@article {pmid38603509, year = {2024}, author = {Coale, TH and Loconte, V and Turk-Kubo, KA and Vanslembrouck, B and Mak, WKE and Cheung, S and Ekman, A and Chen, JH and Hagino, K and Takano, Y and Nishimura, T and Adachi, M and Le Gros, M and Larabell, C and Zehr, JP}, title = {Nitrogen-fixing organelle in a marine alga.}, journal = {Science (New York, N.Y.)}, volume = {384}, number = {6692}, pages = {217-222}, doi = {10.1126/science.adk1075}, pmid = {38603509}, issn = {1095-9203}, abstract = {Symbiotic interactions were key to the evolution of chloroplast and mitochondria organelles, which mediate carbon and energy metabolism in eukaryotes. Biological nitrogen fixation, the reduction of abundant atmospheric nitrogen gas (N2) to biologically available ammonia, is a key metabolic process performed exclusively by prokaryotes. Candidatus Atelocyanobacterium thalassa, or UCYN-A, is a metabolically streamlined N2-fixing cyanobacterium previously reported to be an endosymbiont of a marine unicellular alga. Here we show that UCYN-A has been tightly integrated into algal cell architecture and organellar division and that it imports proteins encoded by the algal genome. These are characteristics of organelles and show that UCYN-A has evolved beyond endosymbiosis and functions as an early evolutionary stage N2-fixing organelle, or "nitroplast."}, }
@article {pmid38601302, year = {2024}, author = {Fukasawa, Y and Driguez, P and Bougouffa, S and Carty, K and Putra, A and Cheung, MS and Ermini, L}, title = {Plasticity of repetitive sequences demonstrated by the complete mitochondrial genome of Eucalyptus camaldulensis.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1339594}, pmid = {38601302}, issn = {1664-462X}, abstract = {The tree Eucalyptus camaldulensis is a ubiquitous member of the Eucalyptus genus, which includes several hundred species. Despite the extensive sequencing and assembly of nuclear genomes from various eucalypts, the genus has only one fully annotated and complete mitochondrial genome (mitogenome). Plant mitochondria are characterized by dynamic genomic rearrangements, facilitated by repeat content, a feature that has hindered the assembly of plant mitogenomes. This complexity is evident in the paucity of available mitogenomes. This study, to the best of our knowledge, presents the first E. camaldulensis mitogenome. Our findings suggest the presence of multiple isomeric forms of the E. camaldulensis mitogenome and provide novel insights into minor rearrangements triggered by nested repeat sequences. A comparative sequence analysis of the E. camaldulensis and E. grandis mitogenomes unveils evolutionary changes between the two genomes. A significant divergence is the evolution of a large repeat sequence, which may have contributed to the differences observed between the two genomes. The largest repeat sequences in the E. camaldulensis mitogenome align well with significant yet unexplained structural variations in the E. grandis mitogenome, highlighting the adaptability of repeat sequences in plant mitogenomes.}, }
@article {pmid38594641, year = {2024}, author = {Shen, B and Shen, A and Liu, L and Tan, Y and Li, S and Tan, Z}, title = {Assembly and comparative analysis of the complete multichromosomal mitochondrial genome of Cymbidium ensifolium, an orchid of high economic and ornamental value.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {255}, pmid = {38594641}, issn = {1471-2229}, support = {Xiangzi Caihuan Zhi (2022) No. 64; Xiangzi Caihuan Zhi (2022) No. 67; Xiangzi Caihuan Zhi (2023) No. 26; Xiangzi Caihuan Zhi (2023) No. 72//the Hunan Provincial Forestry Ecological Protection, Restoration and Development Special Fund Project/ ; 2023JJ50073//the Hunan Provincial Natural Science Foundation/ ; }, mesh = {*Genome, Mitochondrial/genetics ; Phylogeny ; Mitochondria/genetics ; DNA ; *Orchidaceae/genetics ; }, abstract = {BACKGROUND: Orchidaceae is one of the largest groups of angiosperms, and most species have high economic value and scientific research value due to their ornamental and medicinal properties. In China, Chinese Cymbidium is a popular ornamental orchid with high economic value and a long history. However, to date, no detailed information on the mitochondrial genome of any species of Chinese Cymbidium has been published.<br><br>RESULTS: Here, we present the complete assembly and annotation of the mitochondrial genome of Cymbidium ensifolium (L.) Sw. The mitogenome of C. ensifolium was 560,647&#xa0;bp in length and consisted of 19 circular subgenomes ranging in size from 21,995&#xa0;bp to 48,212&#xa0;bp. The genome encoded 35 protein-coding genes, 36 tRNAs, 3 rRNAs, and 3405 ORFs. Repeat sequence analysis and prediction of RNA editing sites revealed a total of 915 dispersed repeats, 162 simple repeats, 45 tandem repeats, and 530 RNA editing sites. Analysis of codon usage showed a preference for codons ending in A/T. Interorganellar DNA transfer was identified in 13 of the 19 chromosomes, with plastid-derived DNA fragments representing 6.81% of the C. ensifolium mitochondrial genome. The homologous fragments of the mitochondrial genome and nuclear genome were also analysed. Comparative analysis showed that the GC content was conserved, but the size, structure, and gene content of the mitogenomes varied greatly among plants with multichromosomal mitogenome structure. Phylogenetic analysis based on the mitogenomes reflected the evolutionary and taxonomic statuses of C. ensifolium. Interestingly, compared with the mitogenomes of Cymbidium lancifolium Hook. and Cymbidium macrorhizon Lindl., the mitogenome of C. ensifolium lost 8 ribosomal protein-coding genes.<br><br>CONCLUSION: In this study, we assembled and annotated the mitogenome of C. ensifolium and compared it with the mitogenomes of other Liliidae and plants with multichromosomal mitogenome structures. Our findings enrich the mitochondrial genome database of orchid plants and reveal the rapid structural evolution of Cymbidium mitochondrial genomes, highlighting the potential for mitochondrial genes to help decipher plant evolutionary history.}, }
@article {pmid38592734, year = {2024}, author = {Kwasniak-Owczarek, M and Janska, H}, title = {Experimental approaches to studying translation in plant semi-autonomous organelles.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/erae151}, pmid = {38592734}, issn = {1460-2431}, abstract = {Plant mitochondria and chloroplasts are semi-autonomous organelles originated from free-living bacteria and retaining respective reduced genomes during evolution. As a consequence, relatively few of the mitochondrial and chloroplast proteins are encoded in the organellar genomes and synthesized by the organellar ribosomes. Since the both organellar genomes encode mainly components of the energy transduction systems, oxidative phosphorylation in mitochondria and photosynthetic apparatus in chloroplasts, understanding the organellar translation is critical to a thorough comprehension of the key aspects of mitochondrial and chloroplast activity affecting plant growth and development. Recent studies have clearly shown that translation is a key regulatory node in the expression of plant organellar genes, underscoring the need for an adequate methodology to study this unique stage of gene expression. The organellar translatome can be analysed by studying newly synthesized proteins or the mRNA pool recruited to the organellar ribosomes. In this review, we present in some detail the experimental approaches used to date for studying translation in the plant bioenergetic organelles. Their benefits and limitations, as well as the critical steps are discussed. Additionally, we briefly mention several recently developed strategies to study organellar translation that have not yet been applied to plants.}, }
@article {pmid38316513, year = {2024}, author = {Liu, X and You, Q and Liu, M and Bo, C and Zhu, Y and Duan, Y and Xue, J and Wang, D and Xue, T}, title = {Assembly and comparative analysis of the complete mitochondrial genome of Pinellia ternata.}, journal = {Functional plant biology : FPB}, volume = {51}, number = {}, pages = {}, doi = {10.1071/FP23256}, pmid = {38316513}, issn = {1445-4416}, mesh = {*Pinellia/genetics ; *Genome, Mitochondrial/genetics ; Phylogeny ; *Plants, Medicinal/genetics ; Plant Tubers ; }, abstract = {Pinellia ternata is an important natural medicinal herb in China. However, it is susceptible to withering when exposed to high temperatures during growth, which limits its tuber production. Mitochondria usually function in stress response. The P . ternata mitochondrial (mt) genome has yet to be explored. Therefore, we integrated PacBio and Illumina sequencing reads to assemble and annotate the mt genome of P . ternata . The circular mt genome of P . ternata is 876 608bp in length and contains 38 protein-coding genes (PCGs), 20 tRNA genes and three rRNA genes. Codon usage, sequence repeats, RNA editing and gene migration from chloroplast (cp) to mt were also examined. Phylogenetic analysis based on the mt genomes of P . ternata and 36 other taxa revealed the taxonomic and evolutionary status of P . ternata . Furthermore, we investigated the mt genome size and GC content by comparing P . ternata with the other 35 species. An evaluation of non-synonymous substitutions and synonymous substitutions indicated that most PCGs in the mt genome underwent negative selection. Our results provide comprehensive information on the P . ternata mt genome, which may facilitate future research on the high-temperature response of P . ternata and provide new molecular insights on the Araceae family.}, }
@article {pmid38587065, year = {2024}, author = {Shen, C and Xu, H and Huang, WZ and Zhao, Q and Zhu, RL}, title = {Is RNA editing truly absent in the complex thalloid liverworts (Marchantiopsida)? Evidence of extensive RNA editing from Cyathodium cavernarum.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.19750}, pmid = {38587065}, issn = {1469-8137}, support = {//East China Normal University/ ; 31970215//National Natural Science Foundation of China/ ; 32370218//National Natural Science Foundation of China/ ; }, abstract = {RNA editing is a crucial modification in plants' organellar transcripts that converts cytidine to uridine (C-to-U; and sometimes uridine to cytidine) in RNA molecules. This post-transcriptional process is controlled by the PLS-class protein with a DYW domain, which belongs to the pentatricopeptide repeat (PPR) protein family. RNA editing is widespread in land plants; however, complex thalloid liverworts (Marchantiopsida) are the only group reported to lack both RNA editing and DYW-PPR protein. The liverwort Cyathodium cavernarum (Marchantiopsida, Cyathodiaceae), typically found in cave habitats, was newly found to have 129 C-to-U RNA editing sites in its chloroplast and 172 sites in its mitochondria. The Cyathodium genus, specifically C. cavernarum, has a large number of PPR editing factor genes, including 251 DYW-type PPR proteins. These DYW-type PPR proteins may be responsible for C-to-U RNA editing in C. cavernarum. Cyathodium cavernarum possesses both PPR DYW proteins and RNA editing. Our analysis suggests that the remarkable RNA editing capability of C. cavernarum may have been acquired alongside the emergence of DYW-type PPR editing factors. These findings provide insight into the evolutionary pattern of RNA editing in land plants.}, }
@article {pmid38568891, year = {2024}, author = {D'Ercole, J and Dapporto, L and Opler, P and Schmidt, CB and Ho, C and Menchetti, M and Zakharov, EV and Burns, JM and Hebert, PDN}, title = {A genetic atlas for the butterflies of continental Canada and United States.}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0300811}, pmid = {38568891}, issn = {1932-6203}, mesh = {Animals ; United States ; *Butterflies/genetics ; Phylogeography ; DNA, Mitochondrial/genetics/chemistry ; Mitochondria/genetics ; Haplotypes ; Genetic Variation ; DNA Barcoding, Taxonomic ; Phylogeny ; }, abstract = {Multi-locus genetic data for phylogeographic studies is generally limited in geographic and taxonomic scope as most studies only examine a few related species. The strong adoption of DNA barcoding has generated large datasets of mtDNA COI sequences. This work examines the butterfly fauna of Canada and United States based on 13,236 COI barcode records derived from 619 species. It compiles i) geographic maps depicting the spatial distribution of haplotypes, ii) haplotype networks (minimum spanning trees), and iii) standard indices of genetic diversity such as nucleotide diversity (π), haplotype richness (H), and a measure of spatial genetic structure (GST). High intraspecific genetic diversity and marked spatial structure were observed in the northwestern and southern North America, as well as in proximity to mountain chains. While species generally displayed concordance between genetic diversity and spatial structure, some revealed incongruence between these two metrics. Interestingly, most species falling in this category shared their barcode sequences with one at least other species. Aside from revealing large-scale phylogeographic patterns and shedding light on the processes underlying these patterns, this work also exposed cases of potential synonymy and hybridization.}, }
@article {pmid38231368, year = {2024}, author = {Nevarez-Lopez, CA and Muhlia-Almazan, A and Gamero-Mora, E and Sanchez-Paz, A and Sastre-Velasquez, CD and Lopez-Martinez, J}, title = {The branched mitochondrial respiratory chain from the jellyfish Stomolophus sp2 as a probable adaptive response to environmental changes.}, journal = {Journal of bioenergetics and biomembranes}, volume = {56}, number = {2}, pages = {101-115}, pmid = {38231368}, issn = {1573-6881}, support = {171862//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; }, mesh = {Animals ; Electron Transport ; Phylogeny ; *Mitochondrial Membranes/metabolism ; *Scyphozoa/chemistry/metabolism ; Mitochondria/metabolism ; Electron Transport Complex IV ; }, abstract = {During their long evolutionary history, jellyfish have faced changes in multiple environmental factors, to which they may selectively fix adaptations, allowing some species to survive and inhabit diverse environments. Previous findings have confirmed the jellyfish's ability to synthesize large ATP amounts, mainly produced by mitochondria, in response to environmental challenges. This study characterized the respiratory chain from the mitochondria of the jellyfish Stomolophus sp2 (previously misidentified as Stomolophus meleagris). The in-gel activity from isolated jellyfish mitochondria confirmed that the mitochondrial respiratory chain contains the four canonical complexes I to IV and F0F1-ATP synthase. Specific additional activity bands, immunodetection, and mass spectrometry identification confirmed the occurrence of four alternative enzymes integrated into a branched mitochondrial respiratory chain of Stomolophus sp2: an alternative oxidase and three dehydrogenases (two NADH type II enzymes and a mitochondrial glycerol-3-phosphate dehydrogenase). The analysis of each transcript sequence, their phylogenetic relationships, and each protein's predicted models confirmed the mitochondrial alternative enzymes' identity and specific characteristics. Although no statistical differences were found among the mean values of transcript abundance of each enzyme in the transcriptomes of jellyfish exposed to three different temperatures, it was confirmed that each gene was expressed at all tested conditions. These first-time reported enzymes in cnidarians suggest the adaptative ability of jellyfish's mitochondria to display rapid metabolic responses, as previously described, to maintain energetic homeostasis and face temperature variations due to climate change.}, }
@article {pmid38561677, year = {2024}, author = {Chen, L and Dong, X and Huang, H and Xu, H and Rono, PC and Cai, X and Hu, G}, title = {Assembly and comparative analysis of the initial complete mitochondrial genome of Primulina hunanensis (Gesneriaceae): a cave-dwelling endangered plant.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {322}, pmid = {38561677}, issn = {1471-2164}, mesh = {*Genome, Mitochondrial ; Phylogeny ; DNA, Mitochondrial/genetics ; *Lamiales/genetics ; Mitochondria/genetics ; *Genome, Chloroplast ; }, abstract = {BACKGROUND: Primulina hunanensis, a troglobitic plant within the Primulina genus of Gesneriaceae family, exhibits robust resilience to arid conditions and holds great horticultural potential as an ornamental plant. The work of chloroplast genome (cpDNA) has been recently accomplished, however, the mitochondrial genome (mtDNA) that is crucial for plant evolution has not been reported.<br><br>RESULTS: In this study, we sequenced and assembled the P. hunanensis complete mtDNA, and elucidated its evolutionary and phylogenetic relationships. The assembled mtDNA spans 575,242&#xa0;bp with 43.54% GC content, encompassing 60 genes, including 37 protein-coding genes (PCGs), 20 tRNA genes, and 3 rRNA genes. Notably, high number of repetitive sequences in the mtDNA and substantial sequence translocation from chloroplasts to mitochondria were observed. To determine the evolutionary and taxonomic positioning of P. hunanensis, a phylogenetic tree was constructed using mitochondrial PCGs from P. hunanensis and 32 other taxa. Furthermore, an exploration of PCGs relative synonymous codon usage, identification of RNA editing events, and an investigation of collinearity with closely related species were conducted.<br><br>CONCLUSIONS: This study reports the initial assembly and annotation of P. hunanensis mtDNA, contributing to the limited mtDNA repository for Gesneriaceae plants and advancing our understanding of their evolution for improved utilization and conservation.}, }
@article {pmid38555796, year = {2024}, author = {Casimir, P and Iwata, R and Vanderhaeghen, P}, title = {Linking mitochondria metabolism, developmental timing, and human brain evolution.}, journal = {Current opinion in genetics &amp; development}, volume = {86}, number = {}, pages = {102182}, doi = {10.1016/j.gde.2024.102182}, pmid = {38555796}, issn = {1879-0380}, abstract = {Changes in developmental timing are an important factor of evolution in organ shape and function. This is particularly striking for human brain development, which, compared with other mammals, is considerably prolonged at the level of the cerebral cortex, resulting in brain neoteny. Here, we review recent findings that indicate that mitochondria and metabolism contribute to species differences in the tempo of cortical neuron development. Mitochondria display species-specific developmental timeline and metabolic activity patterns that are highly correlated with the speed of neuron maturation. Enhancing mitochondrial activity in human cortical neurons results in their accelerated maturation, while its reduction leads to decreased maturation rates in mouse neurons. Together with other global and gene-specific mechanisms, mitochondria thus act as a cellular hourglass of neuronal developmental tempo and may thereby contribute to species-specific features of human brain ontogeny.}, }
@article {pmid38267606, year = {2024}, author = {Sloan, DB and Conover, JL and Grover, CE and Wendel, JF and Sharbrough, J}, title = {Polyploid plants take cytonuclear perturbations in stride.}, journal = {The Plant cell}, volume = {36}, number = {4}, pages = {829-839}, pmid = {38267606}, issn = {1532-298X}, support = {IOS-1829176//National Science Foundation/ ; IOS-2209085//Postdoctoral Research Fellowship in Biology/ ; }, mesh = {*Cell Nucleus/genetics/metabolism ; *Polyploidy ; Plastids/genetics/metabolism ; Mitochondria/genetics ; Hybridization, Genetic ; Genome, Plant/genetics ; Evolution, Molecular ; }, abstract = {Hybridization in plants is often accompanied by nuclear genome doubling (allopolyploidy), which has been hypothesized to perturb interactions between nuclear and organellar (mitochondrial and plastid) genomes by creating imbalances in the relative copy number of these genomes and producing genetic incompatibilities between maternally derived organellar genomes and the half of the allopolyploid nuclear genome from the paternal progenitor. Several evolutionary responses have been predicted to ameliorate these effects, including selection for changes in protein sequences that restore cytonuclear interactions; biased gene retention/expression/conversion favoring maternal nuclear gene copies; and fine-tuning of relative cytonuclear genome copy numbers and expression levels. Numerous recent studies, however, have found that evolutionary responses are inconsistent and rarely scale to genome-wide generalities. The apparent robustness of plant cytonuclear interactions to allopolyploidy may reflect features that are general to allopolyploids such as the lack of F2 hybrid breakdown under disomic inheritance, and others that are more plant-specific, including slow sequence divergence in organellar genomes and preexisting regulatory responses to changes in cell size and endopolyploidy during development. Thus, cytonuclear interactions may only rarely act as the main barrier to establishment of allopolyploid lineages, perhaps helping to explain why allopolyploidy is so pervasive in plant evolution.}, }
@article {pmid38554118, year = {2024}, author = {Laugier, F and Saclier, N and Béthune, K and Braun, A and Konecny, L and Lefébure, T and Luquet, E and Plénet, S and Romiguier, J and David, P}, title = {Both nuclear and cytoplasmic polymorphisms are involved in genetic conflicts over male fertility in the gynodioecious snail Physa acuta.}, journal = {Evolution; international journal of organic evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/evolut/qpae053}, pmid = {38554118}, issn = {1558-5646}, abstract = {Gynodioecy, the coexistence of hermaphrodites with females, often reflects conflicts between cytoplasmic male sterility (CMS) genes and nuclear genes restoring male fertility. CMS is frequent in plants, and has been recently discovered in one animal: the freshwater snail Physa acuta. In this system, CMS was linked to a single divergent mitochondrial genome (D), devoid of apparent nuclear restoration. Our study uncovers a second, novel CMS-associated mitogenome (K) in Physa acuta, demonstrating an extraordinary acceleration of molecular evolution throughout the entire K mitochondrial genome, akin to the previously observed pattern in D. This suggests a pervasive occurrence of accelerated evolution in both CMS-associated lineages. Through a 17-generation introgression experiment, we further show that nuclear polymorphisms in K-mitogenome individuals contribute to the restoration of male function in natural populations. Our results underscore shared characteristics in gynodioecy between plants and animals, emphasizing the presence of multiple CMS mitotypes and cyto-nuclear conflicts. This reaffirms the pivotal role of mitochondria in influencing male function and in generating genomic conflicts that impact reproductive processes in animals.}, }
@article {pmid38548188, year = {2024}, author = {He, X and Qian, Z and Gichira, AW and Chen, J and Li, Z}, title = {Assembly and comparative analysis of the first complete mitochondrial genome of the invasive water hyacinth, Eichhornia crassipes.}, journal = {Gene}, volume = {914}, number = {}, pages = {148416}, doi = {10.1016/j.gene.2024.148416}, pmid = {38548188}, issn = {1879-0038}, abstract = {Eichhornia crassipes is an aquatic plant in tropical and subtropical regions, renowned for its notorious invasive tendencies. In this study, we assembled the complete mitogenome of E. crassipes into a single circle molecule of 397,361 bp. The mitogenome has 58 unique genes, including 37 protein-coding genes (PCGs), 18 tRNA genes, three rRNA genes, and 47 % GC content. Sixteen (6.93 %) homologous fragments, ranging from 31 bp to 8548 bp, were identified, indicating the transfer of genetic material from chloroplasts to mitochondria. In addition, we detected positive selection in six PCGs (ccmB, ccmC, ccmFC, nad3, nad4 and sdh4), along with the identification of 782 RNA editing sites across 37 mt-PCGs. These findings suggest a potential contribution to the robust adaptation of this invasive plant to the stressful environment. Lastly, we inferred that phylogenetic conflicts of E. crassipes between the plastome and mitogenome may be attributed to the difference in nucleotide substitution rates between the two organelle genomes. In conclusion, our study provided vital genomic resources for further understanding the invasive mechanism of this species and exploring the dynamic evolution of mitogenomes within the monocot clade.}, }
@article {pmid38543688, year = {2024}, author = {Ramos-González, PL and Alexandre, MAV and Potsclam-Barro, M and Duarte, LML and Michea Gonzalez, GL and Chabi-Jesus, C and Ramos, AF and Harakava, R and Lorenzi, H and Freitas-Astúa, J and Kitajima, EW}, title = {Two Novel Betarhabdovirins Infecting Ornamental Plants and the Peculiar Intracellular Behavior of the Cytorhabdovirus in the Liana Aristolochia gibertii.}, journal = {Viruses}, volume = {16}, number = {3}, pages = {}, pmid = {38543688}, issn = {1999-4915}, support = {PNPD20132154 - 33141010001P4 - PNPD - IBSP, 88882.157041/2017-01//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; 17/50334-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2019/25078-9//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/02179-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {*Aristolochia/genetics ; *Mirabilis/genetics ; Genome, Viral ; *Rhabdoviridae ; Plants/genetics ; Phylogeny ; Plant Diseases ; }, abstract = {Two novel members of the subfamily Betarhabdovirinae, family Rhabdoviridae, were identified in Brazil. Overall, their genomes have the typical organization 3'-N-P-P3-M-G-L-5' observed in mono-segmented plant-infecting rhabdoviruses. In aristolochia-associated cytorhabdovirus (AaCV), found in the liana aristolochia (Aristolochia gibertii Hook), an additional short orphan ORF encoding a transmembrane helix was detected between P3 and M. The AaCV genome and inferred encoded proteins share the highest identity values, consistently < 60%, with their counterparts of the yerba mate chlorosis-associated virus (Cytorhabdovirus flaviyerbamate). The second virus, false jalap virus (FaJV), was detected in the herbaceous plant false jalap (Mirabilis jalapa L.) and represents together with tomato betanucleorhabdovirus 2, originally found in tomato plants in Slovenia, a tentative new species of the genus Betanucleorhabdovirus. FaJV particles accumulate in the perinuclear space, and electron-lucent viroplasms were observed in the nuclei of the infected cells. Notably, distinct from typical rhabdoviruses, most virions of AaCV were observed to be non-enclosed within membrane-bounded cavities. Instead, they were frequently seen in close association with surfaces of mitochondria or peroxisomes. Unlike FaJV, AaCV was successfully graft-transmitted to healthy plants of three species of the genus Aristolochia, while mechanical and seed transmission proved unsuccessful for both viruses. Data suggest that these viruses belong to two new tentative species within the subfamily Betarhabdovirinae.}, }
@article {pmid38540407, year = {2024}, author = {Zhang, G and Jiao, Y and Zhao, Z and Chen, Q and Wang, Z and Zhu, J and Lv, N and Sun, G}, title = {Genome-Wide and Expression Pattern Analysis of the HIT4 Gene Family Uncovers the Involvement of GHHIT4_4 in Response to Verticillium Wilt in Gossypium hirsutum.}, journal = {Genes}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/genes15030348}, pmid = {38540407}, issn = {2073-4425}, mesh = {*Gossypium/metabolism ; *Verticillium/genetics ; Phylogeny ; Disease Resistance/genetics ; Chromosome Mapping ; }, abstract = {Chromatin remodelers are essential for regulating plant growth, development, and responses to environmental stresses. HIT4 (HEAT-INTOLERANT 4) is a novel stress-induced chromatin remodeling factor that has been less studied in abiotic stress and stress resistance, particularly in cotton. In this study, we conducted a comprehensive analysis of the members of the HIT4 gene family in Gossypium hirsutum using bioinformatics methods, including phylogenetic relationships, gene organization, transcription profiles, phylogenetic connections, selection pressure, and stress response. A total of 18 HIT4 genes were identified in four cotton species, with six HIT4 gene members in upland cotton. Based on the evolutionary relationships shown in the phylogenetic tree, the 18 HIT4 protein sequences were classified into four distinct subgroups. Furthermore, we conducted chromosome mapping to determine the genomic locations of these genes and visually represented the structural characteristics of HIT4 in G. hirsutum. In addition, we predicted the regulatory elements in HIT4 in G. hirsutum and conducted an analysis of repetitive sequences and gene collinearity among HIT4 in four cotton species. Moreover, we calculated the Ka/Ks ratio for homologous genes to assess the selection pressure acting on HIT4. Using RNA-seq, we explored the expression patterns of HIT4 genes in G. hirsutum and Gossypium barbadense. Through weighted gene co-expression network analysis (WGCNA), we found that GHHIT4_4 belonged to the MEblue module, which was mainly enriched in pathways such as DNA replication, phagosome, pentose and glucuronate interconversions, steroid biosynthesis, and starch and sucrose metabolism. This module may regulate the mechanism of upland cotton resistance to Verticillium wilt through DNA replication, phagosome, and various metabolic pathways. In addition, we performed heterologous overexpression of GH_D11G0591 (GHHIT4_4) in tobacco, and the results showed a significant reduction in disease index compared to the wild type, with higher expression levels of disease resistance genes in the transgenic tobacco. After conducting a VIGS (virus-induced gene silencing) experiment in cotton, the results indicated that silencing GHHIT4_4 had a significant impact, the resistance to Verticillium wilt weakened, and the internode length of the plants significantly decreased by 30.7% while the number of true leaves increased by 41.5%. qRT-PCR analysis indicated that GHHIT4_4 mainly enhanced cotton resistance to Verticillium wilt by indirectly regulating the PAL, 4CL, and CHI genes. The subcellular localization results revealed that GHHIT4_4 was predominantly distributed in the mitochondria and nucleus. This study offers preliminary evidence for the involvement of the GHHIT4_4 in cotton resistance to Verticillium wilt and lays the foundation for further research on the disease resistance mechanism of this gene in cotton.}, }
@article {pmid38547729, year = {2024}, author = {Queiroz, MIC and Lazaro, CM and Dos Santos, LMB and Rentz, T and Virgilio-da-Silva, JV and Moraes-Vieira, PMM and Cunha, FAS and Santos, JCC and Vercesi, AE and Leite, ACR and Oliveira, HCF}, title = {In vivo chronic exposure to inorganic mercury worsens hypercholesterolemia, oxidative stress and atherosclerosis in the LDL receptor knockout mice.}, journal = {Ecotoxicology and environmental safety}, volume = {275}, number = {}, pages = {116254}, doi = {10.1016/j.ecoenv.2024.116254}, pmid = {38547729}, issn = {1090-2414}, abstract = {Heavy metal exposure leads to multiple system dysfunctions. The mechanisms are likely multifactorial and involve inflammation and oxidative stress. The aim of this study was to evaluate markers and risk factors for atherosclerosis in the LDL receptor knockout mouse model chronically exposed to inorganic mercury (Hg) in the drinking water. Results revealed that Hg exposed mice present increased plasma levels of cholesterol, without alterations in glucose. As a major source and target of oxidants, we evaluated mitochondrial function. We found that liver mitochondria from Hg treated mice show worse respiratory control, lower oxidative phosphorylation efficiency and increased H2O2 release. In addition, Hg induced mitochondrial membrane permeability transition. Erythrocytes from Hg treated mice showed a 50% reduction in their ability to take up oxygen, lower levels of reduced glutathione (GSH) and of antioxidant enzymes (SOD, catalase and GPx). The Hg treatment disturbed immune system cells counting and function. While lymphocytes were reduced, monocytes, eosinophils and neutrophils were increased. Peritoneal macrophages from Hg treated mice showed increased phagocytic activity. Hg exposed mice tissues present metal impregnation and parenchymal architecture alterations. In agreement, increased systemic markers of liver and kidney dysfunction were observed. Plasma, liver and kidney oxidative damage indicators (MDA and carbonyl) were increased while GSH and thiol groups were diminished by Hg exposure. Importantly, atherosclerotic lesion size in the aorta root of Hg exposed mice were larger than in controls. In conclusion, in vivo chronic exposure to Hg worsens the hypercholesterolemia, impairs mitochondrial bioenergetics and redox function, alters immune cells profile and function, causes several tissues oxidative damage and accelerates atherosclerosis development.}, }
@article {pmid38547143, year = {2024}, author = {Charrasse, S and Racine, V and Saint-Omer, C and Poquillon, T and Lionnard, L and Ledru, M and Gonindard, C and Delaunois, S and Kissa, K and Frye, RE and Pastore, M and Reynes, C and Frechet, M and Chajra, H and Aouacheria, A}, title = {Quantitative imaging and semiotic phenotyping of mitochondrial network morphology in live human cells.}, journal = {PloS one}, volume = {19}, number = {3}, pages = {e0301372}, doi = {10.1371/journal.pone.0301372}, pmid = {38547143}, issn = {1932-6203}, abstract = {The importance of mitochondria in tissue homeostasis, stress responses and human diseases, combined to their ability to transition between various structural and functional states, makes them excellent organelles for monitoring cell health. There is therefore a need for technologies to accurately analyze and quantify changes in mitochondrial organization in a variety of cells and cellular contexts. Here we present an innovative computerized method that enables accurate, multiscale, fast and cost-effective analysis of mitochondrial shape and network architecture from confocal fluorescence images by providing more than thirty features. In order to facilitate interpretation of the quantitative results, we introduced two innovations: the use of Kiviat-graphs (herein named MitoSpider plots) to present highly multidimensional data and visualization of the various mito-cellular configurations in the form of morphospace diagrams (called MitoSigils). We tested our fully automated image analysis tool on rich datasets gathered from live normal human skin cells cultured under basal conditions or exposed to specific stress including UVB irradiation and pesticide exposure. We demonstrated the ability of our proprietary software (named MitoTouch) to sensitively discriminate between control and stressed dermal fibroblasts, and between normal fibroblasts and other cell types (including cancer tissue-derived fibroblasts and primary keratinocytes), showing that our automated analysis captures subtle differences in morphology. Based on this novel algorithm, we report the identification of a protective natural ingredient that mitigates the deleterious impact of hydrogen peroxide (H2O2) on mitochondrial organization. Hence we conceived a novel wet-plus-dry pipeline combining cell cultures, quantitative imaging and semiotic analysis for exhaustive analysis of mitochondrial morphology in living adherent cells. Our tool has potential for broader applications in other research areas such as cell biology and medicine, high-throughput drug screening as well as predictive and environmental toxicology.}, }
@article {pmid38534456, year = {2024}, author = {Casey, W and Kumaran, T and Massey, SE and Mishra, B}, title = {How Mitochondrial Signaling Games May Shape and Stabilize the Nuclear-Mitochondrial Symbiosis.}, journal = {Biology}, volume = {13}, number = {3}, pages = {}, pmid = {38534456}, issn = {2079-7737}, abstract = {The eukaryotic lineage has enjoyed a long-term "stable" mutualism between nucleus and mitochondrion, since mitochondrial endosymbiosis began about 2 billion years ago. This mostly cooperative interaction has provided the basis for eukaryotic expansion and diversification, which has profoundly altered the forms of life on Earth. While we ignore the exact biochemical details of how the alpha-proteobacterial ancestor of mitochondria entered into endosymbiosis with a proto-eukaryote, in more general terms, we present a signaling games perspective of how the cooperative relationship became established, and has been maintained. While games are used to understand organismal evolution, information-asymmetric games at the molecular level promise novel insights into endosymbiosis. Using a previously devised biomolecular signaling games approach, we model a sender-receiver information asymmetric game, in which the informed mitochondrial sender signals and the uninformed nuclear receiver may take actions (involving for example apoptosis, senescence, regeneration and autophagy/mitophagy). The simulation shows that cellularization is a stabilizing mechanism for Pareto efficient sender/receiver strategic interaction. In stark contrast, the extracellular environment struggles to maintain efficient outcomes, as senders are indifferent to the effects of their signals upon the receiver. Our hypothesis has translational implications, such as in cellular therapy, as mitochondrial medicine matures. It also inspires speculative conjectures about how an analogous human-AI endosymbiosis may be engineered.}, }
@article {pmid38525035, year = {2024}, author = {Krasovec, G and Horkan, HR and Quéinnec, &#xc9; and Chambon, JP}, title = {Intrinsic apoptosis is evolutionarily divergent among metazoans.}, journal = {Evolution letters}, volume = {8}, number = {2}, pages = {267-282}, pmid = {38525035}, issn = {2056-3744}, abstract = {Apoptosis is regulated cell death that depends on caspases. A specific initiator caspase is involved upstream of each apoptotic signaling pathway. Characterized in nematode, fly, and mammals, intrinsic apoptosis is considered to be ancestral, conserved among animals, and depends on shared initiators: caspase-9, Apaf-1 and Bcl-2. However, the biochemical role of mitochondria, the pivotal function of cytochrome c and the modality of caspase activation remain highly heterogeneous and hide profound molecular divergence among apoptotic pathways in animals. Uncovering the phylogenetic history of apoptotic actors, especially caspases, is crucial to shed light on the evolutionary history of intrinsic apoptosis. Here, we demonstrate with phylogenetic analyses that caspase-9, the fundamental key of intrinsic apoptosis, is deuterostome-specific, while caspase-2 is ancestral to bilaterians. Our analysis of Bcl-2 and Apaf-1 confirms heterogeneity in functional organization of apoptotic pathways in animals. Our results support emergence of distinct intrinsic apoptotic pathways during metazoan evolution.}, }
@article {pmid38503840, year = {2024}, author = {Duran, DP and Laroche, RA and Roman, SJ and Godwin, W and Herrmann, DP and Bull, E and Egan, SP}, title = {Species delimitation, discovery and conservation in a tiger beetle species complex despite discordant genetic data.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6617}, pmid = {38503840}, issn = {2045-2322}, mesh = {Animals ; Phylogeny ; *DNA, Mitochondrial/genetics ; Mitochondria ; Biodiversity ; *Coleoptera/genetics ; Species Specificity ; }, abstract = {In an age of species declines, delineating and discovering biodiversity is critical for both taxonomic accuracy and conservation. In recent years, there has been a movement away from using exclusively morphological characters to delineate and describe taxa and an increase in the use of molecular markers to describe diversity or through integrative taxonomy, which employs traditional morphological characters, as well as genetic or other data. Tiger beetles are charismatic, of conservation concern, and much work has been done on the morphological delineation of species and subspecies, but few of these taxa have been tested with genetic analyses. In this study, we tested morphologically based taxonomic hypotheses of polymorphic tiger beetles in the Eunota circumpicta (LaFerté-Sénectère, 1841) species complex using multilocus genomic and mtDNA analyses. We find multiple cryptic species within the previous taxonomic concept of Eunota circumpicta, some of which were historically recognized as subspecies. We found that the mtDNA and genomic datasets did not identify the same taxonomic units and that the mtDNA was most at odds with all other genetic and morphological patterns. Overall, we describe new cryptic diversity, which raises important conservation concerns, and provide a working example for testing species and subspecies validity despite discordant data.}, }
@article {pmid38381321, year = {2024}, author = {Liu, T and Ji, D and Li, X and Liu, J and Xu, F and Miao, Z and Chang, Y and Tian, M and Xu, C}, title = {Population genetics reveals new introgression in the nucleus herd of min pigs.}, journal = {Genes &amp; genomics}, volume = {46}, number = {4}, pages = {389-398}, pmid = {38381321}, issn = {2092-9293}, support = {LH2019C017//Natural Science Foundation of Heilongjiang Province/ ; 2022ZX02B10-2//Heilongjiang Provincial Key R&amp;D Program/ ; }, mesh = {Swine/genetics ; Animals ; *Genetic Variation ; *Genetics, Population ; Polymorphism, Genetic ; Mitochondria/genetics ; Heterozygote ; }, abstract = {OBJECTIVE: Min pigs are a unique genetic resource among local pig breeds in China. They have more excellent characteristics in cold and stress resistance, good meat quality, and a high reproductive rate. However, the genetic structure and driving factors remain unclear in the nucleus herd. In this study, the genetic diversity of Min pigs was studied to reveal the formation mechanism of its unique genetic structure. We hope to protect and develop the genetic resources of Min pigs.<br><br>METHODS: We analyzed different types of genes to identify the genetic structure and gene introgression pattern of Min pigs. The nuclear DNA dataset includes information on 21 microsatellite loci and 6 Y-chromosome genes, and the mitochondrial D-loop gene is selected to represent maternal lineages. The above genes are all from the nucleus herd of Min pigs.<br><br>RESULTS: The results of genetic structure identification and analysis of potential exogenous gene introgression patterns indicate that the nucleus herd of Min pigs maintains a high level of genetic diversity (polymorphism information content&#x2009;=&#x2009;0.713, expected heterozygosity&#x2009;=&#x2009;0.662, observed heterozygosity&#x2009;=&#x2009;0.612). Compared with other Asian pig breeds, the formation of Min pig breeds is more special. Gene introgression from European pig breeds to Min pigs has occurred, which is characterized by complete introgression of paternal genes and incomplete introgression of maternal genes.<br><br>CONCLUSION: Gene introgression caused by cross-breeding is not the main factor leading to the formation of the current genetic structure of Min pigs, but this process has increased the level of genetic diversity in the nucleus herd. Compared with the influence of gene introgression, our research suggest that artificial selection and environmental adaptive evolution make Min pigs form unique genetic characteristics.}, }
@article {pmid38503345, year = {2024}, author = {Nuryadi, H and Mandagi, IF and Masengi, KWA and Kusumi, J and Inomata, N and Yamahira, K}, title = {Evidence for hybridization-driven heteroplasmy maintained across generations in a ricefish endemic to a Wallacean ancient lake.}, journal = {Biology letters}, volume = {20}, number = {3}, pages = {20230385}, doi = {10.1098/rsbl.2023.0385}, pmid = {38503345}, issn = {1744-957X}, mesh = {Humans ; Animals ; *Heteroplasmy ; Lakes ; Phylogeny ; *Oryzias/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {Heteroplasmy, the presence of multiple mitochondrial DNA (mtDNA) haplotypes within cells of an individual, is caused by mutation or paternal leakage. However, heteroplasmy is usually resolved to homoplasmy within a few generations because of germ-line bottlenecks; therefore, instances of heteroplasmy are limited in nature. Here, we report heteroplasmy in the ricefish species Oryzias matanensis, endemic to Lake Matano, an ancient lake in Sulawesi Island, in which one individual was known to have many heterozygous sites in the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene. In this study, we cloned the ND2 gene for some additional individuals with heterozygous sites and demonstrated that they are truly heteroplasmic. Phylogenetic analysis revealed that the extra haplotype within the heteroplasmic O. matanensis individuals clustered with haplotypes of O. marmoratus, a congeneric species inhabiting adjacent lakes. This indicated that the heteroplasmy originated from paternal leakage due to interspecific hybridization. The extra haplotype was unique and contained two non-synonymous substitutions. These findings demonstrate that this hybridization-driven heteroplasmy was maintained across generations for a long time to the extent that the extra mitochondria evolved within the new host.}, }
@article {pmid38502499, year = {2024}, author = {Kuntz, M and Dimnet, L and Pullara, S and Moyet, L and Rolland, N}, title = {The Main Functions of Plastids.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2776}, number = {}, pages = {89-106}, pmid = {38502499}, issn = {1940-6029}, mesh = {*Plastids/metabolism ; *Mitochondria/genetics ; }, abstract = {Plastids are semi-autonomous organelles like mitochondria and derive from a cyanobacterial ancestor that was engulfed by a host cell. During evolution, they have recruited proteins originating from the nuclear genome, and only parts of their ancestral metabolic properties were conserved and optimized to limit functional redundancy with other cell compartments. Furthermore, large disparities in metabolic functions exist among various types of plastids, and the characterization of their various metabolic properties is far from being accomplished. In this review, we provide an overview of the main functions, known to be achieved by plastids or shared by plastids and other compartments of the cell. In short, plastids appear at the heart of all main plant functions.}, }
@article {pmid38502495, year = {2024}, author = {Maréchal, E}, title = {How Did Thylakoids Emerge in Cyanobacteria, and How Were the Primary Chloroplast and Chromatophore Acquired?.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2776}, number = {}, pages = {3-20}, pmid = {38502495}, issn = {1940-6029}, abstract = {The emergence of thylakoid membranes in cyanobacteria is a key event in the evolution of all oxygenic photosynthetic cells, from prokaryotes to eukaryotes. Recent analyses show that they could originate from a unique lipid phase transition rather than from a supposed vesicular budding mechanism. Emergence of thylakoids coincided with the great oxygenation event, more than two billion years ago. The acquisition of semi-autonomous organelles, such as the mitochondrion, the chloroplast, and, more recently, the chromatophore, is a critical step in the evolution of eukaryotes. They resulted from primary endosymbiotic events that seem to share general features, i.e., an acquisition of a bacterium/cyanobacteria likely via a phagocytic membrane, a genome reduction coinciding with an escape of genes from the organelle to the nucleus, and, finally, the appearance of an active system translocating nuclear-encoded proteins back to the organelles. An intense mobilization of foreign genes of bacterial origin, via horizontal gene transfers, plays a critical role. Some third partners, like Chlamydia, might have facilitated the transition from cyanobacteria to the early chloroplast. This chapter further details our current understanding of primary endosymbiosis, focusing on primary chloroplasts, thought to have appeared over a billion years ago, and the chromatophore, which appeared around a hundred years ago.}, }
@article {pmid38500026, year = {2024}, author = {Yang, Y and Duan, C}, title = {Mitochondrial genome features and systematic evolution of diospyros kaki thunb 'Taishuu'.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {285}, pmid = {38500026}, issn = {1471-2164}, support = {YCKJ-2021021//Modern Agriculture Project of Yuncheng/ ; YCKJ-2021021//Modern Agriculture Project of Yuncheng/ ; }, abstract = {BACKGROUND: 'Taishuu' has a crisp texture, abundant juice, and sweet flavor with hints of cantaloupe. The availability of mitochondrial genome data of Diospyros species is far from the known number of species.<br><br>RESULTS: The sequencing data were assembled into a closed circular mitochondrial chromosome with a 421,308&#xa0;bp length and a 45.79% GC content. The mitochondrial genome comprised 40 protein-coding, 24 tRNA, and three rRNA genes. The most common codons for arginine (Arg), proline (Pro), glycine (Gly), tryptophan (Trp), valine (Val), alanine (Ala), and leucine (Leu) were AGA, CCA, GGA, UGG, GUA, GCA, and CUA, respectively. The start codon for cox1 and nad4L protein-coding genes was ACG (ATG), whereas the remaining protein-coding genes started with ATG. There are four types of stop codons: CGA, TAA, TAG, and TGA, with TAA being the most frequently used stop codon (45.24%). In the D. kaki Thunb. 'Taishuu' mitochondrial genome, a total of 645 repeat sequences were identified, including 125 SSRs, 7 tandem repeats, and 513 dispersed repeats. Collinearity analysis revealed a close relationship between D. kaki Thunb. 'Taishuu' and Diospyros oleifera, with conserved homologous gene fragments shared among these species in large regions of the mitochondrial genome. The protein-coding genes ccmB and nad4L were observed to undergo positive selection. Analysis of homologous sequences between chloroplasts and mitochondria identified 28 homologous segments, with a total length of 24,075&#xa0;bp, accounting for 5.71% of the mitochondrial genome. These homologous segments contain 8 annotated genes, including 6 tRNA genes and 2 protein-coding genes (rrn18 and ccmC). There are 23 homologous genes between chloroplasts and nuclei. Mitochondria, chloroplasts, and nuclei share two homologous genes, which are trnV-GAC and trnW-CCA.<br><br>CONCLUSION: In conclusion, a high-quality chromosome-level draft genome for D. kaki was generated in this study, which will contribute to further studies of major economic traits in the genus Diospyros.}, }
@article {pmid38492251, year = {2024}, author = {Keeling, PJ and Mtawali, M and Trznadel, M and Livingston, SJ and Wakeman, KC}, title = {Parallel functional reduction in the mitochondria of apicomplexan parasites.}, journal = {European journal of protistology}, volume = {94}, number = {}, pages = {126065}, doi = {10.1016/j.ejop.2024.126065}, pmid = {38492251}, issn = {1618-0429}, abstract = {Extreme functional reduction of mitochondria has taken place in parallel in many distantly related lineages of eukaryotes, leading to a number of recurring metabolic states with variously lost electron transport chain (ETC) complexes, loss of the tricarboxylic acid (TCA) cycle, and/or loss of the mitochondrial genome. The resulting mitochondria-related organelles (MROs) are generally structurally reduced and in the most extreme cases barely recognizable features of the cell with no role in energy metabolism whatsoever (e.g., mitosomes, which generally only make iron-sulfur clusters). Recently, a wide diversity of MROs were discovered to be hiding in plain sight: in gregarine apicomplexans. This diverse group of invertebrate parasites has been known and observed for centuries, but until recent applications of culture-free genomics, their mitochondria were unremarkable. The genomics, however, showed that mitochondrial function has reduced in parallel in multiple gregarine lineages to several different endpoints, including the most reduced mitosomes. Here we review this remarkable case of parallel evolution of MROs, and some of the interesting questions this work raises.}, }
@article {pmid38485499, year = {2024}, author = {Li, CY and Liu, XC and Li, YZ and Wang, Y and Nie, YH and Xu, YT and Zhang, XT and Lu, Y and Sun, Q}, title = {Generation of mitochondrial replacement monkeys by female pronucleus transfer.}, journal = {Zoological research}, volume = {45}, number = {2}, pages = {292-298}, doi = {10.24272/j.issn.2095-8137.2023.287}, pmid = {38485499}, issn = {2095-8137}, mesh = {Mice ; Humans ; Female ; Animals ; *Mitochondrial Diseases/genetics/prevention &amp; control/veterinary ; Haplorhini/genetics ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Primates/genetics ; *Rodent Diseases ; }, abstract = {Mutations in mitochondrial DNA (mtDNA) are maternally inherited and have the potential to cause severe disorders. Mitochondrial replacement therapies, including spindle, polar body, and pronuclear transfers, are promising strategies for preventing the hereditary transmission of mtDNA diseases. While pronuclear transfer has been used to generate mitochondrial replacement mouse models and human embryos, its application in non-human primates has not been previously reported. In this study, we successfully generated four healthy cynomolgus monkeys (Macaca fascicularis) via female pronuclear transfer. These individuals all survived for more than two years and exhibited minimal mtDNA carryover (3.8%-6.7%), as well as relatively stable mtDNA heteroplasmy dynamics during development. The successful establishment of this non-human primate model highlights the considerable potential of pronuclear transfer in reducing the risk of inherited mtDNA diseases and provides a valuable preclinical research model for advancing mitochondrial replacement therapies in humans.}, }
@article {pmid38485105, year = {2024}, author = {Na, I and Campos, C and Lax, G and Kwong, WK and Keeling, PJ}, title = {Phylogenomics reveals Adeleorina are an ancient and distinct subgroup of Apicomplexa.}, journal = {Molecular phylogenetics and evolution}, volume = {195}, number = {}, pages = {108060}, doi = {10.1016/j.ympev.2024.108060}, pmid = {38485105}, issn = {1095-9513}, abstract = {Apicomplexans are a diverse phylum of unicellular eukaryotes that share obligate relationships with terrestrial and aquatic animal hosts. Many well-studied apicomplexans are responsible for several deadly zoonotic and human diseases, most notably malaria caused by Plasmodium. Interest in the evolutionary origin of apicomplexans has also spurred recent work on other more deeply-branching lineages, especially gregarines and sister groups like squirmids and chrompodellids. But a full picture of apicomplexan evolution is still lacking several lineages, and one major, diverse lineage that is notably absent is the adeleorinids. Adeleorina apicomplexans comprises hundreds of described species that infect invertebrate and vertebrate hosts across the globe. Although historically considered coccidians, phylogenetic trees based on limited data have shown conflicting branch positions for this subgroup, leaving this question unresolved. Phylogenomic trees and large-scale analyses comparing cellular functions and metabolism between major subgroups of apicomplexans have not incorporated Adeleorina because only a handful of molecular markers and a couple organellar genomes are available, ultimately excluding this group from contributing to our understanding of apicomplexan evolution and biology. To address this gap, we have generated complete genomes from mitochondria and plastids, as well as multiple deep-coverage single-cell transcriptomes of nuclear genes from two Adeleorina species, Klossia helicina and Legerella nova, and inferred a 206-protein phylogenomic tree of Apicomplexa. We observed distinct structures reported in species descriptions as remnant host structures surrounding adeleorinid oocysts. Klossia helicina and L. nova branched, as expected, with monoxenous adeleorinids within the Adeleorina and their mitochondrial and plastid genomes exhibited similarity to published organellar adeleorinid genomes. We show with a phylogeneomic tree and subsequent phylogenomic analyses that Adeleorina are not closely related to any of the currently sampled apicomplexan subgroups, and instead fall as a sister to a large clade encompassing Coccidia, Protococcidia, Hematozoa, and Nephromycida, collectively. This resolves Adeleorina as a key independently-branching group, separate from coccidians, on the tree of Apicomplexa, which now has all known major lineages sampled.}, }
@article {pmid38480360, year = {2024}, author = {Ghamizi, M and Falniowski, A and Boudellah, A and Hofman, S and Rharras, AE and Assad, N and Moutaouakil, S and Jaszczyska, A}, title = {Two new genera and species of the valvatiform hydrobiid snails (Caenogastropoda: Truncatelloidea: Hydrobiidae) from Morocco.}, journal = {Zootaxa}, volume = {5418}, number = {3}, pages = {223-239}, doi = {10.11646/zootaxa.5418.3.2}, pmid = {38480360}, issn = {1175-5334}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; Morocco ; *Snails/genetics ; Phylogeny ; *Mitochondria/genetics ; }, abstract = {Stygobiont and crenobiont minute gastropods representing the family Hydrobiidae (Caenogastropoda: Truncatelloidea), characterized by the valvatoid low-spired shell, were collected from one spring and four wells in Bouregreg region, NW Morocco. The shells were photographed and measured; shell biometry is illustrated with principal component analysis. Penes were illustrated and described. Mitochondrial cytochrome oxidase subunit 1 (COI) and 16S rRNA, as well as nuclear 18S rRNA sequences were used to infer the phylogeny. The snails represented two genera, both new to science. Their closest relatives were taxa from the Iberian Peninsula, the rough molecular estimate of the time of divergence between these Moroccan and Iberian genera coincided with the Pliocene Flooding, which restored the Strait of Gibraltar to connect the Mediterranean Basin with Atlantic Ocean.}, }
@article {pmid38480282, year = {2024}, author = {Gordon, DP and Quek, ZBR and Huang, D}, title = {Four new species and a ribosomal phylogeny of Rhabdopleura (Hemichordata: Graptolithina) from New Zealand, with a review and key to all described extant taxa.}, journal = {Zootaxa}, volume = {5424}, number = {3}, pages = {323-357}, doi = {10.11646/zootaxa.5424.3.3}, pmid = {38480282}, issn = {1175-5334}, mesh = {Animals ; Phylogeny ; New Zealand ; RNA, Ribosomal, 18S/genetics ; Base Sequence ; *Mitochondria/genetics ; }, abstract = {All eight extant species ofRhabdopleuradescribed between 1869 and 2018 are provisionally accepted as valid based on a review of the literature and new data on two little-known species from the Azores. Additionally, four new species are described from the New Zealand region, increasing global diversity by 50%, and a dichotomous key to all 12 described species is provided based on morphological criteria. The distinction between colony morphologies based on erect-tube inception is regarded as particularly helpful in initial characterization of species. Erect ringed tubes are either produced directly from the surface of creeping-tubes or indirectly, i.e. a short adherent side branch from a creeping tube is interpolated between the creeping tube and an erect tube; such side branches are blind-ending. These two modes of erect-tube origination are here respectively termeddirectandindirect. Species with indirect erect-tube budding are predominant in the North Atlantic whereas species with direct erect-tube budding dominate in New Zealand waters. The only indirect-erect species from New Zealand, Rhabdopleura chathamica n. sp., was discovered on deepwater coral from 10081075 m, constituting the deepest record of the genus to date. Rhabdopleura emancipata n. sp., collected only in a detached state, constitutes a three-dimensional tangled growth that grew freely into the water columna unique morphology hitherto unknown among extant species. Owing to this growth mode, it provided a substratum for epibionts from several phyla. Rhabdopleura francesca n. sp. and Rhabdopleura decipula n. sp. are morphologically very similar but are distinguishable by their distinct placements in a phylogeny based on 16S mitochondrial and 18S nuclear rRNA genes. Phylogenetic reconstructions based on rRNA and mitochondrial genome data contribute to an updated phylogeny of all Rhabdopleura species sequenced thus far, some of which require more molecular sequences and morphological analyses for taxonomic determination.}, }
@article {pmid38480132, year = {2024}, author = {Methou, P and Chen, C and Komai, T}, title = {Revision of the alvinocaridid shrimp genus Rimicaris Williams &amp; Rona, 1986 (Decapoda: Caridea) with description of a new species from the Mariana Arc hydrothermal vents.}, journal = {Zootaxa}, volume = {5406}, number = {4}, pages = {501-518}, doi = {10.11646/zootaxa.5406.4.1}, pmid = {38480132}, issn = {1175-5334}, mesh = {Animals ; Phylogeny ; *Hydrothermal Vents ; *Decapoda ; Mitochondria ; }, abstract = {A new species of alvinocaridid shrimp is reported, from the Northwest Eifuku hydrothermal vent field at 16191667 m depth on the Mariana Arc. A comprehensive phylogenetic reconstruction of Alvinocarididae based on the mitochondrial cytochrome c oxidase subunit I (COI) gene including this new species reveals the paraphyly of the genus Rimicaris Williams &amp; Rona, 1986 with four other generaAlvinocaridinides, Manuscaris, Opaepele, and Shinkaicarisnested within it. We re-examine material of these four problematic genera, and synonymise them under Rimicaris whose diagnosis has been amended, in order to maintain a monophyletic Rimicaris. Our new species, Rimicaris cambonae sp. nov. is genetically close to Rimicaris loihi (Williams &amp; Dobbs, 1995) comb. nov. (previously Opaepele loihi) with which it co-occurs, but can be morphologically distinguished by the less elevated dorsal surface of the rostrum, this being devoid of a median carina, a stronger pterygostomial tooth on the carapace, and a blunt rather than acuminate proximolateral process on the antennular stylocerite. Species previously assigned to the above listed, synonymized genera are also discussed, with new material examined for three key species: R. loihi, R. acuminata, and R. leurokolos. Further, Alvinocaridinides formosa Komai &amp; Chan, 2010 and Manuscaris liui Wang &amp; Sha, 2016 are synonymized under Rimicaris leurokolos (Kikuchi &amp; Hashimoto, 2000) comb. nov. and R. acuminata (Komai &amp; Tsuchida, 2015) comb. nov., respectively. Revised diagnoses are presented for R. loihi, R. acuminata, and R. leurokolos. After the present revision revision, Rimicaris now consists of 15 species.}, }
@article {pmid38475850, year = {2024}, author = {Vesala, L and Basikhina, Y and Tuomela, T and Nurminen, A and Siukola, E and Vale, PF and Salminen, TS}, title = {Mitochondrial perturbation in immune cells enhances cell-mediated innate immunity in Drosophila.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {60}, pmid = {38475850}, issn = {1741-7007}, support = {RPG-2018-369//Leverhulme Trust/ ; 322732//Academy of Finland/ ; 328979//Academy of Finland/ ; 353367//Academy of Finland/ ; 3122800849//Sigrid Jus&#xe9;liuksen S&#xe4;&#xe4;ti&#xf6;/ ; }, mesh = {Animals ; Humans ; *Drosophila ; Drosophila melanogaster/metabolism ; *Wasps/genetics ; Mitochondria ; Immunity, Innate ; Hemocytes/metabolism ; }, abstract = {BACKGROUND: Mitochondria participate in various cellular processes including energy metabolism, apoptosis, autophagy, production of reactive oxygen species, stress responses, inflammation and immunity. However, the role of mitochondrial metabolism in immune cells and tissues shaping the innate immune responses are not yet fully understood. We investigated the effects of tissue-specific mitochondrial perturbation on the immune responses at the organismal level. Genes for oxidative phosphorylation (OXPHOS) complexes cI-cV were knocked down in the fruit fly Drosophila melanogaster, targeting the two main immune tissues, the fat body and the immune cells (hemocytes).<br><br>RESULTS: While OXPHOS perturbation in the fat body was detrimental, hemocyte-specific perturbation led to an enhanced immunocompetence. This was accompanied by the formation of melanized hemocyte aggregates (melanotic nodules), a sign of activation of cell-mediated innate immunity. Furthermore, the hemocyte-specific OXPHOS perturbation induced immune activation of hemocytes, resulting in an infection-like hemocyte profile and an enhanced immune response against parasitoid wasp infection. In addition, OXPHOS perturbation in hemocytes resulted in mitochondrial membrane depolarization and upregulation of genes associated with the mitochondrial unfolded protein response.<br><br>CONCLUSIONS: Overall, we show that while the effects of mitochondrial perturbation on immune responses are highly tissue-specific, mild mitochondrial dysfunction can be beneficial in immune-challenged individuals and contributes to variation in infection outcomes among individuals.}, }
@article {pmid38349189, year = {2024}, author = {Lanza, A and Kimura, S and Hirono, I and Yoshitake, K and Kinoshita, S and Asakawa, S}, title = {Transcriptome analysis of Edwardsiella piscicida during intracellular infection reveals excludons are involved with the activation of a mitochondrion-like energy generation program.}, journal = {mBio}, volume = {15}, number = {3}, pages = {e0352623}, pmid = {38349189}, issn = {2150-7511}, support = {20H00429//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; //Toagosei (Toagosei Co., Ltd.)/ ; }, mesh = {Animals ; Zebrafish ; Phylogeny ; *Edwardsiella/genetics ; Gene Expression Profiling ; *Enterobacteriaceae Infections/microbiology ; *Fish Diseases/microbiology ; }, abstract = {Phylogenetic evidence suggests a shared ancestry between mitochondria and modern Proteobacteria, a phylum including several genera of intracellular pathogens. Studying these diverse pathogens, particularly during intracellular infection of their hosts, can reveal characteristics potentially representative of the mitochondrial-Proteobacterial ancestor by identifying traits shared with mitochondria. While transcriptomic approaches can provide global insights into intracellular acclimatization by pathogens, they are often limited by excess host RNAs in extracts. Here, we developed a method employing magnetic nanoparticles to enrich RNA from an intracellular Gammaproteobacterium, Edwardsiella piscicida, within zebrafish, Danio rerio, fin fibroblasts, enabling comprehensive exploration of the bacterial transcriptome. Our findings revealed that the intracellular E. piscicida transcriptome reflects a mitochondrion-like energy generation program characterized by the suppression of glycolysis and sugar transport, coupled with upregulation of the tricarboxylic acid (TCA) cycle and alternative import of simple organic acids that directly flux into TCA cycle intermediates or electron transport chain donors. Additionally, genes predicted to be members of excludons, loci of gene pairs antagonistically co-regulated by overlapping antisense transcription, are significantly enriched in the set of all genes with perturbed sense and antisense transcription, suggesting a general but important involvement of excludons with intracellular acclimatization. Notably, genes involved with the activation of the mitochondrion-like energy generation program, specifically with metabolite import and glycolysis, are also members of predicted excludons. Other intracellular Proteobacterial pathogens appear to employ a similar mitochondrion-like energy generation program, suggesting a potentially conserved mechanism for optimized energy acquisition from hosts centered around the TCA cycle.IMPORTANCEPhylogenetic evidence suggests that mitochondria and Proteobacteria, a phylum encompassing various intracellular pathogens, share a common ancestral lineage. In this study, we developed a novel method employing magnetic nanoparticles to explore the transcriptome of an aquatic Gammaproteobacterium, Edwardsiella piscicida, during intracellular infection of host cells. We show that the strategy E. piscicida uses to generate energy strikingly mirrors the function of mitochondria-energy generators devoid of glycolytic processes. Notably, several implicated genes are members of excludons-gene pairs antagonistically co-regulated by overlapping antisense transcription. Other intracellular Proteobacterial pathogens appear to adopt a similar mitochondrion-like energy generation program, indicating a possibly conserved strategy for optimized energy acquisition from hosts centered around the tricarboxylic acid cycle.}, }
@article {pmid38474079, year = {2024}, author = {Mourokh, L and Friedman, J}, title = {Mitochondria at the Nanoscale: Physics Meets Biology-What Does It Mean for Medicine?.}, journal = {International journal of molecular sciences}, volume = {25}, number = {5}, pages = {}, doi = {10.3390/ijms25052835}, pmid = {38474079}, issn = {1422-0067}, support = {Award # 66061-00 54//PSC-CUNY/ ; }, abstract = {Mitochondria are commonly perceived as "cellular power plants". Intriguingly, power conversion is not their only function. In the first part of this paper, we review the role of mitochondria in the evolution of eukaryotic organisms and in the regulation of the human body, specifically focusing on cancer and autism in relation to mitochondrial dysfunction. In the second part, we overview our previous works, revealing the physical principles of operation for proton-pumping complexes in the inner mitochondrial membrane. Our proposed simple models reveal the physical mechanisms of energy exchange. They can be further expanded to answer open questions about mitochondrial functions and the medical treatment of diseases associated with mitochondrial disorders.}, }
@article {pmid38135240, year = {2024}, author = {Bľandová, G and Janoštiaková, N and Kodada, D and Pastorek, M and Lipták, R and Hodosy, J and Šebeková, K and Celec, P and Krasňanská, G and Eliaš, V and Wachsmannová, L and Konečný, M and Repiská, V and Baldovič, M}, title = {Mitochondrial DNA variability and Covid-19 in the Slovak population.}, journal = {Mitochondrion}, volume = {75}, number = {}, pages = {101827}, doi = {10.1016/j.mito.2023.101827}, pmid = {38135240}, issn = {1872-8278}, mesh = {Humans ; *DNA, Mitochondrial/genetics ; Phylogeny ; Slovakia/epidemiology ; Haplotypes ; *COVID-19/genetics ; Mitochondria/genetics ; }, abstract = {Recent studies have shown that mitochondria are involved in the pathogenesis of Covid-19. Mitochondria play a role in production of reactive oxygen species and induction of an innate immune response, both important during infections. Common variability of mitochondrial DNA (mtDNA) can affect oxidative phosphorylation and the risk or lethality of cardiovascular, neurodegenerative diseases and sepsis. However, it is unclear whether susceptibility of severe Covid-19 might be affected by mtDNA variation. Thus, we have analyzed mtDNA in a sample of 446 Slovak patients hospitalized due to Covid-19 and a control population group consisting of 1874 individuals. MtDNA variants in the HVRI region have been analyzed and classified into haplogroups at various phylogenetic levels. Binary logistic regression was used to assess the risk of Covid-19. Haplogroups T1, H11, K and variants 16256C > T, 16265A > C, 16293A > G, 16311 T > C and 16399A > G were associated with an increased Covid-19 risk. On contrary, Haplogroup J1, haplogroup clusters H + U5b and T2b + U5b, and the mtDNA variant 16189 T > C were associated with decreased risk of Covid-19. Following the application of the Bonferroni correction, statistical significance was observed exclusively for the cluster of haplogroups H + U5b. Unsurprisingly, the most significant factor contributing to the mortality of patients with Covid-19 is the age of patients. Our findings suggest that mtDNA haplogroups can play a role in Covid-19 pathogenesis, thus potentially useful in identifying susceptibility to its severe form. To confirm these associations, further studies taking into account the nuclear genome or other non-biological influences are needed.}, }
@article {pmid38468766, year = {2022}, author = {Fernández, MB and Bleidorn, C and Calcaterra, LA}, title = {Wolbachia Infection in Native Populations of the Invasive Tawny Crazy Ant Nylanderia fulva.}, journal = {Frontiers in insect science}, volume = {2}, number = {}, pages = {905803}, pmid = {38468766}, issn = {2673-8600}, abstract = {Antagonistic interactions can affect population growth and dispersal of an invasive species. Wolbachia are intracellular endosymbiont bacteria that infect arthropod and nematode hosts and are able to manipulate reproduction, which in some cases leads to cocladogenesis. Moreover, the presence of the strictly maternally transferred Wolbachia in a population can indirectly induce selective sweeps on the hosts' mitochondria. Ants have a Wolbachia infection rate of about 34%, which makes phylogenetic studies using mitochondrial markers vulnerable of being confounded by the effect of the endosymbiont. Nylanderia fulva is an invasive ant native to South America, considered a pest in the United States. Its distribution and biology are poorly known in its native range, and the taxonomic identity of this and its closely related species, Nylanderia pubens, has only recently been understood with the aid of molecular phylogenies. Aiming at estimating robust phylogenetic relationships of N. fulva in its native range, we investigated the presence and pattern of Wolbachia infection in populations of N. fulva from Argentina, part of its native range, to account for its possible effect on the host population structure. Using the ftsZ gene, 30 nests of N. fulva and four from sympatric Nylanderia species were screened for the presence of Wolbachia. We sequenced the MLST genes, the highly variable gene wsp, as well as glyQ, a novel target gene for which new primers were designed. Phylogeny of the ants was estimated using mtDNA (COI). We found supergroup A Wolbachia strains infecting 73% of N. fulva nests and two nests of Nylanderia sp. 1. Wolbachia phylogenetic tree inferred with MLST genes is partially congruent with the host phylogeny topology, with the exception of a lineage of strains shared by ants from different N. fulva clades. Furthermore, by comparing with Wolbachia sequences infecting other ants, we found that the strains infecting different N. fulva clades are not monophyletic. Our findings suggest there are three recent independent horizontally transmitted Wolbachia infections in N. fulva, and we found no evidence of influence of Wolbachia in the host mtDNA based phylogeny.}, }
@article {pmid38468713, year = {2024}, author = {Iverson, ENK}, title = {Conservation Mitonuclear Replacement: Facilitated mitochondrial adaptation for a changing world.}, journal = {Evolutionary applications}, volume = {17}, number = {3}, pages = {e13642}, pmid = {38468713}, issn = {1752-4571}, abstract = {Most species will not be able to migrate fast enough to cope with climate change, nor evolve quickly enough with current levels of genetic variation. Exacerbating the problem are anthropogenic influences on adaptive potential, including the prevention of gene flow through habitat fragmentation and the erosion of genetic diversity in small, bottlenecked populations. Facilitated adaptation, or assisted evolution, offers a way to augment adaptive genetic variation via artificial selection, induced hybridization, or genetic engineering. One key source of genetic variation, particularly for climatic adaptation, are the core metabolic genes encoded by the mitochondrial genome. These genes influence environmental tolerance to heat, drought, and hypoxia, but must interact intimately and co-evolve with a suite of important nuclear genes. These coadapted mitonuclear genes form some of the important reproductive barriers between species. Mitochondrial genomes can and do introgress between species in an adaptive manner, and they may co-introgress with nuclear genes important for maintaining mitonuclear compatibility. Managers should consider the relevance of mitonuclear genetic variability in conservation decision-making, including as a tool for facilitating adaptation. I propose a novel technique dubbed Conservation Mitonuclear Replacement (CmNR), which entails replacing the core metabolic machinery of a threatened species-the mitochondrial genome and key nuclear loci-with those from a closely related species or a divergent population, which may be better-adapted to climatic changes or carry a lower genetic load. The most feasible route to CmNR is to combine CRISPR-based nuclear genetic editing with mitochondrial replacement and assisted reproductive technologies. This method preserves much of an organism's phenotype and could allow populations to persist in the wild when no other suitable conservation options exist. The technique could be particularly important on mountaintops, where rising temperatures threaten an alarming number of species with almost certain extinction in the next century.}, }
@article {pmid38456969, year = {2024}, author = {Ovciarikova, J and Shikha, S and Lacombe, A and Courjol, F and McCrone, R and Hussain, W and Maclean, A and Lemgruber, L and Martins-Duarte, ES and Gissot, M and Sheiner, L}, title = {Two ancient membrane pores mediate mitochondrial-nucleus membrane contact sites.}, journal = {The Journal of cell biology}, volume = {223}, number = {4}, pages = {}, pmid = {38456969}, issn = {1540-8140}, support = {/WT_/Wellcome Trust/United Kingdom ; 217173/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; BB/N003675/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Mitochondrial Membranes/metabolism ; *Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Mitochondria Associated Membranes ; Eukaryotic Cells ; }, abstract = {Coordination between nucleus and mitochondria is essential for cell survival, and thus numerous communication routes have been established between these two organelles over eukaryotic cell evolution. One route for organelle communication is via membrane contact sites, functional appositions formed by molecular tethers. We describe a novel nuclear-mitochondrial membrane contact site in the protozoan Toxoplasma gondii. We have identified specific contacts occurring at the nuclear pore and demonstrated an interaction between components of the nuclear pore and the mitochondrial protein translocon, highlighting them as molecular tethers. Genetic disruption of the nuclear pore or the TOM translocon components, TgNup503 or TgTom40, respectively, result in contact site reduction, supporting their potential involvement in this tether. TgNup503 depletion further leads to specific mitochondrial morphology and functional defects, supporting a role for nuclear-mitochondrial contacts in mediating their communication. The discovery of a contact formed through interaction between two ancient mitochondrial and nuclear complexes sets the ground for better understanding of mitochondrial-nuclear crosstalk in eukaryotes.}, }
@article {pmid38456649, year = {2024}, author = {Kutzer, MAM and Cornish, B and Jamieson, M and Zawistowska, O and Monteith, KM and Vale, PF}, title = {Mitochondrial background can explain variable costs of immune deployment.}, journal = {Journal of evolutionary biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jeb/voae027}, pmid = {38456649}, issn = {1420-9101}, abstract = {Organismal health and survival depend on the ability to mount an effective immune response against infection. Yet immune defence may be energy-demanding, resulting in fitness costs if investment in immune function deprives other physiological processes of resources. While evidence of costly immunity resulting in reduced longevity and reproduction is common, the role of energy-producing mitochondria on the magnitude of these costs is unknown. Here we employed Drosophila melanogaster cybrid lines, where several mitochondrial genotypes (mitotypes) were introgressed onto a single nuclear genetic background, to explicitly test the role of mitochondrial variation on the costs of immune stimulation. We exposed female flies carrying one of nine distinct mitotypes to either a benign, heat-killed bacterial pathogen (stimulating immune deployment while avoiding pathology), or to a sterile control, and measured lifespan, fecundity, and locomotor activity. We observed mitotype-specific costs of immune stimulation and identified a positive genetic correlation between lifespan and the proportion of time cybrids spent moving while alive. Our results suggests that costs of immunity are highly variable depending on the mitochondrial genome, adding to a growing body of work highlighting the important role of mitochondrial variation in host-pathogen interactions.}, }
@article {pmid38449346, year = {2024}, author = {Speijer, D}, title = {How mitochondrial cristae illuminate the important role of oxygen during eukaryogenesis.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e2300193}, doi = {10.1002/bies.202300193}, pmid = {38449346}, issn = {1521-1878}, abstract = {Inner membranes of mitochondria are extensively folded, forming cristae. The observed overall correlation between efficient eukaryotic ATP generation and the area of internal mitochondrial inner membranes both in unicellular organisms and metazoan tissues seems to explain why they evolved. However, the crucial use of molecular oxygen (O2) as final acceptor of the electron transport chain is still not sufficiently appreciated. O2 was an essential prerequisite for cristae development during early eukaryogenesis and could be the factor allowing cristae retention upon loss of mitochondrial ATP generation. Here I analyze illuminating bacterial and unicellular eukaryotic examples. I also discuss formative influences of intracellular O2 consumption on the evolution of the last eukaryotic common ancestor (LECA). These considerations bring about an explanation for the many genes coming from other organisms than the archaeon and bacterium merging at the start of eukaryogenesis.}, }
@article {pmid38422090, year = {2024}, author = {Yu, TS and Park, K and Han, KH and Kwak, IS}, title = {Morphological and genetic analysis for the diversity conservation of rare species, Thamnaconus multilineatus (Tetraodontiformes: Monacanthidae).}, journal = {PloS one}, volume = {19}, number = {2}, pages = {e0292916}, pmid = {38422090}, issn = {1932-6203}, mesh = {Animals ; *Tetraodontiformes ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria ; Biodiversity ; Endangered Species ; }, abstract = {Climate changes have altered biodiversity and ultimately induced community changes that have threatened the survival of certain aquatic organisms such as fish species. Obtaining biological and genetic information on endangered fish species is critical for ecological population management. Thamnaconus multilineatus, registered as an endangered species by the IUCN in 2019, is a Data Deficient (DD) species with a remarkably small number of habitats worldwide and no known information other than its habitat and external form. In this study, we characterized the external and osteological morphology of a T. multilineatus specimen collected from eastern Jeju Island, South Korea, in 2020. We also investigated the phylogenetic relationships among related fish species through complete mitochondrial DNA (mtDNA) analysis of the T. multilineatus specimen. The external and skeletal characteristics of T. multilineatus were similar to those of previous reports describing other fish of the genus Thamnaconus, making it difficult to classify T. multilineatus as a similar species based only on morphological characteristics. As a result of analyzing the complete mtDNA of T. multilineatus, the length of the mtDNA was determined to be 16,435 bp, and the mitochondrial genome was found to have 37 CDCs, including 13 PCGs, 22 tRNAs, and 2 rRNAs. In the phylogenetic analysis within the suborder Balistoidei, T. multilineatus mtDNA formed a cluster with fish of the genus Thamnaconus. This study is the first to report on the skeletal structure and complete mtDNA of T. multilineatus. Since the current research on T. multilineatus has only been reported on morphology, the results of this study will be utilized as important information for the management and restoration of T. multilineatus as an endangered species and significant fishery resource.}, }
@article {pmid38271822, year = {2024}, author = {Alcantara da Silva, JV and Ispada, J and Nociti, RP and da Fonseca Junior, AM and de Lima, CB and Dos Santos, EC and Chiaratti, MR and Milazzotto, MP}, title = {The central role of pyruvate metabolism on the epigenetic maturation and transcriptional profile of bovine oocytes.}, journal = {Reproduction (Cambridge, England)}, volume = {167}, number = {4}, pages = {}, doi = {10.1530/REP-23-0181}, pmid = {38271822}, issn = {1741-7899}, abstract = {IN BRIEF: Pyruvate metabolism is one of the main metabolic pathways during oocyte maturation. This study demonstrates that pyruvate metabolism also regulates the epigenetic and molecular maturation in bovine oocytes.<br><br>ABSTRACT: Pyruvate, the final product of glycolysis, undergoes conversion into acetyl-CoA within the mitochondria of oocytes, serving as a primary fuel source for the tricarboxylic acid (TCA) cycle. The citrate generated in the TCA cycle can be transported to the cytoplasm and converted back into acetyl-CoA. This acetyl-CoA can either fuel lipid synthesis or act as a substrate for histone acetylation. This study aimed to investigate how pyruvate metabolism influences lysine 9 histone 3 acetylation (H3K9ac) dynamics and RNA transcription in bovine oocytes during in vitro maturation (IVM). Bovine cumulus-oocyte complexes were cultured in vitro for 24 h, considering three experimental groups: Control (IVM medium only), DCA (IVM supplemented with sodium dichloroacetate, a stimulant of pyruvate oxidation into acetyl-CoA), or IA (IVM supplemented with sodium iodoacetate, a glycolysis inhibitor). The results revealed significant alterations in oocyte metabolism in both treatments, promoting the utilization of lipids as an energy source. These changes during IVM affected the dynamics of H3K9ac, subsequently influencing the oocyte's transcriptional activity. In the DCA and IA groups, a total of 148 and 356 differentially expressed genes were identified, respectively, compared to the control group. These findings suggest that modifications in pyruvate metabolism trigger the activation of metabolic pathways, particularly lipid metabolism, changing acetyl-CoA availability and H3K9ac levels, ultimately impacting the mRNA content of in vitro matured bovine oocytes.}, }
@article {pmid38419371, year = {2024}, author = {Chen, Z and Xie, X and Jia, C and Zhong, Q and Zhang, Q and Luo, D and Cao, Y and Mu, Y and Ren, C}, title = {Concentration-Driven Evolution of Adaptive Artificial Ion Channels or Nanopores with Specific Anticancer Activities.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {}, number = {}, pages = {e202318811}, doi = {10.1002/anie.202318811}, pmid = {38419371}, issn = {1521-3773}, abstract = {In nature, ceramides are a class of sphingolipids possessing a unique ability to self-assemble into protein-permeable channels with intriguing concentration-dependent adaptive channel cavities. However, within the realm of artificial ion channels, this interesting phenomenon is scarcely recaptured. Herein, we report on a novel class of adaptive artificial channels, Pn-TPPs, based on PEGylated cholic acids bearing triphenylphosphonium (TPP) groups as anion binding motifs. Interestingly, the molecules self-assemble into chloride ion channels at low concentrations, while transforming into small molecule-permeable nanopores at high concentrations. Moreover, the TPP groups endow the molecules with mitochondria-targeting property, enabling them to selectively drill holes on the mitochondrial membrane of cancer cells and subsequently trigger the caspase 9 apoptotic pathway. The anticancer efficacies of Pn-TPPs correlate with their abilities to form nanopores. Significantly, the most active ensembles formed by P5-TPP exhibits impressive anticancer activity against human liver cancer cells, with an IC50 value of 3.8 μM. While demonstrating similar anticancer performance to doxorubicin, P5-TPP exhibits a selectivity index surpassing that of doxorubicin by a factor of 16.8.}, }
@article {pmid38413922, year = {2024}, author = {Xu, L and Wang, J and Zhang, T and Xiao, H and Wang, H}, title = {Characterizing complete mitochondrial genome of Aquilegia amurensis and its evolutionary implications.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {142}, pmid = {38413922}, issn = {1471-2229}, support = {nos. 32070244//National Natural Science Foundation of China/ ; nos.32300187//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Aquilegia is a model system for studying the evolution of adaptive radiation. However, very few studies have been conducted on the Aquilegia mitochondrial genome. Since mitochondria play a key role in plant adaptation to abiotic stress, analyzing the mitochondrial genome may provide a new perspective for understanding adaptive evolution.<br><br>RESULTS: The Aquilegia amurensis mitochondrial genome was characterized by a circular chromosome and two linear chromosomes, with a total length of 538,736&#xa0;bp; the genes included 33 protein-coding genes, 24 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. We subsequently conducted a phylogenetic analysis based on single nucleotide polymorphisms (SNPs) in the mitochondrial genomes of 18 Aquilegia species, which were roughly divided into two clades: the European-Asian clade and the North American clade. Moreover, the genes mttB and rpl5 were shown to be positively selected in European-Asian species, and they may help European and Asian species adapt to environmental changes.<br><br>CONCLUSIONS: In this study, we assembled and annotated the first mitochondrial genome of the adaptive evolution model plant Aquilegia. The subsequent analysis provided us with a basis for further molecular studies on Aquilegia mitochondrial genomes and valuable information on adaptive evolution in Aquilegia.}, }
@article {pmid38411741, year = {2024}, author = {Cardoso, DC and Baldez, BCL and Pereira, AH and Kalapothakis, E and Rosse, IC and Cristiano, MP}, title = {De novo assembly of the complete mitochondrial genome of Mycetophylax simplex Emery, 1888 through organelle targeting revels no substantial expansion of gene spacers, but rather some slightly shorter genes.}, journal = {Molecular genetics and genomics : MGG}, volume = {299}, number = {1}, pages = {16}, pmid = {38411741}, issn = {1617-4623}, support = {PPM199-18//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, abstract = {Mitochondria play a key role in cell biology and have their own genome, residing in a highly oxidative environment that induces faster changes than the nuclear genome. Because of this, mitochondrial markers have been exploited to reconstruct phylogenetic and phylogeographic relationships in studies of adaptation and molecular evolution. In this study, we determined the complete mitogenome of the fungus-farming ant Mycetophylax simplex (Hymenoptera, Formicidae) and conducted a comparative analysis among 29 myrmicine ant mitogenomes. Mycetophylax simplex is an endemic ant that inhabits sand dunes along the southern Atlantic coast. Specifically, the species occur in the ecosystem known as "restinga", within the Atlantic Forest biome. Due to habitat degradation, land use and decline of restinga habitats, the species is considered locally extinct in extremely urban beaches and is listed as vulnerable on the Brazilian Red List (ICMBio). We employed a mitochondrion-targeting approach to obtain the complete mitogenome through high-throughput DNA sequencing technology. This method allowed us to determine the mitogenome with high performance, coverage and low cost. The circular mitogenome has a length of 16,367 base pairs enclosing 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) along with one control region (CR). All the protein-coding genes begin with a typical ATN codon and end with the canonical stop codons. All tRNAs formed the fully paired acceptor stems and fold into the typical cloverleaf-shaped secondary structures. The gene order is consistent with the shared Myrmicinae structure, and the A + T content of the majority strand is 81.51%. Long intergenic spacers were not found but some gene are slightly shorter. The phylogenetic relationships based on concatenated nucleotide and amino acid sequences of the 13 protein-coding genes, using Maximum Likelihood and Bayesian Inference methods, indicated that mitogenome sequences were useful in resolving higher-level relationship within Formicidae.}, }
@article {pmid38411429, year = {2024}, author = {Selosse, MA}, title = {[Mitochondria, organelles or bacteria?].}, journal = {Medecine sciences : M/S}, volume = {40}, number = {2}, pages = {197-198}, doi = {10.1051/medsci/2024001}, pmid = {38411429}, issn = {1958-5381}, }
@article {pmid38410435, year = {2024}, author = {Micchelli, CE and Percopo, C and Traver, M and Brzostowski, J and Amin, SN and Prigge, ST and Sá, JM and Wellems, TE}, title = {Progressive heterogeneity of enlarged and irregularly shaped apicoplasts in P. falciparum persister blood stages after drug treatment.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.01.03.574077}, pmid = {38410435}, abstract = {UNLABELLED: Morphological modifications and shifts in organelle relationships are hallmarks of dormancy in eukaryotic cells. Communications between altered mitochondria and nuclei are associated with metabolic quiescence of cancer cells that can survive chemotherapy. In plants, changes in the pathways between nuclei, mitochondria, and chloroplasts are associated with cold stress and bud dormancy. Plasmodium falciparum parasites, the deadliest agent of malaria in humans, contain a chloroplast-like organelle (apicoplast) derived from an ancient photosynthetic symbiont. Antimalarial treatments can fail because a small fraction of the blood stage parasites enter dormancy and recrudesce after drug exposure. Altered mitochondrial-nuclear interactions in these persisters have been described for P. falciparum , but interactions of the apicoplast remained to be characterized. In the present study, we examined the apicoplasts of dormant persisters obtained after exposure to dihydroartemisinin (a first-line antimalarial drug) followed by sorbitol treatment, or after exposure to sorbitol treatment alone. As previously observed, the mitochondrion of persisters was consistently enlarged and in close association with the nucleus. In contrast, the apicoplast varied from compact and oblate, like those of active ring stage parasites, to enlarged and irregularly shaped. Enlarged apicoplasts became more prevalent later in dormancy, but regular size apicoplasts subsequently predominated when actively replicating parasites recrudesced. All three organelles, nucleus, mitochondrion, and apicoplast, became closer during dormancy. Understanding their relationships in erythrocytic-stage persisters may lead to new strategies to prevent recrudescences and protect the future of malaria chemotherapy.<br><br>SIGNIFICANCE STATEMENT: Dormancy of blood-stage malaria parasites (as persister forms) frequently undermines treatment and may facilitate the evolution of drug resistance. Here, we examine changes that occur in dormancy with two P. falciparum organelles relative to the nucleus: the mitochondrion and the plastid-like apicoplast. As previously reported, the mitochondrion of persisters is consistently enlarged, irregularly shaped, and shifted into close apposition with the nucleus. However, apicoplasts exhibit a greater variety of shapes, volumes, and relative positioning during dormancy: some persisters maintain a regular appearing apicoplast, while others show dramatically altered apicoplasts, reminiscent of the chloroplast swelling and degradation that occurs with death from reactive oxygen species in various plant cells. Improved understanding of these processes will support new approaches in antimalarial chemotherapy.}, }
@article {pmid38402284, year = {2024}, author = {Li, G and Zhang, H and Lin, Z and Li, H and Xu, G and Xu, Y and Ji, R and Luo, W and Qiu, Y and Qiu, S and Tang, H}, title = {Comparative analysis of chloroplast and mitochondrial genomes of sweet potato provides evidence of gene transfer.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4547}, pmid = {38402284}, issn = {2045-2322}, mesh = {*Ipomoea batatas/genetics ; Phylogeny ; *Genome, Mitochondrial/genetics ; *Ipomoea/genetics ; *Genome, Chloroplast/genetics ; Chloroplasts/genetics ; Amino Acids/genetics ; RNA, Transfer/genetics ; }, abstract = {The increasing number of plant mitochondrial DNA genomes (mtDNA) sequenced reveals the extent of transfer from both chloroplast DNA genomes (cpDNA) and nuclear DNA genomes (nDNA). This study created a library and assembled the chloroplast and mitochondrial genomes of the leafy sweet potato better to understand the extent of mitochondrial and chloroplast gene transfer. The full-length chloroplast genome of the leafy sweet potato (OM808940) is 161,387 bp, with 132 genes annotated, including 87 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The mitochondrial genome (OM808941) was 269,578 bp in length and contained 69 functional genes, including 39 protein-coding genes, 6 rRNA genes, and 24 tRNA genes. 68 SSR loci were found in the leafy sweet potato organelle genome, including 54 in the chloroplast genome and 14 in the mitochondria genome. In the sweet potato mitochondrial genome, most genes have RNA editing sites, and the conversion ratio from hydrophilic amino acids to hydrophobic amino acids is the highest, reaching 47.12%. Horizontal transfer occurs in the sweet potato organelle genome and nuclear genome. 40 mitochondrial genome segments share high homology with 14 chloroplast genome segments, 33 of which may be derived from chloroplast genome horizontal transfer. 171 mitochondrial genome sequences come from the horizontal transfer of nuclear genome. The phylogenetic analysis of organelle genes revealed that the leafy sweet potato was closely related to the tetraploid wild species Ipomoea tabascana and the wild diploid species Ipomoea trifida.}, }
@article {pmid38402551, year = {2024}, author = {Xu, R and Li, T and Luo, J and Zhang, X and Wang, T and Wang, Y and Ma, Y and Yang, B and Jia, J and Dmytriw, AA and Li, W and Jiao, L}, title = {PCSK9 increases vulnerability of carotid plaque by promoting mitochondrial dysfunction and apoptosis of vascular smooth muscle cells.}, journal = {CNS neuroscience &amp; therapeutics}, volume = {30}, number = {2}, pages = {e14640}, doi = {10.1111/cns.14640}, pmid = {38402551}, issn = {1755-5949}, support = {DFL20220702//Beijing Hospitals Authority's Ascent Plan/ ; 82171303//National Natural Science Foundation of China/ ; Z201100005520019//Beijing Scientific and Technologic Project/ ; Z201100005520020//Beijing Scientific and Technologic Project/ ; 7244353//Beijing Municipal Natural Science Foundation/ ; }, abstract = {BACKGROUND: Proprotein convertase subtilisin/kexin type 9 (PCSK9) has been recognized as a novel lipid-lowing target. Recent clinical studies suggested the value of inhibiting PCSK9 in decreasing the vulnerability of coronary plaques. However, the evidence of PCSK9-regulated evolution of unstable carotid plaques is unclear, which has limited the use of PCSK9 inhibitor in carotid plaques. This study aimed to determine the effect and molecular mechanisms of PCSK9 on vulnerability of carotid plaques, to provide potential therapeutic targets for stabilizing carotid plaques.<br><br>METHODS: The expression of PCSK9 in stable and unstable carotid plaques were examined in tissue and plasma. Human aortic vascular smooth muscle cells (VSMCs) and carotid VSMCs were employed to transfect lentivirus for overexpression and knockdown of PCSK9, respectively. Morphological and functional changes of mitochondria were observed by live-cell imaging. Cell apoptosis was evaluated by propidium iodide staining. RNA-sequencing and biological examinations were performed to explore and validate the underlying mechanisms. Truncated plasmids were employed to identify the functional domain of PCSK9 in regulation of VSMCs' mitochondrial morphology, function and apoptosis.<br><br>RESULTS: Clinically, PCSK9 was closely related with vulnerability of human carotid plaques. Increased expression of PCSK9 in human VSMCs was accompanied by higher level of apoptosis. At subcellular level of VSMCs, the morphology of mitochondria was shifted toward the fission state, followed by mitochondrial dysfunction. Inhibition of p38 MAPK activation partially rescued the above morphological and behavioral changes caused by PCSK9. Furthermore, inhibiting of dynamin-related protein 1 (DRP1) attenuated PCSK9-related mitochondrial dysfunction and cell apoptosis. The 1-149aa domain of PCSK9 protein was essential to achieve functional regulation to VSMCs.<br><br>CONCLUSION: Our findings demonstrated that PCSK9 induced morphology-related mitochondrial dysfunction and apoptosis of VSMCs, which may be related to increased vulnerability of carotid plaque.}, }
@article {pmid38391484, year = {2024}, author = {Kan, S and Liao, X and Lan, L and Kong, J and Wang, J and Nie, L and Zou, J and An, H and Wu, Z}, title = {Cytonuclear interactions and subgenome dominance shape the evolution of organelle-targeted genes in the Brassica triangle of U.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msae043}, pmid = {38391484}, issn = {1537-1719}, abstract = {The interaction and co-evolution between nuclear and cytoplasmic genomes are one of the fundamental hallmarks of eukaryotic genome evolution and, two billion years later, are still major contributors to the formation of new species. Although many studies have investigated the role of cytonuclear interactions following allopolyploidization, the relative magnitude of the effect of subgenome dominance vs. cytonuclear interaction on genome evolution remains unclear. The Brassica triangle of U features three diploid species that together have formed three separate allotetraploid species on similar evolutionary timescales, providing an ideal system for understanding the contribution of the cytoplasmic donor to hybrid polyploid. Here, we investigated the evolutionary pattern of organelle-targeted genes in B. carinata (BBCC) and two varieties of B. juncea (AABB) at the whole-genome level, with particular focus on cytonuclear enzyme complexes. We found partial evidence that plastid-targeted genes experience selection to match plastid genomes, but no obvious corresponding signal in mitochondria-targeted genes from these two separately formed allopolyploids. Interestingly, selection acting on plastid genomes always reduced the retention rate of plastid-targeted genes encoded by the B subgenome, regardless of whether the B. nigra (BB) subgenome was contributed by the paternal or maternal progenitor. More broadly, this study illustrates the distinct selective pressures experienced by plastid- and mitochondria-targeted genes, despite a shared pattern of inheritance and natural history. Our study also highlights an important role for subgenome dominance in allopolyploid genome evolution, even in genes whose function depends on separately inherited molecules.}, }
@article {pmid38378784, year = {2024}, author = {Li, H and Akella, S and Engstler, C and Omini, JJ and Rodriguez, M and Obata, T and Carrie, C and Cerutti, H and Mower, JP}, title = {Recurrent evolutionary switches of mitochondrial cytochrome c maturation systems in Archaeplastida.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1548}, pmid = {38378784}, issn = {2041-1723}, support = {MCB 2212075//National Science Foundation (NSF)/ ; }, mesh = {Amino Acid Sequence ; *Cytochromes c/genetics/metabolism ; *Mitochondria/genetics/metabolism ; }, abstract = {Mitochondrial cytochrome c maturation (CCM) requires heme attachment via distinct pathways termed systems I and III. The mosaic distribution of these systems in Archaeplastida raises questions about the genetic mechanisms and evolutionary forces promoting repeated evolution. Here, we show a recurrent shift from ancestral system I to the eukaryotic-specific holocytochrome c synthase (HCCS) of system III in 11 archaeplastid lineages. Archaeplastid HCCS is sufficient to rescue mutants of yeast system III and Arabidopsis system I. Algal HCCS mutants exhibit impaired growth and respiration, and altered biochemical and metabolic profiles, likely resulting from deficient CCM and reduced cytochrome c-dependent respiratory activity. Our findings demonstrate that archaeplastid HCCS homologs function as system III components in the absence of system I. These results elucidate the evolutionary trajectory and functional divergence of CCM pathways in Archaeplastida, providing insight into the causes, mechanisms, and consequences of repeated cooption of an entire biological pathway.}, }
@article {pmid38142270, year = {2024}, author = {Khan, MM and Suhail, SM and Majid, HA and Ahmad, I and Sadique, U and Khan, R and Ahmad, I and Ijaz, A and Khan, K and Ali, F and Khan, MS and El-Mansi, AA}, title = {Morpometric and molecular characterization of Surguli goat through CO1 gene in district Kohat.}, journal = {Animal biotechnology}, volume = {35}, number = {1}, pages = {2290528}, doi = {10.1080/10495398.2023.2290528}, pmid = {38142270}, issn = {1532-2378}, mesh = {Animals ; *Goats/genetics ; Phylogeny ; Base Sequence ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; }, abstract = {The present study was designed with the aim to study morphometric characterization as well as phylogeny and diversity of the local Surguli goat at their breeding tract district Kohat through mitochondrial DNA region, i.e., Cytochrome C Oxidase Subunit One (CO1) gene. Morphometric data and blood samples were collected from thirty (30) pure goats. Morphometric analysis showed that sex had significant effect (p < 0.05) on body weight, body length, hearth girth and horn length while no significant effect (p > 0.05) was observed for other characteristics. The results also indicated that age had significant effect (p < 0.05) on height at rump, ear length, horn length and tail length while no significant effect (p > 0.05) was observed for other characteristics. The phylogenetic analysis through CO1 nucleotide sequences within nucleotide range 1-767 showed nine polymorphic sites segregating into eight haplotypes. The mean intraspecific diversity and mean interspecific diversity were calculated as 0.23 and 2.36%, respectively. Phylogenetic tree revealed that Capra Ibex and native Surguli goat have common ancestors. The morphometric and molecular results obtained from the present study can be exploited as a selection tool for breeding and overall improvement.}, }
@article {pmid38368456, year = {2024}, author = {Széliová, D and Müller, S and Zanghellini, J}, title = {Costs of ribosomal RNA stabilization affect ribosome composition at maximum growth rate.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {196}, pmid = {38368456}, issn = {2399-3642}, abstract = {Ribosomes are key to cellular self-fabrication and limit growth rate. While most enzymes are proteins, ribosomes consist of 1/3 protein and 2/3 ribonucleic acid (RNA) (in E. coli).Here, we develop a mechanistic model of a self-fabricating cell, validated across diverse growth conditions. Through resource balance analysis (RBA), we explore the variation in maximum growth rate with ribosome composition, assuming constant kinetic parameters.Our model highlights the importance of RNA instability. If we neglect it, RNA synthesis is always cheaper than protein synthesis, leading to an RNA-only ribosome at maximum growth rate. Upon accounting for RNA turnover, we find that a mixed ribosome composed of RNA and proteins maximizes growth rate. To account for RNA turnover, we explore two scenarios regarding the activity of RNases. In (a) degradation is proportional to RNA content. In (b) ribosomal proteins cooperatively mitigate RNA instability by protecting it from misfolding and subsequent degradation. In both cases, higher protein content elevates protein synthesis costs and simultaneously lowers RNA turnover expenses, resulting in mixed RNA-protein ribosomes. Only scenario (b) aligns qualitatively with experimental data across varied growth conditions.Our research provides fresh insights into ribosome biogenesis and evolution, paving the way for understanding protein-rich ribosomes in archaea and mitochondria.}, }
@article {pmid38363119, year = {2024}, author = {Tetzlaff, S and Hillebrand, A and Drakoulis, N and Gluhic, Z and Maschmann, S and Lyko, P and Wicke, S and Schmitz-Linneweber, C}, title = {Small RNAs from mitochondrial genome recombination sites are incorporated into T. gondii mitoribosomes.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, doi = {10.7554/eLife.95407}, pmid = {38363119}, issn = {2050-084X}, support = {IRTG2290-B01//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The mitochondrial genomes of apicomplexans comprise merely three protein-coding genes, alongside a set of thirty to forty genes encoding small RNAs (sRNAs), many of which exhibit homologies to rRNA from E. coli. The expression status and integration of these short RNAs into ribosomes remains unclear and direct evidence for active ribosomes within apicomplexan mitochondria is still lacking. In this study, we conducted small RNA sequencing on the apicomplexan Toxoplasma gondii to investigate the occurrence and function of mitochondrial sRNAs. To enhance the analysis of sRNA sequencing outcomes, we also re-sequenced the T. gondii mitochondrial genome using an improved organelle enrichment protocol and Nanopore sequencing. It has been established previously that the T. gondii genome comprises 21 sequence blocks that undergo recombination among themselves but that their order is not entirely random. The enhanced coverage of the mitochondrial genome allowed us to characterize block combinations at increased resolution. Employing this refined genome for sRNA mapping, we find that many small RNAs originated from the junction sites between protein-coding blocks and rRNA sequence blocks. Surprisingly, such block border sRNAs were incorporated into polysomes together with canonical rRNA fragments and mRNAs. In conclusion, apicomplexan ribosomes are active within polysomes and are indeed assembled through the integration of sRNAs, including previously undetected sRNAs with merged mRNA-rRNA sequences. Our findings lead to the hypothesis that T. gondii's block-based genome organization enables the dual utilization of mitochondrial sequences as both messenger RNAs and ribosomal RNAs, potentially establishing a link between the regulation of rRNA and mRNA expression.}, }
@article {pmid38361280, year = {2024}, author = {Degli Esposti, M}, title = {Did mitophagy follow the origin of mitochondria?.}, journal = {Autophagy}, volume = {}, number = {}, pages = {1-9}, doi = {10.1080/15548627.2024.2307215}, pmid = {38361280}, issn = {1554-8635}, abstract = {Mitophagy is the process of selective autophagy that removes superfluous and dysfunctional mitochondria. Mitophagy was first characterized in mammalian cells and is now recognized to follow several pathways including basal forms in specific organs. Mitophagy pathways are regulated by multiple, often interconnected factors. The present review aims to streamline this complexity and evaluate common elements that may define the evolutionary origin of mitophagy. Key issues surrounding mitophagy signaling at the mitochondrial surface may fundamentally derive from mitochondrial membrane dynamics. Elements of such membrane dynamics likely originated during the endosymbiosis of the alphaproteobacterial ancestor of our mitochondria but underwent an evolutionary leap forward in basal metazoa that determined the currently known variations in mitophagy signaling.Abbreviations: AGPAT, 1-acylglycerol-3-phosphate O-acyltransferase; ATG, autophagy related; BCL2L13, BCL2 like 13; BNIP3, BCL2 interacting protein 3; BNIP3L, BCL2 interacting protein 3 like; CALCOCO, calcium binding and coiled-coil domain; CL, cardiolipin; ER, endoplasmic reticulum; ERMES, ER-mitochondria encounter structure; FBXL4, F-box and leucine rich repeat protein 4; FUNDC1, FUN14 domain containing 1; GABARAPL1, GABA type A receptor associated protein like 1; HIF, hypoxia inducible factor; IMM, inner mitochondrial membrane; LBPA/BMP, lysobisphosphatidic acid; LIR, LC3-interacting region; LPA, lysophosphatidic acid; MAM, mitochondria-associated membranes; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MCL, monolysocardiolipin; ML, maximum likelihood; NBR1, NBR1 autophagy cargo receptor; OMM, outer mitochondrial membrane; PA, phosphatidic acid; PACS2, phosphofurin acidic cluster sorting protein 2; PC/PLC, phosphatidylcholine; PE, phosphatidylethanolamine; PHB2, prohibitin 2; PINK1, PTEN induced kinase 1; PtdIns, phosphatidylinositol; SAR, Stramenopiles, Apicomplexa and Rhizaria; TAX1BP1, Tax1 binding protein 1; ULK1, unc-51 like autophagy activating kinase 1; VDAC/porin, voltage dependent anion channel.}, }
@article {pmid37847106, year = {2023}, author = {Sharma, A and Ahlawat, S and Sharma, R and Arora, R and Singh, KV and Malik, D and Banik, S and Singh, TR and Tantia, MS}, title = {Tracing the genetic footprints: India's role as a gateway for pig migration and domestication across continents.}, journal = {Animal biotechnology}, volume = {34}, number = {9}, pages = {5173-5179}, doi = {10.1080/10495398.2023.2268683}, pmid = {37847106}, issn = {1532-2378}, mesh = {Swine/genetics ; Animals ; *Domestication ; *Sus scrofa/genetics ; India ; Mitochondria/genetics ; Haplotypes/genetics ; Phylogeny ; Genetic Variation/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {This study explored the maternal genetic diversity in the pig genetic resources of India by analyzing a mitochondrial D-loop fragment and comparing it with the corresponding sequences of previously published studies involving domestic pigs and wild boars. Sequencing of 103 samples representing different domestic pig populations revealed existence of 32 maternal haplotypes. The indices of haplotype and nucleotide diversity in Indian domestic pigs were 0.9421 and 0.015, respectively. Median-Joining network revealed that Indian pigs belong to Clade A and show conformity to 6 haplogroups reported worldwide (D1a, D1a1, D1a2, D1e, D1h and D3a). Among these, D1e and D1a2 were shared with Asian wild boars too. Interestingly, haplotype sharing was evident between Indian pigs and samples from other countries representing Africa, Asia, Europe and Oceania. This study substantiates India's contribution as a possible pig domestication center and highlights the importance of the Indian subcontinent in dispersal of the species to other continents. Additionally, genetic evidence suggested the influence of trading routes and historical interactions in shaping pig genetic exchange. Overall, this investigation provides valuable insights into the genetic diversity, historical migration, and domestication of Indian domestic pigs, contributing to the broader understanding of global pig genetic resources and their evolutionary history.}, }
@article {pmid38351074, year = {2024}, author = {Choudhury, C and Gill, MK and McAleese, CE and Butcher, NJ and Ngo, ST and Steyn, FJ and Minchin, RF}, title = {The Arylamine N-Acetyltransferases as Therapeutic Targets in Metabolic Diseases Associated with Mitochondrial Dysfunction.}, journal = {Pharmacological reviews}, volume = {76}, number = {2}, pages = {300-320}, doi = {10.1124/pharmrev.123.000835}, pmid = {38351074}, issn = {1521-0081}, abstract = {In humans, there are two arylamine N-acetyltransferase genes that encode functional enzymes (NAT1 and NAT2) as well as one pseudogene, all of which are located together on chromosome 8. Although they were first identified by their role in the acetylation of drugs and other xenobiotics, recent studies have shown strong associations for both enzymes in a variety of diseases, including cancer, cardiovascular disease, and diabetes. There is growing evidence that this association may be causal. Consistently, NAT1 and NAT2 are shown to be required for healthy mitochondria. This review discusses the current literature on the role of both NAT1 and NAT2 in mitochondrial bioenergetics. It will attempt to relate our understanding of the evolution of the two genes with biologic function and then present evidence that several major metabolic diseases are influenced by NAT1 and NAT2. Finally, it will discuss current and future approaches to inhibit or enhance NAT1 and NAT2 activity/expression using small-molecule drugs. SIGNIFICANCE STATEMENT: The arylamine N-acetyltransferases (NATs) NAT1 and NAT2 share common features in their associations with mitochondrial bioenergetics. This review discusses mitochondrial function as it relates to health and disease, and the importance of NAT in mitochondrial function and dysfunction. It also compares NAT1 and NAT2 to highlight their functional similarities and differences. Both NAT1 and NAT2 are potential drug targets for diseases where mitochondrial dysfunction is a hallmark of onset and progression.}, }
@article {pmid38346534, year = {2024}, author = {Fehsenfeld, S and Yoon, GR and Quijada-Rodriguez, AR and Kandachi-Toujas, H and Calosi, P and Breton, S and Weihrauch, D}, title = {Short-term exposure to high pCO2 leads to decreased branchial cytochrome C oxidase activity in the presence of octopamine in a decapod.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {}, number = {}, pages = {111603}, doi = {10.1016/j.cbpa.2024.111603}, pmid = {38346534}, issn = {1531-4332}, abstract = {In a recent mechanistic study, octopamine was shown to promote proton transport over the branchial epithelium in green crabs, Carcinus maenas. Here, we follow up on this finding by investigating the involvement of octopamine in an environmental and physiological context that challenges acid-base homeostasis, the response to short-term high pCO2 exposure (400 Pa) in a brackish water environment. We show that hyperregulating green crabs experienced a respiratory acidosis as early as 6 h of exposure to hypercapnia, with a rise in hemolymph pCO2 accompanied by a simultaneous drop of hemolymph pH. The slightly delayed increase in hemolymph HCO3[-] observed after 24 h helped to restore hemolymph pH to initial values by 48 h. Circulating levels of the biogenic amine octopamine were significantly higher in short-term high pCO2 exposed crabs compared to control crabs after 48 h. Whole animal metabolic rates, intracellular levels of octopamine and cAMP, as well as branchial mitochondrial enzyme activities for complex I + III and citrate synthase were unchanged in posterior gill #7 after 48 h of hypercapnia. However, application of octopamine in gill respirometry experiments suppressed branchial metabolic rate in posterior gills of short-term high pCO2 exposed animals. Furthermore, branchial enzyme activity of cytochrome C oxidase decreased in high pCO2 exposed crabs after 48 h. Our results indicate that hyperregulating green crabs are capable of quickly counteracting a hypercapnia-induced respiratory acidosis. The role of octopamine in the acclimation of green crabs to short-term hypercapnia seems to entail the alteration of branchial metabolic pathways, possibly targeting mitochondrial cytochrome C in the gill. Our findings help advancing our current limited understanding of endocrine components in hypercapnia acclimation. SUMMARY STATEMENT: Acid-base compensation upon short-term high pCO2 exposure in hyperregulating green crabs started after 6 h and was accomplished by 48 h with the involvement of the biogenic amine octopamine, accumulation of hemolymph HCO3[-], and regulation of mitochondrial complex IV (cytochrome C oxidase).}, }
@article {pmid38337951, year = {2024}, author = {Guan, J and Zhang, Z and Shi, G}, title = {Genome-Wide Identification of the Ferric Chelate Reductase (FRO) Gene Family in Peanut and Its Diploid Progenitors: Structure, Evolution, and Expression Profiles.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/plants13030418}, pmid = {38337951}, issn = {2223-7747}, abstract = {The ferric chelate reductase (FRO) family plays a vital role in metal ion homeostasis in a variety of locations in the plants. However, little is known about this family in peanut (Arachis hypogaea). This study aimed to identify FRO genes from the genomes of peanut and the two diploid progenitors (A. duranensis and A. ipaensis) and to analyze their gene/protein structures and evolution. In addition, transcriptional responses of AhFRO genes to Fe deficiency and/or Cu exposure were investigated in two peanut cultivars with different Fe deficiency tolerance (Silihong and Fenghua 1). A total of nine, four, and three FRO genes were identified in peanut, A. duranensis, and A. ipaensis, respectively, which were divided into three groups. Most AhFRO genes underwent WGD/segmental duplication, leading to the expansion of the AhFRO gene family. In general, clustered members share similar gene/protein structures. However, significant divergences occurred in AhFRO2 genes. Three out of five AhFRO2 genes were lowly expressed in all tissues under normal conditions, which may be beneficial for avoiding gene loss. Transcription analysis revealed that AhFRO2 and AhFRO7 genes might be involved in the reduction of Fe/Cu in plasma membranes and plastids, respectively. AhFRO8 genes appear to confer Fe reduction in the mitochondria. Moreover, Fe deficiency induced an increase of Cu accumulation in peanut plants in which AhFRO2.2/2.4/2.5 and FRO7.1/7.2 might be involved. Our findings provided new clues for further understanding the roles of AhFRO genes in the Fe/Cu interaction in peanut.}, }
@article {pmid38332473, year = {2024}, author = {Wang, Y and Li, H and Niu, G and Li, Y and Huang, Z and Cheng, S and Zhang, K and Li, H and Fu, Q and Jiang, Y}, title = {Boosting Sono-immunotherapy of Prostate Carcinoma through Amplifying Domino-Effect of Mitochondrial Oxidative Stress Using Biodegradable Cascade-Targeting Nanocomposites.}, journal = {ACS nano}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsnano.3c12511}, pmid = {38332473}, issn = {1936-086X}, abstract = {Sono-immunotherapy faces challenges from poor immunogenicity and low response rate due to complex biological barriers. Herein, we prepared MCTH nanocomposites (NCs) consisting of disulfide bonds (S-S) doped mesoporous organosilica (MONs), Cu-modified protoporphyrin (CuPpIX), mitochondria-targeting triphenylphosphine (TPP), and CD44-targeting hyaluronic acid (HA). MCTH NCs efficiently accumulate at the tumor site due to the overexpressed CD44 receptors on the membrane of the cancer cells. Under the function of HAase and glutathione (GSH), MCTH degrades and exposes TPP to deliver CuPpIX to the mitochondrial site and induce a reactive oxygen species (ROS) burst in situ under ultrasound irradiations, thereby causing severe mitochondria dysfunction. This cascade-targeting ability of MCTH NCs not only reinforces oxidative stress in cancer cells but also amplifies immunogenic cell death (ICD) to stimulate the body's immune response and alleviate the tumor immunosuppressive microenvironment. These NCs significantly enhance the infiltration of immune cells into the tumor, particularly CD8[+] T cells, for a powerful antitumor sono-immunotherapy. The proposed cascade-targeting strategy holds promise for strengthening sono-immunotherapy for prostate cancer treatment and overcoming the limitations of traditional immunotherapy.}, }
@article {pmid38328137, year = {2024}, author = {Iverson, ENK and Criswell, A and Havird, JC}, title = {Stronger evidence for relaxed selection than adaptive evolution in high-elevation animal mtDNA.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.01.20.576402}, pmid = {38328137}, abstract = {Mitochondrial (mt) genes are the subject of many adaptive hypotheses due to the key role of mitochondria in energy production and metabolism. One widespread adaptive hypothesis is that selection imposed by life at high elevation leads to the rapid fixation of beneficial alleles in mtDNA, reflected in the increased rates of mtDNA evolution documented in many high-elevation species. However, the assumption that fast mtDNA evolution is caused by positive, rather than relaxed purifying selection has rarely been tested. Here, we calculated the d N / d S ratio, a metric of nonsynonymous substitution bias, and explicitly tested for relaxed selection in the mtDNA of over 700 species of terrestrial vertebrates, freshwater fishes, and arthropods, with information on elevation and latitudinal range limits, range sizes, and body sizes. We confirmed that mitochondrial genomes of high-elevation taxa have slightly higher d N / d S ratios compared to low-elevation relatives. High-elevation species tend to have smaller ranges, which predict higher d N / d S ratios and more relaxed selection across species and clades, while absolute elevation and latitude do not predict higher d N / d S . We also find a positive relationship between body mass and d N / d S , supporting a role for small effective population size leading to relaxed selection. We conclude that higher mt d N / d S among high-elevation species is more likely to reflect relaxed selection due to smaller ranges and reduced effective population size than adaptation to the environment. Our results highlight the importance of rigorously testing adaptive stories against non-adaptive alternative hypotheses, especially in mt genomes.}, }
@article {pmid38326590, year = {2024}, author = {Murphy, MP and O'Neill, LAJ}, title = {A break in mitochondrial endosymbiosis as a basis for inflammatory diseases.}, journal = {Nature}, volume = {626}, number = {7998}, pages = {271-279}, pmid = {38326590}, issn = {1476-4687}, abstract = {Mitochondria retain bacterial traits due to their endosymbiotic origin, but host cells do not recognize them as foreign because the organelles are sequestered. However, the regulated release of mitochondrial factors into the cytosol can trigger cell death, innate immunity and inflammation. This selective breakdown in the 2-billion-year-old endosymbiotic relationship enables mitochondria to act as intracellular signalling hubs. Mitochondrial signals include proteins, nucleic acids, phospholipids, metabolites and reactive oxygen species, which have many modes of release from mitochondria, and of decoding in the cytosol and nucleus. Because these mitochondrial signals probably contribute to the homeostatic role of inflammation, dysregulation of these processes may lead to autoimmune and inflammatory diseases. A potential reason for the increased incidence of these diseases may be changes in mitochondrial function and signalling in response to such recent phenomena as obesity, dietary changes and other environmental factors. Focusing on the mixed heritage of mitochondria therefore leads to predictions for future insights, research paths and therapeutic opportunities. Thus, whereas mitochondria can be considered 'the enemy within' the cell, evolution has used this strained relationship in intriguing ways, with increasing evidence pointing to the recent failure of endosymbiosis being critical for the pathogenesis of inflammatory diseases.}, }
@article {pmid38243701, year = {2024}, author = {Gangavarapu, K and Ji, X and Baele, G and Fourment, M and Lemey, P and Matsen, FA and Suchard, MA}, title = {Many-core algorithms for high-dimensional gradients on phylogenetic trees.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {2}, pages = {}, doi = {10.1093/bioinformatics/btae030}, pmid = {38243701}, issn = {1367-4811}, support = {R01 AI153044/AI/NIAID NIH HHS/United States ; R01 AI162611/AI/NIAID NIH HHS/United States ; R01 AI153044/NH/NIH HHS/United States ; }, mesh = {Phylogeny ; *Software ; Bayes Theorem ; *Algorithms ; Codon ; Nucleotides ; }, abstract = {MOTIVATION: Advancements in high-throughput genomic sequencing are delivering genomic pathogen data at an unprecedented rate, positioning statistical phylogenetics as a critical tool to monitor infectious diseases globally. This rapid growth spurs the need for efficient inference techniques, such as Hamiltonian Monte Carlo (HMC) in a Bayesian framework, to estimate parameters of these phylogenetic models where the dimensions of the parameters increase with the number of sequences N. HMC requires repeated calculation of the gradient of the data log-likelihood with respect to (wrt) all branch-length-specific (BLS) parameters that traditionally takes O(N2) operations using the standard pruning algorithm. A recent study proposes an approach to calculate this gradient in O(N), enabling researchers to take advantage of gradient-based samplers such as HMC. The CPU implementation of this approach makes the calculation of the gradient computationally tractable for nucleotide-based models but falls short in performance for larger state-space size models, such as Markov-modulated and codon models. Here, we describe novel massively parallel algorithms to calculate the gradient of the log-likelihood wrt all BLS parameters that take advantage of graphics processing units (GPUs) and result in many fold higher speedups over previous CPU implementations.<br><br>RESULTS: We benchmark these GPU algorithms on three computing systems using three evolutionary inference examples exploring complete genomes from 997 dengue viruses, 62 carnivore mitochondria and 49 yeasts, and observe a >128-fold speedup over the CPU implementation for codon-based models and >8-fold speedup for nucleotide-based models. As a practical demonstration, we also estimate the timing of the first introduction of West Nile virus into the continental Unites States under a codon model with a relaxed molecular clock from 104 full viral genomes, an inference task previously intractable.<br><br>We provide an implementation of our GPU algorithms in BEAGLE v4.0.0 (https://github.com/beagle-dev/beagle-lib), an open-source library for statistical phylogenetics that enables parallel calculations on multi-core CPUs and GPUs. We employ a BEAGLE-implementation using the Bayesian phylogenetics framework BEAST (https://github.com/beast-dev/beast-mcmc).}, }
@article {pmid38307786, year = {2024}, author = {Muñoz-Gómez, SA}, title = {The energetic costs of cellular complexity in evolution.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2024.01.003}, pmid = {38307786}, issn = {1878-4380}, abstract = {The evolutionary history of cells has been marked by drastic increases in complexity. Some hypothesize that such cellular complexification requires a massive energy flux as the origin of new features is hypothetically more energetically costly than their evolutionary maintenance. However, it remains unclear how increases in cellular complexity demand more energy. I propose that the early evolution of new genes with weak functions imposes higher energetic costs by overexpression before their functions are evolutionarily refined. In the long term, the accumulation of new genes deviates resources away from growth and reproduction. Accrued cellular complexity further requires additional infrastructure for its maintenance. Altogether, this suggests that larger and more complex cells are defined by increased survival but lower reproductive capacity.}, }
@article {pmid38305563, year = {2024}, author = {McCallum, Q and Askelson, K and Fogarty, FF and Natola, L and Nikelski, E and Huang, A and Irwin, D}, title = {Pronounced differentiation on the Z chromosome and parts of the autosomes in crowned sparrows contrasts with mitochondrial paraphyly: implications for speciation.}, journal = {Journal of evolutionary biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jeb/voae004}, pmid = {38305563}, issn = {1420-9101}, support = {RGPIN-2017-03919//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {When a single species evolves into multiple descendent species, some parts of the genome can play a key role in the evolution of reproductive isolation while other parts flow between the evolving species via interbreeding. Genomic evolution during the speciation process is particularly interesting when major components of the genome-for instance, sex chromosomes vs. autosomes vs. mitochondrial DNA-show widely differing patterns of relationships between three diverging populations. The golden-crowned sparrow (Zonotrichia atricapilla) and the white-crowned sparrow (Zonotrichia leucophrys) are phenotypically differentiated sister species that are largely reproductively isolated despite possessing similar mitochondrial genomes, likely due to recent introgression. We assessed variation in more than 45,000 single nucleotide polymorphisms to determine the structure of nuclear genomic differentiation between these species and between two hybridizing subspecies of Z. leucophrys. The two Z. leucophrys subspecies show moderate levels of relative differentiation and patterns consistent with a history of recurrent selection in both ancestral and daughter populations, with much of the sex chromosome Z and a large region on the autosome 1A showing increased differentiation compared to the rest of the genome. The two species Z. leucophrys and Z. atricapilla show high relative differentiation and strong heterogeneity in the level of differentiation among various chromosomal regions, with a large portion of the sex chromosome (Z) showing highly divergent haplotypes between these species. Studies of speciation often emphasize mitochondrial DNA differentiation, but speciation between Z. atricapilla and Z. leucophrys appears primarily associated with Z chromosome divergence and more moderately associated with autosomal differentiation, whereas mitochondria are highly similar due apparently to recent introgression. These results add to the growing body of evidence for highly heterogeneous patterns of genomic differentiation during speciation, with some genomic regions showing a lack of gene flow between populations many hundreds of thousands of years before other genomic regions.}, }
@article {pmid37489100, year = {2023}, author = {Yordanov, G and Palova, N and Mehandjyiski, I and Hristov, P}, title = {Mitochondrial DNA sequencing illuminates genetic diversity and origin of Hunagrian Nonius horse breed and his relatives - Danubian horse and Serbian Nonius.}, journal = {Animal biotechnology}, volume = {34}, number = {8}, pages = {3897-3907}, doi = {10.1080/10495398.2023.2237533}, pmid = {37489100}, issn = {1532-2378}, mesh = {Animals ; Horses/genetics ; Female ; *DNA, Mitochondrial/genetics ; Serbia ; *Genetic Variation/genetics ; Mitochondria/genetics ; Sequence Analysis, DNA ; Haplotypes/genetics ; Phylogeny ; }, abstract = {From a historical perspective, horse breeding in Bulgaria has been very well developed since the time of the Thracians (early Bronze Age c. 3000 BCE). Archaeological discoveries from this era present us with an extremely rich type diversity, including wild and local primitive horses, the prototype of heavy draft horses, and fine riding horses.The objective of this study was to investigate the genetic structure of unexamined populations of three closely related horse breeds - the Danubian Nonius Hungarian Nonius and Serbian Nonius horses. A 608 bp long fragment of the mtDNA D-loop region was amplified and sequenced. The obtained results showed completely different genetic profiles between the investigated breeds. We identified nine of the 17 haplogroups described in modern horses. Most of the obtained sequences fell into M, L, G, and O'P lineages, which reflects the genetic profiles of the ancestral mares that were probably used at the initial stages of formation of the breeds. The population of the Danubian horse was characterized by a high prevalence of Central Asian specific haplogroup G (45%), followed by Western Eurasian specific haplogroups L and M (both about 21%). In contrast to the Danubian horse, in the Nonius breed the highest frequency of Western Eurasian haplogroup M (43.5%) was found, followed by Middle Eastern haplogroups O'P (26.1%) Central Asian specific E (13.0%) and G (13.1%). The Serbian Nonius horse showed a completely different genetic profile with a prevalence of the rare for Europe haplogroup D (66.7%), followed by Central Asian specific G (16.7%). The high mitochondrial haplotype diversity (Hd = 0.886) found in the investigated samples is evidence for multiple maternal origins in all populations.In conclusion, the obtained results demonstrated a high percentage of haplogroup sharing especially in the Danubian and Hungarian Nonius horse breeds, which reflects the possible common origins of the two breeds. In contrast to these breeds, the Serbian Nonius, despite the small number of investigated animals, showed a specific genetic profile, which could be explained by different and independent origins.}, }
@article {pmid37717227, year = {2024}, author = {Chen, S and Tran, TTT and Yeh, AY and Yang, H and Chen, J and Yang, Y and Wang, X}, title = {The Globodera rostochiensis Gr29D09 Effector with a Role in Defense Suppression Targets the Potato Hexokinase 1 Protein.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {37}, number = {1}, pages = {25-35}, doi = {10.1094/MPMI-07-23-0095-R}, pmid = {37717227}, issn = {0894-0282}, mesh = {Animals ; *Solanum tuberosum ; Hexokinase/genetics ; Reactive Oxygen Species ; Phylogeny ; Proteins/genetics ; *Nematoda ; *Tylenchoidea/physiology ; }, abstract = {The potato cyst nematode (Globodera rostochiensis) is an obligate root pathogen of potatoes. G. rostochiensis encodes several highly expanded effector gene families, including the Gr4D06 family; however, little is known about the function of this effector family. We cloned four 29D09 genes from G. rostochiensis (named Gr29D09v1/v2/v3/v4) that share high sequence similarity and are homologous to the Hg29D09 and Hg4D06 effector genes from the soybean cyst nematode (Heterodera glycines). Phylogenetic analysis revealed that Gr29D09 genes belong to a subgroup of the Gr4D06 family. We showed that Gr29D09 genes are expressed exclusively within the nematode's dorsal gland cell and are dramatically upregulated in parasitic stages, indicating involvement of Gr29D09 effectors in nematode parasitism. Transgenic potato lines overexpressing Gr29D09 variants showed increased susceptibility to G. rostochiensis. Transient expression assays in Nicotiana benthamiana demonstrated that Gr29D09v3 could suppress reactive oxygen species (ROS) production and defense gene expression induced by flg22 and cell death mediated by immune receptors. These results suggest a critical role of Gr29D09 effectors in defense suppression. The use of affinity purification coupled with nanoliquid chromatography-tandem mass spectrometry identified potato hexokinase 1 (StHXK1) as a candidate target of Gr29D09. The Gr29D09-StHXK1 interaction was further confirmed using in planta protein-protein interaction assays. Plant HXKs have been implicated in defense regulation against pathogen infection. Interestingly, we found that StHXK1 could enhance flg22-induced ROS production, consistent with a positive role of plant HXKs in defense. Altogether, our results suggest that targeting StHXK1 by Gr29D09 effectors may impair the positive function of StHXK1 in plant immunity, thereby aiding nematode parasitism. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.}, }
@article {pmid38291287, year = {2024}, author = {Li, X and Zhu, Y and Ruiz-Lozano, P and Wei, K}, title = {Mitochondrial-to-nuclear communications through multiple routes regulate cardiomyocyte proliferation.}, journal = {Cell regeneration (London, England)}, volume = {13}, number = {1}, pages = {2}, pmid = {38291287}, issn = {2045-9769}, support = {2018YFA0800104//Ministry of Science and Technology of the People's Republic of China/ ; 92168205//National Natural Science Foundation of China/ ; 32070823//National Natural Science Foundation of China/ ; 22120230471//Fundamental Research Funds for the Central Universities/ ; }, abstract = {The regenerative capacity of the adult mammalian heart remains a formidable challenge in biological research. Despite extensive investigations into the loss of regenerative potential during evolution and development, unlocking the mechanisms governing cardiomyocyte proliferation remains elusive. Two recent groundbreaking studies have provided fresh perspectives on mitochondrial-to-nuclear communication, shedding light on novel factors that regulate cardiomyocyte proliferation. The studies identified two mitochondrial processes, fatty acid oxidation and protein translation, as key players in restricting cardiomyocyte proliferation. Inhibition of these processes led to increased cell cycle activity in cardiomyocytes, mediated by reduction in H3k4me3 levels through accumulated α-ketoglutarate (αKG), and activation of the mitochondrial unfolded protein response (UPR[mt]), respectively. In this research highlight, we discuss the novel insights into mitochondrial-to-nuclear communication presented in these studies, the broad implications in cardiomyocyte biology and cardiovascular diseases, as well as the intriguing scientific questions inspired by the studies that may facilitate future investigations into the detailed molecular mechanisms of cardiomyocyte metabolism, proliferation, and mitochondrial-to-nuclear communications.}, }
@article {pmid38290047, year = {2024}, author = {Cao, J and Luo, Y and Chen, Y and Wu, Z and Zhang, J and Wu, Y and Hu, W}, title = {Maternal mitochondrial function affects paternal mitochondrial inheritance in Drosophila.}, journal = {Genetics}, volume = {}, number = {}, pages = {}, doi = {10.1093/genetics/iyae014}, pmid = {38290047}, issn = {1943-2631}, abstract = {The maternal inheritance of mitochondria is a widely accepted paradigm, and mechanisms that prevent paternal mitochondria transmission to offspring during spermatogenesis and post-fertilization have been described. Although certain species do retain paternal mitochondria, the factors affecting paternal mitochondria inheritance in these cases are unclear. More importantly, the evolutionary benefit of retaining paternal mitochondria and their ultimate fate are unknown. Here we show that transplanted exogenous paternal D. yakuba mitochondria can be transmitted to offspring when maternal mitochondria are dysfunctional in D. melanogaster. Furthermore, we show that the preserved paternal mitochondria are functional, and can be stably inherited, such that the proportion of paternal mitochondria increases gradually in subsequent generations. Our work has important implications that paternal mitochondria inheritance should not be overlooked as a genetic phenomenon in evolution, especially when paternal mitochondria are of significant differences from the maternal mitochondria or the maternal mitochondria are functionally abnormal. Our results improve the understanding of mitochondrial inheritance and provide a new model system for its study.}, }
@article {pmid38288498, year = {2024}, author = {Meng, X and Wang, D and Pang, Q and Wang, H and Zhou, H}, title = {Multiple independent origins of duplicated mitochondrial control regions indicate an apomorphy in the Thysanoptera (Insecta).}, journal = {Archives of insect biochemistry and physiology}, volume = {115}, number = {1}, pages = {e22087}, doi = {10.1002/arch.22087}, pmid = {38288498}, issn = {1520-6327}, support = {2021YFD1400200//National Key R&amp;D program of China/ ; }, abstract = {The mitochondrial genome (mitogenome) of thrips is characterized by the presence of control region (CR) duplication. However, the evolution pattern of duplicated CRs in thrips is still unclear. In this study, the multiple independent origins of duplicated CR indicated that the CR duplication was not an ancestral state for Thysanoptera. The macroevolutionary pattern suggested that the earliest CR duplication event occurred in the middle Cretaceous (94.85 Ma) coincided with rearrangement events forming the ancestors of Aeolothripidae, but much later than that forming the ancestors of the suborder Terebrantia. The mitogenome with duplicated CRs showed a higher rate of gene rearrangement. The sequence similarity of the CR copies and divergence time were negatively correlated, indicating age-related deterioration of mitochondrial function. No significant differences were found in the mitochondrial DNA, the P123 and P4FD between the single and multiple-CR charactered mitogenomes, which suggested that the duplicated CRs may not affect the replication process in thrip mitogenome. The mitogenomes with duplicated CRs (mean: 0.0088 subs/s/my) show a significantly increased evolutionary rate than that with a single one (mean: 0.0058 subs/s/my). However, it seems that this higher evolutionary rate did not have adaptive mechanisms in Terebrantia. We speculated that the duplicated CRs may cause a more intense production of energy by mitochondria, and an accelerated mutation and substitution rate is expected in such mitogenomes. Our study provided new insights into the presence of CR duplications and their evolution in the mitogenomes of thrips.}, }
@article {pmid38275595, year = {2023}, author = {Li, K and Yu, SW and Hu, H and Feng, YF and Storey, KB and Ma, Y and Zhang, JY and Yu, DN}, title = {The Phylogenetic Relationship of Lamiinae (Coleoptera: Cerambycidae) Using Mitochondrial Genomes.}, journal = {Genes}, volume = {15}, number = {1}, pages = {}, pmid = {38275595}, issn = {2073-4425}, support = {LY23C040002//the Natural Science Foundation of Zhejiang Province/ ; }, mesh = {Animals ; Phylogeny ; *Genome, Mitochondrial ; *Coleoptera/genetics ; Bayes Theorem ; Mitochondria/genetics ; }, abstract = {Lamiinae is the largest subfamily of the Cerambycidae (longhorn beetles), with approximately 21,863 described species. Previous phylogenetic studies of Lamiinae showed that this subfamily was monophyletic, but the relationship between the tribes of Lamiinae is still controversial. Partial molecular data and species morphological characteristics are not sufficient to resolve species phylogenetic studies perfectly. At the same time, the full mitochondrial genome contains more comprehensive genetic data. Benefiting from the development of next-generation sequencing (NGS), mitochondrial genomes can be easily acquired and used as reliable molecular markers to investigate phylogenetic relationships within Cerambycidae. Using NGS technology, we obtained 11 mitochondrial genome sequences of Lamiinae species. Based on this newly generated mitochondrial genome dataset matrix, we reconstructed the phylogeny of Lamiinae. The Bayesian Inference and Maximum Likelihood analyses strongly support the monophyly of four tribes (Lamiini, Batocerini, Mesosini, and Saperdini), whereas the tribe Acanthocinini was identified as paraphyletic. Other mitochondrial structural features were also observed: the start codon in the nad1 gene of all 11 mitochondrial genomes is TTG; 17-22 bp intergenic spacers (IGS) with a 'TACTA' motif were found between trnS2 and nad1. Moreover, two long IGS were found in Mesosa myops and Batocera sp. Tandem repeats were found in the IGS of Batocera sp.}, }
@article {pmid38185291, year = {2024}, author = {Bian, C and Ji, S and Xue, R and Zhou, L and Sun, J and Ji, H}, title = {Molecular cloning and characterization of BNIP3 and NIX1/2 and their role in DHA-induced mitophagy and apoptosis in grass carp (Ctenopharyngodon idellus) adipocytes.}, journal = {Gene}, volume = {899}, number = {}, pages = {148140}, doi = {10.1016/j.gene.2024.148140}, pmid = {38185291}, issn = {1879-0038}, mesh = {Animals ; *Mitophagy/genetics ; *Carps/genetics ; Phylogeny ; Apoptosis/genetics ; Adipocytes/metabolism ; Cloning, Molecular ; Mammals/genetics ; }, abstract = {B-cell lymphoma-2 and adenovirus E1B 19-kDa-interacting protein 3 (BNIP3) and BNIP3 like (BNIP3L or NIX) play a vital role in regulating mitophagy and the intrinsic apoptosis in mammals, but their gene characterizations remain unclear in fish. Herein, bnip3, nix1 and nix2 were isolated and characterized from grass carp (Ctenopharyngodon idellus), which encode peptides of 194, 233 and 222 amino acids, respectively. As typical BH3-only proteins, grass carp BNIP3, NIX1 and NIX2 proteins contain BH3 and C-terminal transmembrane domains for inducing apoptosis. Moreover, the LC3-interacting region motif of BNIP3, NIX1 and NIX2 is also conserved in grass carp. Phylogenetic analyses also demonstrated that nix1 and nix2 may have originated from the genome duplication event. Expression pattern analysis indicated that bnip3, nix1 and nix2 were highest expressed in brain, followed by eye (bnip3) and liver (nix1 and nix2). BNIP3, NIX1 and NIX2 localized to the nucleus and the cytoplasm, with a predominant localization to mitochondria within the cytoplasm. In the present study, we found that 200 μM DHA impaired the mitochondrial function, manifested as the decreased antioxidant ability, cellular ATP content and mitochondrial membrane potential in grass carp adipocytes. In addition, the gene expression and enzyme activities of caspase family were significantly increased in 200 μM DHA group, indicating that adipocyte apoptosis was induced. Meanwhile, DHA increased the gene expression of bnip3, nix1 and nix2 in a dose-dependent manner in grass carp adipocytes. The colocalization of mitochondria and lysosomes was promoted by 200 μM DHA treatment, implying that BNIP3/NIX-related mitophagy was activated in adipocytes. Based on these findings, it can be inferred that BNIP3/NIX-related mitophagy may be involved in the adipocyte apoptosis induced by DHA in grass carp.}, }
@article {pmid38273274, year = {2024}, author = {Butenko, A and Lukeš, J and Speijer, D and Wideman, JG}, title = {Mitochondrial genomes revisited: why do different lineages retain different genes?.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {15}, pmid = {38273274}, issn = {1741-7007}, support = {DBI-2119963//Division of Biological Infrastructure/ ; 23-07695S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 23-06479X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; }, abstract = {The mitochondria contain their own genome derived from an alphaproteobacterial endosymbiont. From thousands of protein-coding genes originally encoded by their ancestor, only between 1 and about 70 are encoded on extant mitochondrial genomes (mitogenomes). Thanks to a dramatically increasing number of sequenced and annotated mitogenomes a coherent picture of why some genes were lost, or relocated to the nucleus, is emerging. In this review, we describe the characteristics of mitochondria-to-nucleus gene transfer and the resulting varied content of mitogenomes across eukaryotes. We introduce a 'burst-upon-drift' model to best explain nuclear-mitochondrial population genetics with flares of transfer due to genetic drift.}, }
@article {pmid38271341, year = {2024}, author = {Serrano, MJ and Goudet, J and Cumer, T}, title = {Characterization of the diversity of barn owl's mitochondrial genome reveals high copy number variations in the control region.}, journal = {PloS one}, volume = {19}, number = {1}, pages = {e0295595}, doi = {10.1371/journal.pone.0295595}, pmid = {38271341}, issn = {1932-6203}, abstract = {Mitochondria are known to play an essential role in the cell. These organelles contain their own DNA, which is divided in a coding and non-coding region (NCR). While much of the NCR's function is unknown, tandem repeats have been observed in several vertebrates, with extreme intra-individual, intraspecific and interspecific variation. Taking advantage of a new complete reference for the mitochondrial genome of the Afro-European Barn Owl (Tyto alba), as well as 172 whole genome-resequencing; we (i) describe the reference mitochondrial genome with a special focus on the repeats in the NCR, (ii) quantify the variation in number of copies between individuals, and (iii) explore the possible factors associated with the variation in the number of repetitions. The reference mitochondrial genome revealed a long (256bp) and a short (80bp) tandem repeat in the NCR region. The re-sequenced genomes showed a great variation in number of copies between individuals, with 4 to 38 copies of the Long and 6 to 135 copies of the short repeat. Among the factors associated with this variation between individuals, the tissue used for extraction was the most significant. The exact mechanisms of the formations of these repeats are still to be discovered and understanding them will help explain the maintenance of the polymorphism in the number of copies, as well as their interactions with the metabolism, the aging and health of the individuals.}, }
@article {pmid38271287, year = {2024}, author = {Harada, R and Hirakawa, Y and Yabuki, A and Kim, E and Yazaki, E and Kamikawa, R and Nakano, K and Eliáš, M and Inagaki, Y}, title = {Encyclopaedia of family A DNA polymerases localized in organelles: Evolutionary contribution of bacteria including the proto-mitochondrion.}, journal = {Molecular biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/molbev/msae014}, pmid = {38271287}, issn = {1537-1719}, abstract = {DNA polymerases (DNAPs) synthesize DNA from deoxyribonucleotides in a semi-conservative manner and serve as the core of DNA replication and repair machineries. In eukaryotic cells, there are two genome-containing organelles, mitochondria and plastids, that were derived from an alphaproteobacterium and a cyanobacterium, respectively. Except for rare cases of genome-lacking mitochondria and plastids, both organelles must be served by nucleus-encoded DNAPs that localize and work in them to maintain their genomes. The evolution of organellar DNAPs has yet to be fully understood because of two unsettled issues. First, the diversity of organellar DNAPs has not been elucidated in the full spectrum of eukaryotes. Second, it is unclear when the DNAPs that were used originally in the endosymbiotic bacteria giving rise to mitochondria and plastids were discarded, as the organellar DNAPs known to date show no phylogenetic affinity to those of the extant alphaproteobacteria or cyanobacteria. In this study, we identified from diverse eukaryotes 134 family A DNAP sequences, which were classified into 10 novel types, and explored their evolutionary origins. The subcellular localizations of selected DNAPs were further examined experimentally. The results presented here suggest that the diversity of organellar DNAPs has been shaped by multiple transfers of the PolI gene from phylogenetically broad bacteria, and their occurrence in eukaryotes was additionally impacted by secondary plastid endosymbioses. Finally, we propose that the last eukaryotic common ancestor may have possessed two mitochondrial DNAPs, POP and a candidate of the direct descendant of the proto-mitochondrial DNAP, rdxPolA, identified in this study.}, }
@article {pmid38267054, year = {2024}, author = {Takusagawa, M and Misumi, O and Nozaki, H and Kato, S and Maruyama, S and Tsujimoto-Inui, Y and Yagisawa, F and Ohnuma, M and Kuroiwa, H and Kuroiwa, T and Matsunaga, S}, title = {Complete mitochondrial and chloroplast DNA sequences of the freshwater green microalga Medakamo hakoo.}, journal = {Genes &amp; genetic systems}, volume = {}, number = {}, pages = {}, doi = {10.1266/ggs.23-00275}, pmid = {38267054}, issn = {1880-5779}, abstract = {We report the complete organellar genome sequences of an ultrasmall green alga, Medakamo hakoo strain M-hakoo 311, which has the smallest known nuclear genome in freshwater green algae. Medakamo hakoo has 90.8-kb chloroplast and 36.5-kb mitochondrial genomes containing 80 and 33 putative protein-coding genes, respectively. The mitochondrial genome is the smallest in the Trebouxiophyceae algae studied so far. The GC content of the nuclear genome is 73%, but those of chloroplast and mitochondrial genomes are 41% and 35%, respectively. Codon usages in the organellar genomes have a different tendency from that in the nuclear genome. The organellar genomes have unique characteristics, such as the biased encoding of mitochondrial genes on a single strand and the absence of operon structures in chloroplast ribosomal genes. Medakamo hakoo will be helpful for understanding the evolution of the organellar genome and the regulation of gene expression in chloroplasts and mitochondria.}, }
@article {pmid38258637, year = {2024}, author = {Li, X and Li, W and Huo, J and Li, L and Chen, B and Guo, Z and Ma, Z}, title = {[Identification and expression analysis of citrate synthase 3 gene family members in apple].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {40}, number = {1}, pages = {137-149}, doi = {10.13345/j.cjb.230166}, pmid = {38258637}, issn = {1872-2075}, mesh = {*Citric Acid ; *Malus/genetics ; Citrate (si)-Synthase ; Phylogeny ; Citrates ; }, abstract = {As one of the key enzymes in cell metabolism, the activity of citrate synthase 3 (CS3) regulates the substance and energy metabolism of organisms. The protein members of CS3 family were identified from the whole genome of apple, and bioinformatics analysis was performed and expression patterns were analyzed to provide a theoretical basis for studying the potential function of CS3 gene in apple. BLASTp was used to identify members of the apple CS3 family based on the GDR database, and the basic information of CS3 protein sequence, subcellular localization, domain composition, phylogenetic relationship and chromosome localization were analyzed by Pfam, SMART, MEGA5.0, clustalx.exe, ExPASy Proteomics Server, MEGAX, SOPMA, MEME, WoLF PSORT and other software. The tissue expression and inducible expression characteristics of 6 CS3 genes in apple were determined by acid content and real-time fluorescence quantitative polymerase chain reaction (qRT-PCR). Apple CS3 gene family contains 6 members, and these CS3 proteins contain 473-608 amino acid residues, with isoelectric point distribution between 7.21 and 8.82. Subcellular localization results showed that CS3 protein was located in mitochondria and chloroplasts, respectively. Phylogenetic analysis divided them into 3 categories, and the number of genes in each subfamily was 2. Chromosome localization analysis showed that CS3 gene was distributed on different chromosomes of apple. The secondary structure of protein is mainly α-helix, followed by random curling, and the proportion of β-angle is the smallest. The 6 members were all expressed in different apple tissues. The overall expression trend from high to low was the highest relative expression content of MdCS3.4, followed by MdCS3.6, and the relative expression level of other members was in the order of MdCS3.3 > MdCS3.2 > MdCS3.1 > MdCS3.5. qRT-PCR results showed that MdCS3.1 and MdCS3.3 genes had the highest relative expression in the pulp of 'Chengji No. 1' with low acid content, and MdCS3.2 and MdCS3.3 genes in the pulp of 'Asda' with higher acid content had the highest relative expression. Therefore, in this study, the relative expression of CS3 gene in apple cultivars with different acid content in different apple varieties was detected, and its role in apple fruit acid synthesis was analyzed. The experimental results showed that the relative expression of CS3 gene in different apple varieties was different, which provided a reference for the subsequent study of the quality formation mechanism of apple.}, }
@article {pmid38262350, year = {2024}, author = {Eglit, Y and Shiratori, T and Jerlström-Hultqvist, J and Williamson, K and Roger, AJ and Ishida, KI and Simpson, AGB}, title = {Meteora sporadica, a protist with incredible cell architecture, is related to Hemimastigophora.}, journal = {Current biology : CB}, volume = {34}, number = {2}, pages = {451-459.e6}, doi = {10.1016/j.cub.2023.12.032}, pmid = {38262350}, issn = {1879-0445}, abstract = {"Kingdom-level" branches are being added to the tree of eukaryotes at a rate approaching one per year, with no signs of slowing down.[1][,][2][,][3][,][4] Some are completely new discoveries, whereas others are morphologically unusual protists that were previously described but lacked molecular data. For example, Hemimastigophora are predatory protists with two rows of flagella that were known since the 19[th] century but proved to represent a new deep-branching eukaryote lineage when phylogenomic analyses were conducted.[2]Meteora sporadica[5] is a protist with a unique morphology; cells glide over substrates along a long axis of anterior and posterior projections while a pair of lateral "arms" swing back and forth, a motility system without any obvious parallels. Originally, Meteora was described by light microscopy only, from a short-term enrichment of deep-sea sediment. A small subunit ribosomal RNA (SSU rRNA) sequence was reported recently, but the phylogenetic placement of Meteora remained unresolved.[6] Here, we investigated two cultivated Meteora sporadica isolates in detail. Transmission electron microscopy showed that both the anterior-posterior projections and the arms are supported by microtubules originating from a cluster of subnuclear microtubule organizing centers (MTOCs). Neither have a flagellar axoneme-like structure. Sequencing the mitochondrial genome showed this to be among the most gene-rich known, outside jakobids. Remarkably, phylogenomic analyses of 254 nuclear protein-coding genes robustly support a close relationship with Hemimastigophora. Our study suggests that Meteora and Hemimastigophora together represent a morphologically diverse "supergroup" and thus are important for resolving the tree of eukaryote life and early eukaryote evolution.}, }
@article {pmid38262211, year = {2024}, author = {Tang, W and Li, X and Ye, B and Shi, B and Zhang, H and Dang, Z and Sun, Y and Danqu, L and Xia, C and Quzhen, D and Zhao, X and Chui, W and Huang, F}, title = {Characterization of the complete mitochondrial genome and phylogenetic analyses of Haemaphysalis tibetensis Hoogstraal, 1965 (Acari: Ixodidae).}, journal = {Ticks and tick-borne diseases}, volume = {15}, number = {2}, pages = {102311}, doi = {10.1016/j.ttbdis.2024.102311}, pmid = {38262211}, issn = {1877-9603}, abstract = {Ticks are specialized ectoparasites that feed on blood, causing physical harm to the host and facilitating pathogen transmission. The genus Haemaphysalis contains vectors for numerous infectious agents. These agents cause various diseases in humans and animals. Mitochondrial genome sequences serve as reliable molecular markers, forming a crucial basis for evolutionary analyses, studying species origins, and exploring molecular phylogeny. We extracted mitochondrial genome from the enriched mitochondria of Haemaphysalis tibetensis and obtained a 14,714-bp sequence. The mitochondrial genome consists of 13 protein-coding genes (PCGs), two ribosomal RNA, 22 transfer RNAs (tRNAs), and two control regions. The nucleotide composition of H. tibetensis mitochondrial genome was 38.38 % for A, 9.61 % for G, 39.32 % for T, and 12.69 % for C. The A + T content of H. tibetensis mitochondrial genome was 77.7 %, significantly higher than the G + C content. The repeat units of H. tibetensis exhibited two identical repeat units of 33 bp in length, positioned downstream of nad1 and rrnL genes. Furthermore, phylogenetic analyses based on the 13 PCGs indicated that Haemaphysalis tibetensis (subgenus Allophysalis) formed a monophyletic clade with Haemaphysalis nepalensis (subgenus Herpetobia) and Haemaphysalis danieli (subgenus Allophysalis). Although the species Haemaphysalis inermis, Haemaphysalis kitaokai, Haemaphysalis kolonini, and Haemaphysalis colasbelcouri belong to the subgenus Alloceraea, which were morphologically primitive hemaphysalines just like H. tibetensis, these four tick species cannot form a single clade with H. tibetensis. In this study, the whole mitochondrial genome sequence of H. tibetensis from Tibet was obtained, which enriched the mitochondrial genome data of ticks and provided genetic markers to study the population heredity and molecular evolution of the genus Haemaphysalis.}, }
@article {pmid38261394, year = {2024}, author = {Sequeira, AN and O'Keefe, IP and Katju, V and Bergthorsson, U}, title = {Friend turned foe: selfish behavior of a spontaneously arising mitochondrial deletion in an experimentally evolved C. elegans population.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkae018}, pmid = {38261394}, issn = {2160-1836}, abstract = {Selfish mitochondrial DNA (mtDNA) mutations are variants that can proliferate within cells and enjoy a replication or transmission bias without fitness benefits for the host. MtDNA deletions in Caenorhabditis elegans can reach high heteroplasmic frequencies despite significantly reducing fitness, illustrating how new mtDNA variants can give rise to genetic conflict between different levels of selection, and between the nuclear and mitochondrial genomes. During a mutation accumulation (MA) experiment in C. elegans, a 1,034 bp deletion originated spontaneously and reached an 81.7% frequency within an experimental evolution line. This heteroplasmic mtDNA deletion, designated as meuDf1, eliminated portions of two protein-coding genes (coxIII and nd4) and tRNA-thr in entirety. MtDNA copy-number in meuDf1 heteroplasmic individuals was 35% higher than in individuals with wildtype mitochondria. After backcrossing into a common genetic background, the meuDf1 mitotype was associated with reduction in several fitness traits and independent competition experiments found a 40% reduction in composite fitness. Experiments that relaxed individual selection by single individual bottlenecks demonstrated that the deletion-bearing mtDNA possessed a strong transmission bias, thereby qualifying it as a novel selfish mitotype.}, }
@article {pmid38259100, year = {2024}, author = {Zhang, Y and Li, H and Wang, Y and Nie, M and Zhang, K and Pan, J and Zhang, Y and Ye, Z and Zufall, RA and Lynch, M and Long, H}, title = {Mitogenomic architecture and evolution of the soil ciliates Colpoda.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0116123}, doi = {10.1128/msystems.01161-23}, pmid = {38259100}, issn = {2379-5077}, abstract = {Colpoda are cosmopolitan unicellular eukaryotes primarily inhabiting soil and benefiting plant growth, but they remain one of the least understood taxa in genetics and genomics within the realm of ciliated protozoa. Here, we investigate the architecture of de novo assembled mitogenomes of six Colpoda species, using long-read sequencing and involving 36 newly isolated natural strains in total. The mitogenome sizes span from 43 to 63 kbp and typically contain 28-33 protein-coding genes. They possess a linear structure with variable telomeres and central repeats, with one Colpoda elliotti strain isolated from Tibet harboring the longest telomeres among all studied ciliates. Phylogenomic analyses reveal that Colpoda species started to diverge more than 326 million years ago, eventually evolving into two distinct groups. Collinearity analyses also reveal significant genomic divergences and a lack of long collinear blocks. One of the most notable features is the exceptionally high level of gene rearrangements between mitochondrial genomes of different Colpoda species, dominated by gene loss events. Population-level mitogenomic analysis on natural strains also demonstrates high sequence divergence, regardless of geographic distance, but the gene order remains highly conserved within species, offering a new species identification criterion for Colpoda species. Furthermore, we identified underlying heteroplasmic sites in the majority of strains of three Colpoda species, albeit without a discernible recombination signal to account for this heteroplasmy. This comprehensive study systematically unveils the mitogenomic structure and evolution of these ancient and ecologically significant Colpoda ciliates, thus laying the groundwork for a deeper understanding of the evolution of unicellular eukaryotes.IMPORTANCEColpoda, one of the most widespread ciliated protozoa in soil, are poorly understood in regard to their genetics and evolution. Our research revealed extreme mitochondrial gene rearrangements dominated by gene loss events, potentially leading to the streamlining of Colpoda mitogenomes. Surprisingly, while interspecific rearrangements abound, our population-level mitogenomic study revealed a conserved gene order within species, offering a potential new identification criterion. Phylogenomic analysis traced their lineage over 326 million years, revealing two distinct groups. Substantial genomic divergence might be associated with the lack of extended collinear blocks and relaxed purifying selection. This study systematically reveals Colpoda ciliate mitogenome structures and evolution, providing insights into the survival and evolution of these vital soil microorganisms.}, }
@article {pmid38255908, year = {2024}, author = {Mirra, S and Marfany, G}, title = {From Beach to the Bedside: Harnessing Mitochondrial Function in Human Diseases Using New Marine-Derived Strategies.}, journal = {International journal of molecular sciences}, volume = {25}, number = {2}, pages = {}, doi = {10.3390/ijms25020834}, pmid = {38255908}, issn = {1422-0067}, support = {PID2022-140957OB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 2021SGR-01093//Government of Catalonia/ ; }, abstract = {Mitochondria are double-membrane organelles within eukaryotic cells that act as cellular power houses owing to their ability to efficiently generate the ATP required to sustain normal cell function. Also, they represent a "hub" for the regulation of a plethora of processes, including cellular homeostasis, metabolism, the defense against oxidative stress, and cell death. Mitochondrial dysfunctions are associated with a wide range of human diseases with complex pathologies, including metabolic diseases, neurodegenerative disorders, and cancer. Therefore, regulating dysfunctional mitochondria represents a pivotal therapeutic opportunity in biomedicine. Marine ecosystems are biologically very diversified and harbor a broad range of organisms, providing both novel bioactive substances and molecules with meaningful biomedical and pharmacological applications. Recently, many mitochondria-targeting marine-derived molecules have been described to regulate mitochondrial biology, thus exerting therapeutic effects by inhibiting mitochondrial abnormalities, both in vitro and in vivo, through different mechanisms of action. Here, we review different strategies that are derived from marine organisms which modulate specific mitochondrial processes or mitochondrial molecular pathways and ultimately aim to find key molecules to treat a wide range of human diseases characterized by impaired mitochondrial function.}, }
@article {pmid38243053, year = {2024}, author = {Seesamut, T and Oba, Y and Jirapatrasilp, P and Martinsson, S and Lindström, M and Erséus, C and Panha, S}, title = {Global species delimitation of the cosmopolitan marine littoral earthworm Pontodrilus litoralis (Grube, 1855).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {1753}, pmid = {38243053}, issn = {2045-2322}, support = {TRF-DPG628001//Thailand Research Fund/ ; BDC-PG2-161002//Center of Excellence on Biodiversity/ ; N35E660138//National Research Council of Thailand/ ; }, mesh = {Animals ; Phylogeny ; *Oligochaeta/genetics ; Mitochondria ; Asia ; Australia ; }, abstract = {The marine littoral earthworm Pontodrilus litoralis (Grube, 1855) is widely distributed and is reported as a single species. This study utilized an integrative taxonomic approach based upon morphological examination, phylogenetic reconstruction, and molecular species delimitation, to test whether the taxon is a single species or a species complex. For this, a total of 114 P. litoralis specimens collected from North America, Africa, Australia and Oceania, Europe and Asia were used. The phylogenetic analyses revealed deeply divergent mitochondrial lineages and a high level of genetic diversity among P. litoralis populations. Both single and multi-locus species delimitation analyses yielded several molecular operational taxonomic units. Therefore, due to the homogeneity of morphological characteristics, it is likely that the morphospecies P. litoralis is a complex of four or more cryptic species, suggesting that more sampling is required and that the population structure genetic data and gene flow need to be investigated.}, }
@article {pmid37877347, year = {2024}, author = {Choi, SW and Yu, HJ and Kim, JK}, title = {Comparative ontogeny and phylogenetic relationships of eight lizardfish species (Synodontidae) from the Northwest Pacific, with a focus on Trachinocephalus monophyly.}, journal = {Journal of fish biology}, volume = {104}, number = {1}, pages = {284-303}, doi = {10.1111/jfb.15595}, pmid = {37877347}, issn = {1095-8649}, support = {R2023001//the National Institute of Fisheries Science/ ; 2023//the National Marine Biodiversity Institute of Korea/ ; }, mesh = {Animals ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Fishes/anatomy &amp; histology ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Larva ; }, abstract = {Lizardfish (Aulopiforms: Synodontidae), distributed broadly in temperate to tropical waters, are represented globally by 83 species across four genera, with 10 species in Korea. Despite these numbers, few studies have been conducted on the early life history of lizardfishes compared to their adult counterparts. Thus, we conducted molecular identification of 123 Synodontidae larvae collected from the Northwest Pacific (Korea Strait, Yellow Sea, East China Sea, and East Sea) between June 2017 and July 2021, using mitochondrial DNA COI and 16S rRNA sequences. Significant morphological differences were observed in the larvae and juvenile, including variation in melanophore, count, morphometric characteristics, and body shape. The morphological traits of eight species (Harpadon nehereus, Saurida macrolepis, Saurida wanieso, Saurida sp., Synodus hoshinonis, Synodus kaianus, Synodus macrops, and Trachinocephalus trachinus) served as vital data for interpreting the phylogenetic relationships within the Northwest Pacific Synodontidae. Ultimately, the identification key revealed by this study will enable accurate identification of Synodontid larvae and juveniles, and further facilitate our understanding of the phylogenetic relationships within this family.}, }
@article {pmid38241813, year = {2024}, author = {Satoh, S and Miyake, K and Adachi, Y and Masuhiro, K and Futami, S and Naito, Y and Shiroyama, T and Koyama, S and Yamaguchi, Y and Konaka, H and Takamatsu, H and Okuzaki, D and Nagatomo, I and Takeda, Y and Kumanogoh, A}, title = {Cancer-associated SNRPD3 mutation confers resistance to hypoxia, which is attenuated by DRP1 inhibition.}, journal = {Biochemical and biophysical research communications}, volume = {696}, number = {}, pages = {149511}, doi = {10.1016/j.bbrc.2024.149511}, pmid = {38241813}, issn = {1090-2104}, abstract = {RNA splicing is a fundamental cellular mechanism performed by spliceosomes that synthesise multiple mature RNA isoforms from a single gene. The association between spliceosome abnormality and solid cancers remains largely unknown. Here, we demonstrated that Sm proteins, which are common components of the spliceosomes and constitute the Sm ring, were overexpressed in multiple cancers and their expression levels were correlated with clinical prognosis. In a pan-cancer mutational hotspot in the Sm ring at SNRPD3 G96V, we found that the G96V substitution confers resistance to hypoxia. RNA-seq detected numerous differentially spliced events between the wild-type and mutation-carrying cells cultured under hypoxia, wherein skipping exons and mutually exclusive exons were frequently observed. This was observed in DNM1L mRNA, which encodes the DRP1 protein that regulates mitochondrial fission. The mitochondria of cells carrying this mutation were excessively fragmented compared with those of wild-type cells. Furthermore, treatment with a DRP1 inhibitor (Mdivi-1) recovered the over-fragmented mitochondria, leading to the attenuation of hypoxia resistance in the mutant cells. These results propose a novel correlation between the cancer-related spliceosome abnormality and mitochondrial fission. Thus, targeting SNRPD3 G96V with a DRP1 inhibitor is a potential treatment strategy for cancers with spliceosome abnormalities.}, }
@article {pmid38238104, year = {2024}, author = {Ali, NA and Song, W and Huang, J and Wu, D and Zhao, X}, title = {Recent advances and biotechnological applications of RNA metabolism in plant chloroplasts and mitochondria.}, journal = {Critical reviews in biotechnology}, volume = {}, number = {}, pages = {1-22}, doi = {10.1080/07388551.2023.2299789}, pmid = {38238104}, issn = {1549-7801}, abstract = {The chloroplast and mitochondrion are semi-autonomous organelles that play essential roles in cell function. These two organelles are embellished with prokaryotic remnants and contain many new features emerging from the co-evolution of organelles and the nucleus. A typical plant chloroplast or mitochondrion genome encodes less than 100 genes, and the regulation of these genes' expression is remarkably complex. The regulation of chloroplast and mitochondrion gene expression can be achieved at multiple levels during development and in response to environmental cues, in which, RNA metabolism, including: RNA transcription, processing, translation, and degradation, plays an important role. RNA metabolism in plant chloroplasts and mitochondria combines bacterial-like traits with novel features evolved in the host cell and is regulated by a large number of nucleus-encoded proteins. Among these, pentatricopeptide repeat (PPR) proteins are deeply involved in multiple aspects of the RNA metabolism of organellar genes. Research over the past decades has revealed new insights into different RNA metabolic events in plant organelles, such as the composition of chloroplast and mitochondrion RNA editosomes. We summarize and discuss the most recent knowledge and biotechnological implications of various RNA metabolism processes in plant chloroplasts and mitochondria, with a focus on the nucleus-encoded factors supporting them, to gain a deeper understanding of the function and evolution of these two organelles in plant cells. Furthermore, a better understanding of the role of nucleus-encoded factors in chloroplast and mitochondrion RNA metabolism will motivate future studies on manipulating the plant gene expression machinery with engineered nucleus-encoded factors.}, }
@article {pmid38235059, year = {2023}, author = {Bayazit, MB and Francois, A and McGrail, E and Accornero, F and Stratton, MS}, title = {mt-tRNAs in the polymerase gamma mutant heart.}, journal = {The journal of cardiovascular aging}, volume = {3}, number = {4}, pages = {}, pmid = {38235059}, issn = {2768-5993}, abstract = {INTRODUCTION: Mice harboring a D257A mutation in the proofreading domain of the mitochondrial DNA polymerase, Polymerase Gamma (POLG), experience severe metabolic dysfunction and display hallmarks of accelerated aging. We previously reported a mitochondrial unfolded protein response (UPT[mt]) - like (UPR[mt]-like) gene and protein expression pattern in the right ventricular tissue of POLG mutant mice.<br><br>AIM: We sought to determine if POLG mutation altered the expression of genes encoded by the mitochondria in a way that might also reduce proteotoxic stress.<br><br>METHODS AND RESULTS: The expression of genes encoded by the mitochondrial DNA was interrogated via RNA-seq and northern blot analysis. A striking, location-dependent effect was seen in the expression of mitochondrial-encoded tRNAs in the POLG mutant as assayed by RNA-seq. These expression changes were negatively correlated with the tRNA partner amino acid's amyloidogenic potential. Direct measurement by northern blot was conducted on candidate mt-tRNAs identified from the RNA-seq. This analysis confirmed reduced expression of MT-TY in the POLG mutant but failed to show increased expression of MT-TP, which was dramatically increased in the RNA-seq data.<br><br>CONCLUSION: We conclude that reduced expression of amyloid-associated mt-tRNAs is another indication of adaptive response to severe mitochondrial dysfunction in the POLG mutant. Incongruence between RNA-seq and northern blot measurement of MT-TP expression points towards the existence of mt-tRNA post-transcriptional modification regulation in the POLG mutant that alters either polyA capture or cDNA synthesis in RNA-seq library generation. Together, these data suggest that 1) evolution has distributed mt-tRNAs across the circular mitochondrial genome to allow chromosomal location-dependent mt-tRNA regulation (either by expression or PTM) and 2) this regulation is cognizant of the tRNA partner amino acid's amyloidogenic properties.}, }
@article {pmid38228651, year = {2024}, author = {Krishnan, N and Csiszár, V and Móri, TF and Garay, J}, title = {Genesis of ectosymbiotic features based on commensalistic syntrophy.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {1366}, pmid = {38228651}, issn = {2045-2322}, support = {955708//Horizon 2020/ ; 125569//NKFIH/ ; }, abstract = {The symbiogenetic origin of eukaryotes with mitochondria is considered a major evolutionary transition. The initial interactions and conditions of symbiosis, along with the phylogenetic affinity of the host, are widely debated. Here, we focus on a possible evolutionary path toward an association of individuals of two species based on unidirectional syntrophy. With the backing of a theoretical model, we hypothesize that the first step in the evolution of such symbiosis could be the appearance of a linking structure on the symbiont's membrane, using which it forms an ectocommensalism with its host. We consider a commensalistic model based on the syntrophy hypothesis in the framework of coevolutionary dynamics and mutant invasion into a monomorphic resident system (evolutionary substitution). We investigate the ecological and evolutionary stability of the consortium (or symbiotic merger), with vertical transmissions playing a crucial role. The impact of the 'effectiveness of vertical transmission' on the dynamics is also analyzed. We find that the transmission of symbionts and the additional costs incurred by the mutant determine the conditions of fixation of the consortia. Additionally, we observe that small and highly metabolically active symbionts are likely to form the consortia.}, }
@article {pmid38221380, year = {2023}, author = {Doniol-Valcroze, P and Coiffard, P and Alstrm, P and Robb, M and Dufour, P and Crochet, PA}, title = {Molecular and acoustic evidence support the species status of Anthus rubescens rubescens and Anthus [rubescens] japonicus (Passeriformes: Motacillidae).}, journal = {Zootaxa}, volume = {5343}, number = {2}, pages = {173-192}, doi = {10.11646/zootaxa.5343.2.4}, pmid = {38221380}, issn = {1175-5334}, mesh = {Animals ; *Passeriformes/genetics ; Plant Breeding ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; }, abstract = {The Buff-bellied Pipit Anthus rubescens comprises two allopatric subspecies groups: A. r. rubescens and A. r. alticola in North America and A. [r.] japonicus in north-east Asia. Despite their great morphological resemblance in breeding plumage, most individuals can be assigned to one or the other subspecies group in non-breeding plumage. Allopatric distributions, morphological differentiation and previously reported molecular divergence suggested the need for additional taxonomic study to assess the rank of these two populations. To resolve the taxonomy of the Buff-bellied Pipit species complex we analysed i) two mitochondrial DNA (mtDNA) loci and ii) nine bioacoustic parameters across 69 sound recordings (338 flight calls) recovered from public databases using principal component analysis and Euclidean distance measures. By comparing our mtDNA and call divergence measures with similar values measured between long-recognised species pairs of the genus, we show that the level of mitochondrial and acoustic divergence between the two Buff-bellied Pipit subspecies groups is typical of species-level divergence in the genus Anthus. Therefore, we recommend splitting the Buff-bellied Pipit species complex into two species: Anthus rubescens (American Pipit) and Anthus japonicus (Siberian Pipit). Our results also suggest that the Water Pipit A. spinoletta deserves taxonomic reassessment as its lineages are highly divergent in acoustics and mtDNA, while mtDNA relationships suggest paraphyly relative to the Rock Pipit A. petrosus. Our work highlights the crucial importance of integrative approaches in taxonomy and the usefulness of bioacoustics in studying cryptic diversity.}, }
@article {pmid38221354, year = {2023}, author = {Hoare, RJB and Patrick, BH and Buckley, TR and Brav-Cubitt, T}, title = {Wing pattern variation and DNA barcodes defy taxonomic splitting in the New Zealand Pimelea Looper Notoreas perornata (Walker) (Lepidoptera: Geometridae: Larentiinae): the importance of populations as conservation units.}, journal = {Zootaxa}, volume = {5346}, number = {1}, pages = {1-27}, doi = {10.11646/zootaxa.5346.1.1}, pmid = {38221354}, issn = {1175-5334}, mesh = {Animals ; *Lepidoptera/genetics ; DNA Barcoding, Taxonomic ; New Zealand ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; *Moths/genetics/anatomy &amp; histology ; Phylogeny ; }, abstract = {The endemic Notoreas perornata (Walker, 1863) complex (Lepidoptera: Geometridae: Larentiinae) from the North Island and northern South Island of New Zealand is reviewed. Larvae feed on Pimelea spp. (Thymelaeaceae), frequently in highly fragmented and threatened shrubland habitats. Allopatric populations tend to differ in size and wing pattern characteristics, but not in genitalia; moreover extensive variation renders recognition of subspecies / allopatric species based on any species concept problematic. A mitochondrial DNA gene tree is not congruent with morphology and indicates rapid recent divergence that has not settled into diagnosable lineages. Based on our results, we synonymise Notoreas simplex Hudson, 1898 with N. perornata (Walker, 1863), and retain N. perornata as a single, highly diverse but monotypic species. All known populations are illustrated to display variation. For conservation purposes, we recommend the continued recognition within the species of 10 populations or groups of populations that appear to be on the way to diverging at subspecific level based on morphological and/or DNA data. The conservation status of all these populations is reviewed. One conservation unit, comprising the populations from Westland, has not been seen since 1998 and is feared possibly extinct.}, }
@article {pmid38221179, year = {2024}, author = {Antoniolli, HRM and Carvalho, TL and Gottschalk, MS and Loreto, ELS and Robe, LJ and Depr, M}, title = {Systematics and spatio-temporal evolutionary patterns of the flavopilosa group of Drosophila (Diptera, Drosophilidae).}, journal = {Zootaxa}, volume = {5399}, number = {1}, pages = {1-18}, doi = {10.11646/zootaxa.5399.1.1}, pmid = {38221179}, issn = {1175-5334}, mesh = {Animals ; *Drosophila/genetics ; Phylogeny ; *Plant Breeding ; Biological Evolution ; Mitochondria/genetics ; }, abstract = {The Drosophila flavopilosa group comprises morphologically cryptic species that are ecologically restricted to feeding, breeding and ovipositing on flowers of Cestrum and Sessea (Solanaceae). Previous studies confirmed the monophyly of the group and the success of DNA barcoding in identifying a subset of its species, but several others remain yet to be evaluated. Furthemore, the taxonomy of the group remains incomplete, with only nine of the 17 species assigned to subgroups. Here, we accessed the phylogenetic relationships and spatio-temporal evolutionary patterns of the flavopilosa group based on a mitochondrial and two nuclear genes, providing the first molecular support to the subdivision of the group and suggesting a new taxonomic scheme for its species. Barcoding proved to be an effective tool, as all species were reciprocally monophyletic and different analyses of species delimitation yielded congruent results. The close relationship of D. flavopilosa with D. cestri and D. cordeiroi was strongly supported, suggesting that the latter should be placed in the flavopilosa subgroup together with the first. Furthermore, D. mariaehelenae was positioned as sister to D. incompta, supporting its inclusion in the nesiota subgroup. Despite new taxonomic assignments, the synapomorphic status of the diagnostic characters proposed for both subgroups was supported. Based on them, each of the remaining species were placed into one of both subgroups. Divergence time estimates suggest that their diversification coincided with the divergence of Sessea and Cestrum, providing an interesting case of coevolution.}, }
@article {pmid38216865, year = {2024}, author = {Cao, L and Chen, P and Hou, X and Ma, J and Yang, N and Lu, Y and Huang, H}, title = {rDNA and mtDNA analysis for the identification of genetic characters in the hybrid grouper derived from hybridization of Cromileptes altivelis (female) × Epinephelus lanceolatus (male).}, journal = {BMC genomic data}, volume = {25}, number = {1}, pages = {5}, pmid = {38216865}, issn = {2730-6844}, support = {YSPTZX202103//The Innovation Platform for Academicians of Hainan Province/ ; RHDRC202010//Scientific Research Foundation of Hainan Tropical Ocean University/ ; 321QN263//Hainan Provincial Natural Science Foundation of China/ ; 32160861//National Natural Science Foundation of China/ ; ZDKJ2021017//The Major Science and Technology plan of Hainan Province/ ; 2020KF001//State Key Laboratory of Developmental Biology of Freshwater Fish/ ; }, mesh = {Animals ; *Bass/genetics/anatomy &amp; histology ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Phylogeny ; Mitochondria/genetics ; }, abstract = {BACKGROUND: Hybridization is a useful strategy to produce offspring with more desirable phenotypic characteristics than those of parents. The hybrid grouper derived from the cross of Cromileptes altivelis (♀, 2n = 48) with Epinephelus lanceolatus (♂, 2n = 48) exhibits improved growth compared with its female parent, which makes it valuable to aquaculture. However, the genetic traits of the hybrid grouper are poorly understood.<br><br>RESULTS: The observations showed that the hybrid grouper was diploid (2n&#x2009;=&#x2009;48) and displayed intermediate morphology with the parent's measurable characteristics. The ribosomal DNA (rDNA) and mitochondria DNA (mtDNA) were characterized at molecular and phylogenetic level. High similarity and low genetic distance of 5S rDNA and mtDNA sequences between the hybrid grouper and C. altivelis showed that the hybrid grouper had a closer genetic relationship with female parents. The reconstructed phylogenetic tree based on COI gene and D-loop region of mtDNA recovered that mtDNA was maternally inherited in the hybrid grouper. Additionally, the DNA methylation level of 5S rDNA intergenic spacers (IGS) sequence was tested in here. The results showed that the DNA methylation status of the hybrid grouper was significantly lower than that of C. altivelis.<br><br>CONCLUSION: Results of this study provide important data on the genetic characteristics of the hybrid derived from the cross of C. altivelis and E. lanceolatus, and contribute the knowledge of both evolution and marine fish breeding.}, }
@article {pmid38206324, year = {2024}, author = {Crino, OL and Head, ML and Jennions, MD and Noble, DWA}, title = {Mitochondrial function and sexual selection: can physiology resolve the 'lek paradox'?.}, journal = {The Journal of experimental biology}, volume = {227}, number = {2}, pages = {}, doi = {10.1242/jeb.245569}, pmid = {38206324}, issn = {1477-9145}, support = {DP210101152//Australian Research Council/ ; }, mesh = {Female ; Male ; Humans ; *Reproduction ; *Biological Evolution ; Exercise ; Food ; Mitochondria/genetics ; }, abstract = {Across many taxa, males use elaborate ornaments or complex displays to attract potential mates. Such sexually selected traits are thought to signal important aspects of male 'quality'. Female mating preferences based on sexual traits are thought to have evolved because choosy females gain direct benefits that enhance their lifetime reproductive success (e.g. greater access to food) and/or indirect benefits because high-quality males contribute genes that increase offspring fitness. However, it is difficult to explain the persistence of female preferences when males only provide genetic benefits, because female preferences should erode the heritable genetic variation in fitness that sexually selected traits signal. This 'paradox of the lek' has puzzled evolutionary biologists for decades, and inspired many hypotheses to explain how heritable variation in sexually selected traits is maintained. Here, we discuss how factors that affect mitochondrial function can maintain variation in sexually selected traits despite strong female preferences. We discuss how mitochondrial function can influence the expression of sexually selected traits, and we describe empirical studies that link the expression of sexually selected traits to mitochondrial function. We explain how mothers can affect mitochondrial function in their offspring by (a) influencing their developmental environment through maternal effects and (b) choosing a mate to increase the compatibility of mitochondrial and nuclear genes (i.e. the 'mitonuclear compatibility model of sexual selection'). Finally, we discuss how incorporating mitochondrial function into models of sexual selection might help to resolve the paradox of the lek, and we suggest avenues for future research.}, }
@article {pmid38203264, year = {2023}, author = {Baleva, MV and Piunova, U and Chicherin, I and Vasilev, R and Levitskii, S and Kamenski, P}, title = {Mitochondrial Protein SLIRP Affects Biosynthesis of Cytochrome c Oxidase Subunits in HEK293T Cells.}, journal = {International journal of molecular sciences}, volume = {25}, number = {1}, pages = {}, pmid = {38203264}, issn = {1422-0067}, support = {21-14-00008//Russian Science Foundation/ ; 24-2-21//Moscow University State Assignment/ ; }, mesh = {Humans ; *Electron Transport Complex IV/genetics ; *Mitochondrial Proteins/genetics ; HEK293 Cells ; Mitochondria/genetics ; Eukaryotic Cells ; RNA-Binding Proteins ; }, abstract = {Mitochondria carry out various vital roles in eukaryotic cells, including ATP energy synthesis, the regulation of apoptosis, Fe-S cluster formation, and the metabolism of fatty acids, amino acids, and nucleotides. Throughout evolution, mitochondria lost most of their ancestor's genome but kept the replication, transcription, and translation machinery. Protein biosynthesis in mitochondria is specialized in the production of highly hydrophobic proteins encoded by mitochondria. These proteins are components of oxidative phosphorylation chain complexes. The coordination of protein synthesis must be precise to ensure the correct assembly of nuclear-encoded subunits for these complexes. However, the regulatory mechanisms of mitochondrial translation in human cells are not yet fully understood. In this study, we examined the contribution of the SLIRP protein in regulating protein biosynthesis in mitochondria. Using a click-chemistry approach, we discovered that deletion of the SLIRP gene disturbs mitochondrial translation, leading to the dysfunction of complexes I and IV, but it has no significant effect on complexes III and V. We have shown that this protein interacts only with the small subunit of the mitochondrial ribosome, which may indicate its involvement in the regulation of the mitochondrial translation initiation stage.}, }
@article {pmid38200446, year = {2024}, author = {Korolija, M and Sukser, V and Vlahoviček, K}, title = {Mitochondrial point heteroplasmy: insights from deep-sequencing of human replicate samples.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {48}, pmid = {38200446}, issn = {1471-2164}, mesh = {Humans ; *Heteroplasmy ; Phylogeny ; *Mitochondria/genetics ; High-Throughput Nucleotide Sequencing ; DNA, Mitochondrial/genetics ; }, abstract = {BACKGROUND: Human mitochondrial heteroplasmy is an extensively investigated phenomenon in the context of medical diagnostics, forensic identification and molecular evolution. However, technical limitations of high-throughput sequencing hinder reliable determination of point heteroplasmies (PHPs) with minor allele frequencies (MAFs) within the noise threshold.<br><br>RESULTS: To investigate the PHP landscape at an MAF threshold down to 0.1%, we sequenced whole mitochondrial genomes at approximately 7.700x coverage, in multiple technical and biological replicates of longitudinal blood and buccal swab samples from 11 human donors (159 libraries in total). The results obtained by two independent sequencing platforms and bioinformatics pipelines indicate distinctive PHP patterns below and above the 1% MAF cut-off. We found a high inter-individual prevalence of low-level PHPs (MAF&#x2009;<&#x2009;1%) at polymorphic positions of the mitochondrial DNA control region (CR), their tissue preference, and a tissue-specific minor allele linkage. We also established the position-dependent potential of minor allele expansion in PHPs, and short-term PHP instability in a mitotically active tissue. We demonstrate that the increase in sensitivity of PHP detection to minor allele frequencies below 1% within a robust experimental and analytical pipeline, provides new information with potential applicative value.<br><br>CONCLUSIONS: Our findings reliably show different mutational loads between tissues at sub-1% allele frequencies, which may serve as an informative medical biomarker of time-dependent, tissue-specific mutational burden, or help discriminate forensically relevant tissues in a single person, close maternal relatives or unrelated individuals of similar phylogenetic background.}, }
@article {pmid38200362, year = {2024}, author = {Liu, J and Hu, JY and Li, DZ}, title = {Remarkable mitochondrial genome heterogeneity in Meniocus linifolius (Brassicaceae).}, journal = {Plant cell reports}, volume = {43}, number = {2}, pages = {36}, pmid = {38200362}, issn = {1432-203X}, support = {XDB31000000//Strategic Priority Research Program (Type-B), Chinese Academy of Science/ ; }, mesh = {*Genome, Mitochondrial/genetics ; *Brassicaceae/genetics ; Phylogeny ; Biological Evolution ; DNA, Mitochondrial/genetics ; }, abstract = {Detailed analyses of 16 genomes identified a remarkable acceleration of mutation rate, hence mitochondrial sequence and structural heterogeneity, in Meniocus linifolius (Brassicaceae). The powerhouse, mitochondria, in plants feature high levels of structural variation, while the encoded genes are normally conserved. However, the substitution rates and spectra of mitochondria DNA within the Brassicaceae, a family with substantial scientific and economic importance, have not been adequately deciphered. Here, by analyzing three newly assembled and 13 known mitochondrial genomes (mitogenomes), we report the highly variable genome structure and mutation rates in Brassicaceae. The genome sizes and GC contents are 196,604 bp and 46.83%, 288,122 bp and 44.79%, and 287,054 bp and 44.93%, for Meniocus linifolius (Mli), Crucihimalaya lasiocarpa (Cla), and Lepidium sativum (Lsa), respectively. In total, 29, 33, and 34 protein-coding genes (PCGs) and 14, 18, and 18 tRNAs are annotated for Mli, Cla, and Lsa, respectively, while all mitogenomes contain one complete circular molecule with three rRNAs and abundant RNA editing sites. The Mli mitogenome features four conformations likely mediated by the two pairs of long repeats, while at the same time seems to have an unusual evolutionary history due to higher GC content, loss of more genes and sequences, but having more repeats and plastid DNA insertions. Corroborating with these, an ambiguous phylogenetic position with long branch length and elevated synonymous substitution rate in nearly all PCGs are observed for Mli. Taken together, our results reveal a high level of mitogenome heterogeneity at the family level and provide valuable resources for further understanding the evolutionary pattern of organelle genomes in Brassicaceae.}, }
@article {pmid38189676, year = {2024}, author = {Huttner, WB and Heide, M and Mora-Bermúdez, F and Namba, T}, title = {Neocortical neurogenesis in development and evolution-Human-specific features.}, journal = {The Journal of comparative neurology}, volume = {}, number = {}, pages = {}, doi = {10.1002/cne.25576}, pmid = {38189676}, issn = {1096-9861}, support = {//Max Planck Society/ ; }, abstract = {In this review, we focus on human-specific features of neocortical neurogenesis in development and evolution. Two distinct topics will be addressed. In the first section, we discuss the expansion of the neocortex during human evolution and concentrate on the human-specific gene ARHGAP11B. We review the ability of ARHGAP11B to amplify basal progenitors and to expand a primate neocortex. We discuss the contribution of ARHGAP11B to neocortex expansion during human evolution and its potential implications for neurodevelopmental disorders and brain tumors. We then review the action of ARHGAP11B in mitochondria as a regulator of basal progenitor metabolism, and how it promotes glutaminolysis and basal progenitor proliferation. Finally, we discuss the increase in cognitive performance due to the ARHGAP11B-induced neocortical expansion. In the second section, we focus on neocortical development in modern humans versus Neanderthals. Specifically, we discuss two recent findings pointing to differences in neocortical neurogenesis between these two hominins that are due to a small number of amino acid substitutions in certain key proteins. One set of such proteins are the kinetochore-associated proteins KIF18a and KNL1, where three modern human-specific amino acid substitutions underlie the prolongation of metaphase during apical progenitor mitosis. This prolongation in turn is associated with an increased fidelity of chromosome segregation to the apical progenitor progeny during modern human neocortical development, with implications for the proper formation of radial units. Another such key protein is transketolase-like 1 (TKTL1), where a single modern human-specific amino acid substitution endows TKTL1 with the ability to amplify basal radial glia, resulting in an increase in upper-layer neuron generation. TKTL1's ability is based on its action in the pentose phosphate pathway, resulting in increased fatty acid synthesis. The data imply greater neurogenesis during neocortical development in modern humans than Neanderthals due to TKTL1, in particular in the developing frontal lobe.}, }
@article {pmid38188667, year = {2023}, author = {Riew, TR and Hwang, JW and Jin, X and Kim, HL and Jung, SJ and Lee, MY}, title = {Astrocytes are involved in the formation of corpora amylacea-like structures from neuronal debris in the CA1 region of the rat hippocampus after ischemia.}, journal = {Frontiers in cellular neuroscience}, volume = {17}, number = {}, pages = {1308247}, pmid = {38188667}, issn = {1662-5102}, abstract = {Recently, we demonstrated that the corpora amylacea (CA), a glycoprotein-rich aggregate frequently found in aged brains, accumulates in the ischemic hippocampus and that osteopontin (OPN) mediates the entire process of CA formation. Therefore, this study aimed to elucidate the mechanisms by which astrocytes and microglia participate in CA formation during the late phase (4-12 weeks) of brain ischemia. Based on various morphological analyses, including immunohistochemistry, in situ hybridization, immunoelectron microscopy, and correlative light and electron microscopy, we propose that astrocytes are the primary cells responsible for CA formation after ischemia. During the subacute phase after ischemia, astrocytes, rather than microglia, express Opn messenger ribonucleic acid and OPN protein, a surrogate marker and key component of CA. Furthermore, the specific localization of OPN in the Golgi complex suggests that it is synthesized and secreted by astrocytes. Astrocytes were in close proximity to type I OPN deposits, which accumulated in the mitochondria of degenerating neurons before fully forming the CA (type III OPN deposits). Throughout CA formation, astrocytes remained closely attached to OPN deposits, with their processes exhibiting well-developed gap junctions. Astrocytic cytoplasmic protein S100β, a calcium-binding protein, was detected within the fully formed CA. Additionally, ultrastructural analysis revealed direct contact between astroglial fibrils and the forming facets of the CA. Overall, we demonstrated that astrocytes play a central role in mediating CA formation from the initial stages of OPN deposit accumulation to the evolution of fully formed CA following transient ischemia in the hippocampus.}, }
@article {pmid38187609, year = {2023}, author = {Sizek, H and Deritei, D and Fleig, K and Harris, M and Regan, PL and Glass, K and Regan, ER}, title = {Unlocking Mitochondrial Dysfunction-Associated Senescence (MiDAS) with NAD [+] - a Boolean Model of Mitochondrial Dynamics and Cell Cycle Control.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.12.18.572194}, pmid = {38187609}, abstract = {UNLABELLED: The steady accumulation of senescent cells with aging creates tissue environments that aid cancer evolution. The secretome of senescent cells promotes chronic inflammation, contains growth and transforming signals, and causes chronic oxidative stress. The latter is primarily due to dysfunctional mitochondria often seen in senescent cells. Aging cell states are highly heterogeneous. 'Deep senescent' cells rely on healthy mitochondria to fuel a strong proinflammatory secretome. In parallel, the triggers of deep senescence also generate cells with mitochondrial dysfunction, and sufficient energy deficit to alter their secretome - a state termed Mitochondrial Dysfunction-Associated Senescence (MiDAS). Here we offer a mechanistic explanation for the molecular processes leading to MiDAS. To do this we have built a Boolean regulatory network model able to reproduce mitochondrial dynamics during cell cycle progression (hyper-fusion at the G1/S boundary, fission in mitosis), apoptosis (fission and dysfunction) and glucose starvation (reversible hyper-fusion), as well as MiDAS in response to SIRT3 knockdown or oxidative stress. Our model also recapitulates the protective role of NAD [+] and external pyruvate. We offer testable predictions about the growth factor- and glucose-dependence of MiDAS and its reversibility at different stages of reactive oxygen species (ROS)-induced senescence. Our model opens the door to modeling distinct stages of DNA-damage induced senescence, the relationship between senescence and epithelial-to-mesenchymal transition in cancer and building multiscale models of tissue aging.<br><br>HIGHLIGHTS: Boolean regulatory network model reproduces mitochondrial dynamics during cell cycle progression, apoptosis, and glucose starvation. Model offers a mechanistic explanation for the positive feedback loop that locks in Mitochondrial Dysfunction-Associated Senescence (MiDAS), involving autophagy-resistant hyperfused but dysfunctional mitochondria. Model reproduces ROS-mediated mitochondrial dysfunction and suggests that MiDAS is part of the early phase of damage-induced senescence. Model predicts that cancer-driving mutations that bypass the G1/S checkpoint generally increase the incidence of MiDAS, with the notable exception of p53 loss.}, }
@article {pmid38186275, year = {2024}, author = {Prokkola, JM and Chew, KK and Anttila, K and Maamela, KS and Yildiz, A and Åsheim, ER and Primmer, CR and Aykanat, T}, title = {Tissue-specific metabolic enzyme levels covary with whole-animal metabolic rates and life-history loci via epistatic effects.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1896}, pages = {20220482}, pmid = {38186275}, issn = {1471-2970}, mesh = {Animals ; Humans ; Anaerobiosis ; Biological Evolution ; Genotype ; Heart ; *Muscles ; *Salmo salar ; Transcription Factors ; Energy Metabolism/physiology ; }, abstract = {Metabolic rates, including standard (SMR) and maximum (MMR) metabolic rate have often been linked with life-history strategies. Variation in context- and tissue-level metabolism underlying SMR and MMR may thus provide a physiological basis for life-history variation. This raises a hypothesis that tissue-specific metabolism covaries with whole-animal metabolic rates and is genetically linked to life history. In Atlantic salmon (Salmo salar), variation in two loci, vgll3 and six6, affects life history via age-at-maturity as well as MMR. Here, using individuals with known SMR and MMR with different vgll3 and six6 genotype combinations, we measured proxies of mitochondrial density and anaerobic metabolism, i.e. maximal activities of the mitochondrial citrate synthase (CS) and lactate dehydrogenase (LDH) enzymes, in four tissues (heart, intestine, liver, white muscle) across low- and high-food regimes. We found enzymatic activities were related to metabolic rates, mainly SMR, in the intestine and heart. Individual loci were not associated with the enzymatic activities, but we found epistatic effects and genotype-by-environment interactions in CS activity in the heart and epistasis in LDH activity in the intestine. These effects suggest that mitochondrial density and anaerobic capacity in the heart and intestine may partly mediate variation in metabolic rates and life history via age-at-maturity. This article is part of the theme issue 'The evolutionary significance of variation in metabolic rates'.}, }
@article {pmid38186271, year = {2024}, author = {Thoral, E and Dargère, L and Medina-Suárez, I and Clair, A and Averty, L and Sigaud, J and Morales, A and Salin, K and Teulier, L}, title = {Non-lethal sampling for assessment of mitochondrial function does not affect metabolic rate and swimming performance.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1896}, pages = {20220483}, pmid = {38186271}, issn = {1471-2970}, mesh = {Animals ; *Swimming ; *Biological Evolution ; Mitochondria ; Muscles ; Oxygen Consumption ; }, abstract = {A fundamental issue in the metabolic field is whether it is possible to understand underlying mechanisms that characterize individual variation. Whole-animal performance relies on mitochondrial function as it produces energy for cellular processes. However, our lack of longitudinal measures to evaluate how mitochondrial function can change within and among individuals and with environmental context makes it difficult to assess individual variation in mitochondrial traits. The aims of this study were to test the repeatability of muscle mitochondrial metabolism by performing two biopsies of red muscle, and to evaluate the effects of biopsies on whole-animal performance in goldfish Carassius auratus. Our results show that basal mitochondrial respiration and net phosphorylation efficiency are repeatable at 14-day intervals. We also show that swimming performance (optimal cost of transport and critical swimming speed) was repeatable in biopsied fish, whereas the repeatability of individual oxygen consumption (standard and maximal metabolic rates) seemed unstable over time. However, we noted that the means of individual and mitochondrial traits did not change over time in biopsied fish. This study shows that muscle biopsies allow the measurement of mitochondrial metabolism without sacrificing animals and that two muscle biopsies 14 days apart affect the intraspecific variation in fish performance without affecting average performance of individuals. This article is part of the theme issue 'The evolutionary significance of variation in metabolic rates'.}, }
@article {pmid38185351, year = {2024}, author = {Zhang, D and Jakovlić, I and Zou, H and Liu, F and Xiang, CY and Gusang, Q and Tso, S and Xue, S and Zhu, WJ and Li, Z and Wu, J and Wang, GT}, title = {Strong mitonuclear discordance in the phylogeny of Neodermata and evolutionary rates of Polyopisthocotylea.}, journal = {International journal for parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijpara.2024.01.001}, pmid = {38185351}, issn = {1879-0135}, abstract = {The genomic evolution of Polyopisthocotylea remains poorly understood in comparison to the remaining three classes of Neodermata: Monopisthocotylea, Cestoda, and Trematoda. Moreover, the evolutionary sequence of major events in the phylogeny of Neodermata remains unresolved. Herein we sequenced the mitogenome and transcriptome of the polyopisthocotylean Diplorchis sp., and conducted comparative evolutionary analyses using nuclear (nDNA) and mitochondrial (mtDNA) genomic datasets of Neodermata. We found strong mitonuclear discordance in the phylogeny of Neodermata. Polyopisthocotylea exhibited striking mitonuclear discordance in relative evolutionary rates: the fastest-evolving mtDNA in Neodermata and a comparatively slowly-evolving nDNA genome. This was largely attributable to its very long stem branch in mtDNA topologies, not exhibited by the nDNA data. We found indications that the fast evolution of mitochondrial genomes of Polyopisthocotylea may be driven both by relaxed purifying selection pressures and elevated levels of directional selection. We identified mitochondria-associated genes encoded in the nuclear genome: they exhibited unique evolutionary rates, but not correlated with the evolutionary rate of mtDNA, and there is no evidence for compensatory evolution (they evolved slower than the rest of the genome). Finally, there appears to exist an exceptionally large (≈6.3 kb) nuclear mitochondrial DNA segment (numt) in the nuclear genome of newly sequenced Diplorchis sp. A 3'-end segment of the 16S rRNA gene encoded by the numt was expressed, suggesting that this gene acquired novel, regulatory functions after the transposition to the nuclear genome. In conclusion, Polyopisthocotylea appears to be the lineage with the fastest-evolving mtDNA sequences among all of Bilateria, but most of the substitutions were accumulated deep in the evolutionary history of this lineage. As the nuclear genome does not exhibit a similar pattern, the circumstances underpinning this evolutionary phenomenon remain a mystery.}, }
@article {pmid38177203, year = {2024}, author = {Yonezawa, T and Mannen, H and Honma, K and Matsunaga, M and Rakotondraparany, F and Ratsoavina, FM and Wu, J and Nishibori, M and Yamamoto, Y}, title = {Origin and spatial population structure of Malagasy native chickens based on mitochondrial DNA.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {569}, pmid = {38177203}, issn = {2045-2322}, support = {21KK0122//JSPS KAKENHI/ ; 21KK0122//JSPS KAKENHI/ ; 21KK0122//JSPS KAKENHI/ ; 21KK0122//JSPS KAKENHI/ ; }, mesh = {Animals ; Africa ; *Chickens/genetics ; *DNA, Mitochondrial/genetics ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Madagascar ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Since Malagasy human culture became established in a multi-layered way by genetic admixture of Austronesian (Indonesia), Bantu (East Africa) and West Asian populations, the Malagasy native livestock should also have originated from these regions. While recent genetic studies revealed that Malagasy native dogs and goats were propagated from Africa, the origin of Malagasy native chickens is still controversial. Here, we conducted a phylogeographic analysis of the native chickens, focusing on the historical relationships among the Indian Ocean rim countries and based on mitochondrial D-loop sequences. Although previous work suggested that the rare Haplogroup D occurs with high frequencies in Island Southeast Asia-Pacific, East Africa and Madagascar, the major mitochondrial lineage in Malagasy populations is actually not Haplogroup D but the Sub-haplogroup C2, which is also observed in East Africa, North Africa, India and West Asia. We demonstrate that the Malagasy native chickens were propagated directly from West Asia (including India and North Africa), and not via East Africa. Furthermore, they display clear genetic differentiation within Madagascar, separated into the Highland and Lowland regions as seen in the human genomic landscape on this island. Our findings provide new insights for better understanding the intercommunion of material/non-material cultures within and around Madagascar.}, }
@article {pmid38174367, year = {2024}, author = {Chi, HM and Davies, MR and Garcia, SM and Montenegro, C and Sharma, S and Lizarraga, M and Wang, Z and Nuthalapati, P and Kim, HT and Liu, X and Feeley, BT}, title = {Defining Endogenous Mitochondrial Transfer in Muscle After Rotator Cuff Injury.}, journal = {The American journal of sports medicine}, volume = {}, number = {}, pages = {3635465231214225}, doi = {10.1177/03635465231214225}, pmid = {38174367}, issn = {1552-3365}, abstract = {BACKGROUND: Rotator cuff muscle degeneration leads to poor clinical outcomes for patients with rotator cuff tears. Fibroadipogenic progenitors (FAPs) are resident muscle stem cells with the ability to differentiate into fibroblasts as well as white and beige adipose tissue. Induction of the beige adipose phenotype in FAPs has been shown to improve muscle quality after rotator cuff tears, but the mechanisms of how FAPs exert their beneficial effects have not been fully elucidated.<br><br>PURPOSE: To study the horizontal transfer of mitochondria from FAPs to myogenic cells and examine the effects of &#x3b2;-agonism on this novel process.<br><br>STUDY DESIGN: Controlled laboratory study.<br><br>METHODS: In mice that had undergone a massive rotator cuff tear, single-cell RNA sequencing was performed on isolated FAPs for genes associated with mitochondrial biogenesis and transfer. Murine FAPs were isolated by fluorescence-activated cell sorting and treated with a &#x3b2;-agonist versus control. FAPs were stained with mitochondrial dyes and cocultured with recipient C2C12 myoblasts, and the rate of transfer was measured after 24 hours by flow cytometry. PdgfraCre[ERT]/MitoTag mice were generated to study the effects of a rotator cuff injury on mitochondrial transfer. PdgfraCre[ERT]/tdTomato mice were likewise generated to perform lineage tracing of PDGFRA[+] cells in this injury model. Both populations of transgenic mice underwent tendon transection and denervation surgery, and MitoTag-labeled mitochondria from Pdgfra[+] FAPs were visualized by fluorescent microscopy, spinning disk confocal microscopy, and 2-photon microscopy; overall mitochondrial quantity was compared between mice treated with &#x3b2;-agonists and dimethyl sulfoxide.<br><br>RESULTS: Single-cell RNA sequencing in mice that underwent rotator cuff tear demonstrated an association between transcriptional markers of adipogenic differentiation and genes associated with mitochondrial biogenesis. In vitro cocultures of murine FAPs with C2C12 cells revealed that treatment of cells with a &#x3b2;-agonist increased mitochondrial transfer compared to control conditions (17.8% &#xb1; 9.9% to 99.6% &#xb1; 0.13% P < .0001). Rotator cuff injury in PdgfraCre[ERT]/MitoTag mice resulted in a robust increase in MitoTag signal in adjacent myofibers compared with uninjured mice. No accumulation of tdTomato signal from PDGFRA[+] cells was seen in injured fibers at 6 weeks after injury, suggesting that FAPs do not fuse with injured muscle fibers but rather contribute their mitochondria.<br><br>CONCLUSION: The authors have described a novel process of endogenous mitochondrial transfer that can occur within the injured rotator cuff between FAPs and myogenic cells. This process may be leveraged therapeutically with &#x3b2;-agonist treatment and represents an exciting target for improving translational therapies available for rotator cuff muscle degeneration.<br><br>CLINICAL RELEVANCE: Promoting endogenous mitochondrial transfer may represent a novel translational strategy to address muscle degeneration after rotator cuff tears.}, }
@article {pmid38170752, year = {2024}, author = {Cui, M and Yamano, K and Yamamoto, K and Yamamoto-Imoto, H and Minami, S and Yamamoto, T and Matsui, S and Kaminishi, T and Shima, T and Ogura, M and Tsuchiya, M and Nishino, K and Layden, BT and Kato, H and Ogawa, H and Oki, S and Okada, Y and Isaka, Y and Kosako, H and Matsuda, N and Yoshimori, T and Nakamura, S}, title = {HKDC1, a target of TFEB, is essential to maintain both mitochondrial and lysosomal homeostasis, preventing cellular senescence.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {2}, pages = {e2306454120}, pmid = {38170752}, issn = {1091-6490}, support = {N/A//China Scholarship Council (CSC)/ ; JPMJCR17H6//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; JP22gm1410014//Japan Agency for Medical Research and Development (AMED)/ ; N/A//Takeda Science Foundation (TSF)/ ; 21H05145//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; 21H02428//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; N/A//Astellas Foundation for Research on Metabolic Disorders/ ; N/A//Mochida Memorial Foundation for Medical and Pharmaceutical Research ()/ ; N/A//Mitsubishi Foundation (The Mitsubishi Foundation)/ ; N/A//NOVARTIS Foundation (Japan) for the Promotion of Science (NOVARTIS Foundation (Japan))/ ; 22H04982//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 23K18140//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 23jm0610091h0001//Japan Agency for Medical Research and Development (AMED)/ ; }, mesh = {*Hexokinase/genetics/metabolism ; Prospective Studies ; *Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics/metabolism ; Mitochondria/metabolism ; Lysosomes/metabolism ; Protein Kinases/metabolism ; Cellular Senescence/genetics ; Homeostasis ; Autophagy/genetics ; }, abstract = {Mitochondrial and lysosomal functions are intimately linked and are critical for cellular homeostasis, as evidenced by the fact that cellular senescence, aging, and multiple prominent diseases are associated with concomitant dysfunction of both organelles. However, it is not well understood how the two important organelles are regulated. Transcription factor EB (TFEB) is the master regulator of lysosomal function and is also implicated in regulating mitochondrial function; however, the mechanism underlying the maintenance of both organelles remains to be fully elucidated. Here, by comprehensive transcriptome analysis and subsequent chromatin immunoprecipitation-qPCR, we identified hexokinase domain containing 1 (HKDC1), which is known to function in the glycolysis pathway as a direct TFEB target. Moreover, HKDC1 was upregulated in both mitochondrial and lysosomal stress in a TFEB-dependent manner, and its function was critical for the maintenance of both organelles under stress conditions. Mechanistically, the TFEB-HKDC1 axis was essential for PINK1 (PTEN-induced kinase 1)/Parkin-dependent mitophagy via its initial step, PINK1 stabilization. In addition, the functions of HKDC1 and voltage-dependent anion channels, with which HKDC1 interacts, were essential for the clearance of damaged lysosomes and maintaining mitochondria-lysosome contact. Interestingly, HKDC1 regulated mitophagy and lysosomal repair independently of its prospective function in glycolysis. Furthermore, loss function of HKDC1 accelerated DNA damage-induced cellular senescence with the accumulation of hyperfused mitochondria and damaged lysosomes. Our results show that HKDC1, a factor downstream of TFEB, maintains both mitochondrial and lysosomal homeostasis, which is critical to prevent cellular senescence.}, }
@article {pmid38170710, year = {2024}, author = {Graham, AM and Lavretsky, P and Wilson, RE and McCracken, KG}, title = {High-altitude adaptation is accompanied by strong signatures of purifying selection in the mitochondrial genomes of three Andean waterfowl.}, journal = {PloS one}, volume = {19}, number = {1}, pages = {e0294842}, pmid = {38170710}, issn = {1932-6203}, mesh = {*Genome, Mitochondrial/genetics ; Altitude ; Genetic Drift ; Mitochondria/genetics ; Environment ; Adaptation, Physiological/genetics ; Selection, Genetic ; }, abstract = {Evidence from a variety of organisms points to convergent evolution on the mitochondria associated with a physiological response to oxygen deprivation or temperature stress, including mechanisms for high-altitude adaptation. Here, we examine whether demography and/or selection explains standing mitogenome nucleotide diversity in high-altitude adapted populations of three Andean waterfowl species: yellow-billed pintail (Anas georgica), speckled teal (Anas flavirostris), and cinnamon teal (Spatula cyanoptera). We compared a total of 60 mitogenomes from each of these three duck species (n = 20 per species) across low and high altitudes and tested whether part(s) or all of the mitogenome exhibited expected signatures of purifying selection within the high-altitude populations of these species. Historical effective population sizes (Ne) were inferred to be similar between high- and low-altitude populations of each species, suggesting that selection rather than genetic drift best explains the reduced genetic variation found in mitochondrial genes of high-altitude populations compared to low-altitude populations of the same species. Specifically, we provide evidence that establishment of these three Andean waterfowl species in the high-altitude environment, coincided at least in part with a persistent pattern of negative purifying selection acting on oxidative phosphorylation (OXPHOS) function of the mitochondria. Our results further reveal that the extent of gene-specific purifying selection has been greatest in the speckled teal, the species with the longest history of high-altitude occupancy.}, }
@article {pmid38164224, year = {2023}, author = {Labbadia, J}, title = {Potential roles for mitochondria-to-HSF1 signaling in health and disease.}, journal = {Frontiers in molecular biosciences}, volume = {10}, number = {}, pages = {1332658}, pmid = {38164224}, issn = {2296-889X}, abstract = {The ability to respond rapidly and efficiently to protein misfolding is crucial for development, reproduction and long-term health. Cells respond to imbalances in cytosolic/nuclear protein homeostasis through the Heat Shock Response, a tightly regulated transcriptional program that enhances protein homeostasis capacity by increasing levels of protein quality control factors. The Heat Shock Response is driven by Heat Shock Factor 1, which is rapidly activated by the appearance of misfolded proteins and drives the expression of genes encoding molecular chaperones and protein degradation factors, thereby restoring proteome integrity. HSF1 is critical for organismal health, and this has largely been attributed to the preservation of cytosolic and nuclear protein homeostasis. However, evidence is now emerging that HSF1 is also a key mediator of mitochondrial function, raising the possibility that many of the health benefits conferred by HSF1 may be due to the maintenance of mitochondrial homeostasis. In this review, I will discuss our current understanding of the interplay between HSF1 and mitochondria and consider how mitochondria-to-HSF1 signaling may influence health and disease susceptibility.}, }
@article {pmid38161329, year = {2023}, author = {Hambardikar, V and Akosah, YA and Scoma, ER and Guitart-Mampel, M and Urquiza, P and Da Costa, RT and Perez, MM and Riggs, LM and Patel, R and Solesio, ME}, title = {Toolkit for cellular studies of mammalian mitochondrial inorganic polyphosphate.}, journal = {Frontiers in cell and developmental biology}, volume = {11}, number = {}, pages = {1302585}, pmid = {38161329}, issn = {2296-634X}, abstract = {Introduction: Inorganic polyphosphate (polyP) is an ancient polymer which is extremely well-conserved throughout evolution, and found in every studied organism. PolyP is composed of orthophosphates linked together by high-energy bonds, similar to those found in ATP. The metabolism and the functions of polyP in prokaryotes and simple eukaryotes are well understood. However, little is known about its physiological roles in mammalian cells, mostly due to its unknown metabolism and lack of systematic methods and effective models for the study of polyP in these organisms. Methods: Here, we present a comprehensive set of genetically modified cellular models to study mammalian polyP. Specifically, we focus our studies on mitochondrial polyP, as previous studies have shown the potent regulatory role of mammalian polyP in the organelle, including bioenergetics, via mechanisms that are not yet fully understood. Results: Using SH-SY5Y cells, our results show that the enzymatic depletion of mitochondrial polyP affects the expression of genes involved in the maintenance of mitochondrial physiology, as well as the structure of the organelle. Furthermore, this depletion has deleterious effects on mitochondrial respiration, an effect that is dependent on the length of polyP. Our results also show that the depletion of mammalian polyP in other subcellular locations induces significant changes in gene expression and bioenergetics; as well as that SH-SY5Y cells are not viable when the amount and/or the length of polyP are increased in mitochondria. Discussion: Our findings expand on the crucial role of polyP in mammalian mitochondrial physiology and place our cell lines as a valid model to increase our knowledge of both mammalian polyP and mitochondrial physiology.}, }
@article {pmid38157451, year = {2024}, author = {Yang, X and Li, G and Lou, P and Zhang, M and Yao, K and Xiao, J and Chen, Y and Xu, J and Tian, S and Deng, M and Pan, Y and Li, M and Wu, X and Liu, R and Shi, X and Tian, Y and Yu, L and Ke, H and Jiao, B and Cong, Y and Plikus, MV and Liu, X and Yu, Z and Lv, C}, title = {Excessive nucleic acid R-loops induce mitochondria-dependent epithelial cell necroptosis and drive spontaneous intestinal inflammation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {1}, pages = {e2307395120}, pmid = {38157451}, issn = {1091-6490}, support = {82025006//MOST | National Natural Science Foundation of China (NSFC)/ ; 82230017//MOST | National Natural Science Foundation of China (NSFC)/ ; 82000498//MOST | National Natural Science Foundation of China (NSFC)/ ; 82270588//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022YFA1104001//National Basic Research Program of China/ ; 2022YFC3602102//National Basic Research Program of China/ ; 2022YFD1300403//National Basic Research Program of China/ ; 2021YFF1000603//National Basic Research Program of China/ ; 82300635//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022M723412//Postdoctoral Science Foundation of China/ ; 88220019//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Humans ; Animals ; Mice ; *Necroptosis ; NAD/metabolism ; R-Loop Structures ; *Inflammatory Bowel Diseases/metabolism ; Epithelial Cells/metabolism ; Intestinal Mucosa/metabolism ; Inflammation/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Mitochondria/metabolism ; }, abstract = {Oxidative stress, which can be activated by a variety of environmental risk factors, has been implicated as an important pathogenic factor for inflammatory bowel disease (IBD). However, how oxidative stress drives IBD onset remains elusive. Here, we found that oxidative stress was strongly activated in inflamed tissues from both ulcerative colitis patients and Crohn's disease patients, and it caused nuclear-to-cytosolic TDP-43 transport and a reduction in the TDP-43 protein level. To investigate the function of TDP-43 in IBD, we inducibly deleted exons 2 to 3 of Tardbp (encoding Tdp-43) in mouse intestinal epithelium, which disrupted its nuclear localization and RNA-processing function. The deletion gave rise to spontaneous intestinal inflammation by inducing epithelial cell necroptosis. Suppression of the necroptotic pathway with deletion of Mlkl or the RIP1 inhibitor Nec-1 rescued colitis phenotypes. Mechanistically, disruption of nuclear TDP-43 caused excessive R-loop accumulation, which triggered DNA damage and genome instability and thereby induced PARP1 hyperactivation, leading to subsequent NAD[+] depletion and ATP loss, consequently activating mitochondrion-dependent necroptosis in intestinal epithelial cells. Importantly, restoration of cellular NAD[+] levels with NAD[+] or NMN supplementation, as well as suppression of ALKBH7, an α-ketoglutarate dioxygenase in mitochondria, rescued TDP-43 deficiency-induced cell death and intestinal inflammation. Furthermore, TDP-43 protein levels were significantly inversely correlated with γ-H2A.X and p-MLKL levels in clinical IBD samples, suggesting the clinical relevance of TDP-43 deficiency-induced mitochondrion-dependent necroptosis. Taken together, these findings identify a unique pathogenic mechanism that links oxidative stress to intestinal inflammation and provide a potent and valid strategy for IBD intervention.}, }
@article {pmid38157080, year = {2023}, author = {Kuprina, K and Smorkatcheva, A and Rudyk, A and Galkina, S}, title = {Numerous insertions of mitochondrial DNA in the genome of the northern mole vole, Ellobius talpinus.}, journal = {Molecular biology reports}, volume = {51}, number = {1}, pages = {36}, pmid = {38157080}, issn = {1573-4978}, mesh = {Animals ; *DNA, Mitochondrial/genetics ; Phylogeny ; Genome ; Mitochondria/genetics ; Arvicolinae/genetics ; Sequence Analysis, DNA ; *Genome, Mitochondrial/genetics ; }, abstract = {BACKGROUND: Ellobius talpinus is a subterranean rodent representing an attractive model in population ecology studies due to its highly special lifestyle and sociality. In such studies, mitochondrial DNA (mtDNA) is widely used. However, if nuclear copies of mtDNA, aka NUMTs, are present, they may co-amplify with the target mtDNA fragment, generating misleading results. The aim of this study was to determine whether NUMTs are present in E. talpinus.<br><br>METHODS AND RESULTS: PCR amplification of the putative mtDNA CytB-D-loop fragment using 'universal' primers from 56 E. talpinus samples produced multiple double peaks in 90% of the sequencing chromatograms. To reveal NUMTs, molecular cloning and sequencing of PCR products of three specimens was conducted, followed by phylogenetic analysis. The pseudogene nature of three out of the seven detected haplotypes was confirmed by their basal positions in relation to other Ellobius haplotypes in the phylogenetic tree. Additionally, 'haplotype B' was basal in relation to other E. talpinus haplotypes and found present in very distant sampling sites. BLASTN search revealed 195 NUMTs in the E. talpinus nuclear genome, including fragments of all four PCR amplified pseudogenes. Although the majority of the NUMTs studied were short, the entire mtDNA had copies in the nuclear genome. The most numerous NUMTs were found for rrnL, COXI, and D-loop.<br><br>CONCLUSIONS: Numerous NUMTs are present in E. talpinus and can be difficult to discriminate against mtDNA sequences. Thus, in future population or phylogenetic studies in E. talpinus, the possibility of cryptic NUMTs amplification should always be taken into account.}, }
@article {pmid38149397, year = {2023}, author = {Shen, Q and Yuan, Y and Jin, J}, title = {[Relationship between Notch signaling pathway and mitochondrial energy metabolism].}, journal = {Zhonghua wei zhong bing ji jiu yi xue}, volume = {35}, number = {12}, pages = {1321-1326}, doi = {10.3760/cma.j.cn121430-20230719-00532}, pmid = {38149397}, issn = {2095-4352}, mesh = {*Signal Transduction/physiology ; *Mitochondria ; Receptors, Notch/metabolism ; Cell Differentiation/physiology ; Energy Metabolism ; }, abstract = {Notch signaling pathway is a highly conserved signaling pathway in the process of evolution. It is composed of three parts: Notch receptor, ligand and effector molecules responsible for intracellular signal transduction. It plays an important role in cell proliferation, differentiation, development, migration, apoptosis and other processes, and has a regulatory effect on tissue homeostasis and homeostasis. Mitochondria are the sites of oxidative metabolism in eukaryotes, where sugars, fats and proteins are finally oxidized to release energy. In recent years, the regulation of Notch signaling pathway on mitochondrial energy metabolism has attracted more and more attention. A large number of data have shown that Notch signaling pathway has a significant effect on mitochondrial energy metabolism, but the relationship between Notch signaling pathway and mitochondrial energy metabolism needs to be specifically and systematically discussed. In this paper, the relationship between Notch signaling pathway and mitochondrial energy metabolism is reviewed, in order to improve the understanding of them and provide new ideas for the treatment of related diseases.}, }
@article {pmid38147995, year = {2023}, author = {Yang, J and Gao, J and Li, W and Liu, J and Huo, J and Ren, Z and Li, L and Chen, B and Mao, J and Ma, Z}, title = {[Identification and expression analysis of apple PDHB-1 gene family].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {39}, number = {12}, pages = {4965-4981}, doi = {10.13345/j.cjb.230011}, pmid = {38147995}, issn = {1872-2075}, mesh = {*Malus/genetics/chemistry/metabolism ; Fruit/genetics ; Protein Structure, Secondary ; }, abstract = {Pyruvate dehydrogenase E1 component subunit beta-1 (PDHB-1) is a gene encoding the β-subunit of pyruvate dehydrogenase complex, which plays an important role in fruit acid accumulation. The aim of this study was to investigate the evolution characteristics of apple PDHB-1 family and its expression in apples with different acid contents. Bioinformatics analysis was performed using databases including NCBI, Pfam and software including ClustalX, MEGA, and TBtools. By combining titratable acid content determination and quantitative real-time PCR (qRT-PCR), the expression of this family genes in the peel and pulp of apple 'Asda' and 'Chengji No.1' with different acid content were obtained, respectively. The family members were mainly located in chloroplast, cytoplasm and mitochondria. α-helix and random coil were the main factors for the formation of secondary structure in this family. Tissue-specific expression profiles showed that the expression of most members were higher in fruit than in other tissues. qRT-PCR results showed that the expression profile of most members was consistent with the profile of titratable acid contents. In the peel, the expression levels of 14 members in 'Asda' apples with high acid content were significantly higher than that in 'Chengji No.1' apples with low acid content, where the expression difference of MdPDHB1-15 was the most significant. In the pulp, the expression levels of 17 members in 'Asda' apples were significantly higher than that in 'Chengji No.1' apples, where MdPDHB1-01 was the most highly expressed. It was predicted that PDHB-1 gene family in apple plays an important role in the regulation of fruit acidity.}, }
@article {pmid38142841, year = {2023}, author = {Buonvicino, D and Pratesi, S and Ranieri, G and Pistolesi, A and Guasti, D and Chiarugi, A}, title = {The mitochondriogenic but not the immunosuppressant effects of mTOR inhibitors prompt neuroprotection and delay disease evolution in a mouse model of progressive multiple sclerosis.}, journal = {Neurobiology of disease}, volume = {191}, number = {}, pages = {106387}, doi = {10.1016/j.nbd.2023.106387}, pmid = {38142841}, issn = {1095-953X}, abstract = {INTRODUCTION: Purportedly, the progression of multiple sclerosis (MS) occurs when neurodegenerative processes due to derangement of axonal bioenergetics take over the autoimmune response. However, a clear picture of the causative interrelationship between autoimmunity and axonal mitochondrial dysfunction in progressive MS (PMS) pathogenesis waits to be provided.<br><br>METHODS: In the present study, by adopting the NOD mouse model of PMS, we compared the pharmacological effects of the immunosuppressants dexamethasone and fingolimod with those of mTOR inhibitors rapamycin and everolimus that, in addition to immunosuppression, also regulate mitochondrial functioning. Female Non-Obese Diabetic (NOD) mice were immunized with MOG35-55 and treated with drugs to evaluate functional, immune and mitochondrial parameters during disease evolution.<br><br>RESULTS: We found that dexamethasone and fingolimod did not affect the pattern of progression as well as survival. Conversely, mTOR inhibitors rapamycin and everolimus delayed disease progression and robustly extended survival of immunized mice. The same effects were obtained when treatment was delayed by 30&#xa0;days after immunization. Remarkably, dexamethasone and fingolimod prompted the same degree of immunosuppression of rapamycin within both spleen and spinal cord of mice. However, only rapamycin prompted mitochondriogenesis by increasing mitochondrial content, and expression of several mitochondrial respiratory complex subunits, thereby preventing mtDNA reduction in the spinal cords of immunized mice. These pharmacodynamic effects were not reproduced in healthy NOD mice, suggesting a disease context-dependent pharmacodynamic effect.<br><br>DISCUSSION: Data corroborate the key role of mitochondriogenesis to treatment of MS progression, and for the first time disclose the translational potential of mTOR inhibitors in PMS therapy.}, }
@article {pmid38140813, year = {2023}, author = {Griseti, E and Bello, AA and Bieth, E and Sabbagh, B and Iacovoni, JS and Bigay, J and Laurell, H and Čopič, A}, title = {Molecular mechanisms of perilipin protein function in lipid droplet metabolism.}, journal = {FEBS letters}, volume = {}, number = {}, pages = {}, doi = {10.1002/1873-3468.14792}, pmid = {38140813}, issn = {1873-3468}, support = {856404/ERC_/European Research Council/International ; }, abstract = {Perilipins are abundant lipid droplet (LD) proteins present in all metazoans and also in Amoebozoa and fungi. Humans express five perilipins, which share a similar domain organization: an amino-terminal PAT domain and an 11-mer repeat region, which can fold into amphipathic helices that interact with LDs, followed by a structured carboxy-terminal domain. Variations of this organization that arose during vertebrate evolution allow for functional specialization between perilipins in relation to the metabolic needs of different tissues. We discuss how different features of perilipins influence their interaction with LDs and their cellular targeting. PLIN1 and PLIN5 play a direct role in lipolysis by regulating the recruitment of lipases to LDs and LD interaction with mitochondria. Other perilipins, particularly PLIN2, appear to protect LDs from lipolysis, but the molecular mechanism is not clear. PLIN4 stands out with its long repetitive region, whereas PLIN3 is most widely expressed and is used as a nascent LD marker. Finally, we discuss the genetic variability in perilipins in connection with metabolic disease, prominent for PLIN1 and PLIN4, underlying the importance of understanding the molecular function of perilipins.}, }
@article {pmid38139163, year = {2023}, author = {He, X and Zhang, X and Deng, Y and Yang, R and Yu, LX and Jia, S and Zhang, T}, title = {Structural Reorganization in Two Alfalfa Mitochondrial Genome Assemblies and Mitochondrial Evolution in Medicago Species.}, journal = {International journal of molecular sciences}, volume = {24}, number = {24}, pages = {}, pmid = {38139163}, issn = {1422-0067}, support = {SJCZFY2022-3//Breeding of New Alfalfa Varieties/ ; 2022JBGS0020//Breeding and Industrialization Demonstration of New High-quality Alfalfa Varieties/ ; }, mesh = {*Genome, Mitochondrial ; Medicago sativa/genetics ; DNA, Mitochondrial/genetics ; Medicago/genetics ; Mitochondria/genetics ; }, abstract = {Plant mitochondria are crucial for species evolution, phylogenetics, classification, and identification as maternal genetic material. However, the presence of numerous repetitive sequences, complex structures, and a low number of genes in the mitochondrial genome has hindered its complete assembly and related research endeavors. In this study, we assembled two mitochondrial genomes of alfalfa varieties of Zhongmu No.1 (299,123 bp) and Zhongmu No.4 (306,983 bp), based on a combination of PacBio, Illumina, and Hi-C sequences. The comparison of genome assemblies revealed that the same number of mitochondrial genes, including thirty-three protein-coding genes, sixteen tRNA genes, and three rRNA genes existed in the two varieties. Additionally, large fragments of repetitive sequences were found underlying frequent mitochondrial recombination events. We observed extensive transfer of mitochondrial fragments into the nuclear genome of Zhongmu No.4. Analysis of the cox1 and rrn18s genes in 35 Medicago accessions revealed the presence of population-level deletions and substitutions in the rrn18s gene. We propose that mitochondrial structural reorganizations may contribute to alfalfa evolution.}, }
@article {pmid38124445, year = {2024}, author = {Uvizl, M and Puechmaille, SJ and Power, S and Pippel, M and Carthy, S and Haerty, W and Myers, EW and Teeling, EC and Huang, Z}, title = {Comparative Genome Microsynteny Illuminates the Fast Evolution of Nuclear Mitochondrial Segments (NUMTs) in Mammals.}, journal = {Molecular biology and evolution}, volume = {41}, number = {1}, pages = {}, pmid = {38124445}, issn = {1537-1719}, mesh = {Animals ; Phylogeny ; *Genomics ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Mammals/genetics ; Sequence Analysis, DNA ; Cell Nucleus/genetics ; *Genome, Mitochondrial ; Evolution, Molecular ; }, abstract = {The escape of DNA from mitochondria into the nuclear genome (nuclear mitochondrial DNA, NUMT) is an ongoing process. Although pervasively observed in eukaryotic genomes, their evolutionary trajectories in a mammal-wide context are poorly understood. The main challenge lies in the orthology assignment of NUMTs across species due to their fast evolution and chromosomal rearrangements over the past 200 million years. To address this issue, we systematically investigated the characteristics of NUMT insertions in 45 mammalian genomes and established a novel, synteny-based method to accurately predict orthologous NUMTs and ascertain their evolution across mammals. With a series of comparative analyses across taxa, we revealed that NUMTs may originate from nonrandom regions in mtDNA, are likely found in transposon-rich and intergenic regions, and unlikely code for functional proteins. Using our synteny-based approach, we leveraged 630 pairwise comparisons of genome-wide microsynteny and predicted the NUMT orthology relationships across 36 mammals. With the phylogenetic patterns of NUMT presence-and-absence across taxa, we constructed the ancestral state of NUMTs given the mammal tree using a coalescent method. We found support on the ancestral node of Fereuungulata within Laurasiatheria, whose subordinal relationships are still controversial. This study broadens our knowledge on NUMT insertion and evolution in mammalian genomes and highlights the merit of NUMTs as alternative genetic markers in phylogenetic inference.}, }
@article {pmid38123538, year = {2023}, author = {Cui, Z and Zhong, Y and Sun, Z and Jiang, Z and Deng, J and Wang, Q and Nielsen, J and Hou, J and Qi, Q}, title = {Reconfiguration of the reductive TCA cycle enables high-level succinic acid production by Yarrowia lipolytica.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {8480}, pmid = {38123538}, issn = {2041-1723}, support = {22208192//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Yarrowia/genetics/metabolism ; Succinic Acid/metabolism ; NAD/metabolism ; Citric Acid Cycle ; Fermentation ; Glucose/metabolism ; Metabolic Engineering ; }, abstract = {Succinic acid (SA) is an important C4-dicarboxylic acid. Microbial production of SA at low pH results in low purification costs and hence good overall process economics. However, redox imbalances limited SA biosynthesis from glucose via the reductive tricarboxylic acid (TCA) cycle in yeast. Here, we engineer the strictly aerobic yeast Yarrowia lipolytica for efficient SA production without pH control. Introduction of the reductive TCA cycle into the cytosol of a succinate dehydrogenase-disrupted yeast strain causes arrested cell growth. Although adaptive laboratory evolution restores cell growth, limited NADH supply restricts SA production. Reconfiguration of the reductive SA biosynthesis pathway in the mitochondria through coupling the oxidative and reductive TCA cycle for NADH regeneration results in improved SA production. In pilot-scale fermentation, the engineered strain produces 111.9 g/L SA with a yield of 0.79 g/g glucose within 62 h. This study paves the way for industrial production of biobased SA.}, }
@article {pmid38112480, year = {2023}, author = {He, Z and Fang, Y and Zhang, F and Liu, Y and Cheng, X and Wang, J and Li, D and Chen, D and Wu, F}, title = {Adenine nucleotide translocase 2 (Ant2) is required for individualization of spermatogenesis of Drosophila melanogaster.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.13309}, pmid = {38112480}, issn = {1744-7917}, support = {CARS-18-SYZ10//China Agricultural Research System of MOF and MARA/ ; 2021-620-000-001-009//Hubei Province Agricultural Science and Technology Innovation Center Project/ ; 2022BBA0079//Hubei Province key Research and Development Project/ ; }, abstract = {Successful completion of spermatogenesis is crucial for the perpetuation of the species. In Drosophila, spermatid individualization, a process involving changes in mitochondrial structure and function is critical to produce functional mature sperm. Ant2, encoding a mitochondrial adenine nucleotide translocase, is highly expressed in male testes and plays a role in energy metabolism in the mitochondria. However, its molecular function remains unclear. Here, we identified an important role of Ant2 in spermatid individualization. In Ant2 knockdown testes, spermatid individualization complexes composed of F-actin cones exhibited a diffuse distribution, and mature sperms were absent in the seminal vesicle, thus leading to male sterility. The most striking effects in Ant2-knockdown spermatids were decrease in tubulin polyglycylation and disruption of proper mitochondria derivatives function. Excessive apoptotic cells were also observed in Ant2-knockdown testes. To further investigate the phenotype of Ant2 knockdown in testes at the molecular level, complementary transcriptome and proteome analyses were performed. At the mRNA level, 868 differentially expressed genes were identified, of which 229 genes were upregulated and 639 were downregulated induced via Ant2 knockdown. iTRAQ-labeling proteome analysis revealed 350 differentially expressed proteins, of which 117 proteins were upregulated and 233 were downregulated. The expression of glutathione transferase (GstD5, GstE5, GstE8, and GstD3), proteins involved in reproduction were significantly regulated at both the mRNA and protein levels. These results indicate that Ant2 is crucial for spermatid maturation by affecting mitochondrial morphogenesis.}, }
@article {pmid38105202, year = {2023}, author = {Baleva, MV and Piunova, UE and Chicherin, IV and Levitskii, SA and Kamenski, PA}, title = {Diversity and Evolution of Mitochondrial Translation Apparatus.}, journal = {Biochemistry. Biokhimiia}, volume = {88}, number = {11}, pages = {1832-1843}, doi = {10.1134/S0006297923110135}, pmid = {38105202}, issn = {1608-3040}, mesh = {*Mitochondria/genetics/metabolism ; Protein Biosynthesis ; *Genome, Mitochondrial ; Mitochondrial Proteins/genetics/metabolism ; }, abstract = {The evolution of mitochondria has proceeded independently in different eukaryotic lines, which is reflected in the diversity of mitochondrial genomes and mechanisms of their expression in eukaryotic species. Mitochondria have lost most of bacterial ancestor genes by transferring them to the nucleus or eliminating them. However, mitochondria of almost all eukaryotic cells still retain relatively small genomes, as well as their replication, transcription, and translation apparatuses. The dependence on the nuclear genome, specific features of mitochondrial transcripts, and synthesis of highly hydrophobic membrane proteins in the mitochondria have led to significant changes in the translation apparatus inherited from the bacterial ancestor, which retained the basic structure necessary for protein synthesis but became more specialized and labile. In this review, we discuss specific properties of translation initiation in the mitochondria and how the evolution of mitochondria affected the functions of main factors initiating protein biosynthesis in these organelles.}, }
@article {pmid38103543, year = {2024}, author = {Wang, S and He, B and Wu, H and Cai, Q and Ramírez-Sánchez, O and Abreu-Goodger, C and Birch, PRJ and Jin, H}, title = {Plant mRNAs move into a fungal pathogen via extracellular vesicles to reduce infection.}, journal = {Cell host &amp; microbe}, volume = {32}, number = {1}, pages = {93-105.e6}, doi = {10.1016/j.chom.2023.11.020}, pmid = {38103543}, issn = {1934-6069}, support = {R35 GM136379/GM/NIGMS NIH HHS/United States ; }, mesh = {RNA, Messenger/genetics/metabolism ; RNA ; *Arabidopsis/genetics/microbiology ; Plants/genetics ; *Extracellular Vesicles ; Plant Diseases/microbiology ; }, abstract = {Cross-kingdom small RNA trafficking between hosts and microbes modulates gene expression in the interacting partners during infection. However, whether other RNAs are also transferred is unclear. Here, we discover that host plant Arabidopsis thaliana delivers mRNAs via extracellular vesicles (EVs) into the fungal pathogen Botrytis cinerea. A fluorescent RNA aptamer reporter Broccoli system reveals host mRNAs in EVs and recipient fungal cells. Using translating ribosome affinity purification profiling and polysome analysis, we observe that delivered host mRNAs are translated in fungal cells. Ectopic expression of two transferred host mRNAs in B. cinerea shows that their proteins are detrimental to infection. Arabidopsis knockout mutants of the genes corresponding to these transferred mRNAs are more susceptible. Thus, plants have a strategy to reduce infection by transporting mRNAs into fungal cells. mRNAs transferred from plants to pathogenic fungi are translated to compromise infection, providing knowledge that helps combat crop diseases.}, }
@article {pmid38100746, year = {2024}, author = {Araujo, TQ and King-Trudeau, S and VanDyke, J and Hochberg, R}, title = {First ultrastructural description of an apomictic opsiblastic egg in freshwater Gastrotricha.}, journal = {Journal of morphology}, volume = {285}, number = {1}, pages = {e21659}, doi = {10.1002/jmor.21659}, pmid = {38100746}, issn = {1097-4687}, support = {//National Science Foundation/ ; }, mesh = {Animals ; Phylogeny ; *Oocytes/ultrastructure ; *Oogenesis ; Endoplasmic Reticulum ; Fresh Water ; }, abstract = {Freshwater gastrotrichs have a biphasic lifecycle that reputedly involves the production of three types of eggs: apomictic and fast hatching (tachyblastic ova), apomictic and delayed hatching (opsiblastic ova), and plaque-bearing eggs (potentially derived from mixis). While some details of oogenesis and eggshell structure are known for tachyblastic ova, there are few details on other egg types. Here, we provide the first ultrastructural description of the oviposited opsiblastic eggs of the freshwater gastrotrich, Lepidodermella squamata. Scanning electron microscopy revealed the eggshell surface to be ornamented with long flattened pillar-like structures centered on polygonal plates that are pitted along their periphery. Transmission electron microscopy showed the pits to lead to a vast labyrinth of tubular spaces and larger cavities throughout the thick apical layer of the shell. The basal layer of the shell is amorphous and connected to a network of fine fibers that traverse an extra-oocyte space and forms a protective sheet around the uncleaved oocyte. The uncleaved oocyte has a dense layer of peripheral ooplasm surrounding a core of organelles including mitochondria, membrane-bound secretion granules, endoplasmic reticulum, and a single nucleus in a granular, ribosome-rich cytoplasm. Secretion granules are the most abundant organelles and presumably contain lipid-rich yolk that will be used as energy for delayed cleavage, thus functioning in temporal dispersal. These data are compared to the fine structure of invertebrate resting eggs across the phylogenetic spectrum to determine the novelty of opsiblastic egg structure in L. squamata.}, }
@article {pmid38097150, year = {2024}, author = {Hew, YX and Ya'cob, Z and Chen, CD and Lau, KW and Sofian-Azirun, M and Muhammad-Rasul, AH and Putt, QY and Tan, TK and Hadi, UK and Suana, IW and Takaoka, H and Low, VL}, title = {Co-occurrence of dual lineages within Simulium (Gomphostilbia) atratum De Meijere in the Indonesian Archipelago along Wallace's Line.}, journal = {Acta tropica}, volume = {250}, number = {}, pages = {107097}, doi = {10.1016/j.actatropica.2023.107097}, pmid = {38097150}, issn = {1873-6254}, mesh = {Animals ; Indonesia ; *Simuliidae/genetics ; Mitochondria ; Phylogeny ; Genetic Variation ; }, abstract = {Mitochondrial cytochrome c oxidase subunit I (COI) sequences were utilized to infer the population genetic structure of Simulium (Gomphostilbia) atratum De Meijere, an endemic simulid species to Indonesia. Both median-joining haplotype network and maximum-likelihood tree revealed two genetic lineages (A and B) within the species, with an overlap distribution in Lombok, which is situated along Wallace's line. Genetic differentiation and gene flow with varying frequencies (FST = 0.02-0.967; Nm = 0.01-10.58) were observed between populations of S. (G.) atratum, of which population pairs of different lineages showed high genetic differentiation. Notably, the high genetic distance of up to 5.92 % observed within S. (G.) atratum in Lombok was attributed to the existence of two genetically distinct lineages. The co-occurrence of distinct lineages in Lombok indicated that Wallace's line did not act as faunistic border for S. (G.) atratum in the present study. Moreover, both lineages also exhibited unimodal distributions and negative values of neutrality tests, suggesting a pattern of population expansion. The expansion and divergence time estimation suggested that the two lineages of S. (G.) atratum diverged and expanded during the Pleistocene era in Indonesia.}, }
@article {pmid38095728, year = {2023}, author = {Chen, W and Zhang, H and Meng, R and Zhang, X and Duo, H and Guo, Z and Shen, X and Chen, C and Li, Z and Fu, Y}, title = {Genome-wide phylogenetic and genetic evolutionary analyses of mitochondria in Hypoderma bovis and H. sinense on the Qinghai-Tibetan Plateau.}, journal = {Parasitology research}, volume = {123}, number = {1}, pages = {43}, pmid = {38095728}, issn = {1432-1955}, mesh = {Animals ; Cattle ; Humans ; Phylogeny ; RNA, Ribosomal, 16S ; Tibet ; *Diptera ; Mitochondria/genetics ; Mammals ; }, abstract = {Hypoderma bovis (H. bovis) and Hypoderma sinense (H. sinense) are insects that cause hypodermosis in yaks and Bos taurus. Hypodermosis is a severe skin condition that not only impairs the development of local animal husbandry but also poses threats to human health as a zoonosis. The Qinghai-Tibetan Plateau (QTP) is known as the "Roof of the World." Its unique geographical environment and climate conditions have supported the growth of a wide range of mammals, providing favorable conditions for Hypoderma spp. to complete their life cycles. In this study, the whole mitochondrial genomes of H. bovis and H. sinense collected from the QTP were sequenced and phylogenetically analyzed. We found that the whole genomes of H. bovis and H. sinense are 16,283 bp and 16,300 bp in length, respectively. Both the H. bovis and H. sinense genomes have 37 mitochondrial genes, which include two rRNA genes (16S rRNA and 12S rRNA), 22 tRNA genes, the control region (D-loop region), the light chain replication initiation region, and 13 protein-coding genes (PCGs). The phylogenetic tree generated based on the 13 PCGs revealed close phylogenetic relationships between H. sinense, H. bovis, and Hypoderma lineatum. A similar result was also found in our phylogenetic analysis based on 18S rRNA and 28S rRNA. However, analysis of cytochrome oxidase subunit I (COI) showed cluster of H. bovis, H. sinense, and Cuterebra spp. on the same branch, all belonging to Oestridae. The differentiation time generated based on 13 PCGs indicates that H. bovis and H. sinense differentiated and formed ~4.69 million years ago (Mya) and ~4.06 Mya, respectively. This timing coincides with the differentiation and appearance of yak and Bos taurus in the Pliocene (~4.7 Mya), indicating that the parasites and mammals diverged in close temporal proximity. Of note, this period also witnessed a rapid uplift of the QTP, causing significant climate and environmental changes. Thus, we conjecture that the differentiation of Hypoderma spp. is potentially related to the differentiation of their host species, as well as climate changes caused by the uplift of the QTP. Overall, our study can provide valuable data to support further studies on the phylogeny and differentiation of Hypoderma spp. on the QTP.}, }
@article {pmid38093186, year = {2023}, author = {Hamza, H and Villa, S and Torre, S and Marchesini, A and Benabderrahim, MA and Rejili, M and Sebastiani, F}, title = {Whole mitochondrial and chloroplast genome sequencing of Tunisian date palm cultivars: diversity and evolutionary relationships.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {772}, pmid = {38093186}, issn = {1471-2164}, support = {GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; GeenPalm//PRIMA/ ; }, mesh = {*Phoeniceae/genetics ; *Genome, Chloroplast ; Phylogeny ; Plant Breeding ; Chloroplasts/genetics ; Mitochondria/genetics ; }, abstract = {BACKGROUND: Date palm (Phoenix dactylifera L.) is the most widespread crop in arid and semi-arid regions and has great traditional and socioeconomic importance, with its fruit well-known for its high nutritional and health value. However, the genetic variation of date palm cultivars is often neglected. The advent of high-throughput sequencing has made possible the resequencing of whole organelle (mitochondria and chloroplast) genomes to explore the genetic diversity and phylogenetic relationships of cultivated plants with unprecedented detail.<br><br>RESULTS: Whole organelle genomes of 171 Tunisian accessions (135 females and 36 males) were sequenced. Targeted bioinformatics pipelines were used to identify date palm haplotypes and genome variants, aiming to provide variant annotation and investigate patterns of evolutionary relationship. Our results revealed the existence of unique haplotypes, identified by 45 chloroplastic and 156 mitochondrial SNPs. Estimation of the effect of these SNPs on genes functions was predicted in silico.<br><br>CONCLUSIONS: The results of this study have important implications, in the light of ongoing environmental changes, for the conservation and sustainable use of the genetic resources of date palm cultivars in Tunisia, where monoculture threatens biodiversity leading to genetic erosion. These data will be useful for breeding and genetic improvement programs of the date palm through selective cross-breeding.}, }
@article {pmid38092275, year = {2024}, author = {Gaudó, P and de Tomás-Mateo, E and Garrido-Pérez, N and Santana, A and Ruiz-Pesini, E and Montoya, J and Bayona-Bafaluy, P}, title = {"ATAD3C regulates ATAD3A assembly and function in the mitochondrial membrane".}, journal = {Free radical biology &amp; medicine}, volume = {211}, number = {}, pages = {114-126}, doi = {10.1016/j.freeradbiomed.2023.12.006}, pmid = {38092275}, issn = {1873-4596}, mesh = {Humans ; *Adenosine Triphosphatases/genetics/metabolism ; ATPases Associated with Diverse Cellular Activities/genetics/chemistry/metabolism ; Gene Duplication ; Membrane Proteins/genetics/metabolism ; Mitochondria/genetics/metabolism ; *Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/metabolism ; }, abstract = {Mitochondrial ATAD3A is an ATPase Associated with diverse cellular Activities (AAA) domain containing enzyme, involved in the structural organization of the inner mitochondrial membrane and of increasing importance in childhood disease. In humans, two ATAD3A paralogs arose by gene duplication during evolution: ATAD3B and ATAD3C. Here we investigate the cellular activities of the ATAD3C paralog that has been considered a pseudogene. We detected unique ATAD3C peptides in HEK 293T cells, with expression similar to that in human tissues, and showed that it is an integral membrane protein that exposes its carboxy-terminus to the intermembrane space. Overexpression of ATAD3C, but not of ATAD3A, in fibroblasts caused a decrease in cell proliferation and oxygen consumption rate, and an increase of cellular ROS. This was due to the incorporation of ATAD3C monomers in ATAD3A complex in the mitochondrial membrane reducing its size. Consistent with a negative regulation of ATAD3A function in mitochondrial membrane organization, ATAD3C expression led to increased accumulation of respiratory chain dimeric CIII in the inner membrane, to the detriment to that assembled in respiratory supercomplexes. Our results demonstrate a negative dominant role of the ATAD3C paralog with implications for mitochondrial OXPHOS function and suggest that its expression regulates ATAD3A in the cell.}, }
@article {pmid38077409, year = {2023}, author = {Santamaria, CA and Griffiths, CL}, title = {Cryptic diversity and phylogeographic patterns of Deto echinata (Isopoda: Detonidae) in southern Africa.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16529}, pmid = {38077409}, issn = {2167-8359}, mesh = {Humans ; Animals ; *Isopoda/genetics ; Phylogeny ; Phylogeography ; Africa, Southern ; Mitochondria ; }, abstract = {Recent phylogeographic studies of poorly-dispersing coastal invertebrates in highly biodiverse regions have led to the discovery of high levels of cryptic diversity and complex phylogeographic patterns that suggest isolation, geological, and ecological processes have shaped their biodiversity. Studies of southern African coastal invertebrates have uncovered cryptic diversity for various taxa and phylogeographic patterns that, although sharing some similarities across taxa, do differ. These findings underscore the need for additional studies to better understand the biodiversity levels, distributional patterns, and processes responsible for producing coastal biodiversity in that region. The coastal isopod Deto echinata is of particular interest, as its complex taxonomic history, poor dispersal capabilities, and broad geographic distribution suggest the potential for cryptic diversity. We use mitochondrial and nuclear sequences to characterize D. echinata individuals from localities ranging from northern Namibia to Glentana, about 2,500 km along the coastline on the south coast of South Africa. These are used to assess whether D. echinata harbors cryptic genetic diversity and whether phylogeographic distributional patterns correlate with those previously documented for other coastal isopods in the region. Analysis of mitochondrial and nuclear sequences revealed two deeply-divergent lineages that exhibit a distributional break in the Cape Peninsula region. These findings suggest D. echinata is a cryptic species complex in need of taxonomic revision and highlight the need for further taxonomic and phylogeographic studies of similarly poorly-dispersing coastal invertebrates in southern Africa.}, }
@article {pmid38075892, year = {2023}, author = {Wolters, JF and LaBella, AL and Opulente, DA and Rokas, A and Hittinger, CT}, title = {Mitochondrial genome diversity across the subphylum Saccharomycotina.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1268944}, pmid = {38075892}, issn = {1664-302X}, support = {R01 AI153356/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; }, abstract = {INTRODUCTION: Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available.<br><br>METHODS: By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades.<br><br>RESULTS: Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales, which includes S. cerevisiae, exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements.<br><br>DISCUSSION: As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.}, }
@article {pmid38073308, year = {2023}, author = {Lin, Y and Yang, H and Liu, H and Lu, X and Cao, H and Li, B and Chang, Y and Guo, Z and Ding, D and Hu, Y and Xue, Y and Liu, Z and Tang, J}, title = {A P-type pentatricopeptide repeat protein ZmRF5 promotes 5' region partial cleavages of atp6c transcripts to restore the fertility of CMS-C maize by recruiting a splicing factor.}, journal = {Plant biotechnology journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/pbi.14263}, pmid = {38073308}, issn = {1467-7652}, support = {32272165//National Natural Science Foundation of China/ ; 31571745//National Natural Science Foundation of China/ ; }, abstract = {A fast evolution within mitochondria genome(s) often generates discords between nuclear and mitochondria, which is manifested as cytoplasmic male sterility (CMS) and fertility restoration (Rf) system. The maize CMS-C trait is regulated by the chimeric mitochondrial gene, atp6c, and can be recovered by the restorer gene ZmRf5. Through positional cloning in this study, we identified the nuclear restorer gene, ZmRf5, which encodes a P-type pentatricopeptide repeat (PPR) family protein. The over-expression of ZmRf5 brought back the fertility to CMS-C plants, whereas its genomic editing by CRISPR/Cas9 induced abortive pollens in the restorer line. ZmRF5 is sorted to mitochondria, and recruited RS31A, a splicing factor, through MORF8 to form a cleaving/restoring complex, which promoted the cleaving of the CMS-associated transcripts atp6c by shifting the major cleavage site from 480th nt to 344 th nt for fast degradation, and preserved just right amount of atp6c RNA for protein translation, providing adequate ATP6C to assembly complex V, thus restoring male fertility. Interestingly, ATP6C in the sterile line CMo17A, with similar cytology and physiology changes to YU87-1A, was accumulated much less than it in NMo17B, exhibiting a contrary trend in the YU87-1 nuclear genome previously reported, and was restored to normal level in the presence of ZmRF5. Collectively these findings unveil a new molecular mechanism underlying fertility restoration by which ZmRF5 cooperates with MORF8 and RS31A to restore CMS-C fertility in maize, complemented and perfected the sterility mechanism, and enrich the perspectives on communications between nucleus and mitochondria.}, }
@article {pmid38070787, year = {2024}, author = {Das, PJ and Kumar, S and Choudhury, M and Banik, S and Pegu, SR and Kumar, S and Deb, R and Gupta, VK}, title = {Characterization of the complete mitochondrial genome and identification of signature sequence of Indian wild pig.}, journal = {Gene}, volume = {897}, number = {}, pages = {148070}, doi = {10.1016/j.gene.2023.148070}, pmid = {38070787}, issn = {1879-0038}, mesh = {Animals ; *Genome, Mitochondrial/genetics ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Genomics ; Sequence Analysis, DNA ; }, abstract = {Mitochondrial DNA (mtDNA) serves as a valuable molecular marker for constructing matrilineal genealogies and tracing the evolutionary history of animals. This study aimed to characterize the complete mitochondrial genome of the Indian wild pig (IWB) (Sus scrofa cristatus) and identify IWB-specific DNA sequences that could be used as genomic signatures to differentiate IWB from domestic Indian pigs (IDP) in forensic cases. For the purpose, three wild IWB from a rescue centre were used for the characterization of the mitochondrial genome of the IWB. The mitochondrial genome was sequenced by the primer walking technique using 30 overlapping primers. The mitochondrial genome of the IWB was found to be 16,689 bp long containing 37 genes coding for 2 rRNAs, 22 tRNAs, 13 protein coding genes, and 1 D-loop region similar to the mitogenome of other pigs. Sequence analysis of the D-loop of IWB with other IDP indicated some signature sequence for IWB like duplication and transition event from 1090[th] to 1099[th] position, deletion of a 10 bp sequence at the 755[th] position, insertion of (CA) at the 137[th] position, and substitution of AT to GA at the 638[th] position. These variations specially the duplication along with transition event causes creation of unique signature sequence (-ACACAAACCT-) in the IWB that could serve as signature sequences for the IWB and be used as markers for differentiation of IWB from IDP breeds in academic as well as forensic or vetero-legal cases. Overall, a total of 36 polymorphic positions were identified in the IWB, with 29 sites being unique to the IWB only and seven being common to the Doom and HDK75 pig breeds. None of the common polymorphic sites were identified in prevailing domestic pig populations. Phylogenetic analysis of the mitochondrial genome revealed the distinct separation of the IWB from IDP. The results of genetic distance evaluation showed that the Doom pig breed was the closest to the IWB. This study provides valuable insights into the mitogenome characterisation, signature sequence and genetic distance analysis of the IWB and establishes a foundation for future studies on the conservation of this protected species.}, }
@article {pmid38062387, year = {2023}, author = {Ouyang, L and Liu, Y and Yao, R and He, D and Yan, L and Chen, Y and Huai, D and Wang, Z and Yu, B and Kang, Y and Jiang, H and Lei, Y and Liao, B and Wang, X}, title = {Genome-wide analysis of UDP-glycosyltransferase gene family and identification of a flavonoid 7-O-UGT (AhUGT75A) enhancing abiotic stress in peanut (Arachis hypogaea L.).}, journal = {BMC plant biology}, volume = {23}, number = {1}, pages = {626}, pmid = {38062387}, issn = {1471-2229}, support = {CARS-13//earmarked fund for China Agricultural Research System/ ; CARS-13//earmarked fund for China Agricultural Research System/ ; CARS-13//earmarked fund for China Agricultural Research System/ ; CAAS-ASTIP-2021-OCRI//Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences/ ; CAAS-ASTIP-2021-OCRI//Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences/ ; CAAS-ASTIP-2021-OCRI//Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences/ ; 32170278//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Arachis/genetics ; Glycosyltransferases/genetics ; Phylogeny ; Flavonoids ; Plant Breeding ; Stress, Physiological/genetics ; *Arabidopsis ; Uridine Diphosphate ; }, abstract = {BACKGROUND: Glycosylation, catalyzed by UDP-glycosyltransferase (UGT), was important for enhancing solubility, bioactivity, and diversity of flavonoids. Peanut (Arachis hypogaea L.) is an important oilseed and cash crop worldwide. In addition to provide high quality of edible oils and proteins, peanut seeds contain a rich source of flavonoid glycosides that benefit human health. However, information of UGT gene family was quite limited in peanut.<br><br>RESULTS: In present study, a total of 267 AhUGTs clustered into 15 phylogenetic groups were identified in peanut genome. Group I has greatly expanded to contain the largest number of AhUGT genes. Segmental duplication was the major driving force for AhUGT gene family expansion. Transcriptomic analysis of gene expression profiles in various tissues and under different abiotic stress treatments indicated AhUGTs were involved in peanut growth and abiotic stress response. AhUGT75A (UGT73CG33), located in mitochondria, was characterized as a flavonoid 7-O-UGT by in vitro enzyme assays. The transcript level of AhUGT75A was strongly induced by abiotic stress. Overexpression of AhUGT75A resulted in accumulating less amount of malondialdehyde (MDA) and superoxide, and enhancing tolerance against drought and/or salt stress in transgenic Arabidopsis. These results indicated AhUGT75A played important roles in conferring abiotic stress tolerance through reactive oxygen species scavenging.<br><br>CONCLUSIONS: Our research only not provides valuable information for functional characterization of UGTs in peanut, but also gives new insights into potential applications in breeding new cultivars with both desirable stress tolerance and health benefits.}, }
@article {pmid38060519, year = {2023}, author = {Novák, LVF and Treitli, SC and Pyrih, J and Hałakuc, P and Pipaliya, SV and Vacek, V and Brzoň, O and Soukal, P and Eme, L and Dacks, JB and Karnkowska, A and Eliáš, M and Hampl, V}, title = {Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria.}, journal = {PLoS genetics}, volume = {19}, number = {12}, pages = {e1011050}, pmid = {38060519}, issn = {1553-7404}, support = {R21 ES021028/ES/NIEHS NIH HHS/United States ; }, mesh = {Phylogeny ; *Eukaryota/genetics ; *Oxymonadida/genetics/metabolism ; Mitochondria/genetics ; Genomics ; }, abstract = {The notion that mitochondria cannot be lost was shattered with the report of an oxymonad Monocercomonoides exilis, the first eukaryote arguably without any mitochondrion. Yet, questions remain about whether this extends beyond the single species and how this transition took place. The Oxymonadida is a group of gut endobionts taxonomically housed in the Preaxostyla which also contains free-living flagellates of the genera Trimastix and Paratrimastix. The latter two taxa harbour conspicuous mitochondrion-related organelles (MROs). Here we report high-quality genome and transcriptome assemblies of two Preaxostyla representatives, the free-living Paratrimastix pyriformis and the oxymonad Blattamonas nauphoetae. We performed thorough comparisons among all available genomic and transcriptomic data of Preaxostyla to further decipher the evolutionary changes towards amitochondriality, endobiosis, and unstacked Golgi. Our results provide insights into the metabolic and endomembrane evolution, but most strikingly the data confirm the complete loss of mitochondria for all three oxymonad species investigated (M. exilis, B. nauphoetae, and Streblomastix strix), suggesting the amitochondriate status is common to a large part if not the whole group of Oxymonadida. This observation moves this unique loss to 100 MYA when oxymonad lineage diversified.}, }
@article {pmid38053364, year = {2023}, author = {Camus, MF and Inwongwan, S}, title = {Mitonuclear interactions modulate nutritional preference.}, journal = {Biology letters}, volume = {19}, number = {12}, pages = {20230375}, pmid = {38053364}, issn = {1744-957X}, mesh = {Animals ; Genotype ; *Mitochondria/genetics ; Haplotypes ; Drosophila/genetics ; *Life History Traits ; DNA, Mitochondrial/genetics ; Cell Nucleus/genetics ; }, abstract = {In nature, organisms are faced with constant nutritional options which fuel key life-history traits. Studies have shown that species can actively make nutritional decisions based on internal and external cues. Metabolism itself is underpinned by complex genomic interactions involving components from both nuclear and mitochondrial genomes. Products from these two genomes must coordinate how nutrients are extracted, used and recycled. Given the complicated nature of metabolism, it is not well understood how nutritional choices are affected by mitonuclear interactions. This is under the rationale that changes in genomic interactions will affect metabolic flux and change physiological requirements. To this end we used a large Drosophila mitonuclear genetic panel, comprising nine isogenic nuclear genomes coupled to nine mitochondrial haplotypes, giving a total of 81 different mitonuclear genotypes. We use a capillary-based feeding assay to screen this panel for dietary preference between carbohydrate and protein. We find significant mitonuclear interactions modulating nutritional choices, with these epistatic interactions also being dependent on sex. Our findings support the notion that complex genomic interactions can place a constraint on metabolic flux. This work gives us deeper insights into how key metabolic interactions can have broad implications on behaviour.}, }
@article {pmid38052127, year = {2023}, author = {Fernández Miyakawa, ME and Casanova, NA and Kogut, MH}, title = {How did antibiotic growth promoters increase growth and feed efficiency in poultry?.}, journal = {Poultry science}, volume = {103}, number = {2}, pages = {103278}, pmid = {38052127}, issn = {1525-3171}, abstract = {It has been hypothesized that reducing the bioenergetic costs of gut inflammation as an explanation for the effect of antibiotic growth promoters (AGPs) on animal efficiency, framing some observations but not explaining the increase in growth rate or the prevention of infectious diseases. The host's ability to adapt to alterations in environmental conditions and to maintain health involves managing all physiological interactions that regulate homeostasis. Thus, metabolic pathways are vital in regulating physiological health as the energetic demands of the host guides most biological functions. Mitochondria are not only the metabolic heart of the cell because of their role in energy metabolism and oxidative phosphorylation, but also a central hub of signal transduction pathways that receive messages about the health and nutritional states of cells and tissues. In response, mitochondria direct cellular and tissue physiological alterations throughout the host. The endosymbiotic theory suggests that mitochondria evolved from prokaryotes, emphasizing the idea that these organelles can be affected by some antibiotics. Indeed, therapeutic levels of several antibiotics can be toxic to mitochondria, but subtherapeutic levels may improve mitochondrial function and defense mechanisms by inducing an adaptive response of the cell, resulting in mitokine production which coordinates an array of adaptive responses of the host to the stressor(s). This adaptive stress response is also observed in several bacteria species, suggesting that this protective mechanism has been preserved during evolution. Concordantly, gut microbiome modulation by subinhibitory concentration of AGPs could be the result of direct stimulation rather than inhibition of determined microbial species. In eukaryotes, these adaptive responses of the mitochondria to internal and external environmental conditions, can promote growth rate of the organism as an evolutionary strategy to overcome potential negative conditions. We hypothesize that direct and indirect subtherapeutic AGP regulation of mitochondria functional output can regulate homeostatic control mechanisms in a manner similar to those involved with disease tolerance.}, }
@article {pmid38047232, year = {2023}, author = {Charrasse, S and Poquillon, T and Saint-Omer, C and Pastore, M and Bordignon, B and Frye, RE and Reynes, C and Racine, V and Aouacheria, A}, title = {Quantitative assessment of mitochondrial morphology relevant for studies on cellular health and environmental toxicity.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {5609-5619}, pmid = {38047232}, issn = {2001-0370}, abstract = {Mitochondria are essential organelles that play crucial roles in cellular energy metabolism, calcium signaling and apoptosis. Their importance in tissue homeostasis and stress responses, combined to their ability to transition between various structural and functional states, make them excellent organelles for monitoring cellular health. Quantitative assessment of mitochondrial morphology can therefore provide valuable insights into environmentally-induced cell damage. High-content screening (HCS) provides a powerful tool for analyzing organelles and cellular substructures. We developed a fully automated and miniaturized HCS wet-plus-dry pipeline (MITOMATICS) exploiting mitochondrial morphology as a marker for monitoring cellular health or damage. MITOMATICS uses an in-house, proprietary software (MitoRadar) to enable fast, exhaustive and cost-effective analysis of mitochondrial morphology and its inherent diversity in live cells. We applied our pipeline and big data analytics software to assess the mitotoxicity of selected chemicals, using the mitochondrial uncoupler CCCP as an internal control. Six different pesticides (inhibiting complexes I, II and III of the mitochondrial respiratory chain) were tested as individual compounds and five other pesticides present locally in Occitanie (Southern France) were assessed in combination to determine acute mitotoxicity. Our results show that the assayed pesticides exhibit specific signatures when used as single compounds or chemical mixtures and that they function synergistically to impact mitochondrial architecture. Study of environment-induced mitochondrial damage has the potential to open new fields in mechanistic toxicology, currently underexplored by regulatory toxicology and exposome research. Such exploration could inform health policy guidelines and foster pharmacological intervention, water, air and soil pollution control and food safety.}, }
@article {pmid38047014, year = {2023}, author = {Kobayashi, G}, title = {Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA).}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16446}, pmid = {38047014}, issn = {2167-8359}, mesh = {Humans ; Animals ; Genes, Mitochondrial ; Phylogeny ; *Annelida ; DNA, Mitochondrial/genetics ; *Polychaeta/genetics ; }, abstract = {BACKGROUND: The mitochondrial genomes (mitogenomes) of metazoans generally include the same set of protein-coding genes, which ensures the homology of mitochondrial genes between species. The mitochondrial genes are often used as reference data for species identification based on genetic data (DNA barcoding). The need for such reference data has been increasing due to the application of environmental DNA (eDNA) analysis for environmental assessments. Recently, the number of publicly available sequence reads obtained with next-generation sequencing (NGS) has been increasing in the public database (the NCBI Sequence Read Archive, SRA). Such freely available NGS reads would be promising sources for assembling mitochondrial protein-coding genes (mPCGs) of organisms whose mitochondrial genes are not available in GenBank. The present study aimed to assemble annelid mPCGs from raw data deposited in the SRA.<br><br>METHODS: The recent progress in the classification of Annelida was briefly introduced. In the present study, the mPCGs of 32 annelid species of 19 families in clitellates and allies in Sedentaria (echiurans and polychaetes) were newly assembled from the reads deposited in the SRA. Assembly was performed with a recently published pipeline mitoRNA, which includes cycles of Bowtie2 mapping and Trinity assembly. Assembled mPCGs were deposited in GenBank as Third Party Data (TPA) data. A phylogenetic tree was reconstructed with maximum likelihood (ML) analysis, together with other mPCGs deposited in GenBank.<br><br>RESULTS AND DISCUSSION: mPCG assembly was largely successful except for Travisia forbesii; only four genes were detected from the assembled contigs of the species probably due to the reads targeting its parasite. Most genes were largely successfully obtained, whereas atp8, nad2, and nad4l were only successful in 22-24 species. The high nucleotide substitution rates of these genes might be relevant to the failure in the assembly although nad6, which showed a similarly high substitution rate, was successfully assembled. Although the phylogenetic positions of several lineages were not resolved in the present study, the phylogenetic relationships of some polychaetes and leeches that were not inferred by transcriptomes were well resolved probably due to a more dense taxon sampling than previous phylogenetic analyses based on transcriptomes. Although NGS data are generally better sources for resolving phylogenetic relationships of both higher and lower classifications, there are ensuring needs for specific loci of the mitochondrial genes for analyses that do not require high resolutions, such as DNA barcoding, eDNA, and phylogenetic analysis among lower taxa. Assembly from publicly available NGS reads would help design specific primers for the mitochondrial gene sequences of species, whose mitochondrial genes are hard to amplify by Sanger sequencing using universal primers.}, }
@article {pmid38042216, year = {2024}, author = {Kong, D and Gan, Z and Li, X}, title = {Phylogenetic relationships and adaptation in deep-sea carideans revealed by mitogenomes.}, journal = {Gene}, volume = {896}, number = {}, pages = {148054}, doi = {10.1016/j.gene.2023.148054}, pmid = {38042216}, issn = {1879-0038}, mesh = {Humans ; Phylogeny ; *Genome, Mitochondrial/genetics ; RNA, Transfer/genetics ; RNA, Ribosomal/genetics ; }, abstract = {The deep-sea environment is characterized by extreme and inhospitable conditions, including oxygen depletion, low temperatures, high pressure, absence of light, and limited food availability. Mitochondria and mitogenomes play a crudial role in aerobic respiration to generate energy for eukaryotes. Here, using the Illumina Hiseq 4000 platform, we performed mitogenome sequencing for five deep-sea caridean species: Lebbeus shinkaiae, Lebbeus Formosus, Glyphocrangon regalis, Heterocarpus dorsalis, and Heterocarpus laevigatus, and five deep-sea caridean mitogenomes were assembled and identified. Each of the five mitogenomes contained 13 protein-coding genes, 2 rRNAs and 22 tRNAs. Specific elements, such as tandem repeats and AT-rich sequences, were observed in the control regions of Lebbeus formosus and Lebbeus shinkaiae, potentially take a role in regulating mitochondrial genome replication and transcription. The gene order of all obtained mitogenomes follows caridean ancestral type organization. Phylogenetic analysis shows a robustly supported phylogenetic tree for the infraorder Caridea. The monophyly of the families included in this study was strongly supported. This study supports the monophyly of Oplophoroidea, but rejects the monophyletic status of Nematocarcinoidea, Crangonoidea, and Alpheoidea. At the genus level, Plesionika is polyphyletic and Rimicaris is paraphyletic in our analysis. Furthermore, Paralebbeus may be considered invalid and synonymous with Lebbeus. Positive selection analysis reveals evidence for adaptive changes in the mitogenome of different deep-sea caridean lineages. Nine residues located in cox1, cox3, atp6, nad1, nad2, nad4, nad5, nad6 and cytb were determined to have undergone positive selection. Mitogenome of different deep-sea lineages experienced different positive selection, and the lineage represented by Alvinocarididae living in deep-sea hydrothermal vents experienced the strongest positive selection. This study provides valuable insights into the adaptive evolution of deep-sea shrimps at the mitochondrial, highlighting the mitogenomic strategy that contribute to their unique adaptations in the deep-sea environment.}, }
@article {pmid38036853, year = {2023}, author = {Ando, R and Shimozono, S and Ago, H and Takagi, M and Sugiyama, M and Kurokawa, H and Hirano, M and Niino, Y and Ueno, G and Ishidate, F and Fujiwara, T and Okada, Y and Yamamoto, M and Miyawaki, A}, title = {StayGold variants for molecular fusion and membrane-targeting applications.}, journal = {Nature methods}, volume = {}, number = {}, pages = {}, pmid = {38036853}, issn = {1548-7105}, support = {JP15dm0207001//Japan Agency for Medical Research and Development (AMED)/ ; JP21am0101070//Japan Agency for Medical Research and Development (AMED)/ ; 21H05041//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; 21H05041//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; 21H05041//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; 19H05794, 19H05795//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; JPM JCR20E2//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; }, abstract = {Although StayGold is a bright and highly photostable fluorescent protein, its propensity for obligate dimer formation may hinder applications in molecular fusion and membrane targeting. To attain monovalent as well as bright and photostable labeling, we engineered tandem dimers of StayGold to promote dispersibility. On the basis of the crystal structure of this fluorescent protein, we disrupted the dimerization to generate a monomeric variant that offers improved photostability and brightness compared to StayGold. We applied the new monovalent StayGold tools to live-cell imaging experiments using spinning-disk laser-scanning confocal microscopy or structured illumination microscopy. We achieved cell-wide, high-spatiotemporal resolution and sustained imaging of dynamic subcellular events, including the targeting of endogenous condensin I to mitotic chromosomes, the movement of the Golgi apparatus and its membranous derivatives along microtubule networks, the distribution of cortical filamentous actin and the remolding of cristae membranes within mobile mitochondria.}, }
@article {pmid38019044, year = {2023}, author = {Osiewacz, HD}, title = {Impact of Mitochondrial Architecture, Function, Redox Homeostasis, and Quality Control on Organismic Aging: Lessons from a Fungal Model System.}, journal = {Antioxidants &amp; redox signaling}, volume = {}, number = {}, pages = {}, doi = {10.1089/ars.2023.0487}, pmid = {38019044}, issn = {1557-7716}, abstract = {SIGNIFICANCE: Mitochondria are eukaryotic organelles with various essential functions. They are both, the source as well as the targets of reactive oxygen species (ROS). Different branches of a mitochondrial quality control system (mQCS), like ROS balancing, degradation of damaged proteins, or whole mitochondria can mitigate the adverse effects of ROS stress. However, the capacity of mQCS is limited. Overwhelming this capacity leads to dysfunctions and aging. Strategies to interfere into mitochondria-dependent human aging with the aim to increase the healthy period of life, the healthspan, rely on the precise knowledge of mitochondrial functions. Experimental models like Podospora anserina, a filamentous fungus with a clear mitochondrial aging etiology, proved to be instrumental to reach this goal.<br><br>RECENT ADVANCES: Investigations of the P. anserina mQCS revealed that it is constituted by a complex network of different branches. Moreover, mitochondrial architecture and lipid homeostasis emerged to affect aging.<br><br>CRITICAL ISSUES: The regulation of the mQCS is only incompletely understood. Details about the involved signaling molecules and interacting pathways remain to be elucidated. Moreover, most of the currently generated experimental data were generated in well-controlled experiments which do not reflect the constantly changing natural life conditions and bear the danger to miss relevant aspects leading to incorrect conclusions.<br><br>FUTURE DIRECTIONS: In P. anserina, the precise impact of redox signaling as well as of molecular damaging for aging remains to be defined. Moreover, natural fluctuation of environmental conditions needs to be considered to generate a realistic picture of aging mechanisms as they developed during evolution.}, }
@article {pmid38007160, year = {2024}, author = {Gao, X and Feng, B and Du, C and Hou, C and Jin, S and Tang, D and Zhu, J and Lv, Y}, title = {Expression dynamics indicate the involvement of SPG7 in the reproduction and spermiogenesis of Phascolosoma esculenta.}, journal = {Gene}, volume = {895}, number = {}, pages = {148028}, doi = {10.1016/j.gene.2023.148028}, pmid = {38007160}, issn = {1879-0038}, mesh = {Animals ; Male ; ATPases Associated with Diverse Cellular Activities/genetics/metabolism ; *Mitochondria/genetics/metabolism ; Spermatogenesis/genetics ; *Spastic Paraplegia, Hereditary/genetics ; Metalloendopeptidases/genetics ; }, abstract = {Spastic paraplegia 7 (SPG7) is an m-AAA protease subunit involved in mitochondrial morphology and physiology. However, its function in animal reproduction is yet to be evaluated. In this study, its molecular features, subcellular localization, and expression dynamics were investigated to analyze its potential function in the reproduction of male Phascolosoma esculenta, an economically important marine species in China. The full-length cDNA of P. esculenta spg7 (Pe-spg7) measures 3053 bp and encodes an 853-amino acid protein (Pe-SPG7). Pe-SPG7 includes two transmembrane domains, an AAA domain and a proteolytic domain. Amino acid sequence alignment revealed that SPG7 was conserved during evolution. The mRNA and protein expression of spg7 indicated its involvement in reproduction. Its expression was the highest in coelomic fluid, where spermatids develop, and it was significantly higher in the breeding stage than in the nonbreeding stage. SPG7 was mainly found in the mitochondria of spermatids in the coelomic fluid, indicating that it functions in this organelle in spermatids. Immunofluorescence experiments showed that SPG7 was expressed and colocalized in the mitochondria during spermiogenesis, suggesting its involvement in P. esculenta spermiogenesis. Therefore, SPG7 may participate in spermiogenesis by functioning in the mitochondria and regulate the reproduction of male P. esculenta. This study provided insights into the function of SPG7 in animal reproduction and P. esculenta gametogenesis.}, }
@article {pmid38006556, year = {2024}, author = {Duplouy, A}, title = {Validating a Mitochondrial Sweep Accompanying the Rapid Spread of a Maternally Inherited Symbiont.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2739}, number = {}, pages = {239-247}, pmid = {38006556}, issn = {1940-6029}, mesh = {*Maternal Inheritance ; *Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Polymorphism, Genetic ; Biological Evolution ; Symbiosis/genetics ; Phylogeny ; }, abstract = {Maternally inherited symbiotic bacteria that interfere with the reproduction of their hosts can contribute to selective sweeps of mitochondrial haplotypes through hitch-hiking or coordinate inheritance of cytoplasmic bacteria and host mitochondria. The sweep will be manifested by genetic variations of mitochondrial genomic DNA of symbiont-infected hosts relative to their uninfected counterparts. In particular, at the population level, infected specimens will show a reduced mitochondrial DNA polymorphism compared to that in the nuclear DNA. This may challenge the use of mitochondrial DNA sequences as neutral genetic markers, as the mitochondrial patterns will reflect the evolutionary history of parasitism, rather than the sole evolutionary history of the host. Here, I describe a detailed step-by-step procedure to infer the occurrence and timing of symbiont-induced mitochondrial sweeps in host species.}, }
@article {pmid38002320, year = {2023}, author = {Nusir, A and Sinclair, P and Kabbani, N}, title = {Mitochondrial Proteomes in Neural Cells: A Systematic Review.}, journal = {Biomolecules}, volume = {13}, number = {11}, pages = {}, pmid = {38002320}, issn = {2218-273X}, mesh = {Humans ; *Proteome/metabolism ; *Neurodegenerative Diseases/metabolism ; Proteomics ; Mitochondria/metabolism ; Neurons/metabolism ; Mitochondrial Proteins/metabolism ; }, abstract = {Mitochondria are ancient endosymbiotic double membrane organelles that support a wide range of eukaryotic cell functions through energy, metabolism, and cellular control. There are over 1000 known proteins that either reside within the mitochondria or are transiently associated with it. These mitochondrial proteins represent a functional subcellular protein network (mtProteome) that is encoded by mitochondrial and nuclear genomes and significantly varies between cell types and conditions. In neurons, the high metabolic demand and differential energy requirements at the synapses are met by specific modifications to the mtProteome, resulting in alterations in the expression and functional properties of the proteins involved in energy production and quality control, including fission and fusion. The composition of mtProteomes also impacts the localization of mitochondria in axons and dendrites with a growing number of neurodegenerative diseases associated with changes in mitochondrial proteins. This review summarizes the findings on the composition and properties of mtProteomes important for mitochondrial energy production, calcium and lipid signaling, and quality control in neural cells. We highlight strategies in mass spectrometry (MS) proteomic analysis of mtProteomes from cultured cells and tissue. The research into mtProteome composition and function provides opportunities in biomarker discovery and drug development for the treatment of metabolic and neurodegenerative disease.}, }
@article {pmid37999092, year = {2023}, author = {Liu, SP and Yin, HD and Li, WJ and Qin, ZH and Yang, Y and Huang, ZZ and Zong, L and Liu, XK and Du, Z and Fan, WL and Zhang, YQ and Zhang, D and Zhang, YE and Liu, XY and Yang, D and Ge, SQ}, title = {The Morphological Transformation of the Thorax during the Eclosion of Drosophila melanogaster (Diptera: Drosophilidae).}, journal = {Insects}, volume = {14}, number = {11}, pages = {}, pmid = {37999092}, issn = {2075-4450}, support = {32270460//National Science Foundation of China/ ; 2021xjkk0605//Third Xinjiang Scientific Expedition Program/ ; }, abstract = {The model organism Drosophila melanogaster, as a species of Holometabola, undergoes a series of transformations during metamorphosis. To deeply understand its development, it is crucial to study its anatomy during the key developmental stages. We describe the anatomical systems of the thorax, including the endoskeleton, musculature, nervous ganglion, and digestive system, from the late pupal stage to the adult stage, based on micro-CT and 3D visualizations. The development of the endoskeleton causes original and insertional changes in muscles. Several muscles change their shape during development in a non-uniform manner with respect to both absolute and relative size; some become longer and broader, while others shorten and become narrower. Muscular shape may vary during development. The number of muscular bundles also increases or decreases. Growing muscles are probably anchored by the tissues in the stroma. Some muscles and tendons are absent in the adult stage, possibly due to the hardened sclerites. Nearly all flight muscles are present by the third day of the pupal stage, which may be due to the presence of more myofibers with enough mitochondria to support flight power. There are sexual differences in the same developmental period. In contrast to the endodermal digestive system, the functions of most thoracic muscles change in the development from the larva to the adult in order to support more complex locomotion under the control of a more structured ventral nerve cord based on the serial homology proposed herein.}, }
@article {pmid37996801, year = {2023}, author = {Song, Y and Du, X and Li, A and Fan, A and He, L and Sun, Z and Niu, Y and Qiao, Y}, title = {Assembly and analysis of the complete mitochondrial genome of Forsythia suspensa (Thunb.) Vahl.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {708}, pmid = {37996801}, issn = {1471-2164}, support = {20210302123390//the Basic Research Program of Shanxi Province/ ; 2023//Shanxi Province Modern Agricultural Chinese Herbal Medicine Industry Technology System Project/ ; CXGC2023041//Shanxi Agricultural University Science and Technology Innovation Promotion Project/ ; }, mesh = {*Forsythia/genetics/chemistry ; *Genome, Mitochondrial/genetics ; Phylogeny ; *Plants, Medicinal/chemistry/genetics ; *Nucleic Acids ; *Genome, Chloroplast ; }, abstract = {BACKGROUND: Forsythia suspensa (Thunb.) Vahl is a valuable ornamental and medicinal plant. Although the nuclear and chloroplast genomes of F. suspensa have been published, its complete mitochondrial genome sequence has yet to be reported. In this study, the genomic DNA of F. suspensa yellowish leaf material was extracted, sequenced by using a mixture of Illumina Novaseq6000 short reads and Oxford Nanopore PromethION long reads, and the sequencing data were assembled and annotated.<br><br>RESULT: The F. suspensa mitochondrial genome was obtained in the length of 535,692&#xa0;bp with a circular structure, and the GC content was 44.90%. The genome contains 60 genes, including 36 protein-coding genes, 21 tRNA genes, and three rRNA genes. We further analyzed RNA editing of the protein-coding genes, relative synonymous codon usage, and sequence repeats based on the genomic data. There were 25 homologous sequences between F. suspensa mitochondria and chloroplast genome, which involved the transfer of 8 mitochondrial genes, and 9473 homologous sequences between mitochondrial and nuclear genomes. Analysis of the nucleic acid substitution rate, nucleic acid diversity, and collinearity of protein-coding genes of the F. suspensa mitochondrial genome revealed that the majority of genes may have undergone purifying selection, exhibiting a slower rate of evolution and a relatively conserved structure. Analysis of the phylogenetic relationships among different species revealed that F. suspensa was most closely related to Olea europaea subsp. Europaea.<br><br>CONCLUSION: In this study, we sequenced, assembled, and annotated a high-quality F. suspensa mitochondrial genome. The results of this study will enrich the mitochondrial genome data of Forsythia, lay a foundation for the phylogenetic development of Forsythia, and promote the evolutionary analysis of Oleaceae species.}, }
@article {pmid37995039, year = {2023}, author = {Lee, YJ and Uh, YR and Kim, YM and Kim, CM and Jang, CS}, title = {Characterization and comparative analysis of the complete organelle genomes of three red macroalgae species (Neoporphyra dentata, Neoporphyra seriata, and Neopyropia yezoensis) and development of molecular makers for their identification.}, journal = {Genes &amp; genomics}, volume = {}, number = {}, pages = {}, pmid = {37995039}, issn = {2092-9293}, support = {20210656//Korea Institute of Marine Science and Technology promotion/ ; }, abstract = {BACKGROUND: Many species of red algae belonging to the phylum Rhodophyta are consumed by humans as raw materials for nutrition and medicine. As the seaweed market grows, the importance of the laver species has increased. The classification of red algal species has changed significantly, and the accuracy of this classification has improved significantly in recent years. Here, we report the complete circular genomes of the chloroplasts (cp) and mitochondria (mt) of three laver species (Neoporphyra dentata, Neoporphyra seriata, and Neopyropia yezoensis).<br><br>OBJECTIVE: This study aims to assemble, annotate, and characterize the organization of the organelle genomes of three laver species, conduct comparative genomic studies, and develop molecular markers based on SNPs.<br><br>METHODS: We analyzed organelle genome structures, repeat sequences, sequence divergence, gene rearrangements, and phylogenetic relationships of three laver species.<br><br>RESULTS: The chloroplast genomes of the three species contained an average of 212 protein-coding genes (PCGs), while the mitochondrial genomes contained an average of 25 PCGs. We reconstructed the phylogenetic trees based on both chloroplast and mitochondrial genomes using 201 and 23 PCGs (in cp and mt genomes, respectively) shared in the class Bangiophyceae (and five species of Florideophyceae class used as an outgroup). In addition, 12 species-specific molecular markers were developed for qRT-PCR analysis.<br><br>CONCLUSIONS: This is the first report of Neoporphyra seriata complete organellar genomes. With the results, this study provides useful genetic information regarding taxonomic discrepancies, the reconstruction of phylogenetic trees, and the evolution of red algae. Moreover, the species-specific markers can be used as fast and easy methods to identify a target species.}, }
@article {pmid37994879, year = {2023}, author = {Záhonová, K and Füssy, Z and Stairs, CW and Leger, MM and Tachezy, J and Čepička, I and Roger, AJ and Hampl, V}, title = {Comparative analysis of mitochondrion-related organelles in anaerobic amoebozoans.}, journal = {Microbial genomics}, volume = {9}, number = {11}, pages = {}, pmid = {37994879}, issn = {2057-5858}, mesh = {Anaerobiosis ; *Mitochondria/genetics ; *Eukaryota ; Iron ; Sulfates ; }, abstract = {Archamoebae comprises free-living or endobiotic amoebiform protists that inhabit anaerobic or microaerophilic environments and possess mitochondrion-related organelles (MROs) adapted to function anaerobically. We compared in silico reconstructed MRO proteomes of eight species (six genera) and found that the common ancestor of Archamoebae possessed very few typical components of the protein translocation machinery, electron transport chain and tricarboxylic acid cycle. On the other hand, it contained a sulphate activation pathway and bacterial iron-sulphur (Fe-S) assembly system of MIS-type. The metabolic capacity of the MROs, however, varies markedly within this clade. The glycine cleavage system is widely conserved among Archamoebae, except in Entamoeba, probably owing to its role in catabolic function or one-carbon metabolism. MRO-based pyruvate metabolism was dispensed within subgroups Entamoebidae and Rhizomastixidae, whereas sulphate activation could have been lost in isolated cases of Rhizomastix libera, Mastigamoeba abducta and Endolimax sp. The MIS (Fe-S) assembly system was duplicated in the common ancestor of Mastigamoebidae and Pelomyxidae, and one of the copies took over Fe-S assembly in their MRO. In Entamoebidae and Rhizomastixidae, we hypothesize that Fe-S cluster assembly in both compartments may be facilitated by dual localization of the single system. We could not find evidence for changes in metabolic functions of the MRO in response to changes in habitat; it appears that such environmental drivers do not strongly affect MRO reduction in this group of eukaryotes.}, }
@article {pmid37988339, year = {2023}, author = {Kang, N and Hu, H}, title = {Adaptive evidence of mitochondrial genes in Pteromalidae and Eulophidae (Hymenoptera: Chalcidoidea).}, journal = {PloS one}, volume = {18}, number = {11}, pages = {e0294687}, pmid = {37988339}, issn = {1932-6203}, mesh = {Animals ; *Hymenoptera/genetics ; Genes, Mitochondrial ; Phylogeny ; Bayes Theorem ; Ecosystem ; Ultraviolet Rays ; Mitochondrial Proteins/genetics ; *Genome, Mitochondrial ; }, abstract = {Pteromalidae and Eulophidae are predominant and abundant taxa within Chalcidoidea (Hymenoptera: Apocrita). These taxa are found in diverse ecosystems, ranging from basin deserts (200 m) to alpine grasslands (4500 m). Mitochondria, cellular powerhouses responsible for energy production via oxidative phosphorylation, are sensitive to various environmental factors such as extreme cold, hypoxia, and intense ultraviolet radiation characteristic of alpine regions. Whether the molecular evolution of mitochondrial genes in these parasitoids corresponds to changes in the energy requirements and alpine environmental adaptations remains unknown. In this study, we performed a comparative analysis of mitochondrial protein-coding genes from 11 alpine species of Pteromalidae and Eulophidae, along with 18 lowland relatives, including 16 newly sequenced species. We further examined the codon usage preferences (RSCU, ENC-GC3s, neutrality, and PR2 bias plot) in these mitochondrial protein-coding sequences and conducted positive selection analysis based on their Bayesian phylogenetic relationships, and identified positive selection sites in the ATP6, ATP8, COX1, COX3, and CYTB genes, emphasizing the crucial role of mitochondrial gene adaptive evolution in the adaptation of Pteromalidae and Eulophidae to alpine environments. The phylogenetically independent contrast (PIC) analysis results verified the ω ratio of 13 PCGs from Pteromalidae and Eulophidae increased with elevation, and results from generalized linear model confirm that ATP6, ATP8, COX3, and ND1 are closely correlated with temperature-related environmental factors. This research not only enriched the molecular data of endemic alpine species but also underscores the significance of mitochondrial genes in facilitating the adaptation of these minor parasitoids to plateau habitats.}, }
@article {pmid37978174, year = {2023}, author = {Mahendrarajah, TA and Moody, ERR and Schrempf, D and Szánthó, LL and Dombrowski, N and Davín, AA and Pisani, D and Donoghue, PCJ and Szöllősi, GJ and Williams, TA and Spang, A}, title = {ATP synthase evolution on a cross-braced dated tree of life.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7456}, pmid = {37978174}, issn = {2041-1723}, mesh = {Phylogeny ; *Bacteria/genetics ; *Archaea/genetics ; Mitochondria/genetics ; Adenosine Triphosphate ; Evolution, Molecular ; Eukaryota/genetics ; Biological Evolution ; }, abstract = {The timing of early cellular evolution, from the divergence of Archaea and Bacteria to the origin of eukaryotes, is poorly constrained. The ATP synthase complex is thought to have originated prior to the Last Universal Common Ancestor (LUCA) and analyses of ATP synthase genes, together with ribosomes, have played a key role in inferring and rooting the tree of life. We reconstruct the evolutionary history of ATP synthases using an expanded taxon sampling set and develop a phylogenetic cross-bracing approach, constraining equivalent speciation nodes to be contemporaneous, based on the phylogenetic imprint of endosymbioses and ancient gene duplications. This approach results in a highly resolved, dated species tree and establishes an absolute timeline for ATP synthase evolution. Our analyses show that the divergence of ATP synthase into F- and A/V-type lineages was a very early event in cellular evolution dating back to more than 4 Ga, potentially predating the diversification of Archaea and Bacteria. Our cross-braced, dated tree of life also provides insight into more recent evolutionary transitions including eukaryogenesis, showing that the eukaryotic nuclear and mitochondrial lineages diverged from their closest archaeal (2.67-2.19 Ga) and bacterial (2.58-2.12 Ga) relatives at approximately the same time, with a slightly longer nuclear stem-lineage.}, }
@article {pmid37958068, year = {2023}, author = {Hui, M and Zhang, Y and Wang, A and Sha, Z}, title = {The First Genome Survey of the Snail Provanna glabra Inhabiting Deep-Sea Hydrothermal Vents.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {21}, pages = {}, pmid = {37958068}, issn = {2076-2615}, support = {XDA22050302 and XDB42000000//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 42025603//National Science Foundation for Distinguished Young Scholars/ ; LSKJ202203104//the Science and Technology Innovation Project of Laoshan Laboratory/ ; }, abstract = {The snail P. glabra is an endemic species in deep-sea chemosynthetic ecosystems of the Northwest Pacific Ocean. To obtain more genetic information on this species and provide the basis for subsequent whole-genome map construction, a genome survey was performed on this snail from the hydrothermal vent of Okinawa Trough. The genomic size of P. glabra was estimated to be 1.44 Gb, with a heterozygosity of 1.91% and a repeated sequence content of 69.80%. Based on the sequencing data, a draft genome of 1.32 Gb was assembled. Transposal elements (TEs) accounted for 40.17% of the entire genome, with DNA transposons taking the highest proportion. It was found that most TEs were inserted in the genome recently. In the simple sequence repeats, the dinucleotide motif was the most enriched microsatellite type, accounting for 53% of microsatellites. A complete mitochondrial genome of P. glabra with a total length of 16,268 bp was assembled from the sequencing data. After comparison with the published mitochondrial genome of Provanna sp. from a methane seep, 331 potential single nucleotide polymorphism (SNP) sites were identified in protein-coding genes (PCGs). Except for the cox1 gene, nad2, nad4, nad5, and cob genes are expected to be candidate markers for population genetic and phylogenetic studies of P. glabra and other deep-sea snails. Compared with shallow-water species, three mitochondrial genes of deep-sea gastropods exhibited a higher evolutionary rate, indicating strong selection operating on mitochondria of deep-sea species. This study provides insights into the genome characteristics of P. glabra and supplies genomic resources for further studies on the adaptive evolution of the snail in extreme deep-sea chemosynthetic environments.}, }
@article {pmid37955101, year = {2023}, author = {Da Costa, RT and Riggs, LM and Solesio, ME}, title = {Inorganic polyphosphate and the regulation of mitochondrial physiology.}, journal = {Biochemical Society transactions}, volume = {51}, number = {6}, pages = {2153-2161}, doi = {10.1042/BST20230735}, pmid = {37955101}, issn = {1470-8752}, support = {R00 AG055701/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Energy Metabolism ; Mammals/metabolism ; *Mitochondria/metabolism ; Mitochondrial Permeability Transition Pore/metabolism ; Polymers ; *Polyphosphates/metabolism ; }, abstract = {Inorganic polyphosphate (polyP) is an ancient polymer that is well-conserved throughout evolution. It is formed by multiple subunits of orthophosphates linked together by phosphoanhydride bonds. The presence of these bonds, which are structurally similar to those found in ATP, and the high abundance of polyP in mammalian mitochondria, suggest that polyP could be involved in the regulation of the physiology of the organelle, especially in the energy metabolism. In fact, the scientific literature shows an unequivocal role for polyP not only in directly regulating oxidative a phosphorylation; but also in the regulation of reactive oxygen species metabolism, mitochondrial free calcium homeostasis, and the formation and opening of mitochondrial permeability transitions pore. All these processes are closely interconnected with the status of mitochondrial bioenergetics and therefore play a crucial role in maintaining mitochondrial and cell physiology. In this invited review, we discuss the main scientific literature regarding the regulatory role of polyP in mammalian mitochondrial physiology, placing a particular emphasis on its impact on energy metabolism. Although the effects of polyP on the physiology of the organelle are evident; numerous aspects, particularly within mammalian cells, remain unclear and require further investigation. These aspects encompass, for example, advancing the development of more precise analytical methods, unraveling the mechanism responsible for sensing polyP levels, and understanding the exact molecular mechanism that underlies the effects of polyP on mitochondrial physiology. By increasing our understanding of the biology of this ancient and understudied polymer, we could unravel new pharmacological targets in diseases where mitochondrial dysfunction, including energy metabolism dysregulation, has been broadly described.}, }
@article {pmid37944010, year = {2024}, author = {Pegan, TM and Berv, JS and Gulson-Castillo, ER and Kimmitt, AA and Winger, BM}, title = {The pace of mitochondrial molecular evolution varies with seasonal migration distance.}, journal = {Evolution; international journal of organic evolution}, volume = {78}, number = {1}, pages = {160-173}, doi = {10.1093/evolut/qpad200}, pmid = {37944010}, issn = {1558-5646}, support = {2146950//National Science Foundation/ ; //Jean Wright Cohn Endowment Fund/ ; //Robert W. Storer Endowment Fund/ ; //Mary Rhoda Swales Museum of Zoology Research Fund/ ; //William G. Fargo Fund/ ; //University of Michigan Museum of Zoology/ ; //William A and Nancy R Klamm Endowment/ ; //Cleveland Museum of Natural History/ ; DGE 1256260//NSF Graduate Research Fellowship/ ; //University of Michigan Rackham Graduate Student Research/ ; }, mesh = {Animals ; Seasons ; *Animal Migration ; Birds/genetics ; Evolution, Molecular ; *Life History Traits ; }, abstract = {Animals that engage in long-distance seasonal migration experience strong selective pressures on their metabolic performance and life history, with potential consequences for molecular evolution. Species with slow life histories typically show lower rates of synonymous substitution (dS) than "fast" species. Previous research suggests long-distance seasonal migrants have a slower life history strategy than short-distance migrants, raising the possibility that rates of molecular evolution may covary with migration distance. Additionally, long-distance migrants may face strong selection on metabolically-important mitochondrial genes due to their long-distance flights. Using over 1,000 mitochondrial genomes, we assessed the relationship between migration distance and mitochondrial molecular evolution in 39 boreal-breeding migratory bird species. We show that migration distance correlates negatively with dS, suggesting that the slow life history associated with long-distance migration is reflected in rates of molecular evolution. Mitochondrial genes in every study species exhibited evidence of purifying selection, but the strength of selection was greater in short-distance migrants, contrary to our predictions. This result may indicate effects of selection for cold tolerance on mitochondrial evolution among species overwintering at high latitudes. Our study demonstrates that the pervasive correlation between life history and molecular evolutionary rates exists in the context of differential adaptations to seasonality.}, }
@article {pmid37940011, year = {2023}, author = {Lopez-Jimenez, J and Herrera, J and Alzate, JF}, title = {Expanding the knowledge frontier of mitoviruses in Cannabis sativa.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {116}, number = {}, pages = {105523}, doi = {10.1016/j.meegid.2023.105523}, pmid = {37940011}, issn = {1567-7257}, mesh = {*Cannabis/genetics ; Phylogeny ; *RNA Viruses/genetics ; Mitochondria/genetics ; Fungi ; }, abstract = {Mitoviruses were initially known for their presence in the mitochondria of fungi and were considered exclusive to these organisms. However, recent studies have shown that they are also present in a large number of plant species. Despite the potential impact that mitoviruses might have on the mitochondria of plant cells, there is a lack of information about these ancient RNA viruses, especially within the Cannabaceae family. Cannabis sativa has been in the spotlight in recent years due to the growing industrial applications of plant derivatives, such as fiber and secondary metabolites. Given the importance of Cannabis in today's agriculture, our study aimed to expand the knowledge frontier of Mitoviruses in C. sativa by increasing the number of reference genomes of CasaMV1 available in public databases and representing a larger number of crops in countries where its industrial-scale growth is legalized. To achieve this goal, we used transcriptomics to sequence the first mitoviral genomes of Colombian crops and analyzed RNA-seq datasets available in the SRA databank. Additionally, the evolutionary analysis performed using the mitovirus genomes revealed two main lineages of CasaMV1, termed CasaMV1_L1 and CasaMV1_L2. These mitoviral lineages showed strong clustering based on the geographic location of the crops and differential expression intensities.}, }
@article {pmid37939146, year = {2023}, author = {Garcia, PS and Barras, F and Gribaldo, S}, title = {Components of iron-Sulfur cluster assembly machineries are robust phylogenetic markers to trace the origin of mitochondria and plastids.}, journal = {PLoS biology}, volume = {21}, number = {11}, pages = {e3002374}, pmid = {37939146}, issn = {1545-7885}, mesh = {Phylogeny ; *Iron-Sulfur Proteins/genetics/metabolism ; Plastids/genetics/metabolism ; Mitochondria/genetics/metabolism ; Iron/metabolism ; Sulfur/metabolism ; }, abstract = {Establishing the origin of mitochondria and plastids is key to understand 2 founding events in the origin and early evolution of eukaryotes. Recent advances in the exploration of microbial diversity and in phylogenomics approaches have indicated a deep origin of mitochondria and plastids during the diversification of Alphaproteobacteria and Cyanobacteria, respectively. Here, we strongly support these placements by analyzing the machineries for assembly of iron-sulfur ([Fe-S]) clusters, an essential function in eukaryotic cells that is carried out in mitochondria by the ISC machinery and in plastids by the SUF machinery. We assessed the taxonomic distribution of ISC and SUF in representatives of major eukaryotic supergroups and analyzed the phylogenetic relationships with their prokaryotic homologues. Concatenation datasets of core ISC proteins show an early branching of mitochondria within Alphaproteobacteria, right after the emergence of Magnetococcales. Similar analyses with the SUF machinery place primary plastids as sister to Gloeomargarita within Cyanobacteria. Our results add to the growing evidence of an early emergence of primary organelles and show that the analysis of essential machineries of endosymbiotic origin provide a robust signal to resolve ancient and fundamental steps in eukaryotic evolution.}, }
@article {pmid37935058, year = {2023}, author = {Smith, CH and Mejia-Trujillo, R and Breton, S and Pinto, BJ and Kirkpatrick, M and Havird, JC}, title = {Mitonuclear Sex Determination? Empirical Evidence from Bivalves.}, journal = {Molecular biology and evolution}, volume = {40}, number = {11}, pages = {}, pmid = {37935058}, issn = {1537-1719}, support = {R35 GM142836/GM/NIGMS NIH HHS/United States ; 1R35GM142836/NH/NIH HHS/United States ; }, mesh = {Female ; Animals ; *Bivalvia/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Genes, Mitochondrial ; *RNA, Small Untranslated ; }, abstract = {Genetic elements encoded in nuclear DNA determine the sex of an individual in many animals. In certain bivalve lineages that possess doubly uniparental inheritance (DUI), mitochondrial DNA (mtDNA) has been hypothesized to contribute to sex determination. In these cases, females transmit a female mtDNA to all offspring, while male mtDNA (M mtDNA) is transmitted only from fathers to sons. Because M mtDNA is inherited in the same way as Y chromosomes, it has been hypothesized that mtDNA may be responsible for sex determination. However, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in DUI bivalves. In this study, we used DNA, RNA, and mitochondrial short noncoding RNA (sncRNA) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel Potamilus streckersoni (Bivalvia: Unionida). We found that the M mtDNA sheds a sncRNA partially within a male-specific mitochondrial gene that targets a pathway hypothesized to be involved in female development and mitophagy. RNA-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncRNAs in gene silencing. These findings support the hypothesis that M mtDNA inhibits female development. Genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex-determining region, although we cannot reject that nuclear factors are involved with sex determination. Our results provide further evidence that mitochondrial loci contribute to diverse, nonrespiratory functions and additional insights into an unorthodox sex-determining system.}, }
@article {pmid37933590, year = {2024}, author = {Khan, M and Joshi, M and Espeland, M and Huemer, P and Lopez-Vaamonde, C and Mutanen, M}, title = {Patterns of speciation in a parapatric pair of Saturnia moths as revealed by target capture.}, journal = {Molecular ecology}, volume = {33}, number = {1}, pages = {e17194}, doi = {10.1111/mec.17194}, pmid = {37933590}, issn = {1365-294X}, support = {314702//Academy of Finland/ ; 101081280//COFUND/ ; 00230503//Suomen Kulttuurirahasto/ ; projectInfoBioS//European Regional Development Fund (ERDF)/ ; EX011185//European Regional Development Fund (ERDF)/ ; }, mesh = {Animals ; Phylogeny ; *Moths/genetics ; Biological Evolution ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; }, abstract = {The focus of this study has been to understand the evolutionary relationships and taxonomy of a widely distributed parapatric species pair of wild silk moths in Europe: Saturnia pavonia and Saturnia pavoniella (Lepidoptera: Saturniidae). To address species delimitation in these parapatric taxa, target enrichment and mtDNA sequencing was employed alongside phylogenetic, admixture, introgression, and species delimitation analyses. The dataset included individuals from both species close to and farther away from the contact zone as well as two hybrids generated in the lab. Nuclear markers strongly supported both S. pavonia and S. pavoniella as two distinct species, with hybrids forming a sister group to S. pavoniella. However, the Maximum Likelihood (ML) tree generated from mtDNA sequencing data presented a different picture, showing both taxa to be phylogenetically intermixed. This inconsistency is likely attributable to mitonuclear discordance, which can arise from biological factors (e.g., introgressive hybridization and/or incomplete lineage sorting). Our analyses indicate that past introgressions have taken place, but that there is no evidence to suggest an ongoing admixture between the two species, demonstrating that the taxa have reached full postzygotic reproductive isolation and hence represent two distinct biological species. Finally, we discuss our results from an evolutionary point of view taking into consideration the past climatic oscillations that have likely shaped the present dynamics between the two species. Overall, our study demonstrates the effectiveness of the target enrichment approach in resolving shallow phylogenetic relationships under complex evolutionary circumstances and that this approach is useful in establishing robust and well-informed taxonomic delimitations involving parapatric taxa.}, }
@article {pmid37931036, year = {2023}, author = {Gu, H and Wen, J and Zhao, X and Zhang, X and Ren, X and Cheng, H and Qu, L}, title = {Evolution, Inheritance, and Strata Formation of the W Chromosome in Duck (Anas platyrhynchos).}, journal = {Genome biology and evolution}, volume = {15}, number = {11}, pages = {}, pmid = {37931036}, issn = {1759-6653}, mesh = {Animals ; Female ; *Ducks/genetics ; *Evolution, Molecular ; Sex Chromosomes ; Birds/genetics ; Inheritance Patterns ; }, abstract = {The nonrecombining female-limited W chromosome is predicted to experience unique evolutionary processes. Difficulties in assembling W chromosome sequences have hindered the identification of duck W-linked sequences and their evolutionary footprint. To address this, we conducted three initial contig-level genome assemblies and developed a rigorous pipeline by which to successfully expand the W-linked data set, including 11 known genes and 24 newly identified genes. Our results indicate that the W chromosome expression may not be subject to female-specific selection; a significant convergent pattern of upregulation associated with increased female-specific selection was not detected. The genetic stability of the W chromosome is also reflected in the strong evolutionary correlation between it and the mitochondria; the complete consistency of the cladogram topology constructed from their gene sequences proves the shared maternal coevolution. By detecting the evolutionary trajectories of W-linked sequences, we have found that recombination suppression started in four distinct strata, of which three were conserved across Neognathae. Taken together, our results have revealed a unique evolutionary pattern and an independent stratum evolutionary pattern for sex chromosomes.}, }
@article {pmid37930986, year = {2023}, author = {Diaz-Recio Lorenzo, C and Patel, T and Arsenault-Pernet, EJ and Poitrimol, C and Jollivet, D and Martinez Arbizu, P and Gollner, S}, title = {Highly structured populations of deep-sea copepods associated with hydrothermal vents across the Southwest Pacific, despite contrasting life history traits.}, journal = {PloS one}, volume = {18}, number = {11}, pages = {e0292525}, pmid = {37930986}, issn = {1932-6203}, mesh = {Animals ; *Copepoda/genetics ; *Hydrothermal Vents ; *Life History Traits ; DNA, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Ecosystem ; }, abstract = {Hydrothermal vents are extreme environments, where abundant communities of copepods with contrasting life history traits co-exist along hydrothermal gradients. Here, we discuss how these traits may contribute to the observed differences in molecular diversity and population genetic structure. Samples were collected from vent locations across the globe including active ridges and back-arc basins and compared to existing deep-sea hydrothermal vent and shallow water data, covering a total of 22 vents and 3 non-vent sites. A total of 806 sequences of mtDNA from the Cox1 gene were used to reconstruct the phylogeny, haplotypic relationship and demography within vent endemic copepods (Dirivultidae, Stygiopontius spp.) and non-vent-endemic copepods (Ameiridae, Miraciidae and Laophontidae). A species complex within Stygiopontius lauensis was studied across five pacific back-arc basins at eight hydrothermal vent fields, with cryptic species being restricted to the basins they were sampled from. Copepod populations from the Lau, North Fiji and Woodlark basins are undergoing demographic expansion, possibly linked to an increase in hydrothermal activity in the last 10 kya. Highly structured populations of Amphiascus aff. varians 2 were also observed from the Lau to the Woodlark basins with populations also undergoing expansion. Less abundant harpacticoids exhibit little to no population structure and stable populations. This study suggests that similarities in genetic structure and demography may arise in vent-associated copepods despite having different life history traits. As structured meta-populations may be at risk of local extinction should major anthropogenic impacts, such as deep-sea mining, occur, we highlight the importance of incorporating a trait-based approach to investigate patterns of genetic connectivity and demography, particularly regarding area-based management tools and environmental management plans.}, }
@article {pmid37929337, year = {2023}, author = {Ibrahim, MK and Haria, A and Mehta, NV and Degani, MS}, title = {Antimicrobial potential of quaternary phosphonium salt compounds: a review.}, journal = {Future medicinal chemistry}, volume = {15}, number = {22}, pages = {2113-2141}, doi = {10.4155/fmc-2023-0188}, pmid = {37929337}, issn = {1756-8927}, mesh = {Phylogeny ; Microbial Sensitivity Tests ; *Anti-Infective Agents/pharmacology/chemistry ; Anti-Bacterial Agents/pharmacology/chemistry ; Mitochondria ; Quaternary Ammonium Compounds/chemistry ; }, abstract = {Given that mitochondrial dysregulation is a biomarker of many cancers, cationic quaternary phosphonium salt (QPS) conjugation is a widely utilized strategy for anticancer drug design. QPS-conjugated compounds exhibit greater cell permeation and accumulation in negatively charged mitochondria, and thus, show enhanced activity. Phylogenetic similarities between mitochondria and bacteria have provided a rationale for exploring the antibacterial properties of mitochondria-targeted compounds. Additionally, due to the importance of mitochondria in the survival of pathogenic microbes, including fungi and parasites, this strategy can be extended to these organisms as well. This review examines recent literature on the antimicrobial activities of various QPS-conjugated compounds and provides future directions for exploring the medicinal chemistry of these compounds.}, }
@article {pmid37924024, year = {2023}, author = {Lu, G and Wang, W and Mao, J and Li, Q and Que, Y}, title = {Complete mitogenome assembly of Selenicereus monacanthus revealed its molecular features, genome evolution, and phylogenetic implications.}, journal = {BMC plant biology}, volume = {23}, number = {1}, pages = {541}, pmid = {37924024}, issn = {1471-2229}, support = {XZ202301ZY0020N//the Science and Technology Program of Tibet Autonomous Region/ ; }, mesh = {Phylogeny ; *Genome, Mitochondrial ; Genomics ; Evolution, Molecular ; *Cactaceae/genetics ; }, abstract = {BACKGROUND: Mitochondria are the powerhouse of the cell and are critical for plant growth and development. Pitaya (Selenicereus or Hylocereus) is the most important economic crop in the family Cactaceae and is grown worldwide, however its mitogenome is unreported.<br><br>RESULTS: This study assembled the complete mitogenome of the red skin and flesh of pitaya (Selenicereus monacanthus). It is a full-length, 2,290,019&#xa0;bp circular molecule encoding 59 unique genes that only occupy 2.17% of the entire length. In addition, 4,459 pairs of dispersed repeats (&#x2265;&#x2009;50&#xa0;bp) were identified, accounting for 84.78% of the total length, and three repeats (394,588, 124,827, and 13,437&#xa0;bp) mediating genomic recombination were identified by long read mapping and Sanger sequencing. RNA editing events were identified in all 32 protein-coding genes (PCGs), among which four sites (nad1-2, nad4L-2, atp9-copy3-223, and ccmFC-1309) were associated with the initiation or termination of PCGs. Seventy-eight homologous fragments of the chloroplast genome were identified in the mitogenome, the longest having 4,523&#xa0;bp. In addition, evolutionary analyses suggest that S. monacanthus may have undergone multiple genomic reorganization events during evolution, with the loss of at least nine PCGs (rpl2, rpl10, rps2, rps3, rps10, rps11, rps14, rps19, and sdh3).<br><br>CONCLUSIONS: This study revealed the genetic basis of the S. monacanthus mitogenome, and provided a scientific basis for further research on phenotypic traits and germplasm resource development.}, }
@article {pmid37919084, year = {2023}, author = {Zhang, X and Lu, YC and Wang, JL}, title = {Assembly and Characterization of the Mitochondrial Genome of Fallopia aubertii (L. Henry) Holub.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {28}, number = {10}, pages = {233}, doi = {10.31083/j.fbl2810233}, pmid = {37919084}, issn = {2768-6698}, mesh = {*Genome, Mitochondrial/genetics ; *Fallopia/genetics ; Phylogeny ; Genes, Mitochondrial ; }, abstract = {BACKGROUND: Fallopia aubertii (L. Henry) Holub is a perennial semi-shrub with both ornamental and medicinal value. The mitochondrial genomes of plants contain valuable genetic traits that can be utilized for the exploitation of genetic resources. The parsing of F. aubertii mitochondrial genome can provide insight into the role of mitochondria in plant growth and development, metabolism regulation, evolution, and response to environmental stress.<br><br>METHODS: In this study, we sequenced the mitochondrial genome of F. aubertii using the Illumina NovaSeq 6000 platform and Nanopore platform. We conducted a comprehensive analysis of the mitochondrial genome of F. aubertii, which involved examining various aspects such as gene composition, repetitive sequences, RNA editing sites, phylogeny, and organelle genome homology. To achieve this, we employed several bioinformatics methods including sequence alignment analysis, repetitive sequence analysis, phylogeny analysis, and more.<br><br>RESULTS: The mitochondrial genome of F. aubertii has 64 genes, including 34 protein-coding genes (PCGs), three rRNAs, and 27 tRNAs. There were 77 short tandem repeat sequences detected in the mitochondrial genome, five tandem repeat sequences identified by Tandem Repeats Finder (TRF), and 50 scattered repeat sequences observed, including 22 forward repeat sequences and 28 palindrome repeat sequences. A total of 367 RNA coding sites were predicted in PCGs, with the highest number (33) found within ccmB. Ka/Ks values estimated for mitochondrial genes of F. aubertii and three closely related species representing Caryophyllales were less than 1 for most of the genes. The maximum likelihood evolutionary tree showed that F. aubertii and Nepenthes &#xd7;ventrata are most closely related.<br><br>CONCLUSIONS: In this study, we obtained basic information on the mitochondrial genome of F. aubertii and this study investigated repeat sequences and homologous segments, predicted RNA editing sites, and utilized the Ka/Ks ratio to estimate the selection pressure on mitochondrial genes of F. aubertii. We also discussed the systematic evolutionary position of F. aubertii based on mitochondrial genome sequences. Our study revealed variations in the sequence and structure of mitochondrial genomes in Caryophyllales. These findings are of great significance for identifying and improving valuable plant traits and serve as a reference for future molecular studies of F. aubertii.}, }
@article {pmid37917792, year = {2023}, author = {Namasivayam, S and Sun, C and Bah, AB and Oberstaller, J and Pierre-Louis, E and Etheridge, RD and Feschotte, C and Pritham, EJ and Kissinger, JC}, title = {Massive invasion of organellar DNA drives nuclear genome evolution in Toxoplasma.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {45}, pages = {e2308569120}, pmid = {37917792}, issn = {1091-6490}, support = {R01 AI068908/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Toxoplasma/genetics ; Genome ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Evolution, Molecular ; Cell Nucleus/genetics ; Sequence Analysis, DNA ; }, abstract = {Toxoplasma gondii is a zoonotic protist pathogen that infects up to one third of the human population. This apicomplexan parasite contains three genome sequences: nuclear (65 Mb); plastid organellar, ptDNA (35 kb); and mitochondrial organellar, mtDNA (5.9 kb of non-repetitive sequence). We find that the nuclear genome contains a significant amount of NUMTs (nuclear integrants of mitochondrial DNA) and NUPTs (nuclear integrants of plastid DNA) that are continuously acquired and represent a significant source of intraspecific genetic variation. NUOT (nuclear DNA of organellar origin) accretion has generated 1.6% of the extant T. gondii ME49 nuclear genome-the highest fraction ever reported in any organism. NUOTs are primarily found in organisms that retain the non-homologous end-joining repair pathway. Significant movement of organellar DNA was experimentally captured via amplicon sequencing of a CRISPR-induced double-strand break in non-homologous end-joining repair competent, but not ku80 mutant, Toxoplasma parasites. Comparisons with Neospora caninum, a species that diverged from Toxoplasma ~28 mya, revealed that the movement and fixation of five NUMTs predates the split of the two genera. This unexpected level of NUMT conservation suggests evolutionary constraint for cellular function. Most NUMT insertions reside within (60%) or nearby genes (23% within 1.5 kb), and reporter assays indicate that some NUMTs have the ability to function as cis-regulatory elements modulating gene expression. Together, these findings portray a role for organellar sequence insertion in dynamically shaping the genomic architecture and likely contributing to adaptation and phenotypic changes in this important human pathogen.}, }
@article {pmid37903625, year = {2024}, author = {Hacker, C and Sendra, K and Keisham, P and Filipescu, T and Lucocq, J and Salimi, F and Ferguson, S and Bhella, D and MacNeill, SA and Embley, M and Lucocq, J}, title = {Biogenesis, inheritance, and 3D ultrastructure of the microsporidian mitosome.}, journal = {Life science alliance}, volume = {7}, number = {1}, pages = {}, pmid = {37903625}, issn = {2575-1077}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Fungal Proteins/metabolism ; Mitochondria/metabolism ; *Microsporidia/genetics/metabolism ; Saccharomyces cerevisiae/metabolism ; Dynamins ; Mammals/metabolism ; }, abstract = {During the reductive evolution of obligate intracellular parasites called microsporidia, a tiny remnant mitochondrion (mitosome) lost its typical cristae, organellar genome, and most canonical functions. Here, we combine electron tomography, stereology, immunofluorescence microscopy, and bioinformatics to characterise mechanisms of growth, division, and inheritance of this minimal mitochondrion in two microsporidia species (grown within a mammalian RK13 culture-cell host). Mitosomes of Encephalitozoon cuniculi (2-12/cell) and Trachipleistophora hominis (14-18/nucleus) displayed incremental/non-phasic growth and division and were closely associated with an organelle identified as equivalent to the fungal microtubule-organising centre (microsporidian spindle pole body; mSPB). The mitosome-mSPB association was resistant to treatment with microtubule-depolymerising drugs nocodazole and albendazole. Dynamin inhibitors (dynasore and Mdivi-1) arrested mitosome division but not growth, whereas bioinformatics revealed putative dynamins Drp-1 and Vps-1, of which, Vps-1 rescued mitochondrial constriction in dynamin-deficient yeast (Schizosaccharomyces pombe). Thus, microsporidian mitosomes undergo incremental growth and dynamin-mediated division and are maintained through ordered inheritance, likely mediated via binding to the microsporidian centrosome (mSPB).}, }
@article {pmid37901222, year = {2023}, author = {Brun, C and Chalet, L and Moulin, F and Bochaton, T and Ducreux, S and Paillard, M and Crola Da Silva, C}, title = {A bibliometric analysis: Ca[2+] fluxes and inflammatory phenotyping by flow cytometry in peripheral blood mononuclear cells.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1272809}, pmid = {37901222}, issn = {1664-3224}, mesh = {Humans ; *Leukocytes, Mononuclear/metabolism ; Flow Cytometry/methods ; Cell Line ; *Signal Transduction ; Inflammation/metabolism ; }, abstract = {BACKGROUND: The immune system, composed of organs, tissues, cells, and proteins, is the key to protecting the body from external biological attacks and inflammation. The latter occurs in several pathologies, such as cancers, type 1 diabetes, and human immunodeficiency virus infection. Immunophenotyping by flow cytometry is the method of choice for diagnosing these pathologies. Under inflammatory conditions, the peripheral blood mononuclear cells (PBMCs) are partially activated and generate intracellular pathways involving Ca[2+]-dependent signaling cascades leading to transcription factor expression. Ca[2+] signaling is typically studied by microscopy in cell lines but can present some limitations to explore human PBMCs, where flow cytometry can be a good alternative.<br><br>OBJECTIVE: In this review, we dived into the research field of inflammation and Ca[2+] signaling in PBMCs. We aimed to investigate the structure and evolution of this field in a physio-pathological context, and then we focused our review on flow cytometry analysis of Ca[2+] fluxes in PBMCs.<br><br>METHODS: From 1984 to 2022, 3865 articles on inflammation and Ca[2+] signaling in PBMCs were published, according to The Clarivate Web of Science (WOS) database used in this review. A bibliometric study was designed for this collection and consisted of a co-citation and bibliographic coupling analysis.<br><br>RESULTS: The co-citation analysis was performed on 133 articles: 4 clusters highlighted the global context of Ca[2+] homeostasis, including chemical probe development, identification of the leading players in Ca[2+] signaling, and the link with chemokine production in immune cell function. Next, the bibliographic coupling analysis combined 998 articles in 8 clusters. This analysis outlined the mechanisms of PBMC activation, from signal integration to cellular response. Further explorations of the bibliographic coupling network, focusing on flow cytometry, revealed 21 articles measuring cytosolic Ca[2+] in PBMCs, with only 5 since 2016. This final query showed that Ca[2+] signaling analysis in human PBMCs using flow cytometry is still underdeveloped and investigates mainly the cytosolic Ca[2+] compartment.<br><br>CONCLUSION: Our review uncovers remaining knowledge gaps of intracellular players involved in Ca[2+] signaling in PBMCs, such as reticulum and mitochondria, and presents flow cytometry as a solid option to supplement gold-standard microscopy studies.}, }
@article {pmid37900311, year = {2023}, author = {Gonzalez-Jimenez, I and Perlin, DS and Shor, E}, title = {Reactive oxidant species induced by antifungal drugs: identity, origins, functions, and connection to stress-induced cell death.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1276406}, pmid = {37900311}, issn = {2235-2988}, support = {R21 AI168729/AI/NIAID NIH HHS/United States ; }, mesh = {*Antifungal Agents/pharmacology/therapeutic use ; Reactive Oxygen Species/metabolism ; *Oxidants ; Echinocandins/pharmacology ; Apoptosis ; }, abstract = {Reactive oxidant species (ROS) are unstable, highly reactive molecules that are produced by cells either as byproducts of metabolism or synthesized by specialized enzymes. ROS can be detrimental, e.g., by damaging cellular macromolecules, or beneficial, e.g., by participating in signaling. An increasing body of evidence shows that various fungal species, including both yeasts and molds, increase ROS production upon exposure to the antifungal drugs currently used in the clinic: azoles, polyenes, and echinocandins. However, the implications of these findings are still largely unclear due to gaps in knowledge regarding the chemical nature, molecular origins, and functional consequences of these ROS. Because the detection of ROS in fungal cells has largely relied on fluorescent probes that lack specificity, the chemical nature of the ROS is not known, and it may vary depending on the specific fungus-drug combination. In several instances, the origin of antifungal drug-induced ROS has been identified as the mitochondria, but further experiments are necessary to strengthen this conclusion and to investigate other potential cellular ROS sources, such as the ER, peroxisomes, and ROS-producing enzymes. With respect to the function of the ROS, several studies have shown that they contribute to the drugs' fungicidal activities and may be part of drug-induced programmed cell death (PCD). However, whether these "pro-death" ROS are a primary consequence of the antifungal mechanism of action or a secondary consequence of drug-induced PCD remains unclear. Finally, several recent studies have raised the possibility that ROS induction can serve an adaptive role, promoting antifungal drug tolerance and the evolution of drug resistance. Filling these gaps in knowledge will reveal a new aspect of fungal biology and may identify new ways to potentiate antifungal drug activity or prevent the evolution of antifungal drug resistance.}, }
@article {pmid37895071, year = {2023}, author = {Olla, S and Siguri, C and Fais, A and Era, B and Fantini, MC and Di Petrillo, A}, title = {Inhibitory Effect of Quercetin on Oxidative Endogen Enzymes: A Focus on Putative Binding Modes.}, journal = {International journal of molecular sciences}, volume = {24}, number = {20}, pages = {}, pmid = {37895071}, issn = {1422-0067}, mesh = {*Quercetin/pharmacology ; Reactive Oxygen Species/metabolism ; *Antioxidants/pharmacology/metabolism ; Molecular Docking Simulation ; Oxidative Stress ; Xanthine Oxidase/metabolism ; Monoamine Oxidase/metabolism ; }, abstract = {Oxidative stress is defined as an imbalance between the production of free radicals and reactive oxygen species (ROS) and the ability of the body to neutralize them by anti-oxidant defense systems. Cells can produce ROS during physiological processes, but excessive ROS can lead to non-specific and irreversible damage to biological molecules, such as DNA, lipids, and proteins. Mitochondria mainly produce endogenous ROS during both physiological and pathological conditions. Enzymes like nicotinamide adenine dinucleotide phosphate oxidase (NOX), xanthine oxidase (XO), lipoxygenase (LOX), myeloperoxidase (MPO), and monoamine oxidase (MAO) contribute to this process. The body has enzymatic and non-enzymatic defense systems to neutralize ROS. The intake of bioactive phenols, like quercetin (Que), can protect against pro-oxidative damage by quenching ROS through a non-enzymatic system. In this study, we evaluate the ability of Que to target endogenous oxidant enzymes involved in ROS production and explore the mechanisms of action underlying its anti-oxidant properties. Que can act as a free radical scavenger by donating electrons through the negative charges in its phenolic and ketone groups. Additionally, it can effectively inhibit the activity of several endogenous oxidative enzymes by binding them with high affinity and specificity. Que had the best molecular docking results with XO, followed by MAO-A, 5-LOX, NOX, and MPO. Que's binding to these enzymes was confirmed by subsequent molecular dynamics, revealing different stability phases depending on the enzyme bound. The 500 ns simulation showed a net evolution of binding for NOX and MPO. These findings suggest that Que has potential as a natural therapy for diseases related to oxidative stress.}, }
@article {pmid37885664, year = {2023}, author = {Ni, Y and Zhang, X and Li, J and Lu, Q and Chen, H and Ma, B and Liu, C}, title = {Genetic diversity of Coffea arabica L. mitochondrial genomes caused by repeat- mediated recombination and RNA editing.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1261012}, pmid = {37885664}, issn = {1664-462X}, abstract = {BACKGROUND: Coffea arabica L. is one of the most important crops widely cultivated in 70 countries across Asia, Africa, and Latin America. Mitochondria are essential organelles that play critical roles in cellular respiration, metabolism, and differentiation. C. arabica's nuclear and chloroplast genomes have been reported. However, its mitochondrial genome remained unreported. Here, we intended to sequence and characterize its mitochondrial genome to maximize the potential of its genomes for evolutionary studies, molecular breeding, and molecular marker developments.<br><br>RESULTS: We sequenced the total DNA of C. arabica using Illumina and Nanopore platforms. We then assembled the mitochondrial genome with a hybrid strategy using Unicycler software. We found that the mitochondrial genome comprised two circular chromosomes with lengths of 867,678 bp and 153,529 bp, encoding 40 protein-coding genes, 26 tRNA genes, and three rRNA genes. We also detected 270 Simple Sequence Repeats and 34 tandem repeats in the mitochondrial genome. We found 515 high-scoring sequence pairs (HSPs) for a self-to-self similarity comparison using BLASTn. Three HSPs were found to mediate recombination by the mapping of long reads. Furthermore, we predicted 472 using deep-mt with the convolutional neural network model. Then we randomly validated 90 RNA editing events by PCR amplification and Sanger sequencing, with the majority being non-synonymous substitutions and only three being synonymous substitutions. These findings provide valuable insights into the genetic characteristics of the C. arabica mitochondrial genome, which can be helpful for future study on coffee breeding and mitochondrial genome evolution.<br><br>CONCLUSION: Our study sheds new light on the evolution of C. arabica organelle genomes and their potential use in genetic breeding, providing valuable data for developing molecular markers that can improve crop productivity and quality. Furthermore, the discovery of RNA editing events in the mitochondrial genome of C. arabica offers insights into the regulation of gene expression in this species, contributing to a better understanding of coffee genetics and evolution.}, }
@article {pmid37871810, year = {2024}, author = {Coto, ALS and Pereira, AA and Oliveira, SD and Moritz, MNO and Franco da Rocha, AM and Dores-Silva, PR and da Silva, NSM and de Araújo Nogueira, AR and Gava, LM and Seraphim, TV and Borges, JC}, title = {Structural characterization of the human DjC20/HscB cochaperone in solution.}, journal = {Biochimica et biophysica acta. Proteins and proteomics}, volume = {1872}, number = {1}, pages = {140970}, doi = {10.1016/j.bbapap.2023.140970}, pmid = {37871810}, issn = {1878-1454}, mesh = {Humans ; Adenosine Triphosphatases/metabolism ; Edetic Acid ; *Heat-Shock Proteins/chemistry ; *HSP70 Heat-Shock Proteins/chemistry ; Molecular Chaperones/chemistry ; }, abstract = {J-domain proteins (JDPs) form a very large molecular chaperone family involved in proteostasis processes, such as protein folding, trafficking through membranes and degradation/disaggregation. JDPs are Hsp70 co-chaperones capable of stimulating ATPase activity as well as selecting and presenting client proteins to Hsp70. In mitochondria, human DjC20/HscB (a type III JDP that possesses only the conserved J-domain in some region of the protein) is involved in [FeS] protein biogenesis and assists human mitochondrial Hsp70 (HSPA9). Human DjC20 possesses a zinc-finger domain in its N-terminus, which closely contacts the J-domain and appears to be essential for its function. Here, we investigated the hDjC20 structure in solution as well as the importance of Zn[+2] for its stability. The recombinant hDjC20 was pure, folded and capable of stimulating HSPA9 ATPase activity. It behaved as a slightly elongated monomer, as attested by small-angle X-ray scattering and SEC-MALS. The presence of Zn[2+] in the hDjC20 samples was verified, a stoichiometry of 1:1 was observed, and its removal by high concentrations of EDTA and DTPA was unfeasible. However, thermal and chemical denaturation in the presence of EDTA led to a reduction in protein stability, suggesting a synergistic action between the chelating agent and denaturators that facilitate protein unfolding depending on metal removal. These data suggest that the affinity of Zn[+2] for the protein is very high, evidencing its importance for the hDjC20 structure.}, }
@article {pmid37859594, year = {2023}, author = {Waters, ER and Bezanilla, M and Vierling, E}, title = {ATAD3 Proteins: Unique Mitochondrial Proteins Essential for Life in Diverse Eukaryotic Lineages.}, journal = {Plant &amp; cell physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/pcp/pcad122}, pmid = {37859594}, issn = {1471-9053}, support = {IOS 1354960 MCB 2215727//National Science Foundation/ ; }, abstract = {ATAD3 proteins (ATPase family AAA domain-containing protein 3) are unique mitochondrial proteins that arose deep in the eukaryotic lineage but that are surprisingly absent from the Fungi and Amoebozoa. These ~600 amino acid proteins are anchored in the inner mitochondrial membrane and are essential in metazoans and Arabidopsis thaliana. ATAD3s comprise a C-terminal AAA+ matrix domain and an ATAD3_N domain that is located primarily in the inner membrane space but potentially extends into cytosol to interact with the ER. Sequence and structural alignments indicate ATAD3 proteins are most similar to classic chaperone unfoldases in AAA+ family, suggesting that they operate in mitochondrial protein quality control. A. thaliana has four ATAD3 genes in two distinct clades that appear first in the seed plants, and both clades are essential for viability. The four genes are generally coordinately expressed, and transcripts are highest in growing apices and imbibed seeds. Plants with disrupted ATAD3 have reduced growth, aberrant mitochondrial morphology, diffuse nucleoids and reduced oxidative phosphorylation complex I. These and other pleiotropic phenotypes are also observed in ATAD3 mutants in metazoans. Here we discuss the distribution of ATAD3 proteins as they have evolved in the plant kingdom, their unique structure, what we know about their function in plants, and the challenges in determining their essential roles in mitochondria.}, }
@article {pmid37850870, year = {2023}, author = {Nicolini, F and Ghiselli, F and Luchetti, A and Milani, L}, title = {Bivalves as Emerging Model Systems to Study the Mechanisms and Evolution of Sex Determination: A Genomic Point of View.}, journal = {Genome biology and evolution}, volume = {15}, number = {10}, pages = {}, pmid = {37850870}, issn = {1759-6653}, mesh = {Humans ; Animals ; Phylogeny ; *Bivalvia/genetics ; Genome ; Genomics ; Mitochondria/genetics ; Sex Determination Processes/genetics ; Biological Evolution ; }, abstract = {Bivalves are a diverse group of molluscs that have recently attained a central role in plenty of biological research fields, thanks to their peculiar life history traits. Here, we propose that bivalves should be considered as emerging model systems also in sex-determination (SD) studies, since they would allow to investigate: 1) the transition between environmental and genetic SD, with respect to different reproductive backgrounds and sexual systems (from species with strict gonochorism to species with various forms of hermaphroditism); 2) the genomic evolution of sex chromosomes (SCs), considering that no heteromorphic SCs are currently known and that homomorphic SCs have been identified only in a few species of scallops; 3) the putative role of mitochondria at some level of the SD signaling pathway, in a mechanism that may resemble the cytoplasmatic male sterility of plants; 4) the evolutionary history of SD-related gene (SRG) families with respect to other animal groups. In particular, we think that this last topic may lay the foundations for expanding our understanding of bivalve SD, as our current knowledge is quite fragmented and limited to a few species. As a matter of fact, tracing the phylogenetic history and diversity of SRG families (such as the Dmrt, Sox, and Fox genes) would allow not only to perform more targeted functional experiments and genomic analyses, but also to foster the possibility of establishing a solid comparative framework.}, }
@article {pmid37844192, year = {2023}, author = {Borghi, F and Saiardi, A}, title = {Evolutionary perspective on mammalian inorganic polyphosphate (polyP) biology.}, journal = {Biochemical Society transactions}, volume = {51}, number = {5}, pages = {1947-1956}, pmid = {37844192}, issn = {1470-8752}, support = {MR/T028904/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Polyphosphates ; *Mammals ; Eukaryotic Cells ; Mitochondria ; Biology ; }, abstract = {Inorganic polyphosphate (polyP), the polymeric form of phosphate, is attracting ever-growing attention due to the many functions it appears to perform within mammalian cells. This essay does not aim to systematically review the copious mammalian polyP literature. Instead, we examined polyP synthesis and functions in various microorganisms and used an evolutionary perspective to theorise key issues of this field and propose solutions. By highlighting the presence of VTC4 in distinct species of very divergent eucaryote clades (Opisthokonta, Viridiplantae, Discoba, and the SAR), we propose that whilst polyP synthesising machinery was present in the ancestral eukaryote, most lineages subsequently lost it during evolution. The analysis of the bacteria-acquired amoeba PPK1 and its unique polyP physiology suggests that eukaryote cells must have developed mechanisms to limit cytosolic polyP accumulation. We reviewed the literature on polyP in the mitochondria from the perspective of its endosymbiotic origin from bacteria, highlighting how mitochondria could possess a polyP physiology reminiscent of their 'bacterial' beginning that is not yet investigated. Finally, we emphasised the similarities that the anionic polyP shares with the better-understood negatively charged polymers DNA and RNA, postulating that the nucleus offers an ideal environment where polyP physiology might thrive.}, }
@article {pmid37843218, year = {2024}, author = {Zhang, J and Zhu, Q and Wang, J and Peng, Z and Zhuang, Z and Hang, C and Li, W}, title = {Mitochondrial dysfunction and quality control lie at the heart of subarachnoid hemorrhage.}, journal = {Neural regeneration research}, volume = {19}, number = {4}, pages = {825-832}, pmid = {37843218}, issn = {1673-5374}, abstract = {The dramatic increase in intracranial pressure after subarachnoid hemorrhage leads to a decrease in cerebral perfusion pressure and a reduction in cerebral blood flow. Mitochondria are directly affected by direct factors such as ischemia, hypoxia, excitotoxicity, and toxicity of free hemoglobin and its degradation products, which trigger mitochondrial dysfunction. Dysfunctional mitochondria release large amounts of reactive oxygen species, inflammatory mediators, and apoptotic proteins that activate apoptotic pathways, further damaging cells. In response to this array of damage, cells have adopted multiple mitochondrial quality control mechanisms through evolution, including mitochondrial protein quality control, mitochondrial dynamics, mitophagy, mitochondrial biogenesis, and intercellular mitochondrial transfer, to maintain mitochondrial homeostasis under pathological conditions. Specific interventions targeting mitochondrial quality control mechanisms have emerged as promising therapeutic strategies for subarachnoid hemorrhage. This review provides an overview of recent research advances in mitochondrial pathophysiological processes after subarachnoid hemorrhage, particularly mitochondrial quality control mechanisms. It also presents potential therapeutic strategies to target mitochondrial quality control in subarachnoid hemorrhage.}, }
@article {pmid37818890, year = {2023}, author = {Chen, H and Shi, BY and Du, LN and Sun, HY}, title = {Description of a New Species of Hua (Gastropoda: Semisulcospiridae) from Guizhou, China, Based on Morphology and Molecular Evidence.}, journal = {Zoological science}, volume = {40}, number = {5}, pages = {414-421}, doi = {10.2108/zs230025}, pmid = {37818890}, issn = {0289-0003}, mesh = {Female ; Animals ; *Gastropoda/anatomy &amp; histology ; Phylogeny ; China ; Mitochondria ; }, abstract = {A new species of Hua, Hua qiannanensis sp. nov., is described from Guizhou Province, China, based on morphological and molecular evidence. The new species can be distinguished from its congeners by the following combination of characters: the smooth shell, only three smaller cusps of lateral teeth on the inner side, outer marginal teeth with eight flattened and rounded denticles, an ovipositor pore in females, and BW/H ≥ 80%, B/H = 76.8-82.3%. Molecular analysis based on partial mitochondrial COI and 16S rDNA also supports the systematic position of the new taxon.}, }
@article {pmid37815994, year = {2023}, author = {Chen, YH and Miller, WB and Hay, A}, title = {Postharvest bacterial succession on cut flowers and vase water.}, journal = {PloS one}, volume = {18}, number = {10}, pages = {e0292537}, pmid = {37815994}, issn = {1932-6203}, mesh = {*Water ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Ecosystem ; *Asteraceae ; Flowers ; Bacteria/genetics ; }, abstract = {In cut flowers, xylem occlusion or blockage by bacteria negatively affects water balance and postharvest quality. Many studies have used culture-based methods to examine bacterial populations in vase water and their effects on flower longevity. It is still unclear if and how bacterial communities at the 16S rRNA gene (16S) level change during the vase period and how such change might correlate with postharvest longevity. This study compared the sequences of 16S amplicons from 4 different types of flowers and their vase water over the course of 7 days (Rosa spp., Gerbera jamesonii, and two Lilium varieties). The relative abundance of plant chloroplast and mitochondria 16S decreased significantly over the course 7 days in all 4 flowers as bacterial diversity increased. Richness and evenness of the bacterial communities increased over time, as did the number of rare taxa and phylogenetic diversity. Bacterial communities varied with time, as well as by flower source, types, and sample location (water, stem surface, whole stem). Some taxa, such as Enterobacteriacea and Bradyhizobiaceae decreased significantly over time while others such as Pseudomonas spp. increased. For example, Pseudomonas veronii, implicated in soft rot of calla lily, increased in both whole stem samples and water samples from Gerbera jamesonii. Erwinia spp., which includes plant pathogenic species, also increased in water samples. This work highlights the dynamic and complex nature of bacterial succession in the flower vase ecosystem. More work is needed to understand if and how bacterial community structure can be managed to improve cut flower vase life.}, }
@article {pmid37810794, year = {2023}, author = {Rodriguez, D and Harding, SF and Sirsi, S and McNichols-O'Rourke, K and Morris, T and Forstner, MRJ and Schwalb, AN}, title = {Mitochondrial sequence data reveal population structure within Pustulosa pustulosa.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15974}, pmid = {37810794}, issn = {2167-8359}, mesh = {Humans ; Animals ; Phylogeny ; Mitochondria ; *Bivalvia ; *Unionidae/genetics ; Texas ; Ontario ; }, abstract = {Unionid mussels are among the most imperiled group of organisms in North America, and Pustulosa pustulosa is a freshwater species with a relatively wide latitudinal distribution that extends from southern Ontario, Canada, to Texas, USA. Considerable morphological and geographic variation in the genus Pustulosa (formerly Cyclonaias) has led to uncertainty over species boundaries, and recent studies have suggested revisions to species-level classifications by synonymizing C. aurea, C. houstonensis, C. mortoni, and C. refulgens with C. pustulosa (currently P. pustulosa). Owing to its wide range and shallow phylogenetic differentiation, we analyzed individuals of P. pustulosa using mitochondrial DNA sequence data under a population genetics framework. We included 496 individuals, which were comprised of 166 samples collected during this study and 330 additional sequences retrieved from GenBank. Pairwise ΦST measures based on ND1 data suggested there may be up to five major geographic groups present within P. pustulosa. Genetic differentiation between regions within Texas was higher compared to populations from the Mississippi and Great Lakes populations, which may reflect differences in historical connectivity. Mitochondrial sequence data also revealed varying demographic histories for each major group suggesting each geographic region has also experienced differential population dynamics in the past. Future surveys should consider exploring variation within species after phylogeographic delimitation has been performed. In this study, we begin to address this need for freshwater mussels via the P. pustulosa system.}, }
@article {pmid37796022, year = {2023}, author = {Usey, MM and Huet, D}, title = {ATP synthase-associated coiled-coil-helix-coiled-coil-helix (CHCH) domain-containing proteins are critical for mitochondrial function in Toxoplasma gondii.}, journal = {mBio}, volume = {14}, number = {5}, pages = {e0176923}, pmid = {37796022}, issn = {2150-7511}, support = {R00 AI137218/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Toxoplasma/genetics/metabolism ; Mitochondria/metabolism ; Proteins/metabolism ; *Parasites/metabolism ; Nitric Oxide Synthase/metabolism ; Adenosine Triphosphate/metabolism ; Protozoan Proteins/genetics/metabolism ; Mitochondrial Proteins/metabolism ; }, abstract = {Members of the coiled-coil-helix-coiled-coil-helix (CHCH) domain protein family are transported into the mitochondrial intermembrane space, where they play important roles in the biogenesis and function of the organelle. Unexpectedly, the ATP synthase of the apicomplexan Toxoplasma gondii harbors CHCH domain-containing subunits of unknown function. As no other ATP synthase studied to date contains this class of proteins, characterizing their function will be of broad interest to the fields of molecular parasitology and mitochondrial evolution. Here, we demonstrate that that two T. gondii ATP synthase subunits containing CHCH domains are required for parasite survival and for stability and function of the ATP synthase. We also show that knockdown disrupts multiple aspects of the mitochondrial morphology of T. gondii and that mutation of key residues in the CHCH domains caused mis-localization of the proteins. This work provides insight into the unique features of the apicomplexan ATP synthase, which could help to develop therapeutic interventions against this parasite and other apicomplexans, such as the malaria-causing parasite Plasmodium falciparum.}, }
@article {pmid37792908, year = {2023}, author = {Motyčková, A and Voleman, L and Najdrová, V and Arbonová, L and Benda, M and Dohnálek, V and Janowicz, N and Malych, R and Šuťák, R and Ettema, TJG and Svärd, S and Stairs, CW and Doležal, P}, title = {Adaptation of the late ISC pathway in the anaerobic mitochondrial organelles of Giardia intestinalis.}, journal = {PLoS pathogens}, volume = {19}, number = {10}, pages = {e1010773}, pmid = {37792908}, issn = {1553-7374}, mesh = {Humans ; *Giardia lamblia/genetics/metabolism ; Anaerobiosis ; *Iron-Sulfur Proteins/genetics/metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins/metabolism ; }, abstract = {Mitochondrial metabolism is entirely dependent on the biosynthesis of the [4Fe-4S] clusters, which are part of the subunits of the respiratory chain. The mitochondrial late ISC pathway mediates the formation of these clusters from simpler [2Fe-2S] molecules and transfers them to client proteins. Here, we characterized the late ISC pathway in one of the simplest mitochondria, mitosomes, of the anaerobic protist Giardia intestinalis that lost the respiratory chain and other hallmarks of mitochondria. In addition to IscA2, Nfu1 and Grx5 we identified a novel BolA1 homologue in G. intestinalis mitosomes. It specifically interacts with Grx5 and according to the high-affinity pulldown also with other core mitosomal components. Using CRISPR/Cas9 we were able to establish full bolA1 knock out, the first cell line lacking a mitosomal protein. Despite the ISC pathway being the only metabolic role of the mitosome no significant changes in the mitosome biology could be observed as neither the number of the mitosomes or their capability to form [2Fe-2S] clusters in vitro was affected. We failed to identify natural client proteins that would require the [2Fe-2S] or [4Fe-4S] cluster within the mitosomes, with the exception of [2Fe-2S] ferredoxin, which is itself part of the ISC pathway. The overall uptake of iron into the cellular proteins remained unchanged as also observed for the grx5 knock out cell line. The pull-downs of all late ISC components were used to build the interactome of the pathway showing specific position of IscA2 due to its interaction with the outer mitosomal membrane proteins. Finally, the comparative analysis across Metamonada species suggested that the adaptation of the late ISC pathway identified in G. intestinalis occurred early in the evolution of this supergroup of eukaryotes.}, }
@article {pmid37783374, year = {2023}, author = {Igamberdiev, AU and Gordon, R}, title = {Macroevolution, differentiation trees, and the growth of coding systems.}, journal = {Bio Systems}, volume = {234}, number = {}, pages = {105044}, doi = {10.1016/j.biosystems.2023.105044}, pmid = {37783374}, issn = {1872-8324}, mesh = {*Cell Differentiation/genetics ; Morphogenesis/genetics ; Phylogeny ; }, abstract = {An open process of evolution of multicellular organisms is based on the rearrangement and growth of the program of differentiation that underlies biological morphogenesis. The maintenance of the final (adult) stable non-equilibrium state (stasis) of a developmental system determines the direction of the evolutionary process. This state is achieved via the sequence of differentiation events representable as differentiation trees. A special type of morphogenetic code, acting as a metacode governing gene expression, may include electromechanical signals appearing as differentiation waves. The excessive energy due to the incorporation of mitochondria in eukaryotic cells resulted not only in more active metabolism but also in establishing the differentiation code for interconnecting cells and forming tissues, which fueled the evolutionary process. The "invention" of "continuing differentiation" distinguishes multicellular eukaryotes from other organisms. The Janus-faced control, involving both top-down control by differentiation waves and bottom-up control via the mechanical consequences of cell differentiations, underlies the process of morphogenesis and results in the achievement of functional stable final states. Duplications of branches of the differentiation tree may be the basis for continuing differentiation and macroevolution, analogous to gene duplication permitting divergence of genes. Metamorphoses, if they are proven to be fusions of disparate species, may be classified according to the topology of fusions of two differentiation trees. In the process of unfolding of morphogenetic structures, microevolution can be defined as changes of the differentiation tree that preserve topology of the tree, while macroevolution represents any change that alters the topology of the differentiation tree.}, }
@article {pmid37778286, year = {2023}, author = {Duarte Hospital, C and Tête, A and Debizet, K and Imler, J and Tomkiewicz-Raulet, C and Blanc, EB and Barouki, R and Coumoul, X and Bortoli, S}, title = {SDHi fungicides: An example of mitotoxic pesticides targeting the succinate dehydrogenase complex.}, journal = {Environment international}, volume = {180}, number = {}, pages = {108219}, doi = {10.1016/j.envint.2023.108219}, pmid = {37778286}, issn = {1873-6750}, mesh = {Animals ; Humans ; *Fungicides, Industrial/toxicity ; *Pesticides ; Succinate Dehydrogenase/genetics/metabolism ; Fungi/metabolism ; Succinic Acid ; Succinates ; }, abstract = {Succinate dehydrogenase inhibitors (SDHi) are fungicides used to control the proliferation of pathogenic fungi in crops. Their mode of action is based on blocking the activity of succinate dehydrogenase (SDH), a universal enzyme expressed by all species harboring mitochondria. The SDH is involved in two interconnected metabolic processes for energy production: the transfer of electrons in the mitochondrial respiratory chain and the oxidation of succinate to fumarate in the Krebs cycle. In humans, inherited SDH deficiencies may cause major pathologies including encephalopathies and cancers. The cellular and molecular mechanisms related to such genetic inactivation have been well described in neuroendocrine tumors, in which it induces an oxidative stress, a pseudohypoxic phenotype, a metabolic, epigenetic and transcriptomic remodeling, and alterations in the migration and invasion capacities of cancer cells, in connection with the accumulation of succinate, an oncometabolite, substrate of the SDH. We will discuss recent studies reporting toxic effects of SDHi in non-target organisms and their implications for risk assessment of pesticides. Recent data show that the SDH structure is highly conserved during evolution and that SDHi can inhibit SDH activity in mitochondria of non-target species, including humans. These observations suggest that SDHi are not specific inhibitors of fungal SDH. We hypothesize that SDHi could have toxic effects in other species, including humans. Moreover, the analysis of regulatory assessment reports shows that most SDHi induce tumors in animals without evidence of genotoxicity. Thus, these substances could have a non-genotoxic mechanism of carcinogenicity that still needs to be fully characterized and that could be related to SDH inhibition. The use of pesticides targeting mitochondrial enzymes encoded by tumor suppressor genes raises questions on the risk assessment framework of mitotoxic pesticides. The issue of SDHi fungicides is therefore a textbook case that highlights the urgent need for changes in regulatory assessment.}, }
@article {pmid37766465, year = {2023}, author = {Dial, DT and Weglarz, KM and Brunet, BMT and Havill, NP and von Dohlen, CD and Burke, GR}, title = {Whole-genome sequence of the Cooley spruce gall adelgid, Adelges cooleyi (Hemiptera: Sternorrhyncha: Adelgidae).}, journal = {G3 (Bethesda, Md.)}, volume = {14}, number = {1}, pages = {}, pmid = {37766465}, issn = {2160-1836}, support = {DEB-1655182//National Science Foundation/ ; //Utah Agricultural Experiment Station/ ; }, mesh = {Animals ; *Hemiptera/genetics ; Ecosystem ; *Aphids/genetics ; Ecology ; North America ; }, abstract = {The adelgids (Adelgidae) are a small family of sap-feeding insects, which, together with true aphids (Aphididae) and phylloxerans (Phylloxeridae), make up the infraorder Aphidomorpha. Some adelgid species are highly destructive to forest ecosystems such as Adelges tsugae, Adelges piceae, Adelges laricis, Pineus pini, and Pineus boerneri. Despite this, there are no high-quality genomic resources for adelgids, hindering advanced genomic analyses within Adelgidae and among Aphidomorpha. Here, we used PacBio continuous long-read and Illumina RNA-sequencing to construct a high-quality draft genome assembly for the Cooley spruce gall adelgid, Adelges cooleyi (Gillette), a gall-forming species endemic to North America. The assembled genome is 270.2 Mb in total size and has scaffold and contig N50 statistics of 14.87 and 7.18 Mb, respectively. There are 24,967 predicted coding sequences, and the assembly completeness is estimated at 98.1 and 99.6% with core BUSCO gene sets of Arthropoda and Hemiptera, respectively. Phylogenomic analysis using the A. cooleyi genome, 3 publicly available adelgid transcriptomes, 4 phylloxera transcriptomes, the Daktulosphaira vitifoliae (grape phylloxera) genome, 4 aphid genomes, and 2 outgroup coccoid genomes fully resolves adelgids and phylloxerans as sister taxa. The mitochondrial genome is 24 kb, among the largest in insects sampled to date, with 39.4% composed of noncoding regions. This genome assembly is currently the only genome-scale, annotated assembly for adelgids and will be a valuable resource for understanding the ecology and evolution of Aphidomorpha.}, }
@article {pmid37761909, year = {2023}, author = {Mendivil, A and Ramírez, R and Morin, J and Ramirez, JL and Siccha-Ramirez, R and Britzke, R and Rivera, F and Ampuero, A and Oliveros, N and Congrains, C}, title = {Comparative Mitogenome Analysis of Two Native Apple Snail Species (Ampullariidae, Pomacea) from Peruvian Amazon.}, journal = {Genes}, volume = {14}, number = {9}, pages = {}, pmid = {37761909}, issn = {2073-4425}, mesh = {Animals ; Peru ; Phylogeny ; *Genome, Mitochondrial/genetics ; Snails/genetics ; Mitochondria/genetics ; }, abstract = {Apple snails of the genus Pomacea Perry, 1810 (Mollusca: Caenogastropoda: Ampullariidae) are native to the Neotropics and exhibit high species diversity, holding cultural and ecological significance as an important protein source in Peru. However, most genetic studies in Pomacea have focused mostly on invasive species, especially in Southeast Asia, where they are considered important pests. In this study, we assembled and annotated the mitochondrial genomes of two Pomacea species native to the Peruvian Amazon: Pomacea reevei Ampuero &amp; Ramírez, 2023 and Pomacea aulanieri (Deville &amp; Hupé, 1850). The mitogenomes of P. reevei and P. aulanieri comprise 15,660 and 16,096 bp, respectively, and contain the typical 37 genes of the animal mitochondria with a large control region of 292 bp in P. reevei and 524 bp in P. aulanieri-which fall within the range of what is currently known in Pomacea. Comparisons with previously published mitogenomes in Pomacea revealed differences in the overlapping of adjacent genes, the size of certain protein-coding genes (PCGs) and the secondary structure of some tRNAs that are consistent with the phylogenetic relationships between these species. These findings provide valuable insights into the systematics and genomics of the genus Pomacea.}, }
@article {pmid37761841, year = {2023}, author = {Koshkina, O and Deniskova, T and Dotsev, A and Kunz, E and Selionova, M and Medugorac, I and Zinovieva, N}, title = {Phylogenetic Analysis of Russian Native Sheep Breeds Based on mtDNA Sequences.}, journal = {Genes}, volume = {14}, number = {9}, pages = {}, pmid = {37761841}, issn = {2073-4425}, mesh = {Sheep/genetics ; Animals ; *DNA, Mitochondrial/genetics ; Phylogeny ; *Mitochondria/genetics ; Animals, Domestic/genetics ; Russia ; }, abstract = {Eurasia is represented by all climatic zones and various environments. A unique breed variety of farm animals has been developed in Russia, whose territory covers a large area of the continent. A total of 69 local breeds and types of dairy, wool, and meat sheep (Ovis aries) are maintained here. However, the genetic diversity and maternal origin of these local breeds have not been comprehensively investigated. In this study, we describe the diversity and phylogeny of Russian sheep breeds inhabiting different geographical regions based on the analysis of complete sequences of mitochondrial genomes (mtDNA). Complete mtDNA sequences of the studied sheep were obtained using next-generation sequencing technology (NGS). All investigated geographical groups of sheep were characterized by high haplotype (Hd = 0.9992) and nucleotide diversity (π = 0.00378). Analysis of the AMOVA results showed that genetic diversity was majorly determined by within-population differences (77.87%). We identified 128 haplotypes in all studied sheep. Haplotypes belonged to the following haplogroups: B (64.8%), A (28.9%), C (5.5%), and D (0.8%). Haplogroup B was predominant in the western part of Russia. A high level of mtDNA polymorphism in the studied groups of local sheep indicates the presence of a significant reserve of unique genotypes in Russia, which is to be explored.}, }
@article {pmid37760086, year = {2023}, author = {Subczynski, WK and Pasenkiewicz-Gierula, M and Widomska, J}, title = {Protecting the Eye Lens from Oxidative Stress through Oxygen Regulation.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {9}, pages = {}, pmid = {37760086}, issn = {2076-3921}, support = {R01 EY015526/EY/NEI NIH HHS/United States ; }, abstract = {Molecular oxygen is a primary oxidant that is involved in the formation of active oxygen species and in the oxidation of lipids and proteins. Thus, controlling oxygen partial pressure (concentration) in the human organism, tissues, and organs can be the first step in protecting them against oxidative stress. However, it is not an easy task because oxygen is necessary for ATP synthesis by mitochondria and in many biochemical reactions taking place in all cells in the human body. Moreover, the blood circulatory system delivers oxygen to all parts of the body. The eye lens seems to be the only organ that is protected from the oxidative stress through the regulation of oxygen partial pressure. The basic mechanism that developed during evolution to protect the eye lens against oxidative damage is based on the maintenance of a very low concentration of oxygen within the lens. This antioxidant mechanism is supported by the resistance of both the lipid components of the lens membrane and cytosolic proteins to oxidation. Any disturbance, continuous or acute, in the working of this mechanism increases the oxygen concentration, in effect causing cataract development. Here, we describe the biophysical basis of the mechanism and its correlation with lens transparency.}, }
@article {pmid37752851, year = {2023}, author = {Togashi, T and Parker, GA and Horinouchi, Y}, title = {Mitochondrial uniparental inheritance achieved after fertilization challenges the nuclear-cytoplasmic conflict hypothesis for anisogamy evolution.}, journal = {Biology letters}, volume = {19}, number = {9}, pages = {20230352}, pmid = {37752851}, issn = {1744-957X}, mesh = {Male ; Humans ; *Mitochondria ; *DNA, Mitochondrial/genetics ; Inheritance Patterns ; Polymerase Chain Reaction ; Fertilization ; }, abstract = {In eukaryotes, a fundamental phenomenon underlying sexual selection is the evolution of gamete size dimorphism between the sexes (anisogamy) from an ancestral gametic system with gametes of the same size in both mating types (isogamy). The nuclear-cytoplasmic conflict hypothesis has been one of the major theoretical hypotheses for the evolution of anisogamy. It proposes that anisogamy evolved as an adaptation for preventing nuclear-cytoplasmic conflict by minimizing male gamete size to inherit organelles uniparentally. In ulvophycean green algae, biparental inheritance of organelles is observed in isogamous species, as the hypothesis assumes. So we tested the hypothesis by examining whether cytoplasmic inheritance is biparental in Monostroma angicava, a slightly anisogamous ulvophycean that produces large male gametes. We tracked the fates of mitochondria in intraspecific crosses with PCR-RFLP markers. We confirmed that mitochondria are maternally inherited. However, paternal mitochondria enter the zygote, where their DNA can be detected for over 14 days. This indicates that uniparental inheritance is enforced by eliminating paternal mitochondrial DNA in the zygote, rather than by decreasing male gamete size to the minimum. Thus, uniparental cytoplasmic inheritance is achieved by an entirely different mechanism, and is unlikely to drive the evolution of anisogamy in ulvophyceans.}, }
@article {pmid37748065, year = {2023}, author = {Zhang, K and Zhao, X and Zhao, Y and Zhang, Z and Liu, Z and Liu, Z and Yu, Y and Li, J and Ma, Y and Dong, Y and Pang, X and Jin, X and Li, N and Liu, B and Wendel, JF and Zhai, J and Long, Y and Wang, T and Gong, L}, title = {Cell type-specific cytonuclear coevolution in three allopolyploid plant species.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {40}, pages = {e2310881120}, pmid = {37748065}, issn = {1091-6490}, mesh = {*Mitochondria/genetics ; *Plastids ; Cell Differentiation ; Problem Solving ; Solitary Nucleus ; }, abstract = {Cytonuclear disruption may accompany allopolyploid evolution as a consequence of the merger of different nuclear genomes in a cellular environment having only one set of progenitor organellar genomes. One path to reconcile potential cytonuclear mismatch is biased expression for maternal gene duplicates (homoeologs) encoding proteins that target to plastids and/or mitochondria. Assessment of this transcriptional form of cytonuclear coevolution at the level of individual cells or cell types remains unexplored. Using single-cell (sc-) and single-nucleus (sn-) RNAseq data from eight tissues in three allopolyploid species, we characterized cell type-specific variations of cytonuclear coevolutionary homoeologous expression and demonstrated the temporal dynamics of expression patterns across development stages during cotton fiber development. Our results provide unique insights into transcriptional cytonuclear coevolution in plant allopolyploids at the single-cell level.}, }
@article {pmid37744223, year = {2023}, author = {Suárez Menéndez, M and Rivera-León, VE and Robbins, J and Berube, M and Palsbøll, PJ}, title = {PHFinder: assisted detection of point heteroplasmy in Sanger sequencing chromatograms.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16028}, pmid = {37744223}, issn = {2167-8359}, mesh = {Animals ; *Heteroplasmy ; Fluorescence ; *Humpback Whale ; Mitochondria ; Nucleotides ; }, abstract = {Heteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets. Here, we present PHFinder, a Python-based, open-source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. The program was tested with Sanger sequencing data from 100 humpback whales (Megaptera novaeangliae) tissue samples with known heteroplasmies. PHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. PHFinder is flexible and enables explicit specification of key parameters to infer double peaks (i.e., heteroplasmies).}, }
@article {pmid37742881, year = {2024}, author = {Zhang, T and Vďačný, P}, title = {Deciphering phylogenetic relationships of and delimiting species boundaries within the controversial ciliate genus Conchophthirus using an integrative morpho-evo approach.}, journal = {Molecular phylogenetics and evolution}, volume = {190}, number = {}, pages = {107931}, doi = {10.1016/j.ympev.2023.107931}, pmid = {37742881}, issn = {1095-9513}, mesh = {Phylogeny ; Sequence Analysis, DNA ; *Oligohymenophorea ; *Ciliophora/genetics ; Mitochondria ; }, abstract = {The phylum Ciliophora (ciliates) comprises about 2600 symbiotic and over 5500 free-living species. The inclusion of symbiotic ciliates in phylogenetic analyses often challenges traditional classification frameworks due to their morphological adaptions to the symbiotic lifestyle. Conchophthirus is such a controversial obligate endocommensal genus whose affinities to other symbiotic and free-living scuticociliates are still poorly understood. Using uni- and multivariate morphometrics as well as 2D-based molecular and phylogenetic analyses, we attempted to test for the monophyly of Conchophthirus, study the boundaries of Conchophthirus species isolated from various bivalves at mesoscale, and reveal the phylogenetic relationships of Conchophthirus to other scuticociliates. Multidimensional analyses of morphometric and cell geometric data generated the same homogenous clusters, as did phylogenetic analyses based on 144 new sequences of two mitochondrial and five nuclear molecular markers. Conchophthirus is not closely related to 'core' scuticociliates represented by the orders Pleuronematida and Philasterida, as assumed in the past using morphological data. Nuclear and mitochondrial markers consistently showed the free-living Dexiotricha and the mouthless endosymbiotic Haptophrya to be the nearest relatives of Conchophthirus. These three highly morphologically and ecologically dissimilar genera represent an orphan clade from the early radiation of scuticociliates in molecular phylogenies.}, }
@article {pmid37735485, year = {2023}, author = {Sidorczuk, K and Mackiewicz, P and Pietluch, F and Gagat, P}, title = {Characterization of signal and transit peptides based on motif composition and taxon-specific patterns.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15751}, pmid = {37735485}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; *Amino Acids ; *Antimicrobial Peptides ; Chloroplasts ; Computational Biology ; }, abstract = {Targeting peptides or presequences are N-terminal extensions of proteins that encode information about their cellular localization. They include signal peptides (SP), which target proteins to the endoplasmic reticulum, and transit peptides (TP) directing proteins to the organelles of endosymbiotic origin: chloroplasts and mitochondria. TPs were hypothesized to have evolved from antimicrobial peptides (AMPs), which are responsible for the host defence against microorganisms, including bacteria, fungi and viruses. In this study, we performed comprehensive bioinformatic analyses of amino acid motifs of targeting peptides and AMPs using a curated set of experimentally verified proteins. We identified motifs frequently occurring in each type of presequence showing specific patterns associated with their amino acid composition, and investigated their position within the presequence. We also compared motif patterns among different taxonomic groups and identified taxon-specific features, providing some evolutionary insights. Considering the functional relevance and many practical applications of targeting peptides and AMPs, we believe that our analyses will prove useful for their design, and better understanding of protein import mechanism and presequence evolution.}, }
@article {pmid37715276, year = {2023}, author = {Leal-Dutra, CA and Yuen, LM and Guedes, BAM and Contreras-Serrano, M and Marques, PE and Shik, JZ}, title = {Evidence that the domesticated fungus Leucoagaricus gongylophorus recycles its cytoplasmic contents as nutritional rewards to feed its leafcutter ant farmers.}, journal = {IMA fungus}, volume = {14}, number = {1}, pages = {19}, pmid = {37715276}, issn = {2210-6340}, support = {ERC-2017-STG-757810/ERC_/European Research Council/International ; }, abstract = {Leafcutter ants farm a fungal cultivar (Leucoagaricus gongylophorus) that converts inedible vegetation into food that sustains colonies with up to millions of workers. Analogous to edible fruits of crops domesticated by humans, L. gongylophorus has evolved specialized nutritional rewards-swollen hyphal cells called gongylidia that package metabolites and are consumed by ant farmers. Yet, little is known about how gongylidia form, and thus how fungal physiology and ant provisioning collectively govern farming performance. We explored the process of gongylidium formation using advanced microscopy to image the cultivar at scales of nanometers, and both in vitro experiments and in silico analyses to examine the mechanisms of gongylidia formation when isolated from ant farmers. We first used transmission electron, fluorescence, and confocal microscopy imaging to see inside hyphal cells. This imaging showed that the cultivar uses a process called autophagy to recycle its own cellular material (e.g. cytosol, mitochondria) and then shuttles the resulting metabolites into a vacuole whose continual expansion displaces other organelles and causes the gongylidium cell's bulging bulb-like appearance. We next used scanning electron microscopy and light microscopy to link this intracellular rearrangement to the external branching patterns of gongylidium cells as they clump together into edible bundles called staphyla. We next confirmed that autophagy plays a critical role in gongylidium formation both: (1) in vitro as gongylidium suppression occurred when isolated fungal cultures were grown on media with autophagy inhibitors, and (2) in silico as differential transcript expression (RNA-seq) analyses showed upregulation of multiple autophagy gene isoforms in gongylidia relative to undifferentiated hyphae. While autophagy is a ubiquitous and often highly derived process across the tree of life, our study reveals a new role for autophagy as a mechanism of functional integration between ant farmers and their fungal crop, and potentially as a signifier of higher-level homeostasis between uniquely life-time committed ectosymbionts.}, }
@article {pmid37708410, year = {2023}, author = {Khachaturyan, M and Reusch, TBH and Dagan, T}, title = {Worldwide Population Genomics Reveal Long-Term Stability of the Mitochondrial Genome Architecture in a Keystone Marine Plant.}, journal = {Genome biology and evolution}, volume = {15}, number = {9}, pages = {}, pmid = {37708410}, issn = {1759-6653}, mesh = {Humans ; Metagenomics ; *Genome, Mitochondrial ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; *Magnoliopsida/genetics ; }, abstract = {Mitochondrial genomes (mitogenomes) of flowering plants are composed of multiple chromosomes. Recombination within and between the mitochondrial chromosomes may generate diverse DNA molecules termed isoforms. The isoform copy number and composition can be dynamic within and among individual plants due to uneven replication and homologous recombination. Nonetheless, despite their functional importance, the level of mitogenome conservation within species remains understudied. Whether the ontogenetic variation translates to evolution of mitogenome composition over generations is currently unknown. Here we show that the mitogenome composition of the seagrass Zostera marina is conserved among worldwide populations that diverged ca. 350,000 years ago. Using long-read sequencing, we characterized the Z. marina mitochondrial genome and inferred the repertoire of recombination-induced configurations. To characterize the mitochondrial genome architecture worldwide and study its evolution, we examined the mitogenome in Z. marina meristematic region sampled in 16 populations from the Pacific and Atlantic oceans. Our results reveal a striking similarity in the isoform relative copy number, indicating a high conservation of the mitogenome composition among distantly related populations and within the plant germline, despite a notable variability during individual ontogenesis. Our study supplies a link between observations of dynamic mitogenomes at the level of plant individuals and long-term mitochondrial evolution.}, }
@article {pmid37685874, year = {2023}, author = {Maffeo, B and Panuzzo, C and Moraca, A and Cilloni, D}, title = {A Leukemic Target with a Thousand Faces: The Mitochondria.}, journal = {International journal of molecular sciences}, volume = {24}, number = {17}, pages = {}, pmid = {37685874}, issn = {1422-0067}, mesh = {Humans ; *Mitochondria ; Cell Division ; Clonal Evolution ; Clone Cells ; *Leukemia ; }, abstract = {In the era of personalized medicine greatly improved by molecular diagnosis and tailor-made therapies, the survival rate of acute myeloid leukemia (AML) at 5 years remains unfortunately low. Indeed, the high heterogeneity of AML clones with distinct metabolic and molecular profiles allows them to survive the chemotherapy-induced changes, thus leading to resistance, clonal evolution, and relapse. Moreover, leukemic stem cells (LSCs), the quiescent reservoir of residual disease, can persist for a long time and activate the recurrence of disease, supported by significant metabolic differences compared to AML blasts. All these points highlight the relevance to develop combination therapies, including metabolism inhibitors to improve treatment efficacy. In this review, we summarized the metabolic differences in AML blasts and LSCs, the molecular pathways related to mitochondria and metabolism are druggable and targeted in leukemia therapies, with a distinct interest for Venetoclax, which has revolutionized the therapeutic paradigms of several leukemia subtype, unfit for intensive treatment regimens.}, }
@article {pmid37667092, year = {2023}, author = {Kar, C and Mariyambi, PC and Raghavan, R and Sureshkumar, S}, title = {Mitochondrial phylogeny of fusilier fishes (family Caesionidae) from the Laccadive archipelago reveals a new species and two new records from the Central Indian Ocean.}, journal = {Journal of fish biology}, volume = {103}, number = {6}, pages = {1445-1451}, doi = {10.1111/jfb.15553}, pmid = {37667092}, issn = {1095-8649}, support = {CRG/2020/004498//Department of Science and Technology, Government of India/ ; 200510341520//University Grants Commission/ ; }, mesh = {Animals ; Phylogeny ; Indian Ocean ; *Fishes/genetics ; *Mitochondria/genetics ; Genes, Mitochondrial ; Pacific Ocean ; }, abstract = {Fusiliers of the family Caesionidae comprise a group of Indo-Pacific reef fishes important in the live bait and artisanal fisheries in many parts of its range, particularly in the Indian Ocean region. Using newly generated mitochondrial COI sequences of 10 species of caesionid fishes from the Laccadive archipelago, we carried out a molecular phylogenetic analysis, which has helped improve our understanding of the diversity, distribution, and systematics of this poorly known group of fishes. The two speciose genera within Caesionidae, Caesio and Pterocaesio, were revealed to be paraphyletic, and as a result, four names earlier considered as subgenera within Caesionidae (Flavicaesio, Odontonectes, Pisinnicaesio, and Squamosicaesio) were elevated to the status of distinct genera. We also discovered the presence of a new lineage in the Central Indian Ocean, sister to Caesio caerulaurea and Caesio xanthalytos, but distinct from both in several morphological characters and a genetic distance of between 2% and 3% in the mitochondrial COI gene. We describe this lineage as Caesio idreesi, a new species, with a distribution spanning the Laccadive Sea and the Bay of Bengal. Our genetic data also helped confirm the first confirmed records of two species, Pisinnicaesio digramma and Squamosicaesio randalli, from the Central Indian Ocean, and a new distribution record for C. xanthalytos in the Laccadive Sea. Combined, these results have helped bridge key biodiversity knowledge gaps of the family Caesionidae and form an excellent baseline for further investigations on their taxonomy, systematics, and life history.}, }
@article {pmid37664184, year = {2023}, author = {Mendoza-Hoffmann, F and Yang, L and Buratto, D and Brito-Sánchez, J and Garduño-Javier, G and Salinas-López, E and Uribe-Álvarez, C and Ortega, R and Sotelo-Serrano, O and Cevallos, M&#xc1; and Ramírez-Silva, L and Uribe-Carvajal, S and Pérez-Hernández, G and Celis-Sandoval, H and García-Trejo, JJ}, title = {Inhibitory to non-inhibitory evolution of the ζ subunit of the F1FO-ATPase of Paracoccus denitrificans and α-proteobacteria as related to mitochondrial endosymbiosis.}, journal = {Frontiers in molecular biosciences}, volume = {10}, number = {}, pages = {1184200}, pmid = {37664184}, issn = {2296-889X}, abstract = {Introduction: The ζ subunit is a potent inhibitor of the F1FO-ATPase of Paracoccus denitrificans (PdF1FO-ATPase) and related α-proteobacteria different from the other two canonical inhibitors of bacterial (ε) and mitochondrial (IF1) F1FO-ATPases. ζ mimics mitochondrial IF1 in its inhibitory N-terminus, blocking the PdF1FO-ATPase activity as a unidirectional pawl-ratchet and allowing the PdF1FO-ATP synthase turnover. ζ is essential for the respiratory growth of P. denitrificans, as we showed by a Δζ knockout. Given the vital role of ζ in the physiology of P. denitrificans, here, we assessed the evolution of ζ across the α-proteobacteria class. Methods: Through bioinformatic, biochemical, molecular biology, functional, and structural analyses of several ζ subunits, we confirmed the conservation of the inhibitory N-terminus of ζ and its divergence toward its C-terminus. We reconstituted homologously or heterologously the recombinant ζ subunits from several α-proteobacteria into the respective F-ATPases, including free-living photosynthetic, facultative symbiont, and intracellular facultative or obligate parasitic α-proteobacteria. Results and discussion: The results show that ζ evolved, preserving its inhibitory function in free-living α-proteobacteria exposed to broad environmental changes that could compromise the cellular ATP pools. However, the ζ inhibitory function was diminished or lost in some symbiotic α-proteobacteria where ζ is non-essential given the possible exchange of nutrients and ATP from hosts. Accordingly, the ζ gene is absent in some strictly parasitic pathogenic Rickettsiales, which may obtain ATP from the parasitized hosts. We also resolved the NMR structure of the ζ subunit of Sinorhizobium meliloti (Sm-ζ) and compared it with its structure modeled in AlphaFold. We found a transition from a compact ordered non-inhibitory conformation into an extended α-helical inhibitory N-terminus conformation, thus explaining why the Sm-ζ cannot exert homologous inhibition. However, it is still able to inhibit the PdF1FO-ATPase heterologously. Together with the loss of the inhibitory function of α-proteobacterial ε, the data confirm that the primary inhibitory function of the α-proteobacterial F1FO-ATPase was transferred from ε to ζ and that ζ, ε, and IF1 evolved by convergent evolution. Some key evolutionary implications on the endosymbiotic origin of mitochondria, as most likely derived from α-proteobacteria, are also discussed.}, }
@article {pmid37662149, year = {2023}, author = {Liu, H and Hou, Z and Xu, L and Ma, Q and Wei, M and Tembrock, LR and Zhang, S and Wu, Z}, title = {Comparative analysis of organellar genomes between diploid and tetraploid Chrysanthemum indicum with its relatives.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1228551}, pmid = {37662149}, issn = {1664-462X}, abstract = {Chrysanthemum indicum, a species native to Eastern Asia is well known as one of the progenitor species of the cultivated Chrysanthemum which is grown for its ornamental and medicinal value. Previous genomic studies on Chrysanthemum have largely ignored the dynamics of plastid genome (plastome) and mitochondria genome (mitogenome) evolution when analyzing this plant lineage. In this study, we sequenced and assembled the plastomes and mitogenomes of diploid and tetraploid C. indicum as well as the morphologically divergent variety C. indicum var. aromaticum. We used published data from 27 species with both plastome and mitogenome complete sequences to explore differences in sequence evolution between the organellar genomes. The size and structure of organellar genome between diploid and tetraploid C. indicum were generally similar but the tetraploid C. indicum and C. indicum var. aromaticum were found to contain unique sequences in the mitogenomes which also contained previously undescribed open reading frames (ORFs). Across Chrysanthemum mitogenome structure varied greatly but sequences transferred from plastomes in to the mitogenomes were conserved. Finally, differences observed between mitogenome and plastome gene trees may be the result of the difference in the rate of sequence evolution between genes in these two genomes. In total the findings presented here greatly expand the resources for studying Chrysanthemum organellar genome evolution with possible applications to conservation, breeding, and gene banking in the future.}, }
@article {pmid37644003, year = {2023}, author = {French, CM and Bertola, LD and Carnaval, AC and Economo, EP and Kass, JM and Lohman, DJ and Marske, KA and Meier, R and Overcast, I and Rominger, AJ and Staniczenko, PPA and Hickerson, MJ}, title = {Global determinants of insect mitochondrial genetic diversity.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5276}, pmid = {37644003}, issn = {2041-1723}, mesh = {Animals ; *Insecta/genetics ; *Mitochondria ; DNA, Mitochondrial/genetics ; Biodiversity ; Genetic Variation ; }, abstract = {Understanding global patterns of genetic diversity is essential for describing, monitoring, and preserving life on Earth. To date, efforts to map macrogenetic patterns have been restricted to vertebrates, which comprise only a small fraction of Earth's biodiversity. Here, we construct a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences, derived from open data. We calculate the mitochondrial genetic diversity mean and genetic diversity evenness of insect assemblages across the globe, identify their environmental correlates, and make predictions of mitochondrial genetic diversity levels in unsampled areas based on environmental data. Using a large single-locus genetic dataset of over 2 million globally distributed and georeferenced mtDNA sequences, we find that mitochondrial genetic diversity evenness follows a quadratic latitudinal gradient peaking in the subtropics. Both mitochondrial genetic diversity mean and evenness positively correlate with seasonally hot temperatures, as well as climate stability since the last glacial maximum. Our models explain 27.9% and 24.0% of the observed variation in mitochondrial genetic diversity mean and evenness in insects, respectively, making an important step towards understanding global biodiversity patterns in the most diverse animal taxon.}, }
@article {pmid37638880, year = {2023}, author = {Gupta, SV and Campos, L and Schmidt, KH}, title = {Mitochondrial superoxide dismutase Sod2 suppresses nuclear genome instability during oxidative stress.}, journal = {Genetics}, volume = {225}, number = {2}, pages = {}, pmid = {37638880}, issn = {1943-2631}, support = {R01GM018245/NH/NIH HHS/United States ; }, mesh = {Antioxidants ; DNA ; Genomic Instability ; Oxidative Stress ; Reactive Oxygen Species ; RecQ Helicases/metabolism ; *Saccharomyces cerevisiae/metabolism ; *Saccharomyces cerevisiae Proteins/genetics/metabolism ; Superoxide Dismutase/genetics/metabolism ; }, abstract = {Oxidative stress can damage DNA and thereby contribute to genome instability. To avoid an imbalance or overaccumulation of reactive oxygen species (ROS), cells are equipped with antioxidant enzymes that scavenge excess ROS. Cells lacking the RecQ-family DNA helicase Sgs1, which contributes to homology-dependent DNA break repair and chromosome stability, are known to accumulate ROS, but the origin and consequences of this oxidative stress phenotype are not fully understood. Here, we show that the sgs1 mutant exhibits elevated mitochondrial superoxide, increased mitochondrial mass, and accumulation of recombinogenic DNA lesions that can be suppressed by antioxidants. Increased mitochondrial mass in the sgs1Δ mutant is accompanied by increased mitochondrial branching, which was also inducible in wildtype cells by replication stress. Superoxide dismutase Sod2 genetically interacts with Sgs1 in the suppression of nuclear chromosomal rearrangements under paraquat (PQ)-induced oxidative stress. PQ-induced chromosome rearrangements in the absence of Sod2 are promoted by Rad51 recombinase and the polymerase subunit Pol32. Finally, the dependence of chromosomal rearrangements on the Rev1/Pol ζ mutasome suggests that under oxidative stress successful DNA synthesis during DNA break repair depends on translesion DNA synthesis.}, }
@article {pmid37636868, year = {2023}, author = {Le Cam, S and Brémaud, J and Malkócs, T and Kreckelbergh, E and Becquet, V and Dubillot, E and Garcia, P and Breton, S and Pante, E}, title = {LAMP-based molecular sexing in a gonochoric marine bivalve (Macoma balthica rubra) with divergent sex-specific mitochondrial genomes.}, journal = {Ecology and evolution}, volume = {13}, number = {8}, pages = {e10320}, pmid = {37636868}, issn = {2045-7758}, abstract = {Taking advantage of the unique system of doubly uniparental inheritance (DUI) of mitochondria, we developed a reliable molecular method to sex individuals of the marine bivalve Macoma balthica rubra. In species with DUI (~100 known bivalves), both sexes transmit their mitochondria: males bear both a male- and female-type mitogenome, while females bear only the female type. Male and female mitotypes are sufficiently divergent to reliably PCR-amplify them specifically. Loop-mediated isothermal amplification (LAMP) is a precise, economical and portable alternative to PCR for molecular sexing and we demonstrate its application in this context. We used 154 individuals sampled along the Atlantic coast of France and sexed microscopically by gonad examination to test for the congruence among gamete type, PCR sexing and LAMP sexing. We show an exact match among the sexing results from these three methods using the male and female mt-cox1 genes. DUI can be disrupted in inter-specific hybrids, causing unexpected distribution of mitogenomes, such as homoplasmic males or heteroplasmic females. To our knowledge, DUI disruption at the intra-specific scale has never been tested. We applied our sexing protocol to control for unexpected heteroplasmy caused by hybridization between divergent genetic lineages and found no evidence of disruption in the mode of mitochondrial inheritance in M. balthica rubra. We propose LAMP as a useful tool to accelerate eco-evolutionary studies of DUI. It offers the opportunity to investigate the potential role of, previously unaccounted-for, sex-specific patterns such as sexual selection or sex-specific dispersal bias in the evolution of free-spawning benthic species.}, }
@article {pmid37636259, year = {2023}, author = {Fiedler, L and Middendorf, M and Bernt, M}, title = {Fully automated annotation of mitochondrial genomes using a cluster-based approach with de Bruijn graphs.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1250907}, pmid = {37636259}, issn = {1664-8021}, abstract = {A wide range of scientific fields, such as forensics, anthropology, medicine, and molecular evolution, benefits from the analysis of mitogenomic data. With the development of new sequencing technologies, the amount of mitochondrial sequence data to be analyzed has increased exponentially over the last few years. The accurate annotation of mitochondrial DNA is a prerequisite for any mitogenomic comparative analysis. To sustain with the growth of the available mitochondrial sequence data, highly efficient automatic computational methods are, hence, needed. Automatic annotation methods are typically based on databases that contain information about already annotated (and often pre-curated) mitogenomes of different species. However, the existing approaches have several shortcomings: 1) they do not scale well with the size of the database; 2) they do not allow for a fast (and easy) update of the database; and 3) they can only be applied to a relatively small taxonomic subset of all species. Here, we present a novel approach that does not have any of these aforementioned shortcomings, (1), (2), and (3). The reference database of mitogenomes is represented as a richly annotated de Bruijn graph. To generate gene predictions for a new user-supplied mitogenome, the method utilizes a clustering routine that uses the mapping information of the provided sequence to this graph. The method is implemented in a software package called DeGeCI (De Bruijn graph Gene Cluster Identification). For a large set of mitogenomes, for which expert-curated annotations are available, DeGeCI generates gene predictions of high conformity. In a comparative evaluation with MITOS2, a state-of-the-art annotation tool for mitochondrial genomes, DeGeCI shows better database scalability while still matching MITOS2 in terms of result quality and providing a fully automated means to update the underlying database. Moreover, unlike MITOS2, DeGeCI can be run in parallel on several processors to make use of modern multi-processor systems.}, }
@article {pmid37634556, year = {2023}, author = {Theriault, JE and Shaffer, C and Dienel, GA and Sander, CY and Hooker, JM and Dickerson, BC and Barrett, LF and Quigley, KS}, title = {A functional account of stimulation-based aerobic glycolysis and its role in interpreting BOLD signal intensity increases in neuroimaging experiments.}, journal = {Neuroscience and biobehavioral reviews}, volume = {153}, number = {}, pages = {105373}, pmid = {37634556}, issn = {1873-7528}, support = {R01 AG071173/AG/NIA NIH HHS/United States ; R01 MH109464/MH/NIMH NIH HHS/United States ; R21 MH129902/MH/NIMH NIH HHS/United States ; R01 MH113234/MH/NIMH NIH HHS/United States ; U01 CA193632/CA/NCI NIH HHS/United States ; R01 CA258269/CA/NCI NIH HHS/United States ; R00 DA043629/DA/NIDA NIH HHS/United States ; }, mesh = {Humans ; *Glycolysis/physiology ; *Adenosine Triphosphate ; Brain/diagnostic imaging/metabolism ; Glucose/metabolism ; Neuroimaging ; }, abstract = {In aerobic glycolysis, oxygen is abundant, and yet cells metabolize glucose without using it, decreasing their ATP per glucose yield by 15-fold. During task-based stimulation, aerobic glycolysis occurs in localized brain regions, presenting a puzzle: why produce ATP inefficiently when, all else being equal, evolution should favor the efficient use of metabolic resources? The answer is that all else is not equal. We propose that a tradeoff exists between efficient ATP production and the efficiency with which ATP is spent to transmit information. Aerobic glycolysis, despite yielding little ATP per glucose, may support neuronal signaling in thin (< 0.5 µm), information-efficient axons. We call this the efficiency tradeoff hypothesis. This tradeoff has potential implications for interpretations of task-related BOLD "activation" observed in fMRI. We hypothesize that BOLD "activation" may index local increases in aerobic glycolysis, which support signaling in thin axons carrying "bottom-up" information, or "prediction error"-i.e., the BIAPEM (BOLD increases approximate prediction error metabolism) hypothesis. Finally, we explore implications of our hypotheses for human brain evolution, social behavior, and mental disorders.}, }
@article {pmid37629135, year = {2023}, author = {Cai, H and Ren, Y and Du, J and Liu, L and Long, L and Yang, M}, title = {Analysis of the RNA Editing Sites and Orthologous Gene Function of Transcriptome and Chloroplast Genomes in the Evolution of Five Deutzia Species.}, journal = {International journal of molecular sciences}, volume = {24}, number = {16}, pages = {}, pmid = {37629135}, issn = {1422-0067}, support = {No.21326301D//Province Key Research and Development Program of Hebei/ ; }, mesh = {*Transcriptome/genetics ; *Genome, Chloroplast ; Phylogeny ; RNA Editing/genetics ; Gene Expression Profiling ; }, abstract = {In this study, the chloroplast genomes and transcriptomes of five Deutzia genus species were sequenced, characterized, combined, and analyzed. A phylogenetic tree was constructed, including 32 other chloroplast genome sequences of Hydrangeoideae species. The results showed that the five Deutzia chloroplast genomes were typical circular genomes 156,860-157,025 bp in length, with 37.58-37.6% GC content. Repeat analysis showed that the Deutzia species had 41-45 scattered repeats and 199-201 simple sequence repeats. Comparative genomic and pi analyses indicated that the genomes are conservative and that the gene structures are stable. According to the phylogenetic tree, Deutzia species appear to be closely related to Kirengeshoma palmata and Philadelphus. By combining chloroplast genomic and transcriptomic analyses, 29-31 RNA editing events and 163-194 orthologous genes were identified. The ndh, rpo, rps, and atp genes had the most editing sites, and all RNA editing events were of the C-to-U type. Most of the orthologous genes were annotated to the chloroplast, mitochondria, and nucleus, with functions including energy production and conversion, translation, and protein transport. Genes related to the biosynthesis of monoterpenoids and flavonoids were also identified from the transcriptome of Deutzia spp. Our results will contribute to further studies of the genomic information and potential uses of the Deutzia spp.}, }
@article {pmid37629077, year = {2023}, author = {Zalewska, A and Antonowicz, B and Szulimowska, J and Zieniewska-Siemieńczuk, I and Leśniewska, B and Borys, J and Zięba, S and Kostecka-Sochoń, P and Żendzian-Piotrowska, M and Lo Giudice, R and Lo Giudice, G and Żukowski, P and Maciejczyk, M}, title = {Mitochondrial Redox Balance of Fibroblasts Exposed to Ti-6Al-4V Microplates Subjected to Different Types of Anodizing.}, journal = {International journal of molecular sciences}, volume = {24}, number = {16}, pages = {}, pmid = {37629077}, issn = {1422-0067}, support = {B.SUB.23.309//Medical University in Bialystok/ ; }, mesh = {Humans ; *Titanium/pharmacology ; *Mitochondria ; Fibroblasts ; Oxidation-Reduction ; }, abstract = {Despite the high biocompatibility of titanium and its alloys, the need to remove titanium implants is increasingly being debated due to the potential for adverse effects associated with long-term retention. Therefore, new solutions are being sought to enhance the biocompatibility of titanium implants. One of them is to increase the thickness of the passive layer of the implant made of titanium dioxide. We were the first to evaluate the effect of hard-anodized (type II) Ti-6Al-4V alloy discs on the cytotoxicity, mitochondrial function, and redox balance of fibroblasts mitochondria compared to standard-anodized (type III) and non-anodized discs. The study used fibroblasts obtained from human gingival tissue. The test discs were applied to the bottom of 12-well plates. Cells were cultured for 24 h and 7, 14, and 21 days and mitochondria were isolated. We demonstrated the occurrence of oxidative stress in the mitochondria of fibroblasts of all tested groups, regardless of the presence and type of anodization. Type II anodization prevented changes in complex II activity (vs. control). The lowest degree of citrate synthase inhibition occurred in mitochondria exposed to titanium discs with type II anodization. In the last phase of culture, the presence of type II anodization reduced the degree of cytochrome c oxidase inhibition compared to the other tests groups and the control group, and prevented apoptosis. Throughout the experiment, the release of titanium, aluminium, and vanadium ions from titanium discs with a hard-anodized passive layer was higher than from the other titanium discs, but decreased with time. The obtained results proved the existence of dysfunction and redox imbalance in the mitochondria of fibroblasts exposed to hard-anodized titanium discs, suggesting the need to search for new materials perhaps biodegradable in tissues of the human body.}, }
@article {pmid37628665, year = {2023}, author = {Havaš Auguštin, D and Šarac, J and Reidla, M and Tamm, E and Grahovac, B and Kapović, M and Novokmet, N and Rudan, P and Missoni, S and Marjanović, D and Korolija, M}, title = {Refining the Global Phylogeny of Mitochondrial N1a, X, and HV2 Haplogroups Based on Rare Mitogenomes from Croatian Isolates.}, journal = {Genes}, volume = {14}, number = {8}, pages = {}, pmid = {37628665}, issn = {2073-4425}, mesh = {Humans ; Phylogeny ; Croatia ; *Genome, Mitochondrial/genetics ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {Mitochondrial DNA (mtDNA) has been used for decades as a predominant tool in population genetics and as a valuable addition to forensic genetic research, owing to its unique maternal inheritance pattern that enables the tracing of individuals along the maternal lineage across numerous generations. The dynamic interplay between evolutionary forces, primarily genetic drift, bottlenecks, and the founder effect, can exert significant influence on genetic profiles. Consequently, the Adriatic islands have accumulated a subset of lineages that exhibits remarkable absence or rarity within other European populations. This distinctive genetic composition underscores the islands' potential as a significant resource in phylogenetic research, with implications reaching beyond regional boundaries to contribute to a global understanding. In the initial attempt to expand the mitochondrial forensic database of the Croatian population with haplotypes from small isolated communities, we sequenced mitogenomes of rare haplogroups from different Croatian island and mainland populations using next-generation sequencing (NGS). In the next step and based on the obtained results, we refined the global phylogeny of haplogroup N1a, HV2, and X by analyzing rare haplotypes, which are absent from the current phylogenetic tree. The trees were based on 16 novel and 52 previously published samples, revealing completely novel branches in the X and HV2 haplogroups and a new European cluster in the ancestral N1a variant, previously believed to be an exclusively African-Asian haplogroup. The research emphasizes the importance of investigating geographically isolated populations and their unique characteristics within a global context.}, }
@article {pmid37628588, year = {2023}, author = {Baldo, MS and Nogueira, C and Pereira, C and Janeiro, P and Ferreira, S and Lourenço, CM and Bandeira, A and Martins, E and Magalhães, M and Rodrigues, E and Santos, H and Ferreira, AC and Vilarinho, L}, title = {Leigh Syndrome Spectrum: A Portuguese Population Cohort in an Evolutionary Genetic Era.}, journal = {Genes}, volume = {14}, number = {8}, pages = {}, pmid = {37628588}, issn = {2073-4425}, mesh = {Child ; Infant ; Humans ; *Leigh Disease/genetics ; Portugal ; DNA, Mitochondrial/genetics ; Mitochondria ; Biological Evolution ; }, abstract = {Mitochondrial diseases are the most common inherited inborn error of metabolism resulting in deficient ATP generation, due to failure in homeostasis and proper bioenergetics. The most frequent mitochondrial disease manifestation in children is Leigh syndrome (LS), encompassing clinical, neuroradiological, biochemical, and molecular features. It typically affects infants but occurs anytime in life. Considering recent updates, LS clinical presentation has been stretched, and is now named LS spectrum (LSS), including classical LS and Leigh-like presentations. Apart from clinical diagnosis challenges, the molecular characterization also progressed from Sanger techniques to NGS (next-generation sequencing), encompassing analysis of nuclear (nDNA) and mitochondrial DNA (mtDNA). This upgrade resumed steps and favored diagnosis. Hereby, our paper presents molecular and clinical data on a Portuguese cohort of 40 positive cases of LSS. A total of 28 patients presented mutation in mtDNA and 12 in nDNA, with novel mutations identified in a heterogeneous group of genes. The present results contribute to the better knowledge of the molecular basis of LS and expand the clinical spectrum associated with this syndrome.}, }
@article {pmid37628587, year = {2023}, author = {Hernández, CL}, title = {Mitochondrial DNA in Human Diversity and Health: From the Golden Age to the Omics Era.}, journal = {Genes}, volume = {14}, number = {8}, pages = {}, pmid = {37628587}, issn = {2073-4425}, mesh = {Humans ; *DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; Anthropology ; Biological Evolution ; Inheritance Patterns ; }, abstract = {Mitochondrial DNA (mtDNA) is a small fraction of our hereditary material. However, this molecule has had an overwhelming presence in scientific research for decades until the arrival of high-throughput studies. Several appealing properties justify the application of mtDNA to understand how human populations are-from a genetic perspective-and how individuals exhibit phenotypes of biomedical importance. Here, I review the basics of mitochondrial studies with a focus on the dawn of the field, analysis methods and the connection between two sides of mitochondrial genetics: anthropological and biomedical. The particularities of mtDNA, with respect to inheritance pattern, evolutionary rate and dependence on the nuclear genome, explain the challenges of associating mtDNA composition and diseases. Finally, I consider the relevance of this single locus in the context of omics research. The present work may serve as a tribute to a tool that has provided important insights into the past and present of humankind.}, }
@article {pmid37604791, year = {2023}, author = {Fernández-Álvarez, F&#xc1; and Sanchez, G and Deville, D and Taite, M and Villanueva, R and Allcock, AL}, title = {Atlantic Oceanic Squids in the "Grey Speciation Zone".}, journal = {Integrative and comparative biology}, volume = {63}, number = {6}, pages = {1214-1225}, pmid = {37604791}, issn = {1557-7023}, support = {IJC2020-043170-I//Generalitat de Catalunya/ ; GOIPD/2019/460//Irish Research Council/ ; 22K15085//Grant-in-Aid for Early-Career Scientists/ ; //Ministerio de Ciencia e Innovaci&#xf3;n/ ; //European Union/ ; CEX2019-000928-S//Spanish Government/ ; CTM2016-78853-R//FEDER/ ; }, mesh = {Animals ; Phylogeny ; *Decapodiformes ; Oceans and Seas ; *Biodiversity ; Mitochondria ; }, abstract = {Cryptic species complexes represent an important challenge for the adequate characterization of Earth's biodiversity. Oceanic organisms tend to have greater unrecognized cryptic biodiversity since the marine realm was often considered to lack hard barriers to genetic exchange. Here, we tested the effect of several Atlantic and Mediterranean oceanic barriers on 16 morphospecies of oceanic squids of the orders Oegopsida and Bathyteuthida using three mitochondrial and one nuclear molecular marker and five species delimitation methods. Number of species recognized within each morphospecies differed among different markers and analyses, but we found strong evidence of cryptic biodiversity in at least four of the studied species (Chtenopteryx sicula, Chtenopteryx canariensis, Ancistrocheirus lesueurii, and Galiteuthis armata). There were highly geographically structured units within Helicocranchia navossae that could either represent recently diverged species or population structure. Although the species studied here can be considered relatively passive with respect to oceanic currents, cryptic speciation patterns showed few signs of being related to oceanic currents. We hypothesize that the bathymetry of the egg masses and duration of the paralarval stage might influence the geographic distribution of oceanic squids. Because the results of different markers and different species delimitation methods are inconsistent and because molecular data encompassing broad geographic sampling areas for oceanic squids are scarce and finding morphological diagnostic characters for early life stages is difficult, it is challenging to assess the species boundaries for many of these species. Thus, we consider many to be in the "grey speciation zone." As many oceanic squids have cosmopolitan distributions, new studies combining genomic and morphological information from specimens collected worldwide are needed to correctly assess the actual oceanic squid biodiversity.}, }
@article {pmid37603398, year = {2023}, author = {Ratliffe, J and Kataura, T and Otten, EG and Korolchuk, VI}, title = {The evolution of selective autophagy as a mechanism of oxidative stress response: The evolutionarily acquired ability of selective autophagy receptors to respond to oxidative stress is beneficial for human longevity.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {11}, pages = {e2300076}, doi = {10.1002/bies.202300076}, pmid = {37603398}, issn = {1521-1878}, support = {EP/W524700/1//EPSRC PhD studentship/ ; BB/M023389/1//BBSRC/ ; BB/R008167/2//BBSRC/ ; //The International Medical Research Foundation/ ; //Uehara Memorial Foundation/ ; }, abstract = {Ageing is associated with a decline in autophagy and elevated reactive oxygen species (ROS), which can breach the capacity of antioxidant systems. Resulting oxidative stress can cause further cellular damage, including DNA breaks and protein misfolding. This poses a challenge for longevous organisms, including humans. In this review, we hypothesise that in the course of human evolution selective autophagy receptors (SARs) acquired the ability to sense and respond to localised oxidative stress. We posit that in the vicinity of protein aggregates and dysfunctional mitochondria oxidation of key cysteine residues in SARs induces their oligomerisation which initiates autophagy. The degradation of damaged cellular components thus could reduce ROS production and restore redox homeostasis. This evolutionarily acquired function of SARs may represent one of the biological adaptations that contributed to longer lifespan. Inversely, loss of this mechanism can lead to age-related diseases associated with impaired autophagy and oxidative stress.}, }
@article {pmid37602330, year = {2023}, author = {Das, P and Pal, S and Das, N and Chakraborty, K and Chatterjee, K and Mal, S and Choudhuri, T}, title = {Endogenous PTEN acts as the key determinant for mTOR inhibitor sensitivity by inducing the stress-sensitized PTEN-mediated death axis in KSHV-associated malignant cells.}, journal = {Frontiers in molecular biosciences}, volume = {10}, number = {}, pages = {1062462}, pmid = {37602330}, issn = {2296-889X}, abstract = {As a part of viral cancer evolution, KSHV-infected human endothelial cells exert a unique transcriptional program via upregulated mTORC1 signaling. This event makes them sensitive to mTOR inhibitors. Master transcriptional regulator PTEN acts as the prime regulator of mTOR and determining factor for mTOR inhibitory drug resistance and sensitivity. PTEN is post-translationally modified in KSHV-associated cell lines and infected tissues. Our current study is an attempt to understand the functional role of upstream modulator PTEN in determining the sensitivity of mTOR inhibitors against KSHV-infected cells in an in vitro stress-responsive model. Our analysis shows that, despite phosphorylation, endogenous levels of intact PTEN in different KSHV-infected cells compared to normal and non-infected cells are quite high. Genetic overexpression of intact PTEN showed functional integrity of this gene in the infected cells in terms of induction of a synchronized cell death process via cell cycle regulation and mitochondria-mediated apoptosis. PTEN overexpression enhanced the mTOR inhibitory drug activity, the silencing of which hampers the process against KSHV-infected cells. Additionally, we have shown that endogenous PTEN acts as a stress balancer molecule inside KSHV-infected cells and can induce stress-sensitized death program post mTOR inhibitor treatment, lined up in the ATM-chk2-p53 axis. Moreover, autophagic regulation was found as a major regulator in mTOR inhibitor-induced PTEN-mediated death axis from our study. The current work critically intersected the PTEN-mediated stress balancing mechanism where autophagy has been utilized as a part of the KSHV stress management system and is specifically fitted and switched toward autophagy-mediated apoptosis directing toward a therapeutic perspective.}, }
@article {pmid37599162, year = {2024}, author = {Braun, HP and Klusch, N}, title = {Promotion of oxidative phosphorylation by complex I-anchored carbonic anhydrases?.}, journal = {Trends in plant science}, volume = {29}, number = {1}, pages = {64-71}, doi = {10.1016/j.tplants.2023.07.007}, pmid = {37599162}, issn = {1878-4372}, mesh = {*Carbonic Anhydrases/chemistry/metabolism ; Oxidative Phosphorylation ; Mitochondria/metabolism ; Plants/metabolism ; Hydrogen-Ion Concentration ; }, abstract = {The mitochondrial NADH-dehydrogenase complex of the respiratory chain, known as complex I, includes a carbonic anhydrase (CA) module attached to its membrane arm on the matrix side in protozoans, algae, and plants. Its physiological role is so far unclear. Recent electron cryo-microscopy (cryo-EM) structures show that the CA module may directly provide protons for translocation across the inner mitochondrial membrane at complex I. CAs can have a central role in adjusting the proton concentration in the mitochondrial matrix. We suggest that CA anchoring in complex I represents the original configuration to secure oxidative phosphorylation (OXPHOS) in the context of early endosymbiosis. After development of 'modern mitochondria' with pronounced cristae structures, this anchoring became dispensable, but has been retained in protozoans, algae, and plants.}, }
@article {pmid37596708, year = {2024}, author = {Golik, P}, title = {RNA processing and degradation mechanisms shaping the mitochondrial transcriptome of budding yeasts.}, journal = {IUBMB life}, volume = {76}, number = {1}, pages = {38-52}, doi = {10.1002/iub.2779}, pmid = {37596708}, issn = {1521-6551}, mesh = {*Transcriptome ; Saccharomyces cerevisiae/genetics/metabolism ; *Saccharomycetales/genetics/metabolism ; Transcription, Genetic ; RNA Processing, Post-Transcriptional ; RNA ; RNA, Transfer/genetics/metabolism ; }, abstract = {Yeast mitochondrial genes are expressed as polycistronic transcription units that contain RNAs from different classes and show great evolutionary variability. The promoters are simple, and transcriptional control is rudimentary. Posttranscriptional mechanisms involving RNA maturation, stability, and degradation are thus the main force shaping the transcriptome and determining the expression levels of individual genes. Primary transcripts are fragmented by tRNA excision by RNase P and tRNase Z, additional processing events occur at the dodecamer site at the 3' end of protein-coding sequences. groups I and II introns are excised in a self-splicing reaction that is supported by protein splicing factors encoded by the nuclear genes, or by the introns themselves. The 3'-to-5' exoribonucleolytic complex called mtEXO is the main RNA degradation activity involved in RNA turnover and processing, supported by an auxiliary 5'-to-3' exoribonuclease Pet127p. tRNAs and, to a lesser extent, rRNAs undergo several different base modifications. This complex gene expression system relies on the coordinated action of mitochondrial and nuclear genes and undergoes rapid evolution, contributing to speciation events. Moving beyond the classical model yeast Saccharomyces cerevisiae to other budding yeasts should provide important insights into the coevolution of both genomes that constitute the eukaryotic genetic system.}, }
@article {pmid37587350, year = {2023}, author = {Merchant, A and Ramirez, BI and Reyes, MN and Van, D and Martinez-Colin, M and Ojo, DO and Mazuca, EL and De La O, HJ and Glenn, AM and Lira, CG and Ehsan, H and Yu, E and Kaneko, G}, title = {Genomic loss of the HSP70cA gene in the vertebrate lineage.}, journal = {Cell stress &amp; chaperones}, volume = {28}, number = {6}, pages = {1053-1067}, pmid = {37587350}, issn = {1466-1268}, mesh = {Animals ; Phylogeny ; *Evolution, Molecular ; *Vertebrates/genetics ; Genome/genetics ; Genomics ; }, abstract = {Metazoan 70 kDa heat shock protein (HSP70) genes have been classified into four lineages: cytosolic A (HSP70cA), cytosolic B (HSP70cB), endoplasmic reticulum (HSP70er), and mitochondria (HSP70m). Because previous studies have identified no HSP70cA genes in vertebrates, we hypothesized that this gene was lost on the evolutionary path to vertebrates. To test this hypothesis, the present study conducted a comprehensive database search followed by phylogenetic and synteny analyses. HSP70cA genes were found in invertebrates and in two of the three subphyla of Chordata, Cephalochordata (lancelets) and Tunicata (tunicates). However, no HSP70cA gene was found in the genomes of Craniata (another subphylum of Chordata; lamprey, hagfish, elephant shark, and coelacanth), suggesting the loss of the HSP70cA gene in the early period of vertebrate evolution. Synteny analysis using available genomic resources indicated that the synteny around the HSP70 genes was generally conserved between tunicates but was largely different between tunicates and lamprey. These results suggest the presence of dynamic chromosomal rearrangement in early vertebrates that possibly caused the loss of the HSP70cA gene in the vertebrate lineage.}, }
@article {pmid37584544, year = {2023}, author = {Yang, C and Li, X and Zhou, J and Gao, C}, title = {Autophagy contributes to positive feedback regulation of SnRK1 signaling in plants.}, journal = {Autophagy}, volume = {19}, number = {12}, pages = {3248-3250}, pmid = {37584544}, issn = {1554-8635}, mesh = {*Arabidopsis Proteins/metabolism ; AMP-Activated Protein Kinases/metabolism ; Feedback ; Autophagy ; *Arabidopsis/metabolism ; Plants/metabolism ; Transcription Factors/metabolism ; Adenosine Monophosphate ; Gene Expression Regulation, Plant ; Protein Serine-Threonine Kinases/metabolism ; Vesicular Transport Proteins/metabolism ; }, abstract = {SnRK1 (SNF1-related protein kinase 1) is a plant ortholog of yeast Snf1 and mammalian adenosine monophosphate-activated protein kinase (AMPK) that acts as a positive regulator of macroautophagy/autophagy. However, whether and how the autophagy pathway modulates SnRK1 activity remains elusive. Recently, we identified a clade of plant-specific FLZ (FCS-like zinc finger) proteins as novel ATG8 (autophagy-related 8)-interacting partners in Arabidopsis thaliana. These AtFLZs, which mainly localize on the surface of mitochondria, can inhibit SnRK1 signaling by repressing the T-loop phosphorylation of its catalytic α subunits, thereby negatively regulating carbon starvation-induced autophagy and plant tolerance to energy deprivation. Upon energy starvation, autophagy is activated to mediate the degradation of these AtFLZs, thus relieving their repression of SnRK1. More importantly, the ATG8-FLZ-SnRK1 regulatory axis appears to be functionally conserved during seed plant evolution. These findings highlight the positive role of autophagy in SnRK1 signaling activation under energy-limiting conditions in plants.Abbreviations: ADS, AIMs docking site; AIM, ATG8-interacting motif; AMPK, adenosine monophosphate-activated protein kinase; ATG, autophagy-related; ESCRT, endosomal sorting complexes required for transport; FLZ, FCS-like zinc finger protein; FREE1, FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING 1; RAPTOR, REGULATORY-ASSOCIATED PROTEIN OF TOR; Snf1, SUCROSE NON-FERMENTING 1; SnRK1, SNF1-related kinase 1; TOR, TARGET OF RAPAMYCIN.}, }
@article {pmid37582787, year = {2023}, author = {Meadows, JRS and Kidd, JM and Wang, GD and Parker, HG and Schall, PZ and Bianchi, M and Christmas, MJ and Bougiouri, K and Buckley, RM and Hitte, C and Nguyen, AK and Wang, C and Jagannathan, V and Niskanen, JE and Frantz, LAF and Arumilli, M and Hundi, S and Lindblad-Toh, K and Ginja, C and Agustina, KK and André, C and Boyko, AR and Davis, BW and Drögemüller, M and Feng, XY and Gkagkavouzis, K and Iliopoulos, G and Harris, AC and Hytönen, MK and Kalthoff, DC and Liu, YH and Lymberakis, P and Poulakakis, N and Pires, AE and Racimo, F and Ramos-Almodovar, F and Savolainen, P and Venetsani, S and Tammen, I and Triantafyllidis, A and vonHoldt, B and Wayne, RK and Larson, G and Nicholas, FW and Lohi, H and Leeb, T and Zhang, YP and Ostrander, EA}, title = {Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {187}, pmid = {37582787}, issn = {1474-760X}, support = {R01 GM140135/GM/NIGMS NIH HHS/United States ; R24 GM082910/GM/NIGMS NIH HHS/United States ; }, mesh = {Dogs ; Animals ; *Wolves/genetics ; Chromosome Mapping ; Alleles ; Polymorphism, Single Nucleotide ; Nucleotides ; Demography ; }, abstract = {BACKGROUND: The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.<br><br>RESULTS: We report the analysis of&#x2009;>&#x2009;48&#xa0;M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50&#xa0;bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.<br><br>CONCLUSIONS: We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.}, }
@article {pmid37577532, year = {2023}, author = {Wolters, JF and LaBella, AL and Opulente, DA and Rokas, A and Hittinger, CT}, title = {Mitochondrial Genome Diversity across the Subphylum Saccharomycotina.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37577532}, support = {R01 AI153356/AI/NIAID NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; }, abstract = {Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales, which includes S. cerevisiae, exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.}, }
@article {pmid37565789, year = {2023}, author = {Yang, Y and Oldenkott, B and Ramanathan, S and Lesch, E and Takenaka, M and Schallenberg-Rüdinger, M and Knoop, V}, title = {DYW cytidine deaminase domains have a long-range impact on RNA recognition by the PPR array of chimeric plant C-to-U RNA editing factors and strongly affect target selection.}, journal = {The Plant journal : for cell and molecular biology}, volume = {116}, number = {3}, pages = {840-854}, doi = {10.1111/tpj.16412}, pmid = {37565789}, issn = {1365-313X}, mesh = {RNA, Plant/metabolism ; *Plant Proteins/metabolism ; *RNA Editing/genetics ; Cytidine Deaminase/chemistry/genetics/metabolism ; Chloroplasts/metabolism ; }, abstract = {The protein factors for the specific C-to-U RNA editing events in plant mitochondria and chloroplasts possess unique arrays of RNA-binding pentatricopeptide repeats (PPRs) linked to carboxy-terminal cytidine deaminase DYW domains via the extension motifs E1 and E2. The E1 and E2 motifs have distant similarities to tetratricopeptide repeats known to mediate protein-protein interactions but their precise function is unclear. Here, we investigate the tolerance of PPR56 and PPR65, two functionally characterized RNA editing factors of the moss Physcomitrium patens, for the creation of chimeras by variably replacing their C-terminal protein regions. Making use of a heterologous RNA editing assay system in Escherichia coli we find that heterologous DYW domains can strongly restrict or widen the spectrum of off-targets in the bacterial transcriptome for PPR56. Surprisingly, our data suggest that these changes are not only caused by the preference of a given heterologous DYW domain for the immediate sequence environment of the cytidine to be edited but also by a long-range impact on the nucleotide selectivity of the upstream PPRs.}, }
@article {pmid37558671, year = {2023}, author = {Kuhle, B and Hirschi, M and Doerfel, LK and Lander, GC and Schimmel, P}, title = {Structural basis for a degenerate tRNA identity code and the evolution of bimodal specificity in human mitochondrial tRNA recognition.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4794}, pmid = {37558671}, issn = {2041-1723}, support = {R21 GM142196/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Humans ; RNA, Mitochondrial ; *RNA, Transfer/genetics/metabolism ; *Amino Acyl-tRNA Synthetases/genetics/metabolism ; Mitochondria/genetics/metabolism ; }, abstract = {Animal mitochondrial gene expression relies on specific interactions between nuclear-encoded aminoacyl-tRNA synthetases and mitochondria-encoded tRNAs. Their evolution involves an antagonistic interplay between strong mutation pressure on mtRNAs and selection pressure to maintain their essential function. To understand the molecular consequences of this interplay, we analyze the human mitochondrial serylation system, in which one synthetase charges two highly divergent mtRNA[Ser] isoacceptors. We present the cryo-EM structure of human mSerRS in complex with mtRNA[Ser(UGA)], and perform a structural and functional comparison with the mSerRS-mtRNA[Ser(GCU)] complex. We find that despite their common function, mtRNA[Ser(UGA)] and mtRNA[Ser(GCU)] show no constrain to converge on shared structural or sequence identity motifs for recognition by mSerRS. Instead, mSerRS evolved a bimodal readout mechanism, whereby a single protein surface recognizes degenerate identity features specific to each mtRNA[Ser]. Our results show how the mutational erosion of mtRNAs drove a remarkable innovation of intermolecular specificity rules, with multiple evolutionary pathways leading to functionally equivalent outcomes.}, }
@article {pmid37557975, year = {2023}, author = {Weaver, RJ and McDonald, AE}, title = {Mitochondrial alternative oxidase across the tree of life: Presence, absence, and putative cases of lateral gene transfer.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1864}, number = {4}, pages = {149003}, doi = {10.1016/j.bbabio.2023.149003}, pmid = {37557975}, issn = {1879-2650}, mesh = {Animals ; *Gene Transfer, Horizontal ; *Plant Proteins/genetics ; Oxidoreductases/genetics ; Mitochondria/genetics ; Plants ; Eukaryota/genetics ; }, abstract = {The alternative oxidase (AOX) is a terminal oxidase in the electron transport system that plays a role in mitochondrial bioenergetics. The past 20 years of research shows AOX has a wide yet patchy distribution across the tree of life. AOX has been suggested to have a role in stress tolerance, growth, and development in plants, but less is known about its function in other groups, including animals. In this study, we analyzed the taxonomic distribution of AOX across >2800 species representatives from prokaryotes and eukaryotes and developed a standardized workflow for finding and verifying the authenticity of AOX sequences. We found that AOX is limited to proteobacteria among prokaryotes, but is widely distributed in eukaryotes, with the highest prevalence in plants, fungi, and protists. AOX is present in many invertebrates, but is absent in others including most arthropods, and is absent from vertebrates. We found aberrant AOX sequences associated with some animal groups. Some of these aberrant AOXs were contaminants, but we also found putative cases of lateral gene transfer of AOX from fungi and protists to nematodes, springtails, fungus gnats, and rotifers. Our findings provide a robust and detailed analysis of the distribution of AOX and a method for identifying and verifying putative AOX sequences, which will be useful as more sequence data becomes available on public repositories.}, }
@article {pmid37556561, year = {2023}, author = {Raval, PK and Martin, WF and Gould, SB}, title = {Mitochondrial evolution: Gene shuffling, endosymbiosis, and signaling.}, journal = {Science advances}, volume = {9}, number = {32}, pages = {eadj4493}, pmid = {37556561}, issn = {2375-2548}, mesh = {*Symbiosis/genetics ; *Mitochondria/genetics ; Eukaryotic Cells/metabolism ; Genes, Mitochondrial ; Phylogeny ; Biological Evolution ; Evolution, Molecular ; }, abstract = {Genes for cardiolipin and ceramide synthesis occur in some alphaproteobacterial genomes. They shed light on mitochondrial origin and signaling in the first eukaryotic cells.}, }
@article {pmid37551058, year = {2023}, author = {Huynh, SD and Melonek, J and Colas des Francs-Small, C and Bond, CS and Small, I}, title = {A unique C-terminal domain contributes to the molecular function of Restorer-of-fertility proteins in plant mitochondria.}, journal = {The New phytologist}, volume = {240}, number = {2}, pages = {830-845}, doi = {10.1111/nph.19166}, pmid = {37551058}, issn = {1469-8137}, mesh = {*Genes, Plant ; Mitochondria/metabolism ; Cytoplasm/metabolism ; Plant Proteins/metabolism ; *Arabidopsis/genetics/metabolism ; Fertility/genetics ; Plant Infertility/genetics ; }, abstract = {Restorer-of-fertility (Rf) genes encode pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria where they specifically bind to transcripts that induce cytoplasmic male sterility and repress their expression. In searching for a molecular signature unique to this class of proteins, we found that a majority of known Rf proteins have a distinct domain, which we called RfCTD (Restorer-of-fertility C-terminal domain), and its presence correlates with the ability to induce cleavage of the mitochondrial RNA target. A screen of 219 angiosperm genomes from 123 genera using a sequence profile that can quickly and accurately identify RfCTD sequences revealed considerable variation in RFL/RfCTD gene numbers across flowering plants. We observed that plant genera with bisexual flowers have significantly higher numbers of RFL genes compared to those with unisexual flowers, consistent with a role of these proteins in restoration of male fertility. We show that removing the RfCTD from the RFL protein RNA PROCESSING FACTOR 2-nad6 prevented cleavage of its RNA target, the nad6 transcript, in Arabidopsis thaliana mitochondria. We provide a simple way of identifying putative Rf candidates in genome sequences, new insights into the molecular mode of action of Rf proteins and the evolution of fertility restoration in flowering plants.}, }
@article {pmid37548336, year = {2023}, author = {Ryan, K and Greenway, R and Landers, J and Arias-Rodriguez, L and Tobler, M and Kelley, JL}, title = {Selection on standing genetic variation mediates convergent evolution in extremophile fish.}, journal = {Molecular ecology}, volume = {32}, number = {18}, pages = {5042-5054}, doi = {10.1111/mec.17081}, pmid = {37548336}, issn = {1365-294X}, mesh = {Animals ; *Hydrogen Sulfide/toxicity ; *Extremophiles ; Ecosystem ; Sulfides ; *Poecilia/genetics ; Genetic Variation/genetics ; Selection, Genetic ; }, abstract = {Hydrogen sulfide is a toxic gas that disrupts numerous biological processes, including energy production in the mitochondria, yet fish in the Poecilia mexicana species complex have independently evolved sulfide tolerance several times. Despite clear evidence for convergence at the phenotypic level in these fishes, it is unclear if the repeated evolution of hydrogen sulfide tolerance is the result of similar genomic changes. To address this gap, we used a targeted capture approach to sequence genes associated with sulfide processes and toxicity from five sulfidic and five nonsulfidic populations in the species complex. By comparing sequence variation in candidate genes to a reference set, we identified similar population structure and differentiation, suggesting that patterns of variation in most genes associated with sulfide processes and toxicity are due to demographic history and not selection. But the presence of tree discordance for a subset of genes suggests that several loci are evolving divergently between ecotypes. We identified two differentiation outlier genes that are associated with sulfide detoxification in the mitochondria that have signatures of selection in all five sulfidic populations. Further investigation into these regions identified long, shared haplotypes among sulfidic populations. Together, these results reveal that selection on standing genetic variation in putatively adaptive genes may be driving phenotypic convergence in this species complex.}, }
@article {pmid37538245, year = {2023}, author = {Zhang, H and Li, X and Fan, W and Pandovski, S and Tian, Y and Dillin, A}, title = {Inter-tissue communication of mitochondrial stress and metabolic health.}, journal = {Life metabolism}, volume = {2}, number = {1}, pages = {}, pmid = {37538245}, issn = {2755-0230}, support = {R01 AG059566/AG/NIA NIH HHS/United States ; R01 ES021667/ES/NIEHS NIH HHS/United States ; }, abstract = {Mitochondria function as a hub of the cellular metabolic network. Mitochondrial stress is closely associated with aging and a variety of diseases, including neurodegeneration and cancer. Cells autonomously elicit specific stress responses to cope with mitochondrial stress to maintain mitochondrial homeostasis. Interestingly, mitochondrial stress responses may also be induced in a non-autonomous manner in cells or tissues that are not directly experiencing such stress. Such non-autonomous mitochondrial stress responses are mediated by secreted molecules called mitokines. Due to their significant translational potential in improving human metabolic health, there has been a surge in mitokine-focused research. In this review, we summarize the findings regarding inter-tissue communication of mitochondrial stress in animal models. In addition, we discuss the possibility of mitokine-mediated intercellular mitochondrial communication originating from bacterial quorum sensing.}, }
@article {pmid37522604, year = {2023}, author = {Chukaew, T and Isomura, N and Mezaki, T and Matsumoto, H and Kitano, YF and Nozawa, Y and Tachikawa, H and Fukami, H}, title = {Molecular Phylogeny and Taxonomy of the Coral Genus Cyphastrea (Cnidaria, Scleractinia, Merulinidae) in Japan, With the First Records of Two Species.}, journal = {Zoological science}, volume = {40}, number = {4}, pages = {326-340}, doi = {10.2108/zs230009}, pmid = {37522604}, issn = {0289-0003}, mesh = {Animals ; Phylogeny ; *Anthozoa/genetics ; Japan ; DNA, Ribosomal/genetics ; Mitochondria/genetics ; Sequence Analysis, DNA ; }, abstract = {The scleractinian coral genus Cyphastrea is widely distributed in the Indo-Pacific region and is common from the subtropical to the warm-temperate regions in Japan. Three new species in this genus have recently been reported from south-eastern Australia or the Red Sea. However, taxonomic and species diversity have been little studied so far in Japan. In this study, we analyzed 112 specimens of Cyphastrea collected from the subtropical to the warm-temperate regions in Japan to clarify the species diversity in the country. This analysis was based on skeletal morphological and molecular analyses using three genetic markers of the nuclear 28S rDNA, histone H3 gene, and the mitochondrial noncoding intergenic region between COI and tRNAmet. The molecular phylogenetic trees showed that our specimens are separated mainly into four clades. Considering the morphological data with the molecular phylogenetic relationships, we confirmed a total of nine species, including two species, C. magna and C. salae, recorded for the first time in Japan. Although eight out of nine species were genetically included within Cyphastrea, one species, C. agassizi, was genetically distant from all other species and was closely related to the genus Leptastrea, suggesting the return of this species to the genus to which it was originally ascribed. Two newly recorded species were reciprocally monophyletic, while the other six species (excluding C. agassizi) clustered in two clades without forming species-specific lineages, including three polyphyletic species. Thus, the species boundary between species in Cyphastrea remains unclear in most species using these three sequenced loci.}, }
@article {pmid37518710, year = {2023}, author = {Russell, PJC and Pateman, JE and Gagarina, AV and Lukhtanov, VA}, title = {Investigations into the Melitaea ornata species complex in the Levant: M. telona and the newly erected species Melitaea klili Benyamini, 2021 (Lepidoptera: Nymphalidae).}, journal = {Zootaxa}, volume = {5285}, number = {1}, pages = {187-195}, doi = {10.11646/zootaxa.5285.1.9}, pmid = {37518710}, issn = {1175-5334}, mesh = {Male ; Animals ; *Butterflies/genetics ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Genes, Mitochondrial ; DNA Barcoding, Taxonomic ; }, abstract = {Melitaea klili Benyamini, 2021 was recently described from Israel as a species closely related to M. telona Fruhstorfer, 1908, but different in phenology, ecological preferences and with an allopatric distribution. Here, based on comparative examinations of mitochondrial DNA-barcodes, male genitalia and larval behaviour under laboratory conditions, we synonymize M. klili with M. telona. The COI barcodes of M. klili were found to be identical to those of M. telona. Analysis of 658 bp fragment of the mitochondrial gene COI demonstrated that the minimum uncorrected p-distance between M. ornata and M. telona was 1.98%. This value is remarkably less than the 3% threshold traditionally accepted as a species boundary in DNA barcoding studies. The morphological differences between these taxa are minimal. In fact, M. ornata and M. telona represent two phylogenetic lineages, the taxonomic status of which (separate species or subspecies of the same species) is intermediate and debatable.}, }
@article {pmid37518527, year = {2023}, author = {Kuhara, N and Nozaki, T and Zhang, AO and Zhou, X}, title = {DNA barcoding facilitates discovery and description of two new species of the Mystacides azureus Species Group (Trichoptera: Leptoceridae) in Japan.}, journal = {Zootaxa}, volume = {5306}, number = {2}, pages = {215-231}, doi = {10.11646/zootaxa.5306.2.3}, pmid = {37518527}, issn = {1175-5334}, mesh = {Female ; Animals ; Male ; Japan ; *DNA Barcoding, Taxonomic ; Phylogeny ; *Holometabola ; Mitochondria ; }, abstract = {We examined adult specimens of the Mystacides azureus Species Group (Trichoptera: Leptoceridae) collected in Japan and confirm three species including M. azureus Linnaeus 1761 and two new species, M. rivularis and M. moritai. Males and females of the new species are described. Mystacides azureus in Japan is shown to have a considerable variation in morphology of the male tergum X. We analyzed mitochondrial COI barcodes of the genus Mystacides including these three species to confirm their species status. A maximum likelihood phylogeny based on COI barcodes shows monophyly of the new species. It also supports the hypothesis that morphological variation of the male tergum X in Japanese populations is intraspecific in only M. azureus.}, }
@article {pmid37518493, year = {2023}, author = {Tomimori, Y and Matsui, M and Okawa, H and Nishikawa, K and Tanabe, S and Kamasaka, R}, title = {Reassessment of species delimitation using nuclear markers in three lentic-breeding salamanders from the Chugoku District of Japan (Amphibia: Caudata: Hynobiidae).}, journal = {Zootaxa}, volume = {5293}, number = {1}, pages = {145-160}, doi = {10.11646/zootaxa.5293.1.6}, pmid = {37518493}, issn = {1175-5334}, mesh = {Animals ; *Urodela/genetics ; Phylogeny ; Japan ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; }, abstract = {Hynobius akiensis sensu lato has recently been split into three species based on short sequence analyses of cyt-b gene of mtDNA and without data of nuclear DNA, and strange sympatric distribution in some areas has been indicated in two species. We analyzed nuclear DNA marker (SNPs) and complete sequence of cyt-b in H. akiensis sensu lato to reassess species delimitation and genetic introgression among species. As a result, we found two lineages with discordant mitochondrial and nuclear DNA in some areas. Of H. akiensis sensu lato, each of the two contains the type locality of two species recently reported (H. sumidai and H. geiyoensis), and the use of these names has been previously advocated. However, their sympatric distribution was rejected based on nuclear DNA data, which we consider is more reliable than mtDNA. We thus clarify geographic boundary of these two species and revise the species delimitations.}, }
@article {pmid37518286, year = {2023}, author = {Zhang, G and Gao, JJ and Takano, KT and Yafuso, M and Suwito, A and Meleng, PA and Toda, MJ}, title = {Phylogenetic classification and palm-inflorescence anthophily of the Colocasiomyia zeylanica species group (Diptera: Drosophilidae), with descriptions of five new species.}, journal = {Zootaxa}, volume = {5278}, number = {2}, pages = {201-238}, doi = {10.11646/zootaxa.5278.2.1}, pmid = {37518286}, issn = {1175-5334}, mesh = {Animals ; *Diptera ; *Drosophilidae/genetics ; Phylogeny ; Inflorescence ; Mitochondria ; }, abstract = {The zeylanica group is one of the six species groups of the anthophilic genus Colocasiomyia de Meijere in the family Drosophilidae. In addition to two known species, five morphospecies have been recognized as members of this species group but left undescribed formally. In this study, species delimitation of these putatively new species was determined by barcoding of the mitochondrial COI (cytochrome c oxydase subunit I) gene and morphological comparison. Phylogenetic relationships within the genus Colocasiomyia were inferred by a cladistic analysis of 89 morphological characters. Based on the results of these analyses, we redefined the zeylanica species group and established two subgroups within it: the zeylanica subgroup comprised of C. zeylanica, C. nepalensis, C. pinangae sp. nov., C. besaris sp. nov. and C. luciphila sp. nov., and the oligochaeta subgroup of C. oligochaeta sp. nov. and C. grimaldii sp. nov. In addition, we briefly address the anthophilic habits of drosophilid flies using palm (Arecaceae) inflorescences, especially of the zeylanica group, compiling scattered collection records from the Oriental and Papuan regions.}, }
@article {pmid37515372, year = {2023}, author = {Fernández-Moncada, I and Rodrigues, RS and Fundazuri, UB and Bellocchio, L and Marsicano, G}, title = {Type-1 cannabinoid receptors and their ever-expanding roles in brain energy processes.}, journal = {Journal of neurochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1111/jnc.15922}, pmid = {37515372}, issn = {1471-4159}, support = {//INSERM/ ; Micabra, ERC-2017-AdG-786467//the European Research Council/ ; DRM20101220445//Fondation pour la Recherche Medicale/ ; ALTF87-2018//EMBO/ ; //the Human Frontiers Science Program/ ; 17219710//Region Aquitaine/ ; CanBrain, AAP2022A-2021-16763610//Region Aquitaine/ ; ANR-19-CE14-0039//French State/Agence Nationale de la Recherche/ ; ERA-Net Neuron CanShank, ANR-21-NEU2-0001-04//French State/Agence Nationale de la Recherche/ ; MitObesity, ANR 18-CE14-0029-01//French State/Agence Nationale de la Recherche/ ; CaCoVi, ANR 18-CE16-0001-02//French State/Agence Nationale de la Recherche/ ; GPR BRAIN_2030//University of Bordeaux's IdEx "Investments for the Future" program/ ; }, abstract = {The brain requires large quantities of energy to sustain its functions. At the same time, the brain is isolated from the rest of the body, forcing this organ to develop strategies to control and fulfill its own energy needs. Likely based on these constraints, several brain-specific mechanisms emerged during evolution. For example, metabolically specialized cells are present in the brain, where intercellular metabolic cycles are organized to separate workload and optimize the use of energy. To orchestrate these strategies across time and space, several signaling pathways control the metabolism of brain cells. One of such controlling systems is the endocannabinoid system, whose main signaling hub in the brain is the type-1 cannabinoid (CB1) receptor. CB1 receptors govern a plethora of different processes in the brain, including cognitive function, emotional responses, or feeding behaviors. Classically, the mechanisms of action of CB1 receptors on brain function had been explained by its direct targeting of neuronal synaptic function. However, new discoveries have challenged this view. In this review, we will present and discuss recent data about how a small fraction of CB1 receptors associated to mitochondrial membranes (mtCB1), are able to exert a powerful control on brain functions and behavior. mtCB1 receptors impair mitochondrial functions both in neurons and astrocytes. In the latter cells, this effect is linked to an impairment of astrocyte glycolytic function, resulting in specific behavioral outputs. Finally, we will discuss the potential implications of (mt)CB1 expression on oligodendrocytes and microglia metabolic functions, with the aim to encourage interdisciplinary approaches to better understand the role of (mt)CB1 receptors in brain function and behavior.}, }
@article {pmid37512520, year = {2023}, author = {Hu, M and Jiang, Y and Xu, JJ}, title = {Characterization of Arabidopsis thaliana Coq9 in the CoQ Biosynthetic Pathway.}, journal = {Metabolites}, volume = {13}, number = {7}, pages = {}, pmid = {37512520}, issn = {2218-1989}, support = {no//Yunnan Revitalization Talent Support Program "Top Team" Project/ ; PFGR202201//Open Fund of Shanghai Key Laboratory of Plant Functional Genomics and Resources under Grant/ ; 222414//Special Fund for Shanghai Landscaping Administration Bureau Program/ ; YDZX20223100001003//Ministry of Science and Technology of the People's Republic of China/ ; }, abstract = {Coenzyme Q, also known as ubiquinone, is a fat-soluble isoprene quinone that serves as a cofactor for numerous enzymes across all domains of life. However, the biosynthetic pathway for this important molecule in plants has been examined in only a limited number of studies. In yeast and mammals, Coq9, an isoprenoid-lipid-binding protein, is essential for CoQ biosynthesis. Previous studies showed that Arabidopsis thaliana Coq9 failed to complement the fission yeast Schizosaccharomyces pombe coq9 null mutant, and its function in plants remains unknown. In this study, we demonstrated that expression of Arabidopsis Coq9 rescued the growth of a yeast temperature-sensitive coq9 mutant and increased CoQ content. Phylogenetic analysis revealed that Coq9 is widely present in green plants. Green fluorescent protein (GFP) fusion experiments showed that Arabidopsis Coq9 is targeted to mitochondria. Disruption of the Coq9 gene in Arabidopsis results in lower amounts of CoQ. Our work suggests that plant Coq9 is required for efficient CoQ biosynthesis. These findings provide new insights into the evolution of CoQ biosynthesis in plants. The identification of Coq9 as a key player in CoQ biosynthesis in plants opens up new avenues for understanding the regulation of this important metabolic pathway.}, }
@article {pmid37511042, year = {2023}, author = {Luo, L and Xu, Y and Wang, S and Zhang, R and Guo, K and Xu, W and Zhao, Z}, title = {Complete Mitochondrial Genome Sequence and Phylogenetic Analysis of Procambarus clarkii and Cambaroides dauricus from China.}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, pmid = {37511042}, issn = {1422-0067}, support = {2020YFD0900402//the National Key Research and Development Project/ ; 2020TD56//the Central Public-interest Scienti&#xfb01;c Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; }, mesh = {Animals ; *Genome, Mitochondrial/genetics ; Astacoidea/genetics ; Phylogeny ; NAD/genetics ; Sequence Analysis, DNA ; }, abstract = {To enhance the management and protection of crayfish genetic diversity and germplasm resources in Cambaroides dauricus (C. dauricus), a common species of Procambarus clarkii (P. clarkii) was used as a control group to compare the whole mitochondrial genome sequence using Illumina sequencing technology. This study found that the mitochondrial genome of C. dauricus is 15580 bp in length, with a base composition of A (31.84%), G (17.66%), C (9.42%), and T (41.08%) and a C + G content of 27.08%. The C + G in the D-loop is rich in 17.06%, indicating a significant preference. The mitochondrial genome of C. dauricus contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes, with most of the genes labeled in the negative direction, except for a few genes that are labeled in the positive direction. The start codons of the ten coding sequences are ATG, and the quintessential TAA and TAG are the stop codons. This study also found that the Ka/Ks ratios of most protein-coding genes in the mitochondria of both shrimps are lower than 1, indicating weak natural selection, except for nad 2, nad 5, and cox 1. The Ka/Ks ratio of cox 3 is the lowest (less than 0.1), indicating that this protein-coding gene bears strong natural selection pressure and functional constraint in the process of mitochondrial genetic evolution of both shrimps. Furthermore, we constructed phylogenetic analyses based on the entire sequence, which effectively distinguishes the high body from other shrimp species of the genus based on the mitochondrial genome. This study provides molecular genetic data for the diversity investigation and protection of fishery resources with Chinese characteristics and a scientific reference for the evolutionary study of Procambarus.}, }
@article {pmid37508434, year = {2023}, author = {Preziuso, A and Piccirillo, S and Cerqueni, G and Serfilippi, T and Terenzi, V and Vinciguerra, A and Orciani, M and Amoroso, S and Magi, S and Lariccia, V}, title = {Exploring the Role of NCX1 and NCX3 in an In Vitro Model of Metabolism Impairment: Potential Neuroprotective Targets for Alzheimer's Disease.}, journal = {Biology}, volume = {12}, number = {7}, pages = {}, pmid = {37508434}, issn = {2079-7737}, support = {2017YH3SXK//Ministry of Education, Universities and Research/ ; }, abstract = {Alzheimer's disease (AD) is a widespread neurodegenerative disorder, affecting a large number of elderly individuals worldwide. Mitochondrial dysfunction, metabolic alterations, and oxidative stress are regarded as cooperating drivers of the progression of AD. In particular, metabolic impairment amplifies the production of reactive oxygen species (ROS), resulting in detrimental alterations to intracellular Ca[2+] regulatory processes. The Na[+]/Ca[2+] exchanger (NCX) proteins are key pathophysiological determinants of Ca[2+] and Na[+] homeostasis, operating at both the plasma membrane and mitochondria levels. Our study aimed to explore the role of NCX1 and NCX3 in retinoic acid (RA) differentiated SH-SY5Y cells treated with glyceraldehyde (GA), to induce impairment of the default glucose metabolism that typically precedes Aβ deposition or Tau protein phosphorylation in AD. By using an RNA interference-mediated approach to silence either NCX1 or NCX3 expression, we found that, in GA-treated cells, the knocking-down of NCX3 ameliorated cell viability, increased the intracellular ATP production, and reduced the oxidative damage. Remarkably, NCX3 silencing also prevented the enhancement of Aβ and pTau levels and normalized the GA-induced decrease in NCX reverse-mode activity. By contrast, the knocking-down of NCX1 was totally ineffective in preventing GA-induced cytotoxicity except for the increase in ATP synthesis. These findings indicate that NCX3 and NCX1 may differently influence the evolution of AD pathology fostered by glucose metabolic dysfunction, thus providing a potential target for preventing AD.}, }
@article {pmid37507225, year = {2023}, author = {Esposti, MD}, title = {Eukaryotes inherited inositol lipids from bacteria: implications for the models of eukaryogenesis.}, journal = {FEBS letters}, volume = {597}, number = {19}, pages = {2484-2496}, doi = {10.1002/1873-3468.14708}, pmid = {37507225}, issn = {1873-3468}, abstract = {The merger of two very different microbes, an anaerobic archaeon and an aerobic bacterium, led to the birth of eukaryotic cells. Current models hypothesize that an archaeon engulfed bacteria through external protrusions that then fused together forming the membrane organelles of eukaryotic cells, including mitochondria. Images of cultivated Lokiarchaea sustain this concept, first proposed in the inside-out model which assumes that the membrane traffic system of archaea drove the merging with bacterial cells through membrane expansions containing inositol lipids, considered to have evolved first in archaea. This assumption has been evaluated here in detail. The data indicate that inositol lipids first emerged in bacteria, not in archaea. The implications of this finding for the models of eukaryogenesis are discussed.}, }
@article {pmid37503831, year = {2023}, author = {Sanchez-Puerta, MV and Ceriotti, LF and Gatica-Soria, LM and Roulet, ME and Garcia, LE and Sato, HA}, title = {Beyond parasitic convergence: unraveling the evolution of the organellar genomes in holoparasites.}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcad108}, pmid = {37503831}, issn = {1095-8290}, abstract = {BACKGROUND: The molecular evolution of organellar genomes in angiosperms has been extensively studied, with some lineages, such as parasitic ones, displaying unique characteristics. Parasitism has emerged 12 times independently in angiosperm evolution. Holoparasitism is the most severe form of parasitism, and comprises approximately 10% of parasitic angiosperms. Although a few holoparasitic species have been examined at the molecular level, most reports involve plastomes instead of mitogenomes. Parasitic plants establish vascular connections with their hosts through haustoria to obtain water and nutrients, which facilitates the exchange of genetic information, making them more susceptible to horizontal gene transfer (HGT). HGT is more prevalent in the mitochondria than in the chloroplast or nuclear compartments.<br><br>SCOPE: This review summarizes the current knowledge on the plastid and mitochondrial genomes of holoparasitic angiosperms, compares the genomic features across the different lineages, and discusses their convergent evolutionary trajectories and distinctive features. We focused on Balanophoraceae (Santalales), which exhibits extraordinary traits in both their organelles.<br><br>CONCLUSIONS: Apart from morphological similarities, plastid genomes of holoparasitic plants also display other convergent features, such as rampant gene loss, biased nucleotide composition, and accelerated evolutionary rates. In addition, the plastomes of Balanophoraceae have extremely low GC and gene content, and two unexpected changes in the genetic code. Limited data on the mitochondrial genomes of holoparasitic plants preclude thorough comparisons. Nonetheless, no obvious genomic features distinguish them from the mitochondria of free-living angiosperms, except for a higher incidence of HGT. HGT appears to be predominant in holoparasitic angiosperms with a long-lasting endophytic stage. Among the Balanophoraceae, mitochondrial genomes exhibit disparate evolutionary paths with notable levels of heteroplasmy in Rhopalocnemis and unprecedented levels of HGT in Lophophytum. Despite their differences, these Balanophoraceae share a multichromosomal mitogenome, a feature also found in a few free-living angiosperms.}, }
@article {pmid37502859, year = {2023}, author = {Cal, K and Leyva, A and Rodríguez-Duarte, J and Ruiz, S and Santos, L and Colella, L and Ingold, M and Vilaseca, C and Galliussi, G and Ziegler, L and Peclat, TR and Bresque, M and Handy, RM and King, R and Dos Reis, LM and Espasandin, C and Breining, P and Dapueto, R and Lopez, A and Thompson, KL and Agorrody, G and DeVallance, E and Meadows, E and Lewis, SE and Barbosa, GCS and de Souza, LOL and Chichierchio, MS and Valez, V and Aicardo, A and Contreras, P and Vendelbo, MH and Jakobsen, S and Kamaid, A and Porcal, W and Calliari, A and Verdes, JM and Du, J and Wang, Y and Hollander, JM and White, TA and Radi, R and Moyna, G and Quijano, C and O'Doherty, R and Moraes-Vieira, P and Holloway, GP and Leonardi, R and Mori, MA and Camacho-Pereira, J and Kelley, EE and Duran, R and Lopez, GV and Batthyány, C and Chini, EN and Escande, C}, title = {A nitroalkene derivative of salicylate alleviates diet-induced obesity by activating creatine metabolism and non-shivering thermogenesis.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37502859}, abstract = {Obesity-related type II diabetes (diabesity) has increased global morbidity and mortality dramatically. Previously, the ancient drug salicylate demonstrated promise for the treatment of type II diabetes, but its clinical use was precluded due to high dose requirements. In this study, we present a nitroalkene derivative of salicylate, 5-(2-nitroethenyl)salicylic acid (SANA), a molecule with unprecedented beneficial effects in diet-induced obesity (DIO). SANA reduces DIO, liver steatosis and insulin resistance at doses up to 40 times lower than salicylate. Mechanistically, SANA stimulated mitochondrial respiration and increased creatine-dependent energy expenditure in adipose tissue. Indeed, depletion of creatine resulted in the loss of SANA action. Moreover, we found that SANA binds to creatine kinases CKMT1/2, and downregulation CKMT1 interferes with the effect of SANA in vivo. Together, these data demonstrate that SANA is a first-in-class activator of creatine-dependent energy expenditure and thermogenesis in adipose tissue and emerges as a candidate for the treatment of diabesity.}, }
@article {pmid37498958, year = {2023}, author = {Schmid, LM and Manavski, N and Chi, W and Meurer, J}, title = {Chloroplast Ribosome Biogenesis Factors.}, journal = {Plant &amp; cell physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/pcp/pcad082}, pmid = {37498958}, issn = {1471-9053}, support = {ME 1794/10 TRR 175 A03//Deutsche Forschungsgemeinschaft/ ; 2022YFF1001700//National Key Research and Development Program of China/ ; }, abstract = {The formation of chloroplasts can be traced back to an ancient event in which a eukaryotic host cell containing mitochondria ingested a cyanobacterium. Since then, chloroplasts have retained many characteristics of their bacterial ancestor, including their transcription and translation machinery. In this review, recent research on the maturation of rRNA and ribosome assembly in chloroplasts is explored, along with their crucial role in plant survival and their implications for plant acclimation to changing environments. A comparison is made between the ribosome composition and auxiliary factors of ancient and modern chloroplasts, providing insights into the evolution of ribosome assembly factors. Although the chloroplast contains ancient proteins with conserved functions in ribosome assembly, newly evolved factors have also emerged to help plants acclimate to changes in their environment and internal signals. Overall, this review offers a comprehensive analysis of the molecular mechanisms underlying chloroplast ribosome assembly and highlights the importance of this process in plant survival, acclimation, and adaptation.}, }
@article {pmid37497665, year = {2023}, author = {Millet, AMC and Coustham, C and Champigny, C and Botella, M and Demeilliers, C and Devin, A and Galinier, A and Belenguer, P and Bordeneuve-Guibé, J and Davezac, N}, title = {OPA1 deficiency impairs oxidative metabolism in cycling cells, underlining a translational approach for degenerative diseases.}, journal = {Disease models &amp; mechanisms}, volume = {16}, number = {9}, pages = {}, pmid = {37497665}, issn = {1754-8411}, mesh = {Humans ; *Optic Atrophy, Autosomal Dominant/genetics/metabolism ; Reactive Oxygen Species/metabolism ; Mitochondria/metabolism ; Cell Respiration ; Oxidative Stress ; GTP Phosphohydrolases/genetics/metabolism ; }, abstract = {Dominant optic atrophy is an optic neuropathy with varying clinical symptoms and progression. A severe disorder is associated with certain OPA1 mutations and includes additional symptoms for >20% of patients. This underscores the consequences of OPA1 mutations in different cellular populations, not only retinal ganglionic cells. We assessed the effects of OPA1 loss of function on oxidative metabolism and antioxidant defences using an RNA-silencing strategy in a human epithelial cell line. We observed a decrease in the mitochondrial respiratory chain complexes, associated with a reduction in aconitase activity related to an increase in reactive oxygen species (ROS) production. In response, the NRF2 (also known as NFE2L2) transcription factor was translocated into the nucleus and upregulated SOD1 and GSTP1. This study highlights the effects of OPA1 deficiency on oxidative metabolism in replicative cells, as already shown in neurons. It underlines a translational process to use cycling cells to circumvent and describe oxidative metabolism. Moreover, it paves the way to predict the evolution of dominant optic atrophy using mathematical models that consider mitochondrial ROS production and their detoxifying pathways.}, }
@article {pmid37493549, year = {2023}, author = {Jagielska, M and Hałakuc, P and Płecha, M and Milanowski, R}, title = {[Mitochondrial genomes – unity and diversity].}, journal = {Postepy biochemii}, volume = {69}, number = {2}, pages = {113-121}, doi = {10.18388/pb.2021_486}, pmid = {37493549}, issn = {0032-5422}, mesh = {*Genome, Mitochondrial ; Evolution, Molecular ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Cell Nucleus ; Phylogeny ; }, abstract = {The emergence of mitochondria was one of the most important events in the history of life on Earth. The engulfed bacterial cell, transformed into a mitochondrion, retained its genome, which then underwent numerous modifications. Through massive loss and numerous gene transfers into the nuclear genome, the autonomous bacterium eventually evolved into the organelle we know today. As a result of changes taking place independently in different evolutionary lineages, we observe a great diversity of mitochondrial genomes with respect to structure and gene content. In most cases, mitochondrial DNA has a circular shape, but linear molecules of mitochondrial DNA are also observed in some eukaryotes. In extreme cases, such as in reduced mitochondrial-derived organelles, the genome has been completely lost. In this article, we discuss the diversity of mitochondrial genome structures within the largest groups of Eukarya.}, }
@article {pmid37491455, year = {2023}, author = {von der Dunk, SHA and Hogeweg, P and Snel, B}, title = {Obligate endosymbiosis enables genome expansion during eukaryogenesis.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {777}, pmid = {37491455}, issn = {2399-3642}, mesh = {Phylogeny ; *Eukaryotic Cells/metabolism ; *Symbiosis/genetics ; Biological Evolution ; Mitochondria/genetics ; }, abstract = {The endosymbiosis of an alpha-proteobacterium that gave rise to mitochondria was one of the key events in eukaryogenesis. One striking outcome of eukaryogenesis was a much more complex cell with a large genome. Despite the existence of many alternative hypotheses for this and other patterns potentially related to endosymbiosis, a constructive evolutionary model in which these hypotheses can be studied is still lacking. Here, we present a theoretical approach in which we focus on the consequences rather than the causes of mitochondrial endosymbiosis. Using a constructive evolutionary model of cell-cycle regulation, we find that genome expansion and genome size asymmetry arise from emergent host-symbiont cell-cycle coordination. We also find that holobionts with large host and small symbiont genomes perform best on long timescales and mimic the outcome of eukaryogenesis. By designing and studying a constructive evolutionary model of obligate endosymbiosis, we uncovered some of the forces that may drive the patterns observed in nature. Our results provide a theoretical foundation for patterns related to mitochondrial endosymbiosis, such as genome size asymmetry, and reveal evolutionary outcomes that have not been considered so far, such as cell-cycle coordination without direct communication.}, }
@article {pmid37491310, year = {2023}, author = {Costa, RD and Thomaz Neto, FJ and Moustafa, MT and Atilano, SR and Chwa, M and Cáceres-Del-Carpi, J and Mohamed, MH and Kenney, MC and Kuppermann, BD}, title = {The role of mitochondrial genes on nuclear gene expression in neovascular age related macular degeneration: analysis of nuclear VEGF gene expression after ranibizumab treatment in cytoplasmic hybrid retinal pigment epithelial cell lines correlated with clinical evolution.}, journal = {International journal of retina and vitreous}, volume = {9}, number = {1}, pages = {44}, pmid = {37491310}, issn = {2056-9920}, abstract = {PURPOSE: The present study tests the hypothesis that mitochondrial genes have retrograde signaling capacity that influences the expression of nuclear genes related to angiogenesis pathways. Cytoplasmic hybrid (cybrid) in vitro cell lines with patient specific mitochondria inserted into an immortalized retinal pigment epithelial cell line (ARPE-19) were used to test this hypothesis. This type of analysis can provide important information to identify the optimal regimen of anti-VEGF treatment, personalizing age-related macular degeneration (AMD) therapies.<br><br>METHODS: Mitochondria deficient ARPE-19 cells (Rho0) were fused with AMD donor's platelets to create individual cybrid cell lines containing mitochondria from patients with phenotypic AMD disease and nuclear DNA from the immortalized RPE cell line. The cybrids were treated with Ranibizumab (Lucentis, Genentech, San Francisco, CA), at 4 different concentrations for 24&#xa0;h, and subsequently the levels of reactive oxygen species (ROS), gene expression for VEGF-A, hypoxia-inducible factor 1-alpha (HIF1-a) and manganese superoxide dismutase (SOD2) were measured. The clinical evolution of the two AMD-donors were correlated with the molecular findings found in their 'personalized' cybrids.<br><br>RESULTS: Cybrids from Patient-01 showed down-regulation of gene expression of VEGF-A and HIF-1a at both 1X and 4X Ranibizumab concentrations. Patient-01 AMD cybrid cultures had an increase in the ROS levels at 1X (P&#x2009;=&#x2009;0.0317), no changes at 2X (P&#x2009;=&#x2009;0.8350) and a decrease at 4X (P&#x2009;=&#x2009;0.0015) and 10X (P&#x2009;=&#x2009;0.0011) of Ranibizumab. Clinically, Patient-01 responded to anti-VEGF therapy but eventually developed geographic atrophy. Patient-02 cybrids demonstrated up-regulation of gene expression of VEGF-A and HIF-1a at Ranibizumab 1X and 4X concentrations. There was decreased ROS levels with Ranibizumab 1X (P&#x2009;=&#x2009;0.1606), 2X (P&#x2009;=&#x2009;0.0388), 4X (P&#x2009;=&#x2009;0.0010) and 10X (P&#x2009;=&#x2009;&#x2009;<&#x2009;0.0001). Clinically, Patient-02 presented with a neovascular lesion associated with a prominent production of intraretinal fluid in clinical follow-up requiring regular and repeated intravitreal injections of Ranibizumab with recurrent subretinal fluid.<br><br>CONCLUSIONS: Our cybrid model has the potential to help personalize the treatment regimen with anti-VEGF drugs in patients with neovascular AMD. Further investigation is needed to better understand the role that the mitochondria play in the cellular response to anti-VEGF drugs. Future studies that focus on this model have the potential to help personalize anti-VEGF treatment.}, }
@article {pmid37481257, year = {2023}, author = {Collington, E and Lobb, B and Mazen, NA and Doxey, AC and Glerum, DM}, title = {Phylogenomic Analysis of 155 Helminth Species Reveals Widespread Absence of Oxygen Metabolic Capacity.}, journal = {Genome biology and evolution}, volume = {15}, number = {8}, pages = {}, pmid = {37481257}, issn = {1759-6653}, mesh = {Animals ; Phylogeny ; Reactive Oxygen Species/metabolism ; *Parasites ; Electron Transport Complex IV/genetics ; Caenorhabditis elegans/genetics/metabolism ; Oxygen/metabolism ; }, abstract = {The terminal electron acceptor of most aerobic respiratory chains, cytochrome c oxidase (COX), has been highly conserved throughout evolution, from aerobic prokaryotes to complex eukaryotes. Oxygen metabolism in parasitic helminths differs significantly from that of most aerobic eukaryotes, as these organisms can switch between aerobic and anaerobic metabolisms throughout their life cycles. Early studies suggested a lack of COX activity in certain parasitic helminths, and the role of COX in helminth mitochondria remains unclear. To determine whether a functional COX is widely present in helminths, we analyzed the phylogenetic distribution of oxygen metabolism systems across 155 helminth genomes, investigating three distinct sets of protein-coding genes involved in different aspects of oxygen metabolism: COX and its assembly factors, peroxisomes, and the most abundant reactive oxygen species (ROS)-metabolizing proteins. While glycolytic and citric acid cycle enzymes are highly conserved in helminthic species, we observed an apparent widespread absence of essential COX genes across 52% of helminth species investigated. While the most common proteins involved in the defense against ROS are highly maintained across virtually all lineages, we also observed an apparent absence of essential peroxisomal protein-coding genes in 42% of species investigated. Our results suggest that a subset of parasitic helminths utilize oxygen differently from related, nonparasitic species such as Caenorhabditis elegans, with significant differences in their mitochondrial electron transport chains and peroxisomes. The identification of substantive differences between parasite and host metabolism offers a new avenue for the development of anthelmintic agents that could target these divergent pathways.}, }
@article {pmid37481145, year = {2023}, author = {DeCicco, LH and DeRaad, DA and Ostrow, EN and Moyle, RG}, title = {A complete species-level phylogeny of the Erythrura parrotfinches (Aves: Estrildidae).}, journal = {Molecular phylogenetics and evolution}, volume = {187}, number = {}, pages = {107883}, doi = {10.1016/j.ympev.2023.107883}, pmid = {37481145}, issn = {1095-9513}, mesh = {Animals ; Phylogeny ; *Passeriformes/genetics ; DNA ; Genes, Mitochondrial ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Sequence Analysis, DNA ; }, abstract = {Identifying species boundaries and phylogenetic relationships among groups of closely related species provides a necessary framework for understanding how biodiversity evolves in natural systems. Here we present a complete phylogeny of the avian genus Erythrura (family Estrildidae) commonly known as parrotfinches, which includes species threatened by habitat loss and the pet trade. Using both mitogenome and reduced-representation genome-wide nuclear DNA sequence data, we reconstructed the evolutionary history of the group by sampling all 12 recognized species, four of which had not previously been studied in a phylogenetic context. We included intra-species geographic sampling that allowed us to comment on species limits in some taxa. We recovered the Gouldian Finch (Chloebia gouldiae) of Australia which has often been placed in the monotypic genus Chloebia, as being sister to a clade comprising all Erythrura species. In addition, we recovered a well-supported clade comprising eight species distributed throughout the Pacific Island eco-region, whereas those species occurring in continental southeast Asia, the Greater Sundas, and the Philippines, were recovered as earlier branching lineages. Of note was the early branching of the Fiji-endemic E. kleinschmidti which corroborates its unique phenotype. We also found a deep phylogenetic split (8.59% corrected, 7.89% uncorrected divergence in the mitochondrial gene ND2) between the Java and Philippine populations of E. hyperythra, indicating unrecognized species-level diversity within this taxon. In contrast, genome-wide nuclear data suggested that the New Guinea endemic species E. papuana is embedded within the widespread species E. trichroa in all phylogenetic reconstructions, corroborating previously published mitochondrial data that suggested a similar pattern. By generating a phylogenetic hypothesis for the relationships among all species of Erythrura parrotfinches, we provide a framework for better understanding the extant diversity and evolutionary history of this group.}, }
@article {pmid37479726, year = {2023}, author = {Falchi, FA and Forti, F and Carnelli, C and Genco, A and Pizzoccheri, R and Manzari, C and Pavesi, G and Briani, F}, title = {Human PNPase causes RNA stabilization and accumulation of R-loops in the Escherichia coli model system.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {11771}, pmid = {37479726}, issn = {2045-2322}, mesh = {Humans ; *Escherichia coli/genetics ; *R-Loop Structures ; Causality ; Gene Expression Regulation ; RNA/genetics ; }, abstract = {Polyribonucleotide phosphorylase (PNPase) is a phosphorolytic RNA exonuclease highly conserved throughout evolution. In Escherichia coli, PNPase controls complex phenotypic traits like biofilm formation and growth at low temperature. In human cells, PNPase is located in mitochondria, where it is implicated in the RNA import from the cytoplasm, the mitochondrial RNA degradation and the processing of R-loops, namely stable RNA-DNA hybrids displacing a DNA strand. In this work, we show that the human PNPase (hPNPase) expressed in E. coli causes oxidative stress, SOS response activation and R-loops accumulation. Hundreds of E. coli RNAs are stabilized in presence of hPNPase, whereas only few transcripts are destabilized. Moreover, phenotypic traits typical of E. coli strains lacking PNPase are strengthened in presence of the human enzyme. We discuss the hypothesis that hPNPase expressed in E. coli may bind, but not degrade, the RNA, in agreement with previous in vitro data showing that phosphate concentrations in the range of those found in the bacterial cytoplasm and, more relevant, in the mitochondria, inhibit its activity.}, }
@article {pmid37479023, year = {2023}, author = {Boël, M and Voituron, Y and Roussel, D}, title = {Body mass dependence of oxidative phosphorylation efficiency in liver mitochondria from mammals.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {284}, number = {}, pages = {111490}, doi = {10.1016/j.cbpa.2023.111490}, pmid = {37479023}, issn = {1531-4332}, mesh = {Animals ; *Oxidative Phosphorylation ; *Mitochondria, Liver/metabolism ; Adenosine Triphosphate/metabolism ; Mitochondria/metabolism ; Mammals/metabolism ; Oxygen Consumption/physiology ; }, abstract = {In eukaryotes, the performances of an organism are dependent on body mass and chemically supported by the mitochondrial production of ATP. Although the relationship between body mass and mitochondrial oxygen consumption is well described, the allometry of the transduction efficiency from oxygen to ATP production (ATP/O) is still poorly understood. Using a comparative approach, we investigated the oxygen consumption and ATP production of liver mitochondria from twelve species of mammals ranging from 5 g to 600 kg. We found that both oxygen consumption and ATP production are mass dependent but not the ATP/O at the maximal phosphorylating state. The results also showed that for sub-maximal phosphorylating states the ATP/O value positively correlated with body mass, irrespective of the metabolic intensity. This result contrasts with previous data obtained in mammalian muscles, suggesting a tissue-dependence of the body mass effect on mitochondrial efficiency.}, }
@article {pmid37464732, year = {2023}, author = {Wang, F and Zhang, N and Zhao, C and Song, Z and Caiyan, X}, title = {Codon usage bias analysis of mitochondrial protein-coding genes in 12 species of Candida.}, journal = {Journal of genetics}, volume = {102}, number = {}, pages = {}, pmid = {37464732}, issn = {0973-7731}, mesh = {Humans ; *Codon Usage ; *Candida/genetics ; Codon/genetics ; Mitochondrial Proteins/genetics ; Mitochondria/genetics ; Nucleotides/genetics ; }, abstract = {The incidence of diseases that are caused by fungal infection is gradually increasing, together with antibiotic abuse and the number of patients with hypoimmunity. The many challenges in clinical anti-fungi treatment include serious adverse effects and drug resistance. The mitochondria of fungi have been found to be closely associated with pathopoiesia and drug resistance. Hence, we investigated patterns in Candida mitochondrial genes codon usage bias to provide new information to guide anti-fungal research. According to the nucleotide composition results, most mitochondrial genes of the analysed Candida tended to use A/T bases rather than G/C bases. The relative synonymous codon usage values demonstrated that UUA, AGU, CCU, GCU, UGA, AGA and GGU were the common preferential codons of mitochondrial genes in 12 Candida species. Codon adaptation index (CAI) analysis indicated that the ATP9 of Candida parapsilosis had the highest value, and the ND6 of C. auris had the lowest value. The CAI clearly correlated with the codon bias index, except in C. maltose and C. viswanathii, and was significantly positively correlated with the average GC content. Together, our results suggested that the codon usage pattern is affected by multiple factors, among which GC content is critical. Nucleotide composition, selection pressure and mutation pressure influence codon bias in Candida mitochondrial genes, with dominant status to mutation pressure. Codon usage bias analyses of Candida mitochondrial genes may provide new insight into its evolution.}, }
@article {pmid37463427, year = {2023}, author = {Warren, JM and Broz, AK and Martinez-Hottovy, A and Elowsky, C and Christensen, AC and Sloan, DB}, title = {Rewiring of Aminoacyl-tRNA Synthetase Localization and Interactions in Plants With Extensive Mitochondrial tRNA Gene Loss.}, journal = {Molecular biology and evolution}, volume = {40}, number = {7}, pages = {}, pmid = {37463427}, issn = {1537-1719}, mesh = {*Amino Acyl-tRNA Synthetases/genetics ; RNA, Transfer/genetics ; Cell Nucleus/genetics ; Mitochondria/genetics ; Genome, Plant ; }, abstract = {The number of tRNAs encoded in plant mitochondrial genomes varies considerably. Ongoing loss of bacterial-like mitochondrial tRNA genes in many lineages necessitates the import of nuclear-encoded counterparts that share little sequence similarity. Because tRNAs are involved in highly specific molecular interactions, this replacement process raises questions about the identity and trafficking of enzymes necessary for the maturation and function of newly imported tRNAs. In particular, the aminoacyl-tRNA synthetases (aaRSs) that charge tRNAs are usually divided into distinct classes that specialize on either organellar (mitochondrial and plastid) or nuclear-encoded (cytosolic) tRNAs. Here, we investigate the evolution of aaRS subcellular localization in a plant lineage (Sileneae) that has experienced extensive and rapid mitochondrial tRNA loss. By analyzing full-length mRNA transcripts (PacBio Iso-Seq), we found predicted retargeting of many ancestrally cytosolic aaRSs to the mitochondrion and confirmed these results with colocalization microscopy assays. However, we also found cases where aaRS localization does not appear to change despite functional tRNA replacement, suggesting evolution of novel interactions and charging relationships. Therefore, the history of repeated tRNA replacement in Sileneae mitochondria reveals that differing constraints on tRNA/aaRS interactions may determine which of these alternative coevolutionary paths is used to maintain organellar translation in plant cells.}, }
@article {pmid37453725, year = {2023}, author = {Shively, CA and Frye, BM and Negrey, JD and Johnson, CSC and Sutphen, CL and Molina, AJA and Yadav, H and Snyder-Mackler, N and Register, TC}, title = {The interactive effects of psychosocial stress and diet composition on health in primates.}, journal = {Neuroscience and biobehavioral reviews}, volume = {152}, number = {}, pages = {105320}, pmid = {37453725}, issn = {1873-7528}, support = {R01 HL087103/HL/NHLBI NIH HHS/United States ; R01 HL122393/HL/NHLBI NIH HHS/United States ; RF1 AG058829/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Primates ; Stress, Psychological ; Anxiety ; *Diet, Mediterranean ; Social Isolation ; }, abstract = {Social disadvantage and diet composition independently impact myriad dimensions of health. They are closely entwined, as social disadvantage often yields poor diet quality, and may interact to fuel differential health outcomes. This paper reviews effects of psychosocial stress and diet composition on health in nonhuman primates and their implications for aging and human health. We examined the effects of social subordination stress and Mediterranean versus Western diet on multiple systems. We report that psychosocial stress and Western diet have independent and additive adverse effects on hypothalamic-pituitary-adrenal and autonomic nervous system reactivity to psychological stressors, brain structure, and ovarian function. Compared to the Mediterranean diet, the Western diet resulted in accelerated aging, nonalcoholic fatty liver disease, insulin resistance, gut microbial changes associated with increased disease risk, neuroinflammation, neuroanatomical perturbations, anxiety, and social isolation. This comprehensive, multisystem investigation lays the foundation for future investigations of the mechanistic underpinnings of psychosocial stress and diet effects on health, and advances the promise of the Mediterranean diet as a therapeutic intervention on psychosocial stress.}, }
@article {pmid37453661, year = {2023}, author = {Dreishpoon, MB and Bick, NR and Petrova, B and Warui, DM and Cameron, A and Booker, SJ and Kanarek, N and Golub, TR and Tsvetkov, P}, title = {FDX1 regulates cellular protein lipoylation through direct binding to LIAS.}, journal = {The Journal of biological chemistry}, volume = {299}, number = {9}, pages = {105046}, pmid = {37453661}, issn = {1083-351X}, support = {R01 CA279550/CA/NCI NIH HHS/United States ; R35 CA242457/CA/NCI NIH HHS/United States ; R35 GM122595/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Humans ; *Ferredoxins/genetics/metabolism ; *Lipoylation/genetics ; Protein Binding ; Cell Respiration/genetics ; Cell Proliferation/genetics ; Metabolome ; *Sulfurtransferases/metabolism ; }, abstract = {Ferredoxins are a family of iron-sulfur (Fe-S) cluster proteins that serve as essential electron donors in numerous cellular processes that are conserved through evolution. The promiscuous nature of ferredoxins as electron donors enables them to participate in many metabolic processes including steroid, heme, vitamin D, and Fe-S cluster biosynthesis in different organisms. However, the unique natural function(s) of each of the two human ferredoxins (FDX1 and FDX2) are still poorly characterized. We recently reported that FDX1 is both a crucial regulator of copper ionophore-induced cell death and serves as an upstream regulator of cellular protein lipoylation, a mitochondrial lipid-based post-translational modification naturally occurring on four mitochondrial enzymes that are crucial for TCA cycle function. Here we show that FDX1 directly regulates protein lipoylation by binding the lipoyl synthase (LIAS) enzyme promoting its functional binding to the lipoyl carrier protein GCSH and not through indirect regulation of cellular Fe-S cluster biosynthesis. Metabolite profiling revealed that the predominant cellular metabolic outcome of FDX1 loss of function is manifested through the regulation of the four lipoylation-dependent enzymes ultimately resulting in loss of cellular respiration and sensitivity to mild glucose starvation. Transcriptional profiling established that FDX1 loss-of-function results in the induction of both compensatory metabolism-related genes and the integrated stress response, consistent with our findings that FDX1 loss-of-function is conditionally lethal. Together, our findings establish that FDX1 directly engages with LIAS, promoting its role in cellular protein lipoylation, a process essential in maintaining cell viability under low glucose conditions.}, }
@article {pmid37451476, year = {2023}, author = {Záhonová, K and Valach, M and Tripathi, P and Benz, C and Opperdoes, FR and Barath, P and Lukáčová, V and Danchenko, M and Faktorová, D and Horváth, A and Burger, G and Lukeš, J and Škodová-Sveráková, I}, title = {Subunit composition of mitochondrial dehydrogenase complexes in diplonemid flagellates.}, journal = {Biochimica et biophysica acta. General subjects}, volume = {1867}, number = {9}, pages = {130419}, doi = {10.1016/j.bbagen.2023.130419}, pmid = {37451476}, issn = {1872-8006}, mesh = {*Mitochondria/metabolism ; *Pyruvate Dehydrogenase Complex/metabolism ; Multienzyme Complexes/metabolism ; Ketoglutarate Dehydrogenase Complex/metabolism ; Pyruvates/metabolism ; }, abstract = {In eukaryotes, pyruvate, a key metabolite produced by glycolysis, is converted by a tripartite mitochondrial pyruvate dehydrogenase (PDH) complex to acetyl-coenzyme A, which is fed into the tricarboxylic acid cycle. Two additional enzyme complexes with analogous composition catalyze similar oxidative decarboxylation reactions albeit using different substrates, the branched-chain ketoacid dehydrogenase (BCKDH) complex and the 2-oxoglutarate dehydrogenase (OGDH) complex. Comparative transcriptome analyses of diplonemids, one of the most abundant and diverse groups of oceanic protists, indicate that the conventional E1, E2, and E3 subunits of the PDH complex are lacking. E1 was apparently replaced in the euglenozoan ancestor of diplonemids by an AceE protein of archaeal type, a substitution that we also document in dinoflagellates. Here, we demonstrate that the mitochondrion of the model diplonemid Paradiplonema papillatum displays pyruvate and 2-oxoglutarate dehydrogenase activities. Protein mass spectrometry of mitochondria reveal that the AceE protein is as abundant as the E1 subunit of BCKDH. This corroborates the view that the AceE subunit is a functional component of the PDH complex. We hypothesize that by acquiring AceE, the diplonemid ancestor not only lost the eukaryotic-type E1, but also the E2 and E3 subunits of the PDH complex, which are present in other euglenozoans. We posit that the PDH activity in diplonemids seems to be carried out by a complex, in which the AceE protein partners with the E2 and E3 subunits from BCKDH and/or OGDH.}, }
@article {pmid37437976, year = {2023}, author = {Atayik, MC and Çakatay, U}, title = {Mitochondria-associated cellular senescence mechanisms: Biochemical and pharmacological perspectives.}, journal = {Advances in protein chemistry and structural biology}, volume = {136}, number = {}, pages = {117-155}, doi = {10.1016/bs.apcsb.2023.03.003}, pmid = {37437976}, issn = {1876-1631}, mesh = {*Mitochondria ; *Cellular Senescence ; Signal Transduction ; }, abstract = {Initially, endosymbiotic relation of mitochondria and other cellular compartments had been continued mutually. However, that evolutionary adaptation impaired because of the deterioration of endosymbiotic crosstalk due to aging and several pathological consequences in cellular redox status are seen, such as deterioration in redox integrity of mitochondria, interfered inter-organelle redox signaling and inefficient antioxidant response element mediated gene expression. Although the dysfunction of mitochondria is known to be a classical pattern of senescence, it is unresolved that why dysfunctional mitochondria is the core of senescence-associated secretory phenotype (SASP). Redox impairment and SASP-related disease development are generally together with weaken immunity. Impaired mitochondrial redox integrity and its ineffectiveness in immunity control render elders to be more prone to age-related diseases. As senotherapeutic agents, senolytics remove senescent cells whilst senomorphics/senostatics inhibits the secretion of SASP. Senotherapeutics and the novel approaches for ameliorating SASP-related unfavorable effects are recently thought to be promising ways as mitochondria-targeted gerotherapeutic options.}, }
@article {pmid37429369, year = {2023}, author = {Ahlawat, S and Sharma, U and Arora, R and Sharma, R and Chhabra, P and Veer Singh, K and Vijh, RK}, title = {Mitogenomic phylogeny reveals the predominance of the Nubian lineage of African wild ass in Indian donkeys.}, journal = {Gene}, volume = {880}, number = {}, pages = {147627}, doi = {10.1016/j.gene.2023.147627}, pmid = {37429369}, issn = {1879-0038}, mesh = {Animals ; Humans ; *Equidae/genetics ; Phylogeny ; *DNA, Mitochondrial/genetics ; Africa ; Domestication ; Haplotypes ; Genetic Variation ; }, abstract = {To contribute to the knowledge of maternal genetic diversity in domestic donkeys, this study investigated the mitochondrial DNA variations and analyzed the genetic structure in Indian donkeys based on 31 mitogenome sequences representing four breeds/populations (Agra, Halari, Kachchhi and Spiti). A total of 27 haplotypes with a haplotype diversity value of 0.989 were evident in the donkey genetic resources of India. The genetic differentiation between the investigated populations was evaluated using population pairwise FST values, which showed maximum differentiation between Kachchhi and Halari donkeys. The Neighbor-Joining (NJ) tree based on the whole mitogenome sequence and the Median-Joining (MJ) network for partial D-loop fragment showed clear demarcation of Indian donkeys into Nubian and Somali clades, substantiating African maternal origin of Indian domestic donkeys. The topology of the MJ network excluded the Asian wild asses as the possible progenitors of Indian donkeys. Halari and Agra donkeys showed conformity exclusively to the Nubian lineage of the African wild asses. However, representation of both the Nubian and Somali lineages was observed in Kachchhi and Spiti donkeys. Comprehensive analysis carried out by retrieving D-loop sequences from different countries representing Asia, Africa, Europe and South America revealed existence of shared haplotypes across geographically isolated regions of the globe. This observation is indicative of utility of donkeys as pack animals across inter-continental trading routes during development of human civilizations. Our results represent a valuable contribution to maternal genetic diversity of Indian donkeys and provide insights into the worldwide spread of the species following initial domestication in Africa.}, }
@article {pmid37429000, year = {2023}, author = {Wan, H and Zhang, Y and Wu, L and Zhou, G and Pan, L and Fernie, AR and Ruan, YL}, title = {Evolution of cytosolic and organellar invertases empowered the colonization and thriving of land plants.}, journal = {Plant physiology}, volume = {193}, number = {2}, pages = {1227-1243}, pmid = {37429000}, issn = {1532-2548}, mesh = {Humans ; Cytosol/metabolism ; *beta-Fructofuranosidase/metabolism ; Plants/genetics/metabolism ; *Embryophyta/metabolism ; Carbon/metabolism ; Evolution, Molecular ; }, abstract = {The molecular innovation underpinning efficient carbon and energy metabolism during evolution of land plants remains largely unknown. Invertase-mediated sucrose cleavage into hexoses is central to fuel growth. Why some cytoplasmic invertases (CINs) function in the cytosol, whereas others operate in chloroplasts and mitochondria, is puzzling. We attempted to shed light on this question from an evolutionary perspective. Our analyses indicated that plant CINs originated from a putatively orthologous ancestral gene in cyanobacteria and formed the plastidic CIN (α1 clade) through endosymbiotic gene transfer, while its duplication in algae with a loss of its signal peptide produced the β clade CINs in the cytosol. The mitochondrial CINs (α2) were derived from duplication of the plastidic CINs and coevolved with vascular plants. Importantly, the copy number of mitochondrial and plastidic CINs increased upon the emergence of seed plants, corresponding with the rise of respiratory, photosynthetic, and growth rates. The cytosolic CIN (β subfamily) kept expanding from algae to gymnosperm, indicating its role in supporting the increase in carbon use efficiency during evolution. Affinity purification mass spectrometry identified a cohort of proteins interacting with α1 and 2 CINs, which points to their roles in plastid and mitochondrial glycolysis, oxidative stress tolerance, and the maintenance of subcellular sugar homeostasis. Collectively, the findings indicate evolutionary roles of α1 and α2 CINs in chloroplasts and mitochondria for achieving high photosynthetic and respiratory rates, respectively, which, together with the expanding of cytosolic CINs, likely underpin the colonization of land plants through fueling rapid growth and biomass production.}, }
@article {pmid37424790, year = {2023}, author = {Margenat, M and Betancour, G and Irving, V and Costábile, A and García-Cedrés, T and Portela, MM and Carrión, F and Herrera, FE and Villarino, A}, title = {Characteristics of Mycobacterium tuberculosis PtpA interaction and activity on the alpha subunit of human mitochondrial trifunctional protein, a key enzyme of lipid metabolism.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1095060}, pmid = {37424790}, issn = {2235-2988}, mesh = {Humans ; Lipid Metabolism ; *Mycobacterium tuberculosis ; Phylogeny ; Ubiquitins ; *Mitochondrial Trifunctional Protein/metabolism ; *Bacterial Proteins/metabolism ; }, abstract = {During Mycobacterium tuberculosis (Mtb) infection, the virulence factor PtpA belonging to the protein tyrosine phosphatase family is delivered into the cytosol of the macrophage. PtpA interacts with numerous eukaryotic proteins modulating phagosome maturation, innate immune response, apoptosis, and potentially host-lipid metabolism, as previously reported by our group. In vitro, the human trifunctional protein enzyme (hTFP) is a bona fide PtpA substrate, a key enzyme of mitochondrial β-oxidation of long-chain fatty acids, containing two alpha and two beta subunits arranged in a tetramer structure. Interestingly, it has been described that the alpha subunit of hTFP (ECHA, hTFPα) is no longer detected in mitochondria during macrophage infection with the virulent Mtb H37Rv. To better understand if PtpA could be the bacterial factor responsible for this effect, in the present work, we studied in-depth the PtpA activity and interaction with hTFPα. With this aim, we performed docking and in vitro dephosphorylation assays defining the P-Tyr-271 as the potential target of mycobacterial PtpA, a residue located in the helix-10 of hTFPα, previously described as relevant for its mitochondrial membrane localization and activity. Phylogenetic analysis showed that Tyr-271 is absent in TFPα of bacteria and is present in more complex eukaryotic organisms. These results suggest that this residue is a specific PtpA target, and its phosphorylation state is a way of regulating its subcellular localization. We also showed that phosphorylation of Tyr-271 can be catalyzed by Jak kinase. In addition, we found by molecular dynamics that PtpA and hTFPα form a stable protein complex through the PtpA active site, and we determined the dissociation equilibrium constant. Finally, a detailed study of PtpA interaction with ubiquitin, a reported PtpA activator, showed that additional factors are required to explain a ubiquitin-mediated activation of PtpA. Altogether, our results provide further evidence supporting that PtpA could be the bacterial factor that dephosphorylates hTFPα during infection, potentially affecting its mitochondrial localization or β-oxidation activity.}, }
@article {pmid37424728, year = {2023}, author = {Gospodaryov, DV and Ballard, JWO and Camus, MF and DeSalle, R and Garvin, MR and Richter, U}, title = {Editorial: Energy-producing organelles and the nucleus: a phenomenal genomic friendship.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1230032}, pmid = {37424728}, issn = {1664-8021}, }
@article {pmid37419430, year = {2023}, author = {Françoso, E and Zuntini, AR and Ricardo, PC and Araujo, NS and Silva, JPN and Brown, MJF and Arias, MC}, title = {The complete mitochondrial genome of Trigonisca nataliae (Hymenoptera, Apidae) assemblage reveals heteroplasmy in the control region.}, journal = {Gene}, volume = {881}, number = {}, pages = {147621}, doi = {10.1016/j.gene.2023.147621}, pmid = {37419430}, issn = {1879-0038}, mesh = {Bees/genetics ; Animals ; *Hymenoptera/genetics ; *Genome, Mitochondrial ; Heteroplasmy ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; }, abstract = {The evolution of mitochondrial genomes in the stingless bees is surprisingly dynamic, making them a model system to understand mitogenome structure, function, and evolution. Out of the seven mitogenomes available in this group, five exhibit atypical characteristics, including extreme rearrangements, rapid evolution and complete mitogenome duplication. To further explore the mitogenome diversity in these bees, we utilized isolated mtDNA and Illumina sequencing to assemble the complete mitogenome of Trigonisca nataliae, a species found in Northern Brazil. The mitogenome of T. nataliae was highly conserved in gene content and structure when compared to Melipona species but diverged in the control region (CR). Using PCR amplification, cloning and Sanger sequencing, six different CR haplotypes, varying in size and content, were recovery. These findings indicate that heteroplasmy, where different mitochondrial haplotypes coexist within individuals, occurs in T. nataliae. Consequently, we argue that heteroplasmy might indeed be a common phenomenon in bees that could be associated with variations in mitogenome size and challenges encountered during the assembly process.}, }
@article {pmid37408307, year = {2023}, author = {Yang, C and Li, X and Yang, L and Chen, S and Liao, J and Li, K and Zhou, J and Shen, W and Zhuang, X and Bai, M and Bassham, DC and Gao, C}, title = {A positive feedback regulation of SnRK1 signaling by autophagy in plants.}, journal = {Molecular plant}, volume = {16}, number = {7}, pages = {1192-1211}, doi = {10.1016/j.molp.2023.07.001}, pmid = {37408307}, issn = {1752-9867}, mesh = {Protein Serine-Threonine Kinases/genetics/metabolism ; *Arabidopsis Proteins/genetics/metabolism ; *Arabidopsis/metabolism ; Feedback ; Autophagy/genetics ; Gene Expression Regulation, Plant ; }, abstract = {SnRK1, an evolutionarily conserved heterotrimeric kinase complex that acts as a key metabolic sensor in maintaining energy homeostasis in plants, is an important upstream activator of autophagy that serves as a cellular degradation mechanism for the healthy growth of plants. However, whether and how the autophagy pathway is involved in regulating SnRK1 activity remains unknown. In this study, we identified a clade of plant-specific and mitochondria-localized FCS-like zinc finger (FLZ) proteins as currently unknown ATG8-interacting partners that actively inhibit SnRK1 signaling by repressing the T-loop phosphorylation of the catalytic α subunits of SnRK1, thereby negatively modulating autophagy and plant tolerance to energy deprivation caused by long-term carbon starvation. Interestingly, these AtFLZs are transcriptionally repressed by low-energy stress, and AtFLZ proteins undergo a selective autophagy-dependent pathway to be delivered to the vacuole for degradation, thereby constituting a positive feedback regulation to relieve their repression of SnRK1 signaling. Bioinformatic analyses show that the ATG8-FLZ-SnRK1 regulatory axis first appears in gymnosperms and seems to be highly conserved during the evolution of seed plants. Consistent with this, depletion of ATG8-interacting ZmFLZ14 confers enhanced tolerance, whereas overexpression of ZmFLZ14 leads to reduced tolerance to energy deprivation in maize. Collectively, our study reveals a previously unknown mechanism by which autophagy contributes to the positive feedback regulation of SnRK1 signaling, thereby enabling plants to better adapt to stressful environments.}, }
@article {pmid37408243, year = {2023}, author = {Frigo, E and Tommasin, L and Lippe, G and Carraro, M and Bernardi, P}, title = {The Haves and Have-Nots: The Mitochondrial Permeability Transition Pore across Species.}, journal = {Cells}, volume = {12}, number = {10}, pages = {}, pmid = {37408243}, issn = {2073-4409}, mesh = {Animals ; *Mitochondrial Permeability Transition Pore/metabolism ; *Mitochondrial Membrane Transport Proteins/metabolism ; Drosophila melanogaster/metabolism ; Mitochondria/metabolism ; Saccharomyces cerevisiae/metabolism ; Adenosine Triphosphate/metabolism ; Mammals/metabolism ; }, abstract = {The demonstration that F1FO (F)-ATP synthase and adenine nucleotide translocase (ANT) can form Ca[2+]-activated, high-conductance channels in the inner membrane of mitochondria from a variety of eukaryotes led to renewed interest in the permeability transition (PT), a permeability increase mediated by the PT pore (PTP). The PT is a Ca[2+]-dependent permeability increase in the inner mitochondrial membrane whose function and underlying molecular mechanisms have challenged scientists for the last 70 years. Although most of our knowledge about the PTP comes from studies in mammals, recent data obtained in other species highlighted substantial differences that could be perhaps attributed to specific features of F-ATP synthase and/or ANT. Strikingly, the anoxia and salt-tolerant brine shrimp Artemia franciscana does not undergo a PT in spite of its ability to take up and store Ca[2+] in mitochondria, and the anoxia-resistant Drosophila melanogaster displays a low-conductance, selective Ca[2+]-induced Ca[2+] release channel rather than a PTP. In mammals, the PT provides a mechanism for the release of cytochrome c and other proapoptotic proteins and mediates various forms of cell death. In this review, we cover the features of the PT (or lack thereof) in mammals, yeast, Drosophila melanogaster, Artemia franciscana and Caenorhabditis elegans, and we discuss the presence of the intrinsic pathway of apoptosis and of other forms of cell death. We hope that this exercise may help elucidate the function(s) of the PT and its possible role in evolution and inspire further tests to define its molecular nature.}, }
@article {pmid37407024, year = {2023}, author = {Healy, TM and Burton, RS}, title = {Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence.}, journal = {Evolution; international journal of organic evolution}, volume = {77}, number = {9}, pages = {2100-2108}, doi = {10.1093/evolut/qpad122}, pmid = {37407024}, issn = {1558-5646}, mesh = {Animals ; *Copepoda/genetics ; Mitochondria/genetics/metabolism ; Chromosomes ; Genome ; Genotype ; DNA, Mitochondrial/genetics ; }, abstract = {All mitochondrial-encoded proteins and RNAs function through interactions with nuclear-encoded proteins, which are critical for mitochondrial performance and eukaryotic fitness. Coevolution maintains inter-genomic (i.e., mitonuclear) compatibility within a taxon, but hybridization can disrupt coevolved interactions, resulting in hybrid breakdown. Thus, mitonuclear incompatibilities may be important mechanisms underlying reproductive isolation and, potentially, speciation. Here we utilize Pool-seq to assess the effects of mitochondrial genotype on nuclear allele frequencies in fast- and slow-developing reciprocal inter-population F2 hybrids between relatively low-divergence populations of the intertidal copepod Tigriopus californicus. We show that mitonuclear interactions lead to elevated frequencies of coevolved (i.e., maternal) nuclear alleles on two chromosomes in crosses between populations with 1.5% or 9.6% fixed differences in mitochondrial DNA nucleotide sequence. However, we also find evidence of excess mismatched (i.e., noncoevolved) alleles on three or four chromosomes per cross, respectively, and of allele frequency differences consistent with effects involving only nuclear loci (i.e., unaffected by mitochondrial genotype). Thus, our results for low-divergence crosses suggest an underlying role for mitonuclear interactions in variation in hybrid developmental rate, but despite substantial effects of mitonuclear coevolution on individual chromosomes, no clear bias favoring coevolved interactions overall.}, }
@article {pmid37406344, year = {2023}, author = {Lamb, IM and Okoye, IC and Mather, MW and Vaidya, AB}, title = {Unique Properties of Apicomplexan Mitochondria.}, journal = {Annual review of microbiology}, volume = {77}, number = {}, pages = {541-560}, doi = {10.1146/annurev-micro-032421-120540}, pmid = {37406344}, issn = {1545-3251}, support = {R01 AI028398/AI/NIAID NIH HHS/United States ; R01 AI100569/AI/NIAID NIH HHS/United States ; R01 AI154499/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Mitochondria/genetics/metabolism ; *Toxoplasma/metabolism ; Biological Evolution ; *Malaria ; }, abstract = {Apicomplexan parasites constitute more than 6,000 species infecting a wide range of hosts. These include important pathogens such as those causing malaria and toxoplasmosis. Their evolutionary emergence coincided with the dawn of animals. Mitochondrial genomes of apicomplexan parasites have undergone dramatic reduction in their coding capacity, with genes for only three proteins and ribosomal RNA genes present in scrambled fragments originating from both strands. Different branches of the apicomplexans have undergone rearrangements of these genes, with Toxoplasma having massive variations in gene arrangements spread over multiple copies. The vast evolutionary distance between the parasite and the host mitochondria has been exploited for the development of antiparasitic drugs, especially those used to treat malaria, wherein inhibition of the parasite mitochondrial respiratory chain is selectively targeted with little toxicity to the host mitochondria. We describe additional unique characteristics of the parasite mitochondria that are being investigated and provide greater insights into these deep-branching eukaryotic pathogens.}, }
@article {pmid37389212, year = {2023}, author = {Stefano, GB and Büttiker, P and Weissenberger, S and Esch, T and Anders, M and Raboch, J and Kream, RM and Ptacek, R}, title = {Independent and sensory human mitochondrial functions reflecting symbiotic evolution.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1130197}, pmid = {37389212}, issn = {2235-2988}, mesh = {Humans ; *Mitochondria ; *Genes, Bacterial ; Quorum Sensing ; Virion ; }, abstract = {The bacterial origin of mitochondria has been a widely accepted as an event that occurred about 1.45 billion years ago and endowed cells with internal energy producing organelle. Thus, mitochondria have traditionally been viewed as subcellular organelle as any other - fully functionally dependent on the cell it is a part of. However, recent studies have given us evidence that mitochondria are more functionally independent than other organelles, as they can function outside the cells, engage in complex "social" interactions, and communicate with each other as well as other cellular components, bacteria and viruses. Furthermore, mitochondria move, assemble and organize upon sensing different environmental cues, using a process akin to bacterial quorum sensing. Therefore, taking all these lines of evidence into account we hypothesize that mitochondria need to be viewed and studied from a perspective of a more functionally independent entity. This view of mitochondria may lead to new insights into their biological function, and inform new strategies for treatment of disease associated with mitochondrial dysfunction.}, }
@article {pmid37386734, year = {2023}, author = {Arnqvist, G and Rowe, L}, title = {Ecology, the pace-of-life, epistatic selection and the maintenance of genetic variation in life-history genes.}, journal = {Molecular ecology}, volume = {32}, number = {17}, pages = {4713-4724}, doi = {10.1111/mec.17062}, pmid = {37386734}, issn = {1365-294X}, mesh = {*Polymorphism, Genetic ; Selection, Genetic ; Biological Evolution ; Alleles ; *Life History Traits ; Models, Genetic ; Genetic Variation ; Epistasis, Genetic ; }, abstract = {Evolutionary genetics has long struggled with understanding how functional genes under selection remain polymorphic in natural populations. Taking as a starting point that natural selection is ultimately a manifestation of ecological processes, we spotlight an underemphasized and potentially ubiquitous ecological effect that may have fundamental effects on the maintenance of genetic variation. Negative frequency dependency is a well-established emergent property of density dependence in ecology, because the relative profitability of different modes of exploiting or utilizing limiting resources tends to be inversely proportional to their frequency in a population. We suggest that this may often generate negative frequency-dependent selection (NFDS) on major effect loci that affect rate-dependent physiological processes, such as metabolic rate, that are phenotypically manifested as polymorphism in pace-of-life syndromes. When such a locus under NFDS shows stable intermediate frequency polymorphism, this should generate epistatic selection potentially involving large numbers of loci with more minor effects on life-history (LH) traits. When alternative alleles at such loci show sign epistasis with a major effect locus, this associative NFDS will promote the maintenance of polygenic variation in LH genes. We provide examples of the kind of major effect loci that could be involved and suggest empirical avenues that may better inform us on the importance and reach of this process.}, }
@article {pmid37381996, year = {2023}, author = {Zhao, JH and Chen, YC and Hua, ZY and Liu, TR and Zhao, YY and Huang, LQ and Yuan, Y}, title = {[Cloning and gene function of dicarboxylate-tricarboxylate carrier protein in Gastrodia elata].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {48}, number = {12}, pages = {3140-3148}, doi = {10.19540/j.cnki.cjcmm.20230310.102}, pmid = {37381996}, issn = {1001-5302}, mesh = {*Gastrodia/genetics ; Phylogeny ; Amino Acids ; Cloning, Molecular ; }, abstract = {The gene GeDTC encoding the dicarboxylate-tricarboxylate carrier protein in Gastrodia elata was cloned by specific primers which were designed based on the transcriptome data of G. elata. Bioinformatics analysis on GeDTC gene was carried out by using ExPASY, ClustalW, MEGA, etc. Positive transgenic plants and potato minituber were obtained by virtue of the potato genetic transformation system. Agronomic characters, such as size, weight, organic acid content, and starch content, of potato minituber were tested and analyzed and GeDTC gene function was preliminarily investigated. The results showed that the open reading frame of GeDTC gene was 981 bp in length and 326 amino acid residues were encoded, with a relative molecular weight of 35.01 kDa. It was predicted that the theoretical isoelectric point of GeDTC protein was 9.83, the instability coefficient was 27.88, and the average index of hydrophilicity was 0.104, which was indicative of a stable hydrophilic protein. GeDTC protein had a transmembrane structure and no signal peptide and was located in the inner membrane of mitochondria. The phylogenetic tree showed that GeDTC was highly homologous with DTC proteins of other plant species, among which GeDTC had the highest homology with DcDTC(XP＿020675804.1) in Dendrobium candidum, reaching 85.89%. GeDTC overexpression vector pCambia1300-35Spro-GeDTC was constructed by double digests, and transgenic potato plants were obtained by Agrobacterium-mediated gene transformation. Compared with the wild-type plants, transgenic potato minituber harvested by transplanting had smaller size, lighter weight, lower organic acid content, and no significant difference in starch content. It is preliminarily induced that GeDTC is the efflux channel of tricarboxylate and related to the tuber development, which lays a foundation for further elucidating the molecular mechanism of G. elata tuber development.}, }
@article {pmid37371486, year = {2023}, author = {Ding, Y and Zhang, S and Guo, Q and Leng, J}, title = {Mitochondrial Diabetes Is Associated with the ND4 G11696A Mutation.}, journal = {Biomolecules}, volume = {13}, number = {6}, pages = {}, pmid = {37371486}, issn = {2218-273X}, mesh = {Adult ; Aged ; Humans ; Middle Aged ; *Diabetes Mellitus, Type 2/genetics ; *DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; Mutation ; *NADH Dehydrogenase/genetics ; Phylogeny ; }, abstract = {Type 2 diabetes mellitus (T2DM) is a common endocrine disorder which remains a large challenge for clinicians. Previous studies have suggested that mitochondrial dysfunction plays an active role in T2DM progression, but a detailed mechanism is still elusive. In the current study, two Han Chinese families with maternally inherited T2DM were evaluated using clinical, genetic, molecular, and biochemical analyses. The mitochondrial genomes were PCR amplified and sequenced. Phylogenetic and bioinformatic analyses were used to assess the potential pathogenicity of mitochondrial DNA (mtDNA) mutations. Interestingly, the matrilineal relatives of these pedigrees exhibited variable severity of T2DM, in particular, the age at onset of T2DM varied from 26 to 65 years, with an average of 49 years. Sequence analysis revealed the presence of ND4 G11696A mutation, which resulted in the substitution of an isoleucine for valine at amino acid (AA) position 312. Indeed, this mutation was present in homoplasmy only in the maternal lineage, not in other members of these families, as well as 200 controls. Furthermore, the m.C5601T in the tRNA[Ala] and novel m.T5813C in the tRNA[Cys], showing high evolutional conservation, may contribute to the phenotypic expression of ND4 G11696A mutation. In addition, biochemical analysis revealed that cells with ND4 G11696A mutation exhibited higher levels of reactive oxygen species (ROS) productions than the controls. In contrast, the levels of mitochondrial membrane potential (MMP), ATP, mtDNA copy number (mtDNA-CN), Complex I activity, and NAD[+]/NADH ratio significantly decreased in cell lines carrying the m.G11696A and tRNA mutations, suggesting that these mutations affected the respiratory chain function and led to mitochondrial dysfunction that was involved in T2DM. Thus, our study broadened the clinical phenotypes of m.G11696A mutation.}, }
@article {pmid37368881, year = {2023}, author = {Tanabe, TS and Grosser, M and Hahn, L and Kümpel, C and Hartenfels, H and Vtulkin, E and Flegler, W and Dahl, C}, title = {Identification of a novel lipoic acid biosynthesis pathway reveals the complex evolution of lipoate assembly in prokaryotes.}, journal = {PLoS biology}, volume = {21}, number = {6}, pages = {e3002177}, pmid = {37368881}, issn = {1545-7885}, mesh = {*Thioctic Acid/genetics/metabolism ; Peptide Synthases/genetics/metabolism ; Phylogeny ; Bacterial Proteins/metabolism ; Sulfur ; }, abstract = {Lipoic acid is an essential biomolecule found in all domains of life and is involved in central carbon metabolism and dissimilatory sulfur oxidation. The machineries for lipoate assembly in mitochondria and chloroplasts of higher eukaryotes, as well as in the apicoplasts of some protozoa, are all of prokaryotic origin. Here, we provide experimental evidence for a novel lipoate assembly pathway in bacteria based on a sLpl(AB) lipoate:protein ligase, which attaches octanoate or lipoate to apo-proteins, and 2 radical SAM proteins, LipS1 and LipS2, which work together as lipoyl synthase and insert 2 sulfur atoms. Extensive homology searches combined with genomic context analyses allowed us to precisely distinguish between the new and established pathways and map them on the tree of life. This not only revealed a much wider distribution of lipoate biogenesis systems than expected, in particular, the novel sLpl(AB)-LipS1/S2 pathway, and indicated a highly modular nature of the enzymes involved, with unforeseen combinations, but also provided a new framework for the evolution of lipoate assembly. Our results show that dedicated machineries for both de novo lipoate biogenesis and scavenging from the environment were implemented early in evolution and that their distribution in the 2 prokaryotic domains was shaped by a complex network of horizontal gene transfers, acquisition of additional genes, fusions, and losses. Our large-scale phylogenetic analyses identify the bipartite archaeal LplAB ligase as the ancestor of the bacterial sLpl(AB) proteins, which were obtained by horizontal gene transfer. LipS1/S2 have a more complex evolutionary history with multiple of such events but probably also originated in the domain archaea.}, }
@article {pmid37367622, year = {2023}, author = {van der Walt, D and Steenkamp, ET and Wingfield, BD and Wilken, PM}, title = {Evidence of Biparental Mitochondrial Inheritance from Self-Fertile Crosses between Closely Related Species of Ceratocystis.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {6}, pages = {}, pmid = {37367622}, issn = {2309-608X}, abstract = {Hybridization is recognized as a notable driver of evolution and adaptation, which closely related species may exploit in the form of incomplete reproductive barriers. Three closely related species of Ceratocystis (i.e., C. fimbriata, C. manginecans and C. eucalypticola) have previously been shown to hybridize. In such studies, naturally occurring self-sterile strains were mated with an unusual laboratory-generated sterile isolate type, which could have impacted conclusions regarding the prevalence of hybridization and inheritance of mitochondria. In the current study, we investigated whether interspecific crosses between fertile isolates of these three species are possible and, if so, how mitochondria are inherited by the progeny. For this purpose, a PCR-RFLP method and a mitochondrial DNA-specific PCR technique were custom-made. These were applied in a novel approach of typing complete ascospore drops collected from the fruiting bodies in each cross to distinguish between self-fertilizations and potential hybridization. These markers showed hybridization between C. fimbriata and C. eucalypticola and between C. fimbriata and C. manginecans, while no hybridization was detected in the crosses involving C. manginecans and C. eucalypticola. In both sets of hybrid progeny, we detected biparental inheritance of mitochondria. This study was the first to successfully produce hybrids from a cross involving self-fertile isolates of Ceratocystis and also provided the first direct evidence of biparental mitochondrial inheritance in the Ceratocystidaceae. This work lays the foundation for further research focused on investigating the role of hybridization in the speciation of Ceratocystis species and if mitochondrial conflict could have influenced the process.}, }
@article {pmid37364695, year = {2023}, author = {Barrera, CA and Ortega, J and Gutierrez-Guerrero, YT and Baeza, JA}, title = {Comparative mitochondrial genomics of American nectar-feeding long-nosed bats Leptonycteris spp. with insights into the phylogeny of the family Phyllostomidae.}, journal = {Gene}, volume = {879}, number = {}, pages = {147588}, doi = {10.1016/j.gene.2023.147588}, pmid = {37364695}, issn = {1879-0038}, mesh = {Animals ; Phylogeny ; *Chiroptera/genetics ; Plant Nectar ; Genomics ; Mitochondria/genetics ; *Genome, Mitochondrial/genetics ; RNA, Transfer/genetics ; }, abstract = {Among leaf-nosed bats (family Phyllostomidae), the genus Leptonycteris (subfamily Glossophaginae), contains three migratory and obligate nectar-dwelling species of great ecological and economic importance; the greater long-nosed bat L. nivalis, the lesser long-nosed bat L. yerbabuenae, and the southern long-nosed bat L. curasoae. According to the IUCN, the three species are categorized as 'vulnerable', 'endangered', and 'near threatened', respectively. In this study, we assembled and characterized in detail the mitochondrial genome of Leptonycteris spp. and examined the phylogenetic position of this genus in the family Phyllostomidae based on protein coding genes (PCGs). The mitogenomes of L. nivalis, L. curasoae, and L. yerbabuenae are 16,708, 16,758, and 16,729 bp in length and each encode 13 PCGs, 22 transfer RNA genes, 2 rRNA genes, and a putative control region (CR). Mitochondrial gene order is identical to that reported before for the family Phyllostomidae. All tRNAs exhibit a 'cloverleaf' secondary structure, except tRNA-Serine-1 that is missing the DHU arm in the three species. All PCGs are exposed to purifying selection with atp8 experiencing the most relaxed purifying selection as the ω ratio was higher for this gene compared to the other PCGs in each species. The CR of each species contains three functional domains: extended termination associated sequence (ETAS), Central, and conserved sequence block domain (CSB). A phylomitogenomic analysis revealed that Leptonycteris is monophyletic and most closely related to the genus Glossophaga. The analysis also supported the monophyly of the family Glossophaginae in the speciose family Phyllostomidae. The mitochondria characterization of these species provides relevant information to develop molecular markers for conservation purposes.}, }
@article {pmid37364099, year = {2023}, author = {Lynch, M}, title = {Mutation pressure, drift, and the pace of molecular coevolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {27}, pages = {e2306741120}, pmid = {37364099}, issn = {1091-6490}, support = {R35 GM122566/GM/NIGMS NIH HHS/United States ; R35-GM122566-01/NH/NIH HHS/United States ; }, mesh = {*Evolution, Molecular ; Mutation ; *Mutation Rate ; Genome ; Genetic Drift ; }, abstract = {Most aspects of the molecular biology of cells involve tightly coordinated intermolecular interactions requiring specific recognition at the nucleotide and/or amino acid levels. This has led to long-standing interest in the degree to which constraints on interacting molecules result in conserved vs. accelerated rates of sequence evolution, with arguments commonly being made that molecular coevolution can proceed at rates exceeding the neutral expectation. Here, a fairly general model is introduced to evaluate the degree to which the rate of evolution at functionally interacting sites is influenced by effective population sizes (Ne), mutation rates, strength of selection, and the magnitude of recombination between sites. This theory is of particular relevance to matters associated with interactions between organelle- and nuclear-encoded proteins, as the two genomic environments often exhibit dramatic differences in the power of mutation and drift. Although genes within low Ne environments can drive the rate of evolution of partner genes experiencing higher Ne, rates exceeding the neutral expectation require that the former also have an elevated mutation rate. Testable predictions, some counterintuitive, are presented on how patterns of coevolutionary rates should depend on the relative intensities of drift, selection, and mutation.}, }
@article {pmid37338543, year = {2023}, author = {Wong, JE and Zíková, A and Gahura, O}, title = {The Ancestral Shape of the Access Proton Path of Mitochondrial ATP Synthases Revealed by a Split Subunit-a.}, journal = {Molecular biology and evolution}, volume = {40}, number = {6}, pages = {}, pmid = {37338543}, issn = {1537-1719}, mesh = {*Mitochondrial Proton-Translocating ATPases/genetics/chemistry/metabolism ; *Proton-Translocating ATPases/metabolism ; Protons ; Eukaryota/metabolism ; Escherichia coli/genetics/metabolism ; Adenosine Triphosphate/metabolism ; }, abstract = {The passage of protons across membranes through F1Fo-ATP synthases spins their rotors and drives the synthesis of ATP. While the principle of torque generation by proton transfer is known, the mechanisms and routes of proton access and release and their evolution are not fully understood. Here, we show that the entry site and path of protons in the lumenal half channel of mitochondrial ATP synthases are largely defined by a short N-terminal α-helix of subunit-a. In Trypanosoma brucei and other Euglenozoa, the α-helix is part of another polypeptide chain that is a product of subunit-a gene fragmentation. This α-helix and other elements forming the proton pathway are widely conserved across eukaryotes and in Alphaproteobacteria, the closest extant relatives of mitochondria, but not in other bacteria. The α-helix blocks one of two proton routes found in Escherichia coli, resulting in a single proton entry site in mitochondrial and alphaproteobacterial ATP synthases. Thus, the shape of the access half channel predates eukaryotes and originated in the lineage from which mitochondria evolved by endosymbiosis.}, }
@article {pmid37336341, year = {2023}, author = {Liu, S and Xu, S and Liu, S and Chen, H}, title = {Importance of DJ-1 in autophagy regulation and disease.}, journal = {Archives of biochemistry and biophysics}, volume = {743}, number = {}, pages = {109672}, doi = {10.1016/j.abb.2023.109672}, pmid = {37336341}, issn = {1096-0384}, mesh = {Humans ; Reactive Oxygen Species/metabolism ; *Oxidative Stress/physiology ; Hypoxia/metabolism ; *Neoplasms ; Autophagy/physiology ; Protein Deglycase DJ-1/metabolism ; }, abstract = {Autophagy is a highly conserved biological process that has evolved across evolution. It can be activated by various external stimuli including oxidative stress, amino acid starvation, infection, and hypoxia. Autophagy is the primary mechanism for preserving cellular homeostasis and is implicated in the regulation of metabolism, cell differentiation, tolerance to starvation conditions, and resistance to aging. As a multifunctional protein, DJ-1 is commonly expressed in vivo and is associated with a variety of biological processes. Its most widely studied role is its function as an oxidative stress sensor that inhibits the production of excessive reactive oxygen species (ROS) in the mitochondria and subsequently the cellular damage caused by oxidative stress. In recent years, many studies have identified DJ-1 as another important factor regulating autophagy; it regulates autophagy in various ways, most commonly by regulating the oxidative stress response. In particular, DJ-1-regulated autophagy is involved in cancer progression and plays a key role in alleviating neurodegenerative diseases(NDS) and defective reperfusion diseases. It could serve as a potential target for the regulation of autophagy and participate in disease treatment as a meaningful modality. Therefore, exploring DJ-1-regulated autophagy could provide new avenues for future disease treatment.}, }
@article {pmid37333265, year = {2023}, author = {Hanson, SE and Doyle, MT and Bernstein, HD}, title = {The patatin-like protein PlpD forms novel structurally dynamic homodimers in the Pseudomonas aeruginosa outer membrane.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37333265}, abstract = {Members of the Omp85 superfamily of outer membrane proteins (OMPs) found in Gram-negative bacteria, mitochondria and chloroplasts are characterized by a distinctive 16-stranded β-barrel transmembrane domain and at least one periplasmic POTRA domain. All previously studied Omp85 proteins promote critical OMP assembly and/or protein translocation reactions. Pseudomonas aeruginosa PlpD is the prototype of an Omp85 protein family that contains an N-terminal patatin-like (PL) domain that is thought to be translocated across the OM by a C-terminal β-barrel domain. Challenging the current dogma, we found that the PlpD PL-domain resides exclusively in the periplasm and, unlike previously studied Omp85 proteins, PlpD forms a homodimer. Remarkably, the PL-domain contains a segment that exhibits unprecedented dynamicity by undergoing transient strand-swapping with the neighboring β-barrel domain. Our results show that the Omp85 superfamily is more structurally diverse than currently believed and suggest that the Omp85 scaffold was utilized during evolution to generate novel functions.}, }
@article {pmid37330026, year = {2023}, author = {Nguyen, TP and Nguyen, BT and Dao, TNL and Ho, TH and Lee, PT}, title = {Investigation of the functional role of UNC93B1 in Nile tilapia (Oreochromis niloticus): mRNA expression, subcellular localization, and physical interaction with fish-specific TLRs.}, journal = {Fish &amp; shellfish immunology}, volume = {139}, number = {}, pages = {108902}, doi = {10.1016/j.fsi.2023.108902}, pmid = {37330026}, issn = {1095-9947}, mesh = {Humans ; Animals ; Mice ; *Cichlids ; Phylogeny ; Fish Proteins/chemistry ; Toll-Like Receptors/genetics/metabolism ; Phagocytosis ; Streptococcus agalactiae/physiology ; *Fish Diseases ; *Streptococcal Infections/veterinary ; Gene Expression Regulation ; Immunity, Innate/genetics ; Membrane Transport Proteins/genetics ; }, abstract = {Nile tilapia (Oreochromis niloticus) is one of the major food fish worldwide. The farming business, on the other hand, has faced considerable obstacles, such as disease infestations. Toll-like receptors (TLRs) play an important function in the activation of the innate immune system in response to infections. Unc-93 homolog B1 (UNC93B1) is a key regulator of nucleic acid (NA)-sensing TLRs. Here the UNC93B1 gene, which was cloned from Nile tilapia tissue for this investigation, had the same genetic structure as a homologous gene in humans and mice. Phylogenetic analysis revealed that Nile tilapia UNC93B1 clustered with UNC93B1 from other species and separately from the UNC93A clade. The gene structure of the Nile tilapia UNC93B1 was found to be identical to that of human UNC93B1. Our gene expression studies revealed that Nile tilapia UNC93B1 was highly expressed in the spleen, followed by other immune-related tissues such as the head kidney, gills, and intestine. Moreover, Nile tilapia UNC93B1 mRNA transcripts were up-regulated in vivo in the head kidney and spleen tissues from poly I:C and Streptococcus agalactiae injected Nile tilapia, as well as in vitro in LPS stimulated Tilapia head kidney (THK) cells. The Nile tilapia UNC93B1-GFP protein signal was detected in the cytosol of THK cells and was co-localized with endoplasmic reticulum and lysosome but not with mitochondria. Moreover, the results of a co-immunoprecipitation and immunostaining analysis showed that Nile tilapia UNC93B1 can be pulled down with fish-specific TLRs such as TLR18 and TLR25 from Nile tilapia, and was found to be co-localized with these fish-specific TLRs in the THK cells. Overall, our findings highlight the potential role of UNC93B1 as an accessory protein in fish-specific TLR signaling.}, }
@article {pmid37327832, year = {2023}, author = {Thacker, CE and Tyler McCraney, W and Harrington, RC and Near, TJ and Shelley, JJ and Adams, M and Hammer, MP and Unmack, PJ}, title = {Diversification of the sleepers (Gobiiformes: Gobioidei: Eleotridae) and evolution of the root gobioid families.}, journal = {Molecular phylogenetics and evolution}, volume = {186}, number = {}, pages = {107841}, doi = {10.1016/j.ympev.2023.107841}, pmid = {37327832}, issn = {1095-9513}, mesh = {Humans ; Animals ; Phylogeny ; *Fishes/genetics ; *Perciformes/genetics ; Mitochondria ; Fossils ; }, abstract = {Eleotridae (sleepers) and five smaller families are the earliest diverging lineages within Gobioidei. Most inhabit freshwaters in and around the Indo-Pacific, but Eleotridae also includes species that have invaded the Neotropics as well as several inland radiations in the freshwaters of Australia, New Zealand, and New Guinea. Previous efforts to infer phylogeny of these families have been based on sets of mitochondrial or nuclear loci and have yielded uncertain resolution of clades within Eleotridae. We expand the taxon sampling of previous studies and use genomic data from nuclear ultraconserved elements (UCEs) to infer phylogeny, then calibrate the hypothesis with recently discovered fossils. Our hypothesis clarifies ambiguously resolved relationships, provides a timescale for divergences, and indicates the core crown Eleotridae diverged over a short period 24.3-26.3 Ma in the late Oligocene. Within Eleotridae, we evaluate diversification dynamics with BAMM and find evidence for an overall slowdown in diversification over the past 35 Ma, but with a sharp increase 3.5 Ma in the genus Mogurnda, a clade of brightly colored species found in the freshwaters of Australia and New Guinea.}, }
@article {pmid37325898, year = {2023}, author = {Sabbah, HN and Taylor, C and Vernon, HJ}, title = {Temporal evolution of the heart failure phenotype in Barth syndrome and treatment with elamipretide.}, journal = {Future cardiology}, volume = {19}, number = {4}, pages = {211-225}, doi = {10.2217/fca-2023-0008}, pmid = {37325898}, issn = {1744-8298}, mesh = {Humans ; *Barth Syndrome/genetics/pathology ; *Heart Failure/drug therapy ; Stroke Volume ; Phenotype ; Cardiolipins ; }, abstract = {Barth syndrome (BTHS) is a rare genetic disorder caused by pathogenic variants in TAFAZZIN leading to reduced remodeled cardiolipin (CL), a phospholipid essential to mitochondrial function and structure. Cardiomyopathy presents in most patients with BTHS, typically appearing as dilated cardiomyopathy (DCM) in infancy and evolving to hypertrophic cardiomyopathy (HCM) resembling heart failure (HF) with preserved ejection fraction (HFpEF) in some patients ≥12 years. Elamipretide localizes to the inner mitochondrial membrane where it associates with CL, improving mitochondrial function, structure and bioenergetics, including ATP synthesis. Numerous preclinical and clinical studies in BTHS and other forms of HF have demonstrated that elamipretide improves left ventricular relaxation by ameliorating mitochondrial dysfunction, making it well suited for therapeutic use in adolescent and adult patients with BTHS.}, }
@article {pmid37311262, year = {2023}, author = {Annes, K and Ferreira, CR and Valente, RS and Marsico, TV and Tannura, JH and da Silveira, JC and Silva, FH and Landim-Alvarenga, FDC and Mesquista, FS and Sudano, MJ}, title = {Contribution of lipids to the organelle differential profile of in vitro-produced bovine embryos.}, journal = {Theriogenology}, volume = {208}, number = {}, pages = {109-118}, doi = {10.1016/j.theriogenology.2023.06.005}, pmid = {37311262}, issn = {1879-3231}, mesh = {Female ; Pregnancy ; Cattle ; Animals ; *Endoplasmic Reticulum ; *Mitochondria ; Lipid Droplets ; Blastocyst ; Ceramides ; }, abstract = {Each living organism is unique because of the lipid identity of its organelles. The diverse distribution of these molecules also contributes to the role of each organelle in cellular activity. The lipid profiles of whole embryos are well documented in the literature. However, this approach can often lead to the loss of relevant information at the subcellular and consequently, metabolic levels, hindering a deeper understanding of key physiological processes during preimplantation development. Therefore, we aimed to characterize four organelles in vitro-produced bovine embryos: lipid droplets (LD), endoplasmic reticulum (ER), mitochondria (MIT), and nuclear membrane (NUC), and evaluate the contribution of the lipid species to each organelle evaluated. Expanded blastocysts were subjected to cell organelle isolation. Thereafter, lipid extraction from cell organelles and lipid analysis using the Multiple Reaction Monitoring (MRM) profiling method were performed. The LD and ER displayed a greater number of lipids (Phosphatidylcholine - PC, Ceramide - Cer, and Sphingomielin - SM) with high signal-to-noise intensities. This result is due to the high rate of biosynthesis, lipid distribution, and ability to store and recycle lipid species of these organelles. The NUC had a more distinct lipid profile than the other three organelles, with high relative intensities of PC, SM, and triacylglycerols (TG), which is consistent with its high nuclear activity. MIT had an intermediate profile that was close to that of LD and ER, which aligns with its autonomous metabolism for some classes of phospholipids (PL). Our study revealed the lipid composition of each organelle studied, and the roles of these lipids could be associated with the characteristic organellar activity. Our findings highlight the lipid species and classes that are relevant for the homeostasis and function of each associated organelle and provide tentative biomarkers for the determination of in vitro embryonic development and quality.}, }
@article {pmid37305924, year = {2023}, author = {Floriano, AM and Batisti Biffignandi, G and Castelli, M and Olivieri, E and Clementi, E and Comandatore, F and Rinaldi, L and Opara, M and Plantard, O and Palomar, AM and Noël, V and Vijay, A and Lo, N and Makepeace, BL and Duron, O and Jex, A and Guy, L and Sassera, D}, title = {The evolution of intramitochondriality in Midichloria bacteria.}, journal = {Environmental microbiology}, volume = {25}, number = {11}, pages = {2102-2117}, doi = {10.1111/1462-2920.16446}, pmid = {37305924}, issn = {1462-2920}, mesh = {Animals ; *Ixodes/microbiology ; Bacteria/genetics ; Mitochondria/genetics ; Phylogeny ; Symbiosis ; }, abstract = {Midichloria spp. are intracellular bacterial symbionts of ticks. Representatives of this genus colonise mitochondria in the cells of their hosts. To shed light on this unique interaction we evaluated the presence of an intramitochondrial localization for three Midichloria in the respective tick host species and generated eight high-quality draft genomes and one closed genome, showing that this trait is non-monophyletic, either due to losses or multiple acquisitions. Comparative genomics supports the first hypothesis, as the genomes of non-mitochondrial symbionts are reduced subsets of those capable of colonising the organelles. We detect genomic signatures of mitochondrial tropism, including the differential presence of type IV secretion system and flagellum, which could allow the secretion of unique effectors and/or direct interaction with mitochondria. Other genes, including adhesion molecules, proteins involved in actin polymerisation, cell wall and outer membrane proteins, are only present in mitochondrial symbionts. The bacteria could use these to manipulate host structures, including mitochondrial membranes, to fuse with the organelles or manipulate the mitochondrial network.}, }
@article {pmid37303610, year = {2023}, author = {Liang, Y and Fang, X and Zheng, L and Wu, H and He, Z and Xiong, Z and Hong, J and Ai, X and Liang, G}, title = {The complete mitochondrial genome of Choristoneura metasequoiacola Liu,1983 (Lepidoptera: Tortricidae).}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {8}, number = {6}, pages = {653-657}, pmid = {37303610}, issn = {2380-2359}, abstract = {Choristoneura metasequoiacola Liu, 1983 is an important caterpillar species that specifically infests the leaves and branches of Metasequoia glyptostroboides Hu &amp; W. C. Cheng 1948 with short larval infestations, long-term dormancy, and has a limited distribution in Lichuan, Hubei, China. The complete mitochondria genome of C. metasequoiacola was determined by using Illumina NovaSeq, and analyzed based on previously annotated sibling species. In total, we obtained mitochondria genome with 15,128 bp in length, circular in shape with a double-stranded closed ring structure, including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and an AT-rich region. Of which the nucleotide composition was highly A + T biased, accounting for 81.98% of the whole mitogenome. Thirteen protein-coding genes (PCGs) were 11,142 bp; Twenty-two tRNA genes and AT-rich region were 1,472 and 199 bp, respectively. Phylogenetically, the relationship between Choristoneura spp. (containing C. metasequoiacola) and Adoxophyes spp. was closer than any other two genera from Tortricidae, and the relationship between C. metasequoiacola and C.murinana was the closest among nine sibling species from that genus, which helps to explain species evolution within the family Tortricidae.}, }
@article {pmid37299482, year = {2023}, author = {Manilla, V and Santopaolo, F and Gasbarrini, A and Ponziani, FR}, title = {Type 2 Diabetes Mellitus and Liver Disease: Across the Gut-Liver Axis from Fibrosis to Cancer.}, journal = {Nutrients}, volume = {15}, number = {11}, pages = {}, pmid = {37299482}, issn = {2072-6643}, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/metabolism ; *Diabetes Mellitus, Type 2/complications/pathology ; *Carcinoma, Hepatocellular/metabolism ; Dysbiosis/complications/pathology ; *Liver Neoplasms/metabolism ; Liver/metabolism ; Liver Cirrhosis ; Fibrosis ; }, abstract = {Type 2 diabetes mellitus is a widespread disease worldwide, and is one of the cornerstones of metabolic syndrome. The existence of a strong relationship between diabetes and the progression of liver fibrosis has been demonstrated by several studies, using invasive and noninvasive techniques. Patients with type 2 diabetes mellitus (T2DM) and nonalcoholic fatty liver disease (NAFLD) show faster progression of fibrosis than patients without diabetes. Many confounding factors make it difficult to determine the exact mechanisms involved. What we know so far is that both liver fibrosis and T2DM are expressions of metabolic dysfunction, and we recognize similar risk factors. Interestingly, both are promoted by metabolic endotoxemia, a low-grade inflammatory condition caused by increased endotoxin levels and linked to intestinal dysbiosis and increased intestinal permeability. There is broad evidence on the role of the gut microbiota in the progression of liver disease, through both metabolic and inflammatory mechanisms. Therefore, dysbiosis that is associated with diabetes can act as a modifier of the natural evolution of NAFLD. In addition to diet, hypoglycemic drugs play an important role in this scenario, and their benefit is also the result of effects exerted in the gut. Here, we provide an overview of the mechanisms that explain why diabetic patients show a more rapid progression of liver disease up to hepatocellular carcinoma (HCC), focusing especially on those involving the gut-liver axis.}, }
@article {pmid37295735, year = {2023}, author = {Gul, I and Abbas, MN and Kausar, S and Luo, J and Gao, X and Mu, Y and Fan, W and Cui, H}, title = {Insight into crustacean cathepsins: Structure-evolutionary relationships and functional roles in physiological processes.}, journal = {Fish &amp; shellfish immunology}, volume = {139}, number = {}, pages = {108852}, doi = {10.1016/j.fsi.2023.108852}, pmid = {37295735}, issn = {1095-9947}, mesh = {Animals ; *Cathepsins/genetics/chemistry ; Proteins ; Biological Evolution ; *Physiological Phenomena ; }, abstract = {Cathepsins belong to a group of proteins that are present in both prokaryotic and eukaryotic organisms and have an extremely high degree of evolutionary conservation. These proteins are functionally active in extracellular environments as soluble enzymatic proteins or attached to plasma membrane receptors. In addition, they occur in cellular secretory vesicles, mitochondria, the cytosol, and within the nuclei of eukaryotic cells. Cathepsins are classified into various groups based on their sequence variations, leading to their structural and functional diversification. The molecular understanding of the physiology of crustaceans has shown that proteases, including cathepsins, are expressed ubiquitously. They also contain one of the central regulatory systems for crustacean reproduction, growth, and immune responses. This review focuses on various aspects of the crustaceans cathepsins and emphasizes their biological roles in different physiological processes such as reproduction, growth, development, and immune responses. We also describe the bioactivity of crustaceans cathepsins. Because of the vital biological roles that cathepsins play as cellular proteases in physiological processes, they have been proposed as potential novel targets for the development of management strategies for the aquaculture industries.}, }
@article {pmid37291154, year = {2023}, author = {Lee, Y and Cho, CH and Noh, C and Yang, JH and Park, SI and Lee, YM and West, JA and Bhattacharya, D and Jo, K and Yoon, HS}, title = {Origin of minicircular mitochondrial genomes in red algae.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3363}, pmid = {37291154}, issn = {2041-1723}, mesh = {Phylogeny ; *Genome, Mitochondrial/genetics ; Eukaryotic Cells ; Mitochondria/genetics ; *Rhodophyta/genetics ; Evolution, Molecular ; }, abstract = {Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.}, }
@article {pmid37289794, year = {2023}, author = {Hebert, PDN and Bock, DG and Prosser, SWJ}, title = {Interrogating 1000 insect genomes for NUMTs: A risk assessment for estimates of species richness.}, journal = {PloS one}, volume = {18}, number = {6}, pages = {e0286620}, pmid = {37289794}, issn = {1932-6203}, mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Genome, Insect ; Mitochondria/genetics ; Insecta/genetics ; Risk Assessment ; Cell Nucleus/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The nuclear genomes of most animal species include NUMTs, segments of the mitogenome incorporated into their chromosomes. Although NUMT counts are known to vary greatly among species, there has been no comprehensive study of their frequency/attributes in the most diverse group of terrestrial organisms, insects. This study examines NUMTs derived from a 658 bp 5' segment of the cytochrome c oxidase I (COI) gene, the barcode region for the animal kingdom. This assessment is important because unrecognized NUMTs can elevate estimates of species richness obtained through DNA barcoding and derived approaches (eDNA, metabarcoding). This investigation detected nearly 10,000 COI NUMTs ≥ 100 bp in the genomes of 1,002 insect species (range = 0-443). Variation in nuclear genome size explained 56% of the mitogenome-wide variation in NUMT counts. Although insect orders with the largest genome sizes possessed the highest NUMT counts, there was considerable variation among their component lineages. Two thirds of COI NUMTs possessed an IPSC (indel and/or premature stop codon) allowing their recognition and exclusion from downstream analyses. The remainder can elevate species richness as they showed 10.1% mean divergence from their mitochondrial homologue. The extent of exposure to "ghost species" is strongly impacted by the target amplicon's length. NUMTs can raise apparent species richness by up to 22% when a 658 bp COI amplicon is examined versus a doubling of apparent richness when 150 bp amplicons are targeted. Given these impacts, metabarcoding and eDNA studies should target the longest possible amplicons while also avoiding use of 12S/16S rDNA as they triple NUMT exposure because IPSC screens cannot be employed.}, }
@article {pmid37286063, year = {2023}, author = {Abalde, S and Crocetta, F and Tenorio, MJ and D'Aniello, S and Fassio, G and Rodríguez-Flores, PC and Uribe, JE and Afonso, CML and Oliverio, M and Zardoya, R}, title = {Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus.}, journal = {Molecular phylogenetics and evolution}, volume = {186}, number = {}, pages = {107838}, doi = {10.1016/j.ympev.2023.107838}, pmid = {37286063}, issn = {1095-9513}, mesh = {Humans ; Animals ; Phylogeny ; *Mitochondria/genetics ; Genetic Speciation ; *Genome, Mitochondrial ; Snails/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red + blue + orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.}, }
@article {pmid37279941, year = {2023}, author = {Sheikh, S and Pánek, T and Gahura, O and Týč, J and Záhonová, K and Lukeš, J and Eliáš, M and Hashimi, H}, title = {A Novel Group of Dynamin-Related Proteins Shared by Eukaryotes and Giant Viruses Is Able to Remodel Mitochondria From Within the Matrix.}, journal = {Molecular biology and evolution}, volume = {40}, number = {6}, pages = {}, pmid = {37279941}, issn = {1537-1719}, mesh = {*Giant Viruses/genetics/metabolism ; Phylogeny ; Mitochondrial Proteins/genetics/metabolism ; Mitochondria/genetics/metabolism ; Dynamins/genetics/metabolism ; Saccharomyces cerevisiae/genetics ; }, abstract = {The diverse GTPases of the dynamin superfamily play various roles in the cell, as exemplified by the dynamin-related proteins (DRPs) Mgm1 and Opa1, which remodel the mitochondrial inner membrane in fungi and metazoans, respectively. Via an exhaustive search of genomic and metagenomic databases, we found previously unknown DRP types occurring in diverse eukaryotes and giant viruses (phylum Nucleocytoviricota). One novel DRP clade, termed MidX, combined hitherto uncharacterized proteins from giant viruses and six distantly related eukaryote taxa (Stramenopiles, Telonemia, Picozoa, Amoebozoa, Apusomonadida, and Choanoflagellata). MidX stood out because it was not only predicted to be mitochondria-targeted but also to assume a tertiary structure not observed in other DRPs before. To understand how MidX affects mitochondria, we exogenously expressed MidX from Hyperionvirus in the kinetoplastid Trypanosoma brucei, which lacks Mgm1 or Opa1 orthologs. MidX massively affected mitochondrial morphology from inside the matrix, where it closely associates with the inner membrane. This unprecedented mode of action contrasts to those of Mgm1 and Opa1, which mediate inner membrane remodeling in the intermembrane space. We speculate that MidX was acquired in Nucleocytoviricota evolution by horizontal gene transfer from eukaryotes and is used by giant viruses to remodel host mitochondria during infection. MidX's unique structure may be an adaptation for reshaping mitochondria from the inside. Finally, Mgm1 forms a sister group to MidX and not Opa1 in our phylogenetic analysis, throwing into question the long-presumed homology of these DRPs with similar roles in sister lineages.}, }
@article {pmid37278219, year = {2023}, author = {Markaki, M and Tsagkari, D and Tavernarakis, N}, title = {Mitophagy and long-term neuronal homeostasis.}, journal = {Journal of cell science}, volume = {136}, number = {11}, pages = {}, doi = {10.1242/jcs.260638}, pmid = {37278219}, issn = {1477-9137}, support = {ERC-GA695190-MANNA/ERC_/European Research Council/International ; }, mesh = {Humans ; *Mitophagy/physiology ; Autophagy/physiology ; Neurons/metabolism ; *Neurodegenerative Diseases/metabolism ; Homeostasis ; }, abstract = {Neurons are highly polarized, post-mitotic cells that are characterized by unique morphological diversity and complexity. As highly differentiated cells that need to survive throughout organismal lifespan, neurons face exceptional energy challenges in time and space. Therefore, neurons are heavily dependent on a healthy mitochondrial network for their proper function and maintenance under both physiological and stress conditions. Multiple quality control systems have evolved to fine-tune mitochondrial number and quality, thus preserving neuronal energy homeostasis. Here, we review the contribution of mitophagy, a selective form of autophagy that targets dysfunctional or superfluous mitochondria for degradation, in maintaining nervous system homeostasis. In addition, we discuss recent evidence implicating defective or dysregulated mitophagy in the pathogenesis of neurodegenerative diseases.}, }
@article {pmid37277654, year = {2023}, author = {Devant, P and Kagan, JC}, title = {Molecular mechanisms of gasdermin D pore-forming activity.}, journal = {Nature immunology}, volume = {24}, number = {7}, pages = {1064-1075}, pmid = {37277654}, issn = {1529-2916}, mesh = {*Intracellular Signaling Peptides and Proteins/genetics/metabolism ; *Gasdermins ; Pyroptosis ; Interleukin-1/metabolism ; Cell Membrane/metabolism ; Inflammasomes/metabolism ; }, abstract = {The regulated disruption of the plasma membrane, which can promote cell death, cytokine secretion or both is central to organismal health. The protein gasdermin D (GSDMD) is a key player in this process. GSDMD forms membrane pores that can promote cytolysis and the release of interleukin-1 family cytokines into the extracellular space. Recent discoveries have revealed biochemical and cell biological mechanisms that control GSDMD pore-forming activity and its diverse downstream immunological effects. Here, we review these multifaceted regulatory activities, including mechanisms of GSDMD activation by proteolytic cleavage, dynamics of pore assembly, regulation of GSDMD activities by posttranslational modifications, membrane repair and the interplay of GSDMD and mitochondria. We also address recent insights into the evolution of the gasdermin family and their activities in species across the kingdoms of life. In doing so, we hope to condense recent progress and inform future studies in this rapidly moving field in immunology.}, }
@article {pmid37276405, year = {2023}, author = {Kumar, P and Babu, KSD and Singh, AK and Singh, DK and Nalli, A and Mukul, SJ and Roy, A and Mazeed, M and Raman, B and Kruparani, SP and Siddiqi, I and Sankaranarayanan, R}, title = {Distinct localization of chiral proofreaders resolves organellar translation conflict in plants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {24}, pages = {e2219292120}, pmid = {37276405}, issn = {1091-6490}, mesh = {*Organelles/metabolism ; Mitochondria/metabolism ; RNA, Transfer, Amino Acyl/metabolism ; Chloroplasts/metabolism ; RNA, Transfer/metabolism ; *Arabidopsis/genetics ; }, abstract = {Plants have two endosymbiotic organelles originated from two bacterial ancestors. The transition from an independent bacterium to a successful organelle would have required extensive rewiring of biochemical networks for its integration with archaeal host. Here, using Arabidopsis as a model system, we show that plant D-aminoacyl-tRNA deacylase 1 (DTD1), of bacterial origin, is detrimental to organellar protein synthesis owing to its changed tRNA recognition code. Plants survive this conflict by spatially restricting the conflicted DTD1 to the cytosol. In addition, plants have targeted archaeal DTD2 to both the organelles as it is compatible with their translation machinery due to its strict D-chiral specificity and lack of tRNA determinants. Intriguingly, plants have confined bacterial-derived DTD1 to work in archaeal-derived cytosolic compartment whereas archaeal DTD2 is targeted to bacterial-derived organelles. Overall, the study provides a remarkable example of the criticality of optimization of biochemical networks for survival and evolution of plant mitochondria and chloroplast.}, }
@article {pmid37275157, year = {2023}, author = {Himmelstrand, K and Brandström Durling, M and Karlsson, M and Stenlid, J and Olson, &#xc5;}, title = {Multiple rearrangements and low inter- and intra-species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1159811}, pmid = {37275157}, issn = {1664-302X}, abstract = {INTRODUCTION: Mitochondria are essential organelles in the eukaryotic cells and responsible for the energy production but are also involved in many other functions including virulence of some fungal species. Although the evolution of fungal mitogenomes have been studied at some taxonomic levels there are still many things to be learned from studies of closely related species.<br><br>METHODS: In this study, we have analyzed 60 mitogenomes in the five species of the Heterobasidion annosum sensu lato complex that all are necrotrophic pathogens on conifers.<br><br>RESULTS AND DISCUSSION: Compared to other fungal genera the genomic and genetic variation between and within species in the complex was low except for multiple rearrangements. Several translocations of large blocks with core genes have occurred between the five species and rearrangements were frequent in intergenic areas. Mitogenome lengths ranged between 108 878 to 116 176 bp, mostly as a result of intron variation. There was a high degree of homology of introns, homing endonuclease genes, and intergenic ORFs among the five Heterobasidion species. Three intergenic ORFs with unknown function (uORF6, uORF8 and uORF9) were found in all five species and was located in conserved synteny blocks. A 13 bp long GC-containing self-complementary palindrome was discovered in many places in the five species that were optional in presence/absence. The within species variation is very low, among 48 H. parviporum mitogenomes, there was only one single intron exchange, and SNP frequency was 0.28% and indel frequency 0.043%. The overall low variation in the Heterobasidion annosum sensu lato complex suggests a slow evolution of the mitogenome.}, }
@article {pmid37269314, year = {2023}, author = {Patriarcheas, D and Momtareen, T and Gallagher, JEG}, title = {Yeast of Eden: microbial resistance to glyphosate from a yeast perspective.}, journal = {Current genetics}, volume = {69}, number = {4-6}, pages = {203-212}, pmid = {37269314}, issn = {1432-0983}, support = {R03 ES034881/ES/NIEHS NIH HHS/United States ; NIH NIEHS R03 ES034881/NH/NIH HHS/United States ; NIH NIEHS R03 ES034881/NH/NIH HHS/United States ; }, mesh = {Saccharomyces cerevisiae/genetics/metabolism ; *Herbicides/pharmacology ; Glycine/pharmacology/metabolism ; Plants ; Amino Acids, Aromatic ; }, abstract = {First marketed as RoundUp, glyphosate is history's most popular herbicide because of its low acute toxicity to metazoans and broad-spectrum effectiveness across plant species. The development of glyphosate-resistant crops has led to increased glyphosate use and consequences from the use of glyphosate-based herbicides (GBH). Glyphosate has entered the food supply, spurred glyphosate-resistant weeds, and exposed non-target organisms to glyphosate. Glyphosate targets EPSPS/AroA/Aro1 (orthologs across plants, bacteria, and fungi), the rate-limiting step in the production of aromatic amino acids from the shikimate pathway. Metazoans lacking this pathway are spared from acute toxicity and acquire their aromatic amino acids from their diet. However, glyphosate resistance is increasing in non-target organisms. Mutations and natural genetic variation discovered in Saccharomyces cerevisiae illustrate similar types of glyphosate resistance mechanisms in fungi, plants, and bacteria, in addition to known resistance mechanisms such as mutations in Aro1 that block glyphosate binding (target-site resistance (TSR)) and mutations in efflux drug transporters non-target-site resistance (NTSR). Recently, genetic variation and mutations in an amino transporter affecting glyphosate resistance have uncovered potential off-target effects of glyphosate in fungi and bacteria. While glyphosate is a glycine analog, it is transported into cells using an aspartic/glutamic acid (D/E) transporter. The size, shape, and charge distribution of glyphosate closely resembles D/E, and, therefore, glyphosate is a D/E amino acid mimic. The mitochondria use D/E in several pathways and mRNA-encoding mitochondrial proteins are differentially expressed during glyphosate exposure. Mutants downstream of Aro1 are not only sensitive to glyphosate but also a broad range of other chemicals that cannot be rescued by exogenous supplementation of aromatic amino acids. Glyphosate also decreases the pH when unbuffered and many studies do not consider the differences in pH that affect toxicity and resistance mechanisms.}, }
@article {pmid37268349, year = {2023}, author = {Pellielo, G and Agyapong, ED and Pinton, P and Rimessi, A}, title = {Control of mitochondrial functions by Pseudomonas aeruginosa in cystic fibrosis.}, journal = {International review of cell and molecular biology}, volume = {377}, number = {}, pages = {19-43}, doi = {10.1016/bs.ircmb.2023.03.008}, pmid = {37268349}, issn = {1937-6448}, mesh = {Humans ; *Cystic Fibrosis ; Pseudomonas aeruginosa/physiology ; Persistent Infection ; Inflammation/genetics ; Mitochondria ; }, abstract = {Cystic fibrosis (CF) is a genetic disease characterized by mutations of cystic fibrosis transmembrane conductance regulator (CFTR) gene, which lead to a dysfunctional chloride and bicarbonate channel. Abnormal mucus viscosity, persistent infections and hyperinflammation that preferentially affect the airways, referred to the pathogenesis of CF lung disease. It has largely demonstrated that Pseudomonas aeruginosa (P. aeruginosa) represents the most important pathogen that affect CF patients, leading to worsen inflammation by stimulating pro-inflammatory mediators release and tissue destruction. The conversion to mucoid phenotype and formation of biofilms, together with the increased frequency of mutations, are only few changes that characterize the P. aeruginosa's evolution during CF lung chronic infection. Recently, mitochondria received increasing attention due to their involvement in inflammatory-related diseases, including in CF. Alteration of mitochondrial homeostasis is sufficient to stimulate immune response. Exogenous or endogenous stimuli that perturb mitochondrial activity are used by cells, which, through the mitochondrial stress, potentiate immunity programs. Studies show the relationship between mitochondria and CF, supporting the idea that mitochondrial dysfunction endorses the exacerbation of inflammatory responses in CF lung. In particular, evidences suggest that mitochondria in CF airway cells are more susceptible to P. aeruginosa infection, with consequent detrimental effects that lead to amplify the inflammatory signals. This review discusses the evolution of P. aeruginosa in relationship with the pathogenesis of CF, a fundamental step to establish chronic infection in CF lung disease. Specifically, we focus on the role of P. aeruginosa in the exacerbation of inflammatory response, by triggering mitochondria in CF.}, }
@article {pmid37267944, year = {2023}, author = {Záhonová, K and Low, RS and Warren, CJ and Cantoni, D and Herman, EK and Yiangou, L and Ribeiro, CA and Phanprasert, Y and Brown, IR and Rueckert, S and Baker, NL and Tachezy, J and Betts, EL and Gentekaki, E and van der Giezen, M and Clark, CG and Jackson, AP and Dacks, JB and Tsaousis, AD}, title = {Evolutionary analysis of cellular reduction and anaerobicity in the hyper-prevalent gut microbe Blastocystis.}, journal = {Current biology : CB}, volume = {33}, number = {12}, pages = {2449-2464.e8}, doi = {10.1016/j.cub.2023.05.025}, pmid = {37267944}, issn = {1879-0445}, mesh = {Animals ; Humans ; *Blastocystis/genetics ; *Gastrointestinal Microbiome/genetics ; Mitochondria/genetics/metabolism ; Organelles/metabolism ; Eukaryota ; }, abstract = {Blastocystis is the most prevalent microbial eukaryote in the human and animal gut, yet its role as commensal or parasite is still under debate. Blastocystis has clearly undergone evolutionary adaptation to the gut environment and possesses minimal cellular compartmentalization, reduced anaerobic mitochondria, no flagella, and no reported peroxisomes. To address this poorly understood evolutionary transition, we have taken a multi-disciplinary approach to characterize Proteromonas lacertae, the closest canonical stramenopile relative of Blastocystis. Genomic data reveal an abundance of unique genes in P. lacertae but also reductive evolution of the genomic complement in Blastocystis. Comparative genomic analysis sheds light on flagellar evolution, including 37 new candidate components implicated with mastigonemes, the stramenopile morphological hallmark. The P. lacertae membrane-trafficking system (MTS) complement is only slightly more canonical than that of Blastocystis, but notably, we identified that both organisms encode the complete enigmatic endocytic TSET complex, a first for the entire stramenopile lineage. Investigation also details the modulation of mitochondrial composition and metabolism in both P. lacertae and Blastocystis. Unexpectedly, we identify in P. lacertae the most reduced peroxisome-derived organelle reported to date, which leads us to speculate on a mechanism of constraint guiding the dynamics of peroxisome-mitochondrion reductive evolution on the path to anaerobiosis. Overall, these analyses provide a launching point to investigate organellar evolution and reveal in detail the evolutionary path that Blastocystis has taken from a canonical flagellated protist to the hyper-divergent and hyper-prevalent animal and human gut microbe.}, }
@article {pmid37262983, year = {2023}, author = {Camus, MF and Dhawanjewar, AS}, title = {Multilevel selection on mitochondrial genomes.}, journal = {Current opinion in genetics &amp; development}, volume = {80}, number = {}, pages = {102050}, doi = {10.1016/j.gde.2023.102050}, pmid = {37262983}, issn = {1879-0380}, mesh = {*Genome, Mitochondrial/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Biological Evolution ; Eukaryota/genetics ; Evolution, Molecular ; }, abstract = {Mitochondria are vital organelles for life in eukaryotes, taking centre stage in the process of cellular respiration. This process is regulated via a series of finely coordinated obligate interactions of molecules encoded by two genomes: nuclear DNA and mitochondrial DNA. Both genomes are required to work harmoniously to provide cellular energy, with detrimental consequences occurring when there is miscommunication between them. Whilst the need for cooperation is strong, vast differences between genomes (ploidy, size, and inheritance) create an arena for conflict. Here, we examine the varying levels of selection operating on the mitochondrial genome and the consequences they have on all these levels. We conclude by highlighting the potential for conflict when selection at different levels is driven by different evolutionary forces.}, }
@article {pmid37254790, year = {2023}, author = {López-García, P and Moreira, D}, title = {The symbiotic origin of the eukaryotic cell.}, journal = {Comptes rendus biologies}, volume = {346}, number = {}, pages = {55-73}, doi = {10.5802/crbiol.118}, pmid = {37254790}, issn = {1768-3238}, mesh = {*Eukaryotic Cells ; *Symbiosis ; Phylogeny ; Archaea/genetics ; Eukaryota/genetics ; Biological Evolution ; }, abstract = {Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.}, }
@article {pmid37249052, year = {2023}, author = {Chen, Y and Guo, Y and Xie, X and Wang, Z and Miao, L and Yang, Z and Jiao, Y and Xie, C and Liu, J and Hu, Z and Xin, M and Yao, Y and Ni, Z and Sun, Q and Peng, H and Guo, W}, title = {Pangenome-based trajectories of intracellular gene transfers in Poaceae unveil high cumulation in Triticeae.}, journal = {Plant physiology}, volume = {193}, number = {1}, pages = {578-594}, pmid = {37249052}, issn = {1532-2548}, mesh = {*Poaceae/genetics ; Triticum/genetics ; Genome, Plant/genetics ; *Oryza/genetics ; Zea mays/genetics ; Evolution, Molecular ; }, abstract = {Intracellular gene transfers (IGTs) between the nucleus and organelles, including plastids and mitochondria, constantly reshape the nuclear genome during evolution. Despite the substantial contribution of IGTs to genome variation, the dynamic trajectories of IGTs at the pangenomic level remain elusive. Here, we developed an approach, IGTminer, that maps the evolutionary trajectories of IGTs using collinearity and gene reannotation across multiple genome assemblies. We applied IGTminer to create a nuclear organellar gene (NOG) map across 67 genomes covering 15 Poaceae species, including important crops. The resulting NOGs were verified by experiments and sequencing data sets. Our analysis revealed that most NOGs were recently transferred and lineage specific and that Triticeae species tended to have more NOGs than other Poaceae species. Wheat (Triticum aestivum) had a higher retention rate of NOGs than maize (Zea mays) and rice (Oryza sativa), and the retained NOGs were likely involved in photosynthesis and translation pathways. Large numbers of NOG clusters were aggregated in hexaploid wheat during 2 rounds of polyploidization, contributing to the genetic diversity among modern wheat accessions. We implemented an interactive web server to facilitate the exploration of NOGs in Poaceae. In summary, this study provides resources and insights into the roles of IGTs in shaping interspecies and intraspecies genome variation and driving plant genome evolution.}, }
@article {pmid37239904, year = {2023}, author = {Rossi, F and Picone, G and Cappadone, C and Sorrentino, A and Columbaro, M and Farruggia, G and Catelli, E and Sciutto, G and Prati, S and Oliete, R and Pasini, A and Pereiro, E and Iotti, S and Malucelli, E}, title = {Shedding Light on Osteosarcoma Cell Differentiation: Impact on Biomineralization and Mitochondria Morphology.}, journal = {International journal of molecular sciences}, volume = {24}, number = {10}, pages = {}, pmid = {37239904}, issn = {1422-0067}, mesh = {Humans ; Osteogenesis ; Biomineralization ; Cell Line, Tumor ; *Osteosarcoma/metabolism ; Cell Differentiation/physiology ; Mitochondria/metabolism ; *Bone Neoplasms/metabolism ; Cell Proliferation/physiology ; }, abstract = {Osteosarcoma (OS) is the most common primary malignant bone tumor and its etiology has recently been associated with osteogenic differentiation dysfunctions. OS cells keep a capacity for uncontrolled proliferation showing a phenotype similar to undifferentiated osteoprogenitors with abnormal biomineralization. Within this context, both conventional and X-ray synchrotron-based techniques have been exploited to deeply characterize the genesis and evolution of mineral depositions in a human OS cell line (SaOS-2) exposed to an osteogenic cocktail for 4 and 10 days. A partial restoration of the physiological biomineralization, culminating with the formation of hydroxyapatite, was observed at 10 days after treatment together with a mitochondria-driven mechanism for calcium transportation within the cell. Interestingly, during differentiation, mitochondria showed a change in morphology from elongated to rounded, indicating a metabolic reprogramming of OS cells possibly linked to an increase in glycolysis contribution to energy metabolism. These findings add a dowel to the genesis of OS giving new insights on the development of therapeutic strategies able to restore the physiological mineralization in OS cells.}, }
@article {pmid37239358, year = {2023}, author = {Ran, B and Zhu, W and Zhao, X and Li, L and Yi, Z and Li, M and Wang, T and Li, D}, title = {Studying Genetic Diversity and Relationships between Mountainous Meihua Chickens Using Mitochondrial DNA Control Region.}, journal = {Genes}, volume = {14}, number = {5}, pages = {}, pmid = {37239358}, issn = {2073-4425}, mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Chickens/genetics ; Genetic Variation/genetics ; Phylogeny ; Mitochondria/genetics ; }, abstract = {The Mountainous Meihua chicken is a unique regional germplasm resource from Tongjiang County, Bazhong City, China, but its genetic structure and evolutionary relationships with other native chicken breeds in the Sichuan region remain unclear. Here, we analyzed a total of 469 sequences, including 199 Mountainous Meihua chicken sequences generated in this study, together with 30 sequences representing 13 clades and 240 sequences from seven different Sichuan local chicken breeds downloaded from NCBI. These sequences were further used to analyze genetic diversity, patterns of population differentiation, and phylogenetic relationships between groups. We show that Mountainous Meihua chicken mtDNA sequences have high haplotypic and nucleotide diversity (0.876 and 0.012, respectively) and with a T bias that is suggestive of good breeding potential. Phylogenetic analysis showed that Mountainous Meihua chickens belong to clades A, B, E, and G and have a low affinity to other chicken breeds, with a moderate degree of differentiation. A non-significant Tajima's D indicates that no demographic expansions occurred in the past. Finally, the four maternal lineages identified in Mountainous Meihua chicken showed unique genetic characteristics.}, }
@article {pmid37239339, year = {2023}, author = {Wu, Z and Yang, T and Qin, R and Liu, H}, title = {Complete Mitogenome and Phylogenetic Analysis of the Carthamus tinctorius L.}, journal = {Genes}, volume = {14}, number = {5}, pages = {}, pmid = {37239339}, issn = {2073-4425}, mesh = {Phylogeny ; *Carthamus tinctorius/genetics ; *Genome, Mitochondrial/genetics ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Carthamus tinctorius L. 1753 (Asteraceae), also called safflower, is a cash crop with both edible and medical properties. We analyzed and reported the safflower mitogenome based on combined short and long reads obtained from Illumina and Pacbio platforms, respectively. This safflower mitogenome mainly contained two circular chromosomes, with a total length of 321,872 bp, and encoded 55 unique genes, including 34 protein-coding genes (PCGs), 3 rRNA genes, and 18 tRNA genes. The total length of repeat sequences greater than 30 bp was 24,953 bp, accounting for 7.75% of the whole mitogenome. Furthermore, we characterized the RNA editing sites of protein-coding genes located in the safflower mitogenome, and the total number of RNA editing sites was 504. Then, we revealed partial sequence transfer events between plastid and mitochondria, in which one plastid-derived gene (psaB) remained intact in the mitogenome. Despite extensive arrangement events among the three mitogenomes of C. tinctorius, Arctium lappa, and Saussurea costus, the constructed phylogenetic tree based on mitogenome PCGs showed that C. tinctorius has a closer relationship with three Cardueae species, A. lappa, A. tomentosum, and S. costus, which is similar to the phylogeny constructed from the PCGs of plastid genomes. This mitogenome not only enriches the genetic information of safflower but also will be useful in the phylogeny and evolution study of the Asteraceae.}, }
@article {pmid37231782, year = {2023}, author = {Shi, J and Yan, S and Li, W and Yang, X and Cui, Z and Li, J and Li, G and Li, Y and Hu, Y and Gao, S}, title = {PacBio full-length transcriptome analysis provides new insights into transcription of chloroplast genomes.}, journal = {RNA biology}, volume = {20}, number = {1}, pages = {248-256}, pmid = {37231782}, issn = {1555-8584}, mesh = {Animals ; *Genome, Chloroplast ; Gene Expression Profiling ; Molecular Sequence Annotation ; Transcriptome ; DNA, Mitochondrial/genetics ; Chloroplasts/genetics ; *Arabidopsis/genetics ; }, abstract = {Chloroplast and mitochondrial DNA (cpDNA and mtDNA) are apart from nuclear DNA (nuDNA) in a eukaryotic cell. The transcription system of chloroplasts differs from those of mitochondria and eukaryotes. In contrast to nuDNA and animal mtDNA, the transcription of cpDNA is still not well understood, primarily due to the unresolved identification of transcription initiation sites (TISs) and transcription termination sites (TTSs) on the genome scale. In the present study, we characterized the transcription of chloroplast (cp) genes with greater accuracy and comprehensive information using PacBio full-length transcriptome data from Arabidopsis thaliana. The major findings included the discovery of four types of artifacts, the validation and correction of cp gene annotations, the exact identification of TISs that start with G, and the discovery of polyA-like sites as TTSs. Notably, we proposed a new model to explain cp transcription initiation and termination at the whole-genome level. Four types of artifacts, degraded RNAs and splicing intermediates deserve the attention from researchers working with PacBio full-length transcriptome data, as these contaminant sequences can lead to incorrect downstream analysis. Cp transcription initiates at multiple promoters and terminates at polyA-like sites. Our study provides new insights into cp transcription and new clues to study the evolution of promoters, TISs, TTSs and polyA tails of eukaryotic genes.}, }
@article {pmid37221926, year = {2023}, author = {Dong, X and Zhang, H and Zhu, X and Wang, K and Xue, H and Ye, Z and Zheng, C and Bu, W}, title = {Mitochondrial introgression and mito-nuclear discordance obscured the closely related species boundaries in Cletus Stål from China (Heteroptera: Coreidae).}, journal = {Molecular phylogenetics and evolution}, volume = {184}, number = {}, pages = {107802}, doi = {10.1016/j.ympev.2023.107802}, pmid = {37221926}, issn = {1095-9513}, mesh = {Animals ; *Heteroptera ; Phylogeny ; China ; *Genome, Mitochondrial ; Mitochondria ; Mitomycin ; }, abstract = {Accurate taxonomy and delimitation are of great importance for pest control strategies and management programs. Here, we focus on Cletus (Insecta: Hemiptera: Coreidae), which includes many crop pests. The species boundaries still conflict and only cytochrome c oxidase subunit I (COI) barcoding has been previously used for molecular studies. We generated new mitochondrial genome and nuclear genome-wide SNPs to explore the species boundaries of 46 Cletus samples from China using multiple species delimitation approaches. All results recovered a monophyly with high support, except for two closely related species in clade I - C. punctiger and C. graminis. Mitochondrial data demonstrated admixture in clade I, while genome-wide SNPs unambiguously identified two separate species, which were confirmed by morphological classification. Inconsistent nuclear and mitochondrial data indicated mito-nuclear discordance. Mitochondrial introgression is the most likely explanation, and more extensive sampling and more comprehensive data are needed to ascertain a pattern. Accurate species delimitation will shed light on species status; thus, an accurate taxonomy is of particular concern, as there is a pressing need to implement precise control of agricultural pests and to perform further research on diversification.}, }
@article {pmid37221210, year = {2023}, author = {Paukszto, &#x141; and Górski, P and Krawczyk, K and Maździarz, M and Szczecińska, M and Ślipiko, M and Sawicki, J}, title = {The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8303}, pmid = {37221210}, issn = {2045-2322}, mesh = {*Hepatophyta ; *Genome, Mitochondrial ; Phylogeny ; Mitochondria ; *Genome, Plastid ; *Anemone ; }, abstract = {Organellar genomes of liverworts are considered as one of the most stable among plants, with rare events of gene loss and structural rearrangements. However, not all lineages of liverworts are equally explored in the field of organellar genomics, and subclass Pellidae is one of the less known. Hybrid assembly, using both short- and long-read technologies enabled the assembly of repeat-rich mitogenomes of Pellia and Apopellia revealing extraordinary reduction of length in the latter which impacts only intergenic spacers. The mitogenomes of Apopellia were revealed to be the smallest among all known liverworts-109 k bp, despite retaining all introns. The study also showed the loss of one tRNA gene in Apopellia mitogenome, although it had no impact on the codon usage pattern of mitochondrial protein coding genes. Moreover, it was revealed that Apopellia and Pellia differ in codon usage by plastome CDSs, despite identical tRNA gene content. Molecular identification of species is especially important where traditional taxonomic methods fail, especially within Pellidae where cryptic speciation is well recognized. The simple morphology of these species and a tendency towards environmental plasticity make them complicated in identification. Application of super-barcodes, based on complete mitochondrial or plastid genomes sequences enable identification of all cryptic lineages within Apopellia and Pellia genera, however in some particular cases, mitogenomes were more efficient in species delimitation than plastomes.}, }
@article {pmid37214873, year = {2023}, author = {Cronin, SJF and Yu, W and Hale, A and Licht-Mayer, S and Crabtree, MJ and Korecka, JA and Tretiakov, EO and Sealey-Cardona, M and Somlyay, M and Onji, M and An, M and Fox, JD and Turnes, BL and Gomez-Diaz, C and da Luz Scheffer, D and Cikes, D and Nagy, V and Weidinger, A and Wolf, A and Reither, H and Chabloz, A and Kavirayani, A and Rao, S and Andrews, N and Latremoliere, A and Costigan, M and Douglas, G and Freitas, FC and Pifl, C and Walz, R and Konrat, R and Mahad, DJ and Koslov, AV and Latini, A and Isacson, O and Harkany, T and Hallett, PJ and Bagby, S and Woolf, CJ and Channon, KM and Je, HS and Penninger, JM}, title = {Crucial neuroprotective roles of the metabolite BH4 in dopaminergic neurons.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37214873}, support = {DOC 33/FWF_/Austrian Science Fund FWF/Austria ; R01 NS112266/NS/NINDS NIH HHS/United States ; R35 NS105076/NS/NINDS NIH HHS/United States ; }, abstract = {Dopa-responsive dystonia (DRD) and Parkinson's disease (PD) are movement disorders caused by the dysfunction of nigrostriatal dopaminergic neurons. Identifying druggable pathways and biomarkers for guiding therapies is crucial due to the debilitating nature of these disorders. Recent genetic studies have identified variants of GTP cyclohydrolase-1 (GCH1), the rate-limiting enzyme in tetrahydrobiopterin (BH4) synthesis, as causative for these movement disorders. Here, we show that genetic and pharmacological inhibition of BH4 synthesis in mice and human midbrain-like organoids accurately recapitulates motor, behavioral and biochemical characteristics of these human diseases, with severity of the phenotype correlating with extent of BH4 deficiency. We also show that BH4 deficiency increases sensitivities to several PD-related stressors in mice and PD human cells, resulting in worse behavioral and physiological outcomes. Conversely, genetic and pharmacological augmentation of BH4 protects mice from genetically- and chemically induced PD-related stressors. Importantly, increasing BH4 levels also protects primary cells from PD-affected individuals and human midbrain-like organoids (hMLOs) from these stressors. Mechanistically, BH4 not only serves as an essential cofactor for dopamine synthesis, but also independently regulates tyrosine hydroxylase levels, protects against ferroptosis, scavenges mitochondrial ROS, maintains neuronal excitability and promotes mitochondrial ATP production, thereby enhancing mitochondrial fitness and cellular respiration in multiple preclinical PD animal models, human dopaminergic midbrain-like organoids and primary cells from PD-affected individuals. Our findings pinpoint the BH4 pathway as a key metabolic program at the intersection of multiple protective mechanisms for the health and function of midbrain dopaminergic neurons, identifying it as a potential therapeutic target for PD.}, }
@article {pmid37212044, year = {2023}, author = {Postel, Z and Sloan, DB and Gallina, S and Godé, C and Schmitt, E and Mangenot, S and Drouard, L and Varré, JS and Touzet, P}, title = {The decoupled evolution of the organellar genomes of Silene nutans leads to distinct roles in the speciation process.}, journal = {The New phytologist}, volume = {239}, number = {2}, pages = {766-777}, doi = {10.1111/nph.18966}, pmid = {37212044}, issn = {1469-8137}, mesh = {*Silene/genetics ; Plant Breeding ; Cell Nucleus/genetics ; Mitochondria/genetics ; *Genome, Mitochondrial/genetics ; Evolution, Molecular ; Phylogeny ; }, abstract = {There is growing evidence that cytonuclear incompatibilities (i.e. disruption of cytonuclear coadaptation) might contribute to the speciation process. In a former study, we described the possible involvement of plastid-nuclear incompatibilities in the reproductive isolation between four lineages of Silene nutans (Caryophyllaceae). Because organellar genomes are usually cotransmitted, we assessed whether the mitochondrial genome could also be involved in the speciation process, knowing that the gynodioecious breeding system of S. nutans is expected to impact the evolutionary dynamics of this genome. Using hybrid capture and high-throughput DNA sequencing, we analyzed diversity patterns in the genic content of the organellar genomes in the four S. nutans lineages. Contrary to the plastid genome, which exhibited a large number of fixed substitutions between lineages, extensive sharing of polymorphisms between lineages was found in the mitochondrial genome. In addition, numerous recombination-like events were detected in the mitochondrial genome, loosening the linkage disequilibrium between the organellar genomes and leading to decoupled evolution. These results suggest that gynodioecy shaped mitochondrial diversity through balancing selection, maintaining ancestral polymorphism and, thus, limiting the involvement of the mitochondrial genome in evolution of hybrid inviability between S. nutans lineages.}, }
@article {pmid37208299, year = {2023}, author = {Dapper, AL and Diegel, AE and Wade, MJ}, title = {Relative rates of evolution of male-beneficial nuclear compensatory mutations and male-harming Mother's Curse mitochondrial alleles.}, journal = {Evolution; international journal of organic evolution}, volume = {77}, number = {9}, pages = {1945-1955}, doi = {10.1093/evolut/qpad087}, pmid = {37208299}, issn = {1558-5646}, mesh = {Female ; Animals ; Male ; Humans ; *Mothers ; Alleles ; *Mitochondria/genetics ; Cell Nucleus/genetics ; Mutation ; }, abstract = {Mother's Curse alleles represent a significant source of potential male fitness defects. The maternal inheritance of mutations with the pattern of sex-specific fitness effects, s♀>0>s♂, allows Mother's Curse alleles to spread through a population even though they reduce male fitness. Although the mitochondrial genomes of animals contain only a handful of protein-coding genes, mutations in many of these genes have been shown to have a direct effect on male fertility. The evolutionary process of nuclear compensation is hypothesized to counteract the male-limited mitochondrial defects that spread via Mother's Curse. Here we use population genetic models to investigate the evolution of compensatory autosomal nuclear mutations that act to restore the loss of fitness caused by mitochondrial mutation pressures. We derive the rate of male fitness deterioration by Mother's Curse and the rate of restoration by nuclear compensatory evolution. We find that the rate of nuclear gene compensation is many times slower than that of its deterioration by cytoplasmic mutation pressure, resulting in a significant lag in the recovery of male fitness. Thus, the numbers of nuclear genes capable of restoring male mitochondrial fitness defects must be large in order to sustain male fitness in the face of mutation pressures.}, }
@article {pmid37199915, year = {2023}, author = {Begeman, A and Babaian, A and Lewis, SC}, title = {Metatranscriptomic analysis uncovers prevalent viral ORFs compatible with mitochondrial translation.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0100222}, pmid = {37199915}, issn = {2379-5077}, support = {R00 GM129456/GM/NIGMS NIH HHS/United States ; R35 GM147218/GM/NIGMS NIH HHS/United States ; T32 GM007232/GM/NIGMS NIH HHS/United States ; R00GM129456/NH/NIH HHS/United States ; }, mesh = {Open Reading Frames ; *RNA Viruses/genetics ; *Viruses/genetics ; Codon ; RNA-Dependent RNA Polymerase/genetics ; }, abstract = {RNA viruses are ubiquitous components of the global virosphere, yet relatively little is known about their genetic diversity or the cellular mechanisms by which they exploit the biology of their diverse eukaryotic hosts. A hallmark of (+)ssRNA (positive single-stranded RNA) viruses is the ability to remodel host endomembranes for their own replication. However, the subcellular interplay between RNA viruses and host organelles that harbor gene expression systems, such as mitochondria, is complex and poorly understood. Here we report the discovery of 763 new virus sequences belonging to the family Mitoviridae by metatranscriptomic analysis, the identification of previously uncharacterized mitovirus clades, and a putative new viral class. With this expanded understanding of the diversity of mitovirus and encoded RNA-dependent RNA polymerases (RdRps), we annotate mitovirus-specific protein motifs and identify hallmarks of mitochondrial translation, including mitochondrion-specific codons. This study expands the known diversity of mitochondrial viruses and provides additional evidence that they co-opt mitochondrial biology for their survival. IMPORTANCE Metatranscriptomic studies have rapidly expanded the cadre of known RNA viruses, yet our understanding of how these viruses navigate the cytoplasmic milieu of their hosts to survive remains poorly characterized. In this study, we identify and assemble 763 new viral sequences belonging to the Mitoviridae, a family of (+)ssRNA viruses thought to interact with and remodel host mitochondria. We exploit this genetic diversity to identify new clades of Mitoviridae, annotate clade-specific sequence motifs that distinguish the mitoviral RdRp, and reveal patterns of RdRp codon usage consistent with translation on host cell mitoribosomes. These results serve as a foundation for understanding how mitoviruses co-opt mitochondrial biology for their proliferation.}, }
@article {pmid37198654, year = {2023}, author = {Kienzle, L and Bettinazzi, S and Choquette, T and Brunet, M and Khorami, HH and Jacques, JF and Moreau, M and Roucou, X and Landry, CR and Angers, A and Breton, S}, title = {A small protein coded within the mitochondrial canonical gene nd4 regulates mitochondrial bioenergetics.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {111}, pmid = {37198654}, issn = {1741-7007}, mesh = {Humans ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; HeLa Cells ; Mitochondria/genetics ; Open Reading Frames ; Peptides ; *NADH Dehydrogenase/genetics ; }, abstract = {BACKGROUND: Mitochondria have a central role in cellular functions, aging, and in certain diseases. They possess their own genome, a vestige of their bacterial ancestor. Over the course of evolution, most of the genes of the ancestor have been lost or transferred to the nucleus. In humans, the mtDNA is a very small circular molecule with a functional repertoire limited to only 37 genes. Its extremely compact nature with genes arranged one after the other and separated by short non-coding regions suggests that there is little room for evolutionary novelties. This is radically different from bacterial genomes, which are also circular but much larger, and in which we can find genes inside other genes. These sequences, different from the reference coding sequences, are called alternatives open reading frames or altORFs, and they are involved in key biological functions. However, whether altORFs exist in mitochondrial protein-coding genes or elsewhere in the human mitogenome has not been fully addressed.<br><br>RESULTS: We found a downstream alternative ATG initiation codon in the&#x2009;+&#x2009;3 reading frame of the human mitochondrial nd4 gene. This newly characterized altORF encodes a 99-amino-acid-long polypeptide, MTALTND4, which is conserved in primates. Our custom antibody, but not the pre-immune serum, was able to immunoprecipitate MTALTND4 from HeLa cell lysates, confirming the existence of an endogenous MTALTND4 peptide. The protein is localized in mitochondria and cytoplasm and is also found in the plasma, and it impacts cell and mitochondrial physiology.<br><br>CONCLUSIONS: Many human mitochondrial translated ORFs might have so far gone unnoticed. By ignoring mtaltORFs, we have underestimated the coding potential of the mitogenome. Alternative mitochondrial peptides such as MTALTND4 may offer a new framework for the investigation of mitochondrial functions and diseases.}, }
@article {pmid37188954, year = {2023}, author = {Lee, SY and Cheah, JS and Zhao, B and Xu, C and Roh, H and Kim, CK and Cho, KF and Udeshi, ND and Carr, SA and Ting, AY}, title = {Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells.}, journal = {Nature methods}, volume = {20}, number = {6}, pages = {908-917}, pmid = {37188954}, issn = {1548-7105}, support = {R01 DK121409/DK/NIDDK NIH HHS/United States ; RC2 DK129964/DK/NIDDK NIH HHS/United States ; T32 GM007276/GM/NIGMS NIH HHS/United States ; }, mesh = {*Proteomics ; *Mitochondria ; Endoplasmic Reticulum ; Biotin ; }, abstract = {The incorporation of light-responsive domains into engineered proteins has enabled control of protein localization, interactions and function with light. We integrated optogenetic control into proximity labeling, a cornerstone technique for high-resolution proteomic mapping of organelles and interactomes in living cells. Through structure-guided screening and directed evolution, we installed the light-sensitive LOV domain into the proximity labeling enzyme TurboID to rapidly and reversibly control its labeling activity with low-power blue light. 'LOV-Turbo' works in multiple contexts and dramatically reduces background in biotin-rich environments such as neurons. We used LOV-Turbo for pulse-chase labeling to discover proteins that traffic between endoplasmic reticulum, nuclear and mitochondrial compartments under cellular stress. We also showed that instead of external light, LOV-Turbo can be activated by bioluminescence resonance energy transfer from luciferase, enabling interaction-dependent proximity labeling. Overall, LOV-Turbo increases the spatial and temporal precision of proximity labeling, expanding the scope of experimental questions that can be addressed with proximity labeling.}, }
@article {pmid37179826, year = {2023}, author = {Casanova, A and Wevers, A and Navarro-Ledesma, S and Pruimboom, L}, title = {Mitochondria: It is all about energy.}, journal = {Frontiers in physiology}, volume = {14}, number = {}, pages = {1114231}, pmid = {37179826}, issn = {1664-042X}, abstract = {Mitochondria play a key role in both health and disease. Their function is not limited to energy production but serves multiple mechanisms varying from iron and calcium homeostasis to the production of hormones and neurotransmitters, such as melatonin. They enable and influence communication at all physical levels through interaction with other organelles, the nucleus, and the outside environment. The literature suggests crosstalk mechanisms between mitochondria and circadian clocks, the gut microbiota, and the immune system. They might even be the hub supporting and integrating activity across all these domains. Hence, they might be the (missing) link in both health and disease. Mitochondrial dysfunction is related to metabolic syndrome, neuronal diseases, cancer, cardiovascular and infectious diseases, and inflammatory disorders. In this regard, diseases such as cancer, Alzheimer's, Parkinson's, amyotrophic lateral sclerosis (ALS), chronic fatigue syndrome (CFS), and chronic pain are discussed. This review focuses on understanding the mitochondrial mechanisms of action that allow for the maintenance of mitochondrial health and the pathways toward dysregulated mechanisms. Although mitochondria have allowed us to adapt to changes over the course of evolution, in turn, evolution has shaped mitochondria. Each evolution-based intervention influences mitochondria in its own way. The use of physiological stress triggers tolerance to the stressor, achieving adaptability and resistance. This review describes strategies that could recover mitochondrial functioning in multiple diseases, providing a comprehensive, root-cause-focused, integrative approach to recovering health and treating people suffering from chronic diseases.}, }
@article {pmid37175542, year = {2023}, author = {Ke, SJ and Liu, DK and Tu, XD and He, X and Zhang, MM and Zhu, MJ and Zhang, DY and Zhang, CL and Lan, SR and Liu, ZJ}, title = {Apostasia Mitochondrial Genome Analysis and Monocot Mitochondria Phylogenomics.}, journal = {International journal of molecular sciences}, volume = {24}, number = {9}, pages = {}, pmid = {37175542}, issn = {1422-0067}, support = {72202200205//Fujian Agriculture and Forestry University/ ; }, mesh = {Phylogeny ; *Genome, Mitochondrial ; Mitochondria/genetics ; RNA, Ribosomal/genetics ; *Orchidaceae/genetics ; }, abstract = {Apostasia shenzhenica belongs to the subfamily Apostasioideae and is a primitive group located at the base of the Orchidaceae phylogenetic tree. However, the A. shenzhenica mitochondrial genome (mitogenome) is still unexplored, and the phylogenetic relationships between monocots mitogenomes remain unexplored. In this study, we discussed the genetic diversity of A. shenzhenica and the phylogenetic relationships within its monocotyledon mitogenome. We sequenced and assembled the complete mitogenome of A. shenzhenica, resulting in a circular mitochondrial draft of 672,872 bp, with an average read coverage of 122× and a GC content of 44.4%. A. shenzhenica mitogenome contained 36 protein-coding genes, 16 tRNAs, two rRNAs, and two copies of nad4L. Repeat sequence analysis revealed a large number of medium and small repeats, accounting for 1.28% of the mitogenome sequence. Selection pressure analysis indicated high mitogenome conservation in related species. RNA editing identified 416 sites in the protein-coding region. Furthermore, we found 44 chloroplast genomic DNA fragments that were transferred from the chloroplast to the mitogenome of A. shenzhenica, with five plastid-derived genes remaining intact in the mitogenome. Finally, the phylogenetic analysis of the mitogenomes from A. shenzhenica and 28 other monocots showed that the evolution and classification of most monocots were well determined. These findings enrich the genetic resources of orchids and provide valuable information on the taxonomic classification and molecular evolution of monocots.}, }
@article {pmid37171259, year = {2023}, author = {Dowling, DK and Wolff, JN}, title = {Evolutionary genetics of the mitochondrial genome: insights from Drosophila.}, journal = {Genetics}, volume = {224}, number = {3}, pages = {}, pmid = {37171259}, issn = {1943-2631}, mesh = {Animals ; *Drosophila/genetics ; *Genome, Mitochondrial ; Eukaryota/genetics ; Mitochondria/genetics ; Oxidative Phosphorylation ; DNA, Mitochondrial ; }, abstract = {Mitochondria are key to energy conversion in virtually all eukaryotes. Intriguingly, despite billions of years of evolution inside the eukaryote, mitochondria have retained their own small set of genes involved in the regulation of oxidative phosphorylation (OXPHOS) and protein translation. Although there was a long-standing assumption that the genetic variation found within the mitochondria would be selectively neutral, research over the past 3 decades has challenged this assumption. This research has provided novel insight into the genetic and evolutionary forces that shape mitochondrial evolution and broader implications for evolutionary ecological processes. Many of the seminal studies in this field, from the inception of the research field to current studies, have been conducted using Drosophila flies, thus establishing the species as a model system for studies in mitochondrial evolutionary biology. In this review, we comprehensively review these studies, from those focusing on genetic processes shaping evolution within the mitochondrial genome, to those examining the evolutionary implications of interactions between genes spanning mitochondrial and nuclear genomes, and to those investigating the dynamics of mitochondrial heteroplasmy. We synthesize the contribution of these studies to shaping our understanding of the evolutionary and ecological implications of mitochondrial genetic variation.}, }
@article {pmid37166639, year = {2023}, author = {Maiti, P and Fontanesi, F}, title = {Metabolic Labeling of Mitochondrial Translation Products in Whole Cells and Isolated Organelles.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2661}, number = {}, pages = {193-215}, pmid = {37166639}, issn = {1940-6029}, mesh = {Animals ; *Protein Biosynthesis ; *Mitochondria/metabolism ; Methionine/metabolism ; Amino Acids/metabolism ; Mitochondrial Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Mammals/genetics ; }, abstract = {Mitochondria retain their own genome and translational apparatus that is highly specialized in the synthesis of a handful of proteins, essential components of the oxidative phosphorylation system. During evolution, the players and mechanisms involved in mitochondrial translation have acquired some unique features, which we have only partially disclosed. The study of the mitochondrial translation process has been historically hampered by the lack of an in vitro translational system and has largely relied on the analysis of the incorporation rate of radiolabeled amino acids into mitochondrial proteins in cellulo or in organello. In this chapter, we describe methods to monitor mitochondrial translation by labeling newly synthesized mitochondrial polypeptides with [S[35]]-methionine in either yeast or mammalian whole cells or isolated mitochondria.}, }
@article {pmid37166631, year = {2023}, author = {Chrzanowska-Lightowlers, ZM and Lightowlers, RN}, title = {Translation in Mitochondrial Ribosomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2661}, number = {}, pages = {53-72}, pmid = {37166631}, issn = {1940-6029}, support = {203105/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Mitochondrial Ribosomes/metabolism ; Cryoelectron Microscopy ; *Mitochondria/genetics/metabolism ; Protein Biosynthesis ; Oxidative Phosphorylation ; Mitochondrial Proteins/genetics/metabolism ; }, abstract = {Mitochondrial protein synthesis is essential for the life of aerobic eukaryotes. Without it, oxidative phosphorylation cannot be coupled. Evolution has shaped a battery of factors and machinery that are key to production of just a handful of critical proteins. In this general concept chapter, we attempt to briefly summarize our current knowledge of the overall process in mitochondria from a variety of species, breaking this down to the four parts of translation: initiation, elongation, termination, and recycling. Where appropriate, we highlight differences between species and emphasize gaps in our understanding. Excitingly, with the current revolution in cryoelectron microscopy and mitochondrial genome editing, it is highly likely that many of these gaps will be resolved in the near future. However, the absence of a faithful in vitro reconstituted system to study mitochondrial translation is still problematic.}, }
@article {pmid37166629, year = {2023}, author = {Agrawal, RK and Majumdar, S}, title = {Evolution: Mitochondrial Ribosomes Across Species.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2661}, number = {}, pages = {7-21}, pmid = {37166629}, issn = {1940-6029}, support = {R01 GM061576/GM/NIGMS NIH HHS/United States ; R01 GM139277/GM/NIGMS NIH HHS/United States ; R01 AI132422/AI/NIAID NIH HHS/United States ; R01 AI155473/AI/NIAID NIH HHS/United States ; }, mesh = {*Mitochondrial Ribosomes/metabolism ; *Mitochondria/genetics/metabolism ; Ribosomes/metabolism ; Eukaryota/genetics/metabolism ; Eukaryotic Cells/metabolism ; Mitochondrial Proteins/metabolism ; Cryoelectron Microscopy ; Ribosomal Proteins/metabolism ; }, abstract = {The ribosome is among the most complex and ancient cellular macromolecular assemblies that plays a central role in protein biosynthesis in all living cells. Its function of translation of genetic information encoded in messenger RNA into protein molecules also extends to subcellular compartments in eukaryotic cells such as apicoplasts, chloroplasts, and mitochondria. The origin of mitochondria is primarily attributed to an early endosymbiotic event between an alpha-proteobacterium and a primitive (archaeal) eukaryotic cell. The timeline of mitochondrial acquisition, the nature of the host, and their diversification have been studied in great detail and are continually being revised as more genomic and structural data emerge. Recent advancements in high-resolution cryo-EM structure determination have provided architectural details of mitochondrial ribosomes (mitoribosomes) from various species, revealing unprecedented diversifications among them. These structures provide novel insights into the evolution of mitoribosomal structure and function. Here, we present a brief overview of the existing mitoribosomal structures in the context of the eukaryotic evolution tree showing their diversification from their last common ancestor.}, }
@article {pmid37162347, year = {2023}, author = {Ezawa, T and Silvestri, A and Maruyama, H and Tawaraya, K and Suzuki, M and Duan, Y and Turina, M and Lanfranco, L}, title = {Structurally distinct mitoviruses: are they an ancestral lineage of the Mitoviridae exclusive to arbuscular mycorrhizal fungi (Glomeromycotina)?.}, journal = {mBio}, volume = {14}, number = {4}, pages = {e0024023}, pmid = {37162347}, issn = {2150-7511}, mesh = {*Mycorrhizae/genetics ; Symbiosis ; Phylogeny ; Ecosystem ; *Glomeromycota/genetics ; Plants/microbiology ; *RNA Viruses/genetics ; RNA-Dependent RNA Polymerase/genetics ; }, abstract = {Mitoviruses in the family Mitoviridae are the mitochondria-replicating "naked RNA viruses" with genomes encoding only the replicase RNA-dependent RNA polymerase (RdRp) and prevalent across fungi, plants, and invertebrates. Arbuscular mycorrhizal fungi in the subphylum Glomeromycotina are obligate plant symbionts that deliver water and nutrients to the host. We discovered distinct mitoviruses in glomeromycotinian fungi, namely "large duamitovirus," encoding unusually large RdRp with a unique N-terminal motif that is endogenized in some host genomes. More than 400 viral sequences similar to the large duamitoviruses are present in metatranscriptome databases. They are globally distributed in soil ecosystems, consistent with the cosmopolitan distribution of glomeromycotinian fungi, and formed the most basal clade of the Mitoviridae in phylogenetic analysis. Given that glomeromycotinian fungi are the only confirmed hosts of these viruses, we propose the hypothesis that large duamitoviruses are the most ancestral lineage of the Mitoviridae that have been maintained exclusively in glomeromycotinian fungi.}, }
@article {pmid37158879, year = {2023}, author = {Shamanskiy, V and Mikhailova, AA and Tretiakov, EO and Ushakova, K and Mikhailova, AG and Oreshkov, S and Knorre, DA and Ree, N and Overdevest, JB and Lukowski, SW and Gostimskaya, I and Yurov, V and Liou, CW and Lin, TK and Kunz, WS and Reymond, A and Mazunin, I and Bazykin, GA and Fellay, J and Tanaka, M and Khrapko, K and Gunbin, K and Popadin, K}, title = {Secondary structure of the human mitochondrial genome affects formation of deletions.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {103}, pmid = {37158879}, issn = {1741-7007}, support = {DOC 33/FWF_/Austrian Science Fund FWF/Austria ; UL1 TR001873/TR/NCATS NIH HHS/United States ; K23 DC019678/DC/NIDCD NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Genome, Mitochondrial ; Mitochondria ; DNA, Mitochondrial/genetics ; Genome, Human ; Protein Structure, Secondary ; DNA, Single-Stranded ; Mammals ; }, abstract = {BACKGROUND: Aging in postmitotic tissues is associated with clonal expansion of somatic mitochondrial deletions, the origin of which is not well understood. Such deletions are often flanked by direct nucleotide repeats, but this alone does not fully explain their distribution. Here, we hypothesized that the close proximity of direct repeats on single-stranded mitochondrial DNA (mtDNA) might play a role in the formation of deletions.<br><br>RESULTS: By analyzing human mtDNA deletions in the major arc of mtDNA, which is single-stranded during replication and is characterized by a high number of deletions, we found a non-uniform distribution with a "hot spot" where one deletion breakpoint occurred within the region of 6-9&#xa0;kb and another within 13-16&#xa0;kb of the mtDNA. This distribution was not explained by the presence of direct repeats, suggesting that other factors, such as the spatial proximity of these two regions, can be the cause. In silico analyses revealed that the single-stranded major arc may be organized as a large-scale hairpin-like loop with a center close to 11&#xa0;kb and contacting regions between 6-9&#xa0;kb and 13-16&#xa0;kb, which would explain the high deletion activity in this contact zone. The direct repeats located within the contact zone, such as the well-known common repeat with a first arm at 8470-8482&#xa0;bp (base pair) and a second arm at 13,447-13,459&#xa0;bp, are three times more likely to cause deletions compared to direct repeats located outside of the contact zone. A comparison of age- and disease-associated deletions demonstrated that the contact zone plays a crucial role in explaining the age-associated deletions, emphasizing its importance in the rate of healthy aging.<br><br>CONCLUSIONS: Overall, we provide topological insights into the mechanism of age-associated deletion formation in human mtDNA, which could be used to predict somatic deletion burden and maximum lifespan in different human haplogroups and mammalian species.}, }
@article {pmid37156858, year = {2023}, author = {Smirnova, J and Loerke, J and Kleinau, G and Schmidt, A and Bürger, J and Meyer, EH and Mielke, T and Scheerer, P and Bock, R and Spahn, CMT and Zoschke, R}, title = {Structure of the actively translating plant 80S ribosome at 2.2 Å resolution.}, journal = {Nature plants}, volume = {9}, number = {6}, pages = {987-1000}, pmid = {37156858}, issn = {2055-0278}, support = {416210002//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 221545957//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 394046635//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 421152132//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; ZO 302/5-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB-TRR 175 (A4)//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 956314//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {Cytosol ; *RNA, Ribosomal/chemistry ; Cryoelectron Microscopy ; Phylogeny ; Models, Molecular ; *Ribosomes/chemistry ; Plants/genetics ; Nicotiana/genetics ; }, abstract = {In plant cells, translation occurs in three compartments: the cytosol, the plastids and the mitochondria. While the structures of the (prokaryotic-type) ribosomes in plastids and mitochondria are well characterized, high-resolution structures of the eukaryotic 80S ribosomes in the cytosol have been lacking. Here the structure of translating tobacco (Nicotiana tabacum) 80S ribosomes was solved by cryo-electron microscopy with a global resolution of 2.2 Å. The ribosome structure includes two tRNAs, decoded mRNA and the nascent peptide chain, thus providing insights into the molecular underpinnings of the cytosolic translation process in plants. The map displays conserved and plant-specific rRNA modifications and the positions of numerous ionic cofactors, and it uncovers the role of monovalent ions in the decoding centre. The model of the plant 80S ribosome enables broad phylogenetic comparisons that reveal commonalities and differences in the ribosomes of plants and those of other eukaryotes, thus putting our knowledge about eukaryotic translation on a firmer footing.}, }
@article {pmid37153218, year = {2023}, author = {Xu, J and Li, B and Jiang, Z and Wang, W and Yang, Y and Yang, M and Ye, X}, title = {Genomic analyses provide insights into the genome evolution and environmental adaptation of the tobacco moth Ephestia elutella.}, journal = {Frontiers in physiology}, volume = {14}, number = {}, pages = {1187522}, pmid = {37153218}, issn = {1664-042X}, abstract = {Ephestia elutella is a major pest responsible for significant damage to stored tobacco over many years. Here, we conduct a comparative genomic analysis on this pest, aiming to explore the genetic bases of environmental adaptation of this species. We find gene families associated with nutrient metabolism, detoxification, antioxidant defense and gustatory receptors are expanded in the E. elutella genome. Detailed phylogenetic analysis of P450 genes further reveals obvious duplications in the CYP3 clan in E. elutella compared to the closely related species, the Indianmeal moth Plodia interpunctella. We also identify 229 rapidly evolving genes and 207 positively selected genes in E. elutella, respectively, and highlight two positively selected heat shock protein 40 (Hsp40) genes. In addition, we find a number of species-specific genes related to diverse biological processes, such as mitochondria biology and development. These findings advance our understanding of the mechanisms underlying processes of environmental adaptation on E. elutella and will enable the development of novel pest management strategies.}, }
@article {pmid37152468, year = {2023}, author = {Kannan, B and Arumugam, P}, title = {The implication of mitochondrial DNA mutation and dysfunction in periodontal diseases.}, journal = {Journal of Indian Society of Periodontology}, volume = {27}, number = {2}, pages = {126-130}, pmid = {37152468}, issn = {0972-124X}, abstract = {Periodontitis is a chronic oral inflammatory disease that is caused by dental plaque pathogens. Periodontal disease development and evolution are based on the host immune system, humoral and cellular immunity, the integrity of the tissues, and certain endocrine and nutritional factors. Mitochondria are significantly involved in periodontal infections and inflammation, which play a role in the inflammatory response in a variety of ways. In general, oxidative stress causes a stressful environment that subsequently leads to tissue damage and chronic inflammation. Several mutations and alterations in mitochondrial DNA lead the disease to an aggressive condition, by causing dysregulated mitochondrial function. Such mutations are significantly associated with various diseases. Numerous studies indicate chronic periodontitis patients have a decreased level of mitochondrial membrane potential, as well as adenosine triphosphate, and an increased level of reactive oxygen species production, which causes cell death in the periodontium and affects tissue growth. Further studies into the association between mitochondria and periodontitis might be helpful for the treatment and prevention of the diseases.}, }
@article {pmid37141262, year = {2023}, author = {Squires, TE and Rödin-Mörch, P and Formenti, G and Tracey, A and Abueg, L and Brajuka, N and Jarvis, E and Halapi, EC and Melsted, P and Höglund, J and Magnússon, KP}, title = {A chromosome-level genome assembly for the Rock Ptarmigan (Lagopus muta).}, journal = {G3 (Bethesda, Md.)}, volume = {13}, number = {7}, pages = {}, pmid = {37141262}, issn = {2160-1836}, mesh = {Animals ; Female ; *Quail ; *Galliformes/genetics ; Repetitive Sequences, Nucleic Acid ; Chromosomes/genetics ; Genome ; Phylogeny ; }, abstract = {The Rock Ptarmigan (Lagopus muta) is a cold-adapted, largely sedentary, game bird with a Holarctic distribution. The species represents an important example of an organism likely to be affected by ongoing climatic shifts across a disparate range. We provide here a high-quality reference genome and mitogenome for the Rock Ptarmigan assembled from PacBio HiFi and Hi-C sequencing of a female bird from Iceland. The total size of the genome is 1.03 Gb with a scaffold N50 of 71.23 Mb and a contig N50 of 17.91 Mb. The final scaffolds represent all 40 predicted chromosomes, and the mitochondria with a BUSCO score of 98.6%. Gene annotation resulted in 16,078 protein-coding genes out of a total 19,831 predicted (81.08% excluding pseudogenes). The genome included 21.07% repeat sequences, and the average length of genes, exons, and introns were 33605, 394, and 4265 bp, respectively. The availability of a new reference-quality genome will contribute to understanding the Rock Ptarmigan's unique evolutionary history, vulnerability to climate change, and demographic trajectories around the globe while serving as a benchmark for species in the family Phasianidae (order Galliformes).}, }
@article {pmid37127113, year = {2023}, author = {Hausdorf, B and Xu, J}, title = {Speciation of rock-dwelling snail species: Disjunct ranges and mosaic patterns reveal the importance of long-distance dispersal in Chilostoma (Cingulifera) in the European Southern Alps.}, journal = {Molecular phylogenetics and evolution}, volume = {184}, number = {}, pages = {107788}, doi = {10.1016/j.ympev.2023.107788}, pmid = {37127113}, issn = {1095-9513}, mesh = {Animals ; Phylogeny ; *Snails/genetics ; Europe ; *Mitochondria ; Genetic Variation ; }, abstract = {To better understand the origin of the high diversity and endemism in the Southern Alps of Europe, we investigated the phylogeny and population structure of the rock-dwelling snail group Chilostoma (Cingulifera) in the Southern Alps. We generated genomic ddRAD data and mitochondrial sequences of 104 Cingulifera specimens from 28 populations and 14 other Ariantinae. Until recently, about 30 Cingulifera taxa were classified as subspecies of a single polytypic species. The phylogenetic and population genetic analyses of the ddRAD data and mitochondrial sequences revealed that Cingulifera in the Southern Alps is differentiated into three species. Each of the three Chilostoma (Cingulifera) species occupies disjunct sub-areas, which are separated by areas occupied by other Chilostoma taxa. Neighbouring populations of different species show little or no admixture. Tests indicating that the genetic differentiation of the three Cingulifera taxa cannot be explained by isolation by distance confirmed their species status. The disjunct range patterns demonstrate the importance of stochastic events such as passive long-distance dispersal for the evolution of population structure and speciation in these snails, and of priority effects and ecological competition as important factors influencing species distributions.}, }
@article {pmid37126705, year = {2023}, author = {Espino-Sanchez, TJ and Wienkers, H and Marvin, RG and Nalder, SA and García-Guerrero, AE and VanNatta, PE and Jami-Alahmadi, Y and Mixon Blackwell, A and Whitby, FG and Wohlschlegel, JA and Kieber-Emmons, MT and Hill, CP and Sigala, PA}, title = {Direct tests of cytochrome c and c1 functions in the electron transport chain of malaria parasites.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {19}, pages = {e2301047120}, pmid = {37126705}, issn = {1091-6490}, support = {P30 GM133894/GM/NIGMS NIH HHS/United States ; T32 DK007115/DK/NIDDK NIH HHS/United States ; R25 HL108828/HL/NHLBI NIH HHS/United States ; R01 GM089778/GM/NIGMS NIH HHS/United States ; U54 DK110858/DK/NIDDK NIH HHS/United States ; R35 GM133764/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cytochromes c ; Electron Transport ; *Parasites ; *Antimalarials ; *Malaria, Falciparum ; Eukaryota ; Cytochromes c1 ; }, abstract = {The mitochondrial electron transport chain (ETC) of Plasmodium malaria parasites is a major antimalarial drug target, but critical cytochrome (cyt) functions remain unstudied and enigmatic. Parasites express two distinct cyt c homologs (c and c-2) with unusually sparse sequence identity and uncertain fitness contributions. P. falciparum cyt c-2 is the most divergent eukaryotic cyt c homolog currently known and has sequence features predicted to be incompatible with canonical ETC function. We tagged both cyt c homologs and the related cyt c1 for inducible knockdown. Translational repression of cyt c and cyt c1 was lethal to parasites, which died from ETC dysfunction and impaired ubiquinone recycling. In contrast, cyt c-2 knockdown or knockout had little impact on blood-stage growth, indicating that parasites rely fully on the more conserved cyt c for ETC function. Biochemical and structural studies revealed that both cyt c and c-2 are hemylated by holocytochrome c synthase, but UV-vis absorbance and EPR spectra strongly suggest that cyt c-2 has an unusually open active site in which heme is stably coordinated by only a single axial amino acid ligand and can bind exogenous small molecules. These studies provide a direct dissection of cytochrome functions in the ETC of malaria parasites and identify a highly divergent Plasmodium cytochrome c with molecular adaptations that defy a conserved role in eukaryotic evolution.}, }
@article {pmid37116483, year = {2023}, author = {George, EE and Barcytė, D and Lax, G and Livingston, S and Tashyreva, D and Husnik, F and Lukeš, J and Eliáš, M and Keeling, PJ}, title = {A single cryptomonad cell harbors a complex community of organelles, bacteria, a phage, and selfish elements.}, journal = {Current biology : CB}, volume = {33}, number = {10}, pages = {1982-1996.e4}, doi = {10.1016/j.cub.2023.04.010}, pmid = {37116483}, issn = {1879-0445}, mesh = {*Cryptophyta ; *Genome ; Eukaryota/genetics ; Cell Nucleus/genetics ; Plastids/genetics ; Bacteria/genetics ; Symbiosis/genetics ; Phylogeny ; }, abstract = {Symbiosis between prokaryotes and microbial eukaryotes (protists) has broadly impacted both evolution and ecology. Endosymbiosis led to mitochondria and plastids, the latter spreading across the tree of eukaryotes by subsequent rounds of endosymbiosis. Present-day endosymbionts in protists remain both common and diverse, although what function they serve is often unknown. Here, we describe a highly complex community of endosymbionts and a bacteriophage (phage) within a single cryptomonad cell. Cryptomonads are a model for organelle evolution because their secondary plastid retains a relict endosymbiont nucleus, but only one previously unidentified Cryptomonas strain (SAG 25.80) is known to harbor bacterial endosymbionts. We carried out electron microscopy and FISH imaging as well as genomic sequencing on Cryptomonas SAG 25.80, which revealed a stable, complex community even after over 50 years in continuous cultivation. We identified the host strain as Cryptomonas gyropyrenoidosa, and sequenced genomes from its mitochondria, plastid, and nucleomorph (and partially its nucleus), as well as two symbionts, Megaira polyxenophila and Grellia numerosa, and one phage (MAnkyphage) infecting M. polyxenophila. Comparing closely related endosymbionts from other hosts revealed similar metabolic and genomic features, with the exception of abundant transposons and genome plasticity in M. polyxenophila from Cryptomonas. We found an abundance of eukaryote-interacting genes as well as many toxin-antitoxin systems, including in the MAnkyphage genome that also encodes several eukaryotic-like proteins. Overall, the Cryptomonas cell is an endosymbiotic conglomeration with seven distinct evolving genomes that all show evidence of inter-lineage conflict but nevertheless remain stable, even after more than 4,000 generations in culture.}, }
@article {pmid37115919, year = {2023}, author = {Al Jewari, C and Baldauf, SL}, title = {An excavate root for the eukaryote tree of life.}, journal = {Science advances}, volume = {9}, number = {17}, pages = {eade4973}, pmid = {37115919}, issn = {2375-2548}, mesh = {*Eukaryota/genetics ; *Eukaryotic Cells ; Biological Evolution ; Phylogeny ; Evolution, Molecular ; }, abstract = {Much of the higher-order phylogeny of eukaryotes is well resolved, but the root remains elusive. We assembled a dataset of 183 eukaryotic proteins of archaeal ancestry to test this root. The resulting phylogeny identifies four lineages of eukaryotes currently classified as "Excavata" branching separately at the base of the tree. Thus, Parabasalia appear as the first major branch of eukaryotes followed sequentially by Fornicata, Preaxostyla, and Discoba. All four excavate branch points receive full statistical support from analyses with commonly used evolutionary models, a protein structure partition model that we introduce here, and various controls for deep phylogeny artifacts. The absence of aerobic mitochondria in Parabasalia, Fornicata, and Preaxostyla suggests that modern eukaryotes arose under anoxic conditions, probably much earlier than expected, and without the benefit of mitochondrial respiration.}, }
@article {pmid37113597, year = {2023}, author = {Mahati, K and Padmasree, K}, title = {Brassinolide promotes interaction between chloroplasts and mitochondria during the optimization of photosynthesis by the mitochondrial electron transport chain in mesophyll cell protoplasts of Arabidopsis thaliana.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1099474}, pmid = {37113597}, issn = {1664-462X}, abstract = {The current experimental data unveils the role of brassinolide (BL), a phytohormone of class brassinosteroids (BRs), in augmenting the cross-talk between the mitochondrial electron transport chain (mETC) and chloroplasts to strengthen the efficiency of the Calvin-Benson cycle (CBC) for higher assimilation of carbon dioxide in the mesophyll cell protoplasts (MCP) of Arabidopsis thaliana. The outcome of total respiration (TR) and photosynthetic carbon assimilation (PCA) was monitored as O2 uptake under dark and NaHCO3-dependent O2 evolution under light, respectively, after pre-incubation of MCP at a broad spectrum of BL concentration from 0.05 pM to 5 pM at 25 °C and optimum light intensity of 1000 μmol m[-2] s[-1]. The addition of optimal concentration (0.5 pM) of BL to MCP stimulated the (i) TR, (ii) PCA, and (iii) para-benzoquinone-dependent O2 evolution (PSII activity). Further, in response to BL, the enzyme activity or transcript levels of redox-regulated CBC enzymes and glucose-6-phosphate raised considerably. Also, the addition of BL to MCP remarkably accelerated the capacity of the cytochrome oxidase (COX) and alternative oxidase (AOX) pathways concurrently with an increase in total cellular pyruvate and reactive oxygen species (ROS) levels. Besides, malate valve components (Malate, Chl-MDH, M-MDH) increased in response to BL. At the same time, the cellular redox ratios of pyridine nucleotides (NADPH and NADH) were kept low in the presence of BL. However, BL could not keep up the CBC activity of photosynthesis along with its associated light-activated enzymes/transcripts when mETC through COX or AOX pathway is restricted by antimycin A (AA) or salicylhydroxamic acid (SHAM), respectively. In contrast, adding BL to MCP under restricted mETC showed aggravation in total cellular ROS, pyruvate, malate, and redox ratio of pyridine nucleotides with a concomitant increase in transcripts associated with malate valve and antioxidant systems. These results suggest that BL enhances the PCA by coordinating in cross-talk of chloroplasts and mitochondria to regulate the cellular redox ratio or ROS through the involvement of COX and AOX pathways along with the malate valve and antioxidant systems.}, }
@article {pmid37107622, year = {2023}, author = {Li, X and Zhe, M and Huang, Y and Fan, W and Yang, J and Zhu, A}, title = {The Evolution of Mitochondrial Genomes between Two Cymbidium Sister Species: Dozens of Circular Chromosomes and the Maintenance and Deterioration of Genome Synteny.}, journal = {Genes}, volume = {14}, number = {4}, pages = {}, pmid = {37107622}, issn = {2073-4425}, mesh = {*Genome, Mitochondrial/genetics ; Synteny ; Introns ; Chromosomes ; *Orchidaceae ; }, abstract = {Plant mitochondrial genomes (mitogenomes) exhibit fluid genome architectures, which could lead to the rapid erosion of genome synteny over a short evolutionary time scale. Among the species-rich orchid family, the leafy Cymbidium lancifolium and leafless Cymbidium macrorhizon are sister species with remarkable differences in morphology and nutritional physiology. Although our understanding of the evolution of mitochondria is incomplete, these sister taxa are ideal for examining this subject. In this study, the complete mitogenomes of C. lancifolium and C. macrorhizon, totaling 704,244 bp and 650,751 bp, respectively, were assembled. In the 2 mitogenomes, 38 protein-coding genes, 18 cis- and 6 trans-spliced introns, and approximately 611 Kb of homologous sequences are identical; overall, they have 99.4% genome-wide similarity. Slight variations in the mitogenomes of C. lancifolium and C. macrorhizon in repeat content (21.0 Kb and 21.6 Kb, respectively) and mitochondrial DNA of plastid origin (MIPT; 38.2 Kb and 37.5 Kb, respectively) were observed. The mitogenome architectures of C. lancifolium and C. macrorhizon are complex and comprise 23 and 22 mini-circular chromosomes, respectively. Pairwise comparisons indicate that the two mitogenomes are largely syntenic, and the disparity in chromosome numbers is likely due to repeat-mediated rearrangements among different chromosomes. Notably, approximately 93.2 Kb C. lancifolium mitochondrial sequences lack any homology in the C. macrorhizon mitogenome, indicating frequent DNA gains and losses, which accounts mainly for the size variation. Our findings provide unique insights into mitogenome evolution in leafy and leafless plants of sister species and shed light on mitogenome dynamics during the transition from mixotrophy to mycoheterotrophy.}, }
@article {pmid37107542, year = {2023}, author = {De, AK and Sawhney, S and Sunder, J and Muthiyan, R and Ponraj, P and Sujatha, T and Malakar, D and Mondal, S and Bera, AK and Kumar, A and Chakurkar, EB and Bhattacharya, D}, title = {Peeping into Mitochondrial Diversity of Andaman Goats: Unveils Possibility of Maritime Transport with Diversified Geographic Signaling.}, journal = {Genes}, volume = {14}, number = {4}, pages = {}, pmid = {37107542}, issn = {2073-4425}, mesh = {Animals ; Cattle ; Swine ; *Goats/genetics ; Phylogeny ; *DNA, Mitochondrial/genetics ; Sequence Analysis, DNA ; Mitochondria/genetics ; }, abstract = {Andaman and Nicobar Islands, a part of South-East Asia, is enriched with the presence of native breeds of livestock (cattle, pig, goat) and poultry. There are two native goat breeds, viz., Andaman local goat and Teressa goat in Andaman and Nicobar Islands. However, to date, the origin and genetic makeup of these two breeds have not been detailed. Therefore, the present study describes the genetic makeup of Andaman goats through analysis of mitochondrial D-loop sequence for sequence polymorphism, phylogeographical signaling and population expansion events. The genetic diversity of the Teressa goat was less compared to the Andaman local goat due to its sole presence on Teressa Island. Out of 38 well-defined haplotypes of Andaman goats, the majority of haplotypes belonged to haplogroup A followed by haplogroup B and haplogroup D. The result of mismatch distribution and neutrality tests indicated no population expansion event of haplogroup A and B. Finally, based on poor geographical signaling, we hypothesize that Andaman goats have been imported to these Islands either through multidirectional diffusion or unidirectional diffusion. We justify our hypothesis of multidirectional diffusion on the basis of observation of the haplotype and nucleotide diversity of Andaman goats. Simultaneously, the probability of unidirectional diffusion of goats in these islands from the Indian subcontinent in different spells of domestication events through maritime routes cannot be ignored.}, }
@article {pmid37100315, year = {2023}, author = {Françoso, E and Zuntini, AR and Ricardo, PC and Santos, PKF and de Souza Araujo, N and Silva, JPN and Gonçalves, LT and Brito, R and Gloag, R and Taylor, BA and Harpur, BA and Oldroyd, BP and Brown, MJF and Arias, MC}, title = {Rapid evolution, rearrangements and whole mitogenome duplication in the Australian stingless bees Tetragonula (Hymenoptera: Apidae): A steppingstone towards understanding mitochondrial function and evolution.}, journal = {International journal of biological macromolecules}, volume = {242}, number = {Pt 1}, pages = {124568}, doi = {10.1016/j.ijbiomac.2023.124568}, pmid = {37100315}, issn = {1879-0003}, mesh = {Animals ; Australia ; *Bees/genetics ; *Genome, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; }, abstract = {The extreme conservation of mitochondrial genomes in metazoans poses a significant challenge to understanding mitogenome evolution. However, the presence of variation in gene order or genome structure, found in a small number of taxa, can provide unique insights into this evolution. Previous work on two stingless bees in the genus Tetragonula (T. carbonaria and T. hockingsi) revealed highly divergent CO1 regions between them and when compared to the bees from the same tribe (Meliponini), indicating rapid evolution. Using mtDNA isolation and Illumina sequencing, we elucidated the mitogenomes of both species. In both species, there has been a duplication of the whole mitogenome to give a total genome size of 30,666 bp in T. carbonaria; and 30,662 bp in T. hockingsi. These duplicated genomes present a circular structure with two identical and mirrored copies of all 13 protein coding genes and 22 tRNAs, with the exception of a few tRNAs that are present as single copies. In addition, the mitogenomes are characterized by rearrangements of two block of genes. We believe that rapid evolution is present in the whole Indo-Malay/Australasian group of Meliponini but is extraordinarily elevated in T. carbonaria and T. hockingsi, probably due to founder effect, low effective population size and the mitogenome duplication. All these features - rapid evolution, rearrangements, and duplication - deviate significantly from the vast majority of the mitogenomes described so far, making the mitogenomes of Tetragonula unique opportunities to address fundamental questions of mitogenome function and evolution.}, }
@article {pmid37087094, year = {2023}, author = {Carella, F and De Vico, G}, title = {Pathology, epidemiology, and phylogeny of mussel egg disease due to the microsporidian Steinhausia mytilovum (Field, 1924) in the Mediterranean mussel (Mytilus galloprovincialis).}, journal = {Journal of invertebrate pathology}, volume = {198}, number = {}, pages = {107927}, doi = {10.1016/j.jip.2023.107927}, pmid = {37087094}, issn = {1096-0805}, mesh = {Female ; Animals ; *Mytilus/microbiology ; *Microsporidia/genetics ; Phylogeny ; Italy ; Seafood ; }, abstract = {Microsporidia are well known fungal pathogens of aquatic animals. However, the taxonomy of microsporidia is generally poorly resolved, which has consequently constrained our understanding of their pathology and epidemiology in marine animals. To date, microsporidia have been reported in both bivalves and gastropods, and microsporidia from mollusks have been classified in different genera. Despite ongoing work to better describe these genera, including detailed microscopic and ultrastructural images, so far we lack information on microsporidian phylogeny and pathogenicity of species within these genera. Here we investigate the microsporidian parasite Steinhausia mytilovum associated with the mussel, Mytilus galloprovincialis, in natural beds and farms along coast of southern Italy. A survey of M. galloprovincialis was conducted in 13 mussel farms and one natural bed between 2009 and 2020. We found the presence of S. mytilovum in 10 of the investigated farms, with a prevalence ranging between 14 and 100% of female mussels, depending on the population and season in which they were sampled. The parasite developed in the oocytes within a sporophorous vesicle (SV) where it produced 1-3 spores per cell, both in the cytoplasm and in the nucleus. Stenhausia mytilovum elicited an infiltrative (24.8%) or a strong capsular inflammatory response (43.4%) at gonadal follicles and surrounding vesicular connective tissue, in some cases accompanied by gonadal atresia (24.8%), leading to loss of gonadal architecture. In 7% of cases no reaction was observed. Ultrastructural observations revealed a mitochondrial re-organization to interact with all the phases of parasite development; the mitochondria were arranged outside the parasitophorous vesicle (PV) or directly interacting with the spore inside vesicle. There are five taxonomic clades of microsporidians as identified by SSU ribosomal gene sequence data. Maximum likelihood analysis assigned S. mytilovum within the Clade IV, defined as the Class Terresporidia, with closest genetic relationship (83.6% identity) to an undetermined invertebrate ovarian microsporidian. The constant presence, prevalence, and severity of S. mytilovum in coastline populations of M. galloprovincialis populations in southern Italy may indirectly reflect immunocompetence at both individual and population levels.}, }
@article {pmid37082671, year = {2023}, author = {Ibodeng, GO and Uche, IN and Mokua, R and Galo, M and Odigwe, B and Galeas, JN and Dasgupta, S}, title = {A snapshot of lung cancer: where are we now?-a narrative review.}, journal = {Annals of translational medicine}, volume = {11}, number = {6}, pages = {261}, pmid = {37082671}, issn = {2305-5839}, abstract = {BACKGROUND AND OBJECTIVE: The global impact of cancer and cancer-related deaths has been a huge challenge and continues to be a setback in the health sector and beyond even in recent times. Cancer is the second leading cause of death globally with lung cancer (LC) being the second most prevalent malignancy and the leading cause of mortality amongst cancers in men and women worldwide. LC still constitutes a major burden despite recent advances in diagnostic and treatment tools. In this article, we review the trends in LC with an emphasis on non-small cell LC. We aimed to identify nuclear and mitochondrial genetic alterations, microbiome dysbiosis, and their significance in non-small cell LC tumorigenesis as well as its relevance in the future management of LCs.<br><br>METHODS: We identified studies for this review by searching the PubMed, Cochrane, Education Resources Information Center (ERIC), and Surveillance, Epidemiology, and End Results (SEER) databases for English-Language articles published from January 1, 2000 through to July 30, 2022, using keywords: lung cancer, non-small cell lung cancer, early detection, treatment, mitochondria, microbiome and epigenetics.<br><br>KEY CONTENT AND FINDINGS: This review will highlight the genomic environment, mitochondrial and nuclear alterations that play a role in the etiopathogenesis of LC and its application in the progression as well as management of the disease. We also elaborate on current molecular tumor biomarkers and their therapeutic targets.<br><br>CONCLUSIONS: LC remains the leading cause of cancer-related deaths globally with poor prognosis despite available treatment options and even recent advances in both diagnostic tools and management guidelines. Human nuclear and mitochondrial alterations clearly play a role in tumorigenesis and progressive genomic evolution is crucial in the early carcinogenesis of LC which is strongly influenced by host immune surveillance. It is imperative that more research and clinical trials be undertaken to appreciate an in-depth understanding of LC from the molecular level to facilitate the discovery of more targeted therapy and overall better management of LC.}, }
@article {pmid37077029, year = {2023}, author = {Park, D and Yu, Y and Kim, JH and Lee, J and Park, J and Hong, K and Seo, JK and Lim, C and Min, KT}, title = {Suboptimal Mitochondrial Activity Facilitates Nuclear Heat Shock Responses for Proteostasis and Genome Stability.}, journal = {Molecules and cells}, volume = {46}, number = {6}, pages = {374-386}, pmid = {37077029}, issn = {0219-1032}, mesh = {Humans ; *Proteostasis ; Reactive Oxygen Species/metabolism ; *Heat-Shock Response/genetics ; HSP70 Heat-Shock Proteins/metabolism ; Mitochondria/metabolism ; Nuclear Proteins/metabolism ; Genomic Instability ; }, abstract = {Thermal stress induces dynamic changes in nuclear proteins and relevant physiology as a part of the heat shock response (HSR). However, how the nuclear HSR is fine-tuned for cellular homeostasis remains elusive. Here, we show that mitochondrial activity plays an important role in nuclear proteostasis and genome stability through two distinct HSR pathways. Mitochondrial ribosomal protein (MRP) depletion enhanced the nucleolar granule formation of HSP70 and ubiquitin during HSR while facilitating the recovery of damaged nuclear proteins and impaired nucleocytoplasmic transport. Treatment of the mitochondrial proton gradient uncoupler masked MRP-depletion effects, implicating oxidative phosphorylation in these nuclear HSRs. On the other hand, MRP depletion and a reactive oxygen species (ROS) scavenger non-additively decreased mitochondrial ROS generation during HSR, thereby protecting the nuclear genome from DNA damage. These results suggest that suboptimal mitochondrial activity sustains nuclear homeostasis under cellular stress, providing plausible evidence for optimal endosymbiotic evolution via mitochondria-to-nuclear communication.}, }
@article {pmid37074804, year = {2023}, author = {Mcguire, JA and Huang, X and Reilly, SB and Iskandar, DT and Wang-Claypool, CY and Werning, S and Chong, RA and Lawalata, SZS and Stubbs, AL and Frederick, JH and Brown, RM and Evans, BJ and Arifin, U and Riyanto, A and Hamidy, A and Arida, E and Koo, MS and Supriatna, J and Andayani, N and Hall, R}, title = {Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation.}, journal = {Systematic biology}, volume = {72}, number = {4}, pages = {885-911}, pmid = {37074804}, issn = {1076-836X}, support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Phylogeny ; Indonesia ; *Lizards/genetics ; Phylogeography ; Genetics, Population ; Genetic Speciation ; }, abstract = {The biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island's long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species-9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present. [Genomics; Indonesia; introgression; mitochondria; phylogenetics; phylogeography; population genetics; reptiles.].}, }
@article {pmid37072481, year = {2023}, author = {Christinaki, AC and Theelen, B and Zania, A and Coutinho, SDA and Cabañes, JF and Boekhout, T and Kouvelis, VN}, title = {Co-evolution of large inverted repeats and G-quadruplex DNA in fungal mitochondria may facilitate mitogenome stability: the case of Malassezia.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {6308}, pmid = {37072481}, issn = {2045-2322}, mesh = {Humans ; *Malassezia/genetics ; Phylogeny ; *Genome, Mitochondrial/genetics ; *G-Quadruplexes ; Mitochondria/genetics ; DNA ; }, abstract = {Mitogenomes are essential due to their contribution to cell respiration. Recently they have also been implicated in fungal pathogenicity mechanisms. Members of the basidiomycetous yeast genus Malassezia are an important fungal component of the human skin microbiome, linked to various skin diseases, bloodstream infections, and they are increasingly implicated in gut diseases and certain cancers. In this study, the comparative analysis of Malassezia mitogenomes contributed to phylogenetic tree construction for all species. The mitogenomes presented significant size and gene order diversity which correlates to their phylogeny. Most importantly, they showed the inclusion of large inverted repeats (LIRs) and G-quadruplex (G4) DNA elements, rendering Malassezia mitogenomes a valuable test case for elucidating the evolutionary mechanisms responsible for this genome diversity. Both LIRs and G4s coexist and convergently evolved to provide genome stability through recombination. This mechanism is common in chloroplasts but, hitherto, rarely found in mitogenomes.}, }
@article {pmid37071674, year = {2023}, author = {Libby, E and Kempes, CP and Okie, JG}, title = {Metabolic compatibility and the rarity of prokaryote endosymbioses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {17}, pages = {e2206527120}, pmid = {37071674}, issn = {1091-6490}, mesh = {Phylogeny ; *Symbiosis/genetics ; *Prokaryotic Cells/metabolism ; Eukaryota/genetics ; Eukaryotic Cells/metabolism ; Biological Evolution ; }, abstract = {The evolution of the mitochondria was a significant event that gave rise to the eukaryotic lineage and most large complex life. Central to the origins of the mitochondria was an endosymbiosis between prokaryotes. Yet, despite the potential benefits that can stem from a prokaryotic endosymbiosis, their modern occurrence is exceptionally rare. While many factors may contribute to their rarity, we lack methods for estimating the extent to which they constrain the appearance of a prokaryotic endosymbiosis. Here, we address this knowledge gap by examining the role of metabolic compatibility between a prokaryotic host and endosymbiont. We use genome-scale metabolic flux models from three different collections (AGORA, KBase, and CarveMe) to assess the viability, fitness, and evolvability of potential prokaryotic endosymbioses. We find that while more than half of host-endosymbiont pairings are metabolically viable, the resulting endosymbioses have reduced growth rates compared to their ancestral metabolisms and are unlikely to gain mutations to overcome these fitness differences. In spite of these challenges, we do find that they may be more robust in the face of environmental perturbations at least in comparison with the ancestral host metabolism lineages. Our results provide a critical set of null models and expectations for understanding the forces that shape the structure of prokaryotic life.}, }
@article {pmid37070190, year = {2023}, author = {Schönherr, S and Weissensteiner, H and Kronenberg, F and Forer, L}, title = {Haplogrep 3 - an interactive haplogroup classification and analysis platform.}, journal = {Nucleic acids research}, volume = {51}, number = {W1}, pages = {W263-W268}, pmid = {37070190}, issn = {1362-4962}, mesh = {Humans ; Phylogeny ; *Software ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Biological Evolution ; }, abstract = {Over the last decade, Haplogrep has become a standard tool for haplogroup classification in the field of human mitochondrial DNA and is widely used by medical, forensic, and evolutionary researchers. Haplogrep scales well for thousands of samples, supports many file formats and provides an intuitive graphical web interface. Nevertheless, the currently available version has limitations when applying it to large biobank-scale data. In this paper, we present a major upgrade to the software by adding (a) haplogroup summary statistics and variant annotations from various publicly available genome databases, (b) an interface to connect new phylogenetic trees, (c) a new state-of-the-art web framework managing large scale data, (d) algorithmic adaptions to improve FASTA classification using BWA-specific alignment rules and (e) a pre-classification quality control step for VCF samples. These improvements will give researchers the opportunity to classify thousands of samples as usual but providing additional ways to investigate the dataset directly in the browser. The web service and its documentation can be accessed freely without any registration at https://haplogrep.i-med.ac.at.}, }
@article {pmid37063179, year = {2023}, author = {Tyszka, AS and Bretz, EC and Robertson, HM and Woodcock-Girard, MD and Ramanauskas, K and Larson, DA and Stull, GW and Walker, JF}, title = {Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1125107}, pmid = {37063179}, issn = {1664-462X}, abstract = {Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring the phylogenetic relationships among land plants. The organelles are predominantly inherited from the same parent, and therefore should exhibit phylogenetic concordance. In this study, we examine the mitochondrion and chloroplast genomes of 226 land plants to infer the degree of similarity between the organelles' evolutionary histories. Our results show largely concordant topologies are inferred between the organelles, aside from four well-supported conflicting relationships that warrant further investigation. Despite broad patterns of topological concordance, our findings suggest that the chloroplast and mitochondrial genomes evolved with significant differences in molecular evolution. The differences result in the genes from the chloroplast and the mitochondrion preferentially clustering with other genes from their respective organelles by a program that automates selection of evolutionary model partitions for sequence alignments. Further investigation showed that changes in compositional heterogeneity are not always uniform across divergences in the land plant tree of life. These results indicate that although the chloroplast and mitochondrial genomes have coexisted for over 1 billion years, phylogenetically, they are still evolving sufficiently independently to warrant separate models of evolution. As genome sequencing becomes more accessible, research into these organelles' evolution will continue revealing insight into the ancient cellular events that shaped not only their history, but the history of plants as a whole.}, }
@article {pmid37045318, year = {2022}, author = {Hasan, ME and Hasan, A and Béarez, P and Shen, KN and Chang, CW and Tran, TTV and Golani, D and Al-Saboonchi, A and Siddiqui, PJA and Durand, JD}, title = {Planiliza lauvergnii (Eydoux &amp; Souleyet, 1850), a senior synonym of Planiliza affinis (Günther, 1861) with a re-evaluation of keeled back mullets&amp;nbsp;(Mugiliformes: Mugilidae).}, journal = {Zootaxa}, volume = {5194}, number = {4}, pages = {497-518}, doi = {10.11646/zootaxa.5194.4.2}, pmid = {37045318}, issn = {1175-5334}, mesh = {Animals ; *Smegmamorpha ; Phylogeny ; Fishes/genetics ; Biological Evolution ; Mitochondria ; }, abstract = {The taxonomic status of the keeled back mullets (Teleostei: Mugilidae) has been reinvestigated. Two nominal mugilid species having keeled backs from East Asia: Mugil lauvergnii Eydoux &amp; Souleyet, 1850 and Mugil affinis Günther, 1861 have been re-evaluated through examination of the holotypes and fresh specimens. Comparison of morpho-meristic characters of the holotypes shows that both species are identical. Phylogenetic analysis based on mitochondrial cytochrome c oxidase 1 (CO1) confirmed morphological data by highlighting presence of a single clade from East Asia. Mugil lauvergnii (=Planiliza lauvergnii) is thus the sole keeled back mullet from East Asia and a senior synonym of Mugil affinis (=Planiliza affinis). The taxonomic status of two other keeled back mullets, Planiliza carinata and P. klunzingeri, is also contentious due to their similar morphology. Meristic and morphometric variation as well as sequence divergence between the two species are limited but phylogenetic analyses delineate well-supported clades consistent with biogeography and currently accepted taxonomy. Planiliza carinata and P. klunzingeri share a recent common ancestor in a Maximum Likelihood tree, with separate distribution ranges while P. lauvergnii formed a paraphyletic lineage. Based on present findings, we suggest maintenance of the taxonomic distinction of P. klunzingeri and P. carinata and discuss its evolutionary significance.}, }
@article {pmid37045317, year = {2022}, author = {Opler, PA and Stout, TL and Back, W and Zhang, J and Cong, Q and Shen, J and Grishin, NV}, title = {DNA barcodes reveal different speciation scenarios in the four North American Anthocharis Boisduval, Rambur, [Duménil] &amp; Graslin, [1833] (Lepidoptera: Pieridae: Pierinae: Anthocharidini) species groups.}, journal = {Zootaxa}, volume = {5194}, number = {4}, pages = {519-539}, doi = {10.11646/zootaxa.5194.4.3}, pmid = {37045317}, issn = {1175-5334}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; *Butterflies/genetics ; DNA, Mitochondrial/genetics ; Mitochondria ; Phylogeny ; }, abstract = {The mitochondrial DNA COI barcode segment sequenced from American Anthocharis specimens across their distribution ranges partitions them into four well-separated species groups and reveals different levels of differentiation within these groups. The lanceolata group experienced the deepest divergence. About 2.7% barcode difference separates the two species: A. lanceolata Lucas, 1852 including A. lanceolata australis (F. Grinnell, 1908), from A. desertolimbus J. Emmel, T. Emmel &amp; Mattoon, 1998. The sara group consists of three species distinctly defined by more than 2% sequence divergence: A. sara Lucas, 1852, A. julia W. H. Edwards, 1872, and A. thoosa (Scudder, 1878). Our treatment is fully consistent with morphological evidence largely based on the characters of fifth instar larvae and pupal cone curvature (Stout, 2005, 2018). In barcodes, it is not possible to see evidence of introgression or hybridization between the three species, and identification by morphology of immature stages always agrees with DNA barcode identification. Interestingly, A. thoosa exhibited the largest intraspecific divergence in DNA barcodes, and several of its metapopulations are identifiable by haplotypes. The cethura group is characterized by the smallest divergence and is best considered as a single species variable in expression of yellow coloration: A cethura C. Felder &amp; R. Felder, 1865. Notably, the most sexually dimorphic subspecies A. cethura morrisoni W. H. Edwards, 1881 is the most distinct by the barcodes. Finally, the midea group barcodes do not always separate A. midea (Hübner, [1809]) and A. limonea (A. Butler, 1871) and we observe gradual accumulation of differences from north (northeastern USA) to south (Hidalgo, Mexico). This barcode gradient suggests a recent origin of the two midea group species and provides another example of vicariant sister species well defined by morphology, ecology and geography, but not necessarily by DNA barcodes.}, }
@article {pmid37044183, year = {2023}, author = {Chen, H and Huang, L and Yu, J and Miao, Y and Liu, C}, title = {Mitochondrial genome of Artemisia argyi L. suggested conserved mitochondrial protein-coding genes among genera Artemisia, Tanacetum and Chrysanthemum.}, journal = {Gene}, volume = {871}, number = {}, pages = {147427}, doi = {10.1016/j.gene.2023.147427}, pmid = {37044183}, issn = {1879-0038}, mesh = {Humans ; *Genome, Mitochondrial ; *Artemisia/genetics ; *Tanacetum/genetics ; *Chrysanthemum/genetics ; Phylogeny ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; }, abstract = {BACKGROUND: Artemisia argyi L., also known as mugwort, is a perennial herb whose leaves are commonly used as a source of traditional medicines. However, the evolution and structure of the mitochondrial genome (mitogenome) in A. argyi remain unclear. In this study, the mitogenome of A. argyi was assembled and characterized for the first time.<br><br>RESULTS: The mitogenome of A. argyi was a circular molecule of 229,354&#xa0;bp. It encodes 56 genes, including 33 protein-coding genes (PCGs), 20 tRNA genes, and three rRNA genes, and three pseudogenes. Five trans-spliced introns were observed in three PCGs namely, nad1, nad2 and nad5. Repeat analysis identified 65 SSRs, 14 tandem repeats, and 167 dispersed repeats. The A. argyi mitogenome contains 12 plastid transfer sequences from 79&#xa0;bp to 2552&#xa0;bp. Five conserved MTPTs were identified in all 18 Asteraceae species. Comparison of mitogenome between A. argyi and one Artemisia specie and two Chrysanthemum species showed 14 conserved gene clusters. Phylogenetic analysis with organelle genomes of A. argyi and 18 other Anthemideae plants showed inconsistent phylogenetic trees, which implied that the evolutionary rates of PCGs and rrna genes derived from mitochondrion and plastid were incongruent. The Ka/Ks ratio of the 27 shared protein-coding genes in the 18 Anthemideae species are all less than 1 indicating that these genes were under the effect of purifying selection. Lastly, a total of 568 RNA editing sites in PCGs were further identified. The average editing frequency of non-synonymous changes was significantly higher than that of synonymous changes (one-sample Student's t-test, p-values&#xa0;&#x2264;&#xa0;0.05) in three tissues (root, leaf and stem).<br><br>CONCLUSIONS: In this study, the gene content, genome size, genome comparison, mitochondrial plastid sequences, dN/dS analysis of mitochondrial protein-coding genes, and RNA-editing events in A. argyi mitogenome were determined, providing insights into the phylogenetic relationships of Asteraceae plant.}, }
@article {pmid37042115, year = {2023}, author = {Metcalfe, NB and Bellman, J and Bize, P and Blier, PU and Crespel, A and Dawson, NJ and Dunn, RE and Halsey, LG and Hood, WR and Hopkins, M and Killen, SS and McLennan, D and Nadler, LE and Nati, JJH and Noakes, MJ and Norin, T and Ozanne, SE and Peaker, M and Pettersen, AK and Przybylska-Piech, A and Rathery, A and Récapet, C and Rodríguez, E and Salin, K and Stier, A and Thoral, E and Westerterp, KR and Westerterp-Plantenga, MS and Wojciechowski, MS and Monaghan, P}, title = {Solving the conundrum of intra-specific variation in metabolic rate: A multidisciplinary conceptual and methodological toolkit: New technical developments are opening the door to an understanding of why metabolic rate varies among individual animals of a species: New technical developments are opening the door to an understanding of why metabolic rate varies among individual animals of a species.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {6}, pages = {e2300026}, doi = {10.1002/bies.202300026}, pmid = {37042115}, issn = {1521-1878}, support = {MC_UU_00014/4/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Humans ; *Basal Metabolism ; Phenotype ; }, abstract = {Researchers from diverse disciplines, including organismal and cellular physiology, sports science, human nutrition, evolution and ecology, have sought to understand the causes and consequences of the surprising variation in metabolic rate found among and within individual animals of the same species. Research in this area has been hampered by differences in approach, terminology and methodology, and the context in which measurements are made. Recent advances provide important opportunities to identify and address the key questions in the field. By bringing together researchers from different areas of biology and biomedicine, we describe and evaluate these developments and the insights they could yield, highlighting the need for more standardisation across disciplines. We conclude with a list of important questions that can now be addressed by developing a common conceptual and methodological toolkit for studies on metabolic variation in animals.}, }
@article {pmid37039888, year = {2023}, author = {Zuccoli, GS and Nascimento, JM and Moraes-Vieira, PM and Rehen, SK and Martins-de-Souza, D}, title = {Mitochondrial, cell cycle control and neuritogenesis alterations in an iPSC-based neurodevelopmental model for schizophrenia.}, journal = {European archives of psychiatry and clinical neuroscience}, volume = {273}, number = {8}, pages = {1649-1664}, pmid = {37039888}, issn = {1433-8491}, support = {2016/04912-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2018/14666-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2014/21035-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2015/15626-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/25588-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2019/00098-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2018/01410-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Adult ; Humans ; *Schizophrenia/metabolism ; *Induced Pluripotent Stem Cells/metabolism ; Cell Differentiation/genetics ; Reactive Oxygen Species/metabolism ; Proteomics ; Cell Cycle Checkpoints ; Mitochondria/metabolism ; }, abstract = {Schizophrenia is a severe psychiatric disorder of neurodevelopmental origin that affects around 1% of the world's population. Proteomic studies and other approaches have provided evidence of compromised cellular processes in the disorder, including mitochondrial function. Most of the studies so far have been conducted on postmortem brain tissue from patients, and therefore, do not allow the evaluation of the neurodevelopmental aspect of the disorder. To circumvent that, we studied the mitochondrial and nuclear proteomes of neural stem cells (NSCs) and neurons derived from induced pluripotent stem cells (iPSCs) from schizophrenia patients versus healthy controls to assess possible alterations related to energy metabolism and mitochondrial function during neurodevelopment in the disorder. Our results revealed differentially expressed proteins in pathways related to mitochondrial function, cell cycle control, DNA repair and neuritogenesis and their possible implication in key process of neurodevelopment, such as neuronal differentiation and axonal guidance signaling. Moreover, functional analysis of NSCs revealed alterations in mitochondrial oxygen consumption in schizophrenia-derived cells and a tendency of higher levels of intracellular reactive oxygen species (ROS). Hence, this study shows evidence that alterations in important cellular processes are present during neurodevelopment and could be involved with the establishment of schizophrenia, as well as the phenotypic traits observed in adult patients. Neural stem cells (NSCs) and neurons were derived from induced pluripotent stem cells (iPSCs) from schizophrenia patients and controls. Proteomic analyses were performed on the enriched mitochondrial and nuclear fractions of NSCs and neurons. Whole-cell proteomic analysis was also performed in neurons. Our results revealed alteration in proteins related to mitochondrial function, cell cycle control, among others. We also performed energy pathway analysis and reactive oxygen species (ROS) analysis of NSCs, which revealed alterations in mitochondrial oxygen consumption and a tendency of higher levels of intracellular ROS in schizophrenia-derived cells.}, }
@article {pmid37029959, year = {2023}, author = {Galindo, LJ and Prokina, K and Torruella, G and López-García, P and Moreira, D}, title = {Maturases and Group II Introns in the Mitochondrial Genomes of the Deepest Jakobid Branch.}, journal = {Genome biology and evolution}, volume = {15}, number = {4}, pages = {}, pmid = {37029959}, issn = {1759-6653}, mesh = {Humans ; Introns ; Phylogeny ; *Genome, Mitochondrial ; Eukaryota/genetics ; Eukaryotic Cells ; }, abstract = {Ophirinina is a recently described suborder of jakobid protists (Excavata) with only one described species to date, Ophirina amphinema. Despite the acquisition and analysis of massive transcriptomic and mitogenomic sequence data from O. amphinema, its phylogenetic position among excavates remained inconclusive, branching as sister group either to all Jakobida or to all Discoba. From a morphological perspective, it has not only several typical jakobid features but also unusual traits for this group, including the morphology of mitochondrial cristae (sac-shaped to flattened-curved cristae) and the presence of two flagellar vanes. In this study, we have isolated, morphologically characterized, and sequenced genome and transcriptome data of two new Ophirinina species: Ophirina chinija sp. nov. and Agogonia voluta gen. et sp. nov. Ophirina chinija differs from O. amphinema in having rounded cell ends, subapically emerging flagella and a posterior cell protrusion. The much more distantly related A. voluta has several unique ultrastructural characteristics, including sac-shaped mitochondrial cristae and a complex "B" fiber. Phylogenomic analyses with a large conserved-marker dataset supported the monophyly of Ophirina and Agogonia within the Ophirinina and, more importantly, resolved the conflicting position of ophirinids as the sister clade to all other jakobids. The characterization of the mitochondrial genomes showed that Agogonia differs from all known gene-rich jakobid mitogenomes by the presence of two group II introns and their corresponding maturase protein genes. A phylogenetic analysis of the diversity of known maturases confirmed that the Agogonia proteins are highly divergent from each other and define distant families among the prokaryotic and eukaryotic maturases. This opens the intriguing possibility that, compared to other jakobids, Ophirinina may have retained additional mitochondrial elements that may help to understand the early diversification of eukaryotes and the evolution of mitochondria.}, }
@article {pmid37023388, year = {2023}, author = {Danial, JSH and Jenner, A and Garcia-Saez, AJ and Cosentino, K}, title = {Real-Time Growth Kinetics Analysis of Macromolecular Assemblies in Cells with Single Molecule Resolution.}, journal = {The journal of physical chemistry. A}, volume = {127}, number = {15}, pages = {3490-3496}, doi = {10.1021/acs.jpca.3c00368}, pmid = {37023388}, issn = {1520-5215}, mesh = {Kinetics ; *Software ; }, abstract = {Single molecule fluorescence microscopy has the unique advantage to provide real-time information on the spatiotemporal assembly of individual protein complexes in cellular membranes. This includes the assembly of proteins into oligomer species of numerous copy numbers. However, there is a need for improved tracing analysis of the real-time growth kinetics of these assemblies in cells with single molecule resolution. Here, we present an automated analysis software to accurately measure the real-time kinetics of assembly of individual high-order oligomer complexes. Our software comes with a simple Graphical User Interface (GUI), is available as a source code and an executable, and can analyze a full data set of several hundred to thousand molecules in less than 2 minutes. Importantly, this software is suitable for the analysis of intracellular protein oligomers, whose stoichiometry is usually more difficult to quantify due to variability in signal detection in the different areas of the cell. We validated our method with simulated ground-truth data and time-lapse images of diffraction-limited oligomeric assemblies of BAX and BAK proteins on mitochondria of cells undergoing apoptosis. Our approach provides the broad community of biologists with a fast, user-friendly tool to trace the compositional evolution of macromolecular assemblies, and potentially model their growth for a deeper understanding of the structural and biophysical mechanisms underlying their functions.}, }
@article {pmid37021319, year = {2023}, author = {Grosser, MR and Sites, SK and Murata, MM and Lopez, Y and Chamusco, KC and Love Harriage, K and Grosser, JW and Graham, JH and Gmitter, FG and Chase, CD}, title = {Plant mitochondrial introns as genetic markers - conservation and variation.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1116851}, pmid = {37021319}, issn = {1664-462X}, abstract = {Plant genomes are comprised of nuclear, plastid and mitochondrial components characterized by different patterns of inheritance and evolution. Genetic markers from the three genomes provide complementary tools for investigations of inheritance, genetic relationships and phenotypic contributions. Plant mitochondrial genomes are challenging for universal marker development because they are highly variable in terms of size, gene order and intergenic sequences and highly conserved with respect to protein-coding sequences. PCR amplification of introns with primers that anneal to conserved, flanking exons is effective for the development of polymorphic nuclear genome markers. The potential for plant mitochondrial intron polymorphisms to distinguish between congeneric species or intraspecific varieties has not been systematically investigated and is possibly constrained by requirements for intron secondary structure and interactions with co-evolved organelle intron splicing factors. To explore the potential for broadly applicable plant mitochondrial intron markers, PCR primer sets based upon conserved sequences flanking 11 introns common to seven angiosperm species were tested across a range of plant orders. PCR-amplified introns were screened for indel polymorphisms among a group of cross-compatible Citrus species and relatives; two Raphanus sativus mitotypes; representatives of the two Phaseolus vulgaris gene pools; and congeneric pairs of Cynodon, Cenchrus, Solanum, and Vaccinium species. All introns were successfully amplified from each plant entry. Length polymorphisms distinguishable by gel electrophoresis were common among genera but infrequent within genera. Sequencing of three introns amplified from 16 entries identified additional short indel polymorphisms and nucleotide substitutions that separated Citrus, Cynodon, Cenchrus and Vaccinium congeners, but failed to distinguish Solanum congeners or representatives of the Phaseolus vulgaris major gene pools. The ability of primer sets to amplify a wider range of plant species' introns and the presence of intron polymorphisms that distinguish congeners was confirmed by in silico analysis. While mitochondrial intron variation is limited in comparison to nuclear introns, these exon-based primer sets provide robust tools for the amplification of mitochondrial introns across a wide range of plant species wherein useful polymorphisms can be identified.}, }
@article {pmid37017198, year = {2023}, author = {Parida, M and Gouda, G and Chidambaranathan, P and Umakanta, N and Katara, JL and Sai, CB and Samantaray, S and Patra, BC and Mohapatra, T}, title = {Mitochondrial markers differentiate two distinct phylogenetic groups in indigenous rice landraces of northeast India: an evolutionary insight.}, journal = {Journal of genetics}, volume = {102}, number = {}, pages = {}, pmid = {37017198}, issn = {0973-7731}, mesh = {Phylogeny ; *Oryza/genetics ; India ; }, abstract = {The inheritance of the mitochondria genome and its diversity is unique for genetic and evolutionary studies relative to nuclear genomes. Northeast India and Himalayan regions are considered as one of the centres of indica rice origin. Also, rice diversity in northeast India is very distinct and highly suited for evolutionary studies. Although reports are available on the genetic diversity of indigenous northeast rice landraces, its relationship with the wild relatives is not yet properly explored and understood. In an attempt, mitochondrial markers were used to study the evolutionary relationship between the 68 landraces of northeast India and wild relatives (O. rufipogon and O. nivara) along with IR64 (indica) and Nipponbare (japonica) were taken as reference cultivars. Phylogenetically, the findings include two distinct clusters in the indigenous northeast India landraces representing indica and japonica groups. Further, the wild relatives and ~60% of northeast India landraces were identified to be closely related to the Nipponbare cluster. Besides, landraces of northeast India grouping with the indica group (IR64) are characterized by the absence of wild relatives. This indicates that there are two distinct evolutionary paths in the origin of northeast Indian rice landraces based on mitochondrial markers diversity and it is proposed that the inheritance of mitochondria, mitonuclear genome interactions, and bottleneck events could have genetically separated these two phylogenetically unique groups of northeast rice landraces.}, }
@article {pmid37009644, year = {2023}, author = {Cheng, B and Zhou, M and Tang, T and Hassan, MJ and Zhou, J and Tan, M and Li, Z and Peng, Y}, title = {A Trifolium repens flavodoxin-like quinone reductase 1 (TrFQR1) improves plant adaptability to high temperature associated with oxidative homeostasis and lipids remodeling.}, journal = {The Plant journal : for cell and molecular biology}, volume = {115}, number = {2}, pages = {369-385}, doi = {10.1111/tpj.16230}, pmid = {37009644}, issn = {1365-313X}, support = {sccxtd-2020-16//Sichuan Forage Innovation Team Program/ ; 2022YFH0059//Sichuan Science and Technology Program/ ; }, mesh = {*Trifolium/genetics/metabolism ; Flavodoxin/genetics/metabolism ; Diglycerides/metabolism ; Phylogeny ; Temperature ; Plant Proteins/genetics/metabolism ; Oxidative Stress ; *Arabidopsis/genetics/metabolism ; Homeostasis ; Gene Expression Regulation, Plant ; Plants, Genetically Modified/metabolism ; }, abstract = {Maintenance of stable mitochondrial respiratory chains could enhance adaptability to high temperature, but the potential mechanism was not elucidated clearly in plants. In this study, we identified and isolated a TrFQR1 gene encoding the flavodoxin-like quinone reductase 1 (TrFQR1) located in mitochondria of leguminous white clover (Trifolium repens). Phylogenetic analysis indicated that amino acid sequences of FQR1 in various plant species showed a high degree of similarities. Ectopic expression of TrFQR1 protected yeast (Saccharomyces cerevisiae) from heat damage and toxic levels of benzoquinone, phenanthraquinone and hydroquinone. Transgenic Arabidopsis thaliana and white clover overexpressing TrFQR1 exhibited significantly lower oxidative damage and better photosynthetic capacity and growth than wild-type in response to high-temperature stress, whereas AtFQR1-RNAi A. thaliana showed more severe oxidative damage and growth retardation under heat stress. TrFQR1-transgenic white clover also maintained better respiratory electron transport chain than wild-type plants, as manifested by significantly higher mitochondrial complex II and III activities, alternative oxidase activity, NAD(P)H content, and coenzyme Q10 content in response to heat stress. In addition, overexpression of TrFQR1 enhanced the accumulation of lipids including phosphatidylglycerol, monogalactosyl diacylglycerol, sulfoquinovosyl diacylglycerol and cardiolipin as important compositions of bilayers involved in dynamic membrane assembly in mitochondria or chloroplasts positively associated with heat tolerance. TrFQR1-transgenic white clover also exhibited higher lipids saturation level and phosphatidylcholine:phosphatidylethanolamine ratio, which could be beneficial to membrane stability and integrity during a prolonged period of heat stress. The current study proves that TrFQR1 is essential for heat tolerance associated with mitochondrial respiratory chain, cellular reactive oxygen species homeostasis, and lipids remodeling in plants. TrFQR1 could be selected as a key candidate marker gene to screen heat-tolerant genotypes or develop heat-tolerant crops via molecular-based breeding.}, }
@article {pmid36994538, year = {2023}, author = {Qiu, L and Dong, J and Li, X and Parey, SH and Tan, K and Orr, M and Majeed, A and Zhang, X and Luo, S and Zhou, X and Zhu, C and Ji, T and Niu, Q and Liu, S and Zhou, X}, title = {Defining honeybee subspecies in an evolutionary context warrants strategized conservation.}, journal = {Zoological research}, volume = {44}, number = {3}, pages = {483-493}, pmid = {36994538}, issn = {2095-8137}, mesh = {Bees/genetics ; Animals ; Phylogeny ; Phenotype ; *Mitochondria ; }, abstract = {Despite the urgent need for conservation consideration, strategic action plans for the preservation of the Asian honeybee, Apis cerana Fabricius, 1793, remain lacking. Both the convergent and divergent adaptations of this widespread insect have led to confusing phenotypical traits and inconsistent infraspecific taxonomy. Unclear subspecies boundaries pose a significant challenge to honeybee conservation efforts, as it is difficult to effectively prioritize conservation targets without a clear understanding of subspecies identities. Here, we investigated genome variations in 362 worker bees representing almost all populations of mainland A. cerana to understand how evolution has shaped its population structure. Whole-genome single nucleotide polymorphisms (SNPs) based on nuclear sequences revealed eight putative subspecies, with all seven peripheral subspecies exhibiting mutually exclusive monophyly and distinct genetic divergence from the widespread central subspecies. Our results demonstrated that most classic morphological traits, including body size, were related to the climatic variables of the local habitats and did not reflect the true evolutionary history of the organism. Thus, such morphological traits were not suitable for subspecific delineation. Conversely, wing vein characters showed relative independence to the environment and supported the subspecies boundaries inferred from nuclear genomes. Mitochondrial phylogeny further indicated that the present subspecies structure was a result of multiple waves of population divergence from a common ancestor. Based on our findings, we propose that criteria for subspecies delineation should be based on evolutionary independence, trait distinction, and geographic isolation. We formally defined and described eight subspecies of mainland A. cerana. Elucidation of the evolutionary history and subspecies boundaries enables a customized conservation strategy for both widespread and endemic honeybee conservation units, guiding colony introduction and breeding.}, }
@article {pmid36993903, year = {2023}, author = {Dalle Carbonare, L and Jiménez, JC and Lichtenauer, S and van Veen, H}, title = {Plant responses to limited aeration: Advances and future challenges.}, journal = {Plant direct}, volume = {7}, number = {3}, pages = {e488}, pmid = {36993903}, issn = {2475-4455}, abstract = {Limited aeration that is caused by tissue geometry, diffusion barriers, high elevation, or a flooding event poses major challenges to plants and is often, but not exclusively, associated with low oxygen. These processes span a broad interest in the research community ranging from whole plant and crop responses, post-harvest physiology, plant morphology and anatomy, fermentative metabolism, plant developmental processes, oxygen sensing by ERF-VIIs, gene expression profiles, the gaseous hormone ethylene, and O2 dynamics at cellular resolution. The International Society for Plant Anaerobiosis (ISPA) gathers researchers from all over the world contributing to understand the causes, responses, and consequences of limited aeration in plants. During the 14th ISPA meeting, major research progress was related to the evolution of O2 sensing mechanisms and the intricate network that balances low O2 signaling. Here, the work moved beyond flooding stress and emphasized novel underexplored roles of low O2 and limited aeration in altitude adaptation, fruit development and storage, and the vegetative development of growth apices. Regarding tolerance towards flooding, the meeting stressed the relevance and regulation of developmental plasticity, aerenchyma, and barrier formation to improve internal aeration. Additional newly explored flood tolerance traits concerned resource balance, senescence, and the exploration of natural genetic variation for novel tolerance loci. In this report, we summarize and synthesize the major progress and future challenges for low O2 and aeration research presented at the conference.}, }
@article {pmid36981035, year = {2023}, author = {Kundu, S and Kamalakannan, M and Mukherjee, T and Banerjee, D and Kim, HW}, title = {Genetic Characterization and Insular Habitat Enveloping of Endangered Leaf-Nosed Bat, Hipposideros nicobarulae (Mammalia: Chiroptera) in India: Phylogenetic Inference and Conservation Implication.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, pmid = {36981035}, issn = {2073-4425}, mesh = {Animals ; *Chiroptera/genetics ; Phylogeny ; Bayes Theorem ; Mammals ; Mitochondria ; }, abstract = {The Nicobar leaf-nosed Bat (Hipposideros nicobarulae) was described in the early 20th century; however, its systematic classification has been debated for over 100 years. This endangered and endemic species has achieved species status through morphological data in the last 10 years. However, the genetic information and phylogenetic relationships of H. nicobarulae remain neglected. The generated mitochondrial cytochrome b gene (mtCytb) sequences (438 bp) of H. nicobarulae contains 53.42-53.65% AT composition and 1.82% variable sites. The studied species, H. nicobarulae maintains an 8.1% to 22.6% genetic distance from other Hipposideros species. The genetic divergence estimated in this study is congruent with the concept of gene speciation in bats. The Bayesian and Maximum-Likelihood phylogenies clearly discriminated all Hipposideros species and showed a sister relationship between H. nicobarulae and H. cf. antricola. Current mtCytb-based investigations of H. nicobarulae have confirmed the species status at the molecular level. Further, the MaxEnt-based species distribution modelling illustrates the most suitable habitat of H. nicobarulae (294 km[2]), of which the majority (171 km[2]) is located on Great Nicobar Island. The present study suggests rigorous sampling across the range, taxonomic coverage, the generation of multiple molecular markers (mitochondrial and nuclear), as well as more ecological information, which will help in understanding population genetic structure, habitat suitability, and the implementation of appropriate conservation action plans for H. nicobarulae and other Hipposideros species.}, }
@article {pmid36980901, year = {2023}, author = {Hammar, F and Miller, DL}, title = {Genetic Diversity in the mtDNA of Physarum polycephalum.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, pmid = {36980901}, issn = {2073-4425}, mesh = {*Physarum polycephalum/genetics ; DNA, Mitochondrial/genetics ; Base Sequence ; Mitochondria/genetics ; Genetic Variation/genetics ; }, abstract = {The mtDNA of the myxomycete Physarum polycephalum can contain as many as 81 genes. These genes can be grouped in three different categories. The first category includes 46 genes that are classically found on the mtDNA of many organisms. However, 43 of these genes are cryptogenes that require a unique type of RNA editing (MICOTREM). A second category of gene is putative protein-coding genes represented by 26 significant open reading frames. However, these genes do not appear to be transcribed during the growth of the plasmodium and are currently unassigned since they do not have any apparent similarity to other classical mitochondrial protein-coding genes. The third category of gene is found in the mtDNA of some strains of P. polycephalum. These genes derive from a linear mitochondrial plasmid with nine significant, but unassigned, open reading frames which can integrate into the mitochondrial DNA by recombination. Here, we review the mechanism and evolution of the RNA editing necessary for cryptogene expression, discuss possible origins for the 26 unassigned open reading frames based on tentative identification of their protein product, and discuss the implications to mtDNA structure and replication of the integration of the linear mitochondrial plasmid.}, }
@article {pmid36977381, year = {2023}, author = {Michels, PAM and Ginger, ML}, title = {Evolution: 'Millefoglie' origin of mitochondrial cristae.}, journal = {Current biology : CB}, volume = {33}, number = {6}, pages = {R219-R221}, doi = {10.1016/j.cub.2023.02.037}, pmid = {36977381}, issn = {1879-0445}, mesh = {*Mitochondria/genetics/metabolism ; *Mitochondrial Proteins/genetics/metabolism ; Mitochondrial Membranes/metabolism ; }, abstract = {Striated intracytoplasmic membranes in alphaproteobacteria are often reminiscent of millefoglie pastries. A new study reveals a protein complex homologous to that responsible for mitochondrial cristae formation drives intracytoplasmic membrane formation, thereby establishing bacterial ancestry for the biogenesis of mitochondrial cristae.}, }
@article {pmid36972795, year = {2023}, author = {Benites, P and Zaldívar-Riverón, A and Meza-Lázaro, RN and Samacá-Sáenz, E and Gutiérrez-Rodríguez, J and Hernández-López, A}, title = {Multiple introgression events during the diversification history of the edible Mexican grasshopper genus Sphenarium (Orthoptera: Pyrgomorphidae).}, journal = {Molecular phylogenetics and evolution}, volume = {183}, number = {}, pages = {107774}, doi = {10.1016/j.ympev.2023.107774}, pmid = {36972795}, issn = {1095-9513}, mesh = {Animals ; Phylogeny ; *Grasshoppers/genetics ; Mexico ; DNA, Mitochondrial/genetics/chemistry ; Mitochondria/genetics ; }, abstract = {Speciation with gene flow often leads to ambiguous phylogenetic reconstructions, reticulate patterns of relatedness and conflicting nuclear versus mitochondrial (mt) lineages. Here we employed a fragment of the COI mtDNA gene and nuclear genome-wide data (3RAD) to assess the diversification history of Sphenarium, an orthopteran genus of great economic importance in Mexico that is presumed to have experienced hybridisation events in some of its species. We carried out separate phylogenetic analyses to evaluate the existence of mito-nuclear discordance in the species relationships, and also assessed the genomic diversity and population genomic structure and investigated the existence of interspecific introgression and species limits of the taxa involved based on the nuclear dataset. The species delineation analyses discriminated all the currently recognised species, but also supported the existence of four undescribed species. The mt and nuclear topologies had four discordant species relationships that can be explained by mt introgression, where the mt haplotypes of S. purpurascens appear to have replaced those of S. purpurascens A and B, S. variabile and S. zapotecum. Moreover, our analyses supported the existence of nuclear introgression events between four species pairs that are distributed in the Sierra Madre del Sur province in southeast Mexico, with three of them occurring in the Tehuantepec Isthmus region. Our study highlights the relevance of genomic data to address the relative importance of allopatric isolation versus gene flow in speciation.}, }
@article {pmid36971557, year = {2023}, author = {Shaliutina-Loginova, A and Francetic, O and Doležal, P}, title = {Bacterial Type II Secretion System and Its Mitochondrial Counterpart.}, journal = {mBio}, volume = {14}, number = {2}, pages = {e0314522}, pmid = {36971557}, issn = {2150-7511}, mesh = {*Type II Secretion Systems/metabolism ; Bacterial Proteins/genetics/metabolism ; Gram-Negative Bacteria/metabolism ; Periplasm/metabolism ; Bacterial Secretion Systems/metabolism ; }, abstract = {Over the billions of years that bacteria have been around, they have evolved several sophisticated protein secretion nanomachines to deliver toxins, hydrolytic enzymes, and effector proteins into their environments. Of these, the type II secretion system (T2SS) is used by Gram-negative bacteria to export a wide range of folded proteins from the periplasm across the outer membrane. Recent findings have demonstrated that components of the T2SS are localized in mitochondria of some eukaryotic lineages, and their behavior is consistent with the presence of a mitochondrial T2SS-derived system (miT2SS). This review focuses on recent advances in the field and discusses open questions concerning the function and evolution of miT2SSs.}, }
@article {pmid36966978, year = {2023}, author = {Edera, AA and Howell, KA and Nevill, PG and Small, I and Sanchez-Puerta, MV}, title = {Evolution of cox2 introns in angiosperm mitochondria and efficient splicing of an elongated cox2i691 intron.}, journal = {Gene}, volume = {869}, number = {}, pages = {147393}, doi = {10.1016/j.gene.2023.147393}, pmid = {36966978}, issn = {1879-0038}, mesh = {Introns/genetics ; *Magnoliopsida/genetics ; Mitochondria/genetics ; RNA Splicing ; Base Sequence ; }, abstract = {In angiosperms, the mitochondrial cox2 gene harbors up to two introns, commonly referred to as cox2i373 and cox2i691. We studied the cox2 from 222 fully-sequenced mitogenomes from 30 angiosperm orders and analyzed the evolution of their introns. Unlike cox2i373, cox2i691 shows a distribution among plants that is shaped by frequent intron loss events driven by localized retroprocessing. In addition, cox2i691 exhibits sporadic elongations, frequently in domain IV of introns. Such elongations are poorly related to repeat content and two of them showed the presence of LINE transposons, suggesting that increasing intron size is very likely due to nuclear intracelular DNA transfer followed by incorporation into the mitochondrial DNA. Surprisingly, we found that cox2i691 is erroneously annotated as absent in 30 mitogenomes deposited in public databases. Although each of the cox2 introns is ∼1.5 kb in length, a cox2i691 of 4.2 kb has been reported in Acacia ligulata (Fabaceae). It is still unclear whether its unusual length is due to a trans-splicing arrangement or the loss of functionality of the interrupted cox2. Through analyzing short-read RNA sequencing of Acacia with a multi-step computational strategy, we found that the Acacia cox2 is functional and its long intron is spliced in cis in a very efficient manner despite its length.}, }
@article {pmid36965057, year = {2023}, author = {Speijer, D}, title = {How mitochondria showcase evolutionary mechanisms and the importance of oxygen.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {6}, pages = {e2300013}, doi = {10.1002/bies.202300013}, pmid = {36965057}, issn = {1521-1878}, mesh = {*Biological Evolution ; *Oxygen/metabolism ; Eukaryota/metabolism ; Bacteria/genetics/metabolism ; Mitochondria/metabolism ; }, abstract = {Darwinian evolution can be simply stated: natural selection of inherited variations increasing differential reproduction. However, formulated thus, links with biochemistry, cell biology, ecology, and population dynamics remain unclear. To understand interactive contributions of chance and selection, higher levels of biological organization (e.g., endosymbiosis), complexities of competing selection forces, and emerging biological novelties (such as eukaryotes or meiotic sex), we must analyze actual examples. Focusing on mitochondria, I will illuminate how biology makes sense of life's evolution, and the concepts involved. First, looking at the bacterium - mitochondrion transition: merging with an archaeon, it lost its independence, but played a decisive role in eukaryogenesis, as an extremely efficient aerobic ATP generator and internal ROS source. Second, surveying later mitochondrion adaptations and diversifications illustrates concepts such as constructive neutral evolution, dynamic interactions between endosymbionts and hosts, the contingency of life histories, and metabolic reprogramming. Without oxygen, mitochondria disappear; with (intermittent) oxygen diversification occurs in highly complex ways, especially upon (temporary) phototrophic substrate supply. These expositions show the Darwinian model to be a highly fruitful paradigm.}, }
@article {pmid36964263, year = {2023}, author = {Jablonski, D and Ribeiro-Júnior, MA and Simonov, E and Šoltys, K and Meiri, S}, title = {A new, rare, small-ranged, and endangered mountain snake of the genus Elaphe from the Southern Levant.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4839}, pmid = {36964263}, issn = {2045-2322}, mesh = {Animals ; Phylogeny ; *Colubridae ; Mitochondria/genetics ; Lebanon ; Syria ; DNA, Mitochondrial/genetics ; }, abstract = {The genus Elaphe Fitzinger, 1833 includes 17 species of charismatic, large-sized, non-venomous, Eurasian snakes. In the Western Palearctic, the genus is represented by three species from the Elaphe quatuorlineata group ranging from the Apennine peninsula to Central Asia. The southernmost population of this group is distributed in the mountains of the Southern Levant, with more than 400 km gap to other Elaphe populations. This population has been known to science for only 50 years and is virtually unstudied due to its extreme rarity. We studied these snakes' morphological and genetic variation from the three countries where they are known to occur, i.e., Israel (Hermon, the Israeli-controlled Golan Heights), Lebanon, and Syria. We used nine mitochondrial and nuclear genes, complete mitogenome sequences, and a comprehensive morphological examination including published data, our own field observations, and museum specimens, to study its relationship to other species in the group. The three currently recognized species of the group (E. quatuorlineata, E. sauromates, E. urartica), and the Levant population, form four deeply divergent, strongly supported clades. Three of these clades correspond to the abovementioned species while the Southern Levant clade, which is genetically and morphologically distinct from all named congeners, is described here as a new species, Elaphe druzei sp. nov. The basal divergence of this group is estimated to be the Late Miocene with subsequent radiation from 5.1 to 3.9 Mya. The revealed biogeography of the E. quatuorlineata group supports the importance of the Levant as a major center of endemism and diversity of biota in Eurasia. The new species is large-sized and is one of the rarest snakes in the Western Palearctic. Because of its small mountain distribution range, in an area affected by land use and climate change, the new Elaphe urgently needs strict protection. Despite political issues, we hope this will be based on the cooperation of all countries where the new species occurs.}, }
@article {pmid36951086, year = {2023}, author = {Sloan, DB and DeTar, RA and Warren, JM}, title = {Aminoacyl-tRNA Synthetase Evolution within the Dynamic Tripartite Translation System of Plant Cells.}, journal = {Genome biology and evolution}, volume = {15}, number = {4}, pages = {}, pmid = {36951086}, issn = {1759-6653}, mesh = {Animals ; *Amino Acyl-tRNA Synthetases/genetics/metabolism ; Plant Cells/metabolism ; Amino Acid Sequence ; Cytosol/metabolism ; RNA, Transfer/genetics/metabolism ; }, abstract = {Eukaryotes maintain separate protein translation systems for nuclear and organellar genes, including distinct sets of tRNAs and aminoacyl-tRNA synthetases (aaRSs). In animals, mitochondrial-targeted aaRSs are expressed at lower levels and are less conserved in sequence than cytosolic aaRSs involved in translation of nuclear mRNAs, likely reflecting lower translational demands in mitochondria. In plants, translation is further complicated by the presence of plastids, which share most aaRSs with mitochondria. In addition, plant mitochondrial tRNA pools have a dynamic history of gene loss and functional replacement by tRNAs from other compartments. To investigate the consequences of these distinctive features of translation in plants, we analyzed sequence evolution in angiosperm aaRSs. In contrast to previously studied eukaryotic systems, we found that plant organellar and cytosolic aaRSs exhibit only a small difference in expression levels, and organellar aaRSs are slightly more conserved than cytosolic aaRSs. We hypothesize that these patterns result from high translational demands associated with photosynthesis in mature chloroplasts. We also investigated aaRS evolution in Sileneae, an angiosperm lineage with extensive mitochondrial tRNA replacement and aaRS retargeting. We predicted positive selection for changes in aaRS sequence resulting from these recent changes in subcellular localization and tRNA substrates but found little evidence for accelerated sequence divergence. Overall, the complex tripartite translation system in plant cells appears to have imposed more constraints on the long-term evolutionary rates of organellar aaRSs compared with other eukaryotic lineages, and plant aaRS protein sequences appear largely robust to more recent perturbations in subcellular localization and tRNA interactions.}, }
@article {pmid36949187, year = {2023}, author = {Mühleip, A and Flygaard, RK and Baradaran, R and Haapanen, O and Gruhl, T and Tobiasson, V and Maréchal, A and Sharma, V and Amunts, A}, title = {Structural basis of mitochondrial membrane bending by the I-II-III2-IV2 supercomplex.}, journal = {Nature}, volume = {615}, number = {7954}, pages = {934-938}, pmid = {36949187}, issn = {1476-4687}, mesh = {*Cryoelectron Microscopy ; Electron Transport ; *Electron Transport Complex III/chemistry/metabolism/ultrastructure ; *Electron Transport Complex IV/chemistry/metabolism/ultrastructure ; *Mitochondria/chemistry/enzymology/metabolism/ultrastructure ; *Mitochondrial Membranes/chemistry/enzymology/metabolism/ultrastructure ; *Electron Transport Complex II/chemistry/metabolism/ultrastructure ; *Electron Transport Complex I/chemistry/metabolism/ultrastructure ; Protein Multimerization ; Protein Subunits/chemistry/metabolism ; Molecular Dynamics Simulation ; Binding Sites ; Evolution, Molecular ; }, abstract = {Mitochondrial energy conversion requires an intricate architecture of the inner mitochondrial membrane[1]. Here we show that a supercomplex containing all four respiratory chain components contributes to membrane curvature induction in ciliates. We report cryo-electron microscopy and cryo-tomography structures of the supercomplex that comprises 150 different proteins and 311 bound lipids, forming a stable 5.8-MDa assembly. Owing to subunit acquisition and extension, complex I associates with a complex IV dimer, generating a wedge-shaped gap that serves as a binding site for complex II. Together with a tilted complex III dimer association, it results in a curved membrane region. Using molecular dynamics simulations, we demonstrate that the divergent supercomplex actively contributes to the membrane curvature induction and tubulation of cristae. Our findings highlight how the evolution of protein subunits of respiratory complexes has led to the I-II-III2-IV2 supercomplex that contributes to the shaping of the bioenergetic membrane, thereby enabling its functional specialization.}, }
@article {pmid36948470, year = {2023}, author = {Cayuela, H and Gaillard, JM and Vieira, C and Ronget, V and Gippet, JMW and Conde García, T and Marais, GAB and Lemaître, JF}, title = {Sex differences in adult lifespan and aging rate across mammals: A test of the 'Mother Curse hypothesis'.}, journal = {Mechanisms of ageing and development}, volume = {212}, number = {}, pages = {111799}, doi = {10.1016/j.mad.2023.111799}, pmid = {36948470}, issn = {1872-6216}, mesh = {Humans ; Animals ; Female ; Male ; *Longevity/genetics ; *Mothers ; Sex Characteristics ; Aging ; DNA, Mitochondrial/genetics ; Drosophila ; Mammals ; }, abstract = {In many animal species, including humans, males have shorter lifespan and show faster survival aging than females. This differential increase in mortality between sexes could result from the accumulation of deleterious mutations in the mitochondrial genome of males due to the maternal mode of mtDNA inheritance. To date, empirical evidence supporting the existence of this mechanism - called the Mother Curse hypothesis - remains largely limited to a few study cases in humans and Drosophila. In this study, we tested whether the Mother Curse hypothesis accounts for sex differences in lifespan and aging rate across 128 populations of mammals (60 and 68 populations studied in wild and captive conditions, respectively) encompassing 104 species. We found that adult lifespan decreases with increasing mtDNA neutral substitution rate in both sexes in a similar way in the wild - but not in captivity. Moreover, the aging rate marginally increased with neutral substitution rate in males and females in the wild. Overall, these results indicate that the Mother Curse hypothesis is not supported across mammals. We further discuss the implication of these findings for our understanding of the evolution of sex differences in mortality and aging.}, }
@article {pmid36948134, year = {2023}, author = {Celik, A and Orfany, A and Dearling, J and Del Nido, PJ and McCully, JD and Bakar-Ates, F}, title = {Mitochondrial transplantation: Effects on chemotherapy in prostate and ovarian cancer cells in vitro and in vivo.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {161}, number = {}, pages = {114524}, doi = {10.1016/j.biopha.2023.114524}, pmid = {36948134}, issn = {1950-6007}, mesh = {Male ; Female ; Humans ; Animals ; Mice ; Prostate/pathology ; Apoptosis ; Cell Line, Tumor ; *Ovarian Neoplasms/pathology ; Mitochondria ; Cisplatin/pharmacology ; Drug Resistance, Neoplasm ; *Antineoplastic Agents/pharmacology/therapeutic use ; }, abstract = {Prostate and ovarian cancers affect the male and female reproductive organs and are among the most common cancers in developing countries. Previous studies have demonstrated that cancer cells have a high rate of aerobic glycolysis that is present in nearly all invasive human cancers and persists even under normoxic conditions. Aerobic glycolysis has been correlated with chemotherapeutic resistance and tumor aggressiveness. These data suggest that mitochondrial dysfunction may confer a significant proliferative advantage during the somatic evolution of cancer. In this study we investigated the effect of direct mitochondria transplantation on cancer cell proliferation and chemotherapeutic sensitivity in prostate and ovarian cancer models, both in vitro and in vivo. Our results show that the transplantation of viable, respiration competent mitochondria has no effect on cancer cell proliferation but significantly decreases migration and alters cell cycle checkpoints. Our results further demonstrate that mitochondrial transplantation significantly increases chemotherapeutic sensitivity, providing similar apoptotic levels with low-dose chemotherapy as that achieved with high-dose chemotherapy. These results suggest that mitochondria transplantation provides a novel approach for early prostate and ovarian cancer therapy, significantly increasing chemotherapeutic sensitivity in in vitro and in vivo murine models.}, }
@article {pmid36944988, year = {2023}, author = {Yu, X and Wei, P and Chen, Z and Li, X and Zhang, W and Yang, Y and Liu, C and Zhao, S and Li, X and Liu, X}, title = {Comparative analysis of the organelle genomes of three Rhodiola species provide insights into their structural dynamics and sequence divergences.}, journal = {BMC plant biology}, volume = {23}, number = {1}, pages = {156}, pmid = {36944988}, issn = {1471-2229}, support = {XZ202001YD0028C//Local Development Funds of Science and Technology Department of Tibet/ ; 413100105//Plateau Ecology Youth Innovative Fund of Wuhan University/ ; }, mesh = {*Rhodiola/genetics ; Phylogeny ; *Genome, Plastid ; Tibet ; Mitochondria/genetics ; *Genome, Mitochondrial/genetics ; Evolution, Molecular ; }, abstract = {BACKGROUND: Plant organelle genomes are a valuable resource for evolutionary biology research, yet their genome architectures, evolutionary patterns and environmental adaptations are poorly understood in many lineages. Rhodiola species is a type of flora mainly distributed in highland habitats, with high medicinal value. Here, we assembled the organelle genomes of three Rhodiola species (R. wallichiana, R. crenulata and R. sacra) collected from the Qinghai-Tibet plateau (QTP), and compared their genome structure, gene content, structural rearrangements, sequence transfer and sequence evolution rates.<br><br>RESULTS: The results demonstrated the contrasting evolutionary pattern between plastomes and mitogenomes in three Rhodiola species, with the former possessing more conserved genome structure but faster evolutionary rates of sequence, while the latter exhibiting structural diversity but slower rates of sequence evolution. Some lineage-specific features were observed in Rhodiola mitogenomes, including chromosome fission, gene loss and structural rearrangement. Repeat element analysis shows that the repeats occurring between the two chromosomes may mediate the formation of multichromosomal structure in the mitogenomes of Rhodiola, and this multichromosomal structure may have recently formed. The identification of homologous sequences between plastomes and mitogenomes reveals several unidirectional protein-coding gene transfer events from chloroplasts to mitochondria. Moreover, we found that their organelle genomes contained multiple fragments of nuclear transposable elements (TEs) and exhibited different preferences for TEs insertion type. Genome-wide scans of positive selection identified one gene matR from the mitogenome. Since the matR is crucial for plant growth and development, as well as for respiration and stress responses, our findings suggest that matR may participate in the adaptive response of Rhodiola species to environmental stress of QTP.<br><br>CONCLUSION: The study analyzed the organelle genomes of three Rhodiola species and demonstrated the contrasting evolutionary pattern between plastomes and mitogenomes. Signals of positive selection were detected in the matR gene of Rhodiola mitogenomes, suggesting the potential role of this gene in Rhodiola adaptation to QTP. Together, the study is expected to enrich the genomic resources and provide valuable insights into the structural dynamics and sequence divergences of Rhodiola species.}, }
@article {pmid36944856, year = {2023}, author = {Niedziałkowska, M and Tarnowska, E and Babik, W and Konczal, M and Gharbi, K and Cezard, T and Jędrzejewska, B}, title = {Different waves of postglacial recolonisation and genomic structure of bank vole populations in NE Poland.}, journal = {Heredity}, volume = {130}, number = {5}, pages = {269-277}, pmid = {36944856}, issn = {1365-2540}, mesh = {Humans ; Animals ; Poland ; Phylogeny ; *DNA, Mitochondrial/genetics ; *Genomics ; Arvicolinae/genetics ; Genetic Variation ; }, abstract = {Previous studies indicated that in some species phylogeographic patterns obtained in the analysis of nuclear and mitochondrial DNA (mtDNA) markers can be different. Such mitonuclear discordance can have important evolutionary and ecological consequences. In the present study, we aimed to check whether there was any discordance between mtDNA and nuclear DNA in the bank vole population in the contact zone of its two mtDNA lineages. We analysed the population genetic structure of bank voles using genome-wide genetic data (SNPs) and diversity of sequenced heart transcriptomes obtained from selected individuals from three populations inhabiting areas outside the contact zone. The SNP genetic structure of the populations confirmed the presence of at least two genetic clusters, and such division was concordant with the patterns obtained in the analysis of other genetic markers and functional genes. However, genome-wide SNP analyses revealed the more detailed structure of the studied population, consistent with more than two bank vole recolonisation waves, as recognised previously in the study area. We did not find any significant differences between individuals representing two separate mtDNA lineages of the species in functional genes coding for protein-forming complexes, which are involved in the process of cell respiration in mitochondria. We concluded that the contemporary genetic structure of the populations and the width of the contact zone were shaped by climatic and environmental factors rather than by genetic barriers. The studied populations were likely isolated in separate Last Glacial Maximum refugia for insufficient amount of time to develop significant genetic differentiation.}, }
@article {pmid36939357, year = {2023}, author = {Macher, JN and Coots, NL and Poh, YP and Girard, EB and Langerak, A and Muñoz-Gómez, SA and Sinha, SD and Jirsová, D and Vos, R and Wissels, R and Gile, GH and Renema, W and Wideman, JG}, title = {Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria).}, journal = {mBio}, volume = {14}, number = {2}, pages = {e0030223}, pmid = {36939357}, issn = {2150-7511}, mesh = {Animals ; *Foraminifera/genetics ; *Genome, Mitochondrial ; Phylogeny ; Codon, Terminator ; *Rhizaria/genetics ; Genomics ; Eukaryota/genetics ; Amino Acids/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {Mitochondria originated from an ancient bacterial endosymbiont that underwent reductive evolution by gene loss and endosymbiont gene transfer to the nuclear genome. The diversity of mitochondrial genomes published to date has revealed that gene loss and transfer processes are ongoing in many lineages. Most well-studied eukaryotic lineages are represented in mitochondrial genome databases, except for the superphylum Retaria-the lineage comprising Foraminifera and Radiolaria. Using single-cell approaches, we determined two complete mitochondrial genomes of Foraminifera and two nearly complete mitochondrial genomes of radiolarians. We report the complete coding content of an additional 14 foram species. We show that foraminiferan and radiolarian mitochondrial genomes contain a nearly fully overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. In contrast to animals and fungi, many protists encode a diverse set of proteins on their mitochondrial genomes, including several ribosomal genes; however, some aerobic eukaryotic lineages (euglenids, myzozoans, and chlamydomonas-like algae) have reduced mitochondrial gene content and lack all ribosomal genes. Similar to these reduced outliers, we show that retarian mitochondrial genomes lack ribosomal protein and tRNA genes, contain truncated and divergent small and large rRNA genes, and contain only 14 or 15 protein-coding genes, including nad1, -3, -4, -4L, -5, and -7, cob, cox1, -2, and -3, and atp1, -6, and -9, with forams and radiolarians additionally carrying nad2 and nad6, respectively. In radiolarian mitogenomes, a noncanonical genetic code was identified in which all three stop codons encode amino acids. Collectively, these results add to our understanding of mitochondrial genome evolution and fill in one of the last major gaps in mitochondrial sequence databases. IMPORTANCE We present the reduced mitochondrial genomes of Retaria, the rhizarian lineage comprising the phyla Foraminifera and Radiolaria. By applying single-cell genomic approaches, we found that foraminiferan and radiolarian mitochondrial genomes contain an overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. An alternative genetic code was identified in radiolarian mitogenomes in which all three stop codons encode amino acids. Collectively, these results shed light on the divergent nature of the mitochondrial genomes from an ecologically important group, warranting further questions into the biological underpinnings of gene content variability and genetic code variation between mitochondrial genomes.}, }
@article {pmid36938916, year = {2023}, author = {Jiao, J and Wang, X and Wei, C and Zhao, Y}, title = {Bioinspired Electrode for the Production and Timely Separation of Nitrile and Hydrogen.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {19}, number = {26}, pages = {e2208044}, doi = {10.1002/smll.202208044}, pmid = {36938916}, issn = {1613-6829}, support = {22102049//National Natural Science Foundation of China/ ; U22A20437//National Natural Science Foundation of China/ ; 222301420005//Joint Fund of Science and Technology R&amp;D Plan of Henan Province/ ; }, abstract = {Replacing electrocatalytic oxygen evolution reaction (OER) with amine oxidation reaction is adopted to boost clean and environment-friendly energy source hydrogen (H2) in water. However, the electrocatalytic reaction is severely restricted by the strong adsorption of product on the catalyst surface. Inspired by the cooperation of flavin adenine dinucleotide and mitochondria membrane in biological system, the catalysis-separation complex electrodes are introduced to promote the desorption of product and hinder its readsorption by applying polytetrafluoroethylene (PTFE)-separation membrane on the one side of electrode, which is benefit for the cleanness of active sites on the catalyst surface for the continuous production and timely separation of nitrile and hydrogen. With the intermolecular force between PTFE and nitrile, the nitrile droplets can be quickly desorbed and separated from catalyst surface of anode, and the size of nitrile droplets on the catalyst surface is only 0.23% to that without PTFE. As a result, the current at 1.49 VRHE from the catalyst with PTFE membrane is about 33 times to that of catalyst without PTFE after long-term operation. Moreover, the cathode with PTFE membrane also achieves the rapid desorption of H2 bubbles and stable cathodic current because of the strong absorption of PTFE to H2 .}, }
@article {pmid36929911, year = {2023}, author = {Biot-Pelletier, D and Bettinazzi, S and Gagnon-Arsenault, I and Dubé, AK and Bédard, C and Nguyen, THM and Fiumera, HL and Breton, S and Landry, CR}, title = {Evolutionary Trajectories are Contingent on Mitonuclear Interactions.}, journal = {Molecular biology and evolution}, volume = {40}, number = {4}, pages = {}, pmid = {36929911}, issn = {1537-1719}, mesh = {*DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Eukaryota/genetics ; Genotype ; *Genome, Mitochondrial ; Cell Nucleus/genetics ; }, abstract = {Critical mitochondrial functions, including cellular respiration, rely on frequently interacting components expressed from both the mitochondrial and nuclear genomes. The fitness of eukaryotic organisms depends on a tight collaboration between both genomes. In the face of an elevated rate of evolution in mtDNA, current models predict that the maintenance of mitonuclear compatibility relies on compensatory evolution of the nuclear genome. Mitonuclear interactions would therefore exert an influence on evolutionary trajectories. One prediction from this model is that the same nuclear genome evolving with different mitochondrial haplotypes would follow distinct molecular paths toward higher fitness. To test this prediction, we submitted 1,344 populations derived from 7 mitonuclear genotypes of Saccharomyces cerevisiae to >300 generations of experimental evolution in conditions that either select for a mitochondrial function or do not strictly require respiration for survival. Performing high-throughput phenotyping and whole-genome sequencing on independently evolved individuals, we identified numerous examples of gene-level evolutionary convergence among populations with the same mitonuclear background. Phenotypic and genotypic data on strains derived from this evolution experiment identify the nuclear genome and the environment as the main determinants of evolutionary divergence, but also show a modulating role for the mitochondrial genome exerted both directly and via interactions with the two other components. We finally recapitulated a subset of prominent loss-of-function alleles in the ancestral backgrounds and confirmed a generalized pattern of mitonuclear-specific and highly epistatic fitness effects. Together, these results demonstrate how mitonuclear interactions can dictate evolutionary divergence of populations with identical starting nuclear genotypes.}, }
@article {pmid36921696, year = {2023}, author = {Lee, C and Ruhlman, TA and Jansen, RK}, title = {Rate accelerations in plastid and mitochondrial genomes of Cyperaceae occur in the same clades.}, journal = {Molecular phylogenetics and evolution}, volume = {182}, number = {}, pages = {107760}, doi = {10.1016/j.ympev.2023.107760}, pmid = {36921696}, issn = {1095-9513}, mesh = {Phylogeny ; Genome, Plant ; *Cyperaceae/genetics ; *Genome, Mitochondrial ; Evolution, Molecular ; *Magnoliopsida/genetics ; Plastids/genetics ; *Genome, Plastid ; }, abstract = {Cyperaceae, the second largest family in the monocot order Poales, comprises >5500 species and includes the genus Eleocharis with ∼ 250 species. A previous study of complete plastomes of two Eleocharis species documented extensive structural heteroplasmy, gene order changes, high frequency of dispersed repeats along with gene losses and duplications. To better understand the phylogenetic distribution of gene and intron content as well as rates and patterns of sequence evolution within and between mitochondrial and plastid genomes of Eleocharis and Cyperaceae, an additional 29 Eleocharis organelle genomes were sequenced and analyzed. Eleocharis experienced extensive gene loss in both genomes while loss of introns was mitochondria-specific. Eleocharis has higher rates of synonymous (dS) and nonsynonymous (dN) substitutions in the plastid and mitochondrion than most sampled angiosperms, and the pattern was distinct from other eudicot lineages with accelerated rates. Several clades showed higher dS and dN in mitochondrial genes than in plastid genes. Furthermore, nucleotide substitution rates of mitochondrial genes were significantly accelerated on the branch leading to Cyperaceae compared to most angiosperms. Mitochondrial genes of Cyperaceae exhibited dramatic loss of RNA editing sites and a negative correlation between RNA editing and dS values was detected among angiosperms. Mutagenic retroprocessing and dysfunction of DNA replication, repair and recombination genes are the most likely cause of striking rate accelerations and loss of edit sites and introns in Eleocharis and Cyperaceae organelle genomes.}, }
@article {pmid36921606, year = {2023}, author = {Muñoz-Gómez, SA and Cadena, LR and Gardiner, AT and Leger, MM and Sheikh, S and Connell, LB and Bilý, T and Kopejtka, K and Beatty, JT and Koblížek, M and Roger, AJ and Slamovits, CH and Lukeš, J and Hashimi, H}, title = {Intracytoplasmic-membrane development in alphaproteobacteria involves the homolog of the mitochondrial crista-developing protein Mic60.}, journal = {Current biology : CB}, volume = {33}, number = {6}, pages = {1099-1111.e6}, doi = {10.1016/j.cub.2023.02.059}, pmid = {36921606}, issn = {1879-0445}, mesh = {*Mitochondrial Proteins/metabolism ; *Alphaproteobacteria/genetics/metabolism ; Mitochondrial Membranes/metabolism ; Mitochondria/metabolism ; Biological Evolution ; }, abstract = {Mitochondrial cristae expand the surface area of respiratory membranes and ultimately allow for the evolutionary scaling of respiration with cell volume across eukaryotes. The discovery of Mic60 homologs among alphaproteobacteria, the closest extant relatives of mitochondria, suggested that cristae might have evolved from bacterial intracytoplasmic membranes (ICMs). Here, we investigated the predicted structure and function of alphaproteobacterial Mic60, and a protein encoded by an adjacent gene Orf52, in two distantly related purple alphaproteobacteria, Rhodobacter sphaeroides and Rhodopseudomonas palustris. In addition, we assessed the potential physical interactors of Mic60 and Orf52 in R. sphaeroides. We show that the three α helices of mitochondrial Mic60's mitofilin domain, as well as its adjacent membrane-binding amphipathic helix, are present in alphaproteobacterial Mic60. The disruption of Mic60 and Orf52 caused photoheterotrophic growth defects, which are most severe under low light conditions, and both their disruption and overexpression led to enlarged ICMs in both studied alphaproteobacteria. We also found that alphaproteobacterial Mic60 physically interacts with BamA, the homolog of Sam50, one of the main physical interactors of eukaryotic Mic60. This interaction, responsible for making contact sites at mitochondrial envelopes, has been conserved in modern alphaproteobacteria despite more than a billion years of evolutionary divergence. Our results suggest a role for Mic60 in photosynthetic ICM development and contact site formation at alphaproteobacterial envelopes. Overall, we provide support for the hypothesis that mitochondrial cristae evolved from alphaproteobacterial ICMs and have therefore improved our understanding of the nature of the mitochondrial ancestor.}, }
@article {pmid36921565, year = {2023}, author = {Huang, L and Zhang, L and Shi, S and Zhou, X and Yuan, H and Song, X and Hu, Y and Pang, W and Yang, G and Gao, L and Chu, G}, title = {Mitochondrial function and E2 synthesis are impaired following alteration of CLOCK gene expression in porcine ovarian granulosa cells.}, journal = {Theriogenology}, volume = {202}, number = {}, pages = {51-60}, doi = {10.1016/j.theriogenology.2023.03.004}, pmid = {36921565}, issn = {1879-3231}, mesh = {Female ; Swine ; Animals ; *Gene Expression Regulation ; Phylogeny ; *Granulosa Cells/physiology ; Estradiol/metabolism ; Mitochondria/metabolism ; Gene Expression ; Mammals ; }, abstract = {Circadian locomotor output cycles kaput (CLOCK) is a critical component of the mammalian circadian clock system and regulates ovarian physiology. However, the functions and mechanisms of CLOCK in porcine granulosa cells (GCs) are poorly understood. The present study focused on CLOCK's effects on estradiol synthesis. Similarity analysis showed that CLOCK is highly conserved between pigs and other species. The phylogenetic tree analysis indicated that porcine CLOCK was most closely related to that in Arabian camels. CLOCK significantly reduced E2 synthesis in GCs. CLOCK reduced the expression of steroidogenesis-related genes at the mRNA and protein levels, including CYP19A1, CYP11A1, and StAR. CYP17A1 levels were significantly downregulated. We demonstrated that CLOCK dramatically decreased ATP content, mitochondrial copy number, and mitochondrial membrane potential (MMP) and increased reactive oxygen species levels in GCs. We observed that mitochondria were severely damaged with fuzzy and fractured cristae and swollen matrix. These findings suggest that mitochondrial function and E2 synthesis are impaired following the alteration of CLOCK gene expression in porcine ovarian GCs.}, }
@article {pmid36916992, year = {2023}, author = {Monné, M and Cianciulli, A and Panaro, MA and Calvello, R and De Grassi, A and Palmieri, L and Mitolo, V and Palmieri, F}, title = {New Insights into the Evolution and Gene Structure of the Mitochondrial Carrier Family Unveiled by Analyzing the Frequent and Conserved Intron Positions.}, journal = {Molecular biology and evolution}, volume = {40}, number = {3}, pages = {}, pmid = {36916992}, issn = {1537-1719}, mesh = {Humans ; Introns ; Phylogeny ; *Mitochondria/genetics/metabolism ; *Membrane Transport Proteins/genetics ; Eukaryota/genetics ; Evolution, Molecular ; Conserved Sequence ; }, abstract = {Mitochondrial carriers (MCs) belong to a eukaryotic protein family of transporters that in higher organisms is called the solute carrier family 25 (SLC25). All MCs have characteristic triplicated sequence repeats forming a 3-fold symmetrical structure of a six-transmembrane α-helix bundle with a centrally located substrate-binding site. Biochemical characterization has shown that MCs altogether transport a wide variety of substrates but can be divided into subfamilies, each transporting a few specific substrates. We have investigated the intron positions in the human MC genes and their orthologs of highly diversified organisms. The results demonstrate that several intron positions are present in numerous MC sequences at the same specific points, of which some are 3-fold symmetry related. Many of these frequent intron positions are also conserved in subfamilies or in groups of subfamilies transporting similar substrates. The analyses of the frequent and conserved intron positions in MCs suggest phylogenetic relationships not only between close but also distant homologs as well as a possible involvement of the intron positions in the evolution of the substrate specificity diversification of the MC family members.}, }
@article {pmid36915058, year = {2023}, author = {Zumkeller, S and Knoop, V}, title = {Categorizing 161 plant (streptophyte) mitochondrial group II introns into 29 families of related paralogues finds only limited links between intron mobility and intron-borne maturases.}, journal = {BMC ecology and evolution}, volume = {23}, number = {1}, pages = {5}, pmid = {36915058}, issn = {2730-7182}, mesh = {Introns/genetics ; *Evolution, Molecular ; *Mitochondria/genetics ; Plants/genetics ; Cell Nucleus ; }, abstract = {Group II introns are common in the two endosymbiotic organelle genomes of the plant lineage. Chloroplasts harbor 22 positionally conserved group II introns whereas their occurrence in land plant (embryophyte) mitogenomes is highly variable and specific for the seven major clades: liverworts, mosses, hornworts, lycophytes, ferns, gymnosperms and flowering plants. Each plant group features "signature selections" of ca. 20-30 paralogues from a superset of altogether 105 group II introns meantime identified in embryophyte mtDNAs, suggesting massive intron gains and losses along the backbone of plant phylogeny. We report on systematically categorizing plant mitochondrial group II introns into "families", comprising evidently related paralogues at different insertion sites, which may even be more similar than their respective orthologues in phylogenetically distant taxa. Including streptophyte (charophyte) algae extends our sampling to 161 and we sort 104 streptophyte mitochondrial group II introns into 25 core families of related paralogues evidently arising from retrotransposition events. Adding to discoveries of only recently created intron paralogues, hypermobile introns and twintrons, our survey led to further discoveries including previously overlooked "fossil" introns in spacer regions or e.g., in the rps8 pseudogene of lycophytes. Initially excluding intron-borne maturase sequences for family categorization, we added an independent analysis of maturase phylogenies and find a surprising incongruence between intron mobility and the presence of intron-borne maturases. Intriguingly, however, we find that several examples of nuclear splicing factors meantime characterized simultaneously facilitate splicing of independent paralogues now placed into the same intron families. Altogether this suggests that plant group II intron mobility, in contrast to their bacterial counterparts, is not intimately linked to intron-encoded maturases.}, }
@article {pmid36913593, year = {2023}, author = {Swainsbury, DJK and Hawkings, FR and Martin, EC and Musiał, S and Salisbury, JH and Jackson, PJ and Farmer, DA and Johnson, MP and Siebert, CA and Hitchcock, A and Hunter, CN}, title = {Cryo-EM structure of the four-subunit Rhodobacter sphaeroides cytochrome bc1 complex in styrene maleic acid nanodiscs.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {12}, pages = {e2217922120}, pmid = {36913593}, issn = {1091-6490}, support = {BB/M000265/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/V006630/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {*Rhodobacter sphaeroides/chemistry ; Cytochromes c ; Cytochromes b ; Styrene ; Cryoelectron Microscopy ; Quinones ; Lipids ; Electron Transport Complex III ; Oxidation-Reduction ; }, abstract = {Cytochrome bc1 complexes are ubiquinol:cytochrome c oxidoreductases, and as such, they are centrally important components of respiratory and photosynthetic electron transfer chains in many species of bacteria and in mitochondria. The minimal complex has three catalytic components, which are cytochrome b, cytochrome c1, and the Rieske iron-sulfur subunit, but the function of mitochondrial cytochrome bc1 complexes is modified by up to eight supernumerary subunits. The cytochrome bc1 complex from the purple phototrophic bacterium Rhodobacter sphaeroides has a single supernumerary subunit called subunit IV, which is absent from current structures of the complex. In this work we use the styrene-maleic acid copolymer to purify the R. sphaeroides cytochrome bc1 complex in native lipid nanodiscs, which retains the labile subunit IV, annular lipids, and natively bound quinones. The catalytic activity of the four-subunit cytochrome bc1 complex is threefold higher than that of the complex lacking subunit IV. To understand the role of subunit IV, we determined the structure of the four-subunit complex at 2.9 Å using single particle cryogenic electron microscopy. The structure shows the position of the transmembrane domain of subunit IV, which lies across the transmembrane helices of the Rieske and cytochrome c1 subunits. We observe a quinone at the Qo quinone-binding site and show that occupancy of this site is linked to conformational changes in the Rieske head domain during catalysis. Twelve lipids were structurally resolved, making contacts with the Rieske and cytochrome b subunits, with some spanning both of the two monomers that make up the dimeric complex.}, }
@article {pmid36897956, year = {2023}, author = {Smith, CH and Pinto, BJ and Kirkpatrick, M and Hillis, DM and Pfeiffer, JM and Havird, JC}, title = {A tale of two paths: The evolution of mitochondrial recombination in bivalves with doubly uniparental inheritance.}, journal = {The Journal of heredity}, volume = {114}, number = {3}, pages = {199-206}, pmid = {36897956}, issn = {1465-7333}, support = {R01 GM116853/GM/NIGMS NIH HHS/United States ; R35-GM142836/NH/NIH HHS/United States ; }, mesh = {Animals ; Female ; Male ; Phylogeny ; Mitochondria/genetics ; *Bivalvia/genetics ; DNA, Mitochondrial/genetics ; Inheritance Patterns ; *Genome, Mitochondrial ; Recombination, Genetic ; }, abstract = {In most animals, mitochondrial DNA is strictly maternally inherited and non-recombining. One exception to this pattern is called doubly uniparental inheritance (DUI), a phenomenon involving the independent transmission of female and male mitochondrial genomes. DUI is known only from the molluskan class Bivalvia. The phylogenetic distribution of male-transmitted mitochondrial DNA (M mtDNA) in bivalves is consistent with several evolutionary scenarios, including multiple independent gains, losses, and varying degrees of recombination with female-transmitted mitochondrial DNA (F mtDNA). In this study, we use phylogenetic methods to test M mtDNA origination hypotheses and infer the prevalence of mitochondrial recombination in bivalves with DUI. Phylogenetic modeling using site concordance factors supported a single origin of M mtDNA in bivalves coupled with recombination acting over long evolutionary timescales. Ongoing mitochondrial recombination is present in Mytilida and Venerida, which results in a pattern of concerted evolution of F mtDNA and M mtDNA. Mitochondrial recombination could be favored to offset the deleterious effects of asexual inheritance and maintain mitonuclear compatibility across tissues. Cardiida and Unionida have gone without recent recombination, possibly due to an extension of the COX2 gene in male mitochondrial DNA. The loss of recombination could be connected to the role of M mtDNA in sex determination or sexual development. Our results support that recombination events may occur throughout the mitochondrial genomes of DUI species. Future investigations may reveal more complex patterns of inheritance of recombinants, which could explain the retention of signal for a single origination of M mtDNA in protein-coding genes.}, }
@article {pmid36893930, year = {2023}, author = {Jesus, PB and Lyra, GM and Zhang, H and Fujii, MT and Nauer, F and Nunes, JMC and Davis, CC and Oliveira, MC}, title = {Phylogenomics and taxon-rich phylogenies of new and historical specimens shed light on the systematics of Hypnea (Cystocloniaceae, Rhodophyta).}, journal = {Molecular phylogenetics and evolution}, volume = {183}, number = {}, pages = {107752}, doi = {10.1016/j.ympev.2023.107752}, pmid = {36893930}, issn = {1095-9513}, mesh = {Phylogeny ; *Rhodophyta/genetics ; Organelles ; Mitochondria ; Chloroplasts ; }, abstract = {Cystocloniacae is a highly diverse family of Rhodophyta, including species of ecological and economic importance, whose phylogeny remains largely unresolved. Species delimitation is unclear, particularly in the most speciose genus, Hypnea, and cryptic diversity has been revealed by recent molecular assessments, especially in the tropics. Here, we carried out the first phylogenomic investigation of Cystocloniaceae, focused on the genus Hypnea, inferred from chloroplast and mitochondrial genomes including taxa sampled from new and historical collections. In this work, molecular synapomorphies (gene losses, InDels and gene inversions) were identified to better characterize clades in our congruent organellar phylogenies. We also present taxon-rich phylogenies based on plastid and mitochondrial markers. Molecular and morphological comparisons of historic collections with contemporary specimens revealed the need for taxonomic updates in Hypnea, the synonymization of H. marchantiae to a later heterotypic synonym of H. cervicornis and the description of three new species: H. davisiana sp. nov., H. djamilae sp. nov. and H. evaristoae sp. nov.}, }
@article {pmid36889655, year = {2023}, author = {Zhu, X and Liu, T and He, A and Zhang, L and Li, J and Li, T and Miao, X and You, M and You, S}, title = {Diversity of Wolbachia infection and its influence on mitochondrial DNA variation in the diamondback moth, Plutella xylostella.}, journal = {Molecular phylogenetics and evolution}, volume = {182}, number = {}, pages = {107751}, doi = {10.1016/j.ympev.2023.107751}, pmid = {36889655}, issn = {1095-9513}, mesh = {Animals ; *Moths/genetics ; *Wolbachia/genetics ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; }, abstract = {Plutella xylostella is a pest that severely damages cruciferous vegetables worldwide and has been shown to be infected with the maternally inherited bacteria Wolbachia, with the main infected strain was plutWB1. In this study, we performed a large-scale global sampling of P. xylostella and amplified 3 mtDNA genes of P. xylostella and 6 Wolbachia genes to analyze the infection status, diversity of Wolbachia in P. xylostella, and its effect on mtDNA variation in P. xylostella. This study provides a conservative estimate of Wolbachia infection rates in P. xylostella, which was found to be 7% (104/1440). The ST 108 (plutWB1) was shared among butterfly species and the moth species P. xylostella, revealing that Wolbachia strain plutWB1 acquisition in P. xylostella may be through horizontal transmission. The Parafit analyses indicated a significant association between Wolbachia and Wolbachia-infected P. xylostella individuals, and individuals infected with plutWB1 tended to cluster in the basal positions of the phylogenetic tree based on the mtDNA data. Additionally, Wolbachia infections were associated with increased mtDNA polymorphism in the infected P. xylostella population. These data suggest that Wolbachia endosymbionts may have a potential effect on mtDNA variation of P. xylostella.}, }
@article {pmid36883292, year = {2023}, author = {Gaugel, SM and Hawlitschek, O and Dey, LS and Husemann, M}, title = {Evolution of mitogenomic gene order in Orthoptera.}, journal = {Insect molecular biology}, volume = {32}, number = {4}, pages = {387-399}, doi = {10.1111/imb.12838}, pmid = {36883292}, issn = {1365-2583}, mesh = {Animals ; Phylogeny ; Gene Order ; *Mitochondria/genetics ; Genomics ; *Gryllidae ; Evolution, Molecular ; }, abstract = {Mitochondrial gene order has contributed to the elucidation of evolutionary relationships in several animal groups. It generally has found its application as a phylogenetic marker for deep nodes. Yet, in Orthoptera limited research has been performed on the gene order, although the group represents one of the oldest insect orders. We performed a comprehensive study on mitochondrial genome rearrangements (MTRs) within Orthoptera in the context of mitogenomic sequence-based phylogeny. We used 280 published mitogenome sequences from 256 species, including three outgroup species, to reconstruct a molecular phylogeny. Using a heuristic approach, we assigned MTR scenarios to the edges of the phylogenetic tree and reconstructed ancestral gene orders to identify possible synapomorphies in Orthoptera. We found all types of MTRs in our dataset: inversions, transpositions, inverse transpositions, and tandem-duplication/random loss events (TDRL). Most of the suggested MTRs were in single and unrelated species. Out of five MTRs which were unique in subgroups of Orthoptera, we suggest four of them to be synapomorphies; those were in the infraorder Acrididea, in the tribe Holochlorini, in the subfamily Pseudophyllinae, and in the two families Phalangopsidae and Gryllidae or their common ancestor (leading to the relationship ((Phalangopsidae + Gryllidae) + Trigonidiidae)). However, similar MTRs have been found in distant insect lineages. Our findings suggest convergent evolution of specific mitochondrial gene orders in several species, deviant from the evolution of the mitogenome DNA sequence. As most MTRs were detected at terminal nodes, a phylogenetic inference of deeper nodes based on MTRs is not supported. Hence, the marker does not seem to aid resolving the phylogeny of Orthoptera, but adds further evidence for the complex evolution of the whole group, especially at the genetic and genomic levels. The results indicate a high demand for more research on patterns and underlying mechanisms of MTR events in Orthoptera.}, }
@article {pmid36883279, year = {2023}, author = {García Pascual, B and Nordbotten, JM and Johnston, IG}, title = {Cellular and environmental dynamics influence species-specific extents of organelle gene retention.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1994}, pages = {20222140}, pmid = {36883279}, issn = {1471-2954}, mesh = {Species Specificity ; *Mitochondria ; *Eukaryotic Cells ; Eukaryota ; }, abstract = {Mitochondria and plastids rely on many nuclear-encoded genes, but retain small subsets of the genes they need to function in their own organelle DNA (oDNA). Different species retain different numbers of oDNA genes, and the reasons for these differences are not completely understood. Here, we use a mathematical model to explore the hypothesis that the energetic demands imposed by an organism's changing environment influence how many oDNA genes it retains. The model couples the physical biology of cell processes of gene expression and transport to a supply-and-demand model for the environmental dynamics to which an organism is exposed. The trade-off between fulfilling metabolic and bioenergetic environmental demands, and retaining genetic integrity, is quantified for a generic gene encoded either in oDNA or in nuclear DNA. Species in environments with high-amplitude, intermediate-frequency oscillations are predicted to retain the most organelle genes, whereas those in less dynamic or noisy environments the fewest. We discuss support for, and insight from, these predictions with oDNA data across eukaryotic taxa, including high oDNA gene counts in sessile organisms exposed to day-night and intertidal oscillations (including plants and algae) and low counts in parasites and fungi.}, }
@article {pmid36882771, year = {2023}, author = {Bu, XL and Zhao, WS and Li, WX and Zou, H and Wu, SG and Li, M and Wang, GT}, title = {Mitochondrial metabolism of the facultative parasite Chilodonella uncinata (Alveolata, Ciliophora).}, journal = {Parasites &amp; vectors}, volume = {16}, number = {1}, pages = {92}, pmid = {36882771}, issn = {1756-3305}, support = {No. 32170437//National Natural Science Foundation of China/ ; No. 2019QZKK0304//the Second Tibetan Plateau Scientific Expedition and Research Program (STEP)/ ; No. CARS-45//the earmarked fund for CARS/ ; }, mesh = {Animals ; *Alveolata ; *Parasites ; Phylogeny ; *Ciliophora/genetics ; Mitochondria ; }, abstract = {BACKGROUND: Chilodonella uncinata is an aerobic ciliate capable of switching between being free-living and parasitic on fish fins and gills, causing tissue damage and host mortality. It is widely used as a model organism for genetic studies, but its mitochondrial metabolism has never been studied. Therefore, we aimed to describe the morphological features and metabolic characteristics of its mitochondria.<br><br>METHODS: Fluorescence&#xa0;staining and transmission electron microscopy (TEM) were used to observe the morphology of mitochondria. Single-cell transcriptome data of C. uncinata were annotated by the Clusters of Orthologous Genes (COG) database. Meanwhile, the metabolic pathways were constructed based on the transcriptomes. The phylogenetic analysis was also made based on the sequenced cytochrome c oxidase subunit 1 (COX1) gene.<br><br>RESULTS: Mitochondria were stained red using Mito-tracker Red staining and were stained slightly blue by DAPI dye. The cristae and double membrane structures of the mitochondria were observed by TEM. Besides, many lipid droplets were evenly distributed around the macronucleus. A total of 2594 unigenes were assigned to 23 functional classifications of COG. Mitochondrial metabolic pathways were depicted. The mitochondria contained enzymes for the complete tricarboxylic acid (TCA) cycle, fatty acid metabolism, amino acid metabolism, and cytochrome-based electron transport chain (ETC), but only partial enzymes involved in the iron-sulfur clusters (ISCs).<br><br>CONCLUSIONS: Our results showed that C. uncinata possess typical mitochondria. Stored lipid droplets inside mitochondria may be the energy storage of C. uncinata that helps its transmission from a free-living to a parasitic lifestyle. These findings also have improved our knowledge of the mitochondrial metabolism of C. uncinata and increased the volume of molecular data for future studies of this facultative parasite.}, }
@article {pmid36877343, year = {2023}, author = {Palacios-Barreto, P and Mar-Silva, AF and Bayona-Vasquez, NJ and Adams, DH and Díaz-Jaimes, P}, title = {Characterization of the complete mitochondrial genome of the brazilian cownose ray Rhinoptera brasiliensis (Myliobatiformes, Rhinopteridae) in the western Atlantic and its phylogenetic implications.}, journal = {Molecular biology reports}, volume = {50}, number = {5}, pages = {4083-4095}, pmid = {36877343}, issn = {1573-4978}, support = {IN207621//Programa de Apoyo a Proyectos de Investigaci&#xf3;n e Innovaci&#xf3;n Tecnol&#xf3;gica (PAPIIT)/ ; 341//LANCAD UNAM-DGTIC/ ; }, mesh = {Animals ; Phylogeny ; *Genome, Mitochondrial/genetics ; Brazil ; DNA, Mitochondrial/genetics ; *Skates, Fish/genetics ; Codon, Terminator ; RNA, Transfer/genetics ; }, abstract = {BACKGROUND: The Brazilian cownose ray, Rhinoptera brasiliensis has undergone a global population reduction and is currently classified by IUCN as Vulnerable. This species is sometimes confused with Rhinoptera bonasus, the only external diagnostic characteristic to distinguish between both species is the number of rows of tooth plates. Both cownose rays overlap geographically from Rio de Janeiro to the western North Atlantic. This calls for a more comprehensive phylogenetic assessment using mitochondria DNA genomes to better understand the relationships and delimitation of these two species.<br><br>METHODS AND RESULTS: The mitochondrial genome sequences of R. brasiliensis was obtained by next-generation sequencing. The length of the mitochondrial genome was 17,759&#xa0;bp containing 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a non-coding control region (D-loop). Each PCG was initiated by an authoritative ATG codon, except for COX1 initiated by a GTG codon. Most of the PCGs were terminated by a complete codon (TAA/TAG), while an incomplete termination codon (TA/T) was found in five out of the 13 PCGs. The phylogenetic analysis showed that R. brasiliensis was closely related to R. steindachneri whereas the reported mitogenome as R. steindachneri (GenBank accession number KM364982), differs from multiple mitocondrial DNA sequences of R. steindachneri and is nearly identical to that of R. javanica.<br><br>CONCLUSION: The new mitogenome determined in this study provides new insight into the phylogenetic relationships in Rhinoptera, while providing new molecular data that can be applied to population genetic studies.}, }
@article {pmid36860172, year = {2023}, author = {Cantó-Santos, J and Valls-Roca, L and Tobías, E and García-García, FJ and Guitart-Mampel, M and Esteve-Codina, A and Martín-Mur, B and Casado, M and Artuch, R and Solsona-Vilarrasa, E and Fernandez-Checa, JC and García-Ruiz, C and Rentero, C and Enrich, C and Moreno-Lozano, PJ and Milisenda, JC and Cardellach, F and Grau-Junyent, JM and Garrabou, G}, title = {Unravelling inclusion body myositis using a patient-derived fibroblast model.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {14}, number = {2}, pages = {964-977}, pmid = {36860172}, issn = {2190-6009}, support = {PI21/00935//Instituto de Salud Carlos III/ ; PI18/00451//Instituto de Salud Carlos III/ ; PI18/00498//Instituto de Salud Carlos III/ ; //APIF Programme (University of Barcelona)/ ; //CIBERER (ISCIII-FEDER)/ ; //CD21/00019 (ISCIII- FSE+)/ ; //Serra H&#xfa;nter Programme (Generalitat de Catalunya)/ ; //Torrons Vicens/ ; //PID2019-111669RB-I00/ ; //PID2020-115055RB-I00/ ; //PT17/0009/0019 (ISCIII-MINECO-FEDER)/ ; }, mesh = {Humans ; *Myositis, Inclusion Body/diagnosis/genetics/metabolism ; *Myositis ; Muscles/metabolism ; Inflammation/pathology ; Biomarkers/metabolism ; }, abstract = {BACKGROUND: Inclusion body myositis (IBM) is an inflammatory myopathy clinically characterized by proximal and distal muscle weakness, with inflammatory infiltrates, rimmed vacuoles and mitochondrial changes in muscle histopathology. There is scarce knowledge on IBM aetiology, and non-established biomarkers or effective treatments are available, partly due to the lack of validated disease models.<br><br>METHODS: We have performed transcriptomics and functional validation of IBM muscle pathological hallmarks in fibroblasts from IBM patients (n&#xa0;=&#xa0;14) and healthy controls (n&#xa0;=&#xa0;12), paired by age and sex. The results comprise an mRNA-seq, together with functional inflammatory, autophagy, mitochondrial and metabolic changes between patients and controls.<br><br>RESULTS: Gene expression profile of IBM vs control fibroblasts revealed 778 differentially expressed genes (P-value adj&#xa0;<&#xa0;0.05) related to inflammation, mitochondria, cell cycle regulation and metabolism. Functionally, an increased inflammatory profile was observed in IBM fibroblasts with higher supernatant cytokine secretion (three-fold increase). Autophagy was reduced considering basal protein mediators (18.4% reduced), time-course autophagosome formation (LC3BII 39% reduced, P-value&#xa0;<&#xa0;0.05), and autophagosome microscopic evaluation. Mitochondria displayed reduced genetic content (by 33.9%, P-value&#xa0;<&#xa0;0.05) and function (30.2%-decrease in respiration, 45.6%-decline in enzymatic activity (P-value&#xa0;<&#xa0;0.001), 14.3%-higher oxidative stress, 135.2%-increased antioxidant defence (P-value&#xa0;<&#xa0;0.05), 11.6%-reduced mitochondrial membrane potential (P-value&#xa0;<&#xa0;0.05) and 42.8%-reduced mitochondrial elongation (P-value&#xa0;<&#xa0;0.05)). In accordance, at the metabolite level, organic acid showed a 1.8-fold change increase, with conserved amino acid profile. Correlating to disease evolution, oxidative stress and inflammation emerge as potential markers of prognosis.<br><br>CONCLUSIONS: These findings confirm the presence of molecular disturbances in peripheral tissues from IBM patients and prompt patients' derived fibroblasts as a promising disease model, which may eventually be exported to other neuromuscular disorders. We additionally identify new molecular players in IBM associated with disease progression, setting the path to deepen in disease aetiology, in the identification of novel biomarkers or in the standardization of biomimetic platforms to assay new therapeutic strategies for preclinical studies.}, }
@article {pmid36858654, year = {2023}, author = {Rubio-Tomás, T and Sotiriou, A and Tavernarakis, N}, title = {The interplay between selective types of (macro)autophagy: Mitophagy and xenophagy.}, journal = {International review of cell and molecular biology}, volume = {374}, number = {}, pages = {129-157}, doi = {10.1016/bs.ircmb.2022.10.003}, pmid = {36858654}, issn = {1937-6448}, mesh = {*Macroautophagy ; *Mitophagy ; Autophagy ; DNA Damage ; Exercise ; }, abstract = {Autophagy is a physiological response, activated by a myriad of endogenous and exogenous cues, including DNA damage, perturbation of proteostasis, depletion of nutrients or oxygen and pathogen infection. Upon sensing those stimuli, cells employ multiple non-selective and selective autophagy pathways to promote fitness and survival. Importantly, there are a variety of selective types of autophagy. In this review we will focus on autophagy of bacteria (xenophagy) and autophagy of mitochondria (mitophagy). We provide a brief introduction to bulk autophagy, as well as xenophagy and mitophagy, highlighting their common molecular factors. We also describe the role of xenophagy and mitophagy in the detection and elimination of pathogens by the immune system and the adaptive mechanisms that some pathogens have developed through evolution to escape the host autophagic response. Finally, we summarize the recent articles (from the last five years) linking bulk autophagy with xenophagy and/or mitophagy in the context on developmental biology, cancer and metabolism.}, }
@article {pmid36858653, year = {2023}, author = {Degli Esposti, M}, title = {The bacterial origin of mitochondria: Incorrect phylogenies and the importance of metabolic traits.}, journal = {International review of cell and molecular biology}, volume = {374}, number = {}, pages = {1-35}, doi = {10.1016/bs.ircmb.2022.11.001}, pmid = {36858653}, issn = {1937-6448}, mesh = {Animals ; Phylogeny ; *Mitochondria ; *Eukaryota ; Oxygen ; Phenotype ; }, abstract = {This article provides an updated review on the evolution of mitochondria from bacteria, which were likely related to extant alphaproteobacteria. Particular attention is given to the timeline of oxygen history on Earth and the entwined phases of eukaryotic evolution that produced the animals that still populate our planet. Mitochondria of early-branching unicellular eukaryotes and plants appear to retain partial or vestigial traits that were directly inherited from the alphaproteobacterial ancestors of the organelles. Most of such traits define the current aerobic physiology of mitochondria. Conversely, the anaerobic traits that would be essential in the syntrophic associations postulated for the evolution of eukaryotic cells are scantly present in extant alphaproteobacteria, and therefore cannot help defining from which bacterial lineage the ancestors of mitochondria originated. This question has recently been addressed quantitatively, reaching the novel conclusion that marine bacteria related to Iodidimonas may be the living relatives of protomitochondria. Additional evidence is presented that either support or does not contrast this novel view of the bacterial origin of mitochondria.}, }
@article {pmid36841519, year = {2023}, author = {Tomita, K and Indo, HP and Sato, T and Tangpong, J and Majima, HJ}, title = {Development of a sensitive double TaqMan Probe-based qPCR Angle-Degree method to detect mutation frequencies.}, journal = {Mitochondrion}, volume = {70}, number = {}, pages = {1-7}, doi = {10.1016/j.mito.2023.02.010}, pmid = {36841519}, issn = {1872-8278}, mesh = {Humans ; Mutation Rate ; *MELAS Syndrome/genetics ; Mutation ; DNA, Mitochondrial/genetics ; *Stroke ; }, abstract = {We designed a method to examine the mutation frequencies of the A3243G mutation of mitochondrial DNA (mtDNA) in patients with mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome. We performed a qPCR assay using the FAM and VIC TaqMan probes, which detect the 3243G (mutated) and 3243A (wild-type) sequences of mtDNA, respectively. The results obtained by "degree" in a series of differential mutation frequencies were used to plot a standard curve of the mutation frequency. The standard curve was then applied for qPCR assays of the desired samples. The standard deviation (%) of the samples calculated using the standard curve for the TaqMan probe was 2.4 ± 1.5%. This method could be used to examine mutation frequencies in the context of diabetes, aging, cancer, and neurodegenerative diseases.}, }
@article {pmid36838260, year = {2023}, author = {Fuerst, PA}, title = {The Status of Molecular Analyses of Isolates of Acanthamoeba Maintained by International Culture Collections.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838260}, issn = {2076-2607}, abstract = {Acanthamoeba is among the most ubiquitous protistan groups in nature. Knowledge of the biological diversity of Acanthamoeba comes in part from the use of strains maintained by the major microbial culture collections, ATCC and CCAP. Standard strains are vital to ensure the comparability of research. The diversity of standard strains of Acanthamoeba in the culture collections is reviewed, emphasizing the extent of genotypic studies based on DNA sequencing of the small subunit ribosomal RNA from the nucleus (18S rRNA gene; Rns) or the mitochondria (16S-like rRNA gene; rns). Over 170 different strains have been maintained at some time by culture centers. DNA sequence information is available for more than 70% of these strains. Determination of the genotypic classification of standard strains within the genus indicates that frequencies of types within culture collections only roughly mirror that from clinical or environmental studies, with significant differences in the frequency of some genotypes. Culture collections include the type of isolate from almost all named species of Acanthamoeba, allowing an evaluation of the validity of species designations. Multiple species are found to share the same Sequence Type, while multiple Sequence Types have been identified for different strains that share the same species name. Issues of sequence reliability and the possibility that a small number of standard strains have been mislabeled when studied are also examined, leading to potential problems for comparative analyses. It is important that all species have reliable genotype designations. The culture collections should be encouraged to assist in completing the molecular inventory of standard strains, while workers in the Acanthamoeba research community should endeavor to ensure that strains representative of genotypes that are missing from the culture collection are provided to the culture centers for preservation.}, }
@article {pmid36835385, year = {2023}, author = {Yang, JX and Dierckxsens, N and Bai, MZ and Guo, YY}, title = {Multichromosomal Mitochondrial Genome of Paphiopedilum micranthum: Compact and Fragmented Genome, and Rampant Intracellular Gene Transfer.}, journal = {International journal of molecular sciences}, volume = {24}, number = {4}, pages = {}, pmid = {36835385}, issn = {1422-0067}, support = {U1804117//National Natural Science Foundation of China/ ; }, mesh = {*Genome, Mitochondrial ; DNA, Mitochondrial ; Mitochondria/genetics ; *Magnoliopsida/genetics ; *Orchidaceae/genetics ; Phylogeny ; }, abstract = {Orchidaceae is one of the largest families of angiosperms. Considering the large number of species in this family and its symbiotic relationship with fungi, Orchidaceae provide an ideal model to study the evolution of plant mitogenomes. However, to date, there is only one draft mitochondrial genome of this family available. Here, we present a fully assembled and annotated sequence of the mitochondrial genome (mitogenome) of Paphiopedilum micranthum, a species with high economic and ornamental value. The mitogenome of P. micranthum was 447,368 bp in length and comprised 26 circular subgenomes ranging in size from 5973 bp to 32,281 bp. The genome encoded for 39 mitochondrial-origin, protein-coding genes; 16 tRNAs (three of plastome origin); three rRNAs; and 16 ORFs, while rpl10 and sdh3 were lost from the mitogenome. Moreover, interorganellar DNA transfer was identified in 14 of the 26 chromosomes. These plastid-derived DNA fragments represented 28.32% (46,273 bp) of the P. micranthum plastome, including 12 intact plastome origin genes. Remarkably, the mitogenome of P. micranthum and Gastrodia elata shared 18% (about 81 kb) of their mitochondrial DNA sequences. Additionally, we found a positive correlation between repeat length and recombination frequency. The mitogenome of P. micranthum had more compact and fragmented chromosomes compared to other species with multichromosomal structures. We suggest that repeat-mediated homologous recombination enables the dynamic structure of mitochondrial genomes in Orchidaceae.}, }
@article {pmid36831240, year = {2023}, author = {Fang, Y and Zhang, F and Zhan, Y and Lu, M and Xu, D and Wang, J and Li, Q and Zhao, L and Su, Y}, title = {RpS3 Is Required for Spermatogenesis of Drosophila melanogaster.}, journal = {Cells}, volume = {12}, number = {4}, pages = {}, pmid = {36831240}, issn = {2073-4409}, mesh = {Animals ; Male ; *Drosophila melanogaster/metabolism ; *Drosophila Proteins/metabolism ; *Ribosomal Proteins/metabolism ; Semen/metabolism ; Spermatogenesis ; }, abstract = {Ribosomal proteins (RPs) constitute the ribosome, thus participating in the protein biosynthesis process. Emerging studies have suggested that many RPs exhibit different expression levels across various tissues and function in a context-dependent manner for animal development. Drosophila melanogaster RpS3 encodes the ribosomal protein S3, one component of the 40S subunit of ribosomes. We found that RpS3 is highly expressed in the reproductive organs of adult flies and its depletion in male germline cells led to severe defects in sperm production and male fertility. Immunofluorescence staining showed that RpS3 knockdown had little effect on early germ cell differentiation, but strongly disrupted the spermatid elongation and individualization processes. Furthermore, we observed abnormal morphology and activity of mitochondrial derivatives in the elongating spermatids of RpS3-knockdown testes, which could cause the failure of axoneme elongation. We also found that RpS3 RNAi inhibited the formation of the individualization complex that takes charge of disassociating the spermatid bundle. In addition, excessive apoptotic cells were detected in the RpS3-knockdown testes, possibly to clean the defective spermatids. Together, our data demonstrated that RpS3 plays an important role in regulating spermatid elongation and individualization processes and, therefore, is required for normal Drosophila spermatogenesis.}, }
@article {pmid36822346, year = {2023}, author = {Cheng, A and Zhang, Y and Sun, J and Huang, D and Sulaiman, JE and Huang, X and Wu, L and Ye, W and Wu, C and Lam, H and Shi, Y and Qian, PY}, title = {Pterosin sesquiterpenoids from Pteris laeta Wall. ex Ettingsh. protect cells from glutamate excitotoxicity by modulating mitochondrial signals.}, journal = {Journal of ethnopharmacology}, volume = {308}, number = {}, pages = {116308}, doi = {10.1016/j.jep.2023.116308}, pmid = {36822346}, issn = {1872-7573}, mesh = {Reactive Oxygen Species/metabolism ; Kelch-Like ECH-Associated Protein 1/metabolism ; Glutamic Acid/metabolism ; *Pteris/metabolism ; NF-E2-Related Factor 2/metabolism ; *Sesquiterpenes/pharmacology ; Mitochondria ; Oxidative Stress ; }, abstract = {The genus Pteris (Pteridaceae) has been used as a traditional herb for a long time. In particular, Pteris laeta Wall. ex Ettingsh. has been widely used in traditional Chinese medicine to treat nervous system diseases and some pterosin sesquiterpenes from Pteris show neuroprotective activity, but their underlying molecular mechanisms remain elusive. Therefore, to investigate the neuroprotective activity and working mechanism of pterosin sesquiterpenes from P. laeta Wall. ex Ettingsh. will provide a better understanding and guidance in using P. laeta Wall. ex Ettingsh. as a traditional Chinese medicine.<br><br>AIM OF THE STUDY: We aim to develop effective treatments for neurodegenerative diseases from pterosin sesquiterpenes by evaluating their neuroprotective activity and investigating their working mechanisms.<br><br>MATERIALS AND METHODS: Primary screening on the glutamate-induced excitotoxicity cell model was assessed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT) assay. Fluorescent-activated cell sorting (FACS) was used to analyze the activation level of glutamate receptors and mitochondria membrane potential after treatment. Transcriptomics and proteomics analysis was performed to identify possible targets of pterosin B. The key pathways were enriched by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis through the Database for Annotation, Visualization, and Integrated Discovery (DAVID). The core targets were visualized by a protein-protein interaction network using STRING. The mRNA and protein expressions were evaluated using real-time quantitative polymerase chain reaction (Q-PCR) and western blot, respectively. Immunocytochemistry was performed to monitor mitochondrial and apoptotic proteins. Cellular reactive oxygen species (ROS) were measured by ROS assay, and Ca[2+] was stained with Fluo-4 AM to quantify intracellular Ca[2+] levels.<br><br>RESULTS: We found pterosin B from Pteris laeta Wall. ex Ettingsh. showed significant neuroprotective activity against glutamate excitotoxicity, enhancing cell viability from 43.8% to 105% (p-value: <0.0001). We demonstrated that pterosin B worked on the downstream signaling pathways of glutamate excitotoxicity rather than directly blocking the activation of glutamate receptors. Pterosin B restored mitochondria membrane potentials, alleviated intracellular calcium overload from 107.4% to 95.47% (p-value: 0.0006), eliminated cellular ROS by 36.55% (p-value: 0.0143), and partially secured cells from LPS-induced inflammation by increasing cell survival from 46.75% to 58.5% (p-value: 0.0114). Notably, pterosin B enhanced the expression of nuclear factor-erythroid factor 2-related factor 2 (NRF2) and heme oxygenase-1 (HO-1) by 2.86-fold (p-value: 0.0006) and 4.24-fold (p-value: 0.0012), and down-regulated Kelch-like ECH-associated protein 1 (KEAP1) expression by 2.5-fold (p-value: 0.0107), indicating that it possibly promotes mitochondrial biogenesis and mitophagy to maintain mitochondria quality control and homeostasis, and ultimately inhibits apoptotic cell death.<br><br>CONCLUSIONS: Our work revealed that pterosin B protected cells from glutamate excitotoxicity by targeting the downstream mitochondrial signals, making it a valuable candidate for developing potential therapeutic agents in treating neurodegenerative diseases.}, }
@article {pmid36810648, year = {2023}, author = {Li, Y and Chen, L and Si, L and Yang, Y and Zhou, C and Yu, F and Xia, G and Wang, H}, title = {Triphenylamine-equipped 1,8-naphthaolactam: a versatile scaffold for the custom design of efficient subcellular imaging agents.}, journal = {Journal of materials chemistry. B}, volume = {11}, number = {11}, pages = {2431-2439}, doi = {10.1039/d2tb02528k}, pmid = {36810648}, issn = {2050-7518}, mesh = {*Optical Imaging ; *Mitochondria ; Amines ; }, abstract = {Fluorescence imaging has enabled much progress in biological fields, while the evolution of commercially available dyes has lagged behind their advanced applications. Herein, we launch triphenylamine-equipped 1,8-naphthaolactam (NP-TPA) as a versatile scaffold for the custom design of an efficient subcellular imaging agent (NP-TPA-Tar), given its bright and constant emissions in various states, significant Stokes shifts, and facile modifiability. The resultant four NP-TPA-Tars maintain excellent emission behavior with targeted modifications and can map the spatial distribution of lysosomes, mitochondria, endoplasmic reticulum, and plasma membrane in Hep G2 cells. Compared to its commercial counterpart, NP-TPA-Tar has a 2.8-25.2 fold increase in Stokes shift, a 1.2-1.9 fold increase in photostability, enhanced targeting capability, and comparable imaging efficiency even at low concentrations of 50 nM. This work will help to accelerate the update of current imaging agents and super-resolution and real-time imaging in biological applications.}, }
@article {pmid36806940, year = {2023}, author = {Rivera-Colón, AG and Rayamajhi, N and Minhas, BF and Madrigal, G and Bilyk, KT and Yoon, V and Hüne, M and Gregory, S and Cheng, CHC and Catchen, JM}, title = {Genomics of Secondarily Temperate Adaptation in the Only Non-Antarctic Icefish.}, journal = {Molecular biology and evolution}, volume = {40}, number = {3}, pages = {}, pmid = {36806940}, issn = {1537-1719}, support = {//National Science Foundation/ ; }, mesh = {Animals ; Antarctic Regions ; *Adaptation, Physiological ; Fishes/genetics ; *Perciformes/genetics ; Genomics ; Antifreeze Proteins ; }, abstract = {White-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is similar in structure and organization to that of its Antarctic congener; however, we observe evidence of chromosomal rearrangements coinciding with regions of elevated genetic divergence in pike icefish populations. We also find several key biological pathways under selection, including genes related to mitochondria and vision, highlighting candidates behind temperate adaptation in C. esox. Substantial antifreeze glycoprotein (AFGP) pseudogenization has occurred in the pike icefish, likely due to relaxed selection following ancestral escape from Antarctica. The canonical AFGP locus organization is conserved in C. esox and C. gunnari, but both show a translocation of two AFGP copies to a separate locus, previously unobserved in cryonotothenioids. Altogether, the study of this secondarily temperate species provides an insight into the mechanisms underlying adaptation to ecologically disparate environments in this otherwise highly specialized group.}, }
@article {pmid36797268, year = {2023}, author = {Preston, AJ and Rogers, A and Sharp, M and Mitchell, G and Toruno, C and Barney, BB and Donovan, LN and Bly, J and Kennington, R and Payne, E and Iovino, A and Furukawa, G and Robinson, R and Shamloo, B and Buccilli, M and Anders, R and Eckstein, S and Fedak, EA and Wright, T and Maley, CC and Kiso, WK and Schmitt, D and Malkin, D and Schiffman, JD and Abegglen, LM}, title = {Elephant TP53-RETROGENE 9 induces transcription-independent apoptosis at the mitochondria.}, journal = {Cell death discovery}, volume = {9}, number = {1}, pages = {66}, pmid = {36797268}, issn = {2058-7716}, support = {U54CA217376//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; }, abstract = {Approximately 20 TP53 retrogenes exist in the African and Asian elephant genomes (Loxodonta Africana, Elephas Maximus) in addition to a conserved TP53 gene that encodes a full-length protein. Elephant TP53-RETROGENE 9 (TP53-R9) encodes a p53 protein (p53-R9) that is truncated in the middle of the canonical DNA binding domain. This C-terminally truncated p53 retrogene protein lacks the nuclear localization signals and oligomerization domain of its full-length counterpart. When expressed in human osteosarcoma cells (U2OS), p53-R9 binds to Tid1, the chaperone protein responsible for mitochondrial translocation of human p53 in response to cellular stress. Tid1 expression is required for p53-R9-induced apoptosis. At the mitochondria, p53-R9 binds to the pro-apoptotic BCL-2 family member Bax, which leads to caspase activation, cytochrome c release, and cell death. Our data show, for the first time, that expression of this truncated elephant p53 retrogene protein induces apoptosis in human cancer cells. Understanding the molecular mechanism by which the additional elephant TP53 retrogenes function may provide evolutionary insight that can be utilized for the development of therapeutics to treat human cancers.}, }
@article {pmid36795453, year = {2023}, author = {Dong, LF and Rohlena, J and Zobalova, R and Nahacka, Z and Rodriguez, AM and Berridge, MV and Neuzil, J}, title = {Mitochondria on the move: Horizontal mitochondrial transfer in disease and health.}, journal = {The Journal of cell biology}, volume = {222}, number = {3}, pages = {}, pmid = {36795453}, issn = {1540-8140}, mesh = {Animals ; Phylogeny ; *Mitochondria/metabolism ; *Neoplasms/genetics/metabolism ; Energy Metabolism ; Mammals ; }, abstract = {Mammalian genes were long thought to be constrained within somatic cells in most cell types. This concept was challenged recently when cellular organelles including mitochondria were shown to move between mammalian cells in culture via cytoplasmic bridges. Recent research in animals indicates transfer of mitochondria in cancer and during lung injury in vivo, with considerable functional consequences. Since these pioneering discoveries, many studies have confirmed horizontal mitochondrial transfer (HMT) in vivo, and its functional characteristics and consequences have been described. Additional support for this phenomenon has come from phylogenetic studies. Apparently, mitochondrial trafficking between cells occurs more frequently than previously thought and contributes to diverse processes including bioenergetic crosstalk and homeostasis, disease treatment and recovery, and development of resistance to cancer therapy. Here we highlight current knowledge of HMT between cells, focusing primarily on in vivo systems, and contend that this process is not only (patho)physiologically relevant, but also can be exploited for the design of novel therapeutic approaches.}, }
@article {pmid36790303, year = {2023}, author = {Sokolova, IM}, title = {Ectotherm mitochondrial economy and responses to global warming.}, journal = {Acta physiologica (Oxford, England)}, volume = {237}, number = {4}, pages = {e13950}, doi = {10.1111/apha.13950}, pmid = {36790303}, issn = {1748-1716}, mesh = {Reactive Oxygen Species/metabolism ; *Global Warming ; *Mitochondria/metabolism ; Energy Metabolism/physiology ; Adenosine Triphosphate/metabolism ; }, abstract = {Temperature is a key abiotic factor affecting ecology, biogeography, and evolution of species. Alterations of energy metabolism play an important role in adaptations and plastic responses to temperature shifts on different time scales. Mitochondrial metabolism affects cellular bioenergetics and redox balance making these organelles an important determinant of organismal performances such as growth, locomotion, or development. Here I analyze the impacts of environmental temperature on the mitochondrial functions (including oxidative phosphorylation, proton leak, production of reactive oxygen species(ROS), and ATP synthesis) of ectotherms and discuss the mechanisms underlying negative shifts in the mitochondrial energy economy caused by supraoptimal temperatures. Owing to the differences in the thermal sensitivity of different mitochondrial processes, elevated temperatures (beyond the species- and population-specific optimal range) cause reallocation of the electron flux and the protonmotive force (Δp) in a way that decreases ATP synthesis efficiency, elevates the relative cost of the mitochondrial maintenance, causes excessive production of ROS and raises energy cost for antioxidant defense. These shifts in the mitochondrial energy economy might have negative consequences for the organismal fitness traits such as the thermal tolerance or growth. Correlation between the thermal sensitivity indices of the mitochondria and the whole organism indicate that these traits experience similar selective pressures but further investigations are needed to establish whether there is a cause-effect relationship between the mitochondrial failure and loss of organismal performance during temperature change.}, }
@article {pmid36790104, year = {2023}, author = {Onuț-Brännström, I and Stairs, CW and Campos, KIA and Thorén, MH and Ettema, TJG and Keeling, PJ and Bass, D and Burki, F}, title = {A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea).}, journal = {Genome biology and evolution}, volume = {15}, number = {3}, pages = {}, pmid = {36790104}, issn = {1759-6653}, support = {MOP-42517//CIHR/Canada ; }, mesh = {Animals ; *Parasites ; *Rhizaria/genetics ; Organelles ; Mitochondria/genetics/metabolism ; Saccharomyces cerevisiae/metabolism ; }, abstract = {Ascetosporea are endoparasites of marine invertebrates that include economically important pathogens of aquaculture species. Owing to their often-minuscule cell sizes, strict intracellular lifestyle, lack of cultured representatives and minimal availability of molecular data, these unicellular parasites remain poorly studied. Here, we sequenced and assembled the genome and transcriptome of Paramikrocytos canceri, an endoparasite isolated from the European edible crab Cancer pagurus. Using bioinformatic predictions, we show that P. canceri likely possesses a mitochondrion-related organelle (MRO) with highly reduced metabolism, resembling the mitosomes of other parasites but with key differences. Like other mitosomes, this MRO is predicted to have reduced metabolic capacity and lack an organellar genome and function in iron-sulfur cluster (ISC) pathway-mediated Fe-S cluster biosynthesis. However, the MRO in P. canceri is uniquely predicted to produce ATP via a partial glycolytic pathway and synthesize phospholipids de novo through the CDP-DAG pathway. Heterologous gene expression confirmed that proteins from the ISC and CDP-DAG pathways retain mitochondrial targeting sequences that are recognized by yeast mitochondria. This represents a unique combination of metabolic pathways in an MRO, including the first reported case of a mitosome-like organelle able to synthesize phospholipids de novo. Some of these phospholipids, such as phosphatidylserine, are vital in other protist endoparasites that invade their host through apoptotic mimicry.}, }
@article {pmid36789533, year = {2023}, author = {Nagarajan-Radha, V and Beekman, M}, title = {G × G × E effect on phenotype expression in a non-conventional model organism, the unicellular slime mould Physarum polycephalum.}, journal = {Biology letters}, volume = {19}, number = {2}, pages = {20220494}, pmid = {36789533}, issn = {1744-957X}, mesh = {*Physarum polycephalum/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Plasmids ; Phenotype ; }, abstract = {In metazoans, the expression of key phenotypic traits is sensitive to two- and three-way interactions between variation in mitochondrial DNA, nuclear DNA and the external environment. Whether gene-by-environment interactions affect phenotypes in single-celled eukaryotes is poorly studied, except in a few species of yeast and fungi. We developed a genetic panel of the unicellular slime mould, Physarum polycephalum containing strains differing in mitochondrial and nuclear DNA haplotypes. The panel also included two strains harbouring a selfishly replicating mitochondrial-fusion (mF) plasmid that could affect phenotype expression. We assayed movement and growth rate differences among the strains across two temperature regimes: 24° and 28°C. We found that the slime mould's growth rate, but not movement, is affected by G × G × E interactions. Predictably, mtDNA × nDNA interactions significantly affected both traits. The inter-trait correlation across the strains in each temperature regime was positive. Surprisingly, the mF plasmid had no negative effects on our chosen traits. Our study is the first to demonstrate genetic regulation of phenotype expression in a unicellular slime mould. The genetic effect on phenotypes manifests via epistatic interactions with the thermal environment, thus shedding new light on the role of G × G × E interactions in trait evolution in protists.}, }
@article {pmid36787792, year = {2022}, author = {Broccard, N and Silva, NM and Currat, M}, title = {Simulated patterns of mitochondrial diversity are consistent with partial population turnover in Bronze Age Central Europe.}, journal = {American journal of biological anthropology}, volume = {177}, number = {1}, pages = {134-146}, pmid = {36787792}, issn = {2692-7691}, mesh = {*Mitochondria/genetics ; Europe ; *DNA, Mitochondrial/genetics ; Emigration and Immigration ; Biological Evolution ; DNA, Ancient ; }, abstract = {OBJECTIVES: The analysis of ancient mitochondrial DNA from osteological remains has challenged previous conclusions drawn from the analysis of mitochondrial DNA from present populations, notably by revealing an absence of genetic continuity between the Neolithic and modern populations in Central Europe. Our study investigates how to reconcile these contradictions at the mitochondrial level using a modeling approach.<br><br>MATERIALS AND METHODS: We used a spatially explicit computational framework to simulate ancient and modern DNA sequences under various evolutionary scenarios of post Neolithic demographic events and compared the genetic diversity of the simulated and observed mitochondrial sequences. We investigated which-if any-scenarios were able to reproduce statistics of genetic diversity similar to those observed, with a focus on the haplogroup N1a, associated with the spread of early Neolithic farmers.<br><br>RESULTS: Demographic fluctuations during the Neolithic transition or subsequent demographic collapses after this period, that is, due to epidemics such as plague, are not sufficient to explain the signal of population discontinuity detected on the mitochondrial DNA in Central Europe. Only a scenario involving a substantial genetic input due to the arrival of migrants after the Neolithic transition, possibly during the Bronze Age, is compatible with observed patterns of genetic diversity.<br><br>DISCUSSION: Our results corroborate paleogenomic studies, since out of the alternative hypotheses tested, the best one that was able to recover observed patterns of mitochondrial diversity in modern and ancient Central European populations was one were immigration of populations from the Pontic steppes during the Bronze Age was explicitly simulated.}, }
@article {pmid36787420, year = {2023}, author = {Zheng, Y and Ye, Z and Xiao, Y}, title = {Subtle Structural Translation Magically Modulates the Super-Resolution Imaging of Self-Blinking Rhodamines.}, journal = {Analytical chemistry}, volume = {95}, number = {8}, pages = {4172-4179}, doi = {10.1021/acs.analchem.2c05298}, pmid = {36787420}, issn = {1520-6882}, mesh = {Rhodamines/chemistry ; *Blinking ; *Fluorescent Dyes/chemistry ; Microscopy, Fluorescence/methods ; Nanotechnology ; }, abstract = {The evolution of super-resolution imaging techniques is benefited from the ongoing competition for optimal rhodamine fluorophores. Yet, it seems blind to construct the desired rhodamine molecule matching the imaging need without the knowledge on imaging impact of even the minimum structural translation. Herein, we have designed a pair of self-blinking sulforhodamines (STMR and SRhB) with the bare distinction of methyl or ethyl substituents and engineered them with Halo protein ligands. Although the two possess similar spectral properties (λab, λfl, ϕ, etc.), they demonstrated unique single-molecule characteristics preferring to individual imaging applications. Experimentally, STMR with high emissive rates was qualified for imaging structures with rapid dynamics (endoplasmic reticulum, and mitochondria), and SRhB with prolonged on-times and photostability was suited for relatively "static" nuclei and microtubules. Using this new knowledge, the mitochondrial morphology during apoptosis and ferroptosis was first super-resolved by STMR. Our study highlights the significance of even the smallest structural modification to the modulation of super-resolution imaging performance and would provide insights for future fluorophore design.}, }
@article {pmid36782130, year = {2023}, author = {Zhang, S and Wang, J and He, W and Kan, S and Liao, X and Jordan, DR and Mace, ES and Tao, Y and Cruickshank, AW and Klein, R and Yuan, D and Tembrock, LR and Wu, Z}, title = {Variation in mitogenome structural conformation in wild and cultivated lineages of sorghum corresponds with domestication history and plastome evolution.}, journal = {BMC plant biology}, volume = {23}, number = {1}, pages = {91}, pmid = {36782130}, issn = {1471-2229}, support = {RCYX20200714114538196//Science, Technology, and Innovation Commission of Shenzhen Municipality/ ; 31970244//National Natural Science Foundation of China/ ; 110243160001007//Chinese Academy of Agricultural Sciences Elite Youth Program/ ; }, mesh = {*Genome, Mitochondrial/genetics ; *Sorghum/genetics ; Phylogeny ; Domestication ; Plants/genetics ; Cell Nucleus ; Evolution, Molecular ; Genome, Plant/genetics ; }, abstract = {BACKGROUND: Mitochondria are organelles within eukaryotic cells that are central to the metabolic processes of cellular respiration and ATP production. However, the evolution of mitochondrial genomes (mitogenomes) in plants is virtually unknown compared to animal mitogenomes or plant plastids, due to complex structural variation and long stretches of repetitive DNA making accurate genome assembly more challenging. Comparing the structural and sequence differences of organellar genomes within and between sorghum species is an essential step in understanding evolutionary processes such as organellar sequence transfer to the nuclear genome as well as improving agronomic traits in sorghum related to cellular metabolism.<br><br>RESULTS: Here, we assembled seven sorghum mitochondrial and plastid genomes and resolved reticulated mitogenome structures with multilinked relationships that could be grouped into three structural conformations that differ in the content of repeats and genes by contig. The grouping of these mitogenome structural types reflects the two domestication events for sorghum in east and west Africa.<br><br>CONCLUSIONS: We report seven mitogenomes of sorghum from different cultivars and wild sources. The assembly method used here will be helpful in resolving complex genomic structures in other plant species. Our findings give new insights into the structure of sorghum mitogenomes that provides an important foundation for future research into the improvement of sorghum traits related to cellular respiration, cytonuclear incompatibly, and disease resistance.}, }
@article {pmid36773750, year = {2023}, author = {Taite, M and Fernández-Álvarez, F&#xc1; and Braid, HE and Bush, SL and Bolstad, K and Drewery, J and Mills, S and Strugnell, JM and Vecchione, M and Villanueva, R and Voight, JR and Allcock, AL}, title = {Genome skimming elucidates the evolutionary history of Octopoda.}, journal = {Molecular phylogenetics and evolution}, volume = {182}, number = {}, pages = {107729}, doi = {10.1016/j.ympev.2023.107729}, pmid = {36773750}, issn = {1095-9513}, mesh = {Animals ; *Octopodiformes/genetics ; Phylogeny ; Bayes Theorem ; Mitochondria/genetics ; *Genome, Mitochondrial ; RNA, Transfer ; }, abstract = {Phylogenies for Octopoda have, until now, been based on morphological characters or a few genes. Here we provide the complete mitogenomes and the nuclear 18S and 28S ribosomal genes of twenty Octopoda specimens, comprising 18 species of Cirrata and Incirrata, representing 13 genera and all five putative families of Cirrata (Cirroctopodidae, Cirroteuthidae, Grimpoteuthidae, Opisthoteuthidae and Stauroteuthidae) and six families of Incirrata (Amphitretidae, Argonautidae, Bathypolypodidae, Eledonidae, Enteroctopodidae, and Megaleledonidae) which were assembled using genome skimming. Phylogenetic trees were built using Maximum Likelihood and Bayesian Inference with several alignment matrices. All mitochondrial genomes had the 'typical' genome composition and gene order previously reported for octopodiforms, except Bathypolypus ergasticus, which appears to lack ND5, two tRNA genes that flank ND5 and two other tRNA genes. Argonautoidea was revealed as sister to Octopodidae by the mitochondrial protein-coding gene dataset, however, it was recovered as sister to all other incirrate octopods with strong support in an analysis using nuclear rRNA genes. Within Cirrata, our study supports two existing classifications suggesting neither is likely in conflict with the true evolutionary history of the suborder. Genome skimming is useful in the analysis of phylogenetic relationships within Octopoda; inclusion of both mitochondrial and nuclear data may be key.}, }
@article {pmid36759539, year = {2023}, author = {Kise, H and Iguchi, A and Ikegami, T and Onishi, Y and Goto, K and Tanaka, Y and Washburn, TW and Nishijima, M and Kunishima, T and Okamoto, N and Suzuki, A}, title = {Genetic population structures of common scavenging species near hydrothermal vents in the Okinawa Trough.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {2348}, pmid = {36759539}, issn = {2045-2322}, mesh = {Animals ; *Hydrothermal Vents ; Phylogeny ; Genetics, Population ; *Decapoda ; Mitochondria/genetics ; Ecosystem ; }, abstract = {Deep-sea mining of hydrothermal deposits off the coast of Japan is currently under consideration, and environmental baseline studies of the area are required to understand possible impacts. The aim of this study is to clarify population structures of dominant benthic megafaunal species near hydrothermal vent fields in the Okinawa Trough, using a population genetics approach. We examined dominant deep-sea scavenging species including eels, several amphipods, and a decapod and performed population genetic analyses based on the mitochondrial cytochrome c oxidase subunit I region. Several sites were sampled within Okinawa Trough to examine intra-population diversity while two other locations 1400-2400 km away were chosen for inter-population comparisons. For synaphobranchid eels Simenchelys parasitica and Synaphobranchus kaupii, our results showed significant intra-population diversity but no inter-population genetic differentiation, suggesting strong genetic connectivity and/or large population sizes. In addition, single nucleotide polymorphism analysis also confirmed strong genetic connectivity for Simenchelys parasitica. Among scavenging amphipods, we detected seven putative species using molecular phylogenetic analysis. We evaluated population structures of the most abundant species of amphipods and a decapod species (Nematocarcinus lanceopes). Our results provide basic information on the genetic population structures of benthic megafaunal species near hydrothermal vent fields, which can be used to select candidate species for future connectivity analysis with high-resolution genetic markers and aid understanding of the potential population impacts of environmental disturbances.}, }
@article {pmid36750641, year = {2023}, author = {Kayastha, P and Stec, D and Sługocki, &#x141; and Gawlak, M and Mioduchowska, M and Kaczmarek, &#x141;}, title = {Integrative taxonomy reveals new, widely distributed tardigrade species of the genus Paramacrobiotus (Eutardigrada: Macrobiotidae).}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {2196}, pmid = {36750641}, issn = {2045-2322}, mesh = {Animals ; *Tardigrada/genetics ; Phylogeny ; Mitochondria/genetics ; Microscopy, Electron, Scanning ; RNA, Ribosomal, 18S/genetics ; }, abstract = {In a moss sample collected in Ribeiro Frio, Madeira, Paramacrobiotus gadabouti sp. nov. was found and described using the integrative taxonomy approach. The new species is described based on morphological and morphometric data from both phase-contrast light microscopy (PCM), as well as scanning electron microscopy (SEM). Moreover, four DNA markers, three nuclear (18S rRNA, 28S rRNA, ITS-2) and one mitochondrial (COI) markers, were used to elucidate the phylogenetic position of the new species within the family Macrobiotidae. The new species has a microplacoid that placed it within Parmacrobiotus richtersi group and exhibit richtersi-type eggs having processes terminated with cap-like structures. Paramacrobiotus gadabouti sp. nov. is most similar to Pam. alekseevi, Pam. filipi and Pam. garynahi, but differs from them mainly in details of egg morphology and morphometrics. Unlike other species from this group, which were confirmed as bisexual and showed limited distribution, Paramacrobiotus gadabouti sp. nov. is yet another parthenogenetic species with a wide distribution, demonstrating that at least some tardigrades confirm to the hypothesis of 'everything is everywhere'.}, }
@article {pmid36748090, year = {2023}, author = {Zhang, Y and Li, W and Bian, Y and Li, Y and Cong, L}, title = {Multifaceted roles of aerobic glycolysis and oxidative phosphorylation in hepatocellular carcinoma.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14797}, pmid = {36748090}, issn = {2167-8359}, mesh = {Humans ; *Carcinoma, Hepatocellular/metabolism ; Oxidative Phosphorylation ; *Liver Neoplasms/metabolism ; Energy Metabolism ; Glycolysis ; }, abstract = {Liver cancer is a common malignancy with high morbidity and mortality rates. Changes in liver metabolism are key factors in the development of primary hepatic carcinoma, and mitochondrial dysfunction is closely related to the occurrence and development of tumours. Accordingly, the study of the metabolic mechanism of mitochondria in primary hepatic carcinomas has gained increasing attention. A growing body of research suggests that defects in mitochondrial respiration are not generally responsible for aerobic glycolysis, nor are they typically selected during tumour evolution. Conversely, the dysfunction of mitochondrial oxidative phosphorylation (OXPHOS) may promote the proliferation, metastasis, and invasion of primary hepatic carcinoma. This review presents the current paradigm of the roles of aerobic glycolysis and OXPHOS in the occurrence and development of hepatocellular carcinoma (HCC). Mitochondrial OXPHOS and cytoplasmic glycolysis cooperate to maintain the energy balance in HCC cells. Our study provides evidence for the targeting of mitochondrial metabolism as a potential therapy for HCC.}, }
@article {pmid36747727, year = {2023}, author = {Espino-Sanchez, TJ and Wienkers, H and Marvin, RG and Nalder, SA and García-Guerrero, AE and VanNatta, PE and Jami-Alahmadi, Y and Blackwell, AM and Whitby, FG and Wohlschlegel, JA and Kieber-Emmons, MT and Hill, CP and Sigala, PA}, title = {Direct Tests of Cytochrome Function in the Electron Transport Chain of Malaria Parasites.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36747727}, support = {R25 HL108828/HL/NHLBI NIH HHS/United States ; R35 GM133764/GM/NIGMS NIH HHS/United States ; T32 DK007115/DK/NIDDK NIH HHS/United States ; U54 DK110858/DK/NIDDK NIH HHS/United States ; }, abstract = {UNLABELLED: The mitochondrial electron transport chain (ETC) of Plasmodium malaria parasites is a major antimalarial drug target, but critical cytochrome functions remain unstudied and enigmatic. Parasites express two distinct cyt c homologs (c and c -2) with unusually sparse sequence identity and uncertain fitness contributions. P. falciparum cyt c -2 is the most divergent eukaryotic cyt c homolog currently known and has sequence features predicted to be incompatible with canonical ETC function. We tagged both cyt c homologs and the related cyt c 1 for inducible knockdown. Translational repression of cyt c and cyt c 1 was lethal to parasites, which died from ETC dysfunction and impaired ubiquinone recycling. In contrast, cyt c -2 knockdown or knock-out had little impact on blood-stage growth, indicating that parasites rely fully on the more conserved cyt c for ETC function. Biochemical and structural studies revealed that both cyt c and c -2 are hemylated by holocytochrome c synthase, but UV-vis absorbance and EPR spectra strongly suggest that cyt c -2 has an unusually open active site in which heme is stably coordinated by only a single axial amino-acid ligand and can bind exogenous small molecules. These studies provide a direct dissection of cytochrome functions in the ETC of malaria parasites and identify a highly divergent Plasmodium cytochrome c with molecular adaptations that defy a conserved role in eukaryotic evolution.<br><br>SIGNIFICANCE STATEMENT: Mitochondria are critical organelles in eukaryotic cells that drive oxidative metabolism. The mitochondrion of Plasmodium malaria parasites is a major drug target that has many differences from human cells and remains poorly studied. One key difference from humans is that malaria parasites express two cytochrome c proteins that differ significantly from each other and play untested and uncertain roles in the mitochondrial electron transport chain (ETC). Our study revealed that one cyt c is essential for ETC function and parasite viability while the second, more divergent protein has unusual structural and biochemical properties and is not required for growth of blood-stage parasites. This work elucidates key biochemical properties and evolutionary differences in the mitochondrial ETC of malaria parasites.}, }
@article {pmid36746982, year = {2023}, author = {de Jong, MJ and Niamir, A and Wolf, M and Kitchener, AC and Lecomte, N and Seryodkin, IV and Fain, SR and Hagen, SB and Saarma, U and Janke, A}, title = {Range-wide whole-genome resequencing of the brown bear reveals drivers of intraspecies divergence.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {153}, pmid = {36746982}, issn = {2399-3642}, mesh = {Animals ; Male ; *Ursidae/genetics ; DNA, Mitochondrial/genetics ; Phylogeography ; Population Dynamics ; Mitochondria/genetics ; }, abstract = {Population-genomic studies can shed new light on the effect of past demographic processes on contemporary population structure. We reassessed phylogeographical patterns of a classic model species of postglacial recolonisation, the brown bear (Ursus arctos), using a range-wide resequencing dataset of 128 nuclear genomes. In sharp contrast to the erratic geographical distribution of mtDNA and Y-chromosomal haplotypes, autosomal and X-chromosomal multi-locus datasets indicate that brown bear population structure is largely explained by recent population connectivity. Multispecies coalescent based analyses reveal cases where mtDNA haplotype sharing between distant populations, such as between Iberian and southern Scandinavian bears, likely results from incomplete lineage sorting, not from ancestral population structure (i.e., postglacial recolonisation). However, we also argue, using forward-in-time simulations, that gene flow and recombination can rapidly erase genomic evidence of former population structure (such as an ancestral population in Beringia), while this signal is retained by Y-chromosomal and mtDNA, albeit likely distorted. We further suggest that if gene flow is male-mediated, the information loss proceeds faster in autosomes than in X chromosomes. Our findings emphasise that contemporary autosomal genetic structure may reflect recent population dynamics rather than postglacial recolonisation routes, which could contribute to mtDNA and Y-chromosomal discordances.}, }
@article {pmid36740932, year = {2023}, author = {Becher, H and Nichols, RA}, title = {Assembly-free quantification of vagrant DNA inserts.}, journal = {Molecular ecology resources}, volume = {23}, number = {5}, pages = {1002-1013}, doi = {10.1111/1755-0998.13764}, pmid = {36740932}, issn = {1755-0998}, support = {PhD studentship awarded to HB//Queen Mary University of London, School of Biological and Chemical Sciences/ ; }, mesh = {Humans ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Eukaryota/genetics ; *Genome, Mitochondrial ; Cell Nucleus/genetics ; Sequence Analysis, DNA ; Phylogeny ; }, abstract = {Inserts of DNA from extranuclear sources, such as organelles and microbes, are common in eukaryote nuclear genomes. However, sequence similarity between the nuclear and extranuclear DNA, and a history of multiple insertions, make the assembly of these regions challenging. Consequently, the number, sequence and location of these vagrant DNAs cannot be reliably inferred from the genome assemblies of most organisms. We introduce two statistical methods to estimate the abundance of nuclear inserts even in the absence of a nuclear genome assembly. The first (intercept method) only requires low-coverage (<1×) sequencing data, as commonly generated for population studies of organellar and ribosomal DNAs. The second method additionally requires that a subset of the individuals carry extranuclear DNA with diverged genotypes. We validated our intercept method using simulations and by re-estimating the frequency of human NUMTs (nuclear mitochondrial inserts). We then applied it to the grasshopper Podisma pedestris, exceptional for both its large genome size and reports of numerous NUMT inserts, estimating that NUMTs make up 0.056% of the nuclear genome, equivalent to >500 times the mitochondrial genome size. We also re-analysed a museomics data set of the parrot Psephotellus varius, obtaining an estimate of only 0.0043%, in line with reports from other species of bird. Our study demonstrates the utility of low-coverage high-throughput sequencing data for the quantification of nuclear vagrant DNAs. Beyond quantifying organellar inserts, these methods could also be used on endosymbiont-derived sequences. We provide an R implementation of our methods called "vagrantDNA" and code to simulate test data sets.}, }
@article {pmid36739946, year = {2023}, author = {Schmitz, JM and Wolters, JF and Murray, NH and Guerra, RM and Bingman, CA and Hittinger, CT and Pagliarini, DJ}, title = {Aim18p and Aim46p are chalcone isomerase domain-containing mitochondrial hemoproteins in Saccharomyces cerevisiae.}, journal = {The Journal of biological chemistry}, volume = {299}, number = {3}, pages = {102981}, pmid = {36739946}, issn = {1083-351X}, support = {R35 GM131795/GM/NIGMS NIH HHS/United States ; P41 GM108538/GM/NIGMS NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; T32 GM008505/GM/NIGMS NIH HHS/United States ; P30 GM138396/GM/NIGMS NIH HHS/United States ; }, mesh = {Flavonoids/metabolism ; *Intramolecular Lyases/chemistry/metabolism ; *Saccharomyces cerevisiae/enzymology/genetics ; *Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {Chalcone isomerases (CHIs) have well-established roles in the biosynthesis of plant flavonoid metabolites. Saccharomyces cerevisiae possesses two predicted CHI-like proteins, Aim18p (encoded by YHR198C) and Aim46p (YHR199C), but it lacks other enzymes of the flavonoid pathway, suggesting that Aim18p and Aim46p employ the CHI fold for distinct purposes. Here, we demonstrate using proteinase K protection assays, sodium carbonate extractions, and crystallography that Aim18p and Aim46p reside on the mitochondrial inner membrane and adopt CHI folds, but they lack select active site residues and possess an extra fungal-specific loop. Consistent with these differences, Aim18p and Aim46p lack CHI activity and also the fatty acid-binding capabilities of other CHI-like proteins, but instead bind heme. We further show that diverse fungal homologs also bind heme and that Aim18p and Aim46p possess structural homology to a bacterial hemoprotein. Collectively, our work reveals a distinct function and cellular localization for two CHI-like proteins, introduces a new variation of a hemoprotein fold, and suggests that ancestral CHI-like proteins were hemoproteins.}, }
@article {pmid36739562, year = {2023}, author = {Fang, JM and Basu, S and Phu, J and Nieh, MP and LoTurco, JJ}, title = {Cellular Localization, Aggregation, and Cytotoxicity of Bicelle-Quantum Dot Nanocomposites.}, journal = {ACS applied bio materials}, volume = {6}, number = {2}, pages = {566-577}, doi = {10.1021/acsabm.2c00827}, pmid = {36739562}, issn = {2576-6422}, mesh = {Humans ; HeLa Cells ; *Quantum Dots/toxicity/chemistry ; HEK293 Cells ; *Nanocomposites/toxicity ; }, abstract = {Bicelles are discoidal lipid nanoparticles (LNPs) in which the planar bilayer and curved rim are, respectively, composed of long- and short-chain lipids. Bicellar LNPs have a hydrophobic core, allowing hydrophobic molecules and large molecular complexes such as quantum dots (QDs) to be encapsulated. In this study, CdSe/ZnS QDs were encapsulated in bicelles made of dipalmitoyl phosphatidylcholine, dihexanoyl phosphatidylcholine, dipalmitoyl phosphatidylglycerol, and distearoyl phosphatidylethanolamine conjugated with polyethylene glycerol amine 2000 to form a well-defined bicelle-QD nanocomplex (known as NANO[2]-QD or bicelle-QD). The bicelle-QD was then incubated with Hek293t cells and HeLa cells for different periods of time to determine changes in their cellular localization. Bicelle-QDs readily penetrated Hek293t cell membranes within 15 min of incubation, localized to the cytoplasm, and associated with mitochondria and intracellular vesicles. After 1 h, the bicelle-QDs enter the cell nucleus. Large aggregates form throughout the cell after 2 h and QDs are nearly absent from the nucleus by 4 h. Previous reports have demonstrated that CdSe/ZnS QDs can be toxic to cells, and we have found that encapsulating QDs in bicelles can attenuate but did not eliminate cytotoxicity. The present research outcome demonstrates the time-resolved pathway of bicelle-encapsulated QDs in Hek293t cells, morphological evolution in cells over time, and cytotoxicity of the bicelle-QDs, providing important insight into the potential application of the nanocomplex for cellular imaging.}, }
@article {pmid36738170, year = {2023}, author = {Rogers, RL and Grizzard, SL and Garner, JT}, title = {Strong, Recent Selective Sweeps Reshape Genetic Diversity in Freshwater Bivalve Megalonaias nervosa.}, journal = {Molecular biology and evolution}, volume = {40}, number = {2}, pages = {}, pmid = {36738170}, issn = {1537-1719}, support = {R35 GM133376/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Selection, Genetic ; Fresh Water ; Genetic Variation ; *Bivalvia ; *Unionidae ; }, abstract = {Freshwater Unionid bivalves have recently faced ecological upheaval through pollution, barriers to dispersal, harvesting, and changes in fish-host prevalence. Currently, over 70% of species in North America are threatened, endangered or extinct. To characterize the genetic response to recent selective pressures, we collected population genetic data for one successful bivalve species, Megalonaias nervosa. We identify megabase-sized regions that are nearly monomorphic across the population, signals of strong, recent selection reshaping diversity across 73 Mb total. These signatures of selection are greater than is commonly seen in population genetic models. We observe 102 duplicate genes with high dN/dS on terminal branches among regions with sweeps, suggesting that gene duplication is a causative mechanism of recent adaptation in M. nervosa. Genes in sweeps reflect functional classes important for Unionid survival, including anticoagulation genes important for fish host parasitization, detox genes, mitochondria management, and shell formation. We identify sweeps in regions with no known functional impacts, suggesting mechanisms of adaptation that deserve greater attention in future work on species survival. In contrast, polymorphic transposable elements (TEs) appear to be detrimental and underrepresented among regions with sweeps. TE site frequency spectra are skewed toward singleton variants, and TEs among regions with sweeps are present at low frequency. Our work suggests that duplicate genes are an essential source of genetic novelty that has helped this species succeed in environments where others have struggled. These results suggest that gene duplications deserve greater attention in non-model population genomics, especially in species that have recently faced sudden environmental challenges.}, }
@article {pmid36737563, year = {2023}, author = {Rottenberg, H}, title = {The evolution of the human mitochondrial bc1 complex- adaptation for reduced rate of superoxide production?.}, journal = {Journal of bioenergetics and biomembranes}, volume = {55}, number = {1}, pages = {15-31}, pmid = {36737563}, issn = {1573-6881}, mesh = {Humans ; Cattle ; Animals ; Mice ; Sheep ; *Ubiquinone/chemistry/metabolism ; *Superoxides/metabolism ; Cytochromes b/metabolism ; Cytochromes c1/metabolism ; Oxidation-Reduction ; Primates/metabolism ; Electron Transport Complex III/metabolism ; Electron Transport ; }, abstract = {The mitochondrial bc1 complex is a major source of mitochondrial superoxide. While bc1-generated superoxide plays a beneficial signaling role, excess production of superoxide lead to aging and degenerative diseases. The catalytic core of bc1 comprises three peptides -cytochrome b, Fe-S protein, and cytochrome c1. All three core peptides exhibit accelerated evolution in anthropoid primates. It has been suggested that the evolution of cytochrome b in anthropoids was driven by a pressure to reduce the production of superoxide. In humans, the bc1 core peptides exhibit anthropoid-specific substitutions that are clustered near functionally critical sites that may affect the production of superoxide. Here we compare the high-resolution structures of bovine, mouse, sheep and human bc1 to identify structural changes that are associated with human-specific substitutions. Several cytochrome b substitutions in humans alter its interactions with other subunits. Most significantly, there is a cluster of seven substitutions, in cytochrome b, the Fe-S protein, and cytochrome c1 that affect the interactions between these proteins at the tether arm of the Fe-S protein and may alter the rate of ubiquinone oxidation and the rate of superoxide production. Another cluster of substitutions near heme bH and the ubiquinone reduction site, Qi, may affect the rate of ubiquinone reduction and thus alter the rate of superoxide production. These results are compatible with the hypothesis that cytochrome b in humans (and other anthropoid primates) evolve to reduce the rate of production of superoxide thus enabling the exceptional longevity and exceptional cognitive ability of humans.}, }
@article {pmid36736695, year = {2023}, author = {Fähnrich, A and Stephan, I and Hirose, M and Haarich, F and Awadelkareem, MA and Ibrahim, S and Busch, H and Wohlers, I}, title = {North and East African mitochondrial genetic variation needs further characterization towards precision medicine.}, journal = {Journal of advanced research}, volume = {54}, number = {}, pages = {59-76}, pmid = {36736695}, issn = {2090-1224}, mesh = {Humans ; *DNA, Mitochondrial/genetics ; *East African People/genetics ; Genetic Variation/genetics ; Haplotypes ; Phylogeny ; Precision Medicine ; Sequence Analysis, DNA ; *North African People/genetics ; }, abstract = {INTRODUCTION: Mitochondria are maternally inherited cell organelles with their own genome, and perform various functions in eukaryotic cells such as energy production and cellular homeostasis. Due to their inheritance and manifold biological roles in health and disease, mitochondrial genetics serves a dual purpose of tracing the history as well as disease susceptibility of human populations across the globe. This work requires a comprehensive catalogue of commonly observed genetic variations in the mitochondrial DNAs for all regions throughout the world. So far, however, certain regions, such as North and East Africa have been understudied.<br><br>OBJECTIVES: To address this shortcoming, we have created the most comprehensive quality-controlled North and East African mitochondrial data set to date and use it for characterizing mitochondrial genetic variation in this region.<br><br>METHODS: We compiled 11 published cohorts with novel data for mitochondrial genomes from 159 Sudanese individuals. We combined these 641 mitochondrial sequences with sequences from the 1000 Genomes (n&#xa0;=&#xa0;2504) and the Human Genome Diversity Project (n&#xa0;=&#xa0;828) and used the tool haplocheck for extensive quality control and detection of in-sample contamination, as well as Nanopore long read sequencing for haplogroup validation of 18 samples.<br><br>RESULTS: Using a subset of high-coverage mitochondrial sequences, we predict 15 potentially novel haplogroups in North and East African subjects and observe likely phylogenetic deviations from the established PhyloTree reference for haplogroups L0a1 and L2a1.<br><br>CONCLUSION: Our findings demonstrate common hitherto unexplored variants in mitochondrial genomes of North and East Africa that lead to novel phylogenetic relationships between haplogroups present in these regions. These observations call for further in-depth population genetic studies in that region to enable the prospective use of mitochondrial genetic variation for precision medicine.}, }
@article {pmid36734850, year = {2023}, author = {Nord, A and Chamkha, I and Elmér, E}, title = {A whole blood approach improves speed and accuracy when measuring mitochondrial respiration in intact avian blood cells.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {37}, number = {3}, pages = {e22766}, doi = {10.1096/fj.202201749R}, pmid = {36734850}, issn = {1530-6860}, mesh = {Animals ; *Mitochondria/metabolism ; *Cell Respiration ; Respiration ; Birds ; Blood Cells ; }, abstract = {Understanding mitochondrial biology and pathology is key to understanding the evolution of animal form and function. However, mitochondrial measurement often involves invasive, or even terminal, sampling, which can be difficult to reconcile in wild models or longitudinal studies. Non-mammal vertebrates contain mitochondria in their red blood cells, which can be exploited for minimally invasive mitochondrial measurement. Several recent bird studies have measured mitochondrial function using isolated blood cells. Isolation adds time in the laboratory and might be associated with physiological complications. We developed and validated a protocol to measure mitochondrial respiration in bird whole blood. Endogenous respiration was comparable between isolated blood cells and whole blood. However, respiration towards oxidative phosphorylation was higher in whole blood, and whole blood mitochondria were better coupled and had higher maximum working capacity. Whole blood measurement was also more reproducible than measurement on isolated cells for all traits considered. Measurements were feasible over a 10-fold range of sample volumes, although both small and large volumes were associated with changes to respiratory traits. The protocol was compatible with long-term storage: after 24 h at 5°C without agitation, all respiration traits but maximum working capacity remained unchanged, the latter decreasing by 14%. Our study suggests that whole blood measurement provides faster, more reproducible, and more biologically and physiologically relevant (mitochondrial integrity) assessment of mitochondrial respiration. We recommend future studies to take a whole blood approach unless specific circumstances require the use of isolated blood cells.}, }
@article {pmid36732530, year = {2023}, author = {Silva, MC and Catry, P and Bried, J and Kawakami, K and Flint, E and Granadeiro, JP}, title = {Contrasting patterns of population structure of Bulwer's petrel (Bulweria bulwerii) between oceans revealed by statistical phylogeography.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {1939}, pmid = {36732530}, issn = {2045-2322}, mesh = {Animals ; Phylogeography ; Oceans and Seas ; *Birds/genetics ; Pacific Ocean ; *Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Phylogeny ; Genetic Variation ; }, abstract = {The patterns of population divergence of mid-latitude marine birds are impacted by only a few biogeographic barriers to dispersal and the effect of intrinsic factors, such as fidelity to natal colonies or wintering grounds, may become more conspicuous. Here we describe, for the first time, the phylogeographic patterns and historical demography of Bulwer's petrel Bulweria bulwerii and provide new insights regarding the drivers of species diversification in the marine environment. We sampled Bulwer's petrels from the main breeding colonies and used a statistical phylogeography approach based on surveying nuclear and mitochondrial loci (~ 9100 bp) to study its mechanisms of global diversification. We uncovered three highly differentiated groups including the Western Pacific, the Central Pacific and the Atlantic. The older divergence occurred within the Pacific Ocean, ca. 850,000 ya, and since then the W Pacific group has been evolving in isolation. Conversely, divergence between the Central Pacific and Atlantic populations occurred within the last 200,000 years. While the Isthmus of Panama is important in restricting gene flow between oceans in Bulwer's petrels, the deepest phylogeographic break is within the Pacific Ocean, where oceanographic barriers are key in driving and maintaining the remarkable structure found in this highly mobile seabird. This is in contrast with the Atlantic, where no structure was detected. Further data will provide insights regarding the extent of lineage divergence of Bulwer's petrels in the Western Pacific.}, }
@article {pmid36727263, year = {2023}, author = {Blair, C}, title = {Organellar DNA continues to provide a rich source of information in the genomics era.}, journal = {Molecular ecology}, volume = {32}, number = {9}, pages = {2144-2150}, doi = {10.1111/mec.16872}, pmid = {36727263}, issn = {1365-294X}, mesh = {Phylogeny ; *Information Sources ; *DNA, Mitochondrial/genetics ; Genomics ; Mitochondria/genetics ; DNA, Chloroplast/genetics ; Sequence Analysis, DNA ; }, abstract = {The genomics revolution continues to change how ecologists and evolutionary biologists study the evolution and maintenance of biodiversity. It is now easier than ever to generate large molecular data sets consisting of hundreds to thousands of independently evolving nuclear loci to estimate a suite of evolutionary and demographic parameters. However, any inferences will be incomplete or inaccurate if incorrect taxonomic identities and perpetuated throughout the analytical pipeline. Due to decades of research and comprehensive online databases, sequencing and analysis of mitochondrial DNA (mtDNA), chloroplast DNA (cpDNA) and select nuclear genes can provide researchers with a cost effective and simple means to verify the species identity of samples prior to subsequent phylogeographic and population genomic analysis. The addition of these sequences to genomic studies can also shed light on other important evolutionary questions such as explanations for gene tree-species tree discordance, species limits, sex-biased dispersal patterns, adaptation, and mtDNA introgression. Although the mtDNA and cpDNA genomes often should not be used exclusively to make historical inferences given their well-known limitations, the addition of these data to modern genomic studies adds little cost and effort while simultaneously providing a wealth of useful data that can have significant implications for both basic and applied research.}, }
@article {pmid36726084, year = {2023}, author = {Li, Y and Gu, M and Liu, X and Lin, J and Jiang, H and Song, H and Xiao, X and Zhou, W}, title = {Sequencing and analysis of the complete mitochondrial genomes of Toona sinensis and Toona ciliata reveal evolutionary features of Toona.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {58}, pmid = {36726084}, issn = {1471-2164}, support = {2011KJCX002,2012KJCX002,2013KJCX002//Guangdong Forestry Science and Technology Innovation Special Project/ ; 2011KJCX002,2012KJCX002,2013KJCX002//Guangdong Forestry Science and Technology Innovation Special Project/ ; 2011KJCX002,2012KJCX002,2013KJCX002//Guangdong Forestry Science and Technology Innovation Special Project/ ; 2011KJCX002,2012KJCX002,2013KJCX002//Guangdong Forestry Science and Technology Innovation Special Project/ ; 2011KJCX002,2012KJCX002,2013KJCX002//Guangdong Forestry Science and Technology Innovation Special Project/ ; 2011KJCX002,2012KJCX002,2013KJCX002//Guangdong Forestry Science and Technology Innovation Special Project/ ; 2011KJCX002,2012KJCX002,2013KJCX002//Guangdong Forestry Science and Technology Innovation Special Project/ ; 2011KJCX002,2012KJCX002,2013KJCX002//Guangdong Forestry Science and Technology Innovation Special Project/ ; }, mesh = {Toona/genetics ; Phylogeny ; *Genome, Mitochondrial ; Plant Breeding ; *Meliaceae/genetics ; }, abstract = {BACKGROUND: Toona is a critical genus in the Meliaceae, and the plants of this group are an asset for both restorative and restorative purposes, the most flexible of which are Toona sinensis and Toona ciliata. To concentrate on the advancement of mitochondrial(Mt) genome variety in T.sinensis and T.ciliata, the Mt genomes of the two species were sequenced in high throughput independently, after de novo assembly and annotation to construct a Mt genome map for comparison in genome structure. Find their repetitive sequences and analyze them in comparison with the chloroplast genome, along with Maximum-likelihood(ML) phylogenetic analysis with 16 other relatives.<br><br>RESULTS: (1)&#xa0;T. sinensis and T.ciliata are both circular structures with lengths of 683482&#xa0;bp and 68300&#xa0;bp, respectively. They share a high degree of similarity in encoding genes and have AT preferences. All of them have the largest Phe concentration and are the most frequently used codons. (2) Both of their Mt genome are highly preserved in terms of structural and functional genes, while the main variability is reflected in the length of tRNA, the number of genes, and the value of RSCU. (3) T. siniensis and T. ciliata were detected to have 94 and 87 SSRs, respectively, of which mononucleotides accounted for the absolute proportion. Besides, the vast majority of their SSRs were found to be poly-A or poly-T. (4)10 and 11 migrating fragments were identified in the comparison with the chloroplast genome, respectively. (5) In the ML evolutionary tree, T.sinensis and T.ciliata clustered individually into a small branch with 100% support, reflecting two species of Toona are very similarly related to each other.<br><br>CONCLUSIONS: This research provides a basis for the exploitation of T.sinensis and T.ciliata in terms of medicinal, edible, and timber resources to avoid confusion; at the same time, it can explore the evolutionary relationship between the Toona and related species, which does not only have an important practical value, but also provides a theoretical basis for future hybrid breeding of forest trees, molecular markers, and evolutionary aspects of plants, which has great scientific significance.}, }
@article {pmid36724679, year = {2023}, author = {Rivero, J and Cutillas, C and Callejón, R}, title = {New genetic lineage of whipworm present in Bactrian camel (Camelus bactrianus).}, journal = {Veterinary parasitology}, volume = {315}, number = {}, pages = {109886}, doi = {10.1016/j.vetpar.2023.109886}, pmid = {36724679}, issn = {1873-2550}, mesh = {Animals ; *Camelus/parasitology ; Trichuris/genetics ; Bayes Theorem ; Phylogeny ; Mitochondria ; *Parasites ; }, abstract = {With a global population of around 35 million in 47 countries, camels play a crucial role in the economy of many marginal and desert areas of the world where they survive in harsh conditions. Nonetheless, there is insufficient knowledge regarding camels' parasite fauna which can reduce their milk and meat production. A molecular study for the Trichuris population of Camelus bactrianus from Spain is presented based on sequences of mitochondrial (cox1, cob, rrnL) and ribosomal (ITS1 and ITS2) DNA regions. Bayesian Inference and Maximum Likelihood methods were used to infer phylogenies for (i) each gene separately, (ii) the combined mitochondrial data, and (iii) the combined mitochondrial and ribosomal dataset. Molecular analyses revealed the existence of two different genetic lineages in the Trichuris parasites populations of C. bactrianus. Future studies should focus on whether there is a coevolution process corresponding to the wild or domestic character of C. bactrianus and Camelus dromedarius. Furthermore, it is necessary to increase integrative taxonomic studies on Trichuris spp. based on morphological, biometric, and molecular data, which will inevitably contribute to our knowledge of the etiology of trichuriasis.}, }
@article {pmid36722300, year = {2023}, author = {Russo, MT and Santin, A and Zuccarotto, A and Leone, S and Palumbo, A and Ferrante, MI and Castellano, I}, title = {The first genetic engineered system for ovothiol biosynthesis in diatoms reveals a mitochondrial localization for the sulfoxide synthase OvoA.}, journal = {Open biology}, volume = {13}, number = {2}, pages = {220309}, pmid = {36722300}, issn = {2046-2441}, mesh = {*Diatoms/genetics ; Genetic Engineering ; Methylhistidines ; Biological Evolution ; }, abstract = {Diatoms represent one of the most abundant groups of microalgae in the ocean and are responsible for approximately 20% of photosynthetically fixed CO2 on Earth. Due to their complex evolutionary history and ability to adapt to different environments, diatoms are endowed with striking molecular biodiversity and unique metabolic activities. Their high growth rate and the possibility to optimize their biomass make them very promising 'biofactories' for biotechnological applications. Among bioactive compounds, diatoms can produce ovothiols, histidine-derivatives, endowed with unique antioxidant and anti-inflammatory properties, and occurring in many marine invertebrates, bacteria and pathogenic protozoa. However, the functional role of ovothiols biosynthesis in organisms remains almost unexplored. In this work, we have characterized the thiol fraction of Phaeodactylum tricornutum, providing the first evidence of the presence of ovothiol B in pennate diatoms. We have used P. tricornutum to overexpress the 5-histidylcysteine sulfoxide synthase ovoA, the gene encoding the key enzyme involved in ovothiol biosynthesis and we have discovered that OvoA localizes in the mitochondria, a finding that uncovers new concepts in cellular redox biochemistry. We have also obtained engineered biolistic clones that can produce higher amount of ovothiol B compared to wild-type cells, suggesting a new strategy for the eco-sustainable production of these molecules.}, }
@article {pmid36720422, year = {2023}, author = {Baltazar-Soares, M and Karell, P and Wright, D and Nilsson, J&#xc5; and Brommer, JE}, title = {Bringing to light nuclear-mitochondrial insertions in the genomes of nocturnal predatory birds.}, journal = {Molecular phylogenetics and evolution}, volume = {181}, number = {}, pages = {107722}, doi = {10.1016/j.ympev.2023.107722}, pmid = {36720422}, issn = {1095-9513}, mesh = {Animals ; Phylogeny ; *Mitochondria/genetics ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; Birds/genetics ; Sequence Analysis, DNA ; Cell Nucleus/genetics ; }, abstract = {Mito-nuclear insertions, or NUMTs, relate to genetic material of mitochondrial origin that have been transferred to the nuclear DNA molecule. The increasing amounts of genomic data currently being produced presents an opportunity to investigate this type of patterns in genome evolution of non-model organisms. Identifying NUMTs across a range of closely related taxa allows one to generalize patterns of insertion and maintenance in autosomes, which is ultimately relevant to the understanding of genome biology and evolution. Here we collected existing pairwise genome-mitogenome data of the order Strigiformes, a group that includes all the nocturnal bird predators. We identified NUMTs by applying percent similarity thresholds after blasting mitochondrial genomes against nuclear genome assemblies. We identified NUMTsin all genomes with numbers ranging from 4 in Bubo bubo to 24 in Ciccaba nigrolineata. Statistical analyses revealed NUMT size to negatively correlate with NUMT's sequence similarity to with original mtDNA region. Lastly, characterizing these nuclear insertions of mitochondrial origin in a comparative genomics framework produced variable phylogenetic patterns, suggesting in some cases that insertions might pre-date speciation events within Strigiformes.}, }
@article {pmid36717448, year = {2022}, author = {Shilovsky, GA and Putyatina, TS and Markov, AV}, title = {Evolution of Longevity as a Species-Specific Trait in Mammals.}, journal = {Biochemistry. Biokhimiia}, volume = {87}, number = {12}, pages = {1579-1599}, doi = {10.1134/S0006297922120148}, pmid = {36717448}, issn = {1608-3040}, mesh = {Animals ; *Longevity ; *Antioxidants ; Reproducibility of Results ; Aging/metabolism ; Mammals ; }, abstract = {From the evolutionary point of view, the priority problem for an individual is not longevity, but adaptation to the environment associated with the need for survival, food supply, and reproduction. We see two main vectors in the evolution of mammals. One is a short lifespan and numerous offspring ensuring reproductive success (r-strategy). The other one is development of valuable skills in order compete successfully (K-strategy). Species with the K-strategy should develop and enhance specific systems (anti-aging programs) aimed at increasing the reliability and adaptability, including lifespan. These systems are signaling cascades that provide cell repair and antioxidant defense. Hence, any arbitrarily selected long-living species should be characterized by manifestation to a different extent of the longevity-favoring traits (e.g., body size, brain development, sociality, activity of body repair and antioxidant defense systems, resistance to xenobiotics and tumor formation, presence of neotenic traits). Hereafter, we will call a set of such traits as the gerontological success of a species. Longevity is not equivalent to the evolutionary or reproductive success. This difference between these phenomena reaches its peak in mammals due to the development of endothermy and cephalization associated with the cerebral cortex expansion, which leads to the upregulated production of oxidative radicals by the mitochondria (and, consequently, accelerated aging), increase in the number of non-dividing differentiated cells, accumulation of the age-related damage in these cells, and development of neurodegenerative diseases. The article presents mathematical indicators used to assess the predisposition to longevity in different species (including the standard mortality rate and basal metabolic rate, as well as their derivatives). The properties of the evolution of mammals (including the differences between modern mammals and their ancestral forms) are also discussed.}, }
@article {pmid36717086, year = {2023}, author = {Nishita, Y and Amaike, Y and Spassov, N and Hristova, L and Kostov, D and Vladova, D and Peeva, S and Raichev, E and Vlaeva, R and Masuda, R}, title = {Diversity of mitochondrial D-loop haplotypes from ancient Thracian horses in Bulgaria.}, journal = {Animal science journal = Nihon chikusan Gakkaiho}, volume = {94}, number = {1}, pages = {e13810}, doi = {10.1111/asj.13810}, pmid = {36717086}, issn = {1740-0929}, support = {Joint Research Project Grant//Japan Society for the Promotion of Science/ ; The Thracians: Genesis and Development of the Ethn//Bulgarian Academy of Sciences/ ; }, mesh = {Horses/genetics ; Animals ; Bulgaria ; Haplotypes/genetics ; Phylogeny ; *Mitochondria/genetics ; *DNA, Mitochondrial/genetics ; Genetic Variation ; }, abstract = {The domestication of the horse began possibly more than 5000 years ago in the western part of the Eurasian steppe, and according to the leading hypothesis, horses first spread from the Steppe toward the region of the Thracian culture, starting in the second half of the 2nd millennium BCE and flourished from the fifth to first centuries BCE, mainly located in present-day Bulgaria. We analyzed 17 horse bone remains excavated from Thracian archaeological sites (fourth to first centuries BCE) in Bulgaria and successfully identified 17 sequences representing 14 different haplotypes of the mitochondrial D-loop. Compared with the mtDNA haplotypes of modern horses around the world, ancient Thracian horses in Bulgaria are thought to be more closely related to modern horses of Southern Europe and less related to those of Central Asia. In addition, the haplotypes we obtained represented 11 previously reported modern horse mtDNA haplogroups: A, B, D, E, G, H, I, L, N, P, and Q. All the haplogroups contain modern and regionally predominant haplotypes occurring in Europe, the Middle East, and Central Asia. Our results indicate that Thracian horses in Bulgaria have had relatively high genetic diversity and are closely related to modern horse breeds.}, }
@article {pmid36702320, year = {2023}, author = {Buonvicino, D and Ranieri, G and Guasti, D and Pistolesi, A and La Rocca, AI and Rapizzi, E and Chiarugi, A}, title = {Early derangement of axonal mitochondria occurs in a mouse model of progressive but not relapsing-remitting multiple sclerosis.}, journal = {Neurobiology of disease}, volume = {178}, number = {}, pages = {106015}, doi = {10.1016/j.nbd.2023.106015}, pmid = {36702320}, issn = {1095-953X}, mesh = {Mice ; Female ; Animals ; *Multiple Sclerosis/pathology ; Hydrogen Peroxide/metabolism ; Mice, Inbred NOD ; *Encephalomyelitis, Autoimmune, Experimental/pathology ; Spinal Cord/pathology ; *Multiple Sclerosis, Relapsing-Remitting/metabolism ; Axons/pathology ; Mitochondria/metabolism ; DNA, Mitochondrial/metabolism ; }, abstract = {INTRODUCTION: Derangement of axonal mitochondrial bioenergetics occurs during progressive multiple sclerosis (PMS). However, whether this is a delayed epiphenomenon or an early causative event of disease progression waits to be understood. Answering this question might further our knowledge of mechanisms underlying neurobiology of PMS and related therapy.<br><br>METHODS: MOG35-55-immunized NOD and PLP139-151-immunized SJL female mice were adopted as models of progressive or relapsing-remitting experimental autoimmune encephalomyelitis (EAE), respectively. Multiple parameters of mitochondrial homeostasis were analyzed in the mouse spinal cord during the early asymptomatic stage, also evaluating the effects of scavenging mitochondrial reactive oxygen species with Mito-TEMPO.<br><br>RESULTS: Almost identical lumbar spinal cord immune infiltrates consisting of Th1 cells and neutrophils without B and Th17 lymphocytes occurred early upon immunization in both mouse strains. Still, only NOD mice showed axon-restricted dysregulation of mitochondrial homeostasis, with reduced mtDNA contents and increased cristae area. Increased expression of mitochondrial respiratory complex subunits Nd2, Cox1, Atp5d, Sdha also exclusively occurred in lumbar spinal cord of NOD and not SJL mice. Accordingly, in this region genes regulating mitochondrial morphology (Opa1, Mfn1, Mfn2 and Atp5j2) and mitochondriogenesis (Pgc1&#x3b1;, Foxo, Hif-1&#x3b1; and Nrf2) were induced early upon immunization. A reduced extent of mitochondrial derangement occurred in the thoracic spinal cord. Notably, the mitochondrial radical scavenger Mito-TEMPO reduced H2O2 content and prevented both mtDNA depletion and cristae remodeling, having no effects on dysregulation of mitochondrial transcriptome.<br><br>DISCUSSION: We provide here the first evidence that axonal-restricted derangement of mitochondrial homeostasis already occurs during the asymptomatic state exclusively in a mouse model of PMS. Data further our understanding of mechanisms related to EAE progression, and point to very early axonal mitochondrial dysfunction as central to the neuropathogenesis of MS evolution.}, }
@article {pmid36695030, year = {2023}, author = {Röhricht, H and Przybyla-Toscano, J and Forner, J and Boussardon, C and Keech, O and Rouhier, N and Meyer, EH}, title = {Mitochondrial ferredoxin-like is essential for forming complex I-containing supercomplexes in Arabidopsis.}, journal = {Plant physiology}, volume = {191}, number = {4}, pages = {2170-2184}, pmid = {36695030}, issn = {1532-2548}, mesh = {*Ferredoxins/genetics/metabolism ; *Arabidopsis/genetics/metabolism ; Phylogeny ; Electron Transport Complex I/genetics/metabolism ; Mitochondria/metabolism ; }, abstract = {In eukaryotes, mitochondrial ATP is mainly produced by the oxidative phosphorylation (OXPHOS) system, which is composed of 5 multiprotein complexes (complexes I-V). Analyses of the OXPHOS system by native gel electrophoresis have revealed an organization of OXPHOS complexes into supercomplexes, but their roles and assembly pathways remain unclear. In this study, we characterized an atypical mitochondrial ferredoxin (mitochondrial ferredoxin-like, mFDX-like). This protein was previously found to be part of the bridge domain linking the matrix and membrane arms of the complex I. Phylogenetic analysis suggested that the Arabidopsis (Arabidopsis thaliana) mFDX-like evolved from classical mitochondrial ferredoxins (mFDXs) but lost one of the cysteines required for the coordination of the iron-sulfur (Fe-S) cluster, supposedly essential for the electron transfer function of FDXs. Accordingly, our biochemical study showed that AtmFDX-like does not bind an Fe-S cluster and is therefore unlikely to be involved in electron transfer reactions. To study the function of mFDX-like, we created deletion lines in Arabidopsis using a CRISPR/Cas9-based strategy. These lines did not show any abnormal phenotype under standard growth conditions. However, the characterization of the OXPHOS system demonstrated that mFDX-like is important for the assembly of complex I and essential for the formation of complex I-containing supercomplexes. We propose that mFDX-like and the bridge domain are required for the correct conformation of the membrane arm of complex I that is essential for the association of complex I with complex III2 to form supercomplexes.}, }
@article {pmid36672951, year = {2023}, author = {Zhang, T and Wang, Y and Song, H}, title = {The Complete Mitochondrial Genome and Gene Arrangement of the Enigmatic Scaphopod Pictodentalium vernedei.}, journal = {Genes}, volume = {14}, number = {1}, pages = {}, pmid = {36672951}, issn = {2073-4425}, mesh = {Animals ; *Genome, Mitochondrial ; Phylogeny ; Gene Order ; Mollusca/genetics ; Mitochondria/genetics ; }, abstract = {The enigmatic scaphopods, or tusk shells, are a small and rare group of molluscs whose phylogenomic position among the Conchifera is undetermined, and the taxonomy within this class also needs revision. Such work is hindered by there only being a very few mitochondrial genomes in this group that are currently available. Here, we present the assembly and annotation of the complete mitochondrial genome from Dentaliida Pictodentalium vernedei, whose mitochondrial genome is 14,519 bp in size, containing 13 protein-coding genes, 22 tRNA genes and two rRNA genes. The nucleotide composition was skewed toward A-T, with a 71.91% proportion of AT content. Due to the mitogenome-based phylogenetic analysis, we defined P. vernedei as a sister to Graptacme eborea in Dentaliida. Although a few re-arrangements occurred, the mitochondrial gene order showed deep conservation within Dentaliida. Yet, such a gene order in Dentaliida largely diverges from Gadilida and other molluscan classes, suggesting that scaphopods have the highest degree of mitogenome arrangement compared to other molluscs.}, }
@article {pmid36671555, year = {2023}, author = {Righetto, I and Gasparotto, M and Casalino, L and Vacca, M and Filippini, F}, title = {Exogenous Players in Mitochondria-Related CNS Disorders: Viral Pathogens and Unbalanced Microbiota in the Gut-Brain Axis.}, journal = {Biomolecules}, volume = {13}, number = {1}, pages = {}, pmid = {36671555}, issn = {2218-273X}, mesh = {Humans ; *COVID-19 ; SARS-CoV-2 ; Brain-Gut Axis ; *Central Nervous System Diseases ; *Gastrointestinal Microbiome ; Mitochondria ; }, abstract = {Billions of years of co-evolution has made mitochondria central to the eukaryotic cell and organism life playing the role of cellular power plants, as indeed they are involved in most, if not all, important regulatory pathways. Neurological disorders depending on impaired mitochondrial function or homeostasis can be caused by the misregulation of "endogenous players", such as nuclear or cytoplasmic regulators, which have been treated elsewhere. In this review, we focus on how exogenous agents, i.e., viral pathogens, or unbalanced microbiota in the gut-brain axis can also endanger mitochondrial dynamics in the central nervous system (CNS). Neurotropic viruses such as Herpes, Rabies, West-Nile, and Polioviruses seem to hijack neuronal transport networks, commandeering the proteins that mitochondria typically use to move along neurites. However, several neurological complications are also associated to infections by pandemic viruses, such as Influenza A virus and SARS-CoV-2 coronavirus, representing a relevant risk associated to seasonal flu, coronavirus disease-19 (COVID-19) and "Long-COVID". Emerging evidence is depicting the gut microbiota as a source of signals, transmitted via sensory neurons innervating the gut, able to influence brain structure and function, including cognitive functions. Therefore, the direct connection between intestinal microbiota and mitochondrial functions might concur with the onset, progression, and severity of CNS diseases.}, }
@article {pmid36670920, year = {2022}, author = {Cruz-Gregorio, A and Aranda-Rivera, AK and Aparicio-Trejo, OE and Medina-Campos, ON and Sciutto, E and Fragoso, G and Pedraza-Chaverri, J}, title = {GK-1 Induces Oxidative Stress, Mitochondrial Dysfunction, Decreased Membrane Potential, and Impaired Autophagy Flux in a Mouse Model of Breast Cancer.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {36670920}, issn = {2076-3921}, support = {IN218822//National Autonomous University of Mexico/ ; IN200922//National Autonomous University of Mexico/ ; 302961//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; A1-S-7495//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 5000-9105//Programa de Apoyo a la Investigaci&#xf3;n y el Posgrado (PAIP), Facultd de Qu&#xed;mica, UNAM/ ; }, abstract = {Breast cancer (BC) is the second most common cancer worldwide in women. During the last decades, the mortality due to breast cancer has progressively decreased due to early diagnosis and the emergence of more effective new treatments. However, human epidermal growth factor receptor 2 (HER2) and triple-negative breast cancer (TNBC) remain with poor prognoses. In our research group, we are proposing the GK-1 immunomodulatory peptide as a new alternative for immunotherapy of these aggressive tumors. GK-1 reduced the growth rate of established tumors and effectively reduced lung metastasis in the 4T1 experimental murine model of breast cancer. Herein, the effect of GK-1 on the redox state, mitochondrial metabolism, and autophagy of triple-negative tumors that can be linked to cancer evolution was studied. GK-1 decreased catalase activity, reduced glutathione (GSH) content and GSH/oxidized glutathione (GSSG) ratio while increased hydrogen peroxide (H2O2) production, GSSG, and protein carbonyl content, inducing oxidative stress (OS) in tumoral tissues. This imbalance between reactive oxygen species (ROS) and antioxidants was related to mitochondrial dysfunction and uncoupling, characterized by reduced mitochondrial respiratory parameters and dissipation of mitochondrial membrane potential (ΔΨm), respectively. Furthermore, GK-1 likely affected autophagy flux, confirmed by elevated levels of p62, a marker of autophagy flux. Overall, the induction of OS, dysfunction, and uncoupling of the mitochondria and the reduction of autophagy could be molecular mechanisms that underlie the reduction of the 4T1 breast cancer induced by GK-1.}, }
@article {pmid36657651, year = {2023}, author = {Moreno-Carmona, M and Montaña-Lozano, P and Prada Quiroga, CF and Baeza, JA}, title = {Comparative analysis of mitochondrial genomes reveals family-specific architectures and molecular features in scorpions (Arthropoda: Arachnida: Scorpiones).}, journal = {Gene}, volume = {859}, number = {}, pages = {147189}, doi = {10.1016/j.gene.2023.147189}, pmid = {36657651}, issn = {1879-0038}, mesh = {Humans ; Animals ; Scorpions/genetics ; *Arachnida/genetics ; *Genome, Mitochondrial/genetics ; Phylogeny ; Mitochondria/genetics ; RNA, Transfer/genetics ; }, abstract = {Scorpions are a group of arachnids with great evolutionary success that comprise more than 2,000 described species. Mitochondrial genomes have been little studied in this clade. We describe and compare different scorpion mitochondrial genomes and analyze their architecture and molecular characteristics. We assembled eight new scorpion mitochondrial genomes from transcriptomic datasets, annotated them, predicted the secondary structures of tRNAs, and compared the nucleotide composition, codon usage, and relative synonymous codon usage of 16 complete scorpion mitochondrial genomes. Lastly, we provided a phylogeny based on all mitochondrial protein coding genes. We characterized the mitogenomes in detail and reported particularities such as dissimilar synteny in the family Buthidae compared to other scorpions, unusual tRNA secondary structures, and unconventional start and stop codons in all scorpions. Our comparative analysis revealed that scorpion mitochondrial genomes exhibit different architectures and features depending on taxonomic identity. We highlight the parvorder Buthida, particularly the family Buthidae, as it invariably exhibited different mitogenome features such as synteny, codon usage, and AT-skew compared to the parvorder Iurida that included the rest of the scorpion families we analyzed in this study. Our results provide a better understanding of the evolution of mitogenome features and phylogenetic relationships in scorpions.}, }
@article {pmid36656997, year = {2023}, author = {Opazo, JC and Vandewege, MW and Hoffmann, FG and Zavala, K and Meléndez, C and Luchsinger, C and Cavieres, VA and Vargas-Chacoff, L and Morera, FJ and Burgos, PV and Tapia-Rojas, C and Mardones, GA}, title = {How Many Sirtuin Genes Are Out There? Evolution of Sirtuin Genes in Vertebrates With a Description of a New Family Member.}, journal = {Molecular biology and evolution}, volume = {40}, number = {2}, pages = {}, pmid = {36656997}, issn = {1537-1719}, mesh = {Animals ; *Sirtuins/genetics ; *Sirtuin 3/genetics ; Evolution, Molecular ; Vertebrates/genetics ; Phylogeny ; Mammals ; }, abstract = {Studying the evolutionary history of gene families is a challenging and exciting task with a wide range of implications. In addition to exploring fundamental questions about the origin and evolution of genes, disentangling their evolution is also critical to those who do functional/structural studies to allow a deeper and more precise interpretation of their results in an evolutionary context. The sirtuin gene family is a group of genes that are involved in a variety of biological functions mostly related to aging. Their duplicative history is an open question, as well as the definition of the repertoire of sirtuin genes among vertebrates. Our results show a well-resolved phylogeny that represents an improvement in our understanding of the duplicative history of the sirtuin gene family. We identified a new sirtuin gene family member (SIRT3.2) that was apparently lost in the last common ancestor of amniotes but retained in all other groups of jawed vertebrates. According to our experimental analyses, elephant shark SIRT3.2 protein is located in mitochondria, the overexpression of which leads to an increase in cellular levels of ATP. Moreover, in vitro analysis demonstrated that it has deacetylase activity being modulated in a similar way to mammalian SIRT3. Our results indicate that there are at least eight sirtuin paralogs among vertebrates and that all of them can be traced back to the last common ancestor of the group that existed between 676 and 615 millions of years ago.}, }
@article {pmid36651963, year = {2023}, author = {Moreira, F and Arenas, M and Videira, A and Pereira, F}, title = {Evolution of TOP1 and TOP1MT Topoisomerases in Chordata.}, journal = {Journal of molecular evolution}, volume = {91}, number = {2}, pages = {192-203}, pmid = {36651963}, issn = {1432-1432}, mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Chordata/genetics ; DNA Topoisomerases, Type I/genetics/chemistry/metabolism ; Mitochondria/genetics ; Cell Nucleus/genetics ; }, abstract = {Type IB topoisomerases relax the torsional stress associated with DNA metabolism in the nucleus and mitochondria and constitute important molecular targets of anticancer drugs. Vertebrates stand out among eukaryotes by having two Type IB topoisomerases acting specifically in the nucleus (TOP1) and mitochondria (TOP1MT). Despite their major importance, the origin and evolution of these paralogues remain unknown. Here, we examine the molecular evolutionary processes acting on both TOP1 and TOP1MT in Chordata, taking advantage of the increasing number of available genome sequences. We found that both TOP1 and TOP1MT evolved under strong purifying selection, as expected considering their essential biological functions. Critical active sites, including those associated with resistance to anticancer agents, were found particularly conserved. However, TOP1MT presented a higher rate of molecular evolution than TOP1, possibly related with its specialized activity on the mitochondrial genome and a less critical role in cells. We could place the duplication event that originated the TOP1 and TOP1MT paralogues early in the radiation of vertebrates, most likely associated with the first round of vertebrate tetraploidization (1R). Moreover, our data suggest that cyclostomes present a specialized mitochondrial Type IB topoisomerase. Interestingly, we identified two missense mutations replacing amino acids in the Linker region of TOP1MT in Neanderthals, which appears as a rare event when comparing the genome of both species. In conclusion, TOP1 and TOP1MT differ in their rates of evolution, and their evolutionary histories allowed us to better understand the evolution of chordates.}, }
@article {pmid36648250, year = {2023}, author = {Graham, AM and Barreto, FS}, title = {Myxozoans (Cnidaria) do not Retain Key Oxygen-Sensing and Homeostasis Toolkit Genes.}, journal = {Genome biology and evolution}, volume = {15}, number = {1}, pages = {}, pmid = {36648250}, issn = {1759-6653}, mesh = {Animals ; *Cnidaria/metabolism ; Oxygen/metabolism ; *Myxozoa/genetics ; Hypoxia/genetics ; Homeostasis ; Hypoxia-Inducible Factor 1, alpha Subunit ; }, abstract = {For aerobic organisms, both the hypoxia-inducible factor pathway and the mitochondrial genomes are key players in regulating oxygen homeostasis. Recent work has suggested that these mechanisms are not as highly conserved as previously thought, prompting more surveys across animal taxonomic levels, which would permit testing of hypotheses about the ecological conditions facilitating evolutionary loss of such genes. The Phylum Cnidaria is known to harbor wide variation in mitochondrial chromosome morphology, including an extreme example, in the Myxozoa, of mitochondrial genome loss. Because myxozoans are obligate endoparasites, frequently encountering hypoxic environments, we hypothesize that variation in environmental oxygen availability could be a key determinant in the evolution of metabolic gene networks associated with oxygen-sensing, hypoxia-response, and energy production. Here, we surveyed genomes and transcriptomes across 46 cnidarian species for the presence of HIF pathway members, as well as for an assortment of hypoxia, mitochondrial, and stress-response toolkit genes. We find that presence of the HIF pathway, as well as number of genes associated with mitochondria, hypoxia, and stress response, do not vary in parallel to mitochondrial genome morphology. More interestingly, we uncover evidence that myxozoans have lost the canonical HIF pathway repression machinery, potentially altering HIF pathway functionality to work under the specific conditions of their parasitic lifestyles. In addition, relative to other cnidarians, myxozoans show loss of large proportions of genes associated with the mitochondrion and involved in response to hypoxia and general stress. Our results provide additional evidence that the HIF regulatory machinery is evolutionarily labile and that variations in the canonical system have evolved in many animal groups.}, }
@article {pmid36646908, year = {2023}, author = {Muñoz-Gómez, SA}, title = {Energetics and evolution of anaerobic microbial eukaryotes.}, journal = {Nature microbiology}, volume = {8}, number = {2}, pages = {197-203}, pmid = {36646908}, issn = {2058-5276}, mesh = {*Eukaryota ; Anaerobiosis ; *Mitochondria/metabolism ; Eukaryotic Cells/metabolism ; Fermentation ; }, abstract = {Mitochondria and aerobic respiration have been suggested to be required for the evolution of eukaryotic cell complexity. Aerobic respiration is several times more energetically efficient than fermentation. Moreover, aerobic respiration occurs at internalized mitochondrial membranes that are not constrained by a sublinear scaling with cell volume. However, diverse and complex anaerobic eukaryotes (for example, free-living and parasitic unicellular, and even small multicellular, eukaryotes) that exclusively rely on fermentation for energy generation have evolved repeatedly from aerobic ancestors. How do fermenting eukaryotes maintain their cell volumes and complexity while relying on such a low energy-yielding process? Here I propose that reduced rates of ATP generation in fermenting versus respiring eukaryotes are compensated for by longer cell cycles that satisfy lifetime energy demands. A literature survey and growth efficiency calculations show that fermenting eukaryotes divide approximately four to six times slower than aerobically respiring counterparts with similar cell volumes. Although ecological advantages such as competition avoidance offset lower growth rates and yields in the short term, fermenting eukaryotes inevitably have fewer physiological and ecological possibilities, which ultimately constrain their long-term evolutionary trajectories.}, }
@article {pmid36644898, year = {2023}, author = {He, W and Xiang, K and Chen, C and Wang, J and Wu, Z}, title = {Master graph: an essential integrated assembly model for the plant mitogenome based on a graph-based framework.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {1}, pages = {}, doi = {10.1093/bib/bbac522}, pmid = {36644898}, issn = {1477-4054}, mesh = {Animals ; *Genome, Mitochondrial ; DNA, Mitochondrial/genetics ; Biological Evolution ; Mitochondria/genetics ; Plants/genetics ; Phylogeny ; }, abstract = {Unlike the typical single circular structure of most animal mitochondrial genomes (mitogenome), the drastic structural variation of plant mitogenomes is a result of a mixture of molecules of various sizes and structures. Obtaining the full panoramic plant mitogenome is still considered a roadblock in evolutionary biology. In this study, we developed a graph-based sequence assembly toolkit (GSAT) to construct the pan-structural landscape of plant mitogenome with high-quality mitochondrial master graphs (MMGs) for model species including rice (Oryza sativa) and thale cress (Arabidopsis thaliana). The rice and thale cress MMGs have total lengths of 346 562 and 358 041 bp, including 9 and 6 contigs and 12 and 8 links, respectively, and could be further divided into 6 and 3 minimum master circles and 4 and 2 minimum secondary circles separately. The nuclear mitochondrial DNA segments (NUMTs) in thale cress strongly affected the frequency evaluation of the homologous structures in the mitogenome, while the effects of NUMTs in rice were relatively weak. The mitochondrial plastid DNA segments (MTPTs) in both species had no effects on the assessment of the MMGs. All potential recombinant structures were evaluated, and the findings revealed that all, except for nuclear-homologous structures, MMG structures are present at a much higher frequency than non-MMG structures are. Investigations of potential circular and linear molecules further supported multiple dominant structures in the mitogenomes and could be completely summarized in the MMG. Our study provided an efficient and accurate model for assembling and applying graph-based plant mitogenomes to assess their pan-structural variations.}, }
@article {pmid36642905, year = {2022}, author = {Zhou, XQ and Ma, J and Wang, RY and Wang, RH and Wu, YQ and Yang, XY and Chen, YJ and Tang, XN and Sun, ET}, title = {[Bacterial community diversity in Dermatophagoides farinae using high-throughput sequencing].}, journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control}, volume = {34}, number = {6}, pages = {630-634}, doi = {10.16250/j.32.1374.2022105}, pmid = {36642905}, issn = {1005-6661}, support = {31870352//National Natural Science Foundation of China/ ; S202110368010//Anhui Provincial University Students' Innovation and Entrepreneurship Training Program/ ; }, mesh = {Humans ; Animals ; *Dermatophagoides farinae/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Phylogeny ; }, abstract = {OBJECTIVE: To investigate the bacterial community diversity in Dermatophagoides farinae.<br><br>METHODS: Laboratory-cultured D. farinae was collected, and the composition of microbial communities was determined by sequence analyses of the V4 region in the bacterial 16S ribosomal RNA (16S rRNA) gene on an Illumina PE250 high-throughput sequencing platform. Following quality control and filtering of the raw sequence files, valid reads were obtained and subjected to operational taxonomic units (OTU) clustering and analysis of the composition of microbial communities and alpha diversity index using the Usearch software, Silva database, and Mothur software.<br><br>RESULTS: A total of 187 616 valid reads were obtained, and 469 OTUs were clustered based on a sequence similarity of more than 97%. OTU annotation showed that the bacteria in D. farinae belonged to 26 phyla, 43 classes, 100 orders, 167 families and 284 genera. The bacteria in D. farinae were mainly annotated to five phyla of Proteobacteria, Firmicutes, Bacteroidota, Actinobacteriota, and Acidobacteriota, with Proteobacteria as the dominant phylum, and mainly annotated to five dominant genera of Ralstonia, norank-f-Mitochondria, Staphylococcus and Sphingomonas, with Wolbachia identified in the non-dominant genus.<br><br>CONCLUSIONS: A high diversity is identified in the composition of the bacterial community in D. farinae, and there are differences in bacterial community diversity and abundance among D. farinae.}, }
@article {pmid36638953, year = {2023}, author = {Gnocchi, D and Sabbà, C and Mazzocca, A}, title = {Lactic acid fermentation: A maladaptive mechanism and an evolutionary throwback boosting cancer drug resistance.}, journal = {Biochimie}, volume = {208}, number = {}, pages = {180-185}, doi = {10.1016/j.biochi.2023.01.005}, pmid = {36638953}, issn = {1638-6183}, mesh = {Humans ; *Lactic Acid/metabolism ; Fermentation ; Glycolysis ; Mitochondria/metabolism ; *Neoplasms/drug therapy/genetics/metabolism ; Drug Resistance, Neoplasm/genetics ; }, abstract = {After four decades of research primarily focused on tumour genetics, the importance of metabolism in tumour biology is receiving renewed attention. Cancer cells undergo energy, biosynthetic and metabolic rewiring, which involves several pathways with a prevalent change from oxidative phosphorylation (OXPHOS) to lactic acid fermentation, known as the Warburg effect. During carcinogenesis, microenvironmental changes can trigger the transition from OXPHOS to lactic acid fermentation, an ancient form of energy supply, mimicking the behaviour of certain anaerobic unicellular organisms according to "atavistic" models of cancer. However, the role of this transition as a mechanism of cancer drug resistance is unclear. Here, we hypothesise that the metabolic rewiring of cancer cells to fermentation can be triggered, enhanced, and sustained by exposure to chronic or high-dose chemotherapy, thereby conferring resistance to drug therapy. We try to expand on the idea that metabolic reprogramming from OXPHOS to lactate fermentation in drug-resistant tumour cells occurs as a general phenotypic mechanism in any type of cancer, regardless of tumour cell heterogeneity, biodiversity, and genetic characteristics. This metabolic response may therefore represent a common feature in cancer biology that could be exploited for therapeutic purposes to overcome chemotherapy resistance, which is currently a major challenge in cancer treatment.}, }
@article {pmid36636864, year = {2023}, author = {Achatz, TJ and Von Holten, ZS and Kipp, JW and Fecchio, A and LaFond, LR and Greiman, SE and Martens, JR and Tkach, VV}, title = {Phylogenetic relationships and further unknown diversity of diplostomids (Diplostomida: Diplostomidae) parasitic in kingfishers.}, journal = {Journal of helminthology}, volume = {97}, number = {}, pages = {e8}, doi = {10.1017/S0022149X22000852}, pmid = {36636864}, issn = {1475-2697}, support = {P20GM103442/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Phylogeny ; *Trematoda ; Fishes/parasitology ; Mitochondria ; Brazil ; }, abstract = {Kingfishers (Alcedinidae Rafinesque) are common inhabitants of wetlands and are known to be definitive hosts to a wide range of digeneans that parasitize fish as second intermediate hosts. Among these digeneans, members of the Diplostomidae Poirier, 1886 (diplostomids) are particularly common. Recent studies of diplostomids collected from kingfishers have revealed that they are probably more diverse than currently known. This particularly concerns the genera Crassiphiala Van Haitsma, 1925 and Uvulifer Yamaguti, 1934. In the present work, we studied seven diplostomid taxa from kingfishers in Brazil, the USA and the Philippines. Partial DNA sequences of the nuclear large ribosomal subunit (28S) and mitochondrial cytochrome c oxidase I (cox1) genes were obtained, and 28S sequences were used to study the phylogenetic interrelationships of these diplostomids. We provide the first DNA sequences from Uvulifer semicircumcisus Dubois et Rausch, 1950 and a member of Subuvulifer Dubois, 1952. Pseudocrassiphiala n. gen. is erected for a previously recognized species-level lineage of Crassiphiala and a new generic diagnosis of Crassiphiala is provided. Crassiphiala jeffreybelli n. sp., Crassiphiala wecksteini n. sp. and Pseudocrassiphiala tulipifera n. sp. are described, and a description of newly collected, high-quality specimens of Crassiphiala bulboglossa Van Haitsma, 1925 (the type-species of the genus) is provided.}, }
@article {pmid36634192, year = {2023}, author = {Osipova, E and Barsacchi, R and Brown, T and Sadanandan, K and Gaede, AH and Monte, A and Jarrells, J and Moebius, C and Pippel, M and Altshuler, DL and Winkler, S and Bickle, M and Baldwin, MW and Hiller, M}, title = {Loss of a gluconeogenic muscle enzyme contributed to adaptive metabolic traits in hummingbirds.}, journal = {Science (New York, N.Y.)}, volume = {379}, number = {6628}, pages = {185-190}, doi = {10.1126/science.abn7050}, pmid = {36634192}, issn = {1095-9203}, mesh = {Animals ; *Birds/genetics/metabolism ; Energy Metabolism/genetics ; *Flight, Animal/physiology ; *Gluconeogenesis/genetics ; *Adaptation, Physiological/genetics ; *Fructose-Bisphosphatase/genetics ; *Muscle, Skeletal/enzymology ; }, abstract = {Hummingbirds possess distinct metabolic adaptations to fuel their energy-demanding hovering flight, but the underlying genomic changes are largely unknown. Here, we generated a chromosome-level genome assembly of the long-tailed hermit and screened for genes that have been specifically inactivated in the ancestral hummingbird lineage. We discovered that FBP2 (fructose-bisphosphatase 2), which encodes a gluconeogenic muscle enzyme, was lost during a time period when hovering flight evolved. We show that FBP2 knockdown in an avian muscle cell line up-regulates glycolysis and enhances mitochondrial respiration, coincident with an increased mitochondria number. Furthermore, genes involved in mitochondrial respiration and organization have up-regulated expression in hummingbird flight muscle. Together, these results suggest that FBP2 loss was likely a key step in the evolution of metabolic muscle adaptations required for true hovering flight.}, }
@article {pmid36634115, year = {2023}, author = {Rossitto De Marchi, B and Gama, AB and Smith, HA}, title = {Evidence of the association between the Q2 mitochondrial group of Bemisia tabaci MED species (Hemiptera: Aleyrodidae) and low competitive displacement capability.}, journal = {PloS one}, volume = {18}, number = {1}, pages = {e0280002}, pmid = {36634115}, issn = {1932-6203}, mesh = {Animals ; Phylogeny ; *Hemiptera/genetics ; Mitochondria/genetics ; Food ; Florida ; }, abstract = {The whitefly, Bemisia tabaci (Gennadius), is one of the most serious agricultural pests worldwide. Bemisia tabaci is a cryptic species complex of more than 40 species among which the invasive MEAM1 and MED species are the most widespread and economically important. Both MEAM1 and MED present intraspecific genetic variability and some haplotypes are reported to be more invasive than others. MED can be further deconstructed into different genetic groups, including MED-Q1 and MED-Q2. However, distinct biological phenotypes discerning the different MED mitochondrial haplotypes are yet to be characterized. Competitive displacement and life-history trials were carried out between MED-Q2 and MEAM1 populations collected in Florida, USA. In addition, a phylogenetic analysis was carried out including populations from previous whitefly competitive displacement studies for identification and comparison of the MED mitochondrial groups. In contrast to other studies with MED-Q1, the MED-Q2 population from Florida is less likely to displace MEAM1 on pepper. In addition, both pepper and watermelon were a more favorable host to MEAM1 compared to MED-Q2 according to the life history trials.}, }
@article {pmid36632145, year = {2023}, author = {Borges, DGF and Carvalho, DS and Bomfim, GC and Ramos, PIP and Brzozowski, J and Góes-Neto, A and Andrade, R and El-Hani, C}, title = {On the origin of mitochondria: a multilayer network approach.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14571}, pmid = {36632145}, issn = {2167-8359}, mesh = {Phylogeny ; *Mitochondria/genetics ; Biological Evolution ; *Alphaproteobacteria/genetics ; Genes, Mitochondrial ; }, abstract = {BACKGOUND: The endosymbiotic theory is widely accepted to explain the origin of mitochondria from a bacterial ancestor. While ample evidence supports the intimate connection of Alphaproteobacteria to the mitochondrial ancestor, pinpointing its closest relative within sampled Alphaproteobacteria is still an open evolutionary debate. Many different phylogenetic methods and approaches have been used to answer this challenging question, further compounded by the heterogeneity of sampled taxa, varying evolutionary rates of mitochondrial proteins, and the inherent biases in each method, all factors that can produce phylogenetic artifacts. By harnessing the simplicity and interpretability of protein similarity networks, herein we re-evaluated the origin of mitochondria within an enhanced multilayer framework, which is an extension and improvement of a previously developed method.<br><br>METHODS: We used a dataset of eight proteins found in mitochondria (N = 6 organisms) and bacteria (N = 80 organisms). The sequences were aligned and resulting identity matrices were combined to generate an eight-layer multiplex network. Each layer corresponded to a protein network, where nodes represented organisms and edges were placed following mutual sequence identity. The Multi-Newman-Girvan algorithm was applied to evaluate community structure, and bifurcation events linked to network partition allowed to trace patterns of divergence between studied taxa.<br><br>RESULTS: In our network-based analysis, we first examined the topology of the 8-layer multiplex when mitochondrial sequences disconnected from the main alphaproteobacterial cluster. The resulting topology lent firm support toward an Alphaproteobacteria-sister placement for mitochondria, reinforcing the hypothesis that mitochondria diverged from the common ancestor of all Alphaproteobacteria. Additionally, we observed that the divergence of Rickettsiales was an early event in the evolutionary history of alphaproteobacterial clades.<br><br>CONCLUSION: By leveraging complex networks methods to the challenging question of circumscribing mitochondrial origin, we suggest that the entire Alphaproteobacteria clade is the closest relative to mitochondria (Alphaproteobacterial-sister hypothesis), echoing recent findings based on different datasets and methodologies.}, }
@article {pmid36629021, year = {2023}, author = {Fang, YK and Vaitová, Z and Hampl, V}, title = {A mitochondrion-free eukaryote contains proteins capable of import into an exogenous mitochondrion-related organelle.}, journal = {Open biology}, volume = {13}, number = {1}, pages = {220238}, pmid = {36629021}, issn = {2046-2441}, mesh = {*Eukaryota/metabolism ; *Protozoan Proteins/metabolism ; Organelles/chemistry/metabolism ; Mitochondria/metabolism ; Protein Transport ; }, abstract = {The endobiotic flagellate Monocercomonoides exilis is the only known eukaryote to have lost mitochondria and all its associated proteins in its evolutionary past. This final stage of the mitochondrial evolutionary pathway may serve as a model to explain events at their very beginning such as the initiation of protein import. We have assessed the capability of proteins from this eukaryote to enter emerging mitochondria using a specifically designed in vitro assay. Hydrogenosomes (reduced mitochondria) of Trichomonas vaginalis were incubated with a soluble protein pool derived from a cytosolic fraction of M. exilis, and proteins entering hydrogenosomes were subsequently detected by mass spectrometry. The assay detected 19 specifically and reproducibly imported proteins, and in 14 cases the import was confirmed by the overexpression of their tagged version in T. vaginalis. In most cases, only a small portion of the signal reached the hydrogenosomes, suggesting specific but inefficient transport. Most of these proteins represent enzymes of carbon metabolism, and none exhibited clear signatures of proteins targeted to hydrogenosomes or mitochondria, which is consistent with their inefficient import. The observed phenomenon may resemble a primaeval type of protein import which might play a role in the establishment of the organelle and shaping of its proteome in the initial stages of endosymbiosis.}, }
@article {pmid36613565, year = {2022}, author = {Bottoni, P and Gionta, G and Scatena, R}, title = {Remarks on Mitochondrial Myopathies.}, journal = {International journal of molecular sciences}, volume = {24}, number = {1}, pages = {}, pmid = {36613565}, issn = {1422-0067}, mesh = {Humans ; *Mitochondria/genetics/metabolism ; *Mitochondrial Myopathies/genetics ; Cell Respiration ; Oxidative Phosphorylation ; NAD/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {Mitochondrial myopathies represent a heterogeneous group of diseases caused mainly by genetic mutations to proteins that are related to mitochondrial oxidative metabolism. Meanwhile, a similar etiopathogenetic mechanism (i.e., a deranged oxidative phosphorylation and a dramatic reduction of ATP synthesis) reveals that the evolution of these myopathies show significant differences. However, some physiological and pathophysiological aspects of mitochondria often reveal other potential molecular mechanisms that could have a significant pathogenetic role in the clinical evolution of these disorders, such as: i. a deranged ROS production both in term of signaling and in terms of damaging molecules; ii. the severe modifications of nicotinamide adenine dinucleotide (NAD)+/NADH, pyruvate/lactate, and α-ketoglutarate (α-KG)/2- hydroxyglutarate (2-HG) ratios. A better definition of the molecular mechanisms at the basis of their pathogenesis could improve not only the clinical approach in terms of diagnosis, prognosis, and therapy of these myopathies but also deepen the knowledge of mitochondrial medicine in general.}, }
@article {pmid36610569, year = {2023}, author = {Ji, X and Tian, Y and Liu, W and Lin, C and He, F and Yang, J and Miao, W and Li, Z}, title = {Mitochondrial characteristics of the powdery mildew genus Erysiphe revealed an extraordinary evolution in protein-coding genes.}, journal = {International journal of biological macromolecules}, volume = {230}, number = {}, pages = {123153}, doi = {10.1016/j.ijbiomac.2023.123153}, pmid = {36610569}, issn = {1879-0003}, mesh = {*Erysiphe ; Phylogeny ; *Ascomycota/genetics ; Plants/microbiology ; Plant Diseases/genetics/microbiology ; }, abstract = {The genus Erysiphe was an obligate parasite causing powdery mildew disease on a wide range of higher plants. However, the knowledge of their mitogenome architecture for lifestyle adaptability was scarce. Here, we assembled the first complete mitogenome (190,559 bp in size) for rubber tree powdery mildew pathogen Erysiphe quercicola. Comparable analysis of the Erysiphe mitogenomes exhibited conserved gene content, genome organization and codon usage bias, but extensive dynamic intron gain/loss events were presented between Erysiphe species. The phylogeny of the Ascomycota species constructed in the phylogenetic analysis showed genetic divergences of the Erysiphe species. Compared with other distant saprophytic and plant pathogenic fungi, Erysiphe had a flat distribution of evolutionary pressures on fungal standard protein-coding genes (PCGs). The Erysiphe PCGs had the highest mean selection pressure. In particular, Erysiphe's cox1, nad1, cob and rps3 genes had the most elevated selection pressures among corresponding PCGs across fungal genera. Altogether, the investigations provided a novel insight into the potential evolutionary pattern of the genus Erysiphe to adapt obligate biotrophic lifestyle and promoted the understanding of the high plasticity and population evolution of fungal mitogenomes.}, }
@article {pmid36605953, year = {2022}, author = {Wu, CS and Chen, CI and Chaw, SM}, title = {Plastid phylogenomics and plastome evolution in the morning glory family (Convolvulaceae).}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1061174}, pmid = {36605953}, issn = {1664-462X}, abstract = {Convolvulaceae, the morning glories or bindweeds, is a large family containing species of economic value, including crops, traditional medicines, ornamentals, and vegetables. However, not only are the phylogenetic relationships within this group still debated at the intertribal and intergeneric levels, but also plastid genome (plastome) complexity within Convolvulaceae is not well surveyed. We gathered 78 plastomes representing 17 genera across nine of the 12 Convolvulaceae tribes. Our plastid phylogenomic trees confirm the monophyly of Convolvulaceae, place the genus Jacquemontia within the subfamily Dicranostyloideae, and suggest that the tribe Merremieae is paraphyletic. In contrast, positions of the two genera Cuscuta and Erycibe are uncertain as the bootstrap support of the branches leading to them is moderate to weak. We show that nucleotide substitution rates are extremely variable among Convolvulaceae taxa and likely responsible for the topological uncertainty. Numerous plastomic rearrangements are detected in Convolvulaceae, including inversions, duplications, contraction and expansion of inverted repeats (IRs), and losses of genes and introns. Moreover, integrated foreign DNA of mitochondrial origin was found in the Jacquemontia plastome, adding a rare example of gene transfer from mitochondria to plastids in angiosperms. In the IR of Dichondra, we discovered an extra copy of rpl16 containing a direct repeat of ca. 200 bp long. This repeat was experimentally demonstrated to trigger effective homologous recombination, resulting in the coexistence of intron-containing and -lacking rpl16 duplicates. Therefore, we propose a hypothetical model to interpret intron loss accompanied by invasion of direct repeats at appropriate positions. Our model complements the intron loss model driven by retroprocessing when genes have lost introns but contain abundant RNA editing sites adjacent to former splicing sites.}, }
@article {pmid36605941, year = {2022}, author = {Locatelli, AG and Cenci, S}, title = {Autophagy and longevity: Evolutionary hints from hyper-longevous mammals.}, journal = {Frontiers in endocrinology}, volume = {13}, number = {}, pages = {1085522}, pmid = {36605941}, issn = {1664-2392}, mesh = {Animals ; Mice ; *Longevity/genetics ; *Aging/genetics/metabolism ; Autophagy/physiology ; Saccharomyces cerevisiae ; Mammals ; }, abstract = {Autophagy is a fundamental multi-tasking adaptive cellular degradation and recycling strategy. Following its causal implication in age-related decline, autophagy is currently among the most broadly studied and challenged mechanisms within aging research. Thanks to these efforts, new cellular nodes interconnected with this phylogenetically ancestral pathway and unexpected roles of autophagy-associated genetic products are unveiled daily, yet the history of functional adaptations of autophagy along its evolutive trail is poorly understood and documented. Autophagy is traditionally studied in canonical and research-wise convenient model organisms such as yeast and mice. However, unconventional animal models endowed with extended longevity and exemption from age-related diseases offer a privileged perspective to inquire into the role of autophagy in the evolution of longevity. In this mini review we retrace the appearance and functions evolved by autophagy in eukaryotic cells and its protective contribution in the pathophysiology of aging.}, }
@article {pmid36602189, year = {2023}, author = {Delling, B and Thörn, F and Norén, M and Irestedt, M}, title = {Museomics reveals the phylogenetic position of the extinct Moroccan trout Salmo pallaryi.}, journal = {Journal of fish biology}, volume = {102}, number = {3}, pages = {619-627}, doi = {10.1111/jfb.15299}, pmid = {36602189}, issn = {1095-8649}, mesh = {Animals ; Phylogeny ; *Trout/genetics ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Sequence Analysis, DNA ; }, abstract = {The authors used museomics to reconstruct the mitochondrial genome from two individuals of the Moroccan, endemic and extinct trout, Salmo pallaryi. They further obtained partial data from 21 nuclear genes previously used for trout phylogenetic analyses. Phylogenetic analyses, including publicly available data from the mitochondrial control region and the cytochrome b gene, and the 21 nuclear genes, place S. pallaryi among other North African trouts. mtDNA places S. pallaryi close to Salmo macrostigma within a single North African clade. Although the nuclear coverage of the genome was low, both specimens were independently positioned as sisters to one of two distantly related North African clades, viz. the Atlas clade with the Dades trout, Salmo multipunctatus. Phylogenetic discordance between mtDNA and nuclear DNA phylogenies is briefly discussed. As several specimens that were extracted failed to produce DNA of sufficient quality, the authors discuss potential reasons for the failure. They suggest that museum specimens in poor physical condition may be better for DNA extraction compared to better-preserved ones, possibly related to the innovation of formalin as a fixative before ethanol storage in the early 20th century.}, }
@article {pmid36601706, year = {2023}, author = {Kashinina, NV and Lushchekina, AA and Sorokin, PA and Tarasyan, KK and Kholodova, MV}, title = {The modern state of the European saiga population (Saiga tatarica tatarica): mtDNA, DRB3 MHC gene, and microsatellite diversity.}, journal = {Integrative zoology}, volume = {18}, number = {4}, pages = {661-676}, doi = {10.1111/1749-4877.12704}, pmid = {36601706}, issn = {1749-4877}, mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Antelopes/genetics ; Mitochondria/genetics ; Alleles ; }, }
@article {pmid36574824, year = {2023}, author = {Baião, GC and Schneider, DI and Miller, WJ and Klasson, L}, title = {Multiple introgressions shape mitochondrial evolutionary history in Drosophila paulistorum and the Drosophila willistoni group.}, journal = {Molecular phylogenetics and evolution}, volume = {180}, number = {}, pages = {107683}, doi = {10.1016/j.ympev.2022.107683}, pmid = {36574824}, issn = {1095-9513}, mesh = {Animals ; *Drosophila/genetics ; Phylogeny ; Nucleic Acid Hybridization ; *Hybridization, Genetic ; }, abstract = {Hybridization and the consequent introgression of genomic elements is an important source of genetic diversity for biological lineages. This is particularly evident in young clades in which hybrid incompatibilities are still incomplete and mixing between species is more likely to occur. Drosophila paulistorum, a representative of the Neotropical Drosophila willistoni subgroup, is a classic model of incipient speciation. The species is divided into six semispecies that show varying degrees of pre- and post-mating incompatibility with each other. In the present study, we investigate the mitochondrial evolutionary history of D. paulistorum and the willistoni subgroup. For that, we perform phylogenetic and comparative analyses of the complete mitochondrial genomes and draft nuclear assemblies of 25 Drosophila lines of the willistoni and saltans species groups. Our results show that the mitochondria of D. paulistorum are polyphyletic and form two non-sister clades that we name α and β. Identification and analyses of nuclear mitochondrial insertions further reveal that the willistoni subgroup has an α-like mitochondrial ancestor and strongly suggest that both the α and β mitochondria of D. paulistorum were acquired through introgression from unknown fly lineages of the willistoni subgroup. We also uncover multiple mitochondrial introgressions across D. paulistorum semispecies and generate novel insight into the evolution of the species.}, }
@article {pmid36563715, year = {2023}, author = {Shukla, P and Mukherjee, S and Patil, A and Joshi, B}, title = {Molecular characterization of variants in mitochondrial DNA encoded genes using next generation sequencing analysis and mitochondrial dysfunction in women with PCOS.}, journal = {Gene}, volume = {855}, number = {}, pages = {147126}, doi = {10.1016/j.gene.2022.147126}, pmid = {36563715}, issn = {1879-0038}, mesh = {Humans ; Female ; DNA, Mitochondrial/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Polycystic Ovary Syndrome/genetics ; Mitochondria/genetics ; RNA, Transfer ; *Genome, Mitochondrial ; }, abstract = {Emerging studies indicates mitochondrial dysfunction and involvement of mitochondrial DNA (mtDNA) variants in the pathogenesis of polycystic ovary syndrome (PCOS). Cumulative effect of mtDNA rare variants are now gaining considerable interest apart from common variants in the pathogenesis of complex diseases. Rare variants may modify the effect of polymorphism or in combination with the common variants may affect the risk of disease. With the evolution of high throughput sequencing techniques, which can be utilized to identify common as well as rare variants along with heteroplasmy levels, comprehensive characterization of the mtDNA variants is possible. Till date, few studies reported common mtDNA variants using traditional sequencing techniques but rare variants in mtDNA encoding genes remain unexplored in women with PCOS. These mtDNA variants may be responsible for mitochondrial dysfunction and may contribute in PCOS pathogenesis. In this study we determined mtDNA copy number, a biomarker of mitochondrial dysfunction and first time analysed variants in mtDNA encoded genes in women with PCOS using mitochondrial Next Generation sequencing (NGS) approach and compared allele frequency from mitochondrial 1000 genome dataset. Variant annotation and prioritization was done using highly automated pipeline, MToolBox that excludes reads mapped from nuclear mitochondrial DNA sequences (NumtS) to identify unique mtDNA reads. The present study identified significant reduction in mtDNA copy number in women with PCOS compared to non-PCOS women. A total of unique 214 prioritized common to rare variants were identified in mtDNA encoded genes, 183 variants in OXPHOS complexes, 14 variants in MT-tRNA and 17 variants in MT-rRNA genes that may be involved in mitochondrial dysfunction in PCOS. Numerous variants were heteroplasmic, pathogenic in nature and occurred in evolutionary conserved region. Heteroplasmic variants were more frequently occurred in MT-CO3 gene. Non-synonymous variants were more than synonymous variants and mainly occurred in OXPHOS complex I and IV. Few variants were found to be associated with diseases in MITOMAP database. The study provides a better understanding towards pathogenesis of PCOS from novel aspects focusing on mitochondrial genetic defects as underlying cause for contributing mitochondrial dysfunction in women with PCOS.}, }
@article {pmid36555867, year = {2022}, author = {Malnick, SDH and Alin, P and Somin, M and Neuman, MG}, title = {Fatty Liver Disease-Alcoholic and Non-Alcoholic: Similar but Different.}, journal = {International journal of molecular sciences}, volume = {23}, number = {24}, pages = {}, pmid = {36555867}, issn = {1422-0067}, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/metabolism ; *Carcinoma, Hepatocellular/metabolism ; *Metabolic Syndrome/metabolism ; *Liver Neoplasms/metabolism ; Liver/metabolism ; *Liver Diseases, Alcoholic/metabolism ; Liver Cirrhosis/metabolism ; Ethanol/metabolism ; }, abstract = {In alcohol-induced liver disease (ALD) and in non-alcoholic fatty liver disease (NAFLD), there are abnormal accumulations of fat in the liver. This phenomenon may be related to excessive alcohol consumption, as well as the combination of alcohol consumption and medications. There is an evolution from simple steatosis to steatohepatitis, fibrosis and cirrhosis leading to hepatocellular carcinoma (HCC). Hepatic pathology is very similar regarding non-alcoholic fatty liver disease (NAFLD) and ALD. Initially, there is lipid accumulation in parenchyma and progression to lobular inflammation. The morphological changes in the liver mitochondria, perivenular and perisinusoidal fibrosis, and hepatocellular ballooning, apoptosis and necrosis and accumulation of fibrosis may lead to the development of cirrhosis and HCC. Medical history of ethanol consumption, laboratory markers of chronic ethanol intake, AST/ALT ratio on the one hand and features of the metabolic syndrome on the other hand, may help in estimating the contribution of alcohol intake and the metabolic syndrome, respectively, to liver steatosis.}, }
@article {pmid36553495, year = {2022}, author = {Kunerth, HD and Tapisso, JT and Valente, R and Mathias, MDL and Alves, PC and Searle, JB and Vega, R and Paupério, J}, title = {Characterising Mitochondrial Capture in an Iberian Shrew.}, journal = {Genes}, volume = {13}, number = {12}, pages = {}, pmid = {36553495}, issn = {2073-4425}, mesh = {Animals ; Phylogeny ; *Shrews/genetics ; *Chromosomes ; Mitochondria/genetics ; Spain ; }, abstract = {Mitochondrial introgression raises questions of biogeography and of the extent of reproductive isolation and natural selection. Previous phylogenetic work on the Sorex araneus complex revealed apparent mitonuclear discordance in Iberian shrews, indicating past hybridisation of Sorex granarius and the Carlit chromosomal race of S. araneus, enabling introgression of the S. araneus mitochondrial genome into S. granarius. To further study this, we genetically typed 61 Sorex araneus/coronatus/granarius from localities in Portugal, Spain, France, and Andorra at mitochondrial, autosomal, and sex-linked loci and combined our data with the previously published sequences. Our data are consistent with earlier data indicating that S. coronatus and S. granarius are the most closely related of the three species, confirming that S. granarius from the Central System mountain range in Spain captured the mitochondrial genome from a population of S. araneus. This mitochondrial capture event can be explained by invoking a biogeographical scenario whereby S. araneus was in contact with S. granarius during the Younger Dryas in central Iberia, despite the two species currently having disjunct distributions. We discuss whether selection favoured S. granarius with an introgressed mitochondrial genome. Our data also suggest recent hybridisation and introgression between S. coronatus and S. granarius, as well as between S. araneus and S. coronatus.}, }
@article {pmid36545736, year = {2023}, author = {He, L and Maheshwari, A}, title = {Mitochondria in Early Life.}, journal = {Current pediatric reviews}, volume = {19}, number = {4}, pages = {395-416}, doi = {10.2174/1573396319666221221110728}, pmid = {36545736}, issn = {1875-6336}, support = {R01 DK120309/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Epigenesis, Genetic ; *Mitochondria/genetics/metabolism ; Signal Transduction ; }, abstract = {Mitochondria are highly-dynamic, membrane-bound organelles that generate most of the chemical energy needed to power the biochemical reactions in eukaryotic cells. These organelles also communicate with the nucleus and other cellular structures to help maintain somatic homeostasis, allow cellular adaptation to stress, and help maintain the developmental trajectory. Mitochondria also perform numerous other functions to support metabolic, energetic, and epigenetic regulation in our cells. There is increasing information on various disorders caused by defects in intrinsic mitochondrial or supporting nuclear genes, on different organ systems. In this review, we have summarized the ultrastructural morphology, structural components, our current understanding of the evolution, biogenesis, dynamics, function, clinical manifestations of mitochondrial dysfunction, and future possibilities. The implications of deficits in mitochondrial dynamics and signaling for embryo viability and offspring health are also explored. We present information from our own clinical and laboratory research in conjunction with information collected from an extensive search in the databases PubMed, EMBASE, and Scopus.}, }
@article {pmid36543969, year = {2023}, author = {Zhu, X and Zhao, Y and Zheng, X and Sun, X}, title = {Genetic Diversity of Four Populations of Silver Carp (Hypophthalmichthys molitrix) Based on Mitochondrial Sequences.}, journal = {Biochemical genetics}, volume = {61}, number = {4}, pages = {1231-1241}, pmid = {36543969}, issn = {1573-4927}, support = {HSY2020K1//Open Project of the National and Local Joint Engineering Laboratory for Freshwater Fish Breeding/ ; }, mesh = {Animals ; *Carps/genetics ; Phylogeny ; Genetic Variation ; Mitochondria/genetics ; DNA, Mitochondrial/genetics ; Haplotypes ; China ; }, abstract = {Three mitochondrial DNA sequences (COI, ATP 8&amp;6, and D-loop) were employed to assess the genetic diversity of four populations of silver carp from three main drainages in China, including the Yangtze River, the Amur River, and the Pearl River. As a result, 98 haplotypes were identified in combined sequences of COI, ATP8&amp;6, and D-loop. A total of 196 variable sites and 116 parsimony-informative sites were observed. AMOVA based on assembled sequences indicated that 12.12% of the variation was among populations, while 87.88% of the variation was within populations. Additionally, the phylogenetic relationships of populations were depicted in a phylogenetic tree based on assembled sequences. Mismatch distribution analysis and the negative significant Fu's Fs values supported population expansion in all populations. Despite the high level of genetic diversity, the establishment of a state-level original breeding farm in the Amur River basin and the Pearl River basin may be an effective conservation strategy for the protection of local unique haplotypes.}, }
@article {pmid36543927, year = {2022}, author = {Cunha, RL and Faleh, AB and Francisco, S and Šanda, R and Vukić, J and Corona, L and Dia, M and Glavičić, I and Kassar, A and Castilho, R and Robalo, JI}, title = {Three mitochondrial lineages and no Atlantic-Mediterranean barrier for the bogue Boops boops across its widespread distribution.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {22124}, pmid = {36543927}, issn = {2045-2322}, mesh = {Humans ; Animals ; Phylogeny ; Phylogeography ; Azores ; Portugal ; *Mitochondria ; *Perciformes/genetics ; Atlantic Ocean ; Genetic Variation ; Mediterranean Sea ; }, abstract = {Marine species exhibiting wide distributional ranges are frequently subdivided into discrete genetic units over limited spatial scales. This is often due to specific life-history traits or oceanographic barriers that prevent gene flow. Fine-scale sampling studies revealed distinct phylogeographic patterns in the northeastern Atlantic and the Mediterranean, ranging from panmixia to noticeable population genetic structure. Here, we used mitochondrial sequence data to analyse connectivity in the bogue Boops boops throughout most of its widespread distribution. Our results identified the existence of three clades, one comprising specimens from the Azores and eastern Atlantic/Mediterranean, another with individuals from the Canary Islands, Madeira and Cape Verde archipelagos, and the third with samples from Mauritania only. One of the branches of the northern subtropical gyre (Azores Current) that drifts towards the Gulf of Cádiz promotes a closer connection between the Azores, southern Portugal and the Mediterranean B. boops populations. The Almería-Oran Front, widely recognised as an oceanographic barrier for many organisms to cross the Atlantic-Mediterranean divide, does not seem to affect the dispersal of this benthopelagic species. The southward movement of the Cape Verde Frontal Zone during the winter, combined with the relatively short duration of the pelagic larval stage of B. boops, may be potential factors for preventing the connectivity between the Atlantic oceanic archipelagos and Mauritania shaping the genetic signature of this species.}, }
@article {pmid36543798, year = {2022}, author = {Zawal, A and Skuza, L and Michoński, G and Bańkowska, A and Szućko-Kociuba, I and Gastineau, R}, title = {Complete mitochondrial genome of Hygrobates turcicus Pešić, Esen &amp; Dabert, 2017 (Acari, Hydrachnidia, Hygrobatoidea).}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {22063}, pmid = {36543798}, issn = {2045-2322}, mesh = {Animals ; Female ; Male ; *Acari/genetics ; *Genome, Mitochondrial ; Mitochondria/genetics ; Codon, Initiator ; RNA, Ribosomal/genetics ; Phylogeny ; Sequence Analysis, DNA ; RNA, Transfer/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {The aim of the study was sequencing of the mitogenome of Hygrobates turcicus Pešić, Esen &amp; Dabert, 2017 to expand knowledge of the polymorphism and cryptic or pseudocryptic diversity within Hydrachnidia. The samples originated from Bulgaria, Vidima River near Debnewo, 42°56'41.4''N, 24°48'44.6''E, depth 0.4 m, stones on the bottom, water flow 0.71 m/s, temperature 10 °C, pH 8.53, oxygen 110%, conductivity 279 µS/cm, hardness 121 CaO mg/l; 11 males, 27 females, 2 deutonymphs 12.x.2019 leg. Zawal, Michoński &amp; Bańkowska; one male and one female dissected and slides mounted. The study was carried out using the following methods: DNA extraction, sequencing, assembly and annotation, comparison with other populations of H. turcicus, and multigene phylogeny. As a result of the study, it was determined that the mitogenome is 15,006 bp long and encodes for 13 proteins, 2 rRNAs, and 22 tRNAs. The genome is colinear with those of H. longiporus and H. taniguchii, the difference in size originating from a non-coding region located between protein-coding genes ND4L and ND3. Five genes have alternative start-codon, and four display premature termination. The multigene phylogeny obtained using all mitochondrial protein-coding genes unambiguously associates H. turcicus with the cluster formed by H. longiporus and H. taniguchii.}, }
@article {pmid36527364, year = {2023}, author = {Knoop, V}, title = {C-to-U and U-to-C: RNA editing in plant organelles and beyond.}, journal = {Journal of experimental botany}, volume = {74}, number = {7}, pages = {2273-2294}, doi = {10.1093/jxb/erac488}, pmid = {36527364}, issn = {1460-2431}, mesh = {*RNA Editing ; Uridine/genetics/metabolism ; *Organelles/genetics/metabolism ; Plants/genetics/metabolism ; Chloroplasts/metabolism ; RNA, Plant/genetics/metabolism ; Plant Proteins/metabolism ; }, abstract = {The genomes in the two energy-converting organelles of plant cells, chloroplasts and mitochondria, contain numerous 'errors' that are corrected at the level of RNA transcript copies. The genes encoded in the two endosymbiotic organelles would not function properly if their transcripts were not altered by site-specific cytidine-to-uridine (C-to-U) exchanges and by additional reverse U-to-C exchanges in hornworts, lycophytes, and ferns. These peculiar processes of plant RNA editing, re-establishing genetic information that could alternatively be present at the organelle genome level, has spurred much research over >30 years. Lately new studies have revealed numerous interesting insights, notably on the biochemical machinery identifying specific pyrimidine nucleobases for conversion from C to U and vice versa. Here, I will summarize prominent research findings that lately have contributed to our better understanding of these phenomena introducing an added layer of information processing in plant cells. Some of this recent progress is based on the successful functional expression of plant RNA editing factors in bacteria and mammalian cells. These research approaches have recapitulated natural processes of horizontal gene transfer through which some protist lineages seem to have acquired plant RNA editing factors and adapted them functionally for their own purposes.}, }
@article {pmid36523555, year = {2022}, author = {Hogg, DW and Reid, AL and Dodsworth, TL and Chen, Y and Reid, RM and Xu, M and Husic, M and Biga, PR and Slee, A and Buck, LT and Barsyte-Lovejoy, D and Locke, M and Lovejoy, DA}, title = {Skeletal muscle metabolism and contraction performance regulation by teneurin C-terminal-associated peptide-1.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {1031264}, pmid = {36523555}, issn = {1664-042X}, abstract = {Skeletal muscle regulation is responsible for voluntary muscular movement in vertebrates. The genes of two essential proteins, teneurins and latrophilins (LPHN), evolving in ancestors of multicellular animals form a ligand-receptor pair, and are now shown to be required for skeletal muscle function. Teneurins possess a bioactive peptide, termed the teneurin C-terminal associated peptide (TCAP) that interacts with the LPHNs to regulate skeletal muscle contractility strength and fatigue by an insulin-independent glucose importation mechanism in rats. CRISPR-based knockouts and siRNA-associated knockdowns of LPHN-1 and-3 in the C2C12 mouse skeletal cell line shows that TCAP stimulates an LPHN-dependent cytosolic Ca[2+] signal transduction cascade to increase energy metabolism and enhance skeletal muscle function via increases in type-1 oxidative fiber formation and reduce the fatigue response. Thus, the teneurin/TCAP-LPHN system is presented as a novel mechanism that regulates the energy requirements and performance of skeletal muscle.}, }
@article {pmid36520311, year = {2023}, author = {Marszalek, J and Craig, EA and Tomiczek, B}, title = {J-Domain Proteins Orchestrate the Multifunctionality of Hsp70s in Mitochondria: Insights from Mechanistic and Evolutionary Analyses.}, journal = {Sub-cellular biochemistry}, volume = {101}, number = {}, pages = {293-318}, pmid = {36520311}, issn = {0306-0225}, mesh = {*Saccharomyces cerevisiae Proteins/metabolism ; HSP70 Heat-Shock Proteins/genetics/metabolism ; Mitochondria/genetics/metabolism ; Molecular Chaperones/genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; }, abstract = {Mitochondrial J-domain protein (JDP) co-chaperones orchestrate the function of their Hsp70 chaperone partner(s) in critical organellar processes that are essential for cell function. These include folding, refolding, and import of mitochondrial proteins, maintenance of mitochondrial DNA, and biogenesis of iron-sulfur cluster(s) (FeS), prosthetic groups needed for function of mitochondrial and cytosolic proteins. Consistent with the organelle's endosymbiotic origin, mitochondrial Hsp70 and the JDPs' functioning in protein folding and FeS biogenesis clearly descended from bacteria, while the origin of the JDP involved in protein import is less evident. Regardless of their origin, all mitochondrial JDP/Hsp70 systems evolved unique features that allowed them to perform mitochondria-specific functions. Their modes of functional diversification and specialization illustrate the versatility of JDP/Hsp70 systems and inform our understanding of system functioning in other cellular compartments.}, }
@article {pmid36519158, year = {2022}, author = {Kim, S and Eom, H and Nandre, R and Choi, YJ and Lee, H and Ryu, H and Ro, HS}, title = {Comparative structural analysis on the mitochondrial DNAs from various strains of Lentinula edodes.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1034387}, pmid = {36519158}, issn = {1664-302X}, abstract = {The evolution of mitochondria through variations in mitochondrial DNA (mtDNA) is one of the intriguing questions in eukaryotic cells. In order to assess the causes of the variations in mitochondria, the mtDNAs of the 21 strains of Lentinula edodes were assembled for this study, and analyzed together with four published mtDNA sequences. The mtDNAs were within the sizes of 117 kb ~ 122 kb. The gene number was observed consistent except for two mtDNAs, which carry a duplicated trnG1-trnG2 unit or a putative gene deletion. The size variation was largely attributed to the number of introns, repeated sequences, transposable elements (TEs), and plasmid-related sequences. Intron loss and gain were found from cox1, rnl, and rns of three mtDNAs. Loss of two introns in cox1 of KY217797.1 reduced its size by 2.7 kb, making it the smallest cox1 gene (8.4 kb) among the cox1s of the 25 mtDNAs, whereas gain of a Group II intron (2.65 kb) and loss of a Group I intron (1.7 kb) in cox1 of MF774813.1 resulted in the longest cox1 (12 kb). In rnl of L. edodes, we discovered four intron insertion consensus sequences which were unique to basidiomycetes but not ascomycetes. Differential incorporation of introns was the primary cause of the rnl size polymorphism. Homing endonucleases (HEGs) were suggestively involved in the mobilization of the introns because all of the introns have HEG genes of the LAGRIDADG or GIY-YIG families with the conserved HEG cleavage sites. TEs contributed to 11.04% of the mtDNA size in average, of which 7.08% was LTR-retrotransposon and 3.96% was DNA transposon, whereas the repeated sequences covered 4.6% of the mtDNA. The repeat numbers were variable in a strain-dependent manner. Both the TEs and repeated sequences were mostly found in the intronic and intergenic regions. Lastly, two major deletions were found in the plasmid-related sequence regions (pol2-pol3 and pol1-atp8) in the five mtDNAs. Particularly, the 6.8 kb-long deletion at pol2-pol3 region made MF774813.1 the shortest mtDNA of all. Our results demonstrate that mtDNA is a dynamic molecule that persistently evolves over a short period of time by insertion/deletion and repetition of DNA segments at the strain level.}, }
@article {pmid36512580, year = {2022}, author = {Guo, S and Lin, X and Song, N}, title = {Mitochondrial phylogenomics reveals deep relationships of scarab beetles (Coleoptera, Scarabaeidae).}, journal = {PloS one}, volume = {17}, number = {12}, pages = {e0278820}, pmid = {36512580}, issn = {1932-6203}, mesh = {Animals ; Phylogeny ; *Coleoptera/genetics ; *Genome, Mitochondrial ; Mitochondria/genetics ; Base Sequence ; }, abstract = {In this study, we newly sequenced the complete mitochondrial genomes (mitogenomes) of two phytophagous scarab beetles, and investigated the deep level relationships within Scarabaeidae combined with other published beetle mitogenome sequences. The complete mitogenomes of Dicronocephalus adamsi Pascoe (Cetoniinae) and Amphimallon sp. (Melolonthinae) are 15,563 bp and 17,433 bp in size, respectively. Both mitogenomes have the typical set of 37 genes (13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes) and an A+T-rich region, with the same gene arrangement found in the majority of beetles. The secondary structures for ribosomal RNA genes (rrnL and rrnS) were inferred by comparative analysis method. Results from phylogenetic analyses provide support for major lineages and current classification of Scarabaeidae. Amino acid data recovered Scarabaeidae as monophyletic. The Scarabaeidae was split into two clades. One clade contained the subfamilies Scarabaeinae and Aphodiinae. The other major clade contained the subfamilies Dynastinae, Rutelinae, Cetoniinae, Melolonthinae and Sericini. The monophyly of Scarabaeinae, Aphodiinae, Dynastinae, Cetoniinae and Sericini were strongly supported. The Scarabaeinae was the sister group of Aphodiinae. The Cetoniinae was sister to the Dynastinae + Rutelinae clade. The Melolonthinae was a non-monophyletic group. The removal of fast-evolving sites from nucleotide dataset using a pattern sorting method (OV-sorting) supported the family Scarabaeidae as a monophyletic group. At the tribe level, the Onthophagini was non-monophyletic with respect to Oniticellini. Ateuchini was sister to a large clade comprising the tribes Onthophagini, Oniticellini and Onitini. Eurysternini was a sister group of the Phanaeini + Ateuchini clade.}, }
@article {pmid36508337, year = {2022}, author = {Xu, R and Martelossi, J and Smits, M and Iannello, M and Peruzza, L and Babbucci, M and Milan, M and Dunham, JP and Breton, S and Milani, L and Nuzhdin, SV and Bargelloni, L and Passamonti, M and Ghiselli, F}, title = {Multi-tissue RNA-Seq Analysis and Long-read-based Genome Assembly Reveal Complex Sex-specific Gene Regulation and Molecular Evolution in the Manila Clam.}, journal = {Genome biology and evolution}, volume = {14}, number = {12}, pages = {}, pmid = {36508337}, issn = {1759-6653}, support = {S10 RR025496/RR/NCRR NIH HHS/United States ; S10 OD010794/OD/NIH HHS/United States ; }, mesh = {Animals ; Female ; Male ; *DNA, Mitochondrial/genetics ; RNA-Seq ; *Bivalvia/genetics ; Mitochondria/genetics ; Evolution, Molecular ; }, abstract = {The molecular factors and gene regulation involved in sex determination and gonad differentiation in bivalve molluscs are unknown. It has been suggested that doubly uniparental inheritance (DUI) of mitochondria may be involved in these processes in species such as the ubiquitous and commercially relevant Manila clam, Ruditapes philippinarum. We present the first long-read-based de novo genome assembly of a Manila clam, and a RNA-Seq multi-tissue analysis of 15 females and 15 males. The highly contiguous genome assembly was used as reference to investigate gene expression, alternative splicing, sequence evolution, tissue-specific co-expression networks, and sexual contrasting SNPs. Differential expression (DE) and differential splicing (DS) analyses revealed sex-specific transcriptional regulation in gonads, but not in somatic tissues. Co-expression networks revealed complex gene regulation in gonads, and genes in gonad-associated modules showed high tissue specificity. However, male gonad-associated modules showed contrasting patterns of sequence evolution and tissue specificity. One gene set was related to the structural organization of male gametes and presented slow sequence evolution but high pleiotropy, whereas another gene set was enriched in reproduction-related processes and characterized by fast sequence evolution and tissue specificity. Sexual contrasting SNPs were found in genes overrepresented in mitochondrial-related functions, providing new candidates for investigating the relationship between mitochondria and sex in DUI species. Together, these results increase our understanding of the role of DE, DS, and sequence evolution of sex-specific genes in an understudied taxon. We also provide resourceful genomic data for studies regarding sex diagnosis and breeding in bivalves.}, }
@article {pmid36502540, year = {2022}, author = {Alsaad, RKA}, title = {Past, present and future of Trichomonas vaginalis: a review study.}, journal = {Annals of parasitology}, volume = {68}, number = {3}, pages = {409-419}, doi = {10.17420/ap6803.447}, pmid = {36502540}, issn = {2299-0631}, mesh = {Male ; Female ; Humans ; *Trichomonas vaginalis/genetics ; *Trichomonas Vaginitis/diagnosis/epidemiology/parasitology ; *Trichomonas Infections/epidemiology ; Metronidazole ; Prevalence ; }, abstract = {Trichomonas vaginalis (TV) is the most common non-viral sexually transmitted infection (STI) microaerophilic protist parasite, which is the causative agent of trichomonosis. Globally, the estimated annual incidence is more than 270 million cases. It is correlated for several health problems including pelvic inflammatory disease (PID), pregnancy miscarriages, cervical carcinoma, prostatitis, prostatic adenocarcinomas, infertility, and the acquisition of human immunodeficiency virus (HIV). Most individuals infected with TV are asymptomatic. Metronidazole (MTZ) has been the treatment of choice for women. Currently, there is no effective vaccine against this pathogen despite efforts at vaccine development. Different socio-economic, demographic, behavioral, and biological factors are associated with the disease. Apart from its role as a pathogenic agent of diseases, it is also a fascinating organism with a surprisingly large genome for a parasite, i.e. larger than 160 Mb, and physiology adapted to its microaerophilic lifestyle. Particularly, the hydrogenosome, a mitochondria-derived organelle that releases hydrogen, attracted much interest in the last decades and rendered TV a model organism for eukaryotic evolution. According to the high prevalence and health consequences associated with TV, there is a requirement for improved screening programs in Iraq. The early diagnosis of asymptomatic diseases and effective treatment regimens are mandatory. Despite being highly prevalent of trichomonosis in the world, there is no review research published that solely focuses on T. vaginalis infections in Iraq.}, }
@article {pmid36501134, year = {2022}, author = {Żmijewski, MA}, title = {Nongenomic Activities of Vitamin D.}, journal = {Nutrients}, volume = {14}, number = {23}, pages = {}, pmid = {36501134}, issn = {2072-6643}, support = {2017/25/B/NZ3/00431//National Science Center/ ; }, mesh = {*Receptors, Calcitriol/genetics ; *Vitamin D/pharmacology/metabolism ; Calcium/metabolism ; Ultraviolet Rays ; Hedgehog Proteins ; Calcitriol/metabolism ; Vitamins ; }, abstract = {Vitamin D shows a variety of pleiotropic activities which cannot be fully explained by the stimulation of classic pathway- and vitamin D receptor (VDR)-dependent transcriptional modulation. Thus, existence of rapid and nongenomic responses to vitamin D was suggested. An active form of vitamin D (calcitriol, 1,25(OH)2D3) is an essential regulator of calcium-phosphate homeostasis, and this process is tightly regulated by VDR genomic activity. However, it seems that early in evolution, the production of secosteroids (vitamin-D-like steroids) and their subsequent photodegradation served as a protective mechanism against ultraviolet radiation and oxidative stress. Consequently, direct cell-protective activities of vitamin D were proven. Furthermore, calcitriol triggers rapid calcium influx through epithelia and its uptake by a variety of cells. Subsequently, protein disulfide-isomerase A3 (PDIA3) was described as a membrane vitamin D receptor responsible for rapid nongenomic responses. Vitamin D was also found to stimulate a release of secondary massagers and modulate several intracellular processes-including cell cycle, proliferation, or immune responses-through wingless (WNT), sonic hedgehog (SSH), STAT1-3, or NF-kappaB pathways. Megalin and its coreceptor, cubilin, facilitate the import of vitamin D complex with vitamin-D-binding protein (DBP), and its involvement in rapid membrane responses was suggested. Vitamin D also directly and indirectly influences mitochondrial function, including fusion-fission, energy production, mitochondrial membrane potential, activity of ion channels, and apoptosis. Although mechanisms of the nongenomic responses to vitamin D are still not fully understood, in this review, their impact on physiology, pathology, and potential clinical applications will be discussed.}, }
@article {pmid36498828, year = {2022}, author = {Ge, Q and Peng, P and Cheng, M and Meng, Y and Cao, Y and Zhang, S and Long, Y and Li, G and Kang, G}, title = {Genome-Wide Identification and Analysis of FKBP Gene Family in Wheat (Triticum asetivum).}, journal = {International journal of molecular sciences}, volume = {23}, number = {23}, pages = {}, pmid = {36498828}, issn = {1422-0067}, mesh = {*Triticum/metabolism ; Genome, Plant ; Phylogeny ; Gene Expression Regulation, Plant ; Tacrolimus Binding Proteins/genetics/metabolism ; Plant Proteins/genetics/metabolism ; Stress, Physiological/genetics ; *Arabidopsis/genetics ; Multigene Family ; }, abstract = {FK506-binding protein (FKBP) genes have been found to play vital roles in plant development and abiotic stress responses. However, limited information is available about this gene family in wheat (Triticum aestivum L.). In this study, a total of 64 FKBP genes were identified in wheat via a genome-wide analysis involving a homologous search of the latest wheat genome data, which was unevenly distributed in 21 chromosomes, encoded 152 to 649 amino acids with molecular weights ranging from 16 kDa to 72 kDa, and was localized in the chloroplast, cytoplasm, nucleus, mitochondria, peroxisome and endoplasmic reticulum. Based on sequence alignment and phylogenetic analysis, 64 TaFKBPs were divided into four different groups or subfamilies, providing evidence of an evolutionary relationship with Aegilops tauschii, Brachypodium distachyon, Triticum dicoccoides, Arabidopsis thaliana and Oryza sativa. Hormone-related, abiotic stress-related and development-related cis-elements were preferentially presented in promoters of TaFKBPs. The expression levels of TaFKBP genes were investigated using transcriptome data from the WheatExp database, which exhibited tissue-specific expression patterns. Moreover, TaFKBPs responded to drought and heat stress, and nine of them were randomly selected for validation by qRT-PCR. Yeast cells expressing TaFKBP19-2B-2 or TaFKBP18-6B showed increased influence on drought stress, indicating their negative roles in drought tolerance. Collectively, our results provide valuable information about the FKBP gene family in wheat and contribute to further characterization of FKBPs during plant development and abiotic stress responses, especially in drought stress.}, }
@article {pmid36497015, year = {2022}, author = {Kozhukhar, N and Alexeyev, MF}, title = {TFAM's Contributions to mtDNA Replication and OXPHOS Biogenesis Are Genetically Separable.}, journal = {Cells}, volume = {11}, number = {23}, pages = {}, pmid = {36497015}, issn = {2073-4409}, support = {S10 OD025089/OD/NIH HHS/United States ; R01 OD010944/OD/NIH HHS/United States ; P01 HL066299/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Humans ; Chickens/genetics ; *DNA Replication ; DNA, Mitochondrial/genetics/metabolism ; *DNA-Binding Proteins/genetics/metabolism ; Mitochondria/genetics/metabolism ; *Mitochondrial Proteins/genetics/metabolism ; Phylogeny ; *Transcription Factors/genetics/metabolism ; }, abstract = {The ability of animal orthologs of human mitochondrial transcription factor A (hTFAM) to support the replication of human mitochondrial DNA (hmtDNA) does not follow a simple pattern of phylogenetic closeness or sequence similarity. In particular, TFAM from chickens (Gallus gallus, chTFAM), unlike TFAM from the "living fossil" fish coelacanth (Latimeria chalumnae), cannot support hmtDNA replication. Here, we implemented the recently developed GeneSwap approach for reverse genetic analysis of chTFAM to obtain insights into this apparent contradiction. By implementing limited "humanization" of chTFAM focused either on amino acid residues that make DNA contacts, or the ones with significant variances in side chains, we isolated two variants, Ch13 and Ch22. The former has a low mtDNA copy number (mtCN) but robust respiration. The converse is true of Ch22. Ch13 and Ch22 complement each other's deficiencies. Opposite directionalities of changes in mtCN and respiration were also observed in cells expressing frog TFAM. This led us to conclude that TFAM's contributions to mtDNA replication and respiratory chain biogenesis are genetically separable. We also present evidence that TFAM residues that make DNA contacts play the leading role in mtDNA replication. Finally, we present evidence for a novel mode of regulation of the respiratory chain biogenesis by regulating the supply of rRNA subunits.}, }
@article {pmid36473440, year = {2022}, author = {Leger, MM and Stairs, C}, title = {Eukaryotic evolution: Spatial proteomics sheds light on mitochondrial reduction.}, journal = {Current biology : CB}, volume = {32}, number = {23}, pages = {R1308-R1311}, doi = {10.1016/j.cub.2022.10.039}, pmid = {36473440}, issn = {1879-0445}, mesh = {*Eukaryota ; *Proteomics ; }, abstract = {Multi-organelle spatial proteomics has revolutionized animal cell biology, but its use in protists has so far been limited. A new study delivers the first such proteome of a free-living protist, uncovering a previously overlooked function of highly reduced mitochondria.}, }
@article {pmid36472108, year = {2022}, author = {Cahill, MA}, title = {Unde venisti PGRMC? Grand-Scale Biology from Early Eukaryotes and Eumetazoan Animal Origins.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {27}, number = {11}, pages = {317}, doi = {10.31083/j.fbl2711317}, pmid = {36472108}, issn = {2768-6698}, mesh = {Animals ; Humans ; *Eukaryota ; *Proteomics ; Epigenesis, Genetic ; Receptors, Progesterone/metabolism ; Glycolysis ; Heme/metabolism ; Mammals/metabolism ; Membrane Proteins/genetics/metabolism ; }, abstract = {The title usage of Unde venisti 'from where have you come' is from a now dead language (Latin) that foundationally influenced modern English (not the major influence, but an essential formative one). This is an apt analogy for how both the ancient eukaryotic and eumetazoan functions of PGRMC proteins (PGRMC1 and PGRMC2 in mammals) probably influence modern human biology: via a formative trajectory from an evolutionarily foundational fulcrum. There is an arguable probability, although not a certainty, that PGRMC-like proteins were involved in eukaryogenesis. If so, then the proto-eukaryotic ancestral protein is modelled as having initiated the oxygen-induced and CYP450 (Cytochrome P450)-mediated synthesis of sterols in the endoplasmic reticulum to regulate proto-mitochondrial activity and heme homeostasis, as well as having enabled sterol transport between endoplasmic reticulum (ER) and mitochondria membranes involving the actin cytoskeleton, transport of heme from mitochondria, and possibly the regulation/origins of mitosis/meiosis. Later, during animal evolution, the last eumetazoan common ancestor (LEUMCA) acquired PGRMC phosphorylated tyrosines coincidentally with the gastrulation organizer, Netrin/deleted in colorectal carcinoma (DCC) signaling, muscle fibers, synapsed neurons, and neural recovery via a sleep-like process. Modern PGRMC proteins regulate multiple functions, including CYP450-mediated steroidogenesis, membrane trafficking, heme homeostasis, glycolysis/Warburg effect, fatty acid metabolism, mitochondrial regulation, and genomic CpG epigenetic regulation of gene expression. The latter imposes the system of differentiation status-sensitive cell-type specific proteomic complements in multi-tissued descendants of the LEUMCA. This paper attempts to trace PGRMC functions through time, proposing that key functions were involved in early eukaryotes, and were later added upon in the LEUMCA. An accompanying paper considers the implications of this awareness for human health and disease.}, }
@article {pmid36470482, year = {2023}, author = {Liu, J and Ni, Y and Liu, C}, title = {Polymeric structure of the Cannabis sativa L. mitochondrial genome identified with an assembly graph model.}, journal = {Gene}, volume = {853}, number = {}, pages = {147081}, doi = {10.1016/j.gene.2022.147081}, pmid = {36470482}, issn = {1879-0038}, mesh = {*Genome, Mitochondrial/genetics ; *Cannabis/genetics ; Plant Breeding ; *Genome, Chloroplast ; Repetitive Sequences, Nucleic Acid ; DNA, Mitochondrial/genetics ; Phylogeny ; Evolution, Molecular ; }, abstract = {Cannabis sativa L. belongs to the family Cannabaceae in Rosales. It has been widely used as medicines, building materials, and textiles. Elucidating its genome is critical for molecular breeding and synthetic biology study. Many studies have shown that the mitochondrial genomes (mitogenomes) and even chloroplast genomes (plastomes) had complex polymeric structures. Using the Nanopore sequencing platform, we sequenced, assembled, and analyzed its mitogenome and plastome. The resulting unitig graph suggested that the mitogenome had a complex polymeric structure. However, a gap-free, circular sequence was further assembled from the unitig graph. In contrast, a circular sequence representing the plastome was obtained. The mitogenome major conformation was 415,837 bp long, and the plastome was 153,927 bp long. To test if the repeat sequences promote recombination, which corresponds to the branch points in the structure, we tested the sequences around repeats by long-read mapping. Among 208 pairs of predicted repeats, the mapping results supported the presence of cross-over around 25 pairs of repeats. Subsequent PCR amplification confirmed the presence of cross-over around 15 of the 25 repeats. By comparing the mitogenome and plastome sequences, we identified 19 mitochondria plastid DNAs, including seven complete genes (trnW-CCA, trnP-UGG, psbJ, trnN-GUU, trnD-GUC, trnH-GUG, trnM-CAU) and nine gene fragments. Furthermore, the selective pressure analysis results showed that five genes (atp1, ccmB, ccmC, cox1, nad7) had 19 positively selected sites. Lastly, we predicted 28 RNA editing sites. A total of 8 RNA editing sites located in the coding regions were successfully validated by PCR amplification and Sanger sequencing, of which four were synonymous, and four were nonsynonymous. In particular, the RNA editing events appeared to be tissue-specific in C. sativa mitogenome. In summary, we have confirmed the major confirmation of C. sativa mitogenome and characterized its structural features in detail. These results provide critical information for future variety breeding and resource development for C. sativa.}, }
@article {pmid36469010, year = {2023}, author = {Penter, L and Ten Hacken, E and Southard, J and Lareau, CA and Ludwig, LS and Li, S and Neuberg, DS and Livak, KJ and Wu, CJ}, title = {Mitochondrial DNA Mutations as Natural Barcodes for Lineage Tracing of Murine Tumor Models.}, journal = {Cancer research}, volume = {83}, number = {5}, pages = {667-672}, pmid = {36469010}, issn = {1538-7445}, support = {R01 CA216273/CA/NCI NIH HHS/United States ; P01 CA206978/CA/NCI NIH HHS/United States ; R01 CA155010/CA/NCI NIH HHS/United States ; R50 CA251956/CA/NCI NIH HHS/United States ; R21 CA267527/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Mice ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Chromatin ; Mutation ; *Neoplasms/genetics ; }, abstract = {UNLABELLED: Murine models are indispensable tools for functional genomic studies and preclinical testing of novel therapeutic approaches. Mitochondrial single-cell assay for transposase-accessible chromatin using sequencing (mtscATAC-seq) enables the dissection of cellular heterogeneity and clonal dynamics by capturing chromatin accessibility, copy-number variations (CNV), and mitochondrial DNA (mtDNA) mutations, yet its applicability to murine studies remains unexplored. By leveraging mtscATAC-seq in novel chronic lymphocytic leukemia and Richter syndrome mouse models, we report the detection of mtDNA mutations, particularly in highly proliferative murine cells, alongside CNV and chromatin state changes indicative of clonal evolution upon secondary transplant. This study thus demonstrates the feasibility and utility of multi-modal single-cell and natural barcoding approaches to characterize murine cancer models.<br><br>SIGNIFICANCE: mtDNA mutations can serve as natural barcodes to enable lineage tracing in murine cancer models, which can be used to provide new insights into disease biology and to identify therapeutic vulnerabilities.}, }
@article {pmid36463410, year = {2023}, author = {Krynická, V and Skotnicová, P and Jackson, PJ and Barnett, S and Yu, J and Wysocka, A and Kaňa, R and Dickman, MJ and Nixon, PJ and Hunter, CN and Komenda, J}, title = {FtsH4 protease controls biogenesis of the PSII complex by dual regulation of high light-inducible proteins.}, journal = {Plant communications}, volume = {4}, number = {1}, pages = {100502}, pmid = {36463410}, issn = {2590-3462}, support = {BB/M000265/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M012166/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Peptide Hydrolases ; Photosystem II Protein Complex/genetics/metabolism ; Phylogeny ; Thylakoids/metabolism ; Chloroplasts/metabolism ; *Arabidopsis/genetics/metabolism ; *Synechocystis/genetics/metabolism ; *Arabidopsis Proteins/genetics/metabolism ; Metalloproteases/genetics/metabolism ; }, abstract = {FtsH proteases are membrane-embedded proteolytic complexes important for protein quality control and regulation of various physiological processes in bacteria, mitochondria, and chloroplasts. Like most cyanobacteria, the model species Synechocystis sp. PCC 6803 contains four FtsH homologs, FtsH1-FtsH4. FtsH1-FtsH3 form two hetero-oligomeric complexes, FtsH1/3 and FtsH2/3, which play a pivotal role in acclimation to nutrient deficiency and photosystem II quality control, respectively. FtsH4 differs from the other three homologs by the formation of a homo-oligomeric complex, and together with Arabidopsis thaliana AtFtsH7/9 orthologs, it has been assigned to another phylogenetic group of unknown function. Our results exclude the possibility that Synechocystis FtsH4 structurally or functionally substitutes for the missing or non-functional FtsH2 subunit in the FtsH2/3 complex. Instead, we demonstrate that FtsH4 is involved in the biogenesis of photosystem II by dual regulation of high light-inducible proteins (Hlips). FtsH4 positively regulates expression of Hlips shortly after high light exposure but is also responsible for Hlip removal under conditions when their elevated levels are no longer needed. We provide experimental support for Hlips as proteolytic substrates of FtsH4. Fluorescent labeling of FtsH4 enabled us to assess its localization using advanced microscopic techniques. Results show that FtsH4 complexes are concentrated in well-defined membrane regions at the inner and outer periphery of the thylakoid system. Based on the identification of proteins that co-purified with the tagged FtsH4, we speculate that FtsH4 concentrates in special compartments in which the biogenesis of photosynthetic complexes takes place.}, }
@article {pmid36463372, year = {2023}, author = {Nikelski, E and Rubtsov, AS and Irwin, D}, title = {High heterogeneity in genomic differentiation between phenotypically divergent songbirds: a test of mitonuclear co-introgression.}, journal = {Heredity}, volume = {130}, number = {1}, pages = {1-13}, pmid = {36463372}, issn = {1365-2540}, mesh = {Animals ; *Songbirds/genetics ; Genome ; Genomics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Comparisons of genomic variation among closely related species often show more differentiation in mitochondrial DNA (mtDNA) and sex chromosomes than in autosomes, a pattern expected due to the differing effective population sizes and evolutionary dynamics of these genomic components. Yet, introgression can cause species pairs to deviate dramatically from general differentiation trends. The yellowhammer (Emberiza citrinella) and pine bunting (E. leucocephalos) are hybridizing avian sister species that differ greatly in appearance and moderately in nuclear DNA, but that show no mtDNA differentiation. This discordance is best explained by adaptive mtDNA introgression-a process that can select for co-introgression at nuclear genes with mitochondrial functions (mitonuclear genes). To better understand these discordant differentiation patterns and characterize nuclear differentiation in this system, we investigated genome-wide differentiation between allopatric yellowhammers and pine buntings and compared it to what was seen previously in mtDNA. We found significant nuclear differentiation that was highly heterogeneous across the genome, with a particularly wide differentiation peak on the sex chromosome Z. We further investigated mitonuclear gene co-introgression between yellowhammers and pine buntings and found support for this process in the direction of pine buntings into yellowhammers. Genomic signals indicative of co-introgression were common in mitonuclear genes coding for subunits of the mitoribosome and electron transport chain complexes. Such introgression of mitochondrial DNA and mitonuclear genes provides a possible explanation for the patterns of high genomic heterogeneity in genomic differentiation seen among some species groups.}, }
@article {pmid36450825, year = {2023}, author = {Missiroli, S and Perrone, M and Gafà, R and Nicoli, F and Bonora, M and Morciano, G and Boncompagni, C and Marchi, S and Lebiedzinska-Arciszewska, M and Vezzani, B and Lanza, G and Kricek, F and Borghi, A and Fiorica, F and Ito, K and Wieckowski, MR and Di Virgilio, F and Abelli, L and Pinton, P and Giorgi, C}, title = {PML at mitochondria-associated membranes governs a trimeric complex with NLRP3 and P2X7R that modulates the tumor immune microenvironment.}, journal = {Cell death and differentiation}, volume = {30}, number = {2}, pages = {429-441}, pmid = {36450825}, issn = {1476-5403}, support = {R01 DK098263/DK/NIDDK NIH HHS/United States ; R01 DK115577/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Cytokines ; Inflammasomes ; Mitochondria ; *NLR Family, Pyrin Domain-Containing 3 Protein/genetics ; *Tumor Microenvironment ; *Receptors, Purinergic P2X7/metabolism ; *Promyelocytic Leukemia Protein/metabolism ; }, abstract = {Uncontrolled inflammatory response arising from the tumor microenvironment (TME) significantly contributes to cancer progression, prompting an investigation and careful evaluation of counter-regulatory mechanisms. We identified a trimeric complex at the mitochondria-associated membranes (MAMs), in which the purinergic P2X7 receptor - NLRP3 inflammasome liaison is fine-tuned by the tumor suppressor PML. PML downregulation drives an exacerbated immune response due to a loss of P2X7R-NLRP3 restraint that boosts tumor growth. PML mislocalization from MAMs elicits an uncontrolled NLRP3 activation, and consequent cytokines blast fueling cancer and worsening the tumor prognosis in different human cancers. New mechanistic insights are provided for the PML-P2X7R-NLRP3 axis to govern the TME in human carcinogenesis, fostering new targeted therapeutic approaches.}, }
@article {pmid36446749, year = {2023}, author = {Li, SP and Jiang, H and Liu, ZB and Yu, WJ and Cai, XS and Liu, C and Xie, WY and Quan, FS and Gao, W and Kim, NH and Yuan, B and Chen, CZ and Zhang, JB}, title = {TBX2 affects proliferation, apoptosis and cholesterol generation by regulating mitochondrial function and autophagy in bovine cumulus cell.}, journal = {Veterinary medicine and science}, volume = {9}, number = {1}, pages = {326-335}, pmid = {36446749}, issn = {2053-1095}, mesh = {Female ; Animals ; Cattle ; *Cumulus Cells/metabolism ; Cell Proliferation ; *Autophagy ; Apoptosis/genetics ; Mitochondria ; Cholesterol/metabolism/pharmacology ; Adenosine Triphosphate/metabolism/pharmacology ; }, abstract = {BACKGROUND: T-box transcription factor 2 (TBX2) is a member of T-box gene family whose members are highly conserved in evolution and encoding genes and are involved in the regulation of developmental processes. The encoding genes play an important role in growth and development. Although TBX2 has been widely studied in cancer cell growth and development, its biological functions in bovine cumulus cells remain unclear.<br><br>OBJECTIVES: This study aimed to investigate the regulatory effects of TBX2 in bovine cumulus cells.<br><br>METHODS: TBX2 gene was knockdown with siRNA to clarify the function in cellular physiological processes. Cell proliferation and cycle changes were determined by xCELLigence cell function analyzer and flow cytometry. Mitochondrial membrane potential and autophagy were detected by fluorescent dye staining and immunofluorescence techniques. Western blot and quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) were used to detect the expression changes of proliferation and autophagy-related proteins. Aadenosine triphosphate (ATP) production, glucose metabolism, and cholesterol synthesis of cumulus cells were measured by optical density and chemiluminescence analysis.<br><br>RESULTS: After inhibition of TBX2, the cell cycle was disrupted. The levels of apoptosis, ratio of light chain 3 beta II/I, and reactive oxygen species were increased. The proliferation, expansion ability, ATP production, and the amount of cholesterol secreted by cumulus cells were significantly decreased.<br><br>CONCLUSIONS: TBX2 plays important roles in regulating the cells' proliferation, expansion, apoptosis, and autophagy; maintaining the mitochondrial function and cholesterol generation of bovine cumulus cells.}, }
@article {pmid36442091, year = {2022}, author = {Insalata, F and Hoitzing, H and Aryaman, J and Jones, NS}, title = {Stochastic survival of the densest and mitochondrial DNA clonal expansion in aging.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {49}, pages = {e2122073119}, pmid = {36442091}, issn = {1091-6490}, mesh = {*DNA, Mitochondrial/genetics ; *Mitochondria ; Cellular Senescence/genetics ; Muscle Fibers, Skeletal ; }, abstract = {The expansion of mitochondrial DNA molecules with deletions has been associated with aging, particularly in skeletal muscle fibers; its mechanism has remained unclear for three decades. Previous accounts have assigned a replicative advantage (RA) to mitochondrial DNA containing deletion mutations, but there is also evidence that cells can selectively remove defective mitochondrial DNA. Here we present a spatial model that, without an RA, but instead through a combination of enhanced density for mutants and noise, produces a wave of expanding mutations with speeds consistent with experimental data. A standard model based on RA yields waves that are too fast. We provide a formula that predicts that wave speed drops with copy number, consonant with experimental data. Crucially, our model yields traveling waves of mutants even if mutants are preferentially eliminated. Additionally, we predict that mutant loads observed in single-cell experiments can be produced by de novo mutation rates that are drastically lower than previously thought for neutral models. Given this exemplar of how spatial structure (multiple linked mtDNA populations), noise, and density affect muscle cell aging, we introduce the mechanism of stochastic survival of the densest (SSD), an alternative to RA, that may underpin other evolutionary phenomena.}, }
@article {pmid36430970, year = {2022}, author = {Pożoga, M and Armbruster, L and Wirtz, M}, title = {From Nucleus to Membrane: A Subcellular Map of the N-Acetylation Machinery in Plants.}, journal = {International journal of molecular sciences}, volume = {23}, number = {22}, pages = {}, pmid = {36430970}, issn = {1422-0067}, support = {Wi 3560/4-1//Deutsche Forschungsgemeinschaft/ ; Wi 3560/7-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; Acetylation ; *Saccharomyces cerevisiae ; *Protein Processing, Post-Translational ; Plants/metabolism ; }, abstract = {N-terminal acetylation (NTA) is an ancient protein modification conserved throughout all domains of life. N-terminally acetylated proteins are present in the cytosol, the nucleus, the plastids, mitochondria and the plasma membrane of plants. The frequency of NTA differs greatly between these subcellular compartments. While up to 80% of cytosolic and 20-30% of plastidic proteins are subject to NTA, NTA of mitochondrial proteins is rare. NTA alters key characteristics of proteins such as their three-dimensional structure, binding properties and lifetime. Since the majority of proteins is acetylated by five ribosome-bound N-terminal acetyltransferases (Nats) in yeast and humans, NTA was long perceived as an exclusively co-translational process in eukaryotes. The recent characterization of post-translationally acting plant Nats, which localize to the plasma membrane and the plastids, has challenged this view. Moreover, findings in humans, yeast, green algae and higher plants uncover differences in the cytosolic Nat machinery of photosynthetic and non-photosynthetic eukaryotes. These distinctive features of the plant Nat machinery might constitute adaptations to the sessile lifestyle of plants. This review sheds light on the unique role of plant N-acetyltransferases in development and stress responses as well as their evolution-driven adaptation to function in different cellular compartments.}, }
@article {pmid36427759, year = {2023}, author = {Munro, D and Rodríguez, E and Blier, PU}, title = {The longest-lived metazoan, Arctica islandica, exhibits high mitochondrial H2O2 removal capacities.}, journal = {Mitochondrion}, volume = {68}, number = {}, pages = {81-86}, doi = {10.1016/j.mito.2022.11.005}, pmid = {36427759}, issn = {1872-8278}, mesh = {Mice ; Animals ; *Hydrogen Peroxide ; Longevity ; Reactive Oxygen Species ; *Bivalvia/physiology ; Mitochondria ; Antioxidants ; }, abstract = {A greater capacity of endogenous matrix antioxidants has recently been hypothesized to characterize mitochondria of long-lived species, curbing bursts of reactive oxygen species (ROS) generated in this organelle. Evidence for this has been obtained from studies comparing the long-lived naked mole rat to laboratory mice. We tested this hypothesis by comparing the longest-lived metazoan, the marine bivalve Arctica islandica (MLSP = 507 y), with shorter-lived and evolutionarily related species. We used a recently developed fluorescent technique to assess mantle and gill tissue mitochondria's capacity to consume hydrogen peroxide (H2O2) in multiple physiological states ex vivo. Depending on the type of respiratory substrate provided, mitochondria of Arctica islandica could consume between 3 and 14 times more H2O2 than shorter-lived species. These findings support the contention that a greater capacity for the elimination of ROS characterizes long-lived species, a novel property of mitochondria thus far demonstrated in two key biogerontological models from distant evolutionary lineages.}, }
@article {pmid36421831, year = {2022}, author = {Tang, Y and Huo, Z and Liu, Y and Wang, Y and Zuo, L and Fang, L and Zhao, W and Tan, Y and Yan, X}, title = {Full Mitochondrial Genomes Reveal Species Differences between the Venerid Clams Ruditapes philippinarum and R. variegatus.}, journal = {Genes}, volume = {13}, number = {11}, pages = {}, pmid = {36421831}, issn = {2073-4425}, mesh = {Animals ; *Genome, Mitochondrial/genetics ; Phylogeny ; Species Specificity ; NADH Dehydrogenase ; *Bivalvia/genetics ; }, abstract = {In natural sea areas along the coast of China, venerid clams Ruditapes philippinarum and R. variegatus exhibit similar adult shell forms and are especially difficult to distinguish as spat and juveniles. This study used comparative mitochondrial genome analysis to reveal differences between these species. The results showed that: (1) the mitochondrial genomes of R. philippinarum and R. variegatus share a large number of similar gene clusters arranged in consistent order, yet they also display noncommon genes, with both gene rearrangements and random losses found; (2) the 13 protein-coding genes in R. philippinarum as well as two-fold and four-fold degenerate sites in R. variegatus have an evident AT bias; (3) the Ka/Ks ratio of the mitochondrial ATP8 gene was significantly higher in R. philippinarum than in R. variegatus, and an analysis of selection pressure revealed that the mitochondrial NADH dehydrogenase subunit 2 gene and NADH dehydrogenase subunit 6 gene of R. variegatus were under great selective pressure during its evolution; and finally, (4) the two species clustered into one branch on a phylogenetic tree, further affirming their phylogenetic closeness. Based on these results, we speculate that the species differences between R. variegatus and R. philippinarum are largely attributable to adaptive evolution to the environment. The present findings provide a reference for the development of germplasm identification.}, }
@article {pmid36421825, year = {2022}, author = {Kyrgiafini, MA and Giannoulis, T and Moutou, KA and Mamuris, Z}, title = {Investigating the Impact of a Curse: Diseases, Population Isolation, Evolution and the Mother's Curse.}, journal = {Genes}, volume = {13}, number = {11}, pages = {}, pmid = {36421825}, issn = {2073-4425}, mesh = {Male ; Female ; Humans ; *Mothers ; DNA, Mitochondrial/genetics ; Maternal Inheritance/genetics ; *Genome, Mitochondrial/genetics ; Mitochondria/genetics ; }, abstract = {The mitochondrion was characterized for years as the energy factory of the cell, but now its role in many more cellular processes is recognized. The mitochondrion and mitochondrial DNA (mtDNA) also possess a set of distinct properties, including maternal inheritance, that creates the Mother's Curse phenomenon. As mtDNA is inherited from females to all offspring, mutations that are harmful to males tend to accumulate more easily. The Mother's Curse is associated with various diseases, and has a significant effect on males, in many cases even affecting their reproductive ability. Sometimes, it even leads to reproductive isolation, as in crosses between different populations, the mitochondrial genome cannot cooperate effectively with the nuclear one resulting in a mito-nuclear incompatibility and reduce the fitness of the hybrids. This phenomenon is observed both in the laboratory and in natural populations, and have the potential to influence their evolution and speciation. Therefore, it turns out that the study of mitochondria is an exciting field that finds many applications, including pest control, and it can shed light on the molecular mechanism of several diseases, improving successful diagnosis and therapeutics. Finally, mito-nuclear co-adaptation, paternal leakage, and kin selection are some mechanisms that can mitigate the impact of the Mother's Curse.}, }
@article {pmid36421375, year = {2022}, author = {Ding, H and Bi, D and Zhang, S and Han, S and Ye, Y and Yi, R and Yang, J and Liu, B and Wu, L and Zhuo, R and Kan, X}, title = {The Mitogenome of Sedum plumbizincicola (Crassulaceae): Insights into RNA Editing, Lateral Gene Transfer, and Phylogenetic Implications.}, journal = {Biology}, volume = {11}, number = {11}, pages = {}, pmid = {36421375}, issn = {2079-7737}, support = {NEL&amp;MARA-003//the Opening Foundation of National Engineering Laboratory of Soil Pollution Control and Remediation Technologies, and Key Laboratory of Heavy Metal Pollution Prevention &amp; Control, Ministry of Agriculture and Rural Affairs/ ; BK20211078//the Basic Research Program (Natural Science Foundation) of Jiangsu Province/ ; YJS20210136//the Scientific Research Project Foundation of Postgraduate of the Anhui Higher Education Institutions of China/ ; }, abstract = {As the largest family within the order Saxifragales, Crassulaceae contains about 34 genera with 1400 species. Mitochondria play a critical role in cellular energy production. Since the first land plant mitogenome was reported in Arabidopsis, more than 400 mitogenomic sequences have been deposited in a public database. However, no entire mitogenome data have been available for species of Crassulaceae to date. To better understand the evolutionary history of the organelles of Crassulaceae, we sequenced and performed comprehensive analyses on the mitogenome of Sedum plumbizincicola. The master mitogenomic circle is 212,159 bp in length, including 31 protein-coding genes (PCGs), 14 tRNA genes, and 3 rRNA genes. We further identified totally 508 RNA editing sites in PCGs, and demonstrated that the second codon positions of mitochondrial genes are most prone to RNA editing events. Notably, by neutrality plot analyses, we observed that the mitochondrial RNA editing events have large effects on the driving forces of plant evolution. Additionally, 4 MTPTs and 686 NUMTs were detected in the mitochondrial and nuclear genomes of S. plumbizincicola, respectively. Additionally, we conducted further analyses on gene transfer, secondary structures of mitochondrial RNAs, and phylogenetic implications. Therefore, the findings presented here will be helpful for future investigations on plant mitogenomes.}, }
@article {pmid36417880, year = {2022}, author = {Aman, Y and Erinjeri, AP and Tataridas-Pallas, N and Williams, R and Wellman, R and Chapman, H and Labbadia, J}, title = {Loss of MTCH-1 suppresses age-related proteostasis collapse through the inhibition of programmed cell death factors.}, journal = {Cell reports}, volume = {41}, number = {8}, pages = {111690}, doi = {10.1016/j.celrep.2022.111690}, pmid = {36417880}, issn = {2211-1247}, support = {BB/P005535/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; *Proteostasis/physiology ; *Proteome/metabolism ; Protein Folding ; Caenorhabditis elegans/metabolism ; Apoptosis ; }, abstract = {The age-related loss of protein homeostasis (proteostasis) is at the heart of numerous neurodegenerative diseases. Therefore, finding ways to preserve proteome integrity in aged cells may be a powerful way to promote long-term health. Here, we show that reducing the activity of a highly conserved mitochondrial outer membrane protein, MTCH-1/MTCH2, suppresses age-related proteostasis collapse in Caenorhabditis elegans without disrupting development, growth, or reproduction. Loss of MTCH-1 does not influence proteostasis capacity in aged tissues through previously described pathways but instead operates by reducing CED-4 levels. This results in the sequestration of HSP-90 by inactive CED-3, which in turn leads to an increase in HSF-1 activity, transcriptional remodeling of the proteostasis network, and maintenance of proteostasis capacity with age. Together, our findings reveal a role for programmed cell death factors in determining proteome health and suggest that inhibiting MTCH-1 activity in adulthood may safeguard the aging proteome and suppress age-related diseases.}, }
@article {pmid36414480, year = {2023}, author = {Sahayasheela, VJ and Yu, Z and Hidaka, T and Pandian, GN and Sugiyama, H}, title = {Mitochondria and G-quadruplex evolution: an intertwined relationship.}, journal = {Trends in genetics : TIG}, volume = {39}, number = {1}, pages = {15-30}, pmid = {36414480}, issn = {0168-9525}, support = {R01 CA236350/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *G-Quadruplexes ; Mitochondria/genetics ; }, abstract = {G-quadruplexes (G4s) are non-canonical structures formed in guanine (G)-rich sequences through stacked G tetrads by Hoogsteen hydrogen bonding. Several studies have demonstrated the existence of G4s in the genome of various organisms, including humans, and have proposed that G4s have a regulatory role in various cellular functions. However, little is known regarding the dissemination of G4s in mitochondria. In this review, we report the observation that the number of potential G4-forming sequences in the mitochondrial genome increases with the evolutionary complexity of different species, suggesting that G4s have a beneficial role in higher-order organisms. We also discuss the possible function of G4s in mitochondrial (mt)DNA and long noncoding (lnc)RNA and their role in various biological processes.}, }
@article {pmid36413915, year = {2023}, author = {Guette-Marquet, S and Roques, C and Bergel, A}, title = {Direct electrochemical detection of trans-plasma membrane electron transfer: A possible alternative pathway for cell respiration.}, journal = {Biosensors &amp; bioelectronics}, volume = {220}, number = {}, pages = {114896}, doi = {10.1016/j.bios.2022.114896}, pmid = {36413915}, issn = {1873-4235}, mesh = {Chlorocebus aethiops ; Animals ; *Electrons ; Vero Cells ; *Biosensing Techniques ; Cell Respiration ; Cell Membrane ; Carbon ; }, abstract = {An electrochemical protocol was designed to enable Vero cells to transfer electrons to an electrode without any added redox mediator. The cells were cultured on the surface of electrodes polarized at the optimal potential of 400 mV/silver pseudo-reference. Gold, carbon, and CNT-coated carbon electrodes displayed similar current record patterns. Extracellular electron transfer was sustained for several days. Its intensity, up to 1.5 pA.cell[-1], was in the range of the electron flows implemented by cell respiration. A large fraction of the current vanished as soon as anoxic conditions were established, which suggests a mitochondrial origin for a large proportion of the electrons. The current records always showed a two-phase pattern. The occurrence of the two phases was not due to an evolution of the cell mat structure, which was fully established during the first day of polarization and did not change significantly thereafter. Increasing the cell seeding density decreased the maximum current reached during the first phase and the duration of the phase. These observations put together lead us to propose a model, in which only the cells adhered on the electrode surface produced current by metabolizing glutamine during the first phase. The possible role of this extracellular electron transfer as an alternative cell respiration pathway is discussed. The key roles it could play in regulating pH and pO2 gradients are considered, specifically to explain the pH gradient reversal observed in cancer cells. These pioneering results pave the way for electrochemical sensors to directly address cellular metabolic pathways.}, }
@article {pmid36412071, year = {2023}, author = {Shimpi, GG and Bentlage, B}, title = {Ancient endosymbiont-mediated transmission of a selfish gene provides a model for overcoming barriers to gene transfer into animal mitochondrial genomes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {2}, pages = {e2200190}, doi = {10.1002/bies.202200190}, pmid = {36412071}, issn = {1521-1878}, mesh = {Animals ; *Genome, Mitochondrial/genetics ; Gene Transfer, Horizontal/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Phylogeny ; Evolution, Molecular ; }, abstract = {In contrast to bilaterian animals, non-bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. Although prevalent in plants, HGT into animal mitochondrial genomes is rare, lacking suitable explanatory models for their occurrence. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral (soft corals and their kin) mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. A review of the available literature suggests that this HGT was mediated by an alveolate endosymbiont infected with a lysogenic phycodnavirus that enabled insertion of the homing endonuclease containing mtMutS into octocoral mitochondrial genomes. We posit that homing endonuclease domains and similar selfish elements play a crucial role in such inter-domain gene transfers. Understanding the role of selfish genetic elements in HGT has the potential to aid development of tools for manipulating animal mitochondrial DNA.}, }
@article {pmid36403966, year = {2022}, author = {Maciszewski, K and Fells, A and Karnkowska, A}, title = {Challenging the Importance of Plastid Genome Structure Conservation: New Insights From Euglenophytes.}, journal = {Molecular biology and evolution}, volume = {39}, number = {12}, pages = {}, pmid = {36403966}, issn = {1537-1719}, mesh = {*Genome, Plastid ; }, abstract = {Plastids, similar to mitochondria, are organelles of endosymbiotic origin, which retained their vestigial genomes (ptDNA). Their unique architecture, commonly referred to as the quadripartite (four-part) structure, is considered to be strictly conserved; however, the bulk of our knowledge on their variability and evolutionary transformations comes from studies of the primary plastids of green algae and land plants. To broaden our perspective, we obtained seven new ptDNA sequences from freshwater species of photosynthetic euglenids-a group that obtained secondary plastids, known to have dynamically evolving genome structure, via endosymbiosis with a green alga. Our analyses have demonstrated that the evolutionary history of euglenid plastid genome structure is exceptionally convoluted, with a patchy distribution of inverted ribosomal operon (rDNA) repeats, as well as several independent acquisitions of tandemly repeated rDNA copies. Moreover, we have shown that inverted repeats in euglenid ptDNA do not share their genome-stabilizing property documented in chlorophytes. We hypothesize that the degeneration of the quadripartite structure of euglenid plastid genomes is connected to the group II intron expansion. These findings challenge the current global paradigms of plastid genome architecture evolution and underscore the often-underestimated divergence between the functionality of shared traits in primary and complex plastid organelles.}, }
@article {pmid36403761, year = {2023}, author = {Shi, F and Yu, T and Xu, Y and Zhang, S and Niu, Y and Ge, S and Tao, J and Zong, S}, title = {Comparative mitochondrial genomic analysis provides new insights into the evolution of the subfamily Lamiinae (Coleoptera: Cerambycidae).}, journal = {International journal of biological macromolecules}, volume = {225}, number = {}, pages = {634-647}, doi = {10.1016/j.ijbiomac.2022.11.125}, pmid = {36403761}, issn = {1879-0003}, mesh = {Animals ; *Coleoptera/genetics ; Phylogeny ; Mitochondria/genetics ; RNA, Transfer/genetics ; Genomics ; }, abstract = {The genus Monochamus within the subfamily Lamiinae is the main vector of Bursaphelenchus xylophilus, which causes pine wilt disease and induces substantial economic and ecological losses. Only three complete mitochondrial genomes of the genus Monochamus have been sequenced to date, and no comparative mitochondrial genomic studies of Lamiinae have been conducted. Here, the mitochondrial genomes of two Monochamus species, M. saltuarius and M. urussovi, were newly sequenced and annotated. The composition and order of genes in the mitochondrial genomes of Monochamus species are conserved. All transfer RNAs exhibit the typical clover-leaf secondary structure, with the exception of trnS1. Similar to other longhorn beetles, Lamiinae mitochondrial genomes have an A + T bias. All 13 protein-coding genes have experienced purifying selection, and tandem repeat sequences are abundant in the A + T-rich region. Phylogenetic analyses revealed congruent topologies among trees inferred from the five datasets, with the monophyly of Acanthocinini, Agapanthiini, Batocerini, Dorcaschematini, Pteropliini, and Saperdini receiving high support. The findings of this study enhance our understanding of mitochondrial genome evolution and will provide a basis for future studies of population genetics and phylogenetic investigations in this group.}, }
@article {pmid36397290, year = {2023}, author = {Mallard, J and Hucteau, E and Schott, R and Trensz, P and Pflumio, C and Kalish-Weindling, M and Favret, F and Pivot, X and Hureau, TJ and Pagano, AF}, title = {Early skeletal muscle deconditioning and reduced exercise capacity during (neo)adjuvant chemotherapy in patients with breast cancer.}, journal = {Cancer}, volume = {129}, number = {2}, pages = {215-225}, pmid = {36397290}, issn = {1097-0142}, mesh = {Humans ; Female ; *Hand Strength/physiology ; Exercise Tolerance ; *Breast Neoplasms/drug therapy ; Quality of Life ; Muscle, Skeletal ; Chemotherapy, Adjuvant/adverse effects ; }, abstract = {BACKGROUND: Fatigue is a hallmark of breast cancer and is associated with skeletal muscle deconditioning. If cancer-related fatigue occurs early during chemotherapy (CT), the development of skeletal muscle deconditioning and its effect on exercise capacity remain unclear. The aim of this study was to investigate the evolution of skeletal muscle deconditioning and exercise capacity in patients with early-stage breast cancer during CT.<br><br>METHODS: Patients with breast cancer had a visit before undergoing CT, at 8&#xa0;weeks, and at the end of chemotherapy (post-CT). Body composition was determined through bioelectrical impedance analysis. Knee extensor, handgrip muscle force and fatigue was quantified by performing maximal voluntary isometric contractions and exercise capacity using the 6-min walking test. Questionnaires were also administered&#xa0;to evaluate quality of life, cancer-related fatigue, and physical activity level.<br><br>RESULTS: Among the 100 patients, reductions were found in muscle mass (-2.3%, p&#xa0;=&#xa0;.002), exercise capacity (-6.7%, p&#xa0;<&#xa0;.001), and knee extensor force (-4.9%, p&#xa0;<&#xa0;.001) post-CT, which occurred within the first 8&#xa0;weeks of treatment with no further decrease thereafter. If muscle fatigue did not change, handgrip muscle force decreased post-CT only (-2.5%, p&#xa0;=&#xa0;.001), and exercise capacity continued to decrease between 8&#xa0;weeks and post-CT (-4.6%, p&#xa0;<&#xa0;.001). Quality of life and cancer-related fatigue were impaired after 8&#xa0;weeks (p&#xa0;<&#xa0;.001) and remained stable thereafter, whereas the physical activity level remained stable during chemotherapy.<br><br>CONCLUSIONS: Similar to cancer-related fatigue, skeletal muscle deconditioning and reduced exercise capacity occurred early during breast cancer CT. Thus, it appears essential to prevent these alterations through exercise training implemented during&#xa0;CT.}, }
@article {pmid36386853, year = {2022}, author = {Radzvilavicius, AL and Johnston, IG}, title = {Organelle bottlenecks facilitate evolvability by traversing heteroplasmic fitness valleys.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {974472}, pmid = {36386853}, issn = {1664-8021}, abstract = {Bioenergetic organelles-mitochondria and plastids-retain their own genomes (mtDNA and ptDNA), and these organelle DNA (oDNA) molecules are vital for eukaryotic life. Like all genomes, oDNA must be able to evolve to suit new environmental challenges. However, mixed oDNA populations in cells can challenge cellular bioenergetics, providing a penalty to the appearance and adaptation of new mutations. Here we show that organelle "bottlenecks," mechanisms increasing cell-to-cell oDNA variability during development, can overcome this mixture penalty and facilitate the adaptation of beneficial mutations. We show that oDNA heteroplasmy and bottlenecks naturally emerge in evolutionary simulations subjected to fluctuating environments, demonstrating that this evolvability is itself evolvable. Usually thought of as a mechanism to clear damaging mutations, organelle bottlenecks therefore also resolve the tension between intracellular selection for pure cellular oDNA populations and the "bet-hedging" need for evolvability and adaptation to new environments. This general theory suggests a reason for the maintenance of organelle heteroplasmy in cells, and may explain some of the observed diversity in organelle maintenance and inheritance across taxa.}, }
@article {pmid36382523, year = {2022}, author = {Watson, ET and Flanagan, BA and Pascar, JA and Edmands, S}, title = {Mitochondrial effects on fertility and longevity in Tigriopus californicus contradict predictions of the mother's curse hypothesis.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1987}, pages = {20221211}, pmid = {36382523}, issn = {1471-2954}, mesh = {Female ; Animals ; *Longevity ; Mitochondria/genetics ; Maternal Inheritance ; Fertility ; *Genome, Mitochondrial ; DNA, Mitochondrial/genetics ; }, abstract = {Strict maternal inheritance of mitochondria favours the evolutionary accumulation of sex-biased fitness effects, as mitochondrial evolution occurs exclusively in female lineages. The 'mother's curse' hypothesis proposes that male-harming mutations should accumulate in mitochondrial genomes when they have neutral or beneficial effects on female fitness. Rigorous empirical tests have largely focused on Drosophila, where support for the predictions of mother's curse has been mixed. We investigated the impact of mother's curse mutations in Tigriopus californicus, a minute crustacean. Using non-recombinant backcrosses, we introgressed four divergent mitochondrial haplotypes into two nuclear backgrounds and recorded measures of fertility and longevity. We found that the phenotypic effects of mitochondrial mutations were context dependent, being influenced by the nuclear background in which they were expressed, as well as the sex of the individual and rearing temperature. Mitochondrial haplotype effects were greater for fertility than longevity, and temperature effects were greater for longevity. However, in opposition to mother's curse expectations, females had higher mitochondrial genetic variance than males for fertility and longevity, little evidence of sexual antagonism favouring females was found, and the impacts of mitonuclear mismatch harmed females but not males. Together, this indicates that selection on mitochondrial variation has not resulted in the accumulation of male mutation load in Tigriopus californicus.}, }
@article {pmid36373631, year = {2023}, author = {Mencía, M}, title = {Acid digestion and symbiont: Proton sharing at the origin of mitochondriogenesis?: Proton production by a symbiotic bacterium may have been the origin of two hallmark eukaryotic features, acid digestion and mitochondria: Proton production by a symbiotic bacterium may have been the origin of two hallmark eukaryotic features, acid digestion and mitochondria.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {1}, pages = {e2200136}, doi = {10.1002/bies.202200136}, pmid = {36373631}, issn = {1521-1878}, mesh = {*Protons ; Phylogeny ; *Eukaryota ; Symbiosis ; Bacteria ; Mitochondria ; Digestion ; Biological Evolution ; }, abstract = {The initial relationships between organisms leading to endosymbiosis and the first eukaryote are currently a topic of hot debate. Here, I present a theory that offers a gradual scenario in which the origins of phagocytosis and mitochondria are intertwined in such a way that the evolution of one would not be possible without the other. In this scenario, the premitochondrial bacterial symbiont became initially associated with a protophagocytic host on the basis of cooperation to kill prey with symbiont-produced toxins and reactive oxygen species (ROS). Subsequently, the cooperation was focused on the digestion stage, through the acidification of the protophagocytic cavities via exportation of protons produced by the aerobic respiration of the symbiont. The host gained an improved phagocytic capacity and the symbiont received organic compounds from prey. As the host gradually lost its membrane energetics to develop lysosomal digestion, respiration was centralized in the premitochondrial symbiont for energy production for the consortium.}, }
@article {pmid36362255, year = {2022}, author = {Zhao, W and Bu, X and Zou, H and Li, W and Wu, S and Li, M and Wang, G}, title = {The Genome of the Mitochondrion-Related Organelle in Cepedea longa, a Large Endosymbiotic Opalinid Inhabiting the Recta of Frogs.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36362255}, issn = {1422-0067}, support = {32170437//National Natural Science Foundation of China/ ; 2021M703435//China Postdoctoral Science Foundation/ ; 2019QZKK0304//Second Tibetan Plateau Scienti&#xfb01;c Expedition and Research Program/ ; CARS-45//earmarked fund for CARS/ ; }, mesh = {Animals ; Phylogeny ; *Anura/genetics ; *Stramenopiles/genetics ; Organelles/metabolism ; Mitochondria/genetics ; }, abstract = {Mitochondrion-related organelles (MROs) are loosely defined as degenerated mitochondria in anaerobic and microaerophilic lineages. Opalinids are commonly regarded as commensals in the guts of cold-blooded amphibians. It may represent an intermediate adaptation stage between the conventional aerobic mitochondria and derived anaerobic MROs. In the present study, we sequenced and analyzed the MRO genome of Cepedea longa. It has a linear MRO genome with large inverted repeat gene regions at both ends. Compared to Blastocystis and Proteromonas lacertae, the MRO genome of C. longa has a higher G + C content and repeat sequences near the central region. Although three Opalinata species have different morphological characteristics, phylogenetic analyses based on eight concatenated nad genes indicate that they are close relatives. The phylogenetic analysis showed that C. longa clustered with P. lacertae with strong support. The 18S rRNA gene-based phylogeny resolved the Opalinea clade as a sister clade to Karotomorpha, which then further grouped with Proteromonas. The paraphyly of Proteromonadea needs to be verified due to the lack of MRO genomes for key species, such as Karotomorpha, Opalina and Protoopalina. Besides, our dataset and analyses offered slight support for the paraphyly of Bigyra.}, }
@article {pmid36361939, year = {2022}, author = {Alves, R and Pazos-Gil, M and Medina-Carbonero, M and Sanz-Alcázar, A and Delaspre, F and Tamarit, J}, title = {Evolution of an Iron-Detoxifying Protein: Eukaryotic and Rickettsia Frataxins Contain a Conserved Site Which Is Not Present in Their Bacterial Homologues.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36361939}, issn = {1422-0067}, support = {PID2020-118296RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n (Spain)/ ; }, mesh = {Humans ; Bacterial Proteins/chemistry/metabolism ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Eukaryota/metabolism ; Friedreich Ataxia/genetics/metabolism ; Iron/metabolism ; *Iron-Binding Proteins/chemistry/metabolism ; *Neurodegenerative Diseases ; *Rickettsia/metabolism ; Tyrosine/metabolism ; Mitochondria/metabolism/microbiology ; Frataxin ; }, abstract = {Friedreich's ataxia is a neurodegenerative disease caused by mutations in the frataxin gene. Frataxin homologues, including bacterial CyaY proteins, can be found in most species and play a fundamental role in mitochondrial iron homeostasis, either promoting iron assembly into metaloproteins or contributing to iron detoxification. While several lines of evidence suggest that eukaryotic frataxins are more effective than bacterial ones in iron detoxification, the residues involved in this gain of function are unknown. In this work, we analyze conservation of amino acid sequence and protein structure among frataxins and CyaY proteins to identify four highly conserved residue clusters and group them into potential functional clusters. Clusters 1, 2, and 4 are present in eukaryotic frataxins and bacterial CyaY proteins. Cluster 3, containing two serines, a tyrosine, and a glutamate, is only present in eukaryotic frataxins and on CyaY proteins from the Rickettsia genus. Residues from cluster 3 are blocking a small cavity of about 40 Å present in E. coli's CyaY. The function of this cluster is unknown, but we hypothesize that its tyrosine may contribute to prevent formation of reactive oxygen species during iron detoxification. This cluster provides an example of gain of function during evolution in a protein involved in iron homeostasis, as our results suggests that Cluster 3 was present in the endosymbiont ancestor of mitochondria and was conserved in eukaryotic frataxins.}, }
@article {pmid36360198, year = {2022}, author = {Boulygina, E and Sharko, F and Cheprasov, M and Gladysheva-Azgari, M and Slobodova, N and Tsygankova, S and Rastorguev, S and Grigorieva, L and Kopp, M and Fernandes, JMO and Novgorodov, G and Boeskorov, G and Protopopov, A and Hwang, WS and Tikhonov, A and Nedoluzhko, A}, title = {Ancient DNA Reveals Maternal Philopatry of the Northeast Eurasian Brown Bear (Ursus arctos) Population during the Holocene.}, journal = {Genes}, volume = {13}, number = {11}, pages = {}, pmid = {36360198}, issn = {2073-4425}, mesh = {Animals ; *Ursidae/genetics ; DNA, Ancient ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; }, abstract = {Significant palaeoecological and paleoclimatic changes that took place during Late Pleistocene-Early Holocene transition are considered important factors that led to megafauna extinctions. Unlike many other species, the brown bear (Ursus arctos) has survived this geological time. Despite the fact that several mitochondrial DNA clades of brown bears became extinct at the end of the Pleistocene, this species is still widely distributed in Northeast Eurasia. Here, using the ancient DNA analysis of a brown bear individual that inhabited Northeast Asia in the Middle Holocene (3460 ± 40 years BP) and comparative phylogenetic analysis, we show a significant mitochondrial DNA similarity of the studied specimen with modern brown bears inhabiting Yakutia and Chukotka. In this study, we clearly demonstrate the maternal philopatry of the Northeastern Eurasian U. arctos population during the several thousand years of the Holocene.}, }
@article {pmid36360182, year = {2022}, author = {Wang, Y and Hua, X and Shi, X and Wang, C}, title = {Origin, Evolution, and Research Development of Donkeys.}, journal = {Genes}, volume = {13}, number = {11}, pages = {}, pmid = {36360182}, issn = {2073-4425}, mesh = {Animals ; *Equidae/genetics ; *Microsatellite Repeats ; Genome/genetics ; Genomics ; Mitochondria/genetics ; }, abstract = {Lack of archaeological and whole-genome diversity data has restricted current knowledge of the evolutionary history of donkeys. With the advancement of science and technology, the discovery of archaeological evidence, the development of molecular genetics, and the improvement of whole-genome sequencing technology, the in-depth understanding of the origin and domestication of donkeys has been enhanced, however. Given the lack of systematic research, the present study carefully screened and collected multiple academic papers and books, journals, and literature on donkeys over the past 15 years. The origin and domestication of donkeys are reviewed in this paper from the aspects of basic information, cultural origin, bioarcheology, mitochondrial and chromosomal microsatellite sequences, and whole-genome sequence comparison. It also highlights and reviews genome assembly technology, by assembling the genome of an individual organism and comparing it with related sample genomes, which can be used to produce more accurate results through big data statistics, analysis, and computational correlation models. Background: The donkey industry in the world and especially in China is developing rapidly, and donkey farming is transforming gradually from the family farming model to large-scale, intensive, and integrated industrial operations, which could ensure the stability of product quality and quantity. However, theoretical research on donkey breeding and its technical development lags far behind that of other livestock, thereby limiting its industrial development. This review provides holistic information for the donkey industry and researchers, that could promote theoretical research, genomic selection (GS), and reproductive management of the donkey population.}, }
@article {pmid36355348, year = {2023}, author = {Klucnika, A and Mu, P and Jezek, J and McCormack, M and Di, Y and Bradshaw, CR and Ma, H}, title = {REC drives recombination to repair double-strand breaks in animal mtDNA.}, journal = {The Journal of cell biology}, volume = {222}, number = {1}, pages = {}, pmid = {36355348}, issn = {1540-8140}, support = {C6946/A24843//Cancer Research UK/United Kingdom ; 203144//Wellcome Trust/United Kingdom ; 203767/Z/16/Z//Wellcome Trust/United Kingdom ; 202269/Z/16/Z//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Humans ; *DNA Repair/genetics ; *DNA, Mitochondrial/genetics ; Drosophila/genetics ; *Drosophila Proteins/genetics ; Homologous Recombination ; Meiosis ; Mitochondria/genetics ; }, abstract = {Mechanisms that safeguard mitochondrial DNA (mtDNA) limit the accumulation of mutations linked to mitochondrial and age-related diseases. Yet, pathways that repair double-strand breaks (DSBs) in animal mitochondria are poorly understood. By performing a candidate screen for mtDNA repair proteins, we identify that REC-an MCM helicase that drives meiotic recombination in the nucleus-also localizes to mitochondria in Drosophila. We show that REC repairs mtDNA DSBs by homologous recombination in somatic and germline tissues. Moreover, REC prevents age-associated mtDNA mutations. We further show that MCM8, the human ortholog of REC, also localizes to mitochondria and limits the accumulation of mtDNA mutations. This study provides mechanistic insight into animal mtDNA recombination and demonstrates its importance in safeguarding mtDNA during ageing and evolution.}, }
@article {pmid36355038, year = {2022}, author = {Raval, PK and Garg, SG and Gould, SB}, title = {Endosymbiotic selective pressure at the origin of eukaryotic cell biology.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36355038}, issn = {2050-084X}, mesh = {*Eukaryotic Cells/physiology ; *Symbiosis/genetics ; Biological Evolution ; Eukaryota/genetics ; Archaea/genetics ; Cell Nucleus ; Meiosis ; Biology ; Phylogeny ; }, abstract = {The dichotomy that separates prokaryotic from eukaryotic cells runs deep. The transition from pro- to eukaryote evolution is poorly understood due to a lack of reliable intermediate forms and definitions regarding the nature of the first host that could no longer be considered a prokaryote, the first eukaryotic common ancestor, FECA. The last eukaryotic common ancestor, LECA, was a complex cell that united all traits characterising eukaryotic biology including a mitochondrion. The role of the endosymbiotic organelle in this radical transition towards complex life forms is, however, sometimes questioned. In particular the discovery of the asgard archaea has stimulated discussions regarding the pre-endosymbiotic complexity of FECA. Here we review differences and similarities among models that view eukaryotic traits as isolated coincidental events in asgard archaeal evolution or, on the contrary, as a result of and in response to endosymbiosis. Inspecting eukaryotic traits from the perspective of the endosymbiont uncovers that eukaryotic cell biology can be explained as having evolved as a solution to housing a semi-autonomous organelle and why the addition of another endosymbiont, the plastid, added no extra compartments. Mitochondria provided the selective pressures for the origin (and continued maintenance) of eukaryotic cell complexity. Moreover, they also provided the energetic benefit throughout eukaryogenesis for evolving thousands of gene families unique to eukaryotes. Hence, a synthesis of the current data lets us conclude that traits such as the Golgi apparatus, the nucleus, autophagosomes, and meiosis and sex evolved as a response to the selective pressures an endosymbiont imposes.}, }
@article {pmid36353057, year = {2022}, author = {Liang, P and Wang, S and Lin, Y and Wang, L and Zhao, L and Liu, S}, title = {The complete mitochondrial genome of Cepola schlegelii from the East China Sea.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {7}, number = {11}, pages = {1925-1927}, pmid = {36353057}, issn = {2380-2359}, abstract = {Cepola schlegelii (Bleeker 1854) belongs to the genus Cepola in the family Cepolidae and order Priacanthiformes. The complete mitochondrial genome of C. schlegelii was sequenced and analyzed by a high-throughput sequencing approach. The full length of the genome is 17,020 bp, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a non-coding control region (D-loop). Phylogenetic analysis based on complete mitochondrial genomes revealed that C. schlegelii was most closely related to Acanthocepola krusensternii. The complete mitochondrial sequence of C. schlegelii will enrich the mitochondrial genome database and provide useful resources for population genetics and evolution analyses.}, }
@article {pmid36351770, year = {2022}, author = {Hénault, M and Marsit, S and Charron, G and Landry, CR}, title = {Hybridization drives mitochondrial DNA degeneration and metabolic shift in a species with biparental mitochondrial inheritance.}, journal = {Genome research}, volume = {32}, number = {11-12}, pages = {2043-2056}, pmid = {36351770}, issn = {1549-5469}, mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Genes, Mitochondrial ; Mitochondria/genetics ; Hybridization, Genetic ; Genotype ; Saccharomyces cerevisiae/genetics ; }, abstract = {Mitochondrial DNA (mtDNA) is a cytoplasmic genome that is essential for respiratory metabolism. Although uniparental mtDNA inheritance is most common in animals and plants, distinct mtDNA haplotypes can coexist in a state of heteroplasmy, either because of paternal leakage or de novo mutations. mtDNA integrity and the resolution of heteroplasmy have important implications, notably for mitochondrial genetic disorders, speciation, and genome evolution in hybrids. However, the impact of genetic variation on the transition to homoplasmy from initially heteroplasmic backgrounds remains largely unknown. Here, we use Saccharomyces yeasts, fungi with constitutive biparental mtDNA inheritance, to investigate the resolution of mtDNA heteroplasmy in a variety of hybrid genotypes. We previously designed 11 crosses along a gradient of parental evolutionary divergence using undomesticated isolates of Saccharomyces paradoxus and Saccharomyces cerevisiae Each cross was independently replicated 48 to 96 times, and the resulting 864 hybrids were evolved under relaxed selection for mitochondrial function. Genome sequencing of 446 MA lines revealed extensive mtDNA recombination, but the recombination rate was not predicted by parental divergence level. We found a strong positive relationship between parental divergence and the rate of large-scale mtDNA deletions, which led to the loss of respiratory metabolism. We also uncovered associations between mtDNA recombination, mtDNA deletion, and genome instability that were genotype specific. Our results show that hybridization in yeast induces mtDNA degeneration through large-scale deletion and loss of function, with deep consequences for mtDNA evolution, metabolism, and the emergence of reproductive isolation.}, }
@article {pmid36336814, year = {2023}, author = {Vilaça, ST and Maroso, F and Lara, P and de Thoisy, B and Chevallier, D and Arantes, LS and Santos, FR and Bertorelle, G and Mazzoni, CJ}, title = {Evidence of backcross inviability and mitochondrial DNA paternal leakage in sea turtle hybrids.}, journal = {Molecular ecology}, volume = {32}, number = {3}, pages = {628-643}, doi = {10.1111/mec.16773}, pmid = {36336814}, issn = {1365-294X}, support = {//Alexander von Humboldt-Stiftung/ ; //Centre National de la Recherche Scientifique/ ; 491292795//Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)/ ; }, mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Turtles/genetics ; Mitochondria/genetics ; Biological Evolution ; Polymerase Chain Reaction ; }, abstract = {Hybridization is known to be part of many species' evolutionary history. Sea turtles have a fascinating hybridization system in which species separated by as much as 43 million years are still capable of hybridizing. Indeed, the largest nesting populations in Brazil of loggerheads (Caretta caretta) and hawksbills (Eretmochelys imbricata) have a high incidence of hybrids between these two species. A third species, olive ridleys (Lepidochelys olivacea), is also known to hybridize although at a smaller scale. Here, we used restriction site-associated DNA sequencing (RAD-Seq) markers, mitogenomes, and satellite-telemetry to investigate the patterns of hybridization and introgression in the Brazilian sea turtle population and their relationship with the migratory behaviours between feeding and nesting aggregations. We also explicitly test if the mixing of two divergent genomes in sea turtle hybrids causes mitochondrial paternal leakage. We developed a new species-specific PCR-assay capable of detecting mitochondrial DNA (mtDNA) inheritance from both parental species and performed ultra-deep sequencing to estimate the abundance of each mtDNA type. Our results show that all adult hybrids are first generation (F1) and most display a loggerhead migratory behaviour. We detected paternal leakage in F1 hybrids and different proportions of mitochondria from maternal and paternal species. Although previous studies showed no significant fitness decrease in hatchlings, our results support genetically-related hybrid breakdown possibly caused by cytonuclear incompatibility. Further research on hybrids from other populations in addition to Brazil and between different species will show if backcross inviability and mitochondrial paternal leakage is observed across sea turtle species.}, }
@article {pmid36331499, year = {2023}, author = {Lestari, SM and Khatun, MF and Acharya, R and Sharma, SR and Shrestha, YK and Jahan, SMH and Aye, TT and Lynn, OM and Win, NKK and Hoat, TX and Thi Dao, H and Tsai, CW and Lee, J and Hwang, HS and Kil, EJ and Lee, S and Kim, SM and Lee, KY}, title = {Genetic diversity of cryptic species of Bemisia tabaci in Asia.}, journal = {Archives of insect biochemistry and physiology}, volume = {112}, number = {2}, pages = {e21981}, doi = {10.1002/arch.21981}, pmid = {36331499}, issn = {1520-6327}, support = {I-1543086-2017-21-01//Exportation Support of Agricultural Products at Animal and Plant Quarantine Agency/ ; Z-1543086-2017-21-01//Exportation Support of Agricultural Products at Animal and Plant Quarantine Agency/ ; }, mesh = {Animals ; Phylogeny ; Asia ; China ; *Mitochondria ; *Hemiptera/genetics ; Genetic Variation ; }, abstract = {Bemisia tabaci is a species complex consisting of various genetically different cryptic species worldwide. To understand the genetic characteristics and geographic distribution of cryptic species of B. tabaci in Asia, we conducted an extensive collection of B. tabaci samples in ten Asian countries (Bangladesh, Indonesia, Japan, Korea, Myanmar, Nepal, Philippines, Singapore, Taiwan, and Vietnam) from 2013 to 2020 and determined 56 different partial sequences of mitochondrial cytochrome oxidase subunit I (COI) DNA. In addition, information on 129 COI sequences of B. tabaci identified from 16 Asian countries was downloaded from the GenBank database. Among the total 185 COI sequences of B. tabaci, the sequence variation reached to 19.68%. In addition, there were 31 cryptic species updated from 16 countries in Asia, that is, Asia I, Asia I India, Asia II (1-13), Asia III, Asia IV, Asia V, China 1-6, MEAM (1, 2, K), MED, Australia/Indonesia, Japan (1 and 2). Further, MED cryptic species consisted of 2 clades, Q1 and Q2. This study provides updated information to understand the genetic variation and geographic diversity of B. tabaci in Asia.}, }
@article {pmid36330786, year = {2022}, author = {De, AK and Bhattacharya, D and Sawhney, S and Bala, P and Sunder, J and Sujatha, T and Ponraj, P and Chakurkar, EB}, title = {Molecular characterization of Rhipicephalus microplus in Andaman and Nicobar Islands, India: an insight into genetic assemblages.}, journal = {Journal of genetics}, volume = {101}, number = {}, pages = {}, pmid = {36330786}, issn = {0973-7731}, mesh = {Animals ; *Rhipicephalus/genetics ; Phylogeny ; Haplotypes ; Geography ; Mitochondria/genetics ; India ; Islands ; }, abstract = {The tick, Rhipicephalus microplus is considered as the most notorious ectoparasite of veterinary importance in tropical and sub-tropical regions of the world. The present study deals with the molecular characterization of R. microplus in different regions of Andaman and Nicobar Islands using sequence information of mitochondrial cytochrome C oxidase subunit I (COX1) and their phylogenetic relationship with other Indian R. microplus genotypes. DNA polymorphism study identified a total of eight haplotypes with haplotype diversity of 0.909 ± 0.065 and nucleotide diversity of 0.01911 ± 0.00493. Currently, R. microplus complex consists of five taxa; R. microplus clade A sensu Burger et al. (2014), R. microplus clade B sensu Burger et al. (2014), R. microplus clade C sensu Low et al. (2015), R. australis and R. annulatus. Phylogenetic analysis revealed the presence of two clades (clade A and clade C) of R. microplus in Andaman and Nicobar isolates; Nicobar isolates belonged to clade A whereas Andaman isolates belonged to clade C of R. microplus complex. All the other Indian sequences retrieved from GenBank belonged to clade C of R. microplus complex. Andaman isolates under clade C of R. microplus were phylogenetically distinct from Indian isolates, which indicates independent speciation under isolated island milieu. In Indian isolates, no host-specific or geographical location-specific sub-clustering was observed which indicates the species jumping potential of the R. microplus tick. Therefore, this study indicated the presence of two different genetic makeup of R. microplus complex in two areas of the Andaman and Nicobar archipelago separated by a natural geographical barrier. This indicates presence of two different founding populations of ticks, one in the south and north-middle Andaman and the other in Nicobar Island.}, }
@article {pmid36327950, year = {2023}, author = {Filimonova, S}, title = {Fine structure of the posterior midgut in the mite Anystis baccarum (L.).}, journal = {Arthropod structure &amp; development}, volume = {72}, number = {}, pages = {101218}, doi = {10.1016/j.asd.2022.101218}, pmid = {36327950}, issn = {1873-5495}, mesh = {Animals ; *Mites/ultrastructure ; Phylogeny ; Digestive System/ultrastructure ; *Arachnida ; Epithelial Cells ; }, abstract = {Homology of the posterior midgut regions (PMG) in different phylogenetic lineages of acariform mites (superorder Acariformes) remains unresolved. In the order Trombidiformes, the ultrastructure of the PMG is known primarily in derived groups; thus this study focuses on species belonging to a relatively basal trombidiform family. PMG of Anystis baccarum consists of the colon and postcolon separated by a small intercolon. The fine structure of the colon and postcolon is close to that of the corresponding organs of sarcoptiform mites with the epithelium showing absorptive and endocytotic activity. The epithelial cells produce a variety of excretory vacuoles and a peritrophic matrix around the feces. Morover, the epithelium of the postcolon is characterized by the highest apical brush border and especially numerous mitochondria suggesting involvement in water and ion absorption. The intercolon functions as a sphincter lined with an epithelium capable of producing excretory granules. A pair of short blind extensions arises assimmetrically from the intercolon into the body cavity. Ultrastructurally, these extensions are similar to the arachnid Malpighian tubules and may be their reduced version. Rare endocrine-like cells have been observed in the colon and postcolon.}, }
@article {pmid36326769, year = {2023}, author = {Kierepka, EM and Preckler-Quisquater, S and Reding, DM and Piaggio, AJ and Riley, SPD and Sacks, BN}, title = {Genomic analyses of gray fox lineages suggest ancient divergence and secondary contact in the southern Great Plains.}, journal = {The Journal of heredity}, volume = {114}, number = {2}, pages = {110-119}, doi = {10.1093/jhered/esac060}, pmid = {36326769}, issn = {1465-7333}, mesh = {Humans ; Animals ; *Foxes/genetics ; Phylogeny ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Genomics ; }, abstract = {The gray fox (Urocyon cinereoargenteus) lineage diverged from all other extant canids at their most basal node and is restricted to the Americas. Previous mitochondrial analysis from coastal populations identified deeply divergent (up to 1 Mya) eastern and western lineages that predate most intraspecific splits in carnivores. We conducted genotyping by sequencing and mitochondrial analysis on gray foxes sampled across North America to determine geographic concordance between nuclear and mitochondrial contact zones and divergence times. We also estimated the admixture within the contact zone between eastern and western gray foxes based on nuclear DNA. Both datasets confirmed that eastern and western lineages met in the southern Great Plains (i.e. Texas and Oklahoma), where they maintained high differentiation. Admixture was generally low, with the majority of admixed individuals carrying <10% ancestry from the other lineage. Divergence times confirmed a mid-Pleistocene split, similar to the mitochondrial estimates. Taken together, findings suggest gray fox lineages represent an ancient divergence event, far older than most intraspecific divergences in North American carnivores. Low admixture may reflect a relatively recent time since secondary contact (e.g. post-Pleistocene) or, alternatively, ecological or reproductive barriers between lineages. Though further research is needed to disentangle these factors, our genomic investigation suggests species-level divergence exists between eastern and western gray fox lineages.}, }
@article {pmid36324074, year = {2022}, author = {Zhao, B and Gao, S and Zhao, M and Lv, H and Song, J and Wang, H and Zeng, Q and Liu, J}, title = {Mitochondrial genomic analyses provide new insights into the "missing" atp8 and adaptive evolution of Mytilidae.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {738}, pmid = {36324074}, issn = {1471-2164}, mesh = {Animals ; *Genome, Mitochondrial ; *Mytilidae/genetics ; Phylogeny ; Genes, Mitochondrial ; Mitochondrial Proton-Translocating ATPases/genetics ; Genomics/methods ; }, abstract = {BACKGROUND: Mytilidae, also known as marine mussels, are widely distributed in the oceans worldwide. Members of Mytilidae show a tremendous range of ecological adaptions, from the species distributed in freshwater to those that inhabit in deep-sea. Mitochondria play an important role in energy metabolism, which might contribute to the adaptation of Mytilidae to different environments. In addition, some bivalve species are thought to lack the mitochondrial protein-coding gene ATP synthase F0 subunit 8. Increasing studies indicated that the absence of atp8 may be caused by annotation difficulties for atp8 gene is characterized by highly divergent, variable length.<br><br>RESULTS: In this study, the complete mitochondrial genomes of three marine mussels (Xenostrobus securis, Bathymodiolus puteoserpentis, Gigantidas vrijenhoeki) were newly assembled, with the lengths of 14,972&#xa0;bp, 20,482, and 17,786&#xa0;bp, respectively. We annotated atp8 in the sequences that we assembled and the sequences lacking atp8. The newly annotated atp8 sequences all have one predicted transmembrane domain, a similar hydropathy profile, as well as the C-terminal region with positively charged amino acids. Furthermore, we reconstructed the phylogenetic trees and performed positive selection analysis. The results showed that the deep-sea bathymodiolines experienced more relaxed evolutionary constraints. And signatures of positive selection were detected in nad4 of Limnoperna fortunei, which may contribute to the survival and/or thriving of this species in freshwater.<br><br>CONCLUSIONS: Our analysis supported that atp8 may not be missing in the Mytilidae. And our results provided evidence that the mitochondrial genes may contribute to the adaptation of Mytilidae to different environments.}, }
@article {pmid36323233, year = {2022}, author = {Picard, M and Shirihai, OS}, title = {Mitochondrial signal transduction.}, journal = {Cell metabolism}, volume = {34}, number = {11}, pages = {1620-1653}, pmid = {36323233}, issn = {1932-7420}, support = {R01 AG066828/AG/NIA NIH HHS/United States ; R21 MH123927/MH/NIMH NIH HHS/United States ; R35 GM119793/GM/NIGMS NIH HHS/United States ; R01 MH119336/MH/NIMH NIH HHS/United States ; R01 MH122706/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Mitochondria/metabolism ; *Signal Transduction ; Cell Communication ; Cell Nucleus/metabolism ; }, abstract = {The analogy of mitochondria as powerhouses has expired. Mitochondria are living, dynamic, maternally inherited, energy-transforming, biosynthetic, and signaling organelles that actively transduce biological information. We argue that mitochondria are the processor of the cell, and together with the nucleus and other organelles they constitute the mitochondrial information processing system (MIPS). In a three-step process, mitochondria (1) sense and respond to both endogenous and environmental inputs through morphological and functional remodeling; (2) integrate information through dynamic, network-based physical interactions and diffusion mechanisms; and (3) produce output signals that tune the functions of other organelles and systemically regulate physiology. This input-to-output transformation allows mitochondria to transduce metabolic, biochemical, neuroendocrine, and other local or systemic signals that enhance organismal adaptation. An explicit focus on mitochondrial signal transduction emphasizes the role of communication in mitochondrial biology. This framework also opens new avenues to understand how mitochondria mediate inter-organ processes underlying human health.}, }
@article {pmid36321837, year = {2022}, author = {McGlynn, SE and Perkins, G and Sim, MS and Mackey, M and Deerinck, TJ and Thor, A and Phan, S and Ballard, D and Ellisman, MH and Orphan, VJ}, title = {A Cristae-Like Microcompartment in Desulfobacterota.}, journal = {mBio}, volume = {13}, number = {6}, pages = {e0161322}, pmid = {36321837}, issn = {2150-7511}, support = {P41 GM103412/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anaerobiosis ; *Bacteria/metabolism ; *Archaea/metabolism ; Methane/metabolism ; Sulfates/metabolism ; Oxidation-Reduction ; Geologic Sediments/microbiology ; Phylogeny ; }, abstract = {Some Alphaproteobacteria contain intracytoplasmic membranes (ICMs) and proteins homologous to those responsible for the mitochondrial cristae, an observation which has given rise to the hypothesis that the Alphaproteobacteria endosymbiont had already evolved cristae-like structures and functions. However, our knowledge of microbial fine structure is still limited, leaving open the possibility of structurally homologous ICMs outside the Alphaproteobacteria. Here, we report on the detailed characterization of lamellar cristae-like ICMs in environmental sulfate-reducing Desulfobacterota that form syntrophic partnerships with anaerobic methane-oxidizing (ANME) archaea. These structures are junction-bound to the cytoplasmic membrane and resemble the form seen in the lamellar cristae of opisthokont mitochondria. Extending these observations, we also characterized similar structures in Desulfovibrio carbinolicus, a close relative of the magnetotactic D. magneticus, which does not contain magnetosomes. Despite a remarkable structural similarity, the key proteins involved in cristae formation have not yet been identified in Desulfobacterota, suggesting that an analogous, but not a homologous, protein organization system developed during the evolution of some members of Desulfobacterota. IMPORTANCE Working with anaerobic consortia of methane oxidizing ANME archaea and their sulfate-reducing bacterial partners recovered from deep sea sediments and with the related sulfate-reducing bacterial isolate D. carbinolicus, we discovered that their intracytoplasmic membranes (ICMs) appear remarkably similar to lamellar cristae. Three-dimensional electron microscopy allowed for the novel analysis of the nanoscale attachment of ICMs to the cytoplasmic membrane, and these ICMs are structurally nearly identical to the crista junction architecture seen in metazoan mitochondria. However, the core junction-forming proteins must be different. The outer membrane vesicles were observed to bud from syntrophic Desulfobacterota, and darkly stained granules were prominent in both Desulfobacterota and D. carbinolicus. These findings expand the taxonomic breadth of ICM-producing microorganisms and add to our understanding of three-dimensional microbial fine structure in environmental microorganisms.}, }
@article {pmid36309009, year = {2022}, author = {Liu, Y and Zhou, J and Zhang, N and Wu, X and Zhang, Q and Zhang, W and Li, X and Tian, Y}, title = {Two sensory neurons coordinate the systemic mitochondrial stress response via GPCR signaling in C. elegans.}, journal = {Developmental cell}, volume = {57}, number = {21}, pages = {2469-2482.e5}, doi = {10.1016/j.devcel.2022.10.001}, pmid = {36309009}, issn = {1878-1551}, mesh = {Animals ; *Caenorhabditis elegans/metabolism ; *Caenorhabditis elegans Proteins/genetics/metabolism ; Mitochondria/metabolism ; Unfolded Protein Response ; Sensory Receptor Cells/metabolism ; Receptors, G-Protein-Coupled/genetics/metabolism ; }, abstract = {Mitochondrial perturbations within neurons communicate stress signals to peripheral tissues, coordinating organismal-wide mitochondrial homeostasis for optimal fitness. However, the neuronal control of the systemic stress regulation remains poorly understood. Here, we identified a G-protein-coupled receptor (GPCR), SRZ-75, that couples with Gαq signaling in a pair of chemosensory ADL neurons to drive the mitochondrial unfolded protein response (UPR[mt]) activation in the intestine via the release of neuropeptides in Caenorhabditis elegans. Constitutive activation of Gαq signaling in the ADL neurons is sufficient to induce the intestinal UPR[mt], leading to increased stress resistance and metabolic adaptations. Ablation of ADL neurons attenuates the intestinal UPR[mt] activation in response to various forms of neuronal mitochondrial dysfunction. Thus, GPCR and its Gαq downstream signaling in two sensory neurons coordinate the systemic UPR[mt] activation, representing a previously uncharacterized, but potentially conserved, neuronal signaling for organismal-wide mitochondrial stress regulation.}, }
@article {pmid36293209, year = {2022}, author = {Liu, Q and Zhang, L and Zou, Y and Tao, Y and Wang, B and Li, B and Liu, R and Wang, B and Ding, L and Cui, Q and Lin, J and Mao, B and Xiong, W and Yu, M}, title = {Modulating p-AMPK/mTOR Pathway of Mitochondrial Dysfunction Caused by MTERF1 Abnormal Expression in Colorectal Cancer Cells.}, journal = {International journal of molecular sciences}, volume = {23}, number = {20}, pages = {}, pmid = {36293209}, issn = {1422-0067}, support = {32160167, 31760331, 31260276, 31601155, 81860531, 81760507, 82160516//National Nature Science Foundation of China/ ; 202001BB0500080, 202001BB050041//the Key Project of Science and Technology Department of Yunnan Province/ ; 202101AT070006//the Applied Basic Research Programs of Science and Technology Department of Yunnan Province/ ; No. 2017HB077//the Reserve Talents of Young and Middle-aged Academic and Technical Leaders of Yunnan Province/ ; 2020267, 2021Y314//d Yunnan University's Research In-novation Fund for Graduate Students/ ; }, mesh = {Humans ; AMP-Activated Protein Kinases/metabolism ; Reactive Oxygen Species/metabolism ; TOR Serine-Threonine Kinases/metabolism ; Cell Proliferation/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/metabolism ; HCT116 Cells ; Cell Line, Tumor ; *Colonic Neoplasms/metabolism ; Adenosine Triphosphate/metabolism ; *Colorectal Neoplasms/pathology ; Gene Expression Regulation, Neoplastic ; }, abstract = {Human mitochondrial transcription termination factor 1 (MTERF1) has been demonstrated to play an important role in mitochondrial gene expression regulation. However, the molecular mechanism of MTERF1 in colorectal cancer (CRC) remains largely unknown. Here, we found that MTERF1 expression was significantly increased in colon cancer tissues compared with normal colorectal tissue by Western blotting, immunohistochemistry, and tissue microarrays (TMA). Overexpression of MTERF1 in the HT29 cell promoted cell proliferation, migration, invasion, and xenograft tumor formation, whereas knockdown of MTERF1 in HCT116 cells appeared to be the opposite phenotype to HT29 cells. Furthermore, MTERF1 can increase mitochondrial DNA (mtDNA) replication, transcription, and protein synthesis in colorectal cancer cells; increase ATP levels, the mitochondrial crista density, mitochondrial membrane potential, and oxygen consumption rate (OCR); and reduce the ROS production in colorectal cancer cells, thereby enhancing mitochondrial oxidative phosphorylation (OXPHOS) activity. Mechanistically, we revealed that MTERF1 regulates the AMPK/mTOR signaling pathway in cancerous cell lines, and we also confirmed the involvement of the AMPK/mTOR signaling pathway in both xenograft tumor tissues and colorectal cancer tissues. In summary, our data reveal an oncogenic role of MTERF1 in CRC progression, indicating that MTERF1 may represent a new therapeutic target in the future.}, }
@article {pmid36288802, year = {2022}, author = {Weaver, RJ and Rabinowitz, S and Thueson, K and Havird, JC}, title = {Genomic Signatures of Mitonuclear Coevolution in Mammals.}, journal = {Molecular biology and evolution}, volume = {39}, number = {11}, pages = {}, pmid = {36288802}, issn = {1537-1719}, support = {R35 GM142836/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *DNA, Mitochondrial/genetics ; *Genes, Mitochondrial ; Mammals/genetics ; Cell Nucleus/genetics ; Mitochondrial Proteins/genetics ; Genomics ; }, abstract = {Mitochondrial (mt) and nuclear-encoded proteins are integrated in aerobic respiration, requiring co-functionality among gene products from fundamentally different genomes. Different evolutionary rates, inheritance mechanisms, and selection pressures set the stage for incompatibilities between interacting products of the two genomes. The mitonuclear coevolution hypothesis posits that incompatibilities may be avoided if evolution in one genome selects for complementary changes in interacting genes encoded by the other genome. Nuclear compensation, in which deleterious mtDNA changes are offset by compensatory nuclear changes, is often invoked as the primary mechanism for mitonuclear coevolution. Yet, direct evidence supporting nuclear compensation is rare. Here, we used data from 58 mammalian species representing eight orders to show strong correlations between evolutionary rates of mt and nuclear-encoded mt-targeted (N-mt) proteins, but not between mt and non-mt-targeted nuclear proteins, providing strong support for mitonuclear coevolution across mammals. N-mt genes with direct mt interactions also showed the strongest correlations. Although most N-mt genes had elevated dN/dS ratios compared to mt genes (as predicted under nuclear compensation), N-mt sites in close contact with mt proteins were not overrepresented for signs of positive selection compared to noncontact N-mt sites (contrary to predictions of nuclear compensation). Furthermore, temporal patterns of N-mt and mt amino acid substitutions did not support predictions of nuclear compensation, even in positively selected, functionally important residues with direct mitonuclear contacts. Overall, our results strongly support mitonuclear coevolution across ∼170 million years of mammalian evolution but fail to support nuclear compensation as the major mode of mitonuclear coevolution.}, }
@article {pmid36282276, year = {2023}, author = {Wang, D and Teng, J and Ning, C and Wang, W and Liu, S and Zhang, Q and Tang, H}, title = {Mitogenome-wide association study on body measurement traits of Wenshang Barred chickens.}, journal = {Animal biotechnology}, volume = {34}, number = {7}, pages = {3154-3161}, doi = {10.1080/10495398.2022.2137035}, pmid = {36282276}, issn = {1532-2378}, mesh = {Animals ; *Chickens/genetics ; *Genome, Mitochondrial/genetics ; Phylogeny ; Phenotype ; Haplotypes/genetics ; Polymorphism, Single Nucleotide/genetics ; DNA, Mitochondrial/genetics ; }, abstract = {Mitochondria are best known for synthesizing ATP through the tricarboxylic acid cycle and oxidative phosphorylation. The cytoplasmic mitochondrial DNA (mtDNA) is important for maintaining the function. This study was designed to reveal the effect of mtDNA on chicken body measurement traits (BMTs). A population of 605 Wenshang Barred chickens were recorded BMTs, including body slope length, keel length, chest width, etc. The single-nucleotide polymorphisms (SNPs) of their mitogenomes were detected by PCR amplification and DNA sequencing. Totally 69 mutations in mitogenome were discovered, including 18 in noncoding region and 51 in coding region. By multi-sequence alignment and haplotype construction, the chickens were clustered into eight haplotypes and further three haplogroups. The association between BMTs and mtDNA SNPs, haplotypes and haplogroups were analyzed in the linear model by ASReml, respectively. Among them, the SNP mt11086 T/C in ND3 was found to significantly affect chest dept (p < .05) and was highly conservative by phylogenetic conservation analyses, which reflected the genetic effect on body size and growth of chickens. No significant association between the mitochondrial haplotypes or haplogroups and BMTs was found. The polymorphic site reflecting body size could be put into chicken breeding programs as the genetic marker.}, }
@article {pmid36281555, year = {2023}, author = {Guo, C and Wang, A and Cheng, H and Chen, L}, title = {New imaging instrument in animal models: Two-photon miniature microscope and large field of view miniature microscope for freely behaving animals.}, journal = {Journal of neurochemistry}, volume = {164}, number = {3}, pages = {270-283}, doi = {10.1111/jnc.15711}, pmid = {36281555}, issn = {1471-4159}, mesh = {Animals ; *Microscopy ; *Optical Imaging/methods ; Mammals ; Neurons/metabolism ; Behavior, Animal/physiology ; }, abstract = {Over the past decade, novel optical imaging tools have been developed for imaging neuronal activities along with the evolution of fluorescence indicators with brighter expression and higher sensitivity. Miniature microscopes, as revolutionary approaches, enable the imaging of large populations of neuron ensembles in freely behaving rodents and mammals, which allows exploring the neural basis of behaviors. Recent progress in two-photon miniature microscopes and mesoscale single-photon miniature microscopes further expand those affordable methods to navigate neural activities during naturalistic behaviors. In this review article, two-photon miniature microscopy techniques are summarized historically from the first documented attempt to the latest ones, and comparisons are made. The driving force behind and their potential for neuroscientific inquiries are also discussed. Current progress in terms of the mesoscale, i.e., the large field-of-view miniature microscopy technique, is addressed as well. Then, pipelines for registering single cells from the data of two-photon and large field-of-view miniature microscopes are discussed. Finally, we present the potential evolution of the techniques.}, }
@article {pmid36280780, year = {2022}, author = {Martijn, J and Vosseberg, J and Guy, L and Offre, P and Ettema, TJG}, title = {Phylogenetic affiliation of mitochondria with Alpha-II and Rickettsiales is an artefact.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {12}, pages = {1829-1831}, pmid = {36280780}, issn = {2397-334X}, mesh = {*Rickettsiales ; Phylogeny ; *Artifacts ; Mitochondria ; }, }
@article {pmid36280779, year = {2022}, author = {Fan, L and Wu, D and Goremykin, V and Trost, K and Knopp, M and Zhang, C and Martin, WF and Zhu, R}, title = {Reply to: Phylogenetic affiliation of mitochondria with Alpha-II and Rickettsiales is an artefact.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {12}, pages = {1832-1835}, pmid = {36280779}, issn = {2397-334X}, mesh = {*Rickettsiales ; Phylogeny ; *Artifacts ; Mitochondria ; }, }
@article {pmid36275864, year = {2022}, author = {Bi, R and Li, Y and Xu, M and Zheng, Q and Zhang, DF and Li, X and Ma, G and Xiang, B and Zhu, X and Zhao, H and Huang, X and Zheng, P and Yao, YG}, title = {Direct evidence of CRISPR-Cas9-mediated mitochondrial genome editing.}, journal = {Innovation (Cambridge (Mass.))}, volume = {3}, number = {6}, pages = {100329}, pmid = {36275864}, issn = {2666-6758}, abstract = {Pathogenic mitochondrial DNA (mtDNA) mutations can cause a variety of human diseases. The recent development of genome-editing technologies to manipulate mtDNA, such as mitochondria-targeted DNA nucleases and base editors, offer a promising way for curing mitochondrial diseases caused by mtDNA mutations. The CRISPR-Cas9 system is a widely used tool for genome editing; however, its application in mtDNA editing is still under debate. In this study, we developed a mito-Cas9 system by adding the mitochondria-targeted sequences and 3' untranslated region of nuclear-encoded mitochondrial genes upstream and downstream of the Cas9 gene, respectively. We confirmed that the mito-Cas9 system was transported into mitochondria and enabled knockin of exogenous single-stranded DNA oligonucleotides (ssODNs) into mtDNA based on proteinase and DNase protection assays. Successful knockin of exogenous ssODNs into mtDNA was further validated using polymerase chain reaction-free third-generation sequencing technology. We also demonstrated that RS-1, an agonist of RAD51, significantly increased knockin efficiency of the mito-Cas9 system. Collectively, we provide direct evidence that mtDNA can be edited using the CRISPR-Cas9 system. The mito-Cas9 system could be optimized as a promising approach for the treatment of mitochondrial diseases caused by pathogenic mtDNA mutations, especially those with homoplasmic mtDNA mutations.}, }
@article {pmid36271979, year = {2022}, author = {Hajibarat, Z and Saidi, A and Gorji, AM and Zeinalabedini, M and Ghaffari, MR and Hajibarat, Z and Nasrollahi, A}, title = {Identification of myosin genes and their expression in response to biotic (PVY, PVX, PVS, and PVA) and abiotic (Drought, Heat, Cold, and High-light) stress conditions in potato.}, journal = {Molecular biology reports}, volume = {49}, number = {12}, pages = {11983-11996}, pmid = {36271979}, issn = {1573-4978}, mesh = {*Solanum tuberosum/genetics/metabolism ; Droughts ; Phylogeny ; Plant Proteins/metabolism ; Hot Temperature ; Plant Breeding ; Stress, Physiological/genetics ; Plants/metabolism ; Myosins/genetics/metabolism ; Gene Expression Regulation, Plant/genetics ; }, abstract = {BACKGROUND: Plant organelles are highly motile where their movement is significant for fast distribution of material around the cell, facilitation of the plant's ability to respond to abiotic and biotic signals, and for appropriate growth. Abiotic and biotic stresses are among the major factors limiting crop yields, and biological membranes are the first target of these stresses. Plants utilize adaptive mechanisms namely myosin to repair injured membranes following exposure to abiotic and biotic stresses.<br><br>OBJECTIVE: Due to the economic importance and cultivation of potato grown under abiotic and biotic stress prone areas, identification and characterization of myosin family members in potato were performed in the present research.<br><br>METHODS: To identify the myosin genes in potato, we performed genome-wide analysis of myosin genes in the S. tuberosum genome using the phytozome. All putative sequences were approved with the interproscan. Bioinformatics analysis was conducted using phylogenetic tree, gene structure, cis-regulatory elements, protein-protein interaction, and gene expression.<br><br>RESULT: The majority of the cell machinery contain actin cytoskeleton and myosins, where motility of organelles are dependent on them. Homology-based analysis was applied to determine seven myosin genes in the potato genome. The members of myosin could be categorized into two groups (XI and VIII). Some of myosin proteins were sub-cellularly located in the nucleus containing 71.5% of myosin proteins and other myosin proteins were localized in the mitochondria, plasma-membrane, and cytoplasm. Determination of co-expressed network, promoter analysis, and gene structure were also performed and gene expression pattern of each gene was surveyed. Number of introns in the gene family members varied from 1 to 39. Gene expression analysis demonstrated that StMyoXI-B and StMyoVIII-2 had the highest transcripts, induced by biotic and abiotic stresses in all three tissues of stem, root, and leaves, respectively. Overall, different cis-elements including abiotic and biotic responsive, hormonal responsive, light responsive, defense responsive elements were found in the myosin promoter sequences. Among the cis-elements, the MYB, G-box, ABRE, JA, and SA contributed the most in the plant growth and development, and in response to abiotic and biotic stress conditions.<br><br>CONCLUSION: Our results showed that myosin genes can be utilized in breeding programs and genetic engineering of plants with the aim of increasing tolerance to abiotic and biotic stresses, especially to viral stresses such as PVY, PVX, PVA, PVS, high light, drought, cold and heat.}, }
@article {pmid36260528, year = {2022}, author = {Zhang, K and Li, J and Li, G and Zhao, Y and Dong, Y and Zhang, Y and Sun, W and Wang, J and Yao, J and Ma, Y and Wang, H and Zhang, Z and Wang, T and Xie, K and Wendel, JF and Liu, B and Gong, L}, title = {Compensatory Genetic and Transcriptional Cytonuclear Coordination in Allopolyploid Lager Yeast (Saccharomyces pastorianus).}, journal = {Molecular biology and evolution}, volume = {39}, number = {11}, pages = {}, pmid = {36260528}, issn = {1537-1719}, mesh = {*Beer ; *Gene Conversion ; Genome ; Cell Nucleus/genetics ; }, abstract = {Cytonuclear coordination between biparental-nuclear genomes and uniparental-cytoplasmic organellar genomes in plants is often resolved by genetic and transcriptional cytonuclear responses. Whether this mechanism also acts in allopolyploid members of other kingdoms is not clear. Additionally, cytonuclear coordination of interleaved allopolyploid cells/individuals within the same population is underexplored. The yeast Saccharomyces pastorianus provides the opportunity to explore cytonuclear coevolution during different growth stages and from novel dimensions. Using S. pastorianus cells from multiple growth stages in the same environment, we show that nuclear mitochondria-targeted genes have undergone both asymmetric gene conversion and growth stage-specific biased expression favoring genes from the mitochondrial genome donor (Saccharomyces eubayanus). Our results suggest that cytonuclear coordination in allopolyploid lager yeast species entails an orchestrated and compensatory genetic and transcriptional evolutionary regulatory shift. The common as well as unique properties of cytonuclear coordination underlying allopolyploidy between unicellular yeasts and higher plants offers novel insights into mechanisms of cytonuclear evolution associated with allopolyploid speciation.}, }
@article {pmid36255631, year = {2023}, author = {Marx, C and Marx-Blümel, L and Sonnemann, J and Wang, ZQ}, title = {Assessment of Mitochondrial Dysfunctions After Sirtuin Inhibition.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2589}, number = {}, pages = {269-291}, pmid = {36255631}, issn = {1940-6029}, mesh = {*Sirtuins/metabolism ; Lysine/metabolism ; Phylogeny ; Acetylation ; Histone Deacetylases/metabolism ; Histone Acetyltransferases/metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins/metabolism ; Histone Deacetylase Inhibitors/pharmacology ; }, abstract = {Posttranslational modifications are important for protein functions and cellular signaling pathways. The acetylation of lysine residues is catalyzed by histone acetyltransferases (HATs) and removed by histone deacetylases (HDACs), with the latter being grouped into four phylogenetic classes. The class III of the HDAC family, the sirtuins (SIRTs), contributes to gene expression, genomic stability, cell metabolism, and tumorigenesis. Thus, several specific SIRT inhibitors (SIRTi) have been developed to target cancer cell proliferation. Here we provide an overview of methods to study SIRT-dependent cell metabolism and mitochondrial functionality. The chapter describes metabolic flux analysis using Seahorse analyzers, methods for normalization of Seahorse data, flow cytometry and fluorescence microscopy to determine the mitochondrial membrane potential, mitochondrial content per cell and mitochondrial network structures, and Western blot analysis to measure mitochondrial proteins.}, }
@article {pmid36253367, year = {2022}, author = {Tobiasson, V and Berzina, I and Amunts, A}, title = {Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6132}, pmid = {36253367}, issn = {2041-1723}, mesh = {*Chlorophyta/metabolism ; Mitochondria/metabolism ; *Mitochondrial Ribosomes/metabolism ; RNA, Ribosomal/metabolism ; RNA, Ribosomal, 5S/metabolism ; Ribosomes/metabolism ; }, abstract = {Mitoribosomes of green algae display a great structural divergence from their tracheophyte relatives, with fragmentation of both rRNA and proteins as a defining feature. Here, we report a 2.9 Å resolution structure of the mitoribosome from the alga Polytomella magna harbouring a reduced rRNA split into 13 fragments. We found that the rRNA contains a non-canonical reduced form of the 5S, as well as a permutation of the LSU domain I. The mt-5S rRNA is stabilised by mL40 that is also found in mitoribosomes lacking the 5S, which suggests an evolutionary pathway. Through comparison to other ribosomes with fragmented rRNAs, we observe that the pattern is shared across large evolutionary distances, and between cellular compartments, indicating an evolutionary convergence and supporting the concept of a primordial fragmented ribosome. On the protein level, eleven peripherally associated HEAT-repeat proteins are involved in the binding of 3' rRNA termini, and the structure features a prominent pseudo-trimer of one of them (mL116). Finally, in the exit tunnel, mL128 constricts the tunnel width of the vestibular area, and mL105, a homolog of a membrane targeting component mediates contacts with an inner membrane bound insertase. Together, the structural analysis provides insight into the evolution of the ribosomal machinery in mitochondria.}, }
@article {pmid36251232, year = {2023}, author = {Giuditta, A and Zucconi, GG and Sadile, A}, title = {Brain Metabolic DNA: A Long Story and Some Conclusions.}, journal = {Molecular neurobiology}, volume = {60}, number = {1}, pages = {228-234}, pmid = {36251232}, issn = {1559-1182}, mesh = {Animals ; Humans ; Mice ; *DNA/metabolism ; *Mitochondria/metabolism ; Brain/metabolism ; Cytoplasm/metabolism ; RNA/metabolism ; DNA, Mitochondrial/metabolism ; }, abstract = {We have previously outlined the main properties of brain metabolic DNA (BMD) and its involvement in circadian oscillations, learning, and post-trial sleep. The presence of BMD in certain subcellular fractions and their behavior in cesium gradients have suggested that BMD originates from cytoplasmic reverse transcription and subsequently acquires a double-stranded configuration. More recently, it has been reported that some DNA sequences of cytoplasmic BMD in learning mice are different from that of the control animals. Furthermore, BMD is located in vicinity of the genes involved in different modifications of synaptic activity, suggesting that BMD may contribute to the brain's response to the changing environment. The present review outlines recent data with a special emphasis on reverse transcription of BMD that may recapitulate the molecular events at the time of the "RNA world" by activating mitochondrial telomerase and generating RNA templates from mitochondrial transcripts. The latter unexpected role of mitochondria is likely to promote a better understanding of mitochondrial contribution to cellular interactions and eukaryotic evolution. An initial step regards the role of human mitochondria in embryonic BMD synthesis, which is exclusively of maternal origin. In addition, mitochondrial transcripts involved in reverse transcription of BMD might possibly reveal unexpected features elucidating mitochondrial involvement in cancer events and neurodegenerative disorders.}, }
@article {pmid36227729, year = {2022}, author = {Loiacono, FV and Walther, D and Seeger, S and Thiele, W and Gerlach, I and Karcher, D and Schöttler, MA and Zoschke, R and Bock, R}, title = {Emergence of Novel RNA-Editing Sites by Changes in the Binding Affinity of a Conserved PPR Protein.}, journal = {Molecular biology and evolution}, volume = {39}, number = {12}, pages = {}, pmid = {36227729}, issn = {1537-1719}, mesh = {RNA Editing ; *Arabidopsis Proteins/genetics/metabolism ; *Arabidopsis/genetics/metabolism ; Chloroplasts/metabolism ; RNA ; Plant Proteins/genetics/metabolism ; }, abstract = {RNA editing converts cytidines to uridines in plant organellar transcripts. Editing typically restores codons for conserved amino acids. During evolution, specific C-to-U editing sites can be lost from some plant lineages by genomic C-to-T mutations. By contrast, the emergence of novel editing sites is less well documented. Editing sites are recognized by pentatricopeptide repeat (PPR) proteins with high specificity. RNA recognition by PPR proteins is partially predictable, but prediction is often inadequate for PPRs involved in RNA editing. Here we have characterized evolution and recognition of a recently gained editing site. We demonstrate that changes in the RNA recognition motifs that are not explainable with the current PPR code allow an ancient PPR protein, QED1, to uniquely target the ndhB-291 site in Brassicaceae. When expressed in tobacco, the Arabidopsis QED1 edits 33 high-confident off-target sites in chloroplasts and mitochondria causing a spectrum of mutant phenotypes. By manipulating the relative expression levels of QED1 and ndhB-291, we show that the target specificity of the PPR protein depends on the RNA:protein ratio. Finally, our data suggest that the low expression levels of PPR proteins are necessary to ensure the specificity of editing site selection and prevent deleterious off-target editing.}, }
@article {pmid36226970, year = {2022}, author = {Chen, L and Kashina, A}, title = {Arginylation Regulates Cytoskeleton Organization and Cell Division and Affects Mitochondria in Fission Yeast.}, journal = {Molecular and cellular biology}, volume = {42}, number = {11}, pages = {e0026122}, pmid = {36226970}, issn = {1098-5549}, support = {R01 NS102435/NS/NINDS NIH HHS/United States ; R35 GM122505/GM/NIGMS NIH HHS/United States ; GM122505//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; NS102435//HHS | NIH | National Institute of Neurological Disorders and Stroke (NINDS)/ ; }, mesh = {Animals ; Mice ; *Schizosaccharomyces/genetics/metabolism ; Arginine/metabolism ; Cytoskeleton/metabolism ; Cell Division ; Mitochondria/metabolism ; *Biological Phenomena ; Mammals/metabolism ; }, abstract = {Protein arginylation mediated by arginyltransferase Ate1 is a posttranslational modification of emerging importance implicated in the regulation of mammalian embryogenesis, the cardiovascular system, tissue morphogenesis, cell migration, neurodegeneration, cancer, and aging. Ate1 deletion results in embryonic lethality in mice but does not affect yeast viability, making yeast an ideal system to study the molecular pathways regulated by arginylation. Here, we conducted a global analysis of cytoskeleton-related arginylation-dependent phenotypes in Schizosaccharomyces pombe, a fission yeast species that shares many fundamental features of higher eukaryotic cells. Our studies revealed roles of Ate1 in cell division, cell polarization, organelle transport, and interphase cytoskeleton organization and dynamics. We also found a role of Ate1 in mitochondria morphology and maintenance. Furthermore, targeted mass spectrometry analysis of the total Sc. pombe arginylome identified a number of arginylated proteins, including those that play direct roles in these processes; lack of their arginylation may be responsible for ate1-knockout phenotypes. Our work outlines global biological processes potentially regulated by arginylation and paves the way to unraveling the functions of protein arginylation that are conserved at multiple levels of evolution and potentially constitute the primary role of this modification in vivo.}, }
@article {pmid36225907, year = {2022}, author = {Zhang, A and Xu, J and Xu, X and Wu, J and Li, P and Wang, B and Fang, H}, title = {Genome-wide identification and characterization of the KCS gene family in sorghum (Sorghum bicolor (L.) Moench).}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14156}, pmid = {36225907}, issn = {2167-8359}, mesh = {*Sorghum/genetics ; Plant Proteins/genetics ; Phylogeny ; Regulatory Sequences, Nucleic Acid ; Promoter Regions, Genetic ; }, abstract = {The aboveground parts of plants are covered with cuticle, a hydrophobic layer composed of cutin polyester and cuticular wax that can protect plants from various environmental stresses. β-Ketoacyl-CoA synthase (KCS) is the key rate-limiting enzyme in plant wax synthesis. Although the properties of KCS family genes have been investigated in many plant species, the understanding of this gene family in sorghum is still limited. Here, a total of 25 SbKCS genes were identified in the sorghum genome, which were named from SbKCS1 to SbKCS25. Evolutionary analysis among different species divided the KCS family into five subfamilies and the SbKCSs were more closely related to maize, implying a closer evolutionary relationship between sorghum and maize. All SbKCS genes were located on chromosomes 1, 2, 3, 4, 5, 6, 9 and 10, respectively, while Chr 1 and Chr 10 contained more KCS genes than other chromosomes. The prediction results of subcellular localization showed that SbKCSs were mainly expressed in the plasma membrane and mitochondria. Gene structure analysis revealed that there was 0-1 intron in the sorghum KCS family and SbKCSs within the same subgroup were similar. Multiple cis-acting elements related to abiotic stress, light and hormone response were enriched in the promoters of SbKCS genes, which indicated the functional diversity among these genes. The three-dimensional structure analysis showed that a compact spherical space structure was formed by various secondary bonds to maintain the stability of SbKCS proteins, which was necessary for their biological activity. qRT-PCR results revealed that nine randomly selected SbKCS genes expressed differently under drought and salt treatments, among which SbKCS8 showed the greatest fold of expression difference at 12 h after drought and salt stresses, which suggested that the SbKCS genes played a potential role in abiotic stress responses. Taken together, these results provided an insight into investigating the functions of KCS family in sorghum and in response to abiotic stress.}, }
@article {pmid36213509, year = {2022}, author = {Kotov, AA and Taylor, DJ}, title = {Daphnia japonica sp. nov. (Crustacea: Cladocera) an eastern Palearctic montane species with mitochondrial discordance.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14113}, pmid = {36213509}, issn = {2167-8359}, mesh = {Animals ; *Cladocera/genetics ; Daphnia/genetics ; Phylogeny ; Mitochondria/genetics ; Genes, Mitochondrial ; DNA ; }, abstract = {The Daphnia longispina complex (Crustacea: Cladocera) contains several keystone freshwater species such as D. longispina O.F. Müller (D. rosea Sars is a junior synonym), D. galeata Sars, D. cucullata Sars, and D. dentifera Forbes. The complex is common throughout the Holarctic, but there are several geographic regions where local forms have been assigned to European species names based on a superficial morphological resemblance. Here we examine the species status of a form that was previously assigned to D. rosea from a montane bog pond on Honshu, Japan. We used two nuclear non-coding loci (nDNA), mitochondrial sequences (the ND2 protein-coding region) and morphology for evidence. The mitochondrial gene evidence supported the existence of a divergent lineage that is more closely related to D. galeata than to D. dentifera. However, morphology and the nuclear DNA data indicated a lineage that is most closely related to D. dentifera. As our evidence supported the existence of a cohesive divergent lineage, we described a new species, Daphnia japonica sp. nov. Recognition of local and subalpine diversity in this group is critical as ongoing anthropogenic disturbance has been associated with introductions, local extirpations, and hybridization.}, }
@article {pmid36212359, year = {2022}, author = {Liu, S and Storti, M and Finazzi, G and Bowler, C and Dorrell, RG}, title = {A metabolic, phylogenomic and environmental atlas of diatom plastid transporters from the model species Phaeodactylum.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {950467}, pmid = {36212359}, issn = {1664-462X}, abstract = {Diatoms are an important group of algae, contributing nearly 40% of total marine photosynthetic activity. However, the specific molecular agents and transporters underpinning the metabolic efficiency of the diatom plastid remain to be revealed. We performed in silico analyses of 70 predicted plastid transporters identified by genome-wide searches of Phaeodactylum tricornutum. We considered similarity with Arabidopsis thaliana plastid transporters, transcriptional co-regulation with genes encoding core plastid metabolic pathways and with genes encoded in the mitochondrial genomes, inferred evolutionary histories using single-gene phylogeny, and environmental expression trends using Tara Oceans meta-transcriptomics and meta-genomes data. Our data reveal diatoms conserve some of the ion, nucleotide and sugar plastid transporters associated with plants, such as non-specific triose phosphate transporters implicated in the transport of phosphorylated sugars, NTP/NDP and cation exchange transporters. However, our data also highlight the presence of diatom-specific transporter functions, such as carbon and amino acid transporters implicated in intricate plastid-mitochondria crosstalk events. These confirm previous observations that substrate non-specific triose phosphate transporters (TPT) may exist as principal transporters of phosphorylated sugars into and out of the diatom plastid, alongside suggesting probable agents of NTP exchange. Carbon and amino acid transport may be related to intricate metabolic plastid-mitochondria crosstalk. We additionally provide evidence from environmental meta-transcriptomic/meta- genomic data that plastid transporters may underpin diatom sensitivity to ocean warming, and identify a diatom plastid transporter (J43171) whose expression may be positively correlated with temperature.}, }
@article {pmid36205366, year = {2022}, author = {Nofrianto, AB and Lawelle, SA and Mokodongan, DF and Masengi, KWA and Inomata, N and Hashiguchi, Y and Kitano, J and Sumarto, BKA and Kakioka, R and Yamahira, K}, title = {Ancient Admixture in Freshwater Halfbeaks of the Genus Nomorhamphus in Southeast Sulawesi.}, journal = {Zoological science}, volume = {39}, number = {5}, pages = {453-458}, doi = {10.2108/zs220023}, pmid = {36205366}, issn = {0289-0003}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Fresh Water ; Indonesia ; *Mitochondria/genetics ; Phylogeny ; Water ; }, abstract = {Freshwater halfbeaks of the genus Nomorhamphus (Zenarchopteridae) uniquely diversified on Sulawesi Island, where tectonic movements have been very active since the Pliocene. Most species of this genus have quite limited distributions, which indicates that geographic isolations have contributed to their diversification. In this study, we demonstrated that secondary contacts and resultant admixtures between long-isolated species/populations may have also been important. We found that the mitochondrial phylogeny of a group of Nomorhamphus in Southeast Sulawesi was discordant with the nuclear phylogeny. Most notably, individuals in the upper and lower streams of the Moramo River, a small river in this region, clustered with each other in the mitochondrial phylogeny but not in the nuclear phylogeny; in the latter, the lower-stream individuals formed a clade with individuals in the Anduna River, a different river with no present water connection to the Moramo River. Phylogenetic network and population structure analyses using genomic data obtained from RNA-seq revealed that the lower-stream Moramo population admixed with the upper-stream Moramo lineage in ancient times. These findings indicate that the observed mito-nuclear discordance was caused by mitochondrial introgression and not incomplete lineage sorting. The phylogenetic network also revealed several other admixtures between ancient lineages. Repeated admixtures were also evidenced by topological incongruence in population trees estimated using the RNA-seq data. We propose that activities of many fault systems dissecting Southeast Sulawesi caused repeated secondary contact.}, }
@article {pmid36203893, year = {2022}, author = {Mondal, S and Singh, SP}, title = {New insights on thioredoxins (Trxs) and glutaredoxins (Grxs) by in silico amino acid sequence, phylogenetic and comparative structural analyses in organisms of three domains of life.}, journal = {Heliyon}, volume = {8}, number = {10}, pages = {e10776}, pmid = {36203893}, issn = {2405-8440}, abstract = {Thioredoxins (Trxs) and Glutaredoxins (Grxs) regulate several cellular processes by controlling the redox state of their target proteins. Trxs and Grxs belong to thioredoxin superfamily and possess characteristic Trx/Grx fold. Several phylogenetic, biochemical and structural studies have contributed to our overall understanding of Trxs and Grxs. However, comparative study of closely related Trxs and Grxs in organisms of all domains of life was missing. Here, we conducted in silico comparative structural analysis combined with amino acid sequence and phylogenetic analyses of 65 Trxs and 88 Grxs from 12 organisms of three domains of life to get insights into evolutionary and structural relationship of two proteins. Outcomes suggested that despite diversity in their amino acids composition in distantly related organisms, both Trxs and Grxs strictly conserved functionally and structurally important residues. Also, position of these residues was highly conserved in all studied Trxs and Grxs. Notably, if any substitution occurred during evolution, preference was given to amino acids having similar chemical properties. Trxs and Grxs were found more different in eukaryotes than prokaryotes due to altered helical conformation. The surface of Trxs was negatively charged, while Grxs surface was positively charged, however, the active site was constituted by uncharged amino acids in both proteins. Also, phylogenetic analysis of Trxs and Grxs in three domains of life supported endosymbiotic origins of chloroplast and mitochondria, and suggested their usefulness in molecular systematics. We also report previously unknown catalytic motifs of two proteins, and discuss in detail about effect of abovementioned parameters on overall structural and functional diversity of Trxs and Grxs.}, }
@article {pmid36198798, year = {2022}, author = {Wei, W and Schon, KR and Elgar, G and Orioli, A and Tanguy, M and Giess, A and Tischkowitz, M and Caulfield, MJ and Chinnery, PF}, title = {Nuclear-embedded mitochondrial DNA sequences in 66,083 human genomes.}, journal = {Nature}, volume = {611}, number = {7934}, pages = {105-114}, pmid = {36198798}, issn = {1476-4687}, support = {212219/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; //Medical Research Council UK/ ; MC_UP_1501/2/MRC_/Medical Research Council/United Kingdom ; MR/S035699/1/MRC_/Medical Research Council/United Kingdom ; MR/S005021/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_00015/9/MRC_/Medical Research Council/United Kingdom ; RPG-2018-408/WT_/Wellcome Trust/United Kingdom ; MC_UU_00028/7/MRC_/Medical Research Council/United Kingdom ; MC_PC_13047/MRC_/Medical Research Council/United Kingdom ; MR/M008886/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Cell Nucleus/genetics/metabolism ; *DNA, Mitochondrial/genetics/metabolism ; *Genome, Human/genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Mutation ; Liposarcoma, Myxoid/genetics ; Neoplasms/genetics ; Germ-Line Mutation ; DNA Breaks, Double-Stranded ; DNA Repair ; }, abstract = {DNA transfer from cytoplasmic organelles to the cell nucleus is a legacy of the endosymbiotic event-the majority of nuclear-mitochondrial segments (NUMTs) are thought to be ancient, preceding human speciation[1-3]. Here we analyse whole-genome sequences from 66,083 people-including 12,509 people with cancer-and demonstrate the ongoing transfer of mitochondrial DNA into the nucleus, contributing to a complex NUMT landscape. More than 99% of individuals had at least one of 1,637 different NUMTs, with 1 in 8 individuals having an ultra-rare NUMT that is present in less than 0.1% of the population. More than 90% of the extant NUMTs that we evaluated inserted into the nuclear genome after humans diverged from apes. Once embedded, the sequences were no longer under the evolutionary constraint seen within the mitochondrion, and NUMT-specific mutations had a different mutational signature to mitochondrial DNA. De novo NUMTs were observed in the germline once in every 10[4] births and once in every 10[3] cancers. NUMTs preferentially involved non-coding mitochondrial DNA, linking transcription and replication to their origin, with nuclear insertion involving multiple mechanisms including double-strand break repair associated with PR domain zinc-finger protein 9 (PRDM9) binding. The frequency of tumour-specific NUMTs differed between cancers, including a probably causal insertion in a myxoid liposarcoma. We found evidence of selection against NUMTs on the basis of size and genomic location, shaping a highly heterogenous and dynamic human NUMT landscape.}, }
@article {pmid36183779, year = {2022}, author = {Moreno, ACR and Olean-Oliveira, A and Olean-Oliveira, T and Nunes, MT and Teixeira, MFS and Seraphim, PM}, title = {Resistance training prevents damage to the mitochondrial function of the skeletal muscle of rats exposed to secondary cigarette smoke.}, journal = {Life sciences}, volume = {309}, number = {}, pages = {121017}, doi = {10.1016/j.lfs.2022.121017}, pmid = {36183779}, issn = {1879-0631}, mesh = {Humans ; Rats ; Animals ; *Resistance Training ; *Cigarette Smoking ; Rats, Wistar ; Muscle, Skeletal/metabolism ; Mitochondria ; Nicotiana/adverse effects ; Oxygen/metabolism ; Adenosine Triphosphate/metabolism ; }, abstract = {AIM: To analyze the consumption of oxygen and to quantify the mitochondrial respiratory chain proteins (OXPHOS) in the gastrocnemius muscle of rats exposed to cigarette smoke and/or RT practitioners.<br><br>MAIN METHODS: Wistar rats were divided into groups: Control (C), Smoker (S), Exercise (E) and Exercise Smoker (ES). Groups F and ES were exposed to the smoke of 4 cigarettes for 30&#xa0;min, 2&#xd7; a day, 5&#xd7; a week, for 16&#xa0;weeks. Groups E and ES performed four climbs with progressive load, 1&#xd7; per day, 5&#xd7; per week, for 16&#xa0;weeks. The gastrocnemius muscle was collected for analysis of OXPHOS content and oxygen consumption. Groups S (vs. C) and ES (vs. C and E) showed lower body weight gain when observing the evolution curve.<br><br>KEY FINDINGS: The S rats showed a reduction in the NDUFB8 proteins of complex 1, SDHB of complex 2, MTC01 of complex 4 and ATP5A of complex 5 (ATP Synthase) compared to Group C. Additionally, S rats also showed increased consumption of O2 in Basal, Leak, Complex I and I/II combined measures compared to the other groups, suggesting that the activity of the mitochondria of these animals increased in terms of coupling and uncoupling parameters.<br><br>SIGNIFICANCE: Our data suggest that exposure to cigarette smoke for 16&#xa0;weeks is capable of causing impairment of mitochondrial function with reduced expression of respiratory chain proteins in skeletal muscle. However, the RT was effective in preventing impairment of mitochondrial function in the skeletal muscle of rats exposed to secondary cigarette smoke.}, }
@article {pmid36180833, year = {2022}, author = {Xiao, S and Xing, J and Nie, T and Su, A and Zhang, R and Zhao, Y and Song, W and Zhao, J}, title = {Comparative analysis of mitochondrial genomes of maize CMS-S subtypes provides new insights into male sterility stability.}, journal = {BMC plant biology}, volume = {22}, number = {1}, pages = {469}, pmid = {36180833}, issn = {1471-2229}, mesh = {*Genome, Mitochondrial/genetics ; Humans ; *Infertility, Male/genetics ; Male ; NADH Dehydrogenase/genetics ; Phylogeny ; Plant Infertility/genetics ; Zea mays/genetics ; }, abstract = {BACKGROUND: Cytoplasmic male sterility (CMS) is a trait of economic importance in the production of hybrid seeds. In CMS-S maize, exerted anthers appear frequently in florets of field-grown female populations where only complete male-sterile plants were expected. It has been reported that these reversions are associated with the loss of sterility-conferring regions or other rearrangements in the mitochondrial genome. However, the relationship between mitochondrial function and sterility stability is largely unknown.<br><br>RESULTS: In this study, we determined the ratio of plants carrying exerted anthers in the population of two CMS-S subtypes. The subtype with a high ratio of exerted anthers was designated as CMS-Sa, and the other with low ratio was designated as CMS-Sb. Through next-generation sequencing, we assembled and compared mitochondrial genomes of two CMS-S subtypes. Phylogenetic analyses revealed strong similarities between the two mitochondrial genomes. The sterility-associated regions, S plasmids, and terminal inverted repeats (TIRs) were intact in both genomes. The two subtypes maintained high transcript levels of the sterility gene orf355 in anther tissue. Most of the functional genes/proteins were identical at the nucleotide sequence and amino acid sequence levels in the two subtypes, except for NADH dehydrogenase subunit 1 (nad1). In the mitochondrial genome of CMS-Sb, a 3.3-kilobase sequence containing nad1-exon1 was absent from the second copy of the 17-kb repeat region. Consequently, we detected two copies of nad1-exon1 in CMS-Sa, but only one copy in CMS-Sb. During pollen development, nad1 transcription and mitochondrial biogenesis were induced in anthers of CMS-Sa, but not in those of CMS-Sb. We suggest that the impaired mitochondrial function in the anthers of CMS-Sb is associated with its more stable sterility.<br><br>CONCLUSIONS: Comprehensive analyses revealed diversity in terms of the copy number of the mitochondrial gene nad1-exon1 between two subtypes of CMS-S maize. This difference in copy number affected the transcript levels of nad1 and mitochondrial biogenesis in anther tissue, and affected the reversion rate of CMS-S maize. The results of this study suggest the involvement of mitochondrial robustness in modulation of sterility stability in CMS-S maize.}, }
@article {pmid36158221, year = {2022}, author = {Ikeda, A and Imai, Y and Hattori, N}, title = {Neurodegeneration-associated mitochondrial proteins, CHCHD2 and CHCHD10-what distinguishes the two?.}, journal = {Frontiers in cell and developmental biology}, volume = {10}, number = {}, pages = {996061}, pmid = {36158221}, issn = {2296-634X}, abstract = {Coiled-coil-helix-coiled-coil-helix domain containing 2 (CHCHD2) and Coiled-coil-helix-coiled-coil-helix domain containing 10 (CHCHD10) are mitochondrial proteins that are thought to be genes which duplicated during evolution and are the causative genes for Parkinson's disease and amyotrophic lateral sclerosis/frontotemporal lobe dementia, respectively. CHCHD2 forms a heterodimer with CHCHD10 and a homodimer with itself, both of which work together within the mitochondria. Various pathogenic and disease-risk variants have been identified; however, how these mutations cause neurodegeneration in specific diseases remains a mystery. This review focuses on important new findings published since 2019 and discusses avenues to solve this mystery.}, }
@article {pmid36146890, year = {2023}, author = {Pierszalowski, SP and Steel, DJ and Gabriele, CM and Neilson, JL and Vanselow, PBS and Cedarleaf, JA and Straley, JM and Baker, CS}, title = {mtDNA heteroplasmy gives rise to a new maternal lineage in North Pacific humpback whales (Megaptera novaeangliae).}, journal = {The Journal of heredity}, volume = {114}, number = {1}, pages = {14-21}, pmid = {36146890}, issn = {1465-7333}, mesh = {Animals ; Female ; Cattle ; *Humpback Whale/genetics ; DNA, Mitochondrial/genetics ; Heteroplasmy ; Mitochondria/genetics ; Cetacea/genetics ; }, abstract = {Heteroplasmy in the mitochondrial genome offers a rare opportunity to track the evolution of a newly arising maternal lineage in populations of non-model species. Here, we identified a previously unreported mitochondrial DNA haplotype while assembling an integrated database of DNA profiles and photo-identification records from humpback whales in southeastern Alaska (SEAK). The haplotype, referred to as A8, was shared by only 2 individuals, a mature female with her female calf, and differed by only a single base pair from a common haplotype in the North Pacific, referred to as A-. To investigate the origins of the A8 haplotype, we reviewed n = 1,089 electropherograms (including replicate samples) of n = 710 individuals with A- haplotypes from an existing collection. From this review, we found 20 individuals with clear evidence of heteroplasmy for A-/A8 (parental/derived) haplotypes. Of these, 15 were encountered in SEAK, 4 were encountered on the Hawaiian breeding ground (the primary migratory destination for whales in SEAK), and 1 was encountered in the northern Gulf of Alaska. We used genotype exclusion and likelihood to identify one of the heteroplasmic females as the likely mother of the A8 cow and grandmother of the A8 calf, establishing the inheritance and germ-line fixation of the new haplotype from the parental heteroplasmy. The mutation leading to this heteroplasmy and the fixation of the A8 haplotype provide an opportunity to document the population dynamics and regional fidelity of a newly arising maternal lineage in a population recovering from exploitation.}, }
@article {pmid36143326, year = {2022}, author = {Govindharaj, GP and Babu, SB and Choudhary, JS and Asad, M and Chidambaranathan, P and Gadratagi, BG and Rath, PC and Naaz, N and Jaremko, M and Qureshi, KA and Kumar, U}, title = {Genome Organization and Comparative Evolutionary Mitochondriomics of Brown Planthopper, Nilaparvata lugens Biotype 4 Using Next Generation Sequencing (NGS).}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {9}, pages = {}, pmid = {36143326}, issn = {2075-1729}, abstract = {Nilaparvata lugens is the main rice pest in India. Until now, the Indian N. lugens mitochondrial genome has not been sequenced, which is a very important basis for population genetics and phylogenetic evolution studies. An attempt was made to sequence two examples of the whole mitochondrial genome of N. lugens biotype 4 from the Indian population for the first time. The mitogenomes of N. lugens are 16,072 and 16,081 bp long with 77.50% and 77.45% A + T contents, respectively, for both of the samples. The mitochondrial genome of N. lugens contains 37 genes, including 13 protein-coding genes (PCGs) (cox1-3, atp6, atp8, nad1-6, nad4l, and cob), 22 transfer RNA genes, and two ribosomal RNA (rrnS and rrnL) subunits genes, which are typical of metazoan mitogenomes. However, both samples of N. lugens mitogenome in the present study retained one extra copy of the trnC gene. Additionally, we also found 93 bp lengths for the atp8 gene in both of the samples, which were 60-70 bp less than that of the other sequenced mitogenomes of hemipteran insects. The phylogenetic analysis of the 19 delphacids mitogenome dataset yielded two identical topologies when rooted with Ugyops sp. in one clade, and the remaining species formed another clade with P. maidis and M. muiri being sisters to the remaining species. Further, the genus Nilaparvata formed a separate subclade with the other genera (Sogatella, Laodelphax, Changeondelphax, and Unkanodes) of Delphacidae. Additionally, the relationship among the biotypes of N. lugens was recovered as the present study samples (biotype-4) were separated from the three biotypes reported earlier. The present study provides the reference mitogenome for N. lugens biotype 4 that may be utilized for biotype differentiation and molecular-aspect-based future studies of N. lugens.}, }
@article {pmid36115336, year = {2022}, author = {Giannakis, K and Arrowsmith, SJ and Richards, L and Gasparini, S and Chustecki, JM and Røyrvik, EC and Johnston, IG}, title = {Evolutionary inference across eukaryotes identifies universal features shaping organelle gene retention.}, journal = {Cell systems}, volume = {13}, number = {11}, pages = {874-884.e5}, doi = {10.1016/j.cels.2022.08.007}, pmid = {36115336}, issn = {2405-4720}, mesh = {*Eukaryota/genetics ; Bayes Theorem ; *Biological Evolution ; Plastids/genetics/metabolism ; Mitochondria/metabolism ; }, abstract = {Mitochondria and plastids power complex life. Why some genes and not others are retained in their organelle DNA (oDNA) genomes remains a debated question. Here, we attempt to identify the properties of genes and associated underlying mechanisms that determine oDNA retention. We harness over 15k oDNA sequences and over 300 whole genome sequences across eukaryotes with tools from structural biology, bioinformatics, machine learning, and Bayesian model selection. Previously hypothesized features, including the hydrophobicity of a protein product, and less well-known features, including binding energy centrality within a protein complex, predict oDNA retention across eukaryotes, with additional influences of nucleic acid and amino acid biochemistry. Notably, the same features predict retention in both organelles, and retention models learned from one organelle type quantitatively predict retention in the other, supporting the universality of these features-which also distinguish gene profiles in more recent, independent endosymbiotic relationships. A record of this paper's transparent peer review process is included in the supplemental information.}, }
@article {pmid36107771, year = {2022}, author = {Lesch, E and Schilling, MT and Brenner, S and Yang, Y and Gruss, OJ and Knoop, V and Schallenberg-Rüdinger, M}, title = {Plant mitochondrial RNA editing factors can perform targeted C-to-U editing of nuclear transcripts in human cells.}, journal = {Nucleic acids research}, volume = {50}, number = {17}, pages = {9966-9983}, pmid = {36107771}, issn = {1362-4962}, mesh = {Amino Acids ; Cytidine ; Humans ; *Plant Proteins/genetics ; RNA/genetics ; RNA, Mitochondrial/genetics ; RNA, Plant/genetics ; *RNA-Binding Proteins/genetics/metabolism ; Uridine/genetics ; }, abstract = {RNA editing processes are strikingly different in animals and plants. Up to thousands of specific cytidines are converted into uridines in plant chloroplasts and mitochondria whereas up to millions of adenosines are converted into inosines in animal nucleo-cytosolic RNAs. It is unknown whether these two different RNA editing machineries are mutually incompatible. RNA-binding pentatricopeptide repeat (PPR) proteins are the key factors of plant organelle cytidine-to-uridine RNA editing. The complete absence of PPR mediated editing of cytosolic RNAs might be due to a yet unknown barrier that prevents its activity in the cytosol. Here, we transferred two plant mitochondrial PPR-type editing factors into human cell lines to explore whether they could operate in the nucleo-cytosolic environment. PPR56 and PPR65 not only faithfully edited their native, co-transcribed targets but also different sets of off-targets in the human background transcriptome. More than 900 of such off-targets with editing efficiencies up to 91%, largely explained by known PPR-RNA binding properties, were identified for PPR56. Engineering two crucial amino acid positions in its PPR array led to predictable shifts in target recognition. We conclude that plant PPR editing factors can operate in the entirely different genetic environment of the human nucleo-cytosol and can be intentionally re-engineered towards new targets.}, }
@article {pmid36101314, year = {2022}, author = {Zhou, S and He, LI and Ma, S and Xu, S and Zhai, Q and Guan, P and Wang, H and Shi, J}, title = {Taxonomic status of Rana nigromaculata mongolia and the validity of Pelophylax tenggerensis (Anura, Ranidae).}, journal = {Zootaxa}, volume = {5165}, number = {4}, pages = {486-500}, doi = {10.11646/zootaxa.5165.4.2}, pmid = {36101314}, issn = {1175-5334}, mesh = {Animals ; *DNA, Mitochondrial/genetics ; Mitochondria/genetics ; Mongolia ; Phylogeny ; *Ranidae/genetics ; }, abstract = {The Black-spotted Pond Frog, Pelophylax nigromaculatus, is widely distributed across mainland China, Korean Peninsula, and Japan. The taxonomic relationships among P. n. nigromaculatus, Rana nigromaculata mongolia (sensu P. n. mongolicus), and P. tenggerensis have long been ambiguous. Here we examine the topotype specimens of P. tenggerensis and R. n. mongolia, and provide phylogenic analyses based on four mitochondrial DNA sequences. The combined evidences from morphology and molecular phylogeny have shown the distinct specific-level of P. n. mongolicus that distant from P. nigromaculatus, while indicating the homogeneity between P. n. mongolicus and P. tenggerensis. Thus, we suggest elevating P. n. mongolicus as a full species Pelophylax mongolicus comb. nov., and place P. tenggerensis to be a secondary synonym of P. mongolicus comb. nov.}, }
@article {pmid36097126, year = {2022}, author = {Joshi, BD and Kumar, V and De, R and Sharma, R and Bhattacharya, A and Dolker, S and Pal, R and Kumar, VP and Sathyakumar, S and Adhikari, BS and Habib, B and Goyal, SP}, title = {Mitochondrial cytochrome b indicates the presence of two paraphyletic diverged lineages of the blue sheep Pseudois nayaur across the Indian Himalaya: conservation implications.}, journal = {Molecular biology reports}, volume = {49}, number = {11}, pages = {11177-11186}, pmid = {36097126}, issn = {1573-4978}, mesh = {Animals ; *Cytochromes b/genetics ; *Genetics, Population ; Haplotypes/genetics ; Phylogeny ; Phylogeography ; Sheep/genetics ; *Mitochondria/metabolism ; }, abstract = {BACKGROUND: Populations exhibit signatures of local adaptive traits due to spatial and environmental heterogeneity resulting in microevolution. The blue sheep is widely distributed across the high Asian mountains and are the snow leopard's principal prey species. These mountains differ in their evolutionary history due to differential glaciation and deglaciation periods, orography, and rainfall patterns, and such factors causes diversification in species.<br><br>METHODS AND RESULTS: Therefore, we assess the phylogeographic status of blue sheep using the mitochondrial cytochrome b gene (220&#xa0;bp) across the Indian Himalayan region (IHR) and its relationship with other populations. Of the observed five haplotypes, two and three were from the western Himalayas (WH) and eastern Himalayas (EH) respectively. One of the haplotypes from WH was shared with the population of Pamir plateau, suggesting historical maternal connectivity between these areas. The phylogenetic analyses split the blue sheep into two paraphyletic clades, and western and eastern populations of IHR were within the Pamir and Tibetan plateau clades, respectively. We observed a relatively higher mean sequence divergence in the EH population than in the WH.<br><br>CONCLUSION: We propose five 'Evolutionary Significant Units' across the blue sheep distribution range based on observed variation in the species' ecological requirements, orography, climatic conditions, and maternal lineages, viz.; Western Himalaya-Pamir plateau (WHPP); Eastern Himalaya-Tibetan plateau (EHTP); Qilian mountains; Helan mountains and Hengduan mountains population. Despite the small sample size, population divergence was observed across the IHR, therefore, we suggest a transboundary, collaborative study on comparative morphology, anatomy, ecology, behaviour, and population genetics using harmonized different genetic markers for identifying the overall taxonomic status of the blue sheep across its range for planning effective conservation strategies.}, }
@article {pmid36085554, year = {2022}, author = {Jacquat, AG and Ulla, SB and Debat, HJ and Muñoz-Adalia, EJ and Theumer, MG and Pedrajas, MDG and Dambolena, JS}, title = {An in silico analysis revealed a novel evolutionary lineage of putative mitoviruses.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {6463-6475}, doi = {10.1111/1462-2920.16202}, pmid = {36085554}, issn = {1462-2920}, mesh = {Genome, Viral ; Mitochondria/genetics ; Phylogeny ; Plant Diseases/microbiology ; *RNA Viruses/genetics ; RNA, Viral ; }, abstract = {Mitoviruses (family Mitoviridae) are small capsid-less RNA viruses that replicate in the mitochondria of fungi and plants. However, to date, the only authentic animal mitovirus infecting an insect was identified as Lutzomyia longipalpis mitovirus 1 (LulMV1). Public databases of transcriptomic studies from several animals may be a good source for identifying the often missed mitoviruses. Consequently, a search of mitovirus-like transcripts at the NCBI transcriptome shotgun assembly (TSA) library, and a search for the mitoviruses previously recorded at the NCBI non-redundant (nr) protein sequences library, were performed in order to identify new mitovirus-like sequences associated with animals. In total, 10 new putative mitoviruses were identified in the TSA database and 8 putative mitoviruses in the nr protein database. To our knowledge, these results represent the first evidence of putative mitoviruses associated with poriferan, cnidarians, echinoderms, crustaceans, myriapods and arachnids. According to different phylogenetic inferences using the maximum likelihood method, these 18 putative mitoviruses form a robust monophyletic lineage with LulMV1, the only known animal-infecting mitovirus. These findings based on in silico procedures provide strong evidence for the existence of a clade of putative mitoviruses associated with animals, which has been provisionally named 'kvinmitovirus'.}, }
@article {pmid36083897, year = {2022}, author = {Ba, Q and Hei, Y and Dighe, A and Li, W and Maziarz, J and Pak, I and Wang, S and Wagner, GP and Liu, Y}, title = {Proteotype coevolution and quantitative diversity across 11 mammalian species.}, journal = {Science advances}, volume = {8}, number = {36}, pages = {eabn0756}, pmid = {36083897}, issn = {2375-2548}, support = {R01 GM137031/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Gene Expression Profiling ; *Mammals/genetics/metabolism ; Proteome/metabolism ; *Proteomics ; Transcriptome ; }, abstract = {Evolutionary profiling has been largely limited to the nucleotide level. Using consistent proteomic methods, we quantified proteomic and phosphoproteomic layers in fibroblasts from 11 common mammalian species, with transcriptomes as reference. Covariation analysis indicates that transcript and protein expression levels and variabilities across mammals remarkably follow functional role, with extracellular matrix-associated expression being the most variable, demonstrating strong transcriptome-proteome coevolution. The biological variability of gene expression is universal at both interindividual and interspecies scales but to a different extent. RNA metabolic processes particularly show higher interspecies versus interindividual variation. Our results further indicate that while the ubiquitin-proteasome system is strongly conserved in mammals, lysosome-mediated protein degradation exhibits remarkable variation between mammalian lineages. In addition, the phosphosite profiles reveal a phosphorylation coevolution network independent of protein abundance.}, }
@article {pmid36083445, year = {2022}, author = {Wang, S and Luo, H}, title = {Estimating the Divergence Times of Alphaproteobacteria Based on Mitochondrial Endosymbiosis and Eukaryotic Fossils.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2569}, number = {}, pages = {95-116}, pmid = {36083445}, issn = {1940-6029}, mesh = {*Alphaproteobacteria/genetics ; Eukaryota ; Evolution, Molecular ; Fossils ; Mitochondria/genetics ; Phylogeny ; Symbiosis/genetics ; }, abstract = {Alphaproteobacteria is one of the most abundant bacterial lineages that successfully colonize diverse marine and terrestrial environments on Earth. In addition, many alphaproteobacterial lineages have established close association with eukaryotes. This makes Alphaproteobacteria a promising system to test the link between the emergence of ecologically important bacteria and related geological events and the co-evolution between symbiotic bacteria and their hosts. Understanding the timescale of evolution of Alphaproteobacteria is key to testing these hypotheses, which is limited by the scarcity of bacterial fossils, however. Based on the mitochondrial endosymbiosis which posits that the mitochondrion originated from an alphaproteobacterial lineage, we propose a new strategy to estimate the divergence times of lineages within the Alphaproteobacteria by leveraging the fossil records of eukaryotes. In this chapter, we describe the workflow of the mitochondria-based method to date Alphaproteobacteria evolution by detailing the software, methods, and commands used for each step. Visualization of data and results is also described. We also provide related notes with background information and alternative options. All codes used to build this protocol are made available to the public, and we strive to make this protocol user-friendly in particular to microbiologists with limited practical skills in bioinformatics.}, }
@article {pmid36071602, year = {2022}, author = {Zhang, M and Zhang, C and Hu, P and Shi, L and Ju, M and Zhang, B and Li, X and Han, X and Wang, K and Li, X and Qiao, R}, title = {Comprehensive analysis of mitogenome of native Henan pig breeds with 58 worldwide pig breeds.}, journal = {Animal genetics}, volume = {53}, number = {6}, pages = {803-813}, doi = {10.1111/age.13261}, pmid = {36071602}, issn = {1365-2052}, support = {U1904115//National Natural Science Foundation of China/ ; 202300410195//Outstanding Youth Foundation of Henan Province/ ; }, mesh = {Animals ; DNA, Mitochondrial/genetics ; Genetic Variation ; *Genome, Mitochondrial ; Haplotypes ; Phylogeny ; Swine/genetics ; }, abstract = {Mitochondria follow non-Mendelian maternal inheritance, and thus can be used to compare genetic diversity and infer the expansion and migration between animal populations. Based on the mitochondrial DNA sequences of 58 pig breeds from Asia, Europe, Oceania, and America, we observed a distinct division of Eurasian pig species into two main Haplogroups (A and B), with the exception of the Berkshire and Yorkshire breeds. Oceanian pigs were much more similar to European and American pigs in Haplogroup A. Additionally, native Chinese pigs exhibited the most abundant genetic polymorphisms and occupied the centre of Haplogroup B. Miyazaki (Japan) and Siberia (Russia) are two distant and disconnected regions; however, most pigs from these regions were clustered into a subcluster, while native pigs from Korea clustered into a second subcluster. This study is the first to report that pigs from Thailand and Vietnam had haplotypes similar to those of Henan, where the earliest evidence of domestic pigs was found from the Yellow River Basin of North China. Local Henan pig breeds are related to many Asian breeds while still having their own mutation identity, such as g.314 delins T>AC/AT/C of the 12S rRNA gene in Yuxi. Some pigs from Palawan, Itbayat, and Batan Islands of the Philippines and Lanyu Island of China were distinct from other Asian pigs and clustered together into Haplogroup C. These findings show that the complexity of domestication of worldwide pig breeds and mitochondria could reflect genetic communication between pig breeds due to geographical proximity and human activities.}, }
@article {pmid36055768, year = {2022}, author = {Khan, K and Van Aken, O}, title = {The colonization of land was a likely driving force for the evolution of mitochondrial retrograde signalling in plants.}, journal = {Journal of experimental botany}, volume = {73}, number = {21}, pages = {7182-7197}, pmid = {36055768}, issn = {1460-2431}, support = {2017-03854//Swedish Research Council/ ; NNF18OC0034822//Novo Nordisk Fonden/ ; UPD2019-0211//Wenner-Gren Foundation/ ; }, mesh = {*Signal Transduction ; Seeds ; Mitochondria ; Eukaryota ; Cyclin-Dependent Kinases ; *Arabidopsis/genetics ; Transcription Factors/genetics ; }, abstract = {Most retrograde signalling research in plants was performed using Arabidopsis, so an evolutionary perspective on mitochondrial retrograde regulation (MRR) is largely missing. Here, we used phylogenetics to track the evolutionary origins of factors involved in plant MRR. In all cases, the gene families can be traced to ancestral green algae or earlier. However, the specific subfamilies containing factors involved in plant MRR in many cases arose during the transition to land. NAC transcription factors with C-terminal transmembrane domains, as observed in the key regulator ANAC017, can first be observed in non-vascular mosses, and close homologs to ANAC017 can be found in seed plants. Cyclin-dependent kinases (CDKs) are common to eukaryotes, but E-type CDKs that control MRR also diverged in conjunction with plant colonization of land. AtWRKY15 can be traced to the earliest land plants, while AtWRKY40 only arose in angiosperms and AtWRKY63 even more recently in Brassicaceae. Apetala 2 (AP2) transcription factors are traceable to algae, but the ABI4 type again only appeared in seed plants. This strongly suggests that the transition to land was a major driver for developing plant MRR pathways, while additional fine-tuning events have appeared in seed plants or later. Finally, we discuss how MRR may have contributed to meeting the specific challenges that early land plants faced during terrestrialization.}, }
@article {pmid36045215, year = {2022}, author = {Monsanto, DM and Main, DC and Janion-Scheepers, C and Emami-Khoyi, A and Deharveng, L and Bedos, A and Potapov, M and Parbhu, SP and Le Roux, JJ and Teske, PR and van Vuuren, BJ}, title = {Mitogenome selection in the evolution of key ecological strategies in the ancient hexapod class Collembola.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {14810}, pmid = {36045215}, issn = {2045-2322}, mesh = {Animals ; *Arthropods/genetics/metabolism ; Evolution, Molecular ; Fossils ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Insecta/genetics ; Phylogeny ; }, abstract = {A longstanding question in evolutionary biology is how natural selection and environmental pressures shape the mitochondrial genomic architectures of organisms. Mitochondria play a pivotal role in cellular respiration and aerobic metabolism, making their genomes functionally highly constrained. Evaluating selective pressures on mitochondrial genes can provide functional and ecological insights into the evolution of organisms. Collembola (springtails) are an ancient hexapod group that includes the oldest terrestrial arthropods in the fossil record, and that are closely associated with soil environments. Of interest is the diversity of habitat stratification preferences (life forms) exhibited by different species within the group. To understand whether signals of positive selection are linked to the evolution of life forms, we analysed 32 published Collembola mitogenomes in a phylomitogenomic framework. We found no evidence that signatures of selection are correlated with the evolution of novel life forms, but rather that mutations have accumulated as a function of time. Our results highlight the importance of nuclear-mitochondrial interactions in the evolution of collembolan life forms and that mitochondrial genomic data should be interpreted with caution, as complex selection signals may complicate evolutionary inferences.}, }
@article {pmid36042193, year = {2022}, author = {Kuhle, B and Hirschi, M and Doerfel, LK and Lander, GC and Schimmel, P}, title = {Structural basis for shape-selective recognition and aminoacylation of a D-armless human mitochondrial tRNA.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5100}, pmid = {36042193}, issn = {2041-1723}, support = {R01 GM125908/GM/NIGMS NIH HHS/United States ; S10 OD032467/OD/NIH HHS/United States ; S10 OD021634/OD/NIH HHS/United States ; }, mesh = {*Amino Acyl-tRNA Synthetases/metabolism ; Aminoacylation/genetics ; Animals ; Humans ; Mammals/genetics ; Mitochondria/metabolism ; RNA, Mitochondrial/metabolism ; *RNA, Transfer/genetics/metabolism ; }, abstract = {Human mitochondrial gene expression relies on the specific recognition and aminoacylation of mitochondrial tRNAs (mtRNAs) by nuclear-encoded mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs). Despite their essential role in cellular energy homeostasis, strong mutation pressure and genetic drift have led to an unparalleled sequence erosion of animal mtRNAs. The structural and functional consequences of this erosion are not understood. Here, we present cryo-EM structures of the human mitochondrial seryl-tRNA synthetase (mSerRS) in complex with mtRNA[Ser(GCU)]. These structures reveal a unique mechanism of substrate recognition and aminoacylation. The mtRNA[Ser(GCU)] is highly degenerated, having lost the entire D-arm, tertiary core, and stable L-shaped fold that define canonical tRNAs. Instead, mtRNA[Ser(GCU)] evolved unique structural innovations, including a radically altered T-arm topology that serves as critical identity determinant in an unusual shape-selective readout mechanism by mSerRS. Our results provide a molecular framework to understand the principles of mito-nuclear co-evolution and specialized mechanisms of tRNA recognition in mammalian mitochondrial gene expression.}, }
@article {pmid36010594, year = {2022}, author = {Liu, Y and Chen, C and Wang, X and Sun, Y and Zhang, J and Chen, J and Shi, Y}, title = {An Epigenetic Role of Mitochondria in Cancer.}, journal = {Cells}, volume = {11}, number = {16}, pages = {}, pmid = {36010594}, issn = {2073-4409}, mesh = {Carcinogenesis/genetics/metabolism ; *Epigenesis, Genetic ; Histones/metabolism ; Humans ; Mitochondria/genetics/metabolism ; *Neoplasms/genetics/metabolism ; Tumor Microenvironment ; }, abstract = {Mitochondria are not only the main energy supplier but are also the cell metabolic center regulating multiple key metaborates that play pivotal roles in epigenetics regulation. These metabolites include acetyl-CoA, α-ketoglutarate (α-KG), S-adenosyl methionine (SAM), NAD[+], and O-linked beta-N-acetylglucosamine (O-GlcNAc), which are the main substrates for DNA methylation and histone post-translation modifications, essential for gene transcriptional regulation and cell fate determination. Tumorigenesis is attributed to many factors, including gene mutations and tumor microenvironment. Mitochondria and epigenetics play essential roles in tumor initiation, evolution, metastasis, and recurrence. Targeting mitochondrial metabolism and epigenetics are promising therapeutic strategies for tumor treatment. In this review, we summarize the roles of mitochondria in key metabolites required for epigenetics modification and in cell fate regulation and discuss the current strategy in cancer therapies via targeting epigenetic modifiers and related enzymes in metabolic regulation. This review is an important contribution to the understanding of the current metabolic-epigenetic-tumorigenesis concept.}, }
@article {pmid36009607, year = {2022}, author = {Wu, L and Tong, Y and Ayivi, SPG and Storey, KB and Zhang, JY and Yu, DN}, title = {The Complete Mitochondrial Genomes of Three Sphenomorphinae Species (Squamata: Scincidae) and the Selective Pressure Analysis on Mitochondrial Genomes of Limbless Isopachys gyldenstolpei.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {16}, pages = {}, pmid = {36009607}, issn = {2076-2615}, support = {31801963//the National Natural Science Foundation of China/ ; }, abstract = {In order to adapt to diverse habitats, organisms often evolve corresponding adaptive mechanisms to cope with their survival needs. The species-rich family of Scincidae contains both limbed and limbless species, which differ fundamentally in their locomotor demands, such as relying on the movement of limbs or only body swing to move. Locomotion requires energy, and different types of locomotion have their own energy requirements. Mitochondria are the energy factories of living things, which provide a lot of energy for various physiological activities of organisms. Therefore, mitochondrial genomes could be tools to explore whether the limb loss of skinks are selected by adaptive evolution. Isopachys gyldenstolpei is a typical limbless skink. Here, we report the complete mitochondrial genomes of I. gyldenstolpei, Sphenomorphus indicus, and Tropidophorus hainanus. The latter two species were included as limbed comparator species to the limbless I. gyldenstolpei. The results showed that the full lengths of the mitochondrial genomes of I. gyldenstolpei, S. indicus, and T. hainanus were 17,210, 16,944, and 17,001 bp, respectively. Three mitochondrial genomes have typical circular double-stranded structures similar to other reptiles, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and the control region. Three mitochondrial genomes obtained in this study were combined with fifteen mitochondrially complete genomes of Scincidae in the NCBI database; the phylogenetic relationship between limbless I. gyldenstolpei and limbed skinks (S. indicus and T. hainanus) is discussed. Through BI and ML trees, Sphenomorphinae and Mabuyinae were monophyletic, while the paraphyly of Scincinae was also recovered. The limbless skink I. gyldenstolpei is closer to the species of Tropidophorus, which has formed a sister group with (T. hainanus + T. hangman). In the mitochondrial genome adaptations between limbless I. gyldenstolpei and limbed skinks, one positively selected site was found in the branch-site model analysis, which was located in ND2 (at position 28, BEB value = 0.907). Through analyzing the protein structure and function of the selected site, we found it was distributed in mitochondrial protein complex I. Positive selection of some mitochondrial genes in limbless skinks may be related to the requirement of energy to fit in their locomotion. Further research is still needed to confirm this conclusion though.}, }
@article {pmid35998817, year = {2022}, author = {Franzolin, GN and Araújo, BL and Zatti, SA and Naldoni, J and Adriano, EA}, title = {Occurrence of the host-parasite system Rhaphiodon vulpinus and Ceratomyxa barbata n. sp. in the two largest watersheds in South America.}, journal = {Parasitology international}, volume = {91}, number = {}, pages = {102651}, doi = {10.1016/j.parint.2022.102651}, pmid = {35998817}, issn = {1873-0329}, mesh = {Animals ; DNA, Ribosomal/genetics ; *Fish Diseases/epidemiology/parasitology ; Fishes ; Gallbladder/parasitology ; *Myxozoa ; *Parasites/genetics ; *Parasitic Diseases, Animal/parasitology ; Phylogeny ; }, abstract = {While around world, species of the genus Ceratomyxa parasite majority marine hosts, growing diversity has been reported in South American freshwater fish. The present study reports Ceratomyxa barbata n. sp. parasitizing the gallbladder of the Rhaphiodon vulpinus fish from the Amazon and La Plata basins. Morphological (light and transmission electron microscopy), molecular (sequencing of small subunit ribosomal DNA - SSU rDNA), and phylogenetic analyses were used to characterize the new species. Worm-like plasmodia endowed with motility were found swimming freely in the bile. The myxospores were elongated, lightly arcuate, with rounded ends and had polar tubules with 3 coils in the polar capsules. Ultrastructural analysis revealed plasmodia composed of an outer cytoplasmic region, where elongated tubular mitochondria, a rough endoplasmic reticulum, sporogonic stages, and a large vacuole occupying the internal area were observed. Phylogenetic analysis, based on SSU rDNA, found that among all South America freshwater Ceratomyxa species, C. barbata n. sp. arises as an earlier divergent species. The present study reveals the occurrence of this host-parasite system (R. vulpinus/C. barbata n. sp.) in the two largest watersheds on the continent.}, }
@article {pmid35997667, year = {2022}, author = {Hirakawa, Y and Hanawa, Y and Yoneda, K and Suzuki, I}, title = {Evolution of a chimeric mitochondrial carbonic anhydrase through gene fusion in a haptophyte alga.}, journal = {FEBS letters}, volume = {596}, number = {23}, pages = {3051-3059}, doi = {10.1002/1873-3468.14475}, pmid = {35997667}, issn = {1873-3468}, support = {LA-2022-011//Institute for Fermentation, Osaka/ ; KAKENHI 18K06358//Japan Society for the Promotion of Science/ ; KAKENHI 19H03280//Japan Society for the Promotion of Science/ ; }, mesh = {*Haptophyta/genetics/metabolism ; *Carbonic Anhydrases/genetics/metabolism ; Plants/metabolism ; Carbon Dioxide/metabolism ; Recombinant Proteins/genetics ; Gene Fusion ; }, abstract = {Carbonic anhydrases (CAs) are a universal enzyme family that catalyses the interconversion of carbon dioxide and bicarbonate, and they are localized in most compartments including mitochondria and plastids. Thus far, eight classes of CAs (α-, β-, γ-, δ-, ζ-, η-, θ- and ι-CA) have been characterized. This study reports an interesting gene encoding a fusion protein of β-CA and ι-CA found in the haptophyte Isochrysis galbana. Recombinant protein assays demonstrated that the C-terminal ι-CA region catalyses CO2 hydration, whereas the N-terminal β-CA region no longer exhibits enzymatic activity. Considering that haptophytes generally have mitochondrion-localized β-CAs and plastid-localized ι-CAs, the fusion CA would show an intermediate stage in which mitochondrial β-CA is replaced by ι-CA in a haptophyte species.}, }
@article {pmid35978085, year = {2022}, author = {Yue, J and Lu, Q and Ni, Y and Chen, P and Liu, C}, title = {Comparative analysis of the plastid and mitochondrial genomes of Artemisia giraldii Pamp.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {13931}, pmid = {35978085}, issn = {2045-2322}, mesh = {*Artemisia/genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; *Genome, Plastid ; Phylogeny ; Plastids/genetics ; }, abstract = {Artemisia giraldii Pamp. is an herbaceous plant distributed only in some areas in China. To understand the evolutionary relationship between plastid and mitochondria in A. giraldii, we sequenced and analysed the plastome and mitogenome of A. giraldii on the basis of Illumina and Nanopore DNA sequencing data. The mitogenome was 194,298 bp long, and the plastome was 151,072 bp long. The mitogenome encoded 56 genes, and the overall GC content was 45.66%. Phylogenetic analysis of the two organelle genomes revealed that A. giraldii is located in the same branching position. We found 13 pairs of homologous sequences between the plastome and mitogenome, and only one of them might have transferred from the plastid to the mitochondria. Gene selection pressure analysis in the mitogenome showed that ccmFc, nad1, nad6, atp9, atp1 and rps12 may undergo positive selection. According to the 18 available plastome sequences, we found 17 variant sites in two hypervariable regions that can be used in completely distinguishing 18 Artemisia species. The most interesting discovery was that the mitogenome of A. giraldii was only 43,226 bp larger than the plastome. To the best of our knowledge, this study represented one of the smallest differences between all sequenced mitogenomes and plastomes from vascular plants. The above results can provide a reference for future taxonomic and molecular evolution studies of Asteraceae species.}, }
@article {pmid35973607, year = {2022}, author = {Holt, AG and Davies, AM}, title = {A comparison of mtDNA deletion mutant proliferation mechanisms.}, journal = {Journal of theoretical biology}, volume = {551-552}, number = {}, pages = {111244}, doi = {10.1016/j.jtbi.2022.111244}, pmid = {35973607}, issn = {1095-8541}, mesh = {Cell Proliferation/genetics ; Clone Cells ; *DNA, Mitochondrial/genetics ; Humans ; *Mitochondria/genetics ; Mutation ; Mutation Rate ; }, abstract = {In this paper we use simulation methods to investigate the proliferation of deletion mutations of mitochondrial DNA in neurons. We simulate three mtDNA proliferation mechanisms, namely, random drift, replicative advantage and vicious cycle. For each mechanism, we investigated the effect mutation rates have on neuron loss within a human host. We also compare heteroplasmy of each mechanism at mutation rates that yield the levels neuron loss that would be associated with dementia. Both random drift and vicious cycle predicted high levels of heteroplasmy, while replicative advantage showed a small number of dominant clones with a low background of heteroplasmy.}, }
@article {pmid35957532, year = {2022}, author = {Wang, G and Wang, Y and Ni, J and Li, R and Zhu, F and Wang, R and Tian, Q and Shen, Q and Yang, Q and Tang, J and Murcha, MW and Wang, G}, title = {An MCIA-like complex is required for mitochondrial complex I assembly and seed development in maize.}, journal = {Molecular plant}, volume = {15}, number = {9}, pages = {1470-1487}, doi = {10.1016/j.molp.2022.08.001}, pmid = {35957532}, issn = {1752-9867}, mesh = {Cell Nucleus/metabolism ; *Electron Transport Complex I/genetics/metabolism ; Humans ; Mitochondria/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Seeds/metabolism ; *Zea mays/metabolism ; }, abstract = {During adaptive radiation, mitochondria have co-evolved with their hosts, leading to gain or loss of subunits and assembly factors of respiratory complexes. Plant mitochondrial complex I harbors ∼40 nuclear- and 9 mitochondrial-encoded subunits, and is formed by stepwise assembly during which different intermediates are integrated via various assembly factors. In mammals, the mitochondrial complex I intermediate assembly (MCIA) complex is required for building the membrane arm module. However, plants have lost almost all of the MCIA complex components, giving rise to the hypothesis that plants follow an ancestral pathway to assemble the membrane arm subunits. Here, we characterize a maize crumpled seed mutant, crk1, and reveal by map-based cloning that CRK1 encodes an ortholog of human complex I assembly factor 1, zNDUFAF1, the only evolutionarily conserved MCIA subunit in plants. zNDUFAF1 is localized in the mitochondria and accumulates in two intermediate complexes that contain complex I membrane arm subunits. Disruption of zNDUFAF1 results in severe defects in complex I assembly and activity, a cellular bioenergetic shift to aerobic glycolysis, and mitochondrial vacuolation. Moreover, we found that zNDUFAF1, the putative mitochondrial import inner membrane translocase ZmTIM17-1, and the isovaleryl-coenzyme A dehydrogenase ZmIVD1 interact each other, and could be co-precipitated from the mitochondria and co-migrate in the same assembly intermediates. Knockout of either ZmTIM17-1 or ZmIVD1 could lead to the significantly reduced complex I stability and activity as well as defective seeds. These results suggest that zNDUFAF1, ZmTIM17-1 and ZmIVD1 probably form an MCIA-like complex that is essential for the biogenesis of mitochondrial complex I and seed development in maize. Our findings also imply that plants and mammals recruit MCIA subunits independently for mitochondrial complex I assembly, highlighting the importance of parallel evolution in mitochondria adaptation to their hosts.}, }
@article {pmid35955668, year = {2022}, author = {Manousaki, A and Bagnall, J and Spiller, D and Balarezo-Cisneros, LN and White, M and Delneri, D}, title = {Quantitative Characterisation of Low Abundant Yeast Mitochondrial Proteins Reveals Compensation for Haplo-Insufficiency in Different Environments.}, journal = {International journal of molecular sciences}, volume = {23}, number = {15}, pages = {}, pmid = {35955668}, issn = {1422-0067}, support = {BB/M011208/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T002123/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptor Proteins, Signal Transducing/metabolism ; GTP Phosphohydrolases/metabolism ; Membrane Proteins/metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins/metabolism ; *Saccharomyces cerevisiae/metabolism ; *Saccharomyces cerevisiae Proteins/metabolism ; }, abstract = {The quantification of low abundant membrane-binding proteins such as transcriptional factors and chaperones has proven difficult, even with the most sophisticated analytical technologies. Here, we exploit and optimise the non-invasive Fluorescence Correlation Spectroscopy (FCS) for the quantitation of low abundance proteins, and as proof of principle, we choose two interacting proteins involved in the fission of mitochondria in yeast, Fis1p and Mdv1p. In Saccharomyces cerevisiae, the recruitment of Fis1p and Mdv1p to mitochondria is essential for the scission of the organelles and the retention of functional mitochondrial structures in the cell. We use FCS in single GFP-labelled live yeast cells to quantify the protein abundance in homozygote and heterozygote cells and to investigate the impact of the environments on protein copy number, bound/unbound protein state and mobility kinetics. Both proteins were observed to localise predominantly at mitochondrial structures, with the Mdv1p bound state increasing significantly in a strictly respiratory environment. Moreover, a compensatory mechanism that controls Fis1p abundance upon deletion of one allele was observed in Fis1p but not in Mdv1p, suggesting differential regulation of Fis1p and Mdv1p protein expression.}, }
@article {pmid35931723, year = {2022}, author = {Silva, NM and Kreutzer, S and Souleles, A and Triantaphyllou, S and Kotsakis, K and Urem-Kotsou, D and Halstead, P and Efstratiou, N and Kotsos, S and Karamitrou-Mentessidi, G and Adaktylou, F and Chondroyianni-Metoki, A and Pappa, M and Ziota, C and Sampson, A and Papathanasiou, A and Vitelli, K and Cullen, T and Kyparissi-Apostolika, N and Lanz, AZ and Peters, J and Rio, J and Wegmann, D and Burger, J and Currat, M and Papageorgopoulou, C}, title = {Ancient mitochondrial diversity reveals population homogeneity in Neolithic Greece and identifies population dynamics along the Danubian expansion axis.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {13474}, pmid = {35931723}, issn = {2045-2322}, support = {31003A_156853/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Bayes Theorem ; DNA, Ancient ; *DNA, Mitochondrial/genetics ; Europe ; Genetics, Population ; Greece ; History, Ancient ; Humans ; *Mitochondria/genetics ; Population Dynamics ; }, abstract = {The aim of the study is to investigate mitochondrial diversity in Neolithic Greece and its relation to hunter-gatherers and farmers who populated the Danubian Neolithic expansion axis. We sequenced 42 mitochondrial palaeogenomes from Greece and analysed them together with European set of 328 mtDNA sequences dating from the Early to the Final Neolithic and 319 modern sequences. To test for population continuity through time in Greece, we use an original structured population continuity test that simulates DNA from different periods by explicitly considering the spatial and temporal dynamics of populations. We explore specific scenarios of the mode and tempo of the European Neolithic expansion along the Danubian axis applying spatially explicit simulations coupled with Approximate Bayesian Computation. We observe a striking genetic homogeneity for the maternal line throughout the Neolithic in Greece whereas population continuity is rejected between the Neolithic and present-day Greeks. Along the Danubian expansion axis, our best-fitting scenario supports a substantial decrease in mobility and an increasing local hunter-gatherer contribution to the gene-pool of farmers following the initial rapid Neolithic expansion. Οur original simulation approach models key demographic parameters rather than inferring them from fragmentary data leading to a better understanding of this important process in European prehistory.}, }
@article {pmid35920138, year = {2022}, author = {Liao, T and Wang, S and Stüeken, EE and Luo, H}, title = {Phylogenomic Evidence for the Origin of Obligate Anaerobic Anammox Bacteria Around the Great Oxidation Event.}, journal = {Molecular biology and evolution}, volume = {39}, number = {8}, pages = {}, pmid = {35920138}, issn = {1537-1719}, mesh = {*Ammonium Compounds ; Anaerobic Ammonia Oxidation ; Anaerobiosis ; Bacteria/genetics ; *Bacteria, Anaerobic/genetics ; Nitrites ; Nitrogen ; Oxidation-Reduction ; Phylogeny ; Quaternary Ammonium Compounds ; }, abstract = {The anaerobic ammonium oxidation (anammox) bacteria can transform ammonium and nitrite to dinitrogen gas, and this obligate anaerobic process accounts for up to half of the global nitrogen loss in surface environments. Yet its origin and evolution, which may give important insights into the biogeochemistry of early Earth, remain enigmatic. Here, we performed a comprehensive phylogenomic and molecular clock analysis of anammox bacteria within the phylum Planctomycetes. After accommodating the uncertainties and factors influencing time estimates, which include implementing both a traditional cyanobacteria-based and a recently developed mitochondria-based molecular dating approach, we estimated a consistent origin of anammox bacteria at early Proterozoic and most likely around the so-called Great Oxidation Event (GOE; 2.32-2.5 Ga) which fundamentally changed global biogeochemical cycles. We further showed that during the origin of anammox bacteria, genes involved in oxidative stress adaptation, bioenergetics, and anammox granules formation were recruited, which might have contributed to their survival on an increasingly oxic Earth. Our findings suggest the rising levels of atmospheric oxygen, which made nitrite increasingly available, was a potential driving force for the emergence of anammox bacteria. This is one of the first studies that link the GOE to the evolution of obligate anaerobic bacteria.}, }
@article {pmid35920046, year = {2022}, author = {Paulino, MG and Rossi, PA and Venturini, FP and Tavares, D and Sakuragui, MM and Moraes, G and Terezan, AP and Fernandes, JB and Giani, A and Fernandes, MN}, title = {Liver dysfunction and energy storage mobilization in traíra, Hoplias malabaricus (Teleostei, Erythrinidae) induced by subchronic exposure to toxic cyanobacterial crude extract.}, journal = {Environmental toxicology}, volume = {37}, number = {11}, pages = {2683-2691}, doi = {10.1002/tox.23628}, pmid = {35920046}, issn = {1522-7278}, support = {Proc GT 346//Companhia Energ&#xe9;tica de Minas Gerais/ ; Proc. 306818/2020-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; Proc. 2276/2011//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; Proc. 2012/00728-1//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; //Programa Nacional de P&#xf3;s-Doutorado/ ; }, mesh = {Acid Phosphatase/metabolism ; Alanine Transaminase/metabolism ; Alkaline Phosphatase/metabolism ; Ammonia ; Animals ; Aspartate Aminotransferases/metabolism ; Bilirubin/metabolism ; *Characiformes ; Complex Mixtures/metabolism/toxicity ; *Cyanobacteria/metabolism ; Glucose/metabolism ; Glycogen/metabolism ; Lactates ; Lipids ; Liver/metabolism ; *Liver Diseases/metabolism ; Microcystins/metabolism/toxicity ; Pyruvates/metabolism ; }, abstract = {Microcystins (MC) are hepatotoxic for organisms. Liver MC accumulation and structural change are intensely studied, but the functional hepatic enzymes and energy metabolism have received little attention. This study investigated the liver and hepatocyte structures and the activity of key hepatic functional enzymes with emphasis on energetic metabolism changes after subchronic fish exposure to cyanobacterial crude extract (CE) containing MC. The Neotropical erythrinid fish, Hoplias malabaricus, were exposed intraperitoneally to CE containing 100 μg MC-LR eq kg[-1] for 30 days and, thereafter, the plasma, liver, and white muscle was sampled for analyses. Liver tissue lost cellular structure organization showing round hepatocytes, hyperemia, and biliary duct obstruction. At the ultrastructural level, the mitochondria and the endoplasmic reticulum exhibited disorganization. Direct and total bilirubin increased in plasma. In the liver, the activity of acid phosphatase (ACP) increased, and the aspartate aminotransferase (AST) decreased; AST increased in plasma. Alkaline phosphatase (ALP) and alanine aminotransferase (ALT) were unchanged in the liver, muscle, and plasma. Glycogen stores and the energetic metabolites as glucose, lactate, and pyruvate decrease in the liver; pyruvate decreased in plasma and lactate decreased in muscle. Ammonia levels increased and protein concentration decreased in plasma. CE alters liver morphology by causing hepatocyte intracellular disorder, obstructive cholestasis, and dysfunction in the activity of key liver enzymes. The increasing energy demand implies glucose mobilization and metabolic adjustments maintaining protein preservation and lipid recruitment to supply the needs for detoxification allowing fish survival.}, }
@article {pmid35915152, year = {2022}, author = {Schavemaker, PE and Muñoz-Gómez, SA}, title = {The role of mitochondrial energetics in the origin and diversification of eukaryotes.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {9}, pages = {1307-1317}, pmid = {35915152}, issn = {2397-334X}, support = {R35 GM122566/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; DNA ; *Eukaryota/genetics ; Mitochondria/genetics/metabolism ; Prokaryotic Cells/metabolism ; }, abstract = {The origin of eukaryotic cell size and complexity is often thought to have required an energy excess supplied by mitochondria. Recent observations show energy demands to scale continuously with cell volume, suggesting that eukaryotes do not have higher energetic capacity. However, respiratory membrane area scales superlinearly with the cell surface area. Furthermore, the consequences of the contrasting genomic architectures between prokaryotes and eukaryotes have not been precisely quantified. Here, we investigated (1) the factors that affect the volumes at which prokaryotes become surface area-constrained, (2) the amount of energy divested to DNA due to contrasting genomic architectures and (3) the costs and benefits of respiring symbionts. Our analyses suggest that prokaryotes are not surface area-constrained at volumes of 10[0]‒10[3] µm[3], the genomic architecture of extant eukaryotes is only slightly advantageous at genomes sizes of 10[6]‒10[7] base pairs and a larger host cell may have derived a greater advantage (lower cost) from harbouring ATP-producing symbionts. This suggests that eukaryotes first evolved without the need for mitochondria since these ranges hypothetically encompass the last eukaryotic common ancestor and its relatives. Our analyses also show that larger and faster-dividing prokaryotes would have a shortage of respiratory membrane area and divest more energy into DNA. Thus, we argue that although mitochondria may not have been required by the first eukaryotes, eukaryote diversification was ultimately dependent on mitochondria.}, }
@article {pmid35910652, year = {2022}, author = {Yu, J and Ran, Z and Zhang, J and Wei, L and Ma, W}, title = {Genome-Wide Insights Into the Organelle Translocation of Photosynthetic NDH-1 Genes During Evolution.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {956578}, pmid = {35910652}, issn = {1664-302X}, abstract = {Translocation of chloroplast-located genes to mitochondria or nucleus is considered to be a safety strategy that impedes mutation of photosynthetic genes and maintains their household function during evolution. The organelle translocation strategy is also developed in photosynthetic NDH-1 (pNDH-1) genes but its understanding is still far from complete. Here, we found that the mutation rate of the conserved pNDH-1 genes was gradually reduced but their selection pressure was maintained at a high level during evolution from cyanobacteria to angiosperm. By contrast, oxygenic photosynthesis-specific (OPS) pNDH-1 genes had an opposite trend, explaining the reason why they were transferred from the reactive oxygen species (ROS)-enriched chloroplast to the ROS-barren nucleus. Further, genome-wide sequence analysis supported the possibility that all conserved pNDH-1 genes lost in chloroplast genomes of Chlorophyceae and Pinaceae were transferred to the ROS-less mitochondrial genome as deduced from their truncated pNDH-1 gene fragments. Collectively, we propose that the organelle translocation strategy of pNDH-1 genes during evolution is necessary to maintain the function of the pNDH-1 complex as an important antioxidant mechanism for efficient photosynthesis.}, }
@article {pmid35899483, year = {2022}, author = {Pani, P and Bal, NC}, title = {Avian adjustments to cold and non-shivering thermogenesis: whats, wheres and hows.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {97}, number = {6}, pages = {2106-2126}, doi = {10.1111/brv.12885}, pmid = {35899483}, issn = {1469-185X}, mesh = {Animals ; *Thermogenesis/physiology ; *Cold Temperature ; Adipose Tissue, Brown/physiology ; Birds ; Muscle, Skeletal/physiology ; Mammals ; Acclimatization/physiology ; }, abstract = {Avian cold adaptation is hallmarked by innovative strategies of both heat conservation and thermogenesis. While minimizing heat loss can reduce the thermogenic demands of body temperature maintenance, it cannot eliminate the requirement for thermogenesis. Shivering and non-shivering thermogenesis (NST) are the two synergistic mechanisms contributing to endothermy. Birds are of particular interest in studies of NST as they lack brown adipose tissue (BAT), the major organ of NST in mammals. Critical analysis of the existing literature on avian strategies of cold adaptation suggests that skeletal muscle is the principal site of NST. Despite recent progress, isolating the mechanisms involved in avian muscle NST has been difficult as shivering and NST co-exist with its primary locomotory function. Herein, we re-evaluate various proposed molecular bases of avian skeletal muscle NST. Experimental evidence suggests that sarco(endo)plasmic reticulum Ca[2+] -ATPase (SERCA) and ryanodine receptor 1 (RyR1) are key in avian muscle NST, through their mediation of futile Ca[2+] cycling and thermogenesis. More recent studies have shown that SERCA regulation by sarcolipin (SLN) facilitates muscle NST in mammals; however, its role in birds is unclear. Ca[2+] signalling in the muscle seems to be common to contraction, shivering and NST, but elucidating its roles will require more precise measurement of local Ca[2+] levels inside avian myofibres. The endocrine control of avian muscle NST is still poorly defined. A better understanding of the mechanistic details of avian muscle NST will provide insights into the roles of these processes in regulatory thermogenesis, which could further inform our understanding of the evolution of endothermy among vertebrates.}, }
@article {pmid35895186, year = {2022}, author = {Atayik, MC and Çakatay, U}, title = {Melatonin-related signaling pathways and their regulatory effects in aging organisms.}, journal = {Biogerontology}, volume = {23}, number = {5}, pages = {529-539}, pmid = {35895186}, issn = {1573-6768}, mesh = {Aging/metabolism ; Antioxidants/metabolism ; Free Radicals/metabolism ; Humans ; *Melatonin ; Signal Transduction ; }, abstract = {Melatonin is a tryptophan-derived ancestral molecule evolved in bacteria. According to the endosymbiotic theory, eukaryotic cells received mitochondria, plastids, and other organelles from bacteria by internalization. After the endosymbiosis, bacteria evolved into organelles and retained their ability of producing melatonin. Melatonin is a small, evolutionarily conserved indole with multiple receptor-mediated, receptor-dependent, and independent actions. Melatonin's initial function was likely a radical scavenger in bacteria that's why there was high intensity of free radicals on primitive atmosphere in the ancient times, and hormetic functions of melatonin, which are effecting through the level of gene expression via prooxidant and antioxidant redox pathways, are developed in throughout the eukaryotic evolution. In the earlier stages of life, endosymbiotic events between mitochondria and other downstream organelles continue with mutual benefits. However, this interaction gradually deteriorates as a result of the imperfection of both mitochondrial and extramitochondrial endosymbiotic crosstalk with the advancing age of eukaryotic organisms. Throughout the aging process melatonin levels tend to reduce and as a manifestation of this, many symptoms in organisms' homeostasis, such as deterioration in adjustment of cellular clocks, are commonly seen. In addition, due to deterioration in mitochondrial integrity and functions, immunity decreases, and lower levels of melatonin renders older individuals to be more susceptible to impaired redox modulation and age-related diseases. Our aim in this paper is to focus on the several redox modulation mechanisms in which melatonin signaling has a central role, to discuss melatonin's gerontological aspects and to provide new research ideas with researchers.}, }
@article {pmid35893881, year = {2022}, author = {Ghanem, J and Passadori, A and Severac, F and Dieterlen, A and Geny, B and Andrès, E}, title = {Effects of Rehabilitation on Long-COVID-19 Patient's Autonomy, Symptoms and Nutritional Observance.}, journal = {Nutrients}, volume = {14}, number = {15}, pages = {}, pmid = {35893881}, issn = {2072-6643}, mesh = {*COVID-19/complications ; Fatigue/complications ; Humans ; *Malnutrition/diagnosis ; Nutrition Assessment ; Nutritional Status ; Post-Acute COVID-19 Syndrome ; }, abstract = {Background: Despite significant improvements in COVID-19 therapy, many patients still present with persistent symptoms and quality-of-life alterations. The aim of this study was to simultaneously investigate the long-term evolution of autonomy, malnutrition and long-lasting symptoms in people infected with COVID-19 and hospitalized in the ICU. Method: Patients’ clinical characteristics; extent of their loss of autonomy based on “Autonomie Gérontologie Groupes Iso-Ressources” (AG-GIR) classification; nutritional status while following the French and Global Leadership Initiative on Malnutrition (GLIM) recommendations; and symptom evolutions before infection, during hospitalization and rehabilitation, and up to 6 months after returning home were determined in thirty-seven patients. Results: Prior to a COVID-19 infection, all patients were autonomous, but upon admission to the rehabilitation center (CRM), 39% of them became highly dependent. After discharge from the center and 6 months after returning home, only 6 and 3%, respectively, still required considerable assistance. Of these thirty-seven patients, 11% were moderately malnourished and 81% presented with severe malnutrition, with a significant correlation being observed between malnutrition and autonomy (p < 0.05). Except for fatigue, which persisted in 70% of the patients 6 months after discharge from rehabilitation, all other symptoms decreased significantly. Conclusions: This study shows a striking decrease in autonomy associated with malnutrition after hospitalization for a COVID-19 infection and a clear beneficial effect from personalized rehabilitation. However, although almost all patients regained autonomy 6 months after returning home, they often still suffer from fatigue. Patient compliance with their nutritional recommendations deserves further improvement, preferably through personalized and persistent follow-up with the patient.}, }
@article {pmid35891364, year = {2022}, author = {Tao, J and Li, B and Cheng, J and Shi, Y and Qiao, C and Lin, Z and Liu, H}, title = {Genomic Divergence Characterization and Quantitative Proteomics Exploration of Type 4 Porcine Astrovirus.}, journal = {Viruses}, volume = {14}, number = {7}, pages = {}, pmid = {35891364}, issn = {1999-4915}, mesh = {Animals ; Antiviral Agents ; *Astroviridae Infections/veterinary ; China ; Genomics ; Humans ; Mamastrovirus ; Mitochondrial Proteins ; Phylogeny ; Proteomics ; Swine ; *Swine Diseases ; }, abstract = {Porcine astrovirus (PAstV) has been identified as an important diarrheic pathogen with a broad global distribution. The PAstV is a potential pathogen to human beings and plays a role in public health. Until now, the divergence characteristics and pathogenesis of the PAstV are still not well known. In this study, the PAstV-4 strain PAstV/CH/2022/CM1 was isolated from the diarrheal feces of a piglet in Shanghai, which was identified to be a recombination of PAstV4/JPN (LC201612) and PAstV4/CHN (JX060808). A time tree based on the ORF2 protein of the astrovirus demonstrated that type 2-5 PAstV (PAstV-2 to 5) diverged from type 1 PAstV (PAstV-1) at a point from 1992 to 2000. To better understand the molecular basis of the virus, we sought to explore the host cell response to the PAstV/CH/2022/CM1 infection using proteomics. The results demonstrate that viral infection elicits global protein changes, and that the mitochondria seems to be a primary and an important target in viral infection. Importantly, there was crosstalk between autophagy and apoptosis, in which ATG7 might be the key mediator. In addition, the NOD-like receptor X1 (NLRX1) in the mitochondria was activated and participated in several important antiviral signaling pathways after the PAstV/CH/2022/CM1 infection, which was closely related to mitophagy. The NLRX1 may be a crucial protein for antagonizing a viral infection through autophagy, but this has yet to be validated. In conclusion, the data in this study provides more information for understanding the virus genomic characterization and the potential antiviral targets in a PAstV infection.}, }
@article {pmid35889091, year = {2022}, author = {Mendoza-Hoffmann, F and Zarco-Zavala, M and Ortega, R and Celis-Sandoval, H and Torres-Larios, A and García-Trejo, JJ}, title = {Evolution of the Inhibitory and Non-Inhibitory ε, ζ, and IF1 Subunits of the F1FO-ATPase as Related to the Endosymbiotic Origin of Mitochondria.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889091}, issn = {2076-2607}, support = {DGAPA-PAPIIT IN217520//National Autonomous University of Mexico/ ; }, abstract = {The F1FO-ATP synthase nanomotor synthesizes >90% of the cellular ATP of almost all living beings by rotating in the “forward” direction, but it can also consume the same ATP pools by rotating in “reverse.” To prevent futile F1FO-ATPase activity, several different inhibitory proteins or domains in bacteria (ε and ζ subunits), mitochondria (IF1), and chloroplasts (ε and γ disulfide) emerged to block the F1FO-ATPase activity selectively. In this study, we analyze how these F1FO-ATPase inhibitory proteins have evolved. The phylogeny of the α-proteobacterial ε showed that it diverged in its C-terminal side, thus losing both the inhibitory function and the ATP-binding/sensor motif that controls this inhibition. The losses of inhibitory function and the ATP-binding site correlate with an evolutionary divergence of non-inhibitory α-proteobacterial ε and mitochondrial δ subunits from inhibitory bacterial and chloroplastidic ε subunits. Here, we confirm the lack of inhibitory function of wild-type and C-terminal truncated ε subunits of P. denitrificans. Taken together, the data show that ζ evolved to replace ε as the primary inhibitor of the F1FO-ATPase of free-living α-proteobacteria. However, the ζ inhibitory function was also partially lost in some symbiotic α-proteobacteria and totally lost in some strictly parasitic α-proteobacteria such as the Rickettsiales order. Finally, we found that ζ and IF1 likely evolved independently via convergent evolution before and after the endosymbiotic origin mitochondria, respectively. This led us to propose the ε and ζ subunits as tracer genes of the pre-endosymbiont that evolved into the actual mitochondria.}, }
@article {pmid35883288, year = {2022}, author = {Shang, Y and Wang, X and Liu, G and Wu, X and Wei, Q and Sun, G and Mei, X and Dong, Y and Sha, W and Zhang, H}, title = {Adaptability and Evolution of Gobiidae: A Genetic Exploration.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {14}, pages = {}, pmid = {35883288}, issn = {2076-2615}, support = {31872242//National Natural Science Foundation of China/ ; 32070405//National Natural Science Foundation of China/ ; 32001228//National Natural Science Foundation of China/ ; 32170530//National Natural Science Foundation of China/ ; }, abstract = {The Gobiidae family occupy one of the most diverse habitat ranges of all fishes. One key reason for their successful colonization of different habitats is their ability to adapt to different energy demands. This energy requirement is related to the ability of mitochondria in cells to generate energy via oxidative phosphorylation (OXPHOS). Here, we assembled three complete mitochondrial genomes of Rhinogobius shennongensis, Rhinogobius wuyanlingensis, and Chaenogobius annularis. These mitogenomes are circular and include 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs, and one non-coding control region (CR). We used comparative mitochondrial DNA (mtDNA) genome and selection pressure analyses to explore the structure and evolutionary rates of Gobiidae mitogenomics in different environments. The CmC model showed that the ω ratios of all mtDNA PCGs were <1, and that the evolutionary rate of adenosine triphosphate 8 (atp8) was faster in Gobiidae than in other mitochondrial DNA PCGs. We also found evidence of positive selection for several sites of NADH dehydrogenase (nd) 6 and atp8 genes. Thus, divergent mechanisms appear to underlie the evolution of mtDNA PCGs, which might explain the ability of Gobiidae to adapt to diverse environments. Our study provides new insights on the adaptive evolution of Gobiidae mtDNA genome and molecular mechanisms of OXPHOS.}, }
@article {pmid35879672, year = {2022}, author = {Ge, H and Xu, J and Hua, M and An, W and Wu, J and Wang, B and Li, P and Fang, H}, title = {Genome-wide identification and analysis of ACP gene family in Sorghum bicolor (L.) Moench.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {538}, pmid = {35879672}, issn = {1471-2164}, support = {32101730//National Natural Science Foundation of China/ ; MS22020033//the Social Livelihood Science and Technology Project of Nantong City,china/ ; 135420609055//Nantong University Scientific Research Start-up project for Introducing Talents/ ; 202110304081Y//the Practice Innovation Training Program Projects for College Students in 2021/ ; }, mesh = {Acyl Carrier Protein/genetics/metabolism ; Droughts ; Gene Expression Regulation, Plant ; Phylogeny ; Plant Proteins/genetics/metabolism ; *Sorghum/metabolism ; Stress, Physiological/genetics ; Zea mays/genetics/metabolism ; }, abstract = {BACKGROUND: Acyl carrier proteins (ACP) constitute a very conserved carrier protein family. Previous studies have found that ACP not only takes part in the fatty acid synthesis process of almost all organisms, but also participates in the regulation of plant growth, development, and metabolism, and makes plants adaptable to stresses. However, this gene family has not been systematically studied in sorghum.<br><br>RESULTS: Nine ACP family members were identified in the sorghum genome, which were located on chromosomes 1, 2, 5, 7, 8 and 9, respectively. Evolutionary analysis among different species divided the ACP family into four subfamilies, showing that the SbACPs were more closely related to maize. The prediction results of subcellular localization showed that SbACPs were mainly distributed in chloroplasts and mitochondria, while fluorescence localization showed that SbACPs were mainly localized in chloroplasts in tobacco leaf. The analysis of gene structure revealed a relatively simple genetic structure, that there were 1-3 introns in the sorghum ACP family, and the gene structure within the same subfamily had high similarity. The amplification method of SbACPs was mainly large fragment replication, and SbACPs were more closely related to ACPs in maize and rice. In addition, three-dimensional structure analysis showed that all ACP genes in sorghum contained four &#x3b1; helices, and the second helix structure was more conserved, implying a key role in function. Cis-acting element analysis indicated that the SbACPs might be involved in light response, plant growth and development regulation, biotic and abiotic stress response, plant hormone regulation, and other physiological processes. What's more, qRT-PCR analysis uncovered that some of SbACPs might be involved in the adaptive regulation of drought and salt stresses, indicating the close relationship between fatty acids and the resistance to abiotic stresses in sorghum.<br><br>CONCLUSIONS: In summary, these results showed a comprehensive overview of the SbACPs and provided a theoretical basis for further studies on the biological functions of SbACPs in sorghum growth, development and abiotic stress responses.}, }
@article {pmid35877596, year = {2022}, author = {Wu, CS and Chaw, SM}, title = {Evolution of mitochondrial RNA editing in extant gymnosperms.}, journal = {The Plant journal : for cell and molecular biology}, volume = {111}, number = {6}, pages = {1676-1687}, pmid = {35877596}, issn = {1365-313X}, mesh = {Amino Acids ; Cycadopsida/genetics ; *Magnoliopsida/genetics ; Mitochondrial Proteins/genetics ; RNA Editing/genetics ; RNA, Mitochondrial ; *Tracheophyta/genetics ; }, abstract = {To unveil the evolution of mitochondrial RNA editing in gymnosperms, we characterized mitochondrial genomes (mitogenomes), plastid genomes, RNA editing sites, and pentatricopeptide repeat (PPR) proteins from 10 key taxa representing four of the five extant gymnosperm clades. The assembled mitogenomes vary in gene content due to massive gene losses in Gnetum and Conifer II clades. Mitochondrial gene expression levels also vary according to protein function, with the most highly expressed genes involved in the respiratory complex. We identified 9132 mitochondrial C-to-U editing sites, as well as 2846 P-class and 8530 PLS-class PPR proteins. Regains of editing sites were demonstrated in Conifer II rps3 transcripts whose corresponding mitogenomic sequences lack introns due to retroprocessing. Our analyses reveal that non-synonymous editing is efficient and results in more codons encoding hydrophobic amino acids. In contrast, synonymous editing, although performed with variable efficiency, can increase the number of U-ending codons that are preferentially utilized in gymnosperm mitochondria. The inferred loss-to-gain ratio of mitochondrial editing sites in gymnosperms is 2.1:1, of which losses of non-synonymous editing are mainly due to genomic C-to-T substitutions. However, such substitutions only explain a small fraction of synonymous editing site losses, indicating distinct evolutionary mechanisms. We show that gymnosperms have experienced multiple lineage-specific duplications in PLS-class PPR proteins. These duplications likely contribute to accumulated RNA editing sites, as a mechanistic correlation between RNA editing and PLS-class PPR proteins is statistically supported.}, }
@article {pmid35875852, year = {2022}, author = {Ebner, JN and Wyss, MK and Ritz, D and von Fumetti, S}, title = {Effects of thermal acclimation on the proteome of the planarian Crenobia alpina from an alpine freshwater spring.}, journal = {The Journal of experimental biology}, volume = {225}, number = {15}, pages = {}, pmid = {35875852}, issn = {1477-9145}, support = {31003A_176234//Schweizerischer Nationalfonds zur Forderung der Wissenschaftlichen Forschung/ ; 31003A_176234//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; //Universitat Basel/ ; }, mesh = {Acclimatization/physiology ; Animals ; Climate Change ; Fresh Water ; Humans ; *Planarians ; *Proteome ; Temperature ; }, abstract = {Species' acclimation capacity and their ability to maintain molecular homeostasis outside ideal temperature ranges will partly predict their success following climate change-induced thermal regime shifts. Theory predicts that ectothermic organisms from thermally stable environments have muted plasticity, and that these species may be particularly vulnerable to temperature increases. Whether such species retained or lost acclimation capacity remains largely unknown. We studied proteome changes in the planarian Crenobia alpina, a prominent member of cold-stable alpine habitats that is considered to be a cold-adapted stenotherm. We found that the species' critical thermal maximum (CTmax) is above its experienced habitat temperatures and that different populations exhibit differential CTmax acclimation capacity, whereby an alpine population showed reduced plasticity. In a separate experiment, we acclimated C. alpina individuals from the alpine population to 8, 11, 14 or 17°C over the course of 168 h and compared their comprehensively annotated proteomes. Network analyses of 3399 proteins and protein set enrichment showed that while the species' proteome is overall stable across these temperatures, protein sets functioning in oxidative stress response, mitochondria, protein synthesis and turnover are lower in abundance following warm acclimation. Proteins associated with an unfolded protein response, ciliogenesis, tissue damage repair, development and the innate immune system were higher in abundance following warm acclimation. Our findings suggest that this species has not suffered DNA decay (e.g. loss of heat-shock proteins) during evolution in a cold-stable environment and has retained plasticity in response to elevated temperatures, challenging the notion that stable environments necessarily result in muted plasticity.}, }
@article {pmid35870233, year = {2022}, author = {Visinoni, F and Delneri, D}, title = {Mitonuclear interplay in yeast: from speciation to phenotypic adaptation.}, journal = {Current opinion in genetics &amp; development}, volume = {76}, number = {}, pages = {101957}, doi = {10.1016/j.gde.2022.101957}, pmid = {35870233}, issn = {1879-0380}, support = {BB/L021471/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adaptation, Physiological/genetics ; *Hybridization, Genetic ; Mitochondria/genetics/metabolism ; Phenotype ; *Proteome/genetics ; }, abstract = {Saccharomyces yeasts have evolved into an important model system to study mitonuclear incompatibilities, thanks to recent advances in the field of sequencing, yeast hybridisation and multigenerational breeding. Yeast hybrids contain two homologous proteomes but retain only one type of mitochondria allowing studies on the effect of mitochondria on phenotype and gene expression. Here, we discuss the recent developments in the growing field of yeast mitogenomics spanning from the impact that this organelle has in shaping yeast fitness and genome evolution to the dissection of molecular determinants of mitonuclear incompatibilities. Applying the state-of-the-art genetic tools to a broader range of natural yeast species from different environments will help progress the field and untap the mitochondrial potential in strain development.}, }
@article {pmid35866365, year = {2022}, author = {McCall, CE and Zhu, X and Zabalawi, M and Long, D and Quinn, MA and Yoza, BK and Stacpoole, PW and Vachharajani, V}, title = {Sepsis, pyruvate, and mitochondria energy supply chain shortage.}, journal = {Journal of leukocyte biology}, volume = {112}, number = {6}, pages = {1509-1514}, pmid = {35866365}, issn = {1938-3673}, mesh = {Mice ; Humans ; Animals ; *Pyruvic Acid/metabolism ; Pyruvate Dehydrogenase Complex/metabolism ; *Sepsis ; Mitochondria/metabolism ; Pyruvate Dehydrogenase Acetyl-Transferring Kinase ; Acetates/pharmacology ; }, abstract = {Balancing high energy-consuming danger resistance and low energy supply of disease tolerance is a universal survival principle that often fails during sepsis. Our research supports the concept that sepsis phosphorylates and deactivates mitochondrial pyruvate dehydrogenase complex control over the tricarboxylic cycle and the electron transport chain. StimulatIng mitochondrial energetics in septic mice and human sepsis cell models can be achieved by inhibiting pyruvate dehydrogenase kinases with the pyruvate structural analog dichloroacetate. Stimulating the pyruvate dehydrogenase complex by dichloroacetate reverses a disruption in the tricarboxylic cycle that induces itaconate, a key mediator of the disease tolerance pathway. Dichloroacetate treatment increases mitochondrial respiration and ATP synthesis, decreases oxidant stress, overcomes metabolic paralysis, regenerates tissue, organ, and innate and adaptive immune cells, and doubles the survival rate in a murine model of sepsis.}, }
@article {pmid35862496, year = {2022}, author = {Cadart, C and Heald, R}, title = {Scaling of biosynthesis and metabolism with cell size.}, journal = {Molecular biology of the cell}, volume = {33}, number = {9}, pages = {}, pmid = {35862496}, issn = {1939-4586}, support = {R35 GM118183/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Evolution ; Cell Size ; Humans ; Mitochondria ; *Ploidies ; *Polyploidy ; }, abstract = {Cells adopt a size that is optimal for their function, and pushing them beyond this limit can cause cell aging and death by senescence or reduce proliferative potential. However, by increasing their genome copy number (ploidy), cells can increase their size dramatically and homeostatically maintain physiological properties such as biosynthesis rate. Recent studies investigating the relationship between cell size and rates of biosynthesis and metabolism under normal, polyploid, and pathological conditions are revealing new insights into how cells attain the best function or fitness for their size by tuning processes including transcription, translation, and mitochondrial respiration. A new frontier is to connect single-cell scaling relationships with tissue and whole-organism physiology, which promises to reveal molecular and evolutionary principles underlying the astonishing diversity of size observed across the tree of life.}, }
@article {pmid35860045, year = {2022}, author = {Jamaludin, NA and Jamaluddin, JAF and Rahim, MA and Mohammed Akib, NA and Ratmuangkhwang, S and Mohd Arshaad, W and Mohd Nor, SA}, title = {Mitochondrial marker implies fishery separate management units for spotted sardinella, Amblygaster sirm (Walbaum, 1792) populations in the South China Sea and the Andaman Sea.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13706}, pmid = {35860045}, issn = {2167-8359}, mesh = {Animals ; Phylogeny ; *Fisheries ; *Conservation of Natural Resources ; Mitochondria/genetics ; Fishes/genetics ; China ; }, abstract = {The spotted sardinella, Amblygaster sirm (Walbaum, 1792), is a commercial sardine commonly caught in Malaysia. Lack of management of these marine species in Malaysian waters could lead to overfishing and potentially declining fish stock populations. Therefore, sustainable management of this species is of paramount importance to ensure its longevity. As such, molecular information is vital in determining the A. sirm population structure and management strategy. In the present study, mitochondrial DNA Cytochrome b was sequenced from 10 A. sirm populations: the Andaman Sea (AS) (two), South China Sea (SCS) (six), Sulu Sea (SS) (one), and Celebes Sea (CS) (one). Accordingly, the intra-population haplotype diversity (Hd) was high (0.91-1.00), and nucleotide diversity (π) was low (0.002-0.009), which suggests a population bottleneck followed by rapid population growth. Based on the phylogenetic trees, minimum spanning network (MSN), population pairwise comparison, and F ST,and supported by analysis of molecular variance (AMOVA) and spatial analysis of molecular variance (SAMOVA) tests, distinct genetic structures were observed (7.2% to 7.6% genetic divergence) between populations in the SCS and its neighboring waters, versus those in the AS. Furthermore, the results defined A. sirm stock boundaries and evolutionary between the west and east coast (which shares the same waters as western Borneo) of Peninsular Malaysia. In addition, genetic homogeneity was revealed throughout the SCS, SS, and CS based on the non-significant F STpairwise comparisons. Based on the molecular evidence, separate management strategies may be required for A. sirm of the AS and the SCS, including its neighboring waters.}, }
@article {pmid35858057, year = {2022}, author = {Brzęk, P and Roussel, D and Konarzewski, M}, title = {Mice selected for a high basal metabolic rate evolved larger guts but not more efficient mitochondria.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1978}, pages = {20220719}, pmid = {35858057}, issn = {1471-2954}, mesh = {Animals ; *Basal Metabolism ; Mice ; *Mitochondria ; Organ Size ; }, abstract = {Intra-specific variation in both the basal metabolic rate (BMR) and mitochondrial efficiency (the amount of ATP produced per unit of oxygen consumed) has profound evolutionary and ecological consequences. However, the functional mechanisms responsible for this variation are not fully understood. Mitochondrial efficiency is negatively correlated with BMR at the interspecific level but it is positively correlated with performance capacity at the intra-specific level. This discrepancy is surprising, as theories explaining the evolution of endothermy assume a positive correlation between BMR and performance capacity. Here, we quantified mitochondrial oxidative phosphorylation activity and efficiency in two lines of laboratory mice divergently selected for either high (H-BMR) or low (L-BMR) levels of BMR. H-BMR mice had larger livers and kidneys (organs that are important predictors of BMR). H-BMR mice also showed higher oxidative phosphorylation activity in liver mitochondria but this difference can be hypothesized to be a direct effect of selection only if the heritability of this trait is low. However, mitochondrial efficiency in all studied organs did not differ between the two lines. We conclude that the rapid evolution of BMR can reflect changes in organ size rather than mitochondrial properties, and does not need to be accompanied obligatorily by changes in mitochondrial efficiency.}, }
@article {pmid35856299, year = {2022}, author = {Carter, CS and Kingsbury, MA}, title = {Oxytocin and oxygen: the evolution of a solution to the 'stress of life'.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1858}, pages = {20210054}, pmid = {35856299}, issn = {1471-2970}, support = {R01 HD098117/HD/NICHD NIH HHS/United States ; R21 HD098603/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Hypothalamo-Hypophyseal System ; Inflammation ; Mammals/metabolism ; Oxygen ; *Oxytocin ; Pituitary-Adrenal System ; Receptors, Oxytocin/metabolism ; }, abstract = {Oxytocin (OT) and the OT receptor occupy essential roles in our current understanding of mammalian evolution, survival, sociality and reproduction. This narrative review examines the hypothesis that many functions attributed to OT can be traced back to conditions on early Earth, including challenges associated with managing life in the presence of oxygen and other basic elements, including sulfur. OT regulates oxidative stress and inflammation especially through effects on the mitochondria. A related nonapeptide, vasopressin, as well as molecules in the hypothalamic-pituitary-adrenal axis, including the corticotropin-releasing hormone family of molecules, have a broad set of functions that interact with OT. Interactions among these molecules have roles in the causes and consequence of social behaviour and the management of threat, fear and stress. Here, we discuss emerging evidence suggesting that unique properties of the OT system allowed vertebrates, and especially mammals, to manage over-reactivity to the 'side effects' of oxygen, including inflammation, oxidation and free radicals, while also supporting high levels of sociality and a perception of safety. This article is part of the theme issue 'Interplays between oxytocin and other neuromodulators in shaping complex social behaviours'.}, }
@article {pmid35850262, year = {2022}, author = {Rottenberg, H}, title = {The accelerated evolution of human cytochrome c oxidase - Selection for reduced rate and proton pumping efficiency?.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1863}, number = {8}, pages = {148595}, doi = {10.1016/j.bbabio.2022.148595}, pmid = {35850262}, issn = {1879-2650}, mesh = {Adenosine Triphosphate ; Animals ; Cattle ; Cytochromes c ; DNA, Mitochondrial ; *Electron Transport Complex IV/genetics/metabolism ; Haplorhini/metabolism ; Humans ; Mammals/metabolism ; Mice ; Oxidoreductases ; Oxygen ; Primates/genetics/metabolism ; *Proton Pumps/genetics ; Protons ; Superoxides ; }, abstract = {The cytochrome c oxidase complex, complex VI (CIV), catalyzes the terminal step of the mitochondrial electron transport chain where the reduction of oxygen to water by cytochrome c is coupled to the generation of a protonmotive force that drive the synthesis of ATP. CIV evolution was greatly accelerated in humans and other anthropoid primates and appears to be driven by adaptive selection. However, it is not known if there are significant functional differences between the anthropoid primates CIV, and other mammals. Comparison of the high-resolution structures of bovine CIV, mouse CIV and human CIV shows structural differences that are associated with anthropoid-specific substitutions. Here I examine the possible effects of these substitutions in four CIV peptides that are known to affect proton pumping: the mtDNA-coded subunits I, II and III, and the nuclear-encoded subunit VIa2. I conclude that many of the anthropoid-specific substitutions could be expected to modulate the rate and/or the efficiency of proton pumping. These results are compatible with the previously proposed hypothesis that the accelerated evolution of CIV in anthropoid primates is driven by selection pressure to lower the mitochondrial protonmotive force and thus decrease the rate of superoxide generation by mitochondria.}, }
@article {pmid37954502, year = {2022}, author = {Politis-Barber, V and Petrick, HL and Raajendiran, A and DesOrmeaux, GJ and Brunetta, HS and Dos Reis, LM and Mori, MA and Wright, DC and Watt, MJ and Holloway, GP}, title = {Ckmt1 is Dispensable for Mitochondrial Bioenergetics Within White/Beige Adipose Tissue.}, journal = {Function (Oxford, England)}, volume = {3}, number = {5}, pages = {zqac037}, pmid = {37954502}, issn = {2633-8823}, mesh = {Animals ; Humans ; Mice ; *Adipose Tissue, Beige/metabolism ; Adipose Tissue, White ; *Creatine/metabolism ; Creatine Kinase/metabolism ; Energy Metabolism/genetics ; Mitochondria/metabolism ; }, abstract = {Within brown adipose tissue (BAT), the brain isoform of creatine kinase (CKB) has been proposed to regulate the regeneration of ADP and phosphocreatine in a futile creatine cycle (FCC) that stimulates energy expenditure. However, the presence of FCC, and the specific creatine kinase isoforms regulating this theoretical model within white adipose tissue (WAT), remains to be fully elucidated. In the present study, creatine did not stimulate respiration in cultured adipocytes, isolated mitochondria or mouse permeabilized WAT. Additionally, while creatine kinase ubiquitous-type, mitochondrial (CKMT1) mRNA and protein were detected in human WAT, shRNA-mediated reductions in Ckmt1 did not decrease submaximal respiration in cultured adipocytes, and ablation of CKMT1 in mice did not alter energy expenditure, mitochondrial responses to pharmacological β3-adrenergic activation (CL 316, 243) or exacerbate the detrimental metabolic effects of consuming a high-fat diet. Taken together, these findings solidify CKMT1 as dispensable in the regulation of energy expenditure, and unlike in BAT, they do not support the presence of FCC within WAT.}, }
@article {pmid35842180, year = {2022}, author = {Biró, B and Gál, Z and Schiavo, G and Ribari, A and Joe Utzeri, V and Brookman, M and Fontanesi, L and Hoffmann, OI}, title = {Nuclear mitochondrial DNA sequences in the rabbit genome.}, journal = {Mitochondrion}, volume = {66}, number = {}, pages = {1-6}, doi = {10.1016/j.mito.2022.07.003}, pmid = {35842180}, issn = {1872-8278}, mesh = {Animals ; Cell Nucleus/genetics ; *DNA, Mitochondrial/chemistry/genetics ; Genome ; *Genome, Mitochondrial ; Mammals/genetics ; Mitochondria/genetics ; Phylogeny ; Rabbits ; Sequence Analysis, DNA ; }, abstract = {Numtogenesis is observable in the mammalian genomes resulting in the integration of mitochondrial segments into the nuclear genomes (numts). To identify numts in rabbit, we aligned mitochondrial and nuclear genomes. Alignment significance threshold was calculated and individual characteristics of numts were analysed. We found 153 numts in the nuclear genome. The GC content of numts were significantly lower than the GC content of their genomic flanking regions or the genome itself. The frequency of three mammalian-wide interspersed repeats were increased in the proximity of numts. The decreased GC content around numts strengthen the theory which supposes a link between DNA structural instability and numt integration.}, }
@article {pmid35836411, year = {2022}, author = {Shen, LL and Waheed, A and Wang, YP and Nkurikiyimfura, O and Wang, ZH and Yang, LN and Zhan, J}, title = {Mitochondrial Genome Contributes to the Thermal Adaptation of the Oomycete Phytophthora infestans.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {928464}, pmid = {35836411}, issn = {1664-302X}, abstract = {As a vital element of climate change, elevated temperatures resulting from global warming present new challenges to natural and agricultural sustainability, such as ecological disease management. Mitochondria regulate the energy production of cells in responding to environmental fluctuation, but studying their contribution to the thermal adaptation of species is limited. This knowledge is needed to predict future disease epidemiology for ecology conservation and food security. Spatial distributions of the mitochondrial genome (mtDNA) in 405 Phytophthora infestans isolates originating from 15 locations were characterized. The contribution of MtDNA to thermal adaptation was evaluated by comparative analysis of mtDNA frequency and intrinsic growth rate, relative population differentiation in nuclear and mtDNA, and associations of mtDNA distribution with local geography climate conditions. Significant variation in frequency, intrinsic growth rate, and spatial distribution was detected in mtDNA. Population differentiation in mtDNA was significantly higher than that in the nuclear genome, and spatial distribution of mtDNA was strongly associated with local climatic conditions and geographic parameters, particularly air temperature, suggesting natural selection caused by a local temperature is the main driver of the adaptation. Dominant mtDNA grew faster than the less frequent mtDNA. Our results provide useful insights into the evolution of pathogens under global warming. Given its important role in biological functions and adaptation to local air temperature, mtDNA intervention has become an increasing necessity for future disease management. To secure ecological integrity and food production under global warming, a synergistic study on the interactive effect of changing temperature on various components of biological and ecological functions of mitochondria in an evolutionary frame is urgently needed.}, }
@article {pmid35809880, year = {2022}, author = {Bononi, G and Masoni, S and Di Bussolo, V and Tuccinardi, T and Granchi, C and Minutolo, F}, title = {Historical perspective of tumor glycolysis: A century with Otto Warburg.}, journal = {Seminars in cancer biology}, volume = {86}, number = {Pt 2}, pages = {325-333}, doi = {10.1016/j.semcancer.2022.07.003}, pmid = {35809880}, issn = {1096-3650}, mesh = {Humans ; *Glycolysis ; *Neoplasms/pathology ; Mitochondria/metabolism ; Oxygen/metabolism ; Lactic Acid/metabolism ; }, abstract = {Tumors have long been known to rewire their metabolism to endorse their proliferation, growth, survival, and invasiveness. One of the common characteristics of these alterations is the enhanced glucose uptake and its subsequent transformation into lactic acid by means of glycolysis, regardless the availability of oxygen or the mitochondria effectiveness. This phenomenon is called the "Warburg effect", which has turned into a century of age now, since its first disclosure by German physiologist Otto Heinrich Warburg. Since then, this peculiar metabolic switch in tumors has been addressed by extensive studies covering several areas of research. In this historical perspective, we aim at illustrating the evolution of these studies over time and their implication in various fields of science.}, }
@article {pmid35808858, year = {2023}, author = {Cassidy-Hanley, DM and Doerder, FP and Hossain, M and Devine, C and Clark, T}, title = {Molecular identification of Tetrahymena species.}, journal = {The Journal of eukaryotic microbiology}, volume = {70}, number = {1}, pages = {e12936}, pmid = {35808858}, issn = {1550-7408}, support = {P40 OD010964/OD/NIH HHS/United States ; P40 RR019688/RR/NCRR NIH HHS/United States ; }, mesh = {*Tetrahymena/genetics ; Mitochondria/genetics ; DNA, Intergenic/genetics ; Phylogeny ; }, abstract = {Mitochondrial cox1 689 bp barcodes are routinely used for identification of Tetrahymena species. Here, we examine whether two shorter nuclear sequences, the 5.8S rRNA gene region and the intergenic region between H3 and H4 histone genes, might also be useful either singly or in combination with each other or cox1. We obtained sequences from ~300 wild isolates deposited at the Tetrahymena Stock Center and analyzed additional sequences obtained from GenBank. The 5.8S rRNA gene and portions of its transcribed flanks identify isolates as to their major clade and uniquely identify some, but not all, species. The ~330 bp H3/H4 intergenic region possesses low intraspecific variability and is unique for most species. However, it fails to distinguish between two pairs of common species and their rarer counterparts, and its use is complicated by the presence of duplicate genes in some species. The results show that while the cox1 sequence is the best single marker for Tetrahymena species identification, 5.8S rRNA, and the H3/H4 intergenic regions sequences are useful, singly or in combination, to confirm cox1 species assignments or as part of a preliminary survey of newly collected Tetrahymena. From our newly collected isolates, the results extend the biogeographical range of T. shanghaiensis and T. malaccensis and identify a new species, Tetrahymena arleneae n. sp. herein described.}, }
@article {pmid35792646, year = {2022}, author = {Gumińska, N and Milanowski, R}, title = {[Types of circular DNA in Eukarya].}, journal = {Postepy biochemii}, volume = {68}, number = {2}, pages = {129-141}, doi = {10.18388/pb.2021_423}, pmid = {35792646}, issn = {0032-5422}, mesh = {Cell Division ; Cytoplasm ; *DNA, Circular/genetics ; *Eukaryota/genetics ; Mitochondria ; }, abstract = {In eukaryotic cells, DNA occurs mainly in a linear chromosomes. In addition, it can also take the form of circular molecules. Mitochondrial and chloroplast genomes are the most thoroughly studied circular DNAs. However, the repertoire of circular DNA in Eukarya is much broader. It also includes extrachromosomal circular DNA (eccDNA): circular forms of rDNA, telomeric circles, small polydisperse DNA, microDNA, and other types of eccDNA of nuclear origin. The occurrence of eccDNA has been confirmed in all organisms tested so far. Previous studies have shown that some eccDNAs are present at every stage of the cell cycle, while others appear and/or accumulate under specific circumstances. It has been proven that eccDNA accumulation accompanies severe genome destabilization caused by malignancies or stress conditions. Despite growing interest in eccDNA, they remain a poorly understood component of eukaryotic genomes. Still little is known about the mechanisms of their formation, evolution and biological functions.}, }
@article {pmid35780856, year = {2022}, author = {Savu, DI and Moisoi, N}, title = {Mitochondria - Nucleus communication in neurodegenerative disease. Who talks first, who talks louder?.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1863}, number = {7}, pages = {148588}, doi = {10.1016/j.bbabio.2022.148588}, pmid = {35780856}, issn = {1879-2650}, mesh = {*Cell Communication ; Cell Nucleus/genetics ; DNA Damage ; Humans ; Mitochondria/metabolism ; *Neurodegenerative Diseases/metabolism ; }, abstract = {Mitochondria - nuclear coadaptation has been central to eukaryotic evolution. The dynamic dialogue between the two compartments within the context of multiorganellar interactions is critical for maintaining cellular homeostasis and directing the balance survival-death in case of cellular stress. The conceptualisation of mitochondria - nucleus communication has so far been focused on the communication from the mitochondria under stress to the nucleus and the consequent signalling responses, as well as from the nucleus to mitochondria in the context of DNA damage and repair. During ageing processes this dialogue may be better viewed as an integrated bidirectional 'talk' with feedback loops that expand beyond these two organelles depending on physiological cues. Here we explore the current views on mitochondria - nucleus dialogue and its role in maintaining cellular health with a focus on brain cells and neurodegenerative disease. Thus, we detail the transcriptional responses initiated by mitochondrial dysfunction in order to protect itself and the general cellular homeostasis. Additionally, we are reviewing the knowledge of the stress pathways initiated by DNA damage which affect mitochondria homeostasis and we add the information provided by the study of combined mitochondrial and genotoxic damage. Finally, we reflect on how each organelle may take the lead in this dialogue in an ageing context where both compartments undergo accumulation of stress and damage and where, perhaps, even the communications' mechanisms may suffer interruptions.}, }
@article {pmid35776057, year = {2022}, author = {Jardim-Messeder, D and Zamocky, M and Sachetto-Martins, G and Margis-Pinheiro, M}, title = {Chloroplastic ascorbate peroxidases targeted to stroma or thylakoid membrane: The chicken or egg dilemma.}, journal = {FEBS letters}, volume = {596}, number = {23}, pages = {2989-3004}, doi = {10.1002/1873-3468.14438}, pmid = {35776057}, issn = {1873-3468}, support = {304583/2018-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 421551/2018-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; E26/111.234/2014//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; VEGA 2/0012/22//Slovak Grant Agency/ ; APVV-20-0284//Slovak Research and Development Agency/ ; }, mesh = {Ascorbate Peroxidases/genetics/metabolism ; *Thylakoids/metabolism ; Phylogeny ; *Peroxidases/genetics/metabolism ; Chloroplasts/metabolism ; Hydrogen Peroxide/metabolism ; Antioxidants ; Gene Expression Regulation, Plant ; }, abstract = {Ascorbate peroxidases (APXs) are heme peroxidases that remove hydrogen peroxide in different subcellular compartments with concomitant ascorbate cycling. Here, we analysed and discussed phylogenetic and molecular features of the APX family. Ancient APX originated as a soluble stromal enzyme, and early during plant evolution, acquired both chloroplast-targeting and mitochondrion-targeting sequences and an alternative splicing mechanism whereby it could be expressed as a soluble or thylakoid membrane-bound enzyme. Later, independent duplication and neofunctionalization events in some angiosperm groups resulted in individual genes encoding stromal, thylakoidal and mitochondrial isoforms. These data reaffirm the complexity of plant antioxidant defenses that allow diverse plant species to acquire new means to adapt to changing environmental conditions.}, }
@article {pmid35766356, year = {2022}, author = {Mondal, S and Kinatukara, P and Singh, S and Shambhavi, S and Patil, GS and Dubey, N and Singh, SH and Pal, B and Shekar, PC and Kamat, SS and Sankaranarayanan, R}, title = {DIP2 is a unique regulator of diacylglycerol lipid homeostasis in eukaryotes.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35766356}, issn = {2050-084X}, support = {/WT_/Wellcome Trust/United Kingdom ; IA/I/15/2/502058/WTDBT_/DBT-Wellcome Trust India Alliance/India ; }, mesh = {Animals ; *Diglycerides/metabolism ; Homeostasis ; Lipid Metabolism ; Mice ; *Saccharomyces cerevisiae/genetics/metabolism ; Triglycerides/metabolism ; }, abstract = {Chain-length-specific subsets of diacylglycerol (DAG) lipids are proposed to regulate differential physiological responses ranging from signal transduction to modulation of the membrane properties. However, the mechanism or molecular players regulating the subsets of DAG species remain unknown. Here, we uncover the role of a conserved eukaryotic protein family, DISCO-interacting protein 2 (DIP2) as a homeostatic regulator of a chemically distinct subset of DAGs using yeast, fly, and mouse models. Genetic and chemical screens along with lipidomics analysis in yeast reveal that DIP2 prevents the toxic accumulation of specific DAGs in the logarithmic growth phase, which otherwise leads to endoplasmic reticulum stress. We also show that the fatty acyl-AMP ligase-like domains of DIP2 are essential for the redirection of the flux of DAG subspecies to storage lipid, triacylglycerols. DIP2 is associated with vacuoles through mitochondria-vacuole contact sites and such modulation of selective DAG abundance by DIP2 is found to be crucial for optimal vacuole membrane fusion and consequently osmoadaptation in yeast. Thus, the study illuminates an unprecedented DAG metabolism route and provides new insights on how cell fine-tunes DAG subspecies for cellular homeostasis and environmental adaptation.}, }
@article {pmid35764832, year = {2022}, author = {Kurt, F and Kurt, B and Filiz, E and Yildiz, K and Akbudak, MA}, title = {Mitochondrial iron transporter (MIT) gene in potato (Solanum tuberosum): comparative bioinformatics, physiological and expression analyses in response to drought and salinity.}, journal = {Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine}, volume = {35}, number = {5}, pages = {875-887}, pmid = {35764832}, issn = {1572-8773}, mesh = {*Arabidopsis/genetics ; Computational Biology ; Droughts ; Gene Expression Regulation, Plant ; Iron/metabolism ; Membrane Transport Proteins/genetics ; Phylogeny ; Plant Proteins/genetics/metabolism ; Plants/metabolism ; Salinity ; *Solanum tuberosum/genetics/metabolism ; Stress, Physiological/genetics ; }, abstract = {Mitochondrial iron transporter (MIT) genes are essential for mitochondrial acquisition/import of iron and vital to proper functioning of mitochondria. Unlike other organisms, research on the MITs in plants is limited. The present study provides comparative bioinformatics assays for the potato MIT gene (StMIT) as well as gene expression analyses. The phylogenetic analyses revealed monocots-dicot divergence in MIT proteins and it was also found clade specific motif diversity. In addition, docking analyses indicated that Asp172 and Gly100 residues to be identified as the closest residues binding to ferrous iron. The percentage of structure overlap of the StMIT 3D protein model with Arabidopsis, maize and rice MIT proteins was found between 80.18% and 85.71%. The transcript analyses exhibited that the expression of StMIT was triggered under drought and salinity stresses. The findings of the present study would provide valuable leads for further studies targeting specifically the MIT gene and generally the plant iron metabolism.}, }
@article {pmid35764697, year = {2022}, author = {Anderson, L and Camus, MF and Monteith, KM and Salminen, TS and Vale, PF}, title = {Variation in mitochondrial DNA affects locomotor activity and sleep in Drosophila melanogaster.}, journal = {Heredity}, volume = {129}, number = {4}, pages = {225-232}, pmid = {35764697}, issn = {1365-2540}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; *DNA, Mitochondrial/genetics ; Drosophila/genetics ; *Drosophila melanogaster/genetics ; Female ; Locomotion/genetics ; Male ; Mitochondria/genetics ; Sleep/genetics ; }, abstract = {Mitochondria are organelles that produce cellular energy in the form of ATP through oxidative phosphorylation, and this primary function is conserved among many taxa. Locomotion is a trait that is highly reliant on metabolic function and expected to be greatly affected by disruptions to mitochondrial performance. To this end, we aimed to examine how activity and sleep vary between Drosophila melanogaster strains with different geographic origins, how these patterns are affected by mitochondrial DNA (mtDNA) variation, and how breaking up co-evolved mito-nuclear gene combinations affect the studied activity traits. Our results demonstrate that Drosophila strains from different locations differ in sleep and activity, and that females are generally more active than males. By comparing activity and sleep of mtDNA variants introgressed onto a common nuclear background in cytoplasmic hybrid (cybrid) strains, we were able to quantify the among-line variance attributable to mitochondrial DNA, and we establish that mtDNA variation affects both activity and sleep, in a sex-specific manner. Altogether our study highlights the important role that mitochondrial genome variation plays on organismal physiology and behaviour.}, }
@article {pmid35764672, year = {2022}, author = {Jenkins, HL and Graham, R and Porter, JS and Vieira, LM and de Almeida, ACS and Hall, A and O'Dea, A and Coppard, SE and Waeschenbach, A}, title = {Unprecedented frequency of mitochondrial introns in colonial bilaterians.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10889}, pmid = {35764672}, issn = {2045-2322}, mesh = {Animals ; *Gene Transfer, Horizontal ; Introns/genetics ; *Mitochondria/genetics ; Phylogeny ; RNA-Directed DNA Polymerase/genetics ; }, abstract = {Animal mitogenomes are typically devoid of introns. Here, we report the largest number of mitochondrial introns ever recorded from bilaterian animals. Mitochondrial introns were identified for the first time from the phylum Bryozoa. They were found in four species from three families (Order Cheilostomatida). A total of eight introns were found in the complete mitogenome of Exechonella vieirai, and five, 17 and 18 introns were found in the partial mitogenomes of Parantropora penelope, Discoporella cookae and Cupuladria biporosa, respectively. Intron-encoded protein domains reverse transcriptase and intron maturase (RVT-IM) were identified in all species. Introns in E. vieirai and P. penelope had conserved Group II intron ribozyme domains V and VI. Conserved domains were lacking from introns in D. cookae and C. biporosa, preventing their further categorization. Putative origins of metazoan introns were explored in a phylogenetic context, using an up-to-date alignment of mitochondrial RVT-IM domains. Results confirmed previous findings of multiple origins of annelid, placozoan and sponge RVT-IM domains and provided evidence for common intron donor sources across metazoan phyla. Our results corroborate growing evidence that some metazoans with regenerative abilities (i.e. placozoans, sponges, annelids and bryozoans) are susceptible to intron integration, most likely via horizontal gene transfer.}, }
@article {pmid35758251, year = {2022}, author = {Garrido, C and Wollman, FA and Lafontaine, I}, title = {The Evolutionary History of Peptidases Involved in the Processing of Organelle-Targeting Peptides.}, journal = {Genome biology and evolution}, volume = {14}, number = {7}, pages = {}, pmid = {35758251}, issn = {1759-6653}, mesh = {*Chloroplasts/genetics/metabolism ; Mitochondria/genetics/metabolism ; *Peptide Hydrolases/genetics/metabolism ; Peptides/genetics/metabolism ; Proteolysis ; }, abstract = {Most of the proteins present in mitochondria and chloroplasts, the organelles acquired via endosymbiotic events, are encoded in the nucleus and translated into the cytosol. Most of such nuclear-encoded proteins are specifically recognized via an N-terminal-encoded targeting peptide (TP) and imported into the organelles via a translocon machinery. Once imported, the TP is degraded by a succession of cleavage steps ensured by dedicated peptidases. Here, we retrace the evolution of the families of the mitochondrial processing peptidase (MPP), stromal processing peptidase (SPP), presequence protease (PreP), and organellar oligo-peptidase (OOP) that play a central role in TP processing and degradation across the tree of life. Their bacterial distributions are widespread but patchy, revealing unsurprisingly complex history of lateral transfers among bacteria. We provide evidence for the eukaryotic acquisition of MPP, OOP, and PreP by lateral gene transfers from bacteria at the time of the mitochondrial endosymbiosis. We show that the acquisition of SPP and of a second copy of OOP and PreP at the time of the chloroplast endosymbiosis was followed by a differential loss of one PreP paralog in photosynthetic eukaryotes. We identified some contrasting sequence conservations between bacterial and eukaryotic homologs that could reflect differences in the functional context of their peptidase activity. The close vicinity of the eukaryotic peptidases MPP and OOP to those of several bacterial pathogens, showing antimicrobial resistance, supports a scenario where such bacteria were instrumental in the establishment of the proteolytic pathway for TP degradation in organelles. The evidence for their role in the acquisition of PreP is weaker, and none is observed for SPP, although it cannot be excluded by the present study.}, }
@article {pmid35743096, year = {2022}, author = {Ždralević, M and Giannattasio, S}, title = {Mitochondrial Research: Yeast and Human Cells as Models.}, journal = {International journal of molecular sciences}, volume = {23}, number = {12}, pages = {}, pmid = {35743096}, issn = {1422-0067}, mesh = {Humans ; *Mitochondria/metabolism ; Organelles/metabolism ; *Saccharomyces cerevisiae/metabolism ; }, abstract = {The evolution of complex eukaryotes would have been impossible without mitochondria, key cell organelles responsible for the oxidative metabolism of sugars and the bulk of ATP production [...].}, }
@article {pmid35741832, year = {2022}, author = {Solana, JC and Chicharro, C and García, E and Aguado, B and Moreno, J and Requena, JM}, title = {Assembly of a Large Collection of Maxicircle Sequences and Their Usefulness for Leishmania Taxonomy and Strain Typing.}, journal = {Genes}, volume = {13}, number = {6}, pages = {}, pmid = {35741832}, issn = {2073-4425}, mesh = {*Genome, Mitochondrial ; Humans ; *Leishmania infantum/genetics ; *Leishmaniasis ; Phylogeny ; *Trypanosoma ; }, abstract = {Parasites of medical importance, such as Leishmania and Trypanosoma, are characterized by the presence of thousands of circular DNA molecules forming a structure known as kinetoplast, within the mitochondria. The maxicircles, which are equivalent to the mitochondrial genome in other eukaryotes, have been proposed as a promising phylogenetic marker. Using whole-DNA sequencing data, it is also possible to assemble maxicircle sequences as shown here and in previous works. In this study, based on data available in public databases and using a bioinformatics workflow previously reported by our group, we assembled the complete coding region of the maxicircles for 26 prototypical strains of trypanosomatid species. Phylogenetic analysis based on this dataset resulted in a robust tree showing an accurate taxonomy of kinetoplastids, which was also able to discern between closely related Leishmania species that are usually difficult to discriminate by classical methodologies. In addition, we provide a dataset of the maxicircle sequences of 60 Leishmania infantum field isolates from America, Western Europe, North Africa, and Eastern Europe. In agreement with previous studies, our data indicate that L. infantum parasites from Brazil are highly homogeneous and closely related to European strains, which were transferred there during the discovery of America. However, this study showed the existence of different L. infantum populations/clades within the Mediterranean region. A maxicircle signature for each clade has been established. Interestingly, two L. infantum clades were found coexisting in the same region of Spain, one similar to the American strains, represented by the Spanish JPCM5 reference strain, and the other, named "non-JPC like", may be related to an important leishmaniasis outbreak that occurred in Madrid a few years ago. In conclusion, the maxicircle sequence emerges as a robust molecular marker for phylogenetic analysis and species typing within the kinetoplastids, which also has the potential to discriminate intraspecific variability.}, }
@article {pmid35741788, year = {2022}, author = {Hawkins, MTR and Bailey, CA and Brown, AM and Tinsman, J and Hagenson, RA and Culligan, RR and Barela, AG and Randriamanana, JC and Ranaivoarisoa, JF and Zaonarivelo, JR and Louis, EE}, title = {Nuclear and Mitochondrial Phylogenomics of the Sifakas Reveal Cryptic Variation in the Diademed Sifaka.}, journal = {Genes}, volume = {13}, number = {6}, pages = {}, pmid = {35741788}, issn = {2073-4425}, mesh = {Animals ; Ecosystem ; Humans ; *Indriidae/classification ; Mitochondria ; Phylogeny ; Sea Urchins ; }, abstract = {The most comprehensive phylogenomic reconstruction to date was generated on all nominal taxa within the lemur genus Propithecus. Over 200 wild-caught individuals were included in this study to evaluate the intra and interspecific relationships across this genus. Ultraconserved Elements (UCEs) resulted in well-supported phylogenomic trees. Complete mitochondrial genomes (CMGs) largely agreed with the UCEs, except where a mitochondrial introgression was detected between one clade of the diademed sifaka (Propithecus diadema) and the Milne-Edwards sifaka (P. edwardsi). Additionally, the crowned (P. coronatus) and Von der Decken’s (P. deckeni) sifakas belonged to a single admixed lineage from UCEs. Further sampling across these two species is warranted to determine if our sampling represents a hybrid zone. P. diadema recovered two well-supported clades, which were dated and estimated as being ancient as the split between the Perrier’s (P. perrierii) and silky (P. candidus) sifakas. The reconstructed demographic history of the two clades also varied over time. We then modeled the modern ecological niches of the two cryptic P. diadema clades and found that they were significantly diverged (p < 0.01). These ecological differences result in a very limited zone of geographic overlap for the P. diadema clades (<60 km2). Niche models also revealed that the Onive River acts as a potential barrier to dispersal between P. diadema and P. edwardsi. Further taxonomic work is required on P. diadema to determine if its taxonomic status should be revised. This first genomic evaluation of the genus resolved the relationships between the taxa and the recovered cryptic diversity within one species.}, }
@article {pmid35741703, year = {2022}, author = {Orlova, VF and Solovyeva, EN and Dunayev, EA and Ananjeva, NB}, title = {Integrative Taxonomy within Eremias multiocellata Complex (Sauria, Lacertidae) from the Western Part of Range: Evidence from Historical DNA.}, journal = {Genes}, volume = {13}, number = {6}, pages = {}, pmid = {35741703}, issn = {2073-4425}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Lizards/genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The Kokshaal racerunner, Eremias kokshaaliensis Eremchenko et Panfilov, 1999, together with other central Asian racerunner species, is included in the Eremias multiocellata complex. In the present work, for the first time, the results of the analysis of historical mitochondrial DNA (barcode) are presented and the taxonomic status and preliminary phylogenetic relationships within the complex are specified. We present, for the first time, the results of the molecular analysis using historical DNA recovered from specimens of several species of this complex (paratypes of the Kokshaal racerunner and historical collections of the Kashgar racerunner E. buechneri from Kashgaria) using DNA barcoding.}, }
@article {pmid35739999, year = {2022}, author = {Martínez-González, JJ and Guevara-Flores, A and Del Arenal Mena, IP}, title = {Evolutionary Adaptations of Parasitic Flatworms to Different Oxygen Tensions.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {11}, number = {6}, pages = {}, pmid = {35739999}, issn = {2076-3921}, support = {IN217920//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico (DGAPA),UNAM/ ; }, abstract = {During the evolution of the Earth, the increase in the atmospheric concentration of oxygen gave rise to the development of organisms with aerobic metabolism, which utilized this molecule as the ultimate electron acceptor, whereas other organisms maintained an anaerobic metabolism. Platyhelminthes exhibit both aerobic and anaerobic metabolism depending on the availability of oxygen in their environment and/or due to differential oxygen tensions during certain stages of their life cycle. As these organisms do not have a circulatory system, gas exchange occurs by the passive diffusion through their body wall. Consequently, the flatworms developed several adaptations related to the oxygen gradient that is established between the aerobic tegument and the cellular parenchyma that is mostly anaerobic. Because of the aerobic metabolism, hydrogen peroxide (H2O2) is produced in abundance. Catalase usually scavenges H2O2 in mammals; however, this enzyme is absent in parasitic platyhelminths. Thus, the architecture of the antioxidant systems is different, depending primarily on the superoxide dismutase, glutathione peroxidase, and peroxiredoxin enzymes represented mainly in the tegument. Here, we discuss the adaptations that parasitic flatworms have developed to be able to transit from the different metabolic conditions to those they are exposed to during their life cycle.}, }
@article {pmid35730682, year = {2022}, author = {P, K and Chakraborty, B and Rani, V and Koner, AL}, title = {Rationally designed far-red emitting styryl chromones and a magnetic nanoconjugate for strip-based 'on-site' detection of metabolic markers.}, journal = {Journal of materials chemistry. B}, volume = {10}, number = {26}, pages = {5071-5085}, doi = {10.1039/d2tb00879c}, pmid = {35730682}, issn = {2050-7518}, mesh = {*Chromones ; Fluorescent Dyes/chemistry ; Molecular Docking Simulation ; *Nanoconjugates ; Serum Albumin ; Spectrometry, Fluorescence ; }, abstract = {The global burden of liver damage and renal failure necessitates technology-aided evolution towards point-of-care (POC) testing of metabolic markers. Hence in the prevalence of current health conditions, achieving on-site detection and quantifying serum albumin (SA) can contribute significantly to halting the increased mortality and morbidity rate. Herein, we have rationally designed and synthesized far-red emitting, solvatofluorochromic styryl chromone (SC) derivatives SC1 and SC2, and SC2-conjugated fluorescent magnetic nanoparticles (SCNPs) for sensing SA with a fluorogenic response via interacting at an atypical drug binding site. In solution, the highly sensitive and selective fluorogenic response was evaluated by the prominent amplification and blue-shift in the emission maxima of the probes from deep red to dark yellow through an intermediate orange emission. The transformation of the fluorogen into a fluorophore was manifested through spectroscopic measurements. The stabilization of the probes at protein pockets was ascribed to the non-covalent interactions, such as H-bonding, cation-π, and hydrophobic interactions, as unveiled by docking studies. The practical applications revealed the novelty of SC derivatives through (a) the capability to detect SA isolated from real blood samples via a turn-on fluorescence response; (b) the design of a simple, cheap, and portable test-strip using a glass-slide loaded with solid-state emissive SC2, which provided differential emission color of the SC2-HSA complex in solution and the solid-state with increasing concentration of HSA. Moreover, a smartphone-based color analysis application was employed to obtain the ratio of green and red (G/R) channels, which was utilized for quantitative detection of HSA; (c) the biocompatibility of the SC1 was ascertained through confocal laser scanning microscopic imaging (CLSM). Detailed investigation showed that SC1 could entirely localize in the mitochondria and evolve as a promising biomarker for distinguishing cancer cells from normal cells. Additionally, the validation of uncommon binding of SC1 and SC2 between domains I and III was determined using competition experiments with a known site-specific binder and molecular docking studies. This unique property of the probes can be further exploited to understand the cellular intake of HSA-drug complexes in the multifaceted biological system. These results find the utility of SC derivatives as small molecule-based chemosensors for at-home SA detection and as a biomarker for cancer.}, }
@article {pmid35711783, year = {2022}, author = {Della Rocca, G and Papini, A and Posarelli, I and Barberini, S and Tani, C and Danti, R and Moricca, S}, title = {Ultrastructure of Terpene and Polyphenol Synthesis in the Bark of Cupressus sempervirens After Seiridium cardinale Infection.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {886331}, pmid = {35711783}, issn = {1664-302X}, abstract = {Cypress Canker Disease (CCD) pandemic caused by Seiridium cardinale is the major constraint of many Cupressaceae worldwide. One of the main symptoms of the disease is the flow of resin from the cankered barks. While inducible phloem axial resin duct-like structures (PARDs) have recently been characterized from an anatomical point of view, their actual resin production is still being debated and has never been demonstrated. Although the involvement of polyphenolic parenchyma cells (PP cells) in the bark of Cupressus sempervirens after S. cardinale infection was revealed in one of our previous studies using light microscopy, their evolution from the phloem parenchyma cells is yet to be clarified. This study investigated functional and ultrastructural aspects of both PARD-like structures and PP cells by means of more in-depth light (LM) and fluorescence microscopy (FM) combined with histochemical staining (using Sudan red, Fluorol Yellow, NADI Aniline blue black, and Toluidine blue staining), in addition to Transmission Electron Microscope (TEM). Two-year-old stem sections of a C. sempervirens canker-resistant clone (var. "Bolgheri"), artificially inoculated with S. cardinale, were sampled 5, 7, 14, 21, and 45 days after inoculation, for time-course observations. FM observation using Fluorol yellow dye clearly showed the presence of lipid material in PARD-like structures lining cells of the cavity and during their secretion into the duct space/cavity. The same tissues were also positive for NADI staining, revealing the presence of terpenoids. The cytoplasm of the ducts' lining cells was also positive for Sudan red. TEM observation highlighted the involvement of plastids and endoplasmic reticulum in the production of terpenoids and the consequent secretion of terpenoids directly through the plasma membrane, without exhibiting vesicle formation. The presence of a high number of mitochondria around the area of terpenoid production suggests that this process is active and consumes ATP. The LM observations showed that PP cells originated from the phloem parenchyma cells (and possibly albuminous cells) through the accumulation of phenolic substances in the vacuole. Here, plastids were again involved in their production. Thus, the findings of this work suggest that the PARD-like structures can actually be considered PARDs or even bark traumatic resin ducts (BTRD).}, }
@article {pmid35706021, year = {2022}, author = {Wu, B and Hao, W and Cox, MP}, title = {Reconstruction of gene innovation associated with major evolutionary transitions in the kingdom Fungi.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {144}, pmid = {35706021}, issn = {1741-7007}, mesh = {Animals ; *Evolution, Molecular ; *Fungi/genetics ; Gene Transfer, Horizontal ; Phylogeny ; Plants/genetics ; }, abstract = {BACKGROUND: Fungi exhibit astonishing diversity with multiple major phenotypic transitions over the kingdom's evolutionary history. As part of this process, fungi developed hyphae, adapted to land environments (terrestrialization), and innovated their sexual structures. These changes also helped fungi establish ecological relationships with other organisms (animals and plants), but the genomic basis of these changes remains largely unknown.<br><br>RESULTS: By systematically analyzing 304 genomes from all major fungal groups, together with a broad range of eukaryotic outgroups, we have identified 188 novel orthogroups associated with major changes during the evolution of fungi. Functional annotations suggest that many of these orthogroups were involved in the formation of key trait innovations in extant fungi and are functionally connected. These innovations include components for cell wall formation, functioning of the spindle pole body, polarisome formation, hyphal growth, and mating group signaling. Innovation of mitochondria-localized proteins occurred widely during fungal transitions, indicating their previously unrecognized importance. We also find that prokaryote-derived horizontal gene transfer provided a small source of evolutionary novelty with such genes involved in key metabolic pathways.<br><br>CONCLUSIONS: The overall picture is one of a relatively small number of novel genes appearing at major evolutionary transitions in the phylogeny of fungi, with most arising de novo and horizontal gene transfer providing only a small additional source of evolutionary novelty. Our findings contribute to an increasingly detailed portrait of the gene families that define fungal phyla and underpin core features of extant fungi.}, }
@article {pmid35701688, year = {2022}, author = {Zheng, J and Zhao, L and Zhao, X and Gao, T and Song, N}, title = {High Genetic Connectivity Inferred from Whole-Genome Resequencing Provides Insight into the Phylogeographic Pattern of Larimichthys polyactis.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {24}, number = {4}, pages = {671-680}, pmid = {35701688}, issn = {1436-2236}, support = {2018YFD0900905//Key Technologies Research and Development Program/ ; 41806180//Innovative Research Group Project of the National Natural Science Foundation of China/ ; }, mesh = {Animals ; Fishes/genetics ; Gene Flow ; Microsatellite Repeats ; *Perciformes/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Compared with terrestrial biota, marine fishes usually present lower genetic differentiation among different geographical populations because of high-level gene flow and lack of physical barriers. Understanding the genetic structure of marine fishes is essential for dividing management unit and making reasonable protection measures. The small yellow croaker (Larimichthys polyactis) belongs to the family Sciaenidae, which is an economic fish and widely distributed in the Western Pacific. To delineate genetic diversity and phylogeographic pattern, whole-genome resequencing was used to evaluate genetic connectivity, genetic diversity, and spatial pattern of L. polyactis for the first time. We obtained 6,645,711 high-quality single nucleotide polymorphisms (SNPs) markers from 40 L. polyactis individuals. The phylogenetic analysis, STRUCTURE, principal component analysis, and Fst results all indicated that no genetic structure consistent with the distribution pattern was found. This result revealed high genetic connectivity of L. polyactis in different sampling sites. High genetic diversity was also detected, indicating that there was sufficient evolutionary potential to maintain its effective population size. Besides, a similar result of high genetic connectivity and genetic diversity was also detected by mitochondria DNA marker. Our study demonstrated the persistence of high levels of genetic connectivity and a lack of population structure across L. polyactis in different sea areas. This study aimed to analyze the division of population structure and the reason for the decline and not exhaustion of L. polyactis resource on a genetic level.}, }
@article {pmid35699132, year = {2022}, author = {Brischigliaro, M and Cabrera-Orefice, A and Sturlese, M and Elurbe, DM and Frigo, E and Fernandez-Vizarra, E and Moro, S and Huynen, MA and Arnold, S and Viscomi, C and Zeviani, M}, title = {CG7630 is the Drosophila melanogaster homolog of the cytochrome c oxidase subunit COX7B.}, journal = {EMBO reports}, volume = {23}, number = {8}, pages = {e54825}, pmid = {35699132}, issn = {1469-3178}, mesh = {Amino Acid Sequence ; Animals ; *Drosophila melanogaster/genetics/metabolism ; *Electron Transport Complex IV/genetics/metabolism ; Mammals/metabolism ; Mitochondria/genetics/metabolism ; Proteomics ; }, abstract = {The mitochondrial respiratory chain (MRC) is composed of four multiheteromeric enzyme complexes. According to the endosymbiotic origin of mitochondria, eukaryotic MRC derives from ancestral proteobacterial respiratory structures consisting of a minimal set of complexes formed by a few subunits associated with redox prosthetic groups. These enzymes, which are the "core" redox centers of respiration, acquired additional subunits, and increased their complexity throughout evolution. Cytochrome c oxidase (COX), the terminal component of MRC, has a highly interspecific heterogeneous composition. Mammalian COX consists of 14 different polypeptides, of which COX7B is considered the evolutionarily youngest subunit. We applied proteomic, biochemical, and genetic approaches to investigate the COX composition in the invertebrate model Drosophila melanogaster. We identified and characterized a novel subunit which is widely different in amino acid sequence, but similar in secondary and tertiary structures to COX7B, and provided evidence that this object is in fact replacing the latter subunit in virtually all protostome invertebrates. These results demonstrate that although individual structures may differ the composition of COX is functionally conserved between vertebrate and invertebrate species.}, }
@article {pmid35697683, year = {2022}, author = {Paredes, GF and Viehboeck, T and Markert, S and Mausz, MA and Sato, Y and Liebeke, M and König, L and Bulgheresi, S}, title = {Differential regulation of degradation and immune pathways underlies adaptation of the ectosymbiotic nematode Laxus oneistus to oxic-anoxic interfaces.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9725}, pmid = {35697683}, issn = {2045-2322}, support = {P28743-B22/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Chromadorea ; *Chromatiaceae ; Hypoxia ; *Nematoda/microbiology ; Oxygen/metabolism ; Sand ; Sulfides ; Sulfur/metabolism ; }, abstract = {Eukaryotes may experience oxygen deprivation under both physiological and pathological conditions. Because oxygen shortage leads to a reduction in cellular energy production, all eukaryotes studied so far conserve energy by suppressing their metabolism. However, the molecular physiology of animals that naturally and repeatedly experience anoxia is underexplored. One such animal is the marine nematode Laxus oneistus. It thrives, invariably coated by its sulfur-oxidizing symbiont Candidatus Thiosymbion oneisti, in anoxic sulfidic or hypoxic sand. Here, transcriptomics and proteomics showed that, whether in anoxia or not, L. oneistus mostly expressed genes involved in ubiquitination, energy generation, oxidative stress response, immune response, development, and translation. Importantly, ubiquitination genes were also highly expressed when the nematode was subjected to anoxic sulfidic conditions, together with genes involved in autophagy, detoxification and ribosome biogenesis. We hypothesize that these degradation pathways were induced to recycle damaged cellular components (mitochondria) and misfolded proteins into nutrients. Remarkably, when L. oneistus was subjected to anoxic sulfidic conditions, lectin and mucin genes were also upregulated, potentially to promote the attachment of its thiotrophic symbiont. Furthermore, the nematode appeared to survive oxygen deprivation by using an alternative electron carrier (rhodoquinone) and acceptor (fumarate), to rewire the electron transfer chain. On the other hand, under hypoxia, genes involved in costly processes (e.g., amino acid biosynthesis, development, feeding, mating) were upregulated, together with the worm's Toll-like innate immunity pathway and several immune effectors (e.g., bactericidal/permeability-increasing proteins, fungicides). In conclusion, we hypothesize that, in anoxic sulfidic sand, L. oneistus upregulates degradation processes, rewires the oxidative phosphorylation and reinforces its coat of bacterial sulfur-oxidizers. In upper sand layers, instead, it appears to produce broad-range antimicrobials and to exploit oxygen for biosynthesis and development.}, }
@article {pmid35695456, year = {2022}, author = {Jiang, X and Coroian, D and Barahona, E and Echavarri-Erasun, C and Castellanos-Rueda, R and Eseverri, &#xc1; and Aznar-Moreno, JA and Burén, S and Rubio, LM}, title = {Functional Nitrogenase Cofactor Maturase NifB in Mitochondria and Chloroplasts of Nicotiana benthamiana.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0026822}, pmid = {35695456}, issn = {2150-7511}, mesh = {*Archaeal Proteins/genetics ; *Azotobacter vinelandii/genetics ; Bacterial Proteins/metabolism ; Chloroplasts/genetics/metabolism ; Fertilizers ; Iron Compounds/*metabolism ; Mitochondria/metabolism ; Nitrogen/metabolism ; Nitrogen Fixation/genetics ; Nitrogenase/genetics/metabolism ; Phylogeny ; Nicotiana/genetics/metabolism ; }, abstract = {Engineering plants to synthesize nitrogenase and assimilate atmospheric N2 will reduce crop dependency on industrial N fertilizers. This technology can be achieved by expressing prokaryotic nitrogen fixation gene products for the assembly of a functional nitrogenase in plants. NifB is a critical nitrogenase component since it catalyzes the first committed step in the biosynthesis of all types of nitrogenase active-site cofactors. Here, we used a library of 30 distinct nifB sequences originating from different phyla and ecological niches to restore diazotrophic growth of an Azotobacter vinelandii nifB mutant. Twenty of these variants rescued the nifB mutant phenotype despite their phylogenetic distance to A. vinelandii. Because multiple protein interactions are required in the iron-molybdenum cofactor (FeMo-co) biosynthetic pathway, the maturation of nitrogenase in a heterologous host can be divided in independent modules containing interacting proteins that function together to produce a specific intermediate. Therefore, nifB functional modules composed of a nifB variant, together with the A. vinelandii NifS and NifU proteins (for biosynthesis of NifB [Fe4S4] clusters) and the FdxN ferredoxin (for NifB function), were expressed in Nicotiana benthamiana chloroplasts and mitochondria. Three archaeal NifB proteins accumulated at high levels in soluble fractions of chloroplasts (Methanosarcina acetivorans and Methanocaldococcus infernus) or mitochondria (M. infernus and Methanothermobacter thermautotrophicus). These NifB proteins were shown to accept [Fe4S4] clusters from NifU and were functional in FeMo-co synthesis in vitro. The accumulation of significant levels of soluble and functional NifB proteins in chloroplasts and mitochondria is critical to engineering biological nitrogen fixation in plants. IMPORTANCE Biological nitrogen fixation is the conversion of inert atmospheric dinitrogen gas into nitrogen-reactive ammonia, a reaction catalyzed by the nitrogenase enzyme of diazotrophic bacteria and archaea. Because plants cannot fix their own nitrogen, introducing functional nitrogenase in cereals and other crop plants would reduce our strong dependency on N fertilizers. NifB is required for the biosynthesis of the active site cofactors of all nitrogenases, which arguably makes it the most important protein in global nitrogen fixation. NifB functionality is therefore a requisite to engineer a plant nitrogenase. The expression of nifB genes from a wide range of prokaryotes into the model diazotroph Azotobacter vinelandii shows a surprising level of genetic complementation suggestive of plasticity in the nitrogenase biosynthetic pathway. In addition, we obtained NifB proteins from both mitochondria and chloroplasts of tobacco that are functional in vitro after reconstitution by providing [Fe4S4] clusters from NifU, paving the way to nitrogenase cofactor biosynthesis in plants.}, }
@article {pmid35688936, year = {2022}, author = {Groux, K and Verschueren, A and Nanteau, C and Clémençon, M and Fink, M and Sahel, JA and Boccara, C and Paques, M and Reichman, S and Grieve, K}, title = {Dynamic full-field optical coherence tomography allows live imaging of retinal pigment epithelium stress model.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {575}, pmid = {35688936}, issn = {2399-3642}, mesh = {Animals ; Fluorescein Angiography ; Humans ; *Macular Degeneration/metabolism ; Mitochondria ; *Retinal Pigment Epithelium/metabolism ; Swine ; Tomography, Optical Coherence/methods ; }, abstract = {Retinal degenerative diseases lead to the blindness of millions of people around the world. In case of age-related macular degeneration (AMD), the atrophy of retinal pigment epithelium (RPE) precedes neural dystrophy. But as crucial as understanding both healthy and pathological RPE cell physiology is for those diseases, no current technique allows subcellular in vivo or in vitro live observation of this critical cell layer. To fill this gap, we propose dynamic full-field OCT (D-FFOCT) as a candidate for live observation of in vitro RPE phenotype. In this way, we monitored primary porcine and human stem cell-derived RPE cells in stress model conditions by performing scratch assays. In this study, we quantified wound healing parameters on the stressed RPE, and observed different cell phenotypes, displayed by the D-FFOCT signal. In order to decipher the subcellular contributions to these dynamic profiles, we performed immunohistochemistry to identify which organelles generate the signal and found mitochondria to be the main contributor to D-FFOCT contrast. Altogether, D-FFOCT appears to be an innovative method to follow degenerative disease evolution and could be an appreciated method in the future for live patient diagnostics and to direct treatment choice.}, }
@article {pmid35683389, year = {2022}, author = {Ruiz, D and Santibañez, M and Lavín, BA and Berja, A and Montalban, C and Vazquez, LA}, title = {Evolution of Mitochondrially Derived Peptides Humanin and MOTSc, and Changes in Insulin Sensitivity during Early Gestation in Women with and without Gestational Diabetes.}, journal = {Journal of clinical medicine}, volume = {11}, number = {11}, pages = {}, pmid = {35683389}, issn = {2077-0383}, abstract = {Our purpose is to study the evolution of mitochondrially derived peptides (MDPs) and their relationship with changes in insulin sensitivity from the early stages of pregnancy in a cohort of pregnant women with and without gestational diabetes (GDM). MDPs (humanin and MOTSc) were assessed in the first and second trimesters of gestation in 28 pregnant women with gestational diabetes mellitus (GDM) and a subgroup of 45 pregnant women without GDM matched by BMI, age, previous gestations, and time of sampling. Insulin resistance (IR) was defined as a HOMA-IR index ≥70th percentile. We observed a significant reduction in both humanin and MOTSc levels from the first to the second trimesters of pregnancy. After adjusting for predefined variables, including BMI, statistically nonsignificant associations between lower levels of humanin and the occurrence of a high HOMA-IR index were obtained (adjusted OR = 2.63 and 3.14 for the first and second trimesters, linear p-trend 0.260 and 0.175, respectively). Regarding MOTSc, an association was found only for the second trimester: adjusted OR = 7.68 (95% CI 1.49-39.67), linear p-trend = 0.012. No significant associations were observed in humanin change with insulin resistance throughout pregnancy, but changes in MOTSc levels were significantly associated with HOMA-IR index: adjusted OR 3.73 (95% CI 1.03-13.50). In conclusion, MOTSc levels, especially a strong decrease from the first to second trimester of gestation, may be involved in increasing insulin resistance during early gestation.}, }
@article {pmid35682820, year = {2022}, author = {Cartalas, J and Coudray, L and Gobert, A}, title = {How RNases Shape Mitochondrial Transcriptomes.}, journal = {International journal of molecular sciences}, volume = {23}, number = {11}, pages = {}, pmid = {35682820}, issn = {1422-0067}, mesh = {Endoribonucleases/metabolism ; Eukaryota/genetics/metabolism ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/metabolism ; RNA/metabolism ; *Ribonucleases/metabolism ; *Transcriptome ; }, abstract = {Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.}, }
@article {pmid35682809, year = {2022}, author = {Eugenin, E and Camporesi, E and Peracchia, C}, title = {Direct Cell-Cell Communication via Membrane Pores, Gap Junction Channels, and Tunneling Nanotubes: Medical Relevance of Mitochondrial Exchange.}, journal = {International journal of molecular sciences}, volume = {23}, number = {11}, pages = {}, pmid = {35682809}, issn = {1422-0067}, support = {MH128082//National Institute of Mental Health/ ; NS105584//National Institute of Neurological Disorders and Stroke/ ; }, mesh = {Animals ; Cell Communication/physiology ; Cell Membrane Structures ; *Gap Junctions/metabolism ; Ion Channels/metabolism ; Mitochondria ; *Nanotubes/chemistry ; }, abstract = {The history of direct cell-cell communication has evolved in several small steps. First discovered in the 1930s in invertebrate nervous systems, it was thought at first to be an exception to the "cell theory", restricted to invertebrates. Surprisingly, however, in the 1950s, electrical cell-cell communication was also reported in vertebrates. Once more, it was thought to be an exception restricted to excitable cells. In contrast, in the mid-1960s, two startling publications proved that virtually all cells freely exchange small neutral and charged molecules. Soon after, cell-cell communication by gap junction channels was reported. While gap junctions are the major means of cell-cell communication, in the early 1980s, evidence surfaced that some cells might also communicate via membrane pores. Questions were raised about the possible artifactual nature of the pores. However, early in this century, we learned that communication via membrane pores exists and plays a major role in medicine, as the structures involved, "tunneling nanotubes", can rescue diseased cells by directly transferring healthy mitochondria into compromised cells and tissues. On the other hand, pathogens/cancer could also use these communication systems to amplify pathogenesis. Here, we describe the evolution of the discovery of these new communication systems and the potential therapeutic impact on several uncurable diseases.}, }
@article {pmid35673874, year = {2022}, author = {Tassé, M and Choquette, T and Angers, A and Stewart, DT and Pante, E and Breton, S}, title = {The longest mitochondrial protein in metazoans is encoded by the male-transmitted mitogenome of the bivalve Scrobicularia plana.}, journal = {Biology letters}, volume = {18}, number = {6}, pages = {20220122}, pmid = {35673874}, issn = {1744-957X}, mesh = {Amino Acids/genetics/metabolism ; Animals ; *Bivalvia/genetics/metabolism ; Cyclooxygenase 2/genetics/metabolism ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; Male ; Mitochondrial Proteins/genetics ; }, abstract = {Cytochrome c oxidase subunit II (COX2) is one of the three mitochondrially encoded proteins of the complex IV of the respiratory chain that catalyses the reduction of oxygen to water. The cox2 gene spans about 690 base pairs in most animal species and produces a protein composed of approximately 230 amino acids. We discovered an extreme departure from this pattern in the male-transmitted mitogenome of the bivalve Scrobicularia plana with doubly uniparental inheritance (DUI) of mitochondrial DNA (mtDNA), which possesses an important in-frame insertion of approximately 4.8 kb in its cox2 gene. This feature-an enlarged male cox2 gene-is found in many species with DUI; the COX2 protein can be up to 420 amino acids long. Through RT-PCRs, immunoassays and comparative genetics, the evolution and functionality of this insertion in S. plana were characterized. The in-frame insertion is conserved among individuals from different populations and bears the signature of purifying selection seemingly indicating maintenance of functionality. Its transcription and translation were confirmed: this gene produces a polypeptide of 1892 amino acids, making it the largest metazoan COX2 protein known to date. We hypothesize that these extreme modifications in the COX2 protein affect the metabolism of mitochondria containing the male-transmitted mtDNA in Scrobicularia plana.}, }
@article {pmid35670055, year = {2022}, author = {Choudhury, S and Ananthanarayanan, V and Ayappa, KG}, title = {Coupling of mitochondrial population evolution to microtubule dynamics in fission yeast cells: a kinetic Monte Carlo study.}, journal = {Soft matter}, volume = {18}, number = {23}, pages = {4483-4492}, doi = {10.1039/d2sm00155a}, pmid = {35670055}, issn = {1744-6848}, mesh = {Kinetics ; Microtubules/metabolism ; Mitochondria ; Monte Carlo Method ; *Schizosaccharomyces/genetics ; }, abstract = {Mitochondrial populations in cells are maintained by cycles of fission and fusion events. Perturbation of this balance has been observed in several diseases such as cancer and neurodegeneration. In fission yeast cells, the association of mitochondria with microtubules inhibits mitochondrial fission [Mehta et al., J. Biol. Chem., 2019, 294, 3385], illustrating the intricate coupling between mitochondria and the dynamic population of microtubules within the cell. In order to understand this coupling, we carried out kinetic Monte Carlo (KMC) simulations to predict the evolution of mitochondrial size distributions for different cases; wild-type cells, cells with short and long microtubules, and cells without microtubules. Comparisons are made with mitochondrial distributions reported in experiments with fission yeast cells. Using experimentally determined mitochondrial fission and fusion frequencies, simulations implemented without the coupling of microtubule dynamics predicted an increase in the mean number of mitochondria, equilibrating within 50 s. The mitochondrial length distribution in these models also showed a higher occurrence of shorter mitochondria, implying a greater tendency for fission, similar to the scenario observed in the absence of microtubules and cells with short microtubules. Interestingly, this resulted in overestimating the mean number of mitochondria and underestimating mitochondrial lengths in cells with wild-type and long microtubules. However, coupling mitochondria's fission and fusion events to the microtubule dynamics effectively captured the mitochondrial number and size distributions in wild-type and cells with long microtubules. Thus, the model provides greater physical insight into the temporal evolution of mitochondrial populations in different microtubule environments, allowing one to study both the short-time evolution as observed in the experiments (<5 minutes) as well as their transition towards a steady-state (>15 minutes). Our study illustrates the critical role of microtubules in mitochondrial dynamics and coupling microtubule growth and shrinkage dynamics is critical to predicting the evolution of mitochondrial populations within the cell.}, }
@article {pmid35666201, year = {2022}, author = {Simon, M and Durand, S and Ricou, A and Vrielynck, N and Mayjonade, B and Gouzy, J and Boyer, R and Roux, F and Camilleri, C and Budar, F}, title = {APOK3, a pollen killer antidote in Arabidopsis thaliana.}, journal = {Genetics}, volume = {221}, number = {4}, pages = {}, pmid = {35666201}, issn = {1943-2631}, mesh = {Alleles ; Antidotes/metabolism ; *Arabidopsis/genetics/metabolism ; *Poisons/metabolism ; Pollen/genetics ; }, abstract = {The principles of heredity state that the two alleles carried by a heterozygote are equally transmitted to the progeny. However, genomic regions that escape this rule have been reported in many organisms. It is notably the case of genetic loci referred to as gamete killers, where one allele enhances its transmission by causing the death of the gametes that do not carry it. Gamete killers are of great interest, particularly to understand mechanisms of evolution and speciation. Although being common in plants, only a few, all in rice, have so far been deciphered to the causal genes. Here, we studied a pollen killer found in hybrids between two accessions of Arabidopsis thaliana. Exploring natural variation, we observed this pollen killer in many crosses within the species. Genetic analyses revealed that three genetically linked elements are necessary for pollen killer activity. Using mutants, we showed that this pollen killer works according to a poison-antidote model, where the poison kills pollen grains not producing the antidote. We identified the gene encoding the antidote, a chimeric protein addressed to mitochondria. De novo genomic sequencing in 12 natural variants with different behaviors regarding the pollen killer revealed a hyper variable locus, with important structural variations particularly in killer genotypes, where the antidote gene recently underwent duplications. Our results strongly suggest that the gene has newly evolved within A. thaliana. Finally, we identified in the protein sequence polymorphisms related to its antidote activity.}, }
@article {pmid35661419, year = {2022}, author = {Dawson, NJ and Scott, GR}, title = {Adaptive increases in respiratory capacity and O2 affinity of subsarcolemmal mitochondria from skeletal muscle of high-altitude deer mice.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {36}, number = {7}, pages = {e22391}, doi = {10.1096/fj.202200219R}, pmid = {35661419}, issn = {1530-6860}, mesh = {*Altitude ; Animals ; Hypoxia ; Mitochondria ; Mitochondria, Muscle ; Muscle, Skeletal ; *Peromyscus/physiology ; }, abstract = {Aerobic energy demands have led to the evolution of complex mitochondrial reticula in highly oxidative muscles, but the extent to which metabolic challenges can be met with adaptive changes in physiology of specific mitochondrial fractions remains unresolved. We examined mitochondrial mechanisms supporting adaptive increases in aerobic performance in deer mice (Peromyscus maniculatus) adapted to the hypoxic environment at high altitude. High-altitude and low-altitude mice were born and raised in captivity, and exposed as adults to normoxia or hypobaric hypoxia (12 kPa O2 for 6-8 weeks). Subsarcolemmal and intermyofibrillar mitochondria were isolated from the gastrocnemius, and a comprehensive substrate titration protocol was used to examine mitochondrial physiology and O2 kinetics by high-resolution respirometry and fluorometry. High-altitude mice had greater yield, respiratory capacity for oxidative phosphorylation, and O2 affinity (lower P50) of subsarcolemmal mitochondria compared to low-altitude mice across environments, but there were no species difference in these traits in intermyofibrillar mitochondria. High-altitude mice also had greater capacities of complex II relative to complexes I + II and higher succinate dehydrogenase activities in both mitochondrial fractions. Exposure to chronic hypoxia reduced reactive oxygen species (ROS) emission in high-altitude mice but not in low-altitude mice. Our findings suggest that functional changes in subsarcolemmal mitochondria contribute to improving aerobic performance in hypoxia in high-altitude deer mice. Therefore, physiological variation in specific mitochondrial fractions can help overcome the metabolic challenges of life at high altitude.}, }
@article {pmid35654156, year = {2022}, author = {Hautekiet, P and Saenen, ND and Aerts, R and Martens, DS and Roels, HA and Bijnens, EM and Nawrot, TS}, title = {Higher buccal mtDNA content is associated with residential surrounding green in a panel study of primary school children.}, journal = {Environmental research}, volume = {213}, number = {}, pages = {113551}, doi = {10.1016/j.envres.2022.113551}, pmid = {35654156}, issn = {1096-0953}, mesh = {Child ; *DNA, Mitochondrial/genetics ; Ethnicity ; Humans ; Mitochondria ; *Parks, Recreational ; Residence Characteristics ; Schools ; }, abstract = {BACKGROUND: Mitochondria are known to respond to environmental stressors but whether green space is associated with mitochondrial abundance is unexplored. Furthermore, as exposures may affect health from early life onwards, we here evaluate if residential green space is associated with mitochondria DNA content (mtDNAc) in children.<br><br>METHODS: In primary schoolchildren (COGNAC study), between 2012 and 2014, buccal mtDNAc was repeatedly (three times) assessed using qPCR. Surrounding low (<3m), high (&#x2265;3m) and total (sum of low and high) green space within different radii (100m-1000m) from the residence and distance to the nearest large green space (>0.5ha) were estimated using a remote sensing derived map. Given the repeated measures design, we applied a mixed-effects model with school and subject as random effect while adjusting for a priori chosen fixed covariates.<br><br>RESULTS: mtDNAc was assessed in 246 children with a total of 436 measurements (mean age 10.3 years). Within a 1000m radius around the residential address, an IQR increment in low (11.0%), high (9.5%), and total (13.9%) green space was associated with a respectively 15.2% (95% CI: 7.2%-23.7%), 10.8% (95% CI: 4.5%-17.5%), and 13.4% (95% CI: 7.4%-19.7%) higher mtDNAc. Conversely, an IQR increment (11.6%) in agricultural area in the same radius was associated with a -3.4% (95% CI: 6.7% to -0.1%) lower mtDNAc. Finally, a doubling in distance to large green space was associated with a -5.2% (95% CI: 7.9 to -2.4%) lower mtDNAc.<br><br>CONCLUSION: To our knowledge, this is the first study evaluating associations between residential surrounding green space and mtDNAc in children. Our results showed that green space was associated with a higher mtDNAc in children, which indicates the importance of the early life environment. To what extent these findings contribute to later life health effects should be further examined.}, }
@article {pmid35642316, year = {2022}, author = {Bremer, N and Tria, FDK and Skejo, J and Garg, SG and Martin, WF}, title = {Ancestral State Reconstructions Trace Mitochondria But Not Phagocytosis to the Last Eukaryotic Common Ancestor.}, journal = {Genome biology and evolution}, volume = {14}, number = {6}, pages = {}, pmid = {35642316}, issn = {1759-6653}, support = {101018894/ERC_/European Research Council/International ; }, mesh = {Animals ; *Biological Evolution ; *Eukaryota/genetics ; Eukaryotic Cells/physiology ; Mitochondria/genetics ; Phagocytosis/physiology ; Phylogeny ; Symbiosis/genetics ; }, abstract = {Two main theories have been put forward to explain the origin of mitochondria in eukaryotes: phagotrophic engulfment (undigested food) and microbial symbiosis (physiological interactions). The two theories generate mutually exclusive predictions about the order in which mitochondria and phagocytosis arose. To discriminate the alternatives, we have employed ancestral state reconstructions (ASR) for phagocytosis as a trait, phagotrophy as a feeding habit, the presence of mitochondria, the presence of plastids, and the multinucleated organization across major eukaryotic lineages. To mitigate the bias introduced by assuming a particular eukaryotic phylogeny, we reconstructed the appearance of these traits across 1789 different rooted gene trees, each having species from opisthokonts, mycetozoa, hacrobia, excavate, archeplastida, and Stramenopiles, Alveolates and Rhizaria. The trees reflect conflicting relationships and different positions of the root. We employed a novel phylogenomic test that summarizes ASR across trees which reconstructs a last eukaryotic common ancestor that possessed mitochondria, was multinucleated, lacked plastids, and was non-phagotrophic as well as non-phagocytic. This indicates that both phagocytosis and phagotrophy arose subsequent to the origin of mitochondria, consistent with findings from comparative physiology. Furthermore, our ASRs uncovered multiple origins of phagocytosis and of phagotrophy across eukaryotes, indicating that, like wings in animals, these traits are useful but neither ancestral nor homologous across groups. The data indicate that mitochondria preceded the origin of phagocytosis, such that phagocytosis cannot have been the mechanism by which mitochondria were acquired.}, }
@article {pmid35639693, year = {2022}, author = {Calatrava, V and Stephens, TG and Gabr, A and Bhaya, D and Bhattacharya, D and Grossman, AR}, title = {Retrotransposition facilitated the establishment of a primary plastid in the thecate amoeba Paulinella.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {23}, pages = {e2121241119}, pmid = {35639693}, issn = {1091-6490}, mesh = {*Amoeba/genetics ; *Biological Evolution ; Eukaryota/genetics ; Plastids/genetics ; *Rhizaria ; *Symbiosis/genetics ; }, abstract = {The evolution of eukaryotic life was predicated on the development of organelles such as mitochondria and plastids. During this complex process of organellogenesis, the host cell and the engulfed prokaryote became genetically codependent, with the integration of genes from the endosymbiont into the host nuclear genome and subsequent gene loss from the endosymbiont. This process required that horizontally transferred genes become active and properly regulated despite inherent differences in genetic features between donor (endosymbiont) and recipient (host). Although this genetic reorganization is considered critical for early stages of organellogenesis, we have little knowledge about the mechanisms governing this process. The photosynthetic amoeba Paulinella micropora offers a unique opportunity to study early evolutionary events associated with organellogenesis and primary endosymbiosis. This amoeba harbors a “chromatophore,” a nascent photosynthetic organelle derived from a relatively recent cyanobacterial association (∼120 million years ago) that is independent of the evolution of primary plastids in plants (initiated ∼1.5 billion years ago). Analysis of the genome and transcriptome of Paulinella revealed that retrotransposition of endosymbiont-derived nuclear genes was critical for their domestication in the host. These retrocopied genes involved in photoprotection in cyanobacteria became expanded gene families and were “rewired,” acquiring light-responsive regulatory elements that function in the host. The establishment of host control of endosymbiont-derived genes likely enabled the cell to withstand photo-oxidative stress generated by oxygenic photosynthesis in the nascent organelle. These results provide insights into the genetic mechanisms and evolutionary pressures that facilitated the metabolic integration of the host–endosymbiont association and sustained the evolution of a photosynthetic organelle.}, }
@article {pmid35638362, year = {2022}, author = {Li, M and Chen, WT and Zhang, QL and Liu, M and Xing, CW and Cao, Y and Luo, FZ and Yuan, ML}, title = {Mitochondrial phylogenomics provides insights into the phylogeny and evolution of spiders (Arthropoda: Araneae).}, journal = {Zoological research}, volume = {43}, number = {4}, pages = {566-584}, pmid = {35638362}, issn = {2095-8137}, mesh = {Animals ; *Arthropods ; *Genome, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Transfer/genetics ; *Spiders/genetics ; }, abstract = {Spiders are among the most varied terrestrial predators, with highly diverse morphology, ecology, and behavior. Morphological and molecular data have greatly contributed to advances in the phylogeny and evolutionary dynamics of spiders. Here, we performed comprehensive mitochondrial phylogenomics analysis on 78 mitochondrial genomes (mitogenomes) representing 29 families; of these, 23 species from eight families were newly generated. Mesothelae retained the same gene arrangement as the arthropod ancestor (Limulus polyphemus), while Opisthothelae showed extensive rearrangement, with 12 rearrangement types in transfer RNAs (tRNAs) and control region. Most spider tRNAs were extremely truncated and lacked typical dihydrouridine or TΨC arms, showing high tRNA structural diversity; in particular, trnS1 exhibited anticodon diversity across the phylogeny. The evolutionary rates of mitochondrial genes were potentially associated with gene rearrangement or truncated tRNAs. Both mitogenomic sequences and rearrangements possessed phylogenetic characteristics, providing a robust backbone for spider phylogeny, as previously reported. The monophyly of suborder, infraorder, retrolateral tibial apophysis clade, and families (except for Pisauridae) was separately supported, and high-level relationships were resolved as (Mesothelae, (Mygalomorphae, (Entelegynae, (Synspermiata, Hypochilidae)))). The phylogenetic positions of several families were also resolved (e.g., Eresidae, Oecobiidae and Titanoecidae). Two reconstructions of ancestral web type obtained almost identical results, indicating that the common ancestor of spiders likely foraged using a silk-lined burrow. This study, the largest mitochondrial phylogenomics analysis of spiders to date, highlights the usefulness of mitogenomic data not only for providing efficient phylogenetic signals for spider phylogeny, but also for characterizing trait diversification in spider evolution.}, }
@article {pmid35637201, year = {2022}, author = {Kodama, Y and Fujishima, M}, title = {Endosymbiotic Chlorella variabilis reduces mitochondrial number in the ciliate Paramecium bursaria.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8216}, pmid = {35637201}, issn = {2045-2322}, mesh = {Antibodies, Monoclonal/metabolism ; *Chlorella/metabolism ; Mitochondria ; *Paramecium/metabolism ; Symbiosis ; }, abstract = {Extant symbioses illustrate endosymbiosis is a driving force for evolution and diversification. In the ciliate Paramecium bursaria, the endosymbiotic alga Chlorella variabilis in perialgal vacuole localizes beneath the host cell cortex by adhesion between the perialgal vacuole membrane and host mitochondria. We investigated whether host mitochondria are also affected by algal endosymbiosis. Transmission electron microscopy of host cells showed fewer mitochondria beneath the algae-bearing host cell cortex than that of alga-free cells. To compare the density and distribution of host mitochondria with or without symbiotic algae, we developed a monoclonal antibody against Paramecium mitochondria. Immunofluorescence microscopy with the monoclonal antibody showed that the mitochondrial density of the algae-bearing P. bursaria was significantly lower than that of the alga-free cells. The total cell protein concentration of alga-free P. bursaria cells was approximately 1.8-fold higher than that of algae-bearing cells, and the protein content of mitochondria was significantly higher in alga-free cells than that in the algae-bearing cells. These results corresponded with those obtained by transmission electron and immunofluorescence microscopies. This paper shows that endosymbiotic algae affect reduced mitochondrial number in the host P. bursaria significantly.}, }
@article {pmid35636077, year = {2022}, author = {Jiang, YJ and Jin, J and Nan, QY and Ding, J and Cui, S and Xuan, MY and Piao, MH and Piao, SG and Zheng, HL and Jin, JZ and Chung, BH and Yang, CW and Li, C}, title = {Coenzyme Q10 attenuates renal fibrosis by inhibiting RIP1-RIP3-MLKL-mediated necroinflammation via Wnt3α/β-catenin/GSK-3β signaling in unilateral ureteral obstruction.}, journal = {International immunopharmacology}, volume = {108}, number = {}, pages = {108868}, doi = {10.1016/j.intimp.2022.108868}, pmid = {35636077}, issn = {1878-1705}, mesh = {Animals ; Fibrosis ; Glycogen Synthase Kinase 3 beta ; Hydrogen Peroxide/pharmacology ; Intracellular Signaling Peptides and Proteins/metabolism ; Kidney/pathology ; *Kidney Diseases/drug therapy/pathology ; Protein Kinases/metabolism ; Rats ; Receptor-Interacting Protein Serine-Threonine Kinases/metabolism ; Ubiquinone/analogs &amp; derivatives ; *Ureteral Obstruction/drug therapy ; beta Catenin ; }, abstract = {OBJECTIVE: Coenzyme Q10 (CoQ10) protects against various types of injury, but its role in preventing renal scarring in chronic kidney disease remains an open question. Herein, we evaluated whether CoQ10 attenuates renal fibrosis by interfering with necroinflammation in a rat model of unilateral ureteral obstruction (UUO) and in vitro.<br><br>METHODS: Rats with UUO were treated daily with CoQ10 or an RIP inhibitor (necrostatin-1 or GSK872) for 7&#xa0;days. The influence of CoQ10 on renal injury caused by UUO was evaluated by histopathology and analysis of gene expression, oxidative stress, intracellular organelles, apoptosis, and Wnt3&#x3b1;/&#x3b2;-catenin/GSK-3&#x3b2; signaling&#xb7;H2O2-exposed human kidney (HK-2) cells were also examined after treatment with CoQ10 or an RIP inhibitor.<br><br>RESULTS: UUO induced marked renal tubular necrosis, upregulation of RIP1-RIP3-MLKL axis proteins, activation of the NLRP3 inflammasome, and evolution of renal fibrosis. UUO-induced oxidative stress evoked excessive endoplasmic reticulum stress and mitochondrial dysfunction, which triggered apoptotic cell death through Wnt3&#x3b1;/&#x3b2;-catenin/GSK-3&#x3b2; signaling. All of these effects were mitigated by CoQ10 or an RIP inhibitor. In H2O2-treated HK-2 cells, CoQ10 or an RIP inhibitor suppressed the expression of RIP1-RIP3-MLKL proteins and pyroptosis-related cytokines, and hindered the production of intracellular reactive oxygen species as shown by MitoSOX Red staining and apoptotic cell death but increased cell viability. The CoQ10 or Wnt/&#x3b2;-catenin inhibitor ICG-001 deactivated H2O2-stimulated activation of Wnt3&#x3b1;/&#x3b2;-catenin/GSK-3&#x3b2; signaling.<br><br>CONCLUSION: These findings suggest that CoQ10 attenuates renal fibrosis by inhibiting RIP1-RIP3-MLKL-mediated necroinflammation via Wnt3&#x3b1;/&#x3b2;-catenin/GSK-3&#x3b2; signaling in UUO.}, }
@article {pmid35633884, year = {2022}, author = {Zhang, L and Liu, K and Zhuan, Q and Liu, Z and Meng, L and Fu, X and Jia, G and Hou, Y}, title = {Mitochondrial Calcium Disorder Affects Early Embryonic Development in Mice through Regulating the ERK/MAPK Pathway.}, journal = {Oxidative medicine and cellular longevity}, volume = {2022}, number = {}, pages = {8221361}, pmid = {35633884}, issn = {1942-0994}, mesh = {Animals ; *Calcium/metabolism ; *Embryonic Development ; *MAP Kinase Signaling System ; Mice ; Mitochondria/metabolism ; *Mitogen-Activated Protein Kinases/metabolism ; Oocytes/metabolism ; }, abstract = {The homeostasis of mitochondrial calcium ([Ca[2+]]mt) in oocytes plays a critical role in maintaining normal reproductive cellular progress such as meiosis. However, little is known about the association between [Ca[2+]]mt homeostasis and early embryonic development. Two in vitro mouse MII oocyte models were established by using a specific agonist or inhibitor targeting mitochondrial calcium uniporters (MCU) to upregulate or downregulate [Ca[2+]]mt concentrations. The imbalance of [Ca[2+]]mt in MII oocytes causes mitochondrial dysfunction and morphological abnormity, leading to an abnormal spindle/chromosome structure. Oocytes in drug-treated groups are less likely to develop into blastocyst during in vitro culture. Abnormal [Ca[2+]]mt concentrations in oocytes hindered epigenetic modification and regulated mitogen-activated protein kinase (MAPK) signaling that is associated with gene expression. We also found that MAPK/ERK signaling is regulating DNA methylation in MII oocytes to modulate epigenetic modification. These data provide a new insight into the protective role of [Ca[2+]]mt homeostasis in early embryonic development and also demonstrate a new mechanism of MAPK signaling regulated by [Ca[2+]]mt that influences epigenetic modification.}, }
@article {pmid35630799, year = {2022}, author = {Xie, DM and Zhang, Q and Xin, LK and Wang, GK and Liu, CB and Qin, MJ}, title = {Cloning and Functional Characterization of Two Germacrene A Oxidases Isolated from Xanthium sibiricum.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {10}, pages = {}, pmid = {35630799}, issn = {1420-3049}, support = {81503190//Dongmei Xie/ ; 2021hxts22//Dongmei Xie/ ; }, mesh = {Cloning, Molecular ; Oxidoreductases/metabolism ; Phylogeny ; Plant Proteins/metabolism ; Sesquiterpenes, Germacrane ; *Xanthium/genetics ; }, abstract = {Sesquiterpene lactones (STLs) from the cocklebur Xanthium sibiricum exhibit significant anti-tumor activity. Although germacrene A oxidase (GAO), which catalyzes the production of Germacrene A acid (GAA) from germacrene A, an important precursor of germacrene-type STLs, has been reported, the remaining GAOs corresponding to various STLs' biosynthesis pathways remain unidentified. In this study, 68,199 unigenes were studied in a de novo transcriptome assembly of X. sibiricum fruits. By comparison with previously published GAO sequences, two candidate X. sibiricum GAO gene sequences, XsGAO1 (1467 bp) and XsGAO2 (1527 bp), were identified, cloned, and predicted to encode 488 and 508 amino acids, respectively. Their protein structure, motifs, sequence similarity, and phylogenetic position were similar to those of other GAO proteins. They were most strongly expressed in fruits, according to a quantitative real-time polymerase chain reaction (qRT-PCR), and both XsGAO proteins were localized in the mitochondria of tobacco leaf epidermal cells. The two XsGAO genes were cloned into the expression vector for eukaryotic expression in Saccharomyces cerevisiae, and the enzyme reaction products were detected by gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) methods. The results indicated that both XsGAO1 and XsGAO2 catalyzed the two-step conversion of germacrene A (GA) to GAA, meaning they are unlike classical GAO enzymes, which catalyze a three-step conversion of GA to GAA. This cloning and functional study of two GAO genes from X. sibiricum provides a useful basis for further elucidation of the STL biosynthesis pathway in X. sibiricum.}, }
@article {pmid35627195, year = {2022}, author = {Popadin, K and Gunbin, K and Peshkin, L and Annis, S and Fleischmann, Z and Franco, M and Kraytsberg, Y and Markuzon, N and Ackermann, RR and Khrapko, K}, title = {Mitochondrial Pseudogenes Suggest Repeated Inter-Species Hybridization among Direct Human Ancestors.}, journal = {Genes}, volume = {13}, number = {5}, pages = {}, pmid = {35627195}, issn = {2073-4425}, support = {R01-HD091439/NH/NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; *Hominidae/genetics ; Humans ; Hybridization, Genetic ; Mitochondria/genetics ; *Pseudogenes/genetics ; }, abstract = {The hypothesis that the evolution of humans involves hybridization between diverged species has been actively debated in recent years. We present the following novel evidence in support of this hypothesis: the analysis of nuclear pseudogenes of mtDNA ("NUMTs"). NUMTs are considered "mtDNA fossils" as they preserve sequences of ancient mtDNA and thus carry unique information about ancestral populations. Our comparison of a NUMT sequence shared by humans, chimpanzees, and gorillas with their mtDNAs implies that, around the time of divergence between humans and chimpanzees, our evolutionary history involved the interbreeding of individuals whose mtDNA had diverged as much as ~4.5 Myr prior. This large divergence suggests a distant interspecies hybridization. Additionally, analysis of two other NUMTs suggests that such events occur repeatedly. Our findings suggest a complex pattern of speciation in primate/human ancestors and provide one potential explanation for the mosaic nature of fossil morphology found at the emergence of the hominin lineage. A preliminary version of this manuscript was uploaded to the preprint server BioRxiv in 2017 (10.1101/134502).}, }
@article {pmid35626633, year = {2022}, author = {Eyenga, P and Rey, B and Eyenga, L and Sheu, SS}, title = {Regulation of Oxidative Phosphorylation of Liver Mitochondria in Sepsis.}, journal = {Cells}, volume = {11}, number = {10}, pages = {}, pmid = {35626633}, issn = {2073-4409}, mesh = {Adenosine Triphosphate/metabolism ; Electron Transport Complex IV/metabolism ; Humans ; Mitochondria, Liver/metabolism ; *Oxidative Phosphorylation ; *Sepsis/metabolism ; }, abstract = {The link between liver dysfunction and decreased mitochondrial oxidative phosphorylation in sepsis has been clearly established in experimental models. Energy transduction is plastic: the efficiency of mitochondrial coupling collapses in the early stage of sepsis but is expected to increase during the recovery phases of sepsis. Among the mechanisms regulating the coupling efficiency of hepatic mitochondria, the slipping reactions at the cytochrome oxidase and ATP synthase seem to be a determining element, whereas other regulatory mechanisms such as those involving proton leakage across the mitochondrial membrane have not yet been formally proven in the context of sepsis. If the dysfunction of hepatic mitochondria is related to impaired cytochrome c oxidase and ATP synthase functions, we need to consider therapeutic avenues to restore their activities for recovery from sepsis. In this review, we discussed previous findings regarding the regulatory mechanism involved in changes in the oxidative phosphorylation of liver mitochondria in sepsis, and propose therapeutic avenues to improve the functions of cytochrome c oxidase and ATP synthase in sepsis.}, }
@article {pmid35614856, year = {2022}, author = {Xu, JJ and Hu, M and Yang, L and Chen, XY}, title = {How plants synthesize coenzyme Q.}, journal = {Plant communications}, volume = {3}, number = {5}, pages = {100341}, pmid = {35614856}, issn = {2590-3462}, mesh = {Mitochondria/metabolism ; Oxidation-Reduction ; *Plants/genetics/metabolism ; *Ubiquinone/metabolism ; }, abstract = {Coenzyme Q (CoQ) is a conserved redox-active lipid that has a wide distribution across the domains of life. CoQ plays a key role in the oxidative electron transfer chain and serves as a crucial antioxidant in cellular membranes. Our understanding of CoQ biosynthesis in eukaryotes has come mostly from studies of yeast. Recently, significant advances have been made in understanding CoQ biosynthesis in plants. Unique mitochondrial flavin-dependent monooxygenase and benzenoid ring precursor biosynthetic pathways have been discovered, providing new insights into the diversity of CoQ biosynthetic pathways and the evolution of phototrophic eukaryotes. We summarize research progress on CoQ biosynthesis and regulation in plants and recent efforts to increase the CoQ content in plant foods.}, }
@article {pmid35609548, year = {2022}, author = {Schärer, L}, title = {Evolution: Mitochondrial lodgers can take over in hermaphroditic snails.}, journal = {Current biology : CB}, volume = {32}, number = {10}, pages = {R477-R479}, doi = {10.1016/j.cub.2022.04.039}, pmid = {35609548}, issn = {1879-0445}, mesh = {Animals ; Cytoplasm ; *Hermaphroditic Organisms ; *Mitochondria ; *Snails ; }, abstract = {Mitochondria - the cell's power stations - are inherited uniparentally via eggs, not sperm. In hermaphroditic plants, they sometimes prevent their hosts from making pollen (and sperm), causing cytoplasmic male sterility. New evidence from a hermaphroditic freshwater snail now documents cytoplasmic male sterility in animals.}, }
@article {pmid35596716, year = {2022}, author = {Yu, G and Nakajima, K and Gruber, A and Rio Bartulos, C and Schober, AF and Lepetit, B and Yohannes, E and Matsuda, Y and Kroth, PG}, title = {Mitochondrial phosphoenolpyruvate carboxylase contributes to carbon fixation in the diatom Phaeodactylum tricornutum at low inorganic carbon concentrations.}, journal = {The New phytologist}, volume = {235}, number = {4}, pages = {1379-1393}, doi = {10.1111/nph.18268}, pmid = {35596716}, issn = {1469-8137}, mesh = {Bicarbonates/metabolism ; Carbon/metabolism ; Carbon Cycle ; Carbon Dioxide/metabolism/pharmacology ; *Diatoms/metabolism ; Mitochondria/metabolism ; Phosphoenolpyruvate Carboxylase/genetics/metabolism ; Photosynthesis ; }, abstract = {Photosynthetic carbon fixation is often limited by CO2 availability, which led to the evolution of CO2 concentrating mechanisms (CCMs). Some diatoms possess CCMs that employ biochemical fixation of bicarbonate, similar to C4 plants, but whether biochemical CCMs are commonly found in diatoms is a subject of debate. In the diatom Phaeodactylum tricornutum, phosphoenolpyruvate carboxylase (PEPC) is present in two isoforms, PEPC1 in the plastids and PEPC2 in the mitochondria. We used real-time quantitative polymerase chain reaction, Western blots, and enzymatic assays to examine PEPC expression and PEPC activity, under low and high concentrations of dissolved inorganic carbon (DIC). We generated and analyzed individual knockout cell lines of PEPC1 and PEPC2, as well as a PEPC1/2 double-knockout strain. While we could not detect an altered phenotype in the PEPC1 knockout strains at ambient, low or high DIC concentrations, PEPC2 and the double-knockout strains grown under ambient air or lower DIC availability conditions showed reduced growth and photosynthetic affinity for DIC while behaving similarly to wild-type (WT) cells at high DIC concentrations. These mutants furthermore exhibited significantly lower [13] C/[12] C ratios compared to the WT. Our data imply that in P. tricornutum at least parts of the CCM rely on biochemical bicarbonate fixation catalyzed by the mitochondrial PEPC2.}, }
@article {pmid35588086, year = {2022}, author = {Santos, HJ and Nozaki, T}, title = {The mitosome of the anaerobic parasitic protist Entamoeba histolytica: A peculiar and minimalist mitochondrion-related organelle.}, journal = {The Journal of eukaryotic microbiology}, volume = {69}, number = {6}, pages = {e12923}, pmid = {35588086}, issn = {1550-7408}, support = {JP20fk0108138//Japan Agency for Medical Research and Development/ ; JP18H02650//Japan Society for the Promotion of Science/ ; JP20K16233//Japan Society for the Promotion of Science/ ; JP21H02723//Japan Society for the Promotion of Science/ ; JPJSCCB20190010//Japan Society for the Promotion of Science/ ; }, mesh = {Humans ; Anaerobiosis ; *Entamoeba histolytica/metabolism ; Membrane Proteins/metabolism ; *Mitochondria/metabolism ; *Organelles/metabolism ; }, abstract = {The simplest class of mitochondrion-related organelles (MROs) is the mitosome, an organelle present in a few anaerobic protozoan parasites such as Entamoeba histolytica, Giardia intestinalis, and Cryptosporidium parvum. E. histolytica causes amoebiasis in humans, deemed as one of the important, yet neglected tropical infections in the world. Much of the enigma of the E. histolytica mitosome circles around the obvious lack of a majority of known mitochondrial components and functions exhibited in other organisms. The identification of enzymes responsible for sulfate activation (AS, IPP, and APSK) and a number of lineage-specific proteins such as the outer membrane beta-barrel protein (MBOMP30), and transmembrane domain-containing proteins that bind to various organellar proteins (ETMP1, ETMP30, EHI_170120, and EHI_099350) showcased the remarkable divergence of this organelle compared to the other MROs of anaerobic protozoa. Here, we summarize the findings regarding the biology of the mitosomes in E. histolytica, from their discovery up to the present understanding of its roles and interactions. We also include current advances and future perspectives on the biology, biochemistry, and evolution of the mitosomes of E. histolytica.}, }
@article {pmid35587988, year = {2022}, author = {Huynen, MA and Elurbe, DM}, title = {Mitochondrial complex complexification.}, journal = {Science (New York, N.Y.)}, volume = {376}, number = {6595}, pages = {794-795}, doi = {10.1126/science.abq0368}, pmid = {35587988}, issn = {1095-9203}, mesh = {*Electron Transport Complex I/chemistry/genetics ; *Electron Transport Complex IV/chemistry/genetics ; Evolution, Molecular ; *Mitochondria/enzymology ; Oxidative Phosphorylation ; Protein Subunits/chemistry/genetics ; *Tetrahymena thermophila/enzymology ; }, abstract = {Variation in complex composition provides clues about the function of individual subunits.}, }
@article {pmid35585601, year = {2022}, author = {Vujovic, F and Hunter, N and Farahani, RM}, title = {Notch ankyrin domain: evolutionary rise of a thermodynamic sensor.}, journal = {Cell communication and signaling : CCS}, volume = {20}, number = {1}, pages = {66}, pmid = {35585601}, issn = {1478-811X}, mesh = {Animals ; *Ankyrins/chemistry/metabolism ; Mice ; *Neural Stem Cells/chemistry/metabolism ; Phylogeny ; Protein Domains ; *Receptors, Notch/chemistry/metabolism ; Signal Transduction ; Thermodynamics ; }, abstract = {Notch signalling pathway plays a key role in metazoan biology by contributing to resolution of binary decisions in the life cycle of cells during development. Outcomes such as proliferation/differentiation dichotomy are resolved by transcriptional remodelling that follows a switch from Notch[on] to Notch[off] state, characterised by dissociation of Notch intracellular domain (NICD) from DNA-bound RBPJ. Here we provide evidence that transitioning to the Notch[off] state is regulated by heat flux, a phenomenon that aligns resolution of fate dichotomies to mitochondrial activity. A combination of phylogenetic analysis and computational biochemistry was utilised to disclose structural adaptations of Notch1 ankyrin domain that enabled function as a sensor of heat flux. We then employed DNA-based micro-thermography to measure heat flux during brain development, followed by analysis in vitro of the temperature-dependent behaviour of Notch1 in mouse neural progenitor cells. The structural capacity of NICD to operate as a thermodynamic sensor in metazoans stems from characteristic enrichment of charged acidic amino acids in β-hairpins of the ankyrin domain that amplify destabilising inter-residue electrostatic interactions and render the domain thermolabile. The instability emerges upon mitochondrial activity which raises the perinuclear and nuclear temperatures to 50 °C and 39 °C, respectively, leading to destabilization of Notch1 transcriptional complex and transitioning to the Notch[off] state. Notch1 functions a metazoan thermodynamic sensor that is switched on by intercellular contacts, inputs heat flux as a proxy for mitochondrial activity in the Notch[on] state via the ankyrin domain and is eventually switched off in a temperature-dependent manner. Video abstract.}, }
@article {pmid35584780, year = {2022}, author = {da Silva E Silva, LH and da Silva, FS and Medeiros, DBA and Cruz, ACR and da Silva, SP and Aragão, AO and Dias, DD and Sena do Nascimento, BL and Júnior, JWR and Vieira, DBR and Monteiro, HAO and Neto, JPN}, title = {Description of the mitogenome and phylogeny of Aedes spp. (Diptera: Culicidae) from the Amazon region.}, journal = {Acta tropica}, volume = {232}, number = {}, pages = {106500}, doi = {10.1016/j.actatropica.2022.106500}, pmid = {35584780}, issn = {1873-6254}, mesh = {*Aedes ; Animals ; *Culicidae/genetics ; *Genome, Mitochondrial/genetics ; Mosquito Vectors/genetics ; Phylogeny ; *Zika Virus/genetics ; *Zika Virus Infection ; }, abstract = {The genus Aedes (Diptera: Culicidae) includes species of great epidemiological relevance, particularly involved in transmission cycles of leading arboviruses in the Brazilian Amazon region, such as the Zika virus (ZIKV), Dengue virus (DENV), Yellow fever virus (YFV), and Chikungunya virus (CHIKV). We report here the first putatively complete sequencing of the mitochondrial genomes of Brazilian populations of the species Aedes albopictus, Aedes scapularis and Aedes serratus. The sequences obtained showed an average length of 14,947 bp, comprising 37 functional subunits, typical in animal mitochondria (13 PCGs, 22 tRNA, and 2 rRNA). The phylogeny reconstructed by Maximum likelihood method, based on the concatenated sequences of all 13 PCGs produced at least two non-directly related groupings, composed of representatives of the subgenus Ochlerotatus and Stegomyia of the genus Aedes. The data and information produced here may be useful for future taxonomic and evolutionary studies of the genus Aedes, as well as the Culicidae family.}, }
@article {pmid35580923, year = {2022}, author = {Maldonado, JA and Firneno, TJ and Hall, AS and Fujita, MK}, title = {Parthenogenesis doubles the rate of amino acid substitution in whiptail mitochondria.}, journal = {Evolution; international journal of organic evolution}, volume = {76}, number = {7}, pages = {1434-1442}, doi = {10.1111/evo.14509}, pmid = {35580923}, issn = {1558-5646}, mesh = {Amino Acid Substitution ; *Genome, Mitochondrial ; Humans ; Male ; Mitochondria/genetics ; Mutation ; Parthenogenesis/genetics ; Phylogeny ; *Reproduction, Asexual/genetics ; }, abstract = {Sexual reproduction is ubiquitous in the natural world, suggesting that sex must have extensive benefits to overcome the cost of males compared to asexual reproduction. One hypothesized advantage of sex with strong theoretical support is that sex plays a role in removing deleterious mutations from the genome. Theory predicts that transitions to asexuality should lead to the suppression of recombination and segregation and, in turn, weakened natural selection, allowing for the accumulation of slightly deleterious mutations. We tested this prediction by estimating the dN/dS ratios in asexual vertebrate lineages in the genus Aspidoscelis using whole mitochondrial genomes from seven asexual and five sexual species. We found higher dN/dS ratios in asexual Aspidoscelis species, indicating that asexual whiptails accumulate nonsynonymous substitutions due to weaker purifying selection. Additionally, we estimated nucleotide diversity and found that asexuals harbor significantly less diversity. Thus, despite their recent origins, slightly deleterious mutations accumulated rapidly enough in asexual lineages to be detected. We provide empirical evidence to corroborate the connection between asexuality and increased amino acid substitutions in asexual vertebrate lineages.}, }
@article {pmid35580797, year = {2022}, author = {Sandamalika, WMG and Udayantha, HMV and Liyanage, DS and Lim, C and Kim, G and Kwon, H and Lee, J}, title = {Identification of reactive oxygen species modulator 1 (Romo 1) from black rockfish (Sebastes schlegelii) and deciphering its molecular characteristics, immune responses, oxidative stress modulation, and wound healing properties.}, journal = {Fish &amp; shellfish immunology}, volume = {125}, number = {}, pages = {266-275}, doi = {10.1016/j.fsi.2022.05.026}, pmid = {35580797}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; *Bass ; DNA, Complementary/genetics ; Female ; Fish Proteins/chemistry ; Immunity, Innate/genetics ; Lipopolysaccharides/metabolism/pharmacology ; Male ; Mammals/genetics/metabolism ; Oxidative Stress ; *Perciformes ; Phylogeny ; Reactive Oxygen Species ; Sequence Alignment ; Wound Healing ; }, abstract = {Reactive oxygen species modulator 1 (Romo1) is a mitochondrial inner membrane protein that induces mitochondrial reactive oxygen species (ROS) generation. In this study, we identified the Romo1 homolog from the black rockfish (Sebastes schlegelii), named it as SsRomo1, and characterized it at the molecular as well as functional levels. An open reading frame consisting of 240 bp was identified in the SsRomo1 complementary DNA (cDNA) sequence that encodes a 79 amino acid-long polypeptide with a molecular weight of 8,293 Da and a theoretical isoelectric point (pI) of 9.89. The in silico analysis revealed the characteristic features of SsRomo1, namely the presence of a transmembrane domain and the lack of a signal peptide. Homology analysis revealed that SsRomo1 exhibits the highest sequence identity with its fish counterparts (>93%) and shares a similar percentage of sequence identity with mammals (>92%). Additionally, it is closely clustered together with the fish clade in the constructed phylogenetic tree. The subcellular localization analysis confirmed its mitochondrial localization within the fathead minnow (FHM) cells. Under normal physiological conditions, the SsRomo1 mRNA is highly expressed in the rockfish ovary, followed by the blood and testis, indicating the abundance of mitochondria in these tissues. Furthermore, the significant upregulation of SsRomo1 in cells treated with lipopolysachharide (LPS), polyinosinic:polycytidylic acid, and Streptococcus iniae suggest that the increased ROS production is induced by SsRomo1 to eliminate pathogens during infections. Incidentally, we believe that this study is the first to determine the involvement of SsRomo1 in LPS-mediated nitric oxide (NO) production in RAW267.4 cells, based on their higher NO production as compared to that in the control. Moreover, overexpression of SsRomo1 enhanced the wound healing ability of FHM cells, indicating its high invasion and migration properties. We also determined the hydrogen peroxide-mediated cell viability of SsRomo1-overexpressed FHM cells and observed a significant reduction in viability, which is possibly due to increased ROS production. Collectively, our observations suggest that SsRomo1 plays an important role in oxidative stress modulation upon immune stimulation and in maintenance of tissue homeostasis in black rockfish.}, }
@article {pmid35577958, year = {2022}, author = {Bates, M and Keller-Findeisen, J and Przybylski, A and Hüper, A and Stephan, T and Ilgen, P and Cereceda Delgado, AR and D'Este, E and Egner, A and Jakobs, S and Sahl, SJ and Hell, SW}, title = {Optimal precision and accuracy in 4Pi-STORM using dynamic spline PSF models.}, journal = {Nature methods}, volume = {19}, number = {5}, pages = {603-612}, pmid = {35577958}, issn = {1548-7105}, mesh = {Animals ; Artifacts ; *Lenses ; Mammals ; Microscopy ; Optical Imaging ; *Single Molecule Imaging ; }, abstract = {Coherent fluorescence imaging with two objective lenses (4Pi detection) enables single-molecule localization microscopy with sub-10 nm spatial resolution in three dimensions. Despite its outstanding sensitivity, wider application of this technique has been hindered by complex instrumentation and the challenging nature of the data analysis. Here we report the development of a 4Pi-STORM microscope, which obtains optimal resolution and accuracy by modeling the 4Pi point spread function (PSF) dynamically while also using a simpler optical design. Dynamic spline PSF models incorporate fluctuations in the modulation phase of the experimentally determined PSF, capturing the temporal evolution of the optical system. Our method reaches the theoretical limits for precision and minimizes phase-wrapping artifacts by making full use of the information content of the data. 4Pi-STORM achieves a near-isotropic three-dimensional localization precision of 2-3 nm, and we demonstrate its capabilities by investigating protein and nucleic acid organization in primary neurons and mammalian mitochondria.}, }
@article {pmid35577294, year = {2022}, author = {Xu, X and Yu, L and Li, F and Wang, B and Liu, F and Li, D}, title = {Phylogenetic placement and species delimitation of the crab spider genus Phrynarachne (Araneae: Thomisidae) from China.}, journal = {Molecular phylogenetics and evolution}, volume = {173}, number = {}, pages = {107521}, doi = {10.1016/j.ympev.2022.107521}, pmid = {35577294}, issn = {1095-9513}, mesh = {Animals ; China ; Mitochondria/genetics ; Phylogeny ; *Spiders/genetics ; }, abstract = {Evolutionary biologists have long been fascinated by the striking resemblance to bird droppings of the sit-and-wait crab spiders of the genus Phrynarachne. In doing so, species of Phrynarachne have evolved not to avoid detection, but rather, to cause predators to misidentify them as inedible and/or inanimate bird droppings. However, the lack of a phylogeny for Phrynarachne impedes our understanding of the evolution of this trait in the genus. Here we explore species boundaries in species of Phrynarachne from China using single- and multi-locus species delimitation approaches based on 30 Phrynarachne samples. All species delimitation approaches supported six species of Phrynarachne in China. We further present the first phylogenetic analysis of the genus Phrynarachne and estimate divergence times using two mitochondrial and three nuclear genes. All of our phylogenetic analyses supported the monophyly of Phrynarachne in China, with the genus still included within the higher 'Thomisus group' based on our results. Our dating analyses place the crown age of Phrynarachne in China to the middle Miocene. Taken together, our study provides a time-calibrated phylogeny of the genus Phrynarachne in China for testing hypotheses regarding the evolution of the lineage and bird dropping masquerade.}, }
@article {pmid35575078, year = {2022}, author = {Lee, J and Willett, CS}, title = {Frequent Paternal Mitochondrial Inheritance and Rapid Haplotype Frequency Shifts in Copepod Hybrids.}, journal = {The Journal of heredity}, volume = {113}, number = {2}, pages = {171-183}, doi = {10.1093/jhered/esab068}, pmid = {35575078}, issn = {1465-7333}, support = {IOS-1155325//National Science Foundation/ ; //University of North Carolina at Chapel Hill/ ; }, mesh = {Animals ; *Copepoda/genetics ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Mitochondria are assumed to be maternally inherited in most animal species, and this foundational concept has fostered advances in phylogenetics, conservation, and population genetics. Like other animals, mitochondria were thought to be solely maternally inherited in the marine copepod Tigriopus californicus, which has served as a useful model for studying mitonuclear interactions, hybrid breakdown, and environmental tolerance. However, we present PCR, Sanger sequencing, and Illumina Nextera sequencing evidence that extensive paternal mitochondrial DNA (mtDNA) transmission is occurring in inter-population hybrids of T. californicus. PCR on four types of crosses between three populations (total sample size of 376 F1 individuals) with 20% genome-wide mitochondrial divergence showed 2% to 59% of F1 hybrids with both paternal and maternal mtDNA, where low and high paternal leakage values were found in different cross directions of the same population pairs. Sequencing methods further verified nucleotide similarities between F1 mtDNA and paternal mtDNA sequences. Interestingly, the paternal mtDNA in F1s from some crosses inherited haplotypes that were uncommon in the paternal population. Compared to some previous research on paternal leakage, we employed more rigorous methods to rule out contamination and false detection of paternal mtDNA due to non-functional nuclear mitochondrial DNA fragments. Our results raise the potential that other animal systems thought to only inherit maternal mitochondria may also have paternal leakage, which would then affect the interpretation of past and future population genetics or phylogenetic studies that rely on mitochondria as uniparental markers.}, }
@article {pmid35563133, year = {2022}, author = {Bonturi, CR and Silva Teixeira, AB and Rocha, VM and Valente, PF and Oliveira, JR and Filho, CMB and Fátima Correia Batista, I and Oliva, MLV}, title = {Plant Kunitz Inhibitors and Their Interaction with Proteases: Current and Potential Pharmacological Targets.}, journal = {International journal of molecular sciences}, volume = {23}, number = {9}, pages = {}, pmid = {35563133}, issn = {1422-0067}, support = {2017/06630-7 and 2019/22243-9//S&#xe3;o Paulo Research Foundation/ ; Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; 301721/2016-5//National Council for Scientific and Technological Development/ ; }, mesh = {Endopeptidases ; Fungi/metabolism ; Humans ; *Plants/metabolism ; *Protease Inhibitors/chemistry/pharmacology/therapeutic use ; Serine Proteases/metabolism ; }, abstract = {The action of proteases can be controlled by several mechanisms, including regulation through gene expression; post-translational modifications, such as glycosylation; zymogen activation; targeting specific compartments, such as lysosomes and mitochondria; and blocking proteolysis using endogenous inhibitors. Protease inhibitors are important molecules to be explored for the control of proteolytic processes in organisms because of their ability to act on several proteases. In this context, plants synthesize numerous proteins that contribute to protection against attacks by microorganisms (fungi and bacteria) and/or invertebrates (insects and nematodes) through the inhibition of proteases in these organisms. These proteins are widely distributed in the plant kingdom, and are present in higher concentrations in legume seeds (compared to other organs and other botanical families), motivating studies on their inhibitory effects in various organisms, including humans. In most cases, the biological roles of these proteins have been assigned based mostly on their in vitro action, as is the case with enzyme inhibitors. This review highlights the structural evolution, function, and wide variety of effects of plant Kunitz protease inhibitors, and their potential for pharmaceutical application based on their interactions with different proteases.}, }
@article {pmid35547863, year = {2021}, author = {Benz, R}, title = {Historical Perspective of Pore-Forming Activity Studies of Voltage-Dependent Anion Channel (Eukaryotic or Mitochondrial Porin) Since Its Discovery in the 70th of the Last Century.}, journal = {Frontiers in physiology}, volume = {12}, number = {}, pages = {734226}, pmid = {35547863}, issn = {1664-042X}, abstract = {Eukaryotic porin, also known as Voltage-Dependent Anion Channel (VDAC), is the most frequent protein in the outer membrane of mitochondria that are responsible for cellular respiration. Mitochondria are most likely descendants of strictly aerobic Gram-negative bacteria from the α-proteobacterial lineage. In accordance with the presumed ancestor, mitochondria are surrounded by two membranes. The mitochondrial outer membrane contains besides the eukaryotic porins responsible for its major permeability properties a variety of other not fully identified channels. It encloses also the TOM apparatus together with the sorting mechanism SAM, responsible for the uptake and assembly of many mitochondrial proteins that are encoded in the nucleus and synthesized in the cytoplasm at free ribosomes. The recognition and the study of electrophysiological properties of eukaryotic porin or VDAC started in the late seventies of the last century by a study of Schein et al., who reconstituted the pore from crude extracts of Paramecium mitochondria into planar lipid bilayer membranes. Whereas the literature about structure and function of eukaryotic porins was comparatively rare during the first 10years after the first study, the number of publications started to explode with the first sequencing of human Porin 31HL and the recognition of the important function of eukaryotic porins in mitochondrial metabolism. Many genomes contain more than one gene coding for homologs of eukaryotic porins. More than 100 sequences of eukaryotic porins are known to date. Although the sequence identity between them is relatively low, the polypeptide length and in particular, the electrophysiological characteristics are highly preserved. This means that all eukaryotic porins studied to date are anion selective in the open state. They are voltage-dependent and switch into cation-selective substates at voltages in the physiological relevant range. A major breakthrough was also the elucidation of the 3D structure of the eukaryotic pore, which is formed by 19 β-strands similar to those of bacterial porin channels. The function of the presumed gate an α-helical stretch of 20 amino acids allowed further studies with respect to voltage dependence and function, but its exact role in channel gating is still not fully understood.}, }
@article {pmid35543999, year = {2022}, author = {Corsaro, D}, title = {Insights into Microsporidia Evolution from Early Diverging Microsporidia.}, journal = {Experientia supplementum (2012)}, volume = {114}, number = {}, pages = {71-90}, pmid = {35543999}, issn = {1664-431X}, mesh = {Animals ; Fungi ; *Microsporidia/genetics ; *Parasites ; Phylogeny ; }, abstract = {Microsporidia have drastically modified genomes and cytology resulting from their high level of adaptation to intracytoplasmic parasitism. Their origins, which had long remained enigmatic, were placed within the line of Rozella, a primitive endoparasitic chytrid. These origins became more and more refined with the discovery of various parasites morphologically similar to the primitive lines of microsporidia (Metchnikovellids and Chytridiopsids) but which possess fungal-like genomes and functional mitochondria. These various parasites turn out to be distinct missing links between a large assemblage of chytrid-like rozellids and the true microsporidians, which are actually a very evolved branch of the rozellids themselves. The question of how to consider the historically known Microsporidia and the various microsporidia-like organisms within paraphyletic rozellids is discussed.}, }
@article {pmid35508562, year = {2022}, author = {Kidd, KK and Evsanaa, B and Togtokh, A and Brissenden, JE and Roscoe, JM and Dogan, M and Neophytou, PI and Gurkan, C and Bulbul, O and Cherni, L and Speed, WC and Murtha, M and Kidd, JR and Pakstis, AJ}, title = {North Asian population relationships in a global context.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {7214}, pmid = {35508562}, issn = {2045-2322}, mesh = {*Asian People/genetics ; Ethnicity/genetics ; Genetic Variation ; *Genetics, Population ; Haplotypes ; Humans ; Phylogeny ; Principal Component Analysis ; }, abstract = {Population genetic studies of North Asian ethnic groups have focused on genetic variation of sex chromosomes and mitochondria. Studies of the extensive variation available from autosomal variation have appeared infrequently. We focus on relationships among population samples using new North Asia microhaplotype data. We combined genotypes from our laboratory on 58 microhaplotypes, distributed across 18 autosomes, on 3945 individuals from 75 populations with corresponding data extracted for 26 populations from the Thousand Genomes consortium and for 22 populations from the GenomeAsia 100 K project. A total of 7107 individuals in 122 total populations are analyzed using STRUCTURE, Principal Component Analysis, and phylogenetic tree analyses. North Asia populations sampled in Mongolia include: Buryats, Mongolians, Altai Kazakhs, and Tsaatans. Available Siberians include samples of Yakut, Khanty, and Komi Zyriane. Analyses of all 122 populations confirm many known relationships and show that most populations from North Asia form a cluster distinct from all other groups. Refinement of analyses on smaller subsets of populations reinforces the distinctiveness of North Asia and shows that the North Asia cluster identifies a region that is ancestral to Native Americans.}, }
@article {pmid35504558, year = {2022}, author = {Zhou, W and Zhao, Z and Yu, Z and Hou, Y and Keerthiga, R and Fu, A}, title = {Mitochondrial transplantation therapy inhibits the proliferation of malignant hepatocellular carcinoma and its mechanism.}, journal = {Mitochondrion}, volume = {65}, number = {}, pages = {11-22}, doi = {10.1016/j.mito.2022.04.004}, pmid = {35504558}, issn = {1872-8278}, mesh = {Animals ; Apoptosis ; *Carcinoma, Hepatocellular/metabolism/pathology/therapy ; Cell Line, Tumor ; Cell Proliferation ; Female ; *Liver Neoplasms/metabolism/pathology/therapy ; Male ; Mice ; Mitochondria/metabolism ; }, abstract = {Mitochondrial dysfunction plays a vital role in growth and malignancy of tumors. In recent scenarios, mitochondrial transplantation therapy is considered as an effective method to remodel mitochondrial function in mitochondria-related diseases. However, the mechanism by which mitochondrial transplantation blocks tumor cell proliferation is still not determined. In addition, mitochondria are maternal inheritance in evolution, and mitochondria obtained from genders exhibit differences in mitochondrial activity. Therefore, the study indicates the inhibitory effect of mitochondria from different genders on hepatocellular carcinoma and explores the molecular mechanism. The results reveal that the healthy mitochondria can retard the proliferation of the hepatocellular carcinoma cells in vitro and in vivo through arresting cell cycle and inducing apoptosis. The molecular mechanism suggests that mitochondrial transplantation therapy can decrease aerobic glycolysis, and down-regulate the expression of cycle-related proteins while up-regulate apoptosis-related proteins in tumor cells. In addition, the antitumor activity of mitochondria from female mice (F-Mito) is relatively higher than that of mitochondria from male mice (M-Mito), which would be related to the evidence that the F-Mito process higher activity than the M-Mito. This study clarifies the mechanism of exogenous mitochondria inhibiting the proliferation of hepatocellular carcinoma and contributes a new biotechnology for therapy of mitochondria-related diseases from different genders.}, }
@article {pmid35503755, year = {2022}, author = {Niu, Y and Lu, Y and Song, W and He, X and Liu, Z and Zheng, C and Wang, S and Shi, C and Liu, J}, title = {Assembly and comparative analysis of the complete mitochondrial genome of three Macadamia species (M. integrifolia, M. ternifolia and M. tetraphylla).}, journal = {PloS one}, volume = {17}, number = {5}, pages = {e0263545}, pmid = {35503755}, issn = {1932-6203}, mesh = {Genome Size ; *Genome, Chloroplast ; *Genome, Mitochondrial/genetics ; Genome, Plant ; Macadamia/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Macadamia is a true dicotyledonous plant that thrives in a mild, humid, low wind environment. It is cultivated and traded internationally due to its high-quality nuts thus, has significant development prospects and scientific research value. However, information on the genetic resources of Macadamia spp. remains scanty.<br><br>RESULTS: The mitochondria (mt) genomes of three economically important Macadamia species, Macadamia integrifolia, M. ternifolia and M. tetraphylla, were assembled through the Illumina sequencing platform. The results showed that each species has 71 genes, including 42 protein-coding genes, 26 tRNAs, and 3 rRNAs. Repeated sequence analysis, RNA editing site prediction, and analysis of genes migrating from chloroplast (cp) to mt were performed in the mt genomes of the three Macadamia species. Phylogenetic analysis based on the mt genome of the three Macadamia species and 35 other species was conducted to reveal the evolution and taxonomic status of Macadamia. Furthermore, the characteristics of the plant mt genome, including genome size and GC content, were studied through comparison with 36 other plant species. The final non-synonymous (Ka) and synonymous (Ks) substitution analysis showed that most of the protein-coding genes in the mt genome underwent negative selections, indicating their importance in the mt genome.<br><br>CONCLUSION: The findings of this study provide a better understanding of the Macadamia genome and will inform future research on the genus.}, }
@article {pmid35501686, year = {2022}, author = {Liu, H and Zhao, W and Hua, W and Liu, J}, title = {A large-scale population based organelle pan-genomes construction and phylogeny analysis reveal the genetic diversity and the evolutionary origins of chloroplast and mitochondrion in Brassica napus L.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {339}, pmid = {35501686}, issn = {1471-2164}, support = {31871664//National Natural Science Foundation of China/ ; CAAS-ZDRW2019003//Agricultural Science and Technology Innovation Program/ ; }, mesh = {Brassica/genetics ; *Brassica napus/genetics ; Brassica rapa/genetics ; Chloroplasts/genetics ; Genetic Variation ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Genome, Plant ; Mitochondria/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Allotetraploid oilseed rape (Brassica napus L.) is an important worldwide oil-producing crop. The origin of rapeseed is still undetermined due to the lack of wild resources. Despite certain genetic architecture and phylogenetic studies have been done focus on large group of Brassica nuclear genomes, the organelle genomes information under global pattern is largely unknown, which provide unique material for phylogenetic studies of B. napus. Here, based on de novo assemblies of 1,579 B. napus accessions collected globally, we constructed the chloroplast and mitochondrial pan-genomes of B. napus, and investigated the genetic diversity, phylogenetic relationships of B. napus, B. rapa and B. oleracea.<br><br>RESULTS: Based on mitotype-specific markers and mitotype-variant ORFs, four main cytoplasmic haplotypes were identified in our groups corresponding the nap, pol, ole, and cam mitotypes, among which the structure of chloroplast genomes was more conserved without any rearrangement than mitochondrial genomes. A total of 2,092 variants were detected in chloroplast genomes, whereas only 326 in mitochondrial genomes, indicating that chloroplast genomes exhibited a higher level of single-base polymorphism than mitochondrial genomes. Based on whole-genome variants diversity analysis, eleven genetic difference regions among different cytoplasmic haplotypes were identified on chloroplast genomes. The phylogenetic tree incorporating accessions of the B. rapa, B. oleracea, natural and synthetic populations of B. napus revealed multiple origins of B. napus cytoplasm. The cam-type and pol-type were both derived from B. rapa, while the ole-type was originated from B. oleracea. Notably, the nap-type cytoplasm was identified in both the B. rapa population and the synthetic B. napus, suggesting that B. rapa might be the maternal ancestor of nap-type B. napus.<br><br>CONCLUSIONS: The phylogenetic results provide novel insights into the organelle genomic evolution of Brassica species. The natural rapeseeds contained at least four cytoplastic haplotypes, of which the predominant nap-type might be originated from B. rapa. Besides, the organelle pan-genomes and the overall variation data offered useful resources for analysis of cytoplasmic inheritance related agronomical important traits of rapeseed, which can substantially facilitate the cultivation and improvement of rapeseed varieties.}, }
@article {pmid35497189, year = {2022}, author = {Chen, Z and Schrödl, M}, title = {How many single-copy orthologous genes from whole genomes reveal deep gastropod relationships?.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13285}, pmid = {35497189}, issn = {2167-8359}, mesh = {Animals ; *Gastropoda/genetics ; Phylogeny ; Mollusca ; Genome/genetics ; Transcriptome ; }, abstract = {The Gastropoda contains 80% of existing mollusks and is the most diverse animal class second only to the Insecta. However, the deep phylogeny of gastropods has been controversial for a long time. Especially the position of Patellogastropoda is a major uncertainty. Morphology and some mitochondria studies concluded that Patellogastropoda is likely to be sister to all other gastropods (Orthogastropoda hypothesis), while transcriptomic and other mitogenomic studies indicated that Patellogastropoda and Vetigastropoda are sister taxa (Psilogastropoda). With the release of high-quality genomes, orthologous genes can be better identified and serve as powerful candidates for phylogenetic analysis. The question is, given the current limitations on the taxon sampling side, how many markers are needed to provide robust results. Here, we identified single-copy orthologous genes (SOGs) from 14 gastropods species with whole genomes available which cover five main gastropod subclasses. We generated different datasets from 395 to 1610 SOGs by allowing species missing in different levels. We constructed gene trees of each SOG, and inferred species trees from different collections of gene trees. We found as the number of SOGs increased, the inferred topology changed from Patellogastropoda being sister to all other gastropods to Patellogastropoda being sister to Vetigastropoda + Neomphalina (Psilogastropoda s.l.), with considerable support. Our study thus rejects the Orthogastropoda concept showing that the selection of the representative species and use of sufficient informative sites greatly influence the analysis of deep gastropod phylogeny.}, }
@article {pmid35490656, year = {2022}, author = {Das, R and Kumar, A and Dalai, R and Goswami, C}, title = {Cytochrome C interacts with the pathogenic mutational hotspot region of TRPV4 and forms complexes that differ in mutation and metal ion-sensitive manner.}, journal = {Biochemical and biophysical research communications}, volume = {611}, number = {}, pages = {172-178}, doi = {10.1016/j.bbrc.2022.04.066}, pmid = {35490656}, issn = {1090-2104}, mesh = {*Cytochromes c/genetics/metabolism ; Ions/metabolism ; Mutation ; *TRPV Cation Channels/metabolism ; }, abstract = {The importance of TRPV4 in physiology and disease has been reported by several groups. Recently we have reported that TRPV4 localizes in the mitochondria in different cellular systems, regulates mitochondrial metabolism and electron transport chain functions. Here, we show that TRPV4 colocalizes with Cytochrome C (Cyt C), both in resting as well as in activated conditions. Amino acid region 592-630 of TRPV4 (termed as Fr592-630) that also covers TM4-Loop-TM5 region (which is also a hotspot of several pathogenic mutations) interacts with Cyt C, in a Ca[2+]-sensitive manner. This interaction is also variable and sensitive to other divalent and trivalent cations (i.e., Cu[2+], Mn[2+], Ni[2+], Zn[2+], Fe[3+]). Key residues of TRPV4 involved in these interactions remain conserved throughout the vertebrate evolution. Accordingly, this interaction is variable in the case of different pathogenic mutations (R616Q, F617L, L618P, V620I). Our data suggest that the TRPV4-Cyt C complex differs due to different mutations and is sensitive to the presence of different metal ions. We propose that TRPV4-Cyt C complex formation is important for physiological functions and relevant for TRPV4-induced channelopathies.}, }
@article {pmid35483362, year = {2022}, author = {David, P and Degletagne, C and Saclier, N and Jennan, A and Jarne, P and Plénet, S and Konecny, L and François, C and Guéguen, L and Garcia, N and Lefébure, T and Luquet, E}, title = {Extreme mitochondrial DNA divergence underlies genetic conflict over sex determination.}, journal = {Current biology : CB}, volume = {32}, number = {10}, pages = {2325-2333.e6}, doi = {10.1016/j.cub.2022.04.014}, pmid = {35483362}, issn = {1879-0445}, mesh = {Animals ; *DNA, Mitochondrial/genetics ; Evolution, Molecular ; Female ; *Genome, Mitochondrial ; Haplotypes ; Mitochondria/genetics ; }, abstract = {Cytoplasmic male sterility (CMS) is a form of genetic conflict over sex determination that results from differences in modes of inheritance between genomic compartments.[1-3] Indeed, maternally transmitted (usually mitochondrial) genes sometimes enhance their transmission by suppressing the male function in a hermaphroditic organism to the detriment of biparentally inherited nuclear genes. Therefore, these hermaphrodites become functionally female and may coexist with regular hermaphrodites in so-called gynodioecious populations.[3] CMS has been known in plants since Darwin's times[4] but is previously unknown in the animal kingdom.[5-8] We relate the first observation of CMS in animals. It occurs in a freshwater snail population, where some individuals appear unable to sire offspring in controlled crosses and show anatomical, physiological, and behavioral characters consistent with a suppression of the male function. Male sterility is associated with a mitochondrial lineage that underwent a spectacular acceleration of DNA substitution rates, affecting the entire mitochondrial genome-this acceleration concerns both synonymous and non-synonymous substitutions and therefore results from increased mitogenome mutation rates. Consequently, mitochondrial haplotype divergence within the population is exceptionally high, matching that observed between snail taxa that diverged 475 million years ago. This result is reminiscent of similar accelerations in mitogenome evolution observed in plant clades where gynodioecy is frequent,[9][,][10] both being consistent with arms-race evolution of genome regions implicated in CMS.[11][,][12] Our study shows that genomic conflicts can trigger independent evolution of similar sex-determination systems in plants and animals and dramatically accelerate molecular evolution.}, }
@article {pmid35480563, year = {2022}, author = {Di-Nizo, CB and Suárez-Villota, EY and Silva, MJJ}, title = {Species limits and recent diversification of Cerradomys (Sigmodontinae: Oryzomyini) during the Pleistocene.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13011}, pmid = {35480563}, issn = {2167-8359}, mesh = {Animals ; *Sigmodontinae ; Phylogeny ; *Biological Evolution ; Mitochondria ; South America ; }, abstract = {Cerradomys is a genus of the tribe Oryzomyini with eight species currently recognized, and a controversial taxonomy. These species are mainly distributed in the South America dry diagonal, but some species extend into Atlantic Forest, reaching the coastal sandy plains known as Restingas. This study aimed to address species limits and patterns of diversification of Cerradomys species. For this purpose, we performed cytogenetic and molecular analyses (phylogeny, coalescent species delimitation, barcoding, and divergence times estimation) using multiple mitochondrial and nuclear markers on a comprehensive sampling, representing all nominal taxa reported so far. Chromosomal information was a robust marker recognizing eight Cerradomys species. Reciprocal monophyly was recovered for all the species, except for C. subflavus. These results together with coalescent analyses recovered eight species as the most congruent species delimitation scenario for the genus (mean C tax : 0.72). Divergence time estimates revealed that Cerradomys' diversification occurred about 1.32 million years ago (Mya) during the Pleistocene. Although our results conservatively support the eight Cerradomys species described so far, different lines of evidence suggest that C. langguthi and C. subflavus could potentially be species-complexes. We discussed this scenario in the light of multiple evolutionary processes within and between species and populations, since Cerradomys comprises a species group with recent diversification affected by Pleistocene climatic changes and by the complex biogeographic history of South America dry diagonal. This work supports that the diversity of Cerradomys is underestimated and reiterates that interdisciplinary approaches are mandatory to identify small rodent species properly, and to unhide cryptic species.}, }
@article {pmid35480047, year = {2022}, author = {De Pinto, V and Mahalakshmi, R and Messina, A}, title = {Editorial: VDAC Structure and Function: An Up-to-Date View.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {871586}, pmid = {35480047}, issn = {1664-042X}, support = {IA/S/20/2/505182/WTDBT_/DBT-Wellcome Trust India Alliance/India ; }, }
@article {pmid35463435, year = {2022}, author = {Yi, L and Liu, B and Nixon, PJ and Yu, J and Chen, F}, title = {Recent Advances in Understanding the Structural and Functional Evolution of FtsH Proteases.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {837528}, pmid = {35463435}, issn = {1664-462X}, abstract = {The FtsH family of proteases are membrane-anchored, ATP-dependent, zinc metalloproteases. They are universally present in prokaryotes and the mitochondria and chloroplasts of eukaryotic cells. Most bacteria bear a single ftsH gene that produces hexameric homocomplexes with diverse house-keeping roles. However, in mitochondria, chloroplasts and cyanobacteria, multiple FtsH homologs form homo- and heterocomplexes with specialized functions in maintaining photosynthesis and respiration. The diversification of FtsH homologs combined with selective pairing of FtsH isomers is a versatile strategy to enable functional adaptation. In this article we summarize recent progress in understanding the evolution, structure and function of FtsH proteases with a focus on the role of FtsH in photosynthesis and respiration.}, }
@article {pmid35460877, year = {2022}, author = {Kodagoda, YK and Liyanage, DS and Omeka, WKM and Kwon, H and Hwang, SD and Lee, J}, title = {Molecular characterization, expression, and functional analysis of cystatin B in the big-belly seahorse (Hippocampus abdominalis).}, journal = {Fish &amp; shellfish immunology}, volume = {124}, number = {}, pages = {442-453}, doi = {10.1016/j.fsi.2022.04.020}, pmid = {35460877}, issn = {1095-9947}, mesh = {Animals ; *Cyprinidae/genetics ; Cystatin B/genetics ; *Cystatins/genetics ; *Fish Diseases ; Fish Proteins/chemistry ; Male ; Phylogeny ; Poly I-C/pharmacology ; Sequence Alignment ; *Smegmamorpha ; }, abstract = {Cystatins are a diverse group of cysteine protease inhibitors widely present among various organisms. Beyond their protease inhibitor function, cystatins play a crucial role in diverse pathophysiological conditions in animals, including neurodegenerative disorders, tumor progression, inflammatory diseases, and immune response. However, the role of cystatins in immunity against viral and bacterial infections in fish remains to be elucidated. In this study, the cystatin B from big-belly seahorse, Hippocampus abdominalis, designated as HaCSTB, was identified and characterized. HaCSTB shared the highest homology with type 1 cystatin family members of teleosts and had three cystatin catalytic domains with no signal peptides or disulfide bonds. HaCSTB transcripts were mainly expressed in peripheral blood cells (PBCs), followed by the testis and pouch of healthy big-belly seahorses. Immune challenge with lipopolysaccharides (LPS), polyinosinic:polycytidylic acid (Poly I:C), and Streptococcus iniae induced upregulation of relative HaCSTB mRNA expression in PBCs. Subcellular localization analysis revealed the distribution of HaCSTB in the cytosol, mitochondria, and nuclei of fathead minnow cells (FHM). Recombinant HaCSTB (rHaCSTB) exhibited potent in vitro inhibitory activity against papain, a cysteine protease, in a concentration-, pH-, and temperature-dependent manner. Overexpression of HaCSTB in viral hemorrhagic septicemia virus (VHSV)-susceptible FHM cells increased cell viability and reduced VHSV-induced apoptosis. Collectively, these results suggest that HaCSTB might engage in the teleostean immune protection against bacteria and viruses.}, }
@article {pmid35460575, year = {2022}, author = {Liu, Q and Iqbal, MF and Yaqub, T and Firyal, S and Zhao, Y and Stoneking, M and Li, M}, title = {The transmission of human mitochondrial DNA in four-generation pedigrees.}, journal = {Human mutation}, volume = {43}, number = {9}, pages = {1259-1267}, doi = {10.1002/humu.24390}, pmid = {35460575}, issn = {1098-1004}, mesh = {*DNA, Mitochondrial/genetics ; Humans ; Mitochondria/genetics ; *Mitochondrial Diseases/genetics ; Pedigree ; Selection, Genetic ; }, abstract = {Most of the pathogenic variants in mitochondrial DNA (mtDNA) exist in a heteroplasmic state (coexistence of mutant and wild-type mtDNA). Understanding how mtDNA is transmitted is crucial for predicting mitochondrial disease risk. Previous studies were based mainly on two-generation pedigree data, which are limited by the randomness in a single transmission. In this study, we analyzed the transmission of heteroplasmies in 16 four-generation families. First, we found that 57.8% of the variants in the great grandmother were transmitted to the fourth generation. The direction and magnitude of the frequency change during transmission appeared to be random. Moreover, no consistent correlation was identified between the frequency changes among the continuous transmissions, suggesting that most variants were functionally neutral or mildly deleterious and thus not subject to strong natural selection. Additionally, we found that the frequency of one nonsynonymous variant (m.15773G>A) showed a consistent increase in one family, suggesting that this variant may confer a fitness advantage to the mitochondrion/cell. We also estimated the effective bottleneck size during transmission to be 21-71. In summary, our study demonstrates the advantages of multigeneration data for studying the transmission of mtDNA for shedding new light on the dynamics of the mutation frequency in successive generations.}, }
@article {pmid35457201, year = {2022}, author = {Juskeviciene, R and Fritz, AK and Brilkova, M and Akbergenov, R and Schmitt, K and Rehrauer, H and Laczko, E and Isnard-Petit, P and Thiam, K and Eckert, A and Schacht, J and Wolfer, DP and Böttger, EC and Shcherbakov, D}, title = {Phenotype of Mrps5-Associated Phylogenetic Polymorphisms Is Intimately Linked to Mitoribosomal Misreading.}, journal = {International journal of molecular sciences}, volume = {23}, number = {8}, pages = {}, pmid = {35457201}, issn = {1422-0067}, mesh = {Animals ; Mice ; *Mitochondrial Proteins/genetics ; Mutation ; Phenotype ; Phylogeny ; Protein Biosynthesis ; *Ribosomal Proteins/genetics ; }, abstract = {We have recently identified point mutation V336Y in mitoribosomal protein Mrps5 (uS5m) as a mitoribosomal ram (ribosomal ambiguity) mutation conferring error-prone mitochondrial protein synthesis. In vivo in transgenic knock-in animals, homologous mutation V338Y was associated with a discrete phenotype including impaired mitochondrial function, anxiety-related behavioral alterations, enhanced susceptibility to noise-induced hearing damage, and accelerated metabolic aging in muscle. To challenge the postulated link between Mrps5 V338Y-mediated misreading and the in vivo phenotype, we introduced mutation G315R into the mouse Mrps5 gene as Mrps5 G315R is homologous to the established bacterial ram mutation RpsE (uS5) G104R. However, in contrast to bacterial translation, the homologous G → R mutation in mitoribosomal Mrps5 did not affect the accuracy of mitochondrial protein synthesis. Importantly, in the absence of mitochondrial misreading, homozygous mutant MrpS5[G315R/G315R] mice did not show a phenotype distinct from wild-type animals.}, }
@article {pmid35453648, year = {2022}, author = {Russo, C and Valle, MS and Casabona, A and Spicuzza, L and Sambataro, G and Malaguarnera, L}, title = {Vitamin D Impacts on Skeletal Muscle Dysfunction in Patients with COPD Promoting Mitochondrial Health.}, journal = {Biomedicines}, volume = {10}, number = {4}, pages = {}, pmid = {35453648}, issn = {2227-9059}, abstract = {Skeletal muscle dysfunction is frequently associated with chronic obstructive pulmonary disease (COPD), which is characterized by a permanent airflow limitation, with a worsening respiratory disorder during disease evolution. In COPD, the pathophysiological changes related to the chronic inflammatory state affect oxidant-antioxidant balance, which is one of the main mechanisms accompanying extra-pulmonary comorbidity such as muscle wasting. Muscle impairment is characterized by alterations on muscle fiber architecture, contractile protein integrity, and mitochondrial dysfunction. Exogenous and endogenous sources of reactive oxygen species (ROS) are present in COPD pathology. One of the endogenous sources of ROS is represented by mitochondria. Evidence demonstrated that vitamin D plays a crucial role for the maintenance of skeletal muscle health. Vitamin D deficiency affects oxidative stress and mitochondrial function influencing disease course through an effect on muscle function in COPD patients. This review will focus on vitamin-D-linked mechanisms that could modulate and ameliorate the damage response to free radicals in muscle fibers, evaluating vitamin D supplementation with enough potent effect to contrast mitochondrial impairment, but which avoids potential severe side effects.}, }
@article {pmid35453370, year = {2022}, author = {Hambardikar, V and Guitart-Mampel, M and Scoma, ER and Urquiza, P and Nagana, GGA and Raftery, D and Collins, JA and Solesio, ME}, title = {Enzymatic Depletion of Mitochondrial Inorganic Polyphosphate (polyP) Increases the Generation of Reactive Oxygen Species (ROS) and the Activity of the Pentose Phosphate Pathway (PPP) in Mammalian Cells.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {11}, number = {4}, pages = {}, pmid = {35453370}, issn = {2076-3921}, support = {R00 AG055701/AG/NIA NIH HHS/United States ; Start Up Funds//Rutgers, The State University of New Jersey/ ; 4R00AG055701-03//National Institute of Health/ ; 1K99AG055701-01A1//National Institute of Health/ ; }, abstract = {Inorganic polyphosphate (polyP) is an ancient biopolymer that is well preserved throughout evolution and present in all studied organisms. In mammals, it shows a high co-localization with mitochondria, and it has been demonstrated to be involved in the homeostasis of key processes within the organelle, including mitochondrial bioenergetics. However, the exact extent of the effects of polyP on the regulation of cellular bioenergetics, as well as the mechanisms explaining these effects, still remain poorly understood. Here, using HEK293 mammalian cells under Wild-type (Wt) and MitoPPX (cells enzymatically depleted of mitochondrial polyP) conditions, we show that depletion of polyP within mitochondria increased oxidative stress conditions. This is characterized by enhanced mitochondrial O2[-] and intracellular H2O2 levels, which may be a consequence of the dysregulation of oxidative phosphorylation (OXPHOS) that we have demonstrated in MitoPPX cells in our previous work. These findings were associated with an increase in basal peroxiredoxin-1 (Prx1), superoxide dismutase-2 (SOD2), and thioredoxin (Trx) antioxidant protein levels. Using [13]C-NMR and immunoblotting, we assayed the status of glycolysis and the pentose phosphate pathway (PPP) in Wt and MitoPPX cells. Our results show that MitoPPX cells display a significant increase in the activity of the PPP and an increase in the protein levels of transaldolase (TAL), which is a crucial component of the non-oxidative phase of the PPP and is involved in the regulation of oxidative stress. In addition, we observed a trend towards increased glycolysis in MitoPPX cells, which corroborates our prior work. Here, for the first time, we show the crucial role played by mitochondrial polyP in the regulation of mammalian redox homeostasis. Moreover, we demonstrate a significant effect of mitochondrial polyP on the regulation of global cellular bioenergetics in these cells.}, }
@article {pmid35453058, year = {2022}, author = {Coleman, PS and Parlo, RA}, title = {Cancer's camouflage: Microvesicle shedding from cholesterol-rich tumor plasma membranes might blindfold first-responder immunosurveillance strategies.}, journal = {European journal of cell biology}, volume = {101}, number = {2}, pages = {151219}, doi = {10.1016/j.ejcb.2022.151219}, pmid = {35453058}, issn = {1618-1298}, mesh = {Animals ; Cell Membrane/metabolism ; Cholesterol/metabolism ; *Lipid Bilayers ; Mammals/metabolism ; Membrane Lipids/metabolism ; Monitoring, Immunologic ; *Neoplasms ; }, abstract = {Intermediary metabolism of tumors is characterized, in part, by a dysregulation of the cholesterol biosynthesis pathway at its rate-controlling enzyme providing the molecular basis for tumor membranes (mitochondria, plasma membrane) to become enriched with cholesterol (Bloch, 1965; Feo et al., 1975; Brown and Goldstein, 1980; Goldstein and Brown, 1990). Cholesterol enriched tumor mitochondria manifest preferential citrate export, thereby providing a continuous supply of substrate precursor for the tumor's dysregulated cholesterogenesis via a "truncated" Krebs/TCA cycle (Kaplan et al., 1986; Coleman et al., 1997). Proliferating tumors shed elevated amounts of plasma membrane-derived extracellular vesicles (pmEV) compared with normal tissues (van Blitterswijk et al., 1979; Black, 1980). Coordination of these metabolic phenomena in tumors supports the enhanced intercalation of cholesterol within the plasma membrane lipid bilayer's cytoplasmic face, the promotion of outward protrusions from the plasma membrane, and the evolution of cholesterol enriched pmEV. The pmEV shed by tumors possess elevated cholesterol and concentrated cell surface antigen clusters found on the tumor cells themselves (Kim et al., 2002). Upon exfoliation, saturation of the extracellular milieu with tumor-derived pmEV could allow early onset mammalian immune surveillance mechanisms to become "blind" to an evolving cancer and lose their ability to detect and initiate strategies to destroy the cancer. However, a molecular mechanism is lacking that would help explain how cholesterol enrichment of the pmEV inner lipid bilayer might allow the tumor cell to evade the host immune system. We offer a hypothesis, endorsed by published mathematical modeling of biomembrane structure as well as by decades of in vivo data with diverse cancers, that a cholesterol enriched inner bilayer leaflet, coupled with a logarithmic expansion in surface area of shed tumor pmEV load relative to its derivative cancer cell, conspire to force exposure of otherwise unfamiliar membrane integral protein domains as antigenic epitopes to the host's circulating immune surveillance system, allowing the tumor cells to evade destruction. We provide elementary numerical estimations comparing the amount of pmEV shed from tumor versus normal cells.}, }
@article {pmid35452707, year = {2022}, author = {Chen, Q and Chen, L and Liao, CQ and Wang, X and Wang, M and Huang, GH}, title = {Comparative mitochondrial genome analysis and phylogenetic relationship among lepidopteran species.}, journal = {Gene}, volume = {830}, number = {}, pages = {146516}, doi = {10.1016/j.gene.2022.146516}, pmid = {35452707}, issn = {1879-0038}, mesh = {Animals ; *Butterflies/genetics ; *Genome, Mitochondrial ; *Lepidoptera/genetics ; Mitochondria/genetics ; *Moths/genetics ; Phylogeny ; RNA, Transfer/genetics ; }, abstract = {Lepidoptera has rich species including many agricultural pests and economical insects around the world. The mitochondrial genomes (mitogenomes) were utilized to explore the phylogenetic relationships between difference taxonomic levels in Lepidoptera. However, the knowledge of mitogenomic characteristics and phylogenetic position about superfamily-level in this order is unresolved. In this study, we integrated 794 mitogenomes consisting of 37 genes and a noncoding control region, which covered 26 lepidopteran superfamilies from newly sequenced and publicly available genomes for comparative genomic and phylogenetic analysis. In primitive taxon, putative start codon of cox1 gene was ATA or ATT instead of CGA, but stop codon of that showed four types, namely TAA, TAG, TA and T. The 7-bp overlap between atp8 and atp6 presented as "ATGATAA". Moreover, the most frequently utilized amino acids were leucine (UUA) in 13 PCGs. Phylogenetic analysis showed that the main backbone relationship in Lepidoptera was (Hepialoidea + (Nepticuloidea + (Adeloidea + (Tischerioidea + (Tineoidea + (Yponomeutoidea + (Gracillarioidea + (Papilionoidea + ((Zygaenoidea + Tortricoidea) + (Gelechioidea + (Pyraloidea + ((Geometroidea + Noctuoidea) + (Lasiocampoidea + Bombycoidea))))))))))))).}, }
@article {pmid35451706, year = {2022}, author = {Vella, A and Vella, N and Acosta-Díaz, C}, title = {The first complete mitochondrial genomes for Serranus papilionaceus and Serranus scriba, and their phylogenetic position within Serranidae.}, journal = {Molecular biology reports}, volume = {49}, number = {7}, pages = {6295-6302}, pmid = {35451706}, issn = {1573-4978}, support = {BioCon_Innovate Research Excellence Grant//University of Malta/ ; FINS//Ministry of Education/ ; }, mesh = {Animals ; *Bass/genetics ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; }, abstract = {BACKGROUND: Butterfly-winged comber, Serranus papilionaceus Valenciennes, 1832, was recently resurrected and so it is no longer considered as a junior synonym of the Painted comber, Serranus scriba (Linneus, 1758). This calls for a more comprehensive phylogenetic assessment using mitochondria DNA genomes to better understand the relationship and delineate these two species.<br><br>METHODS AND RESULTS: Next-generation Sequencing was applied to sequence the genome of these two Serranus species. The data generated was then used to construct the mitochondrial genome of these two species. This produced the first complete mitochondrial genomes for the genus Serranus here represented by Serranus papilionaceus and Serranus scriba. These two mitochondrial genomes are 16,514&#xa0;bp and 16,512&#xa0;bp respectively, and both contained the typical 37 genes found in vertebrates (13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs), together with the OL and the control region.<br><br>CONCLUSIONS: These mitochondrial genomes provide a new insight into the phylogenetic and evolutionary connections between the various subfamilies within Serranidae, while providing new molecular data that can be applied to discriminate between the studied species.}, }
@article {pmid35446942, year = {2022}, author = {Gil Del Alcazar, CR and Trinh, A and Alečković, M and Rojas Jimenez, E and Harper, NW and Oliphant, MUJ and Xie, S and Krop, ED and Lulseged, B and Murphy, KC and Keenan, TE and Van Allen, EM and Tolaney, SM and Freeman, GJ and Dillon, DA and Muthuswamy, SK and Polyak, K}, title = {Insights into Immune Escape During Tumor Evolution and Response to Immunotherapy Using a Rat Model of Breast Cancer.}, journal = {Cancer immunology research}, volume = {10}, number = {6}, pages = {680-697}, pmid = {35446942}, issn = {2326-6074}, support = {P50 CA168504/CA/NCI NIH HHS/United States ; R35 CA197623/CA/NCI NIH HHS/United States ; R35 CA232128/CA/NCI NIH HHS/United States ; T32 CA009172/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Breast Neoplasms/genetics/immunology/therapy ; Female ; Hormones ; Humans ; Immunologic Factors ; Immunotherapy ; Mice ; Rats ; Rats, Sprague-Dawley ; Receptors, Antigen, T-Cell ; }, abstract = {Animal models are critical for the preclinical validation of cancer immunotherapies. Unfortunately, mouse breast cancer models do not faithfully reproduce the molecular subtypes and immune environment of the human disease. In particular, there are no good murine models of estrogen receptor-positive (ER+) breast cancer, the predominant subtype in patients. Here, we show that Nitroso-N-methylurea-induced mammary tumors in outbred Sprague-Dawley rats recapitulate the heterogeneity for mutational profiles, ER expression, and immune evasive mechanisms observed in human breast cancer. We demonstrate the utility of this model for preclinical studies by dissecting mechanisms of response to immunotherapy using combination TGFBR inhibition and PD-L1 blockade. Short-term treatment of early-stage tumors induced durable responses. Gene expression profiling and spatial mapping classified tumors as inflammatory and noninflammatory, and identified IFNγ, T-cell receptor (TCR), and B-cell receptor (BCR) signaling, CD74/MHC II, and epithelium-interacting CD8+ T cells as markers of response, whereas the complement system, M2 macrophage phenotype, and translation in mitochondria were associated with resistance. We found that the expression of CD74 correlated with leukocyte fraction and TCR diversity in human breast cancer. We identified a subset of rat ER+ tumors marked by expression of antigen-processing genes that had an active immune environment and responded to treatment. A gene signature characteristic of these tumors predicted disease-free survival in patients with ER+ Luminal A breast cancer and overall survival in patients with metastatic breast cancer receiving anti-PD-L1 therapy. We demonstrate the usefulness of this preclinical model for immunotherapy and suggest examination to expand immunotherapy to a subset of patients with ER+ disease. See related Spotlight by Roussos Torres, p. 672.}, }
@article {pmid35446419, year = {2022}, author = {Fields, PD and Waneka, G and Naish, M and Schatz, MC and Henderson, IR and Sloan, DB}, title = {Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome.}, journal = {Genome biology and evolution}, volume = {14}, number = {5}, pages = {}, pmid = {35446419}, issn = {1759-6653}, support = {R01 GM118046/GM/NIGMS NIH HHS/United States ; BB/V003984/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Arabidopsis/genetics ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; In Situ Hybridization, Fluorescence ; Mitochondria/genetics ; Sequence Analysis, DNA ; }, abstract = {Intracellular transfers of mitochondrial DNA continue to shape nuclear genomes. Chromosome 2 of the model plant Arabidopsis thaliana contains one of the largest known nuclear insertions of mitochondrial DNA (numts). Estimated at over 600 kb in size, this numt is larger than the entire Arabidopsis mitochondrial genome. The primary Arabidopsis nuclear reference genome contains less than half of the numt because of its structural complexity and repetitiveness. Recent data sets generated with improved long-read sequencing technologies (PacBio HiFi) provide an opportunity to finally determine the accurate sequence and structure of this numt. We performed a de novo assembly using sequencing data from recent initiatives to span the Arabidopsis centromeres, producing a gap-free sequence of the Chromosome 2 numt, which is 641 kb in length and has 99.933% nucleotide sequence identity with the actual mitochondrial genome. The numt assembly is consistent with the repetitive structure previously predicted from fiber-based fluorescent in situ hybridization. Nanopore sequencing data indicate that the numt has high levels of cytosine methylation, helping to explain its biased spectrum of nucleotide sequence divergence and supporting previous inferences that it is transcriptionally inactive. The original numt insertion appears to have involved multiple mitochondrial DNA copies with alternative structures that subsequently underwent an additional duplication event within the nuclear genome. This work provides insights into numt evolution, addresses one of the last unresolved regions of the Arabidopsis reference genome, and represents a resource for distinguishing between highly similar numt and mitochondrial sequences in studies of transcription, epigenetic modifications, and de novo mutations.}, }
@article {pmid35444563, year = {2022}, author = {Mendez-Romero, O and Ricardez-García, C and Castañeda-Tamez, P and Chiquete-Félix, N and Uribe-Carvajal, S}, title = {Thriving in Oxygen While Preventing ROS Overproduction: No Two Systems Are Created Equal.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {874321}, pmid = {35444563}, issn = {1664-042X}, abstract = {From 2.5 to 2.0 billion years ago, atmospheric oxygen concentration [O2] rose thousands of times, leading to the first mass extinction. Reactive Oxygen Species (ROS) produced by the non-catalyzed partial reduction of O2 were highly toxic eliminating many species. Survivors developed different strategies to cope with ROS toxicity. At the same time, using O2 as the final acceptor in respiratory chains increased ATP production manifold. Thus, both O2 and ROS were strong drivers of evolution, as species optimized aerobic metabolism while developing ROS-neutralizing mechanisms. The first line of defense is preventing ROS overproduction and two mechanisms were developed in parallel: 1) Physiological uncoupling systems (PUS), which increase the rate of electron fluxes in respiratory systems. 2) Avoidance of excess [O2]. However, it seems that as avoidance efficiency improved, PUSs became less efficient. PUS includes branched respiratory chains and proton sinks, which may be proton specific, the mitochondrial uncoupling proteins (UCPs) or unspecific, the mitochondrial permeability transition pore (PTP). High [O2] avoidance also involved different strategies: 1) Cell association, as in biofilms or in multi-cellularity allowed gas-permeable organisms (oxyconformers) from bacterial to arthropods to exclude O2. 2) Motility, to migrate from hypoxic niches. 3) Oxyregulator organisms: as early as in fish, and O2-impermeable epithelium excluded all gases and only exact amounts entered through specialized respiratory systems. Here we follow the parallel evolution of PUS and O2-avoidance, PUS became less critical and lost efficiency. In regard, to proton sinks, there is fewer evidence on their evolution, although UCPs have indeed drifted in function while in some species it is not clear whether PTPs exist.}, }
@article {pmid35441886, year = {2022}, author = {Egusquiza-Alvarez, CA and Robles-Flores, M}, title = {An approach to p32/gC1qR/HABP1: a multifunctional protein with an essential role in cancer.}, journal = {Journal of cancer research and clinical oncology}, volume = {148}, number = {8}, pages = {1831-1854}, pmid = {35441886}, issn = {1432-1335}, support = {IV200220//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; IN229420//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; FOSSIS 2017-289600//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; }, mesh = {Carrier Proteins ; Humans ; Ligands ; Mitochondria/metabolism ; *Mitochondrial Proteins/metabolism ; *Neoplasms/pathology ; }, abstract = {P32/gC1qR/HABP1 is a doughnut-shaped acidic protein, highly conserved in eukaryote evolution and ubiquitous in the organism. Although its canonical subcellular localization is the mitochondria, p32 can also be found in the cytosol, nucleus, cytoplasmic membrane, and it can be secreted. Therefore, it is considered a multicompartmental protein. P32 can interact with many physiologically divergent ligands in each subcellular location and modulate their functions. The main ligands are C1q, hyaluronic acid, calreticulin, CD44, integrins, PKC, splicing factor ASF/SF2, and several microbial proteins. Among the functions in which p32 participates are mitochondrial metabolism and dynamics, apoptosis, splicing, immune response, inflammation, and modulates several cell signaling pathways. Notably, p32 is overexpressed in a significant number of epithelial tumors, where its expression level negatively correlates with patient survival. Several studies of gain and/or loss of function in cancer cells have demonstrated that p32 is a promoter of malignant hallmarks such as proliferation, cell survival, chemoresistance, angiogenesis, immunoregulation, migration, invasion, and metastasis. All of this strongly suggests that p32 is a potential diagnostic molecule and therapeutic target in cancer. Indeed, preclinical advances have been made in developing therapeutic strategies using p32 as a target. They include tumor homing peptides, monoclonal antibodies, an intracellular inhibitor, a p32 peptide vaccine, and p32 CAR T cells. These advances are promising and will allow soon to include p32 as part of targeted cancer therapies.}, }
@article {pmid35435757, year = {2022}, author = {Nakabachi, A and Moran, NA}, title = {Extreme Polyploidy of Carsonella, an Organelle-Like Bacterium with a Drastically Reduced Genome.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0035022}, pmid = {35435757}, issn = {2165-0497}, mesh = {Animals ; Bacteria/genetics ; *Gammaproteobacteria ; Genome, Bacterial ; *Hemiptera/genetics/microbiology ; Organelles ; Phylogeny ; Polyploidy ; Symbiosis ; }, abstract = {Polyploidy is the state of having multiple copies of the genome within a nucleus or a cell, which has repeatedly evolved across the domains of life. Whereas most bacteria are monoploid, some bacterial species and endosymbiotic organelles that are derived from bacteria are stably polyploid. In the present study, using absolute quantitative PCR, we assessed the ploidy of Candidatus Carsonella ruddii (Gammaproteobacteria, Oceanospirillales), the obligate symbiont of the hackberry petiole gall psyllid, Pachypsylla venusta (Hemiptera, Psylloidea). The genome of this symbiont is one of the smallest known for cellular organisms, at 160 kb. The analysis revealed that Carsonella within a single bacteriocyte has ∼6 × 10[4] copies of the genome, indicating that some Carsonella cells can contain thousands or even tens of thousands of genomic copies per cell. The basis of polyploidy of Carsonella is unknown, but it potentially plays a role in the repair of DNA damage through homologous recombination. IMPORTANCE Mitochondria and plastids are endosymbiotic organelles in eukaryotic cells and are derived from free-living bacteria. They have many highly reduced genomes from which numerous genes have been transferred to the host nucleus. Similar, but more recently established, symbiotic systems are observed in some insect lineages. Although the genomic sequence data of such bacterial symbionts are rapidly accumulating, little is known about their ploidy. The present study revealed that a bacterium with a drastically reduced genome is an extreme polyploid, which is reminiscent of the case of organelles.}, }
@article {pmid35418016, year = {2022}, author = {Yuan, F and Lan, X}, title = {Sequencing the organelle genomes of Bougainvillea spectabilis and Mirabilis jalapa (Nyctaginaceae).}, journal = {BMC genomic data}, volume = {23}, number = {1}, pages = {28}, pmid = {35418016}, issn = {2730-6844}, mesh = {*Genome, Chloroplast/genetics ; *Genome, Mitochondrial/genetics ; *Mirabilis/genetics ; Mitochondria/genetics ; *Nyctaginaceae/genetics ; }, abstract = {OBJECTIVES: Mirabilis jalapa L. and Bougainvillea spectabilis are two Mirabilis species known for their ornamental and pharmaceutical values. The organelle genomes are highly conserved with a rapid evolution rate making them suitable for evolutionary studies. Therefore, mitochondrial and chloroplast genomes of B. spectabilis and M. jalapa were sequenced to understand their evolutionary relationship with other angiosperms.<br><br>DATA DESCRIPTION: Here, we report the complete mitochondrial genomes of B. spectabilis and M. jalapa (343,746&#xa0;bp and 267,334&#xa0;bp, respectively) and chloroplast genomes of B. spectabilis (154,520&#xa0;bp) and M. jalapa (154,532&#xa0;bp) obtained from Illumina NovaSeq. The mitochondrial genomes of B. spectabilis and M. jalapa consisted of 70 and 72 genes, respectively. Likewise, the chloroplast genomes of B. spectabilis and M. jalapa contained 131 and 132 genes, respectively. The generated genomic data will be useful for molecular characterization and evolutionary studies.}, }
@article {pmid35409414, year = {2022}, author = {Tsai, HC and Hsieh, CH and Hsu, CW and Hsu, YH and Chien, LF}, title = {Cloning and Organelle Expression of Bamboo Mitochondrial Complex I Subunits Nad1, Nad2, Nad4, and Nad5 in the Yeast Saccharomyces cerevisiae.}, journal = {International journal of molecular sciences}, volume = {23}, number = {7}, pages = {}, pmid = {35409414}, issn = {1422-0067}, support = {NSC96-2313-B-005-030-MY2, NSC96-2752-B-005-013-PAE, MOST110-2221-E-005-078//Ministry of Science and Technology of Taiwan/ ; }, mesh = {Cloning, Molecular ; DNA, Mitochondrial/genetics ; *Electron Transport Complex I/genetics ; Mitochondria/genetics ; Phylogeny ; *Saccharomyces cerevisiae/genetics ; }, abstract = {Mitochondrial respiratory complex I catalyzes electron transfer from NADH to ubiquinone and pumps protons from the matrix into the intermembrane space. In particular, the complex I subunits Nad1, Nad2, Nad4, and Nad5, which are encoded by the nad1, nad2, nad4, and nad5 genes, reside at the mitochondrial inner membrane and possibly function as proton (H[+]) and ion translocators. To understand the individual functional roles of the Nad1, Nad2, Nad4, and Nad5 subunits in bamboo, each cDNA of these four genes was cloned into the pYES2 vector and expressed in the mitochondria of the yeast Saccharomyces cerevisiae. The mitochondrial targeting peptide mt gene (encoding MT) and the egfp marker gene (encoding enhanced green fluorescent protein, EGFP) were fused at the 5'-terminal and 3'-terminal ends, respectively. The constructed plasmids were then transformed into yeast. RNA transcripts and fusion protein expression were observed in the yeast transformants. Mitochondrial localizations of the MT-Nad1-EGFP, MT-Nad2-EGFP, MT-Nad4-EGFP, and MT-Nad5-EGFP fusion proteins were confirmed by fluorescence microscopy. The ectopically expressed bamboo subunits Nad1, Nad2, Nad4, and Nad5 may function in ion translocation, which was confirmed by growth phenotype assays with the addition of different concentrations of K[+], Na[+], or H[+].}, }
@article {pmid35409376, year = {2022}, author = {Kasperski, A}, title = {Life Entrapped in a Network of Atavistic Attractors: How to Find a Rescue.}, journal = {International journal of molecular sciences}, volume = {23}, number = {7}, pages = {}, pmid = {35409376}, issn = {1422-0067}, mesh = {Cell Physiological Phenomena ; Cell Transformation, Neoplastic/metabolism ; *Energy Metabolism ; Humans ; Mitochondria/metabolism ; *Neoplasms/metabolism ; }, abstract = {In view of unified cell bioenergetics, cell bioenergetic problems related to cell overenergization can cause excessive disturbances in current cell fate and, as a result, lead to a change of cell-fate. At the onset of the problem, cell overenergization of multicellular organisms (especially overenergization of mitochondria) is solved inter alia by activation and then stimulation of the reversible Crabtree effect by cells. Unfortunately, this apparently good solution can also lead to a much bigger problem when, despite the activation of the Crabtree effect, cell overenergization persists for a long time. In such a case, cancer transformation, along with the Warburg effect, may occur to further reduce or stop the charging of mitochondria by high-energy molecules. Understanding the phenomena of cancer transformation and cancer development has become a real challenge for humanity. To date, many models have been developed to understand cancer-related mechanisms. Nowadays, combining all these models into one coherent universal model of cancer transformation and development can be considered a new challenge. In this light, the aim of this article is to present such a potentially universal model supported by a proposed new model of cellular functionality evolution. The methods of fighting cancer resulting from unified cell bioenergetics and the two presented models are also considered.}, }
@article {pmid35408834, year = {2022}, author = {Scaltsoyiannes, V and Corre, N and Waltz, F and Giegé, P}, title = {Types and Functions of Mitoribosome-Specific Ribosomal Proteins across Eukaryotes.}, journal = {International journal of molecular sciences}, volume = {23}, number = {7}, pages = {}, pmid = {35408834}, issn = {1422-0067}, support = {ANR 16 CE11-0024; ANR 20 CE11-0021//Agence Nationale de la Recherche/ ; }, mesh = {Cryoelectron Microscopy ; Eukaryota/genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; *Mitochondrial Ribosomes/metabolism ; RNA, Ribosomal/metabolism ; *Ribosomal Proteins/metabolism ; }, abstract = {Mitochondria are key organelles that combine features inherited from their bacterial endosymbiotic ancestor with traits that arose during eukaryote evolution. These energy producing organelles have retained a genome and fully functional gene expression machineries including specific ribosomes. Recent advances in cryo-electron microscopy have enabled the characterization of a fast-growing number of the low abundant membrane-bound mitochondrial ribosomes. Surprisingly, mitoribosomes were found to be extremely diverse both in terms of structure and composition. Still, all of them drastically increased their number of ribosomal proteins. Interestingly, among the more than 130 novel ribosomal proteins identified to date in mitochondria, most of them are composed of a-helices. Many of them belong to the nuclear encoded super family of helical repeat proteins. Here we review the diversity of functions and the mode of action held by the novel mitoribosome proteins and discuss why these proteins that share similar helical folds were independently recruited by mitoribosomes during evolution in independent eukaryote clades.}, }
@article {pmid35406135, year = {2022}, author = {Snell, TW and Carberry, J}, title = {Astaxanthin Bioactivity Is Determined by Stereoisomer Composition and Extraction Method.}, journal = {Nutrients}, volume = {14}, number = {7}, pages = {}, pmid = {35406135}, issn = {2072-6643}, mesh = {Animals ; *Antioxidants/pharmacology ; Reactive Oxygen Species/metabolism ; Stereoisomerism ; *Xanthophylls/chemistry/pharmacology ; }, abstract = {Astaxanthin (ASX) is a natural product and one of the most powerful antioxidants known. It has significant effects on the metabolism of many animals, increasing fecundity, egg yolk volume, growth rates, immune responses, and disease resistance. A large part of the bioactivity of ASX is due to its targeting of mitochondria, where it inserts itself into cell membranes. Here, ASX stabilizes membranes and acts as a powerful antioxidant, protecting mitochondria from damage by reactive oxygen species (ROS). ROS are ubiquitous by-products of energy metabolism that must be tightly regulated by cells, lest they bind to and inactivate proteins, DNA and RNA, lipids, and signaling molecules. Most animals cannot synthesize ASX, so they need to acquire it in their diet. ASX is easily thermally denatured during extraction, and its high hydrophobicity limits its bioavailability. Our focus in this review is to contrast the bioactivity of different ASX stereoisomers and how extraction methods can denature ASX, compromising its bioavailability and bioactivity. We discuss the commercial sources of astaxanthin, structure of stereoisomers, relative bioavailability and bioactivity of ASX stereoisomers, mechanisms of ASX bioactivity, evolution of carotenoids, and why mitochondrial targeting makes ASX such an effective antioxidant.}, }
@article {pmid35397926, year = {2022}, author = {Zhu, D and Li, X and Tian, Y}, title = {Mitochondrial-to-nuclear communication in aging: an epigenetic perspective.}, journal = {Trends in biochemical sciences}, volume = {47}, number = {8}, pages = {645-659}, doi = {10.1016/j.tibs.2022.03.008}, pmid = {35397926}, issn = {0968-0004}, mesh = {Cell Nucleus/metabolism ; Epigenesis, Genetic ; *Longevity/physiology ; *Mitochondria/metabolism ; }, abstract = {Age-associated changes in mitochondria are closely involved in aging. Apart from the established roles in bioenergetics and biosynthesis, mitochondria are signaling organelles that communicate their fitness to the nucleus, triggering transcriptional programs to adapt homeostasis stress that is essential for organismal health and aging. Emerging studies revealed that mitochondrial-to-nuclear (mito-nuclear) communication via altered levels of mitochondrial metabolites or stress signals causes various epigenetic changes, facilitating efforts to maintain homeostasis and affect aging. Here, we summarize recent studies on the mechanisms by which mito-nuclear communication modulates epigenomes and their effects on regulating the aging process. Insights into understanding how mitochondrial metabolites serve as prolongevity signals and how aging affects this communication will help us develop interventions to promote longevity and health.}, }
@article {pmid35391231, year = {2022}, author = {Chen, Z and Liu, F and Li, D and Xu, X}, title = {Four new species of the primitively segmented spider genus Songthela (Mesothelae, Liphistiidae) from Chongqing Municipality, China.}, journal = {Zootaxa}, volume = {5091}, number = {4}, pages = {546-558}, doi = {10.11646/zootaxa.5091.4.2}, pmid = {35391231}, issn = {1175-5334}, mesh = {Animals ; China ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Female ; Male ; Mitochondria/genetics ; *Spiders/genetics ; }, abstract = {This paper reports four new species of the primitively segmented spider genus Songthela from Chongqing Municipality, China, based on morphological characters of both males and females: S. jinyun sp. nov., S. longbao sp. nov., S. serriformis sp. nov. and S. wangerbao sp. nov. We also provide the GenBank accession codes of mitochondrial DNA barcode gene, cytochrome c oxidase subunit I (COI), for the holotype of four new species for future identification.}, }
@article {pmid35391113, year = {2022}, author = {Lobon-Rovira, J and Conradie, W and Pinto, PV and Keates, C and Edwards, S and Plessis, AD and Branch, WR}, title = {Systematic revision of Afrogecko ansorgii (Boulenger, 1907) (Sauria: Gekkonidae) from western Angola.}, journal = {Zootaxa}, volume = {5124}, number = {4}, pages = {401-430}, doi = {10.11646/zootaxa.5124.4.1}, pmid = {35391113}, issn = {1175-5334}, mesh = {Angola ; Animals ; Cell Nucleus/genetics ; *Lizards/genetics ; Male ; Mitochondria ; Phylogeny ; }, abstract = {Here we provide the first phylogenetic analysis that include Afrogecko ansorgii and a detailed morphological comparison with other species of leaf-toed geckos. For this purpose, we used two mitochondrial (16S, ND2) and four nuclear (RAG1, RAG2, CMOS, PDC) genes to produce a robust phylogenetic reconstruction. This allowed us to show that A. ansorgii is not related as previously believed to circum-Indian Ocean leaf-toed geckos and is rather more closely related to other Malagasy leaf-toed geckos. Additionally, we explore and compare osteological variation in A. ansorgii skulls through High Resolution X-ray Computed Tomography with previously published material. This allowed us to describe herein a new genus, Bauerius gen. nov., and additionally provide a detailed redescription of the species (including the first description of male material), supplementing the limited original description and type series, which consisted of only two females.}, }
@article {pmid35390830, year = {2021}, author = {Takano, KT and Gao, JJ and Hu, YG and Li, NN and Yafuso, M and Suwito, A and Repin, R and Pungga, RAS and Meleng, PA and Kaliang, CH and Chong, L and Toda, MJ}, title = {Phylogeny, taxonomy and flower-breeding ecology of the Colocasiomyia cristata species group (Diptera: Drosophilidae), with descriptions of ten new species.}, journal = {Zootaxa}, volume = {5079}, number = {1}, pages = {170}, doi = {10.11646/zootaxa.5079.1.1}, pmid = {35390830}, issn = {1175-5334}, mesh = {Animals ; *Diptera ; *Drosophilidae ; Flowers ; Mitochondria ; Phylogeny ; Plant Breeding ; }, abstract = {The phylogeny of the Colocasiomyia cristata species group is reconstructed as a hypothesis, based on DNA sequences of two mitochondrial and six nuclear genes and 51 morphological characters. The resulting tree splits this species group into two clades, one of which corresponds to the colocasiae subgroup. Therefore, a new species subgroup named as the cristata subgroup is established for the other clade. Within the cristata subgroup, three subclades are recognized and each of them is defined as a species complex: the cristata complex composed of five species (including three new ones: C. kinabaluana sp. nov., C. kotana sp. nov. and C. matthewsi sp. nov.), the sabahana complex of two species (C. sabahana sp. nov. and C. sarawakana sp. nov.), and the xenalocasiae complex of five species (including C. sumatrana sp. nov. and C. leucocasiae sp. nov.). There are, however, three new species (C. ecornuta sp. nov., C. grandis sp. nov. and C. vieti sp. nov.) not assigned to any species complex. In addition, breeding habits are described for four cristata-subgroup species, each of which monopolizes its specific host plant. And, data of host-plant use are compiled for all species of the cristata group from records at various localities in the Oriental and Papuan regions. The evolution of host-plant selection and sharing modes is considered by mapping host-plant genera of each species on the phylogenetic tree resulting from the present study.}, }
@article {pmid35390639, year = {2022}, author = {Schneider, A}, title = {Evolution and diversification of mitochondrial protein import systems.}, journal = {Current opinion in cell biology}, volume = {75}, number = {}, pages = {102077}, doi = {10.1016/j.ceb.2022.102077}, pmid = {35390639}, issn = {1879-0410}, mesh = {Animals ; Carrier Proteins/metabolism ; Mammals/metabolism ; Membrane Proteins/metabolism ; Mitochondria/metabolism ; *Mitochondrial Membranes/metabolism ; *Mitochondrial Proteins/genetics/metabolism ; Protein Transport/physiology ; Saccharomyces cerevisiae/metabolism ; }, abstract = {More than 95% of mitochondrial proteins are encoded in the nucleus, synthesised in the cytosol and imported into the organelle. The evolution of mitochondrial protein import systems was therefore a prerequisite for the conversion of the α-proteobacterial mitochondrial ancestor into an organelle. Here, I review that the origin of the mitochondrial outer membrane import receptors can best be understood by convergent evolution. Subsequently, I discuss an evolutionary scenario that was proposed to explain the diversification of the inner membrane carrier protein translocases between yeast and mammals. Finally, I illustrate a scenario that can explain how the two specialised inner membrane protein translocase complexes found in most eukaryotes were reduced to a single multifunctional one in trypanosomes.}, }
@article {pmid35383845, year = {2022}, author = {Sharbrough, J and Conover, JL and Fernandes Gyorfy, M and Grover, CE and Miller, ER and Wendel, JF and Sloan, DB}, title = {Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms.}, journal = {Molecular biology and evolution}, volume = {39}, number = {4}, pages = {}, pmid = {35383845}, issn = {1537-1719}, mesh = {Cell Nucleus/genetics ; Evolution, Molecular ; Genome, Plant ; *Magnoliopsida/genetics ; Plastids/genetics ; Polyploidy ; Ribulose-Bisphosphate Carboxylase/genetics ; }, abstract = {Whole-genome duplications (WGDs) are a prominent process of diversification in eukaryotes. The genetic and evolutionary forces that WGD imposes on cytoplasmic genomes are not well understood, despite the central role that cytonuclear interactions play in eukaryotic function and fitness. Cellular respiration and photosynthesis depend on successful interaction between the 3,000+ nuclear-encoded proteins destined for the mitochondria or plastids and the gene products of cytoplasmic genomes in multi-subunit complexes such as OXPHOS, organellar ribosomes, Photosystems I and II, and Rubisco. Allopolyploids are thus faced with the critical task of coordinating interactions between the nuclear and cytoplasmic genes that were inherited from different species. Because the cytoplasmic genomes share a more recent history of common descent with the maternal nuclear subgenome than the paternal subgenome, evolutionary "mismatches" between the paternal subgenome and the cytoplasmic genomes in allopolyploids might lead to the accelerated rates of evolution in the paternal homoeologs of allopolyploids, either through relaxed purifying selection or strong directional selection to rectify these mismatches. We report evidence from six independently formed allotetraploids that the subgenomes exhibit unequal rates of protein-sequence evolution, but we found no evidence that cytonuclear incompatibilities result in altered evolutionary trajectories of the paternal homoeologs of organelle-targeted genes. The analyses of gene content revealed mixed evidence for whether the organelle-targeted genes are lost more rapidly than the non-organelle-targeted genes. Together, these global analyses provide insights into the complex evolutionary dynamics of allopolyploids, showing that the allopolyploid subgenomes have separate evolutionary trajectories despite sharing the same nucleus, generation time, and ecological context.}, }
@article {pmid35379961, year = {2022}, author = {Mok, BY and Kotrys, AV and Raguram, A and Huang, TP and Mootha, VK and Liu, DR}, title = {CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA.}, journal = {Nature biotechnology}, volume = {40}, number = {9}, pages = {1378-1387}, pmid = {35379961}, issn = {1546-1696}, support = {RM1 HG009490/HG/NHGRI NIH HHS/United States ; R35 GM118062/GM/NIGMS NIH HHS/United States ; R01 EB027793/EB/NIBIB NIH HHS/United States ; R35 GM122455/GM/NIGMS NIH HHS/United States ; T32 GM095450/GM/NIGMS NIH HHS/United States ; U01 AI142756/AI/NIAID NIH HHS/United States ; R01 EB031172/EB/NIBIB NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*CRISPR-Cas Systems ; Cytidine Deaminase/genetics ; DNA, Mitochondrial/genetics ; *Gene Editing ; Humans ; Mitochondria/genetics/metabolism ; }, abstract = {The all-protein cytosine base editor DdCBE uses TALE proteins and a double-stranded DNA-specific cytidine deaminase (DddA) to mediate targeted C•G-to-T•A editing. To improve editing efficiency and overcome the strict TC sequence-context constraint of DddA, we used phage-assisted non-continuous and continuous evolution to evolve DddA variants with improved activity and expanded targeting scope. Compared to canonical DdCBEs, base editors with evolved DddA6 improved mitochondrial DNA (mtDNA) editing efficiencies at TC by 3.3-fold on average. DdCBEs containing evolved DddA11 offered a broadened HC (H = A, C or T) sequence compatibility for both mitochondrial and nuclear base editing, increasing average editing efficiencies at AC and CC targets from less than 10% for canonical DdCBE to 15-30% and up to 50% in cell populations sorted to express both halves of DdCBE. We used these evolved DdCBEs to efficiently install disease-associated mtDNA mutations in human cells at non-TC target sites. DddA6 and DddA11 substantially increase the effectiveness and applicability of all-protein base editing.}, }
@article {pmid35377454, year = {2022}, author = {Monteiro, LB and Prodonoff, JS and Favero de Aguiar, C and Correa-da-Silva, F and Castoldi, A and Bakker, NVT and Davanzo, GG and Castelucci, B and Pereira, JADS and Curtis, J and Büscher, J and Reis, LMD and Castro, G and Ribeiro, G and Virgílio-da-Silva, JV and Adamoski, D and Dias, SMG and Consonni, SR and Donato, J and Pearce, EJ and Câmara, NOS and Moraes-Vieira, PM}, title = {Leptin Signaling Suppression in Macrophages Improves Immunometabolic Outcomes in Obesity.}, journal = {Diabetes}, volume = {71}, number = {7}, pages = {1546-1561}, doi = {10.2337/db21-0842}, pmid = {35377454}, issn = {1939-327X}, mesh = {Adipose Tissue/metabolism ; Animals ; Inflammation/metabolism ; *Insulin Resistance ; *Leptin/metabolism ; Macrophages/metabolism ; Mice ; Mice, Inbred C57BL ; Obesity/metabolism ; }, abstract = {Obesity is a major concern for global health care systems. Systemic low-grade inflammation in obesity is a major risk factor for insulin resistance. Leptin is an adipokine secreted by the adipose tissue that functions by controlling food intake, leading to satiety. Leptin levels are increased in obesity. Here, we show that leptin enhances the effects of LPS in macrophages, intensifying the production of cytokines, glycolytic rates, and morphological and functional changes in the mitochondria through an mTORC2-dependent, mTORC1-independent mechanism. Leptin also boosts the effects of IL-4 in macrophages, leading to increased oxygen consumption, expression of macrophage markers associated with a tissue repair phenotype, and wound healing. In vivo, hyperleptinemia caused by diet-induced obesity increases the inflammatory response by macrophages. Deletion of leptin receptor and subsequently of leptin signaling in myeloid cells (ObR-/-) is sufficient to improve insulin resistance in obese mice and decrease systemic inflammation. Our results indicate that leptin acts as a systemic nutritional checkpoint to regulate macrophage fitness and contributes to obesity-induced inflammation and insulin resistance. Thus, specific interventions aimed at downstream modulators of leptin signaling may represent new therapeutic targets to treat obesity-induced systemic inflammation.}, }
@article {pmid35360860, year = {2022}, author = {Bever, BW and Dietz, ZP and Sullins, JA and Montoya, AM and Bergthorsson, U and Katju, V and Estes, S}, title = {Mitonuclear Mismatch is Associated With Increased Male Frequency, Outcrossing, and Male Sperm Size in Experimentally-Evolved C. elegans.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {742272}, pmid = {35360860}, issn = {1664-8021}, abstract = {We provide a partial test of the mitonuclear sex hypothesis with the first controlled study of how male frequencies and rates of outcrossing evolve in response to mitonuclear mismatch by allowing replicate lineages of C. elegans nematodes containing either mitochondrial or nuclear mutations of electron transport chain (ETC) genes to evolve under three sexual systems: facultatively outcrossing (wildtype), obligately selfing, and obligately outcrossing. Among facultatively outcrossing lines, we found evolution of increased male frequency in at least one replicate line of all four ETC mutant backgrounds tested-nuclear isp-1, mitochondrial cox-1 and ctb-1, and an isp-1 IV; ctb-1M mitonuclear double mutant-and confirmed for a single line set (cox-1) that increased male frequency also resulted in successful outcrossing. We previously found the same result for lines evolved from another nuclear ETC mutant, gas-1. For several lines in the current experiment, however, male frequency declined to wildtype levels (near 0%) in later generations. Male frequency did not change in lines evolved from a wildtype control strain. Additional phenotypic assays of lines evolved from the mitochondrial cox-1 mutant indicated that evolution of high male frequency was accompanied by evolution of increased male sperm size and mating success with tester females, but that it did not translate into increased mating success with coevolved hermaphrodites. Rather, hermaphrodites' self-crossed reproductive fitness increased, consistent with sexually antagonistic coevolution. In accordance with evolutionary theory, males and sexual outcrossing may be most beneficial to populations evolving from a state of low ancestral fitness (gas-1, as previously reported) and less beneficial or deleterious to those evolving from a state of higher ancestral fitness (cox-1). In support of this idea, the obligately outcrossing fog-2 V; cox-1 M lines exhibited no fitness evolution compared to their ancestor, while facultatively outcrossing lines showed slight upward evolution of fitness, and all but one of the obligately selfing xol-1 X; cox-1 M lines evolved substantially increased fitness-even beyond wildtype levels. This work provides a foundation to directly test the effect of reproductive mode on the evolutionary dynamics of mitonuclear genomes, as well as whether compensatory mutations (nuclear or mitochondrial) can rescue populations from mitochondrial dysfunction.}, }
@article {pmid35359176, year = {2022}, author = {Ceriotti, LF and Gatica-Soria, L and Sanchez-Puerta, MV}, title = {Cytonuclear coevolution in a holoparasitic plant with highly disparate organellar genomes.}, journal = {Plant molecular biology}, volume = {109}, number = {6}, pages = {673-688}, pmid = {35359176}, issn = {1573-5028}, support = {PICT-2017-0691//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 06/A724//Universidad Nacional de Cuyo/ ; }, mesh = {*Balanophoraceae/genetics ; Cell Nucleus/genetics ; Chloroplast Proteins/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Plant/genetics ; Phylogeny ; Plants/genetics ; *Plastids/genetics ; }, abstract = {Contrasting substitution rates in the organellar genomes of Lophophytum agree with the DNA repair, replication, and recombination gene content. Plastid and nuclear genes whose products form multisubunit complexes co-evolve. The organellar genomes of the holoparasitic plant Lophophytum (Balanophoraceae) show disparate evolution. In the plastid, the genome has been severely reduced and presents a > 85% AT content, while in the mitochondria most protein-coding genes have been replaced by homologs acquired by horizontal gene transfer (HGT) from their hosts (Fabaceae). Both genomes carry genes whose products form multisubunit complexes with those of nuclear genes, creating a possible hotspot of cytonuclear coevolution. In this study, we assessed the evolutionary rates of plastid, mitochondrial and nuclear genes, and their impact on cytonuclear evolution of genes involved in multisubunit complexes related to lipid biosynthesis and proteolysis in the plastid and those in charge of the oxidative phosphorylation in the mitochondria. Genes from the plastid and the mitochondria (both native and foreign) of Lophophytum showed extremely high and ordinary substitution rates, respectively. These results agree with the biased loss of plastid-targeted proteins involved in angiosperm organellar repair, replication, and recombination machinery. Consistent with the high rate of evolution of plastid genes, nuclear-encoded subunits of plastid complexes showed disproportionate increases in non-synonymous substitution rates, while those of the mitochondrial complexes did not show different rates than the control (i.e. non-organellar nuclear genes). Moreover, the increases in the nuclear-encoded subunits of plastid complexes were positively correlated with the level of physical interaction they possess with the plastid-encoded ones. Overall, these results suggest that a structurally-mediated compensatory factor may be driving plastid-nuclear coevolution in Lophophytum, and that mito-nuclear coevolution was not altered by HGT.}, }
@article {pmid35358979, year = {2022}, author = {Risser, C and Tran Ba Loc, P and Binder-Foucard, F and Fabacher, T and Lefèvre, H and Sauvage, C and Sauleau, EA and Wolff, V}, title = {COVID-19 Impact on Stroke Admissions during France's First Epidemic Peak: An Exhaustive, Nationwide, Observational Study.}, journal = {Cerebrovascular diseases (Basel, Switzerland)}, volume = {51}, number = {5}, pages = {663-669}, pmid = {35358979}, issn = {1421-9786}, mesh = {Bayes Theorem ; *COVID-19/epidemiology ; Cohort Studies ; Communicable Disease Control ; Hospitalization ; Humans ; Pandemics ; *Stroke/diagnosis/epidemiology/therapy ; }, abstract = {INTRODUCTION: The coronavirus disease 2019 (COVID-19) pandemic continues to have great impacts on the care of non-COVID-19 patients. This was especially true during the first epidemic peak in France, which coincided with the national lockdown. The aim of this study was to identify whether a decrease in stroke admissions occurred in spring 2020, by analyzing the evolution of all stroke admissions in France from January 2019 to June 2020.<br><br>METHODS: We conducted a nationwide cohort study using the French national database of hospital admissions (Information Systems Medicalization Program) to extract exhaustive data on all hospitalizations in France with at least one stroke diagnosis between January 1, 2019, and June 30, 2020. The primary endpoint was the difference in the slope gradients of stroke hospitalizations between pre-epidemic, epidemic peak, and post-epidemic peak phases. Modeling was carried out using Bayesian techniques.<br><br>RESULTS: Stroke hospitalizations dropped from March 10, 2020 (slope gradient: -11.70), and began to rise again from March 22 (slope gradient: 2.090) to May 7. In total, there were 23,873 stroke admissions during the period March-April 2020, compared to 29,263 at the same period in 2019, representing a decrease of 18.42%. The percentage change was -15.63%, -25.19%, -18.62% for ischemic strokes, transient ischemic attacks, and hemorrhagic strokes, respectively.<br><br>DISCUSSION/CONCLUSION: Stroke hospitalizations in France experienced a decline during the first lockdown period, which cannot be explained by a sudden change in stroke incidence. This decline is therefore likely to be a direct, or indirect, result of the COVID-19 pandemic.}, }
@article {pmid35353639, year = {2022}, author = {Lipko, NB}, title = {Photobiomodulation: Evolution and Adaptation.}, journal = {Photobiomodulation, photomedicine, and laser surgery}, volume = {40}, number = {4}, pages = {213-233}, doi = {10.1089/photob.2021.0145}, pmid = {35353639}, issn = {2578-5478}, mesh = {Humans ; Lasers ; *Low-Level Light Therapy/methods ; Mitochondria ; }, abstract = {Photobiomodulation (PBM) can be described as the intentional use of low-power laser or light-emitting diode light in the visible and near-infrared light spectra as a medical treatment to living biological tissues. This article describes the evolution of photochemical reactions on Earth, the mitochondria, and their implications in PBM; the science of light and energy (necessary to understand the mechanisms of PBM); and the clinical science of light as therapeutic medicine. Finally, selected reviews of current treatment protocols and ongoing research regarding the possibilities for the use of PBM in the human body are examined.}, }
@article {pmid35351912, year = {2022}, author = {Lessios, HA and Hendler, G}, title = {Mitochondrial phylogeny of the brittle star genus Ophioderma.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {5304}, pmid = {35351912}, issn = {2045-2322}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Echinodermata/genetics ; *Evolution, Molecular ; Mitochondria/genetics ; Phylogeny ; }, abstract = {We reconstructed the mitochondrial phylogeny of the species of the brittle star genus Ophioderma, using sequences of the Cytochrome Oxidase I gene (COI) to address four questions: (i) Are the species of Ophioderma described on morphological evidence reflected in mitochondrial genealogy? (ii) Which species separated from which? (iii) When did speciation events occur? (iv) What is the rate of COI evolution in ophiuroids? We found that most of the 22 described species we sampled coincide with monophyletic clusters of COI sequences, but there are exceptions, most notably in the eastern Pacific, in which three undescribed species were indicated. The COI phylogeny lacks resolution in the deeper nodes, but it does show that there are four species pairs, the members of which are found on either side of the central American Isthmus. Two pairs with a genetic distance of ~ 4% between Atlantic and Pacific members were probably split during the final stages of Isthmus completion roughly 3 million years ago. The rate of divergence provided by these pairs allowed the calibration of a relaxed molecular clock. Estimated dates of divergence indicate that the lineages leading to extant species coalesce at times much older than congeneric species in other classes of echinoderms, suggesting that low extinction rates may be one of the reasons that ophiuroids are species-rich. The mean rate of COI substitution in Ophioderma is three times slower than that of echinoids. Conclusions of previous mitochondrial DNA studies of ophiuroids that relied on echinoid calibrations to determine divergence times need to be revised.}, }
@article {pmid35348760, year = {2022}, author = {Azuma, T and Pánek, T and Tice, AK and Kayama, M and Kobayashi, M and Miyashita, H and Suzaki, T and Yabuki, A and Brown, MW and Kamikawa, R}, title = {An Enigmatic Stramenopile Sheds Light on Early Evolution in Ochrophyta Plastid Organellogenesis.}, journal = {Molecular biology and evolution}, volume = {39}, number = {4}, pages = {}, pmid = {35348760}, issn = {1537-1719}, mesh = {Ecosystem ; Evolution, Molecular ; *Genome, Plastid ; Phylogeny ; Plants/genetics ; Plastids/genetics ; *Stramenopiles/genetics ; }, abstract = {Ochrophyta is an algal group belonging to the Stramenopiles and comprises diverse lineages of algae which contribute significantly to the oceanic ecosystems as primary producers. However, early evolution of the plastid organelle in Ochrophyta is not fully understood. In this study, we provide a well-supported tree of the Stramenopiles inferred by the large-scale phylogenomic analysis that unveils the eukaryvorous (nonphotosynthetic) protist Actinophrys sol (Actinophryidae) is closely related to Ochrophyta. We used genomic and transcriptomic data generated from A. sol to detect molecular traits of its plastid and we found no evidence of plastid genome and plastid-mediated biosynthesis, consistent with previous ultrastructural studies that did not identify any plastids in Actinophryidae. Moreover, our phylogenetic analyses of particular biosynthetic pathways provide no evidence of a current and past plastid in A. sol. However, we found more than a dozen organellar aminoacyl-tRNA synthases (aaRSs) that are of algal origin. Close relationships between aaRS from A. sol and their ochrophyte homologs document gene transfer of algal genes that happened before the divergence of Actinophryidae and Ochrophyta lineages. We further showed experimentally that organellar aaRSs of A. sol are targeted exclusively to mitochondria, although organellar aaRSs in Ochrophyta are dually targeted to mitochondria and plastids. Together, our findings suggested that the last common ancestor of Actinophryidae and Ochrophyta had not yet completed the establishment of host-plastid partnership as seen in the current Ochrophyta species, but acquired at least certain nuclear-encoded genes for the plastid functions.}, }
@article {pmid35342946, year = {2022}, author = {Senarat, S and Kettratad, J and Pairohakul, S and Ampawong, S and Huggins, BP and Coleman, MM and Kaneko, G}, title = {An update on the evolutionary origin of aglomerular kidney with structural and ultrastructural descriptions of the kidney in three fish species.}, journal = {Journal of fish biology}, volume = {100}, number = {5}, pages = {1283-1298}, doi = {10.1111/jfb.15045}, pmid = {35342946}, issn = {1095-8649}, support = {//Johnson Foundation/ ; //Chulalongkorn University/ ; }, mesh = {Animals ; *Batrachoidiformes ; Kidney/ultrastructure ; Kidney Glomerulus/ultrastructure ; Kidney Tubules ; Nephrons/ultrastructure ; *Smegmamorpha ; }, abstract = {The kidney of fish contains numerous nephrons, each of which is divided into the renal corpuscle and renal tubules. This glomerular structure is the filtration unit of the nephron and is important for the kidney function, but it has been reported that the renal corpuscle was lost in at least four independent linages of fish (i.e., aglomerular kidney). In this study, the authors newly described renal structures for three species by histological and ultrastructural observations: two aglomerular kidneys from a seahorse Hippocampus barbouri and a toadfish Allenbatrachus grunniens and a glomerular kidney from a snake eel Pisodonophis boro. The renal development of H. barbouri was also described during 1-35 days after birth. In all species tested, the anterior kidney was comprised of haematopoietic tissues and a few renal tubules, whereas the posterior kidney contained more renal tubules. Although the glomerular structure was present in P. boro, light microscopic observations identified no glomeruli in the kidney of H. barbouri and A. grunniens. Ultrastructurally, abundant deep basal infoldings with mitochondria in the renal tubules were observed in A. grunniens compared to H. barbouri and P. boro, suggesting the possible role of basal infoldings in maintaining the osmotic balance. By integrating the results from the three species and comprehensive literature search, the authors further showed that 56 species have been reported to be aglomerular, and that the aglomerular kidney has evolved at least eight times in bony fishes.}, }
@article {pmid35340599, year = {2022}, author = {Hickey, T and Devaux, J and Rajagopal, V and Power, A and Crossman, D}, title = {Paradoxes of Hymenoptera flight muscles, extreme machines.}, journal = {Biophysical reviews}, volume = {14}, number = {1}, pages = {403-412}, pmid = {35340599}, issn = {1867-2450}, abstract = {In the Carboniferous, insects evolved flight. Intense selection drove for high performance and approximately 100 million years later, Hymenoptera (bees, wasps and ants) emerged. Some species had proportionately small wings, with apparently impossible aerodynamic challenges including a need for high frequency flight muscles (FMs), powered exclusively off aerobic pathways and resulting in extreme aerobic capacities. Modern insect FMs are the most refined and form large dense blocks that occupy 90% of the thorax. These can beat wings at 200 to 230 Hz, more than double that achieved by standard neuromuscular systems. To do so, rapid repolarisation was circumvented through evolution of asynchronous stimulation, stretch activation, elastic recoil and a paradoxically slow Ca[2+] reuptake. While the latter conserves ATP, considerable ATP is demanded at the myofibrils. FMs have diminished sarcoplasmic volumes, and ATP is produced solely by mitochondria, which pack myocytes to maximal limits and have very dense cristae. Gaseous oxygen is supplied directly to mitochondria. While FMs appear to be optimised for function, several unusual paradoxes remain. FMs lack any significant equivalent to the creatine kinase shuttle, and myofibrils are twice as wide as those of within cardiomyocytes. The mitochondrial electron transport systems also release large amounts of reactive oxygen species (ROS) and respiratory complexes do not appear to be present at any exceptional level. Given that the loss of the creatine kinase shuttle and elevated ROS impairs heart function, we question how do FM shuttle adenylates at high rates and tolerate oxidative stress conditions that occur in diseased hearts?}, }
@article {pmid35333655, year = {2022}, author = {Jackson, TD and Crameri, JJ and Muellner-Wong, L and Frazier, AE and Palmer, CS and Formosa, LE and Hock, DH and Fujihara, KM and Stait, T and Sharpe, AJ and Thorburn, DR and Ryan, MT and Stroud, DA and Stojanovski, D}, title = {Sideroflexin 4 is a complex I assembly factor that interacts with the MCIA complex and is required for the assembly of the ND2 module.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {13}, pages = {e2115566119}, pmid = {35333655}, issn = {1091-6490}, mesh = {Adenosine Triphosphate/metabolism ; *Electron Transport Complex I/metabolism ; Humans ; Membrane Proteins ; Mitochondria/genetics/metabolism ; *Mitochondrial Diseases/genetics ; Mitochondrial Proteins/genetics/metabolism ; Mutation ; }, abstract = {SignificanceMitochondria are double-membraned eukaryotic organelles that house the proteins required for generation of ATP, the energy currency of cells. ATP generation within mitochondria is performed by five multisubunit complexes (complexes I to V), the assembly of which is an intricate process. Mutations in subunits of these complexes, or the suite of proteins that help them assemble, lead to a severe multisystem condition called mitochondrial disease. We show that SFXN4, a protein that causes mitochondrial disease when mutated, assists with the assembly of complex I. This finding explains why mutations in SFXN4 cause mitochondrial disease and is surprising because SFXN4 belongs to a family of amino acid transporter proteins, suggesting that it has undergone a dramatic shift in function through evolution.}, }
@article {pmid35325186, year = {2022}, author = {Ye, Z and Zhao, C and Raborn, RT and Lin, M and Wei, W and Hao, Y and Lynch, M}, title = {Genetic Diversity, Heteroplasmy, and Recombination in Mitochondrial Genomes of Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa.}, journal = {Molecular biology and evolution}, volume = {39}, number = {4}, pages = {}, pmid = {35325186}, issn = {1537-1719}, support = {R35 GM122566/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/genetics ; Daphnia/genetics ; *Genome, Mitochondrial ; Heteroplasmy ; *Pulicaria/genetics ; Recombination, Genetic ; }, abstract = {Genetic variants of mitochondrial DNA at the individual (heteroplasmy) and population (polymorphism) levels provide insight into their roles in multiple cellular and evolutionary processes. However, owing to the paucity of genome-wide data at the within-individual and population levels, the broad patterns of these two forms of variation remain poorly understood. Here, we analyze 1,804 complete mitochondrial genome sequences from Daphnia pulex, Daphnia pulicaria, and Daphnia obtusa. Extensive heteroplasmy is observed in D. obtusa, where the high level of intraclonal divergence must have resulted from a biparental-inheritance event, and recombination in the mitochondrial genome is apparent, although perhaps not widespread. Global samples of D. pulex reveal remarkably low mitochondrial effective population sizes, <3% of those for the nuclear genome. In addition, levels of population diversity in mitochondrial and nuclear genomes are uncorrelated across populations, suggesting an idiosyncratic evolutionary history of mitochondria in D. pulex. These population-genetic features appear to be a consequence of background selection associated with highly deleterious mutations arising in the strongly linked mitochondrial genome, which is consistent with polymorphism and divergence data suggesting a predominance of strong purifying selection. Nonetheless, the fixation of mildly deleterious mutations in the mitochondrial genome also appears to be driving positive selection on genes encoded in the nuclear genome whose products are deployed in the mitochondrion.}, }
@article {pmid35322502, year = {2022}, author = {Cantoni, D and Osborne, A and Taib, N and Thompson, G and Martín-Escolano, R and Kazana, E and Edrich, E and Brown, IR and Gribaldo, S and Gourlay, CW and Tsaousis, AD}, title = {Localization and functional characterization of the alternative oxidase in Naegleria.}, journal = {The Journal of eukaryotic microbiology}, volume = {69}, number = {4}, pages = {e12908}, pmid = {35322502}, issn = {1550-7408}, support = {BB/M009971/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Eukaryota ; Mitochondrial Proteins ; *Naegleria ; *Naegleria fowleri ; Oxidoreductases/metabolism ; Plant Proteins ; }, abstract = {The alternative oxidase (AOX) is a protein involved in supporting enzymatic reactions of the Krebs cycle in instances when the canonical (cytochrome-mediated) respiratory chain has been inhibited, while allowing for the maintenance of cell growth and necessary metabolic processes for survival. Among eukaryotes, alternative oxidases have dispersed distribution and are found in plants, fungi, and protists, including Naegleria ssp. Naegleria species are free-living unicellular amoeboflagellates and include the pathogenic species of N. fowleri, the so-called "brain-eating amoeba." Using a multidisciplinary approach, we aimed to understand the evolution, localization, and function of AOX and the role that plays in Naegleria's biology. Our analyses suggest that AOX was present in last common ancestor of the genus and structure prediction showed that all functional residues are also present in Naegleria species. Using cellular and biochemical techniques, we also functionally characterize N. gruberi's AOX in its mitochondria, and we demonstrate that its inactivation affects its proliferation. Consequently, we discuss the benefits of the presence of this protein in Naegleria species, along with its potential pathogenicity role in N. fowleri. We predict that our findings will spearhead new explorations to understand the cell biology, metabolism, and evolution of Naegleria and other free-living relatives.}, }
@article {pmid35318703, year = {2022}, author = {Hammond, M and Dorrell, RG and Speijer, D and Lukeš, J}, title = {Eukaryotic cellular intricacies shape mitochondrial proteomic complexity.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {44}, number = {5}, pages = {e2100258}, doi = {10.1002/bies.202100258}, pmid = {35318703}, issn = {1521-1878}, mesh = {Biological Evolution ; Eukaryota/physiology ; *Eukaryotic Cells/metabolism ; Mitochondria/metabolism ; Organelles/metabolism ; Phylogeny ; *Proteomics ; }, abstract = {Mitochondria have been fundamental to the eco-physiological success of eukaryotes since the last eukaryotic common ancestor (LECA). They contribute essential functions to eukaryotic cells, above and beyond classical respiration. Mitochondria interact with, and complement, metabolic pathways occurring in other organelles, notably diversifying the chloroplast metabolism of photosynthetic organisms. Here, we integrate existing literature to investigate how mitochondrial metabolism varies across the landscape of eukaryotic evolution. We illustrate the mitochondrial remodelling and proteomic changes undergone in conjunction with major evolutionary transitions. We explore how the mitochondrial complexity of the LECA has been remodelled in specific groups to support subsequent evolutionary transitions, such as the acquisition of chloroplasts in photosynthetic species and the emergence of multicellularity. We highlight the versatile and crucial roles played by mitochondria during eukaryotic evolution, extending from its huge contribution to the development of the LECA itself to the dynamic evolution of individual eukaryote groups, reflecting both their current ecologies and evolutionary histories.}, }
@article {pmid35307029, year = {2022}, author = {Smith, AJ and Advani, J and Brock, DC and Nellissery, J and Gumerson, J and Dong, L and Aravind, L and Kennedy, B and Swaroop, A}, title = {GATD3A, a mitochondrial deglycase with evolutionary origins from gammaproteobacteria, restricts the formation of advanced glycation end products.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {68}, pmid = {35307029}, issn = {1741-7007}, support = {ZIAEY000450/EY/NEI NIH HHS/United States ; ZIAEY000546/EY/NEI NIH HHS/United States ; }, mesh = {Animals ; *Gammaproteobacteria/metabolism ; *Glycation End Products, Advanced/metabolism ; Mammals ; Mice ; Mitochondrial Proteins/genetics ; Protein Deglycase DJ-1/metabolism ; }, abstract = {BACKGROUND: Functional complexity of the eukaryotic mitochondrial proteome is augmented by independent gene acquisition from bacteria since its endosymbiotic origins. Mammalian homologs of many ancestral mitochondrial proteins have uncharacterized catalytic activities. Recent forward genetic approaches attributed functions to proteins in established metabolic pathways, thereby limiting the possibility of identifying novel biology relevant to human disease. We undertook a bottom-up biochemistry approach to discern evolutionarily conserved mitochondrial proteins with catalytic potential.<br><br>RESULTS: Here, we identify a Parkinson-associated DJ-1/PARK7-like protein-glutamine amidotransferase-like class 1 domain-containing 3A (GATD3A), with bacterial evolutionary affinities although not from alphaproteobacteria. We demonstrate that GATD3A localizes to the mitochondrial matrix and functions as a deglycase. Through its amidolysis domain, GATD3A removes non-enzymatic chemical modifications produced during the Maillard reaction between dicarbonyls and amines of nucleotides and amino acids. GATD3A interacts with factors involved in mitochondrial mRNA processing and translation, suggestive of a role in maintaining integrity of important biomolecules through its deglycase activity. The loss of GATD3A in mice is associated with accumulation of advanced glycation end products (AGEs) and altered mitochondrial dynamics.<br><br>CONCLUSIONS: An evolutionary perspective helped us prioritize a previously uncharacterized but predicted mitochondrial protein GATD3A, which mediates the removal of early glycation intermediates. GATD3A restricts the formation of AGEs in mitochondria and is a relevant target for diseases where AGE deposition is a pathological hallmark.}, }
@article {pmid35306886, year = {2022}, author = {Zluvova, J and Kubat, Z and Hobza, R and Janousek, B}, title = {Adaptive changes of the autosomal part of the genome in a dioecious clade of Silene.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {377}, number = {1850}, pages = {20210228}, pmid = {35306886}, issn = {1471-2970}, mesh = {Chromosomes, Plant ; Evolution, Molecular ; *Magnoliopsida ; Sex Chromosomes ; *Silene/genetics ; }, abstract = {The genus Silene brings many opportunities for the study of various processes involved in the evolution of dioecy and young sex chromosomes. Here we focus on a dioecious clade in Silene subgenus Silene and closely related species. This study provides improved support for monophyly of this clade (based on inclusion of further dioecious species) and a new estimate of its age (ca 2.3 million years). We observed a rise in adaptive evolution in the autosomal and pseudoautosomal parts of the genome on the branch where dioecy originated. This increase is not a result of the accumulation of sexually antagonistic genes in the pseudoautosomal region. It is also not caused by the coevolution of genes acting in mitochondria (despite the possibility that dioecy along this branch could have evolved from a nucleo-cytoplasmic male sterility-based system). After considering other possibilities, the most parsimonious explanation for the increase seen in the number of positively selected codons is the adaptive evolution of genes involved in the adaptation of the autosomal part of the genome to dioecy, as described in Charnov's sex-allocation theory. As the observed coincidence cannot prove causality, studies in other dioecious clades are necessary to allow the formation of general conclusions. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.}, }
@article {pmid35294555, year = {2022}, author = {Karmin, M and Flores, R and Saag, L and Hudjashov, G and Brucato, N and Crenna-Darusallam, C and Larena, M and Endicott, PL and Jakobsson, M and Lansing, JS and Sudoyo, H and Leavesley, M and Metspalu, M and Ricaut, FX and Cox, MP}, title = {Episodes of Diversification and Isolation in Island Southeast Asian and Near Oceanian Male Lineages.}, journal = {Molecular biology and evolution}, volume = {39}, number = {3}, pages = {}, pmid = {35294555}, issn = {1537-1719}, mesh = {Asia, Southeastern ; *Asian People ; *DNA, Mitochondrial/genetics ; Humans ; Male ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Island Southeast Asia (ISEA) and Oceania host one of the world's richest assemblages of human phenotypic, linguistic, and cultural diversity. Despite this, the region's male genetic lineages are globally among the last to remain unresolved. We compiled ∼9.7 Mb of Y chromosome (chrY) sequence from a diverse sample of over 380 men from this region, including 152 first reported here. The granularity of this data set allows us to fully resolve and date the regional chrY phylogeny. This new high-resolution tree confirms two main population bursts: multiple rapid diversifications following the region's initial settlement ∼50 kya, and extensive expansions <6 kya. Notably, ∼40-25 kya the deep rooting local lineages of C-M130, M-P256, and S-B254 show almost no further branching events in ISEA, New Guinea, and Australia, matching a similar pause in diversification seen in maternal mitochondrial DNA lineages. The main local lineages start diversifying ∼25 kya, at the time of the last glacial maximum. This improved chrY topology highlights localized events with important historical implications, including pre-Holocene contact between Mainland and ISEA, potential interactions between Australia and the Papuan world, and a sustained period of diversification following the flooding of the ancient Sunda and Sahul continents as the insular landscape observed today formed. The high-resolution phylogeny of the chrY presented here thus enables a detailed exploration of past isolation, interaction, and change in one of the world's least understood regions.}, }
@article {pmid35289381, year = {2022}, author = {Drechsel, V and Schneebauer, G and Sandbichler, AM and Fiechtner, B and Pelster, B}, title = {Oxygen consumption and acid secretion in isolated gas gland cells of the European eel Anguilla anguilla.}, journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology}, volume = {192}, number = {3-4}, pages = {447-457}, pmid = {35289381}, issn = {1432-136X}, support = {I2984-B25//&#xd6;sterreichische Forschungsf&#xf6;rderungsgesellschaft/ ; }, mesh = {Air Sacs/metabolism ; *Anguilla/metabolism ; Animals ; Glucose/metabolism ; Oxygen/metabolism ; Oxygen Consumption ; }, abstract = {Swimbladder gas gland cells are known to produce lactic acid required for the acidification of swimbladder blood and decreasing the oxygen carrying capacity of swimbladder blood, i.e., the onset of the Root effect. Gas gland cells have also been shown to metabolize glucose via the pentose phosphate shunt, but the role of the pentose phosphate shunt for acid secretion has not yet been evaluated. Similarly, aerobic metabolism of gas gland cells has been largely neglected so far. In the present study, we therefore simultaneously assessed the role of glycolysis and of the pentose phosphate shunt for acid secretion and recorded oxygen consumption of isolated swimbladder gas gland cells of the European eel. Presence of glucose was essential for acid secretion, and at glucose concentrations of about 1.5 mmol l[-1] acid secretion of gas gland cells reached a maximum, indicating that glucose concentrations in swimbladder blood should not be limiting acid production and secretion under physiological conditions. The data revealed that most of the acid was produced in the glycolytic pathway, but a significant fraction was also contributed by the pentose phosphate shunt. Addition of glucose to gas gland cells incubated in a glucose-free medium resulted in a reduction of oxygen uptake. Inhibition of mitochondrial respiration significantly reduced oxygen consumption, but a fraction of mitochondria-independent respiration remained in presence of rotenone and antimycin A. In the presence of glucose, application of either iodo-acetate inhibiting glycolysis or 6-AN inhibiting the pentose phosphate shunt did not significantly affect oxygen uptake, indicating an independent regulation of oxidative phosphorylation and of acid production. Inhibition of the muscarinic acetylcholine receptor caused a slight elevation in acid secretion, while forskolin caused a concentration-dependent reduction in acid secretion, indicating muscarinic and c-AMP-dependent control of acid secretion in gas gland cells.}, }
@article {pmid35279439, year = {2022}, author = {Zhou, B and Qi, D and Liu, S and Qi, H and Wang, Y and Zhao, K and Tian, F}, title = {Physiological, morphological and transcriptomic responses of Tibetan naked carps (Gymnocypris przewalskii) to salinity variations.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {42}, number = {}, pages = {100982}, doi = {10.1016/j.cbd.2022.100982}, pmid = {35279439}, issn = {1878-0407}, mesh = {Animals ; *Carps ; *Cyprinidae/genetics ; Gills ; Lakes ; Salinity ; Tibet ; Transcriptome ; }, abstract = {Gymnocypris przewalskii is a native cyprinid fish that dwells in the Lake Qinghai with salinity of 12-13‰. It migrates annually to the freshwater rivers for spawning, experiencing the significant changes in salinity. In the present study, we performed the physiological, morphological and transcriptomic analyses to understand the osmoregulation in G. przewalskii. The physiological assay showed that the osmotic pressure of G. przewalskii was almost isosmotic to the brackish lake water. The low salinity reduced its ionic concentrations and osmotic pressure. The plasticity of gill microstructure was linked to the salinity variations, including the presence of mucus and intact tight junctions in brackish water and the development of the mitochondria-rich cells and the loosened tight junctions in freshwater. RNA-seq analysis identified 1926 differentially expressed genes, including 710 and 1216 down- and up-regulated genes in freshwater, which were enriched in ion transport, cell-cell adhesion, and mucus secretion. Genes in ion uptake were activated in low salinity, and mucus pathways and tight junction showed the higher transcription in brackish water. The isosmoticity between the body fluid and the environment suggested G. przewalskii was in the metabolic-saving condition in the brackish water. The decreased salinity disrupted this balance, which activated the ion uptake in freshwater to maintain osmotic homeostasis. The gill remodeling was involved in this process through the development of the mitochondria-rich cells to enhance ion uptake. The current finding provided insights into the potential mechanisms of G. przewalskii to cope with salinity alteration.}, }
@article {pmid35277964, year = {2022}, author = {Lam, SM and Li, J and Sun, H and Mao, W and Lu, Z and Zhao, Q and Han, C and Gong, X and Jiang, B and Chua, GH and Zhao, Z and Meng, F and Shui, G}, title = {Quantitative Lipidomics and Spatial MS-Imaging Uncovered Neurological and Systemic Lipid Metabolic Pathways Underlying Troglomorphic Adaptations in Cave-Dwelling Fish.}, journal = {Molecular biology and evolution}, volume = {39}, number = {4}, pages = {}, pmid = {35277964}, issn = {1537-1719}, mesh = {Animals ; Biological Evolution ; Caves ; *Characidae/genetics ; *Cyprinidae ; *Demyelinating Diseases ; Lipidomics ; Metabolic Networks and Pathways ; Phospholipids ; }, abstract = {Sinocyclocheilus represents a rare, freshwater teleost genus endemic to China that comprises the river-dwelling surface fish and the cave-dwelling cavefish. Using a combinatorial approach of quantitative lipidomics and mass-spectrometry imaging (MSI), we demonstrated that neural compartmentalization of lipid distribution and lipid metabolism is associated with the evolution of troglomorphic traits in Sinocyclocheilus. Attenuated docosahexaenoic acid (DHA) biosynthesis via the Δ4 desaturase pathway led to reductions in DHA-phospholipids in cavefish cerebellum. Instead, cavefish accumulates arachidonic acid-phospholipids that may disfavor retinotectal arbor growth. Importantly, MSI of sulfatides coupled with immunostaining of myelin basic protein and transmission electron microscopy images of hindbrain axons revealed demyelination in cavefish raphe serotonergic neurons. Demyelination in cavefish parallels the loss of neuroplasticity governing social behavior such as aggressive dominance. Outside the brain, quantitative lipidomics and qRT-PCR revealed systemic reductions in membrane esterified DHAs in the liver, attributed to suppression of genes along the Sprecher pathway (elovl2, elovl5, and acox1). Development of fatty livers was observed in cavefish; likely mediated by an impeded mobilization of storage lipids, as evident in the diminished expressions of pnpla2, lipea, lipeb, dagla, and mgll; and suppressed β-oxidation of fatty acyls via both mitochondria and peroxisomes as reflected in the reduced expressions of cpt1ab, hadhaa, cpt2, decr1, and acox1. These neurological and systemic metabolic adaptations serve to reduce energy expenditure, forming the basis of recessive evolution that eliminates nonessential morphological and behavioral traits and giving cavefish a selective advantage to thrive in caves where proper resource allocation becomes a major determinant of survival.}, }
@article {pmid35272287, year = {2022}, author = {Ho, KM and Morgan, DJR}, title = {The Proximal Tubule as the Pathogenic and Therapeutic Target in Acute Kidney Injury.}, journal = {Nephron}, volume = {146}, number = {5}, pages = {494-502}, doi = {10.1159/000522341}, pmid = {35272287}, issn = {2235-3186}, mesh = {*Acute Kidney Injury/drug therapy/pathology ; Humans ; Kidney/pathology ; Kidney Glomerulus/pathology ; *Kidney Tubular Necrosis, Acute ; Kidney Tubules, Proximal/pathology ; }, abstract = {BACKGROUND: In 2004, the term acute kidney injury (AKI) was introduced with the intention of broadening our understanding of rapid declines in renal function and to replace the historical terms of acute renal failure and acute tubular necrosis (ATN). Despite this evolution in terminology, the mechanisms of AKI have stayed largely elusive with the pathophysiological concepts of ATN remaining the mainstay in our understanding of AKI.<br><br>SUMMARY: The proximal tubule (PT), having the highest mitochondrial content in the kidney and relying heavily on oxidative phosphorylation to generate ATP, is vulnerable to ischaemic insults and mitochondrial dysfunction. Histologically, pathological changes in the PT are more consistent than changes to the glomeruli or the loop of Henle in AKI. Physiologically, activation of tubuloglomerular feedback due to PT dysfunction leads to an increase in preglomerular afferent arteriole resistance and a reduction in glomerular filtration. Pharmacologically, frusemide - a drug commonly used in the setting of oliguric AKI - is actively secreted by the PT and its diuretic effect is compromised by its failure to be secreted into the urine and thus be delivered to its site of action at the loop of Henle in AKI. Increases in the urinary, but not plasma biomarkers, of PT injury within 1 h of shock suggest that the PT as the initiation pathogenic target of AKI.<br><br>KEY MESSAGE: Therapeutic agents targeting specifically the PT epithelial cells, in particular its mitochondria - including amino acid ergothioneine and superoxide scavenger MitoTEMPO - show great promises in ameliorating AKI.}, }
@article {pmid35259985, year = {2022}, author = {Perez, M and Breusing, C and Angers, B and Beinart, RA and Won, YJ and Young, CR}, title = {Divergent paths in the evolutionary history of maternally transmitted clam symbionts.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1970}, pages = {20212137}, pmid = {35259985}, issn = {1471-2954}, mesh = {Animals ; Bacteria/genetics ; *Bivalvia/genetics ; *Gammaproteobacteria/genetics ; Genome Size ; Genome, Bacterial ; Phylogeny ; Symbiosis/genetics ; }, abstract = {Vertical transmission of bacterial endosymbionts is accompanied by virtually irreversible gene loss that results in a progressive reduction in genome size. While the evolutionary processes of genome reduction have been well described in some terrestrial symbioses, they are less understood in marine systems where vertical transmission is rarely observed. The association between deep-sea vesicomyid clams and chemosynthetic Gammaproteobacteria is one example of maternally inherited symbioses in the ocean. Here, we assessed the contributions of drift, recombination and selection to genome evolution in two extant vesicomyid symbiont clades by comparing 15 representative symbiont genomes (1.017-1.586 Mb) to those of closely related bacteria and the hosts' mitochondria. Our analyses suggest that drift is a significant force driving genome evolution in vesicomyid symbionts, though selection and interspecific recombination appear to be critical for maintaining symbiont functional integrity and creating divergent patterns of gene conservation. Notably, the two symbiont clades possess putative functional differences in sulfide physiology, anaerobic respiration and dependency on environmental vitamin B12, which probably reflect adaptations to different ecological habitats available to each symbiont group. Overall, these results contribute to our understanding of the eco-evolutionary processes shaping reductive genome evolution in vertically transmitted symbioses.}, }
@article {pmid35258392, year = {2022}, author = {Magalhaes-Novais, S and Blecha, J and Naraine, R and Mikesova, J and Abaffy, P and Pecinova, A and Milosevic, M and Bohuslavova, R and Prochazka, J and Khan, S and Novotna, E and Sindelka, R and Machan, R and Dewerchin, M and Vlcak, E and Kalucka, J and Stemberkova Hubackova, S and Benda, A and Goveia, J and Mracek, T and Barinka, C and Carmeliet, P and Neuzil, J and Rohlenova, K and Rohlena, J}, title = {Mitochondrial respiration supports autophagy to provide stress resistance during quiescence.}, journal = {Autophagy}, volume = {18}, number = {10}, pages = {2409-2426}, pmid = {35258392}, issn = {1554-8635}, mesh = {AMP-Activated Protein Kinases/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; *Autophagy ; Cysteine/metabolism ; DNA, Mitochondrial/metabolism ; Dextrans/metabolism ; Endothelial Cells/metabolism ; Fibroblasts/metabolism ; Formaldehyde/metabolism ; Humans ; *Inflammatory Bowel Diseases/metabolism ; Isothiocyanates ; Lipopolysaccharides/metabolism ; Mechanistic Target of Rapamycin Complex 1/metabolism ; Mice ; Microtubule-Associated Proteins/metabolism ; Mitochondria/metabolism ; Phosphatidylethanolamines/metabolism ; Reactive Oxygen Species/metabolism ; Respiration ; Sirolimus ; }, abstract = {Mitochondrial oxidative phosphorylation (OXPHOS) generates ATP, but OXPHOS also supports biosynthesis during proliferation. In contrast, the role of OXPHOS during quiescence, beyond ATP production, is not well understood. Using mouse models of inducible OXPHOS deficiency in all cell types or specifically in the vascular endothelium that negligibly relies on OXPHOS-derived ATP, we show that selectively during quiescence OXPHOS provides oxidative stress resistance by supporting macroautophagy/autophagy. Mechanistically, OXPHOS constitutively generates low levels of endogenous ROS that induce autophagy via attenuation of ATG4B activity, which provides protection from ROS insult. Physiologically, the OXPHOS-autophagy system (i) protects healthy tissue from toxicity of ROS-based anticancer therapy, and (ii) provides ROS resistance in the endothelium, ameliorating systemic LPS-induced inflammation as well as inflammatory bowel disease. Hence, cells acquired mitochondria during evolution to profit from oxidative metabolism, but also built in an autophagy-based ROS-induced protective mechanism to guard against oxidative stress associated with OXPHOS function during quiescence.Abbreviations: AMPK: AMP-activated protein kinase; AOX: alternative oxidase; Baf A: bafilomycin A1; CI, respiratory complexes I; DCF-DA: 2',7'-dichlordihydrofluorescein diacetate; DHE: dihydroethidium; DSS: dextran sodium sulfate; ΔΨmi: mitochondrial inner membrane potential; EdU: 5-ethynyl-2'-deoxyuridine; ETC: electron transport chain; FA: formaldehyde; HUVEC; human umbilical cord endothelial cells; IBD: inflammatory bowel disease; LC3B: microtubule associated protein 1 light chain 3 beta; LPS: lipopolysaccharide; MEFs: mouse embryonic fibroblasts; MTORC1: mechanistic target of rapamycin kinase complex 1; mtDNA: mitochondrial DNA; NAC: N-acetyl cysteine; OXPHOS: oxidative phosphorylation; PCs: proliferating cells; PE: phosphatidylethanolamine; PEITC: phenethyl isothiocyanate; QCs: quiescent cells; ROS: reactive oxygen species; PLA2: phospholipase A2, WB: western blot.}, }
@article {pmid35255175, year = {2022}, author = {Treidel, LA and Quintanilla Ramirez, GS and Chung, DJ and Menze, MA and Vázquez-Medina, JP and Williams, CM}, title = {Selection on dispersal drives evolution of metabolic capacities for energy production in female wing-polymorphic sand field crickets, Gryllus firmus.}, journal = {Journal of evolutionary biology}, volume = {35}, number = {4}, pages = {599-609}, pmid = {35255175}, issn = {1420-9101}, support = {//Society for Integrative and Comparative Biology (SICB)/ ; //University of California Berkeley/ ; //Hellman Family Foundation/ ; }, mesh = {Animals ; Energy Metabolism ; Female ; *Gryllidae/physiology ; Phenotype ; Wings, Animal/metabolism ; }, abstract = {Life history and metabolism covary, but the mechanisms and individual traits responsible for these linkages remain unresolved. Dispersal capability is a critical component of life history that is constrained by metabolic capacities for energy production. Conflicting relationships between metabolism and life histories may be explained by accounting for variation in dispersal and maximal metabolic rates. We used female wing-polymorphic sand field crickets, Gryllus firmus, selected either for long wings (LW, flight-capable) or short wings (SW, flightless) to test the hypothesis that selection on dispersal capability drives the evolution of metabolic capacities. While resting metabolic rates were similar, long-winged crickets reached higher maximal metabolic rates than short-winged crickets, resulting in improved running performance. We further provided insight into the mechanisms responsible for covariation between life history and metabolism by comparing mitochondrial content of tissues involved in powering locomotion and assessing the function of mitochondria isolated from long- and short-winged crickets. Our results demonstrated that larger metabolic capacities in long-winged crickets were underpinned by increases in mitochondrial content of dorsoventral flight muscle and enhanced bioenergetic capacities of mitochondria within the fat body, a tissue responsible for fuel storage and mobilization. Thus, selection on flight capability correlates with increases in maximal, but not resting metabolic rates, through modifications of tissues powering locomotion at the cellular and organelle levels. This allows organisms to meet high energetic demands of activity for life history. Dispersal capability should therefore explicitly be considered as a potential factor driving the evolution of metabolic capacities.}, }
@article {pmid35248958, year = {2022}, author = {Rodríguez-Martín, D and Murciano, A and Herráiz, M and de Francisco, P and Amaro, F and Gutiérrez, JC and Martín-González, A and Díaz, S}, title = {Arsenate and arsenite differential toxicity in Tetrahymena thermophila.}, journal = {Journal of hazardous materials}, volume = {431}, number = {}, pages = {128532}, doi = {10.1016/j.jhazmat.2022.128532}, pmid = {35248958}, issn = {1873-3336}, mesh = {Animals ; Arsenates/metabolism/toxicity ; *Arsenic/metabolism/toxicity ; *Arsenites/metabolism/toxicity ; Metallothionein ; *Tetrahymena thermophila/genetics ; }, abstract = {A comparative analysis of toxicities of both arsenic forms (arsenite and arsenate) in the model eukaryotic microorganism Tetrahymena thermophila (ciliate protozoa) has shown the presence of various detoxification mechanisms and cellular effects comparable to those of animal cells under arsenic stress. In the wild type strain SB1969 arsenate is almost 2.5 times more toxic than arsenite. According to the concentration addition model used in binary metallic mixtures their toxicities show an additive effect. Using fluorescent assays and flow cytometry, it has been detected that As(V) generates elevated levels of ROS/RNS compared to As(III). Both produce the same levels of superoxide anion, but As(V) also causes greater increases in hydrogen peroxide and peroxynitrite. The mitochondrial membrane potential is affected by both As(V) and As(III), and electron microscopy has also revealed that mitochondria are the main target of both arsenic ionic forms. Fusion/fission and swelling mitochondrial and mitophagy, together with macroautophagy, vacuolization and mucocyst extruction are mainly associated to As(V) toxicity, while As(III) induces an extensive lipid metabolism dysfunction (adipotropic effect). Quantitative RT-PCR analysis of some genes encoding antioxidant proteins or enzymes has shown that glutathione and thioredoxin metabolisms are involved in the response to arsenic stress. Likewise, the function of metallothioneins seems to be crucial in arsenic detoxification processes, after using both metallothionein knockout and knockdown strains and cells overexpressing metallothionein genes from this ciliate. The analysis of the differential toxicity of As(III) and As(V) shown in this study provides cytological and molecular tools to be used as biomarkers for each of the two arsenic ionic forms.}, }
@article {pmid35247316, year = {2022}, author = {Moorthy, BT and Jiang, C and Patel, DM and Ban, Y and O'Shea, CR and Kumar, A and Yuan, T and Birnbaum, MD and Gomes, AV and Chen, X and Fontanesi, F and Lampidis, TJ and Barrientos, A and Zhang, F}, title = {The evolutionarily conserved arginyltransferase 1 mediates a pVHL-independent oxygen-sensing pathway in mammalian cells.}, journal = {Developmental cell}, volume = {57}, number = {5}, pages = {654-669.e9}, pmid = {35247316}, issn = {1878-1551}, support = {R01 GM138557/GM/NIGMS NIH HHS/United States ; R35 GM118141/GM/NIGMS NIH HHS/United States ; }, mesh = {*Aminoacyltransferases/genetics/metabolism ; Animals ; Humans ; Mammals/metabolism ; *Oxygen ; Phylogeny ; Proteolysis ; }, abstract = {The response to oxygen availability is a fundamental process concerning metabolism and survival/death in all mitochondria-containing eukaryotes. However, the known oxygen-sensing mechanism in mammalian cells depends on pVHL, which is only found among metazoans but not in other species. Here, we present an alternative oxygen-sensing pathway regulated by ATE1, an enzyme ubiquitously conserved in eukaryotes that influences protein degradation by posttranslational arginylation. We report that ATE1 centrally controls the hypoxic response and glycolysis in mammalian cells by preferentially arginylating HIF1α that is hydroxylated by PHD in the presence of oxygen. Furthermore, the degradation of arginylated HIF1α is independent of pVHL E3 ubiquitin ligase but dependent on the UBR family proteins. Bioinformatic analysis of human tumor data reveals that the ATE1/UBR and pVHL pathways jointly regulate oxygen sensing in a transcription-independent manner with different tissue specificities. Phylogenetic analysis suggests that eukaryotic ATE1 likely evolved during mitochondrial domestication, much earlier than pVHL.}, }
@article {pmid35243551, year = {2022}, author = {Choi, H and Lee, K and Kim, D and Kim, S and Lee, JH}, title = {The implication of holocytochrome c synthase mutation in Korean familial hypoplastic amelogenesis imperfecta.}, journal = {Clinical oral investigations}, volume = {26}, number = {6}, pages = {4487-4498}, pmid = {35243551}, issn = {1436-3771}, support = {2021R1F1A104718511//National Research Foundation of Korea/ ; 2020R1A6A1A03047902//National Research Foundation of Korea/ ; 2021R1A2B5B01001903//National Research Foundation of Korea/ ; }, mesh = {*Amelogenesis Imperfecta/genetics ; Dentists ; Humans ; Lyases ; Mutation ; Professional Role ; Republic of Korea ; }, abstract = {OBJECTIVES: This study aimed to comprehensively characterise genetic variants of amelogenesis imperfecta in a single Korean family through whole-exome sequencing and bioinformatics analysis.<br><br>MATERIAL AND METHODS: Thirty-one individuals of a Korean family, 9 of whom were affected and 22 unaffected by amelogenesis imperfecta, were enrolled. Whole-exome sequencing was performed on 12 saliva samples, including samples from 8 affected and 4 unaffected individuals. The possible candidate genes associated with the disease were screened by segregation analysis and variant filtering. In silico mutation impact analysis was then performed on the filtered variants based on sequence conservation and protein structure.<br><br>RESULTS: Whole-exome sequencing data revealed an X-linked dominant, heterozygous genomic missense mutation in the mitochondrial gene holocytochrome c synthase (HCCS). We also found that HCCS is potentially related to the role of mitochondria in amelogenesis. The HCCS variant was expected to be deleterious in both evolution-based and large population-based analyses. Further, the variant was predicted to have a negative effect on catalytic function of HCCS by in silico analysis of protein structure. In addition, HCCS had significant association with amelogenesis in literature mining analysis.<br><br>CONCLUSIONS: These findings suggest new evidence for the relationship between amelogenesis and mitochondria function, which could be implicated in the pathogenesis of amelogenesis imperfecta.<br><br>CLINICAL RELEVANCE: The discovery of HCCS mutations and a deeper understanding of the pathogenesis of amelogenesis imperfecta could lead to finding solutions for the fundamental treatment of this disease. Furthermore, it enables dental practitioners to establish predictable prosthetic treatment plans at an early stage by early detection of amelogenesis imperfecta through personalised medicine.}, }
@article {pmid35242350, year = {2022}, author = {Pearman, WS and Wells, SJ and Dale, J and Silander, OK and Freed, NE}, title = {Long-read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod.}, journal = {Royal Society open science}, volume = {9}, number = {1}, pages = {211550}, pmid = {35242350}, issn = {2054-5703}, abstract = {Most animal mitochondrial genomes are small, circular and structurally conserved. However, recent work indicates that diverse taxa possess unusual mitochondrial genomes. In Isopoda, species in multiple lineages have atypical and rearranged mitochondrial genomes. However, more species of this speciose taxon need to be evaluated to understand the evolutionary origins of atypical mitochondrial genomes in this group. In this study, we report the presence of an atypical mitochondrial structure in the New Zealand endemic marine isopod, Isocladus armatus. Data from long- and short-read DNA sequencing suggest that I. armatus has two mitochondrial chromosomes. The first chromosome consists of two mitochondrial genomes that have been inverted and fused together in a circular form, and the second chromosome consists of a single mitochondrial genome in a linearized form. This atypical mitochondrial structure has been detected in other isopod lineages, and our data from an additional divergent isopod lineage (Sphaeromatidae) lends support to the hypothesis that atypical structure evolved early in the evolution of Isopoda. Additionally, we find that an asymmetrical site previously observed across many species within Isopoda is absent in I. armatus, but confirm the presence of two asymmetrical sites recently reported in two other isopod species.}, }
@article {pmid35231030, year = {2022}, author = {Güngör, B and Flohr, T and Garg, SG and Herrmann, JM}, title = {The ER membrane complex (EMC) can functionally replace the Oxa1 insertase in mitochondria.}, journal = {PLoS biology}, volume = {20}, number = {3}, pages = {e3001380}, pmid = {35231030}, issn = {1545-7885}, mesh = {Amino Acid Sequence ; Cell Respiration/genetics ; Electron Transport Complex IV/genetics/*metabolism ; Endoplasmic Reticulum/*metabolism ; Membrane Proteins/genetics/*metabolism ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Mitochondrial Proton-Translocating ATPases/genetics/metabolism ; Mutation ; Nuclear Proteins/genetics/*metabolism ; Phylogeny ; Protein Biosynthesis/genetics ; Protein Transport/genetics ; Saccharomyces cerevisiae/genetics/growth &amp; development/*metabolism ; Saccharomyces cerevisiae Proteins/classification/genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Two multisubunit protein complexes for membrane protein insertion were recently identified in the endoplasmic reticulum (ER): the guided entry of tail anchor proteins (GET) complex and ER membrane complex (EMC). The structures of both of their hydrophobic core subunits, which are required for the insertion reaction, revealed an overall similarity to the YidC/Oxa1/Alb3 family members found in bacteria, mitochondria, and chloroplasts. This suggests that these membrane insertion machineries all share a common ancestry. To test whether these ER proteins can functionally replace Oxa1 in yeast mitochondria, we generated strains that express mitochondria-targeted Get2-Get1 and Emc6-Emc3 fusion proteins in Oxa1 deletion mutants. Interestingly, the Emc6-Emc3 fusion was able to complement an Δoxa1 mutant and restored its respiratory competence. The Emc6-Emc3 fusion promoted the insertion of the mitochondrially encoded protein Cox2, as well as of nuclear encoded inner membrane proteins, although was not able to facilitate the assembly of the Atp9 ring. Our observations indicate that protein insertion into the ER is functionally conserved to the insertion mechanism in bacteria and mitochondria and adheres to similar topological principles.}, }
@article {pmid35222958, year = {2022}, author = {Zárate, D and Lima, TG and Poole, JD and Calfee, E and Burton, RS and Kohn, JR}, title = {Admixture in Africanized honey bees (Apis mellifera) from Panamá to San Diego, California (U.S.A.).}, journal = {Ecology and evolution}, volume = {12}, number = {2}, pages = {e8580}, pmid = {35222958}, issn = {2045-7758}, abstract = {The Africanized honey bee (AHB) is a New World amalgamation of several subspecies of the western honey bee (Apis mellifera), a diverse taxon historically grouped into four major biogeographic lineages: A (African), M (Western European), C (Eastern European), and O (Middle Eastern). In 1956, accidental release of experimentally bred "Africanized" hybrids from a research apiary in Sao Paulo, Brazil initiated a hybrid species expansion that now extends from northern Argentina to northern California (U.S.A.). Here, we assess nuclear admixture and mitochondrial ancestry in 60 bees from four countries (Panamá; Costa Rica, Mexico; U.S.A) across this expansive range to assess ancestry of AHB several decades following initial introduction and test the prediction that African ancestry decreases with increasing latitude. We find that AHB nuclear genomes from Central America and Mexico have predominately African genomes (76%-89%) with smaller contributions from Western and Eastern European lineages. Similarly, nearly all honey bees from Central America and Mexico possess mitochondrial ancestry from the African lineage with few individuals having European mitochondria. In contrast, AHB from San Diego (CA) shows markedly lower African ancestry (38%) with substantial genomic contributions from all four major honey bee lineages and mitochondrial ancestry from all four clades as well. Genetic diversity measures from all New World populations equal or exceed those of ancestral populations. Interestingly, the feral honey bee population of San Diego emerges as a reservoir of diverse admixture and high genetic diversity, making it a potentially rich source of genetic material for honey bee breeding.}, }
@article {pmid35219813, year = {2022}, author = {Xia, L and Cheng, C and Zhao, X and He, X and Yu, X and Li, J and Wang, Y and Chen, J}, title = {Characterization of the mitochondrial genome of Cucumis hystrix and comparison with other cucurbit crops.}, journal = {Gene}, volume = {823}, number = {}, pages = {146342}, doi = {10.1016/j.gene.2022.146342}, pmid = {35219813}, issn = {1879-0038}, mesh = {Crops, Agricultural/genetics ; Cucumis/*genetics ; Cucurbitaceae/classification/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome Size ; *Genome, Mitochondrial ; Genomics ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {The mitochondria ofCucumis genus contain several intriguing features such as paternal inheritance and three-ring genome structure. However, the evolutionary relationships of mitochondria inCucumisremain elusive. Here, we assembled the mitochondrial genome ofC. hystrixand performed a comparative genomic analysis with other crops inthe Cucurbitaceae. The mitochondrial genome ofC. hystrixhas three circular-mapping chromosomes of lengths 1,113,461 bp, 110,683 bp, and 92,288 bp, which contain 73 genes including 38 protein-coding genes, 31tRNAgenes, and 4rRNAgenes. Repeat sequences, RNA editing, and horizontal gene transfer events were identified. The results of phylogenetic analyses, collinearity and gene clusters revealed thatC. hystrixis closer toC. sativus than to C. melo. Meanwhile, wedemonstrated mitochondrial paternal inheritance inC. hystrixbymolecular markers. In comparison with other cucurbitcrops, wefound amarker foridentification of germplasm resources ofCucumis. Collectively, our findings provide a tool to help clarify the paternal lineage within that genus in the evolution of Cucumis.}, }
@article {pmid35215562, year = {2022}, author = {Levy, D and Giannini, M and Oulehri, W and Riou, M and Marcot, C and Pizzimenti, M and Debrut, L and Charloux, A and Geny, B and Meyer, A}, title = {Long Term Follow-Up of Sarcopenia and Malnutrition after Hospitalization for COVID-19 in Conventional or Intensive Care Units.}, journal = {Nutrients}, volume = {14}, number = {4}, pages = {}, pmid = {35215562}, issn = {2072-6643}, mesh = {Aged ; *COVID-19/complications ; Follow-Up Studies ; Hand Strength ; Hospitalization ; Humans ; Intensive Care Units ; *Malnutrition/diagnosis/epidemiology ; Quality of Life ; SARS-CoV-2 ; *Sarcopenia/diagnosis/epidemiology/etiology ; }, abstract = {BACKGROUND: The post-COVID-19 condition, defined as COVID-19-related signs and symptoms lasting at least 2 months and persisting more than 3 months after infection, appears now as a public health issue in terms of frequency and quality of life alterations. Nevertheless, few data are available concerning long term evolution of malnutrition and sarcopenia, which deserve further attention.<br><br>METHOD: Sarcopenia was investigated prospectively, together with weight evolution, at admission and at 3 and 6 months after hospital discharge in 139 COVID-19 patients, using the European Working Group on Sarcopenia in Older People (EWGSOP2) criteria, associating both decreased muscle strength and muscle mass, assessed, respectively, with hand dynamometer and dual-energy X-ray absorptiometry.<br><br>RESULTS: Of the 139 patients, 22 presented with sarcopenia at 3 months; intensive care units (ICU) length of stay was the sole factor associated with sarcopenia after multivariate analysis. Although the entire group did not demonstrate significant weight change, weight decreased significantly in the sarcopenia group (Five and eight patients, showing, respectively, >5 or >10% weight decrease). Interestingly, at 6 months, 16 of the 22 patients recovered from sarcopenia and their weight returned toward baseline values.<br><br>CONCLUSIONS: Sarcopenia and malnutrition are frequently observed in patients hospitalized for COVID-19, even 3 months after infection occurrence, but can largely be reversed at 6 months after discharge. Enhanced patient care is needed in sarcopenic patients, particularly during long stays in an ICU.}, }
@article {pmid35208909, year = {2022}, author = {Cevallos, MA and Degli Esposti, M}, title = {New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient.}, journal = {Microorganisms}, volume = {10}, number = {2}, pages = {}, pmid = {35208909}, issn = {2076-2607}, abstract = {We survey here the Alphaproteobacteria, a large class encompassing physiologically diverse bacteria which are divided in several orders established since 2007. Currently, there is considerable uncertainty regarding the classification of an increasing number of marine metagenome-assembled genomes (MAGs) that remain poorly defined in their taxonomic position within Alphaproteobacteria. The traditional classification of NCBI taxonomy is increasingly complemented by the Genome Taxonomy Database (GTDB), but the two taxonomies differ considerably in the classification of several Alphaproteobacteria, especially from ocean metagenomes. We analyzed the classification of Alphaproteobacteria lineages that are most common in marine environments, using integrated approaches of phylogenomics and functional profiling of metabolic features that define their aerobic metabolism. Using protein markers such as NuoL, the largest membrane subunit of complex I, we have identified new clades of Alphaproteobacteria that are specific to marine niches with steep oxygen gradients (oxycline). These bacteria have relatives among MAGs found in anoxic strata of Lake Tanganyika and together define a lineage that is distinct from either Rhodospirillales or Sneathiellales. We characterized in particular the new 'oxycline' clade. Our analysis of Alphaproteobacteria also reveals new clues regarding the ancestry of mitochondria, which likely evolved in oxycline marine environments.}, }
@article {pmid35207539, year = {2022}, author = {Lei, L and Burton, ZF}, title = {"Superwobbling" and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {35207539}, issn = {2075-1729}, abstract = {The genetic code evolved around the reading of the tRNA anticodon on the primitive ribosome, and tRNA-34 wobble and tRNA-37 modifications coevolved with the code. We posit that EF-Tu, the closing mechanism of the 30S ribosomal subunit, methylation of wobble U34 at the 5-carbon and suppression of wobbling at the tRNA-36 position were partly redundant and overlapping functions that coevolved to establish the code. The genetic code devolved in evolution of mitochondria to reduce the size of the tRNAome (all of the tRNAs of an organism or organelle). "Superwobbling" or four-way wobbling describes a major mechanism for shrinking the mitochondrial tRNAome. In superwobbling, unmodified wobble tRNA-U34 can recognize all four codon wobble bases (A, G, C and U), allowing a single unmodified tRNA-U34 to read a 4-codon box. During code evolution, to suppress superwobbling in 2-codon sectors, U34 modification by methylation at the 5-carbon position appears essential. As expected, at the base of code evolution, tRNA-37 modifications mostly related to the identity of the adjacent tRNA-36 base. TRNA-37 modifications help maintain the translation frame during elongation.}, }
@article {pmid35205291, year = {2022}, author = {Zhang, BQ and Song, XP and Zhang, XQ and Huang, YX and Liang, YJ and Zhou, S and Yang, CF and Yang, LT and Huang, X and Li, YR}, title = {Differential Gene Expression Analysis of SoCBL Family Calcineurin B-like Proteins: Potential Involvement in Sugarcane Cold Stress.}, journal = {Genes}, volume = {13}, number = {2}, pages = {}, pmid = {35205291}, issn = {2073-4425}, mesh = {Calcineurin/genetics ; Cold-Shock Response/genetics ; Gene Expression ; Phylogeny ; *Saccharum/genetics ; }, abstract = {Sugarcan e is a major crop for sugar and biofuel production and is cultivated in tropical and subtropical areas worldwide. Sugarcane growth is constrained because of winter's low-temperature stress, and cold resistance is an important limitation in sugarcane growth enhancement. Therefore, in this study, we identified a gene involved in the low-temperature stress response of sugarcane. Calcineurin B-like (CBL) protein is a calcium signal receptor involved in the cold stress response. Five sugarcane CBL genes were cloned, sequenced, and named SoCBL1, SoCBL3, SoCBL5, SoCBL6, and SoCBL9. The protein sequences of these genes were analyzed. The calculated molecular weight of these proteins was 24.5, 25.9, 25.2, 25.6, and 26.3 kD, respectively. Subcellular localization analysis revealed that SoCBL1, SoCBL3, SoCBL6, and SoCBL9 were situated in the cytoplasm, while SoCBL5 was present in mitochondria. Secondary structure analysis showed that these five CBL proteins had similar secondary structures. Conserved domain analysis displayed that each sugarcane CBL protein contained three conserved EF domains. According to the self-expanding values of the phylogenetic tree, the CBL gene family was divided into four groups. The CBL1 and CBL9 genes were classified into one group, illustrating that these two genes might possess a similar function. The expression analysis of the SoCBL gene under low temperatures showed that SoCBL3 and SoCBL5 were affected significantly, while SoCBL1 and SoCBL9 were less affected. These results demonstrate that the CBL genes in sugarcane have similar characteristics and present differences in genetic diversity and gene expression response to low temperatures. Therefore, these genes might be novel candidates for fighting cold stress in sugarcane.}, }
@article {pmid35205149, year = {2022}, author = {Zhu, Y}, title = {Gap Junction-Dependent and -Independent Functions of Connexin43 in Biology.}, journal = {Biology}, volume = {11}, number = {2}, pages = {}, pmid = {35205149}, issn = {2079-7737}, abstract = {For the first time in animal evolution, the emergence of gap junctions allowed direct exchanges of cellular substances for communication between two cells. Innexin proteins constituted primordial gap junctions until the connexin protein emerged in deuterostomes and took over the gap junction function. After hundreds of millions of years of gene duplication, the connexin gene family now comprises 21 members in the human genome. Notably, GJA1, which encodes the Connexin43 protein, is one of the most widely expressed and commonly studied connexin genes. The loss of Gja1 in mice leads to swelling and a blockage of the right ventricular outflow tract and death of the embryos at birth, suggesting a vital role of Connexin43 gap junction in heart development. Since then, the importance of Connexin43-mediated gap junction function has been constantly expanded to other types of cells. Other than forming gap junctions, Connexin43 can also form hemichannels to release or uptake small molecules from the environment or even mediate many physiological processes in a gap junction-independent manner on plasma membranes. Surprisingly, Connexin43 also localizes to mitochondria in the cell, playing important roles in mitochondrial potassium import and respiration. At the molecular level, Connexin43 mRNA and protein are processed with very distinct mechanisms to yield carboxyl-terminal fragments with different sizes, which have their unique subcellular localization and distinct biological activities. Due to many exciting advancements in Connexin43 research, this review aims to start with a brief introduction of Connexin43 and then focuses on updating our knowledge of its gap junction-independent functions.}, }
@article {pmid35199143, year = {2022}, author = {Helmstetter, N and Chybowska, AD and Delaney, C and Da Silva Dantas, A and Gifford, H and Wacker, T and Munro, C and Warris, A and Jones, B and Cuomo, CA and Wilson, D and Ramage, G and Farrer, RA}, title = {Population genetics and microevolution of clinical Candida glabrata reveals recombinant sequence types and hyper-variation within mitochondrial genomes, virulence genes, and drug targets.}, journal = {Genetics}, volume = {221}, number = {1}, pages = {}, pmid = {35199143}, issn = {1943-2631}, support = {MR/V033417/1/MRC_/Medical Research Council/United Kingdom ; MR/N006364/2//Medical Research Council Centre for Medical Mycology/ ; 214317/Z/18/Z//Wellcome Trust Senior Research Fellowship/ ; 215239/Z/19/Z//Wellcome Trust Seed Award/ ; }, mesh = {Adult ; Antifungal Agents/pharmacology ; *Candida glabrata/genetics ; Drug Resistance, Fungal/genetics ; Genetics, Population ; *Genome, Mitochondrial ; Humans ; Virulence/genetics ; }, abstract = {Candida glabrata is the second most common etiological cause of worldwide systemic candidiasis in adult patients. Genome analysis of 68 isolates from 8 hospitals across Scotland, together with 83 global isolates, revealed insights into the population genetics and evolution of C. glabrata. Clinical isolates of C. glabrata from across Scotland are highly genetically diverse, including at least 19 separate sequence types that have been recovered previously in globally diverse locations, and 1 newly discovered sequence type. Several sequence types had evidence for ancestral recombination, suggesting transmission between distinct geographical regions has coincided with genetic exchange arising in new clades. Three isolates were missing MATα1, potentially representing a second mating type. Signatures of positive selection were identified in every sequence type including enrichment for epithelial adhesins thought to facilitate fungal adhesin to human epithelial cells. In patent microevolution was identified from 7 sets of recurrent cases of candidiasis, revealing an enrichment for nonsynonymous and frameshift indels in cell surface proteins. Microevolution within patients also affected epithelial adhesins genes, and several genes involved in drug resistance including the ergosterol synthesis gene ERG4 and the echinocandin target FKS1/2, the latter coinciding with a marked drop in fluconazole minimum inhibitory concentration. In addition to nuclear genome diversity, the C. glabrata mitochondrial genome was particularly diverse, with reduced conserved sequence and conserved protein-encoding genes in all nonreference ST15 isolates. Together, this study highlights the genetic diversity within the C. glabrata population that may impact virulence and drug resistance, and 2 major mechanisms generating this diversity: microevolution and genetic exchange/recombination.}, }
@article {pmid35197365, year = {2022}, author = {Łabędzka-Dmoch, K and Rażew, M and Gapińska, M and Piątkowski, J and Kolondra, A and Salmonowicz, H and Wenda, JM and Nowotny, M and Golik, P}, title = {The Pet127 protein is a mitochondrial 5'-to-3' exoribonuclease from the PD-(D/E)XK superfamily involved in RNA maturation and intron degradation in yeasts.}, journal = {RNA (New York, N.Y.)}, volume = {28}, number = {5}, pages = {711-728}, pmid = {35197365}, issn = {1469-9001}, mesh = {Candida albicans ; *Exoribonucleases/genetics ; Fungal Proteins/genetics/metabolism ; Introns/genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; *RNA ; }, abstract = {Pet127 is a mitochondrial protein found in multiple eukaryotic lineages, but absent from several taxa, including plants and animals. Distant homology suggests that it belongs to the divergent PD-(D/E)XK superfamily which includes various nucleases and related proteins. Earlier yeast genetics experiments suggest that it plays a nonessential role in RNA degradation and 5' end processing. Our phylogenetic analysis suggests that it is a primordial eukaryotic invention that was retained in diverse groups, and independently lost several times in the evolution of other organisms. We demonstrate for the first time that the fungal Pet127 protein in vitro is a processive 5'-to-3' exoribonuclease capable of digesting various substrates in a sequence nonspecific manner. Mutations in conserved residues essential in the PD-(D/E)XK superfamily active site abolish the activity of Pet127. Deletion of the PET127 gene in the pathogenic yeast Candida albicans results in a moderate increase in the steady-state levels of several transcripts and in accumulation of unspliced precursors and intronic sequences of three introns. Mutations in the active site residues result in a phenotype identical to that of the deletant, confirming that the exoribonuclease activity is related to the physiological role of the Pet127 protein. Pet127 activity is, however, not essential for maintaining the mitochondrial respiratory activity in C. albicans.}, }
@article {pmid35191499, year = {2022}, author = {Zamudio-Ochoa, A and Morozov, YI and Sarfallah, A and Anikin, M and Temiakov, D}, title = {Mechanisms of mitochondrial promoter recognition in humans and other mammalian species.}, journal = {Nucleic acids research}, volume = {50}, number = {5}, pages = {2765-2781}, pmid = {35191499}, issn = {1362-4962}, support = {R35 GM131832/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/genetics ; DNA-Directed RNA Polymerases/metabolism ; Humans ; Mammals/genetics/metabolism ; Mitochondria/enzymology/*genetics ; Mitochondrial Proteins/metabolism ; Transcription Factors/chemistry/genetics ; Transcription Initiation Site ; *Transcription, Genetic ; }, abstract = {Recognition of mammalian mitochondrial promoters requires the concerted action of mitochondrial RNA polymerase (mtRNAP) and transcription initiation factors TFAM and TFB2M. In this work, we found that transcript slippage results in heterogeneity of the human mitochondrial transcripts in vivo and in vitro. This allowed us to correctly interpret the RNAseq data, identify the bona fide transcription start sites (TSS), and assign mitochondrial promoters for > 50% of mammalian species and some other vertebrates. The divergent structure of the mammalian promoters reveals previously unappreciated aspects of mtDNA evolution. The correct assignment of TSS also enabled us to establish the precise register of the DNA in the initiation complex and permitted investigation of the sequence-specific protein-DNA interactions. We determined the molecular basis of promoter recognition by mtRNAP and TFB2M, which cooperatively recognize bases near TSS in a species-specific manner. Our findings reveal a role of mitochondrial transcription machinery in mitonuclear coevolution and speciation.}, }
@article {pmid35189365, year = {2022}, author = {Hawlitschek, O and Ortiz, EM and Noori, S and Webster, KC and Husemann, M and Pereira, RJ}, title = {Transcriptomic data reveals nuclear-mitochondrial discordance in Gomphocerinae grasshoppers (Insecta: Orthoptera: Acrididae).}, journal = {Molecular phylogenetics and evolution}, volume = {170}, number = {}, pages = {107439}, doi = {10.1016/j.ympev.2022.107439}, pmid = {35189365}, issn = {1095-9513}, mesh = {Animals ; *Grasshoppers/genetics ; Hybridization, Genetic ; Mitochondria/genetics ; *Orthoptera/genetics ; Phylogeny ; Transcriptome ; }, abstract = {The phylogeny of many groups of Orthoptera remains poorly understood. Previous phylogenetic studies largely restricted to few mitochondrial markers found many species in the grasshopper subfamily Gomphocerinae to be para- or polyphyletic, presumably because of incomplete lineage sorting and ongoing hybridization between putatively young lineages. Resolving the phylogeny of the Chorthippus biguttulus species complex is important because many morphologically cryptic species occupy overlapping ranges across Eurasia and serve important ecological functions. We investigated whether multispecies coalescent analysis of 540 genes generated by transcriptome sequencing could resolve the phylogeny of the C. biguttulus complex and related Gomphocerinae species. Our divergence time estimates confirm that Gomphocerinae is a very young radiation, with an age estimated at 1.38 (2.35-0.77) mya for the C. biguttulus complex. Our estimated topology based on complete mitogenomes recovered some species as para- or polyphyletic. In contrast, the multispecies coalescent based on nuclear genes retrieved all species as monophyletic clusters, corroborating most taxonomic hypotheses. Our results underline the importance of using nuclear multispecies coalescent methods for studying young radiations and highlight the need of further taxonomic revision in Gomphocerinae grasshoppers.}, }
@article {pmid35188099, year = {2022}, author = {De La Rossa, A and Laporte, MH and Astori, S and Marissal, T and Montessuit, S and Sheshadri, P and Ramos-Fernández, E and Mendez, P and Khani, A and Quairiaux, C and Taylor, EB and Rutter, J and Nunes, JM and Carleton, A and Duchen, MR and Sandi, C and Martinou, JC}, title = {Paradoxical neuronal hyperexcitability in a mouse model of mitochondrial pyruvate import deficiency.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35188099}, issn = {2050-084X}, mesh = {3-Hydroxybutyric Acid/pharmacology ; Animals ; Anion Transport Proteins/genetics/*metabolism ; Biological Transport ; Calcium/physiology ; Gene Expression Regulation/drug effects ; Homeostasis/drug effects/physiology ; Ketone Bodies ; Mice ; Mice, Knockout ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/genetics/*metabolism ; Monocarboxylic Acid Transporters/genetics/*metabolism ; Neurons/drug effects/metabolism ; Oxidation-Reduction ; Pentylenetetrazole/toxicity ; Phosphorylation ; Pyruvic Acid/*metabolism ; Seizures/chemically induced ; Tamoxifen/pharmacology ; }, abstract = {Neuronal excitation imposes a high demand of ATP in neurons. Most of the ATP derives primarily from pyruvate-mediated oxidative phosphorylation, a process that relies on import of pyruvate into mitochondria occuring exclusively via the mitochondrial pyruvate carrier (MPC). To investigate whether deficient oxidative phosphorylation impacts neuron excitability, we generated a mouse strain carrying a conditional deletion of MPC1, an essential subunit of the MPC, specifically in adult glutamatergic neurons. We found that, despite decreased levels of oxidative phosphorylation and decreased mitochondrial membrane potential in these excitatory neurons, mice were normal at rest. Surprisingly, in response to mild inhibition of GABA mediated synaptic activity, they rapidly developed severe seizures and died, whereas under similar conditions the behavior of control mice remained unchanged. We report that neurons with a deficient MPC were intrinsically hyperexcitable as a consequence of impaired calcium homeostasis, which reduced M-type potassium channel activity. Provision of ketone bodies restored energy status, calcium homeostasis and M-channel activity and attenuated seizures in animals fed a ketogenic diet. Our results provide an explanation for the seizures that frequently accompany a large number of neuropathologies, including cerebral ischemia and diverse mitochondriopathies, in which neurons experience an energy deficit.}, }
@article {pmid35187492, year = {2022}, author = {Juhaszova, M and Kobrinsky, E and Zorov, DB and Nuss, HB and Yaniv, Y and Fishbein, KW and de Cabo, R and Montoliu, L and Gabelli, SB and Aon, MA and Cortassa, S and Sollott, SJ}, title = {ATP Synthase K[+]- and H[+]-fluxes Drive ATP Synthesis and Enable Mitochondrial K[+]-"Uniporter" Function: II. Ion and ATP Synthase Flux Regulation.}, journal = {Function (Oxford, England)}, volume = {3}, number = {2}, pages = {zqac001}, pmid = {35187492}, issn = {2633-8823}, mesh = {Bayes Theorem ; Myeloid Cell Leukemia Sequence 1 Protein/metabolism ; Phylogeny ; *Mitochondrial Proton-Translocating ATPases/genetics ; *Mitochondria/metabolism ; Adenosine Triphosphate/metabolism ; }, abstract = {We demonstrated that ATP synthase serves the functions of a primary mitochondrial K[+] "uniporter," i.e., the primary way for K[+] to enter mitochondria. This K[+] entry is proportional to ATP synthesis, regulating matrix volume and energy supply-vs-demand matching. We show that ATP synthase can be upregulated by endogenous survival-related proteins via IF1. We identified a conserved BH3-like domain of IF1 which overlaps its "minimal inhibitory domain" that binds to the β-subunit of F1. Bcl-xL and Mcl-1 possess a BH3-binding-groove that can engage IF1 and exert effects, requiring this interaction, comparable to diazoxide to augment ATP synthase's H[+] and K[+] flux and ATP synthesis. Bcl-xL and Mcl-1, but not Bcl-2, serve as endogenous regulatory ligands of ATP synthase via interaction with IF1 at this BH3-like domain, to increase its chemo-mechanical efficiency, enabling its function as the recruitable mitochondrial KATP-channel that can limit ischemia-reperfusion injury. Using Bayesian phylogenetic analysis to examine potential bacterial IF1-progenitors, we found that IF1 is likely an ancient (∼2 Gya) Bcl-family member that evolved from primordial bacteria resident in eukaryotes, corresponding to their putative emergence as symbiotic mitochondria, and functioning to prevent their parasitic ATP consumption inside the host cell.}, }
@article {pmid35175958, year = {2023}, author = {Buja, LM}, title = {Pathobiology of Myocardial Ischemia and Reperfusion Injury: Models, Modes, Molecular Mechanisms, Modulation, and Clinical Applications.}, journal = {Cardiology in review}, volume = {31}, number = {5}, pages = {252-264}, pmid = {35175958}, issn = {1538-4683}, abstract = {This review presents an integrated approach to the analysis of myocardial ischemia and reperfusion injury and the modulating influence of myocardial conditioning during the evolution of acute myocardial infarction (AMI) and other clinical settings. Experimental studies have involved a spectrum of in vitro, ex vivo, and in vivo models, and guidelines have been developed for the conduct of rigorous preclinical studies and for the identification of various forms of cell injury and death in evolving AMI. AMI in vivo is dominated by oncosis (cell injury with swelling) leading to necroptosis and final necrosis of ischemic cardiomyocytes (CMCs), without or with contraction band formation. Early after coronary occlusion, reperfusion salvages a significant amount of ischemic myocardium in the subepicardium while reperfusion injury contributes up to 50% of the final subendocardial infarct. AMI progression is mediated by damage (or danger)-associated molecular patterns, also known as alarmins, which activate pattern recognition receptors and initiate the inflammatory response. In preclinical studies, lethal reperfusion injury can largely be prevented with preconditioning or postconditioning by pharmacologic or physical means due to effects on both the CMC and microvasculature. Conditioning involves triggers, cytosolic mediators, and intracellular effectors. Mitochondria have a central role in the maintenance and loss of viability of CMCs. Reperfusion of severely ischemic myocardium leads to sustained opening of the mitochondrial permeability transition pore (MPTP). Once the MPTP is opened, the mitochondrial membrane potential (ΔΨm) is rapidly lost and energy production ceases. Conditioning blocks the sustained opening of the MPTP. Translation of conditioning strategies to the clinical management of patients has been challenging. The status of translation of experimental findings to approaches to modulate and ameliorate ischemic and reperfusion injury is discussed for the clinical settings of acute coronary syndromes treated with percutaneous interventions and cardiac preservation during open heart surgery and cardiac transplantation.}, }
@article {pmid35174241, year = {2021}, author = {Ahmad, HI and Afzal, G and Iqbal, MN and Iqbal, MA and Shokrollahi, B and Mansoor, MK and Chen, J}, title = {Positive Selection Drives the Adaptive Evolution of Mitochondrial Antiviral Signaling (MAVS) Proteins-Mediating Innate Immunity in Mammals.}, journal = {Frontiers in veterinary science}, volume = {8}, number = {}, pages = {814765}, pmid = {35174241}, issn = {2297-1769}, abstract = {The regulated production of filamentous protein complexes is essential in many biological processes and provides a new paradigm in signal transmission. The mitochondrial antiviral signaling protein (MAVS) is a critical signaling hub in innate immunity that is activated when a receptor induces a shift in the globular caspase activation and recruitment domain of MAVS into helical superstructures (filaments). It is of interest whether adaptive evolution affects the proteins involved in innate immunity. Here, we explore and confer the role of selection and diversification on mitochondrial antiviral signaling protein in mammalian species. We obtined the MAVS proteins of mammalian species and examined their differences in evolutionary patterns. We discovered evidence for these proteins being subjected to substantial positive selection. We demonstrate that immune system proteins, particularly those encoding recognition proteins, develop under positive selection using codon-based probability methods. Positively chosen regions within recognition proteins cluster in domains involved in microorganism recognition, implying that molecular interactions between hosts and pathogens may promote adaptive evolution in the mammalian immune systems. These significant variations in MAVS development in mammalian species highlights the involvement of MAVS in innate immunity. Our findings highlight the significance of accounting for how non-synonymous alterations affect structure and function when employing sequence-level studies to determine and quantify positive selection.}, }
@article {pmid35163839, year = {2022}, author = {Davoudi, M and Chen, J and Lou, Q}, title = {Genome-Wide Identification and Expression Analysis of Heat Shock Protein 70 (HSP70) Gene Family in Pumpkin (Cucurbita moschata) Rootstock under Drought Stress Suggested the Potential Role of these Chaperones in Stress Tolerance.}, journal = {International journal of molecular sciences}, volume = {23}, number = {3}, pages = {}, pmid = {35163839}, issn = {1422-0067}, support = {BE2021357 and 2021YFD1200201-04//the Key Research and Development Program/ ; }, mesh = {Cucurbita/genetics/*physiology ; *Down-Regulation ; Droughts ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Plant ; Genomics/*methods ; HSP70 Heat-Shock Proteins/*genetics ; Multigene Family ; Phylogeny ; Plant Proteins/genetics ; Promoter Regions, Genetic ; Selection, Genetic ; Stress, Physiological ; }, abstract = {Heat shock protein 70s (HSP70s) are highly conserved proteins that are involved in stress responses. These chaperones play pivotal roles in protein folding, removing the extra amounts of oxidized proteins, preventing protein denaturation, and improving the antioxidant system activities. This conserved family has been characterized in several crops under drought stress conditions. However, there is no study on HSP70s in pumpkin (Cucurbita moschata). Therefore, we performed a comprehensive analysis of this gene family, including phylogenetic relationship, motif and gene structure analysis, gene duplication, collinearity, and promoter analysis. In this research, we found 21 HSP70s that were classified into five groups (from A to E). These genes were mostly localized in the cytoplasm, chloroplast, mitochondria, nucleus, and endoplasmic reticulum (ER). We could observe more similarity in closely linked subfamilies in terms of motifs, the number of introns/exons, and the corresponding cellular compartments. According to the collinearity analysis, gene duplication had occurred as a result of purifying selection. The results showed that the occurrence of gene duplication for all nine gene pairs was due to segmental duplication (SD). Synteny analysis revealed a closer relationship between pumpkin and cucumber than pumpkin and Arabidopsis. Promoter analysis showed the presence of various cis-regulatory elements in the up-stream region of the HSP70 genes, such as hormones and stress-responsive elements, indicating a potential role of this gene family in stress tolerance. We furtherly performed the gene expression analysis of the HSP70s in pumpkin under progressive drought stress. Pumpkin is widely used as a rootstock to improve stress tolerance, as well as fruit quality of cucumber scion. Since stress-responsive mobile molecules translocate through vascular tissue from roots to the whole plant body, we used the xylem of grafted materials to study the expression patterns of the HSP70 (potentially mobile) gene family. The results indicated that all CmoHSP70s had very low expression levels at 4 days after stress (DAS). However, the genes showed different expression patterns by progressing he drought period. For example, the expression of CmoHSP70-4 (in subgroup E) and CmoHSP70-14 (in subgroup C) sharply increased at 6 and 11 DAS, respectively. However, the expression of all genes belonging to subgroup A did not change significantly in response to drought stress. These findings indicated the diverse roles of this gene family under drought stress and provided valuable information for further investigation on the function of this gene family, especially under stressful conditions.}, }
@article {pmid35163579, year = {2022}, author = {Lin, YH and Lim, SN and Chen, CY and Chi, HC and Yeh, CT and Lin, WR}, title = {Functional Role of Mitochondrial DNA in Cancer Progression.}, journal = {International journal of molecular sciences}, volume = {23}, number = {3}, pages = {}, pmid = {35163579}, issn = {1422-0067}, support = {MOST 109-2314-B-182A-068-//Ministry of Science and Technology of the Republic of China/ ; MOST 110-2314-B-182A-095-//Ministry of Science and Technology of the Republic of China/ ; MOST 110-2311-B-182A-001-MY3//Ministry of Science and Technology of the Republic of China/ ; CMRPG3K2292//Chang Gung Memorial Hospital, Taiwan/ ; CMRPG3J0693//Chang Gung Memorial Hospital, Taiwan/ ; CMRPG3J1681//Chang Gung Memorial Hospital, Taiwan/ ; NRRPG3L6011//Chang Gung Memorial Hospital, Taiwan/ ; }, mesh = {*DNA, Mitochondrial/genetics/metabolism ; *DNA, Neoplasm/genetics/metabolism ; Humans ; *Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; *Mutation ; Neoplasm Proteins/genetics/metabolism ; *Neoplasms/genetics/metabolism ; *Polymorphism, Single Nucleotide ; }, abstract = {Mitochondrial DNA (mtDNA) has been identified as a significant genetic biomarker in disease, cancer and evolution. Mitochondria function as modulators for regulating cellular metabolism. In the clinic, mtDNA variations (mutations/single nucleotide polymorphisms) and dysregulation of mitochondria-encoded genes are associated with survival outcomes among cancer patients. On the other hand, nuclear-encoded genes have been found to regulate mitochondria-encoded gene expression, in turn regulating mitochondrial homeostasis. These observations suggest that the crosstalk between the nuclear genome and mitochondrial genome is important for cellular function. Therefore, this review summarizes the significant mechanisms and functional roles of mtDNA variations (DNA level) and mtDNA-encoded genes (RNA and protein levels) in cancers and discusses new mechanisms of crosstalk between mtDNA and the nuclear genome.}, }
@article {pmid35163574, year = {2022}, author = {Falchi, FA and Pizzoccheri, R and Briani, F}, title = {Activity and Function in Human Cells of the Evolutionary Conserved Exonuclease Polynucleotide Phosphorylase.}, journal = {International journal of molecular sciences}, volume = {23}, number = {3}, pages = {}, pmid = {35163574}, issn = {1422-0067}, mesh = {*Evolution, Molecular ; *Exoribonucleases/genetics/metabolism ; Humans ; *Mutation ; *RNA/genetics/metabolism ; *RNA Stability ; *RNA-Binding Proteins/genetics/metabolism ; }, abstract = {Polynucleotide phosphorylase (PNPase) is a phosphorolytic RNA exonuclease highly conserved throughout evolution. Human PNPase (hPNPase) is located in mitochondria and is essential for mitochondrial function and homeostasis. Not surprisingly, mutations in the PNPT1 gene, encoding hPNPase, cause serious diseases. hPNPase has been implicated in a plethora of processes taking place in different cell compartments and involving other proteins, some of which physically interact with hPNPase. This paper reviews hPNPase RNA binding and catalytic activity in relation with the protein structure and in comparison, with the activity of bacterial PNPases. The functions ascribed to hPNPase in different cell compartments are discussed, highlighting the gaps that still need to be filled to understand the physiological role of this ancient protein in human cells.}, }
@article {pmid35163296, year = {2022}, author = {Amaroli, A and Ravera, S and Zekiy, A and Benedicenti, S and Pasquale, C}, title = {A Narrative Review on Oral and Periodontal Bacteria Microbiota Photobiomodulation, through Visible and Near-Infrared Light: From the Origins to Modern Therapies.}, journal = {International journal of molecular sciences}, volume = {23}, number = {3}, pages = {}, pmid = {35163296}, issn = {1422-0067}, mesh = {Bacteria ; Humans ; Infrared Rays ; Light ; Low-Level Light Therapy/methods/*trends ; Microbiota/*radiation effects ; Mitochondria ; Periodontal Diseases/*microbiology/radiotherapy ; Phototherapy/methods/trends ; Stomatitis/radiotherapy ; }, abstract = {Photobiomodulation (PBM) consists of a photon energy transfer to the cell, employing non-ionizing light sources belonging to the visible and infrared spectrum. PBM acts on some intrinsic properties of molecules, energizing them through specific light wavelengths. During the evolution of life, semiconducting minerals were energized by sun radiation. The molecules that followed became photoacceptors and were expressed into the first proto-cells and prokaryote membranes. Afterward, the components of the mitochondria electron transport chain influenced the eukaryotic cell physiology. Therefore, although many organisms have not utilized light as an energy source, many of the molecules involved in their physiology have retained their primordial photoacceptive properties. Thus, in this review, we discuss how PBM can affect the oral microbiota through photo-energization and the non-thermal effect of light on photoacceptors (i.e., cytochromes, flavins, and iron-proteins). Sometimes, the interaction of photons with pigments of an endogenous nature is followed by thermal or photodynamic-like effects. However, the preliminary data do not allow determining reliable therapies but stress the need for further knowledge on light-bacteria interactions and microbiota management in the health and illness of patients through PBM.}, }
@article {pmid35162994, year = {2022}, author = {Phillips, MA and Arnold, KR and Vue, Z and Beasley, HK and Garza-Lopez, E and Marshall, AG and Morton, DJ and McReynolds, MR and Barter, TT and Hinton, A}, title = {Combining Metabolomics and Experimental Evolution Reveals Key Mechanisms Underlying Longevity Differences in Laboratory Evolved Drosophila melanogaster Populations.}, journal = {International journal of molecular sciences}, volume = {23}, number = {3}, pages = {}, pmid = {35162994}, issn = {1422-0067}, mesh = {Aging/*genetics/metabolism ; Animals ; Carbohydrate Metabolism ; Citric Acid Cycle ; Directed Molecular Evolution ; Drosophila melanogaster/genetics/*physiology ; Genomics/*methods ; Longevity ; Metabolomics/*methods ; Mitochondria/metabolism ; Multifactorial Inheritance ; NAD/metabolism ; Polymorphism, Single Nucleotide ; }, abstract = {Experimental evolution with Drosophila melanogaster has been used extensively for decades to study aging and longevity. In recent years, the addition of DNA and RNA sequencing to this framework has allowed researchers to leverage the statistical power inherent to experimental evolution to study the genetic basis of longevity itself. Here, we incorporated metabolomic data into to this framework to generate even deeper insights into the physiological and genetic mechanisms underlying longevity differences in three groups of experimentally evolved D. melanogaster populations with different aging and longevity patterns. Our metabolomic analysis found that aging alters mitochondrial metabolism through increased consumption of NAD[+] and increased usage of the TCA cycle. Combining our genomic and metabolomic data produced a list of biologically relevant candidate genes. Among these candidates, we found significant enrichment for genes and pathways associated with neurological development and function, and carbohydrate metabolism. While we do not explicitly find enrichment for aging canonical genes, neurological dysregulation and carbohydrate metabolism are both known to be associated with accelerated aging and reduced longevity. Taken together, our results provide plausible genetic mechanisms for what might be driving longevity differences in this experimental system. More broadly, our findings demonstrate the value of combining multiple types of omic data with experimental evolution when attempting to dissect mechanisms underlying complex and highly polygenic traits such as aging.}, }
@article {pmid35157851, year = {2022}, author = {Grass, M and McDougal, AD and Blazeski, A and Kamm, RD and García-Cardeña, G and Dewey, CF}, title = {A computational model of cardiomyocyte metabolism predicts unique reperfusion protocols capable of reducing cell damage during ischemia/reperfusion.}, journal = {The Journal of biological chemistry}, volume = {298}, number = {5}, pages = {101693}, pmid = {35157851}, issn = {1083-351X}, support = {T32 HL007627/HL/NHLBI NIH HHS/United States ; }, mesh = {*Computer Simulation ; Humans ; Ischemia/metabolism ; Mitochondria, Heart/metabolism ; *Myocardial Reperfusion Injury/metabolism ; *Myocytes, Cardiac/metabolism/pathology ; Oxygen/metabolism ; Reactive Oxygen Species/metabolism ; Reperfusion/*methods ; }, abstract = {If a coronary blood vessel is occluded and the neighboring cardiomyocytes deprived of oxygen, subsequent reperfusion of the ischemic tissue can lead to oxidative damage due to excessive generation of reactive oxygen species. Cardiomyocytes and their mitochondria are the main energy producers and consumers of the heart, and their metabolic changes during ischemia seem to be a key driver of reperfusion injury. Here, we hypothesized that tracking changes in cardiomyocyte metabolism, such as oxygen and ATP concentrations, would help in identifying points of metabolic failure during ischemia and reperfusion. To track some of these changes continuously from the onset of ischemia through reperfusion, we developed a system of differential equations representing the chemical reactions involved in the production and consumption of 67 molecular species. This model was validated and used to identify conditions present during periods of critical transition in ischemia and reperfusion that could lead to oxidative damage. These simulations identified a range of oxygen concentrations that lead to reverse mitochondrial electron transport at complex I of the respiratory chain and a spike in mitochondrial membrane potential, which are key suspects in the generation of reactive oxygen species at the onset of reperfusion. Our model predicts that a short initial reperfusion treatment with reduced oxygen content (5% of physiological levels) could reduce the cellular damage from both of these mechanisms. This model should serve as an open-source platform to test ideas for treatment of the ischemia reperfusion process by following the temporal evolution of molecular concentrations in the cardiomyocyte.}, }
@article {pmid35148829, year = {2022}, author = {Loconte, V and Singla, J and Li, A and Chen, JH and Ekman, A and McDermott, G and Sali, A and Le Gros, M and White, KL and Larabell, CA}, title = {Soft X-ray tomography to map and quantify organelle interactions at the mesoscale.}, journal = {Structure (London, England : 1993)}, volume = {30}, number = {4}, pages = {510-521.e3}, pmid = {35148829}, issn = {1878-4186}, support = {P30 GM138441/GM/NIGMS NIH HHS/United States ; P41 GM103445/GM/NIGMS NIH HHS/United States ; P41 GM109824/GM/NIGMS NIH HHS/United States ; R01 GM083960/GM/NIGMS NIH HHS/United States ; }, mesh = {*Imaging, Three-Dimensional/methods ; Insulin ; Mitochondria/ultrastructure ; Organelles ; *Tomography, X-Ray/methods ; }, abstract = {Inter-organelle interactions are a vital part of normal cellular function; however, these have proven difficult to quantify due to the range of scales encountered in cell biology and the throughput limitations of traditional imaging approaches. Here, we demonstrate that soft X-ray tomography (SXT) can be used to rapidly map ultrastructural reorganization and inter-organelle interactions in intact cells. SXT takes advantage of the naturally occurring, differential X-ray absorption of the carbon-rich compounds in each organelle. Specifically, we use SXT to map the spatiotemporal evolution of insulin vesicles and their co-localization and interaction with mitochondria in pancreatic β cells during insulin secretion and in response to different stimuli. We quantify changes in the morphology, biochemical composition, and relative position of mitochondria and insulin vesicles. These findings highlight the importance of a comprehensive and unbiased mapping at the mesoscale to characterize cell reorganization that would be difficult to detect with other existing methodologies.}, }
@article {pmid35145105, year = {2022}, author = {Elsemman, IE and Rodriguez Prado, A and Grigaitis, P and Garcia Albornoz, M and Harman, V and Holman, SW and van Heerden, J and Bruggeman, FJ and Bisschops, MMM and Sonnenschein, N and Hubbard, S and Beynon, R and Daran-Lapujade, P and Nielsen, J and Teusink, B}, title = {Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {801}, pmid = {35145105}, issn = {2041-1723}, support = {BB/M025748/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M025756/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Fermentation ; Gene Expression Regulation, Fungal ; Glucose/metabolism ; *Metabolic Networks and Pathways/genetics ; Mitochondria/metabolism ; Proteome/*metabolism ; *Proteomics ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Yeasts/*genetics/growth &amp; development/*metabolism ; }, abstract = {When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the relevant cellular constraints remain to be determined for such cells. Here, we present a comprehensive metabolic model of the yeast cell, based on its full metabolic reaction network extended with protein synthesis and degradation reactions. The model predicts metabolic fluxes and corresponding protein expression by constraining compartment-specific protein pools and maximising growth rate. Comparing model predictions with quantitative experimental data suggests that under glucose limitation, a mitochondrial constraint limits growth at the onset of ethanol formation-known as the Crabtree effect. Under sugar excess, however, a constraint on total cytosolic volume dictates overflow metabolism. Our comprehensive model thus identifies condition-dependent and compartment-specific constraints that can explain metabolic strategies and protein expression profiles from growth rate optimisation, providing a framework to understand metabolic adaptation in eukaryal cells.}, }
@article {pmid35143947, year = {2022}, author = {Sai Satyanarayana, D and Ahlawat, S and Sharma, R and Arora, R and Sharma, A and Tantia, MS and Vijh, RK}, title = {Mitochondrial DNA diversity divulges high levels of haplotype diversity and lack of genetic structure in the Indian camels.}, journal = {Gene}, volume = {820}, number = {}, pages = {146279}, doi = {10.1016/j.gene.2022.146279}, pmid = {35143947}, issn = {1879-0038}, mesh = {Animals ; Biodiversity ; Camelus/*genetics ; DNA, Mitochondrial/*genetics ; Female ; *Genetic Variation ; Haplotypes ; India ; Male ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Camels represent an important genetic resource of the desert ecosystems of India, with the dromedary and Bactrian camels inhabiting the hot and cold deserts, respectively. This study is the first attempt to investigate mitochondrial DNA based genetic diversity in the Indian camel populations and explores their relationship in the context of global genetic diversity of all the three large camel species (Camelus ferus, Camelus bactrianus and Camelus dromedaries). A mitochondrial DNA fragment encompassing part of cytochrome b gene, tRNA[Thr], tRNA[Pro] and the beginning of the control region was amplified and analyzed in 72 dromedary and 8 Bactrian camels of India. Sequence analysis revealed that the haplotype and nucleotide diversity (Hd: 0.937 and π: 0.00431) in the Indian dromedaries was higher than the indices reported so far for the dromedary or Bactrian camels across the globe. The corresponding values in the Indian Bactrian camels were 1.000 and 0.00393, respectively. Signals of population expansion were evident in the dromedaries of India on the basis of mismatch analysis and Fu's Fs values. The analysis of molecular variance attributed most of the genetic variance (92.15%) between the dromedary, wild Bactrian and domestic Bactrian camels indicating separate maternal origins. The existence of three mitochondrial lineages in the old world camels (C. bactrianus: Lineage A; C. ferus: Lineage B and C. dromedarius: Lineage C) was also substantiated by the topology of the Median-Joining network.}, }
@article {pmid35135343, year = {2022}, author = {Horrell, HD and Lindeque, A and Farrell, AP and Seymour, RS and White, CR and Kruger, KM and Snelling, EP}, title = {Relationship between capillaries, mitochondria and maximum power of the heart: a meta-study from shrew to elephant.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1968}, pages = {20212461}, pmid = {35135343}, issn = {1471-2954}, mesh = {Animals ; *Capillaries ; *Elephants ; Humans ; Mitochondria ; Oxygen ; Oxygen Consumption ; Phylogeny ; Shrews ; }, abstract = {This meta-study uses phylogenetic scaling models across more than 30 species, spanning five orders of magnitude in body mass, to show that cardiac capillary numerical density and mitochondrial volume density decrease with body mass raised to the -0.07 ± 0.03 and -0.04 ± 0.01 exponents, respectively. Thus, while an average 10 g mammal has a cardiac capillary density of approximately 4150 mm[-2] and a mitochondrial density of 33%, a 1 t mammal has considerably lower corresponding values of 1850 mm[-2] and 21%. These similar scaling trajectories suggest quantitative matching for the primary oxygen supply and oxygen consuming structures of the heart, supporting economic design at the cellular level of the oxygen cascade in this aerobic organ. These scaling trajectories are nonetheless somewhat shallower than the exponent of -0.11 calculated for the maximum external mechanical power of the cardiac tissue, under conditions of heavy exercise, when oxygen flow between capillaries and mitochondria is probably fully exploited. This mismatch, if substantiated, implies a declining external mechanical efficiency of the heart with increasing body mass, whereby larger individuals put more energy in but get less energy out, a scenario with implications for cardiovascular design, aerobic capacity and limits of body size.}, }
@article {pmid35133488, year = {2022}, author = {Shumenko, PG and Tatonova, YV}, title = {Assessing the population structure of trematode Metagonimus suifunensis using three mitochondrial markers.}, journal = {Parasitology research}, volume = {121}, number = {3}, pages = {915-923}, pmid = {35133488}, issn = {1432-1955}, mesh = {Animals ; DNA, Mitochondrial/chemistry/genetics ; Asia, Eastern ; Genetic Variation ; *Heterophyidae/genetics ; Mitochondria/genetics ; Phylogeny ; Russia ; }, abstract = {In this work, for the first time, the genetic variability of the Metagonimus suifunensis population in the Russian southern Far East was estimated based on the full-length sequences of the nad1 gene of mitochondrial DNA. In addition, for a sample of the same size, the sequences of cox1 and cytb genes, previously used for population studies for M. suifunensis, were reanalysed. Three markers were combined to a common sequence, and the obtained data were studied. Despite the higher level of variability, nad1 and cox1 mtDNA genes did not reveal subdivisions within the population. The combined dataset made it possible to determine that the sample from the Odyr River was the centre of the species' range formation and clarified the continental migration route of the parasite from south to north. According to the data obtained, it was presumed that piscivorous birds participate in the life cycle of the parasite. The subdivision within population revealed that using all three mitochondrial markers is consistent with the features of differentiation within populations of related species, but the reasons for its formation remain unclear due to the insufficient amount of data and the use of different markers in studies of different species.}, }
@article {pmid35132109, year = {2022}, author = {Verma, RK and Kalyakulina, A and Mishra, A and Ivanchenko, M and Jalan, S}, title = {Role of mitochondrial genetic interactions in determining adaptation to high altitude human population.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {2046}, pmid = {35132109}, issn = {2045-2322}, mesh = {Adaptation, Physiological/*genetics ; *Altitude ; Epistasis, Genetic/*genetics ; Ethiopia ; Genes, Mitochondrial/*genetics/*physiology ; Humans ; Mitochondria/*genetics/*physiology ; Polymorphism, Genetic ; South America ; Tibet ; }, abstract = {Physiological and haplogroup studies performed to understand high-altitude adaptation in humans are limited to individual genes and polymorphic sites. Due to stochastic evolutionary forces, the frequency of a polymorphism is affected by changes in the frequency of a near-by polymorphism on the same DNA sample making them connected in terms of evolution. Here, first, we provide a method to model these mitochondrial polymorphisms as "co-mutation networks" for three high-altitude populations, Tibetan, Ethiopian and Andean. Then, by transforming these co-mutation networks into weighted and undirected gene-gene interaction (GGI) networks, we were able to identify functionally enriched genetic interactions of CYB and CO3 genes in Tibetan and Andean populations, while NADH dehydrogenase genes in the Ethiopian population playing a significant role in high altitude adaptation. These co-mutation based genetic networks provide insights into the role of different set of genes in high-altitude adaptation in human sub-populations.}, }
@article {pmid35129136, year = {2022}, author = {Balasubramaniam, S and Soman, M and Katneni, VK and Tomy, S and Gopalapillay, G and Vijayan, KK}, title = {Mitochondrial DNA based diversity studies reveal distinct and substructured populations of pearlspot, Etroplus suratensis (Bloch, 1790) in Indian waters.}, journal = {Journal of genetics}, volume = {101}, number = {}, pages = {}, pmid = {35129136}, issn = {0973-7731}, mesh = {Animals ; *DNA, Mitochondrial/genetics ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; India ; *Mitochondria/genetics ; Phylogeny ; }, abstract = {Pearlspot (Etroplus suratensis) is one of the most commercially important brackish water fish species widely found along the coastal regions of peninsular India and Sri Lanka. Pearlspot is known for its tender flesh, delectable taste, culinary tourism and highyielding market value. Information on the genetic makeup of stocks/populations is extremely vital as it forms the basis for future genetic studies. For this, we utilized ATPase6/8 genes of mtDNA of pearlspot populations collected from nine different locations ranging from Ratnagiri in Maharashtra state on the west coast to Chilika in Odisha on the east coast. Sequence analyses of these genes revealed 33 polymorphic sites, which include 17 singleton and 16 parsimony informative sites. Pair-wise genetic differentiation study (FST = 0.75) indicated significant (P<0.001) differences among all the pairs of stocks except those from Chilika and Nagayalanka. The spatial analysis of molecular variance (SAMOVA) significantly delineated the population into four groups (FCT = 0.69, P = 0.0001), namely northwest (Ratnagiri and Goa); southwest (Mangalore and lakes at Vembanad, Ashtamudi and Vellayani in Kerala); southeast (Pulicat in Tamil Nadu) and northeast (Chilika in Odisha and Nagayalanka in Andhra Pradesh). The above delineation is supported by clades of the phylogenetic tree and also the clusters of median joining haplotype network. The high haplotype diversity (0.84), low nucleotide diversity (0.003), and negative values of Tajima's D (-1.47) and Fu's Fs statistic (-14.89) are characteristic of populations having recently undergone demographic expansion. Mantel test revealed significant isolation by distance. The study identifies highly delineated structured populations with restricted gene flow. If such a stock is overfished, it is highly unlikely that it would recover through migration. For any future breeding programme in this species, it would be desirable to form a base population which incorporates the genetic material from all the locations so that we get a wide gene pool to select from.}, }
@article {pmid35122922, year = {2022}, author = {Baratange, C and Paris-Palacios, S and Bonnard, I and Delahaut, L and Grandjean, D and Wortham, L and Sayen, S and Gallorini, A and Michel, J and Renault, D and Breider, F and Loizeau, JL and Cosio, C}, title = {Metabolic, cellular and defense responses to single and co-exposure to carbamazepine and methylmercury in Dreissena polymorpha.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {300}, number = {}, pages = {118933}, doi = {10.1016/j.envpol.2022.118933}, pmid = {35122922}, issn = {1873-6424}, mesh = {Animals ; Carbamazepine/analysis/toxicity ; *Dreissena/metabolism ; Gills/metabolism ; *Methylmercury Compounds/metabolism/toxicity ; *Water Pollutants, Chemical/analysis ; }, abstract = {Carbamazepine (CBZ) and Hg are widespread and persistent micropollutants in aquatic environments. Both pollutants are known to trigger similar toxicity mechanisms, e.g. reactive oxygen species (ROS) production. Here, their effects were assessed in the zebra mussel Dreissena polymorpha, frequently used as a freshwater model in ecotoxicology and biomonitoring. Single and co-exposures to CBZ (3.9 μg L[-1]) and MeHg (280 ng L[-1]) were performed for 1 and 7 days. Metabolomics analyses evidenced that the co-exposure was the most disturbing after 7 days, reducing the amount of 25 metabolites involved in protein synthesis, energy metabolism, antioxidant response and osmoregulation, and significantly altering cells and organelles' structure supporting a reduction of functions of gills and digestive glands. CBZ alone after 7 days decreased the amount of α-aminobutyric acid and had a moderate effect on the structure of mitochondria in digestive glands. MeHg alone had no effect on mussels' metabolome, but caused a significant alteration of cells and organelles' structure in gills and digestive glands. Single exposures and the co-exposure increased antioxidant responses vs control in gills and digestive glands, without resulting in lipid peroxidation, suggesting an increased ROS production caused by both pollutants. Data globally supported that a higher number of hyperactive cells compensated cellular alterations in the digestive gland of mussels exposed to CBZ or MeHg alone, while CBZ + MeHg co-exposure overwhelmed this compensation after 7 days. Those effects were unpredictable based on cellular responses to CBZ and MeHg alone, highlighting the need to consider molecular toxicity pathways for a better anticipation of effects of pollutants in biota in complex environmental conditions.}, }
@article {pmid35119574, year = {2022}, author = {Munekage, YN and Taniguchi, YY}, title = {A scheme for C4 evolution derived from a comparative analysis of the closely related C3, C3-C4 intermediate, C4-like, and C4 species in the genus Flaveria.}, journal = {Plant molecular biology}, volume = {110}, number = {4-5}, pages = {445-454}, pmid = {35119574}, issn = {1573-5028}, support = {17K07456//Japan Society for the Promotion of Science/ ; 16H06557//Japan Society for the Promotion of Science/ ; 21K05520//Japan Society for the Promotion of Science/ ; }, mesh = {*Flaveria/genetics ; Photosynthesis/physiology ; Mesophyll Cells ; Electron Transport ; Plants ; }, abstract = {A comparative analysis of the genus Flaveria showed a C4 evolutionary process in which the anatomical and metabolic features of C4 photosynthesis were gradually acquired through C3-C4 intermediate stages. C4 photosynthesis has been acquired in multiple lineages of angiosperms during evolution to suppress photorespiration. Crops that perform C4 photosynthesis exhibit high rates of CO2 assimilation and high grain production even under high-temperature in semiarid environments; therefore, engineering C4 photosynthesis in C3 plants is of great importance in the application field. The genus Flaveria contains a large number of C3, C3-C4 intermediate, C4-like, and C4 species, making it a good model genus to study the evolution of C4 photosynthesis, and these studies indicate the direction for C4 engineering. C4 photosynthesis was acquired gradually through the C3-C4 intermediate stage. First, a two-celled C2 cycle called C2 photosynthesis was acquired by localizing glycine decarboxylase activity in the mitochondria of bundle sheath cells. With the development of two-cell metabolism, anatomical features also changed. Next, the replacement of the two-celled C2 cycle by the two-celled C4 cycle was induced by the acquisition of cell-selective expression in addition to the upregulation of enzymes in the C4 cycle during the C3-C4 intermediate stage. This was supported by an increase in cyclic electron transport activity in response to an increase in the ATP/NADPH demand for metabolism. Suppression of the C3 cycle in mesophyll cells was induced after the functional establishment of the C4 cycle, and optimization of electron transport by suppressing the activity of photosystem II also occurred during the final phase of C4 evolution.}, }
@article {pmid35113355, year = {2022}, author = {Singh, P and Lim, B}, title = {Targeting Apoptosis in Cancer.}, journal = {Current oncology reports}, volume = {24}, number = {3}, pages = {273-284}, pmid = {35113355}, issn = {1534-6269}, mesh = {*Antineoplastic Agents/pharmacology/therapeutic use ; Apoptosis ; Humans ; Mitochondria/metabolism ; *Neoplasms/drug therapy/metabolism ; Proto-Oncogene Proteins c-bcl-2 ; }, abstract = {PURPOSE OF REVIEW: Apoptosis is a major mechanism of cancer cell death. Thus, evasion of apoptosis results in therapy resistance. Here, we review apoptosis modulators in cancer and their recent developments, including MDM2 inhibitors and kinase inhibitors that can induce effective apoptosis.<br><br>RECENT FINDINGS: Both extrinsic pathways (external stimuli through cell surface death receptor) and intrinsic pathways (mitochondrial-mediated regulation upon genotoxic stress) regulate the complex process of apoptosis through orchestration of various proteins such as members of the BCL-2 family. Dysregulation within these complex steps can result in evasion of apoptosis. However, via the combined evolution of medicinal chemistry and molecular biology, omics assays have led to innovative inducers of apoptosis and inhibitors of anti-apoptotic regulators. Many of these agents are now being tested in cancer patients in early-phase trials. We believe that despite a sluggish speed of development, apoptosis targeting holds promise as a relevant strategy in cancer therapeutics.}, }
@article {pmid35111395, year = {2022}, author = {Yuan, Z and Jiang, W and Sha, Z}, title = {A review of the common crab genus Macromedaeus Ward, 1942 (Brachyura, Xanthidae) from China Seas with description of a new species using integrative taxonomy methods.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e12735}, pmid = {35111395}, issn = {2167-8359}, mesh = {Animals ; Male ; *Brachyura/anatomy &amp; histology ; Phylogeny ; Oceans and Seas ; Mitochondria ; China ; }, abstract = {Macromedaeus is one of the most common xanthid genera in shallow waters of the Indo-West Pacific. In this study, we describe a new species, Macromedaeus hainanensis sp. nov., and report on two newly recorded species, M. quinquedentatus (Krauss, 1843) and M. orientalis (Takeda &amp; Miyake, 1969) from Hainan Island, South China Sea. M. hainanensis is most related to M. distinguendus (De Haan, 1833-1850) and M. orientalis on the carapace shape and granular appearance, but can be distinguished by unique morphological characteristics especially its front, pereopods and male first gonopod. Taxonomic identities of the six Macromedaeus species recorded from China seas are discussed, and a phylogenetic analyzation is performed on Macromedaeus and related taxa based on three mitochondrial and two nuclear markers (12S, 16S, COI, H3, 18S). Integrated taxonomic evidence is used to support the taxonomic status of each species.}, }
@article {pmid35108076, year = {2022}, author = {Giannotti, D and Boscaro, V and Husnik, F and Vannini, C and Keeling, PJ}, title = {The "Other" Rickettsiales: an Overview of the Family "Candidatus Midichloriaceae".}, journal = {Applied and environmental microbiology}, volume = {88}, number = {6}, pages = {e0243221}, pmid = {35108076}, issn = {1098-5336}, mesh = {*Alphaproteobacteria/genetics ; Animals ; Bacteria ; Phylogeny ; *Rickettsiales ; Symbiosis ; }, abstract = {The family "Candidatus Midichloriaceae" constitutes the most diverse but least studied lineage within the important order of intracellular bacteria Rickettsiales. "Candidatus Midichloriaceae" endosymbionts are found in many hosts, including terrestrial arthropods, aquatic invertebrates, and protists. Representatives of the family are not documented to be pathogenic, but some are associated with diseased fish or corals. Different genera display a range of unusual features, such as full sets of flagellar genes without visible flagella or the ability to invade host mitochondria. Since studies on "Ca. Midichloriaceae" tend to focus on the host, the family is rarely addressed as a unit, and we therefore lack a coherent picture of its diversity. Here, we provide four new midichloriaceae genomes, and we survey molecular and ecological data from the entire family. Features like genome size, ecological context, and host transitions vary considerably even among closely related midichloriaceae, suggesting a high frequency of such shifts, incomplete sampling, or both. Important functional traits involved in energy metabolism, flagella, and secretion systems were independently reduced multiple times with no obvious correspondence to host or habitat, corroborating the idea that many features of these "professional symbionts" are largely independent of host identity. Finally, despite "Ca. Midichloriaceae" being predominantly studied in ticks, our analyses show that the clade is mainly aquatic, with a few terrestrial offshoots. This highlights the importance of considering aquatic hosts, and protists in particular, when reconstructing the evolution of these endosymbionts and by extension all Rickettsiales. IMPORTANCE Among endosymbiotic bacterial lineages, few are as intensely studied as Rickettsiales, which include the causative agents of spotted fever, typhus, and anaplasmosis. However, an important subgroup called "Candidatus Midichloriaceae" receives little attention despite accounting for a third of the diversity of Rickettsiales and harboring a wide range of bacteria with unique features, like the ability to infect mitochondria. Midichloriaceae are found in many hosts, from ticks to corals to unicellular protozoa, and studies on them tend to focus on the host groups. Here, for the first time since the establishment of this clade, we address the genomics, evolution, and ecology of "Ca. Midichloriaceae" as a whole, highlighting trends and patterns, the remaining gaps in our knowledge, and its importance for the understanding of symbiotic processes in intracellular bacteria.}, }
@article {pmid35107193, year = {2022}, author = {Huisman, TAGM and Kralik, SF and Desai, NK and Serrallach, BL and Orman, G}, title = {Neuroimaging of primary mitochondrial disorders in children: A review.}, journal = {Journal of neuroimaging : official journal of the American Society of Neuroimaging}, volume = {32}, number = {2}, pages = {191-200}, doi = {10.1111/jon.12976}, pmid = {35107193}, issn = {1552-6569}, mesh = {Child ; Diagnosis, Differential ; Humans ; Mitochondria/metabolism ; *Mitochondrial Diseases/diagnostic imaging/genetics ; Neuroimaging/methods ; }, abstract = {Mitochondrial disorders represent a diverse and complex group of entities typified by defective energy metabolism. The mitochondrial oxidative phosphorylation system is typically impaired, which is the predominant source of energy production. Because mitochondria are present in nearly all organs, multiple systems may be affected including the central nervous system, skeletal muscles, kidneys, and liver. In particular, those organs that are metabolically active with high energy demands are explicitly vulnerable. Initial diagnostic work up relies on a detailed evaluation of clinical symptoms including physical examination as well as a comprehensive review of the evolution of symptoms over time, relation to possible "triggering" events (eg, fever, infection), blood workup, and family history. High-end neuroimaging plays a pivotal role in establishing diagnosis, narrowing differential diagnosis, monitoring disease progression, and predicting prognosis. The pattern and characteristics of the neuroimaging findings are often highly suggestive of a mitochondrial disorder; unfortunately, in many cases the wide variability of involved metabolic processes prevents a more specific subclassification. Consequently, additional diagnostic steps including muscle biopsy, metabolic workup, and genetic tests are necessary. In the current manuscript, basic concepts of energy production, genetics, and inheritance patterns are reviewed. In addition, the imaging findings of several illustrative mitochondrial disorders are presented to familiarize the involved physicians with pediatric mitochondrial disorders. In addition, the significance of spinal cord imaging and the value of "reversed image-based discovery" for the recognition and correct (re-)classification of mitochondrial disorders is discussed.}, }
@article {pmid35104579, year = {2022}, author = {Gowri, P and Sathish, P and Mahesh Kumar, S and Sundaresan, P}, title = {Mutation profile of neurodegenerative mitochondriopathy - LHON in Southern India.}, journal = {Gene}, volume = {819}, number = {}, pages = {146202}, doi = {10.1016/j.gene.2022.146202}, pmid = {35104579}, issn = {1879-0038}, mesh = {Adolescent ; Adult ; Asian People/genetics ; Child ; Child, Preschool ; DNA, Mitochondrial/metabolism ; Female ; Genes, Mitochondrial ; Genetic Predisposition to Disease ; Genome, Mitochondrial ; Humans ; India ; Male ; Methylation ; Middle Aged ; Mitochondria/*genetics ; *Mutation ; Neurodegenerative Diseases/*genetics ; Optic Atrophy, Hereditary, Leber/*genetics ; Pedigree ; Phylogeny ; Young Adult ; }, abstract = {BACKGROUND: Leber's Hereditary Optic Neuropathy (LHON) is a rare mitochondriopathy causing retinal ganglion cell degeneration resulting in central vision loss. It is caused by mitochondrial DNA (mtDNA) mutations and thus follows maternal inheritance pattern.<br><br>METHODS: We analysed the whole mitochondrial genome in 100 South Indian LHON patients by utilizing Sanger and Next Generation Sequencing approaches. Haplogroup analysis was performed using HaploGrep2 to predict the risk group. Methylation changes in the mtDNA D-loop region were investigated by performing methylation-specific polymerase chain reaction (MSP).<br><br>RESULTS: LHON associated mutations were detected in 55% of the patients of which 42% harboured the primary mutations and 13% harboured potentially pathogenic variants that were previously reported to cause LHON. The candidate mutations identified with confirmed pathogenicity are: m.11778G&#xa0;>&#xa0;A (38%), m.14484&#xa0;T&#xa0;>&#xa0;C (3%), m.4171C&#xa0;>&#xa0;A (1%) and m.11696G&#xa0;>&#xa0;A (1%). MSP results demonstrated that the D-loop region was unmethylated in all the study subjects including mutation-positive patients, mutation-negative patients, asymptomatic carriers, and controls. Haplogroup-M was prevalent (69%) in the study cohort followed by R (14%), U (9%), N (3%), HV (2%), G (2%), and W (1%). The frequency of the predominant mutation m.11778G&#xa0;>&#xa0;A was found lower (&#x334; 11%) in haplogroup-U.<br><br>CONCLUSIONS: South Indian LHON cohort shows a unique profile of mtDNA mutations and haplogroup association presumably with no role of D-loop methylation. MT-ND4, MT-ND5, and MT-ND1 serve as the hotspot genes in this cohort. The presence of LHON associated mutations in patients lacking the common primary mutations insists on the necessity of mitochondrial genome sequencing in individuals suspected with LHON.}, }
@article {pmid35078356, year = {2022}, author = {Munasinghe, M and Haller, BC and Clark, AG}, title = {Migration restores hybrid incompatibility driven by mitochondrial-nuclear sexual conflict.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1967}, pages = {20212561}, pmid = {35078356}, issn = {1471-2954}, mesh = {Cell Nucleus/genetics ; Female ; *Genome, Mitochondrial ; Humans ; Male ; Mitochondria/genetics ; Mutation ; Reproductive Isolation ; }, abstract = {In the mitochondrial genome, sexual asymmetry in transmission allows the accumulation of male-harming mutations since selection acts only on the effect of the mutation in females. Called the 'Mother's Curse', this phenomenon induces a selective pressure for nuclear variants that compensate for this reduction in male fitness. Previous work has demonstrated the existence of these interactions and their potential to act as Dobzhansky-Muller incompatibilities, contributing to reproductive isolation between populations. However, it is not clear how readily they would give rise to and sustain hybrid incompatibilities. Here, we use computer simulations in SLiM 3 to investigate the consequences of sexually antagonistic mitochondrial-nuclear interactions in a subdivided population. We consider distinct migration schemes and vary the chromosomal location, and consequently the transmission pattern, of nuclear restorers. Disrupting these co-evolved interactions results in less-fit males, skewing the sex ratio toward females. Restoration of male fitness depends on both the chromosomal location of nuclear restorer loci and the migration scheme. Our results show that these interactions may act as Dobzhansky-Muller incompatibilities, but their strength is not enough to drive population isolation. Overall, this model shows the varied ways in which populations can respond to migration's disruption of co-evolved mitochondrial-nuclear interactions.}, }
@article {pmid35077696, year = {2022}, author = {Smith, DR}, title = {Genome evolution: Minicircular mtDNA and unusual heteroplasmy in a parasitic plant.}, journal = {Current biology : CB}, volume = {32}, number = {2}, pages = {R86-R89}, doi = {10.1016/j.cub.2021.12.001}, pmid = {35077696}, issn = {1879-0445}, mesh = {*DNA, Mitochondrial/genetics ; *Genome, Mitochondrial/genetics ; Heteroplasmy ; Mitochondria/genetics ; Plants/genetics ; }, abstract = {Minicircular organelle genomes exist in diverse species but have never been observed in plants - that is, until now. The mitochondrial genome of the holoparasite Rhopalocnemis phalloides comprises 21 minicircles, which are extremely heteroplasmic, providing an exceptional example of convergent organelle evolution across disparate lineages.}, }
@article {pmid35066390, year = {2022}, author = {Muthye, V and Mackereth, CD and Stewart, JB and Lavrov, DV}, title = {Large dataset of octocoral mitochondrial genomes provides new insights into mt-mutS evolution and function.}, journal = {DNA repair}, volume = {110}, number = {}, pages = {103273}, doi = {10.1016/j.dnarep.2022.103273}, pmid = {35066390}, issn = {1568-7856}, mesh = {Animals ; *Anthozoa/genetics ; DNA, Mitochondrial/chemistry/genetics ; Escherichia coli Proteins ; Evolution, Molecular ; *Genome, Mitochondrial ; MutS DNA Mismatch-Binding Protein/genetics ; Nucleotides ; Phylogeny ; }, abstract = {All studied octocoral mitochondrial genomes (mt-genomes) contain a homologue of the Escherichia coli mutS gene, a member of a gene family encoding proteins involved in DNA mismatch repair, other types of DNA repair, meiotic recombination, and other functions. Although mutS homologues are found in all domains of life, as well as viruses, octocoral mt-mutS is the only such gene found in an organellar genome. While the function of mtMutS is not known, its domain architecture, conserved sequence, and presence of several characteristic residues suggest its involvement in mitochondrial DNA repair. This inference is supported by exceptionally low rates of mt-sequence evolution observed in octocorals. Previous studies of mt-mutS have been limited by the small number of octocoral mt-genomes available. We utilized sequence-capture data from the recent Quattrini et al. 2020 study [Nature Ecology &amp; Evolution 4:1531-1538] to assemble complete mt-genomes for 94 species of octocorals. Combined with sequences publicly available in GenBank, this resulted in a dataset of 184 complete mt-genomes, which we used to re-analyze the conservation and evolution of mt-mutS. In our analysis, we discovered the first case of mt-mutS loss among octocorals in one of the two Pseudoanthomastus spp. assembled from Quattrini et al. data. This species displayed accelerated rate and changed patterns of nucleotide substitutions in mt-genome, which we argue provide additional evidence for the role of mtMutS in DNA repair. In addition, we found accelerated mt-sequence evolution in the presence of mt-mutS in several octocoral lineages. This accelerated evolution did not appear to be the result of relaxed selection pressure and did not entail changes in patterns of nucleotide substitutions. Overall, our results support previously reported patterns of conservation in mt-mutS and suggest that mtMutS is involved in DNA repair in octocoral mitochondria. They also indicate that the presence of mt-mutS contributes to, but does not fully explain, the low rates of sequence evolution in octocorals.}, }
@article {pmid35063045, year = {2022}, author = {Fan, Y and Zhang, Y and Rui, C and Zhang, H and Xu, N and Wang, J and Han, M and Lu, X and Chen, X and Wang, D and Wang, S and Guo, L and Zhao, L and Huang, H and Wang, J and Sun, L and Chen, C and Ye, W}, title = {Molecular structures and functional exploration of NDA family genes respond tolerant to alkaline stress in Gossypium hirsutum L.}, journal = {Biological research}, volume = {55}, number = {1}, pages = {4}, pmid = {35063045}, issn = {0717-6287}, mesh = {*Gene Expression Regulation, Plant ; Genome, Plant ; *Gossypium/genetics ; Molecular Structure ; Multigene Family/genetics ; Phylogeny ; Plant Proteins/genetics/metabolism ; Stress, Physiological/genetics ; }, abstract = {BACKGROUND: The internal NAD(P)H dehydrogenase (NDA) gene family was a member of the NAD(P)H dehydrogenase (ND) gene family, mainly involved in the non-phosphorylated respiratory pathways in mitochondria and played crucial roles in response to abiotic stress.<br><br>METHODS: The whole genome identification, structure analysis and expression pattern of NDA gene family were conducted to analyze the NDA gene family.<br><br>RESULTS: There were 51, 52, 26, and 24 NDA genes identified in G. hirsutum, G. barbadense, G. arboreum and G. raimondii, respectively. According to the structural characteristics of genes and traits of phylogenetic tree, we divided the NDA gene family into 8 clades. Gene structure analysis showed that the NDA gene family was relatively conservative. The four Gossypium species had good collinearity, and segmental duplication played an important role in the evolution of the NDA gene family. Analysis of cis-elements showed that most GhNDA genes contained cis-elements related to light response and plant hormones (ABA, MeJA and GA). The analysis of the expression patterns of GhNDA genes under different alkaline stress showed that GhNDA genes were actively involved in the response to alkaline stress, possibly through different molecular mechanisms. By analyzing the existing RNA-Seq data after alkaline stress, it was found that an NDA family gene GhNDA32 was expressed, and then theGhNDA32 was silenced by virus-induced gene silencing (VIGS). By observing the phenotype, we found that the wilting degree of silenced plants was much higher than that of the control plant after alkaline treatment, suggesting that GhNDA32 gene was involved in the response to alkaline stress.<br><br>CONCLUSIONS: In this study, GhNDAs participated in response to alkaline stress, especially NaHCO3 stress. It was of great significance for the future research on the molecular mechanism of NDA gene family in responding to abiotic stresses.}, }
@article {pmid35061308, year = {2022}, author = {Choi, IS and Wojciechowski, MF and Steele, KP and Hunter, SG and Ruhlman, TA and Jansen, RK}, title = {Born in the mitochondrion and raised in the nucleus: evolution of a novel tandem repeat family in Medicago polymorpha (Fabaceae).}, journal = {The Plant journal : for cell and molecular biology}, volume = {110}, number = {2}, pages = {389-406}, doi = {10.1111/tpj.15676}, pmid = {35061308}, issn = {1365-313X}, mesh = {*Genome, Mitochondrial/genetics ; Genome, Plant/genetics ; *Medicago/genetics ; Mitochondria/genetics ; Tandem Repeat Sequences/genetics ; }, abstract = {Plant nuclear genomes harbor sequence elements derived from the organelles (mitochondrion and plastid) through intracellular gene transfer (IGT). Nuclear genomes also show a dramatic range of repeat content, suggesting that any sequence can be readily amplified. These two aspects of plant nuclear genomes are well recognized but have rarely been linked. Through investigation of 31 Medicago taxa we detected exceptionally high post-IGT amplification of mitochondrial (mt) DNA sequences containing rps10 in the nuclear genome of Medicago polymorpha and closely related species. The amplified sequences were characterized as tandem arrays of five distinct repeat motifs (2157, 1064, 987, 971, and 587 bp) that have diverged from the mt genome (mitogenome) in the M. polymorpha nuclear genome. The mt rps10-like arrays were identified in seven loci (six intergenic and one telomeric) of the nuclear chromosome assemblies and were the most abundant tandem repeat family, representing 1.6-3.0% of total genomic DNA, a value approximately three-fold greater than the entire mitogenome in M. polymorpha. Compared to a typical mt gene, the mt rps10-like sequence coverage level was 691.5-7198-fold higher in M. polymorpha and closely related species. In addition to the post-IGT amplification, our analysis identified the canonical telomeric repeat and the species-specific satellite arrays that are likely attributable to an ancestral chromosomal fusion in M. polymorpha. A possible relationship between chromosomal instability and the mt rps10-like tandem repeat family in the M. polymorpha clade is discussed.}, }
@article {pmid35058355, year = {2022}, author = {Pei, Y and Forstmeier, W and Ruiz-Ruano, FJ and Mueller, JC and Cabrero, J and Camacho, JPM and Alché, JD and Franke, A and Hoeppner, M and Börno, S and Gessara, I and Hertel, M and Teltscher, K and Knief, U and Suh, A and Kempenaers, B}, title = {Occasional paternal inheritance of the germline-restricted chromosome in songbirds.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {4}, pages = {}, pmid = {35058355}, issn = {1091-6490}, mesh = {Animals ; *Chromosomes ; Cytogenetic Analysis ; DNA, Mitochondrial ; Evolution, Molecular ; Female ; *Germ Cells ; Haplotypes ; Male ; *Paternal Inheritance ; Phylogeny ; Songbirds/classification/*genetics ; Spermatozoa ; }, abstract = {Songbirds have one special accessory chromosome, the so-called germline-restricted chromosome (GRC), which is only present in germline cells and absent from all somatic tissues. Earlier work on the zebra finch (Taeniopygia guttata castanotis) showed that the GRC is inherited only through the female line-like the mitochondria-and is eliminated from the sperm during spermatogenesis. Here, we show that the GRC has the potential to be paternally inherited. Confocal microscopy using GRC-specific fluorescent in situ hybridization probes indicated that a considerable fraction of sperm heads (1 to 19%) in zebra finch ejaculates still contained the GRC. In line with these cytogenetic data, sequencing of ejaculates revealed that individual males from two families differed strongly and consistently in the number of GRCs in their ejaculates. Examining a captive-bred male hybrid of the two zebra finch subspecies (T. g. guttata and T. g. castanotis) revealed that the mitochondria originated from a castanotis mother, whereas the GRC came from a guttata father. Moreover, analyzing GRC haplotypes across nine castanotis matrilines, estimated to have diverged for up to 250,000 y, showed surprisingly little variability among GRCs. This suggests that a single GRC haplotype has spread relatively recently across all examined matrilines. A few diagnostic GRC mutations that arose since this inferred spreading suggest that the GRC has continued to jump across matriline boundaries. Our findings raise the possibility that certain GRC haplotypes could selfishly spread through the population via occasional paternal transmission, thereby outcompeting other GRC haplotypes that were limited to strict maternal inheritance, even if this was partly detrimental to organismal fitness.}, }
@article {pmid35055190, year = {2022}, author = {Belostotsky, R and Frishberg, Y}, title = {Catabolism of Hydroxyproline in Vertebrates: Physiology, Evolution, Genetic Diseases and New siRNA Approach for Treatment.}, journal = {International journal of molecular sciences}, volume = {23}, number = {2}, pages = {}, pmid = {35055190}, issn = {1422-0067}, support = {not relevant//Oxalosis and Hyperoxaluria Foundation/ ; }, mesh = {Animals ; Evolution, Molecular ; Genetic Predisposition to Disease ; Glyoxylates/metabolism ; Humans ; Hydrogen Peroxide/metabolism ; Hydroxyproline/*metabolism ; Hyperoxaluria, Primary/drug therapy/*genetics/metabolism ; Mitochondria/metabolism ; Peroxisomes/metabolism ; RNA, Small Interfering/*pharmacology/therapeutic use ; }, abstract = {Hydroxyproline is one of the most prevalent amino acids in animal proteins. It is not a genetically encoded amino acid, but, rather, it is produced by the post-translational modification of proline in collagen, and a few other proteins, by prolyl hydroxylase enzymes. Although this post-translational modification occurs in a limited number of proteins, its biological significance cannot be overestimated. Considering that hydroxyproline cannot be re-incorporated into pro-collagen during translation, it should be catabolized following protein degradation. A cascade of reactions leads to production of two deleterious intermediates: glyoxylate and hydrogen peroxide, which need to be immediately converted. As a result, the enzymes involved in hydroxyproline catabolism are located in specific compartments: mitochondria and peroxisomes. The particular distribution of catabolic enzymes in these compartments, in different species, depends on their dietary habits. Disturbances in hydroxyproline catabolism, due to genetic aberrations, may lead to a severe disease (primary hyperoxaluria), which often impairs kidney function. The basis of this condition is accumulation of glyoxylate and its conversion to oxalate. Since calcium oxalate is insoluble, children with this rare inherited disorder suffer from progressive kidney damage. This condition has been nearly incurable until recently, as significant advances in substrate reduction therapy using small interference RNA led to a breakthrough in primary hyperoxaluria type 1 treatment.}, }
@article {pmid35052455, year = {2022}, author = {Deng, MX and Xiao, B and Yuan, JX and Hu, JM and Kim, KS and Westbury, MV and Lai, XL and Sheng, GL}, title = {Ancient Mitogenomes Suggest Stable Mitochondrial Clades of the Siberian Roe Deer.}, journal = {Genes}, volume = {13}, number = {1}, pages = {}, pmid = {35052455}, issn = {2073-4425}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/analysis/*genetics ; Deer/*genetics ; *Evolution, Molecular ; Fossils ; *Genetic Variation ; *Genome, Mitochondrial ; Haplotypes ; Mitochondria/*genetics ; *Phylogeny ; }, abstract = {The roe deer (Capreolus spp.) has been present in China since the early Pleistocene. Despite abundant fossils available for detailed morphological analyses, little is known about the phylogenetic relationships of the fossil individuals to contemporary roe deer. We generated near-complete mitochondrial genomes for four roe deer remains from Northeastern China to explore the genetic connection of the ancient roe deer to the extant populations and to investigate the evolutionary history and population dynamics of this species. Phylogenetic analyses indicated the four ancient samples fall into three out of four different haplogroups of the Siberian roe deer. Haplogroup C, distributed throughout Eurasia, have existed in Northeastern China since at least the Late Pleistocene, while haplogroup A and D, found in the east of Lake Baikal, emerged in Northeastern China after the Mid Holocene. The Bayesian estimation suggested that the first split within the Siberian roe deer occurred approximately 0.34 million years ago (Ma). Moreover, Bayesian skyline plot analyses suggested that the Siberian roe deer had a population increase between 325 and 225 thousand years ago (Kya) and suffered a transient decline between 50 and 18 Kya. This study provides novel insights into the evolutionary history and population dynamics of the roe deer.}, }
@article {pmid35051222, year = {2022}, author = {Tsai, CY and Chiou, SJ and Ko, HJ and Cheng, YF and Lin, SY and Lai, YL and Lin, CY and Wang, C and Cheng, JT and Liu, HF and Kwan, AL and Loh, JK and Hong, YR}, title = {Deciphering the evolution of composite-type GSKIP in mitochondria and Wnt signaling pathways.}, journal = {PloS one}, volume = {17}, number = {1}, pages = {e0262138}, pmid = {35051222}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Armadillo Domain Proteins/chemistry/genetics/*metabolism ; Binding Sites ; Cloning, Molecular ; Conserved Sequence ; Evolution, Molecular ; Glycogen Synthase Kinase 3 beta/*metabolism ; Humans ; Mitochondria/*metabolism ; Models, Molecular ; Mutagenesis, Site-Directed ; Phylogeny ; Protein Binding ; Protein Conformation ; RNA-Binding Proteins/chemistry/genetics/*metabolism ; Repressor Proteins/chemistry/*genetics/*metabolism ; Sequence Analysis, DNA ; Two-Hybrid System Techniques ; Wnt Signaling Pathway ; }, abstract = {We previously revealed the origin of mammalian simple-type glycogen synthase kinase interaction protein (GSKIP), which served as a scavenger and a competitor in the Wnt signaling pathway during evolution. In this study, we investigated the conserved and nonconserved regions of the composite-type GSKIP by utilizing bioinformatics tools, site-directed mutagenesis, and yeast two-hybrid methods. The regions were denoted as the pre-GSK3β binding site, which is located at the front of GSK3β-binding sites. Our data demonstrated that clustered mitochondria protein 1 (CLU1), a type of composite-type GSKIP that exists in the mitochondria of all eukaryotic organisms, possesses the protein known as domain of unknown function 727 (DUF727), with a pre-GSK3β-binding site and a mutant GSK3β-binding flanking region. Another type of composite-type GSKIP, armadillo repeat containing 4 (ARMC4), which is known for cilium movement in vertebrates, contains an unintegrated DUF727 flanking region with a pre-GSK3β-binding site (115SPxF118) only. In addition, the sequence of the GSK3β-binding site in CLU1 revealed that Q126L and V130L were not conserved, differing from the ideal GSK3β-binding sequence of simple-type GSKIP. We further illustrated two exceptions, namely 70 kilodalton heat shock proteins (Hsp70/DnaK) and Mitofilin in nematodes, that presented an unexpected ideal GSK3β-binding region with a pre-GSK3β sequence; this composite-type GSKIP could only occur in vertebrate species. Furthermore, we revealed the importance of the pre-GSK3β-binding site (118F or 118Y) and various mutant GSK3β-binding sites of composite-type GSKIP. Collectively, our data suggest that the new composite-type GSKIP starts with a DUF727 domain followed by a pre-GSK3β-binding site, with the subsequent addition of the GSK3β-binding site, which plays vital roles for CLU1, Mitofilin, and ARMC4 in mitochondria and Wnt signaling pathways during evolution.}, }
@article {pmid35039544, year = {2022}, author = {Lebedev, VS and Shenbrot, GI and Krystufek, B and Mahmoudi, A and Melnikova, MN and Solovyeva, EN and Lisenkova, AA and Undrakhbayar, E and Rogovin, KA and Surov, AV and Bannikova, AA}, title = {Phylogenetic relations and range history of jerboas of the Allactaginae subfamily (Dipodidae, Rodentia).}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {842}, pmid = {35039544}, issn = {2045-2322}, support = {21-14-00007//Russian Science Foundation/ ; }, mesh = {Animals ; Ecosystem ; European Union ; Genetic Variation ; Mitochondria/genetics ; *Phylogeny ; Rodentia/classification/*genetics ; Species Specificity ; }, abstract = {Five-toed jerboas of the subfamily Allactaginae comprise several complex taxa occurring over a wide distribution range covering a large part of the Eurasian arid belt. In this study, we employed current methods of molecular phylogenetics based on 15 nuclear genes and the mitochondrial gene cytb to revise relations and systematics within Allactaginae. We also applied species distribution modelling projected on paleo-environmental data to reconstruct the geographic patterns of speciation in Allactaginae. We elucidated the intergeneric relationships within this subfamily and clarified interspecies relations within the genus Scarturus. Moreover, our results demonstrate the species status of S. caprimulga; outline the currently understudied diversity within Orientallactaga, Allactaga, and Pygeretmus; and improve the divergence estimates of these taxa. Based on our results from modelling of geographic range fragmentation in allactagines, we suggest the dating and location of speciation events and present hypotheses regarding general habitat niche conservatism in small mammals.}, }
@article {pmid35038074, year = {2022}, author = {Zhang, H and Qin, J and Lan, X and Zeng, W and Zhou, J and Huang, TE and Xiao, WL and Wang, QQ and Sun, S and Su, W and Nie, W and Yang, S and Yang, J and Gao, Q and Xiang, Y}, title = {Handelin extends lifespan and healthspan of Caenorhabditis elegans by reducing ROS generation and improving motor function.}, journal = {Biogerontology}, volume = {23}, number = {1}, pages = {115-128}, pmid = {35038074}, issn = {1573-6768}, mesh = {Animals ; *Caenorhabditis elegans/physiology ; *Caenorhabditis elegans Proteins/genetics/metabolism ; Ethanol/pharmacology ; Longevity/physiology ; Mammals/metabolism ; Plant Extracts/pharmacology ; Reactive Oxygen Species/metabolism ; Terpenes ; }, abstract = {Aging and aging-related disorders contribute to formidable socioeconomic and healthcare challenges. Several promising small molecules have been identified to target conserved genetic pathways delaying aging to extend lifespan and healthspan in many organisms. We previously found that extract from an edible and medicinal plant Chrysanthemum indicum L. (C. indicum L.) protect skin from UVB-induced photoaging, partially by reducing reactive oxygen species (ROS) generation. Thus, we hypothesized that C. indicum L. and its biological active compound may extend lifespan and health span in vivo. We find that both water and ethanol extracts from C. indicum L. extended lifespan of Caenorhabditis elegans, with better biological effect on life extending for ethanol extracts. As one of the major biological active compounds, handelin extended lifespan of C. elegans too. RNA-seq analysis revealed overall gene expression change of C. elegans post stimulation of handelin focus on several antioxidative proteins. Handelin significantly reduced ROS level and maintained the number and morphology of mitochondria. Moreover, handelin improveed many C. elegans behaviors related to healthspan, including increased pharyngeal pumping and body movement. Muscle fiber imaging analyses revealed that handelin maintains muscle architecture by stabilizing myofilaments. In conclusion, our present study finds a novel compound handelin, from C. indicum L., which bring about biologically beneficial effects by mild stress response, termed as hormetin, that can extend both lifespan and healthspan in vivo on C. elegans. Further study on mammal animal model of natural aging or sarcopenia will verify the potential clinical value of handelin.}, }
@article {pmid35027725, year = {2022}, author = {Muñoz-Gómez, SA and Susko, E and Williamson, K and Eme, L and Slamovits, CH and Moreira, D and López-García, P and Roger, AJ}, title = {Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {3}, pages = {253-262}, pmid = {35027725}, issn = {2397-334X}, mesh = {*Alphaproteobacteria/genetics/metabolism ; Metagenome ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins ; Phylogeny ; }, abstract = {Determining the phylogenetic origin of mitochondria is key to understanding the ancestral mitochondrial symbiosis and its role in eukaryogenesis. However, the precise evolutionary relationship between mitochondria and their closest bacterial relatives remains hotly debated. The reasons include pervasive phylogenetic artefacts as well as limited protein and taxon sampling. Here we developed a new model of protein evolution that accommodates both across-site and across-branch compositional heterogeneity. We applied this site-and-branch-heterogeneous model (MAM60 + GFmix) to a considerably expanded dataset that comprises 108 mitochondrial proteins of alphaproteobacterial origin, and novel metagenome-assembled genomes from microbial mats, microbialites and sediments. The MAM60 + GFmix model fits the data much better and agrees with analyses of compositionally homogenized datasets with conventional site-heterogenous models. The consilience of evidence thus suggests that mitochondria are sister to the Alphaproteobacteria to the exclusion of MarineProteo1 and Magnetococcia. We also show that the ancestral presence of the crista-developing mitochondrial contact site and cristae organizing system (a mitofilin-domain-containing Mic60 protein) in mitochondria and the Alphaproteobacteria only supports their close relationship.}, }
@article {pmid35026224, year = {2022}, author = {Uzarska, MA and Grochowina, I and Soldek, J and Jelen, M and Schilke, B and Marszalek, J and Craig, EA and Dutkiewicz, R}, title = {During FeS cluster biogenesis, ferredoxin and frataxin use overlapping binding sites on yeast cysteine desulfurase Nfs1.}, journal = {The Journal of biological chemistry}, volume = {298}, number = {2}, pages = {101570}, pmid = {35026224}, issn = {1083-351X}, support = {R35 GM127009/GM/NIGMS NIH HHS/United States ; }, mesh = {Binding Sites ; Carbon-Sulfur Lyases/genetics/metabolism ; *Ferredoxins/metabolism ; Iron-Binding Proteins/metabolism ; *Iron-Sulfur Proteins/metabolism ; *Mitochondrial Proteins/metabolism ; Saccharomyces cerevisiae/enzymology/genetics/metabolism ; *Saccharomyces cerevisiae Proteins/metabolism ; *Sulfurtransferases/metabolism ; Frataxin ; }, abstract = {In mitochondria, cysteine desulfurase (Nfs1) plays a central role in the biosynthesis of iron-sulfur (FeS) clusters, cofactors critical for activity of many cellular proteins. Nfs1 functions both as a sulfur donor for cluster assembly and as a binding platform for other proteins functioning in the process. These include not only the dedicated scaffold protein (Isu1) on which FeS clusters are synthesized but also accessory FeS cluster biogenesis proteins frataxin (Yfh1) and ferredoxin (Yah1). Yfh1 has been shown to activate cysteine desulfurase enzymatic activity, whereas Yah1 supplies electrons for the persulfide reduction. While Yfh1 interaction with Nfs1 is well understood, the Yah1-Nfs1 interaction is not. Here, based on the results of biochemical experiments involving purified WT and variant proteins, we report that in Saccharomyces cerevisiae, Yah1 and Yfh1 share an evolutionary conserved interaction site on Nfs1. Consistent with this notion, Yah1 and Yfh1 can each displace the other from Nfs1 but are inefficient competitors when a variant with an altered interaction site is used. Thus, the binding mode of Yah1 and Yfh1 interacting with Nfs1 in mitochondria of S. cerevisiae resembles the mutually exclusive binding of ferredoxin and frataxin with cysteine desulfurase reported for the bacterial FeS cluster assembly system. Our findings are consistent with the generally accepted scenario that the mitochondrial FeS cluster assembly system was inherited from bacterial ancestors of mitochondria.}, }
@article {pmid35025030, year = {2022}, author = {Liu, S and Liu, Y and He, J and Lin, Z and Xue, Q}, title = {The complete mitochondrial genome of Crassostrea hongkongensis from East China Sea indicates species' range may extend northward.}, journal = {Molecular biology reports}, volume = {49}, number = {2}, pages = {1631-1635}, pmid = {35025030}, issn = {1573-4978}, support = {2021S009//Science and Technology Planning Project of Ningbo City/ ; }, mesh = {Animals ; China ; Conservation of Natural Resources/methods ; Crassostrea/*genetics ; Ecosystem ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Crassostrea hongkongensis is an important mariculture shellfish with a relatively narrow distribution range. Recently, larger wild oysters were identified as C. hongkongensis from Sanmen bay in East China Sea. No natural distribution had been reported for this species here, and its origin remains unknown.<br><br>METHODS AND RESULTS: We assembled the complete 18,617&#xa0;bp circular mitochondrial genome of C. hongkongensis from Sanmen bay by next generation sequencing. It included 12 protein-coding genes, 23 tRNAs, and two rRNAs. The A/T content of the mitogenome was higher than its G/C content. Similar values and features were previously found for five other specimens of C. hongkongensis, and were comparable to those of other congeneric species. A phylogenetic analysis based on the 12 protein-coding genes and complete mitochondrial sequence indicated that the six specimens of C. hongkongensis formed a monophyletic group and shared a sister group relationship with C. ariakensis, C. nippona, C. sikamea, C. angulata, C. gigas, and C. iredalei, whereas specimens from the Sanmen bay area clustered later with the five other C. hongkongensis individuals, sharing a sub-clade. The newly sequenced mitogenome had more singleton sites than previously published C. hongkongensis mitogenomes.<br><br>CONCLUSIONS: Crassostrea hongkongensis may be a native species, and the species' range extends further to the north than previously known. Our data may therefore contribute to a better understanding of the species diversity and conservation of Crassostrea oysters.}, }
@article {pmid35022483, year = {2022}, author = {Dash, A and Ghag, SB}, title = {Genome-wide in silico characterization and stress induced expression analysis of BcL-2 associated athanogene (BAG) family in Musa spp.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {625}, pmid = {35022483}, issn = {2045-2322}, mesh = {*Phylogeny ; }, abstract = {Programmed cell death (PCD) is a genetically controlled process for the selective removal of damaged cells. Though understanding about plant PCD has improved over years, the mechanisms are yet to be fully deciphered. Among the several molecular players of PCD in plants, B cell lymphoma 2 (Bcl-2)-associated athanogene (BAG) family of co-chaperones are evolutionary conserved and regulate cell death, growth and development. In this study, we performed a genome-wide in silico analysis of the MusaBAG gene family in a globally important fruit crop banana. Thirteen MusaBAG genes were identified, out of which MusaBAG1, 7 and 8 genes were found to have multiple copies. MusaBAG genes were distributed on seven out of 11 chromosomes in banana. Except for one paralog of MusaBAG8 all the other 12 proteins have characteristic BAG domain. MusaBAG1, 2 and 4 have an additional ubiquitin-like domain whereas MusaBAG5-8 have a calmodulin binding motif. Most of the MusaBAG proteins were predicted to be localized in the nucleus and mitochondria or chloroplast. The in silico cis-regulatory element analysis suggested regulation associated with photoperiodic control, abiotic and biotic stress. The phylogenetic analysis revealed 2 major clusters. Digital gene expression analysis and quantitative real-time RT-PCR depicted the differential expression pattern of MusaBAG genes under abiotic and biotic stress conditions. Further studies are warranted to uncover the role of each of these proteins in growth, PCD and stress responses so as to explore them as candidate genes for engineering transgenic banana plants with improved agronomic traits.}, }
@article {pmid35020439, year = {2022}, author = {Gogoi, J and Bhatnagar, A and Ann, KJ and Pottabathini, S and Singh, R and Mazeed, M and Kuncha, SK and Kruparani, SP and Sankaranarayanan, R}, title = {Switching a conflicted bacterial DTD-tRNA code is essential for the emergence of mitochondria.}, journal = {Science advances}, volume = {8}, number = {2}, pages = {eabj7307}, pmid = {35020439}, issn = {2375-2548}, abstract = {Mitochondria emerged through an endosymbiotic event involving a proteobacterium and an archaeal host. However, the process of optimization of cellular processes required for the successful evolution and survival of mitochondria, which integrates components from two evolutionarily distinct ancestors as well as novel eukaryotic elements, is not well understood. We identify two key switches in the translational machinery—one in the discriminator recognition code of a chiral proofreader DTD [d-aminoacyl–transfer RNA (tRNA) deacylase] and the other in mitochondrial tRNA[Gly]—that enable the compatibility between disparate elements essential for survival. Notably, the mito-tRNA[Gly] discriminator element is the only one to switch from pyrimidine to purine during the bacteria-to-mitochondria transition. We capture this code transition in the Jakobida, an early diverging eukaryotic clade bearing the most bacterial-like mito-genome, wherein both discriminator elements are present. This study underscores the need to explore the fundamental integration strategies critical for mitochondrial and eukaryotic evolution.}, }
@article {pmid35017538, year = {2022}, author = {Li, CH and Haider, S and Boutros, PC}, title = {Age influences on the molecular presentation of tumours.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {208}, pmid = {35017538}, issn = {2041-1723}, support = {P30 CA016042/CA/NCI NIH HHS/United States ; U01 CA214194/CA/NCI NIH HHS/United States ; SVB-145586//CIHR/Canada ; }, mesh = {Age Factors ; Aging/*genetics/metabolism ; CREB-Binding Protein/*genetics/metabolism ; Carcinogenesis/genetics/metabolism/pathology ; Cell Line, Tumor ; Cell Nucleus/metabolism ; Cyclin-Dependent Kinase Inhibitor p16/*genetics/metabolism ; *DNA Repair ; DNA, Neoplasm/*genetics/metabolism ; Datasets as Topic ; Female ; Gene Expression Regulation, Neoplastic ; Humans ; Male ; Mitochondria/metabolism ; Mutation Rate ; Neoplasm Proteins/*genetics/metabolism ; Neoplasms/classification/*genetics/metabolism/pathology ; Repressor Proteins/deficiency/genetics ; Smoking/genetics/metabolism ; Transcriptome ; X-linked Nuclear Protein/genetics/metabolism ; }, abstract = {Cancer is often called a disease of aging. There are numerous ways in which cancer epidemiology and behaviour change with the age of the patient. The molecular bases for these relationships remain largely underexplored. To characterise them, we analyse age-associations in the nuclear and mitochondrial somatic mutational landscape of 20,033 tumours across 35 tumour-types. Age influences both the number of mutations in a tumour (0.077 mutations per megabase per year) and their evolutionary timing. Specific mutational signatures are associated with age, reflecting differences in exogenous and endogenous oncogenic processes such as a greater influence of tobacco use in the tumours of younger patients, but higher activity of DNA damage repair signatures in those of older patients. We find that known cancer driver genes such as CDKN2A and CREBBP are mutated in age-associated frequencies, and these alter the transcriptome and predict for clinical outcomes. These effects are most striking in brain cancers where alterations like SUFU loss and ATRX mutation are age-dependent prognostic biomarkers. Using three cancer datasets, we show that age shapes the somatic mutational landscape of cancer, with clinical implications.}, }
@article {pmid35007655, year = {2022}, author = {Liu, T and Lin, S and Du, Y and Gong, Y and Li, S}, title = {SpBAG3 assisted WSSV infection in mud crab (Scylla paramamosain) by inhibiting apoptosis.}, journal = {Developmental and comparative immunology}, volume = {129}, number = {}, pages = {104349}, doi = {10.1016/j.dci.2022.104349}, pmid = {35007655}, issn = {1879-0089}, mesh = {Animals ; Apoptosis ; Apoptosis Regulatory Proteins/genetics ; Arthropod Proteins/genetics ; Brachyura/*immunology ; Gene Expression Profiling ; Hemocytes/immunology ; Immunity, Innate/genetics ; Membrane Potential, Mitochondrial ; Mitochondria/metabolism ; Phylogeny ; White spot syndrome virus 1/physiology ; }, abstract = {The function of B-cell lymphoma-2 (Bcl-2) family proteins can be divided into two categories: anti-apoptotic and pro-apoptotic. As an anti-apoptotic protein, Bcl2-associated athanogene 3 (BAG3) plays a key role in regulating apoptosis, development, cell movement, and autophagy, and mediating the adaptability of cells to stimulation. However, SpBAG3 has not been reported in mud crab (Scylla paramamosain), and the regulatory effect of SpBAG3 on apoptosis in mud crab and its function in antiviral immunity is still unknown. In this study, SpBAG3 was found, and characterized, which encoded a total of 175 amino acid (molecular mass 19.3 kDa), including a specific conserved domain of the BAG family. SpBAG3 was significantly down-regulated at 0-48 h post-infection with WSSV in vivo. The antiviral effect of SpBAG3 was investigated using RNA interference. The results indicated that SpBAG3 might be involved in assisting the replication of WSSV in the host. SpBAG3 could change the mitochondrial membrane potential (△ψm), and affect cell apoptosis through mitochondrial apoptotic pathways. Therefore, the results of this study suggested that SpBAG3 could assist WSSV infection by inhibiting the apoptosis of the hemocytes in mud crab.}, }
@article {pmid34997986, year = {2022}, author = {Ereskovsky, A and Tokina, D}, title = {Ultrastructural research of spermiogenesis in two sponges, Crellomima imparidens and Hymedesmia irregularis (Demospongiae): New evidence of sperms with acrosome in sponges.}, journal = {Journal of morphology}, volume = {283}, number = {3}, pages = {333-345}, doi = {10.1002/jmor.21446}, pmid = {34997986}, issn = {1097-4687}, mesh = {*Acrosome/ultrastructure ; Animals ; Male ; Phylogeny ; *Porifera ; Spermatids/ultrastructure ; Spermatogenesis ; Spermatozoa ; }, abstract = {Details of spermatogenesis and sperm organization are often useful for reconstructing the phylogeny of closely related taxa of invertebrates. Here, the spermiogenesis and the ultrastructure of sperm were studied in two marine demosponges, Crellomima imparidens and Hymedesmia irregularis (order Poecilosclerida). In C. imparidens and H. irregularis, we found bundles of microtubules arranged along the nucleus during spermiogenesis. These bundles derived from the basal body of axoneme, reaching the apical pole of the cell. In C. imparidens, the microtubules surround the nucleus, forming the manchette. In H. irregularis, the microtubules pass along only one side of the cell periphery. During spermiogenesis, the nucleus stretches and elongates. In both species, the nucleus is twisted into a spiral structure. We suppose that the manchette of microtubules could be responsible for controlling the elongation and shaping of the sperm nucleus to a helical form and for the twisting and/or condensation of chromatin in these sponges. The spermatozoon of both species has an elongated shape. Its apical part has an acrosome, which is dome-shaped in C. imparidens and flattened and lenticular in H. irregularis. The cytoplasm of the spermatozoa contains some small mitochondria, and proximal and distal centrioles arranged at an angle to each other. There is a small volume of residual cytoplasm with dark glycogen-like granules. The axoneme of the spermatid and the flagellum of the sperm of both sponges is located in the deep tunnel-like cytoplasmic depression. The comparison of spermatozoa morphology of different species of the order Poecilosclerida demonstrates that the knowledge of variation within genera and families can give valuable insights into the significance of many characters proposed for phylogenetic studies of this order.}, }
@article {pmid34994554, year = {2022}, author = {Liu, Y and Li, Q and Gu, M and Lu, D and Xiong, X and Zhang, Z and Pan, Y and Liao, Y and Ding, Q and Gong, W and Chen, DS and Guan, M and Wu, J and Tian, Z and Deng, H and Gu, L and Hong, X and Xiao, Y}, title = {A Second Near-Infrared Ru(II) Polypyridyl Complex for Synergistic Chemo-Photothermal Therapy.}, journal = {Journal of medicinal chemistry}, volume = {65}, number = {3}, pages = {2225-2237}, doi = {10.1021/acs.jmedchem.1c01736}, pmid = {34994554}, issn = {1520-4804}, mesh = {Apoptosis/drug effects ; Biocompatible Materials/chemistry/pharmacology/therapeutic use ; Cell Line, Tumor ; Coordination Complexes/*chemistry/pharmacology/therapeutic use ; Drug Design ; Fluorescent Dyes/chemistry/pharmacology/therapeutic use ; G2 Phase Cell Cycle Checkpoints/drug effects ; Humans ; Hyperthermia, Induced ; *Infrared Rays ; Neoplasms/diagnostic imaging/drug therapy/therapy ; Phenazines/chemistry ; Photothermal Therapy/methods ; Polyethylene Glycols/chemistry ; Quantum Theory ; Ruthenium/*chemistry ; Spectroscopy, Near-Infrared ; }, abstract = {The clinical success of cisplatin ushered in a new era of the application of metallodrugs. When it comes to practice, however, drug resistance, tumor recurrence, and drug systemic toxicity make it implausible to completely heal the patients. Herein, we successfully transform an electron acceptor [1, 2, 5]thiadiazolo[3,4-g]quinoxaline into a novel second near-infrared (NIR-II) fluorophore H7. After PEGylation and chelation, HL-PEG2k exhibits a wavelength bathochromic shift, enhanced photothermal conversion efficiency (41.77%), and an antineoplastic effect against glioma. Its potential for in vivo tumor tracking and image-guided chemo-photothermal therapy is explored. High levels of uptake and high-resolution NIR-II imaging results are thereafter obtained. The hyperthermia effect could disrupt the lysosomal membranes, which in turn aggravate the mitochondria dysfunction, arrest the cell cycle in the G2 phase, and finally lead to cancer cell apoptosis. HL-PEG2k displays a superior biocompatibility and thus can be a potential theranostic platform to combat the growth and recurrence of tumors.}, }
@article {pmid34993838, year = {2022}, author = {Jiang, Z and Cai, X and Kong, J and Zhang, R and Ding, Y}, title = {Maternally transmitted diabetes mellitus may be associated with mitochondrial ND5 T12338C and tRNA[Ala] T5587C variants.}, journal = {Irish journal of medical science}, volume = {191}, number = {6}, pages = {2625-2633}, pmid = {34993838}, issn = {1863-4362}, mesh = {Humans ; *RNA, Transfer, Ala ; *Diabetes Mellitus, Type 2/genetics ; Phylogeny ; DNA, Mitochondrial/genetics ; Mitochondria ; Pedigree ; Mutation ; }, abstract = {INTRODUCTION: Mutations/variants in mitochondrial genomes are found to be associated with type 2 diabetes mellitus (T2DM), but the pathophysiology of this disease remains largely unknown.<br><br>AIM: The aim of this study is to investigate the relationship between mitochondrial DNA (mtDNA) variants and T2DM.<br><br>METHODOLOGY: A maternally inherited T2DM pedigree is underwent clinical, genetic, and molecular assessment. Moreover, the complete mitochondrial genomes of the matrilineal relatives of this family are PCR amplified and sequenced. We also utilize the phylogenetic conservation analysis, haplogroup classification, and the pathogenicity scoring system to determine the T2DM-associated potential pathogenic mtDNA variants.<br><br>RESULT: Four of seven matrilineal relatives of this pedigree suffered from T2DM with variable ages of onset. Screening for the entire mtDNA genes of matrilineal members reveals co-existence of ND5 T12338C and tRNA[Ala] T5587C variants, as well as 21 genetic polymorphisms which belong to East Asian haplogroup F2. Interestingly, the T12338C variant causes the alternation of first amino acid Met to Thr, shortened two amino acids of ND5 protein. Furthermore, T5587C variant is located at position 73 in the 3'end of mt-tRNA[Ala] and may have structural and functional consequences.<br><br>CONCLUSIONS: The co-occurrence of ND5 T12338C and tRNA[Ala] T5587C variants may impair the mitochondrial function, which are associated with the development of T2DM in this family.}, }
@article {pmid34976854, year = {2021}, author = {Valdés-Aguayo, JJ and Garza-Veloz, I and Vargas-Rodríguez, JR and Martinez-Vazquez, MC and Avila-Carrasco, L and Bernal-Silva, S and González-Fuentes, C and Comas-García, A and Alvarado-Hernández, DE and Centeno-Ramirez, ASH and Rodriguez-Sánchez, IP and Delgado-Enciso, I and Martinez-Fierro, ML}, title = {Peripheral Blood Mitochondrial DNA Levels Were Modulated by SARS-CoV-2 Infection Severity and Its Lessening Was Associated With Mortality Among Hospitalized Patients With COVID-19.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {754708}, pmid = {34976854}, issn = {2235-2988}, mesh = {*COVID-19 ; DNA, Mitochondrial/genetics ; Humans ; Immunity, Innate ; Mitochondria/genetics ; SARS-CoV-2 ; }, abstract = {INTRODUCTION: During severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, the virus hijacks the mitochondria causing damage of its membrane and release of mt-DNA into the circulation which can trigger innate immunity and generate an inflammatory state. In this study, we explored the importance of peripheral blood mt-DNA as an early predictor of evolution in patients with COVID-19 and to evaluate the association between the concentration of mt-DNA and the severity of the disease and the patient's outcome.<br><br>METHODS: A total 102 patients (51 COVID-19 cases and 51 controls) were included in the study. mt-DNA obtained from peripheral blood was quantified by qRT-PCR using the NADH mitochondrial gene.<br><br>RESULTS: There were differences in peripheral blood mt-DNA between patients with COVID-19 (4.25 ng/&#x3bc;l &#xb1; 0.30) and controls (3.3 ng/&#x3bc;l &#xb1; 0.16) (p = 0.007). Lower mt-DNA concentrations were observed in patients with severe COVID-19 when compared with mild (p= 0.005) and moderate (p= 0.011) cases of COVID-19. In comparison with patients with severe COVID-19 who survived (3.74 &#xb1; 0.26 ng/&#x3bc;l) decreased levels of mt-DNA in patients with severe COVID-19 who died (2.4 &#xb1; 0.65 ng/&#x3bc;l) were also observed (p&#xa0;= 0.037).<br><br>CONCLUSION: High levels of mt-DNA were associated with COVID-19 and its decrease could be used as a potential biomarker to establish a prognosis of severity and mortality of patients with COVID-19.}, }
@article {pmid34972821, year = {2022}, author = {Irwin, NAT and Pittis, AA and Richards, TA and Keeling, PJ}, title = {Systematic evaluation of horizontal gene transfer between eukaryotes and viruses.}, journal = {Nature microbiology}, volume = {7}, number = {2}, pages = {327-336}, pmid = {34972821}, issn = {2058-5276}, mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Host Microbial Interactions ; Phylogeny ; Viruses/*genetics ; }, abstract = {Gene exchange between viruses and their hosts acts as a key facilitator of horizontal gene transfer and is hypothesized to be a major driver of evolutionary change. Our understanding of this process comes primarily from bacteria and phage co-evolution, but the mode and functional importance of gene transfers between eukaryotes and their viruses remain anecdotal. Here we systematically characterized viral-eukaryotic gene exchange across eukaryotic and viral diversity, identifying thousands of transfers and revealing their frequency, taxonomic distribution and projected functions. Eukaryote-derived viral genes, abundant in the Nucleocytoviricota, highlighted common strategies for viral host-manipulation, including metabolic reprogramming, proteolytic degradation and extracellular modification. Furthermore, viral-derived eukaryotic genes implicate genetic exchange in the early evolution and diversification of eukaryotes, particularly through viral-derived glycosyltransferases, which have impacted structures as diverse as algal cell walls, trypanosome mitochondria and animal tissues. These findings illuminate the nature of viral-eukaryotic gene exchange and its impact on the evolution of viruses and their eukaryotic hosts.}, }
@article {pmid34964900, year = {2022}, author = {Rand, DM and Mossman, JA and Spierer, AN and Santiago, JA}, title = {Mitochondria as environments for the nuclear genome in Drosophila: mitonuclear G×G×E.}, journal = {The Journal of heredity}, volume = {113}, number = {1}, pages = {37-47}, pmid = {34964900}, issn = {1465-7333}, support = {R01 GM067862/GM/NIGMS NIH HHS/United States ; R35 GM139607/GM/NIGMS NIH HHS/United States ; 1R35GM139607/NH/NIH HHS/United States ; 2R01GM067862/NH/NIH HHS/United States ; }, mesh = {Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Drosophila/genetics ; Epistasis, Genetic ; *Genome, Mitochondrial ; Mitochondria/genetics ; }, abstract = {Mitochondria evolved from a union of microbial cells belonging to distinct lineages that were likely anaerobic. The evolution of eukaryotes required a massive reorganization of the 2 genomes and eventual adaptation to aerobic environments. The nutrients and oxygen that sustain eukaryotic metabolism today are processed in mitochondria through coordinated expression of 37 mitochondrial genes and over 1000 nuclear genes. This puts mitochondria at the nexus of gene-by-gene (G×G) and gene-by-environment (G×E) interactions that sustain life. Here we use a Drosophila model of mitonuclear genetic interactions to explore the notion that mitochondria are environments for the nuclear genome, and vice versa. We construct factorial combinations of mtDNA and nuclear chromosomes to test for epistatic interactions (G×G), and expose these mitonuclear genotypes to altered dietary environments to examine G×E interactions. We use development time and genome-wide RNAseq analyses to assess the relative contributions of mtDNA, nuclear chromosomes, and environmental effects on these traits (mitonuclear G×G×E). We show that the nuclear transcriptional response to alternative mitochondrial "environments" (G×G) has significant overlap with the transcriptional response of mitonuclear genotypes to altered dietary environments. These analyses point to specific transcription factors (e.g., giant) that mediated these interactions, and identified coexpressed modules of genes that may account for the overlap in differentially expressed genes. Roughly 20% of the transcriptome includes G×G genes that are concordant with G×E genes, suggesting that mitonuclear interactions are part of an organism's environment.}, }
@article {pmid34946978, year = {2021}, author = {Romanova, EV and Bukin, YS and Mikhailov, KV and Logacheva, MD and Aleoshin, VV and Sherbakov, DY}, title = {The Mitochondrial Genome of a Freshwater Pelagic Amphipod Macrohectopus branickii Is among the Longest in Metazoa.}, journal = {Genes}, volume = {12}, number = {12}, pages = {}, pmid = {34946978}, issn = {2073-4425}, mesh = {Amphipoda/*genetics ; Animals ; Gene Order ; Genes, rRNA ; Genome Size ; Genome, Mitochondrial ; Mitochondria/*genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {There are more than 350 species of amphipods (Crustacea) in Lake Baikal, which have emerged predominantly through the course of endemic radiation. This group represents a remarkable model for studying various aspects of evolution, one of which is the evolution of mitochondrial (mt) genome architectures. We sequenced and assembled the mt genome of a pelagic Baikalian amphipod species Macrohectopus branickii. The mt genome is revealed to have an extraordinary length (42,256 bp), deviating significantly from the genomes of other amphipod species and the majority of animals. The mt genome of M. branickii has a unique gene order within amphipods, duplications of the four tRNA genes and Cox2, and a long non-coding region, that makes up about two thirds of the genome's size. The extension of the mt genome was most likely caused by multiple duplications and inversions of regions harboring ribosomal RNA genes. In this study, we analyzed the patterns of mt genome length changes in amphipods and other animal phyla. Through a statistical analysis, we demonstrated that the variability in the mt genome length may be a characteristic of certain phyla and is primarily conferred by expansions of non-coding regions.}, }
@article {pmid34946956, year = {2021}, author = {Tahami, MS and Dincă, V and Lee, KM and Vila, R and Joshi, M and Heikkilä, M and Dapporto, L and Schmid, S and Huemer, P and Mutanen, M}, title = {Genomics Reveal Admixture and Unexpected Patterns of Diversity in a Parapatric Pair of Butterflies.}, journal = {Genes}, volume = {12}, number = {12}, pages = {}, pmid = {34946956}, issn = {2073-4425}, mesh = {Animals ; Balkan Peninsula ; Butterflies/anatomy &amp; histology/*classification/genetics ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Gene Flow ; Genetic Speciation ; Genomics/*methods ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Sympatry ; }, abstract = {We studied the evolutionary relationship of two widely distributed parapatric butterfly species, Melitaea athalia and Melitaea celadussa, using the ddRAD sequencing approach, as well as genital morphology and mtDNA data. M. athalia was retrieved as paraphyletic with respect to M. celadussa. Several cases of mito-nuclear discordance and morpho-genetic mismatch were found in the contact zone. A strongly diverged and marginally sympatric clade of M. athalia from the Balkans was revealed. An in-depth analysis of genomic structure detected high levels of admixture between M. athalia and M. celadussa at the contact zone, though not reaching the Balkan clade. The demographic modelling of populations supported the intermediate genetic make-up of European M. athalia populations with regards to M. celadussa and the Balkan clade. However, the dissimilarity matrix of genotype data (PCoA) suggested the Balkan lineage having a genetic component that is unrelated to the athalia-celadussa group. Although narrowly sympatric, almost no signs of gene flow were found between the main M. athalia group and the Balkan clade. We propose two possible scenarios on the historical evolution of our model taxa and the role of the last glacial maximum in shaping their current distribution. Finally, we discuss the complexities regarding the taxonomic delimitation of parapatric taxa.}, }
@article {pmid34943968, year = {2021}, author = {Singh, LN and Kao, SH and Wallace, DC}, title = {Unlocking the Complexity of Mitochondrial DNA: A Key to Understanding Neurodegenerative Disease Caused by Injury.}, journal = {Cells}, volume = {10}, number = {12}, pages = {}, pmid = {34943968}, issn = {2073-4409}, support = {MH108592/NH/NIH HHS/United States ; P50 HD105354/HD/NICHD NIH HHS/United States ; OD010944/NH/NIH HHS/United States ; W81XWH-21-1-0128//United States Department of Defense/ ; NS021328/NH/NIH HHS/United States ; }, mesh = {Brain Injuries, Traumatic/*genetics/pathology ; DNA, Mitochondrial/*genetics ; Genetic Variation/genetics ; Humans ; Mitochondria/*genetics ; Risk Factors ; Stroke/*genetics/pathology ; }, abstract = {Neurodegenerative disorders that are triggered by injury typically have variable and unpredictable outcomes due to the complex and multifactorial cascade of events following the injury and during recovery. Hence, several factors beyond the initial injury likely contribute to the disease progression and pathology, and among these are genetic factors. Genetics is a recognized factor in determining the outcome of common neurodegenerative diseases. The role of mitochondrial genetics and function in traditional neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases, is well-established. Much less is known about mitochondrial genetics, however, regarding neurodegenerative diseases that result from injuries such as traumatic brain injury and ischaemic stroke. We discuss the potential role of mitochondrial DNA genetics in the progression and outcome of injury-related neurodegenerative diseases. We present a guide for understanding mitochondrial genetic variation, along with the nuances of quantifying mitochondrial DNA variation. Evidence supporting a role for mitochondrial DNA as a risk factor for neurodegenerative disease is also reviewed and examined. Further research into the impact of mitochondrial DNA on neurodegenerative disease resulting from injury will likely offer key insights into the genetic factors that determine the outcome of these diseases together with potential targets for treatment.}, }
@article {pmid34943861, year = {2021}, author = {Key, J and Torres-Odio, S and Bach, NC and Gispert, S and Koepf, G and Reichlmeir, M and West, AP and Prokisch, H and Freisinger, P and Newman, WG and Shalev, S and Sieber, SA and Wittig, I and Auburger, G}, title = {Inactivity of Peptidase ClpP Causes Primary Accumulation of Mitochondrial Disaggregase ClpX with Its Interacting Nucleoid Proteins, and of mtDNA.}, journal = {Cells}, volume = {10}, number = {12}, pages = {}, pmid = {34943861}, issn = {2073-4409}, support = {W81XWH-20-1-0150//Office of the Assistant Secretary for Health/ ; W81XWH-17-1-0052//Office of the Assistant Secretary for Health/ ; R01 HL148153/HL/NHLBI NIH HHS/United States ; GN2494//Action Medical Research/ ; mitoNET, 01GM1906D//German Network for Mitochondrial Disorders/ ; }, mesh = {Adult ; Amino Acids/metabolism ; Brain/metabolism ; Cell Nucleus/*metabolism ; Computational Biology ; Conserved Sequence ; DNA, Mitochondrial/*metabolism ; Endopeptidase Clp/*metabolism ; Fibroblasts/metabolism ; Humans ; Male ; Mitochondria/*metabolism ; Mitochondrial Proteins/metabolism ; Models, Biological ; Protein Binding ; Protein Interaction Maps ; Proteome/metabolism ; Skin/pathology ; Subcellular Fractions/metabolism ; Transcription, Genetic ; }, abstract = {Biallelic pathogenic variants in CLPP, encoding mitochondrial matrix peptidase ClpP, cause a rare autosomal recessive condition, Perrault syndrome type 3 (PRLTS3). It is characterized by primary ovarian insufficiency and early sensorineural hearing loss, often associated with progressive neurological deficits. Mouse models showed that accumulations of (i) its main protein interactor, the substrate-selecting AAA+ ATPase ClpX, (ii) mitoribosomes, and (iii) mtDNA nucleoids are the main cellular consequences of ClpP absence. However, the sequence of these events and their validity in human remain unclear. Here, we studied global proteome profiles to define ClpP substrates among mitochondrial ClpX interactors, which accumulated consistently in ClpP-null mouse embryonal fibroblasts and brains. Validation work included novel ClpP-mutant patient fibroblast proteomics. ClpX co-accumulated in mitochondria with the nucleoid component POLDIP2, the mitochondrial poly(A) mRNA granule element LRPPRC, and tRNA processing factor GFM1 (in mouse, also GRSF1). Only in mouse did accumulated ClpX, GFM1, and GRSF1 appear in nuclear fractions. Mitoribosomal accumulation was minor. Consistent accumulations in murine and human fibroblasts also affected multimerizing factors not known as ClpX interactors, namely, OAT, ASS1, ACADVL, STOM, PRDX3, PC, MUT, ALDH2, PMPCB, UQCRC2, and ACADSB, but the impact on downstream metabolites was marginal. Our data demonstrate the primary impact of ClpXP on the assembly of proteins with nucleic acids and show nucleoid enlargement in human as a key consequence.}, }
@article {pmid34942301, year = {2022}, author = {Bohálová, N and Dobrovolná, M and Brázda, V and Bidula, S}, title = {Conservation and over-representation of G-quadruplex sequences in regulatory regions of mitochondrial DNA across distinct taxonomic sub-groups.}, journal = {Biochimie}, volume = {194}, number = {}, pages = {28-34}, doi = {10.1016/j.biochi.2021.12.006}, pmid = {34942301}, issn = {1638-6183}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *G-Quadruplexes ; Genome ; Humans ; Mitochondria ; Regulatory Sequences, Nucleic Acid/genetics ; }, abstract = {G-quadruplexes have important regulatory roles in the nuclear genome but their distribution and potential roles in mitochondrial DNA (mtDNA) are poorly understood. We analysed 11883 mtDNA sequences from 18 taxonomic sub-groups and identified their frequency and location within mtDNA. Large differences in both the frequency and number of putative quadruplex-forming sequences (PQS) were observed amongst all the organisms and PQS frequency was negatively correlated with an increase in evolutionary age. PQS were over-represented in the 3'UTRs, D-loops, replication origins, and stem loops, indicating regulatory roles for quadruplexes in mtDNA. Variations of the G-quadruplex-forming sequence in the conserved sequence block II (CSBII) region of the human D-loop were conserved amongst other mammals, amphibians, birds, reptiles, and fishes. This D-loop PQS was conserved in the duplicated control regions of some birds and reptiles, indicating its importance to mitochondrial function. The guanine tracts in these PQS also displayed significant length heterogeneity and the length of these guanine tracts were generally longest in bird mtDNA. This information provides further insights into how G4s may contribute to the regulation and function of mtDNA and acts as a database of information for future studies investigating mitochondrial G4s in organisms other than humans.}, }
@article {pmid34941991, year = {2022}, author = {Song, MH and Yan, C and Li, JT}, title = {MEANGS: an efficient seed-free tool for de novo assembling animal mitochondrial genome using whole genome NGS data.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {1}, pages = {}, doi = {10.1093/bib/bbab538}, pmid = {34941991}, issn = {1477-4054}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Software ; Whole Genome Sequencing/*methods ; }, abstract = {Advances in next-generation sequencing (NGS) technologies have led to an exponential increase in the number of whole genome sequences (WGS) in databases. This wealth of WGS data has greatly facilitated the recovery of full mitochondrial genomes (mitogenomes), which are vital for phylogenetic, evolutionary and ecological studies. Unfortunately, most existing software cannot easily assemble mitogenome reference sequences conveniently or efficiently. Therefore, we developed a seed-free de novo assembly tool, MEANGS, which applies the trie-search method to extend contigs from self-discovery seeds and assemble a mitogenome from animal WGS data. We then used data from 16 species with different qualities to compare the performance of MEANGS with three other available programs. MEANGS exhibited the best overall performance since it was the only one that completed all tests, and it assembled full or partial mitogenomes for all of the tested samples while the others failed. Furthermore, MEANGS selects superior assembly sequences and annotates protein-coding genes. Thus, MEANGS can be one of the most efficient software for generating high-quality mitogenomes so far, the further use of it will benefit the study on mitogenome based on whole genome NGS data. MEANGS is available at https://github.com/YanCCscu/meangs.}, }
@article {pmid34938509, year = {2021}, author = {Wade, MJ and Fogarty, L}, title = {Adaptive co-evolution of mitochondria and the Y-chromosome: A resolution to conflict between evolutionary opponents.}, journal = {Ecology and evolution}, volume = {11}, number = {23}, pages = {17307-17313}, pmid = {34938509}, issn = {2045-7758}, abstract = {In most species with motile sperm, male fertility depends upon genes located on the Y-chromosome and in the mitochondrial genome. Coordinated adaptive evolution for the function of male fertility between genes on the Y and the mitochondrion is hampered by their uniparental inheritance in opposing sexes: The Y-chromosome is inherited uniparentally, father to son, and the mitochondrion is inherited maternally, mother to offspring. Preserving male fertility is problematic, because maternal inheritance permits mitochondrial mutations advantageous to females, but deleterious to male fertility, to accumulate in a population. Although uniparental inheritance with sex-restricted adaptation also affects genes on the Y-chromosome, females lack a Y-chromosome and escape the potential maladaptive consequences of male-limited selection. Evolutionary models have shown that mitochondrial mutations deleterious to male fertility can be countered by compensatory evolution of Y-linked mutations that restore it. However, direct adaptive coevolution of Y- and mitochondrial gene combinations has not yet been mathematically characterized. We use population genetic models to show that adaptive coevolution of Y and mitochondrial genes are possible when Y-mt gene combinations have positive effects on male fertility and populations are inbred.}, }
@article {pmid34934212, year = {2021}, author = {Donoso-Fuentes, A and Arriagada-Santis, D}, title = {[Organ dysfunction syndrome and mitochondrial adaptation in the septic patient].}, journal = {Boletin medico del Hospital Infantil de Mexico}, volume = {78}, number = {6}, pages = {597-611}, doi = {10.24875/BMHIM.20000323}, pmid = {34934212}, issn = {1665-1146}, mesh = {Humans ; Microcirculation ; Mitochondria ; *Multiple Organ Failure ; *Shock, Septic ; }, abstract = {The ability to maintain an adequate energy balance and to respond and adapt to environmental stress at the cellular level are cornerstones for the survival and evolution of organisms. Therefore, in the presence of various factors, a cellular protection response is triggered by activation of mitochondrial function-dependent signaling. However, this essential reaction for individual cell survival can be detrimental to organ function (maladaptation), transforming the close balance between the two into the pathogenetic axis of organ dysfunction and eventual recovery in septic patients. Macrocirculatory and microcirculatory disruption undoubtedly contributes to organ dysfunction in the early stage of septic shock, while intrinsic metabolic-bioenergetic failure (cytopathic hypoxia) perpetuates inadequate cellular function. Therefore, mitochondrial dysfunction is a key process in the induction of multiple organ dysfunction syndrome in the septic patient. This syndrome can be considered as a complex hypometabolic adaptive phenomenon in the face of excessive and prolonged inflammatory stimulus to achieve regulation of energy homeostasis and preservation of organ function. In the future, there should be a transition from the current consensus therapeutic options, which are limited to control of the infectious focus, hemodynamic and life support, to metabolic resuscitation based on the molecular and genetic alterations triggered by the infection.}, }
@article {pmid34930424, year = {2021}, author = {Kelly, S}, title = {The economics of organellar gene loss and endosymbiotic gene transfer.}, journal = {Genome biology}, volume = {22}, number = {1}, pages = {345}, pmid = {34930424}, issn = {1474-760X}, mesh = {Arabidopsis/genetics ; Bacteria/*genetics ; Cell Nucleus ; Chloroplasts ; Gene Transfer, Horizontal ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Genome, Plant ; Host Microbial Interactions/genetics ; Mitochondria/genetics ; Proteomics ; Symbiosis/*genetics ; }, abstract = {BACKGROUND: The endosymbiosis of the bacterial progenitors of the mitochondrion and the chloroplast are landmark events in the evolution of life on Earth. While both organelles have retained substantial proteomic and biochemical complexity, this complexity is not reflected in the content of their genomes. Instead, the organellar genomes encode fewer than 5% of the genes found in living relatives of their ancestors. While many of the 95% of missing organellar genes have been discarded, others have been transferred to the host nuclear genome through a process known as endosymbiotic gene transfer.<br><br>RESULTS: Here, we demonstrate that the difference in the per-cell copy number of the organellar and nuclear genomes presents an energetic incentive to the cell to either delete organellar&#xa0;genes or transfer them to the nuclear genome. We show that, for the majority of transferred organellar&#xa0;genes, the energy saved by nuclear transfer exceeds the costs incurred from importing the encoded protein into the organelle where it can provide its function. Finally, we show that the net energy saved by endosymbiotic gene transfer can constitute an appreciable proportion of total cellular energy budgets and is therefore sufficient to impart a selectable advantage to the cell.<br><br>CONCLUSION: Thus, reduced cellular cost and improved energy efficiency likely played a role in the reductive evolution of mitochondrial and chloroplast genomes and the transfer of organellar genes to the nuclear genome.}, }
@article {pmid34925295, year = {2021}, author = {Fonseca, PLC and De-Paula, RB and Araújo, DS and Tomé, LMR and Mendes-Pereira, T and Rodrigues, WFC and Del-Bem, LE and Aguiar, ERGR and Góes-Neto, A}, title = {Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {787283}, pmid = {34925295}, issn = {1664-302X}, abstract = {Fungi comprise a great diversity of species with distinct ecological functions and lifestyles. Similar to other eukaryotes, fungi rely on interactions with prokaryotes and one of the most important symbiotic events was the acquisition of mitochondria. Mitochondria are organelles found in eukaryotic cells whose main function is to generate energy through aerobic respiration. Mitogenomes (mtDNAs) are double-stranded circular or linear DNA from mitochondria that may contain core genes and accessory elements that can be replicated, transcribed, and independently translated from the nuclear genome. Despite their importance, investigative studies on the diversity of fungal mitogenomes are scarce. Herein, we have evaluated 788 curated fungal mitogenomes available at NCBI database to assess discrepancies and similarities among them and to better understand the mechanisms involved in fungal mtDNAs variability. From a total of 12 fungal phyla, four do not have any representative with available mitogenomes, which highlights the underrepresentation of some groups in the current available data. We selected representative and non-redundant mitogenomes based on the threshold of 90% similarity, eliminating 81 mtDNAs. Comparative analyses revealed considerable size variability of mtDNAs with a difference of up to 260 kb in length. Furthermore, variation in mitogenome length and genomic composition are generally related to the number and length of accessory elements (introns, HEGs, and uORFs). We identified an overall average of 8.0 (0-39) introns, 8.0 (0-100) HEGs, and 8.2 (0-102) uORFs per genome, with high variation among phyla. Even though the length of the core protein-coding genes is considerably conserved, approximately 36.3% of the mitogenomes evaluated have at least one of the 14 core coding genes absent. Also, our results revealed that there is not even a single gene shared among all mitogenomes. Other unusual genes in mitogenomes were also detected in many mitogenomes, such as dpo and rpo, and displayed diverse evolutionary histories. Altogether, the results presented in this study suggest that fungal mitogenomes are diverse, contain accessory elements and are absent of a conserved gene that can be used for the taxonomic classification of the Kingdom Fungi.}, }
@article {pmid34919556, year = {2021}, author = {Lima-Cordón, RA and Cahan, SH and McCann, C and Dorn, PL and Justi, SA and Rodas, A and Monroy, MC and Stevens, L}, title = {Insights from a comprehensive study of Trypanosoma cruzi: A new mitochondrial clade restricted to North and Central America and genetic structure of TcI in the region.}, journal = {PLoS neglected tropical diseases}, volume = {15}, number = {12}, pages = {e0010043}, pmid = {34919556}, issn = {1935-2735}, mesh = {Central America ; Chagas Disease/*parasitology ; Electron Transport Complex I/genetics/metabolism ; Electron Transport Complex IV/genetics/metabolism ; Humans ; Mitochondria/*genetics/metabolism ; Phylogeny ; Protozoan Proteins/genetics/metabolism ; South America ; Trypanosoma cruzi/*classification/genetics/*isolation &amp; purification ; }, abstract = {More than 100 years since the first description of Chagas Disease and with over 29,000 new cases annually due to vector transmission (in 2010), American Trypanosomiasis remains a Neglected Tropical Disease (NTD). This study presents the most comprehensive Trypanosoma cruzi sampling in terms of geographic locations and triatomine species analyzed to date and includes both nuclear and mitochondrial genomes. This addresses the gap of information from North and Central America. We incorporate new and previously published DNA sequence data from two mitochondrial genes, Cytochrome oxidase II (COII) and NADH dehydrogenase subunit 1 (ND1). These T. cruzi samples were collected over a broad geographic range including 111 parasite DNA samples extracted from triatomines newly collected across North and Central America, all of which were infected with T. cruzi in their natural environment. In addition, we present parasite reduced representation (Restriction site Associated DNA markers, RAD-tag) genomic nuclear data combined with the mitochondrial gene sequences for a subset of the triatomines (27 specimens) collected from Guatemala and El Salvador. Our mitochondrial phylogenetic reconstruction revealed two of the major mitochondrial lineages circulating across North and Central America, as well as the first ever mitochondrial data for TcBat from a triatomine collected in Central America. Our data also show that within mtTcIII, North and Central America represent an independent, distinct clade from South America, named here as mtTcIIINA-CA, geographically restricted to North and Central America. Lastly, the most frequent lineage detected across North and Central America, mtTcI, was also an independent, distinct clade from South America, noted as mtTcINA-CA. Furthermore, nuclear genome data based on Single Nucleotide Polymorphism (SNP) showed genetic structure of lineage TcI from specimens collected in Guatemala and El Salvador supporting the hypothesis that genetic diversity at a local scale has a geographical component. Our multiscale analysis contributes to the understanding of the independent and distinct evolution of T. cruzi lineages in North and Central America regions.}, }
@article {pmid34917101, year = {2021}, author = {Nunes, JPS and Moraes-Vieira, PM and Chevillard, C and Cunha-Neto, E}, title = {Editorial: Mitochondria at the Crossroads of Immunity and Inflammatory Tissue Damage.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {810787}, doi = {10.3389/fimmu.2021.810787}, pmid = {34917101}, issn = {1664-3224}, support = {P50 AI098461/AI/NIAID NIH HHS/United States ; U19 AI098461/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Humans ; Immunity/*immunology ; Inflammation/*immunology ; Mitochondria/*immunology ; }, }
@article {pmid34911545, year = {2021}, author = {Lewis, AJO and Hegde, RS}, title = {A unified evolutionary origin for the ubiquitous protein transporters SecY and YidC.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {266}, pmid = {34911545}, issn = {1741-7007}, support = {MC_UP_A022_1007/MRC_/Medical Research Council/United Kingdom ; MC_ UP_A022_1007/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacterial Proteins/metabolism ; Cell Membrane/metabolism ; *Escherichia coli Proteins/metabolism ; Hydrophobic and Hydrophilic Interactions ; Membrane Proteins/genetics/metabolism ; Membrane Transport Proteins/genetics ; }, abstract = {BACKGROUND: Protein transporters translocate hydrophilic segments of polypeptide across hydrophobic cell membranes. Two protein transporters are ubiquitous and date back to the last universal common ancestor: SecY and YidC. SecY consists of two pseudosymmetric halves, which together form a membrane-spanning protein-conducting channel. YidC is an asymmetric molecule with a protein-conducting hydrophilic groove that partially spans the membrane. Although both transporters mediate insertion of membrane proteins with short translocated domains, only SecY transports secretory proteins and membrane proteins with long translocated domains. The evolutionary origins of these ancient and essential transporters are not known.<br><br>RESULTS: The features conserved by the two halves of SecY indicate that their common ancestor was an antiparallel homodimeric channel. Structural searches with SecY's halves detect exceptional similarity with YidC homologs. The SecY halves and YidC share a fold comprising a three-helix bundle interrupted by a helical hairpin. In YidC, this hairpin is cytoplasmic and facilitates substrate delivery, whereas in SecY, it is transmembrane and forms the substrate-binding lateral gate helices. In both transporters, the three-helix bundle forms a protein-conducting hydrophilic groove delimited by a conserved hydrophobic residue. Based on these similarities, we propose that SecY originated as a YidC homolog which formed a channel by juxtaposing two hydrophilic grooves in an antiparallel homodimer. We find that archaeal YidC and its eukaryotic descendants use this same dimerisation interface to heterodimerise with a conserved partner. YidC's sufficiency for the function of simple cells is suggested by the results of reductive evolution in mitochondria and plastids, which tend to retain SecY only if they require translocation of large hydrophilic domains.<br><br>CONCLUSIONS: SecY and YidC share previously unrecognised similarities in sequence, structure, mechanism, and function. Our delineation of a detailed correspondence between these two essential and ancient transporters enables a deeper mechanistic understanding of how each functions. Furthermore, key differences between them help explain how SecY performs its distinctive function in the recognition and translocation of secretory proteins. The unified theory presented here explains the evolution of these features, and thus reconstructs a key step in the origin of cells.}, }
@article {pmid34905682, year = {2021}, author = {Niedźwiedzka-Rystwej, P and Bębnowska, D and Kołacz, R and Deptuła, W}, title = {Mitochondria, pattern recognition receptors and autophagy under physiological and pathological conditions, including viral infections.}, journal = {Acta biochimica Polonica}, volume = {69}, number = {1}, pages = {1-10}, doi = {10.18388/abp.2020_5807}, pmid = {34905682}, issn = {1734-154X}, mesh = {Animals ; Autophagy ; DNA, Mitochondrial/genetics ; Mammals/genetics/metabolism ; *Mitochondria/metabolism ; Receptors, Pattern Recognition/metabolism ; *Virus Diseases/metabolism ; }, abstract = {Research on the health of mammals invariably shows how dynamic immunology is and how the role of many elements and immune processes of the macroorganism, developed in the process of evolution in protecting against threats, including infections, is changing. Among these elements conditioning the homeostasis of the macroorganism are mitochondria, PRR receptors (pattern recognition receptors) and the phenomenon of autophagy. In the context of physiological and pathological states in the body, mitochondria perform various functions. The primary function of these organelles is to produce energy in the cell, but on the other hand, they are heavily involved in various cellular processes, including ROS production and calcium homeostasis. They are largely involved in the activation of immune mechanisms during infectious and non-infectious conditions through mtDNA and the mitochondrial MAVS protein. Mitochondrial involvement has been also determined in PRR-related mechanisms as mtDNA has the ability to directly stimulate TLRs. On the other hand, mitochondria are also associated with apoptotic cell death and autophagy.}, }
@article {pmid34904040, year = {2021}, author = {Gopan, A and Sarma, MS}, title = {Mitochondrial hepatopathy: Respiratory chain disorders- 'breathing in and out of the liver'.}, journal = {World journal of hepatology}, volume = {13}, number = {11}, pages = {1707-1726}, pmid = {34904040}, issn = {1948-5182}, abstract = {Mitochondria, the powerhouse of a cell, are closely linked to the pathophysiology of various common as well as not so uncommon disorders of the liver and beyond. Evolution supports a prokaryotic descent, and, unsurprisingly, the organelle is worthy of being labeled an organism in itself. Since highly metabolically active organs require a continuous feed of energy, any dysfunction in the structure and function of mitochondria can have variable impact, with the worse end of the spectrum producing catastrophic consequences with a multisystem predisposition. Though categorized a hepatopathy, mitochondrial respiratory chain defects are not limited to the liver in time and space. The liver involvement is also variable in clinical presentation as well as in age of onset, from acute liver failure, cholestasis, or chronic liver disease. Other organs like eye, muscle, central and peripheral nervous system, gastrointestinal tract, hematological, endocrine, and renal systems are also variably involved. Diagnosis hinges on recognition of subtle clinical clues, screening metabolic investigations, evaluation of the extra-hepatic involvement, and role of genetics and tissue diagnosis. Treatment is aimed at both circumventing the acute metabolic crisis and long-term management including nutritional rehabilitation. This review lists and discusses the burden of mitochondrial respiratory chain defects, including various settings when to suspect, their evolution with time, including certain specific disorders, their tiered evaluation with diagnostic algorithms, management dilemmas, role of liver transplantation, and the future research tools.}, }
@article {pmid37744141, year = {2021}, author = {Clergeot, PH and Olson, &#xc5;}, title = {Mitonuclear Genetic Interactions in the Basidiomycete Heterobasidion parviporum Involve a Non-conserved Mitochondrial Open Reading Frame.}, journal = {Frontiers in fungal biology}, volume = {2}, number = {}, pages = {779337}, pmid = {37744141}, issn = {2673-6128}, abstract = {The mitochondrial and nuclear genomes of Eukaryotes are inherited separately and consequently follow distinct evolutionary paths. Nevertheless, the encoding of many mitochondrial proteins by the nuclear genome shows the high level of integration they have reached, which makes mitonuclear genetic interactions all the more conceivable. For each species, natural selection has fostered the evolution of coadapted alleles in both genomes, but a population-wise divergence of such alleles could lead to important phenotypic variation, and, ultimately, to speciation. In this study in the Basidiomycete Heterobasidion parviporum, we have investigated the genetic basis of phenotypic variation among laboratory-designed heterokaryons carrying the same pair of haploid nuclei, but a different mitochondrial genome. Radial growth rate data of thirteen unrelated homokaryotic parents and of their heterokaryotic offspring were combined with SNP data extracted from parental genome sequences to identify nuclear and mitochondrial loci involved in mitonuclear interactions. Two nuclear loci encoding mitochondrial proteins appeared as best candidates to engage in a genetic interaction affecting radial growth rate with a non-conserved mitochondrial open reading frame of unknown function and not reported apart from the Russulales order of Basidiomycete fungi. We believe our approach could be useful to investigate several important traits of fungal biology where mitonuclear interactions play a role, including virulence of fungal pathogens.}, }
@article {pmid34899176, year = {2021}, author = {Anoar, S and Woodling, NS and Niccoli, T}, title = {Mitochondria Dysfunction in Frontotemporal Dementia/Amyotrophic Lateral Sclerosis: Lessons From Drosophila Models.}, journal = {Frontiers in neuroscience}, volume = {15}, number = {}, pages = {786076}, pmid = {34899176}, issn = {1662-4548}, support = {MR/V003585/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are neurodegenerative disorders characterized by declining motor and cognitive functions. Even though these diseases present with distinct sets of symptoms, FTD and ALS are two extremes of the same disease spectrum, as they show considerable overlap in genetic, clinical and neuropathological features. Among these overlapping features, mitochondrial dysfunction is associated with both FTD and ALS. Recent studies have shown that cells derived from patients' induced pluripotent stem cells (iPSC)s display mitochondrial abnormalities, and similar abnormalities have been observed in a number of animal disease models. Drosophila models have been widely used to study FTD and ALS because of their rapid generation time and extensive set of genetic tools. A wide array of fly models have been developed to elucidate the molecular mechanisms of toxicity for mutations associated with FTD/ALS. Fly models have been often instrumental in understanding the role of disease associated mutations in mitochondria biology. In this review, we discuss how mutations associated with FTD/ALS disrupt mitochondrial function, and we review how the use of Drosophila models has been pivotal to our current knowledge in this field.}, }
@article {pmid34890311, year = {2021}, author = {Zaccaron, AZ and Stergiopoulos, I}, title = {Characterization of the mitochondrial genomes of three powdery mildew pathogens reveals remarkable variation in size and nucleotide composition.}, journal = {Microbial genomics}, volume = {7}, number = {12}, pages = {}, pmid = {34890311}, issn = {2057-5858}, mesh = {Ascomycota/*genetics ; Base Composition ; Cytochromes b/genetics ; Erysiphe/*genetics ; Genome Size ; Genome, Fungal ; *Genome, Mitochondrial ; Introns ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Powdery mildews comprise a large group of economically important phytopathogenic fungi. However, limited information exists on their mitochondrial genomes. Here, we assembled and compared the mitochondrial genomes of the powdery mildew pathogens Blumeria graminis f. sp. tritici, Erysiphe pisi, and Golovinomyces cichoracearum. Included in the comparative analysis was also the mitochondrial genome of Erysiphe necator that was previously analysed. The mitochondrial genomes of the four Erysiphales exhibit a similar gene content and organization but a large variation in size, with sizes ranging from 109800 bp in B. graminis f. sp. tritici to 332165 bp in G. cichoracearum, which is the largest mitochondrial genome of a fungal pathogen reported to date. Further comparative analysis revealed an unusual bimodal GC distribution in the mitochondrial genomes of B. graminis f. sp. tritici and G. cichoracearum that was not previously observed in fungi. The cytochrome b (cob) genes of E. necator, E. pisi, and G. cichoracearum were also exceptionally rich in introns, which in turn harboured rare open reading frames encoding reverse transcriptases that were likely acquired horizontally. Golovinomyces cichoracearum had also the longest cob gene (45 kb) among 703 fungal cob genes analysed. Collectively, these results provide novel insights into the organization of mitochondrial genomes of powdery mildew pathogens and represent valuable resources for population genetics and evolutionary studies.}, }
@article {pmid34887560, year = {2021}, author = {Guberovic, I and Hurtado-Bagès, S and Rivera-Casas, C and Knobloch, G and Malinverni, R and Valero, V and Leger, MM and García, J and Basquin, J and Gómez de Cedrón, M and Frigolé-Vivas, M and Cheema, MS and Pérez, A and Ausió, J and Ramírez de Molina, A and Salvatella, X and Ruiz-Trillo, I and Eirin-Lopez, JM and Ladurner, AG and Buschbeck, M}, title = {Evolution of a histone variant involved in compartmental regulation of NAD metabolism.}, journal = {Nature structural &amp; molecular biology}, volume = {28}, number = {12}, pages = {1009-1019}, pmid = {34887560}, issn = {1545-9985}, mesh = {Cell Nucleus/metabolism ; Chromatin/metabolism ; DNA Repair/genetics ; Energy Metabolism/*physiology ; Eukaryota/metabolism ; Histones/*genetics/*metabolism ; Humans ; NAD/*metabolism ; Poly (ADP-Ribose) Polymerase-1/antagonists &amp; inhibitors ; }, abstract = {NAD metabolism is essential for all forms of life. Compartmental regulation of NAD[+] consumption, especially between the nucleus and the mitochondria, is required for energy homeostasis. However, how compartmental regulation evolved remains unclear. In the present study, we investigated the evolution of the macrodomain-containing histone variant macroH2A1.1, an integral chromatin component that limits nuclear NAD[+] consumption by inhibiting poly(ADP-ribose) polymerase 1 in vertebrate cells. We found that macroH2A originated in premetazoan protists. The crystal structure of the macroH2A macrodomain from the protist Capsaspora owczarzaki allowed us to identify highly conserved principles of ligand binding and pinpoint key residue substitutions, selected for during the evolution of the vertebrate stem lineage. Metabolic characterization of the Capsaspora lifecycle suggested that the metabolic function of macroH2A was associated with nonproliferative stages. Taken together, we provide insight into the evolution of a chromatin element involved in compartmental NAD regulation, relevant for understanding its metabolism and potential therapeutic applications.}, }
@article {pmid34887330, year = {2022}, author = {Zandi, M}, title = {ORF8/ORF8a: a difference between SARS-CoV-2 and SARS-CoV.}, journal = {The European respiratory journal}, volume = {59}, number = {2}, pages = {}, pmid = {34887330}, issn = {1399-3003}, mesh = {Biomarkers ; *COVID-19 ; Humans ; Phylogeny ; *SARS-CoV-2 ; }, abstract = {ORF8 as an accessory protein of SARS-CoV-2 https://bit.ly/3Gr3OTK}, }
@article {pmid34880150, year = {2022}, author = {Hussain, M and Liaqat, I and Mubin, M and Nisar, B and Shahzad, K and Durrani, AI and Zafar, U and Afzaal, M and Ehsan, A and Rubab, S}, title = {DNA Barcoding: Molecular Identification and Phylogenetic Analysis of Pheretimoid Earthworm (Metaphire sp. and Amynthas sp.) Based on Mitochondrial Partial COI Gene from Sialkot, Pakistan.}, journal = {Journal of oleo science}, volume = {71}, number = {1}, pages = {83-93}, doi = {10.5650/jos.ess21246}, pmid = {34880150}, issn = {1347-3352}, mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology/*genetics ; Oligochaeta/anatomy &amp; histology/classification/*genetics ; Pakistan ; *Phylogeny ; Species Specificity ; }, abstract = {The extremely difficult and challenging process is identifying pheretimoid species, genus Metaphire and Amynthas involving increased homoplasy in various morphological characteristics. The molecular identification, phylogenetic relationships, and evolutionary divergence time of earthworms belonging to the pheretimoid complex were investigated in this study using partial mitochondrial COI (cytochrome C oxidase subunit I) gene sequences ranging from 550-680 bp. Results revealed that 86 pheretimoid earthworms were morphologically different from a total of 342 mature worms. Moreover, 11 pheretimoid species were molecularly identified, including Metaphire posthuma (02), M. anomala (01), M. houlleti (02), M. californica (01), M. birmanica (02), Amynthas minimus (01), A. morrisi (01), and M. bununa (01). A phylogenetic tree was constructed with bootstrap values of 95%, which supported a monophyletic lineage of two well-supported clades formed by 12 partial COI sequences and 48 GenBank sequences using Hirudo medicinalis as an outgroup. The monophyly of these obtained genera indicated overall similarity at species level. Today, species like Amynthas, Metaphire and Pheretima have worm diversity in the form of pheretimoid earthworms, which dates to the Late Miocene (11.2-5.3 Mya) and the Pliocene (5.3-2.4 Mya). Compared to all relevant pheretimoid species, genetic p-distance values ranged from 0.0% to 0.57% (less than 1%). These low range values demonstrated that both genera Metaphire and Amynthas, supported the theory, which states that there are shared similarities among the species, despite different morphology. The current study is the first attempt in Pakistan to identify earthworms through DNA barcoding thus providing a genomic stamp. The work explored the significance of COI gene sequences to construct molecular tools that will be useful to overcome the different obstacles in morphologically similar earthworm identification and their phylogenetic study.}, }
@article {pmid34858801, year = {2021}, author = {Dai, SD and Wang, S and Qin, YN and Zhu, JC}, title = {Multiomics Landscape Uncovers the Molecular Mechanism of the Malignant Evolution of Lung Adenocarcinoma Cells to Chronic Low Dose Cadmium Exposure.}, journal = {Frontiers in oncology}, volume = {11}, number = {}, pages = {654687}, pmid = {34858801}, issn = {2234-943X}, abstract = {Cadmium (Cd) from cigarette smoke and polluted air can lead to lung adenocarcinoma after long-term inhalation. However, most studies are based on short-term exposure to this toxic metal at high concentrations. Here, we investigate the effects of long-term exposure of A549 cells (lung adenocarcinoma) to cadmium at low concentrations using morphological and multiomics analyses. First, we treated A549 cells continuously with CdCl2 at 1μM for 8 months and found that CdCl2 promoted cellular migration and invasion. After that, we applied transmission electron and fluorescence microscopies and did not observe significant morphological changes in Golgi apparatus, endoplasmic reticulum, lysosomes, or mitochondria on Cd treated cells; microfilaments, in contrast, accumulated in lamellipodium and adhesion plaques, which suggested that Cd enhanced cellular activity. Second, by using whole-exome sequencing (WES) we detected 4222 unique SNPs in Cd-treated cells, which included 382 unique non-synonymous mutation sites. The corresponding mutated genes, after GO and KEGG enrichments, were involved mainly in cell adhesion, movement, and metabolic pathways. Third, by RNA-seq analysis, we showed that 1250 genes (784 up and 466 down), 1623 mRNAs (1023 up and 591 down), and 679 lncRNAs (375 up and 304 down) were expressed differently. Furthermore, GO enrichment of these RNA-seq results suggested that most differentially expressed genes were related to cell adhesion and organization of the extracellular matrix in biological process terms; KEGG enrichment revealed that the differentially expressed genes took part in 26 pathways, among which the metabolic pathway was the most significant. These findings could be important for unveiling mechanisms of Cd-related cancers and for developing cancer therapies in the future.}, }
@article {pmid34847540, year = {2021}, author = {Fernández Casafuz, AB and De Rossi, MC and Bruno, L}, title = {Morphological fluctuations of individual mitochondria in living cells.}, journal = {Journal of physics. Condensed matter : an Institute of Physics journal}, volume = {34}, number = {9}, pages = {}, doi = {10.1088/1361-648X/ac3e9c}, pmid = {34847540}, issn = {1361-648X}, mesh = {*Cytoskeleton/metabolism ; Microscopy, Confocal ; *Microtubules/metabolism ; Mitochondria/physiology ; Organelles ; }, abstract = {Uncovering the link between mitochondrial morphology, dynamics, positioning and function is challenging. Mitochondria are very flexible organelles that are subject to tension and compression within cells. Recent findings highlighted the importance of these mechanical aspects in the regulation of mitochondria dynamics, arising the question on which are the processes and mechanisms involved in their shape remodeling. In this work we explored in detail the morphological changes and spatio-temporal fluctuations of these organelles in livingXenopus laevismelanophores, a well-characterized cellular model. We developed an automatic method for the classification of mitochondria shapes based on the analysis of the curvature of the contour shape from confocal microscopy images. A persistence length of 2.1μm was measured, quantifying, for the first time, the bending plasticity of mitochondria in their cellular environment. The shape evolution at the single organelle level was followed during a few minutes revealing that mitochondria can bend and unbend in the seconds timescale. Furthermore, the inspection of confocal movies simultaneously registering fluorescent mitochondria and microtubules suggests that the cytoskeleton network architecture and dynamics play a significant role in mitochondria shape remodeling and fluctuations. For instance changes from sinuous to elongated organelles related to transitions from confined behavior to fast directed motion along microtubule tracks were observed.}, }
@article {pmid34836918, year = {2023}, author = {Esteves, AR and Munoz-Pinto, MF and Nunes-Costa, D and Candeias, E and Silva, DF and Magalhães, JD and Pereira-Santos, AR and Ferreira, IL and Alarico, S and Tiago, I and Empadinhas, N and Cardoso, SM}, title = {Footprints of a microbial toxin from the gut microbiome to mesencephalic mitochondria.}, journal = {Gut}, volume = {72}, number = {1}, pages = {73-89}, pmid = {34836918}, issn = {1468-3288}, mesh = {Mice ; Animals ; *Gastrointestinal Microbiome/physiology ; Mesencephalon/metabolism/pathology ; *Parkinson Disease/metabolism ; Inflammation/metabolism ; Mitochondria/metabolism ; }, abstract = {OBJECTIVE: Idiopathic Parkinson's disease (PD) is characterised by alpha-synuclein (aSyn) aggregation and death of dopaminergic neurons in the midbrain. Recent evidence posits that PD may initiate in the gut by microbes or their toxins that promote chronic gut inflammation that will ultimately impact the brain. In this work, we sought to demonstrate that the effects of the microbial toxin β-N-methylamino-L-alanine (BMAA) in the gut may trigger some PD cases, which is especially worrying as this toxin is present in certain foods but not routinely monitored by public health authorities.<br><br>DESIGN: To test the hypothesis, we treated wild-type mice, primary neuronal cultures, cell lines and isolated mitochondria with BMAA, and analysed its impact on gut microbiota composition, barrier permeability, inflammation and aSyn aggregation as well as in brain inflammation, dopaminergic neuronal loss and motor behaviour. To further examine the key role of mitochondria, we also determined the specific effects of BMAA on mitochondrial function and on inflammasome activation.<br><br>RESULTS: BMAA induced extensive depletion of segmented filamentous bacteria (SFB) that regulate gut immunity, thus triggering gut dysbiosis, immune cell migration, increased intestinal inflammation, loss of barrier integrity and caudo-rostral progression of aSyn. Additionally, BMAA induced in vitro and in vivo mitochondrial dysfunction with cardiolipin exposure and consequent activation of neuronal innate immunity. These events primed neuroinflammation, dopaminergic neuronal loss and motor deficits.<br><br>CONCLUSION: Taken together, our results demonstrate that chronic exposure to dietary BMAA can trigger a chain of events that recapitulate the evolution of the PD pathology from the gut to the brain, which is consistent with 'gut-first' PD.}, }
@article {pmid34833151, year = {2021}, author = {Vargas-Mendoza, N and Angeles-Valencia, M and Morales-González, &#xc1; and Madrigal-Santillán, EO and Morales-Martínez, M and Madrigal-Bujaidar, E and Álvarez-González, I and Gutiérrez-Salinas, J and Esquivel-Chirino, C and Chamorro-Cevallos, G and Cristóbal-Luna, JM and Morales-González, JA}, title = {Oxidative Stress, Mitochondrial Function and Adaptation to Exercise: New Perspectives in Nutrition.}, journal = {Life (Basel, Switzerland)}, volume = {11}, number = {11}, pages = {}, pmid = {34833151}, issn = {2075-1729}, abstract = {Cells have the ability to adapt to stressful environments as a part of their evolution. Physical exercise induces an increase of a demand for energy that must be met by mitochondria as the main (ATP) provider. However, this process leads to the increase of free radicals and the so-called reactive oxygen species (ROS), which are necessary for the maintenance of cell signaling and homeostasis. In addition, mitochondrial biogenesis is influenced by exercise in continuous crosstalk between the mitochondria and the nuclear genome. Excessive workloads may induce severe mitochondrial stress, resulting in oxidative damage. In this regard, the objective of this work was to provide a general overview of the molecular mechanisms involved in mitochondrial adaptation during exercise and to understand if some nutrients such as antioxidants may be implicated in blunt adaptation and/or an impact on the performance of exercise by different means.}, }
@article {pmid34831121, year = {2021}, author = {De Gaetano, A and Solodka, K and Zanini, G and Selleri, V and Mattioli, AV and Nasi, M and Pinti, M}, title = {Molecular Mechanisms of mtDNA-Mediated Inflammation.}, journal = {Cells}, volume = {10}, number = {11}, pages = {}, pmid = {34831121}, issn = {2073-4409}, support = {FAR di Dipartimento 2020//University of Modena and Reggio Emilia/ ; NA//Istituto Nazionale per le Ricerche Cardiovascolari/ ; }, mesh = {Biological Evolution ; Body Fluids/metabolism ; DNA, Mitochondrial/*genetics ; Extracellular Vesicles/metabolism ; Humans ; Inflammasomes/metabolism ; Inflammation/*genetics ; }, abstract = {Besides their role in cell metabolism, mitochondria display many other functions. Mitochondrial DNA (mtDNA), the own genome of the organelle, plays an important role in modulating the inflammatory immune response. When released from the mitochondrion to the cytosol, mtDNA is recognized by cGAS, a cGAMP which activates a pathway leading to enhanced expression of type I interferons, and by NLRP3 inflammasome, which promotes the activation of pro-inflammatory cytokines Interleukin-1beta and Interleukin-18. Furthermore, mtDNA can be bound by Toll-like receptor 9 in the endosome and activate a pathway that ultimately leads to the expression of pro-inflammatory cytokines. mtDNA is released in the extracellular space in different forms (free DNA, protein-bound DNA fragments) either as free circulating molecules or encapsulated in extracellular vesicles. In this review, we discussed the latest findings concerning the molecular mechanisms that regulate the release of mtDNA from mitochondria, and the mechanisms that connect mtDNA misplacement to the activation of inflammation in different pathophysiological conditions.}, }
@article {pmid34829656, year = {2021}, author = {Hernández-Camacho, JD and García-Corzo, L and Fernández-Ayala, DJM and Navas, P and López-Lluch, G}, title = {Coenzyme Q at the Hinge of Health and Metabolic Diseases.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {10}, number = {11}, pages = {}, pmid = {34829656}, issn = {2076-3921}, support = {P18-RT-4572//Regional Government of Andalusia/ ; UPO-126247//Regional Government of Andalusia/ ; UPO-1265673//Regional Government of Andalusia/ ; BIO-177//Regional Government of Andalusia/ ; FIS PI20/00541//Instituto de Salud Carlos III/ ; RED2018-102576-T//Centre for Biomedical Network Research on Rare Diseases/ ; FPU16/03264//Ministerio de Educaci&#xf3;n Cultura y Deporte/ ; }, abstract = {Coenzyme Q is a unique lipidic molecule highly conserved in evolution and essential to maintaining aerobic metabolism. It is endogenously synthesized in all cells by a very complex pathway involving a group of nuclear genes that share high homology among species. This pathway is tightly regulated at transcription and translation, but also by environment and energy requirements. Here, we review how coenzyme Q reacts within mitochondria to promote ATP synthesis and also integrates a plethora of metabolic pathways and regulates mitochondrial oxidative stress. Coenzyme Q is also located in all cellular membranes and plasma lipoproteins in which it exerts antioxidant function, and its reaction with different extramitochondrial oxidoreductases contributes to regulate the cellular redox homeostasis and cytosolic oxidative stress, providing a key factor in controlling various apoptosis mechanisms. Coenzyme Q levels can be decreased in humans by defects in the biosynthesis pathway or by mitochondrial or cytosolic dysfunctions, leading to a highly heterogeneous group of mitochondrial diseases included in the coenzyme Q deficiency syndrome. We also review the importance of coenzyme Q levels and its reactions involved in aging and age-associated metabolic disorders, and how the strategy of its supplementation has had benefits for combating these diseases and for physical performance in aging.}, }
@article {pmid34829521, year = {2021}, author = {Olson, KR}, title = {A Case for Hydrogen Sulfide Metabolism as an Oxygen Sensing Mechanism.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {10}, number = {11}, pages = {}, pmid = {34829521}, issn = {2076-3921}, support = {IOS2012106//National Science Foundation USA/ ; }, abstract = {The ability to detect oxygen availability is a ubiquitous attribute of aerobic organisms. However, the mechanism(s) that transduce oxygen concentration or availability into appropriate physiological responses is less clear and often controversial. This review will make the case for oxygen-dependent metabolism of hydrogen sulfide (H2S) and polysulfides, collectively referred to as reactive sulfur species (RSS) as a physiologically relevant O2 sensing mechanism. This hypothesis is based on observations that H2S and RSS metabolism is inversely correlated with O2 tension, exogenous H2S elicits physiological responses identical to those produced by hypoxia, factors that affect H2S production or catabolism also affect tissue responses to hypoxia, and that RSS efficiently regulate downstream effectors of the hypoxic response in a manner consistent with a decrease in O2. H2S-mediated O2 sensing is then compared to the more generally accepted reactive oxygen species (ROS) mediated O2 sensing mechanism and a number of reasons are offered to resolve some of the confusion between the two.}, }
@article {pmid34828378, year = {2021}, author = {Chen, F and Zou, H and Jin, X and Zhang, D and Li, W and Li, M and Wu, S and Wang, G}, title = {Sequencing of the Complete Mitochondrial Genome of Pingus sinensis (Spirurina: Quimperiidae): Gene Arrangements and Phylogenetic Implications.}, journal = {Genes}, volume = {12}, number = {11}, pages = {}, pmid = {34828378}, issn = {2073-4425}, mesh = {Animals ; Bayes Theorem ; Codon Usage ; Evolution, Molecular ; Gene Order ; Genome Size ; Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Spirurina/*genetics/isolation &amp; purification ; }, abstract = {Despite several decades of intensive research on spirurine nematodes, molecular data on some of the main lineages are still absent, which makes taxonomic classification insufficiently resolved. In the present study, we sequenced the first complete mitogenome for the family Quimperiidae, belonging to P. sinensis (Spirurina: Quimperiidae), a parasite living in the intestines of snakehead (Ophiocephalus argus). The circular mitogenome is 13,874 bp long, and it contains the standard nematode gene set: 22 transfer RNAs, 2 ribosomal RNAs and 12 protein-coding genes. There are also two long non-coding regions (NCR), in addition to only 8 other intergenic regions, ranging in size from 1 to 58 bp. To investigate its phylogenetic position and study the relationships among other available Spirurina, we performed the phylogenetic analysis using Bayesian inference and maximum likelihood approaches by concatenating the nucleotide sequences of all 36 genes on a dataset containing all available mitogenomes of the suborder Spirurina from NCBI and compared with gene order phylogenies using the MLGO program. Both supported the closer relationship of Ascaridoidea to Seuratoidea than to Spiruroidea. Pingus formed a sister-group with the Cucullanus genus. The results provide a new insights into the relationships within Spirurina.}, }
@article {pmid34818432, year = {2022}, author = {Jiang, Y and Yue, L and Yang, F and Gillung, JP and Winterton, SL and Price, BW and Contreras-Ramos, A and Hayashi, F and Aspöck, U and Aspöck, H and Yeates, DK and Yang, D and Liu, X}, title = {Similar pattern, different paths: tracing the biogeographical history of Megaloptera (Insecta: Neuropterida) using mitochondrial phylogenomics.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {38}, number = {3}, pages = {374-391}, doi = {10.1111/cla.12494}, pmid = {34818432}, issn = {1096-0031}, mesh = {Animals ; *Genome, Mitochondrial/genetics ; *Holometabola/genetics ; Insecta/genetics ; Mitochondria/genetics ; Phylogeny ; }, abstract = {The sequential breakup of the supercontinent Pangaea since the Middle Jurassic is one of the crucial factors that has driven the biogeographical patterns of terrestrial biotas. Despite decades of effort searching for concordant patterns between diversification and continental fragmentation among taxonomic groups, increasing evidence has revealed more complex and idiosyncratic scenarios resulting from a mixture of vicariance, dispersal and extinction. Aquatic insects with discreet ecological requirements, low vagility and disjunct distributions represent a valuable model for testing biogeographical hypotheses by reconstructing their distribution patterns and temporal divergences. Insects of the order Megaloptera have exclusively aquatic larvae, their adults have low vagility, and the group has a highly disjunct geographical distribution. Here we present a comprehensive phylogeny of Megaloptera based on a large-scale mitochondrial genome sequencing of 99 species representing >90% of the world genera from all major biogeographical regions. Molecular dating suggests that the deep divergence within Megaloptera pre-dates the breakup of Pangaea. Subsequently, the intergeneric divergences within Corydalinae (dobsonflies), Chauliodinae (fishflies) and Sialidae (alderflies) might have been driven by both vicariance and dispersal correlated with the shifting continent during the Cretaceous, but with strikingly different and incongruent biogeographical signals. The austral distribution of many corydalids appears to be a result of colonization from Eurasia through southward dispersal across Europe and Africa during the Cretaceous, whereas a nearly contemporaneous dispersal via northward rafting of Gondwanan landmasses may account for the colonization of extant Eurasian alderflies from the south.}, }
@article {pmid34811145, year = {2021}, author = {Parrinha, D and Marques, MP and Heinicke, MP and Khalid, F and Parker, KL and Tolley, KA and Childers, JL and Conradie, W and Bauer, AM and Ceraco, LMP}, title = {A revision of Angolan species in the genus Pedioplanis Fitzinger (Squamata: Lacertidae), with the description of a new species.}, journal = {Zootaxa}, volume = {5032}, number = {1}, pages = {1-46}, doi = {10.11646/zootaxa.5032.1.1}, pmid = {34811145}, issn = {1175-5334}, mesh = {Animals ; Cell Nucleus ; *Lizards/genetics ; Mitochondria ; Phylogeny ; }, abstract = {The genus Pedioplanis reaches its northernmost limit in western Angola, where it is represented by three species, Pedioplanis benguelensis, P. haackei and P. huntleyi. The taxonomic status of P. benguelensis remains problematic, mainly due to the vague original description and the loss of the original type material. Here we provide a revision of the Angolan representatives of the genus, with the description of a new species, Pedioplanis serodioi sp. nov., from the lowlands of southwestern Angola. Phylogenetic analyses using a combination of mitochondrial (16S and ND2) and nuclear (RAG-1) markers, as well as morphological data, support the recognition of the new species. For purposes of nomenclatural stability, we designate a neotype for P. benguelensis and provide motivation to correct the spelling of the specific epithet to benguelensis. The clarification of the status of P. benguelensis and the description of a new species contribute to a better understanding of the taxonomy and biogeography of the genus Pedioplanis, as well as the general biogeographic context of southwestern Angola, adding to the growing evidence in favor of the recognition of this region as a hotspot of lizard diversity and endemism. An updated key to the genus is also provided.}, }
@article {pmid34810731, year = {2021}, author = {Mousavi-Sabet, H and Eagderi, S and Vatandoust, S and Freyhof, J}, title = {Five new species of the sisorid catfish genus Glyptothorax from Iran (Teleostei: Sisoridae).}, journal = {Zootaxa}, volume = {5067}, number = {4}, pages = {451-484}, doi = {10.11646/zootaxa.5067.4.1}, pmid = {34810731}, issn = {1175-5334}, mesh = {Animals ; *Catfishes/genetics ; DNA, Mitochondrial ; Iran ; Mitochondria ; Rivers ; }, abstract = {Five new species of Glyptothorax are described from Iran. Glyptothorax alidaeii, new species, from the Seimare in the Karkheh drainage, G. galaxias, new species, from the upper Karun drainage, G. hosseinpanahii, new species, from the Zohreh drainage, G. pallens, new species, from the Sirvan drainage, and G. shapuri, new species, from Shapur in the Helleh drainage. Glyptothorax silviae from the Jarrahi drainage is re-diagnosed. All six species are morphologically distinguishable by the structure of the thoracic adhesive apparatus, as well as morphometric characters and details in the colour pattern. They form distinct mitochondrial clades between 1.2% and 4.1% minimum K2P distance based on the mitochondrial DNA barcode region.}, }
@article {pmid34799698, year = {2021}, author = {Vowinckel, J and Hartl, J and Marx, H and Kerick, M and Runggatscher, K and Keller, MA and Mülleder, M and Day, J and Weber, M and Rinnerthaler, M and Yu, JSL and Aulakh, SK and Lehmann, A and Mattanovich, D and Timmermann, B and Zhang, N and Dunn, CD and MacRae, JI and Breitenbach, M and Ralser, M}, title = {The metabolic growth limitations of petite cells lacking the mitochondrial genome.}, journal = {Nature metabolism}, volume = {3}, number = {11}, pages = {1521-1535}, pmid = {34799698}, issn = {2522-5812}, support = {200829/WT_/Wellcome Trust/United Kingdom ; FC001134/MRC_/Medical Research Council/United Kingdom ; FC001134/CRUK_/Cancer Research UK/United Kingdom ; FC001134/WT_/Wellcome Trust/United Kingdom ; 260809/ERC_/European Research Council/International ; }, mesh = {Amino Acids/metabolism ; Biomass ; Cell Proliferation ; Citric Acid Cycle ; *Energy Metabolism ; Fungal Proteins/chemistry/genetics/metabolism ; *Genome, Mitochondrial ; Membrane Potential, Mitochondrial ; Mitochondria/*genetics/*metabolism ; Mutation ; Phenotype ; Structure-Activity Relationship ; Yeasts/*genetics/*metabolism ; }, abstract = {Eukaryotic cells can survive the loss of their mitochondrial genome, but consequently suffer from severe growth defects. 'Petite yeasts', characterized by mitochondrial genome loss, are instrumental for studying mitochondrial function and physiology. However, the molecular cause of their reduced growth rate remains an open question. Here we show that petite cells suffer from an insufficient capacity to synthesize glutamate, glutamine, leucine and arginine, negatively impacting their growth. Using a combination of molecular genetics and omics approaches, we demonstrate the evolution of fast growth overcomes these amino acid deficiencies, by alleviating a perturbation in mitochondrial iron metabolism and by restoring a defect in the mitochondrial tricarboxylic acid cycle, caused by aconitase inhibition. Our results hence explain the slow growth of mitochondrial genome-deficient cells with a partial auxotrophy in four amino acids that results from distorted iron metabolism and an inhibited tricarboxylic acid cycle.}, }
@article {pmid34798191, year = {2021}, author = {Lin, Y and Xiao, Q and Hao, Q and Qian, Z and Li, X and Li, P and Li, H and Chen, L}, title = {Genome-wide identification and functional analysis of the glutathione S-transferase (GST) family in Pomacea canaliculata.}, journal = {International journal of biological macromolecules}, volume = {193}, number = {Pt B}, pages = {2062-2069}, doi = {10.1016/j.ijbiomac.2021.11.038}, pmid = {34798191}, issn = {1879-0003}, mesh = {Animals ; Cold-Shock Response/genetics ; Gastropoda/*genetics ; Genome/*genetics ; Glutathione Transferase/*genetics ; Oxidative Stress/genetics ; Phylogeny ; Reactive Oxygen Species/metabolism ; }, abstract = {Cold causes oxidative stress in living organisms, mainly caused by the accumulation of reactive oxygen species (ROS). In the antioxidant defense systems, Glutathione S-transferases (GSTs) play a vital role in the regulation of detoxification and redox balance of ROS. In this study, the P. canaliculata GST gene family were characterized using a genome-wide search of the conserved domain. Phylogenetic tree and domain composition analysis revealed that 30 PcGSTs belong to seven classes, including five in MAPEG, two in Mu, nine in Omega, 11 in Sigma, one in Rho, Theta and Alpha class, respectively. RNA-seq analysis revealed that most PcGSTs localized in mitochondria highly expressed in hepatopancreas, and most PcGSTs localized in cytoplasm highly expressed in kidney. A total of 12 PcGST genes were significantly up-regulated and PcGST12 was significantly down-regulated after cold acclimation. Ten PcGSTs were identified as DEGs under cold stress after cold acclimation. qRT-PCR revealed that the expression level of five PcGST genes were significantly varied during the cold acclimation. The present study investigated the characterization of the P. canaliculata GST gene family, extending our understanding of GST mediated cold acclimation and cold stress-response mechanisms in this invasive snail.}, }
@article {pmid34797494, year = {2022}, author = {Yamazaki, D and Chiba, S}, title = {Comparing the genetic diversity and population structure of sister marine snails having contrasting habitat specificity.}, journal = {Molecular biology reports}, volume = {49}, number = {1}, pages = {393-401}, pmid = {34797494}, issn = {1573-4978}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Gene Flow ; Genetic Variation ; Genetics, Population ; Japan ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; Snails/*classification/genetics ; Species Specificity ; }, abstract = {BACKGROUND: To grasp the processes of spatial genetic structuring in open and connectable marine environments is the principal study goal in molecular biological studies. Comparative seascape genetics using multiple species are a powerful approach to understand the physical geographic and oceanographic effects on genetic variation. Besides, species-specific ecological traits such as dispersal abilities and habitat specificity are important factors for spatial genetic structuring.<br><br>METHODS AND RESULTS: We focused on the sister marine snail species Tegula kusairo and T. xanthostigma around the Japanese mainland, which have contrasting habitat specificities for wave strength. Tegula kusairo only inhabits sheltered coastal environments, while T. xanthostigma is found mainly on wave-exposed rocky shores facing the open sea. We estimated their genetic diversity indices and levels of population differentiation based on mtDNA. We found that the genetic diversity of T. kusairo was lower than that of T. xanthostigma, while their level of population genetic differentiation was higher than that of T. xanthostigma. Namely, the species specific to weak wave environments had a higher level of population genetic differentiation than the species specific to strong wave action.<br><br>CONCLUSION: Ecological traits linked not only to dispersal abilities but also to habitat specificity can influence genetic variation in a pair of closely related sister species distributed in the same seascape.}, }
@article {pmid34795357, year = {2021}, author = {Mishina, T and Takeshima, H and Takada, M and Iguchi, K and Zhang, C and Zhao, Y and Kawahara-Miki, R and Hashiguchi, Y and Tabata, R and Sasaki, T and Nishida, M and Watanabe, K}, title = {Interploidy gene flow involving the sexual-asexual cycle facilitates the diversification of gynogenetic triploid Carassius fish.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {22485}, pmid = {34795357}, issn = {2045-2322}, support = {18J00928//Japan Society for the Promotion of Science/ ; 21K14919//Japan Society for the Promotion of Science/ ; 15J02066//Japan Society for the Promotion of Science/ ; 26291079//Japan Society for the Promotion of Science/ ; 26250044//Japan Society for the Promotion of Science/ ; 17H03720//Japan Society for the Promotion of Science/ ; 18H01330//Japan Society for the Promotion of Science/ ; 20H03009//Japan Society for the Promotion of Science/ ; }, mesh = {Alleles ; Animals ; Asia ; Biological Evolution ; Cell Nucleus/metabolism ; DNA, Mitochondrial/genetics ; Diploidy ; Europe ; *Gene Flow ; Genetic Markers ; Genetics, Population ; Genotype ; Geography ; Goldfish/*genetics/*physiology ; Heterozygote ; Homozygote ; Japan/epidemiology ; Male ; Mitochondria/metabolism ; Models, Genetic ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; Rivers ; Species Specificity ; Spermatozoa/physiology ; Transcriptome ; Triploidy ; }, abstract = {Asexual vertebrates are rare and at risk of extinction due to their restricted adaptability through the loss of genetic recombination. We explore the mechanisms behind the generation and maintenance of genetic diversity in triploid asexual (gynogenetic) Carassius auratus fish, which is widespread in East Asian fresh waters and exhibits one of the most extensive distribution among asexual vertebrates despite its dependence on host sperm. Our analyses of genetic composition using dozens of genetic markers and genome-wide transcriptome sequencing uncover admixed genetic composition of Japanese asexual triploid Carassius consisting of both the diverged Japanese and Eurasian alleles, suggesting the involvement of Eurasian lineages in its origin. However, coexisting sexual diploid relatives and asexual triploids in Japan show regional genetic similarity in both mitochondrial and nuclear markers. These results are attributed to a unique unidirectional gene flow from diploids to sympatric triploids, with the involvement of occasional sexual reproduction. Additionally, the asexual triploid shows a weaker population structure than the sexual diploid, and multiple triploid lineages coexist in most Japanese rivers. The generated diversity via repeated interploidy gene flow as well as an increased establishment of immigrants is assumed to offset the cost of asexual reproduction and might contribute to the successful broad distribution of this asexual vertebrate.}, }
@article {pmid34789336, year = {2021}, author = {Proust, B and Radić, M and Vidaček, N&#x160; and Cottet, C and Attia, S and Lamarche, F and Ačkar, L and Mikulčić, VG and Tokarska-Schlattner, M and Ćetković, H and Schlattner, U and Bosnar, MH}, title = {NME6 is a phosphotransfer-inactive, monomeric NME/NDPK family member and functions in complexes at the interface of mitochondrial inner membrane and matrix.}, journal = {Cell &amp; bioscience}, volume = {11}, number = {1}, pages = {195}, pmid = {34789336}, issn = {2045-3701}, support = {IP-2016-06-4021//Hrvatska Zaklada za Znanost/ ; IP-2019-04-5382//Hrvatska Zaklada za Znanost/ ; ANR-15-IDEX-02//French National Research Agency within the Investissements d'Avenir program/ ; }, abstract = {BACKGROUND: NME6 is a member of the nucleoside diphosphate kinase (NDPK/NME/Nm23) family which has key roles in nucleotide homeostasis, signal transduction, membrane remodeling and metastasis suppression. The well-studied NME1-NME4 proteins are hexameric and catalyze, via a phospho-histidine intermediate, the transfer of the terminal phosphate from (d)NTPs to (d)NDPs (NDP kinase) or proteins (protein histidine kinase). For the NME6, a gene/protein that emerged early in eukaryotic evolution, only scarce and partially inconsistent data are available. Here we aim to clarify and extend our knowledge on the human NME6.<br><br>RESULTS: We show that NME6 is mostly expressed as a 186 amino acid protein, but that a second albeit much less abundant isoform exists. The recombinant NME6 remains monomeric, and does not assemble into homo-oligomers or hetero-oligomers with NME1-NME4. Consequently, NME6 is unable to catalyze phosphotransfer: it does not generate the phospho-histidine intermediate, and no NDPK activity can be detected. In cells, we could resolve and extend existing contradictory reports by localizing NME6 within mitochondria, largely associated with the mitochondrial inner membrane and matrix space. Overexpressing NME6 reduces ADP-stimulated mitochondrial respiration and complex III abundance, thus linking NME6 to dysfunctional oxidative phosphorylation. However, it did not alter mitochondrial membrane potential, mass, or network characteristics. Our screen for NME6 protein partners revealed its association with NME4 and OPA1, but a direct interaction was observed only with RCC1L, a protein involved in mitochondrial ribosome assembly and mitochondrial translation, and identified as essential for oxidative phosphorylation.<br><br>CONCLUSIONS: NME6, RCC1L and mitoribosomes localize together at the inner membrane/matrix space where NME6, in concert with RCC1L, may be involved in regulation of the mitochondrial translation of essential oxidative phosphorylation subunits. Our findings suggest new functions for NME6, independent of the classical phosphotransfer activity associated with NME proteins.}, }
@article {pmid34786732, year = {2022}, author = {Bykov, YS and Flohr, T and Boos, F and Zung, N and Herrmann, JM and Schuldiner, M}, title = {Widespread use of unconventional targeting signals in mitochondrial ribosome proteins.}, journal = {The EMBO journal}, volume = {41}, number = {1}, pages = {e109519}, pmid = {34786732}, issn = {1460-2075}, mesh = {Amino Acid Motifs ; Bacterial Proteins/chemistry ; Mitochondria/metabolism ; Mitochondrial Proteins/*metabolism ; Mitochondrial Ribosomes/*metabolism ; Models, Biological ; *Protein Sorting Signals ; Saccharomyces cerevisiae/*metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Mitochondrial ribosomes are complex molecular machines indispensable for respiration. Their assembly involves the import of several dozens of mitochondrial ribosomal proteins (MRPs), encoded in the nuclear genome, into the mitochondrial matrix. Proteomic and structural data as well as computational predictions indicate that up to 25% of yeast MRPs do not have a conventional N-terminal mitochondrial targeting signal (MTS). We experimentally characterized a set of 15 yeast MRPs in vivo and found that five use internal MTSs. Further analysis of a conserved model MRP, Mrp17/bS6m, revealed the identity of the internal targeting signal. Similar to conventional MTS-containing proteins, the internal sequence mediates binding to TOM complexes. The entire sequence of Mrp17 contains positive charges mediating translocation. The fact that these sequence properties could not be reliably predicted by standard methods shows that mitochondrial protein targeting is more versatile than expected. We hypothesize that structural constraints imposed by ribosome assembly interfaces may have disfavored N-terminal presequences and driven the evolution of internal targeting signals in MRPs.}, }
@article {pmid34784177, year = {2021}, author = {Holehouse, AS and Ginell, GM and Griffith, D and Böke, E}, title = {Clustering of Aromatic Residues in Prion-like Domains Can Tune the Formation, State, and Organization of Biomolecular Condensates.}, journal = {Biochemistry}, volume = {60}, number = {47}, pages = {3566-3581}, pmid = {34784177}, issn = {1520-4995}, mesh = {Amino Acids, Aromatic/chemistry/genetics/metabolism ; Animals ; Biomolecular Condensates/*metabolism ; Cell Polarity ; Cells, Cultured ; Female ; Intravital Microscopy ; Oocytes/cytology/metabolism ; Phase Transition ; Primary Cell Culture ; Protein Domains/genetics ; Protein Engineering ; T-Box Domain Proteins/chemistry/genetics/*metabolism ; Xenopus Proteins/chemistry/genetics/*metabolism ; Xenopus laevis ; }, abstract = {In immature oocytes, Balbiani bodies are conserved membraneless condensates implicated in oocyte polarization, the organization of mitochondria, and long-term organelle and RNA storage. In Xenopus laevis, Balbiani body assembly is mediated by the protein Velo1. Velo1 contains an N-terminal prion-like domain (PLD) that is essential for Balbiani body formation. PLDs have emerged as a class of intrinsically disordered regions that can undergo various different types of intracellular phase transitions and are often associated with dynamic, liquid-like condensates. Intriguingly, the Velo1 PLD forms solid-like assemblies. Here we sought to understand why Velo1 phase behavior appears to be biophysically distinct from that of other PLD-containing proteins. Through bioinformatic analysis and coarse-grained simulations, we predict that the clustering of aromatic residues and the amino acid composition of residues between aromatics can influence condensate material properties, organization, and the driving forces for assembly. To test our predictions, we redesigned the Velo1 PLD to test the impact of targeted sequence changes in vivo. We found that the Velo1 design with evenly spaced aromatic residues shows rapid internal dynamics, as probed by fluorescent recovery after photobleaching, even when recruited into Balbiani bodies. Our results suggest that Velo1 might have been selected in evolution for distinctly clustered aromatic residues to maintain the structure of Balbiani bodies in long-lived oocytes. In general, our work identifies several tunable parameters that can be used to augment the condensate material state, offering a road map for the design of synthetic condensates.}, }
@article {pmid34783988, year = {2022}, author = {López-Cuamatzi, IL and Ortega, J and Baeza, JA}, title = {The complete mitochondrial genome of the 'Zacatuche' Volcano rabbit (Romerolagus diazi), an endemic and endangered species from the Volcanic Belt of Central Mexico.}, journal = {Molecular biology reports}, volume = {49}, number = {2}, pages = {1141-1149}, pmid = {34783988}, issn = {1573-4978}, mesh = {Animals ; Conservation of Natural Resources/methods ; Endangered Species ; Gene Order ; Genome, Mitochondrial/*genetics ; Lagomorpha/*genetics ; Mexico ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Rabbits/genetics ; }, abstract = {BACKGROUND: The 'Zacatuche', 'Teporingo', or Volcano rabbit (Romerolagus diazi) belongs to the family Leporidae, is an endemic species restricted to the Central part of the Trans-Mexican Volcanic Belt, and is considered 'endangered' by the IUCN Red List of Threatened Species.<br><br>METHODS AND RESULTS: This study reports, for the first time, the complete mitochondrial genome of R. diazi and examined the phylogenetic position of R. diazi among other closely related co-familiar species using mitochondrial protein-coding genes (PCGs). The mitogenome of R. diazi was assembled from short Illumina 150&#xa0;bp pair-end reads with a coverage of 189x. The AT-rich mitochondrial genome of R. diazi is 17,400&#xa0;bp in length and is comprised of 13 PCGs, two ribosomal RNA genes, and 22 transfer RNA genes. The gene order observed in the mitochondrial genome of R. diazi is identical to that reported for other leporids. Phylogenetic analyses based on PCGs support the basal position of Romerolagus within the Leporidae, at least when compared to the genera Oryctolagus and Lepus. Nonetheless, additional mitochondrial genomes from species belonging to the genera Bunolagus, Sylvilagus, and Pronolagus, among others, are needed before a more robust conclusion about the derived vs basal placement of Romerolagus within the family Leporidae can be reached based on mitochondrial PCGs.<br><br>CONCLUSIONS: This is the first genomic resource developed for R. diazi and it represents a tool to improve our understanding about the ecology and evolutionary biology of this iconic and endangered species.}, }
@article {pmid34781749, year = {2021}, author = {Benhamou, S and Rahioui, I and Henri, H and Charles, H and Da Silva, P and Heddi, A and Vavre, F and Desouhant, E and Calevro, F and Mouton, L}, title = {Cytotype Affects the Capability of the Whitefly Bemisia tabaci MED Species To Feed and Oviposit on an Unfavorable Host Plant.}, journal = {mBio}, volume = {12}, number = {6}, pages = {e0073021}, pmid = {34781749}, issn = {2150-7511}, mesh = {Amino Acids/chemistry ; Animals ; Feeding Behavior ; Fertility ; Hemiptera/classification/*physiology ; Hibiscus/chemistry/*parasitology/physiology ; Host Specificity ; Lantana/chemistry/*parasitology/physiology ; Mitochondria/metabolism ; Oviposition ; Symbiosis ; Nicotiana/chemistry/*parasitology/physiology ; }, abstract = {The acquisition of nutritional obligate primary endosymbionts (P-symbionts) allowed phloemo-phageous insects to feed on plant sap and thus colonize novel ecological niches. P-symbionts often coexist with facultative secondary endosymbionts (S-symbionts), which may also influence their hosts' niche utilization ability. The whitefly Bemisia tabaci is a highly diversified species complex harboring, in addition to the P-symbiont "Candidatus Portiera aleyrodidarum," seven S-symbionts whose roles remain poorly understood. Here, we compare the phenotypic and metabolic responses of three B. tabaci lines differing in their S-symbiont community, reared on three different host plants, hibiscus, tobacco, or lantana, and address whether and how S-symbionts influence insect capacity to feed and produce offspring on those plants. We first show that hibiscus, tobacco, and lantana differ in their free amino acid composition. Insects' performance, as well as free amino acid profile and symbiotic load, were shown to be plant dependent, suggesting a critical role for the plant nutritional properties. Insect fecundity was significantly lower on lantana, indicating that it is the least favorable plant. Remarkably, insects reared on this plant show a specific amino acid profile and a higher symbiont density compared to the two other plants. In addition, this plant was the only one for which fecundity differences were observed between lines. Using genetically homogeneous hybrids, we demonstrate that cytotype (mitochondria and symbionts), and not genotype, is a major determinant of females' fecundity and amino acid profile on lantana. As cytotypes differ in their S-symbiont community, we propose that these symbionts may mediate their hosts' suitable plant range. IMPORTANCE Microbial symbionts are universal in eukaryotes, and it is now recognized that symbiotic associations represent major evolutionary driving forces. However, the extent to which symbionts contribute to their hosts' ecological adaptation and subsequent diversification is far from being fully elucidated. The whitefly Bemisia tabaci is a sap feeder associated with multiple coinfecting intracellular facultative symbionts. Here, we show that plant species simultaneously affect whiteflies' performance, amino acid profile, and symbiotic density, which could be partially explained by differences in plant nutritional properties. We also demonstrate that, on lantana, the least favorable plant used in our study, whiteflies' performance is determined by their cytotype. We propose that the host plant utilization in B. tabaci is influenced by its facultative symbiont community composition, possibly through its impact on the host dietary requirements. Altogether, our data provide new insights into the impact of intracellular microorganisms on their animal hosts' ecological niche range and diversification.}, }
@article {pmid34773990, year = {2021}, author = {Liu, Y and Qu, J and Shi, Z and Zhang, P and Ren, M}, title = {Comparative genomic analysis of the tricarboxylic acid cycle members in four Solanaceae vegetable crops and expression pattern analysis in Solanum tuberosum.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {821}, pmid = {34773990}, issn = {1471-2164}, mesh = {Citric Acid Cycle/genetics ; Genomics ; Phylogeny ; *Solanum tuberosum/genetics ; Vegetables ; }, abstract = {BACKGROUND: The tricarboxylic acid (TCA) cycle is crucial for energy supply in animal, plant, and microbial cells. It is not only the main pathway of carbohydrate catabolism but also the final pathway of lipid and protein catabolism. Some TCA genes have been found to play important roles in the growth and development of tomato and potato, but no comprehensive study of TCA cycle genes in Solanaceae crops has been reported.<br><br>RESULTS: In this study, we analyzed TCA cycle genes in four important Solanaceae vegetable crops (potato (Solanum tuberosum), tomato (Solanum lycopersicum), eggplant (Solanum melongena), and pepper (Capsicum annuum)) based on comparative genomics. The four Solanaceae crops had a total of 180 TCA cycle genes: 43 in potato, 44 in tomato, 40 in eggplant, and 53 in pepper. Phylogenetic analysis, collinearity analysis, and tissue expression patterns revealed the conservation of and differences in TCA cycle genes between the four Solanaceae crops and found that there were unique subgroup members in Solanaceae crops that were independent of Arabidopsis genes. The expression analysis of potato TCA cycle genes showed that (1) they were widely expressed in various tissues, and some transcripts like Soltu.DM.01G003320.1(SCoAL) and Soltu.DM.04G021520.1 (SDH) mainly accumulate in vegetative organs, and some transcripts such as Soltu.DM.12G005620.3 (SDH) and Soltu.DM.02G007400.4 (MDH) are preferentially expressed in reproductive organs; (2) several transcripts can be significantly induced by hormones, such as Soltu.DM.08G023870.2 (IDH) and Soltu.DM.06G029290.1 (SDH) under ABA treatment, and Soltu.DM.07G021850.2 (CSY) and Soltu.DM.09G026740.1 (MDH) under BAP treatment, and Soltu.DM.02G000940.1 (IDH) and Soltu.DM.01G031350.4 (MDH) under GA treatment; (3) Soltu.DM.11G024650.1 (SDH) can be upregulated by the three disease resistance inducers including Phytophthora infestans, acibenzolar-S-methyl (BTH), and DL-&#x3b2;-amino-n-butyric acid (BABA); and (4) the levels of Soltu.DM.01G045790.1 (MDH), Soltu.DM.01G028520.3 (CSY), and Soltu.DM.12G028700.1 (CSY) can be activated by both NaCl and mannitol. The subcellular localization results of three potato citrate synthases showed that Soltu.DM.01G028520.3 was localized in mitochondria, while Soltu.DM.12G028700.1 and Soltu.DM.07G021850.1 were localized in the cytoplasm.<br><br>CONCLUSIONS: This study provides a scientific foundation for the comprehensive understanding and functional studies of TCA cycle genes in Solanaceae crops and reveals their potential roles in potato growth, development, and stress response.}, }
@article {pmid34773616, year = {2022}, author = {Skuza, L}, title = {Primer Design for the Analysis of Closely Related Species: Application of Noncoding mtDNA and cpDNA Sequences.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2392}, number = {}, pages = {83-91}, pmid = {34773616}, issn = {1940-6029}, mesh = {Chloroplasts/genetics ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; Phylogeny ; Plants/genetics ; Secale/genetics ; }, abstract = {Noncoding regions of the chloroplast (cpDNA) and mitochondrial (mtDNA) genomes are commonly used in plant phylogenetic and population studies. Consensus primers, which are homologous to most coding regions, but amplify variable noncoding regions, are very useful for this purpose. However, high genetic diversity of plants poses a problem in developing molecular methods that require conserved DNA sequences between species.This chapter describes the protocol for designing PCR primers suitable for analysis of closely related plant species. As an example, we used PCR primer design for cpDNA noncoding regions of the rye (Secale).}, }
@article {pmid34752746, year = {2021}, author = {Erinjeri, AP and Labbadia, J}, title = {The importance of long-lived proteins: Not just nuclear anymore.}, journal = {Developmental cell}, volume = {56}, number = {21}, pages = {2925-2927}, doi = {10.1016/j.devcel.2021.10.015}, pmid = {34752746}, issn = {1878-1551}, mesh = {*Electron Transport Complex IV/metabolism ; *Mitochondria/metabolism ; Mitochondrial Proteins/metabolism ; }, abstract = {The significance of mitochondrial long-lived proteins (mitoLLPs) to tissue health has remained mysterious for over a decade. In this issue of Developmental Cell, Krishna et al. demonstrate that mitochondrial lifetimes are highly heterogeneous and that mitoLLPs promote respiratory capacity by facilitating supercomplex assembly within the electron transport chain.}, }
@article {pmid34748935, year = {2022}, author = {Boël, M and Veyrunes, F and Durieux, AC and Freyssenet, D and Voituron, Y and Roussel, D}, title = {Does high mitochondrial efficiency carry an oxidative cost? The case of the African pygmy mouse (Mus mattheyi).}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {264}, number = {}, pages = {111111}, doi = {10.1016/j.cbpa.2021.111111}, pmid = {34748935}, issn = {1531-4332}, mesh = {Adenosine Diphosphate/metabolism ; Animals ; Hydrogen Peroxide/metabolism ; Mice ; Mice, Inbred C57BL ; Mitochondria, Muscle/*metabolism ; Muscle, Skeletal/metabolism ; Oxidative Phosphorylation ; Oxidative Stress ; Oxygen Consumption ; Reactive Oxygen Species/metabolism ; Species Specificity ; }, abstract = {Skeletal muscle mitochondria of the African pygmy mouse Mus mattheyi exhibit markedly reduced oxygen consumption and ATP synthesis rates but a higher mitochondrial efficiency than what would be expected from allometric trends. In the present study, we assessed whether such reduction of mitochondrial activity in M. mattheyi can limit the oxidative stress associated with an increased generation of mitochondrial reactive oxygen species. We conducted a comparative study of mitochondrial oxygen consumption, H2O2 release, and electron leak (%H2O2/O) in skeletal muscle mitochondria isolated from the extremely small African pygmy mouse (M. mattheyi, ~5 g) and Mus musculus, which is a larger Mus species (~25 g). Mitochondria were energized with pyruvate, malate, and succinate, after which fluxes were measured at different steady-state rates of oxidative phosphorylation. Overall, M. mattheyi exhibited lower oxidative activity and higher electron leak than M. musculus, while the H2O2 release did not differ significantly between these two Mus species. We further found that the high coupling efficiency of skeletal muscle mitochondria from M. mattheyi was associated with high electron leak. Nevertheless, data also show that, despite the higher electron leak, the lower mitochondrial respiratory capacity of M. mattheyi limits the cost of a net increase in H2O2 release, which is lower than that expected for a mammals of this size.}, }
@article {pmid34748608, year = {2021}, author = {Powers, MJ and Martz, LD and Burton, RS and Hill, GE and Weaver, RJ}, title = {Evidence for hybrid breakdown in production of red carotenoids in the marine invertebrate Tigriopus californicus.}, journal = {PloS one}, volume = {16}, number = {11}, pages = {e0259371}, pmid = {34748608}, issn = {1932-6203}, mesh = {Animals ; Aquatic Organisms ; Carotenoids/*metabolism ; Cell Nucleus/genetics/metabolism ; Copepoda/*genetics/metabolism ; *Genetic Fitness ; Hybridization, Genetic ; Invertebrates ; Mitochondria/genetics/metabolism ; Oxidative Phosphorylation ; Xanthophylls/metabolism ; }, abstract = {The marine copepod, Tigriopus californicus, produces the red carotenoid pigment astaxanthin from yellow dietary precursors. This 'bioconversion' of yellow carotenoids to red is hypothesized to be linked to individual condition, possibly through shared metabolic pathways with mitochondrial oxidative phosphorylation. Experimental inter-population crosses of lab-reared T. californicus typically produces low-fitness hybrids is due in large part to the disruption of coadapted sets nuclear and mitochondrial genes within the parental populations. These hybrid incompatibilities can increase variability in life history traits and energy production among hybrid lines. Here, we tested if production of astaxanthin was compromised in hybrid copepods and if it was linked to mitochondrial metabolism and offspring development. We observed no clear mitonuclear dysfunction in hybrids fed a limited, carotenoid-deficient diet of nutritional yeast. However, when yellow carotenoids were restored to their diet, hybrid lines produced less astaxanthin than parental lines. We observed that lines fed a yeast diet produced less ATP and had slower offspring development compared to lines fed a more complete diet of algae, suggesting the yeast-only diet may have obscured effects of mitonuclear dysfunction. Astaxanthin production was not significantly associated with development among lines fed a yeast diet but was negatively related to development in early generation hybrids fed an algal diet. In lines fed yeast, astaxanthin was negatively related to ATP synthesis, but in lines fed algae, the relationship was reversed. Although the effects of the yeast diet may have obscured evidence of hybrid dysfunction, these results suggest that astaxanthin bioconversion may still be related to mitochondrial performance and reproductive success.}, }
@article {pmid34746119, year = {2021}, author = {Thomas, LW and Ashcroft, M}, title = {The Contextual Essentiality of Mitochondrial Genes in Cancer.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {695351}, pmid = {34746119}, issn = {2296-634X}, abstract = {Mitochondria are key organelles in eukaryotic evolution that perform crucial roles as metabolic and cellular signaling hubs. Mitochondrial function and dysfunction are associated with a range of diseases, including cancer. Mitochondria support cancer cell proliferation through biosynthetic reactions and their role in signaling, and can also promote tumorigenesis via processes such as the production of reactive oxygen species (ROS). The advent of (nuclear) genome-wide CRISPR-Cas9 deletion screens has provided gene-level resolution of the requirement of nuclear-encoded mitochondrial genes (NEMGs) for cancer cell viability (essentiality). More recently, it has become apparent that the essentiality of NEMGs is highly dependent on the cancer cell context. In particular, key tumor microenvironmental factors such as hypoxia, and changes in nutrient (e.g., glucose) availability, significantly influence the essentiality of NEMGs. In this mini-review we will discuss recent advances in our understanding of the contribution of NEMGs to cancer from CRISPR-Cas9 deletion screens, and discuss emerging concepts surrounding the context-dependent nature of mitochondrial gene essentiality.}, }
@article {pmid34734993, year = {2022}, author = {Hüdig, M and Tronconi, MA and Zubimendi, JP and Sage, TL and Poschmann, G and Bickel, D and Gohlke, H and Maurino, VG}, title = {Respiratory and C4-photosynthetic NAD-malic enzyme coexist in bundle sheath cell mitochondria and evolved via association of differentially adapted subunits.}, journal = {The Plant cell}, volume = {34}, number = {1}, pages = {597-615}, pmid = {34734993}, issn = {1532-298X}, mesh = {Adaptation, Biological ; Capparaceae/*enzymology ; Cleome/enzymology ; *Evolution, Molecular ; Malate Dehydrogenase/*chemistry/metabolism ; Mitochondria/metabolism ; Plant Proteins/*chemistry/metabolism ; }, abstract = {In plant mitochondria, nicotinamide adenine dinucleotide-malic enzyme (NAD-ME) has a housekeeping function in malate respiration. In different plant lineages, NAD-ME was independently co-opted in C4 photosynthesis. In the C4 Cleome species, Gynandropsis gynandra and Cleome angustifolia, all NAD-ME genes (NAD-MEα, NAD-MEβ1, and NAD-MEβ2) were affected by C4 evolution and are expressed at higher levels than their orthologs in the C3 species Tarenaya hassleriana. In T. hassleriana, the NAD-ME housekeeping function is performed by two heteromers, NAD-MEα/β1 and NAD-MEα/β2, with similar biochemical properties. In both C4 species, this role is restricted to NAD-MEα/β2. In the C4 species, NAD-MEα/β1 is exclusively present in the leaves, where it accounts for most of the enzymatic activity. Gynandropsis gynandra NAD-MEα/β1 (GgNAD-MEα/β1) exhibits high catalytic efficiency and is differentially activated by the C4 intermediate aspartate, confirming its role as the C4-decarboxylase. During C4 evolution, NAD-MEβ1 lost its catalytic activity; its contribution to the enzymatic activity results from a stabilizing effect on the associated α-subunit and the acquisition of regulatory properties. We conclude that in bundle sheath cell mitochondria of C4 species, the functions of NAD-ME as C4 photosynthetic decarboxylase and as a housekeeping enzyme coexist and are performed by isoforms that combine the same α-subunit with differentially adapted β-subunits.}, }
@article {pmid34728739, year = {2021}, author = {Wang, X and Li, LL and Xiao, Y and Chen, XY and Chen, JH and Hu, XS}, title = {A complete sequence of mitochondrial genome of Neolamarckia cadamba and its use for systematic analysis.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {21452}, pmid = {34728739}, issn = {2045-2322}, support = {2018-GDTK-08//Central Finance Forestry Reform and Development Fund/ ; 4400-K16013//South China Agricultural University/ ; }, mesh = {DNA, Mitochondrial/analysis/*genetics ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics/metabolism ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Rubiaceae/*genetics/growth &amp; development ; *Transcriptome ; }, abstract = {Neolamarckia cadamba is an important tropical and subtropical tree for timber industry in southern China and is also a medicinal plant because of the secondary product cadambine. N. cadamba belongs to Rubiaceae family and its taxonomic relationships with other species are not fully evaluated based on genome sequences. Here, we report the complete sequences of mitochondrial genome of N. cadamba, which is 414,980 bp in length and successfully assembled in two genome circles (109,836 bp and 305,144 bp). The mtDNA harbors 83 genes in total, including 40 protein-coding genes (PCGs), 31 transfer RNA genes, 6 ribosomal RNA genes, and 6 other genes. The base composition of the whole genome is estimated as 27.26% for base A, 22.63% for C, 22.53% for G, and 27.56% for T, with the A + T content of 54.82% (54.45% in the small circle and 54.79% in the large circle). Repetitive sequences account for ~ 0.14% of the whole genome. A maximum likelihood (ML) tree based on DNA sequences of 24 PCGs supports that N. cadamba belongs to order Gentianales. A ML tree based on rps3 gene of 60 species in family Rubiaceae shows that N. cadamba is more related to Cephalanthus accidentalis and Hymenodictyon parvifolium and belongs to the Cinchonoideae subfamily. The result indicates that N. cadamba is genetically distant from the species and genera of Rubiaceae in systematic position. As the first sequence of mitochondrial genome of N. cadamba, it will provide a useful resource to investigate genetic variation and develop molecular markers for genetic breeding in the future.}, }
@article {pmid34727288, year = {2022}, author = {Liu, K and Xie, N and Ma, HJ}, title = {Next-generation sequencing reveals the mitogenomic heteroplasmy in the topmouth culter (Culter alburnus Basilewsky, 1855).}, journal = {Molecular biology reports}, volume = {49}, number = {2}, pages = {943-950}, pmid = {34727288}, issn = {1573-4978}, support = {20162012A03//Hangzhou Agricultural &amp; Social Development Research Program/ ; 2019HNCT-01//Science &amp; Technology Innovation Program of Hangzhou Academy of Agricultural Sciences/ ; }, mesh = {Animals ; China ; Cyprinidae/*genetics ; Cypriniformes/genetics ; DNA, Mitochondrial/*genetics ; Fish Proteins/genetics ; Heteroplasmy/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Mitogens/genetics ; Phylogeny ; }, abstract = {BACKGROUND: The mitogenomic heteroplasmy is the presence of multiple haplotypes in the mitochondria, which could cause genetic diseases and is also associated with many critical biological functions. The topmouth culter (Culter alburnus Basilewsky, 1855) is one of the most important freshwater fish in the family of Cyprinidae in China. At present, there are no reports on the topmouth culter's mtDNA heteroplasmy and the existence of which is not known.<br><br>METHODS AND RESULTS: This study aimed to analyze the mitogenomic heteroplasmy in the topmouth culter by the next-generation sequencing of the fins' total DNA. The results confirmed the existence of the heteroplasmy and indicated the presence of the extensive heteroplasmy in the topmouth culter's mitogenome. There were 38 heteroplasmic variations in the protein-coding genes from the three specimens, with 33 non-synonymous substitutions accounting for 86.84% and five synonymous substitutions accounting for 13.16%. Among them, the ND6 had the most heteroplasmic variations but only one synonymous substitution. After removing the putative nuclear mitochondrial DNA fragments, the ratio of primary haplotype in the three specimens was 43.89%, 74.72%, and 32.76%, respectively. The three specimens contained 21, 7, and 21 haplotypes of the mitogenomes, respectively. Due to the extensive heteroplasmy, we reconstructed the phylogenetic tree of the topmouth culter using the RY-coding method, which improved the performance of the phylogenetic tree to some extent.<br><br>CONCLUSIONS: This study reported the mitogenomic heteroplasmy in the topmouth culter and enhanced the knowledge regarding the mitogenomic heteroplasmy in phylogenetic studies. As the topmouth culter is a commercial species, the mitogenomic heteroplasmy is crucial for the fisheries management of the topmouth culter.}, }
@article {pmid34724985, year = {2021}, author = {Wu, Y and Wang, XH and Li, XH and Song, LY and Yu, SL and Fang, ZC and Liu, YQ and Yuan, LY and Peng, CY and Zhang, SY and Cheng, W and Ma, HC and Wang, LF and Tang, JM and Wang, YF and Ji, FY}, title = {Common mtDNA variations at C5178a and A249d/T6392C/G10310A decrease the risk of severe COVID-19 in a Han Chinese population from Central China.}, journal = {Military Medical Research}, volume = {8}, number = {1}, pages = {57}, pmid = {34724985}, issn = {2054-9369}, support = {&#x2116;:2020XGFYZR11//the Special Project of Contingency Research for COVID-19 at Hubei University of Medicine/ ; &#x2116;:2020XGFYZR03//the Special Project of Contingency Research for COVID-19 at Hubei University of Medicine/ ; &#x2116;: 2018QDJZR01//the Cultivating Project for Young Scholar at Hubei University of Medicine/ ; }, mesh = {*COVID-19/genetics ; Case-Control Studies ; China ; *DNA, Mitochondrial/genetics ; Humans ; Mitochondria/genetics ; Phylogeny ; Risk Factors ; }, abstract = {BACKGROUND: Mitochondria have been shown to play vital roles during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and coronavirus disease 2019 (COVID-19) development. Currently, it is unclear whether mitochondrial DNA (mtDNA) variants, which define mtDNA haplogroups and determine oxidative phosphorylation performance and reactive oxygen species production, are associated with COVID-19 risk.<br><br>METHODS: A population-based case-control study was conducted to compare the distribution of mtDNA variations defining mtDNA haplogroups between healthy controls (n&#x2009;=&#x2009;615) and COVID-19 patients (n&#x2009;=&#x2009;536). COVID-19 patients were diagnosed based on molecular diagnostics of the viral genome by qPCR and chest X-ray or computed tomography scanning. The exclusion criteria for the healthy controls were any history of disease in the month preceding the study assessment. MtDNA variants defining mtDNA haplogroups were identified by PCR-RFLPs and HVS-I sequencing and determined based on mtDNA phylogenetic analysis using Mitomap Phylogeny. Student's t-test was used for continuous variables, and Pearson's chi-squared test or Fisher's exact test was used for categorical variables. To assess the independent effect of each mtDNA variant defining mtDNA haplogroups, multivariate logistic regression analyses were performed to calculate the odds ratios (ORs) and 95% confidence intervals (CIs) with adjustments for possible confounding factors of age, sex, smoking and diseases (including cardiopulmonary diseases, diabetes, obesity and hypertension) as determined through clinical and radiographic examinations.<br><br>RESULTS: Multivariate logistic regression analyses revealed that the most common investigated mtDNA variations (>&#x2009;10% in the control population) at C5178a (in NADH dehydrogenase subunit 2 gene, ND2) and A249d (in the displacement loop region, D-loop)/T6392C (in cytochrome c oxidase I gene, CO1)/G10310A (in ND3) were associated with a reduced risk of severe COVID-19 (OR&#x2009;=&#x2009;0.590, 95% CI 0.428-0.814, P&#x2009;=&#x2009;0.001; and OR&#x2009;=&#x2009;0.654, 95% CI 0.457-0.936, P&#x2009;=&#x2009;0.020, respectively), while A4833G (ND2), A4715G (ND2), T3394C (ND1) and G5417A (ND2)/C16257a (D-loop)/C16261T (D-loop) were related to an increased risk of severe COVID-19 (OR&#x2009;=&#x2009;2.336, 95% CI 1.179-4.608, P&#x2009;=&#x2009;0.015; OR&#x2009;=&#x2009;2.033, 95% CI 1.242-3.322, P&#x2009;=&#x2009;0.005; OR&#x2009;=&#x2009;3.040, 95% CI 1.522-6.061, P&#x2009;=&#x2009;0.002; and OR&#x2009;=&#x2009;2.890, 95% CI 1.199-6.993, P&#x2009;=&#x2009;0.018, respectively).<br><br>CONCLUSIONS: This is the first study to explore the association of mtDNA variants with individual's risk of developing severe COVID-19. Based on the case-control study, we concluded that the common mtDNA variants at C5178a and A249d/T6392C/G10310A might contribute to an individual's resistance to developing severe COVID-19, whereas A4833G, A4715G, T3394C and G5417A/C16257a/C16261T might increase an individual's risk of developing severe COVID-19.}, }
@article {pmid34715011, year = {2021}, author = {Hochberg, I and Demain, LAM and Richer, J and Thompson, K and Urquhart, JE and Rea, A and Pagarkar, W and Rodríguez-Palmero, A and Schlüter, A and Verdura, E and Pujol, A and Quijada-Fraile, P and Amberger, A and Deutschmann, AJ and Demetz, S and Gillespie, M and Belyantseva, IA and McMillan, HJ and Barzik, M and Beaman, GM and Motha, R and Ng, KY and O'Sullivan, J and Williams, SG and Bhaskar, SS and Lawrence, IR and Jenkinson, EM and Zambonin, JL and Blumenfeld, Z and Yalonetsky, S and Oerum, S and Rossmanith, W and ,  and Yue, WW and Zschocke, J and Munro, KJ and Battersby, BJ and Friedman, TB and Taylor, RW and O'Keefe, RT and Newman, WG}, title = {Bi-allelic variants in the mitochondrial RNase P subunit PRORP cause mitochondrial tRNA processing defects and pleiotropic multisystem presentations.}, journal = {American journal of human genetics}, volume = {108}, number = {11}, pages = {2195-2204}, pmid = {34715011}, issn = {1537-6605}, mesh = {Adult ; *Alleles ; Female ; *Genetic Pleiotropy ; Humans ; Male ; Mitochondria/*enzymology ; Pedigree ; RNA, Mitochondrial/*genetics ; RNA, Transfer/*genetics ; Ribonuclease P/*genetics ; }, abstract = {Human mitochondrial RNase P (mt-RNase P) is responsible for 5' end processing of mitochondrial precursor tRNAs, a vital step in mitochondrial RNA maturation, and is comprised of three protein subunits: TRMT10C, SDR5C1 (HSD10), and PRORP. Pathogenic variants in TRMT10C and SDR5C1 are associated with distinct recessive or x-linked infantile onset disorders, resulting from defects in mitochondrial RNA processing. We report four unrelated families with multisystem disease associated with bi-allelic variants in PRORP, the metallonuclease subunit of mt-RNase P. Affected individuals presented with variable phenotypes comprising sensorineural hearing loss, primary ovarian insufficiency, developmental delay, and brain white matter changes. Fibroblasts from affected individuals in two families demonstrated decreased steady state levels of PRORP, an accumulation of unprocessed mitochondrial transcripts, and decreased steady state levels of mitochondrial-encoded proteins, which were rescued by introduction of the wild-type PRORP cDNA. In mt-tRNA processing assays performed with recombinant mt-RNase P proteins, the disease-associated variants resulted in diminished mitochondrial tRNA processing. Identification of disease-causing variants in PRORP indicates that pathogenic variants in all three subunits of mt-RNase P can cause mitochondrial dysfunction, each with distinct pleiotropic clinical presentations.}, }
@article {pmid34713507, year = {2022}, author = {Balparda, M and Elsässer, M and Badia, MB and Giese, J and Bovdilova, A and Hüdig, M and Reinmuth, L and Eirich, J and Schwarzländer, M and Finkemeier, I and Schallenberg-Rüdinger, M and Maurino, VG}, title = {Acetylation of conserved lysines fine-tunes mitochondrial malate dehydrogenase activity in land plants.}, journal = {The Plant journal : for cell and molecular biology}, volume = {109}, number = {1}, pages = {92-111}, doi = {10.1111/tpj.15556}, pmid = {34713507}, issn = {1365-313X}, mesh = {Acetylation ; Embryophyta/*enzymology/genetics ; Lysine/metabolism ; Malate Dehydrogenase/genetics/*metabolism ; Mitochondria/enzymology ; Mitochondrial Proteins/genetics/metabolism ; Plant Proteins/genetics/metabolism ; *Protein Processing, Post-Translational ; }, abstract = {Plants need to rapidly and flexibly adjust their metabolism to changes of their immediate environment. Since this necessity results from the sessile lifestyle of land plants, key mechanisms for orchestrating central metabolic acclimation are likely to have evolved early. Here, we explore the role of lysine acetylation as a post-translational modification to directly modulate metabolic function. We generated a lysine acetylome of the moss Physcomitrium patens and identified 638 lysine acetylation sites, mostly found in mitochondrial and plastidial proteins. A comparison with available angiosperm data pinpointed lysine acetylation as a conserved regulatory strategy in land plants. Focusing on mitochondrial central metabolism, we functionally analyzed acetylation of mitochondrial malate dehydrogenase (mMDH), which acts as a hub of plant metabolic flexibility. In P. patens mMDH1, we detected a single acetylated lysine located next to one of the four acetylation sites detected in Arabidopsis thaliana mMDH1. We assessed the kinetic behavior of recombinant A. thaliana and P. patens mMDH1 with site-specifically incorporated acetyl-lysines. Acetylation of A. thaliana mMDH1 at K169, K170, and K334 decreases its oxaloacetate reduction activity, while acetylation of P. patens mMDH1 at K172 increases this activity. We found modulation of the malate oxidation activity only in A. thaliana mMDH1, where acetylation of K334 strongly activated it. Comparative homology modeling of MDH proteins revealed that evolutionarily conserved lysines serve as hotspots of acetylation. Our combined analyses indicate lysine acetylation as a common strategy to fine-tune the activity of central metabolic enzymes with likely impact on plant acclimation capacity.}, }
@article {pmid34710348, year = {2021}, author = {Stairs, CW and Táborský, P and Salomaki, ED and Kolisko, M and Pánek, T and Eme, L and Hradilová, M and Vlček, &#x10c; and Jerlström-Hultqvist, J and Roger, AJ and Čepička, I}, title = {Anaeramoebae are a divergent lineage of eukaryotes that shed light on the transition from anaerobic mitochondria to hydrogenosomes.}, journal = {Current biology : CB}, volume = {31}, number = {24}, pages = {5605-5612.e5}, doi = {10.1016/j.cub.2021.10.010}, pmid = {34710348}, issn = {1879-0445}, mesh = {Anaerobiosis ; *Eukaryota/metabolism ; Mitochondria/genetics/metabolism ; *Organelles/genetics/metabolism ; Oxygen/metabolism ; Phylogeny ; }, abstract = {Discoveries of diverse microbial eukaryotes and their inclusion in comprehensive phylogenomic analyses have crucially re-shaped the eukaryotic tree of life in the 21st century.[1] At the deepest level, eukaryotic diversity comprises 9-10 "supergroups." One of these supergroups, the Metamonada, is particularly important to our understanding of the evolutionary dynamics of eukaryotic cells, including the remodeling of mitochondrial function. All metamonads thrive in low-oxygen environments and lack classical aerobic mitochondria, instead possessing mitochondrion-related organelles (MROs) with metabolisms that are adapted to low-oxygen conditions. These MROs lack an organellar genome, do not participate in the Krebs cycle and oxidative phosphorylation,[2] and often synthesize ATP by substrate-level phosphorylation coupled to hydrogen production.[3][,][4] The events that occurred during the transition from an oxygen-respiring mitochondrion to a functionally streamlined MRO early in metamonad evolution remain largely unknown. Here, we report transcriptomes of two recently described, enigmatic, anaerobic protists from the genus Anaeramoeba.[5] Using phylogenomic analysis, we show that these species represent a divergent, phylum-level lineage in the tree of metamonads, emerging as a sister group of the Parabasalia and reordering the deep branching order of the metamonad tree. Metabolic reconstructions of the Anaeramoeba MROs reveal many "classical" mitochondrial features previously not seen in metamonads, including a disulfide relay import system, propionate production, and amino acid metabolism. Our findings suggest that the cenancestor of Metamonada likely had MROs with more classical mitochondrial features than previously anticipated and demonstrate how discoveries of novel lineages of high taxonomic rank continue to transform our understanding of early eukaryote evolution.}, }
@article {pmid34704591, year = {2021}, author = {Kato, S and Arasaki, K and Tokutomi, N and Imai, Y and Inoshita, T and Hattori, N and Sasaki, T and Sato, M and Wakana, Y and Inoue, H and Tagaya, M}, title = {Syntaxin 17, an ancient SNARE paralog, plays different and conserved roles in different organisms.}, journal = {Journal of cell science}, volume = {134}, number = {22}, pages = {}, doi = {10.1242/jcs.258699}, pmid = {34704591}, issn = {1477-9137}, mesh = {Animals ; Autophagy ; HeLa Cells ; Humans ; *Membrane Fusion ; Qa-SNARE Proteins/genetics ; *SNARE Proteins ; }, abstract = {Mammalian syntaxin 17 (Stx17) has several roles in processes other than membrane fusion, including in mitochondrial division, autophagosome formation and lipid droplet expansion. In contrast to conventional syntaxins, Stx17 has a long C-terminal hydrophobic region with a hairpin-like structure flanked by a basic amino acid-enriched C-terminal tail. Although Stx17 is one of the six ancient SNAREs and is present in diverse eukaryotic organisms, it has been lost in multiple lineages during evolution. In the present study, we compared the localization and function of fly and nematode Stx17s expressed in HeLa cells with those of human Stx17. We found that fly Stx17 predominantly localizes to the cytosol and mediates autophagy, but not mitochondrial division. Nematode Stx17, on the other hand, is predominantly present in mitochondria and facilitates mitochondrial division, but is irrelevant to autophagy. These differences are likely due to different structures in the C-terminal tail. Non-participation of fly Stx17 and nematode Stx17 in mitochondrial division and autophagy, respectively, was demonstrated in individual organisms. Our results provide an insight into the evolution of Stx17 in metazoa. This article has an associated First Person interview with the first author of the paper.}, }
@article {pmid34689722, year = {2022}, author = {Ahuja, P and Ng, CF and Pang, BPS and Chan, WS and Tse, MCL and Bi, X and Kwan, HR and Brobst, D and Herlea-Pana, O and Yang, X and Du, G and Saengnipanthkul, S and Noh, HL and Jiao, B and Kim, JK and Lee, CW and Ye, K and Chan, CB}, title = {Muscle-generated BDNF (brain derived neurotrophic factor) maintains mitochondrial quality control in female mice.}, journal = {Autophagy}, volume = {18}, number = {6}, pages = {1367-1384}, pmid = {34689722}, issn = {1554-8635}, support = {U2C DK093000/DK/NIDDK NIH HHS/United States ; }, mesh = {*AMP-Activated Protein Kinases/metabolism ; Animals ; Autophagy ; *Brain-Derived Neurotrophic Factor/metabolism ; Fatty Acids/metabolism ; Female ; Mice ; *Mitochondria, Muscle/metabolism ; *Muscle, Skeletal/physiology ; }, abstract = {Mitochondrial remodeling is dysregulated in metabolic diseases but the underlying mechanism is not fully understood. We report here that BDNF (brain derived neurotrophic factor) provokes mitochondrial fission and clearance in skeletal muscle via the PRKAA/AMPK-PINK1-PRKN/Parkin and PRKAA-DNM1L/DRP1-MFF pathways. Depleting Bdnf expression in myotubes reduced fatty acid-induced mitofission and mitophagy, which was associated with mitochondrial elongation and impaired lipid handling. Muscle-specific bdnf knockout (MBKO) mice displayed defective mitofission and mitophagy, and accumulation of dysfunctional mitochondria in the muscle when they were fed with a high-fat diet (HFD). These animals also have exacerbated body weight gain, increased intramyocellular lipid deposition, reduced energy expenditure, poor metabolic flexibility, and more insulin resistance. In contrast, consuming a BDNF mimetic (7,8-dihydroxyflavone) increased mitochondrial content, and enhanced mitofission and mitophagy in the skeletal muscles. Hence, BDNF is an essential myokine to maintain mitochondrial quality and function, and its repression in obesity might contribute to impaired metabolism.Abbreviation: 7,8-DHF: 7,8-dihydroxyflavone; ACACA/ACC: acetyl Coenzyme A carboxylase alpha; ACAD: acyl-Coenzyme A dehydrogenase family; ACADVL: acyl-Coenzyme A dehydrogenase, very long chain; ACOT: acyl-CoA thioesterase; CAMKK2: calcium/calmodulin-dependent protein kinase kinase 2, beta; BDNF: brain derived neurotrophic factor; BNIP3: BCL2/adenovirus E1B interacting protein 3; BNIP3L/NIX: BCL2/adenovirus E1B interacting protein 3-like; CCL2/MCP-1: chemokine (C-C motif) ligand 2; CCL5: chemokine (C-C motif) ligand 5; CNS: central nervous system; CPT1B: carnitine palmitoyltransferase 1b, muscle; Cpt2: carnitine palmitoyltransferase 2; CREB: cAMP responsive element binding protein; DNM1L/DRP1: dynamin 1-like; E2: estrogen; EHHADH: enoyl-CoenzymeA hydratase/3-hydroxyacyl CoenzymeA dehydrogenase; ESR1/ER-alpha: estrogen receptor 1 (alpha); FA: fatty acid; FAO: fatty acid oxidation; FCCP: carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone; FFA: free fatty acids; FGF21: fibroblast growth factor 21; FUNDC1: FUN14 domain containing 1; HADHA: hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha; HFD: high-fat diet; iWAT: inguinal white adipose tissues; MAP1LC3A/LC3A: microtubule-associated protein 1 light chain 3 alpha; MBKO; muscle-specific bdnf knockout; IL6/IL-6: interleukin 6; MCEE: methylmalonyl CoA epimerase; MFF: mitochondrial fission factor; NTRK2/TRKB: neurotrophic tyrosine kinase, receptor, type 2; OPTN: optineurin; PA: palmitic acid; PARL: presenilin associated, rhomboid-like; PDH: pyruvate dehydrogenase; PINK1: PTEN induced putative kinase 1; PPARGC1A/PGC-1α: peroxisome proliferative activated receptor, gamma, coactivator 1 alpha; PRKAA/AMPK: protein kinase, AMP-activated, alpha 2 catalytic subunit; ROS: reactive oxygen species; TBK1: TANK-binding kinase 1; TG: triacylglycerides; TNF/TNFα: tumor necrosis factor; TOMM20: translocase of outer mitochondrial membrane 20; ULK1: unc-51 like kinase 1.}, }
@article {pmid34685491, year = {2021}, author = {Kurokawa, H and Taninaka, A and Shigekawa, H and Matsui, H}, title = {Dabigatran Etexilate Induces Cytotoxicity in Rat Gastric Epithelial Cell Line via Mitochondrial Reactive Oxygen Species Production.}, journal = {Cells}, volume = {10}, number = {10}, pages = {}, pmid = {34685491}, issn = {2073-4409}, support = {JP17H06088//Japan Society for the Promotion of Science/ ; JP19H02591//Japan Society for the Promotion of Science/ ; JP19K16854//Japan Society for the Promotion of Science/ ; JPMJCR1875//Core Research for Evolutional Science and Technology/ ; }, mesh = {Animals ; Anticoagulants/*pharmacology ; Benzimidazoles/pharmacology ; Dabigatran/*pharmacology ; Epithelial Cells/*drug effects ; Mitochondria/*drug effects ; Rats ; Reactive Oxygen Species/*metabolism ; Thrombin/metabolism ; }, abstract = {Dabigatran is a novel oral anticoagulant that directly inhibits free and fibrin-bound thrombins and exerts rapid and predictable anticoagulant effects. While the use of this reagent has been associated with an increased risk of gastrointestinal bleeding, the reason why dabigatran use increases gastrointestinal bleeding risk remains unknown. We investigated the cytotoxicity of dabigatran etexilate and tartaric acid, the two primary components of dabigatran. The cytotoxicity of dabigatran etexilate and tartaric acid was measured in a cell viability assay. Intracellular mitochondrial reactive oxygen species (mitROS) production and lipid peroxidation were measured using fluorescence dyes. Cell membrane viscosity was measured using atomic force microscopy. The potential of ascorbic acid as an inhibitor of dabigatran cytotoxicity was also evaluated. The cytotoxicity of dabigatran etexilate was higher than that of tartaric acid. Dabigatran etexilate induced mitROS production and lipid peroxidation and altered the cell membrane viscosity. Ascorbic acid inhibited the cytotoxicity and mitROS production induced by dabigatran etexilate. Therefore, we attributed the cytotoxicity of dabigatran to dabigatran etexilate, and proposed that the cytotoxic effects of dabigatran etexilate are mediated via mitROS production. Additionally, we demonstrated that dabigatran cytotoxicity can be prevented via antioxidant treatment.}, }
@article {pmid34680141, year = {2021}, author = {Picca, A and Guerra, F and Calvani, R and Romano, R and Coelho-Júnior, HJ and Bucci, C and Marzetti, E}, title = {Mitochondrial Dysfunction, Protein Misfolding and Neuroinflammation in Parkinson's Disease: Roads to Biomarker Discovery.}, journal = {Biomolecules}, volume = {11}, number = {10}, pages = {}, pmid = {34680141}, issn = {2218-273X}, mesh = {Biomarkers/metabolism ; Dopaminergic Neurons/metabolism/pathology ; Humans ; Lewy Bodies/genetics/pathology ; Mitochondria/*genetics/pathology ; Neuroinflammatory Diseases/genetics/pathology ; Parkinson Disease/*genetics/pathology ; Protein Aggregates/genetics ; Proteostasis Deficiencies/*genetics/pathology ; Reactive Oxygen Species/metabolism ; alpha-Synuclein/*genetics ; }, abstract = {Parkinson's Disease (PD) is a highly prevalent neurodegenerative disease among older adults. PD neuropathology is marked by the progressive loss of the dopaminergic neurons of the substantia nigra pars compacta and the widespread accumulation of misfolded intracellular α-synuclein (α-syn). Genetic mutations and post-translational modifications, such as α-syn phosphorylation, have been identified among the multiple factors supporting α-syn accrual during PD. A decline in the clearance capacity of the ubiquitin-proteasome and the autophagy-lysosomal systems, together with mitochondrial dysfunction, have been indicated as major pathophysiological mechanisms of PD neurodegeneration. The accrual of misfolded α-syn aggregates into soluble oligomers, and the generation of insoluble fibrils composing the core of intraneuronal Lewy bodies and Lewy neurites observed during PD neurodegeneration, are ignited by the overproduction of reactive oxygen species (ROS). The ROS activate the α-syn aggregation cascade and, together with the Lewy bodies, promote neurodegeneration. However, the molecular pathways underlying the dynamic evolution of PD remain undeciphered. These gaps in knowledge, together with the clinical heterogeneity of PD, have hampered the identification of the biomarkers that may be used to assist in diagnosis, treatment monitoring, and prognostication. Herein, we illustrate the main pathways involved in PD pathogenesis and discuss their possible exploitation for biomarker discovery.}, }
@article {pmid34678674, year = {2021}, author = {Rothmann-Meyer, W and Naidoo, K and de Waal, PJ}, title = {Comparative mitogenomics of Spirocerca lupi from South Africa and China: Variation and possible heteroplasmy.}, journal = {Veterinary parasitology}, volume = {300}, number = {}, pages = {109595}, doi = {10.1016/j.vetpar.2021.109595}, pmid = {34678674}, issn = {1873-2550}, mesh = {Animals ; *Dog Diseases/epidemiology ; Dogs ; Heteroplasmy ; Phylogeny ; South Africa/epidemiology ; *Spirurida Infections/veterinary ; *Thelazioidea/genetics ; }, abstract = {The complete mitochondrial genome of Spirocerca lupi isolated from a dog in South Africa was sequenced using next generation sequencing (NGS) technology and the 12 protein coding genes along with the two rRNA genes were compared to 18 other nematode species as well as S. lupi from China. The mitochondrial genome of S. lupi South Africa had a mean genetic diversity of 6.1 % compared to S. lupi China with some variation in nucleotide composition, gene positioning and size. Pairwise distance results indicated slightly higher variation when compared to the pairwise distances of other closely related species, however, this variation was not high enough for it to be considered a cryptic species. Phylogenetic analysis indicated that S. lupi from the two continents are very similar. In addition, single nucleotide polymorphisms were detected in the nad2 gene with ten sequence variants identified from 10 clones from a single nematode, suggesting possible heteroplasmy. The origin of the heteroplasmy is currently unknown but it is speculated to have arisen from accumulated mutations in the mitochondria during somatic replication.}, }
@article {pmid34678428, year = {2022}, author = {Yu, M and Yu, Y and Song, T and Zhang, Y and Wei, F and Cheng, J and Zhang, B and Zhang, X}, title = {Characterization of the voltage-dependent anion channel (VDAC) gene family in wheat (Triticum aestivum L.) and its potential mechanism in response to drought and salinity stresses.}, journal = {Gene}, volume = {809}, number = {}, pages = {146031}, doi = {10.1016/j.gene.2021.146031}, pmid = {34678428}, issn = {1879-0038}, mesh = {Amino Acid Motifs ; Arabidopsis/genetics ; Chromosomes, Plant ; Droughts ; Gene Expression Regulation, Plant ; Multigene Family ; Oxidoreductases/genetics ; Phylogeny ; Plant Proteins/chemistry/*genetics/metabolism ; Plants, Genetically Modified ; Promoter Regions, Genetic ; Salinity ; Stress, Physiological/*genetics ; Triticum/*genetics/physiology ; Voltage-Dependent Anion Channels/chemistry/*genetics/metabolism ; }, abstract = {Voltage-dependent anion channels (VDACs) are major transport proteins localized in the outer membrane of mitochondria and play critical roles in regulating plant growth and responding to stress. In this study, a total of 26 VDAC genes in common wheat (Triticum aestivum L.) were identified. TaVDACs that contained β-barrel structures were classified into three groups with phylogenetic and sequence alignment. Additionally, the gene structure and protein conserved motif composition varied among diverse subfamilies but were relatively conserved within the same subfamily. The basic elements that were stress- and hormone-related, including TATA-box, CAAT-box, MBS, LTR, TC-rich repeats, ABRE, P-box and TATC-box, were predicted within the promoter region of TaVDAC genes. TaVDAC expression patterns differed among tissues, organs and abiotic stress conditions. Overexpression (OE) of TaVDAC1-B conferred high tolerance to salinity and less resistance to drought stress in Arabidopsis thaliana. TaVDAC1-B interacted with Nucleoredoxin-D1 (TaNRX-D1) protein. Furthermore, compared with WT lines, salinity stress further upregulated the level of AtNRX1 (homologous gene of TaNRX-D1 in Arabidopsis) expression and the activity of superoxide dismutase in TaVDAC1-B OE lines, which led to a decrease in superoxide radical accumulation; drought stress further downregulated AtNRX1 expression and superoxide dismutase activity in TaVDAC1-B OE lines, resulting in the accumulation of superoxide radicals. Our study not only presents comprehensive information for understanding the VDAC gene family in wheat but also proposes a potential mechanism in response to drought and salinity stress.}, }
@article {pmid34678134, year = {2023}, author = {Satyanarayana, DS and Ahlawat, S and Sharma, R and Arora, R and Sharma, A and Tantia, MS and Vijh, RK}, title = {Genetic differentiation of Indian dromedary and Bactrian camel populations based on mitochondrial ATP8 and ATP6 genes.}, journal = {Animal biotechnology}, volume = {34}, number = {3}, pages = {756-760}, doi = {10.1080/10495398.2021.1990079}, pmid = {34678134}, issn = {1532-2378}, mesh = {Animals ; *Camelus/genetics ; Phylogeny ; *Mitochondria/genetics ; Genetic Drift ; DNA, Mitochondrial/genetics ; }, abstract = {Camelids are acknowledged worldwide to endure hostile conditions prevalent in the hot as well cold deserts across the globe. Adaptations to climatic extremes have been associated with mitochondrial protein variants such as ATP8 and ATP6 in different species. The camel genetic resources of India are represented by 9 breeds of dromedary camels which inhabit hot arid and semi-arid zones of the country and a small population of Bactrian camels found in the cold desert of Ladakh. In this study, within and between breed genetic diversity in Indian dromedaries and their divergence from Bactrian camels was investigated based on ATP8/6 genes. Sequence analysis of a mitochondrial DNA fragment encompassing ATP8 and ATP6 genes identified 15 haplotypes in the dromedaries of India and 3 haplotypes in Bactrian camels. The values of haplotype diversity and nucleotide diversity were 0.647 and 0.00187 in the former and 0.679 and 0.00098, respectively in the latter. AMOVA analysis revealed 97.81% variance between the two species. Median-Joining network delineated three distinct mitochondrial haplogroups for Camelus dromedarius, Camelus ferus and Camelus bactrianus. Clear demarcation of the old world (Dromedary and Bactrian camels) and new world camelids (Alpaca, llama, guanaco and vicugna) was evident through the phylogenetic analysis.}, }
@article {pmid34674637, year = {2021}, author = {Lankheet, I and Vicente, M and Barbieri, C and Schlebusch, C}, title = {The performance of common SNP arrays in assigning African mitochondrial haplogroups.}, journal = {BMC genomic data}, volume = {22}, number = {1}, pages = {43}, pmid = {34674637}, issn = {2730-6844}, mesh = {Black People/*genetics ; DNA, Mitochondrial/*genetics ; Datasets as Topic ; Haplotypes/*genetics ; Humans ; Mitochondria/*genetics ; Oligonucleotide Array Sequence Analysis/*standards ; Polymorphism, Single Nucleotide/*genetics ; Software/standards ; }, abstract = {BACKGROUND: Mitochondrial haplogroup assignment is an important tool for forensics and evolutionary genetics. African populations are known to display a high diversity of mitochondrial haplogroups. In this research we explored mitochondrial haplogroup assignment in African populations using commonly used genome-wide SNP arrays.<br><br>RESULTS: We show that, from eight commonly used SNP arrays, two SNP arrays outperform the other arrays when it comes to the correct assignment of African mitochondrial haplogroups. One array enables the recognition of 81% of the African mitochondrial haplogroups from our compiled dataset of full mitochondrial sequences. Other SNP arrays were able to assign 4-62% of the African mitochondrial haplogroups present in our dataset. We also assessed the performance of available software for assigning mitochondrial haplogroups from SNP array data.<br><br>CONCLUSIONS: These results provide the first cross-checked quantification of mitochondrial haplogroup assignment performance from SNP array data. Mitochondrial haplogroup frequencies inferred from most common SNP arrays used for human population analysis should be considered with caution.}, }
@article {pmid34671161, year = {2021}, author = {Wang, Y and Pedersen, MW and Alsos, IG and De Sanctis, B and Racimo, F and Prohaska, A and Coissac, E and Owens, HL and Merkel, MKF and Fernandez-Guerra, A and Rouillard, A and Lammers, Y and Alberti, A and Denoeud, F and Money, D and Ruter, AH and McColl, H and Larsen, NK and Cherezova, AA and Edwards, ME and Fedorov, GB and Haile, J and Orlando, L and Vinner, L and Korneliussen, TS and Beilman, DW and Bjørk, AA and Cao, J and Dockter, C and Esdale, J and Gusarova, G and Kjeldsen, KK and Mangerud, J and Rasic, JT and Skadhauge, B and Svendsen, JI and Tikhonov, A and Wincker, P and Xing, Y and Zhang, Y and Froese, DG and Rahbek, C and Bravo, DN and Holden, PB and Edwards, NR and Durbin, R and Meltzer, DJ and Kjær, KH and Möller, P and Willerslev, E}, title = {Late Quaternary dynamics of Arctic biota from ancient environmental genomics.}, journal = {Nature}, volume = {600}, number = {7887}, pages = {86-92}, pmid = {34671161}, issn = {1476-4687}, support = {/ERC_/European Research Council/International ; 207492/WT_/Wellcome Trust/United Kingdom ; WT220023/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 069906/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Arctic Regions ; *Biota ; Climate Change/history ; DNA, Ancient/*analysis ; DNA, Environmental/*analysis ; Databases, Genetic ; Datasets as Topic ; Extinction, Biological ; Geologic Sediments ; Grassland ; Greenland ; Haplotypes/genetics ; Herbivory/genetics ; History, Ancient ; Humans ; Lakes ; Mammoths ; *Metagenomics ; Mitochondria/genetics ; Perissodactyla ; Permafrost ; Phylogeny ; Plants/genetics ; Population Dynamics ; Rain ; Siberia ; Spatio-Temporal Analysis ; Wetlands ; }, abstract = {During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood[1-8]. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.}, }
@article {pmid34669188, year = {2022}, author = {Fan, Y and Asao, S and Furbank, RT and von Caemmerer, S and Day, DA and Tcherkez, G and Sage, TL and Sage, RF and Atkin, OK}, title = {The crucial roles of mitochondria in supporting C4 photosynthesis.}, journal = {The New phytologist}, volume = {233}, number = {3}, pages = {1083-1096}, doi = {10.1111/nph.17818}, pmid = {34669188}, issn = {1469-8137}, mesh = {Carbon Dioxide/metabolism ; *Malate Dehydrogenase/metabolism ; Mitochondria/metabolism ; *Photosynthesis ; Plant Leaves/physiology ; }, abstract = {C4 photosynthesis involves a series of biochemical and anatomical traits that significantly improve plant productivity under conditions that reduce the efficiency of C3 photosynthesis. We explore how evolution of the three classical biochemical types of C4 photosynthesis (NADP-ME, NAD-ME and PCK types) has affected the functions and properties of mitochondria. Mitochondria in C4 NAD-ME and PCK types play a direct role in decarboxylation of metabolites for C4 photosynthesis. Mitochondria in C4 PCK type also provide ATP for C4 metabolism, although this role for ATP provision is not seen in NAD-ME type. Such involvement has increased mitochondrial abundance/size and associated enzymatic capacity, led to changes in mitochondrial location and ultrastructure, and altered the role of mitochondria in cellular carbon metabolism in the NAD-ME and PCK types. By contrast, these changes in mitochondrial properties are absent in the C4 NADP-ME type and C3 leaves, where mitochondria play no direct role in photosynthesis. From an eco-physiological perspective, rates of leaf respiration in darkness vary considerably among C4 species but does not differ systematically among the three C4 types. This review outlines further mitochondrial research in key areas central to the engineering of the C4 pathway into C3 plants and to the understanding of variation in rates of C4 dark respiration.}, }
@article {pmid34662686, year = {2022}, author = {Omeka, WKM and Liyanage, DS and Jeong, T and Lee, S and Lee, J}, title = {Molecular characterization, immune responses, and functional activities of manganese superoxide dismutase in disk abalone (Haliotis discus discus).}, journal = {Developmental and comparative immunology}, volume = {127}, number = {}, pages = {104299}, doi = {10.1016/j.dci.2021.104299}, pmid = {34662686}, issn = {1879-0089}, mesh = {Animals ; *Gastropoda ; Gene Expression Regulation ; Hydrogen Peroxide ; Immunity, Innate ; Mammals ; Phylogeny ; Superoxide Dismutase/genetics ; *Vibrio parahaemolyticus ; }, abstract = {Superoxide dismutases (SODs) are metalloenzymes that convert superoxide radicals to H2O2 and O2. Although SODs have been extensively studied in mammals and other species, comparative studies in invertebrates, such as abalones, are lacking. Here, we aimed to characterize manganese superoxide dismutase in disk abalone (Haliotis discus discus) (AbMnSOD) by assessing its transcriptional levels at different embryonic developmental stages. Additionally, the temporal expression of AbMnSOD in different abalone tissues in response to bacterial, viral, and pathogen-associated molecular pattern (PAMP) stimuli was investigated. SOD activity was measured at various recombinant protein concentrations via the xanthine oxidase/WST-1 system. Cell viability upon exposure to H2O2, wound healing ability, and subcellular localization were determined in AbMnSOD-transfected cells. AbMnSOD was 681 bp long and contained the SOD-A domain. AbMnSOD expression was higher at the trochophore stage than at the other stages. When challenged with immune stimulants, AbMnSOD showed the highest expression at 6 h post-injection (p.i.) for all stimulants except lipopolysaccharides. In the gills, the highest AbMnSOD expression was observed at 6 h p.i., except for the Vibrio parahaemolyticus challenge. Recombinant AbMnSOD showed concentration-dependent xanthine oxidase activity. Furthermore, AbMnSOD-transfected cells survived H2O2-induced apoptosis and exhibited significant wound gap closure. As expected, AbMnSOD was localized in the mitochondria of the cells. Our findings suggest that AbMnSOD is an essential antioxidant enzyme that participates in regulating developmental processes and defense mechanisms against oxidative stress in hosts.}, }
@article {pmid34660591, year = {2021}, author = {Lim, HJ and Yoon, H and Kim, H and Kang, YW and Kim, JE and Kim, OY and Lee, EY and Twizere, JC and Rak, J and Kim, DK}, title = {Extracellular Vesicle Proteomes Shed Light on the Evolutionary, Interactive, and Functional Divergence of Their Biogenesis Mechanisms.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {734950}, pmid = {34660591}, issn = {2296-634X}, abstract = {Extracellular vesicles (EVs) are membranous structures containing bioactive molecules, secreted by most cells into the extracellular environment. EVs are classified by their biogenesis mechanisms into two major subtypes: ectosomes (enriched in large EVs; lEVs), budding directly from the plasma membrane, which is common in both prokaryotes and eukaryotes, and exosomes (enriched in small EVs; sEVs) generated through the multivesicular bodies via the endomembrane system, which is unique to eukaryotes. Even though recent proteomic analyses have identified key proteins associated with EV subtypes, there has been no systematic analysis, thus far, to support the general validity and utility of current EV subtype separation methods, still largely dependent on physical properties, such as vesicular size and sedimentation. Here, we classified human EV proteomic datasets into two main categories based on distinct centrifugation protocols commonly used for isolating sEV or lEV fractions. We found characteristic, evolutionarily conserved profiles of sEV and lEV proteins linked to their respective biogenetic origins. This may suggest that the evolutionary trajectory of vesicular proteins may result in a membership bias toward specific EV subtypes. Protein-protein interaction (PPI) network analysis showed that vesicular proteins formed distinct clusters with proteins in the same EV fraction, providing evidence for the existence of EV subtype-specific protein recruiters. Moreover, we identified functional modules enriched in each fraction, including multivesicular body sorting for sEV, and mitochondria cellular respiration for lEV proteins. Our analysis successfully captured novel features of EVs embedded in heterogeneous proteomics studies and suggests specific protein markers and signatures to be used as quality controllers in the isolation procedure for subtype-enriched EV fractions.}, }
@article {pmid34655689, year = {2022}, author = {do Amaral, MJ and de Andrade Rosa, I and Andrade, SA and Fang, X and Andrade, LR and Costa, ML and Mermelstein, C}, title = {The perinuclear region concentrates disordered proteins with predicted phase separation distributed in a 3D network of cytoskeletal filaments and organelles.}, journal = {Biochimica et biophysica acta. Molecular cell research}, volume = {1869}, number = {1}, pages = {119161}, pmid = {34655689}, issn = {1879-2596}, support = {R00 HL143210/HL/NHLBI NIH HHS/United States ; R01 HL157115/HL/NHLBI NIH HHS/United States ; R01 HL158761/HL/NHLBI NIH HHS/United States ; }, mesh = {Actin Cytoskeleton/genetics/*metabolism/ultrastructure ; Animals ; Cells, Cultured ; Chick Embryo ; Intrinsically Disordered Proteins/metabolism ; Lysosomes/metabolism/ultrastructure ; Microscopy, Electron, Transmission/methods ; Mitochondria/metabolism/ultrastructure ; Nuclear Envelope/*metabolism/ultrastructure ; Proteome/genetics/metabolism ; Zebrafish ; }, abstract = {Membraneless organelles have emerged during the evolution of eukaryotic cells as intracellular domains in which multiple proteins organize into complex structures to perform specialized functions without the need of a lipid bilayer compartment. Here we describe the perinuclear space of eukaryotic cells as a highly organized network of cytoskeletal filaments that facilitates assembly of biomolecular condensates. Using bioinformatic analyses, we show that the perinuclear proteome is enriched in intrinsic disorder with several proteins predicted to undergo liquid-liquid phase separation. We also analyze immunofluorescence and transmission electron microscopy images showing the association between the nucleus and other organelles, such as mitochondria and lysosomes, or the labeling of specific proteins within the perinuclear region of cells. Altogether our data support the existence of a perinuclear dense sub-micron region formed by a well-organized three-dimensional network of structural and signaling proteins, including several proteins containing intrinsically disordered regions with phase behavior. This network of filamentous cytoskeletal proteins extends a few micrometers from the nucleus, contributes to local crowding, and organizes the movement of molecular complexes within the perinuclear space. Our findings take a key step towards understanding how membraneless regions within eukaryotic cells can serve as hubs for biomolecular condensates assembly, in particular the perinuclear space. Finally, evaluation of the disease context of the perinuclear proteins revealed that alterations in their expression can lead to several pathological conditions, and neurological disorders and cancer are among the most frequent.}, }
@article {pmid34645790, year = {2021}, author = {Frye, RE and Lionnard, L and Singh, I and Karim, MA and Chajra, H and Frechet, M and Kissa, K and Racine, V and Ammanamanchi, A and McCarty, PJ and Delhey, L and Tippett, M and Rose, S and Aouacheria, A}, title = {Mitochondrial morphology is associated with respiratory chain uncoupling in autism spectrum disorder.}, journal = {Translational psychiatry}, volume = {11}, number = {1}, pages = {527}, pmid = {34645790}, issn = {2158-3188}, mesh = {*Autism Spectrum Disorder/metabolism ; Electron Transport ; Electron Transport Complex I ; Humans ; Mitochondria/metabolism ; Oxidation-Reduction ; }, abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental disorder that is associated with unique changes in mitochondrial metabolism, including elevated respiration rates and morphological alterations. We examined electron transport chain (ETC) complex activity in fibroblasts derived from 18 children with ASD as well as mitochondrial morphology measurements in fibroblasts derived from the ASD participants and four typically developing controls. In ASD participants, symptoms severity was measured by the Social Responsiveness Scale and Aberrant Behavior Checklist. Mixed-model regression demonstrated that alterations in mitochondrial morphology were associated with both ETC Complex I+III and IV activity as well as the difference between ETC Complex I+III and IV activity. The subgroup of ASD participants with relative elevation in Complex IV activity demonstrated more typical mitochondrial morphology and milder ASD related symptoms. This study is limited by sample size given the invasive nature of obtaining fibroblasts from children. Furthermore, since mitochondrial function is heterogenous across tissues, the result may be specific to fibroblast respiration. Previous studies have separately described elevated ETC Complex IV activity and changes in mitochondrial morphology in cells derived from children with ASD but this is the first study to link these two findings in mitochondrial metabolism. The association between a difference in ETC complex I+III and IV activity and normal morphology suggests that mitochondrial in individuals with ASD may require ETC uncoupling to function optimally. Further studies should assess the molecular mechanisms behind these unique metabolic changes.Trial registration: Protocols used in this study were registered in clinicaltrials.gov as NCT02000284 and NCT02003170.}, }
@article {pmid34644400, year = {2021}, author = {Szoke, T and Nussbaum-Shochat, A and Amster-Choder, O}, title = {Evolutionarily conserved mechanism for membrane recognition from bacteria to mitochondria.}, journal = {FEBS letters}, volume = {595}, number = {22}, pages = {2805-2815}, doi = {10.1002/1873-3468.14203}, pmid = {34644400}, issn = {1873-3468}, mesh = {*Conserved Sequence ; Escherichia coli ; Escherichia coli Proteins/chemistry/*genetics/metabolism ; *Evolution, Molecular ; Membrane Proteins/chemistry/*genetics/metabolism ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Protein Domains ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins/chemistry/*genetics/metabolism ; }, abstract = {The mechanisms controlling membrane recognition by proteins with one hydrophobic stretch at their carboxyl terminus (tail anchor, TA) are poorly defined. The Escherichia coli TAs of ElaB and YqjD, which share sequential and structural similarity with the Saccharomyces cerevisiae TA of Fis1, were shown to localize to mitochondria. We show that YqjD and ElaB are directed by their TAs to bacterial cell poles. Fis1(TA) expressed in E. coli localizes like the endogenous TAs. The yeast and bacterial TAs are inserted in the E. coli inner membrane, and they all show affiliation to phosphatidic acid (PA), found in the membrane of the bacterial cell poles and of the yeast mitochondria. Our results suggest a mechanism for TA membrane recognition conserved from bacteria to mitochondria and raise the possibility that through their interaction with PA, and TAs play a role across prokaryotes and eukaryotes in controlling cell/organelle fate.}, }
@article {pmid34643951, year = {2022}, author = {Adriano, EA and Zatti, SA and Okamura, B}, title = {How to build single-celled cnidarians with worm-like motility: Lessons from Myxozoa.}, journal = {Journal of anatomy}, volume = {240}, number = {3}, pages = {475-488}, pmid = {34643951}, issn = {1469-7580}, mesh = {Animals ; *Cnidaria ; *Fish Diseases/parasitology ; Gallbladder ; *Myxozoa/physiology/ultrastructure ; Phylogeny ; }, abstract = {Metazoans with worm-like morphologies across diverse and disparate groups typically demonstrate motility generated by hydrostatic skeletons involving tissue layers (muscles and epithelia). Here we present representative morphological, behavioural and molecular data for parasitic cnidarians (myxozoans) that demonstrate unprecedented variation in form and function, developing as cellular hydrostats. Motile elongate plasmodia characterise a remarkable radiation of species in the genus Ceratomyxa. The vermiform plasmodia inhabit gall bladders of a range of South American freshwater fish and exhibit undulatory motility reminiscent of nematodes but achieved at the cellular level. Collective insights from ultrastructure, confocal and light microscopy along with videos depicting movements highlight key features that we propose explain the unique motility of the plasmodia. These features include cytoskeletal elements (net forming microfilaments and microtubules), a large internal vacuole, a relatively rigid outer glycocalyx and peripherally arranged mitochondria. These constituents provide collective evidence for repurposing of the cnidarian epitheliomuscular cell to support worm-like motility at the cellular level. The apparent restriction of vermiform ceratomyxids to South American freshwaters suggests an origination via Cretaceous or Miocene marine transgressions and subsequent radiation.}, }
@article {pmid34633451, year = {2022}, author = {Valera-Calero, JA and Úbeda-D'Ocasar, E and Caballero-Corella, M and Fernández-de-Las-Peñas, C and Sendarrubias, GMG and Arias-Buría, JL}, title = {Cervical Multifidus Morphology and Quality Are Not Associated with Clinical Variables in Women with Fibromyalgia: An Observational Study.}, journal = {Pain medicine (Malden, Mass.)}, volume = {23}, number = {6}, pages = {1138-1143}, doi = {10.1093/pm/pnab297}, pmid = {34633451}, issn = {1526-4637}, mesh = {Cervical Vertebrae/diagnostic imaging ; Female ; *Fibromyalgia/diagnostic imaging ; Humans ; Neck ; Pain ; *Paraspinal Muscles ; }, abstract = {OBJECTIVE: Some studies have reported the presence of histological alterations, such as myofiber disorganization and abnormalities in the number and shape of mitochondria, in patients with fibromyalgia syndrome (FMS). Although Ultrasound imaging (US) is used to quantitatively characterize muscle tissues, US studies in patients with FMS are lacking. Therefore, we aimed to describe morphological and qualitative cervical multifidus (CM) muscle US features in women with FMS and to assess their correlation with clinical indicators.<br><br>DESIGN: Observational study.<br><br>SETTING: AFINSYFACRO Fibromyalgia Association (Madrid, Spain).<br><br>SUBJECTS: Forty-five women with FMS participated.<br><br>METHODS: Sociodemographic variables (e.g., age, height, weight, body mass index) and clinical outcomes (e.g., pain as assessed on a numerical pain rating scale, evolution time, pain-related disability as assessed by the Fibromyalgia Impact Questionnaire) were collected. Images were acquired bilaterally at the cervical spine (C4-C5 level) and measured by an experienced examiner for assessment of muscle morphology (e.g., cross-sectional area, perimeter, and shape) and quality (mean echo intensity and intramuscular fatty infiltration). Side-to-side comparisons and a correlational analysis were conducted.<br><br>RESULTS: No significant side-to-side differences were found for morphology or quality features (P&#x2009;>&#x2009;0.05). None of the clinical indicators were associated with US characteristics (all, P&#x2009;>&#x2009;0.05).<br><br>CONCLUSION: Our results showed no side-to-side differences for CM morphology and quality as assessed with US. No associations between CM muscle morphology or quality and Fibromyalgia Impact Questionnaire, pressure pain threshold, numerical pain rating scale score, or evolution time were observed. Our preliminary data suggest that muscle morphology is not directly related to pain and pain-related disability in women with FMS.}, }
@article {pmid34626646, year = {2021}, author = {Latimer, S and Keene, SA and Stutts, LR and Berger, A and Bernert, AC and Soubeyrand, E and Wright, J and Clarke, CF and Block, AK and Colquhoun, TA and Elowsky, C and Christensen, A and Wilson, MA and Basset, GJ}, title = {A dedicated flavin-dependent monooxygenase catalyzes the hydroxylation of demethoxyubiquinone into ubiquinone (coenzyme Q) in Arabidopsis.}, journal = {The Journal of biological chemistry}, volume = {297}, number = {5}, pages = {101283}, pmid = {34626646}, issn = {1083-351X}, support = {R01 GM139978/GM/NIGMS NIH HHS/United States ; RF1 AG061566/AG/NIA NIH HHS/United States ; }, mesh = {*Arabidopsis/enzymology/genetics ; *Arabidopsis Proteins/genetics/metabolism ; *Mitochondria/enzymology/genetics ; *Mixed Function Oxygenases/genetics/metabolism ; *Phylogeny ; *Ubiquinone/genetics/metabolism ; }, abstract = {Ubiquinone (Coenzyme Q) is a vital respiratory cofactor and liposoluble antioxidant. In plants, it is not known how the C-6 hydroxylation of demethoxyubiquinone, the penultimate step in ubiquinone biosynthesis, is catalyzed. The combination of cross-species gene network modeling along with mining of embryo-defective mutant databases of Arabidopsis thaliana identified the embryo lethal locus EMB2421 (At1g24340) as a top candidate for the missing plant demethoxyubiquinone hydroxylase. In marked contrast with prototypical eukaryotic demethoxyubiquinone hydroxylases, the catalytic mechanism of which depends on a carboxylate-bridged di-iron domain, At1g24340 is homologous to FAD-dependent oxidoreductases that instead use NAD(P)H as an electron donor. Complementation assays in Saccharomyces cerevisiae and Escherichia coli demonstrated that At1g24340 encodes a functional demethoxyubiquinone hydroxylase and that the enzyme displays strict specificity for the C-6 position of the benzoquinone ring. Laser-scanning confocal microscopy also showed that GFP-tagged At1g24340 is targeted to mitochondria. Silencing of At1g24340 resulted in 40 to 74% decrease in ubiquinone content and de novo ubiquinone biosynthesis. Consistent with the role of At1g24340 as a benzenoid ring modification enzyme, this metabolic blockage could not be bypassed by supplementation with 4-hydroxybenzoate, the immediate precursor of ubiquinone's ring. Unlike in yeast, in Arabidopsis overexpression of demethoxyubiquinone hydroxylase did not boost ubiquinone content. Phylogenetic reconstructions indicated that plant demethoxyubiquinone hydroxylase is most closely related to prokaryotic monooxygenases that act on halogenated aromatics and likely descends from an event of horizontal gene transfer between a green alga and a bacterium.}, }
@article {pmid34618964, year = {2020}, author = {Soto Gomez, M and Lin, Q and da Silva Leal, E and Gallaher, TJ and Scherberich, D and Mennes, CB and Smith, SY and Graham, SW}, title = {A bi-organellar phylogenomic study of Pandanales: inference of higher-order relationships and unusual rate-variation patterns.}, journal = {Cladistics : the international journal of the Willi Hennig Society}, volume = {36}, number = {5}, pages = {481-504}, doi = {10.1111/cla.12417}, pmid = {34618964}, issn = {1096-0031}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Genes, Plant ; *Genome, Mitochondrial ; *Genome, Plastid ; Magnoliopsida/*classification/*genetics ; Mitochondria/genetics ; Phylogeny ; Plastids/genetics ; }, abstract = {We used a bi-organellar phylogenomic approach to address higher-order relationships in Pandanales, including the first molecular phylogenetic study of the panama-hat family, Cyclanthaceae. Our genus-level study of plastid and mitochondrial gene sets includes a comprehensive sampling of photosynthetic lineages across the order, and provides a framework for investigating clade ages, biogeographic hypotheses and organellar molecular evolution. Using multiple inference methods and both organellar genomes, we recovered mostly congruent and strongly supported relationships within and between families, including the placement of fully mycoheterotrophic Triuridaceae. Cyclanthaceae and Pandanaceae plastomes have slow substitution rates, contributing to weakly supported plastid-based relationships in Cyclanthaceae. While generally slowly evolving, mitochondrial genomes exhibit sporadic rate elevation across the order. However, we infer well-supported relationships even for slower evolving mitochondrial lineages in Cyclanthaceae. Clade age estimates across photosynthetic lineages are largely consistent with previous studies, are well correlated between the two organellar genomes (with slightly younger inferences from mitochondrial data), and support several biogeographic hypotheses. We show that rapidly evolving non-photosynthetic lineages may bias age estimates upwards at neighbouring photosynthetic nodes, even using a relaxed clock model. Finally, we uncovered new genome structural variants in photosynthetic taxa at plastid inverted repeat boundaries that show promise as interfamilial phylogenetic markers.}, }
@article {pmid34616376, year = {2021}, author = {Lin, R and Xia, Y and Liu, Y and Zhang, D and Xiang, X and Niu, X and Jiang, L and Wang, X and Zheng, A}, title = {Comparative Mitogenomic Analysis and the Evolution of Rhizoctonia solani Anastomosis Groups.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {707281}, pmid = {34616376}, issn = {1664-302X}, abstract = {Mitochondria are the major energy source for cell functions. However, for the plant fungal pathogens, mitogenome variations and their roles during the host infection processes remain largely unknown. Rhizoctonia solani, an important soil-borne pathogen, forms different anastomosis groups (AGs) and adapts to a broad range of hosts in nature. Here, we reported three complete mitogenomes of AG1-IA RSIA1, AG1-IB RSIB1, and AG1-IC, and performed a comparative analysis with nine published Rhizoctonia mitogenomes (AG1-IA XN, AG1-IB 7/3/14, AG3, AG4, and five Rhizoctonia sp. mitogenomes). These mitogenomes encoded 15 typical proteins (cox1-3, cob, atp6, atp8-9, nad1-6, nad4L, and rps3) and several LAGLIDADG/GIY-YIG endonucleases with sizes ranging from 109,017 bp (Rhizoctonia sp. SM) to 235,849 bp (AG3). We found that their large sizes were mainly contributed by repeat sequences and genes encoding endonucleases. We identified the complete sequence of the rps3 gene in 10 Rhizoctonia mitogenomes, which contained 14 positively selected sites. Moreover, we inferred a robust maximum-likelihood phylogeny of 32 Basidiomycota mitogenomes, representing that seven R. solani and other five Rhizoctonia sp. lineages formed two parallel branches in Agaricomycotina. The comparative analysis showed that mitogenomes of Basidiomycota pathogens had high GC content and mitogenomes of R. solani had high repeat content. Compared to other strains, the AG1-IC strain had low substitution rates, which may affect its mitochondrial phylogenetic placement in the R. solani clade. Additionally, with the published RNA-seq data, we investigated gene expression patterns from different AGs during host infection stages. The expressed genes from AG1-IA (host: rice) and AG3 (host: potato) mainly formed four groups by k-mean partitioning analysis. However, conserved genes represented varied expression patterns, and only the patterns of rps3-nad2 and nad1-m3g18/mag28 (an LAGLIDADG endonuclease) were conserved in AG1-IA and AG3 as shown by the correlation coefficient analysis, suggesting regulation of gene repertoires adapting to infect varied hosts. The results of variations in mitogenome characteristics and the gene substitution rates and expression patterns may provide insights into the evolution of R. solani mitogenomes.}, }
@article {pmid34614167, year = {2021}, author = {Sanchez-Contreras, M and Sweetwyne, MT and Kohrn, BF and Tsantilas, KA and Hipp, MJ and Schmidt, EK and Fredrickson, J and Whitson, JA and Campbell, MD and Rabinovitch, PS and Marcinek, DJ and Kennedy, SR}, title = {A replication-linked mutational gradient drives somatic mutation accumulation and influences germline polymorphisms and genome composition in mitochondrial DNA.}, journal = {Nucleic acids research}, volume = {49}, number = {19}, pages = {11103-11118}, pmid = {34614167}, issn = {1362-4962}, support = {T32 AG066574/AG/NIA NIH HHS/United States ; T32 AG000057/AG/NIA NIH HHS/United States ; R21 HG011229/HG/NHGRI NIH HHS/United States ; R21 DK128540/DK/NIDDK NIH HHS/United States ; K01 AG062757/AG/NIA NIH HHS/United States ; R21 CA259780/CA/NCI NIH HHS/United States ; P01 AG001751/AG/NIA NIH HHS/United States ; }, mesh = {Aging/*genetics/metabolism ; Animals ; Chromosome Mapping ; DNA Polymerase gamma/deficiency/genetics ; *DNA Replication ; DNA, Mitochondrial/*genetics/metabolism ; Genetic Speciation ; *Genome, Mitochondrial ; *Germ-Line Mutation ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Mitochondria/*genetics/metabolism ; *Mutation Accumulation ; Mutation Rate ; Polymorphism, Single Nucleotide ; }, abstract = {Mutations in mitochondrial DNA (mtDNA) cause maternally inherited diseases, while somatic mutations are linked to common diseases of aging. Although mtDNA mutations impact health, the processes that give rise to them are under considerable debate. To investigate the mechanism by which de novo mutations arise, we analyzed the distribution of naturally occurring somatic mutations across the mouse and human mtDNA obtained by Duplex Sequencing. We observe distinct mutational gradients in G→A and T→C transitions delimited by the light-strand origin and the mitochondrial Control Region (mCR). The gradient increases unequally across the mtDNA with age and is lost in the absence of DNA polymerase γ proofreading activity. In addition, high-resolution analysis of the mCR shows that important regulatory elements exhibit considerable variability in mutation frequency, consistent with them being mutational 'hot-spots' or 'cold-spots'. Collectively, these patterns support genome replication via a deamination prone asymmetric strand-displacement mechanism as the fundamental driver of mutagenesis in mammalian DNA. Moreover, the distribution of mtDNA single nucleotide polymorphisms in humans and the distribution of bases in the mtDNA across vertebrate species mirror this gradient, indicating that replication-linked mutations are likely the primary source of inherited polymorphisms that, over evolutionary timescales, influences genome composition during speciation.}, }
@article {pmid34610767, year = {2021}, author = {Evans, BJ and Peter, BM and Melnick, DJ and Andayani, N and Supriatna, J and Zhu, J and Tosi, AJ}, title = {Mitonuclear interactions and introgression genomics of macaque monkeys (Macaca) highlight the influence of behaviour on genome evolution.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1960}, pages = {20211756}, pmid = {34610767}, issn = {1471-2954}, mesh = {Animals ; Evolution, Molecular ; Female ; *Genome, Mitochondrial ; Genomics ; Haplorhini ; *Macaca/genetics ; Male ; }, abstract = {In most macaques, females are philopatric and males migrate from their natal ranges, which results in pronounced divergence of mitochondrial genomes within and among species. We therefore predicted that some nuclear genes would have to acquire compensatory mutations to preserve compatibility with diverged interaction partners from the mitochondria. We additionally expected that these sex-differences would have distinctive effects on gene flow in the X and autosomes. Using new genomic data from 29 individuals from eight species of Southeast Asian macaque, we identified evidence of natural selection associated with mitonuclear interactions, including extreme outliers of interspecies differentiation and metrics of positive selection, low intraspecies polymorphism and atypically long runs of homozygosity associated with nuclear-encoded genes that interact with mitochondria-encoded genes. In one individual with introgressed mitochondria, we detected a small but significant enrichment of autosomal introgression blocks from the source species of her mitochondria that contained genes which interact with mitochondria-encoded loci. Our analyses also demonstrate that sex-specific demography sculpts genetic exchange across multiple species boundaries. These findings show that behaviour can have profound but indirect effects on genome evolution by influencing how interacting components of different genomic compartments (mitochondria, the autosomes and the sex chromosomes) move through time and space.}, }
@article {pmid34603395, year = {2021}, author = {Rodríguez, E and Grover Thomas, F and Camus, MF and Lane, N}, title = {Mitonuclear Interactions Produce Diverging Responses to Mild Stress in Drosophila Larvae.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {734255}, pmid = {34603395}, issn = {1664-8021}, abstract = {Mitochondrial function depends on direct interactions between respiratory proteins encoded by genes in two genomes, mitochondrial and nuclear, which evolve in very different ways. Serious incompatibilities between these genomes can have severe effects on development, fitness and viability. The effect of subtle mitonuclear mismatches has received less attention, especially when subject to mild physiological stress. Here, we investigate how two distinct physiological stresses, metabolic stress (high-protein diet) and redox stress [the glutathione precursor N-acetyl cysteine (NAC)], affect development time, egg-to-adult viability, and the mitochondrial physiology of Drosophila larvae with an isogenic nuclear background set against three mitochondrial DNA (mtDNA) haplotypes: one coevolved (WT) and two slightly mismatched (COX and BAR). Larvae fed the high-protein diet developed faster and had greater viability in all haplotypes. The opposite was true of NAC-fed flies, especially those with the COX haplotype. Unexpectedly, the slightly mismatched BAR larvae developed fastest and were the most viable on both treatments, as well as control diets. These changes in larval development were linked to a shift to complex I-driven mitochondrial respiration in all haplotypes on the high-protein diet. In contrast, NAC increased respiration in COX larvae but drove a shift toward oxidation of proline and succinate. The flux of reactive oxygen species was increased in COX larvae treated with NAC and was associated with an increase in mtDNA copy number. Our results support the notion that subtle mitonuclear mismatches can lead to diverging responses to mild physiological stress, undermining fitness in some cases, but surprisingly improving outcomes in other ostensibly mismatched fly lines.}, }
@article {pmid34600156, year = {2021}, author = {Sahebnasagh, A and Hashemi, J and Khoshi, A and Saghafi, F and Avan, R and Faramarzi, F and Azimi, S and Habtemariam, S and Sureda, A and Khayatkashani, M and Safdari, M and Rezai Ghaleno, H and Soltani, H and Khayat Kashani, HR}, title = {Aromatic hydrocarbon receptors in mitochondrial biogenesis and function.}, journal = {Mitochondrion}, volume = {61}, number = {}, pages = {85-101}, doi = {10.1016/j.mito.2021.09.012}, pmid = {34600156}, issn = {1872-8278}, mesh = {Animals ; Cell Cycle ; Evolution, Molecular ; Humans ; Mitochondria/genetics/*metabolism ; Mitogen-Activated Protein Kinases/genetics/metabolism ; *Organelle Biogenesis ; }, abstract = {Mitochondria are ubiquitous membrane-bound organelles that not only play a key role in maintaining cellular energy homeostasis and metabolism but also in signaling and apoptosis. Aryl hydrocarbons receptors (AhRs) are ligand-activated transcription factors that recognize a wide variety of xenobiotics, including polyaromatic hydrocarbons and dioxins, and activate diverse detoxification pathways. These receptors are also activated by natural dietary compounds and endogenous metabolites. In addition, AhRs can modulate the expression of a diverse array of genes related to mitochondrial biogenesis and function. The aim of the present review is to analyze scientific data available on the AhR signaling pathway and its interaction with the intracellular signaling pathways involved in mitochondrial functions, especially those related to cell cycle progression and apoptosis. Various evidence have reported the crosstalk between the AhR signaling pathway and the nuclear factor κB (NF-κB), tyrosine kinase receptor signaling and mitogen-activated protein kinases (MAPKs). The AhR signaling pathway seems to promote cell cycle progression in the absence of exogenous ligands, whereas the presence of exogenous ligands induces cell cycle arrest. However, its effects on apoptosis are controversial since activation or overexpression of AhR has been observed to induce or inhibit apoptosis depending on the cell type. Regarding the mitochondria, although activation by endogenous ligands is related to mitochondrial dysfunction, the effects of endogenous ligands are not well understood but point towards antiapoptotic effects and inducers of mitochondrial biogenesis.}, }
@article {pmid34600050, year = {2022}, author = {Yu, X and Yang, H and Liu, J and Qi, Y and Sun, L and Tian, X}, title = {A strategy for a high enrichment of insect mitochondrial DNA for mitogenomic analysis.}, journal = {Gene}, volume = {808}, number = {}, pages = {145986}, doi = {10.1016/j.gene.2021.145986}, pmid = {34600050}, issn = {1879-0038}, mesh = {Animals ; DNA, Mitochondrial/*genetics/*isolation &amp; purification ; Genome, Insect/genetics ; Genome, Mitochondrial/genetics ; Genomics ; High-Throughput Nucleotide Sequencing/methods ; Insecta/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Next-generation sequencing has dramatically fostered insect mitogenomic research in recent years. However, studies on the insect mitochondrial genome (mitogenome) assembly mainly rely on the sequencing data from total DNA, which is not cost-effective as a huge data from nuclear DNA are wasted. Besides, many mitogenomic studies require genomic information from individual organisms, whereas the DNA yield from small individual insects is too low to meet the sequencing requirements. Here, we describe a strategy for a high enrichment of insect mitochondrial DNA (mtDNA) using rolling circle amplification (RCA) technique. This strategy consists of standard DNA extraction, RCA enrichment, next-generation sequencing and mitogenome assembly. We have evaluated the performance of this strategy on nine insect species representing eight families of insecta, three other invertebrates, and even two vertebrate specimens. Results show that our strategy is especially suitable for insects, which allows almost all tested insect mtDNA contents to reach 80% and above. A further examination of enrichment efficiency of our strategy among different taxa shows that it is also applicable to other invertebrates and even some vertebrates such as Rhacophorus and ptyas species, although its enrichment efficiency in these groups is lower than that of insects. After treatment with our strategy, small flux sequencing data can realize the assembly of mitogenome with deep coverage, providing a solid base for subsequent mitogenome-based studies.}, }
@article {pmid34599203, year = {2021}, author = {Klink, GV and O'Keefe, H and Gogna, A and Bazykin, GA and Elson, JL}, title = {A broad comparative genomics approach to understanding the pathogenicity of Complex I mutations.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19578}, pmid = {34599203}, issn = {2045-2322}, mesh = {Alleles ; Amino Acid Substitution ; Electron Transport Complex I/*genetics/metabolism ; *Genetic Predisposition to Disease ; Genome-Wide Association Study ; *Genomics/methods ; Humans ; Mitochondria/*genetics/metabolism ; *Mutation ; Phylogeny ; Selection, Genetic ; }, abstract = {Disease caused by mutations of mitochondrial DNA (mtDNA) are highly variable in both presentation and penetrance. Over the last 30 years, clinical recognition of this group of diseases has increased. It has been suggested that haplogroup background could influence the penetrance and presentation of disease-causing mutations; however, to date there is only one well-established example of such an effect: the increased penetrance of two Complex I Leber's hereditary optic neuropathy mutations on a haplogroup J background. This paper conducts the most extensive investigation to date into the importance of haplogroup context in the pathogenicity of mtDNA mutations in Complex I. We searched for proven human point mutations across more than 900 metazoans finding human disease-causing mutations and potential masking variants. We found more than a half of human pathogenic variants as compensated pathogenic deviations (CPD) in at least in one animal species from our multiple sequence alignments. Some variants were found in many species, and some were even the most prevalent amino acids across our dataset. Variants were also found in other primates, and in such cases, we looked for non-human amino acids in sites with high probability to interact with the CPD in folded protein. Using this "local interactions" approach allowed us to find potential masking substitutions in other amino acid sites. We suggest that the masking variants might arise in humans, resulting in variability of mutation effect in our species.}, }
@article {pmid34592348, year = {2022}, author = {Li, Y and Wang, S and Zhou, J and Li, T and Jiang, K and Zhang, Y and Zheng, C and Liang, J and Bu, W}, title = {The phylogenic position of aschiphasmatidae in euphasmatodea based on mitochondrial genomic evidence.}, journal = {Gene}, volume = {808}, number = {}, pages = {145974}, doi = {10.1016/j.gene.2021.145974}, pmid = {34592348}, issn = {1879-0038}, mesh = {Animals ; Base Sequence/genetics ; Gene Order/genetics ; Gene Rearrangement/genetics ; Genome, Mitochondrial/*genetics ; Genomics/methods ; Mitochondria/*genetics ; Nematoda/*genetics ; Neoptera/genetics ; Phylogeny ; }, abstract = {The mitochondrial genome (mitogenome) has been regarded as significant source of data to better understand the phylogenetic relationships within the Euphasmatodea, but no mitogenome in Aschiphasmatoidea has been sequenced to date. In this study, two mitogenomes of Orthomeria smaragdinum and Nanhuaphasma hamicercum of Aschiphasmatidae were sequenced and annotated for the first time. The same mitochondrial gene rearrangement structure was present in the two mitogenomes sequenced, showing as the translocation of tRNA-Arg and tRNA-Asn, which conformed to the tandem duplication-random loss and could be used as a possible synapomorphy for Aschiphasmatidae. The phylogenetic results based on the maximum likelihood (ML) and bayesian inference (BI) methods both showed that Aschiphasmatidae and Neophasmatodea in Euphasmatodea are sister taxa. Although the monophyly of Oriophasmata, Occidophasmata, Diapheromeridae, Phasmatidae, Lonchodidae and Bacilloidea has not been solved, the monophyly of Neophasmatodea and Phyllioidea was well supported.}, }
@article {pmid34585988, year = {2021}, author = {Turra, GL and Liedgens, L and Sommer, F and Schneider, L and Zimmer, D and Vilurbina Perez, J and Koncarevic, S and Schroda, M and Mühlhaus, T and Deponte, M}, title = {In Vivo Structure-Function Analysis and Redox Interactomes of Leishmania tarentolae Erv.}, journal = {Microbiology spectrum}, volume = {9}, number = {2}, pages = {e0080921}, pmid = {34585988}, issn = {2165-0497}, mesh = {CRISPR-Cas Systems/genetics ; Leishmania/classification/genetics/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Precursor Protein Import Complex Proteins/*metabolism ; Oxidation-Reduction ; Oxidoreductases Acting on Sulfur Group Donors/*metabolism ; Protein Domains/genetics ; Protein Folding ; Protein Transport/genetics ; Structure-Activity Relationship ; }, abstract = {Import and oxidative folding of proteins in the mitochondrial intermembrane space differ among eukaryotic lineages. While opisthokonts such as yeast rely on the receptor and oxidoreductase Mia40 in combination with the Mia40:cytochrome c oxidoreductase Erv, kinetoplastid parasites and other Excavata/Discoba lack Mia40 but have a functional Erv homologue. Whether excavate Erv homologues rely on a Mia40 replacement or directly interact with imported protein substrates remains controversial. Here, we used the CRISPR-Cas9 system to generate a set of tagged and untagged homozygous mutants of LTERV from the kinetoplastid model parasite Leishmania tarentolae. Modifications of the shuttle cysteine motif of LtErv were lethal, whereas replacement of clamp residue Cys[17] or removal of the kinetoplastida-specific second (KISS) domain had no impact on parasite viability under standard growth conditions. However, removal of the KISS domain rendered parasites sensitive to heat stress and led to the accumulation of homodimeric and mixed LtErv disulfides. We therefore determined and compared the redox interactomes of tagged wild-type LtErv and LtErv[ΔKISS] using stable isotope labeling by amino acids in cell culture (SILAC) and quantitative mass spectrometry. While the Mia40-replacement candidate Mic20 and all but one typical substrate with twin Cx3/9C-motifs were absent in both redox interactomes, we identified a small set of alternative potential interaction partners with putative redox-active cysteine residues. In summary, our study reveals parasite-specific intracellular structure-function relationships and redox interactomes of LtErv with implications for current hypotheses on mitochondrial protein import in nonopisthokonts. IMPORTANCE The discovery of the redox proteins Mia40/CHCHD4 and Erv1/ALR, as well as the elucidation of their relevance for oxidative protein folding in the mitochondrial intermembrane space of yeast and mammals, founded a new research topic in redox biology and mitochondrial protein import. The lack of Mia40/CHCHD4 in protist lineages raises fundamental and controversial questions regarding the conservation and evolution of this essential pathway. Do protist Erv homologues act alone, or do they use the candidate Mic20 or another protein as a Mia40 replacement? Furthermore, we previously showed that Erv homologues in L. tarentolae and the human pathogen L. infantum are not only essential but also differ structurally and mechanistically from yeast and human Erv1/ALR. Here, we analyzed the relevance of such structural differences in vivo and determined the first redox interactomes of a nonopisthokont Erv homologue. Our data challenge recent hypotheses on mitochondrial protein import in nonopisthokonts.}, }
@article {pmid34583583, year = {2021}, author = {Fenton, A and Camus, MF and Hurst, GDD}, title = {Positive selection on mitochondria may eliminate heritable microbes from arthropod populations.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1959}, pages = {20211735}, pmid = {34583583}, issn = {1471-2954}, mesh = {Animals ; *Arthropods/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Mitochondria/genetics ; Symbiosis ; }, abstract = {Diverse eukaryotic taxa carry facultative heritable symbionts, microbes that are passed from mother to offspring. These symbionts are coinherited with mitochondria, and selection favouring either new symbionts, or new symbiont variants, is known to drive loss of mitochondrial diversity as a correlated response. More recently, evidence has accumulated of episodic directional selection on mitochondria, but with currently unknown consequences for symbiont evolution. We therefore employed a population genetic mean field framework to model the impact of selection on mitochondrial DNA (mtDNA) upon symbiont frequency for three generic scenarios of host-symbiont interaction. Our models predict that direct selection on mtDNA can drive symbionts out of the population where a positively selected mtDNA mutation occurs initially in an individual that is uninfected with the symbiont, and the symbiont is initially at low frequency. When, by contrast, the positively selected mtDNA mutation occurs in a symbiont-infected individual, the mutation becomes fixed and in doing so removes symbiont variation from the population. We conclude that the molecular evolution of symbionts and mitochondria, which has previously been viewed from a perspective of selection on symbionts driving the evolution of a neutral mtDNA marker, should be reappraised in the light of positive selection on mtDNA.}, }
@article {pmid34582890, year = {2021}, author = {Weerth, RS and Medlock, AE and Dailey, HA}, title = {Ironing out the distribution of [2Fe-2S] motifs in ferrochelatases.}, journal = {The Journal of biological chemistry}, volume = {297}, number = {5}, pages = {101017}, pmid = {34582890}, issn = {1083-351X}, support = {R01 DK111653/DK/NIDDK NIH HHS/United States ; }, mesh = {*Actinobacteria/chemistry/genetics ; Amino Acid Motifs ; *Bacterial Proteins/chemistry/genetics ; *Ferrochelatase/chemistry/genetics ; Heme/chemistry/genetics ; Iron/*chemistry ; Sulfur/*chemistry ; }, abstract = {Heme, a near ubiquitous cofactor, is synthesized by most organisms. The essential step of insertion of iron into the porphyrin macrocycle is mediated by the enzyme ferrochelatase. Several ferrochelatases have been characterized, and it has been experimentally shown that a fraction of them contain [2Fe-2S] clusters. It has been suggested that all metazoan ferrochelatases have such clusters, but among bacteria, these clusters have been most commonly identified in Actinobacteria and a few other bacteria. Despite this, the function of the [2Fe-2S] cluster remains undefined. With the large number of sequenced genomes currently available, we comprehensively assessed the distribution of putative [2Fe-2S] clusters throughout the ferrochelatase protein family. We discovered that while rare within the bacterial ferrochelatase family, this cluster is prevalent in a subset of phyla. Of note is that genomic data show that the cluster is not common in Actinobacteria, as is currently thought based on the small number of actinobacterial ferrochelatases experimentally examined. With available physiological data for each genome included, we identified a correlation between the presence of the microbial cluster and aerobic metabolism. Additionally, our analysis suggests that Firmicute ferrochelatases are the most ancient and evolutionarily preceded the Alphaproteobacterial precursor to eukaryotic mitochondria. These findings shed light on distribution and evolution of the [2Fe-2S] cluster in ferrochelatases and will aid in determining the function of the cluster in heme synthesis.}, }
@article {pmid34577183, year = {2021}, author = {Koumpoura, CL and Robert, A and Athanassopoulos, CM and Baltas, M}, title = {Antimalarial Inhibitors Targeting Epigenetics or Mitochondria in Plasmodium falciparum: Recent Survey upon Synthesis and Biological Evaluation of Potential Drugs against Malaria.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {18}, pages = {}, pmid = {34577183}, issn = {1420-3049}, mesh = {Animals ; Antimalarials/*chemistry/pharmacology ; DNA/chemistry ; Dihydroorotate Dehydrogenase ; Drug Discovery ; Drug Resistance ; Enzyme Inhibitors/chemistry/pharmacology ; Epigenesis, Genetic ; Histone Deacetylases/metabolism ; Humans ; Malaria, Falciparum/*drug therapy ; Methyltransferases/antagonists &amp; inhibitors ; Mitochondria/*metabolism ; Oxidoreductases Acting on CH-CH Group Donors/antagonists &amp; inhibitors ; Plasmodium falciparum/*drug effects ; Quinazolines/chemistry/pharmacology ; Signal Transduction ; Structure-Activity Relationship ; }, abstract = {Despite many efforts, malaria remains among the most problematic infectious diseases worldwide, mainly due to the development of drug resistance by P. falciparum. Over the past decade, new essential pathways have been emerged to fight against malaria. Among them, epigenetic processes and mitochondrial metabolism appear to be important targets. This review will focus on recent evolutions concerning worldwide efforts to conceive, synthesize and evaluate new drug candidates interfering selectively and efficiently with these two targets and pathways. The focus will be on compounds/scaffolds that possess biological/pharmacophoric properties on DNA methyltransferases and HDAC's for epigenetics, and on cytochrome bc1 and dihydroorotate dehydrogenase for mitochondrion.}, }
@article {pmid34565456, year = {2021}, author = {Bunmee, K and Thaenkham, U and Saralamba, N and Ponlawat, A and Zhong, D and Cui, L and Sattabongkot, J and Sriwichai, P}, title = {Population genetic structure of the malaria vector Anopheles minimus in Thailand based on mitochondrial DNA markers.}, journal = {Parasites &amp; vectors}, volume = {14}, number = {1}, pages = {496}, pmid = {34565456}, issn = {1756-3305}, support = {U19AI089672/NH/NIH HHS/United States ; D43 TW006571/TW/FIC NIH HHS/United States ; D43TW006571/NH/NIH HHS/United States ; U19 AI089672/AI/NIAID NIH HHS/United States ; P0108_19_AF_06.01//Armed Forces Health Surveillance Branch/ ; }, mesh = {Animals ; Anopheles/classification/*genetics/physiology ; Cytochromes b/genetics ; Electron Transport Complex IV/genetics/metabolism ; Gene Flow ; Genetic Markers ; Insect Proteins/*genetics ; Malaria/*transmission ; Mitochondria/*genetics ; Mosquito Vectors/classification/*genetics/physiology ; Phylogeny ; Thailand ; }, abstract = {BACKGROUND: The malaria vector Anopheles minimus has been influenced by external stresses affecting the survival rate and vectorial capacity of the population. Since An. minimus habitats have continuously undergone ecological changes, this study aimed to determine the population genetic structure and the potential gene flow among the An. minimus populations in Thailand.<br><br>METHODS: Anopheles minimus was collected from five malaria transmission areas in Thailand using Centers for Disease Control and Prevention (CDC) light traps. Seventy-nine females from those populations were used as representative samples. The partial mitochondrial cytochrome c oxidase subunit I (COI), cytochrome c oxidase subunit II (COII) and cytochrome b (Cytb) gene sequences were amplified and analyzed to identify species and determine the current population genetic structure. For the past population, we determined the population genetic structure from the 60 deposited COII sequences in GenBank of An. minimus collected from Thailand 20&#xa0;years ago.<br><br>RESULTS: The current populations of An. minimus were genetically divided into two lineages, A and B. Lineage A has high haplotype diversity under gene flow similar to the population in the past. Neutrality tests suggested population expansion of An. minimus, with the detection of abundant rare mutations in all populations, which tend to arise from negative selection.<br><br>CONCLUSIONS: This study revealed that the population genetic structure of An. minimus lineage A was similar between the past and present populations, indicating high adaptability of the species. There was substantial gene flow between the eastern and western An. minimus populations without detection of significant gene flow barriers.}, }
@article {pmid34565318, year = {2021}, author = {Baleva, MV and Piunova, UE and Chicherin, IV and Krasavina, DG and Levitskii, SA and Kamenski, PA}, title = {Yeast Translational Activator Mss51p and Human ZMYND17 - Two Proteins with a Common Origin, but Different Functions.}, journal = {Biochemistry. Biokhimiia}, volume = {86}, number = {9}, pages = {1151-1161}, doi = {10.1134/S0006297921090108}, pmid = {34565318}, issn = {1608-3040}, mesh = {Electron Transport Complex IV/metabolism ; Evolution, Molecular ; Gene Editing ; HeLa Cells ; Humans ; Mitochondria/enzymology/metabolism ; NADH Dehydrogenase/metabolism ; Phylogeny ; Protein Subunits/metabolism ; Proton-Translocating ATPases/metabolism ; RNA, Guide, Kinetoplastida/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/classification/genetics/*metabolism ; Transcription Factors/classification/deficiency/genetics/*metabolism ; }, abstract = {Despite its similarity to protein biosynthesis in bacteria, translation in the mitochondria of modern eukaryotes has several unique features, such as the necessity for coordination of translation of mitochondrial mRNAs encoding proteins of the electron transport chain complexes with translation of other protein components of these complexes in the cytosol. In the mitochondria of baker's yeast Saccharomyces cerevisiae, this coordination is carried out by a system of translational activators that predominantly interact with the 5'-untranslated regions of mitochondrial mRNAs. No such system has been found in human mitochondria, except a single identified translational activator, TACO1. Here, we studied the role of the ZMYND17 gene, an ortholog of the yeast gene for the translational activator Mss51p, on the mitochondrial translation in human cells. Deletion of the ZMYND17 gene did not affect translation in the mitochondria, but led to the decrease in the cytochrome c oxidase activity and increase in the amount of free F1 subunit of ATP synthase. We also investigated the evolutionary history of Mss51p and ZMYND17 and suggested a possible mechanism for the divergence of functions of these orthologous proteins.}, }
@article {pmid34563127, year = {2021}, author = {Deng, J and Assandri, G and Chauhan, P and Futahashi, R and Galimberti, A and Hansson, B and Lancaster, LT and Takahashi, Y and Svensson, EI and Duplouy, A}, title = {Wolbachia-driven selective sweep in a range expanding insect species.}, journal = {BMC ecology and evolution}, volume = {21}, number = {1}, pages = {181}, pmid = {34563127}, issn = {2730-7182}, mesh = {Animals ; Cyprus ; *DNA, Mitochondrial/genetics ; Female ; Genetic Variation ; Odonata/*genetics/*microbiology ; Phylogeny ; *Wolbachia ; }, abstract = {BACKGROUND: Evolutionary processes can cause strong spatial genetic signatures, such as local loss of genetic diversity, or conflicting histories from mitochondrial versus nuclear markers. Investigating these genetic patterns is important, as they may reveal obscured processes and players. The maternally inherited bacterium Wolbachia is among the most widespread symbionts in insects. Wolbachia typically spreads within host species by conferring direct fitness benefits, and/or by manipulating its host reproduction to favour infected over uninfected females. Under sufficient selective advantage, the mitochondrial haplotype associated with the favoured maternally-inherited symbiotic strains will spread (i.e. hitchhike), resulting in low mitochondrial genetic variation across the host species range.<br><br>METHOD: The common bluetail damselfly (Ischnura elegans: van der Linden, 1820) has recently emerged as a model organism for genetics and genomic signatures of range expansion during climate change. Although there is accumulating data on the consequences of such expansion on the genetics of I. elegans, no study has screened for Wolbachia in the damselfly genus Ischnura. Here, we present the biogeographic variation in Wolbachia prevalence and penetrance across Europe and Japan (including samples from 17 populations), and from close relatives in the Mediterranean area (i.e. I. genei: Rambur, 1842; and I. saharensis: Aguesse, 1958).<br><br>RESULTS: Our data reveal (a) multiple Wolbachia-strains, (b) potential transfer of the symbiont through hybridization, (c) higher infection rates at higher latitudes, and (d) reduced mitochondrial diversity in the north-west populations, indicative of hitchhiking associated with the selective sweep of the most common strain. We found low mitochondrial haplotype diversity in the Wolbachia-infected north-western European populations (Sweden, Scotland, the Netherlands, Belgium, France and Italy) of I. elegans, and, conversely, higher mitochondrial diversity in populations with low penetrance of Wolbachia (Ukraine, Greece, Montenegro and Cyprus). The timing of the selective sweep associated with infected lineages was estimated between 20,000 and 44,000&#xa0;years before present, which is consistent with the end of the last glacial period about 20,000 years.<br><br>CONCLUSIONS: Our findings provide an example of how endosymbiont infections can shape spatial variation in their host evolutionary genetics during postglacial expansion. These results also challenge population genetic studies that do not consider the prevalence of symbionts in many insects, which we show can impact geographic patterns of mitochondrial genetic diversity.}, }
@article {pmid34555943, year = {2022}, author = {Lima-Silva, LF and Lee, J and Moraes-Vieira, PM}, title = {Soluble Carrier Transporters and Mitochondria in the Immunometabolic Regulation of Macrophages.}, journal = {Antioxidants &amp; redox signaling}, volume = {36}, number = {13-15}, pages = {906-919}, pmid = {34555943}, issn = {1557-7716}, support = {K01 DK114162/DK/NIDDK NIH HHS/United States ; }, mesh = {Drug Delivery Systems ; *Macrophages/metabolism ; *Mitochondria ; }, abstract = {Significance: Immunometabolic regulation of macrophages is a growing area of research across many fields. Here, we review the contribution of solute carriers (SLCs) in regulating macrophage metabolism. We also highlight key mechanisms that regulate SLC function, their effects on mitochondrial activity, and how these intracellular activities contribute to macrophage fitness in health and disease. Recent Advances: SLCs serve as a major drug absorption pathway and represent a novel category of therapeutic drug targets. SLC dynamics affect cellular nutritional sensors, such as AMP-activated protein kinase and mammalian target of rapamycin, and consequently alter the cellular metabolism and mitochondrial dynamics within macrophages to adapt to a new functional phenotype. Critical Issues: SLC function affects macrophage phenotype, but their mechanisms of action and how their functions contribute to host health remain incompletely defined. Future Directions: Few studies focus on the impact of solute transporters on macrophage function. Identifying which SLCs are present in macrophages and determining their functional roles may reveal novel therapeutic targets with which to treat metabolic and inflammatory diseases. Antioxid. Redox Signal. 36, 906-919.}, }
@article {pmid34547233, year = {2021}, author = {Trefts, E and Shaw, RJ}, title = {AMPK: restoring metabolic homeostasis over space and time.}, journal = {Molecular cell}, volume = {81}, number = {18}, pages = {3677-3690}, pmid = {34547233}, issn = {1097-4164}, support = {R01 DK080425/DK/NIDDK NIH HHS/United States ; R01 CA234047/CA/NCI NIH HHS/United States ; R35 CA220538/CA/NCI NIH HHS/United States ; F32 DK126418/DK/NIDDK NIH HHS/United States ; P30 CA014195/CA/NCI NIH HHS/United States ; P01 CA120964/CA/NCI NIH HHS/United States ; R01 CA172229/CA/NCI NIH HHS/United States ; }, mesh = {AMP-Activated Protein Kinases/genetics/*metabolism ; Animals ; Cytoplasm/metabolism ; Energy Metabolism ; Homeostasis ; Humans ; Mitochondria/metabolism ; Protein Domains ; Signal Transduction ; Structure-Activity Relationship ; }, abstract = {The evolution of AMPK and its homologs enabled exquisite responsivity and control of cellular energetic homeostasis. Recent work has been critical in establishing the mechanisms that determine AMPK activity, novel targets of AMPK action, and the distribution of AMPK-mediated control networks across the cellular landscape. The role of AMPK as a hub of metabolic control has led to intense interest in pharmacologic activation as a therapeutic avenue for a number of disease states, including obesity, diabetes, and cancer. As such, critical work on the compartmentalization of AMPK, its downstream targets, and the systems it influences has progressed in recent years. The variegated distribution of AMPK-mediated control of metabolic homeostasis has revealed key insights into AMPK in normal biology and future directions for AMPK-based therapeutic strategies.}, }
@article {pmid34545486, year = {2022}, author = {O'Leary, BM and Oh, GGK and Millar, AH}, title = {High-Throughput Oxygen Consumption Measurements in Leaf Tissue Using Oxygen Sensitive Fluorophores.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2363}, number = {}, pages = {63-75}, pmid = {34545486}, issn = {1940-6029}, mesh = {Carbon Dioxide/metabolism ; Fluorescent Dyes/metabolism ; Ionophores ; Mitochondria/metabolism ; Oxygen/metabolism ; *Oxygen Consumption ; Plant Leaves ; }, abstract = {Respiratory rate measurements are crucial assays to understand mitochondrial biochemistry as well as metabolic regulation within tissues. Several technologies currently exist that can measure plant respiratory oxygen consumption or carbon dioxide evolution rates over short durations by either isolated mitochondria or plant tissues. Here we describe recently developed alternative methods for measuring tissue oxygen consumption rates (OCRs) using systems reliant on oxygen sensitive fluorophores. The methods described have distinct experimental advantages: they can allow high-throughput and long-duration measurements; and they are particularly suited to investigating the metabolic regulation of respiration by comparing OCRs among treatments or genotypes.}, }
@article {pmid34545138, year = {2021}, author = {Ruíz-Rivero, O and Garcia-Lor, A and Rojas-Panadero, B and Franco, JC and Khamis, FM and Kruger, K and Cifuentes, D and Bielza, P and Tena, A and Urbaneja, A and Pérez-Hedo, M}, title = {Insights into the origin of the invasive populations of Trioza erytreae in Europe using microsatellite markers and mtDNA barcoding approaches.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {18651}, pmid = {34545138}, issn = {2045-2322}, mesh = {Animals ; Citrus/chemistry ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Europe ; Hemiptera/*genetics ; Insect Vectors ; Introduced Species/trends ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Phylogeny ; Plant Diseases ; }, abstract = {The African citrus psyllid Trioza erytreae is one of the major threats to citrus industry as the vector of the incurable disease known as huanglongbing (HLB) or citrus greening. The psyllid invaded the northwest of the Iberian Peninsula 6 years ago. The invasion alarmed citrus growers in the Mediterranean basin, the largest citrus producing area in Europe, which is still free of HLB. Before our study, no research had been carried out on the genetic diversity of T. erytreae populations that have invaded the Iberian Peninsula and the archipelagos of the Macaronesia (Madeira and the Canary Islands). In this study, combining microsatellites markers and mtDNA barcoding analysis, we characterize the genetic diversity, structure and maternal relationship of these new invasive populations of T. erytreae and those from Africa. Our results suggest that the outbreaks of T. erytreae in the Iberian Peninsula may have derived from the Canary Islands. The populations of T. erytreae that invaded Macaronesia and the Iberian Peninsula are likely to have originated from southern Africa. We anticipate our results to be a starting point for tracking the spread of this invasive pest outside of Africa and to be important for optimizing contingency and eradication plans in newly invaded and free areas.}, }
@article {pmid34536995, year = {2021}, author = {Hong, Z and Liao, X and Ye, Y and Zhang, N and Yang, Z and Zhu, W and Gao, W and Sharbrough, J and Tembrock, LR and Xu, D and Wu, Z}, title = {A complete mitochondrial genome for fragrant Chinese rosewood (Dalbergia odorifera, Fabaceae) with comparative analyses of genome structure and intergenomic sequence transfers.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {672}, pmid = {34536995}, issn = {1471-2164}, mesh = {China ; Chloroplasts ; *Dalbergia/genetics ; *Fabaceae/genetics ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Phylogeny ; Plant Breeding ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Dalbergia odorifera is an economically and culturally important species in the Fabaceae because of the high-quality lumber and traditional Chinese medicines made from this plant, however, overexploitation has increased the scarcity of D. odorifera. Given the rarity and the multiple uses of this species, it is important to expand the genomic resources for utilizing in applications such as tracking illegal logging, determining effective population size of wild stands, delineating pedigrees in marker assisted breeding programs, and resolving gene networks in functional genomics studies. Even the nuclear and chloroplast genomes have been published for D. odorifera, the complete mitochondrial genome has not been assembled or assessed for sequence transfer to other genomic compartments until now. Such work is essential in understanding structural and functional genome evolution in a lineage (Fabaceae) with frequent intergenomic sequence transfers.<br><br>RESULTS: We integrated Illumina short-reads and PacBio CLR long-reads to assemble and annotate the complete mitochondrial genome of D. odorifera. The mitochondrial genome was organized as&#xa0;a single circular structure&#xa0;of&#xa0;435 Kb in length containing 33 protein coding genes, 4 rRNA and 17 tRNA genes. Nearly 4.0% (17,386&#x2009;bp) of the genome was annotated as repetitive DNA. From the sequence transfer analysis, it was found that 114 Kb of DNA originating from the mitochondrial genome has been transferred to the nuclear genome, with most of the transfer events having taken place relatively recently. The high frequency of sequence transfers from the mitochondria to the nuclear genome was similar to that of sequence transfer from the chloroplast to the nuclear genome.<br><br>CONCLUSION: For the first-time, the complete mitochondrial genome of D. odorifera was assembled in this study, which will provide a baseline resource in understanding genomic evolution in the highly specious Fabaceae. In particular, the assessment of intergenomic sequence transfer suggests that transfers have been common and recent indicating a possible role in environmental adaptation as has been found in other lineages. The high turnover rate of genomic colinearly and large differences in mitochondrial genome size found in the comparative analyses herein providing evidence for the rapid evolution of mitochondrial genome structure compared to chloroplasts in Faboideae. While phylogenetic analyses using functional genes indicate that mitochondrial genes are very slowly evolving compared to chloroplast genes.}, }
@article {pmid34530136, year = {2021}, author = {Duncan, WP and Machado, RN and Fernandes, MN}, title = {Environmentally-induced osmoregulation in Neotropical freshwater stingrays (Myliobatiformes: Potamotrygoninae) after controlling for phylogeny.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {262}, number = {}, pages = {111076}, doi = {10.1016/j.cbpa.2021.111076}, pmid = {34530136}, issn = {1531-4332}, mesh = {Animals ; Electrolytes/blood/*metabolism ; Fish Proteins/genetics/metabolism ; Fresh Water ; Gills/metabolism ; Kidney/metabolism ; Mitochondria/genetics/*metabolism ; *Osmoregulation ; Osmosis ; Phylogeny ; Renal Reabsorption ; Skates, Fish/blood/genetics/*metabolism ; Sodium-Potassium-Exchanging ATPase/genetics/metabolism ; *Tropical Climate ; }, abstract = {The osmotic physiology of freshwater stingrays was investigated in fifteen species from white (WW), black (BW), and clearwater (CW) rivers of Brazilian hydrographic basins. Regardless of phylogeny, potamotrygonids collected in the BW (Negro, Jutai, Nhamunda, and Manacapuru rivers), and CW (Tapajos, Parana, Mutum, Demeni, and Branco rivers) exhibited lower levels of osmolytes and plasma osmolality than those from WW (Amazon estuary, Solimoes, and Tarauaca rivers). However, the gill and kidney Na[+]/K[+]-ATPase activities were higher in the potamotrygonid species from BW and CW than those from WW. These results may be related to the ability of the potamotrygonids to achieve high ion uptake from ion-poor waters, such as those of BW and/or CW. Additionally, the high kidney Na[+]/K[+]-ATPase activity may help to minimize ion loss and generate diluted urine. Thus, diffusional losses of salts are balanced by uptake of ions in the gill, and reabsorption by the kidney. The physiological traits showed a weak phylogenetic signal, which indicates a strong evolutionary convergence. Multivariate analyses revealed that variations in physiological traits has a significant association with the type of water, as well as its physical and chemical characteristics such as electric conductivity and pH. Therefore, the South American Neotropical freshwater stingrays adjust their osmoregulatory mechanisms according to the environment in which they live.}, }
@article {pmid34528296, year = {2021}, author = {Møller, IM and Rasmusson, AG and Van Aken, O}, title = {Plant mitochondria - past, present and future.}, journal = {The Plant journal : for cell and molecular biology}, volume = {108}, number = {4}, pages = {912-959}, doi = {10.1111/tpj.15495}, pmid = {34528296}, issn = {1365-313X}, mesh = {DNA, Mitochondrial/genetics ; DNA, Plant/*genetics ; Lipids/analysis ; Mitochondria/*metabolism/ultrastructure ; Mitochondrial Proteins/genetics/*metabolism ; NADH Dehydrogenase/genetics/metabolism ; Oxidation-Reduction ; Oxidoreductases/genetics/metabolism ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plants/genetics/*metabolism/ultrastructure ; Proteomics ; Signal Transduction ; }, abstract = {The study of plant mitochondria started in earnest around 1950 with the first isolations of mitochondria from animal and plant tissues. The first 35 years were spent establishing the basic properties of plant mitochondria and plant respiration using biochemical and physiological approaches. A number of unique properties (compared to mammalian mitochondria) were observed: (i) the ability to oxidize malate, glycine and cytosolic NAD(P)H at high rates; (ii) the partial insensitivity to rotenone, which turned out to be due to the presence of a second NADH dehydrogenase on the inner surface of the inner mitochondrial membrane in addition to the classical Complex I NADH dehydrogenase; and (iii) the partial insensitivity to cyanide, which turned out to be due to an alternative oxidase, which is also located on the inner surface of the inner mitochondrial membrane, in addition to the classical Complex IV, cytochrome oxidase. With the appearance of molecular biology methods around 1985, followed by genomics, further unique properties were discovered: (iv) plant mitochondrial DNA (mtDNA) is 10-600 times larger than the mammalian mtDNA, yet it only contains approximately 50% more genes; (v) plant mtDNA has kept the standard genetic code, and it has a low divergence rate with respect to point mutations, but a high recombinatorial activity; (vi) mitochondrial mRNA maturation includes a uniquely complex set of activities for processing, splicing and editing (at hundreds of sites); (vii) recombination in mtDNA creates novel reading frames that can produce male sterility; and (viii) plant mitochondria have a large proteome with 2000-3000 different proteins containing many unique proteins such as 200-300 pentatricopeptide repeat proteins. We describe the present and fairly detailed picture of the structure and function of plant mitochondria and how the unique properties make their metabolism more flexible allowing them to be involved in many diverse processes in the plant cell, such as photosynthesis, photorespiration, CAM and C4 metabolism, heat production, temperature control, stress resistance mechanisms, programmed cell death and genomic evolution. However, it is still a challenge to understand how the regulation of metabolism and mtDNA expression works at the cellular level and how retrograde signaling from the mitochondria coordinates all those processes.}, }
@article {pmid34523684, year = {2021}, author = {Mallo, N and Ovciarikova, J and Martins-Duarte, ES and Baehr, SC and Biddau, M and Wilde, ML and Uboldi, AD and Lemgruber, L and Tonkin, CJ and Wideman, JG and Harding, CR and Sheiner, L}, title = {Depletion of a Toxoplasma porin leads to defects in mitochondrial morphology and contacts with the endoplasmic reticulum.}, journal = {Journal of cell science}, volume = {134}, number = {20}, pages = {}, pmid = {34523684}, issn = {1477-9137}, support = {213455/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 217173/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; BB/N003675/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Endoplasmic Reticulum/genetics/metabolism ; Humans ; Mitochondria/metabolism ; Protein Transport ; *Toxoplasma/genetics/metabolism ; Voltage-Dependent Anion Channels/genetics/metabolism ; }, abstract = {The voltage-dependent anion channel (VDAC) is a ubiquitous channel in the outer membrane of the mitochondrion with multiple roles in protein, metabolite and small molecule transport. In mammalian cells, VDAC protein, as part of a larger complex including the inositol triphosphate receptor, has been shown to have a role in mediating contacts between the mitochondria and endoplasmic reticulum (ER). We identify VDAC of the pathogenic apicomplexan Toxoplasma gondii and demonstrate its importance for parasite growth. We show that VDAC is involved in protein import and metabolite transfer to mitochondria. Further, depletion of VDAC resulted in significant morphological changes in the mitochondrion and ER, suggesting a role in mediating contacts between these organelles in T. gondii. This article has an associated First Person interview with the first author of the paper.}, }
@article {pmid34519912, year = {2022}, author = {Oono, J and Hatakeyama, Y and Yabiku, T and Ueno, O}, title = {Effects of growth temperature and nitrogen nutrition on expression of C3-C4 intermediate traits in Chenopodium album.}, journal = {Journal of plant research}, volume = {135}, number = {1}, pages = {15-27}, pmid = {34519912}, issn = {1618-0860}, support = {JP15K14638//Japan Society for the promotion of Science, KAKENHI/ ; }, mesh = {*Chenopodium album/metabolism ; Glycine Dehydrogenase (Decarboxylating)/metabolism ; Nitrogen ; Photosynthesis ; Plant Leaves/metabolism ; Temperature ; }, abstract = {Proto-Kranz plants represent an initial phase in the evolution from C3 to C3-C4 intermediate to C4 plants. The ecological and adaptive aspects of C3-C4 plants would provide an important clue to understand the evolution of C3-C4 plants. We investigated whether growth temperature and nitrogen (N) nutrition influence the expression of C3-C4 traits in Chenopodium album (proto-Kranz) in comparison with Chenopodium quinoa (C3). Plants were grown during 5 weeks at 20 or 30 °C under standard or low N supply levels (referred to as 20SN, 20LN, 30SN, and 30LN). Net photosynthetic rate and leaf N content were higher in 20SN and 30SN plants than in 20LN and 30LN plants of C. album but did not differ among growth conditions in C. quinoa. The CO2 compensation point (Γ) of C. album was lowest in 30LN plants (36 µmol mol[-1]), highest in 20SN plants (51 µmol mol[-1]), and intermediate in 20LN and 30SN plants, whereas Γ of C. quinoa did not differ among the growth conditions (51-52 µmol mol[-1]). The anatomical structure of leaves was not considerably affected by growth conditions in either species. However, ultrastructural observations in C. album showed that the number of mitochondria per mesophyll or bundle sheath (BS) cell was lower in 20LN and 30LN plants than in 20SN and 30SN plants. Immunohistochemical observations revealed that lower accumulation level of P-protein of glycine decarboxylase (GDC-P) in mesophyll mitochondria than in BS mitochondria is the major factor causing the decrease in Γ values in C. album plants grown under low N supply and high temperature. These results suggest that high growth temperature and low N supply lead to the expression of C3-C4 traits (the reduction of Γ) in the proto-Kranz plants of C. album through the regulation of GDC-P expression.}, }
@article {pmid34504353, year = {2021}, author = {Li, L and Conradson, DM and Bharat, V and Kim, MJ and Hsieh, CH and Minhas, PS and Papakyrikos, AM and Durairaj, AS and Ludlam, A and Andreasson, KI and Partridge, L and Cianfrocco, MA and Wang, X}, title = {A mitochondrial membrane-bridging machinery mediates signal transduction of intramitochondrial oxidation.}, journal = {Nature metabolism}, volume = {3}, number = {9}, pages = {1242-1258}, pmid = {34504353}, issn = {2522-5812}, support = {P30 CA124435/CA/NCI NIH HHS/United States ; R21 AG061315/AG/NIA NIH HHS/United States ; S10 RR026780/RR/NCRR NIH HHS/United States ; S10 RR027425/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Humans ; Mitochondria/*metabolism ; Mitochondrial Membranes/*metabolism ; Oxidation-Reduction ; Protein Conformation ; Reactive Oxygen Species/metabolism ; *Signal Transduction ; }, abstract = {Mitochondria are the main site for generating reactive oxygen species, which are key players in diverse biological processes. However, the molecular pathways of redox signal transduction from the matrix to the cytosol are poorly defined. Here we report an inside-out redox signal of mitochondria. Cysteine oxidation of MIC60, an inner mitochondrial membrane protein, triggers the formation of disulfide bonds and the physical association of MIC60 with Miro, an outer mitochondrial membrane protein. The oxidative structural change of this membrane-crossing complex ultimately elicits cellular responses that delay mitophagy, impair cellular respiration and cause oxidative stress. Blocking the MIC60-Miro interaction or reducing either protein, genetically or pharmacologically, extends lifespan and health-span of healthy fruit flies, and benefits multiple models of Parkinson's disease and Friedreich's ataxia. Our discovery provides a molecular basis for common treatment strategies against oxidative stress.}, }
@article {pmid34498257, year = {2021}, author = {Miyake, T and Nakajima, J and Umemura, K and Onikura, N and Ueda, T and Smith, C and Kawamura, K}, title = {Genetic diversification of the Kanehira bitterling Acheilognathus rhombeus inferred from mitochondrial DNA, with comments on the phylogenetic relationship with its sister species Acheilognathus barbatulus.}, journal = {Journal of fish biology}, volume = {99}, number = {5}, pages = {1677-1695}, doi = {10.1111/jfb.14876}, pmid = {34498257}, issn = {1095-8649}, support = {12575009//Ministry of Education, Science, Sports and Culture, Japan/ ; 10041156//Ministry of Education, Science, Sports and Culture, Japan/ ; }, mesh = {Animals ; *Cypriniformes ; *DNA, Mitochondrial/genetics ; Mitochondria ; Phylogeny ; Phylogeography ; }, abstract = {The Kanehira bitterling, Acheilognathus rhombeus, is a freshwater fish, discontinuously distributed in western Japan and the Korean Peninsula. Unusually among bitterling it is an autumn-spawning species and shows developmental diapause. Consequently, the characterization of its evolutionary history is significant not only in the context of the fish assemblage of East Asia, but also for understanding life-history evolution. This study aimed to investigate the phylogeography of A. rhombeus and its sister species Acheilognathus barbatulus, distributed in China, using a mitochondrial analysis of the ND1 gene from 311 samples collected from 50 localities in Japan and continental Asia. Phylogenetic analysis revealed that A. barbatulus is included in A. rhombeus and genetically closer to Japanese A. rhombeus than to Korean A. rhombeus. Divergence of Korean A. rhombeus and A. barbatulus from Japanese A. rhombeus was estimated to be from the late Pliocene (3.44 Mya) and the early Pleistocene (1.98 Mya), respectively. Each event closely coincided with the time of the Japan Sea opening. Japanese A. rhombeus comprised seven lineages: three in Honshu and four in Kyushu. One lineage in central Kyushu was genetically closer to the Honshu lineages than to other lineages in northern Kyushu. Divergence of Japanese lineages was estimated to be from the early to middle Pleistocene (0.55-0.93 Mya), during a period of geological and paleoclimatic change, including volcanic activity. Population expansion in the late Pleistocene (<0.10 Ma) was suggested in many of the lineages, which accords with other freshwater fishes. Biogeographically the ancestral A. rhombeus/A. barbatulus was likely to have repeatedly colonized Japan from the continent through land bridges in the late Pliocene and the early Pleistocene. However, the close genetic relationship between Japanese A. rhombeus and A. barbatulus suggests another possibility, with the second colonization occurring in reverse, from Japan to China. The small genetic distance between them indicates that the colonization occurred later than colonization events of other freshwater fishes, including other bitterling species.}, }
@article {pmid34493257, year = {2021}, author = {Tůmová, P and Voleman, L and Klingl, A and Nohýnková, E and Wanner, G and Doležal, P}, title = {Inheritance of the reduced mitochondria of Giardia intestinalis is coupled to the flagellar maturation cycle.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {193}, pmid = {34493257}, issn = {1741-7007}, mesh = {Databases, Genetic ; *Giardia lamblia/genetics ; Mitochondria/genetics ; Mitochondrial Dynamics ; Organelles ; }, abstract = {BACKGROUND: The presence of mitochondria is a distinguishing feature between prokaryotic and eukaryotic cells. It is currently accepted that the evolutionary origin of mitochondria coincided with the formation of eukaryotes and from that point control of mitochondrial inheritance was required. Yet, the way the mitochondrial presence has been maintained throughout the eukaryotic cell cycle remains a matter of study. Eukaryotes control mitochondrial inheritance mainly due to the presence of the genetic component; still only little is known about the segregation of mitochondria to daughter cells during cell division. Additionally, anaerobic eukaryotic microbes evolved a variety of genomeless mitochondria-related organelles (MROs), which could be theoretically assembled de novo, providing a distinct mechanistic basis for maintenance of stable mitochondrial numbers. Here, we approach this problem by studying the structure and inheritance of the protist Giardia intestinalis MROs known as mitosomes.<br><br>RESULTS: We combined 2D stimulated emission depletion (STED) microscopy and focused ion beam scanning electron microscopy (FIB/SEM) to show that mitosomes exhibit internal segmentation and conserved asymmetric structure. From a total of about forty mitosomes, a small, privileged population is harnessed to the flagellar apparatus, and their life cycle is coordinated with the maturation cycle of G. intestinalis flagella. The orchestration of mitosomal inheritance with the flagellar maturation cycle is mediated by a microtubular connecting fiber, which physically links the privileged mitosomes to both axonemes of the oldest flagella pair and guarantees faithful segregation of the mitosomes into the daughter cells.<br><br>CONCLUSION: Inheritance of privileged Giardia mitosomes is coupled to the flagellar maturation cycle. We propose that the flagellar system controls segregation of mitochondrial organelles also in other members of this supergroup (Metamonada) of eukaryotes and perhaps reflects the original strategy of early eukaryotic cells to maintain this key organelle before mitochondrial fusion-fission dynamics cycle as observed in Metazoa was established.}, }
@article {pmid34492093, year = {2021}, author = {Phadungsaksawasdi, K and Sunantaraporn, S and Seatamanoch, N and Kongdachalert, S and Phumee, A and Kraivichian, K and Sawaswong, V and Payungporn, S and Brownell, N and Siriyasatien, P}, title = {Molecular analysis of mitochrondrial cytb of Pediculus humanus capitis in Thailand revealed potential historical connection with South Asia.}, journal = {PloS one}, volume = {16}, number = {9}, pages = {e0257024}, pmid = {34492093}, issn = {1932-6203}, mesh = {Animals ; Child ; Cytochromes b/*genetics ; Ectoparasitic Infestations/epidemiology/*genetics/parasitology ; Female ; Genetic Variation/genetics ; Haplotypes/genetics ; Human Migration ; Humans ; Lice Infestations/epidemiology/*genetics/parasitology ; Male ; Mitochondria/genetics ; Pediculus/classification/*genetics/pathogenicity ; Phylogeny ; Thailand/epidemiology ; }, abstract = {BACKGROUND: Pediculus humanus capitis or head louse is an obligate ectoparasite and its infestation remains a major public health issue worldwide. Molecular analysis divides head lice into six clades and intra-clade genetic differences have been identified. Several hypotheses have been formulated to elucidate the discrepancies of the variety of head lice among different regions of the world. It is currently concluded that head lice distribution might be associated with human migration history. This study aims to investigate genetic data of human head lice in Thailand. We believe that the analysis could help establish the correlation between local and global head lice populations.<br><br>METHOD: We investigated mitochondrial cytochrome b (cytb) gene of the collected 214 head lice to evaluate genetic diversity from 15 provinces among 6 regions of Thailand. The head lice genes were added to the global pool for the phylogenetic tree, Bayesian tree, Skyline plot, and median joining network construction. The biodiversity, neutrality tests, and population genetic differentiation among the 6 Thailand geographic regions were analyzed by DNAsp version 6.<br><br>RESULTS: The phylogenetic tree analysis of 214 collected head lice are of clade A and clade C accounting for roughly 65% and 35% respectively. The Bayesian tree revealed a correlation of clade diversification and ancient human dispersal timeline. In Thailand, clade A is widespread in the country. Clade C is confined to only the Central, Southern, and Northeastern regions. We identified 50 novel haplotypes. Statistical analysis showed congruent results between genetic differentiation and population migration especially with South Asia.<br><br>CONCLUSIONS: Pediculosis remains problematic among children in the rural areas in Thailand. Cytb gene analysis of human head lice illustrated clade distribution and intra-clade diversity of different areas. Our study reported novel haplotypes of head lice in Thailand. Moreover, the statistic calculation provided a better understanding of their relationship with human, as an obligate human parasite and might help provide a better insight into the history of human population migration. Determination of the correlation between phylogenetic data and pediculicide resistance gene as well as residing bacteria are of interest for future studies.}, }
@article {pmid34490275, year = {2021}, author = {Moroz, LL and Romanova, DY}, title = {Selective Advantages of Synapses in Evolution.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {726563}, pmid = {34490275}, issn = {2296-634X}, }
@article {pmid34481840, year = {2021}, author = {Montes de Oca Balderas, P}, title = {Mitochondria-plasma membrane interactions and communication.}, journal = {The Journal of biological chemistry}, volume = {297}, number = {4}, pages = {101164}, pmid = {34481840}, issn = {1083-351X}, mesh = {Animals ; Cell Membrane/*metabolism ; Humans ; Mitochondria/*metabolism ; }, abstract = {Mitochondria are known as the powerhouses of eukaryotic cells; however, they perform many other functions besides oxidative phosphorylation, including Ca[2+] homeostasis, lipid metabolism, antiviral response, and apoptosis. Although other hypotheses exist, mitochondria are generally thought as descendants of an α-proteobacteria that adapted to the intracellular environment within an Asgard archaebacteria, which have been studied for decades as an organelle subdued by the eukaryotic cell. Nevertheless, several early electron microscopy observations hinted that some mitochondria establish specific interactions with certain plasma membrane (PM) domains in mammalian cells. Furthermore, recent findings have documented the direct physical and functional interaction of mitochondria and the PM, the organization of distinct complexes, and their communication through vesicular means. In yeast, some molecular players mediating this interaction have been elucidated, but only a few works have studied this interaction in mammalian cells. In addition, mitochondria can be translocated among cells through tunneling nanotubes or by other mechanisms, and free, intact, functional mitochondria have been reported in the blood plasma. Together, these findings challenge the conception of mitochondria as organelles subdued by the eukaryotic cell. This review discusses the evidence of the mitochondria interaction with the PM that has been long disregarded despite its importance in cell function, pathogenesis, and evolution. It also proposes a scheme of mitochondria-PM interactions with the intent to promote research and knowledge of this emerging pathway that promises to shift the current paradigms of cell biology.}, }
@article {pmid34447743, year = {2021}, author = {Mahapatra, K and Banerjee, S and De, S and Mitra, M and Roy, P and Roy, S}, title = {An Insight Into the Mechanism of Plant Organelle Genome Maintenance and Implications of Organelle Genome in Crop Improvement: An Update.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {671698}, pmid = {34447743}, issn = {2296-634X}, abstract = {Besides the nuclear genome, plants possess two small extra chromosomal genomes in mitochondria and chloroplast, respectively, which contribute a small fraction of the organelles' proteome. Both mitochondrial and chloroplast DNA have originated endosymbiotically and most of their prokaryotic genes were either lost or transferred to the nuclear genome through endosymbiotic gene transfer during the course of evolution. Due to their immobile nature, plant nuclear and organellar genomes face continuous threat from diverse exogenous agents as well as some reactive by-products or intermediates released from various endogenous metabolic pathways. These factors eventually affect the overall plant growth and development and finally productivity. The detailed mechanism of DNA damage response and repair following accumulation of various forms of DNA lesions, including single and double-strand breaks (SSBs and DSBs) have been well documented for the nuclear genome and now it has been extended to the organelles also. Recently, it has been shown that both mitochondria and chloroplast possess a counterpart of most of the nuclear DNA damage repair pathways and share remarkable similarities with different damage repair proteins present in the nucleus. Among various repair pathways, homologous recombination (HR) is crucial for the repair as well as the evolution of organellar genomes. Along with the repair pathways, various other factors, such as the MSH1 and WHIRLY family proteins, WHY1, WHY2, and WHY3 are also known to be involved in maintaining low mutation rates and structural integrity of mitochondrial and chloroplast genome. SOG1, the central regulator in DNA damage response in plants, has also been found to mediate endoreduplication and cell-cycle progression through chloroplast to nucleus retrograde signaling in response to chloroplast genome instability. Various proteins associated with the maintenance of genome stability are targeted to both nuclear and organellar compartments, establishing communication between organelles as well as organelles and nucleus. Therefore, understanding the mechanism of DNA damage repair and inter compartmental crosstalk mechanism in various sub-cellular organelles following induction of DNA damage and identification of key components of such signaling cascades may eventually be translated into strategies for crop improvement under abiotic and genotoxic stress conditions. This review mainly highlights the current understanding as well as the importance of different aspects of organelle genome maintenance mechanisms in higher plants.}, }
@article {pmid34447361, year = {2021}, author = {Rolland, C and Andreani, J and Sahmi-Bounsiar, D and Krupovic, M and La Scola, B and Levasseur, A}, title = {Clandestinovirus: A Giant Virus With Chromatin Proteins and a Potential to Manipulate the Cell Cycle of Its Host Vermamoeba vermiformis.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {715608}, pmid = {34447361}, issn = {1664-302X}, abstract = {For several decades, the vast world of DNA viruses has been expanding constantly. Various discoveries in this field have broadened our knowledge and revealed that DNA viruses encode many functional features, which were once thought to be exclusive to cellular life. Here, we report the isolation of a giant virus named "clandestinovirus," grown on the amoebal host Vermamoeba vermiformis. This virus was discovered in a mixed co-culture associated with another giant virus, Faustovirus ST1. Clandestinovirus possesses a linear dsDNA genome of 581,987 base pairs containing 617 genes. Phylogenetically, clandestinovirus is most closely related to Acanthamoeba castellanii medusavirus and was considered a member of the proposed Medusaviridae family. However, clandestinovirus genome is 65% larger than that of medusavirus, emphasizing the considerable genome size variation within this virus family. Functional annotation of the clandestinovirus genes suggests that the virus encodes four core histones. Furthermore, clandestinovirus appears to orchestrate the cell cycle and mitochondrial activities of the infected host by virtue of encoding a panel of protein kinases and phosphatases, and a suite of functionally diverse mitochondrial protein homologs, respectively. Collectively, these observations illuminate a strategy employed by clandestinovirus to optimize the intracellular environment for efficient virus propagation.}, }
@article {pmid34446347, year = {2021}, author = {Satoh, T}, title = {Bird evolution by insulin resistance.}, journal = {Trends in endocrinology and metabolism: TEM}, volume = {32}, number = {10}, pages = {803-813}, doi = {10.1016/j.tem.2021.07.007}, pmid = {34446347}, issn = {1879-3061}, mesh = {Animals ; Birds/metabolism ; Humans ; *Insulin Resistance/genetics ; *Insulins ; Kelch-Like ECH-Associated Protein 1 ; NF-E2-Related Factor 2 ; Oxygen ; Reactive Oxygen Species/metabolism ; }, abstract = {Drift of oxygen concentrations in the atmosphere was one of the main drivers of the evolution of vertebrates. The drop in oxygen concentrations at the Permian-Triassic (PT) boundary may have been the biggest challenge to vertebrates. This hypoxic condition forced theropods to lose certain genes to maximize their efficiency of oxygen usage. Recent studies show that omentin and insulin-sensitive glucose transporter 4 (GLUT4) are missing in the bird genome. Since these gene products play essential roles in maintaining insulin sensitivity, this loss forced theropods to become insulin resistant. Insulin resistance may have been the key to allowing theropods to become hyperathletic under hypoxic conditions and to outcompete mammals during the Triassic period. A second challenge was the gradual increase in oxygen concentrations during the late Jurassic, Cretaceous, and Tertiary periods when reactive oxygen species (ROS) leakage from mitochondria became a problem. Since the simplest solution was the expansion of body size, some theropods became bigger to reduce ROS leakage per volume. Another solution was the development of a constitutively active countermeasure against ROS. A recent study shows that Neoaves have constitutively active nuclear factor erythroid 2-related factor 2 (NRF2) due to deletion of the C-terminal part of the KEAP1 protein, thus allowing Neoaves to express antioxidant enzymes to overcome ROS leakage.}, }
@article {pmid34442643, year = {2021}, author = {Kwak, Y}, title = {An Update on Trichoderma Mitogenomes: Complete De Novo Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma harzianum (Hypocreales, Sordariomycetes), an Ex-Neotype Strain CBS 226.95, and Tracing the Evolutionary Divergences of Mitogenomes in Trichoderma.}, journal = {Microorganisms}, volume = {9}, number = {8}, pages = {}, pmid = {34442643}, issn = {2076-2607}, support = {NRF-2018R1D1A1B07043042, NRF-2021R1I1A1A01042148//National Research Foundation of Korea/ ; }, abstract = {Members of the genus Trichoderma (Hypocreales), widely used as biofungicides, biofertilizers, and as model fungi for the industrial production of CAZymes, have actively been studied for the applications of their biological functions. Recently, the study of the nuclear genomes of Trichoderma has expanded in the directions of adaptation and evolution to gain a better understanding of their ecological traits. However, Trichoderma's mitochondria have received much less attention despite mitochondria being the most necessary element for sustaining cell life. In this study, a mitogenome of the fungus Trichoderma harzianum CBS 226.95 was assembled de novo. A 27,632 bp circular DNA molecule was revealed with specific features, such as the intronless of all core PCGs, one homing endonuclease, and a putative overlapping tRNA, on a closer phylogenetic relationship with T. reesei among hypocrealean fungi. Interestingly, the mitogenome of T. harzianum CBS 226.95 was predicted to have evolved earlier than those of other Trichoderma species and also assumed with a selection pressure in the cox3. Considering the bioavailability, both for the ex-neotype strain of the T. harzianum species complex and the most globally representative commercial fungal biocontrol agent, our results on the T. harzianum CBS 226.95 mitogenome provide crucial information which will be helpful criteria in future studies on Trichoderma.}, }
@article {pmid34440385, year = {2021}, author = {Stewart, DT and Robicheau, BM and Youssef, N and Garrido-Ramos, MA and Chase, EE and Breton, S}, title = {Expanding the Search for Sperm Transmission Elements in the Mitochondrial Genomes of Bivalve Mollusks.}, journal = {Genes}, volume = {12}, number = {8}, pages = {}, pmid = {34440385}, issn = {2073-4425}, mesh = {Animals ; Bivalvia/*genetics ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; Inheritance Patterns ; Male ; Spermatozoa/*physiology ; }, abstract = {Doubly uniparental inheritance (DUI) of mitochondrial DNA (mtDNA) in bivalve mollusks is one of the most notable departures from the paradigm of strict maternal inheritance of mtDNA among metazoans. Recently, work on the Mediterranean mussel Mytilus galloprovincialis suggested that a nucleotide motif in the control region of this species, known as the sperm transmission element (STE), helps protect male-transmitted mitochondria from destruction during spermatogenesis. Subsequent studies found similar, yet divergent, STE motifs in other marine mussels. Here, we extend the in silico search for mtDNA signatures resembling known STEs. This search is carried out for the large unassigned regions of 157 complete mitochondrial genomes from within the Mytiloida, Veneroida, Unionoida, and Ostreoida bivalve orders. Based on a sliding window approach, we present evidence that there are additional putative STE signatures in the large unassigned regions of several marine clams and freshwater mussels with DUI. We discuss the implications of this finding for interpreting the origin of doubly uniparental inheritance in ancestral bivalve mollusks, as well as potential future in vitro and in silico studies that could further refine our understanding of the early evolution of this unusual system of mtDNA inheritance.}, }
@article {pmid34436602, year = {2021}, author = {Petrů, M and Dohnálek, V and Füssy, Z and Doležal, P}, title = {Fates of Sec, Tat, and YidC Translocases in Mitochondria and Other Eukaryotic Compartments.}, journal = {Molecular biology and evolution}, volume = {38}, number = {12}, pages = {5241-5254}, pmid = {34436602}, issn = {1537-1719}, mesh = {*Escherichia coli Proteins/genetics ; *Eukaryota/genetics/metabolism ; Evolution, Molecular ; Membrane Transport Proteins/genetics/metabolism ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Protein Transport ; }, abstract = {Formation of mitochondria by the conversion of a bacterial endosymbiont was a key moment in the evolution of eukaryotes. It was made possible by outsourcing the endosymbiont's genetic control to the host nucleus, while developing the import machinery for proteins synthesized on cytosolic ribosomes. The original protein export machines of the nascent organelle remained to be repurposed or were completely abandoned. This review follows the evolutionary fates of three prokaryotic inner membrane translocases Sec, Tat, and YidC. Homologs of all three translocases can still be found in current mitochondria, but with different importance for mitochondrial function. Although the mitochondrial YidC homolog, Oxa1, became an omnipresent independent insertase, the other two remained only sporadically present in mitochondria. Only a single substrate is known for the mitochondrial Tat and no function has yet been assigned for the mitochondrial Sec. Finally, this review compares these ancestral mitochondrial proteins with their paralogs operating in the plastids and the endomembrane system.}, }
@article {pmid34428409, year = {2021}, author = {Cooper, LN}, title = {Metabolism: Evolution of dolphin sperm endurance.}, journal = {Current biology : CB}, volume = {31}, number = {16}, pages = {R1006-R1008}, doi = {10.1016/j.cub.2021.06.075}, pmid = {34428409}, issn = {1879-0445}, mesh = {Animals ; *Dolphins ; Glycolysis ; Male ; Mammals ; Mitochondria ; Spermatozoa ; }, abstract = {Mammalian sperm have long been known to use energy derived from the metabolism of sugars and fatty acids. A new study shows that sperm of dolphins and their relatives lost functionality of the glycolysis pathway and are fueled only by energy-rich fatty acids that are metabolized by extra-large mitochondria, giving them exceptional endurance.}, }
@article {pmid34419587, year = {2021}, author = {Lyra, GM and Iha, C and Grassa, CJ and Cai, L and Zhang, H and Lane, C and Blouin, N and Oliveira, MC and Nunes, JMC and Davis, CC}, title = {Phylogenomics, divergence time estimation and trait evolution provide a new look into the Gracilariales (Rhodophyta).}, journal = {Molecular phylogenetics and evolution}, volume = {165}, number = {}, pages = {107294}, doi = {10.1016/j.ympev.2021.107294}, pmid = {34419587}, issn = {1095-9513}, mesh = {Genes, Mitochondrial ; *Gracilaria/genetics ; Phylogeny ; Plastids/genetics ; *Rhodophyta/genetics ; }, abstract = {The Gracilariales is a highly diverse, widely distributed order of red algae (Rhodophyta) that forms a well-supported clade. Aside from their ecological importance, species of Gracilariales provide important sources of agarans and possess bioactive compounds with medicinal and pharmaceutical use. Recent phylogenetic analyses from a small number of genes have greatly advanced our knowledge of evolutionary relationships in this clade, yet several key nodes were not especially well resolved. We assembled a phylogenomic data set containing 79 nuclear genes, 195 plastid genes, and 24 mitochondrial genes from species representing all three major Gracilariales lineages, including: Melanthalia, Gracilariopsis, and Gracilaria sensu lato. This data set leads to a fully-resolved phylogeny of Gracilariales, which is highly-consistent across genomic compartments. In agreement with previous findings, Melanthalia obtusata was sister to a clade including Gracilaria s.l. and Gracilariopsis, which were each resolved as well-supported clades. Our results also clarified the long-standing uncertainty about relationships in Gracilaria s.l., not resolved in single and multi-genes approaches. We further characterized the divergence time, organellar genome architecture, and morphological trait evolution in Gracilarales to better facilitate its taxonomic treatment. Gracilariopsis and Gracilaria s.l. are comparable taxonomic ranks, based on the overlapping time range of their divergence. The genomic structure of plastid and mitochondria is highly conserved within each clade but differs slightly among these clades in gene contents. For example, the plastid gene petP is lost in Gracilaria s.l. and the mitochondrial gene trnH is in different positions in the genome of Gracilariopsis and Gracilaria s.l. Our analyses of ancestral character evolution provide evidence that the main characters used to delimitate genera in Gracilariales, such as spermatangia type and features of the cystocarp's anatomy, overlap in subclades of Gracilaria s.l. We discuss the taxonomy of Gracilariales in light of these results and propose an objective and practical classification, which is in agreement with the criteria of monophyly, exclusive characters, predictability and nomenclatural stability.}, }
@article {pmid34418213, year = {2021}, author = {Jakovlić, I and Zou, H and Chen, JH and Lei, HP and Wang, GT and Liu, J and Zhang, D}, title = {Slow crabs - fast genomes: Locomotory capacity predicts skew magnitude in crustacean mitogenomes.}, journal = {Molecular ecology}, volume = {30}, number = {21}, pages = {5488-5502}, doi = {10.1111/mec.16138}, pmid = {34418213}, issn = {1365-294X}, support = {BP0719040//International Collaboration 111 Programme/ ; 31970408//National Natural Science Foundation of China/ ; lzujbky-2019//Fundamental Research Funds for the Central Universities/ ; XDB31010300//Strategic Priority Research Program of Chinese Academy of Sciences/ ; 561120206//Start-up Funds of Introduced Talent in Lanzhou University/ ; }, mesh = {Animals ; Base Composition ; *Brachyura ; Evolution, Molecular ; *Genome, Mitochondrial/genetics ; Mutation ; Phylogeny ; }, abstract = {Base composition skews (G-C/G+C) of mitochondrial genomes are believed to be primarily driven by mutational pressure, which is positively correlated with metabolic rate. In marine animals, metabolic rate is also positively correlated with locomotory capacity. Given the central role of mitochondria in energy metabolism, we hypothesised that selection for locomotory capacity should be positively correlated with the strength of purifying selection (dN/dS), and thus be negatively correlated with the skew magnitude. Therefore, these two models assume diametrically opposite associations between the metabolic rate and skew magnitude: positive correlation in the prevailing paradigm, and negative in our working hypothesis. We examined correlations between the skew magnitude, metabolic rate, locomotory capacity, and several other variables previously associated with mitochondrial evolution on 287 crustacean mitogenomes. Weakly locomotory taxa had higher skew magnitude and ω (dN/dS) values, but not the gene order rearrangement rate. Skew and ω magnitudes were correlated. Multilevel regression analyses indicated that three competing variables, body size, gene order rearrangement rate, and effective population size, had negligible impacts on the skew magnitude. In most crustacean lineages selection for locomotory capacity appears to be the primary factor determining the skew magnitude. Contrary to the prevailing paradigm, this implies that adaptive selection outweighs nonadaptive selection (mutation pressure) in crustaceans. However, we found indications that effective population size (nonadaptive factor) may outweigh the impact of locomotory capacity in sessile crustaceans (Thecostraca). In conclusion, skew magnitude is a product of the interplay between adaptive and nonadaptive factors, the balance of which varies among lineages.}, }
@article {pmid34417525, year = {2021}, author = {Jenkins, EC and O'Connell, MJ and Manfredi, G and Germain, D}, title = {Doxycycline promotes proteasome fitness in the central nervous system.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {17003}, pmid = {34417525}, issn = {2045-2322}, support = {R01 NS084486/NS/NINDS NIH HHS/United States ; R01 GM124079/GM/NIGMS NIH HHS/United States ; R01 NS062055/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Central Nervous System/drug effects/*metabolism ; Cyclic AMP/metabolism ; Doxycycline/*pharmacology ; Estrogen Receptor alpha/metabolism ; Female ; Gene Expression Regulation/drug effects ; Male ; Mice ; Proteasome Endopeptidase Complex/genetics/*metabolism ; Saccharomyces cerevisiae/metabolism ; Transcription, Genetic/drug effects ; Unfolded Protein Response/drug effects ; }, abstract = {Several studies reported that mitochondrial stress induces cytosolic proteostasis in yeast and C. elegans. Notably, inhibition of mitochondrial translation with doxcycyline decreases the toxicity of β-amyloid aggregates, in a C. elegans. However, how mitochondrial stress activates cytosolic proteostasis remains unclear. Further whether doxycycline has this effect in mammals and in disease relevant tissues also remains unclear. We show here that doxycycline treatment in mice drastically reduces the accumulation of proteins destined for degradation by the proteasome in a CNS region-specific manner. This effect is associated with the activation of the ERα axis of the mitochondrial unfolded protein response (UPR[mt]), in both males and females. However, sexually dimorphic mechanisms of proteasome activation were observed. Doxycycline also activates the proteasome in fission yeast, where ERα is not expressed. Rather, the ancient ERα-coactivator Mms19 regulates this response in yeast. Our results suggest that the UPR[mt] initiates a conserved mitochondria-to-cytosol stress signal, resulting in proteasome activation, and that this signal has adapted during evolution, in a sex and tissue specific-manner. Therefore, while our results support the use of doxycycline in the prevention of proteopathic diseases, they also indicate that sex is an important variable to consider in the design of future clinical trials using doxycycline.}, }
@article {pmid34410224, year = {2021}, author = {Bandini, G and Damerow, S and Sempaio Guther, ML and Guo, H and Mehlert, A and Paredes Franco, JC and Beverley, S and Ferguson, MA}, title = {An essential, kinetoplastid-specific GDP-Fuc: β-D-Gal α-1,2-fucosyltransferase is located in the mitochondrion of Trypanosoma brucei.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34410224}, issn = {2050-084X}, support = {/WT_/Wellcome Trust/United Kingdom ; 101842/WT_/Wellcome Trust/United Kingdom ; R01 AI031078/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Cloning, Molecular ; Fucosyltransferases/genetics/*metabolism ; Gene Expression Regulation, Enzymologic ; Humans ; Mitochondria/*enzymology ; Phylogeny ; Trypanosoma brucei brucei/enzymology/*metabolism ; Galactoside 2-alpha-L-fucosyltransferase ; }, abstract = {Fucose is a common component of eukaryotic cell-surface glycoconjugates, generally added by Golgi-resident fucosyltransferases. Whereas fucosylated glycoconjugates are rare in kinetoplastids, the biosynthesis of the nucleotide sugar GDP-Fuc has been shown to be essential in Trypanosoma brucei. Here we show that the single identifiable T. brucei fucosyltransferase (TbFUT1) is a GDP-Fuc: β-D-galactose α-1,2-fucosyltransferase with an apparent preference for a Galβ1,3GlcNAcβ1-O-R acceptor motif. Conditional null mutants of TbFUT1 demonstrated that it is essential for both the mammalian-infective bloodstream form and the insect vector-dwelling procyclic form. Unexpectedly, TbFUT1 was localized in the mitochondrion of T. brucei and found to be required for mitochondrial function in bloodstream form trypanosomes. Finally, the TbFUT1 gene was able to complement a Leishmania major mutant lacking the homologous fucosyltransferase gene (Guo et al., 2021). Together these results suggest that kinetoplastids possess an unusual, conserved and essential mitochondrial fucosyltransferase activity that may have therapeutic potential across trypanosomatids.}, }
@article {pmid34409658, year = {2021}, author = {Karia, P and Yoshioka, K and Moeder, W}, title = {Multiple phosphorylation events of the mitochondrial membrane protein TTM1 regulate cell death during senescence.}, journal = {The Plant journal : for cell and molecular biology}, volume = {108}, number = {3}, pages = {766-780}, doi = {10.1111/tpj.15470}, pmid = {34409658}, issn = {1365-313X}, mesh = {Abscisic Acid/metabolism/pharmacology ; Acid Anhydride Hydrolases/genetics/*metabolism ; Arabidopsis/*cytology/drug effects/*physiology ; Arabidopsis Proteins/genetics/*metabolism ; Cell Death ; Darkness ; Mitochondrial Proteins/genetics/metabolism ; Mitogen-Activated Protein Kinase Kinases/metabolism ; Phosphorylation ; Plant Leaves/drug effects/metabolism ; Plant Senescence/*physiology ; Plants, Genetically Modified ; Serine/metabolism ; }, abstract = {The role of mitochondria in programmed cell death (PCD) during animal growth and development is well documented, but much less is known for plants. We previously showed that the Arabidopsis thaliana triphosphate tunnel metalloenzyme (TTM) proteins TTM1 and TTM2 are tail-anchored proteins that localize in the mitochondrial outer membrane and participate in PCD during senescence and immunity, respectively. Here, we show that TTM1 is specifically involved in senescence induced by abscisic acid (ABA). Moreover, phosphorylation of TTM1 by multiple mitogen-activated protein (MAP) kinases regulates its function and turnover. A combination of proteomics and in vitro kinase assays revealed three major phosphorylation sites of TTM1 (Ser10, Ser437, and Ser490). Ser437, which is phosphorylated upon perception of senescence cues such as ABA and prolonged darkness, is phosphorylated by the MAP kinases MPK3 and MPK4, and Ser437 phosphorylation is essential for TTM1 function in senescence. These MPKs, together with three additional MAP kinases (MPK1, MPK7, and MPK6), also phosphorylate Ser10 and Ser490, marking TTM1 for protein turnover, which likely prevents uncontrolled cell death. Taken together, our results show that multiple MPKs regulate the function and turnover of the mitochondrial protein TTM1 during senescence-associated cell death, revealing a novel link between mitochondria and PCD.}, }
@article {pmid34407123, year = {2021}, author = {Su, HJ and Liang, SL and Nickrent, DL}, title = {Plastome variation and phylogeny of Taxillus (Loranthaceae).}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0256345}, pmid = {34407123}, issn = {1932-6203}, mesh = {DNA, Ribosomal/chemistry/classification/metabolism ; Evolution, Molecular ; Genome, Plastid ; Loranthaceae/*classification/genetics ; Mitochondria/genetics ; NADH Dehydrogenase/classification/genetics ; Phylogeny ; Plastids/*genetics ; RNA, Transfer/genetics ; Ribosomal Proteins/classification/genetics ; }, abstract = {Several molecular phylogenetic studies of the mistletoe family Loranthaceae have been published such that now the general pattern of relationships among the genera and their biogeographic histories are understood. Less is known about species relationships in the larger (> 10 species) genera. This study examines the taxonomically difficult genus Taxillus composed of 35-40 Asian species. The goal was to explore the genetic diversity present in Taxillus plastomes, locate genetically variable hotspots, and test these for their utility as potential DNA barcodes. Using genome skimming, complete plastomes, as well as nuclear and mitochondrial rDNA sequences, were newly generated for eight species. The plastome sequences were used in conjunction with seven publicly available Taxillus sequences and three sequences of Scurrula, a close generic relative. The Taxillus plastomes ranged from 121 to 123 kbp and encoded 90-93 plastid genes. In addition to all of the NADH dehydrogenase complex genes, four ribosomal genes, infA and four intron-containing tRNA genes were lost or pseudogenized in all of the Taxillus and Scurrula plastomes. The topologies of the plastome, mitochondrial rDNA and nuclear rDNA trees were generally congruent, though with discordance at the position of T. chinensis. Several variable regions in the plastomes were identified that have sufficient numbers of parsimony informative sites as to recover the major clades seen in the complete plastome tree. Instead of generating complete plastome sequences, our study showed that accD alone or the concatenation of accD and rbcL can be used in future studies to facilitate identification of Taxillus samples and to generate a molecular phylogeny with robust sampling within the genus.}, }
@article {pmid34403637, year = {2021}, author = {Bettinazzi, S and Milani, L and Blier, PU and Breton, S}, title = {Bioenergetic consequences of sex-specific mitochondrial DNA evolution.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1957}, pages = {20211585}, pmid = {34403637}, issn = {1471-2954}, mesh = {Animals ; *Bivalvia/genetics ; DNA, Mitochondrial/genetics ; Female ; *Genome, Mitochondrial ; Male ; Mitochondria/genetics ; Oxidative Phosphorylation ; }, abstract = {Doubly uniparental inheritance (DUI) represents a notable exception to the general rule of strict maternal inheritance (SMI) of mitochondria in metazoans. This system entails the coexistence of two mitochondrial lineages (F- and M-type) transmitted separately through oocytes and sperm, thence providing an unprecedented opportunity for the mitochondrial genome to evolve adaptively for male functions. In this study, we explored the impact of a sex-specific mitochondrial evolution upon gamete bioenergetics of DUI and SMI bivalve species, comparing the activity of key enzymes of glycolysis, fermentation, fatty acid metabolism, tricarboxylic acid cycle, oxidative phosphorylation and antioxidant metabolism. Our findings suggest reorganized bioenergetic pathways in DUI gametes compared to SMI gametes. This generally results in a decreased enzymatic capacity in DUI sperm with respect to DUI oocytes, a limitation especially prominent at the terminus of the electron transport system. This bioenergetic remodelling fits a reproductive strategy that does not require high energy input and could potentially link with the preservation of the paternally transmitted mitochondrial genome in DUI species. Whether this phenotype may derive from positive or relaxed selection acting on DUI sperm is still uncertain.}, }
@article {pmid34402879, year = {2021}, author = {Muthye, V and Lavrov, DV}, title = {Multiple Losses of MSH1, Gain of mtMutS, and Other Changes in the MutS Family of DNA Repair Proteins in Animals.}, journal = {Genome biology and evolution}, volume = {13}, number = {9}, pages = {}, pmid = {34402879}, issn = {1759-6653}, mesh = {Animals ; DNA Repair ; DNA-Binding Proteins/genetics/metabolism ; Fungal Proteins/genetics ; MutS DNA Mismatch-Binding Protein/genetics/metabolism ; Saccharomyces cerevisiae/genetics ; *Saccharomyces cerevisiae Proteins/genetics ; }, abstract = {MutS is a key component of the mismatch repair (MMR) pathway. Members of the MutS protein family are present in prokaryotes, eukaryotes, and viruses. Six MutS homologs (MSH1-6) have been identified in yeast, of which three function in nuclear MMR, while MSH1 functions in mitochondrial DNA repair. MSH proteins are believed to be well conserved in animals, except for MSH1-which is thought to be lost. Two intriguing exceptions to this general picture have been found, both in the class Anthozoa within the phylum Cnidaria. First, an ortholog of the yeast-MSH1 was reported in one hexacoral species. Second, a MutS homolog (mtMutS) has been found in the mitochondrial genome of all octocorals. To understand the origin and potential functional implications of these exceptions, we investigated the evolution of the MutS family both in Cnidaria and in animals in general. Our study confirmed the acquisition of octocoral mtMutS by horizontal gene transfer from a giant virus. Surprisingly, we identified MSH1 in all hexacorals and several sponges and placozoans. By contrast, MSH1 orthologs were lacking in other cnidarians, ctenophores, and bilaterian animals. Furthermore, while we identified MSH2 and MSH6 in nearly all animals, MSH4, MSH5, and, especially, MSH3 were missing in multiple species. Overall, our analysis revealed a dynamic evolution of the MutS family in animals, with multiple losses of MSH1, MSH3, some losses of MSH4 and MSH5, and a gain of the octocoral mtMutS. We propose that octocoral mtMutS functionally replaced MSH1 that was present in the common ancestor of Anthozoa.}, }
@article {pmid34397090, year = {2021}, author = {Kowalczyk, A and Gbadamosi, O and Kolor, K and Sosa, J and Andrzejczuk, L and Gibson, G and St Croix, C and Chikina, M and Aizenman, E and Clark, N and Kiselyov, K}, title = {Evolutionary rate covariation identifies SLC30A9 (ZnT9) as a mitochondrial zinc transporter.}, journal = {The Biochemical journal}, volume = {478}, number = {17}, pages = {3205-3220}, pmid = {34397090}, issn = {1470-8728}, support = {R01 HG009299/HG/NHGRI NIH HHS/United States ; R21 NS111944/NS/NINDS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Carrier Proteins/*genetics/*metabolism ; Cation Transport Proteins/*genetics/*metabolism ; Cell Cycle Proteins/*genetics/*metabolism ; Computational Biology/*methods ; *Evolution, Molecular ; Gene Knockdown Techniques ; HeLa Cells ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/metabolism ; Phylogeny ; Signal Transduction/*genetics ; Transcription Factors/*genetics/*metabolism ; Transfection ; Whole Genome Sequencing/methods ; Zinc/metabolism ; }, abstract = {Recent advances in genome sequencing have led to the identification of new ion and metabolite transporters, many of which have not been characterized. Due to the variety of subcellular localizations, cargo and transport mechanisms, such characterization is a daunting task, and predictive approaches focused on the functional context of transporters are very much needed. Here we present a case for identifying a transporter localization using evolutionary rate covariation (ERC), a computational approach based on pairwise correlations of amino acid sequence evolutionary rates across the mammalian phylogeny. As a case study, we find that poorly characterized transporter SLC30A9 (ZnT9) coevolves with several components of the mitochondrial oxidative phosphorylation chain, suggesting mitochondrial localization. We confirmed this computational finding experimentally using recombinant human SLC30A9. SLC30A9 loss caused zinc mishandling in the mitochondria, suggesting that under normal conditions it acts as a zinc exporter. We therefore propose that ERC can be used to predict the functional context of novel transporters and other poorly characterized proteins.}, }
@article {pmid34397079, year = {2021}, author = {Wang, T and He, T and Ding, X and Zhang, Q and Yang, L and Nie, Z and Zhao, T and Gai, J and Yang, S}, title = {Confirmation of GmPPR576 as a fertility restorer gene of cytoplasmic male sterility in soybean.}, journal = {Journal of experimental botany}, volume = {72}, number = {22}, pages = {7729-7742}, doi = {10.1093/jxb/erab382}, pmid = {34397079}, issn = {1460-2431}, mesh = {Cytoplasm ; Fertility/genetics ; Phylogeny ; *Plant Infertility/genetics ; *Glycine max/genetics ; }, abstract = {In soybean, heterosis achieved through the three-line system has been gradually applied in breeding to increase yield, but the underlying molecular mechanism remains unknown. We conducted a genetic analysis using the pollen fertility of offspring of the cross NJCMS1A×NJCMS1C. All the pollen of F1 plants was semi-sterile; in F2, the ratio of pollen-fertile plants to pollen-semi-sterile plants was 208:189. This result indicates that NJCMS1A is gametophyte sterile, and the fertility restoration of NJCMS1C to NJCMS1A is a quality trait controlled by a single gene locus. Using bulked segregant analysis, the fertility restorer gene Rf in NJCMS1C was located on chromosome 16 between the markers BARCSOYSSR_16_1067 and BARCSOYSSR_16_1078. Sequence analysis of genes in that region showed that GmPPR576 was non-functional in rf cultivars. GmPPR576 has one functional allele in Rf cultivars but three non-functional alleles in rf cultivars. Phylogenetic analysis showed that the GmPPR576 locus evolved rapidly with the presence of male-sterile cytoplasm. GmPPR576 belongs to the RFL fertility restorer gene family and is targeted to the mitochondria. GmPPR576 was knocked out in soybean N8855 using CRISPR/Cas9. The T1 plants showed sterile pollen, and T2 plants produced few pods at maturity. The results indicate that GmPPR576 is the fertility restorer gene of NJCMS1A.}, }
@article {pmid34390927, year = {2021}, author = {Calderon, RH and Strand, &#xc5;}, title = {How retrograde signaling is intertwined with the evolution of photosynthetic eukaryotes.}, journal = {Current opinion in plant biology}, volume = {63}, number = {}, pages = {102093}, doi = {10.1016/j.pbi.2021.102093}, pmid = {34390927}, issn = {1879-0356}, mesh = {Biological Evolution ; *Eukaryota ; Photosynthesis/genetics ; Phylogeny ; *Plastids/genetics ; Symbiosis/genetics ; }, abstract = {Chloroplasts and mitochondria evolved from free-living prokaryotic organisms that entered the eukaryotic cell through endosymbiosis. The gradual conversion from endosymbiont to organelle during the course of evolution was accompanied by the development of a communication system between the host and the endosymbiont, referred to as retrograde signaling or organelle-to-nucleus signaling. In higher plants, plastid-to-nucleus signaling involves multiple signaling pathways necessary to coordinate plastid function and cellular responses to developmental and environmental stimuli. Phylogenetic reconstructions using sequence information from evolutionarily diverse photosynthetic eukaryotes have begun to provide information about how retrograde signaling pathways were adopted and modified in different lineages over time. A tight communication system was likely a major facilitator of plants conquest of the land because it would have enabled the algal ancestors of land plants to better allocate their cellular resources in response to high light and desiccation, the major stressor for streptophyte algae in a terrestrial habitat. In this review, we aim to give an evolutionary perspective on plastid-to-nucleus signaling.}, }
@article {pmid34388986, year = {2021}, author = {Morrow, JL and Riegler, M}, title = {Genome analyses of four Wolbachia strains and associated mitochondria of Rhagoletis cerasi expose cumulative modularity of cytoplasmic incompatibility factors and cytoplasmic hitchhiking across host populations.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {616}, pmid = {34388986}, issn = {1471-2164}, mesh = {Animals ; Biological Evolution ; Cytoplasm ; Humans ; Mitochondria ; Symbiosis/genetics ; *Tephritidae ; *Wolbachia/genetics ; }, abstract = {BACKGROUND: The endosymbiont Wolbachia can manipulate arthropod reproduction and invade host populations by inducing cytoplasmic incompatibility (CI). Some host species are coinfected with multiple Wolbachia strains which may have sequentially invaded host populations by expressing different types of modular CI factor (cif) genes. The tephritid fruit fly Rhagoletis cerasi is a model for CI and Wolbachia population dynamics. It is associated with at least four Wolbachia strains in various combinations, with demonstrated (wCer2, wCer4), predicted (wCer1) or unknown (wCer5) CI phenotypes.<br><br>RESULTS: We sequenced and assembled the draft genomes of the Wolbachia strains wCer1, wCer4 and wCer5, and compared these with the previously sequenced genome of wCer2 which currently invades R. cerasi populations. We found complete cif gene pairs in all strains: four pairs in wCer2 (three Type I; one Type V), two pairs in wCer1 (both Type I) and wCer4 (one Type I; one Type V), and one pair in wCer5 (Type IV). Wolbachia genome variant analyses across geographically and genetically distant host populations revealed the largest diversity of single nucleotide polymorphisms (SNPs) in wCer5, followed by wCer1 and then wCer2, indicative of their different lengths of host associations. Furthermore, mitogenome analyses of the Wolbachia genome-sequenced individuals in combination with SNP data from six European countries revealed polymorphic mitogenome sites that displayed reduced diversity in individuals infected with wCer2 compared to those without.<br><br>CONCLUSIONS: Coinfections with Wolbachia are common in arthropods and affect options for Wolbachia-based management strategies of pest and vector species already infected by Wolbachia. Our analyses of Wolbachia genomes of a host naturally coinfected&#xa0;by several strains unravelled signatures of the evolutionary dynamics in both Wolbachia and host mitochondrial genomes as a consequence of repeated invasions. Invasion of already infected populations by new Wolbachia strains requires new sets of functionally different cif genes and thereby may select for a cumulative modularity of cif gene diversity in invading strains. Furthermore, we demonstrated at the mitogenomic scale that repeated CI-driven Wolbachia invasions of hosts result in reduced mitochondrial diversity and hitchhiking effects. Already resident Wolbachia strains may experience similar cytoplasmic hitchhiking effects caused by the invading Wolbachia strain.}, }
@article {pmid34388165, year = {2021}, author = {Gul, S and Shah, KN and Rana, RM and Khan, MA and El-Shehawi, AM and Elseehy, MM}, title = {Phylogenetic and expression dynamics of tomato ClpB/Hsp100 gene under heat stress.}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0255847}, pmid = {34388165}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Chloroplasts/metabolism ; Cluster Analysis ; Endopeptidase Clp/classification/*metabolism ; Hot Temperature ; Solanum lycopersicum/*metabolism ; Phylogeny ; Plant Leaves/metabolism ; Plant Proteins/classification/*metabolism ; Seedlings/metabolism ; Sequence Alignment ; }, abstract = {Heat shock proteins (Hsps) are stress-responsive molecular chaperones, which uphold proper protein folding in response to external and internal stresses. The Hsp100 gene family plays a substantial role in thermos-tolerance of plants. This study investigated evolutionary relationship and expression of ClpB/Hsp100 gene family in tomato under heat stress. Six SlHsp100 genes were identified using bioinformatics tools. In silico sub-cellular localization indicated that of these 6 ClpB/Hsp100 members, 4 are found in chloroplast, 1 in mitochondria and 1 in the cytoplasm. For evolutionary study, 36 SlHsp100 genes were included in the phylogenetic tree showing a hierarchical clustering shared by the members of the kingdoms Plantae, Archaea, Chromista, Fungi and Bacteria. A total 4 pairs of orthologous and 5 pairs of paralogous genes were identified. Functional divergence between different Hsp100 clusters showed considerable functional homology. Thermo-tolerance measured in terms of cell viability, cell membrane stability and pollen viability indicated that it was paralleled by thermal resistance of Hsps. Reverse transcriptase polymerase chain reaction was used to analyze gene expression in leaves of five-week-old tomato seedlings following exposure to heat stress (45°C) and control (25°C). Chloroplastic LeHSP110/ClpB gene was upregulated in all tomato genotypes after exposure to heat stress highlighting the crucial role of this gene family in acquired thermo-tolerance.}, }
@article {pmid34387318, year = {2021}, author = {Scott, GR and Dalziel, AC}, title = {Physiological insight into the evolution of complex phenotypes: aerobic performance and the O2 transport pathway of vertebrates.}, journal = {The Journal of experimental biology}, volume = {224}, number = {16}, pages = {}, doi = {10.1242/jeb.210849}, pmid = {34387318}, issn = {1477-9145}, mesh = {*Acclimatization ; Adaptation, Physiological ; *Altitude ; Animals ; Mammals ; Oxygen Consumption ; Phenotype ; }, abstract = {Evolutionary physiology strives to understand how the function and integration of physiological systems influence the way in which organisms evolve. Studies of the O2 transport pathway - the integrated physiological system that transports O2 from the environment to mitochondria - are well suited to this endeavour. We consider the mechanistic underpinnings across the O2 pathway for the evolution of aerobic capacity, focusing on studies of artificial selection and naturally selected divergence among wild populations of mammals and fish. We show that evolved changes in aerobic capacity do not require concerted changes across the O2 pathway and can arise quickly from changes in one or a subset of pathway steps. Population divergence in aerobic capacity can be associated with the evolution of plasticity in response to environmental variation or activity. In some cases, initial evolutionary divergence of aerobic capacity arose exclusively from increased capacities for O2 diffusion and/or utilization in active O2-consuming tissues (muscle), which may often constitute first steps in adaptation. However, continued selection leading to greater divergence in aerobic capacity is often associated with increased capacities for circulatory and pulmonary O2 transport. Increases in tissue O2 diffusing capacity may augment the adaptive benefit of increasing circulatory O2 transport owing to their interactive influence on tissue O2 extraction. Theoretical modelling of the O2 pathway suggests that O2 pathway steps with a disproportionately large influence over aerobic capacity have been more likely to evolve, but more work is needed to appreciate the extent to which such physiological principles can predict evolutionary outcomes.}, }
@article {pmid34384891, year = {2021}, author = {Aboouf, MA and Armbruster, J and Thiersch, M and Gassmann, M and Gödecke, A and Gnaiger, E and Kristiansen, G and Bicker, A and Hankeln, T and Zhu, H and Gorr, TA}, title = {Myoglobin, expressed in brown adipose tissue of mice, regulates the content and activity of mitochondria and lipid droplets.}, journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids}, volume = {1866}, number = {12}, pages = {159026}, doi = {10.1016/j.bbalip.2021.159026}, pmid = {34384891}, issn = {1879-2618}, support = {P30 HD002528/HD/NICHD NIH HHS/United States ; }, mesh = {Adipocytes, Brown/metabolism ; Adipose Tissue, Brown/metabolism ; Animals ; Apoptosis Regulatory Proteins/genetics ; Disease Models, Animal ; Energy Metabolism/genetics ; Humans ; Lipid Droplets/*metabolism ; Mice ; Mice, Knockout ; Mitochondria/genetics/*metabolism ; Muscle, Skeletal/metabolism ; Myoglobin/*genetics/metabolism ; Oxygen/*metabolism ; PPAR alpha/genetics ; Palmitates/metabolism ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/genetics ; Proteins/genetics ; Thermogenesis/genetics ; Uncoupling Protein 1/genetics ; }, abstract = {The identification of novel physiological regulators that stimulate energy expenditure through brown adipose tissue (BAT) activity in substrate catalysis is of utmost importance to understand and treat metabolic diseases. Myoglobin (MB), known to store or transport oxygen in heart and skeletal muscles, has recently been found to bind fatty acids with physiological constants in its oxygenated form (i.e., MBO2). Here, we investigated the in vivo effect of MB expression on BAT activity. In particular, we studied mitochondrial function and lipid metabolism as essential determinants of energy expenditure in this tissue. We show in a MB-null (MBko) mouse model that MB expression in BAT impacts on the activity of brown adipocytes in a twofold manner: i) by elevating mitochondrial density plus maximal respiration capacity, and through that, by stimulating BAT oxidative metabolism along with the organelles` uncoupled respiration; and ii) by influencing the free fatty acids pool towards a palmitate-enriched composition and shifting the lipid droplet (LD) equilibrium towards higher counts of smaller droplets. These metabolic changes were accompanied by the up-regulated expression of thermogenesis markers UCP1, CIDEA, CIDEC, PGC1-α and PPAR-α in the BAT of MB wildtype (MBwt) mice. Along with the emergence of the "browning" BAT morphology, MBwt mice exhibited a leaner phenotype when compared to MBko littermates at 20 weeks of age. Our data shed novel insights into MB's role in linking oxygen and lipid-based thermogenic metabolism. The findings suggest potential new strategies of targeting the MB pathway to treat metabolic disorders related to diminishing energy expenditure.}, }
@article {pmid34384346, year = {2021}, author = {Schäffer, AA and McVeigh, R and Robbertse, B and Schoch, CL and Johnston, A and Underwood, BA and Karsch-Mizrachi, I and Nawrocki, EP}, title = {Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {400}, pmid = {34384346}, issn = {1471-2105}, mesh = {DNA, Ribosomal ; *Databases, Nucleic Acid ; Phylogeny ; *RNA, Ribosomal ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND: The DNA sequences encoding ribosomal RNA genes (rRNAs) are commonly used as markers to identify species, including in metagenomics samples that may combine many organismal communities. The 16S small subunit ribosomal RNA (SSU rRNA) gene is typically used to identify bacterial and archaeal species. The nuclear 18S SSU rRNA gene, and 28S large subunit (LSU) rRNA gene have been used as DNA barcodes and for phylogenetic studies in different eukaryote taxonomic groups. Because of their popularity, the National Center for Biotechnology Information (NCBI) receives a disproportionate number of rRNA sequence submissions and BLAST queries. These sequences vary in quality, length, origin (nuclear, mitochondria, plastid), and organism source and can represent any region of the ribosomal cistron.<br><br>RESULTS: To improve the timely verification of quality, origin and loci boundaries, we developed Ribovore, a software package for sequence analysis of rRNA sequences. The ribotyper and ribosensor programs are used to validate incoming sequences of bacterial and archaeal SSU rRNA. The ribodbmaker program is used to create high-quality datasets of rRNAs from different taxonomic groups. Key algorithmic steps include comparing candidate sequences against rRNA sequence profile hidden Markov models (HMMs) and covariance models of rRNA sequence and secondary-structure conservation, as well as other tests. Nine freely available blastn rRNA databases created and maintained with Ribovore are used for checking incoming GenBank submissions and used by the blastn browser interface at NCBI. Since 2018, Ribovore has been used to analyze more than 50 million prokaryotic SSU rRNA sequences submitted to GenBank, and to select at least 10,435 fungal rRNA RefSeq records from type material of 8350 taxa.<br><br>CONCLUSION: Ribovore combines single-sequence and profile-based methods to improve GenBank processing and analysis of rRNA sequences. It is a standalone, portable, and extensible software package for the alignment, classification and validation of rRNA sequences. Researchers planning on submitting SSU rRNA sequences to GenBank are encouraged to download and use Ribovore to analyze their sequences prior to submission to determine which sequences are likely to be automatically accepted into GenBank.}, }
@article {pmid34378417, year = {2021}, author = {Yap, KN and Zhang, Y}, title = {Revisiting the question of nucleated versus enucleated erythrocytes in birds and mammals.}, journal = {American journal of physiology. Regulatory, integrative and comparative physiology}, volume = {321}, number = {4}, pages = {R547-R557}, doi = {10.1152/ajpregu.00276.2020}, pmid = {34378417}, issn = {1522-1490}, mesh = {Animals ; *Biological Evolution ; Birds/*blood ; Cell Size ; *Energy Metabolism ; Erythroblasts/*metabolism ; Erythrocytes/*metabolism ; Hemoglobins/metabolism ; Organelles/*physiology ; Oxidative Stress ; Phylogeny ; Species Specificity ; }, abstract = {Erythrocyte enucleation is thought to have evolved in mammals to support their energetic cost of high metabolic activities. However, birds face similar selection pressure yet possess nucleated erythrocytes. Current hypotheses on the mammalian erythrocyte enucleation claim that the absence of cell organelles allows erythrocytes to 1) pack more hemoglobin into the cells to increase oxygen carrying capacity and 2) decrease erythrocyte size for increased surface area-to-volume ratio, and improved ability to traverse small capillaries. In this article, we first empirically tested current hypotheses using both conventional and phylogenetically informed analysis comparing literature values of mean cell hemoglobin concentration (MCHC) and mean cell volume (MCV) between 181 avian and 194 mammalian species. We found no difference in MCHC levels between birds and mammals using both conventional and phylogenetically corrected analysis. MCV was higher in birds than mammals according to conventional analysis, but the difference was lost when we controlled for phylogeny. These results suggested that avian and mammalian erythrocytes may employ different strategies to solve a common problem. To further investigate existing hypotheses or develop new hypothesis, we need to understand the functions of various organelles in avian erythrocytes. Consequently, we covered potential physiological functions of various cell organelles in avian erythrocytes based on current knowledge, while making explicit comparisons with their mammalian counterparts. Finally, we proposed by taking an integrative and comparative approach, using tools from molecular biology to evolutionary biology, would allow us to better understand the fundamental physiological functions of various components of avian and mammalian erythrocytes.}, }
@article {pmid34378290, year = {2021}, author = {Liu, X and Xu, L and Hu, K and Ren, S and Weng, M and Yu, J and Li, D and Zhang, J}, title = {New isolate of Loma psittaca (Microsporidia: Glugeidae) infecting the stomach wall of cultured hybrid grouper (Epinephelus lanceolatus♂ × Epinephelus fuscoguttatus♀) in South China.}, journal = {The Journal of eukaryotic microbiology}, volume = {68}, number = {6}, pages = {e12868}, doi = {10.1111/jeu.12868}, pmid = {34378290}, issn = {1550-7408}, mesh = {Animals ; *Bass ; *Fish Diseases ; *Loma ; *Microsporidia ; *Microsporidiosis/veterinary ; Phylogeny ; Stomach ; }, abstract = {Loma psittaca, previously described as inhabiting the intestinal mucosa of an anadromous fish, Colomesus pisttacus, from the Amazon Basin, is reported as being found for the first time in a marine fish, the hybrid grouper (Epinephelus lanceolatus♂×Epinephelus fuscoguttatus♀), from Lingshui city, Hainan Province, China, expanding the geographical distribution and host range of this parasite. Numerous whitish xenomas (0.5-0.7 mm in diameter) of this new isolate of L. psittaca were found distinctly in the muscle layer of the host stomach wall. Electron microscopic observations showed a monokaryotic nucleus in all developmental stages. Round or elongated multinucleate merogonial plasmodia surrounded by numerous mitochondria were observed initially, subsequently transforming into uninucleate sporonts through multiple fissions. Sporonts, each with a large centrally positioned nucleus, further developed into sporoblasts. Each sporoblast mother cell gave rise to two uninucleate sporoblasts by binary fission. Mature spores were ellipsoidal, measuring 4.0 ± 0.3 (3.7-4.3) μm in length and 2.2 ± 0.2 (2.1-2.5) μm in width. Spores possessed a mushroom-like anchoring disk, a bipartite polarplast, isofilar polar filaments arranged in 12-14 turns in one row, and a trilaminar spore wall. The obtained partial SSU rRNA gene sequence of the new isolate was 1330 bp in length and showed 99.4% sequence similarity with an estuary isolate of L. psittaca previously reported in South America. SSU rRNA gene-based phylogenetic analyses demonstrated that the two L. psittaca isolates first clustered together and then formed a dichotomy that included the digestive-tract-infecting Loma species, L. acerinae, with high support values within group I.}, }
@article {pmid34356863, year = {2021}, author = {Cooper, ID and Brookler, KH and Kyriakidou, Y and Elliott, BT and Crofts, CAP}, title = {Metabolic Phenotypes and Step by Step Evolution of Type 2 Diabetes: A New Paradigm.}, journal = {Biomedicines}, volume = {9}, number = {7}, pages = {}, pmid = {34356863}, issn = {2227-9059}, abstract = {Unlike bolus insulin secretion mechanisms, basal insulin secretion is poorly understood. It is essential to elucidate these mechanisms in non-hyperinsulinaemia healthy persons. This establishes a baseline for investigation into pathologies where these processes are dysregulated, such as in type 2 diabetes (T2DM), cardiovascular disease (CVD), certain cancers and dementias. Chronic hyperinsulinaemia enforces glucose fueling, depleting the NAD+ dependent antioxidant activity that increases mitochondrial reactive oxygen species (mtROS). Consequently, beta-cell mitochondria increase uncoupling protein expression, which decreases the mitochondrial ATP surge generation capacity, impairing bolus mediated insulin exocytosis. Excessive ROS increases the Drp1:Mfn2 ratio, increasing mitochondrial fission, which increases mtROS; endoplasmic reticulum-stress and impaired calcium homeostasis ensues. Healthy individuals in habitual ketosis have significantly lower glucagon and insulin levels than T2DM individuals. As beta-hydroxybutyrate rises, hepatic gluconeogenesis and glycogenolysis supply extra-hepatic glucose needs, and osteocalcin synthesis/release increases. We propose insulin's primary role is regulating beta-hydroxybutyrate synthesis, while the role of bone regulates glucose uptake sensitivity via osteocalcin. Osteocalcin regulates the alpha-cell glucagon secretory profile via glucagon-like peptide-1 and serotonin, and beta-hydroxybutyrate synthesis via regulating basal insulin levels. Establishing metabolic phenotypes aids in resolving basal insulin secretion regulation, enabling elucidation of the pathological changes that occur and progress into chronic diseases associated with ageing.}, }
@article {pmid34356526, year = {2021}, author = {Prieto-Carrasco, R and Silva-Palacios, A and Rojas-Morales, P and Aparicio-Trejo, OE and Medina-Reyes, EI and Hernández-Cruz, EY and Sánchez-Garibay, C and Salinas-Lara, C and Pavón, N and Roldán, FJ and Zazueta, C and Tapia, E and Pedraza-Chaverri, J}, title = {Unilateral Ureteral Obstruction for 28 Days in Rats Is Not Associated with Changes in Cardiac Function or Alterations in Mitochondrial Function.}, journal = {Biology}, volume = {10}, number = {7}, pages = {}, pmid = {34356526}, issn = {2079-7737}, support = {A1-S-7495//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 281967//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; IN202219//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; 5000-9105//Programa de Apoyo a la Invstigaci&#xf3;n y el Posgrado-Facultad de Qu&#xed;mica/ ; 2020//Fondos de Gasto Directo Autorizado a la Subdirecci&#xf3;n de Investigaci&#xf3;n B&#xe1;sica-Instituto Nacional de Cardioloig&#xed;a Ignacio Ch&#xe1;vez/ ; }, abstract = {Our work evaluated cardiac function and mitochondrial bioenergetics parameters in hearts from male Wistar rats subjected to the UUO model during 28 days of progression. We measured markers of kidney damage and inflammation in plasma and renal fibrosis by histological analysis and Western blot. Cardiac function was evaluated by echocardiography and proteins involved in cardiac damage by Western blot. Oxygen consumption and transmembrane potential were monitored in cardiac mitochondria using high-resolution respirometry. We also determined the activity of ATP synthase and antioxidant enzymes such as glutathione peroxidase, glutathione reductase, and catalase. Our results show that, although renal dysfunction is established in animals subjected to ureteral obstruction, cardiac function is maintained along with mitochondrial function and antioxidant enzymes activity after 28 days of injury evolution. Our results suggest that renocardiac syndrome might develop but belatedly in obstruction-induced renal damage, opening the opportunity for treatment to prevent this condition.}, }
@article {pmid34344905, year = {2021}, author = {Collado, GA and Torres-Díaz, C and Valladares, MA}, title = {Phylogeography and molecular species delimitation reveal cryptic diversity in Potamolithus (Caenogastropoda: Tateidae) of the southwest basin of the Andes.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {15735}, pmid = {34344905}, issn = {2045-2322}, mesh = {Animals ; Bayes Theorem ; *Biodiversity ; Chile ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics/*metabolism ; Gastropoda/classification/*physiology ; *Genetic Speciation ; *Genetic Variation ; Mitochondria/enzymology/genetics ; *Phylogeography ; }, abstract = {The species of the genus Potamolithus inhabiting the southwestern basin of the Andes are difficult to distinguish due to small size and similar shell morphology. Only Potamolithus australis and Potamolithus santiagensis have been traditionally recognized in this region, but the occurrence of several morphologically similar undescribed populations could increase the regional richness. Here we delimit described and potentially undescribed cryptic species of the genus using partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Network analysis and diversity indices inferred six highly differentiated haplogroups, many of them sympatric and widespread in the study area. Phylogeographic analyses suggest a scenario of recent diversification and the occurrence of multiple refuges during the successive Pleistocene glaciations. Phylogenetic analysis also recovered six major clades that showed no relationship with physiography. Species delimitation analyses consistently recognized three or four candidate species apart from P. australis and P. santiagensis. Divergence times indicate that speciation of Chilean Potamolithus began at the end of the Pliocene, probably driven by climatic rather than geographic events. Considering the high inter- and intra-basin genetic diversity, conservation efforts should be focused on protecting sympatric taxa in the basins with the highest species richness.}, }
@article {pmid34343017, year = {2021}, author = {Gabaldón, T}, title = {Origin and Early Evolution of the Eukaryotic Cell.}, journal = {Annual review of microbiology}, volume = {75}, number = {}, pages = {631-647}, doi = {10.1146/annurev-micro-090817-062213}, pmid = {34343017}, issn = {1545-3251}, mesh = {*Biological Evolution ; Eukaryota/genetics ; *Eukaryotic Cells/metabolism ; Phylogeny ; Prokaryotic Cells/metabolism ; Symbiosis ; }, abstract = {The origin of eukaryotes has been defined as the major evolutionary transition since the origin of life itself. Most hallmark traits of eukaryotes, such as their intricate intracellular organization, can be traced back to a putative common ancestor that predated the broad diversity of extant eukaryotes. However, little is known about the nature and relative order of events that occurred in the path from preexisting prokaryotes to this already sophisticated ancestor. The origin of mitochondria from the endosymbiosis of an alphaproteobacterium is one of the few robustly established events to which most hypotheses on the origin of eukaryotes are anchored, but the debate is still open regarding the time of this acquisition, the nature of the host, and the ecological and metabolic interactions between the symbiotic partners. After the acquisition of mitochondria, eukaryotes underwent a fast radiation into several major clades whose phylogenetic relationships have been largely elusive. Recent progress in the comparative analyses of a growing number of genomes is shedding light on the early events of eukaryotic evolution as well as on the root and branching patterns of the tree of eukaryotes. Here I discuss current knowledge and debates on the origin and early evolution of eukaryotes. I focus particularly on how phylogenomic analyses have challenged some of the early assumptions about eukaryotic evolution, including the widespread idea that mitochondrial symbiosis in an archaeal host was the earliest event in eukaryogenesis.}, }
@article {pmid34341532, year = {2021}, author = {Zhang, Q and Wang, Z and Zhang, W and Wen, Q and Li, X and Zhou, J and Wu, X and Guo, Y and Liu, Y and Wei, C and Qian, W and Tian, Y}, title = {The memory of neuronal mitochondrial stress is inherited transgenerationally via elevated mitochondrial DNA levels.}, journal = {Nature cell biology}, volume = {23}, number = {8}, pages = {870-880}, pmid = {34341532}, issn = {1476-4679}, support = {P40 OD010440/OD/NIH HHS/United States ; }, mesh = {Caenorhabditis elegans Proteins/*genetics ; DNA, Mitochondrial/*metabolism ; *Genes, Mitochondrial ; HEK293 Cells ; Humans ; Longevity/genetics ; *Maternal Inheritance ; Neurons/*metabolism ; Organelle Biogenesis ; Stress, Physiological/*genetics ; Unfolded Protein Response/*genetics ; Wnt Signaling Pathway ; }, abstract = {The memory of stresses experienced by parents can be passed on to descendants as a forecast of the challenges to come. Here, we discovered that the neuronal mitochondrial perturbation-induced systemic mitochondrial unfolded protein response (UPR[mt]) in Caenorhabditis elegans can be transmitted to offspring over multiple generations. The transgenerational activation of UPR[mt] is mediated by maternal inheritance of elevated levels of mitochondrial DNA (mtDNA), which causes the proteostasis stress within mitochondria. Furthermore, results from intercrossing studies using wild C. elegans strains further support that maternal inheritance of higher levels of mtDNA can induce the UPR[mt] in descendants. The mitokine Wnt signalling pathway is required for the transmission of elevated mtDNA levels across generations, thereby conferring lifespan extension and stress resistance to offspring. Collectively, our results reveal that the nervous system can transmit stress signals across generations by increasing mtDNA in the germline, enabling descendants to better cope with anticipated challenges.}, }
@article {pmid34321495, year = {2021}, author = {Scarpassa, VM and Cunha-Machado, AS and Alencar, RB}, title = {Multiple evolutionary lineages for the main vector of Leishmania guyanensis, Lutzomyia umbratilis (Diptera: Psychodidae), in the Brazilian Amazon.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {15323}, pmid = {34321495}, issn = {2045-2322}, mesh = {Animals ; *Biological Evolution ; Brazil/epidemiology ; Cytochromes b/genetics ; Electron Transport Complex IV/genetics ; Female ; Gene Expression ; Genetic Variation ; Haplotypes ; Humans ; Insect Proteins/genetics ; Insect Vectors/classification/*genetics ; Leishmania guyanensis/growth &amp; development/*pathogenicity ; Leishmaniasis, Mucocutaneous/epidemiology/parasitology/*transmission ; Mitochondria/enzymology/genetics ; *Phylogeny ; Phylogeography ; Psychodidae/classification/*genetics ; Rivers/parasitology ; }, abstract = {Lutzomyia umbratilis is the main vector of Leishmania guyanensis in the Brazilian Amazon and in neighboring countries. Previous biological and molecular investigations have revealed significant differences between L. umbratilis populations from the central Brazilian Amazon region. Here, a phylogeographic survey of L. umbratilis populations collected from nine localities in the Brazilian Amazon was conducted using two mitochondrial genes. Statistical analyses focused on population genetics, phylogenetic relationships and species delimitations. COI genetic diversity was very high, whereas Cytb diversity was moderate. COI genealogical haplotypes, population structure and phylogenetic analyses identified a deep genetic differentiation and three main genetic groups. Cytb showed a shallower genetic structure, two main haplogroups and poorly resolved phylogenetic trees. These findings, allied to absence of isolation by distance, support the hypothesis that the Amazon and Negro Rivers and interfluves are the main evolutionary forces driving L. umbratilis diversification. The main three genetic groups observed represent three evolutionary lineages, possibly species. The first lineage occurs north of the Amazon River and east of Negro River, where Le. guyanensis transmission is intense, implying that L. umbratilis is an important vector there. The second lineage is in the interfluve between north of Amazon River and west of Negro River, an area reported to be free of Le. guyanensis transmission. The third lineage, first recorded in this study, is in the interfluve between south of Amazonas River and west of Madeira River, and its involvement in the transmission of this parasite remains to be elucidated.}, }
@article {pmid34320951, year = {2021}, author = {Kan, SL and Shen, TT and Ran, JH and Wang, XQ}, title = {Both Conifer II and Gnetales are characterized by a high frequency of ancient mitochondrial gene transfer to the nuclear genome.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {146}, pmid = {34320951}, issn = {1741-7007}, mesh = {Cycadopsida/genetics ; Evolution, Molecular ; *Genes, Mitochondrial ; *Genome, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; Tracheophyta/genetics ; }, abstract = {BACKGROUND: Mitochondrial gene transfer/loss is common in land plants, and therefore the fate of missing mitochondrial genes has attracted more and more attention. The gene content of gymnosperm mitochondria varies greatly, supplying a system for studying the evolutionary fate of missing mitochondrial genes.<br><br>RESULTS: Here, we studied the tempo and pattern of mitochondrial gene transfer/loss in gymnosperms represented by all 13 families, using high-throughput sequencing of both DNA and cDNA. All 41 mitochondrial protein-coding genes were found in cycads, Ginkgo and Pinaceae, whereas multiple mitochondrial genes were absent in Conifer II and Gnetales. In Conifer II, gene transfer from mitochondria to the nucleus followed by loss of the mitochondrial copy was common, but complete loss of a gene in both mitochondrial and nuclear genomes was rare. In contrast, both gene transfer and loss were commonly found in Gnetales. Notably, in Conifer II and Gnetales, the same five mitochondrial genes were transferred to the nuclear genome, and these gene transfer events occurred, respectively, in ancestors of the two lineages. A two-step transfer mechanism (retroprocessing and subsequent DNA-mediated gene transfer) may be responsible for mitochondrial gene transfer in Conifer II and Gnetales. Moreover, the mitochondrial gene content variation is correlated with gene length, GC content, hydrophobicity, and nucleotide substitution rates in land plants.<br><br>CONCLUSIONS: This study reveals a complete evolutionary scenario for variations of mitochondrial gene transferring in gymnosperms, and the factors responsible for mitochondrial gene content variation in land plants.}, }
@article {pmid34309123, year = {2021}, author = {Fernandes Gyorfy, M and Miller, ER and Conover, JL and Grover, CE and Wendel, JF and Sloan, DB and Sharbrough, J}, title = {Nuclear-cytoplasmic balance: whole genome duplications induce elevated organellar genome copy number.}, journal = {The Plant journal : for cell and molecular biology}, volume = {108}, number = {1}, pages = {219-230}, doi = {10.1111/tpj.15436}, pmid = {34309123}, issn = {1365-313X}, mesh = {Arabidopsis/*genetics ; Cell Nucleus/genetics ; Chloroplasts/genetics ; Cytoplasm/genetics ; *DNA Copy Number Variations ; Diploidy ; Gene Duplication ; Genome, Plant/*genetics ; Genome, Plastid/*genetics ; Mitochondria/genetics ; Plastids/genetics ; Polyploidy ; Triticum/*genetics ; }, abstract = {The plant genome is partitioned across three distinct subcellular compartments: the nucleus, mitochondria, and plastids. Successful coordination of gene expression among these organellar genomes and the nuclear genome is critical for plant function and fitness. Whole genome duplication (WGD) events in the nucleus have played a major role in the diversification of land plants and are expected to perturb the relative copy number (stoichiometry) of nuclear, mitochondrial, and plastid genomes. Thus, elucidating the mechanisms whereby plant cells respond to the cytonuclear stoichiometric imbalance that follows WGDs represents an important yet underexplored question in understanding the evolutionary consequences of genome doubling. We used droplet digital PCR to investigate the relationship between nuclear and organellar genome copy numbers in allopolyploids and their diploid progenitors in both wheat and Arabidopsis. Polyploids exhibit elevated organellar genome copy numbers per cell, largely preserving the cytonuclear stoichiometry observed in diploids despite the change in nuclear genome copy number. To investigate the timescale over which cytonuclear stoichiometry may respond to WGD, we also estimated the organellar genome copy number in Arabidopsis synthetic autopolyploids and in a haploid-induced diploid line. We observed corresponding changes in organellar genome copy number in these laboratory-generated lines, indicating that at least some of the cellular response to cytonuclear stoichiometric imbalance is immediate following WGD. We conclude that increases in organellar genome copy numbers represent a common response to polyploidization, suggesting that maintenance of cytonuclear stoichiometry is an important component in establishing polyploid lineages.}, }
@article {pmid34302870, year = {2021}, author = {Costa, JH and Roque, ALM and Aziz, S and Dos Santos, CP and Germano, TA and Batista, MC and Thiers, KLL and da Cruz Saraiva, KD and Arnholdt-Schmitt, B}, title = {Genome-wide identification of ascorbate-glutathione cycle gene families in soybean (Glycine max) reveals gene duplication events and specificity of gene members linked to development and stress conditions.}, journal = {International journal of biological macromolecules}, volume = {187}, number = {}, pages = {528-543}, doi = {10.1016/j.ijbiomac.2021.07.103}, pmid = {34302870}, issn = {1879-0003}, mesh = {Ascorbate Peroxidases/genetics/metabolism ; Ascorbic Acid/*metabolism ; *Evolution, Molecular ; *Gene Duplication ; Gene Expression Regulation, Plant ; Germination ; Glutathione/*metabolism ; Glutathione Reductase/genetics/metabolism ; Glutathione Transferase/genetics/metabolism ; NADH, NADPH Oxidoreductases/genetics/metabolism ; *Oxidative Stress ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Reactive Oxygen Species/*metabolism ; Glycine max/*genetics/growth &amp; development/metabolism ; }, abstract = {Ascorbate-glutathione (AsA-GSH) cycle plays an important role in tuning beneficial ROS accumulation for intracellular signals and imparts plant tolerance to oxidative stress by detoxifying excess of ROS. Here, we present genome-wide identification of AsA-GSH cycle genes (APX, MDHAR, DHAR, and GR) in several leguminous species and expression analyses in G. max during stress, germination and tissue development. Our data revealed 24 genes in Glycine genus against the maximum of 15 in other leguminous species, which was due to 9 pars of duplicated genes mostly originated from sub/neofunctionalization. Cytosolic APX and MDHAR genes were highly expressed in different tissues and physiological conditions. Germination induced genes encoding AsA-GSH proteins from different cell compartments, whereas vegetative phase (leaves) stimulated predominantly genes related to chloroplast/mitochondria proteins. Moreover, cytosolic APX-1, 2, MDHAR-1a, 1b and GR genes were the primary genes linked to senescence and biotic stresses, while stAPX-a, b and GR (from organelles) were the most abiotic stress related genes. Biotic and abiotic stress tolerant genotypes generally showed increased MDHAR, DHAR and/or GR mRNA levels compared to susceptible genotypes. Overall, these data clarified evolutionary events in leguminous plants and point to the functional specificity of duplicated genes of the AsA-GSH cycle in G. max.}, }
@article {pmid34290263, year = {2021}, author = {Yang, H and Li, W and Yu, X and Zhang, X and Zhang, Z and Liu, Y and Wang, W and Tian, X}, title = {Insights into molecular structure, genome evolution and phylogenetic implication through mitochondrial genome sequence of Gleditsia sinensis.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {14850}, pmid = {34290263}, issn = {2045-2322}, mesh = {*Evolution, Molecular ; Fabaceae/genetics ; Genome, Plant/*genetics ; Gleditsia/*genetics/ultrastructure ; Mitochondria/*genetics ; *Phylogeny ; Species Specificity ; *Whole Genome Sequencing ; }, abstract = {Gleditsia sinensis is an endemic species widely distributed in China with high economic and medicinal value. To explore the genomic evolution and phylogenetic relationships of G. sinensis, the complete mitochondrial (mt) genome of G. sinensis was sequenced and assembled, which was firstly reported in Gleditsia. The mt genome was circular and 594,121 bp in length, including 37 protein-coding genes (PCGs), 19 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. The overall base composition of the G. sinensis mt genome was 27.4% for A, 27.4% for T, 22.6% for G, 22.7% for C. The comparative analysis of PCGs in Fabaceae species showed that most of the ribosomal protein genes and succinate dehydrogenase genes were lost. In addition, we found that the rps4 gene was only lost in G. sinensis, whereas it was retained in other Fabaceae species. The phylogenetic analysis based on shared PCGs of 24 species (22 Fabaceae and 2 Solanaceae) showed that G. sinensis is evolutionarily closer to Senna species. In general, this research will provide valuable information for the evolution of G. sinensis and provide insight into the phylogenetic relationships within the family Fabaceae.}, }
@article {pmid34287642, year = {2021}, author = {Vendramin, R and Katopodi, V and Cinque, S and Konnova, A and Knezevic, Z and Adnane, S and Verheyden, Y and Karras, P and Demesmaeker, E and Bosisio, FM and Kucera, L and Rozman, J and Gladwyn-Ng, I and Rizzotto, L and Dassi, E and Millevoi, S and Bechter, O and Marine, JC and Leucci, E}, title = {Activation of the integrated stress response confers vulnerability to mitoribosome-targeting antibiotics in melanoma.}, journal = {The Journal of experimental medicine}, volume = {218}, number = {9}, pages = {}, pmid = {34287642}, issn = {1540-9538}, mesh = {Aged ; Animals ; Antibiotics, Antineoplastic/*pharmacology ; Cell Line, Tumor ; Doxycycline/pharmacology ; Drug Resistance, Neoplasm/drug effects ; Female ; Humans ; Male ; Melanoma/*drug therapy/genetics/mortality/*pathology ; Mice, Inbred C57BL ; Mice, Nude ; Mitochondrial Ribosomes/*drug effects ; Protein Kinase Inhibitors/pharmacology ; Stress, Physiological/drug effects ; Tigecycline/pharmacology ; Uveal Neoplasms/drug therapy/pathology ; Xenograft Model Antitumor Assays ; }, abstract = {The ability to adapt to environmental stress, including therapeutic insult, contributes to tumor evolution and drug resistance. In suboptimal conditions, the integrated stress response (ISR) promotes survival by dampening cytosolic translation. We show that ISR-dependent survival also relies on a concomitant up-regulation of mitochondrial protein synthesis, a vulnerability that can be exploited using mitoribosome-targeting antibiotics. Accordingly, such agents sensitized to MAPK inhibition, thus preventing the development of resistance in BRAFV600E melanoma models. Additionally, this treatment compromised the growth of melanomas that exhibited elevated ISR activity and resistance to both immunotherapy and targeted therapy. In keeping with this, pharmacological inactivation of ISR, or silencing of ATF4, rescued the antitumoral response to the tetracyclines. Moreover, a melanoma patient exposed to doxycycline experienced complete and long-lasting response of a treatment-resistant lesion. Our study indicates that the repurposing of mitoribosome-targeting antibiotics offers a rational salvage strategy for targeted therapy in BRAF mutant melanoma and a therapeutic option for NRAS-driven and immunotherapy-resistant tumors.}, }
@article {pmid34279226, year = {2021}, author = {Colnaghi, M and Pomiankowski, A and Lane, N}, title = {The need for high-quality oocyte mitochondria at extreme ploidy dictates mammalian germline development.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {34279226}, issn = {2050-084X}, support = {BB/S003681/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/V003542/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Biological Evolution ; Cell Death ; Cell Proliferation ; DNA, Mitochondrial/genetics ; Female ; Follicular Atresia ; Germ Cells/*metabolism ; Humans ; Mammals/genetics ; Mice ; Mitochondria/*genetics/*metabolism ; Mutation ; Oocytes/*metabolism ; Oogenesis ; *Ploidies ; }, abstract = {Selection against deleterious mitochondrial mutations is facilitated by germline processes, lowering the risk of genetic diseases. How selection works is disputed: experimental data are conflicting and previous modeling work has not clarified the issues; here, we develop computational and evolutionary models that compare the outcome of selection at the level of individuals, cells and mitochondria. Using realistic de novo mutation rates and germline development parameters from mouse and humans, the evolutionary model predicts the observed prevalence of mitochondrial mutations and diseases in human populations. We show the importance of organelle-level selection, seen in the selective pooling of mitochondria into the Balbiani body, in achieving high-quality mitochondria at extreme ploidy in mature oocytes. Alternative mechanisms debated in the literature, bottlenecks and follicular atresia, are unlikely to account for the clinical data, because neither process effectively eliminates mitochondrial mutations under realistic conditions. Our findings explain the major features of female germline architecture, notably the longstanding paradox of over-proliferation of primordial germ cells followed by massive loss. The near-universality of these processes across animal taxa makes sense in light of the need to maintain mitochondrial quality at extreme ploidy in mature oocytes, in the absence of sex and recombination.}, }
@article {pmid34277616, year = {2021}, author = {Xu, X and Ma, A and Li, T and Cui, W and Wang, X and Li, J and Li, Q and Pang, Y}, title = {Genetic and Functional Characterization of Novel Brown-Like Adipocytes Around the Lamprey Brain.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {674939}, pmid = {34277616}, issn = {2296-634X}, abstract = {During the process of vertebrate evolution, many thermogenic organs and mechanisms have appeared. Mammalian brown adipose tissue (BAT) generates heat through the uncoupling oxidative phosphorylation of mitochondria, acts as a natural defense against hypothermia and inhibits the development of obesity. Although the existence, cellular origin and molecular identity of BAT in humans have been well studied, the genetic and functional characteristics of BAT from lampreys remain unknown. Here, we identified and characterized a novel, naturally existing brown-like adipocytes at the lamprey brain periphery. Similar to human BAT, the lamprey brain periphery contains brown-like adipocytes that maintain the same morphology as human brown adipocytes, containing multilocular lipid droplets and high mitochondrion numbers. Furthermore, we found that brown-like adipocytes in the periphery of lamprey brains responded to thermogenic reagent treatment and cold exposure and that lamprey UCP2 promoted precursor adipocyte differentiation. Molecular mapping by RNA-sequencing showed that inflammation in brown-like adipocytes treated with LPS and 25HC was enhanced compared to controls. The results of this study provide new evidence for human BAT research and demonstrate the multilocular adipose cell functions of lampreys, including: (1) providing material energy and protecting structure, (2) generating additional heat and contributing to adaptation to low-temperature environments, and (3) resisting external pathogens.}, }
@article {pmid34274481, year = {2021}, author = {Kimball, RT and Guido, M and Hosner, PA and Braun, EL}, title = {When good mitochondria go bad: Cyto-nuclear discordance in landfowl (Aves: Galliformes).}, journal = {Gene}, volume = {801}, number = {}, pages = {145841}, doi = {10.1016/j.gene.2021.145841}, pmid = {34274481}, issn = {1879-0038}, mesh = {Animals ; Cell Nucleus/genetics ; Galliformes/*genetics ; Genome, Mitochondrial/*genetics ; *Phylogeny ; }, abstract = {Mitochondrial sequences were among the first molecular data collected for phylogenetic studies and they are plentiful in DNA sequence archives. However, the future value of mitogenomic data in phylogenetics is uncertain, because its phylogenetic signal sometimes conflicts with that of the nuclear genome. A thorough understanding of the causes and prevalence of cyto-nuclear discordance would aid in reconciling different results owing to sequence data type, and provide a framework for interpreting megaphylogenies when taxa which lack substantial nuclear data are placed using mitochondrial data. Here, we examine the prevalence and possible causes of cyto-nuclear discordance in the landfowl (Aves: Galliformes), leveraging 47 new mitogenomes assembled from off-target reads recovered as part of a target-capture study. We evaluated two hypotheses, that cyto-nuclear discordance is "genuine" and a result of biological processes such as incomplete lineage sorting or introgression, and that cyto-nuclear discordance is an artifact of inaccurate mitochondrial tree estimation (the "inaccurate estimation" hypothesis). We identified seven well-supported topological differences between the mitogenomic tree and trees based on nuclear data. These well-supported topological differences were robust to model selection. An examination of sites suggests these differences were driven by small number of sites, particularly from third-codon positions, suggesting that they were not confounded by convergent directional selection. Hence, the hypothesis of genuine discordance was supported.}, }
@article {pmid34257835, year = {2021}, author = {Cheung, NJ and John Peter, AT and Kornmann, B}, title = {Leri: A web-server for identifying protein functional networks from evolutionary couplings.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {3556-3563}, pmid = {34257835}, issn = {2001-0370}, abstract = {Information on the co-evolution of amino acid pairs in a protein can be used for endeavors such as protein engineering, mutation design, and structure prediction. Here we report a method that captures significant determinants of proteins using estimated co-evolution information to identify networks of residues, termed "residue communities", relevant to protein function. On the benchmark dataset (67 proteins with both catalytic and allosteric residues), the Pearson's correlation between the identified residues in the communities at functional sites is 0.53, and it is higher than 0.8 by taking account of conserved residues derived from the method. On the endoplasmic reticulum-mitochondria encounter structure complex, the results indicate three distinguishable residue communities that are relevant to functional roles in the protein family, suggesting that the residue communities could be general evolutionary signatures in proteins. Based on the method, we provide a webserver for the scientific community to explore the signatures in protein families, which establishes a powerful tool to analyze residue-level profiling for the discovery of functional sites and biological pathway identification. This web-server is freely available for non-commercial users at https://kornmann.bioch.ox.ac.uk/leri/services/ecs.html, neither login nor e-mail required.}, }
@article {pmid34256922, year = {2021}, author = {Husnik, F and Tashyreva, D and Boscaro, V and George, EE and Lukeš, J and Keeling, PJ}, title = {Bacterial and archaeal symbioses with protists.}, journal = {Current biology : CB}, volume = {31}, number = {13}, pages = {R862-R877}, doi = {10.1016/j.cub.2021.05.049}, pmid = {34256922}, issn = {1879-0445}, mesh = {Animals ; *Archaea ; *Bacteria ; *Eukaryota ; *Prokaryotic Cells ; *Symbiosis ; }, abstract = {Most of the genetic, cellular, and biochemical diversity of life rests within single-celled organisms - the prokaryotes (bacteria and archaea) and microbial eukaryotes (protists). Very close interactions, or symbioses, between protists and prokaryotes are ubiquitous, ecologically significant, and date back at least two billion years ago to the origin of mitochondria. However, most of our knowledge about the evolution and functions of eukaryotic symbioses comes from the study of animal hosts, which represent only a small subset of eukaryotic diversity. Here, we take a broad view of bacterial and archaeal symbioses with protist hosts, focusing on their evolution, ecology, and cell biology, and also explore what functions (if any) the symbionts provide to their hosts. With the immense diversity of protist symbioses starting to come into focus, we can now begin to see how these systems will impact symbiosis theory more broadly.}, }
@article {pmid34254168, year = {2021}, author = {Igloi, GL}, title = {The Evolutionary Fate of Mitochondrial Aminoacyl-tRNA Synthetases in Amitochondrial Organisms.}, journal = {Journal of molecular evolution}, volume = {89}, number = {7}, pages = {484-493}, pmid = {34254168}, issn = {1432-1432}, mesh = {Amino Acid Sequence ; *Amino Acyl-tRNA Synthetases/genetics/metabolism ; *Arginine-tRNA Ligase/metabolism ; Mitochondria/genetics/metabolism ; RNA, Transfer ; }, abstract = {During the endosymbiotic evolution of mitochondria, the genes for aminoacyl-tRNA synthetases were transferred to the ancestral nucleus. A further reduction of mitochondrial function resulted in mitochondrion-related organisms (MRO) with a loss of the organelle genome. The fate of the now redundant ancestral mitochondrial aminoacyl-tRNA synthetase genes is uncertain. The derived protein sequence for arginyl-tRNA synthetase from thirty mitosomal organisms have been classified as originating from the ancestral nuclear or mitochondrial gene and compared to the identity element at position 20 of the cognate tRNA that distinguishes the two enzyme forms. The evolutionary choice between loss and retention of the ancestral mitochondrial gene for arginyl-tRNA synthetase reflects the coevolution of arginyl-tRNA synthetase and tRNA identity elements.}, }
@article {pmid34253188, year = {2021}, author = {Gélvez, APC and Diniz Junior, JAP and Brígida, RTSS and Rodrigues, APD}, title = {AgNP-PVP-meglumine antimoniate nanocomposite reduces Leishmania amazonensis infection in macrophages.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {211}, pmid = {34253188}, issn = {1471-2180}, mesh = {Animals ; Antiprotozoal Agents/*pharmacology/*therapeutic use ; Cells, Cultured ; In Vitro Techniques ; Leishmania/*drug effects/physiology/ultrastructure ; Macrophages/parasitology ; Meglumine Antimoniate/chemistry/pharmacology/therapeutic use ; Metal Nanoparticles/chemistry/therapeutic use ; Mice ; Mice, Inbred BALB C ; Nanocomposites/*therapeutic use ; Povidone/chemistry/pharmacology/therapeutic use ; Silver/chemistry/pharmacology/therapeutic use ; }, abstract = {BACKGROUND: Leishmaniasis is an infectious disease caused by parasites of the genus Leishmania and presents different clinical manifestations. The adverse effects, immunosuppression and resistant strains associated with this disease necessitate the development of new drugs. Nanoparticles have shown potential as alternative antileishmanial drugs. We showed in a previous study the biosynthesis, characterization and ideal concentration of a nanocomposite that promoted leishmanicidal activity. In the present study, we conducted a specific analysis to show the mechanism of action of AgNP-PVP-MA (silver nanoparticle-polyvinylpyrrolidone-[meglumine antimoniate (Glucantime®)]) nanocomposite during Leishmania amazonensis infection in vitro.<br><br>RESULTS: Through ultrastructural analysis, we observed significant alterations, such as the presence of small vesicles in the flagellar pocket and in the extracellular membrane, myelin-like structure formation in the Golgi complex and mitochondria, flagellum and plasma membrane rupture, and electrodense material deposition at the edges of the parasite nucleus in both evolutive forms. Furthermore, the Leishmania parasite infection index in macrophages decreased significantly after treatment, and nitric oxide and reactive oxygen species production levels were determined. Additionally, inflammatory, and pro-inflammatory cytokine and chemokine production levels were evaluated. The IL-4, TNF-&#x3b1; and MIP-1&#x3b1; levels increased significantly, while the IL-17&#xa0;A level decreased significantly after treatment.<br><br>CONCLUSIONS: Thus, we demonstrate in this study that the AgNP-PVP-MA nanocomposite has leishmanial potential, and the mechanism of action was demonstrated for the first time, showing that this bioproduct seems to be a potential alternative treatment for leishmaniasis.}, }
@article {pmid34252921, year = {2021}, author = {Anselmetti, Y and El-Mabrouk, N and Lafond, M and Ouangraoua, A}, title = {Gene tree and species tree reconciliation with endosymbiotic gene transfer.}, journal = {Bioinformatics (Oxford, England)}, volume = {37}, number = {Suppl_1}, pages = {i120-i132}, pmid = {34252921}, issn = {1367-4811}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; //Fonds de recherche Nature et Technologie, Qu&#xe9;bec/ ; }, mesh = {Algorithms ; *Evolution, Molecular ; Gene Duplication ; *Gene Transfer, Horizontal ; Genome ; Phylogeny ; Symbiosis/genetics ; }, abstract = {MOTIVATION: It is largely established that all extant mitochondria originated from a unique endosymbiotic event integrating an α-proteobacterial genome into an eukaryotic cell. Subsequently, eukaryote evolution has been marked by episodes of gene transfer, mainly from the mitochondria to the nucleus, resulting in a significant reduction of the mitochondrial genome, eventually completely disappearing in some lineages. However, in other lineages such as in land plants, a high variability in gene repertoire distribution, including genes encoded in both the nuclear and mitochondrial genome, is an indication of an ongoing process of Endosymbiotic Gene Transfer (EGT). Understanding how both nuclear and mitochondrial genomes have been shaped by gene loss, duplication and transfer is expected to shed light on a number of open questions regarding the evolution of eukaryotes, including rooting of the eukaryotic tree.<br><br>RESULTS: We address the problem of inferring the evolution of a gene family through duplication, loss and EGT events, the latter considered as a special case of horizontal gene transfer occurring between the mitochondrial and nuclear genomes of the same species (in one direction or the other). We consider both EGT events resulting in maintaining (EGTcopy) or removing (EGTcut) the gene copy in the source genome. We present a linear-time algorithm for computing the DLE (Duplication, Loss and EGT) distance, as well as an optimal reconciled tree, for the unitary cost, and a dynamic programming algorithm allowing to output all optimal reconciliations for an arbitrary cost of operations. We illustrate the application of our EndoRex software and analyze different costs settings parameters on a plant dataset and discuss the resulting reconciled trees.<br><br>EndoRex implementation and supporting data are available on the GitHub repository via https://github.com/AEVO-lab/EndoRex.}, }
@article {pmid34237359, year = {2021}, author = {Zhang, B and Havird, JC and Wang, E and Lv, J and Xu, X}, title = {Massive gene rearrangement in mitogenomes of phytoseiid mites.}, journal = {International journal of biological macromolecules}, volume = {186}, number = {}, pages = {33-39}, pmid = {34237359}, issn = {1879-0003}, support = {R35 GM142836/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Diet ; *Evolution, Molecular ; Feeding Behavior ; *Gene Order ; *Gene Rearrangement ; *Genome, Mitochondrial ; Mites/*genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Mitochondrial (mt) gene sequences have been widely used to infer phylogeny in animals. The relative order of mt genes in the mitogenome can also be a useful marker for evolution, but the propensity of mt gene rearrangements vary tremendously among taxa. Ticks and mites in Acari exemplify this trend as some families retain the ancestral arthropod gene order, while others show highly divergent gene orders. Mites in Phytoseiidae, many of which are effective biological control agents, show some of the most divergent gene orders. However, the diversity of mitogenome order within this family is little known. We thus sequenced three mt genomes of phytoseiid mites from two of the most speciose genera: Amblyseius swirskii (Athias-Henriot), Amblyseius tsugawai (Ehara) and Neoseiulus womersleyi (Schicha). We find differences in mt GC skew and nucleotide composition, especially between N. womersleyi and the two Amblyseius species. Each species within Phytoseiidae (including three previously available sequences) present a unique gene order. Phytoseiid mitogenomes show some of the highest numbers of breakpoints when compared to the ancestral arthropod order (up to 33), as well as high numbers of breakpoints within the family (14-30). This suggests a history of massive, ongoing mitogenome rearrangements in the family. Phylogenetic analyses of mt sequences confirm that the degree of gene rearrangements follows phylogenetic relatedness. We discuss possible causes for the high degree of mt gene rearrangement within phytoseiid mites as well as selection in the mt and nuclear genome tied to the independent evolution of many diverse feeding strategies in the family. Finally, we suggest N. womersleyi should be used instead of the synonym Amblyseius pseudolongispinosus.}, }
@article {pmid34235856, year = {2022}, author = {Mori, MP and Penjweini, R and Knutson, JR and Wang, PY and Hwang, PM}, title = {Mitochondria and oxygen homeostasis.}, journal = {The FEBS journal}, volume = {289}, number = {22}, pages = {6959-6968}, pmid = {34235856}, issn = {1742-4658}, support = {ZIA HL006051/ImNIH/Intramural NIH HHS/United States ; }, mesh = {*Mitochondria/metabolism ; Free Radicals/metabolism ; *Oxygen/metabolism ; Homeostasis ; Reactive Oxygen Species/metabolism ; Oxidative Stress ; }, abstract = {Molecular oxygen possesses a dual nature due to its highly reactive free radical property: it is capable of oxidizing metabolic substrates to generate cellular energy, but can also serve as a substrate for genotoxic reactive oxygen species generation. As a labile substance upon which aerobic life depends, the mechanisms for handling cellular oxygen have been fine-tuned and orchestrated in evolution. Protection from atmospheric oxygen toxicity as originally posited by the Endosymbiotic Theory of the Mitochondrion is likely to be one basic principle underlying oxygen homeostasis. We briefly review the literature on oxygen homeostasis both in vitro and in vivo with a focus on the role of the mitochondrion where the majority of cellular oxygen is consumed. The insights gleaned from these basic mechanisms are likely to be important for understanding disease pathogenesis and developing strategies for maintaining health.}, }
@article {pmid34233163, year = {2021}, author = {Allouche, J and Rachmin, I and Adhikari, K and Pardo, LM and Lee, JH and McConnell, AM and Kato, S and Fan, S and Kawakami, A and Suita, Y and Wakamatsu, K and Igras, V and Zhang, J and Navarro, PP and Lugo, CM and Noonan, HR and Christie, KA and Itin, K and Mujahid, N and Lo, JA and Won, CH and Evans, CL and Weng, QY and Wang, H and Osseiran, S and Lovas, A and Németh, I and Cozzio, A and Navarini, AA and Hsiao, JJ and Nguyen, N and Kemény, LV and Iliopoulos, O and Berking, C and Ruzicka, T and Gonzalez-José, R and Bortolini, MC and Canizales-Quinteros, S and Acuna-Alonso, V and Gallo, C and Poletti, G and Bedoya, G and Rothhammer, F and Ito, S and Schiaffino, MV and Chao, LH and Kleinstiver, BP and Tishkoff, S and Zon, LI and Nijsten, T and Ruiz-Linares, A and Fisher, DE and Roider, E}, title = {NNT mediates redox-dependent pigmentation via a UVB- and MITF-independent mechanism.}, journal = {Cell}, volume = {184}, number = {16}, pages = {4268-4283.e20}, pmid = {34233163}, issn = {1097-4172}, support = {R01 AR072304/AR/NIAMS NIH HHS/United States ; R00 CA218870/CA/NCI NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; UL1 TR002541/TR/NCATS NIH HHS/United States ; P01 CA163222/CA/NCI NIH HHS/United States ; R01 AR076241/AR/NIAMS NIH HHS/United States ; R01 CA103846/CA/NCI NIH HHS/United States ; P30 DK057521/DK/NIDDK NIH HHS/United States ; R35 GM134957/GM/NIGMS NIH HHS/United States ; BB/I021213/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; P01 HL142494/HL/NHLBI NIH HHS/United States ; P30 ES013508/ES/NIEHS NIH HHS/United States ; R01 CA222871/CA/NCI NIH HHS/United States ; R01 AR043369/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Cell Line ; Cohort Studies ; Cyclic AMP/metabolism ; DNA Damage ; Enzyme Inhibitors/chemistry/pharmacology ; Genetic Predisposition to Disease ; Humans ; Melanocytes/drug effects/metabolism ; Melanosomes/drug effects/metabolism/radiation effects ; Mice ; Mice, Inbred C57BL ; Microphthalmia-Associated Transcription Factor/*metabolism ; Mitochondria/drug effects/metabolism ; Monophenol Monooxygenase/genetics/metabolism ; NADP Transhydrogenases/antagonists &amp; inhibitors/*metabolism ; Oxidation-Reduction/drug effects/radiation effects ; Polymorphism, Single Nucleotide/genetics ; Proteasome Endopeptidase Complex/metabolism ; Proteolysis/drug effects/radiation effects ; RNA, Messenger/genetics/metabolism ; Skin Pigmentation/drug effects/genetics/*radiation effects ; Ubiquitin/metabolism ; *Ultraviolet Rays ; Zebrafish ; }, abstract = {Ultraviolet (UV) light and incompletely understood genetic and epigenetic variations determine skin color. Here we describe an UV- and microphthalmia-associated transcription factor (MITF)-independent mechanism of skin pigmentation. Targeting the mitochondrial redox-regulating enzyme nicotinamide nucleotide transhydrogenase (NNT) resulted in cellular redox changes that affect tyrosinase degradation. These changes regulate melanosome maturation and, consequently, eumelanin levels and pigmentation. Topical application of small-molecule inhibitors yielded skin darkening in human skin, and mice with decreased NNT function displayed increased pigmentation. Additionally, genetic modification of NNT in zebrafish alters melanocytic pigmentation. Analysis of four diverse human cohorts revealed significant associations of skin color, tanning, and sun protection use with various single-nucleotide polymorphisms within NNT. NNT levels were independent of UVB irradiation and redox modulation. Individuals with postinflammatory hyperpigmentation or lentigines displayed decreased skin NNT levels, suggesting an NNT-driven, redox-dependent pigmentation mechanism that can be targeted with NNT-modifying topical drugs for medical and cosmetic purposes.}, }
@article {pmid34222053, year = {2021}, author = {Li, T and Fang, Z and He, Q and Wang, C and Meng, X and Yu, B and Zhou, Z}, title = {Characterizing the Xenoma of Vairimorpha necatrix Provides Insights Into the Most Efficient Mode of Microsporidian Proliferation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {11}, number = {}, pages = {699239}, pmid = {34222053}, issn = {2235-2988}, mesh = {Animals ; Cell Proliferation ; Humans ; In Situ Hybridization, Fluorescence ; *Microsporidia/genetics ; Phylogeny ; }, abstract = {Microsporidia are a group of obligated intracellular parasites that can infect nearly all vertebrates and invertebrates, including humans and economic animals. Microsporidian Vairimorpha necatrix is a natural pathogen of multiple insects and can massively proliferate by making tumor-like xenoma in host tissue. However, little is known about the subcellular structures of this xenoma and the proliferation features of the pathogens inside. Here, we characterized the V. necatrix xenoma produced in muscle cells of silkworm midgut. In result, the whitish xenoma was initially observed on the 12[th] day post infection on the outer surface of the midgut and later became larger and numerous. The observation by scanning electronic microscopy showed that the xenoma is mostly elliptical and spindle with dense pathogen-containing protrusions and spores on the surface, which were likely shedding off the xenoma through exocytosis and could be an infection source of other tissues. Demonstrated with transmission electron microscopy and fluorescent staining, the xenoma was enveloped by a monolayer membrane, and full of vesicle structures, mitochondria, and endoplasmic reticulum around parasites in development, suggesting that high level of energy and nutrients were produced to support the massive proliferation of the parasites. Multiple hypertrophic nuclei were found in one single xenoma, indicating that the cyst was probably formed by fusion of multiple muscle cells. Observed by fluorescence in situ hybridization, pathogens in the xenoma were in merongony, sporogony, and octosporogony, and mature stages. And mature spores were pushed to the center while vegetative pathogens were in the surface layer of the xenoma. The V. necatrix meront usually contained two to three nuclei, and sporont contained two nuclei and was wrapped by a thick membrane with high electron density. The V. necatrix sporogony produces two types of spores, the ordinary dikaryotic spore and unicellular octospores, the latter of which were smaller in size and packed in a sporophorous vesicle. In summary, V. necatrix xenoma is a specialized cyst likely formed by fusion of multiple muscle cells and provides high concentration of energy and nutrients with increased number of mitochondria and endoplasmic reticulum for the massive proliferation of pathogens inside.}, }
@article {pmid34212085, year = {2021}, author = {Sheng, L and Zhou, T and Shi, Z and Pan, X and Weng, X and Ma, J and Wu, S}, title = {The complete mitochondrial genome of Trictenotoma davidi Deyrolle, 1875 (Coleoptera: Trictenotomidae).}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {6}, number = {7}, pages = {2026-2027}, pmid = {34212085}, issn = {2380-2359}, abstract = {Trictenotoma davidi Deyrolle, 1875 is a beetle of the Trictenotomidae family. The length of the complete mitochondria genome of T. davidi was 15,910 bp with 24.1% GC content, including 39.9% A, 15.1% C, 9.0% G, and 36.0% T. The genome encoded 13 protein-coding genes, 22 tRNAs, and 2 rRNAs. Phylogenetic analysis showed that T. davidi was closely related to Vincenzellus ruficollis. This study provided useful genetic information for the evolution of T. davidi and Trictenotomidae insects.}, }
@article {pmid34211444, year = {2021}, author = {Degli Esposti, M and Moya-Beltrán, A and Quatrini, R and Hederstedt, L}, title = {Respiratory Heme A-Containing Oxidases Originated in the Ancestors of Iron-Oxidizing Bacteria.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {664216}, pmid = {34211444}, issn = {1664-302X}, abstract = {Respiration is a major trait shaping the biology of many environments. Cytochrome oxidase containing heme A (COX) is a common terminal oxidase in aerobic bacteria and is the only one in mammalian mitochondria. The synthesis of heme A is catalyzed by heme A synthase (CtaA/Cox15), an enzyme that most likely coevolved with COX. The evolutionary origin of COX in bacteria has remained unknown. Using extensive sequence and phylogenetic analysis, we show that the ancestral type of heme A synthases is present in iron-oxidizing Proteobacteria such as Acidithiobacillus spp. These bacteria also contain a deep branching form of the major COX subunit (COX1) and an ancestral variant of CtaG, a protein that is specifically required for COX biogenesis. Our work thus suggests that the ancestors of extant iron-oxidizers were the first to evolve COX. Consistent with this conclusion, acidophilic iron-oxidizing prokaryotes lived on emerged land around the time for which there is the earliest geochemical evidence of aerobic respiration on earth. Hence, ecological niches of iron oxidation have apparently promoted the evolution of aerobic respiration.}, }
@article {pmid34211399, year = {2021}, author = {García-Casas, P and Alvarez-Illera, P and Gómez-Orte, E and Cabello, J and Fonteriz, RI and Montero, M and Alvarez, J}, title = {The Mitochondrial Na[+]/Ca[2+] Exchanger Inhibitor CGP37157 Preserves Muscle Structure and Function to Increase Lifespan and Healthspan in Caenorhabditis elegans.}, journal = {Frontiers in pharmacology}, volume = {12}, number = {}, pages = {695687}, pmid = {34211399}, issn = {1663-9812}, abstract = {We have reported recently that the mitochondrial Na[+]/Ca[2+] exchanger inhibitor CGP37157 extends lifespan in Caenorhabditis elegans by a mechanism involving mitochondria, the TOR pathway and the insulin/IGF1 pathway. Here we show that CGP37157 significantly improved the evolution with age of the sarcomeric regular structure, delaying development of sarcopenia in C. elegans body wall muscle and increasing the average and maximum speed of the worms. Similarly, CGP37157 favored the maintenance of a regular mitochondrial structure during aging. We have also investigated further the mechanism of the effect of CGP37157 by studying its effect in mutants of aak-1;aak-2/AMP-activated kinase, sir-2.1/sirtuin, rsks-1/S6 kinase and daf-16/FOXO. We found that this compound was still effective increasing lifespan in all these mutants, indicating that these pathways are not involved in the effect. We have then monitored pharynx cytosolic and mitochondrial Ca[2+] signalling and our results suggest that CGP37157 is probably inhibiting not only the mitochondrial Na[+]/Ca[2+] exchanger, but also Ca[2+] entry through the plasma membrane. Finally, a transcriptomic study detected that CGP37157 induced changes in lipid metabolism enzymes and a four-fold increase in the expression of ncx-6, one of the C. elegans mitochondrial Na[+]/Ca[2+] exchangers. In summary, CGP37157 increases both lifespan and healthspan by a mechanism involving changes in cytosolic and mitochondrial Ca[2+] homeostasis. Thus, Ca[2+] signalling could be a promising target to act on aging.}, }
@article {pmid34211040, year = {2021}, author = {Sarkar, BK and Sharma, AR and Bhattacharya, M and Sharma, G and Lee, SS and Chakraborty, C}, title = {Determination of k-mer density in a DNA sequence and subsequent cluster formation algorithm based on the application of electronic filter.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {13701}, pmid = {34211040}, issn = {2045-2322}, mesh = {*Algorithms ; Animals ; Base Sequence ; Cluster Analysis ; DNA/genetics ; DNA, Mitochondrial/genetics ; Genome, Mitochondrial ; Humans ; Phylogeny ; Principal Component Analysis ; Sequence Analysis, DNA/*methods ; beta-Globins/genetics ; }, abstract = {We describe a novel algorithm for information recovery from DNA sequences by using a digital filter. This work proposes a three-part algorithm to decide the k-mer or q-gram word density. Employing a finite impulse response digital filter, one can calculate the sequence's k-mer or q-gram word density. Further principal component analysis is used on word density distribution to analyze the dissimilarity between sequences. A dissimilarity matrix is thus formed and shows the appearance of cluster formation. This cluster formation is constructed based on the alignment-free sequence method. Furthermore, the clusters are used to build phylogenetic relations. The cluster algorithm is in good agreement with alignment-based algorithms. The present algorithm is simple and requires less time for computation than other currently available algorithms. We tested the algorithm using beta hemoglobin coding sequences (HBB) of 10 different species and 18 primate mitochondria genome (mtDNA) sequences.}, }
@article {pmid34204357, year = {2021}, author = {Richtová, J and Sheiner, L and Gruber, A and Yang, SM and Kořený, L and Striepen, B and Oborník, M}, title = {Using Diatom and Apicomplexan Models to Study the Heme Pathway of Chromera velia.}, journal = {International journal of molecular sciences}, volume = {22}, number = {12}, pages = {}, pmid = {34204357}, issn = {1422-0067}, support = {21-03224S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//ERDF/ESF, Centre for Research of Pathogenicity and Virulence of Parasites/ ; }, mesh = {Alveolata/*physiology ; Amino Acid Sequence ; Apicomplexa/*metabolism ; Biological Transport ; Diatoms/*metabolism ; Evolution, Molecular ; Gene Expression Regulation, Enzymologic ; Heme/*metabolism ; *Metabolic Networks and Pathways ; Mitochondria/genetics/metabolism/ultrastructure ; Protozoan Proteins/chemistry/genetics/metabolism ; }, abstract = {Heme biosynthesis is essential for almost all living organisms. Despite its conserved function, the pathway's enzymes can be located in a remarkable diversity of cellular compartments in different organisms. This location does not always reflect their evolutionary origins, as might be expected from the history of their acquisition through endosymbiosis. Instead, the final subcellular localization of the enzyme reflects multiple factors, including evolutionary origin, demand for the product, availability of the substrate, and mechanism of pathway regulation. The biosynthesis of heme in the apicomonad Chromera velia follows a chimeric pathway combining heme elements from the ancient algal symbiont and the host. Computational analyses using different algorithms predict complex targeting patterns, placing enzymes in the mitochondrion, plastid, endoplasmic reticulum, or the cytoplasm. We employed heterologous reporter gene expression in the apicomplexan parasite Toxoplasma gondii and the diatom Phaeodactylum tricornutum to experimentally test these predictions. 5-aminolevulinate synthase was located in the mitochondria in both transfection systems. In T. gondii, the two 5-aminolevulinate dehydratases were located in the cytosol, uroporphyrinogen synthase in the mitochondrion, and the two ferrochelatases in the plastid. In P. tricornutum, all remaining enzymes, from ALA-dehydratase to ferrochelatase, were placed either in the endoplasmic reticulum or in the periplastidial space.}, }
@article {pmid34202821, year = {2021}, author = {Purnomo, GA and Mitchell, KJ and O'Connor, S and Kealy, S and Taufik, L and Schiller, S and Rohrlach, A and Cooper, A and Llamas, B and Sudoyo, H and Teixeira, JC and Tobler, R}, title = {Mitogenomes Reveal Two Major Influxes of Papuan Ancestry across Wallacea Following the Last Glacial Maximum and Austronesian Contact.}, journal = {Genes}, volume = {12}, number = {7}, pages = {}, pmid = {34202821}, issn = {2073-4425}, mesh = {Animals ; Archaeology/history ; Asia ; Australia ; Coleoptera/genetics ; Female ; *Genetics, Population ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; History, Ancient ; Humans ; Male ; New Guinea ; Oceania ; *Phylogeny ; *Phylogeography ; }, abstract = {The tropical archipelago of Wallacea contains thousands of individual islands interspersed between mainland Asia and Near Oceania, and marks the location of a series of ancient oceanic voyages leading to the peopling of Sahul-i.e., the former continent that joined Australia and New Guinea at a time of lowered sea level-by 50,000 years ago. Despite the apparent deep antiquity of human presence in Wallacea, prior population history research in this region has been hampered by patchy archaeological and genetic records and is largely concentrated upon more recent history that follows the arrival of Austronesian seafarers ~3000-4000 years ago (3-4 ka). To shed light on the deeper history of Wallacea and its connections with New Guinea and Australia, we performed phylogeographic analyses on 656 whole mitogenomes from these three regions, including 186 new samples from eight Wallacean islands and three West Papuan populations. Our results point to a surprisingly dynamic population history in Wallacea, marked by two periods of extensive demographic change concentrated around the Last Glacial Maximum ~15 ka and post-Austronesian contact ~3 ka. These changes appear to have greatly diminished genetic signals informative about the original peopling of Sahul, and have important implications for our current understanding of the population history of the region.}, }
@article {pmid34193932, year = {2021}, author = {Ye, L and Yao, T and Lu, J and Jiang, J and Bai, C}, title = {Mitochondrial genomes of two Polydora (Spionidae) species provide further evidence that mitochondrial architecture in the Sedentaria (Annelida) is not conserved.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {13552}, pmid = {34193932}, issn = {2045-2322}, mesh = {Animals ; Annelida/*genetics ; *Evolution, Molecular ; *Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; *Phylogeny ; }, abstract = {Contrary to the early evidence, which indicated that the mitochondrial architecture in one of the two major annelida clades, Sedentaria, is relatively conserved, a handful of relatively recent studies found evidence that some species exhibit elevated rates of mitochondrial architecture evolution. We sequenced complete mitogenomes belonging to two congeneric shell-boring Spionidae species that cause considerable economic losses in the commercial marine mollusk aquaculture: Polydora brevipalpa and Polydora websteri. The two mitogenomes exhibited very similar architecture. In comparison to other sedentarians, they exhibited some standard features, including all genes encoded on the same strand, uncommon but not unique duplicated trnM gene, as well as a number of unique features. Their comparatively large size (17,673 bp) can be attributed to four non-coding regions larger than 500 bp. We identified an unusually large (putative) overlap of 14 bases between nad2 and cox1 genes in both species. Importantly, the two species exhibited completely rearranged gene orders in comparison to all other available mitogenomes. Along with Serpulidae and Sabellidae, Polydora is the third identified sedentarian lineage that exhibits disproportionally elevated rates of mitogenomic architecture rearrangements. Selection analyses indicate that these three lineages also exhibited relaxed purifying selection pressures.}, }
@article {pmid34192514, year = {2021}, author = {Amine, AAA and Liao, CW and Hsu, PC and Opoc, FJG and Leu, JY}, title = {Experimental evolution improves mitochondrial genome quality control in Saccharomyces cerevisiae and extends its replicative lifespan.}, journal = {Current biology : CB}, volume = {31}, number = {16}, pages = {3663-3670.e4}, doi = {10.1016/j.cub.2021.06.026}, pmid = {34192514}, issn = {1879-0445}, mesh = {DNA, Mitochondrial/genetics ; *Directed Molecular Evolution ; *Genome, Mitochondrial ; Longevity ; *Saccharomyces cerevisiae/genetics ; }, abstract = {The mitochondrion is an ancient endosymbiotic organelle that performs many essential functions in eukaryotic cells.[1-3] Mitochondrial impairment often results in physiological defects or diseases.[2-8] Since most mitochondrial genes have been copied into the nuclear genome during evolution,[9] the regulatory and interaction mechanisms between the mitochondrial and nuclear genomes are very complex. Multiple mechanisms, including antioxidant, DNA repair, mitophagy, and mitochondrial biogenesis pathways, have been shown to monitor the quality and quantity of mitochondria.[10-12] Nonetheless, it remains unclear if these pathways can be further modified to enhance mitochondrial stability. Previously, experimental evolution has been used to adapt cells to novel growth conditions. By analyzing the resulting evolved populations, insights have been gained into the underlying molecular mechanisms.[13] Here, we experimentally evolved yeast cells under conditions that selected for efficient respiration while continuously assaulting the mitochondrial genome (mtDNA) with ethidium bromide (EtBr). We found that the ability to maintain functional mtDNA was enhanced in most of the evolved lines when challenged with mtDNA-damaging reagents. We identified mutations of the mitochondrial NADH dehydrogenase NDE1 in most of the evolved lines, but other pathways are also involved. Finally, we show that cells displaying enhanced mtDNA retention also exhibit a prolonged replicative lifespan. Our work reveals potential evolutionary trajectories by which cells can maintain functional mitochondria in response to mtDNA stress, as well as the physiological implications of such adaptations.}, }
@article {pmid34188831, year = {2021}, author = {Yang, M and Dong, D and Li, X}, title = {The complete mitogenome of Phymorhynchus sp. (Neogastropoda, Conoidea, Raphitomidae) provides insights into the deep-sea adaptive evolution of Conoidea.}, journal = {Ecology and evolution}, volume = {11}, number = {12}, pages = {7518-7531}, pmid = {34188831}, issn = {2045-7758}, abstract = {The deep-sea environment is characterized by darkness, hypoxia, and high hydrostatic pressure. Mitochondria play a vital role in energy metabolism; thus, they may endure the selection process during the adaptive evolution of deep-sea organisms. In the present study, the mitogenome of Phymorhynchus sp. from the Haima methane seep was completely assembled and characterized. This mitogenome is 16,681 bp in length and contains 13 protein-coding genes, 2 rRNAs, and 22 tRNAs. The gene order and orientation were identical to those of most sequenced conoidean gastropods. Some special elements, such as tandem repeat sequences and AT-rich sequences, which are involved in the regulation of the replication and transcription of the mitogenome, were observed in the control region. Phylogenetic analysis revealed that Conoidea is divided into two separate clades with high nodal support. Positive selection analysis revealed evidence of adaptive changes in the mitogenomes of deep-sea conoidean gastropods. Eight residues located in atp6, cox1, cytb, nad1, nad4, and nad5 were determined to have undergone positive selection. This study explores the adaptive evolution of deep-sea conoidean gastropods and provides valuable clues at the mitochondrial level regarding the exceptional adaptive ability of organisms in deep-sea environments.}, }
@article {pmid34175396, year = {2021}, author = {Lin, C and Tang, D and Gao, X and Jiang, H and Du, C and Zhu, J}, title = {Molecular characterization, dynamic transcription, and potential function of KIF3A/KIF3B during spermiogenesis in Opsariichthys bidens.}, journal = {Gene}, volume = {798}, number = {}, pages = {145795}, doi = {10.1016/j.gene.2021.145795}, pmid = {34175396}, issn = {1879-0038}, mesh = {Animals ; Cyprinidae/genetics/*physiology ; Kinesins/chemistry/genetics/*physiology ; Male ; Microtubules/metabolism ; Mitochondria/metabolism ; Phylogeny ; Protein Conformation ; RNA, Messenger/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sperm Tail/physiology ; Spermatids/physiology/ultrastructure ; Spermatogenesis/genetics/*physiology ; Testis/metabolism ; Transcription, Genetic ; }, abstract = {Spermiogenesis is the final phase of spermatogenesis, wherein the spermatids differentiate into mature spermatozoa via complex morphological transformation. In this process, kinesin plays an important role. Here, we observed the morphological transformation of spermatids and analyzed the characterization, dynamic transcription, and potential function of kinesin KIF3A/KIF3B during spermiogenesis in Chinese hook snout carp (Opsariichthys bidens). We found that the full-length cDNAs of O. bidens kif3a and kif3b were 2544 and 2806 bp in length comprising 119 bp and 259 bp 5' untranslated region (UTR), 313 bp and 222 bp 3' UTR, and 2112 bp and 2325 bp open reading frame encoding 703 and 774 amino acids, respectively. Ob-KIF3A/KIF3B proteins have three domains, namely N-terminal head, coiled-coil stalk, and C-terminal tail, and exhibit high similarity with homologous proteins in vertebrates and invertebrates. Ob-kif3a/kif3b mRNAs were ubiquitously expressed in all tissues examined, with the highest expression in the brain and stage-IV testis. Immunofluorescence results showed that Ob-KIF3A was co-localized with tubulin and the mitochondria. Particularly, in early spermatids, Ob-KIF3A, tubulin, and the mitochondrial signals were evenly distributed in the cytoplasm, whereas in middle spermatids, they were distributed around the nucleus. In the late stage, the signals were concentrated on one side of the nucleus, where the tail is formed, whereas in mature sperms, they were detected in the midpiece and flagellum. These results indicate that Ob-KIF3A/KIF3B may participate in nuclear reshaping, flagellum formation, and mitochondrial aggregation in the midpiece during spermiogenesis.}, }
@article {pmid34175310, year = {2021}, author = {Parrot, C and Moulinier, L and Bernard, F and Hashem, Y and Dupuy, D and Sissler, M}, title = {Peculiarities of aminoacyl-tRNA synthetases from trypanosomatids.}, journal = {The Journal of biological chemistry}, volume = {297}, number = {2}, pages = {100913}, pmid = {34175310}, issn = {1083-351X}, mesh = {Amino Acid Sequence ; Amino Acids/*metabolism ; Amino Acyl-tRNA Synthetases/chemistry/genetics/*metabolism ; Animals ; Cytosol/metabolism ; Humans ; Leishmania/*enzymology/isolation &amp; purification ; Leishmaniasis/enzymology/parasitology/*pathology ; Mitochondria/metabolism ; Phylogeny ; RNA, Transfer/*genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Trypanosomatid parasites are responsible for various human diseases, such as sleeping sickness, animal trypanosomiasis, or cutaneous and visceral leishmaniases. The few available drugs to fight related parasitic infections are often toxic and present poor efficiency and specificity, and thus, finding new molecular targets is imperative. Aminoacyl-tRNA synthetases (aaRSs) are essential components of the translational machinery as they catalyze the specific attachment of an amino acid onto cognate tRNA(s). In trypanosomatids, one gene encodes both cytosolic- and mitochondrial-targeted aaRSs, with only three exceptions. We identify here a unique specific feature of aaRSs from trypanosomatids, which is that most of them harbor distinct insertion and/or extension sequences. Among the 26 identified aaRSs in the trypanosome Leishmania tarentolae, 14 contain an additional domain or a terminal extension, confirmed in mature mRNAs by direct cDNA nanopore sequencing. Moreover, these RNA-Seq data led us to address the question of aaRS dual localization and to determine splice-site locations and the 5'-UTR lengths for each mature aaRS-encoding mRNA. Altogether, our results provided evidence for at least one specific mechanism responsible for mitochondrial addressing of some L. tarentolae aaRSs. We propose that these newly identified features of trypanosomatid aaRSs could be developed as relevant drug targets to combat the diseases caused by these parasites.}, }
@article {pmid34171617, year = {2021}, author = {Iwata, R and Vanderhaeghen, P}, title = {Regulatory roles of mitochondria and metabolism in neurogenesis.}, journal = {Current opinion in neurobiology}, volume = {69}, number = {}, pages = {231-240}, pmid = {34171617}, issn = {1873-6882}, mesh = {Cell Differentiation ; Cell Proliferation ; Humans ; Mitochondria ; *Neural Stem Cells/metabolism ; *Neurogenesis ; }, abstract = {Neural stem cells (NSCs) undergo massive molecular and cellular changes during neuronal differentiation. These include mitochondria and metabolism remodelling, which were thought to be mostly permissive cues, but recent work indicates that they are causally linked to neurogenesis. Striking remodelling of mitochondria occurs right after mitosis of NSCs, which influences the postmitotic daughter cells towards self-renewal or differentiation. The transitioning to neuronal fate requires metabolic rewiring including increased oxidative phosphorylation activity, which drives transcriptional and epigenetic effects to influence cell fate. Mitochondria metabolic pathways also contribute in an essential way to the regulation of NSC proliferation and self-renewal. The influence of mitochondria and metabolism on neurogenesis is conserved from fly to human systems, but also displays striking differences linked to cell context or species. These new findings have important implications for our understanding of neurodevelopmental diseases and possibly human brain evolution.}, }
@article {pmid34166699, year = {2021}, author = {Xu, XD and Guan, JY and Zhang, ZY and Cao, YR and Storey, KB and Yu, DN and Zhang, JY}, title = {Novel tRNA gene rearrangements in the mitochondrial genomes of praying mantises (Mantodea: Mantidae): Translocation, duplication and pseudogenization.}, journal = {International journal of biological macromolecules}, volume = {185}, number = {}, pages = {403-411}, doi = {10.1016/j.ijbiomac.2021.06.096}, pmid = {34166699}, issn = {1879-0003}, mesh = {Animals ; Evolution, Molecular ; Gene Duplication ; Gene Order ; *Gene Rearrangement ; Genome, Mitochondrial ; Mantodea/*genetics ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; Pseudogenes ; RNA, Plant/genetics ; RNA, Transfer/chemistry/*genetics ; Sequence Analysis, DNA ; Translocation, Genetic ; }, abstract = {Gene rearrangements have been found in several mitochondrial genomes of Mantodea, located in the gene blocks CR-I-Q-M-ND2, COX1-K-D-ATP8 and ND3-A-R-N-S-E-F-ND5. We have sequenced one mitogenome of Amelidae (Yersinia mexicana) and six mitogenomes of Mantidae to discuss the mitochondrial gene rearrangement and the phylogenetic relationship within Mantidae. These mitogenomes showed rearrangements of tRNA genes except for Asiadodis yunnanensis and Hierodula zhangi. These novel gene rearrangements of Mantidae were primarily concentrated in the region of CR-I-Q-M-ND2, including gene translocation, duplication and pseudogenization. For the occurrences of these rearrangements, the tandem duplication-random loss (TDRL) model and slipped-strand mispairing model were suitable to explain. Large non-coding regions (LNCRs) located in the region of CR-I-Q-M-ND2 were detected in most Mantidae species, whereas some LNCRs had high similarity to the control region (CR). Both BI and ML phylogenetic analyses supported the monophyly of Mantidae and the paraphyly of Mantinae. The phylogenetic results with the gene order and the location of NCRs acted as forceful evidence that specific gene rearrangements and special LNCRs may be synapomorphies for several groups of mantises.}, }
@article {pmid34158556, year = {2021}, author = {Soukal, P and Hrdá, &#x160; and Karnkowska, A and Milanowski, R and Szabová, J and Hradilová, M and Strnad, H and Vlček, &#x10c; and Čepička, I and Hampl, V}, title = {Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {13070}, pmid = {34158556}, issn = {2045-2322}, mesh = {Biological Evolution ; Chromatium/genetics/*metabolism ; Euglenida/*genetics/metabolism ; Exons/genetics ; Genome ; Heterotrophic Processes ; Introns/genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Transcriptome/genetics ; }, abstract = {Euglenids represent a group of protists with diverse modes of feeding. To date, only a partial genomic sequence of Euglena gracilis and transcriptomes of several phototrophic and secondarily osmotrophic species are available, while primarily heterotrophic euglenids are seriously undersampled. In this work, we begin to fill this gap by presenting genomic and transcriptomic drafts of a primary osmotroph, Rhabdomonas costata. The current genomic assembly length of 100 Mbp is 14× smaller than that of E. gracilis. Despite being too fragmented for comprehensive gene prediction it provided fragments of the mitochondrial genome and comparison of the transcriptomic and genomic data revealed features of its introns, including several candidates for nonconventional types. A set of 39,456 putative R. costata proteins was predicted from the transcriptome. Annotation of the mitochondrial core metabolism provides the first data on the facultatively anaerobic mitochondrion of R. costata, which in most respects resembles the mitochondrion of E. gracilis with a certain level of streamlining. R. costata can synthetise thiamine by enzymes of heterogenous provenances and haem by a mitochondrial-cytoplasmic C4 pathway with enzymes orthologous to those found in E. gracilis. The low percentage of green algae-affiliated genes supports the ancestrally osmotrophic status of this species.}, }
@article {pmid34155201, year = {2021}, author = {Evers, F and Cabrera-Orefice, A and Elurbe, DM and Kea-Te Lindert, M and Boltryk, SD and Voss, TS and Huynen, MA and Brandt, U and Kooij, TWA}, title = {Composition and stage dynamics of mitochondrial complexes in Plasmodium falciparum.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3820}, pmid = {34155201}, issn = {2041-1723}, mesh = {Electron Transport Chain Complex Proteins/metabolism/ultrastructure ; Evolution, Molecular ; *Life Cycle Stages ; Mitochondria/*metabolism/ultrastructure ; Mitochondrial Proteins/metabolism/ultrastructure ; Multiprotein Complexes/metabolism/ultrastructure ; Oxidative Phosphorylation ; Plasmodium falciparum/growth &amp; development/*metabolism/ultrastructure ; Protozoan Proteins/metabolism/ultrastructure ; Species Specificity ; }, abstract = {Our current understanding of mitochondrial functioning is largely restricted to traditional model organisms, which only represent a fraction of eukaryotic diversity. The unusual mitochondrion of malaria parasites is a validated drug target but remains poorly understood. Here, we apply complexome profiling to map the inventory of protein complexes across the pathogenic asexual blood stages and the transmissible gametocyte stages of Plasmodium falciparum. We identify remarkably divergent composition and clade-specific additions of all respiratory chain complexes. Furthermore, we show that respiratory chain complex components and linked metabolic pathways are up to 40-fold more prevalent in gametocytes, while glycolytic enzymes are substantially reduced. Underlining this functional switch, we find that cristae are exclusively present in gametocytes. Leveraging these divergent properties and stage dynamics for drug development presents an attractive opportunity to discover novel classes of antimalarials and increase our repertoire of gametocytocidal drugs.}, }
@article {pmid34154402, year = {2021}, author = {Comandatore, F and Radaelli, G and Montante, S and Sacchi, L and Clementi, E and Epis, S and Cafiso, A and Serra, V and Pajoro, M and Di Carlo, D and Floriano, AM and Stavru, F and Bandi, C and Sassera, D}, title = {Modeling the Life Cycle of the Intramitochondrial Bacterium "Candidatus Midichloria mitochondrii" Using Electron Microscopy Data.}, journal = {mBio}, volume = {12}, number = {3}, pages = {e0057421}, pmid = {34154402}, issn = {2150-7511}, mesh = {Alphaproteobacteria/*growth &amp; development/*ultrastructure ; Animals ; DNA, Bacterial ; Ixodes/*microbiology ; *Life Cycle Stages ; Microscopy, Electron/*methods ; Mitochondria/microbiology ; Phylogeny ; Symbiosis ; }, abstract = {"Candidatus Midichloria mitochondrii" is a Gram-negative bacterium that lives in strict intracellular symbiosis with the hard tick Ixodes ricinus, forming one of the most intriguing endosymbiosis described to date. The bacterium is capable of durably colonizing the host mitochondria, a peculiar tropism that makes "Ca. Midichloria mitochondrii" a very interesting tool to study the physiology of these cellular organelles. The interaction between the symbiont and the organelle has, however, been difficult to characterize. A parallelism with the predatory bacterium Bdellovibrio bacteriovorus has been drawn, suggesting the hypothesis that "Ca. Midichloria mitochondrii" could prey on mitochondria and consume them to multiply. We studied the life cycle of the bacterium within the host oocytes using a multidisciplinary approach, including electron microscopy, molecular biology, statistics, and systems biology. Our results were not coherent with a predatory-like behavior by "Ca. Midichloria mitochondrii" leading us to propose a novel hypothesis for its life cycle. Based on our results, we here present a novel model called the "mitochondrion-to-mitochondrion hypothesis." Under this model, the bacterium would be able to move from mitochondrion to mitochondrion, possibly within a mitochondrial network. We show that this model presents a good fit with quantitative electron microscopy data. IMPORTANCE Our results suggest that "Candidatus Midichloria mitochondrii," the intramitochondrial bacterium, does not invade mitochondria like predatory bacteria do but instead moves from mitochondrion to mitochondrion within the oocytes of Ixodes ricinus. A better understanding of the lifestyle of "Ca. Midichloria mitochondrii" will allow us to better define the role of this bacterial symbiont in the host physiology.}, }
@article {pmid34145919, year = {2021}, author = {Dymek, AM and Pecio, A and Piprek, RP}, title = {Diversity of Balbiani body formation in internally and externally fertilizing representatives of Osteoglossiformes (Teleostei: Osteoglossomorpha).}, journal = {Journal of morphology}, volume = {282}, number = {9}, pages = {1313-1329}, doi = {10.1002/jmor.21387}, pmid = {34145919}, issn = {1097-4687}, mesh = {Animals ; Fertilization ; Germ Cells ; Male ; Mitochondria ; *Oocytes/metabolism ; *Oogenesis ; }, abstract = {During the early stages of oogenesis, the Balbiani body is formed in the primary oocytes. It consists of the Golgi apparatus, endoplasmic reticulum (ER), and numerous mitochondria aggregated with germ plasm, but its form may differ among animals. Hypothetically, during oogenesis oocytes become adapted to future development in two different environments depending on internal or external fertilization. We aimed to investigate, using light and transmission electron microscopy, the development of the Balbiani body during oogenesis in representatives of Osteoglossiformes, one of the most basal Teleostei groups. We analyzed the structure of oogonia and primary oocytes in the internally fertilizing butterflyfish Pantodon buchholzi and the externally fertilizing Osteoglossum bicirrhosum and Arapaima gigas to compare formation of the Balbiani body in relation to modes of fertilization. We demonstrated that the presence of the germ plasm as well as the fusion and fission of mitochondria are the conserved features of the Bb. However, each species exhibited also some peculiar features, including the presence of three types of ooplasm with different electron density and mitochondria-associated membranes in P. buchholzi; annulate lamellae, complexes of the Golgi apparatus, ER network, and lysosome-like bodies in O. bicirrhosum; as well as karmellae and whorls formed by the lamellae of the ER in A. gigas. Moreover, the form of the germ plasm observed in close contact with mitochondria differed between osteoglossiforms, with a "net-like" structure in P. buchholzi, the presence of numerous strings in O. bicirrhosum, and irregular accumulations in A. gigas. These unique features indicate that the extreme diversity of gamete structure observed so far only in the spermatozoa of osteoglossiforms is also characteristic for oocyte development in these basal teleosts. Possible reason of this variability is a period of about 150 million years of independent evolution of the lineages.}, }
@article {pmid34140474, year = {2021}, author = {Jin, L and Tang, Q and Hu, S and Chen, Z and Zhou, X and Zeng, B and Wang, Y and He, M and Li, Y and Gui, L and Shen, L and Long, K and Ma, J and Wang, X and Chen, Z and Jiang, Y and Tang, G and Zhu, L and Liu, F and Zhang, B and Huang, Z and Li, G and Li, D and Gladyshev, VN and Yin, J and Gu, Y and Li, X and Li, M}, title = {A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3715}, pmid = {34140474}, issn = {2041-1723}, mesh = {Adipose Tissue/*metabolism ; Alternative Splicing ; Animals ; Biological Evolution ; Cell Line ; Cell Lineage ; Cell Nucleus/genetics/metabolism ; Enhancer Elements, Genetic ; Evolution, Molecular ; Gene Expression Profiling ; Gene Regulatory Networks ; MicroRNAs/genetics/*metabolism ; Mitochondria/metabolism ; Molecular Conformation ; Muscle, Skeletal/*metabolism ; Myofibrils/genetics/metabolism ; Phylogeny ; Promoter Regions, Genetic ; RNA, Circular/genetics/*metabolism ; RNA, Long Noncoding/genetics/*metabolism ; RNA, Messenger/genetics/*metabolism ; Spatial Analysis ; Swine ; Transcriptome/*genetics ; }, abstract = {A comprehensive transcriptomic survey of pigs can provide a mechanistic understanding of tissue specialization processes underlying economically valuable traits and accelerate their use as a biomedical model. Here we characterize four transcript types (lncRNAs, TUCPs, miRNAs, and circRNAs) and protein-coding genes in 31 adult pig tissues and two cell lines. We uncover the transcriptomic variability among 47 skeletal muscles, and six adipose depots linked to their different origins, metabolism, cell composition, physical activity, and mitochondrial pathways. We perform comparative analysis of the transcriptomes of seven tissues from pigs and nine other vertebrates to reveal that evolutionary divergence in transcription potentially contributes to lineage-specific biology. Long-range promoter-enhancer interaction analysis in subcutaneous adipose tissues across species suggests evolutionarily stable transcription patterns likely attributable to redundant enhancers buffering gene expression patterns against perturbations, thereby conferring robustness during speciation. This study can facilitate adoption of the pig as a biomedical model for human biology and disease and uncovers the molecular bases of valuable traits.}, }
@article {pmid34136489, year = {2021}, author = {Gažová, I and Lefevre, L and Bush, SJ and Rojo, R and Hume, DA and Lengeling, A and Summers, KM}, title = {CRISPR-Cas9 Editing of Human Histone Deubiquitinase Gene USP16 in Human Monocytic Leukemia Cell Line THP-1.}, journal = {Frontiers in cell and developmental biology}, volume = {9}, number = {}, pages = {679544}, pmid = {34136489}, issn = {2296-634X}, abstract = {USP16 is a histone deubiquitinase which facilitates G2/M transition during the cell cycle, regulates DNA damage repair and contributes to inducible gene expression. We mutated the USP16 gene in a high differentiation clone of the acute monocytic leukemia cell line THP-1 using the CRISPR-Cas9 system and generated four homozygous knockout clones. All were able to proliferate and to differentiate in response to phorbol ester (PMA) treatment. One line was highly proliferative prior to PMA treatment and shut down proliferation upon differentiation, like wild type. Three clones showed sustained expression of the progenitor cell marker MYB, indicating that differentiation had not completely blocked proliferation in these clones. Network analysis of transcriptomic differences among wild type, heterozygotes and homozygotes showed clusters of genes that were up- or down-regulated after differentiation in all cell lines. Prior to PMA treatment, the homozygous clones had lower levels than wild type of genes relating to metabolism and mitochondria, including SRPRB, encoding an interaction partner of USP16. There was also apparent loss of interferon signaling. In contrast, a number of genes were up-regulated in the homozygous cells compared to wild type at baseline, including other deubiquitinases (USP12, BAP1, and MYSM1). However, three homozygotes failed to fully induce USP3 during differentiation. Other network clusters showed effects prior to or after differentiation in the homozygous clones. Thus the removal of USP16 affected the transcriptome of the cells, although all these lines were able to survive, which suggests that the functions attributed to USP16 may be redundant. Our analysis indicates that the leukemic line can adapt to the extreme selection pressure applied by the loss of USP16, and the harsh conditions of the gene editing and selection protocol, through different compensatory pathways. Similar selection pressures occur during the evolution of a cancer in vivo, and our results can be seen as a case study in leukemic cell adaptation. USP16 has been considered a target for cancer chemotherapy, but our results suggest that treatment would select for escape mutants that are resistant to USP16 inhibitors.}, }
@article {pmid34133204, year = {2021}, author = {Cadena, LR and Gahura, O and Panicucci, B and Zíková, A and Hashimi, H}, title = {Mitochondrial Contact Site and Cristae Organization System and F1FO-ATP Synthase Crosstalk Is a Fundamental Property of Mitochondrial Cristae.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {e0032721}, pmid = {34133204}, issn = {2379-5042}, abstract = {Mitochondrial cristae are polymorphic invaginations of the inner membrane that are the fabric of cellular respiration. Both the mitochondrial contact site and cristae organization system (MICOS) and the F1FO-ATP synthase are vital for sculpting cristae by opposing membrane-bending forces. While MICOS promotes negative curvature at crista junctions, dimeric F1FO-ATP synthase is crucial for positive curvature at crista rims. Crosstalk between these two complexes has been observed in baker's yeast, the model organism of the Opisthokonta supergroup. Here, we report that this property is conserved in Trypanosoma brucei, a member of the Discoba clade that separated from the Opisthokonta ∼2 billion years ago. Specifically, one of the paralogs of the core MICOS subunit Mic10 interacts with dimeric F1FO-ATP synthase, whereas the other core Mic60 subunit has a counteractive effect on F1FO-ATP synthase oligomerization. This is evocative of the nature of MICOS-F1FO-ATP synthase crosstalk in yeast, which is remarkable given the diversification that these two complexes have undergone during almost 2 eons of independent evolution. Furthermore, we identified a highly diverged, putative homolog of subunit e, which is essential for the stability of F1FO-ATP synthase dimers in yeast. Just like subunit e, it is preferentially associated with dimers and interacts with Mic10, and its silencing results in severe defects to cristae and the disintegration of F1FO-ATP synthase dimers. Our findings indicate that crosstalk between MICOS and dimeric F1FO-ATP synthase is a fundamental property impacting crista shape throughout eukaryotes. IMPORTANCE Mitochondria have undergone profound diversification in separate lineages that have radiated since the last common ancestor of eukaryotes some eons ago. Most eukaryotes are unicellular protists, including etiological agents of infectious diseases, like Trypanosoma brucei. Thus, the study of a broad range of protists can reveal fundamental features shared by all eukaryotes and lineage-specific innovations. Here, we report that two different protein complexes, MICOS and F1FO-ATP synthase, known to affect mitochondrial architecture, undergo crosstalk in T. brucei, just as in baker's yeast. This is remarkable considering that these complexes have otherwise undergone many changes during their almost 2 billion years of independent evolution. Thus, this crosstalk is a fundamental property needed to maintain proper mitochondrial structure even if the constituent players considerably diverged.}, }
@article {pmid34131078, year = {2021}, author = {Hoshino, Y and Gaucher, EA}, title = {Evolution of bacterial steroid biosynthesis and its impact on eukaryogenesis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {25}, pages = {}, pmid = {34131078}, issn = {1091-6490}, support = {R01 AR069137/AR/NIAMS NIH HHS/United States ; }, mesh = {Archaea/genetics ; Bacteria/genetics/*metabolism ; Bayes Theorem ; *Biosynthetic Pathways/genetics ; Cell Membrane/metabolism ; Eukaryotic Cells/*metabolism ; *Evolution, Molecular ; Genes, Bacterial ; Phylogeny ; Steroids/*biosynthesis ; }, abstract = {Steroids are components of the eukaryotic cellular membrane and have indispensable roles in the process of eukaryotic endocytosis by regulating membrane fluidity and permeability. In particular, steroids may have been a structural prerequisite for the acquisition of mitochondria via endocytosis during eukaryogenesis. While eukaryotes are inferred to have evolved from an archaeal lineage, there is little similarity between the eukaryotic and archaeal cellular membranes. As such, the evolution of eukaryotic cellular membranes has limited our understanding of eukaryogenesis. Despite evolving from archaea, the eukaryotic cellular membrane is essentially a fatty acid bacterial-type membrane, which implies a substantial bacterial contribution to the evolution of the eukaryotic cellular membrane. Here, we address the evolution of steroid biosynthesis in eukaryotes by combining ancestral sequence reconstruction and comprehensive phylogenetic analyses of steroid biosynthesis genes. Contrary to the traditional assumption that eukaryotic steroid biosynthesis evolved within eukaryotes, most steroid biosynthesis genes are inferred to be derived from bacteria. In particular, aerobic deltaproteobacteria (myxobacteria) seem to have mediated the transfer of key genes for steroid biosynthesis to eukaryotes. Analyses of resurrected steroid biosynthesis enzymes suggest that the steroid biosynthesis pathway in early eukaryotes may have been similar to the pathway seen in modern plants and algae. These resurrected proteins also experimentally demonstrate that molecular oxygen was required to establish the modern eukaryotic cellular membrane during eukaryogenesis. Our study provides unique insight into relationships between early eukaryotes and other bacteria in addition to the well-known endosymbiosis with alphaproteobacteria.}, }
@article {pmid34129020, year = {2021}, author = {Mixão, V and Hegedűsová, E and Saus, E and Pryszcz, LP and Cillingová, A and Nosek, J and Gabaldón, T}, title = {Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {28}, number = {3}, pages = {}, pmid = {34129020}, issn = {1756-1663}, support = {//European Union's Horizon 2020 Research and Innovation/ ; }, mesh = {Candida/*genetics/metabolism ; Cell Nucleus/*genetics ; *Genome, Fungal ; *Genome, Mitochondrial ; *Metabolic Networks and Pathways ; Phenols/*metabolism ; Whole Genome Sequencing ; }, abstract = {Candida subhashii belongs to the CUG-Ser clade, a group of phylogenetically closely related yeast species that includes some human opportunistic pathogens, such as Candida albicans. Despite being present in the environment, C. subhashii was initially described as the causative agent of a case of peritonitis. Considering the relevance of whole-genome sequencing and analysis for our understanding of genome evolution and pathogenicity, we sequenced, assembled and annotated the genome of C. subhashii type strain. Our results show that C. subhashii presents a highly heterozygous genome and other signatures that point to a hybrid ancestry. The presence of functional pathways for assimilation of hydroxyaromatic compounds goes in line with the affiliation of this yeast with soil microbial communities involved in lignin decomposition. Furthermore, we observed that different clones of this strain may present circular or linear mitochondrial DNA. Re-sequencing and comparison of strains with differential mitochondrial genome topology revealed five candidate genes potentially associated with this conformational change: MSK1, SSZ1, ALG5, MRPL9 and OYE32.}, }
@article {pmid34118265, year = {2021}, author = {Manoj, KM and Bazhin, NM}, title = {The murburn precepts for aerobic respiration and redox homeostasis.}, journal = {Progress in biophysics and molecular biology}, volume = {167}, number = {}, pages = {104-120}, doi = {10.1016/j.pbiomolbio.2021.05.010}, pmid = {34118265}, issn = {1873-1732}, mesh = {*Adenosine Triphosphate/metabolism ; *Cell Respiration ; Energy Metabolism ; Homeostasis ; Oxidation-Reduction ; Oxidative Phosphorylation ; Respiration ; }, abstract = {Murburn concept is a new perspective to metabolism which posits that certain redox enzymes/proteins mediate catalysis outside their active site, via diffusible reactive oxygen species (DROS, usually deemed as toxic wastes). We have recently questioned the proton-centric chemiosmotic rotary ATP synthesis (CRAS) explanation for mitochondrial oxidative phosphorylation (mOxPhos) and proposed an oxygen-centric murburn model in lieu. Herein, the chemical equations and thermodynamic foundations for this new model of mOxPhos are detailed. Standard transformed Gibbs free energy values of respiratory reactions are calculated to address the spontaneity, control, and efficiency of oxidative phosphorylation. Unlike the deterministic/multi-molecular and 'irreducibly complex' CRAS model, the stochastic/bimolecular and parsimonious murburn reactions afford a more viable precept for the variable and non-integral stoichiometry, higher yield for NADH than FADH2, and origin/evolution of oxygen-centric cellular life. Also, we present tangible DROS-based explanations for the multiple roles of various reaction components, HCN > H2S order of cellular toxicity in aerobes, and explain why oxygen inhibits anaerobes. We highlight the thermodynamic significance of proton deficiency in NADH/mitochondria and link the 'oxygen → DROS → water' metabolic pathway to the macroscopic physiologies of ATP-synthesis, trans-membrane potential, thermogenesis, and homeostasis. We also provide arguments for the extension of the murburn bioenergetics model to life under anoxic and extreme/unique habitats. In the context of mOxPhos, our findings imply that DROS should be seen as an essential requisite for life, and not merely as pathophysiological manifestations.}, }
@article {pmid34111145, year = {2021}, author = {Horoiwa, M and Mandagi, IF and Sutra, N and Montenegro, J and Tantu, FY and Masengi, KWA and Nagano, AJ and Kusumi, J and Yasuda, N and Yamahira, K}, title = {Mitochondrial introgression by ancient admixture between two distant lacustrine fishes in Sulawesi Island.}, journal = {PloS one}, volume = {16}, number = {6}, pages = {e0245316}, pmid = {34111145}, issn = {1932-6203}, mesh = {Animals ; Ecosystem ; Fishes/*genetics ; *Genetic Introgression ; Indonesia ; Islands ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Sulawesi, an island located in a biogeographical transition zone between Indomalaya and Australasia, is famous for its high levels of endemism. Ricefishes (family Adrianichthyidae) are an example of taxa that have uniquely diversified on this island. It was demonstrated that habitat fragmentation due to the Pliocene juxtaposition among tectonic subdivisions of this island was the primary factor that promoted their divergence; however, it is also equally probable that habitat fusions and resultant admixtures between phylogenetically distant species may have frequently occurred. Previous studies revealed that some individuals of Oryzias sarasinorum endemic to a tectonic lake in central Sulawesi have mitochondrial haplotypes that are similar to the haplotypes of O. eversi, which is a phylogenetically related but geologically distant (ca. 190 km apart) adrianichthyid endemic to a small fountain. In this study, we tested if this reflects ancient admixture of O. eversi and O. sarasinorum. Population genomic analyses of genome-wide single-nucleotide polymorphisms revealed that O. eversi and O. sarasinorum are substantially reproductively isolated from each other. Comparison of demographic models revealed that the models assuming ancient admixture from O. eversi to O. sarasinorum was more supported than the models assuming no admixture; this supported the idea that the O. eversi-like mitochondrial haplotype in O. sarasinorum was introgressed from O. eversi. This study is the first to demonstrate ancient admixture of lacustrine or pond organisms in Sulawesi beyond 100 km. The complex geological history of this island enabled such island-wide admixture of lacustrine organisms, which usually experience limited migration.}, }
@article {pmid34109499, year = {2021}, author = {Riyaz, M and Shah, RA and Savarimuthu, I and Kuppusamy, S}, title = {Comparative mitochondrial genome analysis of Eudocima salaminia (Cramer, 1777) (Lepidoptera: Noctuoidea), novel gene rearrangement and phylogenetic relationship within the superfamily Noctuoidea.}, journal = {Molecular biology reports}, volume = {48}, number = {5}, pages = {4449-4463}, pmid = {34109499}, issn = {1573-4978}, support = {EMR/2017/000566//DST/ ; }, mesh = {Animals ; Base Pairing/genetics ; Gene Order ; *Gene Rearrangement ; *Genes, Insect ; *Genome, Mitochondrial ; India ; Insect Proteins/genetics ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Moths/*classification/*genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {The species Eudocima salaminia (Cramer, 1777) commonly known as the fruit-piercing moth belongs to family Erebidae. Its distribution varies from India and across South-east Asia, pacific islands and parts of Australia. The insect is a devastating pest of citrus, longans and lychees. In the present study, complete mitochondrial genome of Eudocima salaminia was sequenced and analyzed using Illumina sequencer. The phylogenetic tree was reconstructed based on nucleotide sequences of 13 PCGs using Maximum likelihood method-General Reversible mitochondrial (mtREV) model. The mitogenome has 15,597 base pairs (bp) in length, comprising of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and A + T-rich region. All protein-coding genes (PCGs) initiate with canonical start codon ATN. The gene order (trnQ-trnI-trnM) of tRNA shows a different rearrangement compared to ancestral insect gene order (trnI-trnQ-trnM). Almost all tRNAs have a typical cloverleaf secondary structure except for trnS1 (AGN) which lacks the dihydrouridine arm. At the beginning of the control region, we observed a conserved polyT", motif "ATTTA" and microsatellite (TA)n element. There are 21 intergenic regions and five overlapping regions ranging from 1 to 73 bp and 1 to 8 bp, respectively. The phylogenetic relationships based on nucleotide sequences of 13 PCGs using Maximum likelihood method showed the family level relationships as (Notodontidae + (Euteliidae + Noctuidae + (Erebidae + Nolidae))). The present study represents the similarity to phylogenetic analysis of Noctuoidea mitogenome. Moreover, the family Erebidae is the sister to the families of (Euteliidae + Noctuidae + Nolidae).}, }
@article {pmid34099752, year = {2021}, author = {Machkour-M'Rabet, S and Hanes, MM and Martínez-Noguez, JJ and Cruz-Medina, J and García-De León, FJ}, title = {The queen conch mitogenome: intra- and interspecific mitogenomic variability in Strombidae and phylogenetic considerations within the Hypsogastropoda.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {11972}, pmid = {34099752}, issn = {2045-2322}, mesh = {Animals ; Base Sequence ; Caribbean Region ; Cell Extracts/genetics ; Gastropoda/*classification/*genetics ; Mitochondria/genetics/metabolism ; NAD/metabolism ; Phylogeny ; RNA, Ribosomal/metabolism ; RNA, Transfer/metabolism ; }, abstract = {Aliger gigas is an economically important and vulnerable marine species. We present a new mitogenome of A. gigas from the Mexican Caribbean and use the eight publicly available Strombidae mitogenomes to analyze intra- and interspecific variation. We present the most complete phylogenomic understanding of Hypsogastropoda to date (17 superfamilies, 39 families, 85 genera, 109 species) to revisit the phylogenetic position of the Stromboidea and evaluate divergence times throughout the phylogeny. The A. gigas mitogenome comprises 15,460 bp including 13 PCGs, 22 tRNAs, and two rRNAs. Nucleotide diversity suggested divergence between the Mexican and Colombian lineages of A. gigas. Interspecific divergence showed high differentiation among Strombidae species and demonstrated a close relationship between A. gigas and Strombus pugilis, between Lambis lambis and Harpago chiragra, and among Tridentarius dentatus/Laevistrombus canarium/Ministrombus variabilis. At the intraspecific level, the gene showing the highest differentiation is ATP8 and the lowest is NAD4L, whereas at the interspecific level the NAD genes show the highest variation and the COX genes the lowest. Phylogenomic analyses confirm that Stromboidea belongs in the non-Latrogastropoda clade and includes Xenophoridea. The phylogenomic position of other superfamilies, including those of previously uncertain affiliation, is also discussed. Finally, our data indicated that Stromboidea diverged into two principal clades in the early Cretaceous while Strombidae diversified in the Paleocene, and lineage diversification within A. gigas took place in the Pleistocene.}, }
@article {pmid34098144, year = {2021}, author = {Spinelli, S and Begani, G and Guida, L and Magnone, M and Galante, D and D'Arrigo, C and Scotti, C and Iamele, L and De Jonge, H and Zocchi, E and Sturla, L}, title = {LANCL1 binds abscisic acid and stimulates glucose transport and mitochondrial respiration in muscle cells via the AMPK/PGC-1α/Sirt1 pathway.}, journal = {Molecular metabolism}, volume = {53}, number = {}, pages = {101263}, pmid = {34098144}, issn = {2212-8778}, mesh = {AMP-Activated Protein Kinases/*metabolism ; Abscisic Acid/*metabolism ; Glucose/metabolism ; HeLa Cells ; Humans ; Mitochondria/metabolism ; Muscle, Skeletal/cytology/metabolism ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/*metabolism ; Receptors, G-Protein-Coupled/genetics/*metabolism ; Sirtuin 1/*metabolism ; }, abstract = {OBJECTIVE: Abscisic acid (ABA) is a plant hormone also present and active in animals. In mammals, ABA regulates blood glucose levels by stimulating insulin-independent glucose uptake and metabolism in adipocytes and myocytes through its receptor LANCL2. The objective of this study was to investigate whether another member of the LANCL protein family, LANCL1, also behaves as an ABA receptor and, if so, which functional effects are mediated by LANCL1.<br><br>METHODS: ABA binding to human recombinant LANCL1 was explored by equilibrium-binding experiments with [[3]H]ABA, circular dichroism, and surface plasmon resonance. Rat L6 myoblasts overexpressing either LANCL1 or LANCL2, or silenced for the expression of both proteins, were used to investigate the basal and ABA-stimulated transport of a fluorescent glucose analog (NBDG) and the signaling pathway downstream of the LANCL proteins using Western blot and qPCR analysis. Finally, glucose tolerance and sensitivity to ABA were compared in LANCL2[-/-] and wild-type (WT) siblings.<br><br>RESULTS: Human recombinant LANCL1 binds ABA with a Kd between 1 and 10&#xa0;&#x3bc;M, depending on the assay (i.e., in a concentration range that lies between the low and high-affinity ABA binding sites of LANCL2). In L6 myoblasts, LANCL1 and LANCL2 similarly, i) stimulate both basal and ABA-triggered NBDG uptake (4-fold), ii) activate the transcription and protein expression of the glucose transporters GLUT4 and GLUT1 (4-6-fold) and the signaling proteins AMPK/PGC-1&#x3b1;/Sirt1 (2-fold), iii) stimulate mitochondrial respiration (5-fold) and the expression of the skeletal muscle (SM) uncoupling proteins sarcolipin (3-fold) and UCP3 (12-fold). LANCL2[-/-] mice have a reduced glucose tolerance compared to WT. They spontaneously overexpress LANCL1 in the SM and respond to chronic ABA treatment (1&#xa0;&#x3bc;g/kg body weight/day) with an improved glycemia response to glucose load and an increased SM transcription of GLUT4 and GLUT1 (20-fold) of the AMPK/PGC-1&#x3b1;/Sirt1 pathway and sarcolipin, UCP3, and NAMPT (4- to 6-fold).<br><br>CONCLUSIONS: LANCL1 behaves as an ABA receptor with a somewhat lower affinity for ABA than LANCL2 but with overlapping effector functions: stimulating glucose uptake and the expression of muscle glucose transporters and mitochondrial uncoupling and respiration via the AMPK/PGC-1&#x3b1;/Sirt1 pathway. Receptor redundancy may have been advantageous in animal evolution, given the role of the ABA/LANCL system in the insulin-independent stimulation of cell glucose uptake and energy metabolism.}, }
@article {pmid34097987, year = {2021}, author = {Capitanio, G and Papa, F and Papa, S}, title = {The allosteric protein interactions in the proton-motive function of mammalian redox enzymes of the respiratory chain.}, journal = {Biochimie}, volume = {189}, number = {}, pages = {1-12}, doi = {10.1016/j.biochi.2021.05.018}, pmid = {34097987}, issn = {1638-6183}, mesh = {Allosteric Regulation ; Animals ; Cytochromes b/*metabolism ; Cytochromes c1/*metabolism ; Electron Transport Complex I/*metabolism ; Electron Transport Complex IV/*metabolism ; Humans ; *Proton-Motive Force ; }, abstract = {Insight into mammalian respiratory complexes defines the role of allosteric protein interactions in their proton-motive activity. In cytochrome c oxidase (CxIV) conformational change of subunit I, caused by O2 binding to heme a3[2+]-CuB[+] and reduction, and stereochemical transitions coupled to oxidation/reduction of heme a and CuA, combined with electrostatic effects, determine the proton pumping activity. In ubiquinone-cytochrome c oxidoreductase (CxIII) conformational movement of Fe-S protein between cytochromes b and c1 is the key element of the proton-motive activity. In NADH-ubiquinone oxidoreductase (CxI) ubiquinone binding and reduction result in conformational changes of subunits in the quinone reaction structure which initiate proton pumping.}, }
@article {pmid34089318, year = {2021}, author = {Vrzoňová, R and Tóth, R and Siváková, B and Moťovská, A and Gaplovská-Kyselá, K and Baráth, P and Tomáška, &#x13d; and Gácser, A and Gabaldón, T and Nosek, J and Neboháčová, M}, title = {OCT1 - a yeast mitochondrial thiolase involved in the 3-oxoadipate pathway.}, journal = {FEMS yeast research}, volume = {21}, number = {5}, pages = {}, doi = {10.1093/femsyr/foab034}, pmid = {34089318}, issn = {1567-1364}, mesh = {Acetyl-CoA C-Acetyltransferase/genetics ; Acetyl-CoA C-Acyltransferase/genetics ; Animals ; Chromatography, Liquid ; Mitochondria ; Phylogeny ; *Saccharomyces cerevisiae/genetics ; *Tandem Mass Spectrometry ; }, abstract = {The 3-oxoacyl-CoA thiolases catalyze the last step of the fatty acid β-oxidation pathway. In yeasts and plants, this pathway takes place exclusively in peroxisomes, whereas in animals it occurs in both peroxisomes and mitochondria. In contrast to baker's yeast Saccharomyces cerevisiae, yeast species from the Debaryomycetaceae family also encode a thiolase with predicted mitochondrial localization. These yeasts are able to utilize a range of hydroxyaromatic compounds via the 3-oxoadipate pathway the last step of which is catalyzed by 3-oxoadipyl-CoA thiolase and presumably occurs in mitochondria. In this work, we studied Oct1p, an ortholog of this enzyme from Candida parapsilosis. We found that the cells grown on a 3-oxoadipate pathway substrate exhibit increased levels of the OCT1 mRNA. Deletion of both OCT1 alleles impairs the growth of C. parapsilosis cells on 3-oxoadipate pathway substrates and this defect can be rescued by expression of the OCT1 gene from a plasmid vector. Subcellular localization experiments and LC-MS/MS analysis of enriched organellar fraction-proteins confirmed the presence of Oct1p in mitochondria. Phylogenetic profiling of Oct1p revealed an intricate evolutionary pattern indicating multiple horizontal gene transfers among different fungal groups.}, }
@article {pmid34087614, year = {2021}, author = {Mazzocca, A and Fais, S}, title = {New hypotheses for cancer generation and progression.}, journal = {Medical hypotheses}, volume = {152}, number = {}, pages = {110614}, doi = {10.1016/j.mehy.2021.110614}, pmid = {34087614}, issn = {1532-2777}, mesh = {Biological Evolution ; Carcinogenesis ; Humans ; Mutation ; *Neoplasms ; Phenotype ; Tumor Microenvironment ; }, abstract = {Since Nixon famously declared war on cancer in 1971, trillions of dollars have been spent on cancer research but the life expectancy for most forms of cancer is still poor. There are many reasons for the partial success of cancer translational research. One of these can be the predominance of certain paradigms that potentially narrowed the vision in interpreting cancer. The main paradigm to explain carcinogenesis is based on DNA mutations, which is well interpreted by the somatic mutation theory (SMT). However, a different theory claims that cancer is instead a tissue disease as proposed by the Tissue Organization Field Theory (TOFT). Here, we propose new hypotheses to explain the origin and pathogenesis of cancer. In this perspective, the systemic-evolutionary theory of cancer (SETOC) is discussed as well as how the microenvironment affects the adaptation of transformed cells and the reversion to a unicellular-like or embryo-like phenotype.}, }
@article {pmid34087289, year = {2021}, author = {Lu, Z and Tang, M and Zhang, M and Li, Y and Shi, F and Zhan, F and Zhao, L and Li, J and Lin, L and Qin, Z}, title = {Expression and functional analysis of the BCL2-Associated agonist of cell death (BAD) gene in grass carp (Ctenopharyngodon idella) during bacterial infection.}, journal = {Developmental and comparative immunology}, volume = {123}, number = {}, pages = {104160}, doi = {10.1016/j.dci.2021.104160}, pmid = {34087289}, issn = {1879-0089}, mesh = {Aeromonas hydrophila/*physiology ; Amino Acid Sequence ; Animals ; Apoptosis ; Carps/*immunology ; Cell Line ; Cloning, Molecular ; Fish Proteins/genetics/*metabolism ; Gram-Negative Bacterial Infections/*immunology ; Immunity, Innate ; Lipopolysaccharides/immunology ; Phylogeny ; Spleen ; Staphylococcal Infections/*immunology ; Staphylococcus aureus/*physiology ; Transcriptome ; Up-Regulation ; bcl-Associated Death Protein/genetics/*metabolism ; }, abstract = {The BCL2-associated agonist of cell death protein is a key participant in apoptosis dependent on mitochondria and in disease progression that involves the regulation of cell death, such as tumorigenesis, diabetes, sepsis shock, and epilepsy. Nevertheless, the mechanisms underlying the immune responses to teleost BAD bacterial infection and mitochondrial-dependent apoptosis remains unclear. In order to elucidate the mechanisms involved, in this study, a Ctenopharyngodon idella (grass carp) BAD gene named GcBAD1 was firstly cloned and characterized. The results indicated that the ORF (open reading frame) of GcBAD1 was 438 bp in length, encoding a 145-amino acid putative protein of 16.66 kDa. This deduced amino acid sequence has a better identity than another teleost species according to a phylogenetic analysis, and contains a Bcl2-BAD-1 domain. In healthy grass carp fish, the mRNA transcripts of GcBAD1 were widely present in the studied tissues, which could be ranked as follows; spleen > brain > middle-kidney > head-kidney > liver > gills > intestines > heart and muscle. In addition, during infection by Aeromonas hydrophila and Staphylococcus aureus, the mRNA transcription and protein levels expression of GcBAD1 in the head-kidney, spleen, and liver tissues of the fish were significantly up-regulated. Moreover, when the C. idellus kidney cell line (CIK) cells were incubated with Lipopolysaccharide (LPS) and lipoteichoic acid (LTA), the GcBAD1 expression transcripts were also significantly up-regulated. Additionally, overexpression of GcBAD1 in CIK cells was able to activate apoptosis-related genes, including those encoding p53, Cytochrome C (CytoC), caspase-3, and caspase-9. Besides, in the TUNEL assays, when pEGFP-BAD1 was over-expressed, the number of red signals associated with apoptosis were significantly increased in the CIK cells infected with LPS or LTA at 12 h. This study demonstrates that GcBAD1 has a significant role in the mitochondrial apoptosis pathway of grass carp's innate immunity. Our findings provide new insight into the potential mechanisms of teleost antibacterial immunity.}, }
@article {pmid34083683, year = {2021}, author = {Feng, JT and Xia, LP and Yan, CR and Miao, J and Ye, YY and Li, JJ and Guo, BY and Lü, ZM}, title = {Characterization of four mitochondrial genomes of family Neritidae (Gastropoda: Neritimorpha) and insight into its phylogenetic relationships.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {11748}, pmid = {34083683}, issn = {2045-2322}, mesh = {Animals ; Base Composition ; Codon ; Computational Biology/methods ; Gastropoda/*classification/*genetics ; Gene Rearrangement ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Genomics/methods ; Mitochondria/*genetics ; Molecular Sequence Annotation ; *Phylogeny ; Selection, Genetic ; }, abstract = {Neritidae is one of the most diverse families of Neritimorpha and possesses euryhaline properties. Members of this family usually live on tropical and subtropical coasts and are mainly gregarious. The phylogenetic relationships between several subclasses of Gastropoda have been controversial for many years. With an increase in the number of described species of Neritidae, the knowledge of the evolutionary relationships in this family has improved. In the present study, we sequenced four complete mitochondrial genomes from two genera (Clithon and Nerita) and compared them with available complete mitochondrial genomes of Neritidae. Gene order exhibited a highly conserved pattern among three genera in the Neritidae family. Our results improved the phylogenetic resolution within Neritidae, and more comprehensive taxonomic sampling of subclass Neritimorpha was proposed. Furthermore, we reconstructed the divergence among the main lineages of 19 Neritimorpha taxa under an uncorrelated relaxed molecular clock.}, }
@article {pmid34083540, year = {2021}, author = {Wang, S and Luo, H}, title = {Dating Alphaproteobacteria evolution with eukaryotic fossils.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {3324}, pmid = {34083540}, issn = {2041-1723}, mesh = {Alphaproteobacteria/*classification/*genetics ; Animals ; Cyanobacteria/classification/genetics ; Eukaryota/*classification/*genetics ; *Evolution, Molecular ; *Fossils/history/microbiology ; Genome, Bacterial ; Genome, Mitochondrial ; History, Ancient ; Mitochondria/genetics/microbiology ; Models, Biological ; Models, Genetic ; Phylogeny ; Rickettsiales/classification/genetics ; Symbiosis/genetics ; Time Factors ; }, abstract = {Elucidating the timescale of the evolution of Alphaproteobacteria, one of the most prevalent microbial lineages in marine and terrestrial ecosystems, is key to testing hypotheses on their co-evolution with eukaryotic hosts and Earth's systems, which, however, is largely limited by the scarcity of bacterial fossils. Here, we incorporate eukaryotic fossils to date the divergence times of Alphaproteobacteria, based on the mitochondrial endosymbiosis that mitochondria evolved from an alphaproteobacterial lineage. We estimate that Alphaproteobacteria arose ~1900 million years (Ma) ago, followed by rapid divergence of their major clades. We show that the origin of Rickettsiales, an order of obligate intracellular bacteria whose hosts are mostly animals, predates the emergence of animals for ~700 Ma but coincides with that of eukaryotes. This, together with reconstruction of ancestral hosts, strongly suggests that early Rickettsiales lineages had established previously underappreciated interactions with unicellular eukaryotes. Moreover, the mitochondria-based approach displays higher robustness to uncertainties in calibrations compared with the traditional strategy using cyanobacterial fossils. Further, our analyses imply the potential of dating the (bacterial) tree of life based on endosymbiosis events, and suggest that previous applications using divergence times of the modern hosts of symbiotic bacteria to date bacterial evolution might need to be revisited.}, }
@article {pmid34082186, year = {2021}, author = {Singh, L and Atilano, SR and Jager, MJ and Kenney, MC}, title = {Mitochondrial DNA polymorphisms and biogenesis genes in primary and metastatic uveal melanoma cell lines.}, journal = {Cancer genetics}, volume = {256-257}, number = {}, pages = {91-99}, doi = {10.1016/j.cancergen.2021.05.002}, pmid = {34082186}, issn = {2210-7762}, mesh = {Cell Line, Tumor ; DNA, Mitochondrial/*genetics ; Gene Dosage ; *Genes, Neoplasm ; Genome, Human ; Haplotypes/genetics ; Heteroplasmy/genetics ; Humans ; Melanoma/*genetics/*pathology ; Neoplasm Metastasis ; *Organelle Biogenesis ; Phylogeny ; *Polymorphism, Genetic ; Polymorphism, Single Nucleotide/genetics ; Uveal Neoplasms/*genetics/*pathology ; }, abstract = {PURPOSE: This study was designed to identify mitochondrial (mt) DNA variations in primary and metastatic uveal melanoma (UM) cell lines and their relation with cell metabolism to gain insight into metastatic progression.<br><br>METHOD: The entire mtDNA genomes were sequenced using Sanger sequencing from two primary UM cell lines (92.1 and MEL270) and two cell lines (OMM2.3 and OMM2.5) derived from liver metastases of the MEL270 patient. The mtDNA copy numbers determined by the ratio of nDNA versus mtDNA. qRT-PCR was used to evaluate expression levels of mitochondrial biogenesis genes.<br><br>RESULTS: Sequencing showed that cell line MEL270 and metastases-derived OMM2.3 and OMM2.5 cell lines had homoplasmic single nucleotide polymorphisms (SNPs) representing J1c7a haplogroup, whereas 92.1 cells had mtDNA H31a haplogroup. mtDNA copy numbers were significantly higher in primary cell lines. The metastatic UM cells showed down-regulation of POLG, TFAM, NRF-1 and SIRT1 compared to their primary MEL270 cells. PGC-1&#x3b1; was downregulated in 92.1 and upregulated in MEL270, OMM2.3 and OMM2.5.<br><br>CONCLUSIONS: Our finding suggests that within metastatic cells, the heteroplasmic SNPs, copy numbers and mitochondrial biogenesis genes are modulated differentially compared to their primary UM cells. Therefore, investigating pathogenic mtDNA variants associated with cancer metabolic susceptibility may provide future therapeutic strategies in metastatic UM.}, }
@article {pmid34077418, year = {2021}, author = {Castro-Pereira, D and Peres, EA and Pinto-da-Rocha, R}, title = {Systematics and phylogeography of the Brazilian Atlantic Forest endemic harvestmen Neosadocus Mello-Leitão, 1926 (Arachnida: Opiliones: Gonyleptidae).}, journal = {PloS one}, volume = {16}, number = {6}, pages = {e0249746}, pmid = {34077418}, issn = {1932-6203}, mesh = {*Animal Distribution ; Animals ; Arachnida/*classification ; *Biological Evolution ; Brazil ; Cell Nucleus/metabolism ; *Forests ; Mitochondria/metabolism ; Phylogeography ; Reproduction ; }, abstract = {Neosadocus harvestmen are endemic to the Southern Brazilian Atlantic Forest. Although they are conspicuous and display great morphological variation, their evolutionary history and the biogeographical events underlying their diversification and distribution are still unknown. This contribution about Neosadocus includes the following: a taxonomic revision; a molecular phylogenetic analysis using mitochondrial and nuclear markers; an investigation of the genetic structure and species' diversity in a phylogeographical framework. Our results show that Neosadocus is a monophyletic group and comprises four species: N. bufo, N. maximus, N. robustus and N. misandrus (which we did not find on fieldwork and only studied the female holotype). There is astonishing male polymorphism in N. robustus, mostly related to reproductive strategies. The following synonymies have resulted from this work: "Bunoweyhia" variabilis Mello-Leitão, 1935 = Neosadocus bufo (Mello-Leitão, 1926); and "Bunoweyhia" minor Mello-Leitão, 1935 = Neosadocus maximus (Giltay, 1928). Most divergences occurred during the Miocene, a geological epoch marked by intense orogenic and climatic events in the Brazilian Atlantic Forest. Intraspecific analyses indicate strong population structure, a pattern congruent with the general behavior and physiological constraints of Neotropical harvestmen.}, }
@article {pmid34073133, year = {2021}, author = {Cramer, ERA and Garcia-Del-Rey, E and Johannessen, LE and Laskemoen, T and Marthinsen, G and Johnsen, A and Lifjeld, JT}, title = {Longer Sperm Swim More Slowly in the Canary Islands Chiffchaff.}, journal = {Cells}, volume = {10}, number = {6}, pages = {}, pmid = {34073133}, issn = {2073-4409}, support = {301592//Norges Forskningsr&#xe5;d/ ; 196554//Norges Forskningsr&#xe5;d/ ; }, mesh = {Animals ; Male ; Mammals/metabolism ; Passeriformes/anatomy &amp; histology/*metabolism ; *Phenotype ; Phylogeny ; Spain ; Sperm Motility/*physiology ; Spermatozoa/*cytology ; }, abstract = {Sperm swimming performance affects male fertilization success, particularly in species with high sperm competition. Understanding how sperm morphology impacts swimming performance is therefore important. Sperm swimming speed is hypothesized to increase with total sperm length, relative flagellum length (with the flagellum generating forward thrust), and relative midpiece length (as the midpiece contains the mitochondria). We tested these hypotheses and tested for divergence in sperm traits in five island populations of Canary Islands chiffchaff (Phylloscopus canariensis). We confirmed incipient mitochondrial DNA differentiation between Gran Canaria and the other islands. Sperm swimming speed correlated negatively with total sperm length, did not correlate with relative flagellum length, and correlated negatively with relative midpiece length (for Gran Canaria only). The proportion of motile cells increased with relative flagellum length on Gran Canaria only. Sperm morphology was similar across islands. We thus add to a growing number of studies on passerine birds that do not support sperm morphology-swimming speed hypotheses. We suggest that the swimming mechanics of passerine sperm are sufficiently different from mammalian sperm that predictions from mammalian hydrodynamic models should no longer be applied for this taxon. While both sperm morphology and sperm swimming speed are likely under selection in passerines, the relationship between them requires further elucidation.}, }
@article {pmid34072215, year = {2021}, author = {Dür, A and Huber, N and Parson, W}, title = {Fine-Tuning Phylogenetic Alignment and Haplogrouping of mtDNA Sequences.}, journal = {International journal of molecular sciences}, volume = {22}, number = {11}, pages = {}, pmid = {34072215}, issn = {1422-0067}, mesh = {Algorithms ; Computational Biology/methods ; DNA, Mitochondrial/chemistry/*genetics ; Genome, Mitochondrial ; Genomics/methods ; *Haplotypes ; Humans ; Mitochondria/genetics ; *Phylogeny ; Regulatory Sequences, Nucleic Acid ; }, abstract = {In this paper, we present a new algorithm for alignment and haplogroup estimation of mitochondrial DNA (mtDNA) sequences. Based on 26,011 vetted full mitogenome sequences, we refined the 5435 original haplogroup motifs of Phylotree Build 17 without changing the haplogroup nomenclature. We adapted 430 motifs (about 8%) and added 966 motifs for yet undetermined subclades. In summary, this led to an 18% increase of haplogroup defining motifs for full mitogenomes and a 30% increase for the mtDNA control region that is of interest for a variety of scientific disciplines, such as medical, population and forensic genetics. The new algorithm is implemented in the EMPOP mtDNA database and is freely accessible.}, }
@article {pmid34070437, year = {2021}, author = {Ai, D and Peng, L and Qin, D and Zhang, Y}, title = {Characterization of Three Complete Mitogenomes of Flatidae (Hemiptera: Fulgoroidea) and Compositional Heterogeneity Analysis in the Planthoppers' Mitochondrial Phylogenomics.}, journal = {International journal of molecular sciences}, volume = {22}, number = {11}, pages = {}, pmid = {34070437}, issn = {1422-0067}, support = {31420103911//National Natural Science Foundation of China/ ; 2015FY210300//Ministry of Science and Technology of the People's Republic of China/ ; 2005DKA21402//Ministry of Science and Technology of the People's Republic of China/ ; }, mesh = {Animals ; Base Composition ; Codon Usage ; Gene Order ; *Genome, Mitochondrial ; Hemiptera/*genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Alignment ; Tandem Repeat Sequences/genetics ; }, abstract = {Although sequences of mitogenomes have been widely used for investigating phylogenetic relationship, population genetics, and biogeography in many members of Fulgoroidea, only one complete mitogenome of a member of Flatidae has been sequenced. Here, the complete mitogenomes of Cerynia lineola, Cromna sinensis, and Zecheuna tonkinensis are sequenced. The gene arrangements of the three new mitogenomes are consistent with ancestral insect mitogenomes. The strategy of using mitogenomes in phylogenetics remains in dispute due to the heterogeneity in base composition and the possible variation in evolutionary rates. In this study, we found compositional heterogeneity and variable evolutionary rates among planthopper mitogenomes. Phylogenetic analysis based on site-homogeneous models showed that the families (Delphacidae and Derbidae) with high values of Ka/Ks and A + T content tended to fall together at a basal position on the trees. Using a site-heterogeneous mixture CAT + GTR model implemented in PhyloBayes yielded almost the same topology. Our results recovered the monophyly of Fulgoroidea. In this study, we apply the heterogeneous mixture model to the planthoppers' phylogenetic analysis for the first time. Our study is based on a large sample and provides a methodological reference for future phylogenetic studies of Fulgoroidea.}, }
@article {pmid34070384, year = {2021}, author = {Di Gregorio, E and Miolo, G and Saorin, A and Steffan, A and Corona, G}, title = {From Metabolism to Genetics and Vice Versa: The Rising Role of Oncometabolites in Cancer Development and Therapy.}, journal = {International journal of molecular sciences}, volume = {22}, number = {11}, pages = {}, pmid = {34070384}, issn = {1422-0067}, mesh = {Cell Transformation, Neoplastic/*metabolism/pathology ; Humans ; Metabolic Diseases/*metabolism/pathology ; Mitochondria/*metabolism/pathology ; Neoplasms/*metabolism/pathology ; *Signal Transduction ; }, abstract = {Over the last decades, the study of cancer metabolism has returned to the forefront of cancer research and challenged the role of genetics in the understanding of cancer development. One of the major impulses of this new trend came from the discovery of oncometabolites, metabolic intermediates whose abnormal cellular accumulation triggers oncogenic signalling and tumorigenesis. These findings have led to reconsideration and support for the long-forgotten hypothesis of Warburg of altered metabolism as oncogenic driver of cancer and started a novel paradigm whereby mitochondrial metabolites play a pivotal role in malignant transformation. In this review, we describe the evolution of the cancer metabolism research from a historical perspective up to the oncometabolites discovery that spawned the new vision of cancer as a metabolic disease. The oncometabolites' mechanisms of cellular transformation and their contribution to the development of new targeted cancer therapies together with their drawbacks are further reviewed and discussed.}, }
@article {pmid34067626, year = {2021}, author = {Yamaguchi, K and Kitamura, S and Furutake, Y and Murakami, R and Yamanoi, K and Taki, M and Ukita, M and Hamanishi, J and Mandai, M}, title = {Acquired Evolution of Mitochondrial Metabolism Regulated by HNF1B in Ovarian Clear Cell Carcinoma.}, journal = {Cancers}, volume = {13}, number = {10}, pages = {}, pmid = {34067626}, issn = {2072-6694}, abstract = {Clear cell carcinoma (CCC) of the ovary exhibits a unique morphology and clinically malignant behavior. The eosinophilic cytoplasm includes abundant glycogen. Although the growth is slow, the prognosis is poor owing to resistance to conventional chemotherapies. CCC often arises in endometriotic cysts and is accompanied by endometriosis. Based on these characteristics, three clinical questions are considered: why does ovarian cancer, especially CCC and endometrioid carcinoma, frequently occur in endometriotic cysts, why do distinct histological subtypes (CCC and endometrioid carcinoma) arise in the endometriotic cyst, and why does ovarian CCC possess unique characteristics? Mutations in AT-rich interacting domain-containing protein 1A and phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit alpha genes may contribute to the carcinogenesis of ovarian CCC, whereas hepatocyte nuclear factor-1-beta (HNF1B) plays crucial roles in sculpting the unique characteristics of ovarian CCC through metabolic alterations. HNF1B increases glutathione synthesis, activates anaerobic glycolysis called the Warburg effect, and suppresses mitochondria. These metabolic changes may be induced in stressful environments. Life has evolved to utilize and control energy; eukaryotes require mitochondria to transform oxygen reduction into useful energy. Because mitochondrial function is suppressed in ovarian CCC, these cancer cells probably acquired further metabolic evolution during the carcinogenic process in order to survive stressful environments.}, }
@article {pmid34065848, year = {2021}, author = {Lyu, D and Msimbira, LA and Nazari, M and Antar, M and Pagé, A and Shah, A and Monjezi, N and Zajonc, J and Tanney, CAS and Backer, R and Smith, DL}, title = {The Coevolution of Plants and Microbes Underpins Sustainable Agriculture.}, journal = {Microorganisms}, volume = {9}, number = {5}, pages = {}, pmid = {34065848}, issn = {2076-2607}, support = {RGPIN 2020-07047.//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Terrestrial plants evolution occurred in the presence of microbes, the phytomicrobiome. The rhizosphere microbial community is the most abundant and diverse subset of the phytomicrobiome and can include both beneficial and parasitic/pathogenic microbes. Prokaryotes of the phytomicrobiome have evolved relationships with plants that range from non-dependent interactions to dependent endosymbionts. The most extreme endosymbiotic examples are the chloroplasts and mitochondria, which have become organelles and integral parts of the plant, leading to some similarity in DNA sequence between plant tissues and cyanobacteria, the prokaryotic symbiont of ancestral plants. Microbes were associated with the precursors of land plants, green algae, and helped algae transition from aquatic to terrestrial environments. In the terrestrial setting the phytomicrobiome contributes to plant growth and development by (1) establishing symbiotic relationships between plant growth-promoting microbes, including rhizobacteria and mycorrhizal fungi, (2) conferring biotic stress resistance by producing antibiotic compounds, and (3) secreting microbe-to-plant signal compounds, such as phytohormones or their analogues, that regulate aspects of plant physiology, including stress resistance. As plants have evolved, they recruited microbes to assist in the adaptation to available growing environments. Microbes serve themselves by promoting plant growth, which in turn provides microbes with nutrition (root exudates, a source of reduced carbon) and a desirable habitat (the rhizosphere or within plant tissues). The outcome of this coevolution is the diverse and metabolically rich microbial community that now exists in the rhizosphere of terrestrial plants. The holobiont, the unit made up of the phytomicrobiome and the plant host, results from this wide range of coevolved relationships. We are just beginning to appreciate the many ways in which this complex and subtle coevolution acts in agricultural systems.}, }
@article {pmid34064566, year = {2021}, author = {Jacome Burbano, MS and Gilson, E}, title = {The Power of Stress: The Telo-Hormesis Hypothesis.}, journal = {Cells}, volume = {10}, number = {5}, pages = {}, pmid = {34064566}, issn = {2073-4409}, support = {ANR-18-CE13-0029-01//Agence Nationale de la Recherche (ANR)/ ; AgeMed//Inserm/ ; }, mesh = {Adaptation, Physiological ; Animals ; DNA ; Hormesis ; Humans ; Hydrogen-Ion Concentration ; Inflammation ; Karyotyping ; Mice ; Mitochondria/metabolism ; *Mutation ; Signal Transduction ; *Stress, Physiological ; Stress, Psychological ; Telomerase/metabolism ; Telomere/*ultrastructure ; Temperature ; }, abstract = {Adaptative response to stress is a strategy conserved across evolution to promote survival. In this context, the groundbreaking findings of Miroslav Radman on the adaptative value of changing mutation rates opened new avenues in our understanding of stress response. Inspired by this work, we explore here the putative beneficial effects of changing the ends of eukaryotic chromosomes, the telomeres, in response to stress. We first summarize basic principles in telomere biology and then describe how various types of stress can alter telomere structure and functions. Finally, we discuss the hypothesis of stress-induced telomere signaling with hormetic effects.}, }
@article {pmid34061855, year = {2021}, author = {Cai, C and Gu, K and Zhao, H and Steinhagen, S and He, P and Wichard, T}, title = {Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea.}, journal = {PloS one}, volume = {16}, number = {6}, pages = {e0250968}, pmid = {34061855}, issn = {1932-6203}, mesh = {China ; Chlorophyta/*genetics ; Genetic Markers/*genetics ; Genome, Chloroplast/genetics ; Phylogeny ; }, abstract = {Over the past decade, Ulva compressa, a cosmopolitan green algal species, has been identified as a component of green tides in the Yellow Sea, China. In the present study, we sequenced and annotated the complete chloroplast genome of U. compressa (alpha-numeric code: RD9023) and focused on the assessment of genome length, homology, gene order and direction, intron size, selection strength, and substitution rate. We compared the chloroplast genome with the mitogenome. The generated phylogenetic tree was analyzed based on single and aligned genes in the chloroplast genome of Ulva compared to mitogenome genes to detect evolutionary trends. U. compressa and U. mutabilis chloroplast genomes had similar gene queues, with individual genes exhibiting high homology levels. Chloroplast genomes were clustered together in the entire phylogenetic tree and shared several forward/palindromic/tandem repetitions, similar to those in U. prolifera and U. linza. However, U. fasciata and U. ohnoi were more divergent, especially in sharing complementary/palindromic repetitions. In addition, phylogenetic analyses of the aligned genes from their chloroplast genomes and mitogenomes confirmed the evolutionary trends of the extranuclear genomes. From phylogenetic analysis, we identified the petA chloroplast genes as potential genetic markers that are similar to the tufA marker. Complementary/forward/palindromic interval repetitions were more abundant in chloroplast genomes than in mitogenomes. Interestingly, a few tandem repetitions were significant for some Ulva subspecies and relatively more evident in mitochondria than in chloroplasts. Finally, the tandem repetition [GAAATATATAATAATA × 3, abbreviated as TRg)] was identified in the mitogenome of U. compressa and the conspecific strain U. mutabilis but not in other algal species of the Yellow Sea. Owing to the high morphological plasticity of U. compressa, the findings of this study have implications for the rapid non-sequencing detection of this species during the occurrence of green tides in the region.}, }
@article {pmid34061590, year = {2021}, author = {Siscar-Lewin, S and Gabaldón, T and Aldejohann, AM and Kurzai, O and Hube, B and Brunke, S}, title = {Transient Mitochondria Dysfunction Confers Fungal Cross-Resistance against Phagocytic Killing and Fluconazole.}, journal = {mBio}, volume = {12}, number = {3}, pages = {e0112821}, pmid = {34061590}, issn = {2150-7511}, mesh = {Antifungal Agents/*pharmacology ; Candida glabrata/*drug effects/*genetics/growth &amp; development/pathogenicity ; Candidiasis/microbiology ; Drug Resistance, Fungal/*genetics ; Fluconazole/*pharmacology ; Gene Expression Regulation, Fungal ; Humans ; Macrophages/microbiology ; Microbial Sensitivity Tests ; Mitochondria/metabolism/*pathology ; Phagocytes ; Phagocytosis ; Virulence/genetics ; }, abstract = {Loss or inactivation of antivirulence genes is an adaptive strategy in pathogen evolution. Candida glabrata is an important opportunistic pathogen related to baker's yeast, with the ability to both quickly increase its intrinsic high level of azole resistance and persist within phagocytes. During C. glabrata's evolution as a pathogen, the mitochondrial DNA polymerase CgMip1 has been under positive selection. We show that CgMIP1 deletion not only triggers loss of mitochondrial function and a petite phenotype, but increases C. glabrata's azole and endoplasmic reticulum (ER) stress resistance and, importantly, its survival in phagocytes. The same phenotype is induced by fluconazole and by exposure to macrophages, conferring a cross-resistance between antifungals and immune cells, and can be found in clinical isolates despite a slow growth of petite strains. This suggests that petite constitutes a bet-hedging strategy of C. glabrata and, potentially, a relevant cause of azole resistance. Mitochondrial function may therefore be considered a potential antivirulence factor. IMPORTANCE Candida glabrata is an opportunistic pathogen whose incidence has been increasing in the last 40 years. It has risen to become the most prominent non-Candida albicans Candida (NCAC) species to cause candidemia, constituting about one-third of isolates in the United States, and steadily increasing in European countries and in Australia. Despite its clinical importance, C. glabrata's pathogenicity strategies remain poorly understood. Our research shows that loss of mitochondrial function and the resulting petite phenotype is advantageous for C. glabrata to cope with infection-related stressors, such as antifungals and host immune defenses. The (cross-)resistance against both these factors may have major implications in the clinical outcome of infections with this major fungal pathogen.}, }
@article {pmid34039261, year = {2021}, author = {Awadi, A and Ben Slimen, H and Schaschl, H and Knauer, F and Suchentrunk, F}, title = {Positive selection on two mitochondrial coding genes and adaptation signals in hares (genus Lepus) from China.}, journal = {BMC ecology and evolution}, volume = {21}, number = {1}, pages = {100}, pmid = {34039261}, issn = {2730-7182}, mesh = {Animals ; China ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; *Hares/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Animal mitochondria play a central role in energy production in the cells through the oxidative phosphorylation (OXPHOS) pathway. Recent studies of selection on different mitochondrial OXPHOS genes have revealed the adaptive implications of amino acid changes in these subunits. In hares, climatic variation and/or introgression were suggested to be at the origin of such adaptation. Here we looked for evidence of positive selection in three mitochondrial OXPHOS genes, using tests of selection, protein structure modelling and effects of amino acid substitutions on the protein function and stability. We also used statistical models to test for climate and introgression effects on sites under positive selection.<br><br>RESULTS: Our results revealed seven sites under positive selection in ND4 and three sites in Cytb. However, no sites under positive selection were observed in the COX1 gene. All three subunits presented a high number of codons under negative selection. Sites under positive selection were mapped on the tridimensional structure of the predicted models for the respective mitochondrial subunit. Of the ten amino acid replacements inferred to have evolved under positive selection for both subunits, six were located in the transmembrane domain. On the other hand, three codons were identified as sites lining proton translocation channels. Furthermore, four codons were identified as destabilizing with a significant variation of &#x394; vibrational entropy energy between wild and mutant type. Moreover, our PROVEAN analysis suggested that among all positively selected sites two fixed amino acid replacements altered the protein functioning. Our statistical models indicated significant effects of climate on the presence of ND4 and Cytb protein variants, but no effect by trans-specific mitochondrial DNA introgression, which is not uncommon in a number of hare species.<br><br>CONCLUSIONS: Positive selection was observed in several codons in two OXPHOS genes. We found that substitutions in the positively selected codons have structural and functional impacts on the encoded proteins. Our results are concordantly suggesting that adaptations have strongly affected the evolution of mtDNA of hare species with potential effects on the protein function. Environmental/climatic changes appear to be a major trigger of this adaptation, whereas trans-specific introgressive hybridization seems to play no major role for the occurrence of protein variants.}, }
@article {pmid34038740, year = {2021}, author = {Wong, HH and Seet, SH and Maier, M and Gurel, A and Traspas, RM and Lee, C and Zhang, S and Talim, B and Loh, AYT and Chia, CY and Teoh, TS and Sng, D and Rensvold, J and Unal, S and Shishkova, E and Cepni, E and Nathan, FM and Sirota, FL and Liang, C and Yarali, N and Simsek-Kiper, PO and Mitani, T and Ceylaner, S and Arman-Bilir, O and Mbarek, H and Gumruk, F and Efthymiou, S and Uğurlu Çi Men, D and Georgiadou, D and Sotiropoulou, K and Houlden, H and Paul, F and Pehlivan, D and Lainé, C and Chai, G and Ali, NA and Choo, SC and Keng, SS and Boisson, B and Yılmaz, E and Xue, S and Coon, JJ and Ly, TTN and Gilani, N and Hasbini, D and Kayserili, H and Zaki, MS and Isfort, RJ and Ordonez, N and Tripolszki, K and Bauer, P and Rezaei, N and Seyedpour, S and Khotaei, GT and Bascom, CC and Maroofian, R and Chaabouni, M and Alsubhi, A and Eyaid, W and Işıkay, S and Gleeson, JG and Lupski, JR and Casanova, JL and Pagliarini, DJ and Akarsu, NA and Maurer-Stroh, S and Cetinkaya, A and Bertoli-Avella, A and Mathuru, AS and Ho, L and Bard, FA and Reversade, B}, title = {Loss of C2orf69 defines a fatal autoinflammatory syndrome in humans and zebrafish that evokes a glycogen-storage-associated mitochondriopathy.}, journal = {American journal of human genetics}, volume = {108}, number = {7}, pages = {1301-1317}, pmid = {34038740}, issn = {1537-6605}, support = {R35 GM131795/GM/NIGMS NIH HHS/United States ; R35 NS105078/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; CRISPR-Cas Systems ; Cell Line ; Encephalitis/*genetics/mortality ; Female ; Genes, Recessive ; Glycogen/metabolism ; Humans ; Inflammation/genetics ; Male ; Membrane Proteins/genetics ; Mitochondrial Diseases/*genetics/mortality ; Pedigree ; Seizures/genetics/mortality ; Zebrafish/genetics ; }, abstract = {Human C2orf69 is an evolutionarily conserved gene whose function is unknown. Here, we report eight unrelated families from which 20 children presented with a fatal syndrome consisting of severe autoinflammation and progredient leukoencephalopathy with recurrent seizures; 12 of these subjects, whose DNA was available, segregated homozygous loss-of-function C2orf69 variants. C2ORF69 bears homology to esterase enzymes, and orthologs can be found in most eukaryotic genomes, including that of unicellular phytoplankton. We found that endogenous C2ORF69 (1) is loosely bound to mitochondria, (2) affects mitochondrial membrane potential and oxidative respiration in cultured neurons, and (3) controls the levels of the glycogen branching enzyme 1 (GBE1) consistent with a glycogen-storage-associated mitochondriopathy. We show that CRISPR-Cas9-mediated inactivation of zebrafish C2orf69 results in lethality by 8 months of age due to spontaneous epileptic seizures, which is preceded by persistent brain inflammation. Collectively, our results delineate an autoinflammatory Mendelian disorder of C2orf69 deficiency that disrupts the development/homeostasis of the immune and central nervous systems.}, }
@article {pmid34037779, year = {2021}, author = {Burskaia, V and Artyushin, I and Potapova, NA and Konovalov, K and Bazykin, GA}, title = {Convergent Adaptation in Mitochondria of Phylogenetically Distant Birds: Does it Exist?.}, journal = {Genome biology and evolution}, volume = {13}, number = {7}, pages = {}, pmid = {34037779}, issn = {1759-6653}, mesh = {Adaptation, Physiological/genetics ; Animals ; Birds/genetics ; *Evolution, Molecular ; *Genome, Mitochondrial ; Mitochondria/genetics ; }, abstract = {In a wide range of taxa, proteins encoded by mitochondrial genomes are involved in adaptation to lifestyle that requires oxygen starvation or elevation of metabolism rate. It remains poorly understood to what extent adaptation to similar conditions is associated with parallel changes in these proteins. We search for a genetic signal of parallel or convergent evolution in recurrent molecular adaptation to high altitude, migration, diving, wintering, unusual flight abilities, or loss of flight in mitochondrial genomes of birds. Developing on previous work, we design an approach for the detection of recurrent coincident changes in genotype and phenotype, indicative of an association between the two. We describe a number of candidate sites involved in recurrent adaptation in ND genes. However, we find that the majority of convergence events can be explained by random coincidences without invoking adaptation.}, }
@article {pmid34034879, year = {2021}, author = {Chowrasia, S and Nishad, J and Pandey, R and Mondal, TK}, title = {Oryza coarctata is a triploid plant with initial events of C4 photosynthesis evolution.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {308}, number = {}, pages = {110878}, doi = {10.1016/j.plantsci.2021.110878}, pmid = {34034879}, issn = {1873-2259}, mesh = {*Biological Evolution ; *Carbon Cycle ; Oryza/*anatomy &amp; histology/genetics ; *Photosynthesis ; Plant Leaves/anatomy &amp; histology ; *Triploidy ; }, abstract = {Oryza coarctata is an obligate halophyte of wild species of rice which thrives well under high saline as well as submerged conditions. We report here for the first time that O. coarctata is triploid (2n = 3x = 36), though it was previously known as tetraploid (2n = 4x = 48). The chromosome number of O. coarctata was determined from mitotic plates of root tips and ploidy level was determined by flow cytometer, where it was found to be triploid (2n = 3x = 36). In addition, this species was found to possess several unique anatomical features in leaves such as presence of Kranz-anatomy, increased vein density and higher ratio of bundle sheath to mesophyll cell area as compared to rice variety (IR-29). Ultra-structure of leaf showed the presence of bundle sheath cells with significant number of chloroplasts and mitochondria which were arranged centrifugally. Chloroplasts lack grana in bundle sheath cell whereas, mesophyll cell contain well-developed grana. These anatomical and ultra structural characteristics indicate that this plant is in initial stage of evolving towards C4 photosynthesis due to high selection pressure which might help it to survive in wide range of ecological conditions i.e. from submerged saline to non-saline terrestrial condition.}, }
@article {pmid34031453, year = {2021}, author = {Kloss-Brandstätter, A and Summerer, M and Horst, D and Horst, B and Streiter, G and Raschenberger, J and Kronenberg, F and Sanguansermsri, T and Horst, J and Weissensteiner, H}, title = {An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {10816}, pmid = {34031453}, issn = {2045-2322}, mesh = {Asian People/ethnology/*genetics ; Cambodia/ethnology ; Female ; Genome, Mitochondrial ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Maternal Inheritance ; Mitochondria/*classification/genetics ; Phylogeny ; Refugees/*classification ; Whole Genome Sequencing/*methods ; }, abstract = {Cambodia harbours a variety of human aboriginal populations that have scarcely been studied in terms of genetic diversity of entire mitochondrial genomes. Here we present the matrilineal gene pool of 299 Cambodian refugees from three different ethnic groups (Cham, Khmer, and Khmer Loeu) deriving from 16 Cambodian districts. After establishing a DNA-saving high-throughput strategy for mitochondrial whole-genome Sanger sequencing, a HaploGrep based workflow was used for quality control, haplogroup classification and phylogenetic reconstruction. The application of diverse phylogenetic algorithms revealed an exciting picture of the genetic diversity of Cambodia, especially in relation to populations from Southeast Asia and from the whole world. A total of 224 unique haplotypes were identified, which were mostly classified under haplogroups B5a1, F1a1, or categorized as newly defined basal haplogroups or basal sub-branches of R, N and M clades. The presence of autochthonous maternal lineages could be confirmed as reported in previous studies. The exceptional homogeneity observed between and within the three investigated Cambodian ethnic groups indicates genetic isolation of the whole population. Between ethnicities, genetic barriers were not detected. The mtDNA data presented here increases the phylogenetic resolution in Cambodia significantly, thereby highlighting the need for an update of the current human mtDNA phylogeny.}, }
@article {pmid34029916, year = {2021}, author = {Zhu, D and Liu, Z and Li, Y and Huang, Q and Xia, L and Li, K}, title = {Delivery of manganese carbonyl to the tumor microenvironment using Tumor-Derived exosomes for cancer gas therapy and low dose radiotherapy.}, journal = {Biomaterials}, volume = {274}, number = {}, pages = {120894}, doi = {10.1016/j.biomaterials.2021.120894}, pmid = {34029916}, issn = {1878-5905}, mesh = {Cell Line, Tumor ; *Exosomes ; Manganese ; *Nanoparticles ; *Neoplasms/radiotherapy ; Tumor Microenvironment ; }, abstract = {The development of novel radiosensitizer with high selectivity and controllability is highly desirable. CO gas could cause damage to mitochondria and thus enhance RT effect. Controlled delivery of CO in tumor is important both to achieve high-efficiency of CO gas therapy and to decrease the risk of CO poisoning. In this study, manganese carbonyl (MnCO) loaded exosome nano-vesicles (MMV) to overcome this conundrum for tumor therapy is developed. After administration, MMV showed its admirable performance in active tumor-targeting, mitochondria damage and radiosensitization therapy. These MMV nanoparticles were able to facilitate robust CO evolution and consequent ROS generation in response to X-ray irradiation both in vitro and in vivo. Significantly, MMV could facilitate a 90% inhibition effect of tumor growth under very low dose (only 2Gy) RT, which is better than high dose (6Gy) radiotherapy. Overall, this study highlights a novel and practical approach to enhancing the efficacy of tumor RT, underscoring the value of future research in the field of CO medicine.}, }
@article {pmid34027666, year = {2021}, author = {Zheng, Y and Ye, Z and Liu, Z and Yang, W and Zhang, X and Yang, Y and Xiao, Y}, title = {Nitroso-Caged Rhodamine: A Superior Green Light-Activatable Fluorophore for Single-Molecule Localization Super-Resolution Imaging.}, journal = {Analytical chemistry}, volume = {93}, number = {22}, pages = {7833-7842}, doi = {10.1021/acs.analchem.1c00175}, pmid = {34027666}, issn = {1520-6882}, mesh = {*Fluorescent Dyes ; Ionophores ; Microscopy, Fluorescence ; Rhodamines ; *Single Molecule Imaging ; }, abstract = {The evolution of super-resolution imaging techniques, especially single-molecule localization microscopy, demands the engineering of switchable fluorophores with labeling functionality. Yet, the switching of these fluorophores depends on the exterior conditions of UV light and enhancing buffers, which is bioincompatible for living-cell applications. Herein, to surpass these limitations, a nitroso-caging strategy is employed to cage rhodamines into leuco forms, which for the first time, is discovered to uncage highly bright zwitterions by green light. Further, clickable construction grants the specificity and versatility for labeling various components in living cells. The simultaneous photoactivation and excitation of these novel probes allow for single-laser super-resolution imaging without any harmful additives. Super-resolution imaging of microtubules in fixed cells or mitochondria and the distribution of glycans and H2B proteins in living cells are achieved at a molecular scale with robust integrity. We envision that our nitroso-caging probes would set a platform for the development of future visible-activatable probes.}, }
@article {pmid34018613, year = {2021}, author = {Stephens, TG and Gabr, A and Calatrava, V and Grossman, AR and Bhattacharya, D}, title = {Why is primary endosymbiosis so rare?.}, journal = {The New phytologist}, volume = {231}, number = {5}, pages = {1693-1699}, pmid = {34018613}, issn = {1469-8137}, support = {80NSSC19K0462/ImNASA/Intramural NASA/United States ; }, mesh = {*Amoeba ; Biological Evolution ; Eukaryota ; Phylogeny ; Plastids ; *Symbiosis ; }, abstract = {Endosymbiosis is a relationship between two organisms wherein one cell resides inside the other. This affiliation, when stable and beneficial for the 'host' cell, can result in massive genetic innovation with the foremost examples being the evolution of eukaryotic organelles, the mitochondria and plastids. Despite its critical evolutionary role, there is limited knowledge about how endosymbiosis is initially established and how host-endosymbiont biology is integrated. Here, we explore this issue, using as our model the rhizarian amoeba Paulinella, which represents an independent case of primary plastid origin that occurred c. 120 million yr ago. We propose the 'chassis and engine' model that provides a theoretical framework for understanding primary plastid endosymbiosis, potentially explaining why it is so rare.}, }
@article {pmid34017941, year = {2021}, author = {Kamrad, S and Rodríguez-López, M and Dey, S and Hoti, M and Wallace, H and Ralser, M and Bähler, J}, title = {Recombination and biased segregation of mitochondrial genomes during crossing and meiosis of different Schizosaccharomyces pombe strains.}, journal = {microPublication biology}, volume = {2021}, number = {}, pages = {}, pmid = {34017941}, issn = {2578-9430}, support = {/WT_/Wellcome Trust/United Kingdom ; FC001134/ARC_/Arthritis Research UK/United Kingdom ; }, abstract = {During meiosis, tethering of parental mitochondria to opposite cell poles inhibits the mixing of mitochondria with different genomes and ensures uniparental inheritance in thestandard laboratory strain of fission yeast. We here investigate mitochondrial inheritance in crosses between natural isolates using tetrad dissection and next-generation sequencing. We find that colonies grown from single spores can sometimes carry a mix of mitochondrial genotypes, that mitochondrial genomes can recombine during meiosis, that in some cases tetrads do not follow the 2:2 segregation pattern, and that certain crosses may feature a weak bias towards one of the parents. Together, these findings paint a more nuanced picture of mitochondrial inheritance in the wild.}, }
@article {pmid34011950, year = {2021}, author = {Horváthová, L and Žárský, V and Pánek, T and Derelle, R and Pyrih, J and Motyčková, A and Klápšťová, V and Vinopalová, M and Marková, L and Voleman, L and Klimeš, V and Petrů, M and Vaitová, Z and Čepička, I and Hryzáková, K and Harant, K and Gray, MW and Chami, M and Guilvout, I and Francetic, O and Franz Lang, B and Vlček, &#x10c; and Tsaousis, AD and Eliáš, M and Doležal, P}, title = {Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {2947}, pmid = {34011950}, issn = {2041-1723}, mesh = {Amino Acid Sequence ; Conserved Sequence ; Eukaryota/classification/genetics/metabolism ; *Evolution, Molecular ; Gram-Negative Bacteria/classification/genetics/metabolism ; Mitochondria/*genetics/*metabolism ; Mitochondrial Proteins/classification/genetics/metabolism ; Models, Biological ; Models, Molecular ; Naegleria/classification/genetics/metabolism ; Peroxisomes/metabolism ; Phylogeny ; Protozoan Proteins/classification/genetics/metabolism ; Sequence Homology, Amino Acid ; Type II Secretion Systems/classification/*genetics/*metabolism ; }, abstract = {The type 2 secretion system (T2SS) is present in some Gram-negative eubacteria and used to secrete proteins across the outer membrane. Here we report that certain representative heteroloboseans, jakobids, malawimonads and hemimastigotes unexpectedly possess homologues of core T2SS components. We show that at least some of them are present in mitochondria, and their behaviour in biochemical assays is consistent with the presence of a mitochondrial T2SS-derived system (miT2SS). We additionally identified 23 protein families co-occurring with miT2SS in eukaryotes. Seven of these proteins could be directly linked to the core miT2SS by functional data and/or sequence features, whereas others may represent different parts of a broader functional pathway, possibly also involving the peroxisome. Its distribution in eukaryotes and phylogenetic evidence together indicate that the miT2SS-centred pathway is an ancestral eukaryotic trait. Our findings thus have direct implications for the functional properties of the early mitochondrion.}, }
@article {pmid34011275, year = {2021}, author = {Porter, TM and Hajibabaei, M}, title = {Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets.}, journal = {BMC bioinformatics}, volume = {22}, number = {1}, pages = {256}, pmid = {34011275}, issn = {1471-2105}, mesh = {Cell Nucleus ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; *Pseudogenes/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcoding and metabarcoding analysis can lead to misleading results. None of the most widely used bioinformatic pipelines used to process marker gene (metabarcode) high throughput sequencing data specifically accounts for the presence of pseudogenes in protein-coding marker genes. The purpose of this study is to develop a method to screen for nuclear mitochondrial DNA segments (nuMTs) in large COI datasets. We do this by: (1) describing gene and nuMT characteristics from an artificial COI barcode dataset, (2) show the impact of two different pseudogene removal methods on perturbed community datasets with simulated nuMTs, and (3) incorporate a pseudogene filtering step in a bioinformatic pipeline that can be used to process Illumina paired-end COI metabarcode sequences. Open reading frame length and sequence bit scores from hidden Markov model (HMM) profile analysis were used to detect pseudogenes.<br><br>RESULTS: Our simulations showed that it was more difficult to identify nuMTs from shorter amplicon sequences such as those typically used in metabarcoding compared with full length DNA barcodes that are used in the construction of barcode libraries. It was also more difficult to identify nuMTs in datasets where there is a high percentage of nuMTs. Existing bioinformatic pipelines used to process metabarcode sequences already remove some nuMTs, especially in the rare sequence removal step, but the addition of a pseudogene filtering step can remove up to 5% of sequences even when other filtering steps are in place.<br><br>CONCLUSIONS: Open reading frame length filtering alone or combined with hidden Markov model profile analysis can be used to effectively screen out apparent pseudogenes from large datasets. There is more to learn from COI nuMTs such as their frequency in DNA barcoding and metabarcoding studies, their taxonomic distribution, and evolution. Thus, we encourage the submission of verified COI nuMTs to public databases to facilitate future studies.}, }
@article {pmid34009340, year = {2021}, author = {Phua, SY and De Smet, B and Remacle, C and Chan, KX and Van Breusegem, F}, title = {Reactive oxygen species and organellar signaling.}, journal = {Journal of experimental botany}, volume = {72}, number = {16}, pages = {5807-5824}, doi = {10.1093/jxb/erab218}, pmid = {34009340}, issn = {1460-2431}, mesh = {Cell Nucleus/metabolism ; Photosynthesis ; *Plant Cells ; Reactive Oxygen Species/metabolism ; *Signal Transduction ; }, abstract = {The evolution of photosynthesis and its associated metabolic pathways has been crucial to the successful establishment of plants, but has also challenged plant cells in the form of production of reactive oxygen species (ROS). Intriguingly, multiple forms of ROS are generated in virtually every plant cell compartment through diverse pathways. As a result, a sophisticated network of ROS detoxification and signaling that is simultaneously tailored to individual organelles and safeguards the entire cell is necessary. Here we take an organelle-centric view on the principal sources and sinks of ROS across the plant cell and provide insights into the ROS-induced organelle to nucleus retrograde signaling pathways needed for operational readjustments during environmental stresses.}, }
@article {pmid34009087, year = {2022}, author = {Ma, ZJ and Li, GZ and Chen, SM and Han, JL and Hanif, Q}, title = {Rich maternal and paternal genetic diversity and divergent lineage composition in wild yak (Bos mutus).}, journal = {Animal biotechnology}, volume = {33}, number = {6}, pages = {1318-1321}, doi = {10.1080/10495398.2021.1895187}, pmid = {34009087}, issn = {1532-2378}, mesh = {Cattle/genetics ; Animals ; Phylogeny ; Haplotypes/genetics ; *DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; Genetic Variation/genetics ; }, abstract = {Wild yak (Bos mutus) is a vulnerable bovine species on the Qinghai-Tibetan Plateau. So far, most studies on the molecular genetic diversity of wild yak have focused on autosomal and mtDNA variations based on the small number of samples. In this study, we analyzed 84 D-loop and 24 whole mitogenome sequences of wild yak to further comprehensively explore its maternal genetic diversity and lineage composition. Meanwhile, using six yak Y-specific polymorphic markers (i.e., SRY4, USP9Y, UTY19, AMELY3, OFD1Y10 and INRA189), we assessed the paternal genetic diversity and lineage composition based on eight wild yak. Our results showed that wild yak exhibited abundant maternal genetic diversity with haplotype diversities of 0.9621 ± 0.0078 and 0.9928 ± 0.0144 in the D-loop and whole mitogenome sequences, respectively. Maternal phylogenetic analysis of wild yak uncovered three defined lineages (mt-I, mt-II and mt-III). Similarly, profuse paternal genetic diversity was observed in wild yak with Y-haplotype diversity at 0.8214 ± 0.1007. Two Y-haplogroups (Y1 and Y2) and four Y-haplotypes (yH1-yH4) were identified in paternal phylogenetic analysis, indicating wild yak to be of two paternal lineages. The present study of genetic diversity and lineage composition of wild yak would provide useful information for the genetic resource conservation and utilization of this vulnerable wild species.}, }
@article {pmid34008202, year = {2021}, author = {Speijer, D}, title = {Zombie ideas about early endosymbiosis: Which entry mechanisms gave us the "endo" in different endosymbionts?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {43}, number = {7}, pages = {e2100069}, doi = {10.1002/bies.202100069}, pmid = {34008202}, issn = {1521-1878}, mesh = {Bacteria/genetics ; Biological Evolution ; Eukaryota ; *Eukaryotic Cells ; Phylogeny ; *Symbiosis ; }, abstract = {Recently, a review regarding the mechanics and evolution of mitochondrial fission appeared in Nature. Surprisingly, it stated authoritatively that the mitochondrial outer membrane, in contrast with the inner membrane of bacterial descent, was acquired from the host, presumably during uptake. However, it has been known for quite some time that this membrane was also derived from the Gram-negative, alpha-proteobacterium related precursor of present-day mitochondria. The zombie idea of the host membrane still surrounding the endosymbiont is not only wrong, but more importantly, might hamper the proper conception of possible scenarios of eukaryogenesis. Why? Because it steers the imagination not only with regard to possible uptake mechanisms, but also regarding what went on before. Here I critically discuss both the evidence for the continuity of the bacterial outer membrane, the reasons for the persistence of the erroneous host membrane hypothesis and the wider implications of these misconceptions for the ideas regarding events occurring during the first steps towards the evolution of the eukaryotes and later major eukaryotic differentiations. I will also highlight some of the latest insights regarding different instances of endosymbiont evolution.}, }
@article {pmid34006275, year = {2021}, author = {Hirakawa, Y and Senda, M and Fukuda, K and Yu, HY and Ishida, M and Taira, M and Kinbara, K and Senda, T}, title = {Characterization of a novel type of carbonic anhydrase that acts without metal cofactors.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {105}, pmid = {34006275}, issn = {1741-7007}, support = {18K06358//Japan Society for the Promotion of Science/ ; 18H05419//Japan Society for the Promotion of Science/ ; JP20am0101071//Japan Agency for Medical Research and Development/ ; 19H03280//Japan Society for the Promotion of Science/ ; 18H05419//Japan Society for the Promotion of Science/ ; }, mesh = {Bacteria/metabolism ; Carbon Dioxide ; Carbonic Anhydrases/genetics/*metabolism ; Eukaryota ; Humans ; Photosynthesis ; Plants/metabolism ; Recombinant Proteins ; }, abstract = {BACKGROUND: Carbonic anhydrases (CAs) are universal metalloenzymes that catalyze the reversible conversion of carbon dioxide (CO2) and bicarbonate (HCO3[-]). They are involved in various biological processes, including pH control, respiration, and photosynthesis. To date, eight evolutionarily unrelated classes of CA families (α, β, γ, δ, ζ, η, θ, and ι) have been identified. All are characterized by an active site accommodating the binding of a metal cofactor, which is assumed to play a central role in catalysis. This feature is thought to be the result of convergent evolution.<br><br>RESULTS: Here, we report that a previously uncharacterized protein group, named "COG4337," constitutes metal-independent CAs from the newly discovered &#x3b9;-class. Genes coding for COG4337 proteins are found in various bacteria and photosynthetic eukaryotic algae. Biochemical assays demonstrated that recombinant COG4337 proteins from a cyanobacterium (Anabaena sp. PCC7120) and a chlorarachniophyte alga (Bigelowiella natans) accelerated CO2 hydration. Unexpectedly, these proteins exhibited their activity under metal-free conditions. Based on X-ray crystallography and point mutation analysis, we identified a metal-free active site within the cone-shaped &#x3b1;+&#x3b2; barrel structure. Furthermore, subcellular localization experiments revealed that COG4337 proteins are targeted into plastids and mitochondria of B. natans, implicating their involvement in CO2 metabolism in these organelles.<br><br>CONCLUSIONS: COG4337 proteins shared a short sequence motif and overall structure with &#x3b9;-class CAs, whereas they were characterized by metal independence, unlike any known CAs. Therefore, COG4337 proteins could be treated as a variant type of &#x3b9;-class CAs. Our findings suggested that this novel type of &#x3b9;-CAs can function even in metal-poor environments (e.g., the open ocean) without competition with other metalloproteins for trace metals. Considering the widespread prevalence of &#x3b9;-CAs across microalgae, this class of CAs may play a role in the global carbon cycle.}, }
@article {pmid34003535, year = {2021}, author = {Pereira, RJ and Lima, TG and Pierce-Ward, NT and Chao, L and Burton, RS}, title = {Recovery from hybrid breakdown reveals a complex genetic architecture of mitonuclear incompatibilities.}, journal = {Molecular ecology}, volume = {30}, number = {23}, pages = {6403-6416}, doi = {10.1111/mec.15985}, pmid = {34003535}, issn = {1365-294X}, support = {//US National Science Foundation/ ; IOS1754347//Division of Integrative Organismal Systems/ ; DEB1556466//Division of Environmental Biology/ ; //Ludwig-Maximilians-Universitaet Muenchen/ ; }, mesh = {Alleles ; Animals ; Cell Nucleus/genetics ; *Copepoda/genetics ; Hybridization, Genetic ; Mitochondria/genetics ; *Reproductive Isolation ; }, abstract = {Reproductive isolation is often achieved when genes that are neutral or beneficial in their genomic background become functionally incompatible in a foreign genomic background, causing inviability, sterility or other forms of low fitness in hybrids. Recent studies suggest that mitonuclear interactions are among the initial incompatibilities to evolve at early stages of population divergence across taxa. Yet, the genomic architecture of mitonuclear incompatibilities has rarely been elucidated. We employ an experimental evolution approach starting with low-fitness F2 interpopulation hybrids of the copepod Tigriopus californicus, in which frequencies of compatible and incompatible nuclear alleles change in response to an alternative mitochondrial background. After about nine generations, we observe a generalized increase in population size and in survivorship, suggesting efficiency of selection against maladaptive phenotypes. Whole genome sequencing of evolved populations showed some consistent allele frequency changes across three replicates of each reciprocal cross, but markedly different patterns between mitochondrial backgrounds. In only a few regions (~6.5% of the genome), the same parental allele was overrepresented irrespective of the mitochondrial background. About 33% of the genome showed allele frequency changes consistent with divergent selection, with the location of these genomic regions strongly differing between mitochondrial backgrounds. In 87% and 89% of these genomic regions, the dominant nuclear allele matched the associated mitochondrial background, consistent with mitonuclear co-adaptation. These results suggest that mitonuclear incompatibilities have a complex polygenic architecture that differs between populations, potentially generating genome-wide barriers to gene flow between closely related taxa.}, }
@article {pmid34001130, year = {2021}, author = {Záhonová, K and Lax, G and Sinha, SD and Leonard, G and Richards, TA and Lukeš, J and Wideman, JG}, title = {Single-cell genomics unveils a canonical origin of the diverse mitochondrial genomes of euglenozoans.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {103}, pmid = {34001130}, issn = {1741-7007}, support = {20-07186S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; ERC CZ LL1601//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; URF\R\191005//Royal Society/ ; 16_019/0000759//Czech Ministry of Education/ ; }, mesh = {DNA, Mitochondrial ; *Euglenida/genetics ; Euglenozoa/genetics ; Europium ; *Genome, Mitochondrial/genetics ; Genomics ; Phylogeny ; RNA, Transfer ; }, abstract = {BACKGROUND: The supergroup Euglenozoa unites heterotrophic flagellates from three major clades, kinetoplastids, diplonemids, and euglenids, each of which exhibits extremely divergent mitochondrial characteristics. Mitochondrial genomes (mtDNAs) of euglenids comprise multiple linear chromosomes carrying single genes, whereas mitochondrial chromosomes are circular non-catenated in diplonemids, but circular and catenated in kinetoplastids. In diplonemids and kinetoplastids, mitochondrial mRNAs require extensive and diverse editing and/or trans-splicing to produce mature transcripts. All known euglenozoan mtDNAs exhibit extremely short mitochondrial small (rns) and large (rnl) subunit rRNA genes, and absence of tRNA genes. How these features evolved from an ancestral bacteria-like circular mitochondrial genome remains unanswered.<br><br>RESULTS: We sequenced and assembled 20 euglenozoan single-cell amplified genomes (SAGs). In our phylogenetic and phylogenomic analyses, three SAGs were placed within kinetoplastids, 14 within diplonemids, one (EU2) within euglenids, and two SAGs with nearly identical small subunit rRNA gene (18S) sequences (EU17/18) branched as either a basal lineage of euglenids, or as a sister to all euglenozoans. Near-complete mitochondrial genomes were identified in EU2 and EU17/18. Surprisingly, both EU2 and EU17/18 mitochondrial contigs contained multiple genes and one tRNA gene. Furthermore, EU17/18 mtDNA possessed&#xa0;several features unique among euglenozoans including full-length rns and rnl genes, six mitoribosomal genes, and nad11,&#xa0;all&#xa0;likely on a single chromosome.<br><br>CONCLUSIONS: Our data strongly suggest that EU17/18 is an early-branching euglenozoan with numerous ancestral mitochondrial features. Collectively these data contribute to untangling the early evolution of euglenozoan mitochondria.}, }
@article {pmid33991648, year = {2021}, author = {Moreno-Carmona, M and Cameron, SL and Prada Quiroga, CF}, title = {How are the mitochondrial genomes reorganized in Hexapoda? Differential evolution and the first report of convergences within Hexapoda.}, journal = {Gene}, volume = {791}, number = {}, pages = {145719}, doi = {10.1016/j.gene.2021.145719}, pmid = {33991648}, issn = {1879-0038}, mesh = {Animals ; Databases, Genetic ; Evolution, Molecular ; Gene Order/genetics ; Gene Rearrangement/genetics ; Genes, Mitochondrial/*genetics ; Genome, Mitochondrial/*genetics ; Insecta/classification/*genetics ; Mitochondria/classification/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The evolution of the Hexapoda mitochondrial genome has been the focus of several genetic and evolutionary studies over the last decades. However, they have concentrated on certain taxonomic orders of economic or health importance. The recent increase of mitochondrial genomes sequencing of diverse taxonomic orders generates an important opportunity to clarify the evolution of this group of organisms. However, there is no comparative study that investigates the evolution of the Hexapoda mitochondrial genome. In order to verify the level of rearrangement and the mitochondrial genome evolution, we performed a comparative genomic analysis of the Hexapoda mitochondrial genome available in the NCBI database. Using a combination of bioinformatics methods to carefully examine the mitochondrial gene rearrangements in 1198 Hexapoda species belonging to 32 taxonomic orders, we determined that there is a great variation in the rate of rearrangement by gene and by taxonomic order. A higher rate of genetic reassortment is observed in Phthiraptera, Thysanoptera, Protura, and Hymenoptera; compared to other taxonomic orders. Twenty-four events of convergence in the genetic order between different taxonomic orders were determined, most of them not previously reported; which proves the great evolutionary dynamics within Hexapoda.}, }
@article {pmid33984441, year = {2021}, author = {Lim, LWK and Chung, HH and Lau, MML and Aziz, F and Gan, HM}, title = {Improving the phylogenetic resolution of Malaysian and Javan mahseer (Cyprinidae), Tor tambroides and Tor tambra: Whole mitogenomes sequencing, phylogeny and potential mitogenome markers.}, journal = {Gene}, volume = {791}, number = {}, pages = {145708}, doi = {10.1016/j.gene.2021.145708}, pmid = {33984441}, issn = {1879-0038}, mesh = {Animals ; Base Sequence/genetics ; Biomarkers ; Cyprinidae/*classification/*genetics ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; Indonesia ; Malaysia ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The true mahseer (Tor spp.) is one of the highest valued fish in the world due to its high nutritional value and great unique taste. Nevertheless, its morphological characterization and single mitochondrial gene phylogeny in the past had yet to resolve the ambiguity in its taxonomical classification. In this study, we sequenced and assembled 11 complete mahseer mitogenomes collected from Java of Indonesia, Pahang and Terengganu of Peninsular Malaysia as well as Sarawak of East Malaysia. The mitogenome evolutionary relationships among closely related Tor spp. samples were investigated based on maximum likelihood phylogenetic tree construction. Compared to the commonly used COX1 gene fragment, the complete COX1, Cytb, ND2, ND4 and ND5 genes appear to be better phylogenetic markers for genetic differentiation at the population level. In addition, a total of six population-specific mitolineage haplotypes were identified among the mahseer samples analyzed, which this offers hints towards its taxonomical landscape.}, }
@article {pmid33983431, year = {2021}, author = {Dellière, S and Hamane, S and Aissaoui, N and Gits-Muselli, M and Bretagne, S and Alanio, A}, title = {Increased sensitivity of a new commercial reverse transcriptase-quantitative PCR for the detection of Pneumocystis jirovecii in respiratory specimens.}, journal = {Medical mycology}, volume = {59}, number = {8}, pages = {845-848}, doi = {10.1093/mmy/myab029}, pmid = {33983431}, issn = {1460-2709}, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Opportunistic Infections/microbiology ; Pneumocystis carinii/genetics/*isolation &amp; purification ; Pneumonia, Pneumocystis/*diagnosis/microbiology ; Real-Time Polymerase Chain Reaction/methods/*standards ; Respiratory System/*microbiology ; Reverse Transcriptase Polymerase Chain Reaction/methods/*standards ; Sensitivity and Specificity ; }, abstract = {UNLABELLED: Optimal sensitivity to detect low Pneumocystis loads is of importance to take individual and collective measures to avoid evolution towards Pneumocystis pneumonia and outbreaks in immunocompromised patients. This study compares two qPCR procedures, a new automated RTqPCR using the GeneLEAD VIII extractor/thermocycler (GLVIII; ∼2.2 h workflow) and a previously validated in-house qPCR assays (IH; ∼5 h workflow) both targeting mtSSU and mtLSU for detecting P. jirovecii in 213 respiratory samples. GLVIII was found to be more sensitive than IH, detecting eight more specimens. Bland-Altman analysis between the two procedures showed a Cq bias of 1.17 ± 0.07 in favor of GLVIII.<br><br>LAY SUMMARY: The fungus Pneumocystis needs to be detected early in respiratory samples to prevent pneumonia in immunocompromised hosts. We evaluated a new commercial RTqPCR on 213 respiratory samples to detect Pneumocystis and found it more sensitive and faster than our routine sensitive in-house qPCR assay.}, }
@article {pmid33975946, year = {2021}, author = {Takusagawa, M and Kobayashi, Y and Fukao, Y and Hidaka, K and Endo, M and Sugiyama, H and Hamaji, T and Kato, Y and Miyakawa, I and Misumi, O and Shikanai, T and Nishimura, Y}, title = {HBD1 protein with a tandem repeat of two HMG-box domains is a DNA clip to organize chloroplast nucleoids in Chlamydomonas reinhardtii.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {20}, pages = {}, pmid = {33975946}, issn = {1091-6490}, mesh = {Chlamydomonas reinhardtii/*genetics/metabolism ; Chloroplast Proteins/classification/*genetics/metabolism ; DNA, Chloroplast/*genetics/metabolism ; Gene Expression Regulation ; Genome, Chloroplast/*genetics ; HMG-Box Domains/*genetics ; Mass Spectrometry/methods ; Mutation ; Phylogeny ; Protein Binding ; Proteomics/methods ; Tandem Repeat Sequences/*genetics ; }, abstract = {Compaction of bulky DNA is a universal issue for all DNA-based life forms. Chloroplast nucleoids (chloroplast DNA-protein complexes) are critical for chloroplast DNA maintenance and transcription, thereby supporting photosynthesis, but their detailed structure remains enigmatic. Our proteomic analysis of chloroplast nucleoids of the green alga Chlamydomonas reinhardtii identified a protein (HBD1) with a tandem repeat of two DNA-binding high mobility group box (HMG-box) domains, which is structurally similar to major mitochondrial nucleoid proteins transcription factor A, mitochondrial (TFAM), and ARS binding factor 2 protein (Abf2p). Disruption of the HBD1 gene by CRISPR-Cas9-mediated genome editing resulted in the scattering of chloroplast nucleoids. This phenotype was complemented when intact HBD1 was reintroduced, whereas a truncated HBD1 with a single HMG-box domain failed to complement the phenotype. Furthermore, ectopic expression of HBD1 in the mitochondria of yeast Δabf2 mutant successfully complemented the defects, suggesting functional similarity between HBD1 and Abf2p. Furthermore, in vitro assays of HBD1, including the electrophoretic mobility shift assay and DNA origami/atomic force microscopy, showed that HBD1 is capable of introducing U-turns and cross-strand bridges, indicating that proteins with two HMG-box domains would function as DNA clips to compact DNA in both chloroplast and mitochondrial nucleoids.}, }
@article {pmid33974849, year = {2021}, author = {Mathur, V and Wakeman, KC and Keeling, PJ}, title = {Parallel functional reduction in the mitochondria of apicomplexan parasites.}, journal = {Current biology : CB}, volume = {31}, number = {13}, pages = {2920-2928.e4}, doi = {10.1016/j.cub.2021.04.028}, pmid = {33974849}, issn = {1879-0445}, mesh = {Animals ; Energy Metabolism ; Genome, Mitochondrial ; Mitochondria/genetics/*metabolism ; Parasites/*cytology/genetics/*metabolism ; *Phylogeny ; Toxoplasma ; }, abstract = {Gregarines are an early-diverging lineage of apicomplexan parasites that hold many clues into the origin and evolution of the group, a remarkable transition from free-living phototrophic algae into obligate parasites of animals.[1] Using single-cell transcriptomics targeting understudied lineages to complement available sequencing data, we characterized the mitochondrial metabolic repertoire across the tree of apicomplexans. In contrast to the large suite of proteins involved in aerobic respiration in well-studied parasites like Toxoplasma or Plasmodium,[2] we find that gregarine trophozoites have significantly reduced energy metabolism: most lack respiratory complexes III and IV, and some lack the electron transport chains (ETCs) and tricarboxylic acid (TCA) cycle entirely. Phylogenomic analyses show that these reductions took place several times in parallel, resulting in a functional range from fully aerobic organelles to extremely reduced "mitosomes" restricted to Fe-S cluster biosynthesis. The mitochondrial genome has also been lost repeatedly: in species with severe functional reduction simply by gene loss but in one species with a complete ETC by relocating cox1 to the nuclear genome. Severe functional reduction of mitochondria is generally associated with structural reduction, resulting in small, nondescript mitochondrial-related organelles (MROs).[3] By contrast, gregarines retain distinctive mitochondria with tubular cristae, even the most functionally reduced cases that also lack genes associated with cristae formation. Overall, the parallel, severe reduction of gregarine mitochondria expands the diversity of organisms that contain MROs and further emphasizes the role of parallel transitions in apicomplexan evolution.}, }
@article {pmid33965538, year = {2021}, author = {Neiber, MT and Chueca, LJ and Caro, A and Teixeira, D and Schlegel, KA and Gómez-Moliner, BJ and Walther, F and Glaubrecht, M and Hausdorf, B}, title = {Incorporating palaeogeography into ancestral area estimation can explain the disjunct distribution of land snails in Macaronesia and the Balearic Islands (Helicidae: Allognathini).}, journal = {Molecular phylogenetics and evolution}, volume = {162}, number = {}, pages = {107196}, doi = {10.1016/j.ympev.2021.107196}, pmid = {33965538}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/genetics ; *Islands ; Mitochondria/genetics ; *Phylogeny ; *Phylogeography ; Snails/*genetics ; Spain ; }, abstract = {The systematics and biogeographical history of the Eastern Mediterranean and Macaronesian land snail tribe Allognathini (Helicidae: Helicinae) is investigated based on mitochondrial and nuclear DNA sequence data. Our molecular phylogenetic analyses indicate that the genus-group systematics of the tribe needs to be revised. We show for the first time that the narrow-range endemics Lampadia and Idiomela from the Madeira Archipelago belong to Allognathini and represent together the sister group of the diverse Canary Island Hemicycla radiation. We therefore suggest synonymising Lampadiini with Allognathini. Sister to these Macaronesian genera was the Balearic Island Allognathus radiation. Pseudotachea was not recovered as a monophyletic group and the two currently recognised species clustered in Iberus. Similarly, Adiverticula was not recovered as a monophyletic group and clustered in Hemicycla. We therefore suggest synonymising Pseudotachea with Iberus and Adiverticula with Hemicycla. The six genera in Allognathini, which we distinguish here (Cepaea, Iberus, Allognathus, Hemicycla, Idiomela and Lampadia), originated in Western to South-western Europe according to our ancestral area estimation and the fossil record. The disjunct distribution of the Balearic Islands and Macaronesian sister clades and the mainly Iberian Iberus clade that separated earlier can be explained by the separation of the Betic-Rif System from the Iberian Peninsula during the late Oligocene to early Miocene, along with independent Miocene dispersals to the Balearic Islands and Macaronesia from the Iberian Peninsula, where the ancestral lineage became extinct.}, }
@article {pmid33963405, year = {2021}, author = {Skejo, J and Garg, SG and Gould, SB and Hendriksen, M and Tria, FDK and Bremer, N and Franjević, D and Blackstone, NW and Martin, WF}, title = {Evidence for a Syncytial Origin of Eukaryotes from Ancestral State Reconstruction.}, journal = {Genome biology and evolution}, volume = {13}, number = {7}, pages = {}, pmid = {33963405}, issn = {1759-6653}, mesh = {Archaea/genetics ; *Biological Evolution ; *Eukaryota/genetics ; Eukaryotic Cells ; Phylogeny ; Prokaryotic Cells ; }, abstract = {Modern accounts of eukaryogenesis entail an endosymbiotic encounter between an archaeal host and a proteobacterial endosymbiont, with subsequent evolution giving rise to a unicell possessing a single nucleus and mitochondria. The mononucleate state of the last eukaryotic common ancestor (LECA) is seldom, if ever, questioned, even though cells harboring multiple (syncytia, coenocytes, and polykaryons) are surprisingly common across eukaryotic supergroups. Here, we present a survey of multinucleated forms. Ancestral character state reconstruction for representatives of 106 eukaryotic taxa using 16 different possible roots and supergroup sister relationships, indicate that LECA, in addition to being mitochondriate, sexual, and meiotic, was multinucleate. LECA exhibited closed mitosis, which is the rule for modern syncytial forms, shedding light on the mechanics of its chromosome segregation. A simple mathematical model shows that within LECA's multinucleate cytosol, relationships among mitochondria and nuclei were neither one-to-one, nor one-to-many, but many-to-many, placing mitonuclear interactions and cytonuclear compatibility at the evolutionary base of eukaryotic cell origin. Within a syncytium, individual nuclei and individual mitochondria function as the initial lower-level evolutionary units of selection, as opposed to individual cells, during eukaryogenesis. Nuclei within a syncytium rescue each other's lethal mutations, thereby postponing selection for viable nuclei and cytonuclear compatibility to the generation of spores, buffering transitional bottlenecks at eukaryogenesis. The prokaryote-to-eukaryote transition is traditionally thought to have left no intermediates, yet if eukaryogenesis proceeded via a syncytial common ancestor, intermediate forms have persisted to the present throughout the eukaryotic tree as syncytia but have so far gone unrecognized.}, }
@article {pmid33958611, year = {2021}, author = {Tuda, M and Iwase, SI and Kébé, K and Haran, J and Skuhrovec, J and Sanaei, E and Tsuji, N and Podlussány, A and Merkl, O and El-Heneidy, AH and Morimoto, K}, title = {Diversification, selective sweep, and body size in the invasive Palearctic alfalfa weevil infected with Wolbachia.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {9664}, pmid = {33958611}, issn = {2045-2322}, mesh = {Animals ; Asia ; Body Size ; Europe ; Female ; Genetic Variation/genetics ; Haplotypes/genetics ; Introduced Species ; Male ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Weevils/genetics/*microbiology ; *Wolbachia ; }, abstract = {The alfalfa weevil Hypera postica, native to the Western Palearctic, is an invasive legume pest with two divergent mitochondrial clades in its invading regions, the Western clade and the Eastern/Egyptian clade. However, knowledge regarding the native populations is limited. The Western clade is infected with the endosymbiotic bacteria Wolbachia that cause cytoplasmic incompatibility in host weevils. Our aim was to elucidate the spatial genetic structure of this insect and the effect of Wolbachia on its population diversity. We analyzed two mitochondrial and two nuclear genes of the weevil from its native ranges. The Western clade was distributed in western/central Europe, whereas the Eastern/Egyptian clade was distributed from the Mediterranean basin to central Asia. Intermediate mitotypes were found from the Balkans to central Asia. Most Western clade individuals in western Europe were infected with an identical Wolbachia strain. Mitochondrial genetic diversity of the infected individuals was minimal. The infected clades demonstrated a higher nonsynonymous/synonymous substitution rate ratio than the uninfected clades, suggesting a higher fixation of nonsynonymous mutations due to a selective sweep by Wolbachia. Trans-Mediterranean and within-European dispersal routes were supported. We suggest that the ancestral populations diversified by geographic isolation due to glaciations and that the diversity was reduced in the west by a recent Wolbachia-driven sweep(s). The intermediate clade exhibited a body size and host plant that differed from the other clades. Pros and cons of the possible use of infected-clade males to control uninfected populations are discussed.}, }
@article {pmid33956890, year = {2021}, author = {Caccavale, F and Osca, D and D'Aniello, S and Crocetta, F}, title = {Molecular taxonomy confirms that the northeastern Atlantic and Mediterranean Sea harbor a single lancelet, Branchiostoma lanceolatum (Pallas, 1774) (Cephalochordata: Leptocardii: Branchiostomatidae).}, journal = {PloS one}, volume = {16}, number = {5}, pages = {e0251358}, pmid = {33956890}, issn = {1932-6203}, mesh = {Animals ; Atlantic Ocean ; DNA/genetics ; Lancelets/classification/*genetics ; Mediterranean Sea ; Mitochondria/genetics ; Multilocus Sequence Typing ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Branchiostomatidae (lancelets or amphioxus) comprises about 30 species, several of which are well-established models in evolutionary development. Our zoological and ecological knowledge of the family is nonetheless limited. Despite evident differences can be found among known populations, the taxonomy of Branchiostoma lanceolatum (type species of the genus Branchiostoma) has never been investigated with modern methods through its range in the northeastern Atlantic and Mediterranean Sea. We address this via a multilocus molecular approach and comparing specimens collected from different European populations. Results obtained here confirm the presence of a single species inhabiting the range between the topotypical localities of B. lanceolatum (Atlantic Ocean) and of its junior synonym B. lubricum (Mediterranean Sea), without evincing geographical structure between populations. This suggests that environment most likely drives the characteristics observed in different geographic areas. The long larval phase and the slow mutation rate in lancelets may have played a key role in the evolutionary history of this iconic species.}, }
@article {pmid33952666, year = {2021}, author = {Reinke, AW}, title = {mSphere of Influence: Where the Pathogen Proteins Are.}, journal = {mSphere}, volume = {6}, number = {3}, pages = {}, pmid = {33952666}, issn = {2379-5042}, mesh = {Animals ; Fungal Proteins/chemistry/*genetics ; *Host-Pathogen Interactions ; Microsporidia/chemistry/*pathogenicity ; Proteomics ; }, abstract = {Aaron Reinke studies microsporidian evolution and how microsporidia interact with their hosts. In this mSphere of Influence article, he reflects on how the papers "A promiscuous biotin ligase fusion protein identifies proximal and interacting proteins in mammalian cells" (K. J. Roux, D. I. Kim, M. Raida, and B. Burke, J Cell Biol 196:801-810, 2012, https://doi.org/10.1083/jcb.201112098) and "Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging" (H.-W. Rhee, P. Zou, N. D. Udeshi, J. D. Martell, et al., Science 339:1328-1331, 2013, https://doi.org/10.1126/science.1230593) impacted his thinking on how to determine where proteins from intracellular pathogens are located within host cells.}, }
@article {pmid33952640, year = {2021}, author = {Fujino, K and Horie, M and Kojima, S and Shimizu, S and Nabekura, A and Kobayashi, H and Makino, A and Honda, T and Tomonaga, K}, title = {A Human Endogenous Bornavirus-Like Nucleoprotein Encodes a Mitochondrial Protein Associated with Cell Viability.}, journal = {Journal of virology}, volume = {95}, number = {14}, pages = {e0203020}, pmid = {33952640}, issn = {1098-5514}, mesh = {Bornaviridae/*genetics ; Cell Survival/*genetics ; Genome, Human ; HEK293 Cells ; HeLa Cells ; Humans ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/*genetics/physiology ; Nucleoproteins/genetics ; RNA, Viral ; RNA-Seq ; Transcriptome ; }, abstract = {Endogenous retroviruses (ERVs) are sequences in animal genomes that originated from ancient retrovirus infections; they provide genetic novelty in hosts by being coopted as functional genes or elements during evolution. Recently, we demonstrated that endogenous elements from not only from retroviruses but also nonretroviral RNA viruses are a possible source of functional genes in host animals. The remnants of ancient bornavirus infections, called endogenous bornavirus-like elements (EBLs), are present in the genomes of a wide variety of vertebrate species, and some express functional products in host cells. Previous studies have predicted that the human EBL locus derived from bornavirus nucleoprotein, termed hsEBLN-2, expresses mRNA encoding a protein, suggesting that hsEBLN-2 has acquired a cellular function during evolution. However, the detailed function of the hsEBLN-2-derived product remains to be elucidated. In this study, we show that the hsEBLN-2-derived protein E2 acts as a mitochondrial protein that interacts with mitochondrial host factors associated with apoptosis, such as HAX-1. We also demonstrate that knockdown of hsEBLN-2-derived RNA increased the levels of PARP and caspase-3 cleavage and markedly decreased cell viability. In contrast, overexpression of E2 enhanced cell viability, as well as the intracellular stability of HAX-1, under stress conditions. Our results suggest that hsEBLN-2 has been coopted as a host gene, the product of which is involved in cell viability by interacting with mitochondrial proteins. IMPORTANCE Our genomes contain molecular fossils of ancient viruses, called endogenous virus elements (EVEs). Mounting evidence suggests that EVEs derived from nonretroviral RNA viruses have acquired functions in host cells during evolution. Previous studies have revealed that a locus encoding a bornavirus-derived EVE, hsEBLN-2, which was generated approximately 43 million years ago in a human ancestor, may be linked to the development of some tumors. However, the function of hsEBLN-2 has not been determined. In this study, we found that the E2 protein, an expression product of hsEBLN-2, interacts with apoptosis-related host proteins as a mitochondrial protein and affects cell viability. This study suggests that nonretroviral RNA viral EVEs have been coopted by hosts with more diverse functions than previously thought, showing a pivotal role for RNA virus infection in evolution.}, }
@article {pmid33951769, year = {2021}, author = {Ndosi, BA and Park, H and Lee, D and Choe, S and Kang, Y and Nath, TC and Bia, MM and Eamudomkarn, C and Jeon, HK and Eom, KS}, title = {Mitochondrial Genome of Spirometra theileri Compared with Other Spirometra Species.}, journal = {The Korean journal of parasitology}, volume = {59}, number = {2}, pages = {139-148}, pmid = {33951769}, issn = {1738-0006}, support = {//International Parasite Resource Bank/ ; 2020-0042//Inclusive Business Solution (IBS) project, Korea/ ; }, mesh = {Animals ; Genome, Helminth ; *Genome, Mitochondrial ; Male ; Panthera/parasitology ; Phylogeny ; Spirometra/classification/*genetics/isolation &amp; purification ; Tanzania ; }, abstract = {This study was carried out to provide information on the taxonomic classification and analysis of mitochondrial genomes of Spirometra theileri. One strobila of S. theileri was collected from the intestine of an African leopard (Panthera pardus) in the Maswa Game Reserve, Tanzania. The complete mtDNA sequence of S. theileri was 13,685 bp encoding 36 genes including 12 protein genes, 22 tRNAs and 2 rRNAs with absence of atp8. Divergences of 12 protein-coding genes were as follow: 14.9% between S. theileri and S. erinaceieuropaei, 14.7% between S. theileri and S. decipiens, and 14.5% between S. theileri with S. ranarum. Divergences of 12 proteins of S. theileri and S. erinaceieuropaei ranged from 2.3% in cox1 to 15.7% in nad5, while S. theileri varied from S. decipiens and S. ranarum by 1.3% in cox1 to 15.7% in nad3. Phylogenetic relationship of S. theileri with eucestodes inferred using the maximum likelihood and Bayesian inferences exhibited identical tree topologies. A clade composed of S. decipiens and S. ranarum formed a sister species to S. erinaceieuropaei, and S. theileri formed a sister species to all species in this clade. Within the diphyllobothridean clade, Dibothriocephalus, Diphyllobothrium and Spirometra formed a monophyletic group, and sister genera were well supported.}, }
@article {pmid33946769, year = {2021}, author = {Oborník, M}, title = {Enigmatic Evolutionary History of Porphobilinogen Deaminase in Eukaryotic Phototrophs.}, journal = {Biology}, volume = {10}, number = {5}, pages = {}, pmid = {33946769}, issn = {2079-7737}, support = {21-03224S//Czech Science Foundation/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//European Regional Development Fund/ ; }, abstract = {In most eukaryotic phototrophs, the entire heme synthesis is localized to the plastid, and enzymes of cyanobacterial origin dominate the pathway. Despite that, porphobilinogen deaminase (PBGD), the enzyme responsible for the synthesis of hydroxymethybilane in the plastid, shows phylogenetic affiliation to α-proteobacteria, the supposed ancestor of mitochondria. Surprisingly, no PBGD of such origin is found in the heme pathway of the supposed partners of the primary plastid endosymbiosis, a primarily heterotrophic eukaryote, and a cyanobacterium. It appears that α-proteobacterial PBGD is absent from glaucophytes but is present in rhodophytes, chlorophytes, plants, and most algae with complex plastids. This may suggest that in eukaryotic phototrophs, except for glaucophytes, either the gene from the mitochondrial ancestor was retained while the cyanobacterial and eukaryotic pseudoparalogs were lost in evolution, or the gene was acquired by non-endosymbiotic gene transfer from an unspecified α-proteobacterium and functionally replaced its cyanobacterial and eukaryotic counterparts.}, }
@article {pmid33931054, year = {2021}, author = {Li, F and Lv, Y and Wen, Z and Bian, C and Zhang, X and Guo, S and Shi, Q and Li, D}, title = {The complete mitochondrial genome of the intertidal spider (Desis jiaxiangi) provides novel insights into the adaptive evolution of the mitogenome and the evolution of spiders.}, journal = {BMC ecology and evolution}, volume = {21}, number = {1}, pages = {72}, pmid = {33931054}, issn = {2730-7182}, mesh = {Animals ; Base Sequence ; *Genome, Mitochondrial/genetics ; Phylogeny ; Silk/genetics ; *Spiders/genetics ; }, abstract = {BACKGROUND: Although almost all extant spider species live in terrestrial environments, a few species live fully submerged in freshwater or seawater. The intertidal spiders (genus Desis) built silk nests within coral crevices can survive submerged in high tides. The diving bell spider, Argyroneta aquatica, resides in a similar dynamic environment but exclusively in freshwater. Given the pivotal role played by mitochondria in supplying most energy for physiological activity via oxidative phosphorylation and the environment, herein we sequenced the complete mitogenome of Desis jiaxiangi to investigate the adaptive evolution of the aquatic spider mitogenomes and the evolution of spiders.<br><br>RESULTS: We assembled a complete mitogenome of the intertidal spider Desis jiaxiangi and performed comparative mitochondrial analyses of data set comprising of Desis jiaxiangi and other 45 previously published spider mitogenome sequences, including that of Argyroneta aquatica. We found a unique transposition of trnL2 and trnN genes in Desis jiaxiangi. Our robust phylogenetic topology clearly deciphered the evolutionary relationships between Desis jiaxiangi and Argyroneta aquatica as well as other spiders. We dated the divergence of Desis jiaxiangi and Argyroneta aquatica to the late Cretaceous at&#x2009;~&#x2009;98&#xa0;Ma. Our selection analyses detected a positive selection signal in the nd4 gene of the aquatic branch comprising both Desis jiaxiangi and Argyroneta aquatica. Surprisingly, Pirata subpiraticus, Hypochilus thorelli, and Argyroneta aquatica each had a higher Ka/Ks value in the 13 PCGs dataset among 46 taxa with complete mitogenomes, and these three species also showed positive selection signal in the nd6 gene.<br><br>CONCLUSIONS: Our finding of the unique transposition of trnL2 and trnN genes indicates that these genes may have experienced rearrangements in the history of intertidal spider evolution. The positive selection signals in the nd4 and nd6 genes might enable a better understanding of the spider metabolic adaptations in relation to different environments. Our construction of a novel mitogenome for the intertidal spider thus sheds light on the evolutionary history of spiders and their mitogenomes.}, }
@article {pmid33929506, year = {2021}, author = {Liao, Z and Schelcher, C and Smirnov, A}, title = {YbeY, éminence grise of ribosome biogenesis.}, journal = {Biochemical Society transactions}, volume = {49}, number = {2}, pages = {727-745}, doi = {10.1042/BST20200669}, pmid = {33929506}, issn = {1470-8752}, mesh = {Amino Acid Sequence ; Animals ; GTP-Binding Proteins/*metabolism ; Humans ; Phylogeny ; Protein Binding ; RNA-Binding Proteins/*metabolism ; Ribonucleases/classification/genetics/*metabolism ; Ribosomal Proteins/*metabolism ; Ribosomes/*metabolism ; Sequence Homology, Amino Acid ; }, abstract = {YbeY is an ultraconserved small protein belonging to the unique heritage shared by most existing bacteria and eukaryotic organelles of bacterial origin, mitochondria and chloroplasts. Studied in more than a dozen of evolutionarily distant species, YbeY is invariably critical for cellular physiology. However, the exact mechanisms by which it exerts such penetrating influence are not completely understood. In this review, we attempt a transversal analysis of the current knowledge about YbeY, based on genetic, structural, and biochemical data from a wide variety of models. We propose that YbeY, in association with the ribosomal protein uS11 and the assembly GTPase Era, plays a critical role in the biogenesis of the small ribosomal subunit, and more specifically its platform region, in diverse genetic systems of bacterial type.}, }
@article {pmid33924228, year = {2021}, author = {Kolchanova, S and Komissarov, A and Kliver, S and Mazo-Vargas, A and Afanador, Y and Velez-Valentín, J and de la Rosa, RV and Castro-Marquez, S and Rivera-Colon, I and Majeske, AJ and Wolfsberger, WW and Hains, T and Corvelo, A and Martinez-Cruzado, JC and Glenn, TC and Robinson, O and Koepfli, KP and Oleksyk, TK}, title = {Molecular Phylogeny and Evolution of Amazon Parrots in the Greater Antilles.}, journal = {Genes}, volume = {12}, number = {4}, pages = {}, pmid = {33924228}, issn = {2073-4425}, mesh = {Amazona/*classification/genetics ; Animals ; Brazil ; Cuba ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; High-Throughput Nucleotide Sequencing ; Jamaica ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Puerto Rico ; Sequence Analysis, DNA/*methods ; }, abstract = {Amazon parrots (Amazona spp.) colonized the islands of the Greater Antilles from the Central American mainland, but there has not been a consensus as to how and when this happened. Today, most of the five remaining island species are listed as endangered, threatened, or vulnerable as a consequence of human activity. We sequenced and annotated full mitochondrial genomes of all the extant Amazon parrot species from the Greater Antillean (A. leucocephala (Cuba), A. agilis, A. collaria (both from Jamaica), A. ventralis (Hispaniola), and A. vittata (Puerto Rico)), A. albifrons from mainland Central America, and A. rhodocorytha from the Atlantic Forest in Brazil. The assembled and annotated mitogenome maps provide information on sequence organization, variation, population diversity, and evolutionary history for the Caribbean species including the critically endangered A. vittata. Despite the larger number of available samples from the Puerto Rican Parrot Recovery Program, the sequence diversity of the A. vittata population in Puerto Rico was the lowest among all parrot species analyzed. Our data support the stepping-stone dispersal and speciation hypothesis that has started approximately 3.47 MYA when the ancestral population arrived from mainland Central America and led to diversification across the Greater Antilles, ultimately reaching the island of Puerto Rico 0.67 MYA. The results are presented and discussed in light of the geological history of the Caribbean and in the context of recent parrot evolution, island biogeography, and conservation. This analysis contributes to understating evolutionary history and empowers subsequent assessments of sequence variation and helps design future conservation efforts in the Caribbean.}, }
@article {pmid33923118, year = {2021}, author = {Filip, E and Skuza, L}, title = {Horizontal Gene Transfer Involving Chloroplasts.}, journal = {International journal of molecular sciences}, volume = {22}, number = {9}, pages = {}, pmid = {33923118}, issn = {1422-0067}, mesh = {Cell Nucleus/*genetics ; Chloroplasts/*genetics ; Endophytes/genetics ; *Gene Transfer, Horizontal ; Genome ; Mitochondria/*genetics ; Plants/genetics ; Plastids/genetics ; }, abstract = {Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments.}, }
@article {pmid33921106, year = {2021}, author = {Bonora, M and Missiroli, S and Perrone, M and Fiorica, F and Pinton, P and Giorgi, C}, title = {Mitochondrial Control of Genomic Instability in Cancer.}, journal = {Cancers}, volume = {13}, number = {8}, pages = {}, pmid = {33921106}, issn = {2072-6694}, support = {IG-23670//Associazione Italiana per la Ricerca sul Cancro/ ; IG-19803//Associazione Italiana per la Ricerca sul Cancro/ ; GGP11139B//Fondazione Telethon/ ; GR-2013-02356747//Ministero della Salute/ ; PRIN2017E5L5P3//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; PRIN20177E9EPY//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca/ ; 853057-InflaPML/ERC_/European Research Council/International ; }, abstract = {Mitochondria are well known to participate in multiple aspects of tumor formation and progression. They indeed can alter the susceptibility of cells to engage regulated cell death, regulate pro-survival signal transduction pathways and confer metabolic plasticity that adapts to specific tumor cell demands. Interestingly, a relatively poorly explored aspect of mitochondria in neoplastic disease is their contribution to the characteristic genomic instability that underlies the evolution of the disease. In this review, we summarize the known mechanisms by which mitochondrial alterations in cancer tolerate and support the accumulation of DNA mutations which leads to genomic instability. We describe recent studies elucidating mitochondrial responses to DNA damage as well as the direct contribution of mitochondria to favor the accumulation of DNA alterations.}, }
@article {pmid33909617, year = {2021}, author = {Gurke, M and Vidal-Gorosquieta, A and Pajimans, JLA and Wȩcek, K and Barlow, A and González-Fortes, G and Hartmann, S and Grandal-d'Anglade, A and Hofreiter, M}, title = {Insight into the introduction of domestic cattle and the process of Neolithization to the Spanish region Galicia by genetic evidence.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0249537}, pmid = {33909617}, issn = {1932-6203}, mesh = {Animals ; Animals, Domestic/*classification/*genetics ; Breeding ; Cattle ; Domestication ; Evolution, Molecular ; Female ; Fossils/*history ; High-Throughput Nucleotide Sequencing ; History, Ancient ; Introduced Species/*history ; Male ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Spain ; }, abstract = {Domestic cattle were brought to Spain by early settlers and agricultural societies. Due to missing Neolithic sites in the Spanish region of Galicia, very little is known about this process in this region. We sampled 18 cattle subfossils from different ages and different mountain caves in Galicia, of which 11 were subject to sequencing of the mitochondrial genome and phylogenetic analysis, to provide insight into the introduction of cattle to this region. We detected high similarity between samples from different time periods and were able to compare the time frame of the first domesticated cattle in Galicia to data from the connecting region of Cantabria to show a plausible connection between the Neolithization of these two regions. Our data shows a close relationship of the early domesticated cattle of Galicia and modern cow breeds and gives a general insight into cattle phylogeny. We conclude that settlers migrated to this region of Spain from Europe and introduced common European breeds to Galicia.}, }
@article {pmid33906412, year = {2021}, author = {Schikora-Tamarit, M&#xc0; and Marcet-Houben, M and Nosek, J and Gabaldón, T}, title = {Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi.}, journal = {Open biology}, volume = {11}, number = {4}, pages = {200362}, pmid = {33906412}, issn = {2046-2441}, mesh = {*Biological Evolution ; Computational Biology/methods ; Electron Transport Complex I/*genetics/*metabolism ; Eukaryota/genetics/metabolism ; Fungi/classification/*physiology ; Genome, Fungal ; Genomics ; Mitochondria/*genetics/*metabolism ; *Oxidative Phosphorylation ; *Oxidative Stress ; Phylogeny ; }, abstract = {Oxidative phosphorylation is among the most conserved mitochondrial pathways. However, one of the cornerstones of this pathway, the multi-protein complex NADH : ubiquinone oxidoreductase (complex I) has been lost multiple independent times in diverse eukaryotic lineages. The causes and consequences of these convergent losses remain poorly understood. Here, we used a comparative genomics approach to reconstruct evolutionary paths leading to complex I loss and infer possible evolutionary scenarios. By mining available mitochondrial and nuclear genomes, we identified eight independent events of mitochondrial complex I loss across eukaryotes, of which six occurred in fungal lineages. We focused on three recent loss events that affect closely related fungal species, and inferred genomic changes convergently associated with complex I loss. Based on these results, we predict novel complex I functional partners and relate the loss of complex I with the presence of increased mitochondrial antioxidants, higher fermentative capabilities, duplications of alternative dehydrogenases, loss of alternative oxidases and adaptation to antifungal compounds. To explain these findings, we hypothesize that a combination of previously acquired compensatory mechanisms and exposure to environmental triggers of oxidative stress (such as hypoxia and/or toxic chemicals) induced complex I loss in fungi.}, }
@article {pmid33901335, year = {2021}, author = {Bilcke, G and Osuna-Cruz, CM and Santana Silva, M and Poulsen, N and D'hondt, S and Bulankova, P and Vyverman, W and De Veylder, L and Vandepoele, K}, title = {Diurnal transcript profiling of the diatom Seminavis robusta reveals adaptations to a benthic lifestyle.}, journal = {The Plant journal : for cell and molecular biology}, volume = {107}, number = {1}, pages = {315-336}, doi = {10.1111/tpj.15291}, pmid = {33901335}, issn = {1365-313X}, mesh = {*Adaptation, Physiological ; Cell Cycle/genetics ; Cell Wall/genetics/metabolism ; Chloroplasts/genetics ; Circadian Rhythm/*genetics ; Diatoms/*cytology/*physiology ; Enzymes/genetics/metabolism ; Evolution, Molecular ; *Gene Expression ; Mitochondria/genetics ; Phylogeny ; Plankton/genetics/physiology ; RNA, Long Noncoding ; }, abstract = {Coastal regions contribute an estimated 20% of annual gross primary production in the oceans, despite occupying only 0.03% of their surface area. Diatoms frequently dominate coastal sediments, where they experience large variations in light regime resulting from the interplay of diurnal and tidal cycles. Here, we report on an extensive diurnal transcript profiling experiment of the motile benthic diatom Seminavis robusta. Nearly 90% (23 328) of expressed protein-coding genes and 66.9% (1124) of expressed long intergenic non-coding RNAs showed significant expression oscillations and are predominantly phasing at night with a periodicity of 24 h. Phylostratigraphic analysis found that rhythmic genes are enriched in highly conserved genes, while diatom-specific genes are predominantly associated with midnight expression. Integration of genetic and physiological cell cycle markers with silica depletion data revealed potential new silica cell wall-associated gene families specific to diatoms. Additionally, we observed 1752 genes with a remarkable semidiurnal (12-h) periodicity, while the expansion of putative circadian transcription factors may reflect adaptations to cope with highly unpredictable external conditions. Taken together, our results provide new insights into the adaptations of diatoms to the benthic environment and serve as a valuable resource for the study of diurnal regulation in photosynthetic eukaryotes.}, }
@article {pmid33892508, year = {2021}, author = {Breton, S and Ghiselli, F and Milani, L}, title = {Mitochondrial Short-Term Plastic Responses and Long-Term Evolutionary Dynamics in Animal Species.}, journal = {Genome biology and evolution}, volume = {13}, number = {7}, pages = {}, pmid = {33892508}, issn = {1759-6653}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Epigenesis, Genetic ; Epigenomics ; *Genome, Mitochondrial ; *Mitochondria/genetics ; }, abstract = {How do species respond or adapt to environmental changes? The answer to this depends partly on mitochondrial epigenetics and genetics, new players in promoting adaptation to both short- and long-term environmental changes. In this review, we explore how mitochondrial epigenetics and genetics mechanisms, such as mtDNA methylation, mtDNA-derived noncoding RNAs, micropeptides, mtDNA mutations, and adaptations, can contribute to animal plasticity and adaptation. We also briefly discuss the challenges in assessing mtDNA adaptive evolution. In sum, this review covers new advances in the field of mitochondrial genomics, many of which are still controversial, and discusses processes still somewhat obscure, and some of which are still quite speculative and require further robust experimentation.}, }
@article {pmid33892099, year = {2021}, author = {Wood, AW and Duda, TF}, title = {Reticulate evolution in Conidae: Evidence of nuclear and mitochondrial introgression.}, journal = {Molecular phylogenetics and evolution}, volume = {161}, number = {}, pages = {107182}, doi = {10.1016/j.ympev.2021.107182}, pmid = {33892099}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/*genetics ; *Evolution, Molecular ; Gastropoda/classification/*genetics ; Genes, Mitochondrial/genetics ; *Genetic Introgression ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Conidae is a hyperdiverse family of marine snails that has many hallmarks of adaptive radiation. Hybridization and introgression may contribute to such instances of rapid diversification by generating novel gene combinations that facilitate exploitation of distinct niches. Here we evaluated whether or not these mechanisms may have contributed to the evolutionary history of a subgenus of Conidae (Virroconus). Several observations hint at evidence of past introgression for members of this group, including incongruence between phylogenetic relationships inferred from mitochondrial gene sequences and morphology and widespread sympatry of many Virroconus species in the Indo-West Pacific. We generated and analyzed transcriptome data of Virroconus species to (i) infer a robust nuclear phylogeny, (ii) assess mitochondrial and nuclear gene tree discordance, and (iii) formally test for introgression of nuclear loci. We identified introgression of mitochondrial genomes and nuclear gene regions between ancestors of one pair of Virroconus species, and mitochondrial introgression between another pair. We also found evidence of adaptive introgression of conotoxin venom loci between a third pair of species. Together, our results demonstrate that hybridization and introgression impacted the evolutionary history of Virroconus and hence may have contributed to the adaptive radiation of Conidae.}, }
@article {pmid33891594, year = {2021}, author = {Milner, DS and Wideman, JG and Stairs, CW and Dunn, CD and Richards, TA}, title = {A functional bacteria-derived restriction modification system in the mitochondrion of a heterotrophic protist.}, journal = {PLoS biology}, volume = {19}, number = {4}, pages = {e3001126}, pmid = {33891594}, issn = {1545-7885}, mesh = {Bacteria/*genetics ; Base Sequence ; DNA Restriction-Modification Enzymes/*genetics ; DNA, Mitochondrial/analysis/genetics ; Escherichia coli/genetics ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Mitochondrial/genetics ; Mitochondria/*genetics ; Organisms, Genetically Modified ; Phylogeny ; Repetitive Sequences, Nucleic Acid/genetics ; Saccharomyces cerevisiae/genetics ; Sequence Analysis, DNA ; }, abstract = {The overarching trend in mitochondrial genome evolution is functional streamlining coupled with gene loss. Therefore, gene acquisition by mitochondria is considered to be exceedingly rare. Selfish elements in the form of self-splicing introns occur in many organellar genomes, but the wider diversity of selfish elements, and how they persist in the DNA of organelles, has not been explored. In the mitochondrial genome of a marine heterotrophic katablepharid protist, we identify a functional type II restriction modification (RM) system originating from a horizontal gene transfer (HGT) event involving bacteria related to flavobacteria. This RM system consists of an HpaII-like endonuclease and a cognate cytosine methyltransferase (CM). We demonstrate that these proteins are functional by heterologous expression in both bacterial and eukaryotic cells. These results suggest that a mitochondrion-encoded RM system can function as a toxin-antitoxin selfish element, and that such elements could be co-opted by eukaryotic genomes to drive biased organellar inheritance.}, }
@article {pmid33891583, year = {2021}, author = {Edwards, DM and Røyrvik, EC and Chustecki, JM and Giannakis, K and Glastad, RC and Radzvilavicius, AL and Johnston, IG}, title = {Avoiding organelle mutational meltdown across eukaryotes with or without a germline bottleneck.}, journal = {PLoS biology}, volume = {19}, number = {4}, pages = {e3001153}, pmid = {33891583}, issn = {1545-7885}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Arabidopsis ; DNA, Mitochondrial/genetics ; Drosophila ; Eukaryota/classification/*genetics ; Gene Expression Regulation, Developmental ; Genetic Speciation ; Germ Cells/*metabolism ; Germ-Line Mutation/physiology ; Humans ; Mice ; Mitochondria/genetics ; Mitochondrial Dynamics/genetics ; Models, Genetic ; Mutagenesis/physiology ; Mutation/*physiology ; Mutation Rate ; Organelle Biogenesis ; Organelles/*genetics/physiology ; }, abstract = {Mitochondrial DNA (mtDNA) and plastid DNA (ptDNA) encode vital bioenergetic apparatus, and mutations in these organelle DNA (oDNA) molecules can be devastating. In the germline of several animals, a genetic "bottleneck" increases cell-to-cell variance in mtDNA heteroplasmy, allowing purifying selection to act to maintain low proportions of mutant mtDNA. However, most eukaryotes do not sequester a germline early in development, and even the animal bottleneck remains poorly understood. How then do eukaryotic organelles avoid Muller's ratchet-the gradual buildup of deleterious oDNA mutations? Here, we construct a comprehensive and predictive genetic model, quantitatively describing how different mechanisms segregate and decrease oDNA damage across eukaryotes. We apply this comprehensive theory to characterise the animal bottleneck with recent single-cell observations in diverse mouse models. Further, we show that gene conversion is a particularly powerful mechanism to increase beneficial cell-to-cell variance without depleting oDNA copy number, explaining the benefit of observed oDNA recombination in diverse organisms which do not sequester animal-like germlines (for example, sponges, corals, fungi, and plants). Genomic, transcriptomic, and structural datasets across eukaryotes support this mechanism for generating beneficial variance without a germline bottleneck. This framework explains puzzling oDNA differences across taxa, suggesting how Muller's ratchet is avoided in different eukaryotes.}, }
@article {pmid33878294, year = {2021}, author = {Kummer, E and Schubert, KN and Schoenhut, T and Scaiola, A and Ban, N}, title = {Structural basis of translation termination, rescue, and recycling in mammalian mitochondria.}, journal = {Molecular cell}, volume = {81}, number = {12}, pages = {2566-2582.e6}, doi = {10.1016/j.molcel.2021.03.042}, pmid = {33878294}, issn = {1097-4164}, mesh = {Animals ; Carboxylic Ester Hydrolases ; Codon, Terminator ; Cryoelectron Microscopy/methods ; Humans ; Mitochondria/metabolism/*physiology ; Mitochondrial Proteins/metabolism ; Mitochondrial Ribosomes/*metabolism ; Peptide Chain Termination, Translational/genetics/*physiology ; Peptide Elongation Factor G/metabolism ; Peptide Termination Factors/metabolism ; Protein Biosynthesis ; Ribosomal Proteins/metabolism/physiology ; Ribosomes/metabolism ; }, abstract = {The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondrial release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present structural models detailing the process of mitochondrial ribosome recycling to explain how a dedicated elongation factor, mitochondrial EFG2 (mtEFG2), has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process.}, }
@article {pmid33871590, year = {2021}, author = {Helfenrath, K and Sauer, M and Kamga, M and Wisniewsky, M and Burmester, T and Fabrizius, A}, title = {The More, the Merrier? Multiple Myoglobin Genes in Fish Species, Especially in Gray Bichir (Polypterus senegalus) and Reedfish (Erpetoichthys calabaricus).}, journal = {Genome biology and evolution}, volume = {13}, number = {7}, pages = {}, pmid = {33871590}, issn = {1759-6653}, mesh = {Animals ; Evolution, Molecular ; *Fishes/genetics ; *Myoglobin/genetics ; Phylogeny ; Vertebrates/genetics ; }, abstract = {The members of the globin superfamily are a classical model system to investigate gene evolution and their fates as well as the diversity of protein function. One of the best-known globins is myoglobin (Mb), which is mainly expressed in heart muscle and transports oxygen from the sarcolemma to the mitochondria. Most vertebrates harbor a single copy of the myoglobin gene, but some fish species have multiple myoglobin genes. Phylogenetic analyses indicate an independent emergence of multiple myoglobin genes, whereby the origin is mostly the last common ancestor of each order. By analyzing different transcriptome data sets, we found at least 15 multiple myoglobin genes in the polypterid gray bichir (Polypterus senegalus) and reedfish (Erpetoichthys calabaricus). In reedfish, the myoglobin genes are expressed in a broad range of tissues but show very different expression values. In contrast, the Mb genes of the gray bichir show a rather scattered expression pattern; only a few Mb genes were found expressed in the analyzed tissues. Both, gray bichir and reedfish possess lungs which enable them to inhabit shallow and swampy waters throughout tropical Africa with frequently fluctuating and low oxygen concentrations. The myoglobin repertoire probably reflects the molecular adaptation to these conditions. The sequence divergence, the substitution rate, and the different expression pattern of multiple myoglobin genes in gray bichir and reedfish imply different functions, probably through sub- and neofunctionalization during evolution.}, }
@article {pmid33871031, year = {2021}, author = {de Melo Teixeira, M and Lang, BF and Matute, DR and Stajich, JE and Barker, BM}, title = {Mitochondrial genomes of the human pathogens Coccidioides immitis and Coccidioides posadasii.}, journal = {G3 (Bethesda, Md.)}, volume = {11}, number = {7}, pages = {}, pmid = {33871031}, issn = {2160-1836}, support = {R01 AI153523/AI/NIAID NIH HHS/United States ; R21 AI128536/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Coccidioides/genetics ; Phylogeny ; *Genome, Mitochondrial ; *Coccidioidomycosis/epidemiology/genetics/microbiology ; }, abstract = {Fungal mitochondrial genomes encode genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and the molecule has been used as a molecular marker for population genetics studies. Coccidioides immitis and C. posadasii are endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. To date, approximately 150 Coccidioides isolates have been sequenced to infer patterns of variation in nuclear genomes. However, less attention has been given to the mitochondrial genomes of Coccidioides. In this report, we describe the assembly and annotation of mitochondrial reference genomes for two representative strains of C. posadasii and C. immitis, as well as assess population variation among 77 selected genomes. The sizes of the circular-mapping molecules are 68.2 Kb in C. immitis and 75.1 Kb in C. posadasii. We identify 14 mitochondrial protein-coding genes common to most fungal mitochondria, which are largely syntenic across different populations and species of Coccidioides. Both Coccidioides species are characterized by a large number of group I and II introns, harboring twice the number of elements as compared to closely related Onygenales. The introns contain complete or truncated ORFs with high similarity to homing endonucleases of the LAGLIDADG and GIY-YIG families. Phylogenetic comparisons of mitochondrial and nuclear genomes show extensive phylogenetic discordance suggesting that the evolution of the two types of genetic material is not identical. This work represents the first assessment of mitochondrial genomes among isolates of both species of Coccidioides, and provides a foundation for future functional work.}, }
@article {pmid33863338, year = {2021}, author = {Salomaki, ED and Terpis, KX and Rueckert, S and Kotyk, M and Varadínová, ZK and Čepička, I and Lane, CE and Kolisko, M}, title = {Gregarine single-cell transcriptomics reveals differential mitochondrial remodeling and adaptation in apicomplexans.}, journal = {BMC biology}, volume = {19}, number = {1}, pages = {77}, pmid = {33863338}, issn = {1741-7007}, support = {CZ.02.2.69/0.0/0.0/16_027/0008357//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy (CZ)/ ; CZ.02.2.69/0.0/0.0/20_079/0017809//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; 1541510//Directorate for Biological Sciences/ ; 1158119//Grantov&#xe1; Agentura, Univerzita Karlova/ ; 19-19297S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 18-28103S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; Fellowship Purkyne//Akademie V&#x11b;d &#x10c;esk&#xe9; Republiky/ ; OIA-1655221//National Science Foundation/ ; GBMF9327//Gordon and Betty Moore Foundation/ ; }, mesh = {Animals ; *Apicomplexa/genetics ; Humans ; *Mitochondria/genetics ; Phylogeny ; Single-Cell Analysis ; Transcriptome ; }, abstract = {BACKGROUND: Apicomplexa is a diverse phylum comprising unicellular endobiotic animal parasites and contains some of the most well-studied microbial eukaryotes including the devastating human pathogens Plasmodium falciparum and Cryptosporidium hominis. In contrast, data on the invertebrate-infecting gregarines remains sparse and their evolutionary relationship to other apicomplexans remains obscure. Most apicomplexans retain a highly modified plastid, while their mitochondria remain metabolically conserved. Cryptosporidium spp. inhabit an anaerobic host-gut environment and represent the known exception, having completely lost their plastid while retaining an extremely reduced mitochondrion that has lost its genome. Recent advances in single-cell sequencing have enabled the first broad genome-scale explorations of gregarines, providing evidence of differential plastid retention throughout the group. However, little is known about the retention and metabolic capacity of gregarine mitochondria.<br><br>RESULTS: Here, we sequenced transcriptomes from five species of gregarines isolated from cockroaches. We combined these data with those from other apicomplexans, performed detailed phylogenomic analyses, and characterized their mitochondrial metabolism. Our results support the placement of Cryptosporidium as the earliest diverging lineage of apicomplexans, which impacts our interpretation of evolutionary events within the phylum. By mapping in silico predictions of core mitochondrial pathways onto our phylogeny, we identified convergently reduced mitochondria. These data show that the electron transport chain has been independently lost three times across the phylum, twice within gregarines.<br><br>CONCLUSIONS: Apicomplexan lineages show variable functional restructuring of mitochondrial metabolism that appears to have been driven by adaptations to parasitism and anaerobiosis. Our findings indicate that apicomplexans are rife with convergent adaptations, with shared features including morphology, energy metabolism, and intracellularity.}, }
@article {pmid33860546, year = {2021}, author = {Brandeis, M}, title = {Were eukaryotes made by sex?: Sex might have been vital for merging endosymbiont and host genomes giving rise to eukaryotes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {43}, number = {6}, pages = {e2000256}, doi = {10.1002/bies.202000256}, pmid = {33860546}, issn = {1521-1878}, mesh = {Archaea/genetics ; *Biological Evolution ; *Eukaryota/genetics ; Eukaryotic Cells ; Phylogeny ; Symbiosis/genetics ; }, abstract = {I hypothesize that the appearance of sex facilitated the merging of the endosymbiont and host genomes during early eukaryote evolution. Eukaryotes were formed by symbiosis between a bacterium that entered an archaeon, eventually giving rise to mitochondria. This entry was followed by the gradual transfer of most bacterial endosymbiont genes into the archaeal host genome. I argue that the merging of the mitochondrial genes into the host genome was vital for the evolution of genuine eukaryotes. At the time this process commenced it was unprecedented and required a novel mechanism. I suggest that this mechanism was meiotic sex, and that its appearance might have been THE crucial step that enabled the evolution of proper eukaryotes from early endosymbiont containing proto-eukaryotes. Sex might continue to be essential today for keeping genome insertions in check. Also see the video abstract here: https://youtu.be/aVMvWMpomac.}, }
@article {pmid33859247, year = {2021}, author = {Louro, M and Kuzmina, TA and Bredtmann, CM and Diekmann, I and de Carvalho, LMM and von Samson-Himmelstjerna, G and Krücken, J}, title = {Genetic variability, cryptic species and phylogenetic relationship of six cyathostomin species based on mitochondrial and nuclear sequences.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {8245}, pmid = {33859247}, issn = {2045-2322}, mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Helminth/analysis/genetics ; DNA, Mitochondrial/analysis ; Genetic Variation ; Germany ; Horse Diseases/parasitology ; Horses/parasitology ; Intestinal Diseases, Parasitic ; Mitochondria/*genetics ; Parasite Egg Count/veterinary ; Phylogeny ; Sequence Analysis, DNA ; *Strongyloidea/classification/genetics ; Ukraine ; }, abstract = {Cyathostomins are important intestinal nematode parasites of equines and include 50 accepted species. Their taxonomy has been frequently revised and the presence of cryptic species suggested. Furthermore, usually molecular- and morphology-based phylogenetic analyses give divergent results. In this study, the nucleotide sequences of the nuclear second internal transcribed spacer (ITS-2) and the mitochondrial partial cytochrome c oxidase subunit I (COI) were determined for adults of six cyathostomin species (Coronocyclus coronatus, Coronocyclus labiatus, Cylicocyclus nassatus, Cylicostephanus calicatus, Cylicostephanus longibursatus, Cylicostephanus minutus) collected from different equine species within two geographic regions. Maximum likelihood trees were calculated for ITS-2, COI, and concatenated data. No obvious differentiation was observed between geographic regions or equine host species. As previously reported, Coronocyclus coronatus and Cylicostephanus calicatus revealed a close relationship. Cryptic species were detected in Cylicostephanus minutus and Cylicostephanus calicatus. Cylicocyclus nassatus and Coronocyclus labiatus showed diverse mitochondrial and nuclear haplotypes occurring in different combinations, while Cylicostephanus longibursatus was comparatively homogenous. In conclusion, a combined analysis of nuclear and mitochondrial haplotypes improved resolution of the phylogeny and should be applied to the remaining cyathostomin species and across additional equine host species and geographic regions.}, }
@article {pmid33857537, year = {2021}, author = {Deonath, A}, title = {Evolution of eukaryotes as a story of survival and growth of mitochondrial DNA over two billion years.}, journal = {Bio Systems}, volume = {206}, number = {}, pages = {104426}, doi = {10.1016/j.biosystems.2021.104426}, pmid = {33857537}, issn = {1872-8324}, mesh = {Animals ; *Biological Evolution ; Cell Survival/physiology ; DNA, Mitochondrial/*physiology ; Eukaryota/genetics/*growth &amp; development ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; Humans ; Mitochondria/physiology ; Time Factors ; }, abstract = {Mitochondria's significance in human diseases and in functioning, health and death of eukaryotic cell has been acknowledged widely. Yet our perspective in cell biology and evolution remains nucleocentric. Mitochondrial DNA, by virtue of its omnipresence and species-level conservation, is used as a barcode in animal taxonomy. This article analyses various levels of containment structures that enclose mitochondrial DNA and advocates a fresh perspective wherein evolution of organic structures of the eukarya domain seem to support and facilitate survival and proliferation of mitochondrial DNA by splitting containers as they age and by directing them along two distinct pathways: destruction of containers with more mutant mitochondrial DNA and rejuvenation of containers with less mutant mitochondrial DNA.}, }
@article {pmid33857516, year = {2021}, author = {Dores-Silva, PR and Kiraly, VTR and Moritz, MNO and Serrão, VHB and Dos Passos, PMS and Spagnol, V and Teixeira, FR and Gava, LM and Cauvi, DM and Ramos, CHI and De Maio, A and Borges, JC}, title = {New insights on human Hsp70-escort protein 1: Chaperone activity, interaction with liposomes, cellular localizations and HSPA's self-assemblies remodeling.}, journal = {International journal of biological macromolecules}, volume = {182}, number = {}, pages = {772-784}, doi = {10.1016/j.ijbiomac.2021.04.048}, pmid = {33857516}, issn = {1879-0003}, mesh = {Active Transport, Cell Nucleus ; Cell Line, Tumor ; Cell Nucleus/*metabolism ; HSP70 Heat-Shock Proteins/metabolism ; Humans ; Intracellular Membranes/metabolism ; Liposomes/*metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins/metabolism ; Molecular Chaperones/*metabolism ; Protein Binding ; Protein Multimerization ; }, abstract = {The 70 kDa heat shock proteins (Hsp70) are prone to self-assembly under thermal stress conditions, forming supramolecular assemblies (SMA), what may have detrimental consequences for cellular viability. In mitochondria, the cochaperone Hsp70-escort protein 1 (Hep1) maintains mitochondrial Hsp70 (mtHsp70) in a soluble and functional state, contributing to preserving proteostasis. Here we investigated the interaction between human Hep1 (hHep1) and HSPA9 (human mtHsp70) or HSPA1A (Hsp70-1A) in monomeric and thermic SMA states to unveil further information about the involved mechanisms. hHep1 was capable of blocking the formation of HSPA SMAs under a thermic treatment and stimulated HSPA ATPase activity in both monomeric and preformed SMA. The interaction of hHep1 with both monomeric and SMA HSPAs displayed a stoichiometric ratio close to 1, suggesting that hHep1 has access to most protomers within the SMA. Interestingly, hHep1 remodeled HSPA9 and HSPA1A SMAs into smaller forms. Furthermore, hHep1 was detected in the mitochondria and nucleus of cells transfected with the respective coding DNA and interacted with liposomes resembling mitochondrial membranes. Altogether, these new features reinforce that hHep1 act as a "chaperone for a chaperone", which may play a critical role in cellular proteostasis.}, }
@article {pmid33848317, year = {2021}, author = {Postic, E and Outreman, Y and Derocles, S and Granado, C and Le Ralec, A}, title = {Genetics of wild and mass-reared populations of a generalist aphid parasitoid and improvement of biological control.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0249893}, pmid = {33848317}, issn = {1932-6203}, mesh = {Animals ; Aphids/classification/*genetics ; Discriminant Analysis ; Electron Transport Complex IV/genetics ; Fragaria/parasitology ; Genetic Variation ; Genetics, Population ; Haplotypes ; Host-Parasite Interactions ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; *Pest Control, Biological ; Phylogeny ; Principal Component Analysis ; }, abstract = {Due to their ability to parasitize various insect species, generalist parasitoids are widely used as biological control agents. They can be mass-reared and released in agroecosystems to control several pest species in various crops. However, the existence of genetic differentiation among populations of generalist parasitoid species is increasingly recognized and this can be associated with an adaptation to local conditions or to a reduced range of host species. Moreover, constraints of mass-rearing conditions can alter genetic variation within parasitoid populations released. These features could be associated with a reduced efficiency of the control of targeted pest species. Here, we focused on strawberry greenhouses where the control of aphids with the generalist parasitoid Aphidius ervi appears to be inefficient. We investigated whether this inefficiency may have both genetic and ecological bases comparing wild and commercial populations of A. ervi. We used two complementary genetic approaches: one based on the mitochondrial marker COI and one based on microsatellite markers. COI analysis showed a genetic differentiation within the A. ervi species, but the structure was neither associated with the commercial/wild status nor with host species factors. On the other hand, using microsatellite markers, we showed a genetic differentiation between commercial and wild A. ervi populations associated with a loss of genetic diversity within the mass-reared populations. Our ecological genetics study may potentially explain the weak efficiency of biological control of aphids in protected strawberry crops and enable to provide some insights to improve biological control.}, }
@article {pmid33848308, year = {2021}, author = {de Meeûs d'Argenteuil, C and Boshuizen, B and Oosterlinck, M and van de Winkel, D and De Spiegelaere, W and de Bruijn, CM and Goethals, K and Vanderperren, K and Delesalle, CJG}, title = {Flexibility of equine bioenergetics and muscle plasticity in response to different types of training: An integrative approach, questioning existing paradigms.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0249922}, pmid = {33848308}, issn = {1932-6203}, mesh = {Amino Acids, Aromatic/metabolism ; Amino Acids, Branched-Chain/metabolism ; Animals ; Citric Acid Cycle ; *Energy Metabolism ; Female ; Glycolysis ; Heart Rate ; Horses ; Lipid Peroxidation ; Male ; Metabolomics ; Mitochondria/metabolism ; Muscle Fibers, Skeletal/physiology ; Muscle, Skeletal/metabolism/pathology/*physiology ; Pentose Phosphate Pathway ; Physical Conditioning, Animal ; }, abstract = {Equine bioenergetics have predominantly been studied focusing on glycogen and fatty acids. Combining omics with conventional techniques allows for an integrative approach to broadly explore and identify important biomolecules. Friesian horses were aquatrained (n = 5) or dry treadmill trained (n = 7) (8 weeks) and monitored for: evolution of muscle diameter in response to aquatraining and dry treadmill training, fiber type composition and fiber cross-sectional area of the M. pectoralis, M. vastus lateralis and M. semitendinosus and untargeted metabolomics of the M. pectoralis and M. vastus lateralis in response to dry treadmill training. Aquatraining was superior to dry treadmill training to increase muscle diameter in the hindquarters, with maximum effect after 4 weeks. After dry treadmill training, the M. pectoralis showed increased muscle diameter, more type I fibers, decreased fiber mean cross sectional area, and an upregulated oxidative metabolic profile: increased β-oxidation (key metabolites: decreased long chain fatty acids and increased long chain acylcarnitines), TCA activity (intermediates including succinyl-carnitine and 2-methylcitrate), amino acid metabolism (glutamine, aromatic amino acids, serine, urea cycle metabolites such as proline, arginine and ornithine) and xenobiotic metabolism (especially p-cresol glucuronide). The M. vastus lateralis expanded its fast twitch profile, with decreased muscle diameter, type I fibers and an upregulation of glycolytic and pentose phosphate pathway activity, and increased branched-chain and aromatic amino acid metabolism (cis-urocanate, carnosine, homocarnosine, tyrosine, tryptophan, p-cresol-glucuronide, serine, methionine, cysteine, proline and ornithine). Trained Friesians showed increased collagen and elastin turn-over. Results show that branched-chain amino acids, aromatic amino acids and microbiome-derived xenobiotics need further study in horses. They feed the TCA cycle at steps further downstream from acetyl CoA and most likely, they are oxidized in type IIA fibers, the predominant fiber type of the horse. These study results underline the importance of reviewing existing paradigms on equine bioenergetics.}, }
@article {pmid33846476, year = {2021}, author = {Elfekih, S and Tay, WT and Polaszek, A and Gordon, KHJ and Kunz, D and Macfadyen, S and Walsh, TK and Vyskočilová, S and Colvin, J and De Barro, PJ}, title = {On species delimitation, hybridization and population structure of cassava whitefly in Africa.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {7923}, pmid = {33846476}, issn = {2045-2322}, mesh = {Africa ; Animals ; Base Sequence ; Electron Transport Complex IV/genetics ; Gene Flow ; Geography ; Hemiptera/*genetics ; *Hybridization, Genetic ; Manihot/*parasitology ; Mitochondria/genetics ; Phylogeny ; Population Dynamics ; Principal Component Analysis ; Species Specificity ; }, abstract = {The Bemisia cassava whitefly complex includes species that cause severe crop damage through vectoring cassava viruses in eastern Africa. Currently, this whitefly complex is divided into species and subgroups (SG) based on very limited molecular markers that do not allow clear definition of species and population structure. Based on 14,358 genome-wide SNPs from 62 Bemisia cassava whitefly individuals belonging to sub-Saharan African species (SSA1, SSA2 and SSA4), and using a well-curated mtCOI gene database, we show clear incongruities in previous taxonomic approaches underpinned by effects from pseudogenes. We show that the SSA4 species is nested within SSA2, and that populations of the SSA1 species comprise well-defined south-eastern (Madagascar, Tanzania) and north-western (Nigeria, Democratic Republic of Congo, Burundi) putative sub-species. Signatures of allopatric incipient speciation, and the presence of a 'hybrid zone' separating the two putative sub-species were also detected. These findings provide insights into the evolution and molecular ecology of a highly cryptic hemipteran insect complex in African, and allow the systematic use of genomic data to be incorporated in the development of management strategies for this cassava pest.}, }
@article {pmid33839167, year = {2021}, author = {García-Catalán, S and González-Moreno, L and Del Arco, A}, title = {Ca[2+]-regulated mitochondrial carriers of ATP-Mg[2+]/Pi: Evolutionary insights in protozoans.}, journal = {Biochimica et biophysica acta. Molecular cell research}, volume = {1868}, number = {7}, pages = {119038}, doi = {10.1016/j.bbamcr.2021.119038}, pmid = {33839167}, issn = {1879-2596}, mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence/genetics ; Animals ; Antiporters/*genetics/*metabolism/physiology ; Calcium/metabolism ; Calcium-Binding Proteins/metabolism ; Calmodulin/metabolism ; Databases, Genetic ; Evolution, Molecular ; Membrane Transport Proteins/metabolism ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins/genetics/metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/*genetics/*metabolism/physiology ; Phylogeny ; Protozoan Proteins/genetics/metabolism ; Sequence Homology ; }, abstract = {In addition to its uptake across the Ca[2+] uniporter, intracellular calcium signals can stimulate mitochondrial metabolism activating metabolite exchangers of the inner mitochondrial membrane belonging to the mitochondrial carrier family (SLC25). One of these Ca[2+]-regulated mitochondrial carriers (CaMCs) are the reversible ATP-Mg[2+]/Pi transporters, or SCaMCs, required for maintaining optimal adenine nucleotide (AdN) levels in the mitochondrial matrix representing an alternative transporter to the ADP/ATP translocases (AAC). This CaMC has a distinctive Calmodulin-like (CaM-like) domain fused to the carrier domain that makes its transport activity strictly dependent on cytosolic Ca[2+] signals. Here we investigate about its origin analysing its distribution and features in unicellular eukaryotes. Unexpectedly, we find two types of ATP-Mg[2+]/Pi carriers, the canonical ones and shortened variants lacking the CaM-like domain. Phylogenetic analysis shows that both SCaMC variants have a common origin, unrelated to AACs, suggesting in turn that recurrent losses of the regulatory module have occurred in the different phyla. They are excluding variants that show a more limited distribution and less conservation than AACs. Interestingly, these truncated variants of SCaMC are found almost exclusively in parasitic protists, such as apicomplexans, kinetoplastides or animal-patogenic oomycetes, and in green algae, suggesting that its lost could be related to certain life-styles. In addition, we find an intricate structural diversity in these variants that may be associated with their pathogenicity. The consequences on SCaMC functions of these new SCaMC-b variants are discussed.}, }
@article {pmid33837778, year = {2021}, author = {Pyrih, J and Pánek, T and Durante, IM and Rašková, V and Cimrhanzlová, K and Kriegová, E and Tsaousis, AD and Eliáš, M and Lukeš, J}, title = {Vestiges of the Bacterial Signal Recognition Particle-Based Protein Targeting in Mitochondria.}, journal = {Molecular biology and evolution}, volume = {38}, number = {8}, pages = {3170-3187}, pmid = {33837778}, issn = {1537-1719}, mesh = {Bacterial Proteins/*genetics ; *Biological Evolution ; Escherichia coli Proteins/*genetics ; *Genome, Mitochondrial ; Naegleria/*genetics ; Receptors, Cytoplasmic and Nuclear/*genetics ; Sequence Homology, Nucleic Acid ; Signal Recognition Particle/*genetics ; }, abstract = {The main bacterial pathway for inserting proteins into the plasma membrane relies on the signal recognition particle (SRP), composed of the Ffh protein and an associated RNA component, and the SRP-docking protein FtsY. Eukaryotes use an equivalent system of archaeal origin to deliver proteins into the endoplasmic reticulum, whereas a bacteria-derived SRP and FtsY function in the plastid. Here we report on the presence of homologs of the bacterial Ffh and FtsY proteins in various unrelated plastid-lacking unicellular eukaryotes, namely Heterolobosea, Alveida, Goniomonas, and Hemimastigophora. The monophyly of novel eukaryotic Ffh and FtsY groups, predicted mitochondrial localization experimentally confirmed for Naegleria gruberi, and a strong alphaproteobacterial affinity of the Ffh group, collectively suggest that they constitute parts of an ancestral mitochondrial signal peptide-based protein-targeting system inherited from the last eukaryotic common ancestor, but lost from the majority of extant eukaryotes. The ability of putative signal peptides, predicted in a subset of mitochondrial-encoded N. gruberi proteins, to target a reporter fluorescent protein into the endoplasmic reticulum of Trypanosoma brucei, likely through their interaction with the cytosolic SRP, provided further support for this notion. We also illustrate that known mitochondrial ribosome-interacting proteins implicated in membrane protein targeting in opisthokonts (Mba1, Mdm38, and Mrx15) are broadly conserved in eukaryotes and nonredundant with the mitochondrial SRP system. Finally, we identified a novel mitochondrial protein (MAP67) present in diverse eukaryotes and related to the signal peptide-binding domain of Ffh, which may well be a hitherto unrecognized component of the mitochondrial membrane protein-targeting machinery.}, }
@article {pmid33836001, year = {2021}, author = {Dey, P and Sharma, SK and Sarkar, I and Ray, SD and Pramod, P and Kochiganti, VHS and Quadros, G and Rathore, SS and Singh, V and Singh, RP}, title = {Complete mitogenome of endemic plum-headed parakeet Psittacula cyanocephala - characterization and phylogenetic analysis.}, journal = {PloS one}, volume = {16}, number = {4}, pages = {e0241098}, pmid = {33836001}, issn = {1932-6203}, mesh = {Animals ; Codon Usage/genetics ; Gene Order/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Mitogens/*genetics ; Phylogeny ; Psittacula/*genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Selection, Genetic/genetics ; }, abstract = {Psittacula cyanocephala is an endemic parakeet from the Indian sub-continent that is widespread in the illegal bird trade. Previous studies on Psittacula parakeets have highlighted taxonomic ambiguities, warranting studies to resolve the issues. Since the mitochondrial genome provides useful information concerning the species evolution and phylogenetics, we sequenced the complete mitogenome of P. cyanocephala using NGS, validated 38.86% of the mitogenome using Sanger Sequencing and compared it with other available whole mitogenomes of Psittacula. The complete mitogenome of the species was 16814 bp in length with 54.08% AT composition. P. cyanocephala mitogenome comprises of 13 protein-coding genes, 2 rRNAs and 22 tRNAs. P. cyanocephala mitogenome organization was consistent with other Psittacula mitogenomes. Comparative codon usage analysis indicated the role of natural selection on Psittacula mitogenomes. Strong purifying selection pressure was observed maximum on nad1 and nad4l genes. The mitochondrial control region of all Psittacula species displayed the ancestral avian CR gene order. Phylogenetic analyses revealed the Psittacula genus as paraphyletic nature, containing at least 4 groups of species within the same genus, suggesting its taxonomic reconsideration. Our results provide useful information for developing forensic tests to control the illegal trade of the species and scientific basis for phylogenetic revision of the genus Psittacula.}, }
@article {pmid33829092, year = {2021}, author = {Lee, SH and Lee, SH}, title = {Complete mitochondrial genome of Oregonia gracilis Dana, 1851 (Crustacea: Decapoda: Majoidea).}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {6}, number = {3}, pages = {1236-1237}, pmid = {33829092}, issn = {2380-2359}, abstract = {The complete mitochondrial genome of the majoid crab, Oregonia gracilis, was determined from a specimen collected in Korea. The mitochondrial genome is 15,737 bp long and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes. A maximum-likelihood phylogenetic tree based on the 13 PCGs of the mitochondria showed that O. gracilis is closely related to the genus Chinoecetes. The complete mitochondrial genome of O. gracilis provides valuable information on the mitochondrial evolution of majoid crabs.}, }
@article {pmid33825987, year = {2021}, author = {Eyenga, P and Roussel, D and Rey, B and Ndille, P and Teulier, L and Eyenga, F and Romestaing, C and Morel, J and Gueguen-Chaignon, V and Sheu, SS}, title = {Mechanical ventilation preserves diaphragm mitochondrial function in a rat sepsis model.}, journal = {Intensive care medicine experimental}, volume = {9}, number = {1}, pages = {19}, pmid = {33825987}, issn = {2197-425X}, abstract = {BACKGROUND: To describe the effect of mechanical ventilation on diaphragm mitochondrial oxygen consumption, ATP production, reactive oxygen species (ROS) generation, and cytochrome c oxidase activity and content, and their relationship to diaphragm strength in an experimental model of sepsis.<br><br>METHODS: A cecal ligation and puncture (CLP) protocol was performed in 12 rats while 12 controls underwent sham operation. Half of the rats in each group were paralyzed and mechanically ventilated. We performed blood gas analysis and lactic acid assays 6&#xa0;h after surgery. Afterwards, we measured diaphragm strength and mitochondrial oxygen consumption, ATP and ROS generation, and cytochrome c oxidase activity. We also measured malondialdehyde (MDA) content as an index of lipid peroxidation, and mRNA expression of the proinflammatory interleukin-1&#x3b2; (IL-1&#x3b2;) in diaphragms.<br><br>RESULTS: CLP rats showed severe hypotension, metabolic acidosis, and upregulation of diaphragm IL-1&#x3b2; mRNA expression. Compared to sham controls, spontaneously breathing CLP rats showed lower diaphragm force and increased susceptibility to fatigue, along with depressed mitochondrial oxygen consumption and ATP production and cytochrome c oxidase activity. These rats also showed increased mitochondrial ROS generation and MDA content. Mechanical ventilation markedly restored mitochondrial oxygen consumption and ATP production in CLP rats; lowered mitochondrial ROS production by the complex 3; and preserved cytochrome c oxidase activity.<br><br>CONCLUSION: In an experimental model of sepsis, early initiation of mechanical ventilation restores diaphragm mitochondrial function.}, }
@article {pmid33818247, year = {2021}, author = {Schwartz, JH}, title = {Evolution, systematics, and the unnatural history of mitochondrial DNA.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {32}, number = {4}, pages = {126-151}, doi = {10.1080/24701394.2021.1899165}, pmid = {33818247}, issn = {2470-1408}, mesh = {*DNA, Mitochondrial/genetics ; *Evolution, Molecular ; *Genome, Mitochondrial ; Mitochondria ; Phylogeny ; }, abstract = {The tenets underlying the use of mtDNA in phylogenetic and systematic analyses are strict maternal inheritance, clonality, homoplasmy, and difference due to mutation: that is, there are species-specific mtDNA sequences and phylogenetic reconstruction is a matter of comparing these sequences and inferring closeness of relatedness from the degree of sequence similarity. Yet, how mtDNA behavior became so defined is mysterious. Even though early studies of fertilization demonstrated for most animals that not only the head, but the sperm's tail and mitochondria-bearing midpiece penetrate the egg, the opposite - only the head enters the egg - became fact, and mtDNA conceived as maternally transmitted. When midpiece/tail penetration was realized as true, the conceptions 'strict maternal inheritance', etc., and their application to evolutionary endeavors, did not change. Yet there is mounting evidence of paternal mtDNA transmission, paternal and maternal combination, intracellular recombination, and intra- and intercellular heteroplasmy. Clearly, these phenomena impact the systematic and phylogenetic analysis of mtDNA sequences.}, }
@article {pmid33813887, year = {2021}, author = {Ghiselli, F and Gomes-Dos-Santos, A and Adema, CM and Lopes-Lima, M and Sharbrough, J and Boore, JL}, title = {Molluscan mitochondrial genomes break the rules.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {376}, number = {1825}, pages = {20200159}, pmid = {33813887}, issn = {1471-2970}, mesh = {Animals ; *Gene Duplication ; *Gene Rearrangement ; *Genome, Mitochondrial ; Heredity ; Mollusca/*genetics ; }, abstract = {The first animal mitochondrial genomes to be sequenced were of several vertebrates and model organisms, and the consistency of genomic features found has led to a 'textbook description'. However, a more broad phylogenetic sampling of complete animal mitochondrial genomes has found many cases where these features do not exist, and the phylum Mollusca is especially replete with these exceptions. The characterization of full mollusc mitogenomes required considerable effort involving challenging molecular biology, but has created an enormous catalogue of surprising deviations from that textbook description, including wide variation in size, radical genome rearrangements, gene duplications and losses, the introduction of novel genes, and a complex system of inheritance dubbed 'doubly uniparental inheritance'. Here, we review the extraordinary variation in architecture, molecular functioning and intergenerational transmission of molluscan mitochondrial genomes. Such features represent a great potential for the discovery of biological history, processes and functions that are novel for animal mitochondrial genomes. This provides a model system for studying the evolution and the manifold roles that mitochondria play in organismal physiology, and many ways that the study of mitochondrial genomes are useful for phylogeny and population biology. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.}, }
@article {pmid33811236, year = {2021}, author = {Alqahtani, AA and Jansen, RK}, title = {The evolutionary fate of rpl32 and rps16 losses in the Euphorbia schimperi (Euphorbiaceae) plastome.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {7466}, pmid = {33811236}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Cell Nucleus/genetics ; Euphorbia/*genetics ; *Evolution, Molecular ; Gene Expression Regulation, Plant ; *Genome, Plastid ; Likelihood Functions ; Phylogeny ; Plant Proteins/chemistry/*genetics ; Ribosomal Proteins/chemistry/*genetics ; Transcriptome/genetics ; }, abstract = {Gene transfers from mitochondria and plastids to the nucleus are an important process in the evolution of the eukaryotic cell. Plastid (pt) gene losses have been documented in multiple angiosperm lineages and are often associated with functional transfers to the nucleus or substitutions by duplicated nuclear genes targeted to both the plastid and mitochondrion. The plastid genome sequence of Euphorbia schimperi was assembled and three major genomic changes were detected, the complete loss of rpl32 and pseudogenization of rps16 and infA. The nuclear transcriptome of E. schimperi was sequenced to investigate the transfer/substitution of the rpl32 and rps16 genes to the nucleus. Transfer of plastid-encoded rpl32 to the nucleus was identified previously in three families of Malpighiales, Rhizophoraceae, Salicaceae and Passifloraceae. An E. schimperi transcript of pt SOD-1-RPL32 confirmed that the transfer in Euphorbiaceae is similar to other Malpighiales indicating that it occurred early in the divergence of the order. Ribosomal protein S16 (rps16) is encoded in the plastome in most angiosperms but not in Salicaceae and Passifloraceae. Substitution of the E. schimperi pt rps16 was likely due to a duplication of nuclear-encoded mitochondrial-targeted rps16 resulting in copies dually targeted to the mitochondrion and plastid. Sequences of RPS16-1 and RPS16-2 in the three families of Malpighiales (Salicaceae, Passifloraceae and Euphorbiaceae) have high sequence identity suggesting that the substitution event dates to the early divergence within Malpighiales.}, }
@article {pmid33809280, year = {2021}, author = {Kusliy, MA and Vorobieva, NV and Tishkin, AA and Makunin, AI and Druzhkova, AS and Trifonov, VA and Iderkhangai, TO and Graphodatsky, AS}, title = {Traces of Late Bronze and Early Iron Age Mongolian Horse Mitochondrial Lineages in Modern Populations.}, journal = {Genes}, volume = {12}, number = {3}, pages = {}, pmid = {33809280}, issn = {2073-4425}, mesh = {Animals ; China ; DNA, Mitochondrial/genetics ; Genetic Variation/genetics ; Genome, Mitochondrial/genetics ; Haplotypes/genetics ; Horses/*genetics ; Italy ; Middle East ; Mitochondria/*genetics ; Mongolia ; }, abstract = {The Mongolian horse is one of the most ancient and relatively unmanaged horse breeds. The population history of the Mongolian horse remains poorly understood due to a lack of information on ancient and modern DNA. Here, we report nearly complete mitochondrial genome data obtained from five ancient Mongolian horse samples of the Khereksur and Deer Stone culture (late 2nd to 1st third of the 1st millennium BC) and one ancient horse specimen from the Xiongnu culture (1st century BC to 1st century AD) using target enrichment and high-throughput sequencing methods. Phylogenetic analysis involving ancient, historical, and modern mitogenomes of horses from Mongolia and other regions showed the presence of three mitochondrial haplogroups in the ancient Mongolian horse populations studied here and similar haplotype composition of ancient and modern horse populations of Mongolia. Our results revealed genetic continuity between the Mongolian horse populations of the Khereksur and Deer Stone culture and those of the Xiongnu culture owing to the presence of related mitotypes. Besides, we report close phylogenetic relationships between haplotypes of the Khereksur and Deer Stone horses and the horses of indigenous breeds of the Middle East (Caspian and Iranian), China (Naqu, Yunnan, and Jinjiang), and Italy (Giara) as well as genetic similarity between the Xiongnu Mongolian horses and those of the most ancient breeds of the Middle East (Arabian) and Central Asia (Akhal-Teke). Despite all the migrations of the Mongolian peoples over the past 3000 years, mitochondrial haplogroup composition of Mongolian horse populations remains almost unchanged.}, }
@article {pmid33808521, year = {2021}, author = {Gînguță, A and Rusu, I and Mircea, C and Ioniță, A and Banciu, HL and Kelemen, B}, title = {Mitochondrial DNA Profiles of Individuals from a 12th Century Necropolis in Feldioara (Transylvania).}, journal = {Genes}, volume = {12}, number = {3}, pages = {}, pmid = {33808521}, issn = {2073-4425}, mesh = {Asia/ethnology ; DNA, Ancient/*analysis ; DNA, Mitochondrial/genetics/*history ; Genetics, Population ; History, Medieval ; Humans ; Mitochondria/*genetics ; Phylogeny ; Population Dynamics ; Romania/ethnology ; White People/*genetics ; }, abstract = {The genetic signature of modern Europeans is the cumulated result of millennia of discrete small-scale exchanges between multiple distinct population groups that performed a repeated cycle of movement, settlement, and interactions with each other. In this study we aimed to highlight one such minute genetic cycle in a sea of genetic interactions by reconstructing part of the genetic story of the migration, settlement, interaction, and legacy of what is today the Transylvanian Saxon. The analysis of the mitochondrial DNA control region of 13 medieval individuals from Feldioara necropolis (Transylvania region, Romania) reveals a genetically heterogeneous group where all identified haplotypes are different. Most of the perceived maternal lineages are of Western Eurasian origin, except for the Central Asiatic haplogroup C seen in only one sample. Comparisons with historical and modern populations describe the contribution of the investigated Saxon settlers to the genetic history of this part of Europe.}, }
@article {pmid33807810, year = {2021}, author = {S Ten, V and Stepanova, AA and Ratner, V and Neginskaya, M and Niatsetskaya, Z and Sosunov, S and Starkov, A}, title = {Mitochondrial Dysfunction and Permeability Transition in Neonatal Brain and Lung Injuries.}, journal = {Cells}, volume = {10}, number = {3}, pages = {}, pmid = {33807810}, issn = {2073-4409}, support = {P01 AG014930/AG/NIA NIH HHS/United States ; R01 NS099109/NS/NINDS NIH HHS/United States ; R01 NS100850/NS/NINDS NIH HHS/United States ; }, mesh = {Brain Injuries/*physiopathology ; Humans ; Infant, Newborn ; Lung Injury/*physiopathology ; Mitochondria/*metabolism/pathology ; Permeability ; }, abstract = {This review discusses the potential mechanistic role of abnormally elevated mitochondrial proton leak and mitochondrial bioenergetic dysfunction in the pathogenesis of neonatal brain and lung injuries associated with premature birth. Providing supporting evidence, we hypothesized that mitochondrial dysfunction contributes to postnatal alveolar developmental arrest in bronchopulmonary dysplasia (BPD) and cerebral myelination failure in diffuse white matter injury (WMI). This review also analyzes data on mitochondrial dysfunction triggered by activation of mitochondrial permeability transition pore(s) (mPTP) during the evolution of perinatal hypoxic-ischemic encephalopathy. While the still cryptic molecular identity of mPTP continues to be a subject for extensive basic science research efforts, the translational significance of mitochondrial proton leak received less scientific attention, especially in diseases of the developing organs. This review is focused on the potential mechanistic relevance of mPTP and mitochondrial dysfunction to neonatal diseases driven by developmental failure of organ maturation or by acute ischemia-reperfusion insult during development.}, }
@article {pmid33807111, year = {2021}, author = {Maár, K and Varga, GIB and Kovács, B and Schütz, O and Maróti, Z and Kalmár, T and Nyerki, E and Nagy, I and Latinovics, D and Tihanyi, B and Marcsik, A and Pálfi, G and Bernert, Z and Gallina, Z and Varga, S and Költő, L and Raskó, I and Török, T and Neparáczki, E}, title = {Maternal Lineages from 10-11th Century Commoner Cemeteries of the Carpathian Basin.}, journal = {Genes}, volume = {12}, number = {3}, pages = {}, pmid = {33807111}, issn = {2073-4425}, mesh = {Cemeteries ; DNA, Mitochondrial/*genetics ; Genetics, Population ; Haplotypes ; High-Throughput Nucleotide Sequencing ; History, Medieval ; Humans ; Hungary/ethnology ; Maternal Inheritance ; Mitochondria/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; Transients and Migrants/*history ; }, abstract = {Nomadic groups of conquering Hungarians played a predominant role in Hungarian prehistory, but genetic data are available only from the immigrant elite strata. Most of the 10-11th century remains in the Carpathian Basin belong to common people, whose origin and relation to the immigrant elite have been widely debated. Mitogenome sequences were obtained from 202 individuals with next generation sequencing combined with hybridization capture. Median joining networks were used for phylogenetic analysis. The commoner population was compared to 87 ancient Eurasian populations with sequence-based (Fst) and haplogroup-based population genetic methods. The haplogroup composition of the commoner population markedly differs from that of the elite, and, in contrast to the elite, commoners cluster with European populations. Alongside this, detectable sub-haplogroup sharing indicates admixture between the elite and the commoners. The majority of the 10-11th century commoners most likely represent local populations of the Carpathian Basin, which admixed with the eastern immigrant groups (which included conquering Hungarians).}, }
@article {pmid33805626, year = {2021}, author = {Schirrmacher, V}, title = {Less Can Be More: The Hormesis Theory of Stress Adaptation in the Global Biosphere and Its Implications.}, journal = {Biomedicines}, volume = {9}, number = {3}, pages = {}, pmid = {33805626}, issn = {2227-9059}, abstract = {A dose-response relationship to stressors, according to the hormesis theory, is characterized by low-dose stimulation and high-dose inhibition. It is non-linear with a low-dose optimum. Stress responses by cells lead to adapted vitality and fitness. Physical stress can be exerted through heat, radiation, or physical exercise. Chemical stressors include reactive species from oxygen (ROS), nitrogen (RNS), and carbon (RCS), carcinogens, elements, such as lithium (Li) and silicon (Si), and metals, such as silver (Ag), cadmium (Cd), and lead (Pb). Anthropogenic chemicals are agrochemicals (phytotoxins, herbicides), industrial chemicals, and pharmaceuticals. Biochemical stress can be exerted through toxins, medical drugs (e.g., cytostatics, psychopharmaceuticals, non-steroidal inhibitors of inflammation), and through fasting (dietary restriction). Key-lock interactions between enzymes and substrates, antigens and antibodies, antigen-presenting cells, and cognate T cells are the basics of biology, biochemistry, and immunology. Their rules do not obey linear dose-response relationships. The review provides examples of biologic stressors: oncolytic viruses (e.g., immuno-virotherapy of cancer) and hormones (e.g., melatonin, stress hormones). Molecular mechanisms of cellular stress adaptation involve the protein quality control system (PQS) and homeostasis of proteasome, endoplasmic reticulum, and mitochondria. Important components are transcription factors (e.g., Nrf2), micro-RNAs, heat shock proteins, ionic calcium, and enzymes (e.g., glutathion redox enzymes, DNA methyltransferases, and DNA repair enzymes). Cellular growth control, intercellular communication, and resistance to stress from microbial infections involve growth factors, cytokines, chemokines, interferons, and their respective receptors. The effects of hormesis during evolution are multifarious: cell protection and survival, evolutionary flexibility, and epigenetic memory. According to the hormesis theory, this is true for the entire biosphere, e.g., archaia, bacteria, fungi, plants, and the animal kingdoms.}, }
@article {pmid33805166, year = {2021}, author = {Lyu, D and Zajonc, J and Pagé, A and Tanney, CAS and Shah, A and Monjezi, N and Msimbira, LA and Antar, M and Nazari, M and Backer, R and Smith, DL}, title = {Plant Holobiont Theory: The Phytomicrobiome Plays a Central Role in Evolution and Success.}, journal = {Microorganisms}, volume = {9}, number = {4}, pages = {}, pmid = {33805166}, issn = {2076-2607}, support = {G250030 AAFC BioFuelNet//Agriculture and Agri-Food Canada/ ; RGPIN 2020-07047.//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Under natural conditions, plants are always associated with a well-orchestrated community of microbes-the phytomicrobiome. The nature and degree of microbial effect on the plant host can be positive, neutral, or negative, and depends largely on the environment. The phytomicrobiome is integral for plant growth and function; microbes play a key role in plant nutrient acquisition, biotic and abiotic stress management, physiology regulation through microbe-to-plant signals, and growth regulation via the production of phytohormones. Relationships between the plant and phytomicrobiome members vary in intimacy, ranging from casual associations between roots and the rhizosphere microbial community, to endophytes that live between plant cells, to the endosymbiosis of microbes by the plant cell resulting in mitochondria and chloroplasts. If we consider these key organelles to also be members of the phytomicrobiome, how do we distinguish between the two? If we accept the mitochondria and chloroplasts as both members of the phytomicrobiome and the plant (entrained microbes), the influence of microbes on the evolution of plants becomes so profound that without microbes, the concept of the "plant" is not viable. This paper argues that the holobiont concept should take greater precedence in the plant sciences when referring to a host and its associated microbial community. The inclusivity of this concept accounts for the ambiguous nature of the entrained microbes and the wide range of functions played by the phytomicrobiome in plant holobiont homeostasis.}, }
@article {pmid33803683, year = {2021}, author = {Proulex, GCR and Meade, MJ and Manoylov, KM and Cahoon, AB}, title = {Mitochondrial mRNA Processing in the Chlorophyte Alga Pediastrum duplex and Streptophyte Alga Chara vulgaris Reveals an Evolutionary Branch in Mitochondrial mRNA Processing.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {3}, pages = {}, pmid = {33803683}, issn = {2223-7747}, abstract = {Mitochondria carry the remnant of an ancestral bacterial chromosome and express those genes with a system separate and distinct from the nucleus. Mitochondrial genes are transcribed as poly-cistronic primary transcripts which are post-transcriptionally processed to create individual translationally competent mRNAs. Algae post-transcriptional processing has only been explored in Chlamydomonas reinhardtii (Class: Chlorophyceae) and the mature mRNAs are different than higher plants, having no 5' UnTranslated Regions (UTRs), much shorter and more variable 3' UTRs and polycytidylated mature mRNAs. In this study, we analyzed transcript termini using circular RT-PCR and PacBio Iso-Seq to survey the 3' and 5' UTRs and termini for two green algae, Pediastrum duplex (Class: Chlorophyceae) and Chara vulgaris (Class: Charophyceae). This enabled the comparison of processing in the chlorophyte and charophyte clades of green algae to determine if the differences in mitochondrial mRNA processing pre-date the invasion of land by embryophytes. We report that the 5' mRNA termini and non-template 3' termini additions in P. duplex resemble those of C. reinhardtii, suggesting a conservation of mRNA processing among the chlorophyceae. We also report that C. vulgaris mRNA UTRs are much longer than chlorophytic examples, lack polycytidylation, and are polyadenylated similar to embryophytes. This demonstrates that some mitochondrial mRNA processing events diverged with the split between chlorophytic and streptophytic algae.}, }
@article {pmid33803147, year = {2021}, author = {Arcila-Galvis, JE and Arango, RE and Torres-Bonilla, JM and Arias, T}, title = {The Mitochondrial Genome of a Plant Fungal Pathogen Pseudocercospora fijiensis (Mycosphaerellaceae), Comparative Analysis and Diversification Times of the Sigatoka Disease Complex Using Fossil Calibrated Phylogenies.}, journal = {Life (Basel, Switzerland)}, volume = {11}, number = {3}, pages = {}, pmid = {33803147}, issn = {2075-1729}, support = {221356934854//Instituto para el desarrollo de la Ciencia y la Tecnolog&#xed;a "Francisco Jos&#xe9; de Caldas/ ; 755-2017//Jovenes Investigadores e Innovadores por la Paz convocatoria/ ; }, abstract = {Mycosphaerellaceae is a highly diverse fungal family containing a variety of pathogens affecting many economically important crops. Mitochondria play a crucial role in fungal metabolism and in the study of fungal evolution. This study aims to: (i) describe the mitochondrial genome of Pseudocercospora fijiensis, and (ii) compare it with closely related species (Sphaerulina musiva, S. populicola, P. musae and P. eumusae) available online, paying particular attention to the Sigatoka disease's complex causal agents. The mitochondrial genome of P. fijiensis is a circular molecule of 74,089 bp containing typical genes coding for the 14 proteins related to oxidative phosphorylation, 2 rRNA genes and a set of 38 tRNAs. P. fijiensis mitogenome has two truncated cox1 copies, and bicistronic transcription of nad2-nad3 and atp6-atp8 confirmed experimentally. Comparative analysis revealed high variability in size and gene order among selected Mycosphaerellaceae mitogenomes likely to be due to rearrangements caused by mobile intron invasion. Using fossil calibrated Bayesian phylogenies, we found later diversification times for Mycosphaerellaceae (66.6 MYA) and the Sigatoka disease complex causal agents, compared to previous strict molecular clock studies. An early divergent Pseudocercospora fijiensis split from the sister species P. musae + P. eumusae 13.31 MYA while their sister group, the sister species P. eumusae and P. musae, split from their shared common ancestor in the late Miocene 8.22 MYA. This newly dated phylogeny suggests that species belonging to the Sigatoka disease complex originated after wild relatives of domesticated bananas (section Eumusae; 27.9 MYA). During this time frame, mitochondrial genomes expanded significantly, possibly due to invasions of introns into different electron transport chain genes.}, }
@article {pmid33802618, year = {2021}, author = {Zhang, T and Li, C and Zhang, X and Wang, C and Roger, AJ and Gao, F}, title = {Characterization and Comparative Analyses of Mitochondrial Genomes in Single-Celled Eukaryotes to Shed Light on the Diversity and Evolution of Linear Molecular Architecture.}, journal = {International journal of molecular sciences}, volume = {22}, number = {5}, pages = {}, pmid = {33802618}, issn = {1422-0067}, support = {31922013//National Natural Science Foundation of China/ ; 32030015//National Natural Science Foundation of China/ ; 31772428//National Natural Science Foundation of China/ ; 201841013//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Amino Acid Sequence ; Cells, Cultured ; Eukaryota/*genetics ; Eukaryotic Cells/physiology ; Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Mitogens/genetics ; Phylogeny ; Plankton/genetics ; Replication Origin/genetics ; }, abstract = {Determination and comparisons of complete mitochondrial genomes (mitogenomes) are important to understand the origin and evolution of mitochondria. Mitogenomes of unicellular protists are particularly informative in this regard because they are gene-rich and display high structural diversity. Ciliates are a highly diverse assemblage of protists and their mitogenomes (linear structure with high A+T content in general) were amongst the first from protists to be characterized and have provided important insights into mitogenome evolution. Here, we report novel mitogenome sequences from three representatives (Strombidium sp., Strombidium cf. sulcatum, and Halteria grandinella) in two dominant ciliate lineages. Comparative and phylogenetic analyses of newly sequenced and previously published ciliate mitogenomes were performed and revealed a number of important insights. We found that the mitogenomes of these three species are linear molecules capped with telomeric repeats that differ greatly among known species. The genomes studied here are highly syntenic, but larger in size and more gene-rich than those of other groups. They also all share an AT-rich tandem repeat region which may serve as the replication origin and modulate initiation of bidirectional transcription. More generally we identified a split version of ccmf, a cytochrome c maturation-related gene that might be a derived character uniting taxa in the subclasses Hypotrichia and Euplotia. Finally, our mitogenome comparisons and phylogenetic analyses support to reclassify Halteria grandinella from the subclass Oligotrichia to the subclass Hypotrichia. These results add to the growing literature on the unique features of ciliate mitogenomes, shedding light on the diversity and evolution of their linear molecular architecture.}, }
@article {pmid33798681, year = {2021}, author = {Ennis, CC and Haeffner, NN and Keyser, CD and Leonard, ST and Macdonald-Shedd, AC and Savoie, AM and Cronin, TJ and Veldsman, WP and Barden, P and Chak, STC and Baeza, JA}, title = {Comparative mitochondrial genomics of sponge-dwelling snapping shrimps in the genus Synalpheus: Exploring differences between eusocial and non-eusocial species and insights into phylogenetic relationships in caridean shrimps.}, journal = {Gene}, volume = {786}, number = {}, pages = {145624}, doi = {10.1016/j.gene.2021.145624}, pmid = {33798681}, issn = {1879-0038}, mesh = {Animals ; Codon Usage ; Decapoda/*classification/genetics ; Genome Size ; Genome, Mitochondrial ; Genomics/*methods ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Selection, Genetic ; }, abstract = {The genus Synalpheus is a cosmopolitan clade of marine shrimps found in most tropical regions. Species in this genus exhibit a range of social organizations, including pair-forming, communal breeding, and eusociality, the latter only known to have evolved within this genus in the marine realm. This study examines the complete mitochondrial genomes of seven species of Synalpheus and explores differences between eusocial and non-eusocial species considering that eusociality has been shown before to affect the strength of purifying selection in mitochondrial protein coding genes. The AT-rich mitochondrial genomes of Synalpheus range from 15,421 bp to 15,782 bp in length and comprise, invariably, 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. A 648 bp to 994 bp long intergenic space is assumed to be the D-loop. Mitochondrial gene synteny is identical among the studied shrimps. No major differences occur between eusocial and non-eusocial species in nucleotide composition and codon usage profiles of PCGs and in the secondary structure of tRNA genes. Maximum likelihood phylogenetic analysis of the complete concatenated PCG complement of 90 species supports the monophyly of the genus Synalpheus and its family Alpheidae. Moreover, the monophyletic status of the caridean families Alvinocaridae, Atyidae, Thoridae, Lysmatidae, Palaemonidae, and Pandalidae within caridean shrimps are fully or highly supported by the analysis. We therefore conclude that mitochondrial genomes contain sufficient phylogenetic information to resolve relationships at high taxonomic levels within the Caridea. Our analysis of mitochondrial genomes in the genus Synalpheus contributes to the understanding of the coevolution between genomic architecture and sociality in caridean shrimps and other marine organisms.}, }
@article {pmid33793863, year = {2021}, author = {Considine, MJ and Foyer, CH}, title = {Oxygen and reactive oxygen species-dependent regulation of plant growth and development.}, journal = {Plant physiology}, volume = {186}, number = {1}, pages = {79-92}, pmid = {33793863}, issn = {1532-2548}, mesh = {Oxygen/*metabolism ; Plant Development/*physiology ; Reactive Oxygen Species/*metabolism ; }, abstract = {Oxygen and reactive oxygen species (ROS) have been co-opted during evolution into the regulation of plant growth, development, and differentiation. ROS and oxidative signals arising from metabolism or phytohormone-mediated processes control almost every aspect of plant development from seed and bud dormancy, liberation of meristematic cells from the quiescent state, root and shoot growth, and architecture, to flowering and seed production. Moreover, the phytochrome and phytohormone-dependent transmissions of ROS waves are central to the systemic whole plant signaling pathways that integrate root and shoot growth. The sensing of oxygen availability through the PROTEOLYSIS 6 (PRT6) N-degron pathway functions alongside ROS production and signaling but how these pathways interact in developing organs remains poorly understood. Considerable progress has been made in our understanding of the nature of hydrogen peroxide sensors and the role of thiol-dependent signaling networks in the transmission of ROS signals. Reduction/oxidation (redox) changes in the glutathione (GSH) pool, glutaredoxins (GRXs), and thioredoxins (TRXs) are important in the control of growth mediated by phytohormone pathways. Although, it is clear that the redox states of proteins involved in plant growth and development are controlled by the NAD(P)H thioredoxin reductase (NTR)/TRX and reduced GSH/GRX systems of the cytosol, chloroplasts, mitochondria, and nucleus, we have only scratched the surface of this multilayered control and how redox-regulated processes interact with other cell signaling systems.}, }
@article {pmid33791336, year = {2021}, author = {Mortz, M and Levivier, A and Lartillot, N and Dufresne, F and Blier, PU}, title = {Long-Lived Species of Bivalves Exhibit Low MT-DNA Substitution Rates.}, journal = {Frontiers in molecular biosciences}, volume = {8}, number = {}, pages = {626042}, pmid = {33791336}, issn = {2296-889X}, abstract = {Bivalves represent valuable taxonomic group for aging studies given their wide variation in longevity (from 1-2 to >500 years). It is well known that aging is associated to the maintenance of Reactive Oxygen Species homeostasis and that mitochondria phenotype and genotype dysfunctions accumulation is a hallmark of these processes. Previous studies have shown that mitochondrial DNA mutation rates are linked to lifespan in vertebrate species, but no study has explored this in invertebrates. To this end, we performed a Bayesian Phylogenetic Covariance model of evolution analysis using 12 mitochondrial protein-coding genes of 76 bivalve species. Three life history traits (maximum longevity, generation time and mean temperature tolerance) were tested against 1) synonymous substitution rates (dS), 2) conservative amino acid replacement rates (Kc) and 3) ratios of radical over conservative amino acid replacement rates (Kr/Kc). Our results confirm the already known correlation between longevity and generation time and show, for the first time in an invertebrate class, a significant negative correlation between dS and longevity. This correlation was not as strong when generation time and mean temperature tolerance variations were also considered in our model (marginal correlation), suggesting a confounding effect of these traits on the relationship between longevity and mtDNA substitution rate. By confirming the negative correlation between dS and longevity previously documented in birds and mammals, our results provide support for a general pattern in substitution rates.}, }
@article {pmid33770399, year = {2021}, author = {Bazer, FW and Seo, H and Johnson, GA and Wu, G}, title = {One-Carbon Metabolism and Development of the Conceptus During Pregnancy: Lessons from Studies with Sheep and Pigs.}, journal = {Advances in experimental medicine and biology}, volume = {1285}, number = {}, pages = {1-15}, pmid = {33770399}, issn = {0065-2598}, mesh = {Animals ; Carbon ; *Embryo, Mammalian ; Endometrium ; Female ; Fetal Development ; *Interferon Type I ; Placenta ; Pregnancy ; Sheep ; Swine ; Uterus ; }, abstract = {The pregnancy recognition signal from the conceptus (embryo/fetus and associated membranes) to the mother is interferon tau (IFNT) in ruminants and estradiol, possibly in concert with interferons gamma and delta in pigs. Those pregnancy recognition signals silence expression of interferon stimulated genes (ISG) in uterine luminal (LE) and superficial glandular (sGE) epithelia while inducing expression of genes for transport of nutrients, including glucose and amino acids, into the uterine lumen to support growth and development of the conceptus. In sheep and pigs, glucose not utilized immediately by the conceptus is converted to fructose. Glucose, fructose, serine and glycine in uterine histotroph can contribute to one carbon (1C) metabolism that provides one-carbon groups for the synthesis of purines and thymidylate, as well as S-adenosylmethionine for epigenetic methylation reactions. Serine and glycine are transported into the mitochondria of cells and metabolized to formate that is transported into the cytoplasm for the synthesis of purines, thymidine and S-adenosylmethionine. The unique aspects of one-carbon metabolism are discussed in the context of the hypoxic uterine environment, aerobic glycolysis, and similarities in metabolism between cancer cells and cells of the rapidly developing fetal-placental tissues during pregnancy. Further, the evolution of anatomical and functional aspects of the placentae of sheep and pigs versus primates is discussed in the context of mechanisms to efficiently obtain, store and utilize nutrients required for rapid fetal growth in the last one-half of gestation.}, }
@article {pmid33751391, year = {2021}, author = {Yi, CH and Yoon, M and Kim, JM and Kim, IH and Cho, IY and An, HS}, title = {Genetic analysis and population genetic structure of hard-shelled mussel, Mytilus coruscus Gould 1861 (Mytiloida: Mytilidae) from the coasts of South Korea based on mitochondrial cytochrome oxidase (COI) gene sequences.}, journal = {Genes &amp; genomics}, volume = {43}, number = {6}, pages = {577-585}, pmid = {33751391}, issn = {2092-9293}, mesh = {Animals ; Bivalvia/enzymology/*genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation/genetics ; Genetics, Population ; Haplotypes/genetics ; Humans ; Microsatellite Repeats/genetics ; Mitochondria/*enzymology ; Mytilus/enzymology/*genetics ; Phylogeny ; Republic of Korea ; }, abstract = {BACKGROUND: Mytilus coruscus Gould, 1861 is a mussel species in the family Mytilidae, native to the Northwest Pacific Ocean, ranging from the East China Sea, the Yellow Sea, and as far as the Peter the Great Gulf in the East Sea. In Korea, this species has been heavily exploited for nutrient-rich food resources and experienced severe reduction in their population.<br><br>OBJECTIVE: The aim of this study was to investigate the genetic diversity and population structure and to provide baseline data to facilitate the conservation and sustainable use of the vulnerable species M. coruscus in South Korea.<br><br>METHODS: Mitochondrial DNA (mtDNA) cytochrome c oxidase I (COI) sequences of 91 adult individuals from four islands and one coastal localities in South Korea were sequenced. We then compared genetic diversity and haplotype data with previously published Chinese wild populations.<br><br>RESULTS: Mytilus coruscus populations on Korean coasts were found to exhibit high genetic diversity despite concerns regarding recent population reduction. A total of 42 haplotypes were defined by 56 polymorphic sites. High-level genetic diversity was observed on four Island sites (Hd&#x2009;=&#x2009;0.906-0.955, &#x3c0;&#x2009;=&#x2009;0.0068-0.0090). The other seashore site represented relatively lower genetic diversity (Hd&#x2009;=&#x2009;0.529, &#x3c0;&#x2009;=&#x2009;0.0011) and was genetically differentiated from the others. In a previous study, wild populations on the East China Sea exhibited similarly high genetic diversity as that observed in our study. Additionally, Chinese M. coruscus populations exhibit a distinct regional haplotype distribution pattern while sharing six haplotypes with Korean populations.<br><br>CONCLUSIONS: The results of this study provide insights that further the current understanding regarding the evolution of M. coruscus species and provides comprehensive genetic data to facilitate the development of an effective conservation strategy.}, }
@article {pmid33750312, year = {2021}, author = {Cheng, Y and He, X and Priyadarshani, SVGN and Wang, Y and Ye, L and Shi, C and Ye, K and Zhou, Q and Luo, Z and Deng, F and Cao, L and Zheng, P and Aslam, M and Qin, Y}, title = {Assembly and comparative analysis of the complete mitochondrial genome of Suaeda glauca.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {167}, pmid = {33750312}, issn = {1471-2164}, support = {31671267//National Natural Science Foundation of China/ ; 31970333//National Natural Science Foundation of China/ ; }, mesh = {*Chenopodiaceae/genetics ; Genome Size ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Phylogeny ; }, abstract = {BACKGROUND: Suaeda glauca (S. glauca) is a halophyte widely distributed in saline and sandy beaches, with strong saline-alkali tolerance. It is also admired as a landscape plant with high development prospects and scientific research value. The S. glauca chloroplast (cp) genome has recently been reported; however, the mitochondria (mt) genome is still unexplored.<br><br>RESULTS: The mt genome of S. glauca were assembled based on the reads from Pacbio and Illumina sequencing platforms. The circular mt genome of S. glauca has a length of 474,330&#x2009;bp. The base composition of the S. glauca mt genome showed A (28.00%), T (27.93%), C (21.62%), and G (22.45%). S. glauca mt genome contains 61 genes, including 27 protein-coding genes, 29 tRNA genes, and 5 rRNA genes. The sequence repeats, RNA editing, and gene migration from cp to mt were observed in S. glauca mt genome. Phylogenetic analysis based on the mt genomes of S. glauca and other 28 taxa reflects an exact evolutionary and taxonomic status of S. glauca. Furthermore, the investigation on mt genome characteristics, including genome size, GC contents, genome organization, and gene repeats of S. gulaca genome, was investigated compared to other land plants, indicating the variation of the mt genome in plants. However, the subsequently Ka/Ks analysis revealed that most of the protein-coding genes in mt genome had undergone negative selections, reflecting the importance of those genes in the mt genomes.<br><br>CONCLUSIONS: In this study, we reported the mt genome assembly and annotation of a halophytic model plant S. glauca. The subsequent analysis provided us a comprehensive understanding of the S. glauca mt genome, which might facilitate the research on the salt-tolerant plant species.}, }
@article {pmid33746976, year = {2021}, author = {Shariq, M and Quadir, N and Sharma, N and Singh, J and Sheikh, JA and Khubaib, M and Hasnain, SE and Ehtesham, NZ}, title = {Mycobacterium tuberculosis RipA Dampens TLR4-Mediated Host Protective Response Using a Multi-Pronged Approach Involving Autophagy, Apoptosis, Metabolic Repurposing, and Immune Modulation.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {636644}, pmid = {33746976}, issn = {1664-3224}, mesh = {Animals ; Apoptosis ; Autophagy ; Bacterial Proteins/genetics/*metabolism ; Cell Differentiation ; HEK293 Cells ; Host-Pathogen Interactions ; Humans ; Immunity, Innate ; Immunomodulation ; Macrophages/*immunology ; Mice ; Mitochondria/*metabolism ; Mycobacterium tuberculosis/*physiology ; NF-kappa B/metabolism ; RAW 264.7 Cells ; Signal Transduction ; Toll-Like Receptor 4/*metabolism ; }, abstract = {Reductive evolution has endowed Mycobacterium tuberculosis (M. tb) with moonlighting in protein functions. We demonstrate that RipA (Rv1477), a peptidoglycan hydrolase, activates the NFκB signaling pathway and elicits the production of pro-inflammatory cytokines, TNF-α, IL-6, and IL-12, through the activation of an innate immune-receptor, toll-like receptor (TLR)4. RipA also induces an enhanced expression of macrophage activation markers MHC-II, CD80, and CD86, suggestive of M1 polarization. RipA harbors LC3 (Microtubule-associated protein 1A/1B-light chain 3) motifs known to be involved in autophagy regulation and indeed alters the levels of autophagy markers LC3BII and P62/SQSTM1 (Sequestosome-1), along with an increase in the ratio of P62/Beclin1, a hallmark of autophagy inhibition. The use of pharmacological agents, rapamycin and bafilomycin A1, reveals that RipA activates PI3K-AKT-mTORC1 signaling cascade that ultimately culminates in the inhibition of autophagy initiating kinase ULK1 (Unc-51 like autophagy activating kinase). This inhibition of autophagy translates into efficient intracellular survival, within macrophages, of recombinant Mycobacterium smegmatis expressing M. tb RipA. RipA, which also localizes into mitochondria, inhibits the production of oxidative phosphorylation enzymes to promote a Warburg-like phenotype in macrophages that favors bacterial replication. Furthermore, RipA also inhibited caspase-dependent programed cell death in macrophages, thus hindering an efficient innate antibacterial response. Collectively, our results highlight the role of an endopeptidase to create a permissive replication niche in host cells by inducing the repression of autophagy and apoptosis, along with metabolic reprogramming, and pointing to the role of RipA in disease pathogenesis.}, }
@article {pmid33744400, year = {2021}, author = {Lazcano, A and Peretó, J}, title = {Prokaryotic symbiotic consortia and the origin of nucleated cells: A critical review of Lynn Margulis hypothesis.}, journal = {Bio Systems}, volume = {204}, number = {}, pages = {104408}, doi = {10.1016/j.biosystems.2021.104408}, pmid = {33744400}, issn = {1872-8324}, mesh = {Basal Bodies ; *Biological Evolution ; Cell Movement ; Centromere ; *Eukaryotic Cells ; Flagella ; Genome, Mitochondrial ; Genome, Plastid ; Microbial Consortia ; Organelles/genetics ; *Prokaryotic Cells ; *Symbiosis ; }, abstract = {The publication in the late 1960s of Lynn Margulis endosymbiotic proposal is a scientific milestone that brought to the fore of evolutionary discussions the issue of the origin of nucleated cells. Although it is true that the times were ripe, the timely publication of Lynn Margulis' original paper was the product of an intellectually bold 29-years old scientist, who based on the critical analysis of the available scientific information produced an all-encompassing, sophisticated narrative scheme on the origin of eukaryotic cells as a result of the evolution of prokaryotic consortia and, in bold intellectual stroke, put it all in the context of planetary evolution. A critical historical reassessment of her original proposal demonstrates that her hypothesis was not a simple archival outline of past schemes, but a renewed historical narrative of prokaryotic evolution and the role of endosymbiosis in the origin of eukaryotes. Although it is now accepted that the closest bacterial relatives of mitochondria and plastids are α-proteobacteria and cyanobacteria, respectively, comparative genomics demonstrates the mosaic character of the organelle genomes. The available evidence has completely refuted Margulis' proposal of an exogenous origin for eukaryotic flagella, the (9 + 2) basal bodies, and centromeres, but we discuss in detail the reasons that led her to devote considerable efforts to argue for a symbiotic origin of the eukaryotic motility. An analysis of the arguments successfully employed by Margulis in her persuasive advocacy of endosymbiosis, combined with the discussions of her flaws and the scientific atmosphere during the period in which she formulated her proposals, are critical for a proper appraisal of the historical conditions that shaped her theory and its acceptance.}, }
@article {pmid33743097, year = {2021}, author = {Ressaissi, Y and Amills, M and Noce, A and Ben Hamouda, M}, title = {Characterizing the Mitochondrial Diversity of Arbi Goats from Tunisia.}, journal = {Biochemical genetics}, volume = {59}, number = {5}, pages = {1225-1232}, pmid = {33743097}, issn = {1573-4927}, support = {AGL2016-76108-R//Ministerio de Econom&#xed;a y Competitividad/ ; }, mesh = {Animals ; DNA, Mitochondrial/analysis/*genetics ; *Genetic Variation ; Goats ; *Haplotypes ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Tunisia ; }, abstract = {Arbi is one of the main local goat breeds in Tunisia, representing an important economic resource in arid and hot areas where cattle and sheep cannot thrive successfully. In the current work, we have characterized the mitochondrial diversity of 26 Arbi goats by partially sequencing the mitochondrial D-loop region. These sequences plus 10 retrieved from GenBank were analyzed with the DnaSP v.5.10.1, evidencing the existence of 12 different haplotypes. Nucleotide and haplotype diversities were 0.02 and 0.96. Moreover, median-joining network analysis showed that all D-loop sequences from Arbi goats correspond to haplogroup A and that in general they do not cluster with sequences from other goat breeds. The high diversity that has been observed in North African goats is compatible with the maritime diffusion of the Neolithic package 10,000-7000 YBP. Moreover, there are evidences that local Tunisian breeds have been extensively crossed with highly productive transboundary breeds in order to improve meat and milk yields. These uncontrolled crossing practices may lead to the loss of alleles that play key roles in the adaptation of Tunisian local breeds to a harsh environment.}, }
@article {pmid33743014, year = {2021}, author = {Zheng, K and Li, T}, title = {Prediction of ATPase cation transporting 13A2 molecule in Petromyzon marinus and pan-cancer analysis into human tumors from an evolutionary perspective.}, journal = {Immunogenetics}, volume = {73}, number = {4}, pages = {277-289}, pmid = {33743014}, issn = {1432-1211}, mesh = {Amino Acid Sequence ; Animals ; Computational Biology ; *Evolution, Molecular ; Fish Proteins/genetics/*metabolism ; Humans ; Neoplasms/genetics/*metabolism/pathology ; Petromyzon/genetics/*metabolism ; *Phylogeny ; Prognosis ; Proton-Translocating ATPases/genetics/*metabolism ; Sequence Homology, Amino Acid ; Survival Rate ; }, abstract = {The ATPase cation transporting 13A2 protein (ATP13A2), which maintains the homeostasis of mitochondria and lysosomes, plays a significant role in human neurodegenerative diseases and cancer. Through constructing a lamprey proteome database, employing multiple sequence alignment and phylogenetic analysis, 5 ATP13A2 proteins from Petromyzon marinus (Pm-ATP13A2) were identified based on the evolutionary perspective. The motif and domain analysis showed that the ATP13A2 protein was conserved. The multiple phosphorylation sites and transmembrane structures highlighted the characteristics of ATP13A2 as the P-ATPase-V cation transporting protein. Based on the information provided by the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, this study was conducted as a preliminary investigation of the carcinogenic effects of the ATP13A2 gene in a variety of tumors. The ATP13A2 was strongly expressed in most tumors, except in two types of nervous system tumors glioblastoma multiforme (GBM) and brain lower grade glioma (LGG). Moreover, the expression of ATP13A2 was strongly correlated with the prognosis of tumor patients. The high expression of ATP13A2 was obviously related to the poor prognosis of LGG. The poor prognosis of LGG patients may affect the ATP13A2 expression through the immune cells and radiotherapy. Also, cancer-related fibroblast infiltration was observed. All in all, this work offers more insights into the molecular evolution of the ATP13A2 protein and facilitates the understanding of the carcinogenic effects of the ATP13A2 in different tumors. Our discussion also promotes the study into the successful evolution of the vertebrate brain and the mechanism of clinical brain-related diseases.}, }
@article {pmid33741537, year = {2021}, author = {Bober, S and Glaubrecht, M and Hausdorf, B and Neiber, MT}, title = {One, two or three? Integrative species delimitation of short-range endemic Hemicycla species (Gastropoda: Helicidae) from the Canary Islands based on morphology, barcoding, AFLP and ddRADseq data.}, journal = {Molecular phylogenetics and evolution}, volume = {161}, number = {}, pages = {107153}, doi = {10.1016/j.ympev.2021.107153}, pmid = {33741537}, issn = {1095-9513}, mesh = {*Amplified Fragment Length Polymorphism Analysis ; Animals ; *DNA Barcoding, Taxonomic ; Mitochondria/genetics ; *Phylogeny ; Polymorphism, Single Nucleotide/*genetics ; Snails/*anatomy &amp; histology/classification/*genetics ; Spain ; }, abstract = {Hemicycla mascaensis and H. diegoi are short-range endemics that occur allopatrically in small areas in the Teno Mountains in the western part of Tenerife (Canary Islands). Both taxa have been recognised as distinct species based on differences in shell morphology and genital anatomy. Preliminary molecular analyses using mitochondrial markers suggested a potential paraphyly of H. diegoi with regard to H. mascaensis. We here use multilocus AFLP data and ddRADseq data as well as distribution data, data on shell morphology and genital anatomy to assess the status of these taxa using phylogenetic analyses, species tree reconstruction and molecular species delimitation based on the multispecies coalescent as implemented in BFD* and BPP in an integrative approach. Our analyses show that, based on the analysis of multilocus data, the two taxa are reciprocally monophyletic. Species delimitation methods, however, tend to recognise all investigated populations as distinct species, albeit neither lending unambiguous support to any of the species hypotheses. The comparison of the anatomy of distal genital organs further suggests differentiation within H. mascaensis. This highlights the need for a balanced weighting of arguments from different lines of evidence to determine species status and calls for cautious interpretations of the results of molecular species delimitation analyses, especially in organisms with low active dispersal capacities and expected distinct population structuring such as land snails. Taking all available evidence into account, we favour to recognise H. mascaensis and H. diegoi as distinct species, acknowledging, though, that the recognition of both taxa as subspecies (with possibly a third yet undescribed) would also be an option as morphological differentiation is within the limits of other land snail species that are traditionally subdivided into subspecies.}, }
@article {pmid33740894, year = {2021}, author = {Pyrih, J and Žárský, V and Fellows, JD and Grosche, C and Wloga, D and Striepen, B and Maier, UG and Tachezy, J}, title = {The iron-sulfur scaffold protein HCF101 unveils the complexity of organellar evolution in SAR, Haptista and Cryptista.}, journal = {BMC ecology and evolution}, volume = {21}, number = {1}, pages = {46}, pmid = {33740894}, issn = {2730-7182}, mesh = {Animals ; *Cryptosporidiosis ; *Cryptosporidium ; Iron ; *Iron-Sulfur Proteins/genetics ; Phylogeny ; Sulfur ; }, abstract = {BACKGROUND: Nbp35-like proteins (Nbp35, Cfd1, HCF101, Ind1, and AbpC) are P-loop NTPases that serve as components of iron-sulfur cluster (FeS) assembly machineries. In eukaryotes, Ind1 is present in mitochondria, and its function is associated with the assembly of FeS clusters in subunits of respiratory Complex I, Nbp35 and Cfd1 are the components of the cytosolic FeS assembly (CIA) pathway, and HCF101 is involved in FeS assembly of photosystem I in plastids of plants (chHCF101). The AbpC protein operates in Bacteria and Archaea. To date, the cellular distribution of these proteins is considered to be highly conserved with only a few exceptions.<br><br>RESULTS: We searched for the genes of all members of the Nbp35-like protein family and analyzed their targeting sequences. Nbp35 and Cfd1 were predicted to reside in the cytoplasm with some exceptions of Nbp35 localization to the mitochondria; Ind1was found in the mitochondria, and HCF101 was predicted to reside in plastids (chHCF101) of all photosynthetically active eukaryotes. Surprisingly, we found a second HCF101 paralog in all members of Cryptista, Haptista, and SAR that was predicted to predominantly target mitochondria (mHCF101), whereas Ind1 appeared to be absent in these organisms. We also identified a few exceptions, as apicomplexans possess mHCF101 predicted to localize in the cytosol and Nbp35 in the mitochondria. Our predictions were experimentally confirmed in selected representatives of Apicomplexa (Toxoplasma gondii), Stramenopila (Phaeodactylum tricornutum, Thalassiosira pseudonana), and Ciliophora (Tetrahymena thermophila) by tagging proteins with a transgenic reporter. Phylogenetic analysis suggested that chHCF101 and mHCF101 evolved from a common ancestral HCF101 independently of the Nbp35/Cfd1 and Ind1 proteins. Interestingly, phylogenetic analysis supports rather a lateral gene transfer of ancestral HCF101 from bacteria than its acquisition being associated with either &#x3b1;-proteobacterial or cyanobacterial endosymbionts.<br><br>CONCLUSION: Our searches for Nbp35-like proteins across eukaryotic lineages revealed that SAR, Haptista, and Cryptista possess mitochondrial HCF101. Because plastid localization of HCF101 was only known thus far, the discovery of its mitochondrial paralog explains confusion regarding the presence of HCF101 in organisms that possibly lost secondary plastids (e.g., ciliates, Cryptosporidium) or possess reduced nonphotosynthetic plastids (apicomplexans).}, }
@article {pmid33739376, year = {2021}, author = {Tria, FDK and Brueckner, J and Skejo, J and Xavier, JC and Kapust, N and Knopp, M and Wimmer, JLE and Nagies, FSP and Zimorski, V and Gould, SB and Garg, SG and Martin, WF}, title = {Gene Duplications Trace Mitochondria to the Onset of Eukaryote Complexity.}, journal = {Genome biology and evolution}, volume = {13}, number = {5}, pages = {}, pmid = {33739376}, issn = {1759-6653}, mesh = {*Biological Evolution ; Eukaryota/*genetics ; Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Mitochondria/*genetics ; }, abstract = {The last eukaryote common ancestor (LECA) possessed mitochondria and all key traits that make eukaryotic cells more complex than their prokaryotic ancestors, yet the timing of mitochondrial acquisition and the role of mitochondria in the origin of eukaryote complexity remain debated. Here, we report evidence from gene duplications in LECA indicating an early origin of mitochondria. Among 163,545 duplications in 24,571 gene trees spanning 150 sequenced eukaryotic genomes, we identify 713 gene duplication events that occurred in LECA. LECA's bacterial-derived genes include numerous mitochondrial functions and were duplicated significantly more often than archaeal-derived and eukaryote-specific genes. The surplus of bacterial-derived duplications in LECA most likely reflects the serial copying of genes from the mitochondrial endosymbiont to the archaeal host's chromosomes. Clustering, phylogenies and likelihood ratio tests for 22.4 million genes from 5,655 prokaryotic and 150 eukaryotic genomes reveal no evidence for lineage-specific gene acquisitions in eukaryotes, except from the plastid in the plant lineage. That finding, and the functions of bacterial genes duplicated in LECA, suggests that the bacterial genes in eukaryotes are acquisitions from the mitochondrion, followed by vertical gene evolution and differential loss across eukaryotic lineages, flanked by concomitant lateral gene transfer among prokaryotes. Overall, the data indicate that recurrent gene transfer via the copying of genes from a resident mitochondrial endosymbiont to archaeal host chromosomes preceded the onset of eukaryotic cellular complexity, favoring mitochondria-early over mitochondria-late hypotheses for eukaryote origin.}, }
@article {pmid33735859, year = {2021}, author = {Kuwana, C and Fujita, H and Tagami, M and Matsuo, T and Miura, I}, title = {Evolution of Sex Chromosome Heteromorphy in Geographic Populations of the Japanese Tago's Brown Frog Complex.}, journal = {Cytogenetic and genome research}, volume = {161}, number = {1-2}, pages = {23-31}, doi = {10.1159/000512964}, pmid = {33735859}, issn = {1424-859X}, mesh = {Animals ; Chromosome Banding ; DNA, Mitochondrial/genetics ; Female ; Geography ; Japan ; Karyotyping ; Likelihood Functions ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ranidae/*genetics ; *Sex Chromosomes ; Species Specificity ; Y Chromosome ; }, abstract = {The sex chromosomes of most anuran amphibians are characterized by homomorphy in both sexes, and evolution to heteromorphy rarely occurs at the species or geographic population level. Here, we report sex chromosome heteromorphy in geographic populations of the Japanese Tago's brown frog complex (2n = 26), comprising Rana sakuraii and R. tagoi. The sex chromosomes of R. sakuraii from the populations in western Japan were homomorphic in both sexes, whereas chromosome 7 from the populations in eastern Japan were heteromorphic in males. Chromosome 7 of R. tagoi, which is distributed close to R. sakuraii in eastern Japan, was highly similar in morphology to the Y chromosome of R. sakuraii. Based on this and on mitochondrial gene sequence analysis, we hypothesize that in the R. sakuraii populations from eastern Japan the XY heteromorphic sex chromosome system was established by the introduction of chromosome 7 from R. tagoi via interspecies hybridization. In contrast, chromosome 13 of R. tagoi from the 2 large islands in western Japan, Shikoku and Kyushu, showed a heteromorphic pattern of constitutive heterochromatin distribution in males, while this pattern was homomorphic in females. Our study reveals that sex chromosome heteromorphy evolved independently at the geographic lineage level in this species complex.}, }
@article {pmid33735765, year = {2021}, author = {Wu, G and Wei, P and Chen, X and Zhang, Z and Jin, Z and Liu, J and Liu, L}, title = {Less is more: biological effects of NiSe2/rGO nanocomposites with low dose provide new insight for risk assessment.}, journal = {Journal of hazardous materials}, volume = {415}, number = {}, pages = {125605}, doi = {10.1016/j.jhazmat.2021.125605}, pmid = {33735765}, issn = {1873-3336}, mesh = {Animals ; *Graphite ; *Nanocomposites/toxicity ; Oxidative Stress ; Rats ; Risk Assessment ; }, abstract = {Nickel selenide nanomaterials (NiSe2 NMs) with different vacancies demonstrated high catalytic activity as electrocatalyst in oxygen evolution reaction. As the growing needs of the industrial applications in electrocatalyst, the increased occupational exposure and environmental releasing of NMs would be unavoidable. While, much efforts have been made to evaluate the ecological safety of such engineered NMs at unrealistically high concentrations, failed to provide the comprehensively guideline for exposure thresholds. To supplement the current knowledge gap, we testified the cytotoxicity of NiSe2/rGO nanocomposites with different surface defects under more realistic exposure mode. Compared with the short-term exposure and repetitive exposure, rat lung macrophages exhibited the augmented oxidative stress, dysfunction of mitochondria, damage of DNA and disorder of calcium homeostasis under the long-term NiSe2/rGO exposure. Noteworthily, no significant differences could be found between the NiSe2/rGO with different surface defects, indicated that the defect type of NMs were not the accurate predictor for real risk assessment. Collectively, the study provided the real potential toxic effects and exposure thresholds of NMs that might be highly possible industrial produced, and appealed the new insight for risk assessments of engineered NMs under the long-term exposure, which exhibited difference from the traditional evaluation of short-term and repetitive exposure.}, }
@article {pmid33735257, year = {2021}, author = {Liu, Y and Yao, L and Ci, Y and Cao, X and Zhao, M and Li, Y and Zhang, X}, title = {Genetic differentiation of geographic populations of Rattus tanezumi based on the mitochondrial Cytb gene.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0248102}, pmid = {33735257}, issn = {1932-6203}, mesh = {Animals ; Cytochromes b/*genetics ; *Gene Flow ; Genes, Mitochondrial ; *Genetic Drift ; Genetic Variation ; Genetics, Population ; Haplotypes ; Mitochondria/*genetics ; Rats/*genetics ; }, abstract = {Rattus tanezumi is a common domestic rat and host of the bubonic plague pathogen in China and Southeast Asia (SEA). The origin, genetic differentiation and dispersal of R. tanezumi have received increasing attention from researchers. The population genetics of R. tanezumi based on its mitochondrial cytochrome b gene have been studied to explain the origin, relationships and dispersal of populations. In this study, we captured a total of 229 rats; morphological and molecular biological identification cytochrome oxidase subunit I (COI) confirmed 131 R. tanezumi individuals collected from 6 provincial areas, and their Cytb gene sequences were analyzed. The results showed that the population in Mohan (MH), Yunnan, had the highest genetic diversity, while that in Ningde (ND), Fujian, had the lowest. Tajima's D statistic for all populations was negative and nonsignificant, indicating the possible expansion of R. tanezumi populations. Low gene flow occurred between the Zhangmu (ZM) R. tanezumi population and other populations, and the genetic differentiation among them was high. Furthermore, our analyses revealed the ZM lineage was the oldest lineage among the groups and diverged ~1.06 Mya, followed by the Luoyang (LY) lineages (~0.51 Mya) and Yunnan lineage (~0.33 Mya). In southeastern Yunnan, the Jinshuihe (JSH) and MH populations were more closely related to the populations in southeastern China (Fuzhou (FZ), ND, Quanzhou (QZ), Nanchang (NC)) and inland areas (Chongqing (CQ), LY) than to those in other areas of Yunnan (Jiegao (JG) and Qingshuihe (QSH)), indicating that R. tanezumi may have spread from southeastern Yunnan to the interior of China. In summary, R. tanezumi may have originated in ZM and adjacent areas, spread to Yunnan, and then spread from the southeast of Yunnan inland or directly eastward from ZM to inland China.}, }
@article {pmid33732288, year = {2021}, author = {Cruz, JO and Silva, AO and Ribeiro, JM and Luizon, MR and Ceron, CS}, title = {Epigenetic Regulation of the N-Terminal Truncated Isoform of Matrix Metalloproteinase-2 (NTT-MMP-2) and Its Presence in Renal and Cardiac Diseases.}, journal = {Frontiers in genetics}, volume = {12}, number = {}, pages = {637148}, pmid = {33732288}, issn = {1664-8021}, abstract = {Several clinical and experimental studies have documented a compelling and critical role for the full-length matrix metalloproteinase-2 (FL-MMP-2) in ischemic renal injury, progressive renal fibrosis, and diabetic nephropathy. A novel N-terminal truncated isoform of MMP-2 (NTT-MMP-2) was recently discovered, which is induced by hypoxia and oxidative stress by the activation of a latent promoter located in the first intron of the MMP2 gene. This NTT-MMP-2 isoform is enzymatically active but remains intracellular in or near the mitochondria. In this perspective article, we first present the findings about the discovery of the NTT-MMP-2 isoform, and its functional and structural differences as compared with the FL-MMP-2 isoform. Based on publicly available epigenomics data from the Encyclopedia of DNA Elements (ENCODE) project, we provide insights into the epigenetic regulation of the latent promoter located in the first intron of the MMP2 gene, which support the activation of the NTT-MMP-2 isoform. We then focus on its functional assessment by covering the alterations found in the kidney of transgenic mice expressing the NTT-MMP-2 isoform. Next, we highlight recent findings regarding the presence of the NTT-MMP-2 isoform in renal dysfunction, in kidney and cardiac diseases, including damage observed in aging, acute ischemia-reperfusion injury (IRI), chronic kidney disease, diabetic nephropathy, and human renal transplants with delayed graft function. Finally, we briefly discuss how our insights may guide further experimental and clinical studies that are needed to elucidate the underlying mechanisms and the role of the NTT-MMP-2 isoform in renal dysfunction, which may help to establish it as a potential therapeutic target in kidney diseases.}, }
@article {pmid33730185, year = {2021}, author = {Arab, DA and Lo, N}, title = {Evolutionary Rates are Correlated Between Buchnera Endosymbionts and the Mitochondrial Genomes of Their Aphid Hosts.}, journal = {Journal of molecular evolution}, volume = {89}, number = {4-5}, pages = {238-248}, pmid = {33730185}, issn = {1432-1432}, mesh = {Animals ; *Aphids/genetics ; Bacteroidetes ; *Buchnera/genetics ; Evolution, Molecular ; *Genome, Mitochondrial/genetics ; Phylogeny ; }, abstract = {The evolution of bacterial endosymbiont genomes is strongly influenced by host-driven selection. Factors affecting host genome evolution will potentially affect endosymbiont genomes in similar ways. One potential outcome is correlations in molecular rates between the genomes of the symbiotic partners. Recently, we presented the first evidence of such correlations between the mitochondrial genomes of cockroaches and the genomes of their endosymbiont (Blattabacterium cuenoti). Here we investigate whether similar patterns are found in additional host-symbiont partners. We use partial genome data from multiple strains of the bacterial endosymbionts Buchnera aphidicola and Sulcia muelleri, and the mitochondrial genomes of their sap-feeding insect hosts. Both endosymbionts show phylogenetic congruence with the mitochondria of their hosts, a result that is expected due to their identical mode of inheritance. We compared root-to-tip distances and branch lengths of phylogenetically independent species pairs. Both analyses showed a highly significant correlation of molecular rates between the genomes of Buchnera and the mitochondrial genomes of their hosts. A similar correlation was detected between Sulcia and their hosts, but was not statistically significant. Our results indicate that evolutionary rate correlations between hosts and long-term symbionts may be a widespread phenomenon.}, }
@article {pmid33729620, year = {2021}, author = {Radzvilavicius, A}, title = {Beyond the "selfish mitochondrion" theory of uniparental inheritance: A unified theory based on mutational variance redistribution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {43}, number = {5}, pages = {e2100009}, doi = {10.1002/bies.202100009}, pmid = {33729620}, issn = {1521-1878}, mesh = {Eukaryota/genetics ; Genome ; *Heredity ; *Mitochondria/genetics ; Mutation/genetics ; }, abstract = {"Selfish" gene theories have offered invaluable insight into eukaryotic genome evolution, but they can also be misleading. The "selfish mitochondrion" hypothesis, developed in the 90s explained uniparental organelle inheritance as a mechanism of conflict resolution, improving cooperation between genetically distinct compartments of the cell. But modern population genetic models provided a more general explanation for uniparental inheritance based on mutational variance redistribution, modulating the efficiency of both purifying and adaptive selection. Nevertheless, as reviewed here, "selfish" conflict theories still dominate the literature. While these hypotheses are rich in metaphor and highly intuitive, selective focus on only one type of mitochondrial mutation limits the generality of our understanding and hinders progress in mito-nuclear evolution theory. Recognizing that uniparental inheritance may have evolved-and is maintained across the eukaryotic tree of life-because of its influence on mutational variance and improved selection will only increase the generality of our evolutionary reasoning, retaining "selfish" conflict explanations as a special case of a much broader theory.}, }
@article {pmid33720930, year = {2021}, author = {Londoño-Burbano, A and Reis, RE}, title = {A combined molecular and morphological phylogeny of the Loricariinae (Siluriformes: Loricariidae), with emphasis on the Harttiini and Farlowellini.}, journal = {PloS one}, volume = {16}, number = {3}, pages = {e0247747}, pmid = {33720930}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; Catfishes/anatomy &amp; histology/classification/*genetics ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Fish Proteins/*genetics ; Genetic Markers ; Mitochondria/genetics ; *Phylogeny ; }, abstract = {We present a combined molecular and morphological phylogenetic analysis of the Loricariinae, with emphasis on the Harttiini (Cteniloricaria, Harttia, and Harttiella) and Farlowellini (Aposturisoma, Farlowella, Lamontichthys, Pterosturisoma, Sturisoma, and Sturisomatichthys). Character sampling comprised seven molecular markers (the mitochondrial Cytb, nd2, 12S and 16S, and the nuclear MyH6, RAG1 and RAG2) and 196 morphological characters. A total of 1,059 specimens, and 159 tissue samples were analized, representing 100 species. A Bayesian Inference analysis was performed using the concatenated data matrix, which is comprised of 6,819 characters. The Loricariinae were found to comprise the tribes (Hartiini (Loricariini, Farlowellini)), the latter two elevated from subtribes. A Maximum Parsimony analysis was also performed using the same data matrix in order to reveal phenotypical synapomorphies to diagnose each clade. Two MP trees were found with a length of 14,704 steps, consistency index of 0.29 and retention index of 0.61, which were summarized in a strict consensus tree. Harttiini includes (Harttiella (Cteniloricaria, Harttia), and Farlowellini includes (Lamontichthys (Pterosturisoma (Sturisoma (Sturisomatichthys, Farlowella)))). Aposturisoma was recovered nested within Farlowella and is synonymyzed to the latter. Sturisoma was corroborated as strictly cis-Andean, while Sturisomatichthys encompasses, besides the valid species already included in the genus, the trans-Andean species once belonging to Sturisoma sensu lato. Identification keys and phylogenetic diagnoses of family-group taxa and genera of both the Harttiini and the Farlowellini are provided.}, }
@article {pmid33713675, year = {2021}, author = {Dumoulin, B and Ufer, C and Kuhn, H and Sofi, S}, title = {Expression Regulation, Protein Chemistry and Functional Biology of the Guanine-Rich Sequence Binding Factor 1 (GRSF1).}, journal = {Journal of molecular biology}, volume = {433}, number = {13}, pages = {166922}, doi = {10.1016/j.jmb.2021.166922}, pmid = {33713675}, issn = {1089-8638}, mesh = {Amino Acid Sequence ; Animals ; Evolution, Molecular ; *Gene Expression Regulation ; Guanine/*metabolism ; Humans ; Poly(A)-Binding Proteins/*chemistry/*genetics ; Protein Binding ; RNA/metabolism ; }, abstract = {In eukaryotic cells RNA-binding proteins have been implicated in virtually all post-transcriptional mechanisms of gene expression regulation. Based on the structural features of their RNA binding domains these proteins have been divided into several subfamilies. The presence of at least two RNA recognition motifs defines the group of heterogenous nuclear ribonucleoproteins H/F and one of its members is the guanine-rich sequence binding factor 1 (GRSF1). GRSF1 was first described 25 years ago and is widely distributed in eukaryotic cells. It is present in the nucleus, the cytoplasm and in mitochondria and has been implicated in a variety of physiological processes (embryogenesis, erythropoiesis, redox homeostasis, RNA metabolism) but also in the pathogenesis of various diseases. This review summarizes our current understanding on GRSF1 biology, critically discusses the literature reports and gives an outlook of future developments in the field.}, }
@article {pmid33711786, year = {2021}, author = {Srivastava, PN and Narwal, SK and Mishra, S}, title = {Mitochondrial apurinic/apyrimidinic endonuclease Apn1 is not critical for the completion of the Plasmodium berghei life cycle.}, journal = {DNA repair}, volume = {101}, number = {}, pages = {103078}, doi = {10.1016/j.dnarep.2021.103078}, pmid = {33711786}, issn = {1568-7856}, mesh = {Amino Acid Sequence ; DNA Damage ; DNA Repair ; DNA, Mitochondrial/metabolism ; DNA-(Apurinic or Apyrimidinic Site) Lyase/chemistry/genetics/*metabolism ; *Life Cycle Stages ; Mitochondria/*enzymology ; Models, Molecular ; Phylogeny ; Plasmodium berghei/*enzymology/growth &amp; development ; Protein Conformation ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {Mitochondrion is an essential organelle in malaria parasite and its DNA must be maintained for optimal function during its complex life cycle. Base excision repair is one of the major pathways by which this is achieved. Apurinic/apyrimidinic (AP) endonucleases are important components of this pathway as they create a nick at the 5'-phosphodiester bond in the AP site and generate free 5'-phosphate and 3'-hydroxyl groups. Two class II AP endonucleases (Apn1 and Ape1) have been annotated in the Plasmodium berghei genome. Using reverse genetic approaches, we provide direct evidence that Apn1 is exclusively localized to the mitochondria of P. berghei. Surprisingly, our gene deletion study revealed a completely dispensable role of Apn1 for the entirety of the P. berghei life cycle. Apn1[-] parasites were found to successfully grow in the blood. They were transmitted normally to the mosquito midguts and salivary glands. Sporozoites obtained from the salivary glands were infective and achieved similar patency as WT. Our results help emphasize the non-availability of this enzyme as a plausible drug target. We also emphasize the importance of genetic validation of antimalarial drug targets before furthering them down the drug discovery pipeline.}, }
@article {pmid33707777, year = {2021}, author = {Zhang, J and Hou, L and Zuo, Z and Ji, P and Zhang, X and Xue, Y and Zhao, F}, title = {Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long.}, journal = {Nature biotechnology}, volume = {39}, number = {7}, pages = {836-845}, pmid = {33707777}, issn = {1546-1696}, mesh = {Animals ; Base Sequence ; Computer Simulation ; Gene Expression Regulation ; Humans ; Mice ; *Nanopore Sequencing ; RNA Isoforms ; RNA, Circular/*genetics ; Reproducibility of Results ; }, abstract = {Reconstructing the sequence of circular RNAs (circRNAs) from short RNA sequencing reads has proved challenging given the similarity of circRNAs and their corresponding linear messenger RNAs. Previous sequencing methods were unable to achieve high-throughput detection of full-length circRNAs. Here we describe a protocol for enrichment and full-length sequencing of circRNA isoforms using nanopore technology. Circular reverse transcription and size selection achieves a 20-fold higher enrichment of circRNAs from total RNA compared to previous methods. We developed an algorithm, called circRNA identifier using long-read sequencing data (CIRI-long), to reconstruct the sequence of circRNAs. The workflow was validated with simulated data and by comparison to Illumina sequencing as well as quantitative real-time RT-PCR. We used CIRI-long to analyze adult mouse brain samples and systematically profile circRNAs, including mitochondria-derived and transcriptional read-through circRNAs. We identified a new type of intronic self-ligated circRNA that exhibits special splicing and expression patterns. Our method takes advantage of nanopore long reads and enables unbiased reconstruction of full-length circRNA sequences.}, }
@article {pmid33704433, year = {2021}, author = {Broz, AK and Waneka, G and Wu, Z and Fernandes Gyorfy, M and Sloan, DB}, title = {Detecting de novo mitochondrial mutations in angiosperms with highly divergent evolutionary rates.}, journal = {Genetics}, volume = {218}, number = {1}, pages = {}, pmid = {33704433}, issn = {1943-2631}, support = {R01 GM118046/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological/genetics ; Biological Evolution ; DNA/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genome/genetics ; Genome, Mitochondrial/genetics ; Genome, Plant/genetics ; Magnoliopsida/genetics ; Mitochondria/*genetics ; Mutation/genetics ; Mutation Rate ; Phylogeny ; Sequence Analysis, DNA/*methods ; Silene/*genetics ; }, abstract = {Although plant mitochondrial genomes typically show low rates of sequence evolution, levels of divergence in certain angiosperm lineages suggest anomalously high mitochondrial mutation rates. However, de novo mutations have never been directly analyzed in such lineages. Recent advances in high-fidelity DNA sequencing technologies have enabled detection of mitochondrial mutations when still present at low heteroplasmic frequencies. To date, these approaches have only been performed on a single plant species (Arabidopsis thaliana). Here, we apply a high-fidelity technique (Duplex Sequencing) to multiple angiosperms from the genus Silene, which exhibits extreme heterogeneity in rates of mitochondrial sequence evolution among close relatives. Consistent with phylogenetic evidence, we found that Silene latifolia maintains low mitochondrial variant frequencies that are comparable with previous measurements in Arabidopsis. Silene noctiflora also exhibited low variant frequencies despite high levels of historical sequence divergence, which supports other lines of evidence that this species has reverted to lower mitochondrial mutation rates after a past episode of acceleration. In contrast, S. conica showed much higher variant frequencies in mitochondrial (but not in plastid) DNA, consistent with an ongoing bout of elevated mitochondrial mutation rates. Moreover, we found an altered mutational spectrum in S. conica heavily biased towards AT→GC transitions. We also observed an unusually low number of mitochondrial genome copies per cell in S. conica, potentially pointing to reduced opportunities for homologous recombination to accurately repair mismatches in this species. Overall, these results suggest that historical fluctuations in mutation rates are driving extreme variation in rates of plant mitochondrial sequence evolution.}, }
@article {pmid33689939, year = {2021}, author = {Dallai, R and Fanciulli, PP and Lupetti, P and Mercati, D}, title = {The ultrastructure of sperm and female sperm storage organs in the water strider Gerris lacustris L. (Heteroptera) and a possible example of genital coevolution.}, journal = {Arthropod structure &amp; development}, volume = {61}, number = {}, pages = {101043}, doi = {10.1016/j.asd.2021.101043}, pmid = {33689939}, issn = {1873-5495}, mesh = {Animals ; *Biological Evolution ; Female ; Genitalia/physiology/ultrastructure ; *Heteroptera/classification/ultrastructure ; Insemination ; Male ; Spermatozoa/ultrastructure ; }, abstract = {The fine structural organization of the male and the female inner reproductive apparatuses of the water-strider Gerris lacustris was studied. The sperm of the species shows a long helicoidal acrosome provided with longitudinal tubules, and a short nucleus. The flagellum is characterized by crescent mitochondrial derivatives and a 9 + 9 + 2 axoneme, as occurs in all Heteroptera. The female reproductive apparatus is characterized by an extremely long spermathecal duct, filled with sperm, which plays the role of the main sperm storage organ. The duct has a thin epithelium surrounded by a complex of secretory and duct-forming cells. The spermathecal duct flows into the gynatrial sac. This region, together with the fertilization chamber, exhibits a simple epithelium with deep apical plasma membrane invaginations, and it does not show conspicuous secretions. The basal cell region shows plasma membrane infoldings forming thin cytoplasmic bands hosting mitochondria and large intercellular spaces. This organization is typical of epithelia active in fluid reabsorption. Two lateral large gynatrial glands open into the gynatrial sac. Such glands also exhibit secretory and duct forming cells. The same structure of these glands is also present along the proximal region of the fecundation canal. The duct forming cells of these regions have very wide ducts with peculiar cuticular finger-like structures at their opening into the gland duct lumen. The results of the present study suggest the occurrence of a coevolution between the sperm and the spermathecal duct lengths.}, }
@article {pmid33684994, year = {2021}, author = {Yang, Y and Tong, J and Ruan, H and Yang, M and Sang, C and Liu, G and Hazihan, W and Xu, B and Hornok, S and Rizabek, K and Gulzhan, K and Liu, Z and Wang, Y}, title = {Genetic Diversity of Hard Ticks (Acari: Ixodidae) in the South and East Regions of Kazakhstan and Northwestern China.}, journal = {The Korean journal of parasitology}, volume = {59}, number = {1}, pages = {103-108}, pmid = {33684994}, issn = {1738-0006}, support = {2018ZX10101002-007//National Key Research &amp; Development Program of China/ ; 2018ZX10101002-003//National Key Research &amp; Development Program of China/ ; 81960379//National Natural Science Foundation of China/ ; 31960709//National Natural Science Foundation of China/ ; 18YJCZH220//Humanities and Social Sciences Research Projects/ ; RCZK2018C04//Shihezi University/ ; 2020E01008//International Cooperation Projects of Xinjiang Uygur Autonomous Region/ ; }, mesh = {Acari/*genetics ; Animals ; China ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Genetic Variation/*genetics ; Kazakhstan ; Mitochondria/enzymology/genetics ; Phylogeny ; }, abstract = {To date, there is no report on the genetic diversity of ticks in these regions. A total of 370 representative ticks from the south and east regions of Kazakhstan (SERK) and Xinjiang Uygur Autonomous Region (XUAR) were selected for molecular comparison. A fragment of the mitochondrial cytochrome c oxidase subunit I (cox1) gene, ranging from 631 bp to 889 bp, was used to analyze genetic diversity among these ticks. Phylogenetic analyses indicated 7 tick species including Hyalomma asiaticum, Hyalomma detritum, Hyalomma anatolicum, Dermacentor marginatus, Rhipicephalus sanguineus, Rhipicephalus turanicus and Haemaphysalis erinacei from the SERK clustered together with conspecific ticks from the XUAR. The network diagram of haplotypes showed that i) Hy. asiaticum from Almaty and Kyzylorda Oblasts together with that from Yuli County of XUAR constituted haplogroup H-2, and the lineage from Chimkent City of South Kazakhstan was newly evolved; and ii) the R. turanicus ticks sampled in Israel, Almaty, South Kazakhstan, Usu City, Ulugqat and Baicheng Counties of XUAR were derivated from an old lineage in Alataw City of XUAR. These findings indicate that: i) Hy. asiaticum, R. turanicus and Ha. erinacei shared genetic similarities between the SERK and XUAR; and ii) Hy. marginatum and D. reticulatus show differences in their evolution.}, }
@article {pmid33684992, year = {2021}, author = {Song, JY and Kim, KY and Choi, SW}, title = {Occurrence and Molecular Identification of Microcotyle sebastis Isolated from Fish Farms of the Korean Rockfish, Sebastes schlegelii.}, journal = {The Korean journal of parasitology}, volume = {59}, number = {1}, pages = {89-95}, pmid = {33684992}, issn = {1738-0006}, support = {R2021065//National Institute of Fisheries Science/ ; }, mesh = {Animals ; Electron Transport Complex IV/genetics ; Fish Diseases/*epidemiology/*parasitology ; *Fisheries ; Microscopy, Electron, Scanning ; Mitochondria/enzymology/genetics ; Phylogeny ; RNA, Ribosomal, 28S ; Republic of Korea/epidemiology ; Trematoda/*genetics/*isolation &amp; purification/ultrastructure ; Trematode Infections/epidemiology/*parasitology/*veterinary ; }, abstract = {Microcotyle sebastis is a gill monogenean ectoparasite that causes serious problems in the mariculture of the Korean rockfish, Sebastes schlegelii. In this study, we isolated the parasite from fish farms along the coasts of Tongyeong, South Korea in 2016, and characterized its infection, morphology and molecular phylogeny. The prevalence of M. sebastis infection during the study period ranged from 46.7% to 96.7%, and the mean intensity was 2.3 to 31.4 ind./fish, indicating that the fish was constantly exposed to parasitic infections throughout the year. Morphological observations under light and scanning electron microscopes of the M. sebastis isolates in this study showed the typical characteristics of the anterior prohaptor and posterior opisthaptor of monogenean parasites. In phylogenetic trees reconstructed using the nuclear 28S ribosomal RNA gene and the mitochondrial cytochrome c oxidase I gene (cox1), they consistently clustered together with their congeneric species, and showed the closest phylogenetic relationships to M. caudata and M. kasago in the cox1 tree.}, }
@article {pmid33684529, year = {2021}, author = {Bogdanova, VS and Shatskaya, NV and Mglinets, AV and Kosterin, OE and Vasiliev, GV}, title = {Discordant evolution of organellar genomes in peas (Pisum L.).}, journal = {Molecular phylogenetics and evolution}, volume = {160}, number = {}, pages = {107136}, doi = {10.1016/j.ympev.2021.107136}, pmid = {33684529}, issn = {1095-9513}, mesh = {Cell Nucleus/genetics ; Cytoplasm/genetics ; Europe ; *Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Hybridization, Genetic ; Pisum sativum/*cytology/*genetics ; *Phylogeny ; Plastids/*genetics ; }, abstract = {Plastids and mitochondria have their own small genomes, which do not undergo meiotic recombination and may have evolutionary fates different from each other and that of the nuclear genome. For the first time, we sequenced mitochondrial genomes of pea (Pisum L.) from 42 accessions mostly representing diverse wild germplasm from throughout the wild pea geographical range. Six structural types of the pea mitochondrial genome were revealed. From the same accessions, plastid genomes were sequenced. Phylogenetic trees based on the plastid and mitochondrial genomes were compared. The topologies of these trees were highly discordant, implying not less than six events of hybridisation between diverged wild peas in the past, with plastids and mitochondria differently inherited by the descendants. Such discordant inheritance of organelles could have been driven by plastid-nuclear incompatibility, which is known to be widespread in crosses involving wild peas and affects organellar inheritance. The topology of the phylogenetic tree based on nucleotide sequences of a nuclear gene, His5, encoding a histone H1 subtype, corresponded to the current taxonomy and resembled that based on the plastid genome. Wild peas (Pisum sativum subsp. elatius s.l.) inhabiting Southern Europe were shown to be of hybrid origin, resulting from crosses of peas related to those presently inhabiting the eastern Mediterranean in a broad sense. These results highlight the roles of hybridisation and cytonuclear conflict in shaping plant microevolution.}, }
@article {pmid33683754, year = {2021}, author = {Shevtsov-Tal, S and Best, C and Matan, R and Chandran, SA and Brown, GG and Ostersetzer-Biran, O}, title = {nMAT3 is an essential maturase splicing factor required for holo-complex I biogenesis and embryo development in Arabidopsis thaliana plants.}, journal = {The Plant journal : for cell and molecular biology}, volume = {106}, number = {4}, pages = {1128-1147}, doi = {10.1111/tpj.15225}, pmid = {33683754}, issn = {1365-313X}, mesh = {Arabidopsis/embryology/*genetics ; Arabidopsis Proteins/genetics/*metabolism ; Cell Nucleus/genetics ; Deoxyribonucleases/genetics/*metabolism ; Electron Transport Complex I/*metabolism ; Introns/genetics ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Phenotype ; RNA Splicing ; RNA Splicing Factors/genetics/metabolism ; RNA-Directed DNA Polymerase/genetics/metabolism ; }, abstract = {Group-II introns are self-splicing mobile genetic elements consisting of catalytic intron-RNA and its related intron-encoded splicing maturase protein cofactor. Group-II sequences are particularly plentiful within the mitochondria of land plants, where they reside within many critical gene loci. During evolution, the plant organellar introns have degenerated, such as they lack regions that are are required for splicing, and also lost their evolutionary related maturase proteins. Instead, for their splicing the organellar introns in plants rely on different host-acting protein cofactors, which may also provide a means to link cellular signals with respiratory functions. The nuclear genome of Arabidopsis thaliana encodes four maturase-related factors. Previously, we showed that three of the maturases, nMAT1, nMAT2 and nMAT4, function in the excision of different group-II introns in Arabidopsis mitochondria. The function of nMAT3 (encoded by the At5g04050 gene locus) was found to be essential during early embryogenesis. Using a modified embryo-rescue method, we show that nMAT3-knockout plants are strongly affected in the splicing of nad1 introns 1, 3 and 4 in Arabidopsis mitochondria, resulting in complex-I biogenesis defects and altered respiratory activities. Functional complementation of nMAT3 restored the organellar defects and embryo-arrested phenotypes associated with the nmat3 mutant line. Notably, nMAT3 and nMA4 were found to act on the same RNA targets but have no redundant functions in the splicing of nad1 transcripts. The two maturases, nMAT3 and nMAT4 are likely to cooperate together in the maturation of nad1 pre-RNAs. Our results provide important insights into the roles of maturases in mitochondria gene expression and the biogenesis of the respiratory system during early plant life.}, }
@article {pmid33678114, year = {2021}, author = {Huang, F and Ye, X and Wang, Z and Ding, Y and Cai, X and Yu, L and Waseem, M and Abbas, F and Ashraf, U and Chen, X and Ke, Y}, title = {The prohibitins (PHB) gene family in tomato: Bioinformatic identification and expression analysis under abiotic and phytohormone stresses.}, journal = {GM crops &amp; food}, volume = {12}, number = {1}, pages = {535-550}, pmid = {33678114}, issn = {2164-5701}, mesh = {Computational Biology ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genome, Plant ; *Solanum lycopersicum/genetics/metabolism ; Multigene Family ; Phylogeny ; Plant Growth Regulators ; Plant Proteins/genetics/metabolism ; Prohibitins ; Stress, Physiological/genetics ; }, abstract = {The prohibitins (PHB) are SPFH domain-containing proteins found in the prokaryotes to eukaryotes. The plant PHBs are associated with a wide range of biological processes, including senescence, development, and responses to biotic and abiotic stresses. The PHB proteins are identified and characterized in the number of plant species, such as Arabidopsis, rice, maize, and soybean. However, no systematic identification of PHB proteins was performed in Solanum lycopersicum. In this study, we identified 16 PHB proteins in the tomato genome. The analysis of conserved motifs and gene structure validated the phylogenetic classification of tomato PHB proteins. It was observed that various members of tomato PHB proteins undergo purifying selection based on the Ka/Ks ratio and are targeted by four families of miRNAs. Moreover, SlPHB proteins displayed a very unique expression pattern in different plant parts including fruits at various development stages. It was found that SlPHBs processed various development-related and phytohormone responsive cis-regulatory elements in their promoter regions. Furthermore, the exogenous phytohormones treatments (Abscisic acid, indole-3-acetic acid, gibberellic acid, methyl jasmonate) salt and drought stresses induce the expression of SlPHB. Moreover, the subcellular localization assay revealed that SlPHB5 and SlPHB10 were located in the mitochondria. This study systematically summarized the general characterization of SlPHBs in the tomato genome and provides a foundation for the functional characterization of PHB genes in tomato and other plant species.}, }
@article {pmid33671025, year = {2021}, author = {Ramzan, R and Kadenbach, B and Vogt, S}, title = {Multiple Mechanisms Regulate Eukaryotic Cytochrome C Oxidase.}, journal = {Cells}, volume = {10}, number = {3}, pages = {}, pmid = {33671025}, issn = {2073-4409}, mesh = {Animals ; Electron Transport Complex IV/*metabolism ; Eukaryota/*metabolism ; Rats ; }, abstract = {Cytochrome c oxidase (COX), the rate-limiting enzyme of mitochondrial respiration, is regulated by various mechanisms. Its regulation by ATP (adenosine triphosphate) appears of particular importance, since it evolved early during evolution and is still found in cyanobacteria, but not in other bacteria. Therefore the "allosteric ATP inhibition of COX" is described here in more detail. Most regulatory properties of COX are related to "supernumerary" subunits, which are largely absent in bacterial COX. The "allosteric ATP inhibition of COX" was also recently described in intact isolated rat heart mitochondria.}, }
@article {pmid33669879, year = {2021}, author = {Zapelloni, F and Jurado-Rivera, JA and Jaume, D and Juan, C and Pons, J}, title = {Comparative Mitogenomics in Hyalella (Amphipoda: Crustacea).}, journal = {Genes}, volume = {12}, number = {2}, pages = {}, pmid = {33669879}, issn = {2073-4425}, mesh = {Amphipoda/classification/*genetics ; Animals ; Codon/genetics ; Codon Usage/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Transfer/genetics ; }, abstract = {We present the sequencing and comparative analysis of 17 mitochondrial genomes of Nearctic and Neotropical amphipods of the genus Hyalella, most from the Andean Altiplano. The mitogenomes obtained comprised the usual 37 gene-set of the metazoan mitochondrial genome showing a gene rearrangement (a reverse transposition and a reversal) between the North and South American Hyalella mitogenomes. Hyalella mitochondrial genomes show the typical AT-richness and strong nucleotide bias among codon sites and strands of pancrustaceans. Protein-coding sequences are biased towards AT-rich codons, with a preference for leucine and serine amino acids. Numerous base changes (539) were found in tRNA stems, with 103 classified as fully compensatory, 253 hemi-compensatory and the remaining base mismatches and indels. Most compensatory Watson-Crick switches were AU -> GC linked in the same haplotype, whereas most hemi-compensatory changes resulted in wobble GU and a few AC pairs. These results suggest a pairing fitness increase in tRNAs after crossing low fitness valleys. Branch-site level models detected positive selection for several amino acid positions in up to eight mitochondrial genes, with atp6 and nad5 as the genes displaying more sites under selection.}, }
@article {pmid33666295, year = {2021}, author = {Salinas-Giegé, T and Ubrig, E and Drouard, L}, title = {Cyanophora paradoxa mitochondrial tRNAs play a double game.}, journal = {The Plant journal : for cell and molecular biology}, volume = {106}, number = {4}, pages = {1105-1115}, doi = {10.1111/tpj.15222}, pmid = {33666295}, issn = {1365-313X}, mesh = {Cyanophora/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; *RNA Processing, Post-Transcriptional ; RNA, Messenger/*genetics ; RNA, Mitochondrial/*genetics ; RNA, Transfer/*genetics ; }, abstract = {Present-day mitochondria derive from a single endosymbiosis of an α-proteobacterium into a proto-eukaryotic cell. Since this monophyletic event, mitochondria have evolved considerably, and unique traits have been independently acquired in the different eukaryotic kingdoms. Mitochondrial genome expression and RNA metabolism have diverged greatly. Here, Cyanophora paradoxa, a freshwater alga considered as a living fossil among photosynthetic organisms, represents an exciting model for studying the evolution of mitochondrial gene expression. As expected, fully mature tRNAs are released from primary transcripts to function in mitochondrial translation. We also show that these tRNAs take part in an mRNA processing punctuation mechanism in a non-conventional manner, leading to mRNA-tRNA hybrids with a CCA triplet at their 3'-extremities. In this case, tRNAs are probably used as stabilizing structures impeding the degradation of mRNA by exonucleases. From our data we propose that the present-day tRNA-like elements (t-elements) found at the 3'-terminals of mitochondrial mRNAs in land plants originate from true tRNAs like those observed in the mitochondria of this basal photosynthetic glaucophyte.}, }
@article {pmid33659931, year = {2021}, author = {Ji, LL and Yeo, D}, title = {Oxidative stress: an evolving definition.}, journal = {Faculty reviews}, volume = {10}, number = {}, pages = {13}, pmid = {33659931}, issn = {2732-432X}, abstract = {Thirty-five years ago, Sies and colleagues insightfully described the universal phenomenon that the generation of reactive oxygen species could modify macromolecules in living organisms, resulting in a wide range of measurable damage. They used the term "oxidative stress" to define the loss of the balance between oxidants and antioxidants in favor of the former. After decades of research, it became increasingly clear that cells are not simply passive receivers of oxidative modification but can act dynamically to resist and adapt to oxidants. Furthermore, many redox-sensitive pathways have been identified wherein certain oxidants (mainly hydrogen peroxide and nitric oxide) are used as messenger molecules to transduce the signals required for these adaptations. Since the turn of the century, redox signaling has developed into a vibrant multidisciplinary field of biology. To reflect the evolution of the study in this field, the definition of oxidative stress is postulated to define a state in which the pro-oxidative processes overwhelm cellular antioxidant defense due to the disruption of redox signaling and adaptation.}, }
@article {pmid33659825, year = {2020}, author = {Poroshina, AA and Sherbakov, DY and Peretolchina, TE}, title = {Diagnosis of the mechanisms of different types of discordances between phylogenies inferred from nuclear and mitochondrial markers.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {24}, number = {4}, pages = {420-426}, doi = {10.18699/VJ20.634}, pmid = {33659825}, issn = {2500-0462}, abstract = {In ancient freshwater lakes, an abnormally large species diversity is observed. The mechanisms that generated extremely high biodiversity in the ancient lakes have not been sufficiently studied and remain only partially known. Sequences of environmental changes in highly complex ecosystems such as Lake Baikal, may induce sophisticated combinations of microevolutionary processes. These processes are likely to result in unusual "patterns" of genetic variability of species. The most unusual patterns include the ones when speciation is followed by incomplete lineage sorting as well as mitochondrial or nuclear introgression. All these phenomena are diagnosed by comparing the topologies of phylogenetic trees inferred from molecular markers of evolution located in mitochondria and nuclei. Mitochondrial and nuclear introgression is a particularly interesting and complex case, which is the process of incorporating the gene alleles of one species into the gene pool of a sister species due to interspecific hybridization (introgressive hybridization). In many cases, existing methods for molecular phylogenetic analysis do not automatically allow the observed patterns of polymorphism to be explained and, therefore, cannot provide hypotheses that would explain the mechanisms which resulted to these patterns. Here we use adaptive dynamics models to study neutral molecular evolution under various scenarios of interaction between sister species and the environment. We propose and justify a set of criteria for detecting how two evolutionary trees may differ, with a special focus on comparing a tree inferred from nuclear DNA to one from mitochondrial DNA. The criteria react to branching pattern and branch lengths, including relative distances from ancestral lineages. Simulations show that the criteria allow fast and automated detection of various types of introgression, secondary breaches of reproductive barriers, and incomplete lineage sorting.}, }
@article {pmid33658719, year = {2021}, author = {Graf, JS and Schorn, S and Kitzinger, K and Ahmerkamp, S and Woehle, C and Huettel, B and Schubert, CJ and Kuypers, MMM and Milucka, J}, title = {Anaerobic endosymbiont generates energy for ciliate host by denitrification.}, journal = {Nature}, volume = {591}, number = {7850}, pages = {445-450}, pmid = {33658719}, issn = {1476-4687}, mesh = {Adenosine Triphosphate/metabolism ; *Anaerobiosis ; Bacteria/genetics/*metabolism ; Biological Evolution ; Cell Respiration ; Ciliophora/chemistry/cytology/*metabolism ; Citric Acid Cycle/genetics ; *Denitrification ; Electron Transport/genetics ; *Energy Metabolism ; Genome, Bacterial/genetics ; *Host Microbial Interactions/genetics ; Mitochondria ; Nitrates/metabolism ; Oxygen/metabolism ; Phylogeny ; *Symbiosis ; }, abstract = {Mitochondria are specialized eukaryotic organelles that have a dedicated function in oxygen respiration and energy production. They evolved about 2 billion years ago from a free-living bacterial ancestor (probably an alphaproteobacterium), in a process known as endosymbiosis[1,2]. Many unicellular eukaryotes have since adapted to life in anoxic habitats and their mitochondria have undergone further reductive evolution[3]. As a result, obligate anaerobic eukaryotes with mitochondrial remnants derive their energy mostly from fermentation[4]. Here we describe 'Candidatus Azoamicus ciliaticola', which is an obligate endosymbiont of an anaerobic ciliate and has a dedicated role in respiration and providing energy for its eukaryotic host. 'Candidatus A. ciliaticola' contains a highly reduced 0.29-Mb genome that encodes core genes for central information processing, the electron transport chain, a truncated tricarboxylic acid cycle, ATP generation and iron-sulfur cluster biosynthesis. The genome encodes a respiratory denitrification pathway instead of aerobic terminal oxidases, which enables its host to breathe nitrate instead of oxygen. 'Candidatus A. ciliaticola' and its ciliate host represent an example of a symbiosis that is based on the transfer of energy in the form of ATP, rather than nutrition. This discovery raises the possibility that eukaryotes with mitochondrial remnants may secondarily acquire energy-providing endosymbionts to complement or replace functions of their mitochondria.}, }
@article {pmid33658670, year = {2021}, author = {Lewis, WH and Ettema, TJG}, title = {A microbial marriage reminiscent of mitochondrial evolution.}, journal = {Nature}, volume = {591}, number = {7850}, pages = {375-376}, pmid = {33658670}, issn = {1476-4687}, mesh = {*Biological Evolution ; *Marriage ; Mitochondria/genetics ; }, }
@article {pmid33658608, year = {2021}, author = {Cabrera, VM}, title = {Human molecular evolutionary rate, time dependency and transient polymorphism effects viewed through ancient and modern mitochondrial DNA genomes.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {5036}, pmid = {33658608}, issn = {2045-2322}, mesh = {DNA, Ancient/analysis ; DNA, Mitochondrial/*genetics/history ; *Evolution, Molecular ; Genetics, Population/*history ; *Genome, Mitochondrial ; Haplotypes ; History, 21st Century ; History, Ancient ; Humans ; Mitochondria/genetics ; *Mutation Rate ; Population Density ; Time Factors ; }, abstract = {Human evolutionary genetics gives a chronological framework to interpret the human history. It is based on the molecular clock hypothesis that suppose a straightforward relationship between the mutation rate and the substitution rate with independence of other factors as demography dynamics. Analyzing ancient and modern human complete mitochondrial genomes we show here that, along the time, the substitution rate can be significantly slower or faster than the average germline mutation rate confirming a time dependence effect mainly attributable to changes in the effective population size of the human populations, with an exponential growth in recent times. We also detect that transient polymorphisms play a slowdown role in the evolutionary rate deduced from haplogroup intraspecific trees. Finally, we propose the use of the most divergent lineages within haplogroups as a practical approach to correct these molecular clock mismatches.}, }
@article {pmid33652602, year = {2021}, author = {Prieto, C and Montecinos, J and Jiménez, G and Riquelme, C and Garrido, D and Hernández, S and Loyola, A and Villanueva, RA}, title = {Phosphorylation of Phylogenetically Conserved Amino Acid Residues Confines HBx within Different Cell Compartments of Human Hepatocarcinoma Cells.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {5}, pages = {}, pmid = {33652602}, issn = {1420-3049}, mesh = {Amino Acid Sequence/genetics ; Carcinoma, Hepatocellular/*genetics/pathology/virology ; Conserved Sequence/genetics ; Gene Expression Regulation, Viral/genetics ; Genome, Viral/genetics ; Hep G2 Cells ; Hepatitis B/*genetics/pathology/virology ; Hepatitis B virus/genetics/pathogenicity ; Humans ; Liver Neoplasms/*genetics/pathology/virology ; Phosphorylation/genetics ; Phylogeny ; Trans-Activators/*genetics ; Viral Regulatory and Accessory Proteins/*genetics ; }, abstract = {Hepatitis B virus (HBV) is a circular, and partially double-stranded DNA virus. Upon infection, the viral genome is translocated into the cell nucleus, generating the covalently closed circular DNA (cccDNA) intermediate, and forming a mini chromosome. HBV HBx is a small protein displaying multiple roles in HBV-infected cells, and in different subcellular locations. In the nucleus, the HBx protein is required to initiate and maintain viral transcription from the viral mini chromosome. In contrast, HBx also functions in the cytoplasm, where it is able to alter multiple cellular functions such as mitochondria metabolism, apoptosis and signal transduction pathways. It has been reported that in cultured cells, at low expression levels, the HBx protein is localized in the nucleus, whereas at high expression levels, it accumulates in the cytoplasm. This dynamic subcellular distribution of HBx might be essential to exert its multiple roles during viral infection. However, the mechanism that regulates different subcellular localizations of the HBx protein is unknown. We have previously taken a bioinformatics approach to investigate whether HBx might be regulated via post-translational modification, and we have proposed that the multiple nucleocytoplasmic functions of HBx might be regulated by an evolutionarily conserved mechanism via phosphorylation. In the current study, phylogenetically conserved amino acids of HBx with a high potential of phosphorylation were targeted for site-directed mutagenesis. Two conserved serine (Ser25 and Ser41), and one conserved threonine (Thr81) amino acids were replaced by either alanine or aspartic acid residues to simulate an unphosphorylated or phosphorylated state, respectively. Human hepatoma cells were transfected with increasing amounts of the HBx DNA constructs, and the cells were analyzed by fluorescence microscopy. Together, our results show that the nucleocytoplasmic distribution of the HBx protein could be regulated by phosphorylation since some of the modified proteins were mainly confined to distinct subcellular compartments. Remarkably, both HBx Ser41A, and HBx Thr81D proteins were predominantly localized within the nuclear compartment throughout the different expression levels of HBx mutants.}, }
@article {pmid33649061, year = {2021}, author = {Fajardo, RG and Fariña, FO and Rey, AM and Rego-Pérez, I and Blanco, FJ and García, JLF}, title = {Relationship Between the Dynamics of Telomere Loss in Peripheral Blood Leukocytes From Knee Osteoarthritis Patients and Mitochondrial DNA Haplogroups.}, journal = {The Journal of rheumatology}, volume = {48}, number = {10}, pages = {1603-1607}, doi = {10.3899/jrheum.201316}, pmid = {33649061}, issn = {1499-2752}, mesh = {DNA, Mitochondrial/genetics ; Haplotypes ; Humans ; Leukocytes ; Mitochondria ; *Osteoarthritis, Knee/diagnostic imaging/genetics ; Telomere/genetics ; }, abstract = {OBJECTIVE: To evaluate the evolution of telomere length from peripheral blood leukocytes (PBLs) in subjects from the Osteoarthritis Initiative (OAI) cohort in relation to the incidence of osteoarthritis (OA), and to explore its possible interactive influence with the mitochondrial DNA (mtDNA) haplogroup.<br><br>METHODS: Dynamics of telomere sequence loss were quantified in PBLs from initially healthy individuals (without symptoms or radiological signs), 78 carrying the mtDNA cluster HV, and 47 with cluster JT, from the OAI, during a 72-month follow-up period. The incidence of knee OA during this period (n = 39) was radiographically established when Kellgren-Lawrence (KL) score increased from < 2 at recruitment, to &#x2265; 2 at the end of 72 months of follow-up. Multivariate analysis using binary logistic regression was performed to assess PBL telomere loss and mtDNA haplogroups as associated risk factors of incidence of knee OA.<br><br>RESULTS: Carriers of cluster HV showed knee OA incidence twice that of the JT carriers (n = 30 vs 9). The rate of PBL telomere loss was higher in cluster HV carriers and in individuals with incident knee OA. Multivariate analysis showed that the dynamics of PBL telomere shortening can be a consistent risk marker of knee OA incidence. Subjects with nonincident knee OA showed a slower telomere loss than those with incident knee OA; the difference was more significant in carriers of cluster JT than in HV.<br><br>CONCLUSION: An increased rate of telomere loss in PBLs may reflect a systemic accelerated senescence phenotype that could be potentiated by the mitochondrial function, increasing the susceptibility of developing knee OA.}, }
@article {pmid33648457, year = {2021}, author = {Bizouerne, E and Buitink, J and Vu, BL and Vu, JL and Esteban, E and Pasha, A and Provart, N and Verdier, J and Leprince, O}, title = {Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour.}, journal = {BMC plant biology}, volume = {21}, number = {1}, pages = {124}, pmid = {33648457}, issn = {1471-2229}, support = {RFI Objectif V&#xe9;g&#xe9;tal//Conseil R&#xe9;gional des Pays de la Loire/ ; }, mesh = {Acclimatization/genetics ; Droughts ; Endosperm/genetics/growth &amp; development ; *Gene Expression Regulation, Plant ; *Gene Regulatory Networks ; Genetic Association Studies ; Solanum lycopersicum/embryology/*genetics/growth &amp; development ; Seeds/*genetics/growth &amp; development ; Transcriptome ; }, abstract = {BACKGROUND: During maturation seeds acquire several physiological traits to enable them to survive drying and disseminate the species. Few studies have addressed the regulatory networks controlling acquisition of these traits at the tissue level particularly in endospermic seeds such as tomato, which matures in a fully hydrated environment and does not undergo maturation drying. Using temporal RNA-seq analyses of the different seed tissues during maturation, gene network and trait-based correlations were used to explore the transcriptome signatures associated with desiccation tolerance, longevity, germination under water stress and dormancy.<br><br>RESULTS: During maturation, 15,173 differentially expressed genes were detected, forming a gene network representing 21 expression modules, with 3 being specific to seed coat and embryo and 5 to the endosperm. A gene-trait significance measure identified a common gene module between endosperm and embryo associated with desiccation tolerance and conserved with non-endospermic seeds. In addition to genes involved in protection such LEA and HSP and ABA response, the module included antioxidant and repair genes. Dormancy was released concomitantly with the increase in longevity throughout fruit ripening until 14&#x2009;days after the red fruit stage. This was paralleled by an increase in SlDOG1-2 and PROCERA transcripts. The progressive increase in seed vigour was captured by three gene modules, one in common between embryo and endosperm and two tissue-specific. The common module was enriched with genes associated with mRNA processing in chloroplast and mitochondria (including penta- and tetratricopeptide repeat-containing proteins) and post-transcriptional regulation, as well several flowering genes. The embryo-specific module contained homologues of ABI4 and CHOTTO1 as hub genes associated with seed vigour, whereas the endosperm-specific module revealed a diverse set of processes that were related to genome stability, defence against pathogens and ABA/GA response genes.<br><br>CONCLUSION: The spatio-temporal co-expression atlas of tomato seed maturation will serve as a valuable resource for the in-depth understanding of the dynamics of gene expression associated with the acquisition of seed vigour at the tissue level.}, }
@article {pmid33644926, year = {2021}, author = {Radzvilavicius, A and Layh, S and Hall, MD and Dowling, DK and Johnston, IG}, title = {Sexually antagonistic evolution of mitochondrial and nuclear linkage.}, journal = {Journal of evolutionary biology}, volume = {34}, number = {5}, pages = {757-766}, doi = {10.1111/jeb.13776}, pmid = {33644926}, issn = {1420-9101}, mesh = {Animals ; *Biological Evolution ; Female ; *Genetic Linkage ; *Genome, Mitochondrial ; Male ; *Models, Genetic ; Mutation ; Recombination, Genetic ; Selection, Genetic ; *Sex Characteristics ; }, abstract = {Across eukaryotes, genes encoding bioenergetic machinery are located in both mitochondrial and nuclear DNA, and incompatibilities between the two genomes can be devastating. Mitochondria are often inherited maternally, and theory predicts sex-specific fitness effects of mitochondrial mutational diversity. Yet how evolution acts on linkage patterns between mitochondrial and nuclear genomes is poorly understood. Using novel mito-nuclear population-genetic models, we show that the interplay between nuclear and mitochondrial genes maintains mitochondrial haplotype diversity within populations, and selects both for sex-independent segregation of mitochondrion-interacting genes and for paternal leakage. These effects of genetic linkage evolution can eliminate male-harming fitness effects of mtDNA mutational diversity. With maternal mitochondrial inheritance, females maintain a tight mitochondrial-nuclear match, but males accumulate mismatch mutations because of the weak statistical associations between the two genomic components. Sex-independent segregation of mitochondria-interacting loci improves the mito-nuclear match. In a sexually antagonistic evolutionary process, male nuclear alleles evolve to increase the rate of recombination, whereas females evolve to suppress it. Paternal leakage of mitochondria can evolve as an alternative mechanism to improve the mito-nuclear linkage. Our modelling framework provides an evolutionary explanation for the observed paucity of mitochondrion-interacting genes on mammalian sex chromosomes and for paternal leakage in protists, plants, fungi and some animals.}, }
@article {pmid33643304, year = {2020}, author = {Kumar, V}, title = {The Trinity of cGAS, TLR9, and ALRs Guardians of the Cellular Galaxy Against Host-Derived Self-DNA.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {624597}, pmid = {33643304}, issn = {1664-3224}, mesh = {Autoimmune Diseases/immunology/pathology ; DNA/*immunology ; DNA-Binding Proteins/*immunology ; Humans ; *Immunity, Innate ; Inflammation/immunology/pathology ; Nucleotidyltransferases/*immunology ; Toll-Like Receptor 9/*immunology ; }, abstract = {The immune system has evolved to protect the host from the pathogens and allergens surrounding their environment. The immune system develops in such a way to recognize self and non-self and develops self-tolerance against self-proteins, nucleic acids, and other larger molecules. However, the broken immunological self-tolerance leads to the development of autoimmune or autoinflammatory diseases. Pattern-recognition receptors (PRRs) are expressed by immunological cells on their cell membrane and in the cytosol. Different Toll-like receptors (TLRs), Nod-like receptors (NLRs) and absent in melanoma-2 (AIM-2)-like receptors (ALRs) forming inflammasomes in the cytosol, RIG (retinoic acid-inducible gene)-1-like receptors (RLRs), and C-type lectin receptors (CLRs) are some of the PRRs. The DNA-sensing receptor cyclic GMP-AMP synthase (cGAS) is another PRR present in the cytosol and the nucleus. The present review describes the role of ALRs (AIM2), TLR9, and cGAS in recognizing the host cell DNA as a potent damage/danger-associated molecular pattern (DAMP), which moves out to the cytosol from its housing organelles (nucleus and mitochondria). The introduction opens with the concept that the immune system has evolved to recognize pathogens, the idea of horror autotoxicus, and its failure due to the emergence of autoimmune diseases (ADs), and the discovery of PRRs revolutionizing immunology. The second section describes the cGAS-STING signaling pathway mediated cytosolic self-DNA recognition, its evolution, characteristics of self-DNAs activating it, and its role in different inflammatory conditions. The third section describes the role of TLR9 in recognizing self-DNA in the endolysosomes during infections depending on the self-DNA characteristics and various inflammatory diseases. The fourth section discusses about AIM2 (an ALR), which also binds cytosolic self-DNA (with 80-300 base pairs or bp) that inhibits cGAS-STING-dependent type 1 IFN generation but induces inflammation and pyroptosis during different inflammatory conditions. Hence, this trinity of PRRs has evolved to recognize self-DNA as a potential DAMP and comes into action to guard the cellular galaxy. However, their dysregulation proves dangerous to the host and leads to several inflammatory conditions, including sterile-inflammatory conditions autoinflammatory and ADs.}, }
@article {pmid33631347, year = {2021}, author = {Kutyumov, VA and Predeus, AV and Starunov, VV and Maltseva, AL and Ostrovsky, AN}, title = {Mitochondrial gene order of the freshwater bryozoan Cristatella mucedo retains ancestral lophotrochozoan features.}, journal = {Mitochondrion}, volume = {59}, number = {}, pages = {96-104}, doi = {10.1016/j.mito.2021.02.003}, pmid = {33631347}, issn = {1872-8278}, mesh = {Animals ; Bryozoa/anatomy &amp; histology/*classification/genetics ; Evolution, Molecular ; Gene Order ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {Bryozoans are aquatic colonial suspension-feeders abundant in many marine and freshwater benthic communities. At the same time, the phylum is under studied on both morphological and molecular levels, and its position on the metazoan tree of life is still disputed. Bryozoa include the exclusively marine Stenolaemata, predominantly marine Gymnolaemata and exclusively freshwater Phylactolaemata. Here we report the mitochondrial genome of the phylactolaemate bryozoan Cristatella mucedo. This species has the largest (21,008 bp) of all currently known bryozoan mitogenomes, containing a typical metazoan gene compendium as well as a number of non-coding regions, three of which are longer than 1500 bp. The trnS1/trnG/nad3 region is presumably duplicated in this species. Comparative analysis of the gene order in C. mucedo and another phylactolaemate bryozoan, Pectinatella magnifica, confirmed their close relationships, and revealed a stronger similarity to mitogenomes of phoronids and other lophotrochozoan species than to marine bryozoans, indicating the ancestral nature of their gene arrangement. We suggest that the ancestral gene order underwent substantial changes in different bryozoan cladesshowing mosaic distribution of conservative gene blocks regardless of their phylogenetic position. Altogether, our results support the early divergence of Phylactolaemata from the rest of Bryozoa.}, }
@article {pmid33618020, year = {2021}, author = {Shinde, P and Whitwell, HJ and Verma, RK and Ivanchenko, M and Zaikin, A and Jalan, S}, title = {Impact of modular mitochondrial epistatic interactions on the evolution of human subpopulations.}, journal = {Mitochondrion}, volume = {58}, number = {}, pages = {111-122}, doi = {10.1016/j.mito.2021.02.004}, pmid = {33618020}, issn = {1872-8278}, support = {MR/R02524X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Epistasis, Genetic ; *Evolution, Molecular ; *Genes, Mitochondrial ; Humans ; Mutation ; Population Groups/*genetics ; }, abstract = {Investigation of human mitochondrial (mt) genome variation has been shown to provide insights to the human history and natural selection. By analyzing 24,167 human mt-genome samples, collected for five continents, we have developed a co-mutation network model to investigate characteristic human evolutionary patterns. The analysis highlighted richer co-mutating regions of the mt-genome, suggesting the presence of epistasis. Specifically, a large portion of COX genes was found to co-mutate in Asian and American populations, whereas, in African, European, and Oceanic populations, there was greater co-mutation bias in hypervariable regions. Interestingly, this study demonstrated hierarchical modularity as a crucial agent for these co-mutation networks. More profoundly, our ancestry-based co-mutation module analyses showed that mutations cluster preferentially in known mitochondrial haplogroups. Contemporary human mt-genome nucleotides most closely resembled the ancestral state, and very few of them were found to be ancestral-variants. Overall, these results demonstrated that subpopulation-based biases may favor mitochondrial gene specific epistasis.}, }
@article {pmid33616640, year = {2021}, author = {Piccinini, G and Iannello, M and Puccio, G and Plazzi, F and Havird, JC and Ghiselli, F}, title = {Mitonuclear Coevolution, but not Nuclear Compensation, Drives Evolution of OXPHOS Complexes in Bivalves.}, journal = {Molecular biology and evolution}, volume = {38}, number = {6}, pages = {2597-2614}, pmid = {33616640}, issn = {1537-1719}, mesh = {Animals ; *Biological Evolution ; Bivalvia/*genetics ; *Genome, Mitochondrial ; *Oxidative Phosphorylation ; }, abstract = {In Metazoa, four out of five complexes involved in oxidative phosphorylation (OXPHOS) are formed by subunits encoded by both the mitochondrial (mtDNA) and nuclear (nuDNA) genomes, leading to the expectation of mitonuclear coevolution. Previous studies have supported coadaptation of mitochondria-encoded (mtOXPHOS) and nuclear-encoded OXPHOS (nuOXPHOS) subunits, often specifically interpreted with regard to the "nuclear compensation hypothesis," a specific form of mitonuclear coevolution where nuclear genes compensate for deleterious mitochondrial mutations due to less efficient mitochondrial selection. In this study, we analyzed patterns of sequence evolution of 79 OXPHOS subunits in 31 bivalve species, a taxon showing extraordinary mtDNA variability and including species with "doubly uniparental" mtDNA inheritance. Our data showed strong and clear signals of mitonuclear coevolution. NuOXPHOS subunits had concordant topologies with mtOXPHOS subunits, contrary to previous phylogenies based on nuclear genes lacking mt interactions. Evolutionary rates between mt and nuOXPHOS subunits were also highly correlated compared with non-OXPHO-interacting nuclear genes. Nuclear subunits of chimeric OXPHOS complexes (I, III, IV, and V) also had higher dN/dS ratios than Complex II, which is formed exclusively by nuDNA-encoded subunits. However, we did not find evidence of nuclear compensation: mitochondria-encoded subunits showed similar dN/dS ratios compared with nuclear-encoded subunits, contrary to most previously studied bilaterian animals. Moreover, no site-specific signals of compensatory positive selection were detected in nuOXPHOS genes. Our analyses extend the evidence for mitonuclear coevolution to a new taxonomic group, but we propose a reconsideration of the nuclear compensation hypothesis.}, }
@article {pmid33616531, year = {2021}, author = {Zarin, T and Strome, B and Peng, G and Pritišanac, I and Forman-Kay, JD and Moses, AM}, title = {Identifying molecular features that are associated with biological function of intrinsically disordered protein regions.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33616531}, issn = {2050-084X}, support = {PJT-148532//CIHR/Canada ; FDN-148375//CIHR/Canada ; }, mesh = {Amino Acid Sequence ; Hydrophobic and Hydrophilic Interactions ; Intrinsically Disordered Proteins/chemistry/*metabolism ; Isoelectric Point ; Mitochondria/metabolism ; Models, Statistical ; Proteome/chemistry/*metabolism ; Saccharomyces cerevisiae/metabolism ; }, abstract = {In previous work, we showed that intrinsically disordered regions (IDRs) of proteins contain sequence-distributed molecular features that are conserved over evolution, despite little sequence similarity that can be detected in alignments (Zarin et al., 2019). Here, we aim to use these molecular features to predict specific biological functions for individual IDRs and identify the molecular features within them that are associated with these functions. We find that the predictable functions are diverse. Examining the associated molecular features, we note some that are consistent with previous reports and identify others that were previously unknown. We experimentally confirm that elevated isoelectric point and hydrophobicity, features that are positively associated with mitochondrial localization, are necessary for mitochondrial targeting function. Remarkably, increasing isoelectric point in a synthetic IDR restores weak mitochondrial targeting. We believe feature analysis represents a new systematic approach to understand how biological functions of IDRs are specified by their protein sequences.}, }
@article {pmid33612083, year = {2022}, author = {Ma, ZJ and Li, GZ and Chen, SM and Han, JL and Hanif, Q}, title = {Rich maternal and paternal genetic diversity and divergent lineage composition in wild yak (Bos mutus).}, journal = {Animal biotechnology}, volume = {33}, number = {6}, pages = {1382-1386}, doi = {10.1080/10495398.2021.1884567}, pmid = {33612083}, issn = {1532-2378}, mesh = {Cattle/genetics ; Animals ; Phylogeny ; Haplotypes/genetics ; *DNA, Mitochondrial/genetics ; *Mitochondria/genetics ; Genetic Variation/genetics ; }, abstract = {Wild yak (Bos mutus) is a vulnerable bovine species on the Qinghai-Tibetan Plateau (QTP). So far, most studies on molecular genetic diversity of wild yak have focused on autosomal and mtDNA variations based on small number of samples. In this study, we analyzed 84 D-loop and 24 whole mitogenome sequences of wild yak to further comprehensively explore its maternal genetic diversity and lineage composition. Meanwhile, using six yak Y-specific polymorphic markers (i.e., SRY4, USP9Y, UTY19, AMELY3, OFD1Y10 and INRA189), we assessed the paternal genetic diversity and lineage composition based on eight wild yak. Our results showed that wild yak exhibited abundant maternal genetic diversity with haplotype diversities of 0.9621 ± 0.0078 and 0.9928 ± 0.0144 in the D-loop and whole mitogenome sequences, respectively. Maternal phylogenetic analysis of wild yak uncovered three defined lineages (mt-I, mt-II and mt-III). Similarly, profuse paternal genetic diversity was observed in wild yak with Y-haplotype diversity (Hd) at 0.8214 ± 0.1007. Two Y-haplogroups (Y1 and Y2) with four Y-haplotypes (yH1-yH4) were identified in paternal phylogenetic analysis, indicating wild yak to be of two paternal lineages. This study of genetic diversity and lineage composition of wild yak would provide useful information for the genetic resource conservation and utilization of this vulnerable wild species.}, }
@article {pmid33606008, year = {2021}, author = {Omarjee, O and Mathieu, AL and Quiniou, G and Moreews, M and Ainouze, M and Frachette, C and Melki, I and Dumaine, C and Gerfaud-Valentin, M and Duquesne, A and Kallinich, T and Tahir Turanli, E and Malcus, C and Viel, S and Pescarmona, R and Georgin-Lavialle, S and Jamilloux, Y and Larbre, JP and Sarrabay, G and Magnotti, F and Rice, GI and Bleicher, F and Reboulet, J and Merabet, S and Henry, T and Crow, YJ and Faure, M and Walzer, T and Belot, A}, title = {LACC1 deficiency links juvenile arthritis with autophagy and metabolism in macrophages.}, journal = {The Journal of experimental medicine}, volume = {218}, number = {3}, pages = {}, pmid = {33606008}, issn = {1540-9538}, mesh = {Adenylate Kinase/metabolism ; Adolescent ; Amino Acid Sequence ; Apoptosis/drug effects ; Arthritis, Juvenile/genetics/*metabolism/*pathology ; *Autophagy/drug effects/genetics ; Autophagy-Related Proteins/metabolism ; Bacteria/metabolism ; Cell Differentiation/drug effects ; Child ; Exome/genetics ; Female ; Homozygote ; Humans ; Inflammasomes/metabolism ; Inflammation/complications/pathology ; Interferons/metabolism ; Intracellular Signaling Peptides and Proteins/chemistry/*deficiency/genetics ; Lipid Droplets/drug effects/metabolism ; Loss of Function Mutation/genetics ; Lysosomes/drug effects/metabolism ; Macrophage Colony-Stimulating Factor/pharmacology ; Macrophages/drug effects/*metabolism ; Male ; Mitochondria/drug effects/metabolism ; Monocytes/drug effects/pathology ; NF-kappa B/metabolism ; Pedigree ; Proteomics ; Receptors for Activated C Kinase/metabolism ; Signal Transduction ; TOR Serine-Threonine Kinases/metabolism ; Young Adult ; }, abstract = {Juvenile idiopathic arthritis is the most common chronic rheumatic disease in children, and its etiology remains poorly understood. Here, we explored four families with early-onset arthritis carrying homozygous loss-of-expression mutations in LACC1. To understand the link between LACC1 and inflammation, we performed a functional study of LACC1 in human immune cells. We showed that LACC1 was primarily expressed in macrophages upon mTOR signaling. We found that LACC1 deficiency had no obvious impact on inflammasome activation, type I interferon response, or NF-κB regulation. Using bimolecular fluorescence complementation and biochemical assays, we showed that autophagy-inducing proteins, RACK1 and AMPK, interacted with LACC1. Autophagy blockade in macrophages was associated with LACC1 cleavage and degradation. Moreover, LACC1 deficiency reduced autophagy flux in primary macrophages. This was associated with a defect in the accumulation of lipid droplets and mitochondrial respiration, suggesting that LACC1-dependent autophagy fuels macrophage bioenergetics metabolism. Altogether, LACC1 deficiency defines a novel form of genetically inherited juvenile arthritis associated with impaired autophagy in macrophages.}, }
@article {pmid33594064, year = {2021}, author = {Uwizeye, C and Decelle, J and Jouneau, PH and Flori, S and Gallet, B and Keck, JB and Bo, DD and Moriscot, C and Seydoux, C and Chevalier, F and Schieber, NL and Templin, R and Allorent, G and Courtois, F and Curien, G and Schwab, Y and Schoehn, G and Zeeman, SC and Falconet, D and Finazzi, G}, title = {Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1049}, pmid = {33594064}, issn = {2041-1723}, mesh = {Acclimatization/radiation effects ; *Energy Metabolism/radiation effects ; *Imaging, Three-Dimensional ; Light ; Microalgae/metabolism/radiation effects/ultrastructure ; Mitochondria/metabolism/radiation effects/ultrastructure ; Phytoplankton/*cytology/*physiology/radiation effects/ultrastructure ; Plastids/metabolism ; Subcellular Fractions/metabolism ; }, abstract = {Eukaryotic phytoplankton have a small global biomass but play major roles in primary production and climate. Despite improved understanding of phytoplankton diversity and evolution, we largely ignore the cellular bases of their environmental plasticity. By comparative 3D morphometric analysis across seven distant phytoplankton taxa, we observe constant volume occupancy by the main organelles and preserved volumetric ratios between plastids and mitochondria. We hypothesise that phytoplankton subcellular topology is modulated by energy-management constraints. Consistent with this, shifting the diatom Phaeodactylum from low to high light enhances photosynthesis and respiration, increases cell-volume occupancy by mitochondria and the plastid CO2-fixing pyrenoid, and boosts plastid-mitochondria contacts. Changes in organelle architectures and interactions also accompany Nannochloropsis acclimation to different trophic lifestyles, along with respiratory and photosynthetic responses. By revealing evolutionarily-conserved topologies of energy-managing organelles, and their role in phytoplankton acclimation, this work deciphers phytoplankton responses at subcellular scales.}, }
@article {pmid33591272, year = {2021}, author = {Zhu, X and Boulet, A and Buckley, KM and Phillips, CB and Gammon, MG and Oldfather, LE and Moore, SA and Leary, SC and Cobine, PA}, title = {Mitochondrial copper and phosphate transporter specificity was defined early in the evolution of eukaryotes.}, journal = {eLife}, volume = {10}, number = {}, pages = {}, pmid = {33591272}, issn = {2050-084X}, support = {R01 GM120211/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; Cell Line ; Copper Transport Proteins/genetics/metabolism ; Eukaryota ; Mice ; Mitochondria ; Mitochondrial Proteins/*genetics/metabolism ; Mutagenesis, Site-Directed ; Phosphate Transport Proteins/genetics/metabolism ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; }, abstract = {The mitochondrial carrier family protein SLC25A3 transports both copper and phosphate in mammals, yet in Saccharomyces cerevisiae the transport of these substrates is partitioned across two paralogs: PIC2 and MIR1. To understand the ancestral state of copper and phosphate transport in mitochondria, we explored the evolutionary relationships of PIC2 and MIR1 orthologs across the eukaryotic tree of life. Phylogenetic analyses revealed that PIC2-like and MIR1-like orthologs are present in all major eukaryotic supergroups, indicating an ancient gene duplication created these paralogs. To link this phylogenetic signal to protein function, we used structural modeling and site-directed mutagenesis to identify residues involved in copper and phosphate transport. Based on these analyses, we generated an L175A variant of mouse SLC25A3 that retains the ability to transport copper but not phosphate. This work highlights the utility of using an evolutionary framework to uncover amino acids involved in substrate recognition by mitochondrial carrier family proteins.}, }
@article {pmid33581918, year = {2021}, author = {Zheng, X and Gao, X and Wang, J and Du, C and Hou, C and Xie, Q and Lou, B and Liu, F and Zhu, J}, title = {KIFC1 functions in nuclear reshaping and midpiece formation during the spermatogenesis of small yellow croaker Larimichthys polyactis.}, journal = {Animal reproduction science}, volume = {226}, number = {}, pages = {106702}, doi = {10.1016/j.anireprosci.2021.106702}, pmid = {33581918}, issn = {1873-2232}, mesh = {Amino Acid Sequence ; Animals ; Cell Nucleus/physiology ; Cloning, Molecular ; DNA, Complementary/genetics ; Fishes/genetics/*physiology ; Gene Expression Regulation/physiology ; Kinesins/genetics/*metabolism ; Male ; Microtubules/physiology ; Mitochondria/physiology ; Phylogeny ; Protein Conformation ; Protein Transport ; RNA, Messenger/genetics/metabolism ; Spermatogenesis/*physiology ; Spermatozoa/*cytology/*physiology ; Testis/*physiology ; Tubulin/genetics/metabolism ; }, abstract = {The C-terminal kinesin motor protein (KIFC1) has essential functions in spermatogenesis. To evaluate molecular mechanisms of KIFC1 during teleost fish spermatogenesis, there was cloning and sequencing the kifc1 cDNA in the testis of Larimichthys polyactis. Quantitative PCR results indicated there were Lp-kifc1 mRNA transcripts in the testes. Results from conducting fluorescence in situ hybridization and immunofluorescence procedures indicated there were trends in relative abundance changes in Lp-kifc1 mRNA transcripts that were associated with abundance of Lp-KIFC1 protein during spermatogenesis. The Lp-KIFC1 protein was detected at all stages of spermatogenesis. There was minimal Lp-KIFC1 in the cytoplasm of spermatogonia, with content being greater and concentrated in the perinuclear region in spermatocytes and during early/mid-stages of development of spermatids. There were large abundances of Lp-KIFC1 in spermatids at the mid-developmental stage. In late-developing spermatids, Lp-KIFC1 content was less and concentrated in the bottom of the nucleus, where the midpiece formed. There was a small Lp-KIFC1 in the midpiece of mature sperm. These findings indicate Lp-KIFC1 may have functions in L. polyactis spermatogenesis. Results from conducting immunofluorescence procedures indicated Lp-KIFC1 was co-localized microtubules and mitochondria throughout spermatogenesis. There were large abundances of Lp-KIFC1 and tubulin in spermatids during the mid-developmental stage, when there is a decrease in size and reshaping of the nucleus. During midpiece formation, there was co-localization of the Lp-KIFC1 and mitochondria in the spermatid perinuclear region to the midpiece. These findings indicate Lp-KIFC1 is involved in nuclear reshaping and midpiece formation during spermatogenesis in L. polyactis.}, }
@article {pmid33569374, year = {2020}, author = {Xu, D and Qian, J and Guan, X and Ren, L and Yang, K and Huang, X and Zhang, S and Chai, Y and Wu, X and Wu, H and Zhang, X and Yang, K and Yu, B}, title = {Copper-Containing Alloy as Immunoregulatory Material in Bone Regeneration via Mitochondrial Oxidative Stress.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {8}, number = {}, pages = {620629}, pmid = {33569374}, issn = {2296-4185}, abstract = {In the mammalian skeletal system, osteogenesis and angiogenesis are closely linked by type H vessels during bone regeneration and repair. Our previous studies confirmed the promotion of these processes by copper-containing metal (CCM) in vitro and in vivo. However, whether and how the coupling of angiogenesis and osteogenesis participates in the promotion of bone regeneration by CCM in vivo is unknown. In this study, M2a macrophages but not M2c macrophages were shown to be immunoregulated by CCM. A CCM, 316L-5Cu, was applied to drilling hole injuries of the tibia of C57/6 mice for comparison. We observed advanced formation of cortical bone and type H vessels beneath the new bone in the 316L-5Cu group 14 and 21 days postinjury. Moreover, the recruitment of CD206-positive M2a macrophages, which are regarded as the primary source of platelet-derived growth factor type BB (PDGF-BB), was significantly promoted at the injury site at days 14 and 21. Under the stimulation of CCM, mitochondria-derived reactive oxygen species were also found to be upregulated in CD206[hi] M2a macrophages in vitro, and this upregulation was correlated with the expression of PDGF-BB. In conclusion, our results indicate that CCM promotes the evolution of callus through the generation of type H vessels during the process of bone repair by upregulating the expression of PDGF-BB derived from M2a macrophages.}, }
@article {pmid33567508, year = {2021}, author = {Mannella, CA}, title = {VDAC-A Primal Perspective.}, journal = {International journal of molecular sciences}, volume = {22}, number = {4}, pages = {}, pmid = {33567508}, issn = {1422-0067}, support = {P41 RR001219/RR/NCRR NIH HHS/United States ; P41RR01219/RR/NCRR NIH HHS/United States ; U01HLI16321/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Ion Channel Gating ; Lipid Bilayers/*metabolism ; *Membrane Potentials ; Mitochondria/*physiology ; Voltage-Dependent Anion Channels/*metabolism ; }, abstract = {The evolution of the eukaryotic cell from the primal endosymbiotic event involved a complex series of adaptations driven primarily by energy optimization. Transfer of genes from endosymbiont to host and concomitant expansion (by infolding) of the endosymbiont's chemiosmotic membrane greatly increased output of adenosine triphosphate (ATP) and placed selective pressure on the membrane at the host-endosymbiont interface to sustain the energy advantage. It is hypothesized that critical functions at this interface (metabolite exchange, polypeptide import, barrier integrity to proteins and DNA) were managed by a precursor β-barrel protein ("pβB") from which the voltage-dependent anion-selective channel (VDAC) descended. VDAC's role as hub for disparate and increasingly complex processes suggests an adaptability that likely springs from a feature inherited from pβB, retained because of important advantages conferred. It is proposed that this property is the remarkable structural flexibility evidenced in VDAC's gating mechanism, a possible origin of which is discussed.}, }
@article {pmid33565245, year = {2021}, author = {Shiiba, I and Takeda, K and Nagashima, S and Ito, N and Tokuyama, T and Yamashita, SI and Kanki, T and Komatsu, T and Urano, Y and Fujikawa, Y and Inatome, R and Yanagi, S}, title = {MITOL promotes cell survival by degrading Parkin during mitophagy.}, journal = {EMBO reports}, volume = {22}, number = {3}, pages = {e49097}, pmid = {33565245}, issn = {1469-3178}, mesh = {Cell Survival ; HeLa Cells ; Humans ; *Mitophagy ; *Ubiquitin-Protein Ligases/genetics/metabolism ; Ubiquitination ; }, abstract = {Parkin promotes cell survival by removing damaged mitochondria via mitophagy. However, although some studies have suggested that Parkin induces cell death, the regulatory mechanism underlying the dual role of Parkin remains unknown. Herein, we report that mitochondrial ubiquitin ligase (MITOL/MARCH5) regulates Parkin-mediated cell death through the FKBP38-dependent dynamic translocation from the mitochondria to the ER during mitophagy. Mechanistically, MITOL mediates ubiquitination of Parkin at lysine 220 residue, which promotes its proteasomal degradation, and thereby fine-tunes mitophagy by controlling the quantity of Parkin. Deletion of MITOL leads to accumulation of the phosphorylated active form of Parkin in the ER, resulting in FKBP38 degradation and enhanced cell death. Thus, we have shown that MITOL blocks Parkin-induced cell death, at least partially, by protecting FKBP38 from Parkin. Our findings unveil the regulation of the dual function of Parkin and provide a novel perspective on the pathogenesis of PD.}, }
@article {pmid33561119, year = {2021}, author = {De, AK and Sawhney, S and Bhattacharya, D and Sujatha, T and Sunder, J and Ponraj, P and Ravi, SK and Mondal, S and Malakar, D and Kundu, A}, title = {Origin, genetic diversity and evolution of Andaman local duck, a native duck germplasm of an insular region of India.}, journal = {PloS one}, volume = {16}, number = {2}, pages = {e0245138}, pmid = {33561119}, issn = {1932-6203}, mesh = {Animals ; Animals, Domestic/genetics ; Biological Evolution ; DNA, Mitochondrial/analysis/*genetics ; Ducks/*genetics ; Genetic Variation/genetics ; Genetics, Population/methods ; Haplotypes/genetics ; India ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Domestic ducks are of paramount importance as a cheap source of protein in rural India. Andaman local duck (ALD) is an indigenous avian genetic resource of Andaman and Nicobar islands (ANI) and is mainly distributed in Middle and Northern parts of these islands. Negligence has brought this breed on the edge of extinction necessitating immediate conservation efforts. Here, we report the genetic diversity, population structure and matrilineal genetic root of ALD. Partial mtDNA D-loop sequences were analyzed in 71 ALD samples and analysis revealed 19 polymorphic sites and 13 haplotypes. Estimated haplotype (Hd ± SD) and nucleotide diversity (π ± SD) were 0.881 ± 0.017 and 0.00897 ± 0.00078 respectively. The high genetic diversity of ALD indicates introgression of genetic material from other local duck breeds. In addition, it can be postulated that ALD bearing high genetic diversity has strong ability to adapt to environmental changes and can withstand impending climate change. Phylogenetic and network analysis indicate that ALD falls under Eurasian clade of mallard and ALD forms three clusters; one cluster is phylogenetically close to Southeast Asian countries, one close to Southern part of mainland India and the third one forms an independent cluster. Therefore, ALD might have migrated either from Southeast Asian countries which enjoy a close cultural bondage with ANI from time immemorial or from Southern part of India. The independent cluster may have evolved locally in these islands and natural selection pressure imposed by environmental conditions might be the driving force for evaluation of these duck haplotypes; which mimics Darwin's theory of natural selection. The results of the study will be beneficial for formulating future breeding programme and conservation strategy towards sustainable development of the duck breed.}, }
@article {pmid33557932, year = {2021}, author = {Pilgrim, J and Siozios, S and Baylis, M and Venter, G and Garros, C and Hurst, GDD}, title = {Cardinium symbiosis as a potential confounder of mtDNA based phylogeographic inference in Culicoides imicola (Diptera: Ceratopogonidae), a vector of veterinary viruses.}, journal = {Parasites &amp; vectors}, volume = {14}, number = {1}, pages = {100}, pmid = {33557932}, issn = {1756-3305}, support = {BB/M011186/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; H2020-MSCA-IF-2014//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; }, mesh = {Animals ; Bacterial Infections/*transmission ; Bacteroidetes/genetics ; Ceratopogonidae/*genetics/*microbiology ; DNA, Mitochondrial/chemistry/*genetics ; Gene Flow ; Horses ; Insect Vectors/*microbiology ; Mediterranean Region ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; South Africa ; *Symbiosis ; }, abstract = {BACKGROUND: Culicoides imicola (Diptera: Ceratopogonidae) is an important Afrotropical and Palearctic vector of disease, transmitting viruses of animal health and economic significance including African horse sickness and bluetongue viruses. Maternally inherited symbiotic bacteria (endosymbionts) of arthropods can alter the frequency of COI (cytochrome c oxidase subunit I) mitochondrial haplotypes (mitotypes) in a population, masking the true patterns of host movement and gene flow. Thus, this study aimed to assess the mtDNA structure of C. imicola in relation to infection with Candidatus Cardinum hertigii (Bacteroides), a common endosymbiont of Culicoides spp.<br><br>METHODS: Using haplotype network analysis, COI Sanger sequences from Cardinium-infected and -uninfected C. imicola individuals were first compared in a population from South Africa. The network was then extended to include mitotypes from a geographic range where Cardinium infection has previously been investigated.<br><br>RESULTS: The mitotype network of the South African population demonstrated the presence of two broad mitotype groups. All Cardinium-infected specimens fell into one group (Fisher's exact test, P&#x2009;=&#x2009;0.00071) demonstrating a linkage disequilibrium between endosymbiont and mitochondria. Furthermore, by extending this haplotype network to include other C. imicola populations from the Mediterranean basin, we revealed mitotype variation between the Eastern and Western Mediterranean basins (EMB and WMB) mirrored Cardinium-infection heterogeneity.<br><br>CONCLUSIONS: These observations suggest that the linkage disequilibrium of Cardinium and mitochondria reflects endosymbiont gene flow within the Mediterranean basin but may not assist in elucidating host gene flow. Subsequently, we urge caution on the single usage of the COI marker to determine population structure and movement in C. imicola and instead suggest the complementary utilisation of additional molecular markers.}, }
@article {pmid33554278, year = {2021}, author = {Ohari, Y and Matsuo, K and Yoshida, A and Nonaka, N and Sato, H and Itagaki, T}, title = {Genetic diversity and population structure analyses based on microsatellite DNA of parthenogenetic Fasciola flukes obtained from cattle and sika deer in Japan.}, journal = {Parasitology research}, volume = {120}, number = {4}, pages = {1341-1350}, pmid = {33554278}, issn = {1432-1955}, mesh = {Animals ; Cattle ; Cattle Diseases/epidemiology/*parasitology ; DNA, Helminth/*genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; Deer/*parasitology ; Fasciola/*genetics/physiology ; Fascioliasis/parasitology/*veterinary ; *Genetic Variation ; Haplotypes ; Helminth Proteins/genetics ; Japan/epidemiology ; Microsatellite Repeats ; Mitochondria/enzymology ; NADH Dehydrogenase/genetics ; Parthenogenesis ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; }, abstract = {Understanding the population structure of Fasciola flukes in domestic and wild animals is important for determining the extent of cross-infection between them. Although the parthenogenetic Fasciola flukes in Japan have been shown to comprise five genetic types based on the ribosomal internal transcribed spacer 1 (ITS1) and mitochondrial NADH dehydrogenase subunit 1 (nad1) regions, these genetic regions are not suitable for analyzing their population structure. In the present study, the genetic diversity and population structure of the parthenogenetic Fasciola flukes in Japan were studied using microsatellite DNA, ITS1, and nad1 regions. A total of 144 parthenogenetic Fasciola flukes, obtained from cattle and sika deer in 16 localities, were individually analyzed using PCR-RFLP for ITS1, PCR-direct sequence analysis for nad1, and post-labeling PCR and capillary electrophoresis for microsatellite DNA regions. The flukes showed higher genetic diversity in the microsatellite DNA regions than ITS1 and nad1. The population structures of parthenogenetic Fasciola flukes were unclear, however, it was suggested that the flukes are more diverse populations. We hypothesized that their distribution throughout Japan is closely related to livestock movement dependent on human activity. Moreover, it is considered that cross-infection of the flukes between cattle and sika deer possibly has occurred in the past.}, }
@article {pmid33550595, year = {2021}, author = {Cainzos, M and Marchetti, F and Popovich, C and Leonardi, P and Pagnussat, G and Zabaleta, E}, title = {Gamma carbonic anhydrases are subunits of the mitochondrial complex I of diatoms.}, journal = {Molecular microbiology}, volume = {116}, number = {1}, pages = {109-125}, doi = {10.1111/mmi.14694}, pmid = {33550595}, issn = {1365-2958}, mesh = {Amino Acid Sequence ; Carbonic Anhydrases/genetics/*metabolism ; Chloroplasts/genetics/metabolism ; Diatoms/genetics/*metabolism ; Electron Transport Complex I/genetics/*metabolism ; Evolution, Molecular ; Mitochondria/genetics/*metabolism ; Phylogeny ; RNA-Seq ; Rhodophyta/genetics ; Sequence Alignment ; Symbiosis/genetics ; }, abstract = {Diatoms are unicellular organisms containing red algal-derived plastids that probably originated as result of serial endosymbioses between an ancestral heterotrophic organism and a red alga or cryptophyta algae from which has only the chloroplast left. Diatom mitochondria are thus believed to derive from the exosymbiont. Unlike animals and fungi, diatoms seem to contain ancestral respiratory chains. In support of this, genes encoding gamma type carbonic anhydrases (CAs) whose products were shown to be intrinsic complex I subunits in plants, Euglena and Acanthamoeba were found in diatoms, a representative of Stramenopiles. In this work, we experimentally show that mitochondrial complex I in diatoms is a large complex containing gamma type CA subunits, supporting an ancestral origin. By using a bioinformatic approach, a complex I integrated CA domain with heterotrimeric subunit composition is proposed.}, }
@article {pmid33549602, year = {2021}, author = {Baluška, F and Lyons, S}, title = {Archaeal Origins of Eukaryotic Cell and Nucleus.}, journal = {Bio Systems}, volume = {203}, number = {}, pages = {104375}, doi = {10.1016/j.biosystems.2021.104375}, pmid = {33549602}, issn = {1872-8324}, mesh = {Actin Cytoskeleton ; Archaea/*cytology ; Biological Evolution ; Cell Biology ; *Cell Nucleus ; Cytoskeleton ; Eukaryota/*cytology ; *Mitochondria ; *Plastids ; *Symbiosis ; Trimethoprim, Sulfamethoxazole Drug Combination ; Tubulin ; }, abstract = {Symbiosis is a major evolutionary force, especially at the cellular level. Here we discuss several older and new discoveries suggesting that besides mitochondria and plastids, eukaryotic nuclei also have symbiotic origins. We propose an archaea-archaea scenario for the evolutionary origin of the eukaryotic cells. We suggest that two ancient archaea-like cells, one based on the actin cytoskeleton and another one based on the tubulin-centrin cytoskeleton, merged together to form the first nucleated eukaryotic cell. This archaeal endosymbiotic origin of eukaryotic cells and their nuclei explains several features of eukaryotic cells which are incompatible with the currently preferred autogenous scenarios of eukaryogenesis.}, }
@article {pmid33546419, year = {2021}, author = {Lee, K and Leister, D and Kleine, T}, title = {Arabidopsis Mitochondrial Transcription Termination Factor mTERF2 Promotes Splicing of Group IIB Introns.}, journal = {Cells}, volume = {10}, number = {2}, pages = {}, pmid = {33546419}, issn = {2073-4409}, support = {KL 2362/1-1 to T.K., and TRR175 to D.L. (project C05) and T.K. (project C01), and a Humboldt fellowship to K.L.//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Arabidopsis ; Arabidopsis Proteins/*metabolism ; Basic-Leucine Zipper Transcription Factors/*metabolism ; Chloroplasts/*metabolism ; Gene Expression Regulation, Plant/*genetics ; Humans ; Introns/*genetics ; Mitochondrial Proteins/*metabolism ; }, abstract = {Plastid gene expression (PGE) is essential for chloroplast biogenesis and function and, hence, for plant development. However, many aspects of PGE remain obscure due to the complexity of the process. A hallmark of nuclear-organellar coordination of gene expression is the emergence of nucleus-encoded protein families, including nucleic-acid binding proteins, during the evolution of the green plant lineage. One of these is the mitochondrial transcription termination factor (mTERF) family, the members of which regulate various steps in gene expression in chloroplasts and/or mitochondria. Here, we describe the molecular function of the chloroplast-localized mTERF2 in Arabidopsis thaliana. The complete loss of mTERF2 function results in embryo lethality, whereas directed, microRNA (amiR)-mediated knockdown of MTERF2 is associated with perturbed plant development and reduced chlorophyll content. Moreover, photosynthesis is impaired in amiR-mterf2 plants, as indicated by reduced levels of photosystem subunits, although the levels of the corresponding messenger RNAs are not affected. RNA immunoprecipitation followed by RNA sequencing (RIP-Seq) experiments, combined with whole-genome RNA-Seq, RNA gel-blot, and quantitative RT-PCR analyses, revealed that mTERF2 is required for the splicing of the group IIB introns of ycf3 (intron 1) and rps12.}, }
@article {pmid33545275, year = {2021}, author = {Kimball, RT and Hosner, PA and Braun, EL}, title = {A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths.}, journal = {Molecular phylogenetics and evolution}, volume = {158}, number = {}, pages = {107091}, doi = {10.1016/j.ympev.2021.107091}, pmid = {33545275}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/genetics ; Databases, Genetic ; Galliformes/*classification/genetics/physiology ; Introns ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Building taxon-rich phylogenies is foundational for macroevolutionary studies. One approach to improve taxon sampling beyond individual studies is to build supermatricies of publicly available data, incorporating taxa sampled across different studies and utilizing different loci. Most existing supermatrix studies have focused on loci commonly sequenced with Sanger technology ("legacy" markers, such as mitochondrial data and small numbers of nuclear loci). However, incorporating phylogenomic studies into supermatrices allows problem nodes to be targeted and resolved with considerable amounts of data, while improving taxon sampling with legacy data. Here we estimate phylogeny from a galliform supermatrix which includes well-known model and agricultural species such as the chicken and turkey. We assembled a supermatrix comprising 4500 ultra-conserved elements (UCEs) collected as part of recent phylogenomic studies in this group and legacy mitochondrial and nuclear (intron and exon) sequences. Our resulting phylogeny included 88% of extant species and recovered well-accepted relationships with strong support. However, branch lengths, which are particularly important in down-stream macroevolutionary studies, appeared vastly skewed. Taxa represented only by rapidly evolving mitochondrial data had high proportions of missing data and exhibited long terminal branches. Conversely, taxa sampled for slowly evolving UCEs with low proportions of missing data exhibited substantially shorter terminal branches. We explored several branch length re-estimation methods with particular attention to terminal branches and conclude that re-estimation using well-sampled mitochondrial sequences may be a pragmatic approach to obtain trees suitable for macroevolutionary analysis.}, }
@article {pmid33542272, year = {2021}, author = {Sucháčková Bartoňová, A and Konvička, M and Marešová, J and Wiemers, M and Ignatev, N and Wahlberg, N and Schmitt, T and Faltýnek Fric, Z}, title = {Wolbachia affects mitochondrial population structure in two systems of closely related Palaearctic blue butterflies.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {3019}, pmid = {33542272}, issn = {2045-2322}, mesh = {Animals ; Butterflies/*genetics/microbiology/ultrastructure ; DNA, Mitochondrial/genetics ; Mitochondria/genetics/microbiology/*ultrastructure ; *Phylogeny ; Wolbachia/*genetics/pathogenicity ; }, abstract = {The bacterium Wolbachia infects many insect species and spreads by diverse vertical and horizontal means. As co-inherited organisms, these bacteria often cause problems in mitochondrial phylogeny inference. The phylogenetic relationships of many closely related Palaearctic blue butterflies (Lepidoptera: Lycaenidae: Polyommatinae) are ambiguous. We considered the patterns of Wolbachia infection and mitochondrial diversity in two systems: Aricia agestis/Aricia artaxerxes and the Pseudophilotes baton species complex. We sampled butterflies across their distribution ranges and sequenced one butterfly mitochondrial gene and two Wolbachia genes. Both butterfly systems had uninfected and infected populations, and harboured several Wolbachia strains. Wolbachia was highly prevalent in A. artaxerxes and the host's mitochondrial structure was shallow, in contrast to A. agestis. Similar bacterial alleles infected both Aricia species from nearby sites, pointing to a possible horizontal transfer. Mitochondrial history of the P. baton species complex mirrored its Wolbachia infection and not the taxonomical division. Pseudophilotes baton and P. vicrama formed a hybrid zone in Europe. Wolbachia could obscure mitochondrial history, but knowledge on the infection helps us to understand the observed patterns. Testing for Wolbachia should be routine in mitochondrial DNA studies.}, }
@article {pmid33540360, year = {2021}, author = {Supaphon, P and Kerdpiboon, S and Vénien, A and Loison, O and Sicard, J and Rouel, J and Astruc, T}, title = {Structural changes in local Thai beef during sous-vide cooking.}, journal = {Meat science}, volume = {175}, number = {}, pages = {108442}, doi = {10.1016/j.meatsci.2021.108442}, pmid = {33540360}, issn = {1873-4138}, mesh = {Animals ; Cattle ; Cooking/*methods ; Microscopy, Electron, Transmission ; Muscle Fibers, Skeletal/*ultrastructure ; Red Meat/*analysis ; Temperature ; Time Factors ; }, abstract = {Thai beef (Bos indicus) samples were sous-vide-cooked at temperatures of 60°C, 70°C or 80°C for 2 to 36 hrs and prepared for microstructure characterization by light and electron microscopy. Muscle fibers showed a first phase of lateral shrinkage during the first 6 hrs of cooking at 60-70°C and the first 2 hrs at 80°C followed by a second phase of significant alternations of shrinkage and swelling independently of water transfers. Swelling peaked at 12 hrs. Microstructural changes were more variable for samples cooked at 60-70°C than for samples cooked at 80°C that showed a larger cross-sectional myofibrillar mass area (CSA). Hypercontracted fibers were evidenced at all temperature-time combinations and were associated with adjacent wavy fibers and a characteristic structural evolution in the mitochondria. The role of thermal denaturation of proteins and the ultrastructural analogy of hypercontracted fibers with cold-shortened fibers are discussed.}, }
@article {pmid33540080, year = {2021}, author = {de Freitas Souza, C and Baldissera, MD and Barroso, D and de Lima, MCM and Baldisserotto, B and Val, AL}, title = {Involvement of purinergic system and electron transport chain in two species of cichlids from the Amazon basin exposed to hypoxia.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {255}, number = {}, pages = {110918}, doi = {10.1016/j.cbpa.2021.110918}, pmid = {33540080}, issn = {1531-4332}, mesh = {Animals ; Cichlids/*metabolism ; Electron Transport ; Fresh Water ; Hydrocortisone/blood ; Hypoxia/*metabolism ; Mitochondria, Liver/metabolism ; Receptors, Purinergic/*metabolism ; South America ; Species Specificity ; }, abstract = {The Amazonian aquatic ecosystem undergoes seasonal variations and daily changes that directly affect the availability of oxygen. During the day the levels of oxygen can reach supersaturation, and at night can drop to zero. In this way, aquatic organisms are exposed daily to physiological challenges regarding the availability of oxygen. The present study revealed significant differences in the physiology and performance of two cichlids: Geophagus proximus (black water cichlid - from Negro River) and Chaetobranchopsis orbicularis (white water cichlid - from Amazon River), exposed to hypoxia. The white water cichlid showed lower value (1.99 ± 0.79 pKa) of critical pressure of oxygen (Pcrit) and a longer time (68.00 ± 14.11 min) for total loss of balance (LOE); however, this species showed 50% mortality during exposure to hypoxia, while the black water cichlid did not show mortality. Both cichlids presented a decrease in O2 consumption rate (OCR) during hypoxia.. In this sense, it was observed that the black water cichlid presented several physiological strategies during hypoxia, such as, a significant increase in plasma cortisol levels, nucleoside triphosphate diphosphohydrolase activity (for adenosine diphosphate (ADP) as a substrate) in the gills, and the activity of adenosine deaminase (ADA) in gills and liver, in addition to a significant increase in the activity of complexes (II-III) in the transporter chain of electrons in both analyzed tissues and succinate dehydrogenase activity of gills' mitochondria. On the other hand, the only physiological change observed in the white water cichlid was a significant reduction in the activity of complexes II-III in gills and liver. Based on our findings, we can hypothesize that the white water cichlid specie has less tolerant to hypoxia when compared to the black water cichlid.}, }
@article {pmid33536648, year = {2021}, author = {Kraus, F and Roy, K and Pucadyil, TJ and Ryan, MT}, title = {Function and regulation of the divisome for mitochondrial fission.}, journal = {Nature}, volume = {590}, number = {7844}, pages = {57-66}, pmid = {33536648}, issn = {1476-4687}, support = {/HHMI/Howard Hughes Medical Institute/United States ; /MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Biological Evolution ; Calcium Signaling ; Cell Death ; Disease ; Dynamins/chemistry/genetics/metabolism ; Health ; Humans ; Mitochondria/*chemistry/*metabolism/pathology ; Mitochondrial Dynamics/*physiology ; }, abstract = {Mitochondria form dynamic networks in the cell that are balanced by the flux of iterative fusion and fission events of the organelles. It is now appreciated that mitochondrial fission also represents an end-point event in a signalling axis that allows cells to sense and respond to external cues. The fission process is orchestrated by membrane-associated adaptors, influenced by organellar and cytoskeletal interactions and ultimately executed by the dynamin-like GTPase DRP1. Here we invoke the framework of the 'mitochondrial divisome', which is conceptually and operationally similar to the bacterial cell-division machinery. We review the functional and regulatory aspects of the mitochondrial divisome and, within this framework, parse the core from the accessory machinery. In so doing, we transition from a phenomenological to a mechanistic understanding of the fission process.}, }
@article {pmid33529628, year = {2021}, author = {Yan, L and Xu, W and Zhang, D and Li, J}, title = {Comparative analysis of the mitochondrial genomes of flesh flies and their evolutionary implication.}, journal = {International journal of biological macromolecules}, volume = {174}, number = {}, pages = {385-391}, doi = {10.1016/j.ijbiomac.2021.01.188}, pmid = {33529628}, issn = {1879-0003}, mesh = {Animals ; Base Composition ; Evolution, Molecular ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Sarcophagidae/*classification/genetics ; Whole Genome Sequencing/*methods ; }, abstract = {Flesh flies (Diptera: Sarcophagidae) include a large and widely distributed rapid radiation within the Calyptratae. They are vital for the ecosystem, as well as economic, forensic, and evolutionary studies, because of their extremely diverse habits as larvae. Phylogenetic studies of Sarcophagidae have been reaching convergence, which leads the opportunity to elucidate the evolution of these fast-evolving insects from the perspective of mitochondrial genome. Complete mitochondrial genomes of eight species were sequenced, and comparative mitochondrial genomic analysis between subfamilies were conducted. Mitochondrial genomes of these flesh flies are conserved in gene content with gene arrangement, same as the inferred ancestral insect, and the nucleotide composition is highly biased towards A + T like other flesh flies. The evolutionary rates of Sarcophagidae vary considerably across subfamilies, with that of Miltogramminae higher than the other two subfamilies. Phylogenetic analysis strongly supports monophyly of Sarcophagidae and each subfamily, with subfamily-level relationship inferred as (Sarcophaginae, (Miltogramminae, Paramacronychiinae)). The main topological inconsistency of all reconstructions is the relationship within Miltogramminae and Sarcophaga, which might be caused by their rapid evolution. Our study indicates that the mitochondrial genomes of flesh flies are highly conserved, and they are practically useful for phylogenetic inference of calyptrates.}, }
@article {pmid33526678, year = {2021}, author = {Rout, S and Oeljeklaus, S and Makki, A and Tachezy, J and Warscheid, B and Schneider, A}, title = {Determinism and contingencies shaped the evolution of mitochondrial protein import.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {6}, pages = {}, pmid = {33526678}, issn = {1091-6490}, mesh = {Animals ; Carrier Proteins/genetics ; *Evolution, Molecular ; Mitochondria/*genetics/metabolism ; Mitochondrial Membrane Transport Proteins/*genetics ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/genetics ; Protein Binding ; Protein Precursors/genetics ; Protein Transport/genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/*genetics ; Trypanosoma brucei brucei/genetics/metabolism/pathogenicity ; }, abstract = {Mitochondrial protein import requires outer membrane receptors that evolved independently in different lineages. Here we used quantitative proteomics and in vitro binding assays to investigate the substrate preferences of ATOM46 and ATOM69, the two mitochondrial import receptors of Trypanosoma brucei The results show that ATOM46 prefers presequence-containing, hydrophilic proteins that lack transmembrane domains (TMDs), whereas ATOM69 prefers presequence-lacking, hydrophobic substrates that have TMDs. Thus, the ATOM46/yeast Tom20 and the ATOM69/yeast Tom70 pairs have similar substrate preferences. However, ATOM46 mainly uses electrostatic, and Tom20 hydrophobic, interactions for substrate binding. In vivo replacement of T. brucei ATOM46 by yeast Tom20 did not restore import. However, replacement of ATOM69 by the recently discovered Tom36 receptor of Trichomonas hydrogenosomes, while not allowing for growth, restored import of a large subset of trypanosomal proteins that lack TMDs. Thus, even though ATOM69 and Tom36 share the same domain structure and topology, they have different substrate preferences. The study establishes complementation experiments, combined with quantitative proteomics, as a highly versatile and sensitive method to compare in vivo preferences of protein import receptors. Moreover, it illustrates the role determinism and contingencies played in the evolution of mitochondrial protein import receptors.}, }
@article {pmid33524071, year = {2021}, author = {Hayward, JA and Rajendran, E and Zwahlen, SM and Faou, P and van Dooren, GG}, title = {Divergent features of the coenzyme Q:cytochrome c oxidoreductase complex in Toxoplasma gondii parasites.}, journal = {PLoS pathogens}, volume = {17}, number = {2}, pages = {e1009211}, pmid = {33524071}, issn = {1553-7374}, mesh = {Animals ; Blotting, Western ; Cells, Cultured ; Electron Transport Complex III/chemistry/*metabolism ; Fluorescent Antibody Technique ; Humans ; Mitochondria/metabolism ; Oxygen/metabolism ; Protein Subunits/chemistry/metabolism ; Smegmamorpha ; Toxoplasma/genetics/*metabolism ; }, abstract = {The mitochondrion is critical for the survival of apicomplexan parasites. Several major anti-parasitic drugs, such as atovaquone and endochin-like quinolones, act through inhibition of the mitochondrial electron transport chain at the coenzyme Q:cytochrome c oxidoreductase complex (Complex III). Despite being an important drug target, the protein composition of Complex III of apicomplexan parasites has not been elucidated. Here, we undertake a mass spectrometry-based proteomic analysis of Complex III in the apicomplexan Toxoplasma gondii. Along with canonical subunits that are conserved across eukaryotic evolution, we identify several novel or highly divergent Complex III components that are conserved within the apicomplexan lineage. We demonstrate that one such subunit, which we term TgQCR11, is critical for parasite proliferation, mitochondrial oxygen consumption and Complex III activity, and establish that loss of this protein leads to defects in Complex III integrity. We conclude that the protein composition of Complex III in apicomplexans differs from that of the mammalian hosts that these parasites infect.}, }
@article {pmid33521839, year = {2021}, author = {Schumm, YR and Bakaloudis, D and Barboutis, C and Cecere, JG and Eraud, C and Fischer, D and Hering, J and Hillerich, K and Lormée, H and Mader, V and Masello, JF and Metzger, B and Rocha, G and Spina, F and Quillfeldt, P}, title = {Prevalence and genetic diversity of avian haemosporidian parasites in wild bird species of the order Columbiformes.}, journal = {Parasitology research}, volume = {120}, number = {4}, pages = {1405-1420}, pmid = {33521839}, issn = {1432-1955}, mesh = {Animal Migration ; Animals ; Bird Diseases/*epidemiology/parasitology ; Columbidae/parasitology ; Columbiformes/*parasitology ; Cytochromes b/genetics ; Genetic Variation ; Global Warming ; Haemosporida/classification/*genetics/growth &amp; development ; Host Specificity ; Mitochondria/genetics ; Multiplex Polymerase Chain Reaction/veterinary ; Phylogeny ; Plasmodium/genetics ; Polymerase Chain Reaction/veterinary ; Prevalence ; Protozoan Infections, Animal/*epidemiology/parasitology ; }, abstract = {Diseases can play a role in species decline. Among them, haemosporidian parasites, vector-transmitted protozoan parasites, are known to constitute a risk for different avian species. However, the magnitude of haemosporidian infection in wild columbiform birds, including strongly decreasing European turtle doves, is largely unknown. We examined the prevalence and diversity of haemosporidian parasites Plasmodium, Leucocytozoon and subgenera Haemoproteus and Parahaemoproteus in six species of the order Columbiformes during breeding season and migration by applying nested PCR, one-step multiplex PCR assay and microscopy. We detected infections in 109 of the 259 screened individuals (42%), including 15 distinct haemosporidian mitochondrial cytochrome b lineages, representing five H. (Haemoproteus), two H. (Parahaemoproteus), five Leucocytozoon and three Plasmodium lineages. Five of these lineages have never been described before. We discriminated between single and mixed infections and determined host species-specific prevalence for each parasite genus. Observed differences among sampled host species are discussed with reference to behavioural characteristics, including nesting and migration strategy. Our results support previous suggestions that migratory birds have a higher prevalence and diversity of blood parasites than resident or short-distance migratory species. A phylogenetic reconstruction provided evidence for H. (Haemoproteus) as well as H. (Parahaemoproteus) infections in columbiform birds. Based on microscopic examination, we quantified parasitemia, indicating the probability of negative effects on the host. This study provides a large-scale baseline description of haemosporidian infections of wild birds belonging to the order Columbiformes sampled in the northern hemisphere. The results enable the monitoring of future changes in parasite transmission areas, distribution and diversity associated with global change, posing a potential risk for declining avian species as the European turtle dove.}, }
@article {pmid33521279, year = {2021}, author = {Kim, J and Jang, SM and Choi, E and Jo, E and Lee, SJ and Kim, SH and Chi, YM and Kim, JH and Park, H}, title = {The complete mitochondrial genome of Eaton's skate, Bathyraja eatonii (Rajiformes, Arhynchobatidae).}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {6}, number = {1}, pages = {91-92}, pmid = {33521279}, issn = {2380-2359}, abstract = {The complete mitochondrial genome of Eaton's skate Bathyraja eatonii was studied using the long-read technology, PacBio Sequel System. The complete mitochondrial genome form of B. eatonii was 16,698 bp and it's comprised of 13 protein-coding genes, 22 tRNA and 2 rRNA. The base composition of B. eatonii is analyzed 31.94% for A, 33.94% for T, 13.49% for G, 20.64% for C, the result of GC content was 33.94%. Phylogenetic analysis showed that B. eatonii was closely related to Bathyraja meridionalis in Arhynchobatidae family, and this first mitochondrial genome of Antarctic skate would provide fundamental information to the evolutional relationship of Antarctic fishes.}, }
@article {pmid33514857, year = {2021}, author = {Macey, JR and Pabinger, S and Barbieri, CG and Buring, ES and Gonzalez, VL and Mulcahy, DG and DeMeo, DP and Urban, L and Hime, PM and Prost, S and Elliott, AN and Gemmell, NJ}, title = {Evidence of two deeply divergent co-existing mitochondrial genomes in the Tuatara reveals an extremely complex genomic organization.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {116}, pmid = {33514857}, issn = {2399-3642}, mesh = {Acclimatization/genetics ; Animals ; Cold Temperature ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Female ; *Genome, Mitochondrial ; Male ; Phylogeny ; Reptiles/*genetics ; }, abstract = {Animal mitochondrial genomic polymorphism occurs as low-level mitochondrial heteroplasmy and deeply divergent co-existing molecules. The latter is rare, known only in bivalvian mollusks. Here we show two deeply divergent co-existing mt-genomes in a vertebrate through genomic sequencing of the Tuatara (Sphenodon punctatus), the sole-representative of an ancient reptilian Order. The two molecules, revealed using a combination of short-read and long-read sequencing technologies, differ by 10.4% nucleotide divergence. A single long-read covers an entire mt-molecule for both strands. Phylogenetic analyses suggest a 7-8 million-year divergence between genomes. Contrary to earlier reports, all 37 genes typical of animal mitochondria, with drastic gene rearrangements, are confirmed for both mt-genomes. Also unique to vertebrates, concerted evolution drives three near-identical putative Control Region non-coding blocks. Evidence of positive selection at sites linked to metabolically important transmembrane regions of encoded proteins suggests these two mt-genomes may confer an adaptive advantage for an unusually cold-tolerant reptile.}, }
@article {pmid33513437, year = {2021}, author = {Li, W and Cao, Y and Chen, Z and Tan, Y and Dai, Y and Wei, J and Xiao, J and Feng, H}, title = {Black carp TRADD suppresses MAVS/IFN signaling during the innate immune activation.}, journal = {Fish &amp; shellfish immunology}, volume = {111}, number = {}, pages = {83-93}, doi = {10.1016/j.fsi.2021.01.006}, pmid = {33513437}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Carps/*genetics/*immunology ; Cell Line ; Fish Diseases/*immunology ; Fish Proteins/chemistry/genetics/immunology ; Gene Expression Profiling/veterinary ; Gene Expression Regulation/*immunology ; HEK293 Cells ; Humans ; Immunity, Innate/*genetics ; Lipopolysaccharides/pharmacology ; Phylogeny ; Poly I-C/pharmacology ; Rhabdoviridae/physiology ; Rhabdoviridae Infections/immunology/veterinary ; Sequence Alignment/veterinary ; TNF Receptor-Associated Death Domain Protein/chemistry/*genetics/*immunology ; }, abstract = {Tumor necrosis factor receptor 1 (TNFR1) associated death domain protein (TRADD) is a pivotal adaptor in TNF signaling pathway and up-regulates MAVS/IFN signaling pathway in human and mammal. However, the role of TRADD in teleost fish remains obscure. To reveal the function of teleost TRADD in the innate immune response, the TRADD homologue (bcTRADD) of black carp (Mylopharyngodon piceus) has been cloned and the function of bcTRADD is investigated in this study, which shares similar functional domain to its mammalian counterpart. bcTRADD mRNA expression level increased in response to different stimuli, including LPS, poly (I:C) and virus infection in host cells. bcTRADD activated the transcriptional activity of NF-κB promoter in the reporter assay; however, showed hardly any effect on the transcriptional activity of IFN promoter. It was interesting that black carp mitochondria antiviral signaling protein (bcMAVS)-activated IFN promoter transcription were dramatically depressed by bcTRADD and the C-terminal death domain of bcTRADD was indispensable for its regulation of bcMAVS. Accordingly, the plaque assay result showed that EPC cells co-expressing bcMAVS and bcTRADD presented much attenuated antiviral activity than EPC cells expressing bcMAVS alone. Knockdown of bcTRADD slightly promoted the antiviral ability of the host cells against SVCV. The current data support the conclusion that bcTRADD suppresses MAVS-mediated antiviral signaling, which is different to its mammalian counterpart.}, }
@article {pmid33510273, year = {2021}, author = {Park, HS and Lee, WK and Lee, SC and Lee, HO and Joh, HJ and Park, JY and Kim, S and Song, K and Yang, TJ}, title = {Inheritance of chloroplast and mitochondrial genomes in cucumber revealed by four reciprocal F1 hybrid combinations.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2506}, pmid = {33510273}, issn = {2045-2322}, mesh = {Cucumis sativus/*genetics ; Evolution, Molecular ; Genetic Markers ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Genomics/methods ; *Hybridization, Genetic ; *Inheritance Patterns ; Plant Breeding ; Polymorphism, Genetic ; }, abstract = {Both genomes in chloroplasts and mitochondria of plant cell are usually inherited from maternal parent, with rare exceptions. To characterize the inheritance patterns of the organelle genomes in cucumber (Cucumis sativus var. sativus), two inbred lines and their reciprocal F1 hybrids were analyzed using an next generation whole genome sequencing data. Their complete chloroplast genome sequences were de novo assembled, and a single SNP was identified between the parental lines. Two reciprocal F1 hybrids have the same chloroplast genomes with their maternal parents. Meanwhile, 292 polymorphic sites were identified between mitochondrial genomes of the two parental lines, which showed the same genotypes with their paternal parents in the two reciprocal F1 hybrids, without any recombination. The inheritance patterns of the chloroplast and mitochondria genomes were also confirmed in four additional cucumber accessions and their six reciprocal F1 hybrids using molecular markers derived from the identified polymorphic sites. Taken together, our results indicate that the cucumber chloroplast genome is maternally inherited, as is typically observed in other plant species, whereas the large cucumber mitochondrial genome is paternally inherited. The combination of DNA markers derived from the chloroplast and mitochondrial genomes will provide a convenient system for purity test of F1 hybrid seeds in cucumber breeding.}, }
@article {pmid33510193, year = {2021}, author = {Zhang, K and Zhu, K and Liu, Y and Zhang, H and Gong, L and Jiang, L and Liu, L and Lü, Z and Liu, B}, title = {Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2411}, pmid = {33510193}, issn = {2045-2322}, mesh = {Animals ; Base Sequence ; Codon ; Eels/*classification/*genetics ; *Gene Rearrangement ; Genes, Mitochondrial ; *Genome, Mitochondrial ; *Genomics/methods ; Nucleic Acid Conformation ; *Phylogeny ; }, abstract = {The structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.}, }
@article {pmid33507977, year = {2021}, author = {Dryomov, SV and Nazhmidenova, AM and Starikovskaya, EB and Shalaurova, SA and Rohland, N and Mallick, S and Bernardos, R and Derevianko, AP and Reich, D and Sukernik, RI}, title = {Mitochondrial genome diversity on the Central Siberian Plateau with particular reference to the prehistory of northernmost Eurasia.}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0244228}, pmid = {33507977}, issn = {1932-6203}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {DNA, Mitochondrial/chemistry/classification/genetics/history ; Genetic Linkage ; Genetic Variation ; *Genome, Mitochondrial ; Haplotypes ; History, Ancient ; Human Migration ; Humans ; Mitochondria/*genetics ; Phylogeny ; Siberia ; }, abstract = {The Central Siberian Plateau was the last geographic area in Eurasia to become habitable by modern humans after the Last Glacial Maximum (LGM). Through a comprehensive dataset of mitochondrial DNA (mtDNA) genomes retained in the remnats of earlier ("Old") Siberians, primarily the Ket, Tofalar, and Todzhi, we explored genetic links between the Yenisei-Sayan region and Northeast Eurasia (best represented by the Yukaghir) over the last 10,000 years. We generated 218 new complete mtDNA sequences and placed them into compound phylogenies with 7 newly obtained and 70 published ancient mitochondrial genomes. We have considerably extended the mtDNA sequence diversity (at the entire mtDNA genome level) of autochthonous Siberians, which remain poorly sampled, and these new data may have a broad impact on the study of human migration. We compared present-day mtDNA diversity in these groups with complete mitochondrial genomes from ancient samples from the region and placed the samples into combined genealogical trees. The resulting components were used to clarify the origins and expansion history of mtDNA lineages that evolved in the refugia of south-central Siberia and beyond, as well as multiple phases of connection between this region and distant parts of Eurasia.}, }
@article {pmid33507545, year = {2021}, author = {Li, J and Meng, Q and Fu, Y and Yu, X and Ji, T and Chao, Y and Chen, Q and Li, Y and Bian, H}, title = {Novel insights: Dynamic foam cells derived from the macrophage in atherosclerosis.}, journal = {Journal of cellular physiology}, volume = {236}, number = {9}, pages = {6154-6167}, doi = {10.1002/jcp.30300}, pmid = {33507545}, issn = {1097-4652}, mesh = {Animals ; Atherosclerosis/*pathology ; Cell Communication ; Cholesterol/metabolism ; Esterification ; Foam Cells/metabolism/*pathology ; Humans ; Metabolome ; }, abstract = {Atherosclerosis can be regarded as a chronic disease derived from the interaction between disordered lipoproteins and an unsuitable immune response. The evolution of foam cells is not only a significant pathological change in the early stage of atherosclerosis but also a key stage in the occurrence and development of atherosclerosis. The formation of foam cells is mainly caused by the imbalance among lipids uptake, lipids treatment, and reverse cholesterol transport. Although a large number of studies have summarized the source of foam cells and the mechanism of foam cells formation, we propose a new idea about foam cells in atherosclerosis. Rather than an isolated microenvironment, the macrophage multiple lipid uptake pathways, lipid internalization, lysosome, mitochondria, endoplasmic reticulum, neutral cholesterol ester hydrolase (NCEH), acyl-coenzyme A-cholesterol acyltransferase (ACAT), and reverse cholesterol transport are mutually influential, and form a dynamic process under multi-factor regulation. The macrophage takes on different uptake lipid statuses depending on multiple uptake pathways and intracellular lipids, lipid metabolites versus pro-inflammatory factors. Except for NCEH and ACAT, the lipid internalization of macrophages also depends on multicellular organelles including the lysosome, mitochondria, and endoplasmic reticulum, which are associated with each other. A dynamic balance between esterification and hydrolysis of cholesterol for macrophages is essential for physiology and pathology. Therefore, we propose that the foam cell in the process of atherosclerosis may be dynamic under multi-factor regulation, and collate this study to provide a holistic and dynamic idea of the foam cell.}, }
@article {pmid33502469, year = {2021}, author = {Han, KL and Barreto, FS}, title = {Pervasive Mitonuclear Coadaptation Underlies Fast Development in Interpopulation Hybrids of a Marine Crustacean.}, journal = {Genome biology and evolution}, volume = {13}, number = {3}, pages = {}, pmid = {33502469}, issn = {1759-6653}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Biological Evolution ; Cell Nucleus/genetics ; Copepoda/*genetics ; *Evolution, Molecular ; Female ; Gene Frequency ; Gene Pool ; Genetic Fitness ; Genome, Mitochondrial/*genetics ; *Hybridization, Genetic ; Male ; Mitochondria/genetics ; Sequence Analysis ; }, abstract = {Cellular energy production requires coordinated interactions between genetic components from the nuclear and mitochondrial genomes. This coordination results in coadaptation of interacting elements within populations. Interbreeding between divergent gene pools can disrupt coadapted loci and result in hybrid fitness breakdown. While specific incompatible loci have been detected in multiple eukaryotic taxa, the extent of the nuclear genome that is influenced by mitonuclear coadaptation is not clear in any species. Here, we used F2 hybrids between two divergent populations of the copepod Tigriopus californicus to examine mitonuclear coadaptation across the nuclear genome. Using developmental rate as a measure of fitness, we found that fast-developing copepods had higher ATP synthesis capacity than slow developers, suggesting variation in developmental rates is at least partly associated with mitochondrial dysfunction. Using Pool-seq, we detected strong biases for maternal alleles across 7 (of 12) chromosomes in both reciprocal crosses in high-fitness hybrids, whereas low-fitness hybrids showed shifts toward the paternal population. Comparison with previous results on a different hybrid cross revealed largely different patterns of strong mitonuclear coadaptation associated with developmental rate. Our findings suggest that functional coadaptation between interacting nuclear and mitochondrial components is reflected in strong polygenic effects on this life-history phenotype, and reveal that molecular coadaptation follows independent evolutionary trajectories among isolated populations.}, }
@article {pmid37309528, year = {2021}, author = {Yang, W and Zou, J and Yu, Y and Long, W and Li, S}, title = {Repeats in mitochondrial and chloroplast genomes characterize the ecotypes of the Oryza.}, journal = {Molecular breeding : new strategies in plant improvement}, volume = {41}, number = {1}, pages = {7}, pmid = {37309528}, issn = {1572-9788}, abstract = {UNLABELLED: Mitochondria and chloroplast are very important organelles for organism, participating in basic life activity. Their genomes contain many repeats which can lead to a variation of genome structure. Oryza is an important genus for human beings' nutrition. Several mitochondrial and chloroplast genomes of Oryza have been sequenced, which help us to insight the distribution and evolution of the repeats in Oryza species. In this paper, we compared six mitochondrial and 13 chloroplast genomes of Oryza and found that the structures of mitochondrial genomes were more diverse than chloroplast genomes. Since repeats can change the structure of the genome, resulting in the structural diversity of the genome, we analyzed all repeats and found 31 repeats in mitochondrial and 13 repeats in chloroplast genomes. Further, we developed 21 pairs of MRS molecular markers and 12 pairs of CRS molecular markers based on mitochondrial repeats and chloroplast repeats, respectively. These molecular markers can be used to detect the repeat-mediated recombination in Oryza mitochondrial and chloroplast genomes by PCR or fluorescence quantification.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-020-01198-6.}, }
@article {pmid35372951, year = {2020}, author = {Chevalier, RL}, title = {Bioenergetic Evolution Explains Prevalence of Low Nephron Number at Birth: Risk Factor for CKD.}, journal = {Kidney360}, volume = {1}, number = {8}, pages = {863-879}, pmid = {35372951}, issn = {2641-7650}, mesh = {Adult ; Energy Metabolism/genetics ; Female ; Humans ; Infant, Newborn ; Male ; *Nephrons ; Placenta/metabolism ; Pregnancy ; *Premature Birth/metabolism ; Prevalence ; *Renal Insufficiency, Chronic/epidemiology ; Risk Factors ; }, abstract = {There is greater than tenfold variation in nephron number of the human kidney at birth. Although low nephron number is a recognized risk factor for CKD, its determinants are poorly understood. Evolutionary medicine represents a new discipline that seeks evolutionary explanations for disease, broadening perspectives on research and public health initiatives. Evolution of the kidney, an organ rich in mitochondria, has been driven by natural selection for reproductive fitness constrained by energy availability. Over the past 2 million years, rapid growth of an energy-demanding brain in Homo sapiens enabled hominid adaptation to environmental extremes through selection for mutations in mitochondrial and nuclear DNA epigenetically regulated by allocation of energy to developing organs. Maternal undernutrition or hypoxia results in intrauterine growth restriction or preterm birth, resulting in low birth weight and low nephron number. Regulated through placental transfer, environmental oxygen and nutrients signal nephron progenitor cells to reprogram metabolism from glycolysis to oxidative phosphorylation. These processes are modulated by counterbalancing anabolic and catabolic metabolic pathways that evolved from prokaryote homologs and by hypoxia-driven and autophagy pathways that evolved in eukaryotes. Regulation of nephron differentiation by histone modifications and DNA methyltransferases provide epigenetic control of nephron number in response to energy available to the fetus. Developmental plasticity of nephrogenesis represents an evolved life history strategy that prioritizes energy to early brain growth with adequate kidney function through reproductive years, the trade-off being increasing prevalence of CKD delayed until later adulthood. The research implications of this evolutionary analysis are to identify regulatory pathways of energy allocation directing nephrogenesis while accounting for the different life history strategies of animal models such as the mouse. The clinical implications are to optimize nutrition and minimize hypoxic/toxic stressors in childbearing women and children in early postnatal development.}, }
@article {pmid34005357, year = {2020}, author = {Mélanie, B and Caroline, R and Claude, D and Frédéric, V and Sabrina, R and Damien, R and Yann, V}, title = {Improved mitochondrial coupling as a response to high mass-specific metabolic rate in extremely small mammals.}, journal = {The Journal of experimental biology}, volume = {}, number = {}, pages = {}, doi = {10.1242/jeb.215558}, pmid = {34005357}, issn = {1477-9145}, abstract = {Mass-specific metabolic rate negatively co-varies with body mass from the whole-animal to the mitochondrial levels. Mitochondria are the mainly consumers of oxygen inspired by mammals to generate ATP or compensate energetic losses dissipated as the form of heat (proton leak) during oxidative phosphorylation. Consequently, ATP synthesis and proton leak thus compete for the same electrochemical gradient. Because proton leak co-varies negatively with body mass, it is unknown if extremely small mammals further decouple their mitochondria to maintain their body temperature or if they implement metabolic innovations to ensure cellular homeostasis. The present study investigates the impact of body mass variation on cellular and mitochondrial functioning in small mammals, comparing the two extremely small African pygmy mice (Mus mattheyi, approx. 5 g and Mus minutoides, approx. 7 g) with the larger house mouse (Mus musculus, approx. 22 g). Oxygen consumption rates were measured from the animal to the mitochondrial levels. We also measured mitochondrial ATP synthesis in order to appreciate the mitochondrial efficiency (ATP/O). At the whole-animal scale, mass- and surface-specific metabolic rates co-varied negatively with body mass, whereas this was not necessarily the case at cellular and mitochondrial levels. M. mattheyi had generally the lowest cellular and mitochondrial fluxes, depending on the tissue considered (liver or skeletal muscle), as well as having higher efficient muscle mitochondria than the other two species. M. mattheyi presents metabolic innovations to ensure its homeostasis, by generating more ATP per oxygen consumed.}, }
@article {pmid33837704, year = {2020}, author = {Chihade, J}, title = {Mitochondrial aminoacyl-tRNA synthetases.}, journal = {The Enzymes}, volume = {48}, number = {}, pages = {175-206}, doi = {10.1016/bs.enz.2020.07.003}, pmid = {33837704}, issn = {0423-2607}, mesh = {*Amino Acyl-tRNA Synthetases/genetics ; Cytosol ; Eukaryotic Cells ; Humans ; Mitochondria/genetics ; RNA, Transfer ; }, abstract = {In all eukaryotic cells, protein synthesis occurs not only in the cytosol, but also in the mitochondria. Translation of mitochondrial genes requires a set of aminoacyl-tRNA synthetases, many of which are often specialized for organellar function. These enzymes have evolved unique mechanisms for tRNA recognition and for ensuring fidelity of translation. Mutations of human mitochondrial synthetases are associated with a wide range of pathogenic phenotypes, both highlighting the importance of their role in maintaining the cellular "powerhouse" and suggesting additional cellular roles.}, }
@article {pmid36659315, year = {2017}, author = {Ye, LQ and Zhao, H and Zhou, HJ and Ren, XD and Liu, LL and Otecko, NO and Wang, ZB and Yang, MM and Zeng, L and Hu, XT and Yao, YG and Zhang, YP and Wu, DD}, title = {The RNA editome of Macaca mulatta and functional characterization of RNA editing in mitochondria.}, journal = {Science bulletin}, volume = {62}, number = {12}, pages = {820-830}, doi = {10.1016/j.scib.2017.05.021}, pmid = {36659315}, issn = {2095-9281}, abstract = {RNA editing was first discovered in mitochondrial RNA molecular. However, whether adenosine-to-inosine (A-to-I) RNA editing has functions in nuclear genes involved in mitochondria remains elusive. Here, we retrieved 707,246 A-to-I RNA editing sites in Macaca mulatta leveraging massive transcriptomes of 30 different tissues and genomes of nine tissues, together with the reported data, and found that A-to-I RNA editing occurred frequently in nuclear genes that have functions in mitochondria. The mitochondrial structure, the level of ATP production, and the expression of some key genes involved in mitochondrial function were dysregulated after knocking down the expression of ADAR1 and ADAR2, the key genes encoding the enzyme responsible for RNA editing. When investigating dynamic changes of RNA editing during brain development, an amino-acid-changing RNA editing site (I234/V) in MFN1, a mediator of mitochondrial fusion, was identified to be significantly correlated with age, and could influence the function of MFN1. When studying transcriptomes of brain disorder, we found that dysregulated RNA editing sites in autism were also enriched within genes having mitochondrial functions. These data indicated that RNA editing had a significant function in mitochondria via their influence on nuclear genes.}, }
@article {pmid33873653, year = {2003}, author = {Logan, DC}, title = {Mitochondrial dynamics.}, journal = {The New phytologist}, volume = {160}, number = {3}, pages = {463-478}, pmid = {33873653}, issn = {1469-8137}, abstract = {Mitochondria cannot be created de novo but instead must arise from the fission (division) of a parental organelle. In addition to fission, mitochondria also fuse with one another and it is thought that a co-ordinated balance of these two processes controls mitochondrial shape, size and number. In the past 5-7 yr, molecular genetics coupled to state-of-the-art cell biology, in particular the use of mitochondrial-targeted green fluorescent protein (GFP), has enabled identification of proteins controlling mitochondrial shape, size and number in yeast and mammalian cells. Little is known about higher plant mitochondrial dynamics. Recently, however, several genes involved in the control of plant mitochondrial dynamics have been identified. The aim of this article is to bring together what is known about mitochondrial dynamics in any organisms and to relate this to our recent knowledge of the underlying processes in higher plants. Contents Summary 463 I. Introduction 464 II. Mitochondrial evolution 464 III. Mitochondria and the cytoskeleton 465 IV. Mitochondrial morphology, biogenesis, proliferation and inheritance 466 V. Mitochondrial fission and fusion 468 VI. Mitochondrial distribution 470 VII. Plant specific proteins playing a role in mitochondrial dynamics 470 VIII. Conclusions 471 Acknowledgements 475 References 475.}, }
@article {pmid37282330, year = {1989}, author = {Andreuccetti, P}, title = {Ultrastructural Observations on the Germ Plasm in the Lizard Podarcis sicula: (germ plasm/germ cells/ultrastructure/reptiles).}, journal = {Development, growth &amp; differentiation}, volume = {31}, number = {3}, pages = {269-273}, doi = {10.1111/j.1440-169X.1989.00269.x}, pmid = {37282330}, issn = {1440-169X}, abstract = {Ultrastructural studies on embryos and adult females of Podarcis sicula revealed fibrogranular electron-dense aggregates in the cytoplasm of primordial germ cells, oogonia, and oocytes. The ultrastructural similarities of these aggregates to fibrogranular aggregates in germ cells of some animal species and their relationship with mitochondria, free ribosomes, as well as cisternae of the rough endoplasmic reticulum strongly suggest that they correspond to the germ plasm.}, }
@article {pmid33873942, year = {1988}, author = {Fahn, A}, title = {Secretory tissues in vascular plants.}, journal = {The New phytologist}, volume = {108}, number = {3}, pages = {229-257}, doi = {10.1111/j.1469-8137.1988.tb04159.x}, pmid = {33873942}, issn = {1469-8137}, abstract = {Secretory tissues occur in most vascular plants. Some of these tissues, such as hydathodes, salt glands and nectaries, secrete unmodified or only slightly modified substances supplied directly or indirectly by the vascular tissues. Other tissues secreting, for instance, polysaccharides, proteins and lipophilic material, produce these substances in their cells. The cells of secretory tissues usually contain numerous mitochondria. The frequency of other cell organelles varies according to the material secreted. In most glandular trichomes the side wall of the lowest stalk cell is completely cutinized. This prevents the secreted material from flowing back into the plant. The salt glands in Atriplex eliminate salt into the central vacuole of the bladder cell but, in other plants, the glands secrete salt to the outside. Different views exist as to the manner in which salt is eliminated from the cytoplasm. According to some authors, the mode of elimination is an eccrine one, while others suggest the involvement of membrane-bound vesicles. Nectar is of phloem origin. The pre-nectar moves to the secretory cells through numerous plasmodesmata present in the nectariferous tissue. Nectar is eliminated from the secretory cells by vesicles of either KR or dictyosomal origin. In some cases, both organelles may be involved but an eccrine mode of nectar secretion has also been suggested by some authors. Carbohydrate mucilages and gums are synthesized by dictyosomes but virtually every cell compartment has been suggested as having a role on the secretion of lipophilic substances. Most commonly, plastids are implicated in the synthesis of lipophilic materials but KR may also play a part. In some cases lipophilic materials may be transported towards the plasmalemma in the KR. Resin and gum ducts of some plants develop normally or in response to external stimuli, such as microorganisms or growth substances. Among the latter, ethylene is the most effective. During the course of evolution, secretory tissues seem to have developed from secretory idioblasts scattered among the cells of the ordinary tissues. Subsequently ducts and cavities developed and finally secretory trichomes. CONTENTS Summary 229 I. Introduction 230 II. Salt glands 231 III. Nectaries 236 IV. Mucilages and gums 241 V. Tissues secreting lipophilic material 242 VI. Factors influencing the development of certain secretory tissues 246 VII. Evolutionary considerations 248 References 250.}, }
@article {pmid33498264, year = {2021}, author = {Gladyck, S and Aras, S and Hüttemann, M and Grossman, LI}, title = {Regulation of COX Assembly and Function by Twin CX9C Proteins-Implications for Human Disease.}, journal = {Cells}, volume = {10}, number = {2}, pages = {}, pmid = {33498264}, issn = {2073-4409}, support = {W81XWH-16-1-0516//U.S. Department of Defense/ ; R01 GM116807/GF/NIH HHS/United States ; HHSN275201300006C/HD/NICHD NIH HHS/United States ; }, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; *Disease ; Electron Transport Complex IV/*chemistry/*metabolism ; Humans ; Phylogeny ; Protein Binding ; Protein Subunits/chemistry/metabolism ; }, abstract = {Oxidative phosphorylation is a tightly regulated process in mammals that takes place in and across the inner mitochondrial membrane and consists of the electron transport chain and ATP synthase. Complex IV, or cytochrome c oxidase (COX), is the terminal enzyme of the electron transport chain, responsible for accepting electrons from cytochrome c, pumping protons to contribute to the gradient utilized by ATP synthase to produce ATP, and reducing oxygen to water. As such, COX is tightly regulated through numerous mechanisms including protein-protein interactions. The twin CX9C family of proteins has recently been shown to be involved in COX regulation by assisting with complex assembly, biogenesis, and activity. The twin CX9C motif allows for the import of these proteins into the intermembrane space of the mitochondria using the redox import machinery of Mia40/CHCHD4. Studies have shown that knockdown of the proteins discussed in this review results in decreased or completely deficient aerobic respiration in experimental models ranging from yeast to human cells, as the proteins are conserved across species. This article highlights and discusses the importance of COX regulation by twin CX9C proteins in the mitochondria via COX assembly and control of its activity through protein-protein interactions, which is further modulated by cell signaling pathways. Interestingly, select members of the CX9C protein family, including MNRR1 and CHCHD10, show a novel feature in that they not only localize to the mitochondria but also to the nucleus, where they mediate oxygen- and stress-induced transcriptional regulation, opening a new view of mitochondrial-nuclear crosstalk and its involvement in human disease.}, }
@article {pmid33495511, year = {2021}, author = {Subramanian, V and Rodemoyer, B and Shastri, V and Rasmussen, LJ and Desler, C and Schmidt, KH}, title = {Bloom syndrome DNA helicase deficiency is associated with oxidative stress and mitochondrial network changes.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2157}, pmid = {33495511}, issn = {2045-2322}, support = {R01 GM081425/GM/NIGMS NIH HHS/United States ; R01 GM139296/GM/NIGMS NIH HHS/United States ; }, mesh = {Autophagy ; Bloom Syndrome/*enzymology/*pathology ; Cyclin B1/metabolism ; DNA Damage ; DNA Replication ; DNA-Binding Proteins/metabolism ; Energy Metabolism ; Fibroblasts/enzymology/pathology ; G1 Phase ; Humans ; Mitochondria/*metabolism/ultrastructure ; Mitochondrial Proteins/metabolism ; Mitosis ; *Oxidative Stress ; Reactive Oxygen Species/metabolism ; RecQ Helicases/*deficiency/metabolism ; Transcription Factors/metabolism ; Up-Regulation ; }, abstract = {Bloom Syndrome (BS; OMIM #210900; ORPHA #125) is a rare genetic disorder that is associated with growth deficits, compromised immune system, insulin resistance, genome instability and extraordinary predisposition to cancer. Most efforts thus far have focused on understanding the role of the Bloom syndrome DNA helicase BLM as a recombination factor in maintaining genome stability and suppressing cancer. Here, we observed increased levels of reactive oxygen species (ROS) and DNA base damage in BLM-deficient cells, as well as oxidative-stress-dependent reduction in DNA replication speed. BLM-deficient cells exhibited increased mitochondrial mass, upregulation of mitochondrial transcription factor A (TFAM), higher ATP levels and increased respiratory reserve capacity. Cyclin B1, which acts in complex with cyclin-dependent kinase CDK1 to regulate mitotic entry and associated mitochondrial fission by phosphorylating mitochondrial fission protein Drp1, fails to be fully degraded in BLM-deficient cells and shows unscheduled expression in G1 phase cells. This failure to degrade cyclin B1 is accompanied by increased levels and persistent activation of Drp1 throughout mitosis and into G1 phase as well as mitochondrial fragmentation. This study identifies mitochondria-associated abnormalities in Bloom syndrome patient-derived and BLM-knockout cells and we discuss how these abnormalities may contribute to Bloom syndrome.}, }
@article {pmid33494532, year = {2021}, author = {Kirkland, C and Farré, M}, title = {Mitochondrial Genome Evolution, Genetic Diversity, and Population Structure in British Water Voles (Arvicola amphibius).}, journal = {Genes}, volume = {12}, number = {2}, pages = {}, pmid = {33494532}, issn = {2073-4425}, mesh = {Animals ; Arvicolinae/classification/*genetics ; *Evolution, Molecular ; *Genetic Variation ; Genetics, Population ; *Genome, Mitochondrial ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {The European water vole (Arvicola amphibius) is a rodent within the subfamily Arvicolinae. In Britain, water voles have declined rapidly during the last century, making them a conservation priority. The relationship of Arvicola to other genera within Arvicolinae remains debated. Additionally, the impact that captive breeding programs in Britain are having on the genetic diversity of water voles is unknown. We use available mitochondrial genomes to construct the phylogeny of species within Arvicolinae, followed by sequencing the mitochondrial DNA control region of 17 individuals from a captive population of water voles in Britain to assess their genetic diversity and population structure. Our study first provides an updated phylogenetic tree of Arvicolinae using the mitochondrial genome of 31 species. Second, our results show considerable genetic diversity in the captive population of water voles, when compared with natural populations in Britain. We confirm the grouping of British water voles into two clades, with all captive individuals found in the English/Welsh clade. Moreover, captive water voles clustered closely with populations in the South East and East of England. The mitochondrial genome provides a useful marker to study the phylogenetics of this rodent clade and in addition, our study provides support for the breeding program at Wildwood Trust and provides a framework for future conservation genetics studies in this species.}, }
@article {pmid33493156, year = {2021}, author = {Neverov, AD and Popova, AV and Fedonin, GG and Cheremukhin, EA and Klink, GV and Bazykin, GA}, title = {Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins.}, journal = {PLoS genetics}, volume = {17}, number = {1}, pages = {e1008711}, pmid = {33493156}, issn = {1553-7404}, mesh = {Amino Acid Substitution/genetics ; Amino Acids/genetics ; Animals ; *Epistasis, Genetic ; *Evolution, Molecular ; Fungi/genetics ; Genome, Mitochondrial/genetics ; Mitochondria/genetics ; Mitochondrial Proteins/*genetics ; Phylogeny ; Protein Conformation ; Protein Interaction Maps/genetics ; *Selection, Genetic ; }, abstract = {The rate of evolution differs between protein sites and changes with time. However, the link between these two phenomena remains poorly understood. Here, we design a phylogenetic approach for distinguishing pairs of amino acid sites that evolve concordantly, i.e., such that substitutions at one site trigger subsequent substitutions at the other; and also pairs of sites that evolve discordantly, so that substitutions at one site impede subsequent substitutions at the other. We distinguish groups of amino acid sites that undergo coordinated evolution and evolve discordantly from other such groups. In mitochondrion-encoded proteins of metazoans and fungi, we show that concordantly evolving sites are clustered in protein structures. By analysing the phylogenetic patterns of substitutions at concordantly and discordantly evolving site pairs, we find that concordant evolution has two distinct causes: epistatic interactions between amino acid substitutions and episodes of selection independently affecting substitutions at different sites. The rate of substitutions at concordantly evolving groups of protein sites changes in the course of evolution, indicating episodes of selection limited to some of the lineages. The phylogenetic positions of these changes are consistent between proteins, suggesting common selective forces underlying them.}, }
@article {pmid33490584, year = {2021}, author = {Eo, JK}, title = {The complete mitogenome of Diaporthe nobilis.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {6}, number = {1}, pages = {6-7}, pmid = {33490584}, issn = {2380-2359}, abstract = {The complete mitogenome of Diaporthe nobilis NIE8444 (KCTC No. 56710) isolated from alpine conifer Abies nephrolepis is determined by the Illumina Hiseq4000 platform in this study. This mitogenome consists of 67,437 bp length with 31.45% G + C content. A total of 51 genes were predicted in this mitogenome: 21 protein-coding genes, 2 rRNAs and 28 tRNAs. Phylogenetic tree based on small subunit ribosomal RNA of mitochondria showed that D. nobilis was close to D. longicolla. This complete mitogenome of D. nobilis provides valuable information on the mitochondrial evolution of endophytic fungi.}, }
@article {pmid33487111, year = {2021}, author = {Wan, KY and Jékely, G}, title = {Origins of eukaryotic excitability.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {376}, number = {1820}, pages = {20190758}, pmid = {33487111}, issn = {1471-2970}, mesh = {*Biological Evolution ; Eukaryota/*physiology ; Eukaryotic Cells/*physiology ; }, abstract = {All living cells interact dynamically with a constantly changing world. Eukaryotes, in particular, evolved radically new ways to sense and react to their environment. These advances enabled new and more complex forms of cellular behaviour in eukaryotes, including directional movement, active feeding, mating, and responses to predation. But what are the key events and innovations during eukaryogenesis that made all of this possible? Here we describe the ancestral repertoire of eukaryotic excitability and discuss five major cellular innovations that enabled its evolutionary origin. The innovations include a vastly expanded repertoire of ion channels, the emergence of cilia and pseudopodia, endomembranes as intracellular capacitors, a flexible plasma membrane and the relocation of chemiosmotic ATP synthesis to mitochondria, which liberated the plasma membrane for more complex electrical signalling involved in sensing and reacting. We conjecture that together with an increase in cell size, these new forms of excitability greatly amplified the degrees of freedom associated with cellular responses, allowing eukaryotes to vastly outperform prokaryotes in terms of both speed and accuracy. This comprehensive new perspective on the evolution of excitability enriches our view of eukaryogenesis and emphasizes behaviour and sensing as major contributors to the success of eukaryotes. This article is part of the theme issue 'Basal cognition: conceptual tools and the view from the single cell'.}, }
@article {pmid33486550, year = {2021}, author = {Christensen, AC}, title = {Plant Mitochondria are a Riddle Wrapped in a Mystery Inside an Enigma.}, journal = {Journal of molecular evolution}, volume = {89}, number = {3}, pages = {151-156}, pmid = {33486550}, issn = {1432-1432}, mesh = {*Cell Nucleus ; *Evolution, Molecular ; Mitochondria/genetics ; Mutation ; Phylogeny ; }, abstract = {A fundamental paradox motivates the study of plant mitochondrial genomics: the mutation rate is very low (lower than in the nucleus) but the rearrangement rate is high. A landmark paper published in Journal of Molecular Evolution in 1988 established these facts and revealed the paradox. Jeffrey Palmer and Laura Herbon did a prodigious amount of work in the pre-genome sequencing era to identify both the high frequency of rearrangements between closely related species, and the low frequency of mutations, observations that have now been confirmed many times by sequencing. This paper was also the first to use molecular data on rearrangements as a phylogenetic trait to build a parsimonious tree. The work was a technical tour-de-force, its findings are still at the heart of plant mitochondrial genomics, and the underlying molecular mechanisms that produce this paradox are still not completely understood.}, }
@article {pmid33482383, year = {2021}, author = {Phillips, MJ and Shazwani Zakaria, S}, title = {Enhancing mitogenomic phylogeny and resolving the relationships of extinct megafaunal placental mammals.}, journal = {Molecular phylogenetics and evolution}, volume = {158}, number = {}, pages = {107082}, doi = {10.1016/j.ympev.2021.107082}, pmid = {33482383}, issn = {1095-9513}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/classification/genetics ; Eutheria/genetics ; Female ; Genetic Heterogeneity ; Likelihood Functions ; Mammals/classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; Pregnancy ; }, abstract = {Mitochondrial genomes provided the first widely used sequences that were sufficiently informative to resolve relationships among animals across a wide taxonomic domain, from within species to between phyla. However, mitogenome studies supported several anomalous relationships and fell partly out of favour as sequencing multiple, independent nuclear loci proved to be highly effective. A tendency to blame mitochondrial DNA (mtDNA) has overshadowed efforts to understand and ameliorate underlying model misspecification. Here we find that influential assessments of the infidelity of mitogenome phylogenies have often been overstated, but nevertheless, substitution saturation and compositional non-stationarity substantially mislead reconstruction. We show that RY coding the mtDNA, excluding protein-coding 3rd codon sites, partitioning models based on amino acid hydrophobicity and enhanced taxon sampling improve the accuracy of mitogenomic phylogeny reconstruction for placental mammals, almost to the level of multi-gene nuclear datasets. Indeed, combined analysis of mtDNA with 3-fold longer nuclear sequence data either maintained or improved upon the nuclear support for all generally accepted clades, even those that mtDNA alone did not favour, thus indicating "hidden support". Confident mtDNA phylogeny reconstruction is especially important for understanding the evolutionary dynamics of mitochondria themselves, and for merging extinct taxa into the tree of life, with ancient DNA often only accessible as mtDNA. Our ancient mtDNA analyses lend confidence to the relationships of three extinct megafaunal taxa: glyptodonts are nested within armadillos, the South American ungulate, Macrauchenia is sister to horses and rhinoceroses, and sabre-toothed and scimitar cats are the monophyletic sister-group of modern cats.}, }
@article {pmid33482382, year = {2021}, author = {Irwin, AR and Strong, EE and Kano, Y and Harper, EM and Williams, ST}, title = {Eight new mitogenomes clarify the phylogenetic relationships of Stromboidea within the caenogastropod phylogenetic framework.}, journal = {Molecular phylogenetics and evolution}, volume = {158}, number = {}, pages = {107081}, doi = {10.1016/j.ympev.2021.107081}, pmid = {33482382}, issn = {1095-9513}, mesh = {Animals ; Gastropoda/classification/*genetics ; *Genome, Mitochondrial ; Mitochondria/classification/*genetics ; Mitochondrial Proteins/classification/genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal, 18S/classification/genetics ; RNA, Transfer/chemistry ; }, abstract = {Members of the gastropod superfamily Stromboidea (Littorinimorpha) are characterised by their elaborate shell morphologies, distinctive mode of locomotion, and often large and colourful eyes. This iconic group comprises over 130 species, including many large and charismatic species. The family Strombidae is of particular interest, largely due to its commercial importance and wide distribution in tropical and subtropical waters. Although a few strombid mitochondrial genomes have been sequenced, data for the other four Recent families in Stromboidea are lacking. In this study we report seven new stromboid mitogenomes obtained from transcriptomic and genomic data, with taxonomic representation from each Recent stromboid family, including the first mitogenomes for Aporrhaidae, Rostellariidae, Seraphsidae and Struthiolariidae. We also report a new mitogenome for the family Xenophoridae. We use these data, along with published sequences, to investigate the relationships among these and other caenogastropod groups. All analyses undertaken in this study support monophyly of Stromboidea as redefined here to include Xenophoridae, a finding consistent with morphological and behavioural data. Consistent with previous morphological and molecular analyses, including those based on mitogenomes, monophyly of Hypsogastropoda is confirmed but monophyly of Littorinimorpha is again rejected.}, }
@article {pmid33481018, year = {2021}, author = {Wazawa, T and Noma, R and Uto, S and Sugiura, K and Washio, T and Nagai, T}, title = {A photoswitchable fluorescent protein for hours-time-lapse and sub-second-resolved super-resolution imaging.}, journal = {Microscopy (Oxford, England)}, volume = {70}, number = {4}, pages = {340-352}, pmid = {33481018}, issn = {2050-5701}, support = {JPMJCR15N3//Core Research for Evolutional Science and Technology/ ; 23115003, 18H03987, 18H05410, 16K07322, 19K05226//Japan Society for the Promotion of Science/ ; }, mesh = {Luminescent Proteins/*chemistry ; Microscopy ; Time-Lapse Imaging/*methods ; }, abstract = {Reversibly photoswitchable fluorescent proteins (RSFPs) are a class of fluorescent proteins whose fluorescence can be turned on and off by light irradiation. RSFPs have become essential tools for super-resolution (SR) imaging. Because most SR imaging techniques require high-power-density illumination, mitigating phototoxicity in cells due to intense light irradiation has been a challenge. Although we previously developed an RSFP named Kohinoor to achieve SR imaging with low phototoxicity, the photoproperties were insufficient to move a step further to explore the cellular dynamics by SR imaging. Here, we show an improved version of RSFP, Kohinoor2.0, which is suitable for SR imaging of cellular processes. Kohinoor2.0 shows a 2.6-fold higher fluorescence intensity, 2.5-fold faster chromophore maturation and 1.5-fold faster off-switching than Kohinoor. The analysis of the pH dependence of the visible absorption band revealed that Kohinoor2.0 and Kohinoor were in equilibria among multiple fluorescently bright and dark states, with the mutations introduced into Kohinoor2.0 bringing about a higher stabilization of the fluorescently bright states compared to Kohinoor. Using Kohinoor2.0 with our SR imaging technique, super-resolution polarization demodulation/on-state polarization angle narrowing, we conducted 4-h time-lapse SR imaging of an actin filament network in mammalian cells with a total acquisition time of 480 s without a noticeable indication of phototoxicity. Furthermore, we demonstrated the SR imaging of mitochondria dynamics at a time resolution of 0.5 s, in which the fusion and fission processes were clearly visualized. Thus, Kohinoor2.0 is shown to be an invaluable RSFP for the SR imaging of cellular dynamics.}, }
@article {pmid33477742, year = {2021}, author = {Sunagar, K and Khochare, S and Senji Laxme, RR and Attarde, S and Dam, P and Suranse, V and Khaire, A and Martin, G and Captain, A}, title = {A Wolf in Another Wolf's Clothing: Post-Genomic Regulation Dictates Venom Profiles of Medically-Important Cryptic Kraits in India.}, journal = {Toxins}, volume = {13}, number = {1}, pages = {}, pmid = {33477742}, issn = {2072-6651}, support = {IAVI/BES/KASU/0002//Department for International Development, UK Government/ ; SR/FST/LS-II/2018/233//DST-FIST/ ; }, mesh = {Animals ; Antivenins/chemistry ; Biological Evolution ; Bungarotoxins/*chemistry ; Bungarus/classification/*genetics/*metabolism ; Gene Expression Profiling ; Gene Regulatory Networks ; Humans ; India ; Male ; Mice ; Mitochondria/genetics ; Molecular Typing ; Pakistan ; Phylogeny ; *Proteome ; Proteomics ; Species Specificity ; }, abstract = {The Common Krait (Bungarus caeruleus) shares a distribution range with many other 'phenotypically-similar' kraits across the Indian subcontinent. Despite several reports of fatal envenomings by other Bungarus species, commercial Indian antivenoms are only manufactured against B. caeruleus. It is, therefore, imperative to understand the distribution of genetically distinct lineages of kraits, the compositional differences in their venoms, and the consequent impact of venom variation on the (pre)clinical effectiveness of antivenom therapy. To address this knowledge gap, we conducted phylogenetic and comparative venomics investigations of kraits in Southern and Western India. Phylogenetic reconstructions using mitochondrial markers revealed a new species of krait, Romulus' krait (Bungarus romulusi sp. nov.), in Southern India. Additionally, we found that kraits with 17 mid-body dorsal scale rows in Western India do not represent a subspecies of the Sind Krait (B. sindanus walli) as previously believed, but are genetically very similar to B. sindanus in Pakistan. Furthermore, venom proteomics and comparative transcriptomics revealed completely contrasting venom profiles. While the venom gland transcriptomes of all three species were highly similar, venom proteomes and toxicity profiles differed significantly, suggesting the prominent role of post-genomic regulatory mechanisms in shaping the venoms of these cryptic kraits. In vitro venom recognition and in vivo neutralisation experiments revealed a strong negative impact of venom variability on the preclinical performance of commercial antivenoms. While the venom of B. caeruleus was neutralised as per the manufacturer's claim, performance against the venoms of B. sindanus and B. romulusi was poor, highlighting the need for regionally-effective antivenoms in India.}, }
@article {pmid33476615, year = {2021}, author = {Li, Q and Wu, P and Li, L and Feng, H and Tu, W and Bao, Z and Xiong, C and Gui, M and Huang, W}, title = {The first eleven mitochondrial genomes from the ectomycorrhizal fungal genus (Boletus) reveal intron loss and gene rearrangement.}, journal = {International journal of biological macromolecules}, volume = {172}, number = {}, pages = {560-572}, doi = {10.1016/j.ijbiomac.2021.01.087}, pmid = {33476615}, issn = {1879-0003}, mesh = {Amino Acid Sequence ; Basidiomycota/classification/*genetics/metabolism ; Biological Evolution ; Exons ; Forests ; Fungal Proteins/classification/*genetics/metabolism ; Genome Size ; *Genome, Mitochondrial ; Introns ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/classification/*genetics/metabolism ; Mycorrhizae/classification/*genetics/metabolism ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; Trees/microbiology ; }, abstract = {In the present study, eleven novel complete mitogenomes of Boletus were assembled and compared. The eleven complete mitogenomes were all composed of circular DNA molecules, with sizes ranging from 32,883 bp to 48,298 bp. The mitochondrial gene arrangement of Boletus varied greatly from other Boletales mitogenomes, and gene position reversal were observed frequently in the evolution of Boletus. Across the 15 core protein-coding genes (PCGs) tested, atp9 had the least and rps3 had the largest genetic distances among the eleven Boletus species, indicating varied evolution rates of core PCGs. In addition, the Ka/Ks value for nad3 gene was >1, suggesting that this gene was subject to possible positive selection pressure. Comparative mitogenomic analysis indicated that the intronic region was significantly correlated with the size of mitogenomes in Boletales. Two large-scale intron loss events were detected in the evolution of Boletus. Phylogenetic analyses based on a combined mitochondrial gene dataset yielded a well-supported (BPP ≥ 0.99; BS =100) phylogenetic tree for 72 Agaricomycetes, and the Boletus species had a close relationship with Paxillus. This study served as the first report on complete mitogenomes in Boletus, which will further promote investigations of the genetics, evolution and phylogeny of the Boletus genus.}, }
@article {pmid33475472, year = {2021}, author = {Fukuda, T and Kanki, T}, title = {Atg43, a novel autophagy-related protein, serves as a mitophagy receptor to bridge mitochondria with phagophores in fission yeast.}, journal = {Autophagy}, volume = {17}, number = {3}, pages = {826-827}, pmid = {33475472}, issn = {1554-8635}, mesh = {Animals ; Autophagosomes ; Autophagy ; Autophagy-Related Proteins ; Mitochondria ; *Mitophagy ; *Schizosaccharomyces ; }, abstract = {Mitophagy is a selective type of autophagy in which damaged or unnecessary mitochondria are sequestered by double-membranous structures called phagophores and delivered to vacuoles/lysosomes for degradation. The molecular mechanisms underlying mitophagy have been studied extensively in budding yeast and mammalian cells. To gain more diverse insights, our recent study identified Atg43 as a mitophagy receptor in the fission yeast Schizosaccharomyces pombe. Atg43 is localized on the mitochondrial outer membrane through the Mim1-Mim2 complex and binds to Atg8, a ubiquitin-like protein conjugated to phagophore membranes. Artificial tethering of Atg8 to mitochondria can bypass the requirement of Atg43 for mitophagy, suggesting that the main role of Atg43 in mitophagy is to stabilize phagophore expansion on mitochondria by interacting with Atg8. Atg43 shares no sequence similarity with mitophagy receptors in other organisms and has a mitophagy-independent function, raising the possibility that Atg43 has acquired the mitophagic function by convergent evolution.}, }
@article {pmid33458207, year = {2020}, author = {Huang, X and Shi, Y and Huang, D and Shen, X and Wang, Y and Chen, J and Cai, Y}, title = {Characterization of the complete mitochondrial DNA sequence of the Lagocephalus guentheri (Tetraodontidae, Tetraodontiformes).}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {5}, number = {3}, pages = {3472-3473}, pmid = {33458207}, issn = {2380-2359}, abstract = {The complete mitochondrial genome of Lagocephalus guentheri was reported in the present study, which was 16,461 bp in length. It consists of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding control region. The overall base composition of the genome is 27.54% for A, 24.80% for T, 31.23% for C and 16.43% for G. The phylogenetic tree, which is based on 12 protein-coding gene sequences, suggested that L. guentheri was closest to L. spadiceus. This study could give impetus to studies focused on population structure and molecular evolution of L. guentheri.}, }
@article {pmid33457843, year = {2020}, author = {Chen, Z and Zhao, J and Qiao, J and Li, W and Li, J and Xu, R and Wang, H and Liu, Z and Xing, B and Wendel, JF and Grover, CE}, title = {Comparative analysis of codon usage between Gossypium hirsutum and G. barbadense mitochondrial genomes.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {5}, number = {3}, pages = {2500-2506}, pmid = {33457843}, issn = {2380-2359}, abstract = {Gossypium hirsutum and G. barbadense mitochondrial genomes were analyzed to understand the factors shaping codon usage. While most analyses of codon usage suggest minimal to no bias, nucleotide composition, specifically GC content, was significantly correlated with codon usage. In general, both mitochondrial genomes favor codons that end in A or U, with a secondary preference for pyrimidine rich codons. These observations are similar to previous reports of codon usage in cotton nuclear genomes, possibly suggestive of a general bias spanning genomic compartment. Although evidence for codon usage bias is weak for most genes, we identified six genes (i.e. atp8, atp9, sdh3, sdh4, mttB and rpl2) with significant nonrandom codon usage. In general, we find multiple factors that influence cotton mitochondrial genome codon usage, which may include selection in a subset of genes.}, }
@article {pmid33457783, year = {2020}, author = {Cevallos, MA and Guerrero, G and Ríos, S and Arroyo, A and Villalobos, MA and Porta, H}, title = {The mitogenome of Pseudocrossidium replicatum, a desiccation-tolerant moss.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {5}, number = {3}, pages = {2339-2341}, pmid = {33457783}, issn = {2380-2359}, abstract = {Bryophytes are the earliest plant group on Earth. They are a fundamental component of many ecosystems around the World. Some of their main roles are related to soil development, water retention, and biogeochemical cycling. Bryophytes include liverworts, hornworts, and mosses. The sequencing of chloroplast and mitochondria genomes has been useful to elucidate the taxonomy of this heterogeneous plant group. To date, despite their ecological importance only 41 mosses mitogenomes have been deposited in the GenBank. Here, the complete mitochondria genome sequence of Pseudocrossidium replicatum, a moss of the Pottiaceae family isolated in Tlaxcala, Mexico, is reported. The mitochondrial genome size of P. replicatum comprises 105,495 bp and contains the groups of genes described for other bryophytes mitogenomes. Our phylogenetic analysis shows that during the evolution of the mosses' mitogenome, nad7, rps4, rpl16, and rpl10 genes were lost independently in several lineages. The complete mitogenome sequence reported here would be a useful tool for our comprehension of the evolutionary and population genetics of this group of plants.}, }
@article {pmid33457738, year = {2020}, author = {Han, X and Li, Y and Lu, C and Liang, G and Zhang, F}, title = {The complete mitochondrial genome of Epicauta ruficeps (Coleoptera: Meloidae).}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {5}, number = {3}, pages = {2049-2050}, pmid = {33457738}, issn = {2380-2359}, abstract = {Epicauta ruficeps is widely distributed in China and some countries in Southeast Asia, and plays an important role in medicine and biological control. The complete mitochondria genome of E. ruficeps was 15,813 bp in length, with 37 genes, including 13 PCGs, 22 tRNA genes (tRNAs), and two rRNA genes (rRNAs). The positions and sequences of genes were consistent with those of known Meloidae species. The nucleotide composition was highly A + T biased, accounting for ∼65% of the whole mitogenome. The complete mitogenome of E. ruficeps would help understand Meloidae evolution.}, }
@article {pmid33455045, year = {2021}, author = {Pamplona, R and Jové, M and Mota-Martorell, N and Barja, G}, title = {Is the NDUFV2 subunit of the hydrophilic complex I domain a key determinant of animal longevity?.}, journal = {The FEBS journal}, volume = {288}, number = {23}, pages = {6652-6673}, doi = {10.1111/febs.15714}, pmid = {33455045}, issn = {1742-4658}, mesh = {Aging/*genetics/metabolism ; Animals ; Biological Evolution ; Electron Transport/genetics ; Electron Transport Complex I/*genetics/metabolism ; Energy Metabolism/*genetics ; Free Radicals/metabolism ; Longevity/*genetics ; Mitochondria/*genetics/metabolism ; Oxygen Consumption/genetics ; Protein Subunits/genetics/metabolism ; }, abstract = {Complex I, a component of the electron transport chain, plays a central functional role in cell bioenergetics and the biology of free radicals. The structural and functional N module of complex I is one of the main sites of the generation of free radicals. The NDUFV2 subunit/N1a cluster is a component of this module. Furthermore, the rate of free radical production is linked to animal longevity. In this review, we explore the hypothesis that NDUFV2 is the only conserved core subunit designed with a regulatory function to ensure correct electron transfer and free radical production, that low gene expression and protein abundance of the NDUFV2 subunit is an evolutionary adaptation needed to achieve a longevity phenotype, and that these features are determinants of the lower free radical generation at the mitochondrial level and a slower rate of aging of long-lived animals.}, }
@article {pmid33454277, year = {2021}, author = {Fuentealba, M and Fabian, DK and Dönertaş, HM and Thornton, JM and Partridge, L}, title = {Transcriptomic profiling of long- and short-lived mutant mice implicates mitochondrial metabolism in ageing and shows signatures of normal ageing in progeroid mice.}, journal = {Mechanisms of ageing and development}, volume = {194}, number = {}, pages = {111437}, pmid = {33454277}, issn = {1872-6216}, support = {WT098565/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Age Factors ; Aging/*genetics/metabolism ; Animals ; Databases, Genetic ; Disease Models, Animal ; Energy Metabolism/*genetics ; *Gene Expression Profiling ; Gene Regulatory Networks ; Mice, Mutant Strains ; Mitochondria/*genetics/metabolism ; Progeria/*genetics/metabolism ; *Transcriptome ; }, abstract = {Genetically modified mouse models of ageing are the living proof that lifespan and healthspan can be lengthened or shortened, and provide a powerful context in which to unravel the molecular mechanisms at work. In this study, we analysed and compared gene expression data from 10 long-lived and 8 short-lived mouse models of ageing. Transcriptome-wide correlation analysis revealed that mutations with equivalent effects on lifespan induce more similar transcriptomic changes, especially if they target the same pathway. Using functional enrichment analysis, we identified 58 gene sets with consistent changes in long- and short-lived mice, 55 of which were up-regulated in long-lived mice and down-regulated in short-lived mice. Half of these sets represented genes involved in energy and lipid metabolism, among which Ppargc1a, Mif, Aldh5a1 and Idh1 were frequently observed. Based on the gene sets with consistent changes, and also the whole transcriptome, the gene expression changes during normal ageing resembled the transcriptome of short-lived models, suggesting that accelerated ageing models reproduce partially the molecular changes of ageing. Finally, we identified new genetic interventions that may ameliorate ageing, by comparing the transcriptomes of 51 mouse mutants not previously associated with ageing to expression signatures of long- and short-lived mice and ageing-related changes.}, }
@article {pmid33453317, year = {2021}, author = {Slijepcevic, P}, title = {Serial Endosymbiosis Theory: From biology to astronomy and back to the origin of life.}, journal = {Bio Systems}, volume = {202}, number = {}, pages = {104353}, doi = {10.1016/j.biosystems.2021.104353}, pmid = {33453317}, issn = {1872-8324}, mesh = {Astronomy/methods/*trends ; *Biological Evolution ; Biology/methods/*trends ; Eukaryota/physiology ; Humans ; *Origin of Life ; Phylogeny ; Symbiosis/*physiology ; }, abstract = {Serial Endosymbiosis Theory, or SET, was conceived and developed by Lynn Margulis, to explain the greatest discontinuity in the history of life, the origin of eukaryotic cells. Some predictions of SET, namely the origin of mitochondria and chloroplasts, withstood the test of the most recent evidence from a variety of disciplines including phylogenetics, biochemistry, and cell biology. Even though some other predictions fared less well, SET remains a seminal theory in biology. In this paper, I focus on two aspects of SET. First, using the concept of "universal symbiogenesis", developed by Freeman Dyson to search for commonalities in astronomy and biology, I propose that SET can be extended beyond eukaryogenesis. The extension refers to the possibility that even prokaryotic organisms, themselves subject to the process of symbiogenesis in SET, could have emerged symbiotically. Second, I contrast a recent "viral eukaryogenesis" hypothesis, according to which the nucleus evolved from a complex DNA virus, with a view closer to SET, according to which the nucleus evolved through the interplay of the archaeal host, the eubacterial symbiont, and a non-LTR transposon, or telomerase. Viruses joined in later, through the process of viral endogenization, to shape eukaryotic chromosomes in the process of karyotype evolution. These two proposals based on SET are a testament to its longevity as a scientific theory.}, }
@article {pmid33452307, year = {2021}, author = {Cui, H and Ding, Z and Zhu, Q and Wu, Y and Qiu, B and Gao, P}, title = {Comparative analysis of nuclear, chloroplast, and mitochondrial genomes of watermelon and melon provides evidence of gene transfer.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {1595}, pmid = {33452307}, issn = {2045-2322}, mesh = {Biological Evolution ; Cell Nucleus/*genetics ; Citrullus/*genetics ; Cucurbitaceae/*genetics ; DNA, Plant/chemistry/metabolism ; Gene Transfer, Horizontal ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Genome, Plant ; Whole Genome Sequencing ; }, abstract = {During plant evolution, there is genetic communication between organelle and nuclear genomes. A comparative analysis was performed on the organelle and nuclear genomes of the watermelon and melon. In the watermelon, chloroplast-derived sequences accounted for 7.6% of the total length of the mitochondrial genome. In the melon, chloroplast-derived sequences accounted for approximately 2.73% of the total mitochondrial genome. In watermelon and melon, the chloroplast-derived small-fragment sequences are either a subset of large-fragment sequences or appeared multiple times in the mitochondrial genome, indicating that these fragments may have undergone multiple independent migration integrations or emerged in the mitochondrial genome after migration, replication, and reorganization. There was no evidence of migration from the mitochondria to chloroplast genome. A sequence with a total length of about 73 kb (47%) in the watermelon chloroplast genome was homologous to a sequence of about 313 kb in the nuclear genome. About 33% of sequences in the watermelon mitochondrial genome was homologous with a 260 kb sequence in the nuclear genome. A sequence with a total length of about 38 kb (25%) in the melon chloroplast genome was homologous with 461 sequences in the nuclear genome, with a total length of about 301 kb. A 3.4 Mb sequence in the nuclear genome was homologous with a melon mitochondrial sequence. These results indicate that, during the evolution of watermelon and melon, a large amount of genetic material was exchanged between the nuclear genome and the two organelle genomes in the cytoplasm.}, }
@article {pmid33446906, year = {2021}, author = {Fachi, JL and Pral, LP and Dos Santos, JAC and Codo, AC and de Oliveira, S and Felipe, JS and Zambom, FFF and Câmara, NOS and Vieira, PMMM and Colonna, M and Vinolo, MAR}, title = {Hypoxia enhances ILC3 responses through HIF-1α-dependent mechanism.}, journal = {Mucosal immunology}, volume = {14}, number = {4}, pages = {828-841}, pmid = {33446906}, issn = {1935-3456}, support = {U01 AI095542/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Clostridium Infections/etiology/metabolism ; Disease Models, Animal ; Disease Susceptibility ; Hypoxia/*immunology/*metabolism ; Hypoxia-Inducible Factor 1, alpha Subunit/genetics/*metabolism ; *Immunity, Innate ; Lymphocyte Activation/genetics/immunology ; Lymphocyte Subsets/*immunology/*metabolism ; Mice ; Mice, Knockout ; Mitochondria/metabolism ; Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism ; Protein Stability ; Signal Transduction ; TOR Serine-Threonine Kinases/metabolism ; }, abstract = {Group 3 innate lymphoid cells (ILC3) have a prominent role in the maintenance of intestine mucosa homeostasis. The hypoxia-inducible factor (HIF) is an important modulator of immune cell activation and a key mechanism for cellular adaptation to oxygen deprivation. However, its role on ILC3 is not well known. In this study, we investigated how a hypoxic environment modulates ILC3 response and the subsequent participation of HIF-1 signaling in this process. We found increased proliferation and activation of intestinal ILC3 at low oxygen levels, a response that was phenocopied when HIF-1α was chemically stabilized and was reversed when HIF-1 was blocked. The increased activation of ILC3 relied on a HIF-1α-dependent transcriptional program, but not on mTOR-signaling or a switch to glycolysis. HIF-1α deficiency in RORyt compartment resulted in impaired IL-17 and IL-22 production by ILC3 in vivo, which reflected in a lower expression of their target genes in the intestinal epithelium and an increased susceptibility to Clostridiodes difficile infection. Taken together, our results show that HIF-1α activation in intestinal ILC3 is relevant for their functions in steady state and infectious conditions.}, }
@article {pmid33442829, year = {2021}, author = {Zhang, K and Liu, Y and Chen, J and Zhang, H and Gong, L and Jiang, L and Liu, L and Lü, Z and Liu, B}, title = {Characterization of the complete mitochondrial genome of Macrotocinclus affinis (Siluriformes; Loricariidae) and phylogenetic studies of Siluriformes.}, journal = {Molecular biology reports}, volume = {48}, number = {1}, pages = {677-689}, pmid = {33442829}, issn = {1573-4978}, support = {NO.41806156//National Natural Science Foundation of China/ ; LMB20201005//State Key Laboratory of Microbial Resources (CN)/ ; No.2019J00048//Starting Research Fund from the Zhejiang Ocean University; Fundamental Research Funds for Zhejiang Provincial Universities and Research Institutes/ ; 2020C21016//Science and Technology Project of Zhoushan/ ; 31702321//National Natural Science Foundation of China/ ; LY20C190008//Zhejiang Provincial Natural Science Foundation of China/ ; }, mesh = {Animals ; Base Composition ; Catfishes/classification/*genetics ; Chromosome Mapping ; DNA, Circular/genetics ; DNA, Mitochondrial/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; *Open Reading Frames ; Phylogeny ; RNA, Ribosomal/classification/genetics ; RNA, Transfer/classification/genetics ; Whole Genome Sequencing ; }, abstract = {The vertebrate mitochondrial genome is typically circular molecules made up of 14,000 to 16,000 bp, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (12 s rRNA and 16 s rRNA) and a control region. Compared with nuclear DNA, mitochondrial DNA has a higher mutation rate, so it is one of the most effective and reliable molecular markers in fish phylogeny. Macrotocinclus affinis was the only species in Macrotocinclus (it was classified as Otocinclus in the past) and currently lacks genetic information. Most of the current researches are based on the mitochondrial Cytb gene and RAG1 and RAG2 nuclear genes to study the phylogenetic analysis of Siluriformes. So, the study provides the characteristic features of the Macrotocinclus affinis mitochondrial genome and this is the first time that the phylogenetic relationship of Siluriformes has been reconstructed based on COI. We aimed to sequence the entire mitochondrial genome of Macrotocinclus affinis using conventional PCR techniques and to clarify its phylogenetic status in Siluriformes by using the COI sequence of mitochondria. In this study, we sequenced the whole mitochondrial genome of this species yielding a 16,632 bp circular assembly composed of the typical vertebrate mitochondrial features. It contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region, and one origin of replication on the light-strand. The overall base composition includes A (30.07%), T (24.43%), C (29.43%) and G (16.01%). The genome composition is A + T biased (54.5%), and exhibits AT-skew (0.1036) and GC-skew (-0.2962). Moreover, the 13 PCGs encode 3850 amino acids in total. The result of the phylogenetic tree supports Macrotocinclus affinis has a closest relationship with Otocinclus cf. hoppei far. These results will help to understand the characteristics of the mitochondrial genome of Macrotocinclus affinis and provide molecular basis for the evolutionary relationship of Loricariidae.}, }
@article {pmid33436634, year = {2021}, author = {Bit, A and Thakur, M and Singh, SK and Joshi, BD and Singh, VK and Sharma, LK and Tripathy, B and Chandra, K}, title = {Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {730}, pmid = {33436634}, issn = {2045-2322}, mesh = {Animals ; DNA, Mitochondrial/analysis/*genetics ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/*genetics ; *Phylogeny ; Ursidae/classification/*genetics ; }, abstract = {The complete mitogenome of Himalayan black bear (Ursus thibetanus laniger) from Indian Himalayan region was assembled following the modified approach of mitochondrial baiting and mapping using the next-generation sequencing reads. The complete mitogenome was of 16,556 bp long, consisted of 37 genes that contained 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 1 control region. The complete base composition was 31.33% A, 15.24% G, 25.45%C, and 27.98%T and gene arrangement was similar to the other sub-species of Asiatic black bear. The relative synonymous codon usage analysis revealed the maximum abundance of Isoleucine, Tyrosine, Leucine and Threonine. The assembled mitogenome of U. t. laniger exhibited 99% similarity with the mitogenomes of Himalayan black bear available from Nepal and Tibetan Plateau-Himalaya region. The findings of the present study has proven low depth sequencing data, adequate and highly efficient in rapid recovering the mitochondrial genome by overcoming the conventional strategies of obtaining long-range PCR and subsequently drawing phylogenetic inferences.}, }
@article {pmid33436278, year = {2021}, author = {Koch, RE and Buchanan, KL and Casagrande, S and Crino, O and Dowling, DK and Hill, GE and Hood, WR and McKenzie, M and Mariette, MM and Noble, DWA and Pavlova, A and Seebacher, F and Sunnucks, P and Udino, E and White, CR and Salin, K and Stier, A}, title = {Integrating Mitochondrial Aerobic Metabolism into Ecology and Evolution.}, journal = {Trends in ecology &amp; evolution}, volume = {36}, number = {4}, pages = {321-332}, doi = {10.1016/j.tree.2020.12.006}, pmid = {33436278}, issn = {1872-8383}, mesh = {Adaptation, Physiological ; Adenosine Triphosphate/metabolism ; *Energy Metabolism ; Humans ; *Mitochondria ; Reactive Oxygen Species/metabolism ; }, abstract = {Biologists have long appreciated the critical role that energy turnover plays in understanding variation in performance and fitness among individuals. Whole-organism metabolic studies have provided key insights into fundamental ecological and evolutionary processes. However, constraints operating at subcellular levels, such as those operating within the mitochondria, can also play important roles in optimizing metabolism over different energetic demands and time scales. Herein, we explore how mitochondrial aerobic metabolism influences different aspects of organismal performance, such as through changing adenosine triphosphate (ATP) and reactive oxygen species (ROS) production. We consider how such insights have advanced our understanding of the mechanisms underpinning key ecological and evolutionary processes, from variation in life-history traits to adaptation to changing thermal conditions, and we highlight key areas for future research.}, }
@article {pmid33432342, year = {2021}, author = {Harada, R and Inagaki, Y}, title = {Phage Origin of Mitochondrion-Localized Family A DNA Polymerases in Kinetoplastids and Diplonemids.}, journal = {Genome biology and evolution}, volume = {13}, number = {2}, pages = {}, pmid = {33432342}, issn = {1759-6653}, mesh = {Bacteriophages/enzymology/*genetics ; DNA-Directed DNA Polymerase/classification/*genetics ; Euglenozoa/enzymology/*genetics ; *Gene Transfer, Horizontal ; Kinetoplastida/enzymology/*genetics ; Mitochondria/enzymology/genetics ; Phylogeny ; }, abstract = {Mitochondria retain their own genomes as other bacterial endosymbiont-derived organelles. Nevertheless, no protein for DNA replication and repair is encoded in any mitochondrial genomes (mtDNAs) assessed to date, suggesting that the nucleus primarily governs the maintenance of mtDNA. As the proteins of diverse evolutionary origins occupy a large proportion of the current mitochondrial proteomes, we anticipate finding the same evolutionary trend in the nucleus-encoded machinery for mtDNA maintenance. Indeed, none of the DNA polymerases (DNAPs) in the mitochondrial endosymbiont, a putative α-proteobacterium, seemingly had been inherited by their descendants (mitochondria), as none of the known types of mitochondrion-localized DNAP showed a specific affinity to the α-proteobacterial DNAPs. Nevertheless, we currently have no concrete idea of how and when the known types of mitochondrion-localized DNAPs emerged. We here explored the origins of mitochondrion-localized DNAPs after the improvement of the samplings of DNAPs from bacteria and phages/viruses. Past studies have revealed that a set of mitochondrion-localized DNAPs in kinetoplastids and diplonemids, namely PolIB, PolIC, PolID, PolI-Perk1/2, and PolI-dipl (henceforth designated collectively as "PolIBCD+") have emerged from a single DNAP. In this study, we recovered an intimate connection between PolIBCD+ and the DNAPs found in a particular group of phages. Thus, the common ancestor of kinetoplastids and diplonemids most likely converted a laterally acquired phage DNAP into a mitochondrion-localized DNAP that was ancestral to PolIBCD+. The phage origin of PolIBCD+ hints at a potentially large contribution of proteins acquired via nonvertical processes to the machinery for mtDNA maintenance in kinetoplastids and diplonemids.}, }
@article {pmid33422563, year = {2021}, author = {Pabis, K}, title = {Triplex and other DNA motifs show motif-specific associations with mitochondrial DNA deletions and species lifespan.}, journal = {Mechanisms of ageing and development}, volume = {194}, number = {}, pages = {111429}, doi = {10.1016/j.mad.2021.111429}, pmid = {33422563}, issn = {1872-6216}, mesh = {Age Factors ; Aging/*genetics/metabolism/pathology ; Animals ; DNA/*genetics/metabolism ; DNA, Mitochondrial/*genetics/metabolism ; G-Quadruplexes ; *Gene Deletion ; Humans ; Longevity/*genetics ; Models, Genetic ; *Mutation ; Nucleic Acid Conformation ; *Nucleotide Motifs ; Phylogeny ; Species Specificity ; }, abstract = {The "theory of resistant biomolecules" posits that long-lived species show resistance to molecular damage at the level of their biomolecules. Here, we test this hypothesis in the context of mitochondrial DNA (mtDNA) as it implies that predicted mutagenic DNA motifs should be inversely correlated with species maximum lifespan (MLS). First, we confirmed that guanine-quadruplex and direct repeat (DR) motifs are mutagenic, as they associate with mtDNA deletions in the human major arc of mtDNA, while also adding mirror repeat (MR) and intramolecular triplex motifs to a growing list of potentially mutagenic features. What is more, triplex motifs showed disease-specific associations with deletions and an apparent interaction with guanine-quadruplex motifs. Surprisingly, even though DR, MR and guanine-quadruplex motifs were associated with mtDNA deletions, their correlation with MLS was explained by the biased base composition of mtDNA. Only triplex motifs negatively correlated with MLS even after adjusting for body mass, phylogeny, mtDNA base composition and effective number of codons. Taken together, our work highlights the importance of base composition for the comparative biogerontology of mtDNA and suggests that future research on mitochondrial triplex motifs is warranted.}, }
@article {pmid33422486, year = {2021}, author = {Austin, S and Nowikovsky, K}, title = {Mitochondrial osmoregulation in evolution, cation transport and metabolism.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1862}, number = {5}, pages = {148368}, doi = {10.1016/j.bbabio.2021.148368}, pmid = {33422486}, issn = {1879-2650}, mesh = {Animals ; Cations/*metabolism ; *Evolution, Molecular ; Humans ; Ion Transport ; Mitochondria/*metabolism ; *Osmoregulation ; }, abstract = {This review provides a retrospective on the role of osmotic regulation in the process of eukaryogenesis. Specifically, it focuses on the adjustments which must have been made by the original colonizing α-proteobacteria that led to the evolution of modern mitochondria. We focus on the cations that are fundamentally involved in volume determination and cellular metabolism and define the transporter landscape in relation to these ions in mitochondria as we know today. We provide analysis on how the cations interplay and together maintain osmotic balance that allows for effective ATP synthesis in the organelle.}, }
@article {pmid33412336, year = {2021}, author = {Bartáková, V and Bryjová, A and Nicolas, V and Lavrenchenko, LA and Bryja, J}, title = {Mitogenomics of the endemic Ethiopian rats: looking for footprints of adaptive evolution in sky islands.}, journal = {Mitochondrion}, volume = {57}, number = {}, pages = {182-191}, doi = {10.1016/j.mito.2020.12.015}, pmid = {33412336}, issn = {1872-8278}, mesh = {Animals ; Evolution, Molecular ; Genetic Introgression ; Mitochondria/*genetics ; Mitochondrial Proteins/chemistry/*genetics ; Models, Molecular ; Murinae/classification/*genetics ; Oxidative Phosphorylation ; Phylogeny ; Selection, Genetic ; Sequence Analysis, DNA/*methods ; }, abstract = {Organisms living in high altitude must adapt to environmental conditions with hypoxia and low temperature, e.g. by changes in the structure and function of proteins associated with oxidative phosphorylation in mitochondria. Here we analysed the signs of adaptive evolution in 27 mitogenomes of endemic Ethiopian rats (Stenocephalemys), where individual species adapted to different elevation. Significant signals of positive selection were detected in 10 of the 13 mitochondrial protein-coding genes, with a majority of functional substitutions in the NADH dehydrogenase complex. Higher frequency of positively selected sites was found in phylogenetic lineages corresponding to Afroalpine specialists.}, }
@article {pmid33412200, year = {2021}, author = {Wang, Q and Wang, J and Wu, Q and Xu, X and Wang, P and Wang, Z}, title = {Insights into the evolution of Brachyura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements.}, journal = {International journal of biological macromolecules}, volume = {170}, number = {}, pages = {717-727}, doi = {10.1016/j.ijbiomac.2020.12.210}, pmid = {33412200}, issn = {1879-0003}, mesh = {Animals ; Brachyura/*genetics ; Gene Order/*genetics ; Gene Rearrangement/*genetics ; Genes, Mitochondrial/*genetics ; Genome, Mitochondrial/genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Brachyura is one of the most species rich and highly derived groups among extant crustaceans, with over 7250 known species. However, brachyuran phylogeny remains controversial and requires further study. Here, we combined 103 brachyuran mitogenomes from GenBank with 10 new mitogenomes to describe gene rearrangement patterns and explore the internal phylogenetic relationships of Brachyura. Most of the 10 novel mitogenomes had the typical 37 genes, except that of Longpotamon depressum, which lacked trnQ. We discovered 15 gene rearrangement patterns among Brachyura and preliminarily determined their rearrangement mechanisms with the help of CREx. We identified seven putative ancestral family gene orders among the 15 rearrangement patterns and expounded systematically upon the mechanisms of their rearrangement. In our phylogenetic analysis, Raninoida shared a sister relationship with an eubrachyuran clade ((Heterotremata [Potamoidea] + Thoracotremata) + Heterotremata) at maximum nodal support rather than Dromiacea, which did not support monophyly of Podotremata. In addition, Potamoidea (Parathelphusidae + Potamidae) retained a close relationship with Thoracotremata rather than their marine relatives in Heterotremata. Our study provides important information for the evolution of Brachyura by using the large taxon sampling currently available for systematic rearrangement and phylogenetic analyses.}, }
@article {pmid33409542, year = {2021}, author = {Yarus, M}, title = {Crick Wobble and Superwobble in Standard Genetic Code Evolution.}, journal = {Journal of molecular evolution}, volume = {89}, number = {1-2}, pages = {50-61}, pmid = {33409542}, issn = {1432-1432}, mesh = {*Anticodon/genetics ; Codon/genetics ; Evolution, Molecular ; *Genetic Code ; RNA ; }, abstract = {Wobble coding is inevitable during evolution of the Standard Genetic Code (SGC). It ultimately splits half of NN U/C/A/G coding boxes with different assignments. Further, it contributes to pervasive SGC order by reinforcing close spacing for identical SGC assignments. But wobble cannot appear too soon, or it will inhibit encoding and more decisively, obstruct evolution of full coding tables. However, these prior results assumed Crick wobble, NN U/C and NN A/G, read by a single adaptor RNA. Superwobble translates NN U/C/A/G codons, using one adaptor RNA with an unmodified 5' anticodon U (appropriate to earliest coding) in modern mitochondria, plastids, and mycoplasma. Assuming the SGC was selected when evolving codes most resembled it, characteristics of the critical selection events can be calculated. For example, continuous superwobble infrequently evolves SGC-like coding tables. So, continuous superwobble is a very improbable origin hypothesis. In contrast, late-arising superwobble shares late Crick wobble's frequent resemblance to SGC order. Thus late superwobble is possible, but yields SGC-like assignments less frequently than late Crick wobble. Ancient coding ambiguity, most simply, arose from Crick wobble alone. This is consistent with SGC assignments to NAN codons.}, }
@article {pmid33408226, year = {2021}, author = {Ferrarini, MG and Nisimura, LM and Girard, RMBM and Alencar, MB and Fragoso, MSI and Araújo-Silva, CA and Veiga, AA and Abud, APR and Nardelli, SC and Vommaro, RC and Silber, AM and France-Sagot, M and Ávila, AR}, title = {Dichloroacetate and Pyruvate Metabolism: Pyruvate Dehydrogenase Kinases as Targets Worth Investigating for Effective Therapy of Toxoplasmosis.}, journal = {mSphere}, volume = {6}, number = {1}, pages = {}, pmid = {33408226}, issn = {2379-5042}, mesh = {Antiprotozoal Agents/*pharmacology ; Apoptosis/*drug effects ; Dichloroacetic Acid/chemistry/*pharmacology ; Fibroblasts/*drug effects/parasitology ; Humans ; Metabolic Networks and Pathways/drug effects ; Mitochondria/metabolism ; Oxidation-Reduction ; Oxidoreductases ; Pyruvate Dehydrogenase Acetyl-Transferring Kinase/*antagonists &amp; inhibitors ; Pyruvates/*metabolism ; Toxoplasma/*drug effects ; Toxoplasmosis/drug therapy ; }, abstract = {Toxoplasmosis, a protozoan infection caused by Toxoplasma gondii, is estimated to affect around 2.5 billion people worldwide. Nevertheless, the side effects of drugs combined with the long period of therapy usually result in discontinuation of the treatment. New therapies should be developed by exploring peculiarities of the parasite's metabolic pathways, similarly to what has been well described in cancer cell metabolism. An example is the switch in the metabolism of cancer that blocks the conversion of pyruvate into acetyl coenzyme A in mitochondria. In this context, dichloroacetate (DCA) is an anticancer drug that reverts the tumor proliferation by inhibiting the enzymes responsible for this switch: the pyruvate dehydrogenase kinases (PDKs). DCA has also been used in the treatment of certain symptoms of malaria; however, there is no evidence of how this drug affects apicomplexan species. In this paper, we studied the metabolism of T. gondii and demonstrate that DCA also inhibits T. gondii's in vitro infection with no toxic effects on host cells. DCA caused an increase in the activity of pyruvate dehydrogenase followed by an unbalanced mitochondrial activity. We also observed morphological alterations frequently in mitochondria and in a few apicoplasts, essential organelles for parasite survival. To date, the kinases that potentially regulate the activity of pyruvate metabolism in both organelles have never been described. Here, we confirmed the presence in the genome of two putative kinases (T. gondii PDK [TgPDK] and T. gondii branched-chain α-keto acid dehydrogenase kinase [TgBCKDK]), verified their cellular localization in the mitochondrion, and provided in silico data suggesting that they are potential targets of DCA.IMPORTANCE Currently, the drugs used for toxoplasmosis have severe toxicity to human cells, and the treatment still lacks effective and safer alternatives. The search for novel drug targets is timely. We report here that the treatment of T. gondii with an anticancer drug, dichloroacetate (DCA), was effective in decreasing in vitro infection without toxicity to human cells. It is known that PDK is the main target of DCA in mammals, and this inactivation increases the conversion of pyruvate into acetyl coenzyme A and reverts the proliferation of tumor cells. Moreover, we verified the mitochondrial localization of two kinases that possibly regulate the activity of pyruvate metabolism in T. gondii, which has never been studied. DCA increased pyruvate dehydrogenase (PDH) activity in T. gondii, followed by an unbalanced mitochondrial activity, in a manner similar to what was previously observed in cancer cells. Thus, we propose the conserved kinases as potential regulators of pyruvate metabolism and interesting targets for new therapies.}, }
@article {pmid33404103, year = {2021}, author = {Lee, DW and Hwang, I}, title = {Understanding the evolution of endosymbiotic organelles based on the targeting sequences of organellar proteins.}, journal = {The New phytologist}, volume = {230}, number = {3}, pages = {924-930}, doi = {10.1111/nph.17167}, pmid = {33404103}, issn = {1469-8137}, mesh = {*Chloroplasts/metabolism ; Mitochondria ; *Organelles ; Phylogeny ; Symbiosis ; }, abstract = {Organellogenesis, a key aspect of eukaryotic cell evolution, critically depends on the successful establishment of organellar protein import mechanisms. Phylogenetic analysis revealed that the evolution of the two endosymbiotic organelles, the mitochondrion and the chloroplast, is thought to have occurred at time periods far from each other. Despite this, chloroplasts and mitochondria have highly similar protein import mechanisms. This raises intriguing questions such as what underlies such similarity in the import mechanisms and how these similar mechanisms have evolved. In this review, we summarise the recent findings regarding sorting and specific targeting of these organellar proteins. Based on these findings, we propose possible evolutionary scenarios regarding how the signal sequences of chloroplasts and mitochondrial proteins ended up having such relationship.}, }
@article {pmid33396901, year = {2020}, author = {Cucini, C and Fanciulli, PP and Frati, F and Convey, P and Nardi, F and Carapelli, A}, title = {Re-Evaluating the Internal Phylogenetic Relationships of Collembola by Means of Mitogenome Data.}, journal = {Genes}, volume = {12}, number = {1}, pages = {}, pmid = {33396901}, issn = {2073-4425}, mesh = {Animals ; Antarctic Regions ; Arthropods/classification/*genetics ; Bayes Theorem ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/genetics ; *Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Collembola are an ancient and early diverging lineage of basal hexapods that occur in virtually all terrestrial habitats on Earth. Phylogenetic relationships between the different orders of Collembola are fiercely debated. Despite a range of studies and the application of both morphological and genetic approaches (singly or in combination) to assess the evolutionary relationships of major lineages in the group, no consensus has been reached. Several mitogenome sequences have been published for key taxa of the class (and their number is increasing rapidly). Here, we describe two new Antarctic Collembola mitogenomes and compare all complete or semi-complete springtail mitogenome sequences available on GenBank in terms of both gene order and DNA sequence analyses in a genome evolution and molecular phylogenetic framework. With minor exceptions, we confirm the monophyly of Poduromorpha and Symphypleona sensu stricto (the latter placed at the most basal position in the springtail phylogenetic tree), whereas monophyly of Neelipleona and Entomobryomorpha is only supported when a handful of critical taxa in these two lineages are excluded. Finally, we review gene order models observed in the class, as well as the overall mitochondrial nucleotide composition.}, }
@article {pmid33396191, year = {2020}, author = {Shimakawa, G and Kohara, A and Miyake, C}, title = {Characterization of Light-Enhanced Respiration in Cyanobacteria.}, journal = {International journal of molecular sciences}, volume = {22}, number = {1}, pages = {}, pmid = {33396191}, issn = {1422-0067}, support = {JPMJCR1503//Core Research for Evolutional Science and Technology/ ; 16J03443//Japan Society for the Promotion of Science/ ; A20J001050//Japan Society for the Promotion of Science/ ; }, mesh = {*Cell Respiration ; Cyanobacteria/*growth &amp; development/metabolism/physiology ; Electron Transport ; *Light ; Oxidation-Reduction ; Oxygen/*metabolism ; *Photosynthesis ; }, abstract = {In eukaryotic algae, respiratory O2 uptake is enhanced after illumination, which is called light-enhanced respiration (LER). It is likely stimulated by an increase in respiratory substrates produced during photosynthetic CO2 assimilation and function in keeping the metabolic and redox homeostasis in the light in eukaryotic cells, based on the interactions among the cytosol, chloroplasts, and mitochondria. Here, we first characterize LER in photosynthetic prokaryote cyanobacteria, in which respiration and photosynthesis share their metabolisms and electron transport chains in one cell. From the physiological analysis, the cyanobacterium Synechocystis sp. PCC 6803 performs LER, similar to eukaryotic algae, which shows a capacity comparable to the net photosynthetic O2 evolution rate. Although the respiratory and photosynthetic electron transports share the interchain, LER was uncoupled from photosynthetic electron transport. Mutant analyses demonstrated that LER is motivated by the substrates directly provided by photosynthetic CO2 assimilation, but not by glycogen. Further, the light-dependent activation of LER was observed even with exogenously added glucose, implying a regulatory mechanism for LER in addition to the substrate amounts. Finally, we discuss the physiological significance of the large capacity of LER in cyanobacteria and eukaryotic algae compared to those in plants that normally show less LER.}, }
@article {pmid33383174, year = {2021}, author = {Mamos, T and Uit de Weerd, D and von Oheimb, PV and Sulikowska-Drozd, A}, title = {Evolution of reproductive strategies in the species-rich land snail subfamily Phaedusinae (Stylommatophora: Clausiliidae).}, journal = {Molecular phylogenetics and evolution}, volume = {158}, number = {}, pages = {107060}, doi = {10.1016/j.ympev.2020.107060}, pmid = {33383174}, issn = {1095-9513}, mesh = {Animals ; *Biological Evolution ; Female ; Mitochondria/genetics ; Oviparity/genetics ; Phylogeny ; Reproduction/*genetics ; Snails/classification/*physiology ; *Viviparity, Nonmammalian/genetics ; }, abstract = {Most of the present knowledge on animal reproductive mode evolution, and possible factors driving transitions between oviparity and viviparity is based on studies on vertebrates. The species rich door snail (Clausiliidae) subfamily Phaedusinae represents a suitable and unique model for further examining parity evolution, as three different strategies, oviparity, viviparity, and the intermediate mode of embryo-retention, occur in this group. The present study reconstructs the evolution of reproductive strategies in Phaedusinae based on time-calibrated molecular phylogenetics, reproductive mode examinations and ancestral state reconstruction. Our phylogenetic analysis employing multiple mitochondrial and nuclear markers identified a well-supported clade (including the tribes Phaedusini and Serrulinini) that contains species exhibiting various reproductive strategies. This clade evolved from an oviparous most recent common ancestor according to our reconstruction. All non-oviparous taxa are confined to a highly supported subclade, coinciding with the tribe Phaedusini. Both oviparity and viviparity occur frequently in different lineages of this subclade that are not closely related. During Phaedusini diversification, multiple transitions in reproductive strategy must have taken place, which could have been promoted by a high fitness of embryo-retaining species. The evolutionary success of this group might result from the maintenance of various strategies.}, }
@article {pmid33372159, year = {2021}, author = {Chen, C and Mahar, R and Merritt, ME and Denlinger, DL and Hahn, DA}, title = {ROS and hypoxia signaling regulate periodic metabolic arousal during insect dormancy to coordinate glucose, amino acid, and lipid metabolism.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {1}, pages = {}, pmid = {33372159}, issn = {1091-6490}, support = {P41 GM122698/GM/NIGMS NIH HHS/United States ; R01 DK105346/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acids/metabolism ; Animals ; Cell Respiration ; Citric Acid Cycle ; Diapause/physiology ; Energy Metabolism ; Glucose/metabolism ; Glycolysis/physiology ; Hypoxia/*metabolism ; Insecta/metabolism ; Lipid Metabolism/physiology ; Lipids/physiology ; Mitochondria/metabolism ; Phosphorylation ; Reactive Oxygen Species/*metabolism ; Sarcophagidae/metabolism ; Signal Transduction ; Torpor/*physiology ; }, abstract = {Metabolic suppression is a hallmark of animal dormancy that promotes overall energy savings. Some diapausing insects and some mammalian hibernators have regular cyclic patterns of substantial metabolic depression alternating with periodic arousal where metabolic rates increase dramatically. Previous studies, largely in mammalian hibernators, have shown that periodic arousal is driven by an increase in aerobic mitochondrial metabolism and that many molecules related to energy metabolism fluctuate predictably across periodic arousal cycles. However, it is still not clear how these rapid metabolic shifts are regulated. We first found that diapausing flesh fly pupae primarily use anaerobic glycolysis during metabolic depression but engage in aerobic respiration through the tricarboxylic acid cycle during periodic arousal. Diapausing pupae also clear anaerobic by-products and regenerate many metabolic intermediates depleted in metabolic depression during arousal, consistent with patterns in mammalian hibernators. We found that decreased levels of reactive oxygen species (ROS) induced metabolic arousal and elevated ROS extended the duration of metabolic depression. Our data suggest ROS regulates the timing of metabolic arousal by changing the activity of two critical metabolic enzymes, pyruvate dehydrogenase and carnitine palmitoyltransferase I by modulating the levels of hypoxia inducible transcription factor (HIF) and phosphorylation of adenosine 5'-monophosphate-activated protein kinase (AMPK). Our study shows that ROS signaling regulates periodic arousal in our insect diapasue system, suggesting the possible importance ROS for regulating other types of of metabolic cycles in dormancy as well.}, }
@article {pmid33370271, year = {2020}, author = {Sorouri, M and Chang, T and Jesudhasan, P and Pinkham, C and Elde, NC and Hancks, DC}, title = {Signatures of host-pathogen evolutionary conflict reveal MISTR-A conserved MItochondrial STress Response network.}, journal = {PLoS biology}, volume = {18}, number = {12}, pages = {e3001045}, pmid = {33370271}, issn = {1545-7885}, support = {R00 GM119126/GM/NIGMS NIH HHS/United States ; R01 GM114514/GM/NIGMS NIH HHS/United States ; T32 AI005284/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Electron Transport Chain Complex Proteins/genetics/metabolism ; Electron Transport Complex IV/genetics/metabolism ; Evolution, Molecular ; Gene Regulatory Networks/genetics ; Host-Pathogen Interactions/*genetics/physiology ; Humans ; MicroRNAs/genetics ; Mitochondria/*genetics/metabolism ; Phylogeny ; Stress, Physiological/*genetics/physiology ; Viruses/genetics ; }, abstract = {Host-pathogen conflicts leave genetic signatures in genes that are critical for host defense functions. Using these "molecular scars" as a guide to discover gene functions, we discovered a vertebrate-specific MItochondrial STress Response (MISTR) circuit. MISTR proteins are associated with electron transport chain (ETC) factors and activated by stress signals such as interferon gamma (IFNγ) and hypoxia. Upon stress, ultraconserved microRNAs (miRNAs) down-regulate MISTR1(NDUFA4) followed by replacement with paralogs MItochondrial STress Response AntiViral (MISTRAV) and/or MItochondrial STress Response Hypoxia (MISTRH). While cells lacking MISTR1(NDUFA4) are more sensitive to chemical and viral apoptotic triggers, cells lacking MISTRAV or expressing the squirrelpox virus-encoded vMISTRAV exhibit resistance to the same insults. Rapid evolution signatures across primate genomes for MISTR1(NDUFA4) and MISTRAV indicate recent and ongoing conflicts with pathogens. MISTR homologs are also found in plants, yeasts, a fish virus, and an algal virus indicating ancient origins and suggesting diverse means of altering mitochondrial function under stress. The discovery of MISTR circuitry highlights the use of evolution-guided studies to reveal fundamental biological processes.}, }
@article {pmid33369015, year = {2021}, author = {Lechuga-Vieco, AV and Justo-Méndez, R and Enríquez, JA}, title = {Not all mitochondrial DNAs are made equal and the nucleus knows it.}, journal = {IUBMB life}, volume = {73}, number = {3}, pages = {511-529}, pmid = {33369015}, issn = {1521-6551}, mesh = {Animals ; Cell Nucleus/*genetics ; Cytoplasm/genetics/metabolism ; *DNA, Mitochondrial/genetics/metabolism ; Evolution, Molecular ; Gene Expression Regulation ; Genome ; Haplotypes ; Humans ; Mitochondria/genetics ; *Oxidative Phosphorylation ; }, abstract = {The oxidative phosphorylation (OXPHOS) system is the only structure in animal cells with components encoded by two genomes, maternally transmitted mitochondrial DNA (mtDNA), and biparentally transmitted nuclear DNA (nDNA). MtDNA-encoded genes have to physically assemble with their counterparts encoded in the nucleus to build together the functional respiratory complexes. Therefore, structural and functional matching requirements between the protein subunits of these molecular complexes are rigorous. The crosstalk between nDNA and mtDNA needs to overcome some challenges, as the nuclear-encoded factors have to be imported into the mitochondria in a correct quantity and match the high number of organelles and genomes per mitochondria that encode and synthesize their own components locally. The cell is able to sense the mito-nuclear match through changes in the activity of the OXPHOS system, modulation of the mitochondrial biogenesis, or reactive oxygen species production. This implies that a complex signaling cascade should optimize OXPHOS performance to the cellular-specific requirements, which will depend on cell type, environmental conditions, and life stage. Therefore, the mitochondria would function as a cellular metabolic information hub integrating critical information that would feedback the nucleus for it to respond accordingly. Here, we review the current understanding of the complex interaction between mtDNA and nDNA.}, }
@article {pmid33367059, year = {2020}, author = {Huang, X and Shi, Y and Shen, X and Huang, D and Wang, Y and Chen, J and Cai, Y}, title = {Characterization of the complete mitochondrial DNA sequence of the Lagocephalus gloveri (Tetraodontidae, Tetraodontiformes).}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {5}, number = {3}, pages = {3683-3684}, pmid = {33367059}, issn = {2380-2359}, abstract = {The complete mitochondrial genome of Lagocephalus gloveri is reported in the present study, which is 16,446 bp in length. It consists of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding control region. The overall base composition of the genome is 27.58% for A, 25.07% for T, 30.83% for C and 16.52% for G. The phylogenetic tree, which is based on 12 protein coding gene sequences, suggested that L. gloveri was closest to L. lagocephalus. This study could give impetus to studies focused on population structure and molecular evolution of L. gloveri.}, }
@article {pmid33366868, year = {2020}, author = {Yang, RS and Chen, YT}, title = {The complete mitochondrial genome of the freshwater fairy shrimp Branchinella kugenumaensis Ishikawa 1894 (Crustacea: Anostraca: Thamnocephalidae).}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {5}, number = {1}, pages = {1048-1049}, pmid = {33366868}, issn = {2380-2359}, abstract = {In this study, we determined and analyzed the complete mitochondrial genome of the freshwater fairy shrimp Branchinella kugenumaensis Ishikawa 1894 (Crustacea: Anostraca: Thamnocephalidae). The mitogenome is 15,127 bp in length, consisted of 37 genes that participate in protein production and energy metabolism of mitochondria. The gene order of the B. kugenumaensis mtDNA exhibits major rearrangements compared with the pancrustacean ancestral pattern or other known anostracan mitogenomes, representing a novel mitochondrial genomic organization within the Crustacea. A maximum-likelihood phylogenetic analysis based on concatenated nucleotide sequences of protein-coding genes places B. kugenumaensis next to Streptocephalus sirindhornae, inside the Anostraca clade. Our study will provide new evidence to the less sampled anostracan evolution and take a further step to the completion of the Branchiopoda tree of life.}, }
@article {pmid33362740, year = {2020}, author = {Li, X and Li, L and Bao, Z and Tu, W and He, X and Zhang, B and Ye, L and Wang, X and Li, Q}, title = {The 287,403 bp Mitochondrial Genome of Ectomycorrhizal Fungus Tuber calosporum Reveals Intron Expansion, tRNA Loss, and Gene Rearrangement.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {591453}, pmid = {33362740}, issn = {1664-302X}, abstract = {In the present study, the mitogenome of Tuber calosporum was assembled and analyzed. The mitogenome of T. calosporum comprises 15 conserved protein-coding genes, two rRNA genes, and 14 tRNAs, with a total size of 287,403 bp. Fifty-eight introns with 170 intronic open reading frames were detected in the T. calosporum mitogenome. The intronic region occupied 69.41% of the T. calosporum mitogenome, which contributed to the T. calosporum mitogenome significantly expand relative to most fungal species. Comparative mitogenomic analysis revealed large-scale gene rearrangements occurred in the mitogenome of T. calosporum, involving gene relocations and position exchanges. The mitogenome of T. calosporum was found to have lost several tRNA genes encoding for cysteine, aspartate, histidine, etc. In addition, a pair of fragments with a total length of 32.91 kb in both the nuclear and mitochondrial genomes of T. calosporum was detected, indicating possible gene transfer events. A total of 12.83% intragenomic duplications were detected in the T. calosporum mitogenome. Phylogenetic analysis based on mitochondrial gene datasets obtained well-supported tree topologies, indicating that mitochondrial genes could be reliable molecular markers for phylogenetic analyses of Ascomycota. This study served as the first report on mitogenome in the family Tuberaceae, thereby laying the groundwork for our understanding of the evolution, phylogeny, and population genetics of these important ectomycorrhizal fungi.}, }
@article {pmid33359769, year = {2021}, author = {Else, PL}, title = {Mammals to membranes: A reductionist story.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {253}, number = {}, pages = {110552}, doi = {10.1016/j.cbpb.2020.110552}, pmid = {33359769}, issn = {1879-1107}, mesh = {Animals ; Cell Membrane/*metabolism ; Energy Metabolism ; Humans ; Mammals/*metabolism ; Oxygen Consumption ; }, abstract = {This is the story of a series of reductionist studies that started with an attempt to explain what underpins the high-level of aerobic metabolism in mammals (i.e. associated with the evolution of endothermy) and almost forty years later had led to investigations into the role of membrane lipids in determining metabolism. Initial studies showed that the increase in aerobic metabolism in mammals was driven by a combination of increases in mitochondrial volume and membrane densities, organ size and changes in the molecular activity of enzymes. The increase in the capacity to produce energy was matched by an increase in energy use, notably driven by increases in H[+], Na[+] and K[+] fluxes. In the case of increased Na[+] flux, it was found this was matched by increases in Na[+]-dependent metabolism at the tissue level and increases in enzyme activity at a cellular level but not by an increase in the number of sodium pumps. To maintain Na[+] gradient across cell membranes, increased Na[+] flux is not controlled by an increase in sodium pump number but rather by an increase in sodium pump molecular activity (i.e. an increase the substrate turnover rate of each sodium pump) in tissues of endotherms. This increase in molecular activity is coupled to an increase in the level of highly unsaturated polyunsaturated fatty acids (PUFA) in membranes, a mechanism similar to that used by ectotherms to ameliorate decreasing activities of metabolic processes in the cold. Determination of how changes in membrane fatty acid composition can change the activities of proteins in membranes will be the next step in this story.}, }
@article {pmid33359125, year = {2021}, author = {Liu, H and Ju, Y and Tamate, H and Wang, T and Xing, X}, title = {Phylogeography of sika deer (Cervus nippon) inferred from mitochondrial cytochrome-b gene and microsatellite DNA.}, journal = {Gene}, volume = {772}, number = {}, pages = {145375}, doi = {10.1016/j.gene.2020.145375}, pmid = {33359125}, issn = {1879-0038}, mesh = {Animals ; Cell Nucleus/genetics ; China ; Cytochromes b/*genetics ; Deer/*classification/genetics ; *Genetic Variation ; Genetics, Population ; Haplotypes ; Japan ; *Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; }, abstract = {The genetic diversity and phylogenetic relationships of sika deer of different subspecies are uncertain. In order to explore the phylogenetic relationship of different sika deer subspecies, this study used a wider sample collection to analyze mitochondrial sequences and nuclear microsatellites of sika deer. The full lengths of cytochrome-b gene of 134 sika deer were sequenced, and 16 haplotypes were obtained. Based on phylogenetic and haplotype networks analysis, the sika deer was not clustered according to subspecies but was divided into four lineages. Lineage I includes individuals from C.n.kopschi, C.n.sichuanicus, and C.n.hortulorum subspecies; Lineage II includes individuals from C.n.hortulorum subspecies; Lineage III includes individuals from C.n.centralis, C.n.yakushime, C.n.mageshimae, and C.n.keramae subspecies, namely southern Japanese population; Lineage IV includes individuals from C.n.centralis and C.n.yesoensis subspecies, namely northern Japanese population. The microsatellite analysis showed that the sika deer in China and Japan originated independently. The three subspecies of China have significant genetic differentiation, while the three subspecies of Japan have no significant differentiation. This study provides reference for the research of genetic diversity and phylogenetic relationship of sika deer, and also provides scientific data for the evaluation, protection, and utilization of sika deer resources.}, }
@article {pmid33338660, year = {2021}, author = {Cairns, NA and Cicchino, AS and Stewart, KA and Austin, JD and Lougheed, SC}, title = {Cytonuclear discordance, reticulation and cryptic diversity in one of North America's most common frogs.}, journal = {Molecular phylogenetics and evolution}, volume = {156}, number = {}, pages = {107042}, doi = {10.1016/j.ympev.2020.107042}, pmid = {33338660}, issn = {1095-9513}, mesh = {Animals ; Anura/*genetics ; Base Sequence ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; *Genetic Variation ; Geography ; Linear Models ; Male ; Mitochondria/genetics ; North America ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Species Specificity ; }, abstract = {Complicated phylogenetic histories benefit from diverse sources of inference. Pseudacris crucifer (spring peeper) spans most of eastern North America and comprises six mtDNA lineages that form multiple contact zones. The putative Miocene or early Pliocene origins of the oldest lineages within Pseudacris crucifer imply sufficient time for species-level divergence. To understand why this species appears unified while congeners have radiated, we analyze and compare male advertisement calls, mitochondrial, and nuclear markers and speak to the complex processes that have potentially influenced its contemporary patterns. We find extensive geographic and topological mitonuclear discordance, with three nuclear lineages containing 6 more-structured mtDNA lineages, and nuclear introgression at some contact zones. Male advertisement call differentiation is incongruent with the genetic structure as only one lineage appears differentiated. Occupying the Interior Highlands of the central United States, this Western lineage also has the most concordant mitochondrial and nuclear geographic patterns. Based on our findings we suggest that the antiquity of common ancestors was not as important as the maintenance of allopatry in the divergence in P. crucifer genetic lineages. We use multiple lines of evidence to generate hypotheses of isolation, reticulation, and discordance within this species and to expand our understanding of the early stages of speciation.}, }
@article {pmid33330486, year = {2020}, author = {Zeng, M and He, Y and Du, H and Yang, J and Wan, H}, title = {Output Regulation and Function Optimization of Mitochondria in Eukaryotes.}, journal = {Frontiers in cell and developmental biology}, volume = {8}, number = {}, pages = {598112}, pmid = {33330486}, issn = {2296-634X}, abstract = {The emergence of endosymbiosis between aerobic alpha-proteobacterium and anaerobic eukaryotic cell precursors opened the chapter of eukaryotic evolution. Multiple functions of mitochondria originated from the ancient precursors of mitochondria and underwent remodeling in eukaryotic cells. Due to the dependence on mitochondrial functions, eukaryotic cells need to constantly adjust mitochondrial output based on energy demand and cellular stress. Meanwhile, eukaryotes conduct the metabolic cooperation between different cells through the involvement of mitochondria. Under some conditions, mitochondria might also be transferred to nearby cells to provide a protective mechanism. However, the endosymbiont relationship determines the existence of various types of mitochondrial injury, such as proteotoxic stress, mutational meltdown, oxidative injure, and immune activation caused by released mitochondrial contents. Eukaryotes have a repertoire of mitochondrial optimization processes, including various mitochondrial quality-control proteins, regulation of mitochondrial dynamics and activation of mitochondrial autophagy. When these quality-control processes fail, eukaryotic cells can activate apoptosis to intercept uncontrolled cell death, thereby minimizing the damage to extracellular tissue. In this review, we describe the intracellular and extracellular context-based regulation of mitochondrial output in eukaryotic cells, and introduce new findings on multifaceted quality-control processes to deal with mitochondrial defects.}, }
@article {pmid33329499, year = {2020}, author = {Oberleitner, L and Poschmann, G and Macorano, L and Schott-Verdugo, S and Gohlke, H and Stühler, K and Nowack, ECM}, title = {The Puzzle of Metabolite Exchange and Identification of Putative Octotrico Peptide Repeat Expression Regulators in the Nascent Photosynthetic Organelles of Paulinella chromatophora.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {607182}, pmid = {33329499}, issn = {1664-302X}, abstract = {The endosymbiotic acquisition of mitochondria and plastids more than one billion years ago was central for the evolution of eukaryotic life. However, owing to their ancient origin, these organelles provide only limited insights into the initial stages of organellogenesis. The cercozoan amoeba Paulinella chromatophora contains photosynthetic organelles-termed chromatophores-that evolved from a cyanobacterium ∼100 million years ago, independently from plastids in plants and algae. Despite the more recent origin of the chromatophore, it shows tight integration into the host cell. It imports hundreds of nucleus-encoded proteins, and diverse metabolites are continuously exchanged across the two chromatophore envelope membranes. However, the limited set of chromatophore-encoded solute transporters appears insufficient for supporting metabolic connectivity or protein import. Furthermore, chromatophore-localized biosynthetic pathways as well as multiprotein complexes include proteins of dual genetic origin, suggesting that mechanisms evolved that coordinate gene expression levels between chromatophore and nucleus. These findings imply that similar to the situation in mitochondria and plastids, also in P. chromatophora nuclear factors evolved that control metabolite exchange and gene expression in the chromatophore. Here we show by mass spectrometric analyses of enriched insoluble protein fractions that, unexpectedly, nucleus-encoded transporters are not inserted into the chromatophore inner envelope membrane. Thus, despite the apparent maintenance of its barrier function, canonical metabolite transporters are missing in this membrane. Instead we identified several expanded groups of short chromatophore-targeted orphan proteins. Members of one of these groups are characterized by a single transmembrane helix, and others contain amphipathic helices. We hypothesize that these proteins are involved in modulating membrane permeability. Thus, the mechanism generating metabolic connectivity of the chromatophore fundamentally differs from the one for mitochondria and plastids, but likely rather resembles the poorly understood mechanism in various bacterial endosymbionts in plants and insects. Furthermore, our mass spectrometric analysis revealed an expanded family of chromatophore-targeted helical repeat proteins. These proteins show similar domain architectures as known organelle-targeted expression regulators of the octotrico peptide repeat type in algae and plants. Apparently these chromatophore-targeted proteins evolved convergently to plastid-targeted expression regulators and are likely involved in gene expression control in the chromatophore.}, }
@article {pmid33314286, year = {2021}, author = {Mutti, LD and Ivanov, VA}, title = {Ultrastructure of the rhyncheal apparatus and other structures of the scolex of Grillotia (Christianella) carvajalregorum (Cestoda: Trypanorhyncha).}, journal = {Journal of morphology}, volume = {282}, number = {2}, pages = {309-324}, doi = {10.1002/jmor.21305}, pmid = {33314286}, issn = {1097-4687}, mesh = {Animals ; Cestoda/*anatomy &amp; histology/cytology/*ultrastructure ; Histocytochemistry ; Phylogeny ; Sensory Receptor Cells/cytology/ultrastructure ; }, abstract = {The scolex ultrastructure was studied in Grillotia (Christianella) carvajalregorum (Cestoda: Trypanorhyncha) using histochemistry and transmission electron microscopy. We show for the first time the presence of scolex glands arranged in two longitudinal acini at the pars vaginalis parenchyma. These glands, along with those scattered in bothrial parenchyma, produce potentially adhesive glycoprotein secretions that are discharged via ducts to the bothrial grooves and apex. A particular type of sensory receptor was found around frontal gland pores, with a possible function in regulating their secretion activity. The internal structure of microtriches varies according to their morphotype and distribution on the scolex, this study providing the first description of the ultrastructure of serrate lanceolate spinitriches. The projections that form serrate margins are an extension of the medulla, differing from similar projections of other spinitriches. The large caps observed in serrate lanceolate spinitriches may reflect their specialization in attachment to and abrasion of intestinal mucosa, while the short caps and large bases of acicular filitriches may reflect their involvement in nutrient absorption. We also describe the rhyncheal apparatus ultrastructure, showing a similar basic structure of tentacular walls than that of other trypanorhynchs. Some differences among species in the number of fibrous layers, composition of the apical cytoplasm and presence of microvilli-like projections were discussed. Finally, our study describes in detail the internal ultrastructure of hollow hooks, evidencing the presence of cytoplasm, mitochondria and fibrils. The location of these fibrils may increase the area of contact surface of hooks on tentacles, possibly allowing for a higher tensile strength than that of solid hooks. We consider that gland location and shape, composition of tentacular wall layers, and hook internal structure may serve as useful characters for the taxonomy and phylogeny of Trypanorhyncha. RESEARCH HIGHLIGHTS: This is the first description of scolex internal ultrastructure in Grillotia carvajalregorum, showing the presence of glands arranged in two longitudinal acini at the pars vaginalis parenchyma, with potentially adhesive functions. The internal ultrastructure of serrate lanceolate spinitriches and acicular filitriches may reflect their specialization in attachment to the host intestinal mucosa and their involvement in nutrient absorption, respectively. Internally, hollow hooks have cytoplasm with mitochondria and fibrils, which are more widely distributed than in solid hooks, possibly increasing their tensile strength.}, }
@article {pmid33314045, year = {2021}, author = {Filograna, R and Mennuni, M and Alsina, D and Larsson, NG}, title = {Mitochondrial DNA copy number in human disease: the more the better?.}, journal = {FEBS letters}, volume = {595}, number = {8}, pages = {976-1002}, pmid = {33314045}, issn = {1873-3468}, mesh = {Animals ; *DNA Copy Number Variations ; *DNA, Mitochondrial/genetics/metabolism ; *DNA, Neoplasm/genetics/metabolism ; Humans ; *Mitochondria/genetics/metabolism ; *Mitochondrial Diseases/genetics/metabolism ; *Neoplasms/genetics/metabolism ; *Neurodegenerative Diseases/genetics/metabolism ; }, abstract = {Most of the genetic information has been lost or transferred to the nucleus during the evolution of mitochondria. Nevertheless, mitochondria have retained their own genome that is essential for oxidative phosphorylation (OXPHOS). In mammals, a gene-dense circular mitochondrial DNA (mtDNA) of about 16.5 kb encodes 13 proteins, which constitute only 1% of the mitochondrial proteome. Mammalian mtDNA is present in thousands of copies per cell and mutations often affect only a fraction of them. Most pathogenic human mtDNA mutations are recessive and only cause OXPHOS defects if present above a certain critical threshold. However, emerging evidence strongly suggests that the proportion of mutated mtDNA copies is not the only determinant of disease but that also the absolute copy number matters. In this review, we critically discuss current knowledge of the role of mtDNA copy number regulation in various types of human diseases, including mitochondrial disorders, neurodegenerative disorders and cancer, and during ageing. We also provide an overview of new exciting therapeutic strategies to directly manipulate mtDNA to restore OXPHOS in mitochondrial diseases.}, }
@article {pmid33311144, year = {2020}, author = {Vasconcelos, R and KÖhler, G and Geniez, P and Crochet, PA}, title = {A new endemic species of Hemidactylus (Squamata: Gekkonidae) from São Nicolau Island, Cabo Verde.}, journal = {Zootaxa}, volume = {4878}, number = {3}, pages = {zootaxa.4878.3.4}, doi = {10.11646/zootaxa.4878.3.4}, pmid = {33311144}, issn = {1175-5334}, mesh = {Animals ; Cabo Verde ; Islands ; *Lizards ; Mitochondria ; Phylogeny ; }, abstract = {A new species of gecko of the genus Hemidactylus (Squamata: Gekkonidae) is described from São Nicolau Island, Cabo Verde Archipelago, and the Sal and Boavista island populations of Hemidactylus boavistensis (i.e., Hemidactylus boavistensis boavistensis comb. nov. and Hemidactylus boavistensis chevalieri comb. nov.) are recognized as subspecies. Hemidactylus nicolauensis sp. nov. is genetically distinct from H. bouvieri, to which it has previously been referred, and from all other closely related endemic Hemidactylus from Cabo Verde Islands in mitochondrial (12S cyt b) and nuclear (RAG2, MC1R) markers. It is characterized morphologically by its distinct colouration and a diagnostically different arrangement of digital lamellae. With the description of this new species, São Nicolau is now known to harbour three single-island endemic gecko species, and the documented reptile diversity in Cabo Verde is raised to 23 endemic species. As a result of our taxonomic changes, existing conservation regulations should be updated and the conservation status of these taxa should be re-evaluated.}, }
@article {pmid33310361, year = {2021}, author = {Bi, YH and Du, AY and Li, JL and Zhou, ZG}, title = {Isolation and characterization of a γ-carbonic anhydrase localized in the mitochondria of Saccharina japonica.}, journal = {Chemosphere}, volume = {266}, number = {}, pages = {129162}, doi = {10.1016/j.chemosphere.2020.129162}, pmid = {33310361}, issn = {1879-1298}, mesh = {Carbon Dioxide ; *Carbonic Anhydrases/genetics ; Escherichia coli ; Mitochondria ; Phylogeny ; }, abstract = {Saccharina japonica is an ecologically and economically important seaweed that is dominant in the rocky shores of cold-temperate regions, forms the major component of productive beds, and affects marine environments. S. japonica exhibits a high photosynthetic efficiency in natural seawater with low dissolved CO2 concentration, thus suggesting the presence of its carbon-concentrating mechanism (CCM). However, the genes, proteins, and pathways involved in the CCM of S. japonica have not been fully identified and characterized. Carbonic anhydrase (CA) is a crucial component of CCM in macroalgae. In this study, the cloning, characterization, and subcellular localization of a specific CA were described. Multisequence alignment and phylogenetic analysis indicated that this CA belonged to the gamma (Sjγ-CA) class. This enzyme has a full-length cDAN of 1370 bp, encodes a protein with 246 amino acids (aa; ca. 25.7 kDa), and contains the mitochondrial transit peptide of 16 aa and LbH_gama_CA_like domain of 159 aa that defined the γ-CA region. The Sjγ-CA was successfully expressed in E. coli BL21 and purified as an active recombinant CA. Immunogold electron microscopy and fluorescence localization illustrated that this enzyme is localized in the mitochondria, and its transcription level is up-regulated by low CO2 concentration. These findings showed that Sjγ-CA is a possible component of the CCM in S. japonica. This work is the first to report about the mtCA of macroalgae and provides a basis for further analysis on seaweed CCM.}, }
@article {pmid33307391, year = {2021}, author = {Harshkova, D and Majewska, M and Pokora, W and Baścik-Remisiewicz, A and Tułodziecki, S and Aksmann, A}, title = {Diclofenac and atrazine restrict the growth of a synchronous Chlamydomonas reinhardtii population via various mechanisms.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {230}, number = {}, pages = {105698}, doi = {10.1016/j.aquatox.2020.105698}, pmid = {33307391}, issn = {1879-1514}, mesh = {Antioxidants/metabolism ; Atrazine/*toxicity ; Catalase/metabolism ; Chlamydomonas reinhardtii/*drug effects/*growth &amp; development/metabolism ; Chlorophyll A/metabolism ; Chloroplasts/metabolism ; Diclofenac/*toxicity ; Electron Transport ; Hydrogen Peroxide/metabolism ; Mitochondria/drug effects/metabolism ; Oxidative Stress/drug effects ; Photosynthesis/drug effects ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Non-steroidal anti-inflammatory drug diclofenac (DCF) is commonly found in freshwater bodies and can have adverse effects on non-target organisms. Among the studies on DCF toxicity, several ones have reported its harmful effects on plants and algae. To gain a better understanding of the mechanisms of DCF toxicity towards green algae, we used a synchronous Chlamydomonas reinhardtii cc-1690 culture and compared DCF (135 mg/L) effects with effects caused by atrazine (ATR; 77.6 μg/L), an herbicide with a well-known mechanism of toxic action. To achieve our goal, cell number and size, photosynthetic oxygen consumption/evolution, chlorophyll a fluorescence in vivo, H2O2 production by the cells, antioxidative enzymes encoding genes expression were analyzed during light phase of the cell cycle. We have found, that DCF and ATR affect C. reinhardtii through different mechanisms. ATR inhibited the photosynthetic electron transport chain and induced oxidative stress in chloroplast. Such chloroplastic energetics disruption indirectly influenced respiration, the intensification of which could partially mitigate low efficiency of photosynthetic energy production. As a result, ATR inhibited the growth of single cell leading to limitation in C. reinhardtii population development. In contrast to ATR-treated algae, in DCF-treated cells the fraction of active PSII reaction centers was diminished without drastic changes in electron transport or oxidative stress symptoms in chloroplast. However, significant increase in transcript level of gene encoding for mitochondria-located catalase indicates respiratory processes as a source of H2O2 overproduced in the DCF-treated cells. Because the single cell growth was not strongly affected by DCF, its adverse effect on progeny cell number seemed to be related rather to arresting of cell divisions. Concluding, although the DCF phytotoxic action appeared to be different from the action of the typical herbicide ATR, it can act as algal growth-inhibiting factor in the environment.}, }
@article {pmid33306962, year = {2021}, author = {Namba, T and Nardelli, J and Gressens, P and Huttner, WB}, title = {Metabolic Regulation of Neocortical Expansion in Development and Evolution.}, journal = {Neuron}, volume = {109}, number = {3}, pages = {408-419}, doi = {10.1016/j.neuron.2020.11.014}, pmid = {33306962}, issn = {1097-4199}, mesh = {Animals ; *Biological Evolution ; Cell Proliferation/*physiology ; Humans ; Metabolic Networks and Pathways/*physiology ; Neocortex/*metabolism ; Neural Stem Cells/*metabolism ; Neurogenesis/*physiology ; Neurons/physiology ; }, abstract = {The neocortex, the seat of our higher cognitive abilities, has expanded in size during the evolution of certain mammals such as primates, including humans. This expansion occurs during development and is linked to the proliferative capacity of neural stem and progenitor cells (NPCs) in the neocortex. A number of cell-intrinsic and cell-extrinsic factors have been implicated in increasing NPC proliferative capacity. However, NPC metabolism has only recently emerged as major regulator of NPC proliferation. In this Perspective, we summarize recent insights into the role of NPC metabolism in neocortical development and neurodevelopmental disorders and its relevance for neocortex evolution. We discuss certain human-specific genes and microcephaly-implicated genes that operate in, or at, the mitochondria of NPCs and stimulate their proliferation by promoting glutaminolysis. We also discuss other metabolic pathways and develop a perspective on how metabolism mechanistically regulates NPC proliferation in neocortical development and how this contributed to neocortex evolution.}, }
@article {pmid33302466, year = {2020}, author = {Geary, DC}, title = {Mitochondrial Functions, Cognition, and the Evolution of Intelligence: Reply to Commentaries and Moving Forward.}, journal = {Journal of Intelligence}, volume = {8}, number = {4}, pages = {}, pmid = {33302466}, issn = {2079-3200}, abstract = {In response to commentaries, I address questions regarding the proposal that general intelligence (g) is a manifestation of the functioning of intramodular and intermodular brain networks undergirded by the efficiency of mitochondrial functioning (Geary 2018). The core issues include the relative contribution of mitochondrial functioning to individual differences in g; studies that can be used to test associated hypotheses; and, the adaptive function of intelligence from an evolutionary perspective. I attempt to address these and related issues, as well as note areas in which other issues remain to be addressed.}, }
@article {pmid33301927, year = {2021}, author = {Jaimes Díaz, H and Martínez Covarrubias, EI and Murcia Garzón, JE and Flores Valdez, M and Muñoz Ramírez, ZY and Ramírez Calzada, CA and Bohra, R and Méndez Tenorio, A}, title = {Phylogenomic study and classification of mitochondrial DNA through virtual genomic fingerprints.}, journal = {Mitochondrion}, volume = {57}, number = {}, pages = {294-299}, doi = {10.1016/j.mito.2020.11.016}, pmid = {33301927}, issn = {1872-8278}, mesh = {Animals ; Computer Simulation ; DNA Fingerprinting/*methods ; DNA, Mitochondrial/classification/*genetics ; Genomics/*methods ; Haplotypes ; Humans ; Mitochondria/*classification/genetics ; Neanderthals/genetics ; Pan paniscus/genetics ; Pan troglodytes/genetics ; Phylogeny ; }, abstract = {In the present study, we evaluated the ability of the Virtual Analysis Method for Phylogenomic fingerprint Estimation (VAMPhyRE) toolkit to classify human mitochondrial DNA (mtDNA) haplogroups. In total, 357 random mtDNA sequences were obtained from different haplogroups, based on the classification of PhyloTree. Additionally, we included a control group of five sequences (Pan paniscus, Pan troglodytes, Homo sapiens neanderthalensis, Yoruba15, and the revised Cambridge reference sequence). VAMPhyRE employs a virtual hybridization technique, using probes that specifically bind to their complementary sequences in the genome. We used 65,536 probes of 8 nucleotides to identify potential sites where hybridization occurs between the mtDNA and the specific probe, forming different heteroduplexes and thus, creating a unique and specific genomic fingerprint for each sequence. Genomic fingerprints were compared, and a table of distances was calculated to obtain a mitochondrial phylogenomic tree with the macrohaplogroups, L, N, M, and R, and their corresponding haplogroups, according to universal nomenclature. The results obtained suggest an accuracy of 97.25% for the distribution of the 357 mtDNA sequences in the four macrohaplogroups and their corresponding haplogroups when compared with other mtDNA classification tools that require reference sequences and do not offer an analysis based on an evolutionary approach. These data are available online at http://biomedbiotec.encb.ipn.mx/VAMPhyRE/.}, }
@article {pmid33301801, year = {2021}, author = {Cortassa, S and Juhaszova, M and Aon, MA and Zorov, DB and Sollott, SJ}, title = {Mitochondrial Ca[2+], redox environment and ROS emission in heart failure: Two sides of the same coin?.}, journal = {Journal of molecular and cellular cardiology}, volume = {151}, number = {}, pages = {113-125}, pmid = {33301801}, issn = {1095-8584}, support = {Z99 AG999999/ImNIH/Intramural NIH HHS/United States ; ZIA AG000250/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Animals ; Calcium/*metabolism ; Heart Failure/*metabolism ; Humans ; Mitochondria, Heart/*metabolism ; Oxidation-Reduction ; Oxidative Stress ; Reactive Oxygen Species/*metabolism ; Sodium/metabolism ; }, abstract = {Heart failure (HF) is a progressive, debilitating condition characterized, in part, by altered ionic equilibria, increased ROS production and impaired cellular energy metabolism, contributing to variable profiles of systolic and diastolic dysfunction with significant functional limitations and risk of premature death. We summarize current knowledge concerning changes of intracellular Na[+] and Ca[2+] control mechanisms during the disease progression and their consequences on mitochondrial Ca[2+] homeostasis and the shift in redox balance. Absent existing biological data, our computational modeling studies advance a new 'in silico' analysis to reconcile existing opposing views, based on different experimental HF models, regarding variations in mitochondrial Ca[2+] concentration that participate in triggering and perpetuating oxidative stress in the failing heart and their impact on cardiac energetics. In agreement with our hypothesis and the literature, model simulations demonstrate the possibility that the heart's redox status together with cytoplasmic Na[+] concentrations act as regulators of mitochondrial Ca[2+] levels in HF and of the bioenergetics response that will ultimately drive ATP supply and oxidative stress. The resulting model predictions propose future directions to study the evolution of HF as well as other types of heart disease, and to develop novel testable mechanistic hypotheses that may lead to improved therapeutics.}, }
@article {pmid33301090, year = {2021}, author = {Duminil, J and Besnard, G}, title = {Utility of the Mitochondrial Genome in Plant Taxonomic Studies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2222}, number = {}, pages = {107-118}, pmid = {33301090}, issn = {1940-6029}, mesh = {*DNA Barcoding, Taxonomic ; *Genome, Mitochondrial ; *Genomics/methods ; Phylogeny ; Phylogeography ; Plants/*classification/*genetics ; Polymorphism, Genetic ; Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {Size, structure, and sequence content lability of plant mitochondrial genome (mtDNA) across species has sharply limited its use in taxonomic studies. Historically, mtDNA variation has been first investigated with RFLPs, while the development of universal primers then allowed studying sequence polymorphisms within short genomic regions (<3 kb). The recent advent of NGS technologies now offers new opportunities by greatly facilitating the assembly of longer mtDNA regions, and even full mitogenomes. Phylogenetic works aiming at comparing signals from different genomic compartments (i.e., nucleus, chloroplast, and mitochondria) have been developed on a few plant lineages, and have been shown especially relevant in groups with contrasted inheritance of organelle genomes. This chapter first reviews the main characteristics of mtDNA and the application offered in taxonomic studies. It then presents tips for best sequencing protocol based on NGS data to be routinely used in mtDNA-based phylogenetic studies.}, }
@article {pmid33297963, year = {2020}, author = {Ren, RC and Yan, XW and Zhao, YJ and Wei, YM and Lu, X and Zang, J and Wu, JW and Zheng, GM and Ding, XH and Zhang, XS and Zhao, XY}, title = {The novel E-subgroup pentatricopeptide repeat protein DEK55 is responsible for RNA editing at multiple sites and for the splicing of nad1 and nad4 in maize.}, journal = {BMC plant biology}, volume = {20}, number = {1}, pages = {553}, pmid = {33297963}, issn = {1471-2229}, support = {91735301//National Natural Science Foundation of China/ ; 2016ZX08003-003//The National Plant Transgenic Program/ ; ts201712024//Taishan Scholar Project of Shandong Province/ ; SYL2017YSTD03//Shandong "Double Tops" Program/ ; dxkt201707//the project from State Key Laboratory of Crop Biology/ ; }, mesh = {Base Sequence ; Binding Sites/genetics ; Electron Transport Complex I/*genetics/metabolism ; Gene Expression Regulation, Plant ; Introns/genetics ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/classification/genetics/metabolism ; Mutation ; NADH Dehydrogenase/*genetics/metabolism ; Phylogeny ; Plant Proteins/classification/*genetics/metabolism ; Plants, Genetically Modified ; *RNA Editing ; *RNA Splicing ; Reverse Transcriptase Polymerase Chain Reaction ; Seeds/genetics/metabolism ; Zea mays/*genetics/metabolism ; }, abstract = {BACKGROUND: Pentatricopeptide repeat (PPR) proteins compose a large protein family whose members are involved in both RNA processing in organelles and plant growth. Previous reports have shown that E-subgroup PPR proteins are involved in RNA editing. However, the additional functions and roles of the E-subgroup PPR proteins are unknown.<br><br>RESULTS: In this study, we developed and identified a new maize kernel mutant with arrested embryo and endosperm development, i.e., defective kernel (dek) 55 (dek55). Genetic and molecular evidence suggested that the defective kernels resulted from a mononucleotide alteration (C to T) at +&#x2009;449&#x2009;bp within the open reading frame (ORF) of Zm00001d014471 (hereafter referred to as DEK55). DEK55 encodes an E-subgroup PPR protein within the mitochondria. Molecular analyses showed that the editing percentage of 24 RNA editing sites decreased and that of seven RNA editing sites increased in dek55 kernels, the sites of which were distributed across 14 mitochondrial gene transcripts. Moreover, the splicing efficiency of nad1 introns 1 and 4 and nad4 intron 1 significantly decreased in dek55 compared with the wild type (WT). These results indicate that DEK55 plays a crucial role in RNA editing at multiple sites as well as in the splicing of nad1 and nad4 introns. Mutation in the DEK55 gene led to the dysfunction of mitochondrial complex I. Moreover, yeast two-hybrid assays showed that DEK55 interacts with two multiple organellar RNA-editing factors (MORFs), i.e., ZmMORF1 (Zm00001d049043) and ZmMORF8 (Zm00001d048291).<br><br>CONCLUSIONS: Our results demonstrated that a mutation in the DEK55 gene affects the mitochondrial function essential for maize kernel development. Our results also provide novel insight into the molecular functions of E-subgroup PPR proteins involved in plant organellar RNA processing.}, }
@article {pmid33296646, year = {2020}, author = {Van Keuren, AM and Tsai, CW and Balderas, E and Rodriguez, MX and Chaudhuri, D and Tsai, MF}, title = {Mechanisms of EMRE-Dependent MCU Opening in the Mitochondrial Calcium Uniporter Complex.}, journal = {Cell reports}, volume = {33}, number = {10}, pages = {108486}, pmid = {33296646}, issn = {2211-1247}, support = {R01 GM129345/GM/NIGMS NIH HHS/United States ; R01 HL141353/HL/NHLBI NIH HHS/United States ; }, mesh = {Calcium/metabolism ; Calcium Channels/*metabolism/physiology/ultrastructure ; Calcium-Binding Proteins/*metabolism/physiology/ultrastructure ; Cation Transport Proteins/*metabolism/physiology/ultrastructure ; HEK293 Cells ; Humans ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins/*metabolism/physiology/ultrastructure ; Mitochondrial Membranes/metabolism ; }, abstract = {The mitochondrial calcium uniporter is a multi-subunit Ca[2+]-activated Ca[2+] channel, made up of the pore-forming MCU protein, a metazoan-specific EMRE subunit, and MICU1/MICU2, which mediate Ca[2+] activation. It has been established that metazoan MCU requires EMRE binding to conduct Ca[2+], but how EMRE promotes MCU opening remains unclear. Here, we demonstrate that EMRE controls MCU activity via its transmembrane helix, while using an N-terminal PKP motif to strengthen binding with MCU. Opening of MCU requires hydrophobic interactions mediated by MCU residues near the pore's luminal end. Enhancing these interactions by single mutation allows human MCU to transport Ca[2+] without EMRE. We further show that EMRE may facilitate MCU opening by stabilizing the open state in a conserved MCU gating mechanism, present also in non-metazoan MCU homologs. These results provide insights into the evolution of the uniporter machinery and elucidate the mechanism underlying the physiologically crucial EMRE-dependent MCU activation process.}, }
@article {pmid33293686, year = {2020}, author = {West, KM and Richards, ZT and Harvey, ES and Susac, R and Grealy, A and Bunce, M}, title = {Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {21479}, pmid = {33293686}, issn = {2045-2322}, mesh = {Animals ; Australia ; *Biodiversity ; Cell Nucleus/genetics ; *DNA Barcoding, Taxonomic/methods ; DNA, Environmental/*genetics ; Eukaryota/genetics ; Indian Ocean ; *Metagenomics/methods ; Mitochondria/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Subterranean ecosystems are understudied and challenging to conventionally survey given the inaccessibility of underground voids and networks. In this study, we conducted a eukaryotic environmental DNA (eDNA) metabarcoding survey across the karst landscape of Christmas Island, (Indian Ocean, Australia) to evaluate the utility of this non-invasive technique to detect subterranean aquatic 'stygofauna' assemblages. Three metabarcoding assays targeting the mitochondrial 16S rRNA and nuclear 18S genes were applied to 159 water and sediment samples collected from 23 caves and springs across the island. Taken together, our assays detected a wide diversity of chordates, cnidarians, porifera, arthropods, molluscs, annelids and bryozoans from 71 families across 60 orders. We report a high level of variation between cave and spring subterranean community compositions which are significantly influenced by varying levels of salinity. Additionally, we show that dissolved oxygen and longitudinal gradients significantly affect biotic assemblages within cave communities. Lastly, we combined eDNA-derived community composition and environmental (water quality) data to predict potential underground interconnectivity across Christmas Island. We identified three cave and spring groups that showed a high degree of biotic and abiotic similarity indicating likely local connectivity. This study demonstrates the applicability of eDNA metabarcoding to detect subterranean eukaryotic communities and explore underground interconnectivity.}, }
@article {pmid33289389, year = {2021}, author = {Sureka, R and Mishra, R}, title = {Identification of Evolutionarily Conserved Nuclear Matrix Proteins and Their Prokaryotic Origins.}, journal = {Journal of proteome research}, volume = {20}, number = {1}, pages = {518-530}, doi = {10.1021/acs.jproteome.0c00550}, pmid = {33289389}, issn = {1535-3907}, mesh = {Animals ; *Drosophila melanogaster/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Nuclear Matrix ; *Nuclear Matrix-Associated Proteins ; Phylogeny ; *Prokaryotic Cells ; }, abstract = {Compared to prokaryotic cells, a typical eukaryotic cell is much more complex along with its endomembrane system and membrane-bound organelles. Although the endosymbiosis theories convincingly explain the evolution of membrane-bound organelles such as mitochondria and chloroplasts, very little is understood about the evolutionary origins of the nucleus, the defining feature of eukaryotes. Most studies on nuclear evolution have not been able to take into consideration the underlying structural framework of the nucleus, attributed to the nuclear matrix (NuMat), a ribonucleoproteinaceous structure. This can largely be attributed to the lack of annotation of its core components. Since NuMat has been shown to provide a structural platform for facilitating a variety of nuclear functions such as replication, transcription, and splicing, it is important to identify its protein components to better understand these processes. In this study, we address this issue using the developing embryos of Drosophila melanogaster and Danio rerio and identify 362 core NuMat proteins that are conserved between the two organisms. We further compare our results with publicly available Mus musculus NuMat dataset and Homo sapiens cellular localization dataset to define the core homologous NuMat proteins consisting of 252 proteins. We find that of them, 86 protein groups have originated from pre-existing proteins in prokaryotes. While 36 were conserved across all eukaryotic supergroups, 14 new proteins evolved before the evolution of the last eukaryotic common ancestor and together, these 50 proteins out of the 252 core conserved NuMat proteins are conserved across all eukaryotes, indicating their indispensable nature for nuclear function for over 1.5 billion years of eukaryotic history. Our analysis paves the way to understand the evolution of the complex internal nuclear architecture and its functions.}, }
@article {pmid33287726, year = {2020}, author = {Urantówka, AD and Kroczak, A and Mackiewicz, P}, title = {New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral gene rearrangement in Aves.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {874}, pmid = {33287726}, issn = {1471-2164}, support = {2017/25/N/NZ8/01197//National Science Centre Poland (Narodowe Centrum Nauki, Polska)/ ; 307//Wroclawskie Centrum Sieciowo-Superkomputerowe, Politechnika Wroclawska/ ; }, mesh = {Animals ; Birds/genetics ; Evolution, Molecular ; Gene Rearrangement ; *Genome, Mitochondrial ; *Palaeognathae ; Phylogeny ; }, abstract = {BACKGROUND: Bird mitogenomes differ from other vertebrates in gene rearrangement. The most common avian gene order, identified first in Gallus gallus, is considered ancestral for all Aves. However, other rearrangements including a duplicated control region and neighboring genes have been reported in many representatives of avian orders. The repeated regions can be easily overlooked due to inappropriate DNA amplification or genome sequencing. This raises a question about the actual prevalence of mitogenomic duplications and the validity of the current view on the avian mitogenome evolution. In this context, Palaeognathae is especially interesting because is sister to all other living birds, i.e. Neognathae. So far, a unique duplicated region has been found in one palaeognath mitogenome, that of Eudromia elegans.<br><br>RESULTS: Therefore, we applied an appropriate PCR strategy to look for omitted duplications in other palaeognaths. The analyses revealed the duplicated control regions with adjacent genes in Crypturellus, Rhea and Struthio as well as ND6 pseudogene in three moas. The copies are very similar and were subjected to concerted evolution. Mapping the presence and absence of duplication onto the Palaeognathae phylogeny indicates that the duplication was an ancestral state for this avian group. This feature was inherited by early diverged lineages and lost two times in others. Comparison of incongruent phylogenetic trees based on mitochondrial and nuclear sequences showed that two variants of mitogenomes could exist in the evolution of palaeognaths. Data collected for other avian mitogenomes revealed that the last common ancestor of all birds and early diverging lineages of Neoaves could also possess the mitogenomic duplication.<br><br>CONCLUSIONS: The duplicated control regions with adjacent genes are more common in avian mitochondrial genomes than it was previously thought. These two regions could increase effectiveness of replication and transcription as well as the number of replicating mitogenomes per organelle. In consequence, energy production by mitochondria may be also more efficient. However, further physiological and molecular analyses are necessary to assess the potential selective advantages of the mitogenome duplications.}, }
@article {pmid33280130, year = {2021}, author = {Dahuja, A and Kumar, RR and Sakhare, A and Watts, A and Singh, B and Goswami, S and Sachdev, A and Praveen, S}, title = {Role of ATP-binding cassette transporters in maintaining plant homeostasis under abiotic and biotic stresses.}, journal = {Physiologia plantarum}, volume = {171}, number = {4}, pages = {785-801}, doi = {10.1111/ppl.13302}, pmid = {33280130}, issn = {1399-3054}, support = {Sanction no. TG-3079//Indian Council of Agricultural Research/ ; sanction no. 21-56 TG3064//Indian Council of Agricultural Research/ ; }, mesh = {*ATP-Binding Cassette Transporters/genetics/metabolism ; Biological Transport ; Homeostasis ; *Plants/metabolism ; Stress, Physiological ; }, abstract = {The ATP-binding cassette (ABC) transporters belong to a large protein family predominantly present in diverse species. ABC transporters are driven by ATP hydrolysis and can act as exporters as well as importers. These proteins are localized in the membranes of chloroplasts, mitochondria, peroxisomes and vacuoles. ABC proteins are involved in regulating diverse biological processes in plants, such as growth, development, uptake of nutrients, tolerance to biotic and abiotic stresses, tolerance to metal toxicity, stomatal closure, shape and size of grains, protection of pollens, transport of phytohormones, etc. In mitochondria and chloroplast, the iron metabolism and its transport across the membrane are mediated by ABC transporters. Tonoplast-localized ABC transporters are involved in internal detoxification of metal ion; thus protecting against the DNA impairment and maintaining cell growth. ABC transporters are involved in the transport of secondary metabolites inside the cells. Microorganisms also engage a large number of ABC transporters to import and expel substrates decisive for their pathogenesis. ABC transporters also suppress the seed embryonic growth until favorable conditions come. This review aims at giving insights on ABC transporters, their evolution, structure, functions and roles in different biological processes for helping the terrestrial plants to survive under adverse environmental conditions. These specialized plant membrane transporters ensure a sustainable economic yield and high-quality products, especially under unfavorable conditions of growth. These transporters can be suitably manipulated to develop 'Plants for the Future'.}, }
@article {pmid33279689, year = {2021}, author = {Sun, D and Niu, Z and Zheng, HX and Wu, F and Jiang, L and Han, TQ and Wei, Y and Wang, J and Jin, L}, title = {A Mitochondrial DNA Variant Elevates the Risk of Gallstone Disease by Altering Mitochondrial Function.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {11}, number = {4}, pages = {1211-1226.e15}, pmid = {33279689}, issn = {2352-345X}, mesh = {Adult ; Aged ; Aged, 80 and over ; Asian People/*genetics ; Case-Control Studies ; China/epidemiology ; Cholesterol/metabolism ; DNA, Mitochondrial/analysis/*genetics ; Female ; Gallstones/epidemiology/genetics/*pathology ; *Genetic Predisposition to Disease ; Humans ; Male ; Middle Aged ; Mitochondria/genetics/*pathology ; *Polymorphism, Single Nucleotide ; Risk Factors ; Young Adult ; }, abstract = {BACKGROUND AND AIMS: Gallstone disease (cholelithiasis) is a cholesterol-related metabolic disorders with strong familial predisposition. Mitochondrial DNA (mtDNA) variants accumulated during human evolution are associated with some metabolic disorders related to modified mitochondrial function. The mechanistic links between mtDNA variants and gallstone formation need further exploration.<br><br>METHODS: In this study, we explored the possible associations of mtDNA variants with gallstone disease by comparing 104 probands and 300 controls in a Chinese population. We constructed corresponding cybrids using trans-mitochondrial technology to investigate the underlying mechanisms of these associations. Mitochondrial respiratory chain complex activity and function and cholesterol metabolism were assessed in the trans-mitochondrial cell models.<br><br>RESULTS: Here, we found a significant association of mtDNA 827A>G with an increased risk of familial gallstone disease in a Chinese population (odds ratio [OR]: 4.5, 95% confidence interval [CI]: 2.1-9.4, P=1.2&#xd7;10[-4]). Compared with 827A cybrids (haplogroups B4a and B4c), 827G cybrids (haplogroups B4b and B4d) had impaired mitochondrial respiratory chain complex activity and function and activated JNK and AMPK signaling pathways. Additionally, the 827G cybrids showed disturbances in cholesterol transport and accelerated development of gallstones. Specifically, cholesterol transport through the transporter ABCG5/8 was increased via activation of the AMPK signaling pathway in 827G cybrids.<br><br>CONCLUSIONS: Our findings reveal that mtDNA 827A>G induces aberrant mitochondrial function and abnormal cholesterol transport, resulting in increased occurrence of gallstones. The results provide an important biological basis for the clinical diagnosis and prevention of gallstone disease in the future.}, }
@article {pmid33278586, year = {2021}, author = {Lee, Y and Ni, G and Shin, J and Kim, T and Kern, EMA and Kim, Y and Kim, SC and Chan, B and Goto, R and Nakano, T and Park, JK}, title = {Phylogeography of Mytilisepta virgata (Mytilidae: Bivalvia) in the northwestern Pacific: Cryptic mitochondrial lineages and mito-nuclear discordance.}, journal = {Molecular phylogenetics and evolution}, volume = {157}, number = {}, pages = {107037}, doi = {10.1016/j.ympev.2020.107037}, pmid = {33278586}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Mitochondria/*genetics ; Mytilidae/*genetics ; Pacific Ocean ; Phylogeny ; *Phylogeography ; Principal Component Analysis ; Time Factors ; }, abstract = {The purplish bifurcate mussel Mytilisepta virgata is widely distributed and represents one of the major components of the intertidal community in the northwestern Pacific (NWP). Here, we characterized population genetic structure of NWP populations throughout nearly their whole distribution range using both mitochondrial (mtDNA cox1) and nuclear (ITS1) markers. Population genetic analyses for mtDNA cox 1 sequences revealed two monophyletic lineages (i.e., southern and northern lineages) geographically distributed according to the two different surface water temperature zones in the NWP. The timing of the lineage split is estimated at the Pliocene- mid-Pleistocene (5.49-1.61 Mya), which is consistent with the timing of the historical isolation of the East Sea/Sea of Japan from the South and East China Seas due to sea level decline during glacial cycles. Historical sea level fluctuation during the Pliocene-Pleistocene and subsequent adaptation of mussels to different surface water temperature zones may have contributed to shaping the contemporary genetic diversity and deep divergence of the two mitochondrial lineages. In contrast to mtDNA sequences, a clear lineage split between the two mitochondrial lineages was not found in ITS1 sequences, which showed a star-like structure composed of a mixture of southern and northern mitochondrial lineages. Possible reasons for this type of mito-nuclear discordance include stochastic divergence in the coalescent processes of the two molecular markers, or balancing selection under different marine environments. Cryptic speciation cannot be ruled out from these results, and future work using genomic analyses is required to address whether the thermal physiology of these mussels corresponds to the deep divergence of their mitochondrial genes and to test for the existence of morphologically indistinguishable but genetically separate cryptic species.}, }
@article {pmid33278511, year = {2021}, author = {Rukavina-Mikusic, IA and Rey, M and Martinefski, M and Tripodi, V and Valdez, LB}, title = {Temporal evolution of cardiac mitochondrial dysfunction in a type 1 diabetes model. Mitochondrial complex I impairment, and H2O2 and NO productions as early subcellular events.}, journal = {Free radical biology &amp; medicine}, volume = {162}, number = {}, pages = {129-140}, doi = {10.1016/j.freeradbiomed.2020.11.033}, pmid = {33278511}, issn = {1873-4596}, mesh = {Animals ; *Diabetes Mellitus, Experimental ; *Diabetes Mellitus, Type 1/chemically induced ; Hydrogen Peroxide ; Male ; Mitochondria, Heart ; Rats ; Rats, Wistar ; }, abstract = {The aim of this work was to study the early events that occur in heart mitochondria and to analyse the temporal evolution of cardiac mitochondrial dysfunction in a type 1 diabetes model. Male Wistar rats were injected with Streptozotocin (STZ, single dose, 60 mg × kg[-1], i.p.) and hyperglycemic state was confirmed 72 h later. The animals were sacrificed 10 or 14 days after STZ-injection. Heart mitochondrial state 3 O2 consumption sustained by malate-glutamate (21%) or by succinate (16%), and complexes I-III (27%), II-III (24%) and IV (22%) activities were lower in STZ group, when animals were sacrificed at day 14, i.e. ~11 days of hyperglycemia. In contrast, after 10 days of STZ-injection (~7 days of hyperglycemia), only the state 3 O2 consumption sustained by malate-glutamate (23%) and its corresponding respiratory control (30%) were lower in diabetic rats, in accordance with complex I-III activity reduction (17%). Therefore, this time (~7 days of hyperglycemia) has been considered as an "early stage" of cardiac mitochondrial dysfunction. At this point, mitochondrial production rates of H2O2 (117%), NO (30%) and ONOO[-] (~225%), and mtNOS expression (29%) were higher; and mitochondrial SOD activity (15%) and [GSH + GSSG] (28%) were lower in diabetic rats. Linear correlations between the modified mitochondrial parameters and glycemias were observed. PGC-1α expression was similar between groups, suggesting that mitochondrial biogenesis was not triggered in this initial phase of mitochondrial dysfunction. Consequently, complex I, H2O2 and NO could be considered early subcellular signals of cardiac mitochondrial dysfunction, with NO and H2O2 being located upstream de novo synthesis of mitochondria.}, }
@article {pmid33270708, year = {2020}, author = {Dell, AC and Curry, MC and Yarnell, KM and Starbuck, GR and Wilson, PB}, title = {Mitochondrial D-loop sequence variation and maternal lineage in the endangered Cleveland Bay horse.}, journal = {PloS one}, volume = {15}, number = {12}, pages = {e0243247}, pmid = {33270708}, issn = {1932-6203}, mesh = {Animals ; Cluster Analysis ; DNA, Mitochondrial/*genetics ; Endangered Species ; Genetic Variation/genetics ; Haplotypes/genetics ; Horses/*genetics ; Maternal Inheritance/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods/veterinary ; }, abstract = {Genetic diversity and maternal ancestry line relationships amongst a sample of 96 Cleveland Bay horses were investigated using a 479bp length of mitochondrial D-loop sequence. The analysis yielded at total of 11 haplotypes with 27 variable positions, all of which have been described in previous equine mitochondrial DNA d-loop studies. Four main haplotype clusters were present in the Cleveland Bay breed describing 89% of the total sample. This suggests that only four principal maternal ancestry lines exist in the present-day global Cleveland Bay population. Comparison of these sequences with other domestic horse haplotypes (Fig 2) shows a close association of the Cleveland Bay horse with Northern European (Clade C), Iberian (Clade A) and North African (Clade B) horse breeds. This indicates that the Cleveland Bay horse may not have evolved exclusively from the now extinct Chapman horse, as previous work as suggested. The Cleveland Bay horse remains one of only five domestic horse breeds classified as Critical on the Rare Breeds Survival Trust (UK) Watchlist and our results provide important information on the origins of this breed and represent a valuable tool for conservation purposes.}, }
@article {pmid33266387, year = {2020}, author = {Schirrmacher, V}, title = {Mitochondria at Work: New Insights into Regulation and Dysregulation of Cellular Energy Supply and Metabolism.}, journal = {Biomedicines}, volume = {8}, number = {11}, pages = {}, pmid = {33266387}, issn = {2227-9059}, abstract = {Mitochondria are of great relevance to health, and their dysregulation is associated with major chronic diseases. Research on mitochondria-156 brand new publications from 2019 and 2020-have contributed to this review. Mitochondria have been fundamental for the evolution of complex organisms. As important and semi-autonomous organelles in cells, they can adapt their function to the needs of the respective organ. They can program their function to energy supply (e.g., to keep heart muscle cells going, life-long) or to metabolism (e.g., to support hepatocytes and liver function). The capacity of mitochondria to re-program between different options is important for all cell types that are capable of changing between a resting state and cell proliferation, such as stem cells and immune cells. Major chronic diseases are characterized by mitochondrial dysregulation. This will be exemplified by cardiovascular diseases, metabolic syndrome, neurodegenerative diseases, immune system disorders, and cancer. New strategies for intervention in chronic diseases will be presented. The tumor microenvironment can be considered a battlefield between cancer and immune defense, competing for energy supply and metabolism. Cancer cachexia is considered as a final stage of cancer progression. Nevertheless, the review will present an example of complete remission of cachexia via immune cell transfer. These findings should encourage studies along the lines of mitochondria, energy supply, and metabolism.}, }
@article {pmid33263877, year = {2020}, author = {Lupette, J and Maréchal, E}, title = {The Puzzling Conservation and Diversification of Lipid Droplets from Bacteria to Eukaryotes.}, journal = {Results and problems in cell differentiation}, volume = {69}, number = {}, pages = {281-334}, pmid = {33263877}, issn = {0080-1844}, mesh = {Bacteria/*chemistry/genetics ; Biological Evolution ; Eukaryota/*chemistry/genetics ; Lipid Droplets/*chemistry ; Organelles ; Plastids ; Symbiosis ; }, abstract = {Membrane compartments are amongst the most fascinating markers of cell evolution from prokaryotes to eukaryotes, some being conserved and the others having emerged via a series of primary and secondary endosymbiosis events. Membrane compartments comprise the system limiting cells (one or two membranes in bacteria, a unique plasma membrane in eukaryotes) and a variety of internal vesicular, subspherical, tubular, or reticulated organelles. In eukaryotes, the internal membranes comprise on the one hand the general endomembrane system, a dynamic network including organelles like the endoplasmic reticulum, the Golgi apparatus, the nuclear envelope, etc. and also the plasma membrane, which are linked via direct lateral connectivity (e.g. between the endoplasmic reticulum and the nuclear outer envelope membrane) or indirectly via vesicular trafficking. On the other hand, semi-autonomous organelles, i.e. mitochondria and chloroplasts, are disconnected from the endomembrane system and request vertical transmission following cell division. Membranes are organized as lipid bilayers in which proteins are embedded. The budding of some of these membranes, leading to the formation of the so-called lipid droplets (LDs) loaded with hydrophobic molecules, most notably triacylglycerol, is conserved in all clades. The evolution of eukaryotes is marked by the acquisition of mitochondria and simple plastids from Gram-positive bacteria by primary endosymbiosis events and the emergence of extremely complex plastids, collectively called secondary plastids, bounded by three to four membranes, following multiple and independent secondary endosymbiosis events. There is currently no consensus view of the evolution of LDs in the Tree of Life. Some features are conserved; others show a striking level of diversification. Here, we summarize the current knowledge on the architecture, dynamics, and multitude of functions of the lipid droplets in prokaryotes and in eukaryotes deriving from primary and secondary endosymbiosis events.}, }
@article {pmid33263876, year = {2020}, author = {Kaczanowski, S}, title = {Symbiotic Origin of Apoptosis.}, journal = {Results and problems in cell differentiation}, volume = {69}, number = {}, pages = {253-280}, pmid = {33263876}, issn = {0080-1844}, mesh = {Animals ; *Apoptosis ; *Biological Evolution ; *Eukaryota ; Mitochondria/*microbiology ; Phylogeny ; *Symbiosis ; }, abstract = {The progress of evolutionary biology has revealed that symbiosis played a basic role in the evolution of complex eukaryotic organisms, including humans. Mitochondria are actually simplified endosymbiotic bacteria currently playing the role of cellular organelles. Mitochondrial domestication occurred at the very beginning of eukaryotic evolution. Mitochondria have two different basic functions: they produce energy using oxidative respiration, and they initiate different forms of apoptotic programmed/regulated cell death. Apoptotic programmed cell death may have different cytological forms. Mechanisms of apoptotic programmed cell death exist even in the unicellular organisms, and they play a basic role in the development of complex multicellular organisms, such as fungi, green plants, and animals. Multicellularity was independently established many times among eukaryotes. There are indications that apoptotic programmed cell death is a trait required for the establishment of multicellularity. Regulated cell death is initiated by many different parallel biochemical pathways. It is generally accepted that apoptosis evolved during mitochondrial domestication. However, there are different hypothetical models of the origin of apoptosis. The phylogenetic studies of my group indicate that apoptosis probably evolved during an evolutionary arms race between host ancestral eukaryotic predators and ancestral prey mitochondria (named protomitochondria). Protomitochondrial prey produced many different toxins as a defense against predators. From these toxins evolved extant apoptotic factors. There are indications that aerobic respiration and apoptosis co-evolved and are functionally linked in extant organisms. Perturbations of apoptosis and oxidative respiration are frequently observed during neoplastic transition. Our group showed that perturbations of apoptosis in yeasts also cause perturbations of oxidative respiration.}, }
@article {pmid33257722, year = {2020}, author = {Mannen, H and Yonezawa, T and Murata, K and Noda, A and Kawaguchi, F and Sasazaki, S and Olivieri, A and Achilli, A and Torroni, A}, title = {Cattle mitogenome variation reveals a post-glacial expansion of haplogroup P and an early incorporation into northeast Asian domestic herds.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {20842}, pmid = {33257722}, issn = {2045-2322}, mesh = {Animals ; Base Sequence/genetics ; Breeding/methods ; Cattle/*genetics ; Chromosomes/genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genetic Variation/genetics ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; Japan ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Surveys of mitochondrial DNA (mtDNA) variation have shown that worldwide domestic cattle are characterized by just a few major haplogroups. Two, T and I, are common and characterize Bos taurus and Bos indicus, respectively, while the other three, P, Q and R, are rare and are found only in taurine breeds. Haplogroup P is typical of extinct European aurochs, while intriguingly modern P mtDNAs have only been found in northeast Asian cattle. These Asian P mtDNAs are extremely rare with the exception of the Japanese Shorthorn breed, where they reach a frequency of 45.9%. To shed light on the origin of this haplogroup in northeast Asian cattle, we completely sequenced 14 Japanese Shorthorn mitogenomes belonging to haplogroup P. Phylogenetic and Bayesian analyses revealed: (1) a post-glacial expansion of aurochs carrying haplogroup P from Europe to Asia; (2) that all Asian P mtDNAs belong to a single sub-haplogroup (P1a), so far never detected in either European or Asian aurochs remains, which was incorporated into domestic cattle of continental northeastern Asia possibly ~ 3700 years ago; and (3) that haplogroup P1a mtDNAs found in the Japanese Shorthorn breed probably reached Japan about 650 years ago from Mongolia/Russia, in agreement with historical evidence.}, }
@article {pmid33255957, year = {2020}, author = {King, MS and Tavoulari, S and Mavridou, V and King, AC and Mifsud, J and Kunji, ERS}, title = {A Single Cysteine Residue in the Translocation Pathway of the Mitosomal ADP/ATP Carrier from Cryptosporidium parvum Confers a Broad Nucleotide Specificity.}, journal = {International journal of molecular sciences}, volume = {21}, number = {23}, pages = {}, pmid = {33255957}, issn = {1422-0067}, support = {MC_UU_00015/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Atractyloside/analogs &amp; derivatives/chemistry ; Bongkrekic Acid/chemistry ; Cryptosporidium parvum/*metabolism ; Cysteine/*metabolism ; Lactococcus lactis/metabolism ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/*chemistry/*metabolism ; Models, Molecular ; Mutant Proteins/chemistry/metabolism ; Nucleotides/*metabolism ; Phylogeny ; Protein Translocation Systems/*metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Structure-Activity Relationship ; Substrate Specificity ; }, abstract = {Cryptosporidiumparvum is a clinically important eukaryotic parasite that causes the disease cryptosporidiosis, which manifests with gastroenteritis-like symptoms. The protist has mitosomes, which are organelles of mitochondrial origin that have only been partially characterized. The genome encodes a highly reduced set of transport proteins of the SLC25 mitochondrial carrier family of unknown function. Here, we have studied the transport properties of one member of the C. parvum carrier family, demonstrating that it resembles the mitochondrial ADP/ATP carrier of eukaryotes. However, this carrier has a broader substrate specificity for nucleotides, transporting adenosine, thymidine, and uridine di- and triphosphates in contrast to its mitochondrial orthologues, which have a strict substrate specificity for ADP and ATP. Inspection of the putative translocation pathway highlights a cysteine residue, which is a serine in mitochondrial ADP/ATP carriers. When the serine residue is replaced by cysteine or larger hydrophobic residues in the yeast mitochondrial ADP/ATP carrier, the substrate specificity becomes broad, showing that this residue is important for nucleotide base selectivity in ADP/ATP carriers.}, }
@article {pmid33253201, year = {2020}, author = {Bjedov, I and Cochemé, HM and Foley, A and Wieser, D and Woodling, NS and Castillo-Quan, JI and Norvaisas, P and Lujan, C and Regan, JC and Toivonen, JM and Murphy, MP and Thornton, J and Kinghorn, KJ and Neufeld, TP and Cabreiro, F and Partridge, L}, title = {Fine-tuning autophagy maximises lifespan and is associated with changes in mitochondrial gene expression in Drosophila.}, journal = {PLoS genetics}, volume = {16}, number = {11}, pages = {e1009083}, pmid = {33253201}, issn = {1553-7404}, support = {MC_UP_1605/6/MRC_/Medical Research Council/United Kingdom ; 214589/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; C416/A25145/CRUK_/Cancer Research UK/United Kingdom ; 102532/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; MC_UP_1102/10/MRC_/Medical Research Council/United Kingdom ; 102531/Z/13/A/WT_/Wellcome Trust/United Kingdom ; MC-A654-5QC80/MRC_/Medical Research Council/United Kingdom ; MR/M02492X/1/MRC_/Medical Research Council/United Kingdom ; MC_UU_00015/3/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Aging/genetics ; Animals ; Autophagy/*genetics ; Autophagy-Related Protein-1 Homolog/genetics/metabolism ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/genetics ; Gene Expression/genetics ; Gene Expression Regulation/genetics ; Genes, Mitochondrial/genetics ; Insulin Receptor Substrate Proteins/genetics/metabolism ; Longevity/*genetics ; Mitochondria/*genetics ; Protein Serine-Threonine Kinases/genetics ; Receptor, Insulin/genetics ; Signal Transduction ; }, abstract = {Increased cellular degradation by autophagy is a feature of many interventions that delay ageing. We report here that increased autophagy is necessary for reduced insulin-like signalling (IIS) to extend lifespan in Drosophila and is sufficient on its own to increase lifespan. We first established that the well-characterised lifespan extension associated with deletion of the insulin receptor substrate chico was completely abrogated by downregulation of the essential autophagy gene Atg5. We next directly induced autophagy by over-expressing the major autophagy kinase Atg1 and found that a mild increase in autophagy extended lifespan. Interestingly, strong Atg1 up-regulation was detrimental to lifespan. Transcriptomic and metabolomic approaches identified specific signatures mediated by varying levels of autophagy in flies. Transcriptional upregulation of mitochondrial-related genes was the signature most specifically associated with mild Atg1 upregulation and extended lifespan, whereas short-lived flies, possessing strong Atg1 overexpression, showed reduced mitochondrial metabolism and up-regulated immune system pathways. Increased proteasomal activity and reduced triacylglycerol levels were features shared by both moderate and high Atg1 overexpression conditions. These contrasting effects of autophagy on ageing and differential metabolic profiles highlight the importance of fine-tuning autophagy levels to achieve optimal healthspan and disease prevention.}, }
@article {pmid33248204, year = {2021}, author = {Beldade, R and Longo, GC and Clements, KD and Robertson, DR and Perez-Matus, A and Itoi, S and Sugita, H and Bernardi, G}, title = {Evolutionary origin of the Atlantic Cabo Verde nibbler (Girella stuebeli), a member of a primarily Pacific Ocean family of antitropical herbivorous reef fishes.}, journal = {Molecular phylogenetics and evolution}, volume = {156}, number = {}, pages = {107021}, doi = {10.1016/j.ympev.2020.107021}, pmid = {33248204}, issn = {1095-9513}, mesh = {Animals ; Atlantic Ocean ; *Biological Evolution ; Cabo Verde ; Calibration ; *Coral Reefs ; Geography ; Mitochondria/genetics ; Pacific Ocean ; Perciformes/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Time Factors ; }, abstract = {Nibblers (family Girellidae) are reef fishes that are mostly distributed in the Indo-Pacific, with one exception: Girella stuebeli, which is found in the Cabo Verde Archipelago, in the Atlantic Ocean. We capitalized on this unusual distribution to study the evolutionary history of the girellids, and determine the relationship between G. stuebeli and the remaining nibbler taxa. Based on thousands of genomic markers (RAD sequences), we identified the closest relatives of G. stuebeli as being a clade of three species endemic to the northwestern Pacific, restricted to the Sea of Japan and vicinity. This clade diverged from G. stuebeli approximately 2.2 Mya. Two alternative potential routes of migration may explain this affinity: a western route, from the Tropical Eastern Pacific and the Tropical Western Atlantic, and an eastern route via the Indian Ocean and Southern Africa. The geological history and oceanography of the regions combined with molecular data presented here, suggest that the eastern route of invasion (via the Indian Ocean and Southern Africa) is a more likely scenario.}, }
@article {pmid33248045, year = {2021}, author = {Song, L and Gao, C and Xue, T and Yang, N and Fu, Q and Zhu, Q and Ge, X and Li, C}, title = {Characterization and expression analysis of mitochondrial localization molecule: NOD-like receptor X1 (Nlrx1) in mucosal tissues of turbot (Scophthalmus maximus) following bacterial challenge.}, journal = {Developmental and comparative immunology}, volume = {116}, number = {}, pages = {103944}, doi = {10.1016/j.dci.2020.103944}, pmid = {33248045}, issn = {1879-0089}, mesh = {Amino Acid Sequence ; Animals ; Cytoplasm/metabolism ; Fish Diseases/immunology/microbiology ; Fish Proteins/genetics/metabolism ; Flatfishes/*immunology/microbiology ; Gene Expression Profiling ; HEK293 Cells ; Humans ; Mitochondrial Proteins/genetics/*immunology/metabolism ; Mucous Membrane/*immunology/microbiology ; Phylogeny ; Protein Interaction Maps ; RNA, Messenger/genetics/metabolism ; Sequence Alignment ; Streptococcus iniae/physiology ; Vibrio/physiology ; }, abstract = {The NOD-like receptor X1 (NLRX1) is a member of highly conserved nucleotide-binding domain (NBD)- and leucine-rich-repeat (LRR)-containing family (known as NLR), that localizes to the mitochondrial outer membrane and regulate the innate immunity by interacting with mitochondrial antiviral-signaling protein (MAVS). As one of cytoplasmic PRRs, NLRX1 plays key roles for pathogen recognition, autophagy and regulating of subsequent immune signaling pathways. In this study, we identified the nlrx1 in turbot as well as its expression profiles in mucosal surfaces following bacterial infection. In our results, the full-length nlrx1 transcript consists of an open reading frame (ORF) of 4,886 bp encoding the putative peptide of 966 amino acids. The phylogenetic analysis revealed the SmNlrx1 showed the closest relationship to Cynoglossus semilaevis. In addition, the Nlrx1 mRNA expression could be detected in all the examined tissues, with the most abundant expression level in head kidney, and the lowest expression level in liver. Moreover, Nlrx1 showed similar expression patterns following Vibrio anguillarum and Streptococcus iniae infection, that were both significantly up-regulated following challenge, especially post S. iniae challenge. Finally, fluorescence microscopy unveiled that the SmNlrx1 localized to mitochondria in HEK293T by N-terminal mitochondrial targeting sequence. Characterization of Nlrx1 might have an important implication in bioenergetic adaptation during metabolic stress, oncogenic transformation and innate immunity and will probably contribute to the development of novel intervention strategies for farming turbot.}, }
@article {pmid33247794, year = {2021}, author = {Bagherfard, S and Najafi, N and Gharzi, A and Akmali, V}, title = {Lack of intraspecific variations of the mitochondrial cytochrome b gene in the greater mouse-tailed bat Rhinopoma microphyllum (Chiroptera: Rhinopomatidae) in Iran.}, journal = {Genetica}, volume = {149}, number = {1}, pages = {37-45}, pmid = {33247794}, issn = {1573-6857}, mesh = {Animals ; Chiroptera/classification/*genetics ; Cytochromes b/*genetics ; DNA, Mitochondrial/*genetics ; *Genetic Speciation ; Genetic Variation/genetics ; Genetics, Population ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeography ; Species Specificity ; }, abstract = {Rhinopoma microphyllum is one of the species of bats that lives in arid and semi-arid areas of Iran. The initial suggestion of the presence of two subspecies R. m. microphyllum and R. m. harrisoni based on their morphological characteristics has been questioned on the basis of small differences between the populations. Later, other researchers assigned Iranian populations of this species to one or two subspecies based on their morphological and molecular characteristics. The present study provides a phylogeographical analysis of this species using 687 bp of the mitochondrial cytochrome b in 81 bats in Iran, Jordan, Levant and Ethiopia. Based on mtDNA sequences, we found a low degree of genetic diversity in the Iranian populations of R. microphyllum (π = 0.0025), which shows a close relationship between the haplotypes. The analysis of genetic distance (0.15-1.93%), phylogenetic trees, and statistical parsimony network showed that all Iranian samples were grouped in the same clade, while Levant, Jordan and Ethiopian samples belonged to a different clade. Molecular dating suggested the Iranian R. microphyllum lineage split from the R. microphyllum of the Levant and Jordan clade during the Pliocene 3.18 (2.11-4.32 Ma). Taking these results into consideration, we can conclude that all Iranian specimens belong to the same subspecies as R. m. harrisoni since molecular results indicate that Iranian samples are differ from Levant subspecies (R. m. microphyllum).}, }
@article {pmid33245800, year = {2021}, author = {Wang, W and Hou, S and Chen, G and Xia, L and Chen, J and Wang, Z and Lu, Y}, title = {Characterization and function study of a glutamyl endopeptidase homolog from Nocardia seriolae.}, journal = {Journal of fish diseases}, volume = {44}, number = {6}, pages = {813-821}, doi = {10.1111/jfd.13311}, pmid = {33245800}, issn = {1365-2761}, support = {KJYF202001-08//Science Technology Innovation and Industrial Development of Shenzhen Dapeng New District/ ; JCYJ20180306173022502//Shenzhen Science and Technology Project/ ; JCYJ20180507183240459//Shenzhen Science and Technology Project/ ; 231419017//Research Projects of Guangdong Ocean University's Top-ranking Discipline Construction/ ; }, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry/*genetics/metabolism ; Base Sequence ; Fish Diseases/microbiology ; Nocardia/*genetics/metabolism ; Nocardia Infections/microbiology/veterinary ; Phylogeny ; Sequence Alignment ; Serine Endopeptidases/chemistry/*genetics/metabolism ; }, abstract = {Glutamic endopeptidases (Glu), belonging to the class of serine proteases, are a subfamily of chymotrypsin-like proteolytic enzymes, which are regarded as important virulence factors in bacteria. However, the roles of glutamic endopeptidases of Nocardia seriolae in pathogenic process still remain uncertain. Here, a glutamic endopeptidase homolog from N. seriolae (GluNS) was cloned and its function was elucidated. GluNS encoded a 414-aa protein which shared 93% identity to N. concava. In the phylogenetic tree, the glutamic endopeptidases of genus Nocardia clustered together firstly and then clustered with Streptomyces species. Moreover, GluNS was identified to be a secreted protein of N. seriolae and localized in the mitochondria of FHM cells. The transient overexpression of GluNS significantly induced increase in caspase-3 activity and decrease in ΔΨm values in FHM cells. The number of apoptotic bodies was remarkably higher than that in control group. Taken together, GluNS overexpression induced apoptotic characteristics in FHM cells. This study provided new insights into the function of glutamic endopeptidase from N. seriolae.}, }
@article {pmid33239750, year = {2020}, author = {Rees, DJ and Poulsen, JY and Sutton, TT and Costa, PAS and Landaeta, MF}, title = {Global phylogeography suggests extensive eucosmopolitanism in Mesopelagic Fishes (Maurolicus: Sternoptychidae).}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {20544}, pmid = {33239750}, issn = {2045-2322}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Fishes/*genetics/metabolism ; Genetic Variation/genetics ; Genotype ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeny ; Phylogeography/methods ; Sequence Analysis, DNA/methods ; Species Specificity ; }, abstract = {Fishes in the mesopelagic zone (200-1000 m) have recently been highlighted for potential exploitation. Here we assess global phylogeography in Maurolicus, the Pearlsides, an ecologically important group. We obtained new sequences from mitochondrial COI and nuclear ITS-2 from multiple locations worldwide, representing 10 described species plus an unknown central South Pacific taxon. Phylogenetic analyses identified five geographically distinct groupings, three of which comprise multiple described species. Species delimitation analyses suggest these may represent four species. Maurolicus muelleri and M. australis are potentially a single species, although as no shared haplotypes are found between the two disjunct groups, we suggest maintenance of these as two species. Maurolicus australis is a predominantly southern hemisphere species found in the Pacific, Indian and southern South Atlantic Oceans, comprising five previously allopatric species. M. muelleri (previously two species) is distributed in the North Atlantic and Mediterranean Sea. Maurolicus weitzmani (previously two species) inhabits the eastern equatorial Atlantic, Gulf of Mexico and western North and South Atlantic. Maurolicus mucronatus is restricted to the Red Sea. No Maurolicus have previously been reported in the central South Pacific but we have identified a distinct lineage from this region, which forms a sister group to Maurolicus from the Red Sea.}, }
@article {pmid33231829, year = {2021}, author = {Mirahmadi, H and Behravan, M and Raz, A and Tasa, D and Namaei, MH and Solgi, R}, title = {Genotyping of the Echinococcus granulosus in Paraffin-Embedded Human Tissue Samples from Iran.}, journal = {Acta parasitologica}, volume = {66}, number = {2}, pages = {535-542}, pmid = {33231829}, issn = {1896-1851}, support = {5303//Birjand University of Medical Sciences/ ; }, mesh = {Animals ; *Echinococcus granulosus/genetics ; Genotype ; Humans ; Iran/epidemiology ; Paraffin Embedding ; Phylogeny ; Sheep ; }, abstract = {PURPOSE: Cystic Echinococcosis (CE) is a medically important disease that is caused by the metacestodes of Echinococcus granulosus. Human hydatid is considered an endemic disease in specific regions of Iran. The goal of the present study was to determine the genetic diversity of E. granulosus from the paraffin-embedded human tissue samples which were collected from the endemic regions of Iran.<br><br>METHODS: Fifty-five formalin-fixed and paraffin-embedded hydatid cysts (FFPE) of humans, which had been removed surgically, were obtained from the South Khorasan and Sistan and Baluchistan provinces. These regions are related to the East and Southeast regions of Iran, respectively. The cox1 and nad1 genes from mitochondria were amplified from the extracted DNA and sequenced. The sequences were edited using the BioEdit software. Furthermore, phylogenetic and genetic diversity analyses were performed.<br><br>RESULTS: Sequencing of the cox1 and nad1 genes from the 44 CE samples was done successfully. Genetic analysis revealed that 38 (86.3%) and 6 (13.6%) of the isolates were G1- and G6-genotypes, respectively. In general, eight and six haplotypes were identified by cox1 and nad1 genes analysis, respectively. For G1 strains, the haplotype diversity index was higher for the cox1 gene (0.6&#x2009;&#xb1;&#x2009;0.07) in comparison with the nad1 gene (0.4&#x2009;&#xb1;&#x2009;0.09).<br><br>CONCLUSION: The findings of the present study showed that the sheep strain (G1) and the less important camel strain (G6) play the main roles in the transmission cycle of CE in the East and Southeast regions of Iran. Therefore, these results could be useful for managing the hydatid disease control programs in the studied and other similar areas.}, }
@article {pmid33230146, year = {2020}, author = {Yu, H and Haja, DK and Schut, GJ and Wu, CH and Meng, X and Zhao, G and Li, H and Adams, MWW}, title = {Structure of the respiratory MBS complex reveals iron-sulfur cluster catalyzed sulfane sulfur reduction in ancient life.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5953}, pmid = {33230146}, issn = {2041-1723}, mesh = {Catalysis ; Catalytic Domain ; Cryoelectron Microscopy ; Electron Transport Complex I/chemistry/metabolism ; Hydrogenase/chemistry/metabolism ; Iron-Sulfur Proteins/*chemistry/*metabolism ; Mitochondrial Membranes/enzymology/metabolism ; Models, Molecular ; Origin of Life ; Oxidation-Reduction ; Oxidoreductases/*chemistry/*metabolism ; Proton Pumps/chemistry ; Pyrococcus furiosus/chemistry/enzymology ; Sodium-Hydrogen Exchangers/chemistry ; Sulfur/*metabolism ; }, abstract = {Modern day aerobic respiration in mitochondria involving complex I converts redox energy into chemical energy and likely evolved from a simple anaerobic system now represented by hydrogen gas-evolving hydrogenase (MBH) where protons are the terminal electron acceptor. Here we present the cryo-EM structure of an early ancestor in the evolution of complex I, the elemental sulfur (S[0])-reducing reductase MBS. Three highly conserved protein loops linking cytoplasmic and membrane domains enable scalable energy conversion in all three complexes. MBS contains two proton pumps compared to one in MBH and likely conserves twice the energy. The structure also reveals evolutionary adaptations of MBH that enabled S[0] reduction by MBS catalyzed by a site-differentiated iron-sulfur cluster without participation of protons or amino acid residues. This is the simplest mechanism proposed for reduction of inorganic or organic disulfides. It is of fundamental significance in the iron and sulfur-rich volcanic environments of early earth and possibly the origin of life. MBS provides a new perspective on the evolution of modern-day respiratory complexes and of catalysis by biological iron-sulfur clusters.}, }
@article {pmid33229320, year = {2020}, author = {Gao, ZW and Wang, L}, title = {[Progress in elucidating the origin of eukaryotes].}, journal = {Yi chuan = Hereditas}, volume = {42}, number = {10}, pages = {929-948}, doi = {10.16288/j.yczz.20-107}, pmid = {33229320}, issn = {0253-9772}, mesh = {Archaea/classification/genetics ; *Biological Evolution ; *Eukaryota/classification/genetics ; Research/trends ; }, abstract = {Knowledge of the origin of eukaryotes is key to broadening our understanding of the eukaryotic genome and the relationship among internal structures within a eukaryotic cell. Since the discovery of archaea in 1977 and the proposal of three-domain tree of life by the American microbiologist Carl Woese, the intimate relationship in evolution between eukaryotes and archaea has been demonstrated by considerable experiments and analyses. From the beginning of the 21st century, with the development of phylogenetic methods and the discovery of new archaeal phyla more related to eukaryotes, increasing evidence has shown that Eukarya and Archaea should be merged into one domain, leading to a two-domain tree of life. Nowadays, the Asgard superphylum discovered via metagenomic analysis is regarded as the closest prokaryotes to eukaryotes. Nevertheless, several key questions are still under debate, such as what the ancestors of the eukaryotes were and when mitochondria emerged. Here, we review the current research progress regarding the changes of the tree of life and the detailed eukaryotic evolutionary mechanism. We show that the recent findings have greatly improved our knowledge on the origin of eukaryotes, which will pave the way for future studies.}, }
@article {pmid33228188, year = {2020}, author = {Peralta-Castro, A and García-Medel, PL and Baruch-Torres, N and Trasviña-Arenas, CH and Juarez-Quintero, V and Morales-Vazquez, CM and Brieba, LG}, title = {Plant Organellar DNA Polymerases Evolved Multifunctionality through the Acquisition of Novel Amino Acid Insertions.}, journal = {Genes}, volume = {11}, number = {11}, pages = {}, pmid = {33228188}, issn = {2073-4425}, mesh = {Amino Acids/genetics/metabolism ; Arabidopsis/genetics ; Arabidopsis Proteins/genetics/metabolism ; DNA End-Joining Repair/physiology ; DNA Repair/*physiology ; DNA-Directed DNA Polymerase/*genetics/metabolism ; Evolution, Molecular ; Organelles/*enzymology ; Plant Proteins/*genetics/metabolism ; }, abstract = {The majority of DNA polymerases (DNAPs) are specialized enzymes with specific roles in DNA replication, translesion DNA synthesis (TLS), or DNA repair. The enzymatic characteristics to perform accurate DNA replication are in apparent contradiction with TLS or DNA repair abilities. For instance, replicative DNAPs incorporate nucleotides with high fidelity and processivity, whereas TLS DNAPs are low-fidelity polymerases with distributive nucleotide incorporation. Plant organelles (mitochondria and chloroplast) are replicated by family-A DNA polymerases that are both replicative and TLS DNAPs. Furthermore, plant organellar DNA polymerases from the plant model Arabidopsis thaliana (AtPOLIs) execute repair of double-stranded breaks by microhomology-mediated end-joining and perform Base Excision Repair (BER) using lyase and strand-displacement activities. AtPOLIs harbor three unique insertions in their polymerization domain that are associated with TLS, microhomology-mediated end-joining (MMEJ), strand-displacement, and lyase activities. We postulate that AtPOLIs are able to execute those different functions through the acquisition of these novel amino acid insertions, making them multifunctional enzymes able to participate in DNA replication and DNA repair.}, }
@article {pmid33227379, year = {2021}, author = {Agafonov, VA and Negrobov, VV and Igamberdiev, AU}, title = {Symbiogenesis as a driving force of evolution: The legacy of Boris Kozo-Polyansky.}, journal = {Bio Systems}, volume = {199}, number = {}, pages = {104302}, doi = {10.1016/j.biosystems.2020.104302}, pmid = {33227379}, issn = {1872-8324}, mesh = {Animals ; *Biological Evolution ; Chloroplasts/metabolism ; Eukaryota/cytology/*metabolism ; Eukaryotic Cells/cytology/*metabolism ; Humans ; Mitochondria/metabolism ; Organelles/metabolism ; Plants/metabolism ; *Symbiosis ; }, abstract = {We analyze evolutionary views of Boris Kozo-Polyansky (1890-1957) who was the first who formulated the symbiotic theory of evolution as a concept in his book, Symbiogenesis: A New Principle of Evolution (1924). Later, starting from 1967, Lynn Margulis independently formulated and further developed the concept of symbiogenesis. Although the ideas on the symbiotic origin of chloroplasts and mitochondria appeared earlier, the book of Kozo-Polyansky presented symbiogenesis as the main factor of complexification in the course of evolution, not only in relation to the origin of eukaryotic cell. Kozo-Polyansky incorporated the ideas of symbiogenesis into a broader paradigm that anticipated the important concepts of the modern Extended Evolutionary Synthesis such as the idea of net of life, the evolutionary role of apoptosis, the ideas of punctuated equilibrium, and the concept of metasystem transition.}, }
@article {pmid33224166, year = {2020}, author = {Khoshravesh, R and Stata, M and Adachi, S and Sage, TL and Sage, RF}, title = {Evolutionary Convergence of C4 Photosynthesis: A Case Study in the Nyctaginaceae.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {578739}, pmid = {33224166}, issn = {1664-462X}, abstract = {C4 photosynthesis evolved over 65 times, with around 24 origins in the eudicot order Caryophyllales. In the Caryophyllales family Nyctaginaceae, the C4 pathway is known in three genera of the tribe Nyctagineae: Allionia, Okenia and Boerhavia. Phylogenetically, Allionia and Boerhavia/Okenia are separated by three genera whose photosynthetic pathway is uncertain. To clarify the distribution of photosynthetic pathways in the Nyctaginaceae, we surveyed carbon isotope ratios of 159 species of the Nyctaginaceae, along with bundle sheath (BS) cell ultrastructure, leaf gas exchange, and C4 pathway biochemistry in five species from the two C4 clades and closely related C3 genera. All species in Allionia, Okenia and Boerhavia are C4, while no C4 species occur in any other genera of the family, including three that branch between Allionia and Boerhavia. This demonstrates that C4 photosynthesis evolved twice in Nyctaginaceae. Boerhavia species use the NADP-malic enzyme (NADP-ME) subtype of C4 photosynthesis, while Allionia species use the NAD-malic enzyme (NAD-ME) subtype. The BS cells of Allionia have many more mitochondria than the BS of Boerhavia. Bundle sheath mitochondria are closely associated with chloroplasts in Allionia which facilitates CO2 refixation following decarboxylation by mitochondrial NAD-ME. The close relationship between Allionia and Boerhavia could provide insights into why NADP-ME versus NAD-ME subtypes evolve, particularly when coupled to analysis of their respective genomes. As such, the group is an excellent system to dissect the organizational hierarchy of convergent versus divergent traits produced by C4 evolution, enabling us to understand when convergence is favored versus when divergent modifications can result in a common phenotype.}, }
@article {pmid33222011, year = {2021}, author = {Liu, H and Liu, M and Zhu, H and Zhong, J and Liao, X and Zhou, Q}, title = {Molecular characterization of a novel mitovirus from the plant‑pathogenic fungus Botryosphaeria dothidea.}, journal = {Archives of virology}, volume = {166}, number = {2}, pages = {633-637}, pmid = {33222011}, issn = {1432-8798}, support = {2018JJ3220//Hunan Provincial Natural Science Fund/ ; CX20190522//Hunan Provincial Innovation Foundation for Postgraduate/ ; }, mesh = {Amino Acids/genetics ; Ascomycota/*virology ; Genome, Viral/*genetics ; Mitochondria/genetics ; Open Reading Frames/genetics ; Phylogeny ; Plants/*microbiology ; RNA Viruses/*genetics ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase ; Viral Proteins/genetics ; }, abstract = {Here, a novel mycovirus, Botryosphaeria dothidea mitovirus 1 (BdMV1), was isolated from a phytopathogenic fungus, Botryosphaeria dothidea, and its molecular characteristics were determined. BdMV1 has a genome of 2,667 nt that contains a single large open reading frame (ORF) using the fungal mitochondrial genetic code. The ORF encodes an RNA-dependent RNA polymerase (RdRp) of 727 amino acids with a molecular mass of 81.64 kDa. BLASTp analysis revealed that the RdRp domain of BdMV1 has 39.59% and 39.18% sequence identity to Plasmopara viticola associated mitovirus 43 and Setosphaeria turcica mitovirus 1, respectively. Phylogenetic analysis further suggested that BdMV1 is a new member of the genus Mitovirus within the family Mitoviridae. To the best of our knowledge, this is the first report of a mitovirus in B. dothidea.}, }
@article {pmid33221746, year = {2020}, author = {Xu, H and Zhou, W and Zhan, L and Sui, H and Zhang, L and Zhao, C and Lu, X}, title = {The ZiBuPiYin recipe regulates proteomic alterations in brain mitochondria-associated ER membranes caused by chronic psychological stress exposure: Implications for cognitive decline in Zucker diabetic fatty rats.}, journal = {Aging}, volume = {12}, number = {23}, pages = {23698-23726}, pmid = {33221746}, issn = {1945-4589}, mesh = {Animals ; Behavior, Animal/*drug effects ; Brain/*drug effects/metabolism ; Chronic Disease ; Cognition/*drug effects ; Cognitive Dysfunction/etiology/metabolism/*prevention &amp; control/psychology ; Diabetes Mellitus/*drug therapy/metabolism ; Disease Models, Animal ; Drugs, Chinese Herbal/*pharmacology ; Endoplasmic Reticulum/*drug effects/metabolism ; Exploratory Behavior/drug effects ; Male ; Memory/drug effects ; Mitochondria/*drug effects/metabolism ; Mitochondrial Membranes/*drug effects/metabolism ; Neuroprotective Agents/*pharmacology ; Protein Interaction Maps ; Proteome/*drug effects ; Proteomics ; Rats, Zucker ; Signal Transduction ; Spatial Learning/drug effects ; Stress, Psychological/complications/*drug therapy/metabolism/psychology ; }, abstract = {Chronic psychological stress (PS) cumulatively affects memory performance through the deleterious effects on hypothalamic-pituitary-adrenal axis regulation. Several functions damaged in cognitive impairment-related diseases are regulated by mitochondria-associated ER membranes (MAMs). To elucidate the role of ZiBuPiYin recipe (ZBPYR) in regulating the MAM proteome to improve PS-induced diabetes-associated cognitive decline (PSD), differentially expressed MAM proteins were identified among Zucker diabetic fatty rats, PSD rats, and PS combined with ZBPYR administration rats via iTRAQ with LC-MS/MS. Proteomic analysis revealed that the expressions of 85 and 33 proteins were altered by PS and ZBPYR treatment, respectively. Among these, 21 proteins were differentially expressed under both PS and ZBPYR treatments, whose functional categories included energy metabolism, lipid and protein metabolism, and synaptic dysfunction. Furthermore, calcium signaling and autophagy-related proteins may play roles in the pathogenesis of PSD and the mechanism of ZBPYR, respectively. Notably, KEGG pathway analysis suggested that 'Alzheimer's disease' and 'oxidative phosphorylation' pathways may be impaired in PSD pathogenesis, while ZBPYR could play a neuroprotective role through regulating the above pathways. Overall, exposure to chronic PS contributes to the evolution of diabetes-associated cognitive decline and ZBPYR might prevent and treat PSD by regulating the MAM proteome.}, }
@article {pmid33220346, year = {2021}, author = {Sweet, AD and Johnson, KP and Cao, Y and de Moya, RS and Skinner, RK and Tan, M and Virrueta Herrera, S and Cameron, SL}, title = {Structure, gene order, and nucleotide composition of mitochondrial genomes in parasitic lice from Amblycera.}, journal = {Gene}, volume = {768}, number = {}, pages = {145312}, doi = {10.1016/j.gene.2020.145312}, pmid = {33220346}, issn = {1879-0038}, mesh = {Amblycera/classification/*genetics ; Animals ; Base Composition ; Base Sequence ; Evolution, Molecular ; Gene Order ; *Genetic Variation ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {Parasitic lice have unique mitochondrial (mt) genomes characterized by rearranged gene orders, variable genome structures, and less AT content compared to most other insects. However, relatively little is known about the mt genomes of Amblycera, the suborder sister to all other parasitic lice. Comparing among nine different genera (including representative of all seven families), we show that Amblycera have variable and highly rearranged mt genomes. Some genera have fragmented genomes that vary considerably in length, whereas others have a single mt chromosome. Notably, these genomes are more AT-biased than most other lice. We also recover genus-level phylogenetic relationships among Amblycera that are consistent with those reported from large nuclear datasets, indicating that mt sequences are reliable for reconstructing evolutionary relationships in Amblycera. However, gene order data cannot reliably recover these same relationships. Overall, our results suggest that the mt genomes of lice, already know to be distinctive, are even more variable than previously thought.}, }
@article {pmid33217579, year = {2021}, author = {Plese, B and Kenny, NJ and Rossi, ME and Cárdenas, P and Schuster, A and Taboada, S and Koutsouveli, V and Riesgo, A}, title = {Mitochondrial evolution in the Demospongiae (Porifera): Phylogeny, divergence time, and genome biology.}, journal = {Molecular phylogenetics and evolution}, volume = {155}, number = {}, pages = {107011}, doi = {10.1016/j.ympev.2020.107011}, pmid = {33217579}, issn = {1095-9513}, mesh = {Animals ; Calibration ; Cell Nucleus/genetics ; Codon, Initiator/genetics ; Codon, Terminator/genetics ; *Evolution, Molecular ; Gene Expression Regulation ; Gene Order ; Gene Rearrangement ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics ; *Phylogeny ; Porifera/*genetics ; Time Factors ; }, abstract = {The sponge class Demospongiae is the most speciose and morphologically diverse in the phylum Porifera, and the species within it are vital components of a range of ecosystems worldwide. Despite their ubiquity, a number of recalcitrant problems still remain to be solved regarding their phylogenetic inter-relationships, the timing of their appearance, and their mitochondrial biology, the latter of which is only beginning to be investigated. Here we generated 14 new demosponge mitochondrial genomes which, alongside previously published mitochondrial resources, were used to address these issues. In addition to phylogenomic analysis, we have used syntenic data and analysis of coding regions to forge a framework for understanding the inter-relationships between Demospongiae sub-classes and orders. We have also leveraged our new resources to study the mitochondrial biology of these clades in terms of codon usage, optimisation and gene expression, to understand how these vital cellular components may have contributed to the success of the Porifera. Our results strongly support a sister relationship between Keratosa and (Verongimorpha + Heteroscleromorpha), contradicting previous studies using nuclear markers. Our study includes one species of Clionaida, and show for the first time support for a grouping of Suberitida+(Clionaida+(Tethyida + Poecilosclerida). The findings of our phylogenetic analyses are supported by in-depth examination of structural and coding-level evidence from our mitochondrial data. A time-calibrated phylogeny estimated the origin of Demospongiae in the Cambrian (~529 Mya), and suggests that most demosponge order crown-groups emerged in the Mesozoic. This work therefore provides a robust basis for considering demosponge phylogenetic relationships, as well as essential mitochondrial data for understanding the biological basis for their success and diversity.}, }
@article {pmid33203574, year = {2021}, author = {Lukeš, J and Kaur, B and Speijer, D}, title = {RNA Editing in Mitochondria and Plastids: Weird and Widespread.}, journal = {Trends in genetics : TIG}, volume = {37}, number = {2}, pages = {99-102}, doi = {10.1016/j.tig.2020.10.004}, pmid = {33203574}, issn = {0168-9525}, mesh = {Mitochondria/*genetics ; Mutation/genetics ; Mutation Rate ; Phylogeny ; Plastids/*genetics ; RNA Editing/*genetics ; Symbiosis/genetics ; }, abstract = {Though widespread, RNA editing is rare, except in endosymbiotic organelles. A combination of higher mutation rates, relaxation of energetic constraints, and high genetic drift is found within plastids and mitochondria and is conducive for evolution and expansion of editing processes, possibly starting as repair mechanisms. To illustrate this, we present an exhaustive phylogenetic overview of editing types.}, }
@article {pmid33197746, year = {2020}, author = {Azim, MF and Burch-Smith, TM}, title = {Organelles-nucleus-plasmodesmata signaling (ONPS): an update on its roles in plant physiology, metabolism and stress responses.}, journal = {Current opinion in plant biology}, volume = {58}, number = {}, pages = {48-59}, doi = {10.1016/j.pbi.2020.09.005}, pmid = {33197746}, issn = {1879-0356}, mesh = {Chloroplasts ; Plant Development ; *Plant Physiological Phenomena ; *Plasmodesmata ; Signal Transduction ; }, abstract = {Plasmodesmata allow movement of metabolites and signaling molecules between plant cells and are, therefore, critical players in plant development and physiology, and in responding to environmental signals and stresses. There is emerging evidence that plasmodesmata are controlled by signaling originating from other organelles, primarily the chloroplasts and mitochondria. These signals act in the nucleus to alter expression of genetic pathways that control both trafficking via plasmodesmata and the plasmodesmatal pores themselves. This control circuit was dubbed organelle-nucleus-plasmodesmata signaling (ONPS). Here we discuss how ONPS arose during plant evolution and highlight the discovery of an ONPS-like module for regulating stomata. We also consider recent findings that illuminate details of the ONPS circuit and its roles in plant physiology, metabolism, and defense.}, }
@article {pmid33185659, year = {2021}, author = {Ettahi, K and Lhee, D and Sung, JY and Simpson, AGB and Park, JS and Yoon, HS}, title = {Evolutionary History of Mitochondrial Genomes in Discoba, Including the Extreme Halophile Pleurostomum flabellatum (Heterolobosea).}, journal = {Genome biology and evolution}, volume = {13}, number = {2}, pages = {}, pmid = {33185659}, issn = {1759-6653}, mesh = {Electron Transport/genetics ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; Genes ; *Genome, Mitochondrial ; Mitochondria/ultrastructure ; Mitochondrial Proteins/genetics ; Phylogeny ; }, abstract = {Data from Discoba (Heterolobosea, Euglenozoa, Tsukubamonadida, and Jakobida) are essential to understand the evolution of mitochondrial genomes (mitogenomes), because this clade includes the most primitive-looking mitogenomes known, as well some extremely divergent genome information systems. Heterolobosea encompasses more than 150 described species, many of them from extreme habitats, but only six heterolobosean mitogenomes have been fully sequenced to date. Here we complete the mitogenome of the heterolobosean Pleurostomum flabellatum, which is extremely halophilic and reportedly also lacks classical mitochondrial cristae, hinting at reduction or loss of respiratory function. The mitogenome of P. flabellatum maps as a 57,829-bp-long circular molecule, including 40 coding sequences (19 tRNA, two rRNA, and 19 orfs). The gene content and gene arrangement are similar to Naegleria gruberi and Naegleria fowleri, the closest relatives with sequenced mitogenomes. The P. flabellatum mitogenome contains genes that encode components of the electron transport chain similar to those of Naegleria mitogenomes. Homology searches against a draft nuclear genome showed that P. flabellatum has two homologs of the highly conserved Mic60 subunit of the MICOS complex, and likely lost Mic19 and Mic10. However, electron microscopy showed no cristae structures. We infer that P. flabellatum, which originates from high salinity (313‰) water where the dissolved oxygen concentration is low, possesses a mitochondrion capable of aerobic respiration, but with reduced development of cristae structure reflecting limited use of this aerobic capacity (e.g., microaerophily).}, }
@article {pmid33180850, year = {2020}, author = {Vorobieva, NV and Makunin, AI and Druzhkova, AS and Kusliy, MA and Trifonov, VA and Popova, KO and Polosmak, NV and Molodin, VI and Vasiliev, SK and Shunkov, MV and Graphodatsky, AS}, title = {High genetic diversity of ancient horses from the Ukok Plateau.}, journal = {PloS one}, volume = {15}, number = {11}, pages = {e0241997}, pmid = {33180850}, issn = {1932-6203}, mesh = {Animals ; Animals, Domestic/*genetics ; Animals, Wild/*genetics ; DNA, Ancient/analysis ; Evolution, Molecular ; Extinction, Biological ; Fossils/history ; Genome, Mitochondrial ; Haplotypes ; High-Throughput Nucleotide Sequencing/veterinary ; History, Ancient ; Horses ; Mitochondria/*genetics ; Phylogeny ; Russia ; Whole Genome Sequencing/*veterinary ; }, abstract = {A growing number of researchers studying horse domestication come to a conclusion that this process happened in multiple locations and involved multiple wild maternal lines. The most promising approach to address this problem involves mitochondrial haplotype comparison of wild and domestic horses from various locations coupled with studies of possible migration routes of the ancient shepherds. Here, we sequenced complete mitochondrial genomes of six horses from burials of the Ukok plateau (Russia, Altai Mountains) dated from 2.7 to 1.4 thousand years before present and a single late Pleistocene wild horse from the neighboring region (Denisova cave). Sequencing data indicates that the wild horse belongs to an extinct pre-domestication lineage. Integration of the domestic horse data with known Eurasian haplotypes of a similar age revealed two distinct groups: the first one widely distributed in Europe and presumably imported to Altai, and the second one specific for Altai Mountains and surrounding area.}, }
@article {pmid33179562, year = {2021}, author = {Khan, S and Nisar, A and Ahmad, H and Mehmood, SA and Hameed, M and Zhao, X and Yang, X and Feng, X}, title = {Analyses of mitogenomic markers shed light on the divergence, population dynamics, and demographic history of Pakistani chickens.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {32}, number = {1}, pages = {34-42}, doi = {10.1080/24701394.2020.1845323}, pmid = {33179562}, issn = {2470-1408}, mesh = {Animals ; Chickens/*classification/genetics ; DNA, Mitochondrial/*genetics ; Feathers/chemistry ; Gene Pool ; Genetic Markers/*genetics ; Genetic Variation ; Haplotypes ; Mitochondria/*genetics ; Pakistan ; Phylogeny ; Population Dynamics ; Sequence Analysis, DNA/*methods ; }, abstract = {Pakistan is one of a few sites, associated with the earliest known independent domestication event in the evolutionary history of chicken, which is socio-economically and historically the most important poultry bird in the country. However, the divergence, past population dynamics, and demographic history of Pakistani chickens have not been addressed so far. Therefore, we herein investigated the indigenous Pakistani chickens using mitogenomic markers. We first prepared individual DNA samples from the chicken feathers, and generated nucleotide sequence data, which was then subjected to various population genetics analyses. In molecular phylogenetic analysis, the Pakistani chickens were clustered under nine different clades. Among the wild fowls, the Indian red jungle fowl (IRJF) shared very close affinities to Pakistani chickens. The Bayesian skyline plot showed an increase in the effective population size of Pakistani chickens during the last 50 years. Finally, a time-calibrated phylogeny inferred molecular divergence of the Pakistani chickens. A molecular rate of 3.6 × 10[-6] mutations/site/year (95% HPD interval: 2.28 × 10[-8] to 9.32 × 10[-6]) was estimated for the data set. In a rooted tree with root-age of 12058 years (95% HPD interval: 1161-38411), the Pakistani chicken haplotypes showed divergence from IRJF haplotypes around 6987 years (95% HPD interval: 1132-20746) ago, and they shared their most recent common ancestor with Gallus gallus spadiceus, and G. g. jabouillei at the root of the tree. Overall, these results suggest that Pakistani chicken haplotypes share their ancestral gene pool with the IRJF as compared to other red jungle fowl subspecies.}, }
@article {pmid33176683, year = {2020}, author = {Dhorne-Pollet, S and Barrey, E and Pollet, N}, title = {A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {785}, pmid = {33176683}, issn = {1471-2164}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial/genetics ; High-Throughput Nucleotide Sequencing ; Horses/genetics ; *Nanopores ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Mitochondrial DNA is remarkably polymorphic. This is why animal geneticists survey mitochondrial genomes variations for fundamental and applied purposes. We present here an approach to sequence whole mitochondrial genomes using nanopore long-read sequencing. Our method relies on the selective elimination of nuclear DNA using an exonuclease treatment and on the amplification of circular mitochondrial DNA using a multiple displacement amplification step.<br><br>RESULTS: We optimized each preparative step to obtain a 100 million-fold enrichment of horse mitochondrial DNA relative to nuclear DNA. We sequenced these amplified mitochondrial DNA using nanopore sequencing technology and obtained mitochondrial DNA reads that represented up to half of the sequencing output. The sequence reads were 2.3&#x2009;kb of mean length and provided an even coverage of the mitochondrial genome. Long-reads spanning half or more of the whole mtDNA provided a coverage that varied between 118X and 488X. We evaluated SNPs identified using these long-reads by Sanger sequencing as ground truth and found a precision of 100.0%; a recall of 93.1% and a F1-score of 0.964 using the Twilight horse mtDNA reference. The choice of the mtDNA reference impacted variant calling efficiency with F1-scores varying between 0.947 and 0.964.<br><br>CONCLUSIONS: Our method to amplify mtDNA and to sequence it using the nanopore technology is usable for mitochondrial DNA variant analysis. With minor modifications, this approach could easily be applied to other large circular DNA molecules.}, }
@article {pmid33165944, year = {2021}, author = {Hirase, S and Tezuka, A and Nagano, AJ and Sato, M and Hosoya, S and Kikuchi, K and Iwasaki, W}, title = {Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population.}, journal = {Evolution; international journal of organic evolution}, volume = {75}, number = {1}, pages = {176-194}, pmid = {33165944}, issn = {1558-5646}, mesh = {Animals ; *Biological Evolution ; *Genome, Mitochondrial ; *Hybridization, Genetic ; Japan ; Perciformes/*genetics ; Phylogeography ; Sequence Analysis, RNA ; }, abstract = {Hybridization between divergent lineages generates new allelic combinations. One mechanism that can hinder the formation of hybrid populations is mitonuclear incompatibility, that is, dysfunctional interactions between proteins encoded in the nuclear and mitochondrial genomes (mitogenomes) of diverged lineages. Theoretically, selective pressure due to mitonuclear incompatibility can affect genotypes in a hybrid population in which nuclear genomes and mitogenomes from divergent lineages admix. To directly and thoroughly observe this key process, we de novo sequenced the 747-Mb genome of the coastal goby, Chaenogobius annularis, and investigated its integrative genomic phylogeographics using RNA-sequencing, RAD-sequencing, genome resequencing, whole mitogenome sequencing, amplicon sequencing, and small RNA-sequencing. Chaenogobius annularis populations have been geographically separated into Pacific Ocean (PO) and Sea of Japan (SJ) lineages by past isolation events around the Japanese archipelago. Despite the divergence history and potential mitonuclear incompatibility between these lineages, the mitogenomes of the PO and SJ lineages have coexisted for generations in a hybrid population on the Sanriku Coast. Our analyses revealed accumulation of nonsynonymous substitutions in the PO-lineage mitogenomes, including two convergent substitutions, as well as signals of mitochondrial lineage-specific selection on mitochondria-related nuclear genes. Finally, our data implied that a microRNA gene was involved in resolving mitonuclear incompatibility. Our integrative genomic phylogeographic approach revealed that mitonuclear incompatibility can affect genome evolution in a natural hybrid population.}, }
@article {pmid33164854, year = {2021}, author = {Ortiz, D and Pekár, S and Bilat, J and Alvarez, N}, title = {Poor performance of DNA barcoding and the impact of RAD loci filtering on the species delimitation of an Iberian ant-eating spider.}, journal = {Molecular phylogenetics and evolution}, volume = {154}, number = {}, pages = {106997}, doi = {10.1016/j.ympev.2020.106997}, pmid = {33164854}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/genetics ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Genetic Loci ; Genetics, Population ; Genomics ; Geography ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; *Restriction Mapping ; *Sequence Analysis, DNA ; Species Specificity ; Spiders/classification/*genetics ; }, abstract = {Genomic data provide unprecedented power for species delimitation. However, current implementations are still time and resource consuming. In addition, bioinformatic processing is contentious and its impact on downstream analyses is insufficiently understood. Here we employ ddRAD sequencing and a thorough sampling for species delimitation in Zodarion styliferum, a widespread Iberian ant-eating spider. We explore the influence of the loci filtering strategy on the downstream phylogenetic analyses, genomic clustering and coalescent species delimitation. We also assess the accuracy of one mitochondrial (COI) and one nuclear (ITS) barcode for fast and inexpensive species delineation in the group. Our genomic data strongly support two morphologically cryptic but ecologically divergent lineages, mainly restricted to the central-eastern and western parts of the Iberian Peninsula, respectively. Larger matrices with more missing data showed increased genomic diversity, supporting that bioinformatic strategies to maximize matrix completion disproportionately exclude loci with the highest mutation rates. Moderate loci filtering gave the best results across analyses: although larger matrices returned concatenated phylogenies with higher support, middle-sized matrices performed better in genetic structure analyses. COI displayed high diversity and a conspicuous barcode gap, revealing 13 mitochondrial lineages. Mitonuclear discordance is consistent with ancestral isolation in multiple groups, probably in glacial refugia, followed by range expansion and secondary contact that produced genomic homogenization. Several apparently (unidirectionally) introgressed specimens further challenge the accuracy of species identification through mitochondrial barcodes in the group. Conversely, ITS failed to separate both lineages of Z. styliferum. This study shows an extreme case of mitonuclear discordance that highlights the limitations of single molecular barcodes for species delimitation, even in presence of distinct barcode gaps, and brings new light on the effects of parameterization on shallow-divergence studies using RAD data.}, }
@article {pmid33164622, year = {2021}, author = {Iketani, G and Pimentel, L and Torres, EDS and Rêgo, PSD and Sampaio, I}, title = {Mitochondrial heteroplasmy and pseudogenes in the freshwater prawn, Macrobrachium amazonicum (Heller, 1862): DNA barcoding and phylogeographic implications.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {32}, number = {1}, pages = {1-11}, doi = {10.1080/24701394.2020.1844677}, pmid = {33164622}, issn = {2470-1408}, mesh = {Animals ; Arthropod Proteins/genetics ; Brazil ; Cell Nucleus/*genetics ; Cloning, Molecular ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Genetics, Population ; Heteroplasmy ; Mitochondria/*genetics ; Palaemonidae/*classification/genetics ; Paraguay ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; }, abstract = {The mitochondrial cytochrome oxidase c subunit 1 (COI) gene has been widely used in phylogenetic studies of crustaceans and analyses in population genetics. As COI studies have become more popular, there has been an increase in the number of reports of the presence of nuclear insertions of mitochondrial DNA (Numts) and mitochondrial heteroplasmy. Here, we provide evidence of both types of event in the COI sequences of Macrobrachium amazonicum, an economically important freshwater prawn, which is widespread in South America. Heteroplasmy and Numts were confirmed by different methods of DNA extraction (genomic, mitochondrial, and nuclear-enriched DNA), cloning, and sequencing, and were observed in 11 of the 14 populations sampled, primarily in the Amazon region. We discuss how the occurrence of these events affects the interpretation of the genetic relationships among the M. amazonicum populations, and we recommend caution when using COI for genetic inferences in prawns of the genus Macrobrachium, and in particular that any analysis should include nuclear markers.}, }
@article {pmid33160039, year = {2021}, author = {Hánová, A and Konečný, A and Nicolas, V and Denys, C and Granjon, L and Lavrenchenko, LA and Šumbera, R and Mikula, O and Bryja, J}, title = {Multilocus phylogeny of African striped grass mice (Lemniscomys): Stripe pattern only partly reflects evolutionary relationships.}, journal = {Molecular phylogenetics and evolution}, volume = {155}, number = {}, pages = {107007}, doi = {10.1016/j.ympev.2020.107007}, pmid = {33160039}, issn = {1095-9513}, mesh = {Africa South of the Sahara ; Animals ; Bayes Theorem ; Calibration ; Climate ; DNA, Mitochondrial/genetics ; *Genetic Loci ; Genetic Variation ; Geography ; Haplotypes/genetics ; Mitochondria/genetics ; *Phylogeny ; Sigmodontinae/*anatomy &amp; histology/*classification ; Species Specificity ; Time Factors ; }, abstract = {Murine rodents are one of the most evolutionary successful groups of extant mammals. They are also important for human as vectors and reservoirs of zoonoses and agricultural pests. Unfortunately, their fast and relatively recent diversification impedes our understanding of phylogenetic relationships and species limits of many murine taxa, including those with very conspicuous phenotype that has been frequently used for taxonomic purposes. One of such groups are the striped grass mice (genus Lemniscomys), distributed across sub-Saharan Africa in 11 currently recognized species. These are traditionally classified into three morphological groups according to different pelage colouration on the back: (a) L. barbarus group (three species) with several continuous pale longitudinal stripes; (b) L. striatus group (four species) with pale stripes diffused into short lines or dots; and (c) L. griselda group (four species) with a single mid-dorsal black stripe. Here we reconstructed the most comprehensive molecular phylogeny of the genus Lemniscomys to date, using the largest currently available multi-locus genetic dataset of all but two species. The results show four main lineages (=species complexes) with the distribution corresponding to the major biogeographical regions of Africa. Surprisingly, the four phylogenetic lineages are only in partial agreement with the morphological classification, suggesting that the single-stripe and/or multi-striped phenotypes evolved independently in multiple lineages. Divergence dating showed the split of Lemniscomys and Arvicanthis genera at the beginning of Pleistocene; most of subsequent speciation processes within Lemniscomys were affected by Pleistocene climate oscillations, with predominantly allopatric diversification in fragmented savanna biome. We propose taxonomic suggestions and directions for future research of this striking group of African rodents.}, }
@article {pmid33159940, year = {2021}, author = {Lin, ZJ and Wang, X and Wang, J and Tan, Y and Tang, X and Werren, JH and Zhang, D and Wang, X}, title = {Comparative analysis reveals the expansion of mitochondrial DNA control region containing unusually high G-C tandem repeat arrays in Nasonia vitripennis.}, journal = {International journal of biological macromolecules}, volume = {166}, number = {}, pages = {1246-1257}, doi = {10.1016/j.ijbiomac.2020.11.007}, pmid = {33159940}, issn = {1879-0003}, mesh = {Animals ; Base Composition/*genetics ; Base Sequence ; CpG Islands/genetics ; DNA Methylation/genetics ; DNA, Mitochondrial/*genetics ; Gene Rearrangement/genetics ; *Genome, Insect ; Genome, Mitochondrial ; Molecular Sequence Annotation ; Phylogeny ; Tandem Repeat Sequences/*genetics ; Wasps/*genetics ; }, abstract = {Insect mitochondrial DNA (mtDNA) ranges from 14 to 19 kbp, and the size difference is attributed to the AT-rich control region. Jewel wasps have a parasitoid lifestyle, which may affect mitochondria function and evolution. We sequenced, assembled, and annotated mitochondrial genomes in Nasonia and outgroup species. Gene composition and order are conserved within Nasonia, but they differ from other parasitoids by two large inversion events that were not reported before. We observed a much higher substitution rate relative to the nuclear genome and mitochondrial introgression between N. giraulti and N. oneida, which is consistent with previous studies. Most strikingly, N. vitripennis mtDNA has an extremely long control region (7665 bp), containing twenty-nine 217 bp tandem repeats and can fold into a super-cruciform structure. In contrast to tandem repeats commonly found in other mitochondria, these high-copy repeats are highly conserved (98.7% sequence identity), much longer in length (approximately 8 Kb), extremely GC-rich (50.7%), and CpG-rich (percent CpG 19.4% vs. 1.1% in coding region), resulting in a 23 kbp mtDNA beyond the typical size range in insects. These N. vitripennis-specific mitochondrial repeats are not related to any known sequences in insect mitochondria. Their evolutionary origin and functional consequences warrant further investigations.}, }
@article {pmid33159171, year = {2020}, author = {Strack, PR and Brodie, EJ and Zhan, H and Schuenemann, VJ and Valente, LJ and Saiyed, T and Lowth, BR and Angley, LM and Perugini, MA and Zeth, K and Truscott, KN and Dougan, DA}, title = {Polymerase delta-interacting protein 38 (PDIP38) modulates the stability and activity of the mitochondrial AAA+ protease CLPXP.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {646}, pmid = {33159171}, issn = {2399-3642}, mesh = {Endopeptidase Clp/genetics/*metabolism ; Gene Expression Regulation ; HeLa Cells ; Humans ; Mitochondria/*metabolism ; Nuclear Proteins/genetics/*metabolism ; Recombinant Proteins ; }, abstract = {Over a decade ago Polymerase δ interacting protein of 38 kDa (PDIP38) was proposed to play a role in DNA repair. Since this time, both the physiological function and subcellular location of PDIP38 has remained ambiguous and our present understanding of PDIP38 function has been hampered by a lack of detailed biochemical and structural studies. Here we show, that human PDIP38 is directed to the mitochondrion in a membrane potential dependent manner, where it resides in the matrix compartment, together with its partner protein CLPX. Our structural analysis revealed that PDIP38 is composed of two conserved domains separated by an α/β linker region. The N-terminal (YccV-like) domain of PDIP38 forms an SH3-like β-barrel, which interacts specifically with CLPX, via the adaptor docking loop within the N-terminal Zinc binding domain of CLPX. In contrast, the C-terminal (DUF525) domain forms an immunoglobin-like β-sandwich fold, which contains a highly conserved putative substrate binding pocket. Importantly, PDIP38 modulates the substrate specificity of CLPX and protects CLPX from LONM-mediated degradation, which stabilises the cellular levels of CLPX. Collectively, our findings shed new light on the mechanism and function of mitochondrial PDIP38, demonstrating that PDIP38 is a bona fide adaptor protein for the mitochondrial protease, CLPXP.}, }
@article {pmid33157103, year = {2021}, author = {Pearson, SA and Cowan, JA}, title = {Evolution of the human mitochondrial ABCB7 [2Fe-2S](GS)4 cluster exporter and the molecular mechanism of an E433K disease-causing mutation.}, journal = {Archives of biochemistry and biophysics}, volume = {697}, number = {}, pages = {108661}, pmid = {33157103}, issn = {1096-0384}, support = {R21 AI072443/AI/NIAID NIH HHS/United States ; }, mesh = {ATP-Binding Cassette Transporters/chemistry/*genetics/*metabolism ; Adenosine Triphosphatases/metabolism ; *Evolution, Molecular ; Humans ; Kinetics ; Models, Molecular ; *Mutation ; Protein Conformation ; }, abstract = {Iron-sulfur cluster proteins play key roles in a multitude of cellular processes. Iron-sulfur cofactors are assembled primarily in mitochondria and are then exported to the cytosol by use of an ABCB7 transporter. It has been shown that the yeast mitochondrial transporter Atm1 can export glutathione-coordinated iron-sulfur clusters, [2Fe-2S](SG)4, providing a source of cluster units for cytosolic iron-sulfur cluster assembly systems. This pathway is consistent with the endosymbiotic model of mitochondrial evolution where homologous bacterial heavy metal transporters, utilizing metal glutathione adducts, were adapted for use in eukaryotic mitochondria. Herein, the basis for endosymbiotic evolution of the human cluster export protein (ABCB7) is developed through a BLAST analysis of transporters from ancient proteobacteria. In addition, a functional comparison of native human protein, versus a disease-causing mutant, demonstrates a key role for residue E433 in promoting cluster transport. Dysfunction in mitochondrial export of Fe-S clusters is a likely cause of the disease condition X-linked sideroblastic anemia.}, }
@article {pmid33153867, year = {2020}, author = {Tort, F and Barredo, E and Parthasarathy, R and Ugarteburu, O and Ferrer-Cortès, X and García-Villoria, J and Gort, L and González-Quintana, A and Martín, MA and Fernández-Vizarra, E and Zeviani, M and Ribes, A}, title = {Biallelic mutations in NDUFA8 cause complex I deficiency in two siblings with favorable clinical evolution.}, journal = {Molecular genetics and metabolism}, volume = {131}, number = {3}, pages = {349-357}, doi = {10.1016/j.ymgme.2020.10.005}, pmid = {33153867}, issn = {1096-7206}, mesh = {Child ; Female ; Fibroblasts/metabolism ; *Genetic Predisposition to Disease ; Humans ; Male ; Metabolism, Inborn Errors/genetics/pathology ; Mitochondria/genetics/pathology ; Mitochondrial Diseases/*genetics/pathology ; NADH Dehydrogenase/*genetics ; *Oxidative Phosphorylation ; Siblings ; Exome Sequencing ; }, abstract = {Isolated complex I (CI) deficiency is the most common cause of oxidative phosphorylation (OXPHOS) dysfunction. Whole-exome sequencing identified biallelic mutations in NDUFA8 (c.[293G > T]; [293G > T], encoding for an accessory subunit of CI, in two siblings with a favorable clinical evolution. The individuals reported here are practically asymptomatic, with the exception of slight failure to thrive and some language difficulties at the age of 6 and 9 years, respectively. These observations are remarkable since the vast majority of patients with CI deficiency, including the only NDUFA8 patient reported so far, showed an extremely poor clinical outcome. Western blot studies demonstrated that NDUFA8 protein was strongly reduced in the patients' fibroblasts and muscle extracts. In addition, there was a marked and specific decrease in the steady-state levels of CI subunits. BN-PAGE demonstrated an isolated defect in the assembly and the activity of CI with impaired supercomplexes formation and abnormal accumulation of CI subassemblies. Confocal microscopy analysis in fibroblasts showed rounder mitochondria and diminished branching degree of the mitochondrial network. Functional complementation studies demonstrated disease-causality for the identified mutation as lentiviral transduction with wild-type NDUFA8 cDNA restored the steady-state levels of CI subunits and completely recovered the deficient enzymatic activity in immortalized mutant fibroblasts. In summary, we provide additional evidence of the involvement of NDUFA8 as a mitochondrial disease-causing gene associated with altered mitochondrial morphology, CI deficiency, impaired supercomplexes formation, and very mild progression of the disease.}, }
@article {pmid33142719, year = {2020}, author = {Penna, E and Pizzella, A and Cimmino, F and Trinchese, G and Cavaliere, G and Catapano, A and Allocca, I and Chun, JT and Campanozzi, A and Messina, G and Precenzano, F and Lanzara, V and Messina, A and Monda, V and Monda, M and Perrone-Capano, C and Mollica, MP and Crispino, M}, title = {Neurodevelopmental Disorders: Effect of High-Fat Diet on Synaptic Plasticity and Mitochondrial Functions.}, journal = {Brain sciences}, volume = {10}, number = {11}, pages = {}, pmid = {33142719}, issn = {2076-3425}, support = {B61G18000470007//Regione Campania/ ; }, abstract = {Neurodevelopmental disorders (NDDs) include diverse neuropathologies characterized by abnormal brain development leading to impaired cognition, communication and social skills. A common feature of NDDs is defective synaptic plasticity, but the underlying molecular mechanisms are only partially known. Several studies have indicated that people's lifestyles such as diet pattern and physical exercise have significant influence on synaptic plasticity of the brain. Indeed, it has been reported that a high-fat diet (HFD, with 30-50% fat content), which leads to systemic low-grade inflammation, has also a detrimental effect on synaptic efficiency. Interestingly, metabolic alterations associated with obesity in pregnant woman may represent a risk factor for NDDs in the offspring. In this review, we have discussed the potential molecular mechanisms linking the HFD-induced metabolic dysfunctions to altered synaptic plasticity underlying NDDs, with a special emphasis on the roles played by synaptic protein synthesis and mitochondrial functions.}, }
@article {pmid33142007, year = {2021}, author = {Russell, S and Jackson, C and Reyes-Prieto, A}, title = {High Sequence Divergence but Limited Architectural Rearrangements in Organelle Genomes of Cyanophora (Glaucophyta) Species.}, journal = {The Journal of eukaryotic microbiology}, volume = {68}, number = {1}, pages = {e12831}, doi = {10.1111/jeu.12831}, pmid = {33142007}, issn = {1550-7408}, mesh = {Biological Evolution ; Cyanophora/*genetics ; DNA, Mitochondrial/analysis ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Mitochondrial ; *Genome, Plastid ; }, abstract = {Cyanophora is the glaucophyte model taxon. Following the sequencing of the nuclear genome of C. paradoxa, studies based on single organelle and nuclear molecular markers revealed previously unrecognized species diversity within this glaucophyte genus. Here, we present the complete plastid (ptDNA) and mitochondrial (mtDNA) genomes of C. kugrensii, C. sudae, and C. biloba. The respective sizes and coding capacities of both ptDNAs and mtDNAs are conserved among Cyanophora species with only minor differences due to specific gene duplications. Organelle phylogenomic analyses consistently recover the species C. kugrensii and C. paradoxa as a clade and C. sudae and C. biloba as a separate group. The phylogenetic affiliations of the four Cyanophora species are consistent with architectural similarities shared at the organelle genomic level. Genetic distance estimations from both organelle sequences are also consistent with phylogenetic and architecture evidence. Comparative analyses confirm that the Cyanophora mitochondrial genes accumulate substitutions at 3-fold higher rates than plastid counterparts, suggesting that mtDNA markers are more appropriate to investigate glaucophyte diversity and evolutionary events that occur at a population level. The study of complete organelle genomes is becoming the standard for species delimitation and is particularly relevant to study cryptic diversity in microbial groups.}, }
@article {pmid33139764, year = {2020}, author = {da Silva, AF and Machado, LC and de Paula, MB and da Silva Pessoa Vieira, CJ and de Morais Bronzoni, RV and de Melo Santos, MAV and Wallau, GL}, title = {Culicidae evolutionary history focusing on the Culicinae subfamily based on mitochondrial phylogenomics.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {18823}, pmid = {33139764}, issn = {2045-2322}, mesh = {Animals ; Culicidae/classification/*genetics/pathogenicity ; *Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Mosquito Vectors ; *Phylogeny ; Species Specificity ; Whole Genome Sequencing ; }, abstract = {Mosquitoes are insects of medical importance due their role as vectors of different pathogens to humans. There is a lack of information about the evolutionary history and phylogenetic positioning of the majority of mosquito species. Here we characterized the mitogenomes of mosquito species through low-coverage whole genome sequencing and data mining. A total of 37 draft mitogenomes of different species were assembled from which 16 are newly-sequenced species. We datamined additional 49 mosquito mitogenomes, and together with our 37 mitogenomes, we reconstructed the evolutionary history of 86 species including representatives from 15 genera and 7 tribes. Our results showed that most of the species clustered in clades with other members of their own genus with exception of Aedes genus which was paraphyletic. We confirmed the monophyletic status of the Mansoniini tribe including both Coquillettidia and Mansonia genus. The Aedeomyiini and Uranotaeniini were consistently recovered as basal to other tribes in the subfamily Culicinae, although the exact relationships among these tribes differed between analyses. These results demonstrate that low-coverage sequencing is effective to recover mitogenomes, establish phylogenetic knowledge and hence generate basic fundamental information that will help in the understanding of the role of these species as pathogen vectors.}, }
@article {pmid33138913, year = {2020}, author = {Fukuda, T and Ebi, Y and Saigusa, T and Furukawa, K and Yamashita, SI and Inoue, K and Kobayashi, D and Yoshida, Y and Kanki, T}, title = {Atg43 tethers isolation membranes to mitochondria to promote starvation-induced mitophagy in fission yeast.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {33138913}, issn = {2050-084X}, support = {17K07330//Japan Society for the Promotion of Science/International ; 20K06552//Japan Society for the Promotion of Science/International ; 18H04858//Japan Society for the Promotion of Science/International ; 19H05712//Japan Society for the Promotion of Science/International ; 19K22419//Japan Society for the Promotion of Science/International ; 20gm6110013h0003//Japan Agency for Medical Research and Development/International ; }, mesh = {Autophagy ; Autophagy-Related Protein 8 Family/*metabolism ; Autophagy-Related Proteins/*metabolism ; Cytosol/metabolism ; Evolution, Molecular ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/*metabolism ; *Mitophagy ; Protein Domains ; Schizosaccharomyces/*metabolism ; Schizosaccharomyces pombe Proteins/*metabolism ; Species Specificity ; Two-Hybrid System Techniques ; }, abstract = {Degradation of mitochondria through mitophagy contributes to the maintenance of mitochondrial function. In this study, we identified that Atg43, a mitochondrial outer membrane protein, serves as a mitophagy receptor in the model organism Schizosaccharomyces pombe to promote the selective degradation of mitochondria. Atg43 contains an Atg8-family-interacting motif essential for mitophagy. Forced recruitment of Atg8 to mitochondria restores mitophagy in Atg43-deficient cells, suggesting that Atg43 tethers expanding isolation membranes to mitochondria. We found that the mitochondrial import factors, including the Mim1-Mim2 complex and Tom70, are crucial for mitophagy. Artificial mitochondrial loading of Atg43 bypasses the requirement of the import factors, suggesting that they contribute to mitophagy through Atg43. Atg43 not only maintains growth ability during starvation but also facilitates vegetative growth through its mitophagy-independent function. Thus, Atg43 is a useful model to study the mechanism and physiological roles, as well as the origin and evolution, of mitophagy in eukaryotes.}, }
@article {pmid33137653, year = {2021}, author = {Ryan, DG and Frezza, C and O'Neill, LA}, title = {TCA cycle signalling and the evolution of eukaryotes.}, journal = {Current opinion in biotechnology}, volume = {68}, number = {}, pages = {72-88}, pmid = {33137653}, issn = {1879-0429}, support = {109443/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_12022/6/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Archaea/genetics ; *Biological Evolution ; *Eukaryota/genetics ; Eukaryotic Cells ; Phylogeny ; Prokaryotic Cells ; Symbiosis ; }, abstract = {A major question remaining in the field of evolutionary biology is how prokaryotic organisms made the leap to complex eukaryotic life. The prevailing theory depicts the origin of eukaryotic cell complexity as emerging from the symbiosis between an α-proteobacterium, the ancestor of present-day mitochondria, and an archaeal host (endosymbiont theory). A primary contribution of mitochondria to eukaryogenesis has been attributed to the mitochondrial genome, which enabled the successful internalisation of bioenergetic membranes and facilitated remarkable genome expansion. It has also been postulated that a key contribution of the archaeal host during eukaryogenesis was in providing 'archaeal histones' that would enable compaction and regulation of an expanded genome. Yet, how the communication between the host and the symbiont evolved is unclear. Here, we propose an evolutionary concept in which mitochondrial TCA cycle signalling was also a crucial player during eukaryogenesis enabling the dynamic control of an expanded genome via regulation of DNA and histone modifications. Furthermore, we discuss how TCA cycle remodelling is a common evolutionary strategy invoked by eukaryotic organisms to coordinate stress responses and gene expression programmes, with a particular focus on the TCA cycle-derived metabolite itaconate.}, }
@article {pmid33135056, year = {2020}, author = {Ji, J and Day, A}, title = {Construction of a highly error-prone DNA polymerase for developing organelle mutation systems.}, journal = {Nucleic acids research}, volume = {48}, number = {21}, pages = {11868-11879}, pmid = {33135056}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Bacterial Outer Membrane Proteins/chemistry/*genetics/metabolism ; Binding Sites ; Chloroplasts/*genetics/*metabolism ; Cloning, Molecular ; DNA Polymerase gamma/chemistry/*genetics/metabolism ; DNA Replication ; Escherichia coli/genetics/metabolism ; Gene Expression ; Genetic Vectors/chemistry/metabolism ; Mitochondria/*genetics/metabolism ; Models, Molecular ; Mutation ; Phylogeny ; Plant Proteins/chemistry/*genetics/metabolism ; Polymorphism, Single Nucleotide ; Porins/chemistry/*genetics/metabolism ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Receptors, Virus/chemistry/*genetics/metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Selection, Genetic ; Sequence Alignment ; Sequence Homology, Amino Acid ; Nicotiana/classification/*genetics/metabolism ; }, abstract = {A novel family of DNA polymerases replicates organelle genomes in a wide distribution of taxa encompassing plants and protozoans. Making error-prone mutator versions of gamma DNA polymerases revolutionised our understanding of animal mitochondrial genomes but similar advances have not been made for the organelle DNA polymerases present in plant mitochondria and chloroplasts. We tested the fidelities of error prone tobacco organelle DNA polymerases using a novel positive selection method involving replication of the phage lambda cI repressor gene. Unlike gamma DNA polymerases, ablation of 3'-5' exonuclease function resulted in a modest 5-8-fold error rate increase. Combining exonuclease deficiency with a polymerisation domain substitution raised the organelle DNA polymerase error rate by 140-fold relative to the wild type enzyme. This high error rate compares favourably with error-rates of mutator versions of animal gamma DNA polymerases. The error prone organelle DNA polymerase introduced mutations at multiple locations ranging from two to seven sites in half of the mutant cI genes studied. Single base substitutions predominated including frequent A:A (template: dNMP) mispairings. High error rate and semi-dominance to the wild type enzyme in vitro make the error prone organelle DNA polymerase suitable for elevating mutation rates in chloroplasts and mitochondria.}, }
@article {pmid33130297, year = {2021}, author = {Raphalo, EM and Cole, ML and Daniels, SR}, title = {Climatic oscillations during the Mio/Pliocene epochs induced cladogenesis in the terrestrial snail genus Gittenedouardia (Mollusca: Gastropoda: Cerastidae) from South Africa.}, journal = {Molecular phylogenetics and evolution}, volume = {155}, number = {}, pages = {107000}, doi = {10.1016/j.ympev.2020.107000}, pmid = {33130297}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; *Climate ; DNA, Mitochondrial/genetics ; Databases, Genetic ; Electron Transport Complex IV/genetics ; Genetic Speciation ; Genetics, Population ; Geography ; Mitochondria/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Snails/*classification/genetics ; South Africa ; Time Factors ; }, abstract = {In South Africa, the terrestrial snail genus Gittenedouardia is the most species-rich member of the Cerastidae, where it is primarily distributed in the highly fragmented Afrotemperate and Indian Ocean coastal belt (IOCB) forest biomes. Phylogenetic relationships and cladogenetic events within the genus remain unstudied. In this respect, we reconstructed a dated phylogeny for eight Gittenedouardia species, and two populations identified to genus level using a combined mitochondrial (16S rRNA and COI) DNA sequencing dataset analysed using Bayesian inference and Maximum Likelihood framework. Furthermore, we investigated the population genetic substructure of the three widely distributed species (Gittenedouardia spadicea, G. natalensis and G. arenicola) for the COI locus, while also subsampling these species using the nuclear DNA ITS-2 locus. Phylogenetic results based on the combined mtDNA dataset supported the monophyly of Gittenedouardia and revealed three major clades and deep genetic structure among the three widely distributed species. Divergence-time estimates suggest that diversification within Gittenedouardia occurred during the middle Miocene/late Pliocene, a period characterised by a decrease in precipitation and the contraction of the Afrotemperate and IOCB forest biomes. We used two species delimitation methods, (PTP and STACEY) to infer putative species in G. spadicea, G. natalensis and G. arenicola. The two methods recovered a large number of evolutionary distinct units, with minimal consensus in the exact number of lineages. Our findings suggest the presence of undescribed diversity, necessitating the need for taxonomic revisionary work on Gittenedouardia. We discuss the climatic factors which may have contributed to the observed cladogenesis and compare our results with other studies of forest dwelling faunal taxa.}, }
@article {pmid33127981, year = {2020}, author = {Zhang, N and Jiang, H and Meng, X and Qian, K and Liu, Y and Song, Q and Stanley, D and Wu, J and Park, Y and Wang, J}, title = {Broad-complex transcription factor mediates opposing hormonal regulation of two phylogenetically distant arginine kinase genes in Tribolium castaneum.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {631}, pmid = {33127981}, issn = {2399-3642}, mesh = {Animals ; Arginine Kinase/*genetics/metabolism ; Cloning, Molecular ; Ecdysterone/metabolism ; Female ; Fertility/genetics ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Enzymologic ; Insect Proteins/*genetics/metabolism ; Juvenile Hormones/metabolism ; Male ; Metamorphosis, Biological/genetics ; Phylogeny ; Pupa/genetics ; Stress, Physiological ; Transcription Factors/*genetics/metabolism ; Tribolium/*genetics/*metabolism ; }, abstract = {The phosphoarginine-arginine kinase shuttle system plays a critical role in maintaining insect cellular energy homeostasis. Insect molting and metamorphosis are coordinated by fluctuations of the ecdysteroid and juvenile hormone. However, the hormonal regulation of insect arginine kinases remain largely elusive. In this report, we comparatively characterized two arginine kinase genes, TcAK1 and TcAK2, in Tribolium castaneum. Functional analysis using RNAi showed that TcAK1 and TcAK2 play similar roles in adult fertility and stress response. TcAK1 was detected in cytoplasm including mitochondria, whereas TcAK2 was detected in cytoplasm excluding mitochondria. Interestingly, TcAK1 expression was negatively regulated by 20-hydroxyecdysone and positively by juvenile hormone, whereas TcAK2 was regulated by the opposite pattern. RNAi, dual-luciferase reporter assays and electrophoretic mobility shift assay further revealed that the opposite hormonal regulation of TcAK1 and TcAK2 was mediated by transcription factor Broad-Complex. Finally, relatively stable AK activities were observed during larval-pupal metamorphosis, which was generally consistent with the constant ATP levels. These results provide new insights into the mechanisms underlying the ATP homeostasis in insects by revealing opposite hormonal regulation of two phylogenetically distant arginine kinase genes.}, }
@article {pmid33124702, year = {2020}, author = {Glare, T and Campbell, M and Biggs, P and Winter, D and Durrant, A and McKinnon, A and Cox, M}, title = {Mitochondrial evolution in the entomopathogenic fungal genus Beauveria.}, journal = {Archives of insect biochemistry and physiology}, volume = {105}, number = {4}, pages = {e21754}, doi = {10.1002/arch.21754}, pmid = {33124702}, issn = {1520-6327}, mesh = {Beauveria/*classification/*genetics ; Evolution, Molecular ; Genome, Fungal ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Species in the fungal genus Beauveria are pathogens of invertebrates and have been commonly used as the active agent in biopesticides. After many decades with few species described, recent molecular approaches to classification have led to over 25 species now delimited. Little attention has been given to the mitochondrial genomes of Beauveria but better understanding may led to insights into the nature of species and evolution in this important genus. In this study, we sequenced the mitochondrial genomes of four new strains belonging to Beauveria bassiana, Beauveria caledonica and Beauveria malawiensis, and compared them to existing mitochondrial sequences of related fungi. The mitochondrial genomes of Beauveria ranged widely from 28,806 to 44,135 base pairs, with intron insertions accounting for most size variation and up to 39% (B. malawiensis) of the mitochondrial length due to introns in genes. Gene order of the common mitochondrial genes did not vary among the Beauveria sequences, but variation was observed in the number of transfer ribonucleic acid genes. Although phylogenetic analysis using whole mitochondrial genomes showed, unsurprisingly, that B. bassiana isolates were the most closely related to each other, mitochondrial codon usage suggested that some B. bassiana isolates were more similar to B. malawiensis and B. caledonica than the other B. bassiana isolates analyzed.}, }
@article {pmid33124220, year = {2021}, author = {Wang, ZJ and Chen, GJ and Zhang, GJ and Zhou, Q}, title = {Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds.}, journal = {Zoological research}, volume = {42}, number = {1}, pages = {51-61}, pmid = {33124220}, issn = {2095-8137}, mesh = {Animals ; *Biological Evolution ; Birds/*genetics ; DNA Transposable Elements/*genetics ; DNA, Mitochondrial/genetics ; Female ; Male ; Multigene Family ; Sex Chromosomes/genetics ; Time Factors ; }, abstract = {Palaeognathae includes ratite and tinamou species that are important for understanding early avian evolution. Here, we analyzed the whole-genome sequences of 15 paleognathous species to infer their demographic histories, which are presently unknown. We found that most species showed a reduction of population size since the beginning of the last glacial period, except for those species distributed in Australasia and in the far south of South America. Different degrees of contraction and expansion of transposable elements (TE) have shaped the paleognathous genome architecture, with a higher transposon removal rate in tinamous than in ratites. One repeat family, AviRTE, likely underwent horizontal transfer from tropical parasites to the ancestor of little and undulated tinamous about 30 million years ago. Our analysis of gene families identified rapid turnover of immune and reproduction-related genes but found no evidence of gene family changes underlying the convergent evolution of flightlessness among ratites. We also found that mitochondrial genes have experienced a faster evolutionary rate in tinamous than in ratites, with the former also showing more degenerated W chromosomes. This result can be explained by the Hill-Robertson interference affecting genetically linked W chromosomes and mitochondria. Overall, we reconstructed the evolutionary history of the Palaeognathae populations, genes, and TEs. Our findings of co-evolution between mitochondria and W chromosomes highlight the key difference in genome evolution between species with ZW sex chromosomes and those with XY sex chromosomes.}, }
@article {pmid33124163, year = {2021}, author = {Kelley, JL and Desvignes, T and McGowan, KL and Perez, M and Rodriguez, LA and Brown, AP and Culumber, Z and Tobler, M}, title = {microRNA expression variation as a potential molecular mechanism contributing to adaptation to hydrogen sulphide.}, journal = {Journal of evolutionary biology}, volume = {34}, number = {6}, pages = {977-988}, doi = {10.1111/jeb.13727}, pmid = {33124163}, issn = {1420-9101}, mesh = {*Adaptation, Biological ; Animals ; Biological Evolution ; Female ; Gene Expression Regulation ; Gills/*metabolism ; *Hydrogen Sulfide ; Male ; MicroRNAs/genetics/*metabolism ; Poecilia/genetics/*metabolism ; }, abstract = {microRNAs (miRNAs) are post-transcriptional regulators of gene expression and can play an important role in modulating organismal development and physiology in response to environmental stress. However, the role of miRNAs in mediating adaptation to diverse environments in natural study systems remains largely unexplored. Here, we characterized miRNAs and their expression in Poecilia mexicana, a species of small fish that inhabits both normal streams and extreme environments in the form of springs rich in toxic hydrogen sulphide (H2 S). We found that P. mexicana has a similar number of miRNA genes as other teleosts. In addition, we identified a large population of mature miRNAs that were differentially expressed between locally adapted populations in contrasting habitats, indicating that miRNAs may contribute to P. mexicana adaptation to sulphidic environments. In silico identification of differentially expressed miRNA-mRNA pairs revealed, in the sulphidic environment, the downregulation of miRNAs predicted to target mRNAs involved in sulphide detoxification and cellular homeostasis, which are pathways essential for life in H2 S-rich springs. In addition, we found that predicted targets of upregulated miRNAs act in the mitochondria (16.6% of predicted annotated targets), which is the main site of H2 S toxicity and detoxification, possibly modulating mitochondrial function. Together, the differential regulation of miRNAs between these natural populations suggests that miRNAs may be involved in H2 S adaptation by promoting functions needed for survival and reducing functions affected by H2 S. This study lays the groundwork for further research to directly demonstrate the role of miRNAs in adaptation to H2 S. Overall, this study provides a critical stepping-stone towards a comprehensive understanding of the regulatory mechanisms underlying the adaptive variation in gene expression in a natural system.}, }
@article {pmid33113229, year = {2021}, author = {Hartmann, FE and Duhamel, M and Carpentier, F and Hood, ME and Foulongne-Oriol, M and Silar, P and Malagnac, F and Grognet, P and Giraud, T}, title = {Recombination suppression and evolutionary strata around mating-type loci in fungi: documenting patterns and understanding evolutionary and mechanistic causes.}, journal = {The New phytologist}, volume = {229}, number = {5}, pages = {2470-2491}, pmid = {33113229}, issn = {1469-8137}, support = {R15 GM119092/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; Fungi/genetics ; *Genes, Mating Type, Fungal/genetics ; Recombination, Genetic/genetics ; Sex Chromosomes ; }, abstract = {Genomic regions determining sexual compatibility often display recombination suppression, as occurs in sex chromosomes, plant self-incompatibility loci and fungal mating-type loci. Regions lacking recombination can extend beyond the genes determining sexes or mating types, by several successive steps of recombination suppression. Here we review the evidence for recombination suppression around mating-type loci in fungi, sometimes encompassing vast regions of the mating-type chromosomes. The suppression of recombination at mating-type loci in fungi has long been recognized and maintains the multiallelic combinations required for correct compatibility determination. We review more recent evidence for expansions of recombination suppression beyond mating-type genes in fungi ('evolutionary strata'), which have been little studied and may be more pervasive than commonly thought. We discuss testable hypotheses for the ultimate (evolutionary) and proximate (mechanistic) causes for such expansions of recombination suppression, including (1) antagonistic selection, (2) association of additional functions to mating-type, such as uniparental mitochondria inheritance, (3) accumulation in the margin of nonrecombining regions of various factors, including deleterious mutations or transposable elements resulting from relaxed selection, or neutral rearrangements resulting from genetic drift. The study of recombination suppression in fungi could thus contribute to our understanding of recombination suppression expansion across a broader range of organisms.}, }
@article {pmid33108945, year = {2022}, author = {Fadhil, IA and Al-Shuhaib, MBS}, title = {Phylogenetic differentiation between Awassi and Hamdani sheep using the mitochondrial 12S rRNA.}, journal = {Animal biotechnology}, volume = {33}, number = {5}, pages = {801-809}, doi = {10.1080/10495398.2020.1837146}, pmid = {33108945}, issn = {1532-2378}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Genetic Markers ; *Genetic Variation/genetics ; Haplotypes/genetics ; Phylogeny ; *RNA, Ribosomal/genetics ; Sheep/genetics ; }, abstract = {This study was conducted to assess the role of the mitochondrial 12S rRNA variations in the phylogenetic discrimination between two Iraqi breeds of sheep that differ in geographical distribution. A total of 122 animals (68 Awassi and 54 Hamdani) were included in the study. Direct sequencing of amplicons followed by the construction of a median-joining network and several trees were performed to identify the possible phylogenetic differences between both involved breeds. Genetic diversity, relative frequencies, and analysis of molecular variance (AMOVA) were performed to assess the genetic correlation between both populations. The median-joining network and minimized tree values showed that all observed haplotypes were separated into two groups according to their breed. Comprehensive phylogenetic data revealed only one Asian ancestor for all observed haplotypes. As indicated by AMOVA, the observed diversity was mostly due to between-population variation (1.24836%), while within-population variation (0.91221%) accounted for much less. The currently investigated rRNA amplicons exhibited different mitochondrial manifestations between Awassi and Hamdani breeds. Due to the ability of these 12S rRNA amplicons to mimic the geographical diversity for the currently investigated breeds, it is highly recommended to be used as potent mitochondrial genetic markers among broader ovine sequences.}, }
@article {pmid33106602, year = {2021}, author = {Vosseberg, J and van Hooff, JJE and Marcet-Houben, M and van Vlimmeren, A and van Wijk, LM and Gabaldón, T and Snel, B}, title = {Timing the origin of eukaryotic cellular complexity with ancient duplications.}, journal = {Nature ecology &amp; evolution}, volume = {5}, number = {1}, pages = {92-100}, pmid = {33106602}, issn = {2397-334X}, support = {724173/ERC_/European Research Council/International ; }, mesh = {Archaea/genetics ; *Biological Evolution ; Eukaryota/genetics ; *Eukaryotic Cells ; Humans ; Phylogeny ; }, abstract = {Eukaryogenesis is one of the most enigmatic evolutionary transitions, during which simple prokaryotic cells gave rise to complex eukaryotic cells. While evolutionary intermediates are lacking, gene duplications provide information on the order of events by which eukaryotes originated. Here we use a phylogenomics approach to reconstruct successive steps during eukaryogenesis. We find that gene duplications roughly doubled the proto-eukaryotic gene repertoire, with families inherited from the Asgard archaea-related host being duplicated most. By relatively timing events using phylogenetic distances, we inferred that duplications in cytoskeletal and membrane-trafficking families were among the earliest events, whereas most other families expanded predominantly after mitochondrial endosymbiosis. Altogether, we infer that the host that engulfed the proto-mitochondrion had some eukaryote-like complexity, which drastically increased upon mitochondrial acquisition. This scenario bridges the signs of complexity observed in Asgard archaeal genomes to the proposed role of mitochondria in triggering eukaryogenesis.}, }
@article {pmid33096232, year = {2021}, author = {van der Mescht, L and Matthee, S and Matthee, CA}, title = {New taxonomic and evolutionary insights relevant to the cat flea, Ctenocephalides felis: A geographic perspective.}, journal = {Molecular phylogenetics and evolution}, volume = {155}, number = {}, pages = {106990}, doi = {10.1016/j.ympev.2020.106990}, pmid = {33096232}, issn = {1095-9513}, mesh = {Africa, Southern ; Animals ; Bayes Theorem ; *Biological Evolution ; Body Size ; Cats/*parasitology ; Ctenocephalides/*classification/genetics ; Electron Transport Complex IV/genetics ; Female ; *Geography ; Haplotypes/genetics ; Head/anatomy &amp; histology ; Male ; Mitochondria/genetics ; Phylogeny ; Principal Component Analysis ; Species Specificity ; }, abstract = {The cat flea, Ctenocephalides felis, is an obligate haematophagous ectoparasite of wildlife and domestic cats and dogs worldwide. Since cat fleas can affect the health of humans and their pets, an uncertain taxonomy of this taxon can greatly inhibit pest and disease management. To address the evolution and taxonomy of the cat flea, we set out to determine 1) how many genetically distinct taxa exist, 2) whether there is morphological support for the genetically distinct taxa, and 3) the role of host range and paleoclimatic events in speciation. We collected a total of 3352 fleas sampled from 576 domestic cats and dogs as well as 10 wildlife species across 30 localities in South Africa. A total of three flea genera, five species, and three of the currently recognized cat flea subspecies, C. f. damarensis, C. f. strongylus and C. f. felis were obtained. Geometric morphometric analyses on head shape were performed on 68 female and 107 male cat flea individuals. Principal component analysis demonstrated large overlap in head shape variation between C. f. strongylus and C. f. felis, rendering this character not useful for phylogenetic inferences. DNA was extracted from 188 Ctenocephalides spp. and mitochondrial COII and nuclear EF1-α sequences were generated. Bayesian and Maximum Likelihood analyses as well as a TCS parsimony haplotype network of the mitochondrial DNA confirmed the presence of three well supported monophyletic clades. These assemblages did not fully corroborate the existence of the three C. felis subspecies. A single well-supported molecular clade included only C. f. damarensis morphotypes that were mostly collected from wildlife. The recognition of this subspecies as a distinct taxon was further corroborated by sequence distances and also the number of plantar spiniform bristles on fore-tarsi V in males. Despite the overall lack of support for the recognition of C. f. damarensis and C. f. strongylus, a geographic trend was visible whereby one genetic lineage corresponded to the western dryer hot subregion, whereas the other was found throughout the region. Bayesian dating suggested that these two clades diverged during the early Pliocene (4.18 mya), a date that corresponds well with the establishment of a dry hot climate in the west of southern Africa. If so, the off-host environment, particularly temperature and humidity, are important factors to consider in the evolution of the cat flea. The present study rejects recent assertions that the three cat flea subspecies are valid entities and rather point to a situation where more sampling is required before the taxonomic status of C. f. damarensis can be resolved.}, }
@article {pmid33093463, year = {2020}, author = {Baltazar-Soares, M and Klein, JD and Correia, SM and Reischig, T and Taxonera, A and Roque, SM and Dos Passos, L and Durão, J and Lomba, JP and Dinis, H and Cameron, SJK and Stiebens, VA and Eizaguirre, C}, title = {Distribution of genetic diversity reveals colonization patterns and philopatry of the loggerhead sea turtles across geographic scales.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {18001}, pmid = {33093463}, issn = {2045-2322}, mesh = {Animals ; *Biological Evolution ; Brazil ; Cabo Verde ; DNA, Mitochondrial/analysis/*genetics ; *Gene Flow ; *Genetic Variation ; *Genetics, Population ; Mediterranean Sea ; Mexico ; Mitochondria/*genetics ; Panama ; Turtles/*genetics ; United States ; }, abstract = {Understanding the processes that underlie the current distribution of genetic diversity in endangered species is a goal of modern conservation biology. Specifically, the role of colonization and dispersal events throughout a species' evolutionary history often remains elusive. The loggerhead sea turtle (Caretta caretta) faces multiple conservation challenges due to its migratory nature and philopatric behaviour. Here, using 4207 mtDNA sequences, we analysed the colonisation patterns and distribution of genetic diversity within a major ocean basin (the Atlantic), a regional rookery (Cabo Verde Archipelago) and a local island (Island of Boa Vista, Cabo Verde). Data analysis using hypothesis-driven population genetic models suggests the colonization of the Atlantic has occurred in two distinct waves, each corresponding to a major mtDNA lineage. We propose the oldest lineage entered the basin via the isthmus of Panama and sequentially established aggregations in Brazil, Cabo Verde and in the area of USA and Mexico. The second lineage entered the Atlantic via the Cape of Good Hope, establishing colonies in the Mediterranean Sea, and from then on, re-colonized the already existing rookeries of the Atlantic. At the Cabo Verde level, we reveal an asymmetric gene flow maintaining links across island-specific nesting groups, despite significant genetic structure. This structure stems from female philopatric behaviours, which could further be detected by weak but significant differentiation amongst beaches separated by only a few kilometres on the island of Boa Vista. Exploring biogeographic processes at diverse geographic scales improves our understanding of the complex evolutionary history of highly migratory philopatric species. Unveiling the past facilitates the design of conservation programmes targeting the right management scale to maintain a species' evolutionary potential.}, }
@article {pmid33086570, year = {2020}, author = {Piłsyk, S and Mieczkowski, A and Golan, MP and Wawrzyniak, A and Kruszewska, JS}, title = {Internalization of the Aspergillus nidulans AstA Transporter into Mitochondria Depends on Growth Conditions, and Affects ATP Levels and Sulfite Oxidase Activity.}, journal = {International journal of molecular sciences}, volume = {21}, number = {20}, pages = {}, pmid = {33086570}, issn = {1422-0067}, mesh = {Adenosine Triphosphate/*metabolism ; Aspergillus nidulans/*growth &amp; development/*metabolism ; Endocytosis ; Endophytes/metabolism ; Fungal Proteins/*metabolism ; Green Fluorescent Proteins/metabolism ; Mitochondria/*metabolism ; Models, Biological ; Oxidation-Reduction ; Phenotype ; Phylogeny ; Sulfite Oxidase/*metabolism ; Sulfur/metabolism ; }, abstract = {The astA gene encoding an alternative sulfate transporter was originally cloned from the genome of the Japanese Aspergillus nidulans isolate as a suppressor of sulfate permease-deficient strains. Expression of the astA gene is under the control of the sulfur metabolite repression system. The encoded protein transports sulfate across the cell membrane. In this study we show that AstA, having orthologs in numerous pathogenic or endophytic fungi, has a second function and, depending on growth conditions, can be translocated into mitochondria. This effect is especially pronounced when an astA-overexpressing strain grows on solid medium at 37 °C. AstA is also recruited to the mitochondria in the presence of mitochondria-affecting compounds such as menadione or antimycin A, which are also detrimental to the growth of the astA-overexpressing strain. Disruption of the Hsp70-Porin1 mitochondrial import system either by methylene blue, an Hsp70 inhibitor, or by deletion of the porin1-encoding gene abolishes AstA translocation into the mitochondria. Furthermore, we observed altered ATP levels and sulfite oxidase activity in the astA-overexpressing strain in a manner dependent on sulfur sources. The presented data indicate that AstA is also involved in the mitochondrial sulfur metabolism in some fungi, and thereby indirectly manages redox potential and energy state.}, }
@article {pmid33076444, year = {2020}, author = {Qu, C and Wang, L and Zhao, Y and Liu, C}, title = {Molecular Evolution of Maize Ascorbate Peroxidase Genes and Their Functional Divergence.}, journal = {Genes}, volume = {11}, number = {10}, pages = {}, pmid = {33076444}, issn = {2073-4425}, mesh = {Ascorbate Peroxidases/*genetics/metabolism ; *Evolution, Molecular ; *Gene Expression Regulation, Plant ; Multigene Family ; Phylogeny ; Plant Proteins/*genetics/*metabolism ; Zea mays/*enzymology/*genetics/growth &amp; development ; }, abstract = {Ascorbate peroxidase (APX) is an important antioxidant enzyme. APXs in maize are encoded by multiple genes and exist as isoenzymes. The evolutionary history and functional divergence of the maize APX gene family were analyzed through comparative genomic and experimental data on the Internet in this paper. APX genes in higher plants were divided into classes A, B, and C. Each type of APX gene in angiosperms only had one ancestral gene that was duplicated along with the genome duplication or local (or tandem) duplication of the angiosperm. A total of eight genes were retained in maize and named APXa1, APXa2, APXa3, APXb1, APXb2, APXc1.1, APXc1.2, and APXc2. The APX genes of class A were located in the chloroplasts or mitochondria, and the class B and C genes were localized in the peroxisomes and cytoplasm, respectively. The expression patterns of eight APXs were different in vegetative and reproductive organs at different growth and development stages. APXa1 and APXb1 of maize may participate in the antioxidant metabolism of vegetative organs under normal conditions. APXa2, APXb2, APXc1.1, and APXc1.2 may be involved in the stress response, and APXb2 and APXc2 may participate in the senescence response. These results provide a basis for cultivating high-yield and resistant maize varieties.}, }
@article {pmid33073395, year = {2020}, author = {Kang, JS and Zhang, HR and Wang, YR and Liang, SQ and Mao, ZY and Zhang, XC and Xiang, QP}, title = {Distinctive evolutionary pattern of organelle genomes linked to the nuclear genome in Selaginellaceae.}, journal = {The Plant journal : for cell and molecular biology}, volume = {104}, number = {6}, pages = {1657-1672}, doi = {10.1111/tpj.15028}, pmid = {33073395}, issn = {1365-313X}, mesh = {Evolution, Molecular ; Gene Rearrangement/genetics ; Genes, Plant/genetics ; Genome, Mitochondrial/genetics ; Genome, Plant/*genetics ; Genome, Plastid/*genetics ; Huperzia/genetics ; Organelles/genetics ; Recombination, Genetic/genetics ; Selaginellaceae/*genetics ; }, abstract = {Plastids and mitochondria are endosymbiotic organelles that store genetic information. The genomes of these organelles generally exhibit contrasting patterns regarding genome architecture and genetic content. However, they have similar genetic features in Selaginellaceae, and little is known about what causes parallel evolution. Here, we document the multipartite plastid genomes (plastomes) and the highly divergent mitochondrial genomes (mitogenomes) from spikemoss obtained by combining short- and long-reads. The 188-kb multipartite plastome has three ribosomal operon copies in the master genomic conformation, creating the alternative subgenomic conformation composed of 110- and 78-kb subgenomes. The long-read data indicated that the two different genomic conformations were present in almost equal proportions in the plastomes of Selaginella nipponica. The mitogenome of S. nipponica was assembled into 27 contigs with a total size of 110 kb. All contigs contained directly arranged repeats at both ends, which introduced multiple conformations. Our results showed that plastomes and mitogenomes share high tRNA losses, GC-biased nucleotides, elevated substitution rates and complicated organization. The exploration of nuclear-encoded organelle DNA replication, recombination and repair proteins indicated that, several single-targeted proteins, particularly plastid-targeted recombinase A1, have been lost in Selaginellaceae; conversely, the dual-targeted proteins remain intact. According to the reported function of recombinase A1, we propose that the plastomes of spikemoss often fail to pair homologous sequences during recombination, and the dual-targeted proteins play a key role in the convergent genetic features of plastomes and mitogenomes. Our results provide a distinctive evolutionary pattern of the organelle genomes in Selaginellaceae and evidence of their convergent evolution.}, }
@article {pmid33072737, year = {2020}, author = {Teulière, J and Bernard, G and Bapteste, E}, title = {The Distribution of Genes Associated With Regulated Cell Death Is Decoupled From the Mitochondrial Phenotypes Within Unicellular Eukaryotic Hosts.}, journal = {Frontiers in cell and developmental biology}, volume = {8}, number = {}, pages = {536389}, pmid = {33072737}, issn = {2296-634X}, abstract = {Genetically regulated cell death (RCD) occurs in all domains of life. In eukaryotes, the evolutionary origin of the mitochondrion and of certain forms of RCD, in particular apoptosis, are thought to coincide, suggesting a central general role for mitochondria in cellular suicide. We tested this mitochondrial centrality hypothesis across a dataset of 67 species of protists, presenting 5 classes of mitochondrial phenotypes, including functional mitochondria, metabolically diversified mitochondria, functionally reduced mitochondria (Mitochondrion Related Organelle or MRO) and even complete absence of mitochondria. We investigated the distribution of genes associated with various forms of RCD. No homologs for described mammalian regulators of regulated necrosis could be identified in our set of 67 unicellular taxa. Protists with MRO and the secondarily a mitochondriate Monocercomonoides exilis display heterogeneous reductions of apoptosis gene sets with respect to typical mitochondriate protists. Remarkably, despite the total lack of mitochondria in M. exilis, apoptosis-associated genes could still be identified. These same species of protists with MRO and M. exilis harbored non-reduced autophagic cell death gene sets. Moreover, transiently multicellular protist taxa appeared enriched in apoptotic and autophagy associated genes compared to free-living protists. This analysis suggests that genes associated with apoptosis in animals and the presence of the mitochondria are significant yet non-essential biological components for RCD in protists. More generally, our results support the hypothesis of a selection for RCD, including both apoptosis and autophagy, as a developmental mechanism linked to multicellularity.}, }
@article {pmid33070735, year = {2020}, author = {Friesen, CR and Noble, DWA and Olsson, M}, title = {The role of oxidative stress in postcopulatory selection.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1813}, pages = {20200065}, pmid = {33070735}, issn = {1471-2970}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; *Biological Evolution ; Humans ; Male ; *Oxidative Stress ; Reactive Oxygen Species/metabolism ; Reproduction/*physiology ; Spermatozoa/*physiology ; }, abstract = {Two decades ago, von Schantz et al. (von Schantz T, Bensch S, Grahn M, Hasselquist D, Wittzell H. 1999 Good genes, oxidative stress and condition-dependent sexual signals. Proc. R. Soc. B 266, 1-12. (doi:10.1098/rspb.1999.0597)) united oxidative stress (OS) biology with sexual selection and life-history theory. This set the scene for analysis of how evolutionary trade-offs may be mediated by the increase in reactive molecules resulting from metabolic processes at reproduction. Despite 30 years of research on OS effects on infertility in humans, one research area that has been left behind in this integration of evolution and OS biology is postcopulatory sexual selection-this integration is long overdue. We review the basic mechanisms in OS biology, why mitochondria are the primary source of ROS and ATP production during oxidative metabolism, and why sperm, and its performance, is uniquely susceptible to OS. We also review how postcopulatory processes select for antioxidation in seminal fluids to counter OS and the implications of the net outcome of these processes on sperm damage, sperm storage, and female and oocyte manipulation of sperm metabolism and repair of DNA to enhance offspring fitness. This article is part of the theme issue 'Fifty years of sperm competition'.}, }
@article {pmid33059071, year = {2021}, author = {van der Merwe, PW and Cotterill, FPD and Kandziora, M and Watters, BR and Nagy, B and Genade, T and Flügel, TJ and Svendsen, DS and Bellstedt, DU}, title = {Genomic fingerprints of palaeogeographic history: The tempo and mode of rift tectonics across tropical Africa has shaped the diversification of the killifish genus Nothobranchius (Teleostei: Cyprinodontiformes).}, journal = {Molecular phylogenetics and evolution}, volume = {158}, number = {}, pages = {106988}, doi = {10.1016/j.ympev.2020.106988}, pmid = {33059071}, issn = {1095-9513}, mesh = {Africa ; Animals ; Cell Nucleus/genetics ; DNA/chemistry/isolation &amp; purification/metabolism ; Electron Transport Complex IV/classification/genetics ; *Genome ; Glycosyltransferases/classification/genetics ; Killifishes/*classification/genetics ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; }, abstract = {This paper reports a phylogeny of the African killifishes (Genus Nothobranchius, Order Cyprinodontiformes) informed by five genetic markers (three nuclear, two mitochondrial) of 80 taxa (seven undescribed and 73 of the 92 recognized species). These short-lived annual fishes occupy seasonally wet habitats in central and eastern Africa, and their distribution coincides largely with the East African Rift System (EARS). The fossil dates of sister clades used to constrain a chronometric tree of all sampled Nothobranchius recovered the origin of the genus at ~13.27 Mya. It was followed by the radiations of six principal clades through the Neogene. An ancestral area estimation tested competing biogeographical hypotheses to constrain the ancestral origin of the genus to the Nilo-Sudan Ecoregion, which seeded a mid-Miocene dispersal event into the Coastal ecoregion, followed closely (~10 Mya) by dispersals southward across the Mozambique coastal plain into the Limpopo Ecoregion. Extending westwards across the Tanzanian plateau, a pulse of radiations through the Pliocene were associated with dispersals and fragmentation of wetlands across the Kalahari and Uganda Ecoregions. We interpret this congruence of drainage rearrangements with dispersals and cladogenic events of Nothobranchius to reflect congruent responses to recurrent uplift and rifting. The coevolution of these freshwater fishes and wetlands is attributed to ultimate control by tectonics, as the EARS extended southwards during the Neogene. Geobiological consilience of the combined evidence supports a tectonic hypothesis for the evolution of Nothobranchius.}, }
@article {pmid33059067, year = {2021}, author = {Bocalini, F and Bolívar-Leguizamón, SD and Silveira, LF and Bravo, GA}, title = {Comparative phylogeographic and demographic analyses reveal a congruent pattern of sister relationships between bird populations of the northern and south-central Atlantic Forest.}, journal = {Molecular phylogenetics and evolution}, volume = {154}, number = {}, pages = {106973}, doi = {10.1016/j.ympev.2020.106973}, pmid = {33059067}, issn = {1095-9513}, mesh = {Animals ; Brazil ; Demography ; *Forests ; Gene Flow ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Mitochondria/genetics ; Passeriformes/*classification/genetics ; Phylogeny ; *Phylogeography ; Polymorphism, Single Nucleotide/genetics ; Species Specificity ; }, abstract = {The Pernambuco Center of Endemism (PCE) is the northernmost strip of the Atlantic Forest (AF). Biogeographic affinities among avifaunas in the PCE, the southern-central Atlantic Forest (SCAF), and Amazonia (AM) have not been studied comprehensively, and current patterns of genetic diversity in the PCE remain unclear. The interplay between species' ecological attributes and historical processes, such as Pleistocene climate fluctuations or the appearance of rivers, may have affected population genetic structures in the PCE. Moreover, the role of past connections between the PCE and AM and the elevational distribution of species in assembling the PCE avifauna remain untested. Here, we investigated the biogeographic history of seven taxa endemic to the PCE within a comparative phylogeographic framework based on a mean of 3,618 independent single nucleotide polymorphisms (SNPs) extracted from flanking regions of ultraconserved elements (UCEs) and one mitochondrial gene. We found that PCE populations were more closely related to SCAF populations than they were to those in AM, regardless of their elevational range, with divergence times placed during the Mid-Pleistocene. These splits were consistent with a pattern of allopatric divergence with gene flow until the upper Pleistocene and no signal of rapid changes in population sizes. Our results support the existence of a Pleistocene refugium driving current genetic diversity in the PCE, thereby rejecting the role of the São Francisco River as a primary barrier for population divergence. Additionally, we found that connections with Amazonia also played a significant role in assembling the PCE avifauna through subsequent migration events.}, }
@article {pmid33058877, year = {2020}, author = {Patel, BV and Yao, F and Howenstine, A and Takenaka, R and Hyatt, JA and Sears, KE and Shewchuk, BM}, title = {Emergent Coordination of the CHKB and CPT1B Genes in Eutherian Mammals: Implications for the Origin of Brown Adipose Tissue.}, journal = {Journal of molecular biology}, volume = {432}, number = {23}, pages = {6127-6145}, pmid = {33058877}, issn = {1089-8638}, support = {R21 OD022988/OD/NIH HHS/United States ; }, mesh = {3-Hydroxyacyl CoA Dehydrogenases/genetics ; Acetyl-CoA C-Acyltransferase/genetics ; Adipose Tissue, Brown/*metabolism ; Animals ; *Biological Evolution ; Carbon-Carbon Double Bond Isomerases/genetics ; Carnitine O-Palmitoyltransferase/*genetics ; Choline Kinase/*genetics ; Enoyl-CoA Hydratase/genetics ; Eutheria/genetics/metabolism ; Female ; Mammals/genetics/metabolism ; Mitochondria/genetics/metabolism ; Phylogeny ; Pregnancy ; Racemases and Epimerases/genetics ; }, abstract = {Mitochondrial fatty acid oxidation (FAO) contributes to the proton motive force that drives ATP synthesis in many mammalian tissues. In eutherian (placental) mammals, brown adipose tissue (BAT) can also dissipate this proton gradient through uncoupling protein 1 (UCP1) to generate heat, but the evolutionary events underlying the emergence of BAT are unknown. An essential step in FAO is the transport of cytoplasmic long chain acyl-coenzyme A (acyl-CoA) into the mitochondrial matrix, which requires the action of carnitine palmitoyltransferase 1B (CPT1B) in striated muscle and BAT. In eutherians, the CPT1B gene is closely linked to the choline kinase beta (CHKB) gene, which is transcribed from the same DNA strand and terminates just upstream of CPT1B. CHKB is a rate-limiting enzyme in the synthesis of phosphatidylcholine (PC), a predominant mitochondrial membrane phospholipid, suggesting that the coordinated expression of CHKB and CPT1B may cooperatively enhance mitochondrial FAO. The present findings show that transcription of the eutherian CHKB and CPT1B genes is linked within a unitary epigenetic domain targeted to the CHKB gene, and that that this regulatory linkage appears to have resulted from an intergenic deletion in eutherians that significantly altered the distribution of CHKB and CPT1B expression. Informed by the timing of this event relative to the emergence of BAT, the phylogeny of CHKB-CPT1B synteny, and the insufficiency of UCP1 to account for eutherian BAT, these data support a mechanism for the emergence of BAT based on the acquisition of a novel capacity for adipocyte FAO in a background of extant UCP1.}, }
@article {pmid33058388, year = {2021}, author = {Lima-Posada, I and Bobadilla, NA}, title = {Understanding the opposite effects of sex hormones in mediating renal injury.}, journal = {Nephrology (Carlton, Vic.)}, volume = {26}, number = {3}, pages = {217-226}, doi = {10.1111/nep.13806}, pmid = {33058388}, issn = {1440-1797}, support = {235855//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 235964//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; 272390//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; A1-S-8715//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; IN223915//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; IN201619//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, mesh = {Age Factors ; *Disease Progression ; Estrogens/*physiology ; Humans ; Incidence ; *Renal Insufficiency, Chronic/epidemiology/metabolism/physiopathology ; *Sex Factors ; Testosterone/*physiology ; }, abstract = {According to epidemiological studies, chronic kidney disease (CKD) affects more women than men, but the incidence of end-stage renal disease is higher in men than in women. However, most of these studies have not considered the incidence of CKD in women of reproductive or post-menopausal age, and even fewer with hormone replacement therapy. Some meta-analyses have reported an exacerbated progression of CKD in men compared with women. Consequently, in most of the experimental models of renal injury, men of reproductive age exhibit more abnormalities in renal function and structure that lead to greater progression to CKD than women, which suggests that these differences are mediated by sex hormones rather than by other factors. This review intends to show the mechanisms regulated by oestrogen or testosterone that may explain the different risks and evolution of renal diseases between men and women. Regardless of the initial cause of kidney disease, sex hormones have been implicated in modulating vascular tone, oxidative stress, inflammation and apoptosis. Finally, our previous study highlights the mechanisms by which the transition from acute kidney injury to CKD does not occur in female rats as commonly as it does in male rats. This review not only identifies sex differences in several kidney diseases but also supports potential therapeutic opportunities to reduce or prevent the progression of CKD and highlights the importance of considering sex differences in the design of any clinical study.}, }
@article {pmid33056981, year = {2020}, author = {Brady, SW and Liu, Y and Ma, X and Gout, AM and Hagiwara, K and Zhou, X and Wang, J and Macias, M and Chen, X and Easton, J and Mulder, HL and Rusch, M and Wang, L and Nakitandwe, J and Lei, S and Davis, EM and Naranjo, A and Cheng, C and Maris, JM and Downing, JR and Cheung, NV and Hogarty, MD and Dyer, MA and Zhang, J}, title = {Pan-neuroblastoma analysis reveals age- and signature-associated driver alterations.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {5183}, pmid = {33056981}, issn = {2041-1723}, support = {P30 CA008748/CA/NCI NIH HHS/United States ; R35 CA220500/CA/NCI NIH HHS/United States ; U10 CA180886/CA/NCI NIH HHS/United States ; U10 CA180899/CA/NCI NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Age Factors ; Anaplastic Lymphoma Kinase/genetics ; Biomarkers, Tumor/*genetics ; Child ; Child, Preschool ; Cohort Studies ; DNA Copy Number Variations ; DNA Mutational Analysis ; Datasets as Topic ; Electron Transport/genetics ; Exome/genetics ; Female ; *Gene Expression Regulation, Neoplastic ; Humans ; Infant ; Infant, Newborn ; Male ; Mitochondrial Ribosomes ; Mutation ; Neuroblastoma/*genetics/pathology ; Receptor, Fibroblast Growth Factor, Type 1/genetics ; Ribosomal Proteins/genetics ; Transcriptome/genetics ; Whole Genome Sequencing ; Young Adult ; }, abstract = {Neuroblastoma is a pediatric malignancy with heterogeneous clinical outcomes. To better understand neuroblastoma pathogenesis, here we analyze whole-genome, whole-exome and/or transcriptome data from 702 neuroblastoma samples. Forty percent of samples harbor at least one recurrent driver gene alteration and most aberrations, including MYCN, ATRX, and TERT alterations, differ in frequency by age. MYCN alterations occur at median 2.3 years of age, TERT at 3.8 years, and ATRX at 5.6 years. COSMIC mutational signature 18, previously associated with reactive oxygen species, is the most common cause of driver point mutations in neuroblastoma, including most ALK and Ras-activating variants. Signature 18 appears early and is continuous throughout disease evolution. Signature 18 is enriched in neuroblastomas with MYCN amplification, 17q gain, and increased expression of mitochondrial ribosome and electron transport-associated genes. Recurrent FGFR1 variants in six patients, and ALK N-terminal structural alterations in five samples, identify additional patients potentially amenable to precision therapy.}, }
@article {pmid33056243, year = {2020}, author = {GÓmez-Zurita, J and Platania, L and Cardoso, A}, title = {A new species of the genus Tricholapita nom. nov. and stat. nov. (Coleoptera: Chrysomelidae, Eumolpinae) from New Caledonia.}, journal = {Zootaxa}, volume = {4858}, number = {1}, pages = {zootaxa.4858.1.5}, doi = {10.11646/zootaxa.4858.1.5}, pmid = {33056243}, issn = {1175-5334}, mesh = {Animals ; *Coleoptera ; Mitochondria ; New Caledonia ; Phylogeny ; }, abstract = {Tricholapita Gómez-Zurita and Cardoso nom. nov. is proposed as the replacement name for the leaf beetle taxon Lapita Gómez-Zurita and Cardoso, 2014, nec Bickel, 2002. Moreover, the rank of Tricholapita stat. nov. is elevated from subgenus of Taophila Heller, 1916 to generic status. Phylogenetic evidence based on mtDNA rrnS sequences and diagnostic morphological characters reveals a new species from the south of Grande Terre in New Caledonia, which is described: Tricholapita reidi sp. nov.}, }
@article {pmid33042846, year = {2020}, author = {da Veiga Moreira, J and Schwartz, L and Jolicoeur, M}, title = {Targeting Mitochondrial Singlet Oxygen Dynamics Offers New Perspectives for Effective Metabolic Therapies of Cancer.}, journal = {Frontiers in oncology}, volume = {10}, number = {}, pages = {573399}, pmid = {33042846}, issn = {2234-943X}, abstract = {The occurrence of mitochondrial respiration has allowed evolution toward more complex and advanced life forms. However, its dysfunction is now also seen as the most probable cause of one of the biggest scourges in human health, cancer. Conventional cancer treatments such as chemotherapy, which mainly focus on disrupting the cell division process, have shown being effective in the attenuation of various cancers but also showing significant limits as well as serious sides effects. Indeed, the idea that cancer is a metabolic disease with mitochondria as the central site of the pathology is now emerging, and we provide here a review supporting this "novel" hypothesis re-actualizing past century Otto Warburg's thoughts. Our conclusion, while integrating literature, is that mitochondrial activity and, in particular, the activity of cytochrome c oxidase, complex IV of the ETC, plays a fundamental role in the effectiveness or non-effectiveness of chemotherapy, immunotherapy and probably radiotherapy treatments. We therefore propose that cancer cells mitochondrial singlet oxygen ([1]O2) dynamics may be an efficient target for metabolic therapy development.}, }
@article {pmid33036486, year = {2020}, author = {Zhu, Y and Berkowitz, O and Selinski, J and Hartmann, A and Narsai, R and Wang, Y and Mao, P and Whelan, J}, title = {Conserved and Opposite Transcriptome Patterns during Germination in Hordeum vulgare and Arabidopsis thaliana.}, journal = {International journal of molecular sciences}, volume = {21}, number = {19}, pages = {}, pmid = {33036486}, issn = {1422-0067}, support = {CE140100008//Centre of Excellence in Plant Energy Biology, Australian Research Council/ ; DE160101536//Australian Research Council/ ; }, mesh = {Arabidopsis/*genetics ; Computational Biology/methods ; Evolution, Molecular ; *Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Germination/*genetics ; Hordeum/*genetics ; Molecular Sequence Annotation ; Seeds/*genetics/metabolism ; *Transcriptome ; }, abstract = {Seed germination is a critical process for completion of the plant life cycle and for global food production. Comparing the germination transcriptomes of barley (Hordeum vulgare) to Arabidopsis thaliana revealed the overall pattern was conserved in terms of functional gene ontology; however, many oppositely responsive orthologous genes were identified. Conserved processes included a set of approximately 6000 genes that peaked early in germination and were enriched in processes associated with RNA metabolism, e.g., pentatricopeptide repeat (PPR)-containing proteins. Comparison of orthologous genes revealed more than 3000 orthogroups containing almost 4000 genes that displayed similar expression patterns including functions associated with mitochondrial tricarboxylic acid (TCA) cycle, carbohydrate and RNA/DNA metabolism, autophagy, protein modifications, and organellar function. Biochemical and proteomic analyses indicated mitochondrial biogenesis occurred early in germination, but detailed analyses revealed the timing involved in mitochondrial biogenesis may vary between species. More than 1800 orthogroups representing 2000 genes displayed opposite patterns in transcript abundance, representing functions of energy (carbohydrate) metabolism, photosynthesis, protein synthesis and degradation, and gene regulation. Differences in expression of basic-leucine zippers (bZIPs) and Apetala 2 (AP2)/ethylene-responsive element binding proteins (EREBPs) point to differences in regulatory processes at a high level, which provide opportunities to modify processes in order to enhance grain quality, germination, and storage as needed for different uses.}, }
@article {pmid33035389, year = {2021}, author = {Novo, N and Ferreira, P and Medina, M}, title = {The apoptosis-inducing factor family: Moonlighting proteins in the crosstalk between mitochondria and nuclei.}, journal = {IUBMB life}, volume = {73}, number = {3}, pages = {568-581}, doi = {10.1002/iub.2390}, pmid = {33035389}, issn = {1521-6551}, mesh = {Animals ; Apoptosis ; Apoptosis Inducing Factor/*chemistry/genetics/*metabolism ; Apoptosis Regulatory Proteins/genetics/metabolism ; Cell Death ; Cell Nucleus/*metabolism ; Humans ; Mitochondria/*metabolism ; Mitochondrial Diseases/genetics/*metabolism/pathology ; Mitochondrial Proteins/genetics/metabolism ; Multigene Family ; Neoplasms/metabolism/pathology ; Phylogeny ; }, abstract = {In Homo sapiens, the apoptosis-inducing factor (AIF) family is represented by three different proteins, known as AIF, AMID and AIFL, that have in common the mitochondrial localisation in healthy cells, the presence of FAD- and NADH-dependent domains involved in an -albeit yet not well understood- oxidoreductase function and their capability to induce programmed cell death. AIF is the best characterised family member, while the information about AMID and AIFL is much scarcer. Nonetheless, available data support different roles as well as mechanisms of action of their particular apoptogenic and redox domains regarding both pro-apoptotic and anti-apoptotic activities. Moreover, diverse cellular functions, to date far from fully clarified, are envisaged for the transcripts corresponding to these three proteins. Here, we review the so far available knowledge on the moonlighting human AIF family from their molecular properties to their relevance in health and disease, through the evaluation of their potential cell death and redox functions in their different subcellular locations. This picture emerging from the current knowledge of the AIF family envisages its contribution to regulate signalling and transcription machineries in the crosstalk among mitochondria, the cytoplasm and the nucleus.}, }
@article {pmid33032063, year = {2020}, author = {Chen, C and Meng, Y and Shopan, J and Whelan, J and Hu, Z and Yang, J and Zhang, M}, title = {Identification and characterization of Arabidopsis thaliana mitochondrial F1F0-ATPase inhibitor factor 1.}, journal = {Journal of plant physiology}, volume = {254}, number = {}, pages = {153264}, doi = {10.1016/j.jplph.2020.153264}, pmid = {33032063}, issn = {1618-1328}, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Green Fluorescent Proteins ; Mitochondria/enzymology/metabolism ; Phylogeny ; Proteins/genetics/*metabolism ; Proton-Translocating ATPases/metabolism ; Real-Time Polymerase Chain Reaction ; Sequence Alignment ; ATPase Inhibitory Protein ; }, abstract = {Mitochondrial F1F0-ATP synthase (F1F0-ATPase) inhibitor factor 1 (IF1) has been extensively characterized as an endogenous inhibitor that prevents the hydrolysis of adenosine-5'-triphosphate (ATP) by mitochondrial ATPases in mammals and yeasts; however, IF1's functions in plants remain unclear. Here, a comprehensive bioinformatic analysis was performed to identify plant mitochondrial F1F0-ATPase IF1 orthologs. Plant IF1s contain a conserved F1F0-ATPase inhibitory domain, but lack the antiparallel α-helical coiled-coil structure compared with mammalian IF1s. A subcellular localization analysis in Arabidopsis thaliana revealed that AtIF1-green fluorescent protein was present only in mitochondria. Additionally, AtIF1 was widely expressed in diverse organs and intense β-glucuronidase staining was observed in reproductive tissues and germinating seeds. Compared with the wild-type and p35S:AtIF1-if1 etiolated seedlings, the ATP/ADP ratio was significantly lower in the AtIF1 T-DNA knockout seedlings (if1 mutant) growing under dark conditions, suggesting that AtIF1 can influence the energy state of cells. A significant reduction in seed yield and strong growth retardation under dark conditions were observed in the if1 mutant line. Furthermore, if1 plants exhibited a substantially decreased sensitivity to abscisic acid. Thus, the A. thaliana mitochondrial IF1, which is a conserved F1F0-ATPase inhibitor, is crucial for plant growth and responses to abscisic acid.}, }
@article {pmid33031928, year = {2021}, author = {Rancilhac, L and Irisarri, I and Angelini, C and Arntzen, JW and Babik, W and Bossuyt, F and Künzel, S and Lüddecke, T and Pasmans, F and Sanchez, E and Weisrock, D and Veith, M and Wielstra, B and Steinfartz, S and Hofreiter, M and Philippe, H and Vences, M}, title = {Phylotranscriptomic evidence for pervasive ancient hybridization among Old World salamanders.}, journal = {Molecular phylogenetics and evolution}, volume = {155}, number = {}, pages = {106967}, doi = {10.1016/j.ympev.2020.106967}, pmid = {33031928}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Genome, Mitochondrial ; *Hybridization, Genetic ; Mitochondria/genetics ; *Phylogeny ; Transcriptome/genetics ; Urodela/*classification/*genetics ; }, abstract = {Hybridization can leave genealogical signatures in an organism's genome, originating from the parental lineages and persisting over time. This potentially confounds phylogenetic inference methods that aim to represent evolution as a strictly bifurcating tree. We apply a phylotranscriptomic approach to study the evolutionary history of, and test for inter-lineage introgression in the Salamandridae, a Holarctic salamanders group of interest in studies of toxicity and aposematism, courtship behavior, and molecular evolution. Although the relationships between the 21 currently recognized salamandrid genera have been the subject of numerous molecular phylogenetic studies, some branches have remained controversial and sometimes affected by discordances between mitochondrial vs. nuclear trees. To resolve the phylogeny of this family, and understand the source of mito-nuclear discordance, we generated new transcriptomic (RNAseq) data for 20 salamandrids and used these along with published data, including 28 mitochondrial genomes, to obtain a comprehensive nuclear and mitochondrial perspective on salamandrid evolution. Our final phylotranscriptomic data set included 5455 gene alignments for 40 species representing 17 of the 21 salamandrid genera. Using concatenation and species-tree phylogenetic methods, we find (1) Salamandrina sister to the clade of the "True Salamanders" (consisting of Chioglossa, Mertensiella, Lyciasalamandra, and Salamandra), (2) Ichthyosaura sister to the Near Eastern genera Neurergus and Ommatotriton, (3) Triturus sister to Lissotriton, and (4) Cynops paraphyletic with respect to Paramesotriton and Pachytriton. Combining introgression tests and phylogenetic networks, we find evidence for introgression among taxa within the clades of "Modern Asian Newts" and "Modern European Newts". However, we could not unambiguously identify the number, position, and direction of introgressive events. Combining evidence from nuclear gene analysis with the observed mito-nuclear phylogenetic discordances, we hypothesize a scenario with hybridization and mitochondrial capture among ancestral lineages of (1) Lissotriton into Ichthyosaura and (2) Triturus into Calotriton, plus introgression of nuclear genes from Triturus into Lissotriton. Furthermore, both mitochondrial capture and nuclear introgression may have occurred among lineages assigned to Cynops. More comprehensive genomic data will, in the future, allow testing this against alternative scenarios involving hybridization with other, extinct lineages of newts.}, }
@article {pmid33031489, year = {2021}, author = {Miyazawa, H and Osigus, HJ and Rolfes, S and Kamm, K and Schierwater, B and Nakano, H}, title = {Mitochondrial Genome Evolution of Placozoans: Gene Rearrangements and Repeat Expansions.}, journal = {Genome biology and evolution}, volume = {13}, number = {1}, pages = {}, pmid = {33031489}, issn = {1759-6653}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Exons ; Gene Order ; *Gene Rearrangement ; *Genome, Mitochondrial ; Haplotypes ; Introns ; Mitochondria/*genetics ; Phylogeny ; Placozoa/*genetics ; RNA, Ribosomal ; RNA, Ribosomal, 16S ; RNA, Transfer ; }, abstract = {Placozoans, nonbilaterian animals with the simplest known metazoan bauplan, are currently classified into 20 haplotypes belonging to three genera, Polyplacotoma, Trichoplax, and Hoilungia. The latter two comprise two and five clades, respectively. In Trichoplax and Hoilungia, previous studies on six haplotypes belonging to four different clades have shown that their mtDNAs are circular chromosomes of 32-43 kb in size, which encode 12 protein-coding genes, 24 tRNAs, and two rRNAs. These mitochondrial genomes (mitogenomes) also show unique features rarely seen in other metazoans, including open reading frames (ORFs) of unknown function, and group I and II introns. Here, we report seven new mitogenomes, covering the five previously described haplotypes H2, H17, H19, H9, and H11, as well as two new haplotypes, H23 (clade III) and H24 (clade VII). The overall gene content is shared between all placozoan mitochondrial genomes, but genome sizes, gene orders, and several exon-intron boundaries vary among clades. Phylogenomic analyses strongly support a tree topology different from previous 16S rRNA analyses, with clade VI as the sister group to all other Hoilungia clades. We found small inverted repeats in all 13 mitochondrial genomes of the Trichoplax and Hoilungia genera and evaluated their distribution patterns among haplotypes. Because Polyplacotoma mediterranea (H0), the sister to the remaining haplotypes, has a small mitochondrial genome with few small inverted repeats and ORFs, we hypothesized that the proliferation of inverted repeats and ORFs substantially contributed to the observed increase in the size and GC content of the Trichoplax and Hoilungia mitochondrial genomes.}, }
@article {pmid33030077, year = {2020}, author = {Han, L and Zhang, JT and Wang, MM and Zhu, KX and Wang, XY}, title = {Mitochondrial DNA diversity and population structure of Laodelphax striatellus across a broad geographic area in China.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {31}, number = {8}, pages = {346-354}, doi = {10.1080/24701394.2020.1830075}, pmid = {33030077}, issn = {2470-1408}, mesh = {Animals ; China ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Genetics, Population ; Haplotypes ; Hemiptera/*classification/genetics ; Mitochondria/*genetics ; Pest Control ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {The small brown planthopper (SBPH), Laodelphax striatellus Fallén (Hemiptera: Delphacidae), is a crucial devastating rice pest in East Asia. To effectively control this pest, we investigate the genetic diversity, genetic differentiation and genetic structure of 49 populations in China based on a 596 bp fragment of the mitochondrial DNA cytochrome c oxidase subunit I (mtDNA COI) gene. Overall, 83 haplotypes were detected in 1253 mtDNA COI sequences. High levels of genetic variability (Hd = 0.756 ± 0.009, π = 0.00416 ± 0.00011) and genetic differentiation (FST = 0.262, p < .001) were observed. Bayesian inference phylogenetic and median-joining haplotype network analyses indicated no obvious geographical distribution pattern among haplotypes. Hierarchical AMOVA and SAMOVA revealed no genetically distinct groups and lack of obvious phylogeographic structure. Isolation by distance (IBD) analysis results demonstrated no correlation between genetic differentiation and geographic distance. Finally, the demographic history of SBPH examined by neutrality tests and mismatch distribution analyses illustrated a sudden population expansion at the large spatial scale in China.}, }
@article {pmid33030068, year = {2020}, author = {Kumar, KS and Chandrika, SK and George, S}, title = {Genetic structure and demographic history of Indirana semipalmata, an endemic frog species of the Western Ghats, India.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {31}, number = {8}, pages = {365-378}, doi = {10.1080/24701394.2020.1830077}, pmid = {33030068}, issn = {2470-1408}, mesh = {Animals ; Anura/*classification/genetics ; Cell Nucleus/*genetics ; Conservation of Natural Resources ; DNA/*genetics ; Evolution, Molecular ; Gene Flow ; Genetics, Population ; India ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The evolutionary potential of a species mainly depends on the level of genetic variation in their populations. Maintenance of gene variation enables populations to adapt more quickly to environmental changes. The geographical gaps also influence the distribution and evolutionary history of many mountain frogs in the world. Hence, a sound knowledge in population genetic structure of a species will help understand its population dynamics and develop conservation strategies. In the context of facing threats to the amphibian fauna of Western Ghats due to habitat loss, we used both mitochondrial and nuclear DNA markers to investigate the genetic structure of an endemic frog species of the Western Ghats (Indirana semipalmata) with restricted distribution. The present study showed the importance of mountain gaps in shaping the species' structuring in the Western Ghats. Though a high genetic diversity was observed for the species when considering a single unit in the southern Western Ghats, the restricted gene flow on/between either side of the Shencottah gap with genetic clustering of the sampled populations may warrant a unique management plan for the species. The habitat fragmentation of the Western Ghats through anthropogenic activities may result in severe setbacks to the survival of the species in the future.}, }
@article {pmid33026033, year = {2020}, author = {Bolmatov, D and Carrillo, JY and Sumpter, BG and Katsaras, J and Lavrentovich, MO}, title = {Double membrane formation in heterogeneous vesicles.}, journal = {Soft matter}, volume = {16}, number = {38}, pages = {8806-8817}, doi = {10.1039/d0sm01167c}, pmid = {33026033}, issn = {1744-6848}, mesh = {*Lipid Bilayers ; *Molecular Dynamics Simulation ; }, abstract = {Lipids are capable of forming a variety of structures, including multi-lamellar vesicles. Layered lipid membranes are found in cell organelles, such as autophagosomes and mitochondria. Here, we present a mechanism for the formation of a double-walled vesicle (i.e., two lipid bilayers) from a unilamellar vesicle through the partitioning and phase separation of a small molecule. Using molecular dynamics simulations, we show that double membrane formation proceeds via a nucleation and growth process - i.e., after a critical concentration of the small molecules, a patch of double membrane nucleates and grows to cover the entire vesicle. We discuss the implications of this mechanism and theoretical approaches for understanding the evolution and formation of double membranes.}, }
@article {pmid33017596, year = {2021}, author = {Mayr, SJ and Mendel, RR and Schwarz, G}, title = {Molybdenum cofactor biology, evolution and deficiency.}, journal = {Biochimica et biophysica acta. Molecular cell research}, volume = {1868}, number = {1}, pages = {118883}, doi = {10.1016/j.bbamcr.2020.118883}, pmid = {33017596}, issn = {1879-2596}, mesh = {Coenzymes/biosynthesis/classification/*genetics ; Eukaryota/*genetics ; Gene Fusion/genetics ; Humans ; Metalloproteins/biosynthesis/classification/*genetics ; Molybdenum/*metabolism ; Molybdenum Cofactors ; Pteridines/classification ; Substrate Specificity ; }, abstract = {The molybdenum cofactor (Moco) represents an ancient metal‑sulfur cofactor, which participates as catalyst in carbon, nitrogen and sulfur cycles, both on individual and global scale. Given the diversity of biological processes dependent on Moco and their evolutionary age, Moco is traced back to the last universal common ancestor (LUCA), while Moco biosynthetic genes underwent significant changes through evolution and acquired additional functions. In this review, focused on eukaryotic Moco biology, we elucidate the benefits of gene fusions on Moco biosynthesis and beyond. While originally the gene fusions were driven by biosynthetic advantages such as coordinated expression of functionally related proteins and product/substrate channeling, they also served as origin for the development of novel functions. Today, Moco biosynthetic genes are involved in a multitude of cellular processes and loss of the according gene products result in severe disorders, both related to Moco biosynthesis and secondary enzyme functions.}, }
@article {pmid33007329, year = {2021}, author = {Braymer, JJ and Freibert, SA and Rakwalska-Bange, M and Lill, R}, title = {Mechanistic concepts of iron-sulfur protein biogenesis in Biology.}, journal = {Biochimica et biophysica acta. Molecular cell research}, volume = {1868}, number = {1}, pages = {118863}, doi = {10.1016/j.bbamcr.2020.118863}, pmid = {33007329}, issn = {1879-2596}, mesh = {Bacteria/genetics ; Cytosol/metabolism ; Humans ; Iron/metabolism ; Iron-Sulfur Proteins/*genetics/metabolism ; Mitochondria/*genetics/metabolism ; Photosynthesis/*genetics ; Respiration/genetics ; Saccharomyces cerevisiae/genetics ; Sulfur/metabolism ; Symbiosis/*genetics ; }, abstract = {Iron-sulfur (Fe/S) proteins are present in virtually all living organisms and are involved in numerous cellular processes such as respiration, photosynthesis, metabolic reactions, nitrogen fixation, radical biochemistry, protein synthesis, antiviral defense, and genome maintenance. Their versatile functions may go back to the proposed role of their Fe/S cofactors in the origin of life as efficient catalysts and electron carriers. More than two decades ago, it was discovered that the in vivo synthesis of cellular Fe/S clusters and their integration into polypeptide chains requires assistance by complex proteinaceous machineries, despite the fact that Fe/S proteins can be assembled chemically in vitro. In prokaryotes, three Fe/S protein biogenesis systems are known; ISC, SUF, and the more specialized NIF. The former two systems have been transferred by endosymbiosis from bacteria to mitochondria and plastids, respectively, of eukaryotes. In their cytosol, eukaryotes use the CIA machinery for the biogenesis of cytosolic and nuclear Fe/S proteins. Despite the structural diversity of the protein constituents of these four machineries, general mechanistic concepts underlie the complex process of Fe/S protein biogenesis. This review provides a comprehensive and comparative overview of the various known biogenesis systems in Biology, and summarizes their common or diverging molecular mechanisms, thereby illustrating both the conservation and diverse adaptions of these four machineries during evolution and under different lifestyles. Knowledge of these fundamental biochemical pathways is not only of basic scientific interest, but is important for the understanding of human 'Fe/S diseases' and can be used in biotechnology.}, }
@article {pmid33004955, year = {2020}, author = {Park, S and Park, S}, title = {Large-scale phylogenomics reveals ancient introgression in Asian Hepatica and new insights into the origin of the insular endemic Hepatica maxima.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {16288}, pmid = {33004955}, issn = {2045-2322}, mesh = {Biological Evolution ; Asia, Eastern ; Genes, Plant/genetics ; Genetic Introgression/genetics ; Genome, Plant/genetics ; Mitochondria/genetics ; Phylogeny ; Plastids/genetics ; Ranunculaceae/*genetics ; }, abstract = {Hepatica maxima is native to Ulleungdo, which is one of the oceanic islands in Korea, and it likely originated via anagenetic speciation from the Korean mainland species H. asiatica. However, the relationships among the Asian lineages remain unresolved. Phylogenomics based on plant genomes can provide new insights into the evolutionary history of plants. We first generated plastid, mitochondrial and transcriptome sequences of the insular endemic species H. maxima. Using the genomic data for H. maxima, we obtained a phylogenomic dataset consisting of 76 plastid, 37 mitochondrial and 413 nuclear genes from Asian Hepatica and two outgroups. Coalescent- and concatenation-based methods revealed cytonuclear and organellar discordance in the lineage. The presence of gynodioecy with cytoplasmic male sterility in Asian Hepatica suggests that the discordance is correlated with potential disruption of linkage disequilibrium between the organellar genomes. Species network analyses revealed a deep history of hybridization and introgression in Asian Hepatica. We discovered that ancient and recent introgression events occurred throughout the evolutionary history of the insular endemic species H. maxima. The introgression may serve as an important source of genetic variation to facilitate adaptation to the Ulleungdo environment.}, }
@article {pmid33002605, year = {2020}, author = {Pacheco, MA and Ceríaco, LMP and Matta, NE and Vargas-Ramírez, M and Bauer, AM and Escalante, AA}, title = {A phylogenetic study of Haemocystidium parasites and other Haemosporida using complete mitochondrial genome sequences.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {85}, number = {}, pages = {104576}, doi = {10.1016/j.meegid.2020.104576}, pmid = {33002605}, issn = {1567-7257}, mesh = {Africa ; Biodiversity ; DNA, Protozoan ; *Genome, Mitochondrial ; *Genomics/methods ; Haemosporida/*classification/*genetics ; High-Throughput Nucleotide Sequencing ; *Phylogeny ; South America ; }, abstract = {Haemosporida are diverse vector-borne parasites associated with terrestrial vertebrates. Driven by the interest in species causing malaria (genus Plasmodium), the diversity of avian and mammalian haemosporidian species has been extensively studied, relying mostly on mitochondrial genes, particularly cytochrome b. However, parasites from reptiles have been neglected in biodiversity surveys. Reptilian haemosporidian parasites include Haemocystidium, a genus that shares morphological features with Plasmodium and Haemoproteus. Here, the first complete Haemocystidium mitochondrial DNA (mtDNA) genomes are studied. In particular, three mtDNA genomes from Haemocystidium spp. sampled in Africa, Oceania, and South America, are described. The Haemocystidium mtDNA genomes showed a high A + T content and a gene organization, including an extreme fragmentation of the rRNAs, found in other Haemosporida. These Haemocystidium mtDNA genomes were incorporated in phylogenetic and molecular clock analyses together with a representative sample of haemosporidian parasites from birds, mammals, and reptiles. The recovered phylogeny supported Haemocystidium as a monophyletic group apart from Plasmodium and other Haemosporida. Both the phylogenetic and molecular clock analyses yielded results consistent with a scenario in which haemosporidian parasites radiated with modern birds. Haemocystidium, like mammalian parasite clades, seems to originate from host switches by avian Haemosporida that allowed for the colonization of new vertebrate hosts. This hypothesis can be tested by investigating additional parasite species from all vertebrate hosts, particularly from reptiles. The mtDNA genomes reported here provide baseline data that can be used to scale up studies in haemosporidian parasites of reptiles using barcode approaches.}, }
@article {pmid32998881, year = {2020}, author = {Popgeorgiev, N and Sa, JD and Jabbour, L and Banjara, S and Nguyen, TTM and Akhavan-E-Sabet, A and Gadet, R and Ralchev, N and Manon, S and Hinds, MG and Osigus, HJ and Schierwater, B and Humbert, PO and Rimokh, R and Gillet, G and Kvansakul, M}, title = {Ancient and conserved functional interplay between Bcl-2 family proteins in the mitochondrial pathway of apoptosis.}, journal = {Science advances}, volume = {6}, number = {40}, pages = {}, pmid = {32998881}, issn = {2375-2548}, mesh = {Animals ; *Apoptosis ; Humans ; Mammals/metabolism ; Mitochondria/metabolism ; Mitochondrial Membranes/metabolism ; *bcl-2 Homologous Antagonist-Killer Protein/chemistry/genetics/metabolism ; }, abstract = {In metazoans, Bcl-2 family proteins are major regulators of mitochondrially mediated apoptosis; however, their evolution remains poorly understood. Here, we describe the molecular characterization of the four members of the Bcl-2 family in the most primitive metazoan, Trichoplax adhaerens All four trBcl-2 homologs are multimotif Bcl-2 group, with trBcl-2L1 and trBcl-2L2 being highly divergent antiapoptotic Bcl-2 members, whereas trBcl-2L3 and trBcl-2L4 are homologs of proapoptotic Bax and Bak, respectively. trBax expression permeabilizes the mitochondrial outer membrane, while trBak operates as a BH3-only sensitizer repressing antiapoptotic activities of trBcl-2L1 and trBcl-2L2. The crystal structure of a trBcl-2L2:trBak BH3 complex reveals that trBcl-2L2 uses the canonical Bcl-2 ligand binding groove to sequester trBak BH3, indicating that the structural basis for apoptosis control is conserved from T. adhaerens to mammals. Finally, we demonstrate that both trBax and trBak BH3 peptides bind selectively to human Bcl-2 homologs to sensitize cancer cells to chemotherapy treatment.}, }
@article {pmid32998193, year = {2020}, author = {Marshall, C and Sturk-Andreaggi, K and Ring, JD and Dür, A and Parson, W}, title = {Pathogenic Variant Filtering for Mitochondrial Genome Haplotype Reporting.}, journal = {Genes}, volume = {11}, number = {10}, pages = {}, pmid = {32998193}, issn = {2073-4425}, mesh = {*Algorithms ; DNA, Mitochondrial/analysis/*genetics ; *Genetic Variation ; *Genetics, Population ; *Genome, Mitochondrial ; *Haplotypes ; Humans ; Mitochondria/*genetics/metabolism/pathology ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Given the enhanced discriminatory power of the mitochondrial DNA (mtDNA) genome (mitogenome) over the commonly sequenced control region (CR) portion, the scientific merit of mitogenome sequencing is generally accepted. However, many laboratories remain beholden to CR sequencing due to privacy policies and legal requirements restricting the use of disease information or coding region (codR) information. In this report, we present an approach to obviate the reporting of sensitive codR data in forensic haplotypes. We consulted the MitoMap database to identify 92 mtDNA codR variants with confirmed pathogenicity. We determined the frequencies of these pathogenic variants in literature-quality and forensic-quality databases to be very low, at 1.2% and 0.36%, respectively. The observed effect of pathogenic variant filtering on random match statistics in 2488 forensic-quality mitogenome haplotypes from four populations was nil. We propose that pathogenic variant filtering should be incorporated into variant calling algorithms for mitogenome haplotype reporting to maximize the discriminatory power of the locus while minimizing the reveal of sensitive genetic information.}, }
@article {pmid32997570, year = {2020}, author = {Friedl, J and Knopp, MR and Groh, C and Paz, E and Gould, SB and Herrmann, JM and Boos, F}, title = {More than just a ticket canceller: the mitochondrial processing peptidase tailors complex precursor proteins at internal cleavage sites.}, journal = {Molecular biology of the cell}, volume = {31}, number = {24}, pages = {2657-2668}, pmid = {32997570}, issn = {1939-4586}, mesh = {Aldehyde Oxidoreductases/metabolism ; Amino Acid Sequence/genetics ; Binding Sites/genetics ; Metalloendopeptidases/*metabolism/physiology ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Multienzyme Complexes/metabolism ; Phosphotransferases (Carboxyl Group Acceptor)/metabolism ; Protein Precursors/metabolism ; Protein Processing, Post-Translational/physiology ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Substrate Specificity/genetics ; Mitochondrial Processing Peptidase ; }, abstract = {Most mitochondrial proteins are synthesized as precursors that carry N-terminal presequences. After they are imported into mitochondria, these targeting signals are cleaved off by the mitochondrial processing peptidase (MPP). Using the mitochondrial tandem protein Arg5,6 as a model substrate, we demonstrate that MPP has an additional role in preprotein maturation, beyond the removal of presequences. Arg5,6 is synthesized as a polyprotein precursor that is imported into mitochondria and subsequently separated into two distinct enzymes. This internal processing is performed by MPP, which cleaves the Arg5,6 precursor at its N-terminus and at an internal site. The peculiar organization of Arg5,6 is conserved across fungi and reflects the polycistronic arginine operon in prokaryotes. MPP cleavage sites are also present in other mitochondrial fusion proteins from fungi, plants, and animals. Hence, besides its role as a "ticket canceller" for removal of presequences, MPP exhibits a second conserved activity as an internal processing peptidase for complex mitochondrial precursor proteins.}, }
@article {pmid32992875, year = {2020}, author = {Tan, DX and Hardeland, R}, title = {Targeting Host Defense System and Rescuing Compromised Mitochondria to Increase Tolerance against Pathogens by Melatonin May Impact Outcome of Deadly Virus Infection Pertinent to COVID-19.}, journal = {Molecules (Basel, Switzerland)}, volume = {25}, number = {19}, pages = {}, pmid = {32992875}, issn = {1420-3049}, mesh = {COVID-19 ; Coronavirus Infections/*drug therapy/metabolism ; Drug Delivery Systems ; Humans ; Melatonin/metabolism/*therapeutic use ; Mitochondria/*drug effects/metabolism ; Pandemics ; Pneumonia, Viral/*drug therapy/metabolism ; Virus Diseases/*drug therapy/*immunology/metabolism ; }, abstract = {Fighting infectious diseases, particularly viral infections, is a demanding task for human health. Targeting the pathogens or targeting the host are different strategies, but with an identical purpose, i.e., to curb the pathogen's spreading and cure the illness. It appears that targeting a host to increase tolerance against pathogens can be of substantial advantage and is a strategy used in evolution. Practically, it has a broader protective spectrum than that of only targeting the specific pathogens, which differ in terms of susceptibility. Methods for host targeting applied in one pandemic can even be effective for upcoming pandemics with different pathogens. This is even more urgent if we consider the possible concomitance of two respiratory diseases with potential multi-organ afflictions such as Coronavirus disease 2019 (COVID-19) and seasonal flu. Melatonin is a molecule that can enhance the host's tolerance against pathogen invasions. Due to its antioxidant, anti-inflammatory, and immunoregulatory activities, melatonin has the capacity to reduce the severity and mortality of deadly virus infections including COVID-19. Melatonin is synthesized and functions in mitochondria, which play a critical role in viral infections. Not surprisingly, melatonin synthesis can become a target of viral strategies that manipulate the mitochondrial status. For example, a viral infection can switch energy metabolism from respiration to widely anaerobic glycolysis even if plenty of oxygen is available (the Warburg effect) when the host cell cannot generate acetyl-coenzyme A, a metabolite required for melatonin biosynthesis. Under some conditions, including aging, gender, predisposed health conditions, already compromised mitochondria, when exposed to further viral challenges, lose their capacity for producing sufficient amounts of melatonin. This leads to a reduced support of mitochondrial functions and makes these individuals more vulnerable to infectious diseases. Thus, the maintenance of mitochondrial function by melatonin supplementation can be expected to generate beneficial effects on the outcome of viral infectious diseases, particularly COVID-19.}, }
@article {pmid32992603, year = {2020}, author = {Laptev, I and Dontsova, O and Sergiev, P}, title = {Epitranscriptomics of Mammalian Mitochondrial Ribosomal RNA.}, journal = {Cells}, volume = {9}, number = {10}, pages = {}, pmid = {32992603}, issn = {2073-4409}, mesh = {Animals ; Evolution, Molecular ; Humans ; Mammals ; Mitochondria/*genetics ; Peptidyl Transferases/genetics ; Pseudouridine/genetics ; RNA, Mitochondrial/*genetics ; RNA, Ribosomal/*genetics ; Ribosomes/*genetics ; }, abstract = {Modified nucleotides are present in all ribosomal RNA molecules. Mitochondrial ribosomes are unique to have a set of methylated residues that includes universally conserved ones, those that could be found either in bacterial or in archaeal/eukaryotic cytosolic ribosomes and those that are present exclusively in mitochondria. A single pseudouridine within the mt-rRNA is located in the peptidyltransferase center at a position similar to that in bacteria. After recent completion of the list of enzymes responsible for the modification of mammalian mitochondrial rRNA it became possible to summarize an evolutionary history, functional role of mt-rRNA modification enzymes and an interplay of the mt-rRNA modification and mitoribosome assembly process, which is a goal of this review.}, }
@article {pmid32987154, year = {2020}, author = {Cheong, A and Lingutla, R and Mager, J}, title = {Expression analysis of mammalian mitochondrial ribosomal protein genes.}, journal = {Gene expression patterns : GEP}, volume = {38}, number = {}, pages = {119147}, pmid = {32987154}, issn = {1872-7298}, support = {R01 HD083311/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Blastocyst/metabolism ; Cells, Cultured ; *Gene Expression Regulation, Developmental ; Mice ; Mice, Inbred C57BL ; Mitochondrial Proteins/*genetics/metabolism ; Ribosomal Proteins/*genetics/metabolism ; }, abstract = {Mitochondrial ribosomal proteins (MRPs) are essential components for the structural and functional integrity of the mitoribosome complex. Throughout evolution, the mammalian mitoribosome has acquired new Mrp genes to compensate for loss of ribosomal RNA. More than 80 MRPs have been identified in mammals. Here we document expression pattern of 79 Mrp genes during mouse development and adult tissues and find that these genes are consistently expressed throughout early embryogenesis with little stage or tissue specificity. Further investigation of the amino acid sequence reveals that this group of proteins has little to no protein similarity. Recent work has shown that the majority of Mrp genes are essential resulting in early embryonic lethality, suggesting no functional redundancy among the group. Taken together, these results indicate that the Mrp genes are not a gene family descended from a single ancestral gene, and that each MRP has unique and essential role in the mitoribosome complex. The lack of functional redundancy is surprising given the importance of the mitoribosome for cellular and organismal viability. Further, these data suggest that genomic variants in Mrp genes may be causative for early pregnancy loss and should be evaluated as clinically.}, }
@article {pmid32966934, year = {2020}, author = {Silva de Souza, S and Machado, RN and Custódio da Costa, J and Campos, DF and Sebrenski da Silva, G and Fonseca de Almeida-Val, VM}, title = {Severe damages caused by Malathion exposure in Colossoma macropomum.}, journal = {Ecotoxicology and environmental safety}, volume = {205}, number = {}, pages = {111340}, doi = {10.1016/j.ecoenv.2020.111340}, pmid = {32966934}, issn = {1090-2414}, mesh = {Animals ; Antioxidants/*metabolism ; Characiformes/genetics/*metabolism ; *DNA Damage ; Gills/drug effects/pathology ; Insecticides/*toxicity ; Lethal Dose 50 ; Malathion/*toxicity ; Mitochondria/drug effects/metabolism ; Proto-Oncogene Mas ; Reactive Oxygen Species/metabolism ; Toxicity Tests, Acute ; Water Pollutants, Chemical/*toxicity ; }, abstract = {The increase in pesticide use in response to agricultural demands poses a risk to non-target organisms, including fish. Integrated analysis of biochemical, histopathological and genetic parameters in fish exposed to Malathion insecticide provide information on the toxicity mechanisms of this pesticide, which is classified as a probable carcinogen for humans. The present study assessed the biological responses of Colossoma macropomum after exposure to Malathion. We started determining the lethal concentration, which is the concentration capable of killing 50% of the subjects in an acute toxicity test (LC50-96 h), which was 15.77 ± 3.30 mgL[-1]. The fish were, then, exposed to Malathion during 96 h at a sublethal concentration, 7.30 mgL[-1]. Overall, we observed an increased activity of biotransformation and antioxidant enzymes, which reduced production of mitochondrial reactive oxygen species after 96 h exposure, as well as kept constant the mitochondrial respiration, Acetylcholinesterase activity and DNA damage. However, fish exposed to insecticide presented severe gill histopathological damage and increased expression of proto-oncogene ras. Taken together, the results suggest that, after four days of exposure to the Malathion, C. macropomum efficiently activates its defense mechanisms, suggesting that the basal response mechanisms are responsive. On the other hand, histopathologic damages evidenced the adverse effects of Malathion on fish, since it promoted gill necrosis and increased the expression of ras oncogene that is directly related to tumorigenesis events.}, }
@article {pmid32960450, year = {2021}, author = {Barbhuiya, PA and Uddin, A and Chakraborty, S}, title = {Codon usage pattern and evolutionary forces of mitochondrial ND genes among orders of class Amphibia.}, journal = {Journal of cellular physiology}, volume = {236}, number = {4}, pages = {2850-2868}, doi = {10.1002/jcp.30050}, pmid = {32960450}, issn = {1097-4652}, mesh = {Amphibian Proteins/genetics/metabolism ; Amphibians/*genetics/metabolism ; Animals ; Anura/genetics/metabolism ; *Codon Usage ; *Evolution, Molecular ; Mitochondria/enzymology/*genetics ; Mitochondrial Proteins/*genetics/metabolism ; NADH Dehydrogenase/*genetics/metabolism ; Species Specificity ; Urodela/genetics/metabolism ; }, abstract = {In this study, we used a bioinformatics approach to analyze the nucleotide composition and pattern of synonymous codon usage in mitochondrial ND genes in three amphibian groups, that is, orders Anura, Caudata, and Gymnophiona to identify the commonality and the differences of codon usage as no research work was reported yet. The high value of the effective number of codons revealed that the codon usage bias (CUB) was low in mitochondrial ND genes among the orders. Nucleotide composition analysis suggested that for each gene, the compositional features differed among Anura, Caudata, and Gymnophiona and the GC content was lower than AT content. Furthermore, a highly significant difference (p < .05) for GC content was found in each gene among the orders. The heat map showed contrasting patterns of codon usage among different ND genes. The regression of GC12 on GC3 suggested a narrow range of GC3 distribution and some points were located in the diagonal, indicating both mutation pressure and natural selection might influence the CUB. Moreover, the slope of the regression line was less than 0.5 in all ND genes among orders, indicating natural selection might have played the dominant role whereas mutation pressure had played a minor role in shaping CUB of ND genes across orders.}, }
@article {pmid32959780, year = {2020}, author = {Camus, MF}, title = {The perils of cheating.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {32959780}, issn = {2050-084X}, mesh = {DNA, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/genetics ; Mitochondrial Dynamics ; Nutrients ; }, abstract = {Experiments on mitochondrial DNA in worms highlight that cheating does not always pay off.}, }
@article {pmid32959778, year = {2020}, author = {Gitschlag, BL and Tate, AT and Patel, MR}, title = {Nutrient status shapes selfish mitochondrial genome dynamics across different levels of selection.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {32959778}, issn = {2050-084X}, support = {F31 GM125344/GM/NIGMS NIH HHS/United States ; R01 GM123260/GM/NIGMS NIH HHS/United States ; GM123260/GM/NIGMS NIH HHS/United States ; 1 F31 GM125344/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Caenorhabditis elegans/genetics/physiology ; Cell Proliferation/genetics ; Genetic Fitness/genetics ; Genome, Mitochondrial/*genetics ; Mitochondrial Dynamics/*genetics ; Nutrients/*metabolism ; Repetitive Sequences, Nucleic Acid/*genetics ; }, abstract = {Cooperation and cheating are widespread evolutionary strategies. While cheating confers an advantage to individual entities within a group, competition between groups favors cooperation. Selfish or cheater mitochondrial DNA (mtDNA) proliferates within hosts while being selected against at the level of host fitness. How does environment shape cheater dynamics across different selection levels? Focusing on food availability, we address this question using heteroplasmic Caenorhabditis elegans. We find that the proliferation of selfish mtDNA within hosts depends on nutrient status stimulating mtDNA biogenesis in the developing germline. Interestingly, mtDNA biogenesis is not sufficient for this proliferation, which also requires the stress-response transcription factor FoxO/DAF-16. At the level of host fitness, FoxO/DAF-16 also prevents food scarcity from accelerating the selection against selfish mtDNA. This suggests that the ability to cope with nutrient stress can promote host tolerance of cheaters. Our study delineates environmental effects on selfish mtDNA dynamics at different levels of selection.}, }
@article {pmid32949792, year = {2020}, author = {Cihlar, JC and Strobl, C and Lagacé, R and Muenzler, M and Parson, W and Budowle, B}, title = {Distinguishing mitochondrial DNA and NUMT sequences amplified with the precision ID mtDNA whole genome panel.}, journal = {Mitochondrion}, volume = {55}, number = {}, pages = {122-133}, doi = {10.1016/j.mito.2020.09.001}, pmid = {32949792}, issn = {1872-8278}, mesh = {Cell Nucleus/*genetics ; Computational Biology/methods ; DNA, Mitochondrial/*classification/isolation &amp; purification ; Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; Mitochondria/*genetics ; Phylogeny ; Whole Genome Sequencing/*methods ; }, abstract = {Nuclear mitochondrial DNA segments (NUMTs) are generated via transfer of portions of the mitochondrial genome into the nuclear genome. Given their common origin, there is the possibility that both the mitochondrial and NUMT segments may co-amplify using the same set of primers. Thus, analysis of the variation of the mitochondrial genome must take into account this co-amplification of mitochondrial and NUMT sequences. The study herein builds on data from the study by Strobl et al. (Strobl et al., 2019), in which multiple point heteroplasmies were called with an "N" to prevent labeling NUMT sequences mimicking mitochondrial heteroplasmy and being interpreted as true mitochondrial in origin sequence variants. Each of these point heteroplasmies was studied in greater detail, both molecularly and bioinformatically, to determine whether NUMT or true mitochondrial DNA variation was present. The bioinformatic and molecular tools available to help distinguish between NUMT and mitochondrial DNA and the effect of NUMT sequences on interpretation were discussed.}, }
@article {pmid32938978, year = {2020}, author = {Ben Chehida, Y and Thumloup, J and Schumacher, C and Harkins, T and Aguilar, A and Borrell, A and Ferreira, M and Rojas-Bracho, L and Robertson, KM and Taylor, BL and Víkingsson, GA and Weyna, A and Romiguier, J and Morin, PA and Fontaine, MC}, title = {Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15190}, pmid = {32938978}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; *Biological Evolution ; Ecosystem ; Evolution, Molecular ; Genetic Speciation ; Genome, Mitochondrial/*genetics ; Genomics/*methods ; Mitochondria/*genetics ; Phylogeny ; Porpoises/*physiology ; Species Specificity ; }, abstract = {Historical variation in food resources is expected to be a major driver of cetacean evolution, especially for the smallest species like porpoises. Despite major conservation issues among porpoise species (e.g., vaquita and finless), their evolutionary history remains understudied. Here, we reconstructed their evolutionary history across the speciation continuum. Phylogenetic analyses of 63 mitochondrial genomes suggest that porpoises radiated during the deep environmental changes of the Pliocene. However, all intra-specific subdivisions were shaped during the Quaternary glaciations. We observed analogous evolutionary patterns in both hemispheres associated with convergent evolution to coastal versus oceanic environments. This suggests that similar mechanisms are driving species diversification in northern (harbor and Dall's) and southern species (spectacled and Burmeister's). In contrast to previous studies, spectacled and Burmeister's porpoises shared a more recent common ancestor than with the vaquita that diverged from southern species during the Pliocene. The low genetic diversity observed in the vaquita carried signatures of a very low population size since the last 5,000 years. Cryptic lineages within Dall's, spectacled and Pacific harbor porpoises suggest a richer evolutionary history than previously suspected. These results provide a new perspective on the mechanisms driving diversification in porpoises and an evolutionary framework for their conservation.}, }
@article {pmid32937139, year = {2020}, author = {Schneider, K and Nelson, GM and Watson, JL and Morf, J and Dalglish, M and Luh, LM and Weber, A and Bertolotti, A}, title = {Protein Stability Buffers the Cost of Translation Attenuation following eIF2α Phosphorylation.}, journal = {Cell reports}, volume = {32}, number = {11}, pages = {108154}, pmid = {32937139}, issn = {2211-1247}, support = {MC_U105185860/MRC_/Medical Research Council/United Kingdom ; 206367/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {5' Untranslated Regions/genetics ; Animals ; Down-Regulation/genetics ; Endoplasmic Reticulum Stress/genetics ; Eukaryotic Initiation Factor-2/*metabolism ; HEK293 Cells ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Mitochondria/metabolism ; Models, Biological ; NIH 3T3 Cells ; Phosphorylation ; Polyribosomes/metabolism ; *Protein Biosynthesis ; Protein Stability ; RNA, Messenger/genetics/metabolism ; Ribosomal Proteins/metabolism ; Transcription, Genetic ; Unfolded Protein Response/genetics ; }, abstract = {Phosphorylation of the translation initiation factor eIF2α is a rapid and vital response to many forms of stress, including protein-misfolding stress in the endoplasmic reticulum (ER stress). It is believed to cause a general reduction in protein synthesis while enabling translation of few transcripts. Such a reduction of protein synthesis comes with the threat of depleting essential proteins, a risk thought to be mitigated by its transient nature. Here, we find that translation attenuation is not uniform, with cytosolic and mitochondrial ribosomal subunits being prominently downregulated. Translation attenuation of these targets persists after translation recovery. Surprisingly, this occurs without a measurable decrease in ribosomal proteins. Explaining this conundrum, translation attenuation preferentially targets long-lived proteins, a finding not only demonstrated by ribosomal proteins but also observed at a global level. This shows that protein stability buffers the cost of translational attenuation, establishing an evolutionary principle of cellular robustness.}, }
@article {pmid32935660, year = {2021}, author = {Li, H and Qiao, H and Liu, Y and Li, S and Tan, J and Hao, D}, title = {Characterization, expression profiling, and thermal tolerance analysis of heat shock protein 70 in pine sawyer beetle, Monochamus alternatus hope (Coleoptera: Cerambycidae).}, journal = {Bulletin of entomological research}, volume = {111}, number = {2}, pages = {217-228}, doi = {10.1017/S0007485320000541}, pmid = {32935660}, issn = {1475-2670}, mesh = {Animals ; *Coleoptera/genetics/metabolism ; Genes, Insect ; *HSP70 Heat-Shock Proteins/genetics/metabolism ; Larva/genetics/metabolism ; Phylogeny ; Thermotolerance/*genetics ; }, abstract = {Monochamus alternatus Hope (Coleoptera: Cerambycidae) warrants attention as a dominant transmission vector of the pinewood nematode, and it exhibits tolerance to high temperature. Heat shock protein 70 (HSP70) family members, including inducible HSP70 and heat shock cognate protein 70 (HSC70), are major contributors to the molecular chaperone networks of insects under heat stress. In this regard, we specifically cloned and characterized three MaltHSP70s and three MaltHSC70s. Bioinformatics analysis on the deduced amino acid sequences showed these genes, having close genetic relationships with HSP70s of Coleopteran species, collectively shared conserved signature structures and ATPase domains. Subcellular localization prediction revealed the HSP70s of M. alternatus were located not only in the cytoplasm and endoplasmic reticulum but also in the nucleus and mitochondria. The transcript levels of MaltHSP70s and MaltHSC70s in each state were significantly upregulated by exposure to 35-50°C for early 3 h, while MaltHSP70s reached a peak after exposure to 45°C for 2-3 h in contrast to less-upregulated MaltHSC70s. In terms of MaltHSP70s, the expression threshold in females was lower than that in males. Also, both fat bodies and Malpighian tubules were the tissues most sensitive to heat stress in M. alternatus larvae. Lastly, the ATPase activity of recombinant MaltHSP70-2 in vitro remained stable at 25-40°C, and this recombinant availably enhanced the thermotolerance of Escherichia coli. Overall, our findings unraveled HSP70s might be the intrinsic mediators of the strong heat tolerance of M. alternatus due to their stabilized structure and bioactivity.}, }
@article {pmid32934270, year = {2020}, author = {Simaika, JP and Ware, JL and Garrison, RW and Samways, MJ}, title = {Phylogeny of the Synlestidae (Odonata: Zygoptera), with an emphasis on Chlorolestes Selys and Ecchlorolestes Barnard.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15088}, pmid = {32934270}, issn = {2045-2322}, mesh = {Animals ; Cell Nucleus/genetics ; Mitochondria/genetics ; Odonata/*genetics ; Phylogeny ; South Africa ; }, abstract = {The Synlestidae (Odonata: Zygoptera) of southern Africa comprise some highly localized species. All but one species are endemic to South Africa, and many to the Cape Floristic Region. Here we present the first phylogenetic reconstruction of the southern African Synlestidae using nuclear and mitochondrial molecular data. The genera Ecchlorolestes and Chlorolestes are monophyletic, and we propose that the Neotropical family Perilestidae consisting of two genera, Perilestes and Perissolestes, be sunk within Synlestidae. We discuss the intra-familial relationships for the southern African Synlestidae.}, }
@article {pmid32933406, year = {2020}, author = {Weaver, RJ and Carrion, G and Nix, R and Maeda, GP and Rabinowitz, S and Iverson, ENK and Thueson, K and Havird, JC}, title = {High mitochondrial mutation rates in Silene are associated with nuclear-mediated changes in mitochondrial physiology.}, journal = {Biology letters}, volume = {16}, number = {9}, pages = {20200450}, pmid = {32933406}, issn = {1744-957X}, mesh = {DNA, Mitochondrial ; Evolution, Molecular ; Genome, Plant ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Mutation ; Mutation Rate ; *Silene/genetics ; }, abstract = {Mitochondrial (mt) respiration depends on proteins encoded both by the mitochondrial and nuclear genomes. Variation in mt-DNA mutation rates exists across eukaryotes, although the functional consequences of elevated mt mutation rates in some lineages remain underexplored. In the angiosperm genus Silene, closely related, ecologically similar species have either 'fast' or 'slow' mt-DNA mutation rates. Here, we investigated the functional consequences of elevated mt-DNA mutation rates on mt respiration profiles of Silene mitochondria. Overall levels of respiration were similar among Species. Fast species had lower respiration efficiency than slow species and relied up to 48% more on nuclear-encoded respiratory enzymes alternative oxidase (AOX) and accessory dehydrogenases (DHex), which participate in stress responses in plants. However, not all fast species showed these trends. Respiratory profiles of some enzymes were correlated, most notably AOX and DHex. We conclude that subtle differences in mt physiology among Silene lineages with dramatically different mt mutation rates may underly similar phenotypes at higher levels of biological organization, betraying the consequences of mt mutations.}, }
@article {pmid32920905, year = {2020}, author = {Ghifari, AS and Teixeira, PF and Kmiec, B and Pružinská, A and Glaser, E and Murcha, MW}, title = {A mitochondrial prolyl aminopeptidase PAP2 releases N-terminal proline and regulates proline homeostasis during stress response.}, journal = {The Plant journal : for cell and molecular biology}, volume = {104}, number = {5}, pages = {1182-1194}, doi = {10.1111/tpj.14987}, pmid = {32920905}, issn = {1365-313X}, mesh = {Amino Acid Motifs ; Aminopeptidases/genetics/*metabolism ; Arabidopsis/cytology/genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Cellular Senescence/physiology ; Darkness ; Green Fluorescent Proteins/genetics ; Loss of Function Mutation ; Mitochondria/metabolism ; Phylogeny ; Plants, Genetically Modified ; Pollen/physiology ; Proline/*metabolism ; Stress, Physiological/*physiology ; Transcription Factors/genetics/*metabolism ; }, abstract = {Most mitochondrial proteins are synthesised in the cytosol and targeted into the organelle via N-terminal targeting peptides that are cleaved upon import. The free targeting peptide is subsequently processed in a stepwise manner, with single amino acids released as final products. Here, we have characterised a proline-cleaving aminopeptidase in Arabidopsis thaliana, prolyl aminopeptidase-2 (PAP2, At3g61540). Activity assays show that PAP2 has a preferred activity to hydrolyse N-terminal proline. Protein localisation studies revealed that PAP2 is exclusively targeted to mitochondria. Characterisation of pap2 mutants show defective pollen, enhanced dark-induced senescence and increased susceptibility to abiotic stresses, which are likely attributed to a reduced level of accumulated free proline. Taken together, these results demonstrate the role of PAP2 in proline cleavage from mitochondrial peptides and proline homeostasis, which is required for the development of male gametophyte, tolerance to abiotic stresses, and leaf senescence.}, }
@article {pmid32917087, year = {2020}, author = {Teske, D and Peters, A and Möllers, A and Fischer, M}, title = {Genomic Profiling: The Strengths and Limitations of Chloroplast Genome-Based Plant Variety Authentication.}, journal = {Journal of agricultural and food chemistry}, volume = {68}, number = {49}, pages = {14323-14333}, doi = {10.1021/acs.jafc.0c03001}, pmid = {32917087}, issn = {1520-5118}, mesh = {Chloroplasts/*genetics ; *Genome, Chloroplast ; *Genome, Plant ; Genomics ; Phylogeny ; Plants/classification/*genetics ; }, abstract = {Genomic profiling is a suitable tool for variety authentication and has applications in both operational quality and regulatory raw material control. It can be used to differentiate species or varieties and to identify admixtures as well as field contaminants. To establish a molecular profile, reliable and very accurate sequence data are required. As a result of the influence of the pollinator plant, nuclear genome-based authentication is in most cases not suitable for a direct application on the fruit. Sequences must be used that come exclusively from the localized mother plant. Parts of the fruit of maternal origin, e.g., components derived from the blossom, are suitable as a basis for this. Alternatively, DNA from cell organelles that are maternally inherited, such as mitochondria or chloroplasts, can be used. The latter will be discussed in this review in closer detail. Although individual gene segments on the chloroplast genome are already used for species differentiation in barcoding studies on plants, little is known about the usefulness of the entire chloroplast genome for intraspecies differentiation in general and for differentiation between modern varieties in particular. Results from the literature as well as from our own work suggest that chloroplast genome sequences are indeed very well-suited for the differentiation of old varieties. On the other hand, they are less or not suitable for the genetic differentiation of modern cultivars, because they are often too closely related.}, }
@article {pmid32916227, year = {2020}, author = {Yamada, Y and Sato, Y and Nakamura, T and Harashima, H}, title = {Evolution of drug delivery system from viewpoint of controlled intracellular trafficking and selective tissue targeting toward future nanomedicine.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {327}, number = {}, pages = {533-545}, pmid = {32916227}, issn = {1873-4995}, mesh = {Drug Delivery Systems ; Gene Transfer Techniques ; Lipids ; *Nanomedicine ; *Nucleic Acids ; }, abstract = {Due to the rapid changes that have occurred in the field of drug discovery and the recent developments in the early 21st century, the role of drug delivery systems (DDS) has become increasingly more important. For the past 20 years, our laboratory has been developing gene delivery systems based on lipid-based delivery systems. One of our efforts has been directed toward developing a multifunctional envelope-type nano device (MEND) by modifying the particle surface with octaarginine, which resulted in a remarkably enhanced cellular uptake and improved intracellular trafficking of plasmid DNA (pDNA). When we moved to in vivo applications, however, we were faced with the PEG-dilemma and we shifted our strategy to the incorporation of ionizable cationic lipids into our system. This resulted in some dramatic improvements over our original design and this can be attributed to the development of a new lipid library. We have also developed a mitochondrial targeting system based on a membrane fusion mechanism using a MITO-Porter, which can deliver nucleic acids/pDNA into the matrix of mitochondria. After the appearance of antibody medicines, Opdivo, an immune checkpoint inhibitor, has established cancer immunology as the 4th strategy in cancer therapy. Our DDS technologies can also be applied to this new field of cancer therapy to cure cancer by controlling our immune mechanisms. The latest studies are summarized in this review article.}, }
@article {pmid32916006, year = {2020}, author = {Gueuning, M and Frey, JE and Praz, C}, title = {Ultraconserved yet informative for species delimitation: Ultraconserved elements resolve long-standing systematic enigma in Central European bees.}, journal = {Molecular ecology}, volume = {29}, number = {21}, pages = {4203-4220}, doi = {10.1111/mec.15629}, pmid = {32916006}, issn = {1365-294X}, mesh = {Animals ; Bees/genetics ; Biodiversity ; Cell Nucleus ; DNA Barcoding, Taxonomic ; *DNA, Mitochondrial/genetics ; Genomics ; *Mitochondria/genetics ; Phylogeny ; }, abstract = {Accurate and testable species hypotheses are essential for measuring, surveying and managing biodiversity. Taxonomists often rely on mitochondrial DNA barcoding to complement morphological species delimitations. Although COI-barcoding has largely proven successful in assisting identifications for most animal taxa, there are nevertheless numerous cases where mitochondrial barcodes do not reflect species hypotheses. For instance, what is regarded as a single species can be associated with two distinct DNA barcodes, which can point either to cryptic diversity or to within-species mitochondrial divergences without reproductive isolation. In contrast, two or more species can share barcodes, for instance due to mitochondrial introgression. These intrinsic limitations of DNA barcoding are commonly addressed with nuclear genomic markers, which are expensive, may have low repeatability and often require high-quality DNA. To overcome these limitations, we examined the use of ultraconserved elements (UCEs) as a quick and robust genomic approach to address such problematic cases of species delimitation in bees. This genomic method was assessed using six different species complexes suspected to harbour cryptic diversity, mitochondrial introgression or mitochondrial paraphyly. The sequencing of UCEs recovered between 686 and 1,860 homologous nuclear loci and provided explicit species delimitation in all investigated species complexes. These results provide strong evidence for the suitability of UCEs as a fast method for species delimitation even in recently diverged lineages. Furthermore, we provide the first evidence for both mitochondrial introgression among distinct bee species, and mitochondrial paraphyly within a single bee species.}, }
@article {pmid32903594, year = {2020}, author = {Mallard, J and Hucteau, E and Schott, R and Petit, T and Demarchi, M and Belletier, C and Ben Abdelghani, M and Carinato, H and Chiappa, P and Fischbach, C and Kalish-Weindling, M and Bousinière, A and Dufour, S and Favret, F and Pivot, X and Hureau, TJ and Pagano, AF}, title = {Evolution of Physical Status From Diagnosis to the End of First-Line Treatment in Breast, Lung, and Colorectal Cancer Patients: The PROTECT-01 Cohort Study Protocol.}, journal = {Frontiers in oncology}, volume = {10}, number = {}, pages = {1304}, pmid = {32903594}, issn = {2234-943X}, abstract = {Background: Cancer cachexia and exacerbated fatigue represent two hallmarks in cancer patients, negatively impacting their exercise tolerance and ultimately their quality of life. However, the characterization of patients' physical status and exercise tolerance and, most importantly, their evolution throughout cancer treatment may represent the first step in efficiently counteracting their development with prescribed and tailored exercise training. In this context, the aim of the PROTECT-01 study will be to investigate the evolution of physical status, from diagnosis to the end of first-line treatment, of patients with one of the three most common cancers (i.e., lung, breast, and colorectal). Methods: The PROTECT-01 cohort study will include 300 patients equally divided between lung, breast and colorectal cancer. Patients will perform a series of assessments at three visits throughout the treatment: (1) between the date of diagnosis and the start of treatment, (2) 8 weeks after the start of treatment, and (3) after the completion of first-line treatment or at the 6-months mark, whichever occurs first. For each of the three visits, subjective and objective fatigue, maximal voluntary force, body composition, cachexia, physical activity level, quality of life, respiratory function, overall physical performance, and exercise tolerance will be assessed. Discussion: The present study is aimed at identifying the nature and severity of maladaptation related to exercise intolerance in the three most common cancers. Therefore, our results should contribute to the delineation of the needs of each group of patients and to the determination of the most valuable exercise interventions in order to counteract these maladaptations. This descriptive and comprehensive approach is a prerequisite in order to elaborate, through future interventional research projects, tailored exercise strategies to counteract specific symptoms that are potentially cancer type-dependent and, in fine, to improve the health and quality of life of cancer patients. Moreover, our concomitant focus on fatigue and cachexia will provide insightful information about two factors that may have substantial interaction but require further investigation. Trial registration: This prospective study has been registered at ClinicalTrials.gov (NCT03956641), May, 2019.}, }
@article {pmid32896572, year = {2021}, author = {Gupta, A and Shrivastava, D and Shakya, AK and Gupta, K and Pratap, JV and Habib, S}, title = {PfKsgA1 functions as a transcription initiation factor and interacts with the N-terminal region of the mitochondrial RNA polymerase of Plasmodium falciparum.}, journal = {International journal for parasitology}, volume = {51}, number = {1}, pages = {23-37}, doi = {10.1016/j.ijpara.2020.07.010}, pmid = {32896572}, issn = {1879-0135}, mesh = {DNA-Directed RNA Polymerases/genetics ; Mitochondria/genetics ; *Mitochondrial Proteins/genetics ; Peptide Initiation Factors ; Phylogeny ; *Plasmodium falciparum/genetics ; RNA, Mitochondrial ; Transcription Factors/genetics ; }, abstract = {The small mitochondrial genome (mtDNA) of the malaria parasite is known to transcribe its genes polycistonically, although promoter element(s) have not yet been identified. An unusually large Plasmodium falciparum candidate mitochondrial phage-like RNA polymerase (PfmtRNAP) with an extended N-terminal region is encoded by the parasite nuclear genome. Using specific antibodies against the enzyme, we established that PfmtRNAP was targeted exclusively to the mitochondrion and interacted with mtDNA. Phylogenetic analysis showed that it is part of a separate apicomplexan clade. A search for PfmtRNAP-associated transcription initiation factors using sequence homology and in silico protein-protein interaction network analysis identified PfKsgA1. PfKsgA1 is a dual cytosol- and mitochondrion-targeted protein that functions as a small subunit rRNA dimethyltransferase in ribosome biogenesis. Chromatin immunoprecipitation showed that PfKsgA1 interacts with mtDNA, and in vivo crosslinking and pull-down experiments confirmed PfmtRNAP-PfKsgA1 interaction. The ability of PfKsgA1 to serve as a transcription initiation factor was demonstrated by complementation of yeast mitochondrial transcription factor Mtf1 function in Rpo41-driven in vitro transcription. Pull-down experiments using PfKsgA1 and PfmtRNAP domains indicated that the N-terminal region of PfmtRNAP interacts primarily with the PfKsgA1 C-terminal domain with some contacts being made with the linker and N-terminal domain of PfKsgA1. In the absence of full-length recombinant PfmtRNAP, solution structures of yeast mitochondrial RNA polymerase Rpo41 complexes with Mtf1 or PfKsgA1 were determined by small-angle X-ray scattering. Protein interaction interfaces thus identified matched with those reported earlier for Rpo41-Mtf1 interaction and overlaid with the PfmtRNAP-interfacing region identified experimentally for PfKsgA1. Our results indicate that in addition to a role in mitochondrial ribosome biogenesis, PfKsgA1 has an independent function as a transcription initiation factor for PfmtRNAP.}, }
@article {pmid32896490, year = {2021}, author = {Zhao, D and Wang, H and Chen, S and Yu, D and Reiter, RJ}, title = {Phytomelatonin: An Emerging Regulator of Plant Biotic Stress Resistance.}, journal = {Trends in plant science}, volume = {26}, number = {1}, pages = {70-82}, doi = {10.1016/j.tplants.2020.08.009}, pmid = {32896490}, issn = {1878-4372}, mesh = {Disease Resistance ; Humans ; *Melatonin ; Plant Growth Regulators ; Reactive Oxygen Species ; *Stress, Physiological ; }, abstract = {Melatonin has diverse functions in plant development and stress tolerance, with recent evidence showing a beneficial role in plant biotic stress tolerance. It has been hypothesized that pathogenic invasion causes the immediate generation of melatonin, reactive oxygen species (ROS), and reactive nitrogen species (RNS), with these being mutually dependent, forming the integrative melatonin-ROS-RNS feedforward loop. Here we discuss how the loop, possibly located in the mitochondria and chloroplasts, maximizes disease resistance in the early pathogen ingress stage, providing on-site protection. We also review how melatonin interacts with phytohormone signaling pathways to mediate defense responses and discuss the evolutionary context from the beginnings of the melatonin receptor-mitogen-activated protein kinase (MAPK) cascade in unicellular green algae, followed by the occurrence of phytohormone pathways in land plants.}, }
@article {pmid32893838, year = {2020}, author = {Chung, HH and Anak Kamar, CK and Kit Lim, LW and Roja, JS and Liao, Y and Tsan-Yuk Lam, T and Chong, YL}, title = {Sequencing and characterization of complete mitogenome DNA of Rasbora tornieri (Cypriniformes: Cyprinidae: Rasbora) and its evolutionary significance.}, journal = {Journal of genetics}, volume = {99}, number = {}, pages = {}, pmid = {32893838}, issn = {0973-7731}, mesh = {Animals ; *Biological Evolution ; Cypriniformes/*genetics ; Fish Proteins/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {The yellowtail rasbora (Rasbora tornieri) is a miniature ray-finned fish categorized under the genus Rasbora in the family of Cyprinidae. In this study, a complete mitogenome sequence of R. tornieri was sequenced using four primers targeting two halves of the mitogenome with overlapping flanking regions. The size of mitogenome was 16,573 bp, housing 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a putative control region. Identical gene organization was detected between this species and other members of Rasbora genus. The heavy strand encompassed 28 genes while the light strand accommodated the other nine genes. Most protein-coding genes execute ATG as start codon, excluding COI and ND3 genes, which utilized GTG instead. The central conserved sequence blocks (CSB-E, CSB-F and CSB-D), variable sequence blocks (CSB-1, CSB-3 and CSB-2) as well as the terminal associated sequence (TAS) were conserved within the control region. The maximum likelihood phylogenetic family tree revealed the divergence of R. tornieri from the basal region of the Rasbora clade, where its evolutionary relationships with other Rasbora members are poorly resolved as indicated by the low bootstrap values. This work acts as window for further population genetics and molecular evolution studies of Rasbora genus in future.}, }
@article {pmid32891682, year = {2020}, author = {Darriba, S and Lee, RS and López, C}, title = {Mikrocytos mytilicoli n.sp. (Cercozoa, Mikrocytida, Mikrocytiidae) infecting the copepod Mytilicola intestinalis (Arthropoda, Cyclopoida, Mytilicolidae), a symbiont of Mytilus galloprovincialis in Galicia (NW Spain).}, journal = {Journal of invertebrate pathology}, volume = {176}, number = {}, pages = {107460}, doi = {10.1016/j.jip.2020.107460}, pmid = {32891682}, issn = {1096-0805}, mesh = {Animals ; Cercozoa/*classification/cytology/genetics/ultrastructure ; Copepoda/*parasitology/physiology ; DNA, Protozoan/analysis ; DNA, Ribosomal Spacer/analysis ; *Host-Parasite Interactions ; Microscopy ; Microscopy, Electron, Transmission ; Mytilus/physiology ; Phylogeny ; RNA, Ribosomal, 18S/analysis ; RNA, Ribosomal, 28S/analysis ; Spain ; Symbiosis ; }, abstract = {During a histopathological survey of Mytilus galloprovincialis in Galicia (NW Spain), microcells were observed infecting several organs of the symbiont copepod Mytilicola intestinalis. Positive results of PCR assay with specific primers for genus Mikrocytos and a clear signal of in situ hybridization with MACKINI-1 digoxigenin- labelled DNA probe (DIG-ISH) indicated a protozoan parasite of Mikrocytos genus. The ultrastructural study revealed intra and extracellular locations, polymorphic nuclei, intracellular round vesicles in the cytoplasm and absence of mitochondria. The present paper reports the characterization of the Mikrocytos sp. infecting M. intestinalis and proposes a novel species in the genus: Mikrocytos mytilicoli n. sp. A sequence of 18S-28S rDNA was obtained with 95.6% maximum identity (query cover 100%) with Mikrocytos mackini. Phylogenetic analysis showed that M. mytilicoli n. sp. and M. mackini share a common ancestor. However, comparison of the ITS1 rDNA region showed low similarity (75.8%) with M. mackini, which, combined with differences in ultrastructural details, host and geographic location, support the designation of a new species. This is the first description of a microcytid parasite of the genus Mikrocytos from a non-bivalve host.}, }
@article {pmid32887610, year = {2020}, author = {Royes, J and Biou, V and Dautin, N and Tribet, C and Miroux, B}, title = {Inducible intracellular membranes: molecular aspects and emerging applications.}, journal = {Microbial cell factories}, volume = {19}, number = {1}, pages = {176}, pmid = {32887610}, issn = {1475-2859}, support = {ANR-11-LABEX-0011-01//Agence Nationale de la Recherche/ ; ANR-17-CE09-0007//Agence Nationale de la Recherche/ ; }, mesh = {Cell Membrane/*physiology/ultrastructure ; Cell Surface Extensions/*metabolism/ultrastructure ; Membrane Proteins/*physiology ; Organelles/*physiology/ultrastructure ; Phospholipids/*physiology ; Protein Conformation ; }, abstract = {Membrane remodeling and phospholipid biosynthesis are normally tightly regulated to maintain the shape and function of cells. Indeed, different physiological mechanisms ensure a precise coordination between de novo phospholipid biosynthesis and modulation of membrane morphology. Interestingly, the overproduction of certain membrane proteins hijack these regulation networks, leading to the formation of impressive intracellular membrane structures in both prokaryotic and eukaryotic cells. The proteins triggering an abnormal accumulation of membrane structures inside the cells (or membrane proliferation) share two major common features: (1) they promote the formation of highly curved membrane domains and (2) they lead to an enrichment in anionic, cone-shaped phospholipids (cardiolipin or phosphatidic acid) in the newly formed membranes. Taking into account the available examples of membrane proliferation upon protein overproduction, together with the latest biochemical, biophysical and structural data, we explore the relationship between protein synthesis and membrane biogenesis. We propose a mechanism for the formation of these non-physiological intracellular membranes that shares similarities with natural inner membrane structures found in α-proteobacteria, mitochondria and some viruses-infected cells, pointing towards a conserved feature through evolution. We hope that the information discussed in this review will give a better grasp of the biophysical mechanisms behind physiological and induced intracellular membrane proliferation, and inspire new applications, either for academia (high-yield membrane protein production and nanovesicle production) or industry (biofuel production and vaccine preparation).}, }
@article {pmid32886780, year = {2020}, author = {Mandel, JR and Ramsey, AJ and Holley, JM and Scott, VA and Mody, D and Abbot, P}, title = {Disentangling Complex Inheritance Patterns of Plant Organellar Genomes: An Example From Carrot.}, journal = {The Journal of heredity}, volume = {111}, number = {6}, pages = {531-538}, doi = {10.1093/jhered/esaa037}, pmid = {32886780}, issn = {1465-7333}, mesh = {Crosses, Genetic ; Daucus carota/*genetics ; Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Genome, Plant/*genetics ; Genome, Plastid/*genetics ; Heteroplasmy/*genetics ; Inheritance Patterns/genetics ; Maternal Inheritance ; Mitochondria/genetics ; Multifactorial Inheritance/*genetics ; Organelles/genetics ; Phylogeny ; Plastids/genetics ; }, abstract = {Plant mitochondria and plastids display an array of inheritance patterns and varying levels of heteroplasmy, where individuals harbor more than 1 version of a mitochondrial or plastid genome. Organelle inheritance in plants has the potential to be quite complex and can vary with plant growth, development, and reproduction. Few studies have sought to investigate these complicated patterns of within-individual variation and inheritance using experimental crosses in plants. We carried out crosses in carrot, Daucus carota L. (Apiaceae), which has previously been shown to exhibit organellar heteroplasmy. We used mitochondrial and plastid markers to begin to disentangle the patterns of organellar inheritance and the fate of heteroplasmic variation, with special focus on cases where the mother displayed heteroplasmy. We also investigated heteroplasmy across the plant, assaying leaf samples at different development stages and ages. Mitochondrial and plastid paternal leakage was rare and offspring received remarkably similar heteroplasmic mixtures to their heteroplasmic mothers, indicating that heteroplasmy is maintained over the course of maternal inheritance. When offspring did differ from their mother, they were likely to exhibit a loss of the genetic variation that was present in their mother. Finally, we found that mitochondrial variation did not vary significantly over plant development, indicating that substantial vegetative sorting did not occur. Our study is one of the first to quantitatively investigate inheritance patterns and heteroplasmy in plants using controlled crosses, and we look forward to future studies making use of whole genome information to study the complex evolutionary dynamics of plant organellar genomes.}, }
@article {pmid32878185, year = {2020}, author = {Karakaidos, P and Rampias, T}, title = {Mitonuclear Interactions in the Maintenance of Mitochondrial Integrity.}, journal = {Life (Basel, Switzerland)}, volume = {10}, number = {9}, pages = {}, pmid = {32878185}, issn = {2075-1729}, abstract = {In eukaryotic cells, mitochondria originated in an α-proteobacterial endosymbiont. Although these organelles harbor their own genome, the large majority of genes, originally encoded in the endosymbiont, were either lost or transferred to the nucleus. As a consequence, mitochondria have become semi-autonomous and most of their processes require the import of nuclear-encoded components to be functional. Therefore, the mitochondrial-specific translation has evolved to be coordinated by mitonuclear interactions to respond to the energetic demands of the cell, acquiring unique and mosaic features. However, mitochondrial-DNA-encoded genes are essential for the assembly of the respiratory chain complexes. Impaired mitochondrial function due to oxidative damage and mutations has been associated with numerous human pathologies, the aging process, and cancer. In this review, we highlight the unique features of mitochondrial protein synthesis and provide a comprehensive insight into the mitonuclear crosstalk and its co-evolution, as well as the vulnerabilities of the animal mitochondrial genome.}, }
@article {pmid32873198, year = {2020}, author = {Yazaki, E and Kume, K and Shiratori, T and Eglit, Y and Tanifuji, G and Harada, R and Simpson, AGB and Ishida, KI and Hashimoto, T and Inagaki, Y}, title = {Barthelonids represent a deep-branching metamonad clade with mitochondrion-related organelles predicted to generate no ATP.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1934}, pages = {20201538}, pmid = {32873198}, issn = {1471-2954}, mesh = {Anaerobiosis ; *Biological Evolution ; Eukaryota/metabolism/*physiology ; Mitochondria/metabolism ; Organelles/metabolism ; *Phylogeny ; }, abstract = {We here report the phylogenetic position of barthelonids, small anaerobic flagellates previously examined using light microscopy alone. Barthelona spp. were isolated from geographically distinct regions and we established five laboratory strains. Transcriptomic data generated from one Barthelona strain (PAP020) were used for large-scale, multi-gene phylogenetic (phylogenomic) analyses. Our analyses robustly placed strain PAP020 at the base of the Fornicata clade, indicating that barthelonids represent a deep-branching metamonad clade. Considering the anaerobic/microaerophilic nature of barthelonids and preliminary electron microscopy observations on strain PAP020, we suspected that barthelonids possess functionally and structurally reduced mitochondria (i.e. mitochondrion-related organelles or MROs). The metabolic pathways localized in the MRO of strain PAP020 were predicted based on its transcriptomic data and compared with those in the MROs of fornicates. We here propose that strain PAP020 is incapable of generating ATP in the MRO, as no mitochondrial/MRO enzymes involved in substrate-level phosphorylation were detected. Instead, we detected a putative cytosolic ATP-generating enzyme (acetyl-CoA synthetase), suggesting that strain PAP020 depends on ATP generated in the cytosol. We propose two separate losses of substrate-level phosphorylation from the MRO in the clade containing barthelonids and (other) fornicates.}, }
@article {pmid32869868, year = {2020}, author = {Seeliger, B and Alesina, PF and Walz, MK and Pop, R and Charles, AL and Geny, B and Messaddeq, N and Kontogeorgos, G and Mascagni, P and Seyller, E and Marescaux, J and Agnus, V and Diana, M}, title = {Intraoperative imaging for remnant viability assessment in bilateral posterior retroperitoneoscopic partial adrenalectomy in an experimental model.}, journal = {The British journal of surgery}, volume = {107}, number = {13}, pages = {1780-1790}, doi = {10.1002/bjs.11839}, pmid = {32869868}, issn = {1365-2168}, support = {10-IAHU-0002//Agence Nationale de la Recherche/ ; //Fondation ARC pour la Recherche sur le Cancer/ ; }, mesh = {Adrenal Glands/*blood supply/*diagnostic imaging/physiology/surgery ; Adrenalectomy/*methods ; Animals ; Biomarkers/metabolism ; Female ; Intraoperative Care/*methods ; Lactic Acid/metabolism ; Male ; Microscopy, Confocal ; Microscopy, Electron ; Mitochondria/metabolism ; Models, Animal ; Optical Imaging ; Postoperative Period ; Sus scrofa ; Tomography, X-Ray Computed ; }, abstract = {BACKGROUND: A surgical approach preserving functional adrenal tissue allows biochemical cure while avoiding the need for lifelong steroid replacement. The aim of this experimental study was to evaluate the impact of intraoperative imaging during bilateral partial adrenalectomy on remnant perfusion and function.<br><br>METHODS: Five pigs underwent bilateral posterior retroperitoneoscopic central adrenal gland division (9 divided glands, 1 undivided). Intraoperative perfusion assessment included computer-assisted quantitative fluorescence imaging, contrast-enhanced CT, confocal laser endomicroscopy (CLE) and local lactate sampling. Specimen analysis after completion adrenalectomy (10 adrenal glands) comprised mitochondrial activity and electron microscopy.<br><br>RESULTS: Fluorescence signal intensity evolution over time was significantly lower in the cranial segment of each adrenal gland (mean(s.d.) 0&#xb7;052(0&#xb7;057) versus 0&#xb7;133(0&#xb7;057) change in intensity per s for cranial versus caudal parts respectively; P&#xa0;=&#xa0;0&#xb7;020). Concordantly, intraoperative CT in the portal phase demonstrated significantly lower contrast uptake in cranial segments (P&#xa0;=&#xa0;0&#xb7;031). In CLE, fluorescein contrast was observed in all caudal segments, but in only four of nine cranial segments (P&#xa0;=&#xa0;0&#xb7;035). Imaging findings favouring caudal perfusion were congruent, with significantly lower local capillary lactate levels caudally (mean(s.d.) 5&#xb7;66(5&#xb7;79) versus 11&#xb7;58(6&#xb7;53) mmol/l for caudal versus cranial parts respectively; P&#xa0;=&#xa0;0&#xb7;008). Electron microscopy showed more necrotic cells cranially (P&#xa0;=&#xa0;0&#xb7;031). There was no disparity in mitochondrial activity (respiratory rates, reactive oxygen species and hydrogen peroxide production) between the different segments.<br><br>CONCLUSION: In a model of bilateral partial adrenalectomy, three intraoperative imaging modalities consistently discriminated between regular and reduced adrenal remnant perfusion. By avoiding circumferential dissection, mitochondrial function was preserved in each segment of the adrenal glands. Surgical relevance Preservation of adrenal tissue to maintain postoperative function is essential in bilateral and hereditary adrenal pathologies. There is interindividual variation in residual adrenocortical stress capacity, and the minimal functional remnant size is unknown. New intraoperative imaging technologies allow improved remnant size and perfusion assessment. Fluorescence imaging and contrast-enhanced intraoperative CT showed congruent results in evaluation of perfusion. Intraoperative imaging can help to visualize the remnant vascular supply in partial adrenalectomy. Intraoperative assessment of perfusion may foster maximal functional tissue preservation in bilateral adrenal pathologies and procedures.}, }
@article {pmid32868785, year = {2020}, author = {Dawson, ER and Patananan, AN and Sercel, AJ and Teitell, MA}, title = {Stable retention of chloramphenicol-resistant mtDNA to rescue metabolically impaired cells.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {14328}, pmid = {32868785}, issn = {2045-2322}, support = {R01GM127985/NH/NIH HHS/United States ; T32CA009120/NH/NIH HHS/United States ; R01 GM073981/GM/NIGMS NIH HHS/United States ; R01 CA185189/CA/NCI NIH HHS/United States ; P30 CA016042/CA/NCI NIH HHS/United States ; R01 GM114188/GM/NIGMS NIH HHS/United States ; R01 GM127985/GM/NIGMS NIH HHS/United States ; R21 MH119020/MH/NIMH NIH HHS/United States ; T32 CA009120/CA/NCI NIH HHS/United States ; T32 GM007185/GM/NIGMS NIH HHS/United States ; R21 CA227480/CA/NCI NIH HHS/United States ; T34 GM008563/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Line, Tumor ; Chloramphenicol ; *DNA, Mitochondrial ; *Gene Transfer Techniques ; HEK293 Cells ; Humans ; *Hybrid Cells ; Mice ; *Mitochondria ; }, abstract = {The permanent transfer of specific mtDNA sequences into mammalian cells could generate improved models of mtDNA disease and support future cell-based therapies. Previous studies documented multiple biochemical changes in recipient cells shortly after mtDNA transfer, but the long-term retention and function of transferred mtDNA remains unknown. Here, we evaluate mtDNA retention in new host cells using 'MitoPunch', a device that transfers isolated mitochondria into mouse and human cells. We show that newly introduced mtDNA is stably retained in mtDNA-deficient (ρ0) recipient cells following uridine-free selection, although exogenous mtDNA is lost from metabolically impaired, mtDNA-intact (ρ+) cells. We then introduced a second selective pressure by transferring chloramphenicol-resistant mitochondria into chloramphenicol-sensitive, metabolically impaired ρ+ mouse cybrid cells. Following double selection, recipient cells with mismatched nuclear (nDNA) and mitochondrial (mtDNA) genomes retained transferred mtDNA, which replaced the endogenous mutant mtDNA and improved cell respiration. However, recipient cells with matched mtDNA-nDNA failed to retain transferred mtDNA and sustained impaired respiration. Our results suggest that exogenous mtDNA retention in metabolically impaired ρ+ recipients depends on the degree of recipient mtDNA-nDNA co-evolution. Uncovering factors that stabilize exogenous mtDNA integration will improve our understanding of in vivo mitochondrial transfer and the interplay between mitochondrial and nuclear genomes.}, }
@article {pmid32865900, year = {2020}, author = {Veena, RK and Carmel, EJ and Ramya, H and Ajith, TA and Wasser, SP and Janardhanan, KK}, title = {Caterpillar Medicinal Mushroom, Cordyceps militaris (Ascomycetes), Mycelia Attenuates Doxorubicin-Induced Oxidative Stress and Upregulates Krebs Cycle Dehydrogenases Activity and ATP Level in Rat Brain.}, journal = {International journal of medicinal mushrooms}, volume = {22}, number = {6}, pages = {593-604}, doi = {10.1615/IntJMedMushrooms.2020035093}, pmid = {32865900}, issn = {1940-4344}, mesh = {Acetylcholinesterase/metabolism ; Adenosine Triphosphate/*metabolism ; Animals ; Antioxidants/metabolism ; Biological Products/*pharmacology ; Body Weight ; Brain/drug effects/*metabolism ; Citric Acid Cycle/*drug effects ; Cordyceps/*chemistry ; Doxorubicin/*pharmacology ; Electron Transport/drug effects ; Glutathione/metabolism ; Lipid Peroxidation/drug effects ; Male ; Mitochondria/enzymology ; Mycelium/chemistry ; Oxidation-Reduction ; Oxidative Stress/*drug effects ; Oxidoreductases/metabolism ; Proteins/metabolism ; Rats ; Rats, Wistar ; Up-Regulation ; }, abstract = {Post-chemotherapy-induced cognitive dysfunction remains one of the challenges in cancer survivors. Cytokine-induced neurotoxicity manifests in subjects at any time after doxorubicin (DOX) chemotherapy. We examined the effect of bioactive Cordyceps militaris mycelia extract (CM) on the energy status, oxidative stress, and acetylcholinesterase activity in the brain of DOX treated rats. The CM (150 and 300 mg/kg b.w.) and DL-α lipoic acid (LA, 100 mg/kg b.w) were administered orally once daily for 5 days to male Wistar rats prior to the DOX administration (18 mg/kg as 3 doses of 6 mg/kg, i.p. b.w.) and continued for 6 more days. Cellular antioxidant status, Krebs cycle dehydrogenases, electron transport chain complexes (ETC) (I, III, and IV), adenosine triphosphate (ATP) level, advanced oxidation of protein products (AOPP), and acetylcholinesterase (AchE) activities were determined in the brain homogenate. The DOX alone treated group of animals showed significant decrease (p < 0.05) of brain antioxidant levels, Krebs cycle dehydrogenases activities, ETC complex activities, and decreased ATP level, while lipid peroxidation and AOPP levels were elevated. CM at 300 mg/kg b.w. or LA at 100 mg/kg b.w. elevated antioxidant status, Krebs cycle dehydrogenases, and complex activities and thus alleviated the toxicity. CM also inhibited the AchE activity in brain. The experimental results thus reveal that CM possessed excellent capacity to attenuate oxidative stress, upregulate respiratory chain complex activity and ATP levels, as well as inhibition of AchE activity.}, }
@article {pmid32861874, year = {2020}, author = {Marotta, R and Chin, J and Chiotis, M and Shuey, N and Collins, SJ}, title = {Long-term screening for primary mitochondrial DNA variants associated with Leber hereditary optic neuropathy: incidence, penetrance and clinical features.}, journal = {Mitochondrion}, volume = {54}, number = {}, pages = {128-132}, doi = {10.1016/j.mito.2020.08.007}, pmid = {32861874}, issn = {1872-8278}, mesh = {Adolescent ; Adult ; Case-Control Studies ; DNA, Mitochondrial/genetics ; Female ; Genetic Predisposition to Disease ; Humans ; Incidence ; Male ; Middle Aged ; Mutation Rate ; NADH Dehydrogenase/*genetics ; Optic Atrophy, Hereditary, Leber/*genetics ; Pedigree ; Penetrance ; *Polymorphism, Single Nucleotide ; }, abstract = {Leber hereditary optic neuropathy (LHON) is a neurodegenerative disorder characterised by bilateral, painless, subacute, central vision loss caused by pathogenic sequence variants in mitochondrial DNA (mtDNA). Over the course of 20 years, 734 people were systematically screened by our diagnostic laboratory for suspected LHON or for being at risk of LHON, with 98 found to harbour one of the three primary pathogenic mtDNA variants. Detection incidences were: 0.95% for NC_012920.1(MT-ND1):m.3460G>A; 9.4% for (MT-ND4):m.11778G>A; and 2.9% for (MT-ND6):m.14484T>C. The median age for symptomatic males was 27.3 years and for females 29.5 years, with a male to female ratio of 4.4:1 (62 males; 14 females). Most pathogenic variant carriers were propositi with the other individuals belonging to one of 14 pedigrees with noteworthy intra-family variability of clinical severity of the disease.}, }
@article {pmid32857636, year = {2020}, author = {Medini, H and Cohen, T and Mishmar, D}, title = {Mitochondria Are Fundamental for the Emergence of Metazoans: On Metabolism, Genomic Regulation, and the Birth of Complex Organisms.}, journal = {Annual review of genetics}, volume = {54}, number = {}, pages = {151-166}, doi = {10.1146/annurev-genet-021920-105545}, pmid = {32857636}, issn = {1545-2948}, mesh = {Animals ; Chromatin/genetics ; Embryonic Development/genetics ; Epigenesis, Genetic/genetics ; Genome/*genetics ; Humans ; Mitochondria/*genetics ; }, abstract = {Out of many intracellular bacteria, only the mitochondria and chloroplasts abandoned their independence billions of years ago and became endosymbionts within the host eukaryotic cell. Consequently, one cannot grow eukaryotic cells without their mitochondria, and the mitochondria cannot divide outside of the cell, thus reflecting interdependence. Here, we argue that such interdependence underlies the fundamental role of mitochondrial activities in the emergence of metazoans. Several lines of evidence support our hypothesis: (a) Differentiation and embryogenesis rely on mitochondrial function; (b) mitochondrial metabolites are primary precursors for epigenetic modifications (such as methyl and acetyl), which are critical for chromatin remodeling and gene expression, particularly during differentiation and embryogenesis; and (c) mitonuclear coregulation adapted to accommodate both housekeeping and tissue-dependent metabolic needs. We discuss the evolution of the unique mitochondrial genetic system, mitochondrial metabolites, mitonuclear coregulation, and their critical roles in the emergence of metazoans and in human disorders.}, }
@article {pmid32853372, year = {2020}, author = {Li, SJ and Zhang, X and Lukeš, J and Li, BQ and Wang, JF and Qu, LH and Hide, G and Lai, DH and Lun, ZR}, title = {Novel organization of mitochondrial minicircles and guide RNAs in the zoonotic pathogen Trypanosoma lewisi.}, journal = {Nucleic acids research}, volume = {48}, number = {17}, pages = {9747-9761}, pmid = {32853372}, issn = {1362-4962}, mesh = {Adenosine Triphosphatases/genetics ; DNA, Protozoan/genetics ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Protein Subunits/genetics ; RNA Editing ; RNA, Guide, Kinetoplastida/*genetics ; RNA, Protozoan/*genetics ; Trypanosoma lewisi/*genetics ; }, abstract = {Kinetoplastid flagellates are known for several unusual features, one of which is their complex mitochondrial genome, known as kinetoplast (k) DNA, composed of mutually catenated maxi- and minicircles. Trypanosoma lewisi is a member of the Stercorarian group of trypanosomes which is, based on human infections and experimental data, now considered a zoonotic pathogen. By assembling a total of 58 minicircle classes, which fall into two distinct categories, we describe a novel type of kDNA organization in T. lewisi. RNA-seq approaches allowed us to map the details of uridine insertion and deletion editing events upon the kDNA transcriptome. Moreover, sequencing of small RNA molecules enabled the identification of 169 unique guide (g) RNA genes, with two differently organized minicircle categories both encoding essential gRNAs. The unprecedented organization of minicircles and gRNAs in T. lewisi broadens our knowledge of the structure and expression of the mitochondrial genomes of these human and animal pathogens. Finally, a scenario describing the evolution of minicircles is presented.}, }
@article {pmid32853350, year = {2020}, author = {Arakawa, T and Kagami, H and Katsuyama, T and Kitazaki, K and Kubo, T}, title = {A Lineage-Specific Paralog of Oma1 Evolved into a Gene Family from Which a Suppressor of Male Sterility-Inducing Mitochondria Emerged in Plants.}, journal = {Genome biology and evolution}, volume = {12}, number = {12}, pages = {2314-2327}, pmid = {32853350}, issn = {1759-6653}, mesh = {Beta vulgaris/*genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Multigene Family ; Phylogeny ; Plant Infertility/*genetics ; Selection, Genetic ; }, abstract = {Cytoplasmic male sterility (MS) in plants is caused by MS-inducing mitochondria, which have emerged frequently during plant evolution. Nuclear restorer-of-fertility (Rf)genes can suppress their cognate MS-inducing mitochondria. Whereas many Rfs encode a class of RNA-binding protein, the sugar beet (Caryophyllales) Rf encodes a protein resembling Oma1, which is involved in the quality control of mitochondria. In this study, we investigated the molecular evolution of Oma1 homologs in plants. We analyzed 37 plant genomes and concluded that a single copy is the ancestral state in Caryophyllales. Among the sugar beet Oma1 homologs, the orthologous copy is located in a syntenic region that is preserved in Arabidopsis thaliana. The sugar beet Rf is a complex locus consisting of a small Oma1 homolog family (RF-Oma1 family) unique to sugar beet. The gene arrangement in the vicinity of the locus is seen in some but not all Caryophyllalean plants and is absent from Ar. thaliana. This suggests a segmental duplication rather than a whole-genome duplication as the mechanism of RF-Oma1 evolution. Of thirty-seven positively selected codons in RF-Oma1, twenty-six of these sites are located in predicted transmembrane helices. Phylogenetic network analysis indicated that homologous recombination among the RF-Oma1 members played an important role to generate protein activity related to suppression. Together, our data illustrate how an evolutionarily young Rf has emerged from a lineage-specific paralog. Interestingly, several evolutionary features are shared with the RNA-binding protein type Rfs. Hence, the evolution of the sugar beet Rf is representative of Rf evolution in general.}, }
@article {pmid32849605, year = {2020}, author = {Pérez-Hernández, CA and Kern, CC and Butkeviciute, E and McCarthy, E and Dockrell, HM and Moreno-Altamirano, MMB and Aguilar-López, BA and Bhosale, G and Wang, H and Gems, D and Duchen, MR and Smith, SG and Sánchez-García, FJ}, title = {Mitochondrial Signature in Human Monocytes and Resistance to Infection in C. elegans During Fumarate-Induced Innate Immune Training.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {1715}, pmid = {32849605}, issn = {1664-3224}, support = {MR/R005850/1/MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 098565/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; 215574/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Caenorhabditis elegans/*drug effects/immunology/metabolism/microbiology ; Calcium Signaling/drug effects ; Cells, Cultured ; Cytokines/metabolism ; Escherichia coli/immunology/*pathogenicity ; Escherichia coli Infections/immunology/metabolism/microbiology/*prevention &amp; control ; Fumarates/*pharmacology ; Host-Pathogen Interactions ; Humans ; Immunity, Innate/*drug effects ; Immunologic Memory/*drug effects ; Membrane Potential, Mitochondrial/drug effects ; Mitochondria/*drug effects/immunology/metabolism ; Mitochondrial Dynamics/drug effects ; Monocytes/*drug effects/immunology/metabolism ; }, abstract = {Monocytes can develop immunological memory, a functional characteristic widely recognized as innate immune training, to distinguish it from memory in adaptive immune cells. Upon a secondary immune challenge, either homologous or heterologous, trained monocytes/macrophages exhibit a more robust production of pro-inflammatory cytokines, such as IL-1β, IL-6, and TNF-α, than untrained monocytes. Candida albicans, β-glucan, and BCG are all inducers of monocyte training and recent metabolic profiling analyses have revealed that training induction is dependent on glycolysis, glutaminolysis, and the cholesterol synthesis pathway, along with fumarate accumulation; interestingly, fumarate itself can induce training. Since fumarate is produced by the tricarboxylic acid (TCA) cycle within mitochondria, we asked whether extra-mitochondrial fumarate has an effect on mitochondrial function. Results showed that the addition of fumarate to monocytes induces mitochondrial Ca[2+] uptake, fusion, and increased membrane potential (Δψm), while mitochondrial cristae became closer to each other, suggesting that immediate (from minutes to hours) mitochondrial activation plays a role in the induction phase of innate immune training of monocytes. To establish whether fumarate induces similar mitochondrial changes in vivo in a multicellular organism, effects of fumarate supplementation were tested in the nematode worm Caenorhabditis elegans. This induced mitochondrial fusion in both muscle and intestinal cells and also increased resistance to infection of the pharynx with E. coli. Together, these findings contribute to defining a mitochondrial signature associated with the induction of innate immune training by fumarate treatment, and to the understanding of whole organism infection resistance.}, }
@article {pmid32849440, year = {2020}, author = {Aguirre-López, B and Escalera-Fanjul, X and Hersch-González, J and Rojas-Ortega, E and El-Hafidi, M and Lezama, M and González, J and Bianchi, MM and López, G and Márquez, D and Scazzocchio, C and Riego-Ruiz, L and González, A}, title = {In Kluyveromyces lactis a Pair of Paralogous Isozymes Catalyze the First Committed Step of Leucine Biosynthesis in Either the Mitochondria or the Cytosol.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1843}, pmid = {32849440}, issn = {1664-302X}, abstract = {Divergence of paralogous pairs, resulting from gene duplication, plays an important role in the evolution of specialized or novel gene functions. Analysis of selected duplicated pairs has elucidated some of the mechanisms underlying the functional diversification of Saccharomyces cerevisiae (S. cerevisiae) paralogous genes. Similar studies of the orthologous pairs extant in pre-whole genome duplication yeast species, such as Kluyveromyces lactis (K. lactis) remain to be addressed. The genome of K. lactis, an aerobic yeast, includes gene pairs generated by sporadic duplications. The genome of this organism comprises the KlLEU4 and KlLEU4BIS paralogous pair, annotated as putative α-isopropylmalate synthases (α-IPMSs), considered to be the orthologs of the S. cerevisiae ScLEU4/ScLEU9 paralogous genes. The enzymes encoded by the latter two genes are mitochondrially located, differing in their sensitivity to leucine allosteric inhibition resulting in ScLeu4-ScLeu4 and ScLeu4-ScLeu9 sensitive dimers and ScLeu9-ScLeu9 relatively resistant homodimers. Previous work has shown that, in a Scleu4Δ mutant, ScLEU9 expression is increased and assembly of ScLeu9-ScLeu9 leucine resistant homodimers results in loss of feedback regulation of leucine biosynthesis, leading to leucine accumulation and decreased growth rate. Here we report that: (i) K. lactis harbors a sporadic gene duplication, comprising the KlLEU4, syntenic with S. cerevisiae ScLEU4 and ScLEU9, and the non-syntenic KlLEU4BIS, arising from a pre-WGD event. (ii) That both, KlLEU4 and KlLEU4BIS encode leucine sensitive α-IPMSs isozymes, located in the mitochondria (KlLeu4) and the cytosol (KlLeu4BIS), respectively. (iii) That both, KlLEU4 or KlLEU4BIS complement the Scleu4Δ Scleu9Δ leucine auxotrophic phenotype and revert the enhanced ScLEU9 transcription observed in a Scleu4Δ ScLEU9 mutant. The Scleu4Δ ScLEU9 growth mutant phenotype is only fully complemented when transformed with the syntenic KlLEU4 mitochondrial isoform. KlLEU4 and KlLEU4BIS underwent a different diversification pathways than that leading to ScLEU4/ScLEU9. KlLEU4 could be considered as the functional ortholog of ScLEU4, since its encoded isozyme can complement both the Scleu4Δ Scleu9Δ leucine auxotrophy and the Scleu4Δ ScLEU9 complex phenotype.}, }
@article {pmid32849413, year = {2020}, author = {Chen, M and Chen, N and Wu, T and Bian, Y and Deng, Y and Xu, Z}, title = {Characterization of Two Mitochondrial Genomes and Gene Expression Analysis Reveal Clues for Variations, Evolution, and Large-Sclerotium Formation in Medical Fungus Wolfiporia cocos.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1804}, pmid = {32849413}, issn = {1664-302X}, abstract = {Wolfiporia cocos, a precious mushroom with a long history as an edible food and Asian traditional medicine, remains unclear in the genetic mechanism underlying the formation of large sclerotia. Here, two complete circular mitogenomes (BL16, 135,686 bp and MD-104 SS10, 124,842 bp, respectively) were presented in detail first. The salient features in the mitogenomes of W. cocos include an intron in the tRNA (trnQ-UUG[2]), and an obvious gene rearrangement identified between the two mitogenomes from the widely geographically separated W. cocos strains. Genome comparison and phylogenetic analyses reveal some variations and evolutional characteristics in W. cocos. Whether the mitochondrion is functional in W. cocos sclerotium development was investigated by analyzing the mitogenome synteny of 10 sclerotium-forming fungi and mitochondrial gene expression patterns in different W. cocos sclerotium-developmental stages. Three common homologous genes identified across ten sclerotium-forming fungi were also found to exhibit significant differential expression levels during W. cocos sclerotium development. Most of the mitogenomic genes are not expressed in the mycelial stage but highly expressed in the sclerotium initial or developmental stage. These results indicate that some of mitochondrial genes may play a role in the development of sclerotium in W. cocos, which needs to be further elucidated in future studies. This study will stimulate new ideas on cytoplasmic inheritance of W. cocos and facilitate the research on the role of mitochondria in large sclerotium formation.}, }
@article {pmid32846873, year = {2020}, author = {Nunes-Nesi, A and Cavalcanti, JHF and Fernie, AR}, title = {Characterization of In Vivo Function(s) of Members of the Plant Mitochondrial Carrier Family.}, journal = {Biomolecules}, volume = {10}, number = {9}, pages = {}, pmid = {32846873}, issn = {2218-273X}, support = {TRR 175/1//Collaborative Research Centers, SFB (Sonderforschungsbereich)/International ; 306818/2016-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/International ; }, mesh = {Amino Acid Transport Systems/genetics/metabolism ; Arabidopsis/genetics/metabolism ; Arabidopsis Proteins/genetics/metabolism ; Coenzyme A/metabolism ; Gene Expression Regulation, Plant ; Iron/metabolism ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins/genetics/*metabolism ; Mitochondrial Uncoupling Proteins/genetics/metabolism ; Models, Biological ; NAD/metabolism ; Organic Anion Transporters/genetics/metabolism ; Phosphate Transport Proteins/genetics/metabolism ; Plant Proteins/genetics/*metabolism ; }, abstract = {Although structurally related, mitochondrial carrier family (MCF) proteins catalyze the specific transport of a range of diverse substrates including nucleotides, amino acids, dicarboxylates, tricarboxylates, cofactors, vitamins, phosphate and H[+]. Despite their name, they do not, however, always localize to the mitochondria, with plasma membrane, peroxisomal, chloroplast and thylakoid and endoplasmic reticulum localizations also being reported. The existence of plastid-specific MCF proteins is suggestive that the evolution of these proteins occurred after the separation of the green lineage. That said, plant-specific MCF proteins are not all plastid-localized, with members also situated at the endoplasmic reticulum and plasma membrane. While by no means yet comprehensive, the in vivo function of a wide range of these transporters is carried out here, and we discuss the employment of genetic variants of the MCF as a means to provide insight into their in vivo function complementary to that obtained from studies following their reconstitution into liposomes.}, }
@article {pmid32841735, year = {2021}, author = {Pallardó, FV and Pagano, G and Rodríguez, LR and Gonzalez-Cabo, P and Lyakhovich, A and Trifuoggi, M}, title = {Friedreich Ataxia: current state-of-the-art, and future prospects for mitochondrial-focused therapies.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {229}, number = {}, pages = {135-141}, doi = {10.1016/j.trsl.2020.08.009}, pmid = {32841735}, issn = {1878-1810}, mesh = {Animals ; Antioxidants/pharmacology/therapeutic use ; Carnitine/pharmacology ; Deferiprone/therapeutic use ; Friedreich Ataxia/*drug therapy/pathology ; Humans ; Iron Chelating Agents/therapeutic use ; Linoleic Acids/pharmacology ; Mitochondria/*drug effects/metabolism/pathology ; Ubiquinone/analogs &amp; derivatives/pharmacology ; }, abstract = {Friedreich's Ataxia is an autosomal recessive genetic disease causing the defective gene product, frataxin. A body of literature has been focused on the attempts to counteract frataxin deficiency and the consequent iron imbalance, in order to mitigate the disease-associated pro-oxidant state and clinical course. The present mini review is aimed at evaluating the basic and clinical reports on the roles and the use of a set of iron chelators, antioxidants and some cofactors involved in the key mitochondrial functions. Extensive literature has focused on the protective roles of iron chelators, coenzyme Q10 and analogs, and vitamin E, altogether with varying outcomes in clinical studies. Other studies have suggested mitoprotective roles for other mitochondrial cofactors, involved in Krebs cycle, such as alpha-lipoic acid and carnitine, involved in acyl transport across the mitochondrial membrane. A body of evidence points to the strong antioxidant properties of these cofactors, and to their potential contribution in mitoprotective strategies in Friedreich's Ataxia clinical evolution. Thus, we suggest the rationale for planning combination strategies based on the 3 mitochondrial cofactors and of some antioxidants and iron binders as mitoprotective cocktails in Friedreich Ataxia patients, calling attention to clinical practitioners of the importance to implement clinical trials.}, }
@article {pmid32827633, year = {2020}, author = {Esch, T and Kream, RM and Stefano, GB}, title = {Emerging regulatory roles of opioid peptides, endogenous morphine, and opioid receptor subtypes in immunomodulatory processes: Metabolic, behavioral, and evolutionary perspectives.}, journal = {Immunology letters}, volume = {227}, number = {}, pages = {28-33}, doi = {10.1016/j.imlet.2020.08.007}, pmid = {32827633}, issn = {1879-0542}, mesh = {Animals ; Behavior ; Biological Evolution ; Humans ; Immunity ; Immunomodulation ; Inflammation/*metabolism ; Morphine/*metabolism ; Nitric Oxide/metabolism ; Opioid Peptides/*metabolism ; Pain/*metabolism ; Receptors, Opioid/genetics/*metabolism ; }, abstract = {Integrated behavioral paradigms such as nociceptive processing coupled to anti-nociceptive responsiveness include systemically-mediated states of alertness, vigilance, motivation, and avoidance. Within a historical and cultural context, opium and its biologically active compounds, codeine and morphine, have been widely used as frontline anti-nociceptive agents. In eukaryotic cells, opiate alkaloids and opioid peptides were evolutionarily fashioned as regulatory factors in neuroimmune, vascular immune, and systemic immune communication and auto-immunoregulation. The significance of opioidergic regulation of immune function was validated by the identification of novel μ and δ opioid receptors on circulating leukocytes. The novel μ3 opioid receptor subtype has been characterized as an opioid peptide-insensitive and opiate alkaloid-selective G protein-coupled receptor (GPCR) that is functionally linked to the activation of constitutive nitric oxide synthase (cNOS). Opioid peptides stimulate granulocyte and immunocyte activation and chemotaxis via activation of a novel leukocyte δ2 receptor subtype. However, opiate alkaloid μ3 receptor agonists inhibit these same cellular activities. Opiate coupling to cNOS and subsequent production and release of mitochondrial nitric oxide (NO) suggests an evolutionary linkage to similar physiological events in prokaryotic cells. A subpopulation of immunocytes from Mytilus edulis and Leucophaea maderae and human granulocytes respond to low opioid concentrations, mediated by the adherence-promoting role of (D-Ala2-D-Met5)-enkephalinamide (DAMA), which is blocked by naloxone in a dose-dependent manner. Neutral endopeptidase 24.11 (NEP), or enkephalinase (CD10), is present on both human and invertebrate immunocytes. Alkaloids, including morphine, are found in both prokaryotic and eukaryotic cells and may have evolved much later in evolution through horizontal gene transfer. It is possible that opioid-mediated regulatory activities were conserved and elaborated during evolution as the central nervous system (CNS) became immunologically isolated by the blood-brain barrier. Thus, opioid receptor coupling became significant for cognitive and behavioural processes. Although opioid peptides and alkaloids work synergistically to suppress nociception, they mediate different actions in immune surveillance. Increased understanding of the evolutionary development of opioid receptors, nociceptive and anti-nociceptive pathways, and immunomodulation may help in the understanding of the development of tolerance to the clinical use of opiates for pain management. The significance of endogenous morphine's importance to evolution can be ascertained by the number of physiological tissues and systems that can be affected by this chemical messenger mechanism, which transcends pain. An integrated review is presented of opioid and opiate receptors, immunomodulation, and pain associated with inflammation, from an evolutionary perspective.}, }
@article {pmid32824295, year = {2020}, author = {Yamada, M and Akashi, K and Ooka, R and Miyado, K and Akutsu, H}, title = {Mitochondrial Genetic Drift after Nuclear Transfer in Oocytes.}, journal = {International journal of molecular sciences}, volume = {21}, number = {16}, pages = {}, pmid = {32824295}, issn = {1422-0067}, mesh = {Gene Editing/methods ; *Genes, Mitochondrial ; *Genetic Drift ; Humans ; Mitochondrial Replacement Therapy/adverse effects/*methods ; Nuclear Transfer Techniques/*adverse effects ; Oocytes/*metabolism ; }, abstract = {Mitochondria are energy-producing intracellular organelles containing their own genetic material in the form of mitochondrial DNA (mtDNA), which codes for proteins and RNAs essential for mitochondrial function. Some mtDNA mutations can cause mitochondria-related diseases. Mitochondrial diseases are a heterogeneous group of inherited disorders with no cure, in which mutated mtDNA is passed from mothers to offspring via maternal egg cytoplasm. Mitochondrial replacement (MR) is a genome transfer technology in which mtDNA carrying disease-related mutations is replaced by presumably disease-free mtDNA. This therapy aims at preventing the transmission of known disease-causing mitochondria to the next generation. Here, a proof of concept for the specific removal or editing of mtDNA disease-related mutations by genome editing is introduced. Although the amount of mtDNA carryover introduced into human oocytes during nuclear transfer is low, the safety of mtDNA heteroplasmy remains a concern. This is particularly true regarding donor-recipient mtDNA mismatch (mtDNA-mtDNA), mtDNA-nuclear DNA (nDNA) mismatch caused by mixing recipient nDNA with donor mtDNA, and mtDNA replicative segregation. These conditions can lead to mtDNA genetic drift and reversion to the original genotype. In this review, we address the current state of knowledge regarding nuclear transplantation for preventing the inheritance of mitochondrial diseases.}, }
@article {pmid32822607, year = {2020}, author = {Deng, J and Xie, XL and Wang, DF and Zhao, C and Lv, FH and Li, X and Yang, J and Yu, JL and Shen, M and Gao, L and Yang, JQ and Liu, MJ and Li, WR and Wang, YT and Wang, F and Li, JQ and Hehua, E and Liu, YG and Shen, ZQ and Ren, YL and Liu, GJ and Chen, ZH and Gorkhali, NA and Rushdi, HE and Salehian-Dehkordi, H and Esmailizadeh, A and Nosrati, M and Paiva, SR and Caetano, AR and Štěpánek, O and Olsaker, I and Weimann, C and Erhardt, G and Curik, I and Kantanen, J and Mwacharo, JM and Hanotte, O and Bruford, MW and Ciani, E and Periasamy, K and Amills, M and Lenstra, JA and Han, JL and Zhang, HP and Li, L and Li, MH}, title = {Paternal Origins and Migratory Episodes of Domestic Sheep.}, journal = {Current biology : CB}, volume = {30}, number = {20}, pages = {4085-4095.e6}, doi = {10.1016/j.cub.2020.07.077}, pmid = {32822607}, issn = {1879-0445}, mesh = {Animals ; Breeding ; Cell Lineage/genetics ; Chromosome Mapping ; DNA, Mitochondrial/*genetics ; Genetic Variation/genetics ; Genome/*genetics ; Male ; Mitochondria/genetics ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide/*genetics ; Sheep ; Sheep, Domestic/classification/*genetics ; Whole Genome Sequencing ; Y Chromosome/*genetics ; }, abstract = {The domestication and subsequent global dispersal of livestock are crucial events in human history, but the migratory episodes during the history of livestock remain poorly documented [1-3]. Here, we first developed a set of 493 novel ovine SNPs of the male-specific region of Y chromosome (MSY) by genome mapping. We then conducted a comprehensive genomic analysis of Y chromosome, mitochondrial DNA, and whole-genome sequence variations in a large number of 595 rams representing 118 domestic populations across the world. We detected four different paternal lineages of domestic sheep and resolved, at the global level, their paternal origins and differentiation. In Northern European breeds, several of which have retained primitive traits (e.g., a small body size and short or thin tails), and fat-tailed sheep, we found an overrepresentation of MSY lineages y-HC and y-HB, respectively. Using an approximate Bayesian computation approach, we reconstruct the demographic expansions associated with the segregation of primitive and fat-tailed phenotypes. These results together with archaeological evidence and historical data suggested the first expansion of early domestic hair sheep and the later expansion of fat-tailed sheep occurred ∼11,800-9,000 years BP and ∼5,300-1,700 years BP, respectively. These findings provide important insights into the history of migration and pastoralism of sheep across the Old World, which was associated with different breeding goals during the Neolithic agricultural revolution.}, }
@article {pmid32817169, year = {2020}, author = {Srivastava, SR and Mahalakshmi, R}, title = {Evolutionary selection of a 19-stranded mitochondrial β-barrel scaffold bears structural and functional significance.}, journal = {The Journal of biological chemistry}, volume = {295}, number = {43}, pages = {14653-14665}, pmid = {32817169}, issn = {1083-351X}, support = {/WT_/Wellcome Trust/United Kingdom ; IA/I/14/1/501305/WTDBT_/DBT-Wellcome Trust India Alliance/India ; }, mesh = {Animals ; Evolution, Molecular ; Humans ; Lipid Bilayers/chemistry/*metabolism ; Mitochondria/chemistry/genetics/metabolism ; Models, Molecular ; Mutation ; Porins/chemistry/genetics/metabolism ; Protein Conformation, beta-Strand ; Protein Engineering ; Protein Stability ; Saccharomyces cerevisiae/chemistry/genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism ; Thermodynamics ; Voltage-Dependent Anion Channel 2/chemistry/genetics/metabolism ; Voltage-Dependent Anion Channels/*chemistry/genetics/*metabolism ; }, abstract = {Transmembrane β-barrels of eukaryotic outer mitochondrial membranes (OMMs) are major channels of communication between the cytosol and mitochondria and are indispensable for cellular homeostasis. A structurally intriguing exception to all known transmembrane β-barrels is the unique odd-stranded, i.e. 19-stranded, structures found solely in the OMM. The molecular origins of this 19-stranded structure and its associated functional significance are unclear. In humans, the most abundant OMM transporter is the voltage-dependent anion channel. Here, using the human voltage-dependent anion channel as our template scaffold, we designed and engineered odd- and even-stranded structures of smaller (V2[16], V2[17], V2[18]) and larger (V2[20], V2[21]) barrel diameters. Determination of the structure, dynamics, and energetics of these engineered structures in bilayer membranes reveals that the 19-stranded barrel surprisingly holds modest to low stability in a lipid-dependent manner. However, we demonstrate that this structurally metastable protein possesses superior voltage-gated channel regulation, efficient mitochondrial targeting, and in vivo cell survival, with lipid-modulated stability, all of which supersede the occurrence of a metastable 19-stranded scaffold. We propose that the unique structural adaptation of these transmembrane transporters exclusively in mitochondria bears strong evolutionary basis and is functionally significant for homeostasis.}, }
@article {pmid32812630, year = {2020}, author = {Shen, H and Zheng, X and Zhou, Z and He, W and Li, M and Su, P and Song, J and Yang, Y}, title = {Oriented immobilization of enzyme-DNA conjugates on magnetic Janus particles for constructing a multicompartment multienzyme system with high activity and stability.}, journal = {Journal of materials chemistry. B}, volume = {8}, number = {36}, pages = {8467-8475}, doi = {10.1039/d0tb01439g}, pmid = {32812630}, issn = {2050-7518}, mesh = {Armoracia/enzymology ; Aspergillus niger/enzymology ; Biocatalysis ; Biomimetics/methods ; DNA/*chemistry ; Enzymes, Immobilized/*chemistry ; Fluoresceins/chemistry ; Fluorescent Dyes/chemistry ; Fungal Proteins/chemistry ; Glucose/analysis/chemistry ; Glucose Oxidase/*chemistry ; Horseradish Peroxidase/*chemistry ; Magnetite Nanoparticles/*chemistry ; Oxidation-Reduction ; Plant Proteins/chemistry ; }, abstract = {Various organelles (e.g., mitochondria and chloroplasts) have a multicompartment structure, providing superior function of material transformation, selective segregation and energy conversion. Enlightened by the elegant evolution of nature, intended isolation of the biochemical process by cooperative multicompartments in cells has become an appealing blueprint to construct bioreactors. In this study, we develop a "soft separation" way to establish a delicate multicompartment multienzyme system (MMS) with polyphenol-encapsulated enzyme-DNA conjugates, which are anchored on magnetic Janus particles, providing a biomimetic catalysis network with the model cascade reactions in confinement. The well-designed MMS exhibits preferable bioactivity benefitting from the dependable DNA bridges and the oriented immobilization of enzymes, while the polyphenol shell further protects the anchored enzymes from exterior attacks, such as heat and enzymatic degradation. Moreover, by applying the MMS as nanomotors, the asymmetrical distribution of enzymes on Janus particles is found to improve mutual elevation between the self-driven locomotion and enzyme-mediated reactions, delivering enhanced dispersal ability and bioactivity. Owing to the excellent enzymatic activity, promoted stability and satisfying biocompatibility, the assembled MMS is proved to be promising for the in vitro and intracellular sensing of glucose, showing significant potential for biochemical analysis applications.}, }
@article {pmid32808073, year = {2020}, author = {Bernacki, LE and Kilpatrick, CW}, title = {Structural Variation of the Turtle Mitochondrial Control Region.}, journal = {Journal of molecular evolution}, volume = {88}, number = {7}, pages = {618-640}, doi = {10.1007/s00239-020-09962-0}, pmid = {32808073}, issn = {1432-1432}, mesh = {Animals ; Base Sequence ; Conserved Sequence ; DNA, Mitochondrial/genetics/*metabolism ; *Evolution, Molecular ; Genetic Variation ; Genome, Mitochondrial ; Mitochondria/genetics ; *Nucleic Acid Conformation ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Turtles/*genetics ; }, abstract = {The present study describes the most comprehensive comparison of turtle mtD-loop regions to date. The primary structure was compared from DNA sequences accessed from GenBank from 48 species in 13 families of extant turtles, and secondary structures of the mtD-loop region were inferred from thermal stabilities, using the program Mfold, for each superfamiliy of turtles. Both primary and secondary structures were found to be highly variable across the order. The Cryptodira showed conservation in the primary structure at conserved sequence blocks (CSBs), but the Pleurodira displayed limited conservation of primary structural characters, other than the coreTAS, a binding site for the helicase TWINKLE, which was highly conserved in the Central and Right Domains across the order. No secondary structure was associated with a TAS, but an AT-rich fold (secondary structure) near the 3' terminus of the mtD-loop region was detected in all turtle superfamilies. Mapping of character states of structural features of the mtD-loop region revealed that most character states were autapomorphies and inferred a number of homoplasies. The Left Domain of turtles, containing no highly conserved structural elements, likely does not serve a functional role; therefore, the Central Domain in turtles is likely equivalent to the Left Domain of mammals. The AT-rich secondary structural element near the 3' terminus of the mtD-loop region may be conserved across turtles because of a functional role, perhaps containing the Light Strand Promotor, or perhaps interacting with the TWINKLE-coreTAS complex in the Central and Right Domains to regulate mtDNA replication and transcription.}, }
@article {pmid32806678, year = {2020}, author = {Santos, HJ and Chiba, Y and Makiuchi, T and Arakawa, S and Murakami, Y and Tomii, K and Imai, K and Nozaki, T}, title = {Import of Entamoeba histolytica Mitosomal ATP Sulfurylase Relies on Internal Targeting Sequences.}, journal = {Microorganisms}, volume = {8}, number = {8}, pages = {}, pmid = {32806678}, issn = {2076-2607}, support = {23117001, 23117005//Ministry of Education, Culture, Sports, Science and Technology/ ; 17K19416; JP18H02650; JP20K16233//Japan Society for the Promotion of Science/ ; }, abstract = {Mitochondrial matrix proteins synthesized in the cytosol often contain amino (N)-terminal targeting sequences (NTSs), or alternately internal targeting sequences (ITSs), which enable them to be properly translocated to the organelle. Such sequences are also required for proteins targeted to mitochondrion-related organelles (MROs) that are present in a few species of anaerobic eukaryotes. Similar to other MROs, the mitosomes of the human intestinal parasite Entamoeba histolytica are highly degenerate, because a majority of the components involved in various processes occurring in the canonical mitochondria are either missing or modified. As of yet, sulfate activation continues to be the only identified role of the relic mitochondria of Entamoeba. Mitosomes influence the parasitic nature of E. histolytica, as the downstream cytosolic products of sulfate activation have been reported to be essential in proliferation and encystation. Here, we investigated the position of the targeting sequence of one of the mitosomal matrix enzymes involved in the sulfate activation pathway, ATP sulfurylase (AS). We confirmed by immunofluorescence assay and subcellular fractionation that hemagluttinin (HA)-tagged EhAS was targeted to mitosomes. However, its ortholog in the δ-proteobacterium Desulfovibrio vulgaris, expressed as DvAS-HA in amoebic trophozoites, indicated cytosolic localization, suggesting a lack of recognizable mitosome targeting sequence in this protein. By expressing chimeric proteins containing swapped sequences between EhAS and DvAS in amoebic cells, we identified the ITSs responsible for mitosome targeting of EhAS. This observation is similar to other parasitic protozoans that harbor MROs, suggesting a convergent feature among various MROs in favoring ITS for the recognition and translocation of targeted proteins.}, }
@article {pmid32788982, year = {2020}, author = {N Miyata, M and Nomura, M and Kageyama, D}, title = {Wolbachia have made it twice: Hybrid introgression between two sister species of Eurema butterflies.}, journal = {Ecology and evolution}, volume = {10}, number = {15}, pages = {8323-8330}, pmid = {32788982}, issn = {2045-7758}, abstract = {Wolbachia, cytoplasmically inherited endosymbionts of arthropods, are known to hijack their host reproduction in various ways to increase their own vertical transmission. This may lead to the selective sweep of associated mitochondria, which can have a large impact on the evolution of mitochondrial lineages. In Japan, two different Wolbacahia strains (wCI and wFem) are found in two sister species of pierid butterflies, Eurema mandarina and Eurema hecabe. In both species, females infected with wCI (C females) produce offspring with a nearly 1:1 sex ratio, while females infected with both wCI and wFem (CF females) produce all-female offspring. Previous studies have suggested the historical occurrence of hybrid introgression in C individuals between the two species. Furthermore, hybrid introgression in CF individuals is suggested by the distinct mitochondrial lineages between C females and CF females of E. mandarina. In this study, we performed phylogenetic analyses based on nuclear DNA and mitochondrial DNA markers of E. hecabe with previously published data on E. mandarina. We found that the nuclear DNA of this species significantly diverged from that of E. mandarina. By contrast, mitochondrial DNA haplotypes comprised two clades, mostly reflecting Wolbachia infection status rather than the individual species. Collectively, our results support the previously suggested occurrence of two independent historical events wherein the cytoplasms of CF females and C females moved between E. hecabe and E. mandarina through hybrid introgression.}, }
@article {pmid32788668, year = {2021}, author = {Lareau, CA and Ludwig, LS and Muus, C and Gohil, SH and Zhao, T and Chiang, Z and Pelka, K and Verboon, JM and Luo, W and Christian, E and Rosebrock, D and Getz, G and Boland, GM and Chen, F and Buenrostro, JD and Hacohen, N and Wu, CJ and Aryee, MJ and Regev, A and Sankaran, VG}, title = {Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling.}, journal = {Nature biotechnology}, volume = {39}, number = {4}, pages = {451-461}, pmid = {32788668}, issn = {1546-1696}, support = {U10 CA180861/CA/NCI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; T32 HG002295/HG/NHGRI NIH HHS/United States ; F31 CA232670/CA/NCI NIH HHS/United States ; UG1 CA233338/CA/NCI NIH HHS/United States ; T32 CA207021/CA/NCI NIH HHS/United States ; P01 CA206978/CA/NCI NIH HHS/United States ; R33 HL120791/HL/NHLBI NIH HHS/United States ; R01 CA208756/CA/NCI NIH HHS/United States ; R01 DK103794/DK/NIDDK NIH HHS/United States ; }, mesh = {Aged, 80 and over ; Cell Differentiation ; Cells, Cultured ; Clonal Evolution ; Clone Cells ; DNA, Mitochondrial/*genetics ; Epigenesis, Genetic ; Female ; Genotyping Techniques ; Hematopoiesis ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Mitochondria/*genetics ; Mutation ; Neoplasms/*genetics ; Sequence Analysis, DNA ; Single-Cell Analysis/*methods ; }, abstract = {Natural mitochondrial DNA (mtDNA) mutations enable the inference of clonal relationships among cells. mtDNA can be profiled along with measures of cell state, but has not yet been combined with the massively parallel approaches needed to tackle the complexity of human tissue. Here, we introduce a high-throughput, droplet-based mitochondrial single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq), a method that combines high-confidence mtDNA mutation calling in thousands of single cells with their concomitant high-quality accessible chromatin profile. This enables the inference of mtDNA heteroplasmy, clonal relationships, cell state and accessible chromatin variation in individual cells. We reveal single-cell variation in heteroplasmy of a pathologic mtDNA variant, which we associate with intra-individual chromatin variability and clonal evolution. We clonally trace thousands of cells from cancers, linking epigenomic variability to subclonal evolution, and infer cellular dynamics of differentiating hematopoietic cells in vitro and in vivo. Taken together, our approach enables the study of cellular population dynamics and clonal properties in vivo.}, }
@article {pmid32788582, year = {2020}, author = {Pittis, AA and Goh, V and Cebrian-Serrano, A and Wettmarshausen, J and Perocchi, F and Gabaldón, T}, title = {Discovery of EMRE in fungi resolves the true evolutionary history of the mitochondrial calcium uniporter.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {4031}, pmid = {32788582}, issn = {2041-1723}, mesh = {Amino Acid Sequence ; Calcium/metabolism ; Calcium Channels/chemistry/*genetics ; Chytridiomycota/genetics ; *Evolution, Molecular ; Fungal Proteins/chemistry/*genetics ; HeLa Cells ; Humans ; Likelihood Functions ; Phylogeny ; Species Specificity ; }, abstract = {Calcium (Ca[2+]) influx into mitochondria occurs through a Ca[2+]-selective uniporter channel, which regulates essential cellular processes in eukaryotic organisms. Previous evolutionary analyses of its pore-forming subunits MCU and EMRE, and gatekeeper MICU1, pinpointed an evolutionary paradox: the presence of MCU homologs in fungal species devoid of any other uniporter components and of mt-Ca[2+] uptake. Here, we trace the mt-Ca[2+] uniporter evolution across 1,156 fully-sequenced eukaryotes and show that animal and fungal MCUs represent two distinct paralogous subfamilies originating from an ancestral duplication. Accordingly, we find EMRE orthologs outside Holoza and uncover the existence of an animal-like uniporter within chytrid fungi, which enables mt-Ca[2+] uptake when reconstituted in vivo in the yeast Saccharomyces cerevisiae. Our study represents the most comprehensive phylogenomic analysis of the mt-Ca[2+] uptake system and demonstrates that MCU, EMRE, and MICU formed the core of the ancestral opisthokont uniporter, with major implications for comparative structural and functional studies.}, }
@article {pmid32771550, year = {2020}, author = {Kornilios, P and Jablonski, D and Sadek, RA and Kumlutaş, Y and Olgun, K and Avci, A and Ilgaz, C}, title = {Multilocus species-delimitation in the Xerotyphlops vermicularis (Reptilia: Typhlopidae) species complex.}, journal = {Molecular phylogenetics and evolution}, volume = {152}, number = {}, pages = {106922}, doi = {10.1016/j.ympev.2020.106922}, pmid = {32771550}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Genetic Variation ; Haplotypes ; Mitochondria/genetics ; *Molecular Typing ; *Phylogeny ; Snakes/*classification/*genetics ; Species Specificity ; }, abstract = {Scolecophidia (worm snakes) are a vertebrate group with high ecomorphological conservatism due to their burrowing lifestyle. The Eurasian or Greek blindsnake Xerotyphlops vermicularis is their only European representative, a species-complex with an old diversification history. However, its systematics and taxonomy has remained untouched. Here, we extend previous work that relied heavily on mitochondrial markers, following a multi-locus approach and applying several species-delimitation methods, including a Bayesian coalescence-based approach (STACEY). Four "species" delimitation analyses based on the mtDNA (ABGD, bGMYC, mPTP, parsimony networks) returned 14, 11, 9 and 10 clusters, respectively. By mitotyping twice as many specimens as before, we have a complete picture of each cluster's distribution. With the exception of the highly-divergent Levantine lineage, the three independent nuclear markers did not help with phylogenetic resolution, as demonstrated in haplotype networks, concatenated and species-trees, a result of incomplete lineage sorting. The prevailing model from the coalescence-based species-delimitation identified two species: the lineage from the Levant and all others. We formally recognize them as distinct species and resurrect Xerotyphlops syriacus (Jan, 1864) to include the Levantine blindsnakes. Finally, X. vermicularis and X. syriacus may represent species-complexes themselves, since they include high levels of cryptic diversity.}, }
@article {pmid32769116, year = {2020}, author = {MacEwen, MJ and Markhard, AL and Bozbeyoglu, M and Bradford, F and Goldberger, O and Mootha, VK and Sancak, Y}, title = {Evolutionary divergence reveals the molecular basis of EMRE dependence of the human MCU.}, journal = {Life science alliance}, volume = {3}, number = {10}, pages = {}, pmid = {32769116}, issn = {2575-1077}, support = {R01 AR071942/AR/NIAMS NIH HHS/United States ; R01 HL130143/HL/NHLBI NIH HHS/United States ; T32 GM007750/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Evolution ; Calcium/metabolism ; Calcium Channels/*metabolism/physiology ; Dictyostelium/genetics/metabolism ; Evolution, Molecular ; HEK293 Cells ; Humans ; Ion Transport/genetics/physiology ; Mitochondria/metabolism ; Protein Domains ; }, abstract = {The mitochondrial calcium uniporter (MCU) is a calcium-activated calcium channel critical for signaling and bioenergetics. MCU, the pore-forming subunit of the uniporter, contains two transmembrane domains and is found in all major eukaryotic taxa. In amoeba and fungi, MCU homologs are sufficient to form a functional calcium channel, whereas human MCU exhibits a strict requirement for the metazoan protein essential MCU regulator (EMRE) for conductance. Here, we exploit this evolutionary divergence to decipher the molecular basis of human MCU's dependence on EMRE. By systematically generating chimeric proteins that consist of EMRE-independent Dictyostelium discoideum MCU and Homo sapiens MCU (HsMCU), we converged on a stretch of 10 amino acids in D. discoideum MCU that can be transplanted to HsMCU to render it EMRE independent. We call this region in human MCU the EMRE dependence domain (EDD). Crosslinking experiments show that EMRE directly interacts with HsMCU at its transmembrane domains as well as the EDD. Our results suggest that EMRE stabilizes the EDD of MCU, permitting both channel opening and calcium conductance, consistent with recently published structures of MCU-EMRE.}, }
@article {pmid32768405, year = {2020}, author = {Bennewitz, B and Sharma, M and Tannert, F and Klösgen, RB}, title = {Dual targeting of TatA points to a chloroplast-like Tat pathway in plant mitochondria.}, journal = {Biochimica et biophysica acta. Molecular cell research}, volume = {1867}, number = {11}, pages = {118816}, doi = {10.1016/j.bbamcr.2020.118816}, pmid = {32768405}, issn = {1879-2596}, mesh = {Arabidopsis/genetics ; Arabidopsis Proteins/genetics/metabolism ; Cell Membrane/genetics/metabolism ; Chloroplasts/*genetics/metabolism ; Electron Transport Complex III/genetics ; Escherichia coli/genetics ; Escherichia coli Proteins/genetics/metabolism ; Membrane Proteins/*genetics ; Membrane Transport Proteins/*genetics/metabolism ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Pisum sativum/genetics ; Plant Proteins/*genetics ; Protein Folding ; Protein Sorting Signals ; Signal Transduction/genetics ; Twin-Arginine-Translocation System/*genetics ; }, abstract = {The biogenesis of membrane-bound electron transport chains requires membrane translocation pathways for folded proteins carrying complex cofactors, like the Rieske Fe/S proteins. Two independent systems were developed during evolution, namely the Twin-arginine translocation (Tat) pathway, which is present in bacteria and chloroplasts, and the Bcs1 pathway found in mitochondria of yeast and mammals. Mitochondria of plants carry a Tat-like pathway which was hypothesized to operate with only two subunits, a TatB-like protein and a TatC homolog (OrfX), but lacking TatA. Here we show that the nuclearly encoded TatA from pea has dual targeting properties, i.e., it can be imported into both, chloroplasts and mitochondria. Dual targeting of TatA was observed with in organello experiments employing chloroplasts and mitochondria isolated from pea as well as after transient expression of suitable reporter constructs in leaf tissue from pea and Nicotiana benthamiana. The extent of transport of these constructs into mitochondria of transiently transformed leaf cells was relatively low, causing a demand for highly sensitive methods to be detected, like the sasplitGFP approach. Yet, the dual import of TatA into mitochondria and chloroplasts observed here points to a common mechanism of Tat transport for folded proteins within both endosymbiotic organelles in plants.}, }
@article {pmid32758535, year = {2020}, author = {Dupuis, JR and Sperling, FAH}, title = {Phylogenomic test of mitochondrial clues to archaic ancestors in a group of hybridizing swallowtail butterflies.}, journal = {Molecular phylogenetics and evolution}, volume = {152}, number = {}, pages = {106921}, doi = {10.1016/j.ympev.2020.106921}, pmid = {32758535}, issn = {1095-9513}, mesh = {Animals ; Biological Evolution ; Butterflies/*classification/*genetics ; DNA, Mitochondrial/genetics ; Genome, Insect/genetics ; Hybridization, Genetic ; Mitochondria/*genetics ; North America ; Nucleic Acid Hybridization ; *Phylogeny ; }, abstract = {Genomics has revolutionized our understanding of hybridization and introgression, but most of the early evidence for these processes came from studies of mitochondrial introgression. To expand these evolutionary insights from mitochondrial patterns, we evaluate phylogenetic discordance across the nuclear genomes of a hybridizing system, the Papilio machaon group of swallowtail butterflies. This species group contains three hybrid lineages (P. brevicauda, P. joanae, and P. m. kahli) that are geographically disjunct across North America and have complete fixation of a mitochondrial lineage that is otherwise primarily found in P. m. hudsonianus, a boreal subspecies of the Holarctic P. machaon. Genome-wide nuclear markers place the three hybrid lineages as a monophyletic group that is sister to P. polyxenes/P. zelicaon rather than P. machaon, although ancient hybridization between a subspecies of P. machaon and the ancestor of these three lineages is also shown by their greater nuclear affinity to P. m. hudsonianus than to other subspecies of P. machaon. Individuals from contemporary hybrid swarms in Alberta, where mitochondrial DNA fixation has not occurred, were more intermediate between their respective parent species, demonstrating diversity in mito-nuclear discordance following hybrid interactions. Our new phylogenetic findings for the P. machaon species group also include: subspecific paraphyly within P. machaon itself across its Holarctic distribution; paraphyly of P. zelicaon relative to P. polyxenes; and more divergent placement of a Mediterranean species, P. hospiton. These results provide the first comprehensive genomic evaluation of relationships within this species group and provide insight into the evolutionary dynamics of hybridization and mitochondrial introgression.}, }
@article {pmid32745723, year = {2020}, author = {Nechushtai, R and Karmi, O and Zuo, K and Marjault, HB and Darash-Yahana, M and Sohn, YS and King, SD and Zandalinas, SI and Carloni, P and Mittler, R}, title = {The balancing act of NEET proteins: Iron, ROS, calcium and metabolism.}, journal = {Biochimica et biophysica acta. Molecular cell research}, volume = {1867}, number = {11}, pages = {118805}, doi = {10.1016/j.bbamcr.2020.118805}, pmid = {32745723}, issn = {1879-2596}, mesh = {Calcium/*metabolism ; Cell Proliferation/genetics ; Endoplasmic Reticulum/metabolism ; Humans ; Iron/chemistry/*metabolism ; Iron-Sulfur Proteins/chemistry/genetics/*metabolism ; Mitochondria/metabolism ; Protein Binding/genetics ; Reactive Oxygen Species/*metabolism ; }, abstract = {NEET proteins belong to a highly conserved group of [2Fe-2S] proteins found across all kingdoms of life. Due to their unique [2Fe2S] cluster structure, they play a key role in the regulation of many different redox and oxidation processes. In eukaryotes, NEET proteins are localized to the mitochondria, endoplasmic reticulum (ER) and the mitochondrial-associated membranes connecting these organelles (MAM), and are involved in the control of multiple processes, ranging from autophagy and apoptosis to ferroptosis, oxidative stress, cell proliferation, redox control and iron and iron‑sulfur homeostasis. Through their different functions and interactions with key proteins such as VDAC and Bcl-2, NEET proteins coordinate different mitochondrial, MAM, ER and cytosolic processes and functions and regulate major signaling molecules such as calcium and reactive oxygen species. Owing to their central role in cells, NEET proteins are associated with numerous human maladies including cancer, metabolic diseases, diabetes, obesity, and neurodegenerative diseases. In recent years, a new and exciting role for NEET proteins was uncovered, i.e., the regulation of mitochondrial dynamics and morphology. This new role places NEET proteins at the forefront of studies into cancer and different metabolic diseases, both associated with the regulation of mitochondrial dynamics. Here we review recent studies focused on the evolution, biological role, and structure of NEET proteins, as well as discuss different studies conducted on NEET proteins function using transgenic organisms. We further discuss the different strategies used in the development of drugs that target NEET proteins, and link these with the different roles of NEET proteins in cells.}, }
@article {pmid32739012, year = {2020}, author = {Smith, SK and Musiek, ES}, title = {Impact of circadian and diurnal rhythms on cellular metabolic function and neurodegenerative diseases.}, journal = {International review of neurobiology}, volume = {154}, number = {}, pages = {393-412}, pmid = {32739012}, issn = {2162-5514}, support = {T32 GM108539/GM/NIGMS NIH HHS/United States ; }, mesh = {Chronobiology Disorders/complications/*metabolism ; Humans ; Mitochondria/*metabolism ; NAD/*metabolism ; Neurodegenerative Diseases/etiology/*metabolism ; Sirtuins/*metabolism ; Sleep Wake Disorders/etiology/*metabolism ; }, abstract = {The 24-h rotational period of the earth has driven evolution of biological systems that serve to synchronize organismal physiology and behavior to this predictable environmental event. In mammals, the circadian (circa, "about" and dia, "a day") clock keeps 24-h time at the organismal and cellular level, optimizing biological function for a given time of day. The most obvious circadian output is the sleep-wake cycle, though countless bodily functions, ranging from hormone levels to cognitive function, are influenced by the circadian clock. Here we discuss the regulation of metabolic pathways by the circadian clock, discuss the evidence implicating circadian and sleep disruption in neurodegenerative diseases, and suggest some possible connections between the clock, metabolism, and neurodegenerative disease.}, }
@article {pmid32735957, year = {2020}, author = {Harasgama, JC and Kasthuriarachchi, TDW and Kwon, H and Wan, Q and Lee, J}, title = {Molecular and functional characterization of a mitochondrial glutathione reductase homolog from redlip mullet (Liza haematocheila): Disclosing its antioxidant properties in the fish immune response mechanism.}, journal = {Developmental and comparative immunology}, volume = {113}, number = {}, pages = {103785}, doi = {10.1016/j.dci.2020.103785}, pmid = {32735957}, issn = {1879-0089}, mesh = {Animals ; Antioxidants/*metabolism ; Cloning, Molecular ; Fish Proteins/*genetics/metabolism ; Gills/*metabolism ; Glutathione Reductase/*genetics/metabolism ; Homeostasis ; Immunity, Innate ; Mitochondria/*metabolism ; Oxidation-Reduction ; Oxidative Stress ; Phylogeny ; Sequence Alignment ; Smegmamorpha/*immunology ; Transcriptome ; }, abstract = {Glutathione reductase (GSHR) is a biologically important enzyme involved in the conversion of oxidized glutathione (GSSG) into its reduced form, reduced glutathione (GSH), with the catalytic activity of NADPH. Most animals and aquatic organisms, including fish, possess high levels of this enzyme system to neutralize oxidative stress in cells. The current study was conducted to broaden our knowledge of GSHR in fish by identifying a mitochondrial isoform of this enzyme (LhGSHRm) in redlip mullet, Liza haematocheila, and clarifying its structure and function. The complete open reading frame of LhGSHRm consists of 1527 base pairs, encoding 508 amino acids, with a predicted molecular weight of 55.43 kDa. Multiple sequence alignment revealed the conservation of important amino acids in this fish. Phylogenetic analysis demonstrated the closest evolutionary relationship between LhGSHRm and other fish GSHRm counterparts. In tissue distribution analysis, the highest mRNA expression of LhGSHRm was observed in the gill tissue under normal physiological conditions. Following pathogenic challenges, the LhGSHRm transcription level was upregulated in a time-dependent manner in the gill and liver tissues, which may modulate the immune reaction against pathogens. rLhGSHRm showed considerable glutathione reductase activity in an enzyme assay. Further, the biological activity of rLhGSHRm in balancing cellular oxidative stress was observed in both disk diffusion and DPPH assays. Collectively, these results support that LhGSHRm has profound effects on modulating the immune reaction in fish to sustain precise redox homeostasis.}, }
@article {pmid32735771, year = {2020}, author = {Williams, R and Laskovs, M and Williams, RI and Mahadevan, A and Labbadia, J}, title = {A Mitochondrial Stress-Specific Form of HSF1 Protects against Age-Related Proteostasis Collapse.}, journal = {Developmental cell}, volume = {54}, number = {6}, pages = {758-772.e5}, doi = {10.1016/j.devcel.2020.06.038}, pmid = {32735771}, issn = {1878-1551}, support = {BB/P005535/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; /BHF_/British Heart Foundation/United Kingdom ; }, mesh = {Aging/*physiology ; Animals ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/*metabolism ; Heat-Shock Response/physiology ; Mitochondria/*metabolism ; Molecular Chaperones/metabolism ; Proteome/metabolism ; Proteostasis/*physiology ; Stress, Physiological/physiology ; Transcription Factors/*metabolism ; }, abstract = {The loss of protein homeostasis (proteostasis) is a primary driver of age-related tissue dysfunction. Recent studies have revealed that the failure of proteostasis with age is triggered by developmental and reproductive cues that repress the activity of proteostasis-related pathways in early adulthood. In Caenorhabditis elegans, reduced mitochondrial electron transport chain (ETC) function during development can override signals that promote proteostasis collapse in aged tissues. However, it is unclear precisely how these beneficial effects are mediated. Here, we reveal that in response to ETC impairment, the PP2A complex generates a dephosphorylated, mitochondrial stress-specific variant of the transcription factor HSF-1. This results in the selective induction of small heat shock proteins in adulthood, thereby protecting against age-related proteostasis collapse. We propose that mitochondrial signals early in life can protect the aging cytosolic proteome by tailoring HSF-1 activity to preferentially drive the expression of non-ATP-dependent chaperones.}, }
@article {pmid32730281, year = {2020}, author = {Pelster, B and Wood, CM and Campos, DF and Val, AL}, title = {Cellular oxygen consumption, ROS production and ROS defense in two different size-classes of an Amazonian obligate air-breathing fish (Arapaima gigas).}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0236507}, pmid = {32730281}, issn = {1932-6203}, support = {I 2984/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Brazil ; Catalase/metabolism ; Fishes/*physiology ; Gills/enzymology/metabolism ; Glutathione/metabolism ; Glutathione Peroxidase/metabolism ; Kidney/metabolism ; Mitochondria/metabolism ; Oxygen Consumption/*physiology ; Reactive Oxygen Species/*metabolism ; Superoxide Dismutase/metabolism ; }, abstract = {In air-breathing fish a reduction of gill surface area reduces the danger of losing oxygen taken up in the air-breathing organ (ABO) to hypoxic water, but it also reduces the surface area available for ion exchange, so that ion regulation may at least in part be transferred to other organs, like the kidney or the gut. In the air-breathing Arapaima gigas, gill lamellae regress as development proceeds, and starting as a water-breathing embryo Arapaima turns into an obligate air-breathing fish with proceeding development, suggesting that ion regulation is shifted away from the gills as the fish grows. In Arapaima the kidney projects medially into the ABO and thus, probably a unique situation among fishes, is in close contact to the gas of the ABO. We therefore hypothesized that the kidney would be predestined to adopt an increased importance for ion homeostasis, because the elevated ATP turnover connected to ion transport can easily be met by aerobic metabolism based on the excellent oxygen supply directly from the ABO. We also hypothesized that in gill tissue the reduced ion regulatory activity should result in a reduced metabolic activity. High metabolic activity and exposure to high oxygen tensions are connected to the production of reactive oxygen species (ROS), therefore the tissues exposed to these conditions should have a high ROS defense capacity. Using in vitro studies, we assessed metabolic activity and ROS production of gill, kidney and ABO tissue, and determined the activity of ROS degrading enzymes in small (~ 5g, 2-3 weeks old) and larger (~ 670 g, 3-4 months old) A. gigas. Comparing the three tissues revealed that kidney tissue oxygen uptake by far exceeded the uptake measured in gill tissue or ABO. ROS production was particularly high in gill tissue, and all three tissues had a high capacity to degrade ROS. Gill tissue was characterized by high activities of enzymes involved in the glutathione pathway to degrade ROS. By contrast, the tissues of the ABO and in particular the kidney were characterized by high catalase activities, revealing different, tissue-specific strategies in ROS defense in this species. Overall the differences in the activity of cells taken from small and larger fish were not as pronounced as expected, while at the tissue level the metabolic activity of kidney cells by far exceeded the activity of ABO and gill cells.}, }
@article {pmid32727571, year = {2020}, author = {Wang, X and Wang, J and Liu, J and Liu, A and He, X and Xiang, Q and Li, Y and Yin, H and Luo, J and Guan, G}, title = {Insights into the phylogenetic relationships and drug targets of Babesia isolates infective to small ruminants from the mitochondrial genomes.}, journal = {Parasites &amp; vectors}, volume = {13}, number = {1}, pages = {378}, pmid = {32727571}, issn = {1756-3305}, support = {2017YFD0501200//the National Key Research and Development Programme of China/ ; 2015CB150300//the 973 Programme/ ; }, mesh = {Animals ; *Babesia/classification/genetics/isolation &amp; purification ; Babesiosis/drug therapy/genetics ; *Classification ; Cytochromes b/genetics ; Drug Delivery Systems ; *Genome, Mitochondrial ; Genome, Protozoan ; Phylogeny ; Sheep ; Sheep Diseases/parasitology ; Tick-Borne Diseases/parasitology ; }, abstract = {BACKGROUND: Babesiosis, a tick-borne disease caused by protozoans of the genus Babesia, is widespread in subtropical and tropical countries. Mitochondria are essential organelles that are responsible for energy transduction and metabolism, calcium homeostasis and cell signaling. Mitochondrial genomes could provide new insights to help elucidate and investigate the biological features, genetic evolution and classification of the protozoans. Nevertheless, there are limited data on the mitochondrial genomes of ovine Babesia spp. in China.<br><br>METHODS: Herein, we sequenced, assembled and annotated the mitochondrial genomes of six ovine Babesia isolates; analyzed the genome size, gene content, genome structure and cytochrome b (cytb) amino acid sequences and performed comparative mitochondrial genomics and phylogenomic analyses among apicomplexan parasites.<br><br>RESULTS: The mitochondrial genomes range from 5767 to 5946 bp in length with a linear form and contain three protein-encoding genes, cytochrome c oxidase subunit 1 (cox1), cytochrome c oxidase subunit 3 (cox3) and cytb, six large subunit rRNA genes (LSU) and two terminal inverted repeats (TIR) on both ends. The cytb gene sequence analysis indicated the binding site of anti-Babesia drugs that targeted the cytochrome bc1 complex. Babesia microti and Babesia rodhaini have a dual flip-flop inversion of 184-1082 bp, whereas other Babesia spp. and Theileria spp. have one pair of TIRs, 25-1563 bp. Phylogenetic analysis indicated that the six ovine Babesia isolates were divided into two clades, Babesia sp. and Babesia motasi. Babesia motasi isolates were further separated into two small clades (B. motasi Hebei/Ningxian and B. motasi Tianzhu/Lintan).<br><br>CONCLUSIONS: The data provided new insights into the taxonomic relationships and drug targets of apicomplexan parasites.}, }
@article {pmid32722672, year = {2020}, author = {Fernando, HSD and Hapugoda, M and Perera, R and Black Iv, WC and De Silva, BGDNK}, title = {Mitochondrial metabolic genes provide phylogeographic relationships of global collections of Aedes aegypti (Diptera: Culicidae).}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0235430}, pmid = {32722672}, issn = {1932-6203}, mesh = {Aedes/classification/*genetics ; Africa ; Africa, Eastern ; Animals ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Gene Flow ; Genes, Mitochondrial/genetics ; Haplotypes ; India ; Mitochondria/*genetics/metabolism ; Pakistan ; Phylogeny ; *Phylogeography ; Sri Lanka ; }, abstract = {Phylogeographic relationships among global collections of the mosquito Aedes aegypti were evaluated using the mitochondrial Cytochrome C Oxidase 1 (CO1) and NADH dehydrogenase subunit 4 (ND4) genes including new sequences from Sri Lanka. Phylogeographic analysis estimated that Ae. aegypti arose as a species ~614 thousand years ago (kya) in the late Pleistocene. At 545 kya an "early" East African clade arose that continued to differentiate in East Africa, and eventually gave rise to three lineages one of which is distributed throughout all tropical and subtropical regions, a second that contains Southeast Asian/Sri Lankan mosquitoes and a third that contains mostly New World mosquitoes. West African collections were not represented in this early clade. The late clade continued to differentiate throughout Africa and gave rise to a lineage that spread globally. The most recent branches of the late clade are represented by South-East Asia and India/Pakistan collections. Analysis of migration rates suggests abundant gene flow between India/Pakistan and the rest of the world with the exception of Africa.}, }
@article {pmid32719405, year = {2020}, author = {Flament-Simon, SC and de Toro, M and Chuprikova, L and Blanco, M and Moreno-González, J and Salas, M and Blanco, J and Redrejo-Rodríguez, M}, title = {High diversity and variability of pipolins among a wide range of pathogenic Escherichia coli strains.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {12452}, pmid = {32719405}, issn = {2045-2322}, mesh = {Animals ; *DNA Transposable Elements ; Escherichia coli/classification/*genetics/isolation &amp; purification/metabolism ; Escherichia coli Infections/*microbiology/*veterinary ; Genetic Variation ; Genome, Bacterial ; Humans ; Phylogeny ; }, abstract = {Self-synthesizing transposons are integrative mobile genetic elements (MGEs) that encode their own B-family DNA polymerase (PolB). Discovered a few years ago, they are proposed as key players in the evolution of several groups of DNA viruses and virus-host interaction machinery. Pipolins are the most recent addition to the group, are integrated in the genomes of bacteria from diverse phyla and also present as circular plasmids in mitochondria. Remarkably, pipolins-encoded PolBs are proficient DNA polymerases endowed with DNA priming capacity, hence the name, primer-independent PolB (piPolB). We have now surveyed the presence of pipolins in a collection of 2,238 human and animal pathogenic Escherichia coli strains and found that, although detected in only 25 positive isolates (1.1%), they are present in E. coli strains from a wide variety of pathotypes, serotypes, phylogenetic groups and sequence types. Overall, the pangenome of strains carrying pipolins is highly diverse, despite the fact that a considerable number of strains belong to only three clonal complexes (CC10, CC23 and CC32). Comparative analysis with a set of 67 additional pipolin-harboring genomes from GenBank database spanning strains from diverse origin, further confirmed these results. The genetic structure of pipolins shows great flexibility and variability, with the piPolB gene and the attachment sites being the only common features. Most pipolins contain one or more recombinases that would be involved in excision/integration of the element in the same conserved tRNA gene. This mobilization mechanism might explain the apparent incompatibility of pipolins with other integrative MGEs such as integrons. In addition, analysis of cophylogeny between pipolins and pipolin-harboring strains showed a lack of congruence between several pipolins and their host strains, in agreement with horizontal transfer between hosts. Overall, these results indicate that pipolins can serve as a vehicle for genetic transfer among circulating E. coli and possibly also among other pathogenic bacteria.}, }
@article {pmid32712152, year = {2020}, author = {Bertgen, L and Mühlhaus, T and Herrmann, JM}, title = {Clingy genes: Why were genes for ribosomal proteins retained in many mitochondrial genomes?.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1861}, number = {11}, pages = {148275}, doi = {10.1016/j.bbabio.2020.148275}, pmid = {32712152}, issn = {1879-2650}, mesh = {Eukaryota/genetics/*metabolism ; *Genome, Mitochondrial ; Mitochondrial Proteins/genetics/*metabolism ; *Protein Biosynthesis ; Ribosomal Proteins/genetics/*metabolism ; Ribosomes/genetics/*metabolism ; }, abstract = {Why mitochondria still retain their own genome is a puzzle given the enormous effort to maintain a mitochondrial translation machinery. Most mitochondrially encoded proteins are membrane-embedded subunits of the respiratory chain. Their hydrophobicity presumably impedes their import into mitochondria. However, many mitochondrial genomes also encode protein subunits of the mitochondrial ribosome. These proteins lack transmembrane domains and hydrophobicity cannot explain why their genes remained in mitochondria. In this review, we provide an overview about mitochondrially encoded subunits of mitochondrial ribosomes of fungi, plants and protists. Moreover, we discuss and evaluate different hypotheses which were put forward to explain why (ribosomal) proteins remained mitochondrially encoded. It seems likely that the synthesis of ribosomal proteins in the mitochondrial matrix is used to regulate the assembly of the mitochondrial ribosome within mitochondria and to avoid problems that mitochondrial proteins might pose for cytosolic proteostasis and for the assembly of cytosolic ribosomes.}, }
@article {pmid32709961, year = {2020}, author = {Cunnane, SC and Trushina, E and Morland, C and Prigione, A and Casadesus, G and Andrews, ZB and Beal, MF and Bergersen, LH and Brinton, RD and de la Monte, S and Eckert, A and Harvey, J and Jeggo, R and Jhamandas, JH and Kann, O and la Cour, CM and Martin, WF and Mithieux, G and Moreira, PI and Murphy, MP and Nave, KA and Nuriel, T and Oliet, SHR and Saudou, F and Mattson, MP and Swerdlow, RH and Millan, MJ}, title = {Brain energy rescue: an emerging therapeutic concept for neurodegenerative disorders of ageing.}, journal = {Nature reviews. Drug discovery}, volume = {19}, number = {9}, pages = {609-633}, pmid = {32709961}, issn = {1474-1784}, support = {MC_UU_00015/3/MRC_/Medical Research Council/United Kingdom ; R15 AG050292/AG/NIA NIH HHS/United States ; R21 AG064479/AG/NIA NIH HHS/United States ; R01 NS107265/NS/NINDS NIH HHS/United States ; MC_U105663142/MRC_/Medical Research Council/United Kingdom ; RF1 AG055549/AG/NIA NIH HHS/United States ; P01 AG026572/AG/NIA NIH HHS/United States ; UH3 NS113776/NS/NINDS NIH HHS/United States ; RF1 AG059093/AG/NIA NIH HHS/United States ; }, mesh = {Aging/*physiology ; Animals ; Brain/*physiology ; Energy Metabolism/*physiology ; Glycolysis/physiology ; Humans ; Neurodegenerative Diseases/*physiopathology ; Oxidative Phosphorylation ; }, abstract = {The brain requires a continuous supply of energy in the form of ATP, most of which is produced from glucose by oxidative phosphorylation in mitochondria, complemented by aerobic glycolysis in the cytoplasm. When glucose levels are limited, ketone bodies generated in the liver and lactate derived from exercising skeletal muscle can also become important energy substrates for the brain. In neurodegenerative disorders of ageing, brain glucose metabolism deteriorates in a progressive, region-specific and disease-specific manner - a problem that is best characterized in Alzheimer disease, where it begins presymptomatically. This Review discusses the status and prospects of therapeutic strategies for countering neurodegenerative disorders of ageing by improving, preserving or rescuing brain energetics. The approaches described include restoring oxidative phosphorylation and glycolysis, increasing insulin sensitivity, correcting mitochondrial dysfunction, ketone-based interventions, acting via hormones that modulate cerebral energetics, RNA therapeutics and complementary multimodal lifestyle changes.}, }
@article {pmid32702525, year = {2020}, author = {Žihala, D and Salamonová, J and Eliáš, M}, title = {Evolution of the genetic code in the mitochondria of Labyrinthulea (Stramenopiles).}, journal = {Molecular phylogenetics and evolution}, volume = {152}, number = {}, pages = {106908}, doi = {10.1016/j.ympev.2020.106908}, pmid = {32702525}, issn = {1095-9513}, mesh = {Codon ; *Evolution, Molecular ; *Genetic Code ; Mitochondria/*genetics ; Phylogeny ; Protein Biosynthesis/genetics ; Stramenopiles/*classification/*genetics ; }, abstract = {Mitochondrial translation often exhibits departures from the standard genetic code, but the full spectrum of these changes has certainly not yet been described and the molecular mechanisms behind the changes in codon meaning are rarely studied. Here we report a detailed analysis of the mitochondrial genetic code in the stramenopile group Labyrinthulea (Labyrinthulomycetes) and their relatives. In the genus Aplanochytrium, UAG is not a termination codon but encodes tyrosine, in contrast to the unaffected meaning of the UAA codon. This change is evolutionarily independent of the reassignment of both UAG and UAA as tyrosine codons recently reported from two uncultivated labyrinthuleans (S2 and S4), which we show are not thraustochytrids as proposed before, but represent the clade LAB14 previously recognised in environmental 18S rRNA gene surveys. We provide rigorous evidence that the UUA codon in the mitochondria of all labyrinthuleans serves as a termination codon instead of encoding leucine, and propose that a sense-to-stop reassignment has also affected the AGG and AGA codons in the LAB14 clade. The distribution of the different forms of sense-to-stop and stop-to-sense reassignments correlates with specific modifications of the mitochondrial release factor mtRF2a in different subsets of labyrinthuleans, and with the unprecedented loss of mtRF1a in Aplanochytrium and perhaps also in the LAB14 clade, pointing towards a possible mechanistic basis of the code changes observed. Curiously, we show that labyrinthulean mitochondria also exhibit a sense-to-sense codon reassignment, manifested as AUA encoding methionine instead of isoleucine. Furthermore, we show that this change evolved independently in the uncultivated stramenopile lineage MAST8b, together with the reassignment of the AGR codons from arginine to serine. Altogether, our study has uncovered novel variants of the mitochondrial genetic code and previously unknown modifications of the mitochondrial translation machinery, further enriching our understanding of the rules governing the evolution of one of the central molecular process in the cell.}, }
@article {pmid32697943, year = {2020}, author = {Codo, AC and Davanzo, GG and Monteiro, LB and de Souza, GF and Muraro, SP and Virgilio-da-Silva, JV and Prodonoff, JS and Carregari, VC and de Biagi Junior, CAO and Crunfli, F and Jimenez Restrepo, JL and Vendramini, PH and Reis-de-Oliveira, G and Bispo Dos Santos, K and Toledo-Teixeira, DA and Parise, PL and Martini, MC and Marques, RE and Carmo, HR and Borin, A and Coimbra, LD and Boldrini, VO and Brunetti, NS and Vieira, AS and Mansour, E and Ulaf, RG and Bernardes, AF and Nunes, TA and Ribeiro, LC and Palma, AC and Agrela, MV and Moretti, ML and Sposito, AC and Pereira, FB and Velloso, LA and Vinolo, MAR and Damasio, A and Proença-Módena, JL and Carvalho, RF and Mori, MA and Martins-de-Souza, D and Nakaya, HI and Farias, AS and Moraes-Vieira, PM}, title = {Elevated Glucose Levels Favor SARS-CoV-2 Infection and Monocyte Response through a HIF-1α/Glycolysis-Dependent Axis.}, journal = {Cell metabolism}, volume = {32}, number = {3}, pages = {437-446.e5}, pmid = {32697943}, issn = {1932-7420}, mesh = {Adult ; Betacoronavirus/*physiology ; Blood Glucose/*metabolism ; COVID-19 ; Cell Line ; Coronavirus Infections/*complications/metabolism ; Diabetes Complications/*complications/metabolism ; Diabetes Mellitus/metabolism ; Female ; Glycolysis ; Humans ; Hypoxia-Inducible Factor 1, alpha Subunit/*metabolism ; Inflammation/complications/metabolism ; Male ; Middle Aged ; Monocytes/*metabolism/virology ; Pandemics ; Pneumonia, Viral/*complications/metabolism ; Reactive Oxygen Species/metabolism ; SARS-CoV-2 ; Signal Transduction ; }, abstract = {COVID-19 can result in severe lung injury. It remained to be determined why diabetic individuals with uncontrolled glucose levels are more prone to develop the severe form of COVID-19. The molecular mechanism underlying SARS-CoV-2 infection and what determines the onset of the cytokine storm found in severe COVID-19 patients are unknown. Monocytes and macrophages are the most enriched immune cell types in the lungs of COVID-19 patients and appear to have a central role in the pathogenicity of the disease. These cells adapt their metabolism upon infection and become highly glycolytic, which facilitates SARS-CoV-2 replication. The infection triggers mitochondrial ROS production, which induces stabilization of hypoxia-inducible factor-1α (HIF-1α) and consequently promotes glycolysis. HIF-1α-induced changes in monocyte metabolism by SARS-CoV-2 infection directly inhibit T cell response and reduce epithelial cell survival. Targeting HIF-1ɑ may have great therapeutic potential for the development of novel drugs to treat COVID-19.}, }
@article {pmid32693134, year = {2020}, author = {Feng, Z and Wu, Y and Yang, C and Gu, X and Wilson, JJ and Li, H and Cai, W and Yang, H and Song, F}, title = {Evolution of tRNA gene rearrangement in the mitochondrial genome of ichneumonoid wasps (Hymenoptera: Ichneumonoidea).}, journal = {International journal of biological macromolecules}, volume = {164}, number = {}, pages = {540-547}, doi = {10.1016/j.ijbiomac.2020.07.149}, pmid = {32693134}, issn = {1879-0003}, mesh = {Animals ; Evolution, Molecular ; Gene Rearrangement ; Genome, Insect ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/*genetics ; Sequence Analysis, DNA/*methods ; Sequence Inversion ; Translocation, Genetic ; Wasps/*classification/genetics ; }, abstract = {Gene rearrangements in the mitochondrial genome (mt genome) are common in certain insect groups and can be an informative character for phylogenetic reconstruction. However, knowledge of the mechanism and biases of gene rearrangement in insect mt genomes is still limited. With an accelerated rate of gene rearrangements, Hymenoptera is an important group for mt genome rearrangements diversity and for understanding the gene rearrangement evolution in mt genomes. Here, we sequenced the complete mt genome of Aphidius gifuensis and analyzed the evolution of tRNA gene rearrangements in the mt genomes of ichneumonoid wasps. Two control regions were detected in A. gifuensis and most of the tRNA rearrangement events occurred around these control regions. tRNA gene rearrangements occurred in almost all of the sequenced mt genomes of Ichneumonoidea and the gene block CR-trnI-trnQ-trnM-ND2-trnW-trnC-trnY was the main hot spot of gene rearrangement. Mapped over the backbone phylogeny of Ichneumonoidea, we found that the inversion and translocation of both trnI and trnM is likely a synapomorphic rearrangement in Braconidae. Our study also demonstrated that the gene block CR-trnI-trnQ-trnM-ND2-trnW-trnC-trnY was important for inferring the gene rearrangement dynamics in Ichneumonoidea.}, }
@article {pmid32693123, year = {2020}, author = {Xu, H and Wu, Y and Wang, Y and Liu, Z}, title = {Comparative analysis of five mitogenomes of Osmylinae (Neuroptera: Osmylidae) and their phylogenetic implications.}, journal = {International journal of biological macromolecules}, volume = {164}, number = {}, pages = {447-455}, doi = {10.1016/j.ijbiomac.2020.07.150}, pmid = {32693123}, issn = {1879-0003}, mesh = {Animals ; Base Composition ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Neoptera/*classification/genetics ; Phylogeny ; RNA Folding ; RNA, Transfer/chemistry ; Sequence Analysis, DNA/*methods ; }, abstract = {In this study, five mitogenomes of Osmylinae species were sequenced: Osmylus fulvicephalus, Osmylus lucalatus, Plethosmylus atomatus, Plethosmylus zheanus, and Plethosmylus sp. These mitogenomes vary from 15,401 bp to 17,136 bp in size. The nucleotide compositions of Osmylinae mitogenomes are biased towards A/T. The gene arrangement of five mitogenomes is congruent with the putative ancestral pattern of the insects. Most of PCGs initiate with typical start codon ATN and terminate with TAA as the stop codon. All tRNA genes are folded into the typical cloverleaf secondary structure with an exception of tRNA[Ser(AGN)]. The phylogenetic relationship was reconstructed by both maximum likelihood and Bayesian methods based on 13 PCGs and two rRNA genes. The sister group relationships between Osmylinae and the clade of Spilosmylinae and Protosmylinae were recovered as expected. The monophyly of Osmylinae was corroborated, but within the subfamily, three species (P. atomatus, P. zheanus, and Plethosmylus sp.) originally belonging to Plethosmylus (transferred to Osmylus by Winterton) were restored as a clade and sister to the clade of Osmylus. The current results implied that it is necessary to reassess the systematic status of Plethosmylus in the future.}, }
@article {pmid32681023, year = {2020}, author = {Folgueira, I and Lamas, J and Sueiro, RA and Leiro, JM}, title = {Molecular characterization and gene expression modulation of the alternative oxidase in a scuticociliate parasite by hypoxia and mitochondrial respiration inhibitors.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {11880}, pmid = {32681023}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cell Respiration/*drug effects ; Female ; Gene Expression ; Genome, Protozoan ; Genomics/methods ; Hypoxia/*metabolism ; Male ; Mitochondria/*drug effects/metabolism/ultrastructure ; Mitochondrial Proteins/chemistry/*genetics ; Models, Molecular ; Oligohymenophorea/classification/*enzymology/*genetics ; Oxidoreductases/chemistry/*genetics ; Phylogeny ; Plant Proteins/chemistry/*genetics ; Protein Conformation ; Structure-Activity Relationship ; }, abstract = {Philasterides dicentrarchi is a marine benthic microaerophilic scuticociliate and an opportunistic endoparasite that can infect and cause high mortalities in cultured turbot (Scophthalmus maximus). In addition to a cytochrome pathway (CP), the ciliate can use a cyanide-insensitive respiratory pathway, which indicates the existence of an alternative oxidase (AOX) in the mitochondrion. Although AOX activity has been described in P. dicentrarchi, based on functional assay results, genetic evidence of the presence of AOX in the ciliate has not previously been reported. In this study, we conducted genomic and transcriptomic analysis of the ciliate and identified the AOX gene and its corresponding mRNA. The AOX gene (size 1,106 bp) contains four exons and three introns that generate an open reading frame of 915 bp and a protein with a predicted molecular weight of 35.6 kDa. The amino acid (aa) sequence of the AOX includes an import signal peptide targeting the mitochondria and the protein is associated with the inner membrane of the mitochondria. Bioinformatic analysis predicted that the peptide is a homodimeric glycoprotein, although monomeric forms may also appear under native conditions, with EXXH motifs associated with the diiron active centers. The aa sequences of the AOX of different P. dicentrarchi isolates are highly conserved and phylogenetically closely related to AOXs of other ciliate species, especially scuticociliates. AOX expression increased significantly during infection in the host and after the addition of CP inhibitors. This confirms the important physiological roles of AOX in respiration under conditions of low levels of O2 and in protecting against oxidative stress generated during infection in the host.}, }
@article {pmid32679802, year = {2020}, author = {Kami, D and Gojo, S}, title = {From Cell Entry to Engraftment of Exogenous Mitochondria.}, journal = {International journal of molecular sciences}, volume = {21}, number = {14}, pages = {}, pmid = {32679802}, issn = {1422-0067}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Endocytosis ; Endosomes/genetics ; Gene Transfer, Horizontal ; Humans ; Mitochondria/genetics/*transplantation ; Pinocytosis ; Symbiosis ; }, abstract = {Mitochondrial transfer has been recognized to play a role in a variety of processes, ranging from fertilization to cancer and neurodegenerative diseases as well as mammalian horizontal gene transfer. It is achieved through either exogeneous or intercellular mitochondrial transfer. From the viewpoint of evolution, exogeneous mitochondrial transfer is quite akin to the initial process of symbiosis between α-protobacterium and archaea, although the progeny have developed more sophisticated machinery to engulf environmental materials, including nutrients, bacteria, and viruses. A molecular-based knowledge of endocytosis, including macropinocytosis and endosomal escape involving bacteria and viruses, could provide mechanistic insights into exogeneous mitochondrial transfer. We focus on exogeneous mitochondrial transfer in this review to facilitate the clinical development of the use of isolated mitochondria to treat various pathological conditions. Several kinds of novel procedures to enhance exogeneous mitochondrial transfer have been developed and are summarized in this review.}, }
@article {pmid32670085, year = {2020}, author = {Praud, C and Jimenez, J and Pampouille, E and Couroussé, N and Godet, E and Le Bihan-Duval, E and Berri, C}, title = {Molecular Phenotyping of White Striping and Wooden Breast Myopathies in Chicken.}, journal = {Frontiers in physiology}, volume = {11}, number = {}, pages = {633}, pmid = {32670085}, issn = {1664-042X}, abstract = {The White Striping (WS) and Wooden Breast (WB) defects are two myopathic syndromes whose occurrence has recently increased in modern fast-growing broilers. The impact of these defects on the quality of breast meat is very important, as they greatly affect its visual aspect, nutritional value, and processing yields. The research conducted to date has improved our knowledge of the biological processes involved in their occurrence, but no solution has been identified so far to significantly reduce their incidence without affecting growing performance of broilers. This study aims to follow the evolution of molecular phenotypes in relation to both fast-growing rate and the occurrence of defects in order to identify potential biomarkers for diagnostic purposes, but also to improve our understanding of physiological dysregulation involved in the occurrence of WS and WB. This has been achieved through enzymatic, histological, and transcriptional approaches by considering breast muscles from a slow- and a fast-growing line, affected or not by WS and WB. Fast-growing muscles produced more reactive oxygen species (ROS) than slow-growing ones, independently of WS and WB occurrence. Within fast-growing muscles, despite higher mitochondria density, muscles affected by WS or WB defects did not show higher cytochrome oxidase activity (COX) activity, suggesting altered mitochondrial function. Among the markers related to muscle remodeling and regeneration, immunohistochemical staining of FN1, NCAM, and MYH15 was higher in fast- compared to slow-growing muscles, and their amount also increased linearly with the presence and severity of WS and WB defects, making them potential biomarkers to assess accurately their presence and severity. Thanks to an innovative histological technique based on fluorescence intensity measurement, they can be rapidly quantified to estimate the injuries induced in case of WS and WB. The muscular expression of several other genes correlates also positively to the presence and severity of the defects like TGFB1 and CTGF, both involved in the development of connective tissue, or Twist1, known as an inhibitor of myogenesis. Finally, our results suggested that a balance between TGFB1 and PPARG would be essential for fibrosis or adiposis induction and therefore for determining WS and WB phenotypes.}, }
@article {pmid32667908, year = {2020}, author = {Arbeithuber, B and Hester, J and Cremona, MA and Stoler, N and Zaidi, A and Higgins, B and Anthony, K and Chiaromonte, F and Diaz, FJ and Makova, KD}, title = {Age-related accumulation of de novo mitochondrial mutations in mammalian oocytes and somatic tissues.}, journal = {PLoS biology}, volume = {18}, number = {7}, pages = {e3000745}, pmid = {32667908}, issn = {1545-7885}, support = {R01 GM116044/GM/NIGMS NIH HHS/United States ; T32 GM102057/GM/NIGMS NIH HHS/United States ; }, mesh = {Aging/*genetics ; Animals ; DNA Mutational Analysis ; DNA, Mitochondrial/genetics ; Female ; Gene Frequency/genetics ; Genetic Drift ; Germ Cells/metabolism ; Inheritance Patterns/genetics ; Logistic Models ; Male ; Mammals/*genetics ; Mice ; Mitochondria/*genetics ; Models, Genetic ; Mutation/*genetics ; Mutation Rate ; Nucleotides/genetics ; Oocytes/*metabolism ; Organ Specificity/*genetics ; Pedigree ; }, abstract = {Mutations create genetic variation for other evolutionary forces to operate on and cause numerous genetic diseases. Nevertheless, how de novo mutations arise remains poorly understood. Progress in the area is hindered by the fact that error rates of conventional sequencing technologies (1 in 100 or 1,000 base pairs) are several orders of magnitude higher than de novo mutation rates (1 in 10,000,000 or 100,000,000 base pairs per generation). Moreover, previous analyses of germline de novo mutations examined pedigrees (and not germ cells) and thus were likely affected by selection. Here, we applied highly accurate duplex sequencing to detect low-frequency, de novo mutations in mitochondrial DNA (mtDNA) directly from oocytes and from somatic tissues (brain and muscle) of 36 mice from two independent pedigrees. We found mtDNA mutation frequencies 2- to 3-fold higher in 10-month-old than in 1-month-old mice, demonstrating mutation accumulation during the period of only 9 mo. Mutation frequencies and patterns differed between germline and somatic tissues and among mtDNA regions, suggestive of distinct mutagenesis mechanisms. Additionally, we discovered a more pronounced genetic drift of mitochondrial genetic variants in the germline of older versus younger mice, arguing for mtDNA turnover during oocyte meiotic arrest. Our study deciphered for the first time the intricacies of germline de novo mutagenesis using duplex sequencing directly in oocytes, which provided unprecedented resolution and minimized selection effects present in pedigree studies. Moreover, our work provides important information about the origins and accumulation of mutations with aging/maturation and has implications for delayed reproduction in modern human societies. Furthermore, the duplex sequencing method we optimized for single cells opens avenues for investigating low-frequency mutations in other studies.}, }
@article {pmid32664529, year = {2020}, author = {Pedriali, G and Morciano, G and Patergnani, S and Cimaglia, P and Morelli, C and Mikus, E and Ferrari, R and Gasbarro, V and Giorgi, C and Wieckowski, MR and Pinton, P}, title = {Aortic Valve Stenosis and Mitochondrial Dysfunctions: Clinical and Molecular Perspectives.}, journal = {International journal of molecular sciences}, volume = {21}, number = {14}, pages = {}, pmid = {32664529}, issn = {1422-0067}, support = {IG-23670//Associazione Italiana per la Ricerca sul Cancro/ ; GGP11139B//Fondazione Telethon/ ; 2017 E5L5P3//Progetti di Rilevante Interesse Nazionale/ ; IG-19803//Associazione Italiana per la Ricerca sul Cancro/ ; GR-2013-02356747//Italian Ministry of Health/ ; ERC, 853057/ERC_/European Research Council/International ; 2017 7E9EPY//Progetti di Rilevante Interesse Nazionale/ ; }, mesh = {Animals ; Aortic Valve/metabolism/*pathology/ultrastructure ; Aortic Valve Stenosis/diagnosis/epidemiology/*metabolism/surgery ; Autophagy ; Basement Membrane/ultrastructure ; Calcinosis/*metabolism ; Disease Progression ; Endothelial Cells/pathology ; Humans ; Inflammation ; Lipids/analysis ; Mitochondria, Heart/*physiology ; Nitric Oxide Synthase Type III/physiology ; Oxidative Stress ; Therapies, Investigational ; Unfolded Protein Response ; }, abstract = {Calcific aortic stenosis is a disorder that impacts the physiology of heart valves. Fibrocalcific events progress in conjunction with thickening of the valve leaflets. Over the years, these events promote stenosis and obstruction of blood flow. Known and common risk factors are congenital defects, aging and metabolic syndromes linked to high plasma levels of lipoproteins. Inflammation and oxidative stress are the main molecular mediators of the evolution of aortic stenosis in patients and these mediators regulate both the degradation and remodeling processes. Mitochondrial dysfunction and dysregulation of autophagy also contribute to the disease. A better understanding of these cellular impairments might help to develop new ways to treat patients since, at the moment, there is no effective medical treatment to diminish neither the advancement of valve stenosis nor the left ventricular function impairments, and the current approaches are surgical treatment or transcatheter aortic valve replacement with prosthesis.}, }
@article {pmid32661403, year = {2020}, author = {Fan, L and Wu, D and Goremykin, V and Xiao, J and Xu, Y and Garg, S and Zhang, C and Martin, WF and Zhu, R}, title = {Phylogenetic analyses with systematic taxon sampling show that mitochondria branch within Alphaproteobacteria.}, journal = {Nature ecology &amp; evolution}, volume = {4}, number = {9}, pages = {1213-1219}, pmid = {32661403}, issn = {2397-334X}, mesh = {*Alphaproteobacteria/genetics ; Mitochondria/genetics ; Phylogeny ; Reproducibility of Results ; }, abstract = {Though it is well accepted that mitochondria originated from an alphaproteobacteria-like ancestor, the phylogenetic relationship of the mitochondrial endosymbiont to extant Alphaproteobacteria is yet unresolved. The focus of much debate is whether the affinity between mitochondria and fast-evolving alphaproteobacterial lineages reflects true homology or artefacts. Approaches such as site exclusion have been claimed to mitigate compositional heterogeneity between taxa, but this comes at the cost of information loss, and the reliability of such methods is so far unproven. Here we demonstrate that site-exclusion methods produce erratic phylogenetic estimates of mitochondrial origin. Thus, previous phylogenetic hypotheses on the origin of mitochondria based on pretreated datasets should be re-evaluated. We applied alternative strategies to reduce phylogenetic noise by systematic taxon sampling while keeping site substitution information intact. Cross-validation based on a series of trees placed mitochondria robustly within Alphaproteobacteria, sharing an ancient common ancestor with Rickettsiales and currently unclassified marine lineages.}, }
@article {pmid32652124, year = {2020}, author = {Wepfer, PH and Nakajima, Y and Sutthacheep, M and Radice, VZ and Richards, Z and Ang, P and Terraneo, T and Sudek, M and Fujimura, A and Toonen, RJ and Mikheyev, AS and Economo, EP and Mitarai, S}, title = {Evolutionary biogeography of the reef-building coral genus Galaxea across the Indo-Pacific ocean.}, journal = {Molecular phylogenetics and evolution}, volume = {151}, number = {}, pages = {106905}, doi = {10.1016/j.ympev.2020.106905}, pmid = {32652124}, issn = {1095-9513}, mesh = {Animals ; Anthozoa/*classification/*genetics ; Base Sequence ; *Coral Reefs ; DNA, Mitochondrial/genetics ; Genetic Variation ; Haplotypes/genetics ; Indian Ocean ; Mitochondria/genetics ; Pacific Ocean ; Phylogeny ; *Phylogeography ; Principal Component Analysis ; }, abstract = {Stony corals (Scleractinia) form the basis for some of the most diverse ecosytems on Earth, but we have much to learn about their evolutionary history and systematic relationships. In order to improve our understanding of species in corals we here investigated phylogenetic relationships between morphologically defined species and genetic lineages in the genus Galaxea (Euphyllidae) using a combined phylogenomic and phylogeographic approach. Previous studies revealed the nominal species G. fascicularis included three genetically well-differentiated lineages (L, S &amp; L+) in the western Pacific, but their distribution and relationship to other species in the genus was unknown. Based on genomic (RAD-seq) and mitochondrial sequence data (non-coding region between cytb and ND2) we investigated whether the morphological taxa represent genetically coherent entities and what is the phylogenetic relationship and spatial distribution of the three lineages of G. fascicularis throughout the observed species range. Using the RAD-seq data, we find that the genus Galaxea is monophyletic and contains three distinct clades: an Indo-Pacific, a Pacific, and a small clade restricted to the Chagos Archipelago. The three lineages of G. fascicularis were associated with different RAD-seq clades, with the 'L' lineage showing some morphological distinction from the other two lineages (larger more asymmetrical polyps). In addition to these, three more genetic lineages in G. fascicularis may be distinguished - a Chagossian, an Ogasawaran, and one from the Indian-Red Sea. Among nominal taxa for which we have multiple samples, G. horrescens was the only monophyletic species. The mitochondrial non-coding region is highly conserved apart of the length polymorphism used to define L, S &amp; L+ lineages and lacks the power to distinguish morphological and genetic groups resolved with genomic RAD-sequencing. The polyphyletic nature of most species warrants a careful examination of the accepted taxonomy of this group with voucher collections and their comparison to type specimens to resolve species boundaries. Further insight to the speciation process in corals will require international cooperation for the sharing of specimens to facilitate scientific discovery.}, }
@article {pmid32651001, year = {2021}, author = {Picard, M and Sandi, C}, title = {The social nature of mitochondria: Implications for human health.}, journal = {Neuroscience and biobehavioral reviews}, volume = {120}, number = {}, pages = {595-610}, pmid = {32651001}, issn = {1873-7528}, support = {R01 MH119336/MH/NIMH NIH HHS/United States ; R01 MH122706/MH/NIMH NIH HHS/United States ; R35 GM119793/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Humans ; *Mitochondria ; Social Behavior ; }, abstract = {Sociality has profound evolutionary roots and is observed from unicellular organisms to multicellular animals. In line with the view that social principles apply across levels of biological complexity, a growing body of data highlights the remarkable social nature of mitochondria - life-sustaining endosymbiotic organelles with their own genome that populate the cell cytoplasm. Here, we draw from organizing principles of behavior in social organisms to reveal that similar to individuals among social networks, mitochondria communicate with each other and with the cell nucleus, exhibit group formation and interdependence, synchronize their behaviors, and functionally specialize to accomplish specific functions within the organism. Mitochondria are social organelles. The extension of social principles across levels of biological complexity is a theoretical shift that emphasizes the role of communication and interdependence in cell biology, physiology, and neuroscience. With the help of emerging computational methods capable of capturing complex dynamic behavioral patterns, the implementation of social concepts in mitochondrial biology may facilitate cross-talk across disciplines towards increasingly holistic and accurate models of human health.}, }
@article {pmid32649783, year = {2020}, author = {Fang, Y and Zhao, C and Xiang, H and Jia, G and Zhong, R}, title = {Melatonin improves cryopreservation of ram sperm by inhibiting mitochondrial permeability transition pore opening.}, journal = {Reproduction in domestic animals = Zuchthygiene}, volume = {55}, number = {9}, pages = {1240-1249}, doi = {10.1111/rda.13771}, pmid = {32649783}, issn = {1439-0531}, support = {KFJ-STS-ZDTP-075//CAS Science and Technology Service Network Initiative/ ; 2015184//the Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 20180201041NY//Jilin Science and Technology Development Plan Project/ ; 2018YFD0501903//National Key Research and Development Program of China/ ; 2017-NK-114//Natural Science Foundation of Qinghai Province/ ; 2017-ZJ-915Q//Natural Science Foundation of Qinghai Province/ ; }, mesh = {Animals ; Cell Membrane ; Cryopreservation/methods/*veterinary ; Cytochromes c/metabolism ; Fertilization in Vitro/veterinary ; Freezing ; Male ; Melatonin/*pharmacology ; Membrane Potential, Mitochondrial ; *Mitochondrial Permeability Transition Pore ; Receptors, Melatonin/agonists/antagonists &amp; inhibitors ; Semen Preservation/veterinary ; Sheep, Domestic ; Spermatozoa/drug effects ; }, abstract = {Cryopreservation damages permeability of sperm mitochondrial membranes, with formation of a mitochondrial permeability transition pore (mPTP). Mitochondria are both a primary synthesis site and principle target for melatonin, which can directly inhibit mPTP formation. The objective was to determine effects of melatonin on mPTP opening of frozen-thawed ram sperm and elucidate underlying pathways by antagonist and agonists of melatonin receptors (MTs), and antagonists of PI3K and GSK 3β treatments; furthermore, plasma membrane integrity, mitochondrial membrane potential (ΔΨm), mitochondrial cytochrome c (Cyt c) release and fertilization were analysed to assess the effect of mPTP status mediated by melatonin on quality of frozen-thawed sperm. Fresh ram semen was diluted in glucose-egg yolk buffer with 0 or 10[-7] M melatonin (frozen and frozen + melatonin groups, respectively) and slow-frozen. In frozen-thawed sperm, melatonin added at initiation of 4°C equilibration was most effective for inhibiting mPTP opening, decreasing peptidyl-prolyl-cis/trans isomerase activity of cyclophilin D and increasing plasma membrane integrity, ΔΨm, mitochondrial Cyt c concentration and fertilizing ability (p < .05). In a mechanistic study, the melatonin receptor (MT)1 antagonist eliminated inhibition of melatonin on mPTP opening, whereas MT1 agonist had opposite effects (p < .05). Neither MT2 antagonist nor agonist had significant effect, but PI3K and/or GSK 3β antagonist decreased inhibition of MT1 agonist on mPTP opening (p < .05). In conclusion, melatonin improved sperm cryopreservation, perhaps by acting on MT1 via the PI3K-Akt-GSK 3β pathway to inhibit mPTP opening.}, }
@article {pmid32649732, year = {2020}, author = {de Oliveira, VC and Gomes Mariano Junior, C and Belizário, JE and Krieger, JE and Fernandes Bressan, F and Roballo, KCS and Fantinato-Neto, P and Meirelles, FV and Chiaratti, MR and Concordet, JP and Ambrósio, CE}, title = {Characterization of post-edited cells modified in the TFAM gene by CRISPR/Cas9 technology in the bovine model.}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0235856}, pmid = {32649732}, issn = {1932-6203}, mesh = {Animals ; *CRISPR-Cas Systems ; Cattle/*genetics ; Cells, Cultured ; DNA Replication ; DNA, Mitochondrial/genetics ; DNA-Binding Proteins/*genetics ; Fibroblasts/metabolism ; Gene Dosage ; *Gene Editing ; Mitochondria/genetics ; Mitochondrial Proteins/*genetics ; Transcription Factors/*genetics ; }, abstract = {Gene editing in large animal models for future applications in translational medicine and food production must be deeply investigated for an increase of knowledge. The mitochondrial transcription factor A (TFAM) is a member of the HMGB subfamily that binds to mtDNA promoters. This gene maintains mtDNA, and it is essential for the initiation of mtDNA transcription. Lately, we generated a new cell line through the disruption of the TFAM gene in bovine fibroblast cells by CRISPR/Cas 9 technology. We showed that the CRISPR/Cas9 design was efficient through the generation of heterozygous mutant clones. In this context, once this gene regulates the mtDNA replication specificity, the study aimed to determine if the post-edited cells are capable of in vitro maintenance and assess if they present changes in mtDNA copies and mitochondrial membrane potential after successive passages in culture. The post-edited cells were expanded in culture, and we performed a growth curve, doubling time, cell viability, mitochondrial DNA copy number, and mitochondrial membrane potential assays. The editing process did not make cell culture unfeasible, even though cell growth rate and viability were decreased compared to control since we observed the cells grow well when cultured in a medium supplemented with uridine and pyruvate. They also exhibited a classical fibroblastoid appearance. The RT-qPCR to determine the mtDNA copy number showed a decrease in the edited clones compared to the non-edited ones (control) in different cell passages. Cell staining with Mitotracker Green and red suggests a reduction in red fluorescence in the edited cells compared to the non-edited cells. Thus, through characterization, we demonstrated that the TFAM gene is critical to mitochondrial maintenance due to its interference in the stability of the mitochondrial DNA copy number in different cell passages and membrane potential confirming the decrease in mitochondrial activity in cells edited in heterozygosis.}, }
@article {pmid32647112, year = {2020}, author = {Lubośny, M and Przyłucka, A and Śmietanka, B and Burzyński, A}, title = {Semimytilus algosus: first known hermaphroditic mussel with doubly uniparental inheritance of mitochondrial DNA.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {11256}, pmid = {32647112}, issn = {2045-2322}, mesh = {Alleles ; Animals ; DNA, Mitochondrial/*genetics ; Female ; Fresh Water ; Genome ; Genome, Mitochondrial ; Heredity ; High-Throughput Nucleotide Sequencing ; *Inheritance Patterns ; Male ; Mitochondria/metabolism ; Models, Genetic ; Mytilus/*genetics ; Open Reading Frames ; Phylogeny ; Polymerase Chain Reaction ; RNA/genetics ; Sex Determination Processes ; }, abstract = {Doubly uniparental inheritance (DUI) of mitochondrial DNA is a rare phenomenon occurring in some freshwater and marine bivalves and is usually characterized by the mitochondrial heteroplasmy of male individuals. Previous research on freshwater Unionida mussels showed that hermaphroditic species do not have DUI even if their closest gonochoristic counterparts do. No records showing DUI in a hermaphrodite have ever been reported. Here we show for the first time that the hermaphroditic mussel Semimytilus algosus (Mytilida), very likely has DUI, based on the complete sequences of both mitochondrial DNAs and the distribution of mtDNA types between male and female gonads. The two mitogenomes show considerable divergence (34.7%). The presumably paternal M type mitogenome dominated the male gonads of most studied mussels, while remaining at very low or undetectable levels in the female gonads of the same individuals. If indeed DUI can function in the context of simultaneous hermaphroditism, a change of paradigm regarding its involvement in sex determination is needed. It is apparently associated with gonadal differentiation rather than with sex determination in bivalves.}, }
@article {pmid32642050, year = {2020}, author = {Porter, SM}, title = {Insights into eukaryogenesis from the fossil record.}, journal = {Interface focus}, volume = {10}, number = {4}, pages = {20190105}, pmid = {32642050}, issn = {2042-8898}, abstract = {Eukaryogenesis-the process by which the eukaryotic cell emerged-has long puzzled scientists. It has been assumed that the fossil record has little to say about this process, in part because important characters such as the nucleus and mitochondria are rarely preserved, and in part because the prevailing model of early eukaryotes implies that eukaryogenesis occurred before the appearance of the first eukaryotes recognized in the fossil record. Here, I propose a different scenario for early eukaryote evolution than is widely assumed. Rather than crown group eukaryotes originating in the late Paleoproterozoic and remaining ecologically minor components for more than half a billion years in a prokaryote-dominated world, I argue for a late Mesoproterozoic origin of the eukaryotic crown group, implying that eukaryogenesis can be studied using the fossil record. I review the proxy records of four crown group characters: the capacity to form cysts as evidenced by the presence of excystment structures; a complex cytoskeleton as evidenced by spines or pylomes; sterol synthesis as evidenced by steranes; and aerobic respiration-and therefore mitochondria-as evidenced by eukaryotes living in oxic environments, and argue that it might be possible to use these proxy records to infer the order in which these characters evolved. The records indicate that both cyst formation and a complex cytoskeleton appeared by late Paleoproterozoic time, and sterol synthesis appeared in the late Mesoproterozioc or early Neoproterozoic. The origin of aerobic respiration cannot as easily be pinned down, but current evidence permits the possibility that it evolved sometime in the Mesoproterozoic.}, }
@article {pmid32636606, year = {2020}, author = {Long, X and Xue, H and Wong, JT}, title = {Descent of Bacteria and Eukarya From an Archaeal Root of Life.}, journal = {Evolutionary bioinformatics online}, volume = {16}, number = {}, pages = {1176934320908267}, pmid = {32636606}, issn = {1176-9343}, abstract = {The 3 biological domains delineated based on small subunit ribosomal RNAs (SSU rRNAs) are confronted by uncertainties regarding the relationship between Archaea and Bacteria, and the origin of Eukarya. The similarities between the paralogous valyl-tRNA and isoleucyl-tRNA synthetases in 5398 species estimated by BLASTP, which decreased from Archaea to Bacteria and further to Eukarya, were consistent with vertical gene transmission from an archaeal root of life close to Methanopyrus kandleri through a Primitive Archaea Cluster to an Ancestral Bacteria Cluster, and to Eukarya. The predominant similarities of the ribosomal proteins (rProts) of eukaryotes toward archaeal rProts relative to bacterial rProts established that an archaeal parent rather than a bacterial parent underwent genome merger with bacteria to generate eukaryotes with mitochondria. Eukaryogenesis benefited from the predominantly archaeal accelerated gene adoption (AGA) phenotype pertaining to horizontally transferred genes from other prokaryotes and expedited genome evolution via both gene-content mutations and nucleotidyl mutations. Archaeons endowed with substantial AGA activity were accordingly favored as candidate archaeal parents. Based on the top similarity bitscores displayed by their proteomes toward the eukaryotic proteomes of Giardia and Trichomonas, and high AGA activity, the Aciduliprofundum archaea were identified as leading candidates of the archaeal parent. The Asgard archaeons and a number of bacterial species were among the foremost potential contributors of eukaryotic-like proteins to Eukarya.}, }
@article {pmid32634032, year = {2020}, author = {Rehman, A and Khan, MF and Bibi, S and Riaz, M and Nouroz, F}, title = {Comparative phylogenetic analysis of Schizothorax plagiostomus and Schizothorax esocinus with other members of subfamilies of cyprinidae on the basis of complete mitochondrial genome and 12S, 16S ribosomal RNA from Northren areas of Pakistan.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {31}, number = {6}, pages = {250-256}, doi = {10.1080/24701394.2020.1787397}, pmid = {32634032}, issn = {2470-1408}, mesh = {Animals ; Cyprinidae/*classification/genetics ; DNA, Ribosomal/*genetics ; Genome, Mitochondrial ; Mitochondria/*genetics ; Pakistan ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Whole Genome Sequencing/*methods ; }, abstract = {We assessed the relationship of Schizothoracinae species with other subfamilies Alburninae, Xenocyprinae, Cultrinae and Squaliobarbinae of family Cyprinidae by creating the phylogenetic trees using complete mitogenome and 12S and 16S RNA. Our representative species show the great affiliation with other but separated from a group composed of Metzia mesembrinum, Metzia longinasus, Metzia lineata and Metzia formosae of subfamily Alburninae while other subfamilies formed distinct group. The members of subfamily Schizothoracinae shows separate line of evolution from subfamily Barbinae.}, }
@article {pmid32628998, year = {2020}, author = {Gonçalves, DJP and Jansen, RK and Ruhlman, TA and Mandel, JR}, title = {Under the rug: Abandoning persistent misconceptions that obfuscate organelle evolution.}, journal = {Molecular phylogenetics and evolution}, volume = {151}, number = {}, pages = {106903}, doi = {10.1016/j.ympev.2020.106903}, pmid = {32628998}, issn = {1095-9513}, mesh = {Base Sequence ; *Biological Evolution ; Genome, Mitochondrial ; Heteroplasmy ; Inheritance Patterns/genetics ; Organelles/genetics/*metabolism ; Phylogeny ; }, abstract = {The advent and advance of next generation sequencing over the past two decades made it possible to accumulate large quantities of sequence reads that could be used to assemble complete or nearly complete organelle genomes (plastome or mitogenome). The result has been an explosive increase in the availability of organelle genome sequences with over 4000 different species of green plants currently available on GenBank. During the same time period, plant molecular biologists greatly enhanced the understanding of the structure, repair, replication, recombination, transcription and translation, and inheritance of organelle DNA. Unfortunately many plant evolutionary biologists are unaware of or have overlooked this knowledge, resulting in misrepresentation of several phenomena that are critical for phylogenetic and evolutionary studies using organelle genomes. We believe that confronting these misconceptions about organelle genome organization, composition, and inheritance will improve our understanding of the evolutionary processes that underly organelle evolution. Here we discuss four misconceptions that can limit evolutionary biology studies and lead to inaccurate phylogenies and incorrect structure of the organellar DNA used to infer organelle evolution.}, }
@article {pmid32616665, year = {2020}, author = {Oldenkott, B and Burger, M and Hein, AC and Jörg, A and Senkler, J and Braun, HP and Knoop, V and Takenaka, M and Schallenberg-Rüdinger, M}, title = {One C-to-U RNA Editing Site and Two Independently Evolved Editing Factors: Testing Reciprocal Complementation with DYW-Type PPR Proteins from the Moss Physcomitrium (Physcomitrella) patens and the Flowering Plants Macadamia integrifolia and Arabidopsis.}, journal = {The Plant cell}, volume = {32}, number = {9}, pages = {2997-3018}, pmid = {32616665}, issn = {1532-298X}, mesh = {Arabidopsis/*genetics ; Arabidopsis Proteins/genetics/*metabolism ; Bryopsida/*genetics ; Evolution, Molecular ; Gene Knockout Techniques ; Genetic Complementation Test ; Macadamia/*genetics ; Mitochondria/genetics/metabolism ; Nuclear Proteins/genetics/*metabolism ; Phylogeny ; Plants, Genetically Modified ; *RNA Editing ; RNA-Binding Proteins/genetics/metabolism ; }, abstract = {Cytidine-to-uridine RNA editing is a posttranscriptional process in plant organelles, mediated by specific pentatricopeptide repeat (PPR) proteins. In angiosperms, hundreds of sites undergo RNA editing. By contrast, only 13 sites are edited in the moss Physcomitrium (Physcomitrella) patens Some are conserved between the two species, like the mitochondrial editing site nad5eU598RC. The PPR proteins assigned to this editing site are known in both species: the DYW-type PPR protein PPR79 in P. patens and the E+-type PPR protein CWM1 in Arabidopsis (Arabidopsis thaliana). CWM1 also edits sites ccmCeU463RC, ccmBeU428SL, and nad5eU609VV. Here, we reciprocally expressed the P. patens and Arabidopsis editing factors in the respective other genetic environment. Surprisingly, the P. patens editing factor edited all target sites when expressed in the Arabidopsis cwm1 mutant background, even when carboxy-terminally truncated. Conversely, neither Arabidopsis CWM1 nor CWM1-PPR79 chimeras restored editing in P. patens ppr79 knockout plants. A CWM1-like PPR protein from the early diverging angiosperm macadamia (Macadamia integrifolia) features a complete DYW domain and fully rescued editing of nad5eU598RC when expressed in P. patens. We conclude that (1) the independently evolved P. patens editing factor PPR79 faithfully operates in the more complex Arabidopsis editing system, (2) truncated PPR79 recruits catalytic DYW domains in trans when expressed in Arabidopsis, and (3) the macadamia CWM1-like protein retains the capacity to work in the less complex P. patens editing environment.}, }
@article {pmid32615754, year = {2020}, author = {Zhu, X and Liu, G and Bu, Y and Zhang, J and Wang, L and Tian, Y and Yu, J and Wu, Z and Zhou, H}, title = {In Situ Monitoring of Mitochondria Regulating Cell Viability by the RNA-Specific Fluorescent Photosensitizer.}, journal = {Analytical chemistry}, volume = {92}, number = {15}, pages = {10815-10821}, doi = {10.1021/acs.analchem.0c02298}, pmid = {32615754}, issn = {1520-6882}, mesh = {Animals ; Apoptosis/drug effects/radiation effects ; Cell Nucleus/drug effects/metabolism/radiation effects ; Cell Survival/drug effects/radiation effects ; HeLa Cells ; Humans ; Mitochondria/drug effects/*metabolism/radiation effects ; Models, Molecular ; Molecular Conformation ; Oxidative Stress/drug effects/radiation effects ; Photosensitizing Agents/*pharmacology ; RNA/*metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {Cell viability is greatly affected by external stimulus eliciting correlated dynamical physiological processes for cells to choose survival or death. A few fluorescent probes have been designed to detect whether the cell is in survival state or apoptotic state, but monitoring the regulation process of the cell undergoing survival to death remains a long-standing challenge. Herein, we highlight the in situ monitor of mitochondria regulating the cell viability by the RNA-specific fluorescent photosensitizer L. At normal conditions, L anchored mitochondria and interacted with mito-RNA to light up the mitochondria with red fluorescence. With external light stimulus, L generated reactive oxide species (ROS) and cause damage to mitochondria, which activated mitochondrial autophagy to prevent death, during which the red fluorescence of L witnessed dynamical distribution in accordance with the evolution of vacuole structures containing damaged mitochondria into autophagosomes. However, with ROS continuously increasing, the mitochondrial apoptosis was eventually commenced and L with red fluorescent was gradually accumulated in the nucleoli, indicating the programmed cell death. This work demonstrated how the delicate balance between survival and death are regulated by mitochondria.}, }
@article {pmid32614920, year = {2020}, author = {Rossi, NA and Menchaca-Rodriguez, A and Antelo, R and Wilson, B and McLaren, K and Mazzotti, F and Crespo, R and Wasilewski, J and Alda, F and Doadrio, I and Barros, TR and Hekkala, E and Alonso-Tabet, M and Alonso-Giménez, Y and Lopez, M and Espinosa-Lopez, G and Burgess, J and Thorbjarnarson, JB and Ginsberg, JR and Vliet, KA and Amato, G}, title = {High levels of population genetic differentiation in the American crocodile (Crocodylus acutus).}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0235288}, pmid = {32614920}, issn = {1932-6203}, mesh = {Alligators and Crocodiles/*genetics ; Animals ; Caribbean Region ; Central America ; DNA, Mitochondrial/genetics ; Genetic Variation ; Genetics, Population ; Haplotypes ; Microsatellite Repeats ; Mitochondria/genetics ; North America ; South America ; }, abstract = {The American crocodile (Crocodylus acutus) is a widely distributed species across coastal and brackish areas of the Neotropical region of the Americas and the Greater Antilles. Available information on patterns of genetic differentiation in C. acutus shows a complex structuring influenced by interspecific interactions (mainly hybridization) and anthropogenic actions (mostly historical hunting, recent poaching, habitat loss and fragmentation, and unintentional translocation of individuals). In this study, we used data on mitochondrial DNA control region and 11 nuclear polymorphic microsatellite loci to assess the degree of population structure of C. acutus in South America, North America, Central America and the Greater Antilles. We used traditional genetic differentiation indices, Bayesian clustering and multivariate methods to create a more comprehensive picture of the genetic relationships within the species across its range. Analyses of mtDNA and microsatellite loci show evidence of a strong population genetic structure in the American crocodile, with unique populations in each sampling locality. Our results support previous findings showing large degrees of genetic differentiation between the continental and the Greater Antillean C. acutus. We report three new haplotypes unique to Venezuela, which are considerably less distant from the Central and North American haplotypes than to the Greater Antillean ones. Our findings reveal genetic population differentiation between Cuban and Jamaican C. acutus and offer the first evidence of strong genetic differentiation among the populations of Greater Antillean C. acutus.}, }
@article {pmid32612534, year = {2020}, author = {Noiret, A and Puch, L and Riffaud, C and Costantini, D and Riou, JF and Aujard, F and Terrien, J}, title = {Sex-Specific Response to Caloric Restriction After Reproductive Investment in Microcebus murinus: An Integrative Approach.}, journal = {Frontiers in physiology}, volume = {11}, number = {}, pages = {506}, pmid = {32612534}, issn = {1664-042X}, abstract = {In seasonal environments, males and females usually maintain high metabolic activity during the whole summer season, exhausting their energy reserves. In the global warming context, unpredictability of food availability during summer could dramatically challenge the energy budget of individuals. Therefore, one can predict that resilience to environmental stress would be dramatically endangered during summer. Here, we hypothesized that females could have greater capacity to survive harsh conditions than males, considering the temporal shift in their respective reproductive energy investment, which can challenge them differently, as well as enhanced flexibility in females' physiological regulation. We tackled this question on the gray mouse lemur (Microcebus murinus), focusing on the late summer period, after the reproductive effort. We monitored six males and six females before and after a 2-weeks 60% caloric restriction (CR), measuring different physiological and cellular parameters in an integrative and comparative multiscale approach. Before CR, females were heavier than males and mostly characterized by high levels of energy expenditure, a more energetic mitochondrial profile and a downregulation of blood antioxidants. We observed a similar energy balance between sexes due to CR, with a decrease in metabolic activity over time only in males. Oxidative damage to DNA was also reduced by different pathways between sexes, which may reflect variability in their physiological status and life-history traits at the end of summer. Finally, females' mitochondria seemed to exhibit greater flexibility and greater metabolic potential than males in response to CR. Our results showed strong differences between males and females in response to food shortage during late summer, underlining the necessity to consider sex as a factor for population dynamics in climate change models.}, }
@article {pmid32605521, year = {2020}, author = {Keaney, TA and Wong, HWS and Dowling, DK and Jones, TM and Holman, L}, title = {Sibling rivalry versus mother's curse: can kin competition facilitate a response to selection on male mitochondria?.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1930}, pages = {20200575}, pmid = {32605521}, issn = {1471-2954}, mesh = {Animals ; Drosophila melanogaster ; Female ; Haplotypes ; Male ; Maternal Inheritance ; *Mitochondria ; *Selection, Genetic ; Siblings ; }, abstract = {Assuming that fathers never transmit mitochondrial DNA (mtDNA) to their offspring, mitochondrial mutations that affect male fitness are invisible to direct selection on males, leading to an accumulation of male-harming alleles in the mitochondrial genome (mother's curse). However, male phenotypes encoded by mtDNA can still undergo adaptation via kin selection provided that males interact with females carrying related mtDNA, such as their sisters. Here, using experiments with Drosophila melanogaster carrying standardized nuclear DNA but distinct mitochondrial DNA, we test whether the mitochondrial haplotype carried by interacting pairs of larvae affects survival to adulthood, as well as the fitness of the adults. Although mtDNA had no detectable direct or indirect genetic effect on larva-to-adult survival, the fitness of male and female adults was significantly affected by their own mtDNA and the mtDNA carried by their social partner in the larval stage. Thus, mtDNA mutations that alter the effect of male larvae on nearby female larvae (which often carry the same mutation, due to kinship) could theoretically respond to kin selection. We discuss the implications of our findings for the evolution of mitochondria and other maternally inherited endosymbionts.}, }
@article {pmid32601224, year = {2020}, author = {Wu, Z and Waneka, G and Broz, AK and King, CR and Sloan, DB}, title = {MSH1 is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {28}, pages = {16448-16455}, pmid = {32601224}, issn = {1091-6490}, support = {R01 GM118046/GM/NIGMS NIH HHS/United States ; }, mesh = {Arabidopsis/*genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Gene Expression Regulation, Plant ; Genome, Mitochondrial ; Genome, Plant ; Genome, Plastid ; Mitochondria/*genetics/metabolism ; MutS DNA Mismatch-Binding Protein/genetics/*metabolism ; Mutation ; Mutation Rate ; Plastids/*genetics/metabolism ; }, abstract = {Mitochondrial and plastid genomes in land plants exhibit some of the slowest rates of sequence evolution observed in any eukaryotic genome, suggesting an exceptional ability to prevent or correct mutations. However, the mechanisms responsible for this extreme fidelity remain unclear. We tested seven candidate genes involved in cytoplasmic DNA replication, recombination, and repair (POLIA, POLIB, MSH1, RECA3, UNG, FPG, and OGG1) for effects on mutation rates in the model angiosperm Arabidopsis thaliana by applying a highly accurate DNA sequencing technique (duplex sequencing) that can detect newly arisen mitochondrial and plastid mutations even at low heteroplasmic frequencies. We find that disrupting MSH1 (but not the other candidate genes) leads to massive increases in the frequency of point mutations and small indels and changes to the mutation spectrum in mitochondrial and plastid DNA. We also used droplet digital PCR to show transmission of de novo heteroplasmies across generations in msh1 mutants, confirming a contribution to heritable mutation rates. This dual-targeted gene is part of an enigmatic lineage within the mutS mismatch repair family that we find is also present outside of green plants in multiple eukaryotic groups (stramenopiles, alveolates, haptophytes, and cryptomonads), as well as certain bacteria and viruses. MSH1 has previously been shown to limit ectopic recombination in plant cytoplasmic genomes. Our results point to a broader role in recognition and correction of errors in plant mitochondrial and plastid DNA sequence, leading to greatly suppressed mutation rates perhaps via initiation of double-stranded breaks and repair pathways based on faithful homologous recombination.}, }
@article {pmid32599078, year = {2020}, author = {Xu, X and Kuntner, M and Bond, JE and Ono, H and Ho, SYW and Liu, F and Yu, L and Li, D}, title = {Molecular species delimitation in the primitively segmented spider genus Heptathela endemic to Japanese islands.}, journal = {Molecular phylogenetics and evolution}, volume = {151}, number = {}, pages = {106900}, doi = {10.1016/j.ympev.2020.106900}, pmid = {32599078}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Geography ; *Islands ; Japan ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Probability ; Species Specificity ; Spiders/*genetics ; }, abstract = {Determining species boundaries forms an important foundation for biological research. However, the results of molecular species delimitation can vary with the data sets and methods that are used. Here we use a two-step approach to delimit species in the genus Heptathela, a group of primitively segmented trapdoor spiders that are endemic to Japanese islands. Morphological evidence suggests the existence of 19 species in the genus. We tested this initial species hypothesis by using six molecular species-delimitation methods to analyse 180 mitochondrial COI sequences of Heptathela sampled from across the known range of the genus. We then conducted a set of more focused analyses by sampling additional genetic markers from the subset of taxa that were inconsistently delimited by the single-locus analyses of mitochondrial DNA. Multilocus species delimitation was performed using two Bayesian approaches based on the multispecies coalescent. Our approach identified 20 putative species among the 180 sampled individuals of Heptathela. We suggest that our two-step approach provides an efficient strategy for delimiting species while minimizing costs and computational time.}, }
@article {pmid32598924, year = {2020}, author = {Moo-Llanes, DA and Pech-May, A and de Oca-Aguilar, ACM and Salomón, OD and Ramsey, JM}, title = {Niche divergence and paleo-distributions of Lutzomyia longipalpis mitochondrial haplogroups (Diptera: Psychodidae).}, journal = {Acta tropica}, volume = {211}, number = {}, pages = {105607}, doi = {10.1016/j.actatropica.2020.105607}, pmid = {32598924}, issn = {1873-6254}, mesh = {Animals ; Argentina ; Brazil ; Caribbean Region ; Central America ; Colombia ; *Ecosystem ; *Haplotypes ; Insect Vectors/*classification/*genetics ; Mexico ; *Mitochondria ; *Phylogeography ; Psychodidae/*classification/*genetics ; Uruguay ; }, abstract = {Lutzomyia longipalpis is a complex of species which has a wide but discontinuous distribution from southeastern Mexico to northern Argentina and Uruguay. To date, eight mitochondrial haplogroups have been identified along its distribution although key environmental tolerances and ecological niche models have been analyzed only at the complex level. The aim of the present study was to analyze whether genetic diversification using three mitochondrial genes of the Lu. longipalpis complex is associated with niche divergence and to explore evolution of distributional projections of all haplogroups between the Last Glacial Maximum (LGM; 21,000 yrs ago) and the present. Current occurrence of all haplogroups was used to develop ecological niche models (ENM) and these were projected in both periods to quantify and identify geographic area shifts. Environmental space was used to estimate niche similarity between major clades and pairwise between individual haplogroups. The two major Lu. longipalpis clades (Mex, CA, Col and Ven vs Arg and Bra) had significantly different environmental space, indicating niche divergence. Environmental space overlap of southern haplogroups was variable, with divergent niche, except between Arg and ArgBra. The most suitable regions for the ArgBra haplogroup were northeastern and southeastern Brazil, and the Gran Chaco region. In contrast, ENM of haplogroups within the northern major clade have significantly similar niche, with highest geographic ENM suitability along both the Caribbean and Pacific coasts. The intensity and coverage of high suitability areas in the LGM decreased for most haplogroups in the present. Integrating ENM and phylogenetic analyses has allowed us to test hypotheses of niche similarity between Lu. longipalpis haplogroups and major clades, and to identify conserved distributional areas of haplogroups since the LGM, with the exception of Arg. Evidence for distributional shifts and overlap of haplogroups is important to analyze Leishmaniasis´ eco-epidemiology and to successfully monitor and control transmission.}, }
@article {pmid32591605, year = {2020}, author = {Goodheart, JA and Minsky, G and Brynjegard-Bialik, MN and Drummond, MS and Munoz, JD and Fallon, TR and Schultz, DT and Weng, JK and Torres, E and Oakley, TH}, title = {Laboratory culture of the California Sea Firefly Vargula tsujii (Ostracoda: Cypridinidae): Developing a model system for the evolution of marine bioluminescence.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {10443}, pmid = {32591605}, issn = {2045-2322}, support = {T32 GM007287/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Aquaculture/methods ; Aquatic Organisms/metabolism ; *Biological Evolution ; California ; Crustacea/embryology/genetics/growth &amp; development/*metabolism ; Female ; Genetics, Population ; Genome/genetics ; Genome, Mitochondrial/genetics ; Life Cycle Stages ; *Luminescence ; Male ; Mitochondria/genetics ; Whole Genome Sequencing ; }, abstract = {Bioluminescence, or the production of light by living organisms via chemical reaction, is widespread across Metazoa. Laboratory culture of bioluminescent organisms from diverse taxonomic groups is important for determining the biosynthetic pathways of bioluminescent substrates, which may lead to new tools for biotechnology and biomedicine. Some bioluminescent groups may be cultured, including some cnidarians, ctenophores, and brittle stars, but those use luminescent substrates (luciferins) obtained from their diets, and therefore are not informative for determination of the biosynthetic pathways of the luciferins. Other groups, including terrestrial fireflies, do synthesize their own luciferin, but culturing them is difficult and the biosynthetic pathway for firefly luciferin remains unclear. An additional independent origin of endogenous bioluminescence is found within ostracods from the family Cypridinidae, which use their luminescence for defense and, in Caribbean species, for courtship displays. Here, we report the first complete life cycle of a luminous ostracod (Vargula tsujii Kornicker &amp; Baker, 1977, the California Sea Firefly) in the laboratory. We also describe the late-stage embryogenesis of Vargula tsujii and discuss the size classes of instar development. We find embryogenesis in V. tsujii ranges from 25-38 days, and this species appears to have five instar stages, consistent with ontogeny in other cypridinid lineages. We estimate a complete life cycle at 3-4 months. We also present the first complete mitochondrial genome for Vargula tsujii. Bringing a luminous ostracod into laboratory culture sets the stage for many potential avenues of study, including learning the biosynthetic pathway of cypridinid luciferin and genomic manipulation of an autogenic bioluminescent system.}, }
@article {pmid32589742, year = {2020}, author = {Greimann, ES and Ward, SF and Woodell, JD and Hennessey, S and Kline, MR and Moreno, JA and Peters, M and Cruise, JL and Montooth, KL and Neiman, M and Sharbrough, J}, title = {Phenotypic Variation in Mitochondria-Related Performance Traits Across New Zealand Snail Populations.}, journal = {Integrative and comparative biology}, volume = {60}, number = {2}, pages = {275-287}, doi = {10.1093/icb/icaa066}, pmid = {32589742}, issn = {1557-7023}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/genetics ; *Genome, Mitochondrial ; *Life History Traits ; New Zealand ; Phenotype ; Reproduction ; Snails/genetics/*physiology ; }, abstract = {Mitochondrial function is critical for energy homeostasis and should shape how genetic variation in metabolism is transmitted through levels of biological organization to generate stability in organismal performance. Mitochondrial function is encoded by genes in two distinct and separately inherited genomes-the mitochondrial genome and the nuclear genome-and selection is expected to maintain functional mito-nuclear interactions. The documented high levels of polymorphism in genes involved in these mito-nuclear interactions and wide variation for mitochondrial function demands an explanation for how and why variability in such a fundamental trait is maintained. Potamopyrgus antipodarum is a New Zealand freshwater snail with coexisting sexual and asexual individuals and, accordingly, contrasting systems of separate vs. co-inheritance of nuclear and mitochondrial genomes. As such, this snail provides a powerful means to dissect the evolutionary and functional consequences of mito-nuclear variation. The lakes inhabited by P. antipodarum span wide environmental gradients, with substantial across-lake genetic structure and mito-nuclear discordance. This situation allows us to use comparisons across reproductive modes and lakes to partition variation in cellular respiration across genetic and environmental axes. Here, we integrated cellular, physiological, and behavioral approaches to quantify variation in mitochondrial function across a diverse set of wild P. antipodarum lineages. We found extensive across-lake variation in organismal oxygen consumption and behavioral response to heat stress and differences across sexes in mitochondrial membrane potential but few global effects of reproductive mode. Taken together, our data set the stage for applying this important model system for sexual reproduction and polyploidy to dissecting the complex relationships between mito-nuclear variation, performance, plasticity, and fitness in natural populations.}, }
@article {pmid32586956, year = {2020}, author = {Greenway, R and Barts, N and Henpita, C and Brown, AP and Arias Rodriguez, L and Rodríguez Peña, CM and Arndt, S and Lau, GY and Murphy, MP and Wu, L and Lin, D and Tobler, M and Kelley, JL and Shaw, JH}, title = {Convergent evolution of conserved mitochondrial pathways underlies repeated adaptation to extreme environments.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {28}, pages = {16424-16430}, pmid = {32586956}, issn = {1091-6490}, support = {MC_UU_00015/3/MRC_/Medical Research Council/United Kingdom ; MC_U105663142/MRC_/Medical Research Council/United Kingdom ; 110159/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 110158/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adaptation, Physiological ; Animals ; Ecosystem ; *Evolution, Molecular ; Extreme Environments ; Genome ; Hydrogen Sulfide/metabolism ; Mitochondria/genetics/*metabolism ; Phylogeny ; Poecilia/genetics/*physiology ; }, abstract = {Extreme environments test the limits of life; yet, some organisms thrive in harsh conditions. Extremophile lineages inspire questions about how organisms can tolerate physiochemical stressors and whether the repeated colonization of extreme environments is facilitated by predictable and repeatable evolutionary innovations. We identified the mechanistic basis underlying convergent evolution of tolerance to hydrogen sulfide (H2S)-a toxicant that impairs mitochondrial function-across evolutionarily independent lineages of a fish (Poecilia mexicana, Poeciliidae) from H2S-rich springs. Using comparative biochemical and physiological analyses, we found that mitochondrial function is maintained in the presence of H2S in sulfide spring P. mexicana but not ancestral lineages from nonsulfidic habitats due to convergent adaptations in the primary toxicity target and a major detoxification enzyme. Genome-wide local ancestry analyses indicated that convergent evolution of increased H2S tolerance in different populations is likely caused by a combination of selection on standing genetic variation and de novo mutations. On a macroevolutionary scale, H2S tolerance in 10 independent lineages of sulfide spring fishes across multiple genera of Poeciliidae is correlated with the convergent modification and expression changes in genes associated with H2S toxicity and detoxification. Our results demonstrate that the modification of highly conserved physiological pathways associated with essential mitochondrial processes mediates tolerance to physiochemical stress. In addition, the same pathways, genes, and-in some instances-codons are implicated in H2S adaptation in lineages that span 40 million years of evolution.}, }
@article {pmid32581834, year = {2020}, author = {Mannella, CA}, title = {Consequences of Folding the Mitochondrial Inner Membrane.}, journal = {Frontiers in physiology}, volume = {11}, number = {}, pages = {536}, pmid = {32581834}, issn = {1664-042X}, support = {P41 RR001219/RR/NCRR NIH HHS/United States ; }, abstract = {A fundamental first step in the evolution of eukaryotes was infolding of the chemiosmotic membrane of the endosymbiont. This allowed the proto-eukaryote to amplify ATP generation while constraining the volume dedicated to energy production. In mitochondria, folding of the inner membrane has evolved into a highly regulated process that creates specialized compartments (cristae) tuned to optimize function. Internalizing the inner membrane also presents complications in terms of generating the folds and maintaining mitochondrial integrity in response to stresses. This review describes mechanisms that have evolved to regulate inner membrane topology and either preserve or (when appropriate) rupture the outer membrane.}, }
@article {pmid32580700, year = {2020}, author = {Deng, Y and Zhang, X and Xie, B and Lin, L and Hsiang, T and Lin, X and Lin, Y and Zhang, X and Ma, Y and Miao, W and Ming, R}, title = {Intra-specific comparison of mitochondrial genomes reveals host gene fragment exchange via intron mobility in Tremella fuciformis.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {426}, pmid = {32580700}, issn = {1471-2164}, support = {31670021//Natural Science Foundation of China/ ; }, mesh = {Basidiomycota/*genetics ; Evolution, Molecular ; Fungal Proteins/genetics ; Gene Order ; Genetic Variation ; Genome Size ; Interspersed Repetitive Sequences ; Introns ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Mitochondrial genomic sequences are known to be variable. Comparative analyses of mitochondrial genomes can reveal the nature and extent of their variation.<br><br>RESULTS: Draft mitochondrial genomes of 16&#x2009;Tremella fuciformis isolates (TF01-TF16) were assembled from Illumina and PacBio sequencing data. Mitochondrial DNA contigs were extracted and assembled into complete circular molecules, ranging from 35,104&#x2009;bp to 49,044&#x2009;bp in size. All mtDNAs contained the same set of 41 conserved genes with identical gene order. Comparative analyses revealed that introns and intergenic regions were variable, whereas genic regions (including coding sequences, tRNA, and rRNA genes) were conserved. Among 24 introns detected, 11 were in protein-coding genes, 3 in tRNA genes, and the other 10 in rRNA genes. In addition, two mobile fragments were found in intergenic regions. Interestingly, six introns containing N-terminal duplication of the host genes were found in five conserved protein-coding gene sequences. Comparison of genes with and without these introns gave rise to the following proposed model: gene fragment exchange with other species can occur via gain or loss of introns with N-terminal duplication of the host genes.<br><br>CONCLUSIONS: Our findings suggest a novel mechanism of fungal mitochondrial gene evolution: partial foreign gene replacement though intron mobility.}, }
@article {pmid32580582, year = {2020}, author = {Nesci, S and Pagliarani, A and Algieri, C and Trombetti, F}, title = {Mitochondrial F-type ATP synthase: multiple enzyme functions revealed by the membrane-embedded FO structure.}, journal = {Critical reviews in biochemistry and molecular biology}, volume = {55}, number = {4}, pages = {309-321}, doi = {10.1080/10409238.2020.1784084}, pmid = {32580582}, issn = {1549-7798}, mesh = {*Adenosine Triphosphate/chemistry/metabolism ; Animals ; Humans ; Mitochondria/*enzymology ; Mitochondrial Membranes/*enzymology ; *Mitochondrial Proton-Translocating ATPases/chemistry/metabolism ; }, abstract = {Of the two main sectors of the F-type ATP synthase, the membrane-intrinsic FO domain is the one which, during evolution, has undergone the highest structural variations and changes in subunit composition. The FO complexity in mitochondria is apparently related to additional enzyme functions that lack in bacterial and thylakoid complexes. Indeed, the F-type ATP synthase has the main bioenergetic role to synthesize ATP by exploiting the electrochemical gradient built by respiratory complexes. The FO membrane domain, essential in the enzyme machinery, also participates in the bioenergetic cost of synthesizing ATP and in the formation of the cristae, thus contributing to mitochondrial morphology. The recent enzyme involvement in a high-conductance channel, which forms in the inner mitochondrial membrane and promotes the mitochondrial permeability transition, highlights a new F-type ATP synthase role. Point mutations which cause amino acid substitutions in FO subunits produce mitochondrial dysfunctions and lead to severe pathologies. The FO variability in different species, pointed out by cryo-EM analysis, mirrors the multiple enzyme functions and opens a new scenario in mitochondrial biology.}, }
@article {pmid32579605, year = {2020}, author = {Pyrih, J and Rašková, V and Škodová-Sveráková, I and Pánek, T and Lukeš, J}, title = {ZapE/Afg1 interacts with Oxa1 and its depletion causes a multifaceted phenotype.}, journal = {PloS one}, volume = {15}, number = {6}, pages = {e0234918}, pmid = {32579605}, issn = {1932-6203}, mesh = {Biotinylation ; Down-Regulation ; Electron Transport Complex I/metabolism ; Electron Transport Complex IV/metabolism ; Eukaryota/genetics ; *Gene Deletion ; Genome, Mitochondrial ; Mitochondria/metabolism ; Mitochondrial Proteins/metabolism ; Phenotype ; Phylogeny ; Protein Binding ; Protozoan Proteins/*metabolism ; Trypanosoma brucei brucei/*metabolism ; }, abstract = {ZapE/Afg1 is a component of the inner cell membrane of some eubacteria and the inner mitochondrial membrane of eukaryotes. This protein is involved in FtsZ-dependent division of eubacteria. In the yeast and human mitochondrion, ZapE/Afg1 likely interacts with Oxa1 and facilitates the degradation of mitochondrion-encoded subunits of respiratory complexes. Furthermore, the depletion of ZapE increases resistance to apoptosis, decreases oxidative stress tolerance, and impacts mitochondrial protein homeostasis. It remains unclear whether ZapE is a multifunctional protein, or whether some of the described effects are just secondary phenotypes. Here, we have analyzed the functions of ZapE in Trypanosoma brucei, a parasitic protist, and an important model organism. Using a newly developed proximity-dependent biotinylation approach (BioID2), we have identified the inner mitochondrial membrane insertase Oxa1 among three putative interacting partners of ZapE, which is present in two paralogs. RNAi-mediated depletion of both ZapE paralogs likely affected the function of respiratory complexes I and IV. Consistently, we show that the distribution of mitochondrial ZapE is restricted only to organisms with Oxa1, respiratory complexes, and a mitochondrial genome. We propose that the evolutionarily conserved interaction of ZapE with Oxa1, which is required for proper insertion of many inner mitochondrial membrane proteins, is behind the multifaceted phenotype caused by the ablation of ZapE.}, }
@article {pmid32569843, year = {2020}, author = {Ricardo, PC and Françoso, E and Arias, MC}, title = {Mitochondrial DNA intra-individual variation in a bumblebee species: A challenge for evolutionary studies and molecular identification.}, journal = {Mitochondrion}, volume = {53}, number = {}, pages = {243-254}, doi = {10.1016/j.mito.2020.06.007}, pmid = {32569843}, issn = {1872-8278}, mesh = {Animals ; Bees/classification/*genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Heteroplasmy ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*veterinary ; }, abstract = {Mitochondrial DNA (mtDNA) regions have been widely used as molecular markers in evolutionary studies and species identification. However, the presence of heteroplasmy and NUMTs may represent obstacles. Heteroplasmy is a state where an organism has different mitochondrial haplotypes. NUMTs are nuclear pseudogenes originating from mtDNA sequences transferred to nuclear DNA. Evidences of heteroplasmy were already verified in the bumblebee Bombus morio in an earlier study. The present work investigated in more detail the presence of intra-individual haplotypes variation in this species. Heteroplasmy was detected in individuals from all the ten sampled locations, with an average of six heteroplasmic haplotypes per individual. In addition, some of these heteroplasmic haplotypes were shared among individuals from different locations, suggesting the existence of stable heteroplasmy in B. morio. These results demonstrated that heteroplasmy is likely to affect inferences based on mtDNA analysis, especially in phylogenetic, phylogeographic and population genetics studies. In addition, NUMTs were also detected. These sequences showed divergence of 2.7% to 12% in relation to the mitochondrial haplotypes. These levels of divergence could mislead conclusions in evolutionary studies and affect species identification through DNA barcoding.}, }
@article {pmid32564730, year = {2020}, author = {Levitskii, SA and Baleva, MV and Chicherin, IV and Krasheninnikov, IA and Kamenski, PA}, title = {Protein Biosynthesis in Mitochondria: Past Simple, Present Perfect, Future Indefinite.}, journal = {Biochemistry. Biokhimiia}, volume = {85}, number = {3}, pages = {257-263}, doi = {10.1134/S0006297920030013}, pmid = {32564730}, issn = {1608-3040}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Biological Evolution ; Cell Nucleus/metabolism ; Cytosol/metabolism ; Gene Transfer Techniques ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/metabolism ; *Oxidative Phosphorylation ; *Protein Biosynthesis ; Saccharomyces cerevisiae/metabolism ; }, abstract = {Mitochondria are obligate organelles of most eukaryotic cells that perform many different functions important for cellular homeostasis. The main role of mitochondria is supplying cells with energy in a form of ATP, which is synthesized in a chain of oxidative phosphorylation reactions on the organelle inner membrane. It is commonly believed now that mitochondria have the endosymbiotic origin. In the course of evolution, they have lost most of their genetic material as a result of genome reduction and gene transfer to the nucleus. The majority of mitochondrial proteins are synthesized in the cytosol and then imported to the mitochondria. However, almost all known mitochondria still contain genomes that are maintained and expressed. The processes of protein biosynthesis in the mitochondria - mitochondrial translation - substantially differs from the analogous processes in bacteria and the cytosol of eukaryotic cells. Mitochondrial translation is characterized by a high degree of specialization and specific regulatory mechanisms. In this review, we analyze available information on the common principles of mitochondrial translation with emphasis on the molecular mechanisms of translation initiation in the mitochondria of yeast and mammalian cells.}, }
@article {pmid32561724, year = {2020}, author = {Nong, W and Cao, J and Li, Y and Qu, Z and Sun, J and Swale, T and Yip, HY and Qian, PY and Qiu, JW and Kwan, HS and Bendena, W and Tobe, S and Chan, TF and Yip, KY and Chu, KH and Ngai, SM and Tsim, KY and Holland, PWH and Hui, JHL}, title = {Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {3051}, pmid = {32561724}, issn = {2041-1723}, mesh = {Animals ; Developmental Biology ; *Genes, Homeobox ; Genome ; Genome, Mitochondrial ; Hormones/genetics ; MicroRNAs/genetics ; Mitochondria/genetics ; *Multigene Family ; Phylogeny ; Plastids/genetics ; RNA/*genetics ; RNA, Small Interfering/genetics ; Scyphozoa/*genetics/*physiology ; Sequence Analysis, DNA ; Species Specificity ; Transcriptome ; }, abstract = {The phylum Cnidaria represents a close outgroup to Bilateria and includes familiar animals including sea anemones, corals, hydroids, and jellyfish. Here we report genome sequencing and assembly for true jellyfish Sanderia malayensis and Rhopilema esculentum. The homeobox gene clusters are characterised by interdigitation of Hox, NK, and Hox-like genes revealing an alternate pathway of ANTP class gene dispersal and an intact three gene ParaHox cluster. The mitochondrial genomes are linear but, unlike in Hydra, we do not detect nuclear copies, suggesting that linear plastid genomes are not necessarily prone to integration. Genes for sesquiterpenoid hormone production, typical for arthropods, are also now found in cnidarians. Somatic and germline cells both express piwi-interacting RNAs in jellyfish revealing a conserved cnidarian feature, and evidence for tissue-specific microRNA arm switching as found in Bilateria is detected. Jellyfish genomes reveal a mosaic of conserved and divergent genomic characters evolved from a shared ancestral genetic architecture.}, }
@article {pmid32555277, year = {2020}, author = {Subramanian, H and Gatenby, RA}, title = {Evolutionary advantage of anti-parallel strand orientation of duplex DNA.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9883}, pmid = {32555277}, issn = {2045-2322}, support = {U54 CA193489/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; DNA/*chemistry/metabolism ; DNA Replication ; *Evolution, Molecular ; Mitochondria/genetics ; Models, Molecular ; Nucleic Acid Conformation ; }, abstract = {DNA in all living systems shares common properties that are remarkably well suited to its function, suggesting refinement by evolution. However, DNA also shares some counter-intuitive properties which confer no obvious benefit, such as strand directionality and anti-parallel strand orientation, which together result in the complicated lagging strand replication. The evolutionary dynamics that led to these properties of DNA remain unknown but their universality suggests that they confer as yet unknown selective advantage to DNA. In this article, we identify an evolutionary advantage of anti-parallel strand orientation of duplex DNA, within a given set of plausible premises. The advantage stems from the increased rate of replication, achieved by dividing the DNA into predictable, independently and simultaneously replicating segments, as opposed to sequentially replicating the entire DNA, thereby parallelizing the replication process. We show that anti-parallel strand orientation is essential for such a replicative organization of DNA, given our premises, the most important of which is the assumption of the presence of sequence-dependent asymmetric cooperativity in DNA.}, }
@article {pmid32553108, year = {2020}, author = {Tobiasson, V and Amunts, A}, title = {Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {32553108}, issn = {2050-084X}, support = {M44/16//Ragnar S&#xf6;derbergs stiftelse/International ; 2017/1041//Cancerfonden/International ; ERC-2018-StG- 805230//H2020 European Research Council/International ; 2018.0080//Knut och Alice Wallenbergs Stiftelse/International ; EMBO Young Investigator Program//European Molecular Biology Organization/International ; FFL15:0325//Swedish Foundation for Strategic Research/International ; NT_2015-04107//Swedish Research Council/International ; }, mesh = {*Biological Evolution ; Evolution, Molecular ; Mitochondrial Ribosomes/*metabolism ; *Protein Biosynthesis ; Tetrahymena thermophila/*metabolism ; }, abstract = {To understand the steps involved in the evolution of translation, we used Tetrahymena thermophila, a ciliate with high coding capacity of the mitochondrial genome, as the model organism and characterized its mitochondrial ribosome (mitoribosome) using cryo-EM. The structure of the mitoribosome reveals an assembly of 94-ribosomal proteins and four-rRNAs with an additional protein mass of ~700 kDa on the small subunit, while the large subunit lacks 5S rRNA. The structure also shows that the small subunit head is constrained, tRNA binding sites are formed by mitochondria-specific protein elements, conserved protein bS1 is excluded, and bacterial RNA polymerase binding site is blocked. We provide evidence for anintrinsic protein targeting system through visualization of mitochondria-specific mL105 by the exit tunnel that would facilitate the recruitment of a nascent polypeptide. Functional protein uS3m is encoded by three complementary genes from the nucleus and mitochondrion, establishing a link between genetic drift and mitochondrial translation. Finally, we reannotated nine open reading frames in the mitochondrial genome that code for mitoribosomal proteins.}, }
@article {pmid32552121, year = {2020}, author = {Kim, P and Han, JH and An, SL}, title = {Genetic identification of species and natural hybridization determination based on mitochondrial DNA and nuclear DNA of genus Zacco in Korea.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {31}, number = {6}, pages = {221-227}, doi = {10.1080/24701394.2020.1777994}, pmid = {32552121}, issn = {2470-1408}, mesh = {Animals ; Breeding ; Cell Nucleus/*genetics ; Chimera ; Cyprinidae/*classification/genetics ; DNA/*genetics ; DNA Barcoding, Taxonomic ; Female ; Genes, RAG-1/genetics ; Genetic Variation ; Male ; Mitochondria/*genetics ; Phylogeny ; Republic of Korea ; }, abstract = {Genus Zacco specimens collected in this study were classified genetically as five species, Zacco platypus, Z. temminckii, Z. koreanus and two unidentified species, using DNA barcoding analysis based on 655 bp of mitochondrial cytochrome c oxidase subunit I (COI) gene. Two of unidentified species (Z. sp.1 and Z. sp.2) were considered to be unrecorded or new species of genus Zacco according to genetic distances between Zacco species. In addition, we determined a natural hybrid based on polymorphic base at the diagnostic positions displayed on nuclear recombination activating gene 1 (RAG1) gene (965 bp), and estimated paternal and maternal species of natural hybrid comparing phylogenetic tree between COI and RAG1, and Z. sp.1♀ × Z. koreanus♂, Z. sp.2♀ × Z. koreanus♂ and Z. koreanus♀ × Z. sp.1♂ individuals were confirmed. The habitat of natural hybrids of Z. koreanus between Z. sp.1 and Z. sp.2 was identified as Geum and Yeongsan River, respectively. In our data, only F1 hybrid generation was identified; however, generations after F1 hybrid or backcross were not demonstrated.}, }
@article {pmid32551463, year = {2020}, author = {Timón-Gómez, A and Barrientos, A}, title = {Mitochondrial respiratory chain composition and organization in response to changing oxygen levels.}, journal = {Journal of life sciences (Westlake Village, Calif.)}, volume = {2}, number = {2}, pages = {}, pmid = {32551463}, issn = {2688-1020}, support = {R35 GM118141/GM/NIGMS NIH HHS/United States ; }, abstract = {Mitochondria are the major consumer of oxygen in eukaryotic cells, owing to the requirement of oxygen to generate ATP through the mitochondrial respiratory chain (MRC) and the oxidative phosphorylation system (OXPHOS). This aerobic energy transduction is more efficient than anaerobic processes such as glycolysis. Hypoxia, a condition in which environmental or intracellular oxygen levels are below the standard range, triggers an adaptive signaling pathway within the cell. When oxygen concentrations are low, hypoxia-inducible factors (HIFs) become stabilized and activated to mount a transcriptional response that triggers modulation of cellular metabolism to adjust to hypoxic conditions. Mitochondrial aerobic metabolism is one of the main targets of the hypoxic response to regulate its functioning and efficiency in the presence of decreased oxygen levels. During evolution, eukaryotic cells and tissues have increased the plasticity of their mitochondrial OXPHOS system to cope with metabolic needs in different oxygen contexts. In mammalian mitochondria, two factors contribute to this plasticity. First, several subunits of the multimeric MRC complexes I and IV exist in multiple tissue-specific and condition-specific isoforms. Second, the MRC enzymes can coexist organized as individual entities or forming supramolecular structures known as supercomplexes, perhaps in a dynamic manner to respond to environmental conditions and cellular metabolic demands. In this review, we will summarize the information currently available on oxygen-related changes in MRC composition and organization and will discuss gaps of knowledge and research opportunities in the field.}, }
@article {pmid32551241, year = {2020}, author = {Monteiro, LB and Davanzo, GG and de Aguiar, CF and Moraes-Vieira, PMM}, title = {Using flow cytometry for mitochondrial assays.}, journal = {MethodsX}, volume = {7}, number = {}, pages = {100938}, pmid = {32551241}, issn = {2215-0161}, abstract = {The understanding of how different cell types adapt their metabolism in the face of challenges has been attracting the attention of researchers for many years. Recently, immunologists also started to focus on how the metabolism of immune cells can impact the way that immunity drives its responses. The presence of a pathogen or damage in a tissue changes severely the way that the immune cells need to respond. When activated, immune cells usually shift their metabolism from a high energy demanding status using mitochondria respiration to a glycolytic based rapid ATP production. The diminished amount of respiration leads to changes in the mitochondrial membrane potential and, consequently, generation of reactive oxygen species. Here, we show how flow cytometry can be used to track changes in mitochondrial mass, membrane potential and superoxide (ROS) production in live immune cells. ● This protocol suggests a quick way of evaluating mitochondrial fitness using flow cytometry. We propose using the probes MitoTraker Green and MitoTracker Red/ MitoSOX at the same time. This way, it is possible to evaluate different parameters of mitochondrial biology in living cells. ● Flow cytometry is a highly used tool by immunologists. With the advances of studies focusing on the metabolism of immune cells, a simplified application of flow cytometry for mitochondrial studies and screenings is a helpful clarifying method for immunology.}, }
@article {pmid32546620, year = {2020}, author = {Valero, C and Colabardini, AC and Chiaratto, J and Pardeshi, L and de Castro, PA and Ferreira Filho, JA and Silva, LP and Rocha, MC and Malavazi, I and Costa, JH and Fill, T and Barros, MH and Wong, SSW and Aimanianda, V and Wong, KH and Goldman, GH}, title = {Aspergillus fumigatus Transcription Factors Involved in the Caspofungin Paradoxical Effect.}, journal = {mBio}, volume = {11}, number = {3}, pages = {}, pmid = {32546620}, issn = {2150-7511}, mesh = {Animals ; Antifungal Agents/pharmacology ; Aspergillosis/microbiology ; Aspergillus fumigatus/*drug effects/*genetics ; Caspofungin/*pharmacology ; Drug Resistance, Fungal/*genetics ; Female ; Fungal Proteins/*metabolism ; Gene Expression Regulation, Fungal ; Gene Library ; Mice ; Mice, Inbred BALB C ; Microbial Sensitivity Tests ; Signal Transduction ; Transcription Factors/*metabolism ; }, abstract = {Aspergillus fumigatus is the leading cause of pulmonary fungal diseases. Azoles have been used for many years as the main antifungal agents to treat and prevent invasive aspergillosis. However, in the last 10 years there have been several reports of azole resistance in A. fumigatus and new strategies are needed to combat invasive aspergillosis. Caspofungin is effective against other human-pathogenic fungal species, but it is fungistatic only against A. fumigatus Resistance to caspofungin in A. fumigatus has been linked to mutations in the fksA gene that encodes the target enzyme of the drug β-1,3-glucan synthase. However, tolerance of high caspofungin concentrations, a phenomenon known as the caspofungin paradoxical effect (CPE), is also important for subsequent adaptation and drug resistance evolution. Here, we identified and characterized the transcription factors involved in the response to CPE by screening an A. fumigatus library of 484 null transcription factors (TFs) in CPE drug concentrations. We identified 11 TFs that had reduced CPE and that encoded proteins involved in the basal modulation of the RNA polymerase II initiation sites, calcium metabolism, and cell wall remodeling. One of these TFs, FhdA, was important for mitochondrial respiratory function and iron metabolism. The ΔfhdA mutant showed decreased growth when exposed to Congo red or to high temperature. Transcriptome sequencing (RNA-seq) analysis and further experimental validation indicated that the ΔfhdA mutant showed diminished respiratory capacity, probably affecting several pathways related to the caspofungin tolerance and resistance. Our results provide the foundation to understand signaling pathways that are important for caspofungin tolerance and resistance.IMPORTANCEAspergillus fumigatus, one of the most important human-pathogenic fungal species, is able to cause aspergillosis, a heterogeneous group of diseases that presents a wide range of clinical manifestations. Invasive pulmonary aspergillosis is the most serious pathology in terms of patient outcome and treatment, with a high mortality rate ranging from 50% to 95% primarily affecting immunocompromised patients. Azoles have been used for many years as the main antifungal agents to treat and prevent invasive aspergillosis. However, there were several reports of evolution of clinical azole resistance in the last decade. Caspofungin, a noncompetitive β-1,3-glucan synthase inhibitor, has been used against A. fumigatus, but it is fungistatic and is recommended as second-line therapy for invasive aspergillosis. More information about caspofungin tolerance and resistance is necessary in order to refine antifungal strategies that target the fungal cell wall. Here, we screened a transcription factor (TF) deletion library for TFs that can mediate caspofungin tolerance and resistance. We have identified 11 TFs that are important for caspofungin sensitivity and/or for the caspofungin paradoxical effect (CPE). These TFs encode proteins involved in the basal modulation of the RNA polymerase II initiation sites, calcium metabolism or cell wall remodeling, and mitochondrial respiratory function. The study of those genes regulated by TFs identified in this work will provide a better understanding of the signaling pathways that are important for caspofungin tolerance and resistance.}, }
@article {pmid32541805, year = {2020}, author = {Viviani, VR and Silva, JR and Amaral, DT and Bevilaqua, VR and Abdalla, FC and Branchini, BR and Johnson, CH}, title = {A new brilliantly blue-emitting luciferin-luciferase system from Orfelia fultoni and Keroplatinae (Diptera).}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9608}, pmid = {32541805}, issn = {2045-2322}, support = {R21 MH116150/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Chromatography, Ion Exchange ; Diptera/enzymology/*metabolism ; Firefly Luciferin/chemistry/isolation &amp; purification/*metabolism ; Gene Expression Profiling ; Luciferases/chemistry/isolation &amp; purification/*metabolism ; Luminescent Measurements ; Mitochondria/enzymology/metabolism ; Spectrometry, Fluorescence ; }, abstract = {Larvae of O. fultoni (Keroplatidae: Keroplatinae), which occur along river banks in the Appalachian Mountains in Eastern United States, produce the bluest bioluminescence among insects from translucent areas associated to black bodies, which are located mainly in the anterior and posterior parts of the body. Although closely related to Arachnocampa spp (Keroplatidae: Arachnocampininae), O.fultoni has a morphologically and biochemically distinct bioluminescent system which evolved independently, requiring a luciferase enzyme, a luciferin, a substrate binding fraction (SBF) that releases luciferin in the presence of mild reducing agents, molecular oxygen, and no additional cofactors. Similarly, the closely related Neoceroplatus spp, shares the same kind of luciferin-luciferase system of Orfelia fultoni. However, the molecular properties, identities and functions of luciferases, SBF and luciferin of Orfelia fultoni and other luminescent members of the Keroplatinae subfamily still remain to be fully elucidated. Using O. fultoni as a source of luciferase, and the recently discovered non-luminescent cave worm Neoditomiya sp as the main source of luciferin and SBF, we isolated and initially characterized these compounds. The luciferase of O. fultoni is a stable enzyme active as an apparent trimer (220 kDa) composed of ~70 kDa monomers, with an optimum pH of 7.8. The SBF, which is found in the black bodies in Orfelia fultoni and in smaller dark granules in Neoditomiya sp, consists of a high molecular weight complex of luciferin and proteins, apparently associated to mitochondria. The luciferin, partially purified from hot extracts by a combination of anion exchange chromatography and TLC, is a very polar and weakly fluorescent compound, whereas its oxidized product displays blue fluorescence with an emission spectrum matching the bioluminescence spectrum (~460 nm), indicating that it is oxyluciferin. The widespread occurrence of luciferin and SBF in both luminescent and non-luminescent Keroplatinae larvae indicate an additional important biological function for the substrate, and therefore the name keroplatin.}, }
@article {pmid32538150, year = {2020}, author = {Li, Y and Nourbakhsh, N and Pham, H and Tham, R and Zuckerman, JE and Singh, P}, title = {Evolution of altered tubular metabolism and mitochondrial function in sepsis-associated acute kidney injury.}, journal = {American journal of physiology. Renal physiology}, volume = {319}, number = {2}, pages = {F229-F244}, pmid = {32538150}, issn = {1522-1466}, support = {I01 BX002175/BX/BLRD VA/United States ; P30 DK079337/DK/NIDDK NIH HHS/United States ; R01 DK107852/DK/NIDDK NIH HHS/United States ; P30-DK 079337//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/International ; }, mesh = {Acute Kidney Injury/etiology/metabolism/*pathology ; Animals ; Disease Models, Animal ; Kidney/*injuries/metabolism ; Kidney Tubules, Proximal/metabolism ; Mice, Inbred C57BL ; Mitochondria/*metabolism ; Sepsis/*complications/metabolism ; }, abstract = {Sepsis-associated acute kidney injury (s-AKI) has a staggering impact in patients and lacks any treatment. Incomplete understanding of the pathogenesis of s-AKI is a major barrier to the development of effective therapies. We address the gaps in knowledge regarding renal oxygenation, tubular metabolism, and mitochondrial function in the pathogenesis of s-AKI using the cecal ligation and puncture (CLP) model in mice. At 24 h after CLP, renal oxygen delivery was reduced; however, fractional oxygen extraction was unchanged, suggesting inefficient renal oxygen utilization despite decreased glomerular filtration rate and filtered load. To investigate the underlying mechanisms, we examined temporal changes in mitochondrial function and metabolism at 4 and 24 h after CLP. At 4 h after CLP, markers of mitochondrial content and biogenesis were increased in CLP kidneys, but mitochondrial oxygen consumption rates were suppressed in proximal tubules. Interestingly, at 24 h, proximal tubular mitochondria displayed high respiratory capacity, but with decreased mitochondrial content, biogenesis, fusion, and ATP levels in CLP kidneys, suggesting decreased ATP synthesis efficiency. We further investigated metabolic reprogramming after CLP and observed reduced expression of fatty acid oxidation enzymes but increased expression of glycolytic enzymes at 24 h. However, assessment of functional glycolysis revealed lower glycolytic capacity, glycolytic reserve, and compensatory glycolysis in CLP proximal tubules, which may explain their susceptibility to injury. In conclusion, we demonstrated significant alterations in renal oxygenation, tubular mitochondrial function, and metabolic reprogramming in s-AKI, which may play an important role in the progression of injury and recovery from AKI in sepsis.}, }
@article {pmid32535166, year = {2020}, author = {Mower, JP}, title = {Variation in protein gene and intron content among land plant mitogenomes.}, journal = {Mitochondrion}, volume = {53}, number = {}, pages = {203-213}, doi = {10.1016/j.mito.2020.06.002}, pmid = {32535166}, issn = {1872-8278}, mesh = {Embryophyta/*genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; Introns ; Mitochondria/*genetics ; Phylogeny ; Trans-Splicing ; }, abstract = {The functional content of the mitochondrial genome (mitogenome) is highly diverse across eukaryotes. Among land plants, our understanding of the variation in mitochondrial gene and intron content is improving from concerted efforts to densely sample mitogenomes from diverse land plants. Here I review the current state of knowledge regarding the diversity in content of protein genes and introns in the mitogenomes of all major land plant lineages. Mitochondrial protein gene content is largely conserved among mosses and liverworts, but it varies substantially among and within other land plant lineages due to convergent losses of genes encoding ribosomal proteins and, to a lesser extent, genes for proteins involved in cytochrome c maturation and oxidative phosphorylation. Mitochondrial intron content is fairly stable within each major land plant lineage, but highly variable among lineages, resulting from occasional gains and many convergent losses over time. Trans-splicing has evolved dozens of times in various vascular plant lineages, particularly those with relatively higher rates of mitogenomic rearrangement. Across eukaryotes, mitochondrial protein gene and intron content has been shaped massive convergent evolution.}, }
@article {pmid32534185, year = {2020}, author = {Mao, X and Rossiter, SJ}, title = {Genome-wide data reveal discordant mitonuclear introgression in the intermediate horseshoe bat (Rhinolophus affinis).}, journal = {Molecular phylogenetics and evolution}, volume = {150}, number = {}, pages = {106886}, doi = {10.1016/j.ympev.2020.106886}, pmid = {32534185}, issn = {1095-9513}, support = {310482/ERC_/European Research Council/International ; }, mesh = {Animals ; Cell Nucleus/genetics ; Chiroptera/*classification/genetics ; DNA, Mitochondrial/classification/genetics ; Gene Flow ; Genome ; Mitochondria/*genetics ; Open Reading Frames/genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; }, abstract = {Closely related taxa often exhibit mitonuclear discordance attributed to introgression of mitochondrial DNA (mtDNA), yet few studies have considered the underlying causes of mtDNA introgression. Here we test for demographic versus adaptive processes as explanations for mtDNA introgression in three subspecies of the intermediate horseshoe bat (Rhinolophus affinis). We generated sequences of 1692 nuclear genes and 13 mitochondrial protein-coding genes for 48 individuals. Phylogenetic reconstructions based on 320 exon sequences and 2217 single nucleotide polymorphisms (SNPs) both revealed conflicts between the species tree and mtDNA tree. These results, together with geographic patterns of mitonuclear discordance, and shared identical or near-identical mtDNA sequences, suggest extensive introgression of mtDNA between the two parapatric mainland subspecies. Under demographic hypotheses, we would also expect to uncover traces of ncDNA introgression, however, population structure and gene flow analyses revealed little nuclear admixture. Furthermore, we found inconsistent estimates of the timing of population expansion and that of the most recent common ancestor for the clade containing introgressed haplotypes. Without a clear demographic explanation, we also examined whether introgression likely arises from adaptation. We found that five mtDNA genes contained fixed amino acid differences between introgressed and non-introgressed individuals, including putative positive selection found in one codon, although this did not show introgression. While our evidence for rejecting demographic hypotheses is arguably stronger than that for rejecting adaptation, we find no definitive support for either explanation. Future efforts will focus on larger-scale resequencing to decipher the underlying causes of discordant mitonuclear introgression in this system.}, }
@article {pmid32534184, year = {2020}, author = {Pozzi, L and Penna, A and Bearder, SK and Karlsson, J and Perkin, A and Disotell, TR}, title = {Cryptic diversity and species boundaries within the Paragalago zanzibaricus species complex.}, journal = {Molecular phylogenetics and evolution}, volume = {150}, number = {}, pages = {106887}, doi = {10.1016/j.ympev.2020.106887}, pmid = {32534184}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cytochromes b/genetics ; Forests ; Galagidae/anatomy &amp; histology/*classification/genetics ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; }, abstract = {The recently described genus Paragalago is a complex of several nocturnal and morphologically cryptic species distributed in the forests of eastern Africa. Species diversity within this genus has been mainly described using species-specific differences in their loud calls. However, molecular data are still lacking for this group and species boundaries remain unclear. In this study, we explore species diversity within the zanzibaricus-complex using a combination of mitochondrial and nuclear data and comparing multiple species delimitation methods. Our results consistently support the existence of three independent lineages, P. cocos, P. zanzibaricus, and P. granti, confirming previous hypotheses based on vocal data. We conclude that these three lineages represent valid cryptic species and we hypothesize that speciation within this complex was characterized by cycles of forest expansion and contraction in the Plio-Pleistocene.}, }
@article {pmid32534171, year = {2020}, author = {Pinevich, AV}, title = {Chloroplast history clarified by the criterion of light-harvesting complex.}, journal = {Bio Systems}, volume = {196}, number = {}, pages = {104173}, doi = {10.1016/j.biosystems.2020.104173}, pmid = {32534171}, issn = {1872-8324}, mesh = {*Biological Evolution ; Chlorophyll/*metabolism ; Chloroplasts/*metabolism ; Cyanobacteria/*metabolism ; Light-Harvesting Protein Complexes/*metabolism ; Pigments, Biological/metabolism ; Plastids/metabolism ; }, abstract = {Bacterial essence of mitochondria and chloroplasts was initially proclaimed in general outline. Later, the remarkable insight gave way to an elaborate hypothesis. Finally, it took shape of a theory confirmed by molecular biology data. In particular, the rrn operon, which is the key phylogeny marker, locates chloroplasts on the tree of Cyanobacteria. Chloroplast ancestry and diversity can be also traced with the rpoС and psbA genes, rbc operon, and other molecular criteria of prime importance. Another criterion, also highly reliable, is light-harvesting complex (LHC). LHC pigment and protein moieties specify light acclimation strategies in evolutionary retrospect and modern biosphere. The onset of symbiosis between eukaryotic host and pre-chloroplast, as well as further mutual adjustment of partners depended on physiological competence of LHC. In this review, the criterion of LHC is applied to the origin and diversity of chloroplasts. In particular, ancient cyanobacterium possessing tandem antenna (encoded by the cbp genes and the pbp genes, correspondingly), and defined as a prochlorophyte, is argued to be chloroplast ancestor.}, }
@article {pmid32534048, year = {2020}, author = {Vertika, S and Singh, KK and Rajender, S}, title = {Mitochondria, spermatogenesis, and male infertility - An update.}, journal = {Mitochondrion}, volume = {54}, number = {}, pages = {26-40}, doi = {10.1016/j.mito.2020.06.003}, pmid = {32534048}, issn = {1872-8278}, mesh = {DNA, Mitochondrial/genetics ; Energy Metabolism ; Humans ; Infertility, Male/*genetics/metabolism ; Male ; Mitochondria/genetics/*metabolism ; *Mutation ; Sperm Motility ; *Spermatogenesis ; Spermatozoa/metabolism/physiology ; }, abstract = {The incorporation of mitochondria in the eukaryotic cell is one of the most enigmatic events in the course of evolution. This important organelle was thought to be only the powerhouse of the cell, but was later learnt to perform many other indispensable functions in the cell. Two major contributions of mitochondria in spermatogenesis concern energy production and apoptosis. Apart from this, mitochondria also participate in a number of other processes affecting spermatogenesis and fertility. Mitochondria in sperm are arranged in the periphery of the tail microtubules to serve to energy demand for motility. Apart from this, the role of mitochondria in germ cell proliferation, mitotic regulation, and the elimination of germ cells by apoptosis are now well recognized. Eventually, mutations in the mitochondrial genome have been reported in male infertility, particularly in sluggish sperm (asthenozoospermia); however, heteroplasmy in the mtDNA and a complex interplay between the nucleus and mitochondria affect their penetrance. In this article, we have provided an update on the role of mitochondria in various events of spermatogenesis and male fertility and on the correlation of mitochondrial DNA mutations with male infertility.}, }
@article {pmid32520982, year = {2021}, author = {Enomoto, H and Mittal, N and Inomata, T and Arimura, T and Izumi, T and Kimura, A and Fukuda, K and Makino, S}, title = {Dilated cardiomyopathy-linked heat shock protein family D member 1 mutations cause up-regulation of reactive oxygen species and autophagy through mitochondrial dysfunction.}, journal = {Cardiovascular research}, volume = {117}, number = {4}, pages = {1118-1131}, doi = {10.1093/cvr/cvaa158}, pmid = {32520982}, issn = {1755-3245}, mesh = {Animals ; Animals, Genetically Modified ; Autophagosomes/genetics/metabolism/ultrastructure ; *Autophagy ; Cardiomyopathy, Dilated/diagnosis/*genetics/metabolism/pathology ; Chaperonin 60/*genetics/metabolism ; Disease Models, Animal ; Female ; Gene Expression Regulation, Developmental ; Genetic Predisposition to Disease ; HEK293 Cells ; Humans ; Male ; Mitochondria, Heart/genetics/*metabolism/ultrastructure ; Mitochondrial Dynamics ; Mitochondrial Proteins/*genetics/metabolism ; Myocytes, Cardiac/*metabolism/ultrastructure ; Nerve Tissue Proteins/*genetics/metabolism ; *Oxidative Stress ; Phenotype ; *Point Mutation ; Reactive Oxygen Species/*metabolism ; Zebrafish/genetics/metabolism ; Zebrafish Proteins/*genetics/metabolism ; }, abstract = {AIMS: During heart failure, the levels of circulatory heat shock protein family D member 1 (HSP60) increase. However, its underlying mechanism is still unknown. The apical domain of heat shock protein family D member 1 (HSPD1) is conserved throughout evolution. We found a point mutation in HSPD1 in a familial dilated cardiomyopathy (DCM) patient. A similar point mutation in HSPD1 in the zebrafish mutant, nbl, led to loss of its regenerative capacity and development of pericardial oedema under heat stress condition. In this study, we aimed to determine the direct involvement of HSPD1 in the development of DCM.<br><br>METHODS AND RESULTS: By Sanger method, we found a point mutation (Thr320Ala) in the apical domain of HSPD1, in one familial DCM patient, which was four amino acids away from the point mutation (Val324Glu) in the nbl mutant zebrafish. The nbl mutants showed atrio-ventricular block and sudden death at 8-month post-fertilization. Histological and microscopic analysis of the nbl mutant hearts showed decreased ventricular wall thickness, elevated level of reactive oxygen species (ROS), increased fibrosis, mitochondrial damage, and increased autophagosomes. mRNA and protein expression of autophagy-related genes significantly increased in nbl mutants. We established HEK293 stable cell lines of wild-type, nbl-type, and DCM-type HSPD1, with tetracycline-dependent expression. Compared to wild-type, both nbl- and DCM-type cells showed decreased cell growth, increased expression of ROS and autophagy-related genes, inhibition of the activity of mitochondrial electron transport chain complexes III and IV, and decreased mitochondrial fission and fusion.<br><br>CONCLUSION: Mutations in HSPD1 caused mitochondrial dysfunction and induced mitophagy. Mitochondrial dysfunction caused increased ROS and cardiac atrophy.}, }
@article {pmid32518318, year = {2020}, author = {Wang, E and Zhang, D and Braun, MS and Hotz-Wagenblatt, A and Pärt, T and Arlt, D and Schmaljohann, H and Bairlein, F and Lei, F and Wink, M}, title = {Can Mitogenomes of the Northern Wheatear (Oenanthe oenanthe) Reconstruct Its Phylogeography and Reveal the Origin of Migrant Birds?.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9290}, pmid = {32518318}, issn = {2045-2322}, mesh = {Animal Migration ; Evolution, Molecular ; *Genetic Speciation ; Genome, Mitochondrial/*genetics ; Germany ; Greece ; Haplotypes/genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; Phylogeny ; Songbirds/*classification/*genetics ; }, abstract = {The Northern Wheatear (Oenanthe oenanthe, including the nominate and the two subspecies O. o. leucorhoa and O. o. libanotica) and the Seebohm's Wheatear (Oenanthe seebohmi) are today regarded as two distinct species. Before, all four taxa were regarded as four subspecies of the Northern Wheatear. Their classification has exclusively been based on ecological and morphological traits, while their molecular characterization is still missing. With this study, we used next-generation sequencing to assemble 117 complete mitochondrial genomes covering O. o. oenanthe, O. o. leucorhoa and O. seebohmi. We compared the resolution power of each individual mitochondrial marker and concatenated marker sets to reconstruct the phylogeny and estimate speciation times of three taxa. Moreover, we tried to identify the origin of migratory wheatears caught on Helgoland (Germany) and on Crete (Greece). Mitogenome analysis revealed two different ancient lineages that separated around 400,000 years ago. Both lineages consisted of a mix of subspecies and species. The phylogenetic trees, as well as haplotype networks are incongruent with the present morphology-based classification. Mitogenome could not distinguish these presumed species. The genetic panmixia among present populations and taxa might be the consequence of mitochondrial introgression between ancient wheatear populations.}, }
@article {pmid32516069, year = {2020}, author = {Khan, KB and Praba, L and Abdul Jaffar Ali, H}, title = {Biological identification of ascidians from Vizhinjam Bay, southwest Coast of India using CO1 gene sequences.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {31}, number = {5}, pages = {209-217}, doi = {10.1080/24701394.2020.1772248}, pmid = {32516069}, issn = {2470-1408}, mesh = {Animals ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; India ; Mitochondria/*genetics ; Phylogeny ; Urochordata/*classification/genetics ; }, abstract = {Ascidians are ecologically important components of marine ecosystems, yet the taxonomy and diversity of ascidians remain largely unexplored. Only <60% of reported ascidian species in India have been taxonomically described and identified and the rest of the species remain unidentified due to uncertainty in the morphology-based identification. We explored the usefulness of CO1 gene sequences for molecular level identification and mtDNA data in assessing phylogenetic relationships of 15 ascidian species. The mean sequence divergences within and among the species fell into the mean divergence ranges found in ascidian group. Species that are most similar grouped together formed a cluster. Clusters of species in a clade indicate that the species are closely related. Species that are highly divergent formed a separate branch. This study has concluded that the CO1 gene sequence is an effective tool to ascertain the molecular taxonomical studies on ascidians.}, }
@article {pmid32512469, year = {2020}, author = {Brown, JA and Sammy, MJ and Ballinger, SW}, title = {An evolutionary, or "Mitocentric" perspective on cellular function and disease.}, journal = {Redox biology}, volume = {36}, number = {}, pages = {101568}, pmid = {32512469}, issn = {2213-2317}, support = {P30 DK079626/DK/NIDDK NIH HHS/United States ; R01 HL103859/HL/NHLBI NIH HHS/United States ; T32 HL007918/HL/NHLBI NIH HHS/United States ; }, mesh = {Cell Nucleus/metabolism ; *DNA, Mitochondrial/genetics/metabolism ; Eukaryotic Cells ; *Mitochondria/genetics ; }, abstract = {The incidence of common, metabolic diseases (e.g. obesity, cardiovascular disease, diabetes) with complex genetic etiology has been steadily increasing nationally and globally. While identification of a genetic model that explains susceptibility and risk for these diseases has been pursued over several decades, no clear paradigm has yet been found to disentangle the genetic basis of polygenic/complex disease development. Since the evolution of the eukaryotic cell involved a symbiotic interaction between the antecedents of the mitochondrion and nucleus (which itself is a genetic hybrid), we suggest that this history provides a rational basis for investigating whether genetic interaction and co-evolution of these genomes still exists. We propose that both mitochondrial and Mendelian, or "mito-Mendelian" genetics play a significant role in cell function, and thus disease risk. This paradigm contemplates the natural variation and co-evolution of both mitochondrial and nuclear DNA backgrounds on multiple mitochondrial functions that are discussed herein, including energy production, cell signaling and immune response, which collectively can influence disease development. At the nexus of these processes is the economy of mitochondrial metabolism, programmed by both mitochondrial and nuclear genomes.}, }
@article {pmid32512195, year = {2020}, author = {Sun, S and Li, Q and Kong, L and Yu, H}, title = {Evolution of mitochondrial gene arrangements in Arcidae (Bivalvia: Arcida) and their phylogenetic implications.}, journal = {Molecular phylogenetics and evolution}, volume = {150}, number = {}, pages = {106879}, doi = {10.1016/j.ympev.2020.106879}, pmid = {32512195}, issn = {1095-9513}, mesh = {Animals ; Arcidae/*classification/genetics ; *Evolution, Molecular ; Gene Order ; Mitochondria/*genetics ; Open Reading Frames/genetics ; Phylogeny ; }, abstract = {Arcidae is a diverse group of ark shells with over 260 described species. The phylogenetic relationships and the evolution of the mitochondrial genomes in this family were poorly understood. Comparisons of mitogenomes have been widely used to explore the phylogenetic relationship among animal taxa. We described the complete mitogenomes of Arca navicularis, Scapharca gubernaculum and one nearly complete mitogenome of Anadara consociata. The mitogenome of A. navicularis (18,103 bp) is currently the smallest known Arcidae mitogenome, while the mitogenomes of S. gubernaculum (45,697 bp) and A. consociata (44,034 bp) are relatively large. The mitochondrial gene orders of the three taxa were substantially different from each other, as well as the patterns found in other ark shells. The relationships among Arcidae species recovered from different mitochondrial characters (nucleotide sequence versus gene order) were in disagreement. The phylogeny based on nucleotide sequences did not support the monophyly of Arcidae, as Cucullaea labiata (Cucullaeidae) appeared as a subgroup within Arcinae, rather than sister group to the family Arcidae. In addition, we presented the first time-calibrated evolutionary tree of Arcidae based on mitochondrial DNA (mtDNA) sequences, which placed the deepest divergence within Arcidae at 342.36 million years ago (Mya), around the Carboniferous (360-300 Mya).}, }
@article {pmid32502904, year = {2020}, author = {Shah, SI and Ong, HL and Demuro, A and Ullah, G}, title = {PunctaSpecks: A tool for automated detection, tracking, and analysis of multiple types of fluorescently labeled biomolecules.}, journal = {Cell calcium}, volume = {89}, number = {}, pages = {102224}, pmid = {32502904}, issn = {1532-1991}, support = {R01 AG053988/AG/NIA NIH HHS/United States ; }, mesh = {Algorithms ; Amyloid beta-Peptides/metabolism ; Automation ; Calcium/metabolism ; Calcium Signaling/drug effects ; Cell Membrane/drug effects/metabolism ; Cerebral Cortex/cytology ; Diffusion ; Fluorescent Dyes/*chemistry ; HEK293 Cells ; Humans ; Inositol 1,4,5-Trisphosphate/pharmacology ; Kinetics ; Neurons/drug effects/metabolism ; ORAI1 Protein/metabolism ; *Software ; Stromal Interaction Molecule 1/metabolism ; }, abstract = {Recent advances in imaging technology and fluorescent probes have made it possible to gain information about the dynamics of subcellular processes at unprecedented spatiotemporal scales. Unfortunately, a lack of automated tools to efficiently process the resulting imaging data encoding fine details of the biological processes remains a major bottleneck in utilizing the full potential of these powerful experimental techniques. Here we present a computational tool, called PunctaSpecks, that can characterize fluorescence signals arising from a wide range of biological molecules under normal and pathological conditions. Among other things, the program can calculate the number, areas, life-times, and amplitudes of fluorescence signals arising from multiple sources, track diffusing fluorescence sources like moving mitochondria, and determine the overlap probability of two processes or organelles imaged using indicator dyes of different colors. We have tested PunctaSpecks on synthetic time-lapse movies containing mobile fluorescence objects of various sizes, mimicking the activity of biomolecules. The robustness of the software is tested by varying the level of noise along with random but known pattern of appearing, disappearing, and movement of these objects. Next, we use PunctaSpecks to characterize protein-protein interaction involved in store-operated Ca[2+] entry through the formation and activation of plasma membrane-bound ORAI1 channel and endoplasmic reticulum membrane-bound stromal interaction molecule (STIM), the evolution of inositol 1,4,5-trisphosphate (IP3)-induced Ca[2+] signals from sub-micrometer size local events into global waves in human cortical neurons, and the activity of Alzheimer's disease-associated β amyloid pores in the plasma membrane. The tool can also be used to study other dynamical processes imaged through fluorescence molecules. The open source algorithm allows for extending the program to analyze more than two types of biomolecules visualized using markers of different colors.}, }
@article {pmid32499047, year = {2020}, author = {Diederich, NJ and Uchihara, T and Grillner, S and Goetz, CG}, title = {The Evolution-Driven Signature of Parkinson's Disease.}, journal = {Trends in neurosciences}, volume = {43}, number = {7}, pages = {475-492}, doi = {10.1016/j.tins.2020.05.001}, pmid = {32499047}, issn = {1878-108X}, mesh = {Axons ; Cerebral Cortex ; Humans ; Mitochondria ; Neurons ; *Parkinson Disease/genetics ; }, abstract = {In this review, we approach Parkinson's disease (PD) in the context of an evolutionary mismatch of central nervous system functions. The neurons at risk have hyperbranched axons, extensive transmitter release sites, display spontaneous spiking, and elevated mitochondrial stress. They function in networks largely unchanged throughout vertebrate evolution, but now connecting to the expanded human cortex. Their breakdown is favoured by longevity. At the cellular level, mitochondrial dysfunction starts at the synapses, then involves axons and cell bodies. At the behavioural level, network dysfunctions provoke the core motor syndrome of parkinsonism including freezing and failed gait automatization, and non-motor deficits including inactive blindsight and autonomic dysregulation. The proposed evolutionary re-interpretation of PD-prone cellular phenotypes and of prototypical clinical symptoms allows a new conceptual framework for future research.}, }
@article {pmid32497832, year = {2020}, author = {Klabacka, RL and Wood, PL and McGuire, JA and Oaks, JR and Grismer, LL and Grismer, JL and Aowphol, A and Sites, JW}, title = {Rivers of Indochina as potential drivers of lineage diversification in the spotted flying lizard (Draco maculatus) species complex.}, journal = {Molecular phylogenetics and evolution}, volume = {150}, number = {}, pages = {106861}, doi = {10.1016/j.ympev.2020.106861}, pmid = {32497832}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Biodiversity ; Brain-Derived Neurotrophic Factor/classification/genetics ; Indochina ; Lizards/*classification/genetics ; Mitochondria/genetics ; NADH Dehydrogenase/classification/genetics ; Phylogeny ; Phylogeography ; Protein Subunits/classification/genetics ; RNA, Ribosomal/classification/genetics ; }, abstract = {Southeast Asia hosts a rich concentration of biodiversity within multiple biodiversity hotspots. Indochina, a region with remarkably high levels of in situ diversification, possesses five major rivers (Ayeyarwady, Chiang Mai, Mekong, Red, and Salween), several of which coincide with phylogenetic breaks of terrestrial taxa. Draco maculatus possesses a range that stretches across Indochina, which widespread geographic distribution along with potential discrete variation within subspecies alludes to the possibility of this taxon constituting multiple divergent lineages. Using sequence data from three mitochondrial (12S, 16S, and ND2) and three nuclear (BDNF, CMOS, and PNN) genes, we provide the first estimated phylogeny of this hypothesized species complex and examine its phylogeographic architecture with maximum likelihood and Bayes factor delimitation (BFD) approaches. Our results support multiple divergent lineages with phylogenetic breaks coincident with rivers, indicating that river barriers may be contributing to the elevated levels of in situ diversification of Indochina.}, }
@article {pmid32497542, year = {2020}, author = {Changbunjong, T and Weluwanarak, T and Sedwisai, P and Ruangsittichai, J and Duvallet, G and Chareonviriyaphap, T}, title = {New records and DNA barcoding of deer flies, Chrysops (Diptera: Tabanidae) in Thailand.}, journal = {Acta tropica}, volume = {210}, number = {}, pages = {105532}, doi = {10.1016/j.actatropica.2020.105532}, pmid = {32497542}, issn = {1873-6254}, mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; Diptera/*classification ; Electron Transport Complex IV/genetics ; Entomology ; Mitochondria/genetics ; Thailand ; }, abstract = {Chrysops spp. or deer flies (Diptera: Tabanidae) are hematophagous flies of medical and veterinary importance and some species are important vectors of Trypanosoma evansi, the causative agent of surra in Thailand. However, data regarding deer fly species and their molecular identification are limited. Accurate species identification will indicate the appropriate control measures. In this study, an entomological survey of deer flies from different sites in Thailand between May 2018 and June 2019 were conducted. In addition, mitochondrial cytochrome oxidase subunit I (COI) barcoding region was used for species identification. A total of 82 females were collected and 6 species were identified. Of these, three species are new records for Thailand: C. designatus, C. fuscomarginalis and C. vanderwulpi bringing the species total found in Thailand to nine. The COI sequences revealed an intraspecific divergence of 0.0%-2.65% and an interspecific divergence of 7.03%-13.47%. Phylogenetic analysis showed that all deer fly species were clearly separated into distinct clusters according to morphologically identified species. These results indicated that COI barcodes were capable in discriminating between deer fly species on the basis of the barcoding gap and phylogenetic analysis. Therefore, DNA barcoding is a valuable tool for species identification of deer flies in Thailand.}, }
@article {pmid32493270, year = {2020}, author = {de Paula Freitas, FC and Lourenço, AP and Nunes, FMF and Paschoal, AR and Abreu, FCP and Barbin, FO and Bataglia, L and Cardoso-Júnior, CAM and Cervoni, MS and Silva, SR and Dalarmi, F and Del Lama, MA and Depintor, TS and Ferreira, KM and Gória, PS and Jaskot, MC and Lago, DC and Luna-Lucena, D and Moda, LM and Nascimento, L and Pedrino, M and Oliveira, FR and Sanches, FC and Santos, DE and Santos, CG and Vieira, J and Barchuk, AR and Hartfelder, K and Simões, ZLP and Bitondi, MMG and Pinheiro, DG}, title = {The nuclear and mitochondrial genomes of Frieseomelitta varia - a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {386}, pmid = {32493270}, issn = {1471-2164}, support = {454103/2014-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 2015/06657-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {Animals ; Bees/classification/genetics/*physiology ; Behavior, Animal ; Cell Nucleus/*genetics ; Computational Biology/*methods ; Gene Order ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Interspersed Repetitive Sequences ; Mitochondria/*genetics ; RNA, Long Noncoding/genetics ; Social Behavior ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Most of our understanding on the social behavior and genomics of bees and other social insects is centered on the Western honey bee, Apis mellifera. The genus Apis, however, is a highly derived branch comprising less than a dozen species, four of which genomically characterized. In contrast, for the equally highly eusocial, yet taxonomically and biologically more diverse Meliponini, a full genome sequence was so far available for a single Melipona species only. We present here the genome sequence of Frieseomelitta varia, a stingless bee that has, as a peculiarity, a completely sterile worker caste.<br><br>RESULTS: The assembly of 243,974,526 high quality Illumina reads resulted in a predicted assembled genome size of 275&#x2009;Mb composed of 2173 scaffolds. A BUSCO analysis for the 10,526 predicted genes showed that these represent 96.6% of the expected hymenopteran orthologs. We also predicted 169,371 repetitive genomic components, 2083 putative transposable elements, and 1946 genes for non-coding RNAs, largely long non-coding RNAs. The mitochondrial genome comprises 15,144&#x2009;bp, encoding 13 proteins, 22 tRNAs and 2 rRNAs. We observed considerable rearrangement in the mitochondrial gene order compared to other bees. For an in-depth analysis of genes related to social biology, we manually checked the annotations for 533 automatically predicted gene models, including 127 genes related to reproductive processes, 104 to development, and 174 immunity-related genes. We also performed specific searches for genes containing transcription factor domains and genes related to neurogenesis and chemosensory communication.<br><br>CONCLUSIONS: The total genome size for F. varia is similar to the sequenced genomes of other bees. Using specific prediction methods, we identified a large number of repetitive genome components and long non-coding RNAs, which could provide the molecular basis for gene regulatory plasticity, including worker reproduction. The remarkable reshuffling in gene order in the mitochondrial genome suggests that stingless bees may be a hotspot for mtDNA evolution. Hence, while being just the second stingless bee genome sequenced, we expect that subsequent targeting of a selected set of species from this diverse clade of highly eusocial bees will reveal relevant evolutionary signals and trends related to eusociality in these important pollinators.}, }
@article {pmid32492081, year = {2020}, author = {Yamamoto, YH and Kasai, A and Omori, H and Takino, T and Sugihara, M and Umemoto, T and Hamasaki, M and Hatta, T and Natsume, T and Morimoto, RI and Arai, R and Waguri, S and Sato, M and Sato, K and Bar-Nun, S and Yoshimori, T and Noda, T and Nagata, K}, title = {ERdj8 governs the size of autophagosomes during the formation process.}, journal = {The Journal of cell biology}, volume = {219}, number = {8}, pages = {}, pmid = {32492081}, issn = {1540-8140}, support = {P01 AG054407/AG/NIA NIH HHS/United States ; R37 AG026647/AG/NIA NIH HHS/United States ; RF1 AG057296/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Animals, Genetically Modified ; Autophagosomes/genetics/*metabolism/ultrastructure ; Autophagy-Related Proteins/genetics/metabolism ; CDP-Diacylglycerol-Inositol 3-Phosphatidyltransferase/genetics/metabolism ; COS Cells ; Caenorhabditis elegans/embryology/genetics/metabolism ; Caenorhabditis elegans Proteins/genetics/metabolism ; Chlorocebus aethiops ; Endoplasmic Reticulum/genetics/*metabolism/ultrastructure ; HSP40 Heat-Shock Proteins/genetics/*metabolism ; HeLa Cells ; Humans ; *Macroautophagy ; Mitochondria/metabolism/ultrastructure ; }, abstract = {In macroautophagy, membrane structures called autophagosomes engulf substrates and deliver them for lysosomal degradation. Autophagosomes enwrap a variety of targets with diverse sizes, from portions of cytosol to larger organelles. However, the mechanism by which autophagosome size is controlled remains elusive. We characterized a novel ER membrane protein, ERdj8, in mammalian cells. ERdj8 localizes to a meshwork-like ER subdomain along with phosphatidylinositol synthase (PIS) and autophagy-related (Atg) proteins. ERdj8 overexpression extended the size of the autophagosome through its DnaJ and TRX domains. ERdj8 ablation resulted in a defect in engulfing larger targets. C. elegans, in which the ERdj8 orthologue dnj-8 was knocked down, could perform autophagy on smaller mitochondria derived from the paternal lineage but not the somatic mitochondria. Thus, ERdj8 may play a critical role in autophagosome formation by providing the capacity to target substrates of diverse sizes for degradation.}, }
@article {pmid32490527, year = {2020}, author = {Luévano-Martínez, LA and Duncan, AL}, title = {Origin and diversification of the cardiolipin biosynthetic pathway in the Eukarya domain.}, journal = {Biochemical Society transactions}, volume = {48}, number = {3}, pages = {1035-1046}, doi = {10.1042/BST20190967}, pmid = {32490527}, issn = {1470-8752}, support = {BB/R00126X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Archaea/*enzymology ; Bacteria/*enzymology ; Binding Sites ; Biosynthetic Pathways ; Cardiolipins/*biosynthesis ; Catalysis ; Eukaryota/*enzymology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Hydrolases/metabolism ; Mitochondria/metabolism ; Models, Molecular ; Phosphatidylglycerols/*metabolism ; Phospholipids/metabolism ; Phosphoric Monoester Hydrolases/metabolism ; Phylogeny ; }, abstract = {Cardiolipin (CL) and its precursor phosphatidylglycerol (PG) are important anionic phospholipids widely distributed throughout all domains of life. They have key roles in several cellular processes by shaping membranes and modulating the activity of the proteins inserted into those membranes. They are synthesized by two main pathways, the so-called eukaryotic pathway, exclusively found in mitochondria, and the prokaryotic pathway, present in most bacteria and archaea. In the prokaryotic pathway, the first and the third reactions are catalyzed by phosphatidylglycerol phosphate synthase (Pgps) belonging to the transferase family and cardiolipin synthase (Cls) belonging to the hydrolase family, while in the eukaryotic pathway, those same reactions are catalyzed by unrelated homonymous enzymes: Pgps of the hydrolase family and Cls of the transferase family. Because of the enzymatic arrangement found in both pathways, it seems that the eukaryotic pathway evolved by convergence to the prokaryotic pathway. However, since mitochondria evolved from a bacterial endosymbiont, it would suggest that the eukaryotic pathway arose from the prokaryotic pathway. In this review, it is proposed that the eukaryote pathway evolved directly from a prokaryotic pathway by the neofunctionalization of the bacterial enzymes. Moreover, after the eukaryotic radiation, this pathway was reshaped by horizontal gene transfers or subsequent endosymbiotic processes.}, }
@article {pmid32486979, year = {2020}, author = {Allen, R and Ryan, H and Davis, BW and King, C and Frantz, L and Irving-Pease, E and Barnett, R and Linderholm, A and Loog, L and Haile, J and Lebrasseur, O and White, M and Kitchener, AC and Murphy, WJ and Larson, G}, title = {A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1928}, pages = {20200690}, pmid = {32486979}, issn = {1471-2954}, mesh = {Animals ; *Biological Evolution ; Fertility ; Genetic Drift ; *Hybridization, Genetic ; Infertility ; *Mammals ; Mitochondria/genetics ; Reproduction ; }, abstract = {Numerous pairs of evolutionarily divergent mammalian species have been shown to produce hybrid offspring. In some cases, F1 hybrids are able to produce F2s through matings with F1s. In other instances, the hybrids are only able to produce offspring themselves through backcrosses with a parent species owing to unisexual sterility (Haldane's Rule). Here, we explicitly tested whether genetic distance, computed from mitochondrial and nuclear genes, can be used as a proxy to predict the relative fertility of the hybrid offspring resulting from matings between species of terrestrial mammals. We assessed the proxy's predictive power using a well-characterized felid hybrid system, and applied it to modern and ancient hominins. Our results revealed a small overlap in mitochondrial genetic distance values that distinguish species pairs whose calculated distances fall within two categories: those whose hybrid offspring follow Haldane's Rule, and those whose hybrid F1 offspring can produce F2s. The strong correlation between genetic distance and hybrid fertility demonstrated here suggests that this proxy can be employed to predict whether the hybrid offspring of two mammalian species will follow Haldane's Rule.}, }
@article {pmid32486081, year = {2020}, author = {Tan, M and Tol, HTAV and Rosenkranz, D and Roovers, EF and Damen, MJ and Stout, TAE and Wu, W and Roelen, BAJ}, title = {PIWIL3 Forms a Complex with TDRKH in Mammalian Oocytes.}, journal = {Cells}, volume = {9}, number = {6}, pages = {}, pmid = {32486081}, issn = {2073-4409}, mesh = {Amino Acid Sequence ; Animals ; Arginine/metabolism ; Argonaute Proteins/chemistry/*metabolism ; Cattle ; Cytoplasm/metabolism ; DNA Transposable Elements/genetics ; Embryonic Development ; Exoribonucleases/metabolism ; Mitochondria/metabolism ; Oocytes/*metabolism ; Protein Binding ; Protein Transport ; RNA, Small Interfering/metabolism ; RNA-Binding Proteins/chemistry/*metabolism ; }, abstract = {P-element induced wimpy testis (PIWIs) are crucial guardians of genome integrity, particularly in germ cells. While mammalian PIWIs have been primarily studied in mouse and rat, a homologue for the human PIWIL3 gene is absent in the Muridae family, and hence the unique function of PIWIL3 in germ cells cannot be effectively modeled by mouse knockouts. Herein, we investigated the expression, distribution, and interaction of PIWIL3 in bovine oocytes. We localized PIWIL3 to mitochondria, and demonstrated that PIWIL3 expression is stringently controlled both spatially and temporally before and after fertilization. Moreover, we identified PIWIL3 in a mitochondrial-recruited three-membered complex with Tudor and KH domain-containing protein (TDRKH) and poly(A)-specific ribonuclease-like domain containing 1 (PNLDC1), and demonstrated by mutagenesis that PIWIL3 N-terminal arginines are required for complex assembly. Finally, we sequenced the piRNAs bound to PIWIL3-TDRKH-PNLDC1 and report here that about 50% of these piRNAs map to transposable elements, recapitulating the important role of PIWIL3 in maintaining genome integrity in mammalian oocytes.}, }
@article {pmid32485941, year = {2020}, author = {Mendoza, H and Perlin, MH and Schirawski, J}, title = {Mitochondrial Inheritance in Phytopathogenic Fungi-Everything Is Known, or Is It?.}, journal = {International journal of molecular sciences}, volume = {21}, number = {11}, pages = {}, pmid = {32485941}, issn = {1422-0067}, support = {GMB180621//National Science Foundation/ ; SCHI 1114/3-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Basidiomycota/genetics ; Cell Nucleus/*genetics ; Cryptococcus neoformans/genetics ; DNA, Mitochondrial/*genetics ; Fungi/*genetics ; Genes, Fungal ; Haploidy ; Saccharomyces/genetics ; }, abstract = {Mitochondria are important organelles in eukaryotes that provide energy for cellular processes. Their function is highly conserved and depends on the expression of nuclear encoded genes and genes encoded in the organellar genome. Mitochondrial DNA replication is independent of the replication control of nuclear DNA and as such, mitochondria may behave as selfish elements, so they need to be controlled, maintained and reliably inherited to progeny. Phytopathogenic fungi meet with special environmental challenges within the plant host that might depend on and influence mitochondrial functions and services. We find that this topic is basically unexplored in the literature, so this review largely depends on work published in other systems. In trying to answer elemental questions on mitochondrial functioning, we aim to introduce the aspect of mitochondrial functions and services to the study of plant-microbe-interactions and stimulate phytopathologists to consider research on this important organelle in their future projects.}, }
@article {pmid32483316, year = {2020}, author = {Lord, E and Collins, C and deFrance, S and LeFebvre, MJ and Pigière, F and Eeckhout, P and Erauw, C and Fitzpatrick, SM and Healy, PF and Martínez-Polanco, MF and Garcia, JL and Ramos Roca, E and Delgado, M and Sánchez Urriago, A and Peña Léon, GA and Toyne, JM and Dahlstedt, A and Moore, KM and Laguer Diaz, C and Zori, C and Matisoo-Smith, E}, title = {Ancient DNA of Guinea Pigs (Cavia spp.) Indicates a Probable New Center of Domestication and Pathways of Global Distribution.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8901}, pmid = {32483316}, issn = {2045-2322}, mesh = {Animals ; Belgium ; Bolivia ; Colombia ; DNA, Ancient/*analysis ; DNA, Mitochondrial/*analysis ; Domestication ; Evolution, Molecular ; Guinea Pigs/*classification/genetics ; Mitochondria/*genetics ; Peru ; Phylogeny ; Phylogeography ; Population Dynamics ; Puerto Rico ; Sequence Analysis, DNA/*veterinary ; United States ; }, abstract = {Guinea pigs (Cavia spp.) have a long association with humans. From as early as 10,000 years ago they were a wild food source. Later, domesticated Cavia porcellus were dispersed well beyond their native range through pre-Columbian exchange networks and, more recently, widely across the globe. Here we present 46 complete mitogenomes of archaeological guinea pigs from sites in Peru, Bolivia, Colombia, the Caribbean, Belgium and the United States to elucidate their evolutionary history, origins and paths of dispersal. Our results indicate an independent centre of domestication of Cavia in the eastern Colombian Highlands. We identify a Peruvian origin for the initial introduction of domesticated guinea pigs (Cavia porcellus) beyond South America into the Caribbean. We also demonstrate that Peru was the probable source of the earliest known guinea pigs transported, as part of the exotic pet trade, to both Europe and the southeastern United States. Finally, we identify a modern reintroduction of guinea pigs to Puerto Rico, where local inhabitants use them for food. This research demonstrates that the natural and cultural history of guinea pigs is more complex than previously known and has implications for other studies regarding regional to global-scale studies of mammal domestication, translocation, and distribution.}, }
@article {pmid32483282, year = {2020}, author = {Ajene, I and Khamis, FM and Pietersen, G and van Asch, B}, title = {Mitochondrial genetic variation reveals phylogeographic structure and cryptic diversity in Trioza erytreae.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8893}, pmid = {32483282}, issn = {2045-2322}, mesh = {Animals ; Citrus/*parasitology ; Ethiopia ; Europe ; *Genetic Variation ; Genome Size ; Genome, Mitochondrial ; Haplotypes ; Hemiptera/*classification/genetics ; Kenya ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; South Africa ; Uganda ; Whole Genome Sequencing/*veterinary ; }, abstract = {Trioza erytreae is the main vector for 'Candidatus Liberibacter africanus', the causative agent of African Citrus Greening disease. The insect is widespread in Africa, and has recently disseminated to Southwestern Europe. This study aimed at generating reference mitogenome sequences for T. erytreae, as a background for future genetic diversity surveys. Complete mitochondrial sequences of three specimens collected in Ethiopia, Uganda and South Africa were recovered using Ion Torrent technology. The mitogenomes of T. erytreae from Uganda and Ethiopia were highly similar, and distinct from that found in South Africa. The phylogeographic structure of T. erytreae was assessed using genetic clustering and pairwise distances, based on a dataset of public COI sequences recorded as T. erytreae. The dataset revealed ten haplotypes with strong phylogeographic structure in Africa and Europe. Three haplotypes found in Kenya on Clausena anisata belonged to pairs separated by distances as high as 11.2%, and were basal to all other sequences. These results indicate that not all sequences identified as T. erytreae belong to the same species, and that some degree of specificity with different plant hosts is likely to exist. This study provides new baseline information on the diversity of T. erytreae, with potential implications for the epidemiology of African Citrus Greening disease.}, }
@article {pmid32482927, year = {2020}, author = {Zou, Y and Xu, M and Ren, S and Liang, N and Han, C and Nan, X and Shi, J}, title = {Taxonomy and phylogenetic relationship of zokors.}, journal = {Journal of genetics}, volume = {99}, number = {}, pages = {}, pmid = {32482927}, issn = {0973-7731}, mesh = {Animals ; Classification/*methods ; Cytochromes b/*genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Rodentia/*genetics ; Tibet ; }, abstract = {Zokor (Myospalacinae) is one of the subterranean rodents, endemic to east Asia. Due to the convergent and parallel evolution induced by its special lifestyles, the controversies in morphological classification of zokor appeared at the level of family and genus. To resolve these controversies about taxonomy and phylogeny, the phylogenetic relationships of 20 species of Muroidea and six species of zokors were studied based on complete mitochondrial genome and mitochondrial Cytb gene, respectively. Phylogeny analysis of 20 species of Muroidea indicated that the zokor belonged to the family Spalacidae, and it was closer to mole rat rather than bamboo rat. Besides, by investigating the phylogenetic relationships of six species of zokors, the status of two genera of Eospalax and Myospalax was affirmed because the two clades differentiated in phylogenetic tree represented two types of zokors, convex occiput type and flat occiput type, respectively. In addition, the two origins in Eospalax were found diverged at 3.71 million years ago (Ma) based on estimation of divergence time. It is suggested that the climate and ecology changes caused by the Qinghai-Tibet Plateau uplift event in 3.6 Ma led to the inner divergence of Eospalax. The intraspecific phylogenetic relationships of partial zokors were well resolved, the two clades of Eospalax cansus represented two geographical populations, respectively, and the divergent pattern of Eospalax baileyi was characterized by allopatric divergence spatially. In this study, we explored the taxonomic status and phylogenetic relationships of Myospalacinae at the molecular level. These works would be significant to understanding the evolutionary process and to clarify the mechanism of differentiation of Myospalacinae.}, }
@article {pmid32475470, year = {2020}, author = {Gibellini, L and De Gaetano, A and Mandrioli, M and Van Tongeren, E and Bortolotti, CA and Cossarizza, A and Pinti, M}, title = {The biology of Lonp1: More than a mitochondrial protease.}, journal = {International review of cell and molecular biology}, volume = {354}, number = {}, pages = {1-61}, doi = {10.1016/bs.ircmb.2020.02.005}, pmid = {32475470}, issn = {1937-6448}, mesh = {ATP-Dependent Proteases/*metabolism ; Animals ; Humans ; Mice ; Mitochondria/*enzymology ; Mitochondrial Proteins/*metabolism ; Neoplasms/enzymology/pathology ; }, abstract = {Initially discovered as a protease responsible for degradation of misfolded or damaged proteins, the mitochondrial Lon protease (Lonp1) turned out to be a multifaceted enzyme, that displays at least three different functions (proteolysis, chaperone activity, binding of mtDNA) and that finely regulates several cellular processes, within and without mitochondria. Indeed, LONP1 in humans is ubiquitously expressed, and is involved in regulation of response to oxidative stress and, heat shock, in the maintenance of mtDNA, in the regulation of mitophagy. Furthermore, its proteolytic activity can regulate several biochemical pathways occurring totally or partially within mitochondria, such as TCA cycle, oxidative phosphorylation, steroid and heme biosynthesis and glutamine production. Because of these multiple activities, Lon protease is highly conserved throughout evolution, and mutations occurring in its gene determines severe diseases in humans, including a rare syndrome characterized by Cerebral, Ocular, Dental, Auricular and Skeletal anomalies (CODAS). Finally, alterations of LONP1 regulation in humans can favor tumor progression and aggressiveness, further highlighting the crucial role of this enzyme in mitochondrial and cellular homeostasis.}, }
@article {pmid32473333, year = {2020}, author = {Kong, L and Li, Y and Kocot, KM and Yang, Y and Qi, L and Li, Q and Halanych, KM}, title = {Mitogenomics reveals phylogenetic relationships of Arcoida (Mollusca, Bivalvia) and multiple independent expansions and contractions in mitochondrial genome size.}, journal = {Molecular phylogenetics and evolution}, volume = {150}, number = {}, pages = {106857}, doi = {10.1016/j.ympev.2020.106857}, pmid = {32473333}, issn = {1095-9513}, mesh = {Animals ; Arcidae/*classification/genetics ; Bayes Theorem ; Evolution, Molecular ; Genome Size ; Mitochondria/*genetics ; Open Reading Frames/genetics ; Phylogeny ; }, abstract = {Arcoida, comprising about 570 species of blood cockles, is an ecologically and economically important lineage of bivalve molluscs. Current classification of arcoids is largely based on morphology, which shows widespread homoplasy. Despite two recent studies employing multi-locus analyses with broad sampling of Arcoida, evolutionary relationships among major lineages remain controversial. Interestingly, mitochondrial genomes of several ark shell species are 2-3 times larger than those found in most bilaterians, and are among the largest bilaterian mitochondrial genomes reported to date. These results highlight the need of detailed phylogenetic study to explore evolutionary relationships within Arcoida so that the evolution of mitochondrial genome size can be understood. To this end, we sequenced 17 mitochondrial genomes and compared them with publicly available data, including those from other lineages of Arcoida with emphasis on the subclade Arcoidea species. Our phylogenetic analyses indicate that Noetiidae, Cucullaeidae and Glycymerididae are nested within a polyphyletic Arcidae. Moreover, we find multiple independent expansions and potential contractions of mitochondrial genome size, suggesting that the large mitochondrial genome is not a shared ancestral feature in Arcoida. We also examined tandem repeats and inverted repeats in non-coding regions and investigated the presence of such repeats with relation to genome size variation. Our results suggest that tandem repeats might facilitate intraspecific mitochondrial genome size variation, and that inverted repeats, which could be derived from transposons, might be responsible for mitochondrial genome expansions and contractions. We show that mitochondrial genome size in Arcoida is more dynamic than previously understood and provide insights into evolution of mitochondrial genome size variation in metazoans.}, }
@article {pmid32468258, year = {2020}, author = {Leelagud, P and Kongsila, S and Vejchasarn, P and Darwell, K and Phansenee, Y and Suthanthangjai, A and Uparang, C and Kawichai, R and Yajai, P and Boonsa-Nga, K and Chamarerk, V and Jairin, J}, title = {Genetic diversity of Asian rice gall midge based on mtCOI gene sequences and identification of a novel resistance locus gm12 in rice cultivar MN62M.}, journal = {Molecular biology reports}, volume = {47}, number = {6}, pages = {4273-4283}, pmid = {32468258}, issn = {1573-4978}, support = {Project No. 27363//Rice Department/ ; }, mesh = {Animals ; Chromosome Mapping/methods ; Cyclooxygenase 1/*genetics/metabolism ; Diptera/genetics ; Genes, Mitochondrial/genetics ; Genetic Linkage/genetics ; Genetic Loci/genetics ; Genetic Markers/genetics ; Genetic Variation/genetics ; Mitochondria/enzymology/genetics ; Nematocera/*genetics ; Oryza/*genetics/parasitology ; Phylogeny ; Plant Diseases/genetics ; }, abstract = {The rice gall midge (RGM), Orseolia oryzae (Wood-Mason), is one of the most destructive insect pests of rice, and it causes significant yield losses annually in Asian countries. The development of resistant rice varieties is considered as the most effective and economical approach for maintaining yield stability by controlling RGM. Identification of resistance genes will help in marker-assisted selection (MAS) to pyramid the resistance genes and develop a durable resistance variety against RGM in areas with frequent outbreaks. In this study, a mitochondrial cytochrome oxidase subunit I (mtCOI) was used to analyze the genetic diversity among Thai RGM populations. The phylogenetic tree indicated that the Thai RGM populations were homogeneously distributed throughout the country. The reactions of the resistant rice varieties carrying different resistance genes revealed different RGM biotypes in Thailand. The Thai rice landrace MN62M showed resistance to all RGM populations used in this study. We identified a novel genetic locus for resistance to RGM, designated as gm12, on the short arm of rice chromosome 2. The locus was identified using linkage analysis in 144 F2 plants derived from a cross between susceptible cultivar KDML105 and RGM-resistant cultivar MN62M with single nucleotide polymorphism (SNP) markers and F2:3 phenotype. The locus was mapped between two flanking markers, S2_76222 and S2_419160. In conclusion, we identified a new RGM resistance gene, gm12, on rice chromosome 2 in the Thai rice landrace MN62M. This finding yielded DNA markers that can be used in MAS to develop cultivars with broad-spectrum resistance to RGM. Moreover, the new resistance gene provides essential information for the identification of RGM biotypes in Thailand and Southeast Asia.}, }
@article {pmid32449459, year = {2020}, author = {Cinget, B and Bélanger, RR}, title = {Discovery of new group I-D introns leads to creation of subtypes and link to an adaptive response of the mitochondrial genome in fungi.}, journal = {RNA biology}, volume = {17}, number = {9}, pages = {1252-1260}, pmid = {32449459}, issn = {1555-8584}, mesh = {*Adaptation, Biological ; Antifungal Agents/pharmacology ; Drug Resistance, Fungal ; Evolution, Molecular ; Fungi/drug effects/*physiology ; Gene Expression Regulation, Fungal ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Genomics/methods ; *Introns ; Mitochondria/*genetics ; }, abstract = {Group I catalytic introns are widespread in bacterial, archaeal, viral, organellar, and some eukaryotic genomes, where they are reported to provide regulatory functions. The group I introns are currently divided into five types (A-E), which are themselves distributed into several subtypes, with the exception of group I type D intron (GI-D). GI-D introns belong to the rarest group with only 17 described to date, including only one with a putative role reported in fungi, where it would interfere with an adaptive response in the cytochrome b (COB) gene to quinone outside inhibitor (QoI) fungicide resistance. Using homology search methods taking into account both conserved sequences and RNA secondary structures, we analysed the mitochondrial genomes or COB genes of 169 fungal species, including some frequently under QoI selection pressure. These analyses have led to the identification of 216 novel GI-D introns, and the definition of three distinct subtypes, one of which being linked with a functional activity. We have further uncovered a homing site for this GI-D intron type, which helps refine the accepted model of quinone outside inhibitor resistance, whereby mobility of the intron across fungal mitochondrial genomes, would influence a fungus ability to develop resistance to QoIs.}, }
@article {pmid32442459, year = {2020}, author = {Neveu, E and Khalifeh, D and Salamin, N and Fasshauer, D}, title = {Prototypic SNARE Proteins Are Encoded in the Genomes of Heimdallarchaeota, Potentially Bridging the Gap between the Prokaryotes and Eukaryotes.}, journal = {Current biology : CB}, volume = {30}, number = {13}, pages = {2468-2480.e5}, doi = {10.1016/j.cub.2020.04.060}, pmid = {32442459}, issn = {1879-0445}, mesh = {Amino Acid Sequence ; Archaea/*genetics/metabolism ; Archaeal Proteins/chemistry/*genetics/metabolism ; *Evolution, Molecular ; Genome, Archaeal ; SNARE Proteins/chemistry/*genetics/metabolism ; }, abstract = {A defining feature of eukaryotic cells is the presence of numerous membrane-bound organelles that subdivide the intracellular space into distinct compartments. How the eukaryotic cell acquired its internal complexity is still poorly understood. Material exchange among most organelles occurs via vesicles that bud off from a source and specifically fuse with a target compartment. Central players in the vesicle fusion process are the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins. These small tail-anchored (TA) membrane proteins zipper into elongated four-helix bundles that pull membranes together. SNARE proteins are highly conserved among eukaryotes but are thought to be absent in prokaryotes. Here, we identified SNARE-like factors in the genomes of uncultured organisms of Asgard archaea of the Heimdallarchaeota clade, which are thought to be the closest living relatives of eukaryotes. Biochemical experiments show that the archaeal SNARE-like proteins can interact with eukaryotic SNARE proteins. We did not detect SNAREs in α-proteobacteria, the closest relatives of mitochondria, but identified several genes encoding for SNARE proteins in γ-proteobacteria of the order Legionellales, pathogens that live inside eukaryotic cells. Very probably, their SNAREs stem from lateral gene transfer from eukaryotes. Together, this suggests that the diverse set of eukaryotic SNAREs evolved from an archaeal precursor. However, whether Heimdallarchaeota actually have a simplified endomembrane system will only be seen when we succeed studying these organisms under the microscope.}, }
@article {pmid32440763, year = {2020}, author = {Roulet, ME and Garcia, LE and Gandini, CL and Sato, H and Ponce, G and Sanchez-Puerta, MV}, title = {Multichromosomal structure and foreign tracts in the Ombrophytum subterraneum (Balanophoraceae) mitochondrial genome.}, journal = {Plant molecular biology}, volume = {103}, number = {6}, pages = {623-638}, doi = {10.1007/s11103-020-01014-x}, pmid = {32440763}, issn = {1573-5028}, support = {PICT-0691//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 06/A724//Universidad Nacional de Cuyo/ ; 1062432//National Science Foundation/ ; }, mesh = {Balanophoraceae/*genetics ; DNA, Mitochondrial/*genetics ; Gene Transfer, Horizontal ; Genome, Mitochondrial/*genetics ; }, abstract = {Horizontal gene transfer (HGT) is frequent in parasitic plant mitochondria as a result of vascular connections established in host-parasite relationships. Recent studies of the holoparasitic plant Lophophytum mirabile (Balanophoraceae) revealed the unprecedented acquisition of a large amount of mitochondrial sequences from its legume host. We focused on a close relative, the generalist holoparasite Ombrophytum subterraneum, to examine the incidence of HGT events in the mitochondrial genome (mtDNA). The mtDNA of O. subterraneum assembles into 54 circular chromosomes, only 34 of which contain the 51 full-length coding regions. Numerous foreign tracts (totaling almost 100 kb, ~ 14% of the mtDNA), including 12 intact genes, were acquired by HGT from the Asteraceae hosts. Nine chromosomes concentrate most of those regions and eight are almost entirely foreign. Native homologs of each foreign gene coexist in the mtDNA and are potentially functional. A large proportion of shorter regions were related to the Fabaceae (a total of ~ 110 kb, 15.4%), some of which were shared with L. mirabile. We also found evidence of foreign sequences donated by angiosperm lineages not reported as hosts (Apocynaceae, Euphorbiaceae, Lamiaceae, and Malvales). We propose an evolutionary hypothesis that involves ancient transfers from legume hosts in the common ancestor of Ombrophytum and Lophophytum followed by more recent transfer events in L. mirabile. Besides, the O. subterraneum mtDNA was also subjected to additional HGT events from diverse angiosperm lineages, including large and recent transfers from the Asteraceae, and also from Lamiaceae.}, }
@article {pmid32437726, year = {2020}, author = {Kovalinka, T and Pánek, T and Kováčová, B and Horváth, A}, title = {Orientation of FtsH protease homologs in Trypanosoma brucei inner mitochondrial membrane and its evolutionary implications.}, journal = {Molecular and biochemical parasitology}, volume = {238}, number = {}, pages = {111282}, doi = {10.1016/j.molbiopara.2020.111282}, pmid = {32437726}, issn = {1872-9428}, mesh = {Animals ; Arabidopsis/classification/enzymology/genetics ; Conserved Sequence ; Euglena gracilis/classification/enzymology/genetics ; Euglena longa/classification/enzymology/genetics ; *Evolution, Molecular ; Gene Expression ; Humans ; Isoenzymes/chemistry/genetics/metabolism ; Leishmania major/classification/enzymology/genetics ; Mice ; Mitochondria/enzymology/genetics ; Mitochondrial Membranes/chemistry/enzymology ; Mitochondrial Proteins/*chemistry/genetics/metabolism ; Peptide Hydrolases/*chemistry/genetics/metabolism ; Phylogeny ; Protein Domains ; Protozoan Proteins/*chemistry/genetics/metabolism ; Saccharomyces cerevisiae/classification/enzymology/genetics ; Trypanosoma brucei brucei/classification/*enzymology/genetics ; }, abstract = {Trypanosoma brucei is an important human pathogen. In this study, we have focused on the characterization of FtsH protease, ATP-dependent membrane-bound mitochondrial enzyme important for regulation of protein abundance. We have determined localization and orientation of all six putative T.brucei FtsH homologs in the inner mitochondrial membrane by in silico analyses, by immunofluorescence, and with protease assay. The evolutionary origin of these homologs has been tested by comparative phylogenetic analysis. Surprisingly, some kinetoplastid FtsH proteins display inverted orientation in the mitochondrial membrane compared to related proteins of other examined eukaryotes. Moreover, our data strongly suggest that during evolution the orientation of FtsH protease in T. brucei varied due to both loss and acquisition of the transmembrane domain.}, }
@article {pmid32433495, year = {2020}, author = {Oka, M and Shimo, S and Ohno, N and Imai, H and Abekura, Y and Koseki, H and Miyata, H and Shimizu, K and Kushamae, M and Ono, I and Nozaki, K and Kawashima, A and Kawamata, T and Aoki, T}, title = {Dedifferentiation of smooth muscle cells in intracranial aneurysms and its potential contribution to the pathogenesis.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8330}, pmid = {32433495}, issn = {2045-2322}, mesh = {Animals ; Becaplermin/metabolism ; *Cell Dedifferentiation ; Cell Movement ; Cells, Cultured ; Chronic Disease ; Disease Models, Animal ; Disease Progression ; Female ; Humans ; Hyperplasia ; Inflammation/etiology ; Intracranial Aneurysm/*etiology/*pathology ; Male ; Muscle, Smooth/*pathology ; Rats ; Rats, Sprague-Dawley ; Tunica Intima/pathology ; }, abstract = {Smooth muscle cells (SMCs) are the major type of cells constituting arterial walls and play a role to maintain stiffness via producing extracellular matrix. Here, the loss and degenerative changes of SMCs become the major histopathological features of an intracranial aneurysm (IA), a major cause of subarachnoid hemorrhage. Considering the important role of SMCs and the loss of this type of cells in IA lesions, we in the present study subjected rats to IA models and examined how SMCs behave during disease progression. We found that, at the neck portion of IAs, SMCs accumulated underneath the internal elastic lamina according to disease progression and formed the intimal hyperplasia. As these SMCs were positive for a dedifferentiation marker, myosin heavy chain 10, and contained abundant mitochondria and rough endoplasmic reticulum, SMCs at the intimal hyperplasia were dedifferentiated and activated. Furthermore, dedifferentiated SMCs expressed some pro-inflammatory factors, suggesting the role in the formation of inflammatory microenvironment to promote the disease. Intriguingly, some SMCs at the intimal hyperplasia were positive for CD68 and contained lipid depositions, indicating similarity with atherosclerosis. We next examined a potential factor mediating dedifferentiation and recruitment of SMCs. Platelet derived growth factor (PDGF)-BB was expressed in endothelial cells at the neck portion of lesions where high wall shear stress (WSS) was loaded. PDGF-BB facilitated migration of SMCs across matrigel-coated pores in a transwell system, promoted dedifferentiation of SMCs and induced expression of pro-inflammatory genes in these cells in vitro. Because, in a stenosis model of rats, PDGF-BB expression was expressed in endothelial cells loaded in high WSS regions, and SMCs present nearby were dedifferentiated, hence a correlation existed between high WSS, PDGFB and dedifferentiation in vivo. In conclusion, dedifferentiated SMCs presumably by PDGF-BB produced from high WSS-loaded endothelial cells accumulate in the intimal hyperplasia to form inflammatory microenvironment leading to the progression of the disease.}, }
@article {pmid32430475, year = {2020}, author = {Speijer, D and Hammond, M and Lukeš, J}, title = {Comparing Early Eukaryotic Integration of Mitochondria and Chloroplasts in the Light of Internal ROS Challenges: Timing is of the Essence.}, journal = {mBio}, volume = {11}, number = {3}, pages = {}, pmid = {32430475}, issn = {2150-7511}, mesh = {Biological Evolution ; Chloroplasts/genetics/*metabolism ; Cyanobacteria/genetics/*metabolism ; Eukaryota/*genetics/*metabolism ; Mitochondria/genetics/*metabolism ; Reactive Oxygen Species/*metabolism ; Time Factors ; }, abstract = {When trying to reconstruct the evolutionary trajectories during early eukaryogenesis, one is struck by clear differences in the developments of two organelles of endosymbiotic origin: the mitochondrion and the chloroplast. From a symbiogenic perspective, eukaryotic development can be interpreted as a process in which many of the defining eukaryotic characteristics arose as a result of mutual adaptions of both prokaryotes (an archaeon and a bacterium) involved. This implies that many steps during the bacterium-to-mitochondrion transition trajectory occurred in an intense period of dramatic and rapid changes. In contrast, the subsequent cyanobacterium-to-chloroplast development in a specific eukaryotic subgroup, leading to the photosynthetic lineages, occurred in a full-fledged eukaryote. The commonalities and differences in the two trajectories shed an interesting light on early, and ongoing, eukaryotic evolutionary driving forces, especially endogenous reactive oxygen species (ROS) formation. Differences between organellar ribosomes, changes to the electron transport chain (ETC) components, and mitochondrial codon reassignments in nonplant mitochondria can be understood when mitochondrial ROS formation, e.g., during high energy consumption in heterotrophs, is taken into account.IMPORTANCE The early eukaryotic evolution was deeply influenced by the acquisition of two endosymbiotic organelles - the mitochondrion and the chloroplast. Here we discuss the possibly important role of reactive oxygen species in these processes.}, }
@article {pmid32430098, year = {2020}, author = {Vecoli, C and Borghini, A and Andreassi, MG}, title = {The molecular biomarkers of vascular aging and atherosclerosis: telomere length and mitochondrial DNA[4977] common deletion.}, journal = {Mutation research. Reviews in mutation research}, volume = {784}, number = {}, pages = {108309}, doi = {10.1016/j.mrrev.2020.108309}, pmid = {32430098}, issn = {1388-2139}, mesh = {Aging/genetics/metabolism/*pathology ; Animals ; Atherosclerosis/*diagnosis/genetics/metabolism ; Biomarkers/*analysis ; DNA, Mitochondrial/*genetics ; *Gene Deletion ; Humans ; Mitochondria/genetics/*pathology ; Risk Factors ; Telomere Shortening/*genetics ; }, abstract = {Age is the dominant risk factor for the most prevalent atherosclerotic vascular diseases, including coronary artery disease, myocardial infarction, cerebrovascular disease and stroke. In human, telomere erosion and mitochondrial DNA (mtDNA) damage play a central role in the mechanisms leading to cellular aging decline. This review summarizes the most relevant findings on the role of telomere shortening and the common mtDNA[4977] deletion in the progression and evolution of atherosclerosis by combining insight from experimental models and human clinical studies. The current evidence shows a link between telomere erosion and compromised mitochondrial function and provides a new perspective regarding their potential role as clinical biomarkers and therapeutic targets.}, }
@article {pmid32429841, year = {2020}, author = {Chang, H and Nie, Y and Zhang, N and Zhang, X and Sun, H and Mao, Y and Qiu, Z and Huang, Y}, title = {MtOrt: an empirical mitochondrial amino acid substitution model for evolutionary studies of Orthoptera insects.}, journal = {BMC evolutionary biology}, volume = {20}, number = {1}, pages = {57}, pmid = {32429841}, issn = {1471-2148}, support = {31872217, 30970346//National Science Foundation of China/International ; 2018JQ8003//Natural Science Basic Research Plan in Shaanxi Province of China/International ; }, mesh = {Amino Acid Sequence ; Amino Acid Substitution/*genetics ; Animals ; Confidence Intervals ; Databases, Genetic ; Genome, Mitochondrial ; Likelihood Functions ; Mitochondria/*genetics ; *Models, Genetic ; Orthoptera/classification/*genetics ; Phylogeny ; *Software ; }, abstract = {BACKGROUND: Amino acid substitution models play an important role in inferring phylogenies from proteins. Although different amino acid substitution models have been proposed, only a few were estimated from mitochondrial protein sequences for specific taxa such as the mtArt model for Arthropoda. The increasing of mitochondrial genome data from broad Orthoptera taxa provides an opportunity to estimate the Orthoptera-specific mitochondrial amino acid empirical model.<br><br>RESULTS: We sequenced complete mitochondrial genomes of 54 Orthoptera species, and estimated an amino acid substitution model (named mtOrt) by maximum likelihood method based on the 283 complete mitochondrial genomes available currently. The results indicated that there are obvious differences between mtOrt and the existing models, and the new model can better fit the Orthoptera mitochondrial protein datasets. Moreover, topologies of trees constructed using mtOrt and existing models are frequently different. MtOrt does indeed have an impact on likelihood improvement as well as tree topologies. The comparisons between the topologies of trees constructed using mtOrt and existing models show that the new model outperforms the existing models in inferring phylogenies from Orthoptera mitochondrial protein data.<br><br>CONCLUSIONS: The new mitochondrial amino acid substitution model of Orthoptera shows obvious differences from the existing models, and outperforms the existing models in inferring phylogenies from Orthoptera mitochondrial protein sequences.}, }
@article {pmid32428499, year = {2020}, author = {Pánek, T and Eliáš, M and Vancová, M and Lukeš, J and Hashimi, H}, title = {Returning to the Fold for Lessons in Mitochondrial Crista Diversity and Evolution.}, journal = {Current biology : CB}, volume = {30}, number = {10}, pages = {R575-R588}, doi = {10.1016/j.cub.2020.02.053}, pmid = {32428499}, issn = {1879-0445}, mesh = {*Biodiversity ; *Biological Evolution ; Eukaryota ; Mitochondria/*ultrastructure ; Mitochondrial Membranes/metabolism/ultrastructure ; Species Specificity ; }, abstract = {Cristae are infoldings of the mitochondrial inner membrane jutting into the organelle's innermost compartment from narrow stems at their base called crista junctions. They are emblematic of aerobic mitochondria, being the fabric for the molecular machinery driving cellular respiration. Electron microscopy revealed that diverse eukaryotes possess cristae of different shapes. Yet, crista diversity has not been systematically examined in light of our current knowledge about eukaryotic evolution. Since crista form and function are intricately linked, we take a holistic view of factors that may underlie both crista diversity and the adherence of cristae to a recognizable form. Based on electron micrographs of 226 species from all major lineages, we propose a rational crista classification system that postulates cristae as variations of two general morphotypes: flat and tubulo-vesicular. The latter is most prevalent and likely ancestral, but both morphotypes are found interspersed throughout the eukaryotic tree. In contrast, crista junctions are remarkably conserved, supporting their proposed role as diffusion barriers that sequester cristae contents. Since cardiolipin, ATP synthase dimers, the MICOS complex, and dynamin-like Opa1/Mgm1 are known to be involved in shaping cristae, we examined their variation in the context of crista diversity. Moreover, we have identified both commonalities and differences that may collectively be manifested as diverse variations of crista form and function.}, }
@article {pmid32428484, year = {2020}, author = {Lane, N}, title = {How energy flow shapes cell evolution.}, journal = {Current biology : CB}, volume = {30}, number = {10}, pages = {R471-R476}, doi = {10.1016/j.cub.2020.03.055}, pmid = {32428484}, issn = {1879-0445}, mesh = {Archaea/genetics/metabolism ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Eukaryota/*genetics/*physiology ; Gene Deletion ; Mitochondria/genetics/*physiology ; }, abstract = {How mitochondria shaped the evolution of eukaryotic complexity has been controversial for decades. The discovery of the Asgard archaea, which harbor close phylogenetic ties to the eukaryotes, supports the idea that a critical endosymbiosis between an archaeal host and a bacterial endosymbiont transformed the selective constraints present at the origin of eukaryotes. Cultured Asgard archaea are typically prokaryotic in both size and internal morphology, albeit featuring extensive protrusions. The acquisition of the mitochondrial predecessor by an archaeal host cell fundamentally altered the topology of genes in relation to bioenergetic membranes. Mitochondria internalised not only the bioenergetic membranes but also the genetic machinery needed for local control of oxidative phosphorylation. Gene loss from mitochondria enabled expansion of the nuclear genome, giving rise to an extreme genomic asymmetry that is ancestral to all extant eukaryotes. This genomic restructuring gave eukaryotes thousands of fold more energy availability per gene. In principle, that difference can support more and larger genes, far more non-coding DNA, greater regulatory complexity, and thousands of fold more protein synthesis per gene. These changes released eukaryotes from the bioenergetic constraints on prokaryotes, facilitating the evolution of morphological complexity.}, }
@article {pmid32428446, year = {2020}, author = {He, Q and Luo, J and Xu, JZ and Meng, XZ and Pan, GQ and Li, T and Zhou, ZY}, title = {Characterization of Hsp70 gene family provides insight into its functions related to microsporidian proliferation.}, journal = {Journal of invertebrate pathology}, volume = {174}, number = {}, pages = {107394}, doi = {10.1016/j.jip.2020.107394}, pmid = {32428446}, issn = {1096-0805}, mesh = {Amino Acid Sequence ; Encephalitozoon/genetics/physiology ; Evolution, Molecular ; Fungal Proteins/chemistry/genetics/metabolism ; Fungi/genetics/physiology ; Genome, Fungal ; *Genome, Protozoan ; HSP70 Heat-Shock Proteins/chemistry/*genetics/metabolism ; Microsporidia/genetics/*physiology ; Nosema/genetics/physiology ; Phylogeny ; Protozoan Proteins/chemistry/*genetics/metabolism ; Sequence Alignment ; }, abstract = {Heat shock protein 70 (Hsp70), a highly conserved protein family, is widely distributed in organisms and plays fundamental roles in biotic and abiotic stress responses. However, reports on Hsp70 genes are scarce in microsporidia, a very large group of obligate intracellular parasites that can infect nearly all animals, including humans. In this study, we identified 37 Hsp70 proteins from eight microsporidian genomes and classified them into four subfamilies (A-D). The number of Hsp70 genes in these microsporidia was significantly fewer than in Rozella allomycis and yeast. All microsporidian species contained genes from each subfamily and similar subcellular locations (mitochondria, endoplasmic reticulum, cytosol, and cytosol and/or nucleus), indicating that each Hsp70 member may fulfil distinct functions. The conserved structures and motifs of the Hsp70 proteins in the same subfamily were highly similar. Expression analysis indicated that the subfamily C cytosol (cyto)-associated Hsp70s is functional during microsporidia development. Immunofluorescence assays revealed that Cyto-NbHsp70 was cytoplasmically located in the proliferation-stage of Nosema bombycis. Cyto-NbHsp70 antiserum also labeled Encephalitozoon hellem within infected cells, suggesting that this antiserum is a potential molecular marker for labeling the proliferative phases of different microsporidian species. The propagation of N. bombycis was significantly inhibited following RNAi of Cyto-NbHsp70, indicating that Cyto-NbHsp70 is important for pathogen proliferation. Our phylogenetic data suggest that Hsp70 proteins evolved during microsporidia adaption to intracellular parasitism, and they play important roles in pathogen development.}, }
@article {pmid32427845, year = {2020}, author = {Cucchi, T and Papayianni, K and Cersoy, S and Aznar-Cormano, L and Zazzo, A and Debruyne, R and Berthon, R and Bălășescu, A and Simmons, A and Valla, F and Hamilakis, Y and Mavridis, F and Mashkour, M and Darvish, J and Siahsarvi, R and Biglari, F and Petrie, CA and Weeks, L and Sardari, A and Maziar, S and Denys, C and Orton, D and Jenkins, E and Zeder, M and Searle, JB and Larson, G and Bonhomme, F and Auffray, JC and Vigne, JD}, title = {Tracking the Near Eastern origins and European dispersal of the western house mouse.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {8276}, pmid = {32427845}, issn = {2045-2322}, mesh = {Animals ; Archaeology ; Asia, Western ; Cyprus ; DNA, Mitochondrial/*genetics ; Europe, Eastern ; Humans ; Introduced Species ; Mice/*classification/genetics ; Mitochondria/*genetics ; Radiometric Dating ; Sequence Analysis, DNA/*veterinary ; }, abstract = {The house mouse (Mus musculus) represents the extreme of globalization of invasive mammals. However, the timing and basis of its origin and early phases of dispersal remain poorly documented. To track its synanthropisation and subsequent invasive spread during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, between 40,000 and 3,000 cal. BP, combining geometric morphometrics numerical taxonomy, ancient mitochondrial DNA and direct radiocarbon dating. We found that large late hunter-gatherer sedentary settlements in the Levant, c. 14,500 cal. BP, promoted the commensal behaviour of the house mouse, which probably led the commensal pathway to cat domestication. House mouse invasive spread was then fostered through the emergence of agriculture throughout the Near East 12,000 years ago. Stowaway transport of house mice to Cyprus can be inferred as early as 10,800 years ago. However, the house mouse invasion of Europe did not happen until the development of proto urbanism and exchange networks - 6,500 years ago in Eastern Europe and 4000 years ago in Southern Europe - which in turn may have driven the first human mediated dispersal of cats in Europe.}, }
@article {pmid32413571, year = {2020}, author = {Arad, M and Waldman, M and Abraham, NG and Hochhauser, E}, title = {Therapeutic approaches to diabetic cardiomyopathy: Targeting the antioxidant pathway.}, journal = {Prostaglandins &amp; other lipid mediators}, volume = {150}, number = {}, pages = {106454}, doi = {10.1016/j.prostaglandins.2020.106454}, pmid = {32413571}, issn = {1098-8823}, mesh = {Animals ; Antioxidants/*pharmacology/therapeutic use ; Diabetes Mellitus/*drug therapy/*metabolism/pathology ; Diabetic Cardiomyopathies/*drug therapy/*metabolism/pathology ; Humans ; Oxidative Stress/*drug effects ; }, abstract = {The global epidemic of cardiovascular disease continues unabated and remains the leading cause of death both in the US and worldwide. We hereby summarize the available therapies for diabetes and cardiovascular disease in diabetics. Clearly, the current approaches to diabetic heart disease often target the manifestations and certain mediators but not the specific pathways leading to myocardial injury, remodeling and dysfunction. Better understanding of the molecular events determining the evolution of diabetic cardiomyopathy will provide insight into the development of specific and targeted therapies. Recent studies largely increased our understanding of the role of enhanced inflammatory response, ROS production, as well as the contribution of Cyp-P450-epoxygenase-derived epoxyeicosatrienoic acid (EET), Peroxisome Proliferator-Activated Receptor Gamma Coactivator-1α (PGC-1α), Heme Oxygenase (HO)-1 and 20-HETE in pathophysiology and therapy of cardiovascular disease. PGC-1α increases production of the HO-1 which has a major role in protecting the heart against oxidative stress, microcirculation and mitochondrial dysfunction. This review describes the potential drugs and their downstream targets, PGC-1α and HO-1, as major loci for developing therapeutic approaches beside diet and lifestyle modification for the treatment and prevention of heart disease associated with obesity and diabetes.}, }
@article {pmid32411111, year = {2020}, author = {Fonseca, PLC and Badotti, F and De-Paula, RB and Araújo, DS and Bortolini, DE and Del-Bem, LE and Azevedo, VA and Brenig, B and Aguiar, ERGR and Góes-Neto, A}, title = {Exploring the Relationship Among Divergence Time and Coding and Non-coding Elements in the Shaping of Fungal Mitochondrial Genomes.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {765}, pmid = {32411111}, issn = {1664-302X}, abstract = {The order Hypocreales (Ascomycota) is composed of ubiquitous and ecologically diverse fungi such as saprobes, biotrophs, and pathogens. Despite their phylogenetic relationship, these species exhibit high variability in biomolecules production, lifestyle, and fitness. The mitochondria play an important role in the fungal biology, providing energy to the cells and regulating diverse processes, such as immune response. In spite of its importance, the mechanisms that shape fungal mitogenomes are still poorly understood. Herein, we investigated the variability and evolution of mitogenomes and its relationship with the divergence time using the order Hypocreales as a study model. We sequenced and annotated for the first time Trichoderma harzianum mitochondrial genome (mtDNA), which was compared to other 34 mtDNAs species that were publicly available. Comparative analysis revealed a substantial structural and size variation on non-coding mtDNA regions, despite the conservation of copy number, length, and structure of protein-coding elements. Interestingly, we observed a highly significant correlation between mitogenome length, and the number and size of non-coding sequences in mitochondrial genome. Among the non-coding elements, group I and II introns and homing endonucleases genes (HEGs) were the main contributors to discrepancies in mitogenomes structure and length. Several intronic sequences displayed sequence similarity among species, and some of them are conserved even at gene position, and were present in the majority of mitogenomes, indicating its origin in a common ancestor. On the other hand, we also identified species-specific introns that advocate for the origin by different mechanisms. Investigation of mitochondrial gene transfer to the nuclear genome revealed that nuclear copies of the nad5 are the most frequent while atp8, atp9, and cox3 could not be identified in any of the nuclear genomes analyzed. Moreover, we also estimated the divergence time of each species and investigated its relationship with coding and non-coding elements as well as with the length of mitogenomes. Altogether, our results demonstrated that introns and HEGs are key elements on mitogenome shaping and its presence on fast-evolving mtDNAs could be mostly explained by its divergence time, although the intron sharing profile suggests the involvement of other mechanisms on the mitochondrial genome evolution, such as horizontal transference.}, }
@article {pmid32407393, year = {2020}, author = {Han, X and He, H and Shen, H and Tang, J and Dong, W and Shi, Y and Wu, S and Zhang, F and Liang, G}, title = {Comparative mitochondrial genome analysis of Dendrolimus houi (Lepidoptera: Lasiocampidae) and phylogenetic relationship among Lasiocampidae species.}, journal = {PloS one}, volume = {15}, number = {5}, pages = {e0232527}, pmid = {32407393}, issn = {1932-6203}, mesh = {Animals ; Chromosome Mapping ; Genome, Insect/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Moths/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Dendrolimus houi is one of the most common caterpillars infesting Gymnosperm trees, and widely distributed in several countries in Southeast Asia, and exists soley or coexists with several congeners and some Lasiocampidae species in various forest habitats. However, natural hybrids occasionally occur among some closely related species in the same habitat, and host preference, extreme climate stress, and geographic isolation probably lead to their uncertain taxonomic consensus. The mitochondrial DNA (mtDNA) of D. houi was extracted and sequenced by using high-throughput technology, and the mitogenome composition and characteristics were compared and analyzed of these species, then the phylogenetic relationship was constructed using the maximum likelihood method (ML) and the Bayesian method (BI) based on their 13 protein-coding genes (PCGs) dataset, which were combined and made available to download which were combined and made available to download among global Lasiocampidae species data. Mitogenome of D. houi was 15,373 bp in length, with 37 genes, including 13 PCGs, 22 tRNA genes (tRNAs) and 2 rRNA genes (rRNAs). The positions and sequences of genes were consistent with those of most known Lasiocampidae species. The nucleotide composition was highly A+T biased, accounting for ~80% of the whole mitogenome. All start codons of PCGs belonged to typical start codons ATN except for COI which used CGA, and most stop codons ended with standard TAA or TAG, while COI, COII, ND4 ended with incomplete T. Only tRNASer (AGN) lacked DHU arm, while the remainder formed a typical "clover-shaped" secondary structure. For Lasiocampidae species, their complete mitochondrial genomes ranged from 15,281 to 15,570 bp in length, and all first genes started from trnM in the same direction. And base composition was biased toward A and T. Finally, both two methods (ML and BI) separately revealed that the same phylogenetic relationship of D. spp. as ((((D. punctatus + D. tabulaeformis) + D. spectabilis) + D. superans) + (D. kikuchii of Hunan population + D. houi) as in previous research, but results were different in that D. kikuchii from a Yunnan population was included, indicating that different geographical populations of insects have differentiated. And the phylogenetic relationship among Lasiocampidae species was ((((Dendrolimus) + Kunugia) + Euthrix) + Trabala). This provides a better theoretical basis for Lasiocampidae evolution and classification for future research directions.}, }
@article {pmid32407378, year = {2020}, author = {Cai, G and Scofield, SR}, title = {Mitochondrial genome sequence of Phytophthora sansomeana and comparative analysis of Phytophthora mitochondrial genomes.}, journal = {PloS one}, volume = {15}, number = {5}, pages = {e0231296}, pmid = {32407378}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Phylogeny ; Phytophthora/*classification/*genetics ; Sequence Homology ; Species Specificity ; }, abstract = {Phytophthora sansomeana infects soybean and causes root rot. It was recently separated from the species complex P. megasperma sensu lato. In this study, we sequenced and annotated its complete mitochondrial genome and compared it to that of nine other Phytophthora species. The genome was assembled into a circular molecule of 39,618 bp with a 22.03% G+C content. Forty-two protein coding genes, 25 tRNA genes and two rRNA genes were annotated in this genome. The protein coding genes include 14 genes in the respiratory complexes, four ATP synthase genes, 16 ribosomal proteins genes, a tatC translocase gene, six conserved ORFs and a unique orf402. The tRNA genes encode tRNAs for 19 amino acids. Comparison among mitochondrial genomes of 10 Phytophthora species revealed three inversions, each covering multiple genes. These genomes were conserved in gene content with few exceptions. A 3' truncated atp9 gene was found in P. nicotianae. All 10 Phytophthora species, as well as other oomycetes and stramenopiles, lacked tRNA genes for threonine in their mitochondria. Phylogenomic analysis using the mitochondrial genomes supported or enhanced previous findings of the phylogeny of Phytophthora spp.}, }
@article {pmid32403285, year = {2020}, author = {Diroma, MA and Varvara, AS and Attimonelli, M and Pesole, G and Picardi, E}, title = {Investigating Human Mitochondrial Genomes in Single Cells.}, journal = {Genes}, volume = {11}, number = {5}, pages = {}, pmid = {32403285}, issn = {2073-4425}, mesh = {Cell Line, Tumor ; Computational Biology ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Datasets as Topic ; *Genome, Mitochondrial ; HT29 Cells ; High-Throughput Nucleotide Sequencing/methods ; Human Umbilical Vein Endothelial Cells ; Humans ; Leukemia, Erythroblastic, Acute/pathology ; *Sequence Alignment ; Single-Cell Analysis/*methods ; *Software ; }, abstract = {Mitochondria host multiple copies of their own small circular genome that has been extensively studied to trace the evolution of the modern eukaryotic cell and discover important mutations linked to inherited diseases. Whole genome and exome sequencing have enabled the study of mtDNA in a large number of samples and experimental conditions at single nucleotide resolution, allowing the deciphering of the relationship between inherited mutations and phenotypes and the identification of acquired mtDNA mutations in classical mitochondrial diseases as well as in chronic disorders, ageing and cancer. By applying an ad hoc computational pipeline based on our MToolBox software, we reconstructed mtDNA genomes in single cells using whole genome and exome sequencing data obtained by different amplification methodologies (eWGA, DOP-PCR, MALBAC, MDA) as well as data from single cell Assay for Transposase Accessible Chromatin with high-throughput sequencing (scATAC-seq) in which mtDNA sequences are expected as a byproduct of the technology. We show that assembled mtDNAs, with the exception of those reconstructed by MALBAC and DOP-PCR methods, are quite uniform and suitable for genomic investigations, enabling the study of various biological processes related to cellular heterogeneity such as tumor evolution, neural somatic mosaicism and embryonic development.}, }
@article {pmid32399193, year = {2020}, author = {Zardoya, R}, title = {Recent advances in understanding mitochondrial genome diversity.}, journal = {F1000Research}, volume = {9}, number = {}, pages = {}, pmid = {32399193}, issn = {2046-1402}, mesh = {Animals ; *Evolution, Molecular ; Fungi/genetics ; *Genome, Mitochondrial ; Introns ; Mitochondria ; Plants/genetics ; RNA Editing ; }, abstract = {Ever since its discovery, the double-stranded DNA contained in the mitochondria of eukaryotes has fascinated researchers because of its bacterial endosymbiotic origin, crucial role in encoding subunits of the respiratory complexes, compact nature, and specific inheritance mechanisms. In the last few years, high-throughput sequencing techniques have accelerated the sequencing of mitochondrial genomes (mitogenomes) and uncovered the great diversity of organizations, gene contents, and modes of replication and transcription found in living eukaryotes. Some early divergent lineages of unicellular eukaryotes retain certain synteny and gene content resembling those observed in the genomes of alphaproteobacteria (the inferred closest living group of mitochondria), whereas others adapted to anaerobic environments have drastically reduced or even lost the mitogenome. In the three main multicellular lineages of eukaryotes, mitogenomes have pursued diverse evolutionary trajectories in which different types of molecules (circular versus linear and single versus multipartite), gene structures (with or without self-splicing introns), gene contents, gene orders, genetic codes, and transfer RNA editing mechanisms have been selected. Whereas animals have evolved a rather compact mitochondrial genome between 11 and 50 Kb in length with a highly conserved gene content in bilaterians, plants exhibit large mitochondrial genomes of 66 Kb to 11.3 Mb with large intergenic repetitions prone to recombination, and fungal mitogenomes have intermediate sizes of 12 to 236 Kb.}, }
@article {pmid32397253, year = {2020}, author = {Kleczewska, M and Grabinska, A and Jelen, M and Stolarska, M and Schilke, B and Marszalek, J and Craig, EA and Dutkiewicz, R}, title = {Biochemical Convergence of Mitochondrial Hsp70 System Specialized in Iron-Sulfur Cluster Biogenesis.}, journal = {International journal of molecular sciences}, volume = {21}, number = {9}, pages = {}, pmid = {32397253}, issn = {1422-0067}, support = {R35 GM127009/GM/NIGMS NIH HHS/United States ; UMO-2015/19/B/NZ1/00237//Narodowe Centrum Nauki/ ; TEAM POIR.04.04.00-00-4114 /17-00//Fundacja na rzecz Nauki Polskiej/ ; R35GM127009//National Institutes of Health/ ; }, mesh = {Adenosine Triphosphatases/genetics/metabolism ; Candida/enzymology/genetics/metabolism ; Circular Dichroism ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/genetics/*metabolism ; Evolution, Molecular ; Gene Duplication ; Gene Ontology ; HSP70 Heat-Shock Proteins/*genetics/*metabolism ; Iron/*metabolism ; Iron-Sulfur Proteins/metabolism ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Models, Molecular ; Molecular Chaperones/genetics/metabolism ; Protein Binding ; Proteome/genetics/metabolism ; Recombinant Proteins ; Saccharomyces/enzymology/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Sulfur/*metabolism ; }, abstract = {Mitochondria play a central role in the biogenesis of iron-sulfur cluster(s) (FeS), protein cofactors needed for many cellular activities. After assembly on scaffold protein Isu, the cluster is transferred onto a recipient apo-protein. Transfer requires Isu interaction with an Hsp70 chaperone system that includes a dedicated J-domain protein co-chaperone (Hsc20). Hsc20 stimulates Hsp70's ATPase activity, thus stabilizing the critical Isu-Hsp70 interaction. While most eukaryotes utilize a multifunctional mitochondrial (mt)Hsp70, yeast employ another Hsp70 (Ssq1), a product of mtHsp70 gene duplication. Ssq1 became specialized in FeS biogenesis, recapitulating the process in bacteria, where specialized Hsp70 HscA cooperates exclusively with an ortholog of Hsc20. While it is well established that Ssq1 and HscA converged functionally for FeS transfer, whether these two Hsp70s possess similar biochemical properties was not known. Here, we show that overall HscA and Ssq1 biochemical properties are very similar, despite subtle differences being apparent - the ATPase activity of HscA is stimulated to a somewhat higher levels by Isu and Hsc20, while Ssq1 has a higher affinity for Isu and for Hsc20. HscA/Ssq1 are a unique example of biochemical convergence of distantly related Hsp70s, with practical implications, crossover experimental results can be combined, facilitating understanding of the FeS transfer process.}, }
@article {pmid32396817, year = {2020}, author = {Seebacher, F}, title = {Is Endothermy an Evolutionary By-Product?.}, journal = {Trends in ecology &amp; evolution}, volume = {35}, number = {6}, pages = {503-511}, doi = {10.1016/j.tree.2020.02.006}, pmid = {32396817}, issn = {1872-8383}, mesh = {Acclimatization ; Adaptation, Physiological ; Animals ; Biological Evolution ; *Energy Metabolism ; *Vertebrates ; }, abstract = {Endothermy alters the energetic relationships between organisms and their environment and thereby influences fundamental niches. Endothermy is closely tied to energy metabolism. Regulation of energy balance is indispensable for all life and regulatory pathways increase in complexity from bacteria to vertebrates. Increasing complexity of metabolic networks also increase the probability for endothermic phenotypes to appear. Adaptive arguments are problematic epistemologically because the regulatory mechanisms enabling endothermy have not evolved for the 'purpose' of endothermy and the utility of current traits is likely to have changed over evolutionary time. It is most parsimonious to view endothermy as the evolutionary by-product of energy balance regulation rather than as an adaptation and interpret its evolution in the context of metabolic networks.}, }
@article {pmid32396758, year = {2020}, author = {Puertas, MJ and González-Sánchez, M}, title = {Insertions of mitochondrial DNA into the nucleus-effects and role in cell evolution.}, journal = {Genome}, volume = {63}, number = {8}, pages = {365-374}, doi = {10.1139/gen-2019-0151}, pmid = {32396758}, issn = {1480-3321}, mesh = {Aging/genetics ; Animals ; Cell Nucleus/*genetics ; Centromere ; DNA, Mitochondrial/genetics/*physiology ; Disease/genetics ; *Evolution, Molecular ; Humans ; *Mutagenesis, Insertional ; Telomere ; }, abstract = {We review the insertion of mitochondrial DNA (mtDNA) fragments into nuclear DNA (NUMTS) as a general and ongoing process that has occurred many times during genome evolution. Fragments of mtDNA are generated during the lifetime of organisms in both somatic and germinal cells, by the production of reactive oxygen species in the mitochondria. The fragments are inserted into the nucleus during the double-strand breaks repair via the non-homologous end-joining machinery, followed by genomic instability, giving rise to the high variability observed in NUMT patterns among species, populations, or genotypes. Some de novo produced mtDNA insertions show harmful effects, being involved in human diseases, carcinogenesis, and ageing. NUMT generation is a non-stop process overpassing the Mendelian transmission. This parasitic property ensures their survival even against their harmful effects. The accumulation of mtDNA fragments mainly at pericentromeric and subtelomeric regions is important to understand the transmission and integration of NUMTs into the genomes. The possible effect of female meiotic drive for mtDNA insertions at centromeres remains to be studied. In spite of the harmful feature of NUMTs, they are important in cell evolution, representing a major source of genomic variation.}, }
@article {pmid32393776, year = {2020}, author = {Wang, L and Fan, J and Han, L and Qi, H and Wang, Y and Wang, H and Chen, S and Du, L and Li, S and Zhang, Y and Tang, W and Ge, G and Pan, W and Hu, P and Cheng, H}, title = {The micropeptide LEMP plays an evolutionarily conserved role in myogenesis.}, journal = {Cell death &amp; disease}, volume = {11}, number = {5}, pages = {357}, pmid = {32393776}, issn = {2041-4889}, mesh = {Amino Acid Sequence ; Animals ; *Cell Differentiation ; Cell Line ; Conserved Sequence ; *Evolution, Molecular ; Mice, Knockout ; *Muscle Development ; Peptides/deficiency/genetics/*metabolism ; Satellite Cells, Skeletal Muscle/*metabolism ; Signal Transduction ; Zebrafish ; Zebrafish Proteins/genetics/*metabolism ; }, abstract = {In recent years, micropeptides have been increasingly identified as important regulators in various biological processes. However, whether micropeptides are functionally conserved remains largely unknown. Here, we uncovered a micropeptide with evolutionarily conserved roles in myogenesis. RNA-seq data analysis of proliferating mouse satellite cells (SCs) and differentiated myotubes identified a previously annotated lncRNA, MyolncR4 (1500011K16RIK), which is upregulated during muscle differentiation. Significantly, MyolncR4 is highly conserved across vertebrate species. Multiple lines of evidence demonstrate that MyolncR4 encodes a 56-aa micropeptide, which was named as LEMP (lncRNA encoded micropeptide). LEMP promotes muscle formation and regeneration in mouse. In zebrafish, MyolncR4 is enriched in developing somites and elimination of LEMP results in impaired muscle development, which could be efficiently rescued by expression of the mouse LEMP. Interestingly, LEMP is localized at both the plasma membrane and mitochondria, and associated with multiple mitochondrial proteins, suggestive of its involvement in mitochondrial functions. Together, our work uncovers a micropeptide that plays an evolutionarily conserved role in skeletal muscle differentiation, pinpointing the functional importance of this growing family of small peptides.}, }
@article {pmid32393264, year = {2020}, author = {De Chiara, M and Friedrich, A and Barré, B and Breitenbach, M and Schacherer, J and Liti, G}, title = {Discordant evolution of mitochondrial and nuclear yeast genomes at population level.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {49}, pmid = {32393264}, issn = {1741-7007}, support = {ANR-10-INBS-09-08//Agence Nationale de la Recherche/International ; }, mesh = {Cell Nucleus/*genetics ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Fungal ; *Genome, Mitochondrial ; Phylogeny ; Saccharomyces cerevisiae/*genetics ; }, abstract = {BACKGROUND: Mitochondria are essential organelles partially regulated by their own genomes. The mitochondrial genome maintenance and inheritance differ from the nuclear genome, potentially uncoupling their evolutionary trajectories. Here, we analysed mitochondrial sequences obtained from the 1011 Saccharomyces cerevisiae strain collection and identified pronounced differences with their nuclear genome counterparts.<br><br>RESULTS: In contrast with pre-whole genome duplication fungal species, S. cerevisiae mitochondrial genomes show higher genetic diversity compared to the nuclear genomes. Strikingly, mitochondrial genomes appear to be highly admixed, resulting in a complex interconnected phylogeny with a weak grouping of isolates, whereas interspecies introgressions are very rare. Complete genome assemblies revealed that structural rearrangements are nearly absent with rare inversions detected. We tracked intron variation in COX1 and COB to infer gain and loss events throughout the species evolutionary history. Mitochondrial genome copy number is connected with the nuclear genome and linearly scale up with ploidy. We observed rare cases of naturally occurring mitochondrial DNA loss, petite, with a subset of them that do not suffer the expected growth defect in fermentable rich media.<br><br>CONCLUSIONS: Overall, our results illustrate how differences in the biology of two genomes coexisting in the same cells can lead to discordant evolutionary histories.}, }
@article {pmid32148763, year = {2019}, author = {Pichon, J and Luscombe, NM and Plessy, C}, title = {Widespread use of the "ascidian" mitochondrial genetic code in tunicates.}, journal = {F1000Research}, volume = {8}, number = {}, pages = {2072}, pmid = {32148763}, issn = {2046-1402}, mesh = {Animals ; Base Sequence ; *Genetic Code ; Mitochondria ; *Phylogeny ; *Urochordata/genetics ; }, abstract = {Background: Ascidians, a tunicate class, use a mitochondrial genetic code that is distinct from vertebrates and other invertebrates. Though it has been used to translate the coding sequences from other tunicate species on a case-by-case basis, it is has not been investigated whether this can be done systematically. This is an important because a) some tunicate mitochondrial sequences are currently translated with the invertebrate code by repositories such as NCBI GenBank, and b) uncertainties about the genetic code to use can complicate or introduce errors in phylogenetic studies based on translated mitochondrial protein sequences. Methods: We collected publicly available nucleotide sequences for non-ascidian tunicates including appendicularians such as Oikopleura dioica, translated them using the ascidian mitochondrial code, and built multiple sequence alignments covering all tunicate classes. Results: All tunicates studied here appear to translate AGR codons to glycine instead of serine (invertebrates) or as a stop codon (vertebrates), as initially described in ascidians. Among Oikopleuridae, we suggest further possible changes in the use of the ATA (Ile → Met) and TGA (Trp → Arg) codons. Conclusions: We recommend using the ascidian mitochondrial code in automatic translation pipelines of mitochondrial sequences for all tunicates. Further investigation is required for additional species-specific differences.}, }
@article {pmid32390938, year = {2020}, author = {Meduri, GU and Chrousos, GP}, title = {General Adaptation in Critical Illness: Glucocorticoid Receptor-alpha Master Regulator of Homeostatic Corrections.}, journal = {Frontiers in endocrinology}, volume = {11}, number = {}, pages = {161}, pmid = {32390938}, issn = {1664-2392}, mesh = {Adaptation, Physiological/drug effects/*physiology ; Animals ; Avitaminosis/complications/genetics/metabolism ; *Critical Illness/rehabilitation ; *Energy Metabolism/drug effects/genetics ; Gene Expression Regulation/drug effects ; Glucocorticoids/deficiency/pharmacology ; Homeostasis/drug effects/*genetics ; Humans ; Mitochondria/drug effects/physiology ; Receptors, Glucocorticoid/*physiology ; }, abstract = {In critical illness, homeostatic corrections representing the culmination of hundreds of millions of years of evolution, are modulated by the activated glucocorticoid receptor alpha (GRα) and are associated with an enormous bioenergetic and metabolic cost. Appreciation of how homeostatic corrections work and how they evolved provides a conceptual framework to understand the complex pathobiology of critical illness. Emerging literature place the activated GRα at the center of all phases of disease development and resolution, including activation and re-enforcement of innate immunity, downregulation of pro-inflammatory transcription factors, and restoration of anatomy and function. By the time critically ill patients necessitate vital organ support for survival, they have reached near exhaustion or exhaustion of neuroendocrine homeostatic compensation, cell bio-energetic and adaptation functions, and reserves of vital micronutrients. We review how critical illness-related corticosteroid insufficiency, mitochondrial dysfunction/damage, and hypovitaminosis collectively interact to accelerate an anti-homeostatic active process of natural selection. Importantly, the allostatic overload imposed by these homeostatic corrections impacts negatively on both acute and long-term morbidity and mortality. Since the bioenergetic and metabolic reserves to support homeostatic corrections are time-limited, early interventions should be directed at increasing GRα and mitochondria number and function. Present understanding of the activated GC-GRα's role in immunomodulation and disease resolution should be taken into account when re-evaluating how to administer glucocorticoid treatment and co-interventions to improve cellular responsiveness. The activated GRα interdependence with functional mitochondria and three vitamin reserves (B1, C, and D) provides a rationale for co-interventions that include prolonged glucocorticoid treatment in association with rapid correction of hypovitaminosis.}, }
@article {pmid32387125, year = {2020}, author = {Gangloff, EJ and Schwartz, TS and Klabacka, R and Huebschman, N and Liu, AY and Bronikowski, AM}, title = {Mitochondria as central characters in a complex narrative: Linking genomics, energetics, pace-of-life, and aging in natural populations of garter snakes.}, journal = {Experimental gerontology}, volume = {137}, number = {}, pages = {110967}, doi = {10.1016/j.exger.2020.110967}, pmid = {32387125}, issn = {1873-6815}, mesh = {Aging/genetics ; Animals ; *Colubridae ; Genomics ; Humans ; Longevity/genetics ; Mitochondria/genetics ; }, abstract = {As a pacesetter for physiological processes, variation in metabolic rate can determine the shape of energetic trade-offs and thereby drive variation in life-history traits. In turn, such variation in metabolic performance and life-histories can have profound consequences for lifespan and lifetime fitness. Thus, the extent to which metabolic rate variation is due to phenotypic plasticity or fixed genetic differences among individuals or populations is likely to be shaped by natural selection. Here, we first present a generalized framework describing the central role of mitochondria in processes linking environmental, genomic, physiological, and aging variation. We then present a test of these relationships in an exemplary system: populations of garter snakes (Thamnophis elegans) exhibiting contrasting life-history strategies - fast-growing, early-reproducing, and fast-aging (FA) versus slow-growing, late-reproducing, and slow-aging (SA). Previous work has characterized divergences in mitochondrial function, reactive oxygen species processing, and whole-organism metabolic rate between these contrasting life-history ecotypes. Here, we report new data on cellular respiration and mitochondrial genomics and synthesize these results with previous work. We test hypotheses about the causes and implications of mitochondrial genome variation within this generalized framework. First, we demonstrate that snakes of the FA ecotype increase cellular metabolic rate across their lifespan, while the opposite pattern holds for SA snakes, implying that reduced energetic throughput is associated with a longer life. Second, we show that variants in mitochondrial genomes are segregating across the landscape in a manner suggesting selection on the physiological consequences of this variation in habitats varying in temperature, food availability, and rates of predation. Third, we demonstrate functional variation in whole-organism metabolic rate related to these mitochondrial genome sequence variants. With this synthesis of numerous datasets, we are able to further characterize how variation across levels of biological organization interact within this generalized framework and how this has resulted in the emergence of distinct life-history ecotypes that vary in their rates of aging and lifespan.}, }
@article {pmid32380284, year = {2020}, author = {Xu, L and Liu, P and Wang, X and Van Damme, K and Du, F}, title = {Phylogenetic relationships and cryptic species in the genus Sthenoteuthis (Cephalopoda: Ommastrephidae) in the South China Sea.}, journal = {Molecular phylogenetics and evolution}, volume = {149}, number = {}, pages = {106846}, doi = {10.1016/j.ympev.2020.106846}, pmid = {32380284}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; China ; DNA, Mitochondrial/genetics ; Decapodiformes/*classification/genetics ; Genetic Variation ; Geography ; Haplotypes/genetics ; Hybridization, Genetic ; Mitochondria/genetics ; *Oceans and Seas ; *Phylogeny ; Species Specificity ; }, abstract = {Large squids of the genus Sthenoteuthis are commercially relevant species that include two truly oceanic squids. They are large nektonic predators being widely distributed throughout tropical and subtropical waters of the Atlantic and Indo-Pacific Ocean. The present study investigates different morphs varying in size at maturity, and assesses the genetic divergence in Sthenotheutis in relation to geographic patterns in the South China Sea. We obtained sequences using a mitochondrial (cytochrome c oxidase subunit I) and a nuclear (Histone H3) gene marker from 111 individuals in 23 locations of the South China Sea. In combination with sequences available in public databases, we performed tests on DNA taxonomy, mostly based on molecular phylogenies. Our results suggest that the genus Sthenoteuthis includes at least three species. The Indo-Pacific purpleback squid Sthenoteuthis oualaniensis contains at least two genetically distinct lineages that can be considered separate species, a dwarf species and a medium-sized species, separated by both the mitochondrial marker and the more conserved nuclear marker. We also assessed whether the few cases of mitonuclear discordance could be the result of genetic introgression and past hybridization or incongruence lineage sorting. The medium-sized species is more widely distributed and dominant in the South China Sea than the dwarf species. The medium-sized species inhabits the whole South China Sea, whereas the dwarf species is restricted to the equatorial waters of the South China Sea. The medium-sized species has two further genetic clades, one distributed in the East Pacific Ocean and the other in the South China Sea. This high level of genetic differentiation is in agreement with the discriminant analysis on the morphological measurements, clearly separating the dwarf and medium-sized species, indicating the presence of a complex of pseudo-cryptic species in S. oualaniensis, clearly identifiable by differences in DNA sequences and in body size, and statistically differentiated in their body measurements.}, }
@article {pmid32372945, year = {2020}, author = {Scorziello, A and Borzacchiello, D and Sisalli, MJ and Di Martino, R and Morelli, M and Feliciello, A}, title = {Mitochondrial Homeostasis and Signaling in Parkinson's Disease.}, journal = {Frontiers in aging neuroscience}, volume = {12}, number = {}, pages = {100}, pmid = {32372945}, issn = {1663-4365}, abstract = {The loss of dopaminergic (DA) neurons in the substantia nigra leads to a progressive, long-term decline of movement and other non-motor deficits. The symptoms of Parkinson's disease (PD) often appear later in the course of the disease, when most of the functional dopaminergic neurons have been lost. The late onset of the disease, the severity of the illness, and its impact on the global health system demand earlier diagnosis and better targeted therapy. PD etiology and pathogenesis are largely unknown. There are mutations in genes that have been linked to PD and, from these complex phenotypes, mitochondrial dysfunction emerged as central in the pathogenesis and evolution of PD. In fact, several PD-associated genes negatively impact on mitochondria physiology, supporting the notion that dysregulation of mitochondrial signaling and homeostasis is pathogenically relevant. Derangement of mitochondrial homeostatic controls can lead to oxidative stress and neuronal cell death. Restoring deranged signaling cascades to and from mitochondria in PD neurons may then represent a viable opportunity to reset energy metabolism and delay the death of dopaminergic neurons. Here, we will highlight the relevance of dysfunctional mitochondrial homeostasis and signaling in PD, the molecular mechanisms involved, and potential therapeutic approaches to restore mitochondrial activities in damaged neurons.}, }
@article {pmid32371392, year = {2020}, author = {Chen, H and Shi, Z and Guo, J and Chang, KJ and Chen, Q and Yao, CH and Haigis, MC and Shi, Y}, title = {The human mitochondrial 12S rRNA m[4]C methyltransferase METTL15 is required for mitochondrial function.}, journal = {The Journal of biological chemistry}, volume = {295}, number = {25}, pages = {8505-8513}, pmid = {32371392}, issn = {1083-351X}, mesh = {CRISPR-Cas Systems/genetics ; Escherichia coli Proteins/metabolism ; Evolution, Molecular ; Gene Editing ; Genome, Mitochondrial ; Glycolysis ; Humans ; Kinetics ; Methylation ; Methyltransferases/genetics/*metabolism ; Microscopy, Fluorescence ; Mitochondria/genetics/*metabolism ; RNA, Messenger/metabolism ; RNA, Mitochondrial/metabolism ; RNA, Ribosomal/genetics/*metabolism ; Substrate Specificity ; }, abstract = {Mitochondrial DNA gene expression is coordinately regulated both pre- and post-transcriptionally, and its perturbation can lead to human pathologies. Mitochondrial rRNAs (mt-rRNAs) undergo a series of nucleotide modifications after release from polycistronic mitochondrial RNA precursors, which is essential for mitochondrial ribosomal biogenesis. Cytosine N[4]-methylation (m[4]C) at position 839 (m[4]C839) of the 12S small subunit mt-rRNA was identified decades ago; however, its biogenesis and function have not been elucidated in detail. Here, using several approaches, including immunofluorescence, RNA immunoprecipitation and methylation assays, and bisulfite mapping, we demonstrate that human methyltransferase-like 15 (METTL15), encoded by a nuclear gene, is responsible for 12S mt-rRNA methylation at m[4]C839 both in vivo and in vitro We tracked the evolutionary history of RNA m[4]C methyltransferases and identified a difference in substrate preference between METTL15 and its bacterial ortholog rsmH. Additionally, unlike the very modest impact of a loss of m[4]C methylation in bacterial small subunit rRNA on the ribosome, we found that METTL15 depletion results in impaired translation of mitochondrial protein-coding mRNAs and decreases mitochondrial respiration capacity. Our findings reveal that human METTL15 is required for mitochondrial function, delineate the evolution of methyltransferase substrate specificities and modification patterns in rRNA, and highlight a differential impact of m[4]C methylation on prokaryotic ribosomes and eukaryotic mitochondrial ribosomes.}, }
@article {pmid32371258, year = {2020}, author = {Sun, L and Zhou, F and Shao, Y and Lv, Z and Li, C}, title = {The iron-sulfur protein subunit of succinate dehydrogenase is critical in driving mitochondrial reactive oxygen species generation in Apostichopus japonicus.}, journal = {Fish &amp; shellfish immunology}, volume = {102}, number = {}, pages = {350-360}, doi = {10.1016/j.fsi.2020.04.060}, pmid = {32371258}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Iron-Sulfur Proteins/*genetics/metabolism ; Lipopolysaccharides/pharmacology ; Mitochondria/metabolism ; Phylogeny ; Reactive Oxygen Species/*metabolism ; Sequence Alignment ; Stichopus/enzymology/*genetics/*immunology/*metabolism ; Succinate Dehydrogenase/genetics/*metabolism ; Vibrio/physiology ; }, abstract = {Succinate dehydrogenase (SDH) is a mitochondrial enzyme with the unique ability to participate in both the tricarboxylic acid cycle and the electron transport chain to produce reactive oxygen species (ROS). The B subunit of SDH is required for succinate oxidation, which is critical for pro-inflammatory response. In this study, we cloned the iron-sulfur protein subunit of SDH from Apostichopus japonicus (denoted as AjSDHB) via RACE technology and explored its role in the immune system as a response to pathogen infection. The full-length cDNA of AjSDHB was 1442 bp with a complete open reading frame of 858 bp encoding 286 amino acids. Simple modular architecture research tool analysis revealed that AjSDHB contained two conserved domains, including a 2Fe-2S iron-sulfur cluster binding domain and a 4Fe-4S dicluster domain, without a signal peptide. Multiple sequence alignment demonstrated that AjSDHB shared a high degree of structural conservation and sequence identities with other counterparts from invertebrates and vertebrates. Phylogenetic analysis supported the finding that AjSDHB is a new member of the SDHB protein subfamily. Tissue distribution analysis revealed that AjSDHB was expressed in all examined tissues and particularly highly expressed in the muscles. AjSDHB transcripts were markedly induced in coelomocytes both by Vibrio splendidus challenge in vivo and lipopolysaccharide exposure in vitro. Function analysis showed that siRNA-mediated AjSDHB knockdown could substantially reduce the mitochondrial membrane potential (ΔΨm) and further decrease mitochondrial ROS production in A. japonicus coelomocytes. By contrast, AjSDHB overexpression considerably increased ΔΨm and mitochondrial ROS production of A. japonicus coelomocytes. These results supported the idea that AjSDHB is involved in the innate immunity of A. japonicus through its participation in mitochondrial ROS generation.}, }
@article {pmid32362267, year = {2020}, author = {Pfannschmidt, T and Terry, MJ and Van Aken, O and Quiros, PM}, title = {Retrograde signals from endosymbiotic organelles: a common control principle in eukaryotic cells.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1801}, pages = {20190396}, pmid = {32362267}, issn = {1471-2970}, mesh = {Eukaryotic Cells/*metabolism ; Organelles/*metabolism ; *Signal Transduction ; Symbiosis/*physiology ; }, abstract = {Endosymbiotic organelles of eukaryotic cells, the plastids, including chloroplasts and mitochondria, are highly integrated into cellular signalling networks. In both heterotrophic and autotrophic organisms, plastids and/or mitochondria require extensive organelle-to-nucleus communication in order to establish a coordinated expression of their own genomes with the nuclear genome, which encodes the majority of the components of these organelles. This goal is achieved by the use of a variety of signals that inform the cell nucleus about the number and developmental status of the organelles and their reaction to changing external environments. Such signals have been identified in both photosynthetic and non-photosynthetic eukaryotes (known as retrograde signalling and retrograde response, respectively) and, therefore, appear to be universal mechanisms acting in eukaryotes of all kingdoms. In particular, chloroplasts and mitochondria both harbour crucial redox reactions that are the basis of eukaryotic life and are, therefore, especially susceptible to stress from the environment, which they signal to the rest of the cell. These signals are crucial for cell survival, lifespan and environmental adjustment, and regulate quality control and targeted degradation of dysfunctional organelles, metabolic adjustments, and developmental signalling, as well as induction of apoptosis. The functional similarities between retrograde signalling pathways in autotrophic and non-autotrophic organisms are striking, suggesting the existence of common principles in signalling mechanisms or similarities in their evolution. Here, we provide a survey for the newcomers to this field of research and discuss the importance of retrograde signalling in the context of eukaryotic evolution. Furthermore, we discuss commonalities and differences in retrograde signalling mechanisms and propose retrograde signalling as a general signalling mechanism in eukaryotic cells that will be also of interest for the specialist. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.}, }
@article {pmid32362253, year = {2020}, author = {Shapiguzov, A and Nikkanen, L and Fitzpatrick, D and Vainonen, JP and Gossens, R and Alseekh, S and Aarabi, F and Tiwari, A and Blokhina, O and Panzarová, K and Benedikty, Z and Tyystjärvi, E and Fernie, AR and Trtílek, M and Aro, EM and Rintamäki, E and Kangasjärvi, J}, title = {Dissecting the interaction of photosynthetic electron transfer with mitochondrial signalling and hypoxic response in the Arabidopsis rcd1 mutant.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1801}, pages = {20190413}, pmid = {32362253}, issn = {1471-2970}, mesh = {Anaerobiosis ; Arabidopsis/*genetics/*physiology ; Arabidopsis Proteins/genetics ; Electron Transport ; Mitochondria/*metabolism ; Nuclear Proteins/genetics ; *Photosynthesis ; *Signal Transduction ; }, abstract = {The Arabidopsis mutant rcd1 is tolerant to methyl viologen (MV). MV enhances the Mehler reaction, i.e. electron transfer from Photosystem I (PSI) to O2, generating reactive oxygen species (ROS) in the chloroplast. To study the MV tolerance of rcd1, we first addressed chloroplast thiol redox enzymes potentially implicated in ROS scavenging. NADPH-thioredoxin oxidoreductase type C (NTRC) was more reduced in rcd1. NTRC contributed to the photosynthetic and metabolic phenotypes of rcd1, but did not determine its MV tolerance. We next tested rcd1 for alterations in the Mehler reaction. In rcd1, but not in the wild type, the PSI-to-MV electron transfer was abolished by hypoxic atmosphere. A characteristic feature of rcd1 is constitutive expression of mitochondrial dysfunction stimulon (MDS) genes that affect mitochondrial respiration. Similarly to rcd1, in other MDS-overexpressing plants hypoxia also inhibited the PSI-to-MV electron transfer. One possible explanation is that the MDS gene products may affect the Mehler reaction by altering the availability of O2. In green tissues, this putative effect is masked by photosynthetic O2 evolution. However, O2 evolution was rapidly suppressed in MV-treated plants. Transcriptomic meta-analysis indicated that MDS gene expression is linked to hypoxic response not only under MV, but also in standard growth conditions. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.}, }
@article {pmid32360615, year = {2020}, author = {Aparicio-Trejo, OE and Avila-Rojas, SH and Tapia, E and Rojas-Morales, P and León-Contreras, JC and Martínez-Klimova, E and Hernández-Pando, R and Sánchez-Lozada, LG and Pedraza-Chaverri, J}, title = {Chronic impairment of mitochondrial bioenergetics and β-oxidation promotes experimental AKI-to-CKD transition induced by folic acid.}, journal = {Free radical biology &amp; medicine}, volume = {154}, number = {}, pages = {18-32}, doi = {10.1016/j.freeradbiomed.2020.04.016}, pmid = {32360615}, issn = {1873-4596}, mesh = {*Acute Kidney Injury/chemically induced/drug therapy/prevention &amp; control ; Disease Progression ; Energy Metabolism ; Folic Acid ; Humans ; Mitochondria/metabolism ; Oxidation-Reduction ; *Renal Insufficiency, Chronic/chemically induced/drug therapy/metabolism ; }, abstract = {Recent studies suggest that mitochondrial bioenergetics and oxidative stress alterations may be common mechanisms involved in the progression of renal damage. However, the evolution of the mitochondrial alterations over time and the possible effects that their prevention could have in the progression of renal damage are not clear. Folic acid (FA)-induced kidney damage is a widely used experimental model to induce acute kidney injury (AKI), which can evolve to chronic kidney disease (CKD). Therefore, it has been extensively applied to study the mechanisms involved in AKI-to-CKD transition. We previously demonstrated that one day after FA administration, N-acetyl-cysteine (NAC) pre-administration prevented the development of AKI induced by FA. Such therapeutic effect was related to mitochondrial preservation. In the present study, we characterized the temporal course of mitochondrial bioenergetics and redox state alterations along the progression of renal damage induced by FA. Mitochondrial function was studied at different time points and showed a sustained impairment in oxidative phosphorylation capacity and a decrease in β-oxidation, decoupling, mitochondrial membrane potential depolarization and a pro-oxidative state, attributed to the reduction in activity of complexes I and III and mitochondrial cristae effacement, thus favoring the transition from AKI to CKD. Furthermore, the mitochondrial protection by NAC administration before AKI prevented not only the long-term deterioration of mitochondrial function at the chronic stage, but also CKD development. Taken together, our results support the idea that the prevention of mitochondrial dysfunction during an AKI event can be a useful strategy to prevent the transition to CKD.}, }
@article {pmid32350251, year = {2020}, author = {Peris, D and Alexander, WG and Fisher, KJ and Moriarty, RV and Basuino, MG and Ubbelohde, EJ and Wrobel, RL and Hittinger, CT}, title = {Synthetic hybrids of six yeast species.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {2085}, pmid = {32350251}, issn = {2041-1723}, mesh = {Directed Molecular Evolution ; Genome Size ; Genome, Fungal ; Genomic Instability ; Genotype ; *Hybridization, Genetic ; Inheritance Patterns/genetics ; Mitochondria/genetics ; Phenotype ; Quantitative Trait, Heritable ; Saccharomyces/*genetics ; }, abstract = {Allopolyploidy generates diversity by increasing the number of copies and sources of chromosomes. Many of the best-known evolutionary radiations, crops, and industrial organisms are ancient or recent allopolyploids. Allopolyploidy promotes differentiation and facilitates adaptation to new environments, but the tools to test its limits are lacking. Here we develop an iterative method of Hybrid Production (iHyPr) to combine the genomes of multiple budding yeast species, generating Saccharomyces allopolyploids of at least six species. When making synthetic hybrids, chromosomal instability and cell size increase dramatically as additional copies of the genome are added. The six-species hybrids initially grow slowly, but they rapidly regain fitness and adapt, even as they retain traits from multiple species. These new synthetic yeast hybrids and the iHyPr method have potential applications for the study of polyploidy, genome stability, chromosome segregation, and bioenergy.}, }
@article {pmid32349679, year = {2020}, author = {Anwar, A and She, M and Wang, K and Ye, X}, title = {Cloning and molecular characterization of Triticum aestivum ornithine amino transferase (TaOAT) encoding genes.}, journal = {BMC plant biology}, volume = {20}, number = {1}, pages = {187}, pmid = {32349679}, issn = {1471-2229}, support = {31771788//National Natural Science Foundation of China/ ; 2019BBF02020//General Key Program of Science and Technology Department of Ningxia/ ; }, mesh = {Chromosomes, Plant ; Droughts ; *Genes, Plant ; Ornithine-Oxo-Acid Transaminase/*genetics ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Polyethylene Glycols/pharmacology ; Polyploidy ; Promoter Regions, Genetic ; Sodium Chloride/pharmacology ; Transcriptome ; Triticum/drug effects/*genetics ; }, abstract = {BACKGROUND: Ornithine aminotransferase (OAT, EC:2.6.1.13), alternatively known as ornithine delta aminotransferase (δOAT), is a pyridoxal phosphate (PLP)-dependent enzyme involved in the conversion of ornithine into glutamyl-5-semi-aldehyde (GSA) and vice versa. Up till now, there has been no study on OAT in wheat despite the success of its isolation from rice, maize, and sorghum. This study focuses on identification and molecular characterization of OAT in wheat.<br><br>RESULTS: In total, three homeologous OAT genes in wheat genome were found on chromosome group 5, named as TaOAT-5AL, TaOAT-5BL, and TaOAT-5DL. Sequence alignment between gDNA and its corresponding cDNA obtained a total of ten exons and nine introns. A phylogenetic tree was constructed and results indicated that OATs shared highly conserved domains between monocots and eudicots, which was further illustrated by using WebLogo to generate a sequence logo. Further subcellular localization analysis indicated that they functioned in mitochondria. Protein-protein interactions supported their role in proline biosynthesis through interactions with genes, such as delta 1-pyrroline-5-carboxylate synthetase (P5CS) and pyrroline-5-carboxylate reductase (P5CR), involved in the proline metabolic pathway. Promoter analysis exposed the presence of several stress responsive elements, implying their involvement in stress regulation. Expression profiling illustrated that TaOAT was highly induced in the wheat plants exposed to drought or salt stress condition. Upregulated expression of TaOATs was observed in stamens and at the heading stage. A potential role of TaOAT genes during floret development was also revealed. Furthermore, the transgenic plants overexpressing TaOAT showed enhanced tolerance to drought stress by increasing proline accumulation. In addition, salt tolerance of the transgenic plants was also enhanced.<br><br>CONCLUSION: TaOATs genes were involved in proline synthesis and nitrogen remobilization because they interacted with genes related to proline biosynthesis enzymes and arginine catabolism. In addition, TaOAT genes had a role in abiotic stress tolerance and a potential role in floret development. The results of this study may propose future research in the improvement of wheat resistance to abiotic stresses.}, }
@article {pmid32345370, year = {2020}, author = {Bateman, A}, title = {Division of labour in a matrix, rather than phagocytosis or endosymbiosis, as a route for the origin of eukaryotic cells.}, journal = {Biology direct}, volume = {15}, number = {1}, pages = {8}, pmid = {32345370}, issn = {1745-6150}, mesh = {*Biological Evolution ; Eukaryotic Cells/*physiology ; Extracellular Space/*physiology ; *Microbial Interactions ; Models, Biological ; Phagocytosis ; Prokaryotic Cells/*physiology ; Symbiosis ; }, abstract = {Two apparently irreconcilable models dominate research into the origin of eukaryotes. In one model, amitochondrial proto-eukaryotes emerged autogenously from the last universal common ancestor of all cells. Proto-eukaryotes subsequently acquired mitochondrial progenitors by the phagocytic capture of bacteria. In the second model, two prokaryotes, probably an archaeon and a bacterial cell, engaged in prokaryotic endosymbiosis, with the species resident within the host becoming the mitochondrial progenitor. Both models have limitations. A search was therefore undertaken for alternative routes towards the origin of eukaryotic cells. The question was addressed by considering classes of potential pathways from prokaryotic to eukaryotic cells based on considerations of cellular topology. Among the solutions identified, one, called here the "third-space model", has not been widely explored. A version is presented in which an extracellular space (the third-space), serves as a proxy cytoplasm for mixed populations of archaea and bacteria to "merge" as a transitionary complex without obligatory endosymbiosis or phagocytosis and to form a precursor cell. Incipient nuclei and mitochondria diverge by division of labour. The third-space model can accommodate the reorganization of prokaryote-like genomes to a more eukaryote-like genome structure. Nuclei with multiple chromosomes and mitosis emerge as a natural feature of the model. The model is compatible with the loss of archaeal lipid biochemistry while retaining archaeal genes and provides a route for the development of membranous organelles such as the Golgi apparatus and endoplasmic reticulum. Advantages, limitations and variations of the "third-space" models are discussed. REVIEWERS: This article was reviewed by Damien Devos, Buzz Baum and Michael Gray.}, }
@article {pmid32345161, year = {2020}, author = {Gyllenhammer, LE and Entringer, S and Buss, C and Wadhwa, PD}, title = {Developmental programming of mitochondrial biology: a conceptual framework and review.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1926}, pages = {20192713}, pmid = {32345161}, issn = {1471-2954}, support = {K99 HD097302/HD/NICHD NIH HHS/United States ; R00 HD097302/HD/NICHD NIH HHS/United States ; R01 AG050455/AG/NIA NIH HHS/United States ; R01 MH105538/MH/NIMH NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Animals ; *Biological Evolution ; Humans ; *Mitochondria ; }, abstract = {Research on mechanisms underlying the phenomenon of developmental programming of health and disease has focused primarily on processes that are specific to cell types, organs and phenotypes of interest. However, the observation that exposure to suboptimal or adverse developmental conditions concomitantly influences a broad range of phenotypes suggests that these exposures may additionally exert effects through cellular mechanisms that are common, or shared, across these different cell and tissue types. It is in this context that we focus on cellular bioenergetics and propose that mitochondria, bioenergetic and signalling organelles, may represent a key cellular target underlying developmental programming. In this review, we discuss empirical findings in animals and humans that suggest that key structural and functional features of mitochondrial biology exhibit developmental plasticity, and are influenced by the same physiological pathways that are implicated in susceptibility for complex, common age-related disorders, and that these targets of mitochondrial developmental programming exhibit long-term temporal stability. We conclude by articulating current knowledge gaps and propose future research directions to bridge these gaps.}, }
@article {pmid32341569, year = {2020}, author = {López-García, P and Moreira, D}, title = {The Syntrophy hypothesis for the origin of eukaryotes revisited.}, journal = {Nature microbiology}, volume = {5}, number = {5}, pages = {655-667}, pmid = {32341569}, issn = {2058-5276}, mesh = {Archaea/genetics/*metabolism ; Bacteria/genetics ; *Biological Evolution ; Cell Nucleus ; Eukaryota/genetics/*metabolism ; Eukaryotic Cells/*metabolism ; Genome, Archaeal ; Hydrogen/metabolism ; Membranes/metabolism ; Mitochondria/metabolism ; Oxidation-Reduction ; *Phylogeny ; Sulfur/metabolism ; Symbiosis/physiology ; }, abstract = {The discovery of Asgard archaea, phylogenetically closer to eukaryotes than other archaea, together with improved knowledge of microbial ecology, impose new constraints on emerging models for the origin of the eukaryotic cell (eukaryogenesis). Long-held views are metamorphosing in favour of symbiogenetic models based on metabolic interactions between archaea and bacteria. These include the classical Searcy's and Hydrogen hypothesis, and the more recent Reverse Flow and Entangle-Engulf-Endogenize models. Two decades ago, we put forward the Syntrophy hypothesis for the origin of eukaryotes based on a tripartite metabolic symbiosis involving a methanogenic archaeon (future nucleus), a fermentative myxobacterial-like deltaproteobacterium (future eukaryotic cytoplasm) and a metabolically versatile methanotrophic alphaproteobacterium (future mitochondrion). A refined version later proposed the evolution of the endomembrane and nuclear membrane system by invagination of the deltaproteobacterial membrane. Here, we adapt the Syntrophy hypothesis to contemporary knowledge, shifting from the original hydrogen and methane-transfer-based symbiosis (HM Syntrophy) to a tripartite hydrogen and sulfur-transfer-based model (HS Syntrophy). We propose a sensible ecological scenario for eukaryogenesis in which eukaryotes originated in early Proterozoic microbial mats from the endosymbiosis of a hydrogen-producing Asgard archaeon within a complex sulfate-reducing deltaproteobacterium. Mitochondria evolved from versatile, facultatively aerobic, sulfide-oxidizing and, potentially, anoxygenic photosynthesizing alphaproteobacterial endosymbionts that recycled sulfur in the consortium. The HS Syntrophy hypothesis accounts for (endo)membrane, nucleus and metabolic evolution in a realistic ecological context. We compare and contrast the HS Syntrophy hypothesis to other models of eukaryogenesis, notably in terms of the mode and tempo of eukaryotic trait evolution, and discuss several model predictions and how these can be tested.}, }
@article {pmid32340511, year = {2020}, author = {Kumar, A and Dewan, S and Lochan, R and Sharma, DK}, title = {Spatial genetic structure of black francolin (Francolinus francolinus asiae) in the North-Western Himalayan region based on mitochondrial control region.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {31}, number = {4}, pages = {163-170}, doi = {10.1080/24701394.2020.1757664}, pmid = {32340511}, issn = {2470-1408}, mesh = {Altitude ; Animals ; DNA, Mitochondrial/*genetics ; Demography ; Ecosystem ; Evolution, Molecular ; Galliformes/*genetics ; Genetic Variation ; India ; Mitochondria/*genetics ; Sequence Analysis, DNA ; }, abstract = {Due to specific habitat preferences and behavioural limitations, black francolin is not uniformly distributed across the northwestern Himalayan landscape, rather is confined to certain land mosaic. The habitable zones are further reduced due to several manmade threats as logging and forest fire leading to sparse distribution. Overall 54 samples were used for partial sequence analysis of mitochondrial control region. A well evident divergence pattern was observed as individuals collected from low altitude, terrai region significantly distanced from high altitude sampled individuals. Also, the individuals at lower elevation sites exhibited higher genetic diversity in comparison to the samples collected at higher elevations. This indicates that patchy distribution and low dispersal rate have resulted in fine-scale patterns of genetic diversity among the black francolin population. Further, habitat loss and forest fragmentation could lead to more small and isolated populations that could suffer from reduced genetic diversity and may be higher extinction rates.}, }
@article {pmid32340081, year = {2020}, author = {Cariou, M and Henri, H and Martinez, S and Duret, L and Charlat, S}, title = {How consistent is RAD-seq divergence with DNA-barcode based clustering in insects?.}, journal = {Molecular ecology resources}, volume = {20}, number = {5}, pages = {1294-1298}, doi = {10.1111/1755-0998.13178}, pmid = {32340081}, issn = {1755-0998}, support = {//Centre National de la Recherche Scientifique/ ; }, mesh = {Animals ; Cluster Analysis ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; *Insecta/classification/genetics ; Phylogeny ; *Sequence Analysis, DNA ; }, abstract = {Promoted by the barcoding approach, mitochondrial DNA is more than ever used as a molecular marker to identify species boundaries. Yet, it has been repeatedly argued that it may be poorly suited for this purpose, especially in insects where mitochondria are often associated with invasive intracellular bacteria that may promote their introgression. Here, we inform this debate by assessing how divergent nuclear genomes can be when mitochondrial barcodes indicate very high proximity. To this end, we obtained RAD-seq data from 92 barcode-based species-like units (operational taxonomic units [OTUs]) spanning four insect orders. In 100% of the cases, the observed median nuclear divergence was lower than 2%, a value that was recently estimated as one below which nuclear gene flow is not uncommon. These results suggest that although mitochondria may occasionally leak between species, this process is rare enough in insects to make DNA barcoding a reliable tool for clustering specimens into species-like units.}, }
@article {pmid32337520, year = {2020}, author = {Pearson, SA and Wachnowsky, C and Cowan, JA}, title = {Defining the mechanism of the mitochondrial Atm1p [2Fe-2S] cluster exporter.}, journal = {Metallomics : integrated biometal science}, volume = {12}, number = {6}, pages = {902-915}, pmid = {32337520}, issn = {1756-591X}, support = {R21 AI072443/AI/NIAID NIH HHS/United States ; }, mesh = {ATP-Binding Cassette Transporters/*metabolism ; Electron Transport ; Glutathione/metabolism ; Humans ; Iron-Sulfur Proteins/*metabolism ; Liposomes/metabolism ; Mitochondria/*metabolism ; Mutagenesis, Site-Directed ; Proteolipids/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/*metabolism ; }, abstract = {Iron-sulfur cluster proteins play key roles in a multitude of physiological processes; including gene expression, nitrogen and oxygen sensing, electron transfer, and DNA repair. Biosynthesis of iron-sulfur clusters occurs in mitochondria on iron-sulfur cluster scaffold proteins in the form of [2Fe-2S] cores that are then transferred to apo targets within metabolic or respiratory pathways. The mechanism by which cytosolic Fe-S cluster proteins mature to their holo forms remains controversial. The mitochondrial inner membrane protein Atm1p can transport glutathione-coordinated iron-sulfur clusters, which may connect the mitochondrial and cytosolic iron-sulfur cluster assembly systems. Herein we describe experiments on the yeast Atm1p/ABCB7 exporter that provide additional support for a glutathione-complexed cluster as the natural physiological substrate and a reflection of the endosymbiotic model of mitochondrial evolution. These studies provide insight on the mechanism of cluster transport and the molecular basis of human disease conditions related to ABCB7. Recruitment of MgATP following cluster binding promotes a structural transition from closed to open conformations that is mediated by coupling helices, with MgATP hydrolysis facilitating the return to the closed state.}, }
@article {pmid32334144, year = {2020}, author = {Waltz, F and Corre, N and Hashem, Y and Giegé, P}, title = {Specificities of the plant mitochondrial translation apparatus.}, journal = {Mitochondrion}, volume = {53}, number = {}, pages = {30-37}, doi = {10.1016/j.mito.2020.04.008}, pmid = {32334144}, issn = {1872-8278}, mesh = {Gene Expression Regulation ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/genetics ; Mitochondrial Ribosomes/*metabolism ; Plant Proteins/genetics ; Plants/genetics/*metabolism ; Protein Biosynthesis ; }, abstract = {Mitochondria are endosymbiotic organelles responsible for energy production in most eukaryotic cells. They host a genome and a fully functional gene expression machinery. In plants this machinery involves hundreds of pentatricopeptide repeat (PPR) proteins. Translation, the final step of mitochondrial gene expression is performed by mitochondrial ribosomes (mitoribosomes). The nature of these molecular machines remained elusive for a very long time. Because of their bacterial origin, it was expected that mitoribosomes would closely resemble bacterial ribosomes. However, recent advances in cryo-electron microscopy have revealed the extraordinary diversity of mitoribosome structure and composition. The plant mitoribosome was characterized for Arabidopsis. In plants, in contrast to other species such as mammals and kinetoplastids where rRNA has been largely reduced, the mitoribosome could be described as a protein/RNA-augmented bacterial ribosome. It has an oversized small subunit formed by expanded ribosomal RNAs and additional protein components when compared to bacterial ribosomes. The same holds true for the large subunit. The small subunit is characterized by a new elongated domain on the head. Among its additional proteins, several PPR proteins are core mitoribosome proteins. They mainly act at the structural level to stabilize and maintain the plant-specific ribosomal RNA expansions but could also be involved in translation initiation. Recent advances in plant mitoribosome composition and structure, its specialization for membrane protein synthesis, translation initiation, the regulation and dynamics of mitochondrial translation are reviewed here and put in perspective with the diversity of mitochondrial translation processes in the green lineage and in the wider context of eukaryote evolution.}, }
@article {pmid32333942, year = {2020}, author = {Kaufer, A and Stark, D and Ellis, J}, title = {A review of the systematics, species identification and diagnostics of the Trypanosomatidae using the maxicircle kinetoplast DNA: from past to present.}, journal = {International journal for parasitology}, volume = {50}, number = {6-7}, pages = {449-460}, doi = {10.1016/j.ijpara.2020.03.003}, pmid = {32333942}, issn = {1879-0135}, mesh = {DNA, Kinetoplast/*genetics ; *Genome, Protozoan ; Phylogeny ; *Trypanosomatina/classification/genetics ; }, abstract = {The Trypanosomatid family are a diverse and widespread group of protozoan parasites that belong to the higher order class Kinetoplastida. Containing predominantly monoxenous species (i.e. those having only a single host) that are confined to invertebrate hosts, this class is primarily known for its pathogenic dixenous species (i.e. those that have two hosts), serving as the aetiological agents of the important neglected tropical diseases including leishmaniasis, American trypanosomiasis (Chagas disease) and human African trypanosomiasis. Over the past few decades, a multitude of studies have investigated the diversity, classification and evolutionary history of the trypanosomatid family using different approaches and molecular targets. The mitochondrial-like DNA of the trypanosomatid parasites, also known as the kinetoplast, has emerged as a unique taxonomic and diagnostic target for exploring the evolution of this diverse group of parasitic eukaryotes. This review discusses recent advancements and important developments that have made a significant impact in the field of trypanosomatid systematics and diagnostics in recent years.}, }
@article {pmid32330419, year = {2020}, author = {Rotterová, J and Salomaki, E and Pánek, T and Bourland, W and Žihala, D and Táborský, P and Edgcomb, VP and Beinart, RA and Kolísko, M and Čepička, I}, title = {Genomics of New Ciliate Lineages Provides Insight into the Evolution of Obligate Anaerobiosis.}, journal = {Current biology : CB}, volume = {30}, number = {11}, pages = {2037-2050.e6}, doi = {10.1016/j.cub.2020.03.064}, pmid = {32330419}, issn = {1879-0445}, mesh = {Anaerobiosis/*genetics/*physiology ; *Biological Evolution ; Ciliophora/*genetics/*physiology/ultrastructure ; *Genomics ; Mitochondria/physiology ; }, abstract = {Oxygen plays a crucial role in energetic metabolism of most eukaryotes. Yet adaptations to low-oxygen concentrations leading to anaerobiosis have independently arisen in many eukaryotic lineages, resulting in a broad spectrum of reduced and modified mitochondrion-related organelles (MROs). In this study, we present the discovery of two new class-level lineages of free-living marine anaerobic ciliates, Muranotrichea, cl. nov. and Parablepharismea, cl. nov., that, together with the class Armophorea, form a major clade of obligate anaerobes (APM ciliates) within the Spirotrichea, Armophorea, and Litostomatea (SAL) group. To deepen our understanding of the evolution of anaerobiosis in ciliates, we predicted the mitochondrial metabolism of cultured representatives from all three classes in the APM clade by using transcriptomic and metagenomic data and performed phylogenomic analyses to assess their evolutionary relationships. The predicted mitochondrial metabolism of representatives from the APM ciliates reveals functional adaptations of metabolic pathways that were present in their last common ancestor and likely led to the successful colonization and diversification of the group in various anoxic environments. Furthermore, we discuss the possible relationship of Parablepharismea to the uncultured deep-sea class Cariacotrichea on the basis of single-gene analyses. Like most anaerobic ciliates, all studied species of the APM clade host symbionts, which we propose to be a significant accelerating factor in the transitions to an obligately anaerobic lifestyle. Our results provide an insight into the evolutionary mechanisms of early transitions to anaerobiosis and shed light on fine-scale adaptations in MROs over a relatively short evolutionary time frame.}, }
@article {pmid32329402, year = {2020}, author = {Ruiz-García, M and Pinedo-Castro, M and Albino, A and Arias-Vásquez, JY and Castellanos, A and Shostell, JM}, title = {Invalidation of taxa within the silvery wooly monkey (Lagothrix lagothricha poeppigii, Atelidae, Primates).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {31}, number = {4}, pages = {147-162}, doi = {10.1080/24701394.2020.1757084}, pmid = {32329402}, issn = {2470-1408}, mesh = {Animals ; Atelinae/*classification/genetics ; Brazil ; Ecuador ; Evolution, Molecular ; Female ; Genetic Variation ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Peru ; Phylogeny ; Phylogeography ; }, abstract = {The systematics of the Humboldt's wooly monkeys (L. lagothricha; Atelidae) is essential to preserve this Neotropical primate species. Traditionally, four morphological subspecies have been described, which recently have been molecularly confirmed. However, no population genetics studies have been carried out throughout the geographical distribution of one of these subspecies, Lagothrix lagothricha poeppigii. For this reason, we analyzed nine mitochondrial genes of L. l. poeppigii mainly collected from the Ecuadorian and Peruvian Amazon in order to better understand the evolutionary history of this taxon. The mitochondrial genetic diversity levels (haplotype and nucleotide diversity) we estimated are likely the highest yet reported for L. lagothricha. Our results did not detect important genetic structure within L. l. poeppigii. Furthermore, our phylogenetic analyses did not detect any relevant molecular cluster in the area where Groves hypothesized the existence of L. poeppigii castelnaui. Therefore, based on these data, castelnaui is not a valid taxon from a molecular perspective. The most differentiated subpopulation within L. l. poeppigii was from Morona-Santiago province (Ecuador) and had a genetic distance of 0.8-1.2% relative to the other subpopulations studied. However, this genetic distance range is within the variability found within a population. We estimated the mitochondrial temporal diversification within L. l. poeppigii to have occurred during the Pleistocene, 1.8-1.2 million years ago. Similarly, all our analyses detected a strong Pleistocene female population expansion for this taxon. Diverse spatial genetic analyses, perhaps with the exception of Monmonier's Algorithm, did not detect differentiated taxa within the area analyzed for L. l. poeppigii. These genetics results could be of importance to conservation efforts to preserve this taxon as one unit.}, }
@article {pmid32326478, year = {2020}, author = {Shu, B and Zhang, J and Veeran, S and Zhong, G}, title = {Pro-Apoptotic Function Analysis of the Reaper Homologue IBM1 in Spodoptera frugiperda.}, journal = {International journal of molecular sciences}, volume = {21}, number = {8}, pages = {}, pmid = {32326478}, issn = {1422-0067}, support = {31572335//National Natural Science Foundation of China/ ; }, mesh = {Amino Acid Chloromethyl Ketones/pharmacology ; Amino Acid Sequence ; Animals ; Apoptosis/drug effects/*genetics/radiation effects ; Baculoviral IAP Repeat-Containing 3 Protein/pharmacology ; Camptothecin/pharmacology ; Caspase Inhibitors/*pharmacology ; Gene Expression Regulation, Developmental ; Insect Proteins/genetics/*metabolism ; Jumonji Domain-Containing Histone Demethylases/genetics/*metabolism ; Limonins/pharmacology ; Mitochondria/drug effects/*metabolism/radiation effects ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sf9 Cells ; Spodoptera/genetics/growth &amp; development/*metabolism/radiation effects ; Ultraviolet Rays ; Up-Regulation ; }, abstract = {As an important type of programmed cell death, apoptosis plays a critical role in lepidopteran insects in response to various internal and external stresses. It is controlled by a network of genes such as those encoding the inhibitor of apoptosis proteins. However, there are few studies on apoptosis-related genes in Spodoptera frugiperda. In this study, an orthologue to the Drosophila reaper gene, named Sf-IBM1, was identified from S. frugiperda, and a full-length sequence was obtained by reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends PCR (RACE-PCR). The expression pattern of Sf-IBM1 was determined in different developmental stages and various tissues. Apoptotic stimuli including azadirachtin, camptothecin, and ultraviolet radiation (UV) induced the expression of Sf-IBM1 at both transcript and protein levels. Overexpression of Sf-IBM1 induced apoptosis in Sf9 cells, and the Sf-IBM1 protein was localized in mitochondria. The apoptosis induced by Sf-IBM1 could be blocked by the caspase universal inhibitor carbobenzoxy-valyl-alanyl-aspartyl-[O-methyl]-fluoromethylketone (Z-VAD-FMK) and Sf-IAP1. Our results provide valuable information that should contribute to a better understanding of the molecular events that lead to apoptosis in lepidopterans.}, }
@article {pmid32322241, year = {2020}, author = {Yang, F and Jin, H and Wang, XQ and Li, Q and Zhang, JT and Cui, N and Jiang, YL and Chen, Y and Wu, QF and Zhou, CZ and Li, WF}, title = {Genomic Analysis of Mic1 Reveals a Novel Freshwater Long-Tailed Cyanophage.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {484}, pmid = {32322241}, issn = {1664-302X}, abstract = {Lake Chaohu, one of the five largest freshwater lakes in China, has been suffering from severe cyanobacterial blooms in the summer for many years. Cyanophages, the viruses that specifically infect cyanobacteria, play a key role in modulating cyanobacterial population, and thus regulate the emergence and decline of cyanobacterial blooms. Here we report a long-tailed cyanophage isolated from Lake Chaohu, termed Mic1, which specifically infects the cyanobacterium Microcystis aeruginosa. Mic1 has an icosahedral head of 88 nm in diameter and a long flexible tail of 400 nm. It possesses a circular genome of 92,627 bp, which contains 98 putative open reading frames. Genome sequence analysis enabled us to define a novel terminase large subunit that consists of two types of intein, indicating that the genome packaging of Mic1 is under fine control via posttranslational maturation of the terminase. Moreover, phylogenetic analysis suggested Mic1 and mitochondria share a common evolutionary origin of DNA polymerase γ gene. All together, these findings provided a start-point for investigating the co-evolution of cyanophages and its cyanobacterial hosts.}, }
@article {pmid32320418, year = {2020}, author = {Medrano-Soto, A and Ghazi, F and Hendargo, KJ and Moreno-Hagelsieb, G and Myers, S and Saier, MH}, title = {Expansion of the Transporter-Opsin-G protein-coupled receptor superfamily with five new protein families.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0231085}, pmid = {32320418}, issn = {1932-6203}, support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence/genetics ; Carrier Proteins/classification/genetics ; Computational Biology ; *Evolution, Molecular ; Humans ; Membrane Transport Proteins/classification/*genetics ; Opsins/classification/*genetics ; Phylogeny ; Receptors, G-Protein-Coupled/classification/*genetics ; Receptors, Peptide/genetics ; }, abstract = {Here we provide bioinformatic evidence that the Organo-Arsenical Exporter (ArsP), Endoplasmic Reticulum Retention Receptor (KDELR), Mitochondrial Pyruvate Carrier (MPC), L-Alanine Exporter (AlaE), and the Lipid-linked Sugar Translocase (LST) protein families are members of the Transporter-Opsin-G Protein-coupled Receptor (TOG) Superfamily. These families share domains homologous to well-established TOG superfamily members, and their topologies of transmembranal segments (TMSs) are compatible with the basic 4-TMS repeat unit characteristic of this Superfamily. These repeat units tend to occur twice in proteins as a result of intragenic duplication events, often with subsequent gain/loss of TMSs in many superfamily members. Transporters within the ArsP family allow microbial pathogens to expel toxic arsenic compounds from the cell. Members of the KDELR family are involved in the selective retrieval of proteins that reside in the endoplasmic reticulum. Proteins of the MPC family are involved in the transport of pyruvate into mitochondria, providing the organelle with a major oxidative fuel. Members of family AlaE excrete L-alanine from the cell. Members of the LST family are involved in the translocation of lipid-linked glucose across the membrane. These five families substantially expand the range of substrates of transport carriers in the superfamily, although KDEL receptors have no known transport function. Clustering of protein sequences reveals the relationships among families, and the resulting tree correlates well with the degrees of sequence similarity documented between families. The analyses and programs developed to detect distant relatedness, provide insights into the structural, functional, and evolutionary relationships that exist between families of the TOG superfamily, and should be of value to many other investigators.}, }
@article {pmid32314625, year = {2020}, author = {Chagas, ATA and Ludwig, S and Pimentel, JDSM and de Abreu, NL and Nunez-Rodriguez, DL and Leal, HG and Kalapothakis, E}, title = {Use of complete mitochondrial genome sequences to identify barcoding markers for groups with low genetic distance.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {31}, number = {4}, pages = {139-146}, doi = {10.1080/24701394.2020.1748609}, pmid = {32314625}, issn = {2470-1408}, mesh = {Animals ; Bayes Theorem ; Characiformes/*classification/genetics ; DNA Barcoding, Taxonomic ; *Genetic Markers ; Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Species Specificity ; }, abstract = {Complete mitochondrial sequences can be rapidly obtained and are widely available, providing a great source of species information and allowing for the discovery of new specific molecular markers. However, for some taxonomic groups, traditional approaches for species delimitation are impaired by the low genetic distance values. In these cases, other species-level markers are used. For Prochilodus, which includes important neotropical fish species, species-level delimitation usually results in poor phylogenetic resolution when using mitochondrial COI/cytB genes as barcoding markers because of low genetic variability and low species-level resolution. Thus, in this study, we developed an approach to design and validate new barcoding markers with high species-level resolution obtained from the D-loop region, using Prochilodus spp. as a model. For the new barcoding marker validation, the amplicon region was used to infer the phylogenetic relationships of Prochilodus spp. through three distinct methods: Bayesian inference (BI), Neighbor-Joining method (NJ), and Maximum Likelihood method (ML). The phylogenetic relationships of Prochilodus spp. revealed high resolution at species-level, nonoverlapping clades, and high branch support. The genetic distance results allied to two different clustering methods (Bayesian Poisson tree processes and automatic barcode gap discovery) revealed the existence of a barcoding gap, thus, validating the use of the barcoding markers designed in this study. The approach proposed here may, therefore, be expanded to other taxa to access and validate new barcoding markers with higher resolution at the species level.}, }
@article {pmid32313974, year = {2020}, author = {Almeida, C and Amaral, MD}, title = {A central role of the endoplasmic reticulum in the cell emerges from its functional contact sites with multiple organelles.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {77}, number = {23}, pages = {4729-4745}, doi = {10.1007/s00018-020-03523-w}, pmid = {32313974}, issn = {1420-9071}, support = {SFRH/BPD/77720/2011//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIM-MEC/2131/2014//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; FCT/02/SAICT/2017/28800//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UID/MULTI/04046/2019//Bioisi/ ; SRC 013//Cystic Fibrosis Trust/ ; }, mesh = {Animals ; Autophagosomes/metabolism ; Endoplasmic Reticulum/*metabolism ; Endosomes/metabolism ; Humans ; Lipid Droplets/metabolism ; Models, Biological ; Organelles/*metabolism ; }, abstract = {Early eukaryotic cells emerged from the compartmentalization of metabolic processes into specific organelles through the development of an endomembrane system (ES), a precursor of the endoplasmic reticulum (ER), which was essential for their survival. Recently, substantial evidence emerged on how organelles communicate among themselves and with the plasma membrane (PM) through contact sites (CSs). From these studies, the ER-the largest single structure in eukaryotic cells-emerges as a central player communicating with all organelles to coordinate cell functions and respond to external stimuli to maintain cellular homeostasis. Herein we review the functional insights into the ER-CSs with other organelles in a physiological perspective. We hypothesize that, in addition to the primitive role by the ES in the appearance of proto-eukaryotes, its successor-the ER-emerges as the key coordinator of inter-organelle/PM communication. The ER thus appears to be the 'maestro' driving eukaryotic cell evolution by incorporating new functions/organelles, while remaining the real coordinator overarching cellular functions and orchestrating them with the external milieu.}, }
@article {pmid32306810, year = {2020}, author = {Lee, EH and Baek, SY and Park, JY and Kim, YW}, title = {Emodin in Rheum undulatum inhibits oxidative stress in the liver via AMPK with Hippo/Yap signalling pathway.}, journal = {Pharmaceutical biology}, volume = {58}, number = {1}, pages = {333-341}, pmid = {32306810}, issn = {1744-5116}, mesh = {AMP-Activated Protein Kinases/*metabolism ; Acetaminophen ; Adaptor Proteins, Signal Transducing/metabolism ; Animals ; Antioxidants/administration &amp; dosage/*pharmacology/therapeutic use ; Cell Cycle Proteins/metabolism ; Cell Line, Tumor ; Cells, Cultured ; Chemical and Drug Induced Liver Injury/*drug therapy/metabolism ; Eicosanoic Acids ; Emodin/administration &amp; dosage/*pharmacology/therapeutic use ; Gene Expression Regulation/drug effects ; Hepatocytes/drug effects ; Hippo Signaling Pathway ; Humans ; Male ; Membrane Potential, Mitochondrial/drug effects ; Mice ; Mice, Inbred C57BL ; Oxidative Stress/*drug effects ; Protein Serine-Threonine Kinases/metabolism ; Reactive Oxygen Species/metabolism ; Rheum/*chemistry ; Signal Transduction/drug effects ; YAP-Signaling Proteins ; }, abstract = {Context: Emodin is a compound in Rheum undulatum Linne (Polygonaceae) that has been reported to exert anti-inflammatory, antibacterial, and antiallergic effects.Objective: Oxidative stress is a causative agent of liver inflammation that may lead to fibrosis and hepato-carcinoma. In this study, we investigated the antioxidant effects of emodin and its mechanism.Materials and methods: We used the hepatocyte stimulated by arachidonic acid (AA) + iron cotreatment and the C57B/6 mice orally injected with acetaminophen (APAP, 500 mg/kg, 6 h), as assessed by immunoblot and next generation sequencing (NGS). Emodin was pre-treated in hepatocyte (3 ∼ 30 μM) for 1 h before AA + iron, and in mice (10 and 30 m/kg, P.O.) for 3 days before APAP.Results: In vitro, emodin treatment inhibited the cell death induced by AA + iron maximally at a dose of 10 μM (EC50 > 3 μM). In addition, emodin attenuated the decrease of anti-apoptotic proteins, and restored mitochondria membrane potential as mediated by the liver kinase B1 (LKB1)-AMP-activated protein kinase (AMPK) pathway. LKB1 mediated AMPK activation was verified using the LKB1 deficient cell line, HeLa. Emodin (10 μM; after 10 min) also induced the phosphorylation of Yes-associated protein 1 (YAP1), the main downstream target of the Hippo signalling pathway that mediated oxidative stress or the ROS-initiated signalling pathway. In vivo, the oral treatment of emodin (10 and 30 m/kg, 3 days) decreased APAP-induced hepatic damage, as indicated by decreases in antioxidant genes as well as tissue damage.Conclusion: Our results show that emodin inhibits oxidative liver injury via the AMPK/YAP mediated pathway.}, }
@article {pmid32299824, year = {2020}, author = {Ravishankar, A and Pupo, A and Gallagher, JEG}, title = {Resistance Mechanisms of Saccharomyces cerevisiae to Commercial Formulations of Glyphosate Involve DNA Damage Repair, the Cell Cycle, and the Cell Wall Structure.}, journal = {G3 (Bethesda, Md.)}, volume = {10}, number = {6}, pages = {2043-2056}, pmid = {32299824}, issn = {2160-1836}, mesh = {Cell Cycle ; Cell Wall ; DNA Damage ; Glycine/analogs &amp; derivatives ; *Herbicides ; *Saccharomyces cerevisiae/genetics ; Glyphosate ; }, abstract = {The use of glyphosate-based herbicides is widespread and despite their extensive use, their effects are yet to be deciphered completely. The additives in commercial formulations of glyphosate, though labeled inert when used individually, have adverse effects when used in combination with other additives along with the active ingredient. As a species, Saccharomyces cerevisiae has a wide range of resistance to glyphosate-based herbicides. To investigate the underlying genetic differences between sensitive and resistant strains, global changes in gene expression were measured, when yeast were exposed to a glyphosate-based herbicide (GBH). Expression of genes involved in numerous pathways crucial to the cell's functioning, such as DNA replication, MAPK signaling, meiosis, and cell wall synthesis changed. Because so many diverse pathways were affected, these strains were then subjected to in-lab-evolutions (ILE) to select mutations that confer increased resistance. Common fragile sites were found to play a role in adaptation to resistance to long-term exposure of GBHs. Copy number increased in approximately 100 genes associated with cell wall proteins, mitochondria, and sterol transport. Taking ILE and transcriptomic data into account it is evident that GBHs affect multiple biological processes in the cell. One such component is the cell wall structure which acts as a protective barrier in alleviating the stress caused by exposure to inert additives in GBHs. Sed1, a GPI-cell wall protein, plays an important role in tolerance of a GBH. Hence, a detailed study of the changes occurring at the genome and transcriptome levels is essential to better understand the effects of an environmental stressor such as a GBH, on the cell as a whole.}, }
@article {pmid32297991, year = {2020}, author = {Waters, ER and Vierling, E}, title = {Plant small heat shock proteins - evolutionary and functional diversity.}, journal = {The New phytologist}, volume = {227}, number = {1}, pages = {24-37}, doi = {10.1111/nph.16536}, pmid = {32297991}, issn = {1469-8137}, mesh = {*Heat-Shock Proteins, Small/genetics ; Molecular Chaperones ; Plant Proteins/genetics ; Plants/genetics ; Seeds ; }, abstract = {Small heat shock proteins (sHSPs) are an ubiquitous protein family found in archaea, bacteria and eukaryotes. In plants, as in other organisms, sHSPs are upregulated by stress and are proposed to act as molecular chaperones to protect other proteins from stress-induced damage. sHSPs share an 'α-crystallin domain' with a β-sandwich structure and a diverse N-terminal domain. Although sHSPs are 12-25 kDa polypeptides, most assemble into oligomers with ≥ 12 subunits. Plant sHSPs are particularly diverse and numerous; some species have as many as 40 sHSPs. In angiosperms this diversity comprises ≥ 11 sHSP classes encoding proteins targeted to the cytosol, nucleus, endoplasmic reticulum, chloroplasts, mitochondria and peroxisomes. The sHSPs underwent a lineage-specific gene expansion, diversifying early in land plant evolution, potentially in response to stress in the terrestrial environment, and expanded again in seed plants and again in angiosperms. Understanding the structure and evolution of plant sHSPs has progressed, and a model for their chaperone activity has been proposed. However, how the chaperone model applies to diverse sHSPs and what processes sHSPs protect are far from understood. As more plant genomes and transcriptomes become available, it will be possible to explore theories of the evolutionary pressures driving sHSP diversification.}, }
@article {pmid32295425, year = {2020}, author = {Rodríguez, M and Valez, V and Cimarra, C and Blasina, F and Radi, R}, title = {Hypoxic-Ischemic Encephalopathy and Mitochondrial Dysfunction: Facts, Unknowns, and Challenges.}, journal = {Antioxidants &amp; redox signaling}, volume = {33}, number = {4}, pages = {247-262}, doi = {10.1089/ars.2020.8093}, pmid = {32295425}, issn = {1557-7716}, mesh = {Adenosine Triphosphate/metabolism ; *Disease Susceptibility ; Electron Transport Complex IV/metabolism ; Homeostasis ; Humans ; Hypoxia-Ischemia, Brain/*etiology/*metabolism/pathology/physiopathology ; Mitochondria/*metabolism ; Neurons/metabolism ; Oxidation-Reduction ; Oxidative Stress ; }, abstract = {Significance: Hypoxic-ischemic events due to intrapartum complications represent the second cause of neonatal mortality and initiate an acute brain disorder known as hypoxic-ischemic encephalopathy (HIE). In HIE, the brain undergoes primary and secondary energy failure phases separated by a latent phase in which partial neuronal recovery is observed. A hypoxic-ischemic event leads to oxygen restriction causing ATP depletion, neuronal oxidative stress, and cell death. Mitochondrial dysfunction and enhanced oxidant formation in brain cells are characteristic phenomena associated with energy failure. Recent Advances: Mitochondrial sources of oxidants in neurons include complex I of the mitochondrial respiratory chain, as a key contributor to O2[•-] production via succinate by a reverse electron transport mechanism. The reaction of O2[•-] with nitric oxide ([•]NO) yields peroxynitrite, a mitochondrial and cellular toxin. Quantitation of the redox state of cytochrome c oxidase, through broadband near-infrared spectroscopy, represents a promising monitoring approach to evaluate mitochondrial dysfunction in vivo in humans, in conjunction with the determination of cerebral oxygenation and their correlation with the severity of brain injury. Critical Issues: The energetic failure being a key phenomenon in HIE connected with the severity of the encephalopathy, measurement of mitochondrial dysfunction in vivo provides an approach to assess evolution, prognosis, and adequate therapies. Restoration of mitochondrial redox homeostasis constitutes a key therapeutic goal. Future Directions: While hypothermia is the only currently accepted therapy in clinical management to preserve mitochondrial function, other mitochondria-targeted and/or redox-based treatments are likely to synergize to ensure further efficacy.}, }
@article {pmid32294100, year = {2020}, author = {Dong, S and Chen, L and Liu, Y and Wang, Y and Zhang, S and Yang, L and Lang, X and Zhang, S}, title = {The draft mitochondrial genome of Magnolia biondii and mitochondrial phylogenomics of angiosperms.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0231020}, pmid = {32294100}, issn = {1932-6203}, mesh = {Conserved Sequence/genetics ; Genes, Plant/genetics ; Genome, Mitochondrial/*genetics ; Genome, Plant/*genetics ; Liriodendron/genetics ; Magnolia/*genetics ; Magnoliopsida/*genetics ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Nymphaea/genetics ; Phylogeny ; }, abstract = {The mitochondrial genomes of flowering plants are well known for their large size, variable coding-gene set and fluid genome structure. The available mitochondrial genomes of the early angiosperms show extreme genetic diversity in genome size, structure, and sequences, such as rampant HGTs in Amborella mt genome, numerous repeated sequences in Nymphaea mt genome, and conserved gene evolution in Liriodendron mt genome. However, currently available early angiosperm mt genomes are still limited, hampering us from obtaining an overall picture of the mitogenomic evolution in angiosperms. Here we sequenced and assembled the draft mitochondrial genome of Magnolia biondii Pamp. from Magnoliaceae (magnoliids) using Oxford Nanopore sequencing technology. We recovered a single linear mitochondrial contig of 967,100 bp with an average read coverage of 122 × and a GC content of 46.6%. This draft mitochondrial genome contains a rich 64-gene set, similar to those of Liriodendron and Nymphaea, including 41 protein-coding genes, 20 tRNAs, and 3 rRNAs. Twenty cis-spliced and five trans-spliced introns break ten protein-coding genes in the Magnolia mt genome. Repeated sequences account for 27% of the draft genome, with 17 out of the 1,145 repeats showing recombination evidence. Although partially assembled, the approximately 1-Mb mt genome of Magnolia is still among the largest in angiosperms, which is possibly due to the expansion of repeated sequences, retention of ancestral mtDNAs, and the incorporation of nuclear genome sequences. Mitochondrial phylogenomic analysis of the concatenated datasets of 38 conserved protein-coding genes from 91 representatives of angiosperm species supports the sister relationship of magnoliids with monocots and eudicots, which is congruent with plastid evidence.}, }
@article {pmid32291084, year = {2020}, author = {Eom, KS and Rim, HJ and Jeon, HK}, title = {Taenia asiatica: Historical overview of taeniasis and cysticercosis with molecular characterization.}, journal = {Advances in parasitology}, volume = {108}, number = {}, pages = {133-173}, doi = {10.1016/bs.apar.2019.12.004}, pmid = {32291084}, issn = {2163-6079}, mesh = {Animals ; Cysticercosis/*parasitology ; Genes, Helminth/genetics ; Humans ; Phylogeny ; Taenia/anatomy &amp; histology/classification/*genetics ; Taeniasis/*parasitology ; }, abstract = {Asian Taenia is a human-infecting Taenia tapeworm known as Taenia asiatica following morphological examination of adult and larval stages of the tapeworm by Eom and Rim (1993). The life cycle of T. asiatica differs from that of T. saginata in its intermediate host (pigs versus cattle) as well as in the infected organs (liver versus muscle). T. asiatica can be differentiated from T. solium and T. saginata by examination of morphological characteristics such as the scolex, mature and gravid proglottids in the adult stage, and the scolex and bladder surface in the larval stage. T. asiatica has been identified in Korea, Taiwan, the Philippines, China, Thailand, Indonesia, Vietnam, Japan, Lao PDR, Nepal and India. The molecular tools employed for T. asiatica identification have been developed to differentiate T. asiatica from other human-infecting Taenia tapeworms based on genetic information such as nucleotide sequence of mitochondrial genes, nuclear ribosomal genes and nuclear genes that lead to development of the subsequent molecular techniques, such as PCR-RFLP, PCR-RAPD, BESST-base, LAMP and qPCR. Investigation of the phylogenetic relationships among human Taenia species revealed that T. asiatica is a sister species with T. saginata, which is genetically more similar than other Taenia species in terms of the nucleotide sequences of cox1, nad1 and 28S rDNA. The mitochondrial genomes of human Taenia tapeworms comprise 13,703bp (T. asiatica), 13,670bp (T. saginata) and 13,709bp (T. solium), and contain 36 genes including 12 protein-coding genes, 2 ribosomal RNAs (rRNAs, a small and a large subunit), and 22 transfer RNAs (tRNAs). Sequence differences in the full genome of T. asiatica and T. saginata mitochondria is 4.6%, while T. solium differs by 11%. Hox gene orthology in T. asiatica was established by comparative analysis with Platyhelminthes Hox genes. T. asiatica Hox revealed six Hox orthologs including two lab/Hox1, two Hox3, one Dfd/Hox4 and one Lox/Lox4. Hybridization between T. asiatica and T. saginata was definitely observed in these species which are sympatrically endemic in the regions of Korea, Thailand, China and Lao PDR. Comparative analyses of T. asiatica, T. saginata and T. solium genomes were also reported with genome features. Taenia asiaticus nomen novum was proposed for T. asiaticaEom and Rim, 1993 which is a homonym of T. asiatica Linstow, 1901 (Davaineidae).}, }
@article {pmid32282807, year = {2020}, author = {Sun, X and Yu, D and Xie, Z and Dong, J and Ding, Y and Yao, H and Greenslade, P}, title = {Phylomitogenomic analyses on collembolan higher taxa with enhanced taxon sampling and discussion on method selection.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0230827}, pmid = {32282807}, issn = {1932-6203}, mesh = {Animals ; Arthropods/*classification/*genetics ; *Genome, Mitochondrial ; *Phylogeny ; }, abstract = {Collembola are a basal group of Hexapoda renowned for both unique morphological characters and significant ecological roles. However, a robust and plausible phylogenetic relationship between its deeply divergent lineages has yet to be achieved. We carried out a mitophylogenomic study based on a so far the most comprehensive mitochondrial genome dataset. Our data matrix contained mitogenomes of 31 species from almost all major families of all four orders, with 16 mitogenomes newly sequenced and annotated. We compared the linear arrangements of genes along mitochondria across species. Then we conducted 13 analyses each under a different combination of character coding, partitioning scheme and heterotachy models, and assessed their performance in phylogenetic inference. Several hypothetical tree topologies were also tested. Mitogenomic structure comparison revealed that most species share the same gene order of putative ancestral pancrustacean pattern, while seven species from Onychiuridae, Poduridae and Symphypleona bear different levels of gene rearrangements, indicating phylogenetic signals. Tomoceroidea was robustly recovered for the first time in the presence of all its families and subfamilies. Monophyly of Onychiuroidea was supported using unpartitioned models alleviating LBA. Paronellidae was revealed polyphyletic with two subfamilies inserted independently into Entomobryidae. Although Entomobryomorpha has not been well supported, more than half of the analyses obtained convincing topologies by placing Tomoceroidea within or near remaining Entomobryomorpha. The relationship between elongate-shaped and spherical-shaped collembolans still remained ambiguous, but Neelipleona tend to occupy the basal position in most trees. This study showed that mitochondrial genomes could provide important information for reconstructing the relationships among Collembola when suitable analytical approaches are implemented. Of all the data refining and model selecting schemes used in this study, the combination of nucleotide sequences, partitioning model and exclusion of third codon positions performed better in generating more reliable tree topology and higher node supports than others.}, }
@article {pmid32278863, year = {2020}, author = {Vargas-Ramírez, M and Caballero, S and Morales-Betancourt, MA and Lasso, CA and Amaya, L and Martínez, JG and das Neves Silva Viana, M and Vogt, RC and Farias, IP and Hrbek, T and Campbell, PD and Fritz, U}, title = {Genomic analyses reveal two species of the matamata (Testudines: Chelidae: Chelus spp.) and clarify their phylogeography.}, journal = {Molecular phylogenetics and evolution}, volume = {148}, number = {}, pages = {106823}, doi = {10.1016/j.ympev.2020.106823}, pmid = {32278863}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Calibration ; Colombia ; DNA, Mitochondrial/genetics ; Female ; Genetics, Population ; *Genomics ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeny ; *Phylogeography ; Principal Component Analysis ; Probability ; Species Specificity ; Time Factors ; Turtles/classification/*genetics ; }, abstract = {The matamata is one of the most charismatic turtles on earth, widely distributed in northern South America. Debates have occurred over whether or not there should be two subspecies or species recognized due to its geographic variation in morphology. Even though the matamata is universally known, its natural history, conservation status and biogeography are largely unexplored. In this study we examined the phylogeographic differentiation of the matamata based on three mitochondrial DNA fragments (2168 bp of the control region, cytochrome oxidase subunit I, and the cytochrome b gene), one nuclear genomic DNA fragment (1068 bp of the R35 intron) and 1661 Single Nucleotide Polymorphisms (SNPs). Our molecular and morphological analyses revealed the existence of two distinct, genetically deeply divergent evolutionary lineages of matamatas that separated in the late Miocene (approximately 12.7 million years ago), corresponding well to the time when the Orinoco Basin was established. As a result of our analyses, we describe the genetically and morphologically highly distinct matamata from the Orinoco and Río Negro Basins and the Essequibo drainage as a species new to science (Chelus orinocensis sp. nov.). Chelus fimbriata sensu stricto is distributed in the Amazon Basin and the Mahury drainage. Additionally, the analyses revealed that each species displays phylogeographic differentiation. For C. orinocensis, there is moderate mitochondrial differentiation between the Orinoco and the Río Negro. For C. fimbriata, there is more pronounced differentiation matching different river systems. One mitochondrial clade was identified from the Amazon, Ucayali, and Mahury Rivers, and another one from the Madeira and Jaci Paraná Rivers. The C. orinocensis in the Essequibo and Branco Rivers have haplotypes that constitute a third clade clustering with C. fimbriata. Phylogenetic analyses of the R35 intron and SNP data link the matamatas from the Essequibo and Branco with the new species, suggesting past gene flow and old mitochondrial introgression. Chelus orinocensis is collected for the pet trade in Colombia and Venezuela. However, neither the extent of the harvest nor its impact are known. Hence, it is crucial to gather more information and to assess its exploitation throughout its distribution range to obtain a better understanding of its conservation status and to design appropriate conservation and management procedures. RESUMEN: La matamata es una de las tortugas más carismáticas del mundo, ampliamente distribuida en el norte de Sudamérica. Debido a su variación morfológica geográfica, se debate sobre el reconocimiento de dos subespecies o especies. A pesar de que la matamata es universalmente conocida, su historia natural, estado de conservación y biogeografía han sido muy poco estudiados. En este estudio examinamos la diferenciación filogeográfica de las matamatas en base a tres fragmentos de ADN mitocondrial (2168 pb de la región de control, la subunidad I del citocromo oxidasa y el gen del citocromo b), un fragmento de ADN genómico nuclear (1068 pb del intrón R35) y 1661 polimorfismos de nucleótido único (SNPs). Nuestros análisis moleculares y morfológicos revelaron la existencia de dos linajes evolutivos distintos de matamatas, genéticamente divergentes que se separaron en el Mioceno tardio (hace aproximadamente 12.7 millones de años), correspondiendo al tiempo en que se estableció la cuenca del Orinoco. Como resultado de nuestros análisis, describimos las genéticamente y morfológicamente distintas matamatas de las cuencas del Orinoco, Río Negro y Essequibo como una especie nueva para la ciencia (Chelus orinocensis sp. nov.). Chelus fimbriata sensu stricto se distribuye en la cuenca del Amazonas y en el drenaje del Mahury. Adicionalmente, los análisis revelaron que cada especie muestra diferenciación filogeográfica. Para C. orinocensis, hay una moderada diferenciación mitocondrial entre el Orinoco y el Río Negro. Para C. fimbriata, hay una diferenciación más pronunciada, concordando con los diferentes sistemas fluviales. Se identificó un clado de los ríos Amazonas, Ucayali y Mahury y otro de los ríos Madeira y Jaci Paraná. Las C. orinocensis de los ríos Essequibo y Branco tienen haplotipos que constituyen un tercer clado que se agrupa con C. fimbriata. Los análisis filogenéticos del intrón R35 y los datos de SNP asocian las matamatas de Essequibo y Branco con la nueva especie, sugiriendo flujo de genes pasado e introgresión mitocondrial antigua. Chelus orinocensis se colecta para el comercio de mascotas en Colombia y Venezuela. Sin embargo, ni se conoce el alcance de las colectas ni su impacto. Por lo tanto, es crucial recopilar más información y evaluar su explotación en todo su rango de distribución, comprender mejor su estado de conservación y para diseñar acciones apropiadas de conservación y manejo.}, }
@article {pmid32268201, year = {2020}, author = {Bolívar-Leguizamón, SD and Silveira, LF and Derryberry, EP and Brumfield, RT and Bravo, GA}, title = {Phylogeography of the Variable Antshrike (Thamnophilus caerulescens), a South American passerine distributed along multiple environmental gradients.}, journal = {Molecular phylogenetics and evolution}, volume = {148}, number = {}, pages = {106810}, doi = {10.1016/j.ympev.2020.106810}, pmid = {32268201}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; *Environment ; Genetic Variation ; Genetics, Population ; Geography ; Information Theory ; Mitochondria/genetics ; Passeriformes/*classification/genetics ; Phylogeny ; *Phylogeography ; Principal Component Analysis ; South America ; Species Specificity ; Time Factors ; }, abstract = {The Neotropics show a wealth of distributional patterns shared by many co-distributed species. A distinctive pattern is the so-called "circum-Amazonian distribution," which is observed in species that do not occur in Amazonia but rather along a belt of forested habitats spanning south and east of Amazonia, the Andean foothills, and often into the Venezuelan Coastal Range and the Tepuis. Although this pattern is widespread across animals and plants, its underlying biogeographic mechanisms remain poorly understood. The Variable Antshrike (Thamnophilus caerulescens) is a sexually dimorphic suboscine passerine that exhibits extreme plumage variation and occurs along the southern portion of the circum-Amazonian belt. We describe broad-scale phylogeographic patterns of T. caerulescens and assess its demographic history using DNA sequences from the mitochondrion and ultraconserved elements (UCEs). We identified three genomic clusters: a) northern Atlantic Forest; b) southeastern Cerrado and central-southern Atlantic Forest, and c) Chaco and Andes. Our results were consistent with Pleistocene divergence followed by gene flow, mainly between the latter two clusters. There were no genetic signatures of rapid population expansions or bottlenecks. The population from the northern Atlantic Forest was the most genetically divergent group within the species. The demographic history of T. caerulescens was probably affected by series of humid and dry periods throughout the Quaternary that generated subtle population expansions and contractions allowing the intermittent connection of habitats along the circum-Amazonian belt. Recognizing the dynamic history of climate-mediated forest expansions, contractions, and connections during the South American Pleistocene is central toward a mechanistic understanding of circum-Amazonian distributions.}, }
@article {pmid32268200, year = {2020}, author = {Li, JN and Liang, D and Wang, YY and Guo, P and Huang, S and Zhang, P}, title = {A large-scale systematic framework of Chinese snakes based on a unified multilocus marker system.}, journal = {Molecular phylogenetics and evolution}, volume = {148}, number = {}, pages = {106807}, doi = {10.1016/j.ympev.2020.106807}, pmid = {32268200}, issn = {1095-9513}, mesh = {Animals ; Biological Evolution ; Cell Nucleus/genetics ; China ; *Genetic Loci ; Genetic Markers ; Mitochondria/genetics ; Phylogeny ; Snakes/*classification/*genetics ; Time Factors ; }, abstract = {Snakes are one of the most diverse groups of terrestrial vertebrates, with approximately 3500 extant species. A robust phylogeny and taxonomy of snakes is crucial for us to know, study and protect them. For a large group such as snakes, broad-scale phylogenetic reconstructions largely rely on data integration. Increasing the compatibility of the data from different researches is thus important, which can be facilitated by standardization of the loci used in systematic analyses. In this study, we proposed a unified multilocus marker system for snake systematics by conflating 5 mitochondrial markers, 19 vertebrate-universal nuclear protein coding (NPC) markers and 72 snake-specific noncoding intron markers. This marker system is an addition to the large squamate conserved locus set (SqCL) for studies preferring a medium-scale data set. We applied this marker system to over 440 snake samples and constructed the currently most comprehensive systematic framework of the snakes in China. Robust snake phylogenetic relationships were recovered at both deep and shallow evolutionary depths, demonstrating the usefulness of this multilocus marker system. Discordance was revealed by a parallel comparison between the snake tree based on the multilocus marker system and that based on only the mitochondrial loci, highlighting the necessity of using multiple types of markers to better understand the snake evolutionary histories. The divergence times of different snake groups were estimated with the nuclear data set. Our comprehensive snake tree not only confirms many important nodes inferred in previous studies but also contributes new insights into many snake phylogenetic relationships. Suggestions are made for the current Chinese snake taxonomy.}, }
@article {pmid32253515, year = {2020}, author = {de Oliveira, BHN and Wairich, A and Turchetto-Zolet, AC and Fett, JP and Ricachenevsky, FK}, title = {The Mitochondrial Iron-Regulated (MIR) gene is Oryza genus specific and evolved before speciation within the Oryza sativa complex.}, journal = {Planta}, volume = {251}, number = {5}, pages = {94}, pmid = {32253515}, issn = {1432-2048}, mesh = {Crops, Agricultural ; Gene Expression Regulation, Plant/*genetics ; Iron/*metabolism ; Iron Deficiencies ; Mitochondria/metabolism ; Oryza/*genetics/metabolism ; Plant Proteins/genetics/*metabolism ; Species Specificity ; }, abstract = {The MIR gene is not an Oryza sativa orphan gene, but an Oryza genus-specific gene that evolved before AA lineage speciation by a complex origination process. Rice (Oryza sativa L.) is a model species and an economically relevant crop. The Oryza genus comprises 25 species, with genomic data available for several Oryza species, making it a model for genetics and evolution. The Mitochondrial Iron-Regulated (MIR) gene was previously implicated in the O. sativa Fe deficiency response, and was considered an orphan gene present only in rice. Here we show that MIR is also found in other Oryza species that belong to the Oryza sativa complex, which have AA genome type and constitute the primary gene pool for O. sativa breeding. Our data suggest that MIR originated in a stepwise process, in which sequences derived from an exon fragment of the raffinose synthase gene were pseudogenized into non-coding, which in turn originated the MIR gene de novo. All species with a putative functional MIR gene conserve their regulation by Fe deficiency, with the exception of Oryza barthii. In O. barthii, the MIR coding sequence was translocated to a different chromosomal position and separated from its regulatory region, leading to a lack of Fe deficiency responsiveness. Moreover, the MIR co-expression subnetwork cluster in O. sativa is responsive to Fe deficiency, evidencing the importance of the newly originated gene in Fe uptake. This work establishes that MIR is not an orphan gene as previously proposed, but a de novo originated gene within the genus Oryza. We also showed that MIR is undergoing genomic changes in one species (O. barthii), with an impact on Fe deficiency response.}, }
@article {pmid32251374, year = {2020}, author = {Waltz, F and Soufari, H and Bochler, A and Giegé, P and Hashem, Y}, title = {Cryo-EM structure of the RNA-rich plant mitochondrial ribosome.}, journal = {Nature plants}, volume = {6}, number = {4}, pages = {377-383}, pmid = {32251374}, issn = {2055-0278}, mesh = {Brassica/genetics/*ultrastructure ; Cryoelectron Microscopy ; Evolution, Molecular ; Mitochondrial Ribosomes/*ultrastructure ; Models, Molecular ; Plant Proteins/ultrastructure ; RNA, Plant/*ultrastructure ; RNA, Ribosomal/*ultrastructure ; Ribosomal Proteins/ultrastructure ; }, abstract = {The vast majority of eukaryotic cells contain mitochondria, essential powerhouses and metabolic hubs[1]. These organelles have a bacterial origin and were acquired during an early endosymbiosis event[2]. Mitochondria possess specialized gene expression systems composed of various molecular machines, including the mitochondrial ribosomes (mitoribosomes). Mitoribosomes are in charge of translating the few essential mRNAs still encoded by mitochondrial genomes[3]. While chloroplast ribosomes strongly resemble those of bacteria[4,5], mitoribosomes have diverged significantly during evolution and present strikingly different structures across eukaryotic species[6-10]. In contrast to animals and trypanosomatids, plant mitoribosomes have unusually expanded ribosomal RNAs and have conserved the short 5S rRNA, which is usually missing in mitoribosomes[11]. We have previously characterized the composition of the plant mitoribosome[6], revealing a dozen plant-specific proteins in addition to the common conserved mitoribosomal proteins. In spite of the tremendous recent advances in the field, plant mitoribosomes remained elusive to high-resolution structural investigations and the plant-specific ribosomal features of unknown structures. Here, we present a cryo-electron microscopy study of the plant 78S mitoribosome from cauliflower at near-atomic resolution. We show that most of the plant-specific ribosomal proteins are pentatricopeptide repeat proteins (PPRs) that deeply interact with the plant-specific rRNA expansion segments. These additional rRNA segments and proteins reshape the overall structure of the plant mitochondrial ribosome, and we discuss their involvement in the membrane association and mRNA recruitment prior to translation initiation. Finally, our structure unveils an rRNA-constructive phase of mitoribosome evolution across eukaryotes.}, }
@article {pmid32246837, year = {2020}, author = {Rank, NE and Mardulyn, P and Heidl, SJ and Roberts, KT and Zavala, NA and Smiley, JT and Dahlhoff, EP}, title = {Mitonuclear mismatch alters performance and reproductive success in naturally introgressed populations of a montane leaf beetle.}, journal = {Evolution; international journal of organic evolution}, volume = {74}, number = {8}, pages = {1724-1740}, doi = {10.1111/evo.13962}, pmid = {32246837}, issn = {1558-5646}, support = {//California Desert Research Legacy Fund/International ; //White Mountain Research Center/International ; 1457335//Division of Integrative Organismal Systems/International ; 1457395//Division of Integrative Organismal Systems/International ; 0844404//Division of Environmental Biology/International ; 0844406//Division of Environmental Biology/International ; }, mesh = {Animals ; California ; Coleoptera/*genetics/growth &amp; development ; Electron Transport Complex IV/genetics ; Female ; Fertility ; *Genetic Fitness ; *Genetic Introgression ; *Genetic Variation ; *Genome, Mitochondrial ; Glucose-6-Phosphate Isomerase/genetics ; Heat-Shock Response ; Larva/growth &amp; development ; Locomotion ; Male ; Phylogeography ; Sexual Behavior, Animal ; }, abstract = {Coordination between nuclear and mitochondrial genomes is critical to metabolic processes underlying animals' ability to adapt to local environments, yet consequences of mitonuclear interactions have rarely been investigated in populations where individuals with divergent mitochondrial and nuclear genomes naturally interbreed. Genetic variation in the leaf beetle Chrysomela aeneicollis was assessed along a latitudinal thermal gradient in California's Sierra Nevada. Variation at mitochondrial cytochrome oxidase II (COII) and the nuclear gene phosphoglucose isomerase (PGI) shows concordance and was significantly greater along a 65 km transect than 10 other loci. STRUCTURE analyses using neutral loci identified a southern and northern subpopulation, which interbreed in the central drainage Bishop Creek. COII and PGI were used as indicators of mitochondrial and nuclear genetic variation in field and laboratory experiments conducted on beetles from this admixed population. Fecundity, larval development rate, running speed and male mating frequency were higher for beetles with geographically "matched" than "mismatched" mitonuclear genotypes. Effects of mitonuclear mismatch were largest for individuals with northern nuclear genotypes possessing southern mitochondria and were most pronounced after heat treatment or at high elevation. These findings suggest that mitonuclear incompatibility diminishes performance and reproductive success in nature, effects that could intensify at environmental extremes.}, }
@article {pmid32245791, year = {2020}, author = {Guan, X and Okazaki, Y and Zhang, R and Saito, K and Nikolau, BJ}, title = {Dual-Localized Enzymatic Components Constitute the Fatty Acid Synthase Systems in Mitochondria and Plastids.}, journal = {Plant physiology}, volume = {183}, number = {2}, pages = {517-529}, pmid = {32245791}, issn = {1532-2548}, mesh = {3-Oxoacyl-(Acyl-Carrier-Protein) Reductase/genetics/metabolism ; Arabidopsis/enzymology/*metabolism ; Arabidopsis Proteins/genetics/metabolism ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)/genetics/metabolism ; Fatty Acid Synthases/*metabolism ; Glycine/metabolism ; Mitochondria/*metabolism ; Multienzyme Complexes/genetics/metabolism ; Plastids/metabolism ; }, abstract = {Plant fatty acid biosynthesis occurs in both plastids and mitochondria. Here, we report the identification and characterization of Arabidopsis (Arabidopsis thaliana) genes encoding three enzymes shared between the mitochondria- and plastid-localized type II fatty acid synthase systems (mtFAS and ptFAS, respectively). Two of these enzymes, β-ketoacyl-acyl carrier protein (ACP) reductase and enoyl-ACP reductase, catalyze two of the reactions that constitute the core four-reaction cycle of the FAS system, which iteratively elongates the acyl chain by two carbon atoms per cycle. The third enzyme, malonyl-coenzyme A:ACP transacylase, catalyzes the reaction that loads the mtFAS system with substrate by malonylating the phosphopantetheinyl cofactor of ACP. GFP fusion experiments revealed that the these enzymes localize to both chloroplasts and mitochondria. This localization was validated by characterization of mutant alleles, which were rescued by transgenes expressing enzyme variants that were retargeted only to plastids or only to mitochondria. The singular retargeting of these proteins to plastids rescued the embryo lethality associated with disruption of the essential ptFAS system, but these rescued plants displayed phenotypes typical of the lack of mtFAS function, including reduced lipoylation of the H subunit of the glycine decarboxylase complex, hyperaccumulation of glycine, and reduced growth. However, these latter traits were reversible in an elevated-CO2 atmosphere, which suppresses mtFAS-associated photorespiration-dependent chemotypes. Sharing enzymatic components between mtFAS and ptFAS systems constrains the evolution of these nonredundant fatty acid biosynthetic machineries.}, }
@article {pmid32244644, year = {2020}, author = {Harada, R and Hirakawa, Y and Yabuki, A and Kashiyama, Y and Maruyama, M and Onuma, R and Soukal, P and Miyagishima, S and Hampl, V and Tanifuji, G and Inagaki, Y}, title = {Inventory and Evolution of Mitochondrion-localized Family A DNA Polymerases in Euglenozoa.}, journal = {Pathogens (Basel, Switzerland)}, volume = {9}, number = {4}, pages = {}, pmid = {32244644}, issn = {2076-0817}, support = {18KK0203 and 19H03280, YI; 17H03723 and 26840123, GT; 17K19434, AY//Japan Society for the Promotion of Science/ ; 16-25280S, VH//the Czech Science foundation/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Centre for research of pathogenicity and virulence of parasites/ ; }, abstract = {The order Trypanosomatida has been well studied due to its pathogenicity and the unique biology of the mitochondrion. In Trypanosoma brucei, four DNA polymerases, namely PolIA, PolIB, PolIC, and PolID, related to bacterial DNA polymerase I (PolI), were shown to be localized in mitochondria experimentally. These mitochondrion-localized DNA polymerases are phylogenetically distinct from other family A DNA polymerases, such as bacterial PolI, DNA polymerase gamma (Polγ) in human and yeasts, "plant and protist organellar DNA polymerase (POP)" in diverse eukaryotes. However, the diversity of mitochondrion-localized DNA polymerases in Euglenozoa other than Trypanosomatida is poorly understood. In this study, we discovered putative mitochondrion-localized DNA polymerases in broad members of three major classes of Euglenozoa-Kinetoplastea, Diplonemea, and Euglenida-to explore the origin and evolution of trypanosomatid PolIA-D. We unveiled distinct inventories of mitochondrion-localized DNA polymerases in the three classes: (1) PolIA is ubiquitous across the three euglenozoan classes, (2) PolIB, C, and D are restricted in kinetoplastids, (3) new types of mitochondrion-localized DNA polymerases were identified in a prokinetoplastid and diplonemids, and (4) evolutionarily distinct types of POP were found in euglenids. We finally propose scenarios to explain the inventories of mitochondrion-localized DNA polymerases in Kinetoplastea, Diplonemea, and Euglenida.}, }
@article {pmid32244414, year = {2020}, author = {Hewitt, SK and Duangrattanalert, K and Burgis, T and Zeef, LAH and Naseeb, S and Delneri, D}, title = {Plasticity of Mitochondrial DNA Inheritance and its Impact on Nuclear Gene Transcription in Yeast Hybrids.}, journal = {Microorganisms}, volume = {8}, number = {4}, pages = {}, pmid = {32244414}, issn = {2076-2607}, support = {BB/F017227/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M017702/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; Development and Promotion of Science and Technology Talent (DPST)//Royal Government of Thailand/ ; BB/L021471/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {Mitochondrial DNA (mtDNA) in yeast is biparentally inherited, but colonies rapidly lose one type of parental mtDNA, thus becoming homoplasmic. Therefore, hybrids between the yeast species possess two homologous nuclear genomes, but only one type of mitochondrial DNA. We hypothesise that the choice of mtDNA retention is influenced by its contribution to hybrid fitness in different environments, and the allelic expression of the two nuclear sub-genomes is affected by the presence of different mtDNAs in hybrids. Saccharomyces cerevisiae/S. uvarum hybrids preferentially retained S. uvarum mtDNA when formed on rich media at colder temperatures, while S. cerevisiae mtDNA was primarily retained on non-fermentable carbon source, at any temperature. Transcriptome data for hybrids harbouring different mtDNA showed a strong environmentally dependent allele preference, which was more important in respiratory conditions. Co-expression analysis for specific biological functions revealed a clear pattern of concerted allelic transcription within the same allele type, which supports the notion that the hybrid cell works preferentially with one set of parental alleles (or the other) for different cellular functions. Given that the type of mtDNA retained in hybrids affects both nuclear expression and fitness, it might play a role in driving hybrid genome evolution in terms of gene retention and loss.}, }
@article {pmid32243910, year = {2020}, author = {Muhammad, N and Suleman,  and Khan, MS and Li, L and Zhao, Q and Ullah, H and Zhu, XQ and Ma, J}, title = {Characterization of the complete mitogenome of Centrorhynchus clitorideus (Meyer, 1931) (Palaeacanthocephala: Centrorhynchidae), the largest mitochondrial genome in Acanthocephala, and its phylogenetic implications.}, journal = {Molecular and biochemical parasitology}, volume = {237}, number = {}, pages = {111274}, doi = {10.1016/j.molbiopara.2020.111274}, pmid = {32243910}, issn = {1872-9428}, mesh = {Acanthocephala/classification/*genetics/isolation &amp; purification ; Animals ; Base Sequence ; Bayes Theorem ; Falconiformes/parasitology ; *Genes, Helminth ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Pakistan ; *Phylogeny ; Strigiformes/parasitology ; Whole Genome Sequencing ; }, abstract = {Species of Centrorhynchus (Polymorphida: Centrorhynchidae) commonly parasitize various falconiform and strigiform birds worldwide. In the present study, the complete mitochondrial (mt) genome sequences of Centrorhynchus clitorideus was sequenced and annotated for the first time based on specimens collected from the little owl Athene noctua (Scopoli) (Strigiformes: Strigidae) in Pakistan. The complete mt genome sequences of C. clitorideus is 15,884 bp in length, and contained 36 genes [two rRNA genes (rrnL and rrnS), 22 tRNA genes and 12 protein-coding genes (PCGs) (lacking atp8)] and two non-coding regions (NCR1 and NCR2), which represents the largest mt genome of acanthocephalan reported so far. In order to assess the systematic position of C. clitorideus and the interrelationship of the family Centrorhynchidae and the other families in order Polymorphida, the phylogenetic tree was constructed using Bayesian inference (BI) based on amino acid sequences of 12 PCGs. Phylogenetic results supported C. clitorideus formed a sister relationship to C. milvus in Centrorhynchidae, which has a sister relationship to the representatives of Polymorphidae + Plagiorhynchidae. Our results revealed the monophyly of Polymorphida and paraphyly of Echinorhynchida in the class Palaeacanthocephala. The validity of the genus Sphaerirostris (Polymorphida: Centrorhynchidae) was also challenged by our phylogenetic results, which seems to be a synonym of Centrorhynchus. Moreover, the present phylogenetic analysis indicated that the family Quadrigyridae and subfamily Pallisentinae (A. cheni and P. celatus) are polyphyletic.}, }
@article {pmid32230997, year = {2020}, author = {Wolf, C and López Del Amo, V and Arndt, S and Bueno, D and Tenzer, S and Hanschmann, EM and Berndt, C and Methner, A}, title = {Redox Modifications of Proteins of the Mitochondrial Fusion and Fission Machinery.}, journal = {Cells}, volume = {9}, number = {4}, pages = {}, pmid = {32230997}, issn = {2073-4409}, mesh = {Animals ; Evolution, Molecular ; Humans ; *Mitochondrial Dynamics ; Mitochondrial Proteins/chemistry/*metabolism ; Oxidation-Reduction ; Phylogeny ; Protein Processing, Post-Translational ; }, abstract = {Mitochondrial fusion and fission tailors the mitochondrial shape to changes in cellular homeostasis. Players of this process are the mitofusins, which regulate fusion of the outer mitochondrial membrane, and the fission protein DRP1. Upon specific stimuli, DRP1 translocates to the mitochondria, where it interacts with its receptors FIS1, MFF, and MID49/51. Another fission factor of clinical relevance is GDAP1. Here, we identify and discuss cysteine residues of these proteins that are conserved in phylogenetically distant organisms and which represent potential sites of posttranslational redox modifications. We reveal that worms and flies possess only a single mitofusin, which in vertebrates diverged into MFN1 and MFN2. All mitofusins contain four conserved cysteines in addition to cysteine 684 in MFN2, a site involved in mitochondrial hyperfusion. DRP1 and FIS1 are also evolutionarily conserved but only DRP1 contains four conserved cysteine residues besides cysteine 644, a specific site of nitrosylation. MFF and MID49/51 are only present in the vertebrate lineage. GDAP1 is missing in the nematode genome and contains no conserved cysteine residues. Our analysis suggests that the function of the evolutionarily oldest proteins of the mitochondrial fusion and fission machinery, the mitofusins and DRP1 but not FIS1, might be altered by redox modifications.}, }
@article {pmid32230306, year = {2020}, author = {Ceríaco, LMP and Agarwal, I and Marques, MP and Bauer, AM}, title = {A review of the genus Hemidactylus Goldfuss, 1820 (Squamata: Gekkonidae) from Angola, with the description of two new species.}, journal = {Zootaxa}, volume = {4746}, number = {1}, pages = {zootaxa.4746.1.1}, doi = {10.11646/zootaxa.4746.1.1}, pmid = {32230306}, issn = {1175-5334}, mesh = {Angola ; Animals ; *Lizards ; Mitochondria ; Phylogeny ; }, abstract = {The genus Hemidactylus in Angola is represented by six species, all of them part of taxonomically and nomenclaturally challenging species complexes. We present a detailed taxonomic revision of the group in the region and describe two new species, Hemidactylus nzingae sp. nov. and Hemidactylus paivae sp. nov., both occuring in and potentially endemic to the highlands of Angola. Phylogenetic analysis using a combination of mitochondrial (ND2) and nuclear (MXRA5, PDC, RAG1) markers, as well as morphological and scalation data support the recognition of the new species. In addition, data support the revalidation of Hemidactylus bayonii Bocage, 1893, and Hemidactylus benguellensis Bocage, 1893. We also provide a redefinition of Hemidactylus longicephalus Bocage, 1873 with which we synonymize Hemidactylus mabouia molleri Bedriaga, 1892, from São Tomé in the Gulf of Guinea. Given that the type material of H. bayonii, H. benguellensis, H. longicephalus and H. mabouia molleri have all been lost or destroyed, we designate neotypes for all of these nomina for purposes of nomenclatural stability. The description of the new species and the revision and revalidation of the Angolan species already described contributes to a better understanding of the taxonomy and biogeography of West and Central African Hemidactylus, as well as to the general biogeographic and evolutionary patterns of Angolan fauna. A key to the Angolan species is also presented.}, }
@article {pmid32229686, year = {2020}, author = {Khosravi, S and Harner, ME}, title = {The MICOS complex, a structural element of mitochondria with versatile functions.}, journal = {Biological chemistry}, volume = {401}, number = {6-7}, pages = {765-778}, doi = {10.1515/hsz-2020-0103}, pmid = {32229686}, issn = {1437-4315}, mesh = {Animals ; Humans ; Mitochondria/*chemistry/metabolism ; Mitochondrial Membranes/*metabolism ; }, abstract = {Mitochondria perform a plethora of functions in various cells of different tissues. Their architecture differs remarkably, for instance in neurons versus steroidogenic cells. Furthermore, aberrant mitochondrial architecture results in mitochondrial dysfunction. This indicates strongly that mitochondrial architecture and function are intimately linked. Therefore, a deep knowledge about the determinants of mitochondrial architecture and their function on a molecular level is of utmost importance. In the past decades, various proteins and protein complexes essential for formation of mitochondrial architecture have been identified. Here we will review the current knowledge of the MICOS complex, one of the major structural elements of mitochondria. MICOS is a multi-subunit complex present in the inner mitochondrial membrane. Multiple interaction partners in the inner and outer mitochondrial membrane point to participation in a multitude of important processes, such as generation of mitochondrial architecture, lipid metabolism, and protein import into mitochondria. Since the MICOS complex is highly conserved in form and function throughout evolution, we will highlight the importance of MICOS for mammals. We will emphasize in particular the current knowledge of the association of MICOS with severe human diseases, including Charcot-Marie-Tooth disease type 2, Alzheimer's disease, Parkinson's disease, Frontotemporal Dementia and Amyotrophic Lateral Sclerosis.}, }
@article {pmid32224234, year = {2020}, author = {Petersen, G and Anderson, B and Braun, HP and Meyer, EH and Møller, IM}, title = {Mitochondria in parasitic plants.}, journal = {Mitochondrion}, volume = {52}, number = {}, pages = {173-182}, doi = {10.1016/j.mito.2020.03.008}, pmid = {32224234}, issn = {1872-8278}, mesh = {Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; *Genome, Mitochondrial ; Magnoliopsida/*genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Plant mitochondrial genomes are renowned for their structural complexity, extreme variation in size and mutation rates, and ability to incorporate foreign DNA. Parasitic flowering plants are no exception, and the close association between parasite and host may even enhance the likelihood of horizontal gene transfer (HGT) between them. Recent studies on mistletoes (Viscum) have revealed that these parasites have lost an exceptional number of mitochondrial genes, including all complex I genes of the respiratory chain. At the same time, an altered respiratory pathway has been demonstrated. Here we review the current understanding of mitochondrial evolution in parasitic plants with a special emphasis on HGT to and from parasite mitochondrial genomes, as well as the uniquely altered mitochondria in Viscum and related plants.}, }
@article {pmid32212876, year = {2020}, author = {Kim, JS and Park, J and Fong, JJ and Zhang, YP and Li, SR and Ota, H and Min, SH and Min, MS and Park, D}, title = {Genetic diversity and inferred dispersal history of the Schlegel's Japanese Gecko (Gekko japonicus) in Northeast Asia based on population genetic analyses and paleo-species distribution modelling.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {31}, number = {3}, pages = {120-130}, doi = {10.1080/24701394.2020.1742332}, pmid = {32212876}, issn = {2470-1408}, mesh = {Alleles ; Animals ; China ; Cytochromes b/*genetics ; DNA, Mitochondrial/genetics ; Ecosystem ; Genes, Mitochondrial/genetics ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Mitochondrial/genetics ; Haplotypes/genetics ; Japan ; Lizards/*genetics ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; NADH Dehydrogenase/*genetics ; Phylogeny ; Phylogeography/methods ; Republic of Korea ; Sequence Analysis, DNA/methods ; }, abstract = {To understand the genetic diversity and dispersal history of Schlegel's Japanese gecko (Gekko japonicus), we performed genetic analyses and paleo-species distributional modelling. For the genetic analysis, we analyzed mitochondrial DNA (mtDNA) (cytochrome b [Cytb] and NADH dehydrogenase 2 [ND2]) and seven microsatellite loci of 353 individuals from 11 populations (2 east coast China, 4 west and central coast Japan and 5 Korea). For the paleo-species distribution modelling, we used 432 occurrence data points (125 China, 291 Japan and 16 Korea) over the Pleistocene and Holocene. China is inferred to be the source population, which had higher genetic diversity (mtDNA) and more private alleles (mtDNA) compared to Japanese and Korean populations. Differences between the three counties were very small in the mtDNA haplotype network despite some genetic structure among the three countries. Microsatellite analysis inferred that genetic exchange has actively occurred among the Chinese, Japanese and Korean populations. Suitable habitats in Japan should have been plentiful by the mid-Holocene, but have only recently become available in Korea. These results suggest that dispersal of G. japonicus occurred after the Holocene warming from the east coast of China to the west and central coasts of Japan and Korea, and gene flow is actively occurring among the three countries.}, }
@article {pmid32208680, year = {2020}, author = {Yue, J and Shen, Y and Liang, L and Cong, L and Xu, W and Shi, W and Liang, C and Xu, S}, title = {Revealing Mitochondrial Microenvironmental Evolution Triggered by Photodynamic Therapy.}, journal = {Analytical chemistry}, volume = {92}, number = {8}, pages = {6081-6087}, doi = {10.1021/acs.analchem.0c00497}, pmid = {32208680}, issn = {1520-6882}, mesh = {Cell Line, Tumor ; Humans ; Hydrogen-Ion Concentration ; Membrane Potential, Mitochondrial/drug effects ; Mitochondria/*drug effects/metabolism ; Optical Imaging ; *Photochemotherapy ; Photosensitizing Agents/*pharmacology ; Reactive Oxygen Species/analysis/metabolism ; }, abstract = {Mitochondrion is one of the most important organelles and becomes a target in many cancer therapeutic strategies. Mitochondrial microenvironments in response to therapeutic methods are the key to understand therapeutic mechanisms. However, they are almost rarely studied. Herein, the mitochondrial microenvironments, including mitochondrial membrane potential (MMP) and reactive oxygen species (ROS) after different photodynamic therapy (PDT) dosages, were monitored by fluorescent imaging and compared among three cell lines (HepG2, MCF-7, and LO2). Furthermore, the fluctuations of intramitochondrial pHs were revealed via a plasmonic mitochondrion-targeting surface-enhanced Raman scattering (SERS) pH nanosensor. Results indicate that the MMP decreases gradually with the ROS generation and the cancerous cells exhibit less response to excess ROS relative to normal cells. On the other hand, the pH value in the mitochondria decreases initially and then increases when the amount of ROS increases. The LO2 cell is preliminarily evidenced to have a higher self-adjustment ability due to its better tolerance to differential intra/extracellular pHs. This study may provide a basis for an in-depth understanding of the mechanisms of the mitochondrial targeting-based PDT therapeutic processes. It is also helpful for more accurate and useful diagnosis according to intramitochondrial microenvironments and improvement on therapy efficiency of cancers.}, }
@article {pmid32206790, year = {2020}, author = {Orton, LM and Fitzek, E and Feng, X and Grayburn, WS and Mower, JP and Liu, K and Zhang, C and Duvall, MR and Yin, Y}, title = {Zygnema circumcarinatum UTEX 1559 chloroplast and mitochondrial genomes provide insight into land plant evolution.}, journal = {Journal of experimental botany}, volume = {71}, number = {11}, pages = {3361-3373}, doi = {10.1093/jxb/eraa149}, pmid = {32206790}, issn = {1460-2431}, mesh = {Base Sequence ; Chloroplasts ; *Embryophyta ; Evolution, Molecular ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Genome, Plant ; Phylogeny ; }, abstract = {The complete chloroplast and mitochondrial genomes of Charophyta have shed new light on land plant terrestrialization. Here, we report the organellar genomes of the Zygnema circumcarinatum strain UTEX 1559, and a comparative genomics investigation of 33 plastomes and 18 mitogenomes of Chlorophyta, Charophyta (including UTEX 1559 and its conspecific relative SAG 698-1a), and Embryophyta. Gene presence/absence was determined across these plastomes and mitogenomes. A comparison between the plastomes of UTEX 1559 (157 548 bp) and SAG 698-1a (165 372 bp) revealed very similar gene contents, but substantial genome rearrangements. Surprisingly, the two plastomes share only 85.69% nucleotide sequence identity. The UTEX 1559 mitogenome size is 215 954 bp, the largest among all sequenced Charophyta. Interestingly, this large mitogenome contains a 50 kb region without homology to any other organellar genomes, which is flanked by two 86 bp direct repeats and contains 15 ORFs. These ORFs have significant homology to proteins from bacteria and plants with functions such as primase, RNA polymerase, and DNA polymerase. We conclude that (i) the previously published SAG 698-1a plastome is probably from a different Zygnema species, and (ii) the 50 kb region in the UTEX 1559 mitogenome might be recently acquired as a mobile element.}, }
@article {pmid32202195, year = {2020}, author = {Yang, C and Zhu, EJ and He, QJ and Yi, CH and Wang, XB and Hu, SJ and Wei, SJ}, title = {Strong genetic differentiation among populations of Cheirotonus gestroi (Coleoptera: Euchiridae) in its native area sheds lights on species conservation.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {31}, number = {3}, pages = {108-119}, doi = {10.1080/24701394.2020.1741565}, pmid = {32202195}, issn = {2470-1408}, mesh = {Animals ; China ; Coleoptera/*genetics ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Ecosystem ; Endangered Species ; Gene Flow ; Genetic Drift ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Mitochondrial/*genetics ; Geography ; Haplotypes/genetics ; Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; }, abstract = {The long-armed scarab (Cheirotonus gestroi) is an endangered large insect in southwestern China and neighboring countries; however, limited information is available regarding its population genetics, hindering conservation efforts. Therefore, we investigated the population genetic structure and evolutionary history of C. gestroi in southwestern China. Twenty-five haplotypes were obtained from 47 specimens across five populations. The Dawei Mountain (DWS) population differed from other populations by a high genetic distance. Population structure analysis generated three distinct clades, corresponding to Hengduan Mountains (HM), Ailao Mountains (AM), and Dawei Mountains (DM), and high-level genetic diversity was found in two HM populations. Collectively, the strong genetic differentiation among populations might be due to limited gene flow, geographical isolation, and habitat fragmentation. Therefore, while developing a conservation strategy, HM, AM, and DM groups should be defined as separate management units. Additionally, the DWS population should be given priority protection due to its uniqueness and low genetic diversity.}, }
@article {pmid32202175, year = {2020}, author = {Mehdizadeh, R and Akmali, V and Sharifi, M}, title = {Population genetic structure and phylogeography of the greater horseshoe bat (Rhinolophus ferrumequinum) along Alborz and Zagros Mts. in Iran.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {31}, number = {3}, pages = {87-97}, doi = {10.1080/24701394.2020.1741562}, pmid = {32202175}, issn = {2470-1408}, mesh = {Animals ; Biological Evolution ; Chiroptera/*genetics ; Cytochromes b/*genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial/genetics ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Mitochondrial/genetics ; Haplotypes/genetics ; Iran ; Mitochondria/genetics ; Phylogeny ; Phylogeography/methods ; Sequence Analysis, DNA/methods ; Turkey ; }, abstract = {In this paper, we investigate the genetic structure and phylogeography of Rhinolophus ferrumequinum, using the mitochondrial cytochrome b gene (1017 bp) in Iran and adjacent regions. The total haplotype and nucleotide diversity are 0.63 ± 0.055 and 0.0021 ± 0.00017, respectively which suggest that R. ferrumequinum exhibits low genetic diversity. AMOVA analysis shows that more variation of genetic differentiation is present among populations of phylogenetic groupings than within populations. Our phylogenetic results support the monophyly of R. ferrumequinum and suggest this taxon comprises three allopatric/parapatric phylogroups that are distributed in Europe-western Turkey, eastern Turkey-northern Iran, and southern Iran. The Europe-western Turkey lineage (clade 2) split from the eastern Turkey-Iran lineage (clade 1) during the middle Pleistocene (0.8534 (ca.I)-0.6454 (ca.II) Ma). The divergence time among subclades A and B occurred during the mid-Pleistocene (0.4849 (ca.I)-0.369 (ca.II) Ma). All phylogenetic analyses also indicate that the Iranian and eastern Turkey R. ferrumequinum diverged from Europe and western Turkey R. ferrumequinum, with the mean percentage sequence differences ranging from 0.92%-0.75% between them. We infer that long-term isolation of R. ferrumequinum in spatially distinct refugia in parts of southwestern and northeastern Iran has promoted distinct phylogeographic lineages during the Pleistocene.}, }
@article {pmid32201093, year = {2020}, author = {de Brito Monteiro, L and Davanzo, GG and de Aguiar, CF and Corrêa da Silva, F and Andrade, JR and Campos Codo, A and Silva Pereira, JAD and Freitas, LP and Moraes-Vieira, PM}, title = {M-CSF- and L929-derived macrophages present distinct metabolic profiles with similar inflammatory outcomes.}, journal = {Immunobiology}, volume = {225}, number = {3}, pages = {151935}, doi = {10.1016/j.imbio.2020.151935}, pmid = {32201093}, issn = {1878-3279}, mesh = {Animals ; Biomarkers ; Cell Line ; Cytokines/metabolism ; Energy Metabolism ; Inflammation Mediators/metabolism ; Macrophage Colony-Stimulating Factor/*metabolism ; Macrophages/*immunology/*metabolism ; *Metabolome ; *Metabolomics/methods ; Mice ; }, abstract = {Macrophages are essential components of the immune system. Macrophages can be derived from the bone marrow of mice with either recombinant M-CSF or L929 supernatant. Recent literature considers recombinant M-CSF- and L929-derived macrophages as equals, even though L929-derived macrophages are exposed to other substances secreted in the L929 supernatant, and not only M-CSF. Thus, we decided to perform a comparative analysis of both inflammatory and metabolic profiles of macrophages differentiated under the aforementioned conditions, which is relevant for standardization and interpretation of in vitro studies. We observed that, when treated with LPS, L929macs secrete lower levels of proinflammatory cytokines (TNF-α, IL-6, IL12) and present higher glycolysis and oxygen consumption when compared with M-CSFmacs. L929macs also have increased mitochondrial mass, with higher percentage of dysfunctional mitochondria. This sort of information can help direct further studies towards a more specific approach for macrophage generation.}, }
@article {pmid32199599, year = {2020}, author = {Noguera, R and Burgos-Panadero, R and Lucantoni, F and de la Cruz-Merino, L and Álvaro Naranjo, T}, title = {[An integral view of cancer (III). Evaluation of new biomarkers and treatment strategies].}, journal = {Revista espanola de patologia : publicacion oficial de la Sociedad Espanola de Anatomia Patologica y de la Sociedad Espanola de Citologia}, volume = {53}, number = {2}, pages = {88-99}, doi = {10.1016/j.patol.2019.08.001}, pmid = {32199599}, issn = {1988-561X}, mesh = {Acidosis ; Antibodies, Neoplasm/immunology ; *Biomarkers, Tumor/metabolism ; CTLA-4 Antigen/immunology ; Cancer Vaccines/therapeutic use ; Cytokines/immunology ; Gastrointestinal Microbiome/immunology ; Humans ; Hypoglycemic Agents/pharmacology ; Immunotherapy/*methods ; Immunotherapy, Adoptive ; Lymphocytes, Tumor-Infiltrating ; Metformin/pharmacology ; Neoplasm Staging/methods ; Neoplasms/*immunology/metabolism/pathology/*therapy ; Oncolytic Virotherapy/methods ; Prognosis ; Programmed Cell Death 1 Receptor/metabolism ; Receptors, Adrenergic/metabolism ; Tumor Hypoxia ; Tumor Microenvironment/*immunology ; }, abstract = {We propose a comprehensive approach to oncological disease, based on a systemic consideration of biology, health and disease. Our two previous review articles focused on tumour microenvironment and the discovery of new biomarkers; here we discuss the practical application of these principles to pathology, through the identification, evaluation and quantitative analysis of new prognostic and predictive factors (Immunoscore, TIME). We also consider the clinical use of promising, better tolerated treatments, such as immunotherapy. The integrative pathologist now has access to the latest improved oncology stratification tools designed to identify effective treatment strategies, based on the natural evolution of clinical and scientific knowledge that transcend the gene-centric theory of cancer.}, }
@article {pmid32199028, year = {2020}, author = {Buonvicino, D and Ranieri, G and Pratesi, S and Gerace, E and Muzzi, M and Guasti, D and Tofani, L and Chiarugi, A}, title = {Neuroprotection induced by dexpramipexole delays disease progression in a mouse model of progressive multiple sclerosis.}, journal = {British journal of pharmacology}, volume = {177}, number = {14}, pages = {3342-3356}, pmid = {32199028}, issn = {1476-5381}, support = {20451 project (P.I. Alberto Chiarugi)//Fondazione CR Firenze under IG 2017/ ; 2014/R/6 (recipient AC)//Italian Foundation for Multiple Sclerosis/ ; 2014/R/6//Italian Foundation for Multiple Sclerosis/ ; //AIRC/ ; //Regione Toscana Rare Disease Projects-Heath Projects 2007 and 2009/ ; }, mesh = {Animals ; *Diabetes Mellitus, Experimental ; Disease Progression ; Female ; Humans ; Mice ; *Multiple Sclerosis/drug therapy ; Neuroprotection ; Pramipexole ; }, abstract = {BACKGROUND AND PURPOSE: Drugs able to counteract progressive multiple sclerosis (MS) represent a largely unmet therapeutic need. Even though the pathogenesis of disease evolution is still obscure, accumulating evidence indicates that mitochondrial dysfunction plays a causative role in neurodegeneration and axonopathy in progressive MS patients. Here, we investigated the effects of dexpramipexole, a compound with a good safety profile in humans and able to sustain mitochondria functioning and energy production, in a mouse model of progressive MS.<br><br>EXPERIMENTAL APPROACH: Female non-obese diabetic mice were immunized with MOG35-55 . Functional, immune and neuropathological parameters were analysed during disease evolution in animals treated or not with dexpramipexole. The compound's effects on bioenergetics and neuroprotection were also evaluated in vitro.<br><br>KEY RESULTS: We found that oral treatment with dexpramipexole at a dose consistent with that well tolerated in humans delayed disability progression, extended survival, counteracted reduction of spinal cord mitochondrial DNA content and reduced spinal cord axonal loss of mice. Accordingly, the drug sustained in vitro bioenergetics of mouse optic nerve and dorsal root ganglia and counteracted neurodegeneration of organotypic mouse cortical cultures exposed to the adenosine triphosphate-depleting agents oligomycin or veratridine. Dexpramipexole, however, was unable to affect the adaptive and innate immune responses both in vivo and in vitro.<br><br>CONCLUSION AND IMPLICATION: The present findings corroborate the hypothesis that neuroprotective agents may be of relevance to counteract MS progression and disclose the translational potential of dexpramipexole to treatment of progressive MS patients as a stand-alone or adjunctive therapy.}, }
@article {pmid32197583, year = {2020}, author = {Achari, SR and Kaur, J and Dinh, Q and Mann, R and Sawbridge, T and Summerell, BA and Edwards, J}, title = {Phylogenetic relationship between Australian Fusarium oxysporum isolates and resolving the species complex using the multispecies coalescent model.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {248}, pmid = {32197583}, issn = {1471-2164}, mesh = {Cell Nucleus/genetics ; Evolution, Molecular ; Fusarium/*classification/genetics/isolation &amp; purification ; Genome, Fungal ; Mitochondria/genetics ; Phylogeny ; Whole Genome Sequencing/*statistics &amp; numerical data ; }, abstract = {BACKGROUND: The Fusarium oxysporum species complex (FOSC) is a ubiquitous group of fungal species readily isolated from agroecosystem and natural ecosystem soils which includes important plant and human pathogens. Genetic relatedness within the complex has been studied by sequencing either the genes or the barcoding gene regions within those genes. Phylogenetic analyses have demonstrated a great deal of diversity which is reflected in the differing number of clades identified: three, five and eight. Genetic limitation within the species in the complex has been studied through Genealogical Concordance Phylogenetic Species Recognition (GCPSR) analyses with varying number of phylogenetic 'species' identified ranging from two to 21. Such differing views have continued to confuse users of these taxonomies.<br><br>RESULTS: The phylogenetic relationships between Australian F. oxysporum isolates from both natural and agricultural ecosystems were determined using three datasets: whole genome, nuclear genes, and mitochondrial genome sequences. The phylogenies were concordant except for three isolates. There were three concordant clades from all the phylogenies suggesting similar evolutionary history for mitochondrial genome and nuclear genes for the isolates in these three clades. Applying a multispecies coalescent (MSC) model on the eight single copy nuclear protein coding genes from the nuclear gene dataset concluded that the three concordant clades correspond to three phylogenetic species within the FOSC. There was 100% posterior probability support for the formation of three species within the FOSC. This is the first report of using the MSC model to estimate species within the F. oxysporum species complex. The findings from this study were compared with previously published phylogenetics and species delimitation studies.<br><br>CONCLUSION: Phylogenetic analyses using three different gene datasets from Australian F. oxysporum isolates have all supported the formation of three major clades which delineated into three species. Species 2 (Clade 3) may be called F. oxysporum as it contains the neotype for F. oxysporum.}, }
@article {pmid32186219, year = {2020}, author = {Zhang, WJ and Wang, JJ and Li, C and Chen, JQ and Li, W and Jiang, SY and Hsu, KC and Zhao, M and Lin, HD and Zhao, J}, title = {Spatial genetic structure of Opsariichthys hainanensis in South China.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {31}, number = {3}, pages = {98-107}, doi = {10.1080/24701394.2020.1741564}, pmid = {32186219}, issn = {2470-1408}, mesh = {Animals ; China ; Cyprinidae/*genetics ; Cytochromes b/*genetics ; DNA, Mitochondrial/genetics ; Fishes/genetics ; Genes, Mitochondrial/genetics ; Genetic Structures/genetics ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Mitochondrial/genetics ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Rivers ; Sequence Analysis, DNA/methods ; }, abstract = {South China presents an excellent opportunity to build a phylogeographic paradigm for complex geological history, including mountain lifting, climate change, and river capture/reversal events. The phylogeography of cyprinids, particularly Opsariichthys hainanensis, an endemic species restricted to South China, was examined to explore the relationship between the populations in Red River, Hainan Island and its adjacent mainland China. A total of 37 haplotypes were genotyped for the mitochondrial cytochrome b (Cyt b) gene in 115 specimens from 11 river systems. Relatively high levels of haplotype diversity (h = 0.946) and low levels of nucleotide diversity (π = 0.014) were detected in O. hainanensis. Four major phylogenetic haplotype groups revealed a relationship between phylogeny and geography. Our results found that (i) the ancestral populations of O. hainanensis were distributed south of the Wuzhishan and Yinggeling mountains, including the Changhua River on Hainan Island, and then spread to the surrounding areas, (ii) the admixtures within lineages occurred between the Red River in North Vietnam and the Changhua River in western Hainan Island and (iii) indicated that the exposure of straits and shelves under water retreat, provides opportunities for population dispersion during glaciations.}, }
@article {pmid32185904, year = {2020}, author = {Stavru, F and Riemer, J and Jex, A and Sassera, D}, title = {When bacteria meet mitochondria: The strange case of the tick symbiont Midichloria mitochondrii[†].}, journal = {Cellular microbiology}, volume = {22}, number = {4}, pages = {e13189}, doi = {10.1111/cmi.13189}, pmid = {32185904}, issn = {1462-5822}, mesh = {Alphaproteobacteria/*physiology ; Animals ; Ixodes/*microbiology ; Mitochondria/*microbiology/physiology ; Phylogeny ; *Symbiosis ; Viral Tropism ; }, abstract = {Mitochondria are key eukaryotic organelles that perform several essential functions. Not surprisingly, many intracellular bacteria directly or indirectly target mitochondria, interfering with innate immunity, energy production or apoptosis, to make the host cell a more hospitable niche for bacterial replication. The alphaproteobacterium Midichloria mitochondrii has taken mitochondrial targeting to another level by physically colonising mitochondria, as shown by transmission electron micrographs of bacteria residing in the mitochondrial intermembrane space. This unique localization provokes a number of questions around the mechanisms allowing, and reasons driving intramitochondrial tropism. We suggest possible scenarios that could lead to this peculiar localization and hypothesize potential costs and benefits of mitochondrial colonisation for the bacterium and its host.}, }
@article {pmid32185389, year = {2020}, author = {Mbadinga Mbadinga, DL and Li, Q and Ranocha, P and Martinez, Y and Dunand, C}, title = {Global analysis of non-animal peroxidases provides insights into the evolution of this gene family in the green lineage.}, journal = {Journal of experimental botany}, volume = {71}, number = {11}, pages = {3350-3360}, doi = {10.1093/jxb/eraa141}, pmid = {32185389}, issn = {1460-2431}, mesh = {Ascorbate Peroxidases ; *Fungi ; *Peroxidases/genetics ; Phylogeny ; Plants ; }, abstract = {The non-animal peroxidases belong to a superfamily of oxidoreductases that reduce hydrogen peroxide and oxidize numerous substrates. Since their initial characterization in 1992, a number of studies have provided an understanding of the origin and evolution of this protein family. Here, we report a comprehensive evolutionary analysis of non-animal peroxidases using integrated in silico and biochemical approaches. Thanks to the availability of numerous genomic sequences from more than 2500 species belonging to 14 kingdoms together with expert and comprehensive annotation of peroxidase sequences that have been centralized in a dedicated database, we have been able to use phylogenetic reconstructions to increase our understanding of the evolutionary processes underlying the diversification of non-animal peroxidases. We analysed the distribution of all non-animal peroxidases in more than 200 eukaryotic organisms in silico. First, we show that the presence or absence of non-animal peroxidases correlates with the presence or absence of certain organelles or with specific biological processes. Examination of almost 2000 organisms determined that ascorbate peroxidases (APxs) and cytochrome c peroxidases (CcPs) are present in those containing chloroplasts and mitochondria, respectively. Plants, which contain both organelles, are an exception and contain only APxs without CcP. Class II peroxidases (CII Prxs) are only found in fungi with wood-decay and plant-degradation abilities. Class III peroxidases (CIII Prxs) are only found in streptophyte algae and land plants, and have been subjected to large family expansion. Biochemical activities of APx, CcP, and CIII Prx assessed using protein extracts from 30 different eukaryotic organisms support the distribution of the sequences resulting from our in silico analysis. The biochemical results confirmed both the presence and classification of the non-animal peroxidase encoding sequences.}, }
@article {pmid32184120, year = {2020}, author = {Warren, JM and Sloan, DB}, title = {Interchangeable parts: The evolutionarily dynamic tRNA population in plant mitochondria.}, journal = {Mitochondrion}, volume = {52}, number = {}, pages = {144-156}, doi = {10.1016/j.mito.2020.03.007}, pmid = {32184120}, issn = {1872-8278}, mesh = {Evolution, Molecular ; Genetic Variation ; Mitochondria/*genetics ; Phylogeny ; Plants/*genetics ; RNA, Mitochondrial/genetics ; RNA, Transfer/*genetics ; Sequence Analysis, RNA ; }, abstract = {Transfer RNAs (tRNAs) remain one of the very few classes of genes still encoded in the mitochondrial genome. These key components of the protein translation system must interact with a large enzymatic network of nuclear-encoded gene products to maintain mitochondrial function. Plants have an evolutionarily dynamic mitochondrial tRNA population, including ongoing tRNA gene loss and replacement by both horizontal gene transfer from diverse sources and import of nuclear-expressed tRNAs from the cytosol. Thus, plant mitochondria represent an excellent model for understanding how anciently divergent genes can act as "interchangeable parts" during the evolution of complex molecular systems. In particular, understanding the integration of the mitochondrial translation system with elements of the corresponding machinery used in cytosolic protein synthesis is a key area for eukaryotic cellular evolution. Here, we review the increasingly detailed phylogenetic data about the evolutionary history of mitochondrial tRNA gene loss, transfer, and functional replacement that has created extreme variation in mitochondrial tRNA populations across plant species. We describe emerging tRNA-seq methods with promise for refining our understanding of the expression and subcellular localization of tRNAs. Finally, we summarize current evidence and identify open questions related to coevolutionary changes in nuclear-encoded enzymes that have accompanied turnover in mitochondrial tRNA populations.}, }
@article {pmid32183692, year = {2020}, author = {Wang, H and Liu, C and Liu, Z and Wang, Y and Ma, L and Xu, B}, title = {The different dietary sugars modulate the composition of the gut microbiota in honeybee during overwintering.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {61}, pmid = {32183692}, issn = {1471-2180}, support = {CARS-45//Agriculture Research System of China/International ; 31572470//Innovative Research Group Project of the National Natural Science Foundation of China/International ; }, mesh = {Animals ; Bacteria/*classification/drug effects/isolation &amp; purification ; Bees/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Dietary Sugars/*adverse effects ; Gastrointestinal Microbiome/drug effects ; High Fructose Corn Syrup/adverse effects ; High-Throughput Nucleotide Sequencing ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Seasons ; Sequence Analysis, DNA/*methods ; Sucrose/adverse effects ; }, abstract = {BACKGROUND: The health of honeybee colonies is critical for bee products and agricultural production, and colony health is closely associated with the bacteria in the guts of honeybees. Although colony loss in winter is now the primary restriction in beekeeping, the effects of different sugars as winter food on the health of honeybee colonies are not well understood. Therefore, in this study, the influence of different sugar diets on honeybee gut bacteria during overwintering was examined.<br><br>RESULTS: The bacterial communities in honeybee midguts and hindguts before winter and after bees were fed honey, sucrose, and high-fructose syrup as winter-food were determined by targeting the V3-V4 region of 16S rDNA using the Illumina MiSeq platform. The dominant microbiota in honeybee guts were the phyla Proteobacteria (63.17%), Firmicutes (17.61%; Lactobacillus, 15.91%), Actinobacteria (4.06%; Bifidobacterium, 3.34%), and Bacteroidetes (1.72%). The dominant taxa were conserved and not affected by season, type of overwintering sugar, or spatial position in the gut. However, the relative abundance of the dominant taxa was affected by those factors. In the midgut, microbial diversity of the sucrose group was higher than that of the honey and high-fructose syrup groups, but in the hindgut, microbial diversity of the honey and high-fructose groups was higher than that in the sucrose group. Sucrose increased the relative abundance of Actinobacteria (Bifidobacteriales Bifidobacteriaceae) and Alphaproteobacteria (Rhizobiales and Mitochondria) of honeybee midgut, and honey enriched the Bacteroidetes and Gammaproteobacteria (Pasteurellales) in honeybee hindgut. High-fructose syrup increased the relative abundance of Betaproteobacteria (Neisseriales: Neisseriaceae) of the midgut.<br><br>CONCLUSION: The type of sugar used as winter food affected the relative abundance of the dominant bacterial communities in honeybee guts, not the taxa, which could affect the health and safety of honeybee colonies during overwintering. The presence of the supernal Alphaproteobacteria, Bifidobacteriales, and Lactobacillaceae in the gut of honeybees fed sucrose and cheaper than honey both indicate that sucrose is very suitable as the overwintering food for honeybees.}, }
@article {pmid32183014, year = {2020}, author = {Choi, IS and Ruhlman, TA and Jansen, RK}, title = {Comparative Mitogenome Analysis of the Genus Trifolium Reveals Independent Gene Fission of ccmFn and Intracellular Gene Transfers in Fabaceae.}, journal = {International journal of molecular sciences}, volume = {21}, number = {6}, pages = {}, pmid = {32183014}, issn = {1422-0067}, support = {DEB-1853024//National Science Foundation/ ; }, mesh = {Evolution, Molecular ; *Genome, Mitochondrial ; *Genome, Plastid ; Phylogeny ; Sequence Homology ; Trifolium/classification/*genetics ; }, abstract = {The genus Trifolium is the largest of the tribe Trifolieae in the subfamily Papilionoideae (Fabaceae). The paucity of mitochondrial genome (mitogenome) sequences has hindered comparative analyses among the three genomic compartments of the plant cell (nucleus, mitochondrion and plastid). We assembled four mitogenomes from the two subgenera (Chronosemium and Trifolium) of the genus. The four Trifolium mitogenomes were compact (294,911-348,724 bp in length) and contained limited repetitive (6.6-8.6%) DNA. Comparison of organelle repeat content highlighted the distinct evolutionary trajectory of plastid genomes in a subset of Trifolium species. Intracellular gene transfer (IGT) was analyzed among the three genomic compartments revealing functional transfer of mitochondrial rps1 to nuclear genome along with other IGT events. Phylogenetic analysis based on mitochondrial and nuclear rps1 sequences revealed that the functional transfer in Trifolieae was independent from the event that occurred in robinioid clade that includes genus Lotus. A novel, independent fission event of ccmFn in Trifolium was identified, caused by a 59 bp deletion. Fissions of this gene reported previously in land plants were reassessed and compared with Trifolium.}, }
@article {pmid32180577, year = {2020}, author = {Ozozan, OV and Dinc, T and Vural, V and Ozogul, C and Ozmen, MM and Coskun, F}, title = {An electron microscopy study of liver and kidney damage in an experimental model of obstructive jaundice.}, journal = {Annali italiani di chirurgia}, volume = {91}, number = {}, pages = {122-130}, pmid = {32180577}, issn = {2239-253X}, mesh = {Animals ; Disease Models, Animal ; Jaundice, Obstructive/complications/*pathology ; Kidney/*pathology/*ultrastructure ; Kidney Diseases/etiology/pathology ; Liver/*pathology/*ultrastructure ; Liver Diseases/etiology/pathology ; Microscopy, Electron ; Rats ; Rats, Wistar ; }, abstract = {UNLABELLED: With this experimental study we investigated the consequences of ligation of the common bile duct (CBD) on hepatic cells and on the renal ultrastructure by electron microscopy and also determine the effects after liberation of the ductus joint in order to clarify the mechanisms of renal failure commonly observed in cholestatic liver disease. The study was conducted on 53 Wistar albino rats divided into 4 subgroups. In the comparison group (sham) we proceeded to the simple laparotomy. After preparation of the common bile duct of all the rats of the four groups, and ligation of the duct at the level of the distal third, eight rats in each group were sacrificed on the 3rd, 7th, 10th and 14th day after surgery, taking blood samples to measure the serum levels of ALP and bilirubin, and liver and renal tissue samples for histological evaluation. In four rats of each group the common bile duct was unligated at the same deadlines to obtain free drainage of the bile for a week. At the end of this week, the rats were sacrificed by collecting blood and liver and kidney tissue samples.<br><br>RESULTS: after CBD ligation in both groups, the ALP value, total and direct bilurubin levels were proportionally increased. After duct release, bilurubin levels decreased significantly. In group II, while large lipid granules were observed to indicate oxidative damage, mitochondrial swelling and crystals were observed after duct liberation. Areas of glycogen and normal mitochondria were observed in group IV. After duct release in this group, increases in Ito granules, lipid granules and normal mitochondria were observed, which may reflect the evolution of hepatic regeneration. When renal tissue was examined in group II, fusion processes in the feet, thickening of the basement membrane and mesengium were observed, and mitochondrial crystals were observed in renal tissue as well as in the liver after duct release. Damage in group III and group IV was increased parallel to prolongation of jaundice and after loosening persistent damage with mitochondrial crystals.<br><br>CONCLUSION: Ultrastructural changes in rat liver tissue in conditions of obstructive jaundice may be reversible after restoration of drainage. On the other hand, ultrastructural changes in renal tissue in cases of prolonged jaundice are irreversible even if the internal drainage is restored.<br><br>KEY WORDS: Bile Duct, Liver, Kidney, Obstructive Jaundice.}, }
@article {pmid32179772, year = {2020}, author = {Naik, VCB and Pusadkar, PP and Waghmare, ST and K P, R and Kranthi, S and Kumbhare, S and Nagrare, VS and Kumar, R and Prabhulinga, T and Gokte-Narkhedkar, N and Waghmare, VN}, title = {Evidence for population expansion of Cotton pink bollworm Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) in India.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {4740}, pmid = {32179772}, issn = {2045-2322}, mesh = {Animals ; Bacillus thuringiensis Toxins ; DNA, Mitochondrial ; Endotoxins ; Genetic Variation ; *Genetics, Population ; Gossypium/*parasitology ; *Haplotypes ; Hemolysin Proteins ; India ; Lepidoptera/*genetics ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Pink bollworm, Pectinophora gossypiella (Saunders) infestation on Bt cotton is a major concern to cotton production in India. The genetic diversity and phylogeographic structure of the insect in light of PBW resistance needs to be revisited. The objective of this study was to identify different haplotypes of pink bollworm and their distribution in India. To achieve this we studied the population structure in 44 cotton growing districts of India. The partial mitochondrial COI sequence analyses of 214 pink bollworm populations collected from 44 geographical locations representing 9 cotton growing states of India were analysed. Genetic diversity analysis exhibited presence of 27 haplotypes, among them Pg_H1 and Pg_H2 were the most common and were present in 143 and 32 populations, respectively. Distributions of pairwise differences obtained with partial COI gene data from the overall Indian populations are unimodal, suggesting population expansion in India. Significant neutrality test on the basis of Tajima' D and Fu's Fs presented a star-shaped haplotype network together with multiple haplotypes. The unimodal mismatch distribution, rejection of neutrality test with significant negative values supported the theory of demographic expansion in cotton pink bollworm populations in India. Genetic data not only provides us with a perspective of population genetics, but also that the two populations of pink bollworm, those occurring early in the season are genetically close to the late season populations with respect to their partial CO1 region. Resistance to Cry toxins does not seem to have had an impact on this region of the mt DNA in populations of pink bollworm.}, }
@article {pmid32178369, year = {2020}, author = {Lu, K and Policar, T and Song, X and Rahimnejad, S}, title = {Molecular Characterization of PGC-1β (PPAR Gamma Coactivator 1β) and its Roles in Mitochondrial Biogenesis in Blunt Snout Bream (Megalobrama amblycephala).}, journal = {International journal of molecular sciences}, volume = {21}, number = {6}, pages = {}, pmid = {32178369}, issn = {1422-0067}, support = {B17162//Outstanding Young Scientific Research Talents Program of Fujian province/ ; 31801969//National Nature Science Foundation of China/ ; LM2018099//Ministry of Education, Youth and Sports of the Czech Republic, project CENAKVA/ ; QK1710310//Ministry of Agriculture of the Czech Republic, project NAZV/ ; }, mesh = {Amino Acids ; Animals ; Cyprinidae/*genetics/*physiology ; DNA, Mitochondrial/genetics ; DNA-Binding Proteins/genetics ; Hepatocytes/physiology ; Liver ; Mitochondria/*genetics/*physiology ; Mitochondrial Proteins/genetics ; Organelle Biogenesis ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/*genetics ; Phylogeny ; Signal Transduction/genetics ; Transcription Factors/genetics ; }, abstract = {This study aimed at achieving the molecular characterization of peroxisome proliferator-activated receptor-gamma coactivator 1β (PGC-1β) and exploring its modulatory roles in mitochondria biogenesis in blunt snout bream (Megalobrama amblycephala). A full-length cDNA of PGC-1β was cloned from liver which covered 3110 bp encoding 859 amino acids. The conserved motifs of PGC-1β family proteins were gained by MEME software, and the phylogenetic analyses showed motif loss and rearrangement of PGC-1β in fish. The function of PGC-1β was evaluated through overexpression and knockdown of PGC-1β in primary hepatocytes of blunt snout bream. We observed overexpression of PGC-1β along with enhanced mitochondrial transcription factor A (TFAM) expression and mtDNA copies in hepatocytes, and its knockdown led to slightly reduced NRF1 expression. However, knockdown of PGC-1β did not significantly influence TFAM expression or mtDNA copies. The alterations in mitochondria biogenesis were assessed following high-fat intake, and the results showed that it induces downregulation of PGC-1β. Furthermore, significant decreases in mitochondrial respiratory chain activities and mitochondria biogenesis were observed by high-fat intake. Our findings demonstrated that overexpression of PGC-1β induces the enhancement of TFAM expression and mtDNA amount but not NRF-1. Therefore, it could be concluded that PGC-1β is involved in mitochondrial biogenesis in blunt snout bream but not through PGC-1β/NRF-1 pathway.}, }
@article {pmid32159766, year = {2020}, author = {Hammond, MJ and Nenarokova, A and Butenko, A and Zoltner, M and Dobáková, EL and Field, MC and Lukeš, J}, title = {A Uniquely Complex Mitochondrial Proteome from Euglena gracilis.}, journal = {Molecular biology and evolution}, volume = {37}, number = {8}, pages = {2173-2191}, pmid = {32159766}, issn = {1537-1719}, support = {/WT_/Wellcome Trust/United Kingdom ; 204697/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Euglena gracilis/*metabolism ; Mitochondrial Proteins/*metabolism ; *Proteome ; }, abstract = {Euglena gracilis is a metabolically flexible, photosynthetic, and adaptable free-living protist of considerable environmental importance and biotechnological value. By label-free liquid chromatography tandem mass spectrometry, a total of 1,786 proteins were identified from the E. gracilis purified mitochondria, representing one of the largest mitochondrial proteomes so far described. Despite this apparent complexity, protein machinery responsible for the extensive RNA editing, splicing, and processing in the sister clades diplonemids and kinetoplastids is absent. This strongly suggests that the complex mechanisms of mitochondrial gene expression in diplonemids and kinetoplastids occurred late in euglenozoan evolution, arising independently. By contrast, the alternative oxidase pathway and numerous ribosomal subunits presumed to be specific for parasitic trypanosomes are present in E. gracilis. We investigated the evolution of unexplored protein families, including import complexes, cristae formation proteins, and translation termination factors, as well as canonical and unique metabolic pathways. We additionally compare this mitoproteome with the transcriptome of Eutreptiella gymnastica, illuminating conserved features of Euglenida mitochondria as well as those exclusive to E. gracilis. This is the first mitochondrial proteome of a free-living protist from the Excavata and one of few available for protists as a whole. This study alters our views of the evolution of the mitochondrion and indicates early emergence of complexity within euglenozoan mitochondria, independent of parasitism.}, }
@article {pmid32157725, year = {2020}, author = {Speijer, D}, title = {Debating Eukaryogenesis-Part 2: How Anachronistic Reasoning Can Lure Us into Inventing Intermediates.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {42}, number = {5}, pages = {e1900153}, doi = {10.1002/bies.201900153}, pmid = {32157725}, issn = {1521-1878}, mesh = {Archaea/genetics ; *Biological Evolution ; *Eukaryota ; Eukaryotic Cells ; Phylogeny ; Symbiosis ; }, abstract = {Eukaryotic origins are inextricably linked with the arrival of a pre-mitochondrion of alphaproteobacterial-like ancestry. However, the nature of the "host" cell and the mode of entry are subject to heavy debate. It is becoming clear that the mutual adaptation of a relatively simple, archaeal host and the endosymbiont has been the defining influence at the beginning of the eukaryotic lineage; however, many still resist such symbiogenic models. In part 1, it is posited that a symbiotic stage before uptake ("pre-symbiosis") seems essential to allow further metabolic integration of the two partners ending in endosymbiosis. Thus, the author argued against phagocytic mechanisms (in which the bacterium is prey or parasite) as the mode of entry. Such positions are still broadly unpopular. Here it is explained why. Evolutionary thinking, especially in the case of eukaryogenesis, is still dominated by anachronistic reasoning, in which highly derived protozoan organisms are seen as in some way representative of intermediate steps during eukaryotic evolution, hence poisoning the debate. This reasoning reflects a mind-set that ignores that Darwinian evolution is a fundamentally historic process. Numerous examples of this kind of erroneous reasoning are given, and some basic precautions against its use are formulated. Also see the video abstract here https://youtu.be/ekqtNleVJpU.}, }
@article {pmid32157325, year = {2020}, author = {Tomáška, &#x13d; and Nosek, J}, title = {Co-evolution in the Jungle: From Leafcutter Ant Colonies to Chromosomal Ends.}, journal = {Journal of molecular evolution}, volume = {88}, number = {4}, pages = {293-318}, pmid = {32157325}, issn = {1432-1432}, support = {APVV-15-0022//Agent&#xfa;ra na Podporu V&#xfd;skumu a V&#xfd;voja/International ; APVV-18-0239//Agent&#xfa;ra na Podporu V&#xfd;skumu a V&#xfd;voja/International ; VEGA 1/0061/20//Ministerstvo &#x161;kolstva, vedy, v&#xfd;skumu a &#x161;portu Slovenskej republiky/International ; VEGA 1/0027/19//Ministerstvo &#x161;kolstva, vedy, v&#xfd;skumu a &#x161;portu Slovenskej republiky/International ; }, mesh = {Animals ; *Ants ; *Biological Coevolution ; DNA ; Genome, Mitochondrial ; *Telomere ; }, abstract = {Biological entities are multicomponent systems where each part is directly or indirectly dependent on the others. In effect, a change in a single component might have a consequence on the functioning of its partners, thus affecting the fitness of the entire system. In this article, we provide a few examples of such complex biological systems, ranging from ant colonies to a population of amino acids within a single-polypeptide chain. Based on these examples, we discuss one of the central and still challenging questions in biology: how do such multicomponent consortia co-evolve? More specifically, we ask how telomeres, nucleo-protein complexes protecting the integrity of linear DNA chromosomes, originated from the ancestral organisms having circular genomes and thus not dealing with end-replication and end-protection problems. Using the examples of rapidly evolving topologies of mitochondrial genomes in eukaryotic microorganisms, we show what means of co-evolution were employed to accommodate various types of telomere-maintenance mechanisms in mitochondria. We also describe an unprecedented runaway evolution of telomeric repeats in nuclei of ascomycetous yeasts accompanied by co-evolution of telomere-associated proteins. We propose several scenarios derived from research on telomeres and supported by other studies from various fields of biology, while emphasizing that the relevant answers are still not in sight. It is this uncertainty and a lack of a detailed roadmap that makes the journey through the jungle of biological systems still exciting and worth undertaking.}, }
@article {pmid32156736, year = {2020}, author = {Healy, TM and Burton, RS}, title = {Strong selective effects of mitochondrial DNA on the nuclear genome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {12}, pages = {6616-6621}, pmid = {32156736}, issn = {1091-6490}, mesh = {Adenosine Triphosphate/*metabolism ; Animals ; Cell Nucleus/*genetics/metabolism ; Copepoda/*genetics/growth &amp; development/metabolism ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genetic Fitness ; *Genome ; Genome, Mitochondrial ; Mitochondria/*genetics/metabolism ; Oxidative Phosphorylation ; }, abstract = {Oxidative phosphorylation, the primary source of cellular energy in eukaryotes, requires gene products encoded in both the nuclear and mitochondrial genomes. As a result, functional integration between the genomes is essential for efficient adenosine triphosphate (ATP) generation. Although within populations this integration is presumably maintained by coevolution, the importance of mitonuclear coevolution in key biological processes such as speciation and mitochondrial disease has been questioned. In this study, we crossed populations of the intertidal copepod Tigriopus californicus to disrupt putatively coevolved mitonuclear genotypes in reciprocal F2 hybrids. We utilized interindividual variation in developmental rate among these hybrids as a proxy for fitness to assess the strength of selection imposed on the nuclear genome by alternate mitochondrial genotypes. Developmental rate varied among hybrid individuals, and in vitro ATP synthesis rates of mitochondria isolated from high-fitness hybrids were approximately two-fold greater than those of mitochondria isolated from low-fitness individuals. We then used Pool-seq to compare nuclear allele frequencies for high- or low-fitness hybrids. Significant biases for maternal alleles were detected on 5 (of 12) chromosomes in high-fitness individuals of both reciprocal crosses, whereas maternal biases were largely absent in low-fitness individuals. Therefore, the most fit hybrids were those with nuclear alleles that matched their mitochondrial genotype on these chromosomes, suggesting that mitonuclear effects underlie individual-level variation in developmental rate and that intergenomic compatibility is critical for high fitness. We conclude that mitonuclear interactions can have profound impacts on both physiological performance and the evolutionary trajectory of the nuclear genome.}, }
@article {pmid32152094, year = {2020}, author = {Vyssokikh, MY and Holtze, S and Averina, OA and Lyamzaev, KG and Panteleeva, AA and Marey, MV and Zinovkin, RA and Severin, FF and Skulachev, MV and Fasel, N and Hildebrandt, TB and Skulachev, VP}, title = {Mild depolarization of the inner mitochondrial membrane is a crucial component of an anti-aging program.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {12}, pages = {6491-6501}, pmid = {32152094}, issn = {1091-6490}, mesh = {Adenosine Diphosphate/metabolism ; *Aging ; Animals ; Chiroptera ; Creatine/metabolism ; Electron Transport ; Embryo, Mammalian ; Glucose/metabolism ; Hexokinase/metabolism ; Membrane Potential, Mitochondrial ; Mice ; Mitochondria/metabolism/*physiology ; Mitochondrial Membranes/enzymology/metabolism/*physiology ; Mitochondrial Proteins/metabolism ; Mole Rats ; Organ Specificity ; Reactive Oxygen Species/metabolism ; Species Specificity ; }, abstract = {The mitochondria of various tissues from mice, naked mole rats (NMRs), and bats possess two mechanistically similar systems to prevent the generation of mitochondrial reactive oxygen species (mROS): hexokinases I and II and creatine kinase bound to mitochondrial membranes. Both systems operate in a manner such that one of the kinase substrates (mitochondrial ATP) is electrophoretically transported by the ATP/ADP antiporter to the catalytic site of bound hexokinase or bound creatine kinase without ATP dilution in the cytosol. One of the kinase reaction products, ADP, is transported back to the mitochondrial matrix via the antiporter, again through an electrophoretic process without cytosol dilution. The system in question continuously supports H[+]-ATP synthase with ADP until glucose or creatine is available. Under these conditions, the membrane potential, ∆ψ, is maintained at a lower than maximal level (i.e., mild depolarization of mitochondria). This ∆ψ decrease is sufficient to completely inhibit mROS generation. In 2.5-y-old mice, mild depolarization disappears in the skeletal muscles, diaphragm, heart, spleen, and brain and partially in the lung and kidney. This age-dependent decrease in the levels of bound kinases is not observed in NMRs and bats for many years. As a result, ROS-mediated protein damage, which is substantial during the aging of short-lived mice, is stabilized at low levels during the aging of long-lived NMRs and bats. It is suggested that this mitochondrial mild depolarization is a crucial component of the mitochondrial anti-aging system.}, }
@article {pmid32145731, year = {2020}, author = {Ran, R and Zhao, Q and Abuzeid, AMI and Huang, Y and Liu, Y and Sun, Y and He, L and Li, X and Liu, J and Li, G}, title = {Mitochondrial Genome Sequence of Echinostoma revolutum from Red-Crowned Crane (Grus japonensis).}, journal = {The Korean journal of parasitology}, volume = {58}, number = {1}, pages = {73-79}, pmid = {32145731}, issn = {1738-0006}, support = {31672541//National Natural Science Foundation of China/ ; 2014A020214005//the Science and Technology Planning Project of Guangdong Province, China/ ; }, mesh = {Animals ; Birds/*parasitology ; Echinostoma/*genetics ; Mitochondria/*genetics ; Phylogeny ; Whole Genome Sequencing ; }, abstract = {Echinostoma revolutum is a zoonotic food-borne intestinal trematode that can cause intestinal bleeding, enteritis, and diarrhea in human and birds. To identify a suspected E. revolutum trematode from a red-crowned crane (Grus japonensis) and to reveal the genetic characteristics of its mitochondrial (mt) genome, the internal transcribed spacer (ITS) and complete mt genome sequence of this trematode were amplified. The results identified the trematode as E. revolutum. Its entire mt genome sequence was 15,714 bp in length, including 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and one non-coding region (NCR), with 61.73% A+T base content and a significant AT preference. The length of the 22 tRNA genes ranged from 59 bp to 70 bp, and their secondary structure showed the typical cloverleaf and D-loop structure. The length of the large subunit of rRNA (rrnL) and the small subunit of rRNA (rrnS) gene was 1,011 bp and 742 bp, respectively. Phylogenetic trees showed that E. revolutum and E. miyagawai clustered together, belonging to Echinostomatidae with Hypoderaeum conoideum. This study may enrich the mitochondrial gene database of Echinostoma trematodes and provide valuable data for studying the molecular identification and phylogeny of some digenean trematodes.}, }
@article {pmid32144830, year = {2021}, author = {Trist, BG and Hilton, JB and Hare, DJ and Crouch, PJ and Double, KL}, title = {Superoxide Dismutase 1 in Health and Disease: How a Frontline Antioxidant Becomes Neurotoxic.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {60}, number = {17}, pages = {9215-9246}, pmid = {32144830}, issn = {1521-3773}, mesh = {Antioxidants/*metabolism ; Biocatalysis ; Central Nervous System Diseases/*metabolism ; Enzyme Stability ; Humans ; Superoxide Dismutase-1/deficiency/genetics/*metabolism ; Superoxides/metabolism ; }, abstract = {Cu/Zn superoxide dismutase (SOD1) is a frontline antioxidant enzyme catalysing superoxide breakdown and is important for most forms of eukaryotic life. The evolution of aerobic respiration by mitochondria increased cellular production of superoxide, resulting in an increased reliance upon SOD1. Consistent with the importance of SOD1 for cellular health, many human diseases of the central nervous system involve perturbations in SOD1 biology. But far from providing a simple demonstration of how disease arises from SOD1 loss-of-function, attempts to elucidate pathways by which atypical SOD1 biology leads to neurodegeneration have revealed unexpectedly complex molecular characteristics delineating healthy, functional SOD1 protein from that which likely contributes to central nervous system disease. This review summarises current understanding of SOD1 biology from SOD1 genetics through to protein function and stability.}, }
@article {pmid32143704, year = {2020}, author = {Cinar, HN and Gopinath, G and Murphy, HR and Almeria, S and Durigan, M and Choi, D and Jang, A and Kim, E and Kim, R and Choi, S and Lee, J and Shin, Y and Lee, J and Qvarnstrom, Y and Benedict, TK and Bishop, HS and da Silva, A}, title = {Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing.}, journal = {Parasites &amp; vectors}, volume = {13}, number = {1}, pages = {122}, pmid = {32143704}, issn = {1756-3305}, mesh = {Base Sequence ; Cluster Analysis ; Computational Biology ; Cyclospora/classification/*genetics/*isolation &amp; purification ; Cyclosporiasis/*diagnosis/parasitology ; DNA, Protozoan/genetics ; Feces/parasitology ; Genome, Mitochondrial/*genetics ; Genotyping Techniques/methods ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Molecular Typing/*methods ; Oocysts/genetics ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; }, abstract = {BACKGROUND: Outbreaks of cyclosporiasis, a diarrheal illness caused by Cyclospora cayetanensis, have been a public health issue in the USA since the mid 1990's. In 2018, 2299 domestically acquired cases of cyclosporiasis were reported in the USA as a result of multiple large outbreaks linked to different fresh produce commodities. Outbreak investigations are hindered by the absence of standardized molecular epidemiological tools for C. cayetanensis. For other apicomplexan coccidian parasites, multicopy organellar DNA such as mitochondrial genomes have been used for detection and molecular typing.<br><br>METHODS: We developed a workflow to obtain complete mitochondrial genome sequences from cilantro samples and clinical samples for typing of C. cayetanensis isolates. The 6.3&#xa0;kb long C. cayetanensis mitochondrial genome was amplified by PCR in four overlapping amplicons from genomic DNA extracted from cilantro, seeded with oocysts, and from stool samples positive for C. cayetanensis by diagnostic methods. DNA sequence libraries of pooled amplicons were prepared and sequenced via next-generation sequencing (NGS). Sequence reads were assembled using a custom bioinformatics pipeline.<br><br>RESULTS: This approach allowed us to sequence complete mitochondrial genomes from the samples studied. Sequence alterations, such as single nucleotide polymorphism (SNP) profiles and insertion and deletions (InDels), in mitochondrial genomes of 24 stool samples from patients with cyclosporiasis diagnosed in 2014, exhibited discriminatory power. The cluster dendrogram that was created based on distance matrices of the complete mitochondrial genome sequences, indicated distinct strain-level diversity among the 2014 C. cayetanensis outbreak isolates analyzed in this study.<br><br>CONCLUSIONS: Our results suggest that genomic analyses of mitochondrial genome sequences may help to link outbreak cases to the source.}, }
@article {pmid32142937, year = {2020}, author = {Mehmood, N and Muqaddas, H and Arshad, M and Ullah, MI and Khan, ZI}, title = {Comprehensive study based on mtDNA signature (nad1) providing insights on Echinococcus granulosus s.s. genotypes from Pakistan and potential role of buffalo-dog cycle.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {81}, number = {}, pages = {104271}, doi = {10.1016/j.meegid.2020.104271}, pmid = {32142937}, issn = {1567-7257}, mesh = {Animals ; Buffaloes/*parasitology ; Cattle ; Cattle Diseases/*parasitology ; DNA, Helminth/genetics ; DNA, Mitochondrial/*genetics ; Echinococcosis/parasitology ; Echinococcus granulosus/*genetics ; Genetic Variation/genetics ; Genotype ; Goat Diseases/parasitology ; Goats/parasitology ; Haplotypes/genetics ; Mitochondria/*genetics ; Pakistan ; Phylogeny ; Sheep/parasitology ; Sheep Diseases/parasitology ; }, abstract = {Pakistan has long been considered neglected endemic region for Echinococcus granulosus. Limited surveillance studies have failed to epidemiologically draw complete picture on geographical presence and etiological agents of cystic echinococcosis. Amidst such lacunae, current study explored main transmission routes of this disease through molecular characterization of hydatid cyst isolates obtained from sheep (n = 35), goats (n = 26), cattle (n = 30) and buffalo (n = 30) from the four provinces of Pakistan. Two strains of E. granulosus sensu stricto, G1/G3, and their haplotypes were observed to be cycling in sympatry in the domestic ungulate populations. G3 genotype had higher prevalence (66.94%) in the hosts compared to G1 genotype (33.06%) which was not surprising, considering the large buffalo population in Pakistan. Haplotypic analysis revealed presence of 9 different haplotypes configured in a double clustered network with two centrally positioned haplotypes referred to as G3 (PKH1) and G1 (PKH6). Population demographics and genetic variability indices suggested expanding parasitic population in multiple host spectrum. Elucidating local transmission patterns of E. granulosus sensu stricto, buffalo-dog cycle emerged as one of the dominant causes of G3 dispersal in contrary to other global studies. Adaptability of G3 to environmental conditions of Pakistan and high affinity for buffaloes emphasize on heterogeneous nature of this strain in contrast to G1. However, more studies involving larger datasets and mitochondrial sequences could confirm this hypothetically formulated inference.}, }
@article {pmid32142472, year = {2020}, author = {Schneider, A}, title = {Evolution of mitochondrial protein import - lessons from trypanosomes.}, journal = {Biological chemistry}, volume = {401}, number = {6-7}, pages = {663-676}, doi = {10.1515/hsz-2019-0444}, pmid = {32142472}, issn = {1437-4315}, mesh = {Mitochondrial Proteins/metabolism ; Protozoan Proteins/*metabolism ; Trypanosoma/*chemistry/metabolism ; }, abstract = {The evolution of mitochondrial protein import and the systems that mediate it marks the boundary between the endosymbiotic ancestor of mitochondria and a true organelle that is under the control of the nucleus. Protein import has been studied in great detail in Saccharomyces cerevisiae. More recently, it has also been extensively investigated in the parasitic protozoan Trypanosoma brucei, making it arguably the second best studied system. A comparative analysis of the protein import complexes of yeast and trypanosomes is provided. Together with data from other systems, this allows to reconstruct the ancestral features of import complexes that were present in the last eukaryotic common ancestor (LECA) and to identify which subunits were added later in evolution. How these data can be translated into plausible scenarios is discussed, providing insights into the evolution of (i) outer membrane protein import receptors, (ii) proteins involved in biogenesis of α-helically anchored outer membrane proteins, and (iii) of the intermembrane space import and assembly system. Finally, it is shown that the unusual presequence-associated import motor of trypanosomes suggests a scenario of how the two ancestral inner membrane protein translocases present in LECA evolved into the single bifunctional one found in extant trypanosomes.}, }
@article {pmid32140958, year = {2020}, author = {Kobayashi, G}, title = {Small-scale population genetic structure of the sand bubbler crab Scopimera ryukyuensis in the Ryukyu Islands, Japan.}, journal = {Molecular biology reports}, volume = {47}, number = {4}, pages = {2619-2626}, pmid = {32140958}, issn = {1573-4978}, mesh = {Animals ; Brachyura/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation/genetics ; Genetics, Population/methods ; Islands ; Japan ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Generally, the gene flow of marine organisms is well maintained, but some local populations of coastal species are genetically differentiated even on a small scale (genetic patchiness). Small-scale isolation can be crucial for understanding genetic diversity within a species. The present study examined the population genetic structure of the sand bubbler crab Scopimera ryukyuensis, which is endemic to the Ryukyu Islands in the northwestern Pacific. A total of 52 haplotypes of mitochondrial cytochrome c oxidase subunit I were recovered from 197 specimens collected from four islands. The haplotype and nucleotide diversities were relatively high in the central Ryukyus (Amami-Oshima and Okinawa Islands) with some exceptions but were low at the southern edge of the geographical distribution of the species, i.e., the southern Ryukyus (Ishigaki and Iriomote Islands). Pairwise FST analysis suggested that the gene flow of S. ryukyuensis was largely restricted. The local populations of the species are differentiated among islands, except for stations on Ishigaki Island and a station on Iriomote Island. Moreover, a clear intra-island population genetic structure was observed within Amami-Oshima and Iriomote Islands, e.g., only 20 km between stations. Small-scale isolation among local populations may be a common tendency for coastal species in the Ryukyu Islands, considering the results of previous studies on corals.}, }
@article {pmid32133457, year = {2019}, author = {Mehta, AR and Walters, R and Waldron, FM and Pal, S and Selvaraj, BT and Macleod, MR and Hardingham, GE and Chandran, S and Gregory, JM}, title = {Targeting mitochondrial dysfunction in amyotrophic lateral sclerosis: a systematic review and meta-analysis.}, journal = {Brain communications}, volume = {1}, number = {1}, pages = {fcz009}, pmid = {32133457}, issn = {2632-1297}, support = {MEHTA/JUL17/948-795/MNDA_/Motor Neurone Disease Association/United Kingdom ; MR/L023784/1/MRC_/Medical Research Council/United Kingdom ; MR/L023784/2/MRC_/Medical Research Council/United Kingdom ; MR/R001162/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Interventions targeting mitochondrial dysfunction have the potential to extend survival in preclinical models of amyotrophic lateral sclerosis. The aim of this systematic review was to assess the efficacy of targeting mitochondria as a potential therapeutic target in amyotrophic lateral sclerosis. Preclinical studies written in the English language were identified with no restrictions on publication date from PubMed, Medline and EMBASE databases. All studies adopting interventions targeting mitochondria to treat amyotrophic lateral sclerosis in genetic or drug-induced organism models were considered for inclusion. A total of 76 studies were included in the analysis. Survival data were extracted, and the meta-analysis was completed in RevMan 5 software. We show that targeting mitochondrial dysfunction in amyotrophic lateral sclerosis results in a statistically significant improvement in survival (Z = 5.31; P<0.00001). The timing of administration of the intervention appears to affect the improvement in survival, with the greatest benefit occurring for interventions given prior to disease onset. Interventions at other time points were not significant, although this is likely to be secondary to a lack of publications examining these timepoints. The quality score had no impact on efficacy, and publication bias revealed an overestimation of the effect size, owing to one outlier study; excluding this led to the recalculated effect size changing from 5.31 to 3.31 (P<0.00001). The extant preclinical literature indicates that targeting mitochondrial dysfunction may prolong survival in amyotrophic lateral sclerosis, particularly if the intervention is administered early. A limitation of current research is a significant bias towards models based on superoxide dismutase 1, with uncertainty about generalisability to amyotrophic lateral sclerosis with an underlying TAR DNA binding protein 43 proteinopathy. However, further mechanistic research is clearly warranted in this field.}, }
@article {pmid32130873, year = {2020}, author = {Hornak, I and Rieger, H}, title = {Stochastic Model of T Cell Repolarization during Target Elimination I.}, journal = {Biophysical journal}, volume = {118}, number = {7}, pages = {1733-1748}, pmid = {32130873}, issn = {1542-0086}, mesh = {Cytoskeleton/metabolism ; *Dyneins/metabolism ; Humans ; Immunological Synapses/metabolism ; *Microtubule-Organizing Center/metabolism ; Microtubules/metabolism ; T-Lymphocytes ; }, abstract = {Cytotoxic T lymphocytes (T) and natural killer cells are the main cytotoxic killer cells of the human body to eliminate pathogen-infected or tumorigenic cells (i.e., target cells). Once a natural killer or T cell has identified a target cell, they form a tight contact zone, the immunological synapse (IS). One then observes a repolarization of the cell involving the rotation of the microtubule (MT) cytoskeleton and a movement of the MT organizing center (MTOC) to a position that is just underneath the plasma membrane at the center of the IS. Concomitantly, a massive relocation of organelles attached to MTs is observed, including the Golgi apparatus, lytic granules, and mitochondria. Because the mechanism of this relocation is still elusive, we devise a theoretical model for the molecular-motor-driven motion of the MT cytoskeleton confined between plasma membrane and nucleus during T cell polarization. We analyze different scenarios currently discussed in the literature, the cortical sliding and capture-shrinkage mechanisms, and compare quantitative predictions about the spatiotemporal evolution of MTOC position and MT cytoskeleton morphology with experimental observations. The model predicts the experimentally observed biphasic nature of the repositioning due to an interplay between MT cytoskeleton geometry and motor forces and confirms the dominance of the capture-shrinkage over the cortical sliding mechanism when the MTOC and IS are initially diametrically opposed. We also find that the two mechanisms act synergistically, thereby reducing the resources necessary for repositioning. Moreover, it turns out that the localization of dyneins in the peripheral supramolecular activation cluster facilitates their interaction with the MTs. Our model also opens a way to infer details of the dynein distribution from the experimentally observed features of the MT cytoskeleton dynamics. In a subsequent publication, we will address the issue of general initial configurations and situations in which the T cell established two ISs.}, }
@article {pmid32122349, year = {2020}, author = {Gray, MW and Burger, G and Derelle, R and Klimeš, V and Leger, MM and Sarrasin, M and Vlček, &#x10c; and Roger, AJ and Eliáš, M and Lang, BF}, title = {The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome.}, journal = {BMC biology}, volume = {18}, number = {1}, pages = {22}, pmid = {32122349}, issn = {1741-7007}, support = {MOP-4124//CIHR/Canada ; MOP-11212//CIHR/Canada ; }, mesh = {Cell Nucleus/genetics ; Eukaryota/*genetics ; *Genome, Mitochondrial ; Mitochondrial Proteins/*genetics/metabolism ; *Proteome ; }, abstract = {BACKGROUND: Comparative analyses have indicated that the mitochondrion of the last eukaryotic common ancestor likely possessed all the key core structures and functions that are widely conserved throughout the domain Eucarya. To date, such studies have largely focused on animals, fungi, and land plants (primarily multicellular eukaryotes); relatively few mitochondrial proteomes from protists (primarily unicellular eukaryotic microbes) have been examined. To gauge the full extent of mitochondrial structural and functional complexity and to identify potential evolutionary trends in mitochondrial proteomes, more comprehensive explorations of phylogenetically diverse mitochondrial proteomes are required. In this regard, a key group is the jakobids, a clade of protists belonging to the eukaryotic supergroup Discoba, distinguished by having the most gene-rich and most bacteria-like mitochondrial genomes discovered to date.<br><br>RESULTS: In this study, we assembled the draft nuclear genome sequence for the jakobid Andalucia godoyi and used a comprehensive in silico approach to infer the nucleus-encoded portion of the mitochondrial proteome of this protist, identifying 864 candidate mitochondrial proteins. The A. godoyi mitochondrial proteome has a complexity that parallels that of other eukaryotes, while exhibiting an unusually large number of ancestral features that have been lost particularly in opisthokont (animal and fungal) mitochondria. Notably, we find no evidence that the A. godoyi nuclear genome has or had a gene encoding a single-subunit, T3/T7 bacteriophage-like RNA polymerase, which functions as the mitochondrial transcriptase in all eukaryotes except the jakobids.<br><br>CONCLUSIONS: As genome and mitochondrial proteome data have become more widely available, a strikingly punctuate phylogenetic distribution of different mitochondrial components has been revealed, emphasizing that the pathways of mitochondrial proteome evolution are likely complex and lineage-specific. Unraveling this complexity will require comprehensive comparative analyses of mitochondrial proteomes from a phylogenetically broad range of eukaryotes, especially protists. The systematic in silico approach described here offers a valuable adjunct to direct proteomic analysis (e.g., via mass spectrometry), particularly in cases where the latter approach is constrained by sample limitation or other practical considerations.}, }
@article {pmid32121321, year = {2020}, author = {Duran, DP and Laroche, RA and Gough, HM and Gwiazdowski, RA and Knisley, CB and Herrmann, DP and Roman, SJ and Egan, SP}, title = {Geographic Life History Differences Predict Genomic Divergence Better than Mitochondrial Barcodes or Phenotype.}, journal = {Genes}, volume = {11}, number = {3}, pages = {}, pmid = {32121321}, issn = {2073-4425}, mesh = {Animals ; Classification/*methods ; Coleoptera/classification/*genetics ; DNA, Mitochondrial/classification/*genetics ; Genetic Variation ; Genome, Insect/genetics ; Haplotypes/genetics ; Life History Traits ; Mitochondria/genetics ; Phenotype ; *Phylogeography ; Polymorphism, Single Nucleotide/genetics ; Species Specificity ; }, abstract = {Species diversity can be inferred using multiple data types, however, results based on genetic data can be at odds with patterns of phenotypic variation. Tiger beetles of the Cicindelidiapolitula (LeConte, 1875) species complex have been taxonomically problematic due to extreme phenotypic variation within and between populations. To better understand the biology and taxonomy of this group, we used mtDNA genealogies and multilocus nuclear analyses of 34,921 SNPs to elucidate its evolutionary history and evaluate the validity of phenotypically circumscribed species and subspecies. Genetic analyses recovered two divergent species that are also ecologically distinct, based on adult life history. These patterns are incongruous with the phenotypic variation that informed prior taxonomy, and most subspecies were not supported as distinct evolutionary lineages. One of the nominal subspecies was found to be a cryptic species; consequently, we elevate C. p.laetipennis (Horn, 1913) to a full species. Although nuclear and mtDNA datasets recovered broadly similar evolutionary units, mito-nuclear discordance was more common than expected, being observed between nearly all geographically overlapping taxonomic pairs. Additionally, a pattern of 'mitochondrial displacement' was observed, where mitochondria from one species unidirectionally displace others. Overall, we found that geographically associated life history factors better predict genomic divergence than phenotype and mitochondrial genealogies, and consequently taxon identifications based on mtDNA (e.g., DNA barcodes) may be misleading.}, }
@article {pmid32117399, year = {2020}, author = {Lee, DW and Lee, S and Min, CK and Park, C and Kim, JM and Hwang, CS and Park, SK and Cho, NH and Hwang, I}, title = {Cross-Species Functional Conservation and Possible Origin of the N-Terminal Specificity Domain of Mitochondrial Presequences.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {64}, pmid = {32117399}, issn = {1664-462X}, abstract = {Plants have two endosymbiotic organelles, chloroplast and mitochondrion. Although they have their own genomes, proteome assembly in these organelles depends on the import of proteins encoded by the nuclear genome. Previously, we elucidated the general design principles of chloroplast and mitochondrial targeting signals, transit peptide, and presequence, respectively, which are highly diverse in primary structure. Both targeting signals are composed of N-terminal specificity domain and C-terminal translocation domain. Especially, the N-terminal specificity domain of mitochondrial presequences contains multiple arginine residues and hydrophobic sequence motif. In this study we investigated whether the design principles of plant mitochondrial presequences can be applied to those in other eukaryotic species. We provide evidence that both presequences and import mechanisms are remarkably conserved throughout the species. In addition, we present evidence that the N-terminal specificity domain of presequence might have evolved from the bacterial TAT (twin-arginine translocation) signal sequence.}, }
@article {pmid32114398, year = {2020}, author = {Chernyshev, AV and Neznanova, SY and Yurchenko, OV}, title = {Spermatozoa ultrastructure of two basal pilidiophoran nemerteans, Hubrechtella juliae and Sonnenemertes cantelli (Nemertea, Pilidiophora).}, journal = {Micron (Oxford, England : 1993)}, volume = {133}, number = {}, pages = {102853}, doi = {10.1016/j.micron.2020.102853}, pmid = {32114398}, issn = {1878-4291}, mesh = {Acrosome/ultrastructure ; Animals ; Invertebrates/*anatomy &amp; histology/classification ; Male ; Microscopy, Electron, Scanning ; Phylogeny ; Spermatozoa/*ultrastructure ; }, abstract = {Nemertea is a phylum of worms with a simple internal morphology; nemerteans' spermatozoon morphology can be used for their classification and phylogenetic analyses. The aim of the present study was to describe spermatozoa of the nemerteans Hubrechtella juliae and Sonnenemertes cantelli from the basal groups of the class Pilidiophora at the ultrastructure level. Both species have primitive ('compact-head' sensu Stricker and Folsom, 1998) spermatozoa with ovoid head and five mitochondria in the midpiece, but differ in the structure of acrosomal complex: in Hubrechtella juliae, the single lens-shaped acrosomal vesicle contains an area of moderate electron density not enclosed by a separate membrane; in Sonnenemertes cantelli, the acrosome shows a unique morphology and contains a few electron-dense vesicles with irregular shapes and positions and one more electron-lucent elongated vesicle. Such a pattern of the acrosomal complex organization is described for Nemertea for the first time. An assumption is made that the states "two or more mitochondria" and "posterior acrosomal ring component" may be synapomorphies of Hubrechtiiformes+Heteronemertea (class Pilidiophora), whereas "the posterior margin of the acrosomes forms an acrosomal ring component" is presumably an autapomorphy of the family Lineidae s.l. The results suggest that spermatozoa provide a useful source of characters for nemertean systematics.}, }
@article {pmid32112190, year = {2020}, author = {Lang, SA and McIlroy, P and Shain, DH}, title = {Structural Evolution of the Glacier Ice Worm Fo ATP Synthase Complex.}, journal = {The protein journal}, volume = {39}, number = {2}, pages = {152-159}, pmid = {32112190}, issn = {1875-8355}, support = {ARRA NIH R15GM093685/NH/NIH HHS/United States ; }, mesh = {ATP Synthetase Complexes/*chemistry/genetics ; Adaptation, Biological ; Animals ; Cold Temperature ; Energy Metabolism ; *Evolution, Molecular ; Oligochaeta/*enzymology/genetics ; Protein Domains ; }, abstract = {The segmented annelid worm, Mesenchytraeus solifugus, is a permanent resident of temperate, maritime glaciers in the Pacific northwestern region of North America, displaying atypically high intracellular ATP levels which have been linked to its unusual ability to thrive in hydrated glacier ice. We have shown previously that ice worms contain a highly basic, carboxy terminal extension on their ATP6 regulatory subunit, likely acquired by horizontal gene transfer from a microbial dietary source. Here we examine the full complement of F1F0 ATP synthase structural subunits with attention to non-conservative, ice worm-specific structural modifications. Our genomics analyses and molecular models identify putative proton shuttling domains on either side of the F0 hemichannel, which predictably function to enhance proton flow across the mitochondrial membrane. Other components of the ice worm ATP synthase complex have remained largely unchanged in the context of Metazoan evolution.}, }
@article {pmid32109602, year = {2020}, author = {Muthye, V and Lavrov, DV}, title = {Causes and consequences of mitochondrial proteome size variation in animals.}, journal = {Mitochondrion}, volume = {52}, number = {}, pages = {100-107}, doi = {10.1016/j.mito.2020.02.007}, pmid = {32109602}, issn = {1872-8278}, mesh = {Acanthamoeba castellanii/metabolism ; Animals ; Caenorhabditis elegans/metabolism ; Drosophila melanogaster/metabolism ; Evolution, Molecular ; Genome Size ; Humans ; Mice ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Proteomics/*methods ; Saccharomyces cerevisiae/metabolism ; }, abstract = {Despite a conserved set of core mitochondrial functions, animal mitochondrial proteomes show a large variation in size. We analyzed putative mechanisms behind and functional significance of this variation by performing comparative analysis of the experimentally-verified mitochondrial proteomes of four bilaterian animals (human, mouse, Caenorhabditis elegans, and Drosophila melanogaster) and two non-animal outgroups (Acanthamoeba castellanii and Saccharomyces cerevisiae). We found that of several factors affecting mitochondrial proteome size, evolution of novel mitochondrial proteins in mammals and loss of ancestral proteins in protostomes were the main contributors. Interestingly, the gain and loss of the N-terminal mitochondrial targeting signal was not a major factor in the proteome size evolution.}, }
@article {pmid32109559, year = {2020}, author = {Derouiche, L and Irzagh, A and Rahmouni, R and Tahri, R and Hadjeloum, M and Bouhadad, R and Fernandes, C}, title = {Deep mitochondrial DNA phylogeographic divergence in the threatened aoudad Ammotragus lervia (Bovidae, Caprini).}, journal = {Gene}, volume = {739}, number = {}, pages = {144510}, doi = {10.1016/j.gene.2020.144510}, pmid = {32109559}, issn = {1879-0038}, mesh = {Africa, Northern ; Animals ; Biological Evolution ; Classification ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Endangered Species ; Mitochondria/genetics ; Phylogeography ; Ruminants/classification/*genetics ; }, abstract = {The aoudad or Barbary sheep (Ammotragus lervia) is a threatened ungulate emblematic of North Africa, whose population structure and subspecific taxonomy have not been examined genetically. This knowledge is essential and urgently needed to inform ongoing conservation and management efforts. We analysed the mitochondrial cytochrome b gene and four nuclear genes (casein kappa, spectrin beta nonerythrocytic 1, thyroglobulin, thyrotropin subunit beta) for the first phylogeographic survey of the aoudad, and uncovered a deep Mediterranean-Saharan mitochondrial split separating two highly distinct evolutionary lineages. Their level of divergence is greater than or comparable to those observed between several pairs of congeneric species of different caprine genera. The split was estimated to have occurred in the Early Pleistocene, about 1.3 million years ago. None of the four nuclear genes surveyed, chosen because they have been used in phylogeographic and species-level phylogenetic studies of bovids, allowed us to detect, likely due to their slow evolutionary rate, the substantial and geographically coherent subdivision revealed by mitochondrial DNA. This study is evidence and testament to the ability of mitochondrial DNA, probably unrivalled by any other single-locus marker, as an exploratory tool for investigating population genealogy and history and identifying potential evolutionarily significant units for conservation in animals.}, }
@article {pmid32105215, year = {2020}, author = {von Känel, C and Muñoz-Gómez, SA and Oeljeklaus, S and Wenger, C and Warscheid, B and Wideman, JG and Harsman, A and Schneider, A}, title = {Homologue replacement in the import motor of the mitochondrial inner membrane of trypanosomes.}, journal = {eLife}, volume = {9}, number = {}, pages = {}, pmid = {32105215}, issn = {2050-084X}, support = {175563/SNSF_/Swiss National Science Foundation/Switzerland ; NCCR RNA and Disease/SNSF_/Swiss National Science Foundation/Switzerland ; Consolidator grant 648235/ERC_/European Research Council/International ; 403222702/SFB 1381//Deutsche Forschungsgemeinschaft/ ; CIBSS - EXC-2189 - Project ID 390939984//Germany's Excellence Strategy/ ; EXC 294 BIOSS//Excellence Initiative of the German Federal and State Governments/ ; 175563//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; NCCR RNA and Disease//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 648235//ERC Consolidator grant/ ; }, mesh = {Mitochondria/*metabolism ; Mitochondrial Membranes/*metabolism ; Molecular Motor Proteins/classification/*metabolism ; Phylogeny ; Protein Binding ; Protein Transport ; Protozoan Proteins/classification/*metabolism ; Trypanosoma brucei brucei/*metabolism ; }, abstract = {Many mitochondrial proteins contain N-terminal presequences that direct them to the organelle. The main driving force for their translocation across the inner membrane is provided by the presequence translocase-associated motor (PAM) which contains the J-protein Pam18. Here, we show that in the PAM of Trypanosoma brucei the function of Pam18 has been replaced by the non-orthologous euglenozoan-specific J-protein TbPam27. TbPam27 is specifically required for the import of mitochondrial presequence-containing but not for carrier proteins. Similar to yeast Pam18, TbPam27 requires an intact J-domain to function. Surprisingly, T. brucei still contains a bona fide Pam18 orthologue that, while essential for normal growth, is not involved in protein import. Thus, during evolution of kinetoplastids, Pam18 has been replaced by TbPam27. We propose that this replacement is linked to the transition from two ancestral and functionally distinct TIM complexes, found in most eukaryotes, to the single bifunctional TIM complex present in trypanosomes.}, }
@article {pmid32099025, year = {2020}, author = {Bettedi, L and Yan, A and Schuster, E and Alic, N and Foukas, LC}, title = {Increased mitochondrial and lipid metabolism is a conserved effect of Insulin/PI3K pathway downregulation in adipose tissue.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3418}, pmid = {32099025}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/M029093/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R014507/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 093115/Z/10/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {3T3-L1 Cells ; Adipose Tissue/*metabolism ; Animals ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster ; Insulin/genetics/*metabolism ; *Lipid Metabolism ; Mice ; Mitochondria/genetics/*metabolism ; Phosphatidylinositol 3-Kinases/genetics/*metabolism ; }, abstract = {The Insulin/IGF-1 signalling (IIS) pathway plays an essential role in the regulation of glucose and lipid homeostasis. At the same time, a reduction in the IIS pathway activity can extend lifespan and healthspan in various model organisms. Amongst a number of body organs that sense and respond to insulin/IGF-1, the adipose tissue has a central role in both the metabolic and lifespan effects of IIS at the organismal level. Genetic inactivation of IIS components specifically in the adipose tissue has been shown before to improve metabolic profile and extend lifespan in various model organisms. We sought to identify conserved molecular mechanisms that may underlie the beneficial effects of IIS inhibition in the adipose tissue, specifically at the level of phosphoinositide 3-kinase (PI3K), a key IIS effector molecule. To this end, we inactivated PI3K by genetic means in the fly fat body and by pharmacological inhibition in mammalian adipocytes. Gene expression studies revealed changes to metabolism and upregulation of mitochondrial activity in mouse adipocytes and fly fat bodies with downregulated PI3K, which were confirmed by biochemical assays in mammalian adipocytes. These data suggest that PI3K inactivation has a conserved effect of upregulating mitochondrial metabolism in both fly and mammalian adipose tissue, which likely contributes to the health- and life-span extending effect of IIS pathway downregulation.}, }
@article {pmid32097597, year = {2020}, author = {Camus, MF and Moore, J and Reuter, M}, title = {Nutritional geometry of mitochondrial genetic effects on male fertility.}, journal = {Biology letters}, volume = {16}, number = {2}, pages = {20190891}, pmid = {32097597}, issn = {1744-957X}, mesh = {Animals ; Cell Nucleus ; *DNA, Mitochondrial ; Female ; Fertility ; *Genome, Mitochondrial ; Male ; Mitochondria/genetics ; }, abstract = {Organismal fitness is partly determined by how well the nutritional intake matches sex-specific metabolic requirements. Metabolism itself is underpinned by complex genomic interactions involving products from both nuclear and mitochondrial genomes. Products from these two genomes must coordinate how nutrients are extracted, used and recycled, processes vital for fuelling reproduction. Given the complicated nature of metabolism, it is not well understood how the functioning of these two genomes is modulated by nutrients. Here we use nutritional geometry techniques on Drosophila lines that only differ in their mtDNA, with the aim to understand if there is nutrient-dependent mitochondrial genetic variance for male reproduction. We first find genetic variance for diet consumption, indicating that flies are consuming different amounts of food to meet new physiological requirements. We then find an interaction between mtDNA and diet for fitness, suggesting that the mtDNA plays a role in modulating diet-dependent fitness. Our results enhance our basic understanding of nutritional health and our chimeric genomes.}, }
@article {pmid32094163, year = {2020}, author = {Yahalomi, D and Atkinson, SD and Neuhof, M and Chang, ES and Philippe, H and Cartwright, P and Bartholomew, JL and Huchon, D}, title = {A cnidarian parasite of salmon (Myxozoa: Henneguya) lacks a mitochondrial genome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {10}, pages = {5358-5363}, pmid = {32094163}, issn = {1091-6490}, mesh = {Animals ; *Genome, Mitochondrial ; *Host-Parasite Interactions ; Myxozoa/*classification/*genetics ; Phylogeny ; Salmon/*parasitology ; }, abstract = {Although aerobic respiration is a hallmark of eukaryotes, a few unicellular lineages, growing in hypoxic environments, have secondarily lost this ability. In the absence of oxygen, the mitochondria of these organisms have lost all or parts of their genomes and evolved into mitochondria-related organelles (MROs). There has been debate regarding the presence of MROs in animals. Using deep sequencing approaches, we discovered that a member of the Cnidaria, the myxozoan Henneguya salminicola, has no mitochondrial genome, and thus has lost the ability to perform aerobic cellular respiration. This indicates that these core eukaryotic features are not ubiquitous among animals. Our analyses suggest that H. salminicola lost not only its mitochondrial genome but also nearly all nuclear genes involved in transcription and replication of the mitochondrial genome. In contrast, we identified many genes that encode proteins involved in other mitochondrial pathways and determined that genes involved in aerobic respiration or mitochondrial DNA replication were either absent or present only as pseudogenes. As a control, we used the same sequencing and annotation methods to show that a closely related myxozoan, Myxobolus squamalis, has a mitochondrial genome. The molecular results are supported by fluorescence micrographs, which show the presence of mitochondrial DNA in M. squamalis, but not in H. salminicola. Our discovery confirms that adaptation to an anaerobic environment is not unique to single-celled eukaryotes, but has also evolved in a multicellular, parasitic animal. Hence, H. salminicola provides an opportunity for understanding the evolutionary transition from an aerobic to an exclusive anaerobic metabolism.}, }
@article {pmid32093266, year = {2020}, author = {Muellner, J and Schmidt, KH}, title = {Yeast Genome Maintenance by the Multifunctional PIF1 DNA Helicase Family.}, journal = {Genes}, volume = {11}, number = {2}, pages = {}, pmid = {32093266}, issn = {2073-4425}, mesh = {DNA Helicases/*genetics/*metabolism ; DNA Repair ; DNA Replication ; G-Quadruplexes ; Genome, Plant/genetics ; Genomic Instability/*genetics ; Saccharomyces cerevisiae/enzymology/genetics/metabolism ; Saccharomyces cerevisiae Proteins/*genetics/*metabolism ; Schizosaccharomyces pombe Proteins/genetics/metabolism ; }, abstract = {The two PIF1 family helicases in Saccharomyces cerevisiae, Rrm3, and ScPif1, associate with thousands of sites throughout the genome where they perform overlapping and distinct roles in telomere length maintenance, replication through non-histone proteins and G4 structures, lagging strand replication, replication fork convergence, the repair of DNA double-strand break ends, and transposable element mobility. ScPif1 and its fission yeast homolog Pfh1 also localize to mitochondria where they protect mitochondrial genome integrity. In addition to yeast serving as a model system for the rapid functional evaluation of human Pif1 variants, yeast cells lacking Rrm3 have proven useful for elucidating the cellular response to replication fork pausing at endogenous sites. Here, we review the increasingly important cellular functions of the yeast PIF1 helicases in maintaining genome integrity, and highlight recent advances in our understanding of their roles in facilitating fork progression through replisome barriers, their functional interactions with DNA repair, and replication stress response pathways.}, }
@article {pmid32093074, year = {2020}, author = {Zhou, J and Wang, Y and Liang, X and Xie, C and Liu, W and Miao, W and Kang, Z and Zheng, L}, title = {Molecular Characterization of a Novel Ourmia-Like Virus Infecting Phoma matteucciicola.}, journal = {Viruses}, volume = {12}, number = {2}, pages = {}, pmid = {32093074}, issn = {1999-4915}, mesh = {Amino Acid Sequence ; Fungal Viruses/*classification/isolation &amp; purification ; *Genome, Viral ; Nucleic Acid Conformation ; Open Reading Frames ; Phoma/*virology ; Phylogeny ; RNA Viruses/*genetics/isolation &amp; purification ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics ; }, abstract = {Here, we report a novel (+) ssRNA mycovirus, Phoma matteucciicola ourmia-like virus 1 (PmOLV1), isolated from Phoma matteucciicola strain LG915-1. The genome of PmOLV1 was 2603 nucleotides long and contained a single open reading frame (ORF), which could be translated into a product of RNA-dependent RNA polymerase (RdRp) by both standard and mitochondrial genetic codons. Cellular fractionation assay indicated that PmOLV1 RNAs are likely more enriched in mitochondria than in cytoplasm. Phylogenetic analysis indicated that PmOLV1 is a new member of the genus Penoulivirus (recently proposed) within the family Botourmiaviridae.}, }
@article {pmid32084398, year = {2020}, author = {Schäfer, K and Künzler, P and Schneider, K and Klingl, A and Eubel, H and Carrie, C}, title = {The Plant Mitochondrial TAT Pathway Is Essential for Complex III Biogenesis.}, journal = {Current biology : CB}, volume = {30}, number = {5}, pages = {840-853.e5}, doi = {10.1016/j.cub.2020.01.001}, pmid = {32084398}, issn = {1879-0445}, mesh = {Arabidopsis/*physiology ; Arginine/*metabolism ; Electron Transport Complex III/*metabolism ; Mitochondria/*metabolism ; *Protein Transport ; *Signal Transduction ; }, abstract = {Twin arginine translocation (TAT) pathways have been extensively studied in bacteria and chloroplasts for their role in membrane translocation of folded proteins. However, an increasing number of organisms have been found to contain mitochondria-located TAT subunits, including plant mitochondria, which contain TAT subunits, though in an unusual arrangement with only TatB and TatC subunits. To date, no confirmed function has been attributed to mitochondrial TAT pathways in any organism. Using a truncation mutant approach, we demonstrate that the plant mitochondrial TatB (MTTATB) is required for complex III biogenesis. More specifically, MTTATB performs at a late stage in complex III biogenesis, conveying the translocation of the C terminus of the Rieske FeS subunit back across the inner membrane. This work confirms that plant mitochondria retained a functional TAT pathway for the Rieske FeS translocation, most likely from the original mitochondrial ancestor. It is hypothesized that the original mitochondria contained a bacteria-derived TAT pathway required for at least the Rieske FeS translocation. In several eukaryotic lineages, this mitochondrial TAT pathway was lost and replaced by BCS1. Interestingly, plant mitochondria appear to assemble complex III in the same subunit order as yeast and mammals but in contrast use bacteria-like assembly factors for this process.}, }
@article {pmid32083134, year = {2020}, author = {Li, K and Wu, L and Liu, J and Lin, W and Qi, Q and Zhao, T}, title = {Maternally Inherited Diabetes Mellitus Associated with a Novel m.15897G&gt;A Mutation in Mitochondrial tRNA[Thr] Gene.}, journal = {Journal of diabetes research}, volume = {2020}, number = {}, pages = {2057187}, pmid = {32083134}, issn = {2314-6753}, mesh = {Adult ; Aged ; Asian People/genetics ; Blotting, Northern ; Blotting, Western ; China ; Diabetes Mellitus, Type 2/*genetics/metabolism ; Electron Transport Chain Complex Proteins/metabolism ; Electrophoresis, Polyacrylamide Gel ; Female ; Genome, Mitochondrial ; Humans ; Male ; Maternal Inheritance ; Membrane Potential, Mitochondrial/genetics ; Middle Aged ; Mitochondria/metabolism ; Pedigree ; Phylogeny ; Point Mutation ; RNA, Transfer, Thr/*genetics ; Reactive Oxygen Species/metabolism ; }, abstract = {We report here the clinical, genetic, and molecular characteristics of type 2 diabetes in a Chinese family. There are differences in the severity and age of onset in diabetes among these families. By molecular analysis of the complete mitochondrial genome in this family, we identified the homoplasmic m.15897G>A mutation underwent sequence analysis of whole mitochondrial DNA genome, which localized at conventional position ten of tRNA[Thr], and distinct sets of mtDNA polymorphisms belonging to haplogroup D4b1. This mutation has been implicated to be important for tRNA identity and stability. Using cybrid cell models, the decreased efficiency of mitochondrial tRNA[Thr] levels caused by the m.15897G>A mutation results in respiratory deficiency, protein synthesis and assembly, mitochondrial ATP synthesis, and mitochondrial membrane potential. These mitochondrial dysfunctions caused an increase in the production of reactive oxygen species in the mutant cell lines. These data provide a direct evidence that a novel tRNA mutation was associated with T2DM. Thus, our findings provide a new insight into the understanding of pathophysiology of maternally inherited diabetes.}, }
@article {pmid32080867, year = {2020}, author = {Speijer, D}, title = {Debating Eukaryogenesis-Part 1: Does Eukaryogenesis Presuppose Symbiosis Before Uptake?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {42}, number = {4}, pages = {e1900157}, doi = {10.1002/bies.201900157}, pmid = {32080867}, issn = {1521-1878}, mesh = {Adaptation, Physiological ; Archaea/*metabolism ; Bacteria/*metabolism ; Biological Evolution ; Eukaryota/*metabolism ; Eukaryotic Cells/*metabolism ; Mitochondria/metabolism ; Phagocytosis/physiology ; Phylogeny ; Reactive Oxygen Species/metabolism ; Signal Transduction/physiology ; Symbiosis/*physiology ; }, abstract = {Eukaryotic origins are heavily debated. The author as well as others have proposed that they are inextricably linked with the arrival of a pre-mitochondrion of alphaproteobacterial-like ancestry, in a so-called symbiogenic scenario. The ensuing mutual adaptation of archaeal host and endosymbiont seems to have been a defining influence during the processes leading to the last eukaryotic common ancestor. An unresolved question in this scenario deals with the means by which the bacterium ends up inside. Older hypotheses revolve around the application of known antagonistic interactions, the bacterium being prey or parasite. Here, in reviewing the field, the author argues that such models share flaws, hence making them less likely, and that a "pre-symbiotic stage" would have eased ongoing metabolic integration. Based on this the author will speculate about the nature of the (endo) symbiosis that started eukaryotic evolution-in the context of bacterial entry being a relatively "early" event-and stress the differences between this uptake and subsequent ones. He will also briefly discuss how the mutual adaptation following the merger progressed and how many eukaryotic hallmarks can be understood in light of coadaptation. Also see the video abstract here https://youtu.be/ekqtNleVJpU.}, }
@article {pmid32080176, year = {2020}, author = {Kuhle, B and Chihade, J and Schimmel, P}, title = {Relaxed sequence constraints favor mutational freedom in idiosyncratic metazoan mitochondrial tRNAs.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {969}, pmid = {32080176}, issn = {2041-1723}, support = {R01 GM125908/GM/NIGMS NIH HHS/United States ; R15 GM071392/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; Amino Acyl-tRNA Synthetases/chemistry/genetics/metabolism ; Animals ; Base Sequence ; Cell Nucleus/genetics/metabolism ; Epistasis, Genetic ; Evolution, Molecular ; Mitochondria/*genetics/metabolism ; Models, Genetic ; Models, Molecular ; *Mutation ; Nucleic Acid Conformation ; Protein Conformation ; RNA Stability/genetics ; RNA, Mitochondrial/chemistry/*genetics ; RNA, Transfer/chemistry/*genetics ; Static Electricity ; }, abstract = {Metazoan complexity and life-style depend on the bioenergetic potential of mitochondria. However, higher aerobic activity and genetic drift impose strong mutation pressure and risk of irreversible fitness decline in mitochondrial (mt)DNA-encoded genes. Bilaterian mitochondria-encoded tRNA genes, key players in mitochondrial activity, have accumulated mutations at significantly higher rates than their cytoplasmic counterparts, resulting in foreshortened and fragile structures. Here we show that fragility of mt tRNAs coincided with the evolution of bilaterian animals. We demonstrate that bilaterians compensated for this reduced structural complexity in mt tRNAs by sequence-independent induced-fit adaption to the cognate mitochondrial aminoacyl-tRNA synthetase (aaRS). Structural readout by nuclear-encoded aaRS partners relaxed the sequence constraints on mt tRNAs and facilitated accommodation of functionally disruptive mutational insults by cis-acting epistatic compensations. Our results thus suggest that mutational freedom in mt tRNA genes is an adaptation to increased mutation pressure that was associated with the evolution of animal complexity.}, }
@article {pmid32074218, year = {2020}, author = {Báez, AL and Lo Presti, MS and Bazán, PC and Strauss, M and Velázquez López, DA and Miler, N and Rivarola, HW and Paglini-Oliva, PA}, title = {Analysis of mitochondrial enzymatic activity in blood lymphomonocyte fractions during infection with different Trypanosoma cruzi strains.}, journal = {Revista do Instituto de Medicina Tropical de Sao Paulo}, volume = {62}, number = {}, pages = {e15}, pmid = {32074218}, issn = {1678-9946}, mesh = {Animals ; Chagas Disease/*enzymology/metabolism/physiopathology ; Citrate (si)-Synthase/*metabolism ; Disease Models, Animal ; Disease Progression ; Electron Transport Complex IV/*metabolism ; Male ; Mitochondria/*enzymology/parasitology/pathology ; Parasitemia ; }, abstract = {Proinflammatory and inflammatory mediators induced by Trypanosoma cruzi infection increase the oxidative stress, generating toxicity for cells targeting mitochondria of different tissues. We studied the activity of citrate synthase and complexes I-IV of respiratory chain in mitochondria of blood lymphomonocyte fraction, from albino Swiss mice infected with different isolates of T. cruzi , during Chagas disease evolution. Complexes I-IV were modified in infected groups (p<0.05) in all the stages, and an inflammatory process of different magnitudes was detected in the heart and skeletal muscle according to the isolate. The citrate synthase activity presented modifications in the SGO Z12 and the Tulahuen group (p<0.05). Hearts showed fiber fragmentation and fibrosis; skeletal muscle presented inflammatory infiltrates and in the Tulahuen infected group, there were also amastigote nests. The inflammatory processes produced an oxidative stress that induced different alterations of mitochondrial enzymes activities in the lymphomonocyte fraction that can be detected by a simple blood extraction, suggesting that they could be used as disease markers, especially in the indeterminate phase of Chagas disease.}, }
@article {pmid32065920, year = {2020}, author = {Sunil, B and Rajsheel, P and Aswani, V and Bapatla, RB and Talla, SK and Raghavendra, AS}, title = {Photosynthesis is sensitive to nitric oxide and respiration sensitive to hydrogen peroxide: Studies with pea mesophyll protoplasts.}, journal = {Journal of plant physiology}, volume = {246-247}, number = {}, pages = {153133}, doi = {10.1016/j.jplph.2020.153133}, pmid = {32065920}, issn = {1618-1328}, mesh = {Hydrogen Peroxide/administration &amp; dosage/*metabolism ; Mesophyll Cells/drug effects/physiology ; Nitric Oxide/administration &amp; dosage/*metabolism ; Nitroprusside/administration &amp; dosage/*metabolism ; Pisum sativum/drug effects/*physiology ; *Photosynthesis ; Plant Leaves/drug effects/physiology ; Protoplasts/drug effects/physiology ; Reactive Oxygen Species/administration &amp; dosage/*metabolism ; }, abstract = {Reports on the effect of nitric oxide (NO) or reactive oxygen species (ROS) on photosynthesis and respiration in leaf tissues are intriguing; therefore, the effects of exogenous addition of sodium nitroprusside (SNP, releases NO) or H2O2 on the photosynthetic O2 evolution and respiratory O2 uptake by mesophyll protoplasts in pea (Pisum sativum) were evaluated in the present study. Low concentrations of SNP or H2O2 were used to minimize nonspecific effects. The effects of NO or H2O2 on respiration and photosynthesis were different. The presence of NO decreased the rate of photosynthesis but caused a marginal stimulation of dark respiration. Conversely, externally administered H2O2 drastically decreased the rate of respiration but only slightly decreased photosynthesis. The PS I activity was more sensitive to NO than PS II. On the other hand, 100 μM H2O2 had no effect on the photochemical reactions of either PS I or PS II. The sensitivity of photosynthesis to antimycin A or SHAM (reflecting the interplay between chloroplasts and mitochondria) was not affected by NO. By contrast, H2O2 markedly decreased the sensitivity of photosynthesis to antimycin A and SHAM. It can be concluded that chloroplasts are the primary targets of NO, while mitochondria are the primary targets of ROS in plant cells. We propose that H2O2 can be an important signal to modulate the crosstalk between chloroplasts and mitochondria.}, }
@article {pmid32060025, year = {2020}, author = {Frank, C and Jendrossek, D}, title = {Acidocalcisomes and Polyphosphate Granules Are Different Subcellular Structures in Agrobacterium tumefaciens.}, journal = {Applied and environmental microbiology}, volume = {86}, number = {8}, pages = {}, pmid = {32060025}, issn = {1098-5336}, mesh = {Agrobacterium tumefaciens/*physiology ; Microscopy, Fluorescence ; Organelles/*metabolism ; Polyphosphates/*metabolism ; }, abstract = {Acidocalcisomes are membrane-enclosed, polyphosphate-containing acidic organelles in lower Eukaryota but have also been described for Agrobacterium tumefaciens (M. Seufferheld, M. Vieira, A. Ruiz, C. O. Rodrigues, S. Moreno, and R. Docampo, J Biol Chem 278:29971-29978, 2003, https://doi.org/10.1074/jbc.M304548200). This study aimed at the characterization of polyphosphate-containing acidocalcisomes in this alphaproteobacterium. Unexpectedly, fluorescence microscopic investigation of A. tumefaciens cells using fluorescent dyes and localization of constructed fusions of polyphosphate kinases (PPKs) and of vacuolar H[+]-translocating pyrophosphatase (HppA) with enhanced yellow fluorescent protein (eYFP) suggested that acidocalcisomes and polyphosphate are different subcellular structures. Acidocalcisomes and polyphosphate granules were frequently located close together, near the cell poles. However, they never shared the same position. Mutant strains of A. tumefaciens with deletions of both ppk genes (Δppk1 Δppk2) were unable to form polyphosphate but still showed cell pole-located eYFP-HppA foci and could be stained with MitoTracker. In conclusion, A. tumefaciens forms polyP granules that are free of a surrounding membrane and thus resemble polyP granules of Ralstonia eutropha and other bacteria. The composition, contents, and function of the subcellular structures that are stainable with MitoTracker and harbor eYFP-HppA remain unclear.IMPORTANCE The uptake of alphaproteobacterium-like cells by ancestors of eukaryotic cells and subsequent conversion of these alphaproteobacterium-like cells to mitochondria are thought to be key steps in the evolution of the first eukaryotic cells. The identification of acidocalcisomes in two alphaproteobacterial species some years ago and the presence of homologs of the vacuolar proton-translocating pyrophosphatase HppA, a marker protein of the acidocalcisome membrane in eukaryotes, in virtually all species within the alphaproteobacteria suggest that eukaryotic acidocalcisomes might also originate from related structures in ancestors of alphaproteobacterial species. Accordingly, alphaproteobacterial acidocalcisomes and eukaryotic acidocalcisomes should have similar features. Since hardly any information is available on bacterial acidocalcisomes, this study aimed at the characterization of organelle-like structures in alphaproteobacterial cells, with A. tumefaciens as an example.}, }
@article {pmid32058540, year = {2020}, author = {Prakash, NR and Chhabra, R and Zunjare, RU and Muthusamy, V and Hossain, F}, title = {Molecular characterization of teosinte branched1 gene governing branching architecture in cultivated maize and wild relatives.}, journal = {3 Biotech}, volume = {10}, number = {2}, pages = {77}, pmid = {32058540}, issn = {2190-572X}, abstract = {We sequenced the entire tb1 gene in six maize inbreds and its wild relatives (parviglumis, mexicana, perennis and luxurians) to characterize it at molecular level. Hopscotch and Tourist transposable elements were observed in the upstream of tb1 in all maize inbreds, while they were absent in wild relatives. In maize, tb1 consisted of 431-443 bp 5'UTR, 1101 bp coding sequence and 211-219 bp 3'UTR. In promoter region, mutations in the light response element in mexicana (~ 35 bp and ~ 55 bp upstream of TSS) and perennis (at ~ 35 bp upstream of TSS) were found. A 6 bp insertion at 420 bp downstream of the polyA signal site was present among teosinte accessions, while it was not observed in maize. A codominant marker flanking the 6 bp InDel was developed, and it differentiated the teosintes from maize. In Tb1 protein, alanine (12.7-14.6%) was the most abundant amino acid with tryptophan as the rarest (0.5-0.9%). The molecular weight of Tb1 protein was 38757.15 g/mol except 'Palomero Toluqueno' and HKI1128. R and TCP motifs in Tb1 protein were highly conserved across maize, teosinte and orthologues, while TCP domain differed for tb1 paralogue. Tb1 possessed important role in light-, auxin-, stress-response and meristem identity maintenance. Presence of molecular signal suggested its localization in mitochondria, nucleus and nucleolus. Parviglumis and mexicana shared closer relationship with maize than perennis and luxurians. A highly conserved 59-60 amino acids long bHLH region was observed across genotypes. Information generated here assumes significance in evolution of tb1 gene and breeding for enhancement of prolificacy in maize.}, }
@article {pmid32054873, year = {2020}, author = {Polovina, ES and Parakatselaki, ME and Ladoukakis, ED}, title = {Paternal leakage of mitochondrial DNA and maternal inheritance of heteroplasmy in Drosophila hybrids.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {2599}, pmid = {32054873}, issn = {2045-2322}, mesh = {Animals ; Chimera/*genetics ; Crosses, Genetic ; DNA, Mitochondrial/*genetics ; Drosophila/*genetics ; Female ; Haplotypes ; Inheritance Patterns ; Male ; Maternal Inheritance ; Mitochondria/genetics ; }, abstract = {Mitochondrial DNA (mtDNA) is maternally transmitted in animals and therefore, individuals are expected to have a single mtDNA haplotype (homoplasmy). Yet, heteroplasmic individuals have been observed in a large number of animal species. Heteroplasmy may emerge as a result of somatic mtDNA mutations, paternal leakage during fertilization or be inherited from a heteroplasmic mother. Understanding the causes of heteroplasmy could shed light into the evolution of mtDNA inheritance. In this study we examined heteroplasmy in progeny from heterospecific crosses of Drosophila for two consecutive generations. We studied the generation of heteroplasmy from paternal leakage and the maternal transmission of heteroplasmy. Our data reveal non-random patterns in the emergence and transmission of heteroplasmy and suggest that heteroplasmy depends on the family of origin.}, }
@article {pmid32050506, year = {2020}, author = {Li, Z and Li, X and Song, N and Tang, H and Yin, X}, title = {The Mitochondrial Genome of Amara aulica (Coleoptera, Carabidae, Harpalinae) and Insights into the Phylogeny of Ground Beetles.}, journal = {Genes}, volume = {11}, number = {2}, pages = {}, pmid = {32050506}, issn = {2073-4425}, mesh = {Animals ; Bayes Theorem ; Coleoptera/classification/*genetics ; Genes, rRNA ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Alignment ; }, abstract = {Carabidae are one of the most species-rich families of beetles, comprising more than 40,000 described species worldwide. Forty-three complete or partial mitochondrial genomes (mitogenomes) from this family have been published in GenBank to date. In this study, we sequenced a nearly complete mitogenome of Amara aulica (Carabidae), using a next-generation sequencing method. This mitogenome was 16,646 bp in length, which encoded the typical 13 mitochondrial protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Combining with the published mitogenomes of Carabidae and five outgroup species from Trachypachidae, Gyrinidae and Dytiscidae, we performed phylogenetic estimates under maximum likelihood and Bayesian inference criteria to investigate the phylogenetic relationships of carabid beetles. The results showed that the family Carabidae was a non-monophyletic assemblage. The subfamilies Cicindelinae, Elaphrinae, Carabinae, Trechinae and Harpalinae were recovered as monophyletic groups. Moreover, the clade (Trechinae + (Brachininae + Harpalinae)) was consistently recovered in all analyses.}, }
@article {pmid32049644, year = {2020}, author = {Kornmann, B}, title = {The endoplasmic reticulum-mitochondria encounter structure: coordinating lipid metabolism across membranes.}, journal = {Biological chemistry}, volume = {401}, number = {6-7}, pages = {811-820}, doi = {10.1515/hsz-2020-0102}, pmid = {32049644}, issn = {1437-4315}, support = {214291/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Cell Membrane/chemistry/*metabolism ; Endoplasmic Reticulum/*metabolism ; Lipid Metabolism ; Lipids/*chemistry ; Mitochondria/chemistry/*metabolism ; }, abstract = {Endosymbiosis, the beginning of a collaboration between an archaeon and a bacterium and a founding step in the evolution of eukaryotes, owes its success to the establishment of communication routes between the host and the symbiont to allow the exchange of metabolites. As far as lipids are concerned, it is the host that has learnt the symbiont's language, as eukaryote lipids appear to have been borrowed from the bacterial symbiont. Mitochondria exchange lipids with the rest of the cell at membrane contact sites. In fungi, the endoplasmic reticulum-mitochondria encounter structure (ERMES) is one of the best understood membrane tethering complexes. Its discovery has yielded crucial insight into the mechanisms of intracellular lipid trafficking. Despite a wealth of data, our understanding of ERMES formation and its exact role(s) remains incomplete. Here, I endeavour to summarise our knowledge on the ERMES complex and to identify lingering gaps.}, }
@article {pmid32045715, year = {2020}, author = {Zhang, J and Kan, X and Miao, G and Hu, S and Sun, Q and Tian, W}, title = {qMGR: A new approach for quantifying mitochondrial genome rearrangement.}, journal = {Mitochondrion}, volume = {52}, number = {}, pages = {20-23}, doi = {10.1016/j.mito.2020.02.004}, pmid = {32045715}, issn = {1872-8278}, mesh = {Animals ; Computational Biology/*methods ; *Gene Rearrangement ; Genome, Mitochondrial ; Mitochondria/*genetics ; Software ; }, abstract = {Rearrangement is one of the most studied features in the animal mitochondrial genomes. The progress in high-throughput sequencing and comparative genomics has brought opportunities for systematic studies of mitochondrial genome rearrangements. However, there are few reports on globally examining mitogenome rearrangement and distinguishing the rearrangement frequency of each gene, which could contribute to a better understanding of its models and evolution. We presented qMGR, a new approach for large-scale quantifying mitogenome rearrangements considering a single gene as a structural unit. Compared to a reference arrangement, qMGR accumulates the changes of two nearest neighbor genes to calculate rearrangement score (RS) and rearrangement frequency (RF) of each single gene in the mitogenomes of a given taxonomic group. By accumulating RS of all genes in one genome, qMGR was developed to calculate each mitogenome rearrangement score, which can be used as a quantitative feature of the mitogenome rearrangement. Based on the frequency of rearrangement of each gene, qMGR can further detect the conserved gene set and high frequency rearrangement segments within the taxon. They may facilitate the assessment of rearrangement distances and understanding rearrangement mechanisms. qMGR web service is freely available at http://qmgr.hnnu.edu.cn/. The source code is available under GNU GPL at https://github.com/zhanglab2019/qMGR.}, }
@article {pmid32041806, year = {2020}, author = {Boël, M and Romestaing, C and Duchamp, C and Veyrunes, F and Renaud, S and Roussel, D and Voituron, Y}, title = {Improved mitochondrial coupling as a response to high mass-specific metabolic rate in extremely small mammals.}, journal = {The Journal of experimental biology}, volume = {223}, number = {Pt 5}, pages = {}, doi = {10.1242/jeb.215558}, pmid = {32041806}, issn = {1477-9145}, mesh = {Animals ; Basal Metabolism ; *Body Weight ; Liver/metabolism ; Male ; Mice/*metabolism ; Mitochondria, Muscle/*metabolism ; Muscle, Skeletal/metabolism ; }, abstract = {Mass-specific metabolic rate negatively co-varies with body mass from the whole-animal to the mitochondrial levels. Mitochondria are the mainly consumers of oxygen inspired by mammals to generate ATP or compensate for energetic losses dissipated as the form of heat (proton leak) during oxidative phosphorylation. Consequently, ATP synthesis and proton leak compete for the same electrochemical gradient. Because proton leak co-varies negatively with body mass, it is unknown whether extremely small mammals further decouple their mitochondria to maintain their body temperature or whether they implement metabolic innovations to ensure cellular homeostasis. The present study investigated the impact of body mass variation on cellular and mitochondrial functioning in small mammals, comparing two extremely small African pygmy mice (Mus mattheyi, ∼5 g, and Mus minutoides, ∼7 g) with the larger house mouse (Mus musculus, ∼22 g). Oxygen consumption rates were measured from the animal to the mitochondrial levels. We also measured mitochondrial ATP synthesis in order to appreciate the mitochondrial efficiency (ATP/O). At the whole-animal scale, mass- and surface-specific metabolic rates co-varied negatively with body mass, whereas this was not necessarily the case at the cellular and mitochondrial levels. Mus mattheyi had generally the lowest cellular and mitochondrial fluxes, depending on the tissue considered (liver or skeletal muscle), as well as having more-efficient muscle mitochondria than the other two species. Mus mattheyi presents metabolic innovations to ensure its homeostasis, by generating more ATP per oxygen consumed.}, }
@article {pmid32041545, year = {2020}, author = {Bhowal, B and Singla-Pareek, SL and Sopory, SK and Kaur, C}, title = {From methylglyoxal to pyruvate: a genome-wide study for the identification of glyoxalases and D-lactate dehydrogenases in Sorghum bicolor.}, journal = {BMC genomics}, volume = {21}, number = {1}, pages = {145}, pmid = {32041545}, issn = {1471-2164}, support = {IFA-14/LSPA-24//Department of Science and Technology, Ministry of Science and Technology/ ; }, mesh = {Genome-Wide Association Study ; Lactate Dehydrogenases/classification/*genetics ; Lactoylglutathione Lyase/classification/*genetics ; Phylogeny ; Plant Proteins/classification/*genetics ; Pyruvaldehyde/*metabolism ; Pyruvic Acid/*metabolism ; Sorghum/*enzymology/genetics ; Stress, Physiological/genetics ; Thiolester Hydrolases/classification/*genetics ; }, abstract = {BACKGROUND: The glyoxalase pathway is evolutionarily conserved and involved in the glutathione-dependent detoxification of methylglyoxal (MG), a cytotoxic by-product of glycolysis. It acts via two metallo-enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII), to convert MG into D-lactate, which is further metabolized to pyruvate by D-lactate dehydrogenases (D-LDH). Since D-lactate formation occurs solely by the action of glyoxalase enzymes, its metabolism may be considered as the ultimate step of MG detoxification. By maintaining steady state levels of MG and other reactive dicarbonyl compounds, the glyoxalase pathway serves as an important line of defence against glycation and oxidative stress in living organisms. Therefore, considering the general role of glyoxalases in stress adaptation and the ability of Sorghum bicolor to withstand prolonged drought, the sorghum glyoxalase pathway warrants an in-depth investigation with regard to the presence, regulation and distribution of glyoxalase and D-LDH genes.<br><br>RESULT: Through this study, we have identified 15 GLYI and 6 GLYII genes in sorghum. In addition, 4 D-LDH genes were also identified, forming the first ever report on genome-wide identification of any plant D-LDH family. Our in silico analysis indicates homology of putatively active SbGLYI, SbGLYII and SbDLDH proteins to several functionally characterised glyoxalases and D-LDHs from Arabidopsis and rice. Further, these three gene families exhibit development and tissue-specific variations in their expression patterns. Importantly, we could predict the distribution of putatively active SbGLYI, SbGLYII and SbDLDH proteins in at least four different sub-cellular compartments namely, cytoplasm, chloroplast, nucleus and mitochondria. Most of the members of the sorghum glyoxalase and D-LDH gene families are indeed found to be highly stress responsive.<br><br>CONCLUSION: This study emphasizes the role of glyoxalases as well as that of D-LDH in the complete detoxification of MG in sorghum. In particular, we propose that D-LDH which metabolizes the specific end product of glyoxalases pathway is essential for complete MG detoxification. By proposing a cellular model for detoxification of MG via glyoxalase pathway in sorghum, we suggest that different sub-cellular organelles are actively involved in MG metabolism in plants.}, }
@article {pmid32039475, year = {2020}, author = {Donin, LM and Ferrer, J and Carvalho, TP}, title = {Taxonomical study of Trichomycterus (Siluriformes: Trichomycteridae) from the Ribeira de Iguape River basin reveals a new species recorded in the early 20th century.}, journal = {Journal of fish biology}, volume = {96}, number = {4}, pages = {886-904}, doi = {10.1111/jfb.14278}, pmid = {32039475}, issn = {1095-8649}, support = {//CNPq/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Animals ; Brazil ; Catfishes/anatomy &amp; histology/*classification/genetics ; Mitochondria/genetics ; *Phylogeny ; Rivers ; Species Specificity ; }, abstract = {A new species of Trichomycterus endemic to the Ribeira de Iguape River basin, southeastern Brazil, was studied based on morphological and molecular evidence. This species had an outer layer of coloration composed of scattered, round, black or dark-brown spots smaller or equivalent in size to the circumference of the eye; eight pectoral-fin rays; 28-29 opercular odontodes; 54-56 interopercular odontodes; and supraorbital line of the laterosensory system not interrupted, with pores s2 absent. Two other species of Trichomycterus from the Ribeira de Iguape River basin are recorded, and their taxonomic status is discussed: Trichomycterus alternatus and Trichomycterus jacupiranga were not differentiated using molecular analysis but may be consistently distinguished based on morphology. The phylogenetic relationships of the co-occurring species, T. alternatus and Cambeva zonata, were inferred using mitochondrial data, reinforcing the taxonomic status of these recently revised species that have a complex taxonomy. In addition, a new combination for Trichomycterus taroba with its inclusion in the genus Cambeva is recommended.}, }
@article {pmid32039050, year = {2019}, author = {Amanzougaghene, N and Fenollar, F and Raoult, D and Mediannikov, O}, title = {Where Are We With Human Lice? A Review of the Current State of Knowledge.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {474}, pmid = {32039050}, issn = {2235-2988}, mesh = {Animals ; Bacteria/classification ; Communicable Disease Control ; Evolution, Molecular ; Genome ; Humans ; Insect Vectors/microbiology ; Insecticide Resistance ; Insecticides ; Lice Infestations/*epidemiology/microbiology/*parasitology/therapy ; Mitochondria ; Pediculus/*classification/drug effects/*genetics ; Phylogeny ; Phylogeography ; }, abstract = {Pediculus humanus is an obligate bloodsucking ectoparasite of human that includes two ecotypes, head louse and body louse, which differ slightly in morphology and biology, but have distinct ecologies. Phylogenetically, they are classified on six mitochondrial clades (A, B, C, D, E, and F), head louse encompasses the full genetic diversity of clades, while body louse belongs to clades A and D. Recent studies suggested that not only body louse, but also head louse can transmit disease, which warrants greater attention as a serious public health problem. The recent sequencing of body louse genome confirmed that P. humanus has the smallest genome of any hemimetabolous insect reported to date, and also revealed numerous interesting characteristics in the nuclear and mitochondrial genomes. The transcriptome analyses showed that body and head lice were almost genetically identical. Indeed, the phenotypic flexibility associated with the emergence of body lice, is probably a result of regulatory changes, perhaps epigenetic in origin, triggered by environmental signals. Current lice control strategies have proven unsuccessful. For instance, ivermectin represents a relatively new and very promising pediculicide. However, ivermectin resistance in the field has begun to be reported. Therefore, novel opportunities for pest control strategies are needed. Our objective here is to review the current state of knowledge on the biology, epidemiology, phylogeny, disease-vector and control of this fascinating and very intimate human parasite.}, }
@article {pmid32029782, year = {2020}, author = {Choi, JW and Graf, L and Peters, AF and Cock, JM and Nishitsuji, K and Arimoto, A and Shoguchi, E and Nagasato, C and Choi, CG and Yoon, HS}, title = {Organelle inheritance and genome architecture variation in isogamous brown algae.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {2048}, pmid = {32029782}, issn = {2045-2322}, mesh = {DNA, Mitochondrial/genetics ; Evolution, Molecular ; Gene Rearrangement ; *Genome, Mitochondrial ; *Genome, Plastid ; Genomics ; *Inheritance Patterns ; Phaeophyceae/*genetics ; Plastids/genetics ; Sequence Analysis, DNA ; }, abstract = {Among the brown algal lineages, Ectocarpales species have isogamous fertilization in which male and female gametes are morphologically similar. In contrast, female gametes are much larger than male gametes in the oogamous species found in many other brown algal lineages. It has been reported that the plastids of isogamous species are biparentally inherited whereas the plastids of oogamous species are maternally inherited. In contrast, in both isogamous and oogamous species, the mitochondria are usually inherited maternally. To investigate whether there is any relationship between the modes of inheritance and organellar genome architecture, we sequenced six plastid genomes (ptDNA) and two mitochondrial genomes (mtDNA) of isogamous species from the Ectocarpales and compared them with previously sequenced organellar genomes. We found that the biparentally inherited ptDNAs of isogamous species presented distinctive structural rearrangements whereas maternally inherited ptDNAs of oogamous species showed no rearrangements. Our analysis permits the hypothesis that structural rearrangements in ptDNAs may be a consequence of the mode of inheritance.}, }
@article {pmid32028035, year = {2020}, author = {Pyron, RA and O'Connell, KA and Lemmon, EM and Lemmon, AR and Beamer, DA}, title = {Phylogenomic data reveal reticulation and incongruence among mitochondrial candidate species in Dusky Salamanders (Desmognathus).}, journal = {Molecular phylogenetics and evolution}, volume = {146}, number = {}, pages = {106751}, doi = {10.1016/j.ympev.2020.106751}, pmid = {32028035}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; Genes, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; Urodela/*classification/genetics ; }, abstract = {Gene flow between evolutionarily distinct lineages is increasingly recognized as a common occurrence. Such processes distort our ability to diagnose and delimit species, as well as confound attempts to estimate phylogenetic relationships. A conspicuous example is Dusky Salamanders (Desmognathus), a common model-system for ecology, evolution, and behavior. Only 22 species are described, 7 in the last 40 years. However, mitochondrial datasets indicate the presence of up to 45 "candidate species" and multiple paraphyletic taxa presenting a complex history of reticulation. Some authors have even suggested that the search for species boundaries in the group may be in vain. Here, we analyze nuclear and mitochondrial data containing 161 individuals from at least 49 distinct evolutionary lineages that we treat as candidate species. Concatenated and species-tree methods do not estimate fully resolved relationships among these taxa. Comparing topologies and applying methods for estimating phylogenetic networks, we find strong support for numerous instances of hybridization throughout the history of the group. We suggest that these processes may be more common than previously thought across the phylogeography-phylogenetics continuum, and that while the search for species boundaries in Desmognathus may not be in vain, it will be complicated by factors such as crypsis, parallelism, and gene-flow.}, }
@article {pmid32028027, year = {2020}, author = {Olsson, U and Alström, P}, title = {A comprehensive phylogeny and taxonomic evaluation of the waxbills (Aves: Estrildidae).}, journal = {Molecular phylogenetics and evolution}, volume = {146}, number = {}, pages = {106757}, doi = {10.1016/j.ympev.2020.106757}, pmid = {32028027}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/genetics ; Mitochondria/genetics ; Passeriformes/*classification/genetics ; Phylogeny ; }, abstract = {We present a revised taxonomy of Estrildidae based on the first time-calibrated phylogeny of the family Estrildidae estimated from a data set including the majority of the species, and all genera except the monospecific Paludipasser, using two mitochondrial and five nuclear markers. We find that most differences in current taxonomy reflect alternative opinions among authors regarding inclusiveness of genera, which are usually not in conflict with the phylogeny. The most notable exception is the current circumscriptions of the genera Neochmia, Nesocharis and Taeniopygia, which are incompatible with the phylogeny. Estrildidae is subdivided into six well supported subclades, which we propose be recognized as the subfamilies Amandavinae, Erythrurinae, Estrildinae, Lagonostictinae, Lonchurinae and Poephilinae.}, }
@article {pmid32027368, year = {2020}, author = {Guo, W and Zhu, A and Fan, W and Adams, RP and Mower, JP}, title = {Extensive Shifts from Cis- to Trans-splicing of Gymnosperm Mitochondrial Introns.}, journal = {Molecular biology and evolution}, volume = {37}, number = {6}, pages = {1615-1620}, doi = {10.1093/molbev/msaa029}, pmid = {32027368}, issn = {1537-1719}, mesh = {Cycadopsida/*genetics ; *Genome, Mitochondrial ; Genome, Plant ; *Introns ; Pinales/*genetics ; *Trans-Splicing ; }, abstract = {Hundreds of plant mitogenomes have been sequenced from angiosperms, but relatively few mitogenomes are available from its sister lineage, gymnosperms. To examine mitogenomic diversity among extant gymnosperms, we generated draft mitogenomes from 11 diverse species and compared them with four previously published mitogenomes. Examined mitogenomes from Pinaceae and cycads retained all 41 protein genes and 26 introns present in the common ancestor of seed plants, whereas gnetophyte and cupressophyte mitogenomes experienced extensive gene and intron loss. In Pinaceae and cupressophyte mitogenomes, an unprecedented number of exons are distantly dispersed, requiring trans-splicing of 50-70% of mitochondrial introns to generate mature transcripts. RNAseq data confirm trans-splicing of these dispersed exons in Pinus. The prevalence of trans-splicing in vascular plant lineages with recombinogenic mitogenomes suggests that genomic rearrangement is the primary cause of shifts from cis- to trans-splicing in plant mitochondria.}, }
@article {pmid32025511, year = {2019}, author = {Gao, J and Chau, S and Meneghini, MD}, title = {Viral attenuation by Endonuclease G during yeast gametogenesis: insights into ancestral roles of programmed cell death?.}, journal = {Microbial cell (Graz, Austria)}, volume = {7}, number = {2}, pages = {32-35}, pmid = {32025511}, issn = {2311-2638}, abstract = {Viruses and other genetic parasites are present in virtually all forms of life. This chronic condition has led to diverse host cell adaptations such as CRISPR and RNAi, whose functions attenuate these parasites. It is hypothesized that programmed cell death (PCD) is an additional adaptation whose origins reside in viral defense. A core event of apoptotic PCD is the regulated release of mitochondrial inter-membrane space proteins into the cytosol, following which these apoptogenic proteins bring about the demise of the cell. The most well studied example of this is found in animals, where the release of mitochondrial cytochrome C nucleates the formation of the apoptosome, which then activates caspase mediated cell death. The release of mitochondrial proteins contributes to PCD in diverse organisms lacking the apoptosome, indicating that regulated mitochondrial release predates the evolution of canonical apoptosis. Using the budding yeast Saccharomyces cerevisiae, we recently confirmed an early study showing that Nuc1, a homolog of the mitochondrial apoptotic driver protein Endonuclease G, attenuates cytosolic double stranded RNA (dsRNA) viruses, which are endemic to yeast and many other organisms. Viral attenuation by Nuc1 occurs most prominently during meiosis and in association with its developmentally programmed relocation from the mitochondria to the cytosol. Intriguingly, meiotic viral attenuation by Nuc1 occurs within the context of meiotic PCD of the superfluous mother cell that we have also discovered. These findings are discussed here.}, }
@article {pmid32025367, year = {2020}, author = {Schultz, DT and Eizenga, JM and Corbett-Detig, RB and Francis, WR and Christianson, LM and Haddock, SHD}, title = {Conserved novel ORFs in the mitochondrial genome of the ctenophore Beroe forskalii.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e8356}, pmid = {32025367}, issn = {2167-8359}, support = {T32 HG008345/HG/NHGRI NIH HHS/United States ; U01 HL137183/HL/NHLBI NIH HHS/United States ; }, abstract = {To date, five ctenophore species' mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria.}, }
@article {pmid32020006, year = {2020}, author = {Taylor, DJ and Connelly, SJ and Kotov, AA}, title = {The Intercontinental phylogeography of neustonic daphniids.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {1818}, pmid = {32020006}, issn = {2045-2322}, mesh = {Animals ; Daphnia/*genetics ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Transfer/genetics ; }, abstract = {Organisms that live at the freshwater surface layer (the neuston) occupy a high energy habitat that is threatened by human activities. Daphniids of the genera Scapholeberis and Megafenestra are adapted to the neuston but are poorly studied for biogeography and diversity. Here we assess the global phylogeography of neustonic daphniids. We obtained 402 new multigene sequences from the 12S rRNA, 16S rRNA, and tRNA (val) regions of the mitochondrial genomes of daphniids from 186 global sites. We assessed the intercontinental origins and boundaries of mitochondrial lineages and the relative rates of evolution in neustonic and planktonic daphniids. We identified 17 divergent lineages in the neustonic daphniids that were associated with biogeographic regions. Six of these lineages had intercontinental ranges - four of these were Transberingian. Patagonian populations of Scapholeberis rammneri were monophyletic and nested within a closely related clade of western North American haplotypes, suggesting an introduction from the Western Nearctic to South America. The Eastern Palearctic was more diverse than other regions, containing eight of the major lineages detected in the Scapholeberinae. The Genus Scapholeberis had high levels of divergence compared to non-neustonic daphniids. Neustonic daphniids have more divergent biogeographic lineages than previously appreciated.}, }
@article {pmid32019493, year = {2020}, author = {Kurbalija Novičić, Z and Sayadi, A and Jelić, M and Arnqvist, G}, title = {Negative frequency dependent selection contributes to the maintenance of a global polymorphism in mitochondrial DNA.}, journal = {BMC evolutionary biology}, volume = {20}, number = {1}, pages = {20}, pmid = {32019493}, issn = {1471-2148}, mesh = {Analysis of Variance ; Animals ; DNA, Mitochondrial/*genetics ; Drosophila/genetics ; Female ; Haplotypes/genetics ; Male ; Phenotype ; *Polymorphism, Genetic ; *Selection, Genetic ; Sympatry ; }, abstract = {BACKGROUND: Understanding the forces that maintain diversity across a range of scales is at the very heart of biology. Frequency-dependent processes are generally recognized as the most central process for the maintenance of ecological diversity. The same is, however, not generally true for genetic diversity. Negative frequency dependent selection, where rare genotypes have an advantage, is often regarded as a relatively weak force in maintaining genetic variation in life history traits because recombination disassociates alleles across many genes. Yet, many regions of the genome show low rates of recombination and genetic variation in such regions (i.e., supergenes) may in theory be upheld by frequency dependent selection.<br><br>RESULTS: We studied what is essentially a ubiquitous life history supergene (i.e., mitochondrial DNA) in the fruit fly Drosophila subobscura, showing sympatric polymorphism with two main mtDNA genotypes co-occurring in populations world-wide. Using an experimental evolution approach involving manipulations of genotype starting frequencies, we show that negative frequency dependent selection indeed acts to maintain genetic variation in this region. Moreover, the strength of selection was affected by food resource conditions.<br><br>CONCLUSIONS: Our work provides novel experimental support for the view that balancing selection through negative frequency dependency acts to maintain genetic variation in life history genes. We suggest that the emergence of negative frequency dependent selection on mtDNA is symptomatic of the fundamental link between ecological processes related to resource use and the maintenance of genetic variation.}, }
@article {pmid32018005, year = {2020}, author = {Wu, H and Liu, Y and Shi, X and Zhang, X and Ye, C and Zhu, KY and Zhu, F and Zhang, J and Ma, E}, title = {Transcriptome analysis of antennal cytochrome P450s and their transcriptional responses to plant and locust volatiles in Locusta migratoria.}, journal = {International journal of biological macromolecules}, volume = {149}, number = {}, pages = {741-753}, doi = {10.1016/j.ijbiomac.2020.01.309}, pmid = {32018005}, issn = {1879-0003}, mesh = {Animals ; Cytochrome P-450 Enzyme System/classification/*genetics/*metabolism ; Cytochrome P450 Family 2/metabolism ; Cytochrome P450 Family 3/metabolism ; Cytochrome P450 Family 4/metabolism ; Gene Expression Profiling/*methods ; Gene Expression Regulation ; Inactivation, Metabolic ; Locusta migratoria/drug effects/*genetics/*metabolism ; Mitochondria/metabolism ; Odorants ; Phylogeny ; Transcriptome ; Volatile Organic Compounds/pharmacology ; }, abstract = {Cytochrome P450 monooxygenases (P450s) constitute a large superfamily of heme-thiolate proteins that are involved in the biosynthesis or degradation of endogenous compounds and detoxification of exogenous chemicals. It has been reported that P450s could serve as odorant-degrading enzymes (ODEs) to inactivate odorants to avoid saturating the antennae. However, there is little information about P450s in the antennae of Locusta migratoria. In the current work, we conducted an antenna transcriptome analysis and identified 92 P450s, including 68 full-length and 24 partial sequences. Phylogenetic analysis showed that 68 full-length P450s were grouped into four clans: CYP2, CYP3, CYP4, and mitochondria clans. Tissue, stage, and sex-dependent expressions of these 68 P450s were investigated. The results showed that 4 P450s were antenna-specific, whereas others were antenna-rich but also expressed in other tissues, implying their various potential roles in the antennae. In addition, the responses of seven selected P450s to five gramineous plant volatiles and four locust volatiles were determined. CYP6MU1 could be induced by almost all compounds tested, suggesting its important roles in odorant processing. Different P450s exhibited diverse responses to odorants, indicating that specific regulation of P450 expression by odorants might modulate the sensitivity of the olfactory responses to various chemicals.}, }
@article {pmid32012851, year = {2020}, author = {Coate, JE and Schreyer, WM and Kum, D and Doyle, JJ}, title = {Robust Cytonuclear Coordination of Transcription in Nascent Arabidopsis thaliana Autopolyploids.}, journal = {Genes}, volume = {11}, number = {2}, pages = {}, pmid = {32012851}, issn = {2073-4425}, mesh = {Arabidopsis/*genetics ; Cell Nucleus/genetics ; Diploidy ; Evolution, Molecular ; Gene Expression Regulation, Plant/*genetics ; Genes, Plant/genetics ; Genome, Plant/genetics ; Mitochondria/genetics ; Organelles/genetics ; Plastids/genetics ; *Polyploidy ; Sequence Analysis, RNA/methods ; Transcriptional Activation/genetics ; }, abstract = {Polyploidy is hypothesized to cause dosage imbalances between the nucleus and the other genome-containing organelles (mitochondria and plastids), but the evidence for this is limited. We performed RNA-seq on Arabidopsis thaliana diploids and their derived autopolyploids to quantify the degree of inter-genome coordination of transcriptional responses to nuclear whole genome duplication in two different organs (sepals and rosette leaves). We show that nuclear and organellar genomes exhibit highly coordinated responses in both organs. First, organelle genome copy number increased in response to nuclear whole genome duplication (WGD), at least partially compensating for altered nuclear genome dosage. Second, transcriptional output of the different cellular compartments is tuned to maintain diploid-like levels of relative expression among interacting genes. In particular, plastid genes and nuclear genes whose products are plastid-targeted show coordinated down-regulation, such that their expression levels relative to each other remain constant across ploidy levels. Conversely, mitochondrial genes and nuclear genes with mitochondrial targeting show either constant or coordinated up-regulation of expression relative to other nuclear genes. Thus, cytonuclear coordination is robust to changes in nuclear ploidy level, with diploid-like balance in transcript abundances achieved within three generations after nuclear whole genome duplication.}, }
@article {pmid32011699, year = {2020}, author = {Gutiérrez Cortés, N and Pertuiset, C and Dumon, E and Börlin, M and Da Costa, B and Le Guédard, M and Stojkovic, T and Loundon, N and Rouillon, I and Nadjar, Y and Letellier, T and Jonard, L and Marlin, S and Rocher, C}, title = {Mutation m.3395A &gt; G in MT-ND1 leads to variable pathologic manifestations.}, journal = {Human molecular genetics}, volume = {29}, number = {6}, pages = {980-989}, doi = {10.1093/hmg/ddaa020}, pmid = {32011699}, issn = {1460-2083}, mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; DNA, Mitochondrial/analysis/*genetics ; Deafness/*classification/genetics/*pathology ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; Mitochondria/genetics/*pathology ; *Mutation ; NADH Dehydrogenase/*genetics ; }, abstract = {A non-synonymous mtDNA mutation, m.3395A > G, which changes tyrosine in position 30 to cysteine in p.MT-ND1, was found in several patients with a wide range of clinical phenotypes such as deafness, diabetes and cerebellar syndrome but no Leber's hereditary optic neuropathy. Although this mutation has already been described, its pathogenicity has not been demonstrated. Here, it was found isolated for the first time, allowing a study to investigate its pathogenicity. To do so, we constructed cybrid cell lines and carried out a functional study to assess the possible consequences of the mutation on mitochondrial bioenergetics. Results obtained demonstrated that this mutation causes an important dysfunction of the mitochondrial respiratory chain with a decrease in both activity and quantity of complex I due to a diminution of p.MT-ND1 quantity. However, no subcomplexes were found in cybrids carrying the mutation, indicating that the quality of the complex I assembly is not affected. Moreover, based on the crystal structure of p.MT-ND1 and the data found in the literature, we propose a hypothesis for the mechanism of the degradation of p.MT-ND1. Our study provides new insights into the pathophysiology of mitochondrial diseases and in particular of MT-ND1 mutations.}, }
@article {pmid32008087, year = {2020}, author = {Zachar, I and Boza, G}, title = {Endosymbiosis before eukaryotes: mitochondrial establishment in protoeukaryotes.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {77}, number = {18}, pages = {3503-3523}, pmid = {32008087}, issn = {1420-9071}, support = {NKFI-K124438//National Research, Development, and Innovation Office/ ; GINOP-2.3.2-15-2016-00057//National Research, Development, and Innovation Office/ ; }, mesh = {Biological Evolution ; Eukaryotic Cells/metabolism ; Microbial Consortia ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/metabolism ; Plastids ; Prokaryotic Cells/*metabolism ; *Symbiosis ; }, abstract = {Endosymbiosis and organellogenesis are virtually unknown among prokaryotes. The single presumed example is the endosymbiogenetic origin of mitochondria, which is hidden behind the event horizon of the last eukaryotic common ancestor. While eukaryotes are monophyletic, it is unlikely that during billions of years, there were no other prokaryote-prokaryote endosymbioses as symbiosis is extremely common among prokaryotes, e.g., in biofilms. Therefore, it is even more precarious to draw conclusions about potentially existing (or once existing) prokaryotic endosymbioses based on a single example. It is yet unknown if the bacterial endosymbiont was captured by a prokaryote or by a (proto-)eukaryote, and if the process of internalization was parasitic infection, slow engulfment, or phagocytosis. In this review, we accordingly explore multiple mechanisms and processes that could drive the evolution of unicellular microbial symbioses with a special attention to prokaryote-prokaryote interactions and to the mitochondrion, possibly the single prokaryotic endosymbiosis that turned out to be a major evolutionary transition. We investigate the ecology and evolutionary stability of inter-species microbial interactions based on dependence, physical proximity, cost-benefit budget, and the types of benefits, investments, and controls. We identify challenges that had to be conquered for the mitochondrial host to establish a stable eukaryotic lineage. Any assumption about the initial interaction of the mitochondrial ancestor and its contemporary host based solely on their modern relationship is rather perilous. As a result, we warn against assuming an initial mutually beneficial interaction based on modern mitochondria-host cooperation. This assumption is twice fallacious: (i) endosymbioses are known to evolve from exploitative interactions and (ii) cooperativity does not necessarily lead to stable mutualism. We point out that the lack of evidence so far on the evolution of endosymbiosis from mutual syntrophy supports the idea that mitochondria emerged from an exploitative (parasitic or phagotrophic) interaction rather than from syntrophy.}, }
@article {pmid32003549, year = {2020}, author = {Wesley, CC and Mishra, S and Levy, DL}, title = {Organelle size scaling over embryonic development.}, journal = {Wiley interdisciplinary reviews. Developmental biology}, volume = {9}, number = {5}, pages = {e376}, pmid = {32003549}, issn = {1759-7692}, support = {R35 GM134885/GM/NIGMS NIH HHS/United States ; P20 GM103432/GM/NIGMS NIH HHS/United States ; R01 GM113028/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Membrane Structures/metabolism/ultrastructure ; Cell Nucleus/metabolism/ultrastructure ; *Embryonic Development ; Endoplasmic Reticulum/metabolism/ultrastructure ; *Organelle Size ; Spindle Apparatus/metabolism/ultrastructure ; }, abstract = {Cell division without growth results in progressive cell size reductions during early embryonic development. How do the sizes of intracellular structures and organelles scale with cell size and what are the functional implications of such scaling relationships? Model organisms, in particular Caenorhabditis elegans worms, Drosophila melanogaster flies, Xenopus laevis frogs, and Mus musculus mice, have provided insights into developmental size scaling of the nucleus, mitotic spindle, and chromosomes. Nuclear size is regulated by nucleocytoplasmic transport, nuclear envelope proteins, and the cytoskeleton. Regulators of microtubule dynamics and chromatin compaction modulate spindle and mitotic chromosome size scaling, respectively. Developmental scaling relationships for membrane-bound organelles, like the endoplasmic reticulum, Golgi, mitochondria, and lysosomes, have been less studied, although new imaging approaches promise to rectify this deficiency. While models that invoke limiting components and dynamic regulation of assembly and disassembly can account for some size scaling relationships in early embryos, it will be exciting to investigate the contribution of newer concepts in cell biology such as phase separation and interorganellar contacts. With a growing understanding of the underlying mechanisms of organelle size scaling, future studies promise to uncover the significance of proper scaling for cell function and embryonic development, as well as how aberrant scaling contributes to disease. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Early Embryonic Development > Fertilization to Gastrulation Comparative Development and Evolution > Model Systems.}, }
@article {pmid32001678, year = {2020}, author = {Barili, V and Fisicaro, P and Montanini, B and Acerbi, G and Filippi, A and Forleo, G and Romualdi, C and Ferracin, M and Guerrieri, F and Pedrazzi, G and Boni, C and Rossi, M and Vecchi, A and Penna, A and Zecca, A and Mori, C and Orlandini, A and Negri, E and Pesci, M and Massari, M and Missale, G and Levrero, M and Ottonello, S and Ferrari, C}, title = {Targeting p53 and histone methyltransferases restores exhausted CD8+ T cells in HCV infection.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {604}, pmid = {32001678}, issn = {2041-1723}, mesh = {Acute Disease ; Adolescent ; Adult ; Aged ; Antiviral Agents/pharmacology/therapeutic use ; Ataxia Telangiectasia Mutated Proteins/metabolism ; CD8-Positive T-Lymphocytes/*immunology ; Chronic Disease ; Epigenesis, Genetic/drug effects ; Gene Expression Profiling ; Gene Regulatory Networks/drug effects ; Glucose/metabolism ; Hepatitis C/blood/genetics/*immunology/virology ; Histone Methyltransferases/*metabolism ; Humans ; Lymphocyte Activation/drug effects/immunology ; Middle Aged ; Mitochondria/drug effects/metabolism ; Principal Component Analysis ; Signal Transduction/drug effects ; Transcription, Genetic/drug effects ; Tumor Suppressor Protein p53/*metabolism ; Young Adult ; }, abstract = {Hepatitis C virus infection (HCV) represents a unique model to characterize, from early to late stages of infection, the T cell differentiation process leading to exhaustion of human CD8+ T cells. Here we show that in early HCV infection, exhaustion-committed virus-specific CD8+ T cells display a marked upregulation of transcription associated with impaired glycolytic and mitochondrial functions, that are linked to enhanced ataxia-telangiectasia mutated (ATM) and p53 signaling. After evolution to chronic infection, exhaustion of HCV-specific T cell responses is instead characterized by a broad gene downregulation associated with a wide metabolic and anti-viral function impairment, which can be rescued by histone methyltransferase inhibitors. These results have implications not only for treatment of HCV-positive patients not responding to last-generation antivirals, but also for other chronic pathologies associated with T cell dysfunction, including cancer.}, }
@article {pmid31992373, year = {2020}, author = {Le, TH and Pham, LTK and Doan, HTT and Le, XTK and Saijuntha, W and Rajapakse, RPVJ and Lawton, SP}, title = {Comparative mitogenomics of the zoonotic parasite Echinostoma revolutum resolves taxonomic relationships within the 'E. revolutum' species group and the Echinostomata (Platyhelminthes: Digenea).}, journal = {Parasitology}, volume = {147}, number = {5}, pages = {566-576}, pmid = {31992373}, issn = {1469-8161}, mesh = {Animals ; Echinostoma/*genetics ; Echinostomatidae/*classification/genetics ; Genome ; Mitochondria/genetics ; Phylogeny ; Trematoda ; }, abstract = {The complete mitochondrial sequence of 17,030 bp was obtained from Echinostoma revolutum and characterized with those of previously reported members of the superfamily Echinostomatoidea, i.e. six echinostomatids, one echinochasmid, five fasciolids, one himasthlid, and two cyclocoelids. Relationship within suborders and between superfamilies, such as Echinostomata, Pronocephalata, Troglotremata, Opisthorchiata, and Xiphiditata, are also considered. It contained 12 protein-coding, two ribosomal RNA, 22 transfer RNA genes and a tandem repetitive consisting non-coding region (NCR). The gene order, one way-positive transcription, the absence of atp8 and the overlapped region by 40 bp between nad4L and nad4 genes were similar as in common trematodes. The NCR located between tRNAGlu (trnE) and cox3 contained 11 long (LRUs) and short repeat units (SRUs) (seven LRUs of 317 bp, four SRUs of 207 bp each), and an internal spacer sequence between LRU7 and SRU4 specifying high-level polymorphism. Special DHU-arm missing tRNAs for Serine were found for both tRNAS1(AGN) and tRNAS2(UCN). Echinostoma revolutum indicated the lowest divergence rate to E. miyagawai and the highest to Tracheophilus cymbius and Echinochasmus japonicus. The usage of ATG/GTG start and TAG/TAA stop codons, the AT composition bias, the negative AT-skewness, and the most for Phe/Leu/Val and the least for Arg/Asn/Asp codons were noted. Topology indicated the monophyletic position of E. revolutum to E. miyagawai. Monophyly of Echinostomatidae and Fasciolidae was clearly solved with respect to Echinochasmidae, Himasthlidae, and Cyclocoelidae which were rendered paraphyletic in the suborder Echinostomata.}, }
@article {pmid31978488, year = {2020}, author = {Souza, DS and Marinoni, L and Monné, ML and Gómez-Zurita, J}, title = {Molecular phylogenetic assessment of the tribal classification of Lamiinae (Coleoptera: Cerambycidae).}, journal = {Molecular phylogenetics and evolution}, volume = {145}, number = {}, pages = {106736}, doi = {10.1016/j.ympev.2020.106736}, pmid = {31978488}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Coleoptera/*classification ; Electron Transport Complex IV/genetics ; Insect Proteins/chemistry/genetics ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Ribosome Subunits, Large/genetics ; }, abstract = {Lamiinae is the most diverse subfamily of longhorned beetles, with about 20,000 described species classified into 80 tribes. Most of the tribes of Lamiinae were proposed during the 19th century and the suprageneric classification of the subfamily has never been assessed under phylogenetic criteria. In this study, we present the first tribal-level phylogeny of Lamiinae, inferred from 130 terminals (representing 46 tribes, prioritizing generic type species of the tribes) and fragments of two mitochondrial and three nuclear markers (cox1, rrnL, Wg, CPS and LSU; 5,024 aligned positions in total). Analyses were performed under Maximum Likelihood and Bayesian methods based on two datasets: a dataset including all taxa available for the study, and a reduced dataset with 111 terminals where taxa only contributing with mitochondrial markers were excluded from the matrix. The monophyly of Lamiinae was corroborated in three of the four analyses and 11 of the 35 tribes with more than one species represented in the analyses were consistently recovered as monophyletic. However, 15 tribes were not retrieved as monophyletic, requiring a revision of their boundaries: Acanthocinini, Acanthoderini, Agapanthiini, Apomecynini, Desmiphorini, Dorcaschematini, Enicodini, Hemilophini, Monochamini, Onciderini, Parmenini, Phytoeciini, Pogonocherini, Pteropliini and Saperdini. Based on these results, when strong support values for paraphyly were recovered, we argue a number of tribe synonymies, including Moneilemini as synonym of Acanthocinini; Onocephalini of Onciderini; Dorcadionini, Gnomini, Monochamini and Rhodopinini of Lamiini; and Obereini and Phytoeciini of Saperdini. Other taxonomic changes proposed in this study based on the criterion of monophyly and supported by morphological characters include the transfer of Tricondyloides and Stenellipsis to Enicodini, and of Dylobolus stat. rest., which is removed as subgenus of Mecas and restituted as genus, to Hemilophini. Furthermore, our analyses suggest that Ostedes and Neohoplonotus should be removed from Acanthocinini and Parmenini, respectively, and Colobotheini should be redefined to encompass several genera currently placed in Acanthocinini.}, }
@article {pmid31974502, year = {2020}, author = {Capt, C and Bouvet, K and Guerra, D and Robicheau, BM and Stewart, DT and Pante, E and Breton, S}, title = {Unorthodox features in two venerid bivalves with doubly uniparental inheritance of mitochondria.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {1087}, pmid = {31974502}, issn = {2045-2322}, mesh = {Animals ; Bivalvia/*genetics/metabolism ; DNA, Mitochondrial/genetics ; Female ; Genome ; Genome, Mitochondrial ; Inheritance Patterns ; Male ; Mitochondria ; Mytilidae/classification/genetics ; Phylogeny ; Species Specificity ; }, abstract = {In animals, strictly maternal inheritance (SMI) of mitochondria is the rule, but one exception (doubly uniparental inheritance or DUI), marked by the transmission of sex-specific mitogenomes, has been reported in bivalves. Associated with DUI is a frequent modification of the mitochondrial cox2 gene, as well as additional sex-specific mitochondrial genes not involved in oxidative phosphorylation. With the exception of freshwater mussels (for 3 families of the order Unionida), these DUI-associated features have only been shown in few species [within Mytilidae (order Mytilida) and Veneridae (order Venerida)] because of the few complete sex-specific mitogenomes published for these orders. Here, we present the complete sex-specific mtDNAs of two recently-discovered DUI species in two families of the order Venerida, Scrobicularia plana (Semelidae) and Limecola balthica (Tellinidae). These species display the largest differences in genome size between sex-specific mitotypes in DUI species (>10 kb), as well as the highest mtDNA divergences (sometimes reaching >50%). An important in-frame insertion (>3.5 kb) in the male cox2 gene is partly responsible for the differences in genome size. The S. plana cox2 gene is the largest reported so far in the Kingdom Animalia. The mitogenomes may be carrying sex-specific genes, indicating that general mitochondrial features are shared among DUI species.}, }
@article {pmid31973163, year = {2020}, author = {Zhang, GJ and Dong, R and Lan, LN and Li, SF and Gao, WJ and Niu, HX}, title = {Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants.}, journal = {International journal of molecular sciences}, volume = {21}, number = {3}, pages = {}, pmid = {31973163}, issn = {1422-0067}, support = {31970240//the National Natural Science foundation of China/ ; }, mesh = {Cell Nucleus/*genetics ; Cell Proliferation/genetics ; DNA End-Joining Repair ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genome Size ; *Genome, Plant ; Mitochondria/genetics ; Mutation ; Plants/*genetics ; Plastids/*genetics ; Sex Chromosomes ; }, abstract = {The transfer of genetic material from the mitochondria and plastid to the nucleus gives rise to nuclear integrants of mitochondrial DNA (NUMTs) and nuclear integrants of plastid DNA (NUPTs). This frequently occurring DNA transfer is ongoing and has important evolutionary implications. In this review, based on previous studies and the analysis of NUMT/NUPT insertions of more than 200 sequenced plant genomes, we analyzed and summarized the general features of NUMTs/NUPTs and highlighted the genetic consequence of organellar DNA insertions. The statistics of organellar DNA integrants among various plant genomes revealed that organellar DNA-derived sequence content is positively correlated with the nuclear genome size. After integration, the nuclear organellar DNA could undergo different fates, including elimination, mutation, rearrangement, fragmentation, and proliferation. The integrated organellar DNAs play important roles in increasing genetic diversity, promoting gene and genome evolution, and are involved in sex chromosome evolution in dioecious plants. The integrating mechanisms, involving non-homologous end joining at double-strand breaks were also discussed.}, }
@article {pmid31972373, year = {2020}, author = {Muthye, V and Kandoi, G and Lavrov, DV}, title = {MMPdb and MitoPredictor: Tools for facilitating comparative analysis of animal mitochondrial proteomes.}, journal = {Mitochondrion}, volume = {51}, number = {}, pages = {118-125}, doi = {10.1016/j.mito.2020.01.001}, pmid = {31972373}, issn = {1872-8278}, mesh = {Acanthamoeba castellanii ; Animals ; Caenorhabditis elegans ; *Databases, Protein ; Drosophila melanogaster ; Energy Metabolism/physiology ; Humans ; *Machine Learning ; Mice ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Proteome/genetics ; Saccharomyces cerevisiae ; }, abstract = {Data on experimentally-characterized animal mitochondrial proteomes (mt-proteomes) are limited to a few model organisms and are scattered across multiple databases, impeding a comparative analysis. We developed two resources to address these problems. First, we re-analyzed proteomic data from six species with experimentally characterized mt-proteomes: animals (Homo sapiens, Mus musculus, Caenorhabditis elegans, and Drosophila melanogaster), and outgroups (Acanthamoeba castellanii and Saccharomyces cerevisiae) and created the Metazoan Mitochondrial Proteome Database (MMPdb) to host the results. Second, we developed a novel pipeline, "MitoPredictor" that uses a Random Forest classifier to infer mitochondrial localization of proteins based on orthology, mitochondrial targeting signal prediction, and protein domain analyses. Both tools generate an R Shiny applet that can be used to visualize and interact with the results and can be used on a personal computer. MMPdb is also available online at https://mmpdb.eeob.iastate.edu/.}, }
@article {pmid31972240, year = {2020}, author = {Chang, H and Qiu, Z and Yuan, H and Wang, X and Li, X and Sun, H and Guo, X and Lu, Y and Feng, X and Majid, M and Huang, Y}, title = {Evolutionary rates of and selective constraints on the mitochondrial genomes of Orthoptera insects with different wing types.}, journal = {Molecular phylogenetics and evolution}, volume = {145}, number = {}, pages = {106734}, doi = {10.1016/j.ympev.2020.106734}, pmid = {31972240}, issn = {1095-9513}, mesh = {Animals ; Biodiversity ; *Biological Evolution ; Mitochondria/*genetics ; Open Reading Frames/genetics ; Orthoptera/anatomy &amp; histology/*classification/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; Wings, Animal/anatomy &amp; histology ; }, abstract = {Orthoptera is the most diverse order of polyneopterans, and the forewing and hindwing of its members exhibit extremely variability from full length to complete loss in many groups; thus, this order provides a good model for studying the effects of insect flight ability on the evolutionary constraints on and evolutionary rate of the mitochondrial genome. Based on a data set of mitochondrial genomes from 171 species, including 43 newly determined, we reconstructed Orthoptera phylogenetic relationships and estimated the divergence times of this group. The results supported Caelifera and Ensifera as two monophyletic groups, and revealed that Orthoptera originated in the Carboniferous (298.997 Mya). The date of divergence between the suborders Caelifera and Ensifera was 255.705 Mya, in the late Permian. The major lineages of Acrididae seemed to have radiated in the Cenozoic, and the six patterns of rearrangement of 171 Orthoptera mitogenomes mostly occurred in the Cretaceous and Cenozoic. Based on phylogenetic relationships and ancestral state reconstruction, we analysed the evolutionary selection pressure on and evolutionary rate of mitochondrial protein-coding genes (mPCGs). The results indicated that during approximately 300 Mya of evolution, these genes experienced purifying selection to maintain their function. Flightless orthopteran insects accumulated more non-synonymous mutations than flying species and experienced more relaxed evolutionary constraints. The different wing types had different evolutionary rates, and the mean evolutionary rate of Orthoptera mitochondrial mPCGs was 13.554 × 10[-9] subs/s/y. The differences in selection pressures and evolutionary rates observed between the mitochondrial genomes suggested that functional constraints due to locomotion play an important role in the evolution of mitochondrial DNA in orthopteran insects with different wing types.}, }
@article {pmid31969697, year = {2020}, author = {Mishmar, D}, title = {mtDNA in the crossroads of evolution and disease.}, journal = {Nature reviews. Molecular cell biology}, volume = {21}, number = {4}, pages = {181}, pmid = {31969697}, issn = {1471-0080}, mesh = {Alleles ; *DNA, Mitochondrial ; Evolution, Molecular ; *Mitochondria ; Phenotype ; }, }
@article {pmid31964548, year = {2020}, author = {Boos, F and Labbadia, J and Herrmann, JM}, title = {How the Mitoprotein-Induced Stress Response Safeguards the Cytosol: A Unified View.}, journal = {Trends in cell biology}, volume = {30}, number = {3}, pages = {241-254}, doi = {10.1016/j.tcb.2019.12.003}, pmid = {31964548}, issn = {1879-3088}, mesh = {Animals ; Cytosol/*metabolism ; Humans ; Mitochondrial Proteins/*metabolism ; Protein Transport ; Proteostasis ; Signal Transduction ; *Stress, Physiological ; }, abstract = {Mitochondrial and cytosolic proteostasis are of central relevance for cellular stress resistance and organismal health. Recently, a number of individual cellular programs were described that counter the fatal consequences of mitochondrial dysfunction. These programs remove arrested import intermediates from mitochondrial protein translocases, stabilize protein homeostasis within mitochondria, and, in particular, increase the levels and activity of chaperones and the proteasome system in the cytosol. Here, we describe the different responses to mitochondrial perturbation and propose to unify the seemingly distinct mitochondrial-cytosolic quality control mechanisms into a single network, the mitoprotein-induced stress response. This holistic view places mitochondrial biogenesis at a central position of the cellular proteostasis network, emphasizing the importance of mitochondrial protein import processes for development, reproduction, and ageing.}, }
@article {pmid31963509, year = {2020}, author = {Toleco, MR and Naake, T and Zhang, Y and Heazlewood, JL and Fernie, AR}, title = {Plant Mitochondrial Carriers: Molecular Gatekeepers That Help to Regulate Plant Central Carbon Metabolism.}, journal = {Plants (Basel, Switzerland)}, volume = {9}, number = {1}, pages = {}, pmid = {31963509}, issn = {2223-7747}, abstract = {The evolution of membrane-bound organelles among eukaryotes led to a highly compartmentalized metabolism. As a compartment of the central carbon metabolism, mitochondria must be connected to the cytosol by molecular gates that facilitate a myriad of cellular processes. Members of the mitochondrial carrier family function to mediate the transport of metabolites across the impermeable inner mitochondrial membrane and, thus, are potentially crucial for metabolic control and regulation. Here, we focus on members of this family that might impact intracellular central plant carbon metabolism. We summarize and review what is currently known about these transporters from in vitro transport assays and in planta physiological functions, whenever available. From the biochemical and molecular data, we hypothesize how these relevant transporters might play a role in the shuttling of organic acids in the various flux modes of the TCA cycle. Furthermore, we also review relevant mitochondrial carriers that may be vital in mitochondrial oxidative phosphorylation. Lastly, we survey novel experimental approaches that could possibly extend and/or complement the widely accepted proteoliposome reconstitution approach.}, }
@article {pmid31960780, year = {2020}, author = {Kumari, K and M, MH and Sinha, A and Koushlesh, SK and Das Sarkar, S and Borah, S and BaItha, R and Behera, BK and Das, BK}, title = {Genetic differentiation and phylogenetic relationship of 11 Asian Sisorinae genera (Siluriformes: Sisoridae) with new record of Pseudolaguvia foveolata.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {31}, number = {1}, pages = {35-41}, doi = {10.1080/24701394.2020.1714605}, pmid = {31960780}, issn = {2470-1408}, mesh = {Animals ; Catfishes/*genetics/metabolism ; DNA-Binding Proteins/*genetics/metabolism ; Electron Transport Complex IV/*genetics/metabolism ; Genes, Mitochondrial/*genetics ; Genome, Mitochondrial/*genetics ; India ; Mitochondria/*genetics/metabolism ; Phylogeny ; }, abstract = {Studies on Sisorinae systematics have been largely restricted to morphological data with few studies on examination of phylogenetic relations. However, no study has been done to evaluate genetic distance of the genera under Sisorinae sub-family and detailed phylogenetic relations within it. We used nuclear recombination activating 2 (rag2) gene and mitochondrial cytochrome c oxidase I (COI) gene from 64 species to examine genetic differentiation and phylogenetic relationships within 11 Asian Sisorinae genera. The range of interspecies K2P distance for rag2 was 0-0.061 and COI was 0-0.204. Phylogenetic analysis based on maximum likelihood (ML) and Bayesian (BI) approaches for each locus individually and for the concatenated rag2 and COI sequences revealed three major subclades viz. Bagariini, Sisorini and Erethistini under subfamily Sisorinae. The analysis based on COI gene showed ((Sisorini, Bagariini), Erethistini) relationship. Rag2 and combined rag2 and COI showed ((Sisorini, Erethistini), Bagariini) relationship. Combined rag2 and COI analyses resulted into better resolved trees with a good bootstrap support. In this study, new record of Pseudolaguvia foveolata (Erethistini) has been documented based on 13 specimens collected from Torsa River, Jaldapara, Alipurduar district, West Bengal, India (26°43'44.66″ N and 89°19'32.34″ E), extending its distribution range in Brahmaputra drainage, India. The genetic distance between the P. foveolata new record and the reported P. foveolata (holotype: UMMZ 244867) was 0.00 at both rag2 and COI locus and it was further grouped with P. foveolata Type specimen (holotype: UMMZ 244867) with 100% bootstrap support. This report gives additional information on occurrence of the species P. foveolata, along with discussion on morphometric, meristic and molecular (COI and rag2 gene) data.}, }
@article {pmid31959914, year = {2020}, author = {Tan, M and Mosaoa, R and Graham, GT and Kasprzyk-Pawelec, A and Gadre, S and Parasido, E and Catalina-Rodriguez, O and Foley, P and Giaccone, G and Cheema, A and Kallakury, B and Albanese, C and Yi, C and Avantaggiati, ML}, title = {Inhibition of the mitochondrial citrate carrier, Slc25a1, reverts steatosis, glucose intolerance, and inflammation in preclinical models of NAFLD/NASH.}, journal = {Cell death and differentiation}, volume = {27}, number = {7}, pages = {2143-2157}, pmid = {31959914}, issn = {1476-5403}, support = {R01 CA193698/CA/NCI NIH HHS/United States ; T32 CA009686/CA/NCI NIH HHS/United States ; P30 CA051008/CA/NCI NIH HHS/United States ; R21 DE028670/DE/NIDCR NIH HHS/United States ; }, mesh = {Acetyl Coenzyme A/metabolism ; Animals ; Blood Glucose/metabolism ; Carrier Proteins/*antagonists &amp; inhibitors/metabolism ; Cell Polarity ; Citric Acid/metabolism ; Diet, High-Fat ; Disease Models, Animal ; Down-Regulation ; Fasting/blood ; Gluconeogenesis ; Glucose Intolerance/blood/*complications ; Hepatomegaly/blood/complications/diagnostic imaging ; Humans ; Hyperglycemia/blood/complications ; Inflammation/blood/*complications ; Insulin Resistance ; Interleukin-6/biosynthesis ; Lipogenesis ; Liver/diagnostic imaging/metabolism/pathology ; Macrophages/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Mitochondria/*metabolism ; Non-alcoholic Fatty Liver Disease/blood/*complications/diagnostic imaging ; Obesity/blood/complications ; Phenotype ; Time Factors ; Triglycerides/metabolism ; Tumor Necrosis Factor-alpha/biosynthesis ; }, abstract = {Nonalcoholic fatty liver disease (NAFLD) and its evolution to inflammatory steatohepatitis (NASH) are the most common causes of chronic liver damage and transplantation that are reaching epidemic proportions due to the upraising incidence of metabolic syndrome, obesity, and diabetes. Currently, there is no approved treatment for NASH. The mitochondrial citrate carrier, Slc25a1, has been proposed to play an important role in lipid metabolism, suggesting a potential role for this protein in the pathogenesis of this disease. Here, we show that Slc25a1 inhibition with a specific inhibitor compound, CTPI-2, halts salient alterations of NASH reverting steatosis, preventing the evolution to steatohepatitis, reducing inflammatory macrophage infiltration in the liver and adipose tissue, while starkly mitigating obesity induced by a high-fat diet. These effects are differentially recapitulated by a global ablation of one copy of the Slc25a1 gene or by a liver-targeted Slc25a1 knockout, which unravel dose-dependent and tissue-specific functions of this protein. Mechanistically, through citrate-dependent activities, Slc25a1 inhibition rewires the lipogenic program, blunts signaling from peroxisome proliferator-activated receptor gamma, a key regulator of glucose and lipid metabolism, and inhibits the expression of gluconeogenic genes. The combination of these activities leads not only to inhibition of lipid anabolic processes, but also to a normalization of hyperglycemia and glucose intolerance as well. In summary, our data show for the first time that Slc25a1 serves as an important player in the pathogenesis of fatty liver disease and thus, provides a potentially exploitable and novel therapeutic target.}, }
@article {pmid31959910, year = {2020}, author = {Tyagi, K and Chakraborty, R and Cameron, SL and Sweet, AD and Chandra, K and Kumar, V}, title = {Rearrangement and evolution of mitochondrial genomes in Thysanoptera (Insecta).}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {695}, pmid = {31959910}, issn = {2045-2322}, mesh = {Animals ; Base Composition ; Evolution, Molecular ; *Gene Rearrangement ; Genetic Variation ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Thysanoptera/classification/*genetics ; }, abstract = {Prior to this study, complete mitochondrial genomes from Order Thysanoptera were restricted to a single family, the Thripidae, resulting in a biased view of their evolution. Here we present the sequences for the mitochondrial genomes of four additional thrips species, adding three extra families and an additional subfamily, thus greatly improving taxonomic coverage. Thrips mitochondrial genomes are marked by high rates of gene rearrangement, duplications of the control region and tRNA mutations. Derived features of mitochondrial tRNAs in thrips include gene duplications, anticodon mutations, loss of secondary structures and high gene translocation rates. Duplicated control regions are found in the Aeolothripidae and the 'core' Thripinae clade but do not appear to promote gene rearrangement as previously proposed. Phylogenetic analysis of thrips mitochondrial sequence data supports the monophyly of two suborders, a sister-group relationship between Stenurothripidae and Thripidae, and suggests a novel set of relationships between thripid genera. Ancestral state reconstructions indicate that genome rearrangements are common, with just eight gene blocks conserved between any thrips species and the ancestral insect mitochondrial genome. Conversely, 71 derived rearrangements are shared between at least two species, and 24 of these are unambiguous synapomorphies for clades identified by phylogenetic analysis. While the reconstructed sequence of genome rearrangements among the protein-coding and ribosomal RNA genes could be inferred across the phylogeny, direct inference of phylogeny from rearrangement data in MLGO resulted in a highly discordant set of relationships inconsistent with both sequence-based phylogenies and previous morphological analysis. Given the demonstrated rates of genomic evolution within thrips, extensive sampling is needed to fully understand these phenomena across the order.}, }
@article {pmid31958218, year = {2020}, author = {Uddin, A and Mazumder, TH and Barbhuiya, PA and Chakraborty, S}, title = {Similarities and dissimilarities of codon usage in mitochondrial ATP genes among fishes, aves, and mammals.}, journal = {IUBMB life}, volume = {72}, number = {5}, pages = {899-914}, doi = {10.1002/iub.2231}, pmid = {31958218}, issn = {1521-6551}, mesh = {Animals ; Avian Proteins/*genetics ; Base Composition ; Biological Evolution ; Birds/*genetics ; *Codon Usage ; Computational Biology/methods ; Ecosystem ; Fish Proteins/*genetics ; Fishes/*genetics ; Gene Expression ; Genes, Mitochondrial ; Mammals/*genetics ; Mitochondria/genetics ; Mitochondrial Proton-Translocating ATPases/*genetics ; Mutation ; Selection, Genetic ; }, abstract = {In this study, we used bioinformatic approach to analyze the compositional features and codon usage bias (CUB) of ATP6 and ATP8 genes among three groups, namely, fishes, aves, and mammals which thrive in three different habitats as no work was reported yet. The coding sequences of these genes were retrieved from the National Center for Biotechnology Information to explore the similarities and dissimilarities of codon usage of each gene among these groups. Low values of synonymous codon usage order in fishes, aves, and mammals for ATP6 and ATP8 genes suggested that the CUB of ATP6 and ATP8 genes was low. In ATP6 gene, overall GC contents in fishes, aves and mammals were (mean ± SD) 44.09 ± 3.10, 46.65 ± 1.90, and 39.41 ± 2.89%, respectively, whereas in ATP8 gene, the overall GC contents were 42.76 ± 4.38, 44.16 ± 2.43, and 34.19 ± 3.82% in fishes, aves, and mammals, that is, both genes were found to be AT rich. In ATP6 gene, the codon AGC was overrepresented in fishes but under-represented in aves and mammals, whereas in ATP8 gene, the codon GCC was overrepresented in fishes but underrepresented in aves and mammals. The pattern of codon usage was different in these genes and varied among groups as evident from correspondence analysis. The slope of the regression line in neutrality plot was lower than 0.5, which revealed that the role of natural selection was higher than mutation pressure in shaping the CUB in ATP6 and ATP8 genes.}, }
@article {pmid31956907, year = {2020}, author = {Ganesh, S and Horvat, F and Drutovic, D and Efenberkova, M and Pinkas, D and Jindrova, A and Pasulka, J and Iyyappan, R and Malik, R and Susor, A and Vlahovicek, K and Solc, P and Svoboda, P}, title = {The most abundant maternal lncRNA Sirena1 acts post-transcriptionally and impacts mitochondrial distribution.}, journal = {Nucleic acids research}, volume = {48}, number = {6}, pages = {3211-3227}, pmid = {31956907}, issn = {1362-4962}, mesh = {Animals ; Gene Knockout Techniques ; Mice ; Mitochondria/*genetics/ultrastructure ; Oocytes/growth &amp; development/*metabolism/ultrastructure ; Polyadenylation/genetics ; RNA, Long Noncoding/*genetics ; RNA, Messenger/*genetics ; RNA, Mitochondrial/*genetics ; Rats ; Transcriptome/genetics ; }, abstract = {Tens of thousands of rapidly evolving long non-coding RNA (lncRNA) genes have been identified, but functions were assigned to relatively few of them. The lncRNA contribution to the mouse oocyte physiology remains unknown. We report the evolutionary history and functional analysis of Sirena1, the most expressed lncRNA and the 10th most abundant poly(A) transcript in mouse oocytes. Sirena1 appeared in the common ancestor of mouse and rat and became engaged in two different post-transcriptional regulations. First, antisense oriented Elob pseudogene insertion into Sirena1 exon 1 is a source of small RNAs targeting Elob mRNA via RNA interference. Second, Sirena1 evolved functional cytoplasmic polyadenylation elements, an unexpected feature borrowed from translation control of specific maternal mRNAs. Sirena1 knock-out does not affect fertility, but causes minor dysregulation of the maternal transcriptome. This includes increased levels of Elob and mitochondrial mRNAs. Mitochondria in Sirena1-/- oocytes disperse from the perinuclear compartment, but do not change in number or ultrastructure. Taken together, Sirena1 contributes to RNA interference and mitochondrial aggregation in mouse oocytes. Sirena1 exemplifies how lncRNAs stochastically engage or even repurpose molecular mechanisms during evolution. Simultaneously, Sirena1 expression levels and unique functional features contrast with the lack of functional importance assessed under laboratory conditions.}, }
@article {pmid31954510, year = {2020}, author = {Eberle, J and Ahrens, D and Mayer, C and Niehuis, O and Misof, B}, title = {A Plea for Standardized Nuclear Markers in Metazoan DNA Taxonomy.}, journal = {Trends in ecology &amp; evolution}, volume = {35}, number = {4}, pages = {336-345}, doi = {10.1016/j.tree.2019.12.003}, pmid = {31954510}, issn = {1872-8383}, mesh = {Animals ; *DNA ; *DNA Barcoding, Taxonomic ; Mitochondria ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The ease of sequencing DNA barcodes promoted a species identification system universally applicable across animal phyla. However, relying on a single mitochondrial DNA fragment has a number of drawbacks that can mislead species delimitation and identification. Implementation of multiple nuclear markers would mitigate the limits of the current barcoding system if these markers are universally applicable across species, carry sufficient information to discriminate between closely related species, and if sequencing and analyzing these markers can be automatized. As sequencing costs continue to fall, we believe that the time is right to extend DNA barcoding. Here we argue that nearly universal single-copy nuclear protein-coding genes deliver the desired characteristics and could be used to reliably delimit and identify animal species.}, }
@article {pmid31953445, year = {2020}, author = {Pascual-Itoiz, MA and Peña-Cearra, A and Martín-Ruiz, I and Lavín, JL and Simó, C and Rodríguez, H and Atondo, E and Flores, JM and Carreras-González, A and Tomás-Cortázar, J and Barriales, D and Palacios, A and García-Cañas, V and Pellón, A and Fullaondo, A and Aransay, AM and Prados-Rosales, R and Martín, R and Anguita, J and Abecia, L}, title = {The mitochondrial negative regulator MCJ modulates the interplay between microbiota and the host during ulcerative colitis.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {572}, pmid = {31953445}, issn = {2045-2322}, support = {R21 AI115091/AI/NIAID NIH HHS/United States ; }, mesh = {ADAM17 Protein/genetics ; Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Colitis, Ulcerative/*genetics/microbiology ; Disease Models, Animal ; Dysbiosis/*genetics ; Gene Deletion ; Gene Expression Regulation ; HSP40 Heat-Shock Proteins/*genetics ; Humans ; Mice ; Microbiota ; Mitochondrial Proteins/*genetics ; Molecular Chaperones/*genetics ; Phylogeny ; Receptors, Tumor Necrosis Factor, Type I/genetics ; Severity of Illness Index ; Tissue Inhibitor of Metalloproteinase-3/genetics ; Tumor Necrosis Factor-alpha/genetics ; }, abstract = {Recent evidences indicate that mitochondrial genes and function are decreased in active ulcerative colitis (UC) patients, in particular, the activity of Complex I of the electron transport chain is heavily compromised. MCJ is a mitochondrial inner membrane protein identified as a natural inhibitor of respiratory chain Complex I. The induction of experimental colitis in MCJ-deficient mice leads to the upregulation of Timp3 expression resulting in the inhibition of TACE activity that likely inhibits Tnf and Tnfr1 shedding from the cell membrane in the colon. MCJ-deficient mice also show higher expression of Myd88 and Tlr9, proinflammatory genes and disease severity. Interestingly, the absence of MCJ resulted in distinct microbiota metabolism and composition, including a member of the gut community in UC patients, Ruminococcus gnavus. These changes provoked an effect on IgA levels. Gene expression analyses in UC patients showed decreased levels of MCJ and higher expression of TIMP3, suggesting a relevant role of mitochondrial genes and function among active UC. The MCJ deficiency disturbs the regulatory relationship between the host mitochondria and microbiota affecting disease severity. Our results indicate that mitochondria function may be an important factor in the pathogenesis. All together support the importance of MCJ regulation during UC.}, }
@article {pmid31952167, year = {2020}, author = {Kleymann, A and Becker, AAMJ and Malik, YS and Kobayashi, N and Ghosh, S}, title = {Detection and Molecular Characterization of Picobirnaviruses (PBVs) in the Mongoose: Identification of a Novel PBV Using an Alternative Genetic Code.}, journal = {Viruses}, volume = {12}, number = {1}, pages = {}, pmid = {31952167}, issn = {1999-4915}, mesh = {Animals ; Feces/virology ; *Genetic Code ; Genetic Variation ; *Genome, Viral ; Genotype ; Herpestidae/*virology ; Host Specificity ; Mitochondria/genetics ; Phylogeny ; Picobirnavirus/classification/*genetics/isolation &amp; purification ; RNA Virus Infections/*veterinary ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics ; Saint Kitts and Nevis ; }, abstract = {We report high rates of detection (35.36%, 29/82) of genogroup-I (GI) picobirnaviruses (PBVs) in non-diarrheic fecal samples from the small Indian mongoose (Urva auropunctata). In addition, we identified a novel PBV-like RNA-dependent RNA polymerase (RdRp) gene sequence that uses an alternative mitochondrial genetic code (that of mold or invertebrate) for translation. The complete/nearly complete gene segment-2/RdRp gene sequences of seven mongoose PBV GI strains and the novel PBV-like strain were obtained by combining a modified non-specific primer-based amplification method with conventional RT-PCRs, facilitated by the inclusion of a new primer targeting the 3'-untranslated region (UTR) of PBV gene segment-2. The mongoose PBV and PBV-like strains retained the various features that are conserved in gene segment-2/RdRps of other PBVs. However, high genetic diversity was observed among the mongoose PBVs within and between host species. This is the first report on detection of PBVs in the mongoose. Molecular characterization of the PBV and PBV-like strains from a new animal species provided important insights into the various features and complex diversity of PBV gene segment-2/putative RdRps. The presence of the prokaryotic ribosomal binding site in the mongoose PBV genomes, and analysis of the novel PBV-like RdRp gene sequence that uses an alternative mitochondrial genetic code (especially that of mold) for translation corroborated recent speculations that PBVs may actually infect prokaryotic or fungal host cells.}, }
@article {pmid31947741, year = {2020}, author = {Chevigny, N and Schatz-Daas, D and Lotfi, F and Gualberto, JM}, title = {DNA Repair and the Stability of the Plant Mitochondrial Genome.}, journal = {International journal of molecular sciences}, volume = {21}, number = {1}, pages = {}, pmid = {31947741}, issn = {1422-0067}, support = {ANR-11-LABX-0057_MITOCROSS//Agence Nationale de la Recherche/ ; }, mesh = {*DNA Repair ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; *Genome, Mitochondrial ; *Genome, Plant ; Genomic Instability ; Mitochondria/genetics ; Plants/*genetics ; }, abstract = {The mitochondrion stands at the center of cell energy metabolism. It contains its own genome, the mtDNA, that is a relic of its prokaryotic symbiotic ancestor. In plants, the mitochondrial genetic information influences important agronomic traits including fertility, plant vigor, chloroplast function, and cross-compatibility. Plant mtDNA has remarkable characteristics: It is much larger than the mtDNA of other eukaryotes and evolves very rapidly in structure. This is because of recombination activities that generate alternative mtDNA configurations, an important reservoir of genetic diversity that promotes rapid mtDNA evolution. On the other hand, the high incidence of ectopic recombination leads to mtDNA instability and the expression of gene chimeras, with potential deleterious effects. In contrast to the structural plasticity of the genome, in most plant species the mtDNA coding sequences evolve very slowly, even if the organization of the genome is highly variable. Repair mechanisms are probably responsible for such low mutation rates, in particular repair by homologous recombination. Herein we review some of the characteristics of plant organellar genomes and of the repair pathways found in plant mitochondria. We further discuss how homologous recombination is involved in the evolution of the plant mtDNA.}, }
@article {pmid31945484, year = {2020}, author = {Huo, LJ and Yang, MC and Wang, JX and Shi, XZ}, title = {Mitochondrial ATPase inhibitor factor 1, MjATPIF1, is beneficial for WSSV replication in kuruma shrimp (Marsupenaeus japonicus).}, journal = {Fish &amp; shellfish immunology}, volume = {98}, number = {}, pages = {245-254}, doi = {10.1016/j.fsi.2020.01.019}, pmid = {31945484}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Arthropod Proteins/genetics/*metabolism ; Gene Expression Regulation ; Hemocytes/metabolism ; Mitochondria/metabolism ; NF-kappa B/genetics/metabolism ; Penaeidae/classification/genetics/*virology ; Phylogeny ; Proteins/genetics/*metabolism ; Recombinant Proteins/genetics/metabolism/pharmacology ; Sequence Alignment ; Superoxides/metabolism ; Survival Rate ; Tissue Distribution ; Virus Replication/drug effects ; White spot syndrome virus 1/*physiology ; ATPase Inhibitory Protein ; }, abstract = {ATPase Inhibitory Factor 1 (IF1) is a mitochondrial protein that functions as a physiological inhibitor of F1F0-ATP synthase. In the present study, a mitochondrial ATPase inhibitor factor 1 (MjATPIF1) was identified from kuruma shrimp (Marsupenaeus japonicus), which was demonstrated to participate in the viral immune reaction of white spot syndrome virus (WSSV). MjATPIF1 contained a mitochondrial ATPase inhibitor (IATP) domain, and was widely distributed in hemocytes, heart, hepatopancreas, gills, stomach, and intestine of shrimp. MjATPIF1 transcription was upregulated in hemocytes and intestines by WSSV. WSSV replication decreased after MjATPIF1 knockdown by RNA interference and increased following recombinant MjATPIF1 protein injection. Further study found that MjATPIF1 promoted the production of superoxide and activated the transcription factor nuclear factor kappa B (NF-κB, Dorsal) to induce the transcription of WSSV RNAs. These results demonstrate that MjATPIF1 benefits WSSV replication in kuruma shrimp by inducing superoxide production and NF-κB activation.}, }
@article {pmid31943222, year = {2020}, author = {Zhou, F and Pichersky, E}, title = {The complete functional characterisation of the terpene synthase family in tomato.}, journal = {The New phytologist}, volume = {226}, number = {5}, pages = {1341-1360}, pmid = {31943222}, issn = {1469-8137}, mesh = {*Alkyl and Aryl Transferases/genetics ; Evolution, Molecular ; *Solanum lycopersicum/genetics ; Monoterpenes ; Phylogeny ; Terpenes ; }, abstract = {Analysis of the updated reference tomato genome found 34 full-length TPS genes and 18 TPS pseudogenes. Biochemical analysis has now identified the catalytic activities of all enzymes encoded by the 34 TPS genes: one isoprene synthase, 10 exclusively or predominantly monoterpene synthases, 17 sesquiterpene synthases and six diterpene synthases. Among the monoterpene and sesquiterpene and diterpene synthases, some use trans-prenyl diphosphates, some use cis-prenyl diphosphates and some use both. The isoprene synthase is cytosolic; six monoterpene synthases are plastidic, and four are cytosolic; the sesquiterpene synthases are almost all cytosolic, with the exception of one found in the mitochondria; and three diterpene synthases are found in the plastids, one in the cytosol and two in the mitochondria. New trans-prenyltransferases (TPTs) were characterised; together with previously characterised TPTs and cis-prenyltransferases (CPTs), tomato plants can make all cis and trans C10 , C15 and C20 prenyl diphosphates. Every type of plant tissue examined expresses some TPS genes and some TPTs and CPTs. Phylogenetic comparison of the TPS genes from tomato and Arabidopsis shows expansions in each clade of the TPS gene family in each lineage (and inferred losses), accompanied by changes in subcellular localisations and substrate specificities.}, }
@article {pmid31940908, year = {2020}, author = {Liu, W and Cai, Y and Zhang, Q and Shu, F and Chen, L and Ma, X and Bian, Y}, title = {Subchromosome-Scale Nuclear and Complete Mitochondrial Genome Characteristics of Morchella crassipes.}, journal = {International journal of molecular sciences}, volume = {21}, number = {2}, pages = {}, pmid = {31940908}, issn = {1422-0067}, mesh = {Ascomycota/genetics/*growth &amp; development ; Chromosome Mapping/*methods ; Gene Expression Regulation, Fungal ; Genome Size ; Genome, Fungal ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Phylogeny ; Whole Genome Sequencing/*methods ; }, abstract = {Morchella crassipes (Vent.) Pers., a typical yellow morel species with high economic value, is mainly distributed in the low altitude plains of Eurasia. However, rare research has been performed on its genomics and polarity, thus limiting its research and development. Here, we reported a fine physical map of the nuclear genome at the subchromosomal-scale and the complete mitochondrial genome of M. crassipes. The complete size of the nuclear genome was 56.7 Mb, and 23 scaffolds were assembled, with eight of them being complete chromosomes. A total of 11,565 encoding proteins were predicted. The divergence time analysis showed that M. crassipes representing yellow morels differentiated with black morels at ~33.98 Mya (million years), with 150 gene families contracted and expanded in M. crassipes versus the two black morels (M. snyderi and M. importuna). Furthermore, 409 CAZYme genes were annotated in M. crassipes, containing almost all plant cell wall degrading enzymes compared with the mycorrhizal fungi (truffles). Genomic annotation of mating type loci and amplification of the mating genes in the monospore population was conducted, the results indicated that M. crassipes is a heterothallic fungus. Additionally, a complete circular mitochondrial genome of M. crassipes was assembled, the size reached as large as 531,195 bp. It can be observed that the strikingly large size was the biggest up till now, coupled with 14 core conserved mitochondrial protein-coding genes, two rRNAs, 31 tRNAs, 51 introns, and 412 ncORFs. The total length of intron sequences accounted for 53.67% of the mitochondrial genome, with 19 introns having a length over 5 kb. Particularly, 221 of 412 ncORFs were distributed within 51 introns, and the total length of the ncORFs sequence accounted for 40.83% of the mitochondrial genome, and 297 ncORFs had expression activity in the mycelium stage, suggesting their potential functions in M. crassipes. Meanwhile, there was a high degree of repetition (51.31%) in the mitochondria of M. crassipes. Thus, the large number of introns, ncORFs and internal repeat sequences may contribute jointly to the largest fungal mitochondrial genome to date. The fine physical maps of nuclear genome and mitochondrial genome obtained in this study will open a new door for better understanding of the mysterious species of M. crassipes.}, }
@article {pmid31939618, year = {2020}, author = {Ding, Y and Ye, YF and Li, MY and Xia, BH and Leng, JH}, title = {Mitochondrial tRNAAla 5601C&gt;T variant may affect the clinical expression of the LHON‑related ND4 11778G&gt;A mutation in a family.}, journal = {Molecular medicine reports}, volume = {21}, number = {1}, pages = {201-208}, pmid = {31939618}, issn = {1791-3004}, mesh = {Adolescent ; Adult ; Asian People/genetics ; Child ; Computational Biology ; DNA, Mitochondrial/*genetics ; Family ; Female ; Humans ; Male ; Middle Aged ; Mitochondria/*genetics ; Mutation ; NADH Dehydrogenase/*genetics ; Optic Atrophy, Hereditary, Leber/blood/*genetics/metabolism/pathology ; Pedigree ; Penetrance ; Phylogeny ; Polymorphism, Genetic ; RNA, Transfer, Ala/chemistry/*genetics ; }, abstract = {Certain mutations in mitochondrial DNA (mtDNA) are associated with Leber's hereditary optic neuropathy (LHON). In particular, the well‑known NADH dehydrogenase 4 (ND4) m.11778G>A mutation is one of the most common LHON‑associated primary mutations worldwide. However, how specific mtDNA mutations, or variants, affect LHON penetrance is not fully understood. The aim of the current study was to explore the relationship between mtDNA mutations and LHON, and to provide useful information for early detection and prevention of this disease. Following the molecular characterization of a Han Chinese family with maternally inherited LHON, four out of eight matrilineal relatives demonstrated varying degrees of both visual impairment and age of onset. Through PCR amplification of mitochondrial genomes and direct Sanger sequencing analysis, a homoplasmic mitochondrial‑encoded ND4 m.11778G>A mutation, alongside a set of genetic variations belonging to human mtDNA haplogroup B5b1 were identified. Among these sequence variants, alanine transfer RNA (tRNA)Ala m.5601C>T was of particular interest. This variant occurred at position 59 in the TψC loop and altered the base pairing, which led to mitochondrial RNA (mt‑RNA) metabolism failure and defects in mitochondrial protein synthesis. Bioinformatics analysis suggested that the m.5601C>T variant altered tRNAAla structure. Therefore, impaired mitochondrial functions caused by the ND4 m.11778G>A mutation may be enhanced by the mt‑tRNAAla m.5601C>T variant. These findings suggested that the tRNAAla m.5601C>T variant might modulate the clinical manifestation of the LHON‑associated primary mutation.}, }
@article {pmid31937820, year = {2020}, author = {Tikochinski, Y and Carreras, C and Tikochinski, G and Vilaça, ST}, title = {Population-specific signatures of intra-individual mitochondrial DNA heteroplasmy and their potential evolutionary advantages.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {211}, pmid = {31937820}, issn = {2045-2322}, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; *Genetics, Population ; Haplotypes ; High-Throughput Nucleotide Sequencing/methods ; Inheritance Patterns ; Mitochondria/*genetics ; Sequence Analysis, DNA/methods ; Turtles/*genetics ; }, abstract = {Heteroplasmy is the existence of more than one mitochondrial DNA (mtDNA) variant within a cell. The evolutionary mechanisms of heteroplasmy are not fully understood, despite being a very common phenomenon. Here we combined heteroplasmy measurements using high throughput sequencing on green turtles (Chelonia mydas) with simulations to understand how heteroplasmy modulates population diversity across generations and under different demographic scenarios. We found heteroplasmy to be widespread in all individuals analysed, with consistent signal in individuals across time and tissue. Significant shifts in haplotype composition were found from mother to offspring, signalling the effect of the cellular bottleneck during oogenesis as included in the model. Our model of mtDNA inheritance indicated that heteroplasmy favoured the increase of population diversity through time and buffered against population bottlenecks, thus indicating the importance of this phenomenon in species with reduced population sizes and frequent population bottlenecks like marine turtles. Individuals with recent haplotypes showed higher levels of heteroplasmy than the individuals with ancient haplotypes, suggesting a potential advantage of maintaining established copies when new mutations arise. We recommend using heteroplasmy through high throughput sequencing in marine turtles, as well as other wildlife populations, for diversity assessment, population genetics, and mixed stock analysis.}, }
@article {pmid31936803, year = {2020}, author = {Wagner, JT and Howe, DK and Estes, S and Denver, DR}, title = {Mitochondrial DNA Variation and Selfish Propagation Following Experimental Bottlenecking in Two Distantly Related Caenorhabditis briggsae Isolates.}, journal = {Genes}, volume = {11}, number = {1}, pages = {}, pmid = {31936803}, issn = {2073-4425}, support = {GM087628/NH/NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/*genetics/metabolism ; Base Sequence/genetics ; Caenorhabditis/*genetics ; DNA Copy Number Variations/genetics ; DNA, Mitochondrial/genetics ; Gene Deletion ; Genetic Variation/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Mutation/genetics ; NADH Dehydrogenase/*genetics/metabolism ; Phylogeny ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Analysis, DNA/methods ; Sequence Deletion/genetics ; }, abstract = {Understanding mitochondrial DNA (mtDNA) evolution and inheritance has broad implications for animal speciation and human disease models. However, few natural models exist that can simultaneously represent mtDNA transmission bias, mutation, and copy number variation. Certain isolates of the nematode Caenorhabditis briggsae harbor large, naturally-occurring mtDNA deletions of several hundred basepairs affecting the NADH dehydrogenase subunit 5 (nduo-5) gene that can be functionally detrimental. These deletion variants can behave as selfish DNA elements under genetic drift conditions, but whether all of these large deletion variants are transmitted in the same preferential manner remains unclear. In addition, the degree to which transgenerational mtDNA evolution profiles are shared between isolates that differ in their propensity to accumulate the nduo-5 deletion is also unclear. We address these knowledge gaps by experimentally bottlenecking two isolates of C. briggsae with different nduo-5 deletion frequencies for up to 50 generations and performing total DNA sequencing to identify mtDNA variation. We observed multiple mutation profile differences and similarities between C. briggsae isolates, a potentially species-specific pattern of copy number dysregulation, and some evidence for genetic hitchhiking in the deletion-bearing isolate. Our results further support C. briggsae as a practical model for characterizing naturally-occurring mtgenome variation and contribute to the understanding of how mtgenome variation persists in animal populations and how it presents in mitochondrial disease states.}, }
@article {pmid31932637, year = {2020}, author = {Kadarusman,  and Sugeha, HY and Pouyaud, L and Hocdé, R and Hismayasari, IB and Gunaisah, E and Widiarto, SB and Arafat, G and Widyasari, F and Mouillot, D and Paradis, E}, title = {A thirteen-million-year divergence between two lineages of Indonesian coelacanths.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {192}, pmid = {31932637}, issn = {2045-2322}, mesh = {Animals ; *Cell Lineage ; DNA, Mitochondrial/analysis/genetics ; *Evolution, Molecular ; Fishes/classification/*genetics ; *Genetic Variation ; *Genome, Mitochondrial ; Indonesia ; Mitochondria/*genetics ; Species Specificity ; }, abstract = {Coelacanth fishes of the genus Latimeria are the only surviving representatives of a basal lineage of vertebrates that originated more than 400 million years ago. Yet, much remains to be unveiled about the diversity and evolutionary history of these 'living fossils' using new molecular data, including the possibility of 'cryptic' species or unknown lineages. Here, we report the discovery of a new specimen in eastern Indonesia allegedly belonging to the species L. menadoensis. Although this specimen was found about 750 km from the known geographical distribution of the species, we found that the molecular divergence between this specimen and others of L. menadoensis was great: 1.8% compared to 0.04% among individuals of L. chalumnae, the other living species of coelacanth. Molecular dating analyses suggested a divergence date of ca. 13 million years ago between the two populations of Indonesian coelacanths. We elaborate a biogeographical scenario to explain the observed genetic divergence of Indonesian coelacanth populations based on oceanic currents and the tectonic history of the region over Miocene to recent. We hypothesize that several populations of coelacanths are likely to live further east of the present capture location, with potentially a new species that remains to be described. Based on this, we call for an international effort to take appropriate measures to protect these fascinating but vulnerable vertebrates which represent among the longest branches on the Tree of Life.}, }
@article {pmid31932444, year = {2020}, author = {Le, T and Žárský, V and Nývltová, E and Rada, P and Harant, K and Vancová, M and Verner, Z and Hrdý, I and Tachezy, J}, title = {Anaerobic peroxisomes in Mastigamoeba balamuthi.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {4}, pages = {2065-2075}, pmid = {31932444}, issn = {1091-6490}, mesh = {Anaerobiosis ; Archamoebae/genetics/*metabolism ; Mitochondria/genetics/metabolism ; Oxidation-Reduction ; Peroxins/genetics/metabolism ; Peroxisomes/genetics/*metabolism ; Protozoan Proteins/genetics/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {The adaptation of eukaryotic cells to anaerobic conditions is reflected by substantial changes to mitochondrial metabolism and functional reduction. Hydrogenosomes belong among the most modified mitochondrial derivative and generate molecular hydrogen concomitant with ATP synthesis. The reduction of mitochondria is frequently associated with loss of peroxisomes, which compartmentalize pathways that generate reactive oxygen species (ROS) and thus protect against cellular damage. The biogenesis and function of peroxisomes are tightly coupled with mitochondria. These organelles share fission machinery components, oxidative metabolism pathways, ROS scavenging activities, and some metabolites. The loss of peroxisomes in eukaryotes with reduced mitochondria is thus not unexpected. Surprisingly, we identified peroxisomes in the anaerobic, hydrogenosome-bearing protist Mastigamoeba balamuthi We found a conserved set of peroxin (Pex) proteins that are required for protein import, peroxisomal growth, and division. Key membrane-associated Pexs (MbPex3, MbPex11, and MbPex14) were visualized in numerous vesicles distinct from hydrogenosomes, the endoplasmic reticulum (ER), and Golgi complex. Proteomic analysis of cellular fractions and prediction of peroxisomal targeting signals (PTS1/PTS2) identified 51 putative peroxisomal matrix proteins. Expression of selected proteins in Saccharomyces cerevisiae revealed specific targeting to peroxisomes. The matrix proteins identified included components of acyl-CoA and carbohydrate metabolism and pyrimidine and CoA biosynthesis, whereas no components related to either β-oxidation or catalase were present. In conclusion, we identified a subclass of peroxisomes, named "anaerobic" peroxisomes that shift the current paradigm and turn attention to the reductive evolution of peroxisomes in anaerobic organisms.}, }
@article {pmid31931136, year = {2020}, author = {Gautério, TB and Machado, S and Loreto, ELDS and Gottschalk, MS and Robe, LJ}, title = {Phylogenetic relationships between fungus-associated Neotropical species of the genera Hirtodrosophila, Mycodrosophila and Zygothrica (Diptera, Drosophilidae), with insights into the evolution of breeding sites usage.}, journal = {Molecular phylogenetics and evolution}, volume = {145}, number = {}, pages = {106733}, doi = {10.1016/j.ympev.2020.106733}, pmid = {31931136}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Breeding ; Cell Nucleus/genetics ; Dopa Decarboxylase/classification/genetics ; Drosophila/genetics ; Drosophilidae/*classification/genetics/growth &amp; development ; Electron Transport Complex IV/classification/genetics ; Fungi/*physiology ; Mitochondria/genetics ; Phylogeny ; }, abstract = {The Neotropical region harbors an astonishing diversity of species, but still encompasses the least studied biogeographic region of the world. These properties apply for different taxonomic groups, and can be exemplified by drosophilids. In fact, high levels of cryptic diversity have recently been discovered for Neotropical species of the Zygothrica genus group, but relationships among these species, or them and other Drosophilidae species still remains to be addressed. Therefore, the aim of this study was to evaluate the phylogenetic relationships between fungus-associated Neotropical species of the genera Hirtodrosophila, Mycodrosophila and Zygothrica, which together with Paramycodrosophila and Paraliodrosophila compose the Zygothrica genus group. For this, fragments of the mitochondrial cytochrome oxidase subunits I (COI) and II (COII) genes, and the nuclear alpha methyldopa (Amd) and dopa decarboxylase (Ddc) genes were newly characterized for 43 Neotropical specimens of fungus-associated drosophilids, and analyzed in the context of 51 additional Drosophilinae sequences plus one Steganinae outgroup. Based on the resulting phylogeny, the evolution of breeding sites usage was also evaluated through ancestral character reconstructions. Our results revealed the Zygothrica genus group as a monophyletic lineage of Drosophila that branches after the subgenera Sophophora and Drosophila. Within this lineage, Mycodrosophila species seem to encompass the early offshoot, followed by a grade of Hirtodrosophila species, with derived branches mostly occupied by representatives of Zygothrica. This genus, in particular, was subdivided into five major clades, two of which include species of Hirtodrosophila, whose generic status needs to be reevatuated. According to our results, the use of fungi as breeding sites encompasses a symplesiomorphy for the Zygothrica genus group, since one of the recovered clades is currently specialized in using flowers as breeding sites whereas a sole species presents a reversal to the use of fruits of a plant of Gentianales. So, in general, this study supports the paraphyly of Drosophila in relation to fungus-associated Neotropical species of Drosophilidae, providing the first molecular insights into the phylogenetic patterns related to the evolution of this diverse group of species and some of its characteristic traits.}, }
@article {pmid31928187, year = {2020}, author = {Jastroch, M and Seebacher, F}, title = {Importance of adipocyte browning in the evolution of endothermy.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1793}, pages = {20190134}, pmid = {31928187}, issn = {1471-2970}, mesh = {Adipocytes/*physiology ; Adipose Tissue, Brown/*physiology ; Adipose Tissue, White/*physiology ; Animals ; *Biological Evolution ; Birds/physiology ; Mammals/*physiology ; *Thermogenesis ; }, abstract = {Endothermy changes the relationship between organisms and their environment fundamentally, and it is therefore of major ecological and evolutionary significance. Endothermy is characterized by non-shivering thermogenesis, that is metabolic heat production in the absence of muscular activity. In many eutherian mammals, brown adipose tissue (BAT) is an evolutionary innovation that facilitates non-shivering heat production in mitochondria by uncoupling food-derived substrate oxidation from chemical energy (ATP) production. Consequently, energy turnover is accelerated resulting in increased heat release. The defining characteristics of BAT are high contents of mitochondria and vascularization, and the presence of uncoupling protein 1. Recent insights, however, reveal that a range of stimuli such as exercise, diet and the immune system can cause the browning of white adipocytes, thereby increasing energy expenditure and heat production even in the absence of BAT. Here, we review the molecular mechanisms that cause browning of white adipose tissue, and their potential contribution to thermoregulation. The significance for palaeophysiology lies in the presence of adipose tissue and the mechanisms that cause its browning and uncoupling in all amniotes. Hence, adipocytes may have played a role in the evolution of endothermy beyond the more specific evolution of BAT in eutherians. This article is part of the theme issue 'Vertebrate palaeophysiology'.}, }
@article {pmid31919449, year = {2020}, author = {De Pierri, CR and Voyceik, R and Santos de Mattos, LGC and Kulik, MG and Camargo, JO and Repula de Oliveira, AM and de Lima Nichio, BT and Marchaukoski, JN and da Silva Filho, AC and Guizelini, D and Ortega, JM and Pedrosa, FO and Raittz, RT}, title = {SWeeP: representing large biological sequences datasets in compact vectors.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {91}, pmid = {31919449}, issn = {2045-2322}, mesh = {Algorithms ; Bacterial Proteins/genetics/*metabolism ; Computational Biology/*methods ; Datasets as Topic ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Phylogeny ; Proteome/*analysis ; Sequence Alignment ; *Software ; }, abstract = {Vectoral and alignment-free approaches to biological sequence representation have been explored in bioinformatics to efficiently handle big data. Even so, most current methods involve sequence comparisons via alignment-based heuristics and fail when applied to the analysis of large data sets. Here, we present "Spaced Words Projection (SWeeP)", a method for representing biological sequences using relatively small vectors while preserving intersequence comparability. SWeeP uses spaced-words by scanning the sequences and generating indices to create a higher-dimensional vector that is later projected onto a smaller randomly oriented orthonormal base. We constructed phylogenetic trees for all organisms with mitochondrial and bacterial protein data in the NCBI database. SWeeP quickly built complete and accurate trees for these organisms with low computational cost. We compared SWeeP to other alignment-free methods and Sweep was 10 to 100 times quicker than the other techniques. A tool to build SWeeP vectors is available at https://sourceforge.net/projects/spacedwordsprojection/.}, }
@article {pmid31915815, year = {2020}, author = {Zumkeller, S and Gerke, P and Knoop, V}, title = {A functional twintron, 'zombie' twintrons and a hypermobile group II intron invading itself in plant mitochondria.}, journal = {Nucleic acids research}, volume = {48}, number = {5}, pages = {2661-2675}, pmid = {31915815}, issn = {1362-4962}, mesh = {Base Sequence ; Conserved Sequence/genetics ; Evolution, Molecular ; Hepatophyta/genetics ; Introns/*genetics ; Lycopodiaceae/*genetics ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; Terminology as Topic ; }, abstract = {The occurrence of group II introns in plant mitochondrial genomes is strikingly different between the six major land plant clades, contrasting their highly conserved counterparts in chloroplast DNA. Their present distribution likely reflects numerous ancient intron gains and losses during early plant evolution before the emergence of seed plants. As a novelty for plant organelles, we here report on five cases of twintrons, introns-within-introns, in the mitogenomes of lycophytes and hornworts. An internal group II intron interrupts an intron-borne maturase of an atp9 intron in Lycopodiaceae, whose splicing precedes splicing of the external intron. An invasive, hypermobile group II intron in cox1, has conquered nine further locations including a previously overlooked sdh3 intron and, most surprisingly, also itself. In those cases, splicing of the external introns does not depend on splicing of the internal introns. Similar cases are identified in the mtDNAs of hornworts. Although disrupting a group I intron-encoded protein in one case, we could not detect splicing of the internal group II intron in this 'mixed' group I/II twintron. We suggest the name 'zombie' twintrons (half-dead, half-alive) for such cases where splicing of external introns does not depend any more on prior splicing of fossilized internal introns.}, }
@article {pmid31915577, year = {2020}, author = {Repetti, SI and Jackson, CJ and Judd, LM and Wick, RR and Holt, KE and Verbruggen, H}, title = {The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e8273}, pmid = {31915577}, issn = {2167-8359}, abstract = {Within the siphonous green algal order Bryopsidales, the size and gene arrangement of chloroplast genomes has been examined extensively, while mitochondrial genomes have been mostly overlooked. The recently published mitochondrial genome of Caulerpa lentillifera is large with expanded noncoding DNA, but it remains unclear if this is characteristic of the entire order. Our study aims to evaluate the evolutionary forces shaping organelle genome dynamics in the Bryopsidales based on the C. lentillifera and Ostreobium quekettii mitochondrial genomes. In this study, the mitochondrial genome of O. quekettii was characterised using a combination of long and short read sequencing, and bioinformatic tools for annotation and sequence analyses. We compared the mitochondrial and chloroplast genomes of O. quekettii and C. lentillifera to examine hypotheses related to genome evolution. The O. quekettii mitochondrial genome is the largest green algal mitochondrial genome sequenced (241,739 bp), considerably larger than its chloroplast genome. As with the mtDNA of C. lentillifera, most of this excess size is from the expansion of intergenic DNA and proliferation of introns. Inflated mitochondrial genomes in the Bryopsidales suggest effective population size, recombination and/or mutation rate, influenced by nuclear-encoded proteins, differ between the genomes of mitochondria and chloroplasts, reducing the strength of selection to influence evolution of their mitochondrial genomes.}, }
@article {pmid31914665, year = {2020}, author = {Draper, ACE and Wilson, Z and Maile, C and Faccenda, D and Campanella, M and Piercy, RJ}, title = {Species-specific consequences of an E40K missense mutation in superoxide dismutase 1 (SOD1).}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {34}, number = {1}, pages = {458-473}, doi = {10.1096/fj.201901455R}, pmid = {31914665}, issn = {1530-6860}, mesh = {Adenosine Triphosphate/*metabolism ; Amyotrophic Lateral Sclerosis/genetics/metabolism/*pathology ; Animals ; Dogs ; Horses ; Humans ; Mitochondria/*metabolism/pathology ; *Mutation, Missense ; Phylogeny ; Species Specificity ; Superoxide Dismutase-1/*genetics ; Transgenes/*physiology ; }, abstract = {A glutamic acid to lysine (E40K) residue substitution in superoxide dismutase 1 (SOD1) is associated with canine degenerative myelopathy: the only naturally occurring large animal model of amyotrophic lateral sclerosis (ALS). The E40 residue is highly conserved across mammals, except the horse, which naturally carries the (dog mutant) K40 residue. Here we hypothesized that in vitro expression of mutant dog SOD1 would recapitulate features of human ALS (ie, SOD1 protein aggregation, reduced cell viability, perturbations in mitochondrial morphology and membrane potential, reduced ATP production, and increased superoxide ion levels); further, we hypothesized that an equivalent equine SOD1 variant would share similar perturbations in vitro, thereby explain horses' susceptibility to certain neurodegenerative diseases. As in human ALS, expression of mutant dog SOD1 was associated with statistically significant increased aggregate formation, raised superoxide levels (ROS), and altered mitochondrial morphology (increased branching (form factor)), when compared to wild-type dog SOD1-expressing cells. Similar deficits were not detected in cells expressing the equivalent horse SOD1 variant. Our data helps explain the ALS-associated cellular phenotype of dogs expressing the mutant SOD1 protein and reveals that species-specific sequence conservation does not necessarily predict pathogenicity. The work improves understanding of the etiopathogenesis of canine degenerative myelopathy.}, }
@article {pmid31914602, year = {2020}, author = {Nagao, T and Shintani, Y and Hayashi, T and Kioka, H and Kato, H and Nishida, Y and Yamazaki, S and Tsukamoto, O and Yashirogi, S and Yazawa, I and Asano, Y and Shinzawa-Itoh, K and Imamura, H and Suzuki, T and Suzuki, T and Goto, YI and Takashima, S}, title = {Higd1a improves respiratory function in the models of mitochondrial disorder.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {34}, number = {1}, pages = {1859-1871}, doi = {10.1096/fj.201800389R}, pmid = {31914602}, issn = {1530-6860}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Animals, Genetically Modified ; Biological Transport/physiology ; Cell Line ; Cytochromes c/metabolism ; Electron Transport/*physiology ; Electron Transport Complex IV/metabolism ; HEK293 Cells ; Humans ; Hypoxia/metabolism ; Intracellular Signaling Peptides and Proteins/*metabolism ; Kinetics ; Mitochondria/*metabolism ; Mitochondrial Diseases/*metabolism ; Mitochondrial Proteins/*metabolism ; Oxidation-Reduction ; Respiration ; Zebrafish/metabolism ; }, abstract = {The respiratory chain (RC) transports electrons to form a proton motive force that is required for ATP synthesis in the mitochondria. RC disorders cause mitochondrial diseases that have few effective treatments; therefore, novel therapeutic strategies are critically needed. We previously identified Higd1a as a positive regulator of cytochrome c oxidase (CcO) in the RC. Here, we test that Higd1a has a beneficial effect by increasing CcO activity in the models of mitochondrial dysfunction. We first demonstrated the tissue-protective effects of Higd1a via in situ measurement of mitochondrial ATP concentrations ([ATP]mito) in a zebrafish hypoxia model. Heart-specific Higd1a overexpression mitigated the decline in [ATP]mito under hypoxia and preserved cardiac function in zebrafish. Based on the in vivo results, we examined the effects of exogenous HIGD1A on three cellular models of mitochondrial disease; notably, HIGD1A improved respiratory function that was coupled with increased ATP synthesis and demonstrated cellular protection in all three models. Finally, enzyme kinetic analysis revealed that Higd1a significantly increased the maximal velocity of the reaction between CcO and cytochrome c without changing the affinity between them, indicating that Higd1a is a positive modulator of CcO. These results corroborate that Higd1a, or its mimic, provides therapeutic options for the treatment of mitochondrial diseases.}, }
@article {pmid31912331, year = {2020}, author = {Wallace, R}, title = {On the Variety of Cognitive Temperatures and Their Symmetry-Breaking Dynamics.}, journal = {Acta biotheoretica}, volume = {68}, number = {4}, pages = {421-439}, doi = {10.1007/s10441-019-09375-7}, pmid = {31912331}, issn = {1572-8358}, mesh = {Adenosine Diphosphate/chemistry ; Adenosine Triphosphate/chemistry ; Animals ; Biological Evolution ; Cognition/*physiology ; Consciousness ; DNA ; Humans ; Hydrolysis ; Mitochondria/physiology ; Models, Biological ; Normal Distribution ; Probability ; Temperature ; Thermodynamics ; }, abstract = {The asymptotic limit theorems of information and control theories permit exploration of a surprising number of temperature-like measures and symmetry-breaking dynamics associated with cognition. Each of several markedly different perspectives produces a distinct temperature-analog, capturing a rich and highly-punctuated behavioral landscape across the complex, hierarchical cognitive phenomena that characterize life at every scale and level of organization. Theories of cognition may be confronted by canonical conundrums similar to those plaguing the study of consciousness and its regulation. In short, there may be a spectrum of interacting cognitive 'temperatures' for organisms, social structures, institutions, information processing machines, and their composite entities, that varies across different systems, and between similar systems having undergone different individual developmental trajectories. The complexities of cognitive failure-leading to a vast array of pathologies-may be far stranger than generally recognized.}, }
@article {pmid31904510, year = {2020}, author = {Kaczmarek, &#x141; and Roszkowska, M and Poprawa, I and Janelt, K and Kmita, H and Gawlak, M and Fiałkowska, E and Mioduchowska, M}, title = {Integrative description of bisexual Paramacrobiotus experimentalis sp. nov. (Macrobiotidae) from republic of Madagascar (Africa) with microbiome analysis.}, journal = {Molecular phylogenetics and evolution}, volume = {145}, number = {}, pages = {106730}, doi = {10.1016/j.ympev.2019.106730}, pmid = {31904510}, issn = {1095-9513}, mesh = {Animals ; Bacteroides/genetics/isolation &amp; purification ; DNA, Bacterial/chemistry/metabolism ; Electron Transport Complex IV/classification/genetics ; Female ; Madagascar ; Male ; *Microbiota ; Mitochondria/genetics ; Phylogeny ; Proteobacteria/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/chemistry/genetics ; RNA, Ribosomal, 18S/classification/genetics ; Symbiosis ; Tardigrada/*classification/genetics/microbiology ; }, abstract = {In a moss samples collected on Madagascar two populations of Paramacrobiotus experimentalis sp. nov. were found. Paramacrobiotus experimentalis sp. nov. with the presence of a microplacoid and areolatus type of eggs is similar to Pam. danielae, Pam. garynahi, Pam. hapukuensis, Pam. peteri, Pam. rioplatensis and Pam. savai, but it differs from them by some morphological and morphometric characters of the eggs. The p-distance between two COI haplotypes of Pam. experimentalis sp. nov. was 0.17%. In turn, the ranges of uncorrected genetic p-distances of all Paramacrobiotus species available in GenBank was from 18.27% (for Pam. lachowskae) to 25.26% (for Pam. arduus) with an average distance of 20.67%. We also found that Pam. experimentalis sp. nov. is bisexual. This observation was congruent on three levels: (i) morphological - specimen size dimorphism; (ii) structural (primary sexual characteristics) - females have an unpaired ovary while males have an unpaired testis and (iii) molecular - heterozygous and homozygous strains of the ITS-2 marker. Although symbiotic associations of hosts with bacteria (including endosymbiotic bacteria) are common in nature and these interactions exert various effects on the evolution, biology and reproductive ecology of hosts, there is still very little information on the bacterial community associated with tardigrades. To fill this gap and characterise the bacterial community of Pam. experimentalis sp. nov. populations and microbiome of its microhabitat, high throughput sequencing of the V3-V4 hypervariable regions in the bacterial 16S rRNA gene fragment was performed. The obtained 16S rRNA gene sequences ranged from 92,665 to 131,163. In total, 135 operational taxonomic units (OTUs) were identified across the rarefied dataset. Overall, both Pam. experimentalis sp. nov. populations were dominated by OTUs ascribed to the phylum Proteobacteria (89-92%) and Firmicutes (6-7%). In the case of samples from tardigrades' laboratory habitat, the most abundant bacterial phylum was Proteobacteria (51-90%) and Bacteroides (9-48%). In all compared microbiome profiles, only 16 of 137 OTUs were shared. We found also significant differences in beta diversity between the partly species-specific microbiome of Pam. experimentalis sp. nov. and its culturing environment. Two OTUs belonging to a putative bacterial endosymbiont were identified - Rickettsiales and Polynucleobacter. We also demonstrated that each bacterial community was rich in genes involved in membrane transport, amino acid metabolism, and carbohydrate metabolism.}, }
@article {pmid31901107, year = {2020}, author = {Yoneva, A and Kuchta, R and Smit, N}, title = {Ultrastructure of the uterus, embryonic envelopes and the coracidium of the enigmatic tapeworm Tetracampos ciliotheca (Cestoda: Bothriocephalidea) from African sharptooth catfish (Clarias gariepinus).}, journal = {Parasitology research}, volume = {119}, number = {3}, pages = {847-858}, pmid = {31901107}, issn = {1432-1955}, mesh = {Animals ; Catfishes/*parasitology ; Cestoda/physiology/*ultrastructure ; Cestode Infections/parasitology/*veterinary ; Female ; Fish Diseases/*parasitology ; Larva/ultrastructure ; Microscopy, Electron, Transmission ; Ovum/ultrastructure ; Uterus/ultrastructure ; }, abstract = {Transmission electron microscopy (TEM) was used to study the ultrastructure of the uterus and egg morphology in the enigmatic bothriocephalidean tapeworm Tetracampos ciliotheca. The uterine wall, underlain by well-developed muscle bundles, consists of a syncytial epithelium which is characterized by the abundance of free ribosomes, mitochondria and cisternae of granular endoplasmic reticulum (GER). On the apical surface of the uterine epithelium, there is an abundant network of cytoplasmic microlamellae projecting into the uterine lumen. The lumen is filled with freely lying eggs which are located close to the uterine wall but do not contact with the microlamellae of the uterine epithelium. The developed eggs possess an oncosphere surrounded by four envelopes: (1) a thin egg shell; (2) an outer envelope; (3) a syncytial, ciliated inner envelope; and (4) the oncospheral membrane. The mature hexacanth is armed with three pairs of oncospheral hooks, as well as somatic and hook muscles and five types of cells (1) binucleated subtegumental cell, (2) somatic cells, (3) penetration gland cells, (4) nerve cells and (5) germinative cells. Considering the relative scarcity of descriptive and comparative studies on the ultrastructure of the uterus and egg morphology in the order Bothriocephalidea, we concluded that Tet. ciliotheca displays a unique type of egg development. Based on these results, we discuss plausible ideas relating to the function of these structures for consideration in future studies.}, }
@article {pmid31894631, year = {2020}, author = {Ghemari, C and Jelassi, R and Khemaissia, H and Waterlot, C and Raimond, M and Souty-Grosset, C and Douay, F and Nasri-Ammar, K}, title = {Physiological and histopathological responses of Porcellio laevis (Isopoda, Crustacea) as indicators of metal trace element contamination.}, journal = {Microscopy research and technique}, volume = {83}, number = {4}, pages = {402-409}, doi = {10.1002/jemt.23428}, pmid = {31894631}, issn = {1097-0029}, mesh = {Animals ; Bioaccumulation ; Biological Monitoring ; Cadmium/*toxicity ; Hepatopancreas/drug effects/*pathology ; Isopoda/*drug effects ; Metals/analysis ; Microscopy, Electron, Transmission ; Plant Leaves ; Quercus ; Soil/chemistry ; Trace Elements/*toxicity ; Zinc/*toxicity ; }, abstract = {This study was designed to assess the impact of the mixture of cadmium (Cd) and zinc (Zn) on the bioaccumulation and the ultrastructural changes in the hepatopancreas of Porcellio laevis (Latreille, 1804) after 4 weeks of exposure to contaminated Quercus leaves under laboratory conditions. For each metal, four concentrations were used with four replicates for each concentration. Metal concentrations in the hepatopancreas and the rest of the body were determined using atomic absorption spectrometry. From the first week until the end of the experiment, a weight gain in P. laevis was observed particularly between the first and the end of exposure from 93.3 ± 18.22 mg fw to 105.22 ± 16.16 mg fw and from 106.4 ± 22.67 mg fw to 125.9 ± 23.9 mg fw for Mix1 and Mix4, respectively. Additionally, the determined metal trace elements (MTE) concentrations in the hepatopancreas were considerably higher compared to those in the rest of the body and seem to be dose-dependent. Using transmission electron microscopy (TEM), some alterations were highlighted in the hepatopancreas. The main observed alterations were (a) the destruction of the microvilli border in a considerable portion of cells, (b) the increase of the lipid droplets with different shapes and sizes, (c) the increase in the number of the mitochondria, and (d) the appearance of TE in the form of B-type granules. The obtained results confirmed the ability of P. laevis to deal with high amounts of MTE, suggesting its possible use in future soil's biomonitoring programs.}, }
@article {pmid31891638, year = {2019}, author = {Tamaki, S and Nishino, K and Ogawa, T and Maruta, T and Sawa, Y and Arakawa, K and Ishikawa, T}, title = {Comparative proteomic analysis of mitochondria isolated from Euglena gracilis under aerobic and hypoxic conditions.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0227226}, pmid = {31891638}, issn = {1932-6203}, mesh = {Anaerobiosis ; Cell Hypoxia ; Esters/metabolism ; Euglena gracilis/*metabolism ; Fermentation ; Mitochondria/*metabolism ; Proteome/*metabolism ; Proteomics ; }, abstract = {The unicellular microalga Euglena gracilis produces wax esters for ATP acquisition under low-oxygen conditions. The regulatory mechanism of wax ester production is not yet understood. Indeed, our previous transcriptomic analysis showed that transcript levels of genes involved in the wax ester synthesis hardly changed under hypoxic conditions, suggesting contribution of post-transcriptional regulation. In this study, we conducted a proteome analysis of E. gracilis mitochondria, as this organelle employs the fatty-acid synthesis pathway under hypoxic conditions. Mitochondria were isolated from E. gracilis SM-ZK strain treated with both aerobic and hypoxic conditions and used for shotgun proteomic analysis. Three independent proteomic analyses succeeded in identifying a total of 714 non-redundant proteins. Of these, 229 were detected in common to all experiments, and 116 were significantly recognized as differentially expressed proteins. GO enrichment analysis suggested dynamic changes in mitochondrial metabolic pathways and redox reactions under aerobic and hypoxic conditions. Protein levels of bifunctional enzymes isocitrate lyase and malate synthase in glyoxylate cycle were 1.35-fold higher under hypoxic conditions. Abundances of the propionyl-CoA synthetic enzymes, succinyl-CoA synthetase and propionyl-CoA carboxylase, were also 1.35- and 1.47-fold higher, respectively, under hypoxic conditions. Protein levels of pyruvate:NADP+ oxidoreductase, a key enzyme for anaerobic synthesis of acetyl-CoA, which serves as a C2 donor for fatty acids, showed a 1.68-fold increase under hypoxic conditions, whereas those of pyruvate dehydrogenase subunits showed a 0.77-0.81-fold decrease. Protein levels of the fatty-acid synthesis enzymes, 3-ketoacyl-CoA thiolase isoforms (KAT1 and KAT2), 3-hydroxyacyl-CoA dehydrogenases, and acyl-CoA dehydrogenase were up-regulated by 1.20- to 1.42-fold in response to hypoxic treatment. Overall, our proteomic analysis revealed that wax ester synthesis-related enzymes are up-regulated at the protein level post-transcriptionally to promote wax ester production in E. gracilis under low-oxygen conditions.}, }
@article {pmid31888949, year = {2020}, author = {Sun, S and Fu, C and Ianiri, G and Heitman, J}, title = {The Pheromone and Pheromone Receptor Mating-Type Locus Is Involved in Controlling Uniparental Mitochondrial Inheritance in Cryptococcus.}, journal = {Genetics}, volume = {214}, number = {3}, pages = {703-717}, pmid = {31888949}, issn = {1943-2631}, support = {R01 AI050113/AI/NIAID NIH HHS/United States ; R01 AI133654/AI/NIAID NIH HHS/United States ; R37 AI039115/AI/NIAID NIH HHS/United States ; }, mesh = {Cryptococcus neoformans/*genetics/pathogenicity ; Evolution, Molecular ; Fungal Proteins/genetics ; Genes, Mating Type, Fungal/*genetics ; Humans ; Mitochondria ; *Pheromones ; Receptors, Pheromone/*genetics ; Reproduction/genetics ; }, abstract = {Mitochondria are inherited uniparentally during sexual reproduction in the majority of eukaryotic species studied, including humans, mice, and nematodes, as well as many fungal species. Mitochondrial uniparental inheritance (mito-UPI) could be beneficial in that it avoids possible genetic conflicts between organelles with different genetic backgrounds, as recently shown in mice, and it could prevent the spread of selfish genetic elements in the mitochondrial genome. Despite the prevalence of observed mito-UPI, the underlying mechanisms and the genes involved in controlling this non-Mendelian inheritance are poorly understood in many species. In Cryptococcus neoformans, a human pathogenic basidiomyceteous fungus, mating types (MATα and MATa) are defined by alternate alleles at the single MAT locus that evolved from fusion of the two MAT loci (P/R encoding pheromones and pheromone receptors, and HD encoding homeodomain transcription factors) that are the ancestral state in the basidiomycota. Mitochondria are inherited uniparentally from the MATa parent in C. neoformans, and this requires the SXI1α and SXI2a HD factors encoded by MAT However, there is evidence that additional genes contribute to the control of mito-UPI in Cryptococcus Here, we show that in C. amylolentus, a sibling species of C. neoformans with unlinked P/R and HD MAT loci, mito-UPI is controlled by the P/R locus and is independent of the HD locus. Consistently, by replacing the MATα alleles of the pheromones (MF) and pheromone receptor (STE3) with the MATa alleles, we show that these P/R locus-defining genes indeed affect mito-UPI in C. neoformans during sexual reproduction. Additionally, we show that during early stages of C. neoformans sexual reproduction, conjugation tubes are always produced by the MATα cells, resulting in unidirectional migration of the MATα nucleus into the MATa cell during zygote formation. This process is controlled by the P/R locus and could serve to physically restrict movement of MATα mitochondria in the zygotes, and thereby contribute to mito-UPI. We propose a model in which both physical and genetic mechanisms function in concert to prevent the coexistence of mitochondria from the two parents in the zygote, and subsequently in the meiotic progeny, thus ensuring mito-UPI in pathogenic Cryptococcus, as well as in closely related nonpathogenic species. The implications of these findings are discussed in the context of the evolution of mito-UPI in fungi and other more diverse eukaryotes.}, }
@article {pmid31888438, year = {2019}, author = {Lichtblau, D}, title = {Alignment-free genomic sequence comparison using FCGR and signal processing.}, journal = {BMC bioinformatics}, volume = {20}, number = {1}, pages = {742}, pmid = {31888438}, issn = {1471-2105}, mesh = {Animals ; Genomics/*methods ; Humans ; Influenza A virus/classification ; Mitochondria/classification ; Phylogeny ; *Software ; }, abstract = {BACKGROUND: Alignment-free methods of genomic comparison offer the possibility of scaling to large data sets of nucleotide sequences comprised of several thousand or more base pairs. Such methods can be used for purposes of deducing "nearby" species in a reference data set, or for constructing phylogenetic trees.<br><br>RESULTS: We describe one such method that gives quite strong results. We use the Frequency Chaos Game Representation (FCGR) to create images from such sequences, We then reduce dimension, first using a Fourier trig transform, followed by a Singular Values Decomposition (SVD). This gives vectors of modest length. These in turn are used for fast sequence lookup, construction of phylogenetic trees, and classification of virus genomic data. We illustrate the accuracy and scalability of this approach on several benchmark test sets.<br><br>CONCLUSIONS: The tandem of FCGR and dimension reductions using Fourier-type transforms and SVD provides a powerful approach for alignment-free genomic comparison. Results compare favorably and often surpass best results reported in prior literature. Good scalability is also observed.}, }
@article {pmid31886415, year = {2019}, author = {Kato, S and Okamura, E and Matsunaga, TM and Nakayama, M and Kawanishi, Y and Ichinose, T and Iwane, AH and Sakamoto, T and Imoto, Y and Ohnuma, M and Nomura, Y and Nakagami, H and Kuroiwa, H and Kuroiwa, T and Matsunaga, S}, title = {Cyanidioschyzon merolae aurora kinase phosphorylates evolutionarily conserved sites on its target to regulate mitochondrial division.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {477}, pmid = {31886415}, issn = {2399-3642}, mesh = {Aurora Kinases/chemistry/*genetics/*metabolism ; *Biological Evolution ; Mitochondria/*genetics/*metabolism ; Mitosis ; Phosphorylation ; Rhodophyta/enzymology/*genetics/*metabolism ; Substrate Specificity ; }, abstract = {The mitochondrion is an organelle that was derived from an endosymbiosis. Although regulation of mitochondrial growth by the host cell is necessary for the maintenance of mitochondria, it is unclear how this regulatory mechanism was acquired. To address this, we studied the primitive unicellular red alga Cyanidioschyzon merolae, which has the simplest eukaryotic genome and a single mitochondrion. Here we show that the C. merolae Aurora kinase ortholog CmAUR regulates mitochondrial division through phosphorylation of mitochondrial division ring components. One of the components, the Drp1 ortholog CmDnm1, has at least four sites phosphorylated by CmAUR. Depletion of the phosphorylation site conserved among eukaryotes induced defects such as mitochondrial distribution on one side of the cell. Taken together with the observation that human Aurora kinase phosphorylates Drp1 in vitro, we suggest that the phosphoregulation is conserved from the simplest eukaryotes to mammals, and was acquired at the primitive stage of endosymbiosis.}, }
@article {pmid31886178, year = {2019}, author = {Mereu, P and Pirastru, M and Satta, V and Frongia, GN and Kassinis, N and Papadopoulos, M and Hadjisterkotis, E and Xirouchakis, S and Manca, L and Naitana, S and Leoni, GG}, title = {Mitochondrial D-loop Sequence Variability in Three Native Insular Griffon Vulture (Gyps fulvus) Populations from the Mediterranean Basin.}, journal = {BioMed research international}, volume = {2019}, number = {}, pages = {2073919}, pmid = {31886178}, issn = {2314-6141}, mesh = {Animals ; Birds/*genetics ; *Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Endangered Species ; Genetic Variation/*genetics ; Genetics, Population ; Haplotypes/genetics ; Humans ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {The islands of Sardinia, Crete, and Cyprus are hosting the last native insular griffon populations in the Mediterranean basin. Their states have been evaluated from "vulnerable" to "critically endangered". The sequence analysis of molecular markers, particularly the mtDNA D-loop region, provides useful information in studying the evolution of closely related taxa and the conservation of endangered species. Therefore, a study of D-loop region sequence was carried out to estimate the genetic diversity and phylogenetic relationship within and among these three populations. Among 84 griffon specimens (44 Sardinian, 33 Cretan, and 7 Cypriot), we detected four haplotypes including a novel haplotype (HPT-D) that was exclusively found in the Cretan population with a frequency of 6.1%. When considered as a unique population, haplotype diversity (Hd) and nucleotide diversity (π) were high at 0.474 and 0.00176, respectively. A similar level of Hd and π was found in Sardinian and Cretan populations, both showing three haplotypes. The different haplotype frequencies and exclusivity detected were in accordance with the limited matrilineal gene flow (FST = 0.07097), probably related to the species reluctance to fly over sea masses. The genetic variability we observe today would therefore be the result of an evolutionary process strongly influenced by isolation leading to the appearance of island variants which deserve to be protected. Furthermore, since nesting sites and food availability are essential elements for colony settlement, we may infer that the island's colonization began when the first domestic animals were transferred by humans during the Neolithic. In conclusion, our research presents a first contribution to the genetic characterization of the griffon vulture populations in the Mediterranean islands of Sardinia, Crete and Cyprus and lays the foundation for conservation and restocking programs.}, }
@article {pmid31884104, year = {2020}, author = {Al-Eitan, L and Saadeh, H and Alnaamneh, A and Darabseh, S and Al-Sarhan, N and Alzihlif, M and Hakooz, N and Ivanova, E and Kelsey, G and Dajani, R}, title = {The genetic landscape of Arab Population, Chechens and Circassians subpopulations from Jordan through HV1 and HV2 regions of mtDNA.}, journal = {Gene}, volume = {729}, number = {}, pages = {144314}, doi = {10.1016/j.gene.2019.144314}, pmid = {31884104}, issn = {1879-0038}, mesh = {Arabs/*genetics ; DNA, Mitochondrial/*genetics ; Ethnicity/*genetics ; Female ; Genetic Variation/genetics ; Genetics, Population/methods ; Haplotypes/genetics ; Humans ; Jordan/epidemiology ; Male ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Mitochondrial DNA (mtDNA) is widely used in several fields including medical genetics, forensic science, genetic genealogy, and evolutionary anthropology. In this study, mtDNA haplotype diversity was determined for 293 unrelated subjects from Jordanian population (Circassians, Chechens, and the original inhabitants of Jordan). A total of 102 haplotypes were identified and analyzed among the populations to describe the maternal lineage landscape. Our results revealed that the distribution of mtDNA haplotype frequencies among the three populations showed disparity and significant differences when compared to each other. We also constructed mitochondrial haplotype classification trees for the three populations to determine the phylogenetic relationship of mtDNA haplotype variants, and we observed clear differences in the distribution of maternal genetic ancestries, especially between Arab and the minority ethnic populations. To our knowledge, this study is the first, to date, to characterize mitochondrial haplotypes and haplotype distributions in a population-based sample from the Jordanian population. It provides a powerful reference for future studies investigating the contribution of mtDNA variation to human health and disease and studying population history and evolution by comparing the mtDNA haplotypes to other populations.}, }
@article {pmid31883789, year = {2020}, author = {Namba, T and Dóczi, J and Pinson, A and Xing, L and Kalebic, N and Wilsch-Bräuninger, M and Long, KR and Vaid, S and Lauer, J and Bogdanova, A and Borgonovo, B and Shevchenko, A and Keller, P and Drechsel, D and Kurzchalia, T and Wimberger, P and Chinopoulos, C and Huttner, WB}, title = {Human-Specific ARHGAP11B Acts in Mitochondria to Expand Neocortical Progenitors by Glutaminolysis.}, journal = {Neuron}, volume = {105}, number = {5}, pages = {867-881.e9}, doi = {10.1016/j.neuron.2019.11.027}, pmid = {31883789}, issn = {1097-4199}, support = {MR/R006237/1/MRC_/Medical Research Council/United Kingdom ; MR/S025065/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {3T3 Cells ; Animals ; Biological Evolution ; Cell Proliferation/genetics ; Citric Acid Cycle ; GTPase-Activating Proteins/genetics/*metabolism ; Gene Expression Regulation, Developmental/genetics ; Glutamic Acid/metabolism ; Glutamine/*metabolism ; Humans ; Mice ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/metabolism ; Mitochondrial Membrane Transport Proteins/metabolism ; Mitochondrial Permeability Transition Pore ; Neocortex/embryology/*metabolism ; Neural Stem Cells/*metabolism ; Neurogenesis/genetics ; }, abstract = {The human-specific gene ARHGAP11B is preferentially expressed in neural progenitors of fetal human neocortex and increases abundance and proliferation of basal progenitors (BPs), which have a key role in neocortex expansion. ARHGAP11B has therefore been implicated in the evolutionary expansion of the human neocortex, but its mode of action has been unknown. Here, we show that ARHGAP11B is imported into mitochondria, where it interacts with the adenine nucleotide translocase (ANT) and inhibits the mitochondrial permeability transition pore (mPTP). BP expansion by ARHGAP11B requires its presence in mitochondria, and pharmacological inhibition of ANT function or mPTP opening mimic BP expansion by ARHGAP11B. Searching for the underlying metabolic basis, we find that BP expansion by ARHGAP11B requires glutaminolysis, the conversion of glutamine to glutamate for the tricarboxylic acid (TCA) cycle. Hence, an ARHGAP11B-induced, mitochondria-based effect on BP metabolism that is a hallmark of highly mitotically active cells appears to underlie its role in neocortex expansion.}, }
@article {pmid31881988, year = {2019}, author = {Liu, Y and Qu, J and Zhang, L and Xu, X and Wei, G and Zhao, Z and Ren, M and Cao, M}, title = {Identification and characterization of the TCA cycle genes in maize.}, journal = {BMC plant biology}, volume = {19}, number = {1}, pages = {592}, pmid = {31881988}, issn = {1471-2229}, support = {2016YFD0101206//National Key Research and Development Program of China/ ; NASC2019TI13//Chengdu Agricultural Science and Technology Center local financial special fund project/ ; 19-001-09//Fundamental Research Funds for the Central Institutes/ ; }, mesh = {Amino Acid Sequence ; Arabidopsis/genetics ; Citric Acid Cycle/*genetics ; Computational Biology ; *Genes, Plant ; Solanum lycopersicum/genetics ; Phylogeny ; Plant Proteins/genetics ; Sequence Alignment ; Transcriptome ; Zea mays/*genetics/metabolism ; }, abstract = {BACKGROUND: The tricarboxylic acid (TCA) cycle is crucial for cellular energy metabolism and carbon skeleton supply. However, the detailed functions of the maize TCA cycle genes remain unclear.<br><br>RESULTS: In this study, 91 TCA genes were identified in maize by a homology search, and they were distributed on 10 chromosomes and 1 contig. Phylogenetic results showed that almost all maize TCA genes could be classified into eight major clades according to their enzyme families. Sequence alignment revealed that several genes in the same subunit shared high protein sequence similarity. The results of cis-acting element analysis suggested that several TCA genes might be involved in signal transduction and plant growth. Expression profile analysis showed that many maize TCA cycle genes were expressed in specific tissues, and replicate genes always shared similar expression patterns. Moreover, qPCR analysis revealed that some TCA genes were highly expressed in the anthers at the microspore meiosis phase. In addition, we predicted the potential interaction networks among the maize TCA genes. Next, we cloned five TCA genes located on different TCA enzyme complexes, Zm00001d008244 (isocitrate dehydrogenase, IDH), Zm00001d017258 (succinyl-CoA synthetase, SCoAL), Zm00001d025258 (&#x3b1;-ketoglutarate dehydrogenase, &#x3b1;KGDH), Zm00001d027558 (aconitase, ACO) and Zm00001d044042 (malate dehydrogenase, MDH). Confocal observation showed that their protein products were mainly localized to the mitochondria; however, Zm00001d025258 and Zm00001d027558 were also distributed in the nucleus, and Zm00001d017258 and Zm00001d044042 were also located in other unknown positions in the cytoplasm. Through the bimolecular fluorescent complimentary (BiFC) method, it was determined that Zm00001d027558 and Zm00001d044042 could form homologous dimers, and both homologous dimers were mainly distributed in the mitochondria. However, no heterodimers were detected between these five genes. Finally, Arabidopsis lines overexpressing the above five genes were constructed, and those transgenic lines exhibited altered primary root length, salt tolerance, and fertility.<br><br>CONCLUSION: Sequence compositions, duplication patterns, phylogenetic relationships, cis-elements, expression patterns, and interaction networks were investigated for all maize TCA cycle genes. Five maize TCA genes were overexpressed in Arabidopsis, and they could alter primary root length, salt tolerance, and fertility. In conclusion, our findings may help to reveal the molecular function of the TCA genes in maize.}, }
@article {pmid31881218, year = {2020}, author = {Ji, SG and Medvedeva, YV and Weiss, JH}, title = {Zn[2+] entry through the mitochondrial calcium uniporter is a critical contributor to mitochondrial dysfunction and neurodegeneration.}, journal = {Experimental neurology}, volume = {325}, number = {}, pages = {113161}, pmid = {31881218}, issn = {1090-2430}, support = {R21 NS096987/NS/NINDS NIH HHS/United States ; R56 NS100494/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Brain/metabolism/pathology ; Calcium Channels/*metabolism ; Dizocilpine Maleate/pharmacology ; Mice ; Mice, Knockout ; Mitochondria/drug effects/*metabolism ; Mitochondrial Proteins/*metabolism ; Nerve Degeneration/*metabolism/pathology ; Neurons/drug effects/*metabolism/pathology ; Neuroprotective Agents/pharmacology ; Zinc/*metabolism ; }, abstract = {Excitotoxic Ca[2+] accumulation contributes to ischemic neurodegeneration, and Ca[2+] can enter the mitochondria through the mitochondrial calcium uniporter (MCU) to promote mitochondrial dysfunction. Yet, Ca[2+]-targeted therapies have met limited success. A growing body of evidence has highlighted the underappreciated importance of Zn[2+], which also accumulates in neurons after ischemia and can induce mitochondrial dysfunction and cell death. While studies have indicated that Zn[2+] can also enter the mitochondria through the MCU, the specificity of the pore's role in Zn[2+]-triggered injury is still debated. Present studies use recently available MCU knockout mice to examine how the deletion of this channel impacts deleterious effects of cytosolic Zn[2+] loading. In cultured cortical neurons from MCU knockout mice, we find significantly reduced mitochondrial Zn[2+] accumulation. Correspondingly, these neurons were protected from both acute and delayed Zn[2+]-triggered mitochondrial dysfunction, including mitochondrial reactive oxygen species generation, depolarization, swelling and inhibition of respiration. Furthermore, when toxic extramitochondrial effects of Ca[2+] entry were moderated, both cultured neurons (exposed to Zn[2+]) and CA1 neurons of hippocampal slices (subjected to prolonged oxygen glucose deprivation to model ischemia) from MCU knockout mice displayed decreased neurodegeneration. Finally, to examine the therapeutic applicability of these findings, we added an MCU blocker after toxic Zn[2+] exposure in wildtype neurons (to induce post-insult MCU blockade). This significantly attenuated the delayed evolution of both mitochondrial dysfunction and neurotoxicity. These data-combining both genetic and pharmacologic tools-support the hypothesis that Zn[2+] entry through the MCU is a critical contributor to ischemic neurodegeneration that could be targeted for neuroprotection.}, }
@article {pmid31873127, year = {2019}, author = {Terrien, J and Seugnet, I and Seffou, B and Herrero, MJ and Bowers, J and Chamas, L and Decherf, S and Duvernois-Berthet, E and Djediat, C and Ducos, B and Demeneix, BA and Clerget-Froidevaux, MS}, title = {Reduced central and peripheral inflammatory responses and increased mitochondrial activity contribute to diet-induced obesity resistance in WSB/EiJ mice.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19696}, pmid = {31873127}, issn = {2045-2322}, mesh = {Animals ; Cytokines/blood ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Energy Metabolism ; Hypothalamus/metabolism/pathology ; Inflammation/genetics/*metabolism ; Inflammation Mediators/metabolism ; Leptin/blood ; Lipid Metabolism ; Male ; Metabolic Networks and Pathways ; Mice ; Mice, Inbred C57BL ; Mitochondria/*metabolism/pathology ; Mitochondrial Dynamics ; Obesity/*etiology/genetics/*metabolism ; Paraventricular Hypothalamic Nucleus/metabolism/pathology ; Species Specificity ; Transcriptome ; }, abstract = {Energy imbalance due to excess of calories is considered to be a major player in the current worldwide obesity pandemic and could be accompanied by systemic and central inflammation and mitochondrial dysfunctions. This hypothesis was tested by comparing the wild-derived diet-induced obesity- (DIO-) resistant mouse strain WSB/EiJ to the obesity-prone C57BL/6J strain. We analysed circulating and hypothalamic markers of inflammatory status and hypothalamic mitochondrial activity in both strains exposed to high-fat diet (HFD). We further analysed the regulations of hypothalamic genes involved in inflammation and mitochondrial pathways by high throughput microfluidic qPCR on RNA extracted from laser micro-dissected arcuate (ARC) and paraventricular (PVN) hypothalamic nuclei. HFD induced increased body weight gain, circulating levels of leptin, cholesterol, HDL and LDL in C57BL/6J whereas WSB/EiJ mice displayed a lower inflammatory status, both peripherally (lower levels of circulating cytokines) and centrally (less activated microglia in the hypothalamus) as well as more reactive mitochondria in the hypothalamus. The gene expression data analysis allowed identifying strain-specific hypothalamic metabolic pathways involved in the respective responses to HFD. Our results point to the involvement of hypothalamic inflammatory and mitochondrial pathways as key factors in the control of energy homeostasis and the resistance to DIO.}, }
@article {pmid31865652, year = {2019}, author = {Hamamcı, B and Açıkgöz, G and Kılıç, E and Karaaslan, K and Çetinkaya, &#xdc; and Durgun Yetim, T and Yetim, &#x130;}, title = {Biochemical Analysis of Germinal Membrane and Cyst Fluid by Raman Spectroscopy in Echinococcosis.}, journal = {Turkiye parazitolojii dergisi}, volume = {43}, number = {4}, pages = {175-181}, doi = {10.4274/tpd.galenos.2019.6293}, pmid = {31865652}, issn = {2146-3077}, mesh = {Animals ; Cyst Fluid/chemistry ; DNA, Helminth/chemistry ; Echinococcosis, Hepatic/*diagnostic imaging/parasitology ; Echinococcus granulosus/*classification/genetics ; Electron Transport Complex IV/genetics ; Humans ; Mitochondria/enzymology ; Phylogeny ; Polymerase Chain Reaction ; Spectrum Analysis, Raman ; Zoonoses/*diagnostic imaging/parasitology ; }, abstract = {OBJECTIVE: Hydatidosis is a zoonotic parasitic infection caused by the larval stage of Echinococcus granulosus. The aim of this study was to investigate the biochemical structures of germinal membrane and cyst fluids obtained from patients with liver involvement during surgery, by Raman spectroscopy at the molecular level.<br><br>METHODS: Molecular characterization of germinal membrane and cyst fluid according to mitochondrial gene region was determined and phylogenetic analysis was performed. Raman spectroscopy was used in samples and spectral bands between 300 and 1800 cm[-1] were examined.<br><br>RESULTS: As a result of PCR, approximately 400 bp DNA band was obtained from germinal membranes and cyst fluids gathered from patients. Peaks were observed at 780, 880, 970, 1151, 1200, 1270 cm[-1] for germinal membrane and at 780 and 1200 cm[-1] for cyst fluid. The highest spectral bands were obtained at 1333-1335 cm[-1] and were determined to be modes indicating the CH3CH2 collagen and polynucleotide chain.<br><br>CONCLUSION: In the identification of microorganisms and biochemical analysis of biological tissues; different diagnostic methods such as molecular, serological and conventional methods are used. In addition to these methods, Raman spectroscopy has been shown in studies to be a fast, non-destructive and noninvasive method. Therefore, it is thought to be an alternative method for analyzing the basic biochemical components of microorganisms at molecular level.}, }
@article {pmid31863129, year = {2020}, author = {Padmanabhan, R and Sarcar, SN and Miller, DL}, title = {Promoter Length Affects the Initiation of T7 RNA Polymerase In Vitro: New Insights into Promoter/Polymerase Co-evolution.}, journal = {Journal of molecular evolution}, volume = {88}, number = {2}, pages = {179-193}, pmid = {31863129}, issn = {1432-1432}, mesh = {Bacteriophage T7/enzymology/genetics ; Base Sequence ; DNA-Directed RNA Polymerases/*genetics ; Mitochondria/enzymology/genetics ; Oligonucleotides/genetics ; *Promoter Regions, Genetic ; *Transcription, Genetic ; Viral Proteins/*genetics ; }, abstract = {Polymerases are integral factors of gene expression and are essential for the maintenance and transmission of genetic information. RNA polymerases (RNAPs) differ from other polymerases in that they can bind promoter sequences and initiate transcription de novo and this promoter recognition requires the presence of specific DNA binding domains in the polymerase. Bacteriophage T7 RNA polymerase (T7RNAP) is the prototype for single subunit RNA polymerases which include bacteriophage and mitochondrial RNAPs, and the structure and mechanistic aspects of transcription by T7 RNAP are well characterized. Here, we describe experiments to determine whether the prototype T7 RNAP is able to recognize and initiate at truncated promoters similar to mitochondrial promoters. Using an in vitro oligonucleotide transcriptional system, we have assayed transcription initiation activity by T7 RNAP. These assays have not only defined the limits of conventional de novo initiation on truncated promoters, but have identified novel activities of initiation of RNA synthesis. We propose that these novel activities may be vestigial activities surviving from the transition of single subunit polymerase initiation using primers to de novo initiation using promoters.}, }
@article {pmid31857199, year = {2020}, author = {Jardim de Queiroz, L and Cardoso, Y and Jacot-des-Combes, C and Bahechar, IA and Lucena, CA and Rapp Py-Daniel, L and Sarmento Soares, LM and Nylinder, S and Oliveira, C and Parente, TE and Torrente-Vilara, G and Covain, R and Buckup, P and Montoya-Burgos, JI}, title = {Evolutionary units delimitation and continental multilocus phylogeny of the hyperdiverse catfish genus Hypostomus.}, journal = {Molecular phylogenetics and evolution}, volume = {145}, number = {}, pages = {106711}, doi = {10.1016/j.ympev.2019.106711}, pmid = {31857199}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Catfishes/*classification/genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Membrane Proteins/genetics ; Mitochondria/genetics ; Nerve Tissue Proteins/genetics ; Phylogeny ; Species Specificity ; }, abstract = {With 149 currently recognized species, Hypostomus is one of the most species-rich catfish genera in the world, widely distributed over most of the Neotropical region. To clarify the evolutionary history of this genus, we reconstructed a comprehensive phylogeny of Hypostomus based on four nuclear and two mitochondrial markers. A total of 206 specimens collected from the main Neotropical rivers were included in the present study. Combining morphology and a Bayesian multispecies coalescent (MSC) approach, we recovered 85 previously recognized species plus 23 putative new species, organized into 118 'clusters'. We presented the Cluster Credibility (CC) index that provides numerical support for every hypothesis of cluster delimitation, facilitating delimitation decisions. We then examined the correspondence between the morphologically identified species and their inter-specific COI barcode pairwise divergence. The mean COI barcode divergence between morphological sisters species was 1.3 ± 1.2%, and only in 11% of the comparisons the divergence was ≥2%. This indicates that the COI barcode threshold of 2% classically used to delimit fish species would seriously underestimate the number of species in Hypostomus, advocating for a taxon-specific COI-based inter-specific divergence threshold to be used only when approximations of species richness are needed. The phylogeny of the 108 Hypostomus species, together with 35 additional outgroup species, confirms the monophyly of the genus. Four well-supported main lineages were retrieved, hereinafter called super-groups: Hypostomus cochliodon, H. hemiurus, H. auroguttatus, and H. plecostomus super-groups. We present a compilation of diagnostic characters for each super-group. Our phylogeny lays the foundation for future studies on biogeography and on macroevolution to better understand the successful radiation of this Neotropical fish genus.}, }
@article {pmid31856711, year = {2019}, author = {Guerra, D and Lopes-Lima, M and Froufe, E and Gan, HM and Ondina, P and Amaro, R and Klunzinger, MW and Callil, C and Prié, V and Bogan, AE and Stewart, DT and Breton, S}, title = {Variability of mitochondrial ORFans hints at possible differences in the system of doubly uniparental inheritance of mitochondria among families of freshwater mussels (Bivalvia: Unionida).}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {229}, pmid = {31856711}, issn = {1471-2148}, mesh = {Animals ; Bivalvia/*classification/cytology/*genetics ; DNA, Mitochondrial/genetics ; Fresh Water ; *Genome, Mitochondrial ; Mitochondrial Proteins/genetics ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Supernumerary ORFan genes (i.e., open reading frames without obvious homology to other genes) are present in the mitochondrial genomes of gonochoric freshwater mussels (Bivalvia: Unionida) showing doubly uniparental inheritance (DUI) of mitochondria. DUI is a system in which distinct female-transmitted and male-transmitted mitotypes coexist in a single species. In families Unionidae and Margaritiferidae, the transition from dioecy to hermaphroditism and the loss of DUI appear to be linked, and this event seems to affect the integrity of the ORFan genes. These observations led to the hypothesis that the ORFans have a role in DUI and/or sex determination. Complete mitochondrial genome sequences are however scarce for most families of freshwater mussels, therefore hindering a clear localization of DUI in the various lineages and a comprehensive understanding of the influence of the ORFans on DUI and sexual systems. Therefore, we sequenced and characterized eleven new mitogenomes from poorly sampled freshwater mussel families to gather information on the evolution and variability of the ORFan genes and their protein products.<br><br>RESULTS: We obtained ten complete plus one almost complete mitogenome sequence from ten representative species (gonochoric and hermaphroditic) of families Margaritiferidae, Hyriidae, Mulleriidae, and Iridinidae. ORFan genes are present only in DUI species from Margaritiferidae and Hyriidae, while non-DUI species from Hyriidae, Iridinidae, and Mulleriidae lack them completely, independently of their sexual system. Comparisons among the proteins translated from the newly characterized ORFans and already known ones provide evidence of conserved structures, as well as family-specific features.<br><br>CONCLUSIONS: The ORFan proteins show a comparable organization of secondary structures among different families of freshwater mussels, which supports a conserved physiological role, but also have distinctive family-specific features. Given this latter observation and the fact that the ORFans can be either highly mutated or completely absent in species that secondarily lost DUI depending on their respective family, we hypothesize that some aspects of the connection among ORFans, sexual systems, and DUI may differ in the various lineages of unionids.}, }
@article {pmid31855060, year = {2020}, author = {Sekar, D and Johnson, J and Biruntha, M and Lakhmanan, G and Gurunathan, D and Ross, K}, title = {Biological and Clinical Relevance of microRNAs in Mitochondrial Diseases/Dysfunctions.}, journal = {DNA and cell biology}, volume = {39}, number = {8}, pages = {1379-1384}, doi = {10.1089/dna.2019.5013}, pmid = {31855060}, issn = {1557-7430}, mesh = {Cell Differentiation/*genetics ; Gene Expression Regulation, Developmental/genetics ; Humans ; MicroRNAs/*genetics ; Mitochondria/*genetics ; Mitochondrial Diseases/*genetics ; RNA, Untranslated/genetics ; Signal Transduction/genetics ; }, abstract = {Mitochondrial dysfunction arises from an inadequate number of mitochondria, an inability to provide necessary substrates to mitochondria, or a dysfunction in their electron transport and a denosine triphosphate synthesis machinery. Occurrences of mitochondrial dysfunction are due to genetic or environmental changes in the mitochondria or in the nuclear DNA that codes mitochondrial components. Currently, drug options are available, yet no treatment exists in sight of this disease and needs a new insight into molecular and signaling pathways for this disease. microRNAs (miRNAs) are small, endogenous, and noncoding RNAs function as a master regulator of gene expression. The evolution of miRNAs in the past two decades emerged as a key regulator of gene expression that controls physiological pathological cellular differentiation processes, and metabolic homeostasis such as development and cancer. It has been known that miRNAs are a potential biomarker in both communicable and noncommunicable diseases. But, in the case of mitochondrial dysfunction in miRNAs, the number of studies and investigations are comparatively less than those on other diseases and dysfunctions. In this review, we have elaborated the roles of miRNAs in the mitochondrial diseases and dysfunctions.}, }
@article {pmid31851687, year = {2019}, author = {Barbosa, AD and Austen, J and Portas, TJ and Friend, JA and Ahlstrom, LA and Oskam, CL and Ryan, UM and Irwin, PJ}, title = {Sequence analyses at mitochondrial and nuclear loci reveal a novel Theileria sp. and aid in the phylogenetic resolution of piroplasms from Australian marsupials and ticks.}, journal = {PloS one}, volume = {14}, number = {12}, pages = {e0225822}, pmid = {31851687}, issn = {1932-6203}, mesh = {Animals ; Australia ; DNA, Protozoan/genetics ; Genetic Loci ; Marsupialia/*parasitology ; Mitochondria/*genetics ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/*genetics ; *Theileria/classification/genetics/isolation &amp; purification ; Theileriasis/*parasitology ; Ticks/*parasitology ; }, abstract = {The order Piroplasmida encompasses two main families: Babesiidae and Theileriidae, containing tick-borne pathogens of veterinary and medical importance worldwide. While only three genera (Babesia, Cytauxzoon and Theileria) comprising piroplasm parasites are currently recognised, phylogenetic studies at the 18S rRNA (18S) gene suggest that these organisms represent at least ten lineages, one of which comprises the relatively unique and highly diverse Theileria spp. from Australian marsupials and ticks. As an alternative to analysing 18S sequences alone, sequencing of mitochondrial genes has proven to be useful for the elucidation of evolutionary relationships amongst some groups of piroplasms. This research aimed to characterise piroplasms from Australian native mammals and ticks using multiple genetic markers (18S, cytochrome c, oxidase subunit III (cox3) and cytochrome B (cytB)) and microscopy. For this, nearly complete piroplasm-18S sequences were obtained from 32 animals belonging to six marsupial species: eastern bettong (Bettongia gaimardi), eastern quoll (Dasyurus viverrinus), eastern grey kangaroo (Macropus giganteus), swamp wallaby (Wallabia bicolor), quokka (Setonix brachyurus) and Gilbert's potoroo (Potorous gilbertii). The organisms detected represented eight novel Theileria genotypes, which formed five sub-clades within the main marsupial clade containing previously reported Australian marsupial and tick-derived Theileria spp. A selection of both novel and previously described Australian piroplasms at the 18S were also successfully characterised, for the first time, at the cox3 and cytB loci, and corroborated the position of Australian native theilerias in a separate, well-supported clade. Analyses of the cox3 and cytB genes also aided in the taxonomic resolution within the clade of Australian Piroplasmida. Importantly, microscopy and molecular analysis at multiple loci led to the discovery of a unique piroplasm species that clustered with the Australian marsupial theilerias, for which we propose the name Theileria lupei n. sp.}, }
@article {pmid31850200, year = {2019}, author = {Tomasetti, M and Gaetani, S and Monaco, F and Neuzil, J and Santarelli, L}, title = {Epigenetic Regulation of miRNA Expression in Malignant Mesothelioma: miRNAs as Biomarkers of Early Diagnosis and Therapy.}, journal = {Frontiers in oncology}, volume = {9}, number = {}, pages = {1293}, pmid = {31850200}, issn = {2234-943X}, abstract = {Asbestos exposure leads to epigenetic and epigenomic modifications that, in association with ROS-induced DNA damage, contribute to cancer onset. Few miRNAs epigenetically regulated in MM have been described in literature; miR-126, however, is one of them, and its expression is regulated by epigenetic mechanisms. Asbestos exposure induces early changes in the miRNAs, which are reversibly expressed as protective species, and their inability to reverse reflects the inability of the cells to restore the physiological miRNA levels despite the cessation of carcinogen exposure. Changes in miRNA expression, which results from genetic/epigenetic changes during tumor formation and evolution, can be detected in fluids and used as cancer biomarkers. This article has reviewed the epigenetic mechanisms involved in miRNA expression in MM, focusing on their role as biomarkers of early diagnosis and therapeutic effects.}, }
@article {pmid31842897, year = {2019}, author = {Souza, F and Rodrigues, R and Reis, E and Lima, M and La Scola, B and Abrahão, J}, title = {In-depth analysis of the replication cycle of Orpheovirus.}, journal = {Virology journal}, volume = {16}, number = {1}, pages = {158}, pmid = {31842897}, issn = {1743-422X}, mesh = {Antigens, Viral/analysis ; DNA Viruses/*growth &amp; development/ultrastructure ; Giant Viruses/*growth &amp; development/ultrastructure ; Lobosea/virology ; Microscopy ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Microscopy, Fluorescence ; Virion/chemistry/ultrastructure ; *Virus Replication ; }, abstract = {BACKGROUND: After the isolation of Acanthamoeba polyphaga mimivirus (APMV), the study and search for new giant viruses has been intensified. Most giant viruses are associated with free-living amoebae of the genus Acanthamoeba; however other giant viruses have been isolated in Vermamoeba vermiformis, such as Faustovirus, Kaumoebavirus and Orpheovirus. These studies have considerably expanded our knowledge about the diversity, structure, genomics, and evolution of giant viruses. Until now, there has been only one Orpheovirus isolate, and many aspects of its life cycle remain to be elucidated.<br><br>METHODS: In this study, we performed an in-depth characterization of the replication cycle and particles of Orpheovirus by transmission and scanning electron microscopy, optical microscopy and IF assays.<br><br>RESULTS: We observed, through optical and IF microscopy, morphological changes in V. vermiformis cells during Orpheovirus infection, as well as increased motility at 12&#x2009;h post infection (h.p.i.). The viral factory formation and viral particle morphogenesis were analysed by transmission electron microscopy, revealing mitochondria and membrane recruitment into and around the electron-lucent viral factories. Membrane traffic inhibitor (Brefeldin A) negatively impacted particle morphogenesis. The first structure observed during particle morphogenesis was crescent-shaped bodies, which extend and are filled by the internal content until the formation of multi-layered mature particles. We also observed the formation of defective particles with different shapes and sizes. Virological assays revealed that viruses are released from the host by exocytosis at 12&#x2009;h.p.i., which is associated with an increase of particle counts in the supernatant.<br><br>CONCLUSIONS: The results presented here contribute to a better understanding of the biology, structures and important steps in the replication cycle of Orpheovirus.}, }
@article {pmid31841597, year = {2019}, author = {Lareau, CA and Ludwig, LS and Sankaran, VG}, title = {Longitudinal assessment of clonal mosaicism in human hematopoiesis via mitochondrial mutation tracking.}, journal = {Blood advances}, volume = {3}, number = {24}, pages = {4161-4165}, pmid = {31841597}, issn = {2473-9537}, support = {F31 CA232670/CA/NCI NIH HHS/United States ; R01 DK103794/DK/NIDDK NIH HHS/United States ; R33 HL120791/HL/NHLBI NIH HHS/United States ; }, mesh = {Clonal Evolution/*genetics ; DNA, Mitochondrial ; Hematopoiesis/*genetics ; Hematopoietic Stem Cells/cytology/*metabolism ; Humans ; Mitochondria/*genetics ; *Mosaicism ; *Mutation ; }, abstract = {Our ability to track cellular dynamics in humans over time in vivo has been limited. Here, we demonstrate how somatic mutations in mitochondrial DNA (mtDNA) can be used to longitudinally track the dynamic output of hematopoietic stem and progenitor cells in humans. Over the course of 3 years of blood sampling in a single individual, our analyses reveal somatic mtDNA sequence variation and evolution reminiscent of models of hematopoiesis established by genetic labeling approaches. Furthermore, we observe fluctuations in mutation heteroplasmy, coinciding with specific clinical events, such as infections, and further identify lineage-specific somatic mtDNA mutations in longitudinally sampled circulating blood cell subsets in individuals with leukemia. Collectively, these observations indicate the significant potential of using tracking of somatic mtDNA sequence variation as a broadly applicable approach to systematically assess hematopoietic clonal dynamics in human health and disease.}, }
@article {pmid31841396, year = {2020}, author = {Showmaker, KC and Cobb, MB and Johnson, AC and Yang, W and Garrett, MR}, title = {Whole genome sequencing and novel candidate genes for CAKUT and altered nephrogenesis in the HSRA rat.}, journal = {Physiological genomics}, volume = {52}, number = {1}, pages = {56-70}, pmid = {31841396}, issn = {1531-2267}, support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; P20 GM104357/GM/NIGMS NIH HHS/United States ; P30 GM103328/GM/NIGMS NIH HHS/United States ; R01 HL137673/HL/NHLBI NIH HHS/United States ; P20 GM121334/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Chromosomes, Mammalian/genetics ; Disease Models, Animal ; *Genetic Association Studies ; *Genetic Predisposition to Disease ; Genome ; Genome, Mitochondrial ; Introns/genetics ; Mitochondria/genetics ; Nephrons/*embryology ; Organogenesis/*genetics ; Phylogeny ; Proto-Oncogene Proteins c-kit/metabolism ; Rats ; Urogenital Abnormalities/*genetics ; Vesico-Ureteral Reflux/*genetics ; *Whole Genome Sequencing ; }, abstract = {The HSRA rat is a model of congenital abnormalities of the kidney and urogenital tract (CAKUT). Our laboratory has used this model to investigate the role of nephron number (functional unit of the kidney) in susceptibility to develop kidney disease as 50-75% offspring are born with a single kidney (HSRA-S), while 25-50% are born with two kidneys (HSRA-C). HSRA-S rats develop increased kidney injury and hypertension with age compared with nephrectomized two-kidney animals (HSRA-UNX), suggesting that even slight differences in nephron number can be an important driver in decline in kidney function. The HSRA rat was selected and inbred from a family of outbred heterogeneous stock (NIH-HS) rats that exhibited a high incidence of CAKUT. The HS model was originally developed from eight inbred strains (ACI, BN, BUF, F344, M520, MR, WKY, and WN). The genetic make-up of the HSRA is therefore a mosaic of these eight inbred strains. Interestingly, the ACI progenitor of the HS model exhibits CAKUT in 10-15% of offspring with the genetic cause being attributed to the presence of a long-term repeat (LTR) within exon 1 of the c-Kit gene. Our hypothesis is that the HSRA and ACI share this common genetic cause, but other alleles in the HSRA genome contribute to the increased penetrance of CAKUT (75% HSRA vs. 15% in ACI). To facilitate genetic studies and better characterize the model, we sequenced the whole genome of the HSRA to a depth of ~50×. A genome-wide variant analysis of high-impact variants identified a number of novel genes that could be linked to CAKUT in the HSRA model. In summary, the identification of new genes/modifiers that lead to CAKUT/loss of one kidney in the HSRA model will provide greater insight into association between kidney development and susceptibility to develop cardiovascular disease later in life.}, }
@article {pmid31840782, year = {2019}, author = {Bloomfield, G}, title = {Sex and macrocyst formation in Dictyostelium.}, journal = {The International journal of developmental biology}, volume = {63}, number = {8-9-10}, pages = {439-446}, doi = {10.1387/ijdb.190183gb}, pmid = {31840782}, issn = {1696-3547}, mesh = {Cell Communication ; Cell Nucleus/metabolism ; Cytoplasm/metabolism ; Dictyostelium/*genetics/*physiology ; Genome ; Germ Cells/*physiology ; Haploidy ; Meiosis ; Mitochondria/metabolism ; Reproduction ; }, abstract = {Sex in Dictyostelia involves a remarkable form of cannibalism in which zygotes attract large numbers of surrounding amoebae and then ingest them. Before they are consumed, the attracted amoebae help the zygote by synthesising an outer wall around the aggregate that traps them inside and helps to protect the mature developed zygotic structure, the macrocyst. Competition between cells vying to contribute genetically to zygotes and through to the next generation seems likely to have promoted the evolution of several unusual features of dictyostelid sex: individual species often have more than two mating types, increasing haploid cells' chances of matching with a compatible partner, and fusion of many gametes to form transient syncytia allows cytoplasmic mixing and lateral transmission of mitochondrial genomes. This review will summarise recent advances in our understanding of mating-type determination, gamete fusion, and inheritance in Dictyostelium, and highlight the key gaps in our understanding of this fascinating set of phenomena.}, }
@article {pmid31830552, year = {2020}, author = {Lee, S and Lee, S}, title = {Multigene phylogeny uncovers oviposition-related evolutionary history of Cerambycinae (Coleoptera: Cerambycidae).}, journal = {Molecular phylogenetics and evolution}, volume = {145}, number = {}, pages = {106707}, doi = {10.1016/j.ympev.2019.106707}, pmid = {31830552}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Coleoptera/*classification/growth &amp; development ; Electron Transport Complex IV/genetics ; Female ; Mitochondria/genetics ; Oviposition/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The correlated evolution of the morphology of reproduction-related organs and biological aspects of insects is intriguing yet poorly understood. As one of the largest subfamilies of phytophagous beetles, Cerambycinae provides a unique opportunity to study this topic because of the wide range of host plants, oviposition strategies, and various forms of ovipositors of its members. Nevertheless, the evolutionary pathway of these traits is unexplored and no robust phylogenetic study of the subfamily has been conducted. In this study, we reconstructed a first multi-locus phylogeny of Cerambycinae representing a wide range of oviposition strategies, host plants, and ovipositor lengths. Ancestral state reconstruction analyses showed that the shortened ovipositor in Cerambycinae evolved at least four times independently and that the use of host plant has evolved from stressed hosts to dead or living hosts and from broad-leaved trees to conifers. The correlated evolution test revealed the correlation between ovipositor length and oviposition strategy. Our study elucidates for the first time the complex evolutionary history of the ovipositor, oviposition strategy, and host plant usage, and their correlations within Cerambycinae.}, }
@article {pmid31830457, year = {2020}, author = {Liu, W and Cai, Y and Zhang, Q and Chen, L and Shu, F and Ma, X and Bian, Y}, title = {The mitochondrial genome of Morchella importuna (272.2 kb) is the largest among fungi and contains numerous introns, mitochondrial non-conserved open reading frames and repetitive sequences.}, journal = {International journal of biological macromolecules}, volume = {143}, number = {}, pages = {373-381}, doi = {10.1016/j.ijbiomac.2019.12.056}, pmid = {31830457}, issn = {1879-0003}, mesh = {Ascomycota/classification/*genetics ; Genome, Mitochondrial/*genetics ; Introns/genetics ; Mitochondria/genetics ; *Molecular Sequence Annotation ; Open Reading Frames/genetics ; Phylogeny ; Repetitive Sequences, Nucleic Acid/genetics ; }, abstract = {The complete mitochondrial genome of Morchella importuna, the famous edible and medicinal mushroom, was assembled as a 272,238 bp single circular dsDNA. As the largest mitogenome among fungi, it exhibits several distinct characteristics. The mitogenome of M. importuna encoded 14 core conserved mitochondrial protein-coding genes and 151 mitochondrial non-conserved open reading frames (ncORFs) were predicted, of which 61 were annotated as homing endonuclease genes, and 108 were confirmed to be expressed during the vegetative growth stages of M. importuna. In addition, 34 introns were identified in seven core genes (cob, cox1, cox2, cox3, nad1, nad4 and nad5) and two rRNA genes (rrnS and rrnL) with a length from 383 bp to 7453 bp, and eight large introns with a length range of 2340 bp to 7453 bp contained multiple intronic mtORFs. Moreover, 34 group I (IA, IB, IC1, IC2, ID and derived group I introns) and four group II intron domains were identified for the 34 introns, including five hybrid ones. Furthermore, the M. importuna mitogenome showed the presence of about 18.7% mitogenomic interspersed repeats. These and the aforementioned ncORFs and introns, contributed to the enlarged size of the mitogenome.}, }
@article {pmid31827252, year = {2020}, author = {Demain, LAM and Gerkes, EH and Smith, RJH and Molina-Ramirez, LP and O'Keefe, RT and Newman, WG}, title = {A recurrent missense variant in HARS2 results in variable sensorineural hearing loss in three unrelated families.}, journal = {Journal of human genetics}, volume = {65}, number = {3}, pages = {305-311}, pmid = {31827252}, issn = {1435-232X}, support = {R01 DC012049/DC/NIDCD NIH HHS/United States ; }, mesh = {Alleles ; Amino Acyl-tRNA Synthetases/*genetics ; Child ; Child, Preschool ; Exome/genetics ; Female ; *Genetic Predisposition to Disease ; Gonadal Dysgenesis, 46,XX/genetics/physiopathology ; Hearing Loss, Sensorineural/*genetics/physiopathology ; Heterozygote ; Histidine-tRNA Ligase/*genetics ; Homozygote ; Humans ; Infant ; Male ; Mitochondria/genetics ; Mutation, Missense/genetics ; Pedigree ; Primary Ovarian Insufficiency/genetics/physiopathology ; }, abstract = {HARS2 encodes mitochondrial histidyl-tRNA synthetase (HARS2), which links histidine to its cognate tRNA in the mitochondrial matrix. Biallelic variants in HARS2 are associated with Perrault syndrome, a rare recessive condition characterized by sensorineural hearing loss in both sexes and primary ovarian insufficiency in 46,XX females. Some individuals with Perrault syndrome have a broader phenotypic spectrum with neurological features, including ataxia and peripheral neuropathy. Here, we report a recurrent variant in HARS2 in association with sensorineural hearing loss. In affected individuals from three unrelated families, the variant HARS2 c.1439G>A p.(Arg480His) is present as a heterozygous variant in trans to a putative pathogenic variant. The low prevalence of the allele HARS2 c.1439G>A p.(Arg480His) in the general population and its presence in three families with hearing loss, confirm the pathogenicity of this variant and illustrate the presentation of Perrault syndrome as nonsyndromic hearing loss in males and prepubertal females.}, }
@article {pmid31827088, year = {2019}, author = {Shiratori, T and Suzuki, S and Kakizawa, Y and Ishida, KI}, title = {Phagocytosis-like cell engulfment by a planctomycete bacterium.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {5529}, pmid = {31827088}, issn = {2041-1723}, mesh = {Alphaproteobacteria/classification/genetics/*physiology/ultrastructure ; Bacterial Proteins/genetics/metabolism ; Biological Evolution ; Genome, Bacterial ; *Phagocytosis ; Phylogeny ; }, abstract = {Phagocytosis is a key eukaryotic feature, conserved from unicellular protists to animals, that enabled eukaryotes to feed on other organisms. It could also be a driving force behind endosymbiosis, a process by which α-proteobacteria and cyanobacteria evolved into mitochondria and plastids, respectively. Here we describe a planctomycete bacterium, 'Candidatus Uab amorphum', which is able to engulf other bacteria and small eukaryotic cells through a phagocytosis-like mechanism. Observations via light and electron microscopy suggest that this bacterium digests prey cells in specific compartments. With the possible exception of a gene encoding an actin-like protein, analysis of the 'Ca. Uab amorphum' genomic sequence does not reveal any genes homologous to eukaryotic phagocytosis genes, suggesting that cell engulfment in this microorganism is probably not homologous to eukaryotic phagocytosis. The discovery of this "phagotrophic" bacterium expands our understanding of the cellular complexity of prokaryotes, and may be relevant to the origin of eukaryotic cells.}, }
@article {pmid31823814, year = {2019}, author = {Dubin, A and Jørgensen, TE and Jakt, LM and Johansen, SD}, title = {The mitochondrial transcriptome of the anglerfish Lophius piscatorius.}, journal = {BMC research notes}, volume = {12}, number = {1}, pages = {800}, pmid = {31823814}, issn = {1756-0500}, mesh = {Adenosine Triphosphatases/genetics ; Animals ; DNA, Mitochondrial/genetics/metabolism ; Electron Transport Complex IV/genetics ; Fishes/*genetics/metabolism ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Intracellular Signaling Peptides and Proteins/genetics ; Mitochondria/*genetics/metabolism ; NADH Dehydrogenase/genetics ; Phylogeny ; RNA, Antisense/genetics ; RNA, Long Noncoding/genetics ; RNA, Messenger/genetics ; RNA, Mitochondrial/genetics ; RNA, Ribosomal/genetics ; Transcriptome/*genetics ; }, abstract = {OBJECTIVE: Analyze key features of the anglerfish Lophius piscatorius mitochondrial transcriptome based on high-throughput total RNA sequencing.<br><br>RESULTS: We determined the complete mitochondrial DNA and corresponding transcriptome sequences of L. piscatorius. Key features include highly abundant mitochondrial ribosomal RNAs (10-100 times that of mRNAs), and that cytochrome oxidase mRNAs appeared&#x2009;>&#x2009;5 times more abundant than both NADH dehydrogenase and ATPase mRNAs. Unusual for a vertebrate mitochondrial mRNA, the polyadenylated COI mRNA was found to harbor a 75 nucleotide 3' untranslated region. The mitochondrial genome expressed several non-canonical genes, including the long noncoding RNAs lncCR-H, lncCR-L and lncCOI. Whereas lncCR-H and lncCR-L mapped to opposite strands in a non-overlapping organization within the control region, lncCOI appeared novel among vertebrates. We found lncCOI to be a highly abundant mitochondrial RNA in antisense to the COI mRNA. Finally, we present the coding potential of a humanin-like peptide within the large subunit ribosomal RNA.}, }
@article {pmid31817290, year = {2019}, author = {Arnedo, M and Latorre-Pellicer, A and Lucia-Campos, C and Gil-Salvador, M and Antoñanzas-Peréz, R and Gómez-Puertas, P and Bueno-Lozano, G and Puisac, B and Pié, J}, title = {More Than One HMG-CoA Lyase: The Classical Mitochondrial Enzyme Plus the Peroxisomal and the Cytosolic Ones.}, journal = {International journal of molecular sciences}, volume = {20}, number = {24}, pages = {}, pmid = {31817290}, issn = {1422-0067}, support = {RTC-2017-6494-1//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/Agencia Estatal de Investigaci&#xf3;n/ ; RTI2018-094434-B-I00//inisterio de Ciencia, Innovaci&#xf3;n y Universidades/Agencia Estatal de Investigaci&#xf3;n/ ; Grupo de Referencia B32_17R//Diputaci&#xf3;n General de Arag&#xf3;n - FEDER: European Social Fund/ ; }, mesh = {Cytosol/*enzymology ; Energy Metabolism ; Evolution, Molecular ; Humans ; Isoenzymes/classification/genetics/metabolism ; Ketone Bodies/metabolism ; Liver/enzymology ; Mitochondria/*enzymology ; Oxo-Acid-Lyases/classification/genetics/*metabolism ; Peroxisomes/*enzymology ; }, abstract = {There are three human enzymes with HMG-CoA lyase activity that are able to synthesize ketone bodies in different subcellular compartments. The mitochondrial HMG-CoA lyase was the first to be described, and catalyzes the cleavage of 3-hydroxy-3-methylglutaryl CoA to acetoacetate and acetyl-CoA, the common final step in ketogenesis and leucine catabolism. This protein is mainly expressed in the liver and its function is metabolic, since it produces ketone bodies as energetic fuels when glucose levels are low. Another isoform is encoded by the same gene for the mitochondrial HMG-CoA lyase (HMGCL), but it is located in peroxisomes. The last HMG-CoA lyase to be described is encoded by a different gene, HMGCLL1, and is located in the cytosolic side of the endoplasmic reticulum membrane. Some activity assays and tissue distribution of this enzyme have shown the brain and lung as key tissues for studying its function. Although the roles of the peroxisomal and cytosolic HMG-CoA lyases remain unknown, recent studies highlight the role of ketone bodies in metabolic remodeling, homeostasis, and signaling, providing new insights into the molecular and cellular function of these enzymes.}, }
@article {pmid31816412, year = {2020}, author = {Baldini, F and Portincasa, P and Grasselli, E and Damonte, G and Salis, A and Bonomo, M and Florio, M and Serale, N and Voci, A and Gena, P and Vergani, L and Calamita, G}, title = {Aquaporin-9 is involved in the lipid-lowering activity of the nutraceutical silybin on hepatocytes through modulation of autophagy and lipid droplets composition.}, journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids}, volume = {1865}, number = {3}, pages = {158586}, doi = {10.1016/j.bbalip.2019.158586}, pmid = {31816412}, issn = {1879-2618}, mesh = {Acyl-CoA Dehydrogenase, Long-Chain/metabolism ; Animals ; Aquaporins/genetics/*metabolism ; *Autophagy ; Cell Line, Tumor ; Hepatocytes/drug effects/*metabolism ; Lipid Droplets/*metabolism ; *Lipid Metabolism ; MicroRNAs/genetics/metabolism ; Mitochondria/drug effects/metabolism ; Rats ; Silybin/*pharmacology ; }, abstract = {Hepatic steatosis is the hallmark of non-alcoholic fatty liver disease (NAFLD), the hepatic manifestation of the metabolic syndrome and insulin resistance with potential evolution towards non-alcoholic steatohepatitis (NASH), cirrhosis and hepatocellular carcinoma. Key roles of autophagy and oxidative stress in hepatic lipid accumulation and NAFLD progression are recognized. Here, we employed a rat hepatoma cell model of NAFLD progression made of FaO cells exposed to oleate/palmitate followed or not by TNFα treatment to investigate the molecular mechanisms through which silybin, a lipid-lowering nutraceutical, may improve hepatic lipid dyshomeostasis. The beneficial effect of silybin was found to involve amelioration of the fatty acids profile of lipid droplets, stimulation of the mitochondrial oxidation and upregulation of a microRNA of pivotal relevance in hepatic fat metabolism, miR-122. Silybin was also found to restore the levels of Aquaporin-9 (AQP9) and glycerol permeability while reducing the activation of the oxidative stress-dependent transcription factor NF-κB, and autophagy turnover. In conclusion, silybin was shown to have molecular effects on signaling pathways that were previously unknown and potentially protect the hepatocyte. These actions intersect TG metabolism, fat-induced autophagy and AQP9-mediated glycerol transport in hepatocytes.}, }
@article {pmid31815198, year = {2019}, author = {Bargelloni, L and Babbucci, M and Ferraresso, S and Papetti, C and Vitulo, N and Carraro, R and Pauletto, M and Santovito, G and Lucassen, M and Mark, FC and Zane, L and Patarnello, T}, title = {Draft genome assembly and transcriptome data of the icefish Chionodraco myersi reveal the key role of mitochondria for a life without hemoglobin at subzero temperatures.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {443}, pmid = {31815198}, issn = {2399-3642}, mesh = {Animals ; *Cold Temperature ; Evolution, Molecular ; Gene Duplication ; Gene Expression Profiling ; Gene Expression Regulation ; *Genome ; *Genomics/methods ; Hemoglobins/*genetics ; Mitochondria/*genetics ; Multigene Family ; Muscles/metabolism ; Organelle Biogenesis ; Perciformes/classification/*genetics ; Phylogeny ; Promoter Regions, Genetic ; *Transcriptome ; }, abstract = {Antarctic fish belonging to Notothenioidei represent an extraordinary example of radiation in the cold. In addition to the absence of hemoglobin, icefish show a number of other striking peculiarities including large-diameter blood vessels, high vascular densities, mitochondria-rich muscle cells, and unusual mitochondrial architecture. In order to investigate the bases of icefish adaptation to the extreme Southern Ocean conditions we sequenced the complete genome of the icefish Chionodraco myersi. Comparative analyses of the icefish genome with those of other teleost species, including two additional white-blooded and five red-blooded notothenioids, provided a new perspective on the evolutionary loss of globin genes. Muscle transcriptome comparative analyses against red-blooded notothenioids as well as temperate fish revealed the peculiar regulation of genes involved in mitochondrial function in icefish. Gene duplication and promoter sequence divergence were identified as genome-wide patterns that likely contributed to the broad transcriptional program underlying the unique features of icefish mitochondria.}, }
@article {pmid31809841, year = {2020}, author = {Ju, Y and Liu, H and He, J and Wang, L and Xu, J and Liu, H and Dong, Y and Zhang, R and Zhao, P and Xing, X}, title = {Genetic diversity of Aoluguya Reindeer based on D-loop region of mtDNA and its conservation implications.}, journal = {Gene}, volume = {733}, number = {}, pages = {144271}, doi = {10.1016/j.gene.2019.144271}, pmid = {31809841}, issn = {1879-0038}, mesh = {Animals ; China ; Conservation of Natural Resources/methods ; DNA, Mitochondrial/*genetics ; Finland ; Genetic Variation/genetics ; Haplotypes ; Introduced Species ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Reindeer/*genetics ; }, abstract = {Aoluguya Reindeer is the only reindeer population in China. In recent years, habitat loss and inbreeding have led to population decline, and population growth has been slow, maintaining a thousand or so. To better protect the Aoluguya Reindeer and improve its fecundity, we have introduced reindeer from Finland, crossbreeding help us to reach this goal. However, it is lacking in the study of genetic diversity of reindeer in China and Finland. Therefore, we used the partial sequences of the D-loop region of mitochondrial DNA to analyze the genetic diversity of Chinese reindeer (Aoluguya Reindeer) and the introduced Finnish reindeer, and identified twenty-six haplotypes, including nineteen in China, five in Finland, and two in Russia. There is no shared haplotype among them. The nucleotide diversity of Aoluguya Reindeer is 0.00752, which is significantly lower than that of reindeer in Finland and other countries. The haplotype and phylogenetic analysis show that reindeer from different geographical origins are not clustered completely according to geographical distribution. Aoluguya Reindeer populations and the introduced reindeer herds from Finland are all closely related to the reindeer from Russia. AMOVA analysis showed that there was significant differentiation between reindeer populations in China and Finland, and mismatch analysis showed that both populations had not experienced expansion. In this study, we identified the genetic diversity of Aoluguya Reindeer and the introduced reindeer, and provided a scientific basis for the conservation and breeding of Aoluguya Reindeer resources.}, }
@article {pmid31806760, year = {2019}, author = {Rosenberg, A and Luth, MR and Winzeler, EA and Behnke, M and Sibley, LD}, title = {Evolution of resistance in vitro reveals mechanisms of artemisinin activity in Toxoplasma gondii.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {52}, pages = {26881-26891}, pmid = {31806760}, issn = {1091-6490}, support = {R01 AI143857/AI/NIAID NIH HHS/United States ; R21 AI130672/AI/NIAID NIH HHS/United States ; R01 AI118426/AI/NIAID NIH HHS/United States ; P30 CA091842/CA/NCI NIH HHS/United States ; T32 GM008666/GM/NIGMS NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; }, abstract = {Artemisinins are effective against a variety of parasites and provide the first line of treatment for malaria. Laboratory studies have identified several mechanisms for artemisinin resistance in Plasmodium falciparum, including mutations in Kelch13 that are associated with delayed clearance in some clinical isolates, although other mechanisms are likely involved. To explore other potential mechanisms of resistance in parasites, we took advantage of the genetic tractability of Toxoplasma gondii, a related parasite that shows moderate sensitivity to artemisinin. Resistant populations of T. gondii were selected by culture in increasing concentrations and whole-genome sequencing identified several nonconservative point mutations that emerged in the population and were fixed over time. Genome editing using CRISPR/Cas9 was used to introduce point mutations conferring amino acid changes in a serine protease homologous to DegP and a serine/threonine protein kinase of unknown function. Single and double mutations conferred a competitive advantage over wild-type parasites in the presence of drug, despite not changing EC50 values. Additionally, the evolved resistant lines showed dramatic amplification of the mitochondria genome, including genes encoding cytochrome b and cytochrome c oxidase I. Prior studies in yeast and mammalian tumor cells implicate the mitochondrion as a target of artemisinins, and treatment of wild-type parasites with high concentrations of drug decreased mitochondrial membrane potential, a phenotype that was stably altered in the resistant parasites. These findings extend the repertoire of mutations associated with artemisinin resistance and suggest that the mitochondrion may be an important target of inhibition of resistance in T. gondii.}, }
@article {pmid31802201, year = {2020}, author = {Yang, J and Khan, MAK and Zhang, H and Zhang, Y and Certik, M and Garre, V and Song, Y}, title = {Mitochondrial Citrate Transport System in the Fungus Mucor circinelloides: Identification, Phylogenetic Analysis, and Expression Profiling During Growth and Lipid Accumulation.}, journal = {Current microbiology}, volume = {77}, number = {2}, pages = {220-231}, pmid = {31802201}, issn = {1432-0991}, support = {31670064//National Natural Science Foundation of China/ ; tscy 20160101//TaiShan Industrial Experts Programme/ ; 2018GNC110039//Key Technology Research and Development Program of Shandong/ ; }, mesh = {Biological Transport ; Citrates/*metabolism ; Gene Expression Regulation, Fungal ; Genome, Fungal ; Lipid Metabolism ; Lipids/*biosynthesis ; Mitochondria/*metabolism ; Mucor/*classification/*metabolism ; *Phylogeny ; }, abstract = {The mitochondrial citrate transport system, composed of citrate and malate transporters (MTs), can regulate the citrate efflux from mitochondria to cytosol, and then citrate is cleaved into OAA and acetyl-CoA which can be used for fatty acid (FA) biosynthesis. However, in the fungus Mucor circinelloides the molecular mechanism of citrate efflux from the mitochondria by this system and its role in FA synthesis is unclear. In the present study, we have analyzed the genome of high lipid-producing strain WJ11 and the low lipid-producing strain CBS 277.49 to find the potential genes involving in this system. Five potential genes are present in the genome of WJ11. These genes encode one citrate transport protein (CT), one tricarboxylate carrier (TCT), one MT, and two 2-oxoglutarate:malate antiporters (SoDIT-a and SoDIT-b). However, the genome of CBS 277.49 contains the same set of genes, except for the presence of just one SoDIT. The proteins from WJ11 had similar properties as their counterparts in CBS 277.49. Moreover, phylogenetic analyses revealed the evolutionary relationship of these proteins and illuminated their typical motifs related to potential functions. Additionally, the expression of these genes was analyzed to predict the possible functions in lipid metabolism in M. circinelloides. This is the first study to report the in silico analysis of structures and functions of the mitochondrial citrate transport system in M. circinelloides. This work showed a new strategy for research for the selection of candidate genes for further detailed functional investigation of the mitochondrial citrate transport system in lipid accumulation.}, }
@article {pmid31801053, year = {2019}, author = {Moraes, CT}, title = {Sorting mtDNA Species-the Role of nDNA-mtDNA Co-evolution.}, journal = {Cell metabolism}, volume = {30}, number = {6}, pages = {1002-1004}, doi = {10.1016/j.cmet.2019.11.005}, pmid = {31801053}, issn = {1932-7420}, support = {R33 ES025673/ES/NIEHS NIH HHS/United States ; R01 AG036871/AG/NIA NIH HHS/United States ; R01 NS079965/NS/NINDS NIH HHS/United States ; }, mesh = {*DNA, Mitochondrial ; Female ; Humans ; Mitochondria ; *Mothers ; }, abstract = {The segregation of heteroplasmic mtDNA species was thought to be mostly stochastic. However, recent findings, including a study by Latorre-Pellicer et al. (2019) published in this issue of Cell Metabolism, provide evidence that nuclear DNA and mitochondrial DNA interactions play an important role in the sorting process.}, }
@article {pmid31797315, year = {2020}, author = {Suk, HY and Bae, HG and Kim, DY and Won, H and Baek, HJ and Lee, CH and Kim, DY and Go, YM and Song, JY and Lee, H and Min, MS}, title = {Genetic and phylogenetic structure of Hynobius quelpaertensis, an endangered endemic salamander species on the Korean Peninsula.}, journal = {Genes &amp; genomics}, volume = {42}, number = {2}, pages = {165-178}, pmid = {31797315}, issn = {2092-9293}, mesh = {Animals ; *Endangered Species ; Genetic Variation ; Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; Republic of Korea ; Urodela/classification/*genetics ; }, abstract = {BACKGROUND: The Korean Peninsula is a small but unique area showing great endemic Hynobius diversity with H. quelpaertensis, H. yangi, H. unisacculus and three species candidates (HC1, HC3 and HC4). H. quelpaertensis is distributed in the southern part and in Jeju Island, while the remaining species have extremely narrow distributions.<br><br>OBJECTIVES: To examine the genetic structure of H. quelpaertensis and the phylogenetic placement in Hynobius.<br><br>METHODS: Three mitochondrial and six microsatellite loci were genotyped for 204 Hynobius quelpaertensis, three H. leechii, three H. yangi, three HC1, two H. unisacculus, three HC3, three HC4 and ten Japanses H. lichenatus.<br><br>RESULTS: A high level of mitochondrial diversity was found in H. quelpaertensis. Our mitochondrial data showed evidence of a historical link between inland and Jeju Island despite the signature of founder effect likely experienced by the early island populations. However, our microsatellite analysis showed the fairly clear signature of isolation history between in- and island populations. Upon phylogenetic analysis, H. quelpaertensis, H. unisacculus and HC1 formed a cluster, whereas H. yangi belonged to a separate cluster. HC3 and HC4 were clustered with either H. quelpaertensis or H. yangi depending on the locus used.<br><br>CONCLUSION: Our results show at least partially the historical imprints engraved by dispersal of Korean endemic Hynobius during Pleistocene, potentially providing a fundamental basis in determining the conservation units and finding management strategies for these species.}, }
@article {pmid31797248, year = {2020}, author = {Hein, A and Brenner, S and Polsakiewicz, M and Knoop, V}, title = {The dual-targeted RNA editing factor AEF1 is universally conserved among angiosperms and reveals only minor adaptations upon loss of its chloroplast or its mitochondrial target.}, journal = {Plant molecular biology}, volume = {102}, number = {1-2}, pages = {185-198}, pmid = {31797248}, issn = {1573-5028}, mesh = {Acclimatization/*genetics ; Arabidopsis/genetics/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Biological Evolution ; Chloroplast Proteins/genetics/metabolism ; Chloroplasts/*genetics ; DNA-Binding Proteins/*genetics ; Genome, Plant ; Magnoliopsida/genetics ; Mitochondria/*genetics ; Phylogeny ; *RNA Editing ; RNA, Chloroplast/genetics ; RNA, Plant/genetics ; RNA-Binding Proteins/metabolism ; Sequence Alignment ; Transcription Factors/*genetics ; }, abstract = {Upon loss of either its chloroplast or mitochondrial target, a uniquely dual-targeted factor for C-to-U RNA editing in angiosperms reveals low evidence for improved molecular adaptation to its remaining target. RNA-binding pentatricopeptide repeat (PPR) proteins specifically recognize target sites for C-to-U RNA editing in the transcriptomes of plant chloroplasts and mitochondria. Among more than 80 PPR-type editing factors that have meantime been characterized, AEF1 (or MPR25) is a special case given its dual targeting to both organelles and addressing an essential mitochondrial (nad5eU1580SL) and an essential chloroplast (atpFeU92SL) RNA editing site in parallel in Arabidopsis. Here, we explored the angiosperm-wide conservation of AEF1 and its two organelle targets. Despite numerous independent losses of the chloroplast editing site by C-to-T conversion and at least four such conversions at the mitochondrial target site in other taxa, AEF1 remains consistently conserved in more than 120 sampled angiosperm genomes. Not a single case of simultaneous loss of the chloroplast and mitochondrial editing target or of AEF1 disintegration or loss could be identified, contrasting previous findings for editing factors targeted to only one organelle. Like in most RNA editing factors, the PPR array of AEF1 reveals potential for conceptually "improved fits" to its targets according to the current PPR-RNA binding code. Surprisingly, we observe only minor evidence for adaptation to the mitochondrial target also after deep losses of the chloroplast target among Asterales, Caryophyllales and Poales or, vice versa, for the remaining chloroplast target after a deep loss of the mitochondrial target among Malvales. The evolutionary observations support the notion that PPR-RNA mismatches may be essential for proper function of editing factors.}, }
@article {pmid31794060, year = {2020}, author = {Kumar, S and Nandi, A and Mahesh, A and Sinha, S and Flores, E and Chakrabarti, R}, title = {Inducible knockout of ∆Np63 alters cell polarity and metabolism during pubertal mammary gland development.}, journal = {FEBS letters}, volume = {594}, number = {6}, pages = {973-985}, pmid = {31794060}, issn = {1873-3468}, support = {R01 CA237243/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Cadherins/genetics/metabolism ; *Cell Polarity ; Female ; Mammary Glands, Animal/*metabolism ; Mice ; Mice, Knockout ; *Sexual Maturation ; Stem Cells/*metabolism ; Trans-Activators/genetics/*metabolism ; beta Catenin/genetics/metabolism ; }, abstract = {The ∆Np63 isoform of the p53-family transcription factor Trp63 is a key regulator of mammary epithelial stem cells that is involved in breast cancer development. To investigate the role of ∆Np63 at different stages of normal mammary gland development, we generated a ∆Np63-inducible conditional knockout (cKO) mouse model. We demonstrate that the deletion of ∆Np63 at puberty results in depletion of mammary stem cell-enriched basal cells, reduces expression of E-cadherin and β-catenin, and leads to a closed ductal lumen. RNA-sequencing analysis reveals reduced expression of oxidative phosphorylation (OXPHOS)-associated proteins and desmosomal polarity proteins. Functional assays show reduced numbers of mitochondria in the mammary epithelial cells of ΔNp63 cKO compared to wild-type, supporting the reduced OXPHOS phenotype. These findings identify a novel role for ∆Np63 in cellular metabolism and mammary epithelial cell polarity.}, }
@article {pmid31787045, year = {2020}, author = {Schaack, S and Ho, EKH and Macrae, F}, title = {Disentangling the intertwined roles of mutation, selection and drift in the mitochondrial genome.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1790}, pages = {20190173}, pmid = {31787045}, issn = {1471-2970}, support = {R15 GM132861/GM/NIGMS NIH HHS/United States ; }, mesh = {*Genetic Drift ; *Genome, Mitochondrial ; *Mutation ; *Selection, Genetic ; }, abstract = {Understanding and quantifying the rates of change in the mitochondrial genome is a major component of many areas of biological inquiry, from phylogenetics to human health. A critical parameter in understanding rates of change is estimating the mitochondrial mutation rate (mtDNA MR). Although the first direct estimates of mtDNA MRs were reported almost 20 years ago, the number of estimates has not grown markedly since that time. This is largely owing to the challenges associated with time- and labour-intensive mutation accumulation (MA) experiments. But even MA experiments do not solve a major problem with estimating mtDNA MRs-the challenge of disentangling the role of mutation from other evolutionary forces acting within the cell. Now that it is widely understood that any newly generated mutant allele in the mitochondria will initially be at very low frequency (1/N, where N is the number of mtDNA molecules in the cell), the importance of understanding the effective population size (Ne) of the mtDNA and the size of genetic bottlenecks during gametogenesis and development has come into the spotlight. In addition to these factors regulating the role of genetic drift, advances in our understanding of mitochondrial replication and turnover allow us to more easily envision how natural selection within the cell might favour or purge mutations in multi-copy organellar genomes. Here, we review the unique features of the mitochondrial genome that pose a challenge for accurate MR estimation and discuss ways to overcome those challenges. Estimates of mtDNA MRs remain one of the most widely used parameters in biology, thus accurate quantification and a deeper understanding of how and why they may vary within and between individuals, populations and species is an important goal. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.}, }
@article {pmid31787042, year = {2020}, author = {Elbassiouny, AA and Lovejoy, NR and Chang, BSW}, title = {Convergent patterns of evolution of mitochondrial oxidative phosphorylation (OXPHOS) genes in electric fishes.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1790}, pages = {20190179}, pmid = {31787042}, issn = {1471-2970}, mesh = {Animals ; Electric Fish/*genetics/metabolism ; *Evolution, Molecular ; Fish Proteins/*genetics/metabolism ; Genome, Mitochondrial ; Mitochondria/*metabolism ; *Multigene Family ; *Oxidative Phosphorylation ; Selection, Genetic ; }, abstract = {The ability to generate and detect electric fields has evolved in several groups of fishes as a means of communication, navigation and, occasionally, predation. The energetic burden required can account for up to 20% of electric fishes' daily energy expenditure. Despite this, molecular adaptations that enable electric fishes to meet the metabolic demands of bioelectrogenesis remain unknown. Here, we investigate the molecular evolution of the mitochondrial oxidative phosphorylation (OXPHOS) complexes in the two most diverse clades of weakly electric fishes-South American Gymnotiformes and African Mormyroidea, using codon-based likelihood approaches. Our analyses reveal that although mitochondrial OXPHOS genes are generally subject to strong purifying selection, this constraint is significantly reduced in electric compared to non-electric fishes, particularly for complexes IV and V. Moreover, analyses of concatenated mitochondrial genes show strong evidence for positive selection in complex I genes on the two branches associated with the independent evolutionary origins of electrogenesis. These results suggest that adaptive evolution of proton translocation in the OXPHOS cellular machinery may be associated with the evolution of bioelectrogenesis. Overall, we find striking evidence for remarkably similar effects of electrogenesis on the molecular evolution of mitochondrial OXPHOS genes in two independently derived clades of electrogenic fishes. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.}, }
@article {pmid31787040, year = {2020}, author = {Bettinazzi, S and Nadarajah, S and Dalpé, A and Milani, L and Blier, PU and Breton, S}, title = {Linking paternally inherited mtDNA variants and sperm performance.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1790}, pages = {20190177}, pmid = {31787040}, issn = {1471-2970}, mesh = {Animals ; Bivalvia/*genetics ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; *Genotype ; Male ; *Maternal Inheritance ; Mercenaria/genetics ; Mytilus edulis/genetics ; *Paternal Inheritance ; Spermatozoa/*physiology ; }, abstract = {Providing robust links between mitochondrial genotype and phenotype is of major importance given that mitochondrial DNA (mtDNA) variants can affect reproductive success. Because of the strict maternal inheritance (SMI) of mitochondria in animals, haplotypes that negatively affect male fertility can become fixed in populations. This phenomenon is known as 'mother's curse'. Doubly uniparental inheritance (DUI) of mitochondria is a stable exception in bivalves, which entails two mtDNA lineages that evolve independently and are transmitted separately through oocytes and sperm. This makes the DUI mitochondrial lineages subject to different sex-specific selective sieves during mtDNA evolution, thus DUI is a unique model to evaluate how direct selection on sperm mitochondria could contribute to male reproductive fitness. In this study, we tested the impact of mtDNA variants on sperm performance and bioenergetics in DUI and SMI species. Analyses also involved measures of sperm performance following inhibition of main energy pathways and sperm response to oocyte presence. Compared to SMI, DUI sperm exhibited (i) low speed and linearity, (ii) a strict OXPHOS-dependent strategy of energy production, and (iii) a partial metabolic shift towards fermentation following egg detection. Discussion embraces the adaptive value of mtDNA variation and suggests a link between male-energetic adaptation, fertilization success and paternal mitochondria preservation. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.}, }
@article {pmid31787038, year = {2020}, author = {Nagarajan-Radha, V and Aitkenhead, I and Clancy, DJ and Chown, SL and Dowling, DK}, title = {Sex-specific effects of mitochondrial haplotype on metabolic rate in Drosophila melanogaster support predictions of the Mother's Curse hypothesis.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1790}, pages = {20190178}, pmid = {31787038}, issn = {1471-2970}, mesh = {Animals ; *Basal Metabolism ; Drosophila melanogaster/*genetics/metabolism ; Female ; *Haplotypes ; Male ; *Maternal Inheritance ; Mitochondria/*genetics ; }, abstract = {Evolutionary theory proposes that maternal inheritance of mitochondria will facilitate the accumulation of mitochondrial DNA (mtDNA) mutations that are harmful to males but benign or beneficial to females. Furthermore, mtDNA haplotypes sampled from across a given species distribution are expected to differ in the number and identity of these 'male-harming' mutations they accumulate. Consequently, it is predicted that the genetic variation which delineates distinct mtDNA haplotypes of a given species should confer larger phenotypic effects on males than females (reflecting mtDNA mutations that are male-harming, but female-benign), or sexually antagonistic effects (reflecting mutations that are male-harming, but female-benefitting). These predictions have received support from recent work examining mitochondrial haplotypic effects on adult life-history traits in Drosophila melanogaster. Here, we explore whether similar signatures of male-bias or sexual antagonism extend to a key physiological trait-metabolic rate. We measured the effects of mitochondrial haplotypes on the amount of carbon dioxide produced by individual flies, controlling for mass and activity, across 13 strains of D. melanogaster that differed only in their mtDNA haplotype. The effects of mtDNA haplotype on metabolic rate were larger in males than females. Furthermore, we observed a negative intersexual correlation across the haplotypes for metabolic rate. Finally, we uncovered a male-specific negative correlation, across haplotypes, between metabolic rate and longevity. These results are consistent with the hypothesis that maternal mitochondrial inheritance has led to the accumulation of a sex-specific genetic load within the mitochondrial genome, which affects metabolic rate and that may have consequences for the evolution of sex differences in life history. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.}, }
@article {pmid31787037, year = {2020}, author = {Camus, MF and O'Leary, M and Reuter, M and Lane, N}, title = {Impact of mitonuclear interactions on life-history responses to diet.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1790}, pages = {20190416}, pmid = {31787037}, issn = {1471-2970}, support = {BB/S003681/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Diet ; Drosophila melanogaster/genetics/*physiology ; Female ; Fertility/*genetics ; Haplotypes ; Life History Traits ; Longevity/*genetics ; Male ; Mitochondria/*genetics ; }, abstract = {Mitochondria are central to both energy metabolism and biosynthesis. Mitochondrial function could therefore influence resource allocation. Critically, mitochondrial function depends on interactions between proteins encoded by the mitochondrial and nuclear genomes. Severe incompatibilities between these genomes can have pervasive effects on both fitness and longevity. How milder deficits in mitochondrial function affect life-history trade-offs is less well understood. Here, we analyse how mitonuclear interactions affect the trade-off between fecundity and longevity in Drosophila melanogaster. We consider a panel of 10 different mitochondrial DNA haplotypes against two contrasting nuclear backgrounds (w[1118] (WE) and Zim53 (ZIM)) in response to high-protein versus standard diet. We report strikingly different responses between the two nuclear backgrounds. WE females have higher fecundity and decreased longevity on high protein. ZIM females have much greater fecundity and shorter lifespan than WE flies on standard diet. High protein doubled their fecundity with no effect on longevity. Mitochondrial haplotype reflected nuclear life-history trade-offs, with a negative correlation between longevity and fecundity in WE flies and no correlation in ZIM flies. Mitonuclear interactions had substantial effects but did not reflect genetic distance between mitochondrial haplotypes. We conclude that mitonuclear interactions can have significant impact on life-history trade-offs, but their effects are not predictable by relatedness. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.}, }
@article {pmid31786061, year = {2019}, author = {Chiang, AC and McCartney, E and O'Farrell, PH and Ma, H}, title = {A Genome-wide Screen Reveals that Reducing Mitochondrial DNA Polymerase Can Promote Elimination of Deleterious Mitochondrial Mutations.}, journal = {Current biology : CB}, volume = {29}, number = {24}, pages = {4330-4336.e3}, pmid = {31786061}, issn = {1879-0445}, support = {202269/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; DNA Polymerase gamma/genetics/*metabolism ; DNA, Mitochondrial/*genetics ; Drosophila Proteins/genetics ; Drosophila melanogaster/genetics ; Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Mutation ; Selection, Genetic/genetics ; }, abstract = {A mutant mitochondrial genome arising amid the pool of mitochondrial genomes within a cell must compete with existing genomes to survive to the next generation. Even weak selective forces can bias transmission of one genome over another to affect the inheritance of mitochondrial diseases and guide the evolution of mitochondrial DNA (mtDNA). Studies in several systems suggested that purifying selection in the female germline reduces transmission of detrimental mitochondrial mutations [1-7]. In contrast, some selfish genomes can take over despite a cost to host fitness [8-13]. Within individuals, the outcome of competition is therefore influenced by multiple selective forces. The nuclear genome, which encodes most proteins within mitochondria, and all external regulators of mitochondrial biogenesis and dynamics can influence the competition between mitochondrial genomes [14-18], yet little is known about how this works. Previously, we established a Drosophila line transmitting two mitochondrial genomes in a stable ratio enforced by purifying selection benefiting one genome and a selfish advantage favoring the other [8]. Here, to find nuclear genes that impact mtDNA competition, we screened heterozygous deletions tiling ∼70% of the euchromatic regions and examined their influence on this ratio. This genome-wide screen detected many nuclear modifiers of this ratio and identified one as the catalytic subunit of mtDNA polymerase gene (POLG), tam. A reduced dose of tam drove elimination of defective mitochondrial genomes. This study suggests that our approach will uncover targets for interventions that would block propagation of pathogenic mitochondrial mutations.}, }
@article {pmid31785298, year = {2020}, author = {Shi, W and Gong, L and Yu, H}, title = {Double control regions of some flatfish mitogenomes evolve in a concerted manner.}, journal = {International journal of biological macromolecules}, volume = {142}, number = {}, pages = {11-17}, doi = {10.1016/j.ijbiomac.2019.11.204}, pmid = {31785298}, issn = {1879-0003}, mesh = {Animals ; DNA Repair/physiology ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Flatfishes/classification/*genetics ; Gene Order ; Genes, rRNA/genetics ; Genetic Variation ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; RNA, Transfer/genetics ; Recombination, Genetic ; Sequence Analysis ; }, abstract = {Mitochondrial genomes (mitogenomes) typically contain 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a single control region (CR). Flatfish mitochondrial genomes (mitogenomes) from three different genera in Bothidae (bothids) contain double CRs that evolved in a concerted manner. How these double CRs maintained identical sequences throughout the evolutionary process is an interesting issue. In the present study, over four hundred arrays of the double CRs of mitogenomes from three bothids (Arnoglossus tenuis, Lophonectes gallus and Psettina iijimae) were performed. Interesting variations between double CRs were observed in P. iijimae mitogenomes, and the networks of CR sequences from P. iijimae indicated a high possibility of genetic information exchange between CRs. No recombination product was detected in our results, indicating that the mechanism of the concerted evolution between the double CRs of P. iijimae was not recombination. We speculate that mismatch repair, a mitochondrial DNA repair mechanism, is a potential explanation for the concerted evolution between these double CRs.}, }
@article {pmid31784872, year = {2020}, author = {Wang, J and Yang, M and Xiao, H and Huang, GH and Deng, F and Hu, Z}, title = {Genome Analysis of Dasineura jujubifolia Toursvirus 2, A Novel Ascovirus.}, journal = {Virologica Sinica}, volume = {35}, number = {2}, pages = {134-142}, pmid = {31784872}, issn = {1995-820X}, mesh = {Animals ; Ascoviridae/classification/*genetics ; DNA, Viral/genetics ; Diptera/*virology ; *Genome, Viral ; Metagenomics ; Mitochondria/genetics ; *Open Reading Frames ; *Phylogeny ; Virus Replication ; }, abstract = {So far, ascoviruses have only been identified from Lepidoptera host insects and their transmission vectors-endoparasitic wasps. Here, we reported the first finding of a complete novel ascovirus genome from a Diptera insect, Dasineura jujubifolia. Initially, sequence fragments with homology to ascoviruses were incidentally identified during metagenomic sequencing of the mitochondria of D. jujubifolia (Cecidomyiidae, Diptera) which is a major pest on Ziziphus jujuba. Then a full circular viral genome was assembled from the metagenomic data, which has an A+T percentage of 74% and contains 142,600 bp with 141 open reading frames (ORFs). Among the 141 ORFs, 37 were conserved in all sequenced ascoviruses (core genes) including proteins predicted to participate in DNA replication, gene transcription, protein modification, virus assembly, lipid metabolism and apoptosis. Multi-gene families including those encode for baculovirus repeated open reading frames (BROs), myristylated membrane proteins, RING/U-box E3 ubiquitin ligases, and ATP-binding cassette (ABC) transporters were found in the virus genome. Phylogenetic analysis showed that the newly identified virus belongs to genus Toursvirus of Ascoviridae, and is therefore named as Dasineura jujubifolia toursvirus 2 (DjTV-2a). The virus becomes the second reported species of the genus after Diadromus pulchellus toursvirus 1 (DpTV-1a). The genome arrangement of DjTV-2a is quite different from that of DpTV-1a, suggesting these two viruses separated in an early time of evolution. The results suggest that the ascoviruses may infect a much broader range of hosts than our previous knowledge, and shed lights on the evolution of ascoviruses and particularly on that of the toursviruses.}, }
@article {pmid31781636, year = {2019}, author = {Owuor, SA and Mamati, EG and Kasili, RW}, title = {Origin, Genetic Diversity, and Population Structure of Rabbits (Oryctolagus cuniculus) in Kenya.}, journal = {BioMed research international}, volume = {2019}, number = {}, pages = {7056940}, pmid = {31781636}, issn = {2314-6141}, mesh = {Animals ; Breeding/methods ; DNA, Mitochondrial/genetics ; Europe ; Genetic Variation/*genetics ; Genetics, Population/methods ; Haplotypes/genetics ; Kenya ; Mitochondria/genetics ; Phylogeny ; Rabbits/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {To evaluate the origin, genetic diversity, and population structure of domesticated rabbits in Kenya, a 263-base pair region of mtDNA D-loop region of 111 rabbits sampled from Kakamega, Vihiga, and Bungoma counties in the western region, Laikipia and Nyandarua counties in the central region, and Kitui, Machakos, and Makueni in the eastern region of the country were analyzed. The average haplotype (0.40702) and nucleotide (0.01494) diversities observed were low, indicating low genetic diversity of domesticated rabbits in Kenya. This study resolved 5 unique haplotypes in the mtDNA D-loop region. A population genetic structure distinguishing Europe grouping and domesticated rabbits in Kenya was obtained on incorporating 32 known haplotypes. Domesticated rabbits in Kenya clustered together with rabbits from other geographic regions, suggesting common origin. The results suggested that the Kenyan domesticated rabbits may have originated from Europe. Integration of exotic breeds into breeding programmes could have contributed to the low genetic diversity. These results provide useful information for breeding and conservation decisions by the relevant stakeholders in the agriculture industry in Kenya.}, }
@article {pmid31780199, year = {2020}, author = {Waltz, F and Giegé, P}, title = {Striking Diversity of Mitochondria-Specific Translation Processes across Eukaryotes.}, journal = {Trends in biochemical sciences}, volume = {45}, number = {2}, pages = {149-162}, doi = {10.1016/j.tibs.2019.10.004}, pmid = {31780199}, issn = {0968-0004}, mesh = {Eukaryotic Cells/metabolism ; Mitochondrial Proteins/metabolism ; Mitochondrial Ribosomes/*metabolism ; *Protein Biosynthesis ; RNA, Ribosomal/metabolism ; RNA, Transfer/metabolism ; }, abstract = {Mitochondria are essential organelles that act as energy conversion powerhouses and metabolic hubs. Their gene expression machineries combine traits inherited from prokaryote ancestors and specific features acquired during eukaryote evolution. Mitochondrial research has wide implications ranging from human health to agronomy. We highlight recent advances in mitochondrial translation. Functional, biochemical, and structural data have revealed an unexpected diversity of mitochondrial translation systems, particularly of their key players, the mitochondrial ribosomes (mitoribosomes). Ribosome assembly and translation mechanisms, such as initiation, are discussed and put in perspective with the prevalence of eukaryote-specific families of mitochondrial translation factors such as pentatricopeptide repeat (PPR) proteins.}, }
@article {pmid31773863, year = {2020}, author = {Gao, H and Li, N and Huang, Y and Qiao, F and Li, J and Li, Z and Li, Y and Wang, Z and Teng, L and Liu, Z}, title = {Taxonomic status of Chinese blue sheep (Pseudois nayaur): new evidence of a distinct subspecies.}, journal = {Integrative zoology}, volume = {15}, number = {3}, pages = {202-212}, doi = {10.1111/1749-4877.12422}, pmid = {31773863}, issn = {1749-4877}, mesh = {Animals ; China ; Genetic Variation ; *Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; Ruminants/*classification/genetics ; Sequence Analysis, DNA/veterinary ; Sheep/classification/genetics ; }, abstract = {The blue sheep is an endemic species to the Qinghai-Tibet Plateau and surrounding regions. It has been regarded as having 2 subspecies: Pseudois nayaur nayaur and P. n. szechuanensis. However, such a classification remains controversial. Herein, we analyze 10 microsatellite loci and part of the mitochondrial control region for clarification in such taxonomic debates. We use samples from 168 individuals from 6 geographic populations covering almost all the distribution areas of the species in China to carry out comparisons. Phylogenetic trees derived from both the microsatellite and mitochondrial markers combined with the discriminant analysis of principal components (DAPC) and the STRUCTURE analysis reveal that the individuals in the Helan Mountains are well grouped with a distinct evolutionary lineage and are significantly different from the other populations of P. n. szechuanensis according to Fst values, implying that this isolated population should be categorized as a valid subspecies; namely, Pseudois nayaur alashanicus. The isolation-by-distance (IBD) analysis shows a significant positive relationship between genetic and geographical distances among the populations.}, }
@article {pmid31772306, year = {2019}, author = {Barbour, AG and Shao, H and Cook, VJ and Baldwin-Brown, J and Tsao, JI and Long, AD}, title = {Genomes, expression profiles, and diversity of mitochondria of the White-footed Deermouse Peromyscus leucopus, reservoir of Lyme disease and other zoonoses.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17618}, pmid = {31772306}, issn = {2045-2322}, support = {AI136523//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/International ; AI126037//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/International ; AI037248//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/International ; P30 CA062203/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Animals, Laboratory/genetics ; Animals, Wild/genetics ; Arachnid Vectors/microbiology ; Borrelia ; Borrelia Infections/genetics/microbiology ; Borrelia burgdorferi/isolation &amp; purification ; DNA, Mitochondrial/*genetics ; *Disease Reservoirs ; Female ; Gene Expression Profiling ; *Genome ; Haplotypes ; Ixodes/microbiology ; Lyme Disease/microbiology/transmission/veterinary ; Muridae/classification/genetics ; Organ Specificity ; Peromyscus/classification/*genetics/microbiology ; Phylogeny ; Pseudogenes ; Rodent Diseases/epidemiology/microbiology/parasitology ; Sequence Homology, Nucleic Acid ; Species Specificity ; Tick Bites/microbiology/veterinary ; United States ; }, abstract = {The cricetine rodents Peromyscus leucopus and P. maniculatus are key reservoirs for several zoonotic diseases in North America. We determined the complete circular mitochondrial genome sequences of representatives of 3 different stock colonies of P. leucopus, one stock colony of P. maniculatus and two wild populations of P. leucopus. The genomes were syntenic with that of the murids Mus musculus and Rattus norvegicus. Phylogenetic analysis confirmed that these two Peromyscus species are sister taxa in a clade with P. polionotus and also uncovered a distinction between P. leucopus populations in the eastern and the central United States. In one P. leucopus lineage four extended regions of mitochondrial pseudogenes were identified in the nuclear genome. RNA-seq analysis revealed transcription of the entire genome and differences from controls in the expression profiles of mitochondrial genes in the blood, but not in liver or brain, of animals infected with the zoonotic pathogen Borrelia hermsii. PCR and sequencing of the D-loop of the mitochondrion identified 32 different haplotypes among 118 wild P. leucopus at a Connecticut field site. These findings help to further establish P. leucopus as a model organism for studies of emerging infectious diseases, ecology, and in other disciplines.}, }
@article {pmid31767921, year = {2019}, author = {Kehlmaier, C and Graciá, E and Campbell, PD and Hofmeyr, MD and Schweiger, S and Martínez-Silvestre, A and Joyce, W and Fritz, U}, title = {Ancient mitogenomics clarifies radiation of extinct Mascarene giant tortoises (Cylindraspis spp.).}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17487}, pmid = {31767921}, issn = {2045-2322}, mesh = {Animals ; DNA, Mitochondrial/*analysis ; Fossils ; Indian Ocean ; Mauritius ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; Reunion ; Sequence Analysis, DNA/*methods ; Turtles/*classification/genetics ; }, abstract = {The five extinct giant tortoises of the genus Cylindraspis belong to the most iconic species of the enigmatic fauna of the Mascarene Islands that went largely extinct after the discovery of the islands. To resolve the phylogeny and biogeography of Cylindraspis, we analysed a data set of 45 mitogenomes that includes all lineages of extant tortoises and eight near-complete sequences of all Mascarene species extracted from historic and subfossil material. Cylindraspis is an ancient lineage that diverged as early as the late Eocene. Diversification of Cylindraspis commenced in the mid-Oligocene, long before the formation of the Mascarene Islands. This rejects any notion suggesting that the group either arrived from nearby or distant continents over the course of the last millions of years or had even been translocated to the islands by humans. Instead, Cylindraspis likely originated on now submerged islands of the Réunion Hotspot and utilized these to island hop to reach the Mascarenes. The final diversification took place both before and after the arrival on the Mascarenes. With Cylindraspis a deeply divergent clade of tortoises became extinct that evolved long before the dodo or the Rodrigues solitaire, two other charismatic species of the lost Mascarene fauna.}, }
@article {pmid31767817, year = {2019}, author = {Abou-Shaara, HF}, title = {Utilizing bioinformatics to detect genetic similarities between African honey bee subspecies.}, journal = {Journal of genetics}, volume = {98}, number = {}, pages = {}, pmid = {31767817}, issn = {0973-7731}, mesh = {Africa ; Animals ; Base Sequence ; Bees/*classification/*genetics ; *Computational Biology ; DNA Primers ; DNA, Mitochondrial/genetics ; Mitochondria/*genetics ; Multigene Family ; Open Reading Frames ; Phylogeny ; Sequence Analysis ; }, abstract = {Various honey bees, especially subspecies Apis mellifera, occur in Africa and are distribute across the continent. The genetic relationships and identical genetic characteristics between honey bee subspecies in Africa (African bee subspecies) have not been widely investigated using sequence analysis. On the other hand, bioinformatics are developed rapidly and have diverse applications. It is anticipated that bioinformatics can show the genetic relationships and similarities among subspecies. These points have high importance, especially subspecies with identical genetic characteristics can be infected with the same group of pathogens, which have implications on honey bee health. In this study, the mitochondrial DNA sequences of four African subspecies and Africanized bees were subjected to the analyses of base composition, phylogeny, shared gene clusters, enzymatic digestion, and open reading frames. High identical base composition was detected in the studied subspecies, and high identical results from all tests were found between A. m. scutellata and A. m. capensis followed by A. m. intermissa and A. m. monticola. The least genetic relationships were found between A. m. lamarckii and the other subspecies. This study presents insights into the genetic aspects of African bee subspecies and highlights similarity and dissimilarity aspects. Also, Africanized honey bees derived from A. m. scutellata showed high genetic similarities to other African bees, especially A. m. capensis. Additionally, specific primers to identify these subspecies were designed and tested.}, }
@article {pmid31767814, year = {2019}, author = {Kumar De, A and Ponraj, P and Malakar, D and Muthiyan, R and Kundu, A and Bhattacharya, D}, title = {Complete mitogenome sequencing of Andaman buffalo: an endangered germplasm of Andaman and Nicobar Islands, India.}, journal = {Journal of genetics}, volume = {98}, number = {}, pages = {}, pmid = {31767814}, issn = {0973-7731}, mesh = {Animals ; Base Composition ; Buffaloes/*genetics ; China ; Codon, Initiator ; Codon, Terminator ; Genes, Mitochondrial/*genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing ; India ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Andaman buffalo is an indigenous buffalo of Andaman and Nicobar Islands, India. Over the last decade, it has witnessed a rapid decline in population, necessitating its immediate characterization and conservation. The present study reports the complete mitogenome profile of Andaman buffalo which is 16,359 bp in length and comprised of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs and two ribosomal RNAs. In addition, one A + T rich region (D-loop) was also present. A biasness towards A and T base was observed in all the genes. All the PCGs except ND6 were present on heavy strand. Start codons for all the 13 PCGs were ATN codon and abbreviated/truncated stop codons were observed in ND1, ND2, COX3, ND3 and ND4. The phylogenetic analysis revealed that the Andaman buffalo is closely related to buffalo from India and China. The results from this study will help in sketching the conservation plan of the threatened breed.}, }
@article {pmid31766564, year = {2019}, author = {Brieba, LG}, title = {Structure-Function Analysis Reveals the Singularity of Plant Mitochondrial DNA Replication Components: A Mosaic and Redundant System.}, journal = {Plants (Basel, Switzerland)}, volume = {8}, number = {12}, pages = {}, pmid = {31766564}, issn = {2223-7747}, support = {13//SEP-Cinvestav/ ; }, abstract = {Plants are sessile organisms, and their DNA is particularly exposed to damaging agents. The integrity of plant mitochondrial and plastid genomes is necessary for cell survival. During evolution, plants have evolved mechanisms to replicate their mitochondrial genomes while minimizing the effects of DNA damaging agents. The recombinogenic character of plant mitochondrial DNA, absence of defined origins of replication, and its linear structure suggest that mitochondrial DNA replication is achieved by a recombination-dependent replication mechanism. Here, I review the mitochondrial proteins possibly involved in mitochondrial DNA replication from a structural point of view. A revision of these proteins supports the idea that mitochondrial DNA replication could be replicated by several processes. The analysis indicates that DNA replication in plant mitochondria could be achieved by a recombination-dependent replication mechanism, but also by a replisome in which primers are synthesized by three different enzymes: Mitochondrial RNA polymerase, Primase-Helicase, and Primase-Polymerase. The recombination-dependent replication model and primers synthesized by the Primase-Polymerase may be responsible for the presence of genomic rearrangements in plant mitochondria.}, }
@article {pmid31762360, year = {2020}, author = {Phukuntsi, MA and Du Plessis, M and Dalton, DL and Jansen, R and Cuozzo, FP and Sauther, ML and Kotze, A}, title = {Population genetic structure of the thick-tailed bushbaby (Otolemur crassicaudatus) from the Soutpansberg Mountain range, Northern South Africa, based on four mitochondrial DNA regions.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {31}, number = {1}, pages = {1-10}, doi = {10.1080/24701394.2019.1694015}, pmid = {31762360}, issn = {2470-1408}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Female ; Galago/*genetics ; Genetic Variation/genetics ; *Genetics, Population ; Genome, Mitochondrial/*genetics ; Male ; Phylogeny ; South Africa ; }, abstract = {Greater bushbabies, strepsirrhine primates, that are distributed across central, eastern and southern Africa, with northern and eastern South Africa representing the species' most southerly distribution. Greater bushbabies are habitat specialists whose naturally fragmented habitats are getting even more fragmented due to anthropogenic activities. Currently, there is no population genetic data or study published on the species. The aim of our study was to investigate the genetic variation in a thick-tailed bushbaby, Otolemur crassicaudatus, population in the Soutpansberg mountain range, Limpopo Province, South Africa. Four mitochondrial regions, ranging from highly conserved to highly variable, were sequenced from 47 individuals. The sequences were aligned and genetic diversity, structure, as well as demographic analyses were performed. Low genetic diversity (π = 0.0007-0.0038 in coding regions and π = 0.0127 in non-coding region; Hd = 0.166-0.569 in coding regions and Hd = 0.584 in non-coding region) and sub-structuring (H = 2-3 in coding regions and H = 4 in non-coding region) was observed with two divergent haplogroups (haplotype pairwise distance = 3-5 in coding region and 6-10 in non-coding region) being identified. This suggests the population may have experienced fixation of mitochondrial haplotypes due to limited female immigration, which is consistent with philopatric species, that alternative haplotypes are not native to this population, and that there may be male mobility from adjacent populations. This study provides the first detailed insights into the mitochondrial genetic diversity of a continental African strepsirrhine primate and demonstrates the utility of mitochondrial DNA in intraspecific genetic population analyses of these primates.}, }
@article {pmid31758495, year = {2020}, author = {Magallón-Gayón, E and Del Río-Portilla, M&#xc1; and de Los Angeles Barriga-Sosa, I}, title = {The complete mitochondrial genomes of two octopods of the eastern Pacific Ocean: Octopus mimus and 'Octopus' fitchi (Cephalopoda: Octopodidae) and their phylogenetic position within Octopoda.}, journal = {Molecular biology reports}, volume = {47}, number = {2}, pages = {943-952}, pmid = {31758495}, issn = {1573-4978}, support = {UAM-147.09.01//Universidad Aut&#xf3;noma Metropolitana (MX)/ ; 04//Universidad Aut&#xf3;noma Metropolitana (MX)/ ; 07//Universidad Aut&#xf3;noma Metropolitana (MX)/ ; 14713349//SEP-PRODEP/ ; }, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; DNA, Mitochondrial/*genetics ; Gene Order ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Octopodiformes/*genetics ; Open Reading Frames ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {The complete mitochondrial genomes of two important octopus species from the eastern Pacific were sequenced, obtaining their complete nucleotide sequences. Octopus mimus is the most important commercially catched species along the eastern Pacific, from Mexico to Chile, whereas 'Octopus' fitchi is a pigmy species with uncertain taxonomic genus. The mitogenomes of Octopus mimus and 'Octopus' fitchi were 15,696 and 15,780 base pairs (bp) in length with an A + T composition of 75.5% and 75.8%, respectively. Each genome contains 13 protein-coding genes, 22 tRNA genes, and two rRNA genes, as well as a control region. Gene order is maintained as reported for other species of the Octopodidae. The phylogenetic analysis based on the concatenated thirteen protein-coding genes confirms that O. mimus belongs to the genus Octopus, which is supported by the genetic distance (11-16%) whereas the position of 'O'. fitchi within this group it is not supported. The analysis also indicated that the phylogenetic position of 'O'. fitchi is closer to Callistoctopus than to the Cistopus or the Amphioctopus clades. Based on the tree topology and the high genetic distance observed (24-25%), we suggest that 'O'. fitchi might represent a different genus.}, }
@article {pmid31754022, year = {2019}, author = {Li, H and Rukina, D and David, FPA and Li, TY and Oh, CM and Gao, AW and Katsyuba, E and Bou Sleiman, M and Komljenovic, A and Huang, Q and Williams, RW and Robinson-Rechavi, M and Schoonjans, K and Morgenthaler, S and Auwerx, J}, title = {Identifying gene function and module connections by the integration of multispecies expression compendia.}, journal = {Genome research}, volume = {29}, number = {12}, pages = {2034-2045}, pmid = {31754022}, issn = {1549-5469}, support = {R01 AG043930/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; *Databases, Nucleic Acid ; *Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; *Gene Regulatory Networks ; Humans ; Mice ; Rats ; Saccharomyces cerevisiae/*genetics ; *Software ; }, abstract = {The functions of many eukaryotic genes are still poorly understood. Here, we developed and validated a new method, termed GeneBridge, which is based on two linked approaches to impute gene function and bridge genes with biological processes. First, Gene-Module Association Determination (G-MAD) allows the annotation of gene function. Second, Module-Module Association Determination (M-MAD) allows predicting connectivity among modules. We applied the GeneBridge tools to large-scale multispecies expression compendia-1700 data sets with over 300,000 samples from human, mouse, rat, fly, worm, and yeast-collected in this study. G-MAD identifies novel functions of genes-for example, DDT in mitochondrial respiration and WDFY4 in T cell activation-and also suggests novel components for modules, such as for cholesterol biosynthesis. By applying G-MAD on data sets from respective tissues, tissue-specific functions of genes were identified-for instance, the roles of EHHADH in liver and kidney, as well as SLC6A1 in brain and liver. Using M-MAD, we identified a list of module-module associations, such as those between mitochondria and proteasome, mitochondria and histone demethylation, as well as ribosomes and lipid biosynthesis. The GeneBridge tools together with the expression compendia are available as an open resource, which will facilitate the identification of connections linking genes, modules, phenotypes, and diseases.}, }
@article {pmid31751694, year = {2020}, author = {Song, N and Li, X and Yin, X and Li, X and Xi, Y}, title = {The mitochondrial genomes of ladybird beetles and implications for evolution and phylogeny.}, journal = {International journal of biological macromolecules}, volume = {147}, number = {}, pages = {1193-1203}, doi = {10.1016/j.ijbiomac.2019.10.089}, pmid = {31751694}, issn = {1879-0003}, mesh = {Animals ; Bayes Theorem ; Codon ; Coleoptera/*genetics/*physiology ; *Genome, Mitochondrial ; Herbivory ; High-Throughput Nucleotide Sequencing ; Likelihood Functions ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Ladybirds formed the most familiar beetle group, namely the family Coccinellidae, whose internal relationships remain unclear. In particular, the subfamily relationships could not be well resolved in previous studies based on the conventional nuclear and/or mitochondrial gene fragments. In this study, we used next-generation sequencing to obtain new mitochondrial genomes (mitogenomes) from 13 species representing four coccinellid subfamilies (i.e., Coccinellinae, Epilachninae, Coccidulinae and Chilocorinae). Together with 24 existing mitogenome sequences of Cucujoidea, we conducted phylogenetic analyses to investigate the deep phylogenetic relationships in Coccinellidae, under maximum likelihood and Bayesian inference criteria. The analyses from nucleotide datasets resulted in a largely identical tree topology, where Epilachninae and Coccinellinae were monophyletic groups. The Scymninae and Coccidulinae were recovered as non-monophyletic. Amino acids differed from nucleotides in that the Epilachninae was retrieved as paraphyletic, with respect to Epilachna admirabilis. Ancestral state reconstruction suggested that the plant eating ladybird beetles arose within an aphidophagous/coccidophagous clade. In addition, three independent shifts toward coccidophagy and one shift toward mycophagy occurred in Coccinellidae.}, }
@article {pmid31751405, year = {2019}, author = {Voleman, L and Doležal, P}, title = {Mitochondrial dynamics in parasitic protists.}, journal = {PLoS pathogens}, volume = {15}, number = {11}, pages = {e1008008}, pmid = {31751405}, issn = {1553-7374}, mesh = {Animals ; *Mitochondrial Dynamics ; Parasites/*pathogenicity ; Parasitic Diseases/*epidemiology/parasitology/*physiopathology ; }, abstract = {The shape and number of mitochondria respond to the metabolic needs during the cell cycle of the eukaryotic cell. In the best-studied model systems of animals and fungi, the cells contain many mitochondria, each carrying its own nucleoid. The organelles, however, mostly exist as a dynamic network, which undergoes constant cycles of division and fusion. These mitochondrial dynamics are driven by intricate protein machineries centered around dynamin-related proteins (DRPs). Here, we review recent advances on the dynamics of mitochondria and mitochondrion-related organelles (MROs) of parasitic protists. In contrast to animals and fungi, many parasitic protists from groups of Apicomplexa or Kinetoplastida carry only a single mitochondrion with a single nucleoid. In these groups, mitochondrial division is strictly coupled to the cell cycle, and the morphology of the organelle responds to the cell differentiation during the parasite life cycle. On the other hand, anaerobic parasitic protists such as Giardia, Entamoeba, and Trichomonas contain multiple MROs that have lost their organellar genomes. We discuss the function of DRPs, the occurrence of mitochondrial fusion, and mitophagy in the parasitic protists from the perspective of eukaryote evolution.}, }
@article {pmid31750917, year = {2020}, author = {Costello, R and Emms, DM and Kelly, S}, title = {Gene Duplication Accelerates the Pace of Protein Gain and Loss from Plant Organelles.}, journal = {Molecular biology and evolution}, volume = {37}, number = {4}, pages = {969-981}, pmid = {31750917}, issn = {1537-1719}, support = {BB/P003117/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J014427/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Evolution, Molecular ; *Gene Duplication ; *Genome ; Mitochondria/metabolism ; *Phylogeny ; Plants/*genetics/metabolism ; Proteome ; }, abstract = {Organelle biogenesis and function is dependent on the concerted action of both organellar-encoded (if present) and nuclear-encoded proteins. Differences between homologous organelles across the Plant Kingdom arise, in part, as a result of differences in the cohort of nuclear-encoded proteins that are targeted to them. However, neither the rate at which differences in protein targeting accumulate nor the evolutionary consequences of these changes are known. Using phylogenomic approaches coupled to ancestral state estimation, we show that the plant organellar proteome has diversified in proportion with molecular sequence evolution such that the proteomes of plant chloroplasts and mitochondria lose or gain on average 3.6 proteins per million years. We further demonstrate that changes in organellar protein targeting are associated with an increase in the rate of molecular sequence evolution and that such changes predominantly occur in genes with regulatory rather than metabolic functions. Finally, we show that gain and loss of protein target signals occurs at a higher rate following gene duplication, revealing that gene and genome duplication are a key facilitator of plant organelle evolution.}, }
@article {pmid31747540, year = {2020}, author = {Anderson, K and Braoudakis, G and Kvist, S}, title = {Genetic variation, pseudocryptic diversity, and phylogeny of Erpobdella (Annelida: Hirudinida: Erpobdelliformes), with emphasis on Canadian species.}, journal = {Molecular phylogenetics and evolution}, volume = {143}, number = {}, pages = {106688}, doi = {10.1016/j.ympev.2019.106688}, pmid = {31747540}, issn = {1095-9513}, mesh = {Animals ; Annelida/classification/*genetics ; Biodiversity ; Canada ; Electron Transport Complex IV/classification/genetics ; *Genetic Variation ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal/classification/genetics ; }, abstract = {Leeches of the family Erpobdellidae are important members of benthic freshwater environments, where they are voracious predators of other invertebrates and an important source of nutrition for several species of vertebrates. Beset by a lack of reliable diagnostic morphological characters and destructive identification processes, molecular approaches have, in recent years, been employed to illuminate the relationships within this family, and DNA barcoding has been employed for identification purposes. However, an understanding of the levels of genetic variation across the geographic distributions of members of the genus is still lacking. Herein, we sequence the mitochondrial COI locus for 249 newly collected North American individuals, representing 5 species, as well as mitochondrial 12S rDNA, nuclear 18S rDNA, and nuclear 28S rDNA for a select subset of these. Our COI dataset was leveraged to detect potential cryptic species, and to calculate genetic distances as a proxy for the degree of gene flow between populations. Augmented by numerous sequences from GenBank, the multilocus dataset was used to reconstruct a phylogenetic hypothesis for worldwide members of the genus. Beyond corroborating previous overarching phylogenetic frameworks, our results show that an undescribed species that is morphologically and genetically similar to Erpobdella punctata exists in sympatry with this species - the new species has likely been overlooked in previous studies due to its morphological similarity with Erpobdella punctata. Erpobdella bucera is reported from Canada for the first time; and Erpobdella microstoma is newly reported from Saskatchewan and placed in a phylogeny for the first time. Finally, we find evidence for genetic structure in both E. cf. punctata and Erpobdella obscura that is correlated with major river drainage basin boundaries in North America.}, }
@article {pmid31742484, year = {2019}, author = {Woodyard, ET and Stilwell, JM and Camus, AC and Rosser, TG}, title = {Molecular and Histopathological Data on Levisunguis subaequalis Curran, Overstreet, Collins &amp; Benz, 2014 (Pentastomida: Eupentastomida: Porocephalida: Porocephaloidea: Sebekidae: Sebekinae) from Gambusia affinis in Alabama, USA.}, journal = {The Journal of parasitology}, volume = {105}, number = {6}, pages = {827-839}, pmid = {31742484}, issn = {1937-2345}, mesh = {Alabama/epidemiology ; Animals ; Bayes Theorem ; Cyprinodontiformes/*parasitology ; DNA/genetics/isolation &amp; purification ; Electron Transport Complex IV/genetics ; Fish Diseases/epidemiology/*parasitology ; Likelihood Functions ; Lung/parasitology ; Mitochondria/enzymology ; Nymph/anatomy &amp; histology ; Parasitic Diseases, Animal/epidemiology/*parasitology ; Pentastomida/anatomy &amp; histology/classification/*genetics ; Phylogeny ; Prevalence ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Turtles/parasitology ; }, abstract = {Levisunguis subaequalis Curran, Overstreet, Collins &amp; Benz, 2014 , was recently described from the lungs of the definitive hosts, softshell turtles, Apalone ferox (Schneider, 1783), and Apalone spinifera aspera (Agassiz, 1857) as well as the viscera of an intermediate host, the western mosquitofish, Gambusia affinis (Baird and Girard, 1853). However, the original account lacked molecular data. Furthermore, histological examination of infected host tissues in the original account of L. subaequalis did not reveal any pathological changes in the intermediate host. The present work provides a robust morphological description of the nymph and novel molecular data from the 18S and 28S ribosomal gene regions and the cytochrome c oxidase subunit 1 (COI) mitochondrial gene. Phylogenetic analyses using Bayesian inference and maximum likelihood analysis with concatenated sequence data from these 3 regions, as well as each region individually, placed the turtle pentastomid L. subaequalis as a sister clade to the crocodilian pentastomids of the genus Sebekia Sambon, 1922. While only concatenated phylogenetic analyses agreed with the currently accepted classification of the Eupentastomida and phylogenetic signal assessment indicated that the concatenated data set yielded the most phylogenetic signal, data from more taxa are still needed for robust phylogenetic inferences to be made. The intensity of infection ranged from 2 to 171 nymphs per fish, compared with the highest previously reported intensity of 6. These high-intensity infections with L. subaequalis were characterized by the nymphs occupying 5-50% of the coelomic cavity of G. affinis. However, despite this heavy parasite infection, fish exhibited minimal pathology. Observed pathology was characterized by compression or effacement of organs adjacent to the nymphs, particularly liver, swim bladder, and intestines, as well as the formation of granulomas around shed pentastomid cuticles. Nonetheless, the morphological and molecular data provided in the present work will bolster future efforts to identify this pentastomid in other hosts where pathology may be present in addition to aiding in the advancement of the field of molecular pentastomid systematics.}, }
@article {pmid31740334, year = {2020}, author = {Feng, JM and Jiang, CQ and Sun, ZY and Hua, CJ and Wen, JF and Miao, W and Xiong, J}, title = {Single-cell transcriptome sequencing of rumen ciliates provides insight into their molecular adaptations to the anaerobic and carbohydrate-rich rumen microenvironment.}, journal = {Molecular phylogenetics and evolution}, volume = {143}, number = {}, pages = {106687}, doi = {10.1016/j.ympev.2019.106687}, pmid = {31740334}, issn = {1095-9513}, mesh = {Adaptation, Physiological ; Anaerobiosis ; Animals ; Carbohydrate Metabolism ; Cellulases/genetics ; Ciliophora/classification/*genetics/physiology ; Gene Transfer, Horizontal ; Glycoside Hydrolases/genetics ; Phylogeny ; Polygalacturonase/genetics ; RNA-Seq ; Rumen/metabolism/*parasitology ; Single-Cell Analysis ; *Transcriptome ; }, abstract = {Rumen ciliates are a specialized group of ciliates exclusively found in the anaerobic, carbohydrate-rich rumen microenvironment. However, the molecular and mechanistic basis of the physiological and behavioral adaptation of ciliates to the rumen microenvironment is undefined. We used single-cell transcriptome sequencing to explore the adaptive evolution of three rumen ciliates: two entodiniomorphids, Entodinium furca and Diplodinium dentatum; and one vestibuliferid, Isotricha intestinalis. We found that all three species are members of monophyletic orders within the class Litostomatea, with E. furca and D. dentatum in Entodiniomorphida and I. intestinalis in Vestibuliferida. The two entodiniomorphids might use H2-producing mitochondria and the vestibuliferid might use anaerobic mitochondria to survive under strictly anaerobic conditions. Moreover, carbohydrate-active enzyme (CAZyme) genes were identified in all three species, including cellulases, hemicellulases, and pectinases. The evidence that all three species have acquired prokaryote-derived genes by horizontal gene transfer (HGT) to digest plant biomass includes a significant enrichment of gene ontology categories such as cell wall macromolecule catabolic process and carbohydrate catabolic process and the identification of genes in common between CAZyme and HGT groups. These findings suggest that HGT might be an important mechanism in the adaptive evolution of ciliates to the rumen microenvironment.}, }
@article {pmid31728830, year = {2020}, author = {Wang, S and Jiao, N and Zhao, L and Zhang, M and Zhou, P and Huang, X and Hu, F and Yang, C and Shu, Y and Li, W and Zhang, C and Tao, M and Chen, B and Ma, M and Liu, S}, title = {Evidence for the paternal mitochondrial DNA in the crucian carp-like fish lineage with hybrid origin.}, journal = {Science China. Life sciences}, volume = {63}, number = {1}, pages = {102-115}, pmid = {31728830}, issn = {1869-1889}, mesh = {Animals ; Base Sequence ; Carps/*classification/*genetics ; DNA, Mitochondrial/*genetics ; Female ; Gene Expression ; Goldfish/*classification/*genetics ; Hybridization, Genetic ; Male ; Mitochondria/genetics ; Ploidies ; }, abstract = {In terms of taxonomic status, common carp (Cyprinus carpio, Cyprininae) and crucian carp (Carassius auratus, Cyprininae) are different species; however, in this study, a newborn homodiploid crucian carp-like fish (2n=100) (2nNCRC) lineage (F1-F3) was established from the interspecific hybridization of female common carp (2n=100)×male blunt snout bream (Megalobrama amblycephala, Cultrinae, 2n=48). The phenotypes and genotypes of 2nNCRC differed from those of its parents but were closely related to those of the existing diploid crucian carp. We further sequenced the whole mitochondrial (mt) genomes of the 2nNCRC lineage from F1 to F3. The paternal mtDNA fragments were stably embedded in the mt-genomes of F1-F3 generations of 2nNCRC to form chimeric DNA fragments. Along with this chimeric process, numerous base sites of F1-F3 generations of 2nNCRC underwent mutations. Most of these mutation sites were consistent with the existing diploid crucian carp. Moreover, the mtDNA organization and nucleotide composition of 2nNCRC were more similar to those of the existing diploid crucian carp than those of the parents. The inheritable chimeric DNA fragments and mutant loci in the mt-genomes of different generations of 2nNCRC provided important evidence of the mtDNA change process in the newborn lineage derived from hybridization of different species. Our findings demonstrated for the first time that the paternal mtDNA were transmitted into the mt-genomes of homodiploid lineage, which provided new insights into the existence of paternal mtDNA in the mtDNA inheritance.}, }
@article {pmid31727366, year = {2020}, author = {Li, J and Xue, C and Gao, Q and Tan, J and Wan, Z}, title = {Mitochondrial DNA heteroplasmy rises in substantial nigra of aged PINK1 KO mice.}, journal = {Biochemical and biophysical research communications}, volume = {521}, number = {4}, pages = {1024-1029}, doi = {10.1016/j.bbrc.2019.10.112}, pmid = {31727366}, issn = {1090-2104}, mesh = {Aging/genetics ; Animals ; Brain/metabolism ; DNA Copy Number Variations/genetics ; DNA, Mitochondrial/*genetics ; Gene Frequency/genetics ; Mice, Knockout ; Mutation Rate ; Protein Kinases/*deficiency/genetics/metabolism ; Substantia Nigra/*metabolism ; }, abstract = {Mutations in PINK1 and Parkin result in early-onset autosomal recessive Parkinson's disease (PD). PINK1/Parkin pathway maintain mitochondrial function by mediating the clearance of damaged mitochondria. However, the role of PINK1/Parkin in maintaining the balance of mtDNA heteroplasmy is still unknown. Here, we isolated mitochondrial DNA (mtDNA) from cortex, striatum and substantia nigra of wildtype (WT), PINK1 knockout (PINK1 KO) and Parkin knockout (Parkin KO) mice to analyze mtDNA heteroplasmy induced by PINK1/Parkin deficiency or aging. Our results showed that the Single Nucleotide Variants (SNVs) of late-onset somatic variants mainly increased with aging. Conversely, the early-onset somatic variants exhibited significant increase in the cortex and substantia nigra of PINK1 KO mice than WT mice of the same age. Increased average variant allele frequency was observed in aged PINK1 KO mice and in substantial nigra of aged Parkin KO mice than in WT mice. Cumulative variant allele frequency in the substantia nigra of PINK1 KO mice was significantly higher than that in WT mice, further supporting the pivotal role of PINK1 in mtDNA maintenance. This study presented a new evidence for PINK1 and Parkin in participating in mitochondrial quality control and provided clues for further revealing the role of PINK1 and Parkin in the pathogenesis of PD.}, }
@article {pmid31726178, year = {2020}, author = {Shen, Y and Wang, X and Guo, S and Qiu, M and Hou, G and Tan, Z}, title = {Evolutionary genomics analysis of human nucleus-encoded mitochondrial genes: implications for the roles of energy production and metabolic pathways in the pathogenesis and pathophysiology of demyelinating diseases.}, journal = {Neuroscience letters}, volume = {715}, number = {}, pages = {134600}, doi = {10.1016/j.neulet.2019.134600}, pmid = {31726178}, issn = {1872-7972}, mesh = {Animals ; Cell Nucleus/genetics/*metabolism ; Demyelinating Diseases/genetics/*metabolism ; Energy Metabolism/*physiology ; Evolution, Molecular ; Genes, Mitochondrial/*physiology ; Genomics/*methods ; Humans ; Metabolic Networks and Pathways/*physiology ; Mice ; Myelin Sheath/genetics/*metabolism ; }, abstract = {The myelin sheath is a plasma membrane extension that lines nerve fibers to protect, support and insulate neurons. The myelination of axons in vertebrates enables fast, saltatory impulse propagation, and this process relies on organelles, especially on mitochondria to supply energy. Approximately 99% of mitochondrial proteins are encoded in the nucleus. Since mitochondria play a central role in the energy production and metabolic pathways, which are essential for myelinogenesis, studying these nucleus-encoded genes (nMGs) may provide new insights into the roles of energy metabolism in demyelinating diseases. In this work, a multiomics-based approach was employed to 1) construct a 1,740 human nMG subset with mitochondrial localization evidence obtained from the Integrated Mitochondrial Protein Index (IMPI) and MitoCarta databases, 2) conduct an evolutionary genomics analysis across mouse, rat, monkey, chimp, and human models, 3) examine dysmyelination phenotype-related genes (nMG subset genes with oligodendrocyte- and myelin-related phenotypes, OMP-nMGs) in MGI mouse lines and human patients, 4) determine the expression discrepancy of OMP-nMGs in brain tissues of cuprizone-treated mice, multiple sclerosis patients, and normal controls, and 5) conduct literature data mining to explore OMP-nMG-associated disease impacts. By contrasting OMP-nMGs with other genes, OMP-nMGs were found to be more ubiquitously expressed (59.1% vs. 16.1%), disease-associated (67.3% vs. 20.2%), and evolutionarily conserved within the human populations. Our multiomics-based analysis identified 110 OMP-nMGs implicated in energy production and lipid and glycan biosynthesis in the pathogenesis and pathophysiology of demyelinating disorders. Future targeted characterization of OMP-nMGs in abnormal myelination conditions may allow the discovery of novel nMG mediated mechanisms underlying myelinogenesis and related diseases.}, }
@article {pmid31719597, year = {2019}, author = {Hao, Y and Ruiz, R and Yang, L and Neto, AG and Amin, MR and Kelly, D and Achlatis, S and Roof, S and Bing, R and Kannan, K and Brown, SM and Pei, Z and Branski, RC}, title = {Mitochondrial somatic mutations and the lack of viral genomic variation in recurrent respiratory papillomatosis.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {16625}, pmid = {31719597}, issn = {2045-2322}, support = {R21 DE025352/DE/NIDCR NIH HHS/United States ; R01 AI110372/AI/NIAID NIH HHS/United States ; U01 CA182370/CA/NCI NIH HHS/United States ; R01 CA204113/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; DNA, Viral/genetics ; Female ; Genetic Variation/genetics ; Genome, Viral/*genetics ; Human papillomavirus 11/*genetics ; Human papillomavirus 6/*genetics ; Humans ; Male ; Middle Aged ; Mitochondria/*genetics ; Mouth/virology ; Multiplex Polymerase Chain Reaction ; Mutation/genetics ; Papillomavirus Infections/diagnosis/genetics/*virology ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Respiratory Tract Infections/diagnosis/genetics/*virology ; }, abstract = {Recurrent Respiratory Papillomatosis (RRP) is a rare disease of the aerodigestive tract caused by the Human Papilloma Virus (HPV) that manifests as profoundly altered phonatory and upper respiratory anatomy. Current therapies are primarily symptomatic; enhanced insight regarding disease-specific biology of RRP is critical to improved therapeutics for this challenging population. Multiplex PCR was performed on oral rinses collected from twenty-three patients with adult-onset RRP every three months for one year. Twenty-two (95.6%) subjects had an initial HPV positive oral rinse. Of those subjects, 77.2% had an additional positive oral rinse over 12 months. A subset of rinses were then compared to tissue samples in the same patient employing HPViewer to determine HPV subtype concordance. Multiple HPV copies (60-787 per human cell) were detected in RRP tissue in each patient, but a single dominant HPV was found in individual samples. These data confirm persistent oral HPV infection in the majority of patients with RRP. In addition, three novel HPV6 isolates were found and identical HPV strains, at very low levels, were identified in oral rinses in two patients suggesting potential HPV subtype concordance. Finally, somatic heteroplasmic mtDNA mutations were observed in RRP tissue with 1.8 mutations per sample and two nonsynonymous variants. These data provide foundational insight into both the underlying pathophysiology of RRP, but also potential targets for intervention in this challenging patient cohort.}, }
@article {pmid31716895, year = {2019}, author = {Tominaga, A and Matsui, M and Tanabe, S and Nishikawa, K}, title = {A revision of Hynobius stejnegeri, a lotic breeding salamander from western Japan, with a description of three new species (Amphibia, Caudata, Hynobiidae).}, journal = {Zootaxa}, volume = {4651}, number = {3}, pages = {zootaxa.4651.3.1}, doi = {10.11646/zootaxa.4651.3.1}, pmid = {31716895}, issn = {1175-5334}, mesh = {Animals ; Breeding ; Japan ; Mitochondria ; Phylogeny ; Tooth ; *Urodela ; }, abstract = {A lotic-breeding salamander Hynobius stejnegeri, formerly called H. yatsui, from western Japan is revised based on genetic and morphological evidence, and three species are described: H. guttatus sp. nov. from Chubu-Kinki districts of Honshu Island, H. tsurugiensis sp. nov. from east highland of Shikoku Island, and H. kuishiensis sp. nov. from other parts of Shikoku Island. Thus, H. stejnegeri sensu stricto is restricted to Kyushu Island. Of these four species, H. kuishiensis sp. nov. contains two distinct mitochondrial lineages, but this split is not reflected in differentiation of allozyme (nuclear genome) markers. These species are morphologically similar to each other but can be differentiated by several characteristics, especially in combination of dorsal coloration, the number of vomerine, upper, and lower jaw teeth, and depth of vomerine teeth series. In coloration, H. guttatus sp. nov. is brown or dark brown mostly with tiny white to brownish white marking, while H. tsurugiensis sp. nov. is dark brown with bright yellow continuous markings. Hynobius kuishiensis sp. nov. is reddish purple or dark brown with small to continuous brownish white markings, in contrast to reddish purple or dark brown with small to large brownish white markings in H. stejnegeri.}, }
@article {pmid31716534, year = {2019}, author = {Braun, MP and Datzmann, T and Arndt, T and Reinschmidt, M and Schnitker, H and Bahr, N and Sauer-Gürth, H and Wink, M}, title = {A molecular phylogeny of the genus Psittacula sensu lato (Aves: Psittaciformes: Psittacidae: Psittacula, Psittinus, Tanygnathus, †Mascarinus) with taxonomic implications.}, journal = {Zootaxa}, volume = {4563}, number = {3}, pages = {zootaxa.4563.3.8}, doi = {10.11646/zootaxa.4563.3.8}, pmid = {31716534}, issn = {1175-5334}, mesh = {Animals ; Base Sequence ; Mitochondria ; *Parrots ; Phylogeny ; *Psittaciformes ; *Psittacula ; }, abstract = {The long-tailed parakeets of the genus Psittacula Cuvier, 1800 have thus far been regarded as a homogeneous and monophyletic group of parrots. We used nucleotide sequences of two genetic markers (mitochondrial CYTB, nuclear RAG-1) to reconstruct the phylogenetic relationships of Psittacula and closely related species. We found that the Asian genus Psittacula is apparently paraphyletic because two genera of short-tailed parrots, Psittinus Blyth, 1842 and Tanygnathus Wagler, 1832, cluster within Psittacula, as does †Mascarinus Lesson, 1830. To create monophyletic genera, we propose recognition of the following genera: Himalayapsitta Braun, 2016 for P. himalayana, P. finschii, P. roseata, and P. cyanocephala; Nicopsitta Braun, 2016 for P. columboides and P. calthrapae; Belocercus S. Müller, 1847 for P. longicauda; Psittacula Cuvier, 1800 for P. alexandri and P. derbiana; Palaeornis Vigors, 1825 for †P. wardi and P. eupatria; and Alexandrinus Braun, 2016 for P. krameri, †P. exsul, and P. (eques) echo. Additionally, Psittacula krameri and P. alexandri are paraphyletic species, which should be split to form monophyletic species.}, }
@article {pmid31716329, year = {2019}, author = {Macià, R and Mally, R and Ylla, J and Gastón, J and Huertas, M}, title = {Integrative revision of the Iberian species of Coscinia Hübner, [1819] sensu lato and Spiris Hübner, [1819], (Lepidoptera: Erebidae, Arctiinae).}, journal = {Zootaxa}, volume = {4615}, number = {3}, pages = {zootaxa.4615.3.1}, doi = {10.11646/zootaxa.4615.3.1}, pmid = {31716329}, issn = {1175-5334}, mesh = {Animals ; Female ; Genitalia ; Male ; Mitochondria ; *Moths ; *Mustelidae ; Phylogeny ; }, abstract = {The Iberian species of the genera Coscinia Hübner, [1819] and Spiris Hübner, [1819], as well as three other species from the Mediterranean area, are revised based on morphological and molecular genetic data. Our results suggest the separation into four morphologically and phylogenetically different genera: Coscinia Hübner, [1819], Lerautia Kemal Koçak, 2006 stat. rev., Sagarriella Macià, Mally, Ylla, Gastón Huertas gen. nov. and Spiris Hübner, [1819]. We conclude that there are eight species of the Coscinia genus group present in the studied area: Coscinia cribraria (Linnaeus, 1758), Coscinia chrysocephala (Hübner, [1810]) stat. rev., Coscinia mariarosae Expósito, 1991, Sagarriella libyssa caligans (Turati, 1907) comb. nov., Sagarriella romei (Sagarra, 1924) (= romeii sensu auctorum) comb. nov., Spiris striata Hübner, [1819], Spiris slovenica (Daniel, 1939) and Lerautia bifasciata (Rambur, 1832) comb. rev. We consider Coscinia cribraria benderi (Marten, 1957) stat. nov., Coscinia c. rippertii (Boisduval, 1834) and Coscinia c. ibicenca Kobes, 1991 stat. rev. to be subspecies of C. cribraria. COI Barcodes of C. cribraria diverge by up to 7.99%, and the investigated specimens group into six different COI Barcode BINs. Both the phylogenetic analysis of mitochondrial and nuclear DNA and the morphological examination of different specimens corroborate the changes in taxonomic status and justify the proposed taxonomic categories. We present images of adults and genitalia of both sexes, the immature stages of some of the species and the subspecies studied, as well as phylogenetic results from the analysis of genetic data. We also include data on life history, foodplants and geographical distribution.}, }
@article {pmid31716318, year = {2019}, author = {Hibbitts, TJ and Ryberg, WA and Harvey, JA and Voelker, G and Lawing, AM and Adams, CS and Neuharth, DB and Dittmer, DE and Duran, CM and Wolaver, BD and Pierre, JP and Labay, BJ and Laduc, TJ}, title = {Phylogenetic structure of Holbrookia lacerata (Cope 1880) (Squamata: Phrynosomatidae): one species or two?.}, journal = {Zootaxa}, volume = {4619}, number = {1}, pages = {zootaxa.4619.1.6}, doi = {10.11646/zootaxa.4619.1.6}, pmid = {31716318}, issn = {1175-5334}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial ; *Lizards ; Mitochondria ; Phylogeny ; Texas ; }, abstract = {Species delimitation attempts to match species-level taxonomy with actual evolutionary lineages. Such taxonomic conclusions are typically, but not always, based on patterns of congruence across multiple data sources and methods of analyses. Here, we use this pluralistic approach to species delimitation to help resolve uncertainty in species boundaries of phrynosomatid sand lizards of the genus Holbrookia. Specifically, the Spot-tailed Earless Lizard (H. lacerata) was historically divided into a northern (H. l. lacerata) and southern (H. l. subcaudalis) subspecies based on differences in morphology and allopatry, but no research has been conducted evaluating genetic differences between these taxa. In this study, patterns in sequence data derived from two genes, one nuclear and one mitochondrial, for 66 individuals sampled across 18 counties in Texas revealed three strongly supported, reciprocally monophyletic lineages, each comprised of individuals from a single geographic region. Distinct genetic variation evident across two of these regions corresponds with differences in morphology, differences in environmental niche, and lines up with the presumed geographic barrier, the Balcones Escarpment, which is the historical subspecies boundary. The combined evidence from genetics, morphology and environmental niche is sufficient to consider these subspecies as distinct species with the lizards north of the Balcones Escarpment retaining the name Holbrookia lacerata, and those south of the Balcones Escarpment being designated as Holbrookia subcaudalis.}, }
@article {pmid31715832, year = {2019}, author = {Han, H and Skou, P and Cheng, R}, title = {Neochloroglyphica, a new genus of Geometrinae from China (Lepidoptera, Geometridae), with description of a new species.}, journal = {Zootaxa}, volume = {4571}, number = {1}, pages = {zootaxa.4571.1.6}, doi = {10.11646/zootaxa.4571.1.6}, pmid = {31715832}, issn = {1175-5334}, mesh = {Animals ; China ; Genitalia ; *Lepidoptera ; Mitochondria ; *Moths ; Phylogeny ; }, abstract = {Neochloroglyphica gen. nov. and its type species N. perbella sp. nov. are described from Yunnan, China. Morphological characters and molecular phylogenetic analysis, based on one mitochondrial and three nuclear genes, support the hypothesis that Neochloroglyphica is a member of the tribe Neohipparchini, and that it is a sister genus to Chloroglyphica. Morphological characters, including those of the genitalia, are figured and compared with related genera, especially Chloroglyphica, Neohipparchus and Chlororithra. Diagnoses for the genus and the species are provided and illustrations of external features and genitalia are presented.}, }
@article {pmid31715688, year = {2019}, author = {Jeon, HK and Eom, KS}, title = {Mitochondrial DNA Sequence Variability of Spirometra Species in Asian Countries.}, journal = {The Korean journal of parasitology}, volume = {57}, number = {5}, pages = {481-487}, pmid = {31715688}, issn = {1738-0006}, support = {2017K1A3A1A09085607//National Research Foundation of Korea/ ; }, mesh = {Animals ; Cestode Infections/*parasitology ; China ; DNA, Helminth/*genetics ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Helminth Proteins/genetics ; Humans ; Japan ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Republic of Korea ; Spirometra/classification/*genetics/isolation &amp; purification ; }, abstract = {Mitochondrial DNA sequence variability of Spirometra erinaceieuropaei in GenBank was observed by reinvestigation of mitochondrial cox1 and cytb sequences. The DNA sequences were analyzed in this study, comprising complete DNA sequences of cox1 (n=239) and cytb (n=213) genes. The 10 complete mitochondrial DNA sequences of Spirometra species were compared with those of Korea, China and Japan. The sequences were analyzed for nucleotide composition, conserved sites, variable sites, singleton sites and parsimony-informative sites. Phylogenetic analyses was done using neighbor joining, maximum parsimony, Bayesian inference and maximum-likelihood on cox1 and cytb sequences of Spirometra species. These polymorphic sites identified 148 (cox1) and 83 (cytb) haplotypes within 239 and 213 isolates from 3 Asian countries. Phylogenetic tree topologies were presented high-level confidence values for the 2 major branches of 2 Spirometra species containing S. erinaceieuropaei and S. decipiens, and S. decipiens sub-clades including all sequences registered as S. erinaceieuropaei in cox1 and cytb genes. These results indicated that mitochondrial haplotypes of S. erinaceieuropaei and S. decipiens were found in the 3 Asian countries.}, }
@article {pmid31711195, year = {2020}, author = {Dourmap, C and Roque, S and Morin, A and Caubrière, D and Kerdiles, M and Béguin, K and Perdoux, R and Reynoud, N and Bourdet, L and Audebert, PA and Moullec, JL and Couée, I}, title = {Stress signalling dynamics of the mitochondrial electron transport chain and oxidative phosphorylation system in higher plants.}, journal = {Annals of botany}, volume = {125}, number = {5}, pages = {721-736}, pmid = {31711195}, issn = {1095-8290}, mesh = {Electron Transport ; *Oxidative Phosphorylation ; Oxidative Stress ; *Plants ; Reactive Oxygen Species ; Signal Transduction ; Stress, Physiological ; }, abstract = {BACKGROUND: Mitochondria play a diversity of physiological and metabolic roles under conditions of abiotic or biotic stress. They may be directly subjected to physico-chemical constraints, and they are also involved in integrative responses to environmental stresses through their central position in cell nutrition, respiration, energy balance and biosyntheses. In plant cells, mitochondria present various biochemical peculiarities, such as cyanide-insensitive alternative respiration, and, besides integration with ubiquitous eukaryotic compartments, their functioning must be coupled with plastid functioning. Moreover, given the sessile lifestyle of plants, their relative lack of protective barriers and present threats of climate change, the plant cell is an attractive model to understand the mechanisms of stress/organelle/cell integration in the context of environmental stress responses.<br><br>SCOPE: The involvement of mitochondria in this integration entails a complex network of signalling, which has not been fully elucidated, because of the great diversity of mitochondrial constituents (metabolites, reactive molecular species and structural and regulatory biomolecules) that are linked to stress signalling pathways. The present review analyses the complexity of stress signalling connexions that are related to the mitochondrial electron transport chain and oxidative phosphorylation system, and how they can be involved in stress perception and transduction, signal amplification or cell stress response modulation.<br><br>CONCLUSIONS: Plant mitochondria are endowed with a diversity of multi-directional hubs of stress signalling that lead to regulatory loops and regulatory rheostats, whose functioning can amplify and diversify some signals or, conversely, dampen and reduce other signals. Involvement in a wide range of abiotic and biotic responses also implies that mitochondrial stress signalling could result in synergistic or conflicting outcomes during acclimation to multiple and complex stresses, such as those arising from climate change.}, }
@article {pmid31706020, year = {2020}, author = {Prous, M and Lee, KM and Mutanen, M}, title = {Cross-contamination and strong mitonuclear discordance in Empria sawflies (Hymenoptera, Tenthredinidae) in the light of phylogenomic data.}, journal = {Molecular phylogenetics and evolution}, volume = {143}, number = {}, pages = {106670}, doi = {10.1016/j.ympev.2019.106670}, pmid = {31706020}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial ; Gene Flow ; Genes, Mitochondrial ; Genome, Mitochondrial ; Genomics ; Hymenoptera/*classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {In several sawfly taxa strong mitonuclear discordance has been observed, with nuclear genes supporting species assignments based on morphology, whereas the barcode region of the mitochondrial COI gene suggests different relationships. As previous studies were based on only a few nuclear genes, the causes and the degree of mitonuclear discordance remain ambiguous. Here, we obtained genomic-scale ddRAD data together with Sanger sequences of mitochondrial COI and two to three nuclear protein coding genes to investigate species limits and mitonuclear discordance in two closely related species groups of the sawfly genus Empria. As found previously based on nuclear ITS and mitochondrial COI sequences, species are in most cases supported as monophyletic based on new nuclear data reported here, but not based on mitochondrial COI. This mitonuclear discordance can be explained by occasional mitochondrial introgression with little or no nuclear gene flow, a pattern that might be common in haplodiploid taxa with slowly evolving mitochondrial genomes. Some species in the E. immersa group are not recovered as monophyletic according to either mitochondrial or nuclear data, but this could partly be because of unresolved taxonomy. Preliminary analyses of ddRAD data did not recover monophyly of E. japonica within the E. longicornis group (three Sanger sequenced nuclear genes strongly supported monophyly), but closer examination of the data and additional Sanger sequencing suggested that both specimens were substantially (possibly 10-20% of recovered loci) cross-contaminated. A reason could be specimen identification tag jumps during sequencing library preparation that in previous studies have been shown to affect up to 2.5% of the sequenced reads. We provide an R script to examine patterns of identical loci among the specimens and estimate that the cross-contamination rate is not unusually high for our ddRAD dataset as a whole (based on counting of identical sequences in the immersa and longicornis groups, which are well separated from each other and probably do not hybridise). The high rate of cross-contamination for both E. japonica specimens might be explained by the small number of recovered loci (~1000) compared to most other specimens (>10 000 in some cases) because of poor sequencing results. We caution against drawing unexpected biological conclusions when closely related specimens are pooled before sequencing and tagged only at one end of the molecule or at both ends using a unique combination of limited number of tags (less than the number of specimens).}, }
@article {pmid31705651, year = {2020}, author = {Igloi, GL}, title = {Molecular evidence for the evolution of the eukaryotic mitochondrial arginyl-tRNA synthetase from the prokaryotic suborder Cystobacterineae.}, journal = {FEBS letters}, volume = {594}, number = {5}, pages = {951-957}, doi = {10.1002/1873-3468.13665}, pmid = {31705651}, issn = {1873-3468}, mesh = {Amino Acid Sequence ; Arginine-tRNA Ligase/*genetics ; Bacterial Proteins/genetics ; Cloning, Molecular ; Data Mining ; Eukaryota/*enzymology/genetics ; Evolution, Molecular ; Mitochondria/*enzymology/genetics ; Myxococcales/*enzymology/genetics ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {The evolutionary origin of the family of eukaryotic aminoacyl-tRNA synthetases that are essential to all living organisms is a matter of debate. In order to shed molecular light on the ancient source of arginyl-tRNA synthetase, a total of 1347 eukaryotic arginyl-tRNA synthetase sequences were mined from databases and analyzed. Their multiple sequence alignment reveals a signature sequence that is characteristic of the nuclear-encoded enzyme, which is imported into mitochondria. Using this molecular beacon, the origins of this gene can be traced to modern prokaryotes. In this way, a previous phylogenetic analysis linking Myxococcus to the emergence of the eukaryotic mitochondrial arginyl-tRNA synthetase is supported by the unique existence of the molecular signature within the suborder Cystobacterineae that includes Myxococcus.}, }
@article {pmid31702777, year = {2020}, author = {Wang, BJ and Xia, JM and Wang, Q and Yu, JL and Song, Z and Zhao, H}, title = {Diet and Adaptive Evolution of Alanine-Glyoxylate Aminotransferase Mitochondrial Targeting in Birds.}, journal = {Molecular biology and evolution}, volume = {37}, number = {3}, pages = {786-798}, doi = {10.1093/molbev/msz266}, pmid = {31702777}, issn = {1537-1719}, mesh = {Animal Feed ; Animals ; Avian Proteins/chemistry/genetics ; Biological Evolution ; Birds/classification/genetics/*physiology ; Carnivora ; Diet ; Evolution, Molecular ; Herbivory ; Mitochondria/*enzymology/genetics ; Phylogeny ; Transaminases/*chemistry/*genetics ; }, abstract = {Adaptations to different diets represent a hallmark of animal diversity. The diets of birds are highly variable, making them an excellent model system for studying adaptive evolution driven by dietary changes. To test whether molecular adaptations to diet have occurred during the evolution of birds, we examined a dietary enzyme alanine-glyoxylate aminotransferase (AGT), which tends to target mitochondria in carnivorous mammals, peroxisomes in herbivorous mammals, and both mitochondria and peroxisomes in omnivorous mammals. A total of 31 bird species were examined in this study, which included representatives of most major avian lineages. Of these, 29 have an intact mitochondrial targeting sequence (MTS) of AGT. This finding is in stark contrast to mammals, which showed a number of independent losses of the MTS. Our cell-based functional assays revealed that the efficiency of AGT mitochondrial targeting was greatly reduced in unrelated lineages of granivorous birds, yet it tended to be high in insectivorous and carnivorous lineages. Furthermore, we found that proportions of animal tissue in avian diets were positively correlated with mitochondrial targeting efficiencies that were experimentally determined, but not with those that were computationally predicted. Adaptive evolution of AGT mitochondrial targeting in birds was further supported by the detection of positive selection on MTS regions. Our study contributes to the understanding of how diet drives molecular adaptations in animals, and suggests that caution must be taken when computationally predicting protein subcellular targeting.}, }
@article {pmid31701178, year = {2019}, author = {Aguirre-Dugua, X and Castellanos-Morales, G and Paredes-Torres, LM and Hernández-Rosales, HS and Barrera-Redondo, J and Sánchez-de la Vega, G and Tapia-Aguirre, F and Ruiz-Mondragón, KY and Scheinvar, E and Hernández, P and Aguirre-Planter, E and Montes-Hernández, S and Lira-Saade, R and Eguiarte, LE}, title = {Evolutionary Dynamics of Transferred Sequences Between Organellar Genomes in Cucurbita.}, journal = {Journal of molecular evolution}, volume = {87}, number = {9-10}, pages = {327-342}, pmid = {31701178}, issn = {1432-1432}, mesh = {Biological Evolution ; Cucurbita/*genetics ; Evolution, Molecular ; Genes, Plant/genetics ; Genome, Mitochondrial/*genetics ; Genome, Plant/genetics ; Mitochondria/genetics ; Phylogeny ; Plastids/*genetics ; Sequence Analysis, DNA ; }, abstract = {Twenty-nine DNA regions of plastid origin have been previously identified in the mitochondrial genome of Cucurbita pepo (pumpkin; Cucurbitaceae). Four of these regions harbor homolog sequences of rbcL, matK, rpl20-rps12 and trnL-trnF, which are widely used as molecular markers for phylogenetic and phylogeographic studies. We extracted the mitochondrial copies of these regions based on the mitochondrial genome of C. pepo and, along with published sequences for these plastome markers from 13 Cucurbita taxa, we performed phylogenetic molecular analyses to identify inter-organellar transfer events in the Cucurbita phylogeny and changes in their nucleotide substitution rates. Phylogenetic reconstruction and tree selection tests suggest that rpl20 and rbcL mitochondrial paralogs arose before Cucurbita diversification whereas the mitochondrial matK and trnL-trnF paralogs emerged most probably later, in the mesophytic Cucurbita clade. Nucleotide substitution rates increased one order of magnitude in all the mitochondrial paralogs compared to their original plastid sequences. Additionally, mitochondrial trnL-trnF sequences obtained by PCR from nine Cucurbita taxa revealed higher nucleotide diversity in the mitochondrial than in the plastid copies, likely related to the higher nucleotide substitution rates in the mitochondrial region and loss of functional constraints in its tRNA genes.}, }
@article {pmid31697708, year = {2019}, author = {Bénit, P and Kahn, A and Chretien, D and Bortoli, S and Huc, L and Schiff, M and Gimenez-Roqueplo, AP and Favier, J and Gressens, P and Rak, M and Rustin, P}, title = {Evolutionarily conserved susceptibility of the mitochondrial respiratory chain to SDHI pesticides and its consequence on the impact of SDHIs on human cultured cells.}, journal = {PloS one}, volume = {14}, number = {11}, pages = {e0224132}, pmid = {31697708}, issn = {1932-6203}, mesh = {Animals ; Antioxidants/metabolism ; Bees/metabolism ; Cells, Cultured ; Drug Resistance, Fungal/drug effects ; Electron Transport/*drug effects ; Fungal Proteins/pharmacology ; Fungi/metabolism ; Humans ; Mitochondrial Membranes/drug effects ; Neurodegenerative Diseases/drug therapy/metabolism ; Oligochaeta/metabolism ; Pesticides/*pharmacology ; Succinate Dehydrogenase/*antagonists &amp; inhibitors/metabolism ; }, abstract = {Succinate dehydrogenase (SDH) inhibitors (SDHIs) are used worldwide to limit the proliferation of molds on plants and plant products. However, as SDH, also known as respiratory chain (RC) complex II, is a universal component of mitochondria from living organisms, highly conserved through evolution, the specificity of these inhibitors toward fungi warrants investigation. We first establish that the human, honeybee, earthworm and fungal SDHs are all sensitive to the eight SDHIs tested, albeit with varying IC50 values, generally in the micromolar range. In addition to SDH, we observed that five of the SDHIs, mostly from the latest generation, inhibit the activity of RC complex III. Finally, we show that the provision of glucose ad libitum in the cell culture medium, while simultaneously providing sufficient ATP and reducing power for antioxidant enzymes through glycolysis, allows the growth of RC-deficient cells, fully masking the deleterious effect of SDHIs. As a result, when glutamine is the major carbon source, the presence of SDHIs leads to time-dependent cell death. This process is significantly accelerated in fibroblasts derived from patients with neurological or neurodegenerative diseases due to RC impairment (encephalopathy originating from a partial SDH defect) and/or hypersensitivity to oxidative insults (Friedreich ataxia, familial Alzheimer's disease).}, }
@article {pmid31696767, year = {2020}, author = {Ayyub, SA and Varshney, U}, title = {Translation initiation in mammalian mitochondria- a prokaryotic perspective.}, journal = {RNA biology}, volume = {17}, number = {2}, pages = {165-175}, pmid = {31696767}, issn = {1555-8584}, mesh = {Animals ; Disease Susceptibility ; Humans ; Mammals/*genetics/metabolism ; Mitochondria/*genetics/metabolism ; Mitochondrial Diseases/genetics/metabolism ; Mitochondrial Ribosomes/chemistry/metabolism ; Models, Molecular ; *Peptide Chain Initiation, Translational ; Prokaryotic Cells/metabolism ; Protein Biosynthesis ; RNA, Messenger/genetics ; RNA, Transfer/genetics ; Ribosomes/chemistry/metabolism ; Structure-Activity Relationship ; }, abstract = {ATP is generated in mitochondria of eukaryotic cells by oxidative phosphorylation (OXPHOS). The OXPHOS complex, which is crucial for cellular metabolism, comprises of both nuclear and mitochondrially encoded subunits. Also, the occurrence of several pathologies because of mutations in the mitochondrial translation apparatus indicates the importance of mitochondrial translation and its regulation. The mitochondrial translation apparatus is similar to its prokaryotic counterpart due to a common origin of evolution. However, mitochondrial translation has diverged from prokaryotic translation in many ways by reductive evolution. In this review, we focus on mammalian mitochondrial translation initiation, a highly regulated step of translation, and present a comparison with prokaryotic translation.}, }
@article {pmid31691343, year = {2020}, author = {Dujon, B}, title = {Mitochondrial genetics revisited.}, journal = {Yeast (Chichester, England)}, volume = {37}, number = {2}, pages = {191-205}, doi = {10.1002/yea.3445}, pmid = {31691343}, issn = {1097-0061}, mesh = {Alleles ; Cell Nucleus ; DNA Replication ; DNA, Mitochondrial ; Evolution, Molecular ; *Genome, Mitochondrial ; Interspersed Repetitive Sequences ; Mitochondria/*genetics ; Saccharomyces cerevisiae/genetics ; Yeasts/*genetics ; }, abstract = {Mitochondrial genetics started decades ago with the discovery of yeast mutants that ignored the Mendelian rules of inheritance. Today, the many known DNA sequences of this second eukaryotic genome illustrate its eccentricity in terms of informational content and functional organisation, suggesting a yet incomplete understanding of its evolution. The hereditary transmission of mitochondrial alleles relies on complex mixes of molecular and cellular mechanisms in which recombination and limited sampling, two sources of rapid genetic changes, play central roles. It is also under the influence of invasive genetic elements whose inconstant distribution in mitochondrial genomes suggests rapid turnovers in evolving populations. This susceptibility to changes contrasts with the development of specific functional interactions between the mitochondrial and nuclear genetic compartments, a trend that is prone to limit the genetic exchanges between distinct lineages. It is perhaps this opposition and the discordant inheritance between mitochondrial and nuclear genomes that best explain the maintenance of a second genome and a second independent protein synthesising machinery in eukaryotic cells.}, }
@article {pmid31687086, year = {2019}, author = {Poljsak, B and Kovac, V and Dahmane, R and Levec, T and Starc, A}, title = {Cancer Etiology: A Metabolic Disease Originating from Life's Major Evolutionary Transition?.}, journal = {Oxidative medicine and cellular longevity}, volume = {2019}, number = {}, pages = {7831952}, pmid = {31687086}, issn = {1942-0994}, mesh = {Animals ; *Biological Evolution ; Drug Resistance, Neoplasm ; Energy Metabolism ; Humans ; Metabolic Diseases/*etiology ; Mitochondria/metabolism ; Neoplasms/*etiology ; }, abstract = {A clear understanding of the origins of cancer is the basis of successful strategies for effective cancer prevention and management. The origin of cancer at the molecular and cellular levels is not well understood. Is the primary cause of the origin of cancer the genomic instability or impaired energy metabolism? An attempt was made to present cancer etiology originating from life's major evolutionary transition. The first evolutionary transition went from simple to complex cells when eukaryotic cells with glycolytic energy production merged with the oxidative mitochondrion (The Endosymbiosis Theory first proposed by Lynn Margulis in the 1960s). The second transition went from single-celled to multicellular organisms once the cells obtained mitochondria, which enabled them to obtain a higher amount of energy. Evidence will be presented that these two transitions, as well as the decline of NAD+ and ATP levels, are the root of cancer diseases. Restoring redox homeostasis and reactivation of mitochondrial oxidative metabolism are important factors in cancer prevention.}, }
@article {pmid31681764, year = {2019}, author = {Naumann, B and Burkhardt, P}, title = {Spatial Cell Disparity in the Colonial Choanoflagellate Salpingoeca rosetta.}, journal = {Frontiers in cell and developmental biology}, volume = {7}, number = {}, pages = {231}, pmid = {31681764}, issn = {2296-634X}, abstract = {Choanoflagellates are the closest unicellular relatives of animals (Metazoa). These tiny protists display complex life histories that include sessile as well as different pelagic stages. Some choanoflagellates have the ability to form colonies as well. Up until recently, these colonies have been described to consist of mostly identical cells showing no spatial cell differentiation, which supported the traditional view that spatial cell differentiation, leading to the co-existence of specific cell types in animals, evolved after the split of the last common ancestor of the Choanoflagellata and Metazoa. The recent discovery of single cells in colonies of the choanoflagellate Salpingoeca rosetta that exhibit unique cell morphologies challenges this traditional view. We have now reanalyzed TEM serial sections, aiming to determine the degree of similarity of S. rosetta cells within a rosette colony. We investigated cell morphologies and nuclear, mitochondrial, and food vacuole volumes of 40 individual cells from four different S. rosetta rosette colonies and compared our findings to sponge choanocytes. Our analysis shows that cells in a choanoflagellate colony differ from each other in respect to cell morphology and content ratios of nuclei, mitochondria, and food vacuoles. Furthermore, cell disparity within S. rosetta colonies is slightly higher compared to cell disparity within sponge choanocytes. Moreover, we discovered the presence of plasma membrane contacts between colonial cells in addition to already described intercellular bridges and filo-/pseudopodial contacts. Our findings indicate that the last common ancestor of Choanoflagellata and Metazoa might have possessed plasma membrane contacts and spatial cell disparity during colonial life history stages.}, }
@article {pmid31679533, year = {2019}, author = {Li, Y and Ma, XX and Lv, QB and Hu, Y and Qiu, HY and Chang, QC and Wang, CR}, title = {Characterization of the complete mitochondrial genome sequence of Tracheophilus cymbius (Digenea), the first representative from the family Cyclocoelidae.}, journal = {Journal of helminthology}, volume = {94}, number = {}, pages = {e101}, doi = {10.1017/S0022149X19000932}, pmid = {31679533}, issn = {1475-2697}, mesh = {Animals ; Base Sequence ; Genome, Helminth ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Trematoda/classification/*genetics/isolation &amp; purification ; }, abstract = {Tracheophilus cymbius (Trematoda: Cyclocoelidae) is a common tracheal fluke of waterfowl, causing serious loss in the poultry industry. However, taxonomic identification of T. cymbius remains controversial and confused. Mitochondrial (mt) genomes can provide genetic markers for the identification of closely related species. We determined the mt genome of T. cymbius and reconstructed phylogenies with other trematodes. The T. cymbius mt genome is 13,760 bp in size, and contains 12 protein-coding genes (cox 1-3, nad 1-6, nad 4L, cyt b and atp 6), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes and one non-coding region. All are transcribed in the same direction. The A + T content is 62.82%. ATG and TAG are the most common initiation and termination codons, respectively. Phylogenetic analyses of concatenated nucleotide sequences show T. cymbius grouping in suborder Echinostomata, and clustering together, with high statistical support, as a sister taxon with Echinochasmus japonicus (Echinochasmidae), the two forming a distinct branch rooted to the ancestor of all Echinostomatidae and Fasciolidae species. This is the first report of the T. cymbius mt genome, and the first reported mt genome within the family Cyclocoelidae. These data will provide a significant resource of molecular markers for studying the taxonomy, population genetics and systematics of trematodes.}, }
@article {pmid31673867, year = {2019}, author = {Puri, RR and Adachi, F and Omichi, M and Saeki, Y and Yamamoto, A and Hayashi, S and Ali, MA and Itoh, K}, title = {Metagenomic study of endophytic bacterial community of sweet potato (Ipomoea batatas) cultivated in different soil and climatic conditions.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {35}, number = {11}, pages = {176}, pmid = {31673867}, issn = {1573-0972}, support = {16KT0032//Japan Society for the Promotion of Science/ ; }, mesh = {Bacteria/*classification/genetics/*metabolism ; Base Sequence ; Biodiversity ; *Climate ; DNA, Bacterial/analysis ; DNA, Mitochondrial/analysis ; Endophytes/*classification/genetics ; Ipomoea batatas/*microbiology ; *Metagenome ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {The aim of this study was to clarify effects of soil and climatic conditions on community structure of sweet potato bacterial endophytes by applying locked nucleic acid oligonucleotide-PCR clamping technique and metagenomic analysis. For this purpose, the soil samples in three locations were transferred each other and sweet potato nursery plants from the same farm were cultivated for ca. 3 months. After removal of plastid, mitochondria and undefined sequences, the averaged numbers of retained sequences and operational taxonomic units per sample were 20,891 and 846, respectively. Proteobacteria (85.0%), Bacteroidetes (6.6%) and Actinobacteria (6.3%) were the three most dominant phyla, accounting for 97.9% of the reads, and γ-Proteobacteria (66.3%) being the most abundant. Top 10 genera represented 81.2% of the overall reads in which Pseudomonas (31.9-45.0%) being the most predominant. The overall endophytic bacterial communities were similar among the samples which indicated that the soil and the climatic conditions did not considerably affect the entire endophytic community. The original endophytic bacterial community might be kept during the cultivation period.}, }
@article {pmid31673019, year = {2019}, author = {Stjelja, S and Fogelqvist, J and Tellgren-Roth, C and Dixelius, C}, title = {The architecture of the Plasmodiophora brassicae nuclear and mitochondrial genomes.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {15753}, pmid = {31673019}, issn = {2045-2322}, mesh = {Cell Nucleus/*genetics ; *Genome, Mitochondrial ; *Genome, Protozoan ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Plant Diseases/genetics/parasitology ; Plasmodiophorida/*genetics ; }, abstract = {Plasmodiophora brassicae is a soil-borne pathogen that attacks roots of cruciferous plants causing clubroot disease. The pathogen belongs to the Plasmodiophorida order in Phytomyxea. Here we used long-read SMRT technology to clarify the P. brassicae e3 genomic constituents along with comparative and phylogenetic analyses. Twenty contigs representing the nuclear genome and one mitochondrial (mt) contig were generated, together comprising 25.1 Mbp. Thirteen of the 20 nuclear contigs represented chromosomes from telomere to telomere characterized by [TTTTAGGG] sequences. Seven active gene candidates encoding synaptonemal complex-associated and meiotic-related protein homologs were identified, a finding that argues for possible genetic recombination events. The circular mt genome is large (114,663 bp), gene dense and intron rich. It shares high synteny with the mt genome of Spongospora subterranea, except in a unique 12 kb region delimited by shifts in GC content and containing tandem minisatellite- and microsatellite repeats with partially palindromic sequences. De novo annotation identified 32 protein-coding genes, 28 structural RNA genes and 19 ORFs. ORFs predicted in the repeat-rich region showed similarities to diverse organisms suggesting possible evolutionary connections. The data generated here form a refined platform for the next step involving functional analysis, all to clarify the complex biology of P. brassicae.}, }
@article {pmid31670799, year = {2020}, author = {Arribas, P and Andújar, C and Moraza, ML and Linard, B and Emerson, BC and Vogler, AP}, title = {Mitochondrial Metagenomics Reveals the Ancient Origin and Phylodiversity of Soil Mites and Provides a Phylogeny of the Acari.}, journal = {Molecular biology and evolution}, volume = {37}, number = {3}, pages = {683-694}, doi = {10.1093/molbev/msz255}, pmid = {31670799}, issn = {1537-1719}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Metagenomics ; Mites/*classification/genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Soil/*parasitology ; }, abstract = {High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites from soils in an area of mixed forest and grassland in southern Iberia. Selected specimens representing the full morphological diversity were shotgun sequenced in bulk, followed by genome assembly of short reads from the mixture, which produced >100 mitochondrial genomes representing diverse acarine lineages. Phylogenetic analyses in combination with taxonomically limited mitogenomes available publicly resulted in plausible trees defining basal relationships of the Acari. Several critical nodes were supported by ancestral-state reconstructions of mitochondrial gene rearrangements. Molecular calibration placed the minimum age for the common ancestor of the superorder Acariformes, which includes most soil-dwelling mites, to the Cambrian-Ordovician (likely within 455-552 Ma), whereas the origin of the superorder Parasitiformes was placed later in the Carboniferous-Permian. Most family-level taxa within the Acariformes were dated to the Jurassic and Triassic. The ancient origin of Acariformes and the early diversification of major extant lineages linked to the soil are consistent with a pioneering role for mites in building the earliest terrestrial ecosystems.}, }
@article {pmid31670613, year = {2019}, author = {Achatz, TJ and Dmytrieva, I and Kuzmin, Y and Tkach, VV}, title = {Phylogenetic Position of Codonocephalus Diesing, 1850 (Digenea, Diplostomoidea), an Unusual Diplostomid with Progenetic Metacercariae.}, journal = {The Journal of parasitology}, volume = {105}, number = {5}, pages = {821-826}, pmid = {31670613}, issn = {1937-2345}, mesh = {Animals ; Bayes Theorem ; DNA, Helminth/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry ; Electron Transport Complex IV/chemistry/genetics ; Life Cycle Stages ; Metacercariae/classification/genetics ; Microscopy, Electron, Scanning/veterinary ; Mitochondria/enzymology ; *Phylogeny ; RNA, Helminth/genetics ; RNA, Nuclear/genetics ; RNA, Ribosomal, 28S/genetics ; Ranidae/*parasitology ; Trematoda/*classification/genetics/ultrastructure ; Trematode Infections/parasitology/*veterinary ; }, abstract = {Codonocephalus is a monotypic genus of diplostomid digeneans and is the only genus in the sub-family Codonocephalinae. The type-species Codonocephalus urniger has an unusual progenetic metacercaria that uses frogs as intermediate hosts and can use snakes as paratenic hosts. Adult C. urniger parasitize ardeid wading birds in the Palearctic. Despite the broad distribution of Codonocephalus, no DNA sequence data are currently available for the genus. In this study, we generated sequence data for nuclear ribosomal and mitochondrial DNA from progenetic metacercaria of the type-species C. urniger from marsh frog, Pelophylax ridibundus, collected in Ukraine. We used partial sequences of the nuclear ribosomal 28S gene to examine for the first time the phylogenetic position of Codonocephalus among the Diplostomoidea.}, }
@article {pmid31670447, year = {2020}, author = {Surana, S and Villarroel-Campos, D and Lazo, OM and Moretto, E and Tosolini, AP and Rhymes, ER and Richter, S and Sleigh, JN and Schiavo, G}, title = {The evolution of the axonal transport toolkit.}, journal = {Traffic (Copenhagen, Denmark)}, volume = {21}, number = {1}, pages = {13-33}, doi = {10.1111/tra.12710}, pmid = {31670447}, issn = {1600-0854}, support = {SCHIAVO/OCT15/880-792/MNDA_/Motor Neurone Disease Association/United Kingdom ; //UK Dementia Research Institute Foundation award/International ; LT000220/2017-L//Human Frontier Science Program/International ; MR/T001976/1/MRC_/Medical Research Council/United Kingdom ; 107116/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; MR/S006990/1/MRC_/Medical Research Council/United Kingdom ; 2016/72170645//Comisi&#xf3;n Nacional de Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/International ; 880-792/MNDA_/Motor Neurone Disease Association/United Kingdom ; 739572//Horizon 2020 Framework Programme/International ; }, mesh = {Animals ; *Axonal Transport ; Axons/metabolism ; Humans ; *Kinesins/metabolism ; Models, Biological ; Neurons/metabolism ; }, abstract = {Neurons are highly polarized cells that critically depend on long-range, bidirectional transport between the cell body and synapse for their function. This continual and highly coordinated trafficking process, which takes place via the axon, has fascinated researchers since the early 20th century. Ramon y Cajal first proposed the existence of axonal trafficking of biological material after observing that dissociation of the axon from the cell body led to neuronal degeneration. Since these first indirect observations, the field has come a long way in its understanding of this fundamental process. However, these advances in our knowledge have been aided by breakthroughs in other scientific disciplines, as well as the parallel development of novel tools, techniques and model systems. In this review, we summarize the evolution of tools used to study axonal transport and discuss how their deployment has refined our understanding of this process. We also highlight innovative tools currently being developed and how their addition to the available axonal transport toolkit might help to address key outstanding questions.}, }
@article {pmid31669617, year = {2020}, author = {Barros, MH and McStay, GP}, title = {Modular biogenesis of mitochondrial respiratory complexes.}, journal = {Mitochondrion}, volume = {50}, number = {}, pages = {94-114}, doi = {10.1016/j.mito.2019.10.008}, pmid = {31669617}, issn = {1872-8278}, mesh = {Animals ; Electron Transport Chain Complex Proteins/*metabolism ; Electron Transport Complex IV/metabolism ; Gene Expression Regulation, Enzymologic/physiology ; Mammals ; Mitochondria/*enzymology/metabolism ; Yeasts ; }, abstract = {Mitochondrial function relies on the activity of oxidative phosphorylation to synthesise ATP and generate an electrochemical gradient across the inner mitochondrial membrane. These coupled processes are mediated by five multi-subunit complexes that reside in this inner membrane. These complexes are the product of both nuclear and mitochondrial gene products. Defects in the function or assembly of these complexes can lead to mitochondrial diseases due to deficits in energy production and mitochondrial functions. Appropriate biogenesis and function are mediated by a complex number of assembly factors that promote maturation of specific complex subunits to form the active oxidative phosphorylation complex. The understanding of the biogenesis of each complex has been informed by studies in both simple eukaryotes such as Saccharomyces cerevisiae and human patients with mitochondrial diseases. These studies reveal each complex assembles through a pathway using specific subunits and assembly factors to form kinetically distinct but related assembly modules. The current understanding of these complexes has embraced the revolutions in genomics and proteomics to further our knowledge on the impact of mitochondrial biology in genetics, medicine, and evolution.}, }
@article {pmid31665278, year = {2019}, author = {Kortsinoglou, AM and Korovesi, AG and Theelen, B and Hagen, F and Boekhout, T and Kouvelis, VN}, title = {The mitochondrial intergenic regions nad1-cob and cob-rps3 as molecular identification tools for pathogenic members of the genus Cryptococcus.}, journal = {FEMS yeast research}, volume = {19}, number = {8}, pages = {}, doi = {10.1093/femsyr/foz077}, pmid = {31665278}, issn = {1567-1364}, mesh = {Cryptococcosis/microbiology ; Cryptococcus/*genetics/*pathogenicity ; DNA, Fungal/*genetics ; *DNA, Intergenic ; DNA, Ribosomal/genetics ; *Genes, Mitochondrial ; Humans ; Membrane Glycoproteins/genetics ; Mitochondria/genetics ; Mycological Typing Techniques ; NADH Dehydrogenase/genetics ; Phylogeny ; Ribosomal Proteins/genetics ; }, abstract = {Cryptococcus spp. are fungal species belonging to Tremellomycetes, Agaricomycotina, Basidiomycota, and several members are responsible for cryptococcosis, one of the most ubiquitous human mycoses. Affecting mainly immunosuppressed patients, but also immunocompetent ones, the members of this genus present a high level of genetic diversity. In this study, two mitochondrial intergenic regions, i.e. nad1-cob and cob-rps3, were tested for the intra- or interspecies discrimination and identification of strains and species of the genus Cryptococcus. Phylogenetic trees were constructed based on individual and concatenated sequences from representative pathogenic strains of the Cryptococcus neoformans/Cryptococcus gattii complex, representing serotypes and AFLP genotypes of all newly introduced species of this complex. Using both intergenic regions, as well as the concatenated dataset, the strains clustered in accordance with the new taxonomy. These results suggest that identification of Cryptococcus strains is possible by employing these mitochondrial intergenic regions using PCR amplification as a quick and effective method to elucidate genotypic and taxonomic differences. Thus, these regions may be applicable to a broad range of clinical studies, leading to a rapid recognition of the clinical profiles of patients.}, }
@article {pmid31648074, year = {2020}, author = {Wu, H and Li, R and Liu, Y and Zhang, X and Zhang, J and Ma, E}, title = {A second intracellular copper/zinc superoxide dismutase and a manganese superoxide dismutase in Oxya chinensis: Molecular and biochemical characteristics and roles in chlorpyrifos stress.}, journal = {Ecotoxicology and environmental safety}, volume = {187}, number = {}, pages = {109830}, doi = {10.1016/j.ecoenv.2019.109830}, pmid = {31648074}, issn = {1090-2414}, mesh = {Animals ; Chlorpyrifos/*metabolism ; Copper/metabolism ; Grasshoppers/classification/*enzymology ; Insect Proteins/chemistry/genetics/metabolism/*physiology ; Manganese/metabolism ; Metals, Heavy/*metabolism ; Phylogeny ; Superoxide Dismutase/chemistry/genetics/metabolism/*physiology ; Zinc/metabolism ; }, abstract = {A second intracellular copper/zinc superoxide dismutase (icCuZnSOD2) and manganese SOD (MnSOD) were cloned and characterized in Oxya chinensis. The open reading frame (ORF) of OcicCuZnSOD2 and OcMnSOD are 462 and 672 bp encoding 153 and 223 amino acids, respectively. OcicCuZnSOD2 contains two signature sequences, one potential N-glycosylation site, and seven copper/zinc binding sites. OcMnSOD includes a mitochondria targeting sequence of 7 amino acids at N-terminal, one signature sequence, two N-glycosylation sites, and four manganese binding sites. The secondary structure and homology model of OcicCuZnSOD2 include nine β sheets, two Greek-key motifs, and one electrostatic loop. OcMnSOD contains nine α-helices and three β-sheets. Phylogenetic analysis shows that OcMnSOD is evolutionarily conserved while OcicCuZnSOD2 may be gene duplication and is paralogous to OcicCuZnSOD1. OcMnSOD expressed widely in all tissues and developmental stages. OcicCuZnSOD2 showed testis-specific expression and expressed highest in the 5th-instar nymph and the adult. The optimum temperatures and pH values of the recombinant OcicCuZnSOD2 and OcMnSOD were 40 °C and 8.0. They were stable at 25-55 °C and at pH 5.0-12.0 and pH 6.0-12.0, respectively. The activity and mRNA expression of each OcSOD were assayed after chlorpyrifos treatments. Total SOD and CuZnSOD activities first increased then declined under chlorpyrifos stress. Chlorpyrifos induced the mRNA expression and activity of OcMnSOD as a dose-dependent manner and inhibited OcicCuZnSOD2 transcription. The role of each OcSOD gene in chlorpyrifos stress was investigated using RNAi and disc diffusion assay with Escherichia coli overexpressing OcSOD proteins. Silencing of OcMnSOD significantly increased ROS content in chlorpyrifos-exposed grasshoppers. Disc diffusion assay showed that the plates with E. coli overexpressing OcMnSOD had the smaller inhibition zones around the chlorpyrifos-soaked filter discs. These results implied that OcMnSOD played a significant role in defense chlorpyrifos-induced oxidative stress.}, }
@article {pmid31647561, year = {2020}, author = {Lewis, WH and Lind, AE and Sendra, KM and Onsbring, H and Williams, TA and Esteban, GF and Hirt, RP and Ettema, TJG and Embley, TM}, title = {Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss.}, journal = {Molecular biology and evolution}, volume = {37}, number = {2}, pages = {524-539}, pmid = {31647561}, issn = {1537-1719}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Aerobiosis ; Anaerobiosis ; Ciliophora/*classification/physiology ; Evolution, Molecular ; Gene Expression Profiling/*methods ; Gene Transfer, Horizontal ; Genome, Mitochondrial ; Hydrogen/metabolism ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Sequence Analysis, RNA ; }, abstract = {Hydrogenosomes are H2-producing mitochondrial homologs found in some anaerobic microbial eukaryotes that provide a rare intracellular niche for H2-utilizing endosymbiotic archaea. Among ciliates, anaerobic and aerobic lineages are interspersed, demonstrating that the switch to an anaerobic lifestyle with hydrogenosomes has occurred repeatedly and independently. To investigate the molecular details of this transition, we generated genomic and transcriptomic data sets from anaerobic ciliates representing three distinct lineages. Our data demonstrate that hydrogenosomes have evolved from ancestral mitochondria in each case and reveal different degrees of independent mitochondrial genome and proteome reductive evolution, including the first example of complete mitochondrial genome loss in ciliates. Intriguingly, the FeFe-hydrogenase used for generating H2 has a unique domain structure among eukaryotes and appears to have been present, potentially through a single lateral gene transfer from an unknown donor, in the common aerobic ancestor of all three lineages. The early acquisition and retention of FeFe-hydrogenase helps to explain the facility whereby mitochondrial function can be so radically modified within this diverse and ecologically important group of microbial eukaryotes.}, }
@article {pmid31640544, year = {2019}, author = {Wang, G and Lin, J and Shi, Y and Chang, X and Wang, Y and Guo, L and Wang, W and Dou, M and Deng, Y and Ming, R and Zhang, J}, title = {Mitochondrial genome in Hypsizygus marmoreus and its evolution in Dikarya.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {765}, pmid = {31640544}, issn = {1471-2164}, support = {KNJ-153011-1//Agricultural technology extension service system for edible fungus industry in Fujian, China/ ; 2016NZ0001//the Science and Technology Major Project of Fujian Province/ ; 31670021//Natural Science Foundation of China/ ; }, mesh = {Agaricales/classification/*genetics ; Ascomycota/classification/genetics ; Basidiomycota/classification/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Fungal Proteins/genetics ; Gene Order ; Genetic Variation ; Genome, Mitochondrial/*genetics ; Phylogeny ; Selection, Genetic ; Species Specificity ; }, abstract = {BACKGROUND: Hypsizygus marmoreus, a high value commercialized edible mushroom is widely cultivated in East Asia, and has become one of the most popular edible mushrooms because of its rich nutritional and medicinal value. Mitochondria are vital organelles, and play various essential roles in eukaryotic cells.<br><br>RESULTS: In this study, we provide the Hypsizygus marmoreus mitochondrial (mt) genome assembly: the circular sequence is 102,752&#x2009;bp in size and contains 15 putative protein-coding genes, 2 ribosomal RNAs subunits and 28 tRNAs. We compared the mt genomes of the 27 fungal species in the Pezizomycotina and Basidiomycotina subphyla, with the results revealing that H. marmoreus is a sister to Tricholoma matsutake and the phylogenetic distribution of this fungus based on the mt genome. Phylogenetic analysis shows that Ascomycetes mitochondria started to diverge earlier than that of Basidiomycetes and supported the robustness of the hyper metric tree. The fungal sequences are highly polymorphic and gene order varies significantly in the dikarya data set, suggesting a correlation between the gene order and divergence time in the fungi mt genome. To detect the mt genome variations in H. marmoreus, we analyzed the mtDNA sequences of 48 strains. The phylogeny and variation sited type statistics of H. marmoreus provide clear-cut evidence for the existence of four well-defined cultivations isolated lineages, suggesting female ancestor origin of H. marmoreus. Furthermore, variations on two loci were further identified to be molecular markers for distinguishing the subgroup containing 32 strains of other strains. Fifteen conserved protein-coding genes of mtDNAs were analyzed, with fourteen revealed to be under purifying selection in the examined fungal species, suggesting the rapid evolution was caused by positive selection of this gene.<br><br>CONCLUSIONS: Our studies have provided new reference mt genomes and comparisons between species and intraspecies with other strains, and provided future perspectives for assessing diversity and origin of H. marmoreus.}, }
@article {pmid31633437, year = {2019}, author = {de Oliveira Simões, R and Fraga-Neto, S and Vilar, EM and Maldonado, A and do Val Vilela, R}, title = {A New Species of Bidigiticauda (Nematoda: Strongylida) from the Bat Artibeus Planirostris (Chiroptera: Phyllostomidae) in the Atlantic Forest and a Molecular Phylogeny of the Molineid Bat Parasites.}, journal = {The Journal of parasitology}, volume = {105}, number = {5}, pages = {783-792}, pmid = {31633437}, issn = {1937-2345}, mesh = {Animals ; Bayes Theorem ; Brazil ; Chiroptera/*parasitology ; DNA Barcoding, Taxonomic/veterinary ; DNA, Helminth/chemistry/isolation &amp; purification ; Electron Transport Complex IV/genetics ; Female ; Forests ; Male ; Mitochondria/enzymology ; *Phylogeny ; RNA, Ribosomal, 28S/genetics ; Trichostrongyloidea/anatomy &amp; histology/*classification/genetics/isolation &amp; purification ; Trichostrongyloidiasis/parasitology/*veterinary ; }, abstract = {The nematode genus Bidigiticauda has 2 species (Bidigiticauda vivipara and Bidigiticauda embryophilum), which are parasites of bats from the Neotropical region. The present paper describes a new species of Bidigiticauda from a male Artibeus planirostris specimen collected in the Pratigi Environmental Protection Area in Bahia state, Brazil. The new species, Bidigiticauda serrafreirei n. sp., differs from B. embryophilum by having longer spicules, rays 5 and 6 arising from a common trunk and bifurcating in its first third, rays 3 and 4 emerging slightly separated from each other, and dorsal rays reaching the margin of the caudal bursa. The new species also differs from B. vivipara by the dorsal ray bifurcating at the extremity of the trunk. A molecular phylogenetic analysis was conducted to determine the evolutionary affinities of Bidigiticauda serrafreirei n. sp. within the Strongylida, which identified a clade that grouped Bidigiticauda with the other members of the Anoplostrongylinae. However, the molineid subfamilies did not group together, indicating that the family Molineidae is polyphyletic. Further analyses, which include additional taxa and genetic markers, should elucidate the complex relationships within the Molineidae, in particular its subfamilies and the evolution of the traits that define these groups.}, }
@article {pmid31632444, year = {2019}, author = {Shen, X and Pu, Z and Chen, X and Murphy, RW and Shen, Y}, title = {Convergent Evolution of Mitochondrial Genes in Deep-Sea Fishes.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {925}, pmid = {31632444}, issn = {1664-8021}, abstract = {Deep seas have extremely harsh conditions including high hydrostatic pressure, total darkness, cold, and little food and oxygen. The adaptations of fishes to deep-sea environment apparently have occurred independently many times. The genetic basis of adaptation for obtaining their energy remains unknown. Mitochondria play a central role in aerobic respiration. Analyses of the available 2,161 complete mitochondrial genomes of 1,042 fishes, including 115 deep-sea species, detect signals of positive selection in mitochondrial genes in nine branches of deep-sea fishes. Aerobic metabolism yields much more energy per unit of source material than anaerobic metabolism. The adaptive evolution of the mtDNA may reflect that aerobic metabolism plays a more important role than anaerobic metabolism in deep-sea fishes, whose energy sources (food) are extremely limited. This strategy maximizes the usage of energy sources. Eleven mitochondrial genes have convergent/parallel amino acid changes between branches of deep-sea fishes. Thus, these amino acid sites may be functionally important in the acquisition of energy, and reflect convergent evolution during their independent invasion of the harsh deep-sea ecological niche.}, }
@article {pmid31631459, year = {2020}, author = {Jelassi, R and Khemaissia, H and Ghemari, C and Raimond, M and Souty-Grosset, C and Nasri-Ammar, K}, title = {The induced damage in the hepatopancreas of Orchestia species after exposure to a mixture of Cu/Zn-An ultrastructural study.}, journal = {Microscopy research and technique}, volume = {83}, number = {2}, pages = {148-155}, doi = {10.1002/jemt.23397}, pmid = {31631459}, issn = {1097-0029}, support = {//Research Laboratory of Diversity, Management and Conservation of Biological Systems, Faculty of Science of Tunis, University of Tunis El Manar/ ; //Erasmus Mundus Al Idrisi II Programme of the European Union/ ; }, mesh = {Amphipoda/*anatomy &amp; histology ; Animals ; Copper/*toxicity ; Environmental Monitoring ; Hepatopancreas/*drug effects/pathology/*ultrastructure ; Metals/analysis ; Microscopy, Electron, Transmission ; Microvilli/drug effects ; Trace Elements/toxicity ; Tunisia ; Water Pollutants, Chemical/toxicity ; Wetlands ; Zinc/*toxicity ; }, abstract = {The hepatopancreas of crustaceans species has been recognized as an essential target organ to assess trace elements' effects. Due to its dynamic and capability of detoxifying trace metal, this organ often indicates distinct pathological disturbances. In the present work, we intend to evaluate the bioaccumulation of trace metal in three Orchestia species (Orchestia montagui, Orchestia gammarellus, and Orchestia mediterranea) living in symmetry in the banks of Bizerte lagoon (37°13'8″N 09°55'1″E) after their exposure during 14 days to a mixture of copper and zinc, and to highlight the effect of these metals on their hepatopancreas ultrastructure using transmission electron microscopy. At the end of the experiment, results showed that the mortality and the body mass varied according to the used nominal concentrations. Significant alterations were noted in all the treatment groups. The degree of these alterations depends on the used concentration, and they are represented especially by the cells remoteness and the border lyses, the reduction of the nuclear volume, the increase in the cytoplasm density with the presence of trace metal in the nucleus as well as in the vacuole, the disorganization and the destruction of microvilli, the condensation of the majority of cellular organelles and mitochondria swelling. Through this study, Orchestia genus could be an attractive candidate for the biochemical study of trace metal toxicity in Tunisian wetlands.}, }
@article {pmid31630458, year = {2020}, author = {Small, ID and Schallenberg-Rüdinger, M and Takenaka, M and Mireau, H and Ostersetzer-Biran, O}, title = {Plant organellar RNA editing: what 30 years of research has revealed.}, journal = {The Plant journal : for cell and molecular biology}, volume = {101}, number = {5}, pages = {1040-1056}, doi = {10.1111/tpj.14578}, pmid = {31630458}, issn = {1365-313X}, mesh = {Cell Nucleus/genetics ; Chloroplasts/genetics ; Mitochondria/genetics ; Plants/*genetics/metabolism ; *RNA Editing ; RNA, Plant/genetics ; RNA-Binding Proteins/genetics ; }, abstract = {The central dogma in biology defines the flow of genetic information from DNA to RNA to protein. Accordingly, RNA molecules generally accurately follow the sequences of the genes from which they are transcribed. This rule is transgressed by RNA editing, which creates RNA products that differ from their DNA templates. Analyses of the RNA landscapes of terrestrial plants have indicated that RNA editing (in the form of C-U base transitions) is highly prevalent within organelles (that is, mitochondria and chloroplasts). Numerous C→U conversions (and in some plants also U→C) alter the coding sequences of many of the organellar transcripts and can also produce translatable mRNAs by creating AUG start sites or eliminating premature stop codons, or affect the RNA structure, influence splicing and alter the stability of RNAs. RNA-binding proteins are at the heart of post-transcriptional RNA expression. The C-to-U RNA editing process in plant mitochondria involves numerous nuclear-encoded factors, many of which have been identified as pentatricopeptide repeat (PPR) proteins that target editing sites in a sequence-specific manner. In this review we report on major discoveries on RNA editing in plant organelles, since it was first documented 30 years ago.}, }
@article {pmid31622439, year = {2019}, author = {Caicedo-Garzón, V and Salgado-Roa, FC and Sánchez-Herrera, M and Hernández, C and Arias-Giraldo, LM and García, L and Vallejo, G and Cantillo, O and Tovar, C and Aristeu da Rosa, J and Carrasco, HJ and Segovia, M and Salazar, C and Ramírez, JD}, title = {Genetic diversification of Panstrongylus geniculatus (Reduviidae: Triatominae) in northern South America.}, journal = {PloS one}, volume = {14}, number = {10}, pages = {e0223963}, pmid = {31622439}, issn = {1932-6203}, mesh = {Animals ; Cell Nucleus/*genetics ; Colombia ; DNA, Ribosomal/*genetics ; Evolution, Molecular ; Genetics, Population ; Mitochondria/*genetics ; Panstrongylus/*classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Triatomines are the vectors of Trypanosoma cruzi, the etiological agent of Chagas disease. Although Triatoma and Rhodnius are the most-studied vector genera, other triatomines, such as Panstrongylus, also transmit T. cruzi, creating new epidemiological scenarios. Panstrongylus has at least 13 reported species but there is limited information about its intraspecific genetic variation and patterns of diversification. Here, we begin to fill this gap by studying populations of P. geniculatus from Colombia and Venezuela and including other epidemiologically important species from the region. We examined the pattern of diversification of P. geniculatus in Colombia using mitochondrial and nuclear ribosomal data. Genetic diversity and differentiation were calculated within and among populations of P. geniculatus. Moreover, we constructed maximum likelihood and Bayesian inference phylogenies and haplotype networks using P. geniculatus and other species from the genus (P. megistus, P. lignarius, P. lutzi, P. tupynambai, P. chinai, P. rufotuberculatus and P. howardi). Using a coalescence framework, we also dated the P. geniculatus lineages. The total evidence tree showed that P. geniculatus is a monophyletic species, with four clades that are concordant with its geographic distribution and are partly explained by the Andes orogeny. However, other factors, including anthropogenic and eco-epidemiological effects must be investigated to explain the existence of recent geographic P. geniculatus lineages. The epidemiological dynamics in structured vector populations, such as those found here, warrant further investigation. Extending our knowledge of P. geniculatus is necessary for the accurate development of effective strategies for the control of Chagas disease vectors.}, }
@article {pmid31621967, year = {2020}, author = {Johnson, RJ and Stenvinkel, P and Andrews, P and Sánchez-Lozada, LG and Nakagawa, T and Gaucher, E and Andres-Hernando, A and Rodriguez-Iturbe, B and Jimenez, CR and Garcia, G and Kang, DH and Tolan, DR and Lanaspa, MA}, title = {Fructose metabolism as a common evolutionary pathway of survival associated with climate change, food shortage and droughts.}, journal = {Journal of internal medicine}, volume = {287}, number = {3}, pages = {252-262}, doi = {10.1111/joim.12993}, pmid = {31621967}, issn = {1365-2796}, support = {R01 AR069137/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; *Climate Change ; Diet ; *Droughts ; Energy Metabolism/*physiology ; Extinction, Biological ; Fructose/*metabolism ; Hominidae ; Humans ; Mutation ; }, abstract = {Mass extinctions occur frequently in natural history. While studies of animals that became extinct can be informative, it is the survivors that provide clues for mechanisms of adaptation when conditions are adverse. Here, we describe a survival pathway used by many species as a means for providing adequate fuel and water, while also providing protection from a decrease in oxygen availability. Fructose, whether supplied in the diet (primarily fruits and honey), or endogenously (via activation of the polyol pathway), preferentially shifts the organism towards the storing of fuel (fat, glycogen) that can be used to provide energy and water at a later date. Fructose causes sodium retention and raises blood pressure and likely helped survival in the setting of dehydration or salt deprivation. By shifting energy production from the mitochondria to glycolysis, fructose reduced oxygen demands to aid survival in situations where oxygen availability is low. The actions of fructose are driven in part by vasopressin and the generation of uric acid. Twice in history, mutations occurred during periods of mass extinction that enhanced the activity of fructose to generate fat, with the first being a mutation in vitamin C metabolism during the Cretaceous-Paleogene extinction (65 million years ago) and the second being a mutation in uricase that occurred during the Middle Miocene disruption (12-14 million years ago). Today, the excessive intake of fructose due to the availability of refined sugar and high-fructose corn syrup is driving 'burden of life style' diseases, including obesity, diabetes and high blood pressure.}, }
@article {pmid31617565, year = {2019}, author = {Žihala, D and Eliáš, M}, title = {Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in a Lineage of Green Algae.}, journal = {Genome biology and evolution}, volume = {11}, number = {10}, pages = {2992-3007}, pmid = {31617565}, issn = {1759-6653}, mesh = {Chlorophyta/*genetics ; *Codon ; Codon, Terminator ; *Evolution, Molecular ; Genome, Mitochondrial ; Mitochondria/*genetics ; Mitochondrial Proteins/chemistry/genetics ; Peptide Termination Factors/chemistry/genetics ; RNA, Transfer/genetics ; }, abstract = {Mitochondria of diverse eukaryotes have evolved various departures from the standard genetic code, but the breadth of possible modifications and their phylogenetic distribution are known only incompletely. Furthermore, it is possible that some codon reassignments in previously sequenced mitogenomes have been missed, resulting in inaccurate protein sequences in databases. Here we show, considering the distribution of codons at conserved amino acid positions in mitogenome-encoded proteins, that mitochondria of the green algal order Sphaeropleales exhibit a diversity of codon reassignments, including previously missed ones and some that are unprecedented in any translation system examined so far, necessitating redefinition of existing translation tables and creating at least seven new ones. We resolve a previous controversy concerning the meaning the UAG codon in Hydrodictyaceae, which beyond any doubt encodes alanine. We further demonstrate that AGG, sometimes together with AGA, encodes alanine instead of arginine in diverse sphaeroplealeans. Further newly detected changes include Arg-to-Met reassignment of the AGG codon and Arg-to-Leu reassignment of the CGG codon in particular species. Analysis of tRNAs specified by sphaeroplealean mitogenomes provides direct support for and molecular underpinning of the proposed reassignments. Furthermore, we point to unique mutations in the mitochondrial release factor mtRF1a that correlate with changes in the use of termination codons in Sphaeropleales, including the two independent stop-to-sense UAG reassignments, the reintroduction of UGA in some Scenedesmaceae, and the sense-to-stop reassignment of UCA widespread in the group. Codon disappearance seems to be the main drive of the dynamic evolution of the mitochondrial genetic code in Sphaeropleales.}, }
@article {pmid31611421, year = {2020}, author = {Khoshravesh, R and Stata, M and Busch, FA and Saladié, M and Castelli, JM and Dakin, N and Hattersley, PW and Macfarlane, TD and Sage, RF and Ludwig, M and Sage, TL}, title = {The Evolutionary Origin of C4 Photosynthesis in the Grass Subtribe Neurachninae.}, journal = {Plant physiology}, volume = {182}, number = {1}, pages = {566-583}, pmid = {31611421}, issn = {1532-2548}, mesh = {Photosynthesis/genetics/physiology ; Plant Leaves/*metabolism/physiology ; Plant Proteins/genetics/*metabolism ; Plasmodesmata/metabolism/physiology ; Poaceae/genetics/physiology ; }, abstract = {The Australian grass subtribe Neurachninae contains closely related species that use C3, C4, and C2 photosynthesis. To gain insight into the evolution of C4 photosynthesis in grasses, we examined leaf gas exchange, anatomy and ultrastructure, and tissue localization of Gly decarboxylase subunit P (GLDP) in nine Neurachninae species. We identified previously unrecognized variation in leaf structure and physiology within Neurachne that represents varying degrees of C3-C4 intermediacy in the Neurachninae. These include inverse correlations between the apparent photosynthetic carbon dioxide (CO2) compensation point in the absence of day respiration (C *) and chloroplast and mitochondrial investment in the mestome sheath (MS), where CO2 is concentrated in C2 and C4 Neurachne species; width of the MS cells; frequency of plasmodesmata in the MS cell walls adjoining the parenchymatous bundle sheath; and the proportion of leaf GLDP invested in the MS tissue. Less than 12% of the leaf GLDP was allocated to the MS of completely C3 Neurachninae species with C * values of 56-61 μmol mol[-1], whereas two-thirds of leaf GLDP was in the MS of Neurachne lanigera, which exhibits a newly-identified, partial C2 phenotype with C * of 44 μmol mol[-1] Increased investment of GLDP in MS tissue of the C2 species was attributed to more MS mitochondria and less GLDP in mesophyll mitochondria. These results are consistent with a model where C4 evolution in Neurachninae initially occurred via an increase in organelle and GLDP content in MS cells, which generated a sink for photorespired CO2 in MS tissues.}, }
@article {pmid31610813, year = {2019}, author = {Motoki, MT and Fonseca, DM and Miot, EF and Demari-Silva, B and Thammavong, P and Chonephetsarath, S and Phommavanh, N and Hertz, JC and Kittayapong, P and Brey, PT and Marcombe, S}, title = {Population genetics of Aedes albopictus (Diptera: Culicidae) in its native range in Lao People's Democratic Republic.}, journal = {Parasites &amp; vectors}, volume = {12}, number = {1}, pages = {477}, pmid = {31610813}, issn = {1756-3305}, mesh = {Aedes/classification/genetics/*physiology/virology ; Algorithms ; Animals ; Asia, Southeastern ; Bayes Theorem ; Cluster Analysis ; DNA/chemistry/isolation &amp; purification ; Electron Transport Complex IV/genetics ; Asia, Eastern ; Female ; Genetic Variation ; Genetics, Population ; Haplotypes ; Italy ; Laos ; Mitochondria/enzymology ; Mosquito Control ; Mosquito Vectors/classification/genetics/*physiology/virology ; Phylogeny ; Sequence Analysis, DNA ; Tropical Climate ; United States ; }, abstract = {BACKGROUND: The Asian tiger mosquito, Aedes (Stegomyia) albopictus (Skuse) is an important worldwide invasive species and can be a locally important vector of chikungunya, dengue and, potentially, Zika. This species is native to Southeast Asia where populations thrive in both temperate and tropical climates. A better understanding of the population structure of Ae. albopictus in Lao PDR is very important in order to support the implementation of strategies for diseases prevention and vector control. In the present study, we investigated the genetic variability of Ae. albopictus across a north-south transect in Lao PDR.<br><br>METHODS: We used variability in a 1337-bp fragment of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1), to assess the population structure of Ae. albopictus in Lao PDR. For context, we also examined variability at the same genetic locus in samples of Ae. albopictus from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA.<br><br>RESULTS: We observed very high levels of genetic polymorphism with 46 novel haplotypes in Ae. albopictus from 9 localities in Lao PDR and Thailand populations. Significant differences were observed between the Luangnamtha population and other locations in Lao PDR. However, we found no evidence of isolation by distance. There was overall little genetic structure indicating ongoing and frequent gene flow among populations or a recent population expansion. Indeed, the neutrality test supported population expansion in Laotian Ae. albopictus and mismatch distribution analyses showed a lack of low frequency alleles, a pattern often seen in bottlenecked populations. When samples from Lao PDR were analyzed together with samples from Thailand, China, Taiwan, Japan, Singapore, Italy and the USA, phylogenetic network and Bayesian cluster analysis showed that most populations from tropical/subtropical regions are more genetically related to each other, than populations from temperate regions. Similarly, most populations from temperate regions are more genetically related to each other, than those from tropical/subtropical regions.<br><br>CONCLUSIONS: Aedes albopictus in Lao PDR are genetically related to populations from tropical/subtropical regions (i.e. Thailand, Singapore, and California and Texas in the USA). The extensive gene flow among locations in Lao PDR indicates that local control is undermined by repeated introductions from untreated sites.}, }
@article {pmid31601645, year = {2019}, author = {Ivanova, A and Gill-Hille, M and Huang, S and Branca, RM and Kmiec, B and Teixeira, PF and Lehtiö, J and Whelan, J and Murcha, MW}, title = {A Mitochondrial LYR Protein Is Required for Complex I Assembly.}, journal = {Plant physiology}, volume = {181}, number = {4}, pages = {1632-1650}, pmid = {31601645}, issn = {1532-2548}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/chemistry/*metabolism ; DNA, Bacterial/genetics ; Electron Transport Complex I/*metabolism ; Gene Deletion ; Gene Expression Regulation, Plant ; Holoenzymes/metabolism ; Iron-Sulfur Proteins/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; Models, Biological ; Organelle Biogenesis ; Phylogeny ; Protein Binding ; Protein Domains ; Protein Subunits/metabolism ; Saccharomyces cerevisiae/metabolism ; Up-Regulation/genetics ; }, abstract = {Complex I biogenesis requires the expression of both nuclear and mitochondrial genes, the import of proteins, cofactor biosynthesis, and the assembly of at least 49 individual subunits. Assembly factors interact with subunits of Complex I but are not part of the final holocomplex. We show that in Arabidopsis (Arabidopsis thaliana), a mitochondrial matrix protein (EMB1793, At1g76060), which we term COMPLEX I ASSEMBLY FACTOR 1 (CIAF1), contains a LYR domain and is required for Complex I assembly. T-DNA insertion mutants of CIAF1 lack Complex I and the Supercomplex I+III. Biochemical characterization shows that the assembly of Complex I is stalled at 650 and 800 kD intermediates in mitochondria isolated from ciaf1 mutant lines.I. Yeast-two-hybrid interaction and complementation assays indicate that CIAF1 specifically interacts with the 23-kD TYKY-1 matrix domain subunit of Complex I and likely plays a role in Fe-S insertion into this subunit. These data show that CIAF1 plays an essential role in assembling the peripheral matrix arm Complex I subunits into the Complex I holoenzyme.}, }
@article {pmid31599941, year = {2019}, author = {Liu, Q and Lin, D and Li, M and Gu, Z and Zhao, Y}, title = {Evidence of Neutral Evolution of Mitochondrial DNA in Human Hepatocellular Carcinoma.}, journal = {Genome biology and evolution}, volume = {11}, number = {10}, pages = {2909-2916}, pmid = {31599941}, issn = {1759-6653}, mesh = {Carcinoma, Hepatocellular/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Exons ; Humans ; Liver Neoplasms/*genetics ; Mutation ; }, abstract = {Many studies have suggested that mitochondria and mitochondrial DNA (mtDNA) might be functionally associated with tumor genesis and development. Although the heterogeneity of tumors is well known, most studies were based on the analysis of a single tumor sample. The extent of mtDNA diversity in the same tumor is unclear, as is whether the diversity is influenced by selection pressure. Here, we analyzed the whole exon data from 1 nontumor sample and 23 tumor samples from different locations of one single tumor tissue from a hepatocellular carcinoma (HCC) patient. Among 18 heteroplasmic sites identified in the tumor, only 2 heteroplasmies were shared among all tumor samples. By investigating the correlations between the occurrence and frequency of heteroplasmy (Het) and sampling locations (Coordinate), relative mitochondrial copy numbers, and single-nucleotide variants in the nuclear genome, we found that the Coordinate was significantly correlated with Het, suggesting no strong purifying selection or positive selection acted on the mtDNA in HCC. By further investigating the allele frequency and proportion of nonsynonymous mutations in the tumor mtDNA, we found that mtDNA in HCC did not undergo extra selection compared with mtDNA in the adjacent nontumor tissue, and they both likely evolved under neutral selection.}, }
@article {pmid31598902, year = {2020}, author = {Baysal, C and Pérez-González, A and Eseverri, &#xc1; and Jiang, X and Medina, V and Caro, E and Rubio, L and Christou, P and Zhu, C}, title = {Recognition motifs rather than phylogenetic origin influence the ability of targeting peptides to import nuclear-encoded recombinant proteins into rice mitochondria.}, journal = {Transgenic research}, volume = {29}, number = {1}, pages = {37-52}, pmid = {31598902}, issn = {1573-9368}, support = {OPP1143172.//Bill and Melinda Gates Foundation/International ; }, mesh = {Amino Acid Motifs ; Arabidopsis/genetics/metabolism ; Cell Nucleus/genetics/*metabolism ; Green Fluorescent Proteins/metabolism ; Mitochondria/genetics/*metabolism ; Oryza/genetics/*metabolism ; Peptide Fragments/genetics/*metabolism ; *Phylogeny ; Plant Proteins/genetics/*metabolism ; Protein Sorting Signals ; Protein Transport ; Recombinant Proteins/genetics/*metabolism ; Nicotiana/genetics/metabolism ; }, abstract = {Mitochondria fulfil essential functions in respiration and metabolism as well as regulating stress responses and apoptosis. Most native mitochondrial proteins are encoded by nuclear genes and are imported into mitochondria via one of several receptors that recognize N-terminal signal peptides. The targeting of recombinant proteins to mitochondria therefore requires the presence of an appropriate N-terminal peptide, but little is known about mitochondrial import in monocotyledonous plants such as rice (Oryza sativa). To gain insight into this phenomenon, we targeted nuclear-encoded enhanced green fluorescent protein (eGFP) to rice mitochondria using six mitochondrial pre-sequences with diverse phylogenetic origins, and investigated their effectiveness by immunoblot analysis as well as confocal and electron microscopy. We found that the ATPA and COX4 (Saccharomyces cerevisiae), SU9 (Neurospora crassa), pFA (Arabidopsis thaliana) and OsSCSb (Oryza sativa) peptides successfully directed most of the eGFP to the mitochondria, whereas the MTS2 peptide (Nicotiana plumbaginifolia) showed little or no evidence of targeting ability even though it is a native plant sequence. Our data therefore indicate that the presence of particular recognition motifs may be required for mitochondrial targeting, whereas the phylogenetic origin of the pre-sequences probably does not play a key role in the success of mitochondrial targeting in dedifferentiated rice callus and plants.}, }
@article {pmid31596994, year = {2019}, author = {McGaughran, A and Terauds, A and Convey, P and Fraser, CI}, title = {Genome-wide SNP data reveal improved evidence for Antarctic glacial refugia and dispersal of terrestrial invertebrates.}, journal = {Molecular ecology}, volume = {28}, number = {22}, pages = {4941-4957}, doi = {10.1111/mec.15269}, pmid = {31596994}, issn = {1365-294X}, mesh = {Animals ; Antarctic Regions ; Biodiversity ; Evolution, Molecular ; Genetic Variation/*genetics ; Genome-Wide Association Study/methods ; Geography ; Ice Cover ; Invertebrates/*genetics ; Islands ; Mitochondria/genetics ; Polymorphism, Single Nucleotide/*genetics ; Refugium ; }, abstract = {Antarctica is isolated, surrounded by the Southern Ocean and has experienced extreme environmental conditions for millions of years, including during recent Pleistocene glacial maxima. How Antarctic terrestrial species might have survived these glaciations has been a topic of intense interest, yet many questions remain unanswered, particularly for Antarctica's invertebrate fauna. We examine whether genetic data from a widespread group of terrestrial invertebrates, springtails (Collembola, Isotomidae) of the genus Cryptopygus, show evidence for long-term survival in glacial refugia along the Antarctic Peninsula. We use genome-wide SNP analyses (via genotyping-by-sequencing, GBS) and mitochondrial data to examine population diversity and differentiation across more than 20 sites spanning >950 km on the Peninsula, and from islands both close to the Peninsula and up to ~1,900 km away. Population structure analysis indicates the presence of strong local clusters of diversity, and we infer that patterns represent a complex interplay of isolation in local refugia coupled with occasional successful long-distance dispersal events. We identified wind and degree days as significant environmental drivers of genetic diversity, with windier and warmer sites hosting higher diversity. Thus, we infer that refugial areas along the Antarctic Peninsula have allowed populations of indigenous springtails to survive in situ throughout glacial periods. Despite the difficulties of dispersal in cold, desiccating conditions, Cryptopygus springtails on the Peninsula appear to have achieved multiple long-distance colonization events, most likely through wind-related dispersal events.}, }
@article {pmid31591397, year = {2019}, author = {Smith, SR and Dupont, CL and McCarthy, JK and Broddrick, JT and Oborník, M and Horák, A and Füssy, Z and Cihlář, J and Kleessen, S and Zheng, H and McCrow, JP and Hixson, KK and Araújo, WL and Nunes-Nesi, A and Fernie, A and Nikoloski, Z and Palsson, BO and Allen, AE}, title = {Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4552}, pmid = {31591397}, issn = {2041-1723}, mesh = {Carbon/metabolism ; Chloroplasts/genetics/metabolism ; Diatoms/*genetics/*metabolism ; Evolution, Molecular ; Gene Expression Profiling/methods ; Gene Expression Regulation ; Metabolic Networks and Pathways/*genetics ; Metabolomics/methods ; Mitochondria/genetics/metabolism ; Models, Biological ; Nitrates/metabolism ; Nitrogen/*metabolism ; Proteomics/methods ; Seawater/microbiology ; Signal Transduction/genetics ; }, abstract = {Diatoms outcompete other phytoplankton for nitrate, yet little is known about the mechanisms underpinning this ability. Genomes and genome-enabled studies have shown that diatoms possess unique features of nitrogen metabolism however, the implications for nutrient utilization and growth are poorly understood. Using a combination of transcriptomics, proteomics, metabolomics, fluxomics, and flux balance analysis to examine short-term shifts in nitrogen utilization in the model pennate diatom in Phaeodactylum tricornutum, we obtained a systems-level understanding of assimilation and intracellular distribution of nitrogen. Chloroplasts and mitochondria are energetically integrated at the critical intersection of carbon and nitrogen metabolism in diatoms. Pathways involved in this integration are organelle-localized GS-GOGAT cycles, aspartate and alanine systems for amino moiety exchange, and a split-organelle arginine biosynthesis pathway that clarifies the role of the diatom urea cycle. This unique configuration allows diatoms to efficiently adjust to changing nitrogen status, conferring an ecological advantage over other phytoplankton taxa.}, }
@article {pmid31587636, year = {2019}, author = {Wideman, JG and Lax, G and Leonard, G and Milner, DS and Rodríguez-Martínez, R and Simpson, AGB and Richards, TA}, title = {A single-cell genome reveals diplonemid-like ancestry of kinetoplastid mitochondrial gene structure.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1786}, pages = {20190100}, pmid = {31587636}, issn = {1471-2970}, mesh = {Euglenozoa/*genetics ; *Genome, Mitochondrial ; *Genome, Protozoan ; Single-Cell Analysis ; }, abstract = {Euglenozoa comprises euglenids, kinetoplastids, and diplonemids, with each group exhibiting different and highly unusual mitochondrial genome organizations. Although they are sister groups, kinetoplastids and diplonemids have very distinct mitochondrial genome architectures, requiring widespread insertion/deletion RNA editing and extensive trans-splicing, respectively, in order to generate functional transcripts. The evolutionary history by which these differing processes arose remains unclear. Using single-cell genomics, followed by small sub unit ribosomal DNA and multigene phylogenies, we identified an isolated marine cell that branches on phylogenetic trees as a sister to known kinetoplastids. Analysis of single-cell amplified genomic material identified multiple mitochondrial genome contigs. These revealed a gene architecture resembling that of diplonemid mitochondria, with small fragments of genes encoded out of order and or on different contigs, indicating that these genes require extensive trans-splicing. Conversely, no requirement for kinetoplastid-like insertion/deletion RNA-editing was detected. Additionally, while we identified some proteins so far only found in kinetoplastids, we could not unequivocally identify mitochondrial RNA editing proteins. These data invite the hypothesis that extensive genome fragmentation and trans-splicing were the ancestral states for the kinetoplastid-diplonemid clade but were lost during the kinetoplastid radiation. This study demonstrates that single-cell approaches can successfully retrieve lineages that represent important new branches on the tree of life, and thus can illuminate major evolutionary and functional transitions in eukaryotes. This article is part of a discussion meeting issue 'Single cell ecology'.}, }
@article {pmid31585116, year = {2019}, author = {Betgiri, AA and Jadhav, SN and Pawde, M and Shukla, A and Mote, C and Pawar, PD and Shanmugam, D and Kundu, K}, title = {Mitochondrial cytochrome oxidase C subunit III (cox3) gene as a sensitive and specific target for molecular detection of Babesia gibsoni infection in dogs.}, journal = {Experimental parasitology}, volume = {206}, number = {}, pages = {107771}, doi = {10.1016/j.exppara.2019.107771}, pmid = {31585116}, issn = {1090-2449}, mesh = {Animals ; Babesia/classification/genetics/*isolation &amp; purification ; Babesiosis/*diagnosis/parasitology ; Base Sequence ; Cross Reactions ; DNA, Ribosomal Spacer/chemistry ; Dog Diseases/*diagnosis/parasitology ; Dogs ; Electron Transport Complex IV/*genetics ; Erythrocytes/parasitology ; Likelihood Functions ; Mitochondria/*enzymology ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Predictive Value of Tests ; RNA, Ribosomal, 18S/analysis ; Sensitivity and Specificity ; Sequence Alignment/veterinary ; }, abstract = {A PCR targeting mitochondrial cytochrome oxidase subunit III (cox3) for molecular detection of Babesia gibsoni infection in dogs has been developed in this study. Fifty blood samples from suspected clinical cases from dogs, brought to the veterinary college clinics, were examined for presence of B. gibsoni using conventional diagnosis by microscopic examination of Giemsa stained thin blood smears. In addition, species specific PCRs targeting ITS-1 region (BgITS-1 PCR) and nested PCR targeting 18S ribosomal RNA gene (Bg18SnPCR) were carried out. A 634 bp PCR fragment of B. gibsoni cox3 gene was amplified in positive samples from three geographical locations of Satara, Wai and Pune in Maharashtra state of India. From analysis of the sequence of the B. gibsoni cox3 gene, we found that the Indian isolate had 96-98% similarity to the isolate from Japan and China. Post sequencing, de-novo diagnostic primer pair for species specific amplification of 164 bp fragment of B. gibsonicox3 was designed and the PCR was standardized. The diagnostic results of de-novo Bgcox3 PCR were compared with BgITS-1 PCR and Bg18S nPCR. Thin blood smears detected 22% (11/50) samples positive for small form of Babesia species. The BgITS-1 PCR detected 25% samples (15/50) as positive and Bg18S nPCR detected 80% (40/50) B. gibsoni positive samples. The de-novo Bgcox3 PCR detected 66% (33/50) samples positive for B. gibsoni (at 95% CI). The analytical sensitivity of cox3 PCR was evaluated as 0.000003% parasitaemia or 09 parasites in 100 μl of blood. The de-novo diagnostic cox3 PCR did not cross react with control positive DNA from other haemoprotozoa and rickettsia like B. vogeli, Hepatozoon canis, Trypanosoma evansi, Ehrlichia canis and Anaplasma platys. Statistically, cox3 PCR had better diagnostic efficiency than ITS-1 PCR in terms of sensitivity (p = 0.0006). No statistically significant difference between results of cox3 PCR and 18S nPCR was observed (p = 0.1760). Kappa values estimated for each test pair showed fair to moderate agreement between the observations. Specificity of Bgcox3 PCR was 100% when compared with microscopy or BgITS-1 PCR. Sensitivity of Bgcox3 PCR was 100% when compared with that of Bg18S nPCR.}, }
@article {pmid31581628, year = {2019}, author = {Mazzocca, A}, title = {The Systemic-Evolutionary Theory of the Origin of Cancer (SETOC): A New Interpretative Model of Cancer as a Complex Biological System.}, journal = {International journal of molecular sciences}, volume = {20}, number = {19}, pages = {}, pmid = {31581628}, issn = {1422-0067}, mesh = {Animals ; *Cell Transformation, Neoplastic ; Humans ; *Models, Biological ; Neoplasms/*etiology/*metabolism/pathology ; }, abstract = {The Systemic-Evolutionary Theory of Cancer (SETOC) is a recently proposed theory based on two important concepts: (i) Evolution, understood as a process of cooperation and symbiosis (Margulian-like), and (ii) The system, in terms of the integration of the various cellular components, so that the whole is greater than the sum of the parts, as in any complex system. The SETOC posits that cancer is generated by the de-emergence of the "eukaryotic cell system" and by the re-emergence of cellular subsystems such as archaea-like (genetic information) and/or prokaryotic-like (mitochondria) subsystems, featuring uncoordinated behaviors. One of the consequences is a sort of "cellular regression" towards ancestral or atavistic biological functions or behaviors similar to those of protists or unicellular organisms in general. This de-emergence is caused by the progressive breakdown of the endosymbiotic cellular subsystem integration (mainly, information = nucleus and energy = mitochondria) as a consequence of long-term injuries. Known cancer-promoting factors, including inflammation, chronic fibrosis, and chronic degenerative processes, cause prolonged damage that leads to the breakdown or failure of this form of integration/endosymbiosis. In normal cells, the cellular "subsystems" must be fully integrated in order to maintain the differentiated state, and this integration is ensured by a constant energy intake. In contrast, when organ or tissue damage occurs, the constant energy intake declines, leading, over time, to energy shortage, failure of endosymbiosis, and the de-differentiated state observed in dysplasia and cancer.}, }
@article {pmid31580787, year = {2019}, author = {Velázquez-Urrieta, Y and Oceguera-Figueroa, A and León-Règagnon, V}, title = {Two New Species of Haematoloechus (Digenea: Plagiorchidae) Parasitizing Rana brownorum (Amphibia: Ranidae) from Southeast Mexico.}, journal = {The Journal of parasitology}, volume = {105}, number = {5}, pages = {724-732}, pmid = {31580787}, issn = {1937-2345}, mesh = {Animals ; Base Sequence ; DNA, Ribosomal/chemistry ; Electron Transport Complex IV/genetics ; Lung/parasitology ; Mexico ; Mitochondria/enzymology ; Phylogeny ; Prevalence ; RNA, Ribosomal, 28S/genetics ; Ranidae/*parasitology ; Sequence Alignment/veterinary ; Trematoda/anatomy &amp; histology/*classification/genetics/isolation &amp; purification ; Trematode Infections/epidemiology/parasitology/*veterinary ; }, abstract = {In an ongoing investigation on the helminths of amphibians in southeastern Mexico, specimens of 2 undescribed species of Haematoloechus were collected from Rana brownorum. Haematoloechus ceciliae n. sp. is morphologically most similar to Haematoloechus meridionalis, but differs in the shape of the oral sucker, in the nature of the acetabulum, and in the distribution of the glandular cells in the pharyngeal region; Haematoloechus celestunensis n. sp. closely resembles Haematoloechus floedae, but differs in the form and size of the testes and measurements of acetabulum. COI and 28S DNA sequences of both new species show high divergence compared to other species of the genus. In the phylogenetic trees, H. ceciliae appears most closely related to Haematoloechus danbrooksi and H. celestunensis to Haematoloechus veracruzanus.}, }
@article {pmid31580785, year = {2019}, author = {Achatz, TJ and Curran, SS and Patitucci, KF and Fecchio, A and Tkach, VV}, title = {Phylogenetic Affinities of Uvulifer Spp. (Digenea: Diplostomidae) in the Americas with Description of Two New Species from Peruvian Amazon.}, journal = {The Journal of parasitology}, volume = {105}, number = {5}, pages = {704-717}, pmid = {31580785}, issn = {1937-2345}, support = {R15 AI092622/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; Bird Diseases/*parasitology ; Birds ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Intestine, Small/parasitology ; Mitochondria/enzymology ; Peru ; *Phylogeny ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal, 28S/genetics ; Rivers ; Sequence Alignment/veterinary ; Trematoda/anatomy &amp; histology/*classification/genetics ; Trematode Infections/parasitology/*veterinary ; }, abstract = {Uvulifer Yamaguti, 1934, is a genus of diplostomoidean digeneans that parasitizes kingfishers worldwide. Species have a Neascus-type metacercaria that encysts in or on fish intermediate hosts, often causing black spot disease. Only 3 prior studies published DNA sequence data for Uvulifer species with only 1 including a single named species (Uvulifer spinatus López-Jiménez, Pérez-Ponce de León, &amp; García-Varela, 2018). Herein we describe 2 new species of Uvulifer from the green-and-rufous kingfisher, Chloroceryle inda (Linnaeus), collected in Peru (Uvulifer batesi n. sp. and Uvulifer pequenae n. sp.). Both new species are readily differentiated from their New World congeners by a combination of morphological characters including distribution of vitelline follicles and prosoma:opisthosoma length ratios. In addition, we used newly generated nuclear 28S rRNA and mitochondrial COI gene sequence data to differentiate among species and examine phylogenetic affinities of Uvulifer. This includes the 2 new species and Uvulifer ambloplitis (Hughes, 1927), as well as Uvulifer elongatus Dubois, 1988 , Uvulifer prosocotyle (Lutz, 1928), and Uvulifer weberi Dubois, 1985 , none of which have been part of prior molecular phylogenetic studies. Our data on Uvulifer revealed 0.1-2.2% interspecific divergence in 28S sequences and 9.3-15.3% in COI sequences. Our 28S phylogeny revealed at least 6 well-supported clades within the genus. In contrast, the branch topology in the COI phylogenetic tree was overall less supported, indicating that although COI sequences are a great tool for species differentiation, they should be used with caution for phylogenetic inference at higher taxonomic levels. Our 28S phylogeny did not reveal any clear patterns of host association between Uvulifer and particular species of kingfishers; however, it identified 2 well-supported clades uniting Uvulifer species from distant geographical locations and more than 1 biogeographic realm, indicating at least 2 independent dispersal events in the evolutionary history of the New World Uvulifer. Our results clearly demonstrate that the diversity of Uvulifer in the New World has been underestimated.}, }
@article {pmid31575774, year = {2019}, author = {Murante, D and Hogan, DA}, title = {New Mitochondrial Targets in Fungal Pathogens.}, journal = {mBio}, volume = {10}, number = {5}, pages = {}, pmid = {31575774}, issn = {2150-7511}, support = {R01 AI127548/AI/NIAID NIH HHS/United States ; }, mesh = {*Candida albicans ; Humans ; *Mitochondria ; Phylogeny ; Saccharomyces cerevisiae ; }, abstract = {In eukaryotic cells, mitochondria are responsible for the synthesis of ATP using power generated by the electron transport chain (ETC). While much of what is known about mitochondria has been gained from a study of a small number of model species, including the yeast Saccharomyces cerevisiae, the general mechanisms of mitochondrial respiration have been recognized as being highly conserved across eukaryotes. Now, Sun et al. (N. Sun, R. S. Parrish, R. A. Calderone, and W. A. Fonzi, mBio 10:e00300-19, 2019, https://doi.org/10.1128/mBio.00300-19) take the next steps in understanding mitochondrial function by identifying proteins that are unique to a smaller phylogenetic group of microbes. Using the combination of in silico, biochemical, and microbiological assays, Sun and colleagues identified seven genes that are unique to the CTG fungal clade, which contains multiple important human pathogens, including Candida albicans, and showed that they are required for full ETC function during respiratory metabolism. Because respiratory metabolism is critical for fungal pathogenesis, these clade-specific mitochondrial factors may represent novel therapeutic targets.}, }
@article {pmid31561749, year = {2019}, author = {Lorenz, C and Alves, JMP and Foster, PG and Sallum, MAM and Suesdek, L}, title = {First record of translocation in Culicidae (Diptera) mitogenomes: evidence from the tribe Sabethini.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {721}, pmid = {31561749}, issn = {1471-2164}, support = {311805/2014-0 and 311984/2018-5//CAPES/ ; 2013/05521-9 and 2015/12784-1//FAPESP/ ; 2014/26229-9//FAPESP/ ; 301877/2016-5//CNPq/ ; }, mesh = {Animals ; Culicidae/*classification/genetics ; Evolution, Molecular ; Gene Order ; Gene Rearrangement ; Genome Size ; Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: The tribe Sabethini (Diptera: Culicidae) contains important vectors of the yellow fever virus and presents remarkable morphological and ecological diversity unequalled in other mosquito groups. However, there is limited information about mitochondrial genomes (mitogenomes) from these species. As mitochondrial genetics has been fundamental for posing evolutionary hypotheses and identifying taxonomical markers, in this study we sequenced the first sabethine mitogenomes: Sabethes undosus, Trichoprosopon pallidiventer, Runchomyia reversa, Limatus flavisetosus, and Wyeomyia confusa. In addition, we performed phylogenetic analyses of Sabethini within Culicidae and compared its mitogenomic architecture to that of other insects.<br><br>RESULTS: Similar to other insects, the Sabethini mitogenome contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. However, the gene order is not the same as that in other mosquitoes; the tyrosine (Y) and cysteine (C) tRNA genes have translocated. In general, mitogenome rearrangements within insects are uncommon events; the translocation reported here is unparalleled among Culicidae and can be considered an autapomorphy for the Neotropical sabethines.<br><br>CONCLUSIONS: Our study provides clear evidence of gene rearrangements in the mitogenomes of these Neotropical genera in the tribe Sabethini. Gene order can be informative at the taxonomic level of tribe. The translocations found, along with the mitogenomic sequence data and other recently published findings, reinforce the status of Sabethini as a well-supported monophyletic taxon. Furthermore, T. pallidiventer was recovered as sister to R. reversa, and both were placed as sisters of other Sabethini genera (Sabethes, Wyeomyia, and Limatus).}, }
@article {pmid31561566, year = {2019}, author = {Varré, JS and D'Agostino, N and Touzet, P and Gallina, S and Tamburino, R and Cantarella, C and Ubrig, E and Cardi, T and Drouard, L and Gualberto, JM and Scotti, N}, title = {Complete Sequence, Multichromosomal Architecture and Transcriptome Analysis of the Solanum tuberosum Mitochondrial Genome.}, journal = {International journal of molecular sciences}, volume = {20}, number = {19}, pages = {}, pmid = {31561566}, issn = {1422-0067}, mesh = {Amino Acid Sequence ; *Gene Expression Profiling ; *Genome, Mitochondrial ; *Genomics/methods ; Open Reading Frames ; Phylogeny ; RNA Editing ; Solanum tuberosum/*genetics ; *Whole Genome Sequencing ; }, abstract = {Mitochondrial genomes (mitogenomes) in higher plants can induce cytoplasmic male sterility and be somehow involved in nuclear-cytoplasmic interactions affecting plant growth and agronomic performance. They are larger and more complex than in other eukaryotes, due to their recombinogenic nature. For most plants, the mitochondrial DNA (mtDNA) can be represented as a single circular chromosome, the so-called master molecule, which includes repeated sequences that recombine frequently, generating sub-genomic molecules in various proportions. Based on the relevance of the potato crop worldwide, herewith we report the complete mtDNA sequence of two S. tuberosum cultivars, namely Cicero and Désirée, and a comprehensive study of its expression, based on high-coverage RNA sequencing data. We found that the potato mitogenome has a multi-partite architecture, divided in at least three independent molecules that according to our data should behave as autonomous chromosomes. Inter-cultivar variability was null, while comparative analyses with other species of the Solanaceae family allowed the investigation of the evolutionary history of their mitogenomes. The RNA-seq data revealed peculiarities in transcriptional and post-transcriptional processing of mRNAs. These included co-transcription of genes with open reading frames that are probably expressed, methylation of an rRNA at a position that should impact translation efficiency and extensive RNA editing, with a high proportion of partial editing implying frequent mis-targeting by the editing machinery.}, }
@article {pmid31559328, year = {2019}, author = {Patita, M and Nunes, G and Alves de Matos, A and Coelho, H and Fonseca, C and Fonseca, J}, title = {Mauriac Syndrome: A Rare Hepatic Glycogenosis in Poorly Controlled Type 1 Diabetes.}, journal = {GE Portuguese journal of gastroenterology}, volume = {26}, number = {5}, pages = {370-374}, pmid = {31559328}, issn = {2341-4545}, abstract = {BACKGROUND: Hepatic glycogenosis (HG) is a complication of poorly controlled type 1 diabetes mellitus (T1DM), characterized by glycogen accumulation in hepatocytes. Mauriac syndrome (MS) is a glycogenic hepatopathy, initially described in 1930, characterized by growth failure, delayed puberty, cushingoid appearance, hepatomegaly with abnormal liver enzymes, and hypercholesterolemia. HG is a condition with good prognosis and fast resolution after adequate glycemic control (although it has potential for relapse), with no case of evolution to end-stage liver disease described.<br><br>CASE: We describe a 26-year-old female, with T1DM complicated by severe retinopathy. The patient maintained poor glycemic control since childhood, presenting glycated hemoglobin persistently higher than 10% and recurrent episodes of ketoacidosis. In adolescence, she developed hepatomegaly and fluctuating elevation of aminotransferases and triglycerides. A small, nonrepresentative hepatic biopsy suggested macrovacuolar steatosis and mild fibrosis. After 15 years of diabetes, the patient was referred for gastroenterology clinic due to chronic diarrhea and exuberant hepatomegaly. Laboratory showed persistent elevation of aminotransferases and triglycerides. Bilirubin, iron metabolism, and coagulation were normal; viral serologies and autoimmune study were negative. Upper endoscopy, ileocolonoscopy, and enteroscopy presented no lesions. Abdominal magnetic resonance imaging displayed massive hepatomegaly. Liver biopsy was repeated showing marked nuclear glycogenization, mild steatosis, and no fibrosis; electron microscopy revealed very large deposits of glycogen and pleomorphic mitochondria with an unusually dense matrix, described for the first time in this entity. The diagnosis of MS variant and diarrhea due to autonomic neuropathy were assumed.<br><br>CONCLUSION: Currently, HG is a well-recognized disease that occurs at any age and can be present without the full spectrum of features initially described for MS. In the era of insulin therapy, this entity represents a rare complication, caused by low therapeutic compliance.}, }
@article {pmid31554701, year = {2019}, author = {Dell'Aglio, E and Giustini, C and Kraut, A and Couté, Y and Costa, A and Decros, G and Gibon, Y and Mazars, C and Matringe, M and Finazzi, G and Curien, G}, title = {Identification of the Arabidopsis Calmodulin-Dependent NAD[+] Kinase That Sustains the Elicitor-Induced Oxidative Burst.}, journal = {Plant physiology}, volume = {181}, number = {4}, pages = {1449-1458}, pmid = {31554701}, issn = {1532-2548}, mesh = {Amino Acid Sequence ; Arabidopsis/*enzymology ; Arabidopsis Proteins/chemistry/*metabolism ; Calcium/metabolism ; Calcium-Calmodulin-Dependent Protein Kinases/metabolism ; Flagellin/metabolism ; Kinetics ; Mitochondria/metabolism ; Models, Biological ; Peptides/metabolism ; Phosphotransferases (Alcohol Group Acceptor)/chemistry/*metabolism ; Photosynthesis ; Phylogeny ; Protein Binding ; Protein Domains ; *Respiratory Burst ; Seedlings/metabolism ; }, abstract = {NADP(H) is an essential cofactor of multiple metabolic processes in all living organisms, and in plants, NADP(H) is required as the substrate of Ca[2+]-dependent NADPH oxidases, which catalyze a reactive oxygen species burst in response to various stimuli. While NADP[+] production in plants has long been known to involve a calmodulin (CaM)/Ca[2+]-dependent NAD[+] kinase, the nature of the enzyme catalyzing this activity has remained enigmatic, as has its role in plant physiology. Here, we used proteomic, biochemical, molecular, and in vivo analyses to identify an Arabidopsis (Arabidopsis thaliana) protein that catalyzes NADP[+] production exclusively in the presence of CaM/Ca[2+] This enzyme, which we named NAD kinase-CaM dependent (NADKc), has a CaM-binding peptide located in its N-terminal region and displays peculiar biochemical properties as well as different domain organization compared with known plant NAD[+] kinases. In response to a pathogen elicitor, the activity of NADKc, which is associated with the mitochondrial periphery, contributes to an increase in the cellular NADP[+] concentration and to the amplification of the elicitor-induced oxidative burst. Based on a phylogenetic analysis and enzymatic assays, we propose that the CaM/Ca[2+]-dependent NAD[+] kinase activity found in photosynthetic organisms is carried out by NADKc-related proteins. Thus, NADKc represents the missing link between Ca[2+] signaling, metabolism, and the oxidative burst.}, }
@article {pmid31553224, year = {2019}, author = {Seligmann, H}, title = {Syntenies Between Cohosted Mitochondrial, Chloroplast, and Phycodnavirus Genomes: Functional Mimicry and/or Common Ancestry?.}, journal = {DNA and cell biology}, volume = {38}, number = {11}, pages = {1257-1268}, doi = {10.1089/dna.2019.4858}, pmid = {31553224}, issn = {1557-7430}, mesh = {Adaptive Immunity/genetics ; Chloroplasts/*genetics ; *Evolution, Molecular ; Genome, Mitochondrial/genetics ; Genome, Viral/genetics ; Host-Pathogen Interactions/genetics/immunology ; Immune Evasion/genetics ; Mitochondria/*genetics ; Molecular Mimicry/*physiology ; Organelles/genetics ; Phycodnaviridae/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Synteny/*genetics ; }, abstract = {Recent analyses suggest bacterial and/or mitochondrion-like ancestry for giant viruses (Megavirales sensu latu): amoeban mitochondrial gene arrangements resemble those of their candidate homologs in megaviral genomes. This presumed ancestral synteny decreases with genome size across megaviral families at large and within Poxviridae. In this study, analyses focus on Phycodnaviridae, a polyphyletic group of giant viruses infecting Haplophyta, Stramenopiles, and other algae, using syntenies between algal mitogene arrangements and chloroplast genomes and Rickettsia prowazekii as positive controls. Mitogene alignment qualities with Rickettsia are much higher than with viral genomes. Mitogenome synteny with some viruses is higher, for others lower than with Rickettsia, despite lower alignments qualities. In some algae, syntenies among cohosted chloroplast, virus, and mitochondrion are higher, in others lower than expected. This suggests gene order coevolution in cohosted genomes, different coregulations of organelle metabolisms for different algae, and viral mitogenome mimicry, to hijack organelle-committed cellular resources and/or escape cellular defenses/genetic immunity systems. This principle might explain high synteny between human mitochondria and the pathogenic endocellular alphaproteobacterium R. prowazekii beyond common ancestry. Results indicate that putative bacteria/mitochondrion-like genomic ancestors of Phycodnaviridae originated before or at the mitochondrion-bacteria split, and ulterior functional constraints on gene arrangements of cohosted genomes.}, }
@article {pmid31551356, year = {2019}, author = {Al-Faresi, RAZ and Lightowlers, RN and Chrzanowska-Lightowlers, ZMA}, title = {Mammalian mitochondrial translation - revealing consequences of divergent evolution.}, journal = {Biochemical Society transactions}, volume = {47}, number = {5}, pages = {1429-1436}, doi = {10.1042/BST20190265}, pmid = {31551356}, issn = {1470-8752}, support = {203105/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Biological Evolution ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/metabolism ; Oxidative Phosphorylation ; RNA Processing, Post-Transcriptional ; RNA, Messenger/metabolism ; }, abstract = {Mitochondria are ubiquitous organelles present in the cytoplasm of all nucleated eukaryotic cells. These organelles are described as arising from a common ancestor but a comparison of numerous aspects of mitochondria between different organisms provides remarkable examples of divergent evolution. In humans, these organelles are of dual genetic origin, comprising ∼1500 nuclear-encoded proteins and thirteen that are encoded by the mitochondrial genome. Of the various functions that these organelles perform, it is only oxidative phosphorylation, which provides ATP as a source of chemical energy, that is dependent on synthesis of these thirteen mitochondrially encoded proteins. A prerequisite for this process of translation are the mitoribosomes. The recent revolution in cryo-electron microscopy has generated high-resolution mitoribosome structures and has undoubtedly revealed some of the most distinctive molecular aspects of the mitoribosomes from different organisms. However, we still lack a complete understanding of the mechanistic aspects of this process and many of the factors involved in post-transcriptional gene expression in mitochondria. This review reflects on the current knowledge and illustrates some of the striking differences that have been identified between mitochondria from a range of organisms.}, }
@article {pmid31550514, year = {2019}, author = {Calì, C and Agus, M and Kare, K and Boges, DJ and Lehväslaiho, H and Hadwiger, M and Magistretti, PJ}, title = {3D cellular reconstruction of cortical glia and parenchymal morphometric analysis from Serial Block-Face Electron Microscopy of juvenile rat.}, journal = {Progress in neurobiology}, volume = {183}, number = {}, pages = {101696}, doi = {10.1016/j.pneurobio.2019.101696}, pmid = {31550514}, issn = {1873-5118}, mesh = {Animals ; Astrocytes/*ultrastructure ; Brain/*cytology/*diagnostic imaging ; *Imaging, Three-Dimensional ; Microglia/*ultrastructure ; Microscopy, Electron ; *Microscopy, Electron, Scanning ; Neurons/*ultrastructure ; Pericytes/*ultrastructure ; Rats ; Somatosensory Cortex/cytology/diagnostic imaging ; }, abstract = {With the rapid evolution in the automation of serial electron microscopy in life sciences, the acquisition of terabyte-sized datasets is becoming increasingly common. High resolution serial block-face imaging (SBEM) of biological tissues offers the opportunity to segment and reconstruct nanoscale structures to reveal spatial features previously inaccessible with simple, single section, two-dimensional images. In particular, we focussed here on glial cells, whose reconstruction efforts in literature are still limited, compared to neurons. We imaged a 750,000 cubic micron volume of the somatosensory cortex from a juvenile P14 rat, with 20 nm accuracy. We recognized a total of 186 cells using their nuclei, and classified them as neuronal or glial based on features of the soma and the processes. We reconstructed for the first time 4 almost complete astrocytes and neurons, 4 complete microglia and 4 complete pericytes, including their intracellular mitochondria, 186 nuclei and 213 myelinated axons. We then performed quantitative analysis on the three-dimensional models. Out of the data that we generated, we observed that neurons have larger nuclei, which correlated with their lesser density, and that astrocytes and pericytes have a higher surface to volume ratio, compared to other cell types. All reconstructed morphologies represent an important resource for computational neuroscientists, as morphological quantitative information can be inferred, to tune simulations that take into account the spatial compartmentalization of the different cell types.}, }
@article {pmid31543463, year = {2019}, author = {Guièze, R and Liu, VM and Rosebrock, D and Jourdain, AA and Hernández-Sánchez, M and Martinez Zurita, A and Sun, J and Ten Hacken, E and Baranowski, K and Thompson, PA and Heo, JM and Cartun, Z and Aygün, O and Iorgulescu, JB and Zhang, W and Notarangelo, G and Livitz, D and Li, S and Davids, MS and Biran, A and Fernandes, SM and Brown, JR and Lako, A and Ciantra, ZB and Lawlor, MA and Keskin, DB and Udeshi, ND and Wierda, WG and Livak, KJ and Letai, AG and Neuberg, D and Harper, JW and Carr, SA and Piccioni, F and Ott, CJ and Leshchiner, I and Johannessen, CM and Doench, J and Mootha, VK and Getz, G and Wu, CJ}, title = {Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies.}, journal = {Cancer cell}, volume = {36}, number = {4}, pages = {369-384.e13}, pmid = {31543463}, issn = {1878-3686}, support = {U10 CA180861/CA/NCI NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; T32 HL007627/HL/NHLBI NIH HHS/United States ; U24 CA210986/CA/NCI NIH HHS/United States ; R35 GM122455/GM/NIGMS NIH HHS/United States ; R21 CA216772/CA/NCI NIH HHS/United States ; R01 CA155010/CA/NCI NIH HHS/United States ; UG1 CA233338/CA/NCI NIH HHS/United States ; U01 CA214125/CA/NCI NIH HHS/United States ; R00 CA190861/CA/NCI NIH HHS/United States ; R01 CA216273/CA/NCI NIH HHS/United States ; R37 NS083524/NS/NINDS NIH HHS/United States ; P01 CA206978/CA/NCI NIH HHS/United States ; R01 CA213442/CA/NCI NIH HHS/United States ; R01 GM095567/GM/NIGMS NIH HHS/United States ; P01 CA081534/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aged, 80 and over ; Animals ; Antineoplastic Combined Chemotherapy Protocols/*pharmacology/therapeutic use ; Apoptosis/drug effects/genetics ; Bridged Bicyclo Compounds, Heterocyclic/*pharmacology/therapeutic use ; Cell Line, Tumor ; Clonal Evolution/drug effects ; Disease Progression ; Drug Resistance, Neoplasm/drug effects/genetics ; Energy Metabolism/drug effects/genetics ; Female ; Gene Expression Regulation, Neoplastic ; Humans ; Leukemia, Lymphocytic, Chronic, B-Cell/*drug therapy/pathology ; Male ; Mice ; Middle Aged ; Mitochondria/drug effects/*pathology ; Myeloid Cell Leukemia Sequence 1 Protein/metabolism ; Oxidative Phosphorylation/drug effects ; Proto-Oncogene Proteins c-bcl-2/*antagonists &amp; inhibitors/metabolism ; Sulfonamides/*pharmacology/therapeutic use ; Treatment Outcome ; Xenograft Model Antitumor Assays ; }, abstract = {Mitochondrial apoptosis can be effectively targeted in lymphoid malignancies with the FDA-approved B cell lymphoma 2 (BCL-2) inhibitor venetoclax, but resistance to this agent is emerging. We show that venetoclax resistance in chronic lymphocytic leukemia is associated with complex clonal shifts. To identify determinants of resistance, we conducted parallel genome-scale screens of the BCL-2-driven OCI-Ly1 lymphoma cell line after venetoclax exposure along with integrated expression profiling and functional characterization of drug-resistant and engineered cell lines. We identified regulators of lymphoid transcription and cellular energy metabolism as drivers of venetoclax resistance in addition to the known involvement by BCL-2 family members, which were confirmed in patient samples. Our data support the implementation of combinatorial therapy with metabolic modulators to address venetoclax resistance.}, }
@article {pmid31542425, year = {2019}, author = {Zheng, F and Colasante, C and Voncken, F}, title = {Characterisation of a mitochondrial iron transporter of the pathogen Trypanosoma brucei.}, journal = {Molecular and biochemical parasitology}, volume = {233}, number = {}, pages = {111221}, doi = {10.1016/j.molbiopara.2019.111221}, pmid = {31542425}, issn = {1872-9428}, support = {BB/G00448X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Cation Transport Proteins/chemistry/genetics/metabolism ; Genes, Fungal ; Genes, Protozoan ; Iron/*metabolism ; Iron-Binding Proteins/chemistry/genetics/metabolism ; Mitochondria/metabolism ; *Mitochondrial Membrane Transport Proteins/chemistry/genetics/metabolism ; Phylogeny ; Protozoan Proteins/chemistry/genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Trypanosoma brucei brucei/*metabolism ; }, abstract = {Similar to higher eukaryotes, the protist parasite T. brucei harbours several iron-containing proteins that regulate DNA and protein processing, oxidative stress defence and mitochondrial respiration. The synthesis of these proteins occurs either in the cytoplasm or within the mitochondrion. For mitochondrial iron cluster protein synthesis, iron needs to be transported across the solute impermeable mitochondrial membrane. In T. brucei we previously identified 24 mitochondrial carrier proteins (TbMCPs) sharing conserved structural and functional features with those from higher eukaryotes. One of these carriers (TbMCP17) displayed high similarity with the iron carriers MRS3, MRS4 from yeast and mitoferrin from mammals, insects and plants. In the present study we demonstrated that TbMCP17 functions as an iron carrier by complementation studies using MRS3/4-deficient yeast. Depletion of TbMCP17 in procyclic form T. brucei resulted in growth deficiency, increased sensitivity to iron deprivation, and lowered mitochondrial iron content. Taken together our results suggest that TbMCP17 functions as a mitochondrial iron transporter in the parasite T. brucei.}, }
@article {pmid31536728, year = {2019}, author = {Buonvicino, D and Ranieri, G and Pratesi, S and Guasti, D and Chiarugi, A}, title = {Neuroimmunological characterization of a mouse model of primary progressive experimental autoimmune encephalomyelitis and effects of immunosuppressive or neuroprotective strategies on disease evolution.}, journal = {Experimental neurology}, volume = {322}, number = {}, pages = {113065}, doi = {10.1016/j.expneurol.2019.113065}, pmid = {31536728}, issn = {1090-2430}, mesh = {Animals ; Bezafibrate/pharmacology ; Biotin/pharmacology ; Dexamethasone/pharmacology ; Encephalomyelitis, Autoimmune, Experimental/*immunology/*pathology ; Immunosuppressive Agents/*pharmacology ; Mice ; Mice, Inbred NOD ; Mitochondria/drug effects ; Multiple Sclerosis, Chronic Progressive ; Neuroprotective Agents/*pharmacology ; Spinal Cord/drug effects/pathology ; }, abstract = {Progressive multiple sclerosis (PMS) is a devastating disorder sustained by neuroimmune interactions still wait to be identified. Recently, immune-independent, neural bioenergetic derangements have been hypothesized as causative of neurodegeneration in PMS patients. To gather information on the immune and neurodegenerative components during PMS, in the present study we investigated the molecular and cellular events occurring in a Non-obese diabetic (NOD) mouse model of experimental autoimmune encephalomyelitis (EAE). In these mice, we also evaluated the effects of clinically-relevant immunosuppressive (dexamethasone) or bioenergetic drugs (bezafibrate and biotin) on functional, immune and neuropathological parameters. We found that immunized NOD mice progressively accumulated disability and severe neurodegeneration in the spinal cord. Unexpectedly, although CD4 and CD8 lymphocytes but not B or NK cells infiltrate the spinal cord linearly with time, their suppression by different dexamethasone treatment schedules did not affect disease progression. Also, the spreading of the autoimmune response towards additional immunogenic myelin antigen occurred neither in the periphery nor in the CNS of EAE mice. Conversely, we found that altered mitochondrial morphology, reduced contents of mtDNA and decreased transcript levels for respiratory complex subunits occurred at early disease stages and preceded axonal degeneration within spinal cord columns. However, the mitochondria boosting drugs, bezafibrate and biotin, were unable to reduce disability progression. Data suggest that EAE NOD mice recapitulate some features of PMS. Also, by showing that bezafibrate or biotin do not affect progression in NOD mice, our study suggests that this model can be harnessed to anticipate experimental information of relevance to innovative treatments of PMS.}, }
@article {pmid31536521, year = {2019}, author = {Yang, M and Gong, L and Sui, J and Li, X}, title = {The complete mitochondrial genome of Calyptogena marissinica (Heterodonta: Veneroida: Vesicomyidae): Insight into the deep-sea adaptive evolution of vesicomyids.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0217952}, pmid = {31536521}, issn = {1932-6203}, mesh = {Adaptation, Biological ; Animals ; Base Sequence ; Bivalvia/*genetics ; Computational Biology/methods ; DNA, Mitochondrial ; Evolution, Molecular ; *Genome, Mitochondrial ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Oceans and Seas ; Phylogeny ; Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {The deep-sea chemosynthetic environment is one of the most extreme environments on the Earth, with low oxygen, high hydrostatic pressure and high levels of toxic substances. Species of the family Vesicomyidae are among the dominant chemosymbiotic bivalves found in this harsh habitat. Mitochondria play a vital role in oxygen usage and energy metabolism; thus, they may be under selection during the adaptive evolution of deep-sea vesicomyids. In this study, the mitochondrial genome (mitogenome) of the vesicomyid bivalve Calyptogena marissinica was sequenced with Illumina sequencing. The mitogenome of C. marissinica is 17,374 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes. All of these genes are encoded on the heavy strand. Some special elements, such as tandem repeat sequences, "G(A)nT" motifs and AT-rich sequences, were observed in the control region of the C. marissinica mitogenome, which is involved in the regulation of replication and transcription of the mitogenome and may be helpful in adjusting the mitochondrial energy metabolism of organisms to adapt to the deep-sea chemosynthetic environment. The gene arrangement of protein-coding genes was identical to that of other sequenced vesicomyids. Phylogenetic analyses clustered C. marissinica with previously reported vesicomyid bivalves with high support values. Positive selection analysis revealed evidence of adaptive change in the mitogenome of Vesicomyidae. Ten potentially important adaptive residues were identified, which were located in cox1, cox3, cob, nad2, nad4 and nad5. Overall, this study sheds light on the mitogenomic adaptation of vesicomyid bivalves that inhabit the deep-sea chemosynthetic environment.}, }
@article {pmid31534121, year = {2019}, author = {Marques, DA and Lucek, K and Sousa, VC and Excoffier, L and Seehausen, O}, title = {Admixture between old lineages facilitated contemporary ecological speciation in Lake Constance stickleback.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {4240}, pmid = {31534121}, issn = {2041-1723}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Gene Flow ; *Genetic Speciation ; Genetics, Population ; Genome/genetics ; Lakes ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Polymorphism, Single Nucleotide/genetics ; Rivers ; Smegmamorpha/*classification/*genetics ; Sympatry/*genetics ; }, abstract = {Ecological speciation can sometimes rapidly generate reproductively isolated populations coexisting in sympatry, but the origin of genetic variation permitting this is rarely known. We previously explored the genomics of very recent ecological speciation into lake and stream ecotypes in stickleback from Lake Constance. Here, we reconstruct the origin of alleles underlying ecological speciation by combining demographic modelling on genome-wide single nucleotide polymorphisms, phenotypic data and mitochondrial sequence data in the wider European biogeographical context. We find that parallel differentiation between lake and stream ecotypes across replicate lake-stream ecotones resulted from recent secondary contact and admixture between old East and West European lineages. Unexpectedly, West European alleles that introgressed across the hybrid zone at the western end of the lake, were recruited to genomic islands of differentiation between ecotypes at the eastern end of the lake. Our results highlight an overlooked outcome of secondary contact: ecological speciation facilitated by admixture variation.}, }
@article {pmid31532710, year = {2020}, author = {Göke, A and Schrott, S and Mizrak, A and Belyy, V and Osman, C and Walter, P}, title = {Mrx6 regulates mitochondrial DNA copy number in Saccharomyces cerevisiae by engaging the evolutionarily conserved Lon protease Pim1.}, journal = {Molecular biology of the cell}, volume = {31}, number = {7}, pages = {527-545}, pmid = {31532710}, issn = {1939-4586}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {ATP-Dependent Proteases/*metabolism ; *Conserved Sequence ; DNA Copy Number Variations/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Gene Deletion ; Genetic Testing ; Mitochondria/metabolism ; Mitochondrial Proteins/*metabolism ; Models, Biological ; Protein Binding ; Protein Domains ; Ribosomal Proteins/chemistry/*metabolism ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; Serine Endopeptidases/*metabolism ; }, abstract = {Mitochondrial function depends crucially on the maintenance of multiple mitochondrial DNA (mtDNA) copies. Surprisingly, the cellular mechanisms regulating mtDNA copy number remain poorly understood. Through a systematic high-throughput approach in Saccharomyces cerevisiae, we determined mtDNA-to-nuclear DNA ratios in 5148 strains lacking nonessential genes. The screen revealed MRX6, a largely uncharacterized gene, whose deletion resulted in a marked increase in mtDNA levels, while maintaining wild type-like mitochondrial structure and cell size. Quantitative superresolution imaging revealed that deletion of MRX6 alters both the size and the spatial distribution of mtDNA nucleoids. We demonstrate that Mrx6 partially colocalizes with mtDNA within mitochondria and interacts with the conserved Lon protease Pim1 in a complex that also includes Mam33 and the Mrx6-related protein Pet20. Acute depletion of Pim1 phenocopied the high mtDNA levels observed in Δmrx6 cells. No further increase in mtDNA copy number was observed upon depletion of Pim1 in Δmrx6 cells, revealing an epistatic relationship between Pim1 and Mrx6. Human and bacterial Lon proteases regulate DNA replication by degrading replication initiation factors, suggesting a model in which Pim1 acts similarly with the Mrx6 complex, providing a scaffold linking it to mtDNA.}, }
@article {pmid31525456, year = {2019}, author = {Corrêa da Silva, F and Aguiar, C and Pereira, JAS and de Brito Monteiro, L and Davanzo, GG and Codo, AC and Pimentel de Freitas, L and Berti, AS and Lopes Ferrucci, D and Castelucci, BG and Consonni, SR and Carvalho, HF and Moraes-Vieira, PMM}, title = {Ghrelin effects on mitochondrial fitness modulates macrophage function.}, journal = {Free radical biology &amp; medicine}, volume = {145}, number = {}, pages = {61-66}, doi = {10.1016/j.freeradbiomed.2019.09.012}, pmid = {31525456}, issn = {1873-4596}, mesh = {Adenosine Triphosphate/genetics ; Animals ; Gene Expression Regulation, Neoplastic/drug effects ; Ghrelin/chemistry/*pharmacology ; Glycolysis/drug effects ; Inflammation/chemically induced/drug therapy/genetics/pathology ; Interleukin-12/*genetics ; Interleukin-1beta/*genetics ; Lipopolysaccharides/toxicity ; Macrophages, Peritoneal/*drug effects/pathology ; Membrane Potential, Mitochondrial/drug effects ; Mice ; Mitochondria/drug effects/ultrastructure ; Nitric Oxide/genetics ; Signal Transduction/genetics ; Tumor Necrosis Factor-alpha/*genetics ; }, abstract = {Over the past years, systemic derived cues that regulate cellular metabolism have been implicated in the regulation of immune responses. Ghrelin is an orexigenic hormone produced by enteroendocrine cells in the gastric mucosa with known immunoregulatory roles. The mechanism behind the function of ghrelin in immune cells, such as macrophages, is still poorly understood. Here, we explored the hypothesis that ghrelin leads to alterations in macrophage metabolism thus modulating macrophage function. We demonstrated that ghrelin exerts an immunomodulatory effect over LPS-activated peritoneal macrophages, as evidenced by inhibition of TNF-α and IL-1β secretion and increased IL-12 production. Concomitantly, ghrelin increased mitochondrial membrane potential and increased respiratory rate. In agreement, ghrelin prevented LPS-induced ultrastructural damage in the mitochondria. Ghrelin also blunted LPS-induced glycolysis. In LPS-activated macrophages, glucose deprivation did not affect ghrelin-induced IL-12 secretion, whereas the inhibition of pyruvate transport and mitochondria-derived ATP abolished ghrelin-induced IL-12 secretion, indicating a dependence on mitochondrial function. Ghrelin pre-treatment of metabolic activated macrophages inhibited the secretion of TNF-α and enhanced IL-12 levels. Moreover, ghrelin effects on IL-12, and not on TNF-α, are dependent on mitochondria elongation, since ghrelin did not enhance IL-12 secretion in metabolic activated mitofusin-2 deficient macrophages. Thus, ghrelin affects macrophage mitochondrial metabolism and the subsequent macrophage function.}, }
@article {pmid31520778, year = {2019}, author = {Dufresnes, C and Mazepa, G and Jablonski, D and Oliveira, RC and Wenseleers, T and Shabanov, DA and Auer, M and Ernst, R and Koch, C and Ramírez-Chaves, HE and Mulder, KP and Simonov, E and Tiutenko, A and Kryvokhyzha, D and Wennekes, PL and Zinenko, OI and Korshunov, OV and Al-Johany, AM and Peregontsev, EA and Masroor, R and Betto-Colliard, C and Denoël, M and Borkin, LJ and Skorinov, DV and Pasynkova, RA and Mazanaeva, LF and Rosanov, JM and Dubey, S and Litvinchuk, S}, title = {Fifteen shades of green: The evolution of Bufotes toads revisited.}, journal = {Molecular phylogenetics and evolution}, volume = {141}, number = {}, pages = {106615}, doi = {10.1016/j.ympev.2019.106615}, pmid = {31520778}, issn = {1095-9513}, mesh = {Animals ; *Biological Evolution ; Bufonidae/classification/genetics/*physiology ; DNA, Mitochondrial/genetics ; Genetic Speciation ; Genome Size ; Genome, Mitochondrial ; Genomics ; Hybridization, Genetic ; Mitochondria/genetics ; Phenotype ; Phylogeny ; Phylogeography ; Principal Component Analysis ; Time Factors ; }, abstract = {The radiation of Palearctic green toads (Bufotes) holds great potential to evaluate the role of hybridization in phylogeography at multiple stages along the speciation continuum. With fifteen species representing three ploidy levels, this model system is particularly attractive to examine the causes and consequences of allopolyploidization, a prevalent yet enigmatic pathway towards hybrid speciation. Despite substantial efforts, the evolutionary history of this species complex remains largely blurred by the lack of consistency among the corresponding literature. To get a fresh, comprehensive view on Bufotes phylogeography, here we combined genome-wide multilocus analyses (RAD-seq) with an extensive compilation of mitochondrial, genome size, niche modelling, distribution and phenotypic (bioacoustics, morphometrics, toxin composition) datasets, representing hundreds of populations throughout Eurasia. We provide a fully resolved nuclear phylogeny for Bufotes and highlight exceptional cyto-nuclear discordances characteristic of complete mtDNA replacement (in 20% of species), mitochondrial surfing during post-glacial expansions, and the formation of homoploid hybrid populations. Moreover, we traced the origin of several allopolyploids down to species level, showing that all were exclusively fathered by the West Himalayan B. latastii but mothered by several diploid forms inhabiting Central Asian lowlands, an asymmetry consistent with hypotheses on mate choice and Dobzhansky-Muller incompatibilities. Their intermediate call phenotypes potentially allowed for rapid reproductive isolation, while toxin compositions converged towards the ecologically-closest parent. Across the radiation, we pinpoint a stepwise progression of reproductive isolation through time, with a threshold below which hybridizability is irrespective of divergence (<6My), above which species barely admix and eventually evolve different mating calls (6-10My), or can successfully cross-breed through allopolyploidization (>15My). Finally, we clarified the taxonomy of Bufotes (including genetic analyses of type series) and formally described two new species, B. cypriensis sp. nov. (endemic to Cyprus) and B. perrini sp. nov. (endemic to Central Asia). Embracing the genomic age, our framework marks the advent of a new exciting era for evolutionary research in these iconic amphibians.}, }
@article {pmid31519789, year = {2019}, author = {Loiacono, FV and Thiele, W and Schöttler, MA and Tillich, M and Bock, R}, title = {Establishment of a Heterologous RNA Editing Event in Chloroplasts.}, journal = {Plant physiology}, volume = {181}, number = {3}, pages = {891-900}, pmid = {31519789}, issn = {1532-2548}, mesh = {Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/genetics/metabolism ; Chloroplasts/*genetics/*metabolism ; Plastids/genetics/metabolism ; RNA Editing/*genetics ; }, abstract = {In chloroplasts and plant mitochondria, specific cytidines in mRNAs are posttranscriptionally converted to uridines by RNA editing. Editing sites are recognized by nucleus-encoded RNA-binding proteins of the pentatricopeptide repeat (PPR) family, which bind upstream of the editing site in a sequence-specific manner and direct the editing activity to the target position. Editing sites have been lost many times during evolution by C-to-T mutations. Loss of an editing site is thought to be accompanied by loss or degeneration of its cognate PPR protein. Consequently, foreign editing sites are usually not recognized when introduced into species lacking the site. Previously, the spinach (Spinacia oleracea) psbF-26 editing site was introduced into the tobacco (Nicotiana tabacum) plastid genome. Tobacco lacks the psbF-26 site and cannot edit it. Expression of the "unedited" PsbF protein resulted in impaired PSII function. In Arabidopsis (Arabidopsis thaliana), the PPR protein LPA66 is required for editing at psbF-26. Here, we show that introduction of the Arabidopsis LPA66 reconstitutes editing of the spinach psbF-26 site in tobacco and restores a wild-type-like phenotype. Our findings define the minimum requirements for establishing new RNA editing sites and suggest that the evolutionary dynamics of editing patterns is largely explained by coevolution of editing sites and PPR proteins.}, }
@article {pmid31519208, year = {2019}, author = {Wang, T and Zhang, S and Pei, T and Yu, Z and Liu, J}, title = {Tick mitochondrial genomes: structural characteristics and phylogenetic implications.}, journal = {Parasites &amp; vectors}, volume = {12}, number = {1}, pages = {451}, pmid = {31519208}, issn = {1756-3305}, support = {31672365//The National Natural Science Foundation of China/ ; BJ2016032//The Natural Science Research Programs of the Educational Department of Hebei Province/ ; L2018J04//The Science Foundation of Hebei Normal University/ ; C2019205064//the Natural Science Foundation of Hebei Province/ ; }, mesh = {Animals ; Base Composition ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Ticks/*genetics ; }, abstract = {Ticks are obligate blood-sucking arachnid ectoparasites from the order Acarina, and many are notorious as vectors of a wide variety of zoonotic pathogens. However, the systematics of ticks in several genera is still controversial. The mitochondrial genome (mt-genome) has been widely used in arthropod phylogeny, molecular evolution and population genetics. With the development of sequencing technologies, an increasing number of tick mt-genomes have been sequenced and annotated. To date, 63 complete tick mt-genomes are available in the NCBI database, and these genomes have become an increasingly important genetic resource and source of molecular markers in phylogenetic studies of ticks in recent years. The present review summarizes all available complete mt-genomes of ticks in the NCBI database and analyses their characteristics, including structure, base composition and gene arrangement. Furthermore, a phylogenetic tree was constructed using mitochondrial protein-coding genes (PCGs) and ribosomal RNA (rRNA) genes from ticks. The results will provide important clues for deciphering new tick mt-genomes and establish a foundation for subsequent taxonomic research.}, }
@article {pmid31515862, year = {2019}, author = {Després, L}, title = {One, two or more species? Mitonuclear discordance and species delimitation.}, journal = {Molecular ecology}, volume = {28}, number = {17}, pages = {3845-3847}, doi = {10.1111/mec.15211}, pmid = {31515862}, issn = {1365-294X}, mesh = {Animals ; Butterflies/genetics ; Cell Nucleus/*genetics ; Climate ; DNA, Mitochondrial/genetics ; Gene Flow ; Geography ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Species Specificity ; }, abstract = {Delimiting species boundaries is central to understand ecological and evolutionary processes, and to monitor biodiversity patterns over time and space. Yet, most of our current knowledge on animal diversity and phylogeny relies on morphological and mitochondrial (mt) DNA variation, a popular molecular marker also used as a barcode to assign samples to species. For morphologically undistinguishable sympatric species (cryptic species), the congruence of several independent markers is necessary to define separate species. Nuclear markers are becoming more accessible, and have confirmed that cryptic species are widespread in all animal phyla (Fišer, Robinson, &amp; Malard, 2018). However, striking differences between the mitochondrial and nuclear variation patterns are also commonly found within single species. Mitonuclear discordance can result from incomplete lineage sorting, sex-biased dispersal, asymmetrical introgression, natural selection or Wolbachia-mediated genetic sweeps. But more generally, the distinct mode of transmission of these two types of markers (maternal vs. biparental) is sufficient to explain their distinct sensitivity to purely demographic events such as spatial range and population size fluctuations over time. In a From the Cover manuscript in this issue of Molecular Ecology, Hijonosa et al. (2019) show that highly divergent mtDNA lineages coexist in a widespread European butterfly (Figure 1). None of the hundreds of nuclear markers analyzed was associated with mt lineages, nor was Wolbachia variation. These findings rule out the presence of cryptic species but shed light on complex demographic history of lineage divergence/fusion during the Pleistocene climatic fluctuations, and pave the way to a better integration of both mt and nuclear information in demographic models.}, }
@article {pmid31513293, year = {2020}, author = {Liu, S and Li, J and Zhang, Y and Liu, N and Viljoen, A and Mostert, D and Zuo, C and Hu, C and Bi, F and Gao, H and Sheng, O and Deng, G and Yang, Q and Dong, T and Dou, T and Yi, G and Ma, LJ and Li, C}, title = {Fusaric acid instigates the invasion of banana by Fusarium oxysporum f. sp. cubense TR4.}, journal = {The New phytologist}, volume = {225}, number = {2}, pages = {913-929}, pmid = {31513293}, issn = {1469-8137}, mesh = {Apoptosis/drug effects ; Biosynthetic Pathways/drug effects/genetics ; Cell Death/drug effects ; Fusaric Acid/biosynthesis/*pharmacology ; Fusarium/drug effects/*pathogenicity ; Gene Expression Regulation, Plant/drug effects ; Mitochondria/drug effects/metabolism ; Models, Biological ; Multigene Family ; Musa/*microbiology ; Phenotype ; Phylogeny ; Plant Stems/microbiology ; Protoplasts/drug effects/metabolism ; Reactive Oxygen Species/metabolism ; Virulence/drug effects ; }, abstract = {Fusaric acid (FSA) is a phytotoxin produced by several Fusarium species and has been associated with plant disease development, although its role is still not well understood. Mutation of key genes in the FSA biosynthetic gene (FUB) cluster in Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) reduced the FSA production, and resulted in decreased disease symptoms and reduced fungal biomass in the host banana plants. When pretreated with FSA, both banana leaves and pseudostems exhibited increased sensitivity to Foc TR4 invasion. Banana embryogenic cell suspensions (ECSs) treated with FSA exhibited a lower rate of O2 uptake, loss of mitochondrial membrane potential, increased reactive oxygen species (ROS) accumulation, and greater nuclear condensation and cell death. Consistently, transcriptomic analysis of FSA-treated ECSs showed that FSA may induce plant cell death through regulating the expression of genes involved in mitochondrial functions. The results herein demonstrated that the FSA from Foc TR4 functions as a positive virulence factor and acts at the early stage of the disease development before the appearance of the fungal hyphae in the infected tissues.}, }
@article {pmid31511073, year = {2019}, author = {Honeycutt, RL and Proudfoot, GA and Silvy, NJ}, title = {Mitochondrial DNA variation of the ruffed grouse (Bonasa umbellus).}, journal = {BMC research notes}, volume = {12}, number = {1}, pages = {570}, pmid = {31511073}, issn = {1756-0500}, support = {DEB 9615163//National Science Foundation/ ; }, mesh = {Animals ; Canada ; DNA, Mitochondrial/*genetics ; Galliformes/classification/*genetics ; Gene Frequency ; *Genetic Variation ; Geography ; Haplotypes ; Mitochondria/*genetics/metabolism ; Phylogeny ; Sequence Analysis, DNA/methods ; United States ; }, abstract = {OBJECTIVE: The ruffed grouse, Bonasa umbellus, is broadly distributed across North America and displays considerable taxonomic diversity. Except for a genetic study of some western populations of ruffed grouse, nothing is known about genetic variation in other regions of Canada and the United States. Our objective is to examine patterns of mitochondrial DNA (mtDNA) variation in the ruffed grouse across western, central, and eastern parts of its distribution. We compare patterns of mtDNA variation to those characterized by morphology and ecology. Additionally, we evaluate the demographic history of the species based on mitochondrial haplotype diversity.<br><br>RESULTS: Patterns of mtDNA variation revealed geographic subdivision, with populations of ruffed grouse subdivided into 3 to 4 genetically distinct groups. This subdivision partially coincided with the ranges of described subspecies. Behavioral traits prohibiting long-distance movement and barriers to dispersal in response to physiography and unsuitable habitat help explain these patterns of subdivision. Historically, the ruffed grouse probably experienced a population expansion, possibly in response to changes during the Pleistocene.}, }
@article {pmid31504759, year = {2019}, author = {Mignerot, L and Nagasato, C and Peters, AF and Perrineau, MM and Scornet, D and Pontheaux, F and Djema, W and Badis, Y and Motomura, T and Coelho, SM and Cock, JM}, title = {Unusual Patterns of Mitochondrial Inheritance in the Brown Alga Ectocarpus.}, journal = {Molecular biology and evolution}, volume = {36}, number = {12}, pages = {2778-2789}, doi = {10.1093/molbev/msz186}, pmid = {31504759}, issn = {1537-1719}, mesh = {*Genes, Mitochondrial ; Genome, Mitochondrial ; Life History Traits ; Parthenogenesis/genetics ; Phaeophyceae/*genetics ; Recombination, Genetic ; }, abstract = {Most eukaryotes inherit their mitochondria from only one of their parents. When there are different sexes, it is almost always the maternal mitochondria that are transmitted. Indeed, maternal uniparental inheritance has been reported for the brown alga Ectocarpus but we show in this study that different strains of Ectocarpus can exhibit different patterns of inheritance: Ectocarpus siliculosus strains showed maternal uniparental inheritance, as expected, but crosses using different Ectocarpus species 7 strains exhibited either paternal uniparental inheritance or an unusual pattern of transmission where progeny inherited either maternal or paternal mitochondria, but not both. A possible correlation between the pattern of mitochondrial inheritance and male gamete parthenogenesis was investigated. Moreover, in contrast to observations in the green lineage, we did not detect any change in the pattern of mitochondrial inheritance in mutant strains affected in life cycle progression. Finally, an analysis of field-isolated strains provided evidence of mitochondrial genome recombination in both Ectocarpus species.}, }
@article {pmid31502197, year = {2019}, author = {Rappocciolo, E and Stiban, J}, title = {Prokaryotic and Mitochondrial Lipids: A Survey of Evolutionary Origins.}, journal = {Advances in experimental medicine and biology}, volume = {1159}, number = {}, pages = {5-31}, doi = {10.1007/978-3-030-21162-2_2}, pmid = {31502197}, issn = {0065-2598}, mesh = {*Biological Evolution ; Cell Membrane/*chemistry ; Ceramides ; Lipids/*chemistry ; Mitochondria/*chemistry ; Prokaryotic Cells/*chemistry ; Sphingolipids ; }, abstract = {Mitochondria and bacteria share a myriad of properties since it is believed that the powerhouses of the eukaryotic cell have evolved from a prokaryotic origin. Ribosomal RNA sequences, DNA architecture and metabolism are strikingly similar in these two entities. Proteins and nucleic acids have been a hallmark for comparison between mitochondria and prokaryotes. In this chapter, similarities (and differences) between mitochondrial and prokaryotic membranes are addressed with a focus on structure-function relationship of different lipid classes. In order to be suitable for the theme of the book, a special emphasis is reserved to the effects of bioactive sphingolipids, mainly ceramide, on mitochondrial membranes and their roles in initiating programmed cell death.}, }
@article {pmid31495025, year = {2019}, author = {Zeh, JA and Zawlodzki, MA and Bonilla, MM and Su-Keene, EJ and Padua, MV and Zeh, DW}, title = {Sperm competitive advantage of a rare mitochondrial haplogroup linked to differential expression of mitochondrial oxidative phosphorylation genes.}, journal = {Journal of evolutionary biology}, volume = {32}, number = {12}, pages = {1320-1330}, pmid = {31495025}, issn = {1420-9101}, support = {P20 GM103440/GM/NIGMS NIH HHS/United States ; U54 GM104944/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Arachnida/*genetics ; Female ; *Genes, Mitochondrial ; *Haplotypes ; Male ; Maternal Inheritance ; *Oxidative Phosphorylation ; Spermatozoa/*physiology ; Testis/physiology ; }, abstract = {Maternal inheritance of mitochondria creates a sex-specific selective sieve through which mitochondrial mutations harmful to males but not females accumulate and contribute to sexual differences in longevity and disease susceptibility. Because eggs and sperm are under disruptive selection, sperm are predicted to be particularly vulnerable to the genetic load generated by maternal inheritance, yet evidence for mitochondrial involvement in male fertility is limited and controversial. Here, we exploit the coexistence of two divergent mitochondrial haplogroups (A and B2) in a Neotropical arachnid to investigate the role of mitochondria in sperm competition. DNA profiling demonstrated that B2-carrying males sired more than three times as many offspring in sperm competition experiments than A males, and this B2 competitive advantage cannot be explained by female mitochondrial haplogroup or male nuclear genetic background. RNA-Seq of testicular tissues implicates differential expression of mitochondrial oxidative phosphorylation (OXPHOS) genes in the B2 competitive advantage, including a 22-fold upregulation of atp8 in B2 males. Previous comparative genomic analyses have revealed functionally significant amino acid substitutions in differentially expressed genes, indicating that the mitochondrial haplogroups differ not only in expression but also in DNA sequence and protein functioning. However, mitochondrial haplogroup had no effect on sperm number or sperm viability, and, when females were mated to a single male, neither male haplogroup, female haplogroup nor the interaction between male/female haplogroup significantly affected female reproductive success. Our findings therefore suggest that mitochondrial effects on male reproduction may often go undetected in noncompetitive contexts and may prove more important in nature than is currently appreciated.}, }
@article {pmid31494084, year = {2020}, author = {Supinski, GS and Schroder, EA and Callahan, LA}, title = {Mitochondria and Critical Illness.}, journal = {Chest}, volume = {157}, number = {2}, pages = {310-322}, pmid = {31494084}, issn = {1931-3543}, support = {I01 BX002132/BX/BLRD VA/United States ; R01 HL112085/HL/NHLBI NIH HHS/United States ; R01 HL113494/HL/NHLBI NIH HHS/United States ; R01 HL141356/HL/NHLBI NIH HHS/United States ; }, mesh = {Acute Lung Injury/*metabolism/therapy ; Alarmins/metabolism ; Antioxidants/therapeutic use ; Cesium/therapeutic use ; Critical Illness ; DNA, Mitochondrial/metabolism ; Humans ; Melatonin/therapeutic use ; Mitochondria/immunology/*metabolism/transplantation ; Muscle, Skeletal ; Muscular Diseases/*metabolism/therapy ; Organelle Biogenesis ; Resveratrol/therapeutic use ; Sepsis/immunology/*metabolism/therapy ; }, abstract = {Classically, mitochondria have largely been believed to influence the development of illness by modulating cell metabolism and determining the rate of production of high-energy phosphate compounds (eg, adenosine triphosphate). It is now recognized that this view is simplistic and that mitochondria play key roles in many other processes, including cell signaling, regulating gene expression, modulating cellular calcium levels, and influencing the activation of cell death pathways (eg, caspase activation). Moreover, these multiple mitochondrial functional characteristics are now known to influence the evolution of cellular and organ function in many disease states, including sepsis, ICU-acquired skeletal muscle dysfunction, acute lung injury, acute renal failure, and critical illness-related immune function dysregulation. In addition, diseased mitochondria generate toxic compounds, most notably released mitochondrial DNA, which can act as danger-associated molecular patterns to induce systemic toxicity and damage multiple organs throughout the body. This article reviews these evolving concepts relating mitochondrial function and acute illness. The discussion is organized into four sections: (1) basics of mitochondrial physiology; (2) cellular mechanisms of mitochondrial pathophysiology; (3) critical care disease processes whose initiation and evolution are shaped by mitochondrial pathophysiology; and (4) emerging treatments for mitochondrial dysfunction in critical illness.}, }
@article {pmid31486889, year = {2019}, author = {Wang, J and Gao, X and Zheng, X and Hou, C and Xie, Q and Lou, B and Zhu, J}, title = {Expression and potential functions of KIF3A/3B to promote nuclear reshaping and tail formation during Larimichthys polyactis spermiogenesis.}, journal = {Development genes and evolution}, volume = {229}, number = {5-6}, pages = {161-181}, pmid = {31486889}, issn = {1432-041X}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cell Nucleus/metabolism ; Cloning, Molecular ; Fish Proteins/chemistry/genetics/*metabolism ; Fishes/*physiology ; Humans ; Kinesins/chemistry/genetics/*metabolism ; Male ; Phylogeny ; Sequence Alignment ; *Spermatogenesis ; Spermatozoa/*cytology/metabolism ; }, abstract = {KIF3A and KIF3B are homologous motor subunits of the Kinesin II protein family. KIF3A, KIF3B, and KAP3 form a heterotrimeric complex and play a significant role in spermatogenesis. Here, we first cloned full-length kif3a/3b cDNAs from Larimichthys polyactis. Lp-kif3a/3b are highly related to their homologs in other animals. The proteins are composed of three domains, an N-terminal head domain, a central stalk domain, and a C-terminus tail domain. Lp-kif3a/3b mRNAs were found to be ubiquitously expressed in the examined tissues, with high expression in the testis. Fluorescence in situ hybridization (FISH) was used to analyze the expression of Lp-kif3a/3b mRNAs during spermiogenesis. The results showed that Lp-kif3a/3b mRNAs had similar expression pattern and were continuously expressed during spermiogenesis. From middle spermatid to mature sperm, Lp-kif3a/3b mRNAs gradually localized to the side of the spermatid where the midpiece and tail form. In addition, we used immunofluorescence (IF) to observe that Lp-KIF3A protein co-localizes with tubulin during spermiogenesis. In early spermatid, Lp-KIF3A protein and microtubule signals were randomly distributed in the cytoplasm. In middle spermatid, however, the protein was detected primarily around the nucleus. In late spermatid, the protein migrated primarily to one side of the nucleus where the tail forms. In mature sperm, Lp-KIF3A and microtubules accumulated in the midpiece. Moreover, Lp-KIF3A co-localized with the mitochondria. In mature sperm, Lp-KIF3A and mitochondria were present in the midpiece. Therefore, Lp-KIF3A/KIF3B may be involved in spermiogenesis in L. polyactis, particularly during nuclear reshaping and tail formation.}, }
@article {pmid31484671, year = {2019}, author = {Yang, H and Deng, L and Liu, H and Fan, S and Hua, W and Liu, J}, title = {Overexpression of BnaAOX1b Confers Tolerance to Osmotic and Salt Stress in Rapeseed.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {10}, pages = {3501-3511}, pmid = {31484671}, issn = {2160-1836}, mesh = {Abscisic Acid ; Amino Acid Sequence ; Brassica napus/*physiology ; Computational Biology/methods ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Ontology ; Germination/genetics ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/chemistry/*genetics ; Osmoregulation/*genetics ; Oxidoreductases/chemistry/*genetics ; Phenotype ; Phylogeny ; Plant Proteins/chemistry/*genetics ; Protein Transport ; Salt Tolerance/*genetics ; Seedlings/genetics ; }, abstract = {Alternative oxidases (AOXs) are the terminal oxidase in the cyanide-resistant respiration pathway in plant mitochondria, which play an important role in abiotic stress and are proposed as a functional marker for high tolerant breeding. In this study, ten AOX genes (BnaAOXs) were identified, and CysI and CysII of AOX isoforms were highly conserved in rapeseed. Among them, Bna.AOX1b was mainly expressed in the ovule and displayed varying expression between rapeseed cultivars which showed different salt resistance in seed germination. We identified its mitochondrial localization of this gene. To investigate the function of BnaAOX1b in rapeseed, transgenic rapeseed lines with overexpressed BnaAOX1b were created and seed germination and seedling establishment assays were performed under osmotic, salt, and ABA treatment. The results indicated that overexpression of BnaAOX1b significantly improved seed germination under osmotic and salt stress and weakened ABA sensitivity. In addition, post-germination seedling growth was improved under high salt condition, but showed hypersensitivity to ABA. RNA-sequencing analysis indicated that the genes involved in electron transport or energy pathway were induced and a number of gene responses to salt stress and ABA were regulated in Bna.AOX1b overexpressing seeds. Taken together, our results imply that Bna.AOX1b confers tolerance to osmotic and salt stress in terms of seed germination and seedling establishment by regulating stress responsive genes and the response to ABA, and could be utilized as a candidate gene in transgenic breeding.}, }
@article {pmid31484504, year = {2019}, author = {Feng, C and Tang, Y and Liu, S and Tian, F and Zhang, C and Zhao, K}, title = {Multiple convergent events created a nominal widespread species: Triplophysa stoliczkae (Steindachner, 1866) (Cobitoidea: Nemacheilidae).}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {177}, pmid = {31484504}, issn = {1471-2148}, mesh = {Animals ; Biological Evolution ; China ; Cypriniformes/*classification/*genetics ; Genetic Speciation ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Tibet ; }, abstract = {BACKGROUND: Triplophysa stoliczkae is the most widespread species in the genus Triplophysa and may have originated from morphological convergence. To understand the evolutionary history of T. stoliczkae, we employed a multilocus approach to investigate the phylogenetics and the morphological evolution of T. stoliczkae on the Qinghai-Tibetan Plateau.<br><br>RESULTS: All phylogenetic analyses (two mitochondrial and five nuclear loci), a genealogical sorting index and species tree inferences suggested that T. stoliczkae consists of distinct lineages that were not closest relatives. The time estimation indicated that the divergence events between "T. stoliczkae" and other Triplophysa species occurred from approximately 0.10 to 4.51&#x2009;Ma. The ancestral state analyses supported the independent evolution of T. stoliczkae morphology in distinct lineages. The morphometric analysis and convergence estimates demonstrated significant phenotypic convergence among "T. stoliczkae" lineages.<br><br>CONCLUSIONS: Triplophysa stoliczkae includes 4 different lineages with similar morphologies. The increasingly harsh environments that have occurred since the Pliocene have driven the occurrences of scrape-feeding fish in the genus Triplophysa. Morphological adaptations associated with scrape-feeding behavior resulted in convergences and the artificial lumping of four different species in the nominal taxon T. stoliczkae. A taxonomic revision for T. stoliczkae is needed.}, }
@article {pmid31482589, year = {2019}, author = {Chen, J and Xia, L and Wang, W and Wang, Z and Hou, S and Xie, C and Cai, J and Lu, Y}, title = {Identification of a mitochondrial-targeting secretory protein from Nocardia seriolae which induces apoptosis in fathead minnow cells.}, journal = {Journal of fish diseases}, volume = {42}, number = {11}, pages = {1493-1507}, doi = {10.1111/jfd.13062}, pmid = {31482589}, issn = {1365-2761}, support = {2017A030313179//Natural Science Foundation of Guangdong Province/ ; 231419017//Research Projects of Guangdong Ocean University's Top-ranking Discipline Construction/ ; JCYJ20170306161613251//Shenzhen Science and Technology Project/ ; KY20160207//Shenzhen Dapeng New District&#xa0;special fund for industry development/ ; PT201901-06//Shenzhen Dapeng New District&#xa0;special fund for industry development/ ; C17377//Natural Science Foundation of Guangdong Ocean University/ ; C13454//Natural Science Foundation of Guangdong Ocean University/ ; }, mesh = {Amino Acid Sequence ; Animals ; *Apoptosis ; Bacterial Proteins/chemistry/genetics/immunology ; Base Sequence ; *Cyprinidae ; Fish Diseases/*immunology/microbiology ; Nocardia/*genetics ; Nocardia Infections/immunology/microbiology/*veterinary ; Phylogeny ; Sequence Alignment/veterinary ; Virulence Factors/*genetics/metabolism ; }, abstract = {Nocardia seriolae is the main pathogen responsible for fish nocardiosis. A mitochondrial-targeting secretory protein (MTSP) 3141 with an N-terminal transit peptide (TP) from N. seriolae was predicted by bioinformatic analysis based on the genomic sequence of the N. seriolae strain ZJ0503. However, the function of the MTSP3141 and its homologs remains totally unknown. In this study, mass spectrometry analysis of the extracellular products from N. seriolae proved that MTSP3141 was a secretory protein, subcellular localization research showed the MTSP3141-GFP fusion protein co-localized with mitochondria in fathead minnow (FHM) cells, the TP played an important role in mitochondria targeting, and only the TP located at N-terminus but not C-terminus can lead to mitochondria directing. Moreover, quantitative assays of mitochondrial membrane potential (ΔΨm) value, caspase-3 activity and apoptosis-related gene (Bcl-2, Bax, Bad, Bid and p53) mRNA expression suggested that cell apoptosis was induced in FHM cells by the overexpression of both MTSP3141 and MTSP3141ΔTP (with the N-terminal TP deleted) proteins. Taken together, the results of this study indicated that the MTSP3141 of N. seriolae was a secretory protein, might target mitochondria, induce apoptosis in host cells and function as a virulence factor.}, }
@article {pmid31477008, year = {2019}, author = {Mossman, JA and Biancani, LM and Rand, DM}, title = {Mitochondrial genomic variation drives differential nuclear gene expression in discrete regions of Drosophila gene and protein interaction networks.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {691}, pmid = {31477008}, issn = {1471-2164}, support = {2R01GM067862/GM/NIGMS NIH HHS/United States ; 1R01AG027849/AG/NIA NIH HHS/United States ; }, mesh = {Amino Acid Motifs/genetics ; Animals ; Cell Nucleus/*genetics/metabolism ; Drosophila/*genetics/growth &amp; development ; Female ; Gene Expression Regulation ; Gene Regulatory Networks/*genetics/physiology ; Genes, Essential/genetics/physiology ; Genetic Variation ; Genome, Mitochondrial/*genetics ; Genotype ; Haplotypes ; Male ; Multigene Family ; Phenotype ; Protein Interaction Maps/genetics/physiology ; RNA, Untranslated/genetics/metabolism ; RNA-Seq ; Transcriptome ; }, abstract = {BACKGROUND: Mitochondria perform many key roles in their eukaryotic hosts, from integrating signaling pathways through to modulating whole organism phenotypes. The > 1 billion years of nuclear and mitochondrial gene co-evolution has necessitated coordinated expression of gene products from both genomes that maintain mitochondrial, and more generally, eukaryotic cellular function. How mitochondrial DNA (mtDNA) variation modifies host fitness has proved a challenging question but has profound implications for evolutionary and medical genetics. In Drosophila, we have previously shown that recently diverged mtDNA haplotypes within-species can have more impact on organismal phenotypes than older, deeply diverged haplotypes from different species. Here, we tested the effects of mtDNA haplotype variation on gene expression in Drosophila under standardized conditions. Using the Drosophila Genetic Reference Panel (DGRP), we constructed a panel of mitonuclear genotypes that consists of factorial variation in nuclear and mtDNA genomes, with mtDNAs originating in D. melanogaster (2x haplotypes) and D. simulans (2x haplotypes).<br><br>RESULTS: We show that mtDNA haplotype variation unequivocally alters nuclear gene expression in both females and males, and mitonuclear interactions are pervasive modifying factors for gene expression. There was appreciable overlap between the sexes for mtDNA-sensitive genes, and considerable transcriptional variation attributed to particular mtDNA contrasts. These genes are generally found in low-connectivity gene co-expression networks, occur in gene clusters along chromosomes, are often flanked by non-coding RNA, and are under-represented among housekeeping genes. Finally, we identify the giant (gt) transcription factor motif as a putative regulatory sequence associated with mtDNA-sensitive genes.<br><br>CONCLUSIONS: There are predictive conditions for nuclear genes that are influenced by mtDNA variation.}, }
@article {pmid31476715, year = {2019}, author = {Dunn, CD and Paavilainen, VO}, title = {Wherever I may roam: organellar protein targeting and evolvability.}, journal = {Current opinion in genetics &amp; development}, volume = {58-59}, number = {}, pages = {9-16}, doi = {10.1016/j.gde.2019.07.012}, pmid = {31476715}, issn = {1879-0380}, support = {R01 GM132649/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence/genetics ; Amoeba/genetics/metabolism ; Endoplasmic Reticulum/metabolism ; Eukaryota/*genetics/metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Mitochondria/genetics/*metabolism ; Molecular Chaperones/genetics/metabolism ; Phylogeny ; Protein Sorting Signals/*genetics/physiology ; Protein Transport/genetics/physiology ; }, abstract = {Many functions of eukaryotic cells are compartmentalized within membrane-bound organelles. One or more cis-encoded signals within a polypeptide sequence typically govern protein targeting to and within destination organelles. Perhaps unexpectedly, organelle targeting does not occur with high specificity, but instead is characterized by considerable degeneracy and inefficiency. Indeed, the same peptide signals can target proteins to more than one location, randomized sequences can easily direct proteins to organelles, and many enzymes appear to traverse different subcellular settings across eukaryotic phylogeny. We discuss the potential benefits provided by flexibility in organelle targeting, with a special emphasis on horizontally transferred and de novo proteins. Moreover, we consider how these new organelle residents can be protected and maintained before they contribute to the needs of the cell and promote fitness.}, }
@article {pmid31474649, year = {2019}, author = {Takeda, A and Saitoh, S and Ohkura, H and Sawin, KE and Goshima, G}, title = {Identification of 15 New Bypassable Essential Genes of Fission Yeast.}, journal = {Cell structure and function}, volume = {44}, number = {2}, pages = {113-119}, pmid = {31474649}, issn = {1347-3700}, support = {203149/WT_/Wellcome Trust/United Kingdom ; 210659/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; 206315/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 094517/WT_/Wellcome Trust/United Kingdom ; 206315/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; 098030/WT_/Wellcome Trust/United Kingdom ; 210659/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Genes, Essential/genetics ; Genes, Fungal/*genetics ; Mutation ; Schizosaccharomyces/*genetics ; }, abstract = {Every organism has a different set of genes essential for its viability. This indicates that an organism can become tolerant to the loss of an essential gene under certain circumstances during evolution, via the manifestation of 'masked' alternative mechanisms. In our quest to systematically uncover masked mechanisms in eukaryotic cells, we developed an extragenic suppressor screening method using haploid spores deleted of an essential gene in the fission yeast Schizosaccharomyces pombe. We screened for the 'bypass' suppressors of lethality of 92 randomly selected genes that are essential for viability in standard laboratory culture conditions. Remarkably, extragenic mutations bypassed the essentiality of as many as 20 genes (22%), 15 of which have not been previously reported. Half of the bypass-suppressible genes were involved in mitochondria function; we also identified multiple genes regulating RNA processing. 18 suppressible genes were conserved in the budding yeast Saccharomyces cerevisiae, but 13 of them were non-essential in that species. These trends suggest that essentiality bypass is not a rare event and that each organism may be endowed with secondary or backup mechanisms that can substitute for primary mechanisms in various biological processes. Furthermore, the robustness of our simple spore-based methodology paves the way for genome-scale screening.Key words: Schizosaccharomyces pombe, extragenic suppressor screening, bypass of essentiality (BOE), cut7 (kinesin-5), hul5 (E3 ubiquitin ligase).}, }
@article {pmid31473860, year = {2019}, author = {Yorimitsu, Y and Kadosono, A and Hatakeyama, Y and Yabiku, T and Ueno, O}, title = {Transition from C3 to proto-Kranz to C3-C4 intermediate type in the genus Chenopodium (Chenopodiaceae).}, journal = {Journal of plant research}, volume = {132}, number = {6}, pages = {839-855}, pmid = {31473860}, issn = {1618-0860}, support = {JP15K14638//Japan Society for the promotion of Science KAKENHI/ ; }, mesh = {*Biological Evolution ; Chenopodium/anatomy &amp; histology/enzymology/*metabolism ; Glycine Dehydrogenase (Decarboxylating)/genetics/metabolism ; *Photosynthesis ; Plant Leaves/anatomy &amp; histology ; Plant Proteins/genetics/metabolism ; }, abstract = {The Chenopodiaceae is one of the families including C4 species among eudicots. In this family, the genus Chenopodium is considered to include only C3 species. However, we report here a transition from C3 photosynthesis to proto-Kranz to C3-C4 intermediate type in Chenopodium. We investigated leaf anatomical and photosynthetic traits of 15 species, of which 8 species showed non-Kranz anatomy and a CO2 compensation point (Γ) typical of C3 plants. However, 5 species showed proto-Kranz anatomy and a C3-like Γ, whereas C. strictum showed leaf anatomy and a Γ typical of C3-C4 intermediates. Chenopodium album accessions examined included both proto-Kranz and C3-C4 intermediate types, depending on locality. Glycine decarboxylase, a key photorespiratory enzyme that is involved in the decarboxylation of glycine, was located predominantly in the mesophyll (M) cells of C3 species, in both M and bundle-sheath (BS) cells in proto-Kranz species, and exclusively in BS cells in C3-C4 intermediate species. The M/BS tissue area ratio, number of chloroplasts and mitochondria per BS cell, distribution of these organelles to the centripetal region of BS cells, the degree of inner positioning (vacuolar side of chloroplasts) of mitochondria in M cells, and the size of BS mitochondria also changed with the change in glycine decarboxylase localization. All Chenopodium species examined were C3-like regarding activities and amounts of C3 and C4 photosynthetic enzymes and δ[13]C values, suggesting that these species perform photosynthesis without contribution of the C4 cycle. This study demonstrates that Chenopodium is not a C3 genus and is valuable for studying evolution of C3-C4 intermediates.}, }
@article {pmid31470232, year = {2019}, author = {Husnik, F and Keeling, PJ}, title = {The fate of obligate endosymbionts: reduction, integration, or extinction.}, journal = {Current opinion in genetics &amp; development}, volume = {58-59}, number = {}, pages = {1-8}, doi = {10.1016/j.gde.2019.07.014}, pmid = {31470232}, issn = {1879-0380}, mesh = {Animals ; *Biological Evolution ; Extinction, Biological ; Mitochondria/*genetics/metabolism ; Phylogeny ; Plastids/genetics/metabolism ; Protein Transport ; Symbiosis/*genetics/physiology ; }, abstract = {Whether mitochondria and plastids originated by endosymbiosis is no longer questioned, but we still do not understand the actual process of integration. Other, younger endosymbiotic systems are, however, relatively common. Traditionally, it was not clear whether these systems could be directly and informatively compared to organelles because they appear sufficiently different. Surprisingly, new data from both organelles and endosymbiotic bacteria are changing this view. As more commonalities are described, the processes underlaying these associations appear to be not so different after all. New models for endosymbiotic associations emphasize the importance of transient stages, conflict more than cooperation, and population genetics forces that lead to genome reduction, which in turn restricts most endosymbionts to one of a few possible evolutionary pathways, commonly ending with extinction.}, }
@article {pmid31466038, year = {2019}, author = {Maciszewski, K and Karnkowska, A}, title = {Should I stay or should I go? Retention and loss of components in vestigial endosymbiotic organelles.}, journal = {Current opinion in genetics &amp; development}, volume = {58-59}, number = {}, pages = {33-39}, doi = {10.1016/j.gde.2019.07.013}, pmid = {31466038}, issn = {1879-0380}, mesh = {Amoebozoa/genetics/metabolism ; Animals ; Biosynthetic Pathways/*genetics/physiology ; Evolution, Molecular ; Genome Size ; Genomics ; Mitochondria/*genetics/metabolism ; Plastids/*genetics/metabolism ; Stramenopiles/genetics/metabolism ; Symbiosis/*genetics/physiology ; Transcriptome/genetics ; }, abstract = {Our knowledge on the variability of the reduced forms of endosymbiotic organelles - mitochondria and plastids - is expanding rapidly, thanks to growing interest in peculiar microbial eukaryotes, along with the availability of the methods used in modern genomics and transcriptomics. The aim of this work is to highlight the most recent advances in understanding these organelles' diversity, physiology and evolution. We also outline the known mechanisms behind the convergence of traits between organelles which have undergone reduction independently, the importance of the earliest evolutionary events in determining the vestigial organelles' eventual fate, and a proposed classification of nonphotosynthetic plastids.}, }
@article {pmid31452134, year = {2019}, author = {Soggiu, A and Roncada, P and Bonizzi, L and Piras, C}, title = {Role of Mitochondria in Host-Pathogen Interaction.}, journal = {Advances in experimental medicine and biology}, volume = {1158}, number = {}, pages = {45-57}, doi = {10.1007/978-981-13-8367-0_3}, pmid = {31452134}, issn = {0065-2598}, mesh = {Apoptosis ; *Host-Pathogen Interactions ; Immunity, Innate ; *Mitochondria/metabolism ; Signal Transduction ; }, abstract = {The centrality of the mitochondrion in the evolution and control of the cellare now supported by many experimental studies. Not only with regard to the energy metabolism but also and especially with regard to the other functions indispensable for the cell such as apoptosis and the control of innate immunity through different complex cell signaling pathways. All this makes them one of the main targets during infections supported by pathogenic microorganisms. The interaction and control of these organelles by pathogens results, from the latest experimental evidence, of fundamental importance in the fate of the host cell and in the progression of infectious diseases.}, }
@article {pmid31449853, year = {2019}, author = {Dorchin, N and Harris, KM and Stireman, JO}, title = {Phylogeny of the gall midges (Diptera, Cecidomyiidae, Cecidomyiinae): Systematics, evolution of feeding modes and diversification rates.}, journal = {Molecular phylogenetics and evolution}, volume = {140}, number = {}, pages = {106602}, doi = {10.1016/j.ympev.2019.106602}, pmid = {31449853}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; *Biodiversity ; Calibration ; Diptera/*classification/genetics ; *Feeding Behavior ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Predatory Behavior ; }, abstract = {Gall midges (Cecidomyiidae) constitute one of the largest and most diverse families of Diptera, with close to 6600 described species and thousands of undescribed species worldwide. The family is divided into six subfamilies, the five basal ones comprising only fungivorous taxa, whereas the largest, youngest and most diverse subfamily Cecidomyiinae includes fungivorous as well as herbivorous and predatory species. The currently accepted classification of the Cecidomyiinae is morphology-based, and the few phylogenetic inferences that have previously been suggested for it were based on fragmentary or limited datasets. In a first comprehensive phylogenetic analysis of the Cecidomyiinae we sampled 142 species representing 88 genera of 13 tribes from all feeding guilds and zoogeographic regions in order to test the validity of the systematic division of the subfamily and gain insight into patterns of diversification and the evolution of feeding modes. We used sequences from five mitochondrial and nuclear genes to reconstruct maximum likelihood and Bayesian, time-calibrated phylogenies and conducted ancestral state reconstruction of feeding modes. Our results corroborate to a great extent the morphology-based classification of the Cecidomyiinae, with strong support for all supertribes and tribes, all were apparently established in the Upper Cretaceous concordant with the major radiation of angiosperms. We infer that transitions from fungus-feeding to plant-feeding occurred only once or twice in the evolution of the subfamily and that predation evolved only once, contrary to previous hypotheses. All herbivorous clades in the subfamily are very species rich and have diversified at a significantly greater rate than expected, but we found no support for the assertion that herbivorous clades associated with symbiotic fungi in their galls diversify faster than clades that do not have such associations. Currently available data also do not support the hypothesis that symbiotic clades have broader host ranges than non-symbiotic clades.}, }
@article {pmid31448547, year = {2019}, author = {Derkarabetian, S and Benavides, LR and Giribet, G}, title = {Sequence capture phylogenomics of historical ethanol-preserved museum specimens: Unlocking the rest of the vault.}, journal = {Molecular ecology resources}, volume = {19}, number = {6}, pages = {1531-1544}, doi = {10.1111/1755-0998.13072}, pmid = {31448547}, issn = {1755-0998}, support = {//Harvard Dean's Fund/ ; DEB-1601208//Division of Environmental Biology/ ; DEB-1754278//Division of Environmental Biology/ ; }, mesh = {Animals ; Biodiversity ; Birds/*genetics ; DNA/genetics ; Ethanol/chemistry ; Formaldehyde/chemistry ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Insecta ; Mitochondria/genetics ; Museums ; Phylogeny ; Preservation, Biological/*methods ; Sequence Analysis, DNA/*methods ; Specimen Handling/methods ; }, abstract = {Natural history collections play a crucial role in biodiversity research, and museum specimens are increasingly being incorporated into modern genetics-based studies. Sequence capture methods have proven incredibly useful for phylogenomics, providing the additional ability to sequence historical museum specimens with highly degraded DNA, which until recently have been deemed less valuable for genetic work. The successful sequencing of ultraconserved elements (UCEs) from historical museum specimens has been demonstrated on multiple tissue types including dried bird skins, formalin-fixed squamates and pinned insects. However, no study has thoroughly demonstrated this approach for historical ethanol-preserved museum specimens. Alongside sequencing of "fresh" specimens preserved in >95% ethanol and stored at -80°C, we used extraction techniques specifically designed for degraded DNA coupled with sequence capture protocols to sequence UCEs from historical museum specimens preserved in 70%-80% ethanol and stored at room temperature, the standard for such ethanol-preserved museum collections. Across 35 fresh and 15 historical museum samples of the arachnid order Opiliones, an average of 345 UCE loci were included in phylogenomic matrices, with museum samples ranging from six to 495 loci. We successfully demonstrate the inclusion of historical ethanol-preserved museum specimens in modern sequence capture phylogenomic studies, show a high frequency of variant bases at the species and population levels, and from off-target reads successfully recover multiple loci traditionally sequenced in multilocus studies including mitochondrial loci and nuclear rRNA loci. The methods detailed in this study will allow researchers to potentially acquire genetic data from millions of ethanol-preserved museum specimens held in collections worldwide.}, }
@article {pmid31445096, year = {2019}, author = {Trasviña-Arenas, CH and Hoyos-Gonzalez, N and Castro-Lara, AY and Rodriguez-Hernandez, A and Sanchez-Sandoval, ME and Jimenez-Sandoval, P and Ayala-García, VM and Díaz-Quezada, C and Lodi, T and Baruffini, E and Brieba, LG}, title = {Amino and carboxy-terminal extensions of yeast mitochondrial DNA polymerase assemble both the polymerization and exonuclease active sites.}, journal = {Mitochondrion}, volume = {49}, number = {}, pages = {166-177}, doi = {10.1016/j.mito.2019.08.005}, pmid = {31445096}, issn = {1872-8278}, mesh = {Catalytic Domain ; DNA Polymerase I/genetics/*metabolism ; DNA Polymerase gamma/genetics/metabolism ; DNA, Fungal/*biosynthesis/genetics ; DNA, Mitochondrial/*biosynthesis/genetics ; Humans ; Mitochondrial Proteins/genetics/*metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; }, abstract = {Human and yeast mitochondrial DNA polymerases (DNAPs), POLG and Mip1, are related by evolution to bacteriophage DNAPs. However, mitochondrial DNAPs contain unique amino and carboxyl-terminal extensions that physically interact. Here we describe that N-terminal deletions in Mip1 polymerases abolish polymerization and decrease exonucleolytic degradation, whereas moderate C-terminal deletions reduce polymerization. Similarly, to the N-terminal deletions, an extended C-terminal deletion of 298 amino acids is deficient in nucleotide addition and exonucleolytic degradation of double and single-stranded DNA. The latter observation suggests that the physical interaction between the amino and carboxyl-terminal regions of Mip1 may be related to the spread of pathogenic POLG mutant along its primary sequence.}, }
@article {pmid31436541, year = {2019}, author = {Watson, E and Ahmad, K and Fraser, CL}, title = {The neuro-ophthalmology of inherited myopathies.}, journal = {Current opinion in ophthalmology}, volume = {30}, number = {6}, pages = {476-483}, doi = {10.1097/ICU.0000000000000610}, pmid = {31436541}, issn = {1531-7021}, mesh = {Eye Diseases, Hereditary/diagnosis/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Mitochondria, Muscle/*pathology ; Mitochondrial Myopathies/diagnosis/*genetics ; Oculomotor Muscles/*pathology ; Ophthalmoplegia, Chronic Progressive External/diagnosis/*genetics ; }, abstract = {PURPOSE OF REVIEW: Inherited myopathies, and in particular mitochondrial myopathies, are heterogeneous disorders, and ocular manifestations may be the presenting feature or offer important diagnostic clues. The ophthalmologist may be key to diagnosis, facilitating recognition of associated potentially life-threatening organ manifestations and an integral part of multidisciplinary care. This review, focusing especially on mitochondrial myopathies, provides updates on clinical features, diagnosis and recent therapeutic developments.<br><br>RECENT FINDINGS: Ptosis and/or ophthalmoplegia is present in over half of patients with mitochondrial disease, and associated clinical features imply specific genetic associations. Advances in next-generation sequencing have led to rapid evolution in the field, improving diagnosis rates, facilitating identification of novel genes, mutations and phenotypes, and providing important insights into disease mechanisms and therapeutic possibilities. Improved understanding of molecular mechanisms in inherited myopathies is enabling the development of experimental molecular therapies with clinical potential.<br><br>SUMMARY: Genetic advances are driving progress in the field of inherited myopathies, influencing diagnosis, understanding of disease and development of therapies. Recognition of key features can impact diagnosis and management of these important conditions.}, }
@article {pmid31434740, year = {2019}, author = {Barbero Barcenilla, B and Shippen, DE}, title = {Back to the future: The intimate and evolving connection between telomere-related factors and genotoxic stress.}, journal = {The Journal of biological chemistry}, volume = {294}, number = {40}, pages = {14803-14813}, pmid = {31434740}, issn = {1083-351X}, support = {R01 GM065383/GM/NIGMS NIH HHS/United States ; R01 GM127402/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA Damage/*genetics ; DNA Repair/genetics ; Eukaryotic Cells ; Gene Expression Regulation/genetics ; Humans ; Mitochondria/genetics ; Oxidative Stress/genetics ; Shelterin Complex ; Telomerase/genetics ; Telomere/*genetics ; Telomere-Binding Proteins/*genetics ; }, abstract = {The conversion of circular genomes to linear chromosomes during molecular evolution required the invention of telomeres. This entailed the acquisition of factors necessary to fulfill two new requirements: the need to fully replicate terminal DNA sequences and the ability to distinguish chromosome ends from damaged DNA. Here we consider the multifaceted functions of factors recruited to perpetuate and stabilize telomeres. We discuss recent theories for how telomere factors evolved from existing cellular machineries and examine their engagement in nontelomeric functions such as DNA repair, replication, and transcriptional regulation. We highlight the remarkable versatility of protection of telomeres 1 (POT1) proteins that was fueled by gene duplication and divergence events that occurred independently across several eukaryotic lineages. Finally, we consider the relationship between oxidative stress and telomeres and the enigmatic role of telomere-associated proteins in mitochondria. These findings point to an evolving and intimate connection between telomeres and cellular physiology and the strong drive to maintain chromosome integrity.}, }
@article {pmid31431166, year = {2019}, author = {Gould, SB and Garg, SG and Handrich, M and Nelson-Sathi, S and Gruenheit, N and Tielens, AGM and Martin, WF}, title = {Adaptation to life on land at high O2 via transition from ferredoxin-to NADH-dependent redox balance.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1909}, pages = {20191491}, pmid = {31431166}, issn = {1471-2954}, mesh = {Adaptation, Physiological/*physiology ; Anaerobiosis ; Animals ; Chlamydomonas reinhardtii/*physiology ; Electron Transport ; Energy Metabolism ; Ferredoxins/*metabolism ; Hydrogenase ; Iron-Sulfur Proteins ; NAD/*metabolism ; Oxygen/metabolism ; }, abstract = {Pyruvate : ferredoxin oxidoreductase (PFO) and iron only hydrogenase ([Fe]-HYD) are common enzymes among eukaryotic microbes that inhabit anaerobic niches. Their function is to maintain redox balance by donating electrons from food oxidation via ferredoxin (Fd) to protons, generating H2 as a waste product. Operating in series, they constitute a soluble electron transport chain of one-electron transfers between FeS clusters. They fulfil the same function-redox balance-served by two electron-transfers in the NADH- and O2-dependent respiratory chains of mitochondria. Although they possess O2-sensitive FeS clusters, PFO, Fd and [Fe]-HYD are also present among numerous algae that produce O2. The evolutionary persistence of these enzymes among eukaryotic aerobes is traditionally explained as adaptation to facultative anaerobic growth. Here, we show that algae express enzymes of anaerobic energy metabolism at ambient O2 levels (21% v/v), Chlamydomonas reinhardtii expresses them with diurnal regulation. High O2 environments arose on Earth only approximately 450 million years ago. Gene presence/absence and gene expression data indicate that during the transition to high O2 environments and terrestrialization, diverse algal lineages retained enzymes of Fd-dependent one-electron-based redox balance, while the land plant and land animal lineages underwent irreversible specialization to redox balance involving the O2-insensitive two-electron carrier NADH.}, }
@article {pmid31430004, year = {2019}, author = {Wu, B and Hao, W}, title = {Mitochondrial-encoded endonucleases drive recombination of protein-coding genes in yeast.}, journal = {Environmental microbiology}, volume = {21}, number = {11}, pages = {4233-4240}, doi = {10.1111/1462-2920.14783}, pmid = {31430004}, issn = {1462-2920}, support = {//Wayne State University/International ; }, mesh = {Endonucleases/genetics/*metabolism ; Genome, Mitochondrial/genetics ; Introns/genetics ; Mitochondria/*genetics ; *Recombination, Genetic ; Saccharomyces/*enzymology/*genetics ; }, abstract = {Mitochondrial recombination in yeast is well recognized, yet the underlying genetic mechanisms are not well understood. Recent progress has suggested that mobile introns in mitochondrial genomes (mitogenomes) can facilitate the recombination of their corresponding intron-containing genes through a mechanism known as intron homing. As many mitochondrial genes lack introns, there is a critical need to determine the extent of recombination and underlying mechanism of intron-lacking genes. This study leverages yeast mitogenomes to address these questions. In Saccharomyces cerevisiae, the 3'-end sequences of at least three intron-lacking mitochondrial genes exhibit elevated nucleotide diversity and recombination hotspots. Each of these 3'-end sequences is immediately adjacent to or even fused as overlapping genes with a stand-alone endonuclease. Our findings suggest that SAEs are responsible for recombination and elevated diversity of adjacent intron-lacking genes. SAEs were also evident to drive recombination of intron-lacking genes in Lachancea kluyveri, a yeast species that diverged from S. cerevisiae more than 100 million years ago. These results suggest SAEs as a common driver in recombination of intron-lacking genes during mitogenome evolution. We postulate that the linkage between intron-lacking gene and its adjacent endonuclease gene is the result of co-evolution.}, }
@article {pmid31419116, year = {2019}, author = {Mehta, AP and Ko, Y and Supekova, L and Pestonjamasp, K and Li, J and Schultz, PG}, title = {Toward a Synthetic Yeast Endosymbiont with a Minimal Genome.}, journal = {Journal of the American Chemical Society}, volume = {141}, number = {35}, pages = {13799-13802}, pmid = {31419116}, issn = {1520-5126}, support = {R01 GM132071/GM/NIGMS NIH HHS/United States ; }, mesh = {Escherichia coli/genetics/*metabolism ; Mitochondria/metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; *Symbiosis/genetics ; }, abstract = {Based on the endosymbiotic theory, one of the key events that occurred during mitochondrial evolution was an extensive loss of nonessential genes from the protomitochondrial endosymbiont genome and transfer of some of the essential endosymbiont genes to the host nucleus. We have developed an approach to recapitulate various aspects of endosymbiont genome minimization using a synthetic system consisting of Escherichia coli endosymbionts within host yeast cells. As a first step, we identified a number of E. coli auxotrophs of central metabolites that can form viable endosymbionts within yeast cells. These studies provide a platform to identify nonessential biosynthetic pathways that can be deleted in the E. coli endosymbionts to investigate the evolutionary adaptations in the host and endosymbiont during the evolution of mitochondria.}, }
@article {pmid31418651, year = {2019}, author = {Sato, C and Sasaki, M and Nabeta, H and Tomioka, M and Uga, S and Nakao, M}, title = {A Philophthalmid Eyefluke from a Human in Japan.}, journal = {The Journal of parasitology}, volume = {105}, number = {4}, pages = {619-623}, pmid = {31418651}, issn = {1937-2345}, mesh = {Animals ; Base Sequence ; Conjunctiva/parasitology ; Conjunctivitis/parasitology ; DNA, Helminth/chemistry ; DNA, Ribosomal/chemistry ; Electron Transport Complex IV/genetics ; Eye Infections, Parasitic/*parasitology ; Female ; Humans ; Japan ; Middle Aged ; Mitochondria/enzymology ; Phylogeny ; RNA, Ribosomal, 28S/genetics ; Trematoda/anatomy &amp; histology/classification/genetics/*isolation &amp; purification ; Trematode Infections/*parasitology ; }, abstract = {Philophthalmid eyeflukes are cosmopolitan parasites of birds and occasionally of mammals, including humans. A gravid adult of Philophthalmus sp. was found from the bulbar conjunctiva of a 64-yr-old woman in Japan, who was diagnosed with acute conjunctivitis. The parasite was morphologically most similar to Philophthalmus hegeneri, but distinctive in lacking an esophagus and in having clearly lobed testes. The DNA sequence analysis of genes for nuclear 28S ribosomal RNA and mitochondrial cytochrome c oxidase subunit 1 supported the identification at generic level. The morphological and molecular analyses strongly suggest that the eyefluke from a human in Japan should be treated as an undescribed species of Philophthalmus. The occurrence of human philophthalmosis is very rare. As far as we know, a total of 11 human cases have been reported worldwide to date.}, }
@article {pmid31416937, year = {2019}, author = {Youle, RJ}, title = {Mitochondria-Striking a balance between host and endosymbiont.}, journal = {Science (New York, N.Y.)}, volume = {365}, number = {6454}, pages = {}, doi = {10.1126/science.aaw9855}, pmid = {31416937}, issn = {1095-9203}, mesh = {Animals ; DNA, Mitochondrial/immunology ; Host Microbial Interactions/*immunology ; Humans ; *Immunity, Innate ; Mitochondria/genetics/*immunology ; Mitophagy/immunology ; Symbiosis/*immunology ; }, abstract = {Mitochondria are organelles with their own genome that arose from α-proteobacteria living within single-celled Archaea more than a billion years ago. This step of endosymbiosis offered tremendous opportunities for energy production and metabolism and allowed the evolution of fungi, plants, and animals. However, less appreciated are the downsides of this endosymbiosis. Coordinating gene expression between the mitochondrial genomes and the nuclear genome is imprecise and can lead to proteotoxic stress. The clonal reproduction of mitochondrial DNA requires workarounds to avoid mutational meltdown. In metazoans that developed innate immune pathways to thwart bacterial and viral infections, mitochondrial components can cross-react with pathogen sensors and invoke inflammation. Here, I focus on the numerous and elegant quality control processes that compensate for or mitigate these challenges of endosymbiosis.}, }
@article {pmid31412712, year = {2020}, author = {Aimo, A and Castiglione, V and Borrelli, C and Saccaro, LF and Franzini, M and Masi, S and Emdin, M and Giannoni, A}, title = {Oxidative stress and inflammation in the evolution of heart failure: From pathophysiology to therapeutic strategies.}, journal = {European journal of preventive cardiology}, volume = {27}, number = {5}, pages = {494-510}, doi = {10.1177/2047487319870344}, pmid = {31412712}, issn = {2047-4881}, mesh = {Animals ; Anti-Inflammatory Agents/adverse effects/*therapeutic use ; Antioxidants/adverse effects/*therapeutic use ; Comorbidity ; Heart/*drug effects/physiopathology ; Heart Disease Risk Factors ; Heart Failure/*drug therapy/epidemiology/metabolism/physiopathology ; Humans ; Inflammation Mediators/*antagonists &amp; inhibitors/metabolism ; Myocardium/*metabolism/pathology ; Oxidative Stress/*drug effects ; Reactive Oxygen Species/*antagonists &amp; inhibitors/metabolism ; Signal Transduction ; }, abstract = {Both oxidative stress and inflammation are enhanced in chronic heart failure. Dysfunction of cardiac mitochondria is a hallmark of heart failure and a leading cause of oxidative stress, which in turn exerts detrimental effects on cellular components, including mitochondria themselves, thus generating a vicious circle. Oxidative stress also causes myocardial tissue damage and inflammation, contributing to heart failure progression. Furthermore, a subclinical inflammatory state may be caused by heart failure comorbidities such as obesity, diabetes mellitus or sleep apnoeas. Some markers of both oxidative stress and inflammation are enhanced in chronic heart failure and hold prognostic significance. For all these reasons, antioxidants or anti-inflammatory drugs may represent interesting additional therapies for subjects either at high risk or with established heart failure. Nonetheless, only a few clinical trials on antioxidants have been carried out so far, with several disappointing results except for vitamin C, elamipretide and coenzyme Q10. With regard to anti-inflammatory drugs, only preliminary data on the interleukin-1 antagonist anakinra are currently available. Therefore, a comprehensive, deep understanding of our current knowledge on oxidative stress and inflammation in chronic heart failure is key to providing some suggestions for future research on this topic.}, }
@article {pmid31407247, year = {2019}, author = {Wang, H and Kim, H and Lim, WA and Ki, JS}, title = {Molecular cloning and oxidative-stress responses of a novel manganese superoxide dismutase (MnSOD) gene in the dinoflagellate Prorocentrum minimum.}, journal = {Molecular biology reports}, volume = {46}, number = {6}, pages = {5955-5966}, pmid = {31407247}, issn = {1573-4978}, mesh = {Amino Acid Sequence/genetics ; Animals ; Base Sequence/genetics ; Cloning, Molecular/methods ; DNA, Complementary/genetics ; Dinoflagellida/*genetics/metabolism ; Open Reading Frames/genetics ; Oxidative Stress/genetics/physiology ; Phylogeny ; RNA, Messenger/genetics ; Reactive Oxygen Species/metabolism ; Sequence Alignment ; Superoxide Dismutase/*genetics/*metabolism ; }, abstract = {Dinoflagellate algae are microeukaryotes that have distinct genomes and gene regulation systems, making them an interesting model for studying protist evolution and genomics. In the present study, we discovered a novel manganese superoxide dismutase (PmMnSOD) gene from the marine dinoflagellate Prorocentrum minimum, examined its molecular characteristics, and evaluated its transcriptional responses to the oxidative stress-inducing contaminants, CuSO4 and NaOCl. Its cDNA was 1238 bp and contained a dinoflagellate spliced leader sequence, a 906 bp open reading frame (301 amino acids), and a poly (A) tail. The gene was coded on the nuclear genome with one 174 bp intron; signal peptide analysis showed that it might be localized to the mitochondria. Real-time PCR analysis revealed an increase in gene expression of MnSOD and SOD activity when P. minimum cells were separately exposed to CuSO4 and NaOCl. In addition, both contaminants considerably decreased chlorophyll autofluorescence, and increased intracellular reactive oxygen species. These results suggest that dinoflagellate MnSOD may be involved in protecting cells against oxidative damage.}, }
@article {pmid31404610, year = {2019}, author = {Kanduma, EG and Bishop, RP and Githaka, NW and Skilton, RA and Heyne, H and Mwacharo, JM}, title = {Mitochondrial and nuclear multilocus phylogeny of Rhipicephalus ticks from Kenya.}, journal = {Molecular phylogenetics and evolution}, volume = {140}, number = {}, pages = {106579}, doi = {10.1016/j.ympev.2019.106579}, pmid = {31404610}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Cell Nucleus/*genetics ; DNA Barcoding, Taxonomic ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; *Genetic Loci ; Haplotypes/genetics ; Kenya ; Mitochondria/*genetics ; *Phylogeny ; Rhipicephalus/anatomy &amp; histology/*classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {The morphological diversity of African ticks of the genus Rhipicephalus and subgenus Boophilus have been studied in detail. However, their taxonomy remains poorly resolved with limited molecular studies performed to improve inter-species discrimination. Herein, ribosomal cytochrome c oxidase I (COI), 12S ribosomal DNA (12S rDNA) and nuclear ribosomal DNA internal transcriber spacer 2 (ITS2) were analyzed in Rhipicephalus tick populations in Kenya. While the morphological and molecular criteria separated R. e. evertsi, R. pulchellus and R. appendiculatus from other members of the genus, except the morphologically similar sibling species R. zambeziensis, this was not the case for other tick populations. COI sequences of Rhipicephalus ticks from Ruma National Park (RNP) in Southwestern Kenya, that were morphologically similar to R. praetextatus/R. simus, a formed distinct clade and barcode gap group. 12S rDNA haplotypes of this population were 99% identical to a GenBank accession of R. muhsamae which is thought to be endemic in West and Central Africa. However, the ITS2 locus indicated that the RNP samples were genetically closest to ticks identified morphologically as R. praetextatus. The COI and 12S rDNA haplotype sequences of R. praetextatus clustered closely with R. simus reference sequences though the two species occurred in distinct barcode gap groups. Our results suggest that the R. simus/R. praetextatus/R. muhsamae comprise a closely related tick species complex found across sub-Saharan Africa and includes the yet to be described RNP population. More studies on the biology, ecology and genomics of all life stages of tick species in the complex may clarify their taxonomic status. A continent-wide study that combines morphology, DNA marker sequencing and emerging methods, such as mass spectrometry and whole-genome resequencing may reveal the diversity and distribution of taxa within the genus Rhipicephalus in sub-Saharan Africa.}, }
@article {pmid31404599, year = {2019}, author = {Zhang, Y and Feng, S and Fekrat, L and Jiang, F and Khathutshelo, M and Li, Z}, title = {The first two complete mitochondrial genome of Dacus bivittatus and Dacus ciliatus (Diptera: Tephritidae) by next-generation sequencing and implications for the higher phylogeny of Tephritidae.}, journal = {International journal of biological macromolecules}, volume = {140}, number = {}, pages = {469-476}, doi = {10.1016/j.ijbiomac.2019.08.076}, pmid = {31404599}, issn = {1879-0003}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; *High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; Molecular Sequence Annotation ; *Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Tephritidae/*genetics ; Whole Genome Sequencing ; }, abstract = {Dacus bivittatus and Dacus ciliatus are destructive pests of Cucurbitaceae crops including cucumber, zucchini and melons. Recent molecular phylogenetic studies conflicted with morphological taxonomy regarding relationships between Bactrocera, Dacus and Zeugodacus. In this study, we sequenced the complete mitochondrial genomes of the above species which are representatives of two subgenera of Dacus (Dacus and Didacus) not previously sequenced and reconstructed the phylogeny of Tephritidae. The mitochondrial genomes of D. bivittatus and D. ciliatus were 15,833 bp and 15,808 bp in length, respectively. The 37 genes, including 13 protein-coding genes (PCGs), 2 rRNA genes and 22 tRNA genes, with a long non-coding region (A + T-rich control region) were in the same arrangement as the ancestral insect mitochondrial genome. Phylogenetic analysis showed that Dacus has a closer relationship of Zeugodacus rather than Bactrocera. Our phylogenetic results further support the recent proposals that Zeugodacus should be considered as a genus not a subgenus of Bactrocera. Whole mitochondrial genomes of D. bivittatus and D. ciliatus could be useful in further studies for species diagnosis, evolution and phylogeny research within Tephritidae.}, }
@article {pmid31402920, year = {2019}, author = {Lee, GR and Shaefi, S and Otterbein, LE}, title = {HO-1 and CD39: It Takes Two to Protect the Realm.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {1765}, pmid = {31402920}, issn = {1664-3224}, support = {K08 GM134220/GM/NIGMS NIH HHS/United States ; R03 AG060179/AG/NIA NIH HHS/United States ; R43 GM125430/GM/NIGMS NIH HHS/United States ; R44 DK111260/DK/NIDDK NIH HHS/United States ; }, mesh = {Adenosine/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Apyrase/*metabolism ; Heme/metabolism ; Heme Oxygenase-1/*metabolism ; Humans ; Immunity, Innate ; }, abstract = {Cellular protective mechanisms exist to ensure survival of the cells and are a fundamental feature of all cells that is necessary for adapting to changes in the environment. Indeed, evolution has ensured that each cell is equipped with multiple overlapping families of genes that safeguard against pathogens, injury, stress, and dysfunctional metabolic processes. Two of the better-known enzymatic systems, conserved through all species, include the heme oxygenases (HO-1/HO-2), and the ectonucleotidases (CD39/73). Each of these systems generates critical bioactive products that regulate the cellular response to a stressor. Absence of these molecules results in the cell being extremely predisposed to collapse and, in most cases, results in the death of the cell. Recent reports have begun to link these two metabolic pathways, and what were once exclusively stand-alone are now being found to be intimately interrelated and do so through their innate ability to generate bioactive products including adenosine, carbon monoxide, and bilirubin. These simple small molecules elicit profound cellular physiologic responses that impact a number of innate immune responses, and participate in the regulation of inflammation and tissue repair. Collectively these enzymes are linked not only because of the mitochondria being the source of their substrates, but perhaps more importantly, because of the impact of their products on specific cellular responses. This review will provide a synopsis of the current state of the field regarding how these systems are linked and how they are now being leveraged as therapeutic modalities in the clinic.}, }
@article {pmid31396441, year = {2019}, author = {Rodriguez, C and Prieto, GI and Vega, IA and Castro-Vazquez, A}, title = {Functional and evolutionary perspectives on gill structures of an obligate air-breathing, aquatic snail.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e7342}, pmid = {31396441}, issn = {2167-8359}, abstract = {Ampullariids are freshwater gastropods bearing a gill and a lung, thus showing different degrees of amphibiousness. In particular, Pomacea canaliculata (Caenogastropoda, Ampullariidae) is an obligate air-breather that relies mainly or solely on the lung for dwelling in poorly oxygenated water, for avoiding predators, while burying in the mud during aestivation, and for oviposition above water level. In this paper, we studied the morphological peculiarities of the gill in this species. We found (1) the gill and lung vasculature and innervation are intimately related, allowing alternation between water and air respiration; (2) the gill epithelium has features typical of a transporting rather than a respiratory epithelium; and (3) the gill has resident granulocytes within intraepithelial spaces that may serve a role for immune defence. Thus, the role in oxygen uptake may be less significant than the roles in ionic/osmotic regulation and immunity. Also, our results provide a morphological background to understand the dependence on aerial respiration of Pomacea canaliculata. Finally, we consider these findings from a functional perspective in the light of the evolution of amphibiousness in the Ampullariidae, and discuss that master regulators may explain the phenotypic convergence of gill structures amongst this molluscan species and those in other phyla.}, }
@article {pmid31392804, year = {2019}, author = {Guo, B and Fang, B and Shikano, T and Momigliano, P and Wang, C and Kravchenko, A and Merilä, J}, title = {A phylogenomic perspective on diversity, hybridization and evolutionary affinities in the stickleback genus Pungitius.}, journal = {Molecular ecology}, volume = {28}, number = {17}, pages = {4046-4064}, doi = {10.1111/mec.15204}, pmid = {31392804}, issn = {1365-294X}, mesh = {Animals ; Cell Nucleus/genetics ; Female ; Gene Flow ; *Genetic Variation ; Geography ; *Hybridization, Genetic ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Smegmamorpha/*classification/*genetics ; Species Specificity ; Time Factors ; }, abstract = {Hybridization and convergent evolution are phenomena of broad interest in evolutionary biology, but their occurrence poses challenges for reconstructing evolutionary affinities among affected taxa. Sticklebacks in the genus Pungitius are a case in point: evolutionary relationships and taxonomic validity of different species and populations in this circumpolarly distributed species complex remain contentious due to convergent evolution of traits regarded as diagnostic in their taxonomy, and possibly also due to frequent hybridization among taxa. To clarify the evolutionary relationships among different Pungitius species and populations globally, as well as to study the prevalence and extent of introgression among recognized species, genomic data sets of both reference genome-anchored single nucleotide polymorphisms and de novo assembled RAD-tag loci were constructed with RAD-seq data. Both data sets yielded topologically identical and well-supported species trees. Incongruence between nuclear and mitochondrial DNA-based trees was found and suggested possibly frequent hybridization and mitogenome capture during the evolution of Pungitius sticklebacks. Further analyses revealed evidence for frequent nuclear genetic introgression among Pungitius species, although the estimated proportions of autosomal introgression were low. Apart from providing evidence for frequent hybridization, the results challenge earlier mitochondrial and morphology-based hypotheses regarding the number of species and their affinities in this genus: at least seven extant species can be recognized on the basis of genetic data. The results also shed new light on the biogeographical history of the Pungitius-complex, including suggestion of several trans-Arctic invasions of Europe from the Northern Pacific. The well-resolved phylogeny should facilitate the utility of this genus as a model system for future comparative evolutionary studies.}, }
@article {pmid31389181, year = {2019}, author = {Tan, K and Chen, Y and Ma, K and Wang, Q and Liu, X and Wang, F}, title = {Spatiotemporally Tracking the Programmable Mitochondrial Membrane Potential Evolutions by a Robust Molecular Rotor.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {15}, number = {40}, pages = {e1903266}, doi = {10.1002/smll.201903266}, pmid = {31389181}, issn = {1613-6829}, mesh = {DNA/metabolism ; Fluorescent Dyes/chemical synthesis/chemistry ; HeLa Cells ; Humans ; Light ; Logic ; MCF-7 Cells ; *Membrane Potential, Mitochondrial ; Mitochondria/metabolism ; Solvents ; Spectrometry, Fluorescence ; Viscosity ; }, abstract = {Mitochondrial membrane potential (MMP) represents an essential parameter of cellular activities, and even a minute MMP variation could significantly affect the biological functions of living organisms. Thus, convenient and accurate MMP detection is highly desirable since conventional MMP probes are always constrained by photobleaching, inconvenience, and irreversibility. Herein, a spatial-dependent fluorescent molecular rotor Mito-Cy is introduced for efficiently tracking the varied MMP status through its restricted intramolecular rotation in mitochondria and nucleus compartments. Based on a systematic investigation, the specifically lit up fluorescent Mito-Cy enables us to explore different MMP situations by determining their varied distributions. Accordingly, Mito-Cy concentrates in mitochondria under normal MMP status. Yet Mito-Cy starts to migrate gradually from mitochondria to the nucleus in decreasing MMP status, as represented by the increasing distribution levels of fluorescent Mito-Cy in the nucleus. Mito-Cy exclusively accumulates in the nucleus at ultimate vanishing MMP status. The facile operation of Mito-Cy, together with its high photostability and sensitivity, facilitates the monitoring of the reversible and programmable MMP evolutions in living cells. The Mito-Cy-involved logic control over MMP, e.g., AND and OR gates, indicates that the robust and versatile Mito-Cy holds great potential for illuminating mitochondrial viscosity-related bioprocesses.}, }
@article {pmid31387118, year = {2019}, author = {Karnkowska, A and Treitli, SC and Brzoň, O and Novák, L and Vacek, V and Soukal, P and Barlow, LD and Herman, EK and Pipaliya, SV and Pánek, T and Žihala, D and Petrželková, R and Butenko, A and Eme, L and Stairs, CW and Roger, AJ and Eliáš, M and Dacks, JB and Hampl, V}, title = {The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion.}, journal = {Molecular biology and evolution}, volume = {36}, number = {10}, pages = {2292-2312}, pmid = {31387118}, issn = {1537-1719}, mesh = {Actin Cytoskeleton ; *Genome, Protozoan ; *Intracellular Membranes ; Introns ; Mitochondrial Dynamics ; Oxymonadida/enzymology/*genetics/ultrastructure ; Proteome ; }, abstract = {The discovery that the protist Monocercomonoides exilis completely lacks mitochondria demonstrates that these organelles are not absolutely essential to eukaryotic cells. However, the degree to which the metabolism and cellular systems of this organism have adapted to the loss of mitochondria is unknown. Here, we report an extensive analysis of the M. exilis genome to address this question. Unexpectedly, we find that M. exilis genome structure and content is similar in complexity to other eukaryotes and less "reduced" than genomes of some other protists from the Metamonada group to which it belongs. Furthermore, the predicted cytoskeletal systems, the organization of endomembrane systems, and biosynthetic pathways also display canonical eukaryotic complexity. The only apparent preadaptation that permitted the loss of mitochondria was the acquisition of the SUF system for Fe-S cluster assembly and the loss of glycine cleavage system. Changes in other systems, including in amino acid metabolism and oxidative stress response, were coincident with the loss of mitochondria but are likely adaptations to the microaerophilic and endobiotic niche rather than the mitochondrial loss per se. Apart from the lack of mitochondria and peroxisomes, we show that M. exilis is a fully elaborated eukaryotic cell that is a promising model system in which eukaryotic cell biology can be investigated in the absence of mitochondria.}, }
@article {pmid31382041, year = {2019}, author = {De, AK and Muthiyan, R and Ponraj, P and Muniswamy, K and Sunder, J and Kundu, A and Karunakaran, D and George, Z and Kundu, MS and Ahmed, SKZ and Malakar, D and Bhattacharya, D}, title = {Mitogenome analysis of Indian isolate of Rhipicephalus microplus clade A sensu (): A first report from Maritime South-East Asia.}, journal = {Mitochondrion}, volume = {49}, number = {}, pages = {135-148}, doi = {10.1016/j.mito.2019.07.014}, pmid = {31382041}, issn = {1872-8278}, mesh = {Animals ; *Genome, Mitochondrial ; India ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Rhipicephalus/*genetics ; }, abstract = {This communication reports a comprehensive profile of mitogenome analysis of Rhipicephalus microplus, isolated and identified from Andaman and Nicobar islands, a part of Maritime South East Asia. Complete mitogenome of Indian isolate of R. microplus (MK234703) was 14,903 bp. Mitochondrial (mt.) genome had 13 protein coding genes (PCGs), 22 tRNAs, two ribosomal subunits and two control regions. All PCGs were located on the H-strand except nad1, nad5, nad4 and nad4L. All start codons were ATN codon and abbreviated stop codons were seen in cox-2-3, nad-5 and cytb. A purine rich tick-box motif has been identified. A tandem repeat unit (TTTATT), described as a region alike to nad1 was identified in 130 bp insertion in between nad1 and tRNA-Glu and in nad1 sequence. Presence of two control regions (CRs) proved that, two CRs have evolved in concert rather than independently. Strong biasness towards A and T in Indian isolate of R. microplus is a typical feature for most of the arthropods. Subtracted values of dn and ds suggested that, there was least effect of nt. sequence of cox1 gene when Indian isolate was compared with other isolates of Rhipicephalus. On the basis of phylogenetic analysis, species of the genus Rhipicephalus could be clustered in three groups; ticks of the genera belonging to sub-family Rhipicephalinae could be grouped in a single cluster. Finally, cox1 sequence of MK234703 indicated that the isolate belonged to clade A sensu Burger et al., 2014 which has not been reported earlier from India.}, }
@article {pmid31380018, year = {2019}, author = {Ngatia, JN and Lan, TM and Dinh, TD and Zhang, L and Ahmed, AK and Xu, YC}, title = {Signals of positive selection in mitochondrial protein-coding genes of woolly mammoth: Adaptation to extreme environments?.}, journal = {Ecology and evolution}, volume = {9}, number = {12}, pages = {6821-6832}, pmid = {31380018}, issn = {2045-7758}, abstract = {The mammoths originated in warm and equatorial Africa and later colonized cold and high-latitude environments. Studies on nuclear genes suggest that woolly mammoth had evolved genetic variations involved in processes relevant to cold tolerance, including lipid metabolism and thermogenesis, and adaptation to extremely varied light and darkness cycles. The mitochondria is a major regulator of cellular energy metabolism, thus the mitogenome of mammoths may also exhibit adaptive evolution. However, little is yet known in this regard. In this study, we analyzed mitochondrial protein-coding genes (MPCGs) sequences of 75 broadly distributed woolly mammoths (Mammuthus primigenius) to test for signatures of positive selection. Results showed that a total of eleven amino acid sites in six genes, namely ND1, ND4, ND5, ND6, CYTB, and ATP6, displayed strong evidence of positive selection. Two sites were located in close proximity to proton-translocation channels in mitochondrial complex I. Biochemical and homology protein structure modeling analyses demonstrated that five amino acid substitutions in ND1, ND5, and ND6 might have influenced the performance of protein-protein interaction among subunits of complex I, and three substitutions in CYTB and ATP6 might have influenced the performance of metabolic regulatory chain. These findings suggest metabolic adaptations in the mitogenome of woolly mammoths in relation to extreme environments and provide a basis for further tests on the significance of the variations on other systems.}, }
@article {pmid31374295, year = {2019}, author = {Tolomeo, AM and Carraro, A and Bakiu, R and Toppo, S and Garofalo, F and Pellegrino, D and Gerdol, M and Ferro, D and Place, SP and Santovito, G}, title = {Molecular characterization of novel mitochondrial peroxiredoxins from the Antarctic emerald rockcod and their gene expression in response to environmental warming.}, journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP}, volume = {225}, number = {}, pages = {108580}, doi = {10.1016/j.cbpc.2019.108580}, pmid = {31374295}, issn = {1532-0456}, mesh = {Amino Acid Sequence ; Animals ; Antarctic Regions ; Fish Proteins/classification/metabolism ; Gene Expression ; Global Warming ; Mitochondria/*enzymology ; Perciformes/*metabolism ; *Peroxiredoxins/classification/metabolism ; Phylogeny ; Protein Isoforms ; Temperature ; }, abstract = {In the present study we describe the molecular characterization of the two paralogous mitochondrial peroxiredoxins from Trematomus bernacchii, a teleost that plays a pivotal role in the Antarctic food chain. The two putative amino acid sequences were compared with orthologs from other fish, highlighting a high percentage of identity and similarity with the respective variant, in particular for the residues that are essential for the characteristic peroxidase activity of these enzymes. The temporal expression of Prdx3 and Prdx5 mRNAs in response to short-term thermal stress showed a general upregulation of prdx3, suggesting that this isoform is the most affected by temperature increase. These data, together with the peculiar differences between the molecular structures of the two mitochondrial Prdxs in T. bernacchii as well as in the tropical species Stegastes partitus, suggest an adaptation that allowed these poikilothermic aquatic vertebrates to colonize very different environments, characterized by different temperature ranges.}, }
@article {pmid31371715, year = {2019}, author = {Mackintosh, A and Laetsch, DR and Hayward, A and Charlesworth, B and Waterfall, M and Vila, R and Lohse, K}, title = {The determinants of genetic diversity in butterflies.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3466}, pmid = {31371715}, issn = {2041-1723}, mesh = {Animals ; Biodiversity ; Body Size ; Butterflies/*classification/*genetics ; Chromosomes ; Evolution, Molecular ; Genetic Drift ; Genetic Variation/*genetics ; Genome ; Genome Size ; Karyotype ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Population Density ; Recombination, Genetic ; *Selection, Genetic ; }, abstract = {Under the neutral theory, genetic diversity is expected to increase with population size. While comparative analyses have consistently failed to find strong relationships between census population size and genetic diversity, a recent study across animals identified a strong correlation between propagule size and genetic diversity, suggesting that r-strategists that produce many small offspring, have greater long-term population sizes. Here we compare genome-wide genetic diversity across 38 species of European butterflies (Papilionoidea), a group that shows little variation in reproductive strategy. We show that genetic diversity across butterflies varies over an order of magnitude and that this variation cannot be explained by differences in current abundance, propagule size, host or geographic range. Instead, neutral genetic diversity is negatively correlated with body size and positively with the length of the genetic map. This suggests that genetic diversity is determined both by differences in long-term population size and the effect of selection on linked sites.}, }
@article {pmid31371451, year = {2019}, author = {Kamikubo, K and Kato, H and Kioka, H and Yamazaki, S and Tsukamoto, O and Nishida, Y and Asano, Y and Imamura, H and Kawahara, H and Shintani, Y and Takashima, S}, title = {A molecular triage process mediated by RING finger protein 126 and BCL2-associated athanogene 6 regulates degradation of G0/G1 switch gene 2.}, journal = {The Journal of biological chemistry}, volume = {294}, number = {40}, pages = {14562-14573}, pmid = {31371451}, issn = {1083-351X}, mesh = {Adenosine Triphosphate/genetics/metabolism ; Alanine/genetics ; Cell Cycle Proteins/chemistry/*genetics ; Gene Expression Regulation/genetics ; HeLa Cells ; Humans ; Hydrophobic and Hydrophilic Interactions ; Mitochondria/genetics/metabolism ; Molecular Chaperones/*genetics/metabolism ; Multiprotein Complexes/chemistry/genetics ; Mutation ; Myocardial Ischemia/*genetics/pathology ; Myocytes, Cardiac/metabolism ; *Oxidative Phosphorylation ; Proteolysis ; Ubiquitin-Protein Ligases/*genetics/metabolism ; Ubiquitination/genetics ; }, abstract = {Oxidative phosphorylation generates most of the ATP in respiring cells. ATP is an essential energy source, especially in cardiomyocytes because of their continuous contraction and relaxation. Previously, we reported that G0/G1 switch gene 2 (G0S2) positively regulates mitochondrial ATP production by interacting with FOF1-ATP synthase. G0S2 overexpression mitigates ATP decline in cardiomyocytes and strongly increases their hypoxic tolerance during ischemia. Here, we show that G0S2 protein undergoes proteasomal degradation via a cytosolic molecular triage system and that inhibiting this process increases mitochondrial ATP production in hypoxia. First, we performed screening with a library of siRNAs targeting ubiquitin-related genes and identified RING finger protein 126 (RNF126) as an E3 ligase involved in G0S2 degradation. RNF126-deficient cells exhibited prolonged G0S2 protein turnover and reduced G0S2 ubiquitination. BCL2-associated athanogene 6 (BAG6), involved in the molecular triage of nascent membrane proteins, enhanced RNF126-mediated G0S2 ubiquitination both in vitro and in vivo Next, we found that Glu-44 in the hydrophobic region of G0S2 acts as a degron necessary for G0S2 polyubiquitination and proteasomal degradation. Because this degron was required for an interaction of G0S2 with BAG6, an alanine-replaced G0S2 mutant (E44A) escaped degradation. In primary cultured cardiomyocytes, both overexpression of the G0S2 E44A mutant and RNF126 knockdown effectively attenuated ATP decline under hypoxic conditions. We conclude that the RNF126/BAG6 complex contributes to G0S2 degradation and that interventions to prevent G0S2 degradation may offer a therapeutic strategy for managing ischemic diseases.}, }
@article {pmid31370303, year = {2019}, author = {Sharaf, A and Gruber, A and Jiroutová, K and Oborník, M}, title = {Characterization of Aminoacyl-tRNA Synthetases in Chromerids.}, journal = {Genes}, volume = {10}, number = {8}, pages = {}, pmid = {31370303}, issn = {2073-4425}, mesh = {Alveolata/classification/enzymology/*genetics ; Amino Acyl-tRNA Synthetases/*genetics ; Phylogeny ; Protozoan Proteins/*genetics ; }, abstract = {Aminoacyl-tRNA synthetases (AaRSs) are enzymes that catalyze the ligation of tRNAs to amino acids. There are AaRSs specific for each amino acid in the cell. Each cellular compartment in which translation takes place (the cytosol, mitochondria, and plastids in most cases), needs the full set of AaRSs; however, individual AaRSs can function in multiple compartments due to dual (or even multiple) targeting of nuclear-encoded proteins to various destinations in the cell. We searched the genomes of the chromerids, Chromera velia and Vitrella brassicaformis, for AaRS genes: 48 genes encoding AaRSs were identified in C. velia, while only 39 AaRS genes were found in V. brassicaformis. In the latter alga, ArgRS and GluRS were each encoded by a single gene occurring in a single copy; only PheRS was found in three genes, while the remaining AaRSs were encoded by two genes. In contrast, there were nine cases for which C. velia contained three genes of a given AaRS (45% of the AaRSs), all of them representing duplicated genes, except AsnRS and PheRS, which are more likely pseudoparalogs (acquired via horizontal or endosymbiotic gene transfer). Targeting predictions indicated that AaRSs are not (or not exclusively), in most cases, used in the cellular compartment from which their gene originates. The molecular phylogenies of the AaRSs are variable between the specific types, and similar between the two investigated chromerids. While genes with eukaryotic origin are more frequently retained, there is no clear pattern of orthologous pairs between C. velia and V. brassicaformis.}, }
@article {pmid31369817, year = {2020}, author = {Garcia-Mayea, Y and Mir, C and Masson, F and Paciucci, R and LLeonart, ME}, title = {Insights into new mechanisms and models of cancer stem cell multidrug resistance.}, journal = {Seminars in cancer biology}, volume = {60}, number = {}, pages = {166-180}, doi = {10.1016/j.semcancer.2019.07.022}, pmid = {31369817}, issn = {1096-3650}, mesh = {ATP-Binding Cassette Transporters/genetics/metabolism ; Animals ; Antineoplastic Agents/*pharmacology/therapeutic use ; Apoptosis/drug effects ; Autophagy ; Biomarkers ; DNA Damage ; Disease Susceptibility ; *Drug Resistance, Multiple ; *Drug Resistance, Neoplasm ; Endoplasmic Reticulum Stress ; Epigenesis, Genetic ; Exosomes/metabolism ; Hippo Signaling Pathway ; Humans ; Mitochondria/drug effects/metabolism ; Neoplasms/drug therapy/etiology/metabolism/pathology ; Neoplastic Stem Cells/*drug effects/*metabolism/pathology ; Protein Serine-Threonine Kinases/metabolism ; Signal Transduction/drug effects ; Tumor Microenvironment/drug effects/genetics ; Unfolded Protein Response ; }, abstract = {The acquisition of genetic alterations, clonal evolution, and the tumor microenvironment promote cancer progression, metastasis and therapy resistance. These events correspond to the establishment of the great phenotypic heterogeneity and plasticity of cancer cells that contribute to tumor progression and resistant disease. Targeting resistant cancers is a major challenge in oncology; however, the underlying processes are not yet fully understood. Even though current treatments can reduce tumor size and increase life expectancy, relapse and multidrug resistance (MDR) ultimately remain the second cause of death in developed countries. Recent evidence points toward stem-like phenotypes in cancer cells, promoted by cancer stem cells (CSCs), as the main culprit of cancer relapse, resistance (radiotherapy, hormone therapy, and/or chemotherapy) and metastasis. Many mechanisms have been proposed for CSC resistance, such as drug efflux through ABC transporters, overactivation of the DNA damage response (DDR), apoptosis evasion, prosurvival pathways activation, cell cycle promotion and/or cell metabolic alterations. Nonetheless, targeted therapy toward these specific CSC mechanisms is only partially effective to prevent or abolish resistance, suggesting underlying additional causes for CSC resilience. This article aims to provide an integrated picture of the MDR mechanisms that operate in CSCs' behavior and to propose a novel model of tumor evolution during chemotherapy. Targeting the pathways mentioned here might hold promise and reveal new strategies for future clinical therapeutic approaches.}, }
@article {pmid31358627, year = {2019}, author = {Kanatsu-Shinohara, M and Yamamoto, T and Toh, H and Kazuki, Y and Kazuki, K and Imoto, J and Ikeo, K and Oshima, M and Shirahige, K and Iwama, A and Nabeshima, Y and Sasaki, H and Shinohara, T}, title = {Aging of spermatogonial stem cells by Jnk-mediated glycolysis activation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {33}, pages = {16404-16409}, pmid = {31358627}, issn = {1091-6490}, mesh = {Adult Germline Stem Cells/metabolism ; Adult Stem Cells/cytology/metabolism ; Aging/*genetics ; Animals ; Cell Proliferation/genetics ; Gene Expression Regulation, Developmental ; Glucuronidase/genetics ; Glycolysis/genetics ; JNK Mitogen-Activated Protein Kinases/*genetics ; Klotho Proteins ; Male ; Mice ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/*genetics ; Polycomb-Group Proteins/genetics ; Proto-Oncogene Proteins/*genetics ; Rats ; Reactive Oxygen Species/metabolism ; Spermatogenesis/*genetics ; Spermatogonia/growth &amp; development/metabolism ; Stem Cell Niche/genetics ; Testis/growth &amp; development/metabolism ; Wnt Proteins/*genetics ; }, abstract = {Because spermatogonial stem cells (SSCs) are immortal by serial transplantation, SSC aging in intact testes is considered to be caused by a deteriorated microenvironment. Here, we report a cell-intrinsic mode of SSC aging by glycolysis activation. Using cultured SSCs, we found that aged SSCs proliferated more actively than young SSCs and showed enhanced glycolytic activity. Moreover, they remained euploid and exhibited stable androgenetic imprinting patterns with robust SSC activity despite having shortened telomeres. Aged SSCs showed increased Wnt7b expression, which was associated with decreased Polycomb complex 2 activity. Our results suggest that aberrant Wnt7b expression activated c-jun N-terminal kinase (JNK), which down-regulated mitochondria numbers by suppressing Ppargc1a Down-regulation of Ppargc1a probably decreased reactive oxygen species and enhanced glycolysis. Analyses of the Klotho-deficient aging mouse model and 2-y-old aged rats confirmed JNK hyperactivation and increased glycolysis. Therefore, not only microenvironment but also intrinsic activation of JNK-mediated glycolysis contributes to SSC aging.}, }
@article {pmid31349102, year = {2019}, author = {Schweizer, M and Warmuth, VM and Alaei Kakhki, N and Aliabadian, M and Förschler, M and Shirihai, H and Ewels, P and Gruselius, J and Olsen, RA and Schielzeth, H and Suh, A and Burri, R}, title = {Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats.}, journal = {Molecular phylogenetics and evolution}, volume = {139}, number = {}, pages = {106568}, doi = {10.1016/j.ympev.2019.106568}, pmid = {31349102}, issn = {1095-9513}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/classification/genetics ; Ecosystem ; *Genome ; Mitochondria/*genetics ; Passeriformes/classification/*genetics ; Phenotype ; Phylogeny ; }, abstract = {In wheatears and related species ('open-habitat chats'), molecular phylogenetics has led to a comprehensively revised understanding of species relationships and species diversity. Phylogenetic analyses have suggested that, in many cases, phenotypic similarities do not reflect species' relationships, revealing traditionally defined genera as non-monophyletic. This led to the suggestion of pervasive parallel evolution of open-habitat chats' plumage coloration and ecological phenotypes. However, to date, the molecular evidence for the phylogenetic relationships among open-habitat chats is mainly limited to mitochondrial DNA. Here, we assessed whether the mitochondrial relationships are supported by genome-wide data. To this end, we reconstructed the species tree among 14 open-habitat chat taxa using multi-species coalescent analyses based on ~1'300 SNPs. Our results confirm previous ones based chiefly on mitochondrial DNA; notably the paraphyly of the Oenanthe lugens complex and the clustering of individual species formerly placed in the genera Cercomela and Myrmecocichla within Oenanthe. Since several variable morphological and ecological characteristics occur in multiple places across the open-habitat chat phylogeny, our study consolidates the evidence for pervasive parallel evolution in the plumage coloration and ecology of open-habitat chats.}, }
@article {pmid31349101, year = {2019}, author = {Caro, A and Neiber, MT and Gómez-Moliner, BJ and Madeira, MJ}, title = {Molecular phylogeny and biogeography of the land snail subfamily Leptaxinae (Gastropoda: Hygromiidae).}, journal = {Molecular phylogenetics and evolution}, volume = {139}, number = {}, pages = {106570}, doi = {10.1016/j.ympev.2019.106570}, pmid = {31349101}, issn = {1095-9513}, mesh = {Animals ; Electron Transport Complex IV/chemistry/classification/genetics ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; RNA, Ribosomal/chemistry/classification/genetics ; Snails/*classification/genetics ; Spain ; }, abstract = {The subfamily Leptaxinae is included within the highly diverse land snail family Hygromiidae. In the absence of clear diagnostic morphological differences, the subfamily status is currently based solely on molecular information and includes three disjunctly distributed tribes, Leptaxini, Cryptosaccini and Metafruticicolini. However, the phylogenetic relationships among these tribes are not fully resolved and the clustering of some of the genera to the tribes is not statistically supported. To resolve the relationships within Leptaxinae and their position within Hygromiidae, we reconstructed their phylogeny using a multi-locus approach with two mitochondrial genes and eight nuclear markers. The phylogeny was further calibrated and an analysis of ancestral area estimation was carried out to infer the biogeographic history of the group. We elevated Metafruticicolini to subfamily level (Metafruticicolinae) and we restricted Leptaxinae to Cryptosaccini and Leptaxini. The Lusitanian genus Portugala was moved to Leptaxini, previously containing only the Macaronesian genus Leptaxis. Within Cryptosaccini, a new genus strictly confined to the Sierra de la Cabrera (Spain) is described, Fractanella gen. nov. According to our results, Leptaxinae originated in the Early Miocene in the Iberian Peninsula, from which the Macaronesian Islands were colonized. Due to the old split recovered for the divergence between Macaronesian and Iberian lineages, we hypothesize that this colonization may have occurred via the once emerged seamounts located between the archipelagos and the European and African continents, although this could also have occurred through the oldest now emerged islands of Macaronesia. In the Iberian Peninsula, the climatic shift that began during the Middle Miocene, changing progressively from subtropical climate towards the present-day Mediterranean climate, was identified as an important factor shaping the subfamily's diversification, along with Pleistocene climatic fluctuations.}, }
@article {pmid31346611, year = {2020}, author = {Huang, G and Cong, Z and Wang, X and Yuan, Y and Xu, R and Lu, Z and Wang, X and Qi, J}, title = {Targeting HSP90 attenuates angiotensin II-induced adventitial remodelling via suppression of mitochondrial fission.}, journal = {Cardiovascular research}, volume = {116}, number = {5}, pages = {1071-1084}, doi = {10.1093/cvr/cvz194}, pmid = {31346611}, issn = {1755-3245}, mesh = {Adventitia/*drug effects/metabolism/pathology ; Angiotensin II ; Animals ; Aorta, Thoracic/*drug effects/metabolism/pathology ; Benzoquinones/*pharmacology ; Calcineurin/metabolism ; Cell Movement/drug effects ; Cell Proliferation/drug effects ; Cells, Cultured ; Disease Models, Animal ; Dynamins/metabolism ; Fibroblasts/*drug effects/metabolism/pathology ; HSP90 Heat-Shock Proteins/*antagonists &amp; inhibitors/metabolism ; Hypertension/chemically induced/*drug therapy/metabolism/pathology ; Lactams, Macrocyclic/*pharmacology ; Male ; Mice, Inbred C57BL ; Mitochondria/*drug effects/metabolism/pathology ; Mitochondrial Dynamics/*drug effects ; Molecular Targeted Therapy ; Phenotype ; Reactive Oxygen Species/metabolism ; Signal Transduction ; Vascular Remodeling/*drug effects ; }, abstract = {AIMS: Adventitial remodelling presenting with the phenotypic switch of adventitial fibroblasts (AFs) to myofibroblasts is reportedly involved in the evolution of several vascular diseases, including hypertension. In our previous study, we reported that heat shock protein 90 (HSP90) inhibition by 17-dime-thylaminoethylamino-17-demethoxygeldanamycin (17-DMAG) markedly attenuates angiotensin II (AngII)-induced abdominal aortic aneurysm formation by simultaneously inhibiting several key signalling and transcriptional pathways in vascular smooth muscle cells; however, little is known about its role on AFs. Given that the AF phenotypic switch is likely to be associated with mitochondrial function and calcineurin (CN), a client protein of HSP90 that mediates mitochondrial fission and function, the aim of this study was to investigate whether mitochondrial fission contributes to phenotypic switch of AF, and if it does, we further aimed to determine whether HSP90 inhibition attenuates mitochondrial fission and subsequently suppresses AF transformation and adventitial remodelling in AngII-induced hypertensive mice.<br><br>METHODS AND RESULTS: In primary mouse AFs, we found that CN-dependent dephosphorylation of Drp1 induced mitochondrial fission and regulated mitochondrial reactive oxygen species production, which stimulated AF proliferation, migration, and phenotypic switching in AngII-treated AFs. Moreover, AngII was found to increase the binding of HSP90 and CN in AFs, while HSP90 inhibition significantly reversed AngII-induced mitochondrial fission and AF phenotypic switching by modulating the CN-dependent dephosphorylation of Drp1. Consistent with the effects in AFs, in an animal model of AngII-induced adventitial remodelling, 17-DMAG markedly reduced mitochondrial fission, AF differentiation, vessel wall thickening, and fibrosis in the aortic adventitia, which were mediated by CN/Drp1 signalling pathways.<br><br>CONCLUSIONS: Our study suggests that CN/Drp1-dependent mitochondrial fission may be essential for understanding adventitial remodelling in hypertension and that HSP90 inhibition may serve as a novel approach for the treatment of adventitial remodelling-related diseases.}, }
@article {pmid31341205, year = {2019}, author = {Tan, MH and Gan, HM and Lee, YP and Bracken-Grissom, H and Chan, TY and Miller, AD and Austin, CM}, title = {Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {10756}, pmid = {31341205}, issn = {2045-2322}, mesh = {Animals ; Decapoda/classification/*genetics ; Evolution, Molecular ; Gene Rearrangement/genetics ; Genomics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {The emergence of cost-effective and rapid sequencing approaches has resulted in an exponential rise in the number of mitogenomes on public databases in recent years, providing greater opportunity for undertaking large-scale comparative genomic and systematic research. Nonetheless, current datasets predominately come from small and disconnected studies on a limited number of related species, introducing sampling biases and impeding research of broad taxonomic relevance. This study contributes 21 crustacean mitogenomes from several under-represented decapod infraorders including Polychelida and Stenopodidea, which are used in combination with 225 mitogenomes available on NCBI to investigate decapod mitogenome diversity and phylogeny. An overview of mitochondrial gene orders (MGOs) reveals a high level of genomic variability within the Decapoda, with a large number of MGOs deviating from the ancestral arthropod ground pattern and unevenly distributed among infraorders. Despite the substantial morphological and ecological variation among decapods, there was limited evidence for correlations between gene rearrangement events and species ecology or lineage specific nucleotide substitution rates. Within a phylogenetic context, predicted scenarios of rearrangements show some MGOs to be informative synapomorphies for some taxonomic groups providing strong independent support for phylogenetic relationships. Additional comparisons for a range of mitogenomic features including nucleotide composition, strand asymmetry, unassigned regions and codon usage indicate several clade-specific trends that are of evolutionary and ecological interest.}, }
@article {pmid31332387, year = {2019}, author = {Barandun, J and Hunziker, M and Vossbrinck, CR and Klinge, S}, title = {Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome.}, journal = {Nature microbiology}, volume = {4}, number = {11}, pages = {1798-1804}, pmid = {31332387}, issn = {2058-5276}, support = {DP2 GM123459/GM/NIGMS NIH HHS/United States ; }, mesh = {Cryoelectron Microscopy ; Evolution, Molecular ; Fungal Proteins/metabolism ; Genome, Fungal ; Microsporidia/*classification/genetics/metabolism ; RNA, Ribosomal/genetics ; Ribosomal Proteins/*metabolism ; Ribosomes/*chemistry/genetics/metabolism ; }, abstract = {Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance[1-3], and are significant opportunistic parasites of humans[4]. They are characterized by having a specialized infection apparatus, an obligate intracellular lifestyle[5], rudimentary mitochondria and the smallest known eukaryotic genomes[5-7]. Extreme genome compaction led to minimal gene sizes affecting even conserved ancient complexes such as the ribosome[8-10]. In the present study, the cryo-electron microscopy structure of the ribosome from the microsporidium Vairimorpha necatrix is presented, which illustrates how genome compaction has resulted in the smallest known eukaryotic cytoplasmic ribosome. Selection pressure led to the loss of two ribosomal proteins and removal of essentially all eukaryote-specific ribosomal RNA (rRNA) expansion segments, reducing the rRNA to a functionally conserved core. The structure highlights how one microsporidia-specific and several repurposed existing ribosomal proteins compensate for the extensive rRNA reduction. The microsporidian ribosome is kept in an inactive state by two previously uncharacterized dormancy factors that specifically target the functionally important E-site, P-site and polypeptide exit tunnel. The present study illustrates the distinct effects of evolutionary pressure on RNA and protein-coding genes, provides a mechanism for ribosome inhibition and can serve as a structural basis for the development of inhibitors against microsporidian parasites.}, }
@article {pmid31329512, year = {2019}, author = {Cronshaw, M and Parker, S and Arany, P}, title = {Feeling the Heat: Evolutionary and Microbial Basis for the Analgesic Mechanisms of Photobiomodulation Therapy.}, journal = {Photobiomodulation, photomedicine, and laser surgery}, volume = {37}, number = {9}, pages = {517-526}, doi = {10.1089/photob.2019.4684}, pmid = {31329512}, issn = {2578-5478}, mesh = {Analgesia/*methods ; Biological Evolution ; Eukaryota/physiology ; Hot Temperature ; Humans ; Low-Level Light Therapy/*methods ; Mitochondria/physiology ; Patient Safety ; }, abstract = {Background: The clinical therapeutic benefits of Photobiomodulation (PBM) therapy have been well established in many clinical scenarios. However, we are far from having developed a complete understanding of the underlying mechanisms of photon-biological tissue interactions. Concurrent to ongoing PBM studies, there are several parallel fields with evidences from cell and tissue physiology such as evolutionary biology, photobiology, and microbiology among others. Objective: This review is focused on extrapolating evidences from an expanded range of studies that may contribute to a better understanding of PBM mechanisms especially focusing on analgesia. Further, the choice of a PBM device source and relevant dosimetry with regards to specific mechanisms are discussed to enable broader clinical use of PBM therapies. Materials and methods: This discussion article is referenced from an expanded range of peer reviewed publications, including literature associated with evolutionary biology, microbiology, oncology, and photo-optical imaging technology, amongst others. Results and discussion: Materials drawn from many disparate disciplines is described. By inference from the current evidence base, a novel theory is offered to partially explain the cellular basis of PBM-induced analgesia. It is proposed that this may involve the activity of a class of transmembrane proteins known as uncoupling proteins. Furthermore, it is proposed that this may activate the heat stress protein response and that intracellur microthermal inclines may be of significance in PBM analgesia. It is suggested that the PBM dose response as a simple binary model of PBM effects as represented by the Arndt-Schulz law is clinically less useful than a multiphasic biological response. Finally, comments are made concerning the nature of photon to tissue interaction that can have significance in regard to the effective choice and delivery of dose to clinical target. Conclusions: It is suggested that a re-evaluation of phototransduction pathways may lead to an improvement in outcome in phototheraphy. An enhanced knowledge of safe parameters and a better knowledge of the mechanics of action at target level will permit more reliable and predictable clinical gain and assist the acceptance of PBM therapy within the wider medical community.}, }
@article {pmid31328352, year = {2019}, author = {Khemaissia, H and Jelassi, R and Ghemari, C and Raimond, M and Souty-Grosset, C and Nasri-Ammar, K}, title = {Effects of trace metal elements on ultrastructural features of hepatopancreas of Armadillidium granulatum Brandt, 1833 (Crustacea, Isopoda).}, journal = {Microscopy research and technique}, volume = {82}, number = {10}, pages = {1819-1831}, doi = {10.1002/jemt.23349}, pmid = {31328352}, issn = {1097-0029}, support = {LR18ES06//Laboratory of Diversity, Management and Conservation of Biological Systems/ ; }, mesh = {Animals ; Aquatic Organisms/chemistry/drug effects ; Hepatopancreas/chemistry/*drug effects/*pathology ; Isopoda/chemistry/*drug effects ; Metals/analysis/*toxicity ; Microscopy, Electron, Transmission ; Spectrophotometry, Atomic ; Tunisia ; Water Pollutants, Chemical/analysis/*toxicity ; }, abstract = {This study was conducted to compare metals bioaccumulation in the terrestrial isopod Armadillidium granulatum collected from Ghar El Melh lagoon. We focused on recognizing the effects of trace elements on hepatopancreas functional role. To this end, isopod specimens were exposed for 3 weeks to sediments contaminated with cadmium, copper, zinc, mercury, and nickel. Three concentrations were used in duplicate for each experimental condition. At the end of the experiment, metal body burdens were determined using flame atomic absorption spectrometry. Results of the bioaccumulation factor (BAF) showed that the species A. granulatum was classified as a Cu macroconcentrator (BAF > 2) and a Zn deconcentrator (BAF < 2). Dose dependent morphological and histological changes were observed in the hepatopancreas cells using transmission electron microscopy. The predominant features were: microvillus border disruption, condensation of the cytoplasm with increasing endoplasmic reticulum, mitochondria, lysosomes and granules that accumulated metals in B and S cells. The number of lipid droplets decreased especially after Cd, Zn, Hg, and Ni treatments. This study demonstrated that the terrestrial isopod A. gramulatum could be a good indicator of soil metal contamination.}, }
@article {pmid33365705, year = {2019}, author = {Salas-Castañeda, MR and Castillo-Páez, A and Rocha-Olivares, A and Cruz-Barraza, JA}, title = {The complete mitogenome of the Eastern Pacific sponge Aplysina gerardogreeni (Demospongiae, Verongida, Aplysinidae).}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {4}, number = {2}, pages = {2734-2735}, pmid = {33365705}, issn = {2380-2359}, abstract = {We report the first mitochondrial genome of a Verongid sponge, Aplysina gerardogreeni from the Pacific Ocean. This has 19,620 bp and includes 14 protein-coding genes, 2 rRNAs genes, and 25 tRNAs genes. The gene arrangement was similar to the one found in two Caribbean Aplysina mitogenomes previously reported. Comparative analyses revealed a few substitutions among congeneric mitogenomes. The mitogenome of A. gerardogreeni could be useful to study the evolution of Verongimorpha group and also to identify adequate genes for its molecular systematics.}, }
@article {pmid31326515, year = {2019}, author = {Zhang, T and Fan, X and Gao, F and Al-Farraj, SA and El-Serehy, HA and Song, W}, title = {Further analyses on the phylogeny of the subclass Scuticociliatia (Protozoa, Ciliophora) based on both nuclear and mitochondrial data.}, journal = {Molecular phylogenetics and evolution}, volume = {139}, number = {}, pages = {106565}, doi = {10.1016/j.ympev.2019.106565}, pmid = {31326515}, issn = {1095-9513}, mesh = {Cell Nucleus/*genetics ; DNA, Ribosomal/chemistry/classification/genetics ; Electron Transport Complex IV/chemistry/classification/genetics ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Oligohymenophorea/*classification/genetics ; Phylogeny ; RNA, Ribosomal/chemistry/classification/genetics ; Sequence Analysis, DNA ; }, abstract = {So far, the phylogenetic studies on ciliated protists have mainly based on single locus, the nuclear ribosomal DNA (rDNA). In order to avoid the limitations of single gene/genome trees and to add more data to systematic analyses, information from mitochondrial DNA sequence has been increasingly used in different lineages of ciliates. The systematic relationships in the subclass Scuticociliatia are extremely confused and largely unresolved based on nuclear genes. In the present study, we have characterized 72 new sequences, including 40 mitochondrial cytochrome oxidase c subunit I (COI) sequences, 29 mitochondrial small subunit ribosomal DNA (mtSSU-rDNA) sequences and three nuclear small subunit ribosomal DNA (nSSU-rDNA) sequences from 47 isolates of 44 morphospecies. Phylogenetic analyses based on single gene as well as concatenated data were performed and revealed: (1) compared to mtSSU-rDNA, COI gene reveals more consistent relationships with those of nSSU-rDNA; (2) the secondary structures of mtSSU-rRNA V4 region are predicted and compared in scuticociliates, which can contribute to discrimination of closely related species; (3) neither nuclear nor mitochondrial data support the monophyly of the order Loxocephalida, which may represent some divergent and intermediate lineages between the subclass Scuticociliatia and Hymenostomatia; (4) the assignments of thigmotrichids to the order Pleuronematida and the confused taxon Sulcigera comosa to the genus Histiobalantium are confirmed by mitochondrial genes; (5) both nuclear and mitochondrial data reveal that the species in the family Peniculistomatidae always group in the genus Pleuronema, suggesting that peniculistomatids are more likely evolved from Pleuronema-like ancestors; (6) mitochondrial genes support the monophyly of the order Philasterida, but the relationships among families of the order Philasterida remain controversial due to the discrepancies between their morphological and molecular data.}, }
@article {pmid31326431, year = {2019}, author = {Fimmel, E and Strüngmann, L}, title = {Linear codes and the mitochondrial genetic code.}, journal = {Bio Systems}, volume = {184}, number = {}, pages = {103990}, doi = {10.1016/j.biosystems.2019.103990}, pmid = {31326431}, issn = {1872-8324}, mesh = {Algorithms ; Amino Acids/genetics ; Base Sequence ; Codon/*genetics ; Evolution, Molecular ; Genetic Code/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Models, Genetic ; Nucleotides/genetics ; }, abstract = {The origin of the genetic code can certainly be regarded as one of the most challenging problems in the theory of molecular evolution. Thus the known variants of the genetic code and a possible common ancestry of them haven been studied extensively in the literature. Gonzalez et al. (2012) developed the theory of a primeval mitochondrial genetic code composed of four base codons. These were called tesserae and it was shown that the tesserae code has some remarkable error detection capabilities. In our paper we will show that using classical coding theory we can construct the tessera code as a linear coding of the standard genetic code and at the same time it can be deduced from the code of all dinucleotides by Plotkin's construction. It shows that the tessera model of the mitochondrial code does not just have a biological explanation but also has a clear mathematical structure. This underlines the role that the tessera model might have played in evolution.}, }
@article {pmid31325209, year = {2020}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {The hologenome concept of evolution: do mothers matter most?.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {127}, number = {2}, pages = {129-137}, doi = {10.1111/1471-0528.15882}, pmid = {31325209}, issn = {1471-0528}, mesh = {Adaptation, Biological/genetics/*physiology ; Adaptation, Physiological/genetics/*physiology ; Adult ; Animals ; Biological Evolution ; Evolution, Molecular ; Female ; Gene Transfer, Horizontal/*genetics ; Genetic Speciation ; Genetic Variation ; Heredity ; Host Microbial Interactions/*physiology ; Humans ; Male ; Microbiota/genetics/*physiology ; *Mothers ; Plants ; Pregnancy ; }, abstract = {The hologenome concept of evolution is discussed, with special emphasis placed upon the microbiome of women. The microbiome is dynamic, changing under different conditions, and differs between women and men. Genetic variation occurs not only in the host, but also in the microbiome by the acquisition of novel microbes, the amplification of specific microbes, and horizontal gene transfer. The majority of unique genes in human holobionts are found in microbiomes, and mothers are responsible for transferring most of these to their offspring during birth, breastfeeding, and physical contact. Thus, mothers are likely to be the primary providers of the majority of genetic information to offspring via mitochondria and the microbiome. TWEETABLE ABSTRACT: Microbiomes differ between women and men. Most genes in humans are in the microbiome. Mothers transfer most of these genes to offspring.}, }
@article {pmid31323336, year = {2019}, author = {Jana, A and Karanth, P}, title = {Multilocus nuclear markers provide new insights into the origin and evolution of the blackbuck (Antilope cervicapra, Bovidae).}, journal = {Molecular phylogenetics and evolution}, volume = {139}, number = {}, pages = {106560}, doi = {10.1016/j.ympev.2019.106560}, pmid = {31323336}, issn = {1095-9513}, mesh = {Animals ; Antelopes/*classification/genetics ; *Biological Evolution ; Cell Nucleus/*genetics ; Fossils ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Evolutionary relationships between members of the Antilopina taxon have been much debated in recent years. The 'true antelope' clade is currently comprised of 4 genera viz., Gazella, Nanger, Eudorcas and the monotypic genus Antilope, that includes A. cervicapra. Most studies have focused on the mitochondrial genome or morphological data to study their relationships. However, signals from mitochondrial data can often be misleading when compared with nuclear markers, as has been shown in multiple taxonomic groups. In this study, we revisit the phylogenetic relationships among members of Antilopina, particularly the phylogenetic position of A. cervicapra, using 12 nuclear markers and compare it with the mitochondrial tree. Furthermore, we explore the implications of the results of this study on the taxonomy and biogeography of Indian antelopes. The nuclear phylogenetic trees built using multiple coalescent and concatenated methods all supported a paraphyletic genus Gazella. Antilope was nested within Gazella as opposed to being sister to it, which was suggested by previous studies and our results based on mitochondrial markers. Our fossil-calibrated larger bovid phylogeny, based on nuclear markers, suggested that the Antilope lineage diverged from its sister species more recently in the Pleistocene, rather than in late Miocene as per previous studies. Our biogeographic analyses suggest that the lineage leading to genus Antilope dispersed into India from the Saharo-Arabian realm around 2 mya, post the expansion of grasslands. We speculate that the adaptations of this savanna-grassland specialist did not allow them to extend their range beyond the Indian subcontinent. Whereas, the only other true antelope in India, G. bennetti, extended its range into India more recently, probably after the establishment of the Thar desert in northwest India.}, }
@article {pmid31319441, year = {2019}, author = {Bouchoucha, A and Waltz, F and Bonnard, G and Arrivé, M and Hammann, P and Kuhn, L and Schelcher, C and Zuber, H and Gobert, A and Giegé, P}, title = {Determination of protein-only RNase P interactome in Arabidopsis mitochondria and chloroplasts identifies a complex between PRORP1 and another NYN domain nuclease.}, journal = {The Plant journal : for cell and molecular biology}, volume = {100}, number = {3}, pages = {549-561}, doi = {10.1111/tpj.14458}, pmid = {31319441}, issn = {1365-313X}, mesh = {5' Untranslated Regions/genetics ; Arabidopsis/*enzymology/genetics ; Arabidopsis Proteins/genetics/*metabolism ; Cell Nucleus/metabolism ; Chloroplasts/enzymology ; Endonucleases/genetics/*metabolism ; Evolution, Molecular ; Mitochondria/enzymology ; Mitochondrial Proteins ; Models, Molecular ; Multiprotein Complexes ; Protein Domains ; RNA Precursors/*genetics ; *RNA Processing, Post-Transcriptional ; Ribonuclease P/genetics/*metabolism ; Ribosomes/metabolism ; }, abstract = {The essential type of endonuclease that removes 5' leader sequences from transfer RNA precursors is called RNase P. While ribonucleoprotein RNase P enzymes containing a ribozyme are found in all domains of life, another type of RNase P called 'PRORP', for 'PROtein-only RNase P', is composed of protein that occurs only in a wide variety of eukaryotes, in organelles and in the nucleus. Here, to find how PRORP functions integrate with other cell processes, we explored the protein interaction network of PRORP1 in Arabidopsis mitochondria and chloroplasts. Although PRORP proteins function as single subunit enzymes in vitro, we found that PRORP1 occurs in protein complexes and is present in high-molecular-weight fractions that contain mitochondrial ribosomes. The analysis of immunoprecipitated protein complexes identified proteins involved in organellar gene expression processes. In particular, direct interaction was established between PRORP1 and MNU2 a mitochondrial nuclease. A specific domain of MNU2 and a conserved signature of PRORP1 were found to be directly accountable for this protein interaction. Altogether, results revealed the existence of an RNA maturation complex in Arabidopsis mitochondria and suggested that PRORP proteins cooperated with other gene expression factors for RNA maturation in vivo.}, }
@article {pmid31318312, year = {2019}, author = {Rubalcava-Gracia, D and García-Rincón, J and Pérez-Montfort, R and Hamel, PP and González-Halphen, D}, title = {Key within-membrane residues and precursor dosage impact the allotopic expression of yeast subunit II of cytochrome c oxidase.}, journal = {Molecular biology of the cell}, volume = {30}, number = {18}, pages = {2358-2366}, pmid = {31318312}, issn = {1939-4586}, mesh = {Cell Nucleus/metabolism ; Cytosol/metabolism ; Electron Transport Complex IV/*genetics/metabolism ; Gene Expression Regulation, Fungal/genetics ; Genes, Mitochondrial ; Membrane Proteins/genetics ; Mitochondria/genetics/metabolism ; Mitochondrial Membrane Transport Proteins/*genetics ; Mitochondrial Proteins/metabolism ; Protein Transport ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; }, abstract = {Experimentally relocating mitochondrial genes to the nucleus for functional expression (allotopic expression) is a challenging process. The high hydrophobicity of mitochondria-encoded proteins seems to be one of the main factors preventing this allotopic expression. We focused on subunit II of cytochrome c oxidase (Cox2) to study which modifications may enable or improve its allotopic expression in yeast. Cox2 can be imported from the cytosol into mitochondria in the presence of the W56R substitution, which decreases the protein hydrophobicity and allows partial respiratory rescue of a cox2-null strain. We show that the inclusion of a positive charge is more favorable than substitutions that only decrease the hydrophobicity. We also searched for other determinants enabling allotopic expression in yeast by examining the COX2 gene in organisms where it was transferred to the nucleus during evolution. We found that naturally occurring variations at within-membrane residues in the legume Glycine max Cox2 could enable yeast COX2 allotopic expression. We also evidence that directing high doses of allotopically synthesized Cox2 to mitochondria seems to be counterproductive because the subunit aggregates at the mitochondrial surface. Our findings are relevant to the design of allotopic expression strategies and contribute to the understanding of gene retention in organellar genomes.}, }
@article {pmid31311504, year = {2019}, author = {Wang, L and Zhuang, H and Zhang, Y and Wei, W}, title = {Diversity of the Bosmina (Cladocera: Bosminidae) in China, revealed by analysis of two genetic markers (mtDNA 16S and a nuclear ITS).}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {145}, pmid = {31311504}, issn = {1471-2148}, mesh = {Animals ; Cell Nucleus/genetics ; China ; Cladocera/*genetics ; DNA, Intergenic/*genetics ; DNA, Mitochondrial/*genetics ; Ecosystem ; Genetic Markers ; *Genetic Variation ; Geography ; Haplotypes/genetics ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Zooplankton/genetics ; }, abstract = {BACKGROUND: China is an important biogeographical zone in which the genetic legacies of the Tertiary and Quaternary periods are abundant, and the contemporary geography environment plays an important role in species distribution. Therefore, many biogeographical studies have focused on the organisms of the region, especially zooplankton, which is essential in the formation of biogeographical principles. Moreover, the generality of endemism also reinforces the need for detailed regional studies of zooplankton. Bosmina, a group of cosmopolitan zooplankton, is difficult to identify by morphology, and no genetic data are available to date to assess this species complex in China. In this study, 48 waterbodies were sampled covering a large geographical and ecological range in China, the goal of this research is to explore the species distribution of Bosmina across China and to reveal the genetic information of this species complex, based on two genetic markers (a mtDNA 16S and a nuclear ITS). The diversity of taxa in the Bosmina across China was investigated using molecular tools for the first time.<br><br>RESULTS: Two main species were detected in 35 waterbodies: an endemic east Asia B. fatalis, and the B. longirostris that has a Holarctic distribution. B. fatalis had lower genetic polymorphism and population differentiation than B. longirostris. B. fatalis was preponderant in central and eastern China, whereas B. longirostris was dominated in western China. The third lineage (B. hagmanni) was only detected in a reservoir (CJR) of eastern China (Guangdong province). Bosmina had limited distribution on the Tibetan plateau.<br><br>CONCLUSIONS: This study revealed that the biogeography of Bosmina appear to be affected by historical events (Pleistocene glaciations) and contemporary environment (such as altitude, eutrophication and isolated habitat).}, }
@article {pmid31300133, year = {2019}, author = {Mirbadie, SR and Najafi Nasab, A and Mohaghegh, MA and Norouzi, P and Mirzaii, M and Spotin, A}, title = {Molecular phylodiagnosis of Echinococcus granulosus sensu lato and Taenia hydatigena determined by mitochondrial Cox1 and SSU-rDNA markers in Iranian dogs: Indicating the first record of pig strain (G7) in definitive host in the Middle East.}, journal = {Comparative immunology, microbiology and infectious diseases}, volume = {65}, number = {}, pages = {88-95}, doi = {10.1016/j.cimid.2019.05.005}, pmid = {31300133}, issn = {1878-1667}, mesh = {Animals ; Cyclooxygenase 1/genetics ; DNA, Ribosomal/genetics ; Dog Diseases/diagnosis/*epidemiology ; Dogs/parasitology ; Echinococcosis/diagnosis/epidemiology/*veterinary ; Echinococcus granulosus/genetics ; Feces/parasitology ; Genotype ; Intestinal Diseases, Parasitic/diagnosis/*veterinary ; Iran/epidemiology ; Middle East/epidemiology ; Mitochondria/genetics ; *Phylogeny ; Prevalence ; Swine/parasitology ; Taenia/genetics ; Taeniasis/diagnosis/epidemiology/*veterinary ; }, abstract = {Unawareness of canine parasitic diseases among at-risk hosts and an uncontrolled program of stray dog population have caused that zoonotic parasites received great attention in endemic regions of the Middle East. A total of 552 faecal samples were collected between December 2016 to January 2018 from stray (n = 408) and domestic (n = 144) dogs of Iran. All specimens were coproscopically observed following concentration and flotation techniques. Subsequently, the DNAs of taeniid eggs were extracted, amplified, and sequenced by targeting of mitochondrial cytochrome oxidase subunit 1 and small-subunit ribosomal DNA markers. The overall prevalence of canine intestinal parasites found 53.6%. The following parasites and their total frequencies were identified: taeniid (10.5%), Dicrocoelium dendriticum (0.7%), Trichuris vulpis (1.2%), Capillaria spp. (2.3%), Blastocystis spp. (5.2%), Ancylostoma spp. (2%), Eimeria spp. (13.2%), Dipylidium caninum (2.3%), Toxocara canis (3.8%), Giardia spp. (8.5%), and Toxascaris leonina (3.6%). Stray dogs were characterized more likely to be poliparasitized and indicated a higher prevalence of taeniid (10.9%), T. canis (4.4%) Giardia spp. (10.1%) than domestic dogs (P > 0.05). Phylogenetic and sequence analysis of Cox1 and SSU-rDNA indicated a low genetic diversity (Haplotype diversity; 0 to 0.495) in E. granulosus sensu lato G1, G3, G7 genotypes, and Taenia hydatigena. The pairwise sequence distances between G7 isolates showed an intra-diversity of 0.7%-1.5% and identity of 98.5%-100%. The first occurrence of pig strain (G7) from Iranian dogs might have substantial implications in the drug treatment of infected dogs due to the shorter maturation time of G7 compared with G1 genotype. Thus, the preventive strategies should be noticed to determine the risk factors, the importance of applying the hygienic practices, and well adjusting deworming programs for the Iranian dogs and at-risk individuals.}, }
@article {pmid31299243, year = {2020}, author = {Montava-Garriga, L and Ganley, IG}, title = {Outstanding Questions in Mitophagy: What We Do and Do Not Know.}, journal = {Journal of molecular biology}, volume = {432}, number = {1}, pages = {206-230}, doi = {10.1016/j.jmb.2019.06.032}, pmid = {31299243}, issn = {1089-8638}, support = {MC_UU_00018/2/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Autophagy/genetics ; *Biological Evolution ; Homeostasis/genetics ; Humans ; Mitochondria/*genetics ; Mitophagy/*genetics ; Signal Transduction/genetics ; }, abstract = {The elimination of mitochondria via autophagy, termed mitophagy, is an evolutionarily conserved mechanism for mitochondrial quality control and homeostasis. Mitophagy, therefore, has an important contribution to cell function and integrity, which extends to the whole organism for development and survival. Research in mitophagy has boomed in recent years, and it is becoming clear that mitophagy is a complex and multi-factorial cellular response that depends on tissue, energetic, stress and signaling contexts. However, we know very little of its physiological regulation and the direct contribution of mitophagy to pathologies like neurodegenerative diseases. In this review, we aim to discuss the outstanding questions (and questions outstanding) in the field and reflect on our current understanding of mitophagy, the current challenges and the future directions to take.}, }
@article {pmid31289699, year = {2019}, author = {Brian, JI and Davy, SK and Wilkinson, SP}, title = {Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e7178}, pmid = {31289699}, issn = {2167-8359}, abstract = {Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondrion; psbA[ncr] region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of next generation sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting or the presence of co-dominance, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.}, }
@article {pmid31286324, year = {2019}, author = {Condori-Apfata, JA and Batista-Silva, W and Medeiros, DB and Vargas, JR and Valente, LML and Heyneke, E and Pérez-Diaz, JL and Fernie, AR and Araújo, WL and Nunes-Nesi, A}, title = {The Arabidopsis E1 subunit of the 2-oxoglutarate dehydrogenase complex modulates plant growth and seed production.}, journal = {Plant molecular biology}, volume = {101}, number = {1-2}, pages = {183-202}, pmid = {31286324}, issn = {1573-5028}, support = {306818/2016-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 402511/2016-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CEX - APQ-02985-14//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; }, mesh = {Arabidopsis/*enzymology/genetics/growth &amp; development ; Arabidopsis Proteins/genetics/metabolism ; Carbon/*metabolism ; Carbon Dioxide/metabolism ; Chlorophyll/metabolism ; Ketoglutarate Dehydrogenase Complex/genetics/*metabolism ; Mitochondria/enzymology ; Mutagenesis, Insertional ; Nitrates/metabolism ; Nitrogen/*metabolism ; Phenotype ; Phylogeny ; Plant Leaves/enzymology/genetics/growth &amp; development ; Protein Isoforms ; Protein Subunits ; Seedlings/enzymology/genetics/growth &amp; development ; Seeds/enzymology/genetics/growth &amp; development ; }, abstract = {Isoforms of 2-OGDH E1 subunit are not functionally redundant in plant growth and development of A. thaliana. The tricarboxylic acid cycle enzyme 2-oxoglutarate dehydrogenase (2-OGDH) converts 2-oxoglutarate (2-OG) to succinyl-CoA concomitant with the reduction of NAD[+]. 2-OGDH has an essential role in plant metabolism, being both a limiting step during mitochondrial respiration as well as a key player in carbon-nitrogen interactions. In Arabidopsis thaliana two genes encode for E1 subunit of 2-OGDH but the physiological roles of each isoform remain unknown. Thus, in the present study we isolated Arabidopsis T-DNA insertion knockout mutant lines for each of the genes encoding the E1 subunit of 2-OGDH enzyme. All mutant plants exhibited substantial reduction in both respiration and CO2 assimilation rates. Furthermore, mutant lines exhibited reduced levels of chlorophylls and nitrate, increased levels of sucrose, malate and fumarate and minor changes in total protein and starch levels in leaves. Despite the similar metabolic phenotypes for the two E1 isoforms the reduction in the expression of each gene culminated in different responses in terms of plant growth and seed production indicating distinct roles for each isoform. Collectively, our results demonstrated the importance of the E1 subunit of 2-OGDH in both autotrophic and heterotrophic tissues and suggest that the two E1 isoforms are not functionally redundant in terms of plant growth in A. thaliana.}, }
@article {pmid31282937, year = {2019}, author = {Forsythe, ES and Sharbrough, J and Havird, JC and Warren, JM and Sloan, DB}, title = {CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis.}, journal = {Genome biology and evolution}, volume = {11}, number = {8}, pages = {2194-2202}, pmid = {31282937}, issn = {1759-6653}, mesh = {Arabidopsis/genetics/*metabolism ; Cell Nucleus/genetics/*metabolism ; Cytoplasm/genetics/*metabolism ; *Evolution, Molecular ; *Genome, Plant ; Plant Proteins/genetics/*metabolism ; Reference Standards ; }, abstract = {The function and evolution of eukaryotic cells depend upon direct molecular interactions between gene products encoded in nuclear and cytoplasmic genomes. Understanding how these cytonuclear interactions drive molecular evolution and generate genetic incompatibilities between isolated populations and species is of central importance to eukaryotic biology. Plants are an outstanding system to investigate such effects because of their two different genomic compartments present in the cytoplasm (mitochondria and plastids) and the extensive resources detailing subcellular targeting of nuclear-encoded proteins. However, the field lacks a consistent classification scheme for mitochondrial- and plastid-targeted proteins based on their molecular interactions with cytoplasmic genomes and gene products, which hinders efforts to standardize and compare results across studies. Here, we take advantage of detailed knowledge about the model angiosperm Arabidopsis thaliana to provide a curated database of plant cytonuclear interactions at the molecular level. CyMIRA (Cytonuclear Molecular Interactions Reference for Arabidopsis) is available at http://cymira.colostate.edu/ and https://github.com/dbsloan/cymira and will serve as a resource to aid researchers in partitioning evolutionary genomic data into functional gene classes based on organelle targeting and direct molecular interaction with cytoplasmic genomes and gene products. It includes 11 categories (and 27 subcategories) of different cytonuclear complexes and types of molecular interactions, and it reports residue-level information for cytonuclear contact sites. We hope that this framework will make it easier to standardize, interpret, and compare studies testing the functional and evolutionary consequences of cytonuclear interactions.}, }
@article {pmid31282925, year = {2019}, author = {McKenzie, JL and Chung, DJ and Healy, TM and Brennan, RS and Bryant, HJ and Whitehead, A and Schulte, PM}, title = {Mitochondrial Ecophysiology: Assessing the Evolutionary Forces That Shape Mitochondrial Variation.}, journal = {Integrative and comparative biology}, volume = {59}, number = {4}, pages = {925-937}, doi = {10.1093/icb/icz124}, pmid = {31282925}, issn = {1557-7023}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/*physiology ; Fundulidae/genetics/*physiology ; Genetic Speciation ; *Genome ; Genome, Mitochondrial ; Mitochondria/genetics/*physiology ; }, abstract = {The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.}, }
@article {pmid31279710, year = {2019}, author = {Parhi, J and Tripathy, PS and Priyadarshi, H and Mandal, SC and Pandey, PK}, title = {Diagnosis of mitogenome for robust phylogeny: A case of Cypriniformes fish group.}, journal = {Gene}, volume = {713}, number = {}, pages = {143967}, doi = {10.1016/j.gene.2019.143967}, pmid = {31279710}, issn = {1879-0038}, mesh = {Animals ; Cypriniformes/*genetics ; *Genes, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Phylogenetic tree using mitochondrial genes and nuclear genes have long been used for augmenting biological classification and understanding evolutionary processes in different lineage of life. But a basic question still exists for finding the most suitable gene for constructing robust phylogenetic tree. Much of the controversy appears due to monophyletic, paraphyletic and polyphyletic clade making deviations from original taxonomy. In the present study we report the first complete mitochondrial genome (mitogenome) of queen loach, generated through next-generation sequencing methods. The assembled mitogenome is a 16,492 bp circular DNA, comprising of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. Further in this study we also investigated the suitability of different mitochondrial region for phylogenetic analysis in Cyprinidae and loach group. For this genetic tree were constructed on COI, COII, COIII, 16S rRNA, 12S rRNA, Cyt b, ATPase 6, D-loop, ND1, ND2, ND3, ND4, ND5, and ND6 along with complete mitogenome. The complete mitogenome based phylogenetic tree got inclusive support from available classical taxonomy for these groups. On individual gene basis Cyt b, 12S rRNA, ND2 and ND3 also produced perfect clade at family and subfamily level. For rest of the genes polyphyly were observed for the fishes belonging to same family or subfamily which makes their use questionable for phylogenetic tree construction.}, }
@article {pmid31278983, year = {2019}, author = {Taylor, RS and Bolton, M and Beard, A and Birt, T and Deane-Coe, P and Raine, AF and González-Solís, J and Lougheed, SC and Friesen, VL}, title = {Cryptic species and independent origins of allochronic populations within a seabird species complex (Hydrobates spp.).}, journal = {Molecular phylogenetics and evolution}, volume = {139}, number = {}, pages = {106552}, doi = {10.1016/j.ympev.2019.106552}, pmid = {31278983}, issn = {1095-9513}, mesh = {Animals ; Atlantic Ocean ; Bayes Theorem ; Biodiversity ; Breeding ; Charadriiformes/*classification/genetics ; DNA, Mitochondrial/genetics ; Gene Flow ; Genetics, Population ; Geography ; Likelihood Functions ; Mitochondria/genetics ; Pacific Ocean ; *Phylogeny ; Principal Component Analysis ; Species Specificity ; }, abstract = {Humans are inherently biased towards naming species based on morphological differences, which can lead to reproductively isolated species being mistakenly classified as one if they are morphologically similar. Recognising cryptic diversity is needed to understand drivers of speciation fully, and for accurate estimates of global biodiversity and assessments for conservation. We investigated cryptic species across the range of band-rumped storm-petrels (Hydrobates spp.): highly pelagic, nocturnal seabirds that breed on tropical and sub-tropical islands in the Atlantic and Pacific Oceans. In many breeding colonies, band-rumped storm-petrels have sympatric but temporally isolated (allochronic) populations; we sampled all breeding locations and allochronic populations. Using mitochondrial control region sequences from 754 birds, cytochrome b sequences from 69 birds, and reduced representation sequencing of the nuclear genomes of 133 birds, we uncovered high levels of genetic structuring. Population genomic analyses revealed up to seven unique clusters, and phylogenomic reconstruction showed that these represent seven monophyletic groups. We uncovered up to six independent breeding season switches across the phylogeny, spanning the continuum from genetically undifferentiated temporal populations to full allochronic species. Thus, band-rumped storm-petrels encompass multiple cryptic species, with non-geographic barriers potentially comprising strong barriers to gene flow.}, }
@article {pmid31264965, year = {2019}, author = {Zarin, T and Strome, B and Nguyen Ba, AN and Alberti, S and Forman-Kay, JD and Moses, AM}, title = {Proteome-wide signatures of function in highly diverged intrinsically disordered regions.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31264965}, issn = {2050-084X}, support = {Alexander Graham Bell Scholarship//Natural Sciences and Engineering Research Council of Canada/International ; Discovery Grant//Natural Sciences and Engineering Research Council of Canada/International ; PJT-148532//CIHR/Canada ; FDN-148375//CIHR/Canada ; Postdoctoral Fellowship//Natural Sciences and Engineering Research Council of Canada/International ; Alexander Graham Bell Scholarship//National Sciences and Engineering Research Council/International ; Discovery Grant//National Sciences and Engineering Research Council/International ; }, mesh = {Amino Acid Sequence ; DNA Repair ; Evolution, Molecular ; Gene Ontology ; Intrinsically Disordered Proteins/chemistry/*metabolism ; Mitochondria/metabolism ; Molecular Sequence Annotation ; Protein Sorting Signals ; Proteome/chemistry/*metabolism ; Saccharomyces cerevisiae/metabolism ; }, abstract = {Intrinsically disordered regions make up a large part of the proteome, but the sequence-to-function relationship in these regions is poorly understood, in part because the primary amino acid sequences of these regions are poorly conserved in alignments. Here we use an evolutionary approach to detect molecular features that are preserved in the amino acid sequences of orthologous intrinsically disordered regions. We find that most disordered regions contain multiple molecular features that are preserved, and we define these as 'evolutionary signatures' of disordered regions. We demonstrate that intrinsically disordered regions with similar evolutionary signatures can rescue function in vivo, and that groups of intrinsically disordered regions with similar evolutionary signatures are strongly enriched for functional annotations and phenotypes. We propose that evolutionary signatures can be used to predict function for many disordered regions from their amino acid sequences.}, }
@article {pmid31257129, year = {2019}, author = {Wein, T and Romero Picazo, D and Blow, F and Woehle, C and Jami, E and Reusch, TBH and Martin, WF and Dagan, T}, title = {Currency, Exchange, and Inheritance in the Evolution of Symbiosis.}, journal = {Trends in microbiology}, volume = {27}, number = {10}, pages = {836-849}, doi = {10.1016/j.tim.2019.05.010}, pmid = {31257129}, issn = {1878-4380}, mesh = {*Biological Evolution ; Chloroplasts ; *Eukaryota ; Host Microbial Interactions/physiology ; Mitochondria ; *Organelles ; *Symbiosis ; *Wills ; }, abstract = {Symbiotic interactions between eukaryotes and prokaryotes are widespread in nature. Here we offer a conceptual framework to study the evolutionary origins and ecological circumstances of species in beneficial symbiosis. We posit that mutual symbiotic interactions are well described by three elements: a currency, the mechanism of currency exchange, and mechanisms of symbiont inheritance. Each of these elements may be at the origin of symbiosis, with the other elements developing with time. The identity of currency in symbiosis depends on the ecological context of the symbiosis, while the specificity of the exchange mechanism underlies molecular adaptations for the symbiosis. The inheritance regime determines the degree of partner dependency and the symbiosis evolutionary trajectory. Focusing on these three elements, we review examples and open questions in the research on symbiosis.}, }
@article {pmid31257025, year = {2019}, author = {Cui, R and Medeiros, T and Willemsen, D and Iasi, LNM and Collier, GE and Graef, M and Reichard, M and Valenzano, DR}, title = {Relaxed Selection Limits Lifespan by Increasing Mutation Load.}, journal = {Cell}, volume = {178}, number = {2}, pages = {385-399.e20}, doi = {10.1016/j.cell.2019.06.004}, pmid = {31257025}, issn = {1097-4172}, mesh = {Aging ; Animals ; DNA Replication ; Evolution, Molecular ; Gene Frequency ; Genome, Mitochondrial ; Killifishes/classification/genetics ; *Longevity ; Mitochondria/genetics/metabolism ; Mutation ; Phylogeny ; Phylogeography ; *Selection, Genetic ; }, abstract = {To uncover the selective forces shaping life-history trait evolution across species, we investigate the genomic basis underlying adaptations to seasonal habitat desiccation in African killifishes, identifying the genetic variants associated with positive and relaxed purifying selection in 45 killifish species and 231 wild individuals distributed throughout sub-Saharan Africa. In annual species, genetic drift led to the expansion of nuclear and mitochondrial genomes and caused the accumulation of deleterious genetic variants in key life-history modulating genes such as mtor, insr, ampk, foxo3, and polg. Relaxation of purifying selection is also significantly associated with mitochondrial function and aging in human populations. We find that relaxation of purifying selection prominently shapes genomes and is a prime candidate force molding the evolution of lifespan and the distribution of genetic variants associated with late-onset diseases in different species. VIDEO ABSTRACT.}, }
@article {pmid31254562, year = {2019}, author = {Chen, J and Gong, Y and Zheng, H and Ma, H and Aweya, JJ and Zhang, Y and Chen, X and Li, SK}, title = {SpBcl2 promotes WSSV infection by suppressing apoptotic activity of hemocytes in mud crab, Scylla paramamosain.}, journal = {Developmental and comparative immunology}, volume = {100}, number = {}, pages = {103421}, doi = {10.1016/j.dci.2019.103421}, pmid = {31254562}, issn = {1879-0089}, mesh = {Animals ; Apoptosis/immunology ; Aquaculture ; Arthropod Proteins/immunology/*metabolism ; Brachyura/*immunology/virology ; Cytochromes c/immunology/metabolism ; Disease Resistance/immunology ; Gene Expression Profiling ; Hemocytes/cytology/immunology/pathology ; *Immunity, Innate ; Mitochondria/immunology/metabolism ; Phylogeny ; Proto-Oncogene Proteins c-bcl-2/immunology/*metabolism ; Up-Regulation/immunology ; White spot syndrome virus 1/*immunology ; }, abstract = {White spot syndrome virus (WSSV) is one of the most virulent and widespread pathogens that infect almost all marine crustaceans and therefore cause huge economic losses in aquaculture. The Bcl2 protein plays a key role in the mitochondrial apoptosis pathway, which is a crucial immune response in invertebrates. However, the role of Bcl2 in apoptosis and immunoregulation in mud crab, Scylla paramamosain, is poorly understood. Here, the Bcl2 homolog (SpBcl2) in S. paramamosain was cloned and its role in WSSV infection explored. The expression of SpBcl2 increased at both the transcriptional level and post-transcriptional level after WSSV infection, while the hemocytes apoptosis decreased significantly. Furthermore, there was increase in the level of cytochrome c coupled with an upregulation in the expression of SpBcl2. These results indicated that SpBcl2 suppressed apoptosis by preventing the release of cytochrome c from mitochondria, thereby promoting WSSV replication in mud crab. The findings here therefore provide novel insight into the immune response of mud crabs to WSSV infection.}, }
@article {pmid31253641, year = {2019}, author = {Aryaman, J and Bowles, C and Jones, NS and Johnston, IG}, title = {Mitochondrial Network State Scales mtDNA Genetic Dynamics.}, journal = {Genetics}, volume = {212}, number = {4}, pages = {1429-1443}, pmid = {31253641}, issn = {1943-2631}, support = {BB/J014575/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_UP_1501/2/MRC_/Medical Research Council/United Kingdom ; RE/13/2/30182/BHF_/British Heart Foundation/United Kingdom ; }, mesh = {DNA, Mitochondrial/*genetics ; *Genetic Variation ; Humans ; *Mitochondrial Dynamics ; *Models, Genetic ; *Mutation ; Selection, Genetic ; }, abstract = {Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. mtDNA is stochastically replicated and degraded, and exists within organelles which undergo dynamic fusion and fission. The role of the resulting mitochondrial networks in the time evolution of the cellular proportion of mutated mtDNA molecules (heteroplasmy), and cell-to-cell variability in heteroplasmy (heteroplasmy variance), remains incompletely understood. Heteroplasmy variance is particularly important since it modulates the number of pathological cells in a tissue. Here, we provide the first wide-reaching theoretical framework which bridges mitochondrial network and genetic states. We show that, under a range of conditions, the (genetic) rate of increase in heteroplasmy variance and de novo mutation are proportionally modulated by the (physical) fraction of unfused mitochondria, independently of the absolute fission-fusion rate. In the context of selective fusion, we show that intermediate fusion:fission ratios are optimal for the clearance of mtDNA mutants. Our findings imply that modulating network state, mitophagy rate, and copy number to slow down heteroplasmy dynamics when mean heteroplasmy is low could have therapeutic advantages for mitochondrial disease and healthy aging.}, }
@article {pmid31249872, year = {2019}, author = {Peyrégne, S and Slon, V and Mafessoni, F and de Filippo, C and Hajdinjak, M and Nagel, S and Nickel, B and Essel, E and Le Cabec, A and Wehrberger, K and Conard, NJ and Kind, CJ and Posth, C and Krause, J and Abrams, G and Bonjean, D and Di Modica, K and Toussaint, M and Kelso, J and Meyer, M and Pääbo, S and Prüfer, K}, title = {Nuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe.}, journal = {Science advances}, volume = {5}, number = {6}, pages = {eaaw5873}, pmid = {31249872}, issn = {2375-2548}, support = {694707/ERC_/European Research Council/International ; }, mesh = {Animals ; Cell Lineage/genetics ; Cell Nucleus/*genetics ; DNA/*genetics ; Europe ; Evolution, Molecular ; Fossils ; Genome/genetics ; Germany ; Mitochondria/genetics ; Neanderthals/*genetics ; }, abstract = {Little is known about the population history of Neandertals over the hundreds of thousands of years of their existence. We retrieved nuclear genomic sequences from two Neandertals, one from Hohlenstein-Stadel Cave in Germany and the other from Scladina Cave in Belgium, who lived around 120,000 years ago. Despite the deeply divergent mitochondrial lineage present in the former individual, both Neandertals are genetically closer to later Neandertals from Europe than to a roughly contemporaneous individual from Siberia. That the Hohlenstein-Stadel and Scladina individuals lived around the time of their most recent common ancestor with later Neandertals suggests that all later Neandertals trace at least part of their ancestry back to these early European Neandertals.}, }
@article {pmid31248014, year = {2019}, author = {Levitskii, S and Baleva, MV and Chicherin, I and Krasheninnikov, IA and Kamenski, P}, title = {S. cerevisiae Strain Lacking Mitochondrial IF3 Shows Increased Levels of Tma19p during Adaptation to Respiratory Growth.}, journal = {Cells}, volume = {8}, number = {7}, pages = {}, pmid = {31248014}, issn = {2073-4409}, mesh = {*Adaptation, Physiological ; Calcium-Binding Proteins ; Electron Transport Complex IV/metabolism ; Eukaryotic Initiation Factors/*genetics/metabolism ; Gene Deletion ; Gene Expression Regulation, Fungal/physiology ; Genes, Mitochondrial/genetics ; Glycolysis/physiology ; Mitochondria/genetics/*metabolism ; Oxidative Stress/physiology ; Protein Biosynthesis/physiology ; Saccharomyces cerevisiae/*physiology ; Saccharomyces cerevisiae Proteins/*genetics/*metabolism ; }, abstract = {After billions of years of evolution, mitochondrion retains its own genome, which gets expressed in mitochondrial matrix. Mitochondrial translation machinery rather differs from modern bacterial and eukaryotic cytosolic systems. Any disturbance in mitochondrial translation drastically impairs mitochondrial function. In budding yeast Saccharomyces cerevisiae, deletion of the gene coding for mitochondrial translation initiation factor 3 - AIM23, leads to an imbalance in mitochondrial protein synthesis and significantly delays growth after shifting from fermentable to non-fermentable carbon sources. Molecular mechanism underlying this adaptation to respiratory growth was unknown. Here, we demonstrate that slow adaptation from glycolysis to respiration in the absence of Aim23p is accompanied by a gradual increase of cytochrome c oxidase activity and by increased levels of Tma19p protein, which protects mitochondria from oxidative stress.}, }
@article {pmid31247505, year = {2019}, author = {Breda, CNS and Davanzo, GG and Basso, PJ and Saraiva Câmara, NO and Moraes-Vieira, PMM}, title = {Mitochondria as central hub of the immune system.}, journal = {Redox biology}, volume = {26}, number = {}, pages = {101255}, pmid = {31247505}, issn = {2213-2317}, mesh = {*Adaptive Immunity ; Animals ; Dendritic Cells/immunology/metabolism ; Glycolysis/immunology ; Humans ; Immune System/*physiology ; *Immunity, Innate ; Inflammasomes/immunology/metabolism ; Lymphocytes/immunology/metabolism ; Macrophages/immunology/metabolism ; Mitochondria/*immunology/metabolism ; Mitochondrial Dynamics/*immunology ; Mitophagy/*immunology ; Neutrophils/immunology/metabolism ; Oxidation-Reduction ; Oxidative Phosphorylation ; }, abstract = {Nearly 130 years after the first insights into the existence of mitochondria, new rolesassociated with these organelles continue to emerge. As essential hubs that dictate cell fate, mitochondria integrate cell physiology, signaling pathways and metabolism. Thus, recent research has focused on understanding how these multifaceted functions can be used to improve inflammatory responses and prevent cellular dysfunction. Here, we describe the role of mitochondria on the development and function of immune cells, highlighting metabolic aspects and pointing out some metabolic- independent features of mitochondria that sustain cell function.}, }
@article {pmid31247339, year = {2019}, author = {Laurimäe, T and Kinkar, L and Romig, T and Umhang, G and Casulli, A and Omer, RA and Sharbatkhori, M and Mirhendi, H and Ponce-Gordo, F and Lazzarini, LE and Soriano, SV and Varcasia, A and Rostami-Nejad, M and Andresiuk, V and Maravilla, P and González, LM and Dybicz, M and Gawor, J and Šarkūnas, M and Šnábel, V and Kuzmina, T and Kia, EB and Saarma, U}, title = {Analysis of nad2 and nad5 enables reliable identification of genotypes G6 and G7 within the species complex Echinococcus granulosus sensu lato.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {74}, number = {}, pages = {103941}, doi = {10.1016/j.meegid.2019.103941}, pmid = {31247339}, issn = {1567-7257}, mesh = {Animals ; Echinococcus granulosus/*classification/genetics ; Genotyping Techniques/*methods ; Helminth Proteins/*genetics ; Mitochondria/genetics ; Multilocus Sequence Typing ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The larval stages of tapeworms in the species complex Echinococcus granulosus sensu lato cause a zoonotic disease known as cystic echinococcosis (CE). Within this species complex, genotypes G6 and G7 are among the most common genotypes associated with human CE cases worldwide. However, our understanding of ecology, biology and epidemiology of G6 and G7 is still limited. An essential first step towards this goal is correct genotype identification, but distinguishing genotypes G6 and G7 has been challenging. A recent analysis based on complete mitogenome data revealed that the conventional sequencing of the cox1 (366 bp) gene fragment mistakenly classified a subset of G7 samples as G6. On the other hand, sequencing complete mitogenomes is not practical if only genotype or haplogroup identification is needed. Therefore, a simpler and less costly method is required to distinguish genotypes G6 and G7. We compared 93 complete mitogenomes of G6 and G7 from a wide geographical range and demonstrate that a combination of nad2 (714 bp) and nad5 (680 bp) gene fragments would be the best option to distinguish G6 and G7. Moreover, this method allows assignment of G7 samples into haplogroups G7a and G7b. However, due to very high genetic variability of G6 and G7, we suggest to construct a phylogenetic network based on the nad2 and nad5 sequences in order to be absolutely sure in genotype assignment. For this we provide a reference dataset of 93 concatenated nad2 and nad5 sequences (1394 bp in total) containing representatives of G6 and G7 (and haplogroups G7a and G7b), which can be used for the reconstruction of phylogenetic networks.}, }
@article {pmid31242450, year = {2019}, author = {Roy, P and Rout, AK and Maharana, J and Sahoo, DR and Panda, SP and Pal, A and Nayak, KK and Behera, BK and Das, BK}, title = {Molecular characterization, constitutive expression and GTP binding mechanism of Cirrhinus mrigala (Hamilton, 1822) Myxovirus resistance (Mx) protein.}, journal = {International journal of biological macromolecules}, volume = {136}, number = {}, pages = {1258-1272}, doi = {10.1016/j.ijbiomac.2019.06.161}, pmid = {31242450}, issn = {1879-0003}, mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Cypriniformes/*genetics ; DNA, Complementary/genetics ; Fish Proteins/chemistry/*genetics/*metabolism ; *Gene Expression Regulation ; Guanosine Triphosphate/*metabolism ; Kinetics ; Molecular Dynamics Simulation ; Myxovirus Resistance Proteins/chemistry/*genetics/*metabolism ; Phylogeny ; Protein Binding ; Protein Domains ; Protein Stability ; RNA, Messenger/genetics ; Thermodynamics ; }, abstract = {Myxovirus resistance (Mx) proteins represents the subclass of the dynamin superfamily of large Guanosine triphosphates (GTPases), play esential role in intracellular vesicle trafficking, endocytosis, organelle homeostasis and mitochondria distribution. These proteins are key players of the vertebrate immune system, induced by type-I and type-III interferons (IFN) of infected host and inhibit viral replication by sequestering its nucleoprotein. In the present study, we report the sequencing and characterization of Cirrhinus mrigala Mx protein (CmMx) for the first time and observed its constitutive expression in different tissues for a period of fourteen days. The synthetic peptide, LSGVALPRGTGI, was dissolved in PBS and injected into a rabbit and the antibody raised against CmMx was used to study the level of its expression. The full length of the CmMx cDNA is 2244 bp with a molecular mass of 70.9 kDa and a predicted isoelectric point of 8.25. The 627 amino acids polypeptide formed of three main functional domains: N-terminal GTPase domain (GD), a middle domain (MD) and GTPase effector domain (GED) with carboxy terminal leucine zipper motif. The 3D models of CmMx protein was modeled based on available close structural homologs and further validated through molecular dynamics (MD) simulations. MD study revealed the importance of G-domain responsible for recognition of GTP, which perfectly corroborate with earlier studies. MM/PBSA binding free energy analysis displayed that van der Waals and electrostatic energy were the key driving force behind molecular recognition of GTP by CmMx protein. The results from this study will illuminate more lights into the ongoing research on myxovirus resistance protein and its role in inhibition of viral replication in other eukaryotic system as well.}, }
@article {pmid31239554, year = {2019}, author = {Ågren, JA and Davies, NG and Foster, KR}, title = {Enforcement is central to the evolution of cooperation.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {7}, pages = {1018-1029}, doi = {10.1038/s41559-019-0907-1}, pmid = {31239554}, issn = {2397-334X}, support = {209397/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Biological Evolution ; *Cooperative Behavior ; Humans ; Symbiosis ; }, abstract = {Cooperation occurs at all levels of life, from genomes, complex cells and multicellular organisms to societies and mutualisms between species. A major question for evolutionary biology is what these diverse systems have in common. Here, we review the full breadth of cooperative systems and find that they frequently rely on enforcement mechanisms that suppress selfish behaviour. We discuss many examples, including the suppression of transposable elements, uniparental inheritance of mitochondria and plastids, anti-cancer mechanisms, reciprocation and punishment in humans and other vertebrates, policing in eusocial insects and partner choice in mutualisms between species. To address a lack of accompanying theory, we develop a series of evolutionary models that show that the enforcement of cooperation is widely predicted. We argue that enforcement is an underappreciated, and often critical, ingredient for cooperation across all scales of biological organization.}, }
@article {pmid31239372, year = {2019}, author = {Sun, N and Parrish, RS and Calderone, RA and Fonzi, WA}, title = {Unique, Diverged, and Conserved Mitochondrial Functions Influencing Candida albicans Respiration.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, pmid = {31239372}, issn = {2150-7511}, mesh = {Candida albicans/genetics/*metabolism ; Electron Transport Complex I/*genetics ; Gene Deletion ; Gene Expression Regulation, Fungal ; *Genes, Fungal ; Mitochondria/*metabolism ; Mitochondrial Proteins/*genetics ; Virulence/genetics ; }, abstract = {Candida albicans is an opportunistic fungal pathogen of major clinical concern. The virulence of this pathogen is intimately intertwined with its metabolism. Mitochondria, which have a central metabolic role, have undergone many lineage-specific adaptations in association with their eukaryotic host. A screen for lineage-specific genes identified seven such genes specific to the CTG clade of fungi, of which C. albicans is a member. Each is required for respiratory growth and is integral to expression of complex I, III, or IV of the electron transport chain. Two genes, NUO3 and NUO4, encode supernumerary subunits of complex I, whereas NUE1 and NUE2 have nonstructural roles in expression of complex I. Similarly, the other three genes have nonstructural roles in expression of complex III (QCE1) or complex IV (COE1 and COE2). In addition to these novel additions, an alternative functional assignment was found for the mitochondrial protein encoded by MNE1MNE1 was required for complex I expression in C. albicans, whereas the distantly related Saccharomyces cerevisiae ortholog participates in expression of complex III. Phenotypic analysis of deletion mutants showed that fermentative metabolism is unable to support optimal growth rates or yields of C. albicans However, yeast-hypha morphogenesis, an important virulence attribute, did not require respiratory metabolism under hypoxic conditions. The inability to respire also resulted in hypersensitivity to the antifungal fluconazole and in attenuated virulence in a Galleria mellonella infection model. The results show that lineage-specific adaptations have occurred in C. albicans mitochondria and highlight the significance of respiratory metabolism in the pathobiology of C. albicansIMPORTANCECandida albicans is an opportunistic fungal pathogen of major clinical concern. The virulence of this pathogen is intimately intertwined with its metabolic behavior, and mitochondria have a central role in that metabolism. Mitochondria have undergone many evolutionary changes, which include lineage-specific adaptations in association with their eukaryotic host. Seven lineage-specific genes required for electron transport chain function were identified in the CTG clade of fungi, of which C. albicans is a member. Additionally, examination of several highly diverged orthologs encoding mitochondrial proteins demonstrated functional reassignment for one of these. Deficits imparted by deletion of these genes revealed the critical role of respiration in virulence attributes of the fungus and highlight important evolutionary adaptations in C. albicans metabolism.}, }
@article {pmid31234590, year = {2019}, author = {Jiang, Z and Watanabe, CKA and Miyagi, A and Kawai-Yamada, M and Terashima, I and Noguchi, K}, title = {Mitochondrial AOX Supports Redox Balance of Photosynthetic Electron Transport, Primary Metabolite Balance, and Growth in Arabidopsis thaliana under High Light.}, journal = {International journal of molecular sciences}, volume = {20}, number = {12}, pages = {}, pmid = {31234590}, issn = {1422-0067}, support = {21114007, 17H05729//Ministry of Education, Culture, Sports, Science and Technology/ ; AL65D21010//Core Research for Evolutional Science and Technology/ ; }, mesh = {Arabidopsis/*physiology/*radiation effects ; Biomarkers ; *Electron Transport ; Energy Metabolism ; Gene Expression Regulation ; *Light ; Mitochondria/*metabolism/*radiation effects ; Mitochondrial Proteins/*metabolism ; *Oxidation-Reduction ; Oxidoreductases/*metabolism ; Photosynthesis/*radiation effects ; Plant Proteins/*metabolism ; }, abstract = {When leaves receive excess light energy, excess reductants accumulate in chloroplasts. It is suggested that some of the reductants are oxidized by the mitochondrial respiratory chain. Alternative oxidase (AOX), a non-energy conserving terminal oxidase, was upregulated in the photosynthetic mutant of Arabidopsis thaliana, pgr5, which accumulated reductants in chloroplast stroma. AOX is suggested to have an important role in dissipating reductants under high light (HL) conditions, but its physiological importance and underlying mechanisms are not yet known. Here, we compared wild-type (WT), pgr5, and a double mutant of AOX1a-knockout plant (aox1a) and pgr5 (aox1a/pgr5) grown under high- and low-light conditions, and conducted physiological analyses. The net assimilation rate (NAR) was lower in aox1a/pgr5 than that in the other genotypes at the early growth stage, while the leaf area ratio was higher in aox1a/pgr5. We assessed detailed mechanisms in relation to NAR. In aox1a/pgr5, photosystem II parameters decreased under HL, whereas respiratory O2 uptake rates increased. Some intermediates in the tricarboxylic acid (TCA) cycle and Calvin cycle decreased in aox1a/pgr5, whereas γ-aminobutyric acid (GABA) and N-rich amino acids increased in aox1a/pgr5. Under HL, AOX may have an important role in dissipating excess reductants to prevent the reduction of photosynthetic electron transport and imbalance in primary metabolite levels.}, }
@article {pmid31234402, year = {2019}, author = {Emelyantsev, S and Prazdnova, E and Chistyakov, V and Alperovich, I}, title = {Biological Effects of C60 Fullerene Revealed with Bacterial Biosensor-Toxic or Rather Antioxidant?.}, journal = {Biosensors}, volume = {9}, number = {2}, pages = {}, pmid = {31234402}, issn = {2079-6374}, support = {16-32-60077 mol_&#x430;_dk//Russian Foundation for Basic Research/ ; }, mesh = {Antioxidants/*pharmacology/toxicity ; Biosensing Techniques/methods ; Escherichia coli/drug effects/metabolism ; Fullerenes/*pharmacology/toxicity ; Hydrogen Peroxide/metabolism ; Nanoparticles/toxicity ; Oxidative Stress/drug effects ; }, abstract = {Nanoparticles have been attracting growing interest for both their antioxidant and toxic effects. Their exact action on cells strongly depends on many factors, including experimental conditions, preparation, and solvents used, which have contributed to the confusion regarding their safety and possible health benefits. In order to clarify the biological effects of the most abundant fullerene C60, its impact on the Escherichia coli model has been studied. The main question was if C60 would have any antioxidant influence on the cell and, if yes, whether and to which extent it would be concentration-dependent. An oxidative stress induced by adding hydrogen peroxide was measured with an E. coli MG1655 pKatG-lux strain sensor, with its time evolution being recorded in the presence of fullerene C60 suspensions of different concentrations. Optimal conditions for the fullerene C60 solubilization in TWEEN 80 2% aqueous solution, together with resulting aggregate sizes, were determined. Results obtained for the bacterial model can be extrapolated on eukaryote mitochondria. The ability of C60 to penetrate through biological membranes, conduct protons, and interact with free radicals is likely responsible for its protective effect detected for E. coli. Thus, fullerene can be considered as a mitochondria-targeted antioxidant, worth further researching as a prospective component of novel medications.}, }
@article {pmid31234016, year = {2019}, author = {Cobley, JN and Noble, A and Jimenez-Fernandez, E and Valdivia Moya, MT and Guille, M and Husi, H}, title = {Catalyst-free Click PEGylation reveals substantial mitochondrial ATP synthase sub-unit alpha oxidation before and after fertilisation.}, journal = {Redox biology}, volume = {26}, number = {}, pages = {101258}, pmid = {31234016}, issn = {2213-2317}, support = {/WT_/Wellcome Trust/United Kingdom ; 212942/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; BB/R014841/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adenosine Triphosphate/biosynthesis ; Amino Acid Sequence ; Animals ; Click Chemistry/*methods ; Disulfides/chemistry ; Embryo, Nonmammalian ; Female ; Fertilization in Vitro ; Glutathione/metabolism ; Heterocyclic Compounds, 1-Ring/chemistry ; Male ; Mitochondria/*chemistry/enzymology ; Mitochondrial Proton-Translocating ATPases/*chemistry/metabolism ; Ovum/*chemistry/cytology/enzymology ; Oxidation-Reduction ; Phylogeny ; Polyethylene Glycols/*chemistry ; *Protein Processing, Post-Translational ; Protein Subunits/*chemistry/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sulfhydryl Compounds/chemistry/metabolism ; Xenopus laevis/classification/embryology/metabolism ; }, abstract = {Using non-reducing Western blotting to assess protein thiol redox state is challenging because most reduced and oxidised forms migrate at the same molecular weight and are, therefore, indistinguishable. While copper catalysed Click chemistry can be used to ligate a polyethylene glycol (PEG) moiety termed Click PEGylation to mass shift the reduced or oxidised form as desired, the potential for copper catalysed auto-oxidation is problematic. Here we define a catalyst-free trans-cyclooctene-methyltetrazine (TCO-Tz) inverse electron demand Diels Alder chemistry approach that affords rapid (k ~2000 M[-1] s[-1]), selective and bio-orthogonal Click PEGylation. We used TCO-Tz Click PEGylation to investigate how fertilisation impacts reversible mitochondrial ATP synthase F1-Fo sub-unit alpha (ATP-α-F1) oxidation-an established molecular correlate of impaired enzyme activity-in Xenopus laevis. TCO-Tz Click PEGylation studies reveal substantial (~65%) reversible ATP-α-F1 oxidation at evolutionary conserved cysteine residues (i.e., C[244] and C[294]) before and after fertilisation. A single thiol is, however, preferentially oxidised likely due to greater solvent exposure during the catalytic cycle. Selective reduction experiments show that: S-glutathionylation accounts for ~50-60% of the reversible oxidation observed, making it the dominant oxidative modification type. Intermolecular disulphide bonds may also contribute due to their relative stability. Substantial reversible ATP-α-F1 oxidation before and after fertilisation is biologically meaningful because it implies low mitochondrial F1-Fo ATP synthase activity. Catalyst-free TCO-Tz Click PEGylation is a valuable new tool to interrogate protein thiol redox state in health and disease.}, }
@article {pmid31233800, year = {2019}, author = {Bodensohn, US and Simm, S and Fischer, K and Jäschke, M and Groß, LE and Kramer, K and Ehmann, C and Rensing, SA and Ladig, R and Schleiff, E}, title = {The intracellular distribution of the components of the GET system in vascular plants.}, journal = {Biochimica et biophysica acta. Molecular cell research}, volume = {1866}, number = {10}, pages = {1650-1662}, doi = {10.1016/j.bbamcr.2019.06.012}, pmid = {31233800}, issn = {1879-2596}, mesh = {Adenosine Triphosphatases ; Arabidopsis/metabolism ; Bryopsida/metabolism ; Chloroplasts ; Cytoplasm/metabolism ; Cytosol/*metabolism ; Embryophyta ; Endoplasmic Reticulum/metabolism ; Green Fluorescent Proteins ; Guanine Nucleotide Exchange Factors ; Solanum lycopersicum/metabolism ; Membrane Proteins/genetics/*metabolism ; Mitochondria/metabolism ; Phylogeny ; Plant Proteins/*metabolism ; Plants/*metabolism ; Protein Transport/*physiology ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins ; Seedlings ; }, abstract = {The guided entry of tail-anchored proteins (GET) pathway facilitates targeting and insertion of tail-anchored proteins into membranes. In plants, such a protein insertion machinery for the endoplasmic reticulum as well as constituents within mitochondrial and chloroplasts were discovered. Previous phylogenetic analysis revealed that Get3 sequences of Embryophyta form two clades representing cytosolic ("a") and organellar ("bc") GET3 homologs, respectively. Cellular fractionation of Arabidopsis thaliana seedlings and usage of the self-assembly GFP system in protoplasts verified the cytosolic (ATGet3a), plastidic (ATGet3b) and mitochondrial (ATGet3c) localization of the different homologs. The identified plant homologs of Get1 and Get4 in A. thaliana are localized in ER and cytosol, respectively, implicating a degree of conservation of the GET pathway in A. thaliana. Transient expression of Get3 homologs of Solanum lycopersicum, Medicago × varia or Physcomitrella patens with the self-assembly GFP technique in homologous and heterologous systems verified that multiple Get3 homologs with differing subcellular localizations are common in plants. Chloroplast localized Get3 homologs were detected in all tested plant systems. In contrast, mitochondrial localized Get3 homologs were not identified in S. lycopersicum, or P. patens, while we confirmed on the example of A. thaliana proteins that mitochondrial localized Get3 proteins are properly targeted in S. lycopersicum as well.}, }
@article {pmid31233646, year = {2019}, author = {Hinojosa, JC and Koubínová, D and Szenteczki, MA and Pitteloud, C and Dincă, V and Alvarez, N and Vila, R}, title = {A mirage of cryptic species: Genomics uncover striking mitonuclear discordance in the butterfly Thymelicus sylvestris.}, journal = {Molecular ecology}, volume = {28}, number = {17}, pages = {3857-3868}, doi = {10.1111/mec.15153}, pmid = {31233646}, issn = {1365-294X}, mesh = {Animals ; Bayes Theorem ; Butterflies/*genetics ; Cell Nucleus/*genetics ; Electron Transport Complex IV/genetics ; Genetic Loci ; *Genomics ; Likelihood Functions ; Mitochondria/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Species Specificity ; }, abstract = {Mitochondrial DNA (mtDNA) sequencing has led to an unprecedented rise in the identification of cryptic species. However, it is widely acknowledged that nuclear DNA (nuDNA) sequence data are also necessary to properly define species boundaries. Next generation sequencing techniques provide a wealth of nuclear genomic data, which can be used to ascertain both the evolutionary history and taxonomic status of putative cryptic species. Here, we focus on the intriguing case of the butterfly Thymelicus sylvestris (Lepidoptera: Hesperiidae). We identified six deeply diverged mitochondrial lineages; three distributed all across Europe and found in sympatry, suggesting a potential case of cryptic species. We then sequenced these six lineages using double-digest restriction-site associated DNA sequencing (ddRADseq). Nuclear genomic loci contradicted mtDNA patterns and genotypes generally clustered according to geography, i.e., a pattern expected under the assumption of postglacial recolonization from different refugia. Further analyses indicated that this strong mtDNA/nuDNA discrepancy cannot be explained by incomplete lineage sorting, sex-biased asymmetries, NUMTs, natural selection, introgression or Wolbachia-mediated genetic sweeps. We suggest that this mitonuclear discordance was caused by long periods of geographic isolation followed by range expansions, homogenizing the nuclear but not the mitochondrial genome. These results highlight T. sylvestris as a potential case of multiple despeciation and/or lineage fusion events. We finally argue, since mtDNA and nuDNA do not necessarily follow the same mechanisms of evolution, their respective evolutionary history reflects complementary aspects of past demographic and biogeographic events.}, }
@article {pmid31233550, year = {2019}, author = {Monteiro, KJL and Calegar, DA and Santos, JP and Bacelar, PAA and Coronato-Nunes, B and Reis, ERC and Boia, MN and Carvalho-Costa, FA and Jaeger, LH}, title = {Genetic diversity of Ascaris spp. infecting humans and pigs in distinct Brazilian regions, as revealed by mitochondrial DNA.}, journal = {PloS one}, volume = {14}, number = {6}, pages = {e0218867}, pmid = {31233550}, issn = {1932-6203}, mesh = {Animals ; Ascariasis/parasitology ; Ascaris lumbricoides/*genetics ; Ascaris suum/*genetics ; Brazil ; Cross-Sectional Studies ; DNA, Mitochondrial/*genetics ; Genetic Variation/*genetics ; Haplotypes/genetics ; Humans ; Mitochondria/*genetics ; Phylogeny ; Swine ; Swine Diseases/parasitology ; }, abstract = {In this study, we assessed the genetic diversity of Ascaris lumbricoides / Ascaris suum circulating in humans and pigs, exploring potential zoonotic cycles in endemic areas in Brazil. We carried out cross-sectional surveys in four municipalities: Santa Isabel do Rio Negro (SIRN-AM) (n = 328); Nossa Senhora de Nazaré (NSN-PI) and Teresina (TER-PI) (n = 605 and n = 297, respectively); and Cachoeiras de Macacu (CAM-RJ) (n = 543). We also studied 61 fecal samples/adult worms obtained from pigs (n = 53 in NSN-PI and n = 8 in TER-PI). A ~450 bp fragment of the Ascaris cytochrome c oxidase subunit 1 (cox1) and ~400 bp of the NADH dehydrogenase subunit 1 (nad1) were amplified and sequenced. Maximum-likelihood (ML) tree and Median-joining (MJ) haplotype network analyses were performed. We also performed scanning electron micrographs of adult specimens. Positivity rates were 93/328 (28.4%) in SIRN-AM, 6/297 (2.0%) in TER-PI, 0/605 (0%) in NSN-PI, and 6/543 (1.1%) in CAM-RJ. In NSN-PI it reached 11/53 (20.7%) in pigs. The MJ network based on cox1 locus (383 bp) revealed three main clusters, one centered around haplotypes H01/H28/H32 and the other around H07/H11. The cox1 haplotypes had a heterogeneous distribution, showing no pattern by geographic region, and high haplotype diversity. The ML trees based on cox1 and nad1 loci showed a similar topology with each other, and with the haplotype networks. Three distinct clusters were observed. Sequences of cox1 and nad1 from humans and animals were distributed throughout the tree and it was not possible to differentiate specimens of human and swine origin. Ascaris populations obtained from humans and swine in different Brazilian regions are not discriminable through the genetic markers used, which indicates the potential for zoonotic transmission and the need for better control of these infections in swine herds, mainly when created in a peridomestic environment.}, }
@article {pmid31229574, year = {2019}, author = {Havird, JC and Noe, GR and Link, L and Torres, A and Logan, DC and Sloan, DB and Chicco, AJ}, title = {Do angiosperms with highly divergent mitochondrial genomes have altered mitochondrial function?.}, journal = {Mitochondrion}, volume = {49}, number = {}, pages = {1-11}, pmid = {31229574}, issn = {1872-8278}, support = {F32 GM116361/GM/NIGMS NIH HHS/United States ; }, mesh = {*Genome, Mitochondrial ; *Genome, Plant ; Silene/*genetics ; }, abstract = {Angiosperm mitochondrial (mt) genes are generally slow-evolving, but multiple lineages have undergone dramatic accelerations in rates of nucleotide substitution and extreme changes in mt genome structure. While molecular evolution in these lineages has been investigated, very little is known about their mt function. Some studies have suggested altered respiration in individual taxa, although there are several reasons why mt variation might be neutral in others. Here, we develop a new protocol to characterize respiration in isolated plant mitochondria and apply it to species of Silene with mt genomes that are rapidly evolving, highly fragmented, and exceptionally large (~11 Mbp). This protocol, complemented with traditional measures of plant fitness, cytochrome c oxidase activity assays, and fluorescence microscopy, was also used to characterize inter- and intraspecific variation in mt function. Contributions of the individual "classic" OXPHOS complexes, the alternative oxidase, and external NADH dehydrogenases to overall mt respiratory flux were found to be similar to previously studied angiosperms with more typical mt genomes. Some differences in mt function could be explained by inter- and intraspecific variation. This study suggests that Silene species with peculiar mt genomes still show relatively normal mt respiration. This may be due to strong purifying selection on mt variants, coevolutionary responses in the nucleus, or a combination of both. Future experiments should explore such questions using a comparative framework and investigating other lineages with unusual mitogenomes.}, }
@article {pmid31227544, year = {2019}, author = {Cooper, BS and Vanderpool, D and Conner, WR and Matute, DR and Turelli, M}, title = {Wolbachia Acquisition by Drosophila yakuba-Clade Hosts and Transfer of Incompatibility Loci Between Distantly Related Wolbachia.}, journal = {Genetics}, volume = {212}, number = {4}, pages = {1399-1419}, pmid = {31227544}, issn = {1943-2631}, support = {R01 GM104325/GM/NIGMS NIH HHS/United States ; R01 GM121750/GM/NIGMS NIH HHS/United States ; R35 GM124701/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Drosophila/*genetics/microbiology/physiology ; Female ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Insect ; Genome, Mitochondrial ; Host-Pathogen Interactions ; Infertility/*genetics ; Male ; Phylogeny ; Wolbachia/*genetics/pathogenicity ; }, abstract = {Maternally transmitted Wolbachia infect about half of insect species, yet the predominant mode(s) of Wolbachia acquisition remains uncertain. Species-specific associations could be old, with Wolbachia and hosts codiversifying (i.e., cladogenic acquisition), or relatively young and acquired by horizontal transfer or introgression. The three Drosophila yakuba-clade hosts [(D. santomea, D. yakuba) D. teissieri] diverged ∼3 MYA and currently hybridize on the West African islands Bioko and São Tomé. Each species is polymorphic for nearly identical Wolbachia that cause weak cytoplasmic incompatibility (CI)-reduced egg hatch when uninfected females mate with infected males. D. yakuba-clade Wolbachia are closely related to wMel, globally polymorphic in D. melanogaster We use draft Wolbachia and mitochondrial genomes to demonstrate that D. yakuba-clade phylogenies for Wolbachia and mitochondria tend to follow host nuclear phylogenies. However, roughly half of D. santomea individuals, sampled both inside and outside of the São Tomé hybrid zone, have introgressed D. yakuba mitochondria. Both mitochondria and Wolbachia possess far more recent common ancestors than the bulk of the host nuclear genomes, precluding cladogenic Wolbachia acquisition. General concordance of Wolbachia and mitochondrial phylogenies suggests that horizontal transmission is rare, but varying relative rates of molecular divergence complicate chronogram-based statistical tests. Loci that cause CI in wMel are disrupted in D. yakuba-clade Wolbachia; but a second set of loci predicted to cause CI are located in the same WO prophage region. These alternative CI loci seem to have been acquired horizontally from distantly related Wolbachia, with transfer mediated by flanking Wolbachia-specific ISWpi1 transposons.}, }
@article {pmid31218630, year = {2019}, author = {Gerlach, L and Gholami, O and Schürmann, N and Kleinschmidt, JH}, title = {Folding of β-Barrel Membrane Proteins into Lipid Membranes by Site-Directed Fluorescence Spectroscopy.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2003}, number = {}, pages = {465-492}, doi = {10.1007/978-1-4939-9512-7_20}, pmid = {31218630}, issn = {1940-6029}, mesh = {Amino Acid Sequence ; Bacterial Outer Membrane Proteins/metabolism ; Cell Membrane/*metabolism ; Escherichia coli/metabolism ; Fluorescence ; Humans ; Kinetics ; Lipid Bilayers/*metabolism ; Membrane Lipids/*metabolism ; Mitochondria/metabolism ; Mutagenesis, Site-Directed/methods ; Protein Folding ; Spectrometry, Fluorescence/methods ; Tryptophan/metabolism ; Voltage-Dependent Anion Channel 1/metabolism ; }, abstract = {Protein-lipid interactions are important for folding and membrane insertion of integral membrane proteins that are composed either of α-helical or of β-barrel structure in their transmembrane domains. While α-helical transmembrane proteins fold co-translationally while they are synthesized by a ribosome, β-barrel transmembrane proteins (β-TMPs) fold and insert posttranslationally-in bacteria after translocation across the cytoplasmic membrane, in cell organelles of eukaryotes after import across the outer membrane of the organelle. β-TMPs can be unfolded in aqueous solutions of chaotropic denaturants like urea and spontaneously refold upon denaturant dilution in the presence of preformed lipid bilayers. This facilitates studies on lipid interactions during folding into lipid bilayers. For several β-TMPs, the kinetics of folding has been reported as strongly dependent on protein-lipid interactions. The kinetics of adsorption/insertion and folding of β-TMPs can be monitored by fluorescence spectroscopy. These fluorescence methods are even more powerful when combined with site-directed mutagenesis for the preparation of mutants of a β-TMP that are site-specifically labeled with a fluorophore or a fluorophore and fluorescence quencher or fluorescence resonance energy acceptor. Single tryptophan or single cysteine mutants of the β-TMP allow for the investigation of local protein-lipid interactions, at specific regions within the protein. To examine the structure formation of β-TMPs in a lipid environment, fluorescence spectroscopy has been used for double mutants of β-TMPs that contain a fluorescent tryptophan and a spin-label, covalently attached to a cysteine as a fluorescence quencher. The sites of mutation are selected so that the tryptophan is in close proximity to the quencher at the cysteine only when the β-TMP is folded. In a folding experiment, the evolution of fluorescence quenching as a function of time at specific sites within the protein can provide important information on the folding mechanism of the β-TMP. Here, we report protocols to examine membrane protein folding for two β-TMPs in a lipid environment, the outer membrane protein A from Escherichia coli, OmpA, and the voltage-dependent anion-selective channel, human isoform 1, hVDAC1, from mitochondria.}, }
@article {pmid31218358, year = {2019}, author = {Krasovec, M and Sanchez-Brosseau, S and Piganeau, G}, title = {First Estimation of the Spontaneous Mutation Rate in Diatoms.}, journal = {Genome biology and evolution}, volume = {11}, number = {7}, pages = {1829-1837}, pmid = {31218358}, issn = {1759-6653}, mesh = {Diatoms/*genetics ; Evolution, Molecular ; Mutagenesis/genetics/physiology ; Mutation Rate ; }, abstract = {Mutations are the origin of genetic diversity, and the mutation rate is a fundamental parameter to understand all aspects of molecular evolution. The combination of mutation-accumulation experiments and high-throughput sequencing enabled the estimation of mutation rates in most model organisms, but several major eukaryotic lineages remain unexplored. Here, we report the first estimation of the spontaneous mutation rate in a model unicellular eukaryote from the Stramenopile kingdom, the diatom Phaeodactylum tricornutum (strain RCC2967). We sequenced 36 mutation accumulation lines for an average of 181 generations per line and identified 156 de novo mutations. The base substitution mutation rate per site per generation is μbs = 4.77 × 10-10 and the insertion-deletion mutation rate is μid = 1.58 × 10-11. The mutation rate varies as a function of the nucleotide context and is biased toward an excess of mutations from GC to AT, consistent with previous observations in other species. Interestingly, the mutation rates between the genomes of organelles and the nucleus differ, with a significantly higher mutation rate in the mitochondria. This confirms previous claims based on indirect estimations of the mutation rate in mitochondria of photosynthetic eukaryotes that acquired their plastid through a secondary endosymbiosis. This novel estimate enables us to infer the effective population size of P. tricornutum to be Ne∼8.72 × 106.}, }
@article {pmid31216623, year = {2019}, author = {Myszczyński, K and Ślipiko, M and Sawicki, J}, title = {Potential of Transcript Editing Across Mitogenomes of Early Land Plants Shows Novel and Familiar Trends.}, journal = {International journal of molecular sciences}, volume = {20}, number = {12}, pages = {}, pmid = {31216623}, issn = {1422-0067}, support = {Grant No. 2017/01/X/NZ8/01094, Grant No. 2016/21/B/NZ8/03325, Grant No. 2015/19/B/NZ8/03970//Narodowe Centrum Nauki/ ; }, mesh = {Base Composition ; Bryophyta/classification/genetics ; Embryophyta/*classification/*genetics ; Genome Size ; *Genome, Mitochondrial ; Genomics/methods ; Open Reading Frames ; Phylogeny ; *RNA Editing ; RNA, Messenger/*genetics ; *RNA, Plant ; }, abstract = {RNA editing alters the identity of nucleotides in an RNA sequence so that the mature transcript differs from the template defined in the genome. This process has been observed in chloroplasts and mitochondria of both seed and early land plants. However, the frequency of RNA editing in plant mitochondria ranges from zero to thousands of editing sites. To date, analyses of RNA editing in mitochondria of early land plants have been conducted on a small number of genes or mitochondrial genomes of a single species. This study provides an overview of the mitogenomic RNA editing potential of the main lineages of these two groups of early land plants by predicting the RNA editing sites of 33 mitochondrial genes of 37 species of liverworts and mosses. For the purpose of the research, we newly assembled seven mitochondrial genomes of liverworts. The total number of liverwort genera with known complete mitogenome sequences has doubled and, as a result, the available complete mitogenome sequences now span almost all orders of liverworts. The RNA editing site predictions revealed that C-to-U RNA editing in liverworts and mosses is group-specific. This is especially evident in the case of liverwort lineages. The average level of C-to-U RNA editing appears to be over three times higher in liverworts than in mosses, while the C-to-U editing frequency of the majority of genes seems to be consistent for each gene across bryophytes.}, }
@article {pmid31211668, year = {2019}, author = {Nascimento, FS and Barta, JR and Whale, J and Hofstetter, JN and Casillas, S and Barratt, J and Talundzic, E and Arrowood, MJ and Qvarnstrom, Y}, title = {Mitochondrial Junction Region as Genotyping Marker for Cyclospora cayetanensis.}, journal = {Emerging infectious diseases}, volume = {25}, number = {7}, pages = {1314-1319}, pmid = {31211668}, issn = {1080-6059}, mesh = {Cyclospora/*classification/*genetics ; Cyclosporiasis/*parasitology/transmission ; *DNA, Mitochondrial ; Genetic Markers ; Genetic Variation ; Genotyping Techniques ; Humans ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Cyclosporiasis is an infection caused by Cyclospora cayetanensis, which is acquired by consumption of contaminated fresh food or water. In the United States, cases of cyclosporiasis are often associated with foodborne outbreaks linked to imported fresh produce or travel to disease-endemic countries. Epidemiologic investigation has been the primary method for linking outbreak cases. A molecular typing marker that can identify genetically related samples would be helpful in tracking outbreaks. We evaluated the mitochondrial junction region as a potential genotyping marker. We tested stool samples from 134 laboratory-confirmed cases in the United States by using PCR and Sanger sequencing. All but 2 samples were successfully typed and divided into 14 sequence types. Typing results were identical among samples within each epidemiologically defined case cluster for 7 of 10 clusters. These findings suggest that this marker can distinguish between distinct case clusters and might be helpful during cyclosporiasis outbreak investigations.}, }
@article {pmid31209489, year = {2019}, author = {Nieuwenhuis, M and van de Peppel, LJJ and Bakker, FT and Zwaan, BJ and Aanen, DK}, title = {Enrichment of G4DNA and a Large Inverted Repeat Coincide in the Mitochondrial Genomes of Termitomyces.}, journal = {Genome biology and evolution}, volume = {11}, number = {7}, pages = {1857-1869}, pmid = {31209489}, issn = {1759-6653}, mesh = {DNA, Mitochondrial/*genetics ; G-Quadruplexes ; Genome, Mitochondrial/*genetics ; Inverted Repeat Sequences/genetics ; Termitomyces/*genetics ; }, abstract = {Mitochondria retain their own genome, a hallmark of their bacterial ancestry. Mitochondrial genomes (mtDNA) are highly diverse in size, shape, and structure, despite their conserved function across most eukaryotes. Exploring extreme cases of mtDNA architecture can yield important information on fundamental aspects of genome biology. We discovered that the mitochondrial genomes of a basidiomycete fungus (Termitomyces spp.) contain an inverted repeat (IR), a duplicated region half the size of the complete genome. In addition, we found an abundance of sequences capable of forming G-quadruplexes (G4DNA); structures that can disrupt the double helical formation of DNA. G4DNA is implicated in replication fork stalling, double-stranded breaks, altered gene expression, recombination, and other effects. To determine whether this occurrence of IR and G4DNA was correlated within the genus Termitomyces, we reconstructed the mitochondrial genomes of 11 additional species including representatives of several closely related genera. We show that the mtDNA of all sampled species of Termitomyces and its sister group, represented by the species Tephrocybe rancida and Blastosporella zonata, are characterized by a large IR and enrichment of G4DNA. To determine whether high mitochondrial G4DNA content is common in fungi, we conducted the first broad survey of G4DNA content in fungal mtDNA, revealing it to be a highly variable trait. The results of this study provide important direction for future research on the function and evolution of G4DNA and organellar IRs.}, }
@article {pmid31207496, year = {2019}, author = {Farooq, MA and Niazi, AK and Akhtar, J and Saifullah,  and Farooq, M and Souri, Z and Karimi, N and Rengel, Z}, title = {Acquiring control: The evolution of ROS-Induced oxidative stress and redox signaling pathways in plant stress responses.}, journal = {Plant physiology and biochemistry : PPB}, volume = {141}, number = {}, pages = {353-369}, doi = {10.1016/j.plaphy.2019.04.039}, pmid = {31207496}, issn = {1873-2690}, mesh = {Acclimatization ; Antioxidants/metabolism ; Arabidopsis/metabolism ; Cell Nucleus/metabolism ; Chloroplasts/metabolism ; Cytosol/metabolism ; Gene Expression Regulation ; Genes, Plant ; Mitochondria/metabolism ; Oryza/metabolism ; *Oxidation-Reduction ; *Oxidative Stress ; Oxygen/metabolism ; Peroxisomes/metabolism ; Photosynthesis ; *Plant Physiological Phenomena ; Populus/metabolism ; Reactive Oxygen Species/*metabolism ; *Signal Transduction ; *Stress, Physiological ; }, abstract = {Reactive oxygen species (ROS) - the byproducts of aerobic metabolism - influence numerous aspects of the plant life cycle and environmental response mechanisms. In plants, ROS act like a double-edged sword; they play multiple beneficial roles at low concentrations, whereas at high concentrations ROS and related redox-active compounds cause cellular damage through oxidative stress. To examine the dual role of ROS as harmful oxidants and/or crucial cellular signals, this review elaborates that (i) how plants sense and respond to ROS in various subcellular organelles and (ii) the dynamics of subsequent ROS-induced signaling processes. The recent understanding of crosstalk between various cellular compartments in mediating their redox state spatially and temporally is discussed. Emphasis on the beneficial effects of ROS in maintaining cellular energy homeostasis, regulating diverse cellular functions, and activating acclimation responses in plants exposed to abiotic and biotic stresses are described. The comprehensive view of cellular ROS dynamics covering the breadth and versatility of ROS will contribute to understanding the complexity of apparently contradictory ROS roles in plant physiological responses in less than optimum environments.}, }
@article {pmid31204914, year = {2019}, author = {Wang, J and Zhou, YA and Su, LP and Li, FM and Chen, M}, title = {[Instability of Mitochondrial DNA D-loop Region Genes in Patients with Leukemia].}, journal = {Zhongguo shi yan xue ye xue za zhi}, volume = {27}, number = {3}, pages = {657-663}, doi = {10.19746/j.cnki.issn.1009-2137.2019.03.005}, pmid = {31204914}, issn = {1009-2137}, mesh = {*DNA, Mitochondrial ; Humans ; *Leukemia ; Mitochondria ; Mutation ; Mutation Rate ; }, abstract = {OBJECTIVE: To study the instability of mitochondrial DNA（mt DNA） D-loop region genes in patients with Leukemia.<br><br>METHODS: The HV-1 and HV-2 regions of D-loop region in 24 patients with leukemia were amplificated and sequenced, then their results were compared with revised Cambridge reference sequence (rCRS) and Databank mtDB. The mutation rate was detected by SPSS 22.0 statistics software.<br><br>RESULTS: The total mutation rate in patients was 95.83% (23/24), the detection showed 82 mutated genes, out of which 47 (57.32%) mutated genes located in HV-1 region, 35 (42.68%) mutated genes in HV-2 region. The comparison showed that the mutation rate in untreated (UT) group and treated (T) group of AML patients was (2.37&#xb1;0.82)&#xd7;10[-3] and (4.76&#xb1;2.45)&#xd7;10[-3] respectively(P&#xff1c;0.01), the mutation rate in PR and CR groups of treated AML patients was (5.10&#xb1;2.56)&#xd7;10[-3] and (4.51&#xb1;2.51)&#xd7;10[-3] respectively (P&#xff1c;0.05), the comparison among M3 group showed that the mutation rates in UT, PR and CR groups were (2.55&#xb1;0.63)&#xd7;10[-3], (5.37&#xb1;3.41)&#xd7;10[-3] and (3.71&#xb1;1.65)&#xd7;10[-3] respectively (P&#xff1e;0.05).<br><br>CONCLUSION: The more high mutation rate and many kinds of mutation types exist in D-loop region, suggesting that the genes in D-loop region display the more strong instability, the chemotherapy may aggravate the instability of genes in D-loop region.}, }
@article {pmid31204704, year = {2019}, author = {Mothay, D and Ramesh, KV}, title = {Evolutionary history and genetic diversity study of heat-shock protein 60 of Rhizophagus irregularis.}, journal = {Journal of genetics}, volume = {98}, number = {2}, pages = {}, pmid = {31204704}, issn = {0973-7731}, mesh = {Chaperonin 60/*genetics/metabolism ; Codon ; Databases, Genetic ; Dyslexia/genetics ; *Evolution, Molecular ; *Genetic Variation ; Genetics, Population ; Glomeromycota/classification/*genetics/metabolism ; Humans ; Meta-Analysis as Topic ; Mitochondria/genetics/metabolism ; Odds Ratio ; Phylogeny ; Polymorphism, Genetic ; Synteny ; }, abstract = {Despite the ubiquitous occurrence of heat-shock protein 60 (Hsp60) and their role in maintenance of cell activity and integrity, this protein remains poorly characterized in many of the symbiotic soil mycorrhizal fungi such as Rhizophagus irregularis. Thus, in the current study, an attempt has been made to elucidate the evolutionary history, time of divergence followed by estimation of population genetic parameters of hsp60 using R. irregularis as a model organism. Sequence alignment reported here identified several close homologues for hsp60 (gene) and Hsp60 (protein) from diverse taxa, while the output from protein-based phylogenetic tree indicates that mitochondrial Hsp60 of R. irregularis shares close evolutionary relationship with classical α-proteobacteria. This is perhaps the first line of evidence elucidating the likelihood of hsp60 from fungal taxa sharing a close evolutionary relationship with classical α-proteobacteria as a common ancestor. Comprehensive analysis of mitochondrial hsp60 from selected fungal taxa from the evolutionary point of view explains the possibility of gene duplication and or horizontal gene transfer of this gene across various fungal species. Synteny relationships and population genetics credibly explain high genetic variability associated with fungal hsp60 presumably brought by random genetic recombination events. The results presented here also confirm a high level of genetic differentiation of hsp60 among all the three fungal populations analysed. In this context, the outcome of the current study, basedon computational approach, stands as a testimony for explaining the possibility of increased genetic differentiation experienced by hsp60 of R. irregularis.}, }
@article {pmid31203477, year = {2019}, author = {Hu, F and Fan, J and Wu, C and Zhu, M and Zhou, Y and Wang, S and Zhang, C and Tao, M and Zhao, R and Tang, C and Luo, K and Qin, Q and Ma, M and Chen, B and Wang, J and Zhou, A and Bai, L and Liu, S}, title = {Analysis of Chromosomal Numbers, Mitochondrial Genome, and Full-Length Transcriptome of Onychostoma brevibarba.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {21}, number = {4}, pages = {515-525}, pmid = {31203477}, issn = {1436-2236}, support = {31802286//National Natural Science Foundation of China/International ; 31430088//National Natural Science Foundation of China/International ; 31730098//National Natural Science Foundation of China/International ; 2018M642986//Postdoctoral Research Foundation of China/International ; CARS-45//Earmarked Fund for China Agriculture Research System/International ; }, mesh = {Animals ; Chromosomes/*chemistry ; Cyprinidae/classification/*genetics ; Gene Ontology ; *Genome ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Karyotype ; Mitochondria/genetics ; Molecular Sequence Annotation ; Phylogeny ; Ploidies ; Sequence Analysis, DNA ; *Transcriptome ; }, abstract = {Onychostoma brevibarba is a new discovered species which is distributed in Xiang Jiang River of the middle Chang Jiang basin in Hunan Province, South China. In this study, the ploidy levels of O. brevibarba were confirmed by counting chromosomal numbers and analyzing karyotype. The complete mitochondrial genome of O. brevibarba was determined and analyzed. Besides, we firstly performed the full-length transcriptome of O. brevibarba derived from 5 different tissues using the PacBio SMRT sequencing. The result shows that O. brevibarba was a diploid with 50 chromosomes [corrected]. The complete mitogenome of O. brevibarba was 16,602 bp in size and very similar (89.1-91.3%) to that of other Onychostoma species but was distinct from all congeners. The full-length transcriptome dataset of O. brevibarba comprised 120,239 unigenes. Among the unigenes, 91,542 were functionally annotated, whereas 26,794 were found to have two or more isoforms. This study could provide many new insights into cytology and molecular characteristics of O. brevibarba; it laid the foundation for further exploration of the genomic signatures of species of Onychostoma.}, }
@article {pmid31203379, year = {2020}, author = {Bloomfield, G}, title = {The molecular foundations of zygosis.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {77}, number = {2}, pages = {323-330}, pmid = {31203379}, issn = {1420-9071}, mesh = {Animals ; Biological Evolution ; Cell Membrane/metabolism/physiology ; Eukaryota/metabolism/physiology ; Germ Cells/metabolism ; Phylogeny ; Transcription Factors/metabolism ; Zygote/metabolism/*physiology ; }, abstract = {Zygosis is the generation of new biological individuals by the sexual fusion of gamete cells. Our current understanding of eukaryotic phylogeny indicates that sex is ancestral to all extant eukaryotes. Although sexual development is extremely diverse, common molecular elements have been retained. HAP2-GCS1, a protein that promotes the fusion of gamete cell membranes that is related in structure to certain viral fusogens, is conserved in many eukaryotic lineages, even though gametes vary considerably in form and behaviour between species. Similarly, although zygotes have dramatically different forms and fates in different organisms, diverse eukaryotes share a common developmental programme in which homeodomain-containing transcription factors play a central role. These common mechanistic elements suggest possible common evolutionary histories that, if correct, would have profound implications for our understanding of eukaryogenesis.}, }
@article {pmid31197948, year = {2019}, author = {Teng, X and Aouacheria, A and Lionnard, L and Metz, KA and Soane, L and Kamiya, A and Hardwick, JM}, title = {KCTD: A new gene family involved in neurodevelopmental and neuropsychiatric disorders.}, journal = {CNS neuroscience &amp; therapeutics}, volume = {25}, number = {7}, pages = {887-902}, pmid = {31197948}, issn = {1755-5949}, support = {P50 MH094268/MH/NIMH NIH HHS/United States ; R21 NS096677/NS/NINDS NIH HHS/United States ; R01 GM077875/GM/NIGMS NIH HHS/United States ; R01 NS083373/NS/NINDS NIH HHS/United States ; R01 DA041208/DA/NIDA NIH HHS/United States ; }, mesh = {Animals ; Humans ; Nervous System Diseases/genetics/metabolism ; Neurodevelopmental Disorders/genetics/*metabolism ; Proteins/genetics/*metabolism ; }, abstract = {The underlying molecular basis for neurodevelopmental or neuropsychiatric disorders is not known. In contrast, mechanistic understanding of other brain disorders including neurodegeneration has advanced considerably. Yet, these do not approach the knowledge accrued for many cancers with precision therapeutics acting on well-characterized targets. Although the identification of genes responsible for neurodevelopmental and neuropsychiatric disorders remains a major obstacle, the few causally associated genes are ripe for discovery by focusing efforts to dissect their mechanisms. Here, we make a case for delving into mechanisms of the poorly characterized human KCTD gene family. Varying levels of evidence support their roles in neurocognitive disorders (KCTD3), neurodevelopmental disease (KCTD7), bipolar disorder (KCTD12), autism and schizophrenia (KCTD13), movement disorders (KCTD17), cancer (KCTD11), and obesity (KCTD15). Collective knowledge about these genes adds enhanced value, and critical insights into potential disease mechanisms have come from unexpected sources. Translation of basic research on the KCTD-related yeast protein Whi2 has revealed roles in nutrient signaling to mTORC1 (KCTD11) and an autophagy-lysosome pathway affecting mitochondria (KCTD7). Recent biochemical and structure-based studies (KCTD12, KCTD13, KCTD16) reveal mechanisms of regulating membrane channel activities through modulation of distinct GTPases. We explore how these seemingly varied functions may be disease related.}, }
@article {pmid31196888, year = {2019}, author = {Pan, Z and Ren, X and Zhao, H and Liu, L and Tan, Z and Qiu, F}, title = {A Mitochondrial Transcription Termination Factor, ZmSmk3, Is Required for nad1 Intron4 and nad4 Intron1 Splicing and Kernel Development in Maize.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {8}, pages = {2677-2686}, pmid = {31196888}, issn = {2160-1836}, mesh = {Basic-Leucine Zipper Transcription Factors/*metabolism ; *Introns ; Mitochondrial Proteins/genetics/metabolism ; Plant Development/*genetics ; *RNA Splicing ; Seedlings/genetics/metabolism ; Zea mays/*physiology ; }, abstract = {The expression systems of the mitochondrial genes are derived from their bacterial ancestors, but have evolved many new features in their eukaryotic hosts. Mitochondrial RNA splicing is a complex process regulated by families of nucleus-encoded RNA-binding proteins, few of which have been characterized in maize (Zea mays L.). Here, we identified the Zea mays small kernel 3 (Zmsmk3) candidate gene, which encodes a mitochondrial transcription termination factor (mTERF) containing two mTERF motifs, which is conserved in monocotyledon; and the target introns were also quite conserved during evolution between monocotyledons and dicotyledons. The mutations of Zmsmk3 led to arrested embryo and endosperm development, resulting in small kernels. A transcriptome of 12 days after pollination endosperm analysis revealed that the starch biosynthetic pathway and the zein gene family were down-regulated in the Zmsmk3 mutant kernels. ZmSMK3 is localized in mitochondria. The reduced expression of ZmSmk3 in the mutant resulted in the splicing deficiency of mitochondrial nad4 intron1 and nad1 intron4, causing a reduction in complex I assembly and activity, impairing mitochondria structure and activating the alternative respiratory pathway. So, the results suggest that ZmSMK3 is required for the splicing of nad4 intron 1 and nad1 intron 4, complex I assembly and kernel development in maize.}, }
@article {pmid31196150, year = {2018}, author = {Gerlitz, M and Knopp, M and Kapust, N and Xavier, JC and Martin, WF}, title = {Elusive data underlying debate at the prokaryote-eukaryote divide.}, journal = {Biology direct}, volume = {13}, number = {1}, pages = {21}, pmid = {31196150}, issn = {1745-6150}, mesh = {*Biological Evolution ; Energy Metabolism ; Eukaryotic Cells/*physiology ; Mitochondria/metabolism ; Prokaryotic Cells/*physiology ; }, abstract = {BACKGROUND: The origin of eukaryotic cells was an important transition in evolution. The factors underlying the origin and evolutionary success of the eukaryote lineage are still discussed. One camp argues that mitochondria were essential for eukaryote origin because of the unique configuration of internalized bioenergetic membranes that they conferred to the common ancestor of all known eukaryotic lineages. A recent paper by Lynch and Marinov concluded that mitochondria were energetically irrelevant to eukaryote origin, a conclusion based on analyses of previously published numbers of various molecules and ribosomes per cell and cell volumes as a presumed proxy for the role of mitochondria in evolution. Their numbers were purportedly extracted from the literature.<br><br>RESULTS: We have examined the numbers upon which the recent study was based. We report that for a sample of 80 numbers that were purportedly extracted from the literature and that underlie key inferences of the recent study, more than 50% of the values do not exist in the cited papers to which the numbers are attributed. The published result cannot be independently reproduced. Other numbers that the recent study reports differ inexplicably from those in the literature to which they are ascribed. We list the discrepancies between the recently published numbers and the purported literature sources of those numbers in a head to head manner so that the discrepancies are readily evident, although the source of error underlying the discrepancies remains obscure.<br><br>CONCLUSION: The data purportedly supporting the view that mitochondria had no impact upon eukaryotic evolution data exhibits notable irregularities. The paper in question evokes the impression that the published numbers are of up to seven significant digit accuracy, when in fact more than half the numbers are nowhere to be found in the literature to which they are attributed. Though the reasons for the discrepancies are unknown, it is important to air these issues, lest the prominent paper in question become a point source of a snowballing error through the literature or become interpreted as a form of evidence that mitochondria were irrelevant to eukaryote evolution.<br><br>REVIEWERS: This article was reviewed by Eric Bapteste, Jianzhi Zhang and Martin Lercher.}, }
@article {pmid31192351, year = {2019}, author = {Zhang, D and Zou, H and Hua, CJ and Li, WX and Mahboob, S and Al-Ghanim, KA and Al-Misned, F and Jakovlić, I and Wang, GT}, title = {Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda.}, journal = {Genome biology and evolution}, volume = {11}, number = {7}, pages = {1797-1812}, pmid = {31192351}, issn = {1759-6653}, mesh = {Algorithms ; Animals ; Genome, Mitochondrial/*genetics ; Isopoda/*genetics ; Mitochondria/*genetics ; Mutation/genetics ; Phylogeny ; }, abstract = {The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.}, }
@article {pmid31192348, year = {2019}, author = {Füssy, Z and Faitová, T and Oborník, M}, title = {Subcellular Compartments Interplay for Carbon and Nitrogen Allocation in Chromera velia and Vitrella brassicaformis.}, journal = {Genome biology and evolution}, volume = {11}, number = {7}, pages = {1765-1779}, pmid = {31192348}, issn = {1759-6653}, mesh = {Algorithms ; Alveolata/*metabolism ; Carbon/*metabolism ; Cytosol/metabolism ; Evolution, Molecular ; Nitrogen/*metabolism ; Photosynthesis/genetics/physiology ; Phylogeny ; Symbiosis/genetics/physiology ; }, abstract = {Endosymbioses necessitate functional cooperation of cellular compartments to avoid pathway redundancy and streamline the control of biological processes. To gain insight into the metabolic compartmentation in chromerids, phototrophic relatives to apicomplexan parasites, we prepared a reference set of proteins probably localized to mitochondria, cytosol, and the plastid, taking advantage of available genomic and transcriptomic data. Training of prediction algorithms with the reference set now allows a genome-wide analysis of protein localization in Chromera velia and Vitrella brassicaformis. We confirm that the chromerid plastids house enzymatic pathways needed for their maintenance and photosynthetic activity, but for carbon and nitrogen allocation, metabolite exchange is necessary with the cytosol and mitochondria. This indeed suggests that the regulatory mechanisms operate in the cytosol to control carbon metabolism based on the availability of both light and nutrients. We discuss that this arrangement is largely shared with apicomplexans and dinoflagellates, possibly stemming from a common ancestral metabolic architecture, and supports the mixotrophy of the chromerid algae.}, }
@article {pmid31183910, year = {2019}, author = {Sun, JT and Duan, XZ and Hoffmann, AA and Liu, Y and Garvin, MR and Chen, L and Hu, G and Zhou, JC and Huang, HJ and Xue, XF and Hong, XY}, title = {Mitochondrial variation in small brown planthoppers linked to multiple traits and probably reflecting a complex evolutionary trajectory.}, journal = {Molecular ecology}, volume = {28}, number = {14}, pages = {3306-3323}, doi = {10.1111/mec.15148}, pmid = {31183910}, issn = {1365-294X}, mesh = {Adaptation, Physiological/genetics ; Animals ; Body Size/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Female ; Fertility/genetics ; Gene Amplification ; Genetics, Population ; Genome, Mitochondrial ; Geography ; Haplotypes/genetics ; Hemiptera/*genetics ; Male ; Mitochondria/*genetics ; Phylogeny ; *Quantitative Trait, Heritable ; Structural Homology, Protein ; Temperature ; }, abstract = {While it has been proposed in several taxa that the mitochondrial genome is associated with adaptive evolution to different climatic conditions, making links between mitochondrial haplotypes and organismal phenotypes remains a challenge. Mitonuclear discordance occurs in the small brown planthopper (SBPH), Laodelphax striatellus, with one mitochondrial haplogroup (HGI) more common in the cold climate region of China relative to another form (HGII) despite strong nuclear gene flow, providing a promising model to investigate climatic adaptation of mitochondrial genomes. We hypothesized that cold adaptation through HGI may be involved, and considered mitogenome evolution, population genetic analyses, and bioassays to test this hypothesis. In contrast to our hypothesis, chill-coma recovery tests and population genetic tests of selection both pointed to HGII being involved in cold adaptation. Phylogenetic analyses revealed that HGII is nested within HGI, and has three nonsynonymous changes in ND2, ND5 and CYTB in comparison to HGI. These molecular changes likely increased mtDNA copy number, cold tolerance and fecundity of SBPH, particularly through a function-altering amino acid change involving M114T in ND2. Nuclear background also influenced fecundity and chill recovery (i.e., mitonuclear epistasis) and protein modelling indicates possible nuclear interactions for the two nonsynonymous changes in ND2 and CYTB. The high occurrence frequency of HGI in the cold climate region of China remains unexplained, but several possible reasons are discussed. Overall, our study points to a link between mtDNA variation and organismal-level evolution and suggests a possible role of mitonuclear interactions in maintaining mtDNA diversity.}, }
@article {pmid31179502, year = {2019}, author = {Schober, AF and Rï O Bï Rtulos, C and Bischoff, A and Lepetit, B and Gruber, A and Kroth, PG}, title = {Organelle Studies and Proteome Analyses of Mitochondria and Plastids Fractions from the Diatom Thalassiosira pseudonana.}, journal = {Plant &amp; cell physiology}, volume = {60}, number = {8}, pages = {1811-1828}, pmid = {31179502}, issn = {1471-9053}, mesh = {Diatoms/*metabolism ; Mitochondria/*metabolism ; Plastids/*metabolism ; Proteome/*metabolism ; Thylakoids/metabolism ; }, abstract = {Diatoms are unicellular algae and evolved by secondary endosymbiosis, a process in which a red alga-like eukaryote was engulfed by a heterotrophic eukaryotic cell. This gave rise to plastids of remarkable complex architecture and ultrastructure that require elaborate protein importing, trafficking, signaling and intracellular cross-talk pathways. Studying both plastids and mitochondria and their distinctive physiological pathways in organello may greatly contribute to our understanding of photosynthesis, mitochondrial respiration and diatom evolution. The isolation of such complex organelles, however, is still demanding, and existing protocols are either limited to a few species (for plastids) or have not been reported for diatoms so far (for mitochondria). In this work, we present the first isolation protocol for mitochondria from the model diatom Thalassiosira pseudonana. Apart from that, we extended the protocol so that it is also applicable for the purification of a high-quality plastids fraction, and provide detailed structural and physiological characterizations of the resulting organelles. Isolated mitochondria were structurally intact, showed clear evidence of mitochondrial respiration, but the fractions still contained residual cell fragments. In contrast, plastid isolates were virtually free of cellular contaminants, featured structurally preserved thylakoids performing electron transport, but lost most of their stromal components as concluded from Western blots and mass spectrometry. Liquid chromatography electrospray-ionization mass spectrometry studies on mitochondria and thylakoids, moreover, allowed detailed proteome analyses which resulted in extensive proteome maps for both plastids and mitochondria thus helping us to broaden our understanding of organelle metabolism and functionality in diatoms.}, }
@article {pmid31177572, year = {2019}, author = {Knerr, I and Colombo, R and Urquhart, J and Morais, A and Merinero, B and Oyarzabal, A and Pérez, B and Jones, SA and Perveen, R and Preece, MA and Rogers, Y and Treacy, EP and Mayne, P and Zampino, G and MacKinnon, S and Wassmer, E and Yue, WW and Robinson, I and Rodríguez-Pombo, P and Olpin, SE and Banka, S}, title = {Expanding the genetic and phenotypic spectrum of branched-chain amino acid transferase 2 deficiency.}, journal = {Journal of inherited metabolic disease}, volume = {42}, number = {5}, pages = {809-817}, doi = {10.1002/jimd.12135}, pmid = {31177572}, issn = {1573-2665}, mesh = {Adolescent ; Adult ; Amino Acid Metabolism, Inborn Errors/*diagnosis/*genetics ; Amino Acids, Branched-Chain/*blood ; Brain/diagnostic imaging/*pathology ; Child ; Child, Preschool ; Female ; Homozygote ; Humans ; Magnetic Resonance Imaging ; Male ; Minor Histocompatibility Antigens/genetics ; Mitochondria/*pathology ; Mutation ; Phenotype ; Pregnancy Proteins/*deficiency/genetics ; Transaminases/*deficiency/genetics ; }, abstract = {The first step in branched-chain amino acid (BCAA) catabolism is catalyzed by the two BCAA transferase isoenzymes, cytoplasmic branched-chain amino acid transferase (BCAT) 1, and mitochondrial BCAT2. Defects in the second step of BCAA catabolism cause maple syrup urine disease (MSUD), a condition which has been far more extensively investigated. Here, we studied the consequences of BCAT2 deficiency, an ultra-rare condition in humans. We present genetic, clinical, and functional data in five individuals from four different families with homozygous or compound heterozygous BCAT2 mutations which were all detected following abnormal biochemical profile results or familial mutation segregation studies. We demonstrate that BCAT2 deficiency has a recognizable biochemical profile with raised plasma BCAAs and, in contrast with MSUD, low-normal branched-chain keto acids (BCKAs) with undetectable l-allo-isoleucine. Interestingly, unlike in MSUD, none of the individuals with BCAT2 deficiency developed acute encephalopathy even with exceptionally high BCAA levels. We observed wide-ranging clinical phenotypes in individuals with BCAT2 deficiency. While one adult was apparently asymptomatic, three individuals had presented with developmental delay and autistic features. We show that the biochemical characteristics of BCAT2 deficiency may be amenable to protein-restricted diet and that early treatment may improve outcome in affected individuals. BCAT2 deficiency is an inborn error of BCAA catabolism. At present, it is unclear whether developmental delay and autism are parts of the variable phenotypic spectrum of this condition or coincidental. Further studies will be required to explore this.}, }
@article {pmid31173843, year = {2019}, author = {Barja, G}, title = {Towards a unified mechanistic theory of aging.}, journal = {Experimental gerontology}, volume = {124}, number = {}, pages = {110627}, doi = {10.1016/j.exger.2019.05.016}, pmid = {31173843}, issn = {1873-6815}, mesh = {Aging/*metabolism ; Animals ; Autophagy ; DNA Damage ; Free Radicals/*metabolism ; Humans ; Longevity/physiology ; Mitochondria/metabolism ; Models, Biological ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; }, abstract = {A large amount of the longevity-modulating genes discovered during the last two decades are highly conserved during evolution from yeast and invertebrates to mammals. Many different kinds of evidence converge in the concept that life extending manipulations like the dietary restrictions or rapamycin signal the nucleus specifically changing gene expression to increase longevity. The response of the cell aging regulation system is to change the level of activity of many different aging effectors to modulate longevity. Aging effectors include mitROS production, lipid unsaturation, autophagy, mitochondrial DNA repair and possibly others like apoptosis, proteostasis, or telomere shortening, corresponding to different classic theories of aging. The constitutive spontaneous activity of this aging regulating system, likely including epigenetics, can also explain species longevity. The aging regulating system reconciles the previously considered independent theories of aging bringing them together into a single unified theory of aging.}, }
@article {pmid31173136, year = {2019}, author = {Montooth, KL and Dhawanjewar, AS and Meiklejohn, CD}, title = {Temperature-Sensitive Reproduction and the Physiological and Evolutionary Potential for Mother's Curse.}, journal = {Integrative and comparative biology}, volume = {59}, number = {4}, pages = {890-899}, pmid = {31173136}, issn = {1557-7023}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; Drosophila melanogaster/genetics/*physiology ; Female ; Male ; Maternal Inheritance/*genetics ; Mitochondria/*genetics ; Mutation/*genetics ; Reproduction/genetics ; Selection, Genetic ; *Temperature ; }, abstract = {Strict maternal transmission of mitochondrial DNA (mtDNA) is hypothesized to permit the accumulation of mitochondrial variants that are deleterious to males but not females, a phenomenon called mother's curse. However, direct evidence that mtDNA mutations exhibit such sexually antagonistic fitness effects is sparse. Male-specific mutational effects can occur when the physiological requirements of the mitochondria differ between the sexes. Such male-specific effects could potentially occur if sex-specific cell types or tissues have energy requirements that are differentially impacted by mutations affecting energy metabolism. Here we summarize findings from a model mitochondrial-nuclear incompatibility in the fruit fly Drosophila that demonstrates sex-biased effects, but with deleterious effects that are generally larger in females. We present new results showing that the mitochondrial-nuclear incompatibility does negatively affect male fertility, but only when males are developed at high temperatures. The temperature-dependent male sterility can be partially rescued by diet, suggesting an energetic basis. Finally, we discuss fruitful paths forward in understanding the physiological scope for sex-specific effects of mitochondrial mutations in the context of the recent discovery that many aspects of metabolism are sexually dimorphic and downstream of sex-determination pathways in Drosophila. A key parameter of these models that remains to be quantified is the fraction of mitochondrial mutations with truly male-limited fitness effects across extrinsic and intrinsic environments. Given the energy demands of reproduction in females, only a small fraction of the mitochondrial mutational spectrum may have the potential to contribute to mother's curse in natural populations.}, }
@article {pmid31170405, year = {2019}, author = {Edgar, JA}, title = {L-ascorbic acid and the evolution of multicellular eukaryotes.}, journal = {Journal of theoretical biology}, volume = {476}, number = {}, pages = {62-73}, doi = {10.1016/j.jtbi.2019.06.001}, pmid = {31170405}, issn = {1095-8541}, mesh = {Aerobiosis/physiology ; Ascorbic Acid/*metabolism ; Eukaryotic Cells/cytology/*metabolism ; *Evolution, Molecular ; Photosynthesis/*physiology ; Plants/*metabolism ; }, abstract = {The lifeless earth was formed around 4.5 billion years ago and the first anaerobic unicellular "organisms" may have appeared half a billion years later. Despite subsequent prokaryotes (bacteria and archaea) evolving quite complex biochemistry and some eukaryote characteristics, the transition from unicellular prokaryotes to multicellular, aerobic eukaryotes took a further 2.5 billion years to begin. The key factor or factors that eventually caused this long-delayed transition is a question that has been a focus of considerable research and a topic of discussion over many years. On the basis of the extensive literature available and consideration of some of the characteristics that distinguish multicellular eukaryotes from prokaryotes, it is proposed that, as well as the development of oxygenic photosynthesis producing high levels of environmental oxygen and the formation of vital organelles such as aerobic adenosine triphosphate-generating mitochondria, the concurrent evolution of the L-ascorbic acid redox system should be considered as a key factor that led to the evolution of multicellular eukaryotes and it remains vitally involved in the maintenance of multicellularity and many other eukaryote characteristics.}, }
@article {pmid31169025, year = {2019}, author = {Black, SM and Nozik-Grayck, E}, title = {Compartmentalization of Redox-Regulated Signaling in the Pulmonary Circulation.}, journal = {Antioxidants &amp; redox signaling}, volume = {31}, number = {12}, pages = {801-803}, pmid = {31169025}, issn = {1557-7716}, support = {R35 HL139726/HL/NHLBI NIH HHS/United States ; P01 HL134610/HL/NHLBI NIH HHS/United States ; R01 HL142212/HL/NHLBI NIH HHS/United States ; R01 HL137282/HL/NHLBI NIH HHS/United States ; T32 HD049303/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Gene Expression Regulation ; Humans ; Hypertension, Pulmonary/*metabolism ; Lung/*blood supply/metabolism ; Mitochondria/metabolism ; Oxidative Stress ; PPAR gamma/metabolism ; *Signal Transduction ; Transcription Factors/metabolism ; }, abstract = {Oxidative stress is well recognized to contribute to the pathogenesis of diverse diseases, including the devastating disease of the lung's blood vessels, pulmonary arterial hypertension (PAH), however, antioxidant-based therapies have been overall disappointing. With the evolution of the field of redox biology, it is now becoming clear that redox reactions are highly selective and targeted, allowing for precise control of redox-regulated signaling in health and disease. This special Forum of the journal describes the current state of knowledge on the regulation of redox-regulated signaling during the development of pulmonary vascular disease, focusing on distinct compartmentalized mechanisms outside and within the cell, including regulation of extracellular and intracellular membrane receptors and channels; responses to changes in biomechanical forces; intracellular thiol redox control; regulation of the nuclear transcription factor, peroxisome proliferator-activated receptor-γ; and regulation of mitochondrial metabolism. Collectively, they exemplify the complex, precise, and localized signaling pathways that drive PAH pathogenesis. This group of authors suggests ways that our increased understanding of these events may pave the way to improved therapeutic approaches for the treatment of this lethal disease.}, }
@article {pmid31168607, year = {2019}, author = {Hood, WR and Williams, AS and Hill, GE}, title = {An Ecologist's Guide to Mitochondrial DNA Mutations and Senescence.}, journal = {Integrative and comparative biology}, volume = {59}, number = {4}, pages = {970-982}, doi = {10.1093/icb/icz097}, pmid = {31168607}, issn = {1557-7023}, mesh = {Aging/*genetics ; Animals ; DNA, Mitochondrial/*genetics ; *Microsatellite Instability ; Mitochondria/genetics/*physiology ; Mutation/*physiology ; Mutation Rate ; }, abstract = {Longevity plays a key role in the fitness of organisms, so understanding the processes that underlie variance in senescence has long been a focus of ecologists and evolutionary biologists. For decades, the performance and ultimate decline of mitochondria have been implicated in the demise of somatic tissue, but exactly why mitochondrial function declines as individual's age has remained elusive. A possible source of decline that has been of intense debate is mutations to the mitochondrial DNA. There are two primary sources of such mutations: oxidative damage, which is widely discussed by ecologists interested in aging, and mitochondrial replication error, which is less familiar to most ecologists. The goal of this review is to introduce ecologists and evolutionary biologists to the concept of mitochondrial replication error and to review the current status of research on the relative importance of replication error in senescence. We conclude by detailing some of the gaps in our knowledge that currently make it difficult to deduce the relative importance of replication error in wild populations and encourage organismal biologists to consider this variable both when interpreting their results and as viable measure to include in their studies.}, }
@article {pmid31163164, year = {2019}, author = {Havird, JC and Forsythe, ES and Williams, AM and Werren, JH and Dowling, DK and Sloan, DB}, title = {Selfish Mitonuclear Conflict.}, journal = {Current biology : CB}, volume = {29}, number = {11}, pages = {R496-R511}, pmid = {31163164}, issn = {1879-0445}, support = {F32 GM116361/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Physiological Phenomena ; *Biological Evolution ; Eukaryota/physiology ; Genome, Mitochondrial/*physiology ; Plastids/physiology ; Symbiosis/physiology ; }, abstract = {Mitochondria, a nearly ubiquitous feature of eukaryotes, are derived from an ancient symbiosis. Despite billions of years of cooperative coevolution - in what is arguably the most important mutualism in the history of life - the persistence of mitochondrial genomes also creates conditions for genetic conflict with the nucleus. Because mitochondrial genomes are present in numerous copies per cell, they are subject to both within- and among-organism levels of selection. Accordingly, 'selfish' genotypes that increase their own proliferation can rise to high frequencies even if they decrease organismal fitness. It has been argued that uniparental (often maternal) inheritance of cytoplasmic genomes evolved to curtail such selfish replication by minimizing within-individual variation and, hence, within-individual selection. However, uniparental inheritance creates conditions for cytonuclear conflict over sex determination and sex ratio, as well as conditions for sexual antagonism when mitochondrial variants increase transmission by enhancing maternal fitness but have the side-effect of being harmful to males (i.e., 'mother's curse'). Here, we review recent advances in understanding selfish replication and sexual antagonism in the evolution of mitochondrial genomes and the mechanisms that suppress selfish interactions, drawing parallels and contrasts with other organelles (plastids) and bacterial endosymbionts that arose more recently. Although cytonuclear conflict is widespread across eukaryotes, it can be cryptic due to nuclear suppression, highly variable, and lineage-specific, reflecting the diverse biology of eukaryotes and the varying architectures of their cytoplasmic genomes.}, }
@article {pmid31154527, year = {2019}, author = {Suleman,  and Khan, MS and Heneberg, P and Zhou, CY and Muhammad, N and Zhu, XQ and Ma, J}, title = {Characterization of the complete mitochondrial genome of Uvitellina sp., representative of the family Cyclocoelidae and phylogenetic implications.}, journal = {Parasitology research}, volume = {118}, number = {7}, pages = {2203-2211}, pmid = {31154527}, issn = {1432-1955}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Birds/parasitology ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Echinostomatidae/classification/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Mitochondrial (mt) DNA has been useful in revealing the phylogenetic relationship of eukaryotic organisms including flatworms. Therefore, the use of mitogenomic data for the comparative and phylogenetic purposes is needed for those families of digenetic trematodes for which the mitogenomic data are still missing. Molecular data with sufficiently rich informative characters that can better resolve species identification, discrimination, and membership in different genera is also required for members of some morphologically difficult families of trematodes bearing few autapomorphic characters among its members. Here, the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (rDNA) and the complete mt genome of the trematode Uvitellina sp. (Cyclocoelidae: Haematotrephinae) was determined and annotated. The mt genome of this avian trematode is 14,217 bp in length, containing 36 genes plus a single non-coding region. The ITS rDNA sequences were used for the pairwise sequence comparison of Uvitellina sp. with European cyclocoelid species, and the mitochondrial 12 protein-coding genes (PCGs) and two ribosomal RNA genes were used to evaluate the position of the family within selected trematodes. The ITS rDNA analysis of Uvitellina sp. showed less nucleotide differences with Hyptiasmus oculeus (16.77%) than with other European cyclocoelids (18.63-23.58%). The Bayesian inference (BI) analysis using the 12 mt PCGs and two rRNA genes supported the placement of the family Cyclocoelidae within the superfamily Echinostomatoidea (Plagiorchiida: Echinostmata). The availability of the mt genome sequences of Uvitellina sp. provides a novel resource of molecular markers for phylogenetic studies of Cyclocoelidae and other trematodes.}, }
@article {pmid31153884, year = {2019}, author = {Wu, Q and Lan, Y and Cao, X and Yao, H and Qiao, D and Xu, H and Cao, Y}, title = {Characterization and diverse evolution patterns of glycerol-3-phosphate dehydrogenase family genes in Dunaliella salina.}, journal = {Gene}, volume = {710}, number = {}, pages = {161-169}, doi = {10.1016/j.gene.2019.05.056}, pmid = {31153884}, issn = {1879-0038}, mesh = {Algal Proteins/chemistry/genetics ; Amino Acid Motifs ; Chlorophyceae/*enzymology/genetics ; Chloroplasts/enzymology ; Data Mining/*methods ; Evolution, Molecular ; Glycerolphosphate Dehydrogenase/*chemistry/*genetics ; Mitochondria/enzymology ; Multigene Family ; Phylogeny ; Protein Domains ; Sequence Analysis, DNA ; }, abstract = {The glycerol-3-phosphate dehydrogenase (GPD) gene family plays a major role in glycerol synthesis and adaptation to abiotic stresses. Few studies on GPD family genes from the halotolerant algae Dunaliella salina are available. In this study, seven DsaGPD genes were identified by mining D. salina sequencing data. Among them, DsaGPD5 contained the canonical NAD[+]-GPD protein domain, called si-GPD. In comparison, DsaGPD1-4 not only contained the canonical NAD[+]-GPD domain but also a unique domain, the haloacid dehalogenase (HAD)-like superfamily domain, in their N-terminal region, called bi-GPD. DsaGPD6, 7 contained the FAD[+]-GPD domain. In the transient expression system, DsaGPD1, 3, 4 were found in the cytosol of Arabidopsis thaliana protoplast, DsaGPD2, 5 in the chloroplast, and DsaGPD6, 7 in the mitochondria. MEME analysis showed that six conserved motifs were present in both si-GPDs and bi-GPDs, whereas seven highly conserved motifs were only present in bi-GPDs. The quantitative real-time PCR results showed significant induction of the DsaGPD genes under abiotic stresses, indicating their tolerance-related role in D. salina. DsaGPD2 and DsaGPD5 may be the osmoregulator form and glyceride form in the chloroplast, respectively. The evolutionary forces acting on si-GPDs and bi-GPDs were different in the same organism: bi-GPDs were under purifying selection, while si-GPDs were mainly under positive selection. Furthermore, evolution of the N_HAD domain and C_GPD domain in bi-GPDs is highly correlated. In summary, this study characterizes DsaGPD gene family members and provides useful information for elucidating the salt tolerance mechanism in D. salina.}, }
@article {pmid31152352, year = {2019}, author = {Lassance, JM and Svensson, GP and Kozlov, MV and Francke, W and Löfstedt, C}, title = {Pheromones and Barcoding Delimit Boundaries between Cryptic Species in the Primitive Moth Genus Eriocrania (Lepidoptera: Eriocraniidae).}, journal = {Journal of chemical ecology}, volume = {45}, number = {5-6}, pages = {429-439}, pmid = {31152352}, issn = {1573-1561}, mesh = {Animals ; DNA/isolation &amp; purification/metabolism ; Electron Transport Complex IV/classification/genetics ; Female ; Genetic Variation ; Glyceraldehyde 3-Phosphate Dehydrogenase (NADP+)/classification/genetics ; Male ; Mitochondria/genetics ; Moths/*genetics ; Phylogeny ; Sex Attractants/*chemistry/metabolism ; }, abstract = {Animal classification is primarily based on morphological characters, even though these may not be the first to diverge during speciation. In many cases, closely related taxa are actually difficult to distinguish based on morphological characters alone, especially when there is no substantial niche separation. As a consequence, the diversity of certain groups is likely to be underestimated. Lepidoptera -moths and butterflies- represent the largest group of herbivorous insects. The extensive diversification in the group is generally assumed to have its origin in the spectacular radiation of flowering plants and the resulting abundance of ecological niches. However, speciation can also occur without strong ecological divergence. For example, reproductive isolation can evolve as the result of divergence in mate preference and the associated pheromone communication system. We combined pheromone trapping and genetic analysis to elucidate the evolutionary relationships within a complex of primitive moth species (Lepidoptera: Eriocraniidae). Mitochondrial and nuclear DNA markers provided evidence that Eriocrania semipurpurella, as currently defined by morphological characters, includes three cryptic species in Northern and Western Europe. Male moths of these cryptic species, as well as of the closely related E. sangii, exhibited relative specificity in terms of their attraction to specific ratios of two major pheromone components, (2S,6Z)-nonen-2-ol and (2R,6Z)-nonen-2-ol. Our data suggest strong assortative mating in these species in the absence of apparent niche separation, indicating that Eriocrania moths may represent an example of non-ecological speciation. Finally, our study argues in favour of combining pheromone investigations and DNA barcoding as powerful tools for identifying and delimitating species boundaries.}, }
@article {pmid31151779, year = {2019}, author = {Sihali-Beloui, O and Aroune, D and Benazouz, F and Hadji, A and El-Aoufi, S and Marco, S}, title = {A hypercaloric diet induces hepatic oxidative stress, infiltration of lymphocytes, and mitochondrial reshuffle in Psammomys obesus, a murine model of insulin resistance.}, journal = {Comptes rendus biologies}, volume = {342}, number = {5-6}, pages = {209-219}, doi = {10.1016/j.crvi.2019.04.003}, pmid = {31151779}, issn = {1768-3238}, mesh = {Animals ; Diet ; Disease Models, Animal ; Disease Progression ; Fatty Liver/metabolism/pathology ; *Gerbillinae ; Glutathione/metabolism ; Hyperphagia/*metabolism/pathology ; Inflammation/metabolism/pathology ; *Insulin Resistance ; Liver/*metabolism/pathology ; Male ; Malondialdehyde/metabolism ; Mitochondria, Liver/*metabolism/pathology ; *Neutrophil Infiltration ; *Oxidative Stress ; }, abstract = {The aim of this study was to show, for the first time, the effect of a hypercaloric diet on the mitochondrial reshuffle of hepatocytes during the progression from steatosis to steatohepatitis to cirrhosis in Psammomys obesus, a typical animal model of the metabolic syndrome. Metabolic and oxidative stresses were induced by feeding the animal through a standard laboratory diet (SD) for nine months. Metabolic parameters, liver malondialdehyde (MDA) and glutathione (GSH), were evaluated. The pathological evolution was examined by histopathology and immunohistochemistry, using CD3 and CD20 antibodies. The dynamics of the mitochondrial structure was followed by transmission electron microscopy. SD induced a steatosis in this animal that evolved under the effect of oxidative and metabolic stress by the appearance of adaptive inflammation and fibrosis leading the animal to the cirrhosis stage with serious hepatocyte damage by the triggering, at first the mitochondrial fusion-fission cycles, which attempted to maintain the mitochondria intact and functional, but the hepatocellular oxidative damage was increased inducing a vicious circle of mitochondrial alteration and dysfunction and their elimination by mitophagy. P. obesus is an excellent animal model of therapeutic research that targets mitochondrial dysfunction in the progression of steatosis.}, }
@article {pmid31150090, year = {2019}, author = {Yin, HZ and Wang, HL and Ji, SG and Medvedeva, YV and Tian, G and Bazrafkan, AK and Maki, NZ and Akbari, Y and Weiss, JH}, title = {Rapid Intramitochondrial Zn2+ Accumulation in CA1 Hippocampal Pyramidal Neurons After Transient Global Ischemia: A Possible Contributor to Mitochondrial Disruption and Cell Death.}, journal = {Journal of neuropathology and experimental neurology}, volume = {78}, number = {7}, pages = {655-664}, pmid = {31150090}, issn = {1554-6578}, support = {UL1 TR001414/TR/NCATS NIH HHS/United States ; R21 NS096987/NS/NINDS NIH HHS/United States ; R56 NS100494/NS/NINDS NIH HHS/United States ; R21 EB024793/EB/NIBIB NIH HHS/United States ; KL2 TR001416/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; CA1 Region, Hippocampal/cytology/*metabolism/pathology ; CA3 Region, Hippocampal/cytology/metabolism/pathology ; Cell Death ; Ischemic Attack, Transient/*metabolism/pathology ; Male ; Mitochondria/*metabolism/pathology/ultrastructure ; Mitochondrial Swelling ; Pyramidal Cells/*metabolism ; Rats ; Rats, Wistar ; Zinc/*metabolism ; }, abstract = {Mitochondrial Zn2+ accumulation, particularly in CA1 neurons, occurs after ischemia and likely contributes to mitochondrial dysfunction and subsequent neurodegeneration. However, the relationship between mitochondrial Zn2+ accumulation and their disruption has not been examined at the ultrastructural level in vivo. We employed a cardiac arrest model of transient global ischemia (TGI), combined with Timm's sulfide silver labeling, which inserts electron dense metallic silver granules at sites of labile Zn2+ accumulation, and used transmission electron microscopy (TEM) to examine subcellular loci of the Zn2+ accumulation. In line with prior studies, TGI-induced damage to CA1 was far greater than to CA3 pyramidal neurons, and was substantially progressive in the hours after reperfusion (being significantly greater after 4- than 1-hour recovery). Intriguingly, TEM examination of Timm's-stained sections revealed substantial Zn2+ accumulation in many postischemic CA1 mitochondria, which was strongly correlated with their swelling and disruption. Furthermore, paralleling the evolution of neuronal injury, both the number of mitochondria containing Zn2+ and the degree of their disruption were far greater at 4- than 1-hour recovery. These data provide the first direct characterization of Zn2+ accumulation in CA1 mitochondria after in vivo TGI, and support the idea that targeting these events could yield therapeutic benefits.}, }
@article {pmid31141182, year = {2019}, author = {de Oliveira Boldrini, V and Dos Santos Farias, A and Degasperi, GR}, title = {Deciphering targets of Th17 cells fate: From metabolism to nuclear receptors.}, journal = {Scandinavian journal of immunology}, volume = {90}, number = {4}, pages = {e12793}, doi = {10.1111/sji.12793}, pmid = {31141182}, issn = {1365-3083}, support = {//CNPq-INCT (Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico-Instituto Nacional de Ci&#xea;ncia e Tecnologia em Neuroimunomodula&#xe7;&#xe3;o)/ ; //CAPES (Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior)/ ; 17/21363-5//FAPESP (Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo)/ ; }, mesh = {Animals ; Autoimmunity ; Cell Differentiation ; Cellular Reprogramming ; Glycolysis ; Humans ; Lymphocyte Activation ; Multiple Sclerosis/*immunology ; Nuclear Receptor Subfamily 1, Group F, Member 3/*metabolism ; Oxidative Phosphorylation ; Peroxisome Proliferator-Activated Receptors/*metabolism ; Th17 Cells/immunology/*metabolism ; }, abstract = {Evidence indicates that reprogramming of metabolism is critically important for the differentiation of CD4 + T lymphocytes, and the manipulation of metabolic pathways in these cells may shape their fate and function. Distinct subgroups from T lymphocytes, such as Th17, adopt specific metabolic programmes to support their needs. Some important metabolic reactions, such as glycolysis, oxidative phosphorylation, are considered important for the differentiation of these lymphocytes. Since their discovery nearly a decade ago, Th17 lymphocytes have received significant attention because of their role in the pathology of several immune-mediated inflammatory diseases such as multiple sclerosis. In this review, it will be discussed as the involvement of T cell metabolism and as metabolic reprogramming in activated T cells dictates fate decisions to Th17. The involvement of nuclear receptors such as RORyt e PPARs in the induction of Th17 cells was also discussed. Understanding the metabolic pathways involved in the differentiation of the distinct subgroups of T lymphocytes helps in the design of promising therapeutic proposals.}, }
@article {pmid31139952, year = {2019}, author = {Ghadery, C and Best, LA and Pavese, N and Tai, YF and Strafella, AP}, title = {PET Evaluation of Microglial Activation in Non-neurodegenerative Brain Diseases.}, journal = {Current neurology and neuroscience reports}, volume = {19}, number = {7}, pages = {38}, pmid = {31139952}, issn = {1534-6293}, mesh = {Animals ; Biomarkers/metabolism ; Brain/*metabolism ; Brain Ischemia ; Central Nervous System/metabolism ; Humans ; Microglia/*metabolism ; Multiple Sclerosis ; Neurodegenerative Diseases/*metabolism ; *Positron-Emission Tomography ; Radiopharmaceuticals ; Receptors, GABA/*metabolism ; Stroke ; }, abstract = {PURPOSE OF THE REVIEW: Microglial cell activation is an important component of neuroinflammation, and it is generally well accepted that chronic microglial activation is indicative of accumulating tissue damage in neurodegenerative conditions, particularly in the earlier stages of disease. Until recently, there has been less focus on the role of neuroinflammation in other forms of neurological and neuropsychiatric conditions. Through this review, we hope to demonstrate the important role TSPO PET imaging has played in illuminating the pivotal role of neuroinflammation and microglial activation underpinning these conditions.<br><br>RECENT FINDINGS: TSPO is an 18&#xa0;kDa protein found on the outer membrane of mitochondria and can act as a marker of microglial activation using nuclear imaging. Through the development of radiopharmaceuticals targeting TSPO, researchers have been able to better characterise the spatial-temporal evolution of chronic neurological conditions, ranging from the focal autoimmune reactions seen in multiple sclerosis to the Wallerian degeneration at remote parts of the brain months following acute cerebral infarction. Development of novel techniques to investigate neuroinflammation within the central nervous system, for the purposes of diagnosis and therapeutics, has flourished over the past few decades. TSPO has proven itself a robust and sensitive biomarker of microglial activation and neuroimaging affords a minimally invasive technique to characterise neuroinflammatory processes in vivo.}, }
@article {pmid31138949, year = {2019}, author = {Storz, JF and Cheviron, ZA and McClelland, GB and Scott, GR}, title = {Evolution of physiological performance capacities and environmental adaptation: insights from high-elevation deer mice (Peromyscus maniculatus).}, journal = {Journal of mammalogy}, volume = {100}, number = {3}, pages = {910-922}, pmid = {31138949}, issn = {0022-2372}, support = {R01 HL087216/HL/NHLBI NIH HHS/United States ; }, abstract = {Analysis of variation in whole-animal performance can shed light on causal connections between specific traits, integrated physiological capacities, and Darwinian fitness. Here, we review and synthesize information on naturally occurring variation in physiological performance capacities and how it relates to environmental adaptation in deer mice (Peromyscus maniculatus). We discuss how evolved changes in aerobic exercise capacity and thermogenic capacity have contributed to adaptation to high elevations. Comparative work on deer mice at high and low elevations has revealed evolved differences in aerobic performance capacities in hypoxia. Highland deer mice have consistently higher aerobic performance capacities under hypoxia relative to lowland natives, consistent with the idea that it is beneficial to have a higher maximal metabolic rate (as measured by the maximal rate of O2 consumption, VO2max) in an environment characterized by lower air temperatures and lower O2 availability. Observed differences in aerobic performance capacities between highland and lowland deer mice stem from changes in numerous subordinate traits that alter the flux capacity of the O2-transport system, the oxidative capacity of tissue mitochondria, and the relationship between O2 consumption and ATP synthesis. Many such changes in physiological phenotype are associated with hypoxia-induced changes in gene expression. Research on natural variation in whole-animal performance forms a nexus between physiological ecology and evolutionary biology that requires insight into the natural history of the study species.}, }
@article {pmid31136801, year = {2019}, author = {Peres, EA and Benedetti, AR and Hiruma, ST and Sobral-Souza, T and Pinto-da-Rocha, R}, title = {Phylogeography of Sodreaninae harvestmen (Arachnida: Opiliones: Gonyleptidae): Insights into the biogeography of the southern Brazilian Atlantic Forest.}, journal = {Molecular phylogenetics and evolution}, volume = {138}, number = {}, pages = {1-16}, doi = {10.1016/j.ympev.2019.05.028}, pmid = {31136801}, issn = {1095-9513}, mesh = {Animals ; Arachnida/*classification/genetics ; Bayes Theorem ; Brazil ; Cell Nucleus/genetics ; *Forests ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeny ; *Phylogeography ; Population Dynamics ; }, abstract = {The Brazilian Atlantic Forest has long been considered a global biodiversity hotspot. In the last decade, the phylogeographic patterns of endemic taxa have been unraveling the biogeographic history of the biome. However, highly diverse invertebrate species have still been poorly studied. Sodreana harvestmen (Gonyleptidae) are distributed in most of the humid coastal forests in the southern portion of the Atlantic Forest, a region that has experienced complex topographic evolution and differing climatic conditions since the Early Cretaceous, which likely affected the geographic distribution and diversification of the group. In this study, we investigated the molecular phylogeny and phylogeography of Sodreana to clarify the species relationships and to make inferences about the historical biogeography of the southern Atlantic Forest. We applied coalescent-based phylogenetic analyses using one mitochondrial and three nuclear markers coupled with an ecological niche modeling approach to verify relationships among species, date the main divergence events in the genus, and make inferences concerning possible changes in the geographical distribution and population dynamics from the past. Our results supported the validity of most Sodreana species and suggested that Paleogene-Neogene geomorphologic processes such as the formation of rivers systems, uplift of mountain ranges and related environmental changes have profoundly affected the evolutionary history of Sodreana. The ecological niche models showed that the areas potentially occupied by the species were greatly reduced during Quaternary glacial periods but no recent lineage divergences or genetic bottlenecks were detected, suggesting that climatically stable micro-habitats could have helped maintain populations during drier periods. Our study highlights the importance of humidity-dependent and poor-dispersal taxa in understanding the effects of ancient geological and climate processes on the Atlantic Forest biota.}, }
@article {pmid31126471, year = {2019}, author = {Mascolo, C and Ceruso, M and Sordino, P and Palma, G and Anastasio, A and Pepe, T}, title = {Comparison of mitochondrial DNA enrichment and sequencing methods from fish tissue.}, journal = {Food chemistry}, volume = {294}, number = {}, pages = {333-338}, doi = {10.1016/j.foodchem.2019.05.026}, pmid = {31126471}, issn = {1873-7072}, mesh = {Animals ; DNA, Mitochondrial/chemistry/*metabolism ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/genetics ; Perciformes/*genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA/*methods ; }, abstract = {Sparid fish species have different commercial values related to their organoleptic features. Mitochondrial (mt) DNA provides a potential tool to distinguish species, but the enrichment of high-quality mtDNA from total genomic DNA is critical to obtain entire mtDNA sequences. Conventional mtDNA isolation is relatively low-cost and proficient. However, high numbers of PCR cycles can lead to artefacts (10[-6] mutations/bp). We describe a rapid protocol for mtDNA extraction and enrichment from fish tissues, based on conventional miniprep columns and paramagnetic bead-based purification, without the need to employ PCR amplification. This newly described method generates a substrate for next-generation sequencing (NGS) analysis and is likely to have wider applications for mitochondrial studies in other fish families to help ensure traceability and differentiation of fish with high commercial values.}, }
@article {pmid31125665, year = {2019}, author = {Liu, W and Chen, B and Chen Li,  and Yao, J and Liu, J and Kuang, M and Wang, F and Wang, Y and Elkady, G and Lu, Y and Zhang, Y and Liu, X}, title = {Identification of fish CMPK2 as an interferon stimulated gene against SVCV infection.}, journal = {Fish &amp; shellfish immunology}, volume = {92}, number = {}, pages = {125-132}, doi = {10.1016/j.fsi.2019.05.032}, pmid = {31125665}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Fish Diseases/*immunology ; Gene Expression Profiling/veterinary ; Gene Expression Regulation/*immunology ; Immunity, Innate/*genetics ; Interferons/metabolism ; Nucleoside-Phosphate Kinase/*genetics/*immunology ; Phylogeny ; Rhabdoviridae/physiology ; Rhabdoviridae Infections/immunology/veterinary ; Sequence Alignment/veterinary ; Zebrafish/*genetics/*immunology ; Zebrafish Proteins/*genetics/*immunology ; }, abstract = {Cytidine/uridine monophosphate kinase 2 (CMPK2) is known as a nucleoside monophosphate kinase in mitochondria to maintains intracellular UTP/CTP, and could be induced by immunostimulants LPS and Poly (I:C) in mammals, suggesting its potential antiviral and antibacterial role. In this study, CMPK2 was cloned and characterized in Fathead minnow (FHM) cells. In vivo analysis of tissue distribution revealed that CMPK2 transcript was detected in all the tissues of zebrafish (Danio rerio) examined in this study, particularly abundant in liver, spleen and kidney. In addition, indirect immunofluorescence showed that CMPK2 was localized in the cytoplasm of FHM cells. Expression of CMPK2 mRNA was significantly up-regulated following challenge with Spring viraemia of carp virus (SVCV), poly(I:C), or zebrafish IFN1 and IFN3 both in vitro and in vivo. Furthermore, overexpression and RNA interference of CMPK2 in SVCV-infected FHM cells showed significantly antiviral effect. In summary, this study for the first time shows the presence and distribution of CMPK2 in different tissues of zebrafish, but also demonstrates its antiviral potential against SVCV infection in vivo. These new findings could contribute to explain the molecular mechanism of the CMPK2 mediated antiviral function.}, }
@article {pmid31121309, year = {2019}, author = {Santos, JCMD and Ferreira, ES and Oliveira, C and Oliveira, TB and Costa, ASLD and Queiroz, AKO and Schneider, H and Sampaio, I and Santos, S}, title = {Phylogeny of the genus Hypophthalmus Cuvier, 1829 (Pimelodidae - Siluriformes), based on a multilocus analysis, indicates diversification and introgression in the Amazon basin.}, journal = {Molecular phylogenetics and evolution}, volume = {137}, number = {}, pages = {285-292}, doi = {10.1016/j.ympev.2019.05.017}, pmid = {31121309}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Catfishes/*classification/*genetics ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Genetic Loci ; *Genetic Variation ; Hybridization, Genetic ; Mitochondria/genetics ; *Phylogeny ; Species Specificity ; }, abstract = {The genus Hypophthalmus encompasses four valid South American freshwater catfish species: H. marginatus, H. edentatus, H. fimbriatus, and H. oremaculatus. More recently two new species were proposed Hypophthalmus n. sp. 1 and Hypophthalmus n. sp. 2. While Hypophthalmus species are a fundamentally important resource for the commercial fisheries that operate in the continental waters of the Amazon basin, their phylogenetic relationships and the true diversity of the genus have yet to be defined conclusively. Given this, the present study analyzed sequences of the mitochondrial COI gene and four nuclear markers (RAG2, Myh6, Plagl2 and Glyt) to evaluate the phylogenetic relationships and the diversity of the species of this genus. All the analyses showed that Hypophthalmus is monophyletic, and the species delimitation tests recovered all the Hypophthalmus taxa as distinct species. The putative new species Hypophthalmus n. sp. 1 and Hypophthalmus n. sp. 2 presented mean genetic divergence similar to or greater than that observed between valid Hypophthalmus taxa. All the analyses showed that H. oremaculatus is the sister group of H. n. sp. 1, which together group with H. fimbriatus. This clade is the sister group of the clade containing H. edentatus and H. n. sp. 2. One specimen, morphologically identified as H. oremaculatus, presented the nuclear genome of this species and the mitochondrial genome of H. n. sp. 1; while another specimen, morphologically identified as H. n. sp. 2, presented the nuclear Myh6 of H. n. sp. 2 and the mitochondrial and RAG2 genome of H. edentatus. These results indicate that hybridization and introgression has occurred between species in Hypophthalmus. The findings of this study indicate that the diversity of the Hypophthalmus is underestimated, emphasize the need for a taxonomic review of the genus, and a more systematic evaluation of the hybridization patterns found, to understanding the role of hybridization and introgression in the evolution of the genus.}, }
@article {pmid31120535, year = {2019}, author = {Sokolova, IM and Sokolov, EP and Haider, F}, title = {Mitochondrial Mechanisms Underlying Tolerance to Fluctuating Oxygen Conditions: Lessons from Hypoxia-Tolerant Organisms.}, journal = {Integrative and comparative biology}, volume = {59}, number = {4}, pages = {938-952}, doi = {10.1093/icb/icz047}, pmid = {31120535}, issn = {1557-7023}, mesh = {*Adaptation, Biological ; Anaerobiosis ; Animals ; Mitochondria/*physiology ; Oxidation-Reduction ; *Oxidative Stress ; Oxygen/*metabolism ; }, abstract = {Oxygen (O2) is essential for most metazoan life due to its central role in mitochondrial oxidative phosphorylation (OXPHOS), which generates >90% of the cellular adenosine triphosphate. O2 fluctuations are an ultimate mitochondrial stressor resulting in mitochondrial damage, energy deficiency, and cell death. This work provides an overview of the known and putative mechanisms involved in mitochondrial tolerance to fluctuating O2 conditions in hypoxia-tolerant organisms including aquatic and terrestrial vertebrates and invertebrates. Mechanisms of regulation of the mitochondrial OXPHOS and electron transport system (ETS) (including alternative oxidases), sulphide tolerance, regulation of redox status and mitochondrial quality control, and the potential role of hypoxia-inducible factor (HIF) in mitochondrial tolerance to hypoxia are discussed. Mitochondrial phenotypes of distantly related animal species reveal common features including conservation and/or anticipatory upregulation of ETS capacity, suppression of reactive oxygen species (ROS)-producing electron flux through ubiquinone, reversible suppression of OXPHOS activity, and investment into the mitochondrial quality control mechanisms. Despite the putative importance of oxidative stress in adaptations to hypoxia, establishing the link between hypoxia tolerance and mitochondrial redox mechanisms is complicated by the difficulties of establishing the species-specific concentration thresholds above which the damaging effects of ROS outweigh their potentially adaptive signaling function. The key gaps in our knowledge about the potential mechanisms of mitochondrial tolerance to hypoxia include regulation of mitochondrial biogenesis and fusion/fission dynamics, and HIF-dependent metabolic regulation that require further investigation in hypoxia-tolerant species. Future physiological, molecular and genetic studies of mitochondrial responses to hypoxia, and reoxygenation in phylogenetically diverse hypoxia-tolerant species could reveal novel solutions to the ubiquitous and metabolically severe problem of O2 deficiency and would have important implications for understanding the evolution of hypoxia tolerance and the potential mitigation of pathological states caused by O2 fluctuations.}, }
@article {pmid31112782, year = {2019}, author = {Gandini, CL and Garcia, LE and Abbona, CC and Sanchez-Puerta, MV}, title = {The complete organelle genomes of Physochlaina orientalis: Insights into short sequence repeats across seed plant mitochondrial genomes.}, journal = {Molecular phylogenetics and evolution}, volume = {137}, number = {}, pages = {274-284}, doi = {10.1016/j.ympev.2019.05.012}, pmid = {31112782}, issn = {1095-9513}, mesh = {Base Sequence ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; *Genome, Plant ; Genome, Plastid ; Introns/genetics ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Phylogeny ; Seeds/*genetics ; Solanaceae/*genetics ; }, abstract = {Short repeats (SR) play an important role in shaping seed plant mitochondrial genomes (mtDNAs). However, their origin, distribution, and relationships across the different plant lineages remain unresolved. We focus on the angiosperm family Solanaceae that shows great variation in repeat content and extend the study to a wide diversity of seed plants. We determined the complete nucleotide sequences of the organellar genomes of the medicinal plant Physochlaina orientalis (Solanaceae), member of the tribe Hyoscyameae. To understand the evolution of the P. orientalis mtDNA we made comparisons with those of five other Solanaceae. P. orientalis mtDNA presents the largest mitogenome (∼685 kb in size) among the Solanaceae and has an unprecedented 8-copy repeat family of ∼8.2 kb in length and a great number of SR arranged in tandem-like structures. We found that the SR in the Solanaceae share a common origin, but these only expanded in members of the tribe Hyoscyameae. We discuss a mechanism that could explain SR formation and expansion in P. orientalis and Hyoscyamus niger. Finally, the great increase in plant mitochondrial data allowed us to systematically extend our repeat analysis to a total of 136 seed plants to characterize and analyze for the first time families of SR among seed plant mtDNAs.}, }
@article {pmid31105043, year = {2019}, author = {Dumesic, PA and Egan, DF and Gut, P and Tran, MT and Parisi, A and Chatterjee, N and Jedrychowski, M and Paschini, M and Kazak, L and Wilensky, SE and Dou, F and Bogoslavski, D and Cartier, JA and Perrimon, N and Kajimura, S and Parikh, SM and Spiegelman, BM}, title = {An Evolutionarily Conserved uORF Regulates PGC1α and Oxidative Metabolism in Mice, Flies, and Bluefin Tuna.}, journal = {Cell metabolism}, volume = {30}, number = {1}, pages = {190-200.e6}, pmid = {31105043}, issn = {1932-7420}, support = {R01 DK095072/DK/NIDDK NIH HHS/United States ; R01 DK054477/DK/NIDDK NIH HHS/United States ; R01 DK061562/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R35 HL139424/HL/NHLBI NIH HHS/United States ; F32 DK112638/DK/NIDDK NIH HHS/United States ; }, mesh = {5' Untranslated Regions/*genetics ; Animals ; Diptera ; Female ; HEK293 Cells ; Humans ; Immunoprecipitation ; Male ; Mice ; Mutation/genetics ; Open Reading Frames/*genetics ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/genetics/*metabolism ; Phylogeny ; Protein Processing, Post-Translational/genetics ; Tuna ; Zebrafish ; }, abstract = {Mitochondrial abundance and function are tightly controlled during metabolic adaptation but dysregulated in pathological states such as diabetes, neurodegeneration, cancer, and kidney disease. We show here that translation of PGC1α, a key governor of mitochondrial biogenesis and oxidative metabolism, is negatively regulated by an upstream open reading frame (uORF) in the 5' untranslated region of its gene (PPARGC1A). We find that uORF-mediated translational repression is a feature of PPARGC1A orthologs from human to fly. Strikingly, whereas multiple inhibitory uORFs are broadly present in fish PPARGC1A orthologs, they are completely absent in the Atlantic bluefin tuna, an animal with exceptionally high mitochondrial content. In mice, an engineered mutation disrupting the PPARGC1A uORF increases PGC1α protein levels and oxidative metabolism and confers protection from acute kidney injury. These studies identify a translational regulatory element governing oxidative metabolism and highlight its potential contribution to the evolution of organismal mitochondrial function.}, }
@article {pmid31095885, year = {2019}, author = {Vesteg, M and Hadariová, L and Horváth, A and Estraño, CE and Schwartzbach, SD and Krajčovič, J}, title = {Comparative molecular cell biology of phototrophic euglenids and parasitic trypanosomatids sheds light on the ancestor of Euglenozoa.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {94}, number = {5}, pages = {1701-1721}, doi = {10.1111/brv.12523}, pmid = {31095885}, issn = {1469-185X}, mesh = {*Biological Evolution ; DNA-Directed RNA Polymerases/genetics/metabolism ; Euglenida/classification/genetics ; Euglenozoa/*classification/genetics ; Genome/physiology ; Introns/physiology ; Mitochondria/genetics ; *Molecular Biology ; Phototrophic Processes ; Phylogeny ; RNA Interference ; RNA, Ribosomal, 28S/genetics ; Trypanosomatina/classification/enzymology/*genetics ; }, abstract = {Parasitic trypanosomatids and phototrophic euglenids are among the most extensively studied euglenozoans. The phototrophic euglenid lineage arose relatively recently through secondary endosymbiosis between a phagotrophic euglenid and a prasinophyte green alga that evolved into the euglenid secondary chloroplast. The parasitic trypanosomatids (i.e. Trypanosoma spp. and Leishmania spp.) and the freshwater phototrophic euglenids (i.e. Euglena gracilis) are the most evolutionary distant lineages in the Euglenozoa phylogenetic tree. The molecular and cell biological traits they share can thus be considered as ancestral traits originating in the common euglenozoan ancestor. These euglenozoan ancestral traits include common mitochondrial presequence motifs, respiratory chain complexes containing various unique subunits, a unique ATP synthase structure, the absence of mitochondria-encoded transfer RNAs (tRNAs), a nucleus with a centrally positioned nucleolus, closed mitosis without dissolution of the nuclear membrane and nucleoli, a nuclear genome containing the unusual 'J' base (β-D-glucosyl-hydroxymethyluracil), processing of nucleus-encoded precursor messenger RNAs (pre-mRNAs) via spliced-leader RNA (SL-RNA) trans-splicing, post-transcriptional gene silencing by the RNA interference (RNAi) pathway and the absence of transcriptional regulation of nuclear gene expression. Mitochondrial uridine insertion/deletion RNA editing directed by guide RNAs (gRNAs) evolved in the ancestor of the kinetoplastid lineage. The evolutionary origin of other molecular features known to be present only in either kinetoplastids (i.e. polycistronic transcripts, compaction of nuclear genomes) or euglenids (i.e. monocistronic transcripts, huge genomes, many nuclear cis-spliced introns, polyproteins) is unclear.}, }
@article {pmid31092607, year = {2019}, author = {Tian, R and Seim, I and Ren, W and Xu, S and Yang, G}, title = {Contraction of the ROS Scavenging Enzyme Glutathione S-Transferase Gene Family in Cetaceans.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {7}, pages = {2303-2315}, pmid = {31092607}, issn = {2160-1836}, mesh = {Adaptation, Physiological ; Animals ; Cytosol/metabolism ; Gene Deletion ; Gene Duplication ; Glutathione Transferase/*genetics/metabolism ; Mammals ; *Multigene Family ; Oxidative Stress ; Phylogeny ; Reactive Oxygen Species/*metabolism ; Whales/classification/*genetics ; }, abstract = {Cetaceans are a group of marine mammals whose ancestors were adaptated for life on land. Life in an aquatic environment poses many challenges for air-breathing mammals. Diving marine mammals have adapted to rapid reoxygenation and reactive oxygen species (ROS)-mediated reperfusion injury. Here, we considered the evolution of the glutathione transferase (GST) gene family which has important roles in the detoxification of endogenously-derived ROS and environmental pollutants. We characterized the cytosolic GST gene family in 21 mammalian species; cetaceans, sirenians, pinnipeds, and their terrestrial relatives. All seven GST classes were identified, showing that GSTs are ubiquitous in mammals. Some GST genes are the product of lineage-specific duplications and losses, in line with a birth-and-death evolutionary model. We detected sites with signatures of positive selection that possibly influence GST structure and function, suggesting that adaptive evolution of GST genes is important for defending mammals from various types of noxious environmental compounds. We also found evidence for loss of alpha and mu GST subclass genes in cetacean lineages. Notably, cetaceans have retained a homolog of at least one of the genes GSTA1, GSTA4, and GSTM1; GSTs that are present in both the cytosol and mitochondria. The observed variation in number and selection pressure on GST genes suggest that the gene family structure is dynamic within cetaceans.}, }
@article {pmid31089765, year = {2019}, author = {Zhang, S and Zhang, YJ and Li, ZL}, title = {Complete mitogenome of the entomopathogenic fungus Sporothrix insectorum RCEF 264 and comparative mitogenomics in Ophiostomatales.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {14}, pages = {5797-5809}, doi = {10.1007/s00253-019-09855-3}, pmid = {31089765}, issn = {1432-0614}, support = {31872162//National Natural Science Foundation of China/ ; 201601D011065//Natural Science Foundation of Shanxi Province/ ; }, mesh = {DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Fungal Proteins/*genetics ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Introns/genetics ; Mitochondria/genetics ; Mutagenesis, Insertional ; Ophiostomatales/*genetics ; Phylogeny ; Sporothrix/*genetics ; }, abstract = {The fungal order Ophiostomatales contains numerous species important in medical fields, agriculture, and forestry, and several species have had available mitogenome information. The nuclear genome of the entomopathogenic fungus Sporothrix insectorum has been reported, while its mitogenome remains unknown. Herein, we firstly described the mitogenome of S. insectorum RCEF 264 and then compared Ophiostomatales mitogenomes from both interspecific and intraspecific perspectives. The mitogenome of S. insectorum RCEF 264 was 31,454 bp in length, containing typical fungal mitochondrial genes plus rnpB. Four group I introns interrupted rnl and cox1. Phylogenetic analyses confirmed the placement of S. insectorum RCEF 264 in Ophiostomatales. Comparison of mitogenomes among seven Ophiostomatales species revealed conserved gene contents and a high synteny, although there were also some differences among them. Their mitogenomes showed more than two-fold variations (26.6-65.1 kb) in size, with a total of 37 intron insertional loci from 11 genes (1-25 introns per species). The sole intron shared by all species was an rps3-encoding intron in rnl (mL2450), and this intron-based phylogeny was highly consistent with those constructed using mitochondrial/nuclear genes, suggesting convergent evolution of this intron with Ophiostomatales species. The dendrogram based on presence/absence patterns at all intron loci was quite different from those based on mitochondrial/nuclear genes. Comparison of mitogenomes among two to three intraspecific individuals in Ophiostoma novo-ulmi subsp. novo-ulmi and Sporothrix schenckii revealed mitogenome size variations due to single-nucleotide polymorphisms (SNPs) and indels but without fluctuation of intron numbers for each species. This study greatly enhanced our understanding of mitogenome evolution in Ophiostomatales.}, }
@article {pmid31088635, year = {2019}, author = {Tan, DX}, title = {Aging: An evolutionary competition between host cells and mitochondria.}, journal = {Medical hypotheses}, volume = {127}, number = {}, pages = {120-128}, doi = {10.1016/j.mehy.2019.04.007}, pmid = {31088635}, issn = {1532-2777}, mesh = {*Aging ; Animals ; Biological Evolution ; Cell Nucleus/metabolism ; Cellular Senescence/genetics ; DNA, Mitochondrial/*metabolism ; Endocytosis ; Evolution, Molecular ; Free Radicals ; Gene Deletion ; Humans ; Immunity, Innate ; Mice ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitosis ; Models, Biological ; Mutation ; Oxidative Stress ; Phenotype ; Reactive Oxygen Species/metabolism ; }, abstract = {Here, a new theory of aging is proposed. This new theory is referred as the Host-Mitochondria Intracellular Innate Immune Theory of Aging (HMIIITA). The main point of this theory is that the aging is rooted from an evolutionary competition, that is, a never ending coevolutionary race between host cells and mitochondria. Mitochondria are the descendants of bacteria. The host cells will inevitably sense their bacterial origin, particularly their circular mtDNA. The host intracellular innate immune pressure (HIIIP) aims to eliminate mtDNA as more as possible while mitochondria have to adapt the HIIIP for survival. Co-evolution is required for both of them. From biological point of view, the larger, the mtDNA, the higher, the chance, it becomes the target of HIIIP. As a result, mitochondria have to reduce their mtDNA size via deletion. This process has last for 1.5-2 billion yeas and the result is that mitochondria have lost excessive 95% of their DNA. This mtDNA deletion is not associated with free radical attack but a unique trait acquired during evolution. In the postmitotic cells, the deletion is passively selected by the mitochondrial fission-fusion cycles. Eventually, the accumulation of deletion will significantly jeopardize the mitochondrial function. The dysfunctional mitochondria no longer provide sufficient ATP to support host cells' continuous demanding for growth. At this stage, the cell or the organism aging is inevitable.}, }
@article {pmid31088494, year = {2019}, author = {Shah, A and Hoffman, JI and Schielzeth, H}, title = {Transcriptome assembly for a colour-polymorphic grasshopper (Gomphocerus sibiricus) with a very large genome size.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {370}, pmid = {31088494}, issn = {1471-2164}, support = {SCHI 1188/1-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; Contig Mapping ; Female ; Gene Expression Profiling/*methods ; Genetic Association Studies ; Genome Size ; Grasshoppers/*genetics ; High-Throughput Nucleotide Sequencing ; Male ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Sequence Analysis, RNA/*methods ; }, abstract = {BACKGROUND: The club-legged grasshopper Gomphocerus sibiricus is a Gomphocerinae grasshopper with a promising future as model species for studying the maintenance of colour-polymorphism, the genetics of sexual ornamentation and genome size evolution. However, limited molecular resources are available for this species. Here, we present a de novo transcriptome assembly as reference resource for gene expression studies. We used high-throughput Illumina sequencing to generate 5,070,036 paired-end reads after quality filtering. We then combined the best-assembled contigs from three different de novo transcriptome assemblers (Trinity, SOAPdenovo-trans and Oases/Velvet) into a single assembly.<br><br>RESULTS: This resulted in 82,251 contigs with a N50 of 1357 and a TransRate assembly score of 0.325, which compares favourably with other orthopteran transcriptome assemblies. Around 87% of the transcripts could be annotated using InterProScan 5, BLASTx and the dammit! annotation pipeline. We identified a number of genes involved in pigmentation and green pigment metabolism pathways. Furthermore, we identified 76,221 putative single nucleotide polymorphisms residing in 8400 contigs. We also assembled the mitochondrial genome and investigated levels of sequence divergence with other species from the genus Gomphocerus. Finally, we detected and assembled Wolbachia sequences, which revealed close sequence similarity to the strain pel wPip.<br><br>CONCLUSIONS: Our study has generated a significant resource for uncovering genotype-phenotype associations in a species with an extraordinarily large genome, while also providing mitochondrial and Wolbachia sequences that will be useful for comparative studies.}, }
@article {pmid31086122, year = {2019}, author = {Santos, HJ and Hanadate, Y and Imai, K and Nozaki, T}, title = {An Entamoeba-Specific Mitosomal Membrane Protein with Potential Association to the Golgi Apparatus.}, journal = {Genes}, volume = {10}, number = {5}, pages = {}, pmid = {31086122}, issn = {2073-4425}, mesh = {Amino Acid Sequence ; Biological Evolution ; Calcium-Transporting ATPases/metabolism ; Computer Simulation ; Entamoeba/*metabolism ; Entamoeba histolytica/genetics/metabolism ; Golgi Apparatus/metabolism ; Membrane Proteins/*metabolism ; Microscopy, Immunoelectron/methods ; Mitochondria/metabolism ; Mitochondrial Membranes/*metabolism ; Organelles/metabolism ; Protein Transport ; Protozoan Proteins ; }, abstract = {The aerobic mitochondrion had undergone evolutionary diversification, most notable among lineages of anaerobic protists. Entamoeba is one of the genera of parasitic protozoans that lack canonical mitochondria, and instead possess mitochondrion-related organelles (MROs), specifically mitosomes. Entamoeba mitosomes exhibit functional reduction and divergence, most exemplified by the organelle's inability to produce ATP and synthesize iron-sulfur cluster. Instead, this organelle is capable of sulfate activation, which has been linked to amoebic stage conversion. In order to understand other unique features and components of this MRO, we utilized an in silico prediction tool to screen transmembrane domain containing proteins in the mitosome proteome. Here, we characterize a novel lineage-specific mitosomal membrane protein, named Entamoeba transmembrane mitosomal protein of 30 kDa (ETMP30; EHI_172170), predicted to contain five transmembrane domains. Immunofluorescence analysis demonstrated colocalization of hemagglutinin (HA)-tagged ETMP30 with the mitosomal marker, adenosine-5'-phosphosulfate kinase. Mitosomal membrane localization was indicated by immunoelectron microscopy analysis, which was supported by carbonate fractionation assay. Transcriptional gene silencing successfully repressed RNA expression by 60%, and led to a defect in growth and partial elongation of mitosomes. Immunoprecipitation of ETMP30 from ETMP30-HA-expressing transformant using anti-HA antibody pulled down one interacting protein of 126 kDa. Protein sequencing by mass spectrometry revealed this protein as a cation-transporting P-type ATPase, previously reported to localize to vacuolar compartments/Golgi-like structures, hinting at a possible mitosome-vacuole/Golgi contact site.}, }
@article {pmid31077734, year = {2019}, author = {Karagozlu, MZ and An, HE and Park, SH and Shin, SE and Kim, CB}, title = {Comparative analyses of the three complete mitochondrial genomes from forensic important beetle genus Dermestes with phylogenetic relationships.}, journal = {Gene}, volume = {706}, number = {}, pages = {146-153}, doi = {10.1016/j.gene.2019.05.020}, pmid = {31077734}, issn = {1879-0038}, mesh = {Animals ; Base Composition/genetics ; Base Sequence ; Coleoptera/*genetics ; Forensic Sciences/methods ; Gene Order/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {Necrophagous Dermestes species have high forensic importance in relation to the estimation of elapsed time since death or death season. To further supplement the genome-level features for related species, the complete mitochondrial genome (mitogenome) of Dermestes species D. essellatocollis, D. frischii and D. coarctatus are amplified, sequenced, annotated, analyzed, and compared with other twelve species of the infraorder Bostrichoidea. The mitochondrial genomes were typical circular molecules with 16,218, 15,873 and 15,873 bp in length, respectively. They included 13 protein coding genes, two rRNAs, and 22 tRNAs, as well as the putative control region. The gene orders and orientations are identical to those of other recorded bostrichiformian species and had the ancestral insect gene composition. Furthermore, phylogenetic analyses based on all the mitochondrial protein coding genes for 13 Bostrichoidea and 16 outgroup taxa were performed using Bayesian and Maximum Likelihood analyses. The inferred trees indicate that the genus Dermestes is monophyletic. The monophyly of infraorder Bostrichiformia is not supported. This study provides genomic data for mitochondrial genome library of the genus Dermestes to investigate evolutionary and systematic studies.}, }
@article {pmid31076245, year = {2019}, author = {Brunk, CF and Martin, WF}, title = {Archaeal Histone Contributions to the Origin of Eukaryotes.}, journal = {Trends in microbiology}, volume = {27}, number = {8}, pages = {703-714}, doi = {10.1016/j.tim.2019.04.002}, pmid = {31076245}, issn = {1878-4380}, mesh = {Archaea/*physiology ; *Biological Evolution ; DNA ; Eukaryotic Cells/*physiology ; Histones/*physiology ; Mitochondria/physiology ; Symbiosis ; }, abstract = {The eukaryotic lineage arose from bacterial and archaeal cells that underwent a symbiotic merger. At the origin of the eukaryote lineage, the bacterial partner contributed genes, metabolic energy, and the building blocks of the endomembrane system. What did the archaeal partner donate that made the eukaryotic experiment a success? The archaeal partner provided the potential for complex information processing. Archaeal histones were crucial in that regard by providing the basic functional unit with which eukaryotes organize DNA into nucleosomes, exert epigenetic control of gene expression, transcribe genes with CCAAT-box promoters, and a manifest cell cycle with condensed chromosomes. While mitochondrial energy lifted energetic constraints on eukaryotic protein production, histone-based chromatin organization paved the path to eukaryotic genome complexity, a critical hurdle en route to the evolution of complex cells.}, }
@article {pmid31073668, year = {2019}, author = {Sakaue, H and Endo, T}, title = {Regulation of the protein entry gate assembly by mitochondrial porin.}, journal = {Current genetics}, volume = {65}, number = {5}, pages = {1161-1163}, pmid = {31073668}, issn = {1432-0983}, support = {15H05705//Japan Society for the Promotion of Science/ ; 2222703//Japan Society for the Promotion of Science/ ; JPMJCR12M1//Core Research for Evolutional Science and Technology/ ; }, mesh = {Carrier Proteins/chemistry/genetics/metabolism ; Mitochondria/*physiology ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/chemistry/*genetics/*metabolism ; Porins/chemistry/*genetics/*metabolism ; Protein Binding ; Protein Multimerization ; Signal Transduction ; }, abstract = {Mitochondrial biogenesis and functions rely on transport of their resident proteins as well as small molecules/ions across their membranes. The TOM complex functions as a protein entry gate for most mitochondrial proteins and mitochondrial porin facilitates transport of small-molecule metabolites and ions. We recently found a novel role of porin in regulation of the TOM complex assembly, the dynamic exchange between the dimer and trimer, and different substrate specificities of the dimer and trimer. Using distinct assembly forms customized for different client proteins, the TOM complex can handle ~ 1000 different mitochondrial protein for their import into mitochondria.}, }
@article {pmid31073215, year = {2019}, author = {Castelli, M and Sabaneyeva, E and Lanzoni, O and Lebedeva, N and Floriano, AM and Gaiarsa, S and Benken, K and Modeo, L and Bandi, C and Potekhin, A and Sassera, D and Petroni, G}, title = {Deianiraea, an extracellular bacterium associated with the ciliate Paramecium, suggests an alternative scenario for the evolution of Rickettsiales.}, journal = {The ISME journal}, volume = {13}, number = {9}, pages = {2280-2294}, pmid = {31073215}, issn = {1751-7370}, mesh = {Alphaproteobacteria/classification ; *Biological Evolution ; Genomics ; Mitochondria/microbiology ; Paramecium/genetics/*microbiology/physiology ; Phylogeny ; Rickettsiales/classification/*genetics/isolation &amp; purification/physiology ; Symbiosis ; }, abstract = {Rickettsiales are a lineage of obligate intracellular Alphaproteobacteria, encompassing important human pathogens, manipulators of host reproduction, and mutualists. Here we report the discovery of a novel Rickettsiales bacterium associated with Paramecium, displaying a unique extracellular lifestyle, including the ability to replicate outside host cells. Genomic analyses show that the bacterium possesses a higher capability to synthesise amino acids, compared to all investigated Rickettsiales. Considering these observations, phylogenetic and phylogenomic reconstructions, and re-evaluating the different means of interaction of Rickettsiales bacteria with eukaryotic cells, we propose an alternative scenario for the evolution of intracellularity in Rickettsiales. According to our reconstruction, the Rickettsiales ancestor would have been an extracellular and metabolically versatile bacterium, while obligate intracellularity would have evolved later, in parallel and independently, in different sub-lineages. The proposed new scenario could impact on the open debate on the lifestyle of the last common ancestor of mitochondria within Alphaproteobacteria.}, }
@article {pmid31068124, year = {2019}, author = {Wu, Z and Hu, K and Yan, M and Song, L and Wen, J and Ma, C and Shen, J and Fu, T and Yi, B and Tu, J}, title = {Mitochondrial genome and transcriptome analysis of five alloplasmic male-sterile lines in Brassica juncea.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {348}, pmid = {31068124}, issn = {1471-2164}, support = {31571746//National Natural Science Foundation of China/ ; 2016YFD0100804//National Key Research and Development Program of China/ ; 2662016PY063//the Fundamental Research Funds for the Central Universities/ ; 2016ABA084//Hubei Key Technological Innovation Project/ ; }, mesh = {Cytoplasm/*genetics ; Gene Expression Regulation, Plant ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Mustard Plant/*genetics/physiology ; Open Reading Frames ; Phylogeny ; *Plant Infertility ; Plant Proteins/*genetics ; }, abstract = {BACKGROUND: Alloplasmic lines, in which the nuclear genome is combined with wild cytoplasm, are often characterized by cytoplasmic male sterility (CMS), regardless of whether it was derived from sexual or somatic hybridization with wild relatives. In this study, we sequenced and analyzed the mitochondrial genomes of five such alloplasmic lines in Brassica juncea.<br><br>RESULTS: The assembled and annotated mitochondrial genomes of the five alloplasmic lines were found to have virtually identical gene contents. They preserved most of the ancestral mitochondrial segments, and the same candidate male sterility gene (orf108) was found harbored in mitotype-specific sequences. We also detected promiscuous sequences of chloroplast origin that were conserved among plants of the Brassicaceae, and found the RNA editing profiles to vary across the five mitochondrial genomes.<br><br>CONCLUSIONS: On the basis of our characterization of the genetic nature of five alloplasmic mitochondrial genomes, we speculated that the putative candidate male sterility gene orf108 may not be responsible for the CMS observed in Brassica oxyrrhina and Diplotaxis catholica. Furthermore, we propose the potential coincidence of CMS in alloplasmic lines. Our findings lay the foundation for further elucidation of male sterility gene.}, }
@article {pmid31066520, year = {2019}, author = {Gobert, A and Bruggeman, M and Giegé, P}, title = {Involvement of PIN-like domain nucleases in tRNA processing and translation regulation.}, journal = {IUBMB life}, volume = {71}, number = {8}, pages = {1117-1125}, doi = {10.1002/iub.2062}, pmid = {31066520}, issn = {1521-6551}, mesh = {Anticodon/chemistry ; Arabidopsis/enzymology ; Chloroplasts/enzymology ; Cullin Proteins/chemistry ; Escherichia coli/enzymology ; *Gene Expression Regulation ; Homeostasis ; Humans ; Mitochondria/enzymology ; Protein Binding ; *Protein Biosynthesis ; Protein Domains ; Protein Interaction Mapping ; Protein Structure, Secondary ; RNA/chemistry ; RNA Precursors ; RNA, Transfer/*chemistry ; Ribonuclease P/*chemistry ; }, abstract = {Transfer RNAs require essential maturation steps to become functional. Among them, RNase P removes 5' leader sequences of pre-tRNAs. Although RNase P was long thought to occur universally as ribonucleoproteins, different types of protein-only RNase P enzymes were discovered in both eukaryotes and prokaryotes. Interestingly, all these enzymes belong to the super-group of PilT N-terminal-like nucleases (PIN)-like ribonucleases. This wide family of enzymes can be subdivided into major subgroups. Here, we review recent studies at both functional and mechanistic levels on three PIN-like ribonucleases groups containing enzymes connected to tRNA maturation and/or translation regulation. The evolutive distribution of these proteins containing PIN-like domains as well as their organization and fusion with various functional domains is discussed and put in perspective with the diversity of functions they acquired during evolution, for the maturation and homeostasis of tRNA and a wider array of RNA substrates. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1117-1125, 2019.}, }
@article {pmid31064825, year = {2019}, author = {Bertolini, MS and Chiurillo, MA and Lander, N and Vercesi, AE and Docampo, R}, title = {MICU1 and MICU2 Play an Essential Role in Mitochondrial Ca[2+] Uptake, Growth, and Infectivity of the Human Pathogen Trypanosoma cruzi.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, pmid = {31064825}, issn = {2150-7511}, support = {R01 AI107663/AI/NIAID NIH HHS/United States ; R56 AI107663/AI/NIAID NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Biological Transport ; CRISPR-Cas Systems ; Calcium/*metabolism ; Calcium-Binding Proteins/genetics/*metabolism ; Cation Transport Proteins ; Cytosol/chemistry/metabolism ; Gene Knockout Techniques ; Humans ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/genetics/*metabolism ; Protozoan Proteins/genetics/*metabolism ; Trypanosoma cruzi/*genetics/pathogenicity ; }, abstract = {The mitochondrial Ca[2+] uptake in trypanosomatids, which belong to the eukaryotic supergroup Excavata, shares biochemical characteristics with that of animals, which, together with fungi, belong to the supergroup Opisthokonta. However, the composition of the mitochondrial calcium uniporter (MCU) complex in trypanosomatids is quite peculiar, suggesting lineage-specific adaptations. In this work, we used Trypanosoma cruzi to study the role of orthologs for mitochondrial calcium uptake 1 (MICU1) and MICU2 in mitochondrial Ca[2+] uptake. T. cruzi MICU1 (TcMICU1) and TcMICU2 have mitochondrial targeting signals, two canonical EF-hand calcium-binding domains, and localize to the mitochondria. Using the CRISPR/Cas9 system (i.e., clustered regularly interspaced short palindromic repeats with Cas9), we generated TcMICU1 and TcMICU2 knockout (-KO) cell lines. Ablation of either TcMICU1 or TcMICU2 showed a significantly reduced mitochondrial Ca[2+] uptake in permeabilized epimastigotes without dissipation of the mitochondrial membrane potential or effects on the AMP/ATP ratio or citrate synthase activity. However, none of these proteins had a gatekeeper function at low cytosolic Ca[2+] concentrations ([Ca[2+]]cyt), as occurs with their mammalian orthologs. TcMICU1-KO and TcMICU2-KO epimastigotes had a lower growth rate and impaired oxidative metabolism, while infective trypomastigotes have a reduced capacity to invade host cells and to replicate within them as amastigotes. The findings of this work, which is the first to study the role of MICU1 and MICU2 in organisms evolutionarily distant from animals, suggest that, although these components were probably present in the last eukaryotic common ancestor (LECA), they developed different roles during evolution of different eukaryotic supergroups. The work also provides new insights into the adaptations of trypanosomatids to their particular life styles.IMPORTANCETrypanosoma cruzi is the etiologic agent of Chagas disease and belongs to the early-branching eukaryotic supergroup Excavata. Its mitochondrial calcium uniporter (MCU) subunit shares similarity with the animal ortholog that was important to discover its encoding gene. In animal cells, the MICU1 and MICU2 proteins act as Ca[2+] sensors and gatekeepers of the MCU, preventing Ca[2+] uptake under resting conditions and favoring it at high cytosolic Ca[2+] concentrations ([Ca[2+]]cyt). Using the CRISPR/Cas9 technique, we generated TcMICU1 and TcMICU2 knockout cell lines and showed that MICU1 and -2 do not act as gatekeepers at low [Ca[2+]]cyt but are essential for normal growth, host cell invasion, and intracellular replication, revealing lineage-specific adaptations.}, }
@article {pmid31057485, year = {2019}, author = {Zhao, D and Yu, Y and Shen, Y and Liu, Q and Zhao, Z and Sharma, R and Reiter, RJ}, title = {Melatonin Synthesis and Function: Evolutionary History in Animals and Plants.}, journal = {Frontiers in endocrinology}, volume = {10}, number = {}, pages = {249}, pmid = {31057485}, issn = {1664-2392}, abstract = {Melatonin is an ancient molecule that can be traced back to the origin of life. Melatonin's initial function was likely that as a free radical scavenger. Melatonin presumably evolved in bacteria; it has been measured in both α-proteobacteria and in photosynthetic cyanobacteria. In early evolution, bacteria were phagocytosed by primitive eukaryotes for their nutrient value. According to the endosymbiotic theory, the ingested bacteria eventually developed a symbiotic association with their host eukaryotes. The ingested α-proteobacteria evolved into mitochondria while cyanobacteria became chloroplasts and both organelles retained their ability to produce melatonin. Since these organelles have persisted to the present day, all species that ever existed or currently exist may have or may continue to synthesize melatonin in their mitochondria (animals and plants) and chloroplasts (plants) where it functions as an antioxidant. Melatonin's other functions, including its multiple receptors, developed later in evolution. In present day animals, via receptor-mediated means, melatonin functions in the regulation of sleep, modulation of circadian rhythms, enhancement of immunity, as a multifunctional oncostatic agent, etc., while retaining its ability to reduce oxidative stress by processes that are, in part, receptor-independent. In plants, melatonin continues to function in reducing oxidative stress as well as in promoting seed germination and growth, improving stress resistance, stimulating the immune system and modulating circadian rhythms; a single melatonin receptor has been identified in land plants where it controls stomatal closure on leaves. The melatonin synthetic pathway varies somewhat between plants and animals. The amino acid, tryptophan, is the necessary precursor of melatonin in all taxa. In animals, tryptophan is initially hydroxylated to 5-hydroxytryptophan which is then decarboxylated with the formation of serotonin. Serotonin is either acetylated to N-acetylserotonin or it is methylated to form 5-methoxytryptamine; these products are either methylated or acetylated, respectively, to produce melatonin. In plants, tryptophan is first decarboxylated to tryptamine which is then hydroxylated to form serotonin.}, }
@article {pmid31044222, year = {2019}, author = {Nagarajan-Radha, V and Rapkin, J and Hunt, J and Dowling, DK}, title = {Interactions Between Mitochondrial Haplotype and Dietary Macronutrient Ratios Confer Sex-Specific Effects on Longevity in Drosophila melanogaster.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {74}, number = {10}, pages = {1573-1581}, doi = {10.1093/gerona/glz104}, pmid = {31044222}, issn = {1758-535X}, mesh = {Animals ; *Diet ; Dietary Carbohydrates ; Dietary Proteins ; Drosophila melanogaster ; Female ; Haplotypes ; Longevity/*physiology ; Male ; Mitochondria/*physiology ; Models, Animal ; Nutrients/*therapeutic use ; Sex Factors ; }, abstract = {Recent studies have demonstrated that modifications to the ratio of dietary macronutrients affect longevity in a diverse range of species. However, the degree to which levels of natural genotypic variation shape these dietary effects on longevity remains unclear. The mitochondria have long been linked to the aging process. The mitochondria possess their own genome, and previous studies have shown that mitochondrial genetic variation affects longevity in insects. Furthermore, the mitochondria are the sites in which dietary nutrients are oxidized to produce adenosine triphosphate, suggesting a capacity for dietary quality to mediate the link between mitochondrial genotype and longevity. Here, we measured longevity of male and female fruit flies, across a panel of genetic strains of Drosophila melanogaster, which vary only in their mitochondrial haplotype, when fed one of the two isocaloric diets that differed in their protein-to-carbohydrate ratio. The mitochondrial haplotype affected the longevity of flies, but the pattern of these effects differed across the two diets in males, but not in females. We discuss the implications of these results in relation to an evolutionary theory linking maternal inheritance of mitochondria to the accumulation of male-harming mitochondrial mutations, and to the theory exploring the evolution of phenotypic plasticity to novel environments.}, }
@article {pmid31042716, year = {2019}, author = {Tiukova, IA and Pettersson, ME and Hoeppner, MP and Olsen, RA and Käller, M and Nielsen, J and Dainat, J and Lantz, H and Söderberg, J and Passoth, V}, title = {Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0215077}, pmid = {31042716}, issn = {1932-6203}, mesh = {Brettanomyces/genetics/*metabolism ; Chromosomes, Fungal/*genetics ; Contig Mapping ; Ethanol/*metabolism ; Evolution, Molecular ; Gene Dosage ; Genetic Variation ; Genome Size ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Whole Genome Sequencing/methods ; }, abstract = {Here, we present the genome of the industrial ethanol production strain Brettanomyces bruxellensis CBS 11270. The nuclear genome was found to be diploid, containing four chromosomes with sizes of ranging from 2.2 to 4.0 Mbp. A 75 Kbp mitochondrial genome was also identified. Comparing the homologous chromosomes, we detected that 0.32% of nucleotides were polymorphic, i.e. formed single nucleotide polymorphisms (SNPs), 40.6% of them were found in coding regions (i.e. 0.13% of all nucleotides formed SNPs and were in coding regions). In addition, 8,538 indels were found. The total number of protein coding genes was 4897, of them, 4,284 were annotated on chromosomes; and the mitochondrial genome contained 18 protein coding genes. Additionally, 595 genes, which were annotated, were on contigs not associated with chromosomes. A number of genes was duplicated, most of them as tandem repeats, including a six-gene cluster located on chromosome 3. There were also examples of interchromosomal gene duplications, including a duplication of a six-gene cluster, which was found on both chromosomes 1 and 4. Gene copy number analysis suggested loss of heterozygosity for 372 genes. This may reflect adaptation to relatively harsh but constant conditions of continuous fermentation. Analysis of gene topology showed that most of these losses occurred in clusters of more than one gene, the largest cluster comprising 33 genes. Comparative analysis against the wine isolate CBS 2499 revealed 88,534 SNPs and 8,133 indels. Moreover, when the scaffolds of the CBS 2499 genome assembly were aligned against the chromosomes of CBS 11270, many of them aligned completely, some have chunks aligned to different chromosomes, and some were in fact rearranged. Our findings indicate a highly dynamic genome within the species B. bruxellensis and a tendency towards reduction of gene number in long-term continuous cultivation.}, }
@article {pmid31040181, year = {2019}, author = {Reis, LMD and Adamoski, D and Ornitz Oliveira Souza, R and Rodrigues Ascenção, CF and Sousa de Oliveira, KR and Corrêa-da-Silva, F and Malta de Sá Patroni, F and Meira Dias, M and Consonni, SR and Mendes de Moraes-Vieira, PM and Silber, AM and Dias, SMG}, title = {Dual inhibition of glutaminase and carnitine palmitoyltransferase decreases growth and migration of glutaminase inhibition-resistant triple-negative breast cancer cells.}, journal = {The Journal of biological chemistry}, volume = {294}, number = {24}, pages = {9342-9357}, pmid = {31040181}, issn = {1083-351X}, mesh = {Benzeneacetamides/*pharmacology ; Carnitine O-Palmitoyltransferase/*antagonists &amp; inhibitors ; Cell Movement/*drug effects ; Cell Proliferation/*drug effects ; Drug Resistance, Neoplasm/*drug effects ; Female ; Glutaminase/*antagonists &amp; inhibitors ; Glutamine/*metabolism ; Humans ; Oxidation-Reduction ; Thiadiazoles/*pharmacology ; Triple Negative Breast Neoplasms/*drug therapy/enzymology/pathology ; Tumor Cells, Cultured ; }, abstract = {Triple-negative breast cancers (TNBCs) lack progesterone and estrogen receptors and do not have amplified human epidermal growth factor receptor 2, the main therapeutic targets for managing breast cancer. TNBCs have an altered metabolism, including an increased Warburg effect and glutamine dependence, making the glutaminase inhibitor CB-839 therapeutically promising for this tumor type. Accordingly, CB-839 is currently in phase I/II clinical trials. However, not all TNBCs respond to CB-839 treatment, and the tumor resistance mechanism is not yet fully understood. Here we classified cell lines as CB-839-sensitive or -resistant according to their growth responses to CB-839. Compared with sensitive cells, resistant cells were less glutaminolytic and, upon CB-839 treatment, exhibited a smaller decrease in ATP content and less mitochondrial fragmentation, an indicator of poor mitochondrial health. Transcriptional analyses revealed that the expression levels of genes linked to lipid metabolism were altered between sensitive and resistant cells and between breast cancer tissues (available from The Cancer Genome Atlas project) with low versus high glutaminase (GLS) gene expression. Of note, CB-839-resistant TNBC cells had increased carnitine palmitoyltransferase 2 (CPT2) protein and CPT1 activity levels. In agreement, CB-839-resistant TNBC cells mobilized more fatty acids into mitochondria for oxidation, which responded to AMP-activated protein kinase and acetyl-CoA carboxylase signaling. Moreover, chemical inhibition of both glutaminase and CPT1 decreased cell proliferation and migration of CB-839-resistant cells compared with single inhibition of each enzyme. We propose that dual targeting of glutaminase and CPT1 activities may have therapeutic relevance for managing CB-839-resistant tumors.}, }
@article {pmid31039434, year = {2019}, author = {Wang, G and Wu, C and Ge, J and Chen, Y and Han, Z and Guo, P and Li, J}, title = {Identification of complete F-type mitochondrial genome in Lamprotula scripta and Lamprotula caveata and analysis on DUI.}, journal = {Gene}, volume = {710}, number = {}, pages = {59-65}, doi = {10.1016/j.gene.2019.04.075}, pmid = {31039434}, issn = {1879-0038}, mesh = {Animals ; Evolution, Molecular ; Genome Size ; *Genome, Mitochondrial ; Maternal Inheritance ; Mitochondria/genetics ; Open Reading Frames ; Phylogeny ; RNA, Transfer/genetics ; RNA, Untranslated/genetics ; Unionidae/*classification/*genetics ; }, abstract = {Mitochondrial DNA is typically passed to offspring through maternal inheritance. However, in mussels, two kinds of mitochondrial DNA exist: F and M type, which are referred to as doubly uniparental inheritance (DUI). Studies have shown that DUI may be related to gender determination. In this study, we obtained the first complete F-type mitochondrial genome of Lamprotula scripta and Lamprotula caveata which were 16,250 bp and 16,641 bp in length, respectively, and had 13 protein coding genes (PCGs), 22 transfer RNAs, 2 ribosomal RNAs and 27 non-coding (NC) regions. The largest NC region of L. scripta was 639 bp and located between ND5 and tRNA[Gln]. The largest NC of L. caveata was 1046 bp and also located between ND5 and tRNA[Gln]. The overall AT content of L. scripta and L. caveata was 58.95% and 58.66%, respectively, which were lower than Lamprotula leai, Lamprotula gottschei and Lamprotula tortuosa. We next compared F and M mitochondrial genomic data on freshwater mussels and established a phylogenetic tree based on amino acid sequences of 13 PCGs and COII gene. Our results showed that F- and M-type mitochondria were significantly separated into two branches, and the basic structure of phylogenetic trees were divided into four distinct groups: Unioninae, Anodontini, Gonideinae and Ambleminae. Relatives of Gonideinae and Ambleminae were more closely related than Unioninae and Anodontini, indicating significant differences in mtDNA between the two mitogenome types. Moreover, we revealed that L. scripta and L. caveata are closely relatives, suggesting that they are both subordinates of the Gonideinae subfamily. Consequently, we speculate that the formation of DUI hinders their disappearance, which provides a basis for further studies into the mechanisms and genetic diversities of DUI formation.}, }
@article {pmid31035578, year = {2019}, author = {Banguera-Hinestroza, E and Ferrada, E and Sawall, Y and Flot, JF}, title = {Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Protein Structure and Function in Stylophora Lineages from Contrasting Environments.}, journal = {Genes}, volume = {10}, number = {5}, pages = {}, pmid = {31035578}, issn = {2073-4425}, mesh = {Animals ; Anthozoa/*genetics ; *Computational Biology ; DNA, Mitochondrial/*genetics ; Ecosystem ; Indian Ocean ; Mitochondria/*genetics ; Open Reading Frames/genetics ; Phylogeny ; Phylogeography ; Protein Conformation ; Tandem Repeat Sequences/genetics ; }, abstract = {More than a decade ago, a new mitochondrial Open Reading Frame (mtORF) was discovered in corals of the family Pocilloporidae and has been used since then as an effective barcode for these corals. Recently, mtORF sequencing revealed the existence of two differentiated Stylophora lineages occurring in sympatry along the environmental gradient of the Red Sea (18.5°C to 33.9°C). In the endemic Red Sea lineage RS_LinB, the mtORF and the heat shock protein gene hsp70 uncovered similar phylogeographic patterns strongly correlated with environmental variations. This suggests that the mtORF too might be involved in thermal adaptation. Here, we used computational analyses to explore the features and putative function of this mtORF. In particular, we tested the likelihood that this gene encodes a functional protein and whether it may play a role in adaptation. Analyses of full mitogenomes showed that the mtORF originated in the common ancestor of Madracis and other pocilloporids, and that it encodes a transmembrane protein differing in length and domain architecture among genera. Homology-based annotation and the relative conservation of metal-binding sites revealed traces of an ancient hydrolase catalytic activity. Furthermore, signals of pervasive purifying selection, lack of stop codons in 1830 sequences analyzed, and a codon-usage bias similar to that of other mitochondrial genes indicate that the protein is functional, i.e., not a pseudogene. Other features, such as intrinsically disordered regions, tandem repeats, and signals of positive selection particularly in StylophoraRS_LinB populations, are consistent with a role of the mtORF in adaptive responses to environmental changes.}, }
@article {pmid31032404, year = {2019}, author = {John, U and Lu, Y and Wohlrab, S and Groth, M and Janouškovec, J and Kohli, GS and Mark, FC and Bickmeyer, U and Farhat, S and Felder, M and Frickenhaus, S and Guillou, L and Keeling, PJ and Moustafa, A and Porcel, BM and Valentin, K and Glöckner, G}, title = {An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome.}, journal = {Science advances}, volume = {5}, number = {4}, pages = {eaav1110}, pmid = {31032404}, issn = {2375-2548}, mesh = {Aerobiosis ; Cell Nucleus/genetics ; Cluster Analysis ; DNA, Complementary/metabolism ; Dinoflagellida/*genetics/*metabolism ; Evolution, Molecular ; Gene Library ; Genome ; *Genome, Mitochondrial ; Likelihood Functions ; Microscopy, Confocal ; Mitochondria/*physiology ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Dinoflagellates are microbial eukaryotes that have exceptionally large nuclear genomes; however, their organelle genomes are small and fragmented and contain fewer genes than those of other eukaryotes. The genus Amoebophrya (Syndiniales) comprises endoparasites with high genetic diversity that can infect other dinoflagellates, such as those forming harmful algal blooms (e.g., Alexandrium). We sequenced the genome (~100 Mb) of Amoebophrya ceratii to investigate the early evolution of genomic characters in dinoflagellates. The A. ceratii genome encodes almost all essential biosynthetic pathways for self-sustaining cellular metabolism, suggesting a limited dependency on its host. Although dinoflagellates are thought to have descended from a photosynthetic ancestor, A. ceratii appears to have completely lost its plastid and nearly all genes of plastid origin. Functional mitochondria persist in all life stages of A. ceratii, but we found no evidence for the presence of a mitochondrial genome. Instead, all mitochondrial proteins appear to be lost or encoded in the A. ceratii nucleus.}, }
@article {pmid31029862, year = {2020}, author = {Rawal, HC and Kumar, PM and Bera, B and Singh, NK and Mondal, TK}, title = {Decoding and analysis of organelle genomes of Indian tea (Camellia assamica) for phylogenetic confirmation.}, journal = {Genomics}, volume = {112}, number = {1}, pages = {659-668}, doi = {10.1016/j.ygeno.2019.04.018}, pmid = {31029862}, issn = {1089-8646}, mesh = {Camellia/*genetics ; Chloroplast Proteins/genetics ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Mitochondrial Proteins/genetics ; *Phylogeny ; RNA, Chloroplast/genetics ; RNA, Mitochondrial/genetics ; }, abstract = {The NCBI database has >15 chloroplast (cp) genome sequences available for different Camellia species but none for C. assamica. There is no report of any mitochondrial (mt) genome in the Camellia genus or Theaceae family. With the strong believes that these organelle genomes can play a great tool for taxonomic and phylogenetic analysis, we successfully assembled and analyzed cp and mt genome of C. assamica. We assembled the complete mt genome of C. assamica in a single circular contig of 707,441 bp length comprising of a total of 66 annotated genes, including 35 protein-coding genes, 29 tRNAs and two rRNAs. The first ever cp genome of C. assamica resulted in a circular contig of 157,353 bp length with a typical quadripartite structure. Phylogenetic analysis based on these organelle genomes showed that C. assamica was closely related to C. sinensis and C. leptophylla. It also supports Caryophyllales as Superasterids.}, }
@article {pmid31028468, year = {2019}, author = {Buddhachat, K and Chontananarth, T}, title = {Is species identification of Echinostoma revolutum using mitochondrial DNA barcoding feasible with high-resolution melting analysis?.}, journal = {Parasitology research}, volume = {118}, number = {6}, pages = {1799-1810}, pmid = {31028468}, issn = {1432-1955}, mesh = {Animals ; Asia, Southeastern ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*chemistry/*genetics ; Echinostoma/chemistry/*classification/genetics/*isolation &amp; purification ; Mitochondria/genetics ; Phylogeny ; Thailand ; Transition Temperature ; }, abstract = {The taxonomic evaluation of Echinostoma species is controversial. Echinostoma species are recognized as complex, leading to problems associated with accurate identification of these species. The aim of this study was to test the feasibility of using DNA barcoding of cytochrome c oxidase subunit I (COI) and NADH dehydrogenase subunit 1 (ND1) conjugated with high-resolution melting (HRM) analysis to identify Echinostoma revolutum. HRM using COI and ND1 was unable to differentiate between species in the "revolutum complex" but did distinguish between two isolates of 37-collar-spined echinostome species, including E. revolutum (Asian lineage) and Echinostoma sp. A from different genera, e.g., Hypoderaeum conoideum, Haplorchoides mehrai, Fasciola gigantica, and Thapariella anastomusa, based on the Tm values derived from HRM analysis. Through phylogenetic analysis, a new clade of the cryptic species known as Echinostoma sp. A was identified. In addition, we found that the E. revolutum clade of ND1 phylogeny obtained from the Thailand strain was from a different lineage than the Eurasian lineage. These findings reveal the complexity of the clade, which is composed of 37-collar-spined echinostome species found in Southeast Asia. Taken together, the systematic aspects of the complex revolutum group are in need of extensive investigation by integrating morphological, biological, and molecular features in order to clarify them, particularly in Southeast Asia.}, }
@article {pmid31018611, year = {2019}, author = {Crottini, A and Orozco-terWengel, P and Rabemananjara, FCE and Hauswaldt, JS and Vences, M}, title = {Mitochondrial Introgression, Color Pattern Variation, and Severe Demographic Bottlenecks in Three Species of Malagasy Poison Frogs, Genus Mantella.}, journal = {Genes}, volume = {10}, number = {4}, pages = {}, pmid = {31018611}, issn = {2073-4425}, mesh = {Animals ; Anura/*classification/genetics ; Biodiversity ; DNA, Mitochondrial/genetics ; Gene Flow ; Genetic Introgression ; Genetics, Population ; Homeodomain Proteins/genetics ; Madagascar ; Microsatellite Repeats ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*veterinary ; Skin Pigmentation/*genetics ; }, abstract = {Madagascar is a biodiversity hotspot particularly rich in amphibian diversity and only a few charismatic Malagasy amphibians have been investigated for their population-level differentiation. The Mantellamadagascariensis group is composed of two rainforest and three swamp forest species of poison frogs. We first confirm the monophyly of this clade using DNA sequences of three nuclear and four mitochondrial genes, and subsequently investigate the population genetic differentiation and demography of the swamp forest species using one mitochondrial, two nuclear and a set of nine microsatellite markers. Our results confirm the occurrence of two main mitochondrial lineages, one dominated by Mantellaaurantiaca (a grouping supported also by our microsatellite-based tree) and the other by Mantellacrocea + Mantellamilotympanum. These two main lineages probably reflect an older divergence in swamp Mantella. Widespread mitochondrial introgression suggests a fairly common occurrence of inter-lineage gene flow. However, nuclear admixture seems to play only a limited role in this group, and the analyses of the RAG-1 marker points to a predominant incomplete lineage sorting scenario between all five species of the group, which probably diverged relatively recently. Our demographic analyses show a common, severe and recent demographic contraction, inferred to be in temporal coincidence with the massive deforestation events that took place in the past 1000 years. Current data do not allow to conclusively delimit independent evolutionary units in these frogs, and we therefore refrain to suggest any taxonomic changes.}, }
@article {pmid31018163, year = {2019}, author = {Torres-Cambas, Y and Ferreira, S and Cordero-Rivera, A and Lorenzo-Carballa, MO}, title = {Mechanisms of allopatric speciation in an Antillean damselfly genus (Odonata, Zygoptera): Vicariance or long-distance dispersal?.}, journal = {Molecular phylogenetics and evolution}, volume = {137}, number = {}, pages = {14-21}, doi = {10.1016/j.ympev.2019.04.018}, pmid = {31018163}, issn = {1095-9513}, mesh = {Animal Migration/*physiology ; Animals ; Base Sequence ; Cell Nucleus/genetics ; Cuba ; DNA, Mitochondrial/genetics ; *Genetic Speciation ; Genetic Variation ; Mitochondria/genetics ; Odonata/*genetics/*physiology ; Phylogeny ; Species Specificity ; Time Factors ; }, abstract = {We have examined divergence times of the Antillean damselfly genus Hypolestes, to elucidate which mechanism of allopatric speciation, vicariance or long-distance dispersal, could better explain the currently observed disjunct distributions of this genus. Samples of the three extant species of the genus, Hypolestes clara (Jamaica), H. hatuey (Hispaniola) and H. trinitatis (Cuba), were collected. Mitochondrial and nuclear DNA gene fragments were amplified to reconstruct phylogenetic relationships and estimate divergence times in this genus. Hypolestes comprises currently three species, which consist in four geographically and genetically isolated lineages located in Jamaica, Hispaniola, Eastern Cuba and Central Cuba. Results of our analyses suggest that the three species diverged between ∼5.91 and 1.69 mya, and that the separation between the lineages from Central Cuba and Eastern Cuba occurred between ∼2.0 and 0.62 mya. Disjunct distributions in the genus Hypolestes can be better explained by a long-distance dispersal mechanism, since the divergence times of the three species do not coincide with the timeline formation of the geographic barriers between Cuba, Hispaniola and Jamaica. The Cuban lineages of H. trinitatis constitute different molecular operational taxonomic units (MOTU). The elevation of these MOTU to the species category requires the analysis of additional characters.}, }
@article {pmid31017302, year = {2019}, author = {Escobar L, MD and Ota, RP and Machado-Allison, A and Andrade-López, J and Farias, IP and Hrbek, T}, title = {A new species of Piaractus (Characiformes: Serrasalmidae) from the Orinoco Basin with a redescription of Piaractus brachypomus.}, journal = {Journal of fish biology}, volume = {95}, number = {2}, pages = {411-427}, doi = {10.1111/jfb.13990}, pmid = {31017302}, issn = {1095-8649}, support = {CNPq 490682/2010-3//Conselho Nacional de Desenvolvimento Cientifico e Tecnol&#xf3;gico/ ; 482662/2013-1 to T.H//Conselho Nacional de Desenvolvimento Cientifico e Tecnol&#xf3;gico/ ; CNPq/PPG7 5570090/2005-9//Conselho Nacional de Desenvolvimento Cientifico e Tecnol&#xf3;gico/ ; CNPq/CT-Amazon 575603/2008-9//Conselho Nacional de Desenvolvimento Cientifico e Tecnol&#xf3;gico/ ; (CAPES 53923790287)//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; CAPES 12002011001P7//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; (306804/2013-3)//CNPq research fellowship/ ; (303646/2010-1)//CNPq research fellowship/ ; }, mesh = {Animal Fins/anatomy &amp; histology ; Animal Scales/anatomy &amp; histology ; Animals ; Brazil ; Characiformes/anatomy &amp; histology/*classification/genetics ; Colombia ; DNA, Mitochondrial/*chemistry ; Electron Transport Complex IV/*genetics ; Fisheries/organization &amp; administration ; Lateral Line System/anatomy &amp; histology ; Likelihood Functions ; Maxilla/anatomy &amp; histology ; Mitochondria/genetics ; Phylogeny ; Pigmentation ; Poisson Distribution ; Rivers ; Sequence Alignment ; Software ; Spine/anatomy &amp; histology ; Terminology as Topic ; }, abstract = {Piaractus orinoquensis, a new species of serrasalmid fish, is described from the Orinoco River basin. The new species differs from congeners by having a slenderer body, relatively smaller head and snout, more compressed mid-body, fewer scales above and below the lateral line and diagnostic molecular characters in the coI mitochondrial gene region. We also provide a re-description of Piaractus brachypomus, restricting its geographic distribution to the Amazon River basin. Both species are economically important in their respective basins and need to be independently managed as distinct species.}, }
@article {pmid31016002, year = {2019}, author = {Pogoda, CS and Keepers, KG and Nadiadi, AY and Bailey, DW and Lendemer, JC and Tripp, EA and Kane, NC}, title = {Genome streamlining via complete loss of introns has occurred multiple times in lichenized fungal mitochondria.}, journal = {Ecology and evolution}, volume = {9}, number = {7}, pages = {4245-4263}, pmid = {31016002}, issn = {2045-7758}, abstract = {Reductions in genome size and complexity are a hallmark of obligate symbioses. The mitochondrial genome displays clear examples of these reductions, with the ancestral alpha-proteobacterial genome size and gene number having been reduced by orders of magnitude in most descendent modern mitochondrial genomes. Here, we examine patterns of mitochondrial evolution specifically looking at intron size, number, and position across 58 species from 21 genera of lichenized Ascomycete fungi, representing a broad range of fungal diversity and niches. Our results show that the cox1gene always contained the highest number of introns out of all the mitochondrial protein-coding genes, that high intron sequence similarity (>90%) can be maintained between different genera, and that lichens have undergone at least two instances of complete, genome-wide intron loss consistent with evidence for genome streamlining via loss of parasitic, noncoding DNA, in Phlyctis boliviensisand Graphis lineola. Notably, however, lichenized fungi have not only undergone intron loss but in some instances have expanded considerably in size due to intron proliferation (e.g., Alectoria fallacina and Parmotrema neotropicum), even between closely related sister species (e.g., Cladonia). These results shed light on the highly dynamic mitochondrial evolution that is occurring in lichens and suggest that these obligate symbiotic organisms are in some cases undergoing recent, broad-scale genome streamlining via loss of protein-coding genes as well as noncoding, parasitic DNA elements.}, }
@article {pmid31012550, year = {2019}, author = {Titov, VN and Sazhina, NN and Evteeva, N&#x41c;}, title = {[Ozone oxidizes oleic fatty acid with the highest rate constant and does not oxidize palmitic acid. Different physicochemical parameters of substrates and their role in phylogenesis.].}, journal = {Klinicheskaia laboratornaia diagnostika}, volume = {64}, number = {3}, pages = {132-139}, doi = {10.18821/0869-2084-2019-64-3-132-139}, pmid = {31012550}, issn = {0869-2084}, mesh = {Animals ; Diet, Vegetarian ; Humans ; Insulin ; Meat ; Oleic Acid/*metabolism ; Ozone/*metabolism ; Palmitic Acid/*metabolism ; }, abstract = {Physicochemical differences between О3 oxidation parameters for palmitic and oleic fatty acids (FA) during phylogenesis (evolution) are fundamental for а) production of palmitoleic monounsaturated fatty (MFA), b) formation of carnitine palmitoyltransferase as a FA transporter to mitochondria, and c) in vivo production of oleic MFA under humoral regulatory effect of insulin. In the strive for the best kinetic parameters of biological organisms without a possibility of modifying physicochemical and biochemical reactions in the mitochondrial matrix, the mitochondria can be provided with a substrate that increases energy production efficiency and the amount of ATP. Physicochemical parameters of oleic MFA has become the standard of an oxidation substrate for in vivo energy production; this MFA was synthesized in organisms for millions of years. Environmental influences are the second factor which determines kinetic perfection of biological organisms during phylogenesis. Are these influences always beneficial? Mostly, they are not. However, they largely stimulate adaptive functions of the organism, including the biological function of locomotion, cognitive function and the function of positioning in the environment. Biological, energy and kinetic perfection formed in vivo can be easily destroyed if phylogenetically herbivorous Homo sapiens abuses the diet of carnivorous animals (meat) which was not consumed by him and his ancestors during phylogenesis. This abuse is the major cause of metabolic pandemias in human population. They are: insulin resistance, atherosclerosis and atheromatosis, obesity and nonalcoholic liver disease. The most effective measures preventing metabolic pandemias, cardiac heart disease and myocardial infarction are extremely simple. People should remain herbivorous.}, }
@article {pmid31010849, year = {2019}, author = {Hsu, J and Reilly, A and Hayes, BJ and Clough, CA and Konnick, EQ and Torok-Storb, B and Gulsuner, S and Wu, D and Becker, PS and Keel, SB and Abkowitz, JL and Doulatov, S}, title = {Reprogramming identifies functionally distinct stages of clonal evolution in myelodysplastic syndromes.}, journal = {Blood}, volume = {134}, number = {2}, pages = {186-198}, pmid = {31010849}, issn = {1528-0020}, support = {P01 CA077852/CA/NCI NIH HHS/United States ; R01 HL031823/HL/NHLBI NIH HHS/United States ; R00 HL123484/HL/NHLBI NIH HHS/United States ; DP2 HL147126/HL/NHLBI NIH HHS/United States ; T32 HL007093/HL/NHLBI NIH HHS/United States ; }, mesh = {*Cellular Reprogramming ; Clonal Evolution/*genetics ; Hematopoietic Stem Cells/*pathology ; Humans ; Myelodysplastic Syndromes/*genetics ; Pluripotent Stem Cells/*pathology ; }, abstract = {Myeloid neoplasms, including myelodysplastic syndromes (MDS), are genetically heterogeneous disorders driven by clonal acquisition of somatic mutations in hematopoietic stem and progenitor cells (HPCs). The order of premalignant mutations and their impact on HPC self-renewal and differentiation remain poorly understood. We show that episomal reprogramming of MDS patient samples generates induced pluripotent stem cells from single premalignant cells with a partial complement of mutations, directly informing the temporal order of mutations in the individual patient. Reprogramming preferentially captured early subclones with fewer mutations, which were rare among single patient cells. To evaluate the functional impact of clonal evolution in individual patients, we differentiated isogenic MDS induced pluripotent stem cells harboring up to 4 successive clonal abnormalities recapitulating a progressive decrease in hematopoietic differentiation potential. SF3B1, in concert with epigenetic mutations, perturbed mitochondrial function leading to accumulation of damaged mitochondria during disease progression, resulting in apoptosis and ineffective erythropoiesis. Reprogramming also informed the order of premalignant mutations in patients with complex karyotype and identified 5q deletion as an early cytogenetic anomaly. The loss of chromosome 5q cooperated with TP53 mutations to perturb genome stability, promoting acquisition of structural and karyotypic abnormalities. Reprogramming thus enables molecular and functional interrogation of preleukemic clonal evolution, identifying mitochondrial function and chromosome stability as key pathways affected by acquisition of somatic mutations in MDS.}, }
@article {pmid31004483, year = {2019}, author = {Tobler, M and Barts, N and Greenway, R}, title = {Mitochondria and the Origin of Species: Bridging Genetic and Ecological Perspectives on Speciation Processes.}, journal = {Integrative and comparative biology}, volume = {59}, number = {4}, pages = {900-911}, doi = {10.1093/icb/icz025}, pmid = {31004483}, issn = {1557-7023}, mesh = {Adaptation, Biological ; Animals ; *Biological Evolution ; *Genetic Variation ; Mitochondria/*genetics ; *Reproductive Isolation ; }, abstract = {Mitochondria have been known to be involved in speciation through the generation of Dobzhansky-Muller incompatibilities, where functionally neutral co-evolution between mitochondrial and nuclear genomes can cause dysfunction when alleles are recombined in hybrids. We propose that adaptive mitochondrial divergence between populations can not only produce intrinsic (Dobzhansky-Muller) incompatibilities, but could also contribute to reproductive isolation through natural and sexual selection against migrants, post-mating prezygotic isolation, as well as by causing extrinsic reductions in hybrid fitness. We describe how these reproductive isolating barriers can potentially arise through adaptive divergence of mitochondrial function in the absence of mito-nuclear coevolution, a departure from more established views. While a role for mitochondria in the speciation process appears promising, we also highlight critical gaps of knowledge: (1) many systems with a potential for mitochondrially-mediated reproductive isolation lack crucial evidence directly linking reproductive isolation and mitochondrial function; (2) it often remains to be seen if mitochondrial barriers are a driver or a consequence of reproductive isolation; (3) the presence of substantial gene flow in the presence of mito-nuclear incompatibilities raises questions whether such incompatibilities are strong enough to drive speciation to completion; and (4) it remains to be tested how mitochondrial effects on reproductive isolation compare when multiple mechanisms of reproductive isolation coincide. We hope this perspective and the proposed research plans help to inform future studies of mitochondrial adaptation in a manner that links genotypic changes to phenotypic adaptations, fitness, and reproductive isolation in natural systems, helping to clarify the importance of mitochondria in the formation and maintenance of biological diversity.}, }
@article {pmid31002891, year = {2019}, author = {Araujo, NS and Arias, MC}, title = {Mitochondrial genome characterization of Melipona bicolor: Insights from the control region and gene expression data.}, journal = {Gene}, volume = {705}, number = {}, pages = {55-59}, doi = {10.1016/j.gene.2019.04.042}, pmid = {31002891}, issn = {1879-0038}, mesh = {Animals ; Base Composition ; Bees/*genetics ; Evolution, Molecular ; Gene Expression Profiling/*methods ; Gene Expression Regulation ; Genome Size ; *Genome, Mitochondrial ; Male ; Mitochondria/*genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; }, abstract = {The stingless bee Melipona bicolor is the only bee in which true polygyny occurs. Its mitochondrial genome was first sequenced in 2008, but it was incomplete and no information about its transcription was known. We combined short and long reads of M. bicolor DNA with RNASeq data to obtain insights about mitochondrial evolution and gene expression in bees. The complete genome has 15,001 bp, including a control region of 255 bp that contains all conserved structures described in honeybees with the highest AT content reported so far for bees (98.1%), displaying a compact but functional region. Gene expression control is similar to other insects however unusual patterns of expression may suggest the existence of different isoforms for the mitochondrially encoded 12S rRNA. Results reveal unique and shared features of the mitochondrial genome in terms of sequence evolution and gene expression making M. bicolor an interesting model to study mitochondrial genomic evolution.}, }
@article {pmid31001816, year = {2019}, author = {Meany, MK and Conner, WR and Richter, SV and Bailey, JA and Turelli, M and Cooper, BS}, title = {Loss of cytoplasmic incompatibility and minimal fecundity effects explain relatively low Wolbachia frequencies in Drosophila mauritiana.}, journal = {Evolution; international journal of organic evolution}, volume = {73}, number = {6}, pages = {1278-1295}, pmid = {31001816}, issn = {1558-5646}, support = {R01 GM104325/GM/NIGMS NIH HHS/United States ; R35 GM124701/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Cytoplasm/microbiology ; Drosophila/*microbiology/*physiology ; Female ; Fertility ; Islands ; Mauritius ; Phylogeny ; Wolbachia/genetics/*physiology ; }, abstract = {Maternally transmitted Wolbachia bacteria infect about half of all insect species. Many Wolbachia cause cytoplasmic incompatibility (CI) and reduced egg hatch when uninfected females mate with infected males. Although CI produces a frequency-dependent fitness advantage that leads to high equilibrium Wolbachia frequencies, it does not aid Wolbachia spread from low frequencies. Indeed, the fitness advantages that produce initial Wolbachia spread and maintain non-CI Wolbachia remain elusive. wMau Wolbachia infecting Drosophila mauritiana do not cause CI, despite being very similar to CI-causing wNo from Drosophila simulans (0.068% sequence divergence over 682,494 bp), suggesting recent CI loss. Using draft wMau genomes, we identify a deletion in a CI-associated gene, consistent with theory predicting that selection within host lineages does not act to increase or maintain CI. In the laboratory, wMau shows near-perfect maternal transmission; but we find no significant effect on host fecundity, in contrast to published data. Intermediate wMau frequencies on the island of Mauritius are consistent with a balance between unidentified small, positive fitness effects and imperfect maternal transmission. Our phylogenomic analyses suggest that group-B Wolbachia, including wMau and wPip, diverged from group-A Wolbachia, such as wMel and wRi, 6-46 million years ago, more recently than previously estimated.}, }
@article {pmid30999558, year = {2019}, author = {Nibert, ML and Debat, HJ and Manny, AR and Grigoriev, IV and De Fine Licht, HH}, title = {Mitovirus and Mitochondrial Coding Sequences from Basal Fungus Entomophthora muscae.}, journal = {Viruses}, volume = {11}, number = {4}, pages = {}, pmid = {30999558}, issn = {1999-4915}, support = {T32 AI007245/AI/NIAID NIH HHS/United States ; }, mesh = {Codon ; Databases, Genetic ; Entomophthora/classification/*genetics/virology ; Evolution, Molecular ; Exons ; Fungal Viruses/classification/*genetics ; Mitochondria/*genetics/virology ; Mitochondrial Proteins/genetics ; Phylogeny ; RNA Viruses/classification/*genetics ; Transcriptome ; }, abstract = {Fungi constituting the Entomophthora muscae species complex (members of subphylum Entomophthoromycotina, phylum Zoopagamycota) commonly kill their insect hosts and manipulate host behaviors in the process. In this study, we made use of public transcriptome data to identify and characterize eight new species of mitoviruses associated with several different E. muscae isolates. Mitoviruses are simple RNA viruses that replicate in host mitochondria and are frequently found in more phylogenetically apical fungi (members of subphylum Glomeromyoctina, phylum Mucoromycota, phylum Basidiomycota and phylum Ascomycota) as well as in plants. E. muscae is the first fungus from phylum Zoopagomycota, and thereby the most phylogenetically basal fungus, found to harbor mitoviruses to date. Multiple UGA (Trp) codons are found not only in each of the new mitovirus sequences from E. muscae but also in mitochondrial core-gene coding sequences newly assembled from E. muscae transcriptome data, suggesting that UGA (Trp) is not a rarely used codon in the mitochondria of this fungus. The presence of mitoviruses in these basal fungi has possible implications for the evolution of these viruses.}, }
@article {pmid30997305, year = {2019}, author = {Kanchan, S and Sharma, P and Chowdhury, S}, title = {Evolution of endonuclease IV protein family: an in silico analysis.}, journal = {3 Biotech}, volume = {9}, number = {5}, pages = {168}, pmid = {30997305}, issn = {2190-572X}, abstract = {DNA repair is one of the key cellular events which balances between evolvability and integrity of the genome. Endonuclease IV enzymes are class II AP endonucleases under base excision repair pathway which act on abasic site and break the phosphodiester bond at the 5' side. The role and activity of endonuclease IV proteins vary among different organisms; even it is absent in higher eukaryotes. The evolution of this protein family was studied by analyzing all homologs of the endonuclease IV protein family through different in silico techniques including phylogenetic tree generation and model building. The sequence analysis revealed four consensus sequence motifs within the AP2EC domain which are functionally important and conserved throughout the evolution process. It was also observed that the species and endonuclease IV gene evolution shape up differently in most of the organisms. Presence of the mitochondria-targeted signal peptides in fungal species Saccharomyces and Coccidioides suggest a possible endosymbiotic transfer of endonuclease IV genes to lower eukaryotes. Evolutionary changes among various clades in the protein-based phylogenetic tree have been investigated by comparison of homology models which suggests the conservation of overall fold of endonuclease IV proteins except for few alterations in loop orientation in few clades.}, }
@article {pmid30996240, year = {2019}, author = {Hirano, T and Saito, T and Tsunamoto, Y and Koseki, J and Ye, B and Do, VT and Miura, O and Suyama, Y and Chiba, S}, title = {Enigmatic incongruence between mtDNA and nDNA revealed by multi-locus phylogenomic analyses in freshwater snails.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6223}, pmid = {30996240}, issn = {2045-2322}, mesh = {Animal Shells/anatomy &amp; histology ; Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Asia, Eastern ; *Genetic Loci ; Genetics, Population ; High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; *Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Snails/classification/*genetics ; }, abstract = {Phylogenetic incongruence has frequently been encountered among different molecular markers. Recent progress in molecular phylogenomics has provided detailed and important information for evolutionary biology and taxonomy. Here we focused on the freshwater viviparid snails (Cipangopaludina chinensis chinensis and C. c. laeta) of East Asia. We conducted phylogenetic analyses and divergence time estimation using two mitochondrial markers. We also performed population genetic analyses using genome-wide SNPs. We investigated how and which phylogenetic patterns reflect shell morphology. The results showed these two species could be separated into four major mitochondrial clades, whereas the nuclear clusters supported two groups. The phylogenetic patterns of both mtDNA and nDNA largely reflected the geographical distribution. Shell morphology reflected the phylogenetic clusters based on nDNA. The findings also showed these two species diversified in the Pliocene to early Pleistocene era, and occurred introgressive hybridisation. The results also raise the taxonomic issue of the two species.}, }
@article {pmid30988357, year = {2019}, author = {Stampar, SN and Broe, MB and Macrander, J and Reitzel, AM and Brugler, MR and Daly, M}, title = {Linear Mitochondrial Genome in Anthozoa (Cnidaria): A Case Study in Ceriantharia.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {6094}, pmid = {30988357}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*classification/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Sequences and structural attributes of mitochondrial genomes have played a critical role in the clarification of relationships among Cnidaria, a key phylum of early-diverging animals. Among the major lineages of Cnidaria, Ceriantharia ("tube anemones") remains one of the most enigmatic in terms of its phylogenetic position. We sequenced the mitochondrial genomes of two ceriantharians to see whether the complete organellar genome would provide more support for the phylogenetic placement of Ceriantharia. For both Isarachnanthus nocturnus and Pachycerianthus magnus, the mitochondrial gene sequences could not be assembled into a single circular genome. Instead, our analyses suggest that both species have mitochondrial genomes consisting of multiple linear fragments. Linear mitogenomes are characteristic of members of Medusozoa, one of the major lineages of Cnidaria, but are unreported for Anthozoa, which includes the Ceriantharia. The inferred number of fragments and variation in gene order between species is much greater within Ceriantharia than among the lineages of Medusozoa. We identify origins of replication for each of the five putative chromosomes of the Isarachnanthus nocturnus mitogenome and for each of the eight putative chromosomes of the Pachycerianthus magnus mitogenome. At 80,923 bp, I. nocturnus now holds the record for the largest animal mitochondrial genome reported to date. The novelty of the mitogenomic structure in Ceriantharia highlights the distinctiveness of this lineage but, because it appears to be both unique to and diverse within Ceriantharia, it is uninformative about the phylogenetic position of Ceriantharia relative to other Anthozoa. The presence of tRNA[Met] and tRNA[Trp] in both ceriantharian mitogenomes supports a closer relationship between Ceriantharia and Hexacorallia than between Ceriantharia and any other cnidarian lineage, but phylogenetic analysis of the genes contained in the mitogenomes suggests that Ceriantharia is sister to a clade containing Octocorallia + Hexacorallia indicating a possible suppression of tRNA[Trp] in Octocorallia.}, }
@article {pmid30981810, year = {2019}, author = {Pazmiño, DA and van Herderden, L and Simpfendorfer, CA and Junge, C and Donnellan, SC and Hoyos-Padilla, EM and Duffy, CAJ and Huveneers, C and Gillanders, BM and Butcher, PA and Maes, GE}, title = {Introgressive hybridisation between two widespread sharks in the east Pacific region.}, journal = {Molecular phylogenetics and evolution}, volume = {136}, number = {}, pages = {119-127}, doi = {10.1016/j.ympev.2019.04.013}, pmid = {30981810}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; California ; Computer Simulation ; DNA, Mitochondrial/genetics ; Geography ; *Hybridization, Genetic ; Mitochondria/genetics ; Pacific Ocean ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Sample Size ; Sharks/*genetics ; }, abstract = {With just a handful of documented cases of hybridisation in cartilaginous fishes, shark hybridisation remains poorly investigated. Small amounts of admixture have been detected between Galapagos (Carcharhinus galapagensis) and dusky (Carcharhinus obscurus) sharks previously, generating a hypothesis of ongoing hybridisation. We sampled a large number of individuals from areas where the species co-occur (contact zones) across the Pacific Ocean and used both mitochondrial and nuclear-encoded SNPs to examine genetic admixture and introgression between the two species. Using empirical analytical approaches and simulations, we first developed a set of 1873 highly informative SNPs for these two species to evaluate the degree of admixture between them. Overall, results indicate a high discriminatory power of nuclear SNPs (FST = 0.47, p < 0.05) between the two species, unlike mitochondrial DNA (ΦST = 0.00 p > 0.05), which failed to differentiate these species. We identified four hybrid individuals (∼1%) and detected bi-directional introgression between C. galapagensis and C. obscurus in the Gulf of California along the east Pacific coast of the Americas. We emphasize the importance of including a combination of mtDNA and diagnostic nuclear markers to properly assess species identification, detect patterns of hybridisation, and better inform management and conservation of these sharks, especially given the morphological similarities within the genus Carcharhinus.}, }
@article {pmid30980669, year = {2019}, author = {Johri, P and Marinov, GK and Doak, TG and Lynch, M}, title = {Population Genetics of Paramecium Mitochondrial Genomes: Recombination, Mutation Spectrum, and Efficacy of Selection.}, journal = {Genome biology and evolution}, volume = {11}, number = {5}, pages = {1398-1416}, pmid = {30980669}, issn = {1759-6653}, support = {R35 GM122566/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Composition ; *Evolution, Molecular ; *Genome, Mitochondrial ; Mutation ; Paramecium/*genetics ; Polymorphism, Single Nucleotide ; RNA, Transfer/genetics ; *Recombination, Genetic ; *Selection, Genetic ; Species Specificity ; }, abstract = {The evolution of mitochondrial genomes and their population-genetic environment among unicellular eukaryotes are understudied. Ciliate mitochondrial genomes exhibit a unique combination of characteristics, including a linear organization and the presence of multiple genes with no known function or detectable homologs in other eukaryotes. Here we study the variation of ciliate mitochondrial genomes both within and across 13 highly diverged Paramecium species, including multiple species from the P. aurelia species complex, with four outgroup species: P. caudatum, P. multimicronucleatum, and two strains that may represent novel related species. We observe extraordinary conservation of gene order and protein-coding content in Paramecium mitochondria across species. In contrast, significant differences are observed in tRNA content and copy number, which is highly conserved in species belonging to the P. aurelia complex but variable among and even within the other Paramecium species. There is an increase in GC content from ∼20% to ∼40% on the branch leading to the P. aurelia complex. Patterns of polymorphism in population-genomic data and mutation-accumulation experiments suggest that the increase in GC content is primarily due to changes in the mutation spectra in the P. aurelia species. Finally, we find no evidence of recombination in Paramecium mitochondria and find that the mitochondrial genome appears to experience either similar or stronger efficacy of purifying selection than the nucleus.}, }
@article {pmid30974201, year = {2019}, author = {Strong, EE and Whelan, NV}, title = {Assessing the diversity of Western North American Juga (Semisulcospiridae, Gastropoda).}, journal = {Molecular phylogenetics and evolution}, volume = {136}, number = {}, pages = {87-103}, doi = {10.1016/j.ympev.2019.04.009}, pmid = {30974201}, issn = {1095-9513}, mesh = {Algorithms ; Animal Shells/anatomy &amp; histology ; Animals ; Bayes Theorem ; California ; Cell Nucleus/genetics ; Gastropoda/anatomy &amp; histology/*genetics ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; }, abstract = {Juga is a genus of freshwater gastropods distributed in Pacific and Interior drainages of the Pacific Northwest from central California to northern Washington. The current classification has relied heavily on features of the shell, which vary within and across drainages, and often intergrade without sharp distinctions between species. The only previous molecular analysis included limited population sampling, which did not allow robust assessment of intra- versus interspecific levels of genetic diversity, and concluded almost every sampled population to be a distinct OTU. We assembled a multilocus mitochondrial (COI, 16S) and nuclear gene (ITS1) dataset for ∼100 populations collected across the range of the genus. We generated primary species hypotheses using ABGD with best-fit model-corrected distances and further explored our data, both individual gene partitions and concatenated datasets, using a diversity of phylogenetic and species delimitation methods (Bayesian inference, maximum likelihood estimation, StarBEAST2, bGMYC, bPTP, BP&amp;P). Our secondary species delimitation hypotheses, based primarily on the criterion of reciprocal monophyly, and informed by a combination of geography and morphology, support the interpretation that Juga comprises a mixture of geographically widespread species and narrow range endemics. As might be expected in taxa with low vagility and poor dispersal capacities, analysis of molecular variance (AMOVA) revealed highly structured populations with up to 80% of the observed genetic variance explained by variation between populations. Analyses with bGMYC, bPTP, and BP&amp;P appeared sensitive to this genetic structure and returned highly dissected species hypotheses that are likely oversplit. The species diversity of Juga is concluded to be lower than presently recognized, and the systematics to require extensive revision. Features of the teleoconch considered significant in species-level and subgeneric classification were found to be variable within some species, sometimes at a single site. Of a number of potentially new species identified in non-peer reviewed reports and field guides, only one was supported as a distinct OTU.}, }
@article {pmid30968307, year = {2019}, author = {Garcia, LE and Zubko, MK and Zubko, EI and Sanchez-Puerta, MV}, title = {Elucidating genomic patterns and recombination events in plant cybrid mitochondria.}, journal = {Plant molecular biology}, volume = {100}, number = {4-5}, pages = {433-450}, pmid = {30968307}, issn = {1573-5028}, support = {M033//Universidad Nacional de Cuyo/ ; PICT1762//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; 1062432//National Science Foundation/ ; }, mesh = {DNA, Mitochondrial/chemistry ; *Genome, Mitochondrial ; Genome, Plant ; Homologous Recombination ; *Hybridization, Genetic ; Hyoscyamus/genetics ; Mitochondria/*genetics ; Nicotiana/genetics ; }, abstract = {Cybrid plant mitochondria undergo homologous recombination, mainly BIR, keep a single allele for each gene, and maintain exclusive sequences of each parent and a single copy of the homologous regions. The maintenance of a dynamic equilibrium between the mitochondrial and nuclear genomes requires continuous communication and a high level of compatibility between them, so that alterations in one genetic compartment need adjustments in the other. The co-evolution of nuclear and mitochondrial genomes has been poorly studied, even though the consequences and effects of this interaction are highly relevant for human health, as well as for crop improvement programs and for genetic engineering. The mitochondria of plants represent an excellent system to understand the mechanisms of genomic rearrangements, chimeric gene formation, incompatibility between nucleus and cytoplasm, and horizontal gene transfer. We carried out detailed analyses of the mtDNA of a repeated cybrid between the solanaceae Nicotiana tabacum and Hyoscyamus niger. The mtDNA of the cybrid was intermediate between the size of the parental mtDNAs and the sum of them. Noticeably, most of the homologous sequences inherited from both parents were lost. In contrast, the majority of the sequences exclusive of a single parent were maintained. The mitochondrial gene content included a majority of N. tabacum derived genes, but also chimeric, two-parent derived, and H. niger-derived genes in a tobacco nuclear background. Any of these alterations in the gene content could be the cause of CMS in the cybrid. The parental mtDNAs interacted through 28 homologous recombination events and a single case of illegitimate recombination. Three main homologous recombination mechanisms were recognized in the cybrid mitochondria. Break induced replication (BIR) pathway was the most frequent. We propose that BIR could be one of the mechanisms responsible for the loss of the majority of the repeated regions derived from H. niger.}, }
@article {pmid30968120, year = {2019}, author = {Mays, JN and Camacho-Villasana, Y and Garcia-Villegas, R and Perez-Martinez, X and Barrientos, A and Fontanesi, F}, title = {The mitoribosome-specific protein mS38 is preferentially required for synthesis of cytochrome c oxidase subunits.}, journal = {Nucleic acids research}, volume = {47}, number = {11}, pages = {5746-5760}, pmid = {30968120}, issn = {1362-4962}, support = {R35 GM118141/GM/NIGMS NIH HHS/United States ; }, mesh = {Arabidopsis/metabolism ; DNA, Mitochondrial/metabolism ; Electron Transport Complex IV/*chemistry ; *Gene Expression Regulation ; *Gene Expression Regulation, Fungal ; Humans ; Kluyveromyces/metabolism ; Mitochondrial Proteins/metabolism ; Mitochondrial Ribosomes/chemistry/*metabolism ; Oryza/metabolism ; Oxidative Phosphorylation ; Polyribosomes/metabolism ; *Protein Biosynthesis ; RNA, Messenger/metabolism ; RNA, Mitochondrial ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Yarrowia/metabolism ; }, abstract = {Message-specific translational regulation mechanisms shape the biogenesis of multimeric oxidative phosphorylation (OXPHOS) enzyme in mitochondria from the yeast Saccharomyces cerevisiae. These mechanisms, driven mainly by the action of mRNA-specific translational activators, help to coordinate synthesis of OXPHOS catalytic subunits by the mitoribosomes with both the import of their nucleus-encoded partners and their assembly to form the holocomplexes. However, little is known regarding the role that the mitoribosome itself may play in mRNA-specific translational regulation. Here, we show that the mitoribosome small subunit protein Cox24/mS38, known to be necessary for mitoribosome-specific intersubunit bridge formation and 15S rRNA H44 stabilization, is required for efficient mitoribogenesis. Consequently, mS38 is necessary to sustain the overall mitochondrial protein synthesis rate, despite an adaptive ∼2-fold increase in mitoribosome abundance in mS38-deleted cells. Additionally, the absence of mS38 preferentially disturbs translation initiation of COX1, COX2, and COX3 mRNAs, without affecting the levels of mRNA-specific translational activators. We propose that mS38 confers the mitochondrial ribosome an intrinsic capacity of translational regulation, probably acquired during evolution from bacterial ribosomes to facilitate the translation of mitochondrial mRNAs, which lack typical anti-Shine-Dalgarno sequences.}, }
@article {pmid30967590, year = {2019}, author = {Kehlmaier, C and Zhang, X and Georges, A and Campbell, PD and Thomson, S and Fritz, U}, title = {Mitogenomics of historical type specimens of Australasian turtles: clarification of taxonomic confusion and old mitochondrial introgression.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5841}, pmid = {30967590}, issn = {2045-2322}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; Turtles/*genetics ; }, abstract = {Diagnosability is central to taxonomy as are type specimens which define taxa. New advances in technologies and the discovery of new informative traits must be matched with previous taxonomic decisions based on name-bearing type specimens. Consequently, the challenge of sequencing highly degraded DNA from historical types becomes an inevitability to resolve the very many taxonomic issues arising from, by modern standards, poor historical species descriptions leading to difficulties to assign names to genetic clusters identified from fresh material. Here we apply high-throughput parallel sequencing and sequence baiting to reconstruct the mitogenomes from 18 type specimens of Australasian side-necked turtles (Chelidae). We resolve a number of important issues that have confused the taxonomy of this family, and analyse the mitogenomes of the types and those of fresh material to improve our understanding of the phylogenetic relationships of this morphologically conservative group. Together with previously published nuclear genomic data, our study provides evidence for multiple old mitochondrial introgressions.}, }
@article {pmid30965625, year = {2019}, author = {Nelson, ED and Grishin, NV}, title = {How Often Do Protein Genes Navigate Valleys of Low Fitness?.}, journal = {Genes}, volume = {10}, number = {4}, pages = {}, pmid = {30965625}, issn = {2073-4425}, support = {GM127390/NH/NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Amino Acid Motifs/*genetics ; *Biological Evolution ; Epistasis, Genetic ; Genetic Fitness/*genetics ; Genotype ; Humans ; Models, Genetic ; Mutation/genetics ; Population Density ; RNA, Transfer/genetics ; Selection, Genetic ; }, abstract = {To escape from local fitness peaks, a population must navigate across valleys of low fitness. How these transitions occur, and what role they play in adaptation, have been subjects of active interest in evolutionary genetics for almost a century. However, to our knowledge, this problem has never been addressed directly by considering the evolution of a gene, or group of genes, as a whole, including the complex effects of fitness interactions among multiple loci. Here, we use a precise model of protein fitness to compute the probability P (s , Δ t) that an allele, randomly sampled from a population at time t, has crossed a fitness valley of depth s during an interval t - Δ t , t in the immediate past. We study populations of model genes evolving under equilibrium conditions consistent with those in mammalian mitochondria. From this data, we estimate that genes encoding small protein motifs navigate fitness valleys of depth 2 N s ≳ 30 with probability P ≳ 0 . 1 on a time scale of human evolution, where N is the (mitochondrial) effective population size. The results are consistent with recent findings for Watson[-]Crick switching in mammalian mitochondrial tRNA molecules.}, }
@article {pmid30959949, year = {2019}, author = {Hirakawa, Y and Watanabe, A}, title = {Organellar DNA Polymerases in Complex Plastid-Bearing Algae.}, journal = {Biomolecules}, volume = {9}, number = {4}, pages = {}, pmid = {30959949}, issn = {2218-273X}, mesh = {DNA-Directed DNA Polymerase/*metabolism ; Phylogeny ; Plastids/*enzymology/genetics ; Rhodophyta/*enzymology ; }, abstract = {DNA replication in plastids and mitochondria is generally regulated by nucleus-encoded proteins. In plants and red algae, a nucleus-encoded enzyme called POP (plant and protist organellar DNA polymerase) is involved in DNA replication in both organelles by virtue of its dual localization. POPs are family A DNA polymerases, which include bacterial DNA polymerase I (PolI). POP homologs have been found in a wide range of eukaryotes, including plants, algae, and non-photosynthetic protists. However, the phylogeny and subcellular localizations of POPs remain unclear in many algae, especially in secondary and tertiary plastid-bearing groups. In this study, we report that chlorarachniophytes possess two evolutionarily distinct POPs, and fluorescent protein-tagging experiments demonstrate that they are targeted to the secondary plastids and mitochondria, respectively. The timing of DNA replication is different between the two organelles in the chlorarachniophyte Bigelowiella natans, and this seems to be correlated to the transcription of respective POP genes. Dinoflagellates also carry two distinct POP genes, possibly for their plastids and mitochondria, whereas haptophytes and ochrophytes have only one. Therefore, unlike plants, some algal groups are likely to have evolved multiple DNA polymerases for various organelles. This study provides a new insight into the evolution of organellar DNA replication in complex plastid-bearing organisms.}, }
@article {pmid30954588, year = {2019}, author = {Sajeela, KA and Gopalakrishnan, A and Basheer, VS and Mandal, A and Bineesh, KK and Grinson, G and Gopakumar, SD}, title = {New insights from nuclear and mitochondrial markers on the genetic diversity and structure of the Indian white shrimp Fenneropenaeus indicus among the marginal seas in the Indian Ocean.}, journal = {Molecular phylogenetics and evolution}, volume = {136}, number = {}, pages = {53-64}, doi = {10.1016/j.ympev.2019.04.007}, pmid = {30954588}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Cell Nucleus/*genetics ; Electron Transport Complex IV/genetics ; Genetic Markers ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Indian Ocean ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Penaeidae/*genetics ; Phylogeny ; Species Specificity ; }, abstract = {Genetic variation in wild stocks of a major commercial shrimp, Fenneropenaeus indicus, from the marginal seas in the Indian Ocean was analysed using polymorphic microsatellite loci and mitochondrial COI gene. The average observed heterozygosity (Ho = 0.44 ± 0.02) and the expected heterozygosity (He = 0.73 ± 0.01) were high across loci and populations indicating high microsatellite variation. Pairwise FST and Bayesian clustering indicated the occurrence of four genetically distinct stocks out of the eight sampled populations with implications for specific management approaches. Mantel test for isolation by distance proved that genetic differentiation is not related to geographic distance between populations. Mitochondrial COI sequence analysis showed concordant differentiation pattern as well indicated the relevance of COI in population genetics of shrimps. Pairwise ɸST and phylogenetic and Bayesian analyses revealed four distinct clades, as observed with nuclear markers. Divergence time analysis revealed the origin and initial divergence of F. indicus corresponds to late Miocene and divergence to phylogroups in the Pleistocene. BSP analysis presented a long stable population size with a slight decrease in the late Pleistocene and gradually expanded to the current status. The information here will be useful in commercial shrimp breeding and selection programmes and management of natural stocks of Indian white shrimp.}, }
@article {pmid30951923, year = {2019}, author = {Kinoshita, G and Nunome, M and Kryukov, AP and Kartavtseva, IV and Han, SH and Yamada, F and Suzuki, H}, title = {Contrasting phylogeographic histories between the continent and islands of East Asia: Massive mitochondrial introgression and long-term isolation of hares (Lagomorpha: Lepus).}, journal = {Molecular phylogenetics and evolution}, volume = {136}, number = {}, pages = {65-75}, doi = {10.1016/j.ympev.2019.04.003}, pmid = {30951923}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Cell Nucleus/genetics ; DNA/genetics ; DNA, Mitochondrial/genetics ; Asia, Eastern ; Genetic Loci ; Geography ; Hares/classification/*genetics ; *Islands ; Mitochondria/*genetics ; Phylogeny ; *Phylogeography ; }, abstract = {Hares of the genus Lepus are distributed worldwide, and introgressive hybridization is thought to be pervasive among species, leading to reticulate evolution and taxonomic confusion. Here, we performed phylogeographic analyses of the following species of hare across East Asia: L. timidus, L. mandshuricus, L. coreanus, and L. brachyurus collected from far-eastern Russia, South Korea, and Japan. Nucleotide sequences of one mitochondrial DNA and eight nuclear gene loci were examined, adding sequences of hares in China from databases. All nuclear DNA analyses supported the clear separation of three phylogroups: L. timidus, L. brachyurus, and the L. mandshuricus complex containing L. coreanus. On the other hand, massive mitochondrial introgression from two L. timidus lineages to the L. mandshuricus complex was suggested in continental East Asia. The northern population of the L. mandshuricus complex was mainly associated with introgression from the continental lineage of L. timidus, possibly since the last glacial period, whereas the southern population of the L. mandshuricus complex experienced introgression from another L. timidus lineage related to the Hokkaido population, possibly before the last glacial period. In contrast to continental hares, no evidence of introgression was found in L. brachyurus in the Japanese Archipelago, which showed the oldest divergence amongst East Asian hare lineages. Our findings suggest that glacial-interglacial climate changes in the circum-Japan Sea region promoted distribution shifts and introgressive hybridization among continental hare species, while the geographic structure of the region contributed to long-term isolation of hares on the islands, preventing inter-species gene flow.}, }
@article {pmid30949694, year = {2019}, author = {Greiner, S and Lehwark, P and Bock, R}, title = {OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes.}, journal = {Nucleic acids research}, volume = {47}, number = {W1}, pages = {W59-W64}, pmid = {30949694}, issn = {1362-4962}, mesh = {Chromosome Mapping ; Genome, Mitochondrial/*genetics ; Genome, Plastid/*genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; Molecular Sequence Annotation ; Organelles/*genetics ; Phylogeny ; Plastids/genetics ; *Software ; }, abstract = {Organellar (plastid and mitochondrial) genomes play an important role in resolving phylogenetic relationships, and next-generation sequencing technologies have led to a burst in their availability. The ongoing massive sequencing efforts require software tools for routine assembly and annotation of organellar genomes as well as their display as physical maps. OrganellarGenomeDRAW (OGDRAW) has become the standard tool to draw graphical maps of plastid and mitochondrial genomes. Here, we present a new version of OGDRAW equipped with a new front end. Besides several new features, OGDRAW now has access to a local copy of the organelle genome database of the NCBI RefSeq project. Together with batch processing of (multi-)GenBank files, this enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades. The new OGDRAW server can be accessed at https://chlorobox.mpimp-golm.mpg.de/OGDraw.html.}, }
@article {pmid30947958, year = {2019}, author = {Kacem, H and Diagne, PM and Miquel, J}, title = {Ultrastructural organisation of the spermatozoon of Allopodocotyle tunisiensis Derbel and Neifar, 2009 (Digenea, Opecoelidae), an intestinal parasite of Solea aegyptiaca Chabanaud, 1927 (Teleostei, Soleidae).}, journal = {Tissue &amp; cell}, volume = {57}, number = {}, pages = {1-7}, doi = {10.1016/j.tice.2019.01.008}, pmid = {30947958}, issn = {1532-3072}, mesh = {Animals ; Flatfishes/parasitology ; Male ; Spermatozoa/*ultrastructure ; Trematoda/*ultrastructure ; }, abstract = {The ultrastructure of the spermatozoon of Allopodocotyle tunisiensis (Digenea, Opecoelidae), an intestinal parasite of Solea aegyptiaca (Teleostei, Soleidae), is described by transmission electron microscopy (TEM). The mature spermatozoon is a filiform cell that exhibits two axonemes of different length with the 9+'1' pattern of trepaxonematan Platyhelminthes. In the anterior spermatozoon extremity, cortical microtubules are absent. They appear after the disappearance of an anterior electron-dense material, being initially in a continuous and submembranous layer. They surround only partially the sperm cell. Later, these cortical microtubules are distributed into two bundles. Additionally, the spermatozoon of A. tunisiensis shows two mitochondria, a nucleus, an external ornamentation of the plasma membrane, spine-like bodies, and a large amount of glycogen granules. According to the location of the external ornamentation, A. tunisiensis presents a Quilichini et al.'s type 2 spermatozoon. With respect to the posterior extremity, the sperm cell of A. tunisiensis corresponds to the Quilichini et al.'s opecoelid type. The morphology of the first mitochondrion with a U-shaped posterior extremity is described for the first time in a digenean spermatozoon.}, }
@article {pmid30945675, year = {2019}, author = {Saikia, M and Nath, R and Devi, D}, title = {Genetic diversity and phylogeny analysis of Antheraea assamensis Helfer (Lepidoptera: Saturniidae) based on mitochondrial DNA sequences.}, journal = {Journal of genetics}, volume = {98}, number = {}, pages = {}, pmid = {30945675}, issn = {0973-7731}, mesh = {Animals ; Bombyx/*classification/*genetics ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; Mitochondria ; Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Antheraea assamensis Helfer, popularly known as Muga silkworm, the golden silk producer of northeast India is economically important and unique among the Saturniid silkworms. In this study, the genetic diversity and phylogeny of semidomesticated and wild morphs of Muga silkwormcollected from different geographical locations of northeast India were investigated based on the sequences of five mitochondrial loci, i.e. 12S rRNA, 16S rRNA, CoxI, Cytb and CR. All the five mitochondrial loci showed a strong bias towards higher 'A' and 'T' contents. Transitional substitutions were found to be more than the transversional substitutions. The rate of nucleotide substitution and average genetic divergence were found to be highest in CR sequences and lowest in 12S rRNA gene sequences among the morphs of Muga silkworm. The morphs collected from same geographical area had identical 12S rRNA, 16S rRNA, CoxI and Cytb gene sequences. Moreover, the 12S rRNA and 16S rRNA gene sequences of somesemi-domesticated and wild morphs collected from different geographical locations were also found to be similar. In the phylogenetic trees generated based on themitochondrial loci, mixing of semi-domesticated and wild morphs was observed as they shared the same group. The information generated in this study will help in formulating strategies to conserve the natural biodiversity present among these unique silkworms in northeast India. In addition, this will be useful in identifying diverse morphs of Muga silkworm, which will help in effective breeding programmes to improve its productivity.}, }
@article {pmid30945667, year = {2019}, author = {Purushothaman, P and Chakraborty, RD and Kuberan, G and Maheswarudu, G}, title = {Integrative taxonomy of commercially important deep water penaeoid shrimps from India.}, journal = {Journal of genetics}, volume = {98}, number = {}, pages = {}, pmid = {30945667}, issn = {0973-7731}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Mitochondria/*genetics ; Penaeidae/*classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {The deep water penaeoid shrimp is an important commercial crustacean resource along the Indian coast. The molecular and morphological information of this group from the Indian coast is scarcely known. In this study, we investigated the identification and phylogenetic relationships of the deep water penaeoid shrimps using three mitochondrial (cytochrome oxidase subunit I (COI), cytochrome b, 16S rRNA) genes, which were compared with 54 morphological characters and further used to evaluate character evolution. Our study revealed remarkable molecular divergence (3.3-33.0%) in nine species from three genera of Solenoceridae, four species from three genera of Penaeidae and one species from Aristeidae using COI. Phylogenetic analysis using maximum likelihood and Bayesian approaches revealed that all species from these families are monophyletic. The present analysis revealed the existence of subgroups in the genus Solenocera suggesting the slow reduction of postrostral carina which corresponds to the increase in distributional depth during the evolutionary process which further indicates the origin of the genus in the continental shelf and extending up to the continental slope. In addition, we generated the DNA barcode database involving these species which can help further to investigate the detailed evolution and biogeography of these valuable crustacean resources.}, }
@article {pmid30941136, year = {2019}, author = {Duvvuri, B and Lood, C}, title = {Cell-Free DNA as a Biomarker in Autoimmune Rheumatic Diseases.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {502}, pmid = {30941136}, issn = {1664-3224}, mesh = {Animals ; Autoimmune Diseases/metabolism ; Biomarkers/*metabolism ; Cell-Free Nucleic Acids/*metabolism ; DNA, Mitochondrial/metabolism ; Disease Progression ; Humans ; Rheumatic Diseases/metabolism ; }, abstract = {Endogenous DNA is primarily found intracellularly in nuclei and mitochondria. However, extracellular, cell-free (cf) DNA, has been observed in several pathological conditions, including autoimmune diseases, prompting the interest of developing cfDNA as a potential biomarker. There is an upsurge in studies considering cfDNA to stratify patients, monitor the treatment response and predict disease progression, thus evaluating the prognostic potential of cfDNA for autoimmune diseases. Since the discovery of elevated cfDNA levels in lupus patients in the 1960s, cfDNA research in autoimmune diseases has mainly focused on the overall quantification of cfDNA and the association with disease activity. However, with recent technological advancements, including genomic and methylomic sequencing, qualitative changes in cfDNA are being explored in autoimmune diseases, similar to the ones used in molecular profiling of cfDNA in cancer patients. Further, the intracellular origin, e.g., if derived from mitochondrial or nuclear source, as well as the complexing with carrier molecules, including LL-37 and HMGB1, has emerged as important factors to consider when analyzing the quality and inflammatory potential of cfDNA. The clinical relevance of cfDNA in autoimmune rheumatic diseases is strengthened by mechanistic insights into the biological processes that result in an enhanced release of DNA into the circulation during autoimmune and inflammatory conditions. Prior work have established an important role of accelerated apoptosis and impaired clearance in leakage of nucleic acids into the extracellular environment. Findings from more recent studies, including our own investigations, have demonstrated that NETosis, a neutrophil cell death process, can result in a selective extrusion of inflammatory mitochondrial DNA; a process which is enhanced in patients with lupus and rheumatoid arthritis. In this review, we will summarize the evolution of cfDNA, both nuclear and mitochondrial DNA, as biomarkers for autoimmune rheumatic diseases and discuss limitations, challenges and implications to establish cfDNA as a biomarker for clinical use. This review will also highlight recent advancements in mechanistic studies demonstrating mitochondrial DNA as a central component of cfDNA in autoimmune rheumatic diseases.}, }
@article {pmid30941110, year = {2019}, author = {Moelling, K and Broecker, F}, title = {Viruses and Evolution - Viruses First? A Personal Perspective.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {523}, pmid = {30941110}, issn = {1664-302X}, abstract = {The discovery of exoplanets within putative habitable zones revolutionized astrobiology in recent years. It stimulated interest in the question about the origin of life and its evolution. Here, we discuss what the roles of viruses might have been at the beginning of life and during evolution. Viruses are the most abundant biological entities on Earth. They are present everywhere, in our surrounding, the oceans, the soil and in every living being. Retroviruses contributed to about half of our genomic sequences and to the evolution of the mammalian placenta. Contemporary viruses reflect evolution ranging from the RNA world to the DNA-protein world. How far back can we trace their contribution? Earliest replicating and evolving entities are the ribozymes or viroids fulfilling several criteria of life. RNA can perform many aspects of life and influences our gene expression until today. The simplest structures with non-protein-coding information may represent models of life built on structural, not genetic information. Viruses today are obligatory parasites depending on host cells. Examples of how an independent lifestyle might have been lost include mitochondria, chloroplasts, Rickettsia and others, which used to be autonomous bacteria and became intracellular parasites or endosymbionts, thereby losing most of their genes. Even in vitro the loss of genes can be recapitulated all the way from coding to non-coding RNA. Furthermore, the giant viruses may indicate that there is no sharp border between living and non-living entities but an evolutionary continuum. Here, it is discussed how viruses can lose and gain genes, and that they are essential drivers of evolution. This discussion may stimulate the thinking about viruses as early possible forms of life. Apart from our view "viruses first", there are others such as "proteins first" and "metabolism first."}, }
@article {pmid30938771, year = {2019}, author = {Lama, S and Broda, M and Abbas, Z and Vaneechoutte, D and Belt, K and Säll, T and Vandepoele, K and Van Aken, O}, title = {Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants.}, journal = {Molecular biology and evolution}, volume = {36}, number = {5}, pages = {974-989}, pmid = {30938771}, issn = {1537-1719}, mesh = {Arabidopsis/*genetics ; DNA Mutational Analysis ; DNA, Bacterial ; F-Box Proteins/genetics ; *Gene Duplication ; Gene Expression ; Genome, Plant ; Mitochondrial Proteins/*genetics ; *Multigene Family ; Mutagenesis, Insertional ; Plant Proteins/genetics ; Signal Transduction ; }, abstract = {Because of their symbiotic origin, many mitochondrial proteins are well conserved across eukaryotic kingdoms. It is however less obvious how specific lineages have obtained novel nuclear-encoded mitochondrial proteins. Here, we report a case of mitochondrial neofunctionalization in plants. Phylogenetic analysis of genes containing the Domain of Unknown Function 295 (DUF295) revealed that the domain likely originated in Angiosperms. The C-terminal DUF295 domain is usually accompanied by an N-terminal F-box domain, involved in ubiquitin ligation via binding with ASK1/SKP1-type proteins. Due to gene duplication, the gene family has expanded rapidly, with 94 DUF295-related genes in Arabidopsis thaliana alone. Two DUF295 family subgroups have uniquely evolved and quickly expanded within Brassicaceae. One of these subgroups has completely lost the F-box, but instead obtained strongly predicted mitochondrial targeting peptides. We show that several representatives of this DUF295 Organellar group are effectively targeted to plant mitochondria and chloroplasts. Furthermore, many DUF295 Organellar genes are induced by mitochondrial dysfunction, whereas F-Box DUF295 genes are not. In agreement, several Brassicaceae-specific DUF295 Organellar genes were incorporated in the evolutionary much older ANAC017-dependent mitochondrial retrograde signaling pathway. Finally, a representative set of DUF295 T-DNA insertion mutants was created. No obvious aberrant phenotypes during normal growth and mitochondrial dysfunction were observed, most likely due to the large extent of gene duplication and redundancy. Overall, this study provides insight into how novel mitochondrial proteins can be created via "intercompartmental" gene duplication events. Moreover, our analysis shows that these newly evolved genes can then be specifically integrated into relevant, pre-existing coexpression networks.}, }
@article {pmid30937430, year = {2019}, author = {Hill, GE}, title = {Reconciling the Mitonuclear Compatibility Species Concept with Rampant Mitochondrial Introgression.}, journal = {Integrative and comparative biology}, volume = {59}, number = {4}, pages = {912-924}, doi = {10.1093/icb/icz019}, pmid = {30937430}, issn = {1557-7023}, mesh = {*Biological Evolution ; Cell Nucleus/*genetics ; Eukaryota/*genetics ; Genetic Introgression ; Genome, Mitochondrial/*genetics ; Genotype ; }, abstract = {The mitonuclear compatibility species concept defines a species as a population that is genetically isolated from other populations by uniquely coadapted mitochondrial (mt) and nuclear genes. A key prediction of this hypothesis is that the mt genotype of each species will be functionally distinct and that introgression of mt genomes will be prevented by mitonuclear incompatibilities that arise when heterospecific mt and nuclear genes attempt to cofunction to enable aerobic respiration. It has been proposed, therefore, that the observation of rampant introgression of mt genotypes from one species to another constitutes a strong refutation of the mitonuclear speciation. The displacement of a mt genotype from a nuclear background with which it co-evolved to a foreign nuclear background will necessarily lead to fitness loss due to mitonuclear incompatibilities. Here I consider two potential benefits of mt introgression between species that may, in some cases, overcome fitness losses arising from mitonuclear incompatibilities. First, the introgressed mt genotype may be better adapted to the local environment than the native mt genotype such that higher fitness is achieved through improved adaptation via introgression. Second, if the mitochondria of the recipient taxa carry a high mutational load, then introgression of a foreign, less corrupt mt genome may enable the recipient taxa to escape its mutational load and gain a fitness advantage. Under both scenarios, fitness gains from novel mt genotypes could theoretically compensate for the fitness that is lost via mitonuclear incompatibility. I also consider the role of endosymbionts in non-adaptive rampant introgression of mt genomes. I conclude that rampant introgression is not necessarily evidence against the idea of tight mitonuclear coadaptation or the mitonuclear compatibility species concept. Rampant mt introgression will typically lead to erasure of species but in some cases could lead to hybrid speciation.}, }
@article {pmid30936856, year = {2019}, author = {Degli Esposti, M and Mentel, M and Martin, W and Sousa, FL}, title = {Oxygen Reductases in Alphaproteobacterial Genomes: Physiological Evolution From Low to High Oxygen Environments.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {499}, pmid = {30936856}, issn = {1664-302X}, abstract = {Oxygen reducing terminal oxidases differ with respect to their subunit composition, heme groups, operon structure, and affinity for O2. Six families of terminal oxidases are currently recognized, all of which occur in alphaproteobacterial genomes, two of which are also present in mitochondria. Many alphaproteobacteria encode several different terminal oxidases, likely reflecting ecological versatility with respect to oxygen levels. Terminal oxidase evolution likely started with the advent of O2 roughly 2.4 billion years ago and terminal oxidases diversified in the Proterozoic, during which oxygen levels remained low, around the Pasteur point (ca. 2 μM O2). Among the alphaproteobacterial genomes surveyed, those from members of the Rhodospirillaceae reveal the greatest diversity in oxygen reductases. Some harbor all six terminal oxidase types, in addition to many soluble enzymes typical of anaerobic fermentations in mitochondria and hydrogenosomes of eukaryotes. Recent data have it that O2 levels increased to current values (21% v/v or ca. 250 μM) only about 430 million years ago. Ecological adaptation brought forth different lineages of alphaproteobacteria and different lineages of eukaryotes that have undergone evolutionary specialization to high oxygen, low oxygen, and anaerobic habitats. Some have remained facultative anaerobes that are able to generate ATP with or without the help of oxygen and represent physiological links to the ancient proteobacterial lineage at the origin of mitochondria and eukaryotes. Our analysis reveals that the genomes of alphaproteobacteria appear to retain signatures of ancient transitions in aerobic metabolism, findings that are relevant to mitochondrial evolution in eukaryotes as well.}, }
@article {pmid30936077, year = {2019}, author = {Mafra, ACP and Dias, SMG}, title = {Several Faces of Glutaminase Regulation in Cells.}, journal = {Cancer research}, volume = {79}, number = {7}, pages = {1302-1304}, doi = {10.1158/0008-5472.CAN-19-0313}, pmid = {30936077}, issn = {1538-7445}, mesh = {Cell Line, Tumor ; Glutaminase/*genetics ; *Mitochondria ; }, abstract = {The cancer target glutaminase (GLS) has proven to be a fascinating protein. Since it was first described to be regulated by the oncogene Myc 10 years ago, several other transcriptional, posttranscriptional, and posttranslational regulatory mechanisms have emerged, and the list is growing. A recent study by Deng and colleagues revealed that an antisense (AS) long noncoding RNA named GLS-AS, which is negatively regulated by Myc, downregulates GLS in pancreatic cancer. The Myc/GLS-AS/GLS regulatory axis is activated by nutrient stress, which is important for the often hypovascular pancreatic cancer, displaying the significance of GLS for the progression of this highly lethal type of cancer.See related article by Deng et al., p. 1398.}, }
@article {pmid30935869, year = {2019}, author = {Zimorski, V and Mentel, M and Tielens, AGM and Martin, WF}, title = {Energy metabolism in anaerobic eukaryotes and Earth's late oxygenation.}, journal = {Free radical biology &amp; medicine}, volume = {140}, number = {}, pages = {279-294}, pmid = {30935869}, issn = {1873-4596}, mesh = {Anaerobiosis/genetics ; Atmosphere ; *Biological Evolution ; Energy Metabolism/genetics ; Eukaryota/*metabolism ; Mitochondria/genetics/metabolism ; Oxygen/*metabolism ; }, abstract = {Eukaryotes arose about 1.6 billion years ago, at a time when oxygen levels were still very low on Earth, both in the atmosphere and in the ocean. According to newer geochemical data, oxygen rose to approximately its present atmospheric levels very late in evolution, perhaps as late as the origin of land plants (only about 450 million years ago). It is therefore natural that many lineages of eukaryotes harbor, and use, enzymes for oxygen-independent energy metabolism. This paper provides a concise overview of anaerobic energy metabolism in eukaryotes with a focus on anaerobic energy metabolism in mitochondria. We also address the widespread assumption that oxygen improves the overall energetic state of a cell. While it is true that ATP yield from glucose or amino acids is increased in the presence of oxygen, it is also true that the synthesis of biomass costs thirteen times more energy per cell in the presence of oxygen than in anoxic conditions. This is because in the reaction of cellular biomass with O2, the equilibrium lies very far on the side of CO2. The absence of oxygen offers energetic benefits of the same magnitude as the presence of oxygen. Anaerobic and low oxygen environments are ancient. During evolution, some eukaryotes have specialized to life in permanently oxic environments (life on land), other eukaryotes have remained specialized to low oxygen habitats. We suggest that the Km of mitochondrial cytochrome c oxidase of 0.1-10 μM for O2, which corresponds to about 0.04%-4% (avg. 0.4%) of present atmospheric O2 levels, reflects environmental O2 concentrations that existed at the time that the eukaryotes arose.}, }
@article {pmid30927526, year = {2019}, author = {Vays, VB and Vangeli, IM and Eldarov, CM and Efeykin, BD and Bakeeva, LE}, title = {Mitochondria in Obliquely Striated Muscles of the Horsehair Worm Gordionus alpestris (Nematomorpha, Gordioidea) with Structural Organization Typical of Cells with Energy-Intensive Processes.}, journal = {Biochemistry. Biokhimiia}, volume = {84}, number = {1}, pages = {56-61}, doi = {10.1134/S0006297919010073}, pmid = {30927526}, issn = {1608-3040}, mesh = {Animals ; Energy Metabolism ; Helminths/*anatomy &amp; histology/cytology ; Mitochondria/*ultrastructure ; Mitochondria, Muscle ; Mitochondrial Membranes ; Muscle, Striated/*ultrastructure ; }, abstract = {The ultrastructure of mitochondria in the flattened circomyarian fibers of the horsehair worm Gordionus alpestris (Nemathelminthes) was examined. In contrast to the previously published data, we showed these mitochondria to be giant elongated organelles that densely fill the central cytoplasmic space of the ribbon-like muscle fibers. No fundamental differences were found in the ultrastructure of the muscle tissue mitochondria in actively moving free-living and parasitic G. alpestris worms. The functional significance of the observed ultrastructural organization of mitochondria is discussed in connection with the necessity for an extended mitochondrial membrane system for a uniform supply of active muscle tissue with energy.}, }
@article {pmid30924880, year = {2019}, author = {Sudianto, E and Chaw, SM}, title = {Two Independent Plastid accD Transfers to the Nuclear Genome of Gnetum and Other Insights on Acetyl-CoA Carboxylase Evolution in Gymnosperms.}, journal = {Genome biology and evolution}, volume = {11}, number = {6}, pages = {1691-1705}, pmid = {30924880}, issn = {1759-6653}, mesh = {Acetyl-CoA Carboxylase/*genetics ; Cell Nucleus/*genetics ; Cycadopsida/classification/genetics ; Evolution, Molecular ; Gnetum/cytology/*enzymology/*genetics ; Mutagenesis, Insertional ; Phylogeny ; Plastids/*genetics ; }, abstract = {Acetyl-CoA carboxylase (ACCase) is the key regulator of fatty acid biosynthesis. In most plants, ACCase exists in two locations (cytosol and plastids) and in two forms (homomeric and heteromeric). Heteromeric ACCase comprises four subunits, three of them (ACCA-C) are nuclear encoded (nr) and the fourth (ACCD) is usually plastid encoded. Homomeric ACCase is encoded by a single nr-gene (ACC). We investigated the ACCase gene evolution in gymnosperms by examining the transcriptomes of newly sequenced Gnetum ula, combined with 75 transcriptomes and 110 plastomes of other gymnosperms. AccD-coding sequences are elongated through the insertion of repetitive DNA in four out of five cupressophyte families (except Sciadopityaceae) and were functionally transferred to the nucleus of gnetophytes and Sciadopitys. We discovered that, among the three genera of gnetophytes, only Gnetum has two copies of nr-accD. Furthermore, using protoplast transient expression assays, we experimentally verified that the nr-accD precursor proteins in Gnetum and Sciadopitys can be delivered to the plastids. Of the two nr-accD copies of Gnetum, one dually targets plastids and mitochondria, whereas the other potentially targets plastoglobuli. The distinct transit peptides, gene architectures, and flanking sequences between the two Gnetum accDs suggest that they have independent origins. Our findings are the first account of two distinctly targeted nr-accDs of any green plants and the most comprehensive analyses of ACCase evolution in gymnosperms to date.}, }
@article {pmid30917630, year = {2020}, author = {Aizawa, S and Brar, G and Tsukamoto, H}, title = {Cell Death and Liver Disease.}, journal = {Gut and liver}, volume = {14}, number = {1}, pages = {20-29}, pmid = {30917630}, issn = {2005-1212}, support = {U01 AA018663/AA/NIAAA NIH HHS/United States ; I01 BX001991/BX/BLRD VA/United States ; R24 AA012885/AA/NIAAA NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; IK6 BX004205/BX/BLRD VA/United States ; }, mesh = {*Cell Death ; Humans ; Liver/*cytology ; Liver Diseases/etiology/*physiopathology ; }, abstract = {Cell death is now reclassified into several types based on the mechanisms and morphologic phenotype. Understanding of such classifications offers insights into the pathogenesis of liver disease, as well as diagnostic or therapeutic implications. Apoptosis is recognized relatively easily due to its unique morphology, but lytic cell death may occur in the form of accidental necrosis, mitochondria permeability transition-driven necrosis, necroptosis, pyroptosis, ferroptosis, and parthanatos. The cell may be engulfed by neighboring cells due to a loss of integrin signaling or cancer cell competition by entosis, a type of cell death. The classification also includes mechanistically termed cell death such as autophagy-dependent cell death and lysosome-dependent cell death. These different types of cell death may occur uniquely in certain liver diseases but may coexist in the evolution of the disease. They occur in parenchymal and non-parenchymal liver cells, as well as inflammatory cells, causing distinct pathologic consequences. This review briefly covers the recently revised classifications of cell death and discusses their relevance to liver diseases of different etiologies.}, }
@article {pmid30912813, year = {2019}, author = {Weaver, RJ}, title = {Hypothesized Evolutionary Consequences of the Alternative Oxidase (AOX) in Animal Mitochondria.}, journal = {Integrative and comparative biology}, volume = {59}, number = {4}, pages = {994-1004}, doi = {10.1093/icb/icz015}, pmid = {30912813}, issn = {1557-7023}, mesh = {Adaptation, Biological/*physiology ; Animals ; Mitochondria/*enzymology ; Oxidation-Reduction ; Oxidoreductases/*genetics/metabolism ; Reactive Oxygen Species/metabolism ; Stress, Physiological ; }, abstract = {The environment in which eukaryotes first evolved was drastically different from what they experience today, and one of the key limiting factors was the availability of oxygen for mitochondrial respiration. During the transition to a fully oxygenated Earth, other compounds such as sulfide posed a considerable constraint on using mitochondrial aerobic respiration for energy production. The ancestors of animals, and those that first evolved from the simpler eukaryotes have mitochondrial respiratory components that are absent from later-evolving animals. Specifically, mitochondria of most basal metazoans have a sulfide-resistant alternative oxidase (AOX), which provides a secondary oxidative pathway to the classical cytochrome pathway. In this essay, I argue that because of its resistance to sulfide, AOX respiration was critical to the evolution of animals by enabling oxidative metabolism under otherwise inhibitory conditions. I hypothesize that AOX allowed for metabolic flexibility during the stochastic oxygen environment of early Earth which shaped the evolution of basal metazoans. I briefly describe the known functions of AOX, with a particular focus on the decreased production of reactive oxygen species (ROS) during stress conditions. Then, I propose three evolutionary consequences of AOX-mediated protection from ROS observed in basal metazoans: 1) adaptation to stressful environments, 2) the persistence of facultative sexual reproduction, and 3) decreased mitochondrial DNA mutation rates. Recognizing the diversity of mitochondrial respiratory systems present in animals may help resolve the mechanisms involved in major evolutionary processes such as adaptation and speciation.}, }
@article {pmid30912143, year = {2019}, author = {Arocena, M and Landeira, M and Di Paolo, A and Silva, A and Sotelo-Silveira, J and Fernández, A and Alonso, J}, title = {Using a variant of coverslip hypoxia to visualize tumor cell alterations at increasing distances from an oxygen source.}, journal = {Journal of cellular physiology}, volume = {234}, number = {10}, pages = {16671-16678}, doi = {10.1002/jcp.28507}, pmid = {30912143}, issn = {1097-4652}, mesh = {*Cell Hypoxia ; Cell Line, Tumor ; Humans ; Hydrogen-Ion Concentration ; Male ; *Oxygen ; *Prostatic Neoplasms ; *Tumor Microenvironment ; }, abstract = {Early stages in tumor development involve growth in confined spaces, where oxygen diffusion is limited and metabolic waste products accumulate. This hostile microenvironment imposes strong selective pressures on tumor cells, leading eventually to the survival and expansion of aggressive subclones that condition further tumor evolution. To model features of this microenvironment in vitro, a diffusional barrier can be introduced in the form of a coverslip placed on top of cells, a method termed coverslip hypoxia. Using a variant of this method, with larger volume between coverslip and cells and with oxygen diffusion occurring only through a small hole in the center of the coverslip, we have visualized alterations in LNCaP tumor cells as a function of their distance to the oxygen source at the center. We observed remarkable morphological changes in LNCaP cells as the distance from the center increases, with cells becoming highly spread, displaying dynamic membrane protrusions and occasionally adopting a migratory phenotype. Concomitantly, cells farther from the center displayed marked increases in the hypoxia marker hypoxyprobe, whereas extracellular pH decreased in the same direction. Cells with altered morphology displayed prominent increases in fibrillar actin, as well as swollen mitochondria with distorted cristae and accumulation of neutral lipid-containing intracellular vesicles. These results show that an in vitro microenvironment that models diffusional barriers encountered by tumors in situ can have profound effects on tumor cells. The coverslip hypoxia variant we describe can be used to characterize in vitro the response of tumor cells to environmental conditions that play crucial roles in early tumor development.}, }
@article {pmid30909863, year = {2019}, author = {Shaari, N'AL and Jaoi-Edward, M and Loo, SS and Salisi, MS and Yusoff, R and Ab Ghani, NI and Saad, MZ and Ahmad, H}, title = {Karyotypic and mtDNA based characterization of Malaysian water buffalo.}, journal = {BMC genetics}, volume = {20}, number = {1}, pages = {37}, pmid = {30909863}, issn = {1471-2156}, mesh = {Animals ; Buffaloes/classification/*genetics ; *DNA, Mitochondrial ; Genetic Variation ; Haplotypes ; Karyotype ; *Karyotyping ; Malaysia ; Mitochondria/genetics ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {BACKGROUND: In Malaysia, the domestic water buffaloes (Bubalus bubalis) are classified into the swamp and the murrah buffaloes. Identification of these buffaloes is usually made via their phenotypic appearances. This study characterizes the subspecies of water buffaloes using karyotype, molecular and phylogenetic analyses. Blood of 105 buffaloes, phenotypically identified as swamp, murrah and crossbred buffaloes were cultured, terminated and harvested using conventional karyotype protocol to determine the number of chromosomes. Then, the D-loop of mitochondrial DNA of 10 swamp, 6 crossbred and 4 murrah buffaloes which were identified earlier by karyotyping were used to construct a phylogenetic tree was constructed.<br><br>RESULTS: Karyotypic analysis confirmed that all 93 animals phenotypically identified as swamp buffaloes with 48 chromosomes, all 7 as crossbreds with 49 chromosomes, and all 5 as murrah buffaloes with 50 chromosomes. The D-loop of mitochondrial DNA analysis showed that 10 haplotypes were observed with haplotype diversity of 0.8000&#x2009;&#xb1;&#x2009;0.089. Sequence characterization revealed 72 variables sites in which 67 were parsimony informative sites with sequence diversity of 0.01906. The swamp and murrah buffaloes clearly formed 2 different clades in the phylogenetic tree, indicating clear maternal divergence from each other. The crossbreds were grouped within the swamp buffalo clade, indicating the dominant maternal swamp buffalo gene in the crossbreds.<br><br>CONCLUSION: Thus, the karyotyping could be used to differentiate the water buffaloes while genotypic analysis could be used to characterize the water buffaloes and their crossbreds.}, }
@article {pmid30897177, year = {2019}, author = {Liao, L and Dong, T and Liu, X and Dong, Z and Qiu, X and Rong, Y and Sun, G and Wang, Z}, title = {Effect of nitrogen supply on nitrogen metabolism in the citrus cultivar 'Huangguogan'.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213874}, pmid = {30897177}, issn = {1932-6203}, mesh = {Citrus/growth &amp; development/*metabolism ; Cytoplasm/metabolism ; Fruit/metabolism ; Gene Expression Regulation, Plant ; Glutamate Dehydrogenase/classification/genetics/metabolism ; Glutamate-Ammonia Ligase/classification/genetics/metabolism ; Nitrate Reductase/classification/genetics/metabolism ; Nitrogen/*metabolism ; Phylogeny ; Plant Leaves/metabolism ; Plant Proteins/classification/genetics/*metabolism ; Plant Roots/metabolism ; Seedlings/growth &amp; development/metabolism ; }, abstract = {Nitrogen metabolism in citrus has received increased attention due to its effects on plant growth and productivity. However, little is known about the effects of nitrogen fertilization on nitrogen metabolism in young trees of citrus cultivar 'Huangguogan' (Citrus reticulata × Citrus sinensis). Here, genes encoding nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), glutamate dehydrogenase (GDH), and asparagine synthetase (AS), represented as HgNR, HgNiR, HgGS, HgGDH, and HgAS, respectively, were cloned from Huangguogan. Deduced protein sequences were analyzed and proteins were confirmed to be localized in their respective cellular organelles. Moreover, pot-cultured 'Huangguogan' seedlings were fertilized with 0 (N1), 1.36 (N2), 1.81 (N3), 2.26 (N4), or 2.72 (N5) kg N/year, for 12 months. Enzyme activity and enzyme-gene expression were studied in roots, leaves, and fruits at different stages. Finally, the effects of N application rate on root activity, leaf N, soluble protein, yield, and fruit quality at the ripening stage were measured. The results showed that: 1) HgNR, HgNiR, HgGDH, and HgAS gene products were found mainly in the cytoplasm and plasma membrane, while HgGS gene product was found mainly in cytoplasm and mitochondria. 2) Gene expression and enzyme activity differed among plant organs. As the root is in permanent direct contact with the soil we suggest that root gene expression and enzyme activity can be used as reference to determine N application rate. 3) Yield, fruit quality, enzyme activity, and enzyme-related gene expression were considerably lower at low than at high-N supply. However, they were all inhibited by excess nitrogen (i.e., 2.72 kg/year). Therefore, we recommend 1.81 kg N/year as the optimal N application rate for young 'Huangguogan' trees.}, }
@article {pmid30893849, year = {2019}, author = {Ding, F and Cheng, J and Fu, Y and Chen, T and Li, B and Jiang, D and Xie, J}, title = {Early Transcriptional Response to DNA Virus Infection in Sclerotinia sclerotiorum.}, journal = {Viruses}, volume = {11}, number = {3}, pages = {}, pmid = {30893849}, issn = {1999-4915}, mesh = {Ascomycota/*genetics/pathogenicity/*virology ; DNA Viruses/*genetics ; *Gene Expression Profiling ; Hyphae/genetics/virology ; Phylogeny ; Sequence Analysis, DNA ; Virion/genetics ; Virulence ; }, abstract = {We previously determined that virions of Sclerotinia sclerotiorum hypovirulence associated DNA virus 1 (SsHADV-1) could directly infect hyphae of Sclerotinia sclerotiorum, resulting in hypovirulence of the fungal host. However, the molecular mechanisms of SsHADV-1 virions disruption of the fungal cell wall barrier and entrance into the host cell are still unclear. To investigate the early response of S. sclerotiorum to SsHADV-1 infection, S. sclerotiorum hyphae were inoculated with purified SsHADV-1 virions. The pre- and post-infection hyphae were collected at one[-]three hours post-inoculation for transcriptome analysis. Further, bioinformatic analysis showed that differentially expressed genes (DEGs) regulated by SsHADV-1 infection were identified in S. sclerotiorum. In total, 187 genes were differentially expressed, consisting of more up-regulated (114) than down-regulated (73) genes. The identified DEGs were involved in several important pathways. Metabolic processes, biosynthesis of antibiotics, and secondary metabolites were the most affected categories in S. sclerotiorum upon SsHADV-1 infection. Cell structure analysis suggested that 26% of the total DEGs were related to membrane tissues. Furthermore, 10 and 27 DEGs were predicted to be located in the cell membrane and mitochondria, respectively. Gene ontology enrichment analyses of the DEGs were performed, followed by functional annotation of the genes. Interestingly, one third of the annotated functional DEGs could be involved in the Ras-small G protein signal transduction pathway. These results revealed that SsHADV-1 virions may be able to bind host membrane proteins and influence signal transduction through Ras-small G protein-coupled receptors during early infection, providing new insight towards the molecular mechanisms of virions infection in S. sclerotiorum.}, }
@article {pmid30893316, year = {2019}, author = {Fregel, R and Ordóñez, AC and Santana-Cabrera, J and Cabrera, VM and Velasco-Vázquez, J and Alberto, V and Moreno-Benítez, MA and Delgado-Darias, T and Rodríguez-Rodríguez, A and Hernández, JC and Pais, J and González-Montelongo, R and Lorenzo-Salazar, JM and Flores, C and Cruz-de-Mercadal, MC and Álvarez-Rodríguez, N and Shapiro, B and Arnay, M and Bustamante, CD}, title = {Mitogenomes illuminate the origin and migration patterns of the indigenous people of the Canary Islands.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0209125}, pmid = {30893316}, issn = {1932-6203}, mesh = {Africa, Northern/ethnology ; Ethnicity/*genetics ; Europe/ethnology ; Genetic Drift ; Genetics, Population ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Middle East ; Mitochondria/*genetics ; Phylogeography ; Sequence Analysis, DNA ; Spain/ethnology ; Transients and Migrants/*classification ; }, abstract = {The Canary Islands' indigenous people have been the subject of substantial archaeological, anthropological, linguistic and genetic research pointing to a most probable North African Berber source. However, neither agreement about the exact point of origin nor a model for the indigenous colonization of the islands has been established. To shed light on these questions, we analyzed 48 ancient mitogenomes from 25 archaeological sites from the seven main islands. Most lineages observed in the ancient samples have a Mediterranean distribution, and belong to lineages associated with the Neolithic expansion in the Near East and Europe (T2c, J2a, X3a…). This phylogeographic analysis of Canarian ancient mitogenomes, the first of its kind, shows that some lineages are restricted to Central North Africa (H1cf, J2a2d and T2c1d3), while others have a wider distribution, including both West and Central North Africa, and, in some cases, Europe and the Near East (U6a1a1, U6a7a1, U6b, X3a, U6c1). In addition, we identify four new Canarian-specific lineages (H1e1a9, H4a1e, J2a2d1a and L3b1a12) whose coalescence dates correlate with the estimated time for the colonization of the islands (1st millennia CE). Additionally, we observe an asymmetrical distribution of mtDNA haplogroups in the ancient population, with certain haplogroups appearing more frequently in the islands closer to the continent. This reinforces results based on modern mtDNA and Y-chromosome data, and archaeological evidence suggesting the existence of two distinct migrations. Comparisons between insular populations show that some populations had high genetic diversity, while others were probably affected by genetic drift and/or bottlenecks. In spite of observing interinsular differences in the survival of indigenous lineages, modern populations, with the sole exception of La Gomera, are homogenous across the islands, supporting the theory of extensive human mobility after the European conquest.}, }
@article {pmid30876291, year = {2019}, author = {Liu, W and Liu, Q and Zhang, Z and Han, Y and Kuang, C and Xu, L and Yang, H and Liu, X}, title = {Three-dimensional super-resolution imaging of live whole cells using galvanometer-based structured illumination microscopy.}, journal = {Optics express}, volume = {27}, number = {5}, pages = {7237-7248}, doi = {10.1364/OE.27.007237}, pmid = {30876291}, issn = {1094-4087}, mesh = {Animals ; Cattle ; Endothelial Cells/*cytology ; Fluorescent Dyes ; *Imaging, Three-Dimensional ; Lighting/*instrumentation ; Microscopy, Fluorescence/*methods ; *Microtubules ; *Mitochondria ; Pulmonary Artery/cytology ; }, abstract = {Imaging and tracking three-dimensional (3D) nanoscale organizations and functions of live cells is essential for biological research but it remains challenging. Among different 3D super-resolution techniques, 3D structured illumination microscopy (SIM) has the intrinsic advantages for live-cell studies; it is based on wide-field imaging and does not require high light intensities or special fluorescent dyes to double 3D resolution. However, the 3D SIM system has developed relatively slowly, especially in live imaging. Here, we report a more flexible 3D SIM system based on two galvanometer sets conveniently controlling the structured illumination pattern's period and orientation, which is able to study dynamics of live whole cells with high speed. We demonstrate our microscope's capabilities with strong optical sectioning and lateral, axial, and volume temporal resolution of 104 nm, 320 nm and 4 s, respectively. We do this by imaging nanoparticle and microtubule organizations and mitochondria evolution. These characteristics enable our galvanometer-based 3D SIM system to broaden the accessible imaging content of SIM-family microscopes and further facilitate their applications in life sciences.}, }
@article {pmid30872700, year = {2019}, author = {Johri, S and Solanki, J and Cantu, VA and Fellows, SR and Edwards, RA and Moreno, I and Vyas, A and Dinsdale, EA}, title = {'Genome skimming' with the MinION hand-held sequencer identifies CITES-listed shark species in India's exports market.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4476}, pmid = {30872700}, issn = {2045-2322}, mesh = {Animals ; Cell Nucleus/*genetics ; DNA/*genetics ; Endangered Species ; Fish Proteins/genetics ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*instrumentation/veterinary ; India ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA/instrumentation/veterinary ; Sharks/*classification/genetics ; }, abstract = {Chondrichthyes - sharks, rays, skates, and chimeras, are among the most threatened and data deficient vertebrate species. Global demand for shark and ray derived products, drives unregulated and exploitative fishing practices, which are in turn facilitated by the lack of ecological data required for effective conservation of these species. Here, we describe a Next Generation Sequencing method (using the MinION, a hand-held portable sequencing device from Oxford Nanopore Technologies), and analyses pipeline for molecular ecological studies in Chondrichthyes. Using this method, the complete mitochondrial genome and nuclear intergenic and protein-coding sequences were obtained by direct sequencing of genomic DNA obtained from shark fin tissue. Recovered loci include mitochondrial barcode sequences- Cytochrome oxidase I, NADH2, 16S rRNA and 12S rRNA- and nuclear genetic loci such as 5.8S rRNA, Internal Transcribed Spacer 2, and 28S rRNA regions, which are commonly used for taxonomic identification. Other loci recovered were the nuclear protein-coding genes for antithrombin or SerpinC, Immunoglobulin lambda light chain, Preprogehrelin, selenium binding protein 1(SBP1), Interleukin-1 beta (IL-1β) and Recombination-Activating Gene 1 (RAG1). The median coverage across all genetic loci was 20x and sequence accuracy was ≥99.8% compared to reference sequences. Analyses of the nuclear ITS2 region and the mitochondrial protein-encoding loci allowed accurate taxonomic identification of the shark specimen as Carcharhinus falciformis, a CITES Appendix II species. MinION sequencing provided 1,152,211 bp of new shark genome, increasing the number of sequenced shark genomes to five. Phylogenetic analyses using both mitochondrial and nuclear loci provided evidence that Prionace glauca is nested within Carcharhinus, suggesting the need for taxonomic reassignment of P. glauca. We increased genomic information about a shark species for ecological and population genetic studies, enabled accurate identification of the shark tissue for biodiversity indexing and resolved phylogenetic relationships among multiple taxa. The method was independent of amplification bias, and adaptable for field assessments of other Chondrichthyes and wildlife species in the future.}, }
@article {pmid30872488, year = {2019}, author = {Dorrell, RG and Azuma, T and Nomura, M and Audren de Kerdrel, G and Paoli, L and Yang, S and Bowler, C and Ishii, KI and Miyashita, H and Gile, GH and Kamikawa, R}, title = {Principles of plastid reductive evolution illuminated by nonphotosynthetic chrysophytes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {14}, pages = {6914-6923}, pmid = {30872488}, issn = {1091-6490}, mesh = {Chloroplast Proteins/genetics ; Chrysophyta/*genetics ; *Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation ; *Genome, Plastid ; Plastids/*genetics ; }, abstract = {The division of life into producers and consumers is blurred by evolution. For example, eukaryotic phototrophs can lose the capacity to photosynthesize, although they may retain vestigial plastids that perform other essential cellular functions. Chrysophyte algae have undergone a particularly large number of photosynthesis losses. Here, we present a plastid genome sequence from a nonphotosynthetic chrysophyte, "Spumella" sp. NIES-1846, and show that it has retained a nearly identical set of plastid-encoded functions as apicomplexan parasites. Our transcriptomic analysis of 12 different photosynthetic and nonphotosynthetic chrysophyte lineages reveals remarkable convergence in the functions of these nonphotosynthetic plastids, along with informative lineage-specific retentions and losses. At one extreme, Cornospumella fuschlensis retains many photosynthesis-associated proteins, although it appears to have lost the reductive pentose phosphate pathway and most plastid amino acid metabolism pathways. At the other extreme, Paraphysomonas lacks plastid-targeted proteins associated with gene expression and all metabolic pathways that require plastid-encoded partners, indicating a complete loss of plastid DNA in this genus. Intriguingly, some of the nucleus-encoded proteins that once functioned in the expression of the Paraphysomonas plastid genome have been retained. These proteins were likely to have been dual targeted to the plastid and mitochondria of the chrysophyte ancestor, and are uniquely targeted to the mitochondria in Paraphysomonas Our comparative analyses provide insights into the process of functional reduction in nonphotosynthetic plastids.}, }
@article {pmid30870981, year = {2019}, author = {Du, Z and Ishikawa, T and Liu, H and Kamitani, S and Tadauchi, O and Cai, W and Li, H}, title = {Phylogeography of the Assassin Bug Sphedanolestes impressicollis in East Asia Inferred From Mitochondrial and Nuclear Gene Sequences.}, journal = {International journal of molecular sciences}, volume = {20}, number = {5}, pages = {}, pmid = {30870981}, issn = {1422-0067}, support = {31772498//National Natural Science Foundation of China/ ; 2018QC089; 2018QC119//Chinese Universities Scientific Fund/ ; }, mesh = {Animals ; Cell Nucleus/*genetics ; Climate ; DNA, Mitochondrial/*genetics ; Ecosystem ; Asia, Eastern ; Genes, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; Phylogeography/methods ; Triatoma/*genetics ; }, abstract = {The assassin bug, Sphedanolestes impressicollis (Hemiptera: Reduviidae), is widely distributed in East Asia. It is an ideal model for evaluating the effects of climatic fluctuation and geographical events on the distribution patterns of East Asian reduviids. Here, we used two mitochondrial genes and one nuclear gene to investigate the phylogeographic pattern of the assassin bug based on comprehensive sampling in China, Japan, South Korea, Vietnam, and Laos. High levels of genetic differentiation were detected among the geographic populations classified into the northern and southern groups. A significant correlation was detected between genetic and geographical distances. The East China Sea land bridge served as a "dispersal corridor" during Pleistocene glaciation. The estimated divergence time indicated that the northern group may have separated from the eastern Chinese populations when the sea level rapidly rose during the "Ryukyu Coral Sea Stage" and the East China Sea land bridge was completely submerged. Demographic history and ecological niche modeling suggested that appropriate climatic conditions may have accounted for the rapid spread across the Korean Peninsula and Japan during the late Pleistocene. Our study underscores the pivotal roles of the Pleistocene sea level changes and climatic fluctuations in determining the distribution patterns of East Asian reduviids.}, }
@article {pmid30862038, year = {2019}, author = {Le Vasseur, M and Chen, VC and Huang, K and Vogl, WA and Naus, CC}, title = {Pannexin 2 Localizes at ER-Mitochondria Contact Sites.}, journal = {Cancers}, volume = {11}, number = {3}, pages = {}, pmid = {30862038}, issn = {2072-6694}, support = {RGPIN-2016-05471//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Endomembrane specialization allows functional compartmentalization but imposes physical constraints to information flow within the cell. However, the evolution of an endomembrane system was associated with the emergence of contact sites facilitating communication between membrane-bound organelles. Contact sites between the endoplasmic reticulum (ER) and mitochondria are highly conserved in terms of their morphological features but show surprising molecular diversity within and across eukaryote species. ER-mitochondria contact sites are thought to regulate key processes in oncogenesis but their molecular composition remains poorly characterized in mammalian cells. In this study, we investigate the localization of pannexin 2 (Panx2), a membrane channel protein showing tumor-suppressing properties in cancer cells. Using a combination of subcellular fractionation, particle tracking in live-cell, and immunogold electron microscopy, we show that Panx2 localizes at ER-mitochondria contact sites in mammalian cells and sensitizes cells to apoptotic stimuli.}, }
@article {pmid30861107, year = {2019}, author = {Sinha, S and Manoj, N}, title = {Molecular evolution of proteins mediating mitochondrial fission-fusion dynamics.}, journal = {FEBS letters}, volume = {593}, number = {7}, pages = {703-718}, doi = {10.1002/1873-3468.13356}, pmid = {30861107}, issn = {1873-3468}, support = {//Indian Institute of Technology Madras/International ; }, mesh = {Animals ; Dynamins/*genetics ; Eukaryota/genetics ; *Evolution, Molecular ; Fungi/genetics ; Mitochondria/genetics ; Mitochondrial Dynamics/*genetics ; Mitochondrial Proteins/*genetics ; Phylogeny ; }, abstract = {Eukaryotes employ a subset of dynamins to mediate mitochondrial fusion and fission dynamics. Here we report the molecular evolution and diversification of the dynamin-related mitochondrial proteins that drive the fission (Drp1) and the fusion processes (mitofusin and OPA1). We demonstrate that the three paralogs emerged concurrently in an early mitochondriate eukaryotic ancestor. Furthermore, multiple independent duplication events from an ancestral bifunctional fission protein gave rise to specialized fission proteins. The evolutionary history of these proteins is marked by transformations that include independent gain and loss events occurring at the levels of entire genes, specific functional domains, and intronic regions. The domain level variations primarily comprise loss-gain of lineage specific domains that are present in the terminal regions of the sequences.}, }
@article {pmid30858078, year = {2019}, author = {Xie, GL and Köhler, F and Huang, XC and Wu, RW and Zhou, CH and Ouyang, S and Wu, XP}, title = {A novel gene arrangement among the Stylommatophora by the complete mitochondrial genome of the terrestrial slug Meghimatium bilineatum (Gastropoda, Arionoidea).}, journal = {Molecular phylogenetics and evolution}, volume = {135}, number = {}, pages = {177-184}, doi = {10.1016/j.ympev.2019.03.002}, pmid = {30858078}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Chromosome Mapping ; Asia, Eastern ; Gastropoda/*genetics ; Gene Order ; *Gene Rearrangement ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Stylommatophora is a main clade of Gastropoda that encompasses approximately 112 gastropod families and may exceed a total of 30,000 species. Twenty-four complete stylommatophoran mitogenomes have been sequenced to date, yet our understanding of mitochondrial evolution in stylommatophorans is still in its infancy. To further expand the set of available mitogenomes, we sequenced the mitogenome of Meghimatium bilineatum (Arionoidea: Philomycidae), a widespread land slug in East Asia. This is the first report on a mitogenome of the superfamily Arionoidea, and indeed on a terrestrial slug. The mitogenome of Meghimatium bilineatum comprises 13,972 bp and exhibits a novel, highly distinctive gene arrangement among the Stylommatophora. Phylogenetic reconstructions based on the sequences of all protein-coding genes consistently recovered Meghimatium bilineatum as sister-group of the Succineidae. A phylogenetic reconstruction based on gene order, however, suggested a highly divergent tree topology, which is less credible when taking into account prior knowledge of stylommatophoran relationships. Our CREx (Common interval Rearrangement Explorer) analysis suggested that three successive events of tandem duplication random loss (TDRL) best explain the evolutionary process of gene order rearrangement in Meghimatium bilineatum from an ancestral stylommatophoran mitogenome. The present example offers new insights into the mechanisms of mitogenome rearrangements in gastropods at large and into the usefulness of mitogenomic gene order as a phylogenetic marker.}, }
@article {pmid30855674, year = {2019}, author = {Dobler, R and Dowling, DK and Morrow, EH and Reinhardt, K}, title = {Reply: Mitochondrial replacement and its effects on human health: accounting for non-independence of data in meta-analyses.}, journal = {Human reproduction update}, volume = {25}, number = {3}, pages = {393-394}, doi = {10.1093/humupd/dmz010}, pmid = {30855674}, issn = {1460-2369}, mesh = {*Germ Cells ; Humans ; *Mitochondria ; }, }
@article {pmid30854666, year = {2019}, author = {Wang, W and Chen, J and Liao, B and Xia, L and Hou, S and Wang, Z and Lu, Y}, title = {Identification and functional characterization of Histone-like DNA-binding protein in Nocardia seriolae (NsHLP) involved in cell apoptosis.}, journal = {Journal of fish diseases}, volume = {42}, number = {5}, pages = {657-666}, doi = {10.1111/jfd.12962}, pmid = {30854666}, issn = {1365-2761}, support = {KY20160207//Shenzhen Dapeng New District special fund for industry development/ ; 2016A050502061//International S&amp;T Cooperation Projects of Guangdong Province/ ; JCYJ20170306161613251//Shenzhen Science and Technology Project/ ; 2017A030313179//Natural Science Foundation of Guangdong Province/ ; C17377//Natural Science Foundation of Guangdong Ocean University/ ; C13454//Natural Science Foundation of Guangdong Ocean University/ ; E10085//Natural Science Foundation of Guangdong Ocean University/ ; }, mesh = {Amino Acid Sequence ; Animals ; *Apoptosis ; Bacterial Proteins/chemistry/*genetics/metabolism ; Base Sequence ; *Cyprinidae ; DNA-Binding Proteins/chemistry/*genetics/metabolism ; Fish Diseases/microbiology/*physiopathology ; Nocardia/genetics/*physiology ; Nocardia Infections/microbiology/physiopathology/*veterinary ; Phylogeny ; Sequence Alignment/veterinary ; }, abstract = {Nocardia seriolae, a facultative intracellular bacterium, is the main pathogen of fish nocardiosis. Bioinformatic analysis showed that the histone-like DNA-binding protein (HLP) gene of N. seriolae (nshlp) encoded a secreted protein and might target the mitochondria in the host cell. To further study the preliminary function of HLP in N. seriolae (NsHLP), the gene cloning, extracellular products identification, subcellular localization, overexpression and apoptosis detection assay were carried out in this study. Mass spectrometry analysis of the extracellular products from N. seriolae showed that NsHLP was a secreted protein. Subcellular localization of HLP-GFP fusion proteins mainly assembled in the nucleus, which indicated that the NsHLP was co-located with the nucleus rather than mitochondria in fathead minnow (FHM) cells. Notably, the expression of NsHLP had changed the distribution of mitochondria into lumps in the FHM cell. In addition, apoptotic features were found in the transfected FHM cells by overexpression of NsHLP. Quantitative assays of mitochondrial membrane potential value, caspase-3 activity and pro-apoptotic genes mRNA (Bad, Bid and Bax) expression level demonstrated that the cell apoptosis was induced in the transfected FHM cells. All the results presented in this study provided insight on the function of NsHLP, which suggested that it may participate in the cell apoptosis regulation and play an important role in the pathogenesis of N. seriolae.}, }
@article {pmid30854477, year = {2019}, author = {Oldenkott, B and Yang, Y and Lesch, E and Knoop, V and Schallenberg-Rüdinger, M}, title = {Plant-type pentatricopeptide repeat proteins with a DYW domain drive C-to-U RNA editing in Escherichia coli.}, journal = {Communications biology}, volume = {2}, number = {}, pages = {85}, pmid = {30854477}, issn = {2399-3642}, mesh = {Amino Acid Sequence ; Escherichia coli/*genetics/*metabolism ; Gene Expression ; Mutation ; Plant Proteins/*chemistry/*genetics ; *Protein Domains ; *RNA Editing ; Recombinant Proteins/chemistry/genetics ; *Repetitive Sequences, Amino Acid ; Sequence Analysis, RNA ; }, abstract = {RNA editing converting cytidines into uridines is a hallmark of gene expression in land plant chloroplasts and mitochondria. Pentatricopeptide repeat (PPR) proteins have a key role in target recognition, but the functional editosome in the plant organelles has remained elusive. Here we show that individual Physcomitrella patens DYW-type PPR proteins alone can perform efficient C-to-U editing in Escherichia coli reproducing the moss mitochondrial editing. Single amino acid exchanges in the DYW domain abolish RNA editing, confirming it as the functional cytidine deaminase. The modification of RNA targets and the identification of numerous off-targets in the E. coli transcriptome reveal nucleotide identities critical for RNA recognition and cytidine conversion. The straightforward amenability of the new E. coli setup will accelerate future studies on RNA target recognition through PPRs, on the C-to-U editing deamination machinery and towards future establishment of transcript editing in other genetic systems.}, }
@article {pmid30853974, year = {2019}, author = {Telschow, A and Gadau, J and Werren, JH and Kobayashi, Y}, title = {Genetic Incompatibilities Between Mitochondria and Nuclear Genes: Effect on Gene Flow and Speciation.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {62}, pmid = {30853974}, issn = {1664-8021}, abstract = {The process of speciation is, according to the biological species concept, the reduction in gene flow between genetically diverging populations. Most of the previous theoretical studies analyzed the effect of nuclear genetic incompatibilities on gene flow. There is, however, an increasing number of empirical examples suggesting that cytoplasmically inherited genetic elements play an important role in speciation. Here, we present a theoretical analysis of mitochondrial driven speciation, in which genetic incompatibilities occur between mitochondrial haplotypes and nuclear alleles. Four population genetic models with mainland-island structure were analyzed that differ with respect to the type of incompatibility and the underlying genetics. Gene flow reduction was measured on selectively neutral alleles of an unlinked locus and quantified by the effective migration rate. Analytical formulae for the different scenarios were derived using the fitness graph method. For the models with haploid genetics, we found that mito-nuclear incompatibilities (MtNI) are as strong as nuclear-nuclear incompatibilities (NNI) in reducing gene flow at the unlinked locus, but only if males and females migrate in equal number. For models with diploid genetics, we found that MtNI reduce gene flow stronger than NNI when incompatibilities are recessive, but weaker when they are dominant. For both haploid and diploid MtNI, we found that gene flow reduction is stronger if females are the migrating sex, but weaker than NNI when males are the migrating sex. These results encourage further examination on the role of mitochondria on genetic divergence and speciation and point toward specific factors (e.g., migrating sex) that could be the focus of an empirical test.}, }
@article {pmid30848125, year = {2019}, author = {Han, Y and Branon, TC and Martell, JD and Boassa, D and Shechner, D and Ellisman, MH and Ting, A}, title = {Directed Evolution of Split APEX2 Peroxidase.}, journal = {ACS chemical biology}, volume = {14}, number = {4}, pages = {619-635}, pmid = {30848125}, issn = {1554-8937}, support = {P41 GM103412/GM/NIGMS NIH HHS/United States ; R01 CA186568/CA/NCI NIH HHS/United States ; R01 GM086197/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Ascorbate Peroxidases/genetics/*metabolism ; Cell Separation ; Directed Molecular Evolution/*methods ; Endoplasmic Reticulum/metabolism ; Flow Cytometry ; HEK293 Cells ; Humans ; Mitochondria/metabolism ; Peptide Library ; Plant Proteins/genetics/*metabolism ; RNA/genetics ; Saccharomyces cerevisiae/genetics ; Glycine max/enzymology ; }, abstract = {APEX is an engineered peroxidase that catalyzes the oxidation of a wide range of substrates, facilitating its use in a variety of applications from subcellular staining for electron microscopy to proximity biotinylation for spatial proteomics and transcriptomics. To further advance the capabilities of APEX, we used directed evolution to engineer a split APEX tool (sAPEX). A total of 20 rounds of fluorescence activated cell sorting (FACS)-based selections from yeast-displayed fragment libraries, using 3 different surface display configurations, produced a 200-amino-acid N-terminal fragment (with 9 mutations relative to APEX2) called "AP" and a 50-amino-acid C-terminal fragment called "EX". AP and EX fragments were each inactive on their own but were reconstituted to give peroxidase activity when driven together by a molecular interaction. We demonstrate sAPEX reconstitution in the mammalian cytosol, on engineered RNA motifs within a non-coding RNA scaffold, and at mitochondria-endoplasmic reticulum contact sites.}, }
@article {pmid30844054, year = {2019}, author = {Thairu, MW and Hansen, AK}, title = {It's a small, small world: unravelling the role and evolution of small RNAs in organelle and endosymbiont genomes.}, journal = {FEMS microbiology letters}, volume = {366}, number = {5}, pages = {}, doi = {10.1093/femsle/fnz049}, pmid = {30844054}, issn = {1574-6968}, mesh = {Bacteria/*genetics ; Evolution, Molecular ; Gene Expression Regulation ; Genome/genetics ; Organelles/*genetics ; RNA, Bacterial/genetics/metabolism ; RNA, Small Untranslated/genetics/metabolism/*physiology ; Symbiosis/*genetics ; }, abstract = {Organelles and host-restricted bacterial symbionts are characterized by having highly reduced genomes that lack many key regulatory genes and elements. Thus, it has been hypothesized that the eukaryotic nuclear genome is primarily responsible for regulating these symbioses. However, with the discovery of organelle- and symbiont-expressed small RNAs (sRNAs) there is emerging evidence that these sRNAs may play a role in gene regulation as well. Here, we compare the diversity of organelle and bacterial symbiont sRNAs recently identified using genome-enabled '-omic' technologies and discuss their potential role in gene regulation. We also discuss how the genome architecture of small genomes may influence the evolution of these sRNAs and their potential function. Additionally, these new studies suggest that some sRNAs are conserved within organelle and symbiont taxa and respond to changes in the environment and/or their hosts. In summary, these results suggest that organelle and symbiont sRNAs may play a role in gene regulation in addition to nuclear-encoded host mechanisms.}, }
@article {pmid30842567, year = {2019}, author = {Matos, I and Machado, MP and Schartl, M and Coelho, MM}, title = {Allele-specific expression variation at different ploidy levels in Squalius alburnoides.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {3688}, pmid = {30842567}, issn = {2045-2322}, mesh = {*Alleles ; Animals ; Chimera ; Cyprinidae/*genetics ; *Diploidy ; Female ; Fish Proteins/genetics ; Genome ; Liver/physiology ; Male ; Polymorphism, Single Nucleotide ; Transcriptome ; *Triploidy ; }, abstract = {Allopolyploid plants are long known to be subject to a homoeolog expression bias of varying degree. The same phenomenon was only much later suspected to occur also in animals based on studies of single selected genes in an allopolyploid vertebrate, the Iberian fish Squalius alburnoides. Consequently, this species became a good model for understanding the evolution of gene expression regulation in polyploid vertebrates. Here, we analyzed for the first time genome-wide allele-specific expression data from diploid and triploid hybrids of S. alburnoides and compared homoeolog expression profiles of adult livers and of juveniles. Co-expression of alleles from both parental genomic types was observed for the majority of genes, but with marked homoeolog expression bias, suggesting homoeolog specific reshaping of expression level patterns in hybrids. Complete silencing of one allele was also observed irrespective of ploidy level, but not transcriptome wide as previously speculated. Instead, it was found only in a restricted number of genes, particularly ones with functions related to mitochondria and ribosomes. This leads us to hypothesize that allelic silencing may be a way to overcome intergenomic gene expression interaction conflicts, and that homoeolog expression bias may be an important mechanism in the achievement of sustainable genomic interactions, mandatory to the success of allopolyploid systems, as in S. alburnoides.}, }
@article {pmid30841657, year = {2019}, author = {Yang, T and Xu, G and Gu, B and Shi, Y and Mzuka, HL and Shen, H}, title = {The Complete Mitochondrial Genome Sequences of the Philomycus bilineatus (Stylommatophora: Philomycidae) and Phylogenetic Analysis.}, journal = {Genes}, volume = {10}, number = {3}, pages = {}, pmid = {30841657}, issn = {2073-4425}, mesh = {Amino Acid Sequence ; Animals ; Gastropoda/*classification/genetics ; Genome Size ; Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Whole Genome Sequencing/*methods ; }, abstract = {The mitochondrial genome (mitogenome) can provide information for phylogenetic analyses and evolutionary biology. We first sequenced, annotated, and characterized the mitogenome of Philomycus bilineatus in this study. The complete mitogenome was 14,347 bp in length, containing 13 protein-coding genes (PCGs), 23 transfer RNA genes, two ribosomal RNA genes, and two non-coding regions (A + T-rich region). There were 15 overlap locations and 18 intergenic spacer regions found throughout the mitogenome of P. bilineatus. The A + T content in the mitogenome was 72.11%. All PCGs used a standard ATN as a start codon, with the exception of cytochrome c oxidase 1 (cox1) and ATP synthase F0 subunit 8 (atp8) with TTG and GTG. Additionally, TAA or TAG was identified as the typical stop codon. All transfer RNA (tRNA) genes had a typical clover-leaf structure, except for trnS1 (AGC), trnS2 (TCA), and trnK (TTT). A phylogenetic analysis with another 37 species of gastropods was performed using Bayesian inference, based on the amino acid sequences of 13 mitochondrial PCGs. The results indicated that P. bilineatus shares a close ancestry with Meghimatium bilineatum. It seems more appropriate to reclassify it as Arionoidea rather than Limacoidea, as previously thought. Our research may provide a new meaningful insight into the evolution of P. bilineatus.}, }
@article {pmid30838029, year = {2019}, author = {Dixit, S and Henderson, JC and Alfonzo, JD}, title = {Multi-Substrate Specificity and the Evolutionary Basis for Interdependence in tRNA Editing and Methylation Enzymes.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {104}, pmid = {30838029}, issn = {1664-8021}, support = {R01 GM084065/GM/NIGMS NIH HHS/United States ; R01 GM132254/GM/NIGMS NIH HHS/United States ; R56 AI131248/AI/NIAID NIH HHS/United States ; }, abstract = {Among tRNA modification enzymes there is a correlation between specificity for multiple tRNA substrates and heteromultimerization. In general, enzymes that modify a conserved residue in different tRNA sequences adopt a heterodimeric structure. Presumably, such changes in the oligomeric state of enzymes, to gain multi-substrate recognition, are driven by the need to accommodate and catalyze a particular reaction in different substrates while maintaining high specificity. This review focuses on two classes of enzymes where the case for multimerization as a way to diversify molecular recognition can be made. We will highlight several new themes with tRNA methyltransferases and will also discuss recent findings with tRNA editing deaminases. These topics will be discussed in the context of several mechanisms by which heterodimerization may have been achieved during evolution and how these mechanisms might impact modifications in different systems.}, }
@article {pmid30837540, year = {2019}, author = {Vai, S and Sarno, S and Lari, M and Luiselli, D and Manzi, G and Gallinaro, M and Mataich, S and Hübner, A and Modi, A and Pilli, E and Tafuri, MA and Caramelli, D and di Lernia, S}, title = {Ancestral mitochondrial N lineage from the Neolithic 'green' Sahara.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {3530}, pmid = {30837540}, issn = {2045-2322}, mesh = {Adult ; Archaeology ; DNA, Mitochondrial/chemistry/classification/genetics ; Female ; Fossils ; Genetic Linkage ; Genome, Mitochondrial ; Haplotypes ; Humans ; Mitochondria/classification/*genetics ; Phylogeny ; Skull/metabolism ; }, abstract = {Because Africa's climate hampers DNA preservation, knowledge of its genetic variability is mainly restricted to modern samples, even though population genetics dynamics and back-migrations from Eurasia may have modified haplotype frequencies, masking ancient genetic scenarios. Thanks to improved methodologies, ancient genetic data for the African continent are now increasingly available, starting to fill in the gap. Here we present newly obtained mitochondrial genomes from two ~7000-year-old individuals from Takarkori rockshelter, Libya, representing the earliest and first genetic data for the Sahara region. These individuals carry a novel mutation motif linked to the haplogroup N root. Our result demonstrates the presence of an ancestral lineage of the N haplogroup in the Holocene "Green Sahara", associated to a Middle Pastoral (Neolithic) context.}, }
@article {pmid30833746, year = {2019}, author = {Bernardo, PH and Sánchez-Ramírez, S and Sánchez-Pacheco, SJ and Álvarez-Castañeda, ST and Aguilera-Miller, EF and Mendez-de la Cruz, FR and Murphy, RW}, title = {Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection, and climate.}, journal = {Heredity}, volume = {123}, number = {3}, pages = {359-370}, pmid = {30833746}, issn = {1365-2540}, support = {PGSD3 NSERC, 442235-2013//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/International ; A3148//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/International ; }, mesh = {Animal Migration ; Animals ; California ; Cell Nucleus/genetics ; Female ; *Gene Flow ; *Genetic Drift ; Genetic Variation ; *Genome, Mitochondrial ; *Inheritance Patterns ; Lizards/*genetics ; Male ; Mexico ; Mitochondria/*genetics ; Polymorphism, Single Nucleotide ; Reproductive Isolation ; Selection, Genetic ; }, abstract = {Nuclear and mitochondrial genomes coexist within cells but are subject to different tempos and modes of evolution. Evolutionary forces such as drift, mutation, selection, and migration are expected to play fundamental roles in the origin and maintenance of diverged populations; however, divergence may lag between genomes subject to different modes of inheritance and functional specialization. Herein, we explore whole mitochondrial genome data and thousands of nuclear single nucleotide polymorphisms to evidence extreme mito-nuclear discordance in the small black-tailed brush lizard, Urosaurus nigricaudus, of the Peninsula of Baja California, Mexico and southern California, USA, and discuss potential drivers. Results show three deeply divergent mitochondrial lineages dating back to the later Miocene (ca. 5.5 Ma) and Pliocene (ca. 2.8 Ma) that likely followed geographic isolation due to trans-peninsular seaways. This contrasts with very low levels of genetic differentiation in nuclear loci (FST < 0.028) between mtDNA lineages. Analyses of protein-coding genes reveal substantial fixed variation between mitochondrial lineages, of which a significant portion comes from non-synonymous mutations. A mixture of drift and selection is likely responsible for the rise of these mtDNA groups, albeit with little evidence of marked differences in climatic niche space between them. Finally, future investigations can look further into the role that mito-nuclear incompatibilities and mating systems play in explaining contrasting nuclear gene flow.}, }
@article {pmid30831270, year = {2019}, author = {Belaiba, E and Marrone, F and Vecchioni, L and Bahri-Sfar, L and Arculeo, M}, title = {An exhaustive phylogeny of the combtooth blenny genus Salaria (Pisces, Blenniidae) shows introgressive hybridization and lack of reciprocal mtDNA monophyly between the marine species Salaria basilisca and Salaria pavo.}, journal = {Molecular phylogenetics and evolution}, volume = {135}, number = {}, pages = {210-221}, doi = {10.1016/j.ympev.2019.02.026}, pmid = {30831270}, issn = {1095-9513}, mesh = {Animals ; Aquatic Organisms/*genetics ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Geography ; Haplotypes/genetics ; *Hybridization, Genetic ; Mitochondria/genetics ; Perciformes/*genetics ; *Phylogeny ; Species Specificity ; }, abstract = {A comprehensive phylogeny of the genus Salaria based on mitochondrial and nuclear markers grouped the extant species of the genus in well-characterised marine and freshwater clades, thus rejecting the hypothesis of a polytypic origin of the freshwater Salaria populations and supporting the occurrence of a single invasion event of the inland waters by the genus. Based on both mitochondrial and nuclear DNA datasets, the Salaria species of the freshwater clade proved to be vicariant taxa originating from a common ancestor which could possibly spread throughout the circum-Mediterranean inland waters during the late Miocene Messinian salinity crisis, then experiencing a process of allopatric differentiation after the re-flooding of the Mediterranean basin. Within the marine clade, although the nuDNA datasets showed the existence of well-supported subclades in accordance to the morphological identification of the studied specimens, one of the two subclades obtained in the phylogenetic tree based on the mtDNA dataset included both S. basilisca and S. pavo specimens, thus failing to find the two species as reciprocally monophyletic. Such a mito-nuclear discordance is here ascribed to multiple mtDNA unidirectional introgression events from S. basilisca to S. pavo, and the molecular diversity pattern of the marine Salaria species is here ascribed to a Pleistocene speciation event nowadays partly concealed by the occurrence of introgressive hybridization phenomena between the two taxa. Our results urge for prudence when implementing DNA barcoding approaches since, in the presence of mito-nuclear discordance phenomena, single-marker mtDNA-only analyses might lead to significant misidentifications.}, }
@article {pmid30824066, year = {2019}, author = {Forgione, I and Bonavita, S and Regina, TMR}, title = {Mitochondria of Cedrus atlantica and allied species: A new chapter in the horizontal gene transfer history.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {281}, number = {}, pages = {93-101}, doi = {10.1016/j.plantsci.2019.01.013}, pmid = {30824066}, issn = {1873-2259}, mesh = {Cedrus/*genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Mitochondrial/*genetics ; Ribosomal Proteins/*genetics ; }, abstract = {The extraordinary incidence of Horizontal Gene Transfer (HGT) mostly in mitochondrial genomes of flowering plants is well known. Here, we report another episode of HGT affecting a large mitochondrial gene region in the evergreen conifer Atlas cedar (Cedrus atlantica). Mitochondria of this Pinaceae species possess an rps3 gene that harbours two introns and shares the same genomic context with a downstream overlapping rpl16 gene, like in the major groups of gymnosperms and angiosperms analyzed so far. Interestingly, C. atlantica contains additional copies of the rps3 and rpl16 sequences that are more closely related to angiosperm counterparts than to those from gymnosperms, as also confirmed by phylogenetic analyses. This suggests that a lateral transfer from a flowering plant donor is the most likely mechanism for the origin of the Atlas cedar extra sequences. Quantitative PCR and reverse-transcription (RT)-PCR analyses demonstrate, respectively, mitochondrial location and lack of expression for the rps3 and rpl16 additional sequences in C. atlantica. Furthermore, our study provides evidence that a similar HGT event takes place in two other Cedrus species, which occurr in Cyprus and North Africa. Only the West Himalayan C. deodara lacks the transferred genes. The potential donor and the molecular mechanism underlying this lateral DNA transfer remain still unclear.}, }
@article {pmid30822116, year = {2019}, author = {Meyer, EH and Welchen, E and Carrie, C}, title = {Assembly of the Complexes of the Oxidative Phosphorylation System in Land Plant Mitochondria.}, journal = {Annual review of plant biology}, volume = {70}, number = {}, pages = {23-50}, doi = {10.1146/annurev-arplant-050718-100412}, pmid = {30822116}, issn = {1545-2123}, mesh = {Animals ; Cell Respiration ; Electron Transport ; *Embryophyta ; Mitochondria ; *Oxidative Phosphorylation ; }, abstract = {Plant mitochondria play a major role during respiration by producing the ATP required for metabolism and growth. ATP is produced during oxidative phosphorylation (OXPHOS), a metabolic pathway coupling electron transfer with ADP phosphorylation via the formation and release of a proton gradient across the inner mitochondrial membrane. The OXPHOS system is composed of large, multiprotein complexes coordinating metal-containing cofactors for the transfer of electrons. In this review, we summarize the current state of knowledge about assembly of the OXPHOS complexes in land plants. We present the different steps involved in the formation of functional complexes and the regulatory mechanisms controlling the assembly pathways. Because several assembly steps have been found to be ancestral in plants-compared with those described in fungal and animal models-we discuss the evolutionary dynamics that lead to the conservation of ancestral pathways in land plant mitochondria.}, }
@article {pmid30813887, year = {2019}, author = {Kuzminkova, AA and Sokol, AD and Ushakova, KE and Popadin, KY and Gunbin, KV}, title = {mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria.}, journal = {BMC evolutionary biology}, volume = {19}, number = {Suppl 1}, pages = {47}, pmid = {30813887}, issn = {1471-2148}, mesh = {Animals ; *Computational Biology ; *Evolution, Molecular ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Phylogeny ; Software ; Solvents/chemistry ; Vertebrates/*genetics ; }, abstract = {BACKGROUND: Heterotachy is the variation in the evolutionary rate of aligned sites in different parts of the phylogenetic tree. It occurs mainly due to epistatic interactions among the substitutions, which are highly complex and make it difficult to study protein evolution. The vast majority of computational evolutionary approaches for studying these epistatic interactions or their evolutionary consequences in proteins require high computational time. However, recently, it has been shown that the evolution of residue solvent accessibility (RSA) is tightly linked with changes in protein fitness and intra-protein epistatic interactions. This provides a computationally fast alternative, based on comparison of evolutionary rates of amino acid replacements with the rates of RSA evolutionary changes in order to recognize any shifts in epistatic interaction.<br><br>RESULTS: Based on RSA information, data randomization and phylogenetic approaches, we constructed a software pipeline, which&#xa0;can be used to analyze the evolutionary consequences of intra-protein epistatic interactions with relatively low computational time. We analyzed the evolution of 512 protein families tightly linked to mitochondrial function in Vertebrates and created "mtProtEvol", the web resource with data on protein evolution. In strict agreement with lifespan and metabolic rate data, we demonstrated that different functional categories of mitochondria-related proteins subjected to selection on accelerated and decelerated RSA rates in rodents and primates. For example, accelerated RSA evolution in rodents has been shown for Krebs cycle enzymes, respiratory chain and reactive oxygen species metabolism, while in primates these functions are stress-response, translation and mtDNA integrity. Decelerated RSA evolution in rodents has been demonstrated for translational machinery and oxidative stress response components.<br><br>CONCLUSIONS: mtProtEvol is an interactive resource focused on evolutionary analysis of epistatic interactions in protein families involved in Vertebrata mitochondria function and available at http://bioinfodbs.kantiana.ru/mtProtEvol /. This resource and the&#xa0;devised software pipeline may be useful tool for researchers in area of protein evolution.}, }
@article {pmid30811487, year = {2019}, author = {Skuza, L and Szućko, I and Filip, E and Strzała, T}, title = {Genetic diversity and relationship between cultivated, weedy and wild rye species as revealed by chloroplast and mitochondrial DNA non-coding regions analysis.}, journal = {PloS one}, volume = {14}, number = {2}, pages = {e0213023}, pmid = {30811487}, issn = {1932-6203}, mesh = {Agriculture ; Bayes Theorem ; Chloroplasts/*genetics ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; *Genetic Variation ; Mitochondria/*genetics ; Phylogeny ; Secale/*classification/genetics ; Sequence Analysis, DNA ; }, abstract = {The genus Secale is small but very diverse. Despite the high economic importance, phylogenetic relationships of rye species have not been fully determined, and they are extremely important for the process of breeding of new cultivars that can be enriched with functional traits derived from wild rye species. The study analyzed the degree of relationship of 35 accessions of the genus Secale, representing 13 most often distinguished species and subspecies, originating from various seed collections in the world, based on the analysis of non-coding regions of the chloroplast (cpDNA) and mitochondrial genome (mtDNA), widely used in phylogenetic and population plant studies, because of a higher rate of evolution than the coding regions. There was no clear genetic structure between different species and subspecies, which may indicated the introgression between these taxa. The obtained data confirmed that S. vavilovii was very similar to S. cereale, which confirmed the assumption that they might share a common ancestor. The results also confirmed the divergence of S. sylvestre from other species and subspecies of rye. Areas that may be useful molecular markers in studies on closely related species of the genus Secale were also indicated.}, }
@article {pmid30809302, year = {2019}, author = {Tan, Y and Zhu, Y and Wen, L and Yang, X and Liu, X and Meng, T and Dai, S and Ping, Y and Yuan, H and Hu, F}, title = {Mitochondria-Responsive Drug Release along with Heat Shock Mediated by Multifunctional Glycolipid Micelles for Precise Cancer Chemo-Phototherapy.}, journal = {Theranostics}, volume = {9}, number = {3}, pages = {691-707}, pmid = {30809302}, issn = {1838-7640}, mesh = {Animals ; Antibiotics, Antineoplastic/*administration &amp; dosage/therapeutic use ; Cell Line, Tumor ; Doxorubicin/*administration &amp; dosage/therapeutic use ; *Drug Liberation ; Female ; Glycolipids/administration &amp; dosage/therapeutic use ; *Heat-Shock Response ; Humans ; Indoles/administration &amp; dosage/*therapeutic use ; Mice ; Mice, Inbred BALB C ; Mice, Nude ; Micelles ; Mitochondria/*drug effects ; *Phototherapy ; Reactive Oxygen Species/metabolism ; }, abstract = {Responsive drug release in tumor mitochondria is a pre-requisite for mitochondria-targeted drug delivery systems to improve the efficacy of this promising therapeutic modality. To this end, a photothermal stimulation strategy for mitochondria-responsive drug release along with heat shock is developed to maximize the antitumor effects with minimal side effects. Methods: This strategy relies on mitochondrial-targeted delivery of doxorubicin (DOX) through a photothermal and lipophilic agent IR-780 iodide (IR780)-modified glycolipid conjugates (CSOSA), which can synergistically triggers high-level reactive oxygen species (ROS) to kill tumor cells. Results: Specifically, upon laser irradiation, the photothermal conversion by IR780-CSOSA can not only weaken the hydrophobic interaction between the core of micelles and DOX and trigger unexpected micelle swelling to release DOX in mitochondria for the amplification of ROS, but also induce mitochondria-specific heat shock to promote the fast evolution of ROS at the same locus to eradicate cancer cells in a more effective way. Furthermore, IR780-CSOSA micelles may independently realize the real-time diagnosis and imaging on multiple tumor models. Deep penetration into tumors by IR780-CSOSA/DOX micelles can be manipulated under laser irradiation. Conclusion: Such multifunctional IR780-CSOSA/DOX micelles with integration of mitochondria-responsive drug release and heat shock are demonstrated to be superior to the non-mitochondria-responsive therapy. This study opens up new avenues for the future cancer diagnosis and treatment.}, }
@article {pmid30809252, year = {2019}, author = {Hirata, A}, title = {Recent Insights Into the Structure, Function, and Evolution of the RNA-Splicing Endonucleases.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {103}, pmid = {30809252}, issn = {1664-8021}, abstract = {RNA-splicing endonuclease (EndA) cleaves out introns from archaeal and eukaryotic precursor (pre)-tRNA and is essential for tRNA maturation. In archaeal EndA, the molecular mechanisms underlying complex assembly, substrate recognition, and catalysis have been well understood. Recently, certain studies have reported novel findings including the identification of new subunit types in archaeal EndA structures, providing insights into the mechanism underlying broad substrate specificity. Further, metagenomics analyses have enabled the acquisition of numerous DNA sequences of EndAs and intron-containing pre-tRNAs from various species, providing information regarding the co-evolution of substrate specificity of archaeal EndAs and tRNA genetic diversity, and the evolutionary pathway of archaeal and eukaryotic EndAs. Although the complex structure of the heterothermic form of eukaryotic EndAs is unknown, previous reports regarding their functions indicated that mutations in human EndA cause neurological disorders including pontocerebellar hypoplasia and progressive microcephaly, and yeast EndA significantly cleaves mitochondria-localized mRNA encoding cytochrome b mRNA processing 1 (Cpb1) for mRNA maturation. This mini-review summarizes the aforementioned results, discusses their implications, and offers my personal opinion regarding future directions for the analysis of the structure and function of EndAs.}, }
@article {pmid30807715, year = {2019}, author = {Matsche, MA and Adams, CR and Blazer, VS}, title = {Newly Described Coccidia Goussia bayae from White Perch Morone americana: Morphology and Phylogenetics Support Emerging Taxonomy of Goussia within Piscine Hosts.}, journal = {The Journal of parasitology}, volume = {105}, number = {1}, pages = {1-10}, pmid = {30807715}, issn = {1937-2345}, mesh = {Animals ; Bass/*parasitology ; Bays ; Bile Ducts, Intrahepatic/parasitology ; Coccidiosis/parasitology/*veterinary ; DNA, Ribosomal/chemistry ; Eimeriidae/*classification/genetics/ultrastructure ; Electron Transport Complex IV/genetics ; Female ; Fish Diseases/*parasitology ; Gallbladder/parasitology ; Male ; Maryland ; Mitochondria/genetics ; Oocysts/ultrastructure ; Phylogeny ; Rivers ; Virginia ; }, abstract = {In March and April 2016, 150 white perch (Morone americana) were collected from various localities in Chesapeake Bay and examined for coccidia. A previously undescribed species of coccidia was observed in the hepatic bile ducts and gallbladder of all white perch (100%) examined. We describe this species using morphological characteristics, histology, and gene sequences of the small-subunit ribosomal DNA (rDNA), large-subunit rDNA, and mitochondrial genes cytochrome oxidase 1 (COI), cytochrome oxidase b (Cytb), and cytochrome oxidase 3 (COIII). Oocysts of Goussia bayae n. sp. were subspherical with a single-layered smooth wall and measured (length [L] × width [W]) 26.2 × 21.8 μm, with a L/W ratio of 1.2. A micropyle was present but a micropyle cap, polar granules, and oocyst residuum were absent. Each oocyst contained 4 sporocysts that were ellipsoidal and measured (L × W) 12.6 × 7.8 μm, with a L/W ratio of 1.6. A pair of sporozoites was present, but sporocysts lacked a Stieda body and residuua. Meronts and gamonts were epicellular in biliary epithelial cells and oocysts were coelozoic in hepatic and common bile ducts and gallbladder. This is the first report of Goussia spp. from white perch and the first mitochondrial DNA sequence reported from a Goussia species. Phylogenetic analysis indicates basal placement of G. bayae to Eimeriidae, Choleoeimeria, and Sarcocystidae.}, }
@article {pmid30807709, year = {2019}, author = {Léveillé, AN and Bland, SK and Carlton, K and Larouche, CB and Kenney, DG and Brouwer, ER and Lillie, BN and Barta, JR}, title = {Klossiella equi Infecting Kidneys of Ontario Horses: Life Cycle Features and Multilocus Sequence-Based Genotyping Confirm the Genus Klossiella Belongs In the Adeleorina (Apicomplexa: Coccidia).}, journal = {The Journal of parasitology}, volume = {105}, number = {1}, pages = {29-40}, pmid = {30807709}, issn = {1937-2345}, mesh = {Animals ; Coccidiosis/epidemiology/parasitology/*veterinary ; DNA, Ribosomal/chemistry ; Electron Transport Complex IV/genetics ; Eucoccidiida/*classification/genetics/growth &amp; development ; Female ; Genotyping Techniques/veterinary ; Horse Diseases/epidemiology/*parasitology ; Horses ; Kidney/parasitology ; Kidney Diseases/epidemiology/parasitology/*veterinary ; Life Cycle Stages ; Male ; Mitochondria/genetics ; Multilocus Sequence Typing/veterinary ; Ontario/epidemiology ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Species in the genus Klossiella Smith and Johnson, 1902 are unique among the suborder Adeleorina because they are monoxenous in mammals exclusively, whereas all other reported members of the Adeleorina use invertebrates as definitive hosts. Unlike other coccidia, all members of the Adeleorina undergo syzygy, the association of microgamonts and macrogamonts before maturation to gametes and syngamy. After fertilization, many members of the Adeleorina produce thin-walled polysporocystic oocysts. Despite being biologically similar to other members of the Adeleorina, the phylogenetic placement of the genus Klossiella has been questioned based on its unique host affinity. In the present study, 2 cases of Klossiella equi were reported from the kidneys of horses in Ontario. Details of the life cycle as well as mitochondrial and nuclear 18S ribosomal DNA (18S rDNA) sequences were analyzed to provide both morphological and molecular evidence for the phylogenetic placement of K. equi. Initially, various stages of the life cycle were identified in histological slides prepared from the kidney tissue, and DNA was isolated from the infected tissue. Polymerase chain reaction and Sanger sequencing were used to generate a complete mitochondrial genome sequence (6,569 bp) and a partial 18S rDNA sequence (1,443 bp). The K. equi 18S rDNA sequence was aligned with various publicly available apicomplexan 18S rDNA sequences. This alignment was used to generate a phylogenetic tree based on Bayesian inference. Multiple K. equi stages were identified including meronts, microgamonts, and macrogamonts associating in syzygy as well as thin-walled oocysts in various stages of sporogonic development. The 18S rDNA sequence of K. equi positioned within the monophyletic Adeleorina clade. The mitochondrial genome of K. equi contained 3 coding sequences for cytochrome c oxidase I, cytochrome c oxidase III, and cytochrome b as well as various fragmented ribosomal sequences. These components were arranged in a unique order that has not been observed in other apicomplexan mitochondrial genomes sequenced to date. Overall, it was concluded that there were sufficient morphological and molecular data to confirm the placement of K. equi and the genus Klossiella among the Adeleorina. The biological and molecular data obtained from these cases may assist with future studies evaluating the prevalence and life history of this seemingly underreported parasite and better define the impact of K. equi on the health of domestic and wild equids.}, }
@article {pmid30804878, year = {2019}, author = {Festoff, BW and Citron, BA}, title = {Thrombin and the Coag-Inflammatory Nexus in Neurotrauma, ALS, and Other Neurodegenerative Disorders.}, journal = {Frontiers in neurology}, volume = {10}, number = {}, pages = {59}, pmid = {30804878}, issn = {1664-2295}, support = {I01 RX001520/RX/RRD VA/United States ; }, abstract = {This review details our current understanding of thrombin signaling in neurodegeneration, with a focus on amyotrophic lateral sclerosis (ALS, Lou Gehrig's disease) as well as future directions to be pursued. The key factors are multifunctional and involved in regulatory pathways, namely innate immune and the coagulation cascade activation, that are essential for normal nervous system function and health. These two major host defense systems have a long history in evolution and include elements and regulators of the coagulation pathway that have significant impacts on both the peripheral and central nervous system in health and disease. The clotting cascade responds to a variety of insults to the CNS including injury and infection. The blood brain barrier is affected by these responses and its compromise also contributes to these detrimental effects. Important molecules in signaling that contribute to or protect against neurodegeneration include thrombin, thrombomodulin (TM), protease activated receptor 1 (PAR1), damage associated molecular patterns (DAMPs), such as high mobility group box protein 1 (HMGB1) and those released from mitochondria (mtDAMPs). Each of these molecules are entangled in choices dependent upon specific signaling pathways in play. For example, the particular cleavage of PAR1 by thrombin vs. activated protein C (APC) will have downstream effects through coupled factors to result in toxicity or neuroprotection. Furthermore, numerous interactions influence these choices such as the interplay between HMGB1, thrombin, and TM. Our hope is that improved understanding of the ways that components of the coagulation cascade affect innate immune inflammatory responses and influence the course of neurodegeneration, especially after injury, will lead to effective therapeutic approaches for ALS, traumatic brain injury, and other neurodegenerative disorders.}, }
@article {pmid30804213, year = {2019}, author = {Tang, K and Li, Y and Yu, C and Wei, Z}, title = {Structural mechanism for versatile cargo recognition by the yeast class V myosin Myo2.}, journal = {The Journal of biological chemistry}, volume = {294}, number = {15}, pages = {5896-5906}, pmid = {30804213}, issn = {1083-351X}, mesh = {Binding Sites ; Evolution, Molecular ; Microtubule-Associated Proteins/chemistry/genetics/metabolism ; Mitochondrial Proteins/chemistry/genetics/metabolism ; Multiprotein Complexes/chemistry/genetics/metabolism ; Myosin Heavy Chains/*chemistry/genetics/*metabolism ; Myosin Type V/*chemistry/genetics/*metabolism ; Protein Domains ; Saccharomyces cerevisiae/*enzymology/genetics ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism ; }, abstract = {Class V myosins are actin-dependent motors, which recognize numerous cellular cargos mainly via the C-terminal globular tail domain (GTD). Myo2, a yeast class V myosin, can transport a broad range of organelles. However, little is known about the capacity of Myo2-GTD to recognize such a diverse array of cargos specifically at the molecular level. Here, we solved crystal structures of Myo2-GTD (at 1.9-3.1 Å resolutions) in complex with three cargo adaptor proteins: Smy1 (for polarization of secretory vesicles), Inp2 (for peroxisome transport), and Mmr1 (for mitochondria transport). The structures of Smy1- and Inp2-bound Myo2-GTD, along with site-directed mutagenesis experiments, revealed a binding site in subdomain-I having a hydrophobic groove with high flexibility enabling Myo2-GTD to accommodate different protein sequences. The Myo2-GTD-Mmr1 complex structure confirmed and complemented a previously identified mitochondrion/vacuole-specific binding region. Moreover, differences between the conformations and locations of cargo-binding sites identified here for Myo2 and those reported for mammalian MyoVA (MyoVA) suggest that class V myosins potentially have co-evolved with their specific cargos. Our structural and biochemical analysis not only uncovers a molecular mechanism that explains the diverse cargo recognition by Myo2-GTD, but also provides structural information useful for future functional studies of class V myosins in cargo transport.}, }
@article {pmid30790556, year = {2019}, author = {Léveillé, AN and Baneth, G and Barta, JR}, title = {Next generation sequencing from Hepatozoon canis (Apicomplexa: Coccidia: Adeleorina): Complete apicoplast genome and multiple mitochondrion-associated sequences.}, journal = {International journal for parasitology}, volume = {49}, number = {5}, pages = {375-387}, doi = {10.1016/j.ijpara.2018.12.001}, pmid = {30790556}, issn = {1879-0135}, mesh = {Animals ; Apicomplexa/classification/*genetics/isolation &amp; purification ; Apicoplasts/*genetics ; Cytochromes b/genetics ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Dog Diseases/parasitology ; Dogs ; Genome, Mitochondrial ; *Genome, Plastid ; Genome, Protozoan ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Protozoan Infections, Animal/parasitology ; }, abstract = {Extrachromosomal genomes of the adeleorinid parasite Hepatozoon canis infecting an Israeli dog were investigated using next-generation and standard sequencing technologies. A complete apicoplast genome and several mitochondrion-associated sequences were generated. The apicoplast genome (31,869 bp) possessed two copies of both large subunit (23S) and small subunit (16S) ribosomal RNA genes (rDNA) within an inverted repeat region, as well as 22 protein-coding sequences, 25 transfer RNA genes (tDNA) and seven open reading frames of unknown function. Although circular-mapping, the apicoplast genome was physically linear according to next-generation data. Unlike other apicoplast genomes, genes encoding ribosomal protein S19 and tDNAs for alanine, aspartic acid, histidine, threonine and valine were not identified. No complete mitochondrial genome was recovered using next-generation data or directed PCR amplifications. Eight mitochondrion-associated (215-3523 bp) contigs assembled from next-generation data encoded a complete cytochrome c oxidase subunit I coding sequence, a complete cytochrome c oxidase subunit III coding sequence, two complete cytochrome B coding sequences, a non-coding, pseudogene for cytochrome B and multiple fragmented mitochondrial rDNA genes (SSUA, SSUB, SSUD, LSUC, LSUG, RNA6, RNA10, RNA14, RNA18). The paucity of NGS reads generating each of the mitochondrion-like sequences suggested that a complete mitochondrial genome at typically high copy number was absent in H. canis. In contrast, the complete nuclear rDNA unit sequence of H. canis (18S rDNA to 28S rDNA, 6977 bp) had >1000-fold next-generation coverage. Multiple divergent (from 93.6% to 99.9% pairwise identities) nuclear 18S rDNA contigs were generated (three types with 10 subtypes total). To our knowledge this is the first apicoplast genome sequenced from any adeleorinid coccidium and the first mitochondrion-associated sequences from this serious pathogen of wild and domestic canids. These newly generated sequences may provide useful genetic loci for high-resolution species-level genotyping that is currently impossible using existing nuclear rDNA targets.}, }
@article {pmid30789345, year = {2019}, author = {Muñoz-Gómez, SA and Hess, S and Burger, G and Lang, BF and Susko, E and Slamovits, CH and Roger, AJ}, title = {An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {30789345}, issn = {2050-084X}, support = {HE7560/1-1//Deutsche Forschungsgemeinschaft/International ; RGPIN/05286-2014//Natural Sciences and Engineering Research Council of Canada/International ; RGPIN-2017-05411//Natural Sciences and Engineering Research Council of Canada/International ; RGPIN/05754-2015//Natural Sciences and Engineering Research Council of Canada/International ; 2016-06792//Natural Sciences and Engineering Research Council of Canada/International ; }, mesh = {Alphaproteobacteria/*classification/*genetics ; Computational Biology ; *Evolution, Molecular ; Genes, Bacterial ; Molecular Biology ; *Phylogeny ; }, abstract = {The Alphaproteobacteria is an extraordinarily diverse and ancient group of bacteria. Previous attempts to infer its deep phylogeny have been plagued with methodological artefacts. To overcome this, we analyzed a dataset of 200 single-copy and conserved genes and employed diverse strategies to reduce compositional artefacts. Such strategies include using novel dataset-specific profile mixture models and recoding schemes, and removing sites, genes and taxa that are compositionally biased. We show that the Rickettsiales and Holosporales (both groups of intracellular parasites of eukaryotes) are not sisters to each other, but instead, the Holosporales has a derived position within the Rhodospirillales. A synthesis of our results also leads to an updated proposal for the higher-level taxonomy of the Alphaproteobacteria. Our robust consensus phylogeny will serve as a framework for future studies that aim to place mitochondria, and novel environmental diversity, within the Alphaproteobacteria.}, }
@article {pmid30785686, year = {2018}, author = {Titov, VN and Aripovskiy, AV and Dmitriev, LF and Medvedev, OS}, title = {[Formation in the phylogenesis of three pulls of cells with expressed different absorption and metabolism of fatty acids. Insulin and medium chains fatty acids.].}, journal = {Klinicheskaia laboratornaia diagnostika}, volume = {63}, number = {12}, pages = {732-740}, doi = {10.18821/0869-2084-2018-63-12-732-740}, pmid = {30785686}, issn = {0869-2084}, mesh = {Animals ; Atherosclerosis ; Diet ; Fatty Acids/*metabolism ; Humans ; Insulin/*metabolism ; Insulin Resistance ; Metabolic Syndrome ; *Phylogeny ; }, abstract = {Somatic cells at the early stages of phylogenesis realized the metabolism of long-chain fatty acids (FA), primarily palmitic saturated FA. It dominated the construction of a bilayer cell membrane and as a substrate for oxidation in mitochondria during energy production. Later, polyene FAs became involved in the construction of the cell membrane, the membranes of intracellular organelles, and became the substrate for the synthesis of biologically active eicosanoids. At later stages of phylogenesis, the metabolism of medium-chain FAs is activated and the formation of ketone bodies as a substrate, which is available for oxidation by the mitochondria of the formed cells of the nervous tissue in the absence of first substrate glucose. In the later stages of phylogenesis, insulin initiated: a) the transformation of carnivorous ancestors of the species Homo sapiens in the ocean into a herbivorous species while living on land; b) the formation of the new biological function of locomotion and c) the dominance of the oleic variant of the metabolism of long-chain fatty acids with higher kinetic parameters of mitochondria oxidation. Metabolites of medium chain FA have become humoral mediators of metabolism and the formation of feedback mechanisms in the function of trophology and cognitive biological function. The formation of an oleic variant of the metabolism of fatty acids under the action of insulin led to the improvement of the energy supply of cells and the high kinetic parameters of many species of herbivorous mammals, including Homo sapiens. The species Homo sapiens was not omnivorous (Omnivores); the insulin's regulatory action during life on land has turned it into a herbivorous species (Herbivore), but with a carnivorous (Carnivore) (fish-eating) past. Seven metabolic pandemics (1. atherosclerosis and atheromatosis; 2. metabolic arterial hypertension; 3. metabolic syndrome; 4. insulin resistance syndrome; 5. obesity; 6. nonalcoholic fatty liver disease and 7. endogenous hyperuricemia) are only functional disorders and can be, in most cases, eliminated. From the standpoint of the phylogenetic theory of general pathology, atherosclerosis and atheromatosis of the arteries have no great future. As soon, as the majority of individuals of the Homo sapiens species realize that in phylogenesis they have formed as herbivores and stop eating excessive amounts of meat food, exogenous palmitic FA, the incidence in the population will begin to decrease. Patients are still obliged to justify the binary, biological name of the species - reasonable man. Prevention and other metabolic pandemics, diseases of civilization, can be discussed. It takes time, an understanding of what happens by the doctors, diligence and the desire of patients to be healthy.}, }
@article {pmid30785203, year = {2019}, author = {Yan, Z and Ye, G and Werren, JH}, title = {Evolutionary Rate Correlation between Mitochondrial-Encoded and Mitochondria-Associated Nuclear-Encoded Proteins in Insects.}, journal = {Molecular biology and evolution}, volume = {36}, number = {5}, pages = {1022-1036}, doi = {10.1093/molbev/msz036}, pmid = {30785203}, issn = {1537-1719}, support = {DEB-1257053//US National Science Foundation/International ; IOS-1456233//US National Science Foundation/International ; }, mesh = {Animals ; *Evolution, Molecular ; Insect Proteins/*genetics ; Insecta/*genetics ; Mitochondrial Proteins/*genetics ; Oxidative Phosphorylation ; }, abstract = {The mitochondrion is a pivotal organelle for energy production, and includes components encoded by both the mitochondrial and nuclear genomes. Functional and evolutionary interactions are expected between the nuclear- and mitochondrial-encoded components. The topic is of broad interest in biology, with implications to genetics, evolution, and medicine. Here, we compare the evolutionary rates of mitochondrial proteins and ribosomal RNAs to rates of mitochondria-associated nuclear-encoded proteins, across the major orders of holometabolous insects. There are significant evolutionary rate correlations (ERCs) between mitochondrial-encoded and mitochondria-associated nuclear-encoded proteins, which are likely driven by different rates of mitochondrial sequence evolution and correlated changes in the interacting nuclear-encoded proteins. The pattern holds after correction for phylogenetic relationships and considering protein conservation levels. Correlations are stronger for both nuclear-encoded OXPHOS proteins that are in contact with mitochondrial OXPHOS proteins and for nuclear-encoded mitochondrial ribosomal amino acids directly contacting the mitochondrial rRNAs. We find that ERC between mitochondrial- and nuclear-encoded proteins is a strong predictor of nuclear-encoded proteins known to interact with mitochondria, and ERC shows promise for identifying new candidate proteins with mitochondrial function. Twenty-three additional candidate nuclear-encoded proteins warrant further study for mitochondrial function based on this approach, including proteins in the minichromosome maintenance helicase complex.}, }
@article {pmid30776435, year = {2019}, author = {Dufresnes, C and Beddek, M and Skorinov, DV and Fumagalli, L and Perrin, N and Crochet, PA and Litvinchuk, SN}, title = {Diversification and speciation in tree frogs from the Maghreb (Hyla meridionalis sensu lato), with description of a new African endemic.}, journal = {Molecular phylogenetics and evolution}, volume = {134}, number = {}, pages = {291-299}, doi = {10.1016/j.ympev.2019.02.009}, pmid = {30776435}, issn = {1095-9513}, mesh = {Africa, Northern ; Animals ; Anura/*genetics ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Genetic Speciation ; *Genetic Variation ; Genetics, Population ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Principal Component Analysis ; }, abstract = {Comparative molecular studies emphasized a new biogeographic paradigm for the terrestrial fauna of North Africa, one of the last uncharted ecoregions of the Western Palearctic: two independent east-west divisions across the Maghreb. Through a comprehensive phylogeography, we assessed how this model suits the genetic diversification documented for the tree frog Hyla meridionalis sensu lato. Analyses of mtDNA variation and thousands of nuclear loci confirmed the old split (low-Pliocene) between Tunisian and Algerian populations. These lineages meet but barely admix in the eastern Maghreb (Algerian-Tunisian border), a sign of putatively advanced reproductive isolation. In the western Maghreb, we report a Pleistocene divergence between Moroccan and Algerian populations. Tree frogs thus follow both predictions: a double east-west break that gave rise to two suture zones characteristic of North-African phylogeography. Moreover, some intraspecific mtDNA variation is not mirrored by the nuclear data, emphasizing that evolutionary units should always be designated by multilocus approaches. Last but not least, we describe the Tunisian lineage as a new species endemic to Africa.}, }
@article {pmid30771209, year = {2019}, author = {Shin, MK and Cheong, JH}, title = {Mitochondria-centric bioenergetic characteristics in cancer stem-like cells.}, journal = {Archives of pharmacal research}, volume = {42}, number = {2}, pages = {113-127}, pmid = {30771209}, issn = {1976-3786}, support = {1020390//Ministry of Health and Welfare/ ; 1320360//Ministry of Health and Welfare/ ; NRF-2017R1D1A1B03032553//National Research Fund, Republic of Korea/ ; 6-2007-0095//Yonsei University College of Medicine/ ; 6-2008-0193//Yonsei University College of Medicine/ ; }, mesh = {Animals ; Antineoplastic Agents/pharmacology ; Energy Metabolism/drug effects/*physiology ; Humans ; Mitochondria/drug effects/*metabolism ; Neoplastic Stem Cells/drug effects/*metabolism ; Oxidative Stress/drug effects/physiology ; Tumor Microenvironment/drug effects/*physiology ; }, abstract = {Metabolic and genotoxic stresses that arise during tumor progression and anti-cancer treatment, respectively, can impose a selective pressure to promote cancer evolution in the tumor microenvironment. This process ultimately selects for the most "fit" clones, which generally have a cancer stem cell like phenotype with features of drug resistance, epithelial-mesenchymal transition, invasiveness, and high metastatic potential. From a bioenergetics perspective, these cancer stem-like cells (CSCs) exhibit mitochondria-centric energy metabolism and are capable of opportunistically utilizing available nutrients such as fatty acids to generate ATP and other metabolic substances, providing a selective advantage for their survival in an impermissible environment and metabolic context. Thus, diverse therapeutic strategies are needed to efficiently tackle these CSCs and eliminate their advantage. Here, we review the metabolic and bioenergetic characteristics and vulnerabilities specific to CSCs, which can provide an unprecedented opportunity to curb CSC-driven cancer mortality rates. We particularly focus on the potential of a CSC bioenergetics-targeted strategy as a versatile therapeutic component of treatment modalities applicable to most cancer types. A cancer bioenergetics-targeted strategy can expand the inventory of combinatorial regimens in the current anti-cancer armamentarium.}, }
@article {pmid30765851, year = {2019}, author = {Garraffoni, ARS and Araújo, TQ and Lourenço, AP and Guidi, L and Balsamo, M}, title = {Integrative taxonomy of a new Redudasys species (Gastrotricha: Macrodasyida) sheds light on the invasion of fresh water habitats by macrodasyids.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {2067}, pmid = {30765851}, issn = {2045-2322}, mesh = {Animals ; Brazil ; Ecosystem ; Evolution, Molecular ; Fresh Water ; Helminths/*classification/*genetics ; Microscopy, Electron, Transmission/methods ; Microscopy, Interference/methods ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; }, abstract = {The order Macrodasyida (Gastrotricha) includes over 350 marine species, and only 3 freshwater species (Marinellina flagellata, Redudasys fornerise, R. neotemperatus). Herein we describe a new freshwater species of Macrodasyida, Redudasys brasiliensis sp. nov., from Brazil through an integrative taxonomic approach. The external morphology and internal anatomy were investigated using differential interference contrast microscopy, confocal microscopy, scanning and transmission electron microscopy. The systematization of the new taxon was inferred by nuclear (18S and 28S) and mitochondrial (COI) genes, and its intra-order relationships were assessed using data from most of available macrodasyids. Phylogenetic analyses yielded congruent trees, in which the new taxon is nested within the family Redudasyidae, but it was genetically distinct from the other species of the genus Redudasys. The new species shares the gross morphology and reproductive traits with other Redudasyidae and the presence of only 1 anterior adhesive tube per side with Redudasys neotemperatus, but it has a specific pattern of ventral ciliation and muscle organization. Results support the hypothesis that dispersion into fresh water habitats by Macrodasyida and Chaetonotida taxa occurred independently and that within Macrodasyida a single lineage invaded the freshwater environment only once. Furthermore, the Neotropical region seems to be peculiar for the evolution of the freshwater macrodasyid clade.}, }
@article {pmid30763758, year = {2019}, author = {Jowers, MJ and Sánchez-Ramírez, S and Lopes, S and Karyakin, I and Dombrovski, V and Qninba, A and Valkenburg, T and Onofre, N and Ferrand, N and Beja, P and Palma, L and Godinho, R}, title = {Unravelling population processes over the Late Pleistocene driving contemporary genetic divergence in Palearctic buzzards.}, journal = {Molecular phylogenetics and evolution}, volume = {134}, number = {}, pages = {269-281}, doi = {10.1016/j.ympev.2019.02.004}, pmid = {30763758}, issn = {1095-9513}, mesh = {Animals ; Arctic Regions ; Bayes Theorem ; Birds/*genetics ; Climate Change ; DNA, Mitochondrial/genetics ; Demography ; Genetic Markers ; *Genetic Variation ; *Genetics, Population ; Haplotypes/genetics ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Mutation Rate ; *Paleontology ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; }, abstract = {Population range expansions and contractions as a response to climate and habitat change throughout the Quaternary are known to have contributed to complex phylogenetic and population genetic events. Speciation patterns and processes in Palearctic buzzards (genus Buteo) are a long-standing example of morphological and genetic data incongruence, attributed to panmixia, habitat range shifts, contact zones, and climate change. Here we assess the systematics, phylogeography and population genetic structure of three nominal species of Palearctic buzzards, Buteo buteo (including B. b. vulpinus), B. rufinus (including B. r. cirtensis) and B. hemilasius. Phylogenetic analyses inferred from mitochondrial data recover B. hemilasius as sister to the sister clades B. r. rufinus and B. buteo complex (B. b. buteo, B. b. vulpinus, but also including B. r. cirtensis). In contrast, we find an unresolved genetic delimitation inferred from four nuclear loci, suggesting an ancestral genetic pool for all species. Time-trees suggest population contractions and expansions throughout the Pleistocene, which likely reflect habitat change and contrasting ecological niche requirements between species. Microsatellite-based extended Bayesian skyline plots reveal relatively constant population sizes for B. hemilasius, B. r. rufinus, and B. b. vulpinus, in contrast to a dramatic population expansion in B. r. cirtensis within the last 3 kya. Overall, our study illustrates how complex population processes over the Late Pleistocene have shaped the patterns of genetic divergence in Palearctic buzzards, due to the joint effects of shared ancestral polymorphisms, population expansions and contractions, with hybridization at contact zones leading to admixture and introgression.}, }
@article {pmid30762166, year = {2019}, author = {Prabhu, VR and Arjun, MS and Bhavana, K and Kamalakkannan, R and Nagarajan, M}, title = {Complete mitochondrial genome of Indian mithun, Bos frontalis and its phylogenetic implications.}, journal = {Molecular biology reports}, volume = {46}, number = {2}, pages = {2561-2566}, pmid = {30762166}, issn = {1573-4978}, support = {EMR/2015/000937//Science and Engineering Research Board/ ; IF160266//DST-INSPIRE/ ; }, mesh = {Animals ; Biological Evolution ; Cattle/*genetics ; Endangered Species ; Genome, Mitochondrial/*genetics ; India ; Mitochondria/*genetics ; Phylogeny ; Species Specificity ; }, abstract = {Mithun (Bos frontalis) is an endangered domestic bovine species native to the hilly areas of China, Bangladesh, Myanmar, Bhutan and India. It is believed to have been domesticated from gaur around 8000 years ago. However, a few studies suggest that mithun is either an independent species or a hybrid descendant of gaur and cattle. Therefore, to understand the evolutionary history of mithun, the complete mitochondrial genome of Indian mithun was sequenced and compared with the mitochondrial genome of closely related Bos species. The mitochondrial genome of mithun was 16,346 bp long and consisted of 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes, and a control region. The phylogenetic assessments of Indian mithun along with other Bos species showed a very close genetic relationship of Indian mithun with gaur suggesting that Indian mithun might have evolved from gaur.}, }
@article {pmid30761963, year = {2019}, author = {Santacruz, A and Ornelas-García, CP and Pérez-Ponce de León, G}, title = {Diversity of Rhabdochona mexicana (Nematoda: Rhabdochonidae), a parasite of Astyanax spp. (Characidae) in Mexico and Guatemala, using mitochondrial and nuclear genes, with the description of a new species.}, journal = {Journal of helminthology}, volume = {94}, number = {}, pages = {e34}, doi = {10.1017/S0022149X19000014}, pmid = {30761963}, issn = {1475-2697}, mesh = {Animals ; Cell Nucleus/*genetics ; Characidae/*parasitology ; Fish Diseases/*parasitology ; Guatemala ; Helminth Proteins/genetics ; Mexico ; Mitochondria/*genetics ; Phylogeny ; Spirurida Infections/parasitology/*veterinary ; Spiruroidea/classification/genetics/growth &amp; development/*isolation &amp; purification ; }, abstract = {Among fish parasitic nematodes Rhabdochona is one of the most speciose genera, with c. 100 species. Twelve congeneric species occur in Mexican freshwater fishes, in a region located between the Nearctic and Neotropical biogeographical regions. Host association and biogeographical history have determined the high species richness of Rhabdochona in Mexico. One of these species, Rhabdochona mexicana, is highly specific to the characid genus Astyanax. Characids are a group of freshwater fish with Neotropical affinity. In this paper, we explore the genetic diversity of R. mexicana through samples obtained from populations of Astyanax spp. across river basins of Mexico and Guatemala. Sequences of one mitochondrial and two ribosomal genes were obtained from 38 individuals and analysed using Maximum Likelihood and Bayesian Inference analysis. Phylogenetic analyses using cox1, and a concatenated alignment of 18S + 28S + cox1 recovered two genetic lineages. One of them corresponded with R. mexicana sensu stricto; this lineage included three reciprocally monophyletic subgroups; the other lineage was highly divergent and represented a putative candidate species. A detailed morphological study was conducted to corroborate the molecular findings. We describe a new species herein and discuss the implications of using molecular tools to increase our knowledge about the diversity of a speciose genus such as Rhabdochona.}, }
@article {pmid30760198, year = {2019}, author = {Pinard, D and Myburg, AA and Mizrachi, E}, title = {The plastid and mitochondrial genomes of Eucalyptus grandis.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {132}, pmid = {30760198}, issn = {1471-2164}, support = {97911//National Research Foundation/ ; 86936//Department of Science and Technology, Republic of South Africa/ ; }, mesh = {Base Sequence ; Cell Nucleus/genetics ; Eucalyptus/cytology/*genetics ; *Genome, Mitochondrial ; *Genome, Plant ; *Genome, Plastid ; Genomics ; Genotype ; Phylogeny ; Plant Cells/physiology ; Polymorphism, Single Nucleotide ; Transcription, Genetic ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Land plant organellar genomes have significant impact on metabolism and adaptation, and as such, accurate assembly and annotation of plant organellar genomes is an important tool in understanding the evolutionary history and interactions between these genomes. Intracellular DNA transfer is ongoing between the nuclear and organellar genomes, and can lead to significant genomic variation between, and within, species that impacts downstream analysis of genomes and transcriptomes.<br><br>RESULTS: In order to facilitate further studies of cytonuclear interactions in Eucalyptus, we report an updated annotation of the E. grandis plastid genome, and the second sequenced and annotated mitochondrial genome of the Myrtales, that of E. grandis. The 478,813&#x2009;bp mitochondrial genome shows the conserved protein coding regions and gene order rearrangements typical of land plants. There have been widespread insertions of organellar DNA into the E. grandis nuclear genome, which span 141 annotated nuclear genes. Further, we identify predicted editing sites to allow for the discrimination of RNA-sequencing reads between nuclear and organellar gene copies, finding that nuclear copies of organellar genes are not expressed in E. grandis.<br><br>CONCLUSIONS: The implications of organellar DNA transfer to the nucleus are often ignored, despite the insight they can give into the ongoing evolution of plant genomes, and the problems they can cause in many applications of genomics. Future comparisons of the transcription and regulation of organellar genes between Eucalyptus genotypes may provide insight to the cytonuclear interactions that impact economically important traits in this widely grown lignocellulosic crop species.}, }
@article {pmid30759299, year = {2019}, author = {Kaila, T and Saxena, S and Ramakrishna, G and Tyagi, A and Tribhuvan, KU and Srivastava, H and Sandhya,  and Chaudhury, A and Singh, NK and Gaikwad, K}, title = {Comparative RNA editing profile of mitochondrial transcripts in cytoplasmic male sterile and fertile pigeonpea reveal significant changes at the protein level.}, journal = {Molecular biology reports}, volume = {46}, number = {2}, pages = {2067-2084}, pmid = {30759299}, issn = {1573-4978}, mesh = {Base Sequence ; Cajanus/*genetics ; Cytoplasm/metabolism ; Cytosol/metabolism ; Fertility/*genetics ; Gene Expression Profiling/methods ; Genes, Mitochondrial/genetics ; Genes, Plant/genetics ; Mitochondria/*genetics ; RNA Editing/genetics/physiology ; RNA, Plant/genetics ; Transcriptome/genetics ; }, abstract = {RNA editing is a process which leads to post-transcriptional alteration of the nucleotide sequence of the corresponding mRNA molecule which may or may not lead to changes at the protein level. Apart from its role in providing variability at the transcript and protein levels, sometimes, such changes may lead to abnormal expression of the mitochondrial gene leading to a cytoplasmic male sterile phenotype. Here we report the editing status of 20 major mitochondrial transcripts in both male sterile (AKCMS11) and male fertile (AKPR303) pigeonpea genotypes. The validation of the predicted editing sites was done by mapping RNA-seq reads onto the amplified mitochondrial genes, and 165 and 159 editing sites were observed in bud tissues of the male sterile and fertile plant respectively. Among the resulting amino acid alterations, the most frequent one was the conversion of hydrophilic amino acids to hydrophobic. The alterations thus detected in our study indicates differential editing, but no major change in terms of the abnormal protein structure was detected. However, the above investigation provides an insight into the behaviour of pigeonpea mitochondrial genome in native and alloplasmic state and could hold clues in identification of editing factors and their role in adaptive evolution in pigeonpea.}, }
@article {pmid30759011, year = {2018}, author = {Tuder, RM}, title = {Bringing Light to Chronic Obstructive Pulmonary Disease Pathogenesis and Resilience.}, journal = {Annals of the American Thoracic Society}, volume = {15}, number = {Suppl 4}, pages = {S227-S233}, pmid = {30759011}, issn = {2325-6621}, support = {R13 HL142192/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Cellular Senescence ; Cigarette Smoking/*adverse effects ; DNA Damage ; Disease Models, Animal ; Epithelial Cells/metabolism/pathology ; Humans ; Iron/metabolism ; Lung/*metabolism/pathology ; Mitochondria/metabolism ; Oxidative Stress ; Pulmonary Disease, Chronic Obstructive/*physiopathology ; Pulmonary Emphysema/*etiology ; Smoke/*adverse effects ; }, abstract = {The pathogenesis of chronic obstructive pulmonary disease remains elusive; investigators in the field have struggled to decipher the cellular and molecular processes underlying chronic bronchitis and emphysema. Studies in the past 20 years have underscored that the tissue destruction, notably in emphysema, involves a multitude of injurious stresses, with progressive engagement of endogenous destructive processes triggered by decades of exposure to cigarette smoke and/or pollutants. These lead to an aged lung, with evidence of macromolecular damage that is unlikely to repair. Here we discuss these key pathogenetic elements in the context of organismal evolution as this concept may best capture the challenges facing chronic obstructive pulmonary disease.}, }
@article {pmid30753887, year = {2019}, author = {Ni, Y and Ma, X and Hu, W and Blair, D and Yin, M}, title = {New lineages and old species: Lineage diversity and regional distribution of Moina (Crustacea: Cladocera) in China.}, journal = {Molecular phylogenetics and evolution}, volume = {134}, number = {}, pages = {87-98}, doi = {10.1016/j.ympev.2019.02.007}, pmid = {30753887}, issn = {1095-9513}, mesh = {Alleles ; Animals ; Bayes Theorem ; China ; Cladocera/anatomy &amp; histology/*classification/*genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Geography ; Haplotypes/genetics ; Mitochondria/genetics ; *Phylogeny ; Time Factors ; }, abstract = {The distribution and genetic diversity of freshwater zooplankton is understudied in the Eastern Palearctic. Here, we explored the lineage diversity and regional distribution of the genus Moina in China. Members of this genus are often keystone components of freshwater ecosystems and have been frequently subjected to toxicological and physiological studies. Four species of Moina were identified, based on morphology, in 50 of 113 Chinese water bodies examined, and their phylogenetic position was analyzed using both a mitochondrial (mitochondrial cytochrome c oxidase subunit I; COI) and a nuclear marker (the nuclear internal transcribed spacer; ITS-1). Both molecular markers identified four clades corresponding broadly to the morphological species. Mitochondrial DNA analysis showed the presence of four species complexes with eleven lineages across China, five of which were new. However, some lineages (and even individual haplotypes) were widespread in Eurasia, suggesting an ability to disperse over long distances. In contrast, a few lineages exhibited restricted distributions. The nuclear phylogeny also recognized four species of Moina within China and seven very distinct clades. Interestingly, one specimen possessing Moina cf. micrura mtDNA had ITS-1 alleles of the M. cf. brachiata clade. This discordance between mtDNA and nuclear ITS-1 phylogenies is indicative of interspecific introgression and hybridization. Additionally, our COI phylogeny showed apparent paraphyly in two Moina species groups, suggesting introgression of their mitochondrial genomes. Our data shows the regional distribution/diversity of the Moina species complex in a Eurasian context.}, }
@article {pmid30753430, year = {2019}, author = {Hein, A and Brenner, S and Knoop, V}, title = {Multifarious Evolutionary Pathways of a Nuclear RNA Editing Factor: Disjunctions in Coevolution of DOT4 and Its Chloroplast Target rpoC1eU488SL.}, journal = {Genome biology and evolution}, volume = {11}, number = {3}, pages = {798-813}, pmid = {30753430}, issn = {1759-6653}, mesh = {Arabidopsis Proteins/*genetics ; *Biological Coevolution ; Chloroplast Proteins/*genetics ; Chloroplasts/metabolism ; *Evolution, Molecular ; Magnoliopsida/*genetics/metabolism ; *RNA Editing ; RNA-Binding Proteins/*genetics ; }, abstract = {Nuclear-encoded pentatricopeptide repeat (PPR) proteins are site-specific factors for C-to-U RNA editing in plant organelles coevolving with their targets. Losing an editing target by C-to-T conversion allows for eventual loss of its editing factor, as recently confirmed for editing factors CLB19, CRR28, and RARE1 targeting ancient chloroplast editing sites in flowering plants. Here, we report on alternative evolutionary pathways for DOT4 addressing rpoC1eU488SL, a chloroplast editing site in the RNA polymerase β' subunit mRNA. Upon loss of rpoC1eU488SL by C-to-T conversion, DOT4 got lost multiple times independently in angiosperm evolution with intermediate states of DOT4 orthologs in various stages of degeneration. Surprisingly, we now also observe degeneration and loss of DOT4 despite retention of a C in the editing position (in Carica, Coffea, Vicia, and Spirodela). We find that the cytidine remains unedited, proving that DOT4 was not replaced by another editing factor. Yet another pathway of DOT4 evolution is observed among the Poaceae. Although the rpoC1eU488SL edit has been lost through C-to-T conversion, DOT4 orthologs not only remain conserved but also have their array of PPRs extended by six additional repeats. Here, the loss of the ancient target has likely allowed DOT4 to adapt for a new function. We suggest rps3 antisense transcripts as previously demonstrated in barley (Hordeum vulgare) arising from promotor sequences newly emerging in the rpl16 intron of Poaceae as a new candidate target for the extended PPR stretch of DOT4. Altogether, DOT4 and its target show more flexible pathways for evolution than the previously explored editing factors CLB19, CRR28, and RARE1. Certain plant clades (e.g., Amaranthus, Vaccinium, Carica, the Poaceae, Fabales, and Caryophyllales) show pronounced dynamics in the evolution of editing sites and corresponding factors.}, }
@article {pmid30745292, year = {2019}, author = {Biebl, MM and Buchner, J}, title = {Structure, Function, and Regulation of the Hsp90 Machinery.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {11}, number = {9}, pages = {}, pmid = {30745292}, issn = {1943-0264}, mesh = {Adenosine Triphosphatases/metabolism ; Animals ; Binding Sites ; Cytosol/*metabolism ; Databases, Protein ; Evolution, Molecular ; *Gene Expression Regulation ; HSP90 Heat-Shock Proteins/*metabolism ; Humans ; Membrane Glycoproteins/metabolism ; Mental Disorders/metabolism ; Mice ; Mitochondria/metabolism ; Molecular Chaperones/*metabolism ; Neurodegenerative Diseases/metabolism ; Peptides/chemistry ; Protein Domains ; Protein Isoforms ; Proteostasis ; }, abstract = {Heat shock protein 90 (Hsp90) is a molecular chaperone involved in the maturation of a plethora of substrates ("clients"), including protein kinases, transcription factors, and E3 ubiquitin ligases, positioning Hsp90 as a central regulator of cellular proteostasis. Hsp90 undergoes large conformational changes during its ATPase cycle. The processing of clients by cytosolic Hsp90 is assisted by a cohort of cochaperones that affect client recruitment, Hsp90 ATPase function or conformational rearrangements in Hsp90. Because of the importance of Hsp90 in regulating central cellular pathways, strategies for the pharmacological inhibition of the Hsp90 machinery in diseases such as cancer and neurodegeneration are being developed. In this review, we summarize recent structural and mechanistic progress in defining the function of organelle-specific and cytosolic Hsp90, including the impact of individual cochaperones on the maturation of specific clients and complexes with clients as well as ways of exploiting Hsp90 as a drug target.}, }
@article {pmid30742851, year = {2019}, author = {Teng, H and Wang, D and Lu, J and Zhou, Y and Pang, Y and Li, Q}, title = {Novel insights into the evolution of the caveolin superfamily and mechanisms of antiapoptotic effects and cell proliferation in lamprey.}, journal = {Developmental and comparative immunology}, volume = {95}, number = {}, pages = {118-128}, doi = {10.1016/j.dci.2019.01.005}, pmid = {30742851}, issn = {1879-0089}, mesh = {Animals ; Apoptosis/genetics/immunology ; Apoptosis Regulatory Proteins/genetics/*immunology ; Caspase 3/metabolism ; Caveolin 1/genetics/*immunology ; Cell Proliferation/genetics ; Cytochromes c/metabolism ; *Evolution, Molecular ; Female ; Fish Proteins/genetics/*immunology ; HeLa Cells ; Humans ; Lampreys/*physiology ; Male ; Mitochondria/immunology/metabolism ; Signal Transduction/immunology ; }, abstract = {Caveolin-1 is the main structural and functional component of caveolin, and it is involved in the regulation of cholesterol transport, endocytosis, and signal transduction. Moreover, changes in caveolin-1 play an important role in tumorigenesis and inflammatory processes. Previous studies have demonstrated that human caveolin-1 is mainly located in the cell membrane and exhibits cell type- and stage-dependent functional differences during cancer development and inflammatory responses. However, the role of Lamprey-caveolin-like (L-caveolin-like) in lamprey remained unknown. Here, we demonstrated that L-caveolin-like performs anti-inflammation and oncogenic functions and the function of caveolin-1 diverged during vertebrate evolution. Moreover, the results reveal the mechanism underlying the antiapoptotic effects of L-caveolin-like. An L-caveolin-like gene from Lampetra japonica (L. japonica) was identified and characterized. L-Caveolin-like was primarily distributed in the leukocytes, intestines and supraneural bodies (Sp-bodies) immune organs as indicated by Q-PCR and immunohistochemistry assays. The mRNA and protein expression levels of L-caveolin exhibited consistent increases in expression at 2 and 72 h in adult tissues after exposure to lipopolysaccharide (LPS) and in leukocytes stimulated by Vibrio anguillarum (V. anguillarum), Staphylococcus aureus (S. aureus), and Poly I:C. Furthermore, the overexpression of pEGFP-N1-L-caveolin-like was associated with a distinct localization in mitochondria, with decreased cytochrome C (Cyt C) and mitochondrial Cyt C oxidase subunit I (CO I) expression. In addition, increased cellular ATP levels suggested that this protein prevented mitochondrial damage. The overexpression of pEGFP-N1-L-caveolin-like led to the altered expression of factors related to apoptosis, such as decreased Caspase-9, Caspase-3, p53, and Bax expression and increased Bcl-2 expression. In addition, the overexpression of pEGFP-N1-L-caveolin-like promoted cell proliferation associated with upregulated EGF, bFGF, and PDGFB expression. Together, these findings indicated that the L-caveolin-like protein from L. japonica induced the activation of antiapoptotic effects via the mitochondrial Cyt C-mediated Caspase-3 signaling pathway. Our analysis further suggests that L-caveolin-like is an oncogene protein product and anti-inflammatory molecule from lamprey that evolved early in vertebrate evolution.}, }
@article {pmid30740458, year = {2019}, author = {Oborník, M}, title = {In the beginning was the word: How terminology drives our understanding of endosymbiotic organelles.}, journal = {Microbial cell (Graz, Austria)}, volume = {6}, number = {2}, pages = {134-141}, pmid = {30740458}, issn = {2311-2638}, abstract = {The names we give objects of research, to some extent, predispose our ways of thinking about them. Misclassifications of Oomycota, Microsporidia, Myxosporidia, and Helicosporidia have obviously affected not only their formal taxonomic names, but also the methods and approaches with which they have been investigated. Therefore, it is important to name biological entities with accurate terms in order to avoid discrepancies in researching them. The endosymbiotic origin of mitochondria and plastids is now the most accepted scenario for their evolution. Since it is apparent that there is no natural definitive border between bacteria and semiautonomous organelles, I propose that mitochondria and plastids should be called bacteria and classified accordingly, in the bacterial classification system. I discuss some consequences of this approach, including: i) the resulting "changes" in the abundances of bacteria, ii) the definitions of terms like microbiome or multicellularity, and iii) the concept of endosymbiotic domestication.}, }
@article {pmid30740457, year = {2019}, author = {Gruber, A}, title = {What's in a name? How organelles of endosymbiotic origin can be distinguished from endosymbionts.}, journal = {Microbial cell (Graz, Austria)}, volume = {6}, number = {2}, pages = {123-133}, pmid = {30740457}, issn = {2311-2638}, abstract = {Mitochondria and plastids evolved from free-living bacteria, but are now considered integral parts of the eukaryotic species in which they live. Therefore, they are implicitly called by the same eukaryotic species name. Historically, mitochondria and plastids were known as "organelles", even before their bacterial origin became fully established. However, since organelle evolution by endosymbiosis has become an established theory in biology, more and more endosymbiotic systems have been discovered that show various levels of host/symbiont integration. In this context, the distinction between "host/symbiont" and "eukaryote/organelle" systems is currently unclear. The criteria that are commonly considered are genetic integration (via gene transfer from the endosymbiont to the nucleus), cellular integration (synchronization of the cell cycles), and metabolic integration (the mutual dependency of the metabolisms). Here, I suggest that these criteria should be evaluated according to the resulting coupling of genetic recombination between individuals and congruence of effective population sizes, which determines if independent speciation is possible for either of the partners. I would like to call this aspect of integration "sexual symbiont integration". If the partners lose their independence in speciation, I think that they should be considered one species. The partner who maintains its genetic recombination mechanisms and life cycle should then be the name giving "host"; the other one would be the organelle. Distinguishing between organelles and symbionts according to their sexual symbiont integration is independent of any particular mechanism or structural property of the endosymbiont/host system under investigation.}, }
@article {pmid30738095, year = {2019}, author = {Gong, L and Jiang, H and Zhu, K and Lu, X and Liu, L and Liu, B and Jiang, L and Ye, Y and Lü, Z}, title = {Large-scale mitochondrial gene rearrangements in the hermit crab Pagurus nigrofascia and phylogenetic analysis of the Anomura.}, journal = {Gene}, volume = {695}, number = {}, pages = {75-83}, doi = {10.1016/j.gene.2019.01.035}, pmid = {30738095}, issn = {1879-0038}, mesh = {Animals ; Anomura/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Gene Rearrangement/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; *Phylogeny ; }, abstract = {Complete mitochondrial genome (mitogenome) provides important information for better understanding of gene rearrangement, molecular evolution and phylogenetic analysis. Currently, only a few Paguridae mitogenomes have been reported. Herein, we described the complete mitogenome of hermit crab Pagurus nigrofascia. The total length was 15,423 bp, containing 13 protein-coding genes (PCGs), two ribosomal RNA, 22 transfer RNA genes, as well as an AT-rich region. The genome composition was highly A + T biased (71.4%), and exhibited a negative AT-skew (-0.006) and GC-skew (-0.138). Eight tRNA genes, two PCGs and an AT-rich region found to be rearranged with respect to the pancrustacean ground pattern gene order. Duplication-random loss and recombination model were adopted to explain the large-scale gene rearrangement events. Two phylogenetic trees of Anomura involving 12 families were constructed. The results showed that all Paguridae species were clustered into one clade except Pagurus longicarpus, which for the first time imposed raises doubt about the morphological taxonomy of this species. Furthermore, the present study found that higher- level phylogenetic relationships within Anomura were controversial, compared with the previous studies. Our results help to better understand gene rearrangements and the evolutionary status of P. nigrofascia and lay foundation for further phylogenetic study of Anomura.}, }
@article {pmid30736942, year = {2019}, author = {Hrazdilová, K and Myśliwy, I and Hildebrand, J and Buńkowska-Gawlik, K and Janaczyk, B and Perec-Matysiak, A and Modrý, D}, title = {Paralogs vs. genotypes? Variability of Babesia canis assessed by 18S rDNA and two mitochondrial markers.}, journal = {Veterinary parasitology}, volume = {266}, number = {}, pages = {103-110}, doi = {10.1016/j.vetpar.2018.12.017}, pmid = {30736942}, issn = {1873-2550}, mesh = {Animals ; Babesia/*genetics ; Babesiosis/blood/diagnosis/parasitology ; Cohort Studies ; DNA, Protozoan/genetics ; Dog Diseases/diagnosis/parasitology ; Dogs ; Europe ; Genetic Markers ; *Genetic Variation ; Genome, Protozoan ; *Genotype ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; }, abstract = {Canine babesiosis caused by Babesia canis sensu stricto became an emerging disease of dogs across Europe calling for attention also in countries where it was an only rare imported disease. An easy accessibility of molecular methods and the growing amount of sequencing data led to the description of intraspecific variability in 18S rDNA sequences designated as "genotypes". Using material from a homogenous cohort of dogs with microscopically confirmed canine babesiosis caused by B. canis, we evaluated Babesia intraspecific variability and amplification sensitivity of three different genes (18S rDNA, COI, Cytb) to assess their potential as diagnostic or phylogenetic markers. In raw sequencing data obtained, we observed at least 3 ambiguous positions in up to 86% of chromatograms within the ∼560 bp fragment of 18S rDNA suggesting the existence of several, not identical copies of this gene. Our COI haplotype analysis resulted in a star-like pattern indicating a recent origin of most haplotypes, but not supporting the existence of two dominant haplotypes. Similarly, the Cytb sequences obtained from samples with all variants of 18S rDNA were identical. We corroborate previous observations from three other European countries and bring the evidence of the existence of 18S rDNA paralogs in B. canis genome replacing currently used "genotype" theory.}, }
@article {pmid30731120, year = {2019}, author = {Brunes, TO and da Silva, AJ and Marques-Souza, S and Rodrigues, MT and Pellegrino, KCM}, title = {Not always young: The first vertebrate ancient origin of true parthenogenesis found in an Amazon leaf litter lizard with evidence of mitochondrial haplotypes surfing on the wave of a range expansion.}, journal = {Molecular phylogenetics and evolution}, volume = {135}, number = {}, pages = {105-122}, doi = {10.1016/j.ympev.2019.01.023}, pmid = {30731120}, issn = {1095-9513}, mesh = {Alleles ; Animals ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Ecosystem ; Haplotypes/*genetics ; Hybridization, Genetic ; Lizards/*genetics ; Male ; Mitochondria/*genetics ; Parthenogenesis/*genetics ; Phylogeny ; Phylogeography ; Plant Leaves/*physiology ; }, abstract = {In vertebrates, true parthenogenesis is found only in squamate reptiles and (mostly) originates via interspecific hybridization after secondary contact. In many cases, parthenogenesis is followed by an increase of ploidy, resulting in triploid lineages. Phylogenetic analyses derived from nuclear and maternally inherited markers can help to clarify the mechanisms of origin and the potential parental species involved. In the Amazon region, parthenogenetic lizards of the Loxopholis percarinatum complex are widely distributed, comprising both diploid and triploid clones. Recently, putative males of L. percarinatum were reported, suggesting the existence of bisexual populations based on morphological data. Here, we used mitochondrial and nuclear data to investigate the origin of parthenogenesis in Loxopholis. Mitochondrial DNA analysis revealed three major lineages: unisexual/2n, unisexual/3n and bisexual, the last of which comprised two sub-lineages placed as the sister taxon to the unisexual/3n lineage. Genetic divergence among the lineages was ∼10% but was lower between the unisexual/3n and bisexual lineages (∼6%). Both mtDNA and nuDNA indicated that individuals from the bisexual lineages might belong to a new species. Nuclear DNA evidence indicates that crossings occasionally occur between unisexual 2n and males from the new bisexual species. Phylogenetic analysis of nuDNA showed L. ferreirai as the closest described bisexual species to the complex. Our results revealed an ancient origin of parthenogenesis in the L. percarinatum complex, in contrast to most young (Pleistocene) parthenogenetic lizards described thus far. Two hybridization events seem to have been involved: the first event occurred in late Miocene, between the ancestral lineage ("A") of the new bisexual species (as a maternal species) and the ancestral lineage of L. ferreirai, as a paternal species of L. percarinatum 2n; and the second event occurred in Pliocene-Pleistocene, in a backcross between L. percarinatum 2n and a male from the common ancestor ("B") of the new bisexual species giving rise to the lineage of L. percarinatum 3n. With these results, we showed that L. percarinatum complex also includes, at least, one undescribed bisexual species in addition to the two known parthenogenetic lineages (2n and 3n). Finally, we present evidence that diploid individuals of L. percarinatum experienced an event of wide demographic expansion over the past million years under an allele surfing model.}, }
@article {pmid30729162, year = {2019}, author = {Li, XC and Peris, D and Hittinger, CT and Sia, EA and Fay, JC}, title = {Mitochondria-encoded genes contribute to evolution of heat and cold tolerance in yeast.}, journal = {Science advances}, volume = {5}, number = {1}, pages = {eaav1848}, pmid = {30729162}, issn = {2375-2548}, support = {R01 GM080669/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Base Sequence ; Cold Temperature ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; *Genes, Mitochondrial ; *Genome, Mitochondrial ; Hot Temperature ; Phenotype ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; Thermotolerance/*genetics ; }, abstract = {Genetic analysis of phenotypic differences between species is typically limited to interfertile species. Here, we conducted a genome-wide noncomplementation screen to identify genes that contribute to a major difference in thermal growth profile between two reproductively isolated yeast species, Saccharomyces cerevisiae and Saccharomyces uvarum. The screen identified only a single nuclear-encoded gene with a moderate effect on heat tolerance, but, in contrast, revealed a large effect of mitochondrial DNA (mitotype) on both heat and cold tolerance. Recombinant mitotypes indicate that multiple genes contribute to thermal divergence, and we show that protein divergence in COX1 affects both heat and cold tolerance. Our results point to the yeast mitochondrial genome as an evolutionary hotspot for thermal divergence.}, }
@article {pmid30728898, year = {2019}, author = {Speirs, MMP and Swensen, AC and Chan, TY and Jones, PM and Holman, JC and Harris, MB and Maschek, JA and Cox, JE and Carson, RH and Hill, JT and Andersen, JL and Prince, JT and Price, JC}, title = {Imbalanced sphingolipid signaling is maintained as a core proponent of a cancerous phenotype in spite of metabolic pressure and epigenetic drift.}, journal = {Oncotarget}, volume = {10}, number = {4}, pages = {449-479}, pmid = {30728898}, issn = {1949-2553}, abstract = {Tumor heterogeneity may arise through genetic drift and environmentally driven clonal selection for metabolic fitness. This would promote subpopulations derived from single cancer cells that exhibit distinct phenotypes while conserving vital pro-survival pathways. We aimed to identify significant drivers of cell fitness in pancreatic adenocarcinoma (PDAC) creating subclones in different nutrient formulations to encourage differential metabolic reprogramming. The genetic and phenotypic expression profiles of each subclone were analyzed relative to a healthy control cell line (hTert-HPNE). The subclones exhibited distinct variations in protein expression and lipid metabolism. Relative to hTert-HPNE, PSN-1 subclones uniformly maintained modified sphingolipid signaling and specifically retained elevated sphingosine-1-phosphate (S1P) relative to C16 ceramide (C16 Cer) ratios. Each clone utilized a different perturbation to this pathway, but maintained this modified signaling to preserve cancerous phenotypes, such as rapid proliferation and defense against mitochondria-mediated apoptosis. Although the subclones were unique in their sensitivity, inhibition of S1P synthesis significantly reduced the ratio of S1P/C16 Cer, slowed cell proliferation, and enhanced sensitivity to apoptotic signals. This reliance on S1P signaling identifies this pathway as a promising drug-sensitizing target that may be used to eliminate cancerous cells consistently across uniquely reprogrammed PDAC clones.}, }
@article {pmid30721704, year = {2019}, author = {Lariccia, V and Macrì, ML and Matteucci, A and Maiolino, M and Amoroso, S and Magi, S}, title = {Effects of ticagrelor on the sodium/calcium exchanger 1 (NCX1) in cardiac derived H9c2 cells.}, journal = {European journal of pharmacology}, volume = {850}, number = {}, pages = {158-166}, doi = {10.1016/j.ejphar.2019.01.067}, pmid = {30721704}, issn = {1879-0712}, mesh = {Calcium/metabolism ; Cell Line ; Cell Survival/drug effects ; Gene Expression Regulation/drug effects ; Humans ; Intracellular Space/drug effects/metabolism ; Mitochondria/drug effects/metabolism ; Myocytes, Cardiac/cytology/*drug effects/*metabolism ; Protein Transport/drug effects ; Sodium-Calcium Exchanger/*antagonists &amp; inhibitors/metabolism ; Ticagrelor/*pharmacology ; }, abstract = {Ticagrelor is a direct acting and reversibly binding P2Y12 antagonist approved for the prevention of thromboembolic events. Clinical effects of ticagrelor cannot be simply accounted for by pure platelet inhibition, and off-target mechanisms can potentially play a role. In particular, recent evidence suggests that ticagrelor may also influence heart function and improve the evolution of myocardial ischemic injury by more direct effects on myocytes. The cardiac sodium/calcium exchanger 1 (NCX1) is a critical player in the generation and control of calcium (Ca[2+]) signals, which orchestrate multiple myocyte activities in health and disease. Altered expression and/or activity of NCX1 can have profound consequences for the function and fate of myocytes. Whether ticagrelor affects cardiac NCX1 has not been investigated yet. To explore this hypothesis, we analyzed the expression, localization and activity of NCX1 in the heart derived H9c2-NCX1 cells following ticagrelor exposure. We found that ticagrelor concentration- and time-dependently reduced the activity of the cardiac NCX1 in H9c2 cells. In particular, the inhibitory effect of ticagrelor on the Ca[2+]-influx mode of NCX1 was evident within 1 h and further developed after 24 h, when NCX1 activity was suppressed by about 55% in cells treated with 1 μM ticagrelor. Ticagrelor-induced inhibition of exchanger activity was reached at clinically relevant concentrations, without affecting the expression levels and subcellular distribution of NCX1. Collectively, these findings suggest that cardiac NCX1 is a new downstream target of ticagrelor, which may contribute to the therapeutic profile of ticagrelor in clinical practice.}, }
@article {pmid30703747, year = {2019}, author = {Gerosa, C and Fanni, D and Congiu, T and Piras, M and Cau, F and Moi, M and Faa, G}, title = {Liver pathology in Wilson's disease: From copper overload to cirrhosis.}, journal = {Journal of inorganic biochemistry}, volume = {193}, number = {}, pages = {106-111}, doi = {10.1016/j.jinorgbio.2019.01.008}, pmid = {30703747}, issn = {1873-3344}, mesh = {Copper/*metabolism ; Copper-Transporting ATPases/genetics/metabolism ; Epigenesis, Genetic ; Hepatolenticular Degeneration/drug therapy/*pathology ; Humans ; Liver/*pathology ; Liver Cirrhosis/drug therapy ; Mitochondria/metabolism/pathology ; Mutation ; Penicillamine/therapeutic use ; }, abstract = {Wilson's disease (WD) is a genetic metabolic disease strictly associated with liver cirrhosis. In this review, the genetic bases of the disease are discussed, with emphasis on the role of ATP7B (the Wilson disease protein) dysfunction as a determinant factor of systemic copper overload. Regarding the different multiple mutations described in WD patients, the peculiarity of Sardinian population is highlighted, Sardinians carrying a rare deletion in the promoter (5' UTR) of the WD gene. The role of epigenetic changes in the clinical presentation and evolution of liver disease in WD patients is also discussed, nutrition probably representing a relevantly risk factor in WD patients. The role of transmission electron microscopy in the diagnosis of WD-related liver disease is underlined. Mitochondrial changes, increased peroxisomes fat droplets, lipolysosomes and intranuclear glycogen inclusions are reported as the most frequent ultrastructural changes in the liver of WD carriers. The role of histochemical stains for copper is analyzed, and the Timm's method is suggested as the most sensitive one for revealing hepatic copper overload in all stage of WD. The marked variability of the histological liver changes occurring in WD is underlined simple steatosis may represent the only pathological changes, frequently associated with glycogenated nuclei. Mallory-Denk bodies lipogranulomas alcoholic and non-alcoholic fatty liver disease ending with bridging fibrosis and cirrhosis. Finally, the reversal of fibrosis as a possible therapeutic objective in WD is discussed.}, }
@article {pmid30700787, year = {2019}, author = {Rusu, I and Modi, A and Radu, C and Mircea, C and Vulpoi, A and Dobrinescu, C and Bodolică, V and Potârniche, T and Popescu, O and Caramelli, D and Kelemen, B}, title = {Mitochondrial ancestry of medieval individuals carelessly interred in a multiple burial from southeastern Romania.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {961}, pmid = {30700787}, issn = {2045-2322}, mesh = {Archaeology ; Bone and Bones/metabolism ; Burial/*history ; DNA, Mitochondrial/genetics ; Female ; Genetics, Population ; Genome, Human ; Genome, Mitochondrial ; Geography ; Haplotypes/genetics ; History, Medieval ; Humans ; Male ; Mitochondria/*genetics ; *Phylogeny ; Romania ; }, abstract = {The historical province of Dobruja, located in southeastern Romania, has experienced intense human population movement, invasions, and conflictual episodes during the Middle Ages, being an important intersection point between Asia and Europe. The most informative source of maternal population histories is the complete mitochondrial genome of archaeological specimens, but currently, there is insufficient ancient DNA data available for the medieval period in this geographical region to complement the archaeological findings. In this study, we reconstructed, by using Next Generation Sequencing, the entire mitochondrial genomes (mitogenomes) of six medieval individuals neglectfully buried in a multiple burial from Capidava necropolis (Dobruja), some presenting signs of a violent death. Six distinct maternal lineages (H11a1, U4d2, J1c15, U6a1a1, T2b, and N1a3a) with different phylogenetic background were identified, pointing out the heterogeneous genetic aspect of the analyzed medieval group. Using population genetic analysis based on high-resolution mitochondrial data, we inferred the genetic affinities of the available medieval dataset from Capidava to other ancient Eurasian populations. The genetic data were integrated with the archaeological and anthropological information in order to sketch a small, local piece of the mosaic that is the image of medieval European population history.}, }
@article {pmid30698742, year = {2019}, author = {Noutahi, E and Calderon, V and Blanchette, M and El-Mabrouk, N and Lang, BF}, title = {Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes.}, journal = {Molecular biology and evolution}, volume = {36}, number = {4}, pages = {766-783}, pmid = {30698742}, issn = {1537-1719}, mesh = {Chlorophyta/*genetics ; *Evolution, Molecular ; *Genetic Code ; *Genome, Mitochondrial ; Phylogeny ; RNA, Transfer/genetics ; }, abstract = {Genetic code deviations involving stop codons have been previously reported in mitochondrial genomes of several green plants (Viridiplantae), most notably chlorophyte algae (Chlorophyta). However, as changes in codon recognition from one amino acid to another are more difficult to infer, such changes might have gone unnoticed in particular lineages with high evolutionary rates that are otherwise prone to codon reassignments. To gain further insight into the evolution of the mitochondrial genetic code in green plants, we have conducted an in-depth study across mtDNAs from 51 green plants (32 chlorophytes and 19 streptophytes). Besides confirming known stop-to-sense reassignments, our study documents the first cases of sense-to-sense codon reassignments in Chlorophyta mtDNAs. In several Sphaeropleales, we report the decoding of AGG codons (normally arginine) as alanine, by tRNA(CCU) of various origins that carry the recognition signature for alanine tRNA synthetase. In Chromochloris, we identify tRNA variants decoding AGG as methionine and the synonymous codon CGG as leucine. Finally, we find strong evidence supporting the decoding of AUA codons (normally isoleucine) as methionine in Pycnococcus. Our results rely on a recently developed conceptual framework (CoreTracker) that predicts codon reassignments based on the disparity between DNA sequence (codons) and the derived protein sequence. These predictions are then validated by an evaluation of tRNA phylogeny, to identify the evolution of new tRNAs via gene duplication and loss, and structural modifications that lead to the assignment of new tRNA identities and a change in the genetic code.}, }
@article {pmid30698308, year = {2019}, author = {El-Sheikh, RM and Mansy, SS and Nessim, IG and Hosni, HN and El Hindawi, A and Hassanein, MH and AbdelFattah, AS}, title = {Carbamoyl phosphate synthetase 1 (CPS1) as a prognostic marker in chronic hepatitis C infection.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {127}, number = {2}, pages = {93-105}, doi = {10.1111/apm.12917}, pmid = {30698308}, issn = {1600-0463}, support = {100//Theodor Bilharz Research Institute (TBRI)/ ; }, mesh = {Adult ; Aged ; Biomarkers/blood ; Carbamoyl-Phosphate Synthase (Ammonia)/*blood ; Female ; Hepatitis C, Chronic/mortality/*pathology ; Humans ; Liver/pathology ; Liver Cirrhosis/*pathology ; Male ; Middle Aged ; Mitochondria/*pathology/ultrastructure ; Prognosis ; Urea/blood ; }, abstract = {This study aims to assess the value of carbamoyl phosphate synthetase 1 (CPS1), as a non-invasive serum marker, for the evolution of chronic HCV infection and hepatic fibrosis. Seventy-two patients with HCV positive serum RNA and 15 health volunteers were enrolled in this study. Out of 72 patients, 10 patients had decompensated liver with ascites. Quantitative analysis of CPS1 was performed in the harvested sera and corresponding liver biopsies using ELISA and immunohistochemistry techniques respectively. Also, mitochondrial count using electron microscopy, urea analysis and conventional liver tests were done. Patients were grouped into (F1 + F2) and (F3 + F4) representing stages of moderate and severe fibrosis respectively. Tissue and serum CPS1 (s.CPS1) correlated significantly in moderate and severe fibrosis. Patients with severe fibrosis showed significantly higher levels of s.CPS1 (p-value ≤ 0.05) and significantly lower mitochondrial counts (p-value = 0.0065) than those with moderate fibrosis. S.urea positively correlated with s.CPS1 only in the decompensated group, at which s.urea reached maximal levels. In conclusion, s.CPS1 is a potential non-invasive marker for the assessment of severity and progression of HCV in relation to mitochondrial dysfunction. Also, increased s.urea with the progression of the disease is mainly due to a concurrent renal malfunction, which needs further investigation.}, }
@article {pmid30670662, year = {2019}, author = {Bloomfield, G and Paschke, P and Okamoto, M and Stevens, TJ and Urushihara, H}, title = {Triparental inheritance in Dictyostelium.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {6}, pages = {2187-2192}, pmid = {30670662}, issn = {1091-6490}, support = {MC_U105115237/MRC_/Medical Research Council/United Kingdom ; MC_U105178783/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Sex promotes the recombination and reassortment of genetic material and is prevalent across eukaryotes, although our knowledge of the molecular details of sexual inheritance is scant in several major lineages. In social amoebae, sex involves a promiscuous mixing of cytoplasm before zygotes consume the majority of cells, but for technical reasons, sexual progeny have been difficult to obtain and study. We report here genome-wide characterization of meiotic progeny in Dictyostelium discoideum We find that recombination occurs at high frequency in pairwise crosses between all three mating types, despite the absence of the Spo11 enzyme that is normally required to initiate crossover formation. Fusions of more than two gametes to form transient syncytia lead to frequent triparental inheritance, with haploid meiotic progeny bearing recombined nuclear haplotypes from two parents and the mitochondrial genome from a third. Cells that do not contribute genetically to the Dictyostelium zygote nucleus thereby have a stake in the next haploid generation. D. discoideum mitochondrial genomes are polymorphic, and our findings raise the possibility that some of this variation might be a result of sexual selection on genes that can promote the spread of individual organelle genomes during sex. This kind of self-interested mitochondrial behavior may have had important consequences during eukaryogenesis and the initial evolution of sex.}, }
@article {pmid30668797, year = {2019}, author = {Backes, S and Garg, SG and Becker, L and Peleh, V and Glockshuber, R and Gould, SB and Herrmann, JM}, title = {Development of the Mitochondrial Intermembrane Space Disulfide Relay Represents a Critical Step in Eukaryotic Evolution.}, journal = {Molecular biology and evolution}, volume = {36}, number = {4}, pages = {742-756}, doi = {10.1093/molbev/msz011}, pmid = {30668797}, issn = {1537-1719}, mesh = {*Biological Evolution ; Cell Respiration ; Disulfides ; Escherichia coli ; Eukaryota/*genetics/metabolism ; Glutathione/metabolism ; Glycoproteins/metabolism ; Mitochondria/*enzymology ; Mitochondrial Membrane Transport Proteins/genetics/*metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/genetics/metabolism ; Organelle Biogenesis ; Oxidation-Reduction ; Oxidoreductases Acting on Sulfur Group Donors/genetics/metabolism ; Protein Disulfide-Isomerases/metabolism ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Thioredoxins/metabolism ; }, abstract = {The mitochondrial intermembrane space evolved from the bacterial periplasm. Presumably as a consequence of their common origin, most proteins of these compartments are stabilized by structural disulfide bonds. The molecular machineries that mediate oxidative protein folding in bacteria and mitochondria, however, appear to share no common ancestry. Here we tested whether the enzymes Erv1 and Mia40 of the yeast mitochondrial disulfide relay could be functionally replaced by corresponding components of other compartments. We found that the sulfhydryl oxidase Erv1 could be replaced by the Ero1 oxidase or the protein disulfide isomerase from the endoplasmic reticulum, however at the cost of respiration deficiency. In contrast to Erv1, the mitochondrial oxidoreductase Mia40 proved to be indispensable and could not be replaced by thioredoxin-like enzymes, including the cytoplasmic reductase thioredoxin, the periplasmic dithiol oxidase DsbA, and Pdi1. From our studies we conclude that the profound inertness against glutathione, its slow oxidation kinetics and its high affinity to substrates renders Mia40 a unique and essential component of mitochondrial biogenesis. Evidently, the development of a specific mitochondrial disulfide relay system represented a crucial step in the evolution of the eukaryotic cell.}, }
@article {pmid30650145, year = {2019}, author = {Tomiyama, T and Goto, K and Tanaka, Y and Maruta, T and Ogawa, T and Sawa, Y and Ito, T and Ishikawa, T}, title = {A major isoform of mitochondrial trans-2-enoyl-CoA reductase is dispensable for wax ester production in Euglena gracilis under anaerobic conditions.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0210755}, pmid = {30650145}, issn = {1932-6203}, mesh = {Anaerobiosis ; Esters/metabolism ; Euglena gracilis/*enzymology/genetics ; Fatty Acids/metabolism ; Fermentation ; Gene Knockdown Techniques ; Isoenzymes/antagonists &amp; inhibitors/genetics/metabolism ; Metabolome ; Metabolomics ; Mitochondria/enzymology ; Oxidoreductases Acting on CH-CH Group Donors/antagonists &amp; inhibitors/genetics/*metabolism ; Waxes/metabolism ; }, abstract = {Under anaerobic conditions, Euglena gracilis produces a large amount of wax ester through mitochondrial fatty acid synthesis from storage polysaccharides termed paramylon, to generate ATP. Trans-2-enoyl-CoA reductases (TERs) in mitochondria have been considered to play a key role in this process, because the enzymes catalyze the reduction of short chain length CoA-substrates (such as crotonyl-CoA). A TER enzyme (EgTER1) has been previously identified and enzymologically characterized; however, its physiological significance remained to be evaluated by genetic analysis. We herein generated EgTER1-knockdown Euglena cells, in which total crotonyl-CoA reductase activity was decreased to 10% of control value. Notably, the knockdown cells showed a severe bleaching phenotype with deficiencies in chlorophylls and glycolipids, but grew normally under heterotrophic conditions (with glucose supplementation). Moreover, the knockdown cells accumulated much greater quantities of wax ester than control cells before and after transfer to anaerobic conditions, which was accompanied by a large metabolomic change. Furthermore, we failed to find any contribution of other potential TER genes in wax ester production. Our findings propose a novel role of EgTER1 in the greening process and demonstrate that this enzyme is dispensable for wax ester production under anaerobic conditions.}, }
@article {pmid30649994, year = {2019}, author = {Kraft, LM and Lackner, LL}, title = {A conserved mechanism for mitochondria-dependent dynein anchoring.}, journal = {Molecular biology of the cell}, volume = {30}, number = {5}, pages = {691-702}, pmid = {30649994}, issn = {1939-4586}, support = {R01 GM120303/GM/NIGMS NIH HHS/United States ; T32 GM008061/GM/NIGMS NIH HHS/United States ; }, mesh = {Cell Membrane/metabolism ; Conserved Sequence ; Dyneins/*metabolism ; Meiosis ; Membrane Lipids/metabolism ; Mitochondria/*metabolism ; Protein Binding ; Protein Domains ; Saccharomyces cerevisiae/metabolism ; Schizosaccharomyces/metabolism ; Schizosaccharomyces pombe Proteins/chemistry/metabolism ; }, abstract = {Mitochondrial anchors have functions that extend beyond simply positioning mitochondria. In budding yeast, mitochondria drive the assembly of the mitochondrial anchor protein Num1 into clusters, which serve to anchor mitochondria as well as dynein to the cell cortex. Here, we explore a conserved role for mitochondria in dynein anchoring by examining the tethering functions of the evolutionarily distant Schizosaccharomyces pombe Num1 homologue. In addition to its function in dynein anchoring, we find that S. pombe Num1, also known as Mcp5, interacts with and tethers mitochondria to the plasma membrane in S. pombe and Saccharomyces cerevisiae. Thus, the mitochondria and plasma membrane-binding domains of the Num1 homologues, as well as the membrane features these domains recognize, are conserved. In S. pombe, we find that mitochondria impact the assembly and cellular distribution of Num1 clusters and that Num1 clusters actively engaged in mitochondrial tethering serve as cortical attachment sites for dynein. Thus, mitochondria play a critical and conserved role in the formation and distribution of dynein-anchoring sites at the cell cortex and, as a consequence, impact dynein function. These findings shed light on an ancient mechanism of mitochondria-dependent dynein anchoring that is conserved over more than 450 million years of evolution, raising the intriguing possibility that the role mitochondria play in dynein anchoring and function extends beyond yeast to higher eukaryotes.}, }
@article {pmid30641272, year = {2019}, author = {Tang, Y and Li, C and Wanghe, K and Feng, C and Tong, C and Tian, F and Zhao, K}, title = {Convergent evolution misled taxonomy in schizothoracine fishes (Cypriniformes: Cyprinidae).}, journal = {Molecular phylogenetics and evolution}, volume = {134}, number = {}, pages = {323-337}, doi = {10.1016/j.ympev.2019.01.008}, pmid = {30641272}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Cyprinidae/*classification/genetics ; DNA, Mitochondrial/genetics ; Diet ; Genome ; Geography ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Tibet ; Time Factors ; }, abstract = {Highly specialized grade (HSG; genera Gymnocypris, Oxygymnocypris, Schizopygopsis, Platypharodon and Chuanchia) of the Schizothoracinae (Cypriniformes: Cyprinidae) are endemic to the Qinghai-Tibet Plateau (QTP). Previously, two distinct ecomorphs were recognized according to trophic traits. One was a limnetic omnivore with normal lower jaw morphology, terminal mouth, and moderate or dense gill rakers, mostly inhabiting in open water of lakes, including Gymnocypris and Oxygymnocypris. Another was a benthic feeder with inferior mouth, sparse gill rakers and sharp horny sheath on the lower jaw for scraping of attached prey off hard substrates, including Schizopygopsis, Platypharodon and Chuanchia. However, traditional taxonomy of HSG based on these trophic traits presented extensive conflicts with the molecular studies in recent years. The possible cause could be convergent evolution in morphology, retention of ancestral polymorphisms or mitochondrial introgression, but these hypotheses could not be assessed due to incomplete taxon sampling and only mitochondrial data employed in previous works. Here, we conducted the most comprehensive molecular analysis on HSG fishes to date, using four mitochondrial loci and 152,464 genome-wide SNPs, and including 21 of 24 putative species and one undescribed Schizopygopsis species. Both SNP and mtDNA trees confirmed extensive paraphyly of genera Gymnocypris and Schizopygopsis, where species often were clustered together by watershed instead of by genus. Basal split into the north clade B and the south clade C (ca. 3.03 Ma) approximately by the Tanggula-Tanitawen Mountains in SLAF tree coincided with a violent uplift of the QTP during the phase A of 'Qingzang movement' (ca. 3.6 Ma). Ancestral state reconstruction of the trophic ecomorph showed that the limnetic omnivore ecomorph had evolved repeatedly in clade B and C. Furthermore, we presented a striking case of convergent evolution between two 'subspecies' Gymnocypris chui chui and G. chui longimandibularis, which had diverged as early as two million years ago (ca. 2.42 Ma). Ecological analyses revealed that similar food utilization, particularly in zooplankton, was the main underlying driving force. This work showed an example of taxonomy with the most extensive errors at the genus/species levels due to convergent evolution and suggested that trophic traits could be misleading in fish taxonomy. Therefore, we propose a major generic revision for HSG species.}, }
@article {pmid30639162, year = {2019}, author = {López Rivero, AS and Rossi, MA and Ceccarelli, EA and Catalano-Dupuy, DL}, title = {A bacterial 2[4Fe4S] ferredoxin as redox partner of the plastidic-type ferredoxin-NADP[+] reductase from Leptospira interrogans.}, journal = {Biochimica et biophysica acta. General subjects}, volume = {1863}, number = {4}, pages = {651-660}, doi = {10.1016/j.bbagen.2019.01.004}, pmid = {30639162}, issn = {1872-8006}, mesh = {Amino Acid Sequence ; Ferredoxin-NADP Reductase/chemistry/*metabolism ; Ferredoxins/chemistry/*metabolism ; Leptospira interrogans/*enzymology ; Models, Molecular ; Oxidation-Reduction ; Phylogeny ; Protein Conformation ; Sequence Alignment ; }, abstract = {BACKGROUND: Ferredoxins are small iron-sulfur proteins that participate as electron donors in various metabolic pathways. They are recognized substrates of ferredoxin-NADP[+] reductases (FNR) in redox metabolisms in mitochondria, plastids, and bacteria. We previously found a plastidic-type FNR in Leptospira interrogans (LepFNR), a parasitic bacterium of animals and humans. Nevertheless, we did not identify plant-type ferredoxins or flavodoxins, the common partners of this kind of FNR.<br><br>METHODS: Sequence alignment, phylogenetical analyses and structural modeling were performed for the identification of a 2[4Fe4S] ferredoxin (LepFd2) as a putative redox partner of LepFNR in L. interrogans. The gene encoding LepFd2 was cloned and the protein overexpressed and purified. The functional properties of LepFd2 and LepFNR-LepFd2 complex were analyzed by kinetic and mutagenesis studies.<br><br>RESULTS: We succeeded in expressing and purifying LepFd2 with its FeS cluster properly bound. We found that LepFd2 exchanges electrons with LepFNR. Moreover, a unique structural subdomain of LepFNR (loop P75-Y91), was shown to be involved in the recognition and binding of LepFd2. This structural subdomain is not found in other FNR homologs.<br><br>CONCLUSIONS: We report for the first time a redox pair in L. interrogans in which a plastidic FNR exchanges electron with a bacterial 2[4Fe4S] ferredoxin. We characterized this reaction and proposed a model for the productive LepFNR-LepFd2 complex.<br><br>GENERAL SIGNIFICANCE: Our findings suggest that the interaction of LepFNR with the iron-sulfur protein would be different from the one previously described for the homolog enzymes. This knowledge would be useful for the design of specific LepFNR inhibitors.}, }
@article {pmid30638448, year = {2019}, author = {Phillips, CB and Tsai, CW and Tsai, MF}, title = {The conserved aspartate ring of MCU mediates MICU1 binding and regulation in the mitochondrial calcium uniporter complex.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {30638448}, issn = {2050-084X}, support = {R01 GM129345/GM/NIGMS NIH HHS/United States ; R01-GM129345/GM/NIGMS NIH HHS/United States ; }, mesh = {Aspartic Acid/*metabolism ; Biological Transport ; Calcium/metabolism ; Calcium Channels/*chemistry/*metabolism ; Calcium-Binding Proteins/*metabolism ; Cation Transport Proteins/*metabolism ; *Conserved Sequence ; Evolution, Molecular ; HEK293 Cells ; Humans ; Mitochondrial Membrane Transport Proteins/*metabolism ; Models, Biological ; Mutation/genetics ; Protein Binding ; Protein Multimerization ; Static Electricity ; Structure-Activity Relationship ; }, abstract = {The mitochondrial calcium uniporter is a Ca[2+] channel that regulates intracellular Ca[2+] signaling, oxidative phosphorylation, and apoptosis. It contains the pore-forming MCU protein, which possesses a DIME sequence thought to form a Ca[2+] selectivity filter, and also regulatory EMRE, MICU1, and MICU2 subunits. To properly carry out physiological functions, the uniporter must stay closed in resting conditions, becoming open only when stimulated by intracellular Ca[2+] signals. This Ca[2+]-dependent activation, known to be mediated by MICU subunits, is not well understood. Here, we demonstrate that the DIME-aspartate mediates a Ca[2+]-modulated electrostatic interaction with MICU1, forming an MICU1 contact interface with a nearby Ser residue at the cytoplasmic entrance of the MCU pore. A mutagenesis screen of MICU1 identifies two highly-conserved Arg residues that might contact the DIME-Asp. Perturbing MCU-MICU1 interactions elicits unregulated, constitutive Ca[2+] flux into mitochondria. These results indicate that MICU1 confers Ca[2+]-dependent gating of the uniporter by blocking/unblocking MCU.}, }
@article {pmid30636322, year = {2019}, author = {Broddrick, JT and Du, N and Smith, SR and Tsuji, Y and Jallet, D and Ware, MA and Peers, G and Matsuda, Y and Dupont, CL and Mitchell, BG and Palsson, BO and Allen, AE}, title = {Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum.}, journal = {The New phytologist}, volume = {222}, number = {3}, pages = {1364-1379}, pmid = {30636322}, issn = {1469-8137}, support = {GMBF3828//Gordon and Betty Moore Foundation/International ; JP15K16156//Japan Society for the Promotion of Science/International ; JP16H06557//Japan Society for the Promotion of Science/International ; JP17K15326//Japan Society for the Promotion of Science/International ; JP24310015//Japan Society for the Promotion of Science/International ; SP16005//Japan Society for the Promotion of Science/International ; //Edna Bailey Sussman Foundation/International ; NSF-MCB-1024913//National Science Foundation/International ; No. 1614398//National Science Foundation/International ; DE-EE0003373//US Department of Energy/International ; DE-SC0008593//US Department of Energy/International ; DE-SC0008595//US Department of Energy/International ; //Individual Special Research Fund of Kwansei Gakuin University/International ; //Promotion and Mutual Aid Corporation for Private Schools of Japan (PMAC)/International ; }, mesh = {Acclimatization/radiation effects ; Alcohol Oxidoreductases/metabolism ; Biomass ; Cell Respiration/radiation effects ; Circadian Rhythm/radiation effects ; Computer Simulation ; Diatoms/*metabolism/*radiation effects ; Electron Transport/radiation effects ; *Light ; Metabolic Networks and Pathways/radiation effects ; Mitochondria/metabolism/radiation effects ; Models, Biological ; Photosynthesis/radiation effects ; Pyruvic Acid/metabolism ; }, abstract = {Photoacclimation consists of short- and long-term strategies used by photosynthetic organisms to adapt to dynamic light environments. Observable photophysiology changes resulting from these strategies have been used in coarse-grained models to predict light-dependent growth and photosynthetic rates. However, the contribution of the broader metabolic network, relevant to species-specific strategies and fitness, is not accounted for in these simple models. We incorporated photophysiology experimental data with genome-scale modeling to characterize organism-level, light-dependent metabolic changes in the model diatom Phaeodactylum tricornutum. Oxygen evolution and photon absorption rates were combined with condition-specific biomass compositions to predict metabolic pathway usage for cells acclimated to four different light intensities. Photorespiration, an ornithine-glutamine shunt, and branched-chain amino acid metabolism were hypothesized as the primary intercompartment reductant shuttles for mediating excess light energy dissipation. Additionally, simulations suggested that carbon shunted through photorespiration is recycled back to the chloroplast as pyruvate, a mechanism distinct from known strategies in photosynthetic organisms. Our results suggest a flexible metabolic network in P. tricornutum that tunes intercompartment metabolism to optimize energy transport between the organelles, consuming excess energy as needed. Characterization of these intercompartment reductant shuttles broadens our understanding of energy partitioning strategies in this clade of ecologically important primary producers.}, }
@article {pmid30630408, year = {2019}, author = {Giannoulis, T and Plageras, D and Stamatis, C and Chatzivagia, E and Tsipourlianos, A and Birtsas, P and Billinis, C and Suchentrunk, F and Mamuris, Z}, title = {Islands and hybrid zones: combining the knowledge from "Natural Laboratories" to explain phylogeographic patterns of the European brown hare.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {17}, pmid = {30630408}, issn = {1471-2148}, mesh = {Alleles ; Animals ; DNA, Mitochondrial/genetics ; Exons/genetics ; Gene Frequency/genetics ; Genetic Variation ; Haplotypes ; Hares/*genetics ; *Hybridization, Genetic ; *Islands ; Major Histocompatibility Complex/genetics ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Phylogeny ; *Phylogeography ; }, abstract = {BACKGROUND: The aim of the study was to use hybrid populations as well as island populations of the European brown hare (Lepus europaeus) to explore the effect of evolutionary events, such as the post-deglaciation translocations, spontaneous and human-mediated, local adaptation and the genetic drift in the shaping of the phylogeographic patterns of the species. For this purpose, we used molecular markers, both nuclear and mitochondrial, that are indicative for local adaptation as well as neutral markers to elucidate the patterns of population differentiation based on geographic isolation and the clade of origin. To broaden our analysis, we included data from our previous studies concerning mainland populations, to explore the genetic differentiation in the base of the geographic origin (mainland/island) of the populations.<br><br>RESULTS: Our results suggest that local adaptation shapes the differentiation in both genomes, favoring specific alleles in nuclear genes (e.g. DQA) or haplotypes in mtDNA (e.g. Control Region, CR). mtDNA variation was found to be in a higher level and was able to give a phylogeographic signal for the populations. Furthermore, the degree of variation was influenced not only by the geographic origin, but also by the clade of origin, since specific island populations of Anatolian origin showed a greater degree of variation compared to specific mainland populations of the European clade. Concerning the hybrid population, we confirmed the existence of both clades in the territory and we provided a possible explanation for the lack of introgression between the clades.<br><br>CONCLUSION: Our results indicate that the Quaternary's climatic oscillations played a major role in the shaping of the phylogeographic patterns of the species, by isolating populations in the distinct refugia, where they adapted and differentiate in allopatry, leading to genome incompatibilities observed nowadays.}, }
@article {pmid30630407, year = {2019}, author = {Ceballos, SG and Roesti, M and Matschiner, M and Fernández, DA and Damerau, M and Hanel, R and Salzburger, W}, title = {Phylogenomics of an extra-Antarctic notothenioid radiation reveals a previously unrecognized lineage and diffuse species boundaries.}, journal = {BMC evolutionary biology}, volume = {19}, number = {1}, pages = {13}, pmid = {30630407}, issn = {1471-2148}, mesh = {Animals ; Antarctic Regions ; Base Sequence ; Calibration ; Fishes/*classification ; Genetic Loci ; Genetic Markers ; Genetic Variation ; Genome ; Haplotypes/genetics ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Phylogeography ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; }, abstract = {BACKGROUND: The impressive adaptive radiation of notothenioid fishes in Antarctic waters is generally thought to have been facilitated by an evolutionary key innovation, antifreeze glycoproteins, permitting the rapid evolution of more than 120 species subsequent to the Antarctic glaciation. By way of contrast, the second-most species-rich notothenioid genus, Patagonotothen, which is nested within the Antarctic clade of Notothenioidei, is almost exclusively found in the non-Antarctic waters of Patagonia. While the drivers of the diversification of Patagonotothen are currently unknown, they are unlikely to be related to antifreeze glycoproteins, given that water temperatures in Patagonia are well above freezing point. Here we performed a phylogenetic analysis based on genome-wide single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RADseq) in a total of twelve Patagonotothen species.<br><br>RESULTS: We present a well-supported, time-calibrated phylogenetic hypothesis including closely and distantly related outgroups, confirming the monophyly of the genus Patagonotothen with an origin approximately 3 million years ago and the paraphyly of both the sister genus Lepidonotothen and the family Notothenidae. Our phylogenomic and population genetic analyses highlight a previously unrecognized linage and provide evidence for shared genetic variation between some closely related species. We also provide a mitochondrial phylogeny showing mitonuclear discordance.<br><br>CONCLUSIONS: Based on a combination of phylogenomic and population genomic approaches, we provide evidence for the existence of a new, potentially cryptic, Patagonotothen species, and demonstrate that genetic boundaries between some closely related species are diffuse, likely due to recent introgression and/or incomplete linage sorting. The detected mitonuclear discordance highlights the limitations of relying on a single locus for species barcoding. In addition, our time-calibrated phylogenetic hypothesis shows that the early burst of diversification roughly coincides with the onset of the intensification of Quaternary glacial cycles and that the rate of species accumulation may have been stepwise rather than constant. Our phylogenetic framework not only advances our understanding of the origin of a high-latitude marine radiation, but also provides the basis for the study of the ecology and life history of the genus Patagonotothen, as well as for their conservation and commercial management.}, }
@article {pmid30630097, year = {2019}, author = {Li, W and Freudenberg, J and Freudenberg, J}, title = {Alignment-free approaches for predicting novel Nuclear Mitochondrial Segments (NUMTs) in the human genome.}, journal = {Gene}, volume = {691}, number = {}, pages = {141-152}, doi = {10.1016/j.gene.2018.12.040}, pmid = {30630097}, issn = {1879-0038}, mesh = {Algorithms ; Cell Nucleus/*genetics ; Evolution, Molecular ; Genome, Human ; Humans ; Mitochondria/*genetics ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; }, abstract = {The nuclear human genome harbors sequences of mitochondrial origin, indicating an ancestral transfer of DNA from the mitogenome. Several Nuclear Mitochondrial Segments (NUMTs) have been detected by alignment-based sequence similarity search, as implemented in the Basic Local Alignment Search Tool (BLAST). Identifying NUMTs is important for the comprehensive annotation and understanding of the human genome. Here we explore the possibility of detecting NUMTs in the human genome by alignment-free sequence similarity search, such as k-mers (k-tuples, k-grams, oligos of length k) distributions. We find that when k=6 or larger, the k-mer approach and BLAST search produce almost identical results, e.g., detect the same set of NUMTs longer than 3 kb. However, when k=5 or k=4, certain signals are only detected by the alignment-free approach, and these may indicate yet unrecognized, and potentially more ancestral NUMTs. We introduce a "Manhattan plot" style representation of NUMT predictions across the genome, which are calculated based on the reciprocal of the Jensen-Shannon divergence between the nuclear and mitochondrial k-mer frequencies. The further inspection of the k-mer-based NUMT predictions however shows that most of them contain long-terminal-repeat (LTR) annotations, whereas BLAST-based NUMT predictions do not. Thus, similarity of the mitogenome to LTR sequences is recognized, which we validate by finding the mitochondrial k-mer distribution closer to those for transposable sequences and specifically, close to some types of LTR.}, }
@article {pmid30629584, year = {2019}, author = {Chiovitti, A and Thorpe, F and Gorman, C and Cuxson, JL and Robevska, G and Szwed, C and Duncan, JC and Vanyai, HK and Cross, J and Siemering, KR and Sumner, J}, title = {A citizen science model for implementing statewide educational DNA barcoding.}, journal = {PloS one}, volume = {14}, number = {1}, pages = {e0208604}, pmid = {30629584}, issn = {1932-6203}, mesh = {Animals ; Australia ; Base Sequence ; *DNA Barcoding, Taxonomic ; Feedback ; Genetic Variation ; Mitochondria/genetics ; *Models, Educational ; Phylogeny ; Reptiles/classification/genetics ; *Science ; Species Specificity ; Students ; }, abstract = {Our aim was to develop a widely available educational program in which students conducted authentic research that met the expectations of both the scientific and educational communities. This paper describes the development and implementation of a citizen science project based on DNA barcoding of reptile specimens obtained from the Museums Victoria frozen tissue collection. The student program was run by the Gene Technology Access Centre (GTAC) and was delivered as a "one day plus one lesson" format incorporating a one-day wet laboratory workshop followed by a single lesson at school utilising online bioinformatics tools. The project leveraged the complementary resources and expertise of the research and educational partners to generate robust scientific data that could be analysed with confidence, meet the requirements of the Victorian state education curriculum, and provide participating students with an enhanced learning experience. During two 1-week stints in 2013 and 2014, 406 students mentored by 44 postgraduate university students participated in the project. Students worked mainly in pairs to process ~200 tissue samples cut from 53 curated reptile specimens representing 17 species. A total of 27 novel Cytochrome Oxidase subunit 1 (CO1) sequences were ultimately generated for 8 south-east Australian reptile species of the families Scincidae and Agamidae.}, }
@article {pmid30621777, year = {2018}, author = {Lynch, M and Marinov, GK}, title = {Response to Martin and colleagues: mitochondria do not boost the bioenergetic capacity of eukaryotic cells.}, journal = {Biology direct}, volume = {13}, number = {1}, pages = {26}, pmid = {30621777}, issn = {1745-6150}, support = {R35 GM122566/GM/NIGMS NIH HHS/United States ; }, mesh = {*Energy Metabolism ; *Eukaryotic Cells ; Mitochondria ; Prokaryotic Cells ; }, abstract = {A recent paper by (Gerlitz et al., Biol Direct 13:21, 2018) questions the validity of the data underlying prior analyses on the bioenergetics capacities of cells, and continues to promote the idea that the mitochondrion endowed eukaryotic cells with energetic superiority over prokaryotes. The former point has been addressed previously, with no resultant changes in the conclusions, and the latter point remains inconsistent with multiple lines of empirical data.}, }
@article {pmid30617214, year = {2019}, author = {Brenner, WG and Mader, M and Müller, NA and Hoenicka, H and Schroeder, H and Zorn, I and Fladung, M and Kersten, B}, title = {High Level of Conservation of Mitochondrial RNA Editing Sites Among Four Populus Species.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {3}, pages = {709-717}, pmid = {30617214}, issn = {2160-1836}, mesh = {Gene Expression Profiling ; Mitochondria/genetics/metabolism ; Phylogeny ; *Polymorphism, Single Nucleotide ; Populus/*genetics/metabolism ; *RNA Editing ; RNA, Mitochondrial/*metabolism ; RNA, Plant/metabolism ; Sequence Analysis, RNA ; }, abstract = {RNA editing occurs in the endosymbiont organelles of higher plants as C-to-U conversions of defined nucleotides. The availability of large quantities of RNA sequencing data makes it possible to identify RNA editing sites and to quantify their editing extent. We have investigated RNA editing in 34 protein-coding mitochondrial transcripts of four Populus species, a genus noteworthy for its remarkably small number of RNA editing sites compared to other angiosperms. 27 of these transcripts were subject to RNA editing in at least one species. In total, 355 RNA editing sites were identified with high confidence, their editing extents ranging from 10 to 100%. The most heavily edited transcripts were ccmB with the highest density of RNA editing sites (53.7 sites / kb) and ccmFn with the highest number of sites (39 sites). Most of the editing events are at position 1 or 2 of the codons, usually altering the encoded amino acid, and are highly conserved among the species, also with regard to their editing extent. However, one SNP was found in the newly sequenced and annotated mitochondrial genome of P. alba resulting in the loss of an RNA editing site compared to P. tremula and P. davidiana This SNP causes a C-to-T transition and an amino acid exchange from Ser to Phe, highlighting the widely discussed role of RNA editing in compensating mutations.}, }
@article {pmid30612859, year = {2019}, author = {Adlakha, J and Karamichali, I and Sangwallek, J and Deiss, S and Bär, K and Coles, M and Hartmann, MD and Lupas, AN and Hernandez Alvarez, B}, title = {Characterization of MCU-Binding Proteins MCUR1 and CCDC90B - Representatives of a Protein Family Conserved in Prokaryotes and Eukaryotic Organelles.}, journal = {Structure (London, England : 1993)}, volume = {27}, number = {3}, pages = {464-475.e6}, doi = {10.1016/j.str.2018.11.004}, pmid = {30612859}, issn = {1878-4186}, mesh = {Archaeal Proteins/chemistry/genetics ; Calcium/metabolism ; Calcium Channels/metabolism ; Carrier Proteins/*chemistry/genetics/*metabolism ; Cell Membrane/metabolism ; Computational Biology/methods ; Conserved Sequence ; Crystallography, X-Ray ; Humans ; Membrane Proteins/*chemistry/genetics/metabolism ; Mitochondrial Proteins/*chemistry/genetics/metabolism ; Multigene Family ; Protein Domains ; Protein Multimerization ; Sequence Analysis, Protein/*methods ; }, abstract = {Membrane-bound coiled-coil proteins are important mediators of signaling, fusion, and scaffolding. Here, we delineate a heterogeneous group of trimeric membrane-anchored proteins in prokaryotes and eukaryotic organelles with a characteristic head-neck-stalk-anchor architecture, in which a membrane-anchored coiled-coil stalk projects an N-terminal head domain via a β-layer neck. Based on sequence analysis, we identify different types of head domains and determine crystal structures of two representatives, the archaeal protein Kcr-0859 and the human CCDC90B, which possesses the most widespread head type. Using mitochondrial calcium uniporter regulator 1 (MCUR1), the functionally characterized paralog of CCDC90B, we study the role of individual domains, and find that the head interacts directly with the mitochondrial calcium uniporter (MCU) and is destabilized upon Ca[2+] binding. Our data provide structural details of a class of membrane-bound coiled-coil proteins and identify the conserved head domain of the most widespread type as a mediator of their function.}, }
@article {pmid30612363, year = {2019}, author = {Jelassi, R and Khemaissia, H and Ghemari, C and Raimond, M and Souty-Grosset, C and Nasri-Ammar, K}, title = {Ecotoxicological effects of trace element contamination in talitrid amphipod Orchestia montagui Audouin, 1826.}, journal = {Environmental science and pollution research international}, volume = {26}, number = {6}, pages = {5577-5587}, pmid = {30612363}, issn = {1614-7499}, mesh = {Amphipoda/drug effects/*physiology ; Animals ; Cadmium ; Copper ; Ecotoxicology ; *Environmental Monitoring ; Hepatopancreas ; Trace Elements/*toxicity ; Water Pollutants, Chemical/*toxicity ; Zinc ; }, abstract = {This study deals with the evaluation of trace element bioaccumulation and histological alterations in the hepatopancreas of the supralittoral amphipod Orchestia montagui Audouin, 1826 due to the exposure to cadmium, copper, and zinc. Orchestia montagui individuals were maintained during 14 days in soils contaminated with different trace elements namely cadmium, copper, and zinc; a control was also prepared. Our results show that the mortality and the body mass vary according to the metal and the nominal concentration used. In general, the mortality increases from the seventh day. However, the body mass shows a decrease with cadmium exposure and an increase with copper and zinc exposures. Furthermore, the concentration factor highlights that this species is considered a macroconcentrator for copper and zinc. The hepatopancreas of unexposed and exposed animals were compared to detect histological changes. Our results show significant alterations in the hepatopancreas of the exposed animals after the experiment. The degree of these alterations was found to be dose-dependent. Among the histological changes in the hepatopancreas in O. montagui, a loss of cell structure was noted, especially cell remoteness and border lyses, the reduction of nuclear volume, an increase in the cytoplasm density with the presence of trace element deposits in both the nucleus and vacuoles, a disorganization and destruction of microvilli, and a condensation of the majority of cell organelles and mitochondria swelling. Through this study, we have confirmed that O. montagui can be a relevant model to assess trace metal element pollution in Tunisian coastal lagoons with the aim of using it in future biomonitoring programs.}, }
@article {pmid30608924, year = {2019}, author = {Makki, A and Rada, P and Žárský, V and Kereïche, S and Kováčik, L and Novotný, M and Jores, T and Rapaport, D and Tachezy, J}, title = {Triplet-pore structure of a highly divergent TOM complex of hydrogenosomes in Trichomonas vaginalis.}, journal = {PLoS biology}, volume = {17}, number = {1}, pages = {e3000098}, pmid = {30608924}, issn = {1545-7885}, mesh = {Carrier Proteins/genetics/*metabolism/physiology ; Membrane Proteins/metabolism ; Membrane Transport Proteins/metabolism ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins/*metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Organelles ; Phylogeny ; Protein Transport/physiology ; Trichomonas vaginalis/*metabolism/pathogenicity/physiology ; }, abstract = {Mitochondria originated from proteobacterial endosymbionts, and their transition to organelles was tightly linked to establishment of the protein import pathways. The initial import of most proteins is mediated by the translocase of the outer membrane (TOM). Although TOM is common to all forms of mitochondria, an unexpected diversity of subunits between eukaryotic lineages has been predicted. However, experimental knowledge is limited to a few organisms, and so far, it remains unsettled whether the triplet-pore or the twin-pore structure is the generic form of TOM complex. Here, we analysed the TOM complex in hydrogenosomes, a metabolically specialised anaerobic form of mitochondria found in the excavate Trichomonas vaginalis. We demonstrate that the highly divergent β-barrel T. vaginalis TOM (TvTom)40-2 forms a translocation channel to conduct hydrogenosomal protein import. TvTom40-2 is present in high molecular weight complexes, and their analysis revealed the presence of four tail-anchored (TA) proteins. Two of them, Tom36 and Tom46, with heat shock protein (Hsp)20 and tetratricopeptide repeat (TPR) domains, can bind hydrogenosomal preproteins and most likely function as receptors. A third subunit, Tom22-like protein, has a short cis domain and a conserved Tom22 transmembrane segment but lacks a trans domain. The fourth protein, hydrogenosomal outer membrane protein 19 (Homp19) has no known homology. Furthermore, our data indicate that TvTOM is associated with sorting and assembly machinery (Sam)50 that is involved in β-barrel assembly. Visualisation of TvTOM by electron microscopy revealed that it forms three pores and has an unconventional skull-like shape. Although TvTOM seems to lack Tom7, our phylogenetic profiling predicted Tom7 in free-living excavates. Collectively, our results suggest that the triplet-pore TOM complex, composed of three conserved subunits, was present in the last common eukaryotic ancestor (LECA), while receptors responsible for substrate binding evolved independently in different eukaryotic lineages.}, }
@article {pmid30604579, year = {2019}, author = {Huang, S and Braun, HP and Gawryluk, RMR and Millar, AH}, title = {Mitochondrial complex II of plants: subunit composition, assembly, and function in respiration and signaling.}, journal = {The Plant journal : for cell and molecular biology}, volume = {98}, number = {3}, pages = {405-417}, doi = {10.1111/tpj.14227}, pmid = {30604579}, issn = {1365-313X}, mesh = {Arabidopsis/*metabolism ; Mitochondria/*metabolism ; Nitric Oxide/metabolism ; Reactive Oxygen Species/metabolism ; Signal Transduction/physiology ; Succinate Dehydrogenase/metabolism ; }, abstract = {Complex II [succinate dehydrogenase (succinate-ubiquinone oxidoreductase); EC 1.3.5.1; SDH] is the only enzyme shared by both the electron transport chain and the tricarboxylic acid (TCA) cycle in mitochondria. Complex II in plants is considered unusual because of its accessory subunits (SDH5-SDH8), in addition to the catalytic subunits of SDH found in all eukaryotes (SDH1-SDH4). Here, we review compositional and phylogenetic analysis and biochemical dissection studies to both clarify the presence and propose a role for these subunits. We also consider the wider functional and phylogenetic evidence for SDH assembly factors and the reports from plants on the control of SDH1 flavination and SDH1-SDH2 interaction. Plant complex II has been shown to influence stomatal opening, the plant defense response and reactive oxygen species-dependent stress responses. Signaling molecules such as salicyclic acid (SA) and nitric oxide (NO) are also reported to interact with the ubiquinone (UQ) binding site of SDH, influencing signaling transduction in plants. Future directions for SDH research in plants and the specific roles of its different subunits and assembly factors are suggested, including the potential for reverse electron transport to explain the succinate-dependent production of reactive oxygen species in plants and new avenues to explore the evolution of plant mitochondrial complex II and its utility.}, }
@article {pmid30598556, year = {2019}, author = {Rathore, S and Berndtsson, J and Marin-Buera, L and Conrad, J and Carroni, M and Brzezinski, P and Ott, M}, title = {Cryo-EM structure of the yeast respiratory supercomplex.}, journal = {Nature structural &amp; molecular biology}, volume = {26}, number = {1}, pages = {50-57}, pmid = {30598556}, issn = {1545-9985}, mesh = {Animals ; Cryoelectron Microscopy/*methods ; Electron Transport/physiology ; Humans ; Lipid Metabolism ; Mitochondria/metabolism/ultrastructure ; Protein Binding ; Saccharomyces cerevisiae/metabolism/ultrastructure ; }, abstract = {Respiratory chain complexes execute energy conversion by connecting electron transport with proton translocation over the inner mitochondrial membrane to fuel ATP synthesis. Notably, these complexes form multi-enzyme assemblies known as respiratory supercomplexes. Here we used single-particle cryo-EM to determine the structures of the yeast mitochondrial respiratory supercomplexes III2IV and III2IV2, at 3.2-Å and 3.5-Å resolutions, respectively. We revealed the overall architecture of the supercomplex, which deviates from the previously determined assemblies in mammals; obtained a near-atomic structure of the yeast complex IV; and identified the protein-protein and protein-lipid interactions implicated in supercomplex formation. Take together, our results demonstrate convergent evolution of supercomplexes in mitochondria that, while building similar assemblies, results in substantially different arrangements and structural solutions to support energy conversion.}, }
@article {pmid30598467, year = {2019}, author = {Clergeot, PH and Rode, NO and Glémin, S and Brandström Durling, M and Ihrmark, K and Olson, &#xc5;}, title = {Estimating the Fitness Effect of Deleterious Mutations During the Two Phases of the Life Cycle: A New Method Applied to the Root-Rot Fungus Heterobasidion parviporum.}, journal = {Genetics}, volume = {211}, number = {3}, pages = {963-976}, pmid = {30598467}, issn = {1943-2631}, mesh = {Basidiomycota/*genetics/growth &amp; development ; Diploidy ; *Genetic Fitness ; Genome, Fungal ; Haploidy ; *Life Cycle Stages ; Models, Genetic ; *Mutation ; }, abstract = {Many eukaryote species, including taxa such as fungi or algae, have a lifecycle with substantial haploid and diploid phases. A recent theoretical model predicts that such haploid-diploid lifecycles are stable over long evolutionary time scales when segregating deleterious mutations have stronger effects in homozygous diploids than in haploids and when they are partially recessive in heterozygous diploids. The model predicts that effective dominance-a measure that accounts for these two effects-should be close to 0.5 in these species. It also predicts that diploids should have higher fitness than haploids on average. However, an appropriate statistical framework to conjointly investigate these predictions is currently lacking. In this study, we derive a new quantitative genetic model to test these predictions using fitness data of two haploid parents and their diploid offspring, and genome-wide genetic distance between haploid parents. We apply this model to the root-rot basidiomycete fungus Heterobasidion parviporum-a species where the heterokaryotic (equivalent to the diploid) phase is longer than the homokaryotic (haploid) phase. We measured two fitness-related traits (mycelium growth rate and the ability to degrade wood) in both homokaryons and heterokaryons, and we used whole-genome sequencing to estimate nuclear genetic distance between parents. Possibly due to a lack of power, we did not find that deleterious mutations were recessive or more deleterious when expressed during the heterokaryotic phase. Using this model to compare effective dominance among haploid-diploid species where the relative importance of the two phases varies should help better understand the evolution of haploid-diploid life cycles.}, }
@article {pmid30595847, year = {2018}, author = {Su-Keene, EJ and Bonilla, MM and Padua, MV and Zeh, DW and Zeh, JA}, title = {Simulated climate warming and mitochondrial haplogroup modulate testicular small non-coding RNA expression in the neotropical pseudoscorpion, Cordylochernes scorpioides.}, journal = {Environmental epigenetics}, volume = {4}, number = {4}, pages = {dvy027}, pmid = {30595847}, issn = {2058-5888}, abstract = {Recent theory suggests that tropical terrestrial arthropods are at significant risk from climate warming. Metabolic rate in such ectothermic species increases exponentially with environmental temperature, and a small temperature increase in a hot environment can therefore have a greater physiological impact than a large temperature increase in a cool environment. In two recent studies of the neotropical pseudoscorpion, Cordylochernes scorpioides, simulated climate warming significantly decreased survival, body size and level of sexual dimorphism. However, these effects were minor compared with catastrophic consequences for male fertility and female fecundity, identifying reproduction as the life stage most vulnerable to climate warming. Here, we examine the effects of chronic high-temperature exposure on epigenetic regulation in C. scorpioides in the context of naturally occurring variation in mitochondrial DNA. Epigenetic mechanisms, including DNA methylation, histone modifications and small non-coding RNA (sncRNA) expression, are particularly sensitive to environmental factors such as temperature, which can induce changes in epigenetic states and phenotypes that may be heritable across generations. Our results indicate that exposure of male pseudoscorpions to elevated temperature significantly altered the expression of >60 sncRNAs in testicular tissue, specifically microRNAs and piwi-interacting RNAs. Mitochondrial haplogroup was also a significant factor influencing both sncRNAs and mitochondrial gene expression. These findings demonstrate that chronic heat stress causes changes in epigenetic profiles that may account for reproductive dysfunction in C. scorpioides males. Moreover, through its effects on epigenetic regulation, mitochondrial DNA polymorphism may provide the potential for an adaptive evolutionary response to climate warming.}, }
@article {pmid30592713, year = {2018}, author = {DiMaio, J and Ruthel, G and Cannon, JJ and Malfara, MF and Povelones, ML}, title = {The single mitochondrion of the kinetoplastid parasite Crithidia fasciculata is a dynamic network.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0202711}, pmid = {30592713}, issn = {1932-6203}, support = {S10 OD021633/OD/NIH HHS/United States ; }, mesh = {Crithidia fasciculata/cytology/*metabolism ; G1 Phase/*physiology ; Mitochondria/*metabolism ; Mitochondrial Dynamics/*physiology ; }, abstract = {Mitochondria are central organelles in cellular metabolism. Their structure is highly dynamic, allowing them to adapt to different energy requirements, to be partitioned during cell division, and to maintain functionality. Mitochondrial dynamics, including membrane fusion and fission reactions, are well studied in yeast and mammals but it is not known if these processes are conserved throughout eukaryotic evolution. Kinetoplastid parasites are some of the earliest-diverging eukaryotes to retain a mitochondrion. Each cell has only a single mitochondrial organelle, making them an interesting model for the role of dynamics in controlling mitochondrial architecture. We have investigated the mitochondrial division cycle in the kinetoplastid Crithidia fasciculata. The majority of mitochondrial biogenesis occurs during the G1 phase of the cell cycle, and the mitochondrion is divided symmetrically in a process coincident with cytokinesis. Live cell imaging revealed that the mitochondrion is highly dynamic, with frequent changes in the topology of the branched network. These remodeling reactions include tubule fission, fusion, and sliding, as well as new tubule formation. We hypothesize that the function of this dynamic remodeling is to homogenize mitochondrial contents and to facilitate rapid transport of mitochondria-encoded gene products from the area containing the mitochondrial nucleoid to other parts of the organelle.}, }
@article {pmid30592414, year = {2019}, author = {Li, J and Liu, X and Zhang, H and Ge, X and Tang, Y and Xu, Z and Tian, L and Yuan, X and Mao, X and Liu, Z}, title = {Ferrocenyl-Triphenyltin Complexes as Lysosome-Targeted Imaging and Anticancer Agents.}, journal = {Inorganic chemistry}, volume = {58}, number = {2}, pages = {1710-1718}, doi = {10.1021/acs.inorgchem.8b03305}, pmid = {30592414}, issn = {1520-510X}, mesh = {A549 Cells ; Antineoplastic Agents ; Cell Death/drug effects ; Cell Proliferation/drug effects ; Drug Screening Assays, Antitumor ; Ferrous Compounds/chemistry/*pharmacology ; Humans ; Lung Neoplasms/*diagnostic imaging/*drug therapy ; Lysosomes/*metabolism ; Metallocenes/chemistry/*pharmacology ; *Optical Imaging ; Organometallic Compounds/chemical synthesis/chemistry/*pharmacology ; Organotin Compounds/chemistry/*pharmacology ; }, abstract = {In this paper, two ferrocenyl-triphenyltin complexes were synthesized and characterized. Complex 2 is constructed as new multifunctional therapeutic platform for lysosome-targeted imaging and displayed much higher cytotoxicity than its analogue 1 by the introduction of a methyl group instead of a hydrogen atom in acylhydrazone. The cyclic voltammograms and reaction with GSH (glutathione) further confirmed that complex 1 has a reversible redox peak and can react with GSH, which indicate that complex 1 might lose its anticancer effect by undergoing reaction with GSH once it enters the cancer cell. Complex 2 could effectively catalyze the oxidation of NADH (the reduced form of nicotinamide adenine dinucleotide) to NAD[+] and induce the production of reactive oxygen species (ROS), lead to caspase-dependent apoptosis through damaged mitochondria, simultaneously, accounting for the mitochondrial vacuolization and karyorrhexis. The caspase-3 activation and cytoplasmic vacuolation karyorrhexis induced by complex 2 revealed that the A549 cell lines might undergo cell death primarily mediated by apoptosis and oncosis; however, 1 cannot reproduce this effect. Taken together, these results indicated that complex 2 has more potential for evolution as a new bioimaging and anticancer agent.}, }
@article {pmid30590727, year = {2019}, author = {Tsitsekian, D and Daras, G and Alatzas, A and Templalexis, D and Hatzopoulos, P and Rigas, S}, title = {Comprehensive analysis of Lon proteases in plants highlights independent gene duplication events.}, journal = {Journal of experimental botany}, volume = {70}, number = {7}, pages = {2185-2197}, pmid = {30590727}, issn = {1460-2431}, mesh = {Base Sequence ; *Evolution, Molecular ; *Gene Duplication ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Plants/*genetics/metabolism ; Protease La/*genetics/metabolism ; Sequence Alignment ; }, abstract = {The degradation of damaged proteins is essential for cell viability. Lon is a highly conserved ATP-dependent serine-lysine protease that maintains proteostasis. We performed a comparative genome-wide analysis to determine the evolutionary history of Lon proteases. Prokaryotes and unicellular eukaryotes retained a single Lon copy, whereas multicellular eukaryotes acquired a peroxisomal copy, in addition to the mitochondrial gene, to sustain the evolution of higher order organ structures. Land plants developed small Lon gene families. Despite the Lon2 peroxisomal paralog, Lon genes triplicated in the Arabidopsis lineage through sequential evolutionary events including whole-genome and tandem duplications. The retention of Lon1, Lon4, and Lon3 triplicates relied on their differential and even contrasting expression patterns, distinct subcellular targeting mechanisms, and functional divergence. Lon1 seems similar to the pre-duplication ancestral gene unit, whereas the duplication of Lon3 and Lon4 is evolutionarily recent. In the wider context of plant evolution, papaya is the only genome with a single ancestral Lon1-type gene. The evolutionary trend among plants is to acquire Lon copies with ambiguous pre-sequences for dual-targeting to mitochondria and chloroplasts, and a substrate recognition domain that deviates from the ancestral Lon1 type. Lon genes constitute a paradigm of dynamic evolution contributing to understanding the functional fate of gene duplicates.}, }
@article {pmid30590568, year = {2019}, author = {Łukasik, P and Chong, RA and Nazario, K and Matsuura, Y and Bublitz, AC and Campbell, MA and Meyer, MC and Van Leuven, JT and Pessacq, P and Veloso, C and Simon, C and McCutcheon, JP}, title = {One Hundred Mitochondrial Genomes of Cicadas.}, journal = {The Journal of heredity}, volume = {110}, number = {2}, pages = {247-256}, pmid = {30590568}, issn = {1465-7333}, support = {P20 GM103546/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anticodon ; DNA, Ribosomal Spacer ; Gene Order ; Genetic Variation ; *Genome, Mitochondrial ; *Genomics/methods ; Genotype ; Hemiptera/*genetics ; Locus Control Region ; Phylogeny ; RNA, Transfer/genetics ; Symbiosis ; }, abstract = {Mitochondrial genomes can provide valuable information on the biology and evolutionary histories of their host organisms. Here, we present and characterize the complete coding regions of 107 mitochondrial genomes (mitogenomes) of cicadas (Insecta: Hemiptera: Auchenorrhyncha: Cicadoidea), representing 31 genera, 61 species, and 83 populations. We show that all cicada mitogenomes retain the organization and gene contents thought to be ancestral in insects, with some variability among cicada clades in the length of a region between the genes nad2 and cox1, which encodes 3 tRNAs. Phylogenetic analyses using these mitogenomes recapitulate a recent 5-gene classification of cicadas into families and subfamilies, but also identify a species that falls outside of the established taxonomic framework. While protein-coding genes are under strong purifying selection, tests of relative evolutionary rates reveal significant variation in evolutionary rates across taxa, highlighting the dynamic nature of mitochondrial genome evolution in cicadas. These data will serve as a useful reference for future research into the systematics, ecology, and evolution of the superfamily Cicadoidea.}, }
@article {pmid30588726, year = {2019}, author = {Hill, GE and Havird, JC and Sloan, DB and Burton, RS and Greening, C and Dowling, DK}, title = {Assessing the fitness consequences of mitonuclear interactions in natural populations.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {94}, number = {3}, pages = {1089-1104}, pmid = {30588726}, issn = {1469-185X}, support = {R01 GM118046/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Animals ; Ecosystem ; Gene Expression Regulation ; *Genetic Fitness ; Mitochondria/*genetics/*physiology ; Oxygen Consumption ; }, abstract = {Metazoans exist only with a continuous and rich supply of chemical energy from oxidative phosphorylation in mitochondria. The oxidative phosphorylation machinery that mediates energy conservation is encoded by both mitochondrial and nuclear genes, and hence the products of these two genomes must interact closely to achieve coordinated function of core respiratory processes. It follows that selection for efficient respiration will lead to selection for compatible combinations of mitochondrial and nuclear genotypes, and this should facilitate coadaptation between mitochondrial and nuclear genomes (mitonuclear coadaptation). Herein, we outline the modes by which mitochondrial and nuclear genomes may coevolve within natural populations, and we discuss the implications of mitonuclear coadaptation for diverse fields of study in the biological sciences. We identify five themes in the study of mitonuclear interactions that provide a roadmap for both ecological and biomedical studies seeking to measure the contribution of intergenomic coadaptation to the evolution of natural populations. We also explore the wider implications of the fitness consequences of mitonuclear interactions, focusing on central debates within the fields of ecology and biomedicine.}, }
@article {pmid30586649, year = {2019}, author = {Bartáková, V and Bryja, J and Šanda, R and Bektas, Y and Stefanov, T and Choleva, L and Smith, C and Reichard, M}, title = {High cryptic diversity of bitterling fish in the southern West Palearctic.}, journal = {Molecular phylogenetics and evolution}, volume = {133}, number = {}, pages = {1-11}, doi = {10.1016/j.ympev.2018.12.025}, pmid = {30586649}, issn = {1095-9513}, mesh = {Animals ; Asia, Western ; Biodiversity ; Cyprinidae/*classification/genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/chemistry ; Demography ; Europe ; Genetic Drift ; Genetic Variation ; Genotype ; Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; }, abstract = {South-east Europe, along with the adjacent region of south-west Asia, is an important biodiversity hotspot with high local endemism largely contributed by contemporary continental lineages that retreated to southern refugia during colder Quaternary periods. We investigated the genetic diversity of the European bitterling fish (Rhodeus amarus) species complex (Cyprinidae) across its range in the western Palearctic, but with a particular emphasis in the region of Balkan, Pontic and Caspian refugia. We genotyped 12 polymorphic microsatellite loci and a partial sequence of mitochondrial gene cytochrome b (CYTB) for a set of 1,038 individuals from 60 populations. We used mtDNA sequences to infer phylogenetic relationships and historical demography, and microsatellite markers to describe fine-scale genetic variability and structure. Our mtDNA analysis revealed six well-supported lineages, with limited local co-occurrence. Two lineages are distributed throughout central and western Europe (lineages "A" and "B"), with two zones of secondary contact. Another two lineages were restricted to the Ponto-Aegean region of Greece (lineages "C" and "D") and the final two lineages were restricted south of the Caucasus mountains (lineage "E" from the Black Sea watershed and lineage "F" from the Caspian watershed). A signal of recent expansion was revealed in the two widespread lineages and the Ponto-Aegean lineage "C". The geographic distribution of clusters detected by nuclear microsatellites corresponded well with mitochondrial lineages and demonstrated finely sub-structured populations. A profound population structure suggested a significant role of genetic drift in differentiation among lineages. Lineage divergence in the Ponto-Aegean and Caspian regions are substantial, supporting the validity of two described endemic species (Rhodeus meridionalis as lineage "D" and Rhodeus colchicus as lineage "E") and invite taxonomic evaluation of the other two southern lineages (Thracean "C" and Caspian "F").}, }
@article {pmid30586406, year = {2018}, author = {Zhao, L and Lin, XM and Li, F and Li, KR and He, B and Zhang, LY and Pan, JJ and Wang, QR and Gao, JM and Johnson, N and Yuan, XF and Lv, JZ and Wu, SQ and Liu, YH}, title = {A survey of argasid ticks and tick-associated pathogens in the Peripheral Oases around Tarim Basin and the first record of Argas japonicus in Xinjiang, China.}, journal = {PloS one}, volume = {13}, number = {12}, pages = {e0208615}, pmid = {30586406}, issn = {1932-6203}, mesh = {Anaplasma/classification/genetics/*isolation &amp; purification/pathogenicity ; Animals ; Argas/classification/genetics/*microbiology ; Cattle ; China ; Disease Vectors ; Mitochondria/genetics ; Ornithodoros/classification/genetics/*microbiology ; Phylogeny ; RNA, Ribosomal/classification/genetics/metabolism ; RNA, Ribosomal, 16S/classification/genetics/metabolism ; Rickettsia/classification/genetics/*isolation &amp; purification/pathogenicity ; Sequence Analysis, DNA ; Sheep ; Tick Infestations/parasitology/pathology/veterinary ; }, abstract = {Argasid ticks (Acari: Argasidae) carry and transmit a variety of pathogens of animals and humans, including viruses, bacteria and parasites. There are several studies reporting ixodid ticks (Acari: Ixodidae) and associated tick-borne pathogens in Xinjiang, China. However, little is known about the argasid ticks and argasid tick-associated pathogens in this area. In this study, a total of 3829 adult argasid ticks infesting livestock were collected at 12 sampling sites of 10 counties in the Peripheral Oases, which carry 90% of the livestock and humans population, around the Tarim Basin (southern Xinjiang) from 2013 to 2016. Tick specimens were identified to two species from different genera by morphology and sequences of mitochondrial 16S rRNA and 12S rRNA were derived to confirm the species designation. The results showed that the dominant argasid ticks infesting livestock in southern Xinjiang were Ornithodoros lahorensis (87.86%, 3364/3829). Ornithodoros lahorensis was distributed widely and were collected from 10 counties of southern Xinjiang. Argas japonicus was collected from Xinjiang for the first time. In addition, we screened these ticks for tick-associated pathogens and showed the presence of DNA sequences of Rickettsia spp. of Spotted fever group and Anaplasma spp. in the argasid ticks. This finding suggests the potential role for Argas japonicus as a vector of pathogens to livestock and humans.}, }
@article {pmid30584918, year = {2019}, author = {Lavin, BR and Girman, DJ}, title = {Phylogenetic relationships and divergence dating in the Glass Lizards (Anguinae).}, journal = {Molecular phylogenetics and evolution}, volume = {133}, number = {}, pages = {128-140}, doi = {10.1016/j.ympev.2018.12.022}, pmid = {30584918}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Geography ; Lizards/*classification/genetics ; Mitochondria/genetics ; *Phylogeny ; Probability ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; }, abstract = {The Glass Lizards are a subfamily (Anguinae) of Anguid Lizards with an elongated limbless body plan that occur throughout the Northern Hemisphere primarily in North America, Europe, and Asia, but also have a presence in North Africa and Indonesia. We used twenty-five nuclear loci (15,191 bp) and 2090 bp of the mtDNA genome to generate a phylogeny containing all known species groups to explore species relationships within the group as well as divergence dating. We also examined the group in the context of a coalescent species tree analysis and species delimitation. All major lineages were found to be monophyletic with potential cryptic diversity in some. The Anguinae first appeared in the Eocene and most lineages were present by the beginning of the Miocene. The Anguinae originated in Europe from an Anguidae ancestor that crossed the Thulean land bridge, spreading to Asia after the drying of the Turgai Sea, then across Beringia as the climate permitted. A species tree analyses found support for the major Anguinae lineages and species delimitation supported accepted species.}, }
@article {pmid30583042, year = {2019}, author = {Elias-Costa, AJ and Confalonieri, VA and Lanteri, AA and Rodriguero, MS}, title = {Game of clones: Is Wolbachia inducing speciation in a weevil with a mixed reproductive mode?.}, journal = {Molecular phylogenetics and evolution}, volume = {133}, number = {}, pages = {42-53}, doi = {10.1016/j.ympev.2018.12.027}, pmid = {30583042}, issn = {1095-9513}, mesh = {Animals ; Argentina ; Biological Evolution ; Brazil ; Cell Nucleus/genetics ; Female ; Genetic Speciation ; Male ; Mitochondria/genetics ; *Parthenogenesis ; Reproduction ; Weevils/classification/genetics/*microbiology/*physiology ; Wolbachia/*physiology ; }, abstract = {Parthenogenesis is widely distributed in Metazoa but it is especially frequent in weevils (Coleoptera, Curculionidae) with one fifth of all known cases. Previous studies have shown that in the tribe Naupactini parthenogenetic reproduction most likely originated with an infection of the endoparasitic bacterium Wolbachia pipientis. In particular, Pantomorus postfasciatus possess a mixed reproductive mode: some populations have males while in others they are absent, and females produce clones by thelytoky. To better understand this scenario, we studied the population structure and infection status in 64 individuals of P. postfasciatus from Argentina and Brazil. We sequenced two mitochondrial (COI and COII) and one nuclear (ITS-1) fragments and obtained two very divergent haplogroups, one corresponding to the sexual populations uninfected with Wolbachia, and another conforming a monophyletic parthenogenetic (or presumptively parthenogenetic) and infected clade. Each of these haplogroups was identified as an independently evolutionary unit by all species delimitation analyses accomplished: multilocus *BEAST and BP&amp;P, and single locus GMYC and K/θ rule. Additionally, present evidence suggests that Wolbachia infection occurred at least twice in all-female populations of P. postfasciatus with two different bacterial strains. Speciation mediated by Wolbachia is a recently described phenomenon and the case of P. postfasciatus is the first known case in a diplo-diploid insect. A model that describes how thelytoky-inducing phenotypes of Wolbachia could generate new lineages is discussed.}, }
@article {pmid30570818, year = {2019}, author = {Williams, AM and Friso, G and van Wijk, KJ and Sloan, DB}, title = {Extreme variation in rates of evolution in the plastid Clp protease complex.}, journal = {The Plant journal : for cell and molecular biology}, volume = {98}, number = {2}, pages = {243-259}, doi = {10.1111/tpj.14208}, pmid = {30570818}, issn = {1365-313X}, mesh = {Cell Nucleus ; Chloroplasts/genetics ; Endopeptidase Clp/chemistry/classification/*genetics ; *Evolution, Molecular ; Gene Expression Regulation, Plant ; Genome, Plant ; Genome, Plastid ; Magnoliopsida/genetics ; Phylogeny ; Plant Proteins/*genetics ; Plants/*genetics ; Plastids/*genetics ; Proteome ; Seeds ; Sequence Alignment ; }, abstract = {Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multi-subunit complexes in mitochondria and plastids. One such complex in plants is the caseinolytic protease (Clp), which plays an essential role in plastid protein turnover. The proteolytic core of Clp comprises subunits from one plastid-encoded gene (clpP1) and multiple nuclear genes. TheclpP1 gene is highly conserved across most green plants, but it is by far the fastest evolving plastid-encoded gene in some angiosperms. To better understand these extreme and mysterious patterns of divergence, we investigated the history ofclpP1 molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find thatclpP1 has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g. a loss of introns andRNA-editing sites) within seed plants. AlthoughclpP1 is often assumed to be a pseudogene in such cases, multiple lines of evidence suggest that this is rarely true. We applied comparative native gel electrophoresis of chloroplast protein complexes followed by protein mass spectrometry in two species within the angiosperm genusSilene, which has highly elevated and heterogeneous rates ofclpP1 evolution. We confirmed thatclpP1 is expressed as a stable protein and forms oligomeric complexes with the nuclear-encoded Clp subunits, even in one of the most divergentSilene species. Additionally, there is a tight correlation between amino acid substitution rates inclpP1 and the nuclear-encoded Clp subunits across a broad sampling of angiosperms, suggesting continuing selection on interactions within this complex.}, }
@article {pmid30569217, year = {2019}, author = {Nie, Y and Wang, L and Cai, Y and Tao, W and Zhang, YJ and Huang, B}, title = {Mitochondrial genome of the entomophthoroid fungus Conidiobolus heterosporus provides insights into evolution of basal fungi.}, journal = {Applied microbiology and biotechnology}, volume = {103}, number = {3}, pages = {1379-1391}, doi = {10.1007/s00253-018-9549-5}, pmid = {30569217}, issn = {1432-0614}, support = {30770008, 31471821 and 31772226//the National Natural Science Foundation of China/ ; 31872162//National Natural Science Foundation of China/ ; 201601D011065//Natural Science Foundation of Shanxi Province/ ; 2017-015//Shanxi Scholarship Council of China/ ; }, mesh = {Base Composition/genetics ; Base Sequence ; Conidiobolus/classification/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genes, Mitochondrial/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Sequence Analysis, DNA ; }, abstract = {Entomophthoroid fungi represent an ecologically important group of fungal pathogens on insects. Here, the whole mitogenome of Conidiobolus heterosporus, one of the entomophthoroid fungi, was described and compared to those early branching fungi with available mitogenomes. The 53,364-bp circular mitogenome of C. heterosporus contained two rRNA genes, 14 standard protein-coding genes, 26 tRNA genes, and three free-standing ORFs. Thirty introns interrupted nine mitochondrial genes. Phylogenetic analysis based on mitochondrion-encoded proteins revealed that C. heterosporus was most close to Zancudomyces culisetae in the Zoopagomycota of basal fungi. Comparison on mitogenomes of 23 basal fungi revealed great variabilities in terms of mitogenome conformation (circular or linear), genetic code (codes 1, 4, or 16), AT contents (53.3-85.5%), etc. These mitogenomes varied from 12.0 to 97.3 kb in sizes, mainly due to different numbers of genes and introns. They showed frequent DNA rearrangement events and a high variability of gene order, although high synteny and conserved gene order were also present between closely related species. By reporting the first mitogenome in Entomophthoromycotina and the second in Zoopagomycota, this study greatly enhanced our understanding on evolution of basal fungi.}, }
@article {pmid30565720, year = {2019}, author = {Morsi, M and Kobeissy, F and Magdeldin, S and Maher, A and Aboelmagd, O and Johar, D and Bernstein, L}, title = {A shared comparison of diabetes mellitus and neurodegenerative disorders.}, journal = {Journal of cellular biochemistry}, volume = {120}, number = {9}, pages = {14318-14325}, doi = {10.1002/jcb.28094}, pmid = {30565720}, issn = {1097-4644}, mesh = {Amyloidogenic Proteins/*metabolism ; Brain/metabolism ; Diabetes Mellitus, Type 1/*metabolism ; Diabetes Mellitus, Type 2/*metabolism ; Humans ; Islets of Langerhans/metabolism ; Kidney Glomerulus/metabolism ; Neurodegenerative Diseases/*metabolism ; Oxidative Stress ; Signal Transduction ; tau Proteins/*metabolism ; }, abstract = {Diabetes mellitus (DM), one of the most prevalent metabolic diseases in the world population, is associated with a number of comorbid conditions including obesity, pancreatic endocrine changes, and renal and cardio-cerebrovascular alterations, coupled with peripheral neuropathy and neurodegenerative disease, some of these disorders are bundled into metabolic syndrome. Type 1 DM (T1DM) is an autoimmune disease that destroys the insulin-secreting islet cells. Type 2 DM (T2DM) is diabetes that is associated with an imbalance in the glucagon/insulin homeostasis that leads to the formation of amyloid deposits in the brain, pancreatic islet cells, and possibly in the kidney glomerulus. There are several layers of molecular pathologic alterations that contribute to the DM metabolic pathophysiology and its associated neuropathic manifestations. In this review, we describe the general signature metabolic features of DM and the cross-talk with neurodegeneration. We will assess the underlying molecular key players associated with DM-induced neuropathic disorders that are associated with both T1DM and T2DM. In this context, we will highlight the role of tau and amyloid protein deposits in the brain as well in the pancreatic islet cells, and possibly in the kidney glomerulus. Furthermore, we will discuss the central role of mitochondria, oxidative stress, and the unfolded protein response in mediating the DM-associated neuropathic degeneration. This study will elucidate the relationship between DM and neurodegeneration which may account for the evolution of other neurodegenerative diseases, particularly Alzheimer's disease and Parkinson's disease as discussed later.}, }
@article {pmid30563833, year = {2019}, author = {Wynn, EL and Christensen, AC}, title = {Repeats of Unusual Size in Plant Mitochondrial Genomes: Identification, Incidence and Evolution.}, journal = {G3 (Bethesda, Md.)}, volume = {9}, number = {2}, pages = {549-559}, pmid = {30563833}, issn = {2160-1836}, mesh = {*Evolution, Molecular ; *Genome, Mitochondrial ; *Genome, Plant ; Genomic Instability ; Plants/genetics ; *Repetitive Sequences, Nucleic Acid ; }, abstract = {Plant mitochondrial genomes have excessive size relative to coding capacity, a low mutation rate in genes and a high rearrangement rate. They also have abundant non-tandem repeats often including pairs of large repeats which cause isomerization of the genome by recombination, and numerous repeats of up to several hundred base pairs that recombine only when the genome is stressed by DNA damaging agents or mutations in DNA repair pathway genes. Early work on mitochondrial genomes led to the suggestion that repeats in the size range from several hundred to a few thousand base pair are underrepresented. The repeats themselves are not well-conserved between species, and are not always annotated in mitochondrial sequence assemblies. We systematically identified and compared these repeats, which are important clues to mechanisms of DNA maintenance in mitochondria. We developed a tool to find and curate non-tandem repeats larger than 50bp and analyzed the complete mitochondrial sequences from 157 plant species. We observed an interesting difference between taxa: the repeats are larger and more frequent in the vascular plants. Analysis of closely related species also shows that plant mitochondrial genomes evolve in dramatic bursts of breakage and rejoining, complete with DNA sequence gain and loss. We suggest an adaptive explanation for the existence of the repeats and their evolution.}, }
@article {pmid30563453, year = {2018}, author = {Harman, A and Barth, C}, title = {The Dictyostelium discoideum homologue of Twinkle, Twm1, is a mitochondrial DNA helicase, an active primase and promotes mitochondrial DNA replication.}, journal = {BMC molecular biology}, volume = {19}, number = {1}, pages = {12}, pmid = {30563453}, issn = {1471-2199}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; DNA Helicases/chemistry/genetics/*metabolism ; DNA Primase/chemistry/genetics/*metabolism ; *DNA Replication ; DNA, Mitochondrial ; Dictyostelium/*genetics/*metabolism ; Gene Dosage ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Protozoan Proteins/chemistry/genetics/metabolism ; RNA Interference ; RNA, Antisense/genetics ; Substrate Specificity ; }, abstract = {BACKGROUND: DNA replication requires contributions from various proteins, such as DNA helicases; in mitochondria Twinkle is important for maintaining and replicating mitochondrial DNA. Twinkle helicases are predicted to also possess primase activity, as has been shown in plants; however this activity appears to have been lost in metazoans. Given this, the study of Twinkle in other organisms is required to better understand the evolution of this family and the roles it performs within mitochondria.<br><br>RESULTS: Here we describe the characterization of a Twinkle homologue, Twm1, in the amoeba Dictyostelium discoideum, a model organism for mitochondrial genetics and disease. We show that Twm1 is important for mitochondrial function as it maintains mitochondrial DNA copy number in vivo. Twm1 is a helicase which unwinds DNA resembling open forks, although it can act upon substrates with a single 3' overhang, albeit less efficiently. Furthermore, unlike human Twinkle, Twm1 has primase activity in vitro. Finally, using a novel in bacterio approach, we demonstrated that Twm1 promotes DNA replication.<br><br>CONCLUSIONS: We conclude that Twm1 is a replicative mitochondrial DNA helicase which is capable of priming DNA for replication. Our results also suggest that non-metazoan Twinkle could function in the initiation of mitochondrial DNA replication. While further work is required, this study has illuminated several alternative processes of mitochondrial DNA maintenance which might also be performed by the Twinkle family of helicases.}, }
@article {pmid30555069, year = {2018}, author = {Idnurm, A}, title = {Mystique of Phycomyces blakesleeanus is a peculiar mitochondrial genetic element that is highly variable in DNA sequence while subjected to strong negative selection.}, journal = {Journal of genetics}, volume = {97}, number = {5}, pages = {1195-1204}, pmid = {30555069}, issn = {0973-7731}, mesh = {Biological Evolution ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; *Genome, Mitochondrial ; *Interspersed Repetitive Sequences ; Mitochondria/*genetics ; Phycomyces/*genetics ; Phylogeny ; *Selection, Genetic ; Sequence Homology ; }, abstract = {A DNA region in the mitochondrial genome of the fungus Phycomyces blakesleeanus (Mucorales, Mucoromycota) was characterized in a population of wild-type strains. The region encodes a predicted protein similar to the reverse transcriptases encoded by mitochondrial retroplasmids of Neurospora species and other Sordariomycetes (Ascomycota), but is uncommon in other fungi. DNA sequences of this element, named mystique, are highly variable between the strains, having greater than 2.5% divergence, yet most of the nucleotide differences fall in codon positions that do not change the amino acid sequence. The high proportion of polymorphisms coupled to the rarity of nonsynonymous changes suggests that mystique is subject to counteracting forces of hypermutation and purifying selection. However, while evidence for negative selection may infer that the element provides a fitness benefit, some strains of P. blakesleeanus do not have the element and grow equivalently well as those strains with it. A mechanism to explain the variability between the mystique alleles is proposed, of error-prone replication through an RNA intermediate, reverse transcription and reintegration of the element into the mitochondrial genome.}, }
@article {pmid30550962, year = {2019}, author = {Feng, C and Zhou, W and Tang, Y and Gao, Y and Chen, J and Tong, C and Liu, S and Wanghe, K and Zhao, K}, title = {Molecular systematics of the Triplophysa robusta (Cobitoidea) complex: Extensive gene flow in a depauperate lineage.}, journal = {Molecular phylogenetics and evolution}, volume = {132}, number = {}, pages = {275-283}, doi = {10.1016/j.ympev.2018.12.009}, pmid = {30550962}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Cypriniformes/*classification/genetics ; Cytochromes b/classification/genetics ; *Gene Flow ; Genetics, Population ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 16S/classification/genetics ; }, abstract = {Gene flow between populations assumed to be isolated frequently leads to incorrect inferences of evolutionary history. Understanding gene flow and its causes has long been a key topic in evolutionary biology. In this study, we explored the evolutionary history of the Triplophysa robusta complex, using a combination of multilocus analyses and coalescent simulation. Our multilocus approach detected conspicuous mitonuclear discordances in the T. robusta complex. Mitochondrial results showed reticular clades, whereas the nuclear results corresponded with the morphological data. Coalescent simulation indicated that gene flow was the source of these discordances. Molecular clock analysis combined with geological processes suggest that intense geological upheavals have shaped a complicated evolutionary history for the T. robusta complex since the late Miocene, causing extensive gene flow which has distorted the molecular systematics of the T. robusta complex. We suggest that frequent gene flow may restrict speciation in the T. robusta complex, leading to such a depauperate lineage. Based on this comprehensive understanding, we provide our proposals for taxonomic revision of the T. robusta complex.}, }
@article {pmid30545443, year = {2019}, author = {Son, JM and Lee, C}, title = {Mitochondria: multifaceted regulators of aging.}, journal = {BMB reports}, volume = {52}, number = {1}, pages = {13-23}, pmid = {30545443}, issn = {1976-670X}, support = {R01 AG052558/AG/NIA NIH HHS/United States ; R01 GM136837/GM/NIGMS NIH HHS/United States ; }, mesh = {Aging/genetics/*physiology ; Animals ; Apoptosis ; DNA Damage/physiology ; DNA, Mitochondrial/genetics ; Free Radicals ; Humans ; Mitochondria/*metabolism/*physiology ; Oxidative Stress/physiology ; Reactive Oxygen Species ; }, abstract = {Aging is accompanied by a time-dependent progressive deterioration of multiple factors of the cellular system. The past several decades have witnessed major leaps in our understanding of the biological mechanisms of aging using dietary, genetic, pharmacological, and physical interventions. Metabolic processes, including nutrient sensing pathways and mitochondrial function, have emerged as prominent regulators of aging. Mitochondria have been considered to play a key role largely due to their production of reactive oxygen species (ROS), resulting in DNA damage that accumulates over time and ultimately causes cellular failure. This theory, known as the mitochondrial free radical theory of aging (MFRTA), was favored by the aging field, but increasing inconsistent evidence has led to criticism and rejection of this idea. However, MFRTA should not be hastily rejected in its entirety because we now understand that ROS is not simply an undesired toxic metabolic byproduct, but also an important signaling molecule that is vital to cellular fitness. Notably, mitochondrial function, a term traditionally referred to bioenergetics and apoptosis, has since expanded considerably. It encompasses numerous other key biological processes, including the following: (i) complex metabolic processes, (ii) intracellular and endocrine signaling/communication, and (iii) immunity/inflammation. Here, we will discuss shortcomings of previous concepts regarding mitochondria in aging and their emerging roles based on recent advances. We will also discuss how the mitochondrial genome integrates with major theories on the evolution of aging. [BMB Reports 2019; 52(1): 13-23].}, }
@article {pmid30523084, year = {2018}, author = {Antonova-Koch, Y and Meister, S and Abraham, M and Luth, MR and Ottilie, S and Lukens, AK and Sakata-Kato, T and Vanaerschot, M and Owen, E and Jado, JC and Maher, SP and Calla, J and Plouffe, D and Zhong, Y and Chen, K and Chaumeau, V and Conway, AJ and McNamara, CW and Ibanez, M and Gagaring, K and Serrano, FN and Eribez, K and Taggard, CM and Cheung, AL and Lincoln, C and Ambachew, B and Rouillier, M and Siegel, D and Nosten, F and Kyle, DE and Gamo, FJ and Zhou, Y and Llinás, M and Fidock, DA and Wirth, DF and Burrows, J and Campo, B and Winzeler, EA}, title = {Open-source discovery of chemical leads for next-generation chemoprotective antimalarials.}, journal = {Science (New York, N.Y.)}, volume = {362}, number = {6419}, pages = {}, pmid = {30523084}, issn = {1095-9203}, support = {P50 GM085764/GM/NIGMS NIH HHS/United States ; R01 AI090141/AI/NIAID NIH HHS/United States ; R01 AI093716/AI/NIAID NIH HHS/United States ; R01 AI103058/AI/NIAID NIH HHS/United States ; }, mesh = {Antimalarials/chemistry/isolation &amp; purification/*pharmacology/therapeutic use ; *Chemoprevention ; *Drug Discovery ; Drug Evaluation, Preclinical ; Humans ; Malaria/*prevention &amp; control ; Mitochondria/drug effects ; Plasmodium/*drug effects/growth &amp; development ; }, abstract = {To discover leads for next-generation chemoprotective antimalarial drugs, we tested more than 500,000 compounds for their ability to inhibit liver-stage development of luciferase-expressing Plasmodium spp. parasites (681 compounds showed a half-maximal inhibitory concentration of less than 1 micromolar). Cluster analysis identified potent and previously unreported scaffold families as well as other series previously associated with chemoprophylaxis. Further testing through multiple phenotypic assays that predict stage-specific and multispecies antimalarial activity distinguished compound classes that are likely to provide symptomatic relief by reducing asexual blood-stage parasitemia from those which are likely to only prevent malaria. Target identification by using functional assays, in vitro evolution, or metabolic profiling revealed 58 mitochondrial inhibitors but also many chemotypes possibly with previously unidentified mechanisms of action.}, }
@article {pmid30537423, year = {2019}, author = {Tsakiri, EN and Gumeni, S and Iliaki, KK and Benaki, D and Vougas, K and Sykiotis, GP and Gorgoulis, VG and Mikros, E and Scorrano, L and Trougakos, IP}, title = {Hyperactivation of Nrf2 increases stress tolerance at the cost of aging acceleration due to metabolic deregulation.}, journal = {Aging cell}, volume = {18}, number = {1}, pages = {e12845}, pmid = {30537423}, issn = {1474-9726}, support = {BIOIMAGING-GR (MIS 5002755)//General Secretariat for Research and Technology, Greece/International ; TASCMAR (EU-H2020/634674)//European Union, H2020/International ; }, mesh = {*Adaptation, Physiological ; Aging/*physiology ; Animals ; Cytoprotection ; Drosophila Proteins/metabolism ; Drosophila melanogaster/*metabolism/*physiology ; Energy Metabolism ; Insulin/metabolism ; Metabolic Networks and Pathways ; Mitochondria/metabolism ; Mitochondrial Dynamics ; NF-E2-Related Factor 2/*metabolism ; Phenotype ; Signal Transduction ; Somatomedins/metabolism ; *Stress, Physiological ; }, abstract = {Metazoans viability depends on their ability to regulate metabolic processes and also to respond to harmful challenges by mounting anti-stress responses; these adaptations were fundamental forces during evolution. Central to anti-stress responses are a number of short-lived transcription factors that by functioning as stress sensors mobilize genomic responses aiming to eliminate stressors. We show here that increased expression of nuclear factor erythroid 2-related factor (Nrf2) in Drosophila activated cytoprotective modules and enhanced stress tolerance. However, while mild Nrf2 activation extended lifespan, high Nrf2 expression levels resulted in developmental lethality or, after inducible activation in adult flies, in altered mitochondrial bioenergetics, the appearance of Diabetes Type 1 hallmarks and aging acceleration. Genetic or dietary suppression of Insulin/IGF-like signaling (IIS) titrated Nrf2 activity to lower levels, largely normalized metabolic pathways signaling, and extended flies' lifespan. Thus, prolonged stress signaling by otherwise cytoprotective short-lived stress sensors perturbs IIS resulting in re-allocation of resources from growth and longevity to somatic preservation and stress tolerance. These findings provide a reasonable explanation of why most (if not all) cytoprotective stress sensors are short-lived proteins, and it also explains the build-in negative feedback loops (shown here for Nrf2); the low basal levels of these proteins, and why their suppressors were favored by evolution.}, }
@article {pmid30535838, year = {2019}, author = {Kumar, V and Santhosh Kumar, TR and Kartha, CC}, title = {Mitochondrial membrane transporters and metabolic switch in heart failure.}, journal = {Heart failure reviews}, volume = {24}, number = {2}, pages = {255-267}, pmid = {30535838}, issn = {1573-7322}, mesh = {ATP-Binding Cassette Transporters/*metabolism ; Animals ; Cardiomegaly/metabolism/pathology ; Electron Transport Chain Complex Proteins/metabolism ; Heart Failure/*metabolism/physiopathology ; Homeostasis/physiology ; Humans ; Iron/metabolism ; Mitochondria, Heart/*metabolism ; Mitochondrial Dynamics/physiology ; Mitochondrial Membrane Transport Proteins/*metabolism ; Mitochondrial Proton-Translocating ATPases/metabolism ; Models, Animal ; Myocytes, Cardiac/*metabolism ; Organelle Biogenesis ; Oxidative Stress/physiology ; Rats ; Reactive Oxygen Species/metabolism ; }, abstract = {Mitochondrial dysfunction is widely recognized as a major factor for the progression of cardiac failure. Mitochondrial uptake of metabolic substrates and their utilization for ATP synthesis, electron transport chain activity, reactive oxygen species levels, ion homeostasis, mitochondrial biogenesis, and dynamics as well as levels of reactive oxygen species in the mitochondria are key factors which regulate mitochondrial function in the normal heart. Alterations in these functions contribute to adverse outcomes in heart failure. Iron imbalance and oxidative stress are also major factors for the evolution of cardiac hypertrophy, heart failure, and aging-associated pathological changes in the heart. Mitochondrial ATP-binding cassette (ABC) transporters have a key role in regulating iron metabolism and maintenance of redox status in cells. Deficiency of mitochondrial ABC transporters is associated with an impaired mitochondrial electron transport chain complex activity, iron overload, and increased levels of reactive oxygen species, all of which can result in mitochondrial dysfunction. In this review, we discuss the role of mitochondrial ABC transporters in mitochondrial metabolism and metabolic switch, alterations in the functioning of ABC transporters in heart failure, and mitochondrial ABC transporters as possible targets for therapeutic intervention in cardiac failure.}, }
@article {pmid30529551, year = {2019}, author = {Liu, J and Yu, J and Zhou, M and Yang, J}, title = {Complete mitochondrial genome of Japalura flaviceps: Deep insights into the phylogeny and gene rearrangements of Agamidae species.}, journal = {International journal of biological macromolecules}, volume = {125}, number = {}, pages = {423-431}, doi = {10.1016/j.ijbiomac.2018.12.068}, pmid = {30529551}, issn = {1879-0003}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Gene Rearrangement/*genetics ; Genome, Mitochondrial/*genetics ; Lizards/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Reptiles/*genetics ; }, abstract = {Japalura flaviceps is a subarboreal species, which is endemically distributed in China. Here, we determined the complete mitogenome of J. flaviceps. This mitogenome was a typical circular molecule of 17,140 bp in size, containing 13 protein-coding genes, 22 transfer-RNA-coding genes, two ribosomal-RNA-coding genes, and one control region. Our phylogenetic result using 15 genes divided all Agamidae lizards into six subfamilies and showed (((((Agaminae, Draconinae), Amphibolurinae), Hydrosaurinae), Uromastycinae), Leiolepinae), which was different from the previous studies. J. flaviceps had a closer relationship to Pseudocalotes species than Acanthosaura species, and they formed a well-supported lineage of Draconinae subfamily. There were nine mitochondrial gene rearrangement types among the 27 Agamidae species, and six of them were found in the Agaminae group. The trnP gene of J. flaviceps mitogenome was encoded on the heavy strand instead of its typical light strand position, providing an example of gene inversion in vertebrate mitogenomes. J. flaviceps shared the same gene arrangement type (inverted trnP gene) with other Draconinae species, strongly implying a single occurrence of the trnP inversion in the ancestral draconine lineage. Our study helps to understand mitogenome evolution and phylogenetic relationship of Agamidae species.}, }
@article {pmid30528084, year = {2019}, author = {Przyboś, E and Rautian, M and Beliavskaia, A and Tarcz, S}, title = {Evaluation of the molecular variability and characteristics of Paramecium polycaryum and Paramecium nephridiatum, within subgenus Cypriostomum (Ciliophora, Protista).}, journal = {Molecular phylogenetics and evolution}, volume = {132}, number = {}, pages = {296-306}, doi = {10.1016/j.ympev.2018.12.003}, pmid = {30528084}, issn = {1095-9513}, mesh = {Bayes Theorem ; DNA, Mitochondrial/genetics/metabolism ; Electron Transport Complex IV/classification/genetics ; Haplotypes ; Likelihood Functions ; Mitochondria/genetics ; Paramecium/*classification ; Phylogeny ; }, abstract = {Although some Paramecium species are suitable research objects in many areas of life sciences, the biodiversity structure of other species is almost unknown. In the current survey, we present a molecular analysis of 60 Cypriostomum strains, which for the first time allows for the study of intra- and interspecific relationships within that subgenus, as well as the assessment of the biogeography patterns of its morphospecies. Analysis of COI mtDNA variation revealed three main clades (separated from each other by approximately 130 nucleotide substitutions), each one with internal sub-clusters (differing by 30 to 70 substitutions - a similar range found between P. aurelia cryptic species and P. bursaria syngens). The first clade is represented exclusively by P. polycaryum; the second one includes only four strains identified as P. calkinsi. The third cluster seems to be paraphyletic, as it includes P. nephridiatum, P. woodruffi, and Eucandidatus P. hungarianum. Some strains, previously identified as P. calkinsi, had COI sequences identical or very similar to P. nephridiatum ones. Morphological reinvestigation of several such strains revealed common morphological features with P. nephridiatum. The paper contains new information concerning speciation within particular species, i.e. existence of cryptic species within P. polycaryum (three) and in P. nephridiatum (six).}, }
@article {pmid30527196, year = {2018}, author = {Kazdal, D and Harms, A and Endris, V and Penzel, R and Oliveira, C and Kriegsmann, M and Longuespée, R and Winter, H and Schneider, MA and Muley, T and Pfarr, N and Weichert, W and Stenzinger, A and Warth, A}, title = {Subclonal evolution of pulmonary adenocarcinomas delineated by spatially distributed somatic mitochondrial mutations.}, journal = {Lung cancer (Amsterdam, Netherlands)}, volume = {126}, number = {}, pages = {80-88}, doi = {10.1016/j.lungcan.2018.10.024}, pmid = {30527196}, issn = {1872-8332}, mesh = {Adenocarcinoma/*genetics/pathology ; Aged ; Clonal Evolution ; DNA, Mitochondrial/classification/*genetics ; Disease-Free Survival ; Female ; Humans ; Lung Neoplasms/*genetics/pathology ; Male ; Middle Aged ; *Mutation ; Mutation Rate ; Phylogeny ; Prognosis ; }, abstract = {OBJECTIVES: The potential role of cancer associated somatic mutations of the mitochondrial genome (mtDNA) is controversial and still poorly understood. Our group and others recently challenged a direct tumorigenic impact and suggested a passenger-like character. In combination with the known increased mutation rate, somatic mtDNA mutations account for an interesting tool to delineate tumor evolution. Here, we comprehensively analyzed the spatial distribution of somatic mtDNA mutations throughout whole tumor sections of pulmonary adenocarcinoma (ADC).<br><br>MATERIALS AND METHODS: Central sections of 19 ADC were analyzed in a segmented manner (11-34 segments/tumor) together with non-neoplastic tissue samples and lymph node metastasis, if present. We performed whole mtDNA sequencing and real-time PCR based quantification of mtDNA copy numbers for all samples. Further, histological growth patterns were determined on H&amp;E sections and the tumor cell content was quantified by digital pathology analyses.<br><br>RESULTS: Somatic mtDNA mutations were present in 96% (18/19) of the analyzed tumors, either ubiquitously or restricted to specific tumor regions. Spatial and histological mapping of the mutations enabled the identification of subclonal structures and phylogenetic relations within a tumor section indicating different progression levels. In this regard, lymph node metastases seem to be related to early events in ADC development. There was no concurrence between histological and mtDNA mutation based clusters. However, micropapillary patterns occurred only in tumors with ubiquitous mutations. ADC with more than two ubiquitous mutations were associated with shorter disease-free survival (p&#x2009;<&#x2009;0.01).<br><br>CONCLUSION: Cancer related mtDNA mutations are interesting candidates for the understanding of subclonal ADC evolution and perspectively for monitoring tumor progression. Our data reveal a potential prognostic relevance of somatic mtDNA mutations.}, }
@article {pmid30526820, year = {2018}, author = {Ndiaye, PI and Marchand, B and Bâ, CT and Justine, JL and Bray, RA and Quilichini, Y}, title = {Ultrastructure of mature spermatozoa of three Bucephalidae (Prosorhynchus longisaccatus, Rhipidocotyle khalili and Bucephalus margaritae) and phylogenetic implications.}, journal = {Parasite (Paris, France)}, volume = {25}, number = {}, pages = {65}, pmid = {30526820}, issn = {1776-1042}, mesh = {Animals ; Axoneme/ultrastructure ; Cell Nucleus/ultrastructure ; Fish Diseases/parasitology ; Fishes ; Male ; Microscopy, Electron, Transmission ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; New Caledonia ; Pacific Ocean ; *Phylogeny ; Spermatozoa/classification/*ultrastructure ; Trematoda/classification/*ultrastructure ; Trematode Infections/parasitology/veterinary ; }, abstract = {We describe here the mature spermatozoa of three species of bucephalids, namely Bucephalus margaritae, Rhipidocotyle khalili and Prosorhynchus longisaccatus. This study provides the first ultrastructural data on the genera Bucephalus and Rhipidocotyle and enabled us to confirm the model of the mature spermatozoon in the Bucephalinae. The spermatozoon exhibits two axonemes with the 9 + "1" pattern of the Trepaxonemata, one of which is very short, lateral expansion, external ornamentation of the plasma membrane located in the anterior extremity of the spermatozoon and associated with cortical microtubules, spine-like bodies, a mitochondrion, and a nucleus. The maximum number of cortical microtubules is located in the anterior part of the spermatozoon. However, more studies are needed to elucidate if spine-like bodies are present in all the Bucephalinae or not. In the Prosorhynchinae, the mature spermatozoon exhibits a similar ultrastructural pattern. Some differences are observed, particularly the axoneme lengths and the arrangement of the spine-like bodies. The posterior extremity of the spermatozoon in the Bucephalinae exhibits only the nucleus, but prosorhynchines have microtubules.}, }
@article {pmid30518034, year = {2018}, author = {Derbikova, K and Kuzmenko, A and Levitskii, S and Klimontova, M and Chicherin, I and Baleva, MV and Krasheninnikov, IA and Kamenski, P}, title = {Biological and Evolutionary Significance of Terminal Extensions of Mitochondrial Translation Initiation Factor 3.}, journal = {International journal of molecular sciences}, volume = {19}, number = {12}, pages = {}, pmid = {30518034}, issn = {1422-0067}, support = {17-14-01005//Russian Science Foundation/ ; 17-54-16005//Russian Foundation for Basic Research/ ; State Assignment AAAA_A16_116021660073_5//Russian Federation Government/ ; }, mesh = {Escherichia coli/metabolism ; *Evolution, Molecular ; Humans ; Mitochondria/*metabolism ; Prokaryotic Initiation Factor-3/*chemistry/*metabolism ; Protein Domains ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; }, abstract = {Protein biosynthesis in mitochondria is organized in a bacterial manner. However, during evolution, mitochondrial translation mechanisms underwent many organelle-specific changes. In particular, almost all mitochondrial translation factors, being orthologous to bacterial proteins, are characterized by some unique elements of primary or secondary structure. In the case of the organellar initiation factor 3 (IF3), these elements are several dozen amino acids long N- and C-terminal extensions. This study focused on the terminal extensions of baker's yeast mitochondrial IF3, Aim23p. By in vivo deletion and complementation analysis, we show that at least one extension is necessary for Aim23p function. At the same time, human mitochondrial IF3 is fully functional in yeast mitochondria even without both terminal extensions. While Escherichia coli IF3 itself is poorly active in yeast mitochondria, adding Aim23p terminal extensions makes the resulting chimeric protein as functional as the cognate factor. Our results show that the terminal extensions of IF3 have evolved as the "adaptors" that accommodate the translation factor of bacterial origin to the evolutionary changed protein biosynthesis system in mitochondria.}, }
@article {pmid30508570, year = {2019}, author = {Hiltunen, JK and Kastaniotis, AJ and Autio, KJ and Jiang, G and Chen, Z and Glumoff, T}, title = {17B-hydroxysteroid dehydrogenases as acyl thioester metabolizing enzymes.}, journal = {Molecular and cellular endocrinology}, volume = {489}, number = {}, pages = {107-118}, doi = {10.1016/j.mce.2018.11.012}, pmid = {30508570}, issn = {1872-8057}, mesh = {17-Hydroxysteroid Dehydrogenases/chemistry/*metabolism ; Animals ; Disease ; Esters/*metabolism ; Fatty Acids, Unsaturated/metabolism ; Humans ; Mitochondria/metabolism ; RNA/metabolism ; }, abstract = {17β-Hydroxysteroid dehydrogenases (HSD17B) catalyze the oxidation/reduction of 17β-hydroxy/keto group in position C17 in C18- and C19 steroids. Most HSD17Bs are also catalytically active with substrates other than steroids. A subset of these enzymes is able to process thioesters of carboxylic acids. This group of enzymes includes HSD17B4, HSD17B8, HSD17B10 and HSD17B12, which execute reactions in intermediary metabolism, participating in peroxisomal β-oxidation of fatty acids, mitochondrial oxidation of 3R-hydroxyacyl-groups, breakdown of isoleucine and fatty acid chain elongation in endoplasmic reticulum. Divergent substrate acceptance capabilities exemplify acquirement of catalytic site adaptiveness during evolution. As an additional common feature these HSD17Bs are multifunctional enzymes that arose either via gene fusions (HSD17B4) or are incorporated as subunits into multifunctional protein complexes (HSD17B8 and HSD17B10). Crystal structures of HSD17B4, HSD17B8 and HSD17B10 give insight into their structure-function relationships. Thus far, deficiencies of HSD17B4 and HSD17B10 have been assigned to inborn errors in humans, underlining their significance as enzymes of metabolism.}, }
@article {pmid30517740, year = {2019}, author = {Petrov, AS and Wood, EC and Bernier, CR and Norris, AM and Brown, A and Amunts, A}, title = {Structural Patching Fosters Divergence of Mitochondrial Ribosomes.}, journal = {Molecular biology and evolution}, volume = {36}, number = {2}, pages = {207-219}, pmid = {30517740}, issn = {1537-1719}, mesh = {Animals ; *Biological Evolution ; Humans ; *Mitochondrial Ribosomes ; Molecular Conformation ; Proteome ; }, abstract = {Mitochondrial ribosomes (mitoribosomes) are essential components of all mitochondria that synthesize proteins encoded by the mitochondrial genome. Unlike other ribosomes, mitoribosomes are highly variable across species. The basis for this diversity is not known. Here, we examine the composition and evolutionary history of mitoribosomes across the phylogenetic tree by combining three-dimensional structural information with a comparative analysis of the secondary structures of mitochondrial rRNAs (mt-rRNAs) and available proteomic data. We generate a map of the acquisition of structural variation and reconstruct the fundamental stages that shaped the evolution of the mitoribosomal large subunit and led to this diversity. Our analysis suggests a critical role for ablation and expansion of rapidly evolving mt-rRNA. These changes cause structural instabilities that are "patched" by the acquisition of pre-existing compensatory elements, thus providing opportunities for rapid evolution. This mechanism underlies the incorporation of mt-tRNA into the central protuberance of the mammalian mitoribosome, and the altered path of the polypeptide exit tunnel of the yeast mitoribosome. We propose that since the toolkits of elements utilized for structural patching differ between mitochondria of different species, it fosters the growing divergence of mitoribosomes.}, }
@article {pmid30517696, year = {2019}, author = {Ilhan, J and Kupczok, A and Woehle, C and Wein, T and Hülter, NF and Rosenstiel, P and Landan, G and Mizrahi, I and Dagan, T}, title = {Segregational Drift and the Interplay between Plasmid Copy Number and Evolvability.}, journal = {Molecular biology and evolution}, volume = {36}, number = {3}, pages = {472-486}, pmid = {30517696}, issn = {1537-1719}, support = {281357/ERC_/European Research Council/International ; }, mesh = {*Biological Evolution ; Chromosomes, Bacterial ; Escherichia coli ; Gene Frequency ; *Genetic Drift ; *Models, Genetic ; Plasmids/*genetics ; }, abstract = {The ubiquity of plasmids in all prokaryotic phyla and habitats and their ability to transfer between cells marks them as prominent constituents of prokaryotic genomes. Many plasmids are found in their host cell in multiple copies. This leads to an increased mutational supply of plasmid-encoded genes and genetically heterogeneous plasmid genomes. Nonetheless, the segregation of plasmid copies into daughter cells during cell division is considered to occur in the absence of selection on the plasmid alleles. We investigate the implications of random genetic drift of multicopy plasmids during cell division-termed here "segregational drift"-to plasmid evolution. Performing experimental evolution of low- and high-copy non-mobile plasmids in Escherichia coli, we find that the evolutionary rate of multicopy plasmids does not reflect the increased mutational supply expected according to their copy number. In addition, simulated evolution of multicopy plasmid alleles demonstrates that segregational drift leads to increased loss frequency and extended fixation time of plasmid mutations in comparison to haploid chromosomes. Furthermore, an examination of the experimentally evolved hosts reveals a significant impact of the plasmid type on the host chromosome evolution. Our study demonstrates that segregational drift of multicopy plasmids interferes with the retention and fixation of novel plasmid variants. Depending on the selection pressure on newly emerging variants, plasmid genomes may evolve slower than haploid chromosomes, regardless of their higher mutational supply. We suggest that plasmid copy number is an important determinant of plasmid evolvability due to the manifestation of segregational drift.}, }
@article {pmid30512221, year = {2019}, author = {Speijer, D}, title = {Can All Major ROS Forming Sites of the Respiratory Chain Be Activated By High FADH2 /NADH Ratios?: Ancient evolutionary constraints determine mitochondrial ROS formation.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {41}, number = {1}, pages = {e1800180}, doi = {10.1002/bies.201800180}, pmid = {30512221}, issn = {1521-1878}, mesh = {Animals ; *Electron Transport ; Eukaryota/metabolism ; Flavin-Adenine Dinucleotide/*metabolism ; Humans ; Mitochondria/*metabolism ; Models, Biological ; NAD/*metabolism ; Oxidation-Reduction ; Reactive Oxygen Species/*metabolism ; }, abstract = {Aspects of peroxisome evolution, uncoupling, carnitine shuttles, supercomplex formation, and missing neuronal fatty acid oxidation (FAO) are linked to reactive oxygen species (ROS) formation in respiratory chains. Oxidation of substrates with high FADH2 /NADH (F/N) ratios (e.g., FAs) initiate ROS formation in Complex I due to insufficient availability of its electron acceptor (Q) and reverse electron transport from QH2 , e.g., during FAO or glycerol-3-phosphate shuttle use. Here it is proposed that the Q-cycle of Complex III contributes to enhanced ROS formation going from low F/N ratio substrates (glucose) to high F/N substrates. This contribution is twofold: 1) Complex III uses Q as substrate, thus also competing with Complex I; 2) Complex III itself will produce more ROS under these conditions. I link this scenario to the universally observed Complex III dimerization. The Q-cycle of Complex III thus again illustrates the tension between efficient ATP generation and endogenous ROS formation. This model can explain recent findings concerning succinate and ROS-induced uncoupling.}, }
@article {pmid30496844, year = {2019}, author = {Boubli, JP and Byrne, H and da Silva, MNF and Silva-Júnior, J and Costa Araújo, R and Bertuol, F and Gonçalves, J and de Melo, FR and Rylands, AB and Mittermeier, RA and Silva, FE and Nash, SD and Canale, G and Alencar, RM and Rossi, RV and Carneiro, J and Sampaio, I and Farias, IP and Schneider, H and Hrbek, T}, title = {On a new species of titi monkey (Primates: Plecturocebus Byrne et al., 2016), from Alta Floresta, southern Amazon, Brazil.}, journal = {Molecular phylogenetics and evolution}, volume = {132}, number = {}, pages = {117-137}, doi = {10.1016/j.ympev.2018.11.012}, pmid = {30496844}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Brazil ; Cytochromes b/genetics ; Ecosystem ; Endangered Species ; Genome ; Mitochondria/genetics ; Phylogeny ; Pitheciidae/anatomy &amp; histology/*classification/genetics ; Polymorphism, Single Nucleotide ; }, abstract = {The taxonomy of the titi monkeys (Callicebinae) has recently received considerable attention. It is now recognised that this subfamily is composed of three genera with 33 species, seven of them described since 2002. Here, we describe a new species of titi, Plecturocebus, from the municipality of Alta Floresta, Mato Grosso, Brazil. We adopt an integrative taxonomic approach that includes phylogenomic analyses, pelage characters, and locality records. A reduced representation genome-wide approach was employed to assess phylogenetic relationships among species of the eastern Amazonian clade of the Plecturocebus moloch group. Using existing records, we calculated the Extent of Occurrence (EOO) of the new species and estimated future habitat loss for the region based on predictive models. We then evaluated the species' conservation status using the IUCN Red list categories and criteria. The new species presents a unique combination of morphological characters: (1) grey agouti colouration on the crown and dorsal parts; (2) entirely bright red-brown venter; (3) an almost entirely black tail with a pale tip; and (4) light yellow colouration of the hair on the cheeks contrasting with bright red-brown hair on the sides of the face. Our phylogenetic reconstructions based on maximum-likelihood and Bayesian methods revealed well-supported species relationships, with the Alta Floresta taxon as sister to P. moloch + P. vieirai. The species EOO is 10,166,653 ha and we predict a total habitat loss of 86% of its original forest habitat under a "business as usual" scenario in the next 24 years, making the newly discovered titi monkey a Critically Endangered species under the IUCN A3c criterion. We give the new titi monkey a specific epithet based on: (1) clear monophyly of this lineage revealed by robust genomic and mitochondrial data; (2) distinct and diagnosable pelage morphology; and (3) a well-defined geographical distribution with clear separation from other closely related taxa. Urgent conservation measures are needed to safeguard the future of this newly discovered and already critically endangered primate.}, }
@article {pmid30487140, year = {2019}, author = {Kolli, R and Soll, J and Carrie, C}, title = {OXA2b is Crucial for Proper Membrane Insertion of COX2 during Biogenesis of Complex IV in Plant Mitochondria.}, journal = {Plant physiology}, volume = {179}, number = {2}, pages = {601-615}, pmid = {30487140}, issn = {1532-2548}, mesh = {Arabidopsis/cytology/*physiology ; Arabidopsis Proteins/genetics/*metabolism ; Electron Transport Complex IV/genetics/*metabolism ; Genetic Complementation Test ; Membrane Proteins/genetics/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Mutation ; Organelle Biogenesis ; Phylogeny ; Plant Cells/metabolism ; Protein Domains ; Seeds/genetics/metabolism ; }, abstract = {The evolutionarily conserved YidC/Oxa1/Alb3 proteins are involved in the insertion of membrane proteins in all domains of life. In plant mitochondria, individual knockouts of OXA1a, OXA2a, and OXA2b are embryo-lethal. In contrast to other members of the protein family, OXA2a and OXA2b contain a tetratricopeptide repeat (TPR) domain at the C-terminus. Here, the role of Arabidopsis (Arabidopsis thaliana) OXA2b was determined by using viable mutant plants that were generated by complementing homozygous lethal OXA2b T-DNA insertional mutants with a C-terminally truncated OXA2b lacking the TPR domain. The truncated-OXA2b-complemented plants displayed severe growth retardation due to a strong reduction in the steady-state abundance and enzyme activity of the mitochondrial respiratory chain complex IV. The TPR domain of OXA2b directly interacts with cytochrome c oxidase subunit 2, aiding in efficient membrane insertion and translocation of its C-terminus. Thus, OXA2b is crucial for the biogenesis of complex IV in plant mitochondria.}, }
@article {pmid30486780, year = {2018}, author = {Fletcher, K and Klosterman, SJ and Derevnina, L and Martin, F and Bertier, LD and Koike, S and Reyes-Chin-Wo, S and Mou, B and Michelmore, R}, title = {Comparative genomics of downy mildews reveals potential adaptations to biotrophy.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {851}, pmid = {30486780}, issn = {1471-2164}, support = {P30 CA093373/CA/NCI NIH HHS/United States ; S10 OD018223/OD/NIH HHS/United States ; S10 RR026825/RR/NCRR NIH HHS/United States ; Endowed Chair in Genomics//Novozymes Inc./ ; C06 RR012088/RR/NCRR NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; *Genomics ; Heterozygote ; Likelihood Functions ; Mitochondria/genetics ; Molecular Sequence Annotation ; Peronospora/*genetics/pathogenicity ; Phylogeny ; Plant Diseases/*microbiology ; Sequence Analysis, RNA ; Terminal Repeat Sequences/genetics ; }, abstract = {BACKGROUND: Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the past 30 years.<br><br>RESULTS: We virulence phenotyped, sequenced, and assembled two isolates of P. effusa from the Salinas Valley, California, U.S.A. that were identified as race 13 and 14. These assemblies are high quality in comparison to assemblies of other downy mildews having low total scaffold count (784 &amp; 880), high contig N50s (48&#xa0;kb &amp; 52&#xa0;kb), high BUSCO completion and low BUSCO duplication scores and share many syntenic blocks with Phytophthora species. Comparative analysis of four downy mildew and three Phytophthora species revealed parallel absences of genes encoding conserved domains linked to transporters, pathogenesis, and carbohydrate activity in the biotrophic species. Downy mildews surveyed that have lost the ability to produce zoospores have a common loss of flagella/motor and calcium domain encoding genes. Our phylogenomic data support multiple origins of downy mildews from hemibiotrophic progenitors and suggest that common gene losses in these downy mildews may be of genes involved in the necrotrophic stages of Phytophthora spp.<br><br>CONCLUSIONS: We present a high-quality draft genome of Peronospora effusa that will serve as a reference for Peronospora spp. We identified several Pfam domains as under-represented in the downy mildews consistent with the loss of zoosporegenesis and necrotrophy. Phylogenomics provides further support for a polyphyletic origin of downy mildews.}, }
@article {pmid30486096, year = {2018}, author = {Agarwal, I and Mahony, S and Giri, VB and Chaitanya, R and Bauer, AM}, title = {Six new Cyrtodactylus (Squamata: Gekkonidae) from northeast India.}, journal = {Zootaxa}, volume = {4524}, number = {5}, pages = {501-535}, doi = {10.11646/zootaxa.4524.5.1}, pmid = {30486096}, issn = {1175-5334}, mesh = {Animals ; *Color ; India ; *Lizards ; Mitochondria ; Myanmar ; Phylogeny ; }, abstract = {We use mitochondrial sequence data to identify divergent lineages within the gekkonid genus Cyrtodactylus in northeast India and use morphological data to describe six new species from within the Indo-Burma clade of Cyrtodactylus. The new species share an irregular colour pattern but differ from described species from the region in morphology and mitochondrial sequence data (>11 % uncorrected pairwise sequence divergence). Three new species are from along the Brahmaputra River and three are from mountains south of the Brahmaputra, including the largest Cyrtodactylus from India and the fifth gecko to be described from a major Indian city, Guwahati.}, }
@article {pmid30484227, year = {2018}, author = {Trosko, JE}, title = {The Role of the Mitochondria in the Evolution of Stem Cells, Including MUSE Stem Cells and Their Biology.}, journal = {Advances in experimental medicine and biology}, volume = {1103}, number = {}, pages = {131-152}, doi = {10.1007/978-4-431-56847-6_7}, pmid = {30484227}, issn = {0065-2598}, mesh = {Adult Stem Cells/cytology ; *Biological Evolution ; Cell Differentiation ; Humans ; Induced Pluripotent Stem Cells/cytology ; Mitochondria/*physiology ; Pluripotent Stem Cells/*cytology ; }, abstract = {From the transition of single-cell organisms to multicellularity of metazoans, evolutionary pressures selected new genes and phenotypes to cope with the oxygenation of the Earth's environment, especially via the symbiotic acquisition of the mitochondrial organelle. There were many new genes and phenotypes that appeared, namely, stem cells, low-oxygen-micro-environments to house these genes ("niches"), new epigenetic mechanisms to regulate , selectively, the gene repertoire to control proliferation, differentiation, apoptosis, senescence and DNA protection mechanisms, including antioxidant genes and DNA repair. This transition required a critical regulation of the metabolism of glucose to produce energy for both the stem cell quiescent state and the energy-requiring differentiated state. While the totipotent-, embryonic-, pluripotent-, and a few adult organ-specific stem cells were recognized, only relatively recently, because of the isolation of somatic cell nuclear transfer (SCNT) stem cells and "induced pluripotent stem" cells, challenges to the origin of these "iPS" cells have been made. The isolation and characterization of human MUSE stem cells and more adult organ-specific adult stem cells have indicated that these MUSE cells have many shared characteristics of the "iPS" cells, yet they do not form teratomas but can give rise to the trigeminal cell layers. While the MUSE cells are a subset of human fibroblastic cells, they have not been characterized, yet, for the mitochondrial metabolic genes, either in the stem cell state or during their differentiation processes. A description of other human adult stem cells will be made to set future studies of how the MUSE stem cells compare to all other stem cells.}, }
@article {pmid30481564, year = {2019}, author = {Xie, B and Wang, S and Jiang, N and Li, JJ}, title = {Cyclin B1/CDK1-regulated mitochondrial bioenergetics in cell cycle progression and tumor resistance.}, journal = {Cancer letters}, volume = {443}, number = {}, pages = {56-66}, pmid = {30481564}, issn = {1872-7980}, support = {R01 CA213830/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; CDC2 Protein Kinase/*metabolism ; Cell Cycle ; Cell Nucleus/metabolism ; Cyclin B1/*metabolism ; *Drug Resistance, Neoplasm ; Energy Metabolism ; Humans ; Mitochondria/metabolism ; Neoplasms/*metabolism ; }, abstract = {A mammalian cell houses two genomes located separately in the nucleus and mitochondria. During evolution, communications and adaptations between these two genomes occur extensively to achieve and sustain homeostasis for cellular functions and regeneration. Mitochondria provide the major cellular energy and contribute to gene regulation in the nucleus, whereas more than 98% of mitochondrial proteins are encoded by the nuclear genome. Such two-way signaling traffic presents an orchestrated dynamic between energy metabolism and consumption in cells. Recent reports have elucidated the way how mitochondrial bioenergetics synchronizes with the energy consumption for cell cycle progression mediated by cyclin B1/CDK1 as the communicator. This review is to recapitulate cyclin B1/CDK1 mediated mitochondrial activities in cell cycle progression and stress response as well as its potential link to reprogram energy metabolism in tumor adaptive resistance. Cyclin B1/CDK1-mediated mitochondrial bioenergetics is applied as an example to show how mitochondria could timely sense the cellular fuel demand and then coordinate ATP output. Such nucleus-mitochondria oscillation may play key roles in the flexible bioenergetics required for tumor cell survival and compromising the efficacy of anti-cancer therapy. Further deciphering the cyclin B1/CDK1-controlled mitochondrial metabolism may invent effect targets to treat resistant cancers.}, }
@article {pmid30480548, year = {2018}, author = {Melvin, RG and Lamichane, N and Havula, E and Kokki, K and Soeder, C and Jones, CD and Hietakangas, V}, title = {Natural variation in sugar tolerance associates with changes in signaling and mitochondrial ribosome biogenesis.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {30480548}, issn = {2050-084X}, mesh = {Animals ; Cellular Reprogramming/genetics ; Diet/methods ; Dietary Sugars/administration &amp; dosage/*metabolism ; Drosophila/drug effects/*genetics/metabolism ; Drosophila Proteins/genetics/metabolism ; Drosophila simulans/drug effects/*genetics/metabolism ; Drug Tolerance/*genetics ; Gene Expression Regulation ; Genetic Variation ; *Genome, Insect ; Larva/drug effects/genetics/metabolism ; Metabolic Networks and Pathways/genetics ; Mitochondria/metabolism ; Organelle Biogenesis ; Protein Phosphatase 1/genetics/metabolism ; Ribosomes/drug effects/metabolism ; Sarcoplasmic Reticulum Calcium-Transporting ATPases/genetics/metabolism ; *Signal Transduction ; Species Specificity ; }, abstract = {How dietary selection affects genome evolution to define the optimal range of nutrient intake is a poorly understood question with medical relevance. We have addressed this question by analyzing Drosophila simulans and sechellia, recently diverged species with differential diet choice. D. sechellia larvae, specialized to a nutrient scarce diet, did not survive on sugar-rich conditions, while the generalist species D. simulans was sugar tolerant. Sugar tolerance in D. simulans was a tradeoff for performance on low-energy diet and was associated with global reprogramming of metabolic gene expression. Hybridization and phenotype-based introgression revealed the genomic regions of D. simulans that were sufficient for sugar tolerance. These regions included genes that are involved in mitochondrial ribosome biogenesis and intracellular signaling, such as PPP1R15/Gadd34 and SERCA, which contributed to sugar tolerance. In conclusion, genomic variation affecting genes involved in global metabolic control defines the optimal range for dietary macronutrient composition.}, }
@article {pmid30477329, year = {2018}, author = {Smith, CF and McGlaughlin, ME and Mackessy, SP}, title = {DNA barcodes from snake venom: a broadly applicable method for extraction of DNA from snake venoms.}, journal = {BioTechniques}, volume = {65}, number = {6}, pages = {339-345}, doi = {10.2144/btn-2018-0096}, pmid = {30477329}, issn = {1940-9818}, mesh = {Alethinophidia/classification/*genetics ; Animals ; Cell Nucleus/genetics ; DNA/*genetics/*isolation &amp; purification ; DNA Barcoding, Taxonomic/*methods ; Mitochondria/genetics ; Phylogeny ; Snake Venoms/classification/*genetics ; }, abstract = {DNA barcoding is a simple technique used to develop a large-scale system of classification that is broadly applicable across a wide variety of taxa. DNA-based analysis of snake venoms can provide a system of classification independent of currently accepted taxonomic relationships by generating DNA barcodes specific to each venom sample. DNA purification from dried snake venoms has previously required large amounts of starting material, has resulted in low yields and inconsistent amplification, and was possible with front-fanged snakes only. Here, we present a modified DNA extraction protocol applied to venoms of both front- and rear-fanged snakes that requires significantly less starting material (1 mg) and yields sufficient amounts of DNA for successful PCR amplification of regions commonly used for DNA barcoding. [Formula: see text].}, }
@article {pmid30474737, year = {2019}, author = {Guo, J and Miao, X and He, P and Li, M and Wang, S and Cui, J and Huang, C and He, L and Zhao, J}, title = {Babesia gibsoni endemic to Wuhan, China: mitochondrial genome sequencing, annotation, and comparison with apicomplexan parasites.}, journal = {Parasitology research}, volume = {118}, number = {1}, pages = {235-243}, pmid = {30474737}, issn = {1432-1955}, support = {2017YFD0500402//National Key Research and Development Program of China/ ; 2015CB150300//National Basic Science Research Program (973 program) of China/ ; 31772729//National Natural Science Foundation of China/ ; 2017CFA020//Natural Science Foundation of Hubei Province/ ; }, mesh = {Amino Acid Sequence ; Animals ; Apicomplexa/classification/genetics/isolation &amp; purification ; Babesia/classification/genetics/*isolation &amp; purification ; Babesiosis/*parasitology ; China/epidemiology ; Cytochromes b/genetics ; DNA Primers/genetics ; Dog Diseases/*parasitology ; Dogs ; *Genome, Mitochondrial ; Molecular Sequence Annotation ; Phylogeny ; Protozoan Infections, Animal/epidemiology/*parasitology ; Sequence Analysis, DNA ; }, abstract = {Babesia gibsoni (B. gibsoni), an intracellular apicomplexan protozoan, poses great threat to canine health. Currently, little information is available about the B. gibsoni (WH58) endemic to Wuhan, China. Here, the mitochondrial (mt) genome of B. gibsoni (WH58) was amplified by five pairs of primers and sequenced and annotated by alignment with the reported mt genome sequences of Babesia canis (B. canis, KC207822), Babesia orientalis (KF218819), Babesia bovis (AB499088), and Theileria equi (AB499091). The evolutionary relationships were analyzed with the amino acid sequences of cytochrome c oxidase I (cox1) and cytochrome b (cob) genes in apicomplexan parasite species. Additionally, the mt genomes of Babesia, Theileria, and Plasmodium spp. were compared in size, host infection, form, distribution, and direction of the protein-coding genes. The full size of the mt genome of B. gibsoni (WH58) was 5865 bp with a linear form, containing terminal-inverted repeats on both ends, six large subunit ribosomal RNA fragments, and three protein-coding genes: cox1, cob, and cytochrome c oxidase III (cox3). Babesia, Theileria, and Plasmodium spp. had a similar mt genome size of about 6000 bp. The mt genomes of parasites that cause canine babesiosis showed a slightly smaller size than the other species. Moreover, Babesia microti (R1 strain) was about 11,100 bp in size, which was twice larger than that of the other species. The mt form was linear for Babesia and Theileria spp. but circular for Plasmodium falciparum and Plasmodium knowlesi. Additionally, all the species contained the three protein-coding genes of cox1, cox3, and cob except Toxoplasma gondii (RH strain) which only contained the cox1 and cob genes. The phylogenetic analysis indicated that B. gibsoni (WH58) was more identical to B. gibsoni (AB499087), B. canis (KC207822), and Babesia rossi (KC207823) and most divergent from Babesia conradae in Babesia spp. Despite the highest similarity to B. gibsoni (AB499087) reported in Japan, B. gibsoni (WH58) showed notable differences in the sequence of nucleotides and amino acids and the property in virulence to host and in vitro cultivation. This study compared the mt genomes of the two B. gibsoni isolates and other parasites in the phylum Apicomplexa and provided new insights into their differences and evolutionary relationships.}, }
@article {pmid30468939, year = {2019}, author = {Weber, AA and Stöhr, S and Chenuil, A}, title = {Species delimitation in the presence of strong incomplete lineage sorting and hybridization: Lessons from Ophioderma (Ophiuroidea: Echinodermata).}, journal = {Molecular phylogenetics and evolution}, volume = {131}, number = {}, pages = {138-148}, doi = {10.1016/j.ympev.2018.11.014}, pmid = {30468939}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial ; Discriminant Analysis ; Echinodermata/*classification/*genetics ; Geography ; *Hybridization, Genetic ; Mitochondria/genetics ; Multigene Family ; *Phylogeny ; Principal Component Analysis ; Species Specificity ; Time Factors ; }, abstract = {Accurate species delimitation is essential to properly assess biodiversity, but also for management and conservation purposes. Yet, it is not always trivial to accurately define species boundaries in closely related species due to incomplete lineage sorting. Additional difficulties may be caused by hybridization, now evidenced as a frequent phenomenon. The brittle star cryptic species complex Ophioderma longicauda encompasses six mitochondrial lineages, including broadcast spawners and internal brooders, yet the actual species boundaries are unknown. Here, we combined three methods to delimit species in the Ophioderma longicauda complex and to infer its divergence history: (i) unsupervised species discovery based on multilocus genotypes; (ii) divergence time estimation using the multi-species coalescent; (iii) divergence scenario testing (including gene flow) using Approximate Bayesian Computation (ABC) methods. 30 sequence markers (transcriptome-based, mitochondrial or non-coding) for 89 O. longicauda and outgroup individuals were used. First, multivariate analyses revealed six genetic clusters, which globally corresponded to the mitochondrial lineages, yet with many exceptions, suggesting ancient hybridization events and challenging traditional mitochondrial barcoding approaches. Second, multi-species coalescent-based analyses confirmed the occurrence of six species and provided divergence time estimates, but the sole use of this method failed to accurately delimit species, highlighting the power of multilocus genotype clustering to delimit recently diverged species. Finally, Approximate Bayesian Computation showed that the most likely scenario involves hybridization between brooders and broadcasters. Our study shows that despite strong incomplete lineage sorting and past hybridization, accurate species delimitation in Ophioderma was possible using a combination of complementary methods. We propose that these methods, especially multilocus genotype clustering, may be useful to resolve other complex speciation histories.}, }
@article {pmid30467693, year = {2019}, author = {Aw, WC and Garvin, MR and Ballard, JWO}, title = {Exogenous Factors May Differentially Influence the Selective Costs of mtDNA Mutations.}, journal = {Advances in anatomy, embryology, and cell biology}, volume = {231}, number = {}, pages = {51-74}, doi = {10.1007/102_2018_2}, pmid = {30467693}, issn = {0301-5556}, mesh = {Cell Nucleus/*metabolism ; DNA, Mitochondrial/*genetics ; Diet ; Electron Transport Complex I/*metabolism ; Energy Metabolism/*genetics/physiology ; Evolution, Molecular ; Genetic Fitness ; Humans ; Mitochondria/genetics/*metabolism ; Mutation ; Nutrients/*metabolism ; Signal Transduction/genetics ; Stress, Physiological ; Temperature ; }, abstract = {In this review, we provide evidence to suggest that the cost of specific mtDNA mutations can be influenced by exogenous factors. We focus on macronutrient-mitochondrial DNA interactions as factors that may differentially influence the consequences of a change as mitochondria must be flexible in its utilization of dietary proteins, carbohydrates, and fats. To understand this fundamental dynamic, we briefly discuss the energy processing pathways in mitochondria. Next, we explore the mitochondrial functions that are initiated during energy deficiency or when cells encounter cellular stress. We consider the anterograde response (nuclear control of mitochondrial function) and the retrograde response (nuclear changes in response to mitochondrial signaling) and how this mito-nuclear crosstalk may be influenced by exogenous factors such as temperature and diet. Finally, we employ Complex I of the mitochondrial electron transport system as a case study and discuss the potential role of the dietary macronutrient ratio as a strong selective force that may shape the frequencies of mitotypes in populations and species. We conclude that this underexplored field likely has implications in the fundamental disciplines of evolutionary biology and quantitative genetics and the more biomedical fields of nutrigenomics and pharmacogenomics.}, }
@article {pmid30466901, year = {2019}, author = {Hampl, V and Čepička, I and Eliáš, M}, title = {Was the Mitochondrion Necessary to Start Eukaryogenesis?.}, journal = {Trends in microbiology}, volume = {27}, number = {2}, pages = {96-104}, doi = {10.1016/j.tim.2018.10.005}, pmid = {30466901}, issn = {1878-4380}, mesh = {Adenosine Triphosphate ; Archaea/physiology ; *Biological Evolution ; Eukaryota/genetics/*physiology ; Eukaryotic Cells/*physiology ; Genome ; Mitochondria/genetics/*physiology ; Phagocytosis ; Prokaryotic Cells/physiology ; Symbiosis ; }, abstract = {Arguments based on cell energetics favour the view that a mitochondrion capable of oxidative phosphorylation was a prerequisite for the evolution of other features of the eukaryotic cell, including increased volume, genome size and, eventually, phagotrophy. Contrary to this we argue that: (i) extant amitochondriate eukaryotes possess voluminous phagotrophic cells with large genomes; (ii) picoeukaryotes demonstrate that phagotrophy is feasible at prokaryotic cell sizes; and (iii) the assumption that evolution of complex features requires extra ATP, often mentioned in this context, is unfounded and should not be used in such considerations. We claim that the diversity of cell organisations and functions observed today in eukaryotes gives no reason to postulate that a mitochondrion must have preceded phagocytosis in eukaryogenesis.}, }
@article {pmid30466434, year = {2018}, author = {Petrů, M and Wideman, J and Moore, K and Alcock, F and Palmer, T and Doležal, P}, title = {Evolution of mitochondrial TAT translocases illustrates the loss of bacterial protein transport machines in mitochondria.}, journal = {BMC biology}, volume = {16}, number = {1}, pages = {141}, pmid = {30466434}, issn = {1741-7007}, mesh = {Escherichia coli/genetics ; Escherichia coli Proteins/chemistry/genetics/metabolism ; Eukaryota/*genetics ; *Evolution, Molecular ; Membrane Transport Proteins/*genetics/*metabolism ; Mitochondria/metabolism ; Protein Transport ; }, abstract = {BACKGROUND: Bacteria and mitochondria contain translocases that function to transport proteins across or insert proteins into their inner and outer membranes. Extant mitochondria retain some bacterial-derived translocases but have lost others. While BamA and YidC were integrated into general mitochondrial protein transport pathways (as Sam50 and Oxa1), the inner membrane TAT translocase, which uniquely transports folded proteins across the membrane, was retained sporadically across the eukaryote tree.<br><br>RESULTS: We have identified mitochondrial TAT machinery in diverse eukaryotic lineages and define three different types of eukaryote-encoded TatABC-derived machineries (TatAC, TatBC and TatC-only). Here, we investigate TatAC and TatC-only machineries, which have not been studied previously. We show that mitochondria-encoded TatAC of the jakobid Andalucia godoyi represent the minimal functional pathway capable of substituting for the Escherichia coli TatABC complex and can transport at least one substrate. However, selected TatC-only machineries, from multiple eukaryotic lineages, were not capable of supporting the translocation of this substrate across the bacterial membrane. Despite the multiple losses of the TatC gene from the mitochondrial genome, the gene was never transferred to the cell nucleus. Although the major constraint preventing nuclear transfer of mitochondrial TatC is likely its high hydrophobicity, we show that in chloroplasts, such transfer of TatC was made possible due to modifications of the first transmembrane domain.<br><br>CONCLUSIONS: At its origin, mitochondria inherited three inner membrane translocases Sec, TAT and Oxa1 (YidC) from its bacterial ancestor. Our work shows for the first time that mitochondrial TAT has likely retained its unique function of transporting folded proteins at least in those few eukaryotes with TatA and TatC subunits encoded in the mitochondrial genome. However, mitochondria, in contrast to chloroplasts, abandoned the machinery multiple times in evolution. The overall lower hydrophobicity of the Oxa1 protein was likely the main reason why this translocase was nearly universally retained in mitochondrial biogenesis pathways.}, }
@article {pmid30464337, year = {2018}, author = {Chen, YL and Chen, LJ and Chu, CC and Huang, PK and Wen, JR and Li, HM}, title = {TIC236 links the outer and inner membrane translocons of the chloroplast.}, journal = {Nature}, volume = {564}, number = {7734}, pages = {125-129}, doi = {10.1038/s41586-018-0713-y}, pmid = {30464337}, issn = {1476-4687}, mesh = {Arabidopsis/*cytology/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Bacterial Outer Membrane Proteins/metabolism ; Chloroplast Proteins/genetics/*metabolism ; Chloroplasts/genetics/*metabolism ; Escherichia coli Proteins/metabolism ; Evolution, Molecular ; Intracellular Membranes/*metabolism ; Membrane Proteins/genetics/*metabolism ; Membrane Transport Proteins/genetics/*metabolism ; Multiprotein Complexes/genetics/metabolism ; Mutation ; Pisum sativum/cytology ; Protein Binding ; Protein Precursors/metabolism ; Protein Transport ; }, abstract = {The two-membrane envelope is a defining feature of chloroplasts. Chloroplasts evolved from a Gram-negative cyanobacterial endosymbiont. During evolution, genes of the endosymbiont have been transferred to the host nuclear genome. Most chloroplast proteins are synthesized in the cytosol as higher-molecular-mass preproteins with an N-terminal transit peptide. Preproteins are transported into chloroplasts by the TOC and TIC (translocons at the outer- and inner-envelope membranes of chloroplasts, respectively) machineries[1,2], but how TOC and TIC are assembled together is unknown. Here we report the identification of the TIC component TIC236; TIC236 is an integral inner-membrane protein that projects a 230-kDa domain into the intermembrane space, which binds directly to the outer-membrane channel TOC75. The knockout mutation of TIC236 is embryonically lethal. In TIC236-knockdown mutants, a smaller amount of the inner-membrane channel TIC20 was associated with TOC75; the amount of TOC-TIC supercomplexes was also reduced. This resulted in a reduced import rate into the stroma, though outer-membrane protein insertion was unaffected. The size and the essential nature of TIC236 indicate that-unlike in mitochondria, in which the outer- and inner-membrane translocons exist as separate complexes and a supercomplex is only transiently assembled during preprotein translocation[3,4]-a long and stable protein bridge in the intermembrane space is required for protein translocation into chloroplasts. Furthermore, TIC236 and TOC75 are homologues of bacterial inner-membrane TamB[5] and outer-membrane BamA, respectively. Our evolutionary analyses show that, similar to TOC75, TIC236 is preserved only in plants and has co-evolved with TOC75 throughout the plant lineage. This suggests that the backbone of the chloroplast protein-import machinery evolved from the bacterial TamB-BamA protein-secretion system.}, }
@article {pmid30456441, year = {2019}, author = {Serrano-Solís, V and Toscano Soares, PE and de Farías, ST}, title = {Genomic Signatures Among Acanthamoeba polyphaga Entoorganisms Unveil Evidence of Coevolution.}, journal = {Journal of molecular evolution}, volume = {87}, number = {1}, pages = {7-15}, pmid = {30456441}, issn = {1432-1432}, mesh = {Acanthamoeba/*genetics ; Amoeba/genetics ; Animals ; Bacteria/genetics ; Biological Coevolution/*genetics ; Codon/genetics ; Evolution, Molecular ; Genome, Viral ; Genomics ; Mimiviridae/*genetics ; Mitochondria/genetics ; Parasites/genetics ; Viral Proteins/genetics ; Virophages/genetics ; }, abstract = {The definition of a genomic signature (GS) is "the total net response to selective pressure". Recent isolation and sequencing of naturally occurring organisms, hereby named entoorganisms, within Acanthamoeba polyphaga, raised the hypothesis of a common genomic signature despite their diverse and unrelated evolutionary origin. Widely accepted and implemented tests for GS detection are oligonucleotide relative frequencies (OnRF) and relative codon usage (RCU) surveys. A common pattern and strong correlations were unveiled from OnRFs among A. polyphaga's Mimivirus and virophage Sputnik. RCU showed a common A-T bias at third codon position. We expanded tests to the amoebal mitochondrial genome and amoeba-resistant bacteria, achieving strikingly coherent results to the aforementioned viral analyses. The GSs in these entoorganisms of diverse evolutionary origin are coevolutionarily conserved within an intracellular environment that provides sanctuary for species of ecological and biomedical relevance.}, }
@article {pmid30446962, year = {2019}, author = {Xie, T and Hu, L and Guo, YX and Li, YC and Chen, F and Zhu, BF}, title = {Genetic polymorphism analysis of mitochondrial DNA from Chinese Xinjiang Kazak ethnic group by a novel mitochondrial DNA genotyping panel.}, journal = {Molecular biology reports}, volume = {46}, number = {1}, pages = {17-25}, pmid = {30446962}, issn = {1573-4978}, support = {81525015//National Natural Science Foundation of China/ ; }, mesh = {Adult ; Alleles ; Asian People/*genetics ; China/ethnology ; DNA, Mitochondrial/blood/*genetics ; Ethnicity/genetics ; Female ; Gene Frequency/genetics ; Genetic Markers ; Genetics, Population/methods ; Genotype ; Genotyping Techniques/*methods ; Haplotypes/genetics ; Healthy Volunteers ; Humans ; Male ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic/genetics ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Genetic polymorphism analysis of 60 mitochondrial DNA (mtDNA) loci in Chinese Xinjiang Kazak group was conducted in this study. Blood samples from 141 unrelated healthy volunteers were randomly collected from Chinese Kazak ethnic group in Ili, Xinjiang Uygur Autonomous region. Among these mtDNA loci, single nucleotide transition was the most commonly observed variant (87.93%). A total of 25 haplogroups and 79 haplotypes were found in Kazak group, and Haplogroup D4 was the most common haplogroup (21.28%). Among the entire 79 haplotypes, 53 of them were observed for only once, 14 for twice. The haplotype diversity was 0.978 ± 0.005, and the nucleotide diversity was 0.17449. The detection of (CA)n and 9-bp deletion polymorphisms could improve the discrimination power of the mtDNA genetic marker. Moreover, Xinjiang Kazak group was compared with other previously reported groups to infer its genetic background. The present results revealed that Xinjiang Kazak ethnic group was genetically closer related to Xinjiang Uygur, Xinjiang Uzbek and Xinjiang Han populations. Meanwhile, our results also indicated the potential closer genetic relationships among Xinjiang Kazak group with Altaian Kazak as well as Xinjiang Xibe group. In conclusion, this novel mtDNA panel could be effectively utilized for forensic applications. Additionally, to further reveal the genetic background of Chinese Kazak group, more relevant populations and genetic markers should be incorporated in our future study.}, }
@article {pmid30446790, year = {2019}, author = {Razzak, MA and Lee, J and Lee, DW and Kim, JH and Yoon, HS and Hwang, I}, title = {Expression of seven carbonic anhydrases in red alga Gracilariopsis chorda and their subcellular localization in a heterologous system, Arabidopsis thaliana.}, journal = {Plant cell reports}, volume = {38}, number = {2}, pages = {147-159}, pmid = {30446790}, issn = {1432-203X}, support = {2016R1E1A1A02922014//Ministry of Fisheries/ ; }, mesh = {Arabidopsis/*genetics ; Carbonic Anhydrases/classification/*metabolism ; Computer Simulation ; Endoplasmic Reticulum/metabolism ; Gene Expression Regulation, Enzymologic ; Glycosylation ; Golgi Apparatus/metabolism ; Green Fluorescent Proteins/metabolism ; Phylogeny ; Plants, Genetically Modified ; Protein Transport ; Protoplasts/metabolism ; Rhodophyta/*enzymology ; Subcellular Fractions/metabolism ; Vacuoles/metabolism ; }, abstract = {Red alga, Gracilariopsis chorda, contains seven carbonic anhydrases that can be grouped into α-, β- and γ-classes. Carbonic anhydrases (CAHs) are metalloenzymes that catalyze the reversible hydration of CO2. These enzymes are present in all living organisms and play roles in various cellular processes, including photosynthesis. In this study, we identified seven CAH genes (GcCAHs) from the genome sequence of the red alga Gracilariopsis chorda and characterized them at the molecular, cellular and biochemical levels. Based on sequence analysis, these seven isoforms were categorized into four α-class, one β-class, and two γ-class isoforms. RNA sequencing revealed that of the seven CAHs isoforms, six genes were expressed in G. chorda in light at room temperature. In silico analysis revealed that these seven isoforms localized to multiple subcellular locations such as the ER, mitochondria and cytosol. When expressed as green fluorescent protein fusions in protoplasts of Arabidopsis thaliana leaf cells, these seven isoforms showed multiple localization patterns. The four α-class GcCAHs with an N-terminal hydrophobic leader sequence localized to the ER and two of them were further targeted to the vacuole. GcCAHβ1 with no noticeable signal sequence localized to the cytosol. The two γ-class GcCAHs also localized to the cytosol, despite the presence of a predicted presequence. Based on these results, we propose that the red alga G. chorda also employs multiple CAH isoforms for various cellular processes such as photosynthesis.}, }
@article {pmid30445187, year = {2019}, author = {Johnston, IG}, title = {Tension and Resolution: Dynamic, Evolving Populations of Organelle Genomes within Plant Cells.}, journal = {Molecular plant}, volume = {12}, number = {6}, pages = {764-783}, doi = {10.1016/j.molp.2018.11.002}, pmid = {30445187}, issn = {1752-9867}, mesh = {Cell Nucleus/metabolism ; Chloroplasts/metabolism ; Mitochondria/*metabolism ; Organelles/metabolism ; Plant Cells/*metabolism ; Plastids/metabolism ; }, abstract = {Mitochondria and plastids form dynamic, evolving populations physically embedded in the fluctuating environment of the plant cell. Their evolutionary heritage has shaped how the cell controls the genetic structure and the physical behavior of its organelle populations. While the specific genes involved in these processes are gradually being revealed, the governing principles underlying this controlled behavior remain poorly understood. As the genetic and physical dynamics of these organelles are central to bioenergetic performance and plant physiology, this challenges both fundamental biology and strategies to engineer better-performing plants. This article reviews current knowledge of the physical and genetic behavior of mitochondria and chloroplasts in plant cells. An overarching hypothesis is proposed whereby organelles face a tension between genetic robustness and individual control and responsiveness, and different species resolve this tension in different ways. As plants are immobile and thus subject to fluctuating environments, their organelles are proposed to favor individual responsiveness, sacrificing genetic robustness. Several notable features of plant organelles, including large genomes, mtDNA recombination, fragmented organelles, and plastid/mitochondrial differences may potentially be explained by this hypothesis. Finally, the ways that quantitative and systems biology can help shed light on the plethora of open questions in this field are highlighted.}, }
@article {pmid30443184, year = {2018}, author = {Dou, X and Chen, L and Lei, M and Zellmer, L and Jia, Q and Ling, P and He, Y and Yang, W and Liao, DJ}, title = {Evaluating the Remote Control of Programmed Cell Death, with or without a Compensatory Cell Proliferation.}, journal = {International journal of biological sciences}, volume = {14}, number = {13}, pages = {1800-1812}, pmid = {30443184}, issn = {1449-2288}, mesh = {Animals ; Apoptosis/genetics/*physiology ; Cell Death/genetics/*physiology ; Cell Proliferation/genetics/*physiology ; Humans ; Necrosis ; }, abstract = {Organisms and their different component levels, whether organelle, cellular or other, come by birth and go by death, and the deaths are often balanced by new births. Evolution on the one hand has built demise program(s) in cells of organisms but on the other hand has established external controls on the program(s). For instance, evolution has established death program(s) in animal cells so that the cells can, when it is needed, commit apoptosis or senescent death (SD) in physiological situations and stress-induced cell death (SICD) in pathological situations. However, these programmed cell deaths are not predominantly regulated by the cells that do the dying but, instead, are controlled externally and remotely by the cells' superior(s), i.e. their host tissue or organ or even the animal's body. Currently, it is still unclear whether a cell has only one death program or has several programs respectively controlling SD, apoptosis and SICD. In animals, apoptosis exterminates, in a physiological manner, healthy but no-longer needed cells to avoid cell redundancy, whereas suicidal SD and SICD, like homicidal necrosis, terminate ill but useful cells, which may be followed by regeneration of the live cells and by scar formation to heal the damaged organ or tissue. Therefore, "who dies" clearly differentiates apoptosis from SD, SICD and necrosis. In animals, apoptosis can occur only in those cell types that retain a lifelong ability of proliferation and never occurs in those cell types that can no longer replicate in adulthood. In cancer cells, SICD is strengthened, apoptosis is dramatically weakened while SD has been lost. Most published studies professed to be about apoptosis are actually about SICD, which has four basic and well-articulated pathways involving caspases or involving pathological alterations in the mitochondria, endoplasmic reticula, or lysosomes.}, }
@article {pmid30433779, year = {2018}, author = {Fujisawa, A and Tamura, T and Yasueda, Y and Kuwata, K and Hamachi, I}, title = {Chemical Profiling of the Endoplasmic Reticulum Proteome Using Designer Labeling Reagents.}, journal = {Journal of the American Chemical Society}, volume = {140}, number = {49}, pages = {17060-17070}, doi = {10.1021/jacs.8b08606}, pmid = {30433779}, issn = {1520-5126}, mesh = {Carboxy-Lyases/analysis/chemistry ; Chromatography, Liquid ; Cyclophilin A/analysis/chemistry ; Endoplasmic Reticulum/*chemistry/metabolism ; Endoplasmic Reticulum Stress/drug effects ; HeLa Cells ; Humans ; Molecular Probes/chemical synthesis/*chemistry ; Multifunctional Enzymes/analysis/chemistry ; Peptide Synthases/analysis/chemistry ; Proteome/*analysis/chemistry ; Proteomics/methods ; Tandem Mass Spectrometry ; Thioredoxins/analysis/chemistry ; Tunicamycin/pharmacology ; Unfolded Protein Response/drug effects ; Xanthenes/chemical synthesis/*chemistry ; }, abstract = {The endoplasmic reticulum (ER) is an organelle that performs a variety of essential cellular functions via interactions with other organelles. Despite its important role, chemical tools for profiling the composition and dynamics of ER proteins remain very limited because of the labile nature of these proteins. Here, we developed ER-localizable reactive molecules (called ERMs) as tools for ER-focused chemical proteomics. ERMs can spontaneously localize in the ER of living cells and selectively label ER-associated proteins with a combined affinity and imaging tag, enabling tag-mediated ER protein enrichment and identification with liquid chromatography tandem mass spectrometry (LC-MS/MS). Using this method, we performed proteomic analysis of the ER of HeLa cells and newly assigned three proteins, namely, PAICS, TXNL1, and PPIA, as ER-associated proteins. The ERM probes could be used simultaneously with the nucleus- and mitochondria-localizable reactive molecules previously developed by our group, which enabled orthogonal organellar chemoproteomics in a single biological sample. Moreover, quantitative analysis of the dynamic changes in ER-associated proteins in response to tunicamycin-induced ER stress was performed by combining ER-specific labeling with SILAC (stable isotope labeling by amino acids in cell culture)-based quantitative MS technology. Our results demonstrated that ERM-based chemical proteomics provides a powerful tool for labeling and profiling ER-related proteins in living cells.}, }
@article {pmid30421421, year = {2019}, author = {Patten, MM}, title = {The X chromosome favors males under sexually antagonistic selection.}, journal = {Evolution; international journal of organic evolution}, volume = {73}, number = {1}, pages = {84-91}, doi = {10.1111/evo.13646}, pmid = {30421421}, issn = {1558-5646}, mesh = {Animals ; *Biological Evolution ; Female ; Male ; Models, Genetic ; *Selection, Genetic ; X Chromosome/*genetics ; }, abstract = {The X chromosome is found twice as often in females as males. This has led to an intuition that X-linked genes for traits experiencing sexually antagonistic selection should tend to evolve toward the female optimum. However, this intuition has never been formally examined. In this paper, I present a simple mathematical model and ask whether the X chromosome is indeed biased toward effecting female-optimal phenotypes. Counter to the intuition, I find that the exact opposite bias exists; the X chromosome is revealed to be a welcome spot for mutations that benefit males at the expense of females. Not only do male-beneficial alleles have an easier time of invading and spreading through a population, but they also achieve higher equilibrium frequencies than comparable female-beneficial alleles. The X chromosome is therefore expected over evolutionary time to nudge phenotypes closer to the male optimum. Consequently, the X chromosome should find itself engaged in perpetual intragenomic conflicts with the autosomes and the mitochondria over developmental outcomes. The X chromosome's male bias and the intragenomic conflicts that ensue bear on the evolution of gene regulation, speciation, and our concept of organismality.}, }
@article {pmid30419142, year = {2018}, author = {Muthye, V and Lavrov, DV}, title = {Characterization of mitochondrial proteomes of nonbilaterian animals.}, journal = {IUBMB life}, volume = {70}, number = {12}, pages = {1289-1301}, doi = {10.1002/iub.1961}, pmid = {30419142}, issn = {1521-6551}, mesh = {Animals ; Cell Nucleus/genetics ; Computational Biology ; Ctenophora/*genetics ; DNA, Mitochondrial ; *Evolution, Molecular ; Humans ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Phylogeny ; Proteome/genetics ; }, abstract = {Mitochondria require ~1,500 proteins for their maintenance and proper functionality, which constitute the mitochondrial proteome (mt-proteome). Although a few of these proteins, mostly subunits of the electron transport chain complexes, are encoded in mitochondrial DNA (mtDNA), the vast majority are encoded in the nuclear genome and imported to the organelle. Previous studies have shown a continuous and complex evolution of mt-proteome among eukaryotes. However, there was less attention paid to mt-proteome evolution within Metazoa, presumably because animal mtDNA and, by extension, animal mitochondria are often considered to be uniform. In this analysis, two bioinformatic approaches (Orthologue-detection and Mitochondrial Targeting Sequence prediction) were used to identify mt-proteins in 23 species from four nonbilaterian phyla: Cnidaria, Ctenophora, Placozoa, and Porifera, as well as two choanoflagellates, the closest animal relatives. Our results revealed a large variation in mt-proteome in nonbilaterian animals in size and composition. Myxozoans, highly reduced cnidarian parasites, possessed the smallest inferred mitochondrial proteomes, while calcareous sponges possessed the largest. About 513 mitochondrial orthologous groups were present in all nonbilaterian phyla and human. Interestingly, 42 human mitochondrial proteins were not identified in any nonbilaterian species studied and represent putative innovations along the bilaterian branch. Several of these proteins were involved in apoptosis and innate immunity, two processes known to evolve within Metazoa. Conversely, several proteins identified as mitochondrial in nonbilaterian phyla and animal outgroups were absent in human, representing cases of possible loss. Finally, a few human cytosolic proteins, such as histones and cytosolic ribosomal proteins, were predicted to be targeted to mitochondria in nonbilaterian animals. Overall, our analysis provides the first step in characterization of mt-proteomes in nonbilaterian animals and understanding evolution of animal mt-proteome. © 2018 IUBMB Life, 70(12):1289-1301, 2018.}, }
@article {pmid30417348, year = {2019}, author = {Lasne, C and Van Heerwaarden, B and Sgrò, CM and Connallon, T}, title = {Quantifying the relative contributions of the X chromosome, autosomes, and mitochondrial genome to local adaptation.}, journal = {Evolution; international journal of organic evolution}, volume = {73}, number = {2}, pages = {262-277}, doi = {10.1111/evo.13647}, pmid = {30417348}, issn = {1558-5646}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Drosophila melanogaster/*genetics ; Female ; Food Deprivation ; Gene Expression Regulation ; Genes, X-Linked ; Genome, Mitochondrial/*genetics ; Hot Temperature ; Male ; Models, Biological ; Water Deprivation ; Wings, Animal/anatomy &amp; histology ; *X Chromosome ; }, abstract = {During local adaptation with gene flow, some regions of the genome are inherently more responsive to selection than others. Recent theory predicts that X-linked genes should disproportionately contribute to local adaptation relative to other genomic regions, yet this prediction remains to be tested. We carried out a multigeneration crossing scheme, using two cline-end populations of Drosophila melanogaster, to estimate the relative contributions of the X chromosome, autosomes, and mitochondrial genome to divergence in four traits involved in local adaptation (wing size, resistance to heat, desiccation, and starvation stresses). We found that the mitochondrial genome and autosomes contributed significantly to clinal divergence in three of the four traits. In contrast, the X made no significant contribution to divergence in these traits. Given the small size of the mitochondrial genome, our results indicate that it plays a surprisingly large role in clinal adaptation. In contrast, the X, which represents roughly 20% of the Drosophila genome, contributes negligibly-a pattern that conflicts with theoretical predictions. These patterns reinforce recent work implying a central role of mitochondria in climatic adaptation, and suggest that different genomic regions may play fundamentally different roles in processes of divergence with gene flow.}, }
@article {pmid30403999, year = {2018}, author = {Wettmarshausen, J and Goh, V and Huang, KT and Arduino, DM and Tripathi, U and Leimpek, A and Cheng, Y and Pittis, AA and Gabaldón, T and Mokranjac, D and Hajnóczky, G and Perocchi, F}, title = {MICU1 Confers Protection from MCU-Dependent Manganese Toxicity.}, journal = {Cell reports}, volume = {25}, number = {6}, pages = {1425-1435.e7}, doi = {10.1016/j.celrep.2018.10.037}, pmid = {30403999}, issn = {2211-1247}, support = {R01 GM102724/GM/NIGMS NIH HHS/United States ; }, mesh = {Apoptosis/drug effects ; Calcium Channels/*metabolism ; Calcium-Binding Proteins/*metabolism ; Cation Transport Proteins/*metabolism ; *Cytoprotection/drug effects ; Eukaryota ; Evolution, Molecular ; HEK293 Cells ; HeLa Cells ; Humans ; Iron/toxicity ; Manganese/*toxicity ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins/*metabolism ; Phylogeny ; Saccharomyces cerevisiae/metabolism ; Stress, Physiological/drug effects ; }, abstract = {The mitochondrial calcium uniporter is a highly selective ion channel composed of species- and tissue-specific subunits. However, the functional role of each component still remains unclear. Here, we establish a synthetic biology approach to dissect the interdependence between the pore-forming subunit MCU and the calcium-sensing regulator MICU1. Correlated evolutionary patterns across 247 eukaryotes indicate that their co-occurrence may have conferred a positive fitness advantage. We find that, while the heterologous reconstitution of MCU and EMRE in vivo in yeast enhances manganese stress, this is prevented by co-expression of MICU1. Accordingly, MICU1 deletion sensitizes human cells to manganese-dependent cell death by disinhibiting MCU-mediated manganese uptake. As a result, manganese overload increases oxidative stress, which can be effectively prevented by NAC treatment. Our study identifies a critical contribution of MICU1 to the uniporter selectivity, with important implications for patients with MICU1 deficiency, as well as neurological disorders arising upon chronic manganese exposure.}, }
@article {pmid30395997, year = {2019}, author = {López-Rubio, A and Suaza-Vasco, JD and Solari, S and Gutiérez-Builes, L and Porter, C and Uribe, SI}, title = {Intraspecific phylogeny of Anopheles (Kerteszia) neivai Howard, Dyar &amp; Knab 1913, based on mitochondrial and nuclear ribosomal genes.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {67}, number = {}, pages = {183-190}, doi = {10.1016/j.meegid.2018.10.013}, pmid = {30395997}, issn = {1567-7257}, mesh = {Animals ; Anopheles/*classification/*genetics ; Central America/epidemiology ; *Genes, Mitochondrial ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/*genetics ; South America/epidemiology ; }, abstract = {Three mitochondrial regions and a fragment of a large nuclear ribosomal subunit was used to study the evolutionary patterns of An. neivai, a mosquito inhabiting mangroves and tropical forest in the lowland and coastal areas of the Yucatan Peninsula through the Pacific Ecuadorian coast. This species exhibits epidemiological importance regarding Malaria transmission in natural ecosystems, particularly in rural areas of the Pacific Colombian coast. The results based on phylogenetic networks and Bayesian inference showed no robust evidence supporting the existence of previously suggested cryptic species. Diversification patterns in geographically widespread species such as this one, are complex and therefore could impact malaria control strategies. Further studies focused on behavior, morphology, and phylogenomics will improve the understanding of the evolutionary patterns within An. neivai and its role as a disease vector.}, }
@article {pmid30395972, year = {2019}, author = {Fan, PC and Zhang, Y and Wang, Y and Wei, W and Zhou, YX and Xie, Y and Wang, X and Qi, YZ and Chang, L and Jia, ZP and Zhou, Z and Guan, H and Zhang, H and Xu, P and Zhou, PK}, title = {Quantitative proteomics reveals mitochondrial respiratory chain as a dominant target for carbon ion radiation: Delayed reactive oxygen species generation caused DNA damage.}, journal = {Free radical biology &amp; medicine}, volume = {130}, number = {}, pages = {436-445}, doi = {10.1016/j.freeradbiomed.2018.10.449}, pmid = {30395972}, issn = {1873-4596}, mesh = {Antioxidants/pharmacology ; Cell Line, Tumor ; DNA Damage/genetics/radiation effects ; DNA Repair/genetics/radiation effects ; Electron Transport/*radiation effects ; Heavy Ion Radiotherapy/adverse effects ; Humans ; Mitochondria/metabolism/*radiation effects ; Neoplasms/genetics/metabolism/*radiotherapy ; *Proteomics ; Reactive Oxygen Species/metabolism ; }, abstract = {Heavy ion radiotherapy has shown great promise for cancer therapy. Understanding the cellular response mechanism to heavy ion radiation is required to explore measures of overcoming devastating side effects. Here, we performed a quantitative proteomic analysis to investigate the mechanism of carbon ion irradiation on human AHH-1 lymphoblastoid cells. We identified 4602 proteins and quantified 4569 proteins showing high coverage in the mitochondria. Data are available via ProteomeXchange with identifier PXD008351. After stringent filtering, 290 proteins were found to be significantly up-regulated and 16 proteins were down-regulated. Functional analysis revealed that these up-regulated proteins were enriched in the process of DNA damage repair, mitochondrial ribosome, and particularly mitochondrial respiratory chain, accounting for approximately 50% of the accumulated proteins. Bioinformatics and functional analysis demonstrated that these up-regulated mitochondrial respiratory chain proteins enhanced ATP production and simultaneously reactive oxygen species release. More importantly, increased reactive oxygen species led to secondary organelle injury and lagged DNA double-strand breaks. Consistently, the expression of antioxidant enzymes was up-regulated for free radical scavenging. The mechanism of lagged secondary injury originated from disturbances in the mitochondrial respiratory chain. Our results provided a novel target for cell self-repair against heavy ion radiation-induced cellular damage.}, }
@article {pmid30394643, year = {2018}, author = {Rand, DM and Mossman, JA and Zhu, L and Biancani, LM and Ge, JY}, title = {Mitonuclear epistasis, genotype-by-environment interactions, and personalized genomics of complex traits in Drosophila.}, journal = {IUBMB life}, volume = {70}, number = {12}, pages = {1275-1288}, pmid = {30394643}, issn = {1521-6551}, support = {R01 GM067862/GM/NIGMS NIH HHS/United States ; R01 AG027849/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Cell Nucleus/genetics ; Drosophila melanogaster/genetics ; Epistasis, Genetic/*genetics ; *Gene-Environment Interaction ; Genome, Mitochondrial/genetics ; Genomics ; Genotype ; Haplotypes ; Humans ; Mitochondria/*genetics ; Multifactorial Inheritance/*genetics ; Phenotype ; Precision Medicine ; }, abstract = {Mitochondrial function requires the coordinated expression of dozens of gene products from the mitochondrial genome and hundreds from the nuclear genomes. The systems that emerge from these interactions convert the food we eat and the oxygen we breathe into energy for life, while regulating a wide range of other cellular processes. These facts beg the question of whether the gene-by-gene interactions (G x G) that enable mitochondrial function are distinct from the gene-by-environment interactions (G x E) that fuel mitochondrial activity. We examine this question using a Drosophila model of mitonuclear interactions in which experimental combinations of mtDNA and nuclear chromosomes generate pairs of mitonuclear genotypes to test for epistatic interactions (G x G). These mitonuclear genotypes are then exposed to altered dietary or oxygen environments to test for G x E interactions. We use development time to assess dietary effects, and genome wide RNAseq analyses to assess hypoxic effects on transcription, which can be partitioned in to mito, nuclear, and environmental (G x G x E) contributions to these complex traits. We find that mitonuclear epistasis is universal, and that dietary and hypoxic treatments alter the epistatic interactions. We further show that the transcriptional response to alternative mitonuclear interactions has significant overlap with the transcriptional response to alternative oxygen environments. Gene coexpression analyses suggest that these shared genes are more central in networks of gene interactions, implying some functional overlap between epistasis and genotype by environment interactions. These results are discussed in the context of evolutionary fitness, the genetic basis of complex traits, and the challenge of achieving precision in personalized medicine. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(12):1275-1288, 2018.}, }
@article {pmid30391331, year = {2019}, author = {Xu, L and Peng, L and Gu, T and Yu, D and Yao, YG}, title = {The 3'UTR of human MAVS mRNA contains multiple regulatory elements for the control of protein expression and subcellular localization.}, journal = {Biochimica et biophysica acta. Gene regulatory mechanisms}, volume = {1862}, number = {1}, pages = {47-57}, doi = {10.1016/j.bbagrm.2018.10.017}, pmid = {30391331}, issn = {1876-4320}, mesh = {3' Untranslated Regions/*genetics ; AU Rich Elements ; Adaptor Proteins, Signal Transducing/*genetics ; Binding Sites ; Cell Line ; Cell Line, Tumor ; Gene Expression Regulation ; Humans ; *Immunity, Innate ; Intracellular Space/metabolism ; MicroRNAs/immunology/metabolism ; Mitochondrial Proteins ; Peptide Fragments ; RNA, Messenger/*genetics ; *Regulatory Sequences, Nucleic Acid ; Vesicular stomatitis Indiana virus/physiology ; Virus Diseases/immunology ; }, abstract = {Post-transcriptional regulation controls the mRNA stability, translation efficiency, and subcellular localization of a protein. The mitochondrial antiviral signaling protein (MAVS) plays a vital role in innate antiviral immunity. The MAVS mRNA has a long 3' untranslated region (UTR, >9 kb) and an understanding of this region may help to explain the post-transcriptional regulation in a key protein. In this study, we aimed to characterize the role of the MAVS 3'UTR during MAVS expression by truncating the 3'UTR into different fragments so as to identify the regulatory elements. We found that the different fragments (H1-H5) of the MAVS 3'UTR play different roles in regulating the subcellular localization and function of MAVS. Three AU-rich elements (AREs) in the MAVS 3'UTR H1 fragment (region 1-3445 in the 3'UTR) repressed MAVS expression by interacting with HuR to destabilize its mRNA. The MAVS 3'UTR H5 fragment (region 5955-7687 in the 3'UTR) affected the cellular localization of MAVS in mitochondria and influenced the subsequent antiviral function. Four miR-27a binding sites were recognized in the MAVS 3'UTR, and treatment of miR-27a inhibited MAVS expression and promoted the replication of the vesicular stomatitis virus (VSV). The identification of multiple regulatory elements in the MAVS 3'UTR offers new insights into the precise control of MAVS expression in innate immunity.}, }
@article {pmid30390623, year = {2018}, author = {Portugez, S and Martin, WF and Hazkani-Covo, E}, title = {Mosaic mitochondrial-plastid insertions into the nuclear genome show evidence of both non-homologous end joining and homologous recombination.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {162}, pmid = {30390623}, issn = {1471-2148}, mesh = {Base Sequence ; Cell Nucleus/*genetics ; DNA End-Joining Repair/*genetics ; DNA, Mitochondrial/genetics ; *Genome, Plant ; Homologous Recombination/*genetics ; Mitochondria/*genetics ; *Mosaicism ; Mutagenesis, Insertional/*genetics ; Plastids/*genetics ; }, abstract = {BACKGROUND: Mitochondrial and plastid DNA fragments are continuously transferred into eukaryotic nuclear genomes, giving rise to nuclear copies of mitochondrial DNA (numts) and nuclear copies of plastid DNA (nupts). Numts and nupts are classified as simple if they are composed of a single organelle fragment or as complex if they are composed of multiple fragments. Mosaic insertions are complex insertions composed of fragments of both mitochondrial and plastid DNA. Simple numts and nupts in eukaryotes have been extensively studied, their mechanism of insertion involves non-homologous end joining (NHEJ). Mosaic insertions have been less well-studied and their mechanisms of integration are unknown.<br><br>RESULTS: Here we estimated the number of nuclear mosaic insertions (numins) in nine plant genomes. We show that numins compose up to 10% of the total nuclear insertions of organelle DNA in these plant genomes. The NHEJ hallmarks typical for numts and nupts were also identified in mosaic insertions. However, the number of identified insertions that integrated via NHEJ mechanism is underestimated, as NHEJ signatures are conserved only in recent insertions and mutationally eroded in older ones. A few complex insertions show signatures of long homology that cannot be attributed to NHEJ, a novel observation that implicates gene conversion or single strand annealing mechanisms in organelle nuclear insertions.<br><br>CONCLUSIONS: The common NHEJ signature that was identified here reveals that, in plant cells, mitochondria and plastid fragments in numins must meet during or prior to integration into the nuclear genome.}, }
@article {pmid30385634, year = {2018}, author = {Loell, K and Nanda, V}, title = {Marginal protein stability drives subcellular proteome isoelectric point.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {46}, pages = {11778-11783}, pmid = {30385634}, issn = {1091-6490}, support = {80NSSC18K0093//Intramural NASA/United States ; DP2 OD006478/OD/NIH HHS/United States ; }, mesh = {Computer Simulation ; Databases, Protein ; Evolution, Molecular ; Humans ; Hydrogen-Ion Concentration ; Isoelectric Point ; Lysosomes/metabolism ; Protein Folding ; Protein Stability ; Proteome/*chemistry/metabolism ; Proteomics/*methods ; Subcellular Fractions/chemistry/metabolism ; }, abstract = {There exists a positive correlation between the pH of subcellular compartments and the median isoelectric point (pI) for the associated proteomes. Proteins in the human lysosome-a highly acidic compartment in the cell-have a median pI of ∼6.5, whereas proteins in the more basic mitochondria have a median pI of ∼8.0. Proposed mechanisms reflect potential adaptations to pH. For example, enzyme active site general acid/base residue pKs are likely evolved to match environmental pH. However, such effects would be limited to a few residues on specific proteins, and might not affect the proteome at large. A protein model that considers residue burial upon folding recapitulates the correlation between proteome pI and environmental pH. This correlation can be fully described by a neutral evolution process; no functional selection is included in the model. Proteins in acidic environments incur a lower energetic penalty for burying acidic residues than basic residues, resulting in a net accumulation of acidic residues in the protein core. The inverse is true under alkaline conditions. The pI distributions of subcellular proteomes are likely not a direct result of functional adaptations to pH, but a molecular spandrel stemming from marginal stability.}, }
@article {pmid30385240, year = {2018}, author = {Palozzi, JM and Jeedigunta, SP and Hurd, TR}, title = {Mitochondrial DNA Purifying Selection in Mammals and Invertebrates.}, journal = {Journal of molecular biology}, volume = {430}, number = {24}, pages = {4834-4848}, doi = {10.1016/j.jmb.2018.10.019}, pmid = {30385240}, issn = {1089-8638}, support = {FRN 159510//CIHR/Canada ; }, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Female ; Humans ; Invertebrates/*genetics/growth &amp; development ; Mammals/*genetics/growth &amp; development ; Maternal Inheritance ; Mitochondria/*genetics ; Ovum/chemistry/*cytology ; Quality Control ; Selection, Genetic ; }, abstract = {Numerous mitochondrial quality control mechanisms exist within cells, but none have been shown to effectively assess and control the quality of mitochondrial DNA (mtDNA). One reason such mechanisms have yet to be elucidated is that they do not appear to be particularly active in most somatic cells, where many studies are conducted. The female germline, the cell lineage that gives rise to eggs, appears to be an exception. In the germline, strong purifying selection pathways act to eliminate deleterious mtDNA. These pathways have apparently evolved to prevent pathogenic mtDNA mutations from accumulating over successive generations and causing a decline of species via Muller's ratchet. Despite their fundamental biological importance, the mechanisms underlying purifying selection remain poorly understood, with no genes involved in this process yet identified. In this review, we discuss recent studies exploring mechanisms of germline mtDNA purifying selection in both mammalian and invertebrate systems. We also discuss the challenges to future major advances. Understanding the molecular basis of purifying selection is not only a fundamental outstanding question in biology, but may also pave the way to controlling selection in somatic tissues, potentially leading to treatments for people suffering from mitochondrial diseases.}, }
@article {pmid30378025, year = {2018}, author = {Gabaldón, T}, title = {Evolution of the Peroxisomal Proteome.}, journal = {Sub-cellular biochemistry}, volume = {89}, number = {}, pages = {221-233}, doi = {10.1007/978-981-13-2233-4_9}, pmid = {30378025}, issn = {0306-0225}, mesh = {Eukaryota/cytology ; Eukaryotic Cells/cytology ; *Evolution, Molecular ; Peroxisomes/*chemistry/*metabolism ; *Phylogeny ; Proteome/*metabolism ; *Proteomics ; }, abstract = {Peroxisomes are single-membrane bound intracellular organelles that can be found in organisms across the tree of eukaryotes, and thus are likely to derive from an ancestral peroxisome in the last eukaryotic common ancestor (LECA). Yet, peroxisomes in different lineages can present a large diversity in terms of their metabolic capabilities, which reflects a highly variable proteomic content. Theories on the evolutionary origin of peroxisomes have shifted in the last decades from scenarios involving an endosymbiotic origin, similar to those of mitochondria and plastids, towards hypotheses purporting an endogenous origin from within the endomembrane system. The peroxisomal proteome is highly dynamic in evolutionary terms, and can evolve via differential loss and gain of proteins, as well as via relocalization of proteins from and to other sub-cellular compartments. Here, I review current knowledge and discussions on the diversity, origin, and evolution of the peroxisomal proteome.}, }
@article {pmid30377874, year = {2018}, author = {Cai, C and Liu, F and Jiang, T and Wang, L and Jia, R and Zhou, L and Gu, K and Ren, J and He, P}, title = {Comparative study on mitogenomes of green tide algae.}, journal = {Genetica}, volume = {146}, number = {6}, pages = {529-540}, pmid = {30377874}, issn = {1573-6857}, support = {18ZR1417400//Shanghai Natural Science Fund/ ; 41576163//National Natural Science Foundation of China/ ; 2016YFC1402105//National Key R&amp;D Program of China/ ; MATHAB2017010//Key Laboratory of Integrated Marine Monitoring and Applied Technologies for Harmful Algal Blooms, S.O.A./ ; }, mesh = {Codon/genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; Microsatellite Repeats ; Open Reading Frames ; RNA, Transfer/genetics ; Sequence Homology, Nucleic Acid ; Ulva/classification/*genetics ; }, abstract = {Since 2007, the annual green tide disaster in the Yellow Sea has brought serious economic losses to China. There is no research on the genetic similarities of four constituent species of green tide algae at the genomic level. We previously determined the mitochondrial genomes of Ulva prolifera, Ulva linza and Ulva flexuosa. In the present work, the mitochondrial genome of another green tide (Ulva compressa) was sequenced and analyzed. With the length of 62,311 bp, it contained 29 encoding genes, 26 tRNAs and 10 open reading frames. By comparing these four mitochondrial genomes, we found that U. compressa was quite different from the other three types of Ulva species. However, there were similarities between U. prolifera and U. linza in the number, distribution and homology of open reading frames, evolutionary and codon variation of tRNA, evolutionary relationship and selection pressure of coding genes. Repetitive sequence analysis of simple sequence repeats, tandem repeat and forward repeats further supposed that they have evolved from the same origin. In addition, we directly analyzed gene homologies and translocation of four green tide algae by Mauve alignment. There were gene order rearrangements among them. With fast-evolving genomes, these four green algal mitochondria have both conservatism and variation, thus opening another window for the understanding of origin and evolution of Ulva.}, }
@article {pmid30373839, year = {2018}, author = {Mehta, AP and Supekova, L and Chen, JH and Pestonjamasp, K and Webster, P and Ko, Y and Henderson, SC and McDermott, G and Supek, F and Schultz, PG}, title = {Engineering yeast endosymbionts as a step toward the evolution of mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {46}, pages = {11796-11801}, pmid = {30373839}, issn = {1091-6490}, support = {P41 GM103445/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Bioengineering/*methods ; Biological Evolution ; Escherichia coli/genetics/metabolism ; Mitochondria/*genetics/metabolism ; Models, Biological ; Saccharomyces cerevisiae/genetics/metabolism ; Symbiosis/*genetics ; Thiamine/metabolism ; }, abstract = {It has been hypothesized that mitochondria evolved from a bacterial ancestor that initially became established in an archaeal host cell as an endosymbiont. Here we model this first stage of mitochondrial evolution by engineering endosymbiosis between Escherichia coli and Saccharomyces cerevisiae An ADP/ATP translocase-expressing E. coli provided ATP to a respiration-deficient cox2 yeast mutant and enabled growth of a yeast-E. coli chimera on a nonfermentable carbon source. In a reciprocal fashion, yeast provided thiamin to an endosymbiotic E. coli thiamin auxotroph. Expression of several SNARE-like proteins in E. coli was also required, likely to block lysosomal degradation of intracellular bacteria. This chimeric system was stable for more than 40 doublings, and GFP-expressing E. coli endosymbionts could be observed in the yeast by fluorescence microscopy and X-ray tomography. This readily manipulated system should allow experimental delineation of host-endosymbiont adaptations that occurred during evolution of the current, highly reduced mitochondrial genome.}, }
@article {pmid30373326, year = {2018}, author = {Bombaça, ACS and Dossow, DV and Barbosa, JMC and Paz, C and Burgos, V and Menna-Barreto, RFS}, title = {TrypanocidalActivity of Natural Sesquiterpenoids Involves Mitochondrial Dysfunction, ROS Production and Autophagic Phenotype in Trypanosomacruzi.}, journal = {Molecules (Basel, Switzerland)}, volume = {23}, number = {11}, pages = {}, pmid = {30373326}, issn = {1420-3049}, mesh = {Autophagy/*drug effects ; Mitochondria/*drug effects/ultrastructure ; Molecular Structure ; Reactive Oxygen Species/*metabolism ; Sesquiterpenes/*chemistry/isolation &amp; purification/*pharmacology ; Trypanocidal Agents/*chemistry/isolation &amp; purification/*pharmacology ; Trypanosoma cruzi/*drug effects/*metabolism/ultrastructure ; }, abstract = {Chagas disease is a neglected tropical disease that is caused by the protozoan Trypanosomacruzi and represents a serious health problem, especially in Latin America. The clinical treatment of Chagas disease is based on two nitroderivatives that present severe side effects and important limitations. In folk medicine, natural products, including sesquiterpenoids, have been employed for the treatment of different parasitic diseases. In this study, the trypanocidal activity of compounds isolated from the Chilean plants Drimys winteri, Podanthus mitiquiand Maytenus boaria on three T. cruzi evolutive forms (epimastigote, trypomastigote and amastigote) was evaluated. Total extracts and seven isolated sesquiterpenoids were assayed on trypomastigotes and epimastigotes. Polygodial (Pgd) from D. winteri, total extract from P. mitiqui (PmTE) and the germacrane erioflorin (Efr) from P. mitiqui were the most bioactive substances. Pgd, Efr and PmTE also presented strong effects on intracellular amastigotes and low host toxicity. Many ultrastructural effects of these substances, including reservosome disruption, cytosolic vacuolization, autophagic phenotype and mitochondrial swelling (in the case of Pgd), were observed. Flow cytometric analysis demonstrated a reduction in mitochondrial membrane potential in treated epimastigotes and an increase in ROS production and high plasma membrane permeability after treatment with Pgd. The promising trypanocidal activity of these natural sesquiterpenoids may be a good starting point for the development of alternative treatmentsforChagas disease.}, }
@article {pmid30368957, year = {2018}, author = {Olsson, M and Friesen, CR and Rollings, N and Sudyka, J and Lindsay, W and Whittington, CM and Wilson, M}, title = {Long-term effects of superoxide and DNA repair on lizard telomeres.}, journal = {Molecular ecology}, volume = {27}, number = {24}, pages = {5154-5164}, doi = {10.1111/mec.14913}, pmid = {30368957}, issn = {1365-294X}, support = {//Swedish Science Council/International ; //Australian Research Council/International ; }, mesh = {Animals ; Australia ; DNA Damage ; *DNA Repair ; Female ; In Situ Hybridization, Fluorescence ; Lizards/*genetics ; Male ; Mitochondria/genetics ; Oxidative Stress ; *Seasons ; Superoxides/*chemistry ; Telomere/*genetics ; Telomere Shortening ; }, abstract = {Telomeres are the non-coding protein-nucleotide "caps" at chromosome ends that contribute to chromosomal stability by protecting the coding parts of the linear DNA from shortening at cell division, and from erosion by reactive molecules. Recently, there has been some controversy between molecular and cell biologists, on the one hand, and evolutionary ecologists on the other, regarding whether reactive molecules erode telomeres during oxidative stress. Many studies of biochemistry and medicine have verified these relationships in cell culture, but other researchers have failed to find such effects in free-living vertebrates. Here, we use a novel approach to measure free radicals (superoxide), mitochondrial "content" (a combined measure of mitochondrial number and size in cells), telomere length and DNA damage at two primary time points during the mating season of an annual lizard species (Ctenophorus pictus). Superoxide levels early in the mating season vary widely and elevated levels predict shorter telomeres both at that time as well as several months later. These effects are likely driven by mitochondrial content, which significantly impacts late season superoxide (cells with more mitochondria have more superoxide), but superoxide effects on telomeres are counteracted by DNA repair as revealed by 8-hydroxy-2'-deoxyguanosine assays. We conclude that reactive oxygen species and DNA repair are fundamental for both short- and long-term regulation of lizard telomere length with pronounced effects of early season cellular stress detectable on telomere length near lizard death.}, }
@article {pmid30364957, year = {2018}, author = {Lee, JM and Song, HJ and Park, SI and Lee, YM and Jeong, SY and Cho, TO and Kim, JH and Choi, HG and Choi, CG and Nelson, WA and Fredericq, S and Bhattacharya, D and Yoon, HS}, title = {Mitochondrial and Plastid Genomes from Coralline Red Algae Provide Insights into the Incongruent Evolutionary Histories of Organelles.}, journal = {Genome biology and evolution}, volume = {10}, number = {11}, pages = {2961-2972}, pmid = {30364957}, issn = {1759-6653}, mesh = {*Biological Evolution ; *Genome, Mitochondrial ; *Genome, Plastid ; Rhodophyta/*genetics ; }, abstract = {Mitochondria and plastids are generally uniparentally inherited and have a conserved gene content over hundreds of millions of years, which makes them potentially useful phylogenetic markers. Organelle single gene-based trees have long been the basis for elucidating interspecies relationships that inform taxonomy. More recently, high-throughput genome sequencing has enabled the construction of massive organelle genome databases from diverse eukaryotes, and these have been used to infer species relationships in deep evolutionary time. Here, we test the idea that despite their expected utility, conflicting phylogenetic signal may exist in mitochondrial and plastid genomes from the anciently diverged coralline red algae (Rhodophyta). We generated complete organelle genome data from five coralline red algae (Lithothamnion sp., Neogoniolithon spectabile, Renouxia sp., Rhodogorgon sp., and Synarthrophyton chejuensis) for comparative analysis with existing organelle genome data from two other species (Calliarthron tuberculosum and Sporolithon durum). We find strong evidence for incongruent phylogenetic signal from both organelle genomes that may be explained by incomplete lineage sorting that has maintained anciently derived gene copies or other molecular evolutionary processes such as hybridization or gene flow during the evolutionary history of coralline red algae.}, }
@article {pmid30358111, year = {2018}, author = {Yu, J and Zhang, L and Li, Y and Zhu, X and Xu, S and Zhou, XM and Wang, H and Zhang, H and Liang, B and Liu, P}, title = {The Adrenal Lipid Droplet is a New Site for Steroid Hormone Metabolism.}, journal = {Proteomics}, volume = {18}, number = {23}, pages = {e1800136}, doi = {10.1002/pmic.201800136}, pmid = {30358111}, issn = {1615-9861}, mesh = {Adrenal Glands/metabolism ; Animals ; Gonadal Steroid Hormones/metabolism ; HeLa Cells ; Humans ; Lipid Droplets/*metabolism ; Lipid Metabolism/physiology ; Macaca ; Progesterone Reductase/metabolism ; }, abstract = {Steroid hormones play essential roles for living organisms. It has been long and well established that the endoplasmic reticulum (ER) and mitochondria are essential sites for steroid hormone biosynthesis because several steroidogenic enzymes are located in these organelles. The adrenal gland lipid droplet (LD) proteomes from human, macaque monkey, and rodent are analyzed, revealing that steroidogenic enzymes are also present in abundance on LDs. The enzymes found include 3β-hydroxysteroid dehydrogenase (HSD3B) and estradiol 17β-dehydrogenase 11 (HSD17B11). Analyses by Western blot and subcellular localization consistently demonstrate that HSD3B2 is localized on LDs. Furthermore, in vitro experiments confirm that the isolated LDs from HeLa cell stably expressing HSD3B2 or from rat adrenal glands have the capacity to convert pregnenolone to progesterone. Collectively, these data suggest that LDs may be important sites of steroid hormone metabolism. These findings may bring novel insights into the biosynthesis and metabolism of steroid hormones and the development of treatments for adrenal disorders.}, }
@article {pmid30358089, year = {2018}, author = {Gray, MW and Mootha, VK}, title = {Evolutionary mitochondrial biology in titisee.}, journal = {IUBMB life}, volume = {70}, number = {12}, pages = {1184-1187}, doi = {10.1002/iub.1958}, pmid = {30358089}, issn = {1521-6551}, mesh = {*Evolution, Molecular ; Humans ; Mitochondria/*genetics/metabolism ; Molecular Biology/*trends ; }, }
@article {pmid30358065, year = {2018}, author = {Paris, Z and Alfonzo, JD}, title = {How the intracellular partitioning of tRNA and tRNA modification enzymes affects mitochondrial function.}, journal = {IUBMB life}, volume = {70}, number = {12}, pages = {1207-1213}, pmid = {30358065}, issn = {1521-6551}, support = {R01 GM084065/GM/NIGMS NIH HHS/United States ; R56 AI131248/AI/NIAID NIH HHS/United States ; U01 AI131348/AI/NIAID NIH HHS/United States ; }, mesh = {Cytoplasm/genetics ; Genome, Mitochondrial/*genetics ; Intracellular Membranes ; Mitochondria/*genetics ; Mitochondrial Membranes/metabolism ; Protein Biosynthesis/*genetics ; RNA Processing, Post-Transcriptional/genetics ; RNA, Transfer/*genetics ; Symbiosis/genetics ; }, abstract = {Organisms have evolved different strategies to seclude certain molecules to specific locations of the cell. This is most pronounced in eukaryotes with their extensive intracellular membrane systems. Intracellular compartmentalization is particularly critical in genome containing organelles, which because of their bacterial evolutionary ancestry still maintain protein-synthesis machinery that resembles more their evolutionary origin than the extant eukaryotic cell they once joined as an endosymbiont. Despite this, it is clear that genome-containing organelles such as the mitochondria are not in isolation and many molecules make it across the mitochondrial membranes from the cytoplasm. In this realm the import of tRNAs and the enzymes that modify them prove most consequential. In this review, we discuss two recent examples of how modifications typically found in cytoplasmic tRNAs affect mitochondrial translation in organisms that forcibly import all their tRNAs from the cytoplasm. In our view, the combination of tRNA import and the compartmentalization of modification enzymes must have played a critical role in the evolution of the organelle. © 2018 IUBMB Life, 70(12):1207-1213, 2018.}, }
@article {pmid30358047, year = {2018}, author = {Gabaldón, T}, title = {Relative timing of mitochondrial endosymbiosis and the "pre-mitochondrial symbioses" hypothesis.}, journal = {IUBMB life}, volume = {70}, number = {12}, pages = {1188-1196}, pmid = {30358047}, issn = {1521-6551}, mesh = {Archaea/genetics/metabolism ; *Biological Evolution ; Eukaryotic Cells/metabolism ; Mitochondria/*genetics ; *Phylogeny ; Prokaryotic Cells/metabolism ; Symbiosis/*genetics ; }, abstract = {The origin of eukaryotes stands as a major open question in biology. Central to this question is the nature and timing of the origin of the mitochondrion, an ubiquitous eukaryotic organelle originated by the endosymbiosis of an alphaproteobacterial ancestor. Different hypotheses disagree, among other aspects, on whether mitochondria were acquired early or late during eukaryogenesis. Similarly, the nature and complexity of the receiving host is debated, with models ranging from a simple prokaryotic host to an already complex proto-eukaryote. Here, I will discuss recent findings from phylogenomics analyses of extant genomes that are shedding light into the evolutionary origins of the eukaryotic ancestor, and which suggest a later acquisition of alpha-proteobacterial derived proteins as compared to those with different bacterial ancestries. I argue that simple eukaryogenesis models that assume a binary symbiosis between an archaeon host and an alpha-proteobacterial proto-mitochondrion cannot explain the complex chimeric nature that is inferred for the eukaryotic ancestor. To reconcile existing hypotheses with the new data, I propose the "pre-mitochondrial symbioses" hypothesis that provides a framework for eukaryogenesis scenarios involving alternative symbiotic interactions that predate the acquisition of mitochondria. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(12):1188-1196, 2018.}, }
@article {pmid30356218, year = {2018}, author = {Katsyuba, E and Mottis, A and Zietak, M and De Franco, F and van der Velpen, V and Gariani, K and Ryu, D and Cialabrini, L and Matilainen, O and Liscio, P and Giacchè, N and Stokar-Regenscheit, N and Legouis, D and de Seigneux, S and Ivanisevic, J and Raffaelli, N and Schoonjans, K and Pellicciari, R and Auwerx, J}, title = {De novo NAD[+] synthesis enhances mitochondrial function and improves health.}, journal = {Nature}, volume = {563}, number = {7731}, pages = {354-359}, pmid = {30356218}, issn = {1476-4687}, mesh = {Animals ; Caenorhabditis elegans/cytology/enzymology/metabolism ; Carboxy-Lyases/antagonists &amp; inhibitors/chemistry/deficiency/*metabolism ; Cell Line ; Choline ; *Conserved Sequence ; Disease Models, Animal ; *Evolution, Molecular ; Female ; Gene Knockdown Techniques ; *Health ; Hepatocytes/cytology/drug effects ; Homeostasis/drug effects ; Humans ; Kidney/cytology/drug effects ; Liver/cytology/drug effects ; Longevity/drug effects ; Male ; Methionine/deficiency ; Mice ; Mice, Inbred C57BL ; Mitochondria/*physiology ; NAD/*biosynthesis ; Non-alcoholic Fatty Liver Disease/physiopathology/prevention &amp; control ; Rats ; Sirtuins/metabolism ; }, abstract = {Nicotinamide adenine dinucleotide (NAD[+]) is a co-substrate for several enzymes, including the sirtuin family of NAD[+]-dependent protein deacylases. Beneficial effects of increased NAD[+] levels and sirtuin activation on mitochondrial homeostasis, organismal metabolism and lifespan have been established across species. Here we show that α-amino-β-carboxymuconate-ε-semialdehyde decarboxylase (ACMSD), the enzyme that limits spontaneous cyclization of α-amino-β-carboxymuconate-ε-semialdehyde in the de novo NAD[+] synthesis pathway, controls cellular NAD[+] levels via an evolutionarily conserved mechanism in Caenorhabditis elegans and mouse. Genetic and pharmacological inhibition of ACMSD boosts de novo NAD[+] synthesis and sirtuin 1 activity, ultimately enhancing mitochondrial function. We also characterize two potent and selective inhibitors of ACMSD. Because expression of ACMSD is largely restricted to kidney and liver, these inhibitors may have therapeutic potential for protection of these tissues from injury. In summary, we identify ACMSD as a key modulator of cellular NAD[+] levels, sirtuin activity and mitochondrial homeostasis in kidney and liver.}, }
@article {pmid30353148, year = {2018}, author = {Ng, NSR and Prawiradilaga, DM and Ng, EYX and Suparno,  and Ashari, H and Trainor, C and Verbelen, P and Rheindt, FE}, title = {A striking new species of leaf warbler from the Lesser Sundas as uncovered through morphology and genomics.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {15646}, pmid = {30353148}, issn = {2045-2322}, mesh = {Acoustics ; Animals ; Cytochromes b/genetics ; *Genomics ; Geography ; Indonesia ; Islands ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Principal Component Analysis ; Songbirds/*anatomy &amp; histology/*genetics ; Sound Spectrography ; Species Specificity ; }, abstract = {Leaf warblers (Aves; Phylloscopidae) are a diverse clade of insectivorous, canopy-dwelling songbirds widespread across the Old World. The taxonomy of Australasian leaf warblers is particularly complex, with multiple species-level divergences between island taxa in the region requiring further scrutiny. We use a combination of morphology, bioacoustics, and analysis of thousands of genome-wide markers to investigate and describe a new species of Phylloscopus leaf warbler from the island of Rote in the Lesser Sundas, Indonesia. We show that this new Rote Leaf Warbler is morphologically and genomically highly distinct from its congenerics, but do not find vocal differentiation between different island taxa. We discuss the behaviour and ecology of this highly distinctive new species, and make recommendations about its conservation status. We believe this constitutes the first description of a novel bird species that is partly based on insights from massive amounts of genome-wide DNA markers.}, }
@article {pmid30350319, year = {2018}, author = {Temereva, EN and Kuzmina, TV}, title = {Spermatogenesis in the deep-sea brachiopod Pelagodiscus atlanticus and the phylogenetic significance of spermatozoon structure.}, journal = {Journal of morphology}, volume = {279}, number = {11}, pages = {1579-1589}, doi = {10.1002/jmor.20887}, pmid = {30350319}, issn = {1097-4687}, support = {17-04-00586//Russian Foundation for Basic Research/International ; #14-50-00034//Russian Science Foundation/International ; #18-14-00082//Russian Science Foundation/International ; }, mesh = {Animals ; Invertebrates/*classification/*physiology ; Male ; Models, Biological ; *Phylogeny ; *Spermatogenesis ; Spermatogonia/cytology/ultrastructure ; Spermatozoa/cytology/*ultrastructure ; }, abstract = {Details of spermatogenesis and sperm organization are often useful for reconstructing the phylogeny of closely related groups of invertebrates. Development in general and gametogenesis in particular usually differ in shallow water and deep-sea invertebrates. Here, the spermatogenesis and ultrastructure of sperm were studied in the deep-sea brachiopod Pelagodiscus atlanticus. The testes of P. atlanticus are voluminous sacs located along the lateral sides of the body. Germ cells develop around the blood capillaries, contact the basal lamina, and contain germ plasm, numerous mitochondria, Golgi apparatus, lipid droplets, and centrioles of the rudimentary cilium. During spermatogenesis, several proacrosomal vesicles appear at the posterior pole of the cell; these vesicles then fuse and migrate to the anterior pole. The spermatozoon has a head with an acrosome, nucleus, eight mitochondria, proximal and distal centrioles orthogonally arranged, and a long tail. Comparative analysis suggests that the spermatozoon of P. atlanticus can be considered the most ancestral among all brachiopods. Such an organization indicates that fertilization is external in this deep-sea species. Spermatozoa of other brachiopods should be regarded as derived from this ancestral type. The transformation of brachiopod spermatozoa might have occurred in three different ways that correspond to the three main clades of recent brachiopods: Linguliformea, Craniiformea, and Rhynchonelliformea.}, }
@article {pmid30347487, year = {2019}, author = {Ligas, J and Pineau, E and Bock, R and Huynen, MA and Meyer, EH}, title = {The assembly pathway of complex I in Arabidopsis thaliana.}, journal = {The Plant journal : for cell and molecular biology}, volume = {97}, number = {3}, pages = {447-459}, doi = {10.1111/tpj.14133}, pmid = {30347487}, issn = {1365-313X}, support = {PIRG256398/MCCC_/Marie Curie/United Kingdom ; }, mesh = {Arabidopsis/*enzymology/genetics ; Electron Transport ; Electron Transport Complex I/genetics/*metabolism ; Evolution, Molecular ; Mitochondria/metabolism ; Proteomics ; }, abstract = {All present-day mitochondria originate from a single endosymbiotic event that gave rise to the last eukaryotic common ancestor more than a billion years ago. However, to date, many aspects of mitochondrial evolution have remained unresolved. Comparative genomics and proteomics have revealed a complex evolutionary origin for many mitochondrial components. To understand the evolution of the respiratory chain, we have examined both the components and the mechanisms of the assembly pathway of complex I. Complex I represents the first enzyme in the respiratory chain, and complex I deficiencies have dramatic consequences in both animals and plants. The complex is located in the mitochondrial inner membrane and possesses two arms: one embedded in the inner membrane and one protruding in the matrix. Here, we describe the assembly pathway of complex I in the model plant Arabidopsis thaliana. Using a proteomics approach called complexome profiling, we have resolved the different steps in the assembly process in plants. We propose a model for the stepwise assembly of complex I, including every subunit. We then compare this pathway with the corresponding pathway in humans and find that complex I assembly in plants follows a different, and likely ancestral, pathway compared with the one in humans. We show that the main evolutionary changes in complex I structure and assembly in humans occurred at the level of the membrane arm, whereas the matrix arm remained rather conserved.}, }
@article {pmid30347227, year = {2019}, author = {Xin, L and Huang, B and Li, C and Bai, C and Wang, C}, title = {Characterization of a nucleus located mollusc mitoferrin and its response to OsHV-1 infection.}, journal = {Biochimica et biophysica acta. General subjects}, volume = {1863}, number = {1}, pages = {255-265}, doi = {10.1016/j.bbagen.2018.10.014}, pmid = {30347227}, issn = {1872-8006}, mesh = {Animals ; Cell Nucleus/*metabolism ; Computational Biology ; Cytosol/metabolism ; DNA Viruses/*physiology ; Female ; Ferritins/metabolism ; Herpesviridae Infections/*veterinary ; Humans ; Immunohistochemistry ; Iron/metabolism ; Membrane Transport Proteins/*chemistry ; Mice ; Mitochondria/metabolism ; Mollusca/*virology ; Phylogeny ; Protein Domains ; Recombinant Proteins/chemistry ; Tissue Distribution ; }, abstract = {Mitoferrin genes as members of SLC25 family are conservatively existed across species, mainly locate on mitochondria and serve an important role in the regulation of whole cellular iron metabolism. Available iron withholding from pathogens presents an important host defense strategy, while the regulation role of mitoferrin against invading pathogens is largely unknown. In this study, a unique mollusc mitoferrin gene was identified in ark clams, named SbmiFn, that showed conserved three-dimensional structure with other mitoferrins, and its iron binding activity was verified by iron chelating assay. Besides cytoplasmic distribution, colocalization between SbmiFn and nuclei was observed by immunohistochemistry assay. Moreover, the response of SbmiFn to viral pathogen OsHV-1 was investigated. The results showed that nucleus located signal of SbmiFn was enhanced, the expressions of SbmiFn and ferritin were coordinately decreased, which might assist host against OsHV-1 replication as the increase of OsHV-1 copies were hardly detected after that. These results refreshed our knowledge on the sequence, structure and functional characteristics of mitoferrin subfamily, and would contribute to further comparative studies on iron metabolism.}, }
@article {pmid30346990, year = {2018}, author = {Costa-Martins, AG and Lima, L and Alves, JMP and Serrano, MG and Buck, GA and Camargo, EP and Teixeira, MMG}, title = {Genome-wide identification of evolutionarily conserved Small Heat-Shock and eight other proteins bearing α-crystallin domain-like in kinetoplastid protists.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0206012}, pmid = {30346990}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Cilia/metabolism ; *Conserved Sequence ; Cytoskeleton/metabolism ; *Evolution, Molecular ; *Genome ; Heat-Shock Proteins, Small/*chemistry/*genetics ; Mitochondria/metabolism ; Mitochondrial Proteins/metabolism ; Phylogeny ; Prokaryotic Cells/metabolism ; Protein Domains ; Synteny/genetics ; Trypanosomatina/*genetics ; alpha-Crystallins/*chemistry ; }, abstract = {Small Heat-Shock Proteins (sHSPs) and other proteins bearing alpha-crystallin domains (ACD) participate in defense against heat and oxidative stress and play important roles in cell cycle, cytoskeleton dynamics, and immunological and pathological mechanisms in eukaryotes. However, little is known about these proteins in early-diverging lineages of protists such as the kinetoplastids. Here, ACD-like proteins (ACDp) were investigated in genomes of 61 species of 12 kinetoplastid genera, including Trypanosoma spp. (23 species of mammals, reptiles and frogs), Leishmania spp. (mammals and lizards), trypanosomatids of insects, Phytomonas spp. of plants, and bodonids. Comparison of ACDps based on domain architecture, predicted tertiary structure, phylogeny and genome organization reveals a kinetoplastid evolutionarily conserved repertoire, which diversified prior to trypanosomatid adaptation to parasitic life. We identified 9 ACDp orthologs classified in 8 families of TryACD: four previously recognized (HSP20, Tryp23A, Tryp23B and ATOM69), and four characterized for the first time in kinetoplastids (TryACDP, TrySGT1, TryDYX1C1 and TryNudC). A single copy of each ortholog was identified in each genome alongside TryNudC1/TrypNudC2 homologs and, overall, ACDPs were under strong selection pressures at main phylogenetic lineages. Transcripts of all ACDPs were identified across the life stages of T. cruzi, T. brucei and Leishmania spp., but proteomic profiles suggested that most ACDPs may be species- and stage-regulated. Our findings establish the basis for functional studies, and provided evolutionary and structural support for an underestimated repertoire of ACDps in the kinetoplastids.}, }
@article {pmid30343708, year = {2018}, author = {Tanaka, A and Leung, PSC and Gershwin, ME}, title = {Evolution of our understanding of PBC.}, journal = {Best practice &amp; research. Clinical gastroenterology}, volume = {34-35}, number = {}, pages = {3-9}, doi = {10.1016/j.bpg.2018.05.008}, pmid = {30343708}, issn = {1532-1916}, mesh = {Animals ; Autoantibodies/blood ; Autoantigens/immunology ; Epitopes ; Humans ; Liver Cirrhosis, Biliary/*immunology/*pathology ; Mitochondria/immunology ; }, abstract = {The discovery of mitochondrial autoantigens recognized by antimitochondrial antibodies (AMAs) in 1987 marked the dawn of a new era in primary biliary cholangitis (PBC) research. Since then, there has been substantial progress in our understanding of PBC partly bestowed by the development of innovative technologies in molecular biology, immunology, and genetics. Here, we review this evolutionary progress in understanding PBC. We now recognize that the epitopes of AMAs, CD4[+], and CD8[+] T cells are all mapped to the same region of the inner lipoyl domain of pyruvate dehydrogenase complex E2 subunit (PDC-E2), and that intrahepatic biliary epithelial cells (BECs) are exclusively targeted in PBC. BECs express PDC-E2 on apotopes in an immunologically intact form during apoptosis, but not other epithelial cells, which could explain the tissue specificity of PBC. In addition, genetic factors, environmental triggers, and epigenetic modifications play crucial roles in the development of PBC. Intact lipoylated PDC-E2, presumably after modification with xenobiotics such as 2-octynamide or 2-nonyamide that are abundantly present in the environment, is endocytosed by antigen-presenting cells and are presented to CD4[+] or CD8[+] T cells. An immune complex consisting of PDC-E2 and anti-PDC-E2 autoantibodies cross-present autoantigens in a more efficient manner. Finally, an adenylate uridine-rich element (ARE) Del -/- mouse model has been established, which presents a disease modeling human PBC, including female dominance as one of its most important features, and can be used to dissect the immunopathology of PBC. Expanding our knowledge of the pathology from a very early stage of the disease will provide the key to cure PBC.}, }
@article {pmid30341492, year = {2019}, author = {Arakawa, T and Ue, S and Sano, C and Matsunaga, M and Kagami, H and Yoshida, Y and Kuroda, Y and Taguchi, K and Kitazaki, K and Kubo, T}, title = {Identification and characterization of a semi-dominant restorer-of-fertility 1 allele in sugar beet (Beta vulgaris).}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {132}, number = {1}, pages = {227-240}, pmid = {30341492}, issn = {1432-2242}, support = {18K05564//Japan Society for the Promotion of Science/ ; 16J01146//Japan Society for the Promotion of Science/ ; Research program on development of innovative technology//Bio-oriented Technology Research Advancement Institution/ ; Grant Number 30001A//Bio-oriented Technology Research Advancement Institution/ ; }, mesh = {Alleles ; Beta vulgaris/*genetics/*physiology ; *Genes, Dominant ; *Genes, Plant ; Genotype ; Mitochondrial Proteins/genetics ; Plant Infertility/*genetics ; Plants, Genetically Modified/physiology ; }, abstract = {The sugar beet Rf1 locus has a number of molecular variants. We found that one of the molecular variants is a weak allele of a previously identified allele. Male sterility (MS) caused by nuclear-mitochondrial interaction is called cytoplasmic male sterility (CMS) in which MS-inducing mitochondria are suppressed by a nuclear gene, restorer-of-fertility. Rf and rf are the suppressing and non-suppressing alleles, respectively. This dichotomic view, however, seems somewhat unsatisfactory to explain the recently discovered molecular diversity of Rf loci. In the present study, we first identified sugar beet line NK-305 as a new source of Rf1. Our crossing experiment revealed that NK-305 Rf1 is likely a semi-dominant allele that restores partial fertility when heterozygous but full fertility when homozygous, whereas Rf1 from another sugar beet line appeared to be a dominant allele. Proper degeneration of anther tapetum is a prerequisite for pollen development; thus, we compared tapetal degeneration in the NK-305 Rf1 heterozygote and the homozygote. Degeneration occurred in both genotypes but to a lesser extent in the heterozygote, suggesting an association between NK-305 Rf1 dose and incompleteness of tapetal degeneration leading to partial fertility. Our protein analyses revealed a quantitative correlation between NK-305 Rf1 dose and a reduction in the accumulation of a 250 kDa mitochondrial protein complex consisting of a CMS-specific mitochondrial protein encoded by MS-inducing mitochondria. The abundance of Rf1 transcripts correlated with NK-305 Rf1 dose. The molecular organization of NK-305 Rf1 suggested that this allele evolved through intergenic recombination. We propose that the sugar beet Rf1 locus has a series of multiple alleles that differ in their ability to restore fertility and are reflective of the complexity of Rf evolution.}, }
@article {pmid30340785, year = {2018}, author = {Dos Santos, RF and Quendera, AP and Boavida, S and Seixas, AF and Arraiano, CM and Andrade, JM}, title = {Major 3'-5' Exoribonucleases in the Metabolism of Coding and Non-coding RNA.}, journal = {Progress in molecular biology and translational science}, volume = {159}, number = {}, pages = {101-155}, doi = {10.1016/bs.pmbts.2018.07.005}, pmid = {30340785}, issn = {1878-0814}, mesh = {Animals ; Disease ; Exoribonucleases/chemistry/*metabolism ; Humans ; Open Reading Frames/genetics ; Phylogeny ; RNA, Untranslated/*genetics ; Substrate Specificity ; }, abstract = {3'-5' exoribonucleases are key enzymes in the degradation of superfluous or aberrant RNAs and in the maturation of precursor RNAs into their functional forms. The major bacterial 3'-5' exoribonucleases responsible for both these activities are PNPase, RNase II and RNase R. These enzymes are of ancient nature with widespread distribution. In eukaryotes, PNPase and RNase II/RNase R enzymes can be found in the cytosol and in mitochondria and chloroplasts; RNase II/RNase R-like enzymes are also found in the nucleus. Humans express one PNPase (PNPT1) and three RNase II/RNase R family members (Dis3, Dis3L and Dis3L2). These enzymes take part in a multitude of RNA surveillance mechanisms that are critical for translation accuracy. Although active against a wide range of both coding and non-coding RNAs, the different 3'-5' exoribonucleases exhibit distinct substrate affinities. The latest studies on these RNA degradative enzymes have contributed to the identification of additional homologue proteins, the uncovering of novel RNA degradation pathways, and to a better comprehension of several disease-related processes and response to stress, amongst many other exciting findings. Here, we provide a comprehensive and up-to-date overview on the function, structure, regulation and substrate preference of the key 3'-5' exoribonucleases involved in RNA metabolism.}, }
@article {pmid30333973, year = {2018}, author = {Lou, E and Zhai, E and Sarkari, A and Desir, S and Wong, P and Iizuka, Y and Yang, J and Subramanian, S and McCarthy, J and Bazzaro, M and Steer, CJ}, title = {Cellular and Molecular Networking Within the Ecosystem of Cancer Cell Communication via Tunneling Nanotubes.}, journal = {Frontiers in cell and developmental biology}, volume = {6}, number = {}, pages = {95}, pmid = {30333973}, issn = {2296-634X}, support = {UL1 TR000114/TR/NCATS NIH HHS/United States ; }, abstract = {Intercellular communication is vital to the ecosystem of cancer cell organization and invasion. Identification of key cellular cargo and their varied modes of transport are important considerations in understanding the basic mechanisms of cancer cell growth. Gap junctions, exosomes, and apoptotic bodies play key roles as physical modalities in mediating intercellular transport. Tunneling nanotubes (TNTs)-narrow actin-based cytoplasmic extensions-are unique structures that facilitate direct, long distance cell-to-cell transport of cargo, including microRNAs, mitochondria, and a variety of other sub cellular components. The transport of cargo via TNTs occurs between malignant and stromal cells and can lead to changes in gene regulation that propagate the cancer phenotype. More notably, the transfer of these varied molecules almost invariably plays a critical role in the communication between cancer cells themselves in an effort to resist death by chemotherapy and promote the growth and metastases of the primary oncogenic cell. The more traditional definition of "Systems Biology" is the computational and mathematical modeling of complex biological systems. The concept, however, is now used more widely in biology for a variety of contexts, including interdisciplinary fields of study that focus on complex interactions within biological systems and how these interactions give rise to the function and behavior of such systems. In fact, it is imperative to understand and reconstruct components in their native context rather than examining them separately. The long-term objective of evaluating cancer ecosystems in their proper context is to better diagnose, classify, and more accurately predict the outcome of cancer treatment. Communication is essential for the advancement and evolution of the tumor ecosystem. This interplay results in cancer progression. As key mediators of intercellular communication within the tumor ecosystem, TNTs are the central topic of this article.}, }
@article {pmid30328804, year = {2018}, author = {Cao, M and Chen, K and Li, W and Ma, J and Xiao, Z and Wang, H and Gao, J}, title = {Genetic characterization of human-derived hydatid fluid based on mitochondrial gene sequencing in individuals from northern and western China.}, journal = {Journal of helminthology}, volume = {94}, number = {}, pages = {e2}, doi = {10.1017/S0022149X18000883}, pmid = {30328804}, issn = {1475-2697}, mesh = {Animals ; China ; Echinococcosis/*parasitology ; Echinococcus/classification/*genetics/*isolation &amp; purification ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Helminth Proteins/genetics ; Humans ; Mitochondria/*genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; Tibet ; }, abstract = {This study investigated Echinococcus genotypes in patients with hydatidosis that reside in Inner Mongolia, Tibet or Qinghai Province by partially sequencing the cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase 1 (nad1) genes. Cyst fluids were collected from 23 patients with hydatidosis and DNA was extracted. Portions of the cox1 and nad1 genes were amplified and subsequently sequenced. Sequencing analysis determined that one of the isolates contained Echinococcus multilocularis, and the other 22 isolates contained E. granulosus sensu lato. The isolates were then further classified based on genotype, and E. granulosus sensu stricto (s.s.) G1 (n = 20), E. granulosus s.s. G3 (n = 1) and E. canadensis G6/7 (n = 1) were identified. Additionally, the sequences were concatenated (pcox1 + pnad1) and 11 haplotypes were identified among the E. granulosus s.s. isolates (G1 and G3), with a shared common haplotype (H1) identified. Overall, these findings provide further understanding of the genetic patterns of Echinococcus in western and northern China.}, }
@article {pmid30328102, year = {2018}, author = {Nakazawa, M and Ando, H and Nishimoto, A and Ohta, T and Sakamoto, K and Ishikawa, T and Ueda, M and Sakamoto, T and Nakano, Y and Miyatake, K and Inui, H}, title = {Anaerobic respiration coupled with mitochondrial fatty acid synthesis in wax ester fermentation by Euglena gracilis.}, journal = {FEBS letters}, volume = {592}, number = {24}, pages = {4020-4027}, pmid = {30328102}, issn = {1873-3468}, mesh = {Acyl-CoA Dehydrogenase/genetics/metabolism ; Adenosine Diphosphate/biosynthesis ; Adenosine Triphosphate/biosynthesis ; Anaerobiosis ; *Cell Respiration ; Esters/chemistry/*metabolism ; Euglena gracilis/cytology/genetics/*metabolism ; Fatty Acids/*biosynthesis ; *Fermentation ; Mitochondria/drug effects/*metabolism ; RNA Interference ; Rotenone/pharmacology ; Uncoupling Agents/pharmacology ; Waxes/chemistry/metabolism ; }, abstract = {In Euglena gracilis, wax ester fermentation produces ATP during anaerobiosis. Here, we report that anaerobic wax ester production is suppressed when the mitochondrial electron transport chain complex I is inhibited by rotenone, whereas it is increased by the uncoupler carbonyl cyanide m-chlorophenylhydrazone (CCCP). The ADP/ATP ratio in anaerobic cells is elevated by treatment with either rotenone or CCCP. Gene silencing experiments indicate that acyl-CoA dehydrogenase, electron transfer flavoprotein (ETF), and rhodoquinone (RQ) participate in wax ester production. These results suggest that fatty acids are synthesized in mitochondria by the reversal of β-oxidation, where trans-2-enoyl-CoA is reduced mainly by acyl-CoA dehydrogenase using the electrons provided by NADH via the electron transport chain complex I, RQ, and ETF, and that ATP production is highly supported by anaerobic respiration utilizing trans-2-enoyl-CoA as a terminal electron acceptor.}, }
@article {pmid30326913, year = {2018}, author = {Zhu, Y and Gu, X and Xu, C}, title = {Mitochondrial DNA 7908-8816 region mutations in maternally inherited essential hypertensive subjects in China.}, journal = {BMC medical genomics}, volume = {11}, number = {1}, pages = {89}, pmid = {30326913}, issn = {1755-8794}, mesh = {Adenosine Triphosphatases/genetics/metabolism ; Aged ; Asian People/*genetics ; Case-Control Studies ; China ; Cyclooxygenase 2/genetics ; DNA, Mitochondrial/*genetics ; Female ; Humans ; Hypertension/*genetics/pathology ; Male ; Maternal Inheritance ; Middle Aged ; Mutation ; RNA, Transfer/genetics ; }, abstract = {BACKGROUND: Nuclear genes or family-based mitochondrial screening have been the focus of genetic studies into essential hypertension. Studies into the role of mitochondria in sporadic Chinese hypertensives are lacking. The objective of the study was to explore the relationship between mitochondrial DNA (mtDNA) variations and the development of maternally inherited essential hypertension (MIEH) in China.<br><br>METHODS: Yangzhou residents who were outpatients or in-patients at the Department of Cardiology in Northern Jiangsu People's Hospital (Jiangsu, China) from June 2009 to June 2015 were recruited in a 1:1 case control study of 600 gender-matched Chinese MIEH subjects and controls. Genomic DNA was isolated from whole blood cells. The most likely sites for hypertension were screened using oligodeoxynucleotides at positions 7908-8816, purified and subsequently analyzed by direct sequencing according to the revised consensus Cambridge sequence. The frequency, density, type and conservative evolution of mtDNA variations were comprehensively analyzed.<br><br>RESULTS: We found a statistical difference between the two groups for body mass index, waist circumference, abdominal circumference, triglyceride, low-density lipoprotein cholesterol, fasting blood glucose, uric acid, creatinine and blood urea nitrogen (P&#x2009;<&#x2009;0.05). More amino-acid changes and RNA variants were found in MIEH subjects than the controls (P&#x2009;<&#x2009;0.01). The detection system simultaneously identified 40 different heteroplasmic or homoplasmic mutations in 4 genes: COXII, tRNA[Lys], ATP8 and ATP 6. The mtDNA variations were mainly distributed in regions of ATP6 binding sites, and the site of highest mutation frequency was m. 8414C&#x2009;>&#x2009;T. Three changes in single bases (C8414T in ATP8, A8701G in ATP6 and G8584A in ATP6) were significantly different in the MIEH patients and the controls (P&#x2009;<&#x2009;0.001). The m.8273_8281del mutation was identified from 59 MIEH patients.<br><br>CONCLUSIONS: Our results indicate that novel mtDNA mutations may be involved in the pathological process of MIEH, and mitochondrial genetic characteristics were identified in MIEH individuals.}, }
@article {pmid30318512, year = {2018}, author = {Ananieva, EA and Bostic, JN and Torres, AA and Glanz, HR and McNitt, SM and Brenner, MK and Boyer, MP and Addington, AK and Hutson, SM}, title = {Mice deficient in the mitochondrial branched-chain aminotransferase (BCATm) respond with delayed tumour growth to a challenge with EL-4 lymphoma.}, journal = {British journal of cancer}, volume = {119}, number = {8}, pages = {1009-1017}, pmid = {30318512}, issn = {1532-1827}, support = {R01 DK034738/DK/NIDDK NIH HHS/United States ; R56 DK034738/DK/NIDDK NIH HHS/United States ; }, mesh = {AMP-Activated Protein Kinases/metabolism ; Amino Acids, Branched-Chain/blood ; Animals ; Disease Progression ; Female ; Lymphoma/*pathology ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Mitochondria/genetics/*metabolism ; Neoplasm Transplantation ; Phosphorylation ; Transaminases/*genetics/*metabolism ; }, abstract = {BACKGROUND: The mitochondrial branched-chain aminotransferase (BCATm) is a recently discovered cancer marker with a poorly defined role in tumour progression.<br><br>METHODS: To understand how a loss of function of BCATm affects cancer, the global knockout mouse BCATmKO was challenged with EL-4 lymphoma under different diet compositions with varying amounts of branched-chain amino acids (BCAAs). Next, the growth and metabolism of EL-4 cells were studied in the presence of different leucine concentrations in the growth medium.<br><br>RESULTS: BCATmKO mice experienced delayed tumour growth when fed standard rodent chow or a normal BCAA diet. Tumour suppression correlated with 37.6- and 18.9-fold increases in plasma and tumour BCAAs, 37.5% and 30.4% decreases in tumour glutamine and alanine, and a 3.5-fold increase in the phosphorylation of tumour AMPK in BCATmKO mice on standard rodent chow. Similar results were obtained with a normal but not with a choice BCAA diet.<br><br>CONCLUSIONS: Global deletion of BCATm caused a dramatic build-up of BCAAs, which could not be utilised for energy or amino acid synthesis, ultimately delaying the growth of lymphoma tumours. Furthermore, physiological, but not high, leucine concentrations promoted the growth of EL-4 cells. BCATm and BCAA metabolism were identified as attractive targets for anti-lymphoma therapy.}, }
@article {pmid30316921, year = {2019}, author = {Gao, XM and Mu, DL and Hou, CC and Zhu, JQ and Jin, S and Wang, CL}, title = {Expression and putative functions of KIFC1 for nuclear reshaping and midpiece formation during spermiogenesis of Phascolosoma esculenta.}, journal = {Gene}, volume = {683}, number = {}, pages = {169-183}, doi = {10.1016/j.gene.2018.10.021}, pmid = {30316921}, issn = {1879-0038}, mesh = {Animals ; Binding Sites ; Cell Nucleus/metabolism ; Gene Expression Regulation ; Kinesins/chemistry/*genetics/*metabolism ; Male ; Microtubules/metabolism ; Models, Molecular ; Phylogeny ; Polychaeta/genetics/*physiology ; Protein Conformation ; Protein Domains ; Protein Transport ; *Spermatogenesis ; }, abstract = {Kinesin-14 KIFC1 plays an important role in vesicular transport, microtubule organization, and spermiogenesis. In this study, we first investigated the microtubule distribution and expression pattern of KIFC1 during spermiogenesis of P. esculenta. Microtubules are abundant during spermiogenesis of P. esculenta and may be related to the generation and maintenance of pseudopodia-like cytoplasmic protrusions and nuclear reshaping. The Pe-KIFC1 protein is conserved with a motor domain where microtubule and ATP binding sites are predicted, a coiled-coil domain and a divergent tail domain. The Pe-kifc1 gene was extensively expressed and showed the highest expression in coelomic fluid where spermiogenesis occurs. We further observed the expression of kifc1 mRNA and protein and found that Pe-KIFC1 protein primarily co-localized with microtubules during spermiogenesis, indicating that KIFC1 might play several roles during this process via its cargo transport and/or microtubule organization function. In addition, co-localization of mitochondria and KIFC1 was also detected during spermiogenesis, which were located in the midpiece in mature sperm, suggesting that mitochondria might be a cargo of Pe-KIFC1 that participates in the intracellular distribution of mitochondria and formation of the midpiece. Based on our detailed observations of the dynamic distribution of microtubules, KIFC1, and mitochondria during spermiogenesis and the conserved function of KIFC1 in cargo transport and microtubule organization, functional models of Pe-KIFC1 during spermiogenesis are proposed, including the participation of KIFC1 in nuclear reshaping and midpiece formation.}, }
@article {pmid30313490, year = {2018}, author = {Katoh, TK and Zhang, G and Zhou, CJ and Gao, JJ}, title = {Taxonomy of the Hirtodrosophila melanderi species group (Diptera: Drosophilidae), with descriptions of four new species from southwestern China.}, journal = {Zootaxa}, volume = {4422}, number = {3}, pages = {345-365}, doi = {10.11646/zootaxa.4422.3.2}, pmid = {30313490}, issn = {1175-5334}, mesh = {Animals ; China ; *Diptera ; *Drosophilidae ; Mitochondria ; Phylogeny ; Tibet ; }, abstract = {The Hirtodrosophila melanderi species group contains nine known species recorded from either the Old or the New World. All these species were thought to be strict fungivorous drosophilids. In the present study, we give supplementary descriptions for three of these known species, all recorded from Yunnan, southwestern China, H. furcapenis, H. furcapenisoides, and H. longifurcapenis, by examining respective type specimen(s). We then describe four new species of the same group, H. seticlasper Katoh Gao, sp. nov., H. spinicerca Katoh Gao, sp. nov., H. serratifurcapenis Katoh Gao, sp. nov., and H. truncifurca Katoh Gao, sp. nov., all discovered recently from high altitudes (ca. 3,500 to 3,800 m a.s.l.) in Tibet (Xizang), southwestern China. The delimitation of these new species is firstly performed in light of morphology and further with the aid of DNA sequences of the mitochondrial COI (cytochrome c oxydase, subunits I) gene. In addition, a key to all the species of the species group is provided.}, }
@article {pmid30311911, year = {2018}, author = {Fischer, J and Müller, SY and Netzker, T and Jäger, N and Gacek-Matthews, A and Scherlach, K and Stroe, MC and García-Altares, M and Pezzini, F and Schoeler, H and Reichelt, M and Gershenzon, J and Krespach, MK and Shelest, E and Schroeckh, V and Valiante, V and Heinzel, T and Hertweck, C and Strauss, J and Brakhage, AA}, title = {Chromatin mapping identifies BasR, a key regulator of bacteria-triggered production of fungal secondary metabolites.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {30311911}, issn = {2050-084X}, support = {SFB-F3703//Austrian Science Fund FWF/Austria ; }, mesh = {Acetylation ; Aspergillus nidulans/genetics/*metabolism ; Chromatin/*metabolism ; Fungal Proteins/genetics/*metabolism ; Gene Expression Regulation, Fungal ; Gene Ontology ; Genome, Fungal ; Histidine/metabolism ; Histones/metabolism ; Lysine/metabolism ; Mitochondria/metabolism ; Multigene Family ; Nitrogen/metabolism ; Phylogeny ; *Secondary Metabolism ; Signal Transduction ; Streptomyces/*metabolism ; Transcription Factors/metabolism ; }, abstract = {The eukaryotic epigenetic machinery can be modified by bacteria to reprogram the response of eukaryotes during their interaction with microorganisms. We discovered that the bacterium Streptomyces rapamycinicus triggered increased chromatin acetylation and thus activation of the silent secondary metabolism ors gene cluster in the fungus Aspergillus nidulans. Using this model, we aim understanding mechanisms of microbial communication based on bacteria-triggered chromatin modification. Using genome-wide ChIP-seq analysis of acetylated histone H3, we uncovered the unique chromatin landscape in A. nidulans upon co-cultivation with S. rapamycinicus and relate changes in the acetylation to that in the fungal transcriptome. Differentially acetylated histones were detected in genes involved in secondary metabolism, in amino acid and nitrogen metabolism, in signaling, and encoding transcription factors. Further molecular analyses identified the Myb-like transcription factor BasR as the regulatory node for transduction of the bacterial signal in the fungus and show its function is conserved in other Aspergillus species.}, }
@article {pmid30309500, year = {2018}, author = {Miquel, J and Poonlaphdecha, S and Ribas, A}, title = {Spermatological characteristics of the family Glypthelminthidae (Digenea, Plagiorchioidea) inferred from the ultrastructural study of Glypthelmins staffordi Tubangui, 1928.}, journal = {Tissue &amp; cell}, volume = {54}, number = {}, pages = {114-119}, doi = {10.1016/j.tice.2018.08.013}, pmid = {30309500}, issn = {1532-3072}, mesh = {Animals ; Male ; Phylogeny ; Spermatozoa/*ultrastructure ; Trematoda/*classification/*ultrastructure ; }, abstract = {The present study describes the ultrastructural organization of the mature spermatozoon of the digenean Glypthelmins staffordi (Glypthelminthidae) by means of transmission electron microscopy. Live digeneans were collected from the Chinese edible frog (Hoplobatrachus rugulosus) in Udon Thani Province (Thailand). The ultrastructural study reveals that the mature spermatozoon of G. staffordi is a filiform cell, which is tapered at both extremities. It exhibits the Bakhoum et al.'s type IV of spermatozoon of digeneans characterized by the 9+'1' axonemes of trepaxonematan Platyhelminthes, the presence of the association "external ornamentation-cortical microtubules", the external ornamentation located in the posterior part of the anterior region, the arrangement of parallel cortical microtubules in two bundles and with its maximum number located in the anterior part of the sperm cell, and the presence of two mitochondria. Other characteristics are the presence of spine-like bodies, a posterior extremity containing only the nucleus, and the presence of a large amount of glycogen granules. Results of the present study are particularly compared with the existing data in other families of the Plagiorchioidea, namely the Brachycoeliidae, the Haematoloechidae, the Omphalometridae and the Plagiorchiidae.}, }
@article {pmid30308027, year = {2018}, author = {Perdices, A and Ozeren, CS and Erkakan, F and Freyhof, J}, title = {Diversity of spined loaches from Asia Minor in a phylogenetic context (Teleostei: Cobitidae).}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0205678}, pmid = {30308027}, issn = {1932-6203}, mesh = {Animals ; Cypriniformes/*genetics ; DNA, Mitochondrial/genetics ; Genetic Variation/genetics ; Homeodomain Proteins/genetics ; Mitochondria/genetics ; Phylogeny ; Turkey ; }, abstract = {Accurate determination of species diversity in areas of high endemicity, particularly those lacking comprehensive systematic knowledge, represents a challenge for both taxonomists and conservationists. This need is particularly evident in areas greatly affected by anthropogenic disturbances such as the Eastern Mediterranean and its freshwater environments. To improve our knowledge of Eastern Mediterranean freshwater fishes, we phylogenetically studied Western Palearctic Cobitis species, focusing on those found in Turkey. Overall, our results provide a robust framework to assess the number of species of Cobitis. Phylogenetic reconstructions based on mitochondrial (cyt b) and nuclear (RAG1) sequences show seven major clades (Clades 1-7) grouping all Western Palearctic Cobitis species, except C. melanoleuca. In general, each major clade comprises Cobitis species that inhabit geographically close areas and have similar secondary sexual characters. Multiple divergent lineages were identified in our analyses, some of which were highly divergent such as the ones inhabiting Turkish freshwaters. Moreover, in some analyses, several of the identified lineages were incongruent with a priori defined species. Furthermore, our analyses identified eight potentially new candidate species, six that had been suggested in previous studies and two that are reported here for the first time. Our results reveal Turkey as the area with the greatest diversity of spined loaches in the Mediterranean.}, }
@article {pmid30304578, year = {2018}, author = {Burger, G and Valach, M}, title = {Perfection of eccentricity: Mitochondrial genomes of diplonemids.}, journal = {IUBMB life}, volume = {70}, number = {12}, pages = {1197-1206}, doi = {10.1002/iub.1927}, pmid = {30304578}, issn = {1521-6551}, support = {MOP-79309//CIHR/Canada ; }, mesh = {Aquatic Organisms/*genetics ; DNA, Mitochondrial/genetics ; Euglenozoa/*genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Introns/genetics ; Mitochondria/*genetics ; }, abstract = {Mitochondria are the sandbox of evolution as exemplified most particularly by the diplonemids, a group of marine microeukaryotes. These protists are uniquely characterized by their highly multipartite mitochondrial genome and systematically fragmented genes whose pieces are spread out over several dozens of chromosomes. The type species Diplonema papillatum was the first member of this group in which the expression of fragmented mitochondrial genes was investigated experimentally. We now know that gene expression involves separate transcription of gene pieces (modules), RNA editing of module transcripts, and module joining to mature mRNAs and rRNAs. The mechanism of cognate module recognition and ligation is distinct from known intron splicing and remains to be uncovered. Here, we review the current status of research on mitochondrial genome architecture, as well as gene complement, structure, and expression modes in diplonemids. Further, we discuss the potential molecular mechanisms of posttranscriptional processing, and finally reflect on the evolutionary trajectories and trends of mtDNA evolution as seen in this protist group. © 2018 IUBMB Life, 70(12):1197-1206, 2018.}, }
@article {pmid30304531, year = {2018}, author = {Urantówka, AD and Kroczak, A and Silva, T and Padrón, RZ and Gallardo, NF and Blanch, J and Blanch, B and Mackiewicz, P}, title = {New Insight into Parrots' Mitogenomes Indicates That Their Ancestor Contained a Duplicated Region.}, journal = {Molecular biology and evolution}, volume = {35}, number = {12}, pages = {2989-3009}, pmid = {30304531}, issn = {1537-1719}, mesh = {Animals ; *Gene Duplication ; Gene Order ; *Genome, Mitochondrial ; Longevity/genetics ; Parrots/anatomy &amp; histology/*genetics ; Phylogeny ; }, abstract = {Mitochondrial genomes of vertebrates are generally thought to evolve under strong selection for size reduction and gene order conservation. Therefore, a growing number of mitogenomes with duplicated regions changes our view on the genome evolution. Among Aves, order Psittaciformes (parrots) is especially noteworthy because of its large morphological, ecological, and taxonomical diversity, which offers an opportunity to study genome evolution in various aspects. Former analyses showed that tandem duplications comprising the control region with adjacent genes are restricted to several lineages in which the duplication occurred independently. However, using an appropriate polymerase chain reaction strategy, we demonstrate that early diverged parrot groups contain mitogenomes with the duplicated region. These findings together with mapping duplication data from other mitogenomes onto parrot phylogeny indicate that the duplication was an ancestral state for Psittaciformes. The state was inherited by main parrot groups and was lost several times in some lineages. The duplicated regions were subjected to concerted evolution with a frequency higher than the rate of speciation. The duplicated control regions may provide a selective advantage due to a more efficient initiation of replication or transcription and a larger number of replicating genomes per organelle, which may lead to a more effective energy production by mitochondria. The mitogenomic duplications were associated with phenotypic features and parrots with the duplicated region can live longer, show larger body mass as well as predispositions to a more active flight. The results have wider implications on the presence of duplications and their evolution in mitogenomes of other avian groups.}, }
@article {pmid30300424, year = {2018}, author = {Kobayashi, G and Araya, JF}, title = {Southernmost records of Escarpia spicata and Lamellibrachia barhami (Annelida: Siboglinidae) confirmed with DNA obtained from dried tubes collected from undiscovered reducing environments in northern Chile.}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0204959}, pmid = {30300424}, issn = {1932-6203}, mesh = {Animals ; Annelida/classification/*genetics/microbiology ; Bacteria/genetics/isolation &amp; purification ; Chile ; DNA/*chemistry/isolation &amp; purification/metabolism ; Electron Transport Complex IV/classification/genetics ; Hemoglobins/classification/genetics ; Mitochondria/genetics ; Phylogeny ; Protein Subunits/classification/genetics ; RNA, Ribosomal, 16S/chemistry/isolation &amp; purification/metabolism ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Deep-sea fishing bycatch enables collection of samples of rare species that are not easily accessible, for research purposes. However, these specimens are often degraded, losing diagnostic morphological characteristics. Several tubes of vestimentiferans, conspicuous annelids endemic to chemosynthetic environments, were obtained from a single batch of deep-sea fishing bycatch at depths of around 1,500 m off Huasco, northern Chile, as part of an ongoing study examining bycatch species. DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene and an intron region within the hemoglobin subunit B2 (hbB2i) were successfully determined using vestimentiferans' dried-up tubes and their degraded inner tissue. Molecular phylogenetic analyses based on DNA sequence identified the samples as Escarpia spicata Jones, 1985, and Lamellibrachia barhami Webb, 1969. These are the southernmost records, vastly extending the geographical ranges of both species from Santa Catalina Island, California to northern Chile for E. spicata (over 8,000 km), and from Vancouver Island Margin to northern Chile for L. barhami (over 10,000 km). We also determined a 16S rRNA sequence of symbiotic bacteria of L. barhami. The sequence of the bacteria is the same as that of E. laminata, Lamellibrachia sp. 1, and Lamellibrachia sp.2 known from the Gulf of Mexico. The present study provides sound evidence forthe presence of reducing environments along the continental margin of northern Chile.}, }
@article {pmid30297026, year = {2018}, author = {Porcelli, V and Vozza, A and Calcagnile, V and Gorgoglione, R and Arrigoni, R and Fontanesi, F and Marobbio, CMT and Castegna, A and Palmieri, F and Palmieri, L}, title = {Molecular identification and functional characterization of a novel glutamate transporter in yeast and plant mitochondria.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1859}, number = {11}, pages = {1249-1258}, doi = {10.1016/j.bbabio.2018.08.001}, pmid = {30297026}, issn = {1879-2650}, mesh = {Amino Acid Transport System X-AG/*metabolism ; Arabidopsis/*metabolism ; Arabidopsis Proteins/*metabolism ; Gene Deletion ; Glutamic Acid/metabolism ; Hydrogen-Ion Concentration ; Kinetics ; Membrane Transport Proteins/*metabolism ; Mitochondria/*metabolism ; Phylogeny ; Proteolipids ; Recombinant Proteins/metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/*metabolism ; Substrate Specificity ; Time Factors ; }, abstract = {The genome of Saccharomyces cerevisiae encodes 35 members of the mitochondrial carrier family (MCF) and 58 MCF members are coded by the genome of Arabidopsis thaliana, most of which have been functionally characterized. Here two members of this family, Ymc2p from S. cerevisiae and BOU from Arabidopsis, have been thoroughly characterized. These proteins were overproduced in bacteria and reconstituted into liposomes. Their transport properties and kinetic parameters demonstrate that Ymc2p and BOU transport glutamate, and to a much lesser extent L-homocysteinesulfinate, but not other amino acids and many other tested metabolites. Transport catalyzed by both carriers was saturable, inhibited by mercuric chloride and dependent on the proton gradient across the proteoliposomal membrane. The growth phenotype of S. cerevisiae cells lacking the genes ymc2 and agc1, which encodes the only other S. cerevisiae carrier capable to transport glutamate besides aspartate, was fully complemented by expressing Ymc2p, Agc1p or BOU. Mitochondrial extracts derived from ymc2Δagc1Δ cells, reconstituted into liposomes, exhibited no glutamate transport at variance with wild-type, ymc2Δ and agc1Δ cells, showing that S. cerevisiae cells grown in the presence of acetate do not contain additional mitochondrial transporters for glutamate besides Ymc2p and Agc1p. Furthermore, mitochondria isolated from wild-type, ymc2Δ and agc1Δ strains, but not from the double mutant ymc2Δagc1Δ strain, swell in isosmotic ammonium glutamate showing that glutamate is transported by Ymc2p and Agc1p together with a H[+]. It is proposed that the function of Ymc2p and BOU is to transport glutamate across the mitochondrial inner membrane and thereby play a role in intermediary metabolism, C1 metabolism and mitochondrial protein synthesis.}, }
@article {pmid30292820, year = {2018}, author = {Cogliati, S and Lorenzi, I and Rigoni, G and Caicci, F and Soriano, ME}, title = {Regulation of Mitochondrial Electron Transport Chain Assembly.}, journal = {Journal of molecular biology}, volume = {430}, number = {24}, pages = {4849-4873}, doi = {10.1016/j.jmb.2018.09.016}, pmid = {30292820}, issn = {1089-8638}, mesh = {Animals ; *Electron Transport ; Evolution, Molecular ; Gene Expression Regulation ; Humans ; Mitochondria/*genetics/metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Multienzyme Complexes/chemistry/metabolism ; Oxidative Phosphorylation ; Phylogeny ; }, abstract = {Mitochondrial function depends on the correct synthesis, transport, and assembly of proteins and cofactors of the electron transport chain. The initial idea that the respiratory chain protein complexes (RCCs) were independent structures in the inner mitochondrial membrane evolved after the identification of higher quaternary structures called supercomplexes (SCs), whose formation is dynamically regulated in order to accommodate cellular metabolic demands. Due to the dual genetic origin of the mitochondrial proteome, electron transport chain and SCs formation must be tightly regulated to coordinate the expression and assembly of components encoded by both genomes. This regulation occurs at different levels from gene transcription to protein, complex or SCs assembly, and might involve the participation of factors that contribute to the formation and stability of the RCCs and SCs. Here we review the cellular pathways and assembly factors that regulate RCCs and SCs formation.}, }
@article {pmid30291814, year = {2018}, author = {Lukeš, J and Wheeler, R and Jirsová, D and David, V and Archibald, JM}, title = {Massive mitochondrial DNA content in diplonemid and kinetoplastid protists.}, journal = {IUBMB life}, volume = {70}, number = {12}, pages = {1267-1274}, pmid = {30291814}, issn = {1521-6551}, support = {MOP-115141//CIHR/Canada ; 103261/Z/13/Z//Wellcome Trust/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {DNA, Mitochondrial/*genetics/isolation &amp; purification/ultrastructure ; Euglenozoa/*genetics ; Kinetoplastida/*genetics ; Mitochondria/*genetics ; Phylogeny ; Trans-Splicing/genetics ; }, abstract = {The mitochondrial DNA of diplonemid and kinetoplastid protists is known for its suite of bizarre features, including the presence of concatenated circular molecules, extensive trans-splicing and various forms of RNA editing. Here we report on the existence of another remarkable characteristic: hyper-inflated DNA content. We estimated the total amount of mitochondrial DNA in four kinetoplastid species (Trypanosoma brucei, Trypanoplasma borreli, Cryptobia helicis, and Perkinsela sp.) and the diplonemid Diplonema papillatum. Staining with 4',6-diamidino-2-phenylindole and RedDot1 followed by color deconvolution and quantification revealed massive inflation in the total amount of DNA in their organelles. This was further confirmed by electron microscopy. The most extreme case is the ∼260 Mbp of DNA in the mitochondrion of Diplonema, which greatly exceeds that in its nucleus; this is, to our knowledge, the largest amount of DNA described in any organelle. Perkinsela sp. has a total mitochondrial DNA content ~6.6× greater than its nuclear genome. This mass of DNA occupies most of the volume of the Perkinsela cell, despite the fact that it contains only six protein-coding genes. Why so much DNA? We propose that these bloated mitochondrial DNAs accumulated by a ratchet-like process. Despite their excessive nature, the synthesis and maintenance of these mtDNAs must incur a relatively low cost, considering that diplonemids are one of the most ubiquitous and speciose protist groups in the ocean. © 2018 IUBMB Life, 70(12):1267-1274, 2018.}, }
@article {pmid30289547, year = {2019}, author = {Hsu, YW and Juan, CT and Wang, CM and Jauh, GY}, title = {Mitochondrial Heat Shock Protein 60s Interact with What's This Factor 9 to Regulate RNA Splicing of ccmFC and rpl2.}, journal = {Plant &amp; cell physiology}, volume = {60}, number = {1}, pages = {116-125}, doi = {10.1093/pcp/pcy199}, pmid = {30289547}, issn = {1471-9053}, mesh = {Amino Acid Sequence ; Arabidopsis/growth &amp; development ; Arabidopsis Proteins/*metabolism ; Base Sequence ; Chaperonin 60/chemistry/*metabolism ; Introns/*genetics ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/metabolism ; Mutation/genetics ; Peptides/chemistry/metabolism ; Phenotype ; Protein Binding ; RNA Splicing/*genetics ; RNA-Binding Proteins/*metabolism ; }, abstract = {Mitochondrial intron splicing is a plant-specific feature that was acquired during the co-evolution of eukaryotic host cells and a-proteobacteria. The elimination of these introns is facilitated by mitochondrial-targeted proteins encoded by its host, nucleus. What's this factor 9 (WTF9), a nuclear-encoded plant organelle RNA recognition (PORR) protein, is involved in the splicing of the mitochondrial group II introns rpl2 and ccmFC. Disruption of WTF9 causes developmental defects associated with the loss of Cyt c and Cyt c1 in Arabidopsis. In the present study, using a co-immunoprecipitation assay, we found that HSP60s interacted with WTF9, which was further confirmed by a pull-down assay. HSP60s are molecular chaperones that assist with protein folding in both eukaryotic and prokaryotic cells. However, accumulating evidence suggests that HSP60s also participate in other biological functions such as RNA metabolism and RNA protection. In this study, we found that consistently with their interaction with WTF9, HSP60s interacted with 48 nucleotides of the ccmFC intron. In mutant studies, the double mutant hsp60-3a1hsp60-3b1 exhibited a small stature phenotype and reduced splicing efficiency for rpl2 and ccmFC. These observations were similar to those in wtf9 mutants and suggest that HSP60s are involved in the RNA splicing of rpl2 and ccmFC introns in mitochondria. Our findings suggest that HSP60s participate in mitochondrial RNA splicing through their RNA-binding ability.}, }
@article {pmid30286121, year = {2018}, author = {Ashrafzadeh, MR and Djan, M and Szendrei, L and Paulauskas, A and Scandura, M and Bagi, Z and Ilie, DE and Kerdikoshvili, N and Marek, P and Soós, N and Kusza, S}, title = {Large-scale mitochondrial DNA analysis reveals new light on the phylogeography of Central and Eastern-European Brown hare (Lepus europaeus Pallas, 1778).}, journal = {PloS one}, volume = {13}, number = {10}, pages = {e0204653}, pmid = {30286121}, issn = {1932-6203}, mesh = {Animals ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Europe ; Haplotypes/genetics ; Hares/*genetics ; Hybridization, Genetic/genetics ; Mitochondria/*genetics ; Phylogeny ; Phylogeography/methods ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {European brown hare, Lepus europaeus, from Central and Eastern European countries (Hungary, Poland, Serbia, Lithuania, Romania, Georgia and Italy) were sampled, and phylogenetic analyses were carried out on two datasets: 1.) 137 sequences (358 bp) of control region mtDNA; and 2.) 105 sequences of a concatenated fragment (916 bp), including the cytochrome b, tRNA-Thr, tRNA-Pro and control region mitochondrial DNA. Our sequences were aligned with additional brown hare sequences from GenBank. A total of 52 and 51 haplotypes were detected within the two datasets, respectively, and assigned to two previously described major lineages: Anatolian/Middle Eastern (AME) and European (EUR). Furthermore, the European lineage was divided into two subclades including South Eastern European (SEE) and Central European (CE). Sympatric distribution of the lineages of the brown hare in South-Eastern and Eastern Europe revealed contact zones there. BAPS analysis assigned sequences from L. europaeus to five genetic clusters, whereas CE individuals were assigned to only one cluster, and AME and SEE sequences were each assigned to two clusters. Our findings uncover numerous novel haplotypes of Anatolian/Middle Eastern brown hare outside their main range, as evidence for the combined influence of Late Pleistocene climatic fluctuations and anthropogenic activities in shaping the phylogeographic structure of the species. Our results support the hypothesis of a postglacial brown hare expansion from Anatolia and the Balkan Peninsula to Central and Eastern Europe, and suggest some slight introgression of individual haplotypes from L. timidus to L. europaeus.}, }
@article {pmid30285603, year = {2018}, author = {Chen, G and Zou, Y and Hu, J and Ding, Y}, title = {Genome-wide analysis of the rice PPR gene family and their expression profiles under different stress treatments.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {720}, pmid = {30285603}, issn = {1471-2164}, support = {31471464//National Nature Science Foundation of China/ ; 2013CB126900//"973" Program of China/ ; }, mesh = {Chromosomes, Plant/genetics ; Droughts ; *Gene Expression Profiling ; Genome, Plant/genetics ; *Genomics ; Intracellular Space/metabolism ; MicroRNAs/genetics ; Oryza/drug effects/*genetics/metabolism/*physiology ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Protein Transport ; Salts/pharmacology ; Stress, Physiological/drug effects/*genetics ; Synteny ; }, abstract = {BACKGROUND: Pentatricopeptide-repeat proteins (PPRs) are characterized by tandem arrays of a degenerate 35-amino-acid (PPR motifs), which can bind RNA strands and participate in post-transcription. PPR proteins family is one of the largest families in land plants and play important roles in organelle RNA metabolism and plant development. However, the functions of PPR genes involved in biotic and abiotic stresses of rice (Oryza sativa L.) remain largely unknown.<br><br>RESULTS: In the present study, a comprehensive genome-wide analysis of PPR genes was performed. A total of 491 PPR genes were found in the rice genome, of which 246 PPR genes belong to the P subfamily, and 245 genes belong to the PLS subfamily. Gene structure analysis showed that most PPR genes lack intron. Chromosomal location analysis indicated that PPR genes were widely distributed in all 12 rice chromosomes. Phylogenetic relationship analysis revealed the distinct difference between the P and PLS subfamilies. Many PPR proteins are predicted to target chloroplasts or mitochondria, and a PPR protein (LOC_Os10g34310) was verified to localize in mitochondria. Furthermore, three PPR genes (LOC_Os03g17634,LOC_Os07g40820,LOC_Os04g51350) were verified as corresponding miRNA targets. The expression pattern analysis showed that many PPR genes could be induced under biotic and abiotic stresses. Finally, seven PPR genes were confirmed with their expression patterns under salinity or drought stress.<br><br>CONCLUSIONS: We found 491 PPR genes in the rice genome, and our genes structure analysis and syntenic analysis indicated that PPR genes might be derived from amplification by retro-transposition. The expression pattern present here suggested that PPR proteins have crucial roles in response to different abiotic stresses in rice. Taken together, our study provides a comprehensive analysis of the PPR gene family and will facilitate further studies on their roles in rice growth and development.}, }
@article {pmid30281911, year = {2018}, author = {van Esveld, SL and Huynen, MA}, title = {Does mitochondrial DNA evolution in metazoa drive the origin of new mitochondrial proteins?.}, journal = {IUBMB life}, volume = {70}, number = {12}, pages = {1240-1250}, doi = {10.1002/iub.1940}, pmid = {30281911}, issn = {1521-6551}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Eukaryota/genetics ; *Evolution, Molecular ; Humans ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Nuclear Proteins/genetics ; Oxidative Phosphorylation ; }, abstract = {Most eukaryotic cells contain mitochondria with a genome that evolved from their α-proteobacterial ancestor. In the course of eukaryotic evolution, the mitochondrial genome underwent a dramatic reduction in size, caused by the loss and translocation of genes. This required adjustments in mitochondrial gene expression mechanisms and resulted in a complex collaborative system of mitochondrially encoded transfer RNAs and ribosomal RNAs with nuclear encoded proteins to express the mitochondrial encoded oxidative phosphorylation (OXPHOS) proteins. In this review, we examine mitochondrial gene expression from an evolutionary point of view: to what extent can we correlate changes in the mitochondrial genome in the evolutionary lineage leading to human with the origin of new nuclear encoded proteins. We dated the evolutionary origin of mitochondrial proteins that interact with mitochondrial DNA or its RNA and/or protein products in a systematic manner and compared them with documented changes in the mitochondrial DNA. We find anecdotal but accumulating evidence that metazoan RNA-interacting proteins arose in conjunction with changes of the mitochondrial DNA. We find no substantial evidence for such compensatory evolution in new OXPHOS proteins, which appear to be constrained by the ability to form supercomplexes. © 2018 IUBMB Life, 70(12):1240-1250, 2018.}, }
@article {pmid30281880, year = {2018}, author = {Harborne, SPD and Kunji, ERS}, title = {Calcium-regulated mitochondrial ATP-Mg/Pi carriers evolved from a fusion of an EF-hand regulatory domain with a mitochondrial ADP/ATP carrier-like domain.}, journal = {IUBMB life}, volume = {70}, number = {12}, pages = {1222-1232}, pmid = {30281880}, issn = {1521-6551}, support = {MC_U105663139/MRC_/Medical Research Council/United Kingdom ; MC_UU_00015/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amino Acid Transport Systems, Acidic/genetics/metabolism ; Animals ; Antiporters/*genetics/metabolism ; Calcium/metabolism ; Calcium Signaling/*genetics ; Calcium-Binding Proteins/metabolism ; Humans ; Mitochondria/*genetics/metabolism ; Mitochondrial ADP, ATP Translocases/*genetics ; Mitochondrial Proteins/*genetics ; Protein Conformation ; Protein Domains/genetics ; Saccharomyces cerevisiae/genetics/metabolism ; }, abstract = {The mitochondrial ATP-Mg/Pi carrier is responsible for the calcium-dependent regulation of adenosine nucleotide concentrations in the mitochondrial matrix, which allows mitochondria to respond to changing energy requirements of the cell. The carrier is expressed in mitochondria of fungi, plants and animals and belongs to the family of mitochondrial carriers. The carrier is unusual as it consists of three separate domains: (i) an N-terminal regulatory domain with four calcium-binding EF-hands similar to calmodulin, (ii) a loop domain containing an amphipathic α-helix and (iii) a mitochondrial carrier domain related to the mitochondrial ADP/ATP carrier. This striking example of three domains coming together from different origins to provide new functions represents an interesting quirk of evolution. In this review, we outline how the carrier was identified and how its physiological role was established with a focus on human isoforms. We exploit the sequence and structural information of the domains to explore the similarities and differences to their closest counterparts; mitochondrial ADP/ATP carriers and proteins with four EF-hands. We discuss how their combined function has led to a mechanism for calcium-regulated transport of adenosine nucleotides. Finally, we compare the ATP-Mg/Pi carrier with the mitochondrial aspartate/glutamate carrier, the only other mitochondrial carrier regulated by calcium, and we will argue that they have arisen by convergent rather than divergent evolution. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(12):1222-1232, 2018.}, }
@article {pmid30280695, year = {2018}, author = {Önder, Z and İnci, A and Yıldırım, A and Çiloğlu, A and Düzlü, &#xd6;}, title = {Molecular Characterization of Myiasis-Causing Moth Flies (Diptera: Psychodidae).}, journal = {Turkiye parazitolojii dergisi}, volume = {42}, number = {3}, pages = {223-228}, doi = {10.5152/tpd.2018.5943}, pmid = {30280695}, issn = {2146-3077}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry ; Mitochondria/genetics ; Myiasis/*parasitology ; Phylogeny ; Psychodidae/classification/*genetics ; Sequence Alignment ; Turkey ; }, abstract = {OBJECTIVE: The aim of this study is to examine the molecular characterization of moth flies (Diptera: Psychodidae) based on their mitochondrial DNA sequences and determine the vectorial potential and damage caused by moth flies in future researches.<br><br>METHODS: A total of 240 adult moth flies were collected from toilet, bathroom, and basement walls of houses from different locations of the Kayseri region between May 2016 and April 2017. The polymerase chain reaction (PCR) analyses were performed using primer pairs, specificaly targeting the mitochondrial cytochrome oxidase c subunit I (mt-COI) gene of adult flies.<br><br>RESULTS: In total, five isolates were gel purified and sequenced for molecular characterization and phylogenetic analyses. Two species, namely Telmatoscopus albipunctatus (ERU-Telmatos3 and ERU-Telmatos6) and Psychodidae sp. (ERU-Psycho1,4,5), were successfully identified with the sequence alignment of isolates. According to the phylogenetic analysis, it was determined that the ERU-Telmatos3 and ERU-Telmatos6 isolates are clustered in the haplogroup A, while the ERU-Psycho1,4,5 isolate was clustered within the haplogroup B. The ERU-Psycho1 isolate was characterized as a new haplotype within the haplogroup B.<br><br>CONCLUSION: This study represents the first molecular characterization and phylogenetic status of moth flies in Turkey. The obtained findings should be the first step in the future investigation based on detecting the transmission of bacterial pathogens by moth flies.}, }
@article {pmid30279542, year = {2018}, author = {Severgnini, M and Lazzari, B and Capra, E and Chessa, S and Luini, M and Bordoni, R and Castiglioni, B and Ricchi, M and Cremonesi, P}, title = {Genome sequencing of Prototheca zopfii genotypes 1 and 2 provides evidence of a severe reduction in organellar genomes.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {14637}, pmid = {30279542}, issn = {2045-2322}, mesh = {Chromosome Mapping ; DNA-Directed RNA Polymerases/genetics ; Genome, Mitochondrial ; Genome, Plant ; Genome, Plastid ; Host-Pathogen Interactions/genetics ; Mitochondria/*genetics ; Photosynthesis/*genetics ; Plastids/*genetics ; Prototheca/*classification/*genetics ; }, abstract = {Prototheca zopfii (P. zopfii, class Trebouxiophyceae, order Chlorellales, family Chlorellaceae), a non-photosynthetic predominantly free-living unicellular alga, is one of the few pathogens belonging to the plant kingdom. This alga can affect many vertebrate hosts, sustaining systemic infections and diseases such as mastitis in cows. The aim of our work was to sequence and assemble the P. zopfii genotype 1 and genotype 2 mitochondrial and plastid genomes. Remarkably, the P. zopfii mitochondrial (38 Kb) and plastid (28 Kb) genomes are models of compaction and the smallest known in the Trebouxiophyceae. As expected, the P. zopfii genotype 1 and 2 plastid genomes lack all the genes involved in photosynthesis, but, surprisingly, they also lack those coding for RNA polymerases. Our results showed that plastid genes are actively transcribed in P. zopfii, which suggests that the missing RNA polymerases are substituted by nuclear-encoded paralogs. The simplified architecture and highly-reduced gene complement of the P. zopfii mitochondrial and plastid genomes are closer to those of P. stagnora and the achlorophyllous obligate parasite Helicosporidium than to those of P. wickerhamii or P. cutis. This similarity is also supported by maximum likelihood phylogenetic analyses inferences. Overall, the P. zopfii sequences reported here, which include nuclear genome drafts for both genotypes, will help provide both a deeper understanding of the evolution of Prototheca spp. and insights into the corresponding host/pathogen interactions.}, }
@article {pmid30265295, year = {2018}, author = {Pereira, J and Lupas, AN}, title = {The Origin of Mitochondria-Specific Outer Membrane β-Barrels from an Ancestral Bacterial Fragment.}, journal = {Genome biology and evolution}, volume = {10}, number = {10}, pages = {2759-2765}, pmid = {30265295}, issn = {1759-6653}, mesh = {Animals ; *Evolution, Molecular ; Mitochondrial Membranes ; Mitochondrial Proteins/*genetics ; }, abstract = {Outer membrane β-barrels (OMBBs) are toroidal arrays of antiparallel β-strands that span the outer membrane of Gram-negative bacteria and eukaryotic organelles. Although homologous, most families of bacterial OMBBs evolved through the independent amplification of an ancestral ββ-hairpin. In mitochondria, one family (SAM50) has a clear bacterial ancestry; the origin of the other family, consisting of 19-stranded OMBBs found only in mitochondria (MOMBBs), is substantially unclear. In a large-scale comparison of mitochondrial and bacterial OMBBs, we find evidence that the common ancestor of all MOMBBs emerged by the amplification of a double ββ-hairpin of bacterial origin, probably at the time of the Last Eukaryotic Common Ancestor. Thus, MOMBBs are indeed descended from bacterial OMBBs, but their fold formed independently in the proto-mitochondria, possibly in response to the need for a general-purpose polypeptide importer. This occurred by a process of amplification, despite the final fold having a prime number of strands.}, }
@article {pmid30265292, year = {2018}, author = {Pyrihová, E and Motycková, A and Voleman, L and Wandyszewska, N and Fišer, R and Seydlová, G and Roger, A and Kolísko, M and Doležal, P}, title = {A Single Tim Translocase in the Mitosomes of Giardia intestinalis Illustrates Convergence of Protein Import Machines in Anaerobic Eukaryotes.}, journal = {Genome biology and evolution}, volume = {10}, number = {10}, pages = {2813-2822}, pmid = {30265292}, issn = {1759-6653}, support = {MOP-142349//CIHR/Canada ; }, mesh = {Amino Acid Sequence ; Anaerobiosis ; *Evolution, Molecular ; Giardia lamblia/*enzymology ; Mitochondria/*enzymology ; Mitochondrial Membrane Transport Proteins/*metabolism ; }, abstract = {Mitochondria have evolved diverse forms across eukaryotic diversity in adaptation to anoxia. Mitosomes are the simplest and the least well-studied type of anaerobic mitochondria. Transport of proteins via TIM complexes, composed of three proteins of the Tim17 protein family (Tim17/22/23), is one of the key unifying aspects of mitochondria and mitochondria-derived organelles. However, multiple experimental and bioinformatic attempts have so far failed to identify the nature of TIM in mitosomes of the anaerobic metamonad protist, Giardia intestinalis, one of the few experimental models for mitosome biology. Here, we present the identification of a single G. intestinalis Tim17 protein (GiTim17), made possible only by the implementation of a metamonad-specific hidden Markov model. While very divergent in primary sequence and in predicted membrane topology, experimental data suggest that GiTim17 is an inner membrane mitosomal protein, forming a disulphide-linked dimer. We suggest that the peculiar GiTim17 sequence reflects adaptation to the unusual, detergent resistant, inner mitosomal membrane. Specific pull-down experiments indicate interaction of GiTim17 with mitosomal Tim44, the tethering component of the import motor complex. Analysis of TIM complexes across eukaryote diversity suggests that a "single Tim" translocase is a convergent adaptation of mitosomes in anaerobic protists, with Tim22 and Tim17 (but not Tim23), providing the protein backbone.}, }
@article {pmid30258733, year = {2018}, author = {Huang, Y and Zheng, S and Mei, X and Yu, B and Sun, B and Li, B and Wei, J and Chen, J and Li, T and Pan, G and Zhou, Z and Li, C}, title = {A secretory hexokinase plays an active role in the proliferation of Nosema bombycis.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5658}, pmid = {30258733}, issn = {2167-8359}, abstract = {The microsporidian Nosema bombycis is an obligate intracellular parasite of Bombyx mori, that lost its intact tricarboxylic acid cycle and mitochondria during evolution but retained its intact glycolysis pathway. N. bombycis hexokinase (NbHK) is not only a rate-limiting enzyme of glycolysis but also a secretory protein. Indirect immunofluorescence assays and recombinant HK overexpressed in BmN cells showed that NbHK localized in the nucleus and cytoplasm of host cell during the meront stage. When N. bombycis matured, NbHK tended to concentrate at the nuclei of host cells. Furthermore, the transcriptional profile of NbHK implied it functioned during N. bombycis' proliferation stages. A knock-down of NbHK effectively suppressed the proliferation of N. bombycis indicating that NbHK is an important protein for parasite to control its host.}, }
@article {pmid30256727, year = {2019}, author = {McClelland, GB and Scott, GR}, title = {Evolved Mechanisms of Aerobic Performance and Hypoxia Resistance in High-Altitude Natives.}, journal = {Annual review of physiology}, volume = {81}, number = {}, pages = {561-583}, doi = {10.1146/annurev-physiol-021317-121527}, pmid = {30256727}, issn = {1545-1585}, mesh = {Altitude ; Animals ; *Atmospheric Pressure ; *Biological Evolution ; Carbohydrate Metabolism ; Humans ; *Hypoxia ; Muscle, Skeletal ; Oxygen/*metabolism ; Oxygen Consumption ; Population Groups/*genetics ; Selection, Genetic ; *Thermogenesis ; }, abstract = {Comparative physiology studies of high-altitude species provide an exceptional opportunity to understand naturally evolved mechanisms of hypoxia resistance. Aerobic capacity (VO2max) is a critical performance trait under positive selection in some high-altitude taxa, and several high-altitude natives have evolved to resist the depressive effects of hypoxia on VO2max. This is associated with enhanced flux capacity through the O2 transport cascade and attenuation of the maladaptive responses to chronic hypoxia that can impair O2 transport. Some highlanders exhibit elevated rates of carbohydrate oxidation during exercise, taking advantage of its high ATP yield per mole of O2. Certain highland native animals have also evolved more oxidative muscles and can sustain high rates of lipid oxidation to support thermogenesis. The underlying mechanisms include regulatory adjustments of metabolic pathways and to gene expression networks. Therefore, the evolution of hypoxia resistance in high-altitude natives involves integrated functional changes in the pathways for O2 and substrate delivery and utilization by mitochondria.}, }
@article {pmid30246391, year = {2019}, author = {Shibata, D}, title = {Somatic cell evolution: how to improve with age.}, journal = {The Journal of pathology}, volume = {247}, number = {1}, pages = {3-5}, pmid = {30246391}, issn = {1096-9896}, support = {U54 CA217376/CA/NCI NIH HHS/United States ; P30 CA014089/CA/NCI NIH HHS/United States ; P30CA014089/NH/NIH HHS/United States ; CA196569/NH/NIH HHS/United States ; P01 CA196569/CA/NCI NIH HHS/United States ; U54CA217376/NH/NIH HHS/United States ; }, mesh = {DNA, Mitochondrial/*genetics ; Mitochondria/genetics ; Mutation ; *Stem Cells ; United Kingdom ; }, abstract = {A recent article published in this journal illuminates a rare example of somatic evolution where cells improve rather than deteriorate with age. In mitotic intestinal crypts, stem cells with higher levels of a deleterious heteroplasmic germline mitochondrial mutation are purged through time, leading to crypts without the mutation. Similar somatic mitochondrial mutations are not purged from crypts, indicating that special conditions are needed to improve with age. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley &amp; Sons, Ltd.}, }
@article {pmid30239827, year = {2019}, author = {Shang, Y and Ren, L and Chen, W and Zha, L and Cai, J and Dong, J and Guo, Y}, title = {Comparative Mitogenomic Analysis of Forensically Important Sarcophagid Flies (Diptera: Sarcophagidae) and Implications of Species Identification.}, journal = {Journal of medical entomology}, volume = {56}, number = {2}, pages = {392-407}, doi = {10.1093/jme/tjy162}, pmid = {30239827}, issn = {1938-2928}, mesh = {Amino Acid Substitution ; Animals ; Entomology/*methods ; Forensic Sciences/*methods ; *Genetic Techniques ; *Genome, Mitochondrial ; Phylogeny ; RNA, Ribosomal/chemistry ; RNA, Transfer/chemistry ; Sarcophagidae/classification/*genetics ; }, abstract = {The flesh flies (Diptera: Sarcophagidae) are significant in forensic investigations. The mitochondrial genome (mitogeome) has been widely used as genetic markers for phylogenetic analysis and species identification. To further understand the mitogenome-level features in Sarcophagidae, the complete mitogenome of Sarcophaga formosensis (Kirneret Lopes, 1961) (Diptera: Sarcophagidae) and Sarcophaga misera (Walker, 1849) (Diptera: Sarcophagidae) was firstly sequenced, annotated, and compared with other 13 Sarcophagidae species. The result indicated that the gene arrangement, gene content, base composition, and codon usage were conserved in the ancestral arthropod. Evolutionary rate of the mitogenome fragments revealed that the nonsynonymous and synonymous substitution rates (Ka and Ks) ratio was less than 1.00, indicating these variable sites under strong purifying selection. Almost all transfer RNA genes (tRNAs) have typical clover-leaf structures within these sarcophagid mitogenomes, except tRNA-Ser (AGN) is lack of the dihydrouridine arm. This comparative mitogenomic analysis sheds light on the architecture and evolution of mitogenomes in the Sarcophagidae. Phylogenetic analyses containing the interspecific distances from different regions in these species provided us new insights into the application of these effective genetic markers for species identification of flesh flies.}, }
@article {pmid30239783, year = {2018}, author = {Hood, WR and Austad, SN and Bize, P and Jimenez, AG and Montooth, KL and Schulte, PM and Scott, GR and Sokolova, I and Treberg, JR and Salin, K}, title = {The Mitochondrial Contribution to Animal Performance, Adaptation, and Life-History Variation.}, journal = {Integrative and comparative biology}, volume = {58}, number = {3}, pages = {480-485}, pmid = {30239783}, issn = {1557-7023}, support = {P30 DK079626/DK/NIDDK NIH HHS/United States ; }, mesh = {*Acclimatization ; Animals ; *Energy Metabolism ; *Life History Traits ; Mitochondria/*physiology ; }, abstract = {Animals display tremendous variation in their rates of growth, reproductive output, and longevity. While the physiological and molecular mechanisms that underlie this variation remain poorly understood, the performance of the mitochondrion has emerged as a key player. Mitochondria not only impact the performance of eukaryotes via their capacity to produce ATP, but they also play a role in producing heat and reactive oxygen species and function as a major signaling hub for the cell. The papers included in this special issue emerged from a symposium titled "Inside the Black Box: The Mitochondrial Basis of Life-history Variation and Animal Performance." Based on studies of diverse animal taxa, three distinct themes emerged from these papers. (1) When linking mitochondrial function to components of fitness, it is crucial that mitochondrial assays are performed in conditions as close as the intracellular conditions experienced by the mitochondria in vivo. (2) Functional plasticity allows mitochondria to retain their performance, as well as that of their host, over a range of exogenous conditions, and selection on mitochondrial and nuclear-derived proteins can optimize the match between the environment and the bioenergetic capacity of the mitochondrion. Finally, (3) studies of wild and wild-derived animals suggest that mitochondria play a central role in animal performance and life history strategy. Taken as a whole, we hope that these papers will foster discussion and inspire new hypotheses and innovations that will further our understanding of the mitochondrial processes that underlie variation in life history traits and animal performance.}, }
@article {pmid30230928, year = {2018}, author = {Isaac, RS and McShane, E and Churchman, LS}, title = {The Multiple Levels of Mitonuclear Coregulation.}, journal = {Annual review of genetics}, volume = {52}, number = {}, pages = {511-533}, doi = {10.1146/annurev-genet-120417-031709}, pmid = {30230928}, issn = {1545-2948}, support = {R01 GM123002/GM/NIGMS NIH HHS/United States ; F32 GM130028/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; Cell Nucleus/genetics ; Genome/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/chemistry/genetics ; Mitochondrial Membranes/chemistry/metabolism ; *Oxidative Phosphorylation ; Protein Biosynthesis ; RNA Processing, Post-Transcriptional/genetics ; Transcription, Genetic ; }, abstract = {Together, the nuclear and mitochondrial genomes encode the oxidative phosphorylation (OXPHOS) complexes that reside in the mitochondrial inner membrane and enable aerobic life. Mitochondria maintain their own genome that is expressed and regulated by factors distinct from their nuclear counterparts. For optimal function, the cell must ensure proper stoichiometric production of OXPHOS subunits by coordinating two physically separated and evolutionarily distinct gene expression systems. Here, we review our current understanding of mitonuclear coregulation primarily at the levels of transcription and translation. Additionally, we discuss other levels of coregulation that may exist but remain largely unexplored, including mRNA modification and stability and posttranslational protein degradation.}, }
@article {pmid30230466, year = {2018}, author = {Cordier-Bussat, M and Thibert, C and Sujobert, P and Genestier, L and Fontaine, &#xc9; and Billaud, M}, title = {[Even the Warburg effect can be oxidized: metabolic cooperation and tumor development].}, journal = {Medecine sciences : M/S}, volume = {34}, number = {8-9}, pages = {701-708}, doi = {10.1051/medsci/20183408017}, pmid = {30230466}, issn = {1958-5381}, mesh = {Cell Transformation, Neoplastic/metabolism/pathology ; Energy Metabolism/*physiology ; Glycolysis/*physiology ; Humans ; Mitochondria/metabolism ; Neoplasms/*metabolism/*pathology ; Oxidation-Reduction ; Tumor Microenvironment/*physiology ; }, abstract = {During tumor development, malignant cells rewire their metabolism to meet the biosynthetic needs required to increase their biomass and to overcome their microenvironment constraints. The sustained activation of aerobic glycolysis, also called Warburg effect, is one of these adaptative mechanisms. The progresses in this area of research have revealed the flexibility of cancer cells that alternate between glycolytic and oxidative metabolism to cope with their conditions of development while sharing their energetic resources. In this survey, we review these recent breakthroughs and discuss a model that likens tumor to an evolutive metabolic ecosystem. We further emphasize the ensuing therapeutic applications that target metabolic weaknesses of neoplastic cells.}, }
@article {pmid30213880, year = {2018}, author = {Ramrath, DJF and Niemann, M and Leibundgut, M and Bieri, P and Prange, C and Horn, EK and Leitner, A and Boehringer, D and Schneider, A and Ban, N}, title = {Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes.}, journal = {Science (New York, N.Y.)}, volume = {362}, number = {6413}, pages = {}, doi = {10.1126/science.aau7735}, pmid = {30213880}, issn = {1095-9203}, mesh = {*Evolution, Molecular ; Mitochondrial Ribosomes/*chemistry/ultrastructure ; Models, Molecular ; Protozoan Proteins/*chemistry/ultrastructure ; RNA, Ribosomal/chemistry/ultrastructure ; Ribosomal Proteins/*chemistry/ultrastructure ; Trypanosoma brucei brucei/*ultrastructure ; }, abstract = {Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of Trypanosoma brucei, a unicellular parasite that causes sleeping sickness in humans. The trypanosomal mitoribosome features the smallest rRNAs and contains more proteins than all known ribosomes. The structure shows how the proteins have taken over the role of architectural scaffold from the rRNA: They form an autonomous outer shell that surrounds the entire particle and stabilizes and positions the functionally important regions of the rRNA. Our results also reveal the "minimal" set of conserved rRNA and protein components shared by all ribosomes that help us define the most essential functional elements.}, }
@article {pmid30211573, year = {2018}, author = {Geary, DC}, title = {Efficiency of mitochondrial functioning as the fundamental biological mechanism of general intelligence (g).}, journal = {Psychological review}, volume = {125}, number = {6}, pages = {1028-1050}, doi = {10.1037/rev0000124}, pmid = {30211573}, issn = {1939-1471}, mesh = {Aging/*physiology ; *Biological Evolution ; *Health Status ; Humans ; Intelligence/genetics/*physiology ; Mitochondria/*physiology ; }, abstract = {General intelligence or g is one of the most thoroughly studied concepts in the behavioral sciences. Measures of intelligence are predictive of a wide range of educational, occupational, and life outcomes, including creative productivity and are systematically related to physical health and successful aging. The nexus of relations suggests 1 or several fundamental biological mechanisms underlie g, health, and aging, among other outcomes. Cell-damaging oxidative stress has been proposed as 1 of many potential mechanisms, but the proposal is underdeveloped and does not capture other important mitochondrial functions. I flesh out this proposal and argue that the overall efficiency of mitochondrial functioning is a core component of g; the most fundamental biological mechanism common to all brain and cognitive processes and that contributes to the relations among intelligence, health, and aging. The proposal integrates research on intelligence with models of the centrality of mitochondria to brain development and functioning, neurological diseases, and health more generally. Moreover, the combination of the maternal inheritance of mitochondrial DNA (mtDNA), the evolution of compensatory nuclear DNA, and the inability of evolutionary processes to purge deleterious mtDNA in males may contribute to the sex difference in variability in intelligence and in other cognitive domains. The proposal unifies many now disparate literatures and generates testable predictions for future studies. (PsycINFO Database Record (c) 2018 APA, all rights reserved).}, }
@article {pmid30209549, year = {2018}, author = {Sandor, S and Zhang, Y and Xu, J}, title = {Fungal mitochondrial genomes and genetic polymorphisms.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {22}, pages = {9433-9448}, doi = {10.1007/s00253-018-9350-5}, pmid = {30209549}, issn = {1432-0614}, support = {531998//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; *Genome, Fungal ; *Genome, Mitochondrial ; Introns ; Mitochondria/*genetics ; Phylogeny ; *Polymorphism, Genetic ; }, abstract = {Mitochondria are the powerhouses of eukaryotic cells, responsible for ATP generation and playing a role in a diversity of cellular and organismal functions. Different from the majority of other intracellular membrane structures, mitochondria contain their own genetic materials that are capable of independent replication and inheritance. In this mini-review, we provide brief summaries of fungal mitochondrial genome structure, size, gene content, inheritance, and genetic variation. We pay special attention to the relative genetic polymorphisms of the mitochondrial vs nuclear genomes at the population level within individual fungal species. Among the 20 species/groups of species reviewed here, there is a range of variation among genes and species in the relative nuclear and mitochondrial genetic polymorphisms. Interestingly, most (15/20) showed a greater genetic diversity for nuclear genes and genomes than for mitochondrial genes and genomes, with the remaining five showing similar or slower nuclear genome genetic variations. This fungal pattern is different from the dominant pattern in animals, but more similar to that in plants. At present, the mechanisms for the variations among fungal species and the overall low level of mitochondrial sequence polymorphisms are not known. The increasing availability of population genomic data should help us reveal the potential genetic and ecological factors responsible for the observed variations.}, }
@article {pmid30208839, year = {2018}, author = {Bono, JM and Pigage, HK and Wettstein, PJ and Prosser, SA and Pigage, JC}, title = {Genome-wide markers reveal a complex evolutionary history involving divergence and introgression in the Abert's squirrel (Sciurus aberti) species group.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {139}, pmid = {30208839}, issn = {1471-2148}, mesh = {Animals ; *Biological Evolution ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Genetic Markers ; *Genetic Variation ; *Genome ; Geography ; Haplotypes/genetics ; Likelihood Functions ; Mitochondria/genetics ; Phylogeography ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; Sciuridae/*genetics ; }, abstract = {BACKGROUND: Genetic introgression between divergent lineages is now considered more common than previously appreciated, with potentially important consequences for adaptation and speciation. Introgression is often asymmetric between populations and patterns can vary for different types of loci (nuclear vs. organellar), complicating phylogeographic reconstruction. The taxonomy of the ecologically specialized Abert's squirrel species group has been controversial, and previous studies based on mitochondrial data have not fully resolved the evolutionary relationships among populations. Moreover, while these studies identified potential areas of secondary contact between divergent lineages, the possibility for introgression has not been tested.<br><br>RESULTS: We used RAD-seq to unravel the complex evolutionary history of the Abert's squirrel species group. Although some of our findings reinforce inferences based on mitochondrial data, we also find significant areas of discordance. Discordant signals generally arise from previously undetected introgression between divergent populations that differentially affected variation at mitochondrial and nuclear loci. Most notably, our results support earlier claims (disputed by mitochondrial data) that S. aberti kaibabensis, found only on the north rim of the Grand Canyon, is highly divergent from other populations. However, we also detected introgression of S. aberti kaibabensis DNA into other S. aberti populations, which likely accounts for the previously inferred close genetic relationship between this population and those south of the Grand Canyon.<br><br>CONCLUSIONS: Overall, the evolutionary history of Abert's squirrels appears to be shaped largely by divergence during periods of habitat isolation. However, we also found evidence for interbreeding during periods of secondary contact resulting in introgression, with variable effects on mitochondrial and nuclear markers. Our results support the emerging view that populations often diversify under scenarios involving both divergence in isolation and gene flow during secondary contact, and highlight the value of genome-wide datasets for resolving such complex evolutionary histories.}, }
@article {pmid30208106, year = {2018}, author = {Viret, A and Tsaparis, D and Tsigenopoulos, CS and Berrebi, P and Sabatini, A and Arculeo, M and Fassatoui, C and Magoulas, A and Marengo, M and Morales-Nin, B and Caill-Milly, N and Durieux, EDH}, title = {Absence of spatial genetic structure in common dentex (Dentex dentex Linnaeus, 1758) in the Mediterranean Sea as evidenced by nuclear and mitochondrial molecular markers.}, journal = {PloS one}, volume = {13}, number = {9}, pages = {e0203866}, pmid = {30208106}, issn = {1932-6203}, mesh = {Alleles ; Animals ; Atlantic Ocean ; Bayes Theorem ; Cell Nucleus/*genetics ; DNA, Mitochondrial/analysis/genetics ; Gene Flow ; Gene Frequency/genetics ; Genetic Variation ; Genetics, Population/methods ; Mediterranean Sea ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; }, abstract = {The common dentex, Dentex dentex, is a fish species which inhabits marine environments in the Mediterranean and Northeast Atlantic regions. This is an important species from an ecological, economic and conservation perspective, however critical information on its population genetic structure is lacking. Most samples were obtained from the Mediterranean Sea (17 sites) with an emphasis around Corsica (5 sites), plus one Atlantic Ocean site. This provided an opportunity to examine genetic structuring at local and broader scales to provide science based data for the management of fishing stocks in the region. Two mitochondrial regions were examined (D-loop and COI) along with eight microsatellite loci. The COI data was combined with publicly available sequences and demonstrated past misidentification of common dentex. All markers indicated the absence of population genetic structure from the Bay of Biscay to the eastern Mediterranean Sea. Bayesian approaches, as well as the statistical tests performed on the allelic frequencies from microsatellite loci, indicated low differentiation between samples; there was only a slight (p = 0.05) indication of isolation by distance. Common dentex is a marine fish species with a unique panmictic population in the Mediterranean and likely in the Atlantic Ocean as well.}, }
@article {pmid30206380, year = {2018}, author = {Jebb, D and Foley, NM and Whelan, CV and Touzalin, F and Puechmaille, SJ and Teeling, EC}, title = {Population level mitogenomics of long-lived bats reveals dynamic heteroplasmy and challenges the Free Radical Theory of Ageing.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {13634}, pmid = {30206380}, issn = {2045-2322}, support = {ERC-2012-StG311000//EC | European Research Council (ERC)/International ; }, mesh = {Aging/*genetics/metabolism ; Animals ; Chiroptera/blood/*genetics ; DNA, Mitochondrial/*genetics ; Free Radicals ; High-Throughput Nucleotide Sequencing ; *Mutation ; }, abstract = {Bats are the only mammals capable of true, powered flight, which drives an extremely high metabolic rate. The "Free Radical Theory of Ageing" (FTRA) posits that a high metabolic rate causes mitochondrial heteroplasmy and the progressive ageing phenotype. Contrary to this, bats are the longest-lived order of mammals given their small size and high metabolic rate. To investigate if bats exhibit increased mitochondrial heteroplasmy with age, we performed targeted, deep sequencing of mitogenomes and measured point heteroplasmy in wild, long lived Myotis myotis. Blood was sampled from 195 individuals, aged between <1 and at 6+ years old, and whole mitochondria deep-sequenced, with a subset sampled over multiple years. The majority of heteroplasmies were at a low frequency and were transitions. Oxidative mutations were present in only a small number of individuals, suggesting local oxidative stress events. Cohort data showed no significant increase in heteroplasmy with age, while longitudinal data from recaptured individuals showed heteroplasmy is dynamic, and does not increase uniformly over time. We show that bats do not suffer from the predicted, inevitable increase in heteroplasmy as posited by the FRTA, instead heteroplasmy was found to be dynamic, questioning its presumed role as a primary driver of ageing.}, }
@article {pmid30204084, year = {2018}, author = {Seidi, A and Muellner-Wong, LS and Rajendran, E and Tjhin, ET and Dagley, LF and Aw, VY and Faou, P and Webb, AI and Tonkin, CJ and van Dooren, GG}, title = {Elucidating the mitochondrial proteome of Toxoplasma gondii reveals the presence of a divergent cytochrome c oxidase.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {30204084}, issn = {2050-084X}, support = {DP110103144//Australian Research Council/International ; }, mesh = {Animals ; Biotinylation ; Computational Biology ; Electron Transport Complex IV/*metabolism ; Gene Knockdown Techniques ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/metabolism ; Oxygen Consumption ; Parasites/growth &amp; development/metabolism ; Phenotype ; Phylogeny ; Proteome/*metabolism ; Proteomics ; Protozoan Proteins/metabolism ; Toxoplasma/growth &amp; development/*metabolism ; }, abstract = {The mitochondrion of apicomplexan parasites is critical for parasite survival, although the full complement of proteins that localize to this organelle has not been defined. Here we undertake two independent approaches to elucidate the mitochondrial proteome of the apicomplexan Toxoplasma gondii. We identify approximately 400 mitochondrial proteins, many of which lack homologs in the animals that these parasites infect, and most of which are important for parasite growth. We demonstrate that one such protein, termed TgApiCox25, is an important component of the parasite cytochrome c oxidase (COX) complex. We identify numerous other apicomplexan-specific components of COX, and conclude that apicomplexan COX, and apicomplexan mitochondria more generally, differ substantially in their protein composition from the hosts they infect. Our study highlights the diversity that exists in mitochondrial proteomes across the eukaryotic domain of life, and provides a foundation for defining unique aspects of mitochondrial biology in an important phylum of parasites.}, }
@article {pmid30201278, year = {2018}, author = {Santos, HJ and Makiuchi, T and Nozaki, T}, title = {Reinventing an Organelle: The Reduced Mitochondrion in Parasitic Protists.}, journal = {Trends in parasitology}, volume = {34}, number = {12}, pages = {1038-1055}, doi = {10.1016/j.pt.2018.08.008}, pmid = {30201278}, issn = {1471-5007}, mesh = {Animals ; Biodiversity ; Biological Evolution ; Eukaryota/classification/cytology/*physiology ; Mitochondria/*physiology ; Parasites/classification/cytology/*physiology ; }, abstract = {Mitochondria originated from the endosymbiotic event commencing from the engulfment of an ancestral α-proteobacterium by the first eukaryotic ancestor. Establishment of niches has led to various adaptations among eukaryotes. In anaerobic parasitic protists, the mitochondria have undergone modifications by combining features shared from the aerobic mitochondria with lineage-specific components and mechanisms; a diversified class of organelles emerged and are generally called mitochondrion-related organelles (MROs). In this review we summarize and discuss the recent advances in the knowledge of MROs from parasitic protists, particularly the themes such as metabolic functions, contribution to parasitism, dynamics, protein targeting, and novel lineage- specific proteins, with emphasis on the diversity among these organelles.}, }
@article {pmid30196672, year = {2018}, author = {Eom, KS and Park, H and Lee, D and Choe, S and Kang, Y and Bia, MM and Lee, SH and Keyyu, J and Fyumagwa, R and Jeon, HK}, title = {Molecular and Morphologic Identification of Spirometra ranarum Found in the Stool of African Lion, Panthera leo in the Serengeti Plain of Tanzania.}, journal = {The Korean journal of parasitology}, volume = {56}, number = {4}, pages = {379-383}, pmid = {30196672}, issn = {1738-0006}, support = {2017R1D1A3B03035976//National Research Foundation of Korea/ ; PRB000720//Parasite Resource Bank of Korea/ ; }, mesh = {Animals ; Cyclooxygenase 1/genetics ; Feces/*parasitology ; Host-Parasite Interactions ; Lions/*parasitology ; Male ; Mitochondria/genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; Spirometra/anatomy &amp; histology/*genetics/*isolation &amp; purification ; Tanzania ; }, abstract = {The present study was performed with morphological and molecular analysis (cox1 and nad1 mitochondrial genes) to identify the proglottids of spirometrid tapeworm found in the stool of an African lion, Panthera leo, in the Serengeti plain of Tanzania. A strand of tapeworm strobila, about 75 cm in length, was obtained in the stool of a male African lion in the Serengeti National Park (34˚ 50' E, 02˚ 30' S), Tanzania, in February 2012. The morphological features of the adult worm examined exhibited 3 uterine coils with a bow tie appearance and adopted a diagonal direction in the second turn. The posterior uterine coils are larger than terminal uterine ball and the feature of uteri are swirling rather than spirally coiling. The sequence difference between the Spirometra species (Tanzania origin) and S. erinaceieuropaei (GenBank no. KJ599680) was 9.4% while those of S. decipiens (GenBank no. KJ599679) differed by 2.1% in the cox1 and nad1 genes. Phylogenetic tree topologies generated using the 2 analytic methods were identical and presented high level of confidence values for the 3 major branches of the 3 Spirometra species in the cox1 gene. The morphological and molecular findings obtained in this study were nearly coincided with those of S. ranarum. Therefore, we can know for the first time that the African lion, Panthera leo, is to the definitive host of this tapeworm.}, }
@article {pmid30195322, year = {2018}, author = {Verechshagina, NA and Konstantinov, YM and Kamenski, PA and Mazunin, IO}, title = {Import of Proteins and Nucleic Acids into Mitochondria.}, journal = {Biochemistry. Biokhimiia}, volume = {83}, number = {6}, pages = {643-661}, doi = {10.1134/S0006297918060032}, pmid = {30195322}, issn = {1608-3040}, mesh = {Biopolymers/metabolism ; Eukaryota/genetics/*metabolism ; Mitochondria/*genetics ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Nucleic Acids/*metabolism ; RNA, Transfer/metabolism ; }, abstract = {Many mitochondrial genes have been transferred to the nucleus in course of evolution. The products of expression of these genes, being still necessary for organelle function, are imported there from the cytosol. Molecular mechanisms of protein import are studied much deeper than those of nucleic acids. The latter, it seems to us, retards the development of mitochondrial genome editing technologies. In this review, we describe mechanisms of DNA, RNA, and protein import into mitochondria of different eukaryotes. The description is given for the natural processes, as well as for artificial targeting of macromolecules into mitochondria for therapy. Also, we discuss different approaches to introduce changes into the mitochondrial DNA sequence.}, }
@article {pmid30194707, year = {2018}, author = {Grandi, G and Astolfi, G and Chicca, M and Pezzi, M}, title = {Ultrastructural investigations on spermatogenesis and spermatozoan morphology in the endangered Adriatic sturgeon, Acipenser naccarii (Chondrostei, Acipenseriformes).}, journal = {Journal of morphology}, volume = {279}, number = {10}, pages = {1376-1396}, doi = {10.1002/jmor.20847}, pmid = {30194707}, issn = {1097-4687}, support = {16-01-14404//Italian Ministry of University and Research (MIUR)/International ; }, mesh = {Acrosome/ultrastructure ; Animals ; *Endangered Species ; Fishes/*anatomy &amp; histology ; Male ; Phylogeny ; Principal Component Analysis ; Spermatids/cytology/ultrastructure ; *Spermatogenesis ; Spermatogonia/ultrastructure ; Spermatozoa/cytology/*ultrastructure ; Testis/ultrastructure ; }, abstract = {Spermatogenesis was investigated in the Adriatic sturgeon, Acipenser naccarii, by light and electron microscopy. The testis of the unrestricted type had a germinal compartment composed of lobules containing germ cells and Sertoli cells, and separated by a basal lamina from the interstitial compartment, in which Leydig and myoid cells were detected for the first time in Acipenseridae. Spermatogenesis occurred in spermatocysts produced when Sertoli cells became associated with type A spermatogonia of subsequent generations, which produced a clone of synchronized aligned spermatogonia. In primary spermatocytes at zygo-pachytene stage, the large spherical nucleus contained synaptonemal complexes. The smaller secondary spermatocytes were ovoid with a central round nucleus and scarce cytoplasm. Spermatids were interconnected by cytoplasmic bridges until early spermiogenesis. Chromatin initially condensed as long, twisted, and nonhomogeneous fibers and finally as a compact structure made of thick filaments. Early spermatids showed the flagellum, the primordia of centriole complex and of "implantation fossa," followed by the acrosomal vesicle formed by Golgi complexes and a fibrous body associated to centriole complex. The spermatozoan head had 10 postero-lateral projections and a trapezoidal nucleus, a cylindrical midpiece with six to eight mitochondria, the centriole complex, and a "9 + 2" flagellum with a pair of lateral fins. Three helical endonuclear canals crossed the nucleus from the acrosome base to the implantation fossa; their spiralization and that of chromatin fibers suggest a spiral twisting of the nucleus during spermiogenesis. The Sertoli cells performed phagocytosis of degenerating spermatids and spermatozoa. Significant interindividual differences were detected in most morphological parameters of spermatozoa. Data on spermatogenesis in A. naccarii and morphometric measurements on mature spermatozoa provide information about the reproductive biology of the species useful not only for phylogenetic studies but also for evaluation of sperm quality for artificial reproduction projects and restocking of this and other critically endangered sturgeon species.}, }
@article {pmid30190598, year = {2018}, author = {Hillen, HS and Temiakov, D and Cramer, P}, title = {Structural basis of mitochondrial transcription.}, journal = {Nature structural &amp; molecular biology}, volume = {25}, number = {9}, pages = {754-765}, pmid = {30190598}, issn = {1545-9985}, support = {R01 GM104231/GM/NIGMS NIH HHS/United States ; R01 GM118941/GM/NIGMS NIH HHS/United States ; }, mesh = {Evolution, Molecular ; Humans ; Mitochondria/enzymology/*metabolism ; Mitochondrial Proteins/*chemistry/*genetics ; Protein Conformation ; Terminator Regions, Genetic ; *Transcription, Genetic ; Transcriptional Elongation Factors/metabolism ; }, abstract = {The mitochondrial genome is transcribed by a single-subunit DNA-dependent RNA polymerase (mtRNAP) and its auxiliary factors. Structural studies have elucidated how mtRNAP cooperates with its dedicated transcription factors to direct RNA synthesis: initiation factors TFAM and TFB2M assist in promoter-DNA binding and opening by mtRNAP while the elongation factor TEFM increases polymerase processivity to the levels required for synthesis of long polycistronic mtRNA transcripts. Here, we review the emerging body of structural and functional studies of human mitochondrial transcription, provide a molecular movie that can be used for teaching purposes and discuss the open questions to guide future directions of investigation.}, }
@article {pmid30187255, year = {2018}, author = {Eyenga, P and Roussel, D and Morel, J and Rey, B and Romestaing, C and Gueguen-Chaignon, V and Sheu, SS and Viale, JP}, title = {Time course of liver mitochondrial function and intrinsic changes in oxidative phosphorylation in a rat model of sepsis.}, journal = {Intensive care medicine experimental}, volume = {6}, number = {1}, pages = {31}, pmid = {30187255}, issn = {2197-425X}, abstract = {BACKGROUND: Tissue ATP depletion and oxidative stress have been associated with the severe outcomes of septic shock. One of the compensatory mechanisms to alleviate the sepsis-induced mitochondrial dysfunction could be the increase in oxidative phosphorylation efficiency (ATP/O). We propose to study liver mitochondrial function and oxidative stress and the regulatory mechanism of mitochondrial oxidative phosphorylation efficiency in an animal model of sepsis.<br><br>METHODS: We induced sepsis in rats by cecal ligation and perforation (CLP). Six, 24, or 36&#xa0;h following CLP, we measured liver mitochondrial respiration, cytochrome c oxidase activity, and membrane permeability. We determine oxidative phosphorylation efficiency, by measuring ATP synthesis related to oxygen consumption at various exogenous ADP concentrations. Finally, we measured radical oxygen species (ROS) generation by liver mitochondria and mRNA concentrations of UCP2, biogenesis factors, and cytokines at the same end points.<br><br>RESULTS: CLP rats presented hypotension, lactic acidosis, liver cytolysis, and upregulation of proinflammatory cytokines mRNA as compared to controls. Liver mitochondria showed a decrease in ATP synthesis and oxygen consumption at 24&#xa0;h following CLP. A marked uncoupling of oxidative phosphorylation appeared 36&#xa0;h following CLP and was associated with a decrease in cytochrome c oxidase activity and content and ATP synthase subunit &#x3b2; content (slip mechanism) and an increase in mitochondrial oligomycin-insensitive respiration, but no change in mitochondrial inner membrane permeability (no leak). Upregulation of UCP2 mRNA resulted in a decrease in mitochondrial ROS generation 24&#xa0;h after the onset of CLP, whereas ROS over-generation associated with slip at cytochrome c oxidase observed at 36&#xa0;h was concomitant with a decrease in UCP2 mRNA expression.<br><br>CONCLUSIONS: Despite a compensatory increase in mitochondrial biogenesis factors, liver mitochondrial functions remain altered after CLP. This suggests that the functional compensatory mechanisms reported in the present study (slip at cytochrome c oxidase and biogenesis factors) were not strong enough to increase oxidative phosphorylation efficiency and failed to limit liver mitochondrial ROS over-generation. These data suggest that treatments based on cytochrome c infusion could have a role in mitochondrial dysfunction and/or ROS generation associated with sepsis.}, }
@article {pmid30185526, year = {2018}, author = {Abbasi, F and Miyata, H and Shimada, K and Morohoshi, A and Nozawa, K and Matsumura, T and Xu, Z and Pratiwi, P and Ikawa, M}, title = {RSPH6A is required for sperm flagellum formation and male fertility in mice.}, journal = {Journal of cell science}, volume = {131}, number = {19}, pages = {}, pmid = {30185526}, issn = {1477-9137}, support = {P01 HD087157/HD/NICHD NIH HHS/United States ; R01 HD088412/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; CRISPR-Cas Systems/genetics ; Conserved Sequence ; Evolution, Molecular ; *Fertility ; Flagella/*metabolism/ultrastructure ; HEK293 Cells ; Humans ; Male ; Mice ; Mice, Mutant Strains ; Mitochondria/metabolism ; Organ Specificity ; Phenotype ; Protein Binding ; Protein Transport ; Proteins/*metabolism ; Sperm Injections, Intracytoplasmic ; Sperm Tail/metabolism ; Spermatozoa/*metabolism/ultrastructure ; Testis/metabolism ; Tubulin/metabolism ; }, abstract = {The flagellum is an evolutionarily conserved appendage used for sensing and locomotion. Its backbone is the axoneme and a component of the axoneme is the radial spoke (RS), a protein complex implicated in flagellar motility regulation. Numerous diseases occur if the axoneme is improperly formed, such as primary ciliary dyskinesia (PCD) and infertility. Radial spoke head 6 homolog A (RSPH6A) is an ortholog of Chlamydomonas RSP6 in the RS head and is evolutionarily conserved. While some RS head proteins have been linked to PCD, little is known about RSPH6A. Here, we show that mouse RSPH6A is testis-enriched and localized in the flagellum. Rsph6a knockout (KO) male mice are infertile as a result of their short immotile spermatozoa. Observation of the KO testis indicates that the axoneme can elongate but is disrupted before accessory structures are formed. Manchette removal is also impaired in the KO testis. Further, RSPH9, another radial spoke protein, disappeared in the Rsph6a KO flagella. These data indicate that RSPH6A is essential for sperm flagellar assembly and male fertility in mice.This article has an associated First Person interview with the first author of the paper.}, }
@article {pmid30181603, year = {2018}, author = {Bisconti, R and Porretta, D and Arduino, P and Nascetti, G and Canestrelli, D}, title = {Hybridization and extensive mitochondrial introgression among fire salamanders in peninsular Italy.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {13187}, pmid = {30181603}, issn = {2045-2322}, mesh = {Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Female ; Gene Flow ; Gene Frequency ; Genetics, Population ; Genomic Imprinting ; *Hybridization, Genetic ; Italy ; Male ; Mitochondria/*genetics ; Phylogeny ; Salamandra/*genetics ; }, abstract = {Discordance between mitochondrial and nuclear patterns of population genetic structure is providing key insights into the eco-evolutionary dynamics between and within species, and their assessment is highly relevant to biodiversity monitoring practices based on DNA barcoding approaches. Here, we investigate the population genetic structure of the fire salamander Salamandra salamandra in peninsular Italy. Both mitochondrial and nuclear markers clearly identified two main population groups. However, nuclear and mitochondrial zones of geographic transition between groups were located 600 km from one another. Recent population declines in central Italy partially erased the genetic imprints of past hybridization dynamics. However, the overall pattern of genetic variation, together with morphological and fossil data, suggest that a rampant mitochondrial introgression triggered the observed mitonuclear discordance, following a post-glacial secondary contact between lineages. Our results clearly show the major role played by reticulate evolution in shaping the structure of Salamandra salamandra populations and, together with similar findings in other regions of the species' range, contribute to identify the fire salamander as a particularly intriguing case to investigate the complexity of mechanisms triggering patterns of mitonuclear discordance in animals.}, }
@article {pmid30179526, year = {2018}, author = {Haenel, GJ and Del Gaizo Moore, V}, title = {Functional Divergence of Mitochondria and Coevolution of Genomes: Cool Mitochondria in Hot Lizards.}, journal = {Physiological and biochemical zoology : PBZ}, volume = {91}, number = {5}, pages = {1068-1081}, doi = {10.1086/699918}, pmid = {30179526}, issn = {1537-5293}, mesh = {Animals ; *Biological Coevolution ; Body Temperature ; Genome ; Hot Temperature ; Lizards/*genetics/*physiology ; Mitochondria/genetics/*physiology ; }, abstract = {Mitochondria play a key role in the ecology and evolution of species through their influence on aerobic metabolism. Mitochondrial DNA (mtDNA) and nuclear genomes must interact for optimal functioning of oxidative phosphorylation to produce ATP, and breakdown of coadaptation components from each may have important evolutionary consequences for hybridization. Introgression of mitochondria in natural populations through hybridization with unidirectional backcrossing allows the testing of coadaptation of mitochondria to different nuclear backgrounds. We compared the function of mitochondria isolated from two species of Urosaurus lizards and hybrid populations. Due to past introgression, hybrids contain the nuclear genome of the "hot-adapted" species (U. graciosus) but the mtDNA of the less heat-tolerant species (U. ornatus). It was found that the function of the parental forms of mitochondria had significantly diverged with the hot-adapted species. There was significant genotype × genotype × environment interactions for mitochondrial membrane potential and genotype × genotype interactions for ATP production. Membrane potential decreased less at a higher temperature, while ATP production was higher at both temperatures in introgressed mitochondria. Oxygen consumption was lower in U. graciosus than in U. ornatus parental-type mitochondria, indicating a likely response to living in hotter environments. Respiratory control ratio values, which provide an indication of the functional quality of isolated mitochondria, were lower in introgressed mitochondria than in parental U. ornatus types, indicating a negative impact on biological function in introgressed mitochondria.}, }
@article {pmid30176805, year = {2018}, author = {Matthee, CA and Engelbrecht, A and Matthee, S}, title = {Comparative phylogeography of parasitic Laelaps mites contribute new insights into the specialist-generalist variation hypothesis (SGVH).}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {131}, pmid = {30176805}, issn = {1471-2148}, support = {Incentive Funding//National Research Foundation/International ; }, mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Genetic Variation ; Geography ; Haplotypes/genetics ; Host Specificity ; Mites/*classification/genetics ; Mitochondria/genetics ; *Models, Biological ; Murinae/genetics/parasitology ; Parasites/*classification/genetics ; *Phylogeography ; }, abstract = {BACKGROUND: The specialist-generalist variation hypothesis (SGVH) in parasites suggests that, due to patchiness in habitat (host availability), specialist species will show more subdivided population structure when compared to generalist species. In addition, since specialist species are more prone to local stochastic extinction events with their hosts, they will show lower levels of intraspecific genetic diversity when compared to more generalist.<br><br>RESULTS: To test the wider applicability of the SGVH we compared 337 cytochrome oxidase I mitochondrial DNA and 268 nuclear tropomyosin DNA sequenced fragments derived from two co-distributed Laelaps mite species and compared the data to 294 COI mtDNA sequences derived from the respective hosts Rhabdomys dilectus, R. bechuanae, Mastomys coucha and M. natalensis. In support of the SGVH, the generalist L. muricola was characterized by a high mtDNA haplotypic diversity of 0.97 (&#xb1;0.00) and a low level of population differentiation (mtDNA Fst&#x2009;=&#x2009;0.56, p&#x2009;<&#x2009;0.05; nuDNA Fst&#x2009;=&#x2009;0.33, P&#x2009;<&#x2009;0.05) while the specialist L. giganteus was overall characterized by a lower haplotypic diversity of 0.77 (&#xb1;0.03) and comparatively higher levels of population differentiation (mtDNA Fst&#x2009;=&#x2009;0.87, P&#x2009;<&#x2009;0.05; nuDNA Fst&#x2009;=&#x2009;0.48, P&#x2009;<&#x2009;0.05). When the two specialist L. giganteus lineages, which occur on two different Rhabdomys species, are respectively compared to the generalist parasite, L. muricola, the SGVH is not fully supported. One of the specialist L. giganteus species occurring on R. dilectus shows similar low levels of population differentiation (mtDNA Fst&#x2009;=&#x2009;0.53, P&#x2009;<&#x2009;0.05; nuDNA Fst&#x2009;=&#x2009;0.12, P&#x2009;<&#x2009;0.05) than that found for the generalist L. muricola. This finding can be correlated to differences in host dispersal: R. bechuanae populations are characterized by a differentiated mtDNA Fst of 0.79 (P&#x2009;<&#x2009;0.05) while R. dilectus populations are less structured with a mtDNA Fst&#x2009;=&#x2009;0.18 (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: These findings suggest that in ectoparasites, host specificity and the vagility of the host are both important drivers for parasite dispersal. It is proposed that the SGHV hypothesis should also incorporate reference to host dispersal since in our case only the specialist species who occur on less mobile hosts showed more subdivided population structure when compared to generalist species.}, }
@article {pmid30176793, year = {2018}, author = {Yin, M and Wang, X and Ma, X and Gießler, S and Petrusek, A and Griebel, J and Hu, W and Wolinska, J}, title = {Cytonuclear diversity and shared mitochondrial haplotypes among Daphnia galeata populations separated by seven thousand kilometres.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {130}, pmid = {30176793}, issn = {1471-2148}, support = {31670380//National Natural Science Foundation of China/International ; 16ZR1402900//Natural Science Foundation of Shanghai/International ; WO 1587/6-1//German Science Foundation/International ; }, mesh = {Alleles ; Animals ; Bayes Theorem ; Cell Nucleus/*genetics ; China ; DNA/genetics ; DNA, Mitochondrial/genetics ; Daphnia/*genetics ; Europe ; Genes, Mitochondrial ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/*genetics ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Phylogeny ; Zooplankton/genetics ; }, abstract = {BACKGROUND: The zooplanktonic cladocerans Daphnia, present in a wide range of water bodies, are an important component of freshwater ecosystems. In contrast to their high dispersal capacity through diapausing eggs carried by waterfowl, Daphnia often exhibit strong population genetic differentiation. Here, to test for common patterns in the population genetic structure of a widespread Holarctic species, D. galeata, we genotyped two sets of populations collected from geographically distant areas: across 13 lakes in Eastern China and 14 lakes in Central Europe. The majority of these populations were genotyped at two types of markers: a mitochondrial gene (for 12S rRNA) and 15 nuclear microsatellite loci.<br><br>RESULTS: Mitochondrial DNA demonstrated relatively shallow divergence within D. galeata, with distinct haplotype compositions in the two study regions but one widely distributed haplotype shared between several of the Chinese as well as European populations. At microsatellite markers, clear separation was observed at both large (between China and Europe) and small (within Europe) geographical scales, as demonstrated by Factorial Correspondence Analyses, Bayesian assignment and a clustering method based on genetic distances. Genetic diversity was comparable between the sets of Chinese and European D. galeata populations for both types of markers. Interestingly, we observed a significant association between genetic distance and geographical distance for D. galeata populations in China but not in Europe.<br><br>CONCLUSIONS: Our results indicate relatively recent spread of D. galeata across wide expanses of the Palaearctic, with one mtDNA lineage of D. galeata successfully establishing over large distances. Despite a clear differentiation of Chinese and European D. galeata at a nuclear level, the pattern of genetic variation is nevertheless similar between both regions. Overall, our findings provide insights into the genetic population structure of a cladoceran species with extremely wide geographical range.}, }
@article {pmid30176236, year = {2019}, author = {Virji, AZ and Thekkiniath, J and Ma, W and Lawres, L and Knight, J and Swei, A and Roch, KL and Mamoun, CB}, title = {Insights into the evolution and drug susceptibility of Babesia duncani from the sequence of its mitochondrial and apicoplast genomes.}, journal = {International journal for parasitology}, volume = {49}, number = {2}, pages = {105-113}, pmid = {30176236}, issn = {1879-0135}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 AI097218/AI/NIAID NIH HHS/United States ; S10 OD016290/OD/NIH HHS/United States ; S10 OD018521/OD/NIH HHS/United States ; R01 GM110506/GM/NIGMS NIH HHS/United States ; R01 AI123321/AI/NIAID NIH HHS/United States ; R43 AI136118/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Babesia/*drug effects/*genetics ; *Drug Resistance ; *Evolution, Molecular ; *Genome, Mitochondrial ; *Genome, Protozoan ; Humans ; Molecular Sequence Annotation ; United States ; Whole Genome Sequencing ; }, abstract = {Babesia microti and Babesia duncani are the main causative agents of human babesiosis in the United States. While significant knowledge about B. microti has been gained over the past few years, nothing is known about B. duncani biology, pathogenesis, mode of transmission or sensitivity to currently recommended therapies. Studies in immunocompetent wild type mice and hamsters have shown that unlike B. microti, infection with B. duncani results in severe pathology and ultimately death. The parasite factors involved in B. duncani virulence remain unknown. Here we report the first known completed sequence and annotation of the apicoplast and mitochondrial genomes of B. duncani. We found that the apicoplast genome of this parasite consists of a 34 kb monocistronic circular molecule encoding functions that are important for apicoplast gene transcription as well as translation and maturation of the organelle's proteins. The mitochondrial genome of B. duncani consists of a 5.9 kb monocistronic linear molecule with two inverted repeats of 48 bp at both ends. Using the conserved cytochrome b (Cytb) and cytochrome c oxidase subunit I (coxI) proteins encoded by the mitochondrial genome, phylogenetic analysis revealed that B. duncani defines a new lineage among apicomplexan parasites distinct from B. microti, Babesia bovis, Theileria spp. and Plasmodium spp. Annotation of the apicoplast and mitochondrial genomes of B. duncani identified targets for development of effective therapies. Our studies set the stage for evaluation of the efficacy of these drugs alone or in combination against B. duncani in culture as well as in animal models.}, }
@article {pmid30172009, year = {2018}, author = {Pavón-Vázquez, CJ and García-Vázquez, UO and Bryson, RW and Feria-Ortiz, M and Manríquez-Morán, NL and de Oca, AN}, title = {Integrative species delimitation in practice: Revealing cryptic lineages within the short-nosed skink Plestiodon brevirostris (Squamata: Scincidae).}, journal = {Molecular phylogenetics and evolution}, volume = {129}, number = {}, pages = {242-257}, doi = {10.1016/j.ympev.2018.08.020}, pmid = {30172009}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Genetic Loci ; Geography ; Lizards/*classification/genetics ; Mexico ; Mitochondria/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Species Specificity ; Time Factors ; }, abstract = {Integrative taxonomy has been generally considered as a goal in systematics for more than a decade. Here, we employed environmental, molecular, and morphological data to evaluate the species boundaries within the short-nosed skink Plestiodon brevirostris from south-central Mexico, one member of the morphologically conservative P. brevirostris group. Our molecular dataset includes one mitochondrial and two nuclear loci. The mitochondrial fragment includes the full length of the gene coding for the NADH dehydrogenase subunit 1 protein, a segment of the gene coding for 16S ribosomal RNA, and flanking tRNAs. The nuclear dataset includes fragments of the genes coding for the megakaryoblastic leukemia 1 and RNA fingerprint 35 proteins. We employed phylogenetic reconstruction, analyses of population structure and morphological variation, and species delimitation methods (including the integration of the three kinds of data in a unified probabilistic framework) to evaluate species limits. Our results suggest that P. brevirostris represents four distinct species. The information provided by each kind of data allowed us to discern between alternative explanations for the observed patterns of geographic structure. Two of the newly recognized lineages are poorly differentiated morphologically but apparently differ in environmental preferences and are allopatric. Additionally, one lineage is microendemic and parapatric with respect to another one. Moreover, our phylogenetic analyses suggest that other taxa within the P. brevirostris group may represent species complexes. We discuss our results in the context of integrative species delimitation.}, }
@article {pmid33474357, year = {2018}, author = {Li, J and Bi, C and Tu, J and Lu, Z}, title = {The complete mitochondrial genome sequence of Boechera stricta.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {3}, number = {2}, pages = {896-897}, pmid = {33474357}, issn = {2380-2359}, abstract = {Boechera stricta (B. stricta) is a wild relative of Arabidopsis, occurring in mostly montane regions of western North America. In this article, we assembled the complete mitochondrial (mt) DNA sequence of B. stricta into a circular genome of length 271,601 bp, including 31 protein-coding genes, 21 tRNA genes, and 3 rRNA genes. From the neighbour-joining phylogenetic tree was constructed, based on the 23 conserved protein-coding genes of B. stricta and other 23 plant species, and the phylogenic relationship and evolution position of B. stricta were determined. The complete mt genome would be useful for further investigation of the genotype-by-environment interactions in mitochondria of Boechera.}, }
@article {pmid31089666, year = {2018}, author = {Cazzolla Gatti, R}, title = {endogenosymbiosis: from hypothesis to empirical evidence towards a Unified Symbiogenetic Theory (UST).}, journal = {Theoretical biology forum}, volume = {111}, number = {1-2}, pages = {13-26}, doi = {10.19272/201811402002}, pmid = {31089666}, issn = {2282-2593}, mesh = {*Biological Evolution ; *Eukaryota ; Eukaryotic Cells ; Phylogeny ; Plastids ; *Symbiosis ; }, abstract = {In 1967 Lynn (Sagan) Margulis proposed that mitochondria, photosynthetic plastids and cilia were acquired prokaryotes and evolved symbiotically to form anaerobic bacteria, photosynthetic bacteria and eventually algae. Although most of this theory is well-accepted now, the hypothesis that endosymbiotic spirochaetes developed into eukaryotic flagella and cilia, and the following proposals of an endosymbiotic origin of other eukaryotic organelles such as peroxisomes, glyoxysomes, etc. have not received much acceptance, since evidence suggests they lack a genome and do not show ultrastructural similarities to bacteria or archaea. Nevertheless, the idea that over millennia mitochondria, plastids, prokaryotic and eukaryotic cells and even flagella and peroxisomes, as either primary or secondary endosymbionts, transferred some or all of their own DNA to the host cell’s nucleus through a process called «endogenosymbiosis» (i.e. a symbiotic gene transfer, such as the internalisation of the endosymbiont’s DNA with lateral transfer) has been recently suggested. This endogenosymbiosis could take place during the evolutionary transition from the symbiotic interacting community, invoked by Margulis, to a fully-integrated (either prokaryotic or eukaryotic) cell. This process could explain the missing evidence of the presence of DNA in flagella and peroxisomes whose ancestor endosymbionts, during the long endogenosymbiotic evolution, could have transferred their whole genome to the host cell that subsequently integrated it in its own genome, directly controlling its expression. Furthermore, the endogenosymbiosis hypothesis could be the explanation of the transition between an RNA to a DNA world and of some cases of true sympatric evolution of species, apparently inexplicable by the canonical speciation processes. Here, after an introduction to the theoretical basis of endogenosymbiosis and a discussion of the empirical confirming evidence, I show a graphical summary of the integration between this and the former endosymbiosis theories. The Serial Endosymbiosis Theory and the Secondary Endosymbiosis are merged with the Endogenosymbiosis Theory in a Unified Symbiogenetic Theory (UST).}, }
@article {pmid33473993, year = {2017}, author = {Zeng, L and Liu, C and Lin, R and Kang, X and Xie, B and Xiong, X}, title = {Complete mitogenome of the high ethanol production fungus Fusarium oxysporum Mh2-2.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {2}, number = {2}, pages = {814-815}, pmid = {33473993}, issn = {2380-2359}, abstract = {Fusarium spp. are significantly important plant pathogens, and some of them are ethanol-producing strains. During infection and/or ethanol production, Fusarium requires a plenty of energy that is mainly provided by mitochondria. Here we report the first mitogenome from a selected Fusarium oxysporum strain mh2-2 that produces ethanol from glucose and xylose. The size of this mitogenome, 46 kb, is different from the size of any reported Fusarium mitogenome. Our results provide insight into the functions and evolution of mitochondrial genes and genomes.}, }
@article {pmid33473765, year = {2017}, author = {Gagat, P and Mackiewicz, D and Mackiewicz, P}, title = {Peculiarities within peculiarities - dinoflagellates and their mitochondrial genomes.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {2}, number = {1}, pages = {191-195}, pmid = {33473765}, issn = {2380-2359}, abstract = {After the establishment of an endosymbiotic relationship between a proto-mitochondrion and its probable archaeal host, mitochondrial genomes underwent a spectacular reductive evolution. An interesting pathway was chosen by mitogenomes of unicellular protists called dinoflagellates, which experienced an additional wave of reduction followed by amplification and rearrangement leading to their secondary complexity. The former resulted in a mitogenome consisting of only three protein-coding genes, the latter in their multiple copies being scattered across numerous chromosomes and the evolution of complex processes for their expression. These stunning features raise a question about the future of the dinoflagellate mitochondrial genome.}, }
@article {pmid33473428, year = {2016}, author = {Dong, L and Maoliang, R and Li, Z and Chen, B}, title = {The complete mitochondrial genome sequence of Meishan pig (Sus Scrofa) and a phylogenetic study.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {1}, number = {1}, pages = {112-113}, pmid = {33473428}, issn = {2380-2359}, abstract = {In this study, we cloned and sequenced the complete mitochondrial genome DNA of Chinese pig, the Meishan pig. The sample was taken from Yencheng City, Jiangsu province in China. The complete genome DNA is 16 708 bp in length. We also performed a comparative analysis of the Meishan pig mitochondrial to the mitogenome sequences of 21 pig breeds which have been deposited in GenBank. Phylogenetic analysis using neighbour-joining computational algorithms showed that the analyzed species are divided into four major clades; the results can be subsequently used to provide information for pig phylogenetic and insights into the evolution of genomes.}, }
@article {pmid32481110, year = {2013}, author = {Gaff, DF and Oliver, M}, title = {The evolution of desiccation tolerance in angiosperm plants: a rare yet common phenomenon.}, journal = {Functional plant biology : FPB}, volume = {40}, number = {4}, pages = {315-328}, doi = {10.1071/FP12321}, pmid = {32481110}, issn = {1445-4416}, abstract = {In a minute proportion of angiosperm species, rehydrating foliage can revive from airdryness or even from equilibration with air of ~0% RH. Such desiccation tolerance is known from vegetative cells of some species of algae and of major groups close to the evolutionary path of the angiosperms. It is also found in the reproductive structures of some algae, moss spores and probably the aerial spores of other terrestrial cryptogamic taxa. The occurrence of desiccation tolerance in the seed plants is overwhelmingly in the aerial reproductive structures; the pollen and seed embryos. Spatially and temporally, pollen and embryos are close ontogenetic derivatives of the angiosperm microspores and megaspores respectively. This suggests that the desiccation tolerance of pollen and embryos derives from the desiccation tolerance of the spores of antecedent taxa and that the basic pollen/embryo mechanism of desiccation tolerance has eventually become expressed also in the vegetative tissue of certain angiosperm species whose drought avoidance is inadequate in micro-habitats that suffer extremely xeric episodes. The protective compounds and processes that contribute to desiccation tolerance in angiosperms are found in the modern groups related to the evolutionary path leading to the angiosperms and are also present in the algae and in the cyanobacteria. The mechanism of desiccation tolerance in the angiosperms thus appears to have its origins in algal ancestors and possibly in the endosymbiotic cyanobacteria-related progenitor of chloroplasts and the bacteria-related progenitor of mitochondria. The mechanism may involve the regulation and timing of the accumulation of protective compounds and of other contributing substances and processes.}, }
@article {pmid31881590, year = {2012}, author = {Lagaudrière-Gesbert, C and Purvina, M and Assrir, N and Rossignol, JM}, title = {Rôle(s) de la protéine cellulaire gC1qR dans les cycles viraux.}, journal = {Virologie (Montrouge, France)}, volume = {16}, number = {2}, pages = {85-94}, doi = {10.1684/vir.2012.0443}, pmid = {31881590}, issn = {1267-8694}, abstract = {The cellular protein gC1qR (also named HABP1, p32, p33 or TAP) has been identified as a partner of several viral proteins belonging to different virus families. gC1qR is a mitochondrial protein also present at the cell surface and in the nucleus. In normal cells, gC1qR seems involved in diverse biological processes related to its cellular localization. gC1qR could be involved in apoptosis in mitochondria, in RNA splicing in the nucleus or in immune and inflammatory responses at the cell surface. The multiple functions of gC1qR, as the variety of its viral partners, raise the question of its possible function(s) in the viral cycle. The goal of this review is to: (i) summarize what is known about gC1qR, (ii) focus on the demonstrated or hypothetical functions of the gC1qR-viral proteins complexes reported in the literature and (iii) propose a model on the possible roles of gC1qR in the viral life cycles.}, }
@article {pmid32689352, year = {2007}, author = {Voznesenskaya, EV and Koteyeva, NK and Chuong, SDX and Ivanova, AN and Barroca, J and Craven, LA and Edwards, GE}, title = {Physiological, anatomical and biochemical characterisation of photosynthetic types in genus Cleome (Cleomaceae).}, journal = {Functional plant biology : FPB}, volume = {34}, number = {4}, pages = {247-267}, doi = {10.1071/FP06287}, pmid = {32689352}, issn = {1445-4416}, abstract = {C4 photosynthesis has evolved many times in 18 different families of land plants with great variation in leaf anatomy, ranging from various forms of Kranz anatomy to C4 photosynthesis occurring within a single type of photosynthetic cell. There has been little research on photosynthetic typing in the family Cleomaceae, in which only one C4 species has been identified, Cleome gynandra L. There is recent interest in selecting and developing a C4 species from the family Cleomaceae as a model C4 system, since it is the most closely related to Arabidopsis, a C3 model system (Brown et al. 2005). From screening more than 230 samples of Cleomaceae species, based on a measure of the carbon isotope composition (δ[13]C) in leaves, we have identified two additional C4 species, C. angustifolia Forssk. (Africa) and C. oxalidea F.Muell. (Australia). Several other species have δ[13]C values around -17‰ to -19‰, suggesting they are C4-like or intermediate species. Eight species of Cleome were selected for physiological, anatomical and biochemical analyses. These included C. gynandra, a NAD-malic enzyme (NAD-ME) type C4 species, C. paradoxa R.Br., a C3-C4 intermediate species, and 6 others which were characterised as C3 species. Cleome gynandra has C4 features based on low CO2 compensation point (Γ), C4 type δ[13]C values, Kranz-type leaf anatomy and bundle sheath (BS) ultrastructure, presence of C4 pathway enzymes, and selective immunolocalisation of Rubisco and phosphoenolpyruvate carboxylase. Cleome paradoxa was identified as a C3-C4 intermediate based on its intermediate Γ (27.5 μmol mol[-1]), ultrastructural features and selective localisation of glycine decarboxylase of the photorespiratory pathway in mitochondria of BS cells. The other six species are C3 plants based on Γ, δ[13]C values, non-Kranz leaf anatomy, and levels of C4 pathway enzymes (very low or absent) typical of C3 plants. The results indicate that this is an interesting family for studying the genetic basis for C4 photosynthesis and its evolution from C3 species.}, }
@article {pmid30326676, year = {1974}, author = {Hinsch, GW and Walker, MH}, title = {The vas deferens of the spider crab, Libinia emarginata.}, journal = {Journal of morphology}, volume = {143}, number = {1}, pages = {1-19}, doi = {10.1002/jmor.1051430102}, pmid = {30326676}, issn = {1097-4687}, abstract = {Sperm enter the anterior vas deferens individually in the spider crab male. There they become surrounded by secretion products from the cells of the vas deferens, and are compartmentalized into spermatophores of varying size. The anterior vas deferens can be divided into three regions. The epithelium of the anterior vas deferens varies regionally from low to high columnar. The cytoplasm contains vast arrays of rough endoplasmic reticulum and Golgi complexes but few mitochondria. Intercellular spaces contain septate junctions, gap junctions and vesicles. Once the spermatophores have been formed in the anterior vas deferens, they are moved posteriorly to the middle vas deferens where they are stored and surrounded by seminal fluids. The epithelial cells of the middle vas deferens contain large amounts of rough endoplasmic reticulum and Golgi complexes. Numerous micropinocytotic vesicles appear, forming at the cell surface and within the apical cytoplasm. Their suggested function is the resorption of secretion products of the anterior vas deferens which initiated compartmentalization of the spermatozoa into spermatophores. The posterior vas deferens functions primarily as a storage center for spermatophores until they are released at the time of copulation. Seminal fluid surrounding the spermatophores is produced in this region as well as in the middle vas deferens. The cells of this region contain vast arrays of vesicular rough endoplasmic reticulum and Golgi complexes. The cells are multinucleate. Microtubules are numerous throughout the length of the cells and appear to insert on the plasma membrane.}, }
@article {pmid30166340, year = {2018}, author = {Valach, M and Léveillé-Kunst, A and Gray, MW and Burger, G}, title = {Respiratory chain Complex I of unparalleled divergence in diplonemids.}, journal = {The Journal of biological chemistry}, volume = {293}, number = {41}, pages = {16043-16056}, pmid = {30166340}, issn = {1083-351X}, support = {MOP-79309//CIHR/Canada ; }, mesh = {DNA, Mitochondrial/*metabolism ; Electron Transport ; Electron Transport Complex I/*metabolism ; Euglenozoa/*genetics/*metabolism ; Mass Spectrometry ; Mitochondria/metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/metabolism ; NADH Dehydrogenase/metabolism ; Phenylalanine/chemistry ; Phylogeny ; Protons ; RNA Editing ; RNA Splicing ; Ubiquinone/chemistry ; }, abstract = {Mitochondrial genes of Euglenozoa (Kinetoplastida, Diplonemea, and Euglenida) are notorious for being barely recognizable, raising the question of whether such divergent genes actually code for functional proteins. Here we demonstrate the translation and identify the function of five previously unassigned y genes encoded by mitochondrial DNA (mtDNA) of diplonemids. As is the rule in diplonemid mitochondria, y genes are fragmented, with gene pieces transcribed separately and then trans-spliced to form contiguous mRNAs. Further, y transcripts undergo massive RNA editing, including uridine insertions that generate up to 16-residue-long phenylalanine tracts, a feature otherwise absent from conserved mitochondrial proteins. By protein sequence analyses, MS, and enzymatic assays in Diplonema papillatum, we show that these y genes encode the subunits Nad2, -3, -4L, -6, and -9 of the respiratory chain Complex I (CI; NADH:ubiquinone oxidoreductase). The few conserved residues of these proteins are essentially those involved in proton pumping across the inner mitochondrial membrane and in coupling ubiquinone reduction to proton pumping (Nad2, -3, -4L, and -6) and in interactions with subunits containing electron-transporting Fe-S clusters (Nad9). Thus, in diplonemids, 10 CI subunits are mtDNA-encoded. Further, MS of D. papillatum CI allowed identification of 26 conventional and 15 putative diplonemid-specific nucleus-encoded components. Most conventional accessory subunits are well-conserved but unusually long, possibly compensating for the streamlined mtDNA-encoded components and for missing, otherwise widely distributed, conventional subunits. Finally, D. papillatum CI predominantly exists as a supercomplex I:III:IV that is exceptionally stable, making this protist an organism of choice for structural studies.}, }
@article {pmid30165810, year = {2018}, author = {Galen, SC and Nunes, R and Sweet, PR and Perkins, SL}, title = {Integrating coalescent species delimitation with analysis of host specificity reveals extensive cryptic diversity despite minimal mitochondrial divergence in the malaria parasite genus Leucocytozoon.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {128}, pmid = {30165810}, issn = {1471-2148}, support = {1358465//National Science Foundation/International ; }, mesh = {Animals ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Genetic Loci ; *Genetic Variation ; Haemosporida/*genetics ; Haplotypes/genetics ; *Host Specificity ; Malaria/*parasitology ; Mitochondria/*genetics ; Parasites/*genetics ; Phylogeny ; Songbirds/parasitology ; Species Specificity ; }, abstract = {BACKGROUND: Coalescent methods that use multi-locus sequence data are powerful tools for identifying putatively reproductively isolated lineages, though this approach has rarely been used for the study of microbial groups that are likely to harbor many unrecognized species. Among microbial symbionts, integrating genetic species delimitation methods with trait data that could indicate reproductive isolation, such as host specificity data, has rarely been used despite its potential to inform species limits. Here we test the ability of an integrative approach combining genetic and host specificity data to delimit species within the avian malaria parasite genus Leucocytozoon in central Alaska.<br><br>RESULTS: We sequenced seven nuclear loci for 69 Leucocytozoon samples and used multiple species delimitation methods (GMYC and BPP models), tested for differences in host infection patterns among putative species based on 406 individual infections, and characterized parasite morphology. We found that cryptic morphology has masked a highly diverse Leucocytozoon assemblage, with most species delimitation methods recovering support for at least 21 separate species that occur sympatrically and have divergent host infection patterns. Reproductive isolation among putative species appears to have evolved despite low mtDNA divergence, and in one instance two Leucocytozoon cytb haplotypes that differed by a single base pair (~&#x2009;0.2% divergence) were supported as separate species. However, there was no consistent association between mtDNA divergence and species limits. Among cytb haplotypes that differed by one to three base pairs we observed idiosyncratic patterns of nuclear and ecological divergence, with cytb haplotype pairs found to be either conspecific, reproductively isolated with no divergence in host specificity, or reproductively isolated with divergent patterns of host specialization.<br><br>CONCLUSION: Integrating multi-locus genetic species delimitation methods and non-traditional ecological data types such as host specificity provide a novel view of the diversity of avian malaria parasites that has been missed previously using morphology and mtDNA barcodes. Species delimitation methods show that Leucocytozoon is highly species-rich in Alaska, and the genus is likely to harbor extraordinary species-level diversity worldwide. Integrating genetic and ecological data will be an important approach for understanding the diversity and evolutionary history of microbial symbionts moving forward.}, }
@article {pmid30160146, year = {2018}, author = {Goh, CJ and Park, D and Kim, H and Sebastiani, F and Hahn, Y}, title = {Novel Divavirus (the family Betaflexiviridae) and Mitovirus (the family Narnaviridae) species identified in basil (Ocimum basilicum).}, journal = {Acta virologica}, volume = {62}, number = {3}, pages = {304-309}, doi = {10.4149/av_2018_224}, pmid = {30160146}, issn = {0001-723X}, mesh = {Flexiviridae/classification/genetics/*isolation &amp; purification/physiology ; Genome, Viral ; Ocimum basilicum/*virology ; Phylogeny ; Plant Diseases/*virology ; RNA-Dependent RNA Polymerase/genetics ; Viral Proteins/genetics ; }, abstract = {Transcriptome data obtained from a plant sample often contain a large number of reads that are derived from associated RNA virus genomes that were co-isolated during RNA preparation. These virus-derived reads can be assembled into a novel plant RNA genome sequence. Here, a basil (Ocimum basilicum) transcriptome dataset was analyzed to identify two new RNA viruses, which were named Ocimum basilicum RNA virus 1 (ObRV1) and Ocimum basilicum RNA virus 2 (ObRV2). A phylogenetic analysis of the ObRV1 RNA-dependent RNA polymerase (RdRp) motif indicated that ObRV1 is a novel species of the genus Divavirus of the family Betaflexiviridae. ObRV1 is the fourth divavirus species to be identified. The ObRV2 RdRp motif showed sequence similarity to viruses of the genus Mitovirus of the family Narnaviridae, which infect fungal mitochondria. Although most of the known mitoviruses do not produce a functional RdRp using the plant mitochondrial genetic code, the ObRV2 encodes a full-length RdRp using both the fungal and plant mitochondrial genetic codes.}, }
@article {pmid30158483, year = {2018}, author = {Kozieł, E and Otulak-Kozieł, K and Bujarski, JJ}, title = {Ultrastructural Analysis of Prune DwarfVirus Intercellular Transport and Pathogenesis.}, journal = {International journal of molecular sciences}, volume = {19}, number = {9}, pages = {}, pmid = {30158483}, issn = {1422-0067}, support = {505-10-011100-Q00190-99//Warsaw Univeristy of Life Sciences WULS-SGGW/ ; }, mesh = {Alfalfa mosaic virus/genetics/*pathogenicity/*ultrastructure ; Biological Transport/genetics/physiology ; Phylogeny ; RNA, Viral ; Viral Proteins/metabolism/ultrastructure ; }, abstract = {Prune dwarf virus (PDV) is an important viral pathogen of plum, sweet cherry, peach, and many herbaceous test plants. Although PDV has been intensively investigated, mainly in the context of phylogenetic relationship of its genes and proteins, many gaps exist in our knowledge about the mechanism of intercellular transport of this virus. The aim of this work was to investigate alterations in cellular organelles and the cell-to-cell transport of PDV in Cucumis sativus cv. Polan at ultrastructural level. To analyze the role of viral proteins in local transport, double-immunogold assays were applied to localize PDV coat protein (CP) and movement protein (MP). We observe structural changes in chloroplasts, mitochondria, and cellular membranes. We prove that PDV is transported as viral particles via MP-generated tubular structures through plasmodesmata. Moreover, the computer-run 3D modeling reveals structural resemblances between MPs of PDV and of Alfalfa mosaic virus (AMV), implying similarities of transport mechanisms for both viruses.}, }
@article {pmid30154842, year = {2018}, author = {Berzabá-Evoli, E and Zazueta, C and Cruz Hernández, JH and Gómez-Crisóstomo, NP and Juárez-Rojop, IE and De la Cruz-Hernández, EN and Martínez-Abundis, E}, title = {Leptin Modifies the Rat Heart Performance Associated with Mitochondrial Dysfunction Independently of Its Prohypertrophic Effects.}, journal = {International journal of endocrinology}, volume = {2018}, number = {}, pages = {6081415}, pmid = {30154842}, issn = {1687-8337}, abstract = {BACKGROUND: Functional receptors for leptin were described on the surface of cardiomyocytes, and there was a prohypertrophic effect with high concentrations of the cytokine. Therefore, leptin could be a link between obesity and the prevalence of cardiovascular diseases. On the other hand, a deleterious effect of leptin on mitochondrial performance was described, which was also associated with the evolution of cardiac hypertrophy to heart failure. The goal of our study was to analyze the effect of the exposure of rat hearts to a high concentration of leptin on cardiac and mitochondrial function.<br><br>METHODS: Rat hearts were perfused continuously with or without 3.1&#x2009;nM leptin for 1, 2, 3, or 4 hours. Homogenates and mitochondria were prepared by centrifugation and analyzed for cardiac actin, STAT3, and pSTAT3 by Western blotting, as well as for mitochondrial oxidative phosphorylation, membrane potential, swelling, calcium transport, and content of oxidized lipids.<br><br>RESULTS: In our results, leptin induced an increased rate-pressure product as a result of increased heart rate and contraction force, as well oxidative stress. In addition, mitochondrial dysfunction expressed as a loss of membrane potential, decreased ability for calcium transport and retention, faster swelling, and less respiratory control was observed.<br><br>CONCLUSIONS: Our results support the role of leptin as a deleterious factor for cardiac function and indicates that mitochondrial dysfunction could be a trigger for cardiac hypertrophy and failure.}, }
@article {pmid30144423, year = {2018}, author = {Pustylnikov, S and Costabile, F and Beghi, S and Facciabene, A}, title = {Targeting mitochondria in cancer: current concepts and immunotherapy approaches.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {202}, number = {}, pages = {35-51}, pmid = {30144423}, issn = {1878-1810}, support = {R01 CA206012/CA/NCI NIH HHS/United States ; R01 CA219871/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/genetics ; Humans ; *Immunotherapy ; Mitochondria/*metabolism ; Mitochondrial Dynamics ; Neoplasms/*immunology/*therapy ; T-Lymphocytes/metabolism ; }, abstract = {An essential advantage during eukaryotic cell evolution was the acquisition of a network of mitochondria as a source of energy for cell metabolism and contrary to conventional wisdom, functional mitochondria are essential for the cancer cell. Multiple aspects of mitochondrial biology beyond bioenergetics support transformation including mitochondrial biogenesis, fission and fusion dynamics, cell death susceptibility, oxidative stress regulation, metabolism, and signaling. In cancer, the metabolism of cells is reprogrammed for energy generation from oxidative phosphorylation to aerobic glycolysis and impacts cancer mitochondrial function. Furthermore cancer cells can also modulate energy metabolism within the cancer microenvironment including immune cells and induce "metabolic anergy" of antitumor immune response. Classical approaches targeting the mitochondria of cancer cells usually aim at inducing changing energy metabolism or directly affecting functions of mitochondrial antiapoptotic proteins but most of such approaches miss the required specificity of action and carry important side effects. Several types of cancers harbor somatic mitochondrial DNA mutations and specific immune response to mutated mitochondrial proteins has been observed. An attractive alternative way to target the mitochondria in cancer cells is the induction of an adaptive immune response against mutated mitochondrial proteins. Here, we review the cancer cell-intrinsic and cell-extrinsic mechanisms through which mitochondria influence all steps of oncogenesis, with a focus on the therapeutic potential of targeting mitochondrial DNA mutations or Tumor Associated Mitochondria Antigens using the immune system.}, }
@article {pmid30143614, year = {2018}, author = {Quintana-Cabrera, R and Quirin, C and Glytsou, C and Corrado, M and Urbani, A and Pellattiero, A and Calvo, E and Vázquez, J and Enríquez, JA and Gerle, C and Soriano, ME and Bernardi, P and Scorrano, L}, title = {The cristae modulator Optic atrophy 1 requires mitochondrial ATP synthase oligomers to safeguard mitochondrial function.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {3399}, pmid = {30143614}, issn = {2041-1723}, support = {IJCI-2015-26225//Ministerio de Econom&#xed;a y Competitividad (Ministry of Economy and Competitiveness)/International ; JPMJCR13M4//JST | Core Research for Evolutional Science and Technology (CREST)/International ; GGP15091//Fondazione Telethon (Telethon Foundation)/International ; GGP14187//Fondazione Telethon (Telethon Foundation)/International ; FP7-282280//EC | European Research Council (ERC)/International ; IG-15748//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/International ; }, mesh = {Animals ; Antimycin A/pharmacology ; Cell Survival/drug effects ; Electrophoresis, Polyacrylamide Gel ; GTP Phosphohydrolases/genetics/*metabolism ; Immunoblotting ; Immunoprecipitation ; Mice ; Microscopy, Electron, Transmission ; Mitochondria/*metabolism ; Mitochondrial Proteins/genetics/metabolism ; Mitochondrial Proton-Translocating ATPases/genetics/*metabolism ; }, abstract = {It is unclear how the mitochondrial fusion protein Optic atrophy 1 (OPA1), which inhibits cristae remodeling, protects from mitochondrial dysfunction. Here we identify the mitochondrial F1Fo-ATP synthase as the effector of OPA1 in mitochondrial protection. In OPA1 overexpressing cells, the loss of proton electrochemical gradient caused by respiratory chain complex III inhibition is blunted and this protection is abolished by the ATP synthase inhibitor oligomycin. Mechanistically, OPA1 and ATP synthase can interact, but recombinant OPA1 fails to promote oligomerization of purified ATP synthase reconstituted in liposomes, suggesting that OPA1 favors ATP synthase oligomerization and reversal activity by modulating cristae shape. When ATP synthase oligomers are genetically destabilized by silencing the key dimerization subunit e, OPA1 is no longer able to preserve mitochondrial function and cell viability upon complex III inhibition. Thus, OPA1 protects mitochondria from respiratory chain inhibition by stabilizing cristae shape and favoring ATP synthase oligomerization.}, }
@article {pmid30141728, year = {2018}, author = {Boratyński, JS and Szafrańska, PA}, title = {Does Basal Metabolism Set the Limit for Metabolic Downregulation during Torpor?.}, journal = {Physiological and biochemical zoology : PBZ}, volume = {91}, number = {5}, pages = {1057-1067}, doi = {10.1086/699917}, pmid = {30141728}, issn = {1537-5293}, mesh = {Animals ; Basal Metabolism/*physiology ; Body Mass Index ; Down-Regulation ; Mammals/*physiology ; Models, Biological ; Torpor/*physiology ; }, abstract = {The evolution of endothermic thermoregulation is rooted in the processes involving high metabolism, which allows the maintenance of high and stable body temperatures (Tb). In turn, selection for high endothermic metabolism correlates with increased size of metabolically active organs and thus with high basal metabolic rate (BMR). Endothermic animals are characterized by an MR several times that of similar-sized ectotherms. However, many small mammals are temporally heterothermic and are able to temporally decrease Tb and MR by entering daily torpor or hibernation. Both BMR and minimum MR during torpor (TMRmin) likely result from oxidative respiration in mitochondria of the same tissues. It should be expected that these two MRs are positively correlated, suggesting that the evolution of endothermy and higher BMR set the limit for the ability to reduce MR while entering torpor. Using published data for 96 mammal species, we tested the hypothesis that, among heterothermic mammals, the processes leading to the evolution of higher BMR limit the ability to downregulate metabolism during torpor. We found that body mass (mb)-adjusted BMR was positively correlated with mb- and Tb-adjusted TMRmin, in a phylogenetically corrected analysis. Phylogenetic path modeling indicated that the mechanisms underlying the evolutionary increase of BMR in endotherms most likely constrain their ability to reduce MR during torpor. Given that heterothermy is considered an ancestral state in mammals, these results suggest an increase in BMR during the evolution of endothermy in homeothermic animals, which leads to the loss of their ability to enter torpor.}, }
@article {pmid30139961, year = {2018}, author = {Liu, J and Kim, SY and Shin, S and Jung, SH and Yim, SH and Lee, JY and Lee, SH and Chung, YJ}, title = {Overexpression of TFF3 is involved in prostate carcinogenesis via blocking mitochondria-mediated apoptosis.}, journal = {Experimental &amp; molecular medicine}, volume = {50}, number = {8}, pages = {1-11}, pmid = {30139961}, issn = {2092-6413}, mesh = {Annexin A5/metabolism ; *Apoptosis ; Carcinogenesis/metabolism/pathology ; Caspase 3/metabolism ; Cell Line, Tumor ; Cell Movement ; Cell Proliferation ; Cytosol/metabolism ; Gene Silencing ; Humans ; Male ; Mitochondria/*metabolism ; Models, Biological ; Prostatic Neoplasms/*metabolism/*pathology ; Trefoil Factor-3/*metabolism ; }, abstract = {The overexpression of trefoil factor family 3 (TFF3) is observed in a variety of cancers, including prostate cancer (PCa), and its potential role in carcinogenesis, such as activating the PI3K/AKT pathway, is suggested. However, its role and its related mechanisms in prostate tumorigenesis remain unknown. To elucidate the role of TFF3 overexpression in PCa, we silenced TFF3 in two PCa cell lines that overexpressed TFF3 and explored the molecular mechanism behind its antiapoptotic role. We also examined TFF3 expression in 108 Korean PCa specimens and 106 normal prostate tissues by immunohistochemistry (IHC) analysis. The mean TFF3 IHC score in the tumor tissues was significantly higher than that in the normal tissues (4.702 vs. 0.311, P = 2.52 × 10[-24]). TFF3-silenced cells showed suppressed tumor cell growth and migration. TFF3 silencing decreased BCL2 and increased BAX expression. The translocation of BAX to the mitochondria was also confirmed. After TFF3 silencing, the expression of the mitochondrial proapoptotic proteins, cytochrome C and Smac/DIABLO, was elevated, and these proteins were released from the mitochondria to the cytosol. Downstream mediators of mitochondrial apoptosis, including cleaved caspase-3, caspase-9, and PARP, were also elevated. Accordingly, the proportion of apoptotic cells was significantly higher among TFF3-silenced cells. There was no difference in extrinsic apoptosis-related molecules after TFF3 silencing. All the results support that TFF3 silencing induces the downstream signaling pathway of mitochondria-mediated apoptosis. This study provides a better understanding of the mechanism of prostate tumorigenesis, suggesting TFF3 as a potential biomarker and therapeutic target of PCa.}, }
@article {pmid30138782, year = {2018}, author = {Treitli, SC and Kotyk, M and Yubuki, N and Jirounková, E and Vlasáková, J and Smejkalová, P and Šípek, P and Čepička, I and Hampl, V}, title = {Molecular and Morphological Diversity of the Oxymonad Genera Monocercomonoides and Blattamonas gen. nov.}, journal = {Protist}, volume = {169}, number = {5}, pages = {744-783}, doi = {10.1016/j.protis.2018.06.005}, pmid = {30138782}, issn = {1618-0941}, mesh = {Genetic Variation ; Microscopy, Electron ; Oxymonadida/*genetics/*growth &amp; development/ultrastructure ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Oxymonads are a group of flagellates living as gut symbionts of insects or vertebrates. They have several unique features, one of them being the absence of mitochondria. Diversity of this group is seriously understudied, which is particularly true for small species from the family Polymastigidae. We isolated 34 strains of oxymonads with Polymastigidae-like morphology from 24 host species and unused cesspits and sequenced the SSU rRNA gene. Our strains formed two clades in the phylogenetic tree with Streblomastix strix branching between them. This topology was also supported by a three-gene phylogenetic analysis. Despite considerable genetic differences between the clades, light and electron microscopy revealed only subtle differences. The larger clade is considered genus Monocercomonoides and the isolates belonging here were classified into three new species (including the first potentially free-living species), two previously described species, and three unclassified lineages. The smaller clade, here described as Blattamonas gen. nov., consists of three newly described species. Concomitantly with the description of Blattamonas, we elevate the Monocercomonoides subgenus Brachymonas to the genus level. Our study shows that, despite their conserved morphology, the molecular diversity of Polymastigidae-like oxymonads is broad and represents a substantial part of the diversity of oxymonads.}, }
@article {pmid30137656, year = {2018}, author = {Kagda, MS and Vu, AL and Ah-Fong, AMV and Judelson, HS}, title = {Phosphagen kinase function in flagellated spores of the oomycete Phytophthora infestans integrates transcriptional regulation, metabolic dynamics and protein retargeting.}, journal = {Molecular microbiology}, volume = {110}, number = {2}, pages = {296-308}, doi = {10.1111/mmi.14108}, pmid = {30137656}, issn = {1365-2958}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Cytoplasm/enzymology ; Flagella/*enzymology ; Gene Expression Regulation/*physiology ; Solanum lycopersicum/genetics/parasitology ; Mitochondria/metabolism ; Phosphotransferases/genetics/*metabolism ; Phytophthora infestans/*enzymology/genetics ; Sporangia/enzymology ; Spores/*enzymology ; Taurine/analogs &amp; derivatives/metabolism ; }, abstract = {Flagellated spores play important roles in the infection of plants and animals by many eukaryotic microbes. The oomycete Phytophthora infestans, which causes potato blight, expresses two phosphagen kinases (PKs). These enzymes store energy in taurocyamine, and are hypothesized to resolve spatial and temporal imbalances between rates of ATP creation and use in zoospores. A dimeric PK is found at low levels in vegetative mycelia, but high levels in ungerminated sporangia and zoospores. In contrast, a monomeric PK protein is at similar levels in all tissues, although is transcribed primarily in mycelia. Subcellular localization studies indicate that the monomeric PK is mitochondrial. In contrast, the dimeric PK is cytoplasmic in mycelia and sporangia but is retargeted to flagellar axonemes during zoosporogenesis. This supports a model in which PKs shuttle energy from mitochondria to and through flagella. Metabolite analysis indicates that deployment of the flagellar PK is coordinated with a large increase in taurocyamine, synthesized by sporulation-induced enzymes that were lost during the evolution of zoospore-lacking oomycetes. Thus, PK function is enabled by coordination of the transcriptional, metabolic and protein targeting machinery during the life cycle. Since plants lack PKs, the enzymes may be useful targets for inhibitors of oomycete plant pathogens.}, }
@article {pmid30127539, year = {2018}, author = {Betts, HC and Puttick, MN and Clark, JW and Williams, TA and Donoghue, PCJ and Pisani, D}, title = {Integrated genomic and fossil evidence illuminates life's early evolution and eukaryote origin.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {10}, pages = {1556-1562}, pmid = {30127539}, issn = {2397-334X}, support = {BB/N000919/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; Eukaryota/*genetics ; *Fossils ; *Genome ; }, abstract = {Establishing a unified timescale for the early evolution of Earth and life is challenging and mired in controversy because of the paucity of fossil evidence, the difficulty of interpreting it and dispute over the deepest branching relationships in the tree of life. Surprisingly, it remains perhaps the only episode in the history of life where literal interpretations of the fossil record hold sway, revised with every new discovery and reinterpretation. We derive a timescale of life, combining a reappraisal of the fossil material with new molecular clock analyses. We find the last universal common ancestor of cellular life to have predated the end of late heavy bombardment (>3.9 billion years ago (Ga)). The crown clades of the two primary divisions of life, Eubacteria and Archaebacteria, emerged much later (<3.4 Ga), relegating the oldest fossil evidence for life to their stem lineages. The Great Oxidation Event significantly predates the origin of modern Cyanobacteria, indicating that oxygenic photosynthesis evolved within the cyanobacterial stem lineage. Modern eukaryotes do not constitute a primary lineage of life and emerged late in Earth's history (<1.84 Ga), falsifying the hypothesis that the Great Oxidation Event facilitated their radiation. The symbiotic origin of mitochondria at 2.053-1.21 Ga reflects a late origin of the total-group Alphaproteobacteria to which the free living ancestor of mitochondria belonged.}, }
@article {pmid30121730, year = {2019}, author = {Radzinski, M and Reichmann, D}, title = {Variety is the spice of life: how to explore a redox-dependent heterogeneity in genomically identical cellular populations.}, journal = {Current genetics}, volume = {65}, number = {1}, pages = {301-306}, pmid = {30121730}, issn = {1432-0983}, support = {1765/13//Israel Science Foundation/ ; 1649/16//legacy Heritage Biomedical Science Partnership/ ; CDA00064/2014//Human Frontier Science Program/ ; 2015056//United States - Israel Binational Science Foundation/ ; }, mesh = {Animals ; Cell Separation/methods ; Cellular Microenvironment/*genetics ; Flow Cytometry/methods ; *Genetic Heterogeneity ; Genomics/*methods ; Green Fluorescent Proteins/genetics/metabolism ; Humans ; Oxidation-Reduction ; Proteomics/*methods ; Saccharomyces cerevisiae/cytology/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {Cellular heterogeneity is a widespread phenomenon, existing across organisms and serving a crucial role in evolution and cell survival. Genetically identical cells may as a result present in a variety of forms with different gene and protein expressions, as well as oxidation level. As a result, a wide range of methodologies and techniques for dissecting different types of genetic, proteomic, and phenotypic heterogeneous traits have emerged in recent years in an effort to better understand how diversity exists within a single population and its effects therein. A key area of interest seeks to establish the ways in which cellular heterogeneity and aging processes interact with each other. Here, we discuss recent developments in defining cellular heterogeneity, specifically focusing on redox-dependent heterogeneity, its characterization, quantification, and behavior. We further expand on potential applications of a cell sorting-based methodology for distinguishing between cells harboring different redox statuses. As an example, we use organelle-specific fluorescence protein-based probes to examine the crosstalk between cytosol and mitochondria in a yeast strain lacking glutathione reductase. Together, these may have wide-reaching implications for future research into redox-associated factors, as well as mechanisms of redox-dependent heterogeneity and its influence on organelles and the cell at large.}, }
@article {pmid30117257, year = {2018}, author = {Wang, L and Zhang, S and Li, JH and Zhang, YJ}, title = {Mitochondrial genome, comparative analysis and evolutionary insights into the entomopathogenic fungus Hirsutella thompsonii.}, journal = {Environmental microbiology}, volume = {20}, number = {9}, pages = {3393-3405}, doi = {10.1111/1462-2920.14379}, pmid = {30117257}, issn = {1462-2920}, support = {201601D011065//Natural Science Foundation of Shanxi Province/International ; }, mesh = {Acari/*microbiology ; Animals ; Evolution, Molecular ; Fungal Proteins/genetics ; Genome, Fungal ; *Genome, Mitochondrial ; Hypocreales/classification/*genetics/isolation &amp; purification ; Introns ; Mitochondria/genetics ; Open Reading Frames ; Phylogeny ; }, abstract = {Nuclear genomes of two isolates of Hirsutella thompsonii, a pathogen causing epizootics among mites, have been reported; in contrast, its mitochondrial genome (mitogenome) has remained unknown, limiting our understanding of its evolution. Herein, we annotated the first complete mitogenome of H. thompsonii, which encoded all standard fungal mitochondrial genes plus three free-standing ORFs. Transcriptional analyses validated the expression of most conserved genes and revealed some interesting transcription patterns of mitochondrial genes. Phylogenetic analyses confirmed its placement in Ophiocordycipitaceae. Comparison of five different isolates originally collected from different locations revealed mitogenome size variations (60.3-66.4 kb) mainly due to different numbers of introns. A total of 15 intron loci were identified, with 11 existing in all 5 isolates and 4 showing presence/absence dynamics. These introns were most likely obtained through horizontal transfer from other fungal organisms. Those common introns might have been in H. thompsonii mitogenomes since the divergence of the fungus from its putative sister species H. minnesotensis, whereas those dynamic introns might have experienced 1-2 gain or loss events. We also detected evidence of degeneration for some introns. Overall, our study shed new insights into the mitochondrial evolution of the acaropathogenic fungus H. thompsonii.}, }
@article {pmid30114217, year = {2018}, author = {Shi, Y and Liu, Y and Zhang, S and Zou, R and Tang, J and Mu, W and Peng, Y and Dong, S}, title = {Assembly and comparative analysis of the complete mitochondrial genome sequence of Sophora japonica 'JinhuaiJ2'.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0202485}, pmid = {30114217}, issn = {1932-6203}, mesh = {Base Composition ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Genes, Plant ; *Genome, Mitochondrial ; Homologous Recombination ; Introns ; Mitochondria/genetics ; Phylogeny ; Plant Proteins/genetics ; RNA, Plant/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Sophora/*genetics ; Whole Genome Sequencing ; }, abstract = {Sophora japonica L. (Faboideae, Leguminosae) is an important traditional Chinese herb with a long history of cultivation. Its flower buds and fruits contain abundant flavonoids, and therefore, the plants are cultivated for the industrial extraction of rutin. Here, we determined the complete nucleotide sequence of the mitochondrial genome of S. japonica 'JinhuaiJ2', the most widely planted variety in Guangxi region of China. The total length of the mtDNA sequence is 484,916 bp, with a GC content of 45.4%. Sophora japonica mtDNA harbors 32 known protein-coding genes, 17 tRNA genes, and three rRNA genes with 17 cis-spliced and five trans-spliced introns disrupting eight protein-coding genes. The gene coding and intron regions, and intergenic spacers account for 7.5%, 5.8% and 86.7% of the genome, respectively. The gene profile of S. japonica mitogenome differs from that of the other Faboideae species by only one or two gene gains or losses. Four of the 17 cis-spliced introns showed distinct length variations in the Faboideae, which could be attributed to the homologous recombination of the short repeats measuring a few bases located precisely at the edges of the putative deletions. This reflects the importance of small repeats in the sequence evolution in Faboideae mitogenomes. Repeated sequences of S. japonica mitogenome are mainly composed of small repeats, with only 20 medium-sized repeats, and one large repeat, adding up to 4% of its mitogenome length. Among the 25 pseudogene fragments detected in the intergenic spacer regions, the two largest ones and their corresponding functional gene copies located in two different sets of medium-sized repeats, point to their origins from homologous recombinations. As we further observed the recombined reads associated with the longest repeats of 2,160 bp with the PacBio long read data set of just 15 × in depth, repeat mediated homologous recombinations may play important role in the mitogenomic evolution of S. japonica. Our study provides insightful knowledge to the genetic background of this important herb species and the mitogenomic evolution in the Faboideae species.}, }
@article {pmid30114187, year = {2018}, author = {Weiss, MC and Preiner, M and Xavier, JC and Zimorski, V and Martin, WF}, title = {The last universal common ancestor between ancient Earth chemistry and the onset of genetics.}, journal = {PLoS genetics}, volume = {14}, number = {8}, pages = {e1007518}, pmid = {30114187}, issn = {1553-7404}, mesh = {Archaea/genetics ; Bacteria/genetics ; Eukaryota/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Code ; Genome ; Mitochondria/genetics ; Nucleic Acid Conformation ; Origin of Life ; *Phylogeny ; Prokaryotic Cells ; }, abstract = {All known life forms trace back to a last universal common ancestor (LUCA) that witnessed the onset of Darwinian evolution. One can ask questions about LUCA in various ways, the most common way being to look for traits that are common to all cells, like ribosomes or the genetic code. With the availability of genomes, we can, however, also ask what genes are ancient by virtue of their phylogeny rather than by virtue of being universal. That approach, undertaken recently, leads to a different view of LUCA than we have had in the past, one that fits well with the harsh geochemical setting of early Earth and resembles the biology of prokaryotes that today inhabit the Earth's crust.}, }
@article {pmid30110634, year = {2018}, author = {Vazquez, JM and Sulak, M and Chigurupati, S and Lynch, VJ}, title = {A Zombie LIF Gene in Elephants Is Upregulated by TP53 to Induce Apoptosis in Response to DNA Damage.}, journal = {Cell reports}, volume = {24}, number = {7}, pages = {1765-1776}, doi = {10.1016/j.celrep.2018.07.042}, pmid = {30110634}, issn = {2211-1247}, mesh = {Animals ; Apoptosis/genetics ; Biological Evolution ; Body Size ; DNA Damage ; Elephants/*genetics/metabolism ; *Gene Dosage ; Gene Duplication ; Gene Expression Regulation ; Humans ; Mitochondria/genetics/metabolism ; Neoplasms/prevention &amp; control ; Phylogeny ; Proboscidea Mammal/classification/genetics ; Protein Isoforms/genetics/metabolism ; Pseudogenes ; Receptors, OSM-LIF/*genetics/metabolism ; Response Elements ; Transcription, Genetic ; Tumor Suppressor Protein p53/*genetics/metabolism ; bcl-2 Homologous Antagonist-Killer Protein/*genetics/metabolism ; bcl-2-Associated X Protein/*genetics/metabolism ; }, abstract = {Large-bodied organisms have more cells that can potentially turn cancerous than small-bodied organisms, imposing an increased risk of developing cancer. This expectation predicts a positive correlation between body size and cancer risk; however, there is no correlation between body size and cancer risk across species ("Peto's paradox"). Here, we show that elephants and their extinct relatives (proboscideans) may have resolved Peto's paradox in part through refunctionalizing a leukemia inhibitory factor pseudogene (LIF6) with pro-apoptotic functions. LIF6 is transcriptionally upregulated by TP53 in response to DNA damage and translocates to the mitochondria where it induces apoptosis. Phylogenetic analyses of living and extinct proboscidean LIF6 genes indicates that its TP53 response element evolved coincident with the evolution of large body sizes in the proboscidean stem lineage. These results suggest that refunctionalizing of a pro-apoptotic LIF pseudogene may have been permissive (although not sufficient) for the evolution of large body sizes in proboscideans.}, }
@article {pmid30109028, year = {2018}, author = {Wideman, JG and Balacco, DL and Fieblinger, T and Richards, TA}, title = {PDZD8 is not the 'functional ortholog' of Mmm1, it is a paralog.}, journal = {F1000Research}, volume = {7}, number = {}, pages = {1088}, pmid = {30109028}, issn = {2046-1402}, mesh = {Animals ; Humans ; Mitochondrial Proteins/*genetics ; *Phylogeny ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/*genetics ; }, abstract = {Authors of a recent paper demonstrate that, like ERMES (ER-mitochondria encounter structure) in fungal cells, PDZD8 (PDZ domain containing 8) tethers mitochondria to the ER in mammalian cells. However, identifying PDZD8 as a "functional ortholog" of yeast Mmm1 (maintenance of mitochondrial morphology protein 1) is at odds with the phylogenetic data. PDZD8 and Mmm1 are paralogs, not orthologs, which affects the interpretation of the data with respect to the evolution of ER-mitochondria tethering. Our phylogenetic analyses show that PDZD8 co-occurs with ERMES components in lineages closely related to animals solidifying its identity as a paralog of Mmm1. Additionally, we identify two related paralogs, one specific to flagellated fungi, and one present only in unicellular relatives of animals. These results point to a complex evolutionary history of ER-mitochondria tethering involving multiple gene gains and losses in the lineage leading to animals and fungi.}, }
@article {pmid30107780, year = {2018}, author = {Dong, S and Zhao, C and Chen, F and Liu, Y and Zhang, S and Wu, H and Zhang, L and Liu, Y}, title = {The complete mitochondrial genome of the early flowering plant Nymphaea colorata is highly repetitive with low recombination.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {614}, pmid = {30107780}, issn = {1471-2164}, support = {31470314//National Natural Science Foundation of China/ ; 31600171//National Natural Science Foundation of China/ ; FLSF2017-03//National Natural Science Foundation of China/ ; 201520//Shenzhen Urban Management Bureau Fund/ ; DEB-1240045//National Science Foundation/ ; JCYJ20150529150409546//Shenzhen Municipal Government of China/ ; }, mesh = {*Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/*genetics ; Nymphaea/*genetics/growth &amp; development ; *Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Mitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. The mitogenome of the earliest angiosperm Amborella is remarkable in carrying rampant foreign DNAs, in contrast to Liriodendron, the other only known early angiosperm mitogenome that is described as 'fossilized'. The distinctive features observed in the two early flowering plant mitogenomes add to the current confusions of what early flowering plants look like. Expanded sampling would provide more details in understanding the mitogenomic evolution of early angiosperms. Here we report the complete mitochondrial genome of water lily Nymphaea colorata from Nymphaeales, one of the three orders of the earliest angiosperms.<br><br>RESULTS: Assembly of data from Pac-Bio long-read sequencing yielded a circular mitochondria chromosome of 617,195&#xa0;bp with an average depth of 601&#xd7;. The genome encoded 41 protein coding genes, 20 tRNA and three rRNA genes with 25 group II introns disrupting 10 protein coding genes. Nearly half of the genome is composed of repeated sequences, which contributed substantially to the intron size expansion, making the gross intron length of the Nymphaea mitochondrial genome one of the longest among angiosperms, including an 11.4-Kb intron in cox2, which is the longest organellar intron reported to date in plants. Nevertheless, repeat mediated homologous recombination is unexpectedly low in Nymphaea evidenced by 74 recombined reads detected from ten recombinationally active repeat pairs among 886,982 repeat pairs examined. Extensive gene order changes were detected in the three early angiosperm mitogenomes, i.e. 38 or 44 events of inversions and translocations are needed to reconcile the mitogenome of Nymphaea with Amborella or Liriodendron, respectively. In contrast to Amborella with six genome equivalents of foreign mitochondrial DNA, not a single horizontal gene transfer event was observed in the Nymphaea mitogenome.<br><br>CONCLUSIONS: The Nymphaea mitogenome resembles the other available early angiosperm mitogenomes by a similarly rich 64-coding gene set, and many conserved gene clusters, whereas stands out by its highly repetitive nature and resultant remarkable intron expansions. The low recombination level in Nymphaea provides evidence for the predominant master conformation in vivo with a highly substoichiometric set of rearranged molecules.}, }
@article {pmid30107223, year = {2018}, author = {Reyes-Ramos, CA and Peregrino-Uriarte, AB and Cota-Ruiz, K and Valenzuela-Soto, EM and Leyva-Carrillo, L and Yepiz-Plascencia, G}, title = {Phosphoenolpyruvate carboxykinase cytosolic and mitochondrial isoforms are expressed and active during hypoxia in the white shrimp Litopenaeus vannamei.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {226}, number = {}, pages = {1-9}, doi = {10.1016/j.cbpb.2018.08.001}, pmid = {30107223}, issn = {1879-1107}, mesh = {Amino Acid Sequence ; Animals ; Aquaculture ; Conserved Sequence ; Cytosol/*enzymology/metabolism ; Databases, Protein ; *Gene Expression Regulation, Developmental ; Gills/enzymology/growth &amp; development/metabolism ; Hepatopancreas/enzymology/growth &amp; development/metabolism ; Hypoxia/*enzymology/metabolism ; Isoenzymes/genetics/metabolism ; Mitochondria/*enzymology/metabolism ; Muscle, Skeletal/enzymology/growth &amp; development/metabolism ; Organ Specificity ; Penaeidae/growth &amp; development/*physiology ; Phosphoenolpyruvate Carboxykinase (GTP)/chemistry/genetics/*metabolism ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Hypoxic zones in marine environments are spreading around the world affecting the survival of many organisms. Marine animals have several strategies to respond to hypoxia, including the regulation of gluconeogenesis. Phosphoenolpyruvate carboxykinase (PEPCK) is a key regulatory enzyme of gluconeogenesis. The objective of this work was to study two isoforms of PEPCK, one mitochondrial (PEPKC-M) and one cytosolic (PEPCK-C), from the white shrimp Litopenaeus vannamei and the response to hypoxia. Both PEPCK isoforms are 72 kDa proteins and have 92% identity at the amino acid level. The mitochondrial isoform has a N-terminal signal peptide for mitochondrial import. Gene expression and enzymatic activity in subcellular fractions were detected in gills, hepatopancreas and muscle in normoxic and hypoxic conditions. Expression of PEPCK-C was higher than PEPCK-M in all the tissues and induced in response to hypoxia at 48 h in hepatopancreas, while the enzymatic activity of PEPCK-M was higher than PEPCK-C in gills and hepatopancreas, but not in muscle and also increased in response to hypoxia in hepatopancreas but decreased in gills and muscle. During limiting oxygen conditions, shrimp tissues obtain energy by inducing anaerobic glycolysis, and although gluconeogenesis implies energy investment, due to the need to maintain glucose homeostasis, these gluconeogenic enzymes are active with contrasting behaviors in the cytosol and mitochondrial cell compartments and appear to be up-regulated in hepatopancreas indicating this tissue pivotal role in gluconeogenesis during the response to hypoxia.}, }
@article {pmid30102976, year = {2018}, author = {Baron, S and van der Merwe, NA and Maritz-Olivier, C}, title = {The genetic relationship between R. microplus and R. decoloratus ticks in South Africa and their population structure.}, journal = {Molecular phylogenetics and evolution}, volume = {129}, number = {}, pages = {60-69}, doi = {10.1016/j.ympev.2018.08.003}, pmid = {30102976}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Cattle ; Cell Nucleus/genetics ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Genetic Markers ; Genetic Variation ; Genetics, Population ; Geography ; Likelihood Functions ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Phylogeny ; Rhipicephalus/classification/*genetics ; South Africa ; }, abstract = {Rhipicephalus microplus and R. decoloratus are one-host ticks that preferentially feed on cattle. They are capable of transmitting various tick-borne pathogens which may be detrimental to the agricultural and livestock industry in South Africa. Previous studies have shown that R. microplus forms five lineages in the R. microplus complex, segregating into different geographical areas based on mitochondrial markers. This study examined the phylogenetic relationship within and between R. microplus and R. decoloratus using the nuclear internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome oxidase subunit I (COI) genes. The results showed that the nuclear ITS2 marker is informative for interspecific variation but lacks the resolution for intraspecific variation. Analysis of the mitochondrial COI gene revealed that R. microplus ticks from South Africa grouped into a clade comprised of ticks from Asia and South America. The population structure of these two tick species was also investigated using novel microsatellite markers. Population structure analyses revealed that both the R. microplus and R. decoloratus populations presented with two genetic clusters. Rhipicephalus microplus ticks from the Kwa-Zulu Natal (KZN) province belonged to cluster 1, and those from the Eastern Cape (EC) province predominantly grouped into cluster 2. No observable population structure was noted for R. decoloratus. The overlap of genetic clusters in both species could be attributed to inbreeding between the regions by unrestricted movement of cattle across provinces. Such movement promotes tick mobility, gene flow and the homogenisation of tick populations.}, }
@article {pmid30102371, year = {2018}, author = {Hillebrand, A and Matz, JM and Almendinger, M and Müller, K and Matuschewski, K and Schmitz-Linneweber, C}, title = {Identification of clustered organellar short (cos) RNAs and of a conserved family of organellar RNA-binding proteins, the heptatricopeptide repeat proteins, in the malaria parasite.}, journal = {Nucleic acids research}, volume = {46}, number = {19}, pages = {10417-10431}, pmid = {30102371}, issn = {1362-4962}, mesh = {Chloroplasts/genetics ; Genome/genetics ; Malaria, Falciparum/*genetics/parasitology ; Mitochondria/chemistry/genetics ; Organelles/*genetics ; Peptides/chemistry/genetics ; Phylogeny ; Plasmodium falciparum/*genetics/pathogenicity ; RNA, Ribosomal/chemistry/genetics ; RNA-Binding Proteins/chemistry/*genetics ; Ribosomes/chemistry/genetics ; }, abstract = {Gene expression in mitochondria of Plasmodium falciparum is essential for parasite survival. The molecular mechanisms of Plasmodium organellar gene expression remain poorly understood. This includes the enigmatic assembly of the mitochondrial ribosome from highly fragmented rRNAs. Here, we present the identification of clustered organellar short RNA fragments (cosRNAs) that are possible footprints of RNA-binding proteins (RBPs) in Plasmodium organelles. In plants, RBPs of the pentatricopeptide repeat (PPR) class produce footprints as a consequence of their function in processing organellar RNAs. Intriguingly, many of the Plasmodium cosRNAs overlap with 5'-ends of rRNA fragments. We hypothesize that these are footprints of RBPs involved in assembling the rRNA fragments into a functioning ribosome. A bioinformatics search of the Plasmodium nuclear genome identified a hitherto unrecognized organellar helical-hairpin-repeat protein family that we term heptatricopeptide repeat (HPR) proteins. We demonstrate that selected HPR proteins are targeted to mitochondria in P. berghei and that one of them, PbHPR1, associates with RNA, but not DNA in vitro. A phylogenetic search identified HPR proteins in a wide variety of eukaryotes. We hypothesize that HPR proteins are required for processing and stabilizing RNAs in Apicomplexa and other taxa.}, }
@article {pmid30097722, year = {2018}, author = {Ding, CQ and Ng, S and Wang, L and Wang, YC and Li, NN and Hao, XY and Zeng, JM and Wang, XC and Yang, YJ}, title = {Genome-wide identification and characterization of ALTERNATIVE OXIDASE genes and their response under abiotic stresses in Camellia sinensis (L.) O. Kuntze.}, journal = {Planta}, volume = {248}, number = {5}, pages = {1231-1247}, pmid = {30097722}, issn = {1432-2048}, support = {1610212017003//Central Public-interest Scientific Institution Basal Research Fund/ ; CARS-19//Earmarked Fund for China Agriculture Research System/ ; 2016C02053-4//The Major Project of Agricultural Science and Technology in Breeding of Tea Plant Variety in Zhejiang Province/ ; ALTF1239-2015//European Molecular Biology Organization/ ; LTFCOFUND2013//FP PEOPLE: Marie cutie actions/ ; GA-2013-609409//FP PEOPLE: Marie cutie actions/ ; }, mesh = {Camellia sinensis/enzymology/*genetics/physiology ; Cloning, Molecular ; Conserved Sequence/genetics ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Mitochondrial Proteins/*genetics/physiology ; Oxidoreductases/*genetics/physiology ; Phylogeny ; Plant Proteins/*genetics/physiology ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Stress, Physiological ; Transcriptome ; }, abstract = {Four typical ALTERNATIVE OXIDASE genes have been identified in tea plants, and their sequence features and gene expression profiles have provided useful information for further studies on function and regulation. Alternative oxidase (AOX) is a terminal oxidase located in the respiratory electron transport chain. AOX catalyzes the oxidation of quinol and the reduction of oxygen into water. In this study, a genome-wide search and subsequent DNA cloning were performed to identify and characterize AOX genes in tea plant (Camellia sinensis (L.) O. Kuntze cv. Longjing43). Our results showed that tea plant possesses four AOX genes, i.e., CsAOX1a, CsAOX1d, CsAOX2a and CsAOX2b. Gene structure and protein sequence analyses revealed that all CsAOXs share a four-exon/three-intron structure with highly conserved regions and amino acid residues, which are necessary for AOX secondary structures, catalytic activities and post-translational regulations. All CsAOX were shown to localize in mitochondria using the green fluorescent protein (GFP)-targeting assay. Both CsAOX1a and CsAOX1d were induced by cold, salt and drought stresses, and with different expression patterns in young and mature leaves. Reactive oxygen species (ROS) accumulated strongly after 72 and 96 h cold treatments in both young and mature leaves, while the polyphenol and total catechin decreased significantly only in mature leaves. In comparison to AtAOX1a in Arabidopsis thaliana, CsAOX1a lost almost all of the stress-responsive cis-acting regulatory elements in its promoter region (1500 bp upstream), but possesses a flavonoid biosynthesis-related MBSII cis-acting regulatory element. These results suggest a link between CsAOX1a function and the metabolism of some secondary metabolites in tea plant. Our studies provide a basis for the further elucidation of the biological function and regulation of the AOX pathway in tea plants.}, }
@article {pmid30086814, year = {2018}, author = {Yurchenko, V and Lukeš, J}, title = {Parasites and their (endo)symbiotic microbes.}, journal = {Parasitology}, volume = {145}, number = {10}, pages = {1261-1264}, doi = {10.1017/S0031182018001257}, pmid = {30086814}, issn = {1469-8161}, mesh = {Animals ; Biological Evolution ; Organelles ; Parasites/*microbiology ; *Symbiosis ; }, abstract = {Thanks to modern molecular biology methods, our understanding of the impact of (endo)symbiotic bacteria on parasitic protists and helminths is growing fast. In this issue, 9 papers have been brought together that describe various facets of the relationships between these microorganisms, reveal their range and high frequency, as well as their capacity to create novel biological complexity. Comparative analyses of these host-endosymbiont interactions indicate that there may be no discrete types of relationships but rather a continuum ranging from a dispensable endosymbiont minimally integrated within the host cell to organelles, such as mitochondria and plastids that evolved into an indispensable, deeply integrated components of the cell. We hope that this series of studies on parasites and (endo)symbiotic bacteria will increase awareness about these relationships and their representation in microbial ecology models.}, }
@article {pmid30086701, year = {2018}, author = {Skoracka, A and Lopes, LF and Alves, MJ and Miller, A and Lewandowski, M and Szydło, W and Majer, A and Różańska, E and Kuczyński, L}, title = {Genetics of lineage diversification and the evolution of host usage in the economically important wheat curl mite, Aceria tosichella Keifer, 1969.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {122}, pmid = {30086701}, issn = {1471-2148}, support = {No. 01/KNOW2/2014//Funding for open access charge: Ministry of Science and Higher Education of the Republic of Poland, from the quality promoting subsidy, under the Leading National Research Centre (KNOW) program for the years 2014-2019/International ; 2011/03/B/NZ8/00129//Narodowe Centrum Nauki/International ; 2011/01/N/NZ8/04540//Narodowe Centrum Nauki/International ; UID/BIA/00329/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/International ; UID/BIA/00329/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/International ; }, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Calibration ; DNA, Mitochondrial/genetics ; Demography ; Gene Flow ; Genetic Variation ; Host-Pathogen Interactions/*genetics ; Mites/*classification/*genetics ; Mitochondria/genetics ; *Phylogeny ; Plant Diseases/*parasitology ; Time Factors ; Triticum/*parasitology ; }, abstract = {BACKGROUND: Understanding the mechanisms that underlie the diversification of herbivores through interactions with their hosts is important for their diversity assessment and identification of expansion events, particularly in a human-altered world where evolutionary processes can be exacerbated. We studied patterns of host usage and genetic structure in the wheat curl mite complex (WCM), Aceria tosichella, a major pest of the world's grain industry, to identify the factors behind its extensive diversification.<br><br>RESULTS: We expanded on previous phylogenetic research, demonstrating deep lineage diversification within the taxon, a complex of distinctive host specialist and generalist lineages more diverse than previously assumed. Time-calibrated phylogenetic reconstruction inferred from mitochondrial DNA sequence data suggests that lineage diversification pre-dates the influence of agricultural practices, and lineages started to radiate in the mid Miocene when major radiations of C4 grasses is known to have occurred. Furthermore, we demonstrated that host specificity is not phylogenetically constrained, while host generalization appears to be a more derived trait coinciding with the expansion of the world's grasslands. Demographic history of specialist lineages have been more stable when compared to generalists, and their expansion pre-dated all generalist lineages. The lack of host-associated genetic structure of generalists indicates gene flow between mite populations from different hosts.<br><br>CONCLUSIONS: Our analyses demonstrated that WCM is an unexpectedly diverse complex of genetic lineages and its differentiation is likely associated with the time of diversification and expansion of its hosts. Signatures of demographic histories and expansion of generalists are consistent with the observed proliferation of the globally most common lineages. The apparent lack of constrains on host use, coupled with a high colonization potential, hinders mite management, which may be further compromised by host range expansion. This study provides a significant contribution to the growing literature on host-association and diversification in herbivorous invertebrates.}, }
@article {pmid30076323, year = {2018}, author = {Duong, NT and Macholdt, E and Ton, ND and Arias, L and Schröder, R and Van Phong, N and Thi Bich Thuy, V and Ha, NH and Thi Thu Hue, H and Thi Xuan, N and Thi Phuong Oanh, K and Hien, LTT and Hoang, NH and Pakendorf, B and Stoneking, M and Van Hai, N}, title = {Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {11651}, pmid = {30076323}, issn = {2045-2322}, mesh = {Asia, Southeastern ; Asian People/genetics ; Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/*genetics ; Ethnicity/genetics ; *Genetics, Population ; Haplotypes ; Humans ; Mitochondria/genetics ; Phylogeny ; *Phylogeography ; Taiwan ; Whole Genome Sequencing ; }, abstract = {Vietnam is an important crossroads within Mainland Southeast Asia (MSEA) and a gateway to Island Southeast Asia, and as such exhibits high levels of ethnolinguistic diversity. However, comparatively few studies have been undertaken of the genetic diversity of Vietnamese populations. In order to gain comprehensive insights into MSEA mtDNA phylogeography, we sequenced 609 complete mtDNA genomes from individuals belonging to five language families (Austroasiatic, Tai-Kadai, Hmong-Mien, Sino-Tibetan and Austronesian) and analyzed them in comparison with sequences from other MSEA countries and Taiwan. Within Vietnam, we identified 399 haplotypes belonging to 135 haplogroups; among the five language families, the sequences from Austronesian groups differ the most from the other groups. Phylogenetic analysis revealed 111 novel Vietnamese mtDNA lineages. Bayesian estimates of coalescence times and associated 95% HPD for these show a peak of mtDNA diversification around 2.5-3 kya, which coincides with the Dong Son culture, and thus may be associated with the agriculturally-driven expansion of this culture. Networks of major MSEA haplogroups emphasize the overall distinctiveness of sequences from Taiwan, in keeping with previous studies that suggested at most a minor impact of the Austronesian expansion from Taiwan on MSEA. We also see evidence for population expansions across MSEA geographic regions and language families.}, }
@article {pmid30075756, year = {2018}, author = {Burke, SV and Ungerer, MC and Duvall, MR}, title = {Investigation of mitochondrial-derived plastome sequences in the Paspalum lineage (Panicoideae; Poaceae).}, journal = {BMC plant biology}, volume = {18}, number = {1}, pages = {152}, pmid = {30075756}, issn = {1471-2229}, support = {DEB-1120856//National Science Foundation/ ; DEB-1120761//National Science Foundation/ ; }, mesh = {DNA, Intergenic/genetics ; DNA, Plant/genetics ; Mitochondria/*genetics ; Paspalum/*genetics ; Phylogeny ; Plastids/*genetics ; Poaceae/genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {BACKGROUND: The grass family (Poaceae), ca. 12,075 species, is a focal point of many recent studies that aim to use complete plastomes to reveal and strengthen relationships within the family. The use of Next Generation Sequencing technology has revealed intricate details in many Poaceae plastomes; specifically the trnI - trnL intergenic spacer region. This study investigates this region and the putative mitochondrial inserts within it in complete plastomes of Paspalum and other Poaceae.<br><br>RESULTS: Nine newly sequenced plastomes, seven of which contain an insert within the trnI - trnL intergenic spacer, were combined into plastome phylogenomic and divergence date analyses with 52 other species. A robust Paspalum topology was recovered, originating at 10.6&#xa0;Ma, with the insert arising at 8.7&#xa0;Ma. The alignment of the insert across Paspalum reveals 21 subregions with pairwise homology in 19. In an analysis of emergent self-organizing maps of tetranucleotide frequencies, the Paspalum insert grouped with mitochondrial DNA.<br><br>CONCLUSIONS: A hypothetical ancestral insert, 17,685&#xa0;bp in size, was found in the trnI - trnL intergenic spacer for the Paspalum lineage. A different insert, 2808&#xa0;bp, was found in the same region for Paraneurachne muelleri. Seven different intrastrand deletion events were found within the Paspalum lineage, suggesting selective pressures to remove large portions of noncoding DNA. Finally, a tetranucleotide frequency analysis was used to determine that the origin of the insert in the Paspalum lineage is mitochondrial DNA.}, }
@article {pmid30074999, year = {2018}, author = {Brew-Appiah, RAT and York, ZB and Krishnan, V and Roalson, EH and Sanguinet, KA}, title = {Genome-wide identification and analysis of the ALTERNATIVE OXIDASE gene family in diploid and hexaploid wheat.}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0201439}, pmid = {30074999}, issn = {1932-6203}, mesh = {Aegilops/*genetics ; Diploidy ; Gene Expression Regulation, Developmental/physiology ; Gene Expression Regulation, Plant/physiology ; Genes, Plant/*genetics ; Genome, Plant/genetics ; Herbicide Resistance/genetics ; Mitochondrial Proteins/*genetics ; Multigene Family/*genetics ; Oxidoreductases/*genetics ; Phylogeny ; Plant Proteins/*genetics ; Polyploidy ; Stress, Physiological/physiology ; Triticum/genetics/*physiology ; Whole Genome Sequencing ; }, abstract = {A comprehensive understanding of wheat responses to environmental stress will contribute to the long-term goal of feeding the planet. ALERNATIVE OXIDASE (AOX) genes encode proteins involved in a bypass of the electron transport chain and are also known to be involved in stress tolerance in multiple species. Here, we report the identification and characterization of the AOX gene family in diploid and hexaploid wheat. Four genes each were found in the diploid ancestors Triticum urartu, and Aegilops tauschii, and three in Aegilops speltoides. In hexaploid wheat (Triticum aestivum), 20 genes were identified, some with multiple splice variants, corresponding to a total of 24 proteins for those with observed transcription and translation. These proteins were classified as AOX1a, AOX1c, AOX1e or AOX1d via phylogenetic analysis. Proteins lacking most or all signature AOX motifs were assigned to putative regulatory roles. Analysis of protein-targeting sequences suggests mixed localization to the mitochondria and other organelles. In comparison to the most studied AOX from Trypanosoma brucei, there were amino acid substitutions at critical functional domains indicating possible role divergence in wheat or grasses in general. In hexaploid wheat, AOX genes were expressed at specific developmental stages as well as in response to both biotic and abiotic stresses such as fungal pathogens, heat and drought. These AOX expression patterns suggest a highly regulated and diverse transcription and expression system. The insights gained provide a framework for the continued and expanded study of AOX genes in wheat for stress tolerance through breeding new varieties, as well as resistance to AOX-targeted herbicides, all of which can ultimately be used synergistically to improve crop yield.}, }
@article {pmid30071112, year = {2018}, author = {Caza, M and Hu, G and Nielson, ED and Cho, M and Jung, WH and Kronstad, JW}, title = {The Sec1/Munc18 (SM) protein Vps45 is involved in iron uptake, mitochondrial function and virulence in the pathogenic fungus Cryptococcus neoformans.}, journal = {PLoS pathogens}, volume = {14}, number = {8}, pages = {e1007220}, pmid = {30071112}, issn = {1553-7374}, support = {R01 AI053721/AI/NIAID NIH HHS/United States ; MOP13234/CAPMC/CIHR/Canada ; }, mesh = {Animals ; Biological Transport ; Cryptococcosis/metabolism/microbiology/pathology ; *Cryptococcus neoformans/genetics/metabolism/pathogenicity ; Female ; Fungal Proteins/*physiology ; Iron/*metabolism ; Mice ; Mice, Inbred BALB C ; Mitochondria/*physiology ; Organisms, Genetically Modified ; Phylogeny ; Virulence/*genetics ; Virulence Factors/genetics/*physiology ; }, abstract = {The battle for iron between invading microorganisms and mammalian hosts is a pivotal determinant of the outcome of infection. The pathogenic fungus, Cryptococcus neoformans, employs multiple mechanisms to compete for iron during cryptococcosis, a disease primarily of immunocompromised hosts. In this study, we examined the role of endocytic trafficking in iron uptake by characterizing a mutant defective in the Sec1/Munc18 (SM) protein Vps45. This protein is known to regulate the machinery for vesicle trafficking and fusion via interactions with SNARE proteins. As expected, a vps45 deletion mutant was impaired in endocytosis and showed sensitivity to trafficking inhibitors. The mutant also showed poor growth on iron-limited media and a defect in transporting the Cfo1 ferroxidase of the high-affinity iron uptake system from the plasma membrane to the vacuole. Remarkably, we made the novel observation that Vps45 also contributes to mitochondrial function in that a Vps45-Gfp fusion protein associated with mitotracker, and a vps45 mutant showed enhanced sensitivity to inhibitors of electron transport complexes as well as changes in mitochondrial membrane potential. Consistent with mitochondrial function, the vps45 mutant was impaired in calcium homeostasis. To assess the relevance of these defects for virulence, we examined cell surface properties of the vps45 mutant and found increased sensitivity to agents that challenge cell wall integrity and to antifungal drugs. A change in cell wall properties was consistent with our observation of altered capsule polysaccharide attachment, and with attenuated virulence in a mouse model of cryptococcosis. Overall, our studies reveal a novel role for Vps45-mediated trafficking for iron uptake, mitochondrial function and virulence.}, }
@article {pmid30071011, year = {2018}, author = {Grinter, R and Hay, ID and Song, J and Wang, J and Teng, D and Dhanesakaran, V and Wilksch, JJ and Davies, MR and Littler, D and Beckham, SA and Henderson, IR and Strugnell, RA and Dougan, G and Lithgow, T}, title = {FusC, a member of the M16 protease family acquired by bacteria for iron piracy against plants.}, journal = {PLoS biology}, volume = {16}, number = {8}, pages = {e2006026}, pmid = {30071011}, issn = {1545-7885}, support = {106077/Z/14/Z//Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/metabolism ; Bacterial Outer Membrane Proteins/metabolism ; Bacterial Proteins/metabolism ; Ferredoxins/metabolism ; Iron/*metabolism ; Membrane Transport Proteins/*metabolism ; Metalloendopeptidases/metabolism ; Pectobacterium/*metabolism ; Phylogeny ; Plant Proteins/metabolism ; Plants/metabolism ; Protein Transport/physiology ; Mitochondrial Processing Peptidase ; }, abstract = {Iron is essential for life. Accessing iron from the environment can be a limiting factor that determines success in a given environmental niche. For bacteria, access of chelated iron from the environment is often mediated by TonB-dependent transporters (TBDTs), which are β-barrel proteins that form sophisticated channels in the outer membrane. Reports of iron-bearing proteins being used as a source of iron indicate specific protein import reactions across the bacterial outer membrane. The molecular mechanism by which a folded protein can be imported in this way had remained mysterious, as did the evolutionary process that could lead to such a protein import pathway. How does the bacterium evolve the specificity factors that would be required to select and import a protein encoded on another organism's genome? We describe here a model whereby the plant iron-bearing protein ferredoxin can be imported across the outer membrane of the plant pathogen Pectobacterium by means of a Brownian ratchet mechanism, thereby liberating iron into the bacterium to enable its growth in plant tissues. This import pathway is facilitated by FusC, a member of the same protein family as the mitochondrial processing peptidase (MPP). The Brownian ratchet depends on binding sites discovered in crystal structures of FusC that engage a linear segment of the plant protein ferredoxin. Sequence relationships suggest that the bacterial gene encoding FusC has previously unappreciated homologues in plants and that the protein import mechanism employed by the bacterium is an evolutionary echo of the protein import pathway in plant mitochondria and plastids.}, }
@article {pmid30067212, year = {2018}, author = {Barthole, G}, title = {[Never alone. Microorganism, ecology, evolution].}, journal = {Medecine sciences : M/S}, volume = {34}, number = {6-7}, pages = {604-607}, doi = {10.1051/medsci/20183406023}, pmid = {30067212}, issn = {1958-5381}, mesh = {Animals ; *Biological Evolution ; Civilization ; *Ecosystem ; Endophytes/*physiology ; Host Microbial Interactions/physiology ; Humans ; Microbial Interactions/physiology ; Mitochondria/physiology ; Plants/microbiology ; Symbiosis/*physiology ; }, }
@article {pmid30063873, year = {2019}, author = {Kumar Jadav, K and Pratap Singh, A and Srivastav, AB and Sarkhel, BC}, title = {Molecular characterization of the complete mitochondrial genome sequence of Indian wild pig (Sus scrofa cristatus).}, journal = {Animal biotechnology}, volume = {30}, number = {2}, pages = {186-191}, doi = {10.1080/10495398.2018.1469506}, pmid = {30063873}, issn = {1532-2378}, mesh = {Animals ; Breeding ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing/veterinary ; Male ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Sus scrofa/*genetics ; }, abstract = {The Indian wild pig is a sub-species (Sus scrofa cristatus) which is different from the other pig breeds and is protected under Schedule-III of the Indian Wildlife (Protection) Act, 1972. In this study, complete mitogenome of two Indian wild pigs was sequenced and characterized by shotgun sequencing and de novo assembly, which revealed sequence size of 16,738 and 16,251 bp, respectively, (Accession no. MG725630 and MG725631). The mitogenome sequence in this study displayed 98% homology with previously reported mitogenome of pigs from different parts of the world. Mitogenome analysis by MITOS Web server revealed similarity of gene organization with the other vertebrates (13 protein-coding, 22 tRNAs, 2 rRNAs genes, and a control region). The mitogenomic sequences of Indian wild pig maintained a separate clade in the phylogenetic tree constructed by using 62 whole mitogenome sequences across the world. The phylogeny derived from mitogenomic sequences revealed distinct separate European-American and Asiatic pig clades. It was concluded that whole mitogenome sequencing using NGS without designing mitogenome-specific primer for amplification, is possible thereby reducing the cost and labor. This study is the first report of complete sequence of mitogenome of Indian wild pig.}, }
@article {pmid30061407, year = {2018}, author = {Nagano, H and Hashimoto, N and Nakayama, A and Suzuki, S and Miyabayashi, Y and Yamato, A and Higuchi, S and Fujimoto, M and Sakuma, I and Beppu, M and Yokoyama, M and Suzuki, Y and Sugano, S and Ikeda, K and Tatsuno, I and Manabe, I and Yokote, K and Inoue, S and Tanaka, T}, title = {p53-inducible DPYSL4 associates with mitochondrial supercomplexes and regulates energy metabolism in adipocytes and cancer cells.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {33}, pages = {8370-8375}, pmid = {30061407}, issn = {1091-6490}, mesh = {Adenosine Triphosphate/biosynthesis ; Adipocytes/*metabolism ; Animals ; Cell Line, Tumor ; *Energy Metabolism ; Humans ; Male ; Mice ; Mice, SCID ; Mitochondria/*metabolism ; Neoplasms/*metabolism ; Nerve Tissue Proteins/*physiology ; Obesity/metabolism ; Oxygen Consumption ; Tumor Suppressor Protein p53/*physiology ; Tumor Suppressor Proteins/physiology ; }, abstract = {The tumor suppressor p53 regulates multiple cellular functions, including energy metabolism. Metabolic deregulation is implicated in the pathogenesis of some cancers and in metabolic disorders and may result from the inactivation of p53 functions. Using RNA sequencing and ChIP sequencing of cancer cells and preadipocytes, we demonstrate that p53 modulates several metabolic processes via the transactivation of energy metabolism genes including dihydropyrimidinase-like 4 (DPYSL4). DPYSL4 is a member of the collapsin response mediator protein family, which is involved in cancer invasion and progression. Intriguingly, DPYSL4 overexpression in cancer cells and preadipocytes up-regulated ATP production and oxygen consumption, while DPYSL4 knockdown using siRNA or CRISPR/Cas9 down-regulated energy production. Furthermore, DPYSL4 was associated with mitochondrial supercomplexes, and deletion of its dihydropyrimidinase-like domain abolished its association and its ability to stimulate ATP production and suppress the cancer cell invasion. Mouse-xenograft and lung-metastasis models indicated that DPYSL4 expression compromised tumor growth and metastasis in vivo. Consistently, database analyses demonstrated that low DPYSL4 expression was significantly associated with poor survival of breast and ovarian cancers in accordance with its reduced expression in certain types of cancer tissues. Moreover, immunohistochemical analysis using the adipose tissue of obese patients revealed that DPYSL4 expression was positively correlated with INFg and body mass index in accordance with p53 activation. Together, these results suggest that DPYSL4 plays a key role in the tumor-suppressor function of p53 by regulating oxidative phosphorylation and the cellular energy supply via its association with mitochondrial supercomplexes, possibly linking to the pathophysiology of both cancer and obesity.}, }
@article {pmid30060189, year = {2018}, author = {Río Bártulos, C and Rogers, MB and Williams, TA and Gentekaki, E and Brinkmann, H and Cerff, R and Liaud, MF and Hehl, AB and Yarlett, NR and Gruber, A and Kroth, PG and van der Giezen, M}, title = {Mitochondrial Glycolysis in a Major Lineage of Eukaryotes.}, journal = {Genome biology and evolution}, volume = {10}, number = {9}, pages = {2310-2325}, pmid = {30060189}, issn = {1759-6653}, support = {//Wellcome Trust/United Kingdom ; 078566/A/05/Z//Wellcome Trust/United Kingdom ; }, mesh = {Biological Evolution ; Blastocystis/cytology/enzymology/genetics/*metabolism ; Diatoms/cytology/enzymology/genetics/*metabolism ; Energy Metabolism ; Genome, Mitochondrial ; *Glycolysis ; Mitochondria/genetics/*metabolism ; Symbiosis ; Transformation, Genetic ; }, abstract = {The establishment of the mitochondrion is seen as a transformational step in the origin of eukaryotes. With the mitochondrion came bioenergetic freedom to explore novel evolutionary space leading to the eukaryotic radiation known today. The tight integration of the bacterial endosymbiont with its archaeal host was accompanied by a massive endosymbiotic gene transfer resulting in a small mitochondrial genome which is just a ghost of the original incoming bacterial genome. This endosymbiotic gene transfer resulted in the loss of many genes, both from the bacterial symbiont as well the archaeal host. Loss of genes encoding redundant functions resulted in a replacement of the bulk of the host's metabolism for those originating from the endosymbiont. Glycolysis is one such metabolic pathway in which the original archaeal enzymes have been replaced by bacterial enzymes from the endosymbiont. Glycolysis is a major catabolic pathway that provides cellular energy from the breakdown of glucose. The glycolytic pathway of eukaryotes appears to be bacterial in origin, and in well-studied model eukaryotes it takes place in the cytosol. In contrast, here we demonstrate that the latter stages of glycolysis take place in the mitochondria of stramenopiles, a diverse and ecologically important lineage of eukaryotes. Although our work is based on a limited sample of stramenopiles, it leaves open the possibility that the mitochondrial targeting of glycolytic enzymes in stramenopiles might represent the ancestral state for eukaryotes.}, }
@article {pmid30059499, year = {2018}, author = {Gao, B and Peng, C and Chen, Q and Zhang, J and Shi, Q}, title = {Mitochondrial genome sequencing of a vermivorous cone snail Conus quercinus supports the correlative analysis between phylogenetic relationships and dietary types of Conus species.}, journal = {PloS one}, volume = {13}, number = {7}, pages = {e0193053}, pmid = {30059499}, issn = {1932-6203}, mesh = {Animals ; Annelida ; Base Composition ; Base Sequence ; Biological Evolution ; Chromosome Mapping ; Conotoxins/*genetics ; Conus Snail/classification/*genetics ; Food Chain ; Gene Ontology ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Open Reading Frames ; Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Transfer/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Tandem Repeat Sequences ; }, abstract = {Complete mitochondrial genome (mitogenome) sequence of a worm-hunting cone snail, Conus quercinus, was reported in this study. Its mitogenome, the longest one (16,460 bp) among reported Conus specie, is composed of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one D-loop region. The mitochondrial gene arrangement is highly-conserved and identical to other reported. However, the D-loop region of C. quercinus is the longest (943 bp) with the higher A+T content (71.3%) and a long AT tandem repeat stretch (68 bp). Subsequent phylogenetic analysis demonstrated that three different dietary types (vermivorous, molluscivorous and piscivorous) of cone snails are clustered separately, suggesting that the phylogenetics of cone snails is related to their dietary types. In conclusion, our current work improves our understanding of the mitogenomic structure and evolutionary status of the vermivorous C. quercinus, which support the putative hypothesis that the Conus ancestor was vermivorous.}, }
@article {pmid30057120, year = {2018}, author = {Zhang, Q and Wu, X and Chen, P and Liu, L and Xin, N and Tian, Y and Dillin, A}, title = {The Mitochondrial Unfolded Protein Response Is Mediated Cell-Non-autonomously by Retromer-Dependent Wnt Signaling.}, journal = {Cell}, volume = {174}, number = {4}, pages = {870-883.e17}, pmid = {30057120}, issn = {1097-4172}, support = {P40 OD010440/OD/NIH HHS/United States ; R01 ES021667/ES/NIEHS NIH HHS/United States ; R37 AG024365/AG/NIA NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Animals, Genetically Modified/genetics/growth &amp; development/*metabolism ; Caenorhabditis elegans/genetics/growth &amp; development/*metabolism ; Caenorhabditis elegans Proteins/genetics/*metabolism ; Carrier Proteins/genetics/metabolism ; Glycoproteins/genetics/metabolism ; Intracellular Signaling Peptides and Proteins ; Mitochondria/genetics/*metabolism ; Neurons/cytology/metabolism ; Polyubiquitin/*metabolism ; Unfolded Protein Response/*physiology ; Vesicular Transport Proteins/genetics/metabolism ; Wnt Proteins/genetics/*metabolism ; }, abstract = {The mitochondrial unfolded protein response (UPR[mt]) can be triggered in a cell-non-autonomous fashion across multiple tissues in response to mitochondrial dysfunction. The ability to communicate information about the presence of mitochondrial stress enables a global response that can ultimately better protect an organism from local mitochondrial challenges. We find that animals use retromer-dependent Wnt signaling to propagate mitochondrial stress signals from the nervous system to peripheral tissues. Specifically, the polyQ40-triggered activation of mitochondrial stress or reduction of cco-1 (complex IV subunit) in neurons of C. elegans results in the Wnt-dependent induction of cell-non-autonomous UPR[mt] in peripheral cells. Loss-of-function mutations of retromer complex components that are responsible for recycling the Wnt secretion-factor/MIG-14 prevent Wnt secretion and thereby suppress cell-non-autonomous UPR[mt]. Neuronal expression of the Wnt ligand/EGL-20 is sufficient to induce cell-non-autonomous UPR[mt] in a retromer complex-, Wnt signaling-, and serotonin-dependent manner, clearly implicating Wnt signaling as a strong candidate for the "mitokine" signal.}, }
@article {pmid30056805, year = {2018}, author = {Seixas, FA and Boursot, P and Melo-Ferreira, J}, title = {The genomic impact of historical hybridization with massive mitochondrial DNA introgression.}, journal = {Genome biology}, volume = {19}, number = {1}, pages = {91}, pmid = {30056805}, issn = {1474-760X}, support = {FCT-ANR/BIA-EVF/0250/2012//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/International ; IF/00033/2014/CP1256/CT0005//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/International ; SFRH/BD/87126/2012//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/International ; ANR-12-ISV7-0002-01//Agence Nationale de la Recherche/International ; NORTE-01-0145-FEDER-000007//NORTE2020, ERDF/International ; }, mesh = {Adaptation, Biological/genetics ; *Animal Migration ; Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Europe ; Genetics, Population ; *Genome ; *Hybridization, Genetic ; Lagomorpha/classification/*genetics ; Mitochondria/genetics ; Models, Genetic ; Phylogeny ; Recombination, Genetic ; Selection, Genetic ; Whole Genome Sequencing ; X Chromosome/chemistry ; }, abstract = {BACKGROUND: The extent to which selection determines interspecific patterns of genetic exchange enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their invasion front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, Lepus granatensis, displays in its northern range extensive mitochondrial DNA introgression from L. timidus, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA.<br><br>RESULTS: Although the average nuclear and mtDNA introgression patterns contrast strongly, they fit a single demographic&#xa0;model of post-glacial invasive replacement of timidus by granatensis. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X chromosome and in low recombining regions.<br><br>CONCLUSIONS: General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits.}, }
@article {pmid30055354, year = {2018}, author = {Linard, B and Crampton-Platt, A and Moriniere, J and Timmermans, MJTN and Andújar, C and Arribas, P and Miller, KE and Lipecki, J and Favreau, E and Hunter, A and Gómez-Rodríguez, C and Barton, C and Nie, R and Gillett, CPDT and Breeschoten, T and Bocak, L and Vogler, AP}, title = {The contribution of mitochondrial metagenomics to large-scale data mining and phylogenetic analysis of Coleoptera.}, journal = {Molecular phylogenetics and evolution}, volume = {128}, number = {}, pages = {1-11}, doi = {10.1016/j.ympev.2018.07.008}, pmid = {30055354}, issn = {1095-9513}, mesh = {Algorithms ; Animals ; Base Sequence ; Coleoptera/classification/*genetics ; Databases, Genetic ; *Metagenomics ; Mitochondria/*genetics ; *Phylogeny ; }, abstract = {A phylogenetic tree at the species level is still far off for highly diverse insect orders, including the Coleoptera, but the taxonomic breadth of public sequence databases is growing. In addition, new types of data may contribute to increasing taxon coverage, such as metagenomic shotgun sequencing for assembly of mitogenomes from bulk specimen samples. The current study explores the application of these techniques for large-scale efforts to build the tree of Coleoptera. We used shotgun data from 17 different ecological and taxonomic datasets (5 unpublished) to assemble a total of 1942 mitogenome contigs of >3000 bp. These sequences were combined into a single dataset together with all mitochondrial data available at GenBank, in addition to nuclear markers widely used in molecular phylogenetics. The resulting matrix of nearly 16,000 species with two or more loci produced trees (RAxML) showing overall congruence with the Linnaean taxonomy at hierarchical levels from suborders to genera. We tested the role of full-length mitogenomes in stabilizing the tree from GenBank data, as mitogenomes might link terminals with non-overlapping gene representation. However, the mitogenome data were only partly useful in this respect, presumably because of the purely automated approach to assembly and gene delimitation, but improvements in future may be possible by using multiple assemblers and manual curation. In conclusion, the combination of data mining and metagenomic sequencing of bulk samples provided the largest phylogenetic tree of Coleoptera to date, which represents a summary of existing phylogenetic knowledge and a defensible tree of great utility, in particular for studies at the intra-familial level, despite some shortcomings for resolving basal nodes.}, }
@article {pmid30055249, year = {2018}, author = {Torrezan-Nitao, E and Figueiredo, RCBQ and Marques-Santos, LF}, title = {Mitochondrial permeability transition pore in sea urchin female gametes.}, journal = {Mechanisms of development}, volume = {154}, number = {}, pages = {208-218}, doi = {10.1016/j.mod.2018.07.008}, pmid = {30055249}, issn = {1872-6356}, mesh = {Animals ; Calcium/metabolism ; Cyclosporine/metabolism ; Female ; Germ Cells/*metabolism ; Membrane Potential, Mitochondrial/physiology ; Mitochondria/*metabolism/physiology ; Mitochondrial Membrane Transport Proteins/*metabolism ; Mitochondrial Permeability Transition Pore ; Sea Urchins/*metabolism/physiology ; }, abstract = {Mitochondrial permeability transition pore (MPTP) has been associated to calcium homeostasis and reactive oxygen species (ROS) generation in several cell types. While extensively investigated in somatic cells, there are few data regarding MPTP phenomenon in gametes. The aim of the present work was to investigate MPTP occurrence in sea urchin female gametes. The protonophores CCCP and FCCP, and the Ca[2+] ionophore ionomycin, were used as pore inductors. Pore opening was monitored by mitochondrial potential sensitive probes and cobalt-quenched calcein assay. The pore desensitizer cyclosporin A (CsA) prevented the loss of mitochondrial inner membrane potential (ΔΨm) and pore opening induced by MPTP activators. The disruption of ΔΨm led to an increase in ROS generation, which was completely prevented by CsA. Our data also demonstrated that the increase in ROS production induced by MPTP opening requires extracellular Ca[2+]. In summary, the current study provides evidence about the occurrence of MPTP in sea urchin eggs in a similar manner as described in vertebrate somatic cells - CsA-sensitive, voltage- and Ca[2+]-triggered - and shows MPTP as a highly conserved physiological event through the evolution.}, }
@article {pmid30046113, year = {2018}, author = {Dhir, A and Dhir, S and Borowski, LS and Jimenez, L and Teitell, M and Rötig, A and Crow, YJ and Rice, GI and Duffy, D and Tamby, C and Nojima, T and Munnich, A and Schiff, M and de Almeida, CR and Rehwinkel, J and Dziembowski, A and Szczesny, RJ and Proudfoot, NJ}, title = {Mitochondrial double-stranded RNA triggers antiviral signalling in humans.}, journal = {Nature}, volume = {560}, number = {7717}, pages = {238-242}, pmid = {30046113}, issn = {1476-4687}, support = {MC_UU_00008/8/MRC_/Medical Research Council/United Kingdom ; 107928/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 339270/ERC_/European Research Council/International ; R01 GM073981/GM/NIGMS NIH HHS/United States ; GM073981/GM/NIGMS NIH HHS/United States ; MC_UU_12010/8/MRC_/Medical Research Council/United Kingdom ; R01 GM114188/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; 107928/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; DEAD-box RNA Helicases/deficiency/genetics/metabolism ; Endoribonucleases/metabolism ; Exoribonucleases/deficiency/genetics/metabolism ; Gene Expression Regulation/immunology ; HeLa Cells ; Herpesvirus 1, Human/genetics/*immunology ; Humans ; Interferon Type I/antagonists &amp; inhibitors/immunology ; Interferon-Induced Helicase, IFIH1/metabolism ; Mice ; Mice, Inbred C57BL ; Multienzyme Complexes/metabolism ; Mutation ; Polyribonucleotide Nucleotidyltransferase/metabolism ; RNA Helicases/metabolism ; RNA, Double-Stranded/*immunology ; RNA, Mitochondrial/*immunology ; Single-Cell Analysis ; bcl-2 Homologous Antagonist-Killer Protein/metabolism ; bcl-2-Associated X Protein/metabolism ; }, abstract = {Mitochondria are descendants of endosymbiotic bacteria and retain essential prokaryotic features such as a compact circular genome. Consequently, in mammals, mitochondrial DNA is subjected to bidirectional transcription that generates overlapping transcripts, which are capable of forming long double-stranded RNA structures[1,2]. However, to our knowledge, mitochondrial double-stranded RNA has not been previously characterized in vivo. Here we describe the presence of a highly unstable native mitochondrial double-stranded RNA species at single-cell level and identify key roles for the degradosome components mitochondrial RNA helicase SUV3 and polynucleotide phosphorylase PNPase in restricting the levels of mitochondrial double-stranded RNA. Loss of either enzyme results in massive accumulation of mitochondrial double-stranded RNA that escapes into the cytoplasm in a PNPase-dependent manner. This process engages an MDA5-driven antiviral signalling pathway that triggers a type I interferon response. Consistent with these data, patients carrying hypomorphic mutations in the gene PNPT1, which encodes PNPase, display mitochondrial double-stranded RNA accumulation coupled with upregulation of interferon-stimulated genes and other markers of immune activation. The localization of PNPase to the mitochondrial inter-membrane space and matrix suggests that it has a dual role in preventing the formation and release of mitochondrial double-stranded RNA into the cytoplasm. This in turn prevents the activation of potent innate immune defence mechanisms that have evolved to protect vertebrates against microbial and viral attack.}, }
@article {pmid30042786, year = {2018}, author = {Riggs, CL and Summers, A and Warren, DE and Nilsson, GE and Lefevre, S and Dowd, WW and Milton, S and Podrabsky, JE}, title = {Small Non-coding RNA Expression and Vertebrate Anoxia Tolerance.}, journal = {Frontiers in genetics}, volume = {9}, number = {}, pages = {230}, pmid = {30042786}, issn = {1664-8021}, abstract = {Background: Extreme anoxia tolerance requires a metabolic depression whose modulation could involve small non-coding RNAs (small ncRNAs), which are specific, rapid, and reversible regulators of gene expression. A previous study of small ncRNA expression in embryos of the annual killifish Austrofundulus limnaeus, the most anoxia-tolerant vertebrate known, revealed a specific expression pattern of small ncRNAs that could play important roles in anoxia tolerance. Here, we conduct a comparative study on the presence and expression of small ncRNAs in the most anoxia-tolerant representatives of several major vertebrate lineages, to investigate the evolution of and mechanisms supporting extreme anoxia tolerance. The epaulette shark (Hemiscyllium ocellatum), crucian carp (Carassius carassius), western painted turtle (Chrysemys picta bellii), and leopard frog (Rana pipiens) were exposed to anoxia and recovery, and small ncRNAs were sequenced from the brain (one of the most anoxia-sensitive tissues) prior to, during, and following exposure to anoxia. Results: Small ncRNA profiles were broadly conserved among species under normoxic conditions, and these expression patterns were largely conserved during exposure to anoxia. In contrast, differentially expressed genes are mostly unique to each species, suggesting that each species may have evolved distinct small ncRNA expression patterns in response to anoxia. Mitochondria-derived small ncRNAs (mitosRNAs) which have a robust response to anoxia in A. limnaeus embryos, were identified in the other anoxia tolerant vertebrates here but did not display a similarly robust response to anoxia. Conclusion: These findings support an overall stabilization of the small ncRNA transcriptome during exposure to anoxic insults, but also suggest that multiple small ncRNA expression pathways may support anoxia tolerance, as no conserved small ncRNA response was identified among the anoxia-tolerant vertebrates studied. This may reflect divergent strategies to achieve the same endpoint: anoxia tolerance. However, it may also indicate that there are multiple cellular pathways that can trigger the same cellular and physiological survival processes, including hypometabolism.}, }
@article {pmid30042493, year = {2019}, author = {Lionnard, L and Duc, P and Brennan, MS and Kueh, AJ and Pal, M and Guardia, F and Mojsa, B and Damiano, MA and Mora, S and Lassot, I and Ravichandran, R and Cochet, C and Aouacheria, A and Potts, PR and Herold, MJ and Desagher, S and Kucharczak, J}, title = {TRIM17 and TRIM28 antagonistically regulate the ubiquitination and anti-apoptotic activity of BCL2A1.}, journal = {Cell death and differentiation}, volume = {26}, number = {5}, pages = {902-917}, pmid = {30042493}, issn = {1476-5403}, mesh = {Apoptosis/*genetics ; Cell Death/genetics ; Cell Line, Tumor ; Doxycycline/pharmacology ; Gene Expression Regulation, Neoplastic/drug effects ; Glycogen Synthase Kinase 3/genetics ; Humans ; Minor Histocompatibility Antigens/*genetics ; Neoplasms/drug therapy/*genetics/pathology ; Phosphorylation/genetics ; Proteasome Endopeptidase Complex/genetics ; Protein Binding/genetics ; Protein Stability ; Proteolysis/drug effects ; Proto-Oncogene Proteins c-bcl-2/*genetics ; Tripartite Motif Proteins/*genetics ; Tripartite Motif-Containing Protein 28/*genetics ; Ubiquitin-Protein Ligases/*genetics ; Ubiquitination/genetics ; }, abstract = {BCL2A1 is an anti-apoptotic member of the BCL-2 family that contributes to chemoresistance in a subset of tumors. BCL2A1 has a short half-life due to its constitutive processing by the ubiquitin-proteasome system. This constitutes a major tumor-suppressor mechanism regulating BCL2A1 function. However, the enzymes involved in the regulation of BCL2A1 protein stability are currently unknown. Here, we provide the first insight into the regulation of BCL2A1 ubiquitination. We present evidence that TRIM28 is an E3 ubiquitin-ligase for BCL2A1. Indeed, endogenous TRIM28 and BCL2A1 bind to each other at the mitochondria and TRIM28 knock-down decreases BCL2A1 ubiquitination. We also show that TRIM17 stabilizes BCL2A1 by blocking TRIM28 from binding and ubiquitinating BCL2A1, and that GSK3 is involved in the phosphorylation-mediated inhibition of BCL2A1 degradation. BCL2A1 and its close relative MCL1 are thus regulated by common factors but with opposite outcome. Finally, overexpression of TRIM28 or knock-out of TRIM17 reduced BCLA1 protein levels and restored sensitivity of melanoma cells to BRAF-targeted therapy. Therefore, our data describe a molecular rheostat in which two proteins of the TRIM family antagonistically regulate BCL2A1 stability and modulate cell death.}, }
@article {pmid30041026, year = {2018}, author = {Bogarín, D and Pérez-Escobar, OA and Groenenberg, D and Holland, SD and Karremans, AP and Lemmon, EM and Lemmon, AR and Pupulin, F and Smets, E and Gravendeel, B}, title = {Anchored hybrid enrichment generated nuclear, plastid and mitochondrial markers resolve the Lepanthes horrida (Orchidaceae: Pleurothallidinae) species complex.}, journal = {Molecular phylogenetics and evolution}, volume = {129}, number = {}, pages = {27-47}, doi = {10.1016/j.ympev.2018.07.014}, pmid = {30041026}, issn = {1095-9513}, mesh = {Cell Nucleus/*genetics ; Cluster Analysis ; Databases, Genetic ; Flowers/anatomy &amp; histology ; Genetic Loci ; Genetic Markers ; *Hybridization, Genetic ; Likelihood Functions ; Mitochondria/*genetics ; Orchidaceae/*genetics ; Phylogeny ; Plastids/*genetics ; Species Specificity ; }, abstract = {Phylogenetic relationships in species complexes and lineages derived from rapid diversifications are often challenging to resolve using morphology or standard DNA barcoding markers. The hyper-diverse genus Lepanthes from Neotropical cloud forest includes over 1200 species and many recent, explosive diversifications that have resulted in poorly supported nodes and morphological convergence across clades. Here, we assess the performance of 446 nuclear-plastid-mitochondrial markers derived from an anchored hybrid enrichment approach (AHE) coupled with coalescence- and species network-based inferences to resolve phylogenetic relationships and improve species recognition in the Lepanthes horrida species group. In addition to using orchid-specific probes to increase enrichment efficiency, we improved gene tree resolution by extending standard angiosperm targets into adjacent exons. We found high topological discordance among individual gene trees, suggesting that hybridization/polyploidy may have promoted speciation in the lineage via formation of new hybrid taxa. In addition, we identified ten loci with the highest phylogenetic informativeness values from these genomes. Most previous phylogenetic sampling in the Pleurothallidinae relies on two regions (ITS and matK), therefore, the evaluation of other markers such as those shown here may be useful in future phylogenetic studies in the orchid family. Coalescent-based species tree estimation methods resolved the phylogenetic relationships of the L. horrida species group. The resolution of the phylogenetic estimations was improved with the inclusion of extended anchor targets. This approach produced longer loci with higher discriminative power. These analyses also disclosed two undescribed species, L. amicitiae and L. genetoapophantica, formally described here, which are also supported by morphology. Our study demonstrates the utility of combined genomic evidence to disentangle phylogenetic relationships at very shallow levels of the tree of life, and in clades showing convergent trait evolution. With a fully resolved phylogeny, is it possible to disentangle traits evolving in parallel or convergently across these orchid lineages such as flower color and size from diagnostic traits such as the shape and orientation of the lobes of the petals and lip.}, }
@article {pmid30040943, year = {2018}, author = {Gawryluk, RMR}, title = {Evolutionary Biology: A New Home for the Powerhouse?.}, journal = {Current biology : CB}, volume = {28}, number = {14}, pages = {R798-R800}, doi = {10.1016/j.cub.2018.05.073}, pmid = {30040943}, issn = {1879-0445}, mesh = {*Alphaproteobacteria ; Biological Evolution ; Biology ; Oceans and Seas ; Phylogeny ; }, abstract = {Metagenomic assemblies of oceanic datasets have unearthed novel and diverse alphaproteobacterial groups. Sophisticated phylogenetic analyses based on these metagenomes suggest that mitochondria do not descend from within Alphaproteobacteria, as typically thought, but from a still undiscovered sister lineage.}, }
@article {pmid30032461, year = {2018}, author = {Sylvester, C and Krishna, MS and Rao, JS and Chandrasekar, A}, title = {Neolithic phylogenetic continuity inferred from complete mitochondrial DNA sequences in a tribal population of Southern India.}, journal = {Genetica}, volume = {146}, number = {4-5}, pages = {383-389}, pmid = {30032461}, issn = {1573-6857}, mesh = {Asian People/genetics ; DNA, Mitochondrial/*genetics ; Ethnicity/*genetics ; Female ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; Humans ; India/ethnology ; Male ; Mitochondria/genetics ; Phylogeny ; Phylogeography/methods ; Sequence Analysis, DNA/methods ; }, abstract = {The subsequent human migrations that dispersed out of Africa, both prehistoric and historic and colonization of India by modern humans is unanimous, and phylogeny of major mitochondrial DNA haplogroups have played a key role in assessing the genetic origin of people of India. To address more such events, complete mitogenomes of 113 Melakudiya tribe of Southern India were sequenced and 46 individuals showed the presence of west Eurasian autochthonous haplogroups HV14 and U7. Phylogenetic analysis revealed two novel subclades HV14a1b and HV14a1b1 and sequences representing haplogroup U7 were included under previously described subclade U7a3a1a2* specific to India. Moreover, the present analysis on complete mtDNA reveals addition information of the spread and distribution of west Eurasian haplogroups in southern India, in tracing an unexplored genetic link between Melakudiya tribe with the people of Iranian Plateau, South Caucasus, and Central Asia. Coalescence ages of HV14 and U7a3a1a2* trees in the present study dates ~ 16.1 ± 4.3 and ~ 13.4 ± 5.6 kya respectively.}, }
@article {pmid30026124, year = {2018}, author = {Ferreira, M and Fernandes, AM and Aleixo, A and Antonelli, A and Olsson, U and Bates, JM and Cracraft, J and Ribas, CC}, title = {Evidence for mtDNA capture in the jacamar Galbula leucogastra/chalcothorax species-complex and insights on the evolution of white-sand ecosystems in the Amazon basin.}, journal = {Molecular phylogenetics and evolution}, volume = {129}, number = {}, pages = {149-157}, doi = {10.1016/j.ympev.2018.07.007}, pmid = {30026124}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Birds/*genetics ; Brazil ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; *Ecosystem ; Gene Flow ; Genetic Loci ; Genome, Mitochondrial ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Jacamar species occur throughout Amazonia, with most species occupying forested habitats. One species-complex, Galbula leucogastra/chalcothorax, is associated to white sand ecosystems (WSE). Previous studies of WSE bird species recovered shallow genetic structure in mtDNA coupled with signs of gene flow among WSE patches. Here, we characterize diversification of the G. leucogastra/chalcothorax species-complex with dense sampling across its distribution using mitochondrial and genomic (Ultraconserved Elements, UCEs) DNA sequences. We performed concatenated likelihood and Bayesian analysis, as well as a species-tree analysis using [∗]BEAST, to establish the phylogenetic relationships among populations. The mtDNA results recovered at least six geographically-structured lineages, with G. chalcothorax embedded within lineages of G. leucogastra. In contrast, both concatenated and species-tree analyses of UCE data recovered G. chalcothorax as sister to all G. leucogastra lineages. We hypothesize that the mitochondrial genome of one of the G. leucogastra lineage (Madeira) was captured into G. chalcothorax in the past. We discuss how WSE evolution and the coevolution of mtDNA and nuclear genes might have played a role in this apparently rare event.}, }
@article {pmid30022808, year = {2018}, author = {Lang, SA and Shain, DH}, title = {Atypical Evolution of the F1Fo Adenosine Triphosphate Synthase Regulatory ATP6 subunit in Glacier Ice Worms (Annelida: Clitellata: Mesenchytraeus).}, journal = {Evolutionary bioinformatics online}, volume = {14}, number = {}, pages = {1176934318788076}, pmid = {30022808}, issn = {1176-9343}, support = {R15 GM093685/GM/NIGMS NIH HHS/United States ; }, abstract = {The glacier ice worm, Mesenchytraeus solifugus, is among a few animals that reside permanently in glacier ice. Their adaptation to cold temperature has been linked to relatively high intracellular adenosine triphosphate (ATP) levels, which compensate for reductions in molecular motion at low physiological temperatures. Here, we show that ATP6-the critical regulatory subunit of the F1Fo-ATP synthase and primary target of mitochondrial disease-acquired an unprecedented histidine-rich, 18-amino acid carboxy-terminal extension, which counters the strong evolutionary trend of mitochondrial genome compaction. Furthermore, sequence analysis suggests that this insertion is not of metazoan origin, but rather is a product of horizontal gene transfer from a microbial dietary source, and may act as a proton shuttle to accelerate the rate of ATP synthesis.}, }
@article {pmid30021129, year = {2018}, author = {Sun, S and Sha, Z and Wang, Y}, title = {Complete mitochondrial genome of the first deep-sea spongicolid shrimp Spongiocaris panglao (Decapoda: Stenopodidea): Novel gene arrangement and the phylogenetic position and origin of Stenopodidea.}, journal = {Gene}, volume = {676}, number = {}, pages = {123-138}, doi = {10.1016/j.gene.2018.07.026}, pmid = {30021129}, issn = {1879-0038}, mesh = {Animals ; Base Composition ; Decapoda/*genetics ; Gene Order ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA/chemistry ; RNA, Mitochondrial ; Sequence Analysis, DNA/*methods ; }, abstract = {Stenopodidea Claus, 1872 (Crustacea: Decapoda) is one of the major groups of decapods crustaceans. Hitherto, only one complete mitochondrial genome (mitogenome) from the family Stenopodidae is available for the infraorder Stenopodidea. Here, we determined the complete mitogenome of Spongiocaris panglao de Grave and Saito, 2016 using Illumina sequencing, representing the first species from the family Spongicolidae. The 15,909 bp genome is a circular molecule and consists of 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. Although the overall genome organization is typical for metazoans, the mitogenome of S. panglao shows some derived characters. A + T content of 77.42% in S. pamglao mitogenome is second-highest among the dacapods described to date. The trnR gene exhibit modified secondary structure with the TψC loop completely missing, which might be a putative autapomorphy of S. pamglao mitogenome. Compared with the shallow-water stenopodidean species S. hispidus, the control region of S. pamglao exhibits three characteristics: larger size, higher A + T content, and more tandem repeat sequences. The gene order exhibited difference from the ancestral mitogenome pattern of the Pancrustacea, with 5 tRNA genes rearrangement. The result from BI was agreed with most morphological characters and molecular evidences, revealing that Stenopodidea and Reptantia had the closest relationship, as the sister group of Caridea. Still, the alternative hypothesis supported from ML topology cannot be completely rejected based on the current data. Estimated times revealed that the two stenopodideans families Stenopodidae and Spongicolidae diverged from each other around 122 Mya. The divergence time of spongicolid shrimp is in good agreement with the origin of their hexactinellid hosts (78-144 Mya).}, }
@article {pmid30019754, year = {2018}, author = {Xiao, H and Zhang, Q and Qin, X and Xu, Y and Ni, C and Huang, J and Zhu, L and Zhong, F and Liu, W and Yao, G and Zhu, Y and Hu, J}, title = {Rice PPS1 encodes a DYW motif-containing pentatricopeptide repeat protein required for five consecutive RNA-editing sites of nad3 in mitochondria.}, journal = {The New phytologist}, volume = {220}, number = {3}, pages = {878-892}, doi = {10.1111/nph.15347}, pmid = {30019754}, issn = {1469-8137}, support = {2016YFD0100804//National Key Research and Development Program of China/International ; 31371698//National Natural Science Foundation of China/International ; 31670310//National Natural Science Foundation of China/International ; SNG2017061//Suzhou science and technology project/International ; }, mesh = {Amino Acid Motifs ; Base Sequence ; Cell Nucleus/metabolism ; Conserved Sequence ; Electron Transport ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Mitochondria/*metabolism/ultrastructure ; Mitochondrial Proteins/chemistry/metabolism ; Oryza/*genetics/ultrastructure ; Phenotype ; Plant Proteins/*chemistry/*metabolism ; Pollen/metabolism/ultrastructure ; Protein Binding ; RNA Editing/*genetics ; RNA Interference ; RNA, Messenger/genetics/metabolism ; Time Factors ; }, abstract = {The pentatricopeptide repeat (PPR) protein family is a large family characterized by tandem arrays of a degenerate 35-amino-acid motif whose members function as important regulators of organelle gene expression at the post-transcriptional level. Despite the roles of PPRs in RNA editing in organelles, their editing activities and the underlying mechanism remain obscure. Here, we show that a novel DYW motif-containing PPR protein, PPS1, is associated with five conserved RNA-editing sites of nad3 located in close proximity to each other in mitochondria, all of which involve conversion from proline to leucine in rice. Both pps1 RNAi and heterozygous plants are characterized by delayed development and partial pollen sterility at vegetative stages and reproductive stage. RNA electrophoresis mobility shift assays (REMSAs) and reciprocal competition assays using different versions of nad3 probes confirm that PPS1 can bind to cis-elements near the five affected sites, which is distinct from the existing mode of PPR-RNA binding because of the continuity of the editing sites. Loss of editing at nad3 in pps1 reduces the activity of several complexes in the mitochondrial electron transport chain and affects mitochondrial morphology. Taken together, our results indicate that PPS1 is required for specific editing sites in nad3 in rice.}, }
@article {pmid30017823, year = {2018}, author = {Chesser, RT and Vaseghi, H and Hosner, PA and Bergner, LM and Cortes-Rodriguez, MN and Welch, AJ and Collins, CT}, title = {Molecular systematics of swifts of the genus Chaetura (Aves: Apodiformes: Apodidae).}, journal = {Molecular phylogenetics and evolution}, volume = {128}, number = {}, pages = {162-171}, doi = {10.1016/j.ympev.2018.07.006}, pmid = {30017823}, issn = {1095-9513}, mesh = {Animals ; Birds/*classification ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; North America ; Panama ; Phylogeny ; Seasons ; South America ; Species Specificity ; }, abstract = {Phylogenetic relationships among swifts of the morphologically conservative genus Chaetura were studied using mitochondrial and nuclear DNA sequences. Taxon sampling included all species and 21 of 30 taxa (species and subspecies) within Chaetura. Our results indicate that Chaetura is monophyletic and support the division of the genus into the two subgenera previously identified using plumage characters. However, our genetic data, when considered in combination with phenotypic data, appear to be at odds with the current classification of some species of Chaetura. We recommend that C. viridipennis, currently generally treated as specifically distinct from C. chapmani, be returned to its former status as C. chapmani viridipennis, and that C. andrei, now generally regarded as synonymous with C. vauxi aphanes, again be recognized as a valid species. Widespread Neotropical species C. spinicaudus is paraphyletic with respect to more range-restricted species C. fumosa, C. egregia, and C. martinica. Geographically structured genetic variation within some other species of Chaetura, especially notable in C. cinereiventris, suggests that future study may lead to recognition of additional species in this genus. Biogeographic analysis indicated that Chaetura originated in South America and identified several dispersal events to Middle and North America following the formation of the Isthmus of Panama.}, }
@article {pmid30016998, year = {2018}, author = {Marais, GAB and Gaillard, JM and Vieira, C and Plotton, I and Sanlaville, D and Gueyffier, F and Lemaitre, JF}, title = {Sex gap in aging and longevity: can sex chromosomes play a role?.}, journal = {Biology of sex differences}, volume = {9}, number = {1}, pages = {33}, pmid = {30016998}, issn = {2042-6410}, mesh = {*Aging ; Animals ; Humans ; *Sex Characteristics ; *Sex Chromosomes ; }, abstract = {It is well known that women live longer than men. This gap is observed in most human populations and can even reach 10-15 years. In addition, most of the known super centenarians (i.e., humans who lived for > 110 years) are women. The differences in life expectancy between men and women are often attributed to cultural differences in common thinking. However, sex hormones seem to influence differences in the prevalence of diseases, in the magnitude of aging, and in the longevity between men and women. Moreover, far from being human specific, the sex gap in longevity is extremely common in non-human animals, especially in mammals. Biological factors clearly contribute to such a sex gap in aging and longevity. Different hypotheses have been proposed to explain why males and females age and die differently. The cost of sexual selection and sexual dimorphism has long been considered the best explanation for the observed sex gap in aging/longevity. However, the way mitochondria are transmitted (i.e., through females in most species) could have an effect, called the mother's curse. Recent data suggest that sex chromosomes may also contribute to the sex gap in aging/longevity through several potential mechanisms, including the unguarded X/Z, the toxic Y/W and the loss of Y/W. We discuss future research directions to test these ideas.}, }
@article {pmid30011013, year = {2018}, author = {Hood, WR and Zhang, Y and Mowry, AV and Hyatt, HW and Kavazis, AN}, title = {Life History Trade-offs within the Context of Mitochondrial Hormesis.}, journal = {Integrative and comparative biology}, volume = {58}, number = {3}, pages = {567-577}, pmid = {30011013}, issn = {1557-7023}, support = {R03 HD083654/HD/NICHD NIH HHS/United States ; }, mesh = {Biological Evolution ; Hormesis/*physiology ; *Life History Traits ; Longevity/*physiology ; Mitochondria/*physiology ; Oxidative Stress/physiology ; Reactive Oxygen Species/metabolism ; Reproduction/*physiology ; }, abstract = {Evolutionary biologists have been interested in the negative interactions among life history traits for nearly a century, but the mechanisms that would create this negative interaction remain poorly understood. One variable that has emerged as a likely link between reproductive effort and longevity is oxidative stress. Specifically, it has been proposed that reproduction generates free radicals that cause oxidative stress and, in turn, oxidative stress damages cellular components and accelerates senescence. We propose that there is limited support for the hypothesis because reactive oxygen species (ROS), the free radicals implicated in oxidative damage, are not consistently harmful. With this review, we define the hormetic response of mitochondria to ROS, termed mitochondrial hormesis, and describe how to test for a mitohormetic response. We interpret existing data using our model and propose that experimental manipulations will further improve our knowledge of this response. Finally, we postulate how the mitohormetic response curve applies to variation in animal performance and longevity.}, }
@article {pmid30005062, year = {2018}, author = {Salunke, R and Mourier, T and Banerjee, M and Pain, A and Shanmugam, D}, title = {Highly diverged novel subunit composition of apicomplexan F-type ATP synthase identified from Toxoplasma gondii.}, journal = {PLoS biology}, volume = {16}, number = {7}, pages = {e2006128}, pmid = {30005062}, issn = {1545-7885}, mesh = {Amino Acid Sequence ; Animals ; Conserved Sequence ; Gene Expression Regulation ; Genetic Variation ; Hemagglutinins/metabolism ; Mitochondria/metabolism ; Mitochondrial Proton-Translocating ATPases/*metabolism ; Parasites/metabolism ; Phylogeny ; Plasmodium falciparum/metabolism ; Protein Multimerization ; Protein Subunits/*metabolism ; Proteome/metabolism ; Proteomics ; Protozoan Proteins/chemistry/isolation &amp; purification/metabolism ; Recombinant Fusion Proteins/metabolism ; Toxoplasma/*enzymology ; }, abstract = {The mitochondrial F-type ATP synthase, a multisubunit nanomotor, is critical for maintaining cellular ATP levels. In T. gondii and other apicomplexan parasites, many subunit components necessary for proper assembly and functioning of this enzyme appear to be missing. Here, we report the identification of 20 novel subunits of T. gondii F-type ATP synthase from mass spectrometry analysis of partially purified monomeric (approximately 600 kDa) and dimeric (>1 MDa) forms of the enzyme. Despite extreme sequence diversification, key FO subunits a, b, and d can be identified from conserved structural features. Orthologs for these proteins are restricted to apicomplexan, chromerid, and dinoflagellate species. Interestingly, their absence in ciliates indicates a major diversion, with respect to subunit composition of this enzyme, within the alveolate clade. Discovery of these highly diversified novel components of the apicomplexan F-type ATP synthase complex could facilitate the development of novel antiparasitic agents. Structural and functional characterization of this unusual enzyme complex will advance our fundamental understanding of energy metabolism in apicomplexan species.}, }
@article {pmid30003876, year = {2018}, author = {Katane, M and Ariyoshi, M and Tateishi, S and Koiwai, S and Takaku, K and Nagai, K and Nakayama, K and Saitoh, Y and Miyamoto, T and Sekine, M and Mita, M and Hamase, K and Matoba, S and Homma, H}, title = {Structural and enzymatic properties of mammalian d-glutamate cyclase.}, journal = {Archives of biochemistry and biophysics}, volume = {654}, number = {}, pages = {10-18}, doi = {10.1016/j.abb.2018.07.005}, pmid = {30003876}, issn = {1096-0384}, mesh = {Animals ; Catalysis ; Dimerization ; Electrophoresis, Polyacrylamide Gel ; Glutamic Acid/metabolism ; Hydro-Lyases/*chemistry/isolation &amp; purification/*metabolism ; Hydrogen-Ion Concentration ; Kinetics ; Manganese/metabolism ; Mice ; Mitochondria/metabolism ; Proline/metabolism ; Protein Conformation ; Recombinant Proteins/chemistry/isolation &amp; purification/metabolism ; Substrate Specificity ; }, abstract = {d-Glutamate cyclase (DGLUCY) is a unique enzyme that reversibly converts free d-glutamate to 5-oxo-d-proline and H2O. Mammalian DGLUCY is highly expressed in the mitochondrial matrix in the heart, and its downregulation disrupts d-glutamate and/or 5-oxo-d-proline levels, contributing to the onset and/or exacerbation of heart failure. However, detailed characterisation of DGLUCY has not yet been performed. Herein, the structural and enzymatic properties of purified recombinant mouse DGLUCY were examined. The results revealed a dimeric oligomerisation state, and both d-glutamate-to-5-oxo-d-proline and 5-oxo-d-proline-to-d-glutamate reactions were catalysed in a stereospecific manner. Catalytic activity is modulated by divalent cations and nucleotides including ATP and ADP. Interestingly, the presence of Mn[2+] completely abolished the 5-oxo-d-proline-to-d-glutamate reaction but stimulated the d-glutamate-to-5-oxo-d-proline reaction. The optimum pH is ∼8.0, similar to that in the mitochondrial matrix, and the catalytic efficiency for d-glutamate is markedly higher than that for 5-oxo-d-proline. These findings suggest that DGLUCY functions as a metalloenzyme that degrades d-glutamate in the mitochondrial matrix in mammalian cells. The results also provide insight into the correlation between DGLUCY enzyme activity and the physiological and pathological roles of d-glutamate and 5-oxo-d-proline in cardiac function, which is of relevance to the risk of onset of heart failure.}, }
@article {pmid29992378, year = {2018}, author = {Kasperski, A and Kasperska, R}, title = {Bioenergetics of life, disease and death phenomena.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {137}, number = {2}, pages = {155-168}, pmid = {29992378}, issn = {1611-7530}, mesh = {Adenosine Triphosphate/chemistry ; Animals ; *Cell Biology ; DNA/analysis ; *Energy Metabolism ; Genome, Human ; Glucose/chemistry ; Humans ; Mitochondria/metabolism ; Models, Biological ; Mutation ; Neoplasms/*genetics/*pathology ; Oxygen/chemistry ; Reactive Oxygen Species/chemistry ; }, abstract = {In this article, some new aspects of unified cell bioenergetics are presented. From the perspective of unified cell bioenergetics certain subsequent stages of cancer development, from initiation stage, through transformation to metastasis, are analyzed. Here we show that after transformation, cancer cells are permanently exposed to reactive oxygen species, that causes continual random DNA mutations and as a result genome and chromosomal destabilizations. The modern cancer attractor hypothesis has been extended in explaining cancer development. Discussion is conducted in light of current cancerogenesis research, including bioenergetic cancer initiation, the somatic mutation theory and the tissue organization field theory. In the article reasons complicating the discovery of patterns of cancer genome changes and cancer evolution are presented. In addition certain cancer therapeutic aspects are given attention to.}, }
@article {pmid29991771, year = {2018}, author = {Okatsu, K and Sato, Y and Yamano, K and Matsuda, N and Negishi, L and Takahashi, A and Yamagata, A and Goto-Ito, S and Mishima, M and Ito, Y and Oka, T and Tanaka, K and Fukai, S}, title = {Structural insights into ubiquitin phosphorylation by PINK1.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {10382}, pmid = {29991771}, issn = {2045-2322}, support = {JP15J10559//Japan Society for the Promotion of Science (JSPS)/International ; JP24687012//Japan Society for the Promotion of Science (JSPS)/International ; JP15H01175//Japan Society for the Promotion of Science (JSPS)/International ; JP16K18545//Japan Society for the Promotion of Science (JSPS)/International ; 17H05888//Japan Society for the Promotion of Science (JSPS)/International ; JP26000014//Japan Society for the Promotion of Science (JSPS)/International ; JP24247014//Japan Society for the Promotion of Science (JSPS)/International ; PRESTO//Japan Science and Technology Agency (JST)/International ; JPMJCR13M3//JST | Core Research for Evolutional Science and Technology (CREST)/International ; JPMJCR12M5//JST | Core Research for Evolutional Science and Technology (CREST)/International ; }, mesh = {Adenosine Triphosphate/metabolism ; Crystallography, X-Ray ; Humans ; Mutation ; Parkinsonian Disorders/etiology ; Phosphorylation ; Protein Binding ; Protein Conformation ; Protein Domains ; Protein Kinases/chemistry/*metabolism ; Ubiquitin/*metabolism ; Ubiquitin-Protein Ligases/metabolism ; }, abstract = {Mutations of PTEN-induced putative kinase 1 (PINK1) and the E3 ubiquitin (Ub) ligase parkin can cause familial parkinsonism. These two proteins are essential for ubiquitylation of damaged mitochondria and subsequent degradation. PINK1 phosphorylates Ser65 of Ub and the Ub-like (UBL) domain of parkin to allosterically relieve the autoinhibition of parkin. To understand the structural mechanism of the Ub/UBL-specific phosphorylation by PINK1, we determined the crystal structure of Tribolium castaneum PINK1 kinase domain (TcPINK1) in complex with a nonhydrolyzable ATP analogue at 2.5 Å resolution. TcPINK1 consists of the N- and C-terminal lobes with the PINK1-specific extension. The ATP analogue is bound in the cleft between the N- and C-terminal lobes. The adenine ring of the ATP analogue is bound to a hydrophobic pocket, whereas the triphosphate group of the ATP analogue and two coordinated Mg ions interact with the catalytic hydrophilic residues. Comparison with protein kinases A and C (PKA and PKC, respectively) unveils a putative Ub/UBL-binding groove, which is wider than the peptide-binding groove of PKA or PKC to accommodate the globular head of Ub or UBL. Further crosslinking analyses suggested a PINK1-interacting surface of Ub. Structure-guided mutational analyses support the findings from the present structural analysis of PINK1.}, }
@article {pmid29989670, year = {2018}, author = {Iha, C and Grassa, CJ and Lyra, GM and Davis, CC and Verbruggen, H and Oliveira, MC}, title = {Organellar genomics: a useful tool to study evolutionary relationships and molecular evolution in Gracilariaceae (Rhodophyta).}, journal = {Journal of phycology}, volume = {54}, number = {6}, pages = {775-787}, doi = {10.1111/jpy.12765}, pmid = {29989670}, issn = {1529-8817}, support = {152939/2014-8//CNPq/International ; 301491/2013-5//CNPq/International ; 406351/2016-3//CNPq/International ; 88881.134422/2016-01//CAPES/International ; TO INT0001/2016//FAPESB/International ; 2013/11833-3//Biota-FAPESP/International ; 2015/50078-1//FAPESP/International ; }, mesh = {*Evolution, Molecular ; Genome, Chloroplast/*genetics ; Genome, Mitochondrial/*genetics ; Phylogeny ; Rhodophyta/*genetics ; Sequence Analysis, DNA ; }, abstract = {Gracilariaceae has a worldwide distribution including numerous economically important species. We applied high-throughput sequencing to obtain organellar genomes (mitochondria and chloroplast) from 10 species of Gracilariaceae and, combined with published genomes, to infer phylogenies and compare genome architecture among species representing main lineages. We obtained similar topologies between chloroplast and mitochondrial genomes phylogenies. However, the chloroplast phylogeny was better resolved with full support. In this phylogeny, Melanthalia intermedia is sister to a monophyletic clade including Gracilaria and Gracilariopsis, which were both resolved as monophyletic genera. Mitochondrial and chloroplast genomes were highly conserved in gene synteny, and variation mainly occurred in regions where insertions of plasmid-derived sequences (PDS) were found. In mitochondrial genomes, PDS insertions were observed in two regions where the transcription direction changes: between the genes cob and trnL, and trnA and trnN. In chloroplast genomes, PDS insertions were in different positions, but generally found between psdD and rrs genes. Gracilariaceae is a good model system to study the impact of PDS in genome evolution due to the frequent presence of these insertions in organellar genomes. Furthermore, the bacterial leuC/leuD operon was found in chloroplast genomes of Gracilaria tenuistipitata, G. chilensis, and M. intermedia, and in extrachromosomal plasmid of G. vermiculophylla. Phylogenetic trees show two different origins of leuC/leuD: genes found in chloroplast and plasmid were placed with proteobacteria, and genes encoded in the nucleus were close to Viridiplantae and cyanobacteria.}, }
@article {pmid29987715, year = {2018}, author = {Rolland, N and Bouchnak, I and Moyet, L and Salvi, D and Kuntz, M}, title = {The Main Functions of Plastids.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1829}, number = {}, pages = {73-85}, doi = {10.1007/978-1-4939-8654-5_5}, pmid = {29987715}, issn = {1940-6029}, mesh = {Biological Evolution ; Energy Metabolism ; Plastids/*physiology/ultrastructure ; }, abstract = {Plastids are semiautonomous organelles like mitochondria, and derive from a cyanobacterial ancestor that was engulfed by a host cell. During evolution, they have recruited proteins originating from the nuclear genome, and only parts of their ancestral metabolic properties were conserved and optimized to limit functional redundancy with other cell compartments. Furthermore, large disparities in metabolic functions exist among various types of plastids, and the characterization of their various metabolic properties is far from being accomplished. In this review, we provide an overview of the main functions, known to be achieved by plastids or shared by plastids and other compartments of the cell. In short, plastids appear at the heart of all main plant functions.}, }
@article {pmid29987711, year = {2018}, author = {Maréchal, E}, title = {Primary Endosymbiosis: Emergence of the Primary Chloroplast and the Chromatophore, Two Independent Events.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1829}, number = {}, pages = {3-16}, doi = {10.1007/978-1-4939-8654-5_1}, pmid = {29987711}, issn = {1940-6029}, mesh = {Alphaproteobacteria/genetics ; Cell Membrane/metabolism ; Chlamydia/genetics/metabolism ; Chloroplasts/*pathology ; Chromatophores/*physiology ; Cyanobacteria/metabolism ; Eukaryota/physiology ; Gene Transfer, Horizontal ; Genes, Bacterial ; Glaucophyta/genetics/metabolism ; Inheritance Patterns ; Mitochondria/genetics/metabolism ; Rhizaria ; *Symbiosis ; }, abstract = {The emergence of semiautonomous organelles, such as the mitochondrion, the chloroplast, and more recently, the chromatophore, are critical steps in the evolution of eukaryotes. They resulted from primary endosymbiotic events that seem to share general features, i.e., an acquisition of a bacterium/cyanobacteria likely via a phagocytic membrane, a genome reduction coinciding with an escape of genes from the organelle to the nucleus, and finally the appearance of an active system translocating nuclear-encoded proteins back to the organelles. An intense mobilization of foreign genes of bacterial origin, via horizontal gene transfers, plays a critical role. Some third partners, like Chlamydia, might have facilitated the transition from cyanobacteria to the early chloroplast. This chapter describes our current understanding of primary endosymbiosis, with a specific focus on primary chloroplasts considered to have emerged more than one billion years ago, and on the chromatophore, having emerged about one hundred million years ago.}, }
@article {pmid29986779, year = {2019}, author = {Wang, HB and Zhang, HJ and Song, LL and Zhu, L and Chen, M and Ren, GJ and Liu, GH and Zhao, GH}, title = {Morphological and molecular confirmation of the validity of Trichuris rhinopiptheroxella in the endangered golden snub-nosed monkey (Rhinopithecus roxellana).}, journal = {Journal of helminthology}, volume = {93}, number = {5}, pages = {601-607}, doi = {10.1017/S0022149X18000500}, pmid = {29986779}, issn = {1475-2697}, mesh = {Animals ; Base Sequence ; China/epidemiology ; Colobinae/*parasitology ; DNA, Mitochondrial/genetics ; Endangered Species ; Female ; Genome, Mitochondrial ; Male ; Mitochondria/genetics ; Phylogeny ; Trichuriasis/epidemiology/*veterinary ; Trichuris/*anatomy &amp; histology/*classification ; }, abstract = {The golden snub-nosed monkey (Rhinopithecus roxellana) is an endangered species endemic to China. Relatively little is known about the taxonomic status of soil-transmitted helminths (STH) in these monkeys. Trichuris spp. (syn. Trichocephalus) are among the most important STHs, causing significant socio-economic losses and public health concerns. To date, five Trichuris species have been reported in golden monkeys, including a novel species, T. rhinopiptheroxella, based on morphology. In the present study, molecular and morphological analysis was conducted on adult Trichuris worms obtained from a dead golden snub-nosed monkey, to better understand their taxonomic status. Morphology indicated that the adult Trichuris worms were similar to T. rhinopiptheroxella. To further ascertain their phylogenetic position, the complete mitochondrial (mt) genome of these worms was sequenced and characterized. The mt genome of T. rhinopiptheroxella is 14,186 bp, encoding 37 genes. Phylogenetic analysis based on the concatenated amino acids of 12 protein-coding genes (with the exception of atp8) indicated that T. rhinopiptheroxella was genetically distinct and exhibited 27.5-27.8% genetic distance between T. rhinopiptheroxella and other Trichuris spp. Our results support T. rhinopiptheroxella as a valid Trichuris species and suggest that mt DNA could serve as a marker for future studies on the classification, evolution and molecular epidemiology of Trichuris spp. from golden snub-nosed monkeys.}, }
@article {pmid29986214, year = {2018}, author = {Angers, B and Chapdelaine, V and Deremiens, L and Vergilino, R and Leung, C and Doucet, SL and Glémet, H and Angers, A}, title = {Gene flow prevents mitonuclear co-adaptation: A comparative portrait of sympatric wild types and cybrids in the fish Chrosomus eos.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {27}, number = {}, pages = {77-84}, doi = {10.1016/j.cbd.2018.06.007}, pmid = {29986214}, issn = {1878-0407}, mesh = {Animals ; Cell Nucleus/genetics ; Cyprinidae/*genetics ; DNA, Mitochondrial/*genetics ; Epigenesis, Genetic ; Female ; *Gene Flow ; Genetic Speciation ; Male ; Mitochondria/genetics ; Sympatry ; }, abstract = {Allospecific mtDNA can occasionally be beneficial for the fitness of populations. It is, however, difficult to assess the effect of mtDNA in natural conditions due to genetic and/or environmental interactions. In the fish Chrosomus eos, the transfer of C. neogaeus mitochondria occurs in a single generation and results in natural cybrids. For a few lakes in Quebec, C. eos can harbor either a C. eos mtDNA (wild types) or a C. neogaeus mtDNA (cybrids). Moreover, mtDNA of cybrids originated either from Mississippian or Atlantic glacial refuges. Such diversity provides a useful system for in situ assessment of allospecific mtDNA effects. We determined genetic, epigenetic and transcriptomic variation as well as mitochondrial enzymatic activity (complex IV) changes among wild types and cybrids either in sympatry or allopatry. Wild types and cybrids did not segregate spatially within a lake. Moreover, no significant genetic differentiation was detected among wild types and cybrids indicating sustained gene flow. Mitochondrial complex IV activity was higher for cybrids in both sympatry and allopatry while no difference was detected among cybrid haplotypes. Epigenetic and transcriptomic analyses revealed only subtle differences between sympatric wild types and cybrids compared to differences between sites. Altogether, these results indicate a limited influence of allospecific mtDNA in nuclear gene expression when controlling for genetic and environmental effects. The absence of a reproductive barrier between wild types and cybrids results in random association of either C. eos or C. neogaeus mtDNA with C. eos nDNA at each generation, and prevents mitonuclear co-adaptation in sympatry.}, }
@article {pmid29984192, year = {2018}, author = {MacDonald, JA and Fowle, WH and Shin, E and Woods, DC}, title = {A method for freeze-fracture and scanning electron microscopy of isolated mitochondria.}, journal = {MethodsX}, volume = {5}, number = {}, pages = {593-598}, pmid = {29984192}, issn = {2215-0161}, abstract = {Electron microscopy as a methodology for the study of mitochondria based on morphological features is a standard technique that has experienced little evolution over the course of several decades. This technology has identified heterogeneity of mitochondria populations across both whole tissues, as well between individual cells, using primarily ultrathin sections for transmission electron microscopy (TEM). However, this technique constrains the evaluation of a sample to a single two-dimensional plane. To overcome this limitation, scanning electron microscopy (SEM) has been successfully utilized to observe three-dimensional mitochondria structures within the complex microenvironment containing total cellular components. In response to these dual technical caveats of existing electron microscopy protocols, we developed a methodology to evaluate the three-dimensional ultrastructure of isolated mitochondria, utilizing a freeze-fracture step and rigorous preservation of sample morphology. This protocol allows for a more high-throughput analysis of mitochondria populations from a specimen of interest, as the sample has been previously purified, as well as a finer resolution of complex intra-mitochondrial structures, using the depth of field created by SEM. •Protocol designed for SEM of isolated mitochondria samples.•SEM visualizes mitochondria ultrastructure in 3-D.•Freeze-fracture creates cross-sectional plane for view of interior organelle structures.}, }
@article {pmid29976842, year = {2018}, author = {He, K and Chen, X and Chen, P and He, SW and Cheng, F and Jiang, XL and Campbell, K}, title = {A new genus of Asiatic short-tailed shrew (Soricidae, Eulipotyphla) based on molecular and morphological comparisons.}, journal = {Zoological research}, volume = {39}, number = {5}, pages = {321-334}, pmid = {29976842}, issn = {2095-8137}, mesh = {Animals ; Biological Evolution ; China ; Mitochondria/genetics ; North America ; Sequence Analysis, DNA ; Shrews/*anatomy &amp; histology/classification/genetics ; Skull/anatomy &amp; histology ; }, abstract = {Blarinellini is a tribe of soricine shrews comprised of nine fossil genera and one extant genus. Blarinelline shrews were once widely distributed throughout Eurasia and North America, though only members of the Asiatic short-tailed shrew genus Blarinella currently persist (mostly in southwestern China and adjacent areas). Only three forms of Blarinella have been recognized as either species or subspecies. However, recent molecular studies indicated a strikingly deep divergence within the genus, implying the existence of a distinct genus-level lineage. We sequenced the complete mitochondrial genomes and one nuclear gene of three Asiatic short-tailed and two North American shrews and analyzed them morphometrically and morphologically. Our molecular analyses revealed that specimens ascribed to B. griselda formed two deeply diverged lineages, one a close relative to B. quadraticauda, whereas the other - comprised of topotype specimens from southern Gansu - diverged from other Blarinella in the middle Miocene (ca. 18.2 million years ago (Ma), 95% confidence interval=13.4-23.6 Ma). Although the skulls were similarly shaped in both lineages, we observed several diagnostic characteristics, including the shape of the upper P[4]. In consideration of the molecular and morphological evidence, we recognize B. griselda as the sole species of a new genus, namely, Pantherina gen. nov. Interestingly, some characteristics of Pantherina griselda are more similar to fossil genera, suggesting it represents an evolutionarily more primitive form than Blarinella. Recognition of this new genus sheds light on the systematics and evolutionary history of the tribe Blarinellini throughout Eurasia and North America.}, }
@article {pmid29973152, year = {2018}, author = {Vanhove, MPM and Briscoe, AG and Jorissen, MWP and Littlewood, DTJ and Huyse, T}, title = {The first next-generation sequencing approach to the mitochondrial phylogeny of African monogenean parasites (Platyhelminthes: Gyrodactylidae and Dactylogyridae).}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {520}, pmid = {29973152}, issn = {1471-2164}, support = {BR/132/PI/TILAPIA//Federaal Wetenschapsbeleid/ ; GB-TAF-2984//SYNTHESYS/ ; GB-TAF-4940//SYNTHESYS/ ; ZRDC2014MP084//Vlaamse Interuniversitaire Raad/ ; P505/12/G112 (ECIP)//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; K220314N//Fonds Wetenschappelijk Onderzoek/ ; Mbisa Congo project//Belgian Development Cooperation/ ; BOF Reserve Fellowship//Universiteit Hasselt/ ; }, mesh = {Animals ; Cichlids/*parasitology ; DNA, Protozoan/chemistry/isolation &amp; purification/metabolism ; Gene Order ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/classification/*genetics ; Phylogeny ; Platyhelminths/*genetics ; Protozoan Proteins/classification/genetics ; RNA, Ribosomal/classification/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Monogenean flatworms are the main ectoparasites of fishes. Representatives of the species-rich families Gyrodactylidae and Dactylogyridae, especially those infecting cichlid fishes and clariid catfishes, are important parasites in African aquaculture, even more so due to the massive anthropogenic translocation of their hosts worldwide. Several questions on their evolution, such as the phylogenetic position of Macrogyrodactylus and the highly speciose Gyrodactylus, remain unresolved with available molecular markers. Also, diagnostics and population-level research would benefit from the development of higher-resolution genetic markers. We aim to offer genetic resources for work on African monogeneans by providing mitogenomic data of four species (two belonging to Gyrodactylidae, two to Dactylogyridae), and analysing their gene sequences and gene order from a phylogenetic perspective.<br><br>RESULTS: Using Illumina technology, the first four mitochondrial genomes of African monogeneans were assembled and annotated for the cichlid parasites Gyrodactylus nyanzae, Cichlidogyrus halli, Cichlidogyrus mbirizei (near-complete mitogenome) and the catfish parasite Macrogyrodactylus karibae (near-complete mitogenome). Complete nuclear ribosomal operons were also retrieved, as molecular vouchers. The start codon TTG is new for Gyrodactylus and for Dactylogyridae, as is the incomplete stop codon TA for Dactylogyridae. Especially the nad2 gene is promising for primer development. Gene order was identical for protein-coding genes and differed between the African representatives of these families only in a tRNA gene transposition. A mitochondrial phylogeny based on an alignment of nearly 12,500&#xa0;bp including 12 protein-coding and two ribosomal RNA genes confirms that the Neotropical oviparous Aglaiogyrodactylus forficulatus takes a sister group position with respect to the other gyrodactylids, instead of the supposedly 'primitive' African Macrogyrodactylus. Inclusion of the African Gyrodactylus nyanzae confirms the paraphyly of Gyrodactylus. The position of the African dactylogyrid Cichlidogyrus is unresolved, although gene order suggests it is closely related to marine ancyrocephalines.<br><br>CONCLUSIONS: The amount of mitogenomic data available for gyrodactylids and dactylogyrids is increased by roughly one-third. Our study underscores the potential of mitochondrial genes and gene order in flatworm phylogenetics, and of next-generation sequencing for marker development for these non-model helminths for which few primers are available.}, }
@article {pmid29970001, year = {2018}, author = {Lenz, H and Hein, A and Knoop, V}, title = {Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {255}, pmid = {29970001}, issn = {1471-2105}, mesh = {Computational Biology/*methods ; Plant Proteins/*genetics ; RNA Editing/*genetics ; RNA, Plant/*genetics ; }, abstract = {BACKGROUND: Gene expression in plant chloroplasts and mitochondria is affected by RNA editing. Numerous C-to-U conversions, accompanied by reverse U-to-C exchanges in some plant clades, alter the genetic information encoded in the organelle genomes. Predicting and analyzing RNA editing, which ranges from only few sites in some species to thousands in other taxa, is bioinformatically demanding.<br><br>RESULTS: Here, we present major enhancements and extensions of PREPACT, a WWW-based service for analysing, predicting and cataloguing plant-type RNA editing. New features in PREPACT's core include direct GenBank accession query input and options to restrict searches to candidate U-to-C editing or to sites where editing has been documented previously in the references. The reference database has been extended by 20 new organelle editomes. PREPACT 3.0 features new modules "EdiFacts" and "TargetScan". EdiFacts integrates information on pentatricopeptide repeat (PPR) proteins characterized as site-specific RNA editing factors. PREPACT's editome references connect into EdiFacts, linking editing events to specific co-factors where known. TargetScan allows position-weighted querying for sequence motifs in the organelle references, optionally restricted to coding regions or sequences around editing sites, or in queries uploaded by the user. TargetScan is mainly intended to evaluate and further refine the proposed PPR-RNA recognition code but may be handy for other tasks as well. We present an analysis for the immediate sequence environment of more than 15,000 documented editing sites finding strong and different bias in the editome data sets.<br><br>CONCLUSIONS: We exemplarily present the novel features of PREPACT 3.0 aimed to enhance the analyses of plant-type RNA editing, including its new modules EdiFacts integrating information on characterized editing factors and TargetScan aimed to analyse RNA editing site recognition specificities.}, }
@article {pmid29967381, year = {2018}, author = {Pietras, Z and Wojcik, MA and Borowski, LS and Szewczyk, M and Kulinski, TM and Cysewski, D and Stepien, PP and Dziembowski, A and Szczesny, RJ}, title = {Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2558}, pmid = {29967381}, issn = {2041-1723}, support = {UMO-2014/12/W/NZ1/00463 to RJS//Narodowe Centrum Nauki (National Science Centre)/International ; UMO-2014/13/D/NZ2/01114 to RJS//Narodowe Centrum Nauki (National Science Centre)/International ; UMO-2013/11/13/NZ1/00089 to PPS//Narodowe Centrum Nauki (National Science Centre)/International ; 309419 PAPs &amp; PUPs to AD//EC | European Research Council (ERC)/International ; }, mesh = {Animals ; DEAD-box RNA Helicases/metabolism ; Endoribonucleases/metabolism ; Exoribonucleases/genetics/metabolism ; *G-Quadruplexes ; Genome, Mitochondrial/*genetics ; HEK293 Cells ; HeLa Cells ; Humans ; Mitochondria/genetics/*metabolism ; Multienzyme Complexes/metabolism ; Phylogeny ; Poly(A)-Binding Proteins/genetics/*metabolism ; Polyribonucleotide Nucleotidyltransferase/metabolism ; RNA Helicases/metabolism ; RNA, Small Interfering/metabolism ; RNA, Untranslated/genetics/*metabolism ; }, abstract = {The GC skew in vertebrate mitochondrial genomes results in synthesis of RNAs that are prone to form G-quadruplexes (G4s). Such RNAs, although mostly non-coding, are transcribed at high rates and are degraded by an unknown mechanism. Here we describe a dedicated mechanism of degradation of G4-containing RNAs, which is based on cooperation between mitochondrial degradosome and quasi-RNA recognition motif (qRRM) protein GRSF1. This cooperation prevents accumulation of G4-containing transcripts in human mitochondria. In vitro reconstitution experiments show that GRSF1 promotes G4 melting that facilitates degradosome-mediated decay. Among degradosome and GRSF1 regulated transcripts we identified one that undergoes post-transcriptional modification. We show that GRSF1 proteins form a distinct qRRM group found only in vertebrates. The appearance of GRSF1 coincided with changes in the mitochondrial genome, which allows the emergence of G4-containing RNAs. We propose that GRSF1 appearance is an evolutionary adaptation enabling control of G4 RNA.}, }
@article {pmid29959984, year = {2018}, author = {Uribe, JE and Zardoya, R and Puillandre, N}, title = {Phylogenetic relationships of the conoidean snails (Gastropoda: Caenogastropoda) based on mitochondrial genomes.}, journal = {Molecular phylogenetics and evolution}, volume = {127}, number = {}, pages = {898-906}, doi = {10.1016/j.ympev.2018.06.037}, pmid = {29959984}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/genetics ; Open Reading Frames/genetics ; *Phylogeny ; Snails/*genetics ; }, abstract = {With more than 5,000 species, Conoidea is one of the most diversified superfamilies of Gastropoda. Recently, the family-level classification of these venomous predator snails has undergone substantial changes, on the basis of a phylogenetic tree reconstructed combining partial mitochondrial and nuclear gene sequences, and up to 16 families are now recognized. However, phylogenetic relationships among these families remain largely unresolved. Here, we sequenced 20 complete or nearly complete mitochondrial (mt) genomes, which were combined with mt genomes available in GenBank to construct a dataset that included representatives of 80% of the known families, although for some we had only one species or genus as representative. Most of the sequenced conoidean mt genomes shared a constant genome organization, and observed rearrangements were limited exclusively to tRNA genes in a few lineages. Phylogenetic trees were reconstructed using probabilistic methods. Two main monophyletic groups, termed "Clade A" and "Clade B", were recovered with strong support within a monophyletic Conoidea. Clade A (including families Clavatulidae, Horaiclavidae, Turridae s.s., Terebridae, Drilliidae, Pseudomelatomidae, and Cochlespiridae) was composed of four main lineages, one of which was additionally supported by a rearrangement in the gene order. Clade B (including families Conidae, Borsoniidae, Clathurellidae, Mangeliidae, Raphitomidae, and Mitromorphidae) was composed of five main lineages. The reconstructed phylogeny rejected the monophyly of Clavatulidae, Horaiclavidae, Turridae, Pseudomelatomidae, and Conidae, indicating that several of the currently accepted families may be ill-defined. The reconstructed tree also revealed new phylogenetic positions for genera characterized as tentative (Gemmuloborsonia, Lucerapex, and Leucosyrinx), enigmatic (Marshallena) or challenging to place (Fusiturris), which will potentially impact the classification of the Conoidea.}, }
@article {pmid29955026, year = {2018}, author = {Liu, SY and He, K and Chen, SD and Jin, W and Murphy, RW and Tang, MK and Liao, R and Li, FJ}, title = {How many species of Apodemus and Rattus occur in China? A survey based on mitochondrial cyt b and morphological analyses.}, journal = {Zoological research}, volume = {39}, number = {5}, pages = {309-320}, pmid = {29955026}, issn = {2095-8137}, mesh = {Animals ; China ; Cytochromes b/*genetics ; Mitochondria/*genetics ; Murinae/anatomy &amp; histology/*genetics ; Phylogeny ; Rats/anatomy &amp; histology/*genetics ; Skull/anatomy &amp; histology ; Surveys and Questionnaires ; Tooth/anatomy &amp; histology ; }, abstract = {Apodemus (mice) and Rattus (rats) are the top rodent reservoirs for zoonoses in China, yet little is known about their diversity. We reexamined the alpha diversity of these two genera based on a new collection of specimens from China and their cyt b sequences in GenBank. We also tested whether species could be identified using external and craniodental measurements exclusively. Measurements from 147 specimens of Apodemus and 236 specimens of Rattus were used for morphological comparisons. We analysed 74 cyt b sequences of Apodemus and 100 cyt b sequences of Rattus to facilitate phylogenetic estimations. Results demonstrated that nine species of Apodemus and seven species of Rattus, plus a new subspecies of Rattus nitidus, are distributed in China. Principal component analysis using external and craniodental measurements revealed that measurements alone could not separate the recognized species. The occurrence of Rattus pyctoris in China remains uncertain.}, }
@article {pmid29953866, year = {2018}, author = {Woodling, NS and Partridge, L}, title = {Parkinson's Disease: Mitochondria Parked at the ER Hit the Snooze Button.}, journal = {Neuron}, volume = {98}, number = {6}, pages = {1059-1061}, doi = {10.1016/j.neuron.2018.06.025}, pmid = {29953866}, issn = {1097-4199}, mesh = {Humans ; Lipids ; Mitochondria ; Mutation ; Neurons ; *Parkinson Disease ; Ubiquitin-Protein Ligases/genetics ; }, abstract = {Parkinson's disease patients report sleep disturbances well ahead of motor symptoms. In this issue of Neuron, Valadas et al. (2018) report that the disease genes pink1 and parkin exert novel, cell-type-specific effects to modulate ER-mitochondria contacts, neuropeptidergic transmission, and sleep patterns.}, }
@article {pmid29950599, year = {2018}, author = {Burgstaller, JP and Kolbe, T and Havlicek, V and Hembach, S and Poulton, J and Piálek, J and Steinborn, R and Rülicke, T and Brem, G and Jones, NS and Johnston, IG}, title = {Large-scale genetic analysis reveals mammalian mtDNA heteroplasmy dynamics and variance increase through lifetimes and generations.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2488}, pmid = {29950599}, issn = {2041-1723}, support = {MR/J010448/1/MRC_/Medical Research Council/United Kingdom ; MR/J013617/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Age Factors ; Animals ; DNA Copy Number Variations/*genetics ; DNA, Mitochondrial/*genetics ; Datasets as Topic ; Female ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; Mice ; Mice, Inbred C57BL ; Mitochondria/metabolism ; Models, Animal ; Oocytes/cytology/immunology ; }, abstract = {Vital mitochondrial DNA (mtDNA) populations exist in cells and may consist of heteroplasmic mixtures of mtDNA types. The evolution of these heteroplasmic populations through development, ageing, and generations is central to genetic diseases, but is poorly understood in mammals. Here we dissect these population dynamics using a dataset of unprecedented size and temporal span, comprising 1947 single-cell oocyte and 899 somatic measurements of heteroplasmy change throughout lifetimes and generations in two genetically distinct mouse models. We provide a novel and detailed quantitative characterisation of the linear increase in heteroplasmy variance throughout mammalian life courses in oocytes and pups. We find that differences in mean heteroplasmy are induced between generations, and the heteroplasmy of germline and somatic precursors diverge early in development, with a haplotype-specific direction of segregation. We develop stochastic theory predicting the implications of these dynamics for ageing and disease manifestation and discuss its application to human mtDNA dynamics.}, }
@article {pmid29950419, year = {2018}, author = {Bilz, NC and Jahn, K and Lorenz, M and Lüdtke, A and Hübschen, JM and Geyer, H and Mankertz, A and Hübner, D and Liebert, UG and Claus, C}, title = {Rubella Viruses Shift Cellular Bioenergetics to a More Oxidative and Glycolytic Phenotype with a Strain-Specific Requirement for Glutamine.}, journal = {Journal of virology}, volume = {92}, number = {17}, pages = {}, pmid = {29950419}, issn = {1098-5514}, mesh = {A549 Cells ; Endothelial Cells/metabolism/virology ; *Energy Metabolism ; Glucose/metabolism/pharmacology ; Glutamine/*metabolism/pharmacology ; Glycolysis/*drug effects ; Homeostasis ; Humans ; Kynurenine/metabolism ; Metabolic Networks and Pathways/drug effects ; Mitochondria/metabolism ; Nucleotides/biosynthesis ; Oxidation-Reduction ; Oxidative Stress ; Oxygen Consumption/drug effects/*physiology ; Phenotype ; Pyruvic Acid/metabolism/pharmacology ; Rubella virus/*metabolism ; Virus Replication/drug effects ; }, abstract = {The flexible regulation of cellular metabolic pathways enables cellular adaptation to changes in energy demand under conditions of stress such as posed by a virus infection. To analyze such an impact on cellular metabolism, rubella virus (RV) was used in this study. RV replication under selected substrate supplementation with glucose, pyruvate, and glutamine as essential nutrients for mammalian cells revealed its requirement for glutamine. The assessment of the mitochondrial respiratory (based on the oxygen consumption rate) and glycolytic (based on the extracellular acidification rate) rate and capacity by respective stress tests through Seahorse technology enabled determination of the bioenergetic phenotype of RV-infected cells. Irrespective of the cellular metabolic background, RV infection induced a shift of the bioenergetic state of epithelial cells (Vero and A549) and human umbilical vein endothelial cells to a higher oxidative and glycolytic level. Interestingly there was a RV strain-specific, but genotype-independent demand for glutamine to induce a significant increase in metabolic activity. While glutaminolysis appeared to be rather negligible for RV replication, glutamine could serve as donor of its amide nitrogen in biosynthesis pathways for important metabolites. This study suggests that the capacity of RVs to induce metabolic alterations could evolve differently during natural infection. Thus, changes in cellular bioenergetics represent an important component of virus-host interactions and could complement our understanding of the viral preference for a distinct host cell population.IMPORTANCE RV pathologies, especially during embryonal development, could be connected with its impact on mitochondrial metabolism. With bioenergetic phenotyping we pursued a rather novel approach in virology. For the first time it was shown that a virus infection could shift the bioenergetics of its infected host cell to a higher energetic state. Notably, the capacity to induce such alterations varied among different RV isolates. Thus, our data add viral adaptation of cellular metabolic activity to its specific needs as a novel aspect to virus-host evolution. In addition, this study emphasizes the implementation of different viral strains in the study of virus-host interactions and the use of bioenergetic phenotyping of infected cells as a biomarker for virus-induced pathological alterations.}, }
@article {pmid29949077, year = {2018}, author = {Lu, Y and Liu, N and Xu, L and Fang, J and Wang, S}, title = {The complete mitochondrial genome of Vanessa indica and phylogenetic analyses of the family Nymphalidae.}, journal = {Genes &amp; genomics}, volume = {40}, number = {10}, pages = {1011-1022}, pmid = {29949077}, issn = {2092-9293}, support = {J10118516034//Undergraduate student scientific research innovation projects of Anhui university/International ; }, mesh = {Animals ; Base Composition ; Butterflies/*classification/cytology/genetics ; Evolution, Molecular ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal/chemistry ; RNA, Ribosomal, 16S/chemistry ; RNA, Transfer/chemistry ; Sequence Analysis, DNA/*methods ; }, abstract = {Vanessa indica is a small butterfly lacking historical molecular and biological research. Vanessa indica belongs to the family Nymphalidae (Lepidoptera: Papilionoidea), which is the largest group of butterflies and are nearly ubiquitous. However, after more than a century of taxonomic and molecular studies, there is no consensus for family classification, and the phylogenetic relationships within Nymphalidae are controversial. The first objective was to sequence and characterize the complete mitochondrial genome of V. indica. The most important objective was to completely reconstruct the phylogenetic relationships for family members within Nymphalidae. The mitochondrial genomic DNA (mtDNA) of V. indica was extracted and amplified by polymerase chain reaction. The complete mitochondrial sequence was annotated and characterized by analyzing sequences with SeqMan program. The phylogenetic analyses were conducted on thirteen protein coding genes (PCGs) in 95 mtDNA of Nymphalidae downloaded from GenBank for reference using the maximum likelihood method and Bayesian inference to ensure the validity of the results. The complete mitogenome was a circular molecule with 15,191 bp consisting of 13 protein coding genes, two ribosomal RNA genes (16S rRNA and 12S rRNA), 22 transfer RNA (tRNA) genes, and an A + T-rich region (D-loop). The nucleotide composition of the genome was highly biased for A + T content, which accounts for 80.0% of the nucleotides. All the tRNAs have putative secondary structures that are characteristic of mitochondrial tRNAs, except tRNA[Ser(AGN)]. All the PCGs started with ATN codons, except cytochrome c oxidase subunit 1 (COX1), which was found to start with an unusual CGA codon. Four genes were observed to have unusual codons: COX1 terminated with atypical TT and the other three genes terminated with a single T. The A + T rich region of 327 bp consisted of repetitive sequences, including a ATAGA motif, a 19-bp poly-T stretch, and two microsatellite-like regions (TA)8. The phylogenetic analyses consistently placed Biblidinae as a sister cluster to Heliconiinae and Calinaginae as a sister clade to Satyrinae. Moreover, the phylogenetic tree identified Libytheinae as a monophyletic group within Nymphalidae. The complete mitogenome of V. indica was 15,191 bp with mitochondrial characterizations common for lepidopteran species, which enriched the mitochondria data of Nymphalid species. And the phylogenetic analysis revealed different classifications and relationships than those previously described. Our results are significant because they would be useful in further understanding of the evolutionary biology of Nymphalidae.}, }
@article {pmid29949074, year = {2018}, author = {Zhang, R and Wang, X}, title = {Characterization and phylogenetic analysis of the complete mitogenome of a rare cavefish, Sinocyclocheilus multipunctatus (Cypriniformes: Cyprinidae).}, journal = {Genes &amp; genomics}, volume = {40}, number = {10}, pages = {1033-1040}, pmid = {29949074}, issn = {2092-9293}, mesh = {Animals ; Base Composition ; Contig Mapping ; Cyprinidae/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {The genus Sinocyclocheilus is a representative group of cave creatures. However, genetic studies on Sinocyclocheilus are rare. The primary objective of this study was to explore the structure and feature of the complete mitochondrial genome of S. multipunctatus, and reconstruct the mitogenomic phylogeny of Sinocyclocheilus. The mitochondrial DNA of S. multipunctatus was amplified by overlapping PCR fragments. The mitogenome was assembled by the SeqMan and annotated using MitoAnnotator. The phylogenetic tree was established using the Bayesian inference and Maximum likelihood methods. The mitogenome of S. multipunctatus is a typical circular molecule of 16,586 bp with base composition A (31.25%), T (25.90%), G (16.35%), and C (26.50%), and consists of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs) genes, two ribosomal RNAs, and a 931 bp control region. Phylogenetic analysis reveals two clades in the Sinocyclocheilus with robust support. S. multipunctatus is close to a newly discovered cavefish, S. ronganensis. We obtained and described the complete mitogenome of S. multipunctatus, and investigated its phylogenetic status, which may provide a valuable resource for future phylogenetic analyses and population genetic studies in Sinocyclocheilus.}, }
@article {pmid29948488, year = {2018}, author = {Yoshida, Y}, title = {The cellular machineries responsible for the division of endosymbiotic organelles.}, journal = {Journal of plant research}, volume = {131}, number = {5}, pages = {727-734}, pmid = {29948488}, issn = {1618-0860}, support = {K05 DA000049/DA/NIDA NIH HHS/United States ; Career Development Award/CDA00049/2018-C//Human Frontier Science Program/ ; KAKENHI/JP18K06325//Japan Society for the Promotion of Science/ ; }, mesh = {Cell Division ; Chloroplasts/physiology/ultrastructure ; Mitochondria/physiology/ultrastructure ; Organelles/physiology/*ultrastructure ; Plastids/physiology/ultrastructure ; Rhodophyta/physiology/*ultrastructure ; *Symbiosis ; }, abstract = {Chloroplasts (plastids) and mitochondria evolved from endosymbiotic bacteria. These organelles perform vital functions in photosynthetic eukaryotes, such as harvesting and converting energy for use in biological processes. Consistent with their evolutionary origins, plastids and mitochondria proliferate by the binary fission of pre-existing organelles. Here, I review the structures and functions of the supramolecular machineries driving plastid and mitochondrial division, which were discovered and first studied in the primitive red alga Cyanidioschyzon merolae. In the past decade, intact division machineries have been isolated from plastids and mitochondria and examined to investigate their underlying structure and molecular mechanisms. A series of studies has elucidated how these division machineries assemble and transform during the fission of these organelles, and which of the component proteins generate the motive force for their contraction. Plastid- and mitochondrial-division machineries have important similarities in their structures and mechanisms despite sharing no component proteins, implying that these division machineries evolved in parallel. The establishment of these division machineries might have enabled the host eukaryotic ancestor to permanently retain these endosymbiotic organelles by regulating their binary fission and the equal distribution of resources to daughter cells. These findings provide key insights into the establishment of endosymbiotic organelles and have opened new avenues of research into their evolution and mechanisms of proliferation.}, }
@article {pmid29948332, year = {2018}, author = {van der Sluis, R}, title = {Analyses of the genetic diversity and protein expression variation of the acyl: CoA medium-chain ligases, ACSM2A and ACSM2B.}, journal = {Molecular genetics and genomics : MGG}, volume = {293}, number = {5}, pages = {1279-1292}, pmid = {29948332}, issn = {1617-4623}, support = {Self-Initiated research grant//South African Medical Research Council/ ; 99323//National Research Foundation/ ; }, mesh = {Coenzyme A Ligases/*genetics/metabolism ; *Genetic Variation ; Glycine/metabolism ; *Haplotypes ; Humans ; Mitochondria, Liver/*enzymology ; Phylogeny ; Substrate Specificity ; Xenobiotics/*metabolism ; }, abstract = {Benzoate (found in milk and widely used as preservative), salicylate (present in fruits and the active component of aspirin), dietary polyphenols produced by gut microbiota, metabolites from organic acidemias, and medium-chain fatty acids (MCFAs) are all metabolised/detoxified by the glycine conjugation pathway. Xenobiotics are first activated to an acyl-CoA by the mitochondrial xenobiotic/medium-chain fatty acid: CoA ligases (ACSMs) and subsequently conjugated to glycine by glycine N-acyltransferase (GLYAT). The MCFAs are activated to acyl-CoA by the ACSMs before entering mitochondrial β-oxidation. This two-step enzymatic pathway has, however, not been thoroughly investigated and the biggest gap in the literature remains the fact that studies continuously characterise the pathway as a one-step reaction. There are no studies available on the interaction/competition of the various substrates involved in the pathway, whilst very little research has been done on the ACSM ligases. To identify variants/haplotypes that should be characterised in future detoxification association studies, this study assessed the naturally observed sequence diversity and protein expression variation of ACSM2A and ACSM2B. The allelic variation, haplotype diversity, Tajima's D values, and phylogenetic analyses indicated that ACSM2A and ACSM2B are highly conserved. This confirmed an earlier hypothesis that the glycine conjugation pathway is highly conserved and essential for life as it maintains the CoA and glycine homeostasis in the liver mitochondria. The protein expression analyses showed that ACSM2A is the predominant transcript in liver. Future studies should investigate the effect of the variants identified in this study on the substrate specificity of these proteins.}, }
@article {pmid29946965, year = {2018}, author = {Sharma, M and Bennewitz, B and Klösgen, RB}, title = {Rather rule than exception? How to evaluate the relevance of dual protein targeting to mitochondria and chloroplasts.}, journal = {Photosynthesis research}, volume = {138}, number = {3}, pages = {335-343}, pmid = {29946965}, issn = {1573-5079}, mesh = {Biological Assay ; Biological Evolution ; Chloroplasts/*metabolism ; Mitochondria/*metabolism ; Protein Transport ; Symbiosis ; }, abstract = {Dual targeting of a nuclearly encoded protein into two different cell organelles is an exceptional event in eukaryotic cells. Yet, the frequency of such dual targeting is remarkably high in case of mitochondria and chloroplasts, the two endosymbiotic organelles of plant cells. In most instances, it is mediated by "ambiguous" transit peptides, which recognize both organelles as the target. A number of different approaches including in silico, in organello as well as both transient and stable in vivo assays are established to determine the targeting specificity of such transit peptides. In this review, we will describe and compare these approaches and discuss the potential role of this unusual targeting process. Furthermore, we will present a hypothetical scenario how dual targeting might have arisen during evolution.}, }
@article {pmid29945721, year = {2018}, author = {Barshad, G and Marom, S and Cohen, T and Mishmar, D}, title = {Mitochondrial DNA Transcription and Its Regulation: An Evolutionary Perspective.}, journal = {Trends in genetics : TIG}, volume = {34}, number = {9}, pages = {682-692}, doi = {10.1016/j.tig.2018.05.009}, pmid = {29945721}, issn = {0168-9525}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; DNA-Binding Proteins/genetics ; DNA-Directed RNA Polymerases/genetics ; *Evolution, Molecular ; Gene Expression Regulation/genetics ; Humans ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics ; Shelterin Complex ; Telomere-Binding Proteins/genetics ; Transcription Factors/genetics ; *Transcription, Genetic ; }, abstract = {The bacterial heritage of mitochondria, as well as its independent genome [mitochondrial DNA (mtDNA)] and polycistronic transcripts, led to the view that mitochondrial transcriptional regulation relies on an evolutionarily conserved, prokaryotic-like system that is separated from the rest of the cell. Indeed, mtDNA transcription was previously thought to be governed by a few dedicated direct regulators, namely, the mitochondrial RNA polymerase (POLRMT), two transcription factors (TFAM and TF2BM), one transcription elongation (TEFM), and one known transcription termination factor (mTERF1). Recent findings have, however, revealed that known nuclear gene expression regulators are also involved in mtDNA transcription and have identified novel transcriptional features consistent with adaptation of the mitochondria to the regulatory environment of the precursor of the eukaryotic cell. Finally, whereas mammals follow the human mtDNA transcription pattern, other organisms notably diverge in terms of mtDNA transcriptional regulation. Hence, mtDNA transcriptional regulation is likely more evolutionary diverse than once thought.}, }
@article {pmid29945248, year = {2018}, author = {Bize, P and Lowe, I and Lehto Hürlimann, M and Heckel, G}, title = {Effects of the Mitochondrial and Nuclear Genomes on Nonshivering Thermogenesis in a Wild Derived Rodent.}, journal = {Integrative and comparative biology}, volume = {58}, number = {3}, pages = {532-543}, doi = {10.1093/icb/icy072}, pmid = {29945248}, issn = {1557-7023}, mesh = {Adipose Tissue, Brown/*physiology ; Animals ; Arvicolinae/classification/genetics/*physiology ; Cell Nucleus/genetics ; Female ; Genome/*physiology ; Genome, Mitochondrial/physiology ; Male ; Thermogenesis/*genetics ; }, abstract = {A key adaptation of mammals to their environment is their ability to maintain a constant high body temperature, even at rest, under a wide range of ambient temperatures. In cold climates, this is achieved by an adaptive production of endogenous heat, known as nonshivering thermogenesis (NST), in the brown adipose tissue (BAT). This organ, unique to mammals, contains a very high density of mitochondria, and BAT correct functioning relies on the correct functioning of its mitochondria. Mitochondria enclose proteins encoded both in the maternally inherited mitochondrial genome and in the biparentally inherited nuclear genome, and one overlooked hypothesis is that both genomes and their interaction may shape NST. By housing under standardized conditions wild-derived common voles (Microtus arvalis) from two distinct evolutionary lineages (Western [W] and Central [C]), we show that W voles had greater NST than C voles. By introgressing those two lineages over at least nine generations, we then experimentally tested the influence of the nuclear and mitochondrial genomes on NST and related phenotypic traits. We found that between-lineage variation in NST and BAT size were significantly influenced by the mitochondrial and nuclear genomes, respectively, with the W mitochondrial genotype being associated with higher NST and the W nuclear genotype with a larger BAT. There were significant mito-nuclear interactions on whole animal body weight and resting metabolic rate (RMR). Hybrid voles were lighter and had higher RMR. Overall, our findings turn new light on the influence of the mitochondrial and nuclear genomes on thermogenesis and building adaptation to the environment in mammals.}, }
@article {pmid29945242, year = {2018}, author = {Buchanan, JL and Meiklejohn, CD and Montooth, KL}, title = {Mitochondrial Dysfunction and Infection Generate Immunity-Fecundity Tradeoffs in Drosophila.}, journal = {Integrative and comparative biology}, volume = {58}, number = {3}, pages = {591-603}, pmid = {29945242}, issn = {1557-7023}, support = {R01 GM067862/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Drosophila melanogaster/genetics/*physiology ; Drosophila simulans/genetics/*physiology ; Female ; Fertility ; *Genotype ; Hybridization, Genetic ; Immunity, Innate ; *Life History Traits ; Male ; Mitochondria/*physiology ; Nutritional Status ; Oxidative Phosphorylation ; Stress, Physiological ; }, abstract = {Physiological responses to short-term environmental stressors, such as infection, can have long-term consequences for fitness, particularly if the responses are inappropriate or nutrient resources are limited. Genetic variation affecting energy acquisition, storage, and usage can limit cellular energy availability and may influence resource-allocation tradeoffs even when environmental nutrients are plentiful. Here, we utilized Drosophila mitochondrial-nuclear genotypes to test whether disrupted mitochondrial function interferes with nutrient-sensing pathways, and whether this disruption has consequences for tradeoffs between immunity and fecundity. We found that an energetically-compromised genotype was relatively resistant to rapamycin-a drug that targets nutrient-sensing pathways and mimics resource limitation. Dietary resource limitation decreased survival of energetically-compromised flies. Furthermore, survival of infection with a natural pathogen was decreased in this genotype, and females of this genotype experienced immunity-fecundity tradeoffs that were not evident in genotypic controls with normal energy metabolism. Together, these results suggest that this genotype may have little excess energetic capacity and fewer cellular nutrients, even when environmental nutrients are not limiting. Genetic variation in energy metabolism may therefore act to limit the resources available for allocation to life-history traits in ways that generate tradeoffs even when environmental resources are not limiting.}, }
@article {pmid29944924, year = {2018}, author = {Chakrabarty, S and Kabekkodu, SP and Singh, RP and Thangaraj, K and Singh, KK and Satyamoorthy, K}, title = {Mitochondria in health and disease.}, journal = {Mitochondrion}, volume = {43}, number = {}, pages = {25-29}, doi = {10.1016/j.mito.2018.06.006}, pmid = {29944924}, issn = {1872-8278}, mesh = {Animals ; Biomedical Research/*trends ; Disease Models, Animal ; Humans ; India ; Mitochondria/*physiology ; Mitochondrial Diseases/diagnosis/*pathology/*physiopathology/therapy ; }, abstract = {Mitochondrial biology has become an area of intense research owing to the unique physiology of the organelle and its role in several types of cancers and other disorders. It has been found that mitochondria-encoded proteins, mitochondrial DNA and even RNA influence the functioning of the cell in more ways than were previously imagined. This may contribute to disease phenotypes which require detailed investigation and communication to the community health care providers. Additionally, this provides several novel avenues in drug designing against various cancers, neurodegenerative diseases and other metabolic disorders. The sixth annual conference of the Society for Mitochondrial Research and Medicine - India (SMRM) titled, 'Mitochondria in Health and Disease' was organized by Rana P. Singh at the School of Life Sciences, Jawaharlal Nehru University in New Delhi, India from 10th to 11th February 2017. The underlying objective of the conference was to provide a platform to discuss the recent advances in basic and translational research in mitochondrial biology and diseases. The conference aimed to translate academic research into clinical practice by providing a forum for basic researchers and clinicians to share their knowledge and build collaborations towards development of advanced therapeutic in mitochondrial diseases. To facilitate the knowledge-sharing, six major themes for the scientific sessions were (1) understanding of mitochondrial biology in disease progression, (2) advances in basic and translational mitochondrial research, (3) mitochondria in evolution and development, (4) targeting mitochondria for cancer prevention and treatment, (5) mitochondria in metabolic and neurological disorders and (6) mitochondria in stem cell and regeneration biology. This report summarizes the major outcomes of the discussions at the conference.}, }
@article {pmid29942045, year = {2018}, author = {Li, D and Waite, DW and Fan, QH and George, S and Semeraro, L and Blacket, MJ}, title = {Molecular detection of small hive beetle Aethina tumida Murray (Coleoptera: Nitidulidae): DNA barcoding and development of a real-time PCR assay.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9623}, pmid = {29942045}, issn = {2045-2322}, mesh = {Animals ; *Bees ; Coleoptera/*classification/*genetics ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Mitochondria/enzymology ; Phylogeny ; *Real-Time Polymerase Chain Reaction ; }, abstract = {Small hive beetle (SHB), Aethina tumida can feed on honey, pollen and brood in honey bee colonies. It was endemic to Africa, but since 1996 has been detected in a number of countries worldwide, including Australia, Brazil, Canada, Italy, Mexico, South Korea, Philippines and the USA where it has had economic effects on local apiculture. To improve SHB identification, we obtained the first reference sequences from the DNA barcoding 5' COI gene region for SHB and some species of the family Nitidulidae associated with beehives. Phylogenetic analysis of SHB COI sequences (3' COI) revealed two divergent lineages, with those from Australia and USA being genetically different from the recent detection in Italy. Many countries, including New Zealand, are currently free from SHB, and require a rapid detection method for biosecurity. Here we present the development and validation of a real-time PCR assay for detection of SHB. The assay showed high specificity and sensitivity for detecting SHB, with no cross-reaction observed with closely related species, such as A. concolor. The real-time PCR is sensitive, detecting the target sequences up to 100 copies/µL. This assay should prove a useful biosecurity tool for rapid detection of SHB worldwide.}, }
@article {pmid29940392, year = {2018}, author = {Wang, Q and Lu, W and Yang, J and Jiang, L and Zhang, Q and Kan, X and Yang, X}, title = {Comparative transcriptomics in three Passerida species provides insights into the evolution of avian mitochondrial complex I.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {28}, number = {}, pages = {27-36}, doi = {10.1016/j.cbd.2018.06.002}, pmid = {29940392}, issn = {1878-0407}, mesh = {Animals ; Avian Proteins/*genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex I/*genetics ; Evolution, Molecular ; *Genes, Mitochondrial ; Genomics ; Phylogeny ; Selection, Genetic ; Sparrows/*genetics ; Species Specificity ; *Transcriptome ; }, abstract = {Recent studies have shown that mitochondria play a crucial role in cellular energy production through the oxidative phosphorylation (OXPHOS) system. Complex I (NADH:ubiquinone oxidoreductase), the first and largest enzyme complex of the OXPHOS system, includes both nuclear- and mitochondrial-encoded proteins. However, the patterns of natural selection and phylogenetic implications of complex I in birds still remain unclear. In this study, we combined transcriptomic and phylogenetic analyses to comprehensively determine the evolution of avian complex I. The transcriptomes of three Passerida species (Leiothrix lutea, Spodiopsar sericeus, and Passer montanus) were obtained using the Illumina HiSeq™ 2500 system. More than 192,000,000 clean reads were assembled in a total of 828,267 transcripts. Evolutionary selection analysis suggested that six genes of the core subunits in avian complex I may have undergone putative positive selection. Notably, we found that the mean dN/dS (ω) ratio for mitochondrial genes of core subunits was significantly lower than that for nuclear genes of non-core subunits within complex I. The constructed maximum-parsimony, maximum-likelihood, and Bayesian inference phylogenetic trees were based on 44 complex I genes. We verified that the family Paridae (represented by Parus major and Pseudopodoces humilis) was clustered with Musicicapoidea. Our results provide new insights into the evolution of avian mitochondrial complex I.}, }
@article {pmid29938587, year = {2019}, author = {Gvozdanović, K and Margeta, V and Margeta, P and Djurkin Kušec, I and Galović, D and Dovč, P and Kušec, G}, title = {Genetic diversity of autochthonous pig breeds analyzed by microsatellite markers and mitochondrial DNA D-loop sequence polymorphism.}, journal = {Animal biotechnology}, volume = {30}, number = {3}, pages = {242-251}, doi = {10.1080/10495398.2018.1478847}, pmid = {29938587}, issn = {1532-2378}, mesh = {Animals ; Breeding ; DNA, Mitochondrial/genetics ; Female ; Gene Frequency ; *Genetic Variation ; Haplotypes ; Male ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Sus scrofa ; Swine/*genetics ; }, abstract = {The evaluation of the genetic structure of autochthonous pig breeds is very important for conservation of local pig breeds and preservation of diversity. In this study, 18 microsatellite loci were used to detect genetic relationship between autochthonous pig breeds [Black Slavonian (BS), Turopolje pig (TP), and Croatian wild boar] and to determine phylogenetic relationship among Croatian autochthonous pig breeds and certain Asian and European pigs using the mitochondrial DNA (mtDNA) D-loop sequence polymorphism. Relatively high degree of genetic variation was found between the observed populations. The analysis of mtDNA showed that haplotypes of the studied pig populations are different from the other European and Chinese haplotypes. BS pigs showed some similarities with Mangalitsa and Duroc breeds. The genetic distances of TP can be explained by high degree of inbreeding during the past century. Despite the European origin of Croatian pig breeds with some impact of Chinese breeds in the past, the results of present study show that genetic diversity is still pronounced within investigated breeds. Furthermore, the genetic diversity is even more pronounced between Croatian breeds and other European and Chinese pig breeds. Thus, conservation of Croatian pig breeds will contribute to overall genetic diversity preservation of pig breeds.}, }
@article {pmid29934612, year = {2018}, author = {Lajbner, Z and Pnini, R and Camus, MF and Miller, J and Dowling, DK}, title = {Experimental evidence that thermal selection shapes mitochondrial genome evolution.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {9500}, pmid = {29934612}, issn = {2045-2322}, mesh = {Animals ; Drosophila melanogaster/genetics ; *Evolution, Molecular ; Female ; Genome, Mitochondrial/*genetics ; Male ; *Selection, Genetic ; *Temperature ; }, abstract = {Mitochondria are essential organelles, found within eukaryotic cells, which contain their own DNA. Mitochondrial DNA (mtDNA) has traditionally been used in population genetic and biogeographic studies as a maternally-inherited and evolutionary-neutral genetic marker. However, it is now clear that polymorphisms within the mtDNA sequence are routinely non-neutral, and furthermore several studies have suggested that such mtDNA polymorphisms are also sensitive to thermal selection. These observations led to the formulation of the "mitochondrial climatic adaptation" hypothesis, for which all published evidence to date is correlational. Here, we use laboratory-based experimental evolution in the fruit fly, Drosophila melanogaster, to test whether thermal selection can shift population frequencies of two mtDNA haplogroups whose natural frequencies exhibit clinal associations with latitude along the Australian east-coast. We present experimental evidence that the thermal regime in which the laboratory populations were maintained drove changes in haplogroup frequencies across generations. Our results strengthen the emerging view that intra-specific mtDNA variants are sensitive to selection, and suggest spatial distributions of mtDNA variants in natural populations of metazoans might reflect adaptation to climatic environments rather than within-population coalescence and diffusion of selectively-neutral haplotypes across populations.}, }
@article {pmid29924334, year = {2018}, author = {Chowdhury, A and Ogura, T and Esaki, M}, title = {Two Cdc48 cofactors Ubp3 and Ubx2 regulate mitochondrial morphology and protein turnover.}, journal = {Journal of biochemistry}, volume = {164}, number = {5}, pages = {349-358}, doi = {10.1093/jb/mvy057}, pmid = {29924334}, issn = {1756-2651}, mesh = {Carrier Proteins/genetics/*metabolism ; Endopeptidases/genetics/*metabolism ; GTP Phosphohydrolases/*metabolism ; Membrane Proteins/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Saccharomyces cerevisiae/growth &amp; development/*metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; }, abstract = {Mitochondria continuously undergo coordinated fusion and fission during vegetative growth to keep their homogeneity and to remove damaged components. A cytosolic AAA ATPase, Cdc48, is implicated in the mitochondrial fusion event and turnover of a fusion-responsible GTPase in the mitochondrial outer membrane, Fzo1, suggesting a possible linkage of mitochondrial fusion and Fzo1 turnover. Here, we identified two Cdc48 cofactor proteins, Ubp3 and Ubx2, involving mitochondria regulation. In the absence of UBP3, mitochondrial fragmentation and aggregation were observed. The turnover of Fzo1 was not affected in Δubp3, but instead a deubiquitylase Ubp12 that removes fusion-required polyubiquitin chains from Fzo1 was stabilized. Thus, excess amount of Ubp12 may lead to mitochondrial fragmentation by removal of fusion-competent ubiquitylated Fzo1. In contrast, deletion of UBX2 perturbed disassembly of Fzo1 oligomers and their degradation without alteration of mitochondrial morphology. The UBX2 deletion led to destabilization of Ubp2 that negatively regulates Fzo1 turnover by removing degradation-signalling polyubiquitin chains, suggesting that Ubx2 would directly facilitate Fzo1 degradation. These results indicated that two different Cdc48-cofactor complexes independently regulate mitochondrial fusion and Fzo1 turnover.}, }
@article {pmid29923829, year = {2018}, author = {Vitali, DG and Käser, S and Kolb, A and Dimmer, KS and Schneider, A and Rapaport, D}, title = {Independent evolution of functionally exchangeable mitochondrial outer membrane import complexes.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {29923829}, issn = {2050-084X}, support = {ITN TAMPting, 607072//Marie Curie/United Kingdom ; }, mesh = {Biological Coevolution ; Gene Deletion ; *Gene Expression Regulation, Fungal ; Genetic Complementation Test ; Membrane Proteins/*genetics/metabolism ; Mitochondria/genetics/metabolism ; Mitochondrial Membrane Transport Proteins/*genetics/metabolism ; Mitochondrial Membranes/*metabolism ; Organelle Biogenesis ; Phosphorylation ; Protein Isoforms/genetics/metabolism ; Protozoan Proteins/*genetics/metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; Trypanosoma brucei brucei/*genetics/metabolism ; }, abstract = {Assembly and/or insertion of a subset of mitochondrial outer membrane (MOM) proteins, including subunits of the main MOM translocase, require the fungi-specific Mim1/Mim2 complex. So far it was unclear which proteins accomplish this task in other eukaryotes. Here, we show by reciprocal complementation that the MOM protein pATOM36 of trypanosomes is a functional analogue of yeast Mim1/Mim2 complex, even though these proteins show neither sequence nor topological similarity. Expression of pATOM36 rescues almost all growth, mitochondrial biogenesis, and morphology defects in yeast cells lacking Mim1 and/or Mim2. Conversely, co-expression of Mim1 and Mim2 restores the assembly and/or insertion defects of MOM proteins in trypanosomes ablated for pATOM36. Mim1/Mim2 and pATOM36 form native-like complexes when heterologously expressed, indicating that additional proteins are not part of these structures. Our findings indicate that Mim1/Mim2 and pATOM36 are the products of convergent evolution and arose only after the ancestors of fungi and trypanosomatids diverged.}, }
@article {pmid29923828, year = {2018}, author = {Tokatlidis, K}, title = {Shaping the import system of mitochondria.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {29923828}, issn = {2050-084X}, support = {MC_PC_17190/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Mitochondria ; *Mitochondrial Membranes ; }, abstract = {Evidence is accumulating that unrelated species have independently evolved the same way of importing proteins in their mitochondria.}, }
@article {pmid29916730, year = {2018}, author = {Chang, CH and Dai, WY and Chen, TY and Lee, AH and Hou, HY and Liu, SH and Jang-Liaw, NH}, title = {DNA barcoding reveals CITES-listed species among Taiwanese government-seized chelonian specimens.}, journal = {Genome}, volume = {61}, number = {8}, pages = {615-624}, doi = {10.1139/gen-2017-0264}, pmid = {29916730}, issn = {1480-3321}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Genetic Markers ; Government ; Mitochondria/*genetics ; Phylogeny ; Species Specificity ; Taiwan ; Turtles/classification/*genetics ; }, abstract = {Compared to traditional morphological identification, DNA barcoding-molecular identification based on sequencing of a segment of mitochondrial cytochrome c oxidase subunit I (COI)-provides a shortcut to authenticating chelonian identifications. Here, we selected 63 government-seized chelonian specimens deposited at Taipei Zoo for DNA barcoding analysis. DNA barcoding and subsequent phylogenetic analysis successfully authenticated 36 chelonian species, including five that are listed in CITES Appendix I. Approximately 90% (57/63) of the specimens were successfully authenticated by our molecular approach, but lack or error of BOLD reference sequences, biological processes such as hybridization, and uncertain species delimitation all reduced the accuracy of DNA barcoding. To increase the accuracy of DNA barcoding, Taipei Zoo will continue to enrich the BOLD database and also establish a genetic database, to include additional genetic markers, by using government-seized chelonian specimens. A fast and accurate method to authenticate seized samples could assist law enforcement agencies to prosecute criminals and restrict illegal exploitation of wild chelonian resources.}, }
@article {pmid29913250, year = {2018}, author = {Seligmann, H}, title = {Giant viruses as protein-coated amoeban mitochondria?.}, journal = {Virus research}, volume = {253}, number = {}, pages = {77-86}, doi = {10.1016/j.virusres.2018.06.004}, pmid = {29913250}, issn = {1872-7492}, mesh = {Acanthamoeba/genetics/metabolism/*virology ; *Biological Evolution ; Gene Order ; Genome Size ; Genome, Viral ; Giant Viruses/*genetics/physiology ; Mitochondria/genetics/metabolism/*virology ; Phylogeny ; Protozoan Proteins/genetics/*metabolism ; }, abstract = {Mimivirus' genome includes parts of 5S, 16S and 23S ribosomal RNAs encoded by Acanthamoeba's mitogenome, the giant virus' host. Two non-exclusive hypotheses for rRNA remnants in giant viruses are examined: 1. mitogenomes invade viral genomes as they do for nuclear chromosomes (producing numts); 2. megaviral genomes evolved from an ancestral mitogenome. Alignment analyses confirm mitochondrial, rather than alphaproteobacterial origins of megaviral rRNAs. Other mitogenes have likely megaviral homologues. These megaviral homologues coevolve to much larger extents than candidate rRNA homologues, suggesting rRNA decay in viruses. Megaviral mitogene homologues overall follow mitochondrial gene order, suggesting mitogenome ancestry. Ancestral synteny decreases with megaviral genome size, suggesting that subsequent mitogene insertions blur ancestral gene order. Putative defenses against DNA invasion conserve mitogene order in short megaviral genomes. Synteny between mitogenome and megaviral genomes confirms the RNA/DNA polymerase-homologies-based hypothesis that giant viruses have mitochondrial-like ancestors, viral rRNA remnants are corollary of mitogenomic origins of megaviral genomes. Note that giant viruses, mitochondria and bacterial spores all have double membranes, spores and viruses have protein coats. Mitochondria might occasionally form spore-like structures that drifted into megaviruses. These missing links could confirm mitogenome ancestry of giant viruses rather than giant virus ancestry of mitochondria.}, }
@article {pmid29913080, year = {2018}, author = {Wilkerson, CD and Mahoney, SP and Carr, SM}, title = {Post-glacial recolonization of insular Newfoundland across the Strait of Belle Isle gave rise to an endemic subspecies of woodland caribou, Rangifer tarandus terranovae (Bangs, 1896): evidence from mtDNA haplotypes.}, journal = {Genome}, volume = {61}, number = {8}, pages = {575-585}, doi = {10.1139/gen-2017-0199}, pmid = {29913080}, issn = {1480-3321}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Forests ; *Genetic Speciation ; Haplotypes/genetics ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Newfoundland and Labrador ; Reindeer/*genetics ; }, abstract = {Post-glacial origins of woodland caribou (Rangifer tarandus subsp.) on the island of Newfoundland and their relationship to mainland populations have been uncertain. Sequence analysis of 2223 bp of the mitochondrial DNA control region and cytochrome b gene from 233 Newfoundland caribou identified 32 haplotypes in four major clades. Comparison with other Nearctic caribou confirms a closer affinity of the basal Clade A with animals from the mainland, and as an outgroup to Clades B, C, and D that are endemic to the island. This indicates re-entry of caribou to post-glacial Newfoundland across the Strait of Belle Isle from Labrador, rather than from southern coastal refugia. Newfoundland caribou are a distinct subspecies, Rangifer tarandus terranovae (Bangs, 1896). Hierarchical AMOVA shows significant clinal differentiation of the major clades from northwest to southeast across the island. The isolated Avalon Peninsula population in the extreme southeast is genetically depauperate. Founder effects are evident in herds introduced to previously unoccupied areas by wildlife managers over the past 40-50 years. Reindeer introduced in the early 20th century have not contributed to mtDNA diversity in Newfoundland caribou.}, }
@article {pmid29910126, year = {2018}, author = {Zambelli, F and Mertens, J and Dziedzicka, D and Sterckx, J and Markouli, C and Keller, A and Tropel, P and Jung, L and Viville, S and Van de Velde, H and Geens, M and Seneca, S and Sermon, K and Spits, C}, title = {Random Mutagenesis, Clonal Events, and Embryonic or Somatic Origin Determine the mtDNA Variant Type and Load in Human Pluripotent Stem Cells.}, journal = {Stem cell reports}, volume = {11}, number = {1}, pages = {102-114}, pmid = {29910126}, issn = {2213-6711}, mesh = {Alleles ; Cell Culture Techniques ; Cell Differentiation/*genetics ; Chromosome Aberrations ; Clonal Evolution/*genetics ; *DNA, Mitochondrial ; Fibroblasts/metabolism ; Gene Expression Profiling ; Genetic Heterogeneity ; Genetic Variation ; Genomic Instability ; Genotype ; Humans ; Mosaicism ; *Mutagenesis ; Pluripotent Stem Cells/*metabolism ; }, abstract = {In this study, we deep-sequenced the mtDNA of human embryonic and induced pluripotent stem cells (hESCs and hiPSCs) and their source cells and found that the majority of variants pre-existed in the cells used to establish the lines. Early-passage hESCs carried few and low-load heteroplasmic variants, similar to those identified in oocytes and inner cell masses. The number and heteroplasmic loads of these variants increased with prolonged cell culture. The study of 120 individual cells of early- and late-passage hESCs revealed a significant diversity in mtDNA heteroplasmic variants at the single-cell level and that the variants that increase during time in culture are always passenger to the appearance of chromosomal abnormalities. We found that early-passage hiPSCs carry much higher loads of mtDNA variants than hESCs, which single-fibroblast sequencing proved pre-existed in the source cells. Finally, we show that these variants are stably transmitted during short-term differentiation.}, }
@article {pmid29909242, year = {2018}, author = {Pinheiro, GMS and Ramos, CHI}, title = {Initial characterization of newly identified mitochondrial and chloroplast small HSPs from sugarcane shows that these chaperones have different oligomerization states and substrate specificities.}, journal = {Plant physiology and biochemistry : PPB}, volume = {129}, number = {}, pages = {285-294}, doi = {10.1016/j.plaphy.2018.06.002}, pmid = {29909242}, issn = {1873-2690}, mesh = {Chloroplasts/*metabolism ; Chromatography, Gel ; Cloning, Molecular ; Heat-Shock Proteins/chemistry/genetics/isolation &amp; purification/*metabolism ; Mitochondria/*metabolism ; Phylogeny ; Plant Proteins/chemistry/genetics/isolation &amp; purification/*metabolism ; Saccharum/genetics/*metabolism ; Sequence Alignment ; Spectrometry, Fluorescence ; Substrate Specificity ; }, abstract = {Chaperones belonging to the small heat shock protein (sHSP) family are ubiquitous and exhibit elevated expression under stresses conditions to protect proteins against aggregation, thereby contributing to the stress tolerance of the organism. Tropical plants are constantly exposed to high temperatures, and the mechanisms by which these plants tolerate heat stress are of foremost importance to basic science as well as applied agrobiotechnology. Therefore, this study aims to characterize sHSPs from different organelles from sugarcane, an important crop that is associated with sugar and bioenergy production. An expression sequence tag database of sugarcane was searched, and sHsp genes of mitochondrial and chloroplast organelles were selected and cloned. The proteins were expressed in Escherichia coli and isolated and purified by two chromatographic steps with high purity as single species. Circular dichroism and fluorescence spectroscopy showed that both proteins were purified in their folded states with a predominant β-sheet secondary structure. Determination of the molecular weight, diffusion coefficient and Stokes radius parameters showed that both chaperones form large spherical-like oligomers in solution. The two sHSPs had different oligomeric states and substrate specificities. The mitochondrial sHSP was a 20-mer with ability to protect model substrates that differ from that of the 16-meric sHSP from chloroplasts. These results indicate that both sHSPs are key agents to protect against stress confirming the importance of the great diversity of sHSP chaperones in plants for homeostasis maintenance. Moreover, to our knowledge, this is the first report about small HSPs from sugarcane organelles.}, }
@article {pmid29904051, year = {2018}, author = {Chen, N and Cai, Y and Chen, Q and Li, R and Wang, K and Huang, Y and Hu, S and Huang, S and Zhang, H and Zheng, Z and Song, W and Ma, Z and Ma, Y and Dang, R and Zhang, Z and Xu, L and Jia, Y and Liu, S and Yue, X and Deng, W and Zhang, X and Sun, Z and Lan, X and Han, J and Chen, H and Bradley, DG and Jiang, Y and Lei, C}, title = {Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {2337}, pmid = {29904051}, issn = {2041-1723}, support = {31501918//National Natural Science Foundation of China (National Science Foundation of China)/International ; }, mesh = {Animals ; *Breeding ; Cattle/*genetics ; China ; Chromosomes/ultrastructure ; Domestication ; Female ; Genetic Variation ; *Genetics, Population ; *Genome ; Geography ; Haplotypes ; Male ; Mitochondria ; Models, Statistical ; Phylogeny ; Polymorphism, Single Nucleotide ; Species Specificity ; Tibet ; }, abstract = {Cattle domestication and the complex histories of East Asian cattle breeds warrant further investigation. Through analysing the genomes of 49 modern breeds and eight East Asian ancient samples, worldwide cattle are consistently classified into five continental groups based on Y-chromosome haplotypes and autosomal variants. We find that East Asian cattle populations are mainly composed of three distinct ancestries, including an earlier East Asian taurine ancestry that reached China at least ~3.9 kya, a later introduced Eurasian taurine ancestry, and a novel Chinese indicine ancestry that diverged from Indian indicine approximately 36.6-49.6 kya. We also report historic introgression events that helped domestic cattle from southern China and the Tibetan Plateau achieve rapid adaptation by acquiring ~2.93% and ~1.22% of their genomes from banteng and yak, respectively. Our findings provide new insights into the evolutionary history of cattle and the importance of introgression in adaptation of cattle to new environmental challenges in East Asia.}, }
@article {pmid29902489, year = {2018}, author = {Uzarska, MA and Przybyla-Toscano, J and Spantgar, F and Zannini, F and Lill, R and Mühlenhoff, U and Rouhier, N}, title = {Conserved functions of Arabidopsis mitochondrial late-acting maturation factors in the trafficking of iron‑sulfur clusters.}, journal = {Biochimica et biophysica acta. Molecular cell research}, volume = {1865}, number = {9}, pages = {1250-1259}, doi = {10.1016/j.bbamcr.2018.06.003}, pmid = {29902489}, issn = {0167-4889}, mesh = {Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Cloning, Molecular ; DNA-Binding Proteins/genetics/metabolism ; Evolution, Molecular ; Iron/metabolism ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Saccharomyces cerevisiae/genetics/*growth &amp; development ; Sulfur/metabolism ; }, abstract = {Numerous proteins require iron‑sulfur (Fe-S) clusters as cofactors for their function. Their biogenesis is a multi-step process occurring in the cytosol and mitochondria of all eukaryotes and additionally in plastids of photosynthetic eukaryotes. A basic model of Fe-S protein maturation in mitochondria has been obtained based on studies achieved in mammals and yeast, yet some molecular details, especially of the late steps, still require investigation. In particular, the late-acting biogenesis factors in plant mitochondria are poorly understood. In this study, we expressed the factors belonging to NFU, BOLA, SUFA/ISCA and IBA57 families in the respective yeast mutant strains. Expression of the Arabidopsis mitochondrial orthologs was usually sufficient to rescue the growth defects observed on specific media and/or to restore the abundance or activity of the defective Fe-S or lipoic acid-dependent enzymes. These data demonstrate that the plant mitochondrial counterparts, including duplicated isoforms, likely retained their ancestral functions. In contrast, the SUFA1 and IBA57.2 plastidial isoforms cannot rescue the lysine and glutamate auxotrophies of the respective isa1-isa2Δ and iba57Δ strains or of the isa1-isa2-iba57Δ triple mutant when expressed in combination. This suggests a specialization of the yeast mitochondrial and plant plastidial factors in these late steps of Fe-S protein biogenesis, possibly reflecting substrate-specific interactions in these different compartments.}, }
@article {pmid29902241, year = {2018}, author = {Yoshino, H and Yamaji, F and Ohsawa, TA}, title = {Genetic structure and dispersal patterns in Limnoria nagatai (Limnoriidae, Isopoda) dwelling in non-buoyant kelps, Eisenia bicyclis and E. arborea, in Japan.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0198451}, pmid = {29902241}, issn = {1932-6203}, mesh = {Animals ; Demography ; Electron Transport Complex IV/*genetics ; Gene Flow ; Isopoda/*classification/physiology ; Japan ; Kelp/*classification/physiology ; Mitochondria/genetics ; Pacific Ocean ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*methods ; }, abstract = {The marine isopod genus Limnoria contains algae-eating species. Previous phylogeographic studies have suggested that Limnoria species feeding on buoyant kelp underwent low genetic differentiation on a large spatial scale because rafting on floating host kelps promotes high levels of gene flow. In this paper, we survey the genetic structure of Limnoria nagatai, which bores into the non-buoyant kelps Eisenia bicyclis and E. arborea. We analyze the mitochondrial DNA (cytochrome oxidase subunit I [COI] gene) and morphological traits of L. nagatai, and the host kelps E. bicyclis and E. arborea from 14 populations along the Japanese archipelago of the Pacific Ocean and the Sea of Japan. Four major lineages are recognized within L. nagatai: three lineages in the Pacific Ocean, and one lineage in the Sea of Japan which might be a cryptic species. For L. nagatai, we show high genetic differentiation between geographically separated habitats in the Pacific Ocean, while low differentiation is found among continuous host kelps habitats in the Pacific Ocean as well as the Sea of Japan. L. nagatai in E. bicyclis in the Pacific Ocean has experienced large population expansion after the Last Glacial Maximum (LGM), whereas the lineage in E. bicyclis in the Sea of Japan has not. We suggest that Limnoria feeding on non-buoyant kelps, may attain low genetic differentiation because they might be able to disperse long distance if the habitat of host kelps is continuous. The historical events affecting Limnoria after the LGM may differ between the coasts of the Pacific Ocean and the Sea of Japan.}, }
@article {pmid29897900, year = {2018}, author = {Chadha, S and Vijayan, R and Gupta, S and Munde, M and Gourinath, S and Madhubala, R}, title = {Genetic manipulation of Leishmania donovani threonyl tRNA synthetase facilitates its exploration as a potential therapeutic target.}, journal = {PLoS neglected tropical diseases}, volume = {12}, number = {6}, pages = {e0006575}, pmid = {29897900}, issn = {1935-2735}, mesh = {Drug Delivery Systems ; Escherichia coli/enzymology/genetics ; Fatty Alcohols/pharmacology ; Gene Expression ; Humans ; Leishmania donovani/drug effects/*enzymology/genetics/pathogenicity ; Leishmaniasis, Visceral/*parasitology ; Organisms, Genetically Modified ; Phylogeny ; Protein Domains ; Protein Transport ; Protozoan Proteins/antagonists &amp; inhibitors/genetics/isolation &amp; purification/metabolism ; Recombinant Proteins ; Sequence Deletion ; Threonine-tRNA Ligase/antagonists &amp; inhibitors/*genetics/isolation &amp; purification/metabolism ; }, abstract = {BACKGROUND: Aminoacyl tRNA synthetases are central enzymes required for protein synthesis. These enzymes are the known drug targets in bacteria and fungi. Here, we for the first time report the functional characterization of threonyl tRNA synthetase (LdThrRS) of Leishmania donovani, a protozoan parasite, the primary causative agent of visceral leishmaniasis.<br><br>METHODOLOGY: Recombinant LdThrRS (rLdThrRS) was expressed in E. coli and purified. The kinetic parameters for rLdThrRS were determined. The subcellular localization of LdThrRS was done by immunofluorescence analysis. Heterozygous mutants of LdThrRS were generated in Leishmania promastigotes. These genetically manipulated parasites were checked for their proliferation, virulence, aminoacylation activity and sensitivity to the known ThrRS inhibitor, borrelidin. An in silico generated structural model of L. donovani ThrRS was compared to that of human.<br><br>CONCLUSIONS: Recombinant LdThrRS displayed aminoacylation activity, and the protein is possibly localized to both the cytosol and mitochondria. The comparison of the 3D-model of LdThrRS to human ThrRS displayed considerable similarity. Heterozygous parasites showed restrictive growth phenotype and had attenuated infectivity. These heterozygous parasites were more susceptible to inhibition by borrelidin. Several attempts to obtain ThrRS homozygous null mutants were not successful, indicating its essentiality for the Leishmania parasite. Borrelidin showed a strong affinity for LdThrRS (KD: 0.04 &#x3bc;M) and was effective in inhibiting the aminoacylation activity of the rLdThrRS (IC50: 0.06 &#x3bc;M). Borrelidin inhibited the promastigotes (IC50: 21 &#x3bc;M) stage of parasites. Our data shows that LdThrRS is essential for L. donovani survival and is likely to bind with small drug-like molecules with strong affinity, thus making it a potential target for drug discovery efforts.}, }
@article {pmid29893915, year = {2018}, author = {Chen, N and Wang, P and Li, C and Wang, Q and Pan, J and Xiao, F and Wang, Y and Zhang, K and Li, C and Yang, B and Sun, C and Deng, X}, title = {A Single Nucleotide Mutation of the IspE Gene Participating in the MEP Pathway for Isoprenoid Biosynthesis Causes a Green-Revertible Yellow Leaf Phenotype in Rice.}, journal = {Plant &amp; cell physiology}, volume = {59}, number = {9}, pages = {1905-1917}, doi = {10.1093/pcp/pcy108}, pmid = {29893915}, issn = {1471-9053}, mesh = {Base Sequence ; Chloroplasts/*metabolism ; Cloning, Molecular ; Gene Expression Regulation, Plant ; Genetic Complementation Test ; Mitochondria/metabolism ; Oryza/*genetics ; Photosynthesis/genetics/physiology ; Phylogeny ; Plant Leaves/*metabolism ; Plant Proteins/metabolism ; *Polymorphism, Single Nucleotide ; Terpenes/*metabolism ; }, abstract = {Plant isoprenoids are dependent on two independent pathways, the cytosolic mevalonate (MVA) pathway and the plastidic methylerythritol phosphate (MEP) pathway. IspE is one of seven known enzymes in the MEP pathway. Currently, no IspE gene has been identified in rice. In addition, no virescent mutants have been reported to result from a gene mutation affecting the MEP pathway. In this study, we isolated a green-revertible yellow leaf mutant gry340 in rice. The mutant exhibited a reduced level of photosynthetic pigments, and an arrested development of chloroplasts and mitochondria in its yellow leaves. Map-based cloning revealed a missense mutation in OsIspE (LOC_Os01g58790) in gry340 mutant plants. OsIspE is constitutively expressed in all tissues, and its encoded protein is targeted to the chloroplast. Further, the mutant phenotype of gry340 was rescued by introduction of the wild-type gene. Therefore, we have successfully identified an IspE gene in monocotyledons via map-based cloning, and confirmed that the green-revertible yellow leaf phenotype of gry340 does result from a single nucleotide mutation in the IspE gene. In addition, the ispE ispF double mutant displayed an etiolation lethal phenotype, indicating that the isoprenoid precursors from the cytosol cannot efficiently compensate for the deficiency of the MEP pathway in rice chloroplasts. Furthermore, real-time quantitative reverse transcription-PCR suggested that this functional defect in OsIspE affected the expression of not only other MEP pathway genes but also that of MVA pathway genes, photosynthetic genes and mitochondrial genes.}, }
@article {pmid29892953, year = {2018}, author = {Liu, W and Hu, C and Xie, W and Chen, P and Zhang, Y and Yao, R and Li, K and Chang, Q}, title = {The mitochondrial genome of red-necked phalarope Phalaropus lobatus (Charadriiformes: Scolopacidae) and phylogeny analysis among Scolopacidae.}, journal = {Genes &amp; genomics}, volume = {40}, number = {5}, pages = {455-463}, pmid = {29892953}, issn = {2092-9293}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Birds/genetics ; Charadriiformes/*genetics ; DNA, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {The red-necked phalarope is a wonderful species with specific morphological characters and lifestyles. Mitochondrial genomes, encoding necessary proteins involved in the system of energy metabolism, are important for the evolution and adaption of species. In this study, we determined the complete mitogenome sequence of Phalaropus lobatus (Charadriiformes: Scolopacidae). The circular genome is 16714 bp in size, containing 13 PCGs, two ribosomal RNAs and 22 tRNAs and a high AT-rich control region. The AT skew and GC skew of major strand is positive and negative respectively. Most of PCGs are biased towards A-rich except ND1. A codon usage analysis shows that 3 start codons (ATG, GTG and ATA), 4 stop codons (TAA, TAG, AGG, AGA) and two incomplete terminate codons (T-). Twenty two transfer RNAs have the typical cloverleaf structure, and a total of ten base pairs are mismatched throughout the nine tRNA genes. The phylogenetic tree based on 13 PCGs and 2 rRNA genes indicates that monophyly of the family and genus Phalaropus is close to genus Xenus plus Tringa. The analysis of selective pressure shows 13 protein-coding genes are evolving under the purifying selection and P. lobatus is different from other Scolopacidae species on the selective pressure of gene ND4. This study helps us know the inherent mechanism of mitochondrial structure and natural selection.}, }
@article {pmid29885222, year = {2017}, author = {Rydin, C and Wikström, N and Bremer, B}, title = {Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny.}, journal = {American journal of botany}, volume = {104}, number = {10}, pages = {1522-1532}, doi = {10.3732/ajb.1700255}, pmid = {29885222}, issn = {1537-2197}, mesh = {Genome, Mitochondrial/*genetics ; Genome, Plant/*genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; Phylogeny ; Rubiaceae/*genetics ; Sequence Analysis, DNA ; }, abstract = {PREMISE OF THE STUDY: Reconstruction of plant phylogeny has heavily relied on single-gene or multigene plastid data. New sequencing methods have led to an increasing number of studies based on data from the entire plastid, but the mitochondrion has rarely been used to infer plant phylogeny because of an assumed information poverty and demonstrated lateral transfer of mitochondrial gene regions between distantly related species.<br><br>METHODS: We explored phylogenetic information from the plant mitochondrion using 57 representatives of the species-rich coffee family as study system and assessed consistency with previous results based (mostly) on plastid data.<br><br>KEY RESULTS: We showed that the mitochondrial genome can provide structured and statistically significant information on plant phylogeny. While most of our results are consistent with those based on plastid data, some surprising and statistically significant conflicts emerge, and our study demonstrates with striking clarity that the phylogeny of Rubiaceae is far from resolved.<br><br>CONCLUSIONS: It appears unlikely that conflicts between results retrieved from the different genomic compartments would be restricted to Rubiaceae. Rather, they are probably a general phenomenon and an important factor behind longstanding "difficult" phylogenetic questions. The biological processes responsible for the conflicting results detected here are unclear, but some conflicts are likely caused by hybridization events that occurred tens of millions of years ago. Whether such ancient events can be reconstructed based on molecular data from extant plants remains to be seen, but future studies of the nuclear genome may provide a way forward.}, }
@article {pmid29883862, year = {2018}, author = {Tyagi, A and Pramanik, R and Vishnubhatla, S and Ali, S and Bakhshi, R and Chopra, A and Singh, A and Bakhshi, S}, title = {Pattern of mitochondrial D-loop variations and their relation with mitochondrial encoded genes in pediatric acute myeloid leukemia.}, journal = {Mutation research}, volume = {810}, number = {}, pages = {13-18}, doi = {10.1016/j.mrfmmm.2018.05.002}, pmid = {29883862}, issn = {1873-135X}, mesh = {Adolescent ; Base Sequence ; Child ; Child, Preschool ; Cyclooxygenase 1/*genetics ; Cytochromes b/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex I/*genetics ; Humans ; Infant ; Leukemia, Myeloid, Acute/*genetics ; Mitochondria/*genetics ; Mitochondrial Proton-Translocating ATPases/*genetics ; *Mutation Rate ; Prospective Studies ; Sequence Analysis, DNA ; }, abstract = {Role of mitochondrial DNA variations, particularly in D loop region, remains investigational in acute myeloid leukaemia (AML). Consecutive 151 pediatric AML patients were prospectively enrolled from June 2013 to August 2016, for evaluating pattern of variations in mitochondrial D-loop region and to determine their association, if any, with expression of mitochondrial-encoded genes. For each patient, D-loop region was sequenced on baseline bone marrow, buccal swab and mother's blood sample. Real time PCR was used for relative gene expression of four mitochondrial DNA encoded genes viz. Nicotinamide-adenine-dineucleotide-dehydrogenase subunit 3 (ND3), Cytochrome-B (Cyt-B), Cytochrome c oxidase-I (COX1) and ATP-synthetase F0 subunit-6 (ATP6). Total 1490 variations were found at 237 positions in D-Loop; 1206 (80.9%) were germline and 284 (19.1%) were somatic. Positions 73-263 were identified as a probable hotspot region. G bases appeared to be most stable nucleotide (least number of single base substitutions) whereas T appeared to be most susceptible to variations with germline T-C being the commonest. Gene expression of Cyt-B was found to be significantly higher for any variation (somatic or germline) at positions 16,192 and 16,327 while it was significantly lower for variations at positions 16,051 and 207. Any variation at positions 152, 207 and 513 significantly decreased COX1 expression while those at positions 16,051 and 152 attenuated ATP6 expression. This first study evaluated type and overall pattern of D-loop variations in AML, and also showed that some of these variations in D loop region might have an effect on the mitochondrial-encoded genes which is new and valuable information in AML genomics.}, }
@article {pmid29880721, year = {2018}, author = {Zhang, H and Burr, SP and Chinnery, PF}, title = {The mitochondrial DNA genetic bottleneck: inheritance and beyond.}, journal = {Essays in biochemistry}, volume = {62}, number = {3}, pages = {225-234}, doi = {10.1042/EBC20170096}, pmid = {29880721}, issn = {1744-1358}, support = {101876/Z/13/Z//Wellcome Trust/United Kingdom ; MC_UP_1501/2//Medical Research Council/United Kingdom ; G0601943//Medical Research Council/United Kingdom ; }, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Gene-Environment Interaction ; Genetic Drift ; *Genetic Predisposition to Disease ; Humans ; Mitochondria/physiology ; Organelle Biogenesis ; Selection, Genetic ; }, abstract = {mtDNA is a multicopy genome. When mutations exist, they can affect a varying proportion of the mtDNA present within every cell (heteroplasmy). Heteroplasmic mtDNA mutations can be maternally inherited, but the proportion of mutated alleles differs markedly between offspring within one generation. This led to the genetic bottleneck hypothesis, explaining the rapid changes in allele frequency seen during transmission from one generation to the next. Although a physical reduction in mtDNA has been demonstrated in several species, a comprehensive understanding of the molecular mechanisms is yet to be revealed. Several questions remain, including the role of selection for and against specific alleles, whether all bottlenecks are the same, and precisely how the bottleneck is controlled during development. Although originally thought to be limited to the germline, there is evidence that bottlenecks exist in other cell types during development, perhaps explaining why different tissues in the same organism contain different levels of mutated mtDNA. Moreover, tissue-specific bottlenecks may occur throughout life in response to environmental influences, adding further complexity to the situation. Here we review key recent findings, and suggest ways forward that will hopefully advance our understanding of the role of mtDNA in human disease.}, }
@article {pmid29879897, year = {2018}, author = {Hein, A and Knoop, V}, title = {Expected and unexpected evolution of plant RNA editing factors CLB19, CRR28 and RARE1: retention of CLB19 despite a phylogenetically deep loss of its two known editing targets in Poaceae.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {85}, pmid = {29879897}, issn = {1471-2148}, mesh = {Arabidopsis/genetics ; Base Sequence ; Cell Nucleus/metabolism ; Chloroplasts/genetics ; *Evolution, Molecular ; Mitochondria/genetics ; *Phylogeny ; Plant Proteins/*genetics/metabolism ; Poaceae/*genetics ; RNA Editing/*genetics ; RNA, Messenger/genetics/metabolism ; RNA, Plant/*genetics/metabolism ; RNA-Binding Proteins/*genetics ; Species Specificity ; }, abstract = {BACKGROUND: C-to-U RNA editing in mitochondria and chloroplasts and the nuclear-encoded, RNA-binding PPR proteins acting as editing factors present a wide field of co-evolution between the different genetic systems in a plant cell. Recent studies on chloroplast editing factors RARE1 and CRR28 addressing one or two chloroplast editing sites, respectively, found them strictly conserved among 65 flowering plants as long as one of their RNA editing targets remained present.<br><br>RESULTS: Extending the earlier sampling to 117 angiosperms with high-quality genome or transcriptome data, we find more evidence confirming previous conclusions but now also identify cases for expected evolutionary transition states such as retention of RARE1 despite loss of its editing target or the degeneration of CRR28 truncating its carboxyterminal DYW domain. The extended angiosperm set was now used to explore CLB19, an "E+"-type PPR editing factor targeting two chloroplast editing sites, rpoAeU200SF and clpPeU559HY, in Arabidopsis thaliana. We found CLB19 consistently conserved if one of the two targets was retained and three independent losses of CLB19 after elimination of both targets. The Ericales show independent regains of the ancestrally lost clpPeU559HY editing, further explaining why multiple-target editing factors are lost much more rarely than single target factors like RARE1. The retention of CLB19 despite loss of both editing targets in some Ericaceae, Apocynaceae and in Camptotheca (Nyssaceae) likely represents evolutionary transitions. However, the retention of CLB19 after a phylogenetic deep loss in the Poaceae rather suggests a yet unrecognized further editing target, for which we suggest editing event ndhAeU473SL.<br><br>CONCLUSION: Extending the scope of studies on plant organelle RNA editing to further taxa and additional nuclear cofactors reveals expected evolutionary transitions, strikingly different evolutionary dynamics for multiple-target editing factors like CLB19 and CRR28 and suggests additional functions for editing factor CLB19 among the Poaceae.}, }
@article {pmid29875327, year = {2018}, author = {Bonsack, F and Sukumari-Ramesh, S}, title = {TSPO: An Evolutionarily Conserved Protein with Elusive Functions.}, journal = {International journal of molecular sciences}, volume = {19}, number = {6}, pages = {}, pmid = {29875327}, issn = {1422-0067}, mesh = {Animals ; Conserved Sequence ; Disease Susceptibility ; Evolution, Molecular ; Humans ; Ligands ; Mitochondria/genetics/metabolism ; Molecular Targeted Therapy ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; Receptors, GABA/chemistry/*genetics/*metabolism ; Steroids/biosynthesis ; }, abstract = {TSPO (18 kDa translocator protein) was identified decades ago in a search for peripheral tissue binding sites for benzodiazepines, and was formerly called the peripheral benzodiazepine receptor. TSPO is a conserved protein throughout evolution and it is implicated in the regulation of many cellular processes, including inflammatory responses, oxidative stress, and mitochondrial homeostasis. TSPO, apart from its broad expression in peripheral tissues, is highly expressed in neuroinflammatory cells, such as activated microglia. In addition, emerging studies employing the ligands of TSPO suggest that TSPO plays an important role in neuropathological settings as a biomarker and therapeutic target. However, the precise molecular function of this protein in normal physiology and neuropathology remains enigmatic. This review provides an overview of recent advances in our understanding of this multifaceted molecule and identifies the knowledge gap in the field for future functional studies.}, }
@article {pmid29873740, year = {2018}, author = {Scott, GR and Guo, KH and Dawson, NJ}, title = {The Mitochondrial Basis for Adaptive Variation in Aerobic Performance in High-Altitude Deer Mice.}, journal = {Integrative and comparative biology}, volume = {58}, number = {3}, pages = {506-518}, doi = {10.1093/icb/icy056}, pmid = {29873740}, issn = {1557-7023}, mesh = {*Acclimatization ; *Altitude ; Animals ; Mitochondria/*physiology ; Peromyscus/*physiology ; }, abstract = {Mitochondria play a central role in aerobic performance. Studies aimed at elucidating how evolved variation in mitochondrial physiology contributes to adaptive variation in aerobic performance can therefore provide a unique and powerful lens to understanding the evolution of complex physiological traits. Here, we review our ongoing work on the importance of changes in mitochondrial quantity and quality to adaptive variation in aerobic performance in high-altitude deer mice. Whole-organism aerobic capacity in hypoxia (VO2max) increases in response to hypoxia acclimation in this species, but high-altitude populations have evolved consistently greater VO2max than populations from low altitude. The evolved increase in VO2max in highlanders is associated with an evolved increase in the respiratory capacity of the gastrocnemius muscle. This appears to result from highlanders having more mitochondria in this tissue, attributed to a higher proportional abundance of oxidative fiber-types and a greater mitochondrial volume density within oxidative fibers. The latter is primarily caused by an over-abundance of subsarcolemmal mitochondria in high-altitude mice, which is likely advantageous for mitochondrial O2 supply because more mitochondria are situated adjacent to the cell membrane and close to capillaries. Evolved changes in gastrocnemius phenotype appear to be underpinned by population differences in the expression of genes involved in energy metabolism, muscle development, and vascular development. Hypoxia acclimation has relatively little effect on respiratory capacity of the gastrocnemius, but it increases respiratory capacity of the diaphragm. However, the mechanisms responsible for this increase differ between populations: lowlanders appear to adjust mitochondrial quantity and quality (i.e., increases in citrate synthase [CS] activity, and mitochondrial respiration relative to CS activity) and they exhibit higher rates of mitochondrial release of reactive oxygen species, whereas highlanders only increase mitochondrial quantity in response to hypoxia acclimation. In contrast to the variation in skeletal muscles, the respiratory capacity of cardiac muscle does not appear to be affected by hypoxia acclimation and varies little between populations. Therefore, evolved changes in mitochondrial quantity and quality make important tissue-specific contributions to adaptive variation in aerobic performance in high-altitude deer mice.}, }
@article {pmid29870859, year = {2018}, author = {Bolstad, KSR and Braid, HE and Strugnell, JM and Lindgren, AR and Lischka, A and Kubodera, T and Laptikhovsky, VL and Roura Labiaga, A}, title = {A mitochondrial phylogeny of the family Onychoteuthidae (Cephalopoda: Oegopsida).}, journal = {Molecular phylogenetics and evolution}, volume = {128}, number = {}, pages = {88-97}, doi = {10.1016/j.ympev.2018.05.032}, pmid = {29870859}, issn = {1095-9513}, mesh = {Animals ; Cephalopoda/*classification/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Mitochondria/*genetics ; *Phylogeny ; Species Specificity ; }, abstract = {The oegopsid squid family Onychoteuthidae was recently revised based on morphology, but sufficient material for a complementary molecular analysis has not been available until now. In the present study, over 250 sequences of cytochrome c oxidase subunit I (COI) and 16S rRNA for 222 individuals were analysed to create a combined phylogeny for the family. Results support monophyly for the family and all seven onychoteuthid genera (including Moroteuthopsis, established herein as the senior genus name for species formerly attributed to Kondakovia); 29 genetically distinct species were recovered, with the BIN (Barcode Index Number) analysis for COI showing good congruence overall with morphological species groupings. No sequences were available for five additional known species, making the total family diversity likely to exceed 34 species. Seven of the BINs formed in this study appear to represent undescribed taxa, suggesting that even in this relatively well-studied family, much additional work remains before a comprehensive understanding of the diversity and evolutionary relationships for the Onychoteuthidae can be achieved.}, }
@article {pmid29864497, year = {2018}, author = {Banerjee, B and Koner, D and Bhuyan, G and Saha, N}, title = {Differential expression of multiple glutamine synthetase genes in air-breathing magur catfish, Clarias magur and their induction under hyper-ammonia stress.}, journal = {Gene}, volume = {671}, number = {}, pages = {85-95}, doi = {10.1016/j.gene.2018.05.111}, pmid = {29864497}, issn = {1879-0038}, mesh = {Ammonia/*pharmacology ; Animals ; Brain/metabolism ; Catfishes/*genetics/metabolism ; Cytosol/metabolism ; Gene Expression Profiling/*methods ; Gene Expression Regulation/drug effects ; Gills/metabolism ; Glutamate-Ammonia Ligase/*genetics ; Kidney/metabolism ; Liver/metabolism ; Mitochondria/metabolism ; Muscle Cells/metabolism ; Phylogeny ; Sequence Analysis, DNA ; Stress, Physiological ; Tissue Distribution ; *Up-Regulation ; }, abstract = {The present study demonstrates the unique presence of three different gs genes (cmgs01, cmgs02, and cmgs03) in air-breathing ureogenic magur catfish (Clarias magur), which is otherwise reported to be encoded by a single gene in higher vertebrates. Of these three genes, two (cmgs01and cmgs03) were identified as 'liver' form, predominantly expressed in liver cells, and the third one as 'brain' form (cmgs02), expressed chiefly in brain cells. Molecular characterization studies have revealed conservation of homologous active site residues in all the three gs genes. In silico analysis, accompanied by GS enzyme assay and Western blot analysis of different GS isoforms in different subcellular fractions indicated the mitochondrial localization of cmGS01 and cmGS03 in liver and kidney cells and cytosolic localization of cmGS02 in brain cells. Further, exposure of magur catfish to high external ammonia (HEA; 25 mM NH4Cl) led to a significant induction of multiple gs genes as evidenced by higher expression of different gs mRNAs at variable levels in different tissues. The cmgs01 and cmgs03 mRNA levels elevated significantly in liver, kidney, muscle, and gills, whereas the cmgs02 mRNA level increased considerably in the brain after 14 days of exposure to HEA. These increases in mRNA levels were associated with a significant rise in cmGS01 and cmGS03 proteins in liver, kidney, muscle, and gills, and the cmGS02 protein in the brain after 14 days of exposure to HEA. Therefore, it can be concluded that the unique differential expression of three gs genes and their induction under high ammonia level probably helps in detoxification of ammonia to glutamine and further to urea via the ornithine-urea cycle in ureogenic as well as non-ureogenic tissues of these magur catfish.}, }
@article {pmid29857468, year = {2018}, author = {Avelange-Macherel, MH and Candat, A and Neveu, M and Tolleter, D and Macherel, D}, title = {Decoding the Divergent Subcellular Location of Two Highly Similar Paralogous LEA Proteins.}, journal = {International journal of molecular sciences}, volume = {19}, number = {6}, pages = {}, pmid = {29857468}, issn = {1422-0067}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/metabolism ; Mitochondrial Proteins/chemistry/genetics/metabolism ; Multigene Family ; Mutation ; Plant Proteins/chemistry/*genetics/*metabolism ; Protein Binding ; Protein Transport ; Proteolysis ; Structure-Activity Relationship ; }, abstract = {Many mitochondrial proteins are synthesized as precursors in the cytosol with an N-terminal mitochondrial targeting sequence (MTS) which is cleaved off upon import. Although much is known about import mechanisms and MTS structural features, the variability of MTS still hampers robust sub-cellular software predictions. Here, we took advantage of two paralogous late embryogenesis abundant proteins (LEA) from Arabidopsis with different subcellular locations to investigate structural determinants of mitochondrial import and gain insight into the evolution of the LEA genes. LEA38 and LEA2 are short proteins of the LEA_3 family, which are very similar along their whole sequence, but LEA38 is targeted to mitochondria while LEA2 is cytosolic. Differences in the N-terminal protein sequences were used to generate a series of mutated LEA2 which were expressed as GFP-fusion proteins in leaf protoplasts. By combining three types of mutation (substitution, charge inversion, and segment replacement), we were able to redirect the mutated LEA2 to mitochondria. Analysis of the effect of the mutations and determination of the LEA38 MTS cleavage site highlighted important structural features within and beyond the MTS. Overall, these results provide an explanation for the likely loss of mitochondrial location after duplication of the ancestral gene.}, }
@article {pmid29855375, year = {2018}, author = {Amzati, GS and Pelle, R and Muhigwa, JB and Kanduma, EG and Djikeng, A and Madder, M and Kirschvink, N and Marcotty, T}, title = {Mitochondrial phylogeography and population structure of the cattle tick Rhipicephalus appendiculatus in the African Great Lakes region.}, journal = {Parasites &amp; vectors}, volume = {11}, number = {1}, pages = {329}, pmid = {29855375}, issn = {1756-3305}, support = {ABC089//Africa Biosciences Challenge Fund (ABCF) program, BecA-ILRI Hub/ ; S0020***10402//Agence Universitaire de la Francophonie/ ; IFS-92890CA3//International Foundation for Science/ ; Bourses institutionnelles-Ceruna//Universit&#xe9; de Namur/ ; 006/014//Communaut&#xe9; &#xe9;conomique des pays des Grands Lacs (CEPGL)/ ; }, mesh = {Africa/epidemiology ; Animals ; Arachnid Vectors/*genetics/parasitology ; Cattle ; Genetic Structures ; *Genetic Variation ; Genetics, Population ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Population Dynamics ; Rhipicephalus/*genetics/parasitology ; Theileria parva/*physiology ; Theileriasis/epidemiology/*parasitology ; }, abstract = {BACKGROUND: The ixodid tick Rhipicephalus appendiculatus is the main vector of Theileria parva, wich causes the highly fatal cattle disease East Coast fever (ECF) in sub-Saharan Africa. Rhipicephalus appendiculatus populations differ in their ecology, diapause behaviour and vector competence. Thus, their expansion in new areas may change the genetic structure and consequently affect the vector-pathogen system and disease outcomes. In this study we investigated the genetic distribution of R. appendiculatus across agro-ecological zones (AEZs) in the African Great Lakes region to better understand the epidemiology of ECF and elucidate R. appendiculatus evolutionary history and biogeographical colonization in Africa.<br><br>METHODS: Sequencing was performed on two mitochondrial genes (cox1 and 12S rRNA) of 218 ticks collected from cattle across six AEZs along an altitudinal gradient in the Democratic Republic of Congo, Rwanda, Burundi and Tanzania. Phylogenetic relationships between tick populations were determined and evolutionary population dynamics models were assessed by mismach distribution.<br><br>RESULTS: Population genetic analysis yielded 22 cox1 and 9 12S haplotypes in a total of 209 and 126 nucleotide sequences, respectively. Phylogenetic algorithms grouped these haplotypes for both genes into two major clades (lineages A and B). We observed significant genetic variation segregating the two lineages and low structure among populations with high degree of migration. The observed high gene flow indicates population admixture between AEZs. However, reduced number of migrants was observed between lowlands and highlands. Mismatch analysis detected a signature of rapid demographic and range expansion of lineage A. The star-like pattern of isolated and published haplotypes indicates that the two lineages evolve independently and have been subjected to expansion across Africa.<br><br>CONCLUSIONS: Two sympatric R. appendiculatus lineages occur in the Great Lakes region. Lineage A, the most diverse and ubiquitous, has experienced rapid population growth and range expansion in all AEZs probably through cattle movement, whereas lineage B, the less abundant, has probably established a founder population from recent colonization events and its occurrence decreases with altitude. These two lineages are sympatric in central and eastern Africa and allopatric in southern Africa. The observed colonization pattern may strongly affect the transmission system and may explain ECF endemic instability in the tick distribution fringes.}, }
@article {pmid29852202, year = {2018}, author = {Wang, M and Teng, Y}, title = {Genome-wide identification and analysis of MICU genes in land plants and their potential role in calcium stress.}, journal = {Gene}, volume = {670}, number = {}, pages = {174-181}, doi = {10.1016/j.gene.2018.05.102}, pmid = {29852202}, issn = {1879-0038}, mesh = {Calcium/metabolism ; Calcium-Binding Proteins/chemistry/*genetics/metabolism ; Down-Regulation ; Embryophyta/classification/genetics/*metabolism ; Evolution, Molecular ; Phylogeny ; Plant Proteins/chemistry/genetics/metabolism ; Protein Domains ; Signal Transduction ; *Stress, Physiological ; }, abstract = {Mitochondrial calcium uptake (MICU) plays a vital role in the regulation of mitochondrial calcium homeostasis, and, consequently, influences calcium signaling transduction. Although genes involved in mitochondrial calcium uptake have been well studied in animals, less is known about their ubiquity and function in plants. In this study, we identified 96 MICU genes in land plants. On the basis of phylogenetic analysis of MICU proteins, they were classified into three clades: MICU from eudicots (Clade I), from monocots (Clade II), and from a basal angiosperm, a bryophyte, and a lycophyte (Clade III). Pairwise identity analysis across all MICU proteins showed that they are highly conserved among land plants at the protein level. Conserved motif analysis showed that most MICU proteins contained three EF-hands, and an additional EF-hand motif first identified in the MICU of Arabidopsis thaliana but not mammals was found in all 96 putative MICU proteins. This suggests that a cellular pathway of calcium uptake and signaling that requires three EF-hand motifs is evolutionarily conserved in plants. In addition, we discovered that MICU-defective mutants of Arabidopsis thaliana exhibited longer roots than wild-type under high calcium stress. Concurrently, the mRNA transcription levels of MICU were decreased under high calcium conditions. These results suggest that loss-of-function mutations of MICU may have potential roles in helping plants resist high calcium stress. This study provides clues to the possible role of plant MICU in mitochondrial calcium uptake, as well as useful information to support further studies on MICU function in plants.}, }
@article {pmid29852093, year = {2018}, author = {Li, Z and You, XL and Wang, LL and Yan, ZT and Zhou, ZY}, title = {Spore morphology and ultrastructure of an Ascosphaera apis strain from the honeybees (Apis mellifera) in southwest China.}, journal = {Mycologia}, volume = {110}, number = {2}, pages = {325-338}, doi = {10.1080/00275514.2018.1442084}, pmid = {29852093}, issn = {1557-2536}, mesh = {Animals ; Bees/*microbiology ; Cell Wall/chemistry ; China ; Chitin/analysis ; Cluster Analysis ; DNA, Fungal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Microscopy ; Microscopy, Confocal ; Microscopy, Electron, Transmission ; Onygenales/classification/*cytology/isolation &amp; purification/*ultrastructure ; Organelles/ultrastructure ; Phylogeny ; RNA, Ribosomal, 5.8S ; Sequence Analysis, DNA ; Spores, Fungal/*cytology/*ultrastructure ; }, abstract = {Ascosphaera apis is an intestinally infective, spore-forming, filamentous fungus that infects honeybees and causes deadly chalkbrood disease. Although A. apis has been known for 60 y, little is known about the ultrastructure of the spores. In this study, the fine morphology and ultrastructure of an isolate, A. apis CQ1 from southwest China, was comprehensively identified by transmission electron microscopy, confocal laser scanning microscopy, scanning electron microscopy, and optical microscopy. The high sequence similarity and phylogenetic data based on nuc rDNA ITS1-5.8S-ITS2 (ITS) supported the hypothesis that the CQ1 strain is a new member of the A. apis species. Morphological observation indicated that the mature spores are long ovals with an average size of 2 × 1.2 µm and are tightly packed inside spherical spore balls. More than 10 spore balls that were 8-16 µm in diameter were wrapped and formed a spherical, nearly hyaline spore cyst of 50-60 µm in diameter. Ultrastructural analysis showed that mature spores have two nuclei with distinctly different sizes. A large nucleus with double nuclear membranes was found in the center of the spore, whereas the small nucleus was only one-fifth of the large nucleus volume and was located near the end of the spore. Numerous ribosomes filled the cytoplasm, and many mitochondria with well-defined structures were arranged along the inner spore wall. The spore wall consists of an electron-dense outer surface layer, an electron-lucent layer, and an inner plasma membrane. Chitin is the major component of the spore wall. The germinated spore was observed as an empty spore coat, whereas the protoplasts, including the nuclei, mitochondria, and ribosomes, had been discharged. In addition to these typical fungal spore organelles, an unknown electron-dense regular structure might be the growing mycelium, which was arranged close to the inner spore wall and almost covered the entire wall area.}, }
@article {pmid29851233, year = {2018}, author = {Solari, KA and Hadly, EA}, title = {Evolution for extreme living: variation in mitochondrial cytochrome c oxidase genes correlated with elevation in pikas (genus Ochotona).}, journal = {Integrative zoology}, volume = {13}, number = {5}, pages = {517-535}, doi = {10.1111/1749-4877.12332}, pmid = {29851233}, issn = {1749-4877}, mesh = {Adaptation, Physiological/*genetics ; Altitude ; Animals ; *Biological Evolution ; Ecosystem ; Electron Transport Complex IV/genetics/*metabolism ; Gene Expression Regulation, Enzymologic ; Lagomorpha/genetics/*physiology ; Mitochondria/*enzymology ; Phylogeny ; }, abstract = {The genus Ochotona (pikas) is a clade of cold-tolerant lagomorphs that includes many high-elevation species. Pikas offer a unique opportunity to study adaptations and potential limitations of an ecologically important mammal to high-elevation hypoxia. We analyzed the evolution of 3 mitochondrial genes encoding the catalytic core of cytochrome c oxidase (COX) in 10 pika species occupying elevations from sea level to 5000 m. COX is an enzyme highly reliant on oxygen and essential for cell function. One amino acid property, the equilibrium constant (ionization of COOH), was found to be under selection in the overall protein complex. We observed a strong relationship between the net value change in this property and the elevation each species occupies, with higher-elevation species having potentially more efficient proteins. We also found evidence of selection in low-elevation species for potentially less efficient COX, perhaps trading efficiency for heat production in the absence of hypoxia. Our results suggest that different pika species may have evolved elevation-specific COX proteins, specialization that may indicate limitations in their ability to shift their elevational ranges in response to future climate change.}, }
@article {pmid29850800, year = {2018}, author = {Guillory, WX and Onyshchenko, A and Ruck, EC and Parks, M and Nakov, T and Wickett, NJ and Alverson, AJ}, title = {Recurrent Loss, Horizontal Transfer, and the Obscure Origins of Mitochondrial Introns in Diatoms (Bacillariophyta).}, journal = {Genome biology and evolution}, volume = {10}, number = {6}, pages = {1504-1515}, pmid = {29850800}, issn = {1759-6653}, mesh = {DNA, Mitochondrial/genetics ; Diatoms/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome, Mitochondrial/*genetics ; Introns/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {We sequenced mitochondrial genomes from five diverse diatoms (Toxarium undulatum, Psammoneis japonica, Eunotia naegelii, Cylindrotheca closterium, and Nitzschia sp.), chosen to fill important phylogenetic gaps and help us characterize broadscale patterns of mitochondrial genome evolution in diatoms. Although gene content was strongly conserved, intron content varied widely across species. The vast majority of introns were of group II type and were located in the cox1 or rnl genes. Although recurrent intron loss appears to be the principal underlying cause of the sporadic distributions of mitochondrial introns across diatoms, phylogenetic analyses showed that intron distributions superficially consistent with a recurrent-loss model were sometimes more complicated, implicating horizontal transfer as a likely mechanism of intron acquisition as well. It was not clear, however, whether diatoms were the donors or recipients of horizontally transferred introns, highlighting a general challenge in resolving the evolutionary histories of many diatom mitochondrial introns. Although some of these histories may become clearer as more genomes are sampled, high rates of intron loss suggest that the origins of many diatom mitochondrial introns are likely to remain unclear.}, }
@article {pmid29848319, year = {2018}, author = {Bronstein, O and Kroh, A and Haring, E}, title = {Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {80}, pmid = {29848319}, issn = {1471-2148}, support = {P 29508/FWF_/Austrian Science Fund FWF/Austria ; P 29508-B25//Austrian Science Fund/International ; }, mesh = {Algorithms ; Animals ; Base Sequence ; DNA Primers/metabolism ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; Genetic Markers ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Transfer/genetics ; Sea Urchins/*genetics ; }, abstract = {BACKGROUND: In Metazoa, mitochondrial markers are the most commonly used targets for inferring species-level molecular phylogenies due to their extremely low rate of recombination, maternal inheritance, ease of use and fast substitution rate in comparison to nuclear DNA. The mitochondrial control region (CR) is the main non-coding area of the mitochondrial genome and contains the mitochondrial origin of replication and transcription. While sequences of the cytochrome oxidase subunit 1 (COI) and 16S rRNA genes are the prime mitochondrial markers in phylogenetic studies, the highly variable CR is typically ignored and not targeted in such analyses. However, the higher substitution rate of the CR can be harnessed to infer the phylogeny of closely related species, and the use of a non-coding region alleviates biases resulting from both directional and purifying selection. Additionally, complete mitochondrial genome assemblies utilizing next generation sequencing (NGS) data often show exceptionally low coverage at specific regions, including the CR. This can only be resolved by targeted sequencing of this region.<br><br>RESULTS: Here we provide novel sequence data for the echinoid mitochondrial control region in over 40 species across the echinoid phylogenetic tree. We demonstrate the advantages of directly targeting the CR and adjacent tRNAs to facilitate complementing low coverage NGS data from complete mitochondrial genome assemblies. Finally, we test the performance of this region as a phylogenetic marker both in the lab and in phylogenetic analyses, and demonstrate its superior performance over the other available mitochondrial markers in echinoids.<br><br>CONCLUSIONS: Our target region of the mitochondrial CR (1) facilitates the first thorough investigation of this region across a wide range of echinoid taxa, (2) provides a tool for complementing missing data in NGS experiments, and (3) identifies the CR as a powerful, novel marker for phylogenetic inference in echinoids due to its high variability, lack of selection, and high compatibility across the entire class, outperforming conventional mitochondrial markers.}, }
@article {pmid29848286, year = {2018}, author = {Darbani, B and Kell, DB and Borodina, I}, title = {Energetic evolution of cellular Transportomes.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {418}, pmid = {29848286}, issn = {1471-2164}, support = {BB/P009042/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 757384//H2020 European Research Council/ ; NNF10CC1016517//The Novo Nordisk Foundation Center for Biosustainability/ ; BB/M006891/1, BB/M017702/1 and BB/P009042/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Energy Metabolism ; *Evolution, Molecular ; *Genomics ; Membrane Transport Proteins/*metabolism ; }, abstract = {BACKGROUND: Transporter proteins mediate the translocation of substances across the membranes of living cells. Many transport processes are energetically expensive and the cells use 20 to 60% of their energy to power the transportomes. We hypothesized that there may be an evolutionary selection pressure for lower energy transporters.<br><br>RESULTS: We performed a genome-wide analysis of the compositional reshaping of the transportomes across the kingdoms of bacteria, archaea, and eukarya. We found that the share of ABC transporters is much higher in bacteria and archaea (ca. 27% of the transportome) than in primitive eukaryotes (13%), algae and plants (10%) and in fungi and animals (5-6%). This decrease is compensated by an increased occurrence of secondary transporters and ion channels. The share of ion channels is particularly high in animals (ca. 30% of the transportome) and algae and plants with (ca. 13%), when compared to bacteria and archaea with only 6-7%. Therefore, our results show a move to a preference for the low-energy-demanding transporters (ion channels and carriers) over the more energy-costly transporter classes (ATP-dependent families, and ABCs in particular) as part of the transition from prokaryotes to eukaryotes. The transportome analysis also indicated seven bacterial species, including Neorickettsia risticii and Neorickettsia sennetsu, as likely origins of the mitochondrion in eukaryotes, based on the phylogenetically restricted presence therein of clear homologues of modern mitochondrial solute carriers.<br><br>CONCLUSIONS: The results indicate that the transportomes of eukaryotes evolved strongly towards a higher energetic efficiency, as ATP-dependent transporters diminished and secondary transporters and ion channels proliferated. These changes have likely been important in the development of tissues performing energetically costly cellular functions.}, }
@article {pmid29843612, year = {2018}, author = {Hartmann, T and Bernt, M and Middendorf, M}, title = {EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements.}, journal = {BMC bioinformatics}, volume = {19}, number = {1}, pages = {192}, pmid = {29843612}, issn = {1471-2105}, mesh = {DNA, Intergenic ; *Evolution, Molecular ; Gene Duplication ; Gene Order ; Genes, Duplicate ; *Genome, Mitochondrial ; *Software ; }, abstract = {BACKGROUND: To study the differences between two unichromosomal circular genomes, e.g., mitochondrial genomes, under the tandem duplication random loss (TDRL) rearrangement it is important to consider the whole set of potential TDRL rearrangement events that could have taken place. The reason is that for two given circular gene orders there can exist different TDRL rearrangements that transform one of the gene orders into the other. Hence, a TDRL event cannot always be reconstructed only from the knowledge of the circular gene order before a TDRL event and the circular gene order after it.<br><br>RESULTS: We present the program EqualTDRL that computes and illustrates the complete set of TDRLs for pairs of circular gene orders that differ by only one TDRL. EqualTDRL considers the circularity of the given genomes and certain restrictions on the TDRL rearrangements. Examples for the latter are sequences of genes that have to be conserved during a TDRL or pairs of genes that frame intergenic regions which might represent remnants of duplicated genes. Additionally, EqualTDRL allows to determine the set of TDRLs that are minimum with respect to the number of duplicated genes.<br><br>CONCLUSION: EqualTDRL supports scientists to study the complete set of TDRLs that possibly could have taken place in the evolution of mitochondrial genomes. EqualTDRL is implemented in C++ using the ggplot2 package of the open source programming language R and is freely available from http://pacosy.informatik.uni-leipzig.de/equaltdrl .}, }
@article {pmid29843598, year = {2018}, author = {Perry, KD and Baker, GJ and Powis, KJ and Kent, JK and Ward, CM and Baxter, SW}, title = {Cryptic Plutella species show deep divergence despite the capacity to hybridize.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {77}, pmid = {29843598}, issn = {1471-2148}, support = {UA00146//University of Adelaide/International ; DAS00094//Grains Research and Development Corporation/International ; DAS00155//Grains Research and Development Corporation/International ; DAS00155//Grains Research and Development Corporation/International ; DAS00155//Grains Research and Development Corporation/International ; DP120100047//Australian Research Council/International ; FT140101303//Australian Research Council/International ; }, mesh = {Animals ; Australia ; Biological Assay ; Crosses, Genetic ; DNA, Mitochondrial/genetics ; Female ; Fertility ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Heterozygote ; *Hybridization, Genetic/drug effects ; Insecticide Resistance/drug effects/genetics ; Insecticides/toxicity ; Likelihood Functions ; Male ; Mitochondria/genetics ; Moths/*genetics/microbiology ; Phylogeny ; Species Specificity ; Sympatry ; Wolbachia/drug effects/physiology ; }, abstract = {BACKGROUND: Understanding genomic and phenotypic diversity among cryptic pest taxa has important implications for the management of pests and diseases. The diamondback moth, Plutella xylostella L., has been intensively studied due to its ability to evolve insecticide resistance and status as the world's most destructive pest of brassicaceous crops. The surprise discovery of a cryptic species endemic to Australia, Plutella australiana Landry &amp; Hebert, raised questions regarding the distribution, ecological traits and pest status of the two species, the capacity for gene flow and whether specific management was required. Here, we collected Plutella from wild and cultivated brassicaceous plants from 75 locations throughout Australia and screened 1447 individuals to identify mtDNA lineages and Wolbachia infections. We genotyped genome-wide SNP markers using RADseq in coexisting populations of each species. In addition, we assessed reproductive compatibility in crossing experiments and insecticide susceptibility phenotypes using bioassays.<br><br>RESULTS: The two Plutella species coexisted on wild brassicas and canola crops, but only 10% of Plutella individuals were P. australiana. This species was not found on commercial Brassica vegetable crops, which are routinely sprayed with insecticides. Bioassays found that P. australiana was 19-306 fold more susceptible to four commonly-used insecticides than P. xylostella. Laboratory crosses revealed that reproductive isolation was incomplete but directionally asymmetric between the species. However, genome-wide nuclear SNPs revealed striking differences in genetic diversity and strong population structure between coexisting wild populations of each species. Nuclear diversity was 1.5-fold higher in P. australiana, yet both species showed limited variation in mtDNA. Infection with a single Wolbachia subgroup B strain was fixed in P. australiana, suggesting that a selective sweep contributed to low mtDNA diversity, while a subgroup A strain infected just 1.5% of P. xylostella.<br><br>CONCLUSIONS: Despite sympatric distributions and the capacity to hybridize, strong genomic and phenotypic divergence exists between these Plutella species that is consistent with contrasting colonization histories and reproductive isolation after secondary contact. Although P. australiana is a potential pest of brassicaceous crops, it is of secondary importance to P. xylostella.}, }
@article {pmid29842994, year = {2018}, author = {Weerts, MJA and Timmermans, EC and van de Stolpe, A and Vossen, RHAM and Anvar, SY and Foekens, JA and Sleijfer, S and Martens, JWM}, title = {Tumor-Specific Mitochondrial DNA Variants Are Rarely Detected in Cell-Free DNA.}, journal = {Neoplasia (New York, N.Y.)}, volume = {20}, number = {7}, pages = {687-696}, pmid = {29842994}, issn = {1476-5586}, mesh = {Aged ; Aged, 80 and over ; Alleles ; *Biomarkers, Tumor ; *Circulating Tumor DNA ; Computational Biology/methods ; *DNA, Mitochondrial ; *DNA, Neoplasm ; Female ; Gene Frequency ; Genetic Heterogeneity ; *Genetic Variation ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Middle Aged ; Neoplasm Staging ; Neoplasms/*genetics/pathology ; Phylogeny ; }, abstract = {The use of blood-circulating cell-free DNA (cfDNA) as a "liquid biopsy" in oncology is being explored for its potential as a cancer biomarker. Mitochondria contain their own circular genomic entity (mitochondrial DNA, mtDNA), up to even thousands of copies per cell. The mutation rate of mtDNA is several orders of magnitude higher than that of the nuclear DNA. Tumor-specific variants have been identified in tumors along the entire mtDNA, and their number varies among and within tumors. The high mtDNA copy number per cell and the high mtDNA mutation rate make it worthwhile to explore the potential of tumor-specific cf-mtDNA variants as cancer marker in the blood of cancer patients. We used single-molecule real-time (SMRT) sequencing to profile the entire mtDNA of 19 tissue specimens (primary tumor and/or metastatic sites, and tumor-adjacent normal tissue) and 9 cfDNA samples, originating from 8 cancer patients (5 breast, 3 colon). For each patient, tumor-specific mtDNA variants were detected and traced in cfDNA by SMRT sequencing and/or digital PCR to explore their feasibility as cancer biomarker. As a reference, we measured other blood-circulating biomarkers for these patients, including driver mutations in nuclear-encoded cfDNA and cancer-antigen levels or circulating tumor cells. Four of the 24 (17%) tumor-specific mtDNA variants were detected in cfDNA, however at much lower allele frequencies compared to mutations in nuclear-encoded driver genes in the same samples. Also, extensive heterogeneity was observed among the heteroplasmic mtDNA variants present in an individual. We conclude that there is limited value in tracing tumor-specific mtDNA variants in blood-circulating cfDNA with the current methods available.}, }
@article {pmid29808012, year = {2018}, author = {Yuan, L and Zhai, L and Qian, L and Huang, D and Ding, Y and Xiang, H and Liu, X and Thompson, JW and Liu, J and He, YH and Chen, XQ and Hu, J and Kong, QP and Tan, M and Wang, XF}, title = {Switching off IMMP2L signaling drives senescence via simultaneous metabolic alteration and blockage of cell death.}, journal = {Cell research}, volume = {28}, number = {6}, pages = {625-643}, pmid = {29808012}, issn = {1748-7838}, support = {R01 CA154586/CA/NCI NIH HHS/United States ; UL1 TR001117/TR/NCATS NIH HHS/United States ; }, mesh = {Aging ; Animals ; Apoptosis Inducing Factor/*metabolism ; Cell Death ; Cell Line ; *Cellular Senescence ; Endopeptidases/*metabolism ; Glycerolphosphate Dehydrogenase/*metabolism ; HEK293 Cells ; HeLa Cells ; Humans ; Mice, Inbred C57BL ; Oxidative Stress ; *Signal Transduction ; }, abstract = {Cellular senescence is a fundamental cell fate playing a significant role throughout the natural aging process. However, the molecular determinants distinguishing senescence from other cell-cycle arrest states such as quiescence and post-mitotic state, and the specified mechanisms underlying cell-fate decisions towards senescence versus cell death in response to cellular stress stimuli remain less understood. Employing multi-omics approaches, we revealed that switching off the specific mitochondrial processing machinery involving the peptidase IMMP2L serves as the foundation of the senescence program, which was also observed during the mammalian aging process. Mechanistically, we demonstrate that IMMP2L processes and thus activates at least two substrates, mitochondrial metabolic enzyme glycerol-3-phosphate dehydrogenase (GPD2) and cell death regulator apoptosis-inducing factor (AIF). For cells destined to senesce, concerted shutdown of the IMMP2L-GPD2 and IMMP2L-AIF signaling axes collaboratively drives the senescent process by reprogramming mitochondria-associated redox status, phospholipid metabolism and signaling network, and simultaneously blocking cell death under oxidative stress conditions.}, }
@article {pmid29806019, year = {2018}, author = {Taborsky, M and Schütz, D and Goffinet, O and van Doorn, GS}, title = {Alternative male morphs solve sperm performance/longevity trade-off in opposite directions.}, journal = {Science advances}, volume = {4}, number = {5}, pages = {eaap8563}, pmid = {29806019}, issn = {2375-2548}, mesh = {Animals ; Cell Survival ; *Cichlids ; Male ; Reproduction ; Semen Analysis ; *Sexual Behavior, Animal ; Sperm Motility ; Spermatozoa/*physiology ; }, abstract = {Males pursuing alternative reproductive tactics have been predicted to face a trade-off between maximizing either swimming performance or endurance of their sperm. However, empirical evidence for this trade-off is equivocal, which may be due to simplistic assumptions. In the shell-brooding cichlid fish Lamprologus callipterus, two Mendelian male morphs compete for fertilization by divergent means: Bourgeois nest males ejaculate sperm, on average, about six times farther from the unfertilized ova than do parasitic dwarf males. This asymmetry is opposite to the usual situation, in which bourgeois males typically benefit from superior fertilization opportunities, suggesting that nest males' sperm should persist longer than dwarf male sperm. The assumed trade-off between sperm swimming performance and longevity predicts that, in turn, sperm of dwarf males should outperform that of nest males in swimming efficiency. Measurement of sperm performance and endurance reveals that dwarf male spermatozoa swim straighter initially than those of nest males, but their motility declines earlier and their velocity slows down more abruptly. Nest male sperm survives longer, which relates to a larger sperm head plus midpiece, implying more mitochondria. Thus, the trade-off between sperm performance and endurance is optimized in opposite directions by alternative male morphs. We argue that the relative success of alternative sperm performance strategies can be influenced strongly by environmental factors such as the time window between gamete release and fertilization, and the position of gamete release. This is an important yet little understood aspect of gametic adaptations to sperm competition.}, }
@article {pmid29802659, year = {2018}, author = {Tilquin, A and Christie, JR and Kokko, H}, title = {Mitochondrial complementation: a possible neglected factor behind early eukaryotic sex.}, journal = {Journal of evolutionary biology}, volume = {31}, number = {8}, pages = {1152-1164}, doi = {10.1111/jeb.13293}, pmid = {29802659}, issn = {1420-9101}, mesh = {Animals ; *Biological Evolution ; Eukaryota/*genetics/*physiology ; *Mitochondria ; Models, Biological ; Reproduction/*genetics/*physiology ; }, abstract = {Sex is ancestral in eukaryotes. Meiotic sex differs from bacterial ways of exchanging genetic material by involving the fusion of two cells. We examine the hypothesis that fusion evolved in early eukaryotes because it was directly beneficial, rather than a passive side effect of meiotic sex. We assume that the uptake of (proto)mitochondria into eukaryotes preceded the evolution of cell fusion and that Muller's ratchet operating within symbiont lineages led to the accumulation of lineage-specific sets of mutations in asexual host cells. We examine whether cell fusion, and the consequent biparental inheritance of symbionts, helps to mitigate the effects of this mutational meltdown of mitochondria. In our model, host cell fitness improves when two independently evolved mitochondrial strains co-inhabit a single cytoplasm, mirroring mitochondrial complementation found in modern eukaryotes. If fusion incurs no cost, we find that an allele coding for fusion can invade a population of nonfusers. If fusion is costly, there are two thresholds. The first describes a maximal fusing rate (probability of fusion per round of cell division) that is able to fix. An allele that codes for a rate above this threshold can reach a polymorphic equilibrium with nonfusers, as long as the rate is below the second threshold, above which the fusion allele is counter-selected. Whenever it evolves, fusion increases the population-wide level of heteroplasmy, which allows mitochondrial complementation and increases population fitness. We conclude that beneficial interactions between mitochondria are a potential factor that selected for cell fusion in early eukaryotes.}, }
@article {pmid29799088, year = {2018}, author = {Li, Q and Chen, C and Xiong, C and Jin, X and Chen, Z and Huang, W}, title = {Comparative mitogenomics reveals large-scale gene rearrangements in the mitochondrial genome of two Pleurotus species.}, journal = {Applied microbiology and biotechnology}, volume = {102}, number = {14}, pages = {6143-6153}, doi = {10.1007/s00253-018-9082-6}, pmid = {29799088}, issn = {1432-0614}, support = {2016NZ0042//The National Science &amp; Technology Pillar Program of Sichuan/ ; 2016NZ0103//the Crop Molecular Breeding Platform in Sichuan/ ; }, mesh = {DNA, Mitochondrial/genetics ; Gene Rearrangement/*genetics ; Genome, Mitochondrial/*genetics ; Phylogeny ; Pleurotus/classification/*genetics ; Species Specificity ; }, abstract = {In the present study, we assembled the mitogenomes of Pleurotus citrinopileatus and Pleurotus platypus. The circular mitogenome of the two Pleurotus species comprises a set of 14 conserved protein-encoding genes (PEGs), 2 RNA genes (small subunit ribosomal RNA and large subunit ribosomal RNA), and 24 tRNAs, with sizes of 60,694 and 73,807 bp, respectively. They contain 4 and 10 introns with 3 and 10 intronic open reading frames (ORFs), respectively. Thirteen position classes (Pcls) of introns were found in the cox1 gene of four Pleurotus species. The number and class of Pcl varied among different Pleurotus species, indicating that numerous events of loss and gain occurred during evolution of Pleurotus. Comparative mitogenomic and collinearity analyses reveal that large-scale gene rearrangements may have occurred during the evolution of Pleurotus citrinopileatus and Pleurotus platypus, including gene rearrangements and inversions, which may be related to the observed high amounts of repetitive DNA elements (5.62 and 5.45%, respectively). Phylogenetic analysis based on concatenated mitochondrial protein sequences reveals that concatenated mitochondrial genes are suitable as molecular markers for phylogenetic analysis. This serves as the first report on large-scale rearrangements in the mitochondria of the genus Pleurotus, thereby improving our understanding of the evolution of the Pleurotus genus and other macrofungi.}, }
@article {pmid29794164, year = {2018}, author = {Ries, LNA and José de Assis, L and Rodrigues, FJS and Caldana, C and Rocha, MC and Malavazi, I and Bayram, &#xd6; and Goldman, GH}, title = {The Aspergillus nidulans Pyruvate Dehydrogenase Kinases Are Essential To Integrate Carbon Source Metabolism.}, journal = {G3 (Bethesda, Md.)}, volume = {8}, number = {7}, pages = {2445-2463}, pmid = {29794164}, issn = {2160-1836}, mesh = {Aspergillus nidulans/classification/genetics/*metabolism ; Carbon/*metabolism ; Catabolite Repression ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Fungal ; Glucose/metabolism ; Hydrolysis ; Metabolic Networks and Pathways ; Metabolome ; Metabolomics/methods ; Multigene Family ; Phylogeny ; Protein Interaction Mapping ; Protein Interaction Maps ; Protein Serine-Threonine Kinases/genetics/*metabolism ; Protein Transport ; Pyruvate Dehydrogenase Acetyl-Transferring Kinase ; }, abstract = {The pyruvate dehydrogenase complex (PDH), that converts pyruvate to acetyl-coA, is regulated by pyruvate dehydrogenase kinases (PDHK) and phosphatases (PDHP) that have been shown to be important for morphology, pathogenicity and carbon source utilization in different fungal species. The aim of this study was to investigate the role played by the three PDHKs PkpA, PkpB and PkpC in carbon source utilization in the reference filamentous fungus Aspergillus nidulans, in order to unravel regulatory mechanisms which could prove useful for fungal biotechnological and biomedical applications. PkpA and PkpB were shown to be mitochondrial whereas PkpC localized to the mitochondria in a carbon source-dependent manner. Only PkpA was shown to regulate PDH activity. In the presence of glucose, deletion of pkpA and pkpC resulted in reduced glucose utilization, which affected carbon catabolite repression (CCR) and hydrolytic enzyme secretion, due to de-regulated glycolysis and TCA cycle enzyme activities. Furthermore, PkpC was shown to be required for the correct metabolic utilization of cellulose and acetate. PkpC negatively regulated the activity of the glyoxylate cycle enzyme isocitrate lyase (ICL), required for acetate metabolism. In summary, this study identified PDHKs important for the regulation of central carbon metabolism in the presence of different carbon sources, with effects on the secretion of biotechnologically important enzymes and carbon source-related growth. This work demonstrates how central carbon metabolism can affect a variety of fungal traits and lays a basis for further investigation into these characteristics with potential interest for different applications.}, }
@article {pmid29794041, year = {2018}, author = {Camus, MF and Dowling, DK}, title = {Mitochondrial genetic effects on reproductive success: signatures of positive intrasexual, but negative intersexual pleiotropy.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1879}, pages = {}, pmid = {29794041}, issn = {1471-2954}, mesh = {Animals ; Drosophila melanogaster/genetics/*physiology ; Female ; Genes, Mitochondrial/*genetics ; *Genetic Pleiotropy ; *Genetic Variation ; *Haplotypes ; Male ; Reproduction ; }, abstract = {Theory predicts that maternal inheritance of mitochondria will facilitate the accumulation of mtDNA mutations that are male biased, or even sexually antagonistic, in effect. While there are many reported cases of mtDNA mutations conferring cytoplasmic male sterility in plants, historically it was assumed such mutations would not persist in the streamlined mitochondrial genomes of bilaterian metazoans. Intriguingly, recent cases of mitochondrial variants exerting male biases in effect have come to light in bilaterians. These cases aside, it remains unknown whether the mitochondrial genetic variation affecting phenotypic expression, and in particular reproductive performance, in bilaterians is routinely composed of sex-biased or sex-specific variation. If selection consistently favours mtDNA variants that augment female fitness, but at cost to males, this could shape patterns of pleiotropy and lead to negative intersexual correlations across mtDNA haplotypes. Here, we show that genetic variation across naturally occurring mitochondrial haplotypes affects components of reproductive success in both sexes, in the fruit fly Drosophila melanogaster We find that intrasexual correlations across mitochondrial haplotypes, for components of reproductive success, are generally positive, while intersexual correlations are negative. These results accord with theoretical predictions, suggesting that maternal inheritance has led to the fixation of numerous mutations of sexually antagonistic effect.}, }
@article {pmid29792772, year = {2018}, author = {Xia, C and Wang, M and Yin, C and Cornejo, OE and Hulbert, SH and Chen, X}, title = {Genome Sequence Resources for the Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) and the Barley Stripe Rust Pathogen (Puccinia striiformis f. sp. hordei).}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {31}, number = {11}, pages = {1117-1120}, doi = {10.1094/MPMI-04-18-0107-A}, pmid = {29792772}, issn = {0894-0282}, mesh = {Basidiomycota/*genetics ; Genome, Fungal/*genetics ; *Genomics ; Genotype ; High-Throughput Nucleotide Sequencing ; Hordeum/*microbiology ; Phenotype ; Plant Diseases/*microbiology ; Sequence Analysis, RNA ; Triticum/*microbiology ; }, abstract = {Puccinia striiformis f. sp. tritici causes devastating stripe (yellow) rust on wheat and P. striiformis f. sp. hordei causes stripe rust on barley. Several P. striiformis f. sp. tritici genomes are available, but no P. striiformis f. sp. hordei genome is available. More genomes of P. striiformis f. sp. tritici and P. striiformis f. sp. hordei are needed to understand the genome evolution and molecular mechanisms of their pathogenicity. We sequenced P. striiformis f. sp. tritici isolate 93-210 and P. striiformis f. sp. hordei isolate 93TX-2, using PacBio and Illumina technologies and RNA sequencing. Their genomic sequences were assembled to contigs with high continuity and showed significant structural differences. The circular mitochondria genomes of both were complete. These genomes provide high-quality resources for deciphering the genomic basis of rapid evolution and host adaptation, identifying genes for avirulence and other important traits, and studying host-pathogen interactions.}, }
@article {pmid29787825, year = {2018}, author = {Long, Z and Li, H and Du, Y and Han, B}, title = {Congenital sideroblastic anemia: Advances in gene mutations and pathophysiology.}, journal = {Gene}, volume = {668}, number = {}, pages = {182-189}, doi = {10.1016/j.gene.2018.05.074}, pmid = {29787825}, issn = {1879-0038}, mesh = {Anemia, Sideroblastic/congenital/*genetics/metabolism ; Heme/biosynthesis ; Humans ; Iron/metabolism ; Mitochondrial Proteins/biosynthesis ; *Mutation ; }, abstract = {Congenital sideroblastic anemia (CSA) is a series of rare, heterogeneous disorders, characterized by iron overload in the mitochondria of erythroblasts and ringed sideroblasts in bone marrow. In recent years, rapid development of next-generation sequencing technology brings great advance in understanding of genetic and pathophysiologic features of CSA. Based on the pathophysiology of mitochondrial iron metabolism, causative genes of CSA can be divided into three subtypes: heme biosynthesis related; iron‑sulfur cluster biosynthesis and transportation related; and mitochondrial respiratory chain synthesis related. Patients with CSA present various clinical manifestation due to relevant mutation gene and require different treatment strategies. The recognition of the causative genes and evolution of pathogenicity is critical. In this review, we summarize the recent progress in mutation genes of CSA, and its potential role in the pathogenesis, diagnosis and treatment.}, }
@article {pmid29787733, year = {2018}, author = {Younas, F and Soltanmohammadi, N and Knapp, O and Benz, R}, title = {The major outer membrane protein of Legionella pneumophila Lpg1974 shows pore-forming characteristics similar to the human mitochondrial outer membrane pore, hVDAC1.}, journal = {Biochimica et biophysica acta. Biomembranes}, volume = {1860}, number = {8}, pages = {1544-1553}, doi = {10.1016/j.bbamem.2018.05.008}, pmid = {29787733}, issn = {0005-2736}, mesh = {Amino Acid Sequence ; Bacterial Outer Membrane Proteins/chemistry/classification/genetics/*metabolism ; Escherichia coli/metabolism ; Humans ; Legionella pneumophila/*metabolism ; Lipid Bilayers/chemistry/metabolism ; Phylogeny ; Protein Structure, Secondary ; Recombinant Proteins/biosynthesis/chemistry/isolation &amp; purification ; Sequence Alignment ; Voltage-Dependent Anion Channel 1/chemistry/*metabolism ; }, abstract = {Legionella pneumophila is an aerobic and nonspore-forming pathogenic Gram-negative bacterium of the genus Legionella. It is the causative agent of Legionnaires' disease, also known as Legionellosis. The hosts of this organism are diverse, ranging from simple water borne protozoans such as amoebae to more complex hosts such as macrophages in humans. Genome analyses have shown the presence of genes coding for eukaryotic like proteins in several Legionella species. The presence of these proteins may assist L. pneumophila in its adaptation to the eukaryotic host. We studied the characteristics of a protein (Lpg1974) of L. pneumophila that shows remarkable homologies in length of the primary sequence and for the identity/homology of many amino acids to the voltage dependent anion channel (human VDAC1, Porin 31HL) of human mitochondria. Two different forms of Lpg1974 were overexpressed in Escherichia coli and purified to homogeneity: the one containing a putative N-terminal signal sequence and one without it. Reconstituted protein containing the signal sequence formed ion-permeable pores in lipid bilayer membranes with a conductance of approximately 5.4 nS in 1 M KCl. When the predicted N-terminal signal peptide of Lpg1974 comprising an α-helical structure similar to that at the N-terminus of hVDAC1 was removed, the channels formed in reconstitution experiments had a conductance of 7.6 nS in 1 M KCl. Both Lpg1974 proteins formed pores that were voltage-dependent and anion-selective similar to the pores formed by hVDAC1. These results suggest that Lpg1974 of L. pneumophila is indeed a structural and functional homologue to hVDAC1.}, }
@article {pmid29787548, year = {2018}, author = {Kaczmarek, E and Hauser, CJ and Kwon, WY and Riça, I and Chen, L and Sandler, N and Otterbein, LE and Campbell, Y and Cook, CH and Yaffe, MB and Marusich, MF and Itagaki, K}, title = {A subset of five human mitochondrial formyl peptides mimics bacterial peptides and functionally deactivates human neutrophils.}, journal = {The journal of trauma and acute care surgery}, volume = {85}, number = {5}, pages = {936-943}, doi = {10.1097/TA.0000000000001971}, pmid = {29787548}, issn = {2163-0763}, mesh = {Calcium/metabolism ; Cells, Cultured ; Chemokine CXCL1/pharmacology ; Chemotaxis/*drug effects ; Computational Biology ; Cyclooxygenase 1/genetics/metabolism ; Cytosol/metabolism ; Electron Transport Complex I/genetics/metabolism ; Evolution, Molecular ; Humans ; Leukotriene B4/pharmacology ; Mitochondria/metabolism ; Mitochondrial Proteins/genetics/metabolism ; N-Formylmethionine Leucyl-Phenylalanine/chemistry/pharmacology ; NADH Dehydrogenase/genetics/metabolism ; Neutrophils/*physiology ; Peptides/*blood/chemistry/genetics/*pharmacology ; Receptors, Formyl Peptide/antagonists &amp; inhibitors/metabolism ; Signal Transduction ; Wounds and Injuries/*blood ; }, abstract = {BACKGROUND: Trauma causes inflammation by releasing mitochondria that act as Danger-Associated Molecular Patterns (DAMPs). Trauma also increases susceptibility to infection. Human mitochondria contain 13 N-formyl peptides (mtFPs). We studied whether mtFPs released into plasma by clinical injury induce neutrophil (PMN) inflammatory responses, whether their potency reflects their similarity to bacterial FPs and how their presence at clinically relevant concentration affects PMN function.<br><br>METHODS: N-terminal sequences of the 13 mtFPs were synthesized. Changes in human PMN cytosolic Ca concentration ([Ca]i) and chemotactic responses to mtFPs were studied. Sequence similarity of mtFPs to the canonical bacterial peptide f-Met-Leu-Phe (fMLF/fMLP) was studied using the BLOcks SUbstitution Matrix 62 (BLOSUM 62) system. The presence of mtFPs in plasma of trauma patients was assayed by Enzyme-linked immunosorbent assay (ELISA). The effects of the most potent mtFP (ND6) on PMN signaling and function were then studied at ambient clinical concentrations by serial exposure of native PMN to ND6, chemokines and leukotrienes.<br><br>RESULTS: Five mtFPs (ND6, ND3, ND4, ND5, and Cox 1) induced [Ca]i flux and chemotaxis in descending order of potency. Evolutionary similarity to fMLF predicted [Ca]i flux and chemotactic potency linearly (R = 0.97, R = 0.95). Chemoattractant potency was also linearly related to [Ca]i flux induction (R = 0.92). Active mtFPs appear to circulate in significant amounts immediately after trauma and persist through the first week. The most active mtFP, ND6, suppresses responses to physiologic alveolar chemoattractants (CXCL-1, leukotriene B4) as well as to fMLF where CXCL-1 and leukotriene B4 do not suppress N-formyl peptide receptor (FPR)-1 responses to mtFPs. Prior FPR-1 inhibition rescues PMN from heterologous suppression of CXCR-1 and BLT-1 by mtFPs.<br><br>CONCLUSION: The data suggest mtFPs released by injured tissue may attract PMN to trauma sites while suppressing PMN responses to other chemoattractants. Inhibition of mtFP-FPR1 interactions might increase PMN recruitment to lung bacterial inoculation after trauma. These findings suggest new paradigms for preventing infections after trauma.<br><br>LEVEL OF EVIDENCE: Therapeutic, Level IV.}, }
@article {pmid29779502, year = {2018}, author = {Buysse, M and Duron, O}, title = {Multi-locus phylogenetics of the Midichloria endosymbionts reveals variable specificity of association with ticks.}, journal = {Parasitology}, volume = {145}, number = {14}, pages = {1969-1978}, doi = {10.1017/S0031182018000793}, pmid = {29779502}, issn = {1469-8161}, mesh = {Alphaproteobacteria/*classification ; Animals ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Female ; Genetic Variation ; Host Specificity ; Ixodes/*microbiology ; Male ; Multilocus Sequence Typing ; *Phylogeny ; *Symbiosis ; }, abstract = {Candidatus Midichloria mitochondrii is a maternally inherited bacterium of ticks with a unique intra-mitochondrial lifestyle. Here, we investigate on the evolutionary history of these associations and the degree of Midichloria-tick specificity. While previous surveys used the 16S rRNA gene as an exclusive molecular marker, we rather developed a multi-locus typing method based on four more variable housekeeping genes (groEL, rpoB, dnaK and ftsZ) and on one flagellum gene (fliC) present in Midichloria genomes. Using this method, multi-locus phylogenetic analyses revealed the structuring of a wide Midichloria genetic diversity into three distinct lineages associated with ticks. Overall, two distinct evolutionary strategies are obvious depending on lineage: two Midichloria lineages are generalists with infections acquired through horizontal transfers between distantly related tick species but one other Midichloria lineage rather show a high specificity degree to the Ixodes tick genus. This pattern suggests a capacity of certain Midichloria strains to maintain infections in only limited range of related tick species. These different infection strategies of Midichloria highlight an unexpected variability in their dependency to their tick hosts. We further conjecture that this pattern is also likely to indicate variability in their effects on ticks.}, }
@article {pmid29770661, year = {2018}, author = {Cang-Lin, Z and Jia, P and Zhen, R and Jin-Rong, Z and Ya-Ming, Y}, title = {[Genotyping and polymorphism analysis of cytochrome c oxidase subunit Ⅰ gene of Pomacea canaliculata from Lincang City in Yunnan Province].}, journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control}, volume = {30}, number = {2}, pages = {179-183}, doi = {10.16250/j.32.1374.2017163}, pmid = {29770661}, issn = {1005-6661}, mesh = {Angiostrongylus cantonensis ; Animals ; China ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Gastropoda/enzymology/*genetics ; Genotype ; Haplotypes ; Phylogeny ; }, abstract = {OBJECTIVE: To analyze the genetic diversity of Pomacea canaliculata based on the mitochondria DNA cytochrome c oxidase subunit Ⅰ (mtDNA COⅠ) gene as a molecular marker in Lincang City of Yunnan Province, so as to provide the scientific data for monitoring Angiostrongylus cantonensis in local areas.<br><br>METHODS: The genotypes and polymorphisms of 38 specimens of P. canaliculata collected from Mengding Town of Lincang City were analyzed by sequencing CO&#x2160; gene. The phylogenetic tree and genetic distances were produced based on the haplotypes from GenBank and the present study by using the neighbourjoining method with the software MEGA version 6.06.<br><br>RESULTS: Totally 31 sequences were acquired in the present study and they produced 3 unique haplotypes. Haplotype 1 showed a higher frequency compared to the others and it accounted for 83.9 % (26/31). The data showed that the least genetic distances ranged from 0 to 0.052 between P. canaliculata and 3 haplotypes, as well as the largest genetic distances ranged from 0.021 to 0.239 between Pila conica and 3 haplotypes. Otherwise, the analysis of the phylogenetic trees based on CO&#x2160; gene sequences of P. canaliculata indicated that all of 3 haplotypes clustered into one big clade with that from Japan (GenBank accession number: AB433769), China (GenBank accession number: KT313034) and USA (GenBank accession number: EU523129), which owned the closet relationship amongst them. Their genetic relationships were distantly related to the GenBank's reference sequences of P. insularum (GenBank accession number: EF514942), P. camena (GenBank accession number: EF515059) and so on.<br><br>CONCLUSIONS: There is a P. canaliculata species in Lincang City of Yunnan Province as well as a high genetic diversity amongst the acquired 3 haplotypes in this study.}, }
@article {pmid29769322, year = {2018}, author = {Krah, A and Zarco-Zavala, M and McMillan, DGG}, title = {Insights into the regulatory function of the ɛ subunit from bacterial F-type ATP synthases: a comparison of structural, biochemical and biophysical data.}, journal = {Open biology}, volume = {8}, number = {5}, pages = {}, pmid = {29769322}, issn = {2046-2441}, mesh = {Adenosine Triphosphate/metabolism ; Bacillaceae/*enzymology/genetics ; Bacillus/enzymology/genetics ; Bacterial Proteins/chemistry/genetics/metabolism ; Binding Sites ; Crystallography, X-Ray ; Escherichia coli/*enzymology/genetics ; Mitochondrial Proton-Translocating ATPases/*chemistry/genetics/*metabolism ; Models, Molecular ; Mutation ; Protein Conformation ; }, abstract = {ATP synthases catalyse the formation of ATP, the most common chemical energy storage unit found in living cells. These enzymes are driven by an electrochemical ion gradient, which allows the catalytic evolution of ATP by a binding change mechanism. Most ATP synthases are capable of catalysing ATP hydrolysis to varying degrees, and to prevent wasteful ATP hydrolysis, bacteria and mitochondria have regulatory mechanisms such as ADP inhibition. Additionally, ɛ subunit inhibition has also been described in three bacterial systems, Escherichia coli, Bacillus PS3 and Caldalkalibacillus thermarum TA2.A1. Previous studies suggest that the ɛ subunit is capable of undergoing an ATP-dependent conformational change from the ATP hydrolytic inhibitory 'extended' conformation to the ATP-induced non-inhibitory 'hairpin' conformation. A recently published crystal structure of the F1 domain of the C. thermarum TA2.A1 F1Fo ATP synthase revealed a mutant ɛ subunit lacking the ability to bind ATP in a hairpin conformation. This is a surprising observation considering it is an organism that performs no ATP hydrolysis in vivo, and appears to challenge the current dogma on the regulatory role of the ɛ subunit. This has prompted a re-examination of present knowledge of the ɛ subunits role in different organisms. Here, we compare published biochemical, biophysical and structural data involving ɛ subunit-mediated ATP hydrolysis regulation in a variety of organisms, concluding that the ɛ subunit from the bacterial F-type ATP synthases is indeed capable of regulating ATP hydrolysis activity in a wide variety of bacteria, making it a potentially valuable drug target, but its exact role is still under debate.}, }
@article {pmid29761268, year = {2018}, author = {Edera, AA and Gandini, CL and Sanchez-Puerta, MV}, title = {Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria.}, journal = {Plant molecular biology}, volume = {97}, number = {3}, pages = {215-231}, pmid = {29761268}, issn = {1573-5028}, mesh = {Base Pair Mismatch ; Codon/genetics ; Genes, Plant/genetics ; Genome, Mitochondrial/genetics ; Magnoliopsida/*genetics ; Mitochondria/*genetics ; Phylogeny ; *RNA Editing/genetics ; Thymidine ; Transcriptome/genetics ; }, abstract = {Our understanding of the dynamic and evolution of RNA editing in angiosperms is in part limited by the few editing sites identified to date. This study identified 10,217 editing sites from 17 diverse angiosperms. Our analyses confirmed the universality of certain features of RNA editing, and offer new evidence behind the loss of editing sites in angiosperms. RNA editing is a post-transcriptional process that substitutes cytidines (C) for uridines (U) in organellar transcripts of angiosperms. These substitutions mostly take place in mitochondrial messenger RNAs at specific positions called editing sites. By means of publicly available RNA-seq data, this study identified 10,217 editing sites in mitochondrial protein-coding genes of 17 diverse angiosperms. Even though other types of mismatches were also identified, we did not find evidence of non-canonical editing processes. The results showed an uneven distribution of editing sites among species, genes, and codon positions. The analyses revealed that editing sites were conserved across angiosperms but there were some species-specific sites. Non-synonymous editing sites were particularly highly conserved (~ 80%) across the plant species and were efficiently edited (80% editing extent). In contrast, editing sites at third codon positions were poorly conserved (~ 30%) and only partially edited (~ 40% editing extent). We found that the loss of editing sites along angiosperm evolution is mainly occurring by replacing editing sites with thymidines, instead of a degradation of the editing recognition motif around editing sites. Consecutive and highly conserved editing sites had been replaced by thymidines as result of retroprocessing, by which edited transcripts are reverse transcribed to cDNA and then integrated into the genome by homologous recombination. This phenomenon was more pronounced in eudicots, and in the gene cox1. These results suggest that retroprocessing is a widespread driving force underlying the loss of editing sites in angiosperm mitochondria.}, }
@article {pmid29760081, year = {2018}, author = {Sharp, NP and Sandell, L and James, CG and Otto, SP}, title = {The genome-wide rate and spectrum of spontaneous mutations differ between haploid and diploid yeast.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {22}, pages = {E5046-E5055}, pmid = {29760081}, issn = {1091-6490}, mesh = {DNA Breaks, Double-Stranded ; DNA Repair/genetics ; DNA Replication/genetics ; DNA, Fungal/*genetics ; *Diploidy ; Genes, Fungal/genetics ; *Haploidy ; Mitochondria/genetics ; Mutation/*genetics ; Mutation Rate ; Saccharomyces cerevisiae/*genetics ; }, abstract = {By altering the dynamics of DNA replication and repair, alternative ploidy states may experience different rates and types of new mutations, leading to divergent evolutionary outcomes. We report a direct comparison of the genome-wide spectrum of spontaneous mutations arising in haploids and diploids following a mutation-accumulation experiment in the budding yeast Saccharomyces cerevisiae Characterizing the number, types, locations, and effects of thousands of mutations revealed that haploids were more prone to single-nucleotide mutations (SNMs) and mitochondrial mutations, while larger structural changes were more common in diploids. Mutations were more likely to be detrimental in diploids, even after accounting for the large impact of structural changes, contrary to the prediction that mutations would have weaker effects, due to masking, in diploids. Haploidy is expected to reduce the opportunity for conservative DNA repair involving homologous chromosomes, increasing the insertion-deletion rate, but we found little support for this idea. Instead, haploids were more susceptible to SNMs in late-replicating genomic regions, resulting in a ploidy difference in the spectrum of substitutions. In diploids, we detect mutation rate variation among chromosomes in association with centromere location, a finding that is supported by published polymorphism data. Diploids are not simply doubled haploids; instead, our results predict that the spectrum of spontaneous mutations will substantially shape the dynamics of genome evolution in haploid and diploid populations.}, }
@article {pmid29757366, year = {2018}, author = {Dobler, R and Dowling, DK and Morrow, EH and Reinhardt, K}, title = {A systematic review and meta-analysis reveals pervasive effects of germline mitochondrial replacement on components of health.}, journal = {Human reproduction update}, volume = {24}, number = {5}, pages = {519-534}, doi = {10.1093/humupd/dmy018}, pmid = {29757366}, issn = {1460-2369}, mesh = {Animals ; Basal Metabolism/genetics ; Gene Expression Regulation/genetics ; Genetic Variation ; Haplotypes ; Humans ; Mitochondria/*genetics ; Mitochondrial Replacement Therapy/*adverse effects ; Risk Assessment ; }, abstract = {BACKGROUND: Mitochondrial replacement, a form of nuclear transfer, has been proposed as a germline therapy to prevent the transmission of mitochondrial diseases. Mitochondrial replacement therapy has been licensed for clinical application in the UK, and already carried out in other countries, but little is known about negative or unintended effects on the health of offspring born using this technique.<br><br>OBJECTIVE AND RATIONALE: Studies in invertebrate models have used techniques that achieve mitochondrial replacement to create offspring with novel combinations of mitochondrial and nuclear genotype. These have demonstrated that the creation of novel mitochondrial-nuclear interactions can lead to alterations in offspring characteristics, such as development rates, fertility and longevity. However, it is currently unclear whether such interactions could similarly affect the outcomes of vertebrate biomedical studies, which have sought to assess the efficacy of the replacement therapy.<br><br>SEARCH METHODS: This systematic review addresses whether the effects of mitochondrial replacement on offspring characteristics differ in magnitude between biological (conducted on invertebrate models, with an ecological or evolutionary focus) and biomedical studies (conducted on vertebrate models, with a clinical focus). Studies were selected based on a key-word search in 'Web of Science', complemented by backward searches of reviews on the topic of mitochondrial-nuclear (mito-nuclear) interactions. In total, 43 of the resulting 116 publications identified in the search contained reliable data to estimate effect sizes of mitochondrial replacement. We found no evidence of publication bias when examining effect-size estimates across sample sizes.<br><br>OUTCOMES: Mitochondrial replacement consistently altered the phenotype, with significant effects at several levels of organismal performance and health, including gene expression, anatomy, metabolism and life-history. Biomedical and biological studies, while differing in the methods used to achieve mitochondrial replacement, showed only marginally significant differences in effect-size estimates (-0.233 [CI: -0.495 to -0.011]), with larger effect-size estimates in biomedical studies (0.697 [CI: 0.450-0.956]) than biological studies (0.462 [CI: 0.287-0.688]). Humans showed stronger effects than other species. Effects of mitochondrial replacement were also stronger in species with a higher basal metabolic rate. Based on our results, we conducted the first formal risk analysis of mitochondrial replacement, and conservatively estimate negative effects in at least one in every 130 resulting offspring born to the therapy.<br><br>WIDER IMPLICATIONS: Our findings suggest that mitochondrial replacement may routinely affect offspring characteristics across a wide array of animal species, and that such effects are likely to extend to humans. Studies in invertebrate models have confirmed mito-nuclear interactions as the underpinning cause of organismal effects following mitochondrial replacement. This therefore suggests that mito-nuclear interactions are also likely to be contributing to effects seen in biomedical studies, on vertebrate models, whose effect sizes exceeded those of biological studies. Our results advocate the use of safeguards that could offset any negative effects (defining any unintended effect as being negative) mediated by mito-nuclear interactions following mitochondrial replacement in humans, such as mitochondrial genetic matching between donor and recipient. Our results also suggest that further research into the molecular nature of mito-nuclear interactions would be beneficial in refining the clinical application of mitochondrial replacement, and in establishing what degree of variation between donor and patient mitochondrial DNA haplotypes is acceptable to ensure 'haplotype matching'.}, }
@article {pmid29754387, year = {2018}, author = {Zhu, C and Chen, P and Han, Y and Ruan, L}, title = {Low Genetic Diversity and Low Gene Flow Corresponded to a Weak Genetic Structure of Ruddy-Breasted Crake (Porzana fusca) in China.}, journal = {Biochemical genetics}, volume = {56}, number = {6}, pages = {586-617}, doi = {10.1007/s10528-018-9862-9}, pmid = {29754387}, issn = {1573-4927}, support = {NSFC no. 30960052//National Science Foundation of China/ ; no. 31260510//National Science Foundation of China/ ; no. KT201537//Water - resource Department of Jiangxi Province Science and Technological Project/ ; }, mesh = {Animals ; Birds/*genetics ; DNA, Mitochondrial ; *Gene Flow ; *Genetic Structures ; *Genetic Variation ; *Genetics, Population ; Haplotypes ; Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; }, abstract = {The Ruddy-breasted Crake (Porzana fusca) is an extremely poorly known species. Although it is not listed as globally endangered, in recent years, with the interference of climate change and human activities, its habitat is rapidly disappearing and its populations have been shrinking. There are two different life history traits for Ruddy-breasted Crake in China, i.e., non-migratory population in the south and migratory population in the north of China. In this study, mitochondrial control sequences and microsatellite datasets of 88 individuals sampled from 8 sites were applied to analyze their genetic diversity, genetic differentiation, and genetic structure. Our results indicated that low genetic diversity and genetic differentiation exit in most populations. The neutrality test suggested significantly negative Fu's Fs value, which, in combination with detection of the mismatch distribution, indicated that population expansion occurred in the interglacier approximately 98,000 years ago, and the time of the most recent common ancestor (TMRCA) was estimated to about 202,705 years ago. Gene flow analysis implied that the gene flow was low, but gene exchange was frequent among adjacent populations. Both phylogenetic and STRUCTURE analyses implied weak genetic structure. In general, the genetic diversity, gene flow, and genetic structure of Ruddy-breasted Crake were low.}, }
@article {pmid29752470, year = {2018}, author = {Goodall-Copestake, WP}, title = {nrDNA:mtDNA copy number ratios as a comparative metric for evolutionary and conservation genetics.}, journal = {Heredity}, volume = {121}, number = {2}, pages = {105-111}, pmid = {29752470}, issn = {1365-2540}, mesh = {Animals ; Cell Nucleus/*genetics ; *DNA Copy Number Variations ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/*genetics ; Evolution, Molecular ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Muscles/metabolism ; Urochordata/*genetics ; }, abstract = {Identifying genetic cues of functional relevance is key to understanding the drivers of evolution and increasingly important for the conservation of biodiversity. This study introduces nuclear ribosomal DNA (nrDNA) to mitochondrial DNA (mtDNA) copy number ratios as a metric with which to screen for this functional genetic variation prior to more extensive omics analyses. To illustrate the metric, quantitative PCR was used to estimate nrDNA (18S) to mtDNA (16S) copy number ratios in muscle tissue from samples of two zooplankton species: Salpa thompsoni caught near Elephant Island (Southern Ocean) and S. fusiformis sampled off Gough Island (South Atlantic). Average 18S:16S ratios in these samples were 9:1 and 3:1, respectively. nrDNA 45S arrays and mitochondrial genomes were then deep sequenced to uncover the sources of intra-individual genetic variation underlying these 18S:16S copy number differences. The deep sequencing profiles obtained were consistent with genetic changes resulting from adaptive processes, including an expansion of nrDNA and damage to mtDNA in S. thompsoni, potentially in response to the polar environment. Beyond this example from zooplankton, nrDNA:mtDNA copy number ratios offer a promising metric to help identify genetic variation of functional relevance in animals more broadly.}, }
@article {pmid29747566, year = {2018}, author = {Oetjens, MT and Martin, A and Veeramah, KR and Kidd, JM}, title = {Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {350}, pmid = {29747566}, issn = {1471-2164}, support = {R01 GM103961/GM/NIGMS NIH HHS/United States ; R01GM103961//National Institute of General Medical Sciences/ ; }, mesh = {Animals ; Coyotes/classification/*genetics ; DNA, Mitochondrial/genetics ; Dogs/classification/*genetics ; *Evolution, Molecular ; Genetic Variation ; Genome ; *Haplotypes ; Male ; *Phylogeny ; Sequence Analysis, DNA/*methods ; Wolves/classification/*genetics ; *Y Chromosome ; }, abstract = {BACKGROUND: Most genetic analyses of ancient and modern dogs have focused on variation in the autosomes or on the mitochondria. Mitochondrial DNA is more easily obtained from ancient samples than nuclear DNA and mitochondrial analyses have revealed important insights into the evolutionary history of canids. Utilizing a recently published dog Y-chromosome reference, we analyzed Y-chromosome sequence across a diverse collection of canids and determined the Y haplogroup of three ancient European dogs.<br><br>RESULTS: We identified 1121 biallelic Y-chromosome SNVs using whole-genome sequences from 118 canids and defined variants diagnostic to distinct dog Y haplogroups. Similar to that of the mitochondria and previous more limited studies of Y diversity, we observe several deep splits in the Y-chromosome tree which may be the result of retained Y-chromosome diversity which predates dog domestication or post-domestication admixture with wolves. We find that Y-chromosomes from three ancient European dogs (4700-7000&#xa0;years old) belong to distinct clades.<br><br>CONCLUSIONS: We estimate that the time to the most recent comment ancestor of dog Y haplogroups is 68-151 thousand years ago. Analysis of three Y-chromosomes from the Neolithic confirms long stranding population structure among European dogs.}, }
@article {pmid29743632, year = {2018}, author = {Sinha, S and Bheemsetty, VA and Inamdar, MS}, title = {A double helical motif in OCIAD2 is essential for its localization, interactions and STAT3 activation.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {7362}, pmid = {29743632}, issn = {2045-2322}, mesh = {Amino Acid Motifs ; Animals ; Cell Line ; Cell Movement ; Conserved Sequence ; Endosomes/metabolism ; Evolution, Molecular ; Gene Duplication ; Gene Expression Regulation ; Humans ; Mitochondria/metabolism ; Neoplasm Proteins/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Transport ; STAT3 Transcription Factor/*metabolism ; }, abstract = {The Ovarian Carcinoma Immunoreactive Antigen domain (OCIAD) - containing proteins OCIAD1/Asrij and OCIAD2, are implicated in several cancers and neurodegenerative diseases. While Asrij has a conserved role in facilitating STAT3 activation for JAK/STAT signaling, the expression and function of OCIAD2 in non-cancerous contexts remains unknown. Here, we report that ociad2 neighbors ociad1/asrij in most vertebrate genomes, and the two genes likely arose by tandem gene duplication, probably somewhere between the Ordovician and Silurian eras. We show that ociad2 expression is higher in the mouse kidney, liver and brain relative to other tissues. OCIAD2 localizes to early endosomes and mitochondria, and interacts with Asrij and STAT3. Knockdown and overexpression studies showed that OCIAD2 is essential for STAT3 activation and cell migration, which could contribute to its role in tumor metastasis. Structure prediction programs, protein disruption studies, biochemical and functional assays revealed a double helical motif in the OCIA domain that is necessary and sufficient for its localization, interactions and STAT3 activation. Given the importance of JAK/STAT signaling in development and disease, our studies shed light on the evolution and conserved function of the OCIA domain in regulating this pathway and will be critical for understanding this clinically important protein family.}, }
@article {pmid29738865, year = {2018}, author = {Feng, S and Stejskal, V and Wang, Y and Li, Z}, title = {The mitochondrial genomes of the barklice, Lepinotus reticulatus and Dorypteryx domestica (Psocodea: Trogiomorpha): Insight into phylogeny of the order Psocodea.}, journal = {International journal of biological macromolecules}, volume = {116}, number = {}, pages = {247-254}, doi = {10.1016/j.ijbiomac.2018.05.021}, pmid = {29738865}, issn = {1879-0003}, mesh = {Animals ; Base Sequence ; Evolution, Molecular ; Gene Order/genetics ; Genome, Mitochondrial/*genetics ; Insecta/*genetics ; Mitochondria/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The order Psocodea which has incorporated the two former orders Psocoptera (barklice and booklice) and Phthiraptera (parasitic lice) attracts much attention for its unusual mitochondrial (mt) genome rearrangements. Available phylogenetic analysis for Psocodea is subjected to partial taxa and a complete one is needed. To further explore the genome rearrangement and phylogeny in Psocodea, we sequenced the mt genomes of two barklice, Lepinotus reticulatus (collected from China) and Dorypteryx domestica (collected from Czech Republic). Both of newly sequenced barklice had typical one-chromosome mt genomes and the same mt gene arrangement with the reported Lepidopsocidae sp. The mt genomes of L. reticulatus and D. domestica contained 37 genes typical of bilateral animals. In contrast with the recent report mt genome of D. domestica, our strain was found with many single nucleotide polymorphisms in intra-specific difference. Phylogenetic relationships were inferred from all available mt genomes of Psocodea data using Maximum Likelihood and Bayesian methods. The mt genome of L. reticulatus is the first representative with complete sequences of the family Trogiidae and our D. domestica data enriched the family Psyllipsocidae, which will contribute to the further study of mt gene rearrangement and phylogeny of Psocodea.}, }
@article {pmid29731304, year = {2018}, author = {Maclean, AE and Hertle, AP and Ligas, J and Bock, R and Balk, J and Meyer, EH}, title = {Absence of Complex I Is Associated with Diminished Respiratory Chain Function in European Mistletoe.}, journal = {Current biology : CB}, volume = {28}, number = {10}, pages = {1614-1619.e3}, doi = {10.1016/j.cub.2018.03.036}, pmid = {29731304}, issn = {1879-0445}, mesh = {Electron Transport/*physiology ; Electron Transport Complex I/*genetics/metabolism ; Mitochondria/*metabolism ; Oxidative Phosphorylation ; Viscum album/*genetics/metabolism ; }, abstract = {Parasitism is a life history strategy found across all domains of life whereby nutrition is obtained from a host. It is often associated with reductive evolution of the genome, including loss of genes from the organellar genomes [1, 2]. In some unicellular parasites, the mitochondrial genome (mitogenome) has been lost entirely, with far-reaching consequences for the physiology of the organism [3, 4]. Recently, mitogenome sequences of several species of the hemiparasitic plant mistletoe (Viscum sp.) have been reported [5, 6], revealing a striking loss of genes not seen in any other multicellular eukaryotes. In particular, the nad genes encoding subunits of respiratory complex I are all absent and other protein-coding genes are also lost or highly diverged in sequence, raising the question what remains of the respiratory complexes and mitochondrial functions. Here we show that oxidative phosphorylation (OXPHOS) in European mistletoe, Viscum album, is highly diminished. Complex I activity and protein subunits of complex I could not be detected. The levels of complex IV and ATP synthase were at least 5-fold lower than in the non-parasitic model plant Arabidopsis thaliana, whereas alternative dehydrogenases and oxidases were higher in abundance. Carbon flux analysis indicates that cytosolic reactions including glycolysis are greater contributors to ATP synthesis than the mitochondrial tricarboxylic acid (TCA) cycle. Our results describe the extreme adjustments in mitochondrial functions of the first reported multicellular eukaryote without complex I.}, }
@article {pmid29730527, year = {2018}, author = {van der Hoek, MD and Madsen, O and Keijer, J and van der Leij, FR}, title = {Evolutionary analysis of the carnitine- and choline acyltransferases suggests distinct evolution of CPT2 versus CPT1 and related variants.}, journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids}, volume = {1863}, number = {8}, pages = {909-918}, doi = {10.1016/j.bbalip.2018.05.001}, pmid = {29730527}, issn = {1388-1981}, mesh = {Animals ; Caenorhabditis elegans/enzymology/genetics ; Carnitine/metabolism ; Carnitine O-Palmitoyltransferase/*genetics/metabolism ; Choline/metabolism ; Drosophila/enzymology/genetics ; *Evolution, Molecular ; Exons/genetics ; Introns/genetics ; Isoenzymes/genetics/metabolism ; Mitochondria/*enzymology ; *Phylogeny ; Yeasts/enzymology/genetics ; }, abstract = {Carnitine/choline acyltransferases play diverse roles in energy metabolism and neuronal signalling. Our knowledge of their evolutionary relationships, important for functional understanding, is incomplete. Therefore, we aimed to determine the evolutionary relationships of these eukaryotic transferases. We performed extensive phylogenetic and intron position analyses. We found that mammalian intramitochondrial CPT2 is most closely related to cytosolic yeast carnitine transferases (Sc-YAT1 and 2), whereas the other members of the family are related to intraorganellar yeast Sc-CAT2. Therefore, the cytosolically active CPT1 more closely resembles intramitochondrial ancestors than CPT2. The choline acetyltransferase is closely related to carnitine acetyltransferase and shows lower evolutionary rates than long chain acyltransferases. In the CPT1 family several duplications occurred during animal radiation, leading to the isoforms CPT1A, CPT1B and CPT1C. In addition, we found five CPT1-like genes in Caenorhabditis elegans that strongly group to the CPT1 family. The long branch leading to mammalian brain isoform CPT1C suggests that either strong positive or relaxed evolution has taken place on this node. The presented evolutionary delineation of carnitine/choline acyltransferases adds to current knowledge on their functions and provides tangible leads for further experimental research.}, }
@article {pmid29728774, year = {2018}, author = {Gong, S and Vamberger, M and Auer, M and Praschag, P and Fritz, U}, title = {Millennium-old farm breeding of Chinese softshell turtles (Pelodiscus spp.) results in massive erosion of biodiversity.}, journal = {Die Naturwissenschaften}, volume = {105}, number = {5-6}, pages = {34}, pmid = {29728774}, issn = {1432-1904}, support = {31471966//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Biodiversity ; *Breeding ; China ; DNA, Mitochondrial/genetics ; Microsatellite Repeats/genetics ; Phylogeny ; Turtles/*classification/*genetics ; }, abstract = {Chinese softshell turtles (Pelodiscus spp.) are widely distributed, ranging from the Amur and Ussuri Rivers in the Russian Far East through the Korean Peninsula, Japan, and eastern, central, and southern China to southern Vietnam. In East and Southeast Asia, Chinese softshell turtles are traditionally exploited for food and have been farm-bred in China since the Spring and Autumn Period, more than 2400 years ago. Currently, the annual production of Pelodiscus amounts to 340,000 t in China alone. Using mitochondrial DNA (2428 bp) and five nuclear loci (3704 bp), we examined broad sampling of wild and farm-bred Pelodiscus to infer genetic and taxonomic differentiation. We discovered four previously unknown mitochondrial lineages, all from China. One lineage from Jiangxi is deeply divergent and sister to the mitochondrial lineage of Pelodiscus axenaria. The nuclear loci supported species status for P. axenaria and the new lineage from Jiangxi. Pelodiscus maackii and P. parviformis, both harboring distinct mitochondrial lineages, were not differentiated from P. sinensis in the studied nuclear markers. The same is true for two new mitochondrial lineages from Zhejiang, China, represented by only one individual each, and another new lineage from Anhui, Guangdong, Jiangxi and Zhejiang, China. However, Vietnamese turtles yielding a mitochondrial lineage clustering within P. sinensis were distinct in nuclear markers, suggesting that these populations could represent another unknown species with introgressed mitochondria. Its species status is also supported by the syntopic occurrence with P. sinensis in northern Vietnam and by morphology. In addition, we confirmed sympatry of P. axenaria and P. parviformis in Guangxi, China, and found evidence for sympatry of P. sinensis and the new putative species from Jiangxi, China. We also discovered evidence for hybridization in turtle farms and for the occurrence of alien lineages in the wild (Zhejiang, China), highlighting the risk of genetic pollution of native stock. In the face of the large-scale breeding of Pelodiscus, we claim that the long-term survival of distinct genetic lineages and species can only be assured when an upscale market segment for pure-bred softshell turtles is established, making the breeding of pure lineages lucrative for turtle farms. Our findings underline that the diversity of Pelodiscus is currently underestimated and threatened by anthropogenic admixture. We recommend mass screening of genetic and morphological variation of Chinese softshell turtles as a first step to understand and preserve their diversity.}, }
@article {pmid29724860, year = {2018}, author = {Garg, SG and Martin, WF}, title = {Asking endosymbionts to do an enzyme's job.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {20}, pages = {E4543-E4544}, pmid = {29724860}, issn = {1091-6490}, mesh = {*Biological Evolution ; Enzymes/*metabolism ; Mitochondria ; *Symbiosis ; }, }
@article {pmid29723685, year = {2019}, author = {Samuilov, VD and Kiselevsky, DB and Oleskin, AV}, title = {Mitochondria-targeted quinones suppress the generation of reactive oxygen species, programmed cell death and senescence in plants.}, journal = {Mitochondrion}, volume = {46}, number = {}, pages = {164-171}, doi = {10.1016/j.mito.2018.04.008}, pmid = {29723685}, issn = {1872-8278}, mesh = {Antioxidants/metabolism ; Apoptosis/*drug effects ; Arabidopsis/drug effects ; Mitochondria/*drug effects/*metabolism ; Pisum sativum/drug effects ; Plant Cells/*drug effects ; Quinones/*metabolism ; Reactive Oxygen Species/*antagonists &amp; inhibitors ; Triticum/drug effects ; }, abstract = {This work focuses on the effect of mitochondria-targeted quinones (SkQs) on plants. SkQs with antioxidant properties are accumulated in the mitochondria of pea cells and suppress the generation of reactive oxygen species. At nanomolar concentrations, SkQs prevented the death of pea leaf epidermal or guard cells caused by chitosan, bacterial lipopolysaccharide or KCN. The protective effect of SkQs was removed by a protonophoric uncoupler. SkQs at micromolar concentrations inhibited the O2 evolution by illuminated chloroplasts and stimulated the respiration of mitochondria. SkQs slowed down the senescence and the death of Arabidopsis thaliana leaves and improved the wheat crop structure.}, }
@article {pmid29722901, year = {2018}, author = {McManus, HA and Fučíková, K and Lewis, PO and Lewis, LA and Karol, KG}, title = {Organellar phylogenomics inform systematics in the green algal family Hydrodictyaceae (Chlorophyceae) and provide clues to the complex evolutionary history of plastid genomes in the green algal tree of life.}, journal = {American journal of botany}, volume = {105}, number = {3}, pages = {315-329}, doi = {10.1002/ajb2.1066}, pmid = {29722901}, issn = {1537-2197}, mesh = {Base Sequence ; Chlorophyceae/*genetics ; Chlorophyta/*genetics ; Chloroplasts ; DNA, Chloroplast/analysis ; DNA, Mitochondrial/analysis ; *Evolution, Molecular ; Genes, Plant ; *Genome, Mitochondrial ; Genome, Plant ; *Genome, Plastid ; Genomics ; Mitochondria ; Organelles/*genetics ; *Phylogeny ; }, abstract = {PREMISE OF THE STUDY: Phylogenomic analyses across the green algae are resolving relationships at the class, order, and family levels and highlighting dynamic patterns of evolution in organellar genomes. Here we present a within-family phylogenomic study to resolve genera and species relationships in the family Hydrodictyaceae (Chlorophyceae), for which poor resolution in previous phylogenetic studies, along with divergent morphological traits, have precluded taxonomic revisions.<br><br>METHODS: Complete plastome sequences and mitochondrial protein-coding gene sequences were acquired from representatives of the Hydrodictyaceae using next-generation sequencing methods. Plastomes were characterized, and gene order and content were compared with plastomes spanning the Sphaeropleales. Single-gene and concatenated-gene phylogenetic analyses of plastid and mitochondrial genes were performed.<br><br>KEY RESULTS: The Hydrodictyaceae contain the largest sphaeroplealean plastomes thus far fully sequenced. Conservation of plastome gene order within Hydrodictyaceae is striking compared with more dynamic patterns revealed across Sphaeropleales. Phylogenetic analyses resolve Hydrodictyon sister to a monophyletic Pediastrum, though the morphologically distinct P. angulosum and P. duplex continue to be polyphyletic. Analyses of plastid data supported the neochloridacean genus Chlorotetra&#xeb;dron as sister to Hydrodictyaceae, while conflicting signal was found in the mitochondrial data.<br><br>CONCLUSIONS: A phylogenomic approach resolved within-family relationships not obtainable with previous phylogenetic analyses. Denser taxon sampling across Sphaeropleales is necessary to capture patterns in plastome evolution, and further taxa and studies are needed to fully resolve the sister lineage to Hydrodictyaceae and polyphyly of Pediastrum angulosum and P. duplex.}, }
@article {pmid29720079, year = {2018}, author = {Dufresnes, C and Lymberakis, P and Kornilios, P and Savary, R and Perrin, N and Stöck, M}, title = {Phylogeography of Aegean green toads (Bufo viridis subgroup): continental hybrid swarm vs. insular diversification with discovery of a new island endemic.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {67}, pmid = {29720079}, issn = {1471-2148}, support = {STO 493/2-2//Deutsche Forschungsgemeinschaft/International ; P2LAP3_171818//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/International ; }, mesh = {Animals ; Base Sequence ; *Biodiversity ; Bufonidae/*classification ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Gene Flow ; Genetic Drift ; Genetics, Population ; Genome ; Greece ; *Islands ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; *Phylogeography ; Reproductive Isolation ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Debated aspects in speciation research concern the amount of gene flow between incipient species under secondary contact and the modes by which post-zygotic isolation accumulates. Secondary contact zones of allopatric lineages, involving varying levels of divergence, provide natural settings for comparative studies, for which the Aegean (Eastern Mediterranean) geography offers unique scenarios. In Palearctic green toads (Bufo viridis subgroup or Bufotes), Plio-Pleistocene (~ 2.6 Mya) diverged species show a sharp transition without contemporary gene flow, while younger lineages, diverged in the Lower-Pleistocene (~ 1.9 Mya), admix over tens of kilometers. Here, we conducted a fine-scale multilocus phylogeographic analysis of continental and insular green toads from the Aegean, where a third pair of taxa, involving Mid-Pleistocene diverged (~ 1.5 Mya) mitochondrial lineages, earlier tentatively named viridis and variabilis, (co-)occurs.<br><br>RESULTS: We discovered a new lineage, endemic to Naxos (Central Cyclades), while coastal islands and Crete feature weak genetic differentiation from the continent. In continental Greece, both lineages, viridis and variabilis, form a hybrid swarm, involving massive mitochondrial and nuclear admixture over hundreds of kilometers, without obvious selection against hybrids.<br><br>CONCLUSIONS: The genetic signatures of insular Aegean toads appear governed by bathymetry and Quaternary sea level changes, resulting in long-term isolation (Central Cyclades: Naxos) and recent land-bridges (coastal islands). Conversely, Crete has been isolated since the end of the Messinian salinity crisis (5.3 My) and Cretan populations thus likely result from human-mediated colonization, at least since Antiquity, from Peloponnese and Anatolia. Comparisons of green toad hybrid zones support the idea that post-zygotic hybrid incompatibilities accumulate gradually over the genome. In this radiation, only one million years of divergence separate a scenario of complete reproductive isolation, from a secondary contact resulting in near panmixia.}, }
@article {pmid29718949, year = {2018}, author = {Lv, C and Li, Q and Kong, L}, title = {Comparative analyses of the complete mitochondrial genomes of Dosinia clams and their phylogenetic position within Veneridae.}, journal = {PloS one}, volume = {13}, number = {5}, pages = {e0196466}, pmid = {29718949}, issn = {1932-6203}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Bayes Theorem ; Bivalvia/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {Mitochondrial genomes have proved to be a powerful tool in resolving phylogenetic relationship. In order to understand the mitogenome characteristics and phylogenetic position of the genus Dosinia, we sequenced the complete mitochondrial genomes of Dosinia altior and Dosinia troscheli (Bivalvia: Veneridae), compared them with that of Dosinia japonica and established a phylogenetic tree for Veneridae. The mitogenomes of D. altior (17,536 bp) and D. troscheli (17,229 bp) are the two smallest in Veneridae, which include 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and non-coding regions. The mitogenomes of the Dosinia species are similar in size, gene content, AT content, AT- and GC- skews, and gene arrangement. The phylogenetic relationships of family Veneridae were established based on 12 concatenated protein-coding genes using maximum likelihood and Bayesian analyses, which supported that Dosininae and Meretricinae have a closer relationship, with Tapetinae being the sister taxon. The information obtained in this study will contribute to further understanding of the molecular features of bivalve mitogenomes and the evolutionary history of the genus Dosinia.}, }
@article {pmid29706933, year = {2018}, author = {Goetzman, ES and Prochownik, EV}, title = {The Role for Myc in Coordinating Glycolysis, Oxidative Phosphorylation, Glutaminolysis, and Fatty Acid Metabolism in Normal and Neoplastic Tissues.}, journal = {Frontiers in endocrinology}, volume = {9}, number = {}, pages = {129}, pmid = {29706933}, issn = {1664-2392}, support = {R01 CA174713/CA/NCI NIH HHS/United States ; R01 DK090242/DK/NIDDK NIH HHS/United States ; }, abstract = {That cancer cells show patterns of metabolism different from normal cells has been known for over 50 years. Yet, it is only in the past decade or so that an appreciation of the benefits of these changes has begun to emerge. Altered cancer cell metabolism was initially attributed to defective mitochondria. However, we now realize that most cancers do not have mitochondrial mutations and that normal cells can transiently adopt cancer-like metabolism during periods of rapid proliferation. Indeed, an encompassing, albeit somewhat simplified, conceptual framework to explain both normal and cancer cell metabolism rests on several simple premises. First, the metabolic pathways used by cancer cells and their normal counterparts are the same. Second, normal quiescent cells use their metabolic pathways and the energy they generate largely to maintain cellular health and organelle turnover and, in some cases, to provide secreted products necessary for the survival of the intact organism. By contrast, undifferentiated cancer cells minimize the latter functions and devote their energy to producing the anabolic substrates necessary to maintain high rates of unremitting cellular proliferation. Third, as a result of the uncontrolled proliferation of cancer cells, a larger fraction of the metabolic intermediates normally used by quiescent cells purely as a source of energy are instead channeled into competing proliferation-focused and energy-consuming anabolic pathways. Fourth, cancer cell clones with the most plastic and rapidly adaptable metabolism will eventually outcompete their less well-adapted brethren during tumor progression and evolution. This attribute becomes increasingly important as tumors grow and as their individual cells compete in a constantly changing and inimical environment marked by nutrient, oxygen, and growth factor deficits. Here, we review some of the metabolic pathways whose importance has gained center stage for tumor growth, particularly those under the control of the c-Myc (Myc) oncoprotein. We discuss how these pathways differ functionally between quiescent and proliferating normal cells, how they are kidnapped and corrupted during the course of transformation, and consider potential therapeutic strategies that take advantage of common features of neoplastic and metabolic disorders.}, }
@article {pmid29703131, year = {2018}, author = {Arafat, H and Alamaru, A and Gissi, C and Huchon, D}, title = {Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {65}, pmid = {29703131}, issn = {1471-2148}, support = {161/15//Israel Science Foundation/International ; }, mesh = {Animals ; Biological Evolution ; Conserved Sequence/genetics ; Ctenophora/*genetics ; DNA, Mitochondrial/genetics ; Gene Order ; *Gene Rearrangement ; *Genes, Mitochondrial ; Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Annotation ; Open Reading Frames/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; }, abstract = {BACKGROUND: Complete mitochondrial (mt) genomes have been sequenced for thousands of animals and represent a molecule of choice for many evolutionary studies. Nevertheless, some animal groups have remained under-sampled. Ctenophora (comb jellies) is one such example, with only two complete mt sequences determined hitherto for this phylum, which encompasses ca. 150-200 described species. This lack of data derives from the extremely fast mt evolutionary rate in this lineage, complicating primer design and DNA amplification. Indeed, in the two ctenophore mt genomes sequenced to date, i.e. those of Mnemiopsis leidyi (order Lobata) and Pleurobrachia bachei (order Cydippida), both rRNA and protein coding genes exhibit an extraordinary size reduction and have highly derived sequences. Additionally, all tRNAs, and the atp6 and atp8 genes are absent. In order to determine whether these characteristics are shared by other ctenophores, we obtained the complete mt genomes of three benthic ctenophores belonging to the so far unsampled order of Platyctenida: Coeloplana loyai, Coeloplana yulianicorum and Vallicula multiformis.<br><br>RESULTS: The mt genomes of benthic ctenophores reveal the same peculiarities found in Mnemiopsis and Pleurobrachia, demonstrating that the fast evolutionary rate is a general trait of the ctenophore mt genomes. Our results also indicate that this high evolutionary rate not only affects the nucleotide substitution but also gene rearrangements. Indeed, gene order was highly rearranged among representatives of the different taxonomic orders in which it was close to random, but also quite variable within Platyctenida, in which the genera Coeloplana and Vallicula share only four conserved synteny blocks. However, the two congeneric Coeloplana species display exactly the same gene order. Because of the extreme evolutionary rate, our phylogenetic analyses were unable to resolve the phylogenetic position of ctenophores within metazoans or the relationships among the different Ctenophora orders. Comparative sequence-analyses allowed us to correct the annotation of the Pleurobrachia mt genome, confirming the absence of tRNAs, the presence of both rRNA genes, and the existence of a reassignment of codon TGA from tryptophan to serine for this species.<br><br>CONCLUSIONS: Since Platyctenida is an early diverging lineage among Ctenophora, our findings suggest that the mt traits described above are ancestral characteristics of this phylum.}, }
@article {pmid29698456, year = {2018}, author = {Peña-Diaz, P and Mach, J and Kriegová, E and Poliak, P and Tachezy, J and Lukeš, J}, title = {Trypanosomal mitochondrial intermediate peptidase does not behave as a classical mitochondrial processing peptidase.}, journal = {PloS one}, volume = {13}, number = {4}, pages = {e0196474}, pmid = {29698456}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Down-Regulation ; Electron Transport Complex IV/metabolism ; Metalloendopeptidases/antagonists &amp; inhibitors/classification/genetics/*metabolism ; Microscopy, Fluorescence ; Mitochondria/*enzymology ; Phylogeny ; Protein Subunits/antagonists &amp; inhibitors/genetics/metabolism ; RNA Interference ; RNA, Small Interfering/metabolism ; Substrate Specificity ; Trypanosoma brucei brucei/*metabolism ; Mitochondrial Processing Peptidase ; }, abstract = {Upon their translocation into the mitochondrial matrix, the N-terminal pre-sequence of nuclear-encoded proteins undergoes cleavage by mitochondrial processing peptidases. Some proteins require more than a single processing step, which involves several peptidases. Down-regulation of the putative Trypanosoma brucei mitochondrial intermediate peptidase (MIP) homolog by RNAi renders the cells unable to grow after 48 hours of induction. Ablation of MIP results in the accumulation of the precursor of the trypanosomatid-specific trCOIV protein, the largest nuclear-encoded subunit of the cytochrome c oxidase complex in this flagellate. However, the trCOIV precursor of the same size accumulates also in trypanosomes in which either alpha or beta subunits of the mitochondrial processing peptidase (MPP) have been depleted. Using a chimeric protein that consists of the N-terminal sequence of a putative subunit of respiratory complex I fused to a yellow fluorescent protein, we assessed the accumulation of the precursor protein in trypanosomes, in which RNAi was induced against the alpha or beta subunits of MPP or MIP. The observed accumulation of precursors indicates MIP depletion affects the activity of the cannonical MPP, or at least one of its subunits.}, }
@article {pmid29697049, year = {2018}, author = {Stairs, CW and Eme, L and Muñoz-Gómez, SA and Cohen, A and Dellaire, G and Shepherd, JN and Fawcett, JP and Roger, AJ}, title = {Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {29697049}, issn = {2050-084X}, support = {MOP 341174//CIHR/Canada ; MOP 142349//CIHR/Canada ; R15 GM096398/GM/NIGMS NIH HHS/United States ; 1R15GM096398-01/NH/NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; *Anaerobiosis ; Bacteria/genetics ; Electron Transport Complex II/*genetics/metabolism ; Eukaryota/*genetics/*physiology ; Fumarates/metabolism ; *Gene Transfer, Horizontal ; Genetic Variation ; Oxidation-Reduction ; Phylogeny ; Ubiquinone/*analogs &amp; derivatives/biosynthesis ; }, abstract = {Under hypoxic conditions, some organisms use an electron transport chain consisting of only complex I and II (CII) to generate the proton gradient essential for ATP production. In these cases, CII functions as a fumarate reductase that accepts electrons from a low electron potential quinol, rhodoquinol (RQ). To clarify the origins of RQ-mediated fumarate reduction in eukaryotes, we investigated the origin and function of rquA, a gene encoding an RQ biosynthetic enzyme. RquA is very patchily distributed across eukaryotes and bacteria adapted to hypoxia. Phylogenetic analyses suggest lateral gene transfer (LGT) of rquA from bacteria to eukaryotes occurred at least twice and the gene was transferred multiple times amongst protists. We demonstrate that RquA functions in the mitochondrion-related organelles of the anaerobic protist Pygsuia and is correlated with the presence of RQ. These analyses reveal the role of gene transfer in the evolutionary remodeling of mitochondria in adaptation to hypoxia.}, }
@article {pmid29695865, year = {2018}, author = {Martijn, J and Vosseberg, J and Guy, L and Offre, P and Ettema, TJG}, title = {Deep mitochondrial origin outside the sampled alphaproteobacteria.}, journal = {Nature}, volume = {557}, number = {7703}, pages = {101-105}, doi = {10.1038/s41586-018-0059-5}, pmid = {29695865}, issn = {1476-4687}, mesh = {Alphaproteobacteria/*cytology/*genetics ; Atlantic Ocean ; Genome, Bacterial/genetics ; Genomics ; Metagenome/genetics ; Mitochondria/*genetics/*metabolism ; Pacific Ocean ; *Phylogeny ; }, abstract = {Mitochondria are ATP-generating organelles, the endosymbiotic origin of which was a key event in the evolution of eukaryotic cells [1] . Despite strong phylogenetic evidence that mitochondria had an alphaproteobacterial ancestry [2] , efforts to pinpoint their closest relatives among sampled alphaproteobacteria have generated conflicting results, complicating detailed inferences about the identity and nature of the mitochondrial ancestor. While most studies support the idea that mitochondria evolved from an ancestor related to Rickettsiales[3-9], an order that includes several host-associated pathogenic and endosymbiotic lineages[10,11], others have suggested that mitochondria evolved from a free-living group[12-14]. Here we re-evaluate the phylogenetic placement of mitochondria. We used genome-resolved binning of oceanic metagenome datasets and increased the genomic sampling of Alphaproteobacteria with twelve divergent clades, and one clade representing a sister group to all Alphaproteobacteria. Subsequent phylogenomic analyses that specifically address long branch attraction and compositional bias artefacts suggest that mitochondria did not evolve from Rickettsiales or any other currently recognized alphaproteobacterial lineage. Rather, our analyses indicate that mitochondria evolved from a proteobacterial lineage that branched off before the divergence of all sampled alphaproteobacteria. In light of this new result, previous hypotheses on the nature of the mitochondrial ancestor[6,15,16] should be re-evaluated.}, }
@article {pmid29691935, year = {2018}, author = {Henry, LP and Newton, ILG}, title = {Mitochondria and Wolbachia titers are positively correlated during maternal transmission.}, journal = {Molecular ecology}, volume = {27}, number = {11}, pages = {2634-2646}, doi = {10.1111/mec.14700}, pmid = {29691935}, issn = {1365-294X}, mesh = {Animals ; Biological Evolution ; Drosophila melanogaster/genetics ; Female ; Gene Expression/genetics ; Genotype ; Infectious Disease Transmission, Vertical ; Mitochondria/*genetics ; NADH Dehydrogenase/genetics ; Symbiosis/genetics ; Wolbachia/*genetics ; }, abstract = {Mothers provide their offspring with symbionts. Maternally transmitted, intracellular symbionts must disperse from mother to offspring with other cytoplasmic elements, like mitochondria. Here, we investigated how the intracellular symbiont Wolbachia interacts with mitochondria during maternal transmission. Mitochondria and Wolbachia may interact antagonistically and compete as each population tries to ensure its own evolutionary success. Alternatively, mitochondria and Wolbachia may cooperate as both benefit from ensuring the fitness of the mother. We characterized the relationship between mitochondria and Wolbachia titers in ovaries of Drosophila melanogaster. We found that mitochondria and Wolbachia titers are positively correlated in common laboratory genotypes of D. melanogaster. We attempted to perturb this covariation through the introduction of Wolbachia variants that colonize at different titers. We also attempted to perturb the covariation through manipulating the female reproductive tract to disrupt maternal transmission. Finally, we also attempted to disrupt the covariation by knocking down gene expression for two loci involved in mitochondrial metabolism: NADH dehydrogenase and a mitochondrial transporter. Overall, we find that mitochondria and Wolbachia titers are commonly positively correlated, but this positive covariation is disrupted at high titers of Wolbachia. Our results suggest that mitochondria and Wolbachia have likely evolved mechanisms to stably coexist, but the competitive dynamics change at high Wolbachia titers. We provide future directions to better understand how their interaction influences the maintenance of the symbiosis.}, }
@article {pmid29689791, year = {2018}, author = {Sadasivan, K and Ramesh, MB and Palot, MJ and Ambekar, M and Mirza, ZA}, title = {A new species of fan-throated lizard of the genus Sitana Cuvier, 1829 from coastal Kerala, southern India.}, journal = {Zootaxa}, volume = {4374}, number = {4}, pages = {545-564}, doi = {10.11646/zootaxa.4374.4.5}, pmid = {29689791}, issn = {1175-5334}, mesh = {Animals ; India ; *Lizards ; Mitochondria ; Phylogeny ; }, abstract = {We here describe Sitana attenboroughii sp. nov., a new species of fan-throated lizard of the genus Sitana Cuvier, 1829 from coastal Kerala in southern India. The new species morphologically is closer to Sitana visiri Deepak, 2016 (in Deepak et al. 2016a), however, differs in having higher numbers of ventral scales and a comparatively short but richly colored dewlap. Genetically the new species shows affinity to Sitana marudhamneydhal Deepak, Khandekar, Varma Chaitanya, 2016 from which it differs in an uncorrected pairwise sequence divergence of 2.2% for a fragment of mitochondrial Nicotinamide adenine dinucleotide dehydrogenase (NADH) subunit 2 gene.}, }
@article {pmid29689215, year = {2018}, author = {McBride, HM}, title = {Mitochondria and endomembrane origins.}, journal = {Current biology : CB}, volume = {28}, number = {8}, pages = {R367-R372}, doi = {10.1016/j.cub.2018.03.052}, pmid = {29689215}, issn = {1879-0445}, mesh = {Animals ; Biological Evolution ; Eukaryota ; Evolution, Molecular ; Humans ; Intracellular Membranes/*physiology ; Mitochondria/*metabolism/*physiology ; Mitochondrial Membranes/metabolism/physiology ; }, abstract = {In this Guest Editorial, Heidi McBride introduces our special issue on membranes with a discussion of the contribution of mitochondria to the emergence of the endomembrane system.}, }
@article {pmid29678141, year = {2018}, author = {Beltrán-López, RG and Domínguez-Domínguez, O and Pérez-Rodríguez, R and Piller, K and Doadrio, I}, title = {Evolving in the highlands: the case of the Neotropical Lerma live-bearing Poeciliopsis infans (Woolman, 1894) (Cyprinodontiformes: Poeciliidae) in Central Mexico.}, journal = {BMC evolutionary biology}, volume = {18}, number = {1}, pages = {56}, pmid = {29678141}, issn = {1471-2148}, mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Climate ; Cyprinodontiformes/genetics/*physiology ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; *Ecosystem ; Fresh Water ; Genes, Mitochondrial ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Mexico ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; Time Factors ; *Tropical Climate ; }, abstract = {BACKGROUND: Volcanic and tectonic activities in conjunction with Quaternary climate are the main events that shaped the geographical distribution of genetic variation of many lineages. Poeciliopsis infans is the only poeciliid species that was able to colonize the temperate highlands of central Mexico. We inferred the phylogenetic relationships, biogeographic history, and historical demography in the widespread Neotropical species P. infans and correlated this with geological events and the Quaternary glacial-interglacial climate in the highlands of central Mexico, using the mitochondrial genes Cytochrome b and Cytochrome oxidase I and two nuclear loci, Rhodopsin and ribosomal protein S7.<br><br>RESULTS: Populations of P. infans were recovered in two well-differentiated clades. The maximum genetic distances between the two clades were 3.3% for cytb, and 1.9% for coxI. The divergence of the two clades occurred ca. 2.83 Myr. Ancestral area reconstruction revealed a complex biogeographical history for P. infans. The Bayesian Skyline Plot showed a demographic decline, although more visible for clade A, and more recently showed a population expansion in the last 0.025 Myr. Finally, the habitat suitability modelling showed that during the LIG, clade B had more areas with high probabilities of presence in comparison to clade A, whereas for the LGM, clade A showed more areas with high probabilities of presence in comparisons to clade B.<br><br>CONCLUSIONS: Poeciliopsis infans has had a complex evolutionary and biogeographic history, which, as in other co-distributed freshwater fishes, seems to be linked to the volcanic and tectonic activities during the Pliocene or early Pleistocene. Populations of P. infans distributed in lowlands showed a higher level of genetic diversity than populations distributed in highlands, which could be linked to more stable and higher temperatures in lowland areas. The fluctuations in population size through time are in agreement with the continuous fluctuations of the climate of central Mexico.}, }
@article {pmid29675902, year = {2018}, author = {Morin, PA and Foote, AD and Baker, CS and Hancock-Hanser, BL and Kaschner, K and Mate, BR and Mesnick, SL and Pease, VL and Rosel, PE and Alexander, A}, title = {Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses.}, journal = {Molecular ecology}, volume = {27}, number = {11}, pages = {2604-2619}, doi = {10.1111/mec.14698}, pmid = {29675902}, issn = {1365-294X}, mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Demography ; Genetic Variation/*genetics ; Genetics, Population/methods ; Haplotypes/genetics ; Mitochondria/*genetics ; Phylogeny ; Phylogeography/methods ; Population Density ; Sperm Whale/*genetics ; }, abstract = {Mitochondrial DNA has been heavily utilized in phylogeography studies for several decades. However, underlying patterns of demography and phylogeography may be misrepresented due to coalescence stochasticity, selection, variation in mutation rates and cultural hitchhiking (linkage of genetic variation to culturally-transmitted traits affecting fitness). Cultural hitchhiking has been suggested as an explanation for low genetic diversity in species with strong social structures, counteracting even high mobility, abundance and limited barriers to dispersal. One such species is the sperm whale, which shows very limited phylogeographic structure and low mtDNA diversity despite a worldwide distribution and large population. Here, we use analyses of 175 globally distributed mitogenomes and three nuclear genomes to evaluate hypotheses of a population bottleneck/expansion vs. a selective sweep due to cultural hitchhiking or selection on mtDNA as the mechanism contributing to low worldwide mitochondrial diversity in sperm whales. In contrast to mtDNA control region (CR) data, mitogenome haplotypes are largely ocean-specific, with only one of 80 shared between the Atlantic and Pacific. Demographic analyses of nuclear genomes suggest low mtDNA diversity is consistent with a global reduction in population size that ended approximately 125,000 years ago, correlated with the Eemian interglacial. Phylogeographic analysis suggests that extant sperm whales descend from maternal lineages endemic to the Pacific during the period of reduced abundance and have subsequently colonized the Atlantic several times. Results highlight the apparent impact of past climate change, and suggest selection and hitchhiking are not the sole processes responsible for low mtDNA diversity in this highly social species.}, }
@article {pmid29675831, year = {2018}, author = {Kauko, A and Lehto, K}, title = {Eukaryote specific folds: Part of the whole.}, journal = {Proteins}, volume = {86}, number = {8}, pages = {868-881}, doi = {10.1002/prot.25517}, pmid = {29675831}, issn = {1097-0134}, mesh = {Archaea/genetics ; Bacteria/classification ; Biological Evolution ; Databases, Protein ; Eukaryota/*classification ; Eukaryotic Cells/classification ; Evolution, Molecular ; Genes, Bacterial ; Genes, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Proteins/genetics ; Symbiosis/*genetics ; }, abstract = {The origin of eukaryotes is one of the central transitions in the history of life; without eukaryotes there would be no complex multicellular life. The most accepted scenarios suggest the endosymbiosis of a mitochondrial ancestor with a complex archaeon, even though the details regarding the host and the triggering factors are still being discussed. Accordingly, phylogenetic analyses have demonstrated archaeal affiliations with key informational systems, while metabolic genes are often related to bacteria, mostly to the mitochondrial ancestor. Despite of this, there exists a large number of protein families and folds found only in eukaryotes. In this study, we have analyzed structural superfamilies and folds that probably appeared during eukaryogenesis. These folds typically represent relatively small binding domains of larger multidomain proteins. They are commonly involved in biological processes that are particularly complex in eukaryotes, such as signaling, trafficking/cytoskeleton, ubiquitination, transcription and RNA processing, but according to recent studies, these processes also have prokaryotic roots. Thus the folds originating from an eukaryotic stem seem to represent accessory parts that have contributed in the expansion of several prokaryotic processes to a new level of complexity. This might have taken place as a co-evolutionary process where increasing complexity and fold innovations have supported each other.}, }
@article {pmid29671881, year = {2018}, author = {Demain, LAM and Antunes, D and O'Sullivan, J and Bhaskhar, SS and O'Keefe, RT and Newman, WG}, title = {A known pathogenic variant in the essential mitochondrial translation gene RMND1 causes a Perrault-like syndrome with renal defects.}, journal = {Clinical genetics}, volume = {94}, number = {2}, pages = {276-277}, doi = {10.1111/cge.13255}, pmid = {29671881}, issn = {1399-0004}, support = {S35/ACT_/RNID/United Kingdom ; /DH_/Department of Health/United Kingdom ; }, mesh = {Cell Cycle Proteins/*genetics ; Female ; *Genetic Predisposition to Disease ; Gonadal Dysgenesis, 46,XX/complications/*genetics/pathology ; Hearing Loss, Sensorineural/complications/*genetics/pathology ; Humans ; Kidney Diseases/complications/*genetics/pathology ; Mitochondria/genetics ; Exome Sequencing ; }, }
@article {pmid29665772, year = {2018}, author = {Padilla-Jacobo, G and Cano-Camacho, H and López-Zavala, R and Cornejo-Pérez, ME and Zavala-Páramo, MG}, title = {Evolutionary history of Mexican domesticated and wild Meleagris gallopavo.}, journal = {Genetics, selection, evolution : GSE}, volume = {50}, number = {1}, pages = {19}, pmid = {29665772}, issn = {1297-9686}, support = {Scholarship No. 359650//Consejo Nacional de Ciencia y Tecnolog&#xed;a/International ; Scholarship//Consejo Nacional de Ciencia y Tecnolog&#xed;a/International ; 2004-C01-201//Consejo Nacional de Ciencia y Tecnolog&#xed;a-SAGARPA (MX)/International ; 2009-05-115938//Fondos Mixtos Consejo Nacional de Ciencia y Tecnolog&#xed;a Gobierno del Estado de Michoac&#xe1;n (MX)/International ; }, mesh = {Animals ; Animals, Domestic/*genetics ; Animals, Wild/genetics ; Canada ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genetic Variation ; Guatemala ; Haplotypes ; Mexico ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*veterinary ; Turkeys/classification/*genetics ; }, abstract = {BACKGROUND: The distribution of the wild turkey (Meleagris gallopavo) extends from Mexico to southeastern Canada and to the eastern and southern regions of the USA. Six subspecies have been described based on morphological characteristics and/or geographical variations in wild and domesticated populations. In this paper, based on DNA sequence data from the mitochondrial D-loop, we investigated the genetic diversity and structure, genealogical relationships, divergence time and demographic history of M. gallopavo populations including domesticated individuals.<br><br>RESULTS: Analyses of 612 wild and domesticated turkey mitochondrial D-loop sequences, including 187 that were collected for this study and 425 from databases, revealed 64 haplotypes with few mutations, some of which are shared between domesticated and wild turkeys. We found a high level of haplotype and nucleotide diversity, which suggests that the total population of this species is large and stable with an old evolutionary history. The results of genetic differentiation, haplotype network, and genealogical relationships analyses revealed three main genetic groups within the species: mexicana as a population relict (C1), merriami (C2), and mexicana/intermedia/silvestris/osceola (C3). Haplotypes detected in domesticated turkeys belong to group C3. Estimates of divergence times agree with range expansion and diversification events of the relict population of M. gallopavo in northwestern Mexico during the Pliocene-Pleistocene and Pleistocene-Holocene boundaries. Demographic reconstruction showed that an expansion of the population occurred 110,000&#xa0;to&#xa0;130,000&#xa0;years ago (Kya), followed by a stable period 100&#xa0;Kya and finally a decline ~&#x2009;10&#xa0;Kya (Pleistocene-Holocene boundary). In Mexico, the Trans-Mexican Volcanic Belt may be responsible for the range expansion of the C3 group. Two haplotypes with different divergence times, MGMDgoB/MICH1 and MICH2, are dominant in domesticated and commercial turkeys.<br><br>CONCLUSIONS: During the Pleistocene, a large and stable population of M. gallopavo covered a wide geographic distribution from the north to the center of America (USA and Mexico). The mexicana, merriami, and mexicana/intermedia/silvestris/osceola genetic groups originated after divergence and range expansion from northwestern Mexico during the Pliocene-Pleistocene and Pleistocene-Holocene boundaries. Old and new maternal lines of the mexicana/intermedia/silvestris/osceola genetic group were distributed within the Trans-Mexican Volcanic Belt where individuals were captured for domestication. Two haplotypes are the main founder maternal lines of domesticated turkeys.}, }
@article {pmid29664320, year = {2018}, author = {Nakano, M}, title = {16S rRNA Gene Primer Validation for Bacterial Diversity Analysis of Vegetable Products.}, journal = {Journal of food protection}, volume = {81}, number = {5}, pages = {848-859}, doi = {10.4315/0362-028X.JFP-17-346}, pmid = {29664320}, issn = {1944-9097}, mesh = {Animals ; Bacteria/genetics ; Bacterial Load ; DNA Primers/genetics ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Microbiota ; RNA, Ribosomal, 16S/*genetics ; Vegetable Products/*microbiology ; }, abstract = {High-throughput sequencing of the 16S rRNA gene enhances understanding of microbial diversity from complex environmental samples. The 16S rRNA gene is currently the most important target in bacterial evolution and ecology studies, particularly for determination of phylogenetic relationships among taxa, exploration of bacterial diversity in a given environment, and quantification of the relative abundance of taxa at various levels. However, some parts of the conserved region of the bacterial 16S rRNA gene are similar to the conserved regions of plant chloroplasts and eukaryotic mitochondria. Therefore, if DNA contains a large amount of nontarget DNA, this nontarget DNA can be coamplified and consequently produce useless sequence reads. We experimentally assessed the primer pair 335f/769r and the widely used bacterial primer pair SD (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21). The primer pair 335f/769r was examined for its ability to amplify bacterial DNA in plant and animal feed samples by using the single-strand confirmation polymorphism method. In our present study, these primer pairs were validated for microbial community structure analysis with complex food matrices by using next-generation sequencing. The sequencing results revealed that the primer pair 335f/769r successfully resulted in fewer chloroplast and mitochondrial sequence reads than generated by the universal primer pair SD and therefore is comparatively suitable for metagenomic analyses of complex food matrices, particularly those that are rich in plant DNA. Additionally, some taxonomic groups were missed entirely when only the SD primer pair was used.}, }
@article {pmid29656105, year = {2018}, author = {Dias, C and Lima, KA and Araripe, J and Aleixo, A and Vallinoto, M and Sampaio, I and Schneider, H and Rêgo, PSD}, title = {Mitochondrial introgression obscures phylogenetic relationships among manakins of the genus Lepidothrix (Aves: Pipridae).}, journal = {Molecular phylogenetics and evolution}, volume = {126}, number = {}, pages = {314-320}, doi = {10.1016/j.ympev.2018.04.017}, pmid = {29656105}, issn = {1095-9513}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Haplotypes/genetics ; Mitochondria/*genetics ; Passeriformes/*classification/*genetics ; *Phylogeny ; }, abstract = {Lepidothrix is the most diverse genus of the family Pipridae, with eight recognized species. Although the genus' monophyly has been supported by both molecular and morphological characters, phylogenetic relationships and species limits within Lepidothrix remain uncertain. In the present study, we combined molecular sequences of mitochondrial (ND2 and COI) and nuclear (MYO, G3PDh and I5BF) markers in a multilocus analysis, to evaluate relationships and inter-specific limits among L. iris, L. nattereri, and L. vilasboasi, which are known to hybridize in eastern Amazonia. The results revealed a complex pattern, whereby events of secondary contact and gene flow after isolation and genetic and phenotypic differentiation prevented the recuperation of reciprocal monophyly among the studied taxa. The mitochondrial data indicate that L. nattereri is divided into two non-sister groups, one monophyletic, and the other, paraphyletic, with L. iris iris being more closely related to one of the two L. nattereri groups, while L. iris eucephala forms an undifferentiated clade with L. vilasboasi, probably resulting from an extensive process of mitochondrial introgression. In agreement with a previous study based on Single Nucleotide Polymorphism (SNP) data, mitochondrial haplotype networks also support that L. vilasboasi does not represent a recent "hybrid swarm" between L. iris and L. nattereri, but instead a genetically divergent lineage with a separate species status. Finally, the sister relationship recovered herein between L. iris iris and some western populations of L. nattereri currently in allopatry is also apparently explained by mitochondrial introgression, as also supported for nuclear genes by SNP data, indicating a complex scenario of past contact and gene flow between currently geographically distant Lepidothrix lineages.}, }
@article {pmid29654216, year = {2018}, author = {Reichold, M and Klootwijk, ED and Reinders, J and Otto, EA and Milani, M and Broeker, C and Laing, C and Wiesner, J and Devi, S and Zhou, W and Schmitt, R and Tegtmeier, I and Sterner, C and Doellerer, H and Renner, K and Oefner, PJ and Dettmer, K and Simbuerger, JM and Witzgall, R and Stanescu, HC and Dumitriu, S and Iancu, D and Patel, V and Mozere, M and Tekman, M and Jaureguiberry, G and Issler, N and Kesselheim, A and Walsh, SB and Gale, DP and Howie, AJ and Martins, JR and Hall, AM and Kasgharian, M and O'Brien, K and Ferreira, CR and Atwal, PS and Jain, M and Hammers, A and Charles-Edwards, G and Choe, CU and Isbrandt, D and Cebrian-Serrano, A and Davies, B and Sandford, RN and Pugh, C and Konecki, DS and Povey, S and Bockenhauer, D and Lichter-Konecki, U and Gahl, WA and Unwin, RJ and Warth, R and Kleta, R}, title = {Glycine Amidinotransferase (GATM), Renal Fanconi Syndrome, and Kidney Failure.}, journal = {Journal of the American Society of Nephrology : JASN}, volume = {29}, number = {7}, pages = {1849-1858}, pmid = {29654216}, issn = {1533-3450}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Aged ; Amidinotransferases/*genetics/metabolism ; Animals ; Computer Simulation ; Fanconi Syndrome/complications/*genetics/metabolism/pathology ; Female ; Heterozygote ; Humans ; Infant ; Inflammasomes/metabolism ; Kidney Failure, Chronic/etiology/*genetics/metabolism/pathology ; Male ; Mice ; Mice, Knockout ; Mitochondria/*metabolism/*pathology ; Molecular Conformation ; Mutation ; Mutation, Missense ; Pedigree ; Reactive Oxygen Species/metabolism ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Background For many patients with kidney failure, the cause and underlying defect remain unknown. Here, we describe a novel mechanism of a genetic order characterized by renal Fanconi syndrome and kidney failure.Methods We clinically and genetically characterized members of five families with autosomal dominant renal Fanconi syndrome and kidney failure. We performed genome-wide linkage analysis, sequencing, and expression studies in kidney biopsy specimens and renal cells along with knockout mouse studies and evaluations of mitochondrial morphology and function. Structural studies examined the effects of recognized mutations.Results The renal disease in these patients resulted from monoallelic mutations in the gene encoding glycine amidinotransferase (GATM), a renal proximal tubular enzyme in the creatine biosynthetic pathway that is otherwise associated with a recessive disorder of creatine deficiency. In silico analysis showed that the particular GATM mutations, identified in 28 members of the five families, create an additional interaction interface within the GATM protein and likely cause the linear aggregation of GATM observed in patient biopsy specimens and cultured proximal tubule cells. GATM aggregates-containing mitochondria were elongated and associated with increased ROS production, activation of the NLRP3 inflammasome, enhanced expression of the profibrotic cytokine IL-18, and increased cell death.Conclusions In this novel genetic disorder, fully penetrant heterozygous missense mutations in GATM trigger intramitochondrial fibrillary deposition of GATM and lead to elongated and abnormal mitochondria. We speculate that this renal proximal tubular mitochondrial pathology initiates a response from the inflammasome, with subsequent development of kidney fibrosis.}, }
@article {pmid29653091, year = {2018}, author = {Islam, W and Lin, W and Qasim, M and Islam, SU and Ali, H and Adnan, M and Arif, M and Du, Z and Wu, Z}, title = {A nation-wide genetic survey revealed a complex population structure of Bemisia tabaci in Pakistan.}, journal = {Acta tropica}, volume = {183}, number = {}, pages = {119-125}, doi = {10.1016/j.actatropica.2018.04.015}, pmid = {29653091}, issn = {1873-6254}, mesh = {Agriculture ; Animals ; Base Sequence ; Electron Transport Complex IV/genetics ; Genetic Speciation ; Genetic Variation ; Hemiptera/*genetics ; Insect Proteins/genetics ; Mitochondria/genetics ; *Molecular Epidemiology ; Pakistan ; *Phylogeny ; }, abstract = {The whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex distributed worldwide. In Pakistan, B. tabaci poses a serious threat to agriculture production. To understand its diversity in Pakistan, a large-scale sampling was conducted from various locations of all four provinces of the country and Mitochondrial cytochrome oxidase I (mtCOI) gene sequencing was used to determine the whiteflies genetically. The study revealed the presence of five different cryptic species in Pakistan namely Asia II-1, Asia II-5, Asia II-7, Asia II-8 and MEAM-1, respectively. Among them, Asia II-1, which was previously reported from a few areas in the country, had been found now to be prevalent all over the country covering 88.7% of all the sequenced samples. Based on the mtCOI sequences and genetic distance analyses, the diversity of Asia II-1 was much greater than all other cryptic species, which exist only in small patches.}, }
@article {pmid29643269, year = {2018}, author = {Mori, S and Matsunami, M}, title = {Signature of positive selection in mitochondrial DNA in Cetartiodactyla.}, journal = {Genes &amp; genetic systems}, volume = {93}, number = {2}, pages = {65-73}, doi = {10.1266/ggs.17-00015}, pmid = {29643269}, issn = {1880-5779}, mesh = {Amino Acid Substitution ; Animals ; Artiodactyla/*genetics ; Biological Evolution ; Cetacea/*genetics ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Evolution, Molecular ; Genomics ; Mammals/genetics ; Mitochondria/genetics ; Phylogeny ; Selection, Genetic/genetics ; }, abstract = {Acceleration of the amino acid substitution rate is a good indicator of positive selection in adaptive evolutionary changes of functional genes. Genomic information about mammals has become readily available in recent years, as many researchers have attempted to clarify the adaptive evolution of mammals by examining evolutionary rate change based on multiple loci. The order Cetartiodactyla (Artiodactyla and Cetacea) is one of the most diverse orders of mammals. Species in this order are found throughout all continents and seas, except Antarctica, and they exhibit wide variation in morphology and habitat. Here, we focused on the metabolism-related genes of mitochondrial DNA (mtDNA) in species of the order Cetartiodactyla using 191 mtDNA sequences available in databases. Based on comparisons of the dN/dS ratio (ω) in 12 protein-coding genes, ATP8 was shown to have a higher ω value (ω = 0.247) throughout Cetartiodactyla than the other 11 genes (ω < 0.05). In a branch-site analysis of ATP8 sequences, a markedly higher ω value of 0.801 was observed in the ancestral lineage of the clade of Cetacea, which is indicative of adaptive evolution. Through efforts to detect positively selected amino acids, codon positions 52 and 54 of ATP8 were shown to have experienced positive selective pressure during the course of evolution; multiple substitutions have occurred at these sites throughout the cetacean lineage. At position 52, glutamic acid was replaced with asparagine, and, at position 54, lysine was replaced with non-charged amino acids. These sites are conserved in most Artiodactyla. These results imply that the ancestor of cetaceans underwent accelerated amino acid changes in ATP8 and replacements at codons 52 and 54, which adjusted metabolism to adapt to the marine environment.}, }
@article {pmid29636759, year = {2018}, author = {Shibata, S and Arimura, SI and Ishikawa, T and Awai, K}, title = {Alterations of Membrane Lipid Content Correlated With Chloroplast and Mitochondria Development in Euglena gracilis.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {370}, pmid = {29636759}, issn = {1664-462X}, abstract = {Euglenoids are unique protists that can grow photoautotrophically, photomixotrophically, and heterotrophically. Here we grew Euglena gracilis under these different growth conditions and determined cellular contents of seven membrane lipids and one storage lipid (triacylglycerol), which account for more than 94 mol% of total membrane lipids. We also describe the relationship among chloroplast and mitochondria developments with lipid contents, protein contents, and oxygen evolution/consumption rates. In photoautotrophic growth conditions, E. gracilis cells accumulated chlorophyll, photosynthetic proteins, and glycolipids typical to thylakoid membranes. The same occurred for the cells grown under photomixotrophic conditions with higher respiration rates. In heterotrophic conditions, E. gracilis cells had higher respiration rates compared to cells grown in other conditions with the accumulation of pyruvate: NADP+ oxidoreductase, a mitochondrial protein and phospholipid common in mitochondria. Cells were also observed using a confocal laser scanning microscope and found to show more chlorophyll autofluorescence when grown photoautotrophically and photomixotrophycally, and fluorescence of MitoTracker when grown photomixotrophically and heterotrophically. These results suggest that under illumination, E. gracilis develops functional thylakoid membranes with membrane lipids and proteins for photosynthesis. In the medium with glucose, the cells develop mitochondria with phospholipids and proteins for respiration. Possible application based on lipid analysis for the enhancement of wax ester or alkene synthesis is discussed.}, }
@article {pmid29626207, year = {2018}, author = {Bundus, JD and Wang, D and Cutter, AD}, title = {Genetic basis to hybrid inviability is more complex than hybrid male sterility in Caenorhabditis nematodes.}, journal = {Heredity}, volume = {121}, number = {2}, pages = {169-182}, pmid = {29626207}, issn = {1365-2540}, mesh = {Animals ; Biological Evolution ; Caenorhabditis/classification/*genetics ; Cell Nucleus/*genetics ; Crosses, Genetic ; Female ; Genomics ; Infertility, Male/*genetics ; Male ; Mitochondria/*genetics ; *Models, Genetic ; }, abstract = {Hybrid male sterility often evolves before female sterility or inviability of hybrids, implying that the accumulation of divergence between separated lineages should lead hybrid male sterility to have a more polygenic basis. However, experimental evidence is mixed. Here, we use the nematodes Caenorhabditis remanei and C. latens to characterize the underlying genetic basis of asymmetric hybrid male sterility and hybrid inviability. We demonstrate that hybrid male sterility is consistent with a simple genetic basis, involving a single X-autosome incompatibility. We also show that hybrid inviability involves more genomic compartments, involving diverse nuclear-nuclear incompatibilities, a mito-nuclear incompatibility, and maternal effects. These findings demonstrate that male sensitivity to genetic perturbation may be genetically simple compared to hybrid inviability in Caenorhabditis and motivates tests of generality for the genetic architecture of hybrid incompatibility across the breadth of phylogeny.}, }
@article {pmid29623424, year = {2018}, author = {Peña-Diaz, P and Lukeš, J}, title = {Fe-S cluster assembly in the supergroup Excavata.}, journal = {Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry}, volume = {23}, number = {4}, pages = {521-541}, pmid = {29623424}, issn = {1432-1327}, mesh = {Eukaryota/cytology/*metabolism ; Iron/metabolism ; Iron-Sulfur Proteins/*metabolism ; Mitochondria/metabolism ; }, abstract = {The majority of established model organisms belong to the supergroup Opisthokonta, which includes yeasts and animals. While enlightening, this focus has neglected protists, organisms that represent the bulk of eukaryotic diversity and are often regarded as primitive eukaryotes. One of these is the "supergroup" Excavata, which comprises unicellular flagellates of diverse lifestyles and contains species of medical importance, such as Trichomonas, Giardia, Naegleria, Trypanosoma and Leishmania. Excavata exhibits a continuum in mitochondrial forms, ranging from classical aerobic, cristae-bearing mitochondria to mitochondria-related organelles, such as hydrogenosomes and mitosomes, to the extreme case of a complete absence of the organelle. All forms of mitochondria house a machinery for the assembly of Fe-S clusters, ancient cofactors required in various biochemical activities needed to sustain every extant cell. In this review, we survey what is known about the Fe-S cluster assembly in the supergroup Excavata. We aim to bring attention to the diversity found in this group, reflected in gene losses and gains that have shaped the Fe-S cluster biogenesis pathways.}, }
@article {pmid29621569, year = {2018}, author = {Seligmann, H}, title = {Alignment-based and alignment-free methods converge with experimental data on amino acids coded by stop codons at split between nuclear and mitochondrial genetic codes.}, journal = {Bio Systems}, volume = {167}, number = {}, pages = {33-46}, doi = {10.1016/j.biosystems.2018.03.002}, pmid = {29621569}, issn = {1872-8324}, mesh = {Amino Acid Sequence ; Amino Acids/*genetics ; Animals ; Anticodon/genetics ; Cell Nucleus/*genetics ; Codon, Terminator/*genetics ; Data Interpretation, Statistical ; Evolution, Molecular ; Genetic Code/*genetics ; Humans ; Mitochondria/*genetics ; }, abstract = {Genetic codes mainly evolve by reassigning punctuation codons, starts and stops. Previous analyses assuming that undefined amino acids translate stops showed greater divergence between nuclear and mitochondrial genetic codes. Here, three independent methods converge on which amino acids translated stops at split between nuclear and mitochondrial genetic codes: (a) alignment-free genetic code comparisons inserting different amino acids at stops; (b) alignment-based blast analyses of hypothetical peptides translated from non-coding mitochondrial sequences, inserting different amino acids at stops; (c) biases in amino acid insertions at stops in proteomic data. Hence short-term protein evolution models reconstruct long-term genetic code evolution. Mitochondria reassign stops to amino acids otherwise inserted at stops by codon-anticodon mismatches (near-cognate tRNAs). Hence dual function (translation termination and translation by codon-anticodon mismatch) precedes mitochondrial reassignments of stops to amino acids. Stop ambiguity increases coded information, compensates endocellular mitogenome reduction. Mitochondrial codon reassignments might prevent viral infections.}, }
@article {pmid29618317, year = {2018}, author = {Doyle, JM and Bell, DA and Bloom, PH and Emmons, G and Fesnock, A and Katzner, TE and LaPré, L and Leonard, K and SanMiguel, P and Westerman, R and Andrew DeWoody, J}, title = {New insights into the phylogenetics and population structure of the prairie falcon (Falco mexicanus).}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {233}, pmid = {29618317}, issn = {1471-2164}, support = {L12AC20102, L11PX02237, L12AC2010//U.S. Bureau of Land Management/ ; University Faculty Scholar program//Provost's Office at Purdue University/ ; PINN645-21//National Park Service/ ; BIO170038//XSEDE/ ; }, mesh = {Animals ; Avian Proteins/*genetics ; California ; Falconiformes/*classification/genetics ; Female ; Genetics, Population ; Idaho ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; *Polymorphism, Single Nucleotide ; Whole Genome Sequencing/*veterinary ; }, abstract = {BACKGROUND: Management requires a robust understanding of between- and within-species genetic variability, however such data are still lacking in many species. For example, although multiple population genetics studies of the peregrine falcon (Falco peregrinus) have been conducted, no similar studies have been done of the closely-related prairie falcon (F. mexicanus) and it is unclear how much genetic variation and population structure exists across the species' range. Furthermore, the phylogenetic relationship of F. mexicanus relative to other falcon species is contested. We utilized a genomics approach (i.e., genome sequencing and assembly followed by single nucleotide polymorphism genotyping) to rapidly address these gaps in knowledge.<br><br>RESULTS: We sequenced the genome of a single female prairie falcon and generated a 1.17 Gb (gigabases) draft genome assembly. We generated maximum likelihood phylogenetic trees using complete mitochondrial genomes as well as nuclear protein-coding genes. This process provided evidence that F. mexicanus is an outgroup to the clade that includes the peregrine falcon and members of the subgenus Hierofalco. We annotated >&#x2009;16,000 genes and almost 600,000 high-quality single nucleotide polymorphisms (SNPs) in the nuclear genome, providing the raw material for a SNP assay design featuring >&#x2009;140 gene-associated markers and a molecular-sexing marker. We subsequently genotyped ~&#x2009;100 individuals from California (including the San Francisco East Bay Area, Pinnacles National Park and the Mojave Desert) and Idaho (Snake River Birds of Prey National Conservation Area). We tested for population structure and found evidence that individuals sampled in California and Idaho represent a single panmictic population.<br><br>CONCLUSIONS: Our study illustrates how genomic resources can rapidly shed light on genetic variability in understudied species and resolve phylogenetic relationships. Furthermore, we found evidence of a single, randomly mating population of prairie falcons across our sampling locations. Prairie falcons are highly mobile and relatively rare long-distance dispersal events may promote gene flow throughout the range. As such, California's prairie falcons might be managed as a single population, indicating that management actions undertaken to benefit the species at the local level have the potential to influence the species as a whole.}, }
@article {pmid29618295, year = {2018}, author = {Derbikova, KS and Levitsky, SA and Chicherin, IV and Vinogradova, EN and Kamenski, PA}, title = {Activation of Yeast Mitochondrial Translation: Who Is in Charge?.}, journal = {Biochemistry. Biokhimiia}, volume = {83}, number = {2}, pages = {87-97}, doi = {10.1134/S0006297918020013}, pmid = {29618295}, issn = {1608-3040}, mesh = {Cytochromes b/genetics/metabolism ; Electron Transport Complex IV/genetics/metabolism ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/metabolism ; RNA, Messenger/metabolism ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Transcriptional Activation ; }, abstract = {Mitochondrial genome has undergone significant reduction in a course of evolution; however, it still contains a set of protein-encoding genes and requires translational machinery for their expression. Mitochondrial translation is of the prokaryotic type with several remarkable differences. This review is dedicated to one of the most puzzling features of mitochondrial protein synthesis, namely, the system of translational activators, i.e., proteins that specifically regulate translation of individual mitochondrial mRNAs and couple protein biosynthesis with the assembly of mitochondrial respiratory chain complexes. The review does not claim to be a comprehensive analysis of all published data; it is rather focused on the idea of the "core component" of the translational activator system.}, }
@article {pmid29616678, year = {2018}, author = {Nie, WH and Wang, JH and Su, WT and Hu, Y and He, SW and Jiang, XL and He, K}, title = {Species identification of crested gibbons (Nomascus) in captivity in China using karyotyping- and PCR-based approaches.}, journal = {Zoological research}, volume = {39}, number = {5}, pages = {356-363}, pmid = {29616678}, issn = {2095-8137}, mesh = {Animals ; Animals, Zoo ; Cell Nucleus/genetics ; China ; Endangered Species ; Genes/genetics ; Hylobates/classification/*genetics ; In Situ Hybridization, Fluorescence ; Karyotype ; Karyotyping ; Mitochondria/genetics ; Polymerase Chain Reaction ; }, abstract = {Gibbons and siamangs (Hylobatidae) are well-known for their rapid chromosomal evolution, which has resulted in high speciation rate within the family. On the other hand, distinct karyotypes do not prevent speciation, allowing interbreeding between individuals in captivity, and the unwanted hybrids are ethically problematic as all gibbon species are endangered or critically endangered. Thus, accurate species identification is crucial for captive breeding, particularly in China where studbooks are unavailable. Identification based on external morphology is difficult, especially for hybrids, because species are usually similar in appearance. In this study, we employed G-banding karyotyping and fluorescence in situ hybridization (FISH) as well as a PCR-based approach to examine karyotypic characteristics and identify crested gibbons of the genus Nomascus from zoos and nature reserves in China. We characterized and identified five karyotypes from 21 individuals of Nomascus. Using karyotypes and mitochondrial and nuclear genes, we identified three purebred species and three hybrids, including one F2 hybrid between N. gabriellae and N. siki. Our results also supported that N. leucogenys and N. siki shared the same inversion on chromosome 7, which resolves arguments from previous studies. Our results demonstrated that both karyotyping and DNA-based approaches were suitable for identifying purebred species, though neither was ideal for hybrid identification. The advantages and disadvantages of both approaches are discussed. Our results further highlight the importance of animal ethics and welfare, which are critical for endangered species in captivity.}, }
@article {pmid29614345, year = {2018}, author = {Fan, Z and Zhou, A and Osada, N and Yu, J and Jiang, J and Li, P and Du, L and Niu, L and Deng, J and Xu, H and Xing, J and Yue, B and Li, J}, title = {Ancient hybridization and admixture in macaques (genus Macaca) inferred from whole genome sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {127}, number = {}, pages = {376-386}, doi = {10.1016/j.ympev.2018.03.038}, pmid = {29614345}, issn = {1095-9513}, support = {R00 HG005846/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; *Gene Flow ; Genetic Variation ; *Genome ; Heterozygote ; *Hybridization, Genetic ; Macaca mulatta/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; *Whole Genome Sequencing ; }, abstract = {The evolutionary history of the stump-tailed macaque (Macaca arctoides) and its genetic relationship to other macaques is a subject of continuing controversy. Here, we have reported the first genome sequences of two stump-tailed macaques and one Assamese macaque (M. assamensis). Additionally, we have investigated the genetic diversity between macaque species and analyzed ancient hybridization events. Genome-wide analyses demonstrated that the stump-tailed macaque is more closely related to sinica species than to fascicularis/mulatta species. This topology contradicts the mitochondrial sequence-based phylogeny that places the stump-tailed macaque into the fascicularis/mulatta group. However, our results further show that stump-tailed macaques have genetic backgrounds distinct from sinica species, and present evidence of gene flows with rhesus macaques. We suggest that an ancient introgression occurred after stump-tailed macaques diverged from sinica species. The distinct gene flow between proto-arctoides and proto-mulatta resulted in the transfer of rhesus macaque-type mitochondria into proto-arctoides. The rhesus macaque-type mitochondria remained in populations because of genetic drift during the bottleneck. The PSMC results and morphological and geographic evidence are consistent with the mitochondria capture pattern in the stump-tailed macaque. The molecular clock estimates suggest that the mitochondrial transference into stump-tailed macaques occurred 0.4-1.4 million years ago. Furthermore, we detected extensive admixtures between different macaque species, indicating that gene flow has played an important role in the evolutionary history of the genus Macaca.}, }
@article {pmid29609620, year = {2018}, author = {Hornok, S and Beck, R and Farkas, R and Grima, A and Otranto, D and Kontschán, J and Takács, N and Horváth, G and Szőke, K and Szekeres, S and Majoros, G and Juhász, A and Salant, H and Hofmann-Lehmann, R and Stanko, M and Baneth, G}, title = {High mitochondrial sequence divergence in synanthropic flea species (Insecta: Siphonaptera) from Europe and the Mediterranean.}, journal = {Parasites &amp; vectors}, volume = {11}, number = {1}, pages = {221}, pmid = {29609620}, issn = {1756-3305}, support = {115854//OTKA/International ; }, mesh = {Animals ; *Base Sequence ; Ctenocephalides/classification/genetics ; Europe ; Flea Infestations/parasitology ; *Genetic Variation ; Haplotypes ; Humans ; Insect Vectors/classification/genetics ; Mediterranean Region ; Mitochondria/*genetics ; Phylogeny ; Siphonaptera/*classification/*genetics ; }, abstract = {BACKGROUND: Adult fleas are haematophagous ectoparasites of warm-blooded vertebrates, particularly mammals. Among them, the cat flea (Ctenocephalides felis) and the human flea (Pulex irritans) have high veterinary-medical significance, owing to their cosmopolitan distribution and role in the transmission of important vector-borne pathogens. While the taxonomy of Ct. felis has been investigated on a morphological basis during the past decades, its molecular-phylogenetic analyses have been only recently conducted. This study expands the knowledge on Ct. felis from hitherto less studied geographical regions, and includes representatives from additional flea families, less investigated with molecular approaches.<br><br>METHODS: Fleas were collected in four countries of the Mediterranean Basin (Croatia, Italy, Malta and Israel), as well as in Hungary, from domestic and wild carnivores, rodents and humans. The DNA extracts of representative fleas (n = 148), belonging to ten species of eight genera, were used for PCR amplification of part of their cytochrome c oxidase subunits 1, 2 (cox1, cox2) and 18S rRNA genes, followed by sequencing and phylogenetic analyses.<br><br>RESULTS: The majority (65.6%) of Ct. felis felis cox2 sequences showed 99.4-100% similarity to each other (haplogroup A), whereas those from Malta and Israel had 98.1-98.7% sequence similarity (haplogroup B), and a third sequence from Israel (haplotype C) had as low as 96.3% sequence similarity in comparison with a reference sequence from group "A". Except for the shape of the head, no consistent morphological differences (e.g. in chaetotaxy) were found between haplogroups "A" and "C". Haplotypes of Ct. canis were genetically more homogenous, with 99.6-100% sequence similarity to each other. However, when P. irritans collected from humans was compared to those from three species of wild carnivores, these only had 96.6% cox2 similarity. The mouse flea, Leptopsylla segnis and the northern rat flea, Nosopsyllus fasciatus were both shown to have haplotypes with low intraspecific cox2 similarities (96.2 and 94.4%, respectively). Taken together, differences between mitochondrial lineages within four flea species exceeded that observed between two Chaetopsylla spp. (which had 97.3% cox2 similarity). The topologies of cox1 and cox2 phylogenetic trees were in line with relevant sequence comparisons. Conversely, 18S rRNA gene analyses only resolved differences above the species level.<br><br>CONCLUSIONS: Ctenocephalides felis felis, P. irritans, L. segnis and N. fasciatus were shown to have such a high level of mitochondrial gene heterogeneity, that the uniformity of these flea taxa should be reconsidered. Although the present results are limited (especially in the case of L. segnis and N. fasciatus), there appears to be no geographical or host restriction, which could explain the divergence of these genetic lineages.}, }
@article {pmid29587633, year = {2018}, author = {Chase, EE and Robicheau, BM and Veinot, S and Breton, S and Stewart, DT}, title = {The complete mitochondrial genome of the hermaphroditic freshwater mussel Anodonta cygnea (Bivalvia: Unionidae): in silico analyses of sex-specific ORFs across order Unionoida.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {221}, pmid = {29587633}, issn = {1471-2164}, support = {217175//Natural Sciences and Engineering Research Council of Canada/International ; }, mesh = {Animals ; Computer Simulation ; DNA, Mitochondrial/genetics ; Disorders of Sex Development/*genetics ; Female ; Fresh Water ; *Genome, Mitochondrial ; Male ; Mitochondrial Proteins/genetics ; *Open Reading Frames ; Phylogeny ; Sex Factors ; Unionidae/classification/*genetics ; }, abstract = {BACKGROUND: Doubly uniparental inheritance (DUI) of mitochondrial DNA in bivalves is a fascinating exception to strictly maternal inheritance as practiced by all other animals. Recent work on DUI suggests that there may be unique regions of the mitochondrial genomes that play a role in sex determination and/or sexual development in freshwater mussels (order Unionoida). In this study, one complete mitochondrial genome of the hermaphroditic swan mussel, Anodonta cygnea, is sequenced and compared to the complete mitochondrial genome of the gonochoric duck mussel, Anodonta anatina. An in silico assessment of novel proteins found within freshwater bivalve species (known as F-, H-, and M-open reading frames or ORFs) is conducted, with special attention to putative transmembrane domains (TMs), signal peptides (SPs), signal cleavage sites (SCS), subcellular localization, and potential control regions. Characteristics of TMs are also examined across freshwater mussel lineages.<br><br>RESULTS: In silico analyses suggests the presence of SPs and SCSs and provides some insight into possible function(s) of these novel ORFs. The assessed confidence in these structures and functions was highly variable, possibly due to the novelty of these proteins. The number and topology of putative TMs appear to be maintained among both F- and H-ORFs, however, this is not the case for M-ORFs. There does not appear to be a typical control region in H-type mitochondrial DNA, especially given the loss of tandem repeats in unassigned regions when compared to F-type mtDNA.<br><br>CONCLUSION: In silico analyses provides a useful tool to discover patterns in DUI and to navigate further in situ analyses related to DUI in freshwater mussels. In situ analysis will be necessary to further explore the intracellular localizations and possible role of these open reading frames in the process of sex determination in freshwater mussel.}, }
@article {pmid29579296, year = {2018}, author = {Caspermeyer, J}, title = {Cockroach Ancient Geographic and Genomic History Traced Back to Last Supercontinent.}, journal = {Molecular biology and evolution}, volume = {35}, number = {4}, pages = {1035}, doi = {10.1093/molbev/msy039}, pmid = {29579296}, issn = {1537-1719}, mesh = {Animals ; *Cockroaches ; Genomics ; Mitochondria ; *Phylogeny ; }, }
@article {pmid29575366, year = {2018}, author = {Ivanov, V and Lee, KM and Mutanen, M}, title = {Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression.}, journal = {Molecular ecology}, volume = {27}, number = {7}, pages = {1681-1695}, doi = {10.1111/mec.14564}, pmid = {29575366}, issn = {1365-294X}, mesh = {Animals ; Cell Nucleus/*genetics ; Electron Transport Complex IV/genetics ; Genetic Loci ; *Genome, Mitochondrial ; *Genomics ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; Spiders/*genetics ; }, abstract = {Systematists and taxonomists have benefited greatly from the emergence of molecular methods. Species identification has become straightforward through DNA barcoding and the rapid build-up of massive DNA barcode reference libraries. In animals, mitonuclear discordance can significantly complicate the process of species identification and delimitation. The causes of mitonuclear discordance are either biological (e.g., introgression, incomplete lineage sorting, horizontal gene transfer androgenesis) or induced by operational factors (e.g., human error with specimen misidentification or incorrect species delimitation). Moreover, endosymbionts may play an important role in promoting fixation of mitochondrial genomes. Here, we study the mitonuclear discordance of wolf spiders species (Lycosidae) (independent cases from Alopecosa aculeata and Pardosa pullata groups) that share identical COI DNA barcodes. We approached the case utilizing double-digest restriction site-associated DNA sequencing (ddRADseq) to obtain and analyse genomic-scale data. Our results suggest that the observed cases of mitonuclear discordance are not due to operational reasons but result from biological processes. Further analysis indicated introgression and that incomplete lineage sorting is unlikely to have been responsible for the observed discrepancy. Additional survey of endosymbionts provided ideas on further research and their role in shaping mitochondrial DNA distribution patterns. Thus, ddRADseq grants an efficient way to study the taxonomy of problematic groups with insight into underlying evolutionary processes.}, }
@article {pmid29567505, year = {2018}, author = {O'Connell, KA and Smith, EN}, title = {The effect of missing data on coalescent species delimitation and a taxonomic revision of whipsnakes (Colubridae: Masticophis).}, journal = {Molecular phylogenetics and evolution}, volume = {127}, number = {}, pages = {356-366}, doi = {10.1016/j.ympev.2018.03.018}, pmid = {29567505}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Biodiversity ; Cell Nucleus/genetics ; Colubridae/*classification ; Cytochromes c/genetics ; Geography ; Mitochondria/genetics ; *Phylogeny ; Species Specificity ; }, abstract = {A stable alpha taxonomy is essential to understanding evolutionary processes and achieving effective conservation aims. Taxonomy depends on the identification of independently evolving lineages, and the delimitation of these lineages based on multiple lines of evidence. Coalescent species delimitation within an integrative framework has increased the rigor of the delimitation process. Here we use genome-wide SNP data and coalescent species delimitation to explore lineage relationships within several North American whipsnake species, test the species status of several lineages, and test the effect of missing data on species delimitation. We find support for the elevation of several previously recognized subspecies to full species status, and formally elevate two species. This study demonstrates the power of molecular data and model-based delimitation methods to identify evolutionary relationships, and finds that missing data have little impact on the outcome of delimitation analyses.}, }
@article {pmid29563878, year = {2018}, author = {Zeth, K and Zachariae, U}, title = {Ten Years of High Resolution Structural Research on the Voltage Dependent Anion Channel (VDAC)-Recent Developments and Future Directions.}, journal = {Frontiers in physiology}, volume = {9}, number = {}, pages = {108}, pmid = {29563878}, issn = {1664-042X}, abstract = {Mitochondria are evolutionarily related to Gram-negative bacteria and both comprise two membrane systems with strongly differing protein composition. The major protein in the outer membrane of mitochondria is the voltage-dependent anion channel (VDAC), which mediates signal transmission across the outer membrane but also the exchange of metabolites, most importantly ADP and ATP. More than 30 years after its discovery three identical high-resolution structures were determined in 2008. These structures show a 19-stranded anti-parallel beta-barrel with an N-terminal helix located inside. An odd number of beta-strands is also shared by Tom40, another member of the VDAC superfamily. This indicates that this superfamily is evolutionarily relatively young and that it has emerged in the context of mitochondrial evolution. New structural information obtained during the last decade on Tom40 can be used to cross-validate the structure of VDAC and vice versa. Interpretation of biochemical and biophysical studies on both protein channels now rests on a solid basis of structural data. Over the past 10 years, complementary structural and functional information on proteins of the VDAC superfamily has been collected from in-organello, in-vitro, and in silico studies. Most of these findings have confirmed the validity of the original structures. This short article briefly reviews the most important advances on the structure and function of VDAC superfamily members collected during the last decade and summarizes how they enhanced our understanding of the channel.}, }
@article {pmid29562168, year = {2018}, author = {Haroon, S and Li, A and Weinert, JL and Fritsch, C and Ericson, NG and Alexander-Floyd, J and Braeckman, BP and Haynes, CM and Bielas, JH and Gidalevitz, T and Vermulst, M}, title = {Multiple Molecular Mechanisms Rescue mtDNA Disease in C. elegans.}, journal = {Cell reports}, volume = {22}, number = {12}, pages = {3115-3125}, pmid = {29562168}, issn = {2211-1247}, support = {R01 CA204894/CA/NCI NIH HHS/United States ; T32 ES019851/ES/NIEHS NIH HHS/United States ; R01 ES026222/ES/NIEHS NIH HHS/United States ; R01 GM124532/GM/NIGMS NIH HHS/United States ; R37 AG047182/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/*metabolism ; DNA, Mitochondrial/*genetics ; Disease Progression ; Mice ; Mitochondria/*metabolism ; Models, Animal ; }, abstract = {Genetic instability of the mitochondrial genome (mtDNA) plays an important role in human aging and disease. Thus far, it has proven difficult to develop successful treatment strategies for diseases that are caused by mtDNA instability. To address this issue, we developed a model of mtDNA disease in the nematode C. elegans, an animal model that can rapidly be screened for genes and biological pathways that reduce mitochondrial pathology. These worms recapitulate all the major hallmarks of mtDNA disease in humans, including increased mtDNA instability, loss of respiration, reduced neuromuscular function, and a shortened lifespan. We found that these phenotypes could be rescued by intervening in numerous biological pathways, including IGF-1/insulin signaling, mitophagy, and the mitochondrial unfolded protein response, suggesting that it may be possible to ameliorate mtDNA disease through multiple molecular mechanisms.}, }
@article {pmid29555947, year = {2018}, author = {Islam, T and Ghosh, A}, title = {Genome-wide dissection and expression profiling of unique glyoxalase III genes in soybean reveal the differential pattern of transcriptional regulation.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {4848}, pmid = {29555947}, issn = {2045-2322}, mesh = {Aldehyde Oxidoreductases/chemistry/*genetics ; Amino Acid Sequence ; Environment ; Evolution, Molecular ; *Gene Expression Profiling ; *Genomics ; Glycine max/*genetics/growth &amp; development ; *Transcription, Genetic ; }, abstract = {Reactive carbonyl species, such as methylglyoxal and glyoxal are very toxic in nature and can inactivate various cellular macromolecules such as DNA, RNA, and protein by forming advanced glycation end products. Conventional glyoxalase pathway with two enzymes- glyoxalase I and glyoxalase II, detoxify MG into D-lactate with the help of reduced glutathione. However, DJ-1/PfpI domain(s) containing DJ-1/ Hsp31 proteins do the same in a single step, and thus termed as "glyoxalase III". A comprehensive genome-wide analysis of soybean identified eleven putative glyoxalase III proteins with DJ-1/PfpI domain encoded by seven genes. Most of these proteins are predicted to be mitochondria and chloroplast localized. In spite of similar function, a differential evolution pattern was observed between Hsp31 and DJ-1 proteins. Expression of GmDJ-1A, GmDJ-1B, and GmDJ-1D2 transcripts was found to be constitutive in different tissues and developmental stages. Transcript profiling revealed the strong substrate-specific upregulation of GmDJ-1 genes in response to exogenous methylglyoxal exposure. Out of seven genes, GmDJ-1D1 and GmDJ-1D2 showed maximum upregulation against salinity, dehydration, and oxidative stresses. Moreover, GmDJ-1D2 showed functional glyoxalase III enzyme activity by utilizing MG as a substrate. Overall, this study identifies some novel tissue-specific and abiotic stress-responsive GmDJ-1 genes that could be investigated further.}, }
@article {pmid29554738, year = {2018}, author = {Braz-Mota, S and Campos, DF and MacCormack, TJ and Duarte, RM and Val, AL and Almeida-Val, VMF}, title = {Mechanisms of toxic action of copper and copper nanoparticles in two Amazon fish species: Dwarf cichlid (Apistogramma agassizii) and cardinal tetra (Paracheirodon axelrodi).}, journal = {The Science of the total environment}, volume = {630}, number = {}, pages = {1168-1180}, doi = {10.1016/j.scitotenv.2018.02.216}, pmid = {29554738}, issn = {1879-1026}, mesh = {Animals ; Characidae/*physiology ; Cichlids/*physiology ; Copper/*toxicity ; Metal Nanoparticles/*toxicity ; Mitochondria/drug effects ; Stress, Physiological/drug effects ; Toxicity Tests ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Copper oxide nanoparticles (nCuO) are widely used in boat antifouling paints and are released into the environment, potentially inducing toxicity to aquatic organisms. The present study aimed to understand the effects of nCuO and dissolved copper (Cu) on two ornamental Amazon fish species: dwarf cichlid (Apistogramma agassizii) and cardinal tetra (Paracheirodon axelrodi). Fish were exposed to 50% of the LC50 for nCuO (dwarf cichlid 58.31μgL[-1] and cardinal tetra 69.6μgL[-1]) and Cu (dwarf cichlid 20μgL[-1] and cardinal tetra 22.9μgL[-1]) for 24, 48, 72 and 96h. Following exposure, aerobic metabolic rate (ṀO2), gill osmoregulatory physiology and mitochondrial function, oxidative stress markers, and morphological damage were evaluated. Our results revealed species specificity in metabolic stress responses. An increase of ṀO2 was noted in cardinal tetra exposed to Cu, but not nCuO, whereas ṀO2 in dwarf cichlid showed little change with either treatment. In contrast, mitochondria from dwarf cichlid exhibited increased proton leak and a resulting decrease in respiratory control ratios in response to nCuO and Cu exposure. This uncoupling was directly related to an increase in reactive oxygen species (ROS) levels. Our findings reveal different metabolic responses between these two species in response to nCuO and Cu, which are probably caused by the differences between species natural histories, indicating that different mechanisms of toxic action of the contaminants are associated to differential osmoregulatory strategies among species.}, }
@article {pmid29551757, year = {2018}, author = {McLean, BS and Nyamsuren, B and Tchabovsky, A and Cook, JA}, title = {Impacts of late Quaternary environmental change on the long-tailed ground squirrel (Urocitellus undulatus) in Mongolia.}, journal = {Zoological research}, volume = {39}, number = {5}, pages = {364-372}, pmid = {29551757}, issn = {2095-8137}, mesh = {Animals ; Climate Change ; Cytochromes b/genetics ; Electron Transport Complex IV/genetics ; Environment ; Genotyping Techniques ; Mitochondria/genetics ; Mongolia ; Phylogeny ; Phylogeography ; Sciuridae/classification/*genetics ; }, abstract = {Impacts of Quaternary environmental changes on mammal faunas of central Asia remain poorly understood due to a lack of geographically comprehensive phylogeographic sampling for most species. To help address this knowledge gap, we conducted the most extensive molecular analysis to date of the long-tailed ground squirrel (Urocitellus undulatus Pallas 1778) in Mongolia, a country that comprises the southern core of this species' range. Drawing on material from recent collaborative field expeditions, we genotyped 128 individuals at 2 mitochondrial genes (cytochrome b and cytochrome oxidase I; 1 797 bp total). Phylogenetic inference supports the existence of two deeply divergent infraspecific lineages (corresponding to subspecies U. u. undulatus and U. u. eversmanni), a result in agreement with previous molecular investigations but discordant with patterns of range-wide craniometric and external phenotypic variation. In the widespread westerneversmanni lineage, we recovered geographically-associated clades from the: (a) Khangai, (b) Mongolian Altai, and (c) Govi Altai mountain ranges. Phylogeographic structure in U. u. eversmanni is consistent with an isolation-by-distance model; however, genetic distances are significantly lower than among subspecies, and intra-clade relationships are largely unresolved. The latter patterns, as well as the relatively higher nucleotide polymorphism of populations from the Great Lakes Depression of northwestern Mongolia, suggest a history of range shifts into these lowland areas in response to Pleistocene glaciation and environmental change, followed by upslope movements and mitochondrial lineage sorting with Holocene aridification. Our study illuminates possible historical mechanisms responsible for U. undulatus genetic structure and contributes to a framework for ongoing exploration of mammalian response to past and present climate change in central Asia.}, }
@article {pmid29547666, year = {2018}, author = {Oxusoff, L and Préa, P and Perez, Y}, title = {A complete logical approach to resolve the evolution and dynamics of mitochondrial genome in bilaterians.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194334}, pmid = {29547666}, issn = {1932-6203}, mesh = {Algorithms ; *Evolution, Molecular ; *Genome, Mitochondrial ; *Genomics/methods ; Mitochondria/genetics ; Models, Genetic ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {Investigating how recombination might modify gene order during the evolution has become a routine part of mitochondrial genome analysis. A new method of genomic maps analysis based on formal logic is described. The purpose of this method is to 1) use mitochondrial gene order of current taxa as datasets 2) calculate rearrangements between all mitochondrial gene orders and 3) reconstruct phylogenetic relationships according to these calculated rearrangements within a tree under the assumption of maximum parsimony. Unlike existing methods mainly based on the probabilistic approach, the main strength of this new approach is that it calculates all the exact tree solutions with completeness and provides logical consequences as highly robust results. Moreover, this method infers all possible hypothetical ancestors and reconstructs character states for all internal nodes of the trees. We started by testing our method using the deuterostomes as a study case. Then, with sponges as an outgroup, we investigated the evolutionary history of mitochondrial genomes of 47 bilaterian phyla and emphasised the peculiar case of chaetognaths. This pilot work showed that the use of formal logic in a hypothetico-deductive background such as phylogeny (where experimental testing of hypotheses is impossible) is very promising to explore mitochondrial gene order in deuterostomes and should be applied to many other bilaterian clades.}, }
@article {pmid29543917, year = {2018}, author = {Visser, JH and Bennett, NC and Jansen van Vuuren, B}, title = {Spatial genetic diversity in the Cape mole-rat, Georychus capensis: Extreme isolation of populations in a subterranean environment.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194165}, pmid = {29543917}, issn = {1932-6203}, mesh = {Animal Distribution ; Animals ; Cytochromes b/genetics ; Ecosystem ; *Genetic Variation ; Genetics, Population ; Mitochondria/genetics ; Mole Rats/*genetics ; Phylogeny ; Phylogeography ; South Africa ; }, abstract = {The subterranean niche harbours animals with extreme adaptations. These adaptations decrease the vagility of taxa and, along with other behavioural adaptations, often result in isolated populations characterized by small effective population sizes, high inbreeding, population bottlenecks, genetic drift and consequently, high spatial genetic structure. Although information is available for some species, estimates of genetic diversity and whether this variation is spatially structured, is lacking for the Cape mole-rat (Georychus capensis). By adopting a range-wide sampling regime and employing two variable mitochondrial markers (cytochrome b and control region), we report on the effects that life-history, population demography and geographic barriers had in shaping genetic variation and population genetic patterns in G. capensis. We also compare our results to information available for the sister taxon of the study species, Bathyergus suillus. Our results show that Georychus capensis exhibits low genetic diversity relative to the concomitantly distributed B. suillus, most likely due to differences in habitat specificity, habitat fragmentation and historical population declines. In addition, the isolated nature of G. capensis populations and low levels of population connectivity has led to small effective population sizes and genetic differentiation, possibly aided by genetic drift. Not surprisingly therefore, G. capensis exhibits pronounced spatial structure across its range in South Africa. Along with geographic distance and demography, other factors shaping the genetic structure of G. capensis include the historical and contemporary impacts of mountains, rivers, sea-level fluctuations and elevation. Given the isolation and differentiation among G. capensis populations, the monotypic genus Georychus may represent a species complex.}, }
@article {pmid29543844, year = {2018}, author = {Bekker, EI and Karabanov, DP and Galimov, YR and Haag, CR and Neretina, TV and Kotov, AA}, title = {Phylogeography of Daphnia magna Straus (Crustacea: Cladocera) in Northern Eurasia: Evidence for a deep longitudinal split between mitochondrial lineages.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194045}, pmid = {29543844}, issn = {1932-6203}, mesh = {Animals ; Cell Lineage/*genetics ; Cladocera/*genetics ; DNA, Mitochondrial/genetics ; Daphnia/*genetics ; Europe ; Asia, Eastern ; Haplotypes/genetics ; Lakes ; Mitochondria/*genetics ; North America ; Phylogeny ; Phylogeography/methods ; Siberia ; }, abstract = {Species with a large geographic distributions present a challenge for phylogeographic studies due to logistic difficulties of obtaining adequate sampling. For instance, in most species with a Holarctic distribution, the majority of studies has concentrated on the European or North American part of the distribution, with the Eastern Palearctic region being notably understudied. Here, we study the phylogeography of the freshwater cladoceran Daphnia magna Straus, 1820 (Crustacea: Cladocera), based on partial mitochondrial COI sequences and using specimens from populations spread longitudinally from westernmost Europe to easternmost Asia, with many samples from previously strongly understudied regions in Siberia and Eastern Asia. The results confirm the previously suspected deep split between Eastern and Western mitochondrial haplotype super-clades. We find a narrow contact zone between these two super-clades in the eastern part of Western Siberia, with proven co-occurrence in a single lake in the Novosibirsk region. However, at present there is no evidence suggesting that the two mitochondrial super-clades represent cryptic species. Rather, they may be explained by secondary contact after expansion from different refugia. Interestingly, Central Siberia has previously been found to be an important contact zone also in other cladoceran species, and may thus be a crucial area for understanding the Eurasian phylogeography of freshwater invertebrates. Together, our study provides an unprecedented complete, while still not global, picture of the phylogeography of this important model species.}, }
@article {pmid29543809, year = {2018}, author = {Abdollahi, N and Albani, A and Anthony, E and Baud, A and Cardon, M and Clerc, R and Czernecki, D and Conte, R and David, L and Delaune, A and Djerroud, S and Fourgoux, P and Guiglielmoni, N and Laurentie, J and Lehmann, N and Lochard, C and Montagne, R and Myrodia, V and Opuu, V and Parey, E and Polit, L and Privé, S and Quignot, C and Ruiz-Cuevas, M and Sissoko, M and Sompairac, N and Vallerix, A and Verrecchia, V and Delarue, M and Guérois, R and Ponty, Y and Sacquin-Mora, S and Carbone, A and Froidevaux, C and Le Crom, S and Lespinet, O and Weigt, M and Abboud, S and Bernardes, J and Bouvier, G and Dequeker, C and Ferré, A and Fuchs, P and Lelandais, G and Poulain, P and Richard, H and Schweke, H and Laine, E and Lopes, A}, title = {Meet-U: Educating through research immersion.}, journal = {PLoS computational biology}, volume = {14}, number = {3}, pages = {e1005992}, pmid = {29543809}, issn = {1553-7358}, mesh = {Computational Biology/*education/*methods ; Humans ; Research/*education ; Research Design ; Students ; Universities ; }, abstract = {We present a new educational initiative called Meet-U that aims to train students for collaborative work in computational biology and to bridge the gap between education and research. Meet-U mimics the setup of collaborative research projects and takes advantage of the most popular tools for collaborative work and of cloud computing. Students are grouped in teams of 4-5 people and have to realize a project from A to Z that answers a challenging question in biology. Meet-U promotes "coopetition," as the students collaborate within and across the teams and are also in competition with each other to develop the best final product. Meet-U fosters interactions between different actors of education and research through the organization of a meeting day, open to everyone, where the students present their work to a jury of researchers and jury members give research seminars. This very unique combination of education and research is strongly motivating for the students and provides a formidable opportunity for a scientific community to unite and increase its visibility. We report on our experience with Meet-U in two French universities with master's students in bioinformatics and modeling, with protein-protein docking as the subject of the course. Meet-U is easy to implement and can be straightforwardly transferred to other fields and/or universities. All the information and data are available at www.meet-u.org.}, }
@article {pmid29540429, year = {2018}, author = {Czarnoleski, M and Labecka, AM and Dragosz-Kluska, D and Pis, T and Pawlik, K and Kapustka, F and Kilarski, WM and Kozłowski, J}, title = {Concerted evolution of body mass and cell size: similar patterns among species of birds (Galliformes) and mammals (Rodentia).}, journal = {Biology open}, volume = {7}, number = {4}, pages = {}, pmid = {29540429}, issn = {2046-6390}, abstract = {Cell size plays a role in body size evolution and environmental adaptations. Addressing these roles, we studied body mass and cell size in Galliformes birds and Rodentia mammals, and collected published data on their genome sizes. In birds, we measured erythrocyte nuclei and basal metabolic rates (BMRs). In birds and mammals, larger species consistently evolved larger cells for five cell types (erythrocytes, enterocytes, chondrocytes, skin epithelial cells, and kidney proximal tubule cells) and evolved smaller hepatocytes. We found no evidence that cell size differences originated through genome size changes. We conclude that the organism-wide coordination of cell size changes might be an evolutionarily conservative characteristic, and the convergent evolutionary body size and cell size changes in Galliformes and Rodentia suggest the adaptive significance of cell size. Recent theory predicts that species evolving larger cells waste less energy on tissue maintenance but have reduced capacities to deliver oxygen to mitochondria and metabolize resources. Indeed, birds with larger size of the abovementioned cell types and smaller hepatocytes have evolved lower mass-specific BMRs. We propose that the inconsistent pattern in hepatocytes derives from the efficient delivery system to hepatocytes, combined with their intense involvement in supracellular function and anabolic activity.}, }
@article {pmid29538419, year = {2018}, author = {Bocak, L and Motyka, M and Bocek, M and Bocakova, M}, title = {Incomplete sclerotization and phylogeny: The phylogenetic classification of Plastocerus (Coleoptera: Elateroidea).}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0194026}, pmid = {29538419}, issn = {1932-6203}, mesh = {Animals ; Coleoptera/*genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Female ; Luminescence ; Male ; Mitochondria/genetics ; Phylogeny ; }, abstract = {The relationships of the monogeneric family Plastoceridae Crowson, 1972 (Coleoptera: Elateroidea) have remained contentious due to its modified morphology, incorrect information on incomplete metamorphosis of females and the absence of molecular data. We produced the sequences for P. angulosus (Germar, 1844) (the type-species of Plastocerus Schaum, 1852) and performed molecular phylogenetic analyses to estimate its position. The analyses of Elateroidea (186 spp.) and Elateridae (110 spp.) molecular datasets of two mitochondrial and two nuclear gene fragments repeatedly placed Plastocerus Schaum, 1852 in relationships with the elaterid genera Oxynopterus Hope, 1842 and Pectocera Hope, 1842. Alternative topologies were rejected by likelihood tests. Therefore, Plastoceridae Crowson, 1972 are down-ranked to the subfamily Plastocerinae in Elateridae Leach, 1815. We suggest that the morphology-based placement and high rank for some elateroid lineages were inferred from the presence of homoplasies which evolved due to incomplete sclerotization. Distantly related soft-bodied elateroids share freely movable and transverse coxae, a shortened prosternum, and a weakly sclerotized abdomen with free ventrites. Importantly, the apomorphic structures characteristic for their closest relatives, such as the prosternal process, mesoventral cavity, and intercoxal keel in the first abdominal ventrite are regularly absent. Consequently, morphology-based phylogenetic analyses suggest deeply rooted positions for lineages without expressed apomorphic character states. Molecular data represent an independent character system that is not affected by the convergent morphological evolution, and therefore molecular phylogenies can elucidate the relationships of incompletely sclerotized lineages.}, }
@article {pmid29533769, year = {2018}, author = {Marsit, S and Dion-Côté, AM and Barbash, DA}, title = {Did Mitochondria Kill the Frog?.}, journal = {Developmental cell}, volume = {44}, number = {5}, pages = {539-541}, doi = {10.1016/j.devcel.2018.02.020}, pmid = {29533769}, issn = {1878-1551}, mesh = {*Genome ; Genomics ; Hybridization, Genetic ; Mitochondria ; *Reproductive Isolation ; }, abstract = {Genomic divergence can cause reproductive isolation between species. The molecular mechanisms underlying reproductive isolation can thus reveal which genomic features evolve rapidly and become unstable or incompatible in hybrids. In a recent paper in Nature, Gibeaux et al. (2018) report paternal genome instability and metabolic imbalance in hybrids between frog species.}, }
@article {pmid29531011, year = {2018}, author = {Wolters, JF and Charron, G and Gaspary, A and Landry, CR and Fiumera, AC and Fiumera, HL}, title = {Mitochondrial Recombination Reveals Mito-Mito Epistasis in Yeast.}, journal = {Genetics}, volume = {209}, number = {1}, pages = {307-319}, pmid = {29531011}, issn = {1943-2631}, support = {R01 GM101320/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Mitochondrial ; *Epistasis, Genetic ; Genotype ; Haplotypes ; Mitochondria/*genetics ; Quantitative Trait Loci ; *Recombination, Genetic ; Stress, Physiological ; Yeasts/*genetics ; }, abstract = {Genetic variation in mitochondrial DNA (mtDNA) provides adaptive potential although the underlying genetic architecture of fitness components within mtDNAs is not known. To dissect functional variation within mtDNAs, we first identified naturally occurring mtDNAs that conferred high or low fitness in Saccharomyces cerevisiae by comparing growth in strains containing identical nuclear genotypes but different mtDNAs. During respiratory growth under temperature and oxidative stress conditions, mitotype effects were largely independent of nuclear genotypes even in the presence of mito-nuclear interactions. Recombinant mtDNAs were generated to determine fitness components within high- and low-fitness mtDNAs. Based on phenotypic distributions of isogenic strains containing recombinant mtDNAs, we found that multiple loci contributed to mitotype fitness differences. These mitochondrial loci interacted in epistatic, nonadditive ways in certain environmental conditions. Mito-mito epistasis (i.e., nonadditive interactions between mitochondrial loci) influenced fitness in progeny from four different crosses, suggesting that mito-mito epistasis is a widespread phenomenon in yeast and other systems with recombining mtDNAs. Furthermore, we found that interruption of coadapted mito-mito interactions produced recombinant mtDNAs with lower fitness. Our results demonstrate that mito-mito epistasis results in functional variation through mitochondrial recombination in fungi, providing modes for adaptive evolution and the generation of mito-mito incompatibilities.}, }
@article {pmid29530548, year = {2018}, author = {Zhang, P and Liu, Y and Wang, M and Dong, M and Liu, Z and Jia, Z and Wang, W and Zhang, A and Wang, L and Song, L}, title = {Chinese mitten crab (Eriocheir sinensis) iron-sulphur cluster assembly protein 2 (EsIscA2) is differentially regulated after immune and oxidative stress challenges.}, journal = {Developmental and comparative immunology}, volume = {84}, number = {}, pages = {343-352}, doi = {10.1016/j.dci.2018.03.007}, pmid = {29530548}, issn = {1879-0089}, mesh = {Aeromonas hydrophila/*immunology ; Animals ; Arthropod Proteins/genetics/*metabolism ; Brachyura/*physiology ; Cells, Cultured ; Cloning, Molecular ; Gene Expression Regulation ; Gram-Negative Bacterial Infections/*immunology ; Hemocytes/*physiology ; Immunity, Innate/genetics ; Invertebrates ; Iron/metabolism ; Iron-Sulfur Proteins/genetics/*metabolism ; Lipopolysaccharides/immunology ; Mitochondria/*physiology ; Oxidative Stress/genetics ; Protein Binding ; Sequence Alignment ; }, abstract = {Iron-sulphur clusters (ISCs), one of the oldest and most versatile cofactors of proteins, are involved in catalysis reactions, electron transport reactions, regulation processes as well as sensing of ambient conditions. Iron-sulphur cluster assembly protein (IscA) is a scaffold protein member of ISC formation system, which plays a significant role in the assembly and maturation process of ISC proteins. In the present study, the cDNA sequence of iron-sulphur cluster assembly protein 2 (designated as EsIscA2) was cloned from Eriocheir sinensis. The open reading frame (ORF) of EsIscA2 was of 507 bp, encoding a peptide of 168 amino acids with a typically conserved Fe-S domain. A tetrameric form was predicated by the SWISS-MODEL prediction algorithm, and three conserved cysteine residues (Cys-93, Cys-158, Cys-160) from each IscA monomer were predicted to form a 'cysteine pocket'. The deduced amino acid sequence of EsIscA2 shared over 50% similarity with that of other IscAs. EsIscA2 was clustered with IscA2 proteins from invertebrates and vertebrates, indicating that the protein was highly conservative in the evolution. rEsIscA2 exhibited a high iron binding affinity in the concentration ranging from 2 to 200 μM. EsIscA2 transcripts were detected in all the tested tissues including gonad, hemocytes, gill, muscle, heart, hepatopancreas and eyestalk, and EsIscA2 protein was detected in the mitochondria of hemocytes. The highest mRNA expression level of EsIscA2 was detected in muscle and hepatopancreas, which was about 34.66-fold (p < 0.05) and 27.07-fold (p < 0.05) of that in hemocytes, respectively. After Aeromonas hydrophila and lipopolysaccharide (LPS) stimulations, the mRNA expression of EsIscA2 in hemocytes was down-regulated and reached the lowest level at 24 h (0.31-fold, p < 0.05) and 48 h (0.29-fold, p < 0.05) compared to control group, respectively. And the expression of EsIscA2 mRNA in hepatopancreas was repressed from 6 h to 48 h post stimulation (p < 0.05). When the primary cultured crab hemocytes were incubated with different concentrations of H2O2 for 15 min, the expression level of EsIscA2 mRNA was significantly repressed to the 0.34-0.44-fold of that in the control group. After A. hydrophila stimulation, the mRNA expression of EsGrx2 was up-regulated at 3 h (3.22-fold compared to control group, p < 0.05) and reached the peak at 12 h (4.88-fold, p < 0.05). All these results suggested that EsIscA2 had iron-binding capabilities as observed in IscA proteins from other organisms, supporting the role of EsIscA2 as a mitochondrial iron donor for ISC synthesis in Chinese mitten crab. Its differential mRNA expression after immune and oxidative stress challenges suggested the adaptations of ISC synthesis rates to these stress conditions.}, }
@article {pmid29529094, year = {2018}, author = {Bourret, TB and Choudhury, RA and Mehl, HK and Blomquist, CL and McRoberts, N and Rizzo, DM}, title = {Multiple origins of downy mildews and mito-nuclear discordance within the paraphyletic genus Phytophthora.}, journal = {PloS one}, volume = {13}, number = {3}, pages = {e0192502}, pmid = {29529094}, issn = {1932-6203}, mesh = {Cell Nucleus/genetics ; Likelihood Functions ; Mitochondria/genetics ; Peronospora/*genetics ; *Phylogeny ; Phytophthora/*genetics ; Plant Diseases/parasitology ; }, abstract = {Phylogenetic relationships between thirteen species of downy mildew and 103 species of Phytophthora (plant-pathogenic oomycetes) were investigated with two nuclear and four mitochondrial loci, using several likelihood-based approaches. Three Phytophthora taxa and all downy mildew taxa were excluded from the previously recognized subgeneric clades of Phytophthora, though all were strongly supported within the paraphyletic genus. Downy mildews appear to be polyphyletic, with graminicolous downy mildews (GDM), brassicolous downy mildews (BDM) and downy mildews with colored conidia (DMCC) forming a clade with the previously unplaced Phytophthora taxon totara; downy mildews with pyriform haustoria (DMPH) were placed in their own clade with affinities to the obligate biotrophic P. cyperi. Results suggest the recognition of four additional clades within Phytophthora, but few relationships between clades could be resolved. Trees containing all twenty extant downy mildew genera were produced by adding partial coverage of seventeen additional downy mildew taxa; these trees supported the monophyly of the BDMs, DMCCs and DMPHs but suggested that the GDMs are paraphyletic in respect to the BDMs or polyphyletic. Incongruence between nuclear-only and mitochondrial-only trees suggests introgression may have occurred between several clades, particularly those containing biotrophs, questioning whether obligate biotrophic parasitism and other traits with polyphyletic distributions arose independently or were horizontally transferred. Phylogenetic approaches may be limited in their ability to resolve some of the complex relationships between the "subgeneric" clades of Phytophthora, which include twenty downy mildew genera and hundreds of species.}, }
@article {pmid29529025, year = {2018}, author = {Tas, D and Stickley, L and Miozzo, F and Koch, R and Loncle, N and Sabado, V and Gnägi, B and Nagoshi, E}, title = {Parallel roles of transcription factors dFOXO and FER2 in the development and maintenance of dopaminergic neurons.}, journal = {PLoS genetics}, volume = {14}, number = {3}, pages = {e1007271}, pmid = {29529025}, issn = {1553-7404}, mesh = {Animals ; Autophagy ; Basic Helix-Loop-Helix Transcription Factors/genetics/*metabolism ; Cell Survival ; Dopaminergic Neurons/*metabolism/*pathology ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster ; Forkhead Transcription Factors/genetics/*metabolism ; Mitochondria/metabolism ; Mutation ; *Neuroprotection ; Parkinson Disease/metabolism/*pathology ; }, abstract = {Forkhead box (FOXO) proteins are evolutionarily conserved, stress-responsive transcription factors (TFs) that can promote or counteract cell death. Mutations in FOXO genes are implicated in numerous pathologies, including age-dependent neurodegenerative disorders, such as Parkinson's disease (PD). However, the complex regulation and downstream mechanisms of FOXOs present a challenge in understanding their roles in the pathogenesis of PD. Here, we investigate the involvement of FOXO in the death of dopaminergic (DA) neurons, the key pathological feature of PD, in Drosophila. We show that dFOXO null mutants exhibit a selective loss of DA neurons in the subgroup crucial for locomotion, the protocerebral anterior medial (PAM) cluster, during development as well as in adulthood. PAM neuron-targeted adult-restricted knockdown demonstrates that dFOXO in adult PAM neurons tissue-autonomously promotes neuronal survival during aging. We further show that dFOXO and the bHLH-TF 48-related-2 (FER2) act in parallel to protect PAM neurons from different forms of cellular stress. Remarkably, however, dFOXO and FER2 share common downstream processes leading to the regulation of autophagy and mitochondrial morphology. Thus, overexpression of one can rescue the loss of function of the other. These results indicate a role of dFOXO in neuroprotection and highlight the notion that multiple genetic and environmental factors interact to increase the risk of DA neuron degeneration and the development of PD.}, }
@article {pmid29524652, year = {2018}, author = {Berriman, JS and Ellingson, RA and Awbrey, JD and Rico, DM and Valdés, &#xc1;A and Wilson, NG and Aguilar, A and Herbert, DG and Hirano, YM and Trowbridge, CD and Krug, PJ}, title = {A biting commentary: Integrating tooth characters with molecular data doubles known species diversity in a lineage of sea slugs that consume "killer algae".}, journal = {Molecular phylogenetics and evolution}, volume = {126}, number = {}, pages = {356-370}, pmid = {29524652}, issn = {1095-9513}, support = {R25 GM061331/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; Biodiversity ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Eukaryota/*physiology ; Gastropoda/*physiology ; Genetic Variation ; Haplotypes/genetics ; Mitochondria/genetics ; *Phylogeny ; Species Specificity ; Tooth/*physiology ; }, abstract = {Predicting biotic resistance to highly invasive strains of "killer algae" (Caulerpa spp.) requires understanding the diversity and feeding preferences of native consumers, including sea slugs in family Oxynoidae. Past studies reported low algal host specificity for Oxynoe (6 spp.) and Lobiger (4 spp.), but these taxonomically challenging slugs may represent species complexes of unrecognized specialists that prefer different Caulerpa spp. Here, we assess global diversity of these genera by integrating gene sequences with morphological data from microscopic teeth and internal shells, the only hard parts in these soft-bodied invertebrates. Four delimitation methods applied to datasets comprising mtDNA and/or nuclear alleles yielded up to 16 species hypotheses for samples comprising five nominal taxa, including five highly divergent species in Lobiger and five in Oxynoe. Depending on the analysis, a further four to six species were recovered in the O. antillarum-viridis complex, a clade in which mitochondrial divergence was low and nuclear alleles were shared among lineages. Bayesian species delimitation using only morphological data supported most candidate species, however, and integrative analyses combining morphological and genetic data fully supported all complex members. Collectively, our findings double the recognized biodiversity in Oxynoidae, and illustrate the value of including data from traits that mediate fast-evolving ecological interactions during species delimitation. Preference for Caulerpa spp. and radular tooth characteristics covaried among newly delimited species, highlighting an unappreciated degree of host specialization and coevolution in these taxa that may help predict their role in containing outbreaks of invasive algae.}, }
@article {pmid29523798, year = {2018}, author = {Fu, YB}, title = {Oat evolution revealed in the maternal lineages of 25 Avena species.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {4252}, pmid = {29523798}, issn = {2045-2322}, mesh = {Avena/*genetics ; *Evolution, Molecular ; Genetic Speciation ; Genome, Chloroplast ; Genome, Mitochondrial ; Ploidies ; Polymorphism, Single Nucleotide ; }, abstract = {Cultivated hexaploid oat has three different sets of nuclear genomes (A, C, D), but its evolutionary history remains elusive. A multiplexed shotgun sequencing procedure was explored to acquire maternal phylogenetic signals from chloroplast and mitochondria genomes of 25 Avena species. Phylogenetic analyses of the acquired organelle SNP data revealed a new maternal pathway towards hexaploids of oat genome evolution involving three diploid species (A. ventricosa, A. canariensis and A. longiglumis) and two tetraploid species (A. insularis and A. agadiriana). Cultivated hexaploid A. sativa acquired its maternal genome from an AC genome tetraploid close to A. insularis. Both AC genome A. insularis and AB genome A. agadiriana obtained a maternal genome from an ancient A, not C, genome diploid close to A. longiglumis. Divergence dating showed the major divergences of C genome species 19.9-21.2 million years ago (Mya), of the oldest A genome A. canariensis 13-15 Mya, and of the clade with hexaploids 8.5-9.5 Mya. These findings not only advance our knowledge on oat genome evolution, but also have implications for oat germplasm conservation and utilization in breeding.}, }
@article {pmid29521101, year = {2018}, author = {Wyżewski, Z and Gregorczyk, KP and Szczepanowska, J and Szulc-Dąbrowska, L}, title = {Functional role of Hsp60 as a positive regulator of human viral infection progression.}, journal = {Acta virologica}, volume = {62}, number = {1}, pages = {33-40}, doi = {10.4149/av_2018_104}, pmid = {29521101}, issn = {0001-723X}, mesh = {Chaperonin 60/genetics/*metabolism ; HIV Infections/*metabolism ; Hepatitis B/*metabolism ; Humans ; Influenza, Human/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; }, abstract = {Heat shock proteins (Hsps) are a family of proteins highly conserved in evolution. Members of the Hsp family are mainly responsible for proper protein folding, however they perform many other functions in living organisms. Hsp60 is a molecular chaperone that is present in mitochondria and cytosol of eukaryotic cells, as well as on their surface. It is also found in the extracellular space and in the peripheral blood. Apart from its role in assisting protein folding in cooperation with Hsp10, Hsp60 contributes to regulation of apoptosis, as well as participates in modulation of the immune system activity. Hsp60 may favor oncogenesis by promoting survival or growth of some tumor cell types. Hsp60 is a subject of medical research due to its role in pathogenesis of certain tumors and infectious diseases. In this review we discuss mechanisms by which Hsp60 promotes development and progression of infections caused by three human viruses: hepatitis B virus (HBV), human immunodeficiency virus (HIV) and influenza A virus.}, }
@article {pmid29515095, year = {2018}, author = {Suwannapoom, C and Wu, YJ and Chen, X and Adeola, AC and Chen, J and Wang, WZ}, title = {Complete mitochondrial genome of the Thai Red Junglefowl (Gallus gallus) and phylogenetic analysis.}, journal = {Zoological research}, volume = {39}, number = {2}, pages = {127-129}, pmid = {29515095}, issn = {2095-8137}, mesh = {Animals ; Chickens/*genetics ; DNA, Mitochondrial/genetics ; Genome/genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Thailand ; }, abstract = {In this study, we sequenced the complete mitochondrial genome (mitogenome) of the Thai Red Junglefowl (RJF; Gallus gallus) using the next-generation sequencing (NGS) platform of the Ion Torrent PGM. Samples were taken from Mae Wang District, Chiang Mai Province, northern Thailand. Our data showed the complete mitogenome to be 16 785 bp in length, composed by 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. The genome nucleotide composition was 30.3% A, 23.7% T, 32.5% C, and 13.5% G, resulting in a high percentage of A+T (50.4%). Phylogenetic analysis revealed that the mitogenome belonged to haplogroup X, whereas those of all domestic chickens belong to haplogroups A to G. This newly released mitogenome sequence will advance further evolutionary and population genetics study of the RJF and domestic chicken. The availability of the G. gallus mitogenome will also contribute to further conservation genetics research of a unique species, listed as 'data deficient' in Thailand.}, }
@article {pmid29514071, year = {2018}, author = {Zeng, R and Smith, E and Barrientos, A}, title = {Yeast Mitoribosome Large Subunit Assembly Proceeds by Hierarchical Incorporation of Protein Clusters and Modules on the Inner Membrane.}, journal = {Cell metabolism}, volume = {27}, number = {3}, pages = {645-656.e7}, pmid = {29514071}, issn = {1932-7420}, support = {R01 GM112179/GM/NIGMS NIH HHS/United States ; R35 GM118141/GM/NIGMS NIH HHS/United States ; }, mesh = {Membrane Proteins/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/*metabolism ; Mitochondrial Ribosomes/*metabolism ; Protein Biosynthesis ; Ribosomal Proteins/*metabolism ; Saccharomyces cerevisiae/*metabolism ; }, abstract = {Mitoribosomes are specialized for the synthesis of hydrophobic membrane proteins encoded by mtDNA, all essential for oxidative phosphorylation. Despite their linkage to human mitochondrial diseases and the recent cryoelectron microscopy reconstruction of yeast and mammalian mitoribosomes, how they are assembled remains obscure. Here, we dissected the yeast mitoribosome large subunit (mtLSU) assembly process by systematic genomic deletion of 44 mtLSU proteins (MRPs). Analysis of the strain collection unveiled 37 proteins essential for functional mtLSU assembly, three of which are critical for mtLSU 21S rRNA stability. Hierarchical cluster analysis of mtLSU subassemblies accumulated in mutant strains revealed co-operative assembly of protein sets forming structural clusters and preassembled modules. It also indicated crucial roles for mitochondrion-specific membrane-binding MRPs in anchoring newly transcribed 21S rRNA to the inner membrane, where assembly proceeds. Our results define the yeast mtLSU assembly landscape in vivo and provide a foundation for studies of mitoribosome assembly across evolution.}, }
@article {pmid29511984, year = {2018}, author = {Zhao, YQ and Mu, DL and Wang, D and Han, YL and Hou, CC and Zhu, JQ}, title = {Analysis of the function of KIF3A and KIF3B in the spermatogenesis in Boleophthalmus pectinirostris.}, journal = {Fish physiology and biochemistry}, volume = {44}, number = {3}, pages = {769-788}, pmid = {29511984}, issn = {1573-5168}, support = {No. 31272642//National Natural Science Foundation of China (CN)/ ; No. 2015C110005//Scientific and Technical Project of Ningbo/ ; No.2016A610081//Ningbo Natural Science Foundation/ ; }, mesh = {Animals ; *Fish Proteins/chemistry/genetics/metabolism ; Gills/metabolism ; Kidney/metabolism ; *Kinesins/chemistry/genetics/metabolism ; Liver/metabolism ; Male ; Microscopy, Electron, Transmission ; Muscles/metabolism ; Myocardium/metabolism ; *Perciformes ; Phylogeny ; RNA, Messenger/metabolism ; Sequence Analysis, DNA ; Spermatogenesis/genetics/*physiology ; Spermatozoa/metabolism/ultrastructure ; Spleen/metabolism ; Testis/metabolism ; }, abstract = {Spermatogenesis represents one of the most complicated morphological transformation procedures. During this process, the assembly and maintenance of the flagella and intracellular transport of membrane-bound organelles required KIF3A and KIF3B. Our main goal was to test KIF3A and KIF3B location during spermatogenesis of Boleophthalmus pectinirostris. We cloned complete cDNA of KIF3A/3B from the testis of B. pectinirostris by PCR and rapid amplification of cDNA ends (RACE). The predicted secondary and tertiary structures of B. pectinirostris KIF3A/3B contained three domains: (a) the head region, (b) the stalk region, and (c) the tail region. Real-time quantitative PCR (qPCR) results revealed that KIF3A and KIF3B mRNA were presented in all the tissues examined, with the highest expression seen in the testis. In situ hybridization (ISH) showed that KIF3A and KIF3B were distributed in the periphery of the nuclear in the spermatocyte and the early spermatid. In the late spermatid and mature sperm, the KIF3A and KIF3B mRNA were gradually gathered to one side where the flagella formed. Immunofluorescence (IF) showed that KIF3A, tubulin, and mitochondria were co-localized in different stages during spermiogenesis in B. pectinirostris. The temporal and spatial expression dynamics of KIF3A/3B indicate that KIF3A and KIF3B might be involved in flagellar assembly and maintenance at the mRNA and protein levels. Moreover, these proteins may transport the mitochondria resulting in flagellum formation in B. pectinirostris.}, }
@article {pmid29509408, year = {2018}, author = {Wisnovsky, S and Sack, T and Pagliarini, DJ and Laposa, RR and Kelley, SO}, title = {DNA Polymerase θ Increases Mutational Rates in Mitochondrial DNA.}, journal = {ACS chemical biology}, volume = {13}, number = {4}, pages = {900-908}, pmid = {29509408}, issn = {1554-8937}, support = {R01 GM115591/GM/NIGMS NIH HHS/United States ; R01 GM116886/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Line, Tumor ; DNA Replication ; DNA, Mitochondrial/*genetics ; DNA-Directed DNA Polymerase/*physiology ; Humans ; *Mutation Rate ; Neoplasms/genetics ; Oxidative Stress ; DNA Polymerase theta ; }, abstract = {Replication and maintenance of mitochondrial DNA (mtDNA) is essential for cellular function, yet few DNA polymerases are known to function in mitochondria. Here, we conclusively demonstrate that DNA polymerase θ (Polθ) localizes to mitochondria and explore whether this protein is overexpressed in patient-derived cells and tumors. Polθ appears to play an important role in facilitating mtDNA replication under conditions of oxidative stress, and this error-prone polymerase was found to introduce mutations into mtDNA. In patient-derived cells bearing a pathogenic mtDNA mutation, Polθ expression levels were increased, indicating that the oxidative conditions in these cells promote higher expression levels for Polθ. Heightened Polθ expression levels were also associated with elevated mtDNA mutation rates in a selected panel of human tumor tissues, suggesting that this protein can influence mutational frequencies in tumors. The results reported indicate that the mitochondrial function of Polθ may have relevance to human disease.}, }
@article {pmid29495437, year = {2018}, author = {Mansilla, N and Racca, S and Gras, DE and Gonzalez, DH and Welchen, E}, title = {The Complexity of Mitochondrial Complex IV: An Update of Cytochrome c Oxidase Biogenesis in Plants.}, journal = {International journal of molecular sciences}, volume = {19}, number = {3}, pages = {}, pmid = {29495437}, issn = {1422-0067}, mesh = {Animals ; Catalytic Domain ; Electron Transport Complex IV/chemistry/genetics/*metabolism ; *Energy Metabolism ; Enzyme Activation ; Gene Expression Regulation, Plant ; Humans ; Mammals/genetics/metabolism ; Mitochondria/genetics/*metabolism ; Mutation ; Plant Development ; Plant Physiological Phenomena ; Plants/genetics/*metabolism ; Protein Subunits ; Yeasts/genetics/metabolism ; }, abstract = {Mitochondrial respiration is an energy producing process that involves the coordinated action of several protein complexes embedded in the inner membrane to finally produce ATP. Complex IV or Cytochrome c Oxidase (COX) is the last electron acceptor of the respiratory chain, involved in the reduction of O2 to H2O. COX is a multimeric complex formed by multiple structural subunits encoded in two different genomes, prosthetic groups (heme a and heme a3), and metallic centers (CuA and CuB). Tens of accessory proteins are required for mitochondrial RNA processing, synthesis and delivery of prosthetic groups and metallic centers, and for the final assembly of subunits to build a functional complex. In this review, we perform a comparative analysis of COX composition and biogenesis factors in yeast, mammals and plants. We also describe possible external and internal factors controlling the expression of structural proteins and assembly factors at the transcriptional and post-translational levels, and the effect of deficiencies in different steps of COX biogenesis to infer the role of COX in different aspects of plant development. We conclude that COX assembly in plants has conserved and specific features, probably due to the incorporation of a different set of subunits during evolution.}, }
@article {pmid29487229, year = {2018}, author = {Weiss, AKH and Loeffler, JR and Liedl, KR and Gstach, H and Jansen-Dürr, P}, title = {The fumarylacetoacetate hydrolase (FAH) superfamily of enzymes: multifunctional enzymes from microbes to mitochondria.}, journal = {Biochemical Society transactions}, volume = {46}, number = {2}, pages = {295-309}, doi = {10.1042/BST20170518}, pmid = {29487229}, issn = {1470-8752}, mesh = {Amino Acid Sequence ; Carboxy-Lyases/metabolism ; Humans ; Hydrolases/chemistry/*metabolism ; *Microbiota ; Mitochondria/*enzymology ; Sequence Homology, Amino Acid ; Tyrosine/metabolism ; }, abstract = {Prokaryotic and eukaryotic fumarylacetoacetate hydrolase (FAH) superfamily members, sharing conserved regions that form the so-called FAH-domain, catalyze a remarkable variety of reactions. These enzymes are essential in the metabolic pathways to degrade aromatic compounds in prokaryotes and eukaryotes. It appears that prokaryotic FAH superfamily members evolved mainly to allow microbes to generate energy and useful metabolites from complex carbon sources. We review recent findings, indicating that both prokaryotic and eukaryotic members of the FAH superfamily also display oxaloacetate decarboxylase (ODx) activity. The identification of human FAH domain-containing protein 1 as mitochondrial ODx regulating mitochondrial function supports the new concept that, during evolution, eukaryotic FAH superfamily members have acquired important regulatory functions beyond catabolism of complex carbon sources. Molecular studies on the evolution and function of FAH superfamily members are expected to provide new mechanistic insights in their physiological roles.}, }
@article {pmid29486692, year = {2017}, author = {Skulachev, MV and Skulachev, VP}, title = {Programmed Aging of Mammals: Proof of Concept and Prospects of Biochemical Approaches for Anti-aging Therapy.}, journal = {Biochemistry. Biokhimiia}, volume = {82}, number = {12}, pages = {1403-1422}, doi = {10.1134/S000629791712001X}, pmid = {29486692}, issn = {1608-3040}, mesh = {Aging/drug effects/*physiology ; Animals ; Antioxidants/pharmacology ; Humans ; Longevity/drug effects ; Mitochondria/metabolism ; Mole Rats ; Plastoquinone/analogs &amp; derivatives/pharmacology ; Reactive Oxygen Species/metabolism ; }, abstract = {(i) In 2015-2017 we compared possible reasons for longevity of two mammalian highly social species, i.e. naked mole rats and humans. We proposed that in both cases longevity is a result of neoteny, prolongation of youth by deceleration of late ontogeny (Skulachev, V. P. (2015) Abst. 11th Conf. on Mitochondrial Physiology (MiP2015), Lucni Bouda, Czech Republic, pp. 64-66; Skulachev, V. P., Holtze, S., Vyssokikh, M. Y., Bakeeva, L. E., Skulachev, M. V., Markov, A. V., Hildebrandt, T. B., and Sadovnichii, V. A. (2017) Physiol. Rev., 97, 699-720). Both naked mole rats and humans strongly decreased the pressure of natural selection, although in two different manners. Naked mole rats preferred an "aristocratic" pathway when reproduction (and, hence, involvement in evolution) is monopolized by the queen and her several husbands. Huge number of subordinates who have no right to take part in reproduction and hence in evolution serves the small queen's family. Humans used an alternative, "democratic" pathway, namely technical progress facilitating adaptation to the changing environmental conditions. This pathway is open to all humankind. (ii) As a result, aging as a mechanism increasing evolvability by means of facilitation of natural selection became unnecessary for naked mole rats and humans due to strong attenuation of this selection. This is apparently why aging became a counterproductive atavism for these two species and was strongly shifted to late ages. This shift is direct evidence of the hypothesis that aging is programmed, being the last step of late ontogeny. (iii) Further deceleration of aging for humans by means of neoteny is unrealistic since the development of neoteny probably takes million years. (iv) However, if biological aging is a program, an alternative and much simpler way to avoid it seems possible. We mean inhibition of an essential step of this program. (v) At present, the most probable scheme of the aging program assumes that it is a mechanism of slow poisoning of an organism by reactive oxygen species produced by mitochondria. If this is the case, a mitochondria-targeted antioxidant might be an inhibitor of the aging program. During the last 12 years, such an antioxidant, namely SkQ1, was synthesized and studied in detail in our group. It consists of plastoquinone and decyltriphenylphosphonium (a penetrating cation responsible for electrophoretic accumulation of SkQ1 in mitochondria). It was shown that long-term treatment with SkQ1 increased the lifespan of plants, fungi, invertebrates, fish, and mammals. Moreover, SkQ1 is effective in the therapy of various age-related diseases. It was also shown that a single SkQ1 injection could save life in certain models of sudden death of animals. (vi) A tentative scheme is proposed considering aging as a process of chronic phenoptosis, which eventually results in initiation of acute phenoptosis and death. This scheme also suggests that under certain conditions chronic phenoptosis can be neutralized by an anti-aging program that is activated by food restriction regarded by an organism as a signal of starvation. As for acute phenoptosis, it is apparently controlled by receptors responsible for measuring key parameters of homeostasis. The first experimental indications have been already obtained indicating that both chronic and acute phenoptosis are suppressed by SkQ1.}, }
@article {pmid29486209, year = {2019}, author = {Kenny, NJ and Noreña, C and Damborenea, C and Grande, C}, title = {Probing recalcitrant problems in polyclad evolution and systematics with novel mitochondrial genome resources.}, journal = {Genomics}, volume = {111}, number = {3}, pages = {343-355}, doi = {10.1016/j.ygeno.2018.02.009}, pmid = {29486209}, issn = {1089-8646}, mesh = {Animals ; *Evolution, Molecular ; *Genome, Mitochondrial ; *Phylogeny ; Platyhelminths/classification/*genetics ; }, abstract = {For their apparent morphological simplicity, the Platyhelminthes or "flatworms" are a diverse clade found in a broad range of habitats. Their body plans have however made them difficult to robustly classify. Molecular evidence is only beginning to uncover the true evolutionary history of this clade. Here we present nine novel mitochondrial genomes from the still undersampled orders Polycladida and Rhabdocoela, assembled from short Illumina reads. In particular we present for the first time in the literature the mitochondrial sequence of a Rhabdocoel, Bothromesostoma personatum (Typhloplanidae, Mesostominae). The novel mitochondrial genomes examined generally contained the 36 genes expected in the Platyhelminthes, with all possessing 12 of the 13 protein-coding genes normally found in metazoan mitochondrial genomes (ATP8 being absent from all Platyhelminth mtDNA sequenced to date), along with two ribosomal RNA genes. The majority presented possess 22 transfer RNA genes, and a single tRNA gene was absent from two of the nine assembled genomes. By comparison of mitochondrial gene order and phylogenetic analysis of the protein coding and ribosomal RNA genes contained within these sequences with those of previously sequenced species we are able to gain a firm molecular phylogeny for the inter-relationships within this clade. Our phylogenetic reconstructions, using both nucleotide and amino acid sequences under several models and both Bayesian and Maximum Likelihood methods, strongly support the monophyly of Polycladida, and the monophyly of Acotylea and Cotylea within that clade. They also allow us to speculate on the early emergence of Macrostomida, the monophyly of a "Turbellarian-like" clade, the placement of Rhabditophora, and that of Platyhelminthes relative to the Lophotrochozoa (=Spiralia). The data presented here therefore represent a significant advance in our understanding of platyhelminth phylogeny, and will form the basis of a range of future research in the still-disputed classifications within this taxon.}, }
@article {pmid29483657, year = {2018}, author = {Curson, ARJ and Williams, BT and Pinchbeck, BJ and Sims, LP and Martínez, AB and Rivera, PPL and Kumaresan, D and Mercadé, E and Spurgin, LG and Carrión, O and Moxon, S and Cattolico, RA and Kuzhiumparambil, U and Guagliardo, P and Clode, PL and Raina, JB and Todd, JD}, title = {DSYB catalyses the key step of dimethylsulfoniopropionate biosynthesis in many phytoplankton.}, journal = {Nature microbiology}, volume = {3}, number = {4}, pages = {430-439}, doi = {10.1038/s41564-018-0119-5}, pmid = {29483657}, issn = {2058-5276}, mesh = {Chloroplasts/*enzymology/genetics/metabolism ; Diatoms/enzymology/genetics ; Dinoflagellida/enzymology/genetics ; Haptophyta/*enzymology/genetics ; Methyltransferases/*genetics/metabolism ; Mitochondria/*enzymology/genetics/metabolism ; Phytoplankton/metabolism ; Sulfonium Compounds/*metabolism ; }, abstract = {Dimethylsulfoniopropionate (DMSP) is a globally important organosulfur molecule and the major precursor for dimethyl sulfide. These compounds are important info-chemicals, key nutrients for marine microorganisms, and are involved in global sulfur cycling, atmospheric chemistry and cloud formation[1-3]. DMSP production was thought to be confined to eukaryotes, but heterotrophic bacteria can also produce DMSP through the pathway used by most phytoplankton [4] , and the DsyB enzyme catalysing the key step of this pathway in bacteria was recently identified [5] . However, eukaryotic phytoplankton probably produce most of Earth's DMSP, yet no DMSP biosynthesis genes have been identified in any such organisms. Here we identify functional dsyB homologues, termed DSYB, in many phytoplankton and corals. DSYB is a methylthiohydroxybutryate methyltransferase enzyme localized in the chloroplasts and mitochondria of the haptophyte Prymnesium parvum, and stable isotope tracking experiments support these organelles as sites of DMSP synthesis. DSYB transcription levels increased with DMSP concentrations in different phytoplankton and were indicative of intracellular DMSP. Identification of the eukaryotic DSYB sequences, along with bacterial dsyB, provides the first molecular tools to predict the relative contributions of eukaryotes and prokaryotes to global DMSP production. Furthermore, evolutionary analysis suggests that eukaryotic DSYB originated in bacteria and was passed to eukaryotes early in their evolution.}, }
@article {pmid29476907, year = {2018}, author = {Layton, KKS and Gosliner, TM and Wilson, NG}, title = {Flexible colour patterns obscure identification and mimicry in Indo-Pacific Chromodoris nudibranchs (Gastropoda: Chromodorididae).}, journal = {Molecular phylogenetics and evolution}, volume = {124}, number = {}, pages = {27-36}, doi = {10.1016/j.ympev.2018.02.008}, pmid = {29476907}, issn = {1095-9513}, mesh = {Animals ; Biodiversity ; DNA, Mitochondrial/genetics ; Gastropoda/genetics/*physiology ; Geography ; Likelihood Functions ; Mitochondria/genetics ; Molecular Mimicry/*genetics ; Phylogeny ; Pigmentation/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Chromodoris is a genus of colourful nudibranchs that feed on sponges and is found across the Indo-Pacific. While this was once the most diverse chromodorid genus, recent work has shown that the genus should be restricted to a monophyletic lineage that contains only 22 species, all of which exhibit black pigmentation and planar spawning behaviour. Earlier phylogenies of this group are poorly resolved and thus additional work is needed to clarify species boundaries within Chromodoris. This study presents a maximum-likelihood phylogeny based on mitochondrial loci (COI, 16S) for 345 Chromodoris specimens, including data from 323 new specimens and 22 from GenBank, from across the Indo-Pacific. Species hypotheses and phylogenetic analysis uncovered 39 taxa in total containing 18 undescribed species, with only five of 39 taxa showing stable colour patterns and distinct morphotypes. This study also presents the first evidence for regional mimicry in this genus, with C. colemani and C. joshi displaying geographically-based variation in colour patterns which appear to match locally abundant congenerics, highlighting the flexibility of these colour patterns in Chromodoris nudibranchs. The current phylogeny contains short branch lengths, polytomies and poor support at interior nodes, which is indicative of a recent radiation. As such, future work will employ a transcriptome-based exon capture approach for resolving the phylogeny of this group. In all, this study included 21 of the 22 described species in the Chromodoris sensu stricto group with broad sampling coverage from across the Indo-Pacific, constituting the most comprehensive sampling of this group to date. This work highlights several cases of undocumented diversity, ultimately expanding our knowledge of species boundaries in this group, while also demonstrating the limitations of colour patterns for species identification in this genus.}, }
@article {pmid29472284, year = {2018}, author = {Raina, JB and Eme, L and Pollock, FJ and Spang, A and Archibald, JM and Williams, TA}, title = {Symbiosis in the microbial world: from ecology to genome evolution.}, journal = {Biology open}, volume = {7}, number = {2}, pages = {}, pmid = {29472284}, issn = {2046-6390}, abstract = {The concept of symbiosis - defined in 1879 by de Bary as 'the living together of unlike organisms' - has a rich and convoluted history in biology. In part, because it questioned the concept of the individual, symbiosis fell largely outside mainstream science and has traditionally received less attention than other research disciplines. This is gradually changing. In nature organisms do not live in isolation but rather interact with, and are impacted by, diverse beings throughout their life histories. Symbiosis is now recognized as a central driver of evolution across the entire tree of life, including, for example, bacterial endosymbionts that provide insects with vital nutrients and the mitochondria that power our own cells. Symbioses between microbes and their multicellular hosts also underpin the ecological success of some of the most productive ecosystems on the planet, including hydrothermal vents and coral reefs. In November 2017, scientists working in fields spanning the life sciences came together at a Company of Biologists' workshop to discuss the origin, maintenance, and long-term implications of symbiosis from the complementary perspectives of cell biology, ecology, evolution and genomics, taking into account both model and non-model organisms. Here, we provide a brief synthesis of the fruitful discussions that transpired.}, }
@article {pmid29466431, year = {2018}, author = {Ravago-Gotanco, R and de la Cruz, TL and Pante, MJ and Borsa, P}, title = {Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea.}, journal = {PloS one}, volume = {13}, number = {2}, pages = {e0193220}, pmid = {29466431}, issn = {1932-6203}, mesh = {Animals ; Fishes/classification/*genetics ; *Genetic Loci ; *Genotype ; *Microsatellite Repeats ; Mitochondria/*genetics ; Oceans and Seas ; *Phylogeny ; }, abstract = {The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P < 0.001); (2) low frequency of later-generation hybrids; (3) significant association with mitochondrial Clade A and Clade B, respectively; and (4) subtle yet significant body shape differences as inferred from geometric morphometric analysis. The divergence between mitochondrial Clade C and the two other clades was not matched by genetic differences at microsatellite marker loci. The occurrence of discordant mitonuclear combinations (20.5% of the total number of individuals) is thought to result from mitochondrial introgression, consistent with a scenario of demographic, and presumably spatial, post-Pleistocene expansion of populations from northern regions into a secondary contact zone in the South China Sea. Mitonuclear discordance due to introgression obscures phylogenetic relationships for recently-diverged lineages, and cautions against the use of mitochondrial markers alone for species identification within the mottled rabbitfish species complex in the South China Sea region.}, }
@article {pmid29464567, year = {2018}, author = {Schlattner, U and Kay, L and Tokarska-Schlattner, M}, title = {Mitochondrial Proteolipid Complexes of Creatine Kinase.}, journal = {Sub-cellular biochemistry}, volume = {87}, number = {}, pages = {365-408}, doi = {10.1007/978-981-10-7757-9_13}, pmid = {29464567}, issn = {0306-0225}, mesh = {Animals ; *Creatine Kinase/chemistry/metabolism ; Cytosol/chemistry/metabolism ; Humans ; *Mitochondria/chemistry/metabolism ; *Mitochondrial Membranes/chemistry/metabolism ; *Mitochondrial Proteins/chemistry/metabolism ; *Phospholipids/chemistry/metabolism ; Reactive Oxygen Species/chemistry/metabolism ; Thermogenesis/physiology ; }, abstract = {Isoforms of creatine kinase (CK) generate and use phosphocreatine, a concentrated and highly diffusible cellular "high energy" intermediate, for the main purpose of energy buffering and transfer in order to maintain cellular energy homeostasis. The mitochondrial CK isoform (mtCK) localizes to the mitochondrial intermembrane and cristae space, where it assembles into peripherally membrane-bound, large cuboidal homooctamers. These are part of proteolipid complexes wherein mtCK directly interacts with cardiolipin and other anionic phospholipids, as well as with the VDAC channel in the outer membrane. This leads to a stabilization and cross-linking of inner and outer mitochondrial membrane, forming so-called contact sites. Also the adenine nucleotide translocator of the inner membrane can be recruited into these proteolipid complexes, probably mediated by cardiolipin. The complexes have functions mainly in energy transfer to the cytosol and stimulation of oxidative phosphorylation, but also in restraining formation of reactive oxygen species and apoptosis. In vitro evidence indicates a putative role of mtCK in mitochondrial phospholipid distribution, and most recently a role in thermogenesis has been proposed. This review summarizes the essential structural and functional data of these mtCK complexes and describes in more detail the more recent advances in phospholipid interaction, thermogenesis, cancer and evolution of mtCK.}, }
@article {pmid29463212, year = {2018}, author = {Wagner, JT and Singh, PP and Romney, AL and Riggs, CL and Minx, P and Woll, SC and Roush, J and Warren, WC and Brunet, A and Podrabsky, JE}, title = {The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {155}, pmid = {29463212}, issn = {1471-2164}, support = {R24 OD011198/OD/NIH HHS/United States ; R24 RR032658/RR/NCRR NIH HHS/United States ; CEHG Fellowship//Stanford University/International ; IOS-1354549//National Science Foundation/International ; }, mesh = {Adaptation, Biological/*genetics ; Animals ; Base Composition ; Biological Evolution ; Chickens ; Embryo, Nonmammalian ; Embryonic Development/*genetics ; Gene Expression Regulation ; *Genome ; Genome Size ; Genomics/methods ; Killifishes/*embryology/genetics/*physiology ; Mitochondria/genetics/metabolism ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Stress, Physiological/*genetics ; Vertebrates ; Zebrafish ; }, abstract = {BACKGROUND: The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in northern Venezuela, South America, and is an emerging extremophile model for vertebrate diapause, stress tolerance, and evolution. Embryos of A. limnaeus regularly experience extended periods of desiccation and anoxia as a part of their natural history and have unique metabolic and developmental adaptations. Currently, there are limited genomic resources available for gene expression and evolutionary studies that can take advantage of A. limnaeus as a unique model system.<br><br>RESULTS: We describe the first draft genome sequence of A. limnaeus. The genome was assembled de novo using a merged assembly strategy and was annotated using the NCBI Eukaryotic Annotation Pipeline. We show that the assembled genome has a high degree of completeness in genic regions that is on par with several other teleost genomes. Using RNA-seq and phylogenetic-based approaches, we identify several candidate genes that may be important for embryonic stress tolerance and post-diapause development in A. limnaeus. Several of these genes include heat shock proteins that have unique expression patterns in A. limnaeus embryos and at least one of these may be under positive selection.<br><br>CONCLUSION: The A. limnaeus genome is the first South American annual killifish genome made publicly available. This genome will be a valuable resource for comparative genomics to determine the genetic and evolutionary mechanisms that support the unique biology of annual killifishes. In a broader context, this genome will be a valuable tool for exploring genome-environment interactions and their impacts on vertebrate physiology and evolution.}, }
@article {pmid29460123, year = {2018}, author = {Larsen, PA and Hunnicutt, KE and Larsen, RJ and Yoder, AD and Saunders, AM}, title = {Warning SINEs: Alu elements, evolution of the human brain, and the spectrum of neurological disease.}, journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology}, volume = {26}, number = {1-2}, pages = {93-111}, pmid = {29460123}, issn = {1573-6849}, support = {S10 OD018164/OD/NIH HHS/United States ; }, mesh = {Alu Elements/*physiology ; *Biological Evolution ; Brain/*physiology ; Genome, Human ; Humans ; Nervous System Diseases/*genetics ; Neurogenesis ; Retroelements ; }, abstract = {Alu elements are a highly successful family of primate-specific retrotransposons that have fundamentally shaped primate evolution, including the evolution of our own species. Alus play critical roles in the formation of neurological networks and the epigenetic regulation of biochemical processes throughout the central nervous system (CNS), and thus are hypothesized to have contributed to the origin of human cognition. Despite the benefits that Alus provide, deleterious Alu activity is associated with a number of neurological and neurodegenerative disorders. In particular, neurological networks are potentially vulnerable to the epigenetic dysregulation of Alu elements operating across the suite of nuclear-encoded mitochondrial genes that are critical for both mitochondrial and CNS function. Here, we highlight the beneficial neurological aspects of Alu elements as well as their potential to cause disease by disrupting key cellular processes across the CNS. We identify at least 37 neurological and neurodegenerative disorders wherein deleterious Alu activity has been implicated as a contributing factor for the manifestation of disease, and for many of these disorders, this activity is operating on genes that are essential for proper mitochondrial function. We conclude that the epigenetic dysregulation of Alu elements can ultimately disrupt mitochondrial homeostasis within the CNS. This mechanism is a plausible source for the incipient neuronal stress that is consistently observed across a spectrum of sporadic neurological and neurodegenerative disorders.}, }
@article {pmid29455315, year = {2018}, author = {Caparroz, R and Rocha, AV and Cabanne, GS and Tubaro, P and Aleixo, A and Lemmon, EM and Lemmon, AR}, title = {Mitogenomes of two neotropical bird species and the multiple independent origin of mitochondrial gene orders in Passeriformes.}, journal = {Molecular biology reports}, volume = {45}, number = {3}, pages = {279-285}, pmid = {29455315}, issn = {1573-4978}, support = {564036/2010-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 445025/2014-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 457444/2012-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 202796/2014-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; PIP 2012-2014 0862//Consejo Nacional de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas/ ; PICT 2014-2154//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; }, mesh = {Animals ; Base Sequence/genetics ; Gene Order ; Genes, Mitochondrial ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/*genetics ; Passeriformes/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {At least four mitogenome arrangements occur in Passeriformes and differences among them are derived from an initial tandem duplication involving a segment containing the control region (CR), followed by loss or reduction of some parts of this segment. However, it is still unclear how often duplication events have occurred in this bird order. In this study, the mitogenomes from two species of Neotropical passerines (Sicalis olivascens and Lepidocolaptes angustirostris) with different gene arrangements were first determined. We also estimated how often duplication events occurred in Passeriformes and if the two CR copies demonstrate a pattern of concerted evolution in Sylvioidea. One tissue sample for each species was used to obtain the mitogenomes as a byproduct using next generation sequencing. The evolutionary history of mitogenome rearrangements was reconstructed mapping these characters onto a mitogenome Bayesian phylogenetic tree of Passeriformes. Finally, we performed a Bayesian analysis for both CRs from some Sylvioidea species in order to evaluate the evolutionary process involving these two copies. Both mitogenomes described comprise 2 rRNAs, 22 tRNAs, 13 protein-codon genes and the CR. However, S. olivascens has 16,768 bp showing the ancestral avian arrangement, while L. angustirostris has 16,973 bp and the remnant CR2 arrangement. Both species showed the expected gene order compared to their closest relatives. The ancestral state reconstruction suggesting at least six independent duplication events followed by partial deletions or loss of one copy in some lineages. Our results also provide evidence that both CRs in some Sylvioidea species seem to be maintained in an apparently functional state, perhaps by concerted evolution, and that this mechanism may be important for the evolution of the bird mitogenome.}, }
@article {pmid29451846, year = {2018}, author = {Briosio-Aguilar, R and Pinto, HA and Rodríguez-Santiago, MA and López-García, K and García-Varela, M and de León, GP}, title = {Link Between the Adult and the Metacercaria of Clinostomum heluans Braun, 1899 (Trematoda: Clinostomidae) Through DNA Sequences, and its Phylogenetic Position Within the Genus Clinostomum Leidy, 1856.}, journal = {The Journal of parasitology}, volume = {104}, number = {3}, pages = {292-296}, doi = {10.1645/17-183}, pmid = {29451846}, issn = {1937-2345}, mesh = {Animals ; Base Sequence ; Bird Diseases/*parasitology ; Birds ; Brazil ; Cichlids/parasitology ; DNA Barcoding, Taxonomic/veterinary ; DNA, Helminth/*chemistry/genetics ; Electron Transport Complex IV/chemistry/genetics ; Fish Diseases/*parasitology ; Metacercariae/classification/genetics ; Mexico ; Mitochondria/enzymology/genetics ; *Phylogeny ; Trematoda/*classification/genetics/growth &amp; development ; Trematode Infections/parasitology/*veterinary ; }, abstract = {The phylogenetic position of Clinostomum heluans Braun, 1899 within the genus Clinostomum Leidy, 1856 is reported in this study based on sequences of the barcoding region of the mitochondrial cytochrome c oxidase subunit 1 gene (COX1). Additionally, molecular data are used to link the adult and the metacercariae of the species. The metacercariae of C. heluans were found encysted infecting the cichlid fish Australoheros sp. in Minas Gerais, Brazil, whereas the adults were obtained from the mouth cavity of the Great White Egret, Ardea alba, in Campeche, Mexico. The COX1 sequences obtained for the Mexican clinostomes and the Brazilian metacercaria were almost identical (0.2% molecular divergence), indicating conspecificity. Similar molecular divergence (0.2-0.4%) was found between sequences of C. heluans reported here and Clinostomum sp. 6 previously obtained from a metacercaria recovered from the cichlid Cichlasoma boliviense in Santa Cruz, Bolivia. Both maximum likelihood and Bayesian inference analyses unequivocally showed the conspecificity between C. heluans and Clinostomum sp. 6, which form a monophyletic clade with high nodal support and very low genetic divergence. Moreover, tree topology reveals that C. heluans occupies a basal position with respect to New World species of Clinostomum, although a denser taxon sampling of species within the genus is further required. The metacercaria of C. heluans seems to be specific to cichlid fish because both samples from South America were recovered from species of this fish family, although not closely related.}, }
@article {pmid29449618, year = {2018}, author = {Shinde, P and Sarkar, C and Jalan, S}, title = {Codon based co-occurrence network motifs in human mitochondria.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {3060}, pmid = {29449618}, issn = {2045-2322}, mesh = {Africa ; Americas ; Asia ; Codon/genetics ; DNA, Mitochondrial/*genetics ; Europe ; *Evolution, Molecular ; Genome, Human/*genetics ; Genome, Mitochondrial/*genetics ; Humans ; Mitochondria/*genetics ; Models, Genetic ; Mutation ; Oceania ; Selection, Genetic ; }, abstract = {The nucleotide polymorphism in the human mitochondrial genome (mtDNA) tolled by codon position bias plays an indispensable role in human population dispersion and expansion. Herein, genome-wide nucleotide co-occurrence networks were constructed using data comprised of five different geographical regions and around 3000 samples for each region. We developed a powerful network model to describe complex mitochondrial evolutionary patterns among codon and non-codon positions. We found evidence that the evolution of human mitochondria DNA is dominated by adaptive forces, particularly mutation and selection, which was supported by many previous studies. The diversity observed in the mtDNA was compared with mutations, co-occurring mutations, network motifs considering codon positions as causing agent. This comparison showed that long-range nucleotide co-occurrences have a large effect on genomic diversity. Most notably, codon motifs apparently underpinned the preferences among codon positions for co-evolution which is probably highly biased during the origin of the genetic code. Our analysis also showed that variable nucleotide positions of different human sub-populations implemented the independent mtDNA evolution to its geographical dispensation. Ergo, this study has provided both a network framework and a codon glance to investigate co-occurring genomic variations that are critical in underlying complex mitochondrial evolution.}, }
@article {pmid29447215, year = {2018}, author = {Keleher, MR and Zaidi, R and Shah, S and Oakley, ME and Pavlatos, C and El Idrissi, S and Xing, X and Li, D and Wang, T and Cheverud, JM}, title = {Maternal high-fat diet associated with altered gene expression, DNA methylation, and obesity risk in mouse offspring.}, journal = {PloS one}, volume = {13}, number = {2}, pages = {e0192606}, pmid = {29447215}, issn = {1932-6203}, support = {P30 DK020579/NH/NIH HHS/United States ; P30 CA91842/NH/NIH HHS/United States ; UL1 TR000448/TR/NCATS NIH HHS/United States ; P30 CA091842/CA/NCI NIH HHS/United States ; UL1 TR002345/TR/NCATS NIH HHS/United States ; UL1TR000448/NH/NIH HHS/United States ; P30 DK020579/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *DNA Methylation ; *Diet, High-Fat ; Female ; *Gene Expression ; Mice ; *Mothers ; Obesity/*epidemiology ; Risk Factors ; }, abstract = {We investigated maternal obesity in inbred SM/J mice by assigning females to a high-fat diet or a low-fat diet at weaning, mating them to low-fat-fed males, cross-fostering the offspring to low-fat-fed SM/J nurses at birth, and weaning the offspring onto a high-fat or low-fat diet. A maternal high-fat diet exacerbated obesity in the high-fat-fed daughters, causing them to weigh more, have more fat, and have higher serum levels of leptin as adults, accompanied by dozens of gene expression changes and thousands of DNA methylation changes in their livers and hearts. Maternal diet particularly affected genes involved in RNA processing, immune response, and mitochondria. Between one-quarter and one-third of differentially expressed genes contained a differentially methylated region associated with maternal diet. An offspring high-fat diet reduced overall variation in DNA methylation, increased body weight and organ weights, increased long bone lengths and weights, decreased insulin sensitivity, and changed the expression of 3,908 genes in the liver. Although the offspring were more affected by their own diet, their maternal diet had epigenetic effects lasting through adulthood, and in the daughters these effects were accompanied by phenotypic changes relevant to obesity and diabetes.}, }
@article {pmid29440651, year = {2018}, author = {Petit, D and Teppa, E and Cenci, U and Ball, S and Harduin-Lepers, A}, title = {Reconstruction of the sialylation pathway in the ancestor of eukaryotes.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2946}, pmid = {29440651}, issn = {2045-2322}, mesh = {Amino Acid Sequence ; *Computational Biology ; Eukaryota/*metabolism ; N-Acetylneuraminic Acid/*metabolism ; Phylogeny ; *Protein Processing, Post-Translational ; }, abstract = {The biosynthesis of sialylated molecules of crucial relevance for eukaryotic cell life is achieved by sialyltransferases (ST) of the CAZy family GT29. These enzymes are widespread in the Deuterostoma lineages and more rarely described in Protostoma, Viridiplantae and various protist lineages raising the question of their presence in the Last eukaryotes Common Ancestor (LECA). If so, it is expected that the main enzymes associated with sialic acids metabolism are also present in protists. We conducted phylogenomic and protein sequence analyses to gain insights into the origin and ancient evolution of ST and sialic acid pathway in eukaryotes, Bacteria and Archaea. Our study uncovered the unreported occurrence of bacterial GT29 ST and evidenced the existence of 2 ST groups in the LECA, likely originating from the endosymbiotic event that generated mitochondria. Furthermore, distribution of the major actors of the sialic acid pathway in the different eukaryotic phyla indicated that these were already present in the LECA, which could also access to this essential monosaccharide either endogenously or via a sialin/sialidase uptake mechanism involving vesicles. This pathway was lost in several basal eukaryotic lineages including Archaeplastida despite the presence of two different ST groups likely assigned to other functions.}, }
@article {pmid29438872, year = {2018}, author = {Nibert, ML and Vong, M and Fugate, KK and Debat, HJ}, title = {Evidence for contemporary plant mitoviruses.}, journal = {Virology}, volume = {518}, number = {}, pages = {14-24}, pmid = {29438872}, issn = {1096-0341}, support = {R01 GM033050/GM/NIGMS NIH HHS/United States ; T32 GM007598/GM/NIGMS NIH HHS/United States ; }, mesh = {Crops, Agricultural/*virology ; Evolution, Molecular ; Gene Expression Regulation, Viral/physiology ; Phylogeny ; Plant Diseases/*virology ; Plant Viruses/*classification/physiology ; RNA Viruses/*classification ; RNA, Viral/genetics ; Viral Proteins/genetics/metabolism ; }, abstract = {Mitoviruses have small RNA(+) genomes, replicate in mitochondria, and have been shown to infect only fungi to date. For this report, sequences that appear to represent nearly complete plant mitovirus genomes were recovered from publicly available transcriptome data. Twenty of the refined sequences, 2684-2898 nt long and derived from 10 different species of land plants, appear to encompass the complete coding regions of contemporary plant mitoviruses, which furthermore constitute a monophyletic cluster within genus Mitovirus. Complete coding sequences of several of these viruses were recovered from multiple transcriptome (but not genome) studies of the same plant species and also from multiple plant tissues. Crop plants among implicated hosts include beet and hemp. Other new results suggest that such genuine plant mitoviruses were immediate ancestors to endogenized mitovirus elements now widespread in land plant genomes. Whether these mitoviruses are wholly cryptic with regard to plant health remains to be investigated.}, }
@article {pmid29435647, year = {2018}, author = {Karmi, O and Marjault, HB and Pesce, L and Carloni, P and Onuchic, JN and Jennings, PA and Mittler, R and Nechushtai, R}, title = {The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease.}, journal = {Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry}, volume = {23}, number = {4}, pages = {599-612}, pmid = {29435647}, issn = {1432-1327}, support = {R01 GM101467/GM/NIGMS NIH HHS/United States ; }, mesh = {*Disease ; *Health ; Humans ; Hydrophobic and Hydrophilic Interactions ; Iron-Sulfur Proteins/*chemistry/*metabolism ; Protein Domains ; *Protein Folding ; }, abstract = {NEET proteins comprise a new class of [2Fe-2S] cluster proteins. In human, three genes encode for NEET proteins: cisd1 encodes mitoNEET (mNT), cisd2 encodes the Nutrient-deprivation autophagy factor-1 (NAF-1) and cisd3 encodes MiNT (Miner2). These recently discovered proteins play key roles in many processes related to normal metabolism and disease. Indeed, NEET proteins are involved in iron, Fe-S, and reactive oxygen homeostasis in cells and play an important role in regulating apoptosis and autophagy. mNT and NAF-1 are homodimeric and reside on the outer mitochondrial membrane. NAF-1 also resides in the membranes of the ER associated mitochondrial membranes (MAM) and the ER. MiNT is a monomer with distinct asymmetry in the molecular surfaces surrounding the clusters. Unlike its paralogs mNT and NAF-1, it resides within the mitochondria. NAF-1 and mNT share similar backbone folds to the plant homodimeric NEET protein (At-NEET), while MiNT's backbone fold resembles a bacterial MiNT protein. Despite the variation of amino acid composition among these proteins, all NEET proteins retained their unique CDGSH domain harboring their unique 3Cys:1His [2Fe-2S] cluster coordination through evolution. The coordinating exposed His was shown to convey the lability to the NEET proteins' [2Fe-2S] clusters. In this minireview, we discuss the NEET fold and its structural elements. Special attention is given to the unique lability of the NEETs' [2Fe-2S] cluster and the implication of the latter to the NEET proteins' cellular and systemic function in health and disease.}, }
@article {pmid29433421, year = {2018}, author = {Li, Q and Dong, K and Xu, L and Jia, X and Wu, J and Sun, W and Zhang, X and Fu, S}, title = {The distribution of three candidate cold-resistant SNPs in six minorities in North China.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {134}, pmid = {29433421}, issn = {1471-2164}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Adaptation, Physiological/*genetics ; Asian People/genetics ; Carnitine O-Palmitoyltransferase/genetics ; China ; *Cold Temperature ; Ethnicity/classification/*genetics ; Fatty Acid Desaturases/genetics ; Gene Frequency ; Genotype ; Humans ; Linkage Disequilibrium ; Phylogeny ; *Polymorphism, Single Nucleotide ; }, abstract = {BACKGROUND: Heilongjiang Province located in northeast China is a multi-ethnic region with people who have lived in cold conditions for several generations. Fatty acids are important to people with cold resistance. CPT1A encodes a protein that imports long-chain fatty acids into the mitochondria for fatty-acid oxidation. FADS is an essential enzyme for the synthesis of long-chain polyunsaturated fatty acids.<br><br>RESULTS: In the present study, we investigated the distributions of three cold resistance-related SNPs (rs80356779 G&#x2009;>&#x2009;A in CPT1A, rs7115739 T&#x2009;>&#x2009;G in FADS3 and rs174570 C&#x2009;>&#x2009;T in FADS2) from six populations that included 1093 individuals who have lived in Heilongjiang Province for at least three generations. The frequencies of rs174570 and rs7115739 were different in our six north minorities compared to the Chinese Dai in Xishuangbanna (CDX) in southern China. All the SNPs in Hezhen were significantly different from other five studied populations. In addition, the genetic distribution of rs174570 in Daur was significantly different from Manchu and Korea, and the frequency of rs7115739 in Ewenki was significantly different from the other populations. The results also showed that the frequencies of the three SNPs in the six minorities were different from those of Greenlandic Inuit and Siberian population.<br><br>CONCLUSIONS: Our results showed the distributions of the three cold resistance-related SNPs from six populations that included 1093 individuals in northern China. Distributions of the allele frequencies for the cold resistance-related SNPs in northern China were statistically different from those in southern China. These data help to establish the DNA genome database for the six populations and fully preserve existing minority genetic information.}, }
@article {pmid29432738, year = {2018}, author = {Qin, Q and Jin, J and He, F and Zheng, Y and Li, T and Zhang, Y and He, J}, title = {Humanin promotes mitochondrial biogenesis in pancreatic MIN6 β-cells.}, journal = {Biochemical and biophysical research communications}, volume = {497}, number = {1}, pages = {292-297}, doi = {10.1016/j.bbrc.2018.02.071}, pmid = {29432738}, issn = {1090-2104}, mesh = {Animals ; Cell Line ; Insulin-Secreting Cells/cytology/*drug effects/*physiology ; Intracellular Signaling Peptides and Proteins/*administration &amp; dosage/*metabolism ; Mice ; Mitochondria/*drug effects/*physiology/ultrastructure ; *Organelle Biogenesis ; Treatment Outcome ; }, abstract = {Mitochondrial dysfunction is associated with β-cell failure and insulin resistance in diabetes. Humanin is an endogenous cytoprotective peptide. In the current study, we aimed to define the effects of Humanin on mitochondrial biogenesis in pancreatic β-cells. Our findings demonstrated that Humanin treatment significantly increased the expression of PGC-1α and its downstream target genes NRF1 and TFAM in MIN6 β-cells. Notably, Humanin treatment significantly promoted mitochondrial biogenesis by increasing mitochondrial mass, elevating mtDNA/nDNA ratio, and stimulating the expression of cytochrome B, which were suppressed by the specific AMPK inhibitor compound C. Indeed, Humanin treatment caused the phosphorylation of AMPK, which was involved in the induction of PGC-1α, NRF1, and TFAM by Humanin. Importantly, our findings indicate that Humanin treatment led to a possible functional gain of the mitochondria by increasing ATP levels and respiratory rate. Our findings provided a new insight into the molecular mechanisms of action by which Humanin improves pancreatic β-cell function via enhanced mitochondrial mass and performance.}, }
@article {pmid29428509, year = {2018}, author = {Sahoo, RK and Lohman, DJ and Wahlberg, N and Müller, CJ and Brattström, O and Collins, SC and Peggie, D and Aduse-Poku, K and Kodandaramaiah, U}, title = {Evolution of Hypolimnas butterflies (Nymphalidae): Out-of-Africa origin and Wolbachia-mediated introgression.}, journal = {Molecular phylogenetics and evolution}, volume = {123}, number = {}, pages = {50-58}, doi = {10.1016/j.ympev.2018.02.001}, pmid = {29428509}, issn = {1095-9513}, mesh = {Africa ; Animals ; Base Sequence ; Bayes Theorem ; Biodiversity ; *Biological Evolution ; Butterflies/*genetics/*microbiology ; DNA, Mitochondrial/genetics ; Haplotypes/genetics ; Larva/physiology ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Wolbachia/*physiology ; }, abstract = {Hypolimnas butterflies (Nymphalidae), commonly known as eggflies, are a popular model system for studying a wide range of ecological questions including mimicry, polymorphism, wing pattern evolution, and Wolbachia-host interactions. The lack of a time-calibrated phylogeny for this group has precluded understanding its evolutionary history. We reconstruct a species-level phylogeny using a nine gene dataset and estimate species divergence times. Based on the resulting tree, we investigate the taxon's historical biogeography, examine the evolution of host plant preferences, and test the hypothesis that the endosymbiotic bacterium Wolbachia mediates gene transfer between species. Our analyses indicate that the species are grouped within three strongly supported, deeply divergent clades. However, relationships among these three clades are uncertain. In addition, many Hypolimnas species are not monophyletic or monophyletic with weak support, suggesting widespread incomplete lineage sorting and/or introgression. Biogeographic analysis strongly indicates that the genus diverged from its ancestor in Africa and subsequently dispersed to Asia; the strength of this result is not affected by topological uncertainties. While the larvae of African species feed almost exclusively on Urticaceae, larvae of species found further east often feed on several additional families. Interestingly, we found an identical mitochondrial haplotype in two Hypolimnas species, H. bolina and H. alimena, and a strong association between this mitotype and the Wolbachia strain wBol1a. Future investigations should explore the plausibility of Wolbachia-mediated introgression between species.}, }
@article {pmid29427777, year = {2019}, author = {Prager, M}, title = {Unweaving a taxon tangle: Comments on De Silva et al. (2017).}, journal = {Molecular phylogenetics and evolution}, volume = {131}, number = {}, pages = {229-232}, doi = {10.1016/j.ympev.2018.02.005}, pmid = {29427777}, issn = {1095-9513}, mesh = {Animals ; Biomarkers ; *Birds ; Cell Nucleus ; *Mitochondria ; Phylogeny ; }, }
@article {pmid29426933, year = {2018}, author = {Allu, PK and Boggula, Y and Karri, S and Marada, A and Krishnamoorthy, T and Sepuri, NBV}, title = {A conserved R type Methionine Sulfoxide Reductase reverses oxidized GrpEL1/Mge1 to regulate Hsp70 chaperone cycle.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2716}, pmid = {29426933}, issn = {2045-2322}, mesh = {Adenosine Triphosphatases/genetics/metabolism ; Cysteine/metabolism ; Ferredoxin-NADP Reductase/genetics/*metabolism ; Genetic Complementation Test ; HSP70 Heat-Shock Proteins/genetics/*metabolism ; Humans ; Methionine/metabolism ; Methionine Sulfoxide Reductases/genetics/*metabolism ; Mitochondria/genetics/*metabolism ; Mitochondrial Membrane Transport Proteins/chemistry/genetics/*metabolism ; Models, Molecular ; Molecular Chaperones/chemistry/genetics/*metabolism ; Mutant Proteins/genetics/metabolism ; Oxidation-Reduction ; Oxidative Stress ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; }, abstract = {Cells across evolution employ reversible oxidative modification of methionine and cysteine amino acids within proteins to regulate responses to redox stress. Previously we have shown that mitochondrial localized methionine sulfoxide reductase (Mxr2) reversibly regulates oxidized yeast Mge1 (yMge1), a co-chaperone of Hsp70/Ssc1 to maintain protein homeostasis during oxidative stress. However, the specificity and the conservation of the reversible methionine oxidation mechanism in higher eukaryotes is debatable as human GrpEL1 (hGrpEL1) unlike its homolog yMge1 harbors two methionine residues and multiple cysteines besides the mammalian mitochondria hosting R and S types of Mxrs/Msrs. In this study, using yeast as a surrogate system, we show that hGRPEL1 and R type MSRs but not the S type MSRs complement the deletion of yeast MGE1 or MXR2 respectively. Our investigations show that R type Msrs interact selectively with oxidized hGrpEL1/yMge1 in an oxidative stress dependent manner, reduce the conserved hGrpEL1-Met146-SO and rescue the Hsp70 ATPase activity. In addition, a single point mutation in hGrpEL1-M146L rescues the slow growth phenotype of yeast MXR2 deletion under oxidative duress. Our study illustrates the evolutionarily conserved formation of specific Met-R-SO in hGrpEL1/yMge1 and the essential and canonical role of R type Msrs/Mxrs in mitochondrial redox mechanism.}, }
@article {pmid29424926, year = {2019}, author = {Sweetman, C and Soole, KL and Jenkins, CLD and Day, DA}, title = {Genomic structure and expression of alternative oxidase genes in legumes.}, journal = {Plant, cell &amp; environment}, volume = {42}, number = {1}, pages = {71-84}, doi = {10.1111/pce.13161}, pmid = {29424926}, issn = {1365-3040}, mesh = {Cicer/enzymology/*genetics/metabolism ; Electrophoresis, Polyacrylamide Gel ; *Gene Expression Regulation, Plant ; Genes, Plant/*genetics ; Immunoblotting ; Mitochondria/enzymology/metabolism ; Mitochondrial Proteins/*genetics/metabolism ; Oxidoreductases/*genetics/metabolism ; Oxygen Consumption ; Plant Proteins/*genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Mitochondria isolated from chickpea (Cicer arietinum) possess substantial alternative oxidase (AOX) activity, even in non-stressed plants, and one or two AOX protein bands were detected immunologically, depending on the organ. Four different AOX isoforms were identified in the chickpea genome: CaAOX1 and CaAOX2A, B and D. CaAOX2A was the most highly expressed form and was strongly expressed in photosynthetic tissues, whereas CaAOX2D was found in all organs examined. These results are very similar to those of previous studies with soybean and siratro. Searches of available databases showed that this pattern of AOX genes and their expression was common to at least 16 different legume species. The evolution of the legume AOX gene family is discussed, as is the in vivo impact of an inherently high AOX capacity in legumes on growth and responses to environmental stresses.}, }
@article {pmid29417658, year = {2018}, author = {Pogoda, CS and Keepers, KG and Lendemer, JC and Kane, NC and Tripp, EA}, title = {Reductions in complexity of mitochondrial genomes in lichen-forming fungi shed light on genome architecture of obligate symbioses.}, journal = {Molecular ecology}, volume = {27}, number = {5}, pages = {1155-1169}, doi = {10.1111/mec.14519}, pmid = {29417658}, issn = {1365-294X}, mesh = {Biological Evolution ; Evolution, Molecular ; Fungal Proteins/genetics ; Fungi/genetics ; Genes, Fungal ; *Genome, Fungal ; *Genome, Mitochondrial ; Genomics ; Lichens/*genetics ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Symbiosis/*genetics ; Synteny ; }, abstract = {Symbioses among co-evolving taxa are often marked by genome reductions such as a loss of protein-coding genes in at least one of the partners as a means of reducing redundancy or intergenomic conflict. To explore this phenomenon in an iconic yet under-studied group of obligate symbiotic organisms, mitochondrial genomes of 22 newly sequenced and annotated species of lichenized fungi were compared to 167 mitochondrial genomes of nonlichenized fungi. Our results demonstrate the first broad-scale loss of atp9 from mitochondria of lichenized fungi. Despite key functions in mitochondrial energy production, we show that atp9 has been independently lost in three different lineages spanning 10 of the 22 studied species. A search for predicted, functional copies of atp9 among genomes of other symbionts involved in each lichen revealed the full-length, presumably functional copies of atp9 in either the photosynthetic algal partner or in other symbiotic fungi in all 10 instances. Together, these data yield evidence of an obligate symbiotic relationship in which core genomic processes have been streamlined, likely due to co-evolution.}, }
@article {pmid29413517, year = {2018}, author = {Gavish, M and Veenman, L}, title = {Regulation of Mitochondrial, Cellular, and Organismal Functions by TSPO.}, journal = {Advances in pharmacology (San Diego, Calif.)}, volume = {82}, number = {}, pages = {103-136}, doi = {10.1016/bs.apha.2017.09.004}, pmid = {29413517}, issn = {1557-8925}, mesh = {Animals ; Evolution, Molecular ; Genes, Essential ; Homeostasis ; Humans ; Mitochondria/*metabolism ; Reactive Oxygen Species/metabolism ; Receptors, GABA/*metabolism ; }, abstract = {In 1999, the enigma of the 18kDa mitochondrial translocator protein (TSPO), also known as the peripheral-type benzodiazepine receptor, was the seeming disparity of the many functions attributed to TSPO, ranging from the potential of TSPO acting as a housekeeping gene at molecular biological levels to adaptations to stress, and even involvement in higher emotional and cognitive functioning, such as anxiety and depression. In the years since then, knowledge regarding the many functions modulated by TSPO has expanded, and understanding has deepened. In addition, new functions could be firmly associated with TSPO, such as regulation of programmed cell death and modulation of gene expression. Interestingly, control by the mitochondrial TSPO over both of these life and death functions appears to include Ca[++] homeostasis, generation of reactive oxygen species (ROS), and ATP production. Other mitochondrial functions under TSPO control are considered to be steroidogenesis and tetrapyrrole metabolism. As TSPO effects on gene expression and on programmed cell death can be related to the wide range of functions that can be associated with TSPO, several of these five elements of Ca[++], ROS, ATP, steroids, and tetrapyrroles may indeed form the basis of TSPO's capability to operate as a multifunctional housekeeping gene to maintain homeostasis of the cell and of the whole multicellular organism.}, }
@article {pmid29410353, year = {2018}, author = {Rose, JP and Kleist, TJ and Löfstrand, SD and Drew, BT and Schönenberger, J and Sytsma, KJ}, title = {Phylogeny, historical biogeography, and diversification of angiosperm order Ericales suggest ancient Neotropical and East Asian connections.}, journal = {Molecular phylogenetics and evolution}, volume = {122}, number = {}, pages = {59-79}, doi = {10.1016/j.ympev.2018.01.014}, pmid = {29410353}, issn = {1095-9513}, mesh = {Animals ; *Biodiversity ; Chloroplasts/genetics ; Asia, Eastern ; Fossils/history ; Genetic Speciation ; History, Ancient ; Magnoliopsida/*classification/genetics ; Mitochondria/genetics ; *Phylogeny ; Phylogeography/history ; Ribosomes/genetics ; }, abstract = {Inferring interfamilial relationships within the eudicot order Ericales has remained one of the more recalcitrant problems in angiosperm phylogenetics, likely due to a rapid, ancient radiation. As a result, no comprehensive time-calibrated tree or biogeographical analysis of the order has been published. Here, we elucidate phylogenetic relationships within the order and then conduct time-dependent biogeographical and diversification analyses by using a taxon and locus-rich supermatrix approach on one-third of the extant species diversity calibrated with 23 macrofossils and two secondary calibration points. Our results corroborate previous studies and also suggest several new but poorly supported relationships. Newly suggested relationships are: (1) holoparasitic Mitrastemonaceae is sister to Lecythidaceae, (2) the clade formed by Mitrastemonaceae + Lecythidaceae is sister to Ericales excluding balsaminoids, (3) Theaceae is sister to the styracoids + sarracenioids + ericoids, and (4) subfamilial relationships with Ericaceae suggest that Arbutoideae is sister to Monotropoideae and Pyroloideae is sister to all subfamilies excluding Arbutoideae, Enkianthoideae, and Monotropoideae. Our results indicate Ericales began to diversify 110 Mya, within Indo-Malaysia and the Neotropics, with exchange between the two areas and expansion out of Indo-Malaysia becoming an important area in shaping the extant diversity of many families. Rapid cladogenesis occurred along the backbone of the order between 104 and 106 Mya. Jump dispersal is important within the order in the last 30 My, but vicariance is the most important cladogenetic driver of disjunctions at deeper levels of the phylogeny. We detect between 69 and 81 shifts in speciation rate throughout the order, the vast majority of which occurred within the last 30 My. We propose that range shifting may be responsible for older shifts in speciation rate, but more recent shifts may be better explained by morphological innovation.}, }
@article {pmid29408286, year = {2018}, author = {Yuan, ML and Zhang, QL and Zhang, L and Jia, CL and Li, XP and Yang, XZ and Feng, RQ}, title = {Mitochondrial phylogeny, divergence history and high-altitude adaptation of grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) inhabiting the Tibetan Plateau.}, journal = {Molecular phylogenetics and evolution}, volume = {122}, number = {}, pages = {116-124}, doi = {10.1016/j.ympev.2018.01.016}, pmid = {29408286}, issn = {1095-9513}, mesh = {*Adaptation, Physiological/genetics ; *Altitude ; Animals ; Biodiversity ; DNA/chemistry/isolation &amp; purification/metabolism ; Grassland ; Mitochondria/*genetics ; Moths/*classification/genetics ; Open Reading Frames/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Tibet ; }, abstract = {Grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) are the most important pests in alpine meadows of the Tibetan Plateau (TP) and have well adapted to high-altitude environments. To further understand the evolutionary history and their adaptation to the TP, we newly determined seven complete TP Gynaephora mitogenomes. Compared to single genes, whole mitogenomes provided the best phylogenetic signals and obtained robust results, supporting the monophyly of the TP Gynaephora species and a phylogeny of Arctiinae + (Aganainae + Lymantriinae). Incongruent phylogenetic signals were found among single mitochondrial genes, none of which recovered the same phylogeny as the whole mitogenome. We identified six best-performing single genes using Shimodaira-Hasegawa tests and found that the combinations of rrnS and either cox1 or cox3 generated the same phylogeny as the whole mitogenome, indicating the phylogenetic potential of these three genes for future evolutionary studies of Gynaephora. The TP Gynaephora species were estimated to radiate on the TP during the Pliocene and Quaternary, supporting an association of the diversification and speciation of the TP Gynaephora species with the TP uplifts and associated climate changes during this time. Selection analyses revealed accelerated evolutionary rates of the mitochondrial protein-coding genes in the TP Gynaephora species, suggesting that they accumulated more nonsynonymous substitutions that may benefit their adaptation to high altitudes. Furthermore, signals of positive selection were detected in nad5 of two Gynaephora species with the highest altitude-distributions, indicating that this gene may contribute to Gynaephora's adaptation to divergent altitudes. This study adds to the understanding of the TP Gynaephora evolutionary relationships and suggests a link between mitogenome evolution and ecological adaptation to high-altitude environments in grassland caterpillars.}, }
@article {pmid29405334, year = {2018}, author = {Hill, GE}, title = {Mitonuclear Mate Choice: A Missing Component of Sexual Selection Theory?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {40}, number = {3}, pages = {}, doi = {10.1002/bies.201700191}, pmid = {29405334}, issn = {1521-1878}, mesh = {Animals ; Cell Nucleus/*genetics/metabolism ; Ducks ; Evolution, Molecular ; Female ; Finches ; *Genome, Mitochondrial ; Genotype ; Male ; Mating Preference, Animal/*physiology ; Mitochondria/*genetics/metabolism ; Models, Biological ; *Oxidative Phosphorylation ; Reproduction ; *Selection, Genetic ; Spheniscidae ; }, abstract = {The fitness of a eukaryote hinges on the coordinated function of the products of its nuclear and mitochondrial genomes in achieving oxidative phosphorylation (OXPHOS). I propose that sexual selection plays a key role in the maintenance of mitonuclear coadaptation across generations because it enables pre-zygotic sorting for coadapted mitonuclear genotypes. At each new generation, sexual reproduction creates new combinations of nuclear and mitochondrial genes, and the potential arises for mitonuclear incompatibilities and reduced fitness. In reviewing the literature, I hypothesize that individuals engaged in mate choice select partners with correct species-typical mitochondrial and nuclear genotypes as well as individuals with highly functional cellular respiration. The implication is that mate choice for compatible nuclear and mitochondrial genes can play a significant role in generating the patterns of ornamentation and preferences observed in animals. A number of testable predictions emerge from this mitonuclear compatibility hypothesis of sexual selection.}, }
@article {pmid29404746, year = {2018}, author = {Jaleta, TG and Rödelsperger, C and Abanda, B and Eisenbarth, A and Achukwi, MD and Renz, A and Streit, A}, title = {Full mitochondrial and nuclear genome comparison confirms that Onchocerca sp. "Siisa" is Onchocerca ochengi.}, journal = {Parasitology research}, volume = {117}, number = {4}, pages = {1069-1077}, pmid = {29404746}, issn = {1432-1955}, support = {AOBJ:602317//Deutsche Forschungsgemeinschaft/ ; N/A//Max-Planck-Gesellschaft/ ; }, mesh = {Animals ; Cattle/parasitology ; Cattle Diseases/parasitology ; Genome, Mitochondrial/*genetics ; Genome, Protozoan/*genetics ; Humans ; Insect Vectors/parasitology ; Mitochondria/genetics ; Onchocerca/*classification/*genetics/isolation &amp; purification ; Onchocerciasis/parasitology ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Simuliidae/parasitology ; Skin/parasitology ; }, abstract = {Onchocerca ochengi is a nodule-forming filarial nematode parasite of cattle. It is the closest known relative of the human parasite Onchocerca volvulus, with which it shares the black fly vector Simulium damnosum. Onchocerca sp. "Siisa" was described in black flies and in cattle and, based on limited mitochondrial sequence information, appeared to be about equally phylogenetically distant from O. ochengi and O. volvulus. Based on molecular genetic markers and apparent interbreeding, we later proposed that O. sp. "Siisa" belongs to the species O. ochengi. However, we did not demonstrate directly that the hybrids were fertile, and we were still unable to resolve the phylogenetic relationship of O. ochengi, O. sp. "Siisa," and O. volvulus, leaving some concerns with the conclusion mentioned above. Here, we present fully assembled, manually curated mitochondrial genomes of O. ochengi and O. sp. "Siisa," and we compare multiple individuals of these two taxa with respect to their whole mitochondrial and nuclear genomes. Based on the mitochondrial genomes, O. ochengi and O. sp. "Siisa" are phylogenetically much closer to each other than to O. volvulus. The differences between them are well within the range of what is expected for within-species variation. The nuclear genome comparison provided no indication of genetic separation of O. ochengi and O. sp. "Siisa." From this, in combination with the earlier literature, we conclude that O. ochengi and O. sp. "Siisa" should be considered one species.}, }
@article {pmid29401406, year = {2018}, author = {Abboud, TG and Zubaer, A and Wai, A and Hausner, G}, title = {The complete mitochondrial genome of the Dutch elm disease fungus Ophiostoma novo-ulmi subsp. novo-ulmi.}, journal = {Canadian journal of microbiology}, volume = {64}, number = {5}, pages = {339-348}, doi = {10.1139/cjm-2017-0605}, pmid = {29401406}, issn = {1480-3275}, mesh = {Base Sequence ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Fungal Proteins/genetics ; Genes, Fungal ; *Genome, Mitochondrial ; Mitochondria/genetics ; Open Reading Frames ; Ophiostoma/*genetics ; Phylogeny ; Plant Diseases/*microbiology ; Ulmus/microbiology ; }, abstract = {Ophiostoma novo-ulmi, a member of the Ophiostomatales (Ascomycota), is the causal agent of the current Dutch elm disease pandemic in Europe and North America. The complete mitochondrial genome (mtDNA) of Ophiostoma novo-ulmi subsp. novo-ulmi, the European component of O. novo-ulmi, has been sequenced and annotated. Gene order (synteny) among the currently available members of the Ophiostomatales was examined and appears to be conserved, and mtDNA size variability among the Ophiostomatales is due in part to the presence of introns and their encoded open reading frames. Phylogenetic analysis of concatenated mitochondrial protein-coding genes yielded phylogenetic estimates for various members of the Ophiostomatales, with strong statistical support showing that mtDNA analysis may provide valuable insights into the evolution of the Ophiostomatales.}, }
@article {pmid29400318, year = {2018}, author = {Luo, F and Shinzawa-Itoh, K and Hagimoto, K and Shimada, A and Shimada, S and Yamashita, E and Yoshikawa, S and Tsukihara, T}, title = {Structure of bovine cytochrome c oxidase in the ligand-free reduced state at neutral pH.}, journal = {Acta crystallographica. Section F, Structural biology communications}, volume = {74}, number = {Pt 2}, pages = {92-98}, pmid = {29400318}, issn = {2053-230X}, support = {JPMJCR12M3//Japan Science and Technology Agency, Core Research for Evolutional Science and Technology/International ; 26291033//Japan Society for the Promotion of Science/International ; 15K18493//Japan Society for the Promotion of Science/International ; }, mesh = {Animals ; Cattle ; Electron Transport Complex IV/*chemistry/*metabolism ; Hydrogen-Ion Concentration ; Ligands ; Oxidation-Reduction ; Protein Structure, Secondary ; Protein Structure, Tertiary ; X-Ray Diffraction/methods ; }, abstract = {Cytochrome c oxidase (CcO), the terminal oxidase in cellular respiration, couples proton pumping to O2 reduction. Mammalian CcO resides in the inner mitochondrial membrane. Previously, a model of H-pathway proton pumping was proposed based on various CcO crystal structures. However, all previously determined structures were solved using crystals obtained at pH 5.7, which differs from the environmental pH of CcO in the inner membrane. The structures of fully oxidized and ligand-free reduced CcO at pH 7.3 have now been determined. Structural comparison between the oxidized and reduced states revealed that the structural alterations that occurred upon redox change at pH 5.7 in Asp51, the magnesium-containing cluster, haem groups and helix X, which provide important structural evidence for the H-pathway proton-pumping proposal, also occur at pH 7.3. These structural alterations were restricted to a local region of CcO; no domain movement was detected, nor were significant structural alterations detected in peripheral regions at either pH value. These observations indicate that the small and precise structural alterations that occur over the course of the reaction cycle are not affected by pH change, and that isolated CcO precisely performs proton pumping via the H-pathway over a wide pH range. Because the pH is not uniform across the molecular surface of CcO, the fact that the overall structure of CcO is not affected by pH changes ensures the high enzymatic efficiency of this protein in the mitochondria.}, }
@article {pmid29385875, year = {2018}, author = {Mustafa, SI and Schwarzacher, T and Heslop-Harrison, JS}, title = {Complete mitogenomes from Kurdistani sheep: abundant centromeric nuclear copies representing diverse ancestors.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {8}, pages = {1180-1193}, doi = {10.1080/24701394.2018.1431226}, pmid = {29385875}, issn = {2470-1408}, mesh = {Animals ; Breeding ; Centromere/*genetics ; *Evolution, Molecular ; Female ; *Genetic Speciation ; *Genome, Mitochondrial ; Male ; Polymorphism, Single Nucleotide ; Sex Chromosomes/genetics ; Sheep/*genetics ; }, abstract = {The geographical centre of domestication and species diversity for sheep (Ovis aries) lies around the Kurdistan region of Northern Iraq, within the 'Fertile Crescent'. From whole genome sequence reads, we assembled the mitochondrial genomes (mtDNA or mitogenome) of five animals of the two main Kurdistani sheep breeds Hamdani and Karadi and found they fitted into known sheep haplogroups (or matrilineages), with some SNPs. Haplotyping 31 animals showed presence of the main Asian (hpgA) and European (hpgB) haplogroups, as well as the rarer Anatolian haplogroup hpgC. From the sequence reads, near-complete genomes of mitochondria from wild sheep species (or subspecies), and even many sequences similar to goat (Capra) mitochondria, could be extracted. Analysis suggested that these polymorphic reads were nuclear mitochondrial DNA segments (numts). In situ hybridization with seven regions of mitochondria chosen from across the whole genome showed strong hybridization to the centromeric regions of all autosomal sheep chromosomes, but not the Y. Centromeres of the three submetacentric pairs and the X chromosomes showed fewer copies of numts, with varying abundance of different mitochondrial regions. Some mitochondrial-nuclear transfer presumably occurred before species divergence within the genus, and there has been further introgression of sheep mitochondrial sequences more recently. This high abundance of nuclear mitochondrial sequences is not reflected in the whole nuclear genome assemblies, and the accumulation near major satellite sequences at centromeres was unexpected. Mitochondrial variants including SNPs, numts and heteroplasmy must be rigorously validated to interpret correctly mitochondrial phylogenies and SNPs.}, }
@article {pmid29383422, year = {2018}, author = {Yu, H and Wang, D and Zou, L and Zhang, Z and Xu, H and Zhu, F and Ren, X and Xu, B and Yuan, J and Liu, J and Spencer, PS and Yang, X}, title = {Proteomic alterations of brain subcellular organelles caused by low-dose copper exposure: implication for Alzheimer's disease.}, journal = {Archives of toxicology}, volume = {92}, number = {4}, pages = {1363-1382}, doi = {10.1007/s00204-018-2163-6}, pmid = {29383422}, issn = {1432-0738}, support = {2014A030313715//National Natural Science Foundation of China/ ; }, mesh = {Alzheimer Disease/*chemically induced/*metabolism ; Animals ; Brain/*drug effects/metabolism/ultrastructure ; Copper/*toxicity ; Hippocampus/drug effects/metabolism/ultrastructure ; Memory Disorders ; Mice ; Mice, Transgenic ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Proteomics ; Spatial Memory ; }, abstract = {Excessive copper intake can lead to neurotoxicity, but there is a lack of comprehensive understanding on the potential impact of copper exposure especially at a low-dose on brain. We used 3xTg-AD mice to explore the potential neurotoxicity of chronic, low-dose copper treatment (0.13 ppm copper chloride in drinking water) on behavior and the brain hippocampal mitochondrial and nuclear proteome. Low-dose copper increased the spatial memory impairment of these animals, increased accumulation of intracellular amyloid 1-42 (Aβ1-42), decreased ATP content, increased the positive staining of 8-hydroxyguanosine (8-OHdG), a marker of DNA oxidative damage, and caused apoptosis and a decrease in synaptic proteins. Mitochondrial proteomic analysis by two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) revealed modulation of 24 hippocampal mitochondrial proteins (14 increased and 10 decreased) in copper-treated vs. untreated 3xTg-AD mice. Nuclear proteomic analysis revealed 43 modulated hippocampal nuclear proteins (25 increased and 18 decreased) in copper-treated 3xTg-AD vs. untreated mice. Classification of modulated mitochondrial and nuclear proteins included functional categories such as energy metabolism, synaptic-related proteins, DNA damage and apoptosis-related proteins, and oxidative stress-related proteins. Among these differentially expressed mitochondrial and nuclear proteins, nine proteins were abnormally expressed in both hippocampus mitochondria and nuclei, including electron transport chain-related proteins NADH dehydrogenase 1 alpha subcomplex subunit 10 (NDUAA), cytochrome b-c1 complex subunit Rieske (UCRI), cytochrome c oxidase subunit 5B (COX5B), and ATP synthase subunit d (ATP5H), glycolytic-related pyruvate kinase PKM (KPYM) and pyruvate dehydrogenase E1 component subunit alpha (ODPA). Furthermore, we found coenzyme Q10 (CoQ10), an endogenous mitochondrial protective factor/antioxidant, modulated the expression of 12 differentially expressed hippocampal proteins (4 increased and 8 decreased), which could be classified in functional categories such as glycolysis and synaptic-related proteins, oxidative stress-related proteins, implying that CoQ10 improved synaptic function, suppress oxidative stress, and regulate glycolysis. For the proteomics study, we validated the expression of several proteins related to synapses, DNA and apoptosis. The data confirmed that synapsin-2, a synaptic-related protein, was significantly decreased in both mitochondria and nuclei of copper-exposed 3xTg-AD mice. In mitochondria, dynamin-1 (DYN1), an apoptosis-related proteins, was significantly decreased. In the cellular nuclei, paraspeckle protein 1 (PSPC1) and purin-rich element-binding protein alpha (Purα), two DNA damage-related proteins, were significantly decreased and increased, respectively. We conclude that low-dose copper exposure exacerbates the spatial memory impairment of 3xTg-AD mice and perturbs multiple biological/pathogenic processes by dysregulating the mitochondrial and nuclear proteome. Exposure to copper might therefore contribute to the evolution of AD.}, }
@article {pmid29382768, year = {2018}, author = {Zachar, I and Szilágyi, A and Számadó, S and Szathmáry, E}, title = {Farming the mitochondrial ancestor as a model of endosymbiotic establishment by natural selection.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {7}, pages = {E1504-E1510}, pmid = {29382768}, issn = {1091-6490}, support = {294332/ERC_/European Research Council/International ; }, mesh = {Animals ; Bacteria/pathogenicity ; *Biological Evolution ; Computational Biology ; Erythrocytes/*microbiology ; Eukaryota ; Humans ; Mitochondria/*physiology ; *Models, Biological ; Predatory Behavior ; *Selection, Genetic ; Symbiosis/*physiology ; }, abstract = {The origin of mitochondria was a major evolutionary transition leading to eukaryotes, and is a hotly debated issue. It is unknown whether mitochondria were acquired early or late, and whether it was captured via phagocytosis or syntrophic integration. We present dynamical models to directly simulate the emergence of mitochondria in an ecoevolutionary context. Our results show that regulated farming of prey bacteria and delayed digestion can facilitate the establishment of stable endosymbiosis if prey-rich and prey-poor periods alternate. Stable endosymbiosis emerges without assuming any initial metabolic benefit provided by the engulfed partner, in a wide range of parameters, despite that during good periods farming is costly. Our approach lends support to the appearance of mitochondria before any metabolic coupling has emerged, but after the evolution of primitive phagocytosis by the urkaryote.}, }
@article {pmid29381758, year = {2018}, author = {Song, N and Lin, A and Zhao, X}, title = {Insight into higher-level phylogeny of Neuropterida: Evidence from secondary structures of mitochondrial rRNA genes and mitogenomic data.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0191826}, pmid = {29381758}, issn = {1932-6203}, mesh = {Animals ; Genes, Insect ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Neoptera/*classification/genetics ; Nucleic Acid Conformation ; *Phylogeny ; RNA, Ribosomal/*genetics ; }, abstract = {It is well known that the rRNA structure information is important to assist phylogenetic analysis through identifying homologous positions to improve alignment accuracy. In addition, the secondary structure of some conserved motifs is highly stable among distantly related taxa, which can provide potentially informative characters for estimating phylogeny. In this paper, we applied the high-throughput pooled sequencing approach to the determination of neuropteran mitogenomes. Four complete mitogenome sequences were obtained: Micromus angulatus (Hemerobiidae), Chrysoperla nipponensis (Chrysopidae), Rapisma sp. (Ithonidae), and Thaumatosmylus sp. (Osmylidae). This allowed us to sample more complete mitochondrial RNA gene sequences. Secondary structure diagrams for the complete mitochondrial small and large ribosomal subunit RNA genes of eleven neuropterid species were predicted. Comparative analysis of the secondary structures indicated a closer relationship of Megaloptera and Neuroptera. This result was congruent with the resulting phylogeny inferred from sequence alignments of all 37 mitochondrial genes, namely the hypothesis of (Raphidioptera + (Megaloptera + Neuroptera)).}, }
@article {pmid29374514, year = {2018}, author = {Godahewa, GI and Perera, NCN and Nam, BH and Lee, J}, title = {Antioxidative properties and structural features of atypical 2-Cys peroxiredoxin from Sebastes schlegelii.}, journal = {Developmental and comparative immunology}, volume = {82}, number = {}, pages = {152-164}, doi = {10.1016/j.dci.2018.01.015}, pmid = {29374514}, issn = {1879-0089}, mesh = {Animals ; Antioxidants ; Cloning, Molecular ; Cysteine/genetics ; Fish Proteins/*genetics/metabolism ; Fishes/*metabolism ; Gills/*metabolism ; Insulin/metabolism ; Liver/*metabolism ; Mitochondria/*metabolism ; Oxidation-Reduction ; Oxidative Stress ; Peroxiredoxins/*genetics/metabolism ; Phylogeny ; Reactive Oxygen Species/metabolism ; Streptococcal Infections/*immunology ; Streptococcus iniae/*immunology ; Structure-Activity Relationship ; Transcriptome ; Vertebrates ; }, abstract = {Atypical 2-Cys peroxiredoxin (Prx5) is an antioxidant protein that exerts its antioxidant function by detoxifying different reactive oxygen species (ROS). Here, we identified mitochondrial Prx5 from rockfish (SsPrx5) and described its specific structural and functional characteristics. The open reading frame (ORF) of SsPrx5 (570 bp) was translated into a 190-amino acid polypeptide that contained a mitochondrial targeting sequence (MTS), thioredoxin 2 domain, two Prx-specific signature motifs, and three conserved cysteine residues. Sequence comparison indicated that the SsPrx5 protein sequence shared greatest identity with teleost orthologs, where the phylogenetic results showed an evolutionary position within the fish Prx5. The coding sequence of SsPrx5 was scattered in six exons as found in other vertebrates. Additionally, the potent antioxidant functions of recombinantly expressed SsPrx5 protein was demonstrated by insulin reduction and extracellular H2O2 scavenging both in vitro and in vivo. Quantitative real time PCR (qPCR) detected ubiquitous mRNA expression of SsPrx5 in healthy rockfish tissues, with remarkable expression observed in gill, liver, and reproductive tissues. Prompt transcription of SsPrx5 was shown in the immune-stimulated gill and liver tissues against Streptococcus iniae and lipopolysaccharide injection. Taken together, present results suggest the indispensable role of SsPrx5 in the rockfish antioxidant defense system against oxidative stresses and its role in maintaining redox balance upon pathogen invasion.}, }
@article {pmid29374209, year = {2018}, author = {Giordano, L and Sillo, F and Garbelotto, M and Gonthier, P}, title = {Mitonuclear interactions may contribute to fitness of fungal hybrids.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1706}, pmid = {29374209}, issn = {2045-2322}, mesh = {*Adaptation, Biological ; Basidiomycota/*genetics/*growth &amp; development ; DNA, Mitochondrial/*genetics ; *Genetic Fitness ; *Hybrid Vigor ; *Recombination, Genetic ; }, abstract = {Hybridization between species is being recognized as a major force in the rapid adaptive evolution of fungal plant pathogens. The first stages of interspecific hybridization necessarily involve nuclear-mitochondrial chimeras. In their 2001 publication, Olson and Stenlid reported that mitochondria control the virulence of first generation hybrids between the North American fungal pathogen Heterobasidion irregulare and its congeneric H. occidentale. By assessing saprobic ability and gene expression of H. irregulare × H. annosum sensu stricto hybrids and of their parental genotypes, we demonstrate that mitochondria also influence saprobic growth of hybrids. Moreover, gene expression data suggest that fungal fitness is modulated by an intimate interplay between nuclear genes and mitochondrial type, and is dependent on the specific mitonuclear combination.}, }
@article {pmid29370159, year = {2018}, author = {Lane, N}, title = {Hot mitochondria?.}, journal = {PLoS biology}, volume = {16}, number = {1}, pages = {e2005113}, pmid = {29370159}, issn = {1545-7885}, mesh = {Animals ; Energy Metabolism ; Fluorescent Dyes ; Hot Temperature ; Humans ; Membrane Proteins ; Mitochondria/*physiology ; Temperature ; Thermogenesis/*physiology ; Xanthenes ; }, abstract = {Mitochondria generate most of the heat in endotherms. Given some impedance of heat transfer across protein-rich bioenergetic membranes, mitochondria must operate at a higher temperature than body temperature in mammals and birds. But exactly how much hotter has been controversial, with physical calculations suggesting that maximal heat gradients across cells could not be greater than 10(-5) K. Using the thermosensitive mitochondrial-targeted fluorescent dye Mito Thermo Yellow (MTY), Chrétien and colleagues suggest that mitochondria are optimised to nearly 50 °C, 10 °C hotter than body temperature. This extreme value questions what temperature really means in confined far-from-equilibrium systems but encourages a reconsideration of thermal biology.}, }
@article {pmid29362421, year = {2018}, author = {Carreras, C and Pascual, M and Tomás, J and Marco, A and Hochscheid, S and Castillo, JJ and Gozalbes, P and Parga, M and Piovano, S and Cardona, L}, title = {Sporadic nesting reveals long distance colonisation in the philopatric loggerhead sea turtle (Caretta caretta).}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1435}, pmid = {29362421}, issn = {2045-2322}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Ecosystem ; Mediterranean Sea ; *Microsatellite Repeats ; Mitochondria/genetics ; *Nesting Behavior ; Population Dynamics ; Sequence Analysis, DNA/*methods ; Temperature ; Turtles/genetics/*physiology ; }, abstract = {The colonisation of new suitable habitats is crucial for species survival at evolutionary scale under changing environmental conditions. However, colonisation potential may be limited by philopatry that facilitates exploiting successful habitats across generations. We examine the mechanisms of long distance dispersal of the philopatric loggerhead sea turtle (Caretta caretta) by analysing 40 sporadic nesting events in the western Mediterranean. The analysis of a fragment of the mitochondrial DNA and 7 microsatellites of 121 samples from 18 of these nesting events revealed that these nests were colonising events associated with juveniles from distant populations feeding in nearby foraging grounds. Considering the temperature-dependent sex determination of the species, we simulated the effect of the incubation temperature and propagule pressure on a potential colonisation scenario. Our results indicated that colonisation will succeed if warm temperature conditions, already existing in some of the beaches in the area, extend to the whole western Mediterranean. We hypothesize that the sporadic nesting events in developmental foraging grounds may be a mechanism to overcome philopatry limitations thus increasing the dispersal capabilities of the species and the adaptability to changing environments. Sporadic nesting in the western Mediterranean can be viewed as potential new populations in a scenario of rising temperatures.}, }
@article {pmid29360606, year = {2018}, author = {Hou, CC and Gao, XM and Ni, J and Mu, DL and Yang, HY and Liu, C and Zhu, JQ}, title = {The expression pattern and potential functions of PHB in the spermiogenesis of Phascolosoma esculenta.}, journal = {Gene}, volume = {652}, number = {}, pages = {25-38}, doi = {10.1016/j.gene.2018.01.056}, pmid = {29360606}, issn = {1879-0038}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Escherichia coli/genetics/metabolism ; Gene Expression ; Genetic Vectors/chemistry/metabolism ; Male ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Models, Molecular ; Phylogeny ; Polychaeta/classification/*genetics/growth &amp; development/metabolism ; Polyubiquitin/genetics/metabolism ; Prohibitins ; Protein Domains ; Protein Structure, Secondary ; Recombinant Proteins/chemistry/genetics/metabolism ; Repressor Proteins/chemistry/*genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Spermatogenesis/*genetics ; Spermatozoa/growth &amp; development/*metabolism ; }, abstract = {Prohibitin (PHB) is a ubiquitous, evolutionarily conserved protein that is mainly localized in the inner mitochondrial membrane and exerts various mitochondrial functions. Here, we first cloned the phb gene from P. esculenta. The Pe-PHB protein has high homology and a similar protein structure to that of other animals, and it can be divided into the N-terminal hydrophobic/transmembrane domain, SPFH domain, and C-terminal coiled-coil domain. The Pe-phb gene is widely expressed, and the gene expression of phb is highest in coelomic fluid where spermiogenesis occurs, indicating a specific function in the coelom. We further observed continuous expression of the phb gene and localization of PHB proteins in mitochondria during spermiogenesis, indicating that PHB, as a mitochondrial component, may play a role during this process via its mitochondrial function. In addition, ubiquitination of mitochondria was detected, and the PHB signal was co-localized with the poly-ubiquitin signal during spermiogenesis. Mature sperm also showed ubiquitination of mitochondria and PHB. Therefore, PHB may be a substrate of poly-ubiquitin to regulate the ubiquitination of mitochondria and even subsequent elimination during P. esculenta spermiogenesis, and it has a potential role in guaranteeing the maternal inheritance of mitochondria. Taken together, these results support the hypothesis that PHB participates in the spermiogenesis of P. esculenta by maintaining the normal function of mitochondria and regulating the degradation of mitochondria.}, }
@article {pmid29359358, year = {2018}, author = {Zhang, MY and Wei, D and Li, R and Jia, HT and Liu, YW and Taning, CNT and Wang, JJ and Smagghe, G}, title = {Cytoplasmic glutamine synthetase gene expression regulates larval development in Bactrocera dorsalis (Hendel).}, journal = {Archives of insect biochemistry and physiology}, volume = {97}, number = {4}, pages = {}, doi = {10.1002/arch.21447}, pmid = {29359358}, issn = {1520-6327}, mesh = {Amino Acid Sequence ; Animals ; Female ; Glutamate-Ammonia Ligase/genetics/*metabolism ; Insect Proteins/metabolism ; Larva/enzymology/growth &amp; development ; Methionine Sulfoximine ; Phylogeny ; RNA Interference ; Tephritidae/*enzymology/genetics/*growth &amp; development ; }, abstract = {In insects, glutamine synthetase (GS), a key enzyme in the synthesis of glutamine, has been reported to be associated with embryonic development, heat shock response, and fecundity regulation. However, little is known about the influence of GS on postembryonic development. In this study, we demonstrate that blocking the activity of GS in the oriental fruit fly (Bactrocera dorsalis) with use of a GS-specific inhibitor (L-methionine S-sulfoximine), led to a significant delay in larval development, pupal weight loss, and inhibition of pupation. We further identify cloned and characterized two GS genes (BdGS-c and BdGS-m) from B. dorsalis. The two GS genes identified in B. dorsalis were predicted to be located in the cytosol (BdGS-c) and mitochondria (BdGS-m), and homology analysis indicated that both genes were similar to homologs from other Dipterans, such as Drosophila melanogaster and Aedes aegypti. BdGS-c was highly expressed in the larval stages, suggesting that cytosolic GS plays a predominant role in larval development. Furthermore, RNA interference experiments against BdGS-c, to specifically decrease the expression of cytosolic GS, resulted in delay in larval development as well as pupal weight loss. This study presents the prominent role played by BdGS-c in regulating larval development and suggests that the observed effect could have been modulated through ecdysteroid synthesis, agreeing with the reduced expression of the halloween gene spook. Also, the direct effects of BdGS-c silencing on B. dorsalis, such as larval lethality, delayed pupation, and late emergence, can be further exploited as novel insecticide target in the context of pest management.}, }
@article {pmid29359182, year = {2018}, author = {Shevade, A and Strogolova, V and Orlova, M and Yeo, CT and Kuchin, S}, title = {Mitochondrial Voltage-Dependent Anion Channel Protein Por1 Positively Regulates the Nuclear Localization of Saccharomyces cerevisiae AMP-Activated Protein Kinase.}, journal = {mSphere}, volume = {3}, number = {1}, pages = {}, pmid = {29359182}, issn = {2379-5042}, abstract = {Snf1 protein kinase of the yeast Saccharomyces cerevisiae is a member of the highly conserved eukaryotic AMP-activated protein kinase (AMPK) family, which is involved in regulating responses to energy limitation. Under conditions of carbon/energy stress, such as during glucose depletion, Snf1 is catalytically activated and enriched in the nucleus to regulate transcription. Snf1 catalytic activation requires phosphorylation of its conserved activation loop threonine (Thr210) by upstream kinases. Catalytic activation is also a prerequisite for Snf1's subsequent nuclear enrichment, a process that is mediated by Gal83, one of three alternate β-subunits of the Snf1 kinase complex. We previously reported that the mitochondrial voltage-dependent anion channel (VDAC) proteins Por1 and Por2 play redundant roles in promoting Snf1 catalytic activation by Thr210 phosphorylation. Here, we show that the por1Δ mutation alone, which by itself does not affect Snf1 Thr210 phosphorylation, causes defects in Snf1 and Gal83 nuclear enrichment and Snf1's ability to stimulate transcription. We present evidence that Por1 promotes Snf1 nuclear enrichment by promoting the nuclear enrichment of Gal83. Overexpression of Por2, which is not believed to have channel activity, can suppress the localization and transcription activation defects of the por1Δ mutant, suggesting that the regulatory role played by Por1 is separable from its channel function. Thus, our findings expand the positive roles of the yeast VDACs in carbon/energy stress signaling upstream of Snf1. Since AMPK/Snf1 and VDAC proteins are conserved in evolution, our findings in yeast may have implications for AMPK regulation in other eukaryotes, including humans. IMPORTANCE AMP-activated protein kinases (AMPKs) sense energy limitation and regulate transcription and metabolism in eukaryotes from yeast to humans. In mammals, AMPK responds to increased AMP-to-ATP or ADP-to-ATP ratios and is implicated in diabetes, heart disease, and cancer. Mitochondria produce ATP and are generally thought to downregulate AMPK. Indeed, some antidiabetic drugs activate AMPK by affecting mitochondrial respiration. ATP release from mitochondria is mediated by evolutionarily conserved proteins known as voltage-dependent anion channels (VDACs). One would therefore expect VDACs to serve as negative regulators of AMPK. However, our experiments in yeast reveal the existence of an opposite relationship. We previously showed that Saccharomyces cerevisiae VDACs Por1 and Por2 positively regulate AMPK/Snf1 catalytic activation. Here, we show that Por1 also plays an important role in promoting AMPK/Snf1 nuclear localization. Our counterintuitive findings could inform research in areas ranging from diabetes to cancer to fungal pathogenesis.}, }
@article {pmid29358597, year = {2018}, author = {Eimanifar, A and Kimball, RT and Braun, EL and Ellis, JD}, title = {Mitochondrial genome diversity and population structure of two western honey bee subspecies in the Republic of South Africa.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {1333}, pmid = {29358597}, issn = {2045-2322}, mesh = {Animals ; Bees/*classification/cytology/genetics ; Evolution, Molecular ; Genetic Variation ; *Genome, Mitochondrial ; Haplotypes ; Introduced Species ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; South Africa ; }, abstract = {Apis mellifera capensis Eschscholtz and A.m. scutellata Lepeletier are subspecies of western honey bees that are indigenous to the Republic of South Africa (RSA). Both subspecies have invasive potential and are organisms of concern for areas outside their native range, though they are important bees to beekeepers, agriculture, and the environment where they are native. The aim of the present study was to examine genetic differentiation among these subspecies and estimate their phylogenetic relationships using complete mitochondrial genomes sequences. We used 25 individuals that were either assigned to one of the subspecies or designated hybrids using morphometric analyses. Phylogenetic analyses of mitogenome sequences by maximum likelihood (ML) and Bayesian inference identified a monophyletic RSA clade, subdivided into two clades. A haplotype network was consistent with the phylogenetic trees. However, members of both subspecies occurred in both clades, indicating that A.m. capensis and A.m. scutellata are neither reciprocally monophyletic nor do they exhibit paraphyly with one subspecies nested within the other subspecies. Furthermore, no mitogenomic features were diagnostic to either subspecies. All bees analyzed from the RSA expressed a substantial level of haplotype diversity (most samples had unique haplotypes) but limited nucleotide diversity. The number of variable codons across protein-coding genes (PCGs) differed among loci, with CO3 exhibiting the most variation and ATP6 the least.}, }
@article {pmid29356455, year = {2017}, author = {Antunes, CD and Lucena, MN and Garçon, DP and Leone, FA and McNamara, JC}, title = {Low salinity-induced alterations in epithelial ultrastructure, Na[+]/K[+]-ATPase immunolocalization and enzyme kinetic characteristics in the gills of the thinstripe hermit crab, Clibanarius vittatus (Anomura, Diogenidae).}, journal = {Journal of experimental zoology. Part A, Ecological and integrative physiology}, volume = {327}, number = {6}, pages = {380-397}, doi = {10.1002/jez.2109}, pmid = {29356455}, issn = {2471-5646}, mesh = {Animals ; Anomura/*drug effects/physiology ; Enzymes/*metabolism ; Epithelial Cells ; Epithelium/*ultrastructure ; Gills/*drug effects/physiology ; Protein Transport/drug effects/physiology ; *Salinity ; Sodium/chemistry/pharmacology ; Sodium-Potassium-Exchanging ATPase/*metabolism ; }, abstract = {Fresh caught Clibanarius vittatus [SW, 31‰ salinity (S)] were acclimated to a dilute medium (15‰ S) for 10 days, employing silver staining to locate gill ion transporting tissue, immunofluorescence to localize the Na[+]/K[+]-ATPase α-subunit in the lamellae, and electron microscopy to portray ultrastructural changes in the gill epithelia. Na[+]/K[+]-ATPase activity was characterized kinetically in a gill microsomal fraction, including synergistic stimulation by NH4[+] plus K[+]. Silver staining revealed that all 26 phyllobranchiate arthro- and pleurobranchiae participate in ion transport. Na[+]/K[+]-ATPase α-subunit staining was weak in SW crabs and distributed exclusively and irregularly within the intralamellar septal cells, particularly at the septal-pillar cell body junctions, and septal cell cytoplasm facing the hemolymph space. In 15‰ S crabs, α-subunit localization was intense, occupying the entire thickened septum. Pillar cells and flanges did not stain. Mitochondria and membrane foldings increased in the pillar cell flanges and intralamellar septal cells, greatly amplifying surface area. Only a single ATP binding site (VM = 130.8 ± 10.5 nmol min[-1] mg protein[-1]; K0.5 = 55.3 ± 1.7 μmol l[-1]) obeying Michaelis-Menten kinetics was disclosed. Na[+]/K[+]-ATPase activity was modulated by Mg[2+], Na[+], and NH4[+], exhibiting site-site interactions; K[+] modulation showed Michaelis-Menten kinetics. K[+] plus NH4[+] synergistically stimulated activity ≈ 1.7-fold. Ouabain inhibited total ATPase activity by ≈ 70% (KI = 220-300 μmol l[-1]), revealing phosphohydrolytic activities other than the Na[+]/K[+]-ATPase. Despite ample phylogenetic separation, the phyllobranchiate lamellae of the Anomura and Caridea share many ultrastructural features, that is, an intralamellar septum and opposed abutting pillar cells, similar Na[+]/K[+]-ATPase distribution, and comparable kinetic characteristics. These findings suggest either convergent evolution at the structural and biochemical levels, or preservation of traits present in a remote common ancestor.}, }
@article {pmid29343698, year = {2018}, author = {Li, X and Zhou, TC and Wu, CH and Tao, LL and Bi, R and Chen, LJ and Deng, DY and Liu, C and Otecko, NO and Tang, Y and Lai, X and Zhang, L and Wei, J}, title = {Correlations between mitochondrial DNA haplogroup D5 and chronic hepatitis B virus infection in Yunnan, China.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {869}, pmid = {29343698}, issn = {2045-2322}, mesh = {Adult ; Biomarkers ; Case-Control Studies ; China ; *DNA, Mitochondrial ; Female ; *Haplotypes ; *Hepatitis B virus ; Hepatitis B, Chronic/*genetics/metabolism/*virology ; Humans ; Liver Function Tests ; Male ; Middle Aged ; Odds Ratio ; Viral Load ; }, abstract = {Mitochondrial abnormality is frequently reported in individuals with hepatitis B virus (HBV) infection, but the associated hosts' mitochondrial genetic factors remain obscure. We hypothesized that mitochondria may affect host susceptibility to HBV infection. In this study, we aimed to detect the association between chronic HBV infection and mitochondrial DNA in Chinese from Yunnan, Southwest China. A total of 272 individuals with chronic HBV infection (CHB), 310 who had never been infected by HBV (healthy controls, HC) and 278 with a trace of HBV infection (spontaneously recovered, SR) were analysed for mtDNA sequence variations and classified into respective haplogroups. Haplogroup frequencies were compared between HBV infected patients, HCs and SRs. Haplogroup D5 presented a higher frequency in CHBs than in HCs (P = 0.017, OR = 2.87, 95% confidence interval [CI] = (1.21-6.81)) and SRs (P = 0.049, OR = 2.90, 95% CI = 1.01-8.35). The network of haplogroup D5 revealed a distinct distribution pattern between CHBs and non-CHBs. A trend of higher viral load among CHBs with haplogroup D5 was observed. Our results indicate the risk potential of mtDNA haplogroup D5 in chronic HBV infection in Yunnan, China.}, }
@article {pmid29343499, year = {2018}, author = {Wilton, PR and Zaidi, A and Makova, K and Nielsen, R}, title = {A Population Phylogenetic View of Mitochondrial Heteroplasmy.}, journal = {Genetics}, volume = {208}, number = {3}, pages = {1261-1274}, pmid = {29343499}, issn = {1943-2631}, support = {R01 GM116044/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Bayes Theorem ; Computer Simulation ; *Genetics, Population ; Mitochondria/*genetics ; *Models, Genetic ; *Phylogeny ; }, abstract = {The mitochondrion has recently emerged as an active player in myriad cellular processes. Additionally, it was recently shown that >200 diseases are known to be linked to variants in mitochondrial DNA or in nuclear genes interacting with mitochondria. This has reinvigorated interest in its biology and population genetics. Mitochondrial heteroplasmy, or genotypic variation of mitochondria within an individual, is now understood to be common in humans and important in human health. However, it is still not possible to make quantitative predictions about the inheritance of heteroplasmy and its proliferation within the body, partly due to the lack of an appropriate model. Here, we present a population-genetic framework for modeling mitochondrial heteroplasmy as a process that occurs on an ontogenetic phylogeny, with genetic drift and mutation changing heteroplasmy frequencies during the various developmental processes represented in the phylogeny. Using this framework, we develop a Bayesian inference method for inferring rates of mitochondrial genetic drift and mutation at different stages of human life. Applying the method to previously published heteroplasmy frequency data, we demonstrate a severe effective germline bottleneck comprised of the cumulative genetic drift occurring between the divergence of germline and somatic cells in the mother, and the separation of germ layers in the offspring. Additionally, we find that the two somatic tissues we analyze here undergo tissue-specific bottlenecks during embryogenesis, less severe than the effective germline bottleneck, and that these somatic tissues experience little additional genetic drift during adulthood. We conclude with a discussion of possible extensions of the ontogenetic phylogeny framework and its possible applications to other ontogenetic processes in addition to mitochondrial heteroplasmy.}, }
@article {pmid29339819, year = {2018}, author = {Sharma, I and Sharma, V and Khan, A and Kumar, P and Rai, E and Bamezai, RNK and Vilar, M and Sharma, S}, title = {Ancient Human Migrations to and through Jammu Kashmir- India were not of Males Exclusively.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {851}, pmid = {29339819}, issn = {2045-2322}, mesh = {DNA, Mitochondrial/chemistry/classification/metabolism ; Female ; Genetic Variation ; Haplotypes ; *Human Migration ; Humans ; India ; Male ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Jammu and Kashmir (J&amp;K), the Northern most State of India, has been under-represented or altogether absent in most of the phylogenetic studies carried out in literature, despite its strategic location in the Himalayan region. Nonetheless, this region may have acted as a corridor to various migrations to and from mainland India, Eurasia or northeast Asia. The belief goes that most of the migrations post-late-Pleistocene were mainly male dominated, primarily associated with population invasions, where female migration may thus have been limited. To evaluate female-centered migration patterns in the region, we sequenced 83 complete mitochondrial genomes of unrelated individuals belonging to different ethnic groups from the state. We observed a high diversity in the studied maternal lineages, identifying 19 new maternal sub-haplogroups (HGs). High maternal diversity and our phylogenetic analyses suggest that the migrations post-Pleistocene were not strictly paternal, as described in the literature. These preliminary observations highlight the need to carry out an extensive study of the endogamous populations of the region to unravel many facts and find links in the peopling of India.}, }
@article {pmid29338715, year = {2018}, author = {Ramos, B and González-Acuña, D and Loyola, DE and Johnson, WE and Parker, PG and Massaro, M and Dantas, GPM and Miranda, MD and Vianna, JA}, title = {Landscape genomics: natural selection drives the evolution of mitogenome in penguins.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {53}, pmid = {29338715}, issn = {1471-2164}, support = {11110060 and 1150517//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (CL)/International ; INACH T12-13//Instituto Ant&#xe1;rtico Chileno/International ; DI-410-13/I//Universidad Andres Bello/International ; 482501/2013-8 and 490403/2008-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (BR)/International ; 2009/08624//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/International ; ANT 0944411//Directorate for Biological Sciences/International ; C01X1001//Ministry of Science and Innovation, New Zealand/International ; }, mesh = {Animals ; DNA, Mitochondrial/chemistry ; *Evolution, Molecular ; Gene-Environment Interaction ; *Genome, Mitochondrial ; Genomics ; *Selection, Genetic ; Spheniscidae/*genetics ; }, abstract = {BACKGROUND: Mitochondria play a key role in the balance of energy and heat production, and therefore the mitochondrial genome is under natural selection by environmental temperature and food availability, since starvation can generate more efficient coupling of energy production. However, selection over mitochondrial DNA (mtDNA) genes has usually been evaluated at the population level. We sequenced by NGS 12 mitogenomes and with four published genomes, assessed genetic variation in ten penguin species distributed from the equator to Antarctica. Signatures of selection of 13 mitochondrial protein-coding genes were evaluated by comparing among species within and among genera (Spheniscus, Pygoscelis, Eudyptula, Eudyptes and Aptenodytes). The genetic data were correlated with environmental data obtained through remote sensing (sea surface temperature [SST], chlorophyll levels [Chl] and a combination of SST and Chl [COM]) through the distribution of these species.<br><br>RESULTS: We identified the complete mtDNA genomes of several penguin species, including ND6 and 8 tRNAs on the light strand and 12 protein coding genes, 14 tRNAs and two rRNAs positioned on the heavy strand. The highest diversity was found in NADH dehydrogenase genes and the lowest in COX genes. The lowest evolutionary divergence among species was between Humboldt (Spheniscus humboldti) and Galapagos (S. mendiculus) penguins (0.004), while the highest was observed between little penguin (Eudyptula minor) and Ad&#xe9;lie penguin (Pygoscelis adeliae) (0.097). We identified a signature of purifying selection (Ka/Ks&#x2009;<&#x2009;1) across the mitochondrial genome, which is consistent with the hypothesis that purifying selection is constraining mitogenome evolution to maintain Oxidative phosphorylation (OXPHOS) proteins and functionality. Pairwise species maximum-likelihood analyses of selection at codon sites suggest positive selection has occurred on ATP8 (Fixed-Effects Likelihood, FEL) and ND4 (Single Likelihood Ancestral Counting, SLAC) in all penguins. In contrast, COX1 had a signature of strong negative selection. ND4 Ka/Ks ratios were highly correlated with SST (Mantel, p-value: 0.0001; GLM, p-value: 0.00001) and thus may be related to climate adaptation throughout penguin speciation.<br><br>CONCLUSIONS: These results identify mtDNA candidate genes under selection which could be involved in broad-scale adaptations of penguins to their environment. Such knowledge may be particularly useful for developing predictive models of how these species may respond to severe climatic changes in the future.}, }
@article {pmid29337274, year = {2018}, author = {Ballesteros, JA and Hormiga, G}, title = {Species delimitation of the North American orchard-spider Leucauge venusta (Walckenaer, 1841) (Araneae, Tetragnathidae).}, journal = {Molecular phylogenetics and evolution}, volume = {121}, number = {}, pages = {183-197}, doi = {10.1016/j.ympev.2018.01.002}, pmid = {29337274}, issn = {1095-9513}, mesh = {Animals ; Brazil ; Calibration ; Canada ; Ecosystem ; Florida ; Geography ; Male ; Mexico ; Mitochondria/genetics ; North America ; *Phylogeny ; Probability ; Species Specificity ; Spiders/classification/*genetics ; Time Factors ; United States ; }, abstract = {The orchard spider, Leucauge venusta (Walckenaer, 1841) is one of the most common and abundant orb-weavers in North America. This species has a broad geographic distribution extending across tropical and temperate regions of the Americas from Canada to Brazil. Guided by a preliminary observation of the barcode gap between sequences from specimens of L. venusta collected in Florida and other North American localities, we collected across a transect through the southeastern USA to investigate the observed genetic divide. The dataset, complemented with additional samples from Mexico, and Brazil was analyzed for species delimitation using STACEY and bGMYC based on sequences from one nuclear (ITS2) and one mitochondrial marker (COI). The analyses clearly separate USA samples into two deeply divergent and geographically structured groups (north-south) which we interpret as two different species. We generated ecological niche models for these two groups rejecting a niche equivalence hypothesis for these lineages. Taxonomic changes are proposed based on these findings, Leucauge venusta is restricted to denote the northern clade, and its known distribution restricted to the USA. Leucauge argyrobapta (White, 1841) is removed from synonymy to denote the populations in Florida, Mexico and Brazil. Although the delimitation analyses suggest each of these geographic clusters within the L. argyrobapta samples represent different species, more specimens from Central and South America are needed to properly test the cohesion of L. argyrobapta populations.}, }
@article {pmid29335382, year = {2018}, author = {Aviv, A}, title = {The mitochondrial genome, paternal age and telomere length in humans.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {373}, number = {1741}, pages = {}, pmid = {29335382}, issn = {1471-2970}, support = {R01 HL116446/HL/NHLBI NIH HHS/United States ; R01 HD071180/HD/NICHD NIH HHS/United States ; R01 HL134840/HL/NHLBI NIH HHS/United States ; }, mesh = {Biological Evolution ; *Genome, Mitochondrial ; Humans ; Male ; *Paternal Age ; Polymorphism, Genetic ; Reactive Oxygen Species/metabolism ; Spermatozoa/metabolism ; Stem Cells ; Telomere/*metabolism ; *Telomere Homeostasis ; }, abstract = {Telomere length (TL) in humans is highly heritable and undergoes progressive age-dependent shortening in somatic cells. By contrast, sperm donated by older men display comparatively long telomeres, presumably because in the male germline, telomeres become longer with age. This puzzling phenomenon might explain why TL in the offspring correlates positively with paternal age. The present communication proposes that mitochondrial DNA polymorphisms and heteroplasmy cause variation in the production of reactive oxygen species, which, in turn, mediate age-dependent selection of germ stem cells with long telomeres and hence sperm with long telomeres. These long telomeres are then inherited by the offspring. The effect of paternal age on the offspring TL might be an evolutionarily driven mechanism that helps regulate TL across the human population.This article is part of the theme issue 'Understanding diversity in telomere dynamics'.}, }
@article {pmid29334409, year = {2018}, author = {Lamb, AM and Gan, HM and Greening, C and Joseph, L and Lee, YP and Morán-Ordóñez, A and Sunnucks, P and Pavlova, A}, title = {Climate-driven mitochondrial selection: A test in Australian songbirds.}, journal = {Molecular ecology}, volume = {27}, number = {4}, pages = {898-918}, doi = {10.1111/mec.14488}, pmid = {29334409}, issn = {1365-294X}, mesh = {Amino Acids/genetics ; Animals ; Australia ; Bayes Theorem ; *Climate ; Codon/genetics ; Genes, Mitochondrial ; Mitochondria/*genetics ; NADH Dehydrogenase ; Open Reading Frames/genetics ; Phylogeny ; Phylogeography ; *Selection, Genetic ; Songbirds/*genetics ; Species Specificity ; Structural Homology, Protein ; }, abstract = {Diversifying selection between populations that inhabit different environments can promote lineage divergence within species and ultimately drive speciation. The mitochondrial genome (mitogenome) encodes essential proteins of the oxidative phosphorylation (OXPHOS) system and can be a strong target for climate-driven selection (i.e., associated with inhabiting different climates). We investigated whether Pleistocene climate changes drove mitochondrial selection and evolution within Australian birds. First, using phylogeographic analyses of the mitochondrial ND2 gene for 17 songbird species, we identified mitochondrial clades (mitolineages). Second, using distance-based redundancy analyses, we tested whether climate predicts variation in intraspecific genetic divergence beyond that explained by geographic distances and geographic position. Third, we analysed 41 complete mitogenome sequences representing each mitolineage of 17 species using codon models in a phylogenetic framework and a biochemical approach to identify signals of selection on OXPHOS protein-coding genes and test for parallel selection in mitolineages of different species existing in similar climates. Of 17 species examined, 13 had multiple mitolineages (range: 2-6). Climate was a significant predictor of mitochondrial variation in eight species. At least two amino acid replacements in OXPHOS complex I could have evolved under positive selection in specific mitolineages of two species. Protein homology modelling showed one of these to be in the loop region of the ND6 protein channel and the other in the functionally critical helix HL region of ND5. These findings call for direct tests of the functional and evolutionary significance of mitochondrial protein candidates for climate-associated selection.}, }
@article {pmid29330875, year = {2018}, author = {Wai, KT and Barash, M and Gunn, P}, title = {Performance of the Early Access AmpliSeq™ Mitochondrial Panel with degraded DNA samples using the Ion Torrent™ platform.}, journal = {Electrophoresis}, volume = {39}, number = {21}, pages = {2776-2784}, doi = {10.1002/elps.201700371}, pmid = {29330875}, issn = {1522-2683}, mesh = {DNA, Mitochondrial/*genetics ; Female ; Forensic Genetics/*methods ; Heating ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; Mitochondria/genetics ; Nucleic Acid Denaturation ; Phylogeny ; }, abstract = {The Early Access AmpliSeq™ Mitochondrial Panel amplifies whole mitochondrial genomes for phylogenetic and kinship identifications, using Ion Torrent™ technology. There is currently limited information on its performance with degraded DNA, a common occurrence in forensic samples. This study evaluated the performance of the Panel with DNA samples degraded in vitro, to mimic conditions commonly found in forensic investigations. Purified DNA from five individuals was heat-treated at five time points each (125°C for 0, 30, 60, 120, and 240 min; total n = 25). The quality of DNA was assessed via a real-time DNA assay of genomic DNA and prepared for massively parallel sequencing on the Ion Torrent™ platform. Mitochondrial sequences were obtained for all samples and had an amplicon coverage averaging between 66X to 2803X. Most amplicons (157/162) displayed high coverages (452 ± 333X), while reads with less than 100X coverage were recorded in five amplicons only (90 ± 5X). Amplicon coverage was decreased with prolonged heating. At 72% strand balance, reads were well balanced between forward and reverse strands. Using a coverage threshold of ten reads per SNP, complete sequences were recovered in all samples and resolved kinship and, haplogroup relations. Additionally, the HV1 and HV2 regions of the reference and 240-min heat-treated samples (n = 10) were Sanger-sequenced for concordance. Overall, this study demonstrates the efficacy of a novel forensic Panel that recovers high quality mitochondrial sequences from degraded DNA samples.}, }
@article {pmid29318727, year = {2018}, author = {Kaur, B and Valach, M and Peña-Diaz, P and Moreira, S and Keeling, PJ and Burger, G and Lukeš, J and Faktorová, D}, title = {Transformation of Diplonema papillatum, the type species of the highly diverse and abundant marine microeukaryotes Diplonemida (Euglenozoa).}, journal = {Environmental microbiology}, volume = {20}, number = {3}, pages = {1030-1040}, doi = {10.1111/1462-2920.14041}, pmid = {29318727}, issn = {1462-2920}, support = {MOP 70309//CIHR/Canada ; }, mesh = {Aquatic Organisms ; Drug Resistance ; Euglenozoa/genetics/*physiology ; Eukaryota/genetics ; Gene Expression Regulation ; Mitochondria ; Phylogeny ; Puromycin/pharmacology ; RNA, Messenger/genetics/metabolism ; *Transformation, Genetic ; }, abstract = {Diplonema papillatum is the type species of diplonemids, which are among the most abundant and diverse heterotrophic microeukaryotes in the world's oceans. Diplonemids are also known for a unique form of post-transcriptional processing in mitochondria. However, the lack of reverse genetics methodologies in these protists has hampered elucidation of their cellular and molecular biology. Here we report a protocol for D. papillatum transformation. We have identified several antibiotics to which D. papillatum is sensitive and thus are suitable selectable markers, and focus in particular on puromycin. Constructs were designed encoding antibiotic resistance markers, fluorescent tags, and additional genomic sequences from D. papillatum to facilitate vector integration into chromosomes. We established conditions for effective electroporation, and demonstrate that electroporated constructs can be stably integrated in the D. papillatum nuclear genome. In D. papillatum transformants, the heterologous puromycin resistance gene is transcribed into mRNA and translated into protein, as determined by Southern hybridization, reverse transcription, and Western blot analyses. This is the first documented case of transformation in a euglenozoan protist outside the well-studied kinetoplastids, making D. papillatum a genetically tractable organism and potentially a model system for marine microeukaryotes.}, }
@article {pmid29312883, year = {2017}, author = {Lemasters, JJ}, title = {Evolution of Voltage-Dependent Anion Channel Function: From Molecular Sieve to Governator to Actuator of Ferroptosis.}, journal = {Frontiers in oncology}, volume = {7}, number = {}, pages = {303}, pmid = {29312883}, issn = {2234-943X}, support = {R01 AA021191/AA/NIAAA NIH HHS/United States ; P30 CA138313/CA/NCI NIH HHS/United States ; P20 GM103542/GM/NIGMS NIH HHS/United States ; R01 DK073336/DK/NIDDK NIH HHS/United States ; R01 CA184456/CA/NCI NIH HHS/United States ; R01 DE016572/DE/NIDCR NIH HHS/United States ; }, abstract = {The voltage-dependent anion channel (VDAC) is well known as the pathway for passive diffusion of anionic hydrophilic mitochondrial metabolites across the outer membrane, but a more complex functionality of the three isoforms of VDAC has emerged, as addressed in the Frontiers in Oncology Research Topic on "Uncovering the Function of the Mitochondrial Protein VDAC in Health and Disease: from Structure-Function to Novel Therapeutic Strategies." VDAC as the single most abundant protein in mitochondrial outer membranes is typically involved in isoform-specific interactions of the mitochondrion with its surroundings as, for example, during mitochondria-dependent pathways of cell death. VDAC closure can also act as an adjustable limiter (governator) of global mitochondrial metabolism, as during hepatic ethanol metabolism to promote selective oxidation of membrane-permeant acetaldehyde. In cancer cells, high free tubulin inhibits VDAC1 and VDAC2, contributing to suppression of mitochondrial function in the Warburg phenomenon. Erastin, the canonical inducer of ferroptosis, opens VDAC in the presence of tubulin and hyperpolarizes mitochondria, leading to mitochondrial production of reactive oxygen species, mitochondrial dysfunction, and cell death. Our understanding of VDAC function continues to evolve.}, }
@article {pmid29307851, year = {2018}, author = {Bai, J and Xu, S and Nie, Z and Wang, Y and Zhu, C and Wang, Y and Min, W and Cai, Y and Zou, J and Zhou, X}, title = {The complete mitochondrial genome of Huananpotamon lichuanense (Decapoda: Brachyura) with phylogenetic implications for freshwater crabs.}, journal = {Gene}, volume = {646}, number = {}, pages = {217-226}, doi = {10.1016/j.gene.2018.01.015}, pmid = {29307851}, issn = {1879-0038}, mesh = {Animals ; Brachyura/*genetics ; Evolution, Molecular ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Male ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Selection, Genetic ; Sequence Analysis, DNA/*methods ; }, abstract = {In the present study, we determined the complete mitochondrial genome of Huananpotamon lichuanense (Decapoda: Brachyura) for the first time. The genome is 15,380bp in length and typically consists of 37 genes. When the gene order was compared to the ancestral crustacean type, two tRNA genes (tRNA[His] and tRNA[Gln]) were rearranged in H. lichuanense, and the translocation of tRNA[Gln] appeared only in Potamoidea crabs, such as Geothelphusa dehaani and Sinopotamon xiushuiense, supporting the monophyly of the Potamoidea superfamily. Thirteen protein-coding genes and 2 rRNA genes were divided into five complexes to perform the phylogenetic analysis, and the results showed that the trees constructed by complex I (ND1-ND6 and ND4L), complex IV (COX1-COX3) and rRNA genes better accord with the morphological classification system, suggesting that molecular markers of higher-level phylogeny can be developed in these three complexes in the future. The estimated divergence time for freshwater crabs is approximately 133.58Ma, and G. dehaani from Japan diverged from the freshwater crabs of mainland China approximately 60.66Ma. A selective pressure analysis based on current data revealed obviously increasing dN/dS ratios (except for ATP6 and ND4L) of freshwater crabs, and the accumulation of nonsynonymous mutations suggests that terrestrial habitats provide a relatively relaxed selective pressure environment for this group.}, }
@article {pmid29301905, year = {2018}, author = {Dai, D and Luan, S and Chen, X and Wang, Q and Feng, Y and Zhu, C and Qi, W and Song, R}, title = {Maize Dek37 Encodes a P-type PPR Protein That Affects cis-Splicing of Mitochondrial nad2 Intron 1 and Seed Development.}, journal = {Genetics}, volume = {208}, number = {3}, pages = {1069-1082}, pmid = {29301905}, issn = {1943-2631}, mesh = {Cloning, Molecular ; *Gene Expression Regulation, Plant ; *Introns ; Mitochondria/genetics ; Mitochondrial Proteins/*genetics ; Mutation ; NADH Dehydrogenase/metabolism ; Phenotype ; Phylogeny ; Plant Proteins/*genetics ; Protein Transport ; *RNA Splicing ; Seeds/*genetics ; Zea mays/*genetics ; }, abstract = {Mitochondrial group II introns require the participation of numerous nucleus-encoded general and specific factors to achieve efficient splicing in vivo Pentatricopeptide repeat (PPR) proteins have been implicated in assisting group II intron splicing. Here, we identified and characterized a new maize seed mutant, defective kernel 37 (dek37), which has significantly delayed endosperm and embryo development. Dek37 encodes a classic P-type PPR protein that targets mitochondria. The dek37 mutation causes no detectable DEK37 protein in mutant seeds. Mitochondrial transcripts analysis indicated that dek37 mutation decreases splicing efficiency of mitochondrial nad2 intron 1, leading to reduced assembly and NADH dehydrogenase activity of complex I. Transmission Electron Microscopy (TEM) revealed severe morphological defects of mitochondria in dek37 Transcriptome analysis of dek37 endosperm indicated enhanced expression in the alternative respiratory pathway and extensive differentially expressed genes related to mitochondrial function. These results indicated that Dek37 is involved in cis-splicing of mitochondrial nad2 intron 1 and is required for complex I assembly, mitochondrial function, and seed development in maize.}, }
@article {pmid29299440, year = {2017}, author = {Awadi, A}, title = {Host species and pathogenicity effects in the evolution of the mitochondrial genomes of Eimeria species (Apicomplexa; Coccidia; Eimeriidae).}, journal = {Journal of biological research (Thessalonike, Greece)}, volume = {24}, number = {}, pages = {13}, pmid = {29299440}, issn = {1790-045X}, abstract = {BACKGROUND: Mitochondria are fundamental organelles responsible for cellular metabolism and energy production in eukaryotes via the oxidative phosphorylation pathway. Mitochondrial DNA is often used in population and species studies with the assumption of neutral evolution. However, evidence of positive selection in mitochondrial coding genes of various animal species has accumulated suggesting that amino acid changes in mtDNA might be adaptive. The functional and physiological implications of the inferred positively selected sites are usually unknown and are only evaluated based on available structural and functional models. Such studies are absent in unicellular organisms that show several crucial differences to the electron transport chain of animal mitochondria. In the present study, we explored Eimeria mitogenomes for positive selection. We also tested for association between mtDNA polymorphism and environmental variation (i.e. host species), parasite life cycle (i.e. sporulation period), and efficient host cell invasion (i.e. pathogenicity, prepatent period).<br><br>FINDINGS: We used site- and branch-site tests to estimate the extent of purifying and positive selection at each site and each lineage of several Eimeria parasite mitogenomes retrieved from GenBank. We founded sixteen codons in the three mtDNA-encoded proteins to be under positive selection compared to a strong purifying selection. Variation in the ratios of non-synonymous to synonymous changes of the studied parasites was associated with their different host species (F&#xa0;=&#xa0;13.748; p&#xa0;<&#xa0;0.001), whereas pathogenicity levels were associated with both synonymous and non-synonymous changes. This association was also confirmed by the multiple regression analysis.<br><br>CONCLUSIONS: Our results suggest that host species and pathogenicity are important factors that might shape mitochondrial variation in Eimeria parasites. This supports the important role of mtDNA variations in the evolution and adaptation of these parasites.}, }
@article {pmid29297348, year = {2017}, author = {Logacheva, MD and Krinitsina, AA and Belenikin, MS and Khafizov, K and Konorov, EA and Kuptsov, SV and Speranskaya, AS}, title = {Comparative analysis of inverted repeats of polypod fern (Polypodiales) plastomes reveals two hypervariable regions.}, journal = {BMC plant biology}, volume = {17}, number = {Suppl 2}, pages = {255}, pmid = {29297348}, issn = {1471-2229}, mesh = {DNA, Plant/genetics ; Genes, Plant/genetics ; Genome, Plant/genetics ; Inverted Repeat Sequences/*genetics ; Phylogeny ; Plastids/*genetics ; Tracheophyta/*genetics ; }, abstract = {BACKGROUND: Ferns are large and underexplored group of vascular plants (~ 11 thousands species). The genomic data available by now include low coverage nuclear genomes sequences and partial sequences of mitochondrial genomes for six species and several plastid genomes.<br><br>RESULTS: We characterized plastid genomes of three species of Dryopteris, which is one of the largest fern genera, using sequencing of chloroplast DNA enriched samples and performed comparative analysis with available plastomes of Polypodiales, the most species-rich group of ferns. We also sequenced the plastome of Adianthum hispidulum (Pteridaceae). Unexpectedly, we found high variability in the IR region, including duplication of rrn16 in D. blanfordii, complete loss of trnI-GAU in D. filix-mas, its pseudogenization due to the loss of an exon in D. blanfordii. Analysis of previously reported plastomes of Polypodiales demonstrated that Woodwardia unigemmata and Lepisorus clathratus have unusual insertions in the IR region. The sequence of these inserted regions has high similarity to several LSC fragments of ferns outside of Polypodiales and to spacer between tRNA-CGA and tRNA-TTT genes of mitochondrial genome of Asplenium nidus. We suggest that this reflects the ancient DNA transfer from mitochondrial to plastid genome occurred in a common ancestor of ferns. We determined the marked conservation of gene content and relative evolution rate of genes and intergenic spacers in the IRs of Polypodiales. Faster evolution of the four intergenic regions had been demonstrated (trnA- orf42, rrn16-rps12, rps7-psbA and ycf2-trnN).<br><br>CONCLUSIONS: IRs of Polypodiales plastomes are dynamic, driven by such events as gene loss, duplication and putative lateral transfer from mitochondria.}, }
@article {pmid29294404, year = {2018}, author = {Qu, M and Tang, W and Liu, Q and Wang, D and Ding, S}, title = {Genetic diversity within grouper species and a method for interspecific hybrid identification using DNA barcoding and RYR3 marker.}, journal = {Molecular phylogenetics and evolution}, volume = {121}, number = {}, pages = {46-51}, doi = {10.1016/j.ympev.2017.12.031}, pmid = {29294404}, issn = {1095-9513}, mesh = {Animals ; Biomarkers/*metabolism ; Cell Nucleus/genetics ; China ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/genetics ; Fishes/*genetics ; *Genetic Variation ; Geography ; *Hybridization, Genetic ; Mitochondria/genetics ; Oceans and Seas ; Phylogeny ; Ryanodine Receptor Calcium Release Channel/*genetics ; Species Specificity ; }, abstract = {Groupers (family Epinephelidae) are an assemblage of coral reef fishes comprising more than 160 species in 16 genera, many of which are both environmentally and economically valuable. Because of their similar morphology, variable color patterns, and tendency for interspecies hybridization, morphological identification of groupers usually leads to taxonomic confusion. To find an effective method for identifying different grouper species and hybrids, evaluate genetic diversity and uncover any synonymous or cryptic species, we sampled a total of 221 specimens representing 57 species in 9 genera in the China Seas. Both mitochondrial (mt) cytochrome oxidase subunit I (COI) and NADH dehydrogenase subunit 2 (ND2) were found to be effective barcoding genes. We also developed an efficient protocol for identifying hybrid groupers using mt markers and the nuclear RYR3 gene and found the first record of wide interspecies hybridization in genus Epinephelus. This barcoding study revealed high genetic divergence in many widespread species and possible synonyms. In addition to providing a molecular method for identifying grouper species, this study offers important resources for the further study of grouper conservation genetics, speciation, hybridization and other evolutionary traits.}, }
@article {pmid29293597, year = {2018}, author = {Silva, SR and Michael, TP and Meer, EJ and Pinheiro, DG and Varani, AM and Miranda, VFO}, title = {Comparative genomic analysis of Genlisea (corkscrew plants-Lentibulariaceae) chloroplast genomes reveals an increasing loss of the ndh genes.}, journal = {PloS one}, volume = {13}, number = {1}, pages = {e0190321}, pmid = {29293597}, issn = {1932-6203}, mesh = {Chloroplasts/*genetics ; *Genome, Chloroplast ; Magnoliopsida/classification/*genetics ; NADPH Dehydrogenase/*genetics ; Phylogeny ; }, abstract = {In the carnivorous plant family Lentibulariaceae, all three genome compartments (nuclear, chloroplast, and mitochondria) have some of the highest rates of nucleotide substitutions across angiosperms. While the genera Genlisea and Utricularia have the smallest known flowering plant nuclear genomes, the chloroplast genomes (cpDNA) are mostly structurally conserved except for deletion and/or pseudogenization of the NAD(P)H-dehydrogenase complex (ndh) genes known to be involved in stress conditions of low light or CO2 concentrations. In order to determine how the cpDNA are changing, and to better understand the evolutionary history within the Genlisea genus, we sequenced, assembled and analyzed complete cpDNA from six species (G. aurea, G. filiformis, G. pygmaea, G. repens, G. tuberosa and G. violacea) together with the publicly available G. margaretae cpDNA. In general, the cpDNA structure among the analyzed Genlisea species is highly similar. However, we found that the plastidial ndh genes underwent a progressive process of degradation similar to the other terrestrial Lentibulariaceae cpDNA analyzed to date, but in contrast to the aquatic species. Contrary to current thinking that the terrestrial environment is a more stressful environment and thus requiring the ndh genes, we provide evidence that in the Lentibulariaceae the terrestrial forms have progressive loss while the aquatic forms have the eleven plastidial ndh genes intact. Therefore, the Lentibulariaceae system provides an important opportunity to understand the evolutionary forces that govern the transition to an aquatic environment and may provide insight into how plants manage water stress at a genome scale.}, }
@article {pmid29284403, year = {2017}, author = {Wojtkowska, M and Buczek, D and Suzuki, Y and Shabardina, V and Makałowski, W and Kmita, H}, title = {The emerging picture of the mitochondrial protein import complexes of Amoebozoa supergroup.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {997}, pmid = {29284403}, issn = {1471-2164}, support = {MPD/2010/3//Fundacja na rzecz Nauki Polskiej/International ; 01/KNOW2/2014//Polish Ministry of Science and Higher Education/International ; }, mesh = {Acanthamoeba castellanii/genetics ; Amoebozoa/classification/*genetics ; Cells, Cultured ; Dictyostelium/genetics ; Gene Expression Profiling ; Genomics ; Mitochondrial Membrane Transport Proteins/classification/*genetics ; Phylogeny ; Protein Subunits/genetics ; }, abstract = {BACKGROUND: The existence of mitochondria-related organelles (MROs) is proposed for eukaryotic organisms. The Amoebozoa includes some organisms that are known to have mitosomes but also organisms that have aerobic mitochondria. However, the mitochondrial protein apparatus of this supergroup remains largely unsampled, except for the mitochondrial outer membrane import complexes studied recently. Therefore, in this study we investigated the mitochondrial inner membrane and intermembrane space complexes, using the available genome and transcriptome sequences.<br><br>RESULTS: When compared with the canonical cognate complexes described for the yeast Saccharomyces cerevisiae, amoebozoans with aerobic mitochondria, display lower differences in the number of subunits predicted for these complexes than the mitochondrial outer membrane complexes, although the predicted subunits appear to display different levels of diversity in regard to phylogenetic position and isoform numbers. For the putative mitosome-bearing amoebozoans, the number of predicted subunits suggests the complex elimination distinctly more pronounced than in the case of the outer membrane ones.<br><br>CONCLUSION: The results concern the problem of mitochondrial and mitosome protein import machinery structural variability and the reduction of their complexity within the currently defined supergroup of Amoebozoa. This results are crucial for better understanding of the Amoebozoa taxa of both biomedical and evolutionary importance.}, }
@article {pmid29281973, year = {2017}, author = {Chong, RA and Mueller, RL}, title = {Polymorphic duplicate genes and persistent non-coding sequences reveal heterogeneous patterns of mitochondrial DNA loss in salamanders.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {992}, pmid = {29281973}, issn = {1471-2164}, support = {1210900//Division of Environmental Biology/International ; 1021489//Division of Environmental Biology/International ; }, mesh = {Animals ; Cell Nucleus/genetics ; DNA, Intergenic/chemistry ; DNA, Mitochondrial/*chemistry ; *Evolution, Molecular ; Gene Duplication ; *Gene Order ; *Genes, Duplicate ; *Genes, Mitochondrial ; Genes, rRNA ; Genetic Variation ; Mitochondrial Proteins/genetics ; Phylogeny ; RNA, Transfer/genetics ; Urodela/classification/*genetics ; }, abstract = {BACKGROUND: Mitochondria are the site of the citric acid cycle and oxidative phosphorylation (OXPHOS). In metazoans, the mitochondrial genome is a small, circular molecule averaging 16.5 kb in length. Despite evolutionarily conserved gene content, metazoan mitochondrial genomes show a diversity of gene orders most commonly explained by the duplication-random loss (DRL) model. In the DRL model, (1) a sequence of genes is duplicated in tandem, (2) one paralog sustains a loss-of-function mutation, resulting in selection to retain the other copy, and (3) the non-functional paralog is eventually deleted from the genome. Despite its apparent role in generating mitochondrial gene order diversity, little is known about the tempo and mode of random gene loss after duplication events. Here, we determine mitochondrial gene order across the salamander genus Aneides, which was previously shown to include at least two DRL-mediated rearrangement events. We then analyze these gene orders in a phylogenetic context to reveal patterns of DNA loss after mitochondrial gene duplication.<br><br>RESULTS: We identified two separate duplication events that resulted in mitochondrial gene rearrangements in Aneides; one occurred at the base of the clade tens of millions of years ago, while the other occurred much more recently (i.e. within a single species), resulting in gene order polymorphism and paralogs that are readily identifiable. We demonstrate that near-complete removal of duplicate rRNA genes has occurred since the recent duplication event, whereas duplicate protein-coding genes persist as pseudogenes and duplicate tRNAs persist as functionally intact paralogs. In addition, we show that non-coding DNA duplicated at the base of the clade has persisted across species for tens of millions of years.<br><br>CONCLUSIONS: The evolutionary history of the mitochondrial genome, from its inception as a bacterial endosymbiont, includes massive genomic reduction. Consistent with this overall trend, selection for efficiency of mitochondrial replication and transcription has been hypothesized to favor elimination of extra sequence. Our results, however, suggest that there may be no strong disadvantage to extraneous sequences in salamander mitochondrial genomes, although duplicate rRNA genes may be deleterious.}, }
@article {pmid29280079, year = {2018}, author = {de Brito Vieira, WH and Ferraresi, C and Schwantes, MLB and de Andrade Perez, SE and Baldissera, V and Cerqueira, MS and Parizotto, NA}, title = {Photobiomodulation increases mitochondrial citrate synthase activity in rats submitted to aerobic training.}, journal = {Lasers in medical science}, volume = {33}, number = {4}, pages = {803-810}, pmid = {29280079}, issn = {1435-604X}, mesh = {Animals ; Citrate (si)-Synthase/*metabolism ; Infrared Rays ; L-Lactate Dehydrogenase/metabolism ; Low-Level Light Therapy ; Male ; Mitochondria, Muscle/*enzymology/radiation effects ; Muscle, Skeletal/enzymology/radiation effects ; Myocardium/enzymology ; Physical Conditioning, Animal ; Rats ; Rats, Wistar ; Running ; }, abstract = {This study investigated the effects of photobiomodulation by low-laser laser therapy (LLLT) on the activities of citrate synthase (CS) and lactate dehydrogenase (LDH) and the anaerobic threshold (AT) in rats submitted to treadmill exercise. Fifty-four rats were allocated into four groups: rest control (RCG), rest laser (RLG), exercise control (ECG), and exercise laser (ELG). The infrared LLLT was applied daily on the quadriceps, gluteus maximum, soleus, and tibialis anterior muscles. Muscle samples (soleus, tibialis anterior, and cardiac muscles) were removed 48 h after the last exercise session for spectrophotometric analysis of the CS and LDH. The CS activity (μmol/protein) in ELG (16.02 and 0.49) was significantly greater (P < 0.05) than RCG (2.34 and 0.24), RLG (6.25 and 0.17), and ECG (6.76 and 0.26) in the cardiac and soleus muscles, respectively. The LDH activity (in 1 Mm/protein) in soleus muscle was smaller (P < 0.05) for ELG (0.33) compared to ECG (0.97), RLG (0.79), and RCG (1.07). For cardiac muscle, the LDH activity was smaller (P < 0.05) in ELG (1.38) compared to ECG (1.91) and RCG (2.55). The ECG and ELG showed increases in the maximum speed and a shift of the AT to higher effort levels after the training period, but no differences occurred between the exercised groups. In conclusion, the aerobic treadmill training combined with LLLT promotes an increase of oxidative capacity in this rat model, mainly in muscles with greater aerobic capacity.}, }
@article {pmid29279407, year = {2018}, author = {Łukasik, P and Nazario, K and Van Leuven, JT and Campbell, MA and Meyer, M and Michalik, A and Pessacq, P and Simon, C and Veloso, C and McCutcheon, JP}, title = {Multiple origins of interdependent endosymbiotic complexes in a genus of cicadas.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {2}, pages = {E226-E235}, pmid = {29279407}, issn = {1091-6490}, mesh = {Animals ; Bacteria/*classification/*genetics ; Bacterial Physiological Phenomena/*genetics ; Biological Evolution ; Chile ; Genetic Variation ; Genome, Bacterial ; Hemiptera/*microbiology ; Phylogeny ; Symbiosis/*physiology ; }, abstract = {Bacterial endosymbionts that provide nutrients to hosts often have genomes that are extremely stable in structure and gene content. In contrast, the genome of the endosymbiont Hodgkinia cicadicola has fractured into multiple distinct lineages in some species of the cicada genus Tettigades To better understand the frequency, timing, and outcomes of Hodgkinia lineage splitting throughout this cicada genus, we sampled cicadas over three field seasons in Chile and performed genomics and microscopy on representative samples. We found that a single ancestral Hodgkinia lineage has split at least six independent times in Tettigades over the last 4 million years, resulting in complexes of between two and six distinct Hodgkinia lineages per host. Individual genomes in these symbiotic complexes differ dramatically in relative abundance, genome size, organization, and gene content. Each Hodgkinia lineage retains a small set of core genes involved in genetic information processing, but the high level of gene loss experienced by all genomes suggests that extensive sharing of gene products among symbiont cells must occur. In total, Hodgkinia complexes that consist of multiple lineages encode nearly complete sets of genes present on the ancestral single lineage and presumably perform the same functions as symbionts that have not undergone splitting. However, differences in the timing of the splits, along with dissimilar gene loss patterns on the resulting genomes, have led to very different outcomes of lineage splitting in extant cicadas.}, }
@article {pmid29279306, year = {2018}, author = {Kawano, S and Tamura, Y and Kojima, R and Bala, S and Asai, E and Michel, AH and Kornmann, B and Riezman, I and Riezman, H and Sakae, Y and Okamoto, Y and Endo, T}, title = {Structure-function insights into direct lipid transfer between membranes by Mmm1-Mdm12 of ERMES.}, journal = {The Journal of cell biology}, volume = {217}, number = {3}, pages = {959-974}, pmid = {29279306}, issn = {1540-8140}, mesh = {Biological Transport, Active/physiology ; Endoplasmic Reticulum/genetics/*metabolism ; Kluyveromyces/genetics/*metabolism ; Membrane Proteins/genetics/*metabolism ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Multiprotein Complexes/genetics/*metabolism ; Phospholipids/genetics/*metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Structure-Activity Relationship ; }, abstract = {The endoplasmic reticulum (ER)-mitochondrial encounter structure (ERMES) physically links the membranes of the ER and mitochondria in yeast. Although the ER and mitochondria cooperate to synthesize glycerophospholipids, whether ERMES directly facilitates the lipid exchange between the two organelles remains controversial. Here, we compared the x-ray structures of an ERMES subunit Mdm12 from Kluyveromyces lactis with that of Mdm12 from Saccharomyces cerevisiae and found that both Mdm12 proteins possess a hydrophobic pocket for phospholipid binding. However in vitro lipid transfer assays showed that Mdm12 alone or an Mmm1 (another ERMES subunit) fusion protein exhibited only a weak lipid transfer activity between liposomes. In contrast, Mdm12 in a complex with Mmm1 mediated efficient lipid transfer between liposomes. Mutations in Mmm1 or Mdm12 impaired the lipid transfer activities of the Mdm12-Mmm1 complex and furthermore caused defective phosphatidylserine transport from the ER to mitochondrial membranes via ERMES in vitro. Therefore, the Mmm1-Mdm12 complex functions as a minimal unit that mediates lipid transfer between membranes.}, }
@article {pmid29277086, year = {2018}, author = {Hagström, E and Andersson, SG}, title = {The challenges of integrating two genomes in one cell.}, journal = {Current opinion in microbiology}, volume = {41}, number = {}, pages = {89-94}, doi = {10.1016/j.mib.2017.12.003}, pmid = {29277086}, issn = {1879-0364}, mesh = {Bacteria/*genetics/metabolism/pathogenicity ; Cell Nucleus/genetics ; *Evolution, Molecular ; *Genome ; Genome, Mitochondrial ; Humans ; Mitochondria/*genetics ; Oxygen/metabolism ; Phylogeny ; Respiration ; Symbiosis/genetics ; }, abstract = {Mutualistic bacteria and mitochondria have small genomes that harbor host-essential genes. A major question is why a distinct bacterial or mitochondrial genome is needed to encode these functions. The dual location of genes demand two sets of information processing systems, coordination of gene expression and elaborate transport systems. A simpler solution would be to harbor all genes in a single genome. Functional gene transfers to the host nuclear genome is uncommon in mutualistic bacteria and lost gene functions are rather rescued by co-symbiotic bacteria. Recent findings suggest that the mitochondrial genome is retained to avoid conflicting signals between protein targeting pathways in the cell. However, if the selective pressure for oxygenic respiration is lost, the mitochondrial genome will start to deteriorate and soon be lost.}, }
@article {pmid29271525, year = {2018}, author = {Corrêa-da-Silva, F and Pereira, JAS and de Aguiar, CF and de Moraes-Vieira, PMM}, title = {Mitoimmunity-when mitochondria dictates macrophage function.}, journal = {Cell biology international}, volume = {42}, number = {6}, pages = {651-655}, doi = {10.1002/cbin.10921}, pmid = {29271525}, issn = {1095-8355}, mesh = {Animals ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism ; Inflammasomes/metabolism ; Inflammation/metabolism/*pathology ; Macrophages/cytology/*immunology/metabolism ; Mitochondria/*metabolism ; Mitochondrial Dynamics ; NADP/metabolism ; Reactive Oxygen Species/metabolism ; Succinate Dehydrogenase/metabolism ; }, abstract = {In the past decade, several reports have appointed the importance of mitochondria in the immune response. Our understanding of mitochondria evolved from a simple supplier of energy into a platform necessary for immunorregulation. Proinflammatory responses are associated with enhanced glycolytic activity and breakdown of the TCA cycle. Mitochondrial reactive species of oxygen (mROS) are key regulators of classically activated macrophages, with substantial impact in the anti-microbicidal activity and pro-inflammatory cytokine secretion of macrophages. The inflammasome activation in macrophages is dependent on mROS production and mitochondrial regulation and mitochondrial dynamics and functionality direct impact inflammatory responses. Alternative activated macrophage metabolism relies on fatty acid oxidation, and the mechanism responsible for this phenotype is not fully elucidated. Thus, cellular metabolism and mitochondria function is a key immunoregulatory feature of macrophage biology. In this review, we will provide insights into recently reported evidences of mitochondria-related metabolic nodes, which are important for macrophage physiology.}, }
@article {pmid29262786, year = {2017}, author = {Dai, C and Hao, Y and He, Y and Lei, F}, title = {The absence of reproductive isolation between non-sister and deeply diverged mitochondrial lineages of the black-throated tit (Aegithalos concinnus) revealed by a multilocus genetic analysis in a contact zone.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {266}, pmid = {29262786}, issn = {1471-2148}, support = {31401965//National Natural Science Foundation of China/International ; }, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; *Genetic Loci ; Genetic Speciation ; Genetic Variation ; Geography ; Haplotypes/genetics ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Passeriformes/*genetics ; *Phylogeny ; Probability ; *Reproductive Isolation ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: A deep divergence of mitochondrial DNA is common in species delimitated by morphological traits. Several hypotheses can explain such variations, such as cryptic species, introgression, allopatric divergence and ancestral lineage. The black-throated tit harbors several deeply divergent mitochondrial lineages. Two lineages with 5% divergence, but having a high level of gene flow, have been detected in its subspecies, A. C. concinnus and A. c. talifuenses. In this study, we conducted a genetic analysis at a contact zone of these two lineages to identify whether these lineages either reflect a high level of intraspecific variation in mitochondrial loci or represent incipient speciation. Mitochondrial ND2 and 11 microsatellite loci were used to conduct phylogenetic and population structure analyses.<br><br>RESULTS: ND2 haplotypes actually diverged into two groups within subspecies A. c. talifuenses; however, they formed a non-sister relationship when including all available GenBank ND2 sequences. Analyses of microsatellite data indicated no existing population structure and showed a pattern of isolation by distance. Individuals sampled at the contact zone were almost identified as F2 hybrids.<br><br>CONCLUSIONS: Isolation for 2.4&#xa0;Ma, as suggested by a previous study, appeared to be insufficient to develop robust reproductive barriers. Reproductive barriers were weak, or even absent between the divergent lineages, highlighting that incipient speciation was unlikely to be the case. Considering the results from previous studies, the divergent lineages may be better explained by secondary contact after allopatric isolation because of Pleistocene climate changes, but other hypotheses cannot be definitively ruled out because of the lack of representative samples from the other distribution region and its relatives. Considering that divergence in morphology was hardly observed and the particular split in genetics, the two subspecies might be better merged. The current findings also highlight the likely contribution of male-biased dispersal to male-biased gene flow among mitochondrial lineages; more efforts are needed to illustrate the evolutionary history of the black-throated tit.}, }
@article {pmid29253894, year = {2017}, author = {Wei, W and Gomez-Duran, A and Hudson, G and Chinnery, PF}, title = {Background sequence characteristics influence the occurrence and severity of disease-causing mtDNA mutations.}, journal = {PLoS genetics}, volume = {13}, number = {12}, pages = {e1007126}, pmid = {29253894}, issn = {1553-7404}, support = {//Wellcome Trust/United Kingdom ; MC_UP_1501/2/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Alleles ; Base Sequence ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Founder Effect ; Gene Frequency ; Genetic Variation ; Haplotypes ; Humans ; Mitochondria/genetics ; *Mutation ; Optic Atrophy, Hereditary, Leber/*genetics ; Phylogeny ; }, abstract = {Inherited mitochondrial DNA (mtDNA) mutations have emerged as a common cause of human disease, with mutations occurring multiple times in the world population. The clinical presentation of three pathogenic mtDNA mutations is strongly associated with a background mtDNA haplogroup, but it is not clear whether this is limited to a handful of examples or is a more general phenomenon. To address this, we determined the characteristics of 30,506 mtDNA sequences sampled globally. After performing several quality control steps, we ascribed an established pathogenicity score to the major alleles for each sequence. The mean pathogenicity score for known disease-causing mutations was significantly different between mtDNA macro-haplogroups. Several mutations were observed across all haplogroup backgrounds, whereas others were only observed on specific clades. In some instances this reflected a founder effect, but in others, the mutation recurred but only within the same phylogenetic cluster. Sequence diversity estimates showed that disease-causing mutations were more frequent on young sequences, and genomes with two or more disease-causing mutations were more common than expected by chance. These findings implicate the mtDNA background more generally in recurrent mutation events that have been purified through natural selection in older populations. This provides an explanation for the low frequency of mtDNA disease reported in specific ethnic groups.}, }
@article {pmid29250469, year = {2017}, author = {Klink, GV and Golovin, AV and Bazykin, GA}, title = {Substitutions into amino acids that are pathogenic in human mitochondrial proteins are more frequent in lineages closely related to human than in distant lineages.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e4143}, pmid = {29250469}, issn = {2167-8359}, abstract = {Propensities for different amino acids within a protein site change in the course of evolution, so that an amino acid deleterious in a particular species may be acceptable at the same site in a different species. Here, we study the amino acid-changing variants in human mitochondrial genes, and analyze their occurrence in non-human species. We show that substitutions giving rise to such variants tend to occur in lineages closely related to human more frequently than in more distantly related lineages, indicating that a human variant is more likely to be deleterious in more distant species. Unexpectedly, substitutions giving rise to amino acids that correspond to alleles pathogenic in humans also more frequently occur in more closely related lineages. Therefore, a pathogenic variant still tends to be more acceptable in human mitochondria than a variant that may only be fit after a substantial perturbation of the protein structure.}, }
@article {pmid29249204, year = {2018}, author = {Stentiford, GD and Ross, S and Minardi, D and Feist, SW and Bateman, KS and Gainey, PA and Troman, C and Bass, D}, title = {Evidence for trophic transfer of Inodosporus octospora and Ovipleistophora arlo n. sp. (Microsporidia) between crustacean and fish hosts.}, journal = {Parasitology}, volume = {145}, number = {8}, pages = {1105-1117}, doi = {10.1017/S0031182017002256}, pmid = {29249204}, issn = {1469-8161}, mesh = {Animals ; DNA, Ribosomal ; Fishes/*microbiology ; Microscopy, Electron, Transmission ; Microsporidia/genetics/*isolation &amp; purification/ultrastructure ; Microsporidiosis/transmission/*veterinary ; Muscles/*microbiology ; Oocytes/microbiology ; Palaemonidae/*microbiology ; Phylogeny ; Polymerase Chain Reaction ; Viral Tropism ; }, abstract = {Within aquatic habitats, the hyper-abundant Order Crustacea appear to be the predominant host group for members of the Phylum Microsporidia. The musculature, a common site of infection, provides access to biochemical (carbohydrate-rich) and physiological (mitochondria-rich) conditions conducive to prolific parasite replication and maturation. The significant proportion of body plan devoted to skeletal musculature in Crustacea provides the location for a highly efficient intracellular parasite factory. In this study, we utilize histological, ultrastructural and phylogenetic evidence to describe a previously known (Inodosporus octospora) and novel (Ovipleistophora arlo n. sp.) microsporidian parasites infecting the musculature of the common prawn (Palaemon serratus) from the same site, at the same time of year. Despite similar clinical signs of infection, both parasites are otherwise distinct in terms of pathogenesis, morphology and phylogeny. Based upon partial subunit ribosomal RNA (SSU rDNA) sequence, we show that that I. octospora may be identical to a Kabatana sp. previously described infecting two-spot goby (Gobiusculus flavescens) in Europe, or at least that Inodosporus and Kabatana genera are synonyms. In addition, SSU rDNA sequence for O. arlo places it within a distinct clade containing Ovipleistophora mirandellae and Ovipleistophora ovariae, both infecting the oocytes of freshwater fish in Europe. Taken together, our data provide strong evidence for trophic-transfer between crustacean and fish hosts for two different microsporidians within clade 5 of the phylum. Furthermore, it demonstrates that morphologically and phylogenetically distinct microsporidians can infect the same tissues of the same host species to impart clinical signs which mimic infection with the other.}, }
@article {pmid29247559, year = {2018}, author = {Lee, K and Lee, HY and Back, K}, title = {Rice histone deacetylase 10 and Arabidopsis histone deacetylase 14 genes encode N-acetylserotonin deacetylase, which catalyzes conversion of N-acetylserotonin into serotonin, a reverse reaction for melatonin biosynthesis in plants.}, journal = {Journal of pineal research}, volume = {64}, number = {2}, pages = {}, doi = {10.1111/jpi.12460}, pmid = {29247559}, issn = {1600-079X}, mesh = {Arabidopsis/*metabolism ; Arylalkylamine N-Acetyltransferase/metabolism ; Histone Deacetylases/*metabolism ; Melatonin/*biosynthesis ; Oryza/*metabolism ; Phylogeny ; Plant Proteins/*metabolism ; Serotonin/analogs &amp; derivatives/metabolism ; }, abstract = {In plants, melatonin production is strictly regulated, unlike the production of its precursor, serotonin, which is highly inducible in response to stimuli, such as senescence and pathogen exposure. Exogenous serotonin treatment does not greatly induce the production of N-acetylserotonin (NAS) and melatonin in plants, which suggests the possible existence of one or more regulatory genes in the pathway for the biosynthesis of melatonin from serotonin. In this report, we found that NAS was rapidly and abundantly converted into serotonin in rice seedlings, indicating the presence of an N-acetylserotonin deacetylase (ASDAC). To clone the putative ASDAC gene, we screened 4 genes that were known as histone deacetylase (HDAC) genes, but encoded proteins targeted into chloroplasts or mitochondria rather than nuclei. Of 4 recombinant Escherichia coli strains expressing these genes, one E. coli strain expressing the rice HDAC10 gene was found to be capable of producing serotonin in response to treatment with NAS. The recombinant purified rice HDAC10 (OsHDAC10) protein exhibited ASDAC enzyme activity toward NAS, N-acetyltyramine (NAT), N-acetyltryptamine, and melatonin, with the highest ASDAC activity for NAT. In addition, its Arabidopsis ortholog, AtHDAC14, showed similar ASDAC activity to that of OsHDAC10. Both OsHDAC10 and AtHDAC14 were found to be expressed in chloroplasts. Phylogenetic analysis indicated that ASDAC homologs were present in archaea, but not in cyanobacteria, which differs from the distribution of serotonin N-acetyltransferase (SNAT). This suggests that SNAT and ASDAC may have evolved differently from ancestral eukaryotic cells.}, }
@article {pmid29245571, year = {2017}, author = {Pickersgill, M and Zimkus, BM and Raw, LRG}, title = {A new species of Phrynobatrachus (Anura: Phrynobatrachidae) from the Eastern Arc Mountians of Tanzania.}, journal = {Zootaxa}, volume = {4350}, number = {1}, pages = {151-163}, doi = {10.11646/zootaxa.4350.1.9}, pmid = {29245571}, issn = {1175-5334}, mesh = {Animals ; *Anura ; Male ; Mitochondria ; Phylogeny ; RNA, Ribosomal, 16S ; Tanzania ; }, abstract = {Phrynobatrachus discogularis sp. nov. (Anura, Phrynobatrachidae) is described from the Eastern Arc Mountains in Tanzania. It occupies upland grasslands and while it morphologically most resembles West and Central African P. gutturosus (Chabanaud, 1921), P. rungwensis (Loveridge, 1932), and P. anotis Schmidt and Inger, 1959, preliminary analysis of mitochondrial 16S rRNA indicates that the new species differs from all other species with published sequence data by a minimum distance of 4.1% and has affinities with P. rungwensis, P. uzungwensis Grandison and Howell, 1983 and P. keniensis Barbour and Loveridge, 1928-all diminutive upland eastern African taxa. The shape and colour of the male's external gular apparatus distinguish this species from all other described Phrynobatrachus species. Although geographically either sympatric or closely allopatric with P. uzungwensis, the lack of overlapping morphological characters indicates the two forms are distinct species. The new taxon is compared with other species from the region.}, }
@article {pmid29244187, year = {2017}, author = {Salinas-Giegé, T and Cavaiuolo, M and Cognat, V and Ubrig, E and Remacle, C and Duchêne, AM and Vallon, O and Maréchal-Drouard, L}, title = {Polycytidylation of mitochondrial mRNAs in Chlamydomonas reinhardtii.}, journal = {Nucleic acids research}, volume = {45}, number = {22}, pages = {12963-12973}, pmid = {29244187}, issn = {1362-4962}, mesh = {Base Sequence ; Chlamydomonas reinhardtii/*genetics/metabolism ; Chlorophyta/classification/genetics ; Genome, Mitochondrial/genetics ; Mitochondria/*genetics/metabolism ; Phylogeny ; Poly C/metabolism ; RNA, Messenger/*genetics/metabolism ; RNA, Mitochondrial ; Sequence Homology, Nucleic Acid ; *Transcription, Genetic ; }, abstract = {The unicellular photosynthetic organism, Chlamydomonas reinhardtii, represents a powerful model to study mitochondrial gene expression. Here, we show that the 5'- and 3'-extremities of the eight Chlamydomonas mitochondrial mRNAs present two unusual characteristics. First, all mRNAs start primarily at the AUG initiation codon of the coding sequence which is often marked by a cluster of small RNAs. Second, unusual tails are added post-transcriptionally at the 3'-extremity of all mRNAs. The nucleotide composition of the tails is distinct from that described in any other systems and can be partitioned between A/U-rich tails, predominantly composed of Adenosine and Uridine, and C-rich tails composed mostly of Cytidine. Based on 3' RACE experiments, 22% of mRNAs present C-rich tails, some of them composed of up to 20 consecutive Cs. Polycytidylation is specific to mitochondria and occurs primarily on mRNAs. This unprecedented post-transcriptional modification seems to be a specific feature of the Chlorophyceae class of green algae and points out the existence of novel strategies in mitochondrial gene expression.}, }
@article {pmid29241459, year = {2017}, author = {Carrie, C and Soll, J}, title = {To Mia or not to Mia: stepwise evolution of the mitochondrial intermembrane space disulfide relay.}, journal = {BMC biology}, volume = {15}, number = {1}, pages = {119}, pmid = {29241459}, issn = {1741-7007}, mesh = {*Arabidopsis ; *Arabidopsis Proteins ; Disulfides ; Mitochondria ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins ; Oxidation-Reduction ; Oxidoreductases Acting on Sulfur Group Donors ; Saccharomyces cerevisiae ; *Saccharomyces cerevisiae Proteins ; }, abstract = {The disulfide relay system found in the intermembrane space (IMS) of mitochondria is an essential pathway for the import and oxidative folding of IMS proteins. Erv1, an essential member of this pathway, has been previously found to be ubiquitously present in mitochondria-containing eukaryotes. However, the other essential protein, Mia40, was found to be absent or not required in some organisms, raising questions about how the disulfide relay functions in these organisms. A recent study published in BMC Biology demonstrates for the first time that some Erv1 proteins can function in oxidative folding independently of a Mia40 protein, providing for the first time strong evidence that the IMS disulfide relay evolved in a stepwise manner.See research article: 10.1186/s12915-017-0445-8.}, }
@article {pmid29241457, year = {2017}, author = {Yalvac, ME and Amornvit, J and Braganza, C and Chen, L and Hussain, SA and Shontz, KM and Montgomery, CL and Flanigan, KM and Lewis, S and Sahenk, Z}, title = {Impaired regeneration in calpain-3 null muscle is associated with perturbations in mTORC1 signaling and defective mitochondrial biogenesis.}, journal = {Skeletal muscle}, volume = {7}, number = {1}, pages = {27}, pmid = {29241457}, issn = {2044-5040}, mesh = {AMP-Activated Protein Kinases/metabolism ; Animals ; Calpain/genetics/*metabolism ; Cells, Cultured ; Disease Models, Animal ; Genetic Therapy ; Mechanistic Target of Rapamycin Complex 1/*metabolism ; Mice, Inbred C57BL ; Mice, Knockout ; MicroRNAs/metabolism ; Muscle Proteins/genetics/*metabolism ; Muscle, Skeletal/metabolism/pathology/*physiology ; Muscular Dystrophies, Limb-Girdle/metabolism/physiopathology ; *Organelle Biogenesis ; Proto-Oncogene Proteins c-akt/metabolism ; *Regeneration ; Signal Transduction ; Transforming Growth Factor beta/metabolism ; }, abstract = {BACKGROUND: Previous studies in patients with limb-girdle muscular dystrophy type 2A (LGMD2A) have suggested that calpain-3 (CAPN3) mutations result in aberrant regeneration in muscle.<br><br>METHODS: To gain insight into pathogenesis of aberrant muscle regeneration in LGMD2A, we used a paradigm of cardiotoxin (CTX)-induced cycles of muscle necrosis and regeneration in the CAPN3-KO mice to simulate the early features of the dystrophic process in LGMD2A. The temporal evolution of the regeneration process was followed by assessing the oxidative state, size, and the number of metabolic fiber types at 4 and 12&#xa0;weeks after last CTX injection. Muscles isolated at these time points were further investigated for the key regulators of the pathways involved in various cellular processes such as protein synthesis, cellular energy status, metabolism, and cell stress to include Akt/mTORC1 signaling, mitochondrial biogenesis, and AMPK signaling. TGF-&#x3b2; and microRNA (miR-1, miR-206, miR-133a) regulation were also assessed. Additional studies included in vitro assays for quantifying fusion index of myoblasts from CAPN3-KO mice and development of an in vivo gene therapy paradigm for restoration of impaired regeneration using the adeno-associated virus vector carrying CAPN3 gene in the muscle.<br><br>RESULTS: At 4 and 12&#xa0;weeks after last CTX injection, we found impaired regeneration in CAPN3-KO muscle characterized by excessive numbers of small lobulated fibers belonging to oxidative metabolic type (slow twitch) and increased connective tissue. TGF-&#x3b2; transcription levels in the regenerating CAPN3-KO muscles were significantly increased along with microRNA dysregulation compared to wild type (WT), and the attenuated radial growth of muscle fibers was accompanied by perturbed Akt/mTORC1 signaling, uncoupled from protein synthesis, through activation of AMPK pathway, thought to be triggered by energy shortage in the CAPN3-KO muscle. This was associated with failure to increase mitochondria content, PGC-1&#x3b1;, and ATP5D transcripts in the regenerating CAPN3-KO muscles compared to WT. In vitro studies showed defective myotube fusion in CAPN3-KO myoblast cultures. Replacement of CAPN3 by gene therapy in vivo increased the fiber size and decreased the number of small oxidative fibers.<br><br>CONCLUSION: Our findings provide insights into understanding of the impaired radial growth phase of regeneration in calpainopathy.}, }
@article {pmid29221178, year = {2017}, author = {Díaz-Carballo, D and Klein, J and Acikelli, AH and Wilk, C and Saka, S and Jastrow, H and Wennemuth, G and Dammann, P and Giger-Pabst, U and Khosrawipour, V and Rassow, J and Nienen, M and Strumberg, D}, title = {Cytotoxic stress induces transfer of mitochondria-associated human endogenous retroviral RNA and proteins between cancer cells.}, journal = {Oncotarget}, volume = {8}, number = {56}, pages = {95945-95964}, pmid = {29221178}, issn = {1949-2553}, abstract = {About 8 % of the human genome consists of human endogenous retroviruses (HERVs), which are relicts of ancient exogenous retroviral infections incurred during evolution. Although the majority of HERVs have functional gene defects or epigenetic modifications, many of them are still able to produce retroviral proteins that have been proposed to be involved in cellular transformation and cancer development. We found that, in chemo-resistant U87[RETO] glioblastoma cells, cytotoxic stress induced by etoposide promotes accumulation and large-scale fission of mitochondria, associated with the detection of HERV-WE1 (syncytin-1) and HERV-FRD1 (syncytin-2) in these organelles. In addition, mitochondrial preparations also contained the corresponding receptors, i.e. ASCT2 and MFSD2. We clearly demonstrated that mitochondria associated with HERV-proteins were shuttled between adjacent cancer cells not only via tunneling tubes, but also by direct cellular uptake across the cell membrane. Furthermore, anti-syncytin-1 and anti-syncytin-2 antibodies were able to specifically block this direct cellular uptake of mitochondria even more than antibodies targeting the cognate receptors. Here, we suggest that the association of mitochondria with syncytin-1/syncytin-2 together with their respective receptors could represent a novel mechanism of cell-to-cell transfer. In chemotherapy-refractory cancer cells, this might open up attractive avenues to novel mitochondria-targeting therapies.}, }
@article {pmid29210936, year = {2018}, author = {Litts, KM and Zhang, Y and Freund, KB and Curcio, CA}, title = {OPTICAL COHERENCE TOMOGRAPHY AND HISTOLOGY OF AGE-RELATED MACULAR DEGENERATION SUPPORT MITOCHONDRIA AS REFLECTIVITY SOURCES.}, journal = {Retina (Philadelphia, Pa.)}, volume = {38}, number = {3}, pages = {445-461}, pmid = {29210936}, issn = {1539-2864}, support = {P30 EY003039/EY/NEI NIH HHS/United States ; R01 EY006109/EY/NEI NIH HHS/United States ; R01 EY024378/EY/NEI NIH HHS/United States ; R21 EY021903/EY/NEI NIH HHS/United States ; }, mesh = {Bruch Membrane/pathology ; Humans ; Macular Degeneration/diagnostic imaging/*pathology ; Mitochondria/*ultrastructure ; Retinal Cone Photoreceptor Cells/pathology ; Retinal Photoreceptor Cell Outer Segment/*pathology ; Retinal Pigment Epithelium/pathology ; Tomography, Optical Coherence/*methods ; }, abstract = {PURPOSE: Widespread adoption of optical coherence tomography has revolutionized the diagnosis and management of retinal disease. If the cellular and subcellular sources of reflectivity in optical coherence tomography can be identified, the value of this technology will be advanced even further toward precision medicine, mechanistic thinking, and molecular discovery. Four hyperreflective outer retinal bands are created by the exquisite arrangement of photoreceptors, Müller cells, retinal pigment epithelium, and Bruch membrane. Because of massed effects of these axially compartmentalized and transversely aligned cells, reflectivity can be localized to the subcellular level. This review focuses on the second of the four bands, called ellipsoid zone in a consensus clinical lexicon, with the central thesis that mitochondria in photoreceptor inner segments are a major independent reflectivity source in this band, because of Mie scattering and waveguiding.<br><br>METHODS: We review the evolution of Band 2 nomenclature in published literature and discuss the origins of imaging signals from photoreceptor mitochondria that could make these organelles visible in vivo.<br><br>RESULTS: Our recent data pertain to outer retinal tubulation, a unique neurodegenerative and gliotic structure with a highly reflective border, prominent in late age-related macular degeneration. High-resolution histology and multimodal imaging of outer retinal tubulation together provide evidence that inner segment mitochondria undergoing fission and translocation toward the nucleus provide the reflectivity signal.<br><br>CONCLUSION: Our data support adoption of the ellipsoid zone nomenclature. Identifying subcellular signal sources will newly inform clinical.}, }
@article {pmid29207267, year = {2017}, author = {Petitjean, C and Williams, TA}, title = {Evolution: New Gene-Rich Mitochondria Found across the Eukaryotic Tree.}, journal = {Current biology : CB}, volume = {27}, number = {23}, pages = {R1270-R1271}, doi = {10.1016/j.cub.2017.10.028}, pmid = {29207267}, issn = {1879-0445}, mesh = {Eukaryota/*genetics ; Eukaryotic Cells ; Evolution, Molecular ; *Genome, Mitochondrial ; Mitochondria/genetics ; Symbiosis/genetics ; Trees/genetics ; }, abstract = {Mitochondria are the energy-generating organelles that power eukaryotic cells. Originally descended from endosymbiotic bacteria, their genomes have shrunk during evolution. New analyses suggest that large, gene-rich mitochondrial genomes are more common than previously thought, with interesting implications for eukaryotic genome evolution.}, }
@article {pmid29202688, year = {2017}, author = {Abrahamian, M and Kagda, M and Ah-Fong, AMV and Judelson, HS}, title = {Rethinking the evolution of eukaryotic metabolism: novel cellular partitioning of enzymes in stramenopiles links serine biosynthesis to glycolysis in mitochondria.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {241}, pmid = {29202688}, issn = {1471-2148}, mesh = {Animals ; *Biological Evolution ; Cytosol ; Eukaryotic Cells/*metabolism ; Genes ; *Glycolysis ; Mitochondria/genetics/*metabolism ; Oomycetes/metabolism ; Phosphorylation ; Phylogeny ; Phytophthora infestans/metabolism ; Serine/*biosynthesis ; Stramenopiles/*enzymology/*metabolism ; }, abstract = {BACKGROUND: An important feature of eukaryotic evolution is metabolic compartmentalization, in which certain pathways are restricted to the cytosol or specific organelles. Glycolysis in eukaryotes is described as a cytosolic process. The universality of this canon has been challenged by recent genome data that suggest that some glycolytic enzymes made by stramenopiles bear mitochondrial targeting peptides.<br><br>RESULTS: Mining of oomycete, diatom, and brown algal genomes indicates that stramenopiles encode two forms of enzymes for the second half of glycolysis, one with and the other without mitochondrial targeting peptides. The predicted mitochondrial targeting was confirmed by using fluorescent tags to localize phosphoglycerate kinase, phosphoglycerate mutase, and pyruvate kinase in Phytophthora infestans, the oomycete that causes potato blight. A genome-wide search for other enzymes with atypical mitochondrial locations identified phosphoglycerate dehydrogenase, phosphoserine aminotransferase, and phosphoserine phosphatase, which form a pathway for generating serine from the glycolytic intermediate 3-phosphoglycerate. Fluorescent tags confirmed the delivery of these serine biosynthetic enzymes to P. infestans mitochondria. A cytosolic form of this serine biosynthetic pathway, which occurs in most eukaryotes, is missing from oomycetes and most other stramenopiles. The glycolysis and serine metabolism pathways of oomycetes appear to be mosaics of enzymes with different ancestries. While some of the noncanonical oomycete mitochondrial enzymes have the closest affinity in phylogenetic analyses with proteins from other stramenopiles, others cluster with bacterial, plant, or animal proteins. The genes encoding the mitochondrial phosphoglycerate kinase and serine-forming enzymes are physically linked on oomycete chromosomes, which suggests a shared origin.<br><br>CONCLUSIONS: Stramenopile metabolism appears to have been shaped through the acquisition of genes by descent and lateral or endosymbiotic gene transfer, along with the targeting of the proteins to locations that are novel compared to other eukaryotes. Colocalization of the glycolytic and serine biosynthesis enzymes in mitochondria is apparently necessary since they share a common intermediate. The results indicate that descriptions of metabolism in textbooks do not cover the full diversity of eukaryotic biology.}, }
@article {pmid29202174, year = {2018}, author = {Wragg, D and Techer, MA and Canale-Tabet, K and Basso, B and Bidanel, JP and Labarthe, E and Bouchez, O and Le Conte, Y and Clémencet, J and Delatte, H and Vignal, A}, title = {Autosomal and Mitochondrial Adaptation Following Admixture: A Case Study on the Honeybees of Reunion Island.}, journal = {Genome biology and evolution}, volume = {10}, number = {1}, pages = {220-238}, pmid = {29202174}, issn = {1759-6653}, mesh = {Acclimatization ; Adaptation, Physiological ; Animals ; Bees/*genetics/physiology ; DNA, Mitochondrial/genetics ; Female ; Genome, Insect ; Genome, Mitochondrial ; Male ; Mitochondria/*genetics/metabolism ; Reunion ; }, abstract = {The honeybee population of the tropical Reunion Island is a genetic admixture of the Apis mellifera unicolor subspecies, originally described in Madagascar, and of European subspecies, mainly A. m. carnica and A. m. ligustica, regularly imported to the island since the late 19th century. We took advantage of this population to study genetic admixing of the tropical-adapted indigenous and temperate-adapted European genetic backgrounds. Whole genome sequencing of 30 workers and 6 males from Reunion, compared with samples from Europe, Madagascar, Mauritius, Rodrigues, and the Seychelles, revealed the Reunion honeybee population to be composed on an average of 53.2 ± 5.9% A. m. unicolor nuclear genomic background, the rest being mainly composed of A. m. carnica and to a lesser extent A. m. ligustica. In striking contrast to this, only 1 out of the 36 honeybees from Reunion had a mitochondrial genome of European origin, suggesting selection has favored the A. m. unicolor mitotype, which is possibly better adapted to the island's bioclimate. Local ancestry was determined along the chromosomes for all Reunion samples, and a test for preferential selection for the A. m. unicolor or European background revealed 15 regions significantly associated with the A. m. unicolor lineage and 9 regions with the European lineage. Our results provide insights into the long-term consequences of introducing exotic specimen on the nuclear and mitochondrial genomes of locally adapted populations.}, }
@article {pmid29199107, year = {2018}, author = {Solano-Zavaleta, I and Nieto-Montes de Oca, A}, title = {Species limits in the Morelet's Alligator lizard (Anguidae: Gerrhonotinae).}, journal = {Molecular phylogenetics and evolution}, volume = {120}, number = {}, pages = {16-27}, doi = {10.1016/j.ympev.2017.11.011}, pmid = {29199107}, issn = {1095-9513}, mesh = {Alligators and Crocodiles/*physiology ; Animals ; Bayes Theorem ; Cell Nucleus/genetics ; Central America ; DNA, Mitochondrial/genetics ; Lizards/genetics/*physiology ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Species Specificity ; Time Factors ; }, abstract = {The widely distributed, Central American anguid lizard Mesaspis moreletii is currently recognized as a polytypic species with five subspecies (M. m. fulvus, M. m. moreletii, M. m. rafaeli, M. m. salvadorensis, and M. m. temporalis). We reevaluated the species limits within Mesaspis moreletii using DNA sequences of one mitochondrial and three nuclear genes. The multi-locus data set included samples of all of the subspecies of M. moreletii, the other species of Mesaspis in Central America (M. cuchumatanus and M. monticola), and some populations assignable to M. moreletii but of uncertain subspecific identity from Honduras and Nicaragua. We first used a tree-based method for delimiting species based on mtDNA data to identify potential evolutionary independent lineages, and then analized the multilocus dataset with two species delimitation methods that use the multispecies coalescent model to evaluate different competing species delimitation models: the Bayes factors species delimitation method (BFD) implemented in [∗]BEAST, and the Bayesian Phylogenetics and Phylogeography (BP&amp;P) method. Our results suggest that M. m. moreletii, M. m. rafaeli, M. m. salvadorensis, and M. m. temporalis represent distinct evolutionary independent lineages, and that the populations of uncertain status from Honduras and Nicaragua may represent additional undescribed species. Our results also suggest that M. m. fulvus is a synonym of M. m. moreletii. The biogeography of the Central American lineages of Mesaspis is discussed.}, }
@article {pmid29196205, year = {2018}, author = {Medina, CD and Avila, LJ and Sites, JW and Santos, J and Morando, M}, title = {Alternative methods of phylogenetic inference for the Patagonian lizard group Liolaemus elongatus-kriegi (Iguania: Liolaemini) based on mitochondrial and nuclear markers.}, journal = {Molecular phylogenetics and evolution}, volume = {120}, number = {}, pages = {158-169}, doi = {10.1016/j.ympev.2017.11.017}, pmid = {29196205}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/*genetics ; Cytochromes b/classification/genetics/metabolism ; DNA/chemistry/isolation &amp; purification/metabolism ; Databases, Genetic ; Lizards/*classification/genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/chemistry/classification/genetics ; Sequence Analysis, DNA ; }, abstract = {We present different approaches to a multi-locus phylogeny for the Liolaemus elongatus-kriegi group, including almost all species and recognized lineages. We sequenced two mitochondrial and five nuclear gene regions for 123 individuals from 35 taxa, and compared relationships resolved from concatenated and species tree methods. The L. elongatus-kriegi group was inferred as monophyletic in three of the five analyses (concatenated mitochondrial, concatenated mitochondrial + nuclear gene trees, and SVD quartet species tree). The mitochondrial gene tree resolved four haploclades, three corresponding to the previously recognized complexes: L. elongatus, L. kriegi and L. petrophilus complexes, and the L. punmahuida group. The BEAST species tree approach included the L. punmahuida group within the L. kriegi complex, but the SVD quartet method placed it as sister to the L. elongatus-kriegi group. BEAST inferred species of the L. elongatus and L. petrophilus complexes as one clade, while SVDquartet inferred these two complexes as monophyletic (although with no statistical support for the L. petrophilus complex). The species tree approach also included the L. punmahuida group as part of the L. elongatus-kriegi group. Our study provides detailed multilocus phylogenetic hypotheses for the L. elongatus-kriegi group, and we discuss possible reasons for differences in the concatenation and species tree methods.}, }
@article {pmid29195856, year = {2018}, author = {Chakraborty, S and Uddin, A and Mazumder, TH and Choudhury, MN and Malakar, AK and Paul, P and Halder, B and Deka, H and Mazumder, GA and Barbhuiya, RA and Barbhuiya, MA and Devi, WJ}, title = {Codon usage and expression level of human mitochondrial 13 protein coding genes across six continents.}, journal = {Mitochondrion}, volume = {42}, number = {}, pages = {64-76}, doi = {10.1016/j.mito.2017.11.006}, pmid = {29195856}, issn = {1872-8278}, mesh = {*Codon ; Computational Biology ; Electron Transport Chain Complex Proteins/*genetics ; *Gene Expression Profiling ; Global Health ; Humans ; Mitochondrial Proteins/*genetics ; Phylogeography ; Selection, Genetic ; }, abstract = {The study of codon usage coupled with phylogenetic analysis is an important tool to understand the genetic and evolutionary relationship of a gene. The 13 protein coding genes of human mitochondria are involved in electron transport chain for the generation of energy currency (ATP). However, no work has yet been reported on the codon usage of the mitochondrial protein coding genes across six continents. To understand the patterns of codon usage in mitochondrial genes across six different continents, we used bioinformatic analyses to analyze the protein coding genes. The codon usage bias was low as revealed from high ENC value. Correlation between codon usage and GC3 suggested that all the codons ending with G/C were positively correlated with GC3 but vice versa for A/T ending codons with the exception of ND4L and ND5 genes. Neutrality plot revealed that for the genes ATP6, COI, COIII, CYB, ND4 and ND4L, natural selection might have played a major role while mutation pressure might have played a dominant role in the codon usage bias of ATP8, COII, ND1, ND2, ND3, ND5 and ND6 genes. Phylogenetic analysis indicated that evolutionary relationships in each of 13 protein coding genes of human mitochondria were different across six continents and further suggested that geographical distance was an important factor for the origin and evolution of 13 protein coding genes of human mitochondria.}, }
@article {pmid29193148, year = {2018}, author = {Damerau, M and Freese, M and Hanel, R}, title = {Multi-gene phylogeny of jacks and pompanos (Carangidae), including placement of monotypic vadigo Campogramma glaycos.}, journal = {Journal of fish biology}, volume = {92}, number = {1}, pages = {190-202}, doi = {10.1111/jfb.13509}, pmid = {29193148}, issn = {1095-8649}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus ; DNA, Mitochondrial ; Fishes/*genetics ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {In this study, the phylogenetic trees of jacks and pompanos (Carangidae), an ecologically and morphologically diverse, globally distributed fish family, are inferred from a complete, concatenated data set of two mitochondrial (cytochrome c oxidase I, cytochrome b) loci and one nuclear (myosin heavy chain 6) locus. Maximum likelihood and Bayesian inferences are largely congruent and show a clear separation of Carangidae into the four subfamilies: Scomberoidinae, Trachinotinae, Naucratinae and Caranginae. The inclusion of the carangid sister lineages Coryphaenidae (dolphinfishes) and Rachycentridae (cobia), however, render Carangidae paraphyletic. The phylogenetic trees also show with high statistical support that the monotypic vadigo Campogramma glaycos is the sister to all other species within the Naucratinae.}, }
@article {pmid29191733, year = {2018}, author = {Chatterjee, K and Nostramo, RT and Wan, Y and Hopper, AK}, title = {tRNA dynamics between the nucleus, cytoplasm and mitochondrial surface: Location, location, location.}, journal = {Biochimica et biophysica acta. Gene regulatory mechanisms}, volume = {1861}, number = {4}, pages = {373-386}, pmid = {29191733}, issn = {1874-9399}, support = {R01 GM027930/GM/NIGMS NIH HHS/United States ; R01 GM122884/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Transport ; Cell Nucleus/*metabolism ; Cytoplasm/*metabolism ; Endoribonucleases/metabolism ; Evolution, Molecular ; Fungal Proteins/metabolism ; HSP70 Heat-Shock Proteins/metabolism ; Mitochondrial Membranes/*metabolism ; Nuclear Pore Complex Proteins/metabolism ; Nucleocytoplasmic Transport Proteins/*metabolism ; Plant Proteins/metabolism ; RNA Precursors/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Transfer/*metabolism ; RNA-Binding Proteins/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Transcription, Genetic ; Vertebrates/metabolism ; Yeasts/metabolism ; }, abstract = {Although tRNAs participate in the essential function of protein translation in the cytoplasm, tRNA transcription and numerous processing steps occur in the nucleus. This subcellular separation between tRNA biogenesis and function requires that tRNAs be efficiently delivered to the cytoplasm in a step termed "primary tRNA nuclear export". Surprisingly, tRNA nuclear-cytoplasmic traffic is not unidirectional, but, rather, movement is bidirectional. Cytoplasmic tRNAs are imported back to the nucleus by the "tRNA retrograde nuclear import" step which is conserved from budding yeast to vertebrate cells and has been hijacked by viruses, such as HIV, for nuclear import of the viral reverse transcription complex in human cells. Under appropriate environmental conditions cytoplasmic tRNAs that have been imported into the nucleus return to the cytoplasm via the 3rd nuclear-cytoplasmic shuttling step termed "tRNA nuclear re-export", that again is conserved from budding yeast to vertebrate cells. We describe the 3 steps of tRNA nuclear-cytoplasmic movements and their regulation. There are multiple tRNA nuclear export and import pathways. The different tRNA nuclear exporters appear to possess substrate specificity leading to the tantalizing possibility that the cellular proteome may be regulated at the level of tRNA nuclear export. Moreover, in some organisms, such as budding yeast, the pre-tRNA splicing heterotetrameric endonuclease (SEN), which removes introns from pre-tRNAs, resides on the cytoplasmic surface of the mitochondria. Therefore, we also describe the localization of the SEN complex to mitochondria and splicing of pre-tRNA on mitochondria, which occurs prior to the participation of tRNAs in protein translation. This article is part of a Special Issue entitled: SI: Regulation of tRNA synthesis and modification in physiological conditions and disease edited by Dr. Boguta Magdalena.}, }
@article {pmid29191512, year = {2018}, author = {Shimada, S and Oosaki, M and Takahashi, R and Uene, S and Yanagisawa, S and Tsukihara, T and Shinzawa-Itoh, K}, title = {A unique respiratory adaptation in Drosophila independent of supercomplex formation.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1859}, number = {2}, pages = {154-163}, doi = {10.1016/j.bbabio.2017.11.007}, pmid = {29191512}, issn = {0005-2728}, mesh = {*Adaptation, Physiological ; Animals ; Cattle ; Drosophila Proteins/chemistry/*metabolism ; Drosophila melanogaster ; Electron Transport/physiology ; Electron Transport Chain Complex Proteins/chemistry/*metabolism ; Mice ; Mitochondria, Heart/*metabolism ; Reactive Oxygen Species/chemistry/*metabolism ; Swine ; }, abstract = {Large assemblies of respiratory chain complexes, known as supercomplexes, are present in the mitochondrial membrane in mammals and yeast, as well as in some bacterial membranes. The formation of supercomplexes is thought to contribute to efficient electron transfer, stabilization of each enzyme complex, and inhibition of reactive oxygen species (ROS) generation. In this study, mitochondria from various organisms were solubilized with digitonin, and then the solubilized complexes were separated by blue native PAGE (BN-PAGE). The results revealed a supercomplex consisting of complexes I, III, and IV in mitochondria from bovine and porcine heart, and a supercomplex consisting primarily of complexes I and III in mitochondria from mouse heart and liver. However, supercomplexes were barely detectable in Drosophila flight-muscle mitochondria, and only dimeric complex V was present. Drosophila mitochondria exhibited the highest rates of oxygen consumption and NADH oxidation, and the concentrations of the electron carriers, cytochrome c and quinone were higher than in other species. Respiratory chain complexes were tightly packed in the mitochondrial membrane containing abundant phosphatidylethanolamine with the fatty acid palmitoleic acid (C16:1), which is relatively high oxidation-resistant as compared to poly-unsaturated fatty acid. These properties presumably allow efficient electron transfer in Drosophila. These findings reveal the existence of a new mechanism of biological adaptation independent of supercomplex formation.}, }
@article {pmid29187976, year = {2017}, author = {Conner, WR and Blaxter, ML and Anfora, G and Ometto, L and Rota-Stabelli, O and Turelli, M}, title = {Genome comparisons indicate recent transfer of wRi-like Wolbachia between sister species Drosophila suzukii and D. subpulchrella.}, journal = {Ecology and evolution}, volume = {7}, number = {22}, pages = {9391-9404}, pmid = {29187976}, issn = {2045-7758}, support = {R01 GM104325/GM/NIGMS NIH HHS/United States ; }, abstract = {Wolbachia endosymbionts may be acquired by horizontal transfer, by introgression through hybridization between closely related species, or by cladogenic retention during speciation. All three modes of acquisition have been demonstrated, but their relative frequency is largely unknown. Drosophila suzukii and its sister species D. subpulchrella harbor Wolbachia, denoted wSuz and wSpc, very closely related to wRi, identified in California populations of D. simulans. However, these variants differ in their induced phenotypes: wRi causes significant cytoplasmic incompatibility (CI) in D. simulans, but CI has not been detected in D. suzukii or D. subpulchrella. Our draft genomes of wSuz and wSpc contain full-length copies of 703 of the 734 single-copy genes found in wRi. Over these coding sequences, wSuz and wSpc differ by only 0.004% (i.e., 28 of 704,883 bp); they are sisters relative to wRi, from which each differs by 0.014%-0.015%. Using published data from D. melanogaster, Nasonia wasps and Nomada bees to calibrate relative rates of Wolbachia versus host nuclear divergence, we conclude that wSuz and wSpc are too similar-by at least a factor of 100-to be plausible candidates for cladogenic transmission. These three wRi-like Wolbachia, which differ in CI phenotype in their native hosts, have different numbers of orthologs of genes postulated to contribute to CI; and the CI loci differ at several nucleotides that may account for the CI difference. We discuss the general problem of distinguishing alternative modes of Wolbachia acquisition, focusing on the difficulties posed by limited knowledge of variation in absolute and relative rates of molecular evolution for host nuclear genomes, mitochondria, and Wolbachia.}, }
@article {pmid29182013, year = {2017}, author = {Dickerson, T and Jauregui, CE and Teng, Y}, title = {Friend or foe? Mitochondria as a pharmacological target in cancer treatment.}, journal = {Future medicinal chemistry}, volume = {9}, number = {18}, pages = {2197-2210}, doi = {10.4155/fmc-2017-0110}, pmid = {29182013}, issn = {1756-8927}, mesh = {ATPases Associated with Diverse Cellular Activities/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Antineoplastic Agents/pharmacology/therapeutic use ; DNA, Mitochondrial/drug effects/metabolism ; Energy Metabolism/drug effects ; Humans ; Membrane Proteins/metabolism ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/metabolism ; Neoplasms/*drug therapy/metabolism/pathology ; Reactive Oxygen Species/metabolism ; Signal Transduction/drug effects ; }, abstract = {Mitochondria have acquired numerous functions over the course of evolution, such as those involved in controlling energy production, cellular metabolism, cell survival, apoptosis and autophagy within host cells. Tumor cells can develop defects in mitochondrial function, presenting a potential strategy for designing selective anticancer therapies. Therefore, cancer has been the main focus of recent research to uncover possible mitochondrial targets for therapeutic benefit. This comprehensive review covers not only the recent discoveries of the roles of mitochondria in cancer development, progression and therapeutic implications but also the findings regarding emerging mitochondrial therapeutic targets and mitochondria-targeted agents. Current challenges and future directions for developments and applications of mitochondrial-targeted therapeutics are also discussed.}, }
@article {pmid29179728, year = {2017}, author = {Li, D and Du, X and Guo, X and Zhan, L and Li, X and Yin, C and Chen, C and Li, M and Li, B and Yang, H and Xing, J}, title = {Site-specific selection reveals selective constraints and functionality of tumor somatic mtDNA mutations.}, journal = {Journal of experimental &amp; clinical cancer research : CR}, volume = {36}, number = {1}, pages = {168}, pmid = {29179728}, issn = {1756-9966}, mesh = {Amino Acids/genetics ; Codon/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Databases, Genetic ; Humans ; Mitochondria/chemistry/*genetics ; Mutation Rate ; Neoplasms/*genetics ; *Point Mutation ; Selection, Genetic ; }, abstract = {BACKGROUND: Previous studies have indicated that tumor mitochondrial DNA (mtDNA) mutations are primarily shaped by relaxed negative selection, which is contradictory to the critical roles of mtDNA mutations in tumorigenesis. Therefore, we hypothesized that site-specific selection may influence tumor mtDNA mutations.<br><br>METHODS: To test our hypothesis, we developed the largest collection of tumor mtDNA mutations to date and evaluated how natural selection shaped mtDNA mutation patterns.<br><br>RESULTS: Our data demonstrated that both positive and negative selections acted on specific positions or functional units of tumor mtDNAs, although the landscape of these mutations was consistent with the relaxation of negative selection. In particular, mutation rate (mutation number in a region/region bp length) in complex V and tRNA coding regions, especially in ATP8 within complex V and in loop and variable regions within tRNA, were significantly lower than those in other regions. While the mutation rate of most codons and amino acids were consistent with the expectation under neutrality, several codons and amino acids had significantly different rates. Moreover, the mutations under selection were enriched for changes that are predicted to be deleterious, further supporting the evolutionary constraints on these regions.<br><br>CONCLUSION: These results indicate the existence of site-specific selection and imply the important role of the mtDNA mutations at some specific sites in tumor development.}, }
@article {pmid29178068, year = {2017}, author = {Wang, L and Liebmen, MN and Wang, X}, title = {Roles of Mitochondrial DNA Signaling in Immune Responses.}, journal = {Advances in experimental medicine and biology}, volume = {1038}, number = {}, pages = {39-53}, doi = {10.1007/978-981-10-6674-0_4}, pmid = {29178068}, issn = {0065-2598}, mesh = {Animals ; *Autophagy/genetics/immunology ; *CRISPR-Cas Systems ; *DNA, Mitochondrial/genetics/immunology ; *Gene Editing ; Humans ; *Immune System Diseases/genetics/immunology/therapy ; *Mitochondria/genetics/immunology/pathology ; Toll-Like Receptor 9/genetics/immunology ; }, abstract = {Mitochondrial DNA (mtDNA) plays an important role in immune responses during the evolution. The present chapter systemically describes its role on immune-related diseases and its interaction on immune responses. It is important to explore the main function and mechanisms of mtDNA in immune responses by which mtDNA regulates the signaling pathways of Toll-like receptor 9, autophagy, and STING. There are potentials to discover therapeutic targets of mtDNA in immune diseases and inflammation. It will be more exciting if the CRISPR-Cas9 method can be applied for mtDNA gene editing to cure diseases and provide a novel insight of mtDNA in immune responses as well as new therapies.}, }
@article {pmid29177973, year = {2017}, author = {Niu, Y and Moghimyfiroozabad, S and Safaie, S and Yang, Y and Jonas, EA and Alavian, KN}, title = {Phylogenetic Profiling of Mitochondrial Proteins and Integration Analysis of Bacterial Transcription Units Suggest Evolution of F1Fo ATP Synthase from Multiple Modules.}, journal = {Journal of molecular evolution}, volume = {85}, number = {5-6}, pages = {219-233}, pmid = {29177973}, issn = {1432-1432}, support = {R01 NS045876/NS/NINDS NIH HHS/United States ; R01 NS081746/NS/NINDS NIH HHS/United States ; R21 NS104249/NS/NINDS NIH HHS/United States ; R37 NS045876/NS/NINDS NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/biosynthesis ; Evolution, Molecular ; Humans ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Mitochondrial Proton-Translocating ATPases/*genetics/*metabolism ; Phylogeny ; Protein Domains ; Protein Structural Elements/genetics ; Transcription, Genetic/genetics ; }, abstract = {ATP synthase is a complex universal enzyme responsible for ATP synthesis across all kingdoms of life. The F-type ATP synthase has been suggested to have evolved from two functionally independent, catalytic (F1) and membrane bound (Fo), ancestral modules. While the modular evolution of the synthase is supported by studies indicating independent assembly of the two subunits, the presence of intermediate assembly products suggests a more complex evolutionary process. We analyzed the phylogenetic profiles of the human mitochondrial proteins and bacterial transcription units to gain additional insight into the evolution of the F-type ATP synthase complex. In this study, we report the presence of intermediary modules based on the phylogenetic profiles of the human mitochondrial proteins. The two main intermediary modules comprise the α3β3 hexamer in the F1 and the c-subunit ring in the Fo. A comprehensive analysis of bacterial transcription units of F1Fo ATP synthase revealed that while a long and constant order of F1Fo ATP synthase genes exists in a majority of bacterial genomes, highly conserved combinations of separate transcription units are present among certain bacterial classes and phyla. Based on our findings, we propose a model that includes the involvement of multiple modules in the evolution of F1Fo ATP synthase. The central and peripheral stalk subunits provide a link for the integration of the F1/Fo modules.}, }
@article {pmid29176839, year = {2017}, author = {Peçanha, WT and Althoff, SL and Galiano, D and Quintela, FM and Maestri, R and Gonçalves, GL and Freitas, TRO}, title = {Pleistocene climatic oscillations in Neotropical open areas: Refuge isolation in the rodent Oxymycterus nasutus endemic to grasslands.}, journal = {PloS one}, volume = {12}, number = {11}, pages = {e0187329}, pmid = {29176839}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Brazil ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Genetic Markers ; Genetic Variation ; Geography ; *Grassland ; Haplotypes/genetics ; Mitochondria/genetics ; Models, Theoretical ; *Paleontology ; Phylogeny ; Rodentia/genetics/*physiology ; Skull/anatomy &amp; histology ; Species Specificity ; Time Factors ; *Tropical Climate ; Uruguay ; }, abstract = {Pleistocene climatic oscillations favoured the expansion of grassland ecosystems and open vegetation landscapes throughout the Neotropics, and influenced the evolutionary history of species adapted to such environments. In this study, we sampled populations of the rodent Oxymycterus nasutus endemic to open areas in the Pampas and Atlantic Forest biomes to assess the tempo and mode of population divergence using an integrative approach, including coalescence theory, ecological niche models, and morphometry. Our results indicated that these O. nasutus populations exhibited high levels of genetic structure. Six major mtDNA clades were found, structuring these biomes into distinct groups. Estimates of their divergence times was indicated to be 0.571 myr. The high degree of genetic structure is reflected in the analyses of geometric morphometric; skull differences between lineages in the two ecoregions were detected. During the last glacial maximum, there was a strong increase in suitable abiotic conditions for O. nasutus. Distinct molecular markers revealed a population expansion over time, with a possible demographic retraction during the post-glacial period. Considering that all clades coalesce with the last interglacial maximum, our results indicated that reduction in suitable conditions during this period may have resulted in a possible vicariance associated with refuge isolation.}, }
@article {pmid29174633, year = {2018}, author = {Praefcke, GJK}, title = {Regulation of innate immune functions by guanylate-binding proteins.}, journal = {International journal of medical microbiology : IJMM}, volume = {308}, number = {1}, pages = {237-245}, doi = {10.1016/j.ijmm.2017.10.013}, pmid = {29174633}, issn = {1618-0607}, mesh = {Animals ; Autophagy/immunology ; Cytoplasm/*immunology/microbiology/parasitology/virology ; GTP Phosphohydrolases/immunology/metabolism ; GTP-Binding Proteins/chemistry/immunology/metabolism/*physiology ; Humans ; *Immunity, Innate ; Inflammasomes/immunology/metabolism ; Interferons/immunology/metabolism ; Vacuoles/metabolism/microbiology/parasitology/virology ; }, abstract = {Guanylate-binding proteins (GBP) are a family of dynamin-related large GTPases which are expressed in response to interferons and other pro-inflammatory cytokines. GBPs mediate a broad spectrum of innate immune functions against intracellular pathogens ranging from viruses to bacteria and protozoa. Several binding partners for individual GBPs have been identified and several different mechanisms of action have been proposed depending on the organisms, the cell type and the pathogen used. Many of these anti-pathogenic functions of GBPs involve the recruitment to and the subsequent destruction of pathogen containing vacuolar compartments, the assembly of large oligomeric innate immune complexes such as the inflammasome, or the induction of autophagy. Furthermore, GBPs often cooperate with immunity-related GTPases (IRGs), another family of dynamin-related GTPases, to exert their anti-pathogenic function, but since most IRGs have been lost in the evolution of higher primates, the anti-pathogenic function of human GBPs seems to be IRG-independent. GBPs and IRGs share biochemical and structural properties with the other members of the dynamin superfamily such as low nucleotide affinity and a high intrinsic GTPase activity which can be further enhanced by oligomerisation. Furthermore, GBPs and IRGs can interact with lipid membranes. In the case of three human and murine GBP isoforms this interaction is mediated by C-terminal isoprenylation. Based on cell biological studies, and in analogy to the function of other dynamins in membrane scission events, it has been postulated that both GBPs and IRGs might actively disrupt the outer membrane of pathogen-containing vacuole leading to the detection and destruction of the pathogen by the cytosolic innate immune system of the host. Recent evidence, however, indicates that GBPs might rather function by mediating membrane tethering events similar to the dynamin-related atlastin and mitofusin proteins, which mediate fusion of the ER and mitochondria, respectively. The aim of this review is to highlight the current knowledge on the function of GBPs in innate immunity and to combine it with the recent progress in the biochemical characterisation of this protein family.}, }
@article {pmid29171872, year = {2017}, author = {Luévano-Martínez, LA and Kowaltowski, AJ}, title = {Topological characterization of the mitochondrial phospholipid scramblase 3.}, journal = {FEBS letters}, volume = {591}, number = {24}, pages = {4056-4066}, doi = {10.1002/1873-3468.12917}, pmid = {29171872}, issn = {1873-3468}, mesh = {Animals ; Cardiolipins/chemistry/metabolism ; Crystallography, X-Ray ; Intracellular Membranes/metabolism ; Male ; Mitochondria/*enzymology ; Models, Molecular ; Phospholipid Transfer Proteins/*chemistry/genetics/metabolism ; Phylogeny ; Rats ; Rats, Sprague-Dawley ; Saccharomyces cerevisiae ; }, abstract = {Scramblases redistribute phospholipids in biological membranes. Phospholipid scramblase 3 (PLSCR3), which is located in mitochondria, has been reported to be involved in cardiolipin distribution from the inner to the outer membrane, thus regulating cellular processes such as apoptosis or mitophagy. However, the localization and topology of this protein has not been convincingly addressed to support a role in intermembrane phospholipid transfer. Here, we studied PLSCR3 topology within mitochondria. We show that PLSCR3 inserts in the inner membrane (IM) via its C-terminal transmembrane helix, whereas its N-terminal portion is oriented toward the intermembrane space where it is activated by calcium. Our results suggest that PLSCR3, via its C-terminal transmembrane domain, participates in the bidirectional movement of phospholipids within the IM.}, }
@article {pmid29171834, year = {2017}, author = {Quandt, CA and Beaudet, D and Corsaro, D and Walochnik, J and Michel, R and Corradi, N and James, TY}, title = {The genome of an intranuclear parasite, Paramicrosporidium saccamoebae, reveals alternative adaptations to obligate intracellular parasitism.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {29171834}, issn = {2050-084X}, mesh = {*Adaptation, Biological ; Amoeba/microbiology ; Animals ; Fungi/*genetics ; *Genome, Fungal ; *Host-Parasite Interactions ; Molecular Sequence Annotation ; Sequence Analysis, DNA ; }, abstract = {Intracellular parasitism often results in gene loss, genome reduction, and dependence upon the host for cellular functioning. Rozellomycota is a clade comprising many such parasites and is related to the diverse, highly reduced, animal parasites, Microsporidia. We sequenced the nuclear and mitochondrial genomes of Paramicrosporidium saccamoebae [Rozellomycota], an intranuclear parasite of amoebae. A canonical fungal mitochondrial genome was recovered from P. saccamoebae that encodes genes necessary for the complete oxidative phosphorylation pathway including Complex I, differentiating it from most endoparasites including its sequenced relatives in Rozellomycota and Microsporidia. Comparative analysis revealed that P. saccamoebae shares more gene content with distantly related Fungi than with its closest relatives, suggesting that genome evolution in Rozellomycota and Microsporidia has been affected by repeated and independent gene losses, possibly as a result of variation in parasitic strategies (e.g. host and subcellular localization) or due to multiple transitions to parasitism.}, }
@article {pmid29168500, year = {2017}, author = {Bohnert, KA and Kenyon, C}, title = {A lysosomal switch triggers proteostasis renewal in the immortal C. elegans germ lineage.}, journal = {Nature}, volume = {551}, number = {7682}, pages = {629-633}, pmid = {29168500}, issn = {1476-4687}, support = {P40 OD010440/OD/NIH HHS/United States ; R01 AG011816/AG/NIA NIH HHS/United States ; R37 AG011816/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Caenorhabditis elegans/*cytology/*metabolism ; Caenorhabditis elegans Proteins/metabolism ; *Cell Lineage ; Female ; Fertilization ; Hormones/metabolism ; Hydrogen-Ion Concentration ; Lysosomes/*metabolism ; Male ; Mitochondria/metabolism ; Oocytes/*cytology/enzymology/*metabolism ; Oogenesis ; Protein Aggregation, Pathological/metabolism ; *Proteostasis ; Signal Transduction ; Spermatozoa/metabolism ; Vacuolar Proton-Translocating ATPases/biosynthesis/metabolism ; Xenopus ; }, abstract = {Although individuals age and die with time, an animal species can continue indefinitely, because of its immortal germ-cell lineage. How the germline avoids transmitting damage from one generation to the next remains a fundamental question in biology. Here we identify a lysosomal switch that enhances germline proteostasis before fertilization. We find that Caenorhabditis elegans oocytes whose maturation is arrested by the absence of sperm exhibit hallmarks of proteostasis collapse, including protein aggregation. Remarkably, sperm-secreted hormones re-establish oocyte proteostasis once fertilization becomes imminent. Key to this restoration is activation of the vacuolar H[+]-ATPase (V-ATPase), a proton pump that acidifies lysosomes. Sperm stimulate V-ATPase activity in oocytes by signalling the degradation of GLD-1, a translational repressor that blocks V-ATPase synthesis. Activated lysosomes, in turn, promote a metabolic shift that mobilizes protein aggregates for degradation, and reset proteostasis by enveloping and clearing the aggregates. Lysosome acidification also occurs during Xenopus oocyte maturation; thus, a lysosomal switch that enhances oocyte proteostasis in anticipation of fertilization may be conserved in other species.}, }
@article {pmid29162845, year = {2017}, author = {Chatre, L and Fernandes, J and Michel, V and Fiette, L and Avé, P and Arena, G and Jain, U and Haas, R and Wang, TC and Ricchetti, M and Touati, E}, title = {Helicobacter pylori targets mitochondrial import and components of mitochondrial DNA replication machinery through an alternative VacA-dependent and a VacA-independent mechanisms.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {15901}, pmid = {29162845}, issn = {2045-2322}, mesh = {Animals ; Bacterial Proteins/*metabolism ; Cell Line ; Cytosol/metabolism ; DNA Polymerase gamma/metabolism ; *DNA Replication ; DNA, Mitochondrial/*metabolism ; DNA-Binding Proteins/metabolism ; Helicobacter Infections/metabolism/microbiology ; Helicobacter pylori/*metabolism ; High Mobility Group Proteins/metabolism ; Humans ; Mice ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/metabolism ; Models, Biological ; Protein Transport ; }, abstract = {Targeting mitochondria is a powerful strategy for pathogens to subvert cell physiology and establish infection. Helicobacter pylori is a bacterial pathogen associated with gastric cancer development that is known to target mitochondria directly and exclusively through its pro-apoptotic and vacuolating cytotoxin VacA. By in vitro infection of gastric epithelial cells with wild-type and VacA-deficient H. pylori strains, treatment of cells with purified VacA proteins and infection of a mouse model, we show that H. pylori deregulates mitochondria by two novel mechanisms, both rather associated with host cell survival. First, early upon infection VacA induces transient increase of mitochondrial translocases and a dramatic accumulation of the mitochondrial DNA replication and maintenance factors POLG and TFAM. These events occur when VacA is not detected intracellularly, therefore do not require the direct interaction of the cytotoxin with the organelle, and are independent of the toxin vacuolating activity. In vivo, these alterations coincide with the evolution of gastric lesions towards severity. Second, H. pylori also induces VacA-independent alteration of mitochondrial replication and import components, suggesting the involvement of additional H. pylori activities in mitochondria-mediated effects. These data unveil two novel mitochondrial effectors in H. pylori-host interaction with links on gastric pathogenesis.}, }
@article {pmid29161481, year = {2017}, author = {Arrivillaga-Henríquez, J and Enríquez, S and Romero, V and Echeverría, G and Pérez-Barrera, J and Poveda, A and Navarro, JC and Warburg, A and Benítez, W}, title = {[Eco-epidemiological aspects, natural detection and molecular identification of Leishmania spp. in Lutzomyia reburra, Lutzomyia barrettoi majuscula and Lutzomyia trapidoi].}, journal = {Biomedica : revista del Instituto Nacional de Salud}, volume = {37}, number = {0}, pages = {83-97}, doi = {10.7705/biomedica.v37i0.3536}, pmid = {29161481}, issn = {2590-7379}, mesh = {Animals ; Cell Nucleus/enzymology ; DNA Topoisomerases, Type II/genetics ; DNA, Protozoan/analysis ; DNA, Ribosomal Spacer/analysis ; Ecuador ; Feeding Behavior ; Female ; Insect Vectors/*parasitology ; Leishmania/genetics/*isolation &amp; purification/physiology ; Leishmaniasis, Cutaneous/parasitology/*transmission ; Mitochondria/enzymology ; Phylogeny ; Phylogeography ; Protozoan Proteins/genetics ; Psychodidae/*parasitology ; Species Specificity ; }, abstract = {INTRODUCTION: The province of Pichincha in Ecuador is an endemic area of cutaneous leishmaniasis, where anthropophilic sand flies with natural infection by Leishmania, have been reported as vectors. However, the role in transmission of zoophilic species has not been evaluated.<br><br>OBJECTIVE: To evaluate natural infection by Leishmania in two zoophilic phlebotomine sand fly species, Lutzomyia reburra and Lu. barrettoi majuscula, and one anthropophilic species, Lu. trapidoi, as well as the endophagy and synanthropism of these species in the northwest of Pichincha.<br><br>MATERIALS AND METHODS: Phlebotomines were collected using CDC light traps in different habitats and altitudes with presence of cutaneous leishmaniasis. Leishmania infection was detected using genomic DNA from females of the collected sand flies. We amplified the internal transcribed spacer gene of ribosomal RNA I (ITS1), the mitochondrial topoisomerase II gene (mtTOPOII), and the nuclear topoisomerase II gene (TopoII). Percentages of positivity for Leishmania, at spatio-temporal scale, proportion of endophagy and synanthropism index were calculated.<br><br>RESULTS: Natural infection was determined for Le. amazonensis in Lu. reburra (9.5%) and Lu. b. majuscula (23.8%), while in Lu. trapidoi we detected Le. amazonensis, Le. brazilienis and Le. naiffi-lainsoni. Phlebotomines were asynanthropic and with low endophagy.<br><br>CONCLUSION: Natural infection with Le. amazonensis was recorded for the first time in Lu. reburra and Lu. b. majuscula, demonstrating the importance of zoophilic phlebotomines in the maintenance of the Leishmania transmission cycle in endemic foci.}, }
@article {pmid29160602, year = {2018}, author = {Guedes-Monteiro, RF and Ferreira-Junior, JR and Bleicher, L and Nóbrega, FG and Barrientos, A and Barros, MH}, title = {Mitochondrial ribosome bL34 mutants present diminished translation of cytochrome c oxidase subunits.}, journal = {Cell biology international}, volume = {42}, number = {6}, pages = {630-642}, pmid = {29160602}, issn = {1095-8355}, support = {R35 GM118141/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Electron Transport Complex IV/genetics/*metabolism ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/metabolism ; Mitochondrial Ribosomes/*metabolism ; Mutagenesis, Site-Directed ; Protein Biosynthesis ; RGS Proteins/genetics/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Sequence Alignment ; }, abstract = {Saccharomyces cerevisiae mitoribosomes are specialized in the translation of a few number of highly hydrophobic membrane proteins, components of the oxidative phosphorylation system. Mitochondrial characteristics, such as the membrane system and its redox state driven mitoribosomes evolution through great diversion from their bacterial and cytosolic counterparts. Therefore, mitoribosome presents a considerable number of mitochondrial-specific proteins, as well as new protein extensions. In this work we characterize temperature sensitive mutants of the subunit bL34 present in the 54S large subunit. Although bL34 has bacterial homologs, in yeast it has a long 65 aminoacids mitochondrial N-terminal addressing sequence, here we demonstrate that it can be replaced by the mitochondrial addressing sequence of Neurospora crassa ATP9 gene. The bL34 temperature sensitive mutants present lowered translation of mitochondrial COX1 and COX3, which resulted in reduced cytochrome c oxidase activity and respiratory growth deficiency. The sedimentation properties of bL34 in sucrose gradients suggest that similarly to its bacterial homolog, bL34 is also a later participant in the process of mitoribosome biogenesis.}, }
@article {pmid29155472, year = {2018}, author = {Wang, D and Gu, J and David, R and Wang, Z and Yang, S and Searle, IR and Zhu, JK and Timmis, JN}, title = {Experimental reconstruction of double-stranded break repair-mediated plastid DNA insertion into the tobacco nucleus.}, journal = {The Plant journal : for cell and molecular biology}, volume = {93}, number = {2}, pages = {227-234}, doi = {10.1111/tpj.13769}, pmid = {29155472}, issn = {1365-313X}, mesh = {Cell Nucleus/genetics ; *DNA Breaks, Double-Stranded ; *DNA Repair ; DNA, Chloroplast/genetics ; Genome, Plant/*genetics ; Plastids/genetics ; Symbiosis ; Nicotiana/*genetics ; }, abstract = {The mitochondria and plastids of eukaryotic cells evolved from endosymbiotic prokaryotes. DNA from the endosymbionts has bombarded nuclei since the ancestral prokaryotes were engulfed by a precursor of the nucleated eukaryotic host. An experimental confirmation regarding the molecular mechanisms responsible for organelle DNA incorporation into nuclei has not been performed until the present analysis. Here we introduced double-stranded DNA breaks into the nuclear genome of tobacco through inducible expression of I-SceI, and showed experimentally that tobacco chloroplast DNAs insert into nuclear genomes through double-stranded DNA break repair. Microhomology-mediated linking of disparate segments of chloroplast DNA occurs frequently during healing of induced nuclear double-stranded breaks (DSB) but the resulting nuclear integrants are often immediately unstable. Non-Mendelian inheritance of a selectable marker (neo), used to identify plastid DNA transfer, was observed in the progeny of about 50% of lines emerging from the screen. The instability of these de novo nuclear insertions of plastid DNA (nupts) was shown to be associated with deletion not only of the nupt itself but also of flanking nuclear DNA within one generation of transfer. This deletion of pre-existing nuclear DNA suggests that the genetic impact of organellar DNA transfer to the nucleus is potentially far greater than previously thought.}, }
@article {pmid29155008, year = {2018}, author = {McDonald, AE and Pichaud, N and Darveau, CA}, title = {"Alternative" fuels contributing to mitochondrial electron transport: Importance of non-classical pathways in the diversity of animal metabolism.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {224}, number = {}, pages = {185-194}, doi = {10.1016/j.cbpb.2017.11.006}, pmid = {29155008}, issn = {1879-1107}, mesh = {Animals ; Citric Acid Cycle/*physiology ; Electron Transport/physiology ; Glycolysis/*physiology ; Humans ; Mitochondria/*physiology ; *Oxidative Phosphorylation ; }, abstract = {The study of glycolysis, the TCA cycle, and oxidative phosphorylation in animals has yielded a wealth of information about bioenergetics. Less is known about how animals use fuels other than glucose and less characterized enzymes that are also used to provide electrons to the electron transport system. It has become clear that bioenergetic flexibility is employed by a wide variety of animals in order to successfully grow, maintain cells, and reproduce, and has contributed to the exploitation of new environments and ecological niches through evolution. In most cases, the discovery of these "alternative" fuels and non-classical pathways is relatively recent, but is starting to call into question long believed paradigms about the diversity of animal bioenergetics. We present several specific examples of these "alternatives" and the animals that use them and present some implications for animal mitochondrial physiology research.}, }
@article {pmid29154466, year = {2018}, author = {Wei, X and Li, H and Zhao, G and Yang, J and Li, L and Huang, Y and Lan, X and Ma, Y and Hu, L and Zheng, H and Chen, H}, title = {ΔFosB regulates rosiglitazone-induced milk fat synthesis and cell survival.}, journal = {Journal of cellular physiology}, volume = {233}, number = {12}, pages = {9284-9298}, doi = {10.1002/jcp.26218}, pmid = {29154466}, issn = {1097-4652}, mesh = {Animals ; Apoptosis/drug effects/genetics ; Calcium/metabolism ; Cell Proliferation/drug effects ; Cell Survival/drug effects/genetics ; Cells, Cultured ; Cytoprotection/drug effects/genetics ; Epithelial Cells/drug effects/metabolism ; Female ; Gene Expression Regulation/drug effects ; Goats ; Lipid Droplets/drug effects/metabolism ; Lipid Metabolism/genetics ; Lipids/*biosynthesis ; Mammary Glands, Animal/*cytology ; Matrix Metalloproteinase 9/metabolism ; Milk/*chemistry ; Mitochondria/drug effects/metabolism ; PPAR gamma/metabolism ; Proto-Oncogene Proteins c-bcl-2 ; Proto-Oncogene Proteins c-fos/*metabolism ; Rosiglitazone/*pharmacology ; Triglycerides/biosynthesis ; }, abstract = {Rosiglitazone induces adipogenesis in adipocyte and regulates cell survival and differentiation in number of cell types. However, whether PPARγ regulates the synthesis of milk fat and cell survival in goat mammary gland remains unknown. Rosiglitazone strongly enhanced cellular triacylglycerol content and accumulation of lipid droplet in goat mammary epithelial cells (GMEC). Furthermore, ΔFosB decreased the expression of PPARγ at both mRNA and protein levels, and rosiglitazone-induced milk fat synthesis was abolished by ΔFosB overexpression. ΔFosB reduced milk fat synthesis and enhanced saturated fatty acid concentration. Rosiglitazone increased the number of GMEC in G0/G1 phase and inhibited cell proliferation, and these effects were improved by overexpression of ΔFosB. ΔFosB was found to promote the expression of Bcl-2 and suppress the expression of Bax, and protected GMEC from apoptosis induced by rosiglitazone. Intracellular calcium trafficking assay revealed that rosiglitazone markedly increased intracellular calcium concentration. ΔFosB protected GMEC from apoptosis induced by intracellular Ca[2+] overload. ΔFosB increased MMP-9 gelatinolytic activity. SB-3CT, an MMP-9 inhibitor, suppressed the expression of Bcl-2, and increased intracellular calcium levels, and this effect was abolished by ΔFosB overexpression. SB-3CT induced GMEC apoptosis and this effect was inhibited by ΔFosB overexpression. These findings suggest that ΔFosB regulates rosiglitazone-induced milk fat synthesis and cell survival. Therefore, ΔFosB may be an important checkpoint to control milk fat synthesis and cell apoptosis.}, }
@article {pmid29154412, year = {2018}, author = {Shaw, RE and Banks, SC and Peakall, R}, title = {The impact of mating systems and dispersal on fine-scale genetic structure at maternally, paternally and biparentally inherited markers.}, journal = {Molecular ecology}, volume = {27}, number = {1}, pages = {66-82}, doi = {10.1111/mec.14433}, pmid = {29154412}, issn = {1365-294X}, mesh = {Animal Migration ; Animals ; DNA, Mitochondrial/genetics ; Female ; Genetic Markers ; Inheritance Patterns/*genetics ; Male ; Mammals/*genetics ; *Sexual Behavior, Animal ; Y Chromosome/genetics ; }, abstract = {For decades, studies have focused on how dispersal and mating systems influence genetic structure across populations or social groups. However, we still lack a thorough understanding of how these processes and their interaction shape spatial genetic patterns over a finer scale (tens-hundreds of metres). Using uniparentally inherited markers may help answer these questions, yet their potential has not been fully explored. Here, we use individual-level simulations to investigate the effects of dispersal and mating system on fine-scale genetic structure at autosomal, mitochondrial and Y chromosome markers. Using genetic spatial autocorrelation analysis, we found that dispersal was the major driver of fine-scale genetic structure across maternally, paternally and biparentally inherited markers. However, when dispersal was restricted (mean distance = 100 m), variation in mating behaviour created strong differences in the comparative level of structure detected at maternally and paternally inherited markers. Promiscuity reduced spatial genetic structure at Y chromosome loci (relative to monogamy), whereas structure increased under polygyny. In contrast, mitochondrial and autosomal markers were robust to differences in the specific mating system, although genetic structure increased across all markers when reproductive success was skewed towards fewer individuals. Comparing males and females at Y chromosome vs. mitochondrial markers, respectively, revealed that some mating systems can generate similar patterns to those expected under sex-biased dispersal. This demonstrates the need for caution when inferring ecological and behavioural processes from genetic results. Comparing patterns between the sexes, across a range of marker types, may help us tease apart the processes shaping fine-scale genetic structure.}, }
@article {pmid29149282, year = {2017}, author = {Skibinski, DOF and Ghiselli, F and Diz, AP and Milani, L and Mullins, JGL}, title = {Structure-Related Differences between Cytochrome Oxidase I Proteins in a Stable Heteroplasmic Mitochondrial System.}, journal = {Genome biology and evolution}, volume = {9}, number = {12}, pages = {3265-3281}, pmid = {29149282}, issn = {1759-6653}, mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Substitution ; Animals ; Bivalvia/cytology/enzymology/*genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*chemistry/classification/genetics ; *Evolution, Molecular ; Female ; Inheritance Patterns ; Male ; Membrane Potential, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Protein Conformation ; Protein Structure, Secondary ; Protein Subunits ; Sequence Analysis, DNA ; }, abstract = {Many bivalve species have two types of mitochondrial DNA passed independently through the female line (F genome) and male line (M genome). Here we study the cytochrome oxidase I protein in such bivalve species and provide evidence for differences between the F and M proteins in amino acid property values, particularly relating to hydrophobicity and helicity. The magnitude of these differences varies between different regions of the protein and the change from the ancestor is most marked in the M protein. The observed changes occur in parallel and in the same direction in the different species studied. Two possible causes are considered, first relaxation of purifying selection with drift and second positive selection. These may operate in different ways in different regions of the protein. Many different amino acid substitutions contribute in a small way to the observed variation, but substitutions involving alanine and serine have a quantitatively large effect. Some of these substitutions are potential targets for phosphorylation and some are close to residues of functional importance in the catalytic mechanism. We propose that the observed changes in the F and M proteins might contribute to functional differences between them relating to ATP production and mitochondrial membrane potential with implications for sperm function.}, }
@article {pmid29145028, year = {2018}, author = {Sun, S and Hui, M and Wang, M and Sha, Z}, title = {The complete mitochondrial genome of the alvinocaridid shrimp Shinkaicaris leurokolos (Decapoda, Caridea): Insight into the mitochondrial genetic basis of deep-sea hydrothermal vent adaptation in the shrimp.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {25}, number = {}, pages = {42-52}, doi = {10.1016/j.cbd.2017.11.002}, pmid = {29145028}, issn = {1878-0407}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Arthropod Proteins/*genetics ; Base Sequence ; Conserved Sequence ; Decapoda/*genetics/physiology ; *Genome, Mitochondrial ; *Hydrothermal Vents ; Open Reading Frames ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Deep-sea hydrothermal vent is one of the most extreme environments on Earth with low oxygen and high levels of toxins. Decapod species from the family Alvinocarididae have colonized and successfully adapted to this extremely harsh environment. Mitochondria plays a vital role in oxygen usage and energy metabolism, thus it may be under selection in the adaptive evolution of the hydrothermal vent shrimps. In this study, the mitochondrial genome (mitogenome) of alvinocaridid shrimp Shinkaicaris leurokolos (Kikuchi &amp; Hashimoto, 2000) was determined through Illumina sequencing. The mitogenome of S. leurokolos was 15,903bp in length, containing 13 protein-coding genes, 2 rRNAs, and 22 tRNAs. The gene order and orientation were identical to those of sequenced alvinocaridids. It has the longest concatenated sequences of protein-coding genes, tRNAs and shortest pooled rRNAs among the alvinocaridids. The control regions (CRs) of alvinocaridid were significantly longer (p<0.01) than those of the other caridaen. The alignment of the alvinocaridid CRs revealed two conserved sequence blocks (CSBs), and each of the CSBs included a noncanonical open reading frame (ORF), which may be involved in adjusting mitochondrial energy metabolism to adapt to the hydrothermal environment. Phylogenetic analysis supported that the deep-sea hydrothermal vent shrimps may have originated from those living in shallow area. Positive selection analysis reveals the evidence of adaptive change in the mitogenome of Alvinocarididae. Thirty potentially important adaptive residues were identified, which were located in atp6, cox1, cox3, cytb and nad1-5. This study explores the mitochondrial genetic basis of hydrothermal vent adaptation in alvinocaridid for the first time, and provides valuable clues regarding the adaptation.}, }
@article {pmid29141880, year = {2017}, author = {Lague, SL and Chua, B and Alza, L and Scott, GR and Frappell, PB and Zhong, Y and Farrell, AP and McCracken, KG and Wang, Y and Milsom, WK}, title = {Divergent respiratory and cardiovascular responses to hypoxia in bar-headed geese and Andean birds.}, journal = {The Journal of experimental biology}, volume = {220}, number = {Pt 22}, pages = {4186-4194}, doi = {10.1242/jeb.168799}, pmid = {29141880}, issn = {1477-9145}, mesh = {*Altitude ; Anaerobiosis ; Animal Migration ; Animals ; Biological Evolution ; Ducks/*physiology ; Female ; Geese/*physiology ; *Life History Traits ; Male ; *Oxygen Consumption ; Phylogeny ; *Respiration ; Species Specificity ; }, abstract = {Many high-altitude vertebrates have evolved increased capacities in their oxygen transport cascade (ventilation, pulmonary diffusion, circulation and tissue diffusion), enhancing oxygen transfer from the atmosphere to mitochondria. However, the extent of interspecies variation in the control processes that dictate hypoxia responses remains largely unknown. We compared the metabolic, cardiovascular and respiratory responses to progressive decreases in inspired oxygen levels of bar-headed geese (Anser indicus), birds that biannually migrate across the Himalayan mountains, with those of Andean geese (Chloephaga melanoptera) and crested ducks (Lophonetta specularioides), lifelong residents of the high Andes. We show that Andean geese and crested ducks have evolved fundamentally different mechanisms for maintaining oxygen supply during low oxygen (hypoxia) from those of bar-headed geese. Bar-headed geese respond to hypoxia with robust increases in ventilation and heart rate, whereas Andean species increase lung oxygen extraction and cardiac stroke volume. We propose that transient high-altitude performance has favoured the evolution of robust convective oxygen transport recruitment in hypoxia, whereas life-long high-altitude residency has favoured the evolution of structural enhancements to the lungs and heart that increase lung diffusion and stroke volume.}, }
@article {pmid29141015, year = {2017}, author = {Bozler, J and Kacsoh, BZ and Bosco, G}, title = {Nematocytes: Discovery and characterization of a novel anculeate hemocyte in Drosophila falleni and Drosophila phalerata.}, journal = {PloS one}, volume = {12}, number = {11}, pages = {e0188133}, pmid = {29141015}, issn = {1932-6203}, support = {DP1 MH110234/MH/NIMH NIH HHS/United States ; P30 CA023108/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Drosophila/*classification/immunology ; *Hemocytes ; Immunity, Innate ; Microscopy, Fluorescence ; Phylogeny ; Species Specificity ; }, abstract = {Immune challenges, such as parasitism, can be so pervasive and deleterious that they constitute an existential threat to a species' survival. In response to these ecological pressures, organisms have developed a wide array of novel behavioral, cellular, and molecular adaptations. Research into these immune defenses in model systems has resulted in a revolutionary understanding of evolution and functional biology. As the field has expanded beyond the limited number of model organisms our appreciation of evolutionary innovation and unique biology has widened as well. With this in mind, we have surveyed the hemolymph of several non-model species of Drosophila. Here we identify and describe a novel hemocyte, type-II nematocytes, found in larval stages of numerous Drosophila species. Examined in detail in Drosophila falleni and Drosophila phalerata, we find that these remarkable cells are distinct from previously described hemocytes due to their anucleate state (lacking a nucleus) and unusual morphology. Type-II nematocytes are long, narrow cells with spindle-like projections extending from a cell body with high densities of mitochondria and microtubules, and exhibit the ability to synthesize proteins. These properties are unexpected for enucleated cells, and together with our additional characterization, we demonstrate that these type-II nematocytes represent a biological novelty. Surprisingly, despite the absence of a nucleus, we observe through live cell imaging that these cells remain motile with a highly dynamic cellular shape. Furthermore, these cells demonstrate the ability to form multicellular structures, which we suggest may be a component of the innate immune response to macro-parasites. In addition, live cell imaging points to a large nucleated hemocyte, type-I nematocyte, as the progenitor cell, leading to enucleation through a budding or asymmetrical division process rather than nuclear ejection: This study is the first to report such a process of enucleation. Here we describe these cells in detail for the first time and examine their evolutionary history in Drosophila.}, }
@article {pmid29138502, year = {2017}, author = {Pannek, M and Simic, Z and Fuszard, M and Meleshin, M and Rotili, D and Mai, A and Schutkowski, M and Steegborn, C}, title = {Crystal structures of the mitochondrial deacylase Sirtuin 4 reveal isoform-specific acyl recognition and regulation features.}, journal = {Nature communications}, volume = {8}, number = {1}, pages = {1513}, pmid = {29138502}, issn = {2041-1723}, mesh = {Acylation ; Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; Humans ; Isoenzymes/chemistry/genetics/metabolism ; Lysine/*chemistry/genetics/metabolism ; Mitochondrial Proteins/*chemistry/genetics/metabolism ; Models, Molecular ; Phylogeny ; Protein Conformation ; Sequence Homology, Amino Acid ; Sirtuins/*chemistry/genetics/metabolism ; Xenopus ; Xenopus Proteins/*chemistry/genetics/metabolism ; }, abstract = {Sirtuins are evolutionary conserved NAD[+]-dependent protein lysine deacylases. The seven human isoforms, Sirt1-7, regulate metabolism and stress responses and are considered therapeutic targets for aging-related diseases. Sirt4 locates to mitochondria and regulates fatty acid metabolism and apoptosis. In contrast to the mitochondrial deacetylase Sirt3 and desuccinylase Sirt5, no prominent deacylase activity and structural information are available for Sirt4. Here we describe acyl substrates and crystal structures for Sirt4. The enzyme shows isoform-specific acyl selectivity, with significant activity against hydroxymethylglutarylation. Crystal structures of Sirt4 from Xenopus tropicalis reveal a particular acyl binding site with an additional access channel, rationalizing its activities. The structures further identify a conserved, isoform-specific Sirt4 loop that folds into the active site to potentially regulate catalysis. Using these results, we further establish efficient Sirt4 activity assays, an unusual Sirt4 regulation by NADH, and Sirt4 effects of pharmacological modulators.}, }
@article {pmid29137980, year = {2018}, author = {El Haddad, S and Serrano, A and Normand, T and Robin, C and Dubois, M and Brulé-Morabito, F and Mollet, L and Charpentier, S and Legrand, A}, title = {Interaction of Alpha-synuclein with Cytogaligin, a protein encoded by the proapoptotic gene GALIG.}, journal = {Biochemical and biophysical research communications}, volume = {495}, number = {1}, pages = {787-792}, doi = {10.1016/j.bbrc.2017.11.078}, pmid = {29137980}, issn = {1090-2104}, mesh = {Apoptosis ; Apoptosis Regulatory Proteins ; Blood Proteins/*metabolism ; Extracellular Fluid/*metabolism ; Galectins/*metabolism ; HeLa Cells ; Humans ; Protein Binding ; Protein Interaction Mapping ; Subcellular Fractions/*metabolism ; alpha-Synuclein/*metabolism ; }, abstract = {GALIG, an internal gene to the human galectin-3 gene, encodes two distinct proteins, Mitogaligin and Cytogaligin through translation of a unique mRNA in two overlapping alternative reading frames. When overexpressed GALIG induces apoptosis. In cultured cells, Mitogaligin destabilizes mitochondria membranes through interaction with cardiolipin. Little is known regarding the role of Cytogaligin. This protein displays multiple subcellular localizations; cytosol, nucleus, and mitochondria. We illustrate here that Cytogaligin is also secreted in the extracellular medium. Cytogaligin is shown to interact with α-Synuclein, the major component of Lewy bodies in Parkinson's disease. Overexpression of Cytogaligin reduces α-Synuclein dimerization raising a possible role in the evolution of α-Synuclein aggregation, a key molecular event underlying the pathogenesis of Parkinson's disease.}, }
@article {pmid29137957, year = {2018}, author = {Saunders, GW and Jackson, C and Salomaki, ED}, title = {Phylogenetic analyses of transcriptome data resolve familial assignments for genera of the red-algal Acrochaetiales-Palmariales Complex (Nemaliophycidae).}, journal = {Molecular phylogenetics and evolution}, volume = {119}, number = {}, pages = {151-159}, doi = {10.1016/j.ympev.2017.11.002}, pmid = {29137957}, issn = {1095-9513}, mesh = {Base Sequence ; DNA Barcoding, Taxonomic ; DNA, Intergenic/genetics ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Rhodophyta/*classification/*genetics ; Transcriptome/*genetics ; }, abstract = {Phylogenetic analyses of transcriptome data for representatives of the red algal Acrochaetiales-Palmariales Complex provided robust support for the assignment of genera to the constituent families. In the Acrochaetiales, the genera Acrochaetium, Grania, and an unnamed genus-level lineage (Acrochaetiac sp._1Aus) were assigned to the Acrochaetiaceae, while Audouinella is placed in a resurrected Audouinellaceae and Rhodochorton and Rhododrewia constitute the resurrected Rhodochortonaceae. For the Palmariales, transcriptome data solidly support the inclusion of Camontagnea and Rhodothamniella in the Rhodothamniellaceae, Meiodiscus and Rubrointrusa in the Meiodiscaceae, Rhodonematella and Rhodophysema in the Rhodophysemataceae, while Devaleraea and Palmaria remained in the Palmariaceae. These analyses, however, questioned the monophyly of Palmaria, which prompted a second round of analyses using eight common red algal phylogenetic markers and including a broader sampling of red algal genera in our analyses. These results supported transfer of Palmaria callophylloides and P. mollis to the genus Devaleraea necessitating new combinations, and further added the genus Halosaccion to the Palmariaceae and the genera Kallymenicola and Rhodophysemopsis to the Meiodiscaceae. Finally, DNA barcode (mitochondrial COI-5P) and ITS data were explored and supported the continued recognition of Palmaria palmata as a single species in the North Atlantic.}, }
@article {pmid29129605, year = {2018}, author = {Pogozheva, ID and Lomize, AL}, title = {Evolution and adaptation of single-pass transmembrane proteins.}, journal = {Biochimica et biophysica acta. Biomembranes}, volume = {1860}, number = {2}, pages = {364-377}, doi = {10.1016/j.bbamem.2017.11.002}, pmid = {29129605}, issn = {0005-2736}, mesh = {*Adaptation, Physiological ; Arabidopsis/genetics/metabolism ; Cell Membrane/*metabolism ; Databases, Protein ; Dictyostelium/genetics/metabolism ; Escherichia coli/genetics/metabolism ; *Evolution, Molecular ; Humans ; Membrane Proteins/chemistry/genetics/*metabolism ; Methanocaldococcus/genetics/metabolism ; Protein Conformation, alpha-Helical ; Protein Multimerization ; Proteome/chemistry/genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Species Specificity ; }, abstract = {A comparative analysis of 6039 single-pass (bitopic) membrane proteins from six evolutionarily distant organisms was performed based on data from the Membranome database. The observed repertoire of bitopic proteins is significantly enlarged in eukaryotic cells and especially in multicellular organisms due to the diversification of enzymes, emergence of proteins involved in vesicular trafficking, and expansion of receptors, structural, and adhesion proteins. The majority of bitopic proteins in multicellular organisms are located in the plasma membrane (PM) and involved in cell communication. Bitopic proteins from different membranes significantly diverge in terms of their biological functions, size, topology, domain architecture, physical properties of transmembrane (TM) helices and propensity to form homodimers. Most proteins from eukaryotic PM and endoplasmic reticulum (ER) have the N-out topology. The predicted lengths of TM helices and hydrophobic thicknesses, stabilities and hydrophobicities of TM α-helices are the highest for proteins from eukaryotic PM, intermediate for proteins from prokaryotic cells, ER and Golgi apparatus, and lowest for proteins from mitochondria, chloroplasts, and peroxisomes. Tyr and Phe residues accumulate at the cytoplasmic leaflet of PM and at the outer leaflet of membranes of bacteria, Golgi apparatus, and nucleus. The propensity for dimerization increases from unicellular to multicellular eukaryotes, from enzymes to receptors, and from intracellular membrane proteins to PM proteins. More than half of PM proteins form homodimers with a 2:1 ratio of right-handed to left-handed helix packing arrangements. The inverse ratio (1:2) was observed for dimers from the ER, Golgi and vesicles.}, }
@article {pmid29129532, year = {2017}, author = {Campbell, MA and Łukasik, P and Simon, C and McCutcheon, JP}, title = {Idiosyncratic Genome Degradation in a Bacterial Endosymbiont of Periodical Cicadas.}, journal = {Current biology : CB}, volume = {27}, number = {22}, pages = {3568-3575.e3}, pmid = {29129532}, issn = {1879-0445}, support = {NNA17BB05A/ImNASA/Intramural NASA/United States ; }, mesh = {Animals ; Bacteria/genetics ; Biological Evolution ; DNA, Circular/genetics ; Genome, Bacterial ; Genomics ; Hemiptera/*genetics/*microbiology ; Phylogeny ; Sequence Analysis, DNA/methods ; Symbiosis/*genetics ; }, abstract = {When a free-living bacterium transitions to a host-beneficial endosymbiotic lifestyle, it almost invariably loses a large fraction of its genome [1, 2]. The resulting small genomes often become stable in size, structure, and coding capacity [3-5], as exemplified by Sulcia muelleri, a nutritional endosymbiont of cicadas. Sulcia's partner endosymbiont, Hodgkinia cicadicola, similarly remains co-linear in some cicadas diverged by millions of years [6, 7]. But in the long-lived periodical cicada Magicicada tredecim, the Hodgkinia genome has split into dozens of tiny, gene-sparse circles that sometimes reside in distinct Hodgkinia cells [8]. Previous data suggested that all other Magicicada species harbor complex Hodgkinia populations, but the timing, number of origins, and outcomes of the splitting process were unknown. Here, by sequencing Hodgkinia metagenomes from the remaining six Magicicada and two sister species, we show that each Magicicada species harbors Hodgkinia populations of at least 20 genomic circles. We find little synteny among the 256 Hodgkinia circles analyzed except between the most closely related cicada species. Gene phylogenies show multiple Hodgkinia lineages in the common ancestor of Magicicada and its closest known relatives but that most splitting has occurred within Magicicada and has given rise to highly variable Hodgkinia gene dosages among species. These data show that Hodgkinia genome degradation has proceeded down different paths in different Magicicada species and support a model of genomic degradation that is stochastic in outcome and nonadaptive for the host. These patterns mirror the genomic instability seen in some mitochondria.}, }
@article {pmid29126122, year = {2018}, author = {Pacheco, MA and Matta, NE and Valkiunas, G and Parker, PG and Mello, B and Stanley, CE and Lentino, M and Garcia-Amado, MA and Cranfield, M and Kosakovsky Pond, SL and Escalante, AA}, title = {Mode and Rate of Evolution of Haemosporidian Mitochondrial Genomes: Timing the Radiation of Avian Parasites.}, journal = {Molecular biology and evolution}, volume = {35}, number = {2}, pages = {383-403}, pmid = {29126122}, issn = {1537-1719}, support = {R01 GM080586/GM/NIGMS NIH HHS/United States ; R01 GM093939/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; *Genome, Mitochondrial ; *Genome, Protozoan ; Haemosporida/*genetics ; Selection, Genetic ; }, abstract = {Haemosporidians are a diverse group of vector-borne parasitic protozoa that includes the agents of human malaria; however, most of the described species are found in birds and reptiles. Although our understanding of these parasites' diversity has expanded by analyses of their mitochondrial genes, there is limited information on these genes' evolutionary rates. Here, 114 mitochondrial genomes (mtDNA) were studied from species belonging to four genera: Leucocytozoon, Haemoproteus, Hepatocystis, and Plasmodium. Contrary to previous assertions, the mtDNA is phylogenetically informative. The inferred phylogeny showed that, like the genus Plasmodium, the Leucocytozoon and Haemoproteus genera are not monophyletic groups. Although sensitive to the assumptions of the molecular dating method used, the estimated times indicate that the diversification of the avian haemosporidian subgenera/genera took place after the Cretaceous-Paleogene boundary following the radiation of modern birds. Furthermore, parasite clade differences in mtDNA substitution rates and strength of negative selection were detected. These differences may affect the biological interpretation of mtDNA gene lineages used as a proxy to species in ecological and parasitological investigations. Given that the mitochondria are critically important in the parasite life cycle stages that take place in the vector and that the transmission of parasites belonging to particular clades has been linked to specific insect families/subfamilies, this study suggests that differences in vectors have affected the mode of evolution of haemosporidian mtDNA genes. The observed patterns also suggest that the radiation of haemosporidian parasites may be the result of community-level evolutionary processes between their vertebrate and invertebrate hosts.}, }
@article {pmid29123225, year = {2017}, author = {Eme, L and Spang, A and Lombard, J and Stairs, CW and Ettema, TJG}, title = {Archaea and the origin of eukaryotes.}, journal = {Nature reviews. Microbiology}, volume = {15}, number = {12}, pages = {711-723}, pmid = {29123225}, issn = {1740-1534}, mesh = {Archaea/*genetics ; *Biological Evolution ; Eukaryota/*genetics ; Pharmacogenomic Variants ; }, abstract = {Woese and Fox's 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features. Although it has been generally accepted for some time that mitochondria descend from endosymbiotic alphaproteobacteria, the precise evolutionary relationship between eukaryotes and archaea has continued to be a subject of debate. In this Review, we outline a brief history of the changing shape of the tree of life and examine how the recent discovery of a myriad of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes. Furthermore, we revisit central questions regarding the process of eukaryogenesis and discuss what can currently be inferred about the evolutionary transition from the first to the last eukaryotic common ancestor.}, }
@article {pmid29122550, year = {2018}, author = {VandenBrooks, JM and Gstrein, G and Harmon, J and Friedman, J and Olsen, M and Ward, A and Parker, G}, title = {Supply and demand: How does variation in atmospheric oxygen during development affect insect tracheal and mitochondrial networks?.}, journal = {Journal of insect physiology}, volume = {106}, number = {Pt 3}, pages = {217-223}, doi = {10.1016/j.jinsphys.2017.11.001}, pmid = {29122550}, issn = {1879-1611}, mesh = {Animals ; Drosophila/anatomy &amp; histology/*growth &amp; development ; Male ; *Mitochondria, Muscle ; Muscles/anatomy &amp; histology ; Oxygen/*physiology ; Trachea/anatomy &amp; histology/growth &amp; development ; }, abstract = {Atmospheric oxygen is one of the most important atmospheric component for all terrestrial organisms. Variation in atmospheric oxygen has wide ranging effects on animal physiology, development, and evolution. This variation in oxygen has the potential to affect both respiratory systems (the supply side) and mitochondrial networks (the demand side) in animals. Insect respiratory systems supplying oxygen to tissues in the gas phase through blind ended tracheal systems are particularly susceptible to this variation. While the large conducting tracheae have previously been shown to respond developmentally to changes in rearing oxygen, the effect of oxygen on the tracheolar network has been relatively unexplored, especially in adult insects. Similarly, mitochondrial networks that meet energy demand in insects and other animals are dynamic and their enzyme activities have been shown to vary in the presence of oxygen. These two systems together should be under selective pressure to meet the aerobic metabolic requirements of insects. To test this hypothesis, we reared Mito-YFP Drosophila under three different oxygen concentrations hypoxia (12%), normoxia (21%), and hyperoxia (31%) and imaged their tracheolar and mitochondrial networks within their flight muscle using confocal microscopy. In terms of oxygen supply, hypoxia increased mean (mid-length) tracheolar diameters, tracheolar tip diameters, the number of tracheoles per main branch and affected tracheal branching patterns, while the opposite was observed in hyperoxia. In terms of oxygen demand, hypoxia increased mitochondrial investment and mitochondrial to tracheolar volume ratios; while the opposite was observed in hyperoxia. Generally, hypoxia had a stronger effect on both systems than hyperoxia. These results show that insects are capable of developmentally changing investment in both their supply and demand networks to increase overall fitness.}, }
@article {pmid29117860, year = {2017}, author = {Peleh, V and Zannini, F and Backes, S and Rouhier, N and Herrmann, JM}, title = {Erv1 of Arabidopsis thaliana can directly oxidize mitochondrial intermembrane space proteins in the absence of redox-active Mia40.}, journal = {BMC biology}, volume = {15}, number = {1}, pages = {106}, pmid = {29117860}, issn = {1741-7007}, mesh = {Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Mitochondrial Membrane Transport Proteins/*genetics/metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/genetics/*metabolism ; Oxidation-Reduction ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; }, abstract = {BACKGROUND: Many proteins of the mitochondrial intermembrane space (IMS) contain structural disulfide bonds formed by the mitochondrial disulfide relay. In fungi and animals, the sulfhydryl oxidase Erv1 'generates' disulfide bonds that are passed on to the oxidoreductase Mia40, which oxidizes substrate proteins. A different structural organization of plant Erv1 proteins compared to that of animal and fungal orthologs was proposed to explain its inability to complement the corresponding yeast mutant.<br><br>RESULTS: Herein, we have revisited the biochemical and functional properties of Arabidopsis thaliana Erv1 by both in vitro reconstituted activity assays and complementation of erv1 and mia40 yeast mutants. These mutants were viable, however, they showed severe defects in the biogenesis of IMS proteins. The plant Erv1 was unable to oxidize yeast Mia40 and rather even blocked its activity. Nevertheless, it was able to mediate the import and folding of mitochondrial proteins.<br><br>CONCLUSIONS: We observed that plant Erv1, unlike its homologs in fungi and animals, can promote protein import and oxidative protein folding in the IMS independently of the oxidoreductase Mia40. In accordance to the absence of Mia40 in many protists, our study suggests that the mitochondrial disulfide relay evolved in a stepwise reaction from an Erv1-only system to which Mia40 was added in order to improve substrate specificity. Graphical Abstract The mitochondrial disulfide relay evolved in a step-wise manner from an Erv1-only system.}, }
@article {pmid29117562, year = {2017}, author = {Redrejo-Rodríguez, M and Ordóñez, CD and Berjón-Otero, M and Moreno-González, J and Aparicio-Maldonado, C and Forterre, P and Salas, M and Krupovic, M}, title = {Primer-Independent DNA Synthesis by a Family B DNA Polymerase from Self-Replicating Mobile Genetic Elements.}, journal = {Cell reports}, volume = {21}, number = {6}, pages = {1574-1587}, pmid = {29117562}, issn = {2211-1247}, support = {340440/ERC_/European Research Council/International ; }, mesh = {Amino Acid Sequence ; Bacteriophage M13/genetics ; DNA/*biosynthesis ; DNA Primers/*metabolism ; DNA, Single-Stranded/biosynthesis ; DNA-Directed DNA Polymerase/chemistry/classification/genetics/*metabolism ; Databases, Genetic ; Escherichia coli/enzymology ; Phylogeny ; Plasmids/genetics/metabolism ; Recombinant Proteins/biosynthesis/isolation &amp; purification ; Sequence Alignment ; Transcription, Genetic ; }, abstract = {Family B DNA polymerases (PolBs) play a central role during replication of viral and cellular chromosomes. Here, we report the discovery of a third major group of PolBs, which we denote primer-independent PolB (piPolB), that might be a link between the previously known protein-primed and RNA/DNA-primed PolBs. PiPolBs are encoded by highly diverse mobile genetic elements, pipolins, integrated in the genomes of diverse bacteria and also present as circular plasmids in mitochondria. Biochemical characterization showed that piPolB displays efficient DNA polymerization activity that can use undamaged and damaged templates and is endowed with proofreading and strand displacement capacities. Remarkably, the protein is also capable of template-dependent de novo DNA synthesis, i.e., DNA-priming activity, thereby breaking the long-standing dogma that replicative DNA polymerases require a pre-existing primer for DNA synthesis. We suggest that piPolBs are involved in self-replication of pipolins and may also contribute to bacterial DNA damage tolerance.}, }
@article {pmid29117555, year = {2017}, author = {Labbadia, J and Brielmann, RM and Neto, MF and Lin, YF and Haynes, CM and Morimoto, RI}, title = {Mitochondrial Stress Restores the Heat Shock Response and Prevents Proteostasis Collapse during Aging.}, journal = {Cell reports}, volume = {21}, number = {6}, pages = {1481-1494}, pmid = {29117555}, issn = {2211-1247}, support = {P01 AG049665/AG/NIA NIH HHS/United States ; R37 AG026647/AG/NIA NIH HHS/United States ; RF1 AG057296/AG/NIA NIH HHS/United States ; }, mesh = {*Aging ; Animals ; Caenorhabditis elegans/*metabolism ; Caenorhabditis elegans Proteins/antagonists &amp; inhibitors/genetics/metabolism ; Cytoplasm/metabolism ; Electron Transport Chain Complex Proteins/antagonists &amp; inhibitors/metabolism ; Heat-Shock Proteins/genetics/metabolism ; Heat-Shock Response/*genetics ; Longevity ; Mitochondria/drug effects/*metabolism ; Protein Binding ; Proteostasis/physiology ; RNA Interference ; RNA Polymerase II/genetics/metabolism ; RNA, Small Interfering/metabolism ; Reactive Oxygen Species/metabolism ; Stress, Physiological ; Temperature ; Transcription Factors/genetics/metabolism ; Xenobiotics/pharmacology ; }, abstract = {In Caenorhabditis elegans, the programmed repression of the heat shock response (HSR) accompanies the transition to reproductive maturity, leaving cells vulnerable to environmental stress and protein aggregation with age. To identify the factors driving this event, we performed an unbiased genetic screen for suppressors of stress resistance and identified the mitochondrial electron transport chain (ETC) as a central regulator of the age-related decline of the HSR and cytosolic proteostasis. Mild downregulation of ETC activity, either by genetic modulation or exposure to mitochondria-targeted xenobiotics, maintained the HSR in adulthood by increasing HSF-1 binding and RNA polymerase II recruitment at HSF-1 target genes. This resulted in a robust restoration of cytoplasmic proteostasis and increased vitality later in life, without detrimental effects on fecundity. We propose that low levels of mitochondrial stress regulate cytoplasmic proteostasis and healthspan during aging by coordinating the long-term activity of HSF-1 with conditions preclusive to optimal fitness.}, }
@article {pmid29117544, year = {2017}, author = {Nave, KA and Tzvetanova, ID and Schirmeier, S}, title = {Glial Cell Evolution: The Origins of a Lipid Store.}, journal = {Cell metabolism}, volume = {26}, number = {5}, pages = {701-702}, doi = {10.1016/j.cmet.2017.10.011}, pmid = {29117544}, issn = {1932-7420}, mesh = {Animals ; Apolipoproteins E ; *Lactic Acid ; *Lipid Droplets ; Lipids ; Neuroglia ; Neurons ; Reactive Oxygen Species ; }, abstract = {In Drosophila, neuronal mitochondria that lack OXPHOS generate ROS-protective fatty acids and lipid droplets in associated glia. In this issue, Liu et al. (2017) demonstrate that neuronal lipid synthesis is driven by the glial lactate shuttle. This lipoprotein-dependent deposition of lipids may be at the origin of glial specializations evolving in vertebrates.}, }
@article {pmid29112874, year = {2017}, author = {Roger, AJ and Muñoz-Gómez, SA and Kamikawa, R}, title = {The Origin and Diversification of Mitochondria.}, journal = {Current biology : CB}, volume = {27}, number = {21}, pages = {R1177-R1192}, doi = {10.1016/j.cub.2017.09.015}, pmid = {29112874}, issn = {1879-0445}, mesh = {Adenosine Triphosphate/biosynthesis/metabolism ; Alphaproteobacteria/*genetics/growth &amp; development ; *Biological Evolution ; Eukaryotic Cells/*metabolism ; Genome, Mitochondrial/genetics ; Membrane Transport Proteins/genetics ; *Mitochondria/genetics/metabolism/physiology ; Protein Transport/genetics/physiology ; Symbiosis/genetics/physiology ; }, abstract = {Mitochondria are best known for their role in the generation of ATP by aerobic respiration. Yet, research in the past half century has shown that they perform a much larger suite of functions and that these functions can vary substantially among diverse eukaryotic lineages. Despite this diversity, all mitochondria derive from a common ancestral organelle that originated from the integration of an endosymbiotic alphaproteobacterium into a host cell related to Asgard Archaea. The transition from endosymbiotic bacterium to permanent organelle entailed a massive number of evolutionary changes including the origins of hundreds of new genes and a protein import system, insertion of membrane transporters, integration of metabolism and reproduction, genome reduction, endosymbiotic gene transfer, lateral gene transfer and the retargeting of proteins. These changes occurred incrementally as the endosymbiont and the host became integrated. Although many insights into this transition have been gained, controversy persists regarding the nature of the original endosymbiont, its initial interactions with the host and the timing of its integration relative to the origin of other features of eukaryote cells. Since the establishment of the organelle, proteins have been gained, lost, transferred and retargeted as mitochondria have specialized into the spectrum of functional types seen across the eukaryotic tree of life.}, }
@article {pmid29107619, year = {2018}, author = {Chueca, LJ and Gómez-Moliner, BJ and Madeira, MJ and Pfenninger, M}, title = {Molecular phylogeny of Candidula (Geomitridae) land snails inferred from mitochondrial and nuclear markers reveals the polyphyly of the genus.}, journal = {Molecular phylogenetics and evolution}, volume = {118}, number = {}, pages = {357-368}, doi = {10.1016/j.ympev.2017.10.022}, pmid = {29107619}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Cell Nucleus/*genetics ; Electron Transport Complex IV/chemistry/genetics ; Evolution, Molecular ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/genetics ; RNA, Ribosomal, 28S/chemistry/genetics ; RNA, Ribosomal, 5.8S/chemistry/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Snails/*classification/genetics ; }, abstract = {The genus Candidula (Geomitridae), consisting of 28 species in Western Europe as currently described, has a disjunct distribution in the Iberian Peninsula, Italy, the Balkans, the Aegean Islands, and one species on the Canary Islands. Although the genus is seemingly well defined by characters of the reproductive system, the relationships within the genus are still unclear and some authors have indicated a possible subgeneric division based on the internal morphology of the dart sac. Despite substantial phylogenetic incongruence, we present a well-resolved molecular phylogeny of Candidula based on two mitochondrial genes (COI and 16S rRNA), the nuclear rDNA region (5.8S rNRA + ITS2 + 28S rRNA) and seven additional nuclear DNA regions developed specifically for this genus (60SL13, 60SL17, 60SL7, RPL14, 40SS6, 60SL9, 60SL13a), in total 5595 bp. Six reciprocally monophyletic entities including Candidula species were recovered, grouping into two major clades. The incorporation of additional geomitrid genera allowed us to unequivocally demonstrate the polyphyly of the genus Candidula. One major clade grouped species from southern France and Italy with the widely distributed species C. unifasciata. The second major clade grouped all the species from the Iberian Peninsula, including C. intersecta and C. gigaxii. Candidula ultima from the Canary Islands was recovered as separated lineage within the latter clade and related to African taxa. The six monophyla were defined as six new genera belonging to different tribes within the Helicellinae. Thus, we could show that similar structures of the stimulatory apparatus of the genital system in different taxa do not necessarily indicate a close phylogenetic relationship in the Geomitridae. More genera of the family are needed to clarify their evolutionary relationships, and to fully understand the evolution of the stimulatory apparatus of the genital system within the Geomitridae.}, }
@article {pmid29107618, year = {2018}, author = {da Cruz, MOR and Weksler, M}, title = {Impact of tree priors in species delimitation and phylogenetics of the genus Oligoryzomys (Rodentia: Cricetidae).}, journal = {Molecular phylogenetics and evolution}, volume = {119}, number = {}, pages = {1-12}, doi = {10.1016/j.ympev.2017.10.021}, pmid = {29107618}, issn = {1095-9513}, mesh = {Animals ; Arvicolinae/*classification ; Bayes Theorem ; Mitochondria/metabolism ; *Phylogeny ; Probability ; Species Specificity ; Time Factors ; }, abstract = {The use of genetic data and tree-based algorithms to delimit evolutionary lineages is becoming an important practice in taxonomic identification, especially in morphologically cryptic groups. The effects of different phylogenetic and/or coalescent models in the analyses of species delimitation, however, are not clear. In this paper, we assess the impact of different evolutionary priors in phylogenetic estimation, species delimitation, and molecular dating of the genus Oligoryzomys (Mammalia: Rodentia), a group with complex taxonomy and morphological cryptic species. Phylogenetic and coalescent analyses included 20 of the 24 recognized species of the genus, comprising of 416 Cytochrome b sequences, 26 Cytochrome c oxidase I sequences, and 27 Beta-Fibrinogen Intron 7 sequences. For species delimitation, we employed the General Mixed Yule Coalescent (GMYC) and Bayesian Poisson tree processes (bPTP) analyses, and contrasted 4 genealogical and phylogenetic models: Pure-birth (Yule), Constant Population Size Coalescent, Multiple Species Coalescent, and a mixed Yule-Coalescent model. GMYC analyses of trees from different genealogical models resulted in similar species delimitation and phylogenetic relationships, with incongruence restricted to areas of poor nodal support. bPTP results, however, significantly differed from GMYC for 5 taxa. Oligoryzomys early diversification was estimated to have occurred in the Early Pleistocene, between 0.7 and 2.6 MYA. The mixed Yule-Coalescent model, however, recovered younger dating estimates for Oligoryzomys diversification, and for the threshold for the speciation-coalescent horizon in GMYC. Eight of the 20 included Oligoryzomys species were identified as having two or more independent evolutionary units, indicating that current taxonomy of Oligoryzomys is still unsettled.}, }
@article {pmid29106540, year = {2017}, author = {Degli Esposti, M}, title = {A Journey across Genomes Uncovers the Origin of Ubiquinone in Cyanobacteria.}, journal = {Genome biology and evolution}, volume = {9}, number = {11}, pages = {3039-3053}, pmid = {29106540}, issn = {1759-6653}, mesh = {Bacterial Proteins/genetics ; Biosynthetic Pathways ; Cyanobacteria/enzymology/*genetics/metabolism ; Databases, Protein ; Escherichia coli/enzymology/genetics/metabolism ; *Evolution, Molecular ; Genome, Bacterial/*genetics ; Mitochondria/enzymology/genetics/metabolism ; Phylogeny ; Proteobacteria/enzymology/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Ubiquinone/biosynthesis/classification/*genetics ; }, abstract = {Ubiquinone (Q) is an isoprenoid quinone that functions as membrane electron carrier in mitochondria and bacterial organisms belonging to the alpha, beta, and gamma class of proteobacteria. The biosynthesis of Q follows various biochemical steps catalyzed by diverse proteins that are, in general, homologous in mitochondria and bacteria. Nonorthologous proteins can also contribute to some biochemical steps as originally uncovered in Escherichia coli, which is the best studied organism for Q biosynthesis in prokaryotes. However, the origin of the biosynthetic pathway of Q has remained obscure. Here, I show by genome analysis that Q biosynthesis originated in cyanobacteria and then diversified in anaerobic alpha proteobacteria which have extant relatives in members of the Rhodospirillaceae family. Two distinct biochemical pathways diverged when ambient oxygen reached current levels on earth, one leading to the well-known series of Ubi genes found in E. coli, and the other containing CoQ proteins originally found in eukaryotes. Extant alpha proteobacteria show Q biosynthesis pathways that are more similar to that present in mitochondria than to that of E. coli. Hence, this work clarifies not only the origin but also the evolution of Q biosynthesis from bacteria to mitochondria.}, }
@article {pmid29106528, year = {2017}, author = {Ostersetzer-Biran, O and Lane, N and Pomiankowski, A and Burton, R and Arnqvist, G and Filipovska, A and Huchon, D and Mishmar, D}, title = {The First Mitochondrial Genomics and Evolution SMBE-Satellite Meeting: A New Scientific Symbiosis.}, journal = {Genome biology and evolution}, volume = {9}, number = {11}, pages = {3054-3058}, pmid = {29106528}, issn = {1759-6653}, mesh = {Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genome, Mitochondrial/*genetics ; *Genomics ; Humans ; Maternal Inheritance ; Mitochondria/*genetics/metabolism ; }, abstract = {The central role of the mitochondrion for cellular and organismal metabolism is well known, yet its functional role in evolution has rarely been featured in leading international conferences. Moreover, the contribution of mitochondrial genetics to complex disease phenotypes is particularly important, and although major advances have been made in the field of genomics, mitochondrial genomic data have in many cases been overlooked. Accumulating data and new knowledge support a major contribution of this maternally inherited genome, and its interactions with the nucleus, to both major evolutionary processes and diverse disease phenotypes. These advances encouraged us to assemble the first Mitochondrial Genomics and Evolution (MGE) meeting-an SMBE satellite and Israeli Science foundation international conference (Israel, September 2017). Here, we report the content and outcome of the MGE meeting (https://www.mge2017.com/; last accessed November 5, 2017).}, }
@article {pmid29104545, year = {2017}, author = {Dobson, GP and Arsyad, A and Letson, HL}, title = {The Adenosine Hypothesis Revisited: Modulation of Coupling between Myocardial Perfusion and Arterial Compliance.}, journal = {Frontiers in physiology}, volume = {8}, number = {}, pages = {824}, pmid = {29104545}, issn = {1664-042X}, abstract = {For over four decades the thoracic aortic ring model has become one of the most widely used methods to study vascular reactivity and electromechanical coupling. A question that is rarely asked, however, is what function does a drug-mediated relaxation (or contraction) in this model serve in the intact system? The physiological significance of adenosine relaxation in rings isolated from large elastic conduit arteries from a wide range of species remains largely unknown. We propose that adenosine relaxation increases aortic compliance in acute stress states and facilitates ventricular-arterial (VA) coupling, and thereby links compliance and coronary artery perfusion to myocardial energy metabolism. In 1963 Berne argued that adenosine acts as a local negative feedback regulator between oxygen supply and demand in the heart during hypoxic/ischemic stress. The adenosine VA coupling hypothesis extends and enhances Berne's "adenosine hypothesis" from a local regulatory scheme in the heart to include conduit arterial function. In multicellular organisms, evolution may have selected adenosine, nitric oxide, and other vascular mediators, to modulate VA coupling for optimal transfer of oxygen (and nutrients) from the lung, heart, large conduit arteries, arterioles and capillaries to respiring mitochondria. Finally, a discussion of the potential clinical significance of adenosine modulation of VA coupling is extended to vascular aging and disease, including hypertension, diabetes, obesity, coronary artery disease and heart failure.}, }
@article {pmid29104141, year = {2018}, author = {Lüddecke, T and Krehenwinkel, H and Canning, G and Glaw, F and Longhorn, SJ and Tänzler, R and Wendt, I and Vences, M}, title = {Discovering the silk road: Nuclear and mitochondrial sequence data resolve the phylogenetic relationships among theraphosid spider subfamilies.}, journal = {Molecular phylogenetics and evolution}, volume = {119}, number = {}, pages = {63-70}, doi = {10.1016/j.ympev.2017.10.015}, pmid = {29104141}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Silk/*genetics ; Spiders/*classification/*genetics ; }, abstract = {The mygalomorph spiders in the family Theraphosidae, also known as "tarantulas", are one of the most popular and diverse groups of arachnids, but their evolutionary history remains poorly understood because morphological analyses have only provided mostly controversial results, and a broad molecular perspective has been lacking until now. In this study we provide a preliminary molecular phylogenetic hypothesis of relationships among theraphosid subfamilies, based on 3.5 kbp of three nuclear and three mitochondrial markers, for 52 taxa representing 10 of the 11 commonly accepted subfamilies. Our analysis confirms the monophyly of the Theraphosidae and of most recognized theraphosid subfamilies, supports the validity of the Stromatopelminae and Poecilotheriinae, and indicates paraphyly of the Schismatothelinae. The placement of representatives of Schismatothelinae also indicates possible non-monophyly of Aviculariinae and supports the distinction of the previously contentious subfamily Psalmopoeinae. Major clades typically corresponded to taxa occurring in the same biogeographic region, with two of them each occurring in Africa, South America and Asia. Because relationships among these major clades were poorly supported, more extensive molecular data sets are required to test the hypothesis of independent colonization and multiple dispersal events among these continents.}, }
@article {pmid29100916, year = {2018}, author = {Krishnan, R and Girish Babu, P and Jeena, K and Tripathi, G and Pani Prasad, K}, title = {Molecular characterization, ontogeny and expression profiling of mitochondrial antiviral signaling adapter, MAVS from Asian seabass Lates calcarifer, Bloch (1790).}, journal = {Developmental and comparative immunology}, volume = {79}, number = {}, pages = {175-185}, doi = {10.1016/j.dci.2017.10.019}, pmid = {29100916}, issn = {1879-0089}, mesh = {Adaptor Proteins, Signal Transducing/*genetics ; Animals ; Bass/*immunology ; Cloning, Molecular ; Fish Diseases/*immunology ; Fish Proteins ; Gene Expression Profiling ; Immunity, Innate ; Mitochondria/*metabolism ; Nodaviridae/*physiology ; Phylogeny ; RNA Virus Infections/*immunology ; Signal Transduction ; Spleen/*metabolism ; Zebrafish Proteins/genetics ; }, abstract = {Mitochondrial antiviral signaling protein (MAVS), an innate immune signaling adapter coordinates the signals received from two independent cytosolic pathogen recognition receptors (RIG-1 and MDA5) to induce antiviral genes. In the present study the MAVS gene of Lates calcarifer (LcMAVS) was cloned and characterized. The complete cDNA sequence of LcMAVS was 3160 bp and encodes a poly peptide of 577 amino acids. Structural analysis of LcMAVS revealed an N-terminal CARD-like domain, central proline-rich domain and a C-terminal transmembrane domain. Phylogenetic analysis indicated that LcMAVS exhibited the closest relationship to P. olivaceous MAVS. LcMAVS was ubiquitously expressed in all tested tissues of healthy fish viz., brain, gill, heart, liver, spleen, kidney and intestine, with highest transcript level in spleen. The mRNA transcript level of LcMAVS in different developmental stages showed constitutive expression in all the stages tested suggesting the maternal transfer of the gene. Significant up regulation in MAVS expression was observed post nervous necrosis virus (NNV) challenge in vivo in all the selected tissues. Further, time course analysis showed that LcMAVS transcripts significantly increased in the brain and spleen tissues after NNV infection. These findings provide useful information for further elucidating the function of LcMAVS in antiviral innate immune response against NNV in Asian seabass.}, }
@article {pmid29099633, year = {2017}, author = {Kotarska, K and Doniec, A and Bednarska, M and Polański, Z and Styrna, J}, title = {Aging deteriorates quality of sperm produced by male mice with partial Yq deletion.}, journal = {Systems biology in reproductive medicine}, volume = {63}, number = {6}, pages = {360-363}, doi = {10.1080/19396368.2017.1391888}, pmid = {29099633}, issn = {1939-6376}, mesh = {Aging/*physiology ; Animals ; Azoospermia/genetics ; *Chromosome Deletion ; Fertilization ; Infertility, Male/genetics ; Male ; Mice ; Mice, Congenic/genetics ; Mitochondria/physiology ; Sperm Motility/genetics ; Spermatogenesis/genetics ; Spermatozoa/*physiology/ultrastructure ; Y Chromosome/*genetics ; }, abstract = {UNLABELLED: The aim of the study was to assess the cumulative effects of aging and Y-chromosome long arm deletion on sperm quality parameters. Motility, mitochondrial activity, and head morphology were evaluated for sperm of 3- and 12-month-old males from B10.BR-Y[del] and B10.BR congenic mouse strains. The study revealed that quality and fertilizing potential of sperm produced by younger and older B10.BR males persist on similar levels, but worsen significantly with age of B10.BR-Y[del] males. The findings imply that partial Yq deletions might be more harmful for spermiogenesis in advancing age and may be applicable to other species including humans.<br><br>ABBREVIATIONS: AZF: azoospermia factor; MSYq: male-specific region of the Y-chromosome long arm.}, }
@article {pmid29080362, year = {2018}, author = {Fernandez-Martell, A and Johari, YB and James, DC}, title = {Metabolic phenotyping of CHO cells varying in cellular biomass accumulation and maintenance during fed-batch culture.}, journal = {Biotechnology and bioengineering}, volume = {115}, number = {3}, pages = {645-660}, doi = {10.1002/bit.26485}, pmid = {29080362}, issn = {1097-0290}, mesh = {Animals ; *Biomass ; CHO Cells ; Cell Culture Techniques/*methods ; Cricetulus ; *Glycolysis ; Mitochondria/*metabolism ; Oxidation-Reduction ; }, abstract = {CHO cell lines capable of high-level recombinant protein product biosynthesis during fed-batch culture are still generally obtained by intensive empirical screening of transfected cells rather than knowledge-guided cellular engineering. In this study, we investigate how CHO cell lines create and maintain cellular biosynthetic capacity during fed-batch culture to achieve the optimal combination of rapid exponential proliferation and extended maintenance of high cell biomass concentration. We perform a comparative meta-analysis of mitochondrial and glycolytic functions of 22 discrete parental CHO cell lineages varying in fed-batch culture performance to test the hypotheses that (i) "biomass-intensive" CHO cells exhibit conserved differences in metabolic programming and (ii) it is possible to isolate parental CHO cell lines with a biomass-intensive phenotype to support fed-batch bioproduction processes. We show that for most parental CHO cell lines, rapid proliferation and high late-stage culture performance are mutually exclusive objectives. However, quantitative dissection of mitochondrial and glycolytic functions revealed that a small proportion of clones utilize a conserved metabolic program that significantly enhances cellular glycolytic and mitochondrial oxidative capacity at the onset of late-stage culture. We reveal the central importance of dynamic metabolic re-programming to activate oxidative mitochondrial function as a necessary mechanism to support CHO cell biosynthetic performance during culture.}, }
@article {pmid29079378, year = {2018}, author = {Yoshizawa, K and Johnson, KP and Sweet, AD and Yao, I and Ferreira, RL and Cameron, SL}, title = {Mitochondrial phylogenomics and genome rearrangements in the barklice (Insecta: Psocodea).}, journal = {Molecular phylogenetics and evolution}, volume = {119}, number = {}, pages = {118-127}, doi = {10.1016/j.ympev.2017.10.014}, pmid = {29079378}, issn = {1095-9513}, mesh = {Animals ; Evolution, Molecular ; *Gene Order ; *Genome, Mitochondrial ; Insecta/*classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Annotation ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The mitochondrial genome arrangement in the insect order Psocodea (booklice, barklice, and parasitic lice) is extremely variable. Genome organization ranges from the rearrangement of a few tRNAs and protein coding genes, through extensive tRNA and protein coding gene rearrangements, to subdivision into multiple mini-chromosomes. Evolution of the extremely modified mitochondrial genome in parasitic lice (Phthiraptera) has been the subject of several studies, but limited information is available regarding the mitochondrial genome organization of the more plesiomorphic, free-living Psocodea (formerly known as the "Psocoptera"). In particular, the ancestral state of the psocodean mitochondrial genome arrangement and the evolutionary pathway to the rearranged conditions are still unknown. In this study, we addressed mitochondrial evolutionary questions within the Psocodea by using mitochondrial genome sequences obtained from a wide range of Psocoptera, covering all three suborders. We identified seven types of mitochondrial genome arrangements in Psocoptera, including the first example in Psocodea of retention of the ancestral pancrustacean condition in Prionoglaris (Prionoglarididae). Two methods (condition-based parsimony reconstruction and common-interval genome distances) were applied to estimate the ancestral mitochondrial arrangement in Psocodea, and both provided concordant results. Specifically, the common ancestor of Psocodea retained the ancestral pancrustacean condition, and most of the gene arrangement types have originated independently from this ancestral condition. We also utilized the genomic data for phylogenetic estimation. The tree estimated from the mitochondrial genomic data was well resolved, strongly supported, and in agreement with previously estimated phylogenies. It also provided the first robust support for the family Prionoglarididae, as its monophyly was uncertain in previous morphological and molecular studies.}, }
@article {pmid29075935, year = {2017}, author = {Glasgow, RIC and Thompson, K and Barbosa, IA and He, L and Alston, CL and Deshpande, C and Simpson, MA and Morris, AAM and Neu, A and Löbel, U and Hall, J and Prokisch, H and Haack, TB and Hempel, M and McFarland, R and Taylor, RW}, title = {Novel GFM2 variants associated with early-onset neurological presentations of mitochondrial disease and impaired expression of OXPHOS subunits.}, journal = {Neurogenetics}, volume = {18}, number = {4}, pages = {227-235}, pmid = {29075935}, issn = {1364-6753}, support = {01GM1603, 01GM1207//German Bundesministerium f&#xfc;r Bildung und Forschung (BMBF) and Horizon2020/ ; NIHR-HCS-D12-03-04//NIHR/CSO Healthcare Science Research Fellowship/ ; G0800674//Mitochondrial Disease Patient Cohort (UK)/ ; 203105/Z/16/Z//Wellcome Centre for Mitochondrial Research/ ; 633974//EU Horizon2020 Collaborative Research Project SOUND/ ; NIHR-HCS-D12-03-04/DH_/Department of Health/United Kingdom ; FKZ 01ZX1405C//German Federal Ministry of Education and Research (BMBF)/ ; }, mesh = {Child ; Exome/genetics ; Female ; Homozygote ; Humans ; Male ; Mitochondria/*genetics/metabolism ; Mitochondrial Diseases/*genetics ; Mitochondrial Proteins/genetics/*metabolism ; Mutation/genetics ; Pedigree ; Peptide Elongation Factor G/*genetics ; Phenotype ; }, abstract = {Mitochondrial diseases are characterised by clinical, molecular and functional heterogeneity, reflecting their bi-genomic control. The nuclear gene GFM2 encodes mtEFG2, a protein with an essential role during the termination stage of mitochondrial translation. We present here two unrelated patients harbouring different and previously unreported compound heterozygous (c.569G>A, p.(Arg190Gln); c.636delA, p.(Glu213Argfs*3)) and homozygous (c.275A>C, p.(Tyr92Ser)) recessive variants in GFM2 identified by whole exome sequencing (WES) together with histochemical and biochemical findings to support the diagnoses of pathological GFM2 variants in each case. Both patients presented similarly in early childhood with global developmental delay, raised CSF lactate and abnormalities on cranial MRI. Sanger sequencing of familial samples confirmed the segregation of bi-allelic GFM2 variants with disease, while investigations into steady-state mitochondrial protein levels revealed respiratory chain subunit defects and loss of mtEFG2 protein in muscle. These data demonstrate the effects of defective mtEFG2 function, caused by previously unreported variants, confirming pathogenicity and expanding the clinical phenotypes associated with GFM2 variants.}, }
@article {pmid29074460, year = {2018}, author = {Smith, CH and Johnson, NA and Pfeiffer, JM and Gangloff, MM}, title = {Molecular and morphological data reveal non-monophyly and speciation in imperiled freshwater mussels (Anodontoides and Strophitus).}, journal = {Molecular phylogenetics and evolution}, volume = {119}, number = {}, pages = {50-62}, doi = {10.1016/j.ympev.2017.10.018}, pmid = {29074460}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Bivalvia/*anatomy &amp; histology/*genetics ; Florida ; *Fresh Water ; *Genetic Speciation ; Geography ; Haplotypes/genetics ; Louisiana ; Mitochondria/metabolism ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Accurate taxonomic placement is vital to conservation efforts considering many intrinsic biological characteristics of understudied species are inferred from closely related taxa. The rayed creekshell, Anodontoides radiatus (Conrad, 1834), exists in the Gulf of Mexico drainages from western Florida to Louisiana and has been petitioned for listing under the Endangered Species Act. We set out to resolve the evolutionary history of A. radiatus, primarily generic placement and species boundaries, using phylogenetic, morphometric, and geographic information. Our molecular matrix contained 3 loci: cytochrome c oxidase subunit I, NADH dehydrogenase subunit I, and the nuclear-encoded ribosomal internal transcribed spacer I. We employed maximum likelihood and Bayesian inference to estimate a phylogeny and test the monophyly of Anodontoides and Strophitus. We implemented two coalescent-based species delimitation models to test seven species models and evaluate species boundaries within A. radiatus. Concomitant to molecular data, we also employed linear morphometrics and geographic information to further evaluate species boundaries. Molecular and morphological evidence supports the inclusion of A. radiatus in the genus Strophitus, and we resurrect the binomial Strophitus radiatus to reflect their shared common ancestry. We also found strong support for polyphyly in Strophitus and advocate the resurrection of the genus Pseudodontoideus to represent 'Strophitus' connasaugaensis and 'Strophitus' subvexus. Strophitus radiatus exists in six well-supported clades that were distinguished as evolutionary independent lineages using Bayesian inference, maximum likelihood, and coalescent-based species delimitation models. Our integrative approach found evidence for as many as 4 evolutionary divergent clades within S. radiatus. Therefore, we formally describe two new species from the S. radiatus species complex (Strophitus williamsi and Strophitus pascagoulaensis) and recognize the potential for a third putative species (Strophitus sp. cf. pascagoulaensis). Our findings aid stakeholders in establishing conservation and management strategies for the members of Anodontoides, Strophitus, and Pseudodontoideus.}, }
@article {pmid29073898, year = {2017}, author = {Radzvilavicius, AL and Lane, N and Pomiankowski, A}, title = {Sexual conflict explains the extraordinary diversity of mechanisms regulating mitochondrial inheritance.}, journal = {BMC biology}, volume = {15}, number = {1}, pages = {94}, pmid = {29073898}, issn = {1741-7007}, mesh = {Animals ; *Evolution, Molecular ; Female ; *Genes, Mitochondrial ; *Inheritance Patterns ; Male ; Spermatogenesis ; }, abstract = {BACKGROUND: Mitochondria are predominantly inherited from the maternal gamete, even in unicellular organisms. Yet an extraordinary array of mechanisms enforce uniparental inheritance, which implies shifting selection pressures and multiple origins.<br><br>RESULTS: We consider how this high turnover in mechanisms controlling uniparental inheritance arises using a novel evolutionary model in which control of mitochondrial transmission occurs either during spermatogenesis (by paternal nuclear genes) or at/after fertilization (by maternal nuclear genes). The model treats paternal leakage as an evolvable trait. Our evolutionary analysis shows that maternal control consistently favours strict uniparental inheritance with complete exclusion of sperm mitochondria, whereas some degree of paternal leakage of mitochondria is an expected outcome under paternal control. This difference arises because mito-nuclear linkage builds up with maternal control, allowing the greater variance created by asymmetric inheritance to boost the efficiency of purifying selection and bring benefits in the long term. In contrast, under paternal control, mito-nuclear linkage tends to be much weaker, giving greater advantage to the mixing of cytotypes, which improves mean fitness in the short term, even though it imposes a fitness cost to both mating types in the long term.<br><br>CONCLUSIONS: Sexual conflict is an inevitable outcome when there is competition between maternal and paternal control of mitochondrial inheritance. If evolution has led to complete uniparental inheritance through maternal control, it creates selective pressure on the paternal nucleus in favour of subversion through paternal leakage, and vice versa. This selective divergence provides a reason for the repeated evolution of novel mechanisms that regulate the transmission of paternal mitochondria, both in the fertilized egg and spermatogenesis. Our analysis suggests that the widespread occurrence of paternal leakage and prevalence of heteroplasmy are natural outcomes of this sexual conflict.}, }
@article {pmid29070589, year = {2017}, author = {Cantarero, A and Alonso-Alvarez, C}, title = {Mitochondria-targeted molecules determine the redness of the zebra finch bill.}, journal = {Biology letters}, volume = {13}, number = {10}, pages = {}, pmid = {29070589}, issn = {1744-957X}, mesh = {Animals ; Beak/*physiology ; Carotenoids/*metabolism ; Finches/*physiology ; Male ; Mitochondria/*metabolism ; Onium Compounds/metabolism ; Organophosphorus Compounds/metabolism ; *Pigmentation ; Ubiquinone/analogs &amp; derivatives/metabolism ; }, abstract = {The evolution and production mechanisms of red carotenoid-based ornaments in animals are poorly understood. Recently, it has been suggested that enzymes transforming yellow carotenoids to red pigments (ketolases) in animal cells may be positioned in the inner mitochondrial membrane (IMM) intimately linked to the electron transport chain. These enzymes may mostly synthesize coenzyme Q10 (coQ10), a key redox-cycler antioxidant molecularly similar to yellow carotenoids. It has been hypothesized that this shared pathway favours the evolution of red traits as sexually selected individual quality indices by revealing a well-adjusted oxidative metabolism. We administered mitochondria-targeted molecules to male zebra finches (Taeniopygia guttata) measuring their bill redness, a trait produced by transforming yellow carotenoids. One molecule included coQ10 (mitoquinone mesylate, MitoQ) and the other one (decyl-triphenylphosphonium; dTPP) has the same structure without the coQ10 aromatic ring. At the highest dose, the bill colour of MitoQ and dTPP birds strongly differed: MitoQ birds' bills were redder and dTPP birds showed paler bills even compared to birds injected with saline only. These results suggest that ketolases are indeed placed at the IMM and that coQ10 antioxidant properties may improve their efficiency. The implications for evolutionary theories of sexual signalling are discussed.}, }
@article {pmid29069345, year = {2017}, author = {Christy, SF and Wernick, RI and Lue, MJ and Velasco, G and Howe, DK and Denver, DR and Estes, S}, title = {Adaptive Evolution under Extreme Genetic Drift in Oxidatively Stressed Caenorhabditis elegans.}, journal = {Genome biology and evolution}, volume = {9}, number = {11}, pages = {3008-3022}, pmid = {29069345}, issn = {1759-6653}, mesh = {Adaptation, Physiological/genetics ; Animals ; *Biological Evolution ; Caenorhabditis elegans/*genetics ; Genes, Helminth/*genetics ; *Genetic Drift ; Genetic Fitness ; Mitochondria/genetics ; Models, Genetic ; Mutation Accumulation ; Mutation Rate ; Oxidative Stress/*genetics ; Polymorphism, Single Nucleotide ; Selection, Genetic ; }, abstract = {A mutation-accumulation (MA) experiment with Caenorhabditis elegans nematodes was conducted in which replicate, independently evolving lines were initiated from a low-fitness mitochondrial electron transport chain mutant, gas-1. The original intent of the study was to assess the effect of electron transport chain dysfunction involving elevated reactive oxygen species production on patterns of spontaneous germline mutation. In contrast to results of standard MA experiments, gas-1 MA lines evolved slightly higher mean fitness alongside reduced among-line genetic variance compared with their ancestor. Likewise, the gas-1 MA lines experienced partial recovery to wildtype reactive oxygen species levels. Whole-genome sequencing and analysis revealed that the molecular spectrum but not the overall rate of nuclear DNA mutation differed from wildtype patterns. Further analysis revealed an enrichment of mutations in loci that occur in a gas-1-centric region of the C. elegans interactome, and could be classified into a small number of functional-genomic categories. Characterization of a backcrossed four-mutation set isolated from one gas-1 MA line revealed this combination to be beneficial on both gas-1 mutant and wildtype genetic backgrounds. Our combined results suggest that selection favoring beneficial mutations can be powerful even under unfavorable population genetic conditions, and agree with fitness landscape theory predicting an inverse relationship between population fitness and the likelihood of adaptation.}, }
@article {pmid29068466, year = {2017}, author = {Martin, WF}, title = {Too Much Eukaryote LGT.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {12}, pages = {}, doi = {10.1002/bies.201700115}, pmid = {29068466}, issn = {1521-1878}, mesh = {Animals ; Eukaryota/classification/*genetics ; Eukaryotic Cells/cytology/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genome ; Mitochondria/genetics ; Phylogeny ; Plants/classification/genetics ; Plastids/genetics ; Prokaryotic Cells/cytology/metabolism ; Symbiosis/*genetics ; }, abstract = {The realization that prokaryotes naturally and frequently disperse genes across steep taxonomic boundaries via lateral gene transfer (LGT) gave wings to the idea that eukaryotes might do the same. Eukaryotes do acquire genes from mitochondria and plastids and they do transfer genes during the process of secondary endosymbiosis, the spread of plastids via eukaryotic algal endosymbionts. From those observations it, however, does not follow that eukaryotes transfer genes either in the same ways as prokaryotes do, or to a quantitatively similar degree. An important illustration of the difference is that eukaryotes do not exhibit pangenomes, though prokaryotes do. Eukaryotes reveal no detectable cumulative effects of LGT, though prokaryotes do. A critical analysis suggests that something is deeply amiss with eukaryote LGT theories.}, }
@article {pmid29064673, year = {2018}, author = {Li, S and Shen, G and Li, W}, title = {Intramembrane Thiol Oxidoreductases: Evolutionary Convergence and Structural Controversy.}, journal = {Biochemistry}, volume = {57}, number = {3}, pages = {258-266}, pmid = {29064673}, issn = {1520-4995}, support = {R01 HL121718/HL/NHLBI NIH HHS/United States ; R21 EY028705/EY/NEI NIH HHS/United States ; }, mesh = {Catalysis ; Conserved Sequence ; Disulfides/chemistry ; *Evolution, Molecular ; Humans ; Isomerism ; Oxidoreductases Acting on Sulfur Group Donors/*chemistry ; Protein Folding ; Protein Structure, Secondary ; Sulfhydryl Compounds/*chemistry ; Vitamin K Epoxide Reductases/*chemistry ; }, abstract = {During oxidative protein folding, disulfide bond formation is catalyzed by thiol oxidoreductases. Through dedicated relay pathways, the disulfide is generated in donor enzymes, passed to carrier enzymes, and subsequently delivered to target proteins. The eukaryotic disulfide donors are flavoenzymes, Ero1 in the endoplasmic reticulum and Erv1 in mitochondria. In prokaryotes, disulfide generation is coupled to quinone reduction, catalyzed by intramembrane donor enzymes, DsbB and VKOR. To catalyze de novo disulfide formation, these different disulfide donors show striking structural convergence at several levels. They share a four-helix bundle core structure at their active site, which contains a CXXC motif at a helical end. They have also evolved a flexible loop with shuttle cysteines to transfer electrons to the active site and relay the disulfide bond to the carrier enzymes. Studies of the prokaryotic VKOR, however, have stirred debate about whether the human homologue adopts the same topology with four transmembrane helices and uses the same electron-transfer mechanism. The controversies have recently been resolved by investigating the human VKOR structure and catalytic process in living cells with a mass spectrometry-based approach. Structural convergence between human VKOR and the disulfide donors is found to underlie cofactor reduction, disulfide generation, and electron transfer.}, }
@article {pmid29061908, year = {2017}, author = {Yang, Y and Zhu, G and Li, R and Yan, S and Fu, D and Zhu, B and Tian, H and Luo, Y and Zhu, H}, title = {The RNA Editing Factor SlORRM4 Is Required for Normal Fruit Ripening in Tomato.}, journal = {Plant physiology}, volume = {175}, number = {4}, pages = {1690-1702}, pmid = {29061908}, issn = {1532-2548}, mesh = {CRISPR-Cas Systems ; Fruit/*physiology ; Gene Expression Regulation, Developmental/physiology ; Gene Expression Regulation, Plant/*physiology ; Gene Silencing ; Solanum lycopersicum/genetics/*physiology ; Mitochondria ; Mutation ; Phylogeny ; Plant Development/genetics/physiology ; Plant Proteins/genetics/*metabolism ; RNA Editing/genetics/*physiology ; }, abstract = {RNA editing plays a key posttranscriptional role in gene expression. Existing studies on cytidine-to-uridine RNA editing in plants have focused on maize (Zea mays), rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana). However, the importance and regulation of RNA editing in several critical agronomic processes are not well understood, a notable example of which is fruit ripening. Here, we analyzed the expression profile of 33 RNA editing factors and identified 11 putative tomato (Solanum lycopersicum) fruit ripening-related factors. A rapid virus-induced gene silencing assay indicated that the organelle RNA recognition motif-containing protein SlORRM4 affected tomato fruit ripening. Knocking out SlORRM4 expression using a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 genome editing strategy delayed tomato fruit ripening by lowering respiratory rate and ethylene production. Additionally, the expression of numerous genes associated with fruit ripening and mitochondrial functions changed significantly when SlORRM4 was knocked out. Moreover, the loss of SlORRM4 function significantly reduced RNA editing of many mitochondrial transcripts, leading to low-level expression of some core subunits that are critical for mitochondrial complex assembly (i.e. Nad3, Cytc1, and COX II). Taken together, these results indicate that SlORRM4 is involved in RNA editing of transcripts in ripening fruit that influence mitochondrial function and key aspects of fruit ripening.}, }
@article {pmid29056456, year = {2017}, author = {Wang, P and Khoshravesh, R and Karki, S and Tapia, R and Balahadia, CP and Bandyopadhyay, A and Quick, WP and Furbank, R and Sage, TL and Langdale, JA}, title = {Re-creation of a Key Step in the Evolutionary Switch from C3 to C4 Leaf Anatomy.}, journal = {Current biology : CB}, volume = {27}, number = {21}, pages = {3278-3287.e6}, pmid = {29056456}, issn = {1879-0445}, mesh = {Biological Evolution ; Chloroplasts/*genetics/physiology ; Mitochondria/genetics ; Oryza/*genetics ; Photosynthesis/*genetics ; Plant Leaves/anatomy &amp; histology/genetics/*metabolism ; Plant Proteins/*genetics ; Transcription Factors/*genetics ; Zea mays/*genetics ; }, abstract = {The C4 photosynthetic pathway accounts for ∼25% of primary productivity on the planet despite being used by only 3% of species. Because C4 plants are higher yielding than C3 plants, efforts are underway to introduce the C4 pathway into the C3 crop rice. This is an ambitious endeavor; however, the C4 pathway evolved from C3 on multiple independent occasions over the last 30 million years, and steps along the trajectory are evident in extant species. One approach toward engineering C4 rice is to recapitulate this trajectory, one of the first steps of which was a change in leaf anatomy. The transition from C3 to so-called "proto-Kranz" anatomy requires an increase in organelle volume in sheath cells surrounding leaf veins. Here we induced chloroplast and mitochondrial development in rice vascular sheath cells through constitutive expression of maize GOLDEN2-LIKE genes. Increased organelle volume was accompanied by the accumulation of photosynthetic enzymes and by increased intercellular connections. This suite of traits reflects that seen in "proto-Kranz" species, and, as such, a key step toward engineering C4 rice has been achieved.}, }
@article {pmid29048531, year = {2017}, author = {Wu, B and Macielog, AI and Hao, W}, title = {Origin and Spread of Spliceosomal Introns: Insights from the Fungal Clade Zymoseptoria.}, journal = {Genome biology and evolution}, volume = {9}, number = {10}, pages = {2658-2667}, pmid = {29048531}, issn = {1759-6653}, mesh = {Ascomycota/*genetics ; DNA Transposable Elements ; DNA, Intergenic/genetics ; *Evolution, Molecular ; Genome, Fungal ; *Introns ; Spliceosomes/*genetics ; }, abstract = {Spliceosomal introns are a key feature of eukaryote genome architecture and have been proposed to originate from selfish group II introns from an endosymbiotic bacterium, that is, the ancestor of mitochondria. However, the mechanisms underlying the wide spread of spliceosomal introns across eukaryotic genomes have been obscure. In this study, we characterize the dynamic evolution of spliceosomal introns in the fungal genus Zymoseptoria at different evolutionary scales, that is, within a genome, among conspecific strains within species, and between different species. Within the genome, spliceosomal introns can proliferate in unrelated genes and intergenic regions. Among conspecific strains, spliceosomal introns undergo rapid turnover (gains and losses) and frequent sequence exchange between geographically distinct strains. Furthermore, spliceosomal introns could undergo introgression between distinct species, which can further promote intron invasion and proliferation. The dynamic invasion and proliferation processes of spliceosomal introns resemble the life cycles of mobile selfish (group I/II) introns, and these intron movements, at least in part, account for the dramatic processes of intron gain and intron loss during eukaryotic evolution.}, }
@article {pmid29048527, year = {2017}, author = {Sayadi, A and Immonen, E and Tellgren-Roth, C and Arnqvist, G}, title = {The Evolution of Dark Matter in the Mitogenome of Seed Beetles.}, journal = {Genome biology and evolution}, volume = {9}, number = {10}, pages = {2697-2706}, pmid = {29048527}, issn = {1759-6653}, mesh = {Animals ; Coleoptera/classification/*genetics ; DNA, Intergenic/genetics ; *Evolution, Molecular ; *Genome, Insect ; *Genome, Mitochondrial ; Phylogeny ; Selection, Genetic ; Tandem Repeat Sequences ; *Transcriptome ; }, abstract = {Animal mitogenomes are generally thought of as being economic and optimized for rapid replication and transcription. We use long-read sequencing technology to assemble the remarkable mitogenomes of four species of seed beetles. These are the largest circular mitogenomes ever assembled in insects, ranging from 24,496 to 26,613 bp in total length, and are exceptional in that some 40% consists of non-coding DNA. The size expansion is due to two very long intergenic spacers (LIGSs), rich in tandem repeats. The two LIGSs are present in all species but vary greatly in length (114-10,408 bp), show very low sequence similarity, divergent tandem repeat motifs, a very high AT content and concerted length evolution. The LIGSs have been retained for at least some 45 my but must have undergone repeated reductions and expansions, despite strong purifying selection on protein coding mtDNA genes. The LIGSs are located in two intergenic sites where a few recent studies of insects have also reported shorter LIGSs (>200 bp). These sites may represent spaces that tolerate neutral repeat array expansions or, alternatively, the LIGSs may function to allow a more economic translational machinery. Mitochondrial respiration in adult seed beetles is based almost exclusively on fatty acids, which reduces the need for building complex I of the oxidative phosphorylation pathway (NADH dehydrogenase). One possibility is thus that the LIGSs may allow depressed transcription of NAD genes. RNA sequencing showed that LIGSs are partly transcribed and transcriptional profiling suggested that all seven mtDNA NAD genes indeed show low levels of transcription and co-regulation of transcription across sexes and tissues.}, }
@article {pmid29044162, year = {2017}, author = {Makiuchi, T and Santos, HJ and Tachibana, H and Nozaki, T}, title = {Hetero-oligomer of dynamin-related proteins participates in the fission of highly divergent mitochondria from Entamoeba histolytica.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {13439}, pmid = {29044162}, issn = {2045-2322}, mesh = {Dynamins/chemistry/genetics/*metabolism ; Entamoeba histolytica/genetics/*metabolism ; Evolution, Molecular ; *Mitochondrial Dynamics ; Protein Binding ; Protozoan Proteins/chemistry/genetics/*metabolism ; }, abstract = {Entamoeba histolytica is an anaerobic parasitic protist and possesses mitosomes, one of the most highly divergent mitochondrion-related organelles (MROs). Although unique metabolism and protein/metabolite transport machinery have been demonstrated in Entamoeba mitosomes, the mechanism of mitosomal fusion and fission remains to be elucidated. In this study, we demonstrate that two dynamin-related proteins (DRPs) are cooperatively involved in the fission of Entamoeba mitosomes. Expression of a dominant negative form of EhDrpA and EhDrpB, and alternatively, repression of gene expression of EhDrpA and EhDrpB genes, caused elongation of mitosomes, reflecting inhibition of mitosomal fission. Moreover, EhDrpA and EhDrpB formed an unprecedented hetero-oligomeric complex with an approximate 1:2 to 1:3 ratio, suggesting that the observed elongation of mitosomes is likely caused by the disruption and instability of the complex caused by an imbalance in the two DRPs. Altogether, this is the first report of a hetero-oligomeric DRP complex which participates in the fission of mitochondria and MROs.}, }
@article {pmid29036556, year = {2018}, author = {Kang, C and Badr, MA and Kyrychenko, V and Eskelinen, EL and Shirokova, N}, title = {Deficit in PINK1/PARKIN-mediated mitochondrial autophagy at late stages of dystrophic cardiomyopathy.}, journal = {Cardiovascular research}, volume = {114}, number = {1}, pages = {90-102}, pmid = {29036556}, issn = {1755-3245}, support = {R01 HL093342/HL/NHLBI NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/metabolism ; Animals ; *Autophagy ; Cardiomyopathies/*enzymology/etiology/genetics/pathology ; Cellular Senescence ; Disease Models, Animal ; Mice, Inbred mdx ; Microtubule-Associated Proteins/metabolism ; Mitochondria, Heart/*enzymology/ultrastructure ; *Mitophagy ; Muscular Dystrophy, Duchenne/*complications/enzymology/genetics ; Myocytes, Cardiac/*enzymology/ultrastructure ; Phosphorylation ; Protein Kinases/*metabolism ; Signal Transduction ; Ubiquitin-Protein Ligases/*metabolism ; }, abstract = {AIMS: Duchenne muscular dystrophy (DMD) is an inherited devastating muscle disease with severe and often lethal cardiac complications. Emerging evidence suggests that the evolution of the pathology in DMD is accompanied by the accumulation of mitochondria with defective structure and function. Here, we investigate whether defects in the housekeeping autophagic pathway contribute to mitochondrial and metabolic dysfunctions in dystrophic cardiomyopathy.<br><br>METHODS AND RESULTS: We employed various biochemical and imaging techniques to assess mitochondrial structure and function as well as to evaluate autophagy, and specific mitochondrial autophagy (mitophagy), in hearts of mdx mice, an animal model of DMD. Our results indicate substantial structural damage of mitochondria and a significant decrease in ATP production in hearts of mdx animals, which developed cardiomyopathy. In these hearts, we also detected enhanced autophagy but paradoxically, mitophagy appeared to be suppressed. In addition, we found decreased levels of several proteins involved in the PINK1/PARKIN mitophagy pathway as well as an insignificant amount of PARKIN protein phosphorylation at the S65 residue upon induction of mitophagy.<br><br>CONCLUSIONS: Our results suggest faulty mitophagy in dystrophic hearts due to defects in the PINK1/PARKIN pathway.}, }
@article {pmid29032499, year = {2017}, author = {Hu, L and Yang, Y and Zhao, Y and Niu, D and Yang, R and Wang, R and Lu, Z and Li, X}, title = {DNA barcoding for molecular identification of Demodex based on mitochondrial genes.}, journal = {Parasitology research}, volume = {116}, number = {12}, pages = {3285-3290}, pmid = {29032499}, issn = {1432-1955}, support = {81471972//National Natural Science Foundation of China/ ; 81271856//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Base Sequence ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; Dog Diseases ; Dogs ; *Genes, Mitochondrial ; Mite Infestations/parasitology/veterinary ; Mites/*classification ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {There has been no widely accepted DNA barcode for species identification of Demodex. In this study, we attempted to solve this issue. First, mitochondrial cox1-5' and 12S gene fragments of Demodex folloculorum, D. brevis, D. canis, and D. caprae were amplified, cloned, and sequenced for the first time; intra/interspecific divergences were computed and phylogenetic trees were reconstructed. Then, divergence frequency distribution plots of those two gene fragments were drawn together with mtDNA cox1-middle region and 16S obtained in previous studies. Finally, their identification efficiency was evaluated by comparing barcoding gap. Results indicated that 12S had the higher identification efficiency. Specifically, for cox1-5' region of the four Demodex species, intraspecific divergences were less than 2.0%, and interspecific divergences were 21.1-31.0%; for 12S, intraspecific divergences were less than 1.4%, and interspecific divergences were 20.8-26.9%. The phylogenetic trees demonstrated that the four Demodex species clustered separately, and divergence frequency distribution plot showed that the largest intraspecific divergence of 12S (1.4%) was less than cox1-5' region (2.0%), cox1-middle region (3.1%), and 16S (2.8%). The barcoding gap of 12S was 19.4%, larger than cox1-5' region (19.1%), cox1-middle region (11.3%), and 16S (13.0%); the interspecific divergence span of 12S was 6.2%, smaller than cox1-5' region (10.0%), cox1-middle region (14.1%), and 16S (11.4%). Moreover, 12S has a moderate length (517 bp) for sequencing at once. Therefore, we proposed mtDNA 12S was more suitable than cox1 and 16S to be a DNA barcode for classification and identification of Demodex at lower category level.}, }
@article {pmid29032142, year = {2017}, author = {Ali, RA and Mehdi, AM and Rothnagel, R and Hamilton, NA and Gerle, C and Landsberg, MJ and Hankamer, B}, title = {RAZA: A Rapid 3D z-crossings algorithm to segment electron tomograms and extract organelles and macromolecules.}, journal = {Journal of structural biology}, volume = {200}, number = {2}, pages = {73-86}, doi = {10.1016/j.jsb.2017.10.002}, pmid = {29032142}, issn = {1095-8657}, mesh = {*Algorithms ; Electron Microscope Tomography/*methods ; Humans ; Imaging, Three-Dimensional/*methods ; Mitochondria/*ultrastructure ; Molecular Docking Simulation/*methods ; Ribosomes/*ultrastructure ; }, abstract = {Resolving the 3D architecture of cells to atomic resolution is one of the most ambitious challenges of cellular and structural biology. Central to this process is the ability to automate tomogram segmentation to identify sub-cellular components, facilitate molecular docking and annotate detected objects with associated metadata. Here we demonstrate that RAZA (Rapid 3D z-crossings algorithm) provides a robust, accurate, intuitive, fast, and generally applicable segmentation algorithm capable of detecting organelles, membranes, macromolecular assemblies and extrinsic membrane protein domains. RAZA defines each continuous contour within a tomogram as a discrete object and extracts a set of 3D structural fingerprints (major, middle and minor axes, surface area and volume), enabling selective, semi-automated segmentation and object extraction. RAZA takes advantage of the fact that the underlying algorithm is a true 3D edge detector, allowing the axes of a detected object to be defined, independent of its random orientation within a cellular tomogram. The selectivity of object segmentation and extraction can be controlled by specifying a user-defined detection tolerance threshold for each fingerprint parameter, within which segmented objects must fall and/or by altering the number of search parameters, to define morphologically similar structures. We demonstrate the capability of RAZA to selectively extract subgroups of organelles (mitochondria) and macromolecular assemblies (ribosomes) from cellular tomograms. Furthermore, the ability of RAZA to define objects and their contours, provides a basis for molecular docking and rapid tomogram annotation.}, }
@article {pmid29024751, year = {2018}, author = {Mokodongan, DF and Montenegro, J and Mochida, K and Fujimoto, S and Ishikawa, A and Kakioka, R and Yong, L and Mulis,  and Hadiaty, RK and Mandagi, IF and Masengi, KWA and Wachi, N and Hashiguchi, Y and Kitano, J and Yamahira, K}, title = {Phylogenomics reveals habitat-associated body shape divergence in Oryzias woworae species group (Teleostei: Adrianichthyidae).}, journal = {Molecular phylogenetics and evolution}, volume = {118}, number = {}, pages = {194-203}, doi = {10.1016/j.ympev.2017.10.005}, pmid = {29024751}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Ecosystem ; Female ; *Genomics ; Geography ; Indonesia ; Male ; Mitochondria/genetics ; Oryzias/*anatomy &amp; histology/*genetics ; *Phylogeny ; Principal Component Analysis ; Species Specificity ; }, abstract = {The Oryzias woworae species group, composed of O. asinua, O. wolasi, and O. woworae, is widely distributed in southeastern Sulawesi, an island in the Indo-Australian Archipelago. Deep-elongated body shape divergence is evident among these three species to the extent that it is used as a species-diagnostic character. These fishes inhabit a variety of habitats, ranging from upper streams to ponds, suggesting that the body shape divergence among the three species may reflect adaptation to local environments. First, our geometric morphometrics among eight local populations of this species group revealed that the three species cannot be separated by body shape and that riverine populations had more elongated bodies and longer caudal parts than lacustrine populations. Second, their phylogenetic relationships did not support the presence of three species; phylogenies using mitochondrial DNA and genomic data obtained from RNA-Seq revealed that the eight populations could not be sorted into three different clades representing three described species. Third, phylogenetic corrections of body shape variations and ancestral state reconstruction of body shapes demonstrated that body shape divergence between riverine and lacustrine populations persisted even if the phylogenies were considered and that body shape evolved rapidly irrespective of phylogeny. Sexual dimorphism in body shape was also evident, but the degree of dimorphism did not significantly differ between riverine and lacustrine populations after phylogenetic corrections, suggesting that sexual selection may not substantially contribute to geographical variations in body shape. Overall, these results indicate that the deep-elongated body shape divergence of the O. woworae species group evolved locally in response to habitat environments, such as water currents, and that a thorough taxonomic reexamination of the O. woworae species group may be necessary.}, }
@article {pmid29021915, year = {2017}, author = {Klein, KA and Warren, AK and Baumal, CR and Hedges, TR}, title = {Optical coherence tomography findings in methanol toxicity.}, journal = {International journal of retina and vitreous}, volume = {3}, number = {}, pages = {36}, pmid = {29021915}, issn = {2056-9920}, abstract = {BACKGROUND: Methanol toxicity poses a significant public health problem in developing countries, and in Southeast Asia, where the most common source of poisoning is via adulterated liquor in local drinks. Methanol toxicity can have devastating visual consequences and retinal specialists should be aware of the features of this toxic optic neuropathy. The authors report a case of severe systemic methanol toxicity and relatively mild optic neuropathy demonstrating unique retinal changes on optical coherence tomography (OCT).<br><br>CASE PRESENTATION: A previously healthy student developed ataxia, difficulty breathing and loss of consciousness hours after drinking homemade alcohol while traveling in Indonesia. She was found to have a serum pH of 6.79 and elevated methanol levels. She was treated with intravenous ethanol, methylprednisolone and sodium bicarbonate. When she awoke she had bilateral central scotomas. At presentation, she had central depression on visual field testing. OCT of the retinal nerve fiber layer (RNFL) was normal but ganglion cell layer analysis (GCL) showed highly selective loss of the nasal fibers in both eyes. Further, OCT of the macula demonstrated inner nuclear layer (INL) microcysts in the corresponding area of selective GCL loss in both eyes.<br><br>CONCLUSIONS: The selective involvement of the papillomacular bundle fibers is common in toxic optic neuropathies and represents damage to the small caliber axons rich in mitochondria. Despite severe systemic toxicity, the relative sparing of the optic nerve in this case enabled characterization of the evolution of methanol toxicity with segmental GCL involvement and preservation of the RNFL, corresponding to the papillomacular bundle. This is the first reported case of INL microcysts in methanol optic neuropathy and supports that they are a non-specific finding, and may represent preferential damage to the papillomacular bundle.}, }
@article {pmid28993269, year = {2017}, author = {Bombaça, ACS and Dias, FA and Ennes-Vidal, V and Garcia-Gomes, ADS and Sorgine, MHF and d'Avila-Levy, CM and Menna-Barreto, RFS}, title = {Hydrogen peroxide resistance in Strigomonas culicis: Effects on mitochondrial functionality and Aedes aegypti interaction.}, journal = {Free radical biology &amp; medicine}, volume = {113}, number = {}, pages = {255-266}, doi = {10.1016/j.freeradbiomed.2017.10.006}, pmid = {28993269}, issn = {1873-4596}, mesh = {Adenosine Triphosphate/biosynthesis ; Aedes/*parasitology ; Animals ; Antioxidants/metabolism ; Betaproteobacteria/metabolism ; Biological Evolution ; Drug Resistance ; Electron Transport Chain Complex Proteins/*genetics/metabolism ; Energy Metabolism/*genetics ; Gastrointestinal Tract/parasitology ; Gene Expression Regulation ; *Host-Parasite Interactions ; Hydrogen Peroxide/*pharmacology ; Mitochondria/drug effects/genetics/metabolism ; Oxidation-Reduction ; Oxidative Stress ; Protozoan Proteins/*genetics/metabolism ; Signal Transduction ; Symbiosis/physiology ; Trypanosomatina/drug effects/genetics/*metabolism/microbiology ; }, abstract = {Reactive oxygen species (ROS) are toxic molecules involved in several biological processes such as cellular signaling, proliferation, differentiation and cell death. Adaptations to oxidative environments are crucial for the success of the colonization of insects by protozoa. Strigomonas culicis is a monoxenic trypanosomatid found in the midgut of mosquitoes and presenting a life cycle restricted to the epimastigote form. Among S. culicis peculiarities, there is an endosymbiotic bacterium in the cytoplasm, which completes essential biosynthetic routes of the host cell and may represent an intermediary evolutive step in organelle origin, thus constituting an interesting model for evolutive researches. In this work, we induced ROS resistance in wild type S. culicis epimastigotes by the incubation with increasing concentrations of hydrogen peroxide (H2O2), and compared the oxidative and energetic metabolisms among wild type, wild type-H2O2 resistant and aposymbiotic strains. Resistant protozoa were less sensitive to the oxidative challenge and more dependent on oxidative phosphorylation, which was demonstrated by higher oxygen consumption and mitochondrial membrane potential, increased activity of complexes II-III and IV, increased complex II gene expression and higher ATP production. Furthermore, the wild type-H2O2 resistant strain produced reduced ROS levels and showed lower lipid peroxidation, as well as an increase in gene expression of antioxidant enzymes and thiol-dependent peroxidase activity. On the other hand, the aposymbiotic strain showed impaired mitochondrial function, higher H2O2 production and deficient antioxidant response. The induction of H2O2 resistance also led to a remarkable increase in Aedes aegypti midgut binding in vitro and colonization in vivo, indicating that both the pro-oxidant environment in the mosquito gut and the oxidative stress susceptibility regulate S. culicis population in invertebrates.}, }
@article {pmid28989067, year = {2018}, author = {Ogedengbe, ME and El-Sherry, S and Ogedengbe, JD and Chapman, HD and Barta, JR}, title = {Phylogenies based on combined mitochondrial and nuclear sequences conflict with morphologically defined genera in the eimeriid coccidia (Apicomplexa).}, journal = {International journal for parasitology}, volume = {48}, number = {1}, pages = {59-69}, doi = {10.1016/j.ijpara.2017.07.008}, pmid = {28989067}, issn = {1879-0135}, mesh = {Animals ; Cell Nucleus/*genetics/metabolism ; DNA, Protozoan/*genetics/metabolism ; DNA, Ribosomal/*genetics/metabolism ; Eimeria/classification/*genetics/growth &amp; development/metabolism ; Electron Transport Complex IV/genetics/metabolism ; Mitochondria/*genetics/metabolism ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Partial mitochondrial (mt) cytochrome c oxidase subunit I (COI) and near-complete nuclear (nu) 18S rDNA sequences were obtained from various eimeriid coccidia infecting vertebrates. New and published sequences were used in phylogenetic reconstructions based on nu 18S rDNA, mt COI and concatenated sequence datasets. Bayesian analyses of nu 18S rDNA sequences used secondary structure-based alignments with a doublet nucleotide substitution model; the codon nucleotide substitution model was applied to COI sequences. Although alignment of the mt COI sequences was unambiguous, substitution saturation was evident for comparisons of COI sequences between ingroup (eimeriid) and outgroup (sarcocystid) taxa. Consequently, a combined dataset applying partition-specific analytical and alignment improvements was used to generate a robust molecular phylogeny. Most eimeriid parasites that infect closely related definitive hosts were found in close proximity on the resulting tree, frequently in a single clade. Whether this represents coevolution or co-accommodation or a combination remains an open point. Unlike host associations, basic oocyst configuration (number of sporocysts per oocyst and sporozoites per sporocyst) was not correlated with phylogeny. Neither 'Eimeria-type' nor 'Isospora-type' oocyst morphotypes formed monophyletic groups. In the combined dataset tree (representing only a tiny fraction of described eimeriid coccidia), at least 10 clades of Eimeria spp. would need to be re-assigned to nine distinct genera to resolve their paraphyly. The apparent lack of congruence between morphotype and genotype will require taxonomists to balance nomenclatural stability and diagnostic ease against the ideal of monophyletic genera. For now, recognition of paraphyletic eimeriid genera defined by basic oocyst configuration may be necessary for reasons of taxonomic stability and diagnostic utility. Future taxonomic revisions to produce monophyletic eimeriid genera will ultimately require the identification of reliable phenotypic characters that agree with the molecular phylogeny of these parasites or, less optimally, acceptance that genotyping may be needed to support monophyletic supraspecific taxonomic groups.}, }
@article {pmid28988150, year = {2017}, author = {Semenova, GA and Fomina, IR and Kosobryukhov, AA and Lyubimov, VY and Nadezhkina, ES and Balakhnina, TI}, title = {Mesophyll cell ultrastructure of wheat leaves etiolated by lead and selenium.}, journal = {Journal of plant physiology}, volume = {219}, number = {}, pages = {37-44}, doi = {10.1016/j.jplph.2017.09.008}, pmid = {28988150}, issn = {1618-1328}, mesh = {Chlorophyll/*metabolism ; *Etiolation ; Hydrogen Peroxide/*metabolism ; Lead/*metabolism ; Mesophyll Cells/drug effects/ultrastructure ; Oxygen/*metabolism ; Plant Leaves/drug effects/growth &amp; development/metabolism/ultrastructure ; Selenium/*metabolism ; Stress, Physiological ; Triticum/drug effects/*growth &amp; development/metabolism/ultrastructure ; }, abstract = {The ultrastructure of mesophyll cells was studied in leaves of the Triticum aestivum L. cv. "Trizo" seedlings after two weeks of growth on soil contaminated by Pb and/or Se. The soil treatments: control; (Pb1) 50mgkg[-1]; (Pb2) 100mgkg[-1]; (Se1) 0.4mgkg[-1]; (Se2) 0.8mgkg[-1]; (Pb1+Se1); (Pb1+Se2); (P2+Se1); and (Pb2+Se2) were used. Light and other conditions were optimal for plant growth. The (Se1)-plants showed enhanced growth and biomass production; (Pb1+Se1)-plants did not lag behind the controls, though O2 evolution decreased; chlorophyll content did not differ statistically in these treatments. Other treatments led to statistically significant growth suppression, chlorophyll content reduction, inhibition of photosynthesis, stress development tested by H2O2 and leaf etiolation at the end of 14-days experiment. The tops of etiolated leaves remained green, while the main leaf parts were visually white. Plastids in mesophyll cells of etiolated parts of leaves were mainly represented by etioplasts and an insignificant amount of degraded chloroplasts. Other cellular organelles remained intact in most mesophyll cells of the plants, except (Pb2+Se2)-plants. Ruptured tonoplast and etioplast envelope, swelled cytoplasm and mitochondria, and electron transparent matrix of gialoplasm were observed in the mesophyll cells at (Pb2+Se2)-treatment, that caused maximal inhibition of plant growth. The results indicate that Pb and Se effects on growth of wheat leaves are likely to target meristem in which the development of proplastids to chloroplasts under the light is determined by chlorophyll biosynthesis. Antagonistic effect of low concentration of Se and Pb in combination may retard etiolation process.}, }
@article {pmid28986237, year = {2018}, author = {Liu, Y and Song, F and Jiang, P and Wilson, JJ and Cai, W and Li, H}, title = {Compositional heterogeneity in true bug mitochondrial phylogenomics.}, journal = {Molecular phylogenetics and evolution}, volume = {118}, number = {}, pages = {135-144}, doi = {10.1016/j.ympev.2017.09.025}, pmid = {28986237}, issn = {1095-9513}, mesh = {Animals ; Base Composition ; Base Sequence ; Bayes Theorem ; Genetic Variation ; *Genome, Mitochondrial ; Heteroptera/*genetics ; Likelihood Functions ; Mitochondria/*genetics ; *Phylogeny ; }, abstract = {Mitochondrial phylogenomics is often controversial, in particular for inferring deep relationships. The recent rapid increase of mitochondrial genome data provides opportunities for better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and mutation rates. Here, we gathered 76 mitochondrial genome sequences for Heteroptera representing all seven infraorders, including 17 newly sequenced mitochondrial genomes. We found strong heterogeneity in base composition and contrasting evolutionary rates among heteropteran mitochondrial genomes, which affected analyses with various datasets and partitioning schemes under site-homogeneous models and produced false groupings of unrelated taxa exhibiting similar base composition and accelerated evolutionary rates. Bayesian analyses using a site-heterogeneous mixture CAT+GTR model showed high congruence of topologies with the currently accepted phylogeny of Heteroptera. The results confirm the monophyly of the six infraorders within Heteroptera, except for Cimicomorpha which was recovered as two paraphyletic clades. The monophyly of Terheteroptera (Cimicomorpha and Pentatomomorpha) and Panheteroptera (Nepomorpha, Leptopodomorpha and Terheteroptera) was recovered demonstrating a significant improvement over previous studies using mitochondrial genome data. Our study shows the power of the site-heterogeneous mixture models for resolving phylogenetic relationships with Heteroptera and provides one more case showing that model adequacy is critical for accurate tree reconstruction in mitochondrial phylogenomics.}, }
@article {pmid28986236, year = {2018}, author = {Matenaar, D and Fingerle, M and Heym, E and Wirtz, S and Hochkirch, A}, title = {Phylogeography of the endemic grasshopper genus Betiscoides (Lentulidae) in the South African Cape Floristic Region.}, journal = {Molecular phylogenetics and evolution}, volume = {118}, number = {}, pages = {318-329}, doi = {10.1016/j.ympev.2017.09.024}, pmid = {28986236}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Biological Evolution ; DNA/chemistry/isolation &amp; purification/metabolism ; Genetic Variation ; Grasshoppers/*classification/genetics ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Sequence Alignment ; Sequence Analysis, DNA ; South Africa ; }, abstract = {Vicariance and dispersal are two important processes shaping biodiversity patterns. The South African Cape Floristic Region (CFR) is known for its high biotic diversity and endemism. However, studies on the phylogeography of endemic invertebrates in this biodiversity hotspot are still scarce. Here, we present a phylogenetic study of the flightless grasshopper genus Betiscoides, which is endemic to the CFR and strongly associated with restio plants (Restionaceae). We hypothesized that the genus originated in the southwestern part of the CFR, that differentiation within the genus is mainly an effect of vicariance and that the three known species only represent a minor fraction of the real genetic diversity of the genus. We inferred the phylogeny based on sequences of three mitochondrial and two nuclear genes from 99 Betiscoides specimens collected across the CFR. Furthermore, we conducted a SDIVA analysis to detect distributions of ancestral nodes and the possible spatial origin of these lineages. Strong differentiation among genetic lineages was shown. The ancestor of this genus was most likely distributed in the southwestern CFR. Five major lineages were detected, three of which were ancestrally distributed in the southwestern CFR. The ancestors of the two other lineages were distributed in the northern and eastern margins of the CFR. A total of 24 divergent evolutionary lineages were found, reflecting the geographical isolation of restio-dominated fynbos habitats. Dispersal played a more prominent role than expected in differentiation of Betiscoides. While the five main lineages were separated during a first phase via dispersal, differentiation occurred later and on smaller spatial scale, predominantly driven by isolation in montane refugia (i.e. vicariance). Our study also suggests that flightless insect taxa likely show high levels of differentiation in biodiversity hotspots with their taxonomy often being incomplete.}, }
@article {pmid28985476, year = {2017}, author = {Court, DA and Khetoo, S and Shuvo, SR and Reitmeier, SD and Hausner, G}, title = {In silico analysis of coevolution among ERMES proteins, Pex11, and Lam6.}, journal = {Canadian journal of microbiology}, volume = {63}, number = {12}, pages = {984-997}, doi = {10.1139/cjm-2017-0460}, pmid = {28985476}, issn = {1480-3275}, mesh = {Antiporters/genetics ; *Computer Simulation ; *Evolution, Molecular ; Membrane Proteins/genetics ; Peroxins/genetics ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; }, abstract = {In eukaryotic cells, communication and dynamic interactions among different organelles are important for maintaining cellular homeostasis. The endoplasmic reticulum (ER) mitochondria encounter structure (ERMES) complex establishes membrane contact sites between ER and mitochondria and is essential for phospholipid transport, protein import, and mitochondrial dynamics and inheritance. In this work, in silico analyses were used to probe the intramolecular interactions in ERMES proteins and the interactions that support the ERMES complex. Based on mutual information (MI), sites of intramolecular coevolution are predicted in the core proteins Mmm1, Mdm10, Mdm12, Mdm34, the peroxisomal protein Pex11, and cytoplasmic Lam6; these sites are linked to structural features of the proteins. Intermolecular coevolution is predicted among the synaptotagmin-like mitochondrial lipid-binding protein (SMP) domains of Mmm1, Mdm12, and Mdm34. Segments of Pex11 and Lam6 also share MI with the SMP domains of Mmm1 and Mdm12 and with the N terminus of Mdm34, implicating Mdm34 as part of a hub for interactions between ERMES and other complexes. In contrast, evidence of limited intermolecular coevolution involving the outer membrane protein Mdm10 was detected only with Mmm1 and Pex11. The results support models for the organization of these interacting proteins and suggest roles for Pex11 and Lam6 in regulating complex formation.}, }
@article {pmid28985295, year = {2017}, author = {Eslamieh, M and Williford, A and Betrán, E}, title = {Few Nuclear-Encoded Mitochondrial Gene Duplicates Contribute to Male Germline-Specific Functions in Humans.}, journal = {Genome biology and evolution}, volume = {9}, number = {10}, pages = {2782-2790}, pmid = {28985295}, issn = {1759-6653}, support = {R01 GM071813/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Nucleus/*genetics ; Drosophila melanogaster/genetics ; Evolution, Molecular ; Gene Duplication/*genetics ; Gene Expression Profiling ; Gene Ontology ; Genes, Insect/genetics ; Genes, Mitochondrial/*genetics ; Genome, Human/*genetics ; Humans ; Male ; Mitochondria/genetics/metabolism/physiology ; Species Specificity ; Spermatogenesis/genetics ; Spermatozoa/metabolism/*physiology ; Testis/physiology ; }, abstract = {Most of the genes encoding proteins that function in the mitochondria are located in the nucleus and are called nuclear-encoded mitochondrial genes, or N-mt genes. In Drosophila melanogaster , about 23% of N-mt genes fall into gene families, and all duplicates with tissue-biased expression (76%) are testis biased. These genes are enriched for energy-related functions and tend to be older than other duplicated genes in the genome. These patterns reveal strong selection for the retention of new genes for male germline mitochondrial functions. The two main forces that are likely to drive changes in mitochondrial functions are maternal inheritance of mitochondria and male-male competition for fertilization. Both are common among animals, suggesting similar N-mt gene duplication patterns in different species. To test this, we analyzed N-mt genes in the human genome. We find that about 18% of human N-mt genes fall into gene families, but unlike in Drosophila , only 28% of the N-mt duplicates have tissue-biased expression and only 36% of these have testis-biased expression. In addition, human testis-biased duplicated genes are younger than other duplicated genes in the genome and have diverse functions. These contrasting patterns between species might reflect either differences in selective pressures for germline energy-related or other mitochondrial functions during spermatogenesis and fertilization, or differences in the response to similar pressures.}, }
@article {pmid28981721, year = {2017}, author = {Allio, R and Donega, S and Galtier, N and Nabholz, B}, title = {Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker.}, journal = {Molecular biology and evolution}, volume = {34}, number = {11}, pages = {2762-2772}, doi = {10.1093/molbev/msx197}, pmid = {28981721}, issn = {1537-1719}, mesh = {Animals ; Biological Evolution ; Biomarkers ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; Genetic Speciation ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome/genetics ; Mitochondria/genetics ; Mutation ; *Mutation Rate ; Phylogeny ; Polymorphism, Genetic/genetics ; Population Density ; Selection, Genetic/genetics ; }, abstract = {It is commonly assumed that mitochondrial DNA (mtDNA) evolves at a faster rate than nuclear DNA (nuDNA) in animals. This has contributed to the popularity of mtDNA as a molecular marker in evolutionary studies. Analyzing 121 multilocus data sets and four phylogenomic data sets encompassing 4,676 species of animals, we demonstrate that the ratio of mitochondrial over nuclear mutation rate is highly variable among animal taxa. In nonvertebrates, such as insects and arachnids, the ratio of mtDNA over nuDNA mutation rate varies between 2 and 6, whereas it is above 20, on average, in vertebrates such as scaled reptiles and birds. Interestingly, this variation is sufficient to explain the previous report of a similar level of mitochondrial polymorphism, on average, between vertebrates and nonvertebrates, which was originally interpreted as reflecting the effect of pervasive positive selection. Our analysis rather indicates that the among-phyla homogeneity in within-species mtDNA diversity is due to a negative correlation between mtDNA per-generation mutation rate and effective population size, irrespective of the action of natural selection. Finally, we explore the variation in the absolute per-year mutation rate of both mtDNA and nuDNA using a reduced data set for which fossil calibration is available, and discuss the potential determinants of mutation rate variation across genomes and taxa. This study has important implications regarding DNA-based identification methods in predicting that mtDNA barcoding should be less reliable in nonvertebrates than in vertebrates.}, }
@article {pmid28979209, year = {2017}, author = {Gaudry, MJ and Campbell, KL}, title = {Evolution of UCP1 Transcriptional Regulatory Elements Across the Mammalian Phylogeny.}, journal = {Frontiers in physiology}, volume = {8}, number = {}, pages = {670}, pmid = {28979209}, issn = {1664-042X}, abstract = {Uncoupling protein 1 (UCP1) permits non-shivering thermogenesis (NST) when highly expressed in brown adipose tissue (BAT) mitochondria. Exclusive to placental mammals, BAT has commonly been regarded to be advantageous for thermoregulation in hibernators, small-bodied species, and the neonates of larger species. While numerous regulatory control motifs associated with UCP1 transcription have been proposed for murid rodents, it remains unclear whether these are conserved across the eutherian mammal phylogeny and hence essential for UCP1 expression. To address this shortcoming, we conducted a broad comparative survey of putative UCP1 transcriptional regulatory elements in 139 mammals (135 eutherians). We find no evidence for presence of a UCP1 enhancer in monotremes and marsupials, supporting the hypothesis that this control region evolved in a stem eutherian ancestor. We additionally reveal that several putative promoter elements (e.g., CRE-4, CCAAT) identified in murid rodents are not conserved among BAT-expressing eutherians, and together with the putative regulatory region (PRR) and CpG island do not appear to be crucial for UCP1 expression. The specificity and importance of the upTRE, dnTRE, URE1, CRE-2, RARE-2, NBRE, BRE-1, and BRE-2 enhancer elements first described from rats and mice are moreover uncertain as these motifs differ substantially-but generally remain highly conserved-in other BAT-expressing eutherians. Other UCP1 enhancer motifs (CRE-3, PPRE, and RARE-3) as well as the TATA box are also highly conserved in nearly all eutherian lineages with an intact UCP1. While these transcriptional regulatory motifs are generally also maintained in species where this gene is pseudogenized, the loss or degeneration of key basal promoter (e.g., TATA box) and enhancer elements in other UCP1-lacking lineages make it unlikely that the enhancer region is pleiotropic (i.e., co-regulates additional genes). Importantly, differential losses of (or mutations within) putative regulatory elements among the eutherian lineages with an intact UCP1 suggests that the transcriptional control of gene expression is not highly conserved in this mammalian clade.}, }
@article {pmid28978045, year = {2017}, author = {Ozsvari, B and Fiorillo, M and Bonuccelli, G and Cappello, AR and Frattaruolo, L and Sotgia, F and Trowbridge, R and Foster, R and Lisanti, MP}, title = {Mitoriboscins: Mitochondrial-based therapeutics targeting cancer stem cells (CSCs), bacteria and pathogenic yeast.}, journal = {Oncotarget}, volume = {8}, number = {40}, pages = {67457-67472}, pmid = {28978045}, issn = {1949-2553}, abstract = {The "endo-symbiotic theory of mitochondrial evolution" states that mitochondrial organelles evolved from engulfed aerobic bacteria, after millions of years of symbiosis and adaptation. Here, we have exploited this premise to design new antibiotics and novel anti-cancer therapies, using a convergent approach. First, virtual high-throughput screening (vHTS) and computational chemistry were used to identify novel compounds binding to the 3D structure of the mammalian mitochondrial ribosome. The resulting library of ∼880 compounds was then subjected to phenotypic drug screening on human cancer cells, to identify which compounds functionally induce ATP-depletion, which is characteristic of mitochondrial inhibition. Notably, the top ten "hit" compounds define four new classes of mitochondrial inhibitors. Next, we further validated that these novel mitochondrial inhibitors metabolically target mitochondrial respiration in cancer cells and effectively inhibit the propagation of cancer stem-like cells in vitro. Finally, we show that these mitochondrial inhibitors possess broad-spectrum antibiotic activity, preventing the growth of both gram-positive and gram-negative bacteria, as well as C. albicans - a pathogenic yeast. Remarkably, these novel antibiotics also were effective against methicillin-resistant Staphylococcus aureus (MRSA). Thus, this simple, yet systematic, approach to the discovery of mitochondrial ribosome inhibitors could provide a plethora of anti-microbials and anti-cancer therapies, to target drug-resistance that is characteristic of both i) tumor recurrence and ii) infectious disease. In summary, we have successfully used vHTS combined with phenotypic drug screening of human cancer cells to identify several new classes of broad-spectrum antibiotics that target both bacteria and pathogenic yeast. We propose the new term "mitoriboscins" to describe these novel mitochondrial-related antibiotics. Thus far, we have identified four different classes of mitoriboscins, such as: 1) mitoribocyclines, 2) mitoribomycins, 3) mitoribosporins and 4) mitoribofloxins. However, we broadly define mitoriboscins as any small molecule(s) or peptide(s) that bind to the mitoribosome (large or small subunits) and, as a consequence, inhibit mitochondrial function, i.e., mitoribosome inhibitors.}, }
@article {pmid28977708, year = {2017}, author = {Cariou, M and Duret, L and Charlat, S}, title = {The global impact of Wolbachia on mitochondrial diversity and evolution.}, journal = {Journal of evolutionary biology}, volume = {30}, number = {12}, pages = {2204-2210}, doi = {10.1111/jeb.13186}, pmid = {28977708}, issn = {1420-9101}, mesh = {Animals ; Arthropods/*genetics/microbiology ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; Female ; Genetic Variation ; Male ; Phylogeny ; Wolbachia/*physiology ; }, abstract = {The spread of maternally inherited microorganisms, such as Wolbachia bacteria, can induce indirect selective sweeps on host mitochondria, to which they are linked within the cytoplasm. The resulting reduction in effective population size might lead to smaller mitochondrial diversity and reduced efficiency of natural selection. While documented in several host species, it is currently unclear if such a scenario is common enough to globally impact the diversity and evolution of mitochondria in Wolbachia-infected lineages. Here, we address this question using a mapping of Wolbachia acquisition/extinction events on a large mitochondrial DNA tree, including over 1000 species. Our analyses indicate that on a large phylogenetic scale, other sources of variation, such as mutation rates, tend to hide the effects of Wolbachia. However, paired comparisons between closely related infected and uninfected taxa reveal that Wolbachia is associated with a twofold reduction in silent mitochondrial polymorphism, and a 13% increase in nonsynonymous substitution rates. These findings validate the conjecture that the widespread distribution of Wolbachia infections throughout arthropods impacts the effective population size of mitochondria. These effects might in part explain the disconnection between genetic diversity and demographic population size in mitochondria, and also fuel red-queen-like cytonuclear co-evolution through the fixation of deleterious mitochondrial alleles.}, }
@article {pmid28969942, year = {2018}, author = {Chen, S and Wu, Z and Zhang, J and Wang, M and Jia, R and Zhu, D and Liu, M and Sun, K and Yang, Q and Wu, Y and Zhao, X and Cheng, A}, title = {Duck stimulator of interferon genes plays an important role in host anti-duck plague virus infection through an IFN-dependent signalling pathway.}, journal = {Cytokine}, volume = {102}, number = {}, pages = {191-199}, doi = {10.1016/j.cyto.2017.09.008}, pmid = {28969942}, issn = {1096-0023}, mesh = {Amino Acid Sequence ; Animals ; Avian Proteins/genetics/immunology ; Bird Diseases/*genetics/*immunology/virology ; Ducks/*genetics/*immunology/virology ; Host-Pathogen Interactions/genetics/immunology ; Humans ; Immunity, Innate/genetics ; Interferon-beta/genetics ; Mardivirus/*immunology/*pathogenicity/physiology ; Marek Disease/*genetics/*immunology/virology ; NF-kappa B/metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; Signal Transduction ; Virus Replication ; }, abstract = {The human stimulator of interferon gene (STING) is an important molecule in innate immunity that stimulates type I interferon (IFN) production. However, the role of duck STING (duSTING) in innate immunity has yet to be explained. In this study, the full length of the duSTING cDNA sequence (1149bp), which encodes 382 amino acid (aa) residues, was reported and showed the highest sequence similarity with chicken STINGs. The phylogenetic analysis based on STING aa showed that duSTING was grouped onto the birds clade. According to the tissue distribution spectrum analysis, duSTING was highly present in the bursa of Fabricius, glandular stomach, liver, pancreas, and small intestine of ducklings, as well as in the blood and pancreas of the adult duck. DuSTING mainly colocalized with the endoplasmic reticulum (ER) and mitochondria in transfected Baby Hamster Syrian Kidney (BHK21) and duck embryo fibroblasts (DEF) cells by an indirect immunofluorescence assay. The transfection of the DEFs with duSTING activated NF-κB, which induced the transcription of IFN-β, and the activated IFN induced the interferon-stimulated response element (ISRE). Furthermore, the overexpression of duSTING significantly upregulated the mRNA level of duck IFN-β and IFN-stimulated genes (ISGs), such as duMx and duOASL and inhibited the replication of the double-stranded DNA duck plague virus (DPV) in vitro. In addition, the knockdown of endogenous duSTING by shRNA significantly reduced the poly (I:C) (pIC), poly (dA:dT), and Tembusu virus (TMUV), induced IFN-β production and significantly promoted DPV replication in vitro. In general, these data demonstrate that duSTING is vital for duck type I interferon induction and plays an important role in the host defence of DPV infection.}, }
@article {pmid28967179, year = {2018}, author = {Dayan, FE and Barker, A and Tranel, PJ}, title = {Origins and structure of chloroplastic and mitochondrial plant protoporphyrinogen oxidases: implications for the evolution of herbicide resistance.}, journal = {Pest management science}, volume = {74}, number = {10}, pages = {2226-2234}, doi = {10.1002/ps.4744}, pmid = {28967179}, issn = {1526-4998}, mesh = {Amaranthus/drug effects/enzymology/genetics ; Chloroplast Proteins/genetics/metabolism ; *Evolution, Molecular ; Glycine/analogs &amp; derivatives/pharmacology ; Herbicide Resistance/*genetics ; Herbicides/*pharmacology ; Mitochondrial Proteins/genetics/metabolism ; Plant Weeds/drug effects/enzymology/*genetics ; Protoporphyrinogen Oxidase/*genetics/metabolism ; Glyphosate ; }, abstract = {Protoporphyrinogen IX oxidase (PPO)-inhibiting herbicides are effective tools to control a broad spectrum of weeds, including those that have evolved resistance to glyphosate. Their utility is being threatened by the appearance of biotypes that are resistant to PPO inhibitors. While the chloroplastic PPO1 isoform is thought to be the primary target of PPO herbicides, evolved resistance mechanisms elucidated to date are associated with changes to the mitochondrial PPO2 isoform, suggesting that the importance of PPO2 has been underestimated. Our investigation of the evolutionary and structural biology of plant PPOs provides some insight into the potential reasons why PPO2 is the preferred target for evolution of resistance. The most common target-site mutation imparting resistance involved the deletion of a key glycine codon. The genetic environment that facilitates this deletion is apparently only present in the gene encoding PPO2 in a few species. Additionally, both species with this mutation (Amaranthus tuberculatus and Amaranthus palmeri) have dual targeting of PPO2 to both the chloroplast and the mitochondria, which might be a prerequisite to impart herbicide resistance. The most recent target-site mutations have substituted a key arginine residue involved in stabilizing the substrate in the catalytic domain of PPO2. This arginine is highly conserved across all plant PPOs, suggesting that its substitution could be equally likely on PPO1 and PPO2, yet it has only occurred on PPO2, underscoring the importance of this isoform for the evolution of herbicide resistance. © 2017 Society of Chemical Industry.}, }
@article {pmid28966595, year = {2017}, author = {Wiens, L and Banh, S and Sotiri, E and Jastroch, M and Block, BA and Brand, MD and Treberg, JR}, title = {Comparison of Mitochondrial Reactive Oxygen Species Production of Ectothermic and Endothermic Fish Muscle.}, journal = {Frontiers in physiology}, volume = {8}, number = {}, pages = {704}, pmid = {28966595}, issn = {1664-042X}, support = {R01 AG033542/AG/NIA NIH HHS/United States ; }, abstract = {Recently we demonstrated that the capacity of isolated muscle mitochondria to produce reactive oxygen species, measured as H2O2 efflux, is temperature-sensitive in isolated muscle mitochondria of ectothermic fish and the rat, a representative endothermic mammal. However, at physiological temperatures (15° and 37°C for the fish and rat, respectively), the fraction of total mitochondrial electron flux that generated H2O2, the fractional electron leak (FEL), was far lower in the rat than in fish. Those results suggested that the elevated body temperatures associated with endothermy may lead to a compensatory decrease in mitochondrial ROS production relative to respiratory capacity. To test this hypothesis we compare slow twitch (red) muscle mitochondria from the endothermic Pacific bluefin tuna (Thunnus orientalis) with mitochondria from three ectothermic fishes [rainbow trout (Oncorhynchus mykiss), common carp (Cyprinus carpio), and the lake sturgeon (Acipenser fulvescens)] and the rat. At a common assay temperature (25°C) rates of mitochondrial respiration and H2O2 efflux were similar in tuna and the other fishes. The thermal sensitivity of fish mitochondria was similar irrespective of ectothermy or endothermy. Comparing tuna to the rat at a common temperature, respiration rates were similar, or lower depending on mitochondrial substrates. FEL was not different across fish species at a common assay temperature (25°C) but was markedly higher in fishes than in rat. Overall, endothermy and warming of Pacific Bluefin tuna red muscle may increase the potential for ROS production by muscle mitochondria but the evolution of endothermy in this species is not necessarily associated with a compensatory reduction of ROS production relative to the respiratory capacity of mitochondria.}, }
@article {pmid28963083, year = {2018}, author = {Eldridge, RA and Achmadi, AS and Giarla, TC and Rowe, KC and Esselstyn, JA}, title = {Geographic isolation and elevational gradients promote diversification in an endemic shrew on Sulawesi.}, journal = {Molecular phylogenetics and evolution}, volume = {118}, number = {}, pages = {306-317}, doi = {10.1016/j.ympev.2017.09.018}, pmid = {28963083}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; DNA/chemistry/isolation &amp; purification/metabolism ; Gene Flow ; Genetic Variation ; Genetics, Population ; Indonesia ; Islands ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Sequence Alignment ; Sequence Analysis, DNA ; Shrews/*classification ; }, abstract = {Phylogeographic research on endemic primates and amphibians inhabiting the Indonesian island of Sulawesi revealed the existence of seven areas of endemism (AoEs). Here, we use phylogenetic and population genetic analyses of one mitochondrial gene and 15 nuclear loci to assess geographic patterns of genetic partitioning in a shrew (Crocidura elongata) that is endemic to Sulawesi, but occurs across the island. We uncover substantial genetic diversity in this species both between and within AoEs, but we also identify close relationships between populations residing in different AoEs. One of the earliest divergences within C. elongata distinguishes a high-elevation clade from low-elevation clades. In addition, on one mountain, we observe three distinct genetic groups from low, middle, and high elevations, suggesting divergence along a single elevational gradient. In general, our results show that C. elongata, like several other Sulawesi endemic taxa, harbors extensive genetic diversity. This diversity is structured in part by known AoE boundaries, but also by elevational gradients and geographic isolation within AoEs.}, }
@article {pmid28961859, year = {2017}, author = {Cheng, J and Guo, X and Cai, P and Cheng, X and Piškur, J and Ma, Y and Jiang, H and Gu, Z}, title = {Parallel Evolution of Chromatin Structure Underlying Metabolic Adaptation.}, journal = {Molecular biology and evolution}, volume = {34}, number = {11}, pages = {2870-2878}, doi = {10.1093/molbev/msx220}, pmid = {28961859}, issn = {1537-1719}, mesh = {Aerobiosis/*genetics/physiology ; Anaerobiosis/genetics ; Biological Evolution ; Chromatin/*genetics/physiology ; Dekkera/genetics/metabolism ; Evolution, Molecular ; Fermentation/genetics ; Gene Expression/genetics ; Glucose/metabolism ; Phylogeny ; Promoter Regions, Genetic/genetics ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {Parallel evolution occurs when a similar trait emerges in independent evolutionary lineages. Although changes in protein coding and gene transcription have been investigated as underlying mechanisms for parallel evolution, parallel changes in chromatin structure have never been reported. Here, Saccharomyces cerevisiae and a distantly related yeast species, Dekkera bruxellensis, are investigated because both species have independently evolved the capacity of aerobic fermentation. By profiling and comparing genome sequences, transcriptomic landscapes, and chromatin structures, we revealed that parallel changes in nucleosome occupancy in the promoter regions of mitochondria-localized genes led to concerted suppression of mitochondrial functions by glucose, which can explain the metabolic convergence in these two independent yeast species. Further investigation indicated that similar mutational processes in the promoter regions of these genes in the two independent evolutionary lineages underlay the parallel changes in chromatin structure. Our results indicate that, despite several hundred million years of separation, parallel changes in chromatin structure, can be an important adaptation mechanism for different organisms. Due to the important role of chromatin structure changes in regulating gene expression and organism phenotypes, the novel mechanism revealed in this study could be a general phenomenon contributing to parallel adaptation in nature.}, }
@article {pmid28952250, year = {2017}, author = {Chen, YJ and Rong, QX and Jiang, D and Shen, Y and Huang, LQ}, title = {[Bioinformatics analysis of geranylgeranyl pyrophosphate synthase coding gene and amino acid sequence in Lamiaceae].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {42}, number = {3}, pages = {465-472}, doi = {10.19540/j.cnki.cjcmm.20170103.030}, pmid = {28952250}, issn = {1001-5302}, mesh = {Amino Acid Sequence ; Computational Biology ; Geranylgeranyl-Diphosphate Geranylgeranyltransferase/*genetics ; Lamiaceae/enzymology/*genetics ; Phylogeny ; Plant Proteins/*genetics ; }, abstract = {Geranylgeranyl pyrophosphate synthase enzyme is one of the key enzymes in the synthesis pathway of diterpenoid. Nine Lamiaceae genus GGPS synthase in Genebank was analyzed in this article. GGPS synthase the nucleic acid sequences and amino acid sequences, physicochemical properties, the signal peptide, leader peptides, transmembrane topological structure, hydrophobic, hydrophilic, subcellular localization, secondary structure, function domain, tertiary structure and evolutional relationship were predicted by using bioinformatics methods.Phylogenetic tree was constructed for the geranylgeranyl pyrophosphate synthase enzyme protein family. The results showed that GGPS amino acid sequence of the physical and chemical properties were basically identical, mainly hydrophilic protein, there existed chloroplast transit peptide, and no signal peptide and membrane structure domain, which mainly located in the chloroplast, the minor part located in mitochondria. The main secondary structures of the proteins are alpha helix and random coil. All these proteins have catalytic residues, aspartate-rich region, active site lid residues, substrate-Mg2+ binding site. The results provide theoretical reference for study on both the enzymatic characteristics of GGPS and the biosynthesis pathway of diterpenoid.}, }
@article {pmid28947489, year = {2017}, author = {Majsec, K and Bhuiyan, NH and Sun, Q and Kumari, S and Kumar, V and Ware, D and van Wijk, KJ}, title = {The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis.}, journal = {The Plant cell}, volume = {29}, number = {11}, pages = {2687-2710}, pmid = {28947489}, issn = {1532-298X}, mesh = {Arabidopsis Proteins/genetics/*metabolism ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Gene Regulatory Networks/genetics ; Mitochondria/*enzymology/genetics ; Peptide Hydrolases/classification/genetics/*metabolism ; Phylogeny ; Plastids/*enzymology/genetics ; Proteome/genetics/metabolism ; Proteostasis/genetics ; }, abstract = {Plant plastids and mitochondria have dynamic proteomes. Protein homeostasis in these organelles is maintained by a proteostasis network containing protein chaperones, peptidases, and their substrate recognition factors. However, many peptidases, as well as their functional connections and substrates, are poorly characterized. This review provides a systematic insight into the organellar peptidase network in Arabidopsis thaliana We present a compendium of known and putative Arabidopsis peptidases and inhibitors, and compare the distribution of plastid and mitochondrial peptidases to the total peptidase complement. This comparison shows striking biases, such as the (near) absence of cysteine and aspartic peptidases and peptidase inhibitors, whereas other peptidase families were exclusively organellar; reasons for such biases are discussed. A genome-wide mRNA-based coexpression data set was generated based on quality controlled and normalized public data, and used to infer additional plastid peptidases and to generate a coexpression network for 97 organellar peptidase baits (1742 genes, making 2544 edges). The graphical network includes 10 modules with specialized/enriched functions, such as mitochondrial protein maturation, thermotolerance, senescence, or enriched subcellular locations such as the thylakoid lumen or chloroplast envelope. The peptidase compendium, including the autophagy and proteosomal systems, and the annotation based on the MEROPS nomenclature of peptidase clans and families, is incorporated into the Plant Proteome Database.}, }
@article {pmid28943271, year = {2017}, author = {Chaturvedi, D and Mahalakshmi, R}, title = {Transmembrane β-barrels: Evolution, folding and energetics.}, journal = {Biochimica et biophysica acta. Biomembranes}, volume = {1859}, number = {12}, pages = {2467-2482}, pmid = {28943271}, issn = {0005-2736}, support = {/WT_/Wellcome Trust/United Kingdom ; IA/I/14/1/501305/WTDBT_/DBT-Wellcome Trust India Alliance/India ; }, mesh = {Amino Acid Sequence ; Bacteria/genetics/*metabolism ; Bacterial Outer Membrane Proteins/*chemistry/genetics/metabolism ; *Biological Evolution ; Eukaryota/genetics/metabolism ; Gene Expression ; Mitochondria/chemistry/*metabolism ; Mitochondrial Proteins/*chemistry/genetics/metabolism ; Molecular Chaperones/*chemistry/genetics/metabolism ; Protein Binding ; Protein Conformation, beta-Strand ; Protein Folding ; Protein Interaction Domains and Motifs ; Sequence Alignment ; Sequence Homology, Amino Acid ; Thermodynamics ; }, abstract = {The biogenesis of transmembrane β-barrels (outer membrane proteins, or OMPs) is an elaborate multistep orchestration of the nascent polypeptide with translocases, barrel assembly machinery, and helper chaperone proteins. Several theories exist that describe the mechanism of chaperone-assisted OMP assembly in vivo and unassisted (spontaneous) folding in vitro. Structurally, OMPs of bacterial origin possess even-numbered strands, while mitochondrial β-barrels are even- and odd-stranded. Several underlying similarities between prokaryotic and eukaryotic β-barrels and their folding machinery are known; yet, the link in their evolutionary origin is unclear. While OMPs exhibit diversity in sequence and function, they share similar biophysical attributes and structure. Similarly, it is important to understand the intricate OMP assembly mechanism, particularly in eukaryotic β-barrels that have evolved to perform more complex functions. Here, we deliberate known facets of β-barrel evolution, folding, and stability, and attempt to highlight outstanding questions in β-barrel biogenesis and proteostasis.}, }
@article {pmid28942768, year = {2017}, author = {Bakhoum, AJS and Miquel, J and Ndiaye, PI and Justine, JL and Falchi, A and Bâ, CT and Marchand, B and Quilichini, Y}, title = {Advances in Spermatological Characters in the Digenea: Review and Proposal of Spermatozoa Models and Their Phylogenetic Importance.}, journal = {Advances in parasitology}, volume = {98}, number = {}, pages = {111-165}, doi = {10.1016/bs.apar.2017.04.001}, pmid = {28942768}, issn = {2163-6079}, mesh = {Animals ; Axoneme/*ultrastructure ; Male ; Microtubules ; *Phylogeny ; Spermatozoa/*ultrastructure ; Trematoda/*classification/cytology ; }, abstract = {The wide biodiversity and economic importance of digeneans have motivated a great deal of research in the last decade, focussing on their phylogenetic positions. Molecular research was instrumental for our understanding of phylogeny in the Digenea, but spermatological studies have also provided many results, which are potentially useful for phylogeny; however, the complete spermatological data set has never been reviewed in a whole phylogenetic perspective. Spermatological data are now available for more than 100 species, belonging to 15 superfamilies and 46 families. In this paper, we try to summarize the current knowledge about sperm structure in the digeneans and propose a classification of digenean spermatozoa into five basic models. The main ultrastructural characters used are (1) the type of axoneme, (2) the lateral expansion, (3) the association 'external ornamentation of the plasma membrane + cortical microtubules', (4) the field of cortical microtubules and its number, (5) the location of the external ornamentation, (6) the location of the maximum number of cortical microtubules and (7) the number of mitochondria. We also outline the most interesting features for phylogenetic inference and their possible value in the context of digenean systematics, phylogeny and evolution. Associations between sperm models and superfamilies were found as follows: Type 1 in the Schistosomatoidea; Type 2 in the Hemiuroidea; Type 3 in the Opecoeloidea, Lepocreadioidea, Haploporoidea and Opisthorchioidea; Type 4 in the Gorgoderoidea, Microphalloidea, Plagiorchioidea and Gymnophalloidea; Type 5 in the Echinostomatoidea, Microscaphidioidea, Paramphistomoidea, Pronocephaloidea and Brachylaimoidea.}, }
@article {pmid28938742, year = {2017}, author = {Wells, D and Ravichandran, K and McCaffrey, C and Grifo, J and Morales, A and Perloe, M and Munne, S and Fragouli, E}, title = {Reply: Mitochondrial DNA Quantification-the devil in the detail.}, journal = {Human reproduction (Oxford, England)}, volume = {32}, number = {10}, pages = {2150-2151}, doi = {10.1093/humrep/dex279}, pmid = {28938742}, issn = {1460-2350}, mesh = {*DNA, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria ; Phylogeny ; }, }
@article {pmid28937858, year = {2018}, author = {Kramer, P and Bressan, P}, title = {Our (Mother's) Mitochondria and Our Mind.}, journal = {Perspectives on psychological science : a journal of the Association for Psychological Science}, volume = {13}, number = {1}, pages = {88-100}, pmid = {28937858}, issn = {1745-6924}, mesh = {Animals ; Biological Evolution ; Humans ; Mental Disorders/physiopathology ; Mental Processes/*physiology ; Mitochondria/genetics/*physiology ; }, abstract = {Most of the energy we get to spend is furnished by mitochondria, minuscule living structures sitting inside our cells or dispatched back and forth within them to where they are needed. Mitochondria produce energy by burning down what remains of our meal after we have digested it, but at the cost of constantly corroding themselves and us. Here we review how our mitochondria evolved from invading bacteria and have retained a small amount of independence from us; how we inherit them only from our mother; and how they are heavily implicated in learning, memory, cognition, and virtually every mental or neurological affliction. We discuss why counteracting mitochondrial corrosion with antioxidant supplements is often unwise, and why our mitochondria, and therefore we ourselves, benefit instead from exercise, meditation, sleep, sunshine, and particular eating habits. Finally, we describe how malfunctioning mitochondria force rats to become socially subordinate to others, how such disparity can be evened off by a vitamin, and why these findings are relevant to us.}, }
@article {pmid28932931, year = {2018}, author = {Gorgulho, R and Jacinto, R and Lopes, SS and Pereira, SA and Tranfield, EM and Martins, GG and Gualda, EJ and Derks, RJE and Correia, AC and Steenvoorden, E and Pintado, P and Mayboroda, OA and Monteiro, EC and Morello, J}, title = {Usefulness of zebrafish larvae to evaluate drug-induced functional and morphological renal tubular alterations.}, journal = {Archives of toxicology}, volume = {92}, number = {1}, pages = {411-423}, doi = {10.1007/s00204-017-2063-1}, pmid = {28932931}, issn = {1432-0738}, support = {Gulbenkian Professorship 121986/2012//Funda&#xe7;&#xe3;o Calouste Gulbenkian/ ; ANR/BEX-BID/0153/2012//Foundation for Science and Technology/ ; IF/00951/2012//Foundation for Science and Technology/ ; PD/BD/52420/2013//Foundation for Science and Technology/ ; SFRH/BSAB/114291/2016//Foundation for Science and Technology/ ; LISBOA-01-0145-FEDER-007344//iNOVA Health Research Unit/ ; }, mesh = {Acetaminophen/adverse effects/pharmacokinetics ; Acute Kidney Injury/*chemically induced/mortality/pathology ; Animals ; Animals, Genetically Modified ; Gentamicins/adverse effects/pharmacokinetics ; Inactivation, Metabolic ; Kidney Function Tests ; Kidney Tubules, Proximal/*drug effects/pathology ; Larva ; Mitochondria/drug effects/pathology/ultrastructure ; Prodrugs/adverse effects/pharmacokinetics ; Tenofovir/adverse effects/pharmacokinetics ; Toxicity Tests/*methods ; *Zebrafish/genetics ; }, abstract = {Prediction and management of drug-induced renal injury (DIRI) rely on the knowledge of the mechanisms of drug insult and on the availability of appropriate animal models to explore it. Zebrafish (Danio rerio) offers unique advantages for assessing DIRI because the larval pronephric kidney has a high homology with its human counterpart and it is fully mature at 3.5 days post-fertilization. Herein, we aimed to evaluate the usefulness of zebrafish larvae as a model of renal tubular toxicity through a comprehensive analysis of the renal alterations induced by the lethal concentrations for 10% of the larvae for gentamicin, paracetamol and tenofovir. We evaluated drug metabolic profile by mass spectrometry, renal function with the inulin clearance assay, the 3D morphology of the proximal convoluted tubule by two-photon microscopy and the ultrastructure of proximal convoluted tubule mitochondria by transmission electron microscopy. Paracetamol was metabolized by conjugation and oxidation with further detoxification with glutathione. Renal clearance was reduced with gentamicin and paracetamol. Proximal tubules were enlarged with paracetamol and tenofovir. All drugs induced mitochondrial alterations including dysmorphic shapes ("donuts", "pancakes" and "rods"), mitochondrial swelling, cristae disruption and/or loss of matrix granules. These results are in agreement with the tubular effects of gentamicin, paracetamol and tenofovir in man and demonstrate that zebrafish larvae might be a good model to assess functional and structural damage associated with DIRI.}, }
@article {pmid28918565, year = {2017}, author = {Scala, A and Mirabella, R and Goedhart, J and de Vries, M and Haring, MA and Schuurink, RC}, title = {Forward genetic screens identify a role for the mitochondrial HER2 in E-2-hexenal responsiveness.}, journal = {Plant molecular biology}, volume = {95}, number = {4-5}, pages = {399-409}, pmid = {28918565}, issn = {1573-5028}, support = {818.02.017//NWO/ ; }, mesh = {Aldehydes/*pharmacology ; Arabidopsis/cytology/drug effects/*genetics/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Mitochondria/drug effects/metabolism ; Mutation ; Oxidation-Reduction/drug effects ; Phylogeny ; Plant Leaves/cytology/drug effects/genetics/physiology ; Plant Roots/cytology/drug effects/genetics/physiology ; Receptor, ErbB-2/genetics/*metabolism ; Seedlings/cytology/drug effects/genetics/physiology ; Signal Transduction/drug effects ; }, abstract = {This work adds a new player, HER2, downstream of the perception of E-2-hexenal, a green leaf volatile, and shows that E-2-hexenal specifically changes the redox status of the mitochondria. It is widely accepted that plants produce and respond to green leaf volatiles (GLVs), but the molecular components involved in transducing their perception are largely unknown. The GLV E-2-hexenal inhibits root elongation in seedlings and, using this phenotype, we isolated E-2-hexenal response (her) Arabidopsis thaliana mutants. Using map-based cloning we positioned the her2 mutation to the At5g63620 locus, resulting in a phenylalanine instead of serine on position 223. Knockdown and overexpression lines of HER2 confirmed the role of HER2, which encodes an oxidoreductase, in the responsiveness to E-2-hexenal. Since E-2-hexenal is a reactive electrophile species, which are known to influence the redox status of cells, we utilized redox sensitive GFP2 (roGFP2) to determine the redox status of E-2-hexenal-treated root cells. Since the signal peptide of HER2 directed mCherry to the mitochondria, we targeted the expression of roGFP2 to this organelle besides the cytosol. E-2-hexenal specifically induced a change in the redox status in the mitochondria. We did not see a difference in the redox status in her2 compared to wild-type Arabidopsis. Still, the mitochondrial redox status did not change with Z-3-hexenol, another abundant GLV. These results indicate that HER2 is involved in transducing the perception of E-2-hexenal, which changes the redox status of the mitochondria.}, }
@article {pmid28916841, year = {2017}, author = {Dunn, CD}, title = {Some Liked It Hot: A Hypothesis Regarding Establishment of the Proto-Mitochondrial Endosymbiont During Eukaryogenesis.}, journal = {Journal of molecular evolution}, volume = {85}, number = {3-4}, pages = {99-106}, pmid = {28916841}, issn = {1432-1432}, support = {637649/ERC_/European Research Council/International ; }, mesh = {Archaea/*genetics/metabolism ; Bacteria/genetics ; *Biological Evolution ; Energy Metabolism ; Eukaryota/*genetics/metabolism ; *Hot Temperature ; Mitochondria/genetics/*metabolism/physiology ; *Symbiosis ; }, abstract = {Eukaryotic cells are characterized by a considerable increase in subcellular compartmentalization when compared to prokaryotes. Most evidence suggests that the earliest eukaryotes consisted of mitochondria derived from an α-proteobacterial ancestor enclosed within an archaeal host cell. However, what benefits the archaeal host and the proto-mitochondrial endosymbiont might have obtained at the beginning of this endosymbiotic relationship remains unclear. In this work, I argue that heat generated by the proto-mitochondrion initially permitted an archaeon living at high temperatures to colonize a cooler environment, thereby removing apparent limitations on cellular complexity. Furthermore, heat generation by the endosymbiont would have provided phenotypic flexibility not available through fixed alleles selected for fitness at specific temperatures. Finally, a role for heat production by the proto-mitochondrion bridges a conceptual gap between initial endosymbiont entry to the archaeal host and a later role for mitochondrial ATP production in permitting increased cellular complexity.}, }
@article {pmid28911184, year = {2017}, author = {Xia, L and Liang, H and Xu, L and Chen, J and Bekaert, M and Zhang, H and Lu, Y}, title = {Subcellular localization and function study of a secreted phospholipase C from Nocardia seriolae.}, journal = {FEMS microbiology letters}, volume = {364}, number = {17}, pages = {}, doi = {10.1093/femsle/fnx143}, pmid = {28911184}, issn = {1574-6968}, mesh = {Animals ; Apoptosis ; Cell Line ; Cloning, Molecular ; Cyprinidae/*microbiology ; Cytoplasm/*enzymology ; Epithelial Cells/cytology/microbiology/ultrastructure ; Escherichia coli/genetics ; Gene Expression ; Green Fluorescent Proteins/genetics ; Host-Pathogen Interactions ; Microscopy, Fluorescence ; Mitochondria/enzymology/ultrastructure ; Nocardia/cytology/*enzymology/genetics ; Phylogeny ; Recombinant Fusion Proteins/metabolism ; Transfection ; Type C Phospholipases/*chemistry/genetics/*metabolism ; Virulence Factors/chemistry/*metabolism ; }, abstract = {Fish nocardiosis is a chronic systemic granulomatous disease, and Nocardia seriolae is the main pathogen that causes it. The pathogenesis and virulence factors of N. seriolae are not fully understood. A phospholipase C (PLC), which is likely to be a secreted protein targeting host cell mitochondria, was found by a bioinformatics analysis of the whole genome sequence of N. seriolae. In order to determine the subcellular localization and study the preliminary function of PLC from N. seriolae (NsPLC), in this study gene cloning, secreted protein identification, subcellular localization in host cells and apoptosis detection of NsPLC were carried out. Mass spectrometry analysis of extracellular products from N. seriolae showed that NsPLC was a secreted protein. Subcellular localization of NsPLC-GFP fusion protein in fathead minnow (FHM) cells revealed that the green fluorescence exhibited a punctate distribution near the nucleus and did not co-localize with mitochondria. In addition, an apoptosis assay suggested that apoptosis was induced in FHM cells by the overexpression of NsPLC. This study may lay the foundations for further studies on the function of NsPLC and promote the understanding of the virulence factors and pathogenic mechanism of N. seriolae.}, }
@article {pmid28910691, year = {2017}, author = {Tyml, T and Dyková, I}, title = {Phylogeny and taxonomy of new and re-examined strains of Tubulinea (Amoebozoa).}, journal = {European journal of protistology}, volume = {61}, number = {Pt A}, pages = {41-47}, doi = {10.1016/j.ejop.2017.08.002}, pmid = {28910691}, issn = {1618-0429}, mesh = {Lobosea/*classification/cytology ; Norway ; *Phylogeny ; Species Specificity ; }, abstract = {Morphological and molecular characterizations of three newly isolated tubulinean strains and re-examination of five strains formerly considered representatives of Saccamoeba and one strain formerly considered as Trichamoeba resulted in (a) the determination of strain BA02, isolated from a dripping rock ledge in Skansbukta (Billefjorden, Svalbard), as a new representative of Ptolemeba bulliensis Brown et al., 2014; (b) identification of strain ATCC[®] 50249™, deposited in the American Type Culture Collection as Trichamoeba, as the same species (P. bulliensis); (c) characterization of the new strain POHL into the Saccamoeba clade as a member closely related to S. lacustris; and (d) changing the generic residence of three strains formerly considered as representatives of Saccamoeba (strain PV67 to the P. bulliensis clade, and W187G and DP7 into the sister group of Ptolemeba noxubium Brown et al., 2014) whereas two other strains (MSED6, NTSHR) retain their original Saccamoeba clade position. Within the individual clades, the ultrastructure (especially the inner architecture of mitochondria) is congruent and thus of superior taxonomic value to that of light microscopic (morphometric) features.}, }
@article {pmid28904365, year = {2017}, author = {Ma, X and Yao, L and Yang, B and Lee, YK and Chen, F and Liu, J}, title = {RNAi-mediated silencing of a pyruvate dehydrogenase kinase enhances triacylglycerol biosynthesis in the oleaginous marine alga Nannochloropsis salina.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11485}, pmid = {28904365}, issn = {2045-2322}, mesh = {Biomarkers ; Carbohydrate Metabolism ; Gene Expression Regulation ; Gene Knockdown Techniques ; *Gene Silencing ; Genotype ; Lipid Metabolism ; Microalgae/classification/*genetics/*metabolism ; Photosynthesis ; Phylogeny ; Protein Serine-Threonine Kinases/chemistry/*genetics ; Protein Transport ; Pyruvate Dehydrogenase Acetyl-Transferring Kinase ; *RNA Interference ; Sequence Analysis, DNA ; Triglycerides/*biosynthesis ; }, abstract = {Oleaginous microalgae have been emerging as the third-generation feedstocks for biofuel production. Genetic manipulation for improving triacylglycerol (TAG) accumulation represents a promising approach towards the economics of microalgal biofuels. Acetyl-CoA, the essential carbon precursor for de novo fatty acid biosynthesis, can be derived from pyruvate catalyzed by pyruvate dehydrogenase, which is negatively regulated by pyruvate dehydrogenase kinase (PDK). In the present study, we characterized a PDK gene (NsPDK) from Nannochloropsis salina. Subcellular localization assay assisted by green fluorescence protein (GFP) fusion indicated the localization of NsPDK in mitochondria of N. salina cells. NsPDK knockdown via RNA interference strategy attenuated NsPDK expression at the mRNA level and its enzymatic activity in vivo, leading to faster TAG accumulation without compromising cell growth under high light stress conditions. Interestingly, the TAG increase was accompanied by a decline in membrane polar lipids. NsPDK knockdown also altered fatty acid profile in N. salina. Furthermore, transcriptional analysis suggested that the carbon metabolic pathways might be influenced by NsPDK knockdown leading to diverted carbon flux towards TAG synthesis. Taken together, our results demonstrate the role of NsPDK in regulating TAG accumulation and provide valuable insights into future manipulation of oleaginous microalgae for improving biofuel production.}, }
@article {pmid28903620, year = {2018}, author = {Kim, IH and Park, J and Suk, HY and Bae, HG and Min, MS and Tsai, TS and Park, D}, title = {Phylogenetic relationships of three representative sea krait species (genus Laticauda; elapidae; serpentes) based on 13 mitochondrial genes.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {772-777}, doi = {10.1080/24701394.2017.1357710}, pmid = {28903620}, issn = {2470-1408}, mesh = {Animals ; Biological Evolution ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/genetics ; Elapidae/*genetics ; Genes, Mitochondrial/genetics ; Genetic Speciation ; Genome, Mitochondrial/*genetics ; Laticauda/*genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 16S ; Snakes/genetics ; }, abstract = {To investigate the phylogenetic relationships of the genus Laticauda to related higher taxa, we compared the sequences of four mitochondrial genes (12S rRNA, 16S rRNA, ND4, Cytb) from three Laticauda species (L. colubrina, L. laticaudata, and L. semifasciata) with those of 55 Asian and Australo-Melanesian elapid species. We also characterized the complete mitogenomes of the three Laticauda species and compared the sequences of 13 mitochondrial genes from Laticauda species with five terrestrial elapid and one viperid species to estimate phylogenetic relationships and divergence times. Our results showed that the genus Laticauda is paraphyletic to terrestrial elapids and diverged from the Asian elapids approximately 16.23 Mya. The mitogenomes of the three Laticauda species commonly encoded 13 proteins, 22 tRNAs, 12S and 16S rRNAs and two control regions and ranged from 17,170 and 17,450 bp in size. The L. colubrina mitogenome was more similar to that of L. laticaudata than that of L. semifasciata. The divergence time among the three Laticauda clades was estimated at 8-10 Mya, and a close phylogenetic relationship between L. colubrina and L. laticaudata was found. Our results contribute to our understanding of the evolutionary history of sea kraits.}, }
@article {pmid28902190, year = {2017}, author = {Lindsey, ARI and Stouthamer, R}, title = {The effects of outbreeding on a parasitoid wasp fixed for infection with a parthenogenesis-inducing Wolbachia symbiont.}, journal = {Heredity}, volume = {119}, number = {6}, pages = {411-417}, pmid = {28902190}, issn = {1365-2540}, mesh = {Animals ; Biological Coevolution ; Crosses, Genetic ; Female ; Fertility ; Heterozygote ; Homozygote ; Male ; Models, Genetic ; *Parthenogenesis ; *Sex Ratio ; Symbiosis ; Wasps/*genetics/microbiology ; *Wolbachia ; }, abstract = {Trichogramma wasps can be rendered asexual by infection with the maternally inherited symbiont Wolbachia. Previous studies indicate the Wolbachia strains infecting Trichogramma wasps are host-specific, inferred by failed horizontal transfer of Wolbachia to novel Trichogramma hosts. Additionally, Trichogramma can become dependent upon their Wolbachia infection for the production of female offspring, leaving them irreversibly asexual, further linking host and symbiont. We hypothesized Wolbachia strains infecting irreversibly asexual, resistant to horizontal transfer Trichogramma would show adaptation to a particular host genetic background. To test this, we mated Wolbachia-dependent females with males from a Wolbachia-naïve population to create heterozygous wasps. We measured sex ratios and fecundity, a proxy for Wolbachia fitness, produced by heterozygous wasps, and by their recombinant offspring. We find a heterozygote advantage, resulting in higher fitness for Wolbachia, as wasps will produce more offspring without any reduction in the proportion of females. While recombinant wasps did not differ in total fecundity after 10 days, recombinants produced fewer offspring early on, leading to an increased female-biased sex ratio for the whole brood. Despite the previously identified barriers to horizontal transfer of Wolbachia to and from Trichogramma pretiosum, there were no apparent barriers for Wolbachia to induce parthenogenesis in these non-native backgrounds. This is likely due to the route of infection being introgression rather than horizontal transfer, and possibly the co-evolution of Wolbachia with the mitochondria rather than the nuclear genome. These results help to elucidate the mechanisms by which Wolbachia adapt to hosts and the evolution of host-symbiont phenotypes.}, }
@article {pmid28893855, year = {2017}, author = {Radzvilavicius, AL and Kokko, H and Christie, JR}, title = {Mitigating Mitochondrial Genome Erosion Without Recombination.}, journal = {Genetics}, volume = {207}, number = {3}, pages = {1079-1088}, pmid = {28893855}, issn = {1943-2631}, mesh = {Eukaryota ; Genome, Mitochondrial/*genetics ; Maternal Inheritance ; Mitochondrial Dynamics ; *Models, Genetic ; *Mutation Accumulation ; Recombination, Genetic ; Selection, Genetic ; }, abstract = {Mitochondria are ATP-producing organelles of bacterial ancestry that played a key role in the origin and early evolution of complex eukaryotic cells. Most modern eukaryotes transmit mitochondrial genes uniparentally, often without recombination among genetically divergent organelles. While this asymmetric inheritance maintains the efficacy of purifying selection at the level of the cell, the absence of recombination could also make the genome susceptible to Muller's ratchet. How mitochondria escape this irreversible defect accumulation is a fundamental unsolved question. Occasional paternal leakage could in principle promote recombination, but it would also compromise the purifying selection benefits of uniparental inheritance. We assess this tradeoff using a stochastic population-genetic model. In the absence of recombination, uniparental inheritance of freely-segregating genomes mitigates mutational erosion, while paternal leakage exacerbates the ratchet effect. Mitochondrial fusion-fission cycles ensure independent genome segregation, improving purifying selection. Paternal leakage provides opportunity for recombination to slow down the mutation accumulation, but always at a cost of increased steady-state mutation load. Our findings indicate that random segregation of mitochondrial genomes under uniparental inheritance can effectively combat the mutational meltdown, and that homologous recombination under paternal leakage might not be needed.}, }
@article {pmid28893840, year = {2018}, author = {de Vries, J and Gould, SB}, title = {The monoplastidic bottleneck in algae and plant evolution.}, journal = {Journal of cell science}, volume = {131}, number = {2}, pages = {}, doi = {10.1242/jcs.203414}, pmid = {28893840}, issn = {1477-9137}, mesh = {*Biological Evolution ; Inheritance Patterns/genetics ; Mitochondria/genetics ; Plants/*metabolism ; Plastids/*metabolism ; Symbiosis/genetics ; }, abstract = {Plastids in plants and algae evolved from the endosymbiotic integration of a cyanobacterium by a heterotrophic eukaryote. New plastids can only emerge through fission; thus, the synchronization of bacterial division with the cell cycle of the eukaryotic host was vital to the origin of phototrophic eukaryotes. Most of the sampled algae house a single plastid per cell and basal-branching relatives of polyplastidic lineages are all monoplastidic, as are some non-vascular plants during certain stages of their life cycle. In this Review, we discuss recent advances in our understanding of the molecular components necessary for plastid division, including those of the peptidoglycan wall (of which remnants were recently identified in moss), in a wide range of phototrophic eukaryotes. Our comparison of the phenotype of 131 species harbouring plastids of either primary or secondary origin uncovers that one prerequisite for an algae or plant to house multiple plastids per nucleus appears to be the loss of the bacterial genes minD and minE from the plastid genome. The presence of a single plastid whose division is coupled to host cytokinesis was a prerequisite of plastid emergence. An escape from such a monoplastidic bottleneck succeeded rarely and appears to be coupled to the evolution of additional layers of control over plastid division and a complex morphology. The existence of a quality control checkpoint of plastid transmission remains to be demonstrated and is tied to understanding the monoplastidic bottleneck.}, }
@article {pmid28889978, year = {2017}, author = {Singer, A and Poschmann, G and Mühlich, C and Valadez-Cano, C and Hänsch, S and Hüren, V and Rensing, SA and Stühler, K and Nowack, ECM}, title = {Massive Protein Import into the Early-Evolutionary-Stage Photosynthetic Organelle of the Amoeba Paulinella chromatophora.}, journal = {Current biology : CB}, volume = {27}, number = {18}, pages = {2763-2773.e5}, doi = {10.1016/j.cub.2017.08.010}, pmid = {28889978}, issn = {1879-0445}, mesh = {Cercozoa/*physiology ; Chromatophores/*physiology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Mass Spectrometry ; Metabolic Networks and Pathways ; Proteome/*analysis ; Protozoan Proteins/*analysis ; Sequence Analysis, Protein ; Symbiosis ; }, abstract = {The endosymbiotic acquisition of mitochondria and plastids more than 1 Ga ago profoundly impacted eukaryote evolution. At the heart of understanding organelle evolution is the re-arrangement of the endosymbiont proteome into a host-controlled organellar proteome. However, early stages in this process as well as the timing of events that underlie organelle integration remain poorly understood. The amoeba Paulinella chromatophora contains cyanobacterium-derived photosynthetic organelles, termed "chromatophores," that were acquired more recently (around 100 Ma ago). To explore the re-arrangement of an organellar proteome during its integration into a eukaryotic host cell, here we characterized the chromatophore proteome by protein mass spectrometry. Apparently, genetic control over the chromatophore has shifted substantially to the nucleus. Two classes of nuclear-encoded proteins-which differ in protein length-are imported into the chromatophore, most likely through independent pathways. Long imported proteins carry a putative, conserved N-terminal targeting signal, and many specifically fill gaps in chromatophore-encoded metabolic pathways or processes. Surprisingly, upon heterologous expression in a plant cell, the putative chromatophore targeting signal conferred chloroplast localization. This finding suggests common features in the protein import pathways of chromatophores and plastids, two organelles that evolved independently and more than 1 Ga apart from each other. By combining experimental data with in silico predictions, we provide a comprehensive catalog of almost 450 nuclear-encoded, chromatophore-targeted proteins. Interestingly, most imported proteins seem to derive from ancestral host genes, suggesting that the re-targeting of nuclear-encoded proteins that resulted from endosymbiotic gene transfers plays only a minor role at the onset of chromatophore integration.}, }
@article {pmid28883650, year = {2017}, author = {Liu, M and Guo, X}, title = {A novel and stress adaptive alternative oxidase derived from alternative splicing of duplicated exon in oyster Crassostrea virginica.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10785}, pmid = {28883650}, issn = {2045-2322}, mesh = {*Alternative Splicing ; Animals ; Crassostrea/genetics/*physiology ; *Exons ; Gene Expression Regulation ; Mitochondria/metabolism ; Mitochondrial Proteins/*genetics/*metabolism ; Models, Biological ; Oxidoreductases/*genetics/*metabolism ; Phylogeny ; Plant Proteins/*genetics/*metabolism ; *Stress, Physiological ; }, abstract = {Alternative oxidase (AOX) is a mitochondrial inner-membrane oxidase that accepts electrons directly from ubiquinol and reduces oxygen to water without involving cytochrome-linked electron transport chain. It is highly conserved in many non-vertebrate taxa and may protect cells against hypoxia and oxidative stress. We identified two AOX mRNAs in eastern oyster Crassostrea virginica, CvAOXA and CvAOXB, which differ by 170 bp but encode AOXs of the same size. Sequence analyses indicate that CvAOX has 10 exons with a tandem duplication of exon 10, and 3' alternative splicing using either the first or second exon 10 produces the two variants CvAOXB or CvAOXA, respectively. The second exon 10 in CvAOXA is more conserved across taxa, while the first exon 10 in CvAOXB contains novel mutations surrounding key functional sites. Both variants are expressed in all organs with the expression of CvAOXA higher than that of CvAOXB under normal condition. Under stress by air exposure, CvAOXB showed significantly higher expression than CvAOXA and became the dominant variant. This is the first case of alternative splicing of duplicated exon in a mollusc that produces a novel variant adaptive to stress, highlighting genome's versatility in generating diversity and phenotypic plasticity.}, }
@article {pmid28882896, year = {2017}, author = {Sultana, S and Solotchi, M and Ramachandran, A and Patel, SS}, title = {Transcriptional fidelities of human mitochondrial POLRMT, yeast mitochondrial Rpo41, and phage T7 single-subunit RNA polymerases.}, journal = {The Journal of biological chemistry}, volume = {292}, number = {44}, pages = {18145-18160}, pmid = {28882896}, issn = {1083-351X}, support = {R35 GM118086/GM/NIGMS NIH HHS/United States ; }, mesh = {8-Hydroxy-2'-Deoxyguanosine ; Bacteriophage T7/enzymology ; Base Pair Mismatch ; DNA Damage ; DNA-Directed RNA Polymerases/genetics/*metabolism ; Deoxyguanosine/analogs &amp; derivatives/metabolism ; Fluorescence Polarization ; Humans ; Mitochondrial Proteins/genetics/*metabolism ; *Mutation ; Mutation Rate ; Oxidation-Reduction ; Recombinant Fusion Proteins/metabolism ; Recombinant Proteins/metabolism ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Substrate Specificity ; *Transcription Elongation, Genetic ; Transcription Factors/metabolism ; Viral Proteins/genetics/*metabolism ; }, abstract = {Single-subunit RNA polymerases (RNAPs) are present in phage T7 and in mitochondria of all eukaryotes. This RNAP class plays important roles in biotechnology and cellular energy production, but we know little about its fidelity and error rates. Herein, we report the error rates of three single-subunit RNAPs measured from the catalytic efficiencies of correct and all possible incorrect nucleotides. The average error rates of T7 RNAP (2 × 10[-6]), yeast mitochondrial Rpo41 (6 × 10[-6]), and human mitochondrial POLRMT (RNA polymerase mitochondrial) (2 × 10[-5]) indicate high accuracy/fidelity of RNA synthesis resembling those of replicative DNA polymerases. All three RNAPs exhibit a distinctly high propensity for GTP misincorporation opposite dT, predicting frequent A→G errors in RNA with rates of ∼10[-4] The A→C, G→A, A→U, C→U, G→U, U→C, and U→G errors mostly due to pyrimidine-purine mismatches were relatively frequent (10[-5]-10[-6]), whereas C→G, U→A, G→C, and C→A errors from purine-purine and pyrimidine-pyrimidine mismatches were rare (10[-7]-10[-10]). POLRMT also shows a high C→A error rate on 8-oxo-dG templates (∼10[-4]). Strikingly, POLRMT shows a high mutagenic bypass rate, which is exacerbated by TEFM (transcription elongation factor mitochondrial). The lifetime of POLRMT on terminally mismatched elongation substrate is increased in the presence of TEFM, which allows POLRMT to efficiently bypass the error and continue with transcription. This investigation of nucleotide selectivity on normal and oxidatively damaged DNA by three single-subunit RNAPs provides the basic information to understand the error rates in mitochondria and, in the case of T7 RNAP, to assess the quality of in vitro transcribed RNAs.}, }
@article {pmid28878314, year = {2017}, author = {Sun, S and Li, Q and Kong, L and Yu, H}, title = {Limited locomotive ability relaxed selective constraints on molluscs mitochondrial genomes.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {10628}, pmid = {28878314}, issn = {2045-2322}, mesh = {Animals ; Evolution, Molecular ; *Genome, Mitochondrial ; Genomics/methods ; *Locomotion ; Mitochondria/*genetics/*metabolism ; Mollusca/*physiology ; Open Reading Frames ; Phylogeny ; Selection, Genetic ; }, abstract = {Mollusca are the second largest phylum in the animal kingdom with different types of locomotion. Some molluscs are poor-migrating, while others are free-moving or fast-swimming. Most of the energy required for locomotion is provided by mitochondria via oxidative phosphorylation. Here, we conduct a comparative genomic analysis of 256 molluscs complete mitochondrial genomes and evaluate the role of energetic functional constraints on the protein-coding genes, providing a new insight into mitochondrial DNA (mtDNA) evolution. The weakly locomotive molluscs, compared to strongly locomotive molluscs, show significantly higher Ka/Ks ratio, which suggest they accumulated more nonsynonymous mutations in mtDNA and have experienced more relaxed evolutionary constraints. Eleven protein-coding genes (CoxI, CoxII, ATP6, Cytb, ND1-6, ND4L) show significant difference for Ka/Ks ratios between the strongly and weakly locomotive groups. The relaxation of selective constraints on Atp8 arise in the common ancestor of bivalves, and the further relaxation occurred in marine bivalves lineage. Our study thus demonstrates that selective constraints relevant to locomotive ability play an essential role in evolution of molluscs mtDNA.}, }
@article {pmid28870618, year = {2017}, author = {Sato, N}, title = {Revisiting the theoretical basis of the endosymbiotic origin of plastids in the original context of Lynn Margulis on the origin of mitosing, eukaryotic cells.}, journal = {Journal of theoretical biology}, volume = {434}, number = {}, pages = {104-113}, doi = {10.1016/j.jtbi.2017.08.028}, pmid = {28870618}, issn = {1095-8541}, mesh = {Chromosomes ; DNA Replication ; History, 20th Century ; Mitosis/*genetics ; *Models, Theoretical ; Plastids ; *Symbiosis ; }, abstract = {Fifty years ago, Lynn Margulis proposed a comprehensive hypothesis on the origin of eukaryotic cells with an emphasis on the origin of mitosis. This hypothesis postulated that the eukaryotic cell is a composite of different parts as a result of the symbiosis of various different bacteria. In this hypothesis, she integrated previously proposed ideas that mitochondria and chloroplasts were descendants of endosymbionts that originated from aerobic bacteria and blue-green algae (now cyanobacteria), respectively. However, the major part of her hypothesis, which she believed to be original, was the origin of mitosis. The core of her postulate involved a chromosome partition mechanism dependent on DNA-microtubule binding, which originated from a hypothetical centriole-DNA complex, with an ability to replicate. Surprisingly, her complete lack of real experimental works in the cytoskeleton, cell motility, or paleontology did not prevent this 29-year-old junior scientist from assembling archival knowledge and constructing a narrative on the evolution of all organisms. Whether the centriole-DNA complex originated from a spirochete or not was a minor anecdote in this initial postulate. Unfortunately, this hypothesis on the origin of mitosis, which she believed to be a holistic unity, testable by experiments, was entirely refuted. Despite falsification of her original narrative as a whole, her success as a founder of endosymbiotic theory on the origin of mitochondria and chloroplasts is undoubted. We will discuss the reasons for her success in terms of the historical situation in the latter half of the 20th century.}, }
@article {pmid28870165, year = {2017}, author = {Kollmar, M and Mühlhausen, S}, title = {Myosin repertoire expansion coincides with eukaryotic diversification in the Mesoproterozoic era.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {211}, pmid = {28870165}, issn = {1471-2148}, mesh = {Eukaryota/*classification/*genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Speciation ; Genome ; Introns ; Myosins/chemistry/*genetics ; Phylogeny ; Spliceosomes ; }, abstract = {BACKGROUND: The last eukaryotic common ancestor already had an amazingly complex cell possessing genomic and cellular features such as spliceosomal introns, mitochondria, cilia-dependent motility, and a cytoskeleton together with several intracellular transport systems. In contrast to the microtubule-based dyneins and kinesins, the actin-filament associated myosins are considerably divergent in extant eukaryotes and a unifying picture of their evolution has not yet emerged.<br><br>RESULTS: Here, we manually assembled and annotated 7852 myosins from 929 eukaryotes providing an unprecedented dense sequence and taxonomic sampling. For classification we complemented phylogenetic analyses with gene structure comparisons resulting in 79 distinct myosin classes. The intron pattern analysis and the taxonomic distribution of the classes suggest two myosins in the last eukaryotic common ancestor, a class-1 prototype and another myosin, which is most likely the ancestor of all other myosin classes. The sparse distribution of class-2 and class-4 myosins outside their major lineages contradicts their presence in the last eukaryotic common ancestor but instead strongly suggests early eukaryote-eukaryote horizontal gene transfer.<br><br>CONCLUSIONS: By correlating the evolution of myosin diversity with the history of Earth we found that myosin innovation occurred in independent major "burst" events in the major eukaryotic lineages. Most myosin inventions happened in the Mesoproterozoic era. In the late Neoproterozoic era, a process of extensive independent myosin loss began simultaneously with further eukaryotic diversification. Since the Cambrian explosion, myosin repertoire expansion is driven by lineage- and species-specific gene and genome duplications leading to subfunctionalization and fine-tuning of myosin functions.}, }
@article {pmid28864909, year = {2017}, author = {Reiter, RJ and Rosales-Corral, S and Tan, DX and Jou, MJ and Galano, A and Xu, B}, title = {Melatonin as a mitochondria-targeted antioxidant: one of evolution's best ideas.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {74}, number = {21}, pages = {3863-3881}, pmid = {28864909}, issn = {1420-9071}, mesh = {Animals ; Antioxidants/*pharmacology ; Free Radicals/*metabolism ; Humans ; Melatonin/*pharmacology ; Mitochondria/drug effects/*metabolism ; Oxidation-Reduction ; }, abstract = {Melatonin is an ancient antioxidant. After its initial development in bacteria, it has been retained throughout evolution such that it may be or may have been present in every species that have existed. Even though it has been maintained throughout evolution during the diversification of species, melatonin's chemical structure has never changed; thus, the melatonin present in currently living humans is identical to that present in cyanobacteria that have existed on Earth for billions of years. Melatonin in the systemic circulation of mammals quickly disappears from the blood presumably due to its uptake by cells, particularly when they are under high oxidative stress conditions. The measurement of the subcellular distribution of melatonin has shown that the concentration of this indole in the mitochondria greatly exceeds that in the blood. Melatonin presumably enters mitochondria through oligopeptide transporters, PEPT1, and PEPT2. Thus, melatonin is specifically targeted to the mitochondria where it seems to function as an apex antioxidant. In addition to being taken up from the circulation, melatonin may be produced in the mitochondria as well. During evolution, mitochondria likely originated when melatonin-forming bacteria were engulfed as food by ancestral prokaryotes. Over time, engulfed bacteria evolved into mitochondria; this is known as the endosymbiotic theory of the origin of mitochondria. When they did so, the mitochondria retained the ability to synthesize melatonin. Thus, melatonin is not only taken up by mitochondria but these organelles, in addition to many other functions, also probably produce melatonin as well. Melatonin's high concentrations and multiple actions as an antioxidant provide potent antioxidant protection to these organelles which are exposed to abundant free radicals.}, }
@article {pmid28863891, year = {2017}, author = {Lu, L and Wang, X and Wu, S and Song, X and Zou, Z and Xie, X and Xiao, J and Chen, S and Feng, H}, title = {Black carp STING functions importantly in innate immune defense against RNA virus.}, journal = {Fish &amp; shellfish immunology}, volume = {70}, number = {}, pages = {13-24}, doi = {10.1016/j.fsi.2017.08.037}, pmid = {28863891}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Carps/*genetics/*immunology ; Fish Diseases/*immunology ; Fish Proteins/chemistry/genetics/immunology ; Gene Expression Profiling ; Gene Expression Regulation/*immunology ; Immunity, Innate/*genetics ; Membrane Proteins/chemistry/*genetics/*immunology ; Phylogeny ; Reoviridae/physiology ; Reoviridae Infections/immunology ; Rhabdoviridae/physiology ; Rhabdoviridae Infections/immunology ; }, abstract = {Stimulator of interferon genes (STING) is a central and multifaceted mediator in the innate immune response of higher vertebrates. To explore its role in teleost fish, the STING homolog of black carp (Mylopharyngodon piceus) (bcSTING) has been cloned and characterized in this paper. bcSTING transcription in Mylopharyngodon piceus fin (MPF) cells increased remarkably in response to GCRV and SVCV infection, or poly (I:C) stimulation. bcSTING migrated around 42 KDa in immunoblot assay and was identified as a cytosolic protein locating on ER majorly through immunofluorescence staining. Under condition of SVCV/GCRV infection or poly (I:C) stimulation, the subcellular distribution of bcSTING majorly displayed on mitochondria, which overlapped with that of bcMAVS. HA-bcSTING instead of bcSTING-HA presented strong IFN-inducing activity in reporter assay and antiviral ability against both SVCV and GCRV in plaque assay. Site mutation of serine (S) on C-terminus of bcSTING demonstrated that both S371 and S379 were crucial for its mediated signaling. Taken together, our study support the conclusion that bcSTING plays an important role in host innate immune defense against RNA virus such as SVCV and GCRV, in which its C-terminus functions crucially.}, }
@article {pmid28859174, year = {2017}, author = {Hudson, W}, title = {Whole-loop mitochondrial DNA D-loop sequence variability in Egyptian Arabian equine matrilines.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0184309}, pmid = {28859174}, issn = {1932-6203}, mesh = {Agriculture ; Animals ; DNA, Mitochondrial/*genetics ; Egypt ; Haplotypes/genetics ; Horses/*genetics ; Mitochondria/genetics ; Pedigree ; *Phylogeny ; }, abstract = {BACKGROUND: Egyptian Arabian horses have been maintained in a state of genetic isolation for over a hundred years. There is only limited genetic proof that the studbook records of female lines of Egyptian Arabian pedigrees are reliable. This study characterized the mitochondrial DNA (mtDNA) signatures of 126 horses representing 14 matrilines in the Egyptian Agricultural Organization (EAO) horse-breeding program.<br><br>FINDINGS: Analysis of the whole D-loop sequence yielded additional information compared to hypervariable region-1 (HVR1) analysis alone, with 42 polymorphic sites representing ten haplotypes compared to 16 polymorphic sites representing nine haplotypes, respectively. Most EAO haplotypes belonged to ancient haplogroups, suggesting origin from a wide geographical area over many thousands of years, although one haplotype was novel.<br><br>CONCLUSIONS: Historical families share haplotypes and some individuals from different strains belonged to the same haplogroup: the classical EAO strain designation is not equivalent to modern monophyletic matrilineal groups. Phylogenetic inference showed that the foundation mares of the historical haplotypes were highly likely to have the same haplotypes as the animals studied (p > 0.998 in all cases), confirming the reliability of EAO studbook records and providing the opportunity for breeders to confirm the ancestry of their horses.}, }
@article {pmid28855414, year = {2017}, author = {Sloan, DB}, title = {Nuclear and mitochondrial RNA editing systems have opposite effects on protein diversity.}, journal = {Biology letters}, volume = {13}, number = {8}, pages = {}, pmid = {28855414}, issn = {1744-957X}, mesh = {Base Sequence ; Inosine ; Phylogeny ; Proteins ; RNA ; *RNA Editing ; RNA, Mitochondrial ; }, abstract = {RNA editing can yield protein products that differ from those directly encoded by genomic DNA. This process is pervasive in the mitochondria of many eukaryotes, where it predominantly results in the restoration of ancestral protein sequences. Nuclear mRNAs in metazoans also undergo editing (adenosine-to-inosine or 'A-to-I' substitutions), and most of these edits appear to be nonadaptive 'misfirings' of adenosine deaminases. However, recent analysis of cephalopod transcriptomes found that many editing sites are shared by anciently divergent lineages within this group, suggesting they play some adaptive role. Recent discoveries have also revealed that some fungi have an independently evolved A-to-I editing mechanism, resulting in extensive recoding of their nuclear mRNAs. Here, phylogenetic comparisons were used to determine whether RNA editing generally restores ancestral protein sequences or creates derived variants. Unlike in mitochondrial systems, RNA editing in metazoan and fungal nuclear transcripts overwhelmingly leads to novel sequences not found in inferred ancestral proteins. Even for the subset of RNA editing sites shared by deeply divergent cephalopod lineages, the primary effect of nuclear editing is an increase-not a decrease-in protein divergence. These findings suggest fundamental differences in the forces responsible for the evolution of RNA editing in nuclear versus mitochondrial systems.}, }
@article {pmid28854633, year = {2017}, author = {Park, S and Ruhlman, TA and Weng, ML and Hajrah, NH and Sabir, JSM and Jansen, RK}, title = {Contrasting Patterns of Nucleotide Substitution Rates Provide Insight into Dynamic Evolution of Plastid and Mitochondrial Genomes of Geranium.}, journal = {Genome biology and evolution}, volume = {9}, number = {6}, pages = {1766-1780}, pmid = {28854633}, issn = {1759-6653}, mesh = {Base Sequence ; *Evolution, Molecular ; *Genome, Mitochondrial ; Genome, Plant ; *Genome, Plastid ; Geranium/chemistry/classification/*genetics ; Mitochondria/genetics ; Mutation ; Phylogeny ; Plastids/genetics ; }, abstract = {Geraniaceae have emerged as a model system for investigating the causes and consequences of variation in plastid and mitochondrial genomes. Incredible structural variation in plastid genomes (plastomes) and highly accelerated evolutionary rates have been reported in selected lineages and functional groups of genes in both plastomes and mitochondrial genomes (mitogenomes), and these phenomena have been implicated in cytonuclear incompatibility. Previous organelle genome studies have included limited sampling of Geranium, the largest genus in the family with over 400 species. This study reports on rates and patterns of nucleotide substitutions in plastomes and mitogenomes of 17 species of Geranium and representatives of other Geraniaceae. As detected across other angiosperms, substitution rates in the plastome are 3.5 times higher than the mitogenome in most Geranium. However, in the branch leading to Geranium brycei/Geranium incanum mitochondrial genes experienced significantly higher dN and dS than plastid genes, a pattern that has only been detected in one other angiosperm. Furthermore, rate accelerations differ in the two organelle genomes with plastomes having increased dN and mitogenomes with increased dS. In the Geranium phaeum/Geranium reflexum clade, duplicate copies of clpP and rpoA genes that experienced asymmetric rate divergence were detected in the single copy region of the plastome. In the case of rpoA, the branch leading to G. phaeum/G. reflexum experienced positive selection or relaxation of purifying selection. Finally, the evolution of acetyl-CoA carboxylase is unusual in Geraniaceae because it is only the second angiosperm family where both prokaryotic and eukaryotic ACCases functionally coexist in the plastid.}, }
@article {pmid28854623, year = {2017}, author = {Marlétaz, F and Le Parco, Y and Liu, S and Peijnenburg, KTCA}, title = {Extreme Mitogenomic Variation in Natural Populations of Chaetognaths.}, journal = {Genome biology and evolution}, volume = {9}, number = {6}, pages = {1374-1384}, pmid = {28854623}, issn = {1759-6653}, support = {/WT_/Wellcome Trust/United Kingdom ; 268513/ERC_/European Research Council/International ; }, mesh = {Animals ; DNA, Mitochondrial/genetics ; Eukaryota/classification/*genetics ; Evolution, Molecular ; *Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; }, abstract = {The extent of within-species genetic variation across the diversity of animal life is an underexplored problem in ecology and evolution. Although neutral genetic variation should scale positively with population size, mitochondrial diversity levels are believed to show little variation across animal species. Here, we report an unprecedented case of extreme mitochondrial diversity within natural populations of two morphospecies of chaetognaths (arrow worms). We determine that this diversity is composed of deep sympatric mitochondrial lineages, which are in some cases as divergent as human and platypus. Additionally, based on 54 complete mitogenomes, we observed mitochondrial gene order differences between several of these lineages. We examined nuclear divergence patterns (18S, 28S, and an intron) to determine the possible origin of these lineages, but did not find congruent patterns between mitochondrial and nuclear markers. We also show that extreme mitochondrial divergence in chaetognaths is not driven by positive selection. Hence, we propose that the extreme levels of mitochondrial variation could be the result of either a complex scenario of reproductive isolation, or a combination of large population size and accelerated mitochondrial mutation rate. These findings emphasize the importance of characterizing genome-wide levels of nuclear variation in these species and promote chaetognaths as a remarkable model to study mitochondrial evolution.}, }
@article {pmid28854615, year = {2017}, author = {Mak, SST and Gopalakrishnan, S and Carøe, C and Geng, C and Liu, S and Sinding, MS and Kuderna, LFK and Zhang, W and Fu, S and Vieira, FG and Germonpré, M and Bocherens, H and Fedorov, S and Petersen, B and Sicheritz-Pontén, T and Marques-Bonet, T and Zhang, G and Jiang, H and Gilbert, MTP}, title = {Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing.}, journal = {GigaScience}, volume = {6}, number = {8}, pages = {1-13}, pmid = {28854615}, issn = {2047-217X}, support = {681396/ERC_/European Research Council/International ; U01 MH106874/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Base Composition ; DNA/chemistry ; DNA, Mitochondrial/chemistry ; Genomics/*methods/*standards ; High-Throughput Nucleotide Sequencing/*methods/*standards ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform on DNA extracted from 8 historic and ancient dog and wolf samples. The data generated were largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (P = 0.371) and average sequence length (P = 0718) of endogenous nuclear DNA, sequence GC content (P = 0.311), double-stranded DNA damage rate (v. 0.309), and sequence clonality (P = 0.093). Small significant differences were found in single-strand DNA damage rate (δS; slightly lower for the BGISEQ-500, P = 0.011) and the background rate of difference from the reference genome (θ; slightly higher for BGISEQ-500, P = 0.012). This may result from the differences in amplification cycles used to polymerase chain reaction-amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (P = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from 3 of the samples with overall very low levels of endogenous DNA. Although we acknowledge that our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent a valid and potentially valuable alternative platform for palaeogenomic data generation that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.}, }
@article {pmid28854599, year = {2017}, author = {Rauch, C and Christa, G and de Vries, J and Woehle, C and Gould, SB}, title = {Mitochondrial Genome Assemblies of Elysia timida and Elysia cornigera and the Response of Mitochondrion-Associated Metabolism during Starvation.}, journal = {Genome biology and evolution}, volume = {9}, number = {7}, pages = {1873-1879}, pmid = {28854599}, issn = {1759-6653}, mesh = {Animals ; Chloroplasts/metabolism ; DNA, Mitochondrial/genetics ; Gastropoda/classification/*genetics/*metabolism ; *Genome, Mitochondrial ; Mitochondria/genetics/metabolism ; Photosynthesis ; Plastids/metabolism ; }, abstract = {Some sacoglossan sea slugs sequester functional plastids (kleptoplasts) from their food, which continue to fix CO2 in a light dependent manner inside the animals. In plants and algae, plastid and mitochondrial metabolism are linked in ways that reach beyond the provision of energy-rich carbon compounds through photosynthesis, but how slug mitochondria respond to starvation or alterations in plastid biochemistry has not been explored. We assembled the mitochondrial genomes of the plastid-sequestering sea slugs Elysia timida and Elysia cornigera from RNA-Seq data that was complemented with standard sequencing of mitochondrial DNA through primer walking. Our data confirm the sister species relationship of the two Sacoglossa and from the analysis of changes in mitochondrial-associated metabolism during starvation we speculate that kleptoplasts might aid in the rerouting or recycling of reducing power independent of, yet maybe improved by, photosynthesis.}, }
@article {pmid28848044, year = {2017}, author = {Srivastava, S and Savanur, MA and Sinha, D and Birje, A and R, V and Saha, PP and D'Silva, P}, title = {Regulation of mitochondrial protein import by the nucleotide exchange factors GrpEL1 and GrpEL2 in human cells.}, journal = {The Journal of biological chemistry}, volume = {292}, number = {44}, pages = {18075-18090}, pmid = {28848044}, issn = {1083-351X}, mesh = {Biomarkers/metabolism ; Genetic Complementation Test ; Green Fluorescent Proteins/genetics/metabolism ; HEK293 Cells ; HSP70 Heat-Shock Proteins/chemistry/*metabolism ; HeLa Cells ; Humans ; Immunoprecipitation ; Intracellular Signaling Peptides and Proteins/antagonists &amp; inhibitors/chemistry/genetics/*metabolism ; Ligands ; Mitochondria/*metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; *Models, Molecular ; Molecular Chaperones/antagonists &amp; inhibitors/chemistry/genetics/*metabolism ; Oxidative Stress ; Phylogeny ; Protein Isoforms/metabolism ; Protein Multimerization ; Protein Stability ; Protein Transport ; RNA Interference ; Recombinant Fusion Proteins/chemistry/metabolism ; }, abstract = {Mitochondria are organelles indispensable for maintenance of cellular energy homeostasis. Most mitochondrial proteins are nuclearly encoded and are imported into the matrix compartment where they are properly folded. This process is facilitated by the mitochondrial heat shock protein 70 (mtHsp70), a chaperone contributing to mitochondrial protein quality control. The affinity of mtHsp70 for its protein clients and its chaperone function are regulated by binding of ATP/ADP to mtHsp70's nucleotide-binding domain. Nucleotide exchange factors (NEFs) play a crucial role in exchanging ADP for ATP at mtHsp70's nucleotide-binding domain, thereby modulating mtHsp70's chaperone activity. A single NEF, Mge1, regulates mtHsp70's chaperone activity in lower eukaryotes, but the mammalian orthologs are unknown. Here, we report that two putative NEF orthologs, GrpE-like 1 (GrpEL1) and GrpEL2, modulate mtHsp70's function in human cells. We found that both GrpEL1 and GrpEL2 associate with mtHsp70 as a hetero-oligomeric subcomplex and regulate mtHsp70 function. The formation of this subcomplex was critical for conferring stability to the NEFs, helped fine-tune mitochondrial protein quality control, and regulated crucial mtHsp70 functions, such as import of preproteins and biogenesis of Fe-S clusters. Our results also suggested that GrpEL2 has evolved as a possible stress resistance protein in higher vertebrates to maintain chaperone activity under stress conditions. In conclusion, our findings support the idea that GrpEL1 has a role as a stress modulator in mammalian cells and highlight that multiple NEFs are involved in controlling protein quality in mammalian mitochondria.}, }
@article {pmid28846455, year = {2017}, author = {Bock, R}, title = {Witnessing Genome Evolution: Experimental Reconstruction of Endosymbiotic and Horizontal Gene Transfer.}, journal = {Annual review of genetics}, volume = {51}, number = {}, pages = {1-22}, doi = {10.1146/annurev-genet-120215-035329}, pmid = {28846455}, issn = {1545-2948}, mesh = {Cell Nucleus/genetics/metabolism ; Chloroplasts/genetics/metabolism ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genetic Speciation ; *Genome, Plant ; Genomics/methods ; Mitochondria/genetics/metabolism ; Plant Cells/metabolism ; Plants/*genetics ; Symbiosis/*genetics ; }, abstract = {Present day mitochondria and plastids (chloroplasts) evolved from formerly free-living bacteria that were acquired through endosymbiosis more than a billion years ago. Conversion of the bacterial endosymbionts into cell organelles involved the massive translocation of genetic material from the organellar genomes to the nucleus. The development of transformation technologies for organellar genomes has made it possible to reconstruct this endosymbiotic gene transfer in laboratory experiments and study the mechanisms involved. Recently, the horizontal transfer of genetic information between organisms has also become amenable to experimental investigation. It led to the discovery of horizontal genome transfer as an asexual process generating new species and new combinations of nuclear and organellar genomes. This review describes experimental approaches towards studying endosymbiotic and horizontal gene transfer processes, discusses the new knowledge gained from these approaches about both the evolutionary significance of gene transfer and the underlying molecular mechanisms, and highlights exciting possibilities to exploit gene and genome transfer in biotechnology and synthetic biology.}, }
@article {pmid28842472, year = {2017}, author = {Kraus, F and Ryan, MT}, title = {The constriction and scission machineries involved in mitochondrial fission.}, journal = {Journal of cell science}, volume = {130}, number = {18}, pages = {2953-2960}, doi = {10.1242/jcs.199562}, pmid = {28842472}, issn = {1477-9137}, mesh = {Actins/metabolism ; Animals ; Endoplasmic Reticulum/metabolism ; Humans ; Lipids/chemistry ; *Mitochondrial Dynamics ; Mitochondrial Proteins/metabolism ; Models, Biological ; }, abstract = {A key event in the evolution of eukaryotic cells was the engulfment of an aerobic bacterium by a larger anaerobic archaebacterium, leading to a close relationship between the host and the newly formed endosymbiont. Mitochondria, originating from this event, have evolved to be the main place of cellular ATP production. Maintaining elements of their independence, mitochondria undergo growth and division in the cell, thereby ensuring that new daughter cells inherit a mitochondrial complement. Mitochondrial division is also important for other processes, including quality control, mitochondrial (mt)DNA inheritance, transport and cell death. However, unlike bacterial fission, which uses a dynamin-related protein to constrict the membrane at its inner face, mitochondria use dynamin and dynamin-related proteins to constrict the outer membrane from the cytosolic face. In this Review, we summarize the role of proteins from the dynamin superfamily in mitochondrial division. This includes recent findings highlighting that dynamin-2 (Dnm2) is involved in mitochondrial scission, which led to the reappraisal of the role of dynamin-related protein 1 (Drp1; also known as Dnm1l) and its outer membrane adaptors as components of the mitochondrial constriction machinery along with ER components and actin.}, }
@article {pmid28837072, year = {2017}, author = {Hikmat, O and Eichele, T and Tzoulis, C and Bindoff, LA}, title = {Understanding the Epilepsy in POLG Related Disease.}, journal = {International journal of molecular sciences}, volume = {18}, number = {9}, pages = {}, pmid = {28837072}, issn = {1422-0067}, mesh = {Animals ; Cerebral Cortex/pathology ; DNA Polymerase gamma/*genetics/*metabolism ; Disease Susceptibility ; Electroencephalography ; Epilepsy/diagnosis/*etiology/*metabolism/therapy ; Humans ; Magnetic Resonance Imaging/methods ; Neurons/metabolism ; }, abstract = {Epilepsy is common in polymerase gamma (POLG) related disease and is associated with high morbidity and mortality. Epileptiform discharges typically affect the occipital regions initially and focal seizures, commonly evolving to bilateral convulsive seizures which are the most common seizure types in both adults and children. Our work has shown that mtDNA depletion-i.e., the quantitative loss of mtDNA-in neurones is the earliest and most important factor of the subsequent development of cellular dysfunction. Loss of mtDNA leads to loss of mitochondrial respiratory chain (MRC) components that, in turn, progressively disables energy metabolism. This critically balanced neuronal energy metabolism leads to both a chronic and continuous attrition (i.e., neurodegeneration) and it leaves the neurone unable to cope with increased demand that can trigger a potentially catastrophic cycle that results in acute focal necrosis. We believe that it is the onset of epilepsy that triggers the cascade of damage. These events can be identified in the stepwise evolution that characterizes the clinical, Electroencephalography (EEG), neuro-imaging, and neuropathology findings. Early recognition with prompt and aggressive seizure management is vital and may play a role in modifying the epileptogenic process and improving survival.}, }
@article {pmid28830831, year = {2017}, author = {Banker, SE and Wade, EJ and Simon, C}, title = {The confounding effects of hybridization on phylogenetic estimation in the New Zealand cicada genus Kikihia.}, journal = {Molecular phylogenetics and evolution}, volume = {116}, number = {}, pages = {172-181}, doi = {10.1016/j.ympev.2017.08.009}, pmid = {28830831}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Haplotypes/genetics ; Hemiptera/*genetics ; *Hybridization, Genetic ; Mitochondria/genetics ; New Zealand ; *Phylogeny ; Species Specificity ; }, abstract = {Phylogenetic studies of multiple independently inherited nuclear genes considered in combination with patterns of inheritance of organelle DNA have provided considerable insight into the history of species evolution. In particular, investigations of cicadas in the New Zealand genus Kikihia have identified interesting cases where mitochondrial DNA (mtDNA) crosses species boundaries in some species pairs but not others. Previous phylogenetic studies focusing on mtDNA largely corroborated Kikihia species groups identified by song, morphology and ecology with the exception of a unique South Island mitochondrial haplotype clade-the Westlandica group. This newly identified group consists of diverse taxa previously classified as belonging to three different sub-generic clades. We sequenced five nuclear loci from multiple individuals from every species of Kikihia to assess the nuclear gene concordance for this newly-identified mtDNA lineage. Bayes Factor analysis of the constrained phylogeny suggests some support for the mtDNA-based hypotheses, despite the fact that neither concatenation nor multiple species tree methods resolve the Westlandica group as monophyletic. The nuclear analyses suggest a geographic distinction between clearly defined monophyletic North Island clades and unresolved South Island clades. We suggest that more extreme habitat modification on South Island during the Pliocene and Pleistocene resulted in secondary contact and hybridization between species pairs and a series of mitochondrial capture events followed by subsequent lineage evolution.}, }
@article {pmid28829360, year = {2017}, author = {Vasileiou, PVS and Mourouzis, I and Pantos, C}, title = {Principal Aspects Regarding the Maintenance of Mammalian Mitochondrial Genome Integrity.}, journal = {International journal of molecular sciences}, volume = {18}, number = {8}, pages = {}, pmid = {28829360}, issn = {1422-0067}, mesh = {Animals ; DNA Damage ; DNA Repair ; DNA, Mitochondrial ; Evolution, Molecular ; *Genome, Mitochondrial ; Genomic Instability ; Genomic Structural Variation ; *Genomics/methods ; *Homeostasis ; Humans ; Mammals/*genetics ; Mitochondrial Dynamics/genetics ; Mitophagy/genetics ; }, abstract = {Mitochondria have emerged as key players regarding cellular homeostasis not only due to their contribution regarding energy production through oxidative phosphorylation, but also due to their involvement in signaling, ion regulation, and programmed cell death. Indeed, current knowledge supports the notion that mitochondrial dysfunction is a hallmark in the pathogenesis of various diseases. Mitochondrial biogenesis and function require the coordinated action of two genomes: nuclear and mitochondrial. Unfortunately, both intrinsic and environmental genotoxic insults constantly threaten the integrity of nuclear as well as mitochondrial DNA. Despite the extensive research that has been made regarding nuclear genome instability, the importance of mitochondrial genome integrity has only recently begun to be elucidated. The specific architecture and repair mechanisms of mitochondrial DNA, as well as the dynamic behavior that mitochondria exert regarding fusion, fission, and autophagy participate in mitochondrial genome stability, and therefore, cell homeostasis.}, }
@article {pmid28822138, year = {2017}, author = {Khoshravesh, R and Lundsgaard-Nielsen, V and Sultmanis, S and Sage, TL}, title = {Light Microscopy, Transmission Electron Microscopy, and Immunohistochemistry Protocols for Studying Photorespiration.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1653}, number = {}, pages = {243-270}, doi = {10.1007/978-1-4939-7225-8_17}, pmid = {28822138}, issn = {1940-6029}, mesh = {Arabidopsis/*physiology/ultrastructure ; Carbon Dioxide/metabolism ; Chloroplasts/metabolism/ultrastructure ; Cytosol/metabolism/ultrastructure ; Glycolates/metabolism ; Immunohistochemistry/*methods ; Microscopy, Electron, Transmission/instrumentation/*methods ; Microtomy/instrumentation/methods ; Mitochondria/metabolism/ultrastructure ; Oxygen/metabolism ; Oxygen Consumption/*physiology ; Peroxisomes/metabolism/ultrastructure ; Photosynthesis/*physiology ; Plant Leaves/*physiology/ultrastructure ; Ribulose-Bisphosphate Carboxylase/metabolism ; Staining and Labeling/instrumentation/methods ; Tissue Embedding/methods ; Tissue Fixation/methods ; }, abstract = {High-resolution images obtained from plant tissues processed for light microscopy, transmission electron microscopy, and immunohistochemistry have provided crucial links between plant subcellular structure and physiology during photorespiration as well as the impact of photorespiration on plant evolution and development. This chapter presents established protocols to guide researchers in the preparation of plant tissues for high-resolution imaging with a light and transmission electron microscope and detection of proteins using immunohistochemistry. Discussion of concepts and theory behind each step in the process from tissue preservation to staining of resin-embedded tissues is included to enhance the understanding of all steps in the procedure. We also include a brief protocol for quantification of cellular parameters from high-resolution images to help researchers rigorously test hypotheses.}, }
@article {pmid28821609, year = {2017}, author = {Lyons, A and Coleman, M and Riis, S and Favre, C and O'Flanagan, CH and Zhdanov, AV and Papkovsky, DB and Hursting, SD and O'Connor, R}, title = {Insulin-like growth factor 1 signaling is essential for mitochondrial biogenesis and mitophagy in cancer cells.}, journal = {The Journal of biological chemistry}, volume = {292}, number = {41}, pages = {16983-16998}, pmid = {28821609}, issn = {1083-351X}, support = {P30 CA016086/CA/NCI NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; R35 CA197627/CA/NCI NIH HHS/United States ; }, mesh = {Carrier Proteins/genetics/metabolism ; Cell Survival/genetics ; Humans ; Insulin-Like Growth Factor I/genetics/*metabolism ; MCF-7 Cells ; Membrane Proteins/genetics/metabolism ; Mitochondria/genetics/*metabolism ; *Mitochondrial Dynamics ; *Mitophagy ; NF-E2-Related Factor 2/genetics/metabolism ; Neoplasm Proteins/genetics/*metabolism ; Neoplasms/genetics/*metabolism/pathology ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/genetics/metabolism ; Proto-Oncogene Proteins/genetics/metabolism ; RNA-Binding Proteins ; Receptor, IGF Type 1 ; Receptors, Somatomedin/genetics/metabolism ; *Signal Transduction ; Tumor Suppressor Proteins/genetics/metabolism ; }, abstract = {Mitochondrial activity and metabolic reprogramming influence the phenotype of cancer cells and resistance to targeted therapy. We previously established that an insulin-like growth factor 1 (IGF-1)-inducible mitochondrial UTP carrier (PNC1/SLC25A33) promotes cell growth. This prompted us to investigate whether IGF signaling is essential for mitochondrial maintenance in cancer cells and whether this contributes to therapy resistance. Here we show that IGF-1 stimulates mitochondrial biogenesis in a range of cell lines. In MCF-7 and ZR75.1 breast cancer cells, IGF-1 induces peroxisome proliferator-activated receptor γ coactivator 1β (PGC-1β) and PGC-1α-related coactivator (PRC). Suppression of PGC-1β and PRC with siRNA reverses the effects of IGF-1 and disrupts mitochondrial morphology and membrane potential. IGF-1 also induced expression of the redox regulator nuclear factor-erythroid-derived 2-like 2 (NFE2L2 alias NRF-2). Of note, MCF-7 cells with acquired resistance to an IGF-1 receptor (IGF-1R) tyrosine kinase inhibitor exhibited reduced expression of PGC-1β, PRC, and mitochondrial biogenesis. Interestingly, these cells exhibited mitochondrial dysfunction, indicated by reactive oxygen species expression, reduced expression of the mitophagy mediators BNIP3 and BNIP3L, and impaired mitophagy. In agreement with this, IGF-1 robustly induced BNIP3 accumulation in mitochondria. Other active receptor tyrosine kinases could not compensate for reduced IGF-1R activity in mitochondrial protection, and MCF-7 cells with suppressed IGF-1R activity became highly dependent on glycolysis for survival. We conclude that IGF-1 signaling is essential for sustaining cancer cell viability by stimulating both mitochondrial biogenesis and turnover through BNIP3 induction. This core mitochondrial protective signal is likely to strongly influence responses to therapy and the phenotypic evolution of cancer.}, }
@article {pmid28819183, year = {2017}, author = {Zhang, H and Seol, Y and Agama, K and Neuman, KC and Pommier, Y}, title = {Distribution bias and biochemical characterization of TOP1MT single nucleotide variants.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8614}, pmid = {28819183}, issn = {2045-2322}, support = {Z01 BC006161//Intramural NIH HHS/United States ; Z01 HL001056//Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Cell Line, Tumor ; Cell Nucleus/enzymology/*genetics ; DNA Topoisomerases, Type I/chemistry/*genetics/metabolism ; DNA, Superhelical/chemistry/genetics/metabolism ; Gene Frequency ; Genetic Predisposition to Disease/genetics ; Humans ; Mitochondria/enzymology/*genetics ; Models, Molecular ; Neoplasms/enzymology/genetics/pathology ; Nucleic Acid Conformation ; *Polymorphism, Single Nucleotide ; Protein Binding ; Protein Domains ; Sequence Homology, Amino Acid ; }, abstract = {Mitochondrial topoisomerase I (TOP1MT) is a type IB topoisomerase encoded in the nucleus of vertebrate cells. In contrast to the other five human topoisomerases, TOP1MT possesses two high frequency single nucleotide variants (SNVs), rs11544484 (V256I, Minor Allele Frequency = 0.27) and rs2293925 (R525W, MAF = 0.45), which tend to be mutually exclusive across different human ethnic groups and even more clearly in a cohort of 129 US patients with breast cancer and in the NCI-60 cancer cell lines. We expressed these two TOP1MT variants and the double-variant (V256I-R525W) as recombinant proteins, as well as a less common variant E168G (rs200673353, MAF = 0.001), and studied their biochemical properties by magnetic tweezers-based supercoil relaxation and classical DNA relaxation assays. Variants showed reduced DNA relaxation activities, especially the V256I variant towards positively supercoiled DNA. We also found that the V256I variant was enriched to MAF = 0.64 in NCI-60 lung carcinoma cell lines, whereas the TOP1MT R525W was enriched to MAF = 0.65 in the NCI-60 melanoma cell lines. Moreover, TOP1MT expression correlated with the 256 variants in the NCI-60 lung carcinoma cell lines, valine with high expression and isoleucine with low expression. Our results are discussed in the context of evolution between the nuclear and mitochondrial topoisomerases and potential cancer predisposition.}, }
@article {pmid28818345, year = {2017}, author = {Novikova, O and Belfort, M}, title = {Mobile Group II Introns as Ancestral Eukaryotic Elements.}, journal = {Trends in genetics : TIG}, volume = {33}, number = {11}, pages = {773-783}, pmid = {28818345}, issn = {0168-9525}, support = {R01 GM039422/GM/NIGMS NIH HHS/United States ; R01 GM044844/GM/NIGMS NIH HHS/United States ; R37 GM039422/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Eukaryotic Cells ; Interspersed Repetitive Sequences ; *Introns ; RNA, Catalytic/genetics ; Spliceosomes ; }, abstract = {The duality of group II introns, capable of carrying out both self-splicing and retromobility reactions, is hypothesized to have played a profound role in the evolution of eukaryotes. These introns likely provided the framework for the emergence of eukaryotic retroelements, spliceosomal introns and other key components of the spliceosome. Group II introns are found in all three domains of life and are therefore considered to be exceptionally successful mobile genetic elements. Initially identified in organellar genomes, group II introns are found in bacteria, chloroplasts, and mitochondria of plants and fungi, but not in nuclear genomes. Although there is no doubt that prokaryotic and organellar group II introns are evolutionary related, there are remarkable differences in survival strategies between them. Furthermore, an evolutionary relationship of group II introns to eukaryotic retroelements, including telomeres, and spliceosomes is unmistakable.}, }
@article {pmid28812460, year = {2017}, author = {Martín-Hernández, E and García-Silva, MT and Quijada-Fraile, P and Rodríguez-García, ME and Rivera, H and Hernández-Laín, A and Coca-Robinot, D and Fernández-Toral, J and Arenas, J and Martín, MA and Martínez-Azorín, F}, title = {Myopathic mtDNA Depletion Syndrome Due to Mutation in TK2 Gene.}, journal = {Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society}, volume = {20}, number = {5}, pages = {416-420}, doi = {10.1177/1093526616686439}, pmid = {28812460}, issn = {1093-5266}, mesh = {Child ; Female ; Genetic Markers ; Homozygote ; Humans ; Mitochondrial Diseases/diagnosis/*genetics ; Muscular Diseases/diagnosis/*genetics ; *Mutation ; Thymidine Kinase/*genetics ; Exome Sequencing ; }, abstract = {Whole-exome sequencing was used to identify the disease gene(s) in a Spanish girl with failure to thrive, muscle weakness, mild facial weakness, elevated creatine kinase, deficiency of mitochondrial complex III and depletion of mtDNA. With whole-exome sequencing data, it was possible to get the whole mtDNA sequencing and discard any pathogenic variant in this genome. The analysis of whole exome uncovered a homozygous pathogenic mutation in thymidine kinase 2 gene (TK2; NM_004614.4:c.323 C>T, p.T108M). TK2 mutations have been identified mainly in patients with the myopathic form of mtDNA depletion syndromes. This patient presents an atypical TK2-related myopathic form of mtDNA depletion syndromes, because despite having a very low content of mtDNA (<20%), she presents a slower and less severe evolution of the disease. In conclusion, our data confirm the role of TK2 gene in mtDNA depletion syndromes and expanded the phenotypic spectrum.}, }
@article {pmid28811531, year = {2017}, author = {Moghaddam, MB and Gross, T and Becker, A and Vilcinskas, A and Rahnamaeian, M}, title = {The selective antifungal activity of Drosophila melanogaster metchnikowin reflects the species-dependent inhibition of succinate-coenzyme Q reductase.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8192}, pmid = {28811531}, issn = {2045-2322}, mesh = {Animals ; Antifungal Agents/*pharmacology ; Antimicrobial Cationic Peptides/genetics/*pharmacology ; Cell Line ; Drosophila Proteins/genetics/*pharmacology ; Drosophila melanogaster/genetics/*metabolism ; Electron Transport Complex II/*antagonists &amp; inhibitors/genetics ; Enzyme Inhibitors/*pharmacology ; Mitochondria/enzymology/genetics ; Phylogeny ; Recombinant Proteins/pharmacology ; }, abstract = {Insect-derived antifungal peptides have a significant economic potential, particularly for the engineering of pathogen-resistant crops. However, the nonspecific antifungal activity of such peptides could result in detrimental effects against beneficial fungi, whose interactions with plants promote growth or increase resistance against biotic and abiotic stress. The antifungal peptide metchnikowin (Mtk) from Drosophila melanogaster acts selectively against pathogenic Ascomycota, including Fusarium graminearum, without affecting Basidiomycota such as the beneficial symbiont Piriformospora indica. Here we investigated the mechanism responsible for the selective antifungal activity of Mtk by using the peptide to probe a yeast two-hybrid library of F. graminearum cDNAs. We found that Mtk specifically targets the iron-sulfur subunit (SdhB) of succinate-coenzyme Q reductase (SQR). A functional assay based on the succinate dehydrogenase (SDH) activity of mitochondrial complex II clearly demonstrated that Mtk inhibited the SDH activity of F. graminearum mitochondrial SQR by up to 52%, but that the equivalent enzyme in P. indica was unaffected. A phylogenetic analysis of the SdhB family revealed a significant divergence between the Ascomycota and Basidiomycota. SQR is one of the key targets of antifungal agents and we therefore propose Mtk as an environmentally sustainable and more selective alternative to chemical fungicides.}, }
@article {pmid28806979, year = {2017}, author = {Zachar, I and Szathmáry, E}, title = {Breath-giving cooperation: critical review of origin of mitochondria hypotheses : Major unanswered questions point to the importance of early ecology.}, journal = {Biology direct}, volume = {12}, number = {1}, pages = {19}, pmid = {28806979}, issn = {1745-6150}, mesh = {*Biological Evolution ; Energy Metabolism ; Genome, Mitochondrial ; *Mitochondria ; *Models, Biological ; Phagocytosis ; Phylogeny ; }, abstract = {UNLABELLED: The origin of mitochondria is a unique and hard evolutionary problem, embedded within the origin of eukaryotes. The puzzle is challenging due to the egalitarian nature of the transition where lower-level units took over energy metabolism. Contending theories widely disagree on ancestral partners, initial conditions and unfolding of events. There are many open questions but there is no comparative examination of hypotheses. We have specified twelve questions about the observable facts and hidden processes leading to the establishment of the endosymbiont that a valid hypothesis must address. We have objectively compared contending hypotheses under these questions to find the most plausible course of events and to draw insight on missing pieces of the puzzle. Since endosymbiosis borders evolution and ecology, and since a realistic theory has to comply with both domains' constraints, the conclusion is that the most important aspect to clarify is the initial ecological relationship of partners. Metabolic benefits are largely irrelevant at this initial phase, where ecological costs could be more disruptive. There is no single theory capable of answering all questions indicating a severe lack of ecological considerations. A new theory, compliant with recent phylogenomic results, should adhere to these criteria.<br><br>REVIEWERS: This article was reviewed by Michael W. Gray, William F. Martin and Purificaci&#xf3;n L&#xf3;pez-Garc&#xed;a.}, }
@article {pmid28801771, year = {2017}, author = {Schmitt, C and Betz, O}, title = {Morphology and ultrastructure of the tarsal adhesive organs of the Madagascar hissing cockroach Gromphadorhina portentosa.}, journal = {Cell and tissue research}, volume = {370}, number = {2}, pages = {243-265}, doi = {10.1007/s00441-017-2661-5}, pmid = {28801771}, issn = {1432-0878}, mesh = {Adhesives/*analysis ; Animals ; Cockroaches/*anatomy &amp; histology/cytology/*ultrastructure ; Cryoelectron Microscopy ; Epidermal Cells ; Epidermis/anatomy &amp; histology/ultrastructure ; Female ; Male ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Walking ; }, abstract = {The present transmission and scanning electron microscopic study of the ultramorphology of the pliable attachment pads (arolium, euplantulae) of the Madagascar hissing cockroach Gromphadorhina portentosa reveals structural evidence for their function in producing, storing, and secreting an adhesion-mediating secretion and releasing it to the exterior. The exocrine epidermal tissue of both the arolium and the euplantula is significantly enlarged by numerous invaginations stretching into the hemolymph cavity. Its cells show large nuclei, numerous mitochondria, Golgi complexes, and a prominent rough-surfaced endoplasmic reticulum integrated within an electron-dense cytoplasm that contains numerous vesicles of diverse electron density and size. Invaginations of the cell membrane provide evidence for strong membrane turnover. The glandular epithelium of both the arolium and the euplantula releases the adhesion-mediating secretion into a subcuticular void from which it has to permeate the thick cuticle of the adhesive pads. The subcuticular void is compartmentalized by cuticle bands through which the adhesion-mediating secretion permeates via small canals. The secretion subsequently enters a larger storage reservoir before being received by a prominent sponge-like cuticle. The structural differences between the arolium and the euplantula consist of the number and length of the interdigitations spanning the hemolymph cavity, of the subdivision of the subcuticular reservoir by cuticle bands, and of the thickness of the sponge-like cuticle. The structural results are discussed with respect to the production of a chemically complex (emulsion-like) adhesive, its controlled release to the exterior, and the micromechanical properties of the cuticle of the pliable pad.}, }
@article {pmid28798696, year = {2017}, author = {Wu, X and Wu, FH and Wu, Q and Zhang, S and Chen, S and Sima, M}, title = {Phylogenetic and Molecular Evolutionary Analysis of Mitophagy Receptors under Hypoxic Conditions.}, journal = {Frontiers in physiology}, volume = {8}, number = {}, pages = {539}, pmid = {28798696}, issn = {1664-042X}, abstract = {As animals evolved to use oxygen as the main strategy to produce ATP through the process of mitochondrial oxidative phosphorylation, the ability to adapt to fluctuating oxygen concentrations is a crucial component of evolutionary pressure. Three mitophagy receptors, FUNDC1, BNIP3 and NIX, induce the removal of dysfunctional mitochondria (mitophagy) under prolonged hypoxic conditions in mammalian cells, to maintain oxygen homeostasis and prevent cell death. However, the evolutionary origins and structure-function relationships of these receptors remain poorly understood. Here, we found that FUN14 domain-containing proteins are present in archaeal, bacterial and eukaryotic genomes, while the family of BNIP3 domain-containing proteins evolved from early animals. We investigated conservation patterns of the critical amino acid residues of the human mitophagy receptors. These residues are involved in receptor regulation, mainly through phosphorylation, and in interaction with LC3 on the phagophore. Whereas FUNDC1 may be able to bind to LC3 under the control of post-translational regulations during the early evolution of vertebrates, BINP3 and NIX had already gained the ability for LC3 binding in early invertebrates. Moreover, FUNDC1 and BNIP3 each lack a layer of phosphorylation regulation in fishes that is conserved in land vertebrates. Molecular evolutionary analysis revealed that BNIP3 and NIX, as the targets of oxygen sensing HIF-1α, showed higher rates of substitution in fishes than in mammals. Conversely, FUNDC1 and its regulator MARCH5 showed higher rates of substitution in mammals. Thus, we postulate that the structural traces of mitophagy receptors in land vertebrates and fishes may reflect the process of vertebrate transition from water onto land, during which the changes in atmospheric oxygen concentrations acted as a selection force in vertebrate evolution. In conclusion, our study, combined with previous experimental results, shows that hypoxia-induced mitophagy regulated by FUDNC1/MARCH5 might use a different mechanism from the HIF-1α-dependent mitophagy regulated by BNIP3/NIX.}, }
@article {pmid28798357, year = {2017}, author = {Xiang, H and Gao, J and Cai, D and Luo, Y and Yu, B and Liu, L and Liu, R and Zhou, H and Chen, X and Dun, W and Wang, X and Hofreiter, M and Zhao, X}, title = {Origin and dispersal of early domestic pigs in northern China.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5602}, pmid = {28798357}, issn = {2045-2322}, mesh = {Animals ; Animals, Domestic/*genetics ; China ; DNA, Mitochondrial/genetics ; Domestication ; Evolution, Molecular ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Sus scrofa/*genetics ; }, abstract = {It is widely accepted that modern pigs were domesticated independently at least twice, and Chinese native pigs are deemed as direct descendants of the first domesticated pigs in the corresponding domestication centers. By analyzing mitochondrial DNA sequences of an extensive sample set spanning 10,000 years, we find that the earliest pigs from the middle Yellow River region already carried the maternal lineages that are dominant in both younger archaeological populations and modern Chinese pigs. Our data set also supports early Neolithic pig utilization and a long-term in situ origin for northeastern Chinese pigs during 8,000-3,500 BP, suggesting a possibly independent domestication in northeast China. Additionally, we observe a genetic replacement in ancient northeast Chinese pigs since 3,500 BP. The results not only provide increasing evidence for pig origin in the middle Yellow River region but also depict an outline for the process of early pig domestication in northeast China.}, }
@article {pmid28794432, year = {2017}, author = {Izumikawa, K and Nobe, Y and Yoshikawa, H and Ishikawa, H and Miura, Y and Nakayama, H and Nonaka, T and Hasegawa, M and Egawa, N and Inoue, H and Nishikawa, K and Yamano, K and Simpson, RJ and Taoka, M and Yamauchi, Y and Isobe, T and Takahashi, N}, title = {TDP-43 stabilises the processing intermediates of mitochondrial transcripts.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {7709}, pmid = {28794432}, issn = {2045-2322}, mesh = {Cell Line ; DNA-Binding Proteins/genetics/*metabolism ; Gene Expression ; *Genes, Mitochondrial ; Humans ; Mitochondria/*genetics/*metabolism/ultrastructure ; Protein Binding ; Protein Transport ; *RNA Processing, Post-Transcriptional ; RNA Stability ; RNA, Transfer/genetics ; *Transcription, Genetic ; }, abstract = {The 43-kDa trans-activating response region DNA-binding protein 43 (TDP-43) is a product of a causative gene for amyotrophic lateral sclerosis (ALS). Despite of accumulating evidence that mitochondrial dysfunction underlies the pathogenesis of TDP-43-related ALS, the roles of wild-type TDP-43 in mitochondria are unknown. Here, we show that the small TDP-43 population present in mitochondria binds directly to a subset of mitochondrial tRNAs and precursor RNA encoded in L-strand mtDNA. Upregulated expression of TDP-43 stabilised the processing intermediates of mitochondrial polycistronic transcripts and their products including the components of electron transport and 16S mt-rRNA, similar to the phenotype observed in cells deficient for mitochondrial RNase P. Conversely, TDP-43 deficiency reduced the population of processing intermediates and impaired mitochondrial function. We propose that TDP-43 has a novel role in maintaining mitochondrial homeostasis by regulating the processing of mitochondrial transcripts.}, }
@article {pmid28792749, year = {2017}, author = {Thompson, AD and Bewersdorf, J and Toomre, D and Schepartz, A}, title = {HIDE Probes: A New Toolkit for Visualizing Organelle Dynamics, Longer and at Super-Resolution.}, journal = {Biochemistry}, volume = {56}, number = {39}, pages = {5194-5201}, pmid = {28792749}, issn = {1520-4995}, support = {F31 GM119259/GM/NIGMS NIH HHS/United States ; R01 GM118486/GM/NIGMS NIH HHS/United States ; P30 DK045735/DK/NIDDK NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; 095927/A/11/Z/WT_/Wellcome Trust/United Kingdom ; R01 GM131372/GM/NIGMS NIH HHS/United States ; 203285/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; R01 GM083257/GM/NIGMS NIH HHS/United States ; }, mesh = {HeLa Cells ; Humans ; Intracellular Membranes/metabolism ; Molecular Imaging/*methods ; Organelles/*metabolism ; Signal-To-Noise Ratio ; Time Factors ; }, abstract = {Living cells are complex and dynamic assemblies that carefully sequester and orchestrate multiple diverse processes that enable growth, division, regulation, movement, and communication. Membrane-bound organelles such as the endoplasmic reticulum, mitochondria, plasma membrane, and others are integral to these processes, and their functions demand dynamic reorganization in both space and time. Visualizing these dynamics in live cells over long time periods demands probes that label discrete organelles specifically, at high density, and withstand long-term irradiation. Here we describe the evolution of our work on the development of a set of high-density environmentally sensitive (HIDE) membrane probes that enable long-term, live-cell nanoscopy of the dynamics of multiple organelles in live cells using single-molecule switching and stimulated emission depletion imaging modalities.}, }
@article {pmid28791889, year = {2018}, author = {Greenberg, EF and Vatolin, S}, title = {Symbiotic Origin of Aging.}, journal = {Rejuvenation research}, volume = {21}, number = {3}, pages = {225-231}, doi = {10.1089/rej.2017.1973}, pmid = {28791889}, issn = {1557-8577}, mesh = {*Aging ; Animals ; *Apoptosis ; Biological Evolution ; Caloric Restriction ; Cell Differentiation ; Cell Line ; Cell Proliferation ; Cell Survival ; Cellular Senescence ; Eukaryotic Cells ; Gene Deletion ; Humans ; Mice ; Mitochondria/*genetics/metabolism ; Models, Theoretical ; Mutation ; Reactive Oxygen Species/metabolism ; *Symbiosis ; }, abstract = {Normally aging cells are characterized by an unbalanced mitochondrial dynamic skewed toward punctate mitochondria. Genetic and pharmacological manipulation of mitochondrial fission/fusion cycles can contribute to both accelerated and decelerated cellular or organismal aging. In this work, we connect these experimental data with the symbiotic theory of mitochondrial origin to generate new insight into the evolutionary origin of aging. Mitochondria originated from autotrophic α-proteobacteria during an ancient endosymbiotic event early in eukaryote evolution. To expand beyond individual host cells, dividing α-proteobacteria initiated host cell lysis; apoptosis is a product of this original symbiont cell lytic exit program. Over the course of evolution, the host eukaryotic cell attenuated the harmful effect of symbiotic proto-mitochondria, and modern mitochondria are now functionally interdependent with eukaryotic cells; they retain their own circular genomes and independent replication timing. In nondividing differentiated or multipotent eukaryotic cells, intracellular mitochondria undergo repeated fission/fusion cycles, favoring fission as organisms age. The discordance between cellular quiescence and mitochondrial proliferation generates intracellular stress, eventually leading to a gradual decline in host cell performance and age-related pathology. Hence, aging evolved from a conflict between maintenance of a quiescent, nonproliferative state and the evolutionarily conserved propagation program driving the life cycle of former symbiotic organisms: mitochondria.}, }
@article {pmid28782594, year = {2017}, author = {Poliseno, A and Feregrino, C and Sartoretto, S and Aurelle, D and Wörheide, G and McFadden, CS and Vargas, S}, title = {Comparative mitogenomics, phylogeny and evolutionary history of Leptogorgia (Gorgoniidae).}, journal = {Molecular phylogenetics and evolution}, volume = {115}, number = {}, pages = {181-189}, doi = {10.1016/j.ympev.2017.08.001}, pmid = {28782594}, issn = {1095-9513}, mesh = {Animals ; Anthozoa/*classification/genetics ; Biological Evolution ; DNA/chemistry/isolation &amp; purification/metabolism ; Genetic Variation ; Mitochondria/*genetics ; Mitochondrial Proton-Translocating ATPases/classification/genetics ; Phylogeny ; RNA, Ribosomal/classification/genetics ; Sequence Analysis, DNA ; }, abstract = {Molecular analyses of the ecologically important gorgonian octocoral genus Leptogorgia are scant and mostly deal with few species from restricted geographical regions. Here we explore the phylogenetic relationships and the evolutionary history of Leptogorgia using the complete mitochondrial genomes of six Leptogorgia species from different localities in the Atlantic, Mediterranean and eastern Pacific as well as four other genera of Gorgoniidae and Plexauridae. Our mitogenomic analyses showed high inter-specific diversity, variable nucleotide substitution rates and, for some species, novel genomic features such as ORFs of unknown function. The phylogenetic analyses using complete mitogenomes and an extended mtMutS dataset recovered Leptogorgia as polyphyletic, and the species considered in the analyses were split into two defined groups corresponding to different geographic regions, namely the eastern Pacific and the Atlantic-Mediterranean. Our phylogenetic analysis based on mtMutS also showed a clear separation between the eastern Atlantic and South African Leptogorgia, suggesting the need of a taxonomic revision for these forms. A time-calibrated phylogeny showed that the separation of eastern Pacific and western Atlantic species started ca. 20Mya and suggested a recent divergence for eastern Pacific species and for L. sarmentosa-L. capverdensis. Our results also revealed high inter-specific diversity among eastern Atlantic and South African species, highlighting a potential role of the geographical diversification processes and geological events occurring during the last 30Ma in the Atlantic on the evolutionary history of these organisms.}, }
@article {pmid28782202, year = {2017}, author = {Speijer, D}, title = {Evolution of peroxisomes illustrates symbiogenesis.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {9}, pages = {}, doi = {10.1002/bies.201700050}, pmid = {28782202}, issn = {1521-1878}, mesh = {Adaptation, Biological/physiology ; Animals ; Biological Evolution ; Eukaryotic Cells/metabolism/physiology ; Humans ; Mitochondria/metabolism/physiology ; Oxidation-Reduction ; Peroxisomes/*metabolism/*physiology ; Reactive Oxygen Species/metabolism ; Saccharomyces cerevisiae/physiology ; }, abstract = {Recently, the group of McBride reported a stunning observation regarding peroxisome biogenesis: newly born peroxisomes are hybrids of mitochondrial and ER-derived pre-peroxisomes. What was stunning? Studies performed with the yeast Saccharomyces cerevisiae had convincingly shown that peroxisomes are ER-derived, without indications for mitochondrial involvement. However, the recent finding using fibroblasts dovetails nicely with a mechanism inferred to be driving the eukaryotic invention of peroxisomes: reduction of mitochondrial reactive oxygen species (ROS) generation associated with fatty acid (FA) oxidation. This not only explains the mitochondrial involvement, but also its apparent absence in yeast. The latest results allow a reconstruction of the evolution of the yeast's highly derived metabolism and its limitations as a model organism in this instance. As I review here, peroxisomes are eukaryotic inventions reflecting mutual host endosymbiont adaptations: this is predicted by symbiogenetic theory, which states that the defining eukaryotic characteristics evolved as a result of mutual adaptations of two merging prokaryotes.}, }
@article {pmid28780151, year = {2017}, author = {Addy, F and Wassermann, M and Kagendo, D and Ebi, D and Zeyhle, E and Elmahdi, IE and Umhang, G and Casulli, A and Harandi, MF and Aschenborn, O and Kern, P and Mackenstedt, U and Romig, T}, title = {Genetic differentiation of the G6/7 cluster of Echinococcus canadensis based on mitochondrial marker genes.}, journal = {International journal for parasitology}, volume = {47}, number = {14}, pages = {923-931}, doi = {10.1016/j.ijpara.2017.06.003}, pmid = {28780151}, issn = {1879-0135}, mesh = {Africa ; Animals ; Camelus ; Cattle ; DNA, Mitochondrial/chemistry ; Deer ; Dogs ; Echinococcus/classification/*genetics ; Europe ; Genetic Markers/*genetics ; Genetic Variation/*genetics ; Goats ; Haplotypes/genetics ; Humans ; Middle East ; Mitochondria/*genetics ; Multigene Family/*genetics ; Phylogeny ; Polymorphism, Genetic ; Swine ; Wolves ; }, abstract = {Among the genotype/species causing cystic echinococcosis, the taxonomic status of Echinococcus canadensis is only partially resolved. Within E. canadensis, four genotypes (G6, G7, G8 and G10) have been described based on short mitochondrial sequences, of which G6 and G7 (the 'camel' and the 'pig' strain, respectively) are closely related and variously regarded as microvariants of a single strain G6/7. Globally, this G6/7 cluster is the second most important agent of human cystic echinococcosis and is the predominant Echinococcus taxon in large parts of sub-Saharan Africa. To add data on the internal structure and the geographical distribution of this cluster, we analysed diversity and population structure of 296 isolates of E. canadensis from sub-Saharan Africa, the Middle East and Europe using the complete mitochondrial cytochrome c oxidase subunit 1 (cox1) (1,608bp) and NADH dehydrogenase subunit 1 (nad1) (894bp) gene sequences. Polymorphism of the mtDNA loci gave 51 (cox1), 33 (nad1) and 73 (cox1-nad1 concatenated) haplotypes. African and Middle Eastern isolates mainly grouped in a star-like structure around a predominant haplotype, while the European isolates produced more diversified networks. Although the cox1 diagnostic sequence for G6 is frequent in the African/Middle Eastern sub-cluster, and that for G7 is common in the European isolates, numerous intermediate variants prevent a clear distinction into 'G6' or 'G7', and the entire taxon is best treated as a common haplotype cluster G6/7. Meanwhile, the G6/7 cluster is clearly distinct from sequences of wildlife isolates of G8 and G10 from the northern hemisphere, and sequences of the latter genotypes were remarkably distant from each other. It is clear from the present study that, based on mitochondrial data, G6/7 is a coherent genotypic entity within E. canadensis that retains substantial intraspecific variance, and sub-populations share common ancestral polymorphisms and haplotypes. This study provides the basis for wider biogeographic comparison and population genetics studies of this taxon.}, }
@article {pmid28779732, year = {2016}, author = {Aziz, NMA and Esa, Y and Arshad, A}, title = {DNA barcoding and phylogenetic analysis of Malaysian groupers (Subfamily: Epinephelinae) using mitochondrial Cytochrome c oxidase I (COI) gene.}, journal = {Journal of environmental biology}, volume = {37}, number = {4 Spec No}, pages = {725-733}, pmid = {28779732}, issn = {0254-8704}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Fishes/*genetics ; Haplotypes ; Mitochondria/*enzymology ; *Phylogeny ; Species Specificity ; }, abstract = {The present study was carried out to examine the species identification and phylogenetic relationships of groupers in Malaysia using mitochondrial Cytochrome c Oxidase I (COI) gene, commonly known as barcoding gene. A total of 63 individuals comprising 10 species from three genera were collected from the coastal areas of Johor, Kelantan, Pahang, Perak, Selangor and Terengganu. All the individuals were morphologically identified and molecular works involved polymerase chain reaction (PCR) and sequencing of COI barcoding fragment (655 base pairs). Results from the BLAST search showed that 55 sequences could be assigned to 10 grouper species with high percentage identity index (≥95% to 100%), while eight grouper individuals showed discrepancies in their taxonomic identification based on the morphology and the COI barcoding results. The histogram of distances showed that there was a clear-cut barcode gap present in the sequences indicating a clear separation between intraspecific and interspecific distances. The pairwise genetic distances showed lowest pairwise distance between P. leopardus and P. maculatus (4.4%), while the highest pairwise distance was between E. bleekeri and P. maculatus (23.5%), supporting their morphological and habitat similarities and differences. Phylogenetic analysis (Neighbor-Joining) showed the presence of two major clades (1) genus Epinephelus vs (2) genus Plectropomus and Cephalopholis). In conclusion, the present study has managed to show the accuracy of DNA barcoding method for species identification, and utilization of COI gene for phylogenetic study among groupers. ?}, }
@article {pmid28778567, year = {2018}, author = {Chen, XJ and Clark-Walker, GD}, title = {Unveiling the mystery of mitochondrial DNA replication in yeasts.}, journal = {Mitochondrion}, volume = {38}, number = {}, pages = {17-22}, pmid = {28778567}, issn = {1872-8278}, support = {R01 AG023731/AG/NIA NIH HHS/United States ; R21 AG047400/AG/NIA NIH HHS/United States ; }, mesh = {*DNA Replication ; DNA, Mitochondrial/*metabolism ; Models, Biological ; Recombination, Genetic ; Saccharomyces cerevisiae/*genetics ; }, abstract = {Conventional DNA replication is initiated from specific origins and requires the synthesis of RNA primers for both the leading and lagging strands. In contrast, the replication of yeast mitochondrial DNA is origin-independent. The replication of the leading strand is likely primed by recombinational structures and proceeded by a rolling circle mechanism. The coexistent linear and circular DNA conformers facilitate the recombination-based initiation. The replication of the lagging strand is poorly understood. Re-evaluation of published data suggests that the rolling circle may also provide structures for the synthesis of the lagging-strand by mechanisms such as template switching. Thus, the coupling of recombination with rolling circle replication and possibly, template switching, may have been selected as an economic replication mode to accommodate the reductive evolution of mitochondria. Such a replication mode spares the need for conventional replicative components, including those required for origin recognition/remodelling, RNA primer synthesis and lagging-strand processing.}, }
@article {pmid28766501, year = {2017}, author = {Hu, JJ and Huang, S and Wen, T and Esch, GW and Liang, Y and Li, HL}, title = {Sarcocystis spp. in domestic sheep in Kunming City, China: prevalence, morphology, and molecular characteristics.}, journal = {Parasite (Paris, France)}, volume = {24}, number = {}, pages = {30}, pmid = {28766501}, issn = {1776-1042}, mesh = {Animals ; China/epidemiology ; DNA, Protozoan/chemistry/isolation &amp; purification ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Genetic Markers ; Microscopy, Electron, Transmission/veterinary ; Mitochondria/enzymology ; Muscles/parasitology ; Phylogeny ; Prevalence ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Sarcocystis/classification/genetics/*isolation &amp; purification/ultrastructure ; Sarcocystosis/epidemiology/parasitology/*veterinary ; Sheep ; Sheep Diseases/epidemiology/*parasitology ; }, abstract = {Sheep (Ovis aries) are intermediate hosts for at least six named species of Sarcocystis: S. tenella, S. arieticanis, S. gigantea, S. medusiformis, S. mihoensis, and S. microps. Here, only two species, S. tenella and S. arieticanis, were found in 79 of 86 sheep (91.9%) in Kunming, China, based on their morphological characteristics. Four genetic markers, i.e., 18S rRNA gene, 28S rRNA gene, mitochondrial cox1 gene, and ITS-1 region, were sequenced and characterized for the two species of Sarcocystis. Sequences of the three former markers for S. tenella shared high identities with those of S. capracanis in goats, i.e., 99.0%, 98.3%, and 93.6%, respectively; the same three marker sequences of S. arieticanis shared high identities with those of S. hircicanis in goats, i.e., 98.5%, 96.5%, and 92.5%, respectively. No sequences in GenBank were found to significantly resemble the ITS-1 regions of S. tenella and S. arieticanis. Identities of the four genetic markers for S. tenella and S. arieticanis were 96.3%, 95.4%, 82.5%, and 66.2%, respectively.}, }
@article {pmid28763510, year = {2017}, author = {Oliveira Da Silva, W and Pieczarka, JC and Ferguson-Smith, MA and O'Brien, PCM and Mendes-Oliveira, AC and Sampaio, I and Carneiro, J and Nagamachi, CY}, title = {Chromosomal diversity and molecular divergence among three undescribed species of Neacomys (Rodentia, Sigmodontinae) separated by Amazonian rivers.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0182218}, pmid = {28763510}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; *Biodiversity ; Brazil ; *Chromosome Mapping ; Chromosome Painting ; Chromosomes/*ultrastructure ; Cytochromes b/metabolism ; Electron Transport Complex IV/metabolism ; Female ; Genetic Variation ; Geography ; Haplotypes ; In Situ Hybridization, Fluorescence ; Karyotyping ; Likelihood Functions ; Male ; Mitochondria/genetics ; Phylogeny ; Rodentia/classification/*genetics ; }, abstract = {The Neacomys genus (Rodentia, Sigmodontinae) is distributed in the Amazon region, with some species limited to a single endemic area, while others may occur more widely. The number of species within the genus and their geographical boundaries are not known accurately, due to their high genetic diversity and difficulties in taxonomic identification. In this work we collected Neacomys specimens from both banks of the Tapajós River in eastern Amazon, and studied them using chromosome painting with whole chromosome probes of Hylaeamys megacephalus (HME; Rodentia, Sigmodontinae), and molecular analysis using haplotypes of mitochondrial genes COI and Cytb. Chromosome painting shows that Neacomys sp. A (NSP-A, 2n = 58/FN = 68) and Neacomys sp. B (NSP-B, 2n = 54/FN = 66) differ by 11 fusion/fission events, one translocation, four pericentric inversions and four heterochromatin amplification events. Using haplotypes of the concatenated mitochondrial genes COI and Cyt b, Neacomys sp. (2n = 58/FN = 64 and 70) shows a mean divergence of 6.2% for Neacomys sp. A and 9.1% for Neacomys sp. B, while Neacomys sp. A and Neacomys sp. B presents a medium nucleotide divergence of 7.4%. Comparisons were made with other published Neacomys data. The Tapajós and Xingu Rivers act as geographic barriers that define the distribution of these Neacomys species. Furthermore, our HME probes reveal four synapomorphies for the Neacomys genus (associations HME 20/[13,22]/4, 6a/21, [9,10]/7b/[9,10] and 12/[16,17]) and demonstrate ancestral traits of the Oryzomyini tribe (HME 8a and 8b, 18 and 25) and Sigmodontinae subfamily (HME 15 and 24), which can be used as taxonomic markers for these groups.}, }
@article {pmid28763193, year = {2017}, author = {Stutz, K and Müller, AT and Hiss, JA and Schneider, P and Blatter, M and Pfeiffer, B and Posselt, G and Kanfer, G and Kornmann, B and Wrede, P and Altmann, KH and Wessler, S and Schneider, G}, title = {Peptide-Membrane Interaction between Targeting and Lysis.}, journal = {ACS chemical biology}, volume = {12}, number = {9}, pages = {2254-2259}, doi = {10.1021/acschembio.7b00504}, pmid = {28763193}, issn = {1554-8937}, mesh = {Amino Acid Sequence ; Anti-Infective Agents/*chemistry/metabolism/*pharmacology ; Antimicrobial Cationic Peptides/*chemistry/metabolism/*pharmacology ; Cell Membrane/drug effects/metabolism ; Cell Membrane Permeability ; HeLa Cells ; Humans ; Liposomes/*metabolism ; Mitochondria/*drug effects/metabolism ; Models, Molecular ; Staphylococcal Infections/drug therapy ; Staphylococcus aureus/*drug effects/growth &amp; development ; }, abstract = {Certain cationic peptides interact with biological membranes. These often-complex interactions can result in peptide targeting to the membrane, or in membrane permeation, rupture, and cell lysis. We investigated the relationship between the structural features of membrane-active peptides and these effects, to better understand these processes. To this end, we employed a computational method for morphing a membranolytic antimicrobial peptide into a nonmembranolytic mitochondrial targeting peptide by "directed simulated evolution." The results obtained demonstrate that superficially subtle sequence modifications can strongly affect the peptides' membranolytic and membrane-targeting abilities. Spectroscopic and computational analyses suggest that N- and C-terminal structural flexibility plays a crucial role in determining the mode of peptide-membrane interaction.}, }
@article {pmid28758818, year = {2018}, author = {Manger, A and Behere, GT and Firake, DM and Sharma, B and Deshmukh, NA and Firake, PD and Azad Thakur, NS and Ngachan, SV}, title = {Genetic characterization of Bactrocera fruit flies (Diptera: Tephritidae) from Northeastern India based on DNA barcodes.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {792-799}, doi = {10.1080/24701394.2017.1357713}, pmid = {28758818}, issn = {2470-1408}, mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Speciation ; Genome, Mitochondrial/genetics ; India ; Mitochondria/genetics ; Perciformes/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Tephritidae/*genetics ; }, abstract = {The Northeastern region of India, one of the mega biodiversity hot spots has enormous potential for the production of fruits and vegetables. Fruit flies of the genus Bactrocera Macquart are important pests of fruits and vegetables, and one of the limiting factors in successful production of these commodities. The relationship among some of the species is unclear due to their high molecular and morphological similarities. Moreover, due to the significant morphological resemblance between fruit fly species, reliable identification is very difficult task. We genetically characterized 10 fruit fly species of the genus Bactrocera by using standard DNA barcoding region of COI gene. The characterization and identification of eight species were straight forward. This study was unable to establish the molecular identity of Bactrocera sp. 2. Within the 547 bp region of partial COI gene, there were 157 variable sites of which 110 sites were parsimony informative, 153 were synonymous substitutions and 4 were non-synonymous substitutions. The estimate of genetic divergence among the ten species was in the range of 0-21.9% and the pairwise genetic distance of Bactrocera. (Bactrocera) dorsalis (Hendel) with B. (B.) carambolae was only 0.7%. Phylogenetic analysis formed separate clades for fruit and vegetable infesting fruit flies. B. (B.) aethriobasis Hardy, B. (B.) thailandica and B. (B.) tuberculata (Bezzi) have been reported for the first time from the Northeastern India. The information generated from this study would certainly have implications for pest management, taxonomy, quarantine and trade.}, }
@article {pmid28756720, year = {2018}, author = {Li, YX and Gao, YL and He, XL and Cao, SX}, title = {Exploration of mtDNA control region sequences in Chinese Tibetan Mastiffs.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {800-804}, doi = {10.1080/24701394.2017.1357714}, pmid = {28756720}, issn = {2470-1408}, mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Dogs/*genetics ; Evolution, Molecular ; Genetic Speciation ; Genetic Variation ; Genetics, Population ; Genome, Mitochondrial/genetics ; Haplotypes ; India ; Mitochondria/genetics ; Perciformes/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Tibet ; }, abstract = {The control region of mitochondrial DNA (mtDNA) was obtained from 40 purebred Chinese Tibetan Mastiffs (TMs). Sequence structure and genetic diversity were analyzed, and a phylogenetic tree was constructed. The TM mtDNA control region was composed of ETAS (extended termination associated sequences), CD (a central domain) and CSBs (conserved sequenced blocks) and sequence length showed some diversity, which was mainly caused by the number of 10 nucleotide repeat units [5'-GTA CAC GT (G/A) C-3'] between CSB I and CSB II, which ranged from 27 to 35 among individuals. Seventy-five polymorphic sites were identified, which defined 37 haplotypes; the haplotype diversity was 0.990, and the nucleotide diversity was 1.201. Based on the control region sequences, Chinese TMs were divided into three categories, which were consistent with the origin and geographical classification of TMs. Phylogenetic analysis of 538-bp HVR-I sequences revealed that TMs were most closely related to Labrador Retrievers.}, }
@article {pmid28756717, year = {2018}, author = {Feng, X and He, D and Sui, X and Chen, Y and Chen, Y}, title = {Morphological and genetic divergence between lake and river populations of Triplophysa in Ngangtse Co, Tibet.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {778-784}, doi = {10.1080/24701394.2017.1357711}, pmid = {28756717}, issn = {2470-1408}, mesh = {Animals ; Biological Evolution ; Cypriniformes/*genetics ; DNA ; DNA, Mitochondrial/genetics ; Ecosystem ; Genetic Drift ; Genetic Speciation ; Genetic Variation/genetics ; Genome, Mitochondrial/*genetics ; Lakes ; Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; Rivers ; Tibet ; }, abstract = {Ngangtse Co (4535 m a.s.l., 840 km[2]) is a typical endorheic lake in Tibet. In 2015, we investigated the fish resource in this lake and its rivers and collected two Triplophysa species, including T. brevicauda and T. stewarti. To understand the evolutionary dynamics of Triplophysa in Ngangtse Co, the adaptive and genetic divergence between river and lake populations were investigated by analysing their morphological characteristics and mitochondrial COI and Cytb sequences. Among all of 277 samples, the ratios of the number of T. brevicauda to T. stewarti were 27:8, 34:11, 14:24, 37:0, 16:23 and 0:83 in river populations RA, RB, RC, RD, lakeside population LSE and lake population L, respectively. For T. brevicauda, a small but significant genetic divergence (mean FST = 0.0890) was detected between population RD and other three river populations, and significant morphological differences of body length/body height and body length/caudal peduncle length were observed between population RD and RA, RB, suggesting an association between differentiation and geographical distance. For T. stewarti, very high levels of genetic differentiation was observed between population L and other populations with the FST values ranging from 0.4737 (L-RA) to 0.7074 (L-RC). In addition, significant differences of most of morphological characteristics were observed between the lake (L) and river (RC) populations, indicating that lake fish of T. stewarti was a population that showed a long-term adaptation to the saltwater lake. These results provide insights on the evolutionary dynamics of Triplophysa in Ngangtse Co and help us to understand the fish speciation in endorheic lakes on the Qinghai-Tibetan Plateau.}, }
@article {pmid28755372, year = {2017}, author = {Negroni, L and Zivy, M and Lemaire, C}, title = {Mass Spectrometry of Mitochondrial Membrane Protein Complexes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1635}, number = {}, pages = {233-246}, doi = {10.1007/978-1-4939-7151-0_12}, pmid = {28755372}, issn = {1940-6029}, mesh = {Chromatography, Liquid ; Electrophoresis, Polyacrylamide Gel ; Membrane Proteins/*metabolism ; Mitochondrial Membranes/*metabolism ; Oxidative Phosphorylation ; Protein Subunits/metabolism ; Proteomics ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Tandem Mass Spectrometry ; }, abstract = {The ATP production (oxidative phosphorylation) involves five complexes embedded in the inner membrane of mitochondria. The yeast Saccharomyces cerevisiae is mainly used as a model for the study of oxidative phosphorylation; mutants are easy to produce and are still viable due to their ability to grow using the fermentation pathway. Here, we present a process for analyzing mitochondrial respiratory complexes using native electrophoresis (BN-PAGE) coupled to LC-MS/MS. BN-PAGE (1) permits the separation of functional respiratory complexes, thus allowing in-gel activity detection of most of the respiratory complexes and (2) provides convenient samples for bottom-up proteomics. Combining BN-PAGE and LC-MS/MS leads to the identification of the subunit composition of membrane complexes and offers the possibility of highlighting potential interacting proteins.}, }
@article {pmid28755245, year = {2018}, author = {Díaz, ML and Cuppari, S and Soresi, D and Carrera, A}, title = {In Silico Analysis of Fatty Acid Desaturase Genes and Proteins in Grasses.}, journal = {Applied biochemistry and biotechnology}, volume = {184}, number = {2}, pages = {484-499}, doi = {10.1007/s12010-017-2556-7}, pmid = {28755245}, issn = {1559-0291}, support = {PGI (24/B228)//Universidad Nacional del Sur/ ; PICT 2188//Agencia Nacional de Promoci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; }, mesh = {Amino Acid Motifs ; *Computer Simulation ; Databases, Genetic ; *Fatty Acid Desaturases/biosynthesis/chemistry/genetics ; Gene Expression Regulation, Enzymologic/*physiology ; Gene Expression Regulation, Plant/*physiology ; Genes, Plant/*physiology ; *Plant Proteins/biosynthesis/chemistry/genetics ; *Poaceae/enzymology/genetics ; }, abstract = {Fatty acid desaturases (FADs) catalyze the introduction of a double bond into acyl chains. Two FAD groups have been identified in plants: acyl-acyl carrier proteins (ACPs) and acyl-lipid or membrane-bound FAD. The former catalyze the conversion of 18:0 to 18:1 and to date have only been identified in plants. The latter are found in eukaryotes and bacteria and are responsible for multiple desaturations. In this study, we identified 82 desaturase gene and protein sequences from 10 grass species deposited in GenBank that were analyzed using bioinformatic approaches. Subcellular localization predictions of desaturase family revealed their localization in plasma membranes, chloroplasts, endoplasmic reticula, and mitochondria. The in silico mapping showed multiple chromosomal locations in most species. Furthermore, the presence of the characteristic histidine domains, the predicted motifs, and the finding of transmembrane regions strongly support the protein functionality. The identification of putative regulatory sites in the promotor and the expression profiles revealed the wide range of pathways in which fatty acid desaturases are involved. This study is an updated survey on desaturases of grasses that provides a comprehensive insight into diversity and evolution. This characterization is a necessary first step before considering these genes as candidates for new biotechnological approaches.}, }
@article {pmid28754286, year = {2017}, author = {Harish, A and Kurland, CG}, title = {Mitochondria are not captive bacteria.}, journal = {Journal of theoretical biology}, volume = {434}, number = {}, pages = {88-98}, doi = {10.1016/j.jtbi.2017.07.011}, pmid = {28754286}, issn = {1095-8541}, mesh = {Biological Coevolution ; *Biological Evolution ; Mitochondria/chemistry/*genetics ; *Phylogeny ; *Proteome ; Symbiosis ; }, abstract = {Lynn Sagan's conjecture (1967) that three of the fundamental organelles observed in eukaryote cells, specifically mitochondria, plastids and flagella were once free-living primitive (prokaryotic) cells was accepted after considerable opposition. Even though the idea was swiftly refuted for the specific case of origins of flagella in eukaryotes, the symbiosis model in general was accepted for decades as a realistic hypothesis to describe the endosymbiotic origins of eukaryotes. However, a systematic analysis of the origins of the mitochondrial proteome based on empirical genome evolution models now indicates that 97% of modern mitochondrial protein domains as well their homologues in bacteria and archaea were present in the universal common ancestor (UCA) of the modern tree of life (ToL). These protein domains are universal modular building blocks of modern genes and genomes, each of which is identified by a unique tertiary structure and a specific biochemical function as well as a characteristic sequence profile. Further, phylogeny reconstructed from genome-scale evolution models reveals that Eukaryotes and Akaryotes (archaea and bacteria) descend independently from UCA. That is to say, Eukaryotes and Akaryotes are both primordial lineages that evolved in parallel. Finally, there is no indication of massive inter-lineage exchange of coding sequences during the descent of the two lineages. Accordingly, we suggest that the evolution of the mitochondrial proteome was autogenic (endogenic) and not endosymbiotic (exogenic).}, }
@article {pmid28752775, year = {2018}, author = {Wang, ZD and Liao, J and Huang, CQ and Long, SS and Zhang, S and Guo, YS and Liu, L and Liu, CW}, title = {Significant genetic differentiation of Gobiopterus lacustris, a newly recorded transparent goby in China.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {785-791}, doi = {10.1080/24701394.2017.1357712}, pmid = {28752775}, issn = {2470-1408}, mesh = {Animals ; China ; Cyclooxygenase 1/*genetics ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/genetics ; Gene Flow ; Genetic Drift ; Genetic Variation/genetics ; Genetics, Population ; Genome, Mitochondrial/genetics ; Haplotypes ; Mitochondria/genetics ; Perciformes/*genetics ; Phenotype ; Philippines ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/methods ; }, abstract = {In our recent survey, the transparent small Lacustrine goby, Gobiopterus lacustris had reported as the endemic species of Luzon, Philippines, was identified as an abundant species in mangroves of Leizhou Peninsula, China. Here, high diversity and significant differentiation of five sites of samples representing the west and east populations were revealed by mitochondrial DNA sequences. Five haplotypes of 56 cytochrome oxidase subunit I (Cox1) with the lengths of 623 base pairs (bp) have the high pairwise identity (>98.8%). Moreover, a total of 31 haplotypes for 129 partial D-loop regions were clustered into two clades corresponding to the east and west sampling sites. The strong population structure was confirmed (ΦST = 0.43017, p < .0001) with high haplotype diversity (h = 0.880 ± 0.017) and low nucleotide diversity (p=.00484). Moreover, both the mismatch distribution analysis and neutral test of D-loop revealed that the west group might experience a recent demographic expansion. Lastly, the isolation-with-migration analysis supported the expansion and indicated that the east-west split happened at approximately 7.1 kyr ago. Given the distribution and diversity, G. lacustris could be a good model for the study of the sea-level fluctuations and coast evolution of the South China Sea.}, }
@article {pmid28752773, year = {2018}, author = {Koroiva, R and Kvist, S}, title = {Estimating the barcoding gap in a global dataset of cox1 sequences for Odonata: close, but no cigar.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {765-771}, doi = {10.1080/24701394.2017.1357709}, pmid = {28752773}, issn = {2470-1408}, mesh = {Animals ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Speciation ; Genetic Variation ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Odonata/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {We evaluated the extent of intraspecific and interspecific genetic distances for two highly diverse infraorders of Odonata: Anisoptera and Zygoptera. All cytochrome c oxidase subunit I sequences (cox1), the region chosen for zoological DNA barcoding, present in GenBank for each infraorder were downloaded and curated. For Anisoptera, the final dataset consisted of 2,961 individual cox1 sequences for 536 species and the equivalent numbers for Zygoptera were 2,477 sequences for 497 species. More than 7 million individual genetic comparisons were made and the results indicated that there is a tendency towards a barcoding gap, but that the size of the gap may not be sufficient to robustly infer identities for some taxa. DNA barcoding may be of less use for some odonate taxa, perhaps pertaining to misidentifications in global databases. However, at local scales or with more confined taxonomical sampling, this tool may yet be beneficial in identifying these charismatic organisms.}, }
@article {pmid28749584, year = {2017}, author = {Kopečná, M and Vigouroux, A and Vilím, J and Končitíková, R and Briozzo, P and Hájková, E and Jašková, L and von Schwartzenberg, K and Šebela, M and Moréra, S and Kopečný, D}, title = {The ALDH21 gene found in lower plants and some vascular plants codes for a NADP[+] -dependent succinic semialdehyde dehydrogenase.}, journal = {The Plant journal : for cell and molecular biology}, volume = {92}, number = {2}, pages = {229-243}, doi = {10.1111/tpj.13648}, pmid = {28749584}, issn = {1365-313X}, mesh = {Bryophyta/enzymology/*genetics ; Ferns/enzymology/*genetics ; Genes, Plant/*genetics/physiology ; Phylogeny ; Protein Conformation ; Structure-Activity Relationship ; Substrate Specificity ; Succinate-Semialdehyde Dehydrogenase/*genetics/metabolism ; Succinic Acid/metabolism ; gamma-Aminobutyric Acid/analogs &amp; derivatives/metabolism ; }, abstract = {Lower plant species including some green algae, non-vascular plants (bryophytes) as well as the oldest vascular plants (lycopods) and ferns (monilophytes) possess a unique aldehyde dehydrogenase (ALDH) gene named ALDH21, which is upregulated during dehydration. However, the gene is absent in flowering plants. Here, we show that ALDH21 from the moss Physcomitrella patens codes for a tetrameric NADP[+] -dependent succinic semialdehyde dehydrogenase (SSALDH), which converts succinic semialdehyde, an intermediate of the γ-aminobutyric acid (GABA) shunt pathway, into succinate in the cytosol. NAD[+] is a very poor coenzyme for ALDH21 unlike for mitochondrial SSALDHs (ALDH5), which are the closest related ALDH members. Structural comparison between the apoform and the coenzyme complex reveal that NADP[+] binding induces a conformational change of the loop carrying Arg-228, which seals the NADP[+] in the coenzyme cavity via its 2'-phosphate and α-phosphate groups. The crystal structure with the bound product succinate shows that its carboxylate group establishes salt bridges with both Arg-121 and Arg-457, and a hydrogen bond with Tyr-296. While both arginine residues are pre-formed for substrate/product binding, Tyr-296 moves by more than 1 Å. Both R121A and R457A variants are almost inactive, demonstrating a key role of each arginine in catalysis. Our study implies that bryophytes but presumably also some green algae, lycopods and ferns, which carry both ALDH21 and ALDH5 genes, can oxidize SSAL to succinate in both cytosol and mitochondria, indicating a more diverse GABA shunt pathway compared with higher plants carrying only the mitochondrial ALDH5.}, }
@article {pmid28745560, year = {2018}, author = {Bhatti, S and Abbas, S and Aslamkhan, M and Attimonelli, M and Trinidad, MS and Aydin, HH and de Souza, EMS and Gonzalez, GR}, title = {Genetic perspective of uniparental mitochondrial DNA landscape on the Punjabi population, Pakistan.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {714-726}, doi = {10.1080/24701394.2017.1350951}, pmid = {28745560}, issn = {2470-1408}, mesh = {Adult ; Asian People/genetics ; DNA, Mitochondrial/*genetics ; Ethnicity/genetics ; Gene Pool ; Genetic Variation ; Genetics, Population/methods ; Genome, Mitochondrial/genetics ; Haplotypes ; Humans ; Male ; Mitochondria/genetics ; Pakistan ; Phylogeny ; Phylogeography ; Social Class ; White People/genetics ; }, abstract = {To investigate the uniparental genetic structure of the Punjabi population from mtDNA aspect and to set up an appropriate mtDNA forensic database, we studied maternally unrelated Punjabi (N = 100) subjects from two caste groups (i.e. Arain and Gujar) belonging to territory of Punjab. The complete control region was elucidated by Sanger sequencing and the subsequent 58 different haplotypes were designated into appropriate haplogroups according to the most recently updated mtDNA phylogeny. We found a homogenous dispersal of Eurasian haplogroup uniformity among the Punjab Province and exhibited a strong connotation with the European populations. Punjabi castes are primarily a composite of substantial South Asian, East Asian and West Eurasian lineages. Moreover, for the first time we have defined the newly sub-haplogroup M52b1 characterized by 16223 T, 16275 G and 16438 A in Gujar caste. The vast array of mtDNA variants displayed in this study suggested that the haplogroup composition radiates signals of extensive genetic conglomeration, population admixture and demographic expansion that was equipped with diverse origin, whereas matrilineal gene pool was phylogeographically homogenous across the Punjab. This context was further fully acquainted with the facts supported by PCA scatterplot that Punjabi population clustered with South Asian populations. Finally, the high power of discrimination (0.8819) and low random match probability (0.0085%) proposed a worthy contribution of mtDNA control region dataset as a forensic database that considered a gold standard of today to get deeper insight into the genetic ancestry of contemporary matrilineal phylogeny.}, }
@article {pmid28745537, year = {2018}, author = {Nakazawa, T and Liu, SV and Sakai, Y and Araki, KS and Tsai, CH and Okuda, N}, title = {Spatial genetic structure and body size divergence in endangered Gymnogobius isaza in ancient Lake Biwa.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {756-764}, doi = {10.1080/24701394.2017.1357708}, pmid = {28745537}, issn = {2470-1408}, mesh = {Animals ; Body Size/*genetics ; DNA, Mitochondrial/genetics ; Endangered Species ; Genetic Variation/genetics ; Genome, Mitochondrial/genetics ; Japan ; Lakes ; Mitochondria/genetics ; Perciformes/*genetics ; Phenotype ; Phylogeny ; }, abstract = {Gymnogobius isaza is a freshwater goby endemic to ancient Lake Biwa, the largest lake in Japan. The species is now listed as 'Critically Endangered' in the Red Data Book of Japan. Nevertheless, it remains subject to fishing without any specific management strategies. Previous studies using mitochondrial DNA markers showed that this fish species has two cryptic lineages. However, little is known about spatial genetic structure and ecological differences across the broad lakescape. In this study, we collected fish samples at nine locations along the lakeshore during the breeding season and tested for the presence of spatial heterogeneity in the lineage's composition while measuring body size as the most fundamental biological trait. The results showed that the major lineage dominated all the sampling locations whereas the minor lineage consisted of only 11% (16/143) of samples. Furthermore, although their spatial distributions overlapped (i.e. the two lineages may be well mixed), we found it possible that the minor lineage may have a potentially narrower distribution than the major lineage. In addition, we found that the two lineages differ in body size; specifically, the minor lineage is smaller in size. From the viewpoint of genetic diversity conservation and sustainable resource use, this fish should be managed as two genetic stocks and spatial and/or body size-based fishery management is desirable, with particular attention to the minor (smaller sized) lineage.}, }
@article {pmid28743941, year = {2017}, author = {Yum, LK and Baumgarten, S and Röthig, T and Roder, C and Roik, A and Michell, C and Voolstra, CR}, title = {Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6442}, pmid = {28743941}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*genetics/physiology ; Glycolysis/genetics ; Indian Ocean ; Mitochondria/genetics/metabolism ; Oxygen/metabolism ; *Transcriptome ; }, abstract = {Despite the importance of deep-sea corals, our current understanding of their ecology and evolution is limited due to difficulties in sampling and studying deep-sea environments. Moreover, a recent re-evaluation of habitat limitations has been suggested after characterization of deep-sea corals in the Red Sea, where they live at temperatures of above 20 °C at low oxygen concentrations. To gain further insight into the biology of deep-sea corals, we produced reference transcriptomes and studied gene expression of three deep-sea coral species from the Red Sea, i.e. Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. Our analyses suggest that deep-sea coral employ mitochondrial hypometabolism and anaerobic glycolysis to manage low oxygen conditions present in the Red Sea. Notably, we found expression of genes related to surface cilia motion that presumably enhance small particle transport rates in the oligotrophic deep-sea environment. This is the first study to characterize transcriptomes and in situ gene expression for deep-sea corals. Our work offers several mechanisms by which deep-sea corals might cope with the distinct environmental conditions present in the Red Sea As such, our data provide direction for future research and further insight to organismal response of deep-sea coral to environmental change and ocean warming.}, }
@article {pmid28742928, year = {2017}, author = {Choo, LQ and Crampton-Platt, A and Vogler, AP}, title = {Shotgun mitogenomics across body size classes in a local assemblage of tropical Diptera: Phylogeny, species diversity and mitochondrial abundance spectrum.}, journal = {Molecular ecology}, volume = {26}, number = {19}, pages = {5086-5098}, doi = {10.1111/mec.14258}, pmid = {28742928}, issn = {1365-294X}, mesh = {Animals ; *Body Size ; Borneo ; Contig Mapping ; DNA, Mitochondrial/genetics ; Diptera/anatomy &amp; histology/*classification ; *Genome, Mitochondrial ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Mitochondrial genomes can be assembled readily from shotgun-sequenced DNA mixtures of mass-trapped arthropods ("mitochondrial metagenomics"), speeding up the taxonomic characterization. Bulk sequencing was conducted on some 800 individuals of Diptera obtained by canopy fogging of a single tree in Borneo dominated by small (<1.5 mm) individuals. Specimens were split into five body size classes for DNA extraction, to equalize read numbers across specimens and to study how body size, a key ecological trait, interacts with species and phylogenetic diversity. Genome assembly produced 304 orthologous mitochondrial contigs presumed to each represent a different species. The small-bodied fraction was the by far most species-rich (187 contigs). Identification of contigs was through phylogenetic analysis together with 56 reference mitogenomes, which placed most of the Bornean community into seven clades of small-bodied species, indicating phylogenetic conservation of body size. Mapping of shotgun reads against the mitogenomes showed wide ranges of read abundances within each size class. Ranked read abundance plots were largely log-linear, indicating a uniformly filled abundance spectrum, especially for small-bodied species. Small-bodied species differed greatly from other size classes in neutral metacommunity parameters, exhibiting greater levels of immigration, besides greater total community size. We suggest that the established uses of mitochondrial metagenomics for analysis of species and phylogenetic diversity can be extended to parameterize recent theories of community ecology and biodiversity, and by focusing on the number mitochondria, rather than individuals, a new theoretical framework for analysis of mitochondrial abundance spectra can be developed that incorporates metabolic activity approximated by the count of mitochondria.}, }
@article {pmid28742865, year = {2017}, author = {Yan, C and Mou, B and Meng, Y and Tu, F and Fan, Z and Price, M and Yue, B and Zhang, X}, title = {A novel mitochondrial genome of Arborophila and new insight into Arborophila evolutionary history.}, journal = {PloS one}, volume = {12}, number = {7}, pages = {e0181649}, pmid = {28742865}, issn = {1932-6203}, mesh = {Animals ; Asia, Southeastern ; Biological Evolution ; Frameshift Mutation/genetics ; Galliformes/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; }, abstract = {The lineage of the Bar-backed Partridge (Arborophila brunneopectus) was investigated to determine the phylogenetic relationships within Arborophila as the species is centrally distributed within an area covered by the distributions of 22 South-east Asian hill partridge species. The complete mitochondrial genome (mitogenome) of A. brunneopectus was determined and compared with four other hill partridge species mitogenomes. NADH subunit genes are radical in hill partridge mitogenomes and contain the most potential positive selective sites around where variable sites are abundant. Together with 44 other mitogenomes of closely related species, we reconstructed highly resolved phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) analyses and calculated the divergence and dispersal history of Arborophila using combined datasets composed of their 13-protein coding sequences. Arborophila is reportedly be the oldest group in Phasianidae whose ancestors probably originated in Asia. A. rufipectus shares a closer relationship with A. ardens and A. brunneopectus compared to A. gingica and A. rufogularis, and such relationships were supported and profiled by NADH dehydrogenase subunit 5 (ND5). The intragenus divergence of all five Arborophila species occurred in the Miocene (16.84~5.69 Mya) when there were periods of climate cooling. We propose that these cooling events in the Miocene forced hill partridges from higher to lower altitudes, which led to geographic isolation and speciation. We demonstrated that the apparently deleterious +1 frameshift mutation in NADH dehydrogenase subunit 3 (ND3) found in all Arborophila is an ancient trait that has been eliminated in some younger lineages, such as Passeriformes. It is unclear of the biological advantages of this elimination for the relevant taxa and this requires further investigation.}, }
@article {pmid28741861, year = {2018}, author = {López-Escardó, D and López-García, P and Moreira, D and Ruiz-Trillo, I and Torruella, G}, title = {Parvularia atlantis gen. et sp. nov., a Nucleariid Filose Amoeba (Holomycota, Opisthokonta).}, journal = {The Journal of eukaryotic microbiology}, volume = {65}, number = {2}, pages = {170-179}, pmid = {28741861}, issn = {1550-7408}, support = {322669/ERC_/European Research Council/International ; 616960/ERC_/European Research Council/International ; }, mesh = {Amoeba/*genetics/*ultrastructure ; Animals ; Microscopy, Electron, Transmission ; *Phylogeny ; RNA, Ribosomal, 18S/analysis ; Sequence Analysis, RNA ; }, abstract = {The opisthokonts constitute a eukaryotic supergroup divided into two main clades: the holozoans, which include animals and their unicellular relatives, and the holomycotans, which include fungi, opisthosporidians, and nucleariids. Nucleariids are phagotrophic filose amoebae that phenotypically resemble more their distant holozoan cousins than their holomycotan phylogenetic relatives. Despite their evolutionary interest, the diversity and internal phylogenetic relationships within the nucleariids remain poorly studied. Here, we formally describe and characterize by molecular phylogeny and microscopy observations Parvularia atlantis gen. et sp. nov. (formerly Nuclearia sp. ATCC 50694), and compare its features with those of other nucleariid genera. Parvularia is an amoebal genus characterized by radiating knobbed and branching filopodia. It exhibits prominent vacuoles observable under light microscopy, a cyst-like stage, and completely lacks cilia. P. atlantis possesses one or two nuclei with a central nucleolus, and mitochondria with flat or discoid cristae. These morphological features, although typical of nucleariids, represent a combination of characters different to those of any other described Nuclearia species. Likewise, 18S rRNA-based phylogenetic analyses show that P. atlantis represents a distinct lineage within the nucleariids.}, }
@article {pmid28738827, year = {2017}, author = {Lutfullahoğlu-Bal, G and Keskin, A and Seferoğlu, AB and Dunn, CD}, title = {Bacterial tail anchors can target to the mitochondrial outer membrane.}, journal = {Biology direct}, volume = {12}, number = {1}, pages = {16}, pmid = {28738827}, issn = {1745-6150}, support = {637649/ERC_/European Research Council/International ; }, mesh = {Escherichia coli Proteins/chemistry/*metabolism ; Eukaryotic Cells/metabolism/ultrastructure ; Mitochondria/metabolism ; Mitochondrial Membranes/*metabolism ; Organelle Biogenesis ; Protein Sorting Signals/physiology ; Protein Transport ; Saccharomyces cerevisiae/*metabolism/ultrastructure ; }, abstract = {BACKGROUND: During the generation and evolution of the eukaryotic cell, a proteobacterial endosymbiont was re-fashioned into the mitochondrion, an organelle that appears to have been present in the ancestor of all present-day eukaryotes. Mitochondria harbor proteomes derived from coding information located both inside and outside the organelle, and the rate-limiting step toward the formation of eukaryotic cells may have been development of an import apparatus allowing protein entry to mitochondria. Currently, a widely conserved translocon allows proteins to pass from the cytosol into mitochondria, but how proteins encoded outside of mitochondria were first directed to these organelles at the dawn of eukaryogenesis is not clear. Because several proteins targeted by a carboxyl-terminal tail anchor (TA) appear to have the ability to insert spontaneously into the mitochondrial outer membrane (OM), it is possible that self-inserting, tail-anchored polypeptides obtained from bacteria might have formed the first gate allowing proteins to access mitochondria from the cytosol.<br><br>RESULTS: Here, we tested whether bacterial TAs are capable of targeting to mitochondria. In a survey of proteins encoded by the proteobacterium Escherichia coli, predicted TA sequences were directed to specific subcellular locations within the yeast Saccharomyces cerevisiae. Importantly, TAs obtained from DUF883 family members ElaB and YqjD were abundantly localized to and inserted at the mitochondrial OM.<br><br>CONCLUSIONS: Our results support the notion that eukaryotic cells are able to utilize membrane-targeting signals present in bacterial proteins obtained by lateral gene transfer, and our findings make plausible a model in which mitochondrial protein translocation was first driven by tail-anchored proteins.<br><br>REVIEWERS: This article was reviewed by Michael Ryan and Thomas Simmen.}, }
@article {pmid28736036, year = {2017}, author = {Campos-Silva, C and Reyes-Torres, I and Rivera, M and Meza-Torres, C and Hernández-Camacho, JD and Rodríguez-Bies, E and Navas, P and López-Lluch, G}, title = {[Regulation of the expression of coenzyme Q-synthesis complex during ageing].}, journal = {Revista espanola de geriatria y gerontologia}, volume = {52}, number = {6}, pages = {307-312}, doi = {10.1016/j.regg.2017.03.003}, pmid = {28736036}, issn = {1578-1747}, mesh = {Aging/genetics/*metabolism ; Animals ; Gene Expression Regulation ; Male ; Mice ; Mice, Inbred C57BL ; Ubiquinone/*biosynthesis/genetics ; }, abstract = {INTRODUCTION: Coenzyme Q is an essential component in the activity of the mitochondrial electron transport chain. Its synthesis involves, at least, a complex of ten different proteins. In this study, an attempt is made to determine the evolution of the expression of the genes involved in coenzyme Q synthesis during mouse ageing.<br><br>MATERIAL AND METHODS: The messenger RNA (mRNA) of different organs, such as brain, liver, kidney and skeletal muscle from young (8 months), mature (18 months), and old (24 months) mice was extracted by using Trizol and was then analysed by real time PCR (qPCR) using specific primers for all the known components of the coenzyme Q-synthesis complex (COQ genes).<br><br>RESULTS: Liver showed the highest age-dependent changes in mRNA levels of the different components of Q-synthesis complex, affecting the extent of the variation as well as the significance of the change. In most of the cases, mRNA levels of the different components were higher in mature animals compared to young and old animals. When mRNAs of young and old animals were compared, only minor reductions of mRNA levels were found. Kidney showed a pattern similar to that found in liver as regards the changes in expression, although with lower increases in mature animals than those observed in the liver. Brain and skeletal muscle showed low variations, with muscle being the tissue with less changes, although a pattern similar to that found in liver and kidney was found, with slight increases in mature animals.<br><br>DISCUSSION: The results of this study indicate that ageing is an important factor affecting COQ gene expression, but its effect depends on the organ, and that mature animals show higher levels of mRNA than young and old animals. Taken into consideration the importance of coenzyme Q in cell metabolism and ageing, a more detailed study is needed to understand the gene regulation of the coenzyme Q-synthesis mechanisms during ageing.}, }
@article {pmid28733587, year = {2017}, author = {Översti, S and Onkamo, P and Stoljarova, M and Budowle, B and Sajantila, A and Palo, JU}, title = {Identification and analysis of mtDNA genomes attributed to Finns reveal long-stagnant demographic trends obscured in the total diversity.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {6193}, pmid = {28733587}, issn = {2045-2322}, mesh = {Bayes Theorem ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Evolution, Molecular ; Finland ; Genetics, Population/*methods ; Humans ; Mitochondria/*genetics ; Phylogeny ; Population Density ; Sequence Analysis, DNA/*methods ; }, abstract = {In Europe, modern mitochondrial diversity is relatively homogeneous and suggests an ubiquitous rapid population growth since the Neolithic revolution. Similar patterns also have been observed in mitochondrial control region data in Finland, which contrasts with the distinctive autosomal and Y-chromosomal diversity among Finns. A different picture emerges from the 843 whole mitochondrial genomes from modern Finns analyzed here. Up to one third of the subhaplogroups can be considered as Finn-characteristic, i.e. rather common in Finland but virtually absent or rare elsewhere in Europe. Bayesian phylogenetic analyses suggest that most of these attributed Finnish lineages date back to around 3,000-5,000 years, coinciding with the arrival of Corded Ware culture and agriculture into Finland. Bayesian estimation of past effective population sizes reveals two differing demographic histories: 1) the 'local' Finnish mtDNA haplotypes yielding small and dwindling size estimates for most of the past; and 2) the 'immigrant' haplotypes showing growth typical of most European populations. The results based on the local diversity are more in line with that known about Finns from other studies, e.g., Y-chromosome analyses and archaeology findings. The mitochondrial gene pool thus may contain signals of local population history that cannot be readily deduced from the total diversity.}, }
@article {pmid28733390, year = {2017}, author = {Ung, H and Karia, P and Ebine, K and Ueda, T and Yoshioka, K and Moeder, W}, title = {Triphosphate Tunnel Metalloenzyme Function in Senescence Highlights a Biological Diversification of This Protein Superfamily.}, journal = {Plant physiology}, volume = {175}, number = {1}, pages = {473-485}, pmid = {28733390}, issn = {1532-2548}, mesh = {Acid Anhydride Hydrolases/genetics/*metabolism ; Arabidopsis/*enzymology/genetics/physiology/radiation effects ; Arabidopsis Proteins/genetics/*metabolism ; Cell Death ; Darkness ; Gene Knockout Techniques ; Genes, Reporter ; Mitochondria/enzymology ; Mutation ; Organ Specificity ; Phenotype ; Plant Leaves/enzymology/genetics/physiology/radiation effects ; Polyphosphates/metabolism ; Protein Domains ; Pyrophosphatases/genetics/*metabolism ; Nicotiana/enzymology/genetics/physiology ; }, abstract = {The triphosphate tunnel metalloenzyme (TTM) superfamily comprises a group of enzymes that hydrolyze organophosphate substrates. They exist in all domains of life, yet the biological role of most family members is unclear. Arabidopsis (Arabidopsis thaliana) encodes three TTM genes. We have previously reported that AtTTM2 displays pyrophosphatase activity and is involved in pathogen resistance. Here, we report the biochemical activity and biological function of AtTTM1 and diversification of the biological roles between AtTTM1 and 2 Biochemical analyses revealed that AtTTM1 displays pyrophosphatase activity similar to AtTTM2, making them the only TTMs characterized so far to act on a diphosphate substrate. However, knockout mutant analysis showed that AtTTM1 is not involved in pathogen resistance but rather in leaf senescence. AtTTM1 is transcriptionally up-regulated during leaf senescence, and knockout mutants of AtTTM1 exhibit delayed dark-induced and natural senescence. The double mutant of AtTTM1 and AtTTM2 did not show synergistic effects, further indicating the diversification of their biological function. However, promoter swap analyses revealed that they functionally can complement each other, and confocal microscopy revealed that both proteins are tail-anchored proteins that localize to the mitochondrial outer membrane. Additionally, transient overexpression of either gene in Nicotiana benthamiana induced senescence-like cell death upon dark treatment. Taken together, we show that two TTMs display the same biochemical properties but distinct biological functions that are governed by their transcriptional regulation. Moreover, this work reveals a possible connection of immunity-related programmed cell death and senescence through novel mitochondrial tail-anchored proteins.}, }
@article {pmid28717207, year = {2017}, author = {Brennan, IG and Bauer, AM and Van Tri, N and Wang, YY and Wang, WZ and Zhang, YP and Murphy, RW}, title = {Barcoding utility in a mega-diverse, cross-continental genus: keeping pace with Cyrtodactylus geckos.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5592}, pmid = {28717207}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Ecosystem ; *Evolution, Molecular ; Geography ; Lizards/*classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Over the past decade, DNA barcoding has become a staple of low-cost molecular systematic investigations. The availability of universal primers and subsidized sequencing projects (PolarBOL, SharkBOL, SpongeBOL) have driven this popularity, often without appropriate investigation into the utility of barcoding data for the taxonomic group of interest. Here, our primary aim is to determine the phylogenetic value of DNA barcoding (mitochondrial locus COI) within the gecko genus Cyrtodactylus. With >40 new species described since last systematic investigation, Cyrtodactylus represents one of the most diverse extant squamate genera, and their contemporary distribution spans the Indian subcontinent, eastward through Indochina, and into AustraloPapua. The complex biogeographic history of this group, and morphology-only designation of many species have complicated our phylogenetic understanding of Cyrtodactylus. To highlight the need for continued inclusive molecular assessment, we use Vietnamese Cyrtodactylus as a case study showing the geopolitically paraphyletic nature of their history. We compare COI to the legacy marker ND2, and discuss the value of COI as an interspecific marker, as well as its shortcomings at deeper evolutionary scales. We draw attention back to the Cold Code as a subsidized method for incorporating molecular methods into species descriptions in the effort to maintain accurate phylogenies.}, }
@article {pmid28716740, year = {2017}, author = {Ochoa, LE and Roxo, FF and DoNascimiento, C and Sabaj, MH and Datovo, A and Alfaro, M and Oliveira, C}, title = {Multilocus analysis of the catfish family Trichomycteridae (Teleostei: Ostariophysi: Siluriformes) supporting a monophyletic Trichomycterinae.}, journal = {Molecular phylogenetics and evolution}, volume = {115}, number = {}, pages = {71-81}, doi = {10.1016/j.ympev.2017.07.007}, pmid = {28716740}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Catfishes/*classification/genetics ; Cytochromes b/classification/genetics ; DNA/chemistry/isolation &amp; purification/metabolism ; Electron Transport Complex IV/classification/genetics ; Mitochondria/genetics ; Myosin Heavy Chains/classification/genetics ; Nuclear Proteins/classification/genetics ; Phylogeny ; RNA, Ribosomal, 16S/classification/genetics ; Sequence Analysis, DNA ; }, abstract = {Trichomycteridae is the second most diverse family of the order Siluriformes, its members are widely distributed through the freshwaters of Central and South America, exhibiting an exceptional ecological and phenotypic disparity. The most diverse subfamily, Trichomycterinae, represented mainly by the genus Trichomycterus, historically has been recognized as non-monophyletic and various characters used to unite or divide its constituents are repeatedly called into question. No comprehensive molecular phylogenetic hypothesis regarding relationships of trichomycterids has been produced, and the present study is the first extensive phylogeny for the family Trichomycteridae, based on a multilocus dataset of three mitochondrial loci and two nuclear markers (3284bp total). Our analysis has the most comprehensive taxon-sampling of the Trichomycteridae published so far, including members of all subfamilies and a vast representation of Trichomycterus diversity. Analysis of these data showed a phylogenetic hypothesis with broad agreement between the Bayesian (BI) and maximum-likelihood (ML) trees. The results provided overwhelming support for the monophyletic status of Copionodontinae, Stegophilinae, Trichomycterinae, and Vandelliinae, but not Sarcoglanidinae and Glanapteryginae. A major feature of our results is the support to the current conceptualization of Trichomycterinae, which includes Ituglanis and Scleronema and excludes the "Trichomycterus" hasemani group. Divergence time analysis based on DNA substitution rates suggested a Lower Cretaceous origin of the family and the divergence events at subfamilial level shaped by Paleogene events in the geohistory of South America. This hypothesis lays a foundation for an array of future studies of evolution and biogeography of the family.}, }
@article {pmid28712321, year = {2018}, author = {Wang, ZL and Yang, XQ and Wang, TZ and Yu, X}, title = {Assessing the effectiveness of mitochondrial COI and 16S rRNA genes for DNA barcoding of farmland spiders in China.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {695-702}, doi = {10.1080/24701394.2017.1350949}, pmid = {28712321}, issn = {2470-1408}, mesh = {Animals ; China ; DNA ; DNA Barcoding, Taxonomic/methods ; Electron Transport Complex IV/*genetics ; Farms ; Genetic Speciation ; Genetic Variation ; Genome, Insect/*genetics ; Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Spiders/*genetics ; }, abstract = {DNA barcoding has been widely used to identify and discover new species in a wide range of taxa. In order to assess the effectiveness of COI (cytochrome C oxidase subunit I) and 16S (16S ribosomal RNA) in the discrimination of spiders, we have generated 289 barcodes for a total of 56 farmland spider species from 14 different families for the first time in China. Our results reveal that the standard barcoding marker COI can be used to distinguish the farmland spiders both in species and family level by NJ tree-based method, despite the absence of a barcode gap between the intra- and inter-specific genetic divergences. 16S has a lower species identification success as compared with COI. However, almost 98% of the species can be correctly distinguished for both COI and 16S when a threshold of 3% nucleotide divergence was used for species discrimination. Our study significantly improves the barcode reference sequence library for Chinese farmland spiders, and will be very useful in pest management and eco-environmental monitoring and protection.}, }
@article {pmid28712317, year = {2018}, author = {Han, CC and Fang, LS and Chang, IM and Lin, HD}, title = {Genetic variation of the land-locked freshwater shrimp Caridina pseudodenticulata (Decapoda: Atyidae: Caridina) in Taiwan.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {687-694}, doi = {10.1080/24701394.2017.1350948}, pmid = {28712317}, issn = {2470-1408}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Decapoda/*genetics ; Electron Transport Complex IV/*genetics ; Fresh Water ; Genetic Variation ; Genetics, Population/methods ; Genome, Mitochondrial/genetics ; Mitochondria/genetics ; Phylogeny ; Rivers ; Sequence Analysis, DNA/methods ; Shellfish ; Taiwan ; }, abstract = {Caridina pseudodenticulata is a land-locked freshwater shrimp, which is endemic to North and West Taiwan. It is listed as Vulnerable under criteria A1ce in the IUCN Red List. Our study used mitochondrial DNA fragment sequences of the cytochrome oxidase subunit I (COI) gene to examine its genetic structure. In total, 204 sequences were analyzed from 22 populations, and all 39 haplotypes were identified. Our study (1) found that the genetic diversity within population of this species was similar to that of other land-locked freshwater prawn in Taiwan; (2) displayed that during glaciation, the Taiwan Strait was largely above water, an event which created opportunities for colonization Taiwan and dispersal widely; (3) showed that although the phylogenetic analysis showed the lack of a population genetic structure, the AMOVA and haplotypes distribution pattern revealed geographically divided; (4) indicated that C. pseudodenticulata could across to neighbor rivers through the mouths of rivers, which confluent with each other during floods.}, }
@article {pmid28711665, year = {2017}, author = {Pérez, T and Rodríguez, F and Fernández, M and Albornoz, J and Domínguez, A}, title = {Ancient mitochondrial pseudogenes reveal hybridization between distant lineages in the evolution of the Rupicapra genus.}, journal = {Gene}, volume = {628}, number = {}, pages = {63-71}, doi = {10.1016/j.gene.2017.07.035}, pmid = {28711665}, issn = {1879-0038}, mesh = {Animals ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; *Hybridization, Genetic ; Mitochondria/genetics ; Phylogeny ; *Pseudogenes ; Rupicapra/classification/*genetics ; }, abstract = {Mitochondrial pseudogenes (numts) inserted in the nuclear genome are frequently found in population studies. Its presence is commonly connected with problems and errors when they are confounded with true mitochondrial sequences. In the opposite side, numts can provide valuable phylogenetic information when they are copies of ancient mitochondrial lineages. We show that Rupicapra individuals of different geographic origin from the Cantabrian Mountains to the Apennines and the Caucasus share a nuclear COI fragment. The numt copies are monophyletic, and their pattern of differentiation shows two outstanding features: a long evolution as differentiated true mitochondrial lineage, and a recent integration and spread through the chamois populations. The COI pseudogene is much older than the present day mitochondrial clades of Rupicapra and occupies a basal position within the Rupicapra-Ammotragus-Arabitragus node. Joint analysis of this numt and a cytb pseudogene with a similar pattern of evolution places the source mitochondrial lineage as a sister branch that separated from the Ammotragus-Arabitragus lineage 6millionyearsago (Mya). The occurrence of this sequence in the nucleus of chamois suggests hybridization between highly divergent lineages. The integration event seems to be very recent, more recent than the split of the present day mtDNA lineages of Rupicapra (1.9Mya). This observation invites to think of the spread across the genus by horizontal transfer through recent male-biased dispersal.}, }
@article {pmid28709986, year = {2017}, author = {Barba-Montoya, J and Dos Reis, M and Yang, Z}, title = {Comparison of different strategies for using fossil calibrations to generate the time prior in Bayesian molecular clock dating.}, journal = {Molecular phylogenetics and evolution}, volume = {114}, number = {}, pages = {386-400}, pmid = {28709986}, issn = {1095-9513}, support = {BB/N000609/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Calibration ; Cytochromes b/classification/genetics ; Electron Transport Complex IV/classification/genetics ; *Fossils/history ; History, Ancient ; Mitochondria/genetics ; NADH Dehydrogenase/classification/genetics ; Phylogeny ; Plants/classification/genetics ; Primates/classification/genetics ; }, abstract = {Fossil calibrations are the utmost source of information for resolving the distances between molecular sequences into estimates of absolute times and absolute rates in molecular clock dating analysis. The quality of calibrations is thus expected to have a major impact on divergence time estimates even if a huge amount of molecular data is available. In Bayesian molecular clock dating, fossil calibration information is incorporated in the analysis through the prior on divergence times (the time prior). Here, we evaluate three strategies for converting fossil calibrations (in the form of minimum- and maximum-age bounds) into the prior on times, which differ according to whether they borrow information from the maximum age of ancestral nodes and minimum age of descendent nodes to form constraints for any given node on the phylogeny. We study a simple example that is analytically tractable, and analyze two real datasets (one of 10 primate species and another of 48 seed plant species) using three Bayesian dating programs: MCMCTree, MrBayes and BEAST2. We examine how different calibration strategies, the birth-death process, and automatic truncation (to enforce the constraint that ancestral nodes are older than descendent nodes) interact to determine the time prior. In general, truncation has a great impact on calibrations so that the effective priors on the calibration node ages after the truncation can be very different from the user-specified calibration densities. The different strategies for generating the effective prior also had considerable impact, leading to very different marginal effective priors. Arbitrary parameters used to implement minimum-bound calibrations were found to have a strong impact upon the prior and posterior of the divergence times. Our results highlight the importance of inspecting the joint time prior used by the dating program before any Bayesian dating analysis.}, }
@article {pmid28708996, year = {2017}, author = {Bushell, E and Gomes, AR and Sanderson, T and Anar, B and Girling, G and Herd, C and Metcalf, T and Modrzynska, K and Schwach, F and Martin, RE and Mather, MW and McFadden, GI and Parts, L and Rutledge, GG and Vaidya, AB and Wengelnik, K and Rayner, JC and Billker, O}, title = {Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes.}, journal = {Cell}, volume = {170}, number = {2}, pages = {260-272.e8}, pmid = {28708996}, issn = {1097-4172}, support = {R01 AI028398/AI/NIAID NIH HHS/United States ; 098051//Wellcome Trust/United Kingdom ; G0501670/MRC_/Medical Research Council/United Kingdom ; R56 AI028398/AI/NIAID NIH HHS/United States ; //Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Biological Evolution ; Female ; Gene Knockout Techniques ; Genes, Essential ; *Genome, Protozoan ; Host-Parasite Interactions ; Metabolic Networks and Pathways ; Mice ; Mice, Inbred BALB C ; Plasmodium berghei/*genetics/*growth &amp; development/metabolism ; Saccharomyces cerevisiae/genetics ; Toxoplasma/genetics ; Trypanosoma brucei brucei/genetics ; }, abstract = {The genomes of malaria parasites contain many genes of unknown function. To assist drug development through the identification of essential genes and pathways, we have measured competitive growth rates in mice of 2,578 barcoded Plasmodium berghei knockout mutants, representing >50% of the genome, and created a phenotype database. At a single stage of its complex life cycle, P. berghei requires two-thirds of genes for optimal growth, the highest proportion reported from any organism and a probable consequence of functional optimization necessitated by genomic reductions during the evolution of parasitism. In contrast, extreme functional redundancy has evolved among expanded gene families operating at the parasite-host interface. The level of genetic redundancy in a single-celled organism may thus reflect the degree of environmental variation it experiences. In the case of Plasmodium parasites, this helps rationalize both the relative successes of drugs and the greater difficulty of making an effective vaccine.}, }
@article {pmid28704930, year = {2017}, author = {Lai, YC and Baker, JS and Donti, T and Graham, BH and Craigen, WJ and Anderson, AE}, title = {Mitochondrial Dysfunction Mediated by Poly(ADP-Ribose) Polymerase-1 Activation Contributes to Hippocampal Neuronal Damage Following Status Epilepticus.}, journal = {International journal of molecular sciences}, volume = {18}, number = {7}, pages = {}, pmid = {28704930}, issn = {1422-0067}, support = {K08 NS063117/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Blotting, Western ; Electroencephalography ; Hippocampus/*metabolism/*pathology ; Mitochondria/*metabolism/*pathology ; Neurons/*metabolism/*pathology ; Poly (ADP-Ribose) Polymerase-1/*metabolism ; Rats ; Rats, Sprague-Dawley ; Status Epilepticus/*metabolism/*pathology ; }, abstract = {Mitochondrial dysfunction plays a central role in the neuropathology associated with status epilepticus (SE) and is implicated in the development of epilepsy. While excitotoxic mechanisms are well-known mediators affecting mitochondrial health following SE, whether hyperactivation of poly(ADP-ribose) polymerase-1 (PARP-1) also contributes to SE-induced mitochondrial dysfunction remains to be examined. Here we first evaluated the temporal evolution of poly-ADP-ribosylated protein levels in hippocampus following kainic acid-induced SE as a marker for PARP-1 activity, and found that PARP-1 was hyperactive at 24 h following SE. We evaluated oxidative metabolism and found decreased NAD[+] levels by enzymatic cycling, and impaired NAD[+]-dependent mitochondrial respiration as measured by polarography at 24 h following SE. Stereological estimation showed significant cell loss in the hippocampal CA1 and CA3 subregions 72 h following SE. PARP-1 inhibition using N-(6-Oxo-5,6-dihydro-phenanthridin-2-yl)- N,N-dimethylacetamide (PJ-34) in vivo administration was associated with preserved NAD[+] levels and NAD[+]-dependent mitochondrial respiration, and improved CA1 neuronal survival. These findings suggest that PARP-1 hyperactivation contributes to SE-associated mitochondrial dysfunction and CA1 hippocampal damage. The deleterious effects of PARP-1 hyperactivation on mitochondrial respiration are in part mediated through intracellular NAD[+] depletion. Therefore, modulating PARP-1 activity may represent a potential therapeutic target to preserve intracellular energetics and mitochondrial function following SE.}, }
@article {pmid28703292, year = {2017}, author = {Bonnet, T and Leblois, R and Rousset, F and Crochet, PA}, title = {A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes.}, journal = {Evolution; international journal of organic evolution}, volume = {71}, number = {9}, pages = {2140-2158}, doi = {10.1111/evo.13296}, pmid = {28703292}, issn = {1558-5646}, mesh = {Computer Simulation ; *DNA, Mitochondrial ; *Genome, Mitochondrial ; *Hybridization, Genetic ; Mitochondria ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Hybridization is increasingly recognized as a significant evolutionary process, in particular because it can lead to introgression of genes from one species to another. A striking pattern of discordance in the amount of introgression between mitochondrial and nuclear markers exists such that substantial mitochondrial introgression is often found in combination with no or little nuclear introgression. Multiple mechanisms have been proposed to explain this discordance, including positive selection for introgressing mitochondrial variants, several types of sex-biases, drift, negative selection against introgression in the nuclear genome, and spatial expansion. Most of these hypotheses are verbal, and have not been quantitatively evaluated so far. We use individual-based, multilocus, computer simulations of secondary contact under a wide range of demographic and genetic scenarios to evaluate the ability of the different mechanisms to produce discordant introgression. Sex-biases and spatial expansions fail to produce substantial mito-nuclear discordance. Drift and nuclear selection can produce strong discordance, but only under a limited range of conditions. In contrast, selection on the mitochondrial genome produces strong discordance, particularly when dispersal rates are low. However, commonly used statistical tests have little power to detect this selection. Altogether, these results dismiss several popular hypotheses, and provide support for adaptive mitochondrial introgression.}, }
@article {pmid28699890, year = {2017}, author = {Brandt, T and Mourier, A and Tain, LS and Partridge, L and Larsson, NG and Kühlbrandt, W}, title = {Changes of mitochondrial ultrastructure and function during ageing in mice and Drosophila.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {28699890}, issn = {2050-084X}, mesh = {Aging/*physiology ; Animals ; Cryoelectron Microscopy ; DNA, Mitochondrial/genetics ; Drosophila melanogaster/*physiology ; Energy Metabolism ; Imaging, Three-Dimensional ; Mice ; Mitochondria/metabolism/*ultrastructure ; Organ Specificity ; Tomography ; }, abstract = {Ageing is a progressive decline of intrinsic physiological functions. We examined the impact of ageing on the ultrastructure and function of mitochondria in mouse and fruit flies (Drosophila melanogaster) by electron cryo-tomography and respirometry. We discovered distinct age-related changes in both model organisms. Mitochondrial function and ultrastructure are maintained in mouse heart, whereas subpopulations of mitochondria from mouse liver show age-related changes in membrane morphology. Subpopulations of mitochondria from young and old mouse kidney resemble those described for apoptosis. In aged flies, respiratory activity is compromised and the production of peroxide radicals is increased. In about 50% of mitochondria from old flies, the inner membrane organization breaks down. This establishes a clear link between inner membrane architecture and functional decline. Mitochondria were affected by ageing to very different extents, depending on the organism and possibly on the degree to which tissues within the same organism are protected against mitochondrial damage.}, }
@article {pmid28695851, year = {2017}, author = {Luo, F and Shinzawa-Itoh, K and Hagimoto, K and Shimada, A and Shimada, S and Yamashita, E and Yoshikawa, S and Tsukihara, T}, title = {Structure of bovine cytochrome c oxidase crystallized at a neutral pH using a fluorinated detergent.}, journal = {Acta crystallographica. Section F, Structural biology communications}, volume = {73}, number = {Pt 7}, pages = {416-422}, pmid = {28695851}, issn = {2053-230X}, support = {JPMJCR12M3//Japan Science and Technology Agency, Core Research for Evolutional Science and Technology/ ; 26291033//Japan Society for the Promotion of Science/ ; 15K18493//Japan Society for the Promotion of Science/ ; }, mesh = {Amino Acid Motifs ; Animals ; Binding Sites ; Cattle ; Crystallography, X-Ray ; Detergents/*chemistry ; Electron Transport Complex IV/*chemistry/isolation &amp; purification/metabolism ; Hydrocarbons, Fluorinated/*chemistry ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Maltose/*analogs &amp; derivatives/chemistry ; Mitochondria, Heart/*chemistry/enzymology ; Models, Molecular ; Myocardium/chemistry ; Oxidation-Reduction ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Subunits/*chemistry/isolation &amp; purification/metabolism ; *Protons ; }, abstract = {Cytochrome c oxidase (CcO) couples proton pumping to O2 reduction. Its enzymatic activity depends sensitively on pH over a wide range. However, owing to difficulty in crystallizing this protein, X-ray structure analyses of bovine CcO aimed at understanding its reaction mechanism have been conducted using crystals prepared at pH 5.7, which is significantly lower than that in the cell. Here, oxidized CcO at pH 7.3 was crystallized using a fluorinated octyl-maltoside derivative, and the structure was determined at 1.77 Å resolution. No structural differences between crystals obtained at the neutral pH and the acidic pH were detected within the molecules. On the other hand, some differences in intermolecular interactions were detected between the two types of crystal. The influence of pH on the molecular surface is likely to contribute to the pH dependency of the aerobic oxidation of ferrocytochrome c.}, }
@article {pmid28690821, year = {2017}, author = {Zhang, B and Zhang, YH and Wang, X and Zhang, HX and Lin, Q}, title = {The mitochondrial genome of a sea anemone Bolocera sp. exhibits novel genetic structures potentially involved in adaptation to the deep-sea environment.}, journal = {Ecology and evolution}, volume = {7}, number = {13}, pages = {4951-4962}, pmid = {28690821}, issn = {2045-7758}, abstract = {The deep sea is one of the most extensive ecosystems on earth. Organisms living there survive in an extremely harsh environment, and their mitochondrial energy metabolism might be a result of evolution. As one of the most important organelles, mitochondria generate energy through energy metabolism and play an important role in almost all biological activities. In this study, the mitogenome of a deep-sea sea anemone (Bolocera sp.) was sequenced and characterized. Like other metazoans, it contained 13 energy pathway protein-coding genes and two ribosomal RNAs. However, it also exhibited some unique features: just two transfer RNA genes, two group I introns, two transposon-like noncanonical open reading frames (ORFs), and a control region-like (CR-like) element. All of the mitochondrial genes were coded by the same strand (the H-strand). The genetic order and orientation were identical to those of most sequenced actiniarians. Phylogenetic analyses showed that this species was closely related to Bolocera tuediae. Positive selection analysis showed that three residues (31 L and 42 N in ATP6, 570 S in ND5) of Bolocera sp. were positively selected sites. By comparing these features with those of shallow sea anemone species, we deduced that these novel gene features may influence the activity of mitochondrial genes. This study may provide some clues regarding the adaptation of Bolocera sp. to the deep-sea environment.}, }
@article {pmid28690785, year = {2017}, author = {Láruson, &#xc1;J}, title = {Rates and relations of mitochondrial genome evolution across the Echinoidea, with special focus on the superfamily Odontophora.}, journal = {Ecology and evolution}, volume = {7}, number = {13}, pages = {4543-4551}, pmid = {28690785}, issn = {2045-7758}, abstract = {In order to better characterize the placement of genus Tripneustes, as a representative of the Toxopneustidae family within the broader sea urchin mitochondrial (MT) phylogeny, the complete MT genome of Tripneustes gratilla was generated and compared with all published echinoid MT genomes currently available on NCBI GenBank. The MT genome phylogeny supports the existence of the superfamily Odontophora (consisting of the families Strongylocentrotidae, Echinometridae, and Toxopneustidae). A relaxed molecular-clock time calibration suggests a split between the three key Odontophore MT lineages occurred during the late Eocene/Oligocene. Major global oceanographic changes have been inferred during this time frame, potentially driving species diversification through environmental selection pressures. To test for signatures of selection acting on the mitochondria, the historical rate of gene evolution of individual MT genes was assessed through a branch-site comparison of nonsynonymous to synonymous substitution ratios (ω). Models of positive selection and neutral evolution, as compared via a likelihood ratio test, show no evidence of strong historical positive selection on mitochondrial genes at the genesis of the Odontophora. However, while pairwise ω comparison revealed signatures of strong negative selection, relatively elevated ω values were observed within the Strongylocentrotus genus.}, }
@article {pmid28690127, year = {2017}, author = {Nacer, DF and Raposo do Amaral, F}, title = {Striking pseudogenization in avian phylogenetics: Numts are large and common in falcons.}, journal = {Molecular phylogenetics and evolution}, volume = {115}, number = {}, pages = {1-6}, doi = {10.1016/j.ympev.2017.07.002}, pmid = {28690127}, issn = {1095-9513}, mesh = {Animals ; Cytochromes b/classification/genetics ; Electron Transport Complex IV/classification/genetics ; Falconiformes/*classification ; Mitochondria/genetics ; NADH Dehydrogenase/classification/genetics ; Phylogeny ; }, abstract = {Nuclear copies of mitochondrial genes (numts) are a well-known feature of eukaryotic genomes and a concern in systematics, as they can mislead phylogenetic inferences when inadvertently used. Studies on avian numts initially based on the chicken genome suggest that numts may be uncommon and relatively short among birds. Here we ask how common numts are in falcons, based on recently sequenced genomes of the Saker falcon (Falco cherrug) and Peregrine falcon (F. peregrinus). We identified numts by BLASTN searches and then extracted CYTB, ND2 and COI sequences from them, which were then used for phylogeny inference along with several sequences from other species in Falconiformes. Our results indicate that avian numts may be much more frequent and longer than previously thought. Phylogenetic inferences revealed multiple independent nuclear insertions throughout the history of the Falconiformes, including cases of sequences available in public databases and wrongly identified as authentic mtDNA. New sequencing technologies and ongoing efforts for whole genome sequencing will provide exciting opportunities for avian numt research in the near future.}, }
@article {pmid28689725, year = {2017}, author = {Polymeropoulos, ET and Oelkrug, R and White, CR and Jastroch, M}, title = {Phylogenetic analysis of the allometry of metabolic rate and mitochondrial basal proton leak.}, journal = {Journal of thermal biology}, volume = {68}, number = {Pt A}, pages = {83-88}, doi = {10.1016/j.jtherbio.2017.01.013}, pmid = {28689725}, issn = {0306-4565}, mesh = {Animals ; *Basal Metabolism ; Biological Evolution ; Mitochondria/physiology ; *Phylogeny ; Protons ; }, abstract = {The mitochondrial basal proton leak (MBPL) significantly contributes to high body temperatures (Tb) and basal metabolic rates (BMR) in endotherms. In endotherms at a given body mass (M), liver MBPL is higher than in ectotherms, supporting the notion that MBPL may partly explain the evolutionary increase in metabolic rate (MR), fostering endothermy. Here, we re-addressed this assumption by performing a phylogenetic analysis comparing all available liver MBPL data for ecto- and endotherms. While MBPL within endotherms negatively scales with M and BMR as shown previously, MBPL of ectotherms does not scale allometrically with M. Phylogenetic analysis reveals that this result is confounded by a positive scaling coefficient for MBPL with M for reptiles. Strikingly, the reptilian MBPL reaches endothermic levels above a body mass of 6.6kg. Thus, phylogenetic scaling of MBPL supports previous claims of endotherm-like physiological characteristics in large reptiles. It appears that diversification of ancestral ectothermic tetrapods to a body mass of at least 6kg may have been required to reach a MBPL that is beneficial for sustained high body temperatures. Novel MBPL data for the lesser hedgehog tenrec, a protoendothermic eutherian that displays reptile-like thermoregulatory patterns, fall within the endo- and ectothermic allometric regressions. Finally, we add additional evidence that within endotherms, phylogenetic differences in MR do not correlate with MBPL. Collectively, these data suggest that MBPL does not universally scale with metabolic rate in ecto- or endotherms and that an increasing MBPL with M may have played an important physiological role in the evolutionary history of reptilian thermoregulation.}, }
@article {pmid28689636, year = {2017}, author = {Zhao, YQ and Yang, HY and Zhang, DD and Han, YL and Hou, CC and Zhu, JQ}, title = {Dynamic transcription and expression patterns of KIF3A and KIF3B genes during spermiogenesis in the shrimp, Palaemon carincauda.}, journal = {Animal reproduction science}, volume = {184}, number = {}, pages = {59-77}, doi = {10.1016/j.anireprosci.2017.06.017}, pmid = {28689636}, issn = {1873-2232}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Gene Expression Regulation/*physiology ; Kinesins/genetics/*metabolism ; Male ; Models, Molecular ; Palaemonidae/*metabolism ; Phylogeny ; Protein Conformation ; RNA, Messenger/genetics/metabolism ; Spermatogenesis/*physiology ; }, abstract = {Spermiogenesis is a highly ordered and complex process in the male germ cell differentiation. The microtubule-based motor proteins KIF3A and KIF3B are required for the progression of the stages of spermiogenesis. In this study, the main goal was to determine whether KIF3A and KIF3B have a key role in spermiogenesis in Palaemon carincauda. The complete cDNA of KIF3A/3B from the testis of P. carincauda was cloned by using PCR and rapid amplification of cDNA ends (RACE). The predicted secondary and tertiary structures of KIF3A/3B contained three domains which were the: a) head region, b) stalk region, and c) tail region. Real-time quantitative PCR (qPCR) results revealed that KIF3A and KIF3B mRNAs were obtained for all the tissues examined, with the greatest gene expression in the testis. In situ hybridization indicated the KIF3A and KIF3B mRNAs were distributed in the periphery of the nuclear in the early spermatid of spermiogenesis. In the middle and late spermatid stages, KIF3A and KIF3B mRNAs were gradually upregulated and assembled to one side where acrosome biogenesis begins. In the mature sperm, KIF3A and KIF3B mRNAs were distributed in the acrosome cap and spike. Immunofluorescence studies indicated that KIF3A, tubulin, mitochondria, and Golgi were co-localized in different stages during spermiogenesis in P. carincauda. The temporal and spatial gene expression dynamics of KIF3A/3B indicate that KIF3A and KIF3B proteins may be involved in acrosome formation and nucleus shaping. Moreover, these proteins can transport the mitochondria and Golgi that facilitate acrosome formation in P. carincauda.}, }
@article {pmid28684295, year = {2017}, author = {Lazcano, A and Peretó, J}, title = {On the origin of mitosing cells: A historical appraisal of Lynn Margulis endosymbiotic theory.}, journal = {Journal of theoretical biology}, volume = {434}, number = {}, pages = {80-87}, doi = {10.1016/j.jtbi.2017.06.036}, pmid = {28684295}, issn = {1095-8541}, mesh = {*Biological Evolution ; Chloroplasts ; Eukaryota/genetics ; Genome ; History, 20th Century ; Metabolic Networks and Pathways ; Mitochondria ; Symbiosis/*physiology ; }, abstract = {Although for a long-time symbiosis was considered to be quite rare and with no role in evolutionary processes, Lynn Margulis demonstrated that endosymbiotic events played a key role in the origin and evolution of eukaryotic cells. Starting with her seminal assay in the Journal of Theoretical Biology in 1967 (authored as Lynn Sagan), her lifelong work on eukaryogenesis and the role of symbiosis in evolution stands as a valid and authoritative contribution to science. As was quick to acknowledge, she was not the first to discuss the significance of symbiosis to explain the origin of mitochondria and chloroplasts, but no one else had done it to her extent and depth, nor had anyone provided a variety of testable hypotheses. While it is true that some of her proposals were incomplete or mistaken, morphological, biochemical and geochemical evidence together with phylogenomic analyses of mitochondria, chloroplasts and eukaryotic nuclear genomes have demonstrated the validity of her evolutionary scheme, as well that of her specific predictions on the chimeric nature of genomes and the mosaicism of metabolic pathways in eukaryotic cells.}, }
@article {pmid28682310, year = {2017}, author = {Li, Y and Zhang, L and Qu, T and Tang, X and Li, L and Zhang, G}, title = {Conservation and divergence of mitochondrial apoptosis pathway in the Pacific oyster, Crassostrea gigas.}, journal = {Cell death &amp; disease}, volume = {8}, number = {7}, pages = {e2915}, pmid = {28682310}, issn = {2041-4889}, mesh = {Animals ; Apoptosis/drug effects/*genetics/radiation effects ; Apoptotic Protease-Activating Factor 1/*genetics/metabolism ; Biological Evolution ; Carbonyl Cyanide m-Chlorophenyl Hydrazone/pharmacology ; Caspases/*genetics/metabolism ; Conserved Sequence ; Crassostrea/classification/drug effects/*metabolism/radiation effects ; Cytochromes c/metabolism ; Gene Expression Regulation ; Genetic Variation ; Hemocytes/drug effects/metabolism/radiation effects ; Mitochondria/drug effects/*metabolism/radiation effects ; Mitochondrial Membranes/drug effects/metabolism/radiation effects ; Permeability ; Phylogeny ; Proto-Oncogene Proteins c-bcl-2/*genetics/metabolism ; Proton Ionophores/pharmacology ; Signal Transduction ; Ultraviolet Rays ; }, abstract = {Apoptosis is considered a crucial part of the host defense system in oysters according to previous reports; however, the exact process by which this occurs remains unclear. Besides, mitochondrial apoptosis is the primary method of apoptosis in vertebrate cells, but has been poorly studied in invertebrates and is quite controversial. In this study, we investigated the molecular mechanism of mitochondrial apoptosis in the Pacific oyster Crassostrea gigas. Notably, we show that most key elements involved in the vertebrate mitochondrial apoptosis pathway - including mitochondrial outer membrane permeabilization, cytochrome c release, and caspase activation - are also present in C. gigas. In contrast, the lack of Bcl-2 homology 3-only subfamily members and apoptotic protease activating factor-1 (APAF-1) protein revealed evolutionary diversity from other phyla. Our results support that mitochondrial apoptosis in animals predates the emergence of vertebrates, but suggest that an unexpectedly diverse mitochondrial apoptosis pathway may exist in invertebrates. In addition, our work provided new clues for an improved understanding of how bivalve acclimate themselves to an inconstant environment.}, }
@article {pmid28673190, year = {2018}, author = {Koç, H and Bülbül, U and Kurnaz, M and İhsan Eroğlu, A and Kutrup, B}, title = {Phylogenetic relationships of Podarcis siculus (Rafinesque-Schmaltz, 1810) and Podarcis tauricus (Pallas, 1814) in Turkey, based on mitochondrial DNA.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {664-673}, doi = {10.1080/24701394.2017.1342245}, pmid = {28673190}, issn = {2470-1408}, mesh = {Animals ; DNA ; DNA, Mitochondrial/*genetics ; Genetic Speciation ; Genome, Mitochondrial/*genetics ; Lizards/*genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Turkey ; }, abstract = {The Italian wall lizard and the Balkan wall lizard have a series of taxonomic revisions. However, their phylogenetic relationships still remain uncertain in Turkey. In the present study, we have assessed taxonomic relationships, both of Podarcis siculus and Podarcis tauricus through estimation of phylogenetic relationships among 43 and 42 specimens, respectively, using mtDNA (16 S rRNA and cytb) from great main populations in Turkey. The genetic distances among the populations of P. siculus in Turkey were very low and they were ranged from 0.2 to 1.6% in 16 S rRNA while they were ranged from 0.0% to 3.3% in cytb. On the other hand, the p-distances among the populations of P. tauricus were ranged from 0.0 to 0.6% in 16 S rRNA while they were 0.2% cytb in Turkey. Finally, most of the topologically identical trees of phylogenetic analyses and p-distances showed that monophyly was found in extant populations of P. siculus and P. tauricus. The nominate subspecies, P. s. siculus and P. t. tauricus are representatives of these lizards in Turkey.}, }
@article {pmid28671726, year = {2018}, author = {Liu, M and Zhang, J and Zhang, Z and Zhou, L and Jiang, Y and Wang, J and Xiao, J and Wu, Y}, title = {Phenotypic spectrum of mutations in IBA57, a candidate gene for cavitating leukoencephalopathy.}, journal = {Clinical genetics}, volume = {93}, number = {2}, pages = {235-241}, doi = {10.1111/cge.13090}, pmid = {28671726}, issn = {1399-0004}, mesh = {Carrier Proteins/*genetics ; Child ; Child, Preschool ; Female ; Genetic Association Studies ; Humans ; Infant ; Leukoencephalopathies/diagnostic imaging/*genetics/pathology ; Magnetic Resonance Imaging ; Male ; Mitochondria/*genetics/pathology ; Mutation ; Phenotype ; }, abstract = {IBA57 is involved in the biogenesis of mitochondrial [4Fe-4S] proteins. Eighteen cases with IBA57 mutations have been reported to date. We described a novel phenotype in 11 children with cavitating leukoencephalopathy and summarized the phenotypic spectrum of IBA57 mutations. The median age of onset was 9 months, with an initial presentation of motor regression. Deterioration of neurological function reached its peak within 4 months. The median interval between onset and last follow-up was 2.9 years (0.4-10.0). All cases survived and remained stable. Severe motor handicap was observed in 50.0% of the patients, 52.9% to 71.4% had a delay in communication, problem solving or personal-social skills, and 20.0% had mild symptomatic fluctuations. In the peak phase, magnetic resonance imaging (MRI) lesions were mainly observed in the periventricular/central white matter, and cavitating lesions and patchy high diffusion-weighted imaging (DWI) signals were observed. The numbers and extent of restricted diffusional lesions were reduced, and atrophy was prominent in the recovery phase. Eight novel mutations in IBA57 were identified in our study. This study provided more information about the natural history and evolution of neuroimaging. Combined with previously reported patient studies, our findings suggest that defects in IBA57 can produce diverse phenotypes. IBA57 should be considered a candidate gene for cavitating leukoencephalopathy.}, }
@article {pmid28667781, year = {2018}, author = {Papadopoulos, V and Fan, J and Zirkin, B}, title = {Translocator protein (18 kDa): an update on its function in steroidogenesis.}, journal = {Journal of neuroendocrinology}, volume = {30}, number = {2}, pages = {}, pmid = {28667781}, issn = {1365-2826}, support = {R01 AG021092/AG/NIA NIH HHS/United States ; R21 AG051259/AG/NIA NIH HHS/United States ; R37 AG021092/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Apoptosis/physiology ; Cell Proliferation/physiology ; Female ; Gonadal Steroid Hormones/*biosynthesis ; Male ; Mice ; Mitochondria/*metabolism ; Receptors, GABA/*metabolism ; }, abstract = {Translocator protein (18 kDa) (TSPO) is a ubiquitous mitochondrial protein. Studies of its responses to drug and endogenous ligands have shown TSPO to be involved either directly or indirectly in numerous biological functions, including mitochondrial cholesterol transport and steroid hormone biosynthesis, porphyrin transport and heme synthesis, apoptosis, cell proliferation, and anion transport. Localised to the outer mitochondrial membrane of steroidogenic cells, TSPO has been shown to associate with cytosolic and mitochondrial proteins as part of a large multiprotein complex involved in mitochondrial cholesterol transport, the rate-limiting step in steroidogenesis. There is general agreement as to the structure and pharmacology of TSPO. Stimulation of TSPO has been shown to have therapeutic use as anxiolytics by inducing allopregnanolone production in the brain, and also potentially for re-establishing androgen levels in hypogonadal ageing animals. Until recently, there has been general agreement regarding the role of TSPO in steroidogenesis. However, recent studies involving genetic depletion of TSPO in mice have created controversy about the role of this protein in steroid and heme synthesis. We review the data on the structure and function of TSPO, as well as the recent results obtained using various genetic animal models. Taken together, these studies suggest that TSPO is a unique mitochondrial pharmacological target for diseases that involve increased mitochondrial activity, including steroidogenesis. Although there is no known mammalian species that lacks TSPO, it is likely that, because of the importance of this ancient protein in evolution and mitochondrial function, redundant mechanisms may exist to replace it under circumstances when it is removed.}, }
@article {pmid28667281, year = {2017}, author = {Yang, F and Jiang, Y and Yang, D and Liu, X}, title = {Mitochondrial genomes of two Australian fishflies with an evolutionary timescale of Chauliodinae.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4481}, pmid = {28667281}, issn = {2045-2322}, mesh = {Animals ; Australia ; Base Composition ; Codon ; Computational Biology/methods ; *Evolution, Molecular ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Genomics/methods ; Insecta/*classification/*genetics ; Mitochondria/genetics ; Nucleic Acid Conformation ; Phylogeny ; }, abstract = {Fishflies (Corydalidae: Chauliodinae) with a total of ca. 130 extant species are one of the major groups of the holometabolous insect order Megaloptera. As a group which originated during the Mesozoic, the phylogeny and historical biogeography of fishflies are of high interest. The previous hypothesis on the evolutionary history of fishflies was based primarily on morphological data. To further test the existing phylogenetic relationships and to understand the divergence pattern of fishflies, we conducted a molecule-based study. We determined the complete mitochondrial (mt) genomes of two Australian fishfly species, Archichauliodes deceptor Kimmins, 1954 and Protochauliodes biconicus Kimmins, 1954, both members of a major subgroup of Chauliodinae with high phylogenetic significance. A phylogenomic analysis was carried out based on 13 mt protein coding genes (PCGs) and two rRNAs genes from the megalopteran species with determined mt genomes. Both maximum likelihood and Bayesian inference analyses recovered the Dysmicohermes clade as the sister group of the Archichauliodes clade + the Protochauliodes clade, which is consistent with the previous morphology-based hypothesis. The divergence time estimation suggested that the divergence among the three major subgroups of fishflies occurred during the Late Jurassic and Early Cretaceous when the supercontinent Pangaea was undergoing sequential breakup.}, }
@article {pmid28665258, year = {2017}, author = {Hu, JJ and Huang, S and Wen, T and Esch, GW and Liang, Y and Li, HL}, title = {Morphology, Molecular Characteristics, and Demonstration of a Definitive Host for Sarcocystis rommeli from Cattle (Bos taurus) in China.}, journal = {The Journal of parasitology}, volume = {103}, number = {5}, pages = {471-476}, doi = {10.1645/16-187}, pmid = {28665258}, issn = {1937-2345}, mesh = {Animals ; Cat Diseases/parasitology ; Cats ; Cattle ; Cattle Diseases/*parasitology ; China ; Cloning, Molecular ; DNA, Protozoan/chemistry/isolation &amp; purification ; Electron Transport Complex IV/genetics ; Feces/parasitology ; Intestine, Small/parasitology ; Life Cycle Stages ; Microscopy, Electron, Transmission/veterinary ; Mitochondria/enzymology ; Phylogeny ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal, 18S/genetics ; Sarcocystis/classification/*genetics/growth &amp; development/*ultrastructure ; Sarcocystosis/parasitology/*veterinary ; Sequence Alignment/veterinary ; Sequence Analysis, DNA ; }, abstract = {Sarcocysts of Sarcocystis rommeli were found for the first time in 6 of 34 (17.6%) cattle (Bos taurus) in China. With light microscopy, sarcocysts of S. rommeli were up to 1,130 μm long, with a striated, 4-8-μm-thick cyst wall. Using transmission electron microscopy, the villar protrusions (vp) were 4.7-5.2 × 0.2-0.3 μm, and 0.3-0.5 μm apart from each other. The vp contained microtubules extending from the top of the vp to the middle of the ground substance layer (gsl). A BLAST search of the near full-length 18S rRNA and partial mitochondrial cox1 sequences of S. rommeli revealed 98.7% identity and 99.2% identity with sequences of Sarcocystis bovini in GenBank, respectively. Two domestic cats (Felis catus) fed sarcocysts of S. rommeli shed oocysts/sporocysts in their feces with a prepatent period of 14 to 15 days; the partial mitochondrial cox1 sequences of these oocysts/sporocysts shared the high identities, that is, 99.4% and 99.5%, with cox1 sequences of S. rommeli sarcocysts and S. bovini sarcocysts, respectively. This is the first demonstration of a definitive host for S. rommeli.}, }
@article {pmid28657486, year = {2018}, author = {Suk, HY and Lee, MY and Bae, HG and Lee, SJ and Poyarkov, N and Lee, H and Min, MS}, title = {Phylogenetic structure and ancestry of Korean clawed salamander, Onychodactylus koreanus (Caudata: Hynobiidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {650-658}, doi = {10.1080/24701394.2017.1339187}, pmid = {28657486}, issn = {2470-1408}, mesh = {Animals ; China ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Genes, Mitochondrial ; *Genetic Speciation ; *Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Republic of Korea ; Species Specificity ; Urodela/*genetics ; }, abstract = {Onychodactylus koreanus, a hynobiid salamander species endemic to the Korean Peninsula, can be regarded as a strict ecological specialist, probably vulnerable to anthropogenic environmental modifications and climate change. We used mitochondrial cytochrome b gene to analyze the genetic diversity and phylogenetic structure of O. koreanus from 19 populations collected in an attempt to cover its major distribution within South Korea. A total of 76 haplotypes of O. koreanus obtained in our analyses could be subdivided into three phylogenetic clades, KR, NE and SE. Clade KR haplotypes occur in most of the regions throughout the Korean Peninsula with four distinct subclades (KR I-IV). Clade NE and SE haplotypes were only observed in two populations YY and YS, respectively. Haplotype sharing was scarce even among populations in geographical proximity, and most of the populations were represented by a single clade or subclade, indicating the low level of gene flow among populations. O. koreanus likely originated from the historical southward dispersal of its ancestral lineages following divergence from Chinese O. zhaoermii that was recovered as the sister of O. koreanus in our phylogenetic analysis. Our results have critical implications for the taxonomic status of O. koreanus and its long-term management plan.}, }
@article {pmid28655921, year = {2017}, author = {Liu, H and Li, H and Song, F and Gu, W and Feng, J and Cai, W and Shao, R}, title = {Novel insights into mitochondrial gene rearrangement in thrips (Insecta: Thysanoptera) from the grass thrips, Anaphothrips obscurus.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4284}, pmid = {28655921}, issn = {2045-2322}, mesh = {Animals ; Evolution, Molecular ; *Gene Rearrangement ; Genes, Mitochondrial ; Genome, Mitochondrial ; Genomics/methods ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; Thysanoptera/classification/*genetics ; }, abstract = {We sequenced the mitochondrial (mt) genome of the grass thrips, Anaphothrips obscurus, which is highly rearranged and differs from the four thrips species reported previously in the arrangement of both tRNA genes and a protein-coding gene, nad3, and in the copy number of the control region (CR). We reconstructed the phylogeny of the thrips with mt genome sequences, and used it as a framework to gain insights into mt genome evolution in thrips. It is evident that A. obscurus is less rearranged in mt genome organization than the other four known thrips. nad3 is in its ancestral location in A. obscurus but was translocated in other four thrips. Also, A. obscurus has one CR, which is ancestral to hexapods whereas other thrips have two or three CRs. All of the five thrips whose mt genomes have been sequenced to date are from the subfamily Thripinae, which represents about a quarter of the species richness in the order Thysanoptera. The high variation in mt genome organization observed in a subfamily challenges our knowledge about animal mt genomes. It remains to be investigated why mt genomes evolved so fast in the subfamily Thripinae and how mt genomes evolved in other lineages of thrips.}, }
@article {pmid28655915, year = {2017}, author = {Bernardino, AF and Li, Y and Smith, CR and Halanych, KM}, title = {Multiple introns in a deep-sea Annelid (Decemunciger: Ampharetidae) mitochondrial genome.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4295}, pmid = {28655915}, issn = {2045-2322}, mesh = {Animals ; Annelida/classification/*genetics ; Genes, Mitochondrial ; *Genome, Mitochondrial ; *Introns ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Wood falls provide episodic fluxes of energy to the sea floor that are degraded by a species-rich benthic fauna. Part of this rich diversity includes annelid polychaetes but unfortunately, our understanding of such fauna is limited and their genetic variability and evolutionary origins remain poorly known. In this study, we sequenced complete mitochondrial genomes from three congeneric Decemunciger (Ampharetidae) individuals that had colonized multiple wood falls in the deep (~1600 m) NE Pacific Ocean. Mitochondrial gene order within Decemunciger was similar to the three other available Terebellomorpha genomes, consistent with the relatively conserved nature of mitochondrial genomes within annelids. Unexpectedly, we found introns within the cox1, nad1 and nad4 genes of all three genomes assembled. This is the greatest number of introns observed in annelid mtDNA genomes, and possibly in bilaterians. Interestingly, the introns were of variable sizes suggesting possible evolutionary differences in the age and origins of introns. The sequence of the introns within cox1 is similar to Group II introns previously identified, suggesting that introns in the mitochondrial genome of annelids may be more widespread then realized. Phylogenetically, Decemunciger appears to be a sister clade among current vent and seep deep-sea Ampharetinae.}, }
@article {pmid28655342, year = {2017}, author = {Li, WX and Zhang, D and Boyce, K and Xi, BW and Zou, H and Wu, SG and Li, M and Wang, GT}, title = {The complete mitochondrial DNA of three monozoic tapeworms in the Caryophyllidea: a mitogenomic perspective on the phylogeny of eucestodes.}, journal = {Parasites &amp; vectors}, volume = {10}, number = {1}, pages = {314}, pmid = {28655342}, issn = {1756-3305}, mesh = {Animals ; Cestoda/*genetics ; Cestode Infections/parasitology/*veterinary ; DNA, Mitochondrial/genetics ; Fish Diseases/*parasitology ; Fishes ; *Gene Order ; Gene Rearrangement ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/veterinary ; }, abstract = {BACKGROUND: External segmentation and internal proglottization are important evolutionary characters of the Eucestoda. The monozoic caryophyllideans are considered the earliest diverging eucestodes based on partial mitochondrial genes and nuclear rDNA sequences, yet, there are currently no complete mitogenomes available. We have therefore sequenced the complete mitogenomes of three caryophyllideans, as well as the polyzoic Schyzocotyle acheilognathi, explored the phylogenetic relationships of eucestodes and compared the gene arrangements between unsegmented and segmented cestodes.<br><br>RESULTS: The circular mitogenome of Atractolytocestus huronensis was 15,130&#xa0;bp, the longest sequence of all the available cestodes, 14,620&#xa0;bp for Khawia sinensis, 14,011&#xa0;bp for Breviscolex orientalis and 14,046&#xa0;bp for Schyzocotyle acheilognathi. The A-T content of the three caryophyllideans was found to be lower than any other published mitogenome. Highly repetitive regions were detected among the non-coding regions (NCRs) of the four cestode species. The evolutionary relationship determined between the five orders (Caryophyllidea, Diphyllobothriidea, Bothriocephalidea, Proteocephalidea and Cyclophyllidea) is consistent with that expected from morphology and the large fragments of mtDNA when reconstructed using all 36 genes. Examination of the 54 mitogenomes from these five orders, revealed a unique arrangement for each order except for the Cyclophyllidea which had two types that were identical to that of the Diphyllobothriidea and the Proteocephalidea. When comparing gene order between the unsegmented and segmented cestodes, the segmented cestodes were found to have the lower similarities due to a long distance transposition event. All rearrangement events between the four arrangement categories took place at the junction of rrnS-tRNA [Arg] (P1) where NCRs are common.<br><br>CONCLUSIONS: Highly repetitive regions are detected among NCRs of the four cestode species. A long distance transposition event is inferred between the unsegmented and segmented cestodes. Gene arrangements of Taeniidae and the rest of the families in the Cyclophyllidea are found be identical to those of the sister order Proteocephalidea and the relatively basal order Diphyllobothriidea, respectively.}, }
@article {pmid28655155, year = {2017}, author = {Lau, GY and Mandic, M and Richards, JG}, title = {Evolution of Cytochrome c Oxidase in Hypoxia Tolerant Sculpins (Cottidae, Actinopterygii).}, journal = {Molecular biology and evolution}, volume = {34}, number = {9}, pages = {2153-2162}, doi = {10.1093/molbev/msx179}, pmid = {28655155}, issn = {1537-1719}, mesh = {Animals ; Electron Transport/physiology ; Electron Transport Complex IV/*genetics/*metabolism ; Hypoxia/genetics/metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Oxygen/*metabolism ; Perciformes/genetics/metabolism ; Phylogeny ; Protein Structural Elements ; Protein Structure, Tertiary ; Pyrones ; Respiration/genetics ; }, abstract = {Vertebrate hypoxia tolerance can emerge from modifications to the oxygen (O2) transport cascade, but whether there is adaptive variation to O2 binding at the terminus of this cascade, mitochondrial cytochrome c oxidase (COX), is not known. In order to address the hypothesis that hypoxia tolerance is associated with enhanced O2 binding by mitochondria we undertook a comparative analysis of COX O2 kinetics across species of intertidal sculpins (Cottidae, Actinopterygii) that vary in hypoxia tolerance. Our analysis revealed a significant relationship between hypoxia tolerance (critical O2 tension of O2 consumption rate; Pcrit), mitochondrial O2 binding affinity (O2 tension at which mitochondrial respiration was half maximal; P50), and COX O2-binding affinity (apparent Michaelis-Menten constant for O2 binding to COX; Km,app O2). The more hypoxia tolerant species had both a lower mitochondrial P50 and lower COX Km,app O2, facilitating the maintenance of mitochondrial function to a lower O2 tension than in hypoxia intolerant species. Additionally, hypoxia tolerant species had a lower overall COX Vmax but higher mitochondrial COX respiration rate when expressed relative to maximal electron transport system respiration rate. In silico analyses of the COX3 subunit postulated as the entry point for O2 into the COX protein catalytic core, points to variation in COX3 protein stability (estimated as free energy of unfolding) contributing to the variation in COX Km,app O2. We propose that interactions between COX3 and cardiolipin at four amino acid positions along the same alpha-helix forming the COX3 v-cleft represent likely determinants of interspecific differences in COX Km,app O2.}, }
@article {pmid28651548, year = {2017}, author = {Thai, QK and Chung, DA and Tran, HD}, title = {Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database.}, journal = {BMC genetics}, volume = {18}, number = {1}, pages = {60}, pmid = {28651548}, issn = {1471-2156}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Databases, Genetic ; Genetic Variation ; *Haplotypes ; *Internet ; Mitochondria/genetics ; Phylogeny ; Wolves/*genetics ; }, abstract = {BACKGROUND: Canine and wolf mitochondrial DNA haplotypes, which can be used for forensic or phylogenetic analyses, have been defined in various schemes depending on the region analyzed. In recent studies, the 582 bp fragment of the HV1 region is most commonly used. 317 different canine HV1 haplotypes have been reported in the rapidly growing public database GenBank. These reported haplotypes contain several inconsistencies in their haplotype information. To overcome this issue, we have developed a Canis mtDNA HV1 database. This database collects data on the HV1 582 bp region in dog mitochondrial DNA from the GenBank to screen and correct the inconsistencies. It also supports users in detection of new novel mutation profiles and assignment of new haplotypes.<br><br>DESCRIPTION: The Canis mtDNA HV1 database (CHD) contains 5567 nucleotide entries originating from 15 subspecies in the species Canis lupus. Of these entries, 3646 were haplotypes and grouped into 804 distinct sequences. 319 sequences were recognized as previously assigned haplotypes, while the remaining 485 sequences had new mutation profiles and were marked as new haplotype candidates awaiting further analysis for haplotype assignment. Of the 3646 nucleotide entries, only 414 were annotated with correct haplotype information, while 3232 had insufficient or lacked haplotype information and were corrected or modified before storing in the CHD. The CHD can be accessed at http://chd.vnbiology.com . It provides sequences, haplotype information, and a web-based tool for mtDNA HV1 haplotyping. The CHD is updated monthly and supplies all data for download.<br><br>CONCLUSIONS: The Canis mtDNA HV1 database contains information about canine mitochondrial DNA HV1 sequences with reconciled annotation. It serves as a tool for detection of inconsistencies in GenBank and helps identifying new HV1 haplotypes. Thus, it supports the scientific community in naming new HV1 haplotypes and to reconcile existing annotation of HV1 582&#xa0;bp sequences.}, }
@article {pmid28651540, year = {2017}, author = {Srirattana, K and McCosker, K and Schatz, T and St John, JC}, title = {Cattle phenotypes can disguise their maternal ancestry.}, journal = {BMC genetics}, volume = {18}, number = {1}, pages = {59}, pmid = {28651540}, issn = {1471-2156}, mesh = {Animals ; Cattle/classification/*genetics/physiology ; Cells, Cultured ; DNA, Mitochondrial/*genetics ; Embryo, Mammalian/cytology/metabolism ; Female ; Genetic Speciation ; *Maternal Inheritance ; Mitochondria/genetics ; Oocytes/cytology/metabolism ; *Phenotype ; Phylogeny ; }, abstract = {BACKGROUND: Cattle are bred for, amongst other factors, specific traits, including parasite resistance and adaptation to climate. However, the influence and inheritance of mitochondrial DNA (mtDNA) are not usually considered in breeding programmes. In this study, we analysed the mtDNA profiles of cattle from Victoria (VIC), southern Australia, which is a temperate climate, and the Northern Territory (NT), the northern part of Australia, which has a tropical climate, to determine if the mtDNA profiles of these cattle are indicative of breed and phenotype, and whether these profiles are appropriate for their environments.<br><br>RESULTS: A phylogenetic tree of the full mtDNA sequences of different breeds of cattle, which were obtained from the NCBI database, showed that the mtDNA profiles of cattle do not always reflect their phenotype as some cattle with Bos taurus phenotypes had Bos indicus mtDNA, whilst some cattle with Bos indicus phenotypes had Bos taurus mtDNA. Using D-loop sequencing, we were able to contrast the phenotypes and mtDNA profiles from different species of cattle from the 2 distinct cattle breeding regions of Australia. We found that 67 of the 121 cattle with Bos indicus phenotypes from NT (55.4%) had Bos taurus mtDNA. In VIC, 92 of the 225 cattle with Bos taurus phenotypes (40.9%) possessed Bos indicus mtDNA. When focusing on oocytes from cattle with the Bos taurus phenotype in VIC, their respective oocytes with Bos indicus mtDNA had significantly lower levels of mtDNA copy number compared with oocytes possessing Bos taurus mtDNA (P&#xa0;<&#xa0;0.01). However, embryos derived from oocytes with Bos indicus mtDNA had the same ability to develop to the blastocyst stage and the levels of mtDNA copy number in their blastocysts were similar to blastocysts derived from oocytes harbouring Bos taurus mtDNA. Nevertheless, oocytes originating from the Bos indicus phenotype exhibited lower developmental potential due to low mtDNA copy number when compared with oocytes from cattle with a Bos taurus phenotype.<br><br>CONCLUSIONS: The phenotype of cattle is not always related to their mtDNA profiles. MtDNA profiles should be considered for breeding programmes as they also influence phenotypic traits and reproductive capacity in terms of oocyte quality.}, }
@article {pmid28646582, year = {2017}, author = {Heiske, M and Letellier, T and Klipp, E}, title = {Comprehensive mathematical model of oxidative phosphorylation valid for physiological and pathological conditions.}, journal = {The FEBS journal}, volume = {284}, number = {17}, pages = {2802-2828}, doi = {10.1111/febs.14151}, pmid = {28646582}, issn = {1742-4658}, mesh = {Adenosine Triphosphate/biosynthesis ; Algorithms ; Animals ; Biocatalysis ; Cattle ; Kinetics ; Metabolic Flux Analysis ; Mitochondria, Heart/metabolism ; *Models, Biological ; *Oxidative Phosphorylation ; }, abstract = {We developed a mathematical model of oxidative phosphorylation (OXPHOS) that allows for a precise description of mitochondrial function with respect to the respiratory flux and the ATP production. The model reproduced flux-force relationships under various experimental conditions (state 3 and 4, uncoupling, and shortage of respiratory substrate) as well as time courses, exhibiting correct P/O ratios. The model was able to reproduce experimental threshold curves for perturbations of the respiratory chain complexes, the F1 F0 -ATP synthase, the ADP/ATP carrier, the phosphate/OH carrier, and the proton leak. Thus, the model is well suited to study complex interactions within the OXPHOS system, especially with respect to physiological adaptations or pathological modifications, influencing substrate and product affinities or maximal catalytic rates. Moreover, it could be a useful tool to study the role of OXPHOS and its capacity to compensate or enhance physiopathologies of the mitochondrial and cellular energy metabolism.}, }
@article {pmid28646188, year = {2017}, author = {Wang, J and Xiang, H and Liu, L and Kong, M and Yin, T and Zhao, X}, title = {Mitochondrial haplotypes influence metabolic traits across bovine inter- and intra-species cybrids.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4179}, pmid = {28646188}, issn = {2045-2322}, mesh = {Acids/metabolism ; Animals ; Cattle/*genetics ; DNA, Mitochondrial/genetics ; Female ; Gene Dosage ; Gene Expression Regulation ; Genome, Mitochondrial ; Haplotypes/*genetics ; Hybrid Cells/metabolism ; *Hybridization, Genetic ; Lipids/biosynthesis ; Mitochondria/*genetics/*metabolism ; Organelle Biogenesis ; Oxygen Consumption ; Phylogeny ; *Quantitative Trait, Heritable ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {In bovine species, mitochondrial DNA polymorphisms and their correlation to productive or reproductive performances have been widely reported across breeds and individuals. However, experimental evidence of this correlation has never been provided. In order to identify differences among bovine mtDNA haplotypes, transmitochondrial cybrids were generated, with the nucleus from MAC-T cell line, derived from a Holstein dairy cow (Bos taurus) and mitochondria from either primary cell line derived from a domestic Chinese native beef Luxi cattle breed or central Asian domestic yak (Bos grunniens). Yak primary cells illustrated a stronger metabolic capacity than that of Luxi. However, all yak cybrid parameters illustrated a drop in relative yak mtDNA compared to Luxi mtDNA, in line with a mitonuclear imbalance in yak interspecies cybrid. Luxi has 250 divergent variations relative to the mitogenome of Holsteins. In cybrids there were generally higher rates of oxygen consumption (OCR) and extracellular acidification (ECAR), and lower mRNA expression levels of nuclear-encoded mitochondrial genes, potentially reflecting active energy metabolism and cellular stress resistance. The results demonstrate that functional differences exist between bovine cybrid cells. While cybrid viability was similar between Holstein and Luxi breeds, the mitonuclear mismatch caused a marked metabolic dysfunction in cattle:yak cybrid species.}, }
@article {pmid28640391, year = {2017}, author = {Christie, JR and Beekman, M}, title = {Selective sweeps of mitochondrial DNA can drive the evolution of uniparental inheritance.}, journal = {Evolution; international journal of organic evolution}, volume = {71}, number = {8}, pages = {2090-2099}, doi = {10.1111/evo.13291}, pmid = {28640391}, issn = {1558-5646}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Haplotypes ; Heredity ; Inheritance Patterns ; Mitochondria ; Mutation ; }, abstract = {Although the uniparental (or maternal) inheritance of mitochondrial DNA (mtDNA) is widespread, the reasons for its evolution remain unclear. Two main hypotheses have been proposed: selection against individuals containing different mtDNAs (heteroplasmy) and selection against "selfish" mtDNA mutations. Recently, uniparental inheritance was shown to promote adaptive evolution in mtDNA, potentially providing a third hypothesis for its evolution. Here, we explore this hypothesis theoretically and ask if the accumulation of beneficial mutations provides a sufficient fitness advantage for uniparental inheritance to invade a population in which mtDNA is inherited biparentally. In a deterministic model, uniparental inheritance increases in frequency but cannot replace biparental inheritance if only a single beneficial mtDNA mutation sweeps through the population. When we allow successive selective sweeps of mtDNA, however, uniparental inheritance can replace biparental inheritance. Using a stochastic model, we show that a combination of selection and drift facilitates the fixation of uniparental inheritance (compared to a neutral trait) when there is only a single selective mtDNA sweep. When we consider multiple mtDNA sweeps in a stochastic model, uniparental inheritance becomes even more likely to replace biparental inheritance. Our findings thus suggest that selective sweeps of beneficial mtDNA haplotypes can drive the evolution of uniparental inheritance.}, }
@article {pmid28637217, year = {2017}, author = {Camus, MF and Wolff, JN and Sgrò, CM and Dowling, DK}, title = {Experimental Support That Natural Selection Has Shaped the Latitudinal Distribution of Mitochondrial Haplotypes in Australian Drosophila melanogaster.}, journal = {Molecular biology and evolution}, volume = {34}, number = {10}, pages = {2600-2612}, doi = {10.1093/molbev/msx184}, pmid = {28637217}, issn = {1537-1719}, mesh = {Acclimatization/*genetics ; Adaptation, Physiological/genetics ; Altitude ; Animals ; Australia ; Biological Evolution ; Cold Temperature ; DNA, Mitochondrial/*genetics ; Drosophila melanogaster/*genetics ; Genetic Variation/genetics ; Haplotypes/genetics ; Hot Temperature ; Mitochondria/genetics ; Selection, Genetic/genetics ; Temperature ; }, abstract = {Cellular metabolism is regulated by enzyme complexes within the mitochondrion, the function of which are sensitive to the prevailing temperature. Such thermal sensitivity, coupled with the observation that population frequencies of mitochondrial haplotypes tend to associate with latitude, altitude, or climatic regions across species distributions, led to the hypothesis that thermal selection has played a role in shaping standing variation in the mitochondrial DNA (mtDNA) sequence. This hypothesis, however, remains controversial, and requires evidence that the distribution of haplotypes observed in nature corresponds with the capacity of these haplotypes to confer differences in thermal tolerance. Specifically, haplotypes predominating in tropical climates are predicted to encode increased tolerance to heat stress, but decreased tolerance to cold stress. We present direct evidence for these predictions, using mtDNA haplotypes sampled from the Australian distribution of Drosophila melanogaster. We show that the ability of flies to tolerate extreme thermal challenges is affected by sequence variation across mtDNA haplotypes, and that the thermal performance associated with each haplotype corresponds with its latitudinal prevalence. The haplotype that predominates at low (subtropical) latitudes confers greater resilience to heat stress, but lower resilience to cold stress, than haplotypes predominating at higher (temperate) latitudes. We explore molecular mechanisms that might underlie these responses, presenting evidence that the effects are in part regulated by SNPs that do not change the protein sequence. Our findings suggest that standing variation in the mitochondrial genome can be shaped by thermal selection, and could therefore contribute to evolutionary adaptation under climatic stress.}, }
@article {pmid28629794, year = {2017}, author = {Rey, B and Duchamp, C and Roussel, D}, title = {Uncoupling effect of palmitate is exacerbated in skeletal muscle mitochondria of sea-acclimatized king penguins (Aptenodytes patagonicus).}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {211}, number = {}, pages = {56-60}, doi = {10.1016/j.cbpa.2017.06.009}, pmid = {28629794}, issn = {1531-4332}, mesh = {*Adaptation, Physiological ; Animals ; Dose-Response Relationship, Drug ; Mitochondria, Muscle/*drug effects/metabolism ; Muscle, Skeletal/*drug effects/metabolism ; Oxygen Consumption ; Palmitic Acid/*pharmacology ; Spheniscidae/*metabolism/physiology ; }, abstract = {In king penguin juveniles, the environmental transition from a terrestrial to a marine habitat, occurring at fledging, drastically stimulates lipid catabolism and the remodelling of muscle mitochondria to sustain extensive swimming activity and thermoregulation in the cold circumpolar oceans. However, the exact nature of these mechanisms remains only partially resolved. Here we investigated, in vitro, the uncoupling effect of increasing doses of fatty acids in pectoralis muscle intermyofibrillar mitochondria isolated, either from terrestrial never-immersed or experimentally cold water immersed pre-fledging king penguins or from sea-acclimatized fledged penguins. Mitochondria exhibited much greater palmitate-induced uncoupling respiration and higher maximal oxidative capacity after acclimatization to marine life. Such effects were not reproduced experimentally after repeated immersions in cold water, suggesting that the plasticity of mitochondrial characteristics may not be primarily driven by cold exposure per se but by other aspects of sea acclimatization.}, }
@article {pmid28622748, year = {2018}, author = {Iswarya Deepti, V and Kandula, S and Khedkar, GD}, title = {DNA barcoding of five species of groupers (Pisces: Serranidae) off Visakhapatnam, central eastern coast of India.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {5}, pages = {659-663}, doi = {10.1080/24701394.2017.1339188}, pmid = {28622748}, issn = {2470-1408}, mesh = {Animals ; Bass/*genetics ; DNA ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Genetic Speciation ; Genome, Mitochondrial/*genetics ; India ; Mitochondria/genetics ; Perciformes/genetics ; Phylogeny ; }, abstract = {Grouper species of Epinephelus - E. epistictus, E. heniochus, E. latifasciatus, E. magniscuttis and E. radiatus exhibit overlapping colour pattern that often leads to misidentification in the field. Even the colour pattern of juveniles of these species in different size groups varies considerably with that of adults. DNA barcoding of these five species was carried out to reinforce our knowledge on existing taxonomic relationships derived based on morphological and biochemical genetic studies that were previously done from Indian waters. Mean interspecific genetic distance is in the range 0.079-0.164.The phylogeny tree revealed distinct clades for species that are in concurrence with previous taxonomic and allozyme electrophoretic studies carried out from central eastern coast of India. Barcode sequences generated for the first time for species E. heniochus from Indian waters for E. magniscuttis so far there are no reference sequences in GenBank.}, }
@article {pmid28615286, year = {2017}, author = {Martin, WF and Tielens, AGM and Mentel, M and Garg, SG and Gould, SB}, title = {The Physiology of Phagocytosis in the Context of Mitochondrial Origin.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {81}, number = {3}, pages = {}, pmid = {28615286}, issn = {1098-5557}, mesh = {Adenosine Triphosphate/metabolism ; Archaea/genetics ; Biological Evolution ; Endocytosis/physiology ; Energy Metabolism ; Eukaryotic Cells/*physiology ; Metagenomics ; Mitochondria/*physiology ; Phagocytosis/*physiology ; Phylogeny ; Prokaryotic Cells/*physiology ; Symbiosis ; }, abstract = {How mitochondria came to reside within the cytosol of their host has been debated for 50 years. Though current data indicate that the last eukaryote common ancestor possessed mitochondria and was a complex cell, whether mitochondria or complexity came first in eukaryotic evolution is still discussed. In autogenous models (complexity first), the origin of phagocytosis poses the limiting step at eukaryote origin, with mitochondria coming late as an undigested growth substrate. In symbiosis-based models (mitochondria first), the host was an archaeon, and the origin of mitochondria was the limiting step at eukaryote origin, with mitochondria providing bacterial genes, ATP synthesis on internalized bioenergetic membranes, and mitochondrion-derived vesicles as the seed of the eukaryote endomembrane system. Metagenomic studies are uncovering new host-related archaeal lineages that are reported as complex or phagocytosing, although images of such cells are lacking. Here we review the physiology and components of phagocytosis in eukaryotes, critically inspecting the concept of a phagotrophic host. From ATP supply and demand, a mitochondrion-lacking phagotrophic archaeal fermenter would have to ingest about 34 times its body weight in prokaryotic prey to obtain enough ATP to support one cell division. It would lack chemiosmotic ATP synthesis at the plasma membrane, because phagocytosis and chemiosmosis in the same membrane are incompatible. It would have lived from amino acid fermentations, because prokaryotes are mainly protein. Its ATP yield would have been impaired relative to typical archaeal amino acid fermentations, which involve chemiosmosis. In contrast, phagocytosis would have had great physiological benefit for a mitochondrion-bearing cell.}, }
@article {pmid28608363, year = {2017}, author = {Moulinier, L and Ripp, R and Castillo, G and Poch, O and Sissler, M}, title = {MiSynPat: An integrated knowledge base linking clinical, genetic, and structural data for disease-causing mutations in human mitochondrial aminoacyl-tRNA synthetases.}, journal = {Human mutation}, volume = {38}, number = {10}, pages = {1316-1324}, pmid = {28608363}, issn = {1098-1004}, mesh = {Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/chemistry/*genetics ; *Databases, Genetic ; Evolution, Molecular ; Genetic Diseases, Inborn/genetics ; Humans ; Mitochondria/*enzymology/genetics ; Molecular Structure ; Mutation/*genetics ; Protein Conformation ; }, abstract = {Numerous mutations in each of the mitochondrial aminoacyl-tRNA synthetases (aaRSs) have been implicated in human diseases. The mutations are autosomal and recessive and lead mainly to neurological disorders, although with pleiotropic effects. The processes and interactions that drive the etiology of the disorders associated with mitochondrial aaRSs (mt-aaRSs) are far from understood. The complexity of the clinical, genetic, and structural data requires concerted, interdisciplinary efforts to understand the molecular biology of these disorders. Toward this goal, we designed MiSynPat, a comprehensive knowledge base together with an ergonomic Web server designed to organize and access all pertinent information (sequences, multiple sequence alignments, structures, disease descriptions, mutation characteristics, original literature) on the disease-linked human mt-aaRSs. With MiSynPat, a user can also evaluate the impact of a possible mutation on sequence-conservation-structure in order to foster the links between basic and clinical researchers and to facilitate future diagnosis. The proposed integrated view, coupled with research on disease-related mt-aaRSs, will help to reveal new functions for these enzymes and to open new vistas in the molecular biology of the cell. The purpose of MiSynPat, freely available at http://misynpat.org, is to constitute a reference and a converging resource for scientists and clinicians.}, }
@article {pmid28607415, year = {2017}, author = {Hofmann, S and Stöck, M and Zheng, Y and Ficetola, FG and Li, JT and Scheidt, U and Schmidt, J}, title = {Molecular Phylogenies indicate a Paleo-Tibetan Origin of Himalayan Lazy Toads (Scutiger).}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3308}, pmid = {28607415}, issn = {2045-2322}, mesh = {Animals ; Anura/*classification ; Calibration ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Genetic Markers ; Geography ; Mitochondria/genetics ; *Phylogeny ; Tibet ; Time Factors ; }, abstract = {The Himalaya presents an outstanding geologically active orogen and biodiversity hotspot. However, our understanding of the historical biogeography of its fauna is far from comprehensive. Many taxa are commonly assumed to have originated from China-Indochina and dispersed westward along the Himalayan chain. Alternatively, the "Tibetan-origin hypothesis" suggests primary diversification of lineages in Paleo-Tibet, and secondary diversification along the slopes of the later uplifted Greater Himalaya. We test these hypotheses in high-mountain megophryid anurans (Scutiger). Extensive sampling from High Asia, and analyses of mitochondrial (2839 bp) and nuclear DNA (2208 bp), using Bayesian and Maximum likelihood phylogenetics, suggest that the Himalayan species form a distinct clade, possibly older than those from the eastern Himalaya-Tibet orogen. While immigration from China-Indochina cannot be excluded, our data may indicate that Himalayan Scutiger originated to the north of the Himalaya by colonization from Paleo-Tibet and then date back to the Oligocene. High intraspecific diversity of Scutiger implies limited migration across mountains and drainages along the Himalaya. While our study strengthens support for a "Tibetan-origin hypothesis", current sampling (10/22 species; 1 revalidated: S. occidentalis) remains insufficient to draw final conclusions on Scutiger but urges comparative phylogeographers to test alternative, geologically supported hypotheses for a true future understanding of Himalayan biogeography.}, }
@article {pmid28606446, year = {2017}, author = {Dennerlein, S and Wang, C and Rehling, P}, title = {Plasticity of Mitochondrial Translation.}, journal = {Trends in cell biology}, volume = {27}, number = {10}, pages = {712-721}, doi = {10.1016/j.tcb.2017.05.004}, pmid = {28606446}, issn = {1879-3088}, mesh = {Animals ; Humans ; Mitochondria/*metabolism/*physiology ; Mitochondrial Proteins/*metabolism ; Multienzyme Complexes/metabolism ; Nuclear Proteins/metabolism ; Oxidative Phosphorylation ; Protein Biosynthesis/*physiology ; Protein Transport/physiology ; RNA, Messenger/metabolism ; Ribosomes/metabolism/physiology ; }, abstract = {Mitochondria maintained a genome during evolution to synthesize core subunits of the oxidative phosphorylation system. Expression of the mitochondrial genome requires intraorganellar replication, transcription, and translation. Membrane-associated ribosomes translate mitochondrial-encoded proteins and facilitate co-translational insertion of newly synthesized polypeptides into the inner membrane. Considering that mitochondrial-encoded proteins assemble with imported, nuclear-encoded proteins into enzyme complexes of the oxidative phosphorylation system, it is expected that expression of mitochondrial genes should adapt to the availability of their nuclear-encoded partners. Recent work shows that mitochondrial translation is influenced by the cellular environment. We discuss how mitochondrial translation is affected by the cellular environment and propose models of translational plasticity that modulate mitochondrial translation in response to the availability of imported proteins.}, }
@article {pmid28606351, year = {2017}, author = {Powell, MJ and Letcher, PM and James, TY}, title = {Ultrastructural characterization of the host-parasite interface between Allomyces anomalus (Blastocladiomycota) and Rozella allomycis (Cryptomycota).}, journal = {Fungal biology}, volume = {121}, number = {6-7}, pages = {561-572}, doi = {10.1016/j.funbio.2017.03.002}, pmid = {28606351}, issn = {1878-6146}, mesh = {Fungi/*ultrastructure ; *Host-Parasite Interactions ; Microscopy, Electron ; Organelles/ultrastructure ; }, abstract = {Rozella allomycis is an obligate endoparasite of the water mold Allomyces and a member of a clade (= Opisthosporidia) sister to the traditional Fungi. Gaining insights into Rozella's development as a phylogenetically pivotal endoparasite can aid our understanding of structural adaptations and evolution of the Opisthosporidia clade, especially within the context of genomic information. The purpose of this study is to characterize the interface between R. allomycis and Allomyces anomalus. Electron microscopy of developing plasmodia of R. allomycis in host hyphae shows that the interface consists of three-membrane layers, interpreted as the parasite's plasma membrane (inner one layer) and a host cisterna (outer two layers). As sporangial and resting spore plasmodia develop, host mitochondria typically cluster at the surface of the parasite and eventually align parallel to the three-membrane layered interface. The parasite's mitochondria have only a few cristae and the mitochondrial matrix is sparse, clearly distinguishing parasite mitochondria from those of the host. Consistent with the expected organellar topology if the parasite plasmodia phagocytize host cytoplasm, phagocytic vacuoles are at first bounded by three-membrane layers with host-type mitochondria lining the inner membrane. Thus, Rozella's nutrition, at least in part, is phagotrophic in contrast to osmotrophic nutrition of traditional fungi.}, }
@article {pmid28606055, year = {2017}, author = {Le, VS and Dang, CC and Le, QS}, title = {Improved mitochondrial amino acid substitution models for metazoan evolutionary studies.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {136}, pmid = {28606055}, issn = {1471-2148}, mesh = {Amino Acid Substitution ; Animals ; Evolution, Molecular ; Humans ; Invertebrates/*genetics ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; *Models, Genetic ; *Phylogeny ; Sequence Homology, Amino Acid ; Vertebrates/*genetics ; }, abstract = {BACKGROUND: Amino acid substitution models play an essential role in inferring phylogenies from mitochondrial protein data. However, only few empirical models have been estimated from restricted mitochondrial protein data of a hundred species. The existing models are unlikely to represent appropriately the amino acid substitutions from hundred thousands metazoan mitochondrial protein sequences.<br><br>RESULTS: We selected 125,935 mitochondrial protein sequences from 34,448 species in the metazoan kingdom to estimate new amino acid substitution models targeting metazoa, vertebrates and invertebrate groups. The new models help to find significantly better likelihood phylogenies in comparison with the existing models. We noted remarkable distances from phylogenies with the existing models to the maximum likelihood phylogenies that indicate a considerable number of incorrect bipartitions in phylogenies with the existing models. Finally, we used the new models and mitochondrial protein data to certify that Testudines, Aves, and Crocodylia form one separated clade within amniotes.<br><br>CONCLUSIONS: We introduced new mitochondrial amino acid substitution models for metazoan mitochondrial proteins. The new models outperform the existing models in inferring phylogenies from metazoan mitochondrial protein data. We strongly recommend researchers to use the new models in analysing metazoan mitochondrial protein data.}, }
@article {pmid28605672, year = {2017}, author = {Tadokoro, R and Takahashi, Y}, title = {Intercellular transfer of organelles during body pigmentation.}, journal = {Current opinion in genetics &amp; development}, volume = {45}, number = {}, pages = {132-138}, doi = {10.1016/j.gde.2017.05.001}, pmid = {28605672}, issn = {1879-0380}, mesh = {Animals ; Cell Membrane/metabolism ; Exocytosis ; Keratinocytes/metabolism ; Melanocytes/*metabolism ; Melanosomes/metabolism ; Microscopy, Electron/methods ; Organelles/metabolism ; Pigmentation/*physiology ; Pseudopodia/metabolism ; Skin/*cytology ; }, abstract = {The intercellular transfer of the melanin-producing organelle, called melanosome, from melanocytes to adjacent keratinocytes, is largely responsible for the coat colors and skin pigmentation of amniotes (birds, reptiles, and mammals). Although several hypotheses of melanin-transfer were proposed mainly by in vitro studies and electron microscopies, how the melanosome transfer takes place in the actual skin remained unclear. With advances in technologies of gene manipulations and high-resolution microscopy that allow direct visualization of plasma membrane, we are beginning to understand the amazing behaviors and dynamics of melanocytes. Studies in melanosome transfer further provide a clue to understand a general principle of intercellular organelle transport, including the intercellular translocations of mitochondria.}, }
@article {pmid28602831, year = {2017}, author = {Turissini, DA and Gomez, OM and Teixeira, MM and McEwen, JG and Matute, DR}, title = {Species boundaries in the human pathogen Paracoccidioides.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {106}, number = {}, pages = {9-25}, pmid = {28602831}, issn = {1096-0937}, support = {R01 GM121750/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Mitochondrial/genetics ; Gene Flow ; Genetic Loci ; *Genetic Speciation ; Genome, Fungal ; Humans ; Microsatellite Repeats ; Mitochondria/genetics ; Paracoccidioides/*classification/*genetics ; Phylogeny ; Polymorphism, Genetic ; Recombination, Genetic ; Sequence Analysis, DNA ; Statistics, Nonparametric ; }, abstract = {The use of molecular taxonomy for identifying recently diverged species has transformed the study of speciation in fungi. The pathogenic fungus Paracoccidioides spp has been hypothesized to be composed of five phylogenetic species, four of which compose the brasiliensis species complex. Nuclear gene genealogies support this divergence scenario, but mitochondrial loci do not; while all species from the brasiliensis complex are differentiated at nuclear coding loci, they are not at mitochondrial loci. We addressed the source of this incongruity using 11 previously published gene fragments, 10 newly-sequenced nuclear non-coding loci, and 10 microsatellites. We hypothesized and further demonstrated that the mito-nuclear incongruence in the brasiliensis species complex results from interspecific hybridization and mitochondrial introgression, a common phenomenon in eukaryotes. Additional population genetic analyses revealed possible nuclear introgression but much less than that seen in the mitochondrion. Our results are consistent with a divergence scenario of secondary contact and subsequent mitochondrial introgression despite the continued persistence of species boundaries. We also suggest that yeast morphology slightly-but significantly-differs across all five Paracoccidioides species and propose to elevate four of these phylogenetic species to formally described taxonomic species.}, }
@article {pmid28602572, year = {2017}, author = {van Riemsdijk, I and Arntzen, JW and Bogaerts, S and Franzen, M and Litvinchuk, SN and Olgun, K and Wielstra, B}, title = {The Near East as a cradle of biodiversity: A phylogeography of banded newts (genus Ommatotriton) reveals extensive inter- and intraspecific genetic differentiation.}, journal = {Molecular phylogenetics and evolution}, volume = {114}, number = {}, pages = {73-81}, doi = {10.1016/j.ympev.2017.05.028}, pmid = {28602572}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; *Biodiversity ; Biological Evolution ; Cytochromes b/classification/genetics ; Electron Transport Complex IV/classification/genetics ; Fossils ; Gene Flow ; *Genetic Variation ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Population Dynamics ; Salamandridae/*classification/genetics ; }, abstract = {The banded newt (genus Ommatotriton) is widely distributed in the Near East (Anatolia, Caucasus and the Levant) - an understudied region from the perspective of phylogeography. The genus is polytypic, but the number of species included and the phylogenetic relationships between them are not settled. We sequenced two mitochondrial and two nuclear DNA markers throughout the range of Ommatotriton. For mtDNA we constructed phylogenetic trees, estimated divergence times using fossil calibration, and investigated changes in effective population size with Bayesian skyline plots and mismatch analyses. For nuDNA we constructed phylogenetic trees and haplotype networks. Species trees were constructed for all markers and nuDNA only. Species distribution models were projected on current and Last Glacial Maximum climate layers. We confirm the presence of three Ommatotriton species: O. nesterovi, O. ophryticus and O. vittatus. These species are genetically distinct and their most recent common ancestor was dated at ∼25Ma (Oligocene). No evidence of recent gene flow between species was found. The species show deep intraspecific genetic divergence, represented by geographically structured clades, with crown nodes of species dated ∼8-13Ma (Miocene to Early Quaternary); evidence of long-term in situ evolution and survival in multiple glacial refugia. While a species tree based on nuDNA suggested a sister species relationship between O. vittatus and O. ophryticus, when mtDNA was included, phylogenetic relationships were unresolved, and we refrain from accepting a particular phylogenetic hypothesis at this stage. While species distribution models suggest reduced and fragmented ranges during the Last Glacial Maximum, we found no evidence for strong population bottlenecks. We discuss our results in the light of other phylogeographic studies from the Near East. Our study underlines the important role of the Near East in generating and sustaining biodiversity.}, }
@article {pmid28599069, year = {2017}, author = {Wang, L and Feng, C and Zheng, X and Guo, Y and Zhou, F and Shan, D and Liu, X and Kong, J}, title = {Plant mitochondria synthesize melatonin and enhance the tolerance of plants to drought stress.}, journal = {Journal of pineal research}, volume = {63}, number = {3}, pages = {}, doi = {10.1111/jpi.12429}, pmid = {28599069}, issn = {1600-079X}, mesh = {Amino Acid Sequence ; Arabidopsis ; Arylalkylamine N-Acetyltransferase/genetics/*metabolism ; Gene Expression Regulation, Plant ; Malus/*enzymology/genetics ; Melatonin/*biosynthesis ; Mitochondria/*enzymology ; *Oxidative Stress ; Phylogeny ; Plants, Genetically Modified ; Sequence Homology, Amino Acid ; }, abstract = {Synthesis of melatonin in mitochondria was reported in animals. However, there is no report on whether plant mitochondria also produce melatonin. Herein, we show that plant mitochondria are a major site for melatonin synthesis. In an in vitro study, isolated apple mitochondria had the capacity to generate melatonin. Subcellular localization analysis documented that an apple SNAT isoform, MzSNAT5, was localized in the mitochondria of both Arabidopsis protoplasts and apple callus cells. The kinetic analysis revealed that the recombinant MzSNAT5 protein exhibited high enzymatic activity to catalyze serotonin to N-acetylserotonin with the Km and Vmax of 55 μmol/L and 0.909 pmol/min/mg protein at 35°C, respectively; this pathway functioned over a wide range of temperatures from 5 to 75°C. In an in vivo study, MzSNAT5 was drought inducible. The transgenic Arabidopsis ectopically expressing MzSNAT5 elevated the melatonin level and, hence, enhanced drought tolerance. The mechanistic study indicated that the ectopically expressing MzSNAT5 allows plant mitochondria to increase melatonin synthesis. As a potent free radical scavenger, melatonin reduces the oxidative stress caused by the elevated reactive oxygen species which are generated under drought stress in plants. Our findings provide evidence that engineered melatonin-enriched plants exhibit enhanced oxidative tolerance.}, }
@article {pmid28596084, year = {2017}, author = {Ivanovic, Z}, title = {Stem cell evolutionary paradigm and cell engineering.}, journal = {Transfusion clinique et biologique : journal de la Societe francaise de transfusion sanguine}, volume = {24}, number = {3}, pages = {251-255}, doi = {10.1016/j.tracli.2017.05.004}, pmid = {28596084}, issn = {1953-8022}, mesh = {Aerobiosis ; Anaerobiosis ; Animals ; Atmosphere ; *Biological Evolution ; Cell Culture Techniques ; Cell Division ; *Cell Engineering ; Eukaryotic Cells/*cytology/metabolism ; Hematopoietic Stem Cells/*cytology/metabolism ; Humans ; Mesenchymal Stem Cells/*cytology/metabolism ; Metabolic Networks and Pathways ; Mitochondria/physiology ; Origin of Life ; Oxygen/metabolism ; }, abstract = {Studying hematopoietic and mesenchymal stem cells for almost three decades revealed some similarities between the stem cell entity and the single-celled eukaryotes exhibiting the anaerobic/facultative aerobic metabolic features. A careful analysis of nowadays knowledge concerning the early eukaryotic evolution allowed us to reveal some analogies between stem cells in the metazoan tissues and the single-celled eukaryotes which existed during the first phase of eukaryotes evolution in mid-Proterozoic era. In fact, it is possible to trace the principle of the self-renewal back to the first eukaryotic common ancestor, the first undifferentiated nucleated cell possessing the primitive, mostly anaerobically-respiring mitochondria and a capacity to reproduction by a simple cell division "à l'identique". Similarly, the diversification of these single-cell eukaryotes and acquiring of complex life cycle allowed/conditioned by the increase of O2 in atmosphere (and consequently in the water environment) represents a prototype for the phenomenon of commitment/differentiation. This point of view allowed to predict the ex-vivo behavior of stem cells with respect to the O2 availability and metabolic profile which enabled to conceive the successful protocols of stem cell expansion and ex vivo conditioning based on "respecting" this relationship between the anaerobiosis and stemness. In this review, the basic elements of this paradigm and a possible application in cell engineering were discussed.}, }
@article {pmid28595493, year = {2018}, author = {Gu, XB and Wang, BJ and Zhao, XB and Li, YF and Yang, GY and Lai, WM and Zhong, ZJ and Peng, GN}, title = {Genetic variation in mitochondrial cox2 of Heterakis gallinarum from poultry in Sichuan, China.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {629-634}, doi = {10.1080/24701394.2017.1334771}, pmid = {28595493}, issn = {2470-1408}, mesh = {Animals ; Ascaridida/*genetics/isolation &amp; purification ; Ascaridida Infections/parasitology ; Base Sequence ; Cecum/parasitology ; China ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Genetics, Population ; *Genome, Mitochondrial ; Haplotypes ; Mitochondria/enzymology/*genetics ; Phylogeny ; Poultry ; }, abstract = {Heterakis gallinarum is one of the common parasitic nematodes found in the caecum of poultry. To investigate the genetic diversity and genetic structure of the H. gallinarum population in Sichuan, we amplified and sequenced the complete mitochondrial (mt) cytochrome c oxidase subunit II (cox2) gene of 59 H. gallinarum isolates from seven different geographical regions, then analyzed their genetic polymorphisms. All cox2 genes of the 59 H. gallinarum isolates were 696 bp in length, with an average A + T content of 67.1%. Fifty-nine sequences contained 34 variable sites, and were classified into 23 haplotypes (HS1-HS23). The values of haplotype diversity (Hd) and nucleotide diversity (π) were 0.688 and 0.00288, respectively. Based on values of FST and Nm (FST = 0.01929, Nm = 12.71), there was a frequent gene flow but no significant genetic differentiation observed among the populations. The network map showed that the most prominent haplotype was HS1, and the other haplotypes (HS2-HS23) were centered on HS1 with a star-like topology, indicating that H. gallinarum had previously experienced a population expansion. To our knowledge, this is the first research on the population genetics of H. gallinarum based on mitochondrial cox2.}, }
@article {pmid28595327, year = {2017}, author = {Klink, GV and Bazykin, GA}, title = {Parallel Evolution of Metazoan Mitochondrial Proteins.}, journal = {Genome biology and evolution}, volume = {9}, number = {5}, pages = {1341-1350}, pmid = {28595327}, issn = {1759-6653}, mesh = {Alleles ; Amino Acid Substitution ; Amino Acids/*genetics ; Animals ; *Epistasis, Genetic ; *Evolution, Molecular ; Mitochondrial Proteins/*genetics ; Models, Genetic ; *Phylogeny ; }, abstract = {Amino acid propensities at amino acid sites change with time due to epistatic interactions or changing environment, affecting the probabilities of fixation of different amino acids. Such changes should lead to an increased rate of homoplasies (reversals, parallelisms, and convergences) at closely related species. Here, we reconstruct the phylogeny of twelve mitochondrial proteins from several thousand metazoan species, and measure the phylogenetic distances between branches at which either the same allele originated repeatedly due to homoplasies, or different alleles originated due to divergent substitutions. The mean phylogenetic distance between parallel substitutions is ∼20% lower than the mean phylogenetic distance between divergent substitutions, indicating that a variant fixed in a species is more likely to be deleterious in a more phylogenetically remote species, compared with a more closely related species. These findings are robust to artefacts of phylogenetic reconstruction or of pooling of sites from different conservation classes or functional groups, and imply that single-position fitness landscapes change at rates similar to rates of amino acid changes.}, }
@article {pmid28591857, year = {2017}, author = {Escalona, T and Weadick, CJ and Antunes, A}, title = {Adaptive Patterns of Mitogenome Evolution Are Associated with the Loss of Shell Scutes in Turtles.}, journal = {Molecular biology and evolution}, volume = {34}, number = {10}, pages = {2522-2536}, pmid = {28591857}, issn = {1537-1719}, mesh = {Adaptation, Physiological/genetics ; Animal Shells/metabolism/*physiology ; Animals ; Biological Evolution ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Oxidative Phosphorylation ; Phylogeny ; Turtles/*genetics/metabolism ; }, abstract = {The mitochondrial genome encodes several protein components of the oxidative phosphorylation (OXPHOS) pathway and is critical for aerobic respiration. These proteins have evolved adaptively in many taxa, but linking molecular-level patterns with higher-level attributes (e.g., morphology, physiology) remains a challenge. Turtles are a promising system for exploring mitochondrial genome evolution as different species face distinct respiratory challenges and employ multiple strategies for ensuring efficient respiration. One prominent adaptation to a highly aquatic lifestyle in turtles is the secondary loss of keratenized shell scutes (i.e., soft-shells), which is associated with enhanced swimming ability and, in some species, cutaneous respiration. We used codon models to examine patterns of selection on mitochondrial protein-coding genes along the three turtle lineages that independently evolved soft-shells. We found strong evidence for positive selection along the branches leading to the pig-nosed turtle (Carettochelys insculpta) and the softshells clade (Trionychidae), but only weak evidence for the leatherback (Dermochelys coriacea) branch. Positively selected sites were found to be particularly prevalent in OXPHOS Complex I proteins, especially subunit ND2, along both positively selected lineages, consistent with convergent adaptive evolution. Structural analysis showed that many of the identified sites are within key regions or near residues involved in proton transport, indicating that positive selection may have precipitated substantial changes in mitochondrial function. Overall, our study provides evidence that physiological challenges associated with adaptation to a highly aquatic lifestyle have shaped the evolution of the turtle mitochondrial genome in a lineage-specific manner.}, }
@article {pmid28588260, year = {2017}, author = {Lemieux, H and Blier, PU and Gnaiger, E}, title = {Remodeling pathway control of mitochondrial respiratory capacity by temperature in mouse heart: electron flow through the Q-junction in permeabilized fibers.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2840}, pmid = {28588260}, issn = {2045-2322}, mesh = {Animals ; *Cell Respiration ; *Electron Transport ; Electron Transport Complex IV/metabolism ; Mice ; Mitochondria, Heart/*metabolism ; Models, Biological ; Oxidative Phosphorylation ; Oxygen Consumption ; Permeability ; *Signal Transduction ; Temperature ; }, abstract = {Fuel substrate supply and oxidative phosphorylation are key determinants of muscle performance. Numerous studies of mammalian mitochondria are carried out (i) with substrate supply that limits electron flow, and (ii) far below physiological temperature. To analyze potentially implicated biases, we studied mitochondrial respiratory control in permeabilized mouse myocardial fibers using high-resolution respirometry. The capacity of oxidative phosphorylation at 37 °C was nearly two-fold higher when fueled by physiological substrate combinations reconstituting tricarboxylic acid cycle function, compared with electron flow measured separately through NADH to Complex I or succinate to Complex II. The relative contribution of the NADH pathway to physiological respiratory capacity increased with a decrease in temperature from 37 to 25 °C. The apparent excess capacity of cytochrome c oxidase above physiological pathway capacity increased sharply under hypothermia due to limitation by NADH-linked dehydrogenases. This mechanism of mitochondrial respiratory control in the hypothermic mammalian heart is comparable to the pattern in ectotherm species, pointing towards NADH-linked mt-matrix dehydrogenases and the phosphorylation system rather than electron transfer complexes as the primary drivers of thermal sensitivity at low temperature. Delineating the link between stress and remodeling of oxidative phosphorylation is important for understanding metabolic perturbations in disease evolution and cardiac protection.}, }
@article {pmid28582680, year = {2017}, author = {Dumack, K and Mylnikov, AP and Bonkowski, M}, title = {Evolutionary Relationship of the Scale-Bearing Kraken (incertae sedis, Monadofilosa, Cercozoa, Rhizaria): Combining Ultrastructure Data and a Two-Gene Phylogeny.}, journal = {Protist}, volume = {168}, number = {3}, pages = {362-373}, doi = {10.1016/j.protis.2017.04.004}, pmid = {28582680}, issn = {1618-0941}, mesh = {Biological Evolution ; Cercozoa/*classification/genetics/ultrastructure ; DNA, Protozoan/analysis/*genetics ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The genus Kraken represents a distinct lineage of filose amoebae within the Cercozoa. Currently a single species, Kraken carinae, has been described. SSU rDNA phylogeny showed an affiliation to the Cercomonadida, branching with weak support at its base, close to Paracercomonas, Metabolomonas, and Brevimastigomonas. Light microscopical analyses showed several unique features of the genus Kraken, but ultrastructure data were lacking. In this study, K. carinae has been studied by electron microscopy, these data conjoined with a two-gene phylogeny were used to give more insight into the evolutionary relationship of the genus Kraken within Cercozoa. The data confirmed the absence of flagella, but also showed novel characteristics, such as the presence of extrusomes, osmiophilic bodies, and mitochondria with flat cristae. Surprising was the presence of single-tier scales which are carried by cell outgrowths, much of what is expected of the last common ancestor of the class Imbricatea. The phylogenetic analyses however confirmed previous results, indicating Kraken as a sister group to Paracercomonas in Sarcomonadea with an increased but still low support of 0.98 PP/63 BP. Based on the unique features of Kraken we establish the Krakenidae fam. nov. that we, due to contradictory results in morphology and phylogeny, assign incertae sedis, Monadofilosa.}, }
@article {pmid28578677, year = {2017}, author = {Sarvašová, A and Kočišová, A and Candolfi, E and Mathieu, B}, title = {Description of Culicoides (Culicoides) bysta n. sp., a new member of the Pulicaris group (Diptera: Ceratopogonidae) from Slovakia.}, journal = {Parasites &amp; vectors}, volume = {10}, number = {1}, pages = {279}, pmid = {28578677}, issn = {1756-3305}, mesh = {Animals ; Arboviruses ; Bluetongue/transmission ; Bluetongue virus ; Ceratopogonidae/anatomy &amp; histology/*classification/genetics/virology ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Female ; Genes, Mitochondrial/genetics ; Insect Vectors/anatomy &amp; histology/*classification/genetics/virology ; Male ; Mitochondria/enzymology/genetics ; *Phylogeny ; Slovakia ; Species Specificity ; }, abstract = {BACKGROUND: Species of the genus Culicoides Latreille, 1809 (Diptera: Ceratopogonidae) are mainly known as vectors of arboviruses such as bluetongue (BTV) and Schmallenberg (SBV). Among the known vectors, few species within the subgenus Culicoides Latreille, 1809 have been implicated in the transmission of BTV and SBV. Nevertheless, phylogenetic studies had revealed the presence of cryptic and undescribed species in Europe, raising questions about their vectorial role. A previous integrative study, associating morphology and barcode data, raised the hypothesis of the presence of undescribed species in Slovakia. The present study, combining morphological and molecular approaches, is aimed to support the hypothesis and a description of Culicoides bysta n. sp. is provided.<br><br>METHODS: Series of male and female specimens were dissected and several of them were sequenced for the barcode region of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1). Bayesian inference phylogenetic analyses based on 72 cox1 sequences of the species belonging to the Pulicaris group of the subgenus Culicoides, were carried out and the frequencies of intra/interspecific variations were analyzed. The morphology of abundant material of the new species (31 females and 12 males) was examined and compared with the paratypes of Culicoides boyi Nielsen, Kristensen &amp; Pape, 2015 and with specimens of Culicoides pulicaris Linnaeus, 1758. For females, suture distances on the eyes were newly evaluated as a diagnostic character and for males we assessed a new measurement on the ninth tergite and on the apicolateral processes.<br><br>RESULTS: Both phylogenetic analysis and barcode distances supported the distinct status of the new species, Culicoides bysta n. sp. described as a member of the Pulicaris group based on the morphology of males and females. The new species is closely related to C. boyi and C. pulicaris but can be distinguished on the basis of the wing pattern and the ratio between the two eye sutures. Both newly evaluated characters, i.e. eyes in females and male genitalia appeared to be diagnostic for distinguishing the new species described herein.<br><br>CONCLUSIONS: The vector potential of the recently described species C. boyi and C. bysta n. sp. to transmit arboviruses, such as BTV and SBV, is unknown. When considering these two species as being close to C. pulicaris, the previous data, such as the vector implication for C. pulicaris in BTV transmission, should be revaluated in future.}, }
@article {pmid28577575, year = {2017}, author = {Minard, G and Tran Van, V and Tran, FH and Melaun, C and Klimpel, S and Koch, LK and Ly Huynh Kim, K and Huynh Thi Thuy, T and Tran Ngoc, H and Potier, P and Mavingui, P and Valiente Moro, C}, title = {Identification of sympatric cryptic species of Aedes albopictus subgroup in Vietnam: new perspectives in phylosymbiosis of insect vector.}, journal = {Parasites &amp; vectors}, volume = {10}, number = {1}, pages = {276}, pmid = {28577575}, issn = {1756-3305}, mesh = {Aedes/anatomy &amp; histology/*classification/genetics/*microbiology ; Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Culicidae ; Insect Vectors/classification/*microbiology ; Microbiota ; Mitochondria ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; Vietnam ; Wolbachia/classification/pathogenicity ; }, abstract = {BACKGROUND: The Aedes (Stegomyia) albopictus subgroup includes 11 cryptic species of which Ae. albopictus is the most widely distributed. Its global expansion associated with a documented vector competence for several emerging arboviruses raise obvious concerns in the recently colonized regions. While several studies have provided important insights regarding medical importance of Ae. albopicus, the investigations of the other sibling species are scarce. In Asia, indigenous populations within the Ae. albopictus subgroup can be found in sympatry. In the present study, we aimed to describe and compare molecular, morphological and bacterial symbionts composition among sympatric individuals from the Ae. albopictus subgroup inhabiting a Vietnamese protected area.<br><br>RESULTS: Based on morphological structure of the cibarial armarture, we identified a cryptic species in the forest park at B&#xf9; Gia M&#x1ead;p in the south-eastern region of Vietnam. Analysis of nuclear (ITS1-5.8S-ITS2) and mitochondrial (cox1, nad5) markers confirmed the divergence between the cryptic species and Ae. albopictus. Analysis of midgut bacterial microbiota revealed a strong similarity among the two species with a notable difference; contrary to Ae. albopictus, the cryptic species did not harbour any Wolbachia infection.<br><br>CONCLUSIONS: These results could reflect either a recent invasion of Wolbachia in Ae. albopictus or alternatively a loss of this symbiont in the cryptic species. We argue that neglected species of the Ae. albopictus subgroup are of main importance in order to estimate variation of host-symbionts interactions across evolution.}, }
@article {pmid28573928, year = {2018}, author = {Wang, XC and Chen, H and Yang, D and Liu, C}, title = {Diversity of mitochondrial plastid DNAs (MTPTs) in seed plants.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {635-642}, doi = {10.1080/24701394.2017.1334772}, pmid = {28573928}, issn = {2470-1408}, mesh = {DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Genetic Variation ; Genome, Mitochondrial ; Genome, Plastid ; Mitochondria/*genetics ; Multigene Family ; Phylogeny ; Plants/classification/*genetics ; Plastids/*genetics ; Seeds/genetics ; }, abstract = {Mitochondrial plastid DNAs (MTPTs) refer to plastid-derived DNA fragments in mitochondrial genomes. While the MTPTs have been described for numerous species, its overall patterns have not been examined in details. Here, we carried out a systematic analysis of MTPTs among 73 plant species, including 28 algae, 1 liverwort, 2 moss, 1 lycophyte, 1 gymnosperm, 1 magnoliid, 12 monocots, 26 eudicots and 1 relic angiosperm Amborella trichopoda. A total of 300 MTPT gene clusters were found in 39 seed plants, which represented 144 MTPT gene cluster types. The detected MTPT gene clusters were evaluated in seven aspects, and they were found to be enriched particularly in monocots and asterids of eudicots. Some MTPT gene clusters were found to be shared by closely related species. All chloroplast genes were found in MTPTs, suggesting that there is no functional relevancy for genes that were transferred. However, after calculation of the frequency of the 115 chloroplast genes, five hot spots and three cold spots were discovered in chloroplast genome. In summary, this study demonstrated the high degree of diversity in MTPTs. The discovered MTPTs would facilitate the accurate assembly of chloroplast and mitochondrial genomes as well as the understanding of organelle genome evolution.}, }
@article {pmid28564594, year = {2017}, author = {Hall, CE and Yao, Z and Choi, M and Tyzack, GE and Serio, A and Luisier, R and Harley, J and Preza, E and Arber, C and Crisp, SJ and Watson, PMD and Kullmann, DM and Abramov, AY and Wray, S and Burley, R and Loh, SHY and Martins, LM and Stevens, MM and Luscombe, NM and Sibley, CR and Lakatos, A and Ule, J and Gandhi, S and Patani, R}, title = {Progressive Motor Neuron Pathology and the Role of Astrocytes in a Human Stem Cell Model of VCP-Related ALS.}, journal = {Cell reports}, volume = {19}, number = {9}, pages = {1739-1749}, pmid = {28564594}, issn = {2211-1247}, support = {616417/ERC_/European Research Council/International ; MR/L01095X/1/MRC_/Medical Research Council/United Kingdom ; MC_U132674518/MRC_/Medical Research Council/United Kingdom ; MR/P008658/1/MRC_/Medical Research Council/United Kingdom ; MR/L012677/1/MRC_/Medical Research Council/United Kingdom ; 101149/Z/13/A/WT_/Wellcome Trust/United Kingdom ; MR/M02492X/1/MRC_/Medical Research Council/United Kingdom ; G116/147/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amyotrophic Lateral Sclerosis/*metabolism/*pathology ; Astrocytes/*pathology ; Cell Survival ; DNA-Binding Proteins/metabolism ; Endoplasmic Reticulum/metabolism/ultrastructure ; Endoplasmic Reticulum Stress ; Humans ; Induced Pluripotent Stem Cells/metabolism ; Membrane Potential, Mitochondrial ; Mitochondria/metabolism/ultrastructure ; *Models, Biological ; Motor Neurons/*pathology ; Mutation/genetics ; Nerve Degeneration/pathology ; Neurogenesis ; Oxidative Stress ; Phenotype ; Synapses/pathology ; Valosin Containing Protein/*metabolism ; }, abstract = {Motor neurons (MNs) and astrocytes (ACs) are implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS), but their interaction and the sequence of molecular events leading to MN death remain unresolved. Here, we optimized directed differentiation of induced pluripotent stem cells (iPSCs) into highly enriched (> 85%) functional populations of spinal cord MNs and ACs. We identify significantly increased cytoplasmic TDP-43 and ER stress as primary pathogenic events in patient-specific valosin-containing protein (VCP)-mutant MNs, with secondary mitochondrial dysfunction and oxidative stress. Cumulatively, these cellular stresses result in synaptic pathology and cell death in VCP-mutant MNs. We additionally identify a cell-autonomous VCP-mutant AC survival phenotype, which is not attributable to the same molecular pathology occurring in VCP-mutant MNs. Finally, through iterative co-culture experiments, we uncover non-cell-autonomous effects of VCP-mutant ACs on both control and mutant MNs. This work elucidates molecular events and cellular interplay that could guide future therapeutic strategies in ALS.}, }
@article {pmid28562139, year = {2018}, author = {Sun, P and Tang, B and Yin, F}, title = {Population genetic structure and genetic diversity of Chinese pomfret at the coast of the East China Sea and the South China Sea.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {643-649}, doi = {10.1080/24701394.2017.1334773}, pmid = {28562139}, issn = {2470-1408}, mesh = {Animals ; China ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Genetics, Population ; Genome, Mitochondrial ; Haplotypes ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; }, abstract = {The Chinese pomfret Pampus chinensis is one of the most economic and ecological important marine fish species in China. In the present study, the population genetic structure and genetic diversity of P. chinensis were evaluated from a total sample size of 180 individuals representing six populations from the East China Sea and the South China Sea using mitochondrial cytochrome c oxidase subunit I (COI) gene. A total of 24 variable sites (including 3 singleton sites and 21 parsimony information sites) were observed, and 18 haplotypes were defined. The haplotype diversity (Hd) of the populations ranged from 0.559 to 0.775, and the nucleotide diversity (π) ranged from 0.330 to 1.090%. Analysis of molecular variance (AMOVA) reveals that the main variation (66.02%) was among individuals within populations. The average pairwise differences and ϕST values indicated significant genetic differentiation between Dongxing population and the other populations. The results of the present study are helpful for the sustainable management and utilization of this species.}, }
@article {pmid28554774, year = {2017}, author = {Wong, LH and Levine, TP}, title = {Tubular lipid binding proteins (TULIPs) growing everywhere.}, journal = {Biochimica et biophysica acta. Molecular cell research}, volume = {1864}, number = {9}, pages = {1439-1449}, pmid = {28554774}, issn = {0167-4889}, support = {BB/M011801/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacterial Proteins/chemistry/genetics/*metabolism ; Binding Sites ; Cholesterol Ester Transfer Proteins/chemistry/genetics/*metabolism ; Evolution, Molecular ; Humans ; Lipid Metabolism ; Phospholipid Transfer Proteins/chemistry/genetics/*metabolism ; Protein Binding ; }, abstract = {Tubular lipid binding proteins (TULIPs) have become a focus of interest in the cell biology of lipid signalling, lipid traffic and membrane contact sites. Each tubular domain has an internal pocket with a hydrophobic lining that can bind a hydrophobic molecule such as a lipid. This allows TULIP proteins to carry lipids through the aqueous phase. TULIP domains were first found in a large family of extracellular proteins related to the bacterial permeability-inducing protein (BPI) and cholesterol ester transfer protein (CETP). Since then, the same fold and lipid transfer capacity have been found in SMP domains (so-called for their occurrence in synaptotagmin, mitochondrial and lipid binding proteins), which localise to intracellular membrane contact sites. Here the methods for identifying known TULIPs are described, and used to find previously unreported TULIPs, one in the silk polymer and another in prokaryotes illustrated by the E. coli protein YceB. The bacterial TULIP alters views on the likely evolution of the domain, suggesting its presence in the last universal common ancestor. The major function of TULIPs is to handle lipids, but we still do not know how they work in detail, or how many more remain to be discovered. This article is part of a Special Issue entitled: Membrane Contact Sites edited by Christian Ungermann and Benoit Kornmann.}, }
@article {pmid28554771, year = {2017}, author = {Jain, A and Holthuis, JCM}, title = {Membrane contact sites, ancient and central hubs of cellular lipid logistics.}, journal = {Biochimica et biophysica acta. Molecular cell research}, volume = {1864}, number = {9}, pages = {1450-1458}, doi = {10.1016/j.bbamcr.2017.05.017}, pmid = {28554771}, issn = {0167-4889}, mesh = {Animals ; Cell Membrane/*metabolism ; Evolution, Molecular ; Humans ; *Lipid Metabolism ; Phospholipid Transfer Proteins/genetics/metabolism ; Secretory Pathway ; }, abstract = {Membrane contact sites (MCSs) are regions where two organelles are closely apposed to facilitate molecular communication and promote a functional integration of compartmentalized cellular processes. There is growing evidence that MCSs play key roles in controlling intracellular lipid flows and distributions. Strikingly, even organelles connected by vesicular trafficking exchange lipids en bulk via lipid transfer proteins that operate at MCSs. Herein, we describe how MCSs developed into central hubs of lipid logistics during the evolution of eukaryotic cells. We then focus on how modern eukaryotes exploit MCSs to help solve a major logistical problem, namely to preserve the unique lipid mixtures of their early and late secretory organelles in the face of extensive vesicular trafficking. This article is part of a Special Issue entitled: Membrane Contact Sites edited by Christian Ungermann and Benoit Kornmann.}, }
@article {pmid28551806, year = {2017}, author = {Sharma, K}, title = {Mitochondrial Dysfunction in the Diabetic Kidney.}, journal = {Advances in experimental medicine and biology}, volume = {982}, number = {}, pages = {553-562}, doi = {10.1007/978-3-319-55330-6_28}, pmid = {28551806}, issn = {0065-2598}, mesh = {Animals ; Blood Glucose/metabolism ; Diabetic Nephropathies/*metabolism/pathology/physiopathology/prevention &amp; control ; *Energy Metabolism/drug effects ; Humans ; Kidney/drug effects/*metabolism/pathology/physiopathology ; Mitochondria/drug effects/*metabolism/pathology ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; Signal Transduction ; }, abstract = {The role of mitochondria in diabetic complications has been viewed as a source of excess superoxide production leading to cell dysfunction. However, with the lack of benefit of non-specific anti-oxidant approaches this view needs to be re-evaluated. With recent studies using real-time imaging of superoxide, metabolomics, flux studies, transcriptomics and proteomics a new appreciation for the role of mitochondria in the evolution of diabetic kidney disease has emerged. Ongoing studies to further unravel the time course and mechanisms that reduce mitochondrial function will be relevant to novel therapies that could have a major impact on diabetic kidney disease and other diabetic complications.}, }
@article {pmid28550453, year = {2017}, author = {Weiss, RA}, title = {Exchange of Genetic Sequences Between Viruses and Hosts.}, journal = {Current topics in microbiology and immunology}, volume = {407}, number = {}, pages = {1-29}, doi = {10.1007/82_2017_21}, pmid = {28550453}, issn = {0070-217X}, mesh = {Animals ; Endogenous Retroviruses/genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Viral/*genetics ; Host Specificity/*genetics ; Proviruses/*genetics ; Viruses/*genetics ; }, abstract = {Although genetic transfer between viruses and vertebrate hosts occurs less frequently than gene flow between bacteriophages and prokaryotes, it is extensive and has affected the evolution of both parties. With retroviruses, the integration of proviral DNA into chromosomal DNA can result in the activation of adjacent host gene expression and in the transduction of host transcripts into retroviral genomes as oncogenes. Yet in contrast to lysogenic phage, there is little evidence that viral oncogenes persist in a chain of natural transmission or that retroviral transduction is a significant driver of the horizontal spread of host genes. Conversely, integration of proviruses into the host germ line has generated endogenous retroviral genomes (ERV) in all vertebrate genomes sequenced to date. Some of these genomes retain potential infectivity and upon reactivation may transmit to other host species. During mammalian evolution, sequences of retroviral origin have been repurposed to serve host functions, such as the viral envelope glycoproteins crucial to the development of the placenta. Beyond retroviruses, DNA viruses with complex genomes have acquired numerous genes of host origin which influence replication, pathogenesis and immune evasion, while host species have accumulated germline sequences of both DNA and RNA viruses. A codicil is added on lateral transmission of cancer cells between hosts and on migration of host mitochondria into cancer cells.}, }
@article {pmid28545148, year = {2017}, author = {Petersen, G and Cuenca, A and Zervas, A and Ross, GT and Graham, SW and Barrett, CF and Davis, JI and Seberg, O}, title = {Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0177606}, pmid = {28545148}, issn = {1932-6203}, mesh = {Alismatales/classification/*genetics ; Biological Evolution ; Chromosome Mapping ; DNA, Plant/chemistry/metabolism ; *Genome, Mitochondrial ; Hydrocharitaceae/genetics ; Mitochondria/*genetics/metabolism ; Phylogeny ; Ribosomal Proteins/*genetics ; Sequence Analysis, DNA ; Zosteraceae/genetics ; }, abstract = {The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant. Using a broad sample of the Alismatales, the evolutionary history of ribosomal protein gene loss is analyzed. In Zostera almost all ribosomal protein genes are lost from the mitogenome, but only some can be found in the nucleus.}, }
@article {pmid28542596, year = {2017}, author = {Stram, AR and Wagner, GR and Fogler, BD and Pride, PM and Hirschey, MD and Payne, RM}, title = {Progressive mitochondrial protein lysine acetylation and heart failure in a model of Friedreich's ataxia cardiomyopathy.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0178354}, pmid = {28542596}, issn = {1932-6203}, mesh = {Acetylation ; Adult ; Animals ; Cardiomyopathies/metabolism/*pathology ; Disease Models, Animal ; Friedreich Ataxia/metabolism/*pathology ; Heart Failure/metabolism/*pathology ; Humans ; Iron-Binding Proteins/metabolism ; Lysine/*metabolism ; Male ; Mice ; Middle Aged ; Mitochondria/metabolism/*pathology ; Mitochondrial Proteins/*metabolism ; Sirtuin 3/metabolism ; Frataxin ; }, abstract = {INTRODUCTION: The childhood heart disease of Friedreich's Ataxia (FRDA) is characterized by hypertrophy and failure. It is caused by loss of frataxin (FXN), a mitochondrial protein involved in energy homeostasis. FRDA model hearts have increased mitochondrial protein acetylation and impaired sirtuin 3 (SIRT3) deacetylase activity. Protein acetylation is an important regulator of cardiac metabolism and loss of SIRT3 increases susceptibility of the heart to stress-induced cardiac hypertrophy and ischemic injury. The underlying pathophysiology of heart failure in FRDA is unclear. The purpose of this study was to examine in detail the physiologic and acetylation changes of the heart that occur over time in a model of FRDA heart failure. We predicted that increased mitochondrial protein acetylation would be associated with a decrease in heart function in a model of FRDA.<br><br>METHODS: A conditional mouse model of FRDA cardiomyopathy with ablation of FXN (FXN KO) in the heart was compared to healthy controls at postnatal days 30, 45 and 65. We evaluated hearts using echocardiography, cardiac catheterization, histology, protein acetylation and expression.<br><br>RESULTS: Acetylation was temporally progressive and paralleled evolution of heart failure in the FXN KO model. Increased acetylation preceded detectable abnormalities in cardiac function and progressed rapidly with age in the FXN KO mouse. Acetylation was also associated with cardiac fibrosis, mitochondrial damage, impaired fat metabolism, and diastolic and systolic dysfunction leading to heart failure. There was a strong inverse correlation between level of protein acetylation and heart function.<br><br>CONCLUSION: These results demonstrate a close relationship between mitochondrial protein acetylation, physiologic dysfunction and metabolic disruption in FRDA hypertrophic cardiomyopathy and suggest that abnormal acetylation contributes to the pathophysiology of heart disease in FRDA. Mitochondrial protein acetylation may represent a therapeutic target for early intervention.}, }
@article {pmid28542197, year = {2017}, author = {Osigus, HJ and Eitel, M and Schierwater, B}, title = {Deep RNA sequencing reveals the smallest known mitochondrial micro exon in animals: The placozoan cox1 single base pair exon.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0177959}, pmid = {28542197}, issn = {1932-6203}, mesh = {Animals ; Base Pairing ; Base Sequence ; Electron Transport Complex IV/*genetics ; Exons/*genetics ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/enzymology/genetics ; Placozoa/enzymology/*genetics ; RNA Splicing ; RNA, Messenger/chemistry/genetics/*metabolism ; RNA, Mitochondrial ; Sequence Alignment ; Sequence Analysis, RNA ; }, abstract = {The phylum Placozoa holds a key position for our understanding of the evolution of mitochondrial genomes in Metazoa. Placozoans possess large mitochondrial genomes which harbor several remarkable characteristics such as a fragmented cox1 gene and trans-splicing cox1 introns. A previous study also suggested the existence of cox1 mRNA editing in Trichoplax adhaerens, yet the only formally described species in the phylum Placozoa. We have analyzed RNA-seq data of the undescribed sister species, Placozoa sp. H2 ("Panama" clone), with special focus on the mitochondrial mRNA. While we did not find support for a previously postulated cox1 mRNA editing mechanism, we surprisingly found two independent transcripts representing intermediate cox1 mRNA splicing stages. Both transcripts consist of partial cox1 exon as well as overlapping intron fragments. The data suggest that the cox1 gene harbors a single base pair (cytosine) micro exon. Furthermore, conserved group I intron structures flank this unique micro exon also in other placozoans. We discuss the evolutionary origin of this micro exon in the context of a self-splicing intron gain in the cox1 gene of the last common ancestor of extant placozoans.}, }
@article {pmid28541477, year = {2017}, author = {Wu, Z and Sloan, DB and Brown, CW and Rosenblueth, M and Palmer, JD and Ong, HC}, title = {Mitochondrial Retroprocessing Promoted Functional Transfers of rpl5 to the Nucleus in Grasses.}, journal = {Molecular biology and evolution}, volume = {34}, number = {9}, pages = {2340-2354}, pmid = {28541477}, issn = {1537-1719}, support = {R01 GM035087/GM/NIGMS NIH HHS/United States ; R01 GM070612/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence/genetics ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Gene Conversion/genetics ; Genes, Mitochondrial/genetics ; Genes, Plant ; Genome, Mitochondrial ; Magnoliopsida/genetics ; Mitochondria/*genetics ; Phylogeny ; Plant Proteins/genetics ; Poaceae/*genetics ; Pseudogenes/genetics ; RNA Editing ; Ribosomal Proteins/genetics ; Sequence Homology, Amino Acid ; }, abstract = {Functional gene transfers from the mitochondrion to the nucleus are ongoing in angiosperms and have occurred repeatedly for all 15 ribosomal protein genes, but it is not clear why some of these genes are transferred more often than others nor what the balance is between DNA- and RNA-mediated transfers. Although direct insertion of mitochondrial DNA into the nucleus occurs frequently in angiosperms, case studies of functional mitochondrial gene transfer have implicated an RNA-mediated mechanism that eliminates introns and RNA editing sites, which would otherwise impede proper expression of mitochondrial genes in the nucleus. To elucidate the mechanisms that facilitate functional gene transfers and the evolutionary dynamics of the coexisting nuclear and mitochondrial gene copies that are established during these transfers, we have analyzed rpl5 genes from 90 grasses (Poaceae) and related monocots. Multiple lines of evidence indicate that rpl5 has been functionally transferred to the nucleus at least three separate times in the grass family and that at least seven species have intact and transcribed (but not necessarily functional) copies in both the mitochondrion and nucleus. In two grasses, likely functional nuclear copies of rpl5 have been subject to recent gene conversion events via secondarily transferred mitochondrial copies in what we believe are the first described cases of mitochondrial-to-nuclear gene conversion. We show that rpl5 underwent a retroprocessing event within the mitochondrial genome early in the evolution of the grass family, which we argue predisposed the gene towards successful, DNA-mediated functional transfer by generating a "pre-edited" sequence.}, }
@article {pmid28539364, year = {2017}, author = {Guo, X and Niemi, NM and Coon, JJ and Pagliarini, DJ}, title = {Integrative proteomics and biochemical analyses define Ptc6p as the Saccharomyces cerevisiae pyruvate dehydrogenase phosphatase.}, journal = {The Journal of biological chemistry}, volume = {292}, number = {28}, pages = {11751-11759}, pmid = {28539364}, issn = {1083-351X}, support = {R01 DK098672/DK/NIDDK NIH HHS/United States ; R35 GM118110/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Biochemistry/methods ; Conserved Sequence ; Databases, Protein ; Enzyme Activation ; Gene Knockout Techniques ; Immunoprecipitation ; Phosphoprotein Phosphatases/genetics/*metabolism ; Phosphorylation ; Phylogeny ; *Protein Processing, Post-Translational ; Proteomics/methods ; Pyruvate Dehydrogenase Complex/*metabolism ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/*enzymology ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {The pyruvate dehydrogenase complex (PDC) is the primary metabolic checkpoint connecting glycolysis and mitochondrial oxidative phosphorylation and is important for maintaining cellular and organismal glucose homeostasis. Phosphorylation of the PDC E1 subunit was identified as a key inhibitory modification in bovine tissue ∼50 years ago, and this regulatory process is now known to be conserved throughout evolution. Although Saccharomyces cerevisiae is a pervasive model organism for investigating cellular metabolism and its regulation by signaling processes, the phosphatase(s) responsible for activating the PDC in S. cerevisiae has not been conclusively defined. Here, using comparative mitochondrial phosphoproteomics, analyses of protein-protein interactions by affinity enrichment-mass spectrometry, and in vitro biochemistry, we define Ptc6p as the primary PDC phosphatase in S. cerevisiae Our analyses further suggest additional substrates for related S. cerevisiae phosphatases and describe the overall phosphoproteomic changes that accompany mitochondrial respiratory dysfunction. In summary, our quantitative proteomics and biochemical analyses have identified Ptc6p as the primary-and likely sole-S. cerevisiae PDC phosphatase, closing a key knowledge gap about the regulation of yeast mitochondrial metabolism. Our findings highlight the power of integrative omics and biochemical analyses for annotating the functions of poorly characterized signaling proteins.}, }
@article {pmid28539070, year = {2018}, author = {Emami-Khoyi, A and Paterson, AM and Hartley, DA and Boren, LJ and Cruickshank, RH and Ross, JG and Murphy, EC and Else, TA}, title = {Mitogenomics data reveal effective population size, historical bottlenecks, and the effects of hunting on New Zealand fur seals (Arctocephalus forsteri).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {567-580}, doi = {10.1080/24701394.2017.1325478}, pmid = {28539070}, issn = {2470-1408}, mesh = {Animals ; Breeding ; *Feeding Behavior ; Fur Seals/*genetics ; *Genome, Mitochondrial ; Mitochondria/*genetics ; *Phylogeny ; Population Density ; Recreation ; }, abstract = {The New Zealand fur seal (Arctocephalus forsteri) passed through a population bottleneck due to commercial sealing during the eighteenth to nineteenth centuries. To facilitate future management options, we reconstructed the demographic history of New Zealand fur seals in a Bayesian framework using maternally inherited, mitochondrial DNA sequences. Mitogenomic data suggested two separate clades (most recent common ancestor 5000 years ago) of New Zealand fur seals that survived large-scale human harvest. Mitochondrial haplotype diversity was high, with 45 singletons identified from 46 individuals although mean nucleotide diversity was low (0.012 ± 0.0061). Variation was not constrained geographically. Analyses of mitogenomes support the hypothesis for a population bottleneck approximately 35 generations ago, which coincides with the peak of commercial sealing. Mitogenomic data are consistent with a pre-human effective population size of approximately 30,000 that first declined to around 10,000 (due to the impact of Polynesian colonization, particularly in the first 100 years of their arrival into New Zealand), and then to 100-200 breeding individuals during peak of commercial sealing.}, }
@article {pmid28533386, year = {2017}, author = {Horscroft, JA and Kotwica, AO and Laner, V and West, JA and Hennis, PJ and Levett, DZH and Howard, DJ and Fernandez, BO and Burgess, SL and Ament, Z and Gilbert-Kawai, ET and Vercueil, A and Landis, BD and Mitchell, K and Mythen, MG and Branco, C and Johnson, RS and Feelisch, M and Montgomery, HE and Griffin, JL and Grocott, MPW and Gnaiger, E and Martin, DS and Murray, AJ}, title = {Metabolic basis to Sherpa altitude adaptation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {24}, pages = {6382-6387}, pmid = {28533386}, issn = {1091-6490}, support = {BB/F016581/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; FS/09/050/BHF_/British Heart Foundation/United Kingdom ; MR/P01836X/1/MRC_/Medical Research Council/United Kingdom ; MR/P011705/1/MRC_/Medical Research Council/United Kingdom ; MC_UP_A090_1006/MRC_/Medical Research Council/United Kingdom ; MC_PC_13030/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Adaptation, Physiological/genetics ; Adult ; *Altitude ; Atmospheric Pressure ; Citric Acid Cycle ; Energy Metabolism ; *Ethnicity/genetics ; Fatty Acids/metabolism ; Female ; Gene Frequency ; Glucose/metabolism ; Glycolysis ; Humans ; Hypoxia/genetics/*metabolism/physiopathology ; Male ; Mitochondria, Muscle/metabolism ; Muscle, Skeletal/metabolism ; Nepal ; Nitric Oxide/blood ; Oxidative Phosphorylation ; Oxidative Stress ; Oxygen Consumption ; PPAR alpha/genetics/metabolism ; Polymorphism, Single Nucleotide ; Tibet/ethnology ; }, abstract = {The Himalayan Sherpas, a human population of Tibetan descent, are highly adapted to life in the hypobaric hypoxia of high altitude. Mechanisms involving enhanced tissue oxygen delivery in comparison to Lowlander populations have been postulated to play a role in such adaptation. Whether differences in tissue oxygen utilization (i.e., metabolic adaptation) underpin this adaptation is not known, however. We sought to address this issue, applying parallel molecular, biochemical, physiological, and genetic approaches to the study of Sherpas and native Lowlanders, studied before and during exposure to hypobaric hypoxia on a gradual ascent to Mount Everest Base Camp (5,300 m). Compared with Lowlanders, Sherpas demonstrated a lower capacity for fatty acid oxidation in skeletal muscle biopsies, along with enhanced efficiency of oxygen utilization, improved muscle energetics, and protection against oxidative stress. This adaptation appeared to be related, in part, to a putatively advantageous allele for the peroxisome proliferator-activated receptor A (PPARA) gene, which was enriched in the Sherpas compared with the Lowlanders. Our findings suggest that metabolic adaptations underpin human evolution to life at high altitude, and could have an impact upon our understanding of human diseases in which hypoxia is a feature.}, }
@article {pmid28531368, year = {2018}, author = {Kang, L and Zhang, S and Wu, C and Liu, X and Xu, MY and Jiang, L}, title = {Molecular phylogeny of Loliginidae inferred from mitochondrial DNA sequence variation.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {600-605}, doi = {10.1080/24701394.2017.1325482}, pmid = {28531368}, issn = {2470-1408}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Decapodiformes/classification/*genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; *Genes, Mitochondrial ; *Genetic Variation ; Genome, Mitochondrial ; Mitochondria/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Loliginidae includes many economically important species in trophic systems worldwide. Here, we investigated genetic relationships and diversity in this family. Sequence comparisons and phylogenetic analyses revealed considerable variations between mitochondrial 16 S rRNA gene and cytochrome coxidase subunit I gene among nine Loliginid species. We identified three similar non-coding regions in eight Loliginid species, but not in Sepioteuthislessoniana. We detected a single extended termination-associated sequence and three conserved sequence blocks among these eight species. Our results suggest that Loliginidae forms a major lineage, with S. lessoniana located at the most basal position and forming an individual clade as sister to the remaining species. Loligobeka, Loliolusjaponica, Loliolusuyii, Loligochinensis, Loligoedulis, Loligoduvauceli, Loligobleekeri, and Loligoopalescensare clustered into a monophyletic group. We identified repetitive elements and repeat numbers in the control regions.}, }
@article {pmid28526134, year = {2017}, author = {Matic, I and Strobbe, D and Di Guglielmo, F and Campanella, M}, title = {Molecular Biology Digest of Cell Mitophagy.}, journal = {International review of cell and molecular biology}, volume = {332}, number = {}, pages = {233-258}, doi = {10.1016/bs.ircmb.2016.12.003}, pmid = {28526134}, issn = {1937-6448}, support = {BB/M010384/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N007042/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; G1100809/2//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Humans ; *Mitophagy ; Models, Biological ; *Molecular Biology ; Ubiquitin-Protein Ligases/metabolism ; }, abstract = {The homeostasis of eukaryotic cells relies on efficient mitochondrial function. The control of mitochondrial quality is framed by the combination of distinct but interdependent mechanisms spanning biogenesis, regulation of dynamic network, and finely tuned degradation either through ubiquitin-proteasome system or autophagy (mitophagy). There is continuous evolution on the pathways orchestrating the mitochondrial response to stress signals and the organelle adaptation to quality control during acute and subtle dysfunctions. Notably, it remains indeed ill-defined whether active mitophagy leads to cell survival or death by defective mitochondrial degradation. Above all, uncharted is whether and how pharmacologically tackle these mechanisms may lead to conceive novel therapeutic strategies for treating conditions associated with the defective mitochondria. Here, we attempt to provide a chronological and comprehensive overview of the determining discoveries, which have led to the current knowledge of mitophagy.}, }
@article {pmid28524717, year = {2018}, author = {Adhikari, P and Han, SH and Kim, YK and Kim, TW and Thapa, TB and Subedi, N and Adhikari, P and Oh, HS}, title = {First molecular evidence of Mus musculus bactrianus in Nepal inferred from the mitochondrial DNA cytochrome B gene sequences.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {561-566}, doi = {10.1080/24701394.2017.1320994}, pmid = {28524717}, issn = {2470-1408}, mesh = {Animals ; *Biological Evolution ; Cytochromes b/*genetics ; DNA, Mitochondrial/*genetics ; Genome, Mitochondrial ; Mice/classification/*genetics ; Mitochondria/*genetics ; Nepal ; Phylogeny ; }, abstract = {To identify the house mice collected in Pokhara and Lumbini of Nepal at the subspecies level, morphological and molecular analyses were carried out. Morphologically, two populations collected in Pokhara and Lumbini were distinguished by fur colour, but there was no significant difference in external measurements (p > .05). The phylogenetic analysis results revealed that the haplotypes sequences of mitochondrial DNA (mtDNA) Cytochrome B (CytB) gene distinguished into two distinct clades on a phylogenetic tree representing two subspecies, Mus musculus bactrianus and M. m. castaneus in Pokhara and Lumbini, respectively. In Nepal, the subspecies M. m. bactrianus was not reported before this study. These findings concluded that at least two subspecies, M. m. bactrianus and M. m. castaneus currently exist in Nepal. We estimated that these two subspecies could have introduced together with human migration, while further study is required to understand their evolutionary history and current distribution.}, }
@article {pmid28521046, year = {2017}, author = {Melvin, RG and Ballard, JWO}, title = {Cellular and population level processes influence the rate, accumulation and observed frequency of inherited and somatic mtDNA mutations.}, journal = {Mutagenesis}, volume = {32}, number = {3}, pages = {323-334}, doi = {10.1093/mutage/gex004}, pmid = {28521046}, issn = {1464-3804}, mesh = {Animals ; *Genome, Mitochondrial ; Humans ; *Mutation ; }, abstract = {Mitochondria are found in all animals and have the unique feature of containing multiple copies of their own small, circular DNA genome (mtDNA). The rate and pattern of mutation accumulation in the mtDNA are influenced by molecular, cellular and population level processes. We distinguish between inherited and somatic mtDNA mutations and review evidence for the often-made assumption that mutations accumulate at a higher rate in mtDNA than in nuclear DNA (nDNA). We conclude that the whole genome mutation accumulation rate is higher for mtDNA than for nDNA but include the caveat that rates overlap considerably between the individual mtDNA- and nDNA-encoded genes. Next, we discuss the postulated causal mechanisms for the high rate of mtDNA mutation accumulation in both inheritance and in somatic cells. Perhaps unexpectedly, mtDNA is resilient to many mutagens of nDNA but is prone to errors of replication. We then consider the influence of maternal inheritance, recombination and selection on the observed accumulation pattern of inherited mtDNA mutations. Finally, we discuss environmental influences of temperature and diet on the observed frequency of inherited and somatic mtDNA mutations. We conclude that it is necessary to understand the cellular processes to fully interpret the pattern of mutations and how they influence our interpretations of evolution and disease.}, }
@article {pmid28511886, year = {2017}, author = {Singh, KK and Choudhury, AR and Tiwari, HK}, title = {Numtogenesis as a mechanism for development of cancer.}, journal = {Seminars in cancer biology}, volume = {47}, number = {}, pages = {101-109}, pmid = {28511886}, issn = {1096-3650}, support = {I01 BX001716/BX/BLRD VA/United States ; R01 CA204430/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Cell Nucleus/genetics/*metabolism ; Cell Transformation, Neoplastic/*genetics/*metabolism ; DNA, Mitochondrial ; Disease Susceptibility ; Environment ; Genome ; Humans ; Mitochondria/*genetics/*metabolism ; Neoplasms/*etiology/*metabolism ; }, abstract = {Transfer of genetic material from cytoplasmic organelles to the nucleus, an ongoing process, has implications in evolution, aging, and human pathologies such as cancer. The transferred mitochondrial DNA (mtDNA) fragments in the nuclear genome are called nuclear mtDNA or NUMTs. We have named the process numtogenesis, defining the term as the transfer of mtDNA into the nuclear genome, or, less specifically, the transfer of mitochondria or mitochondrial components into the nucleus. There is increasing evidence of the involvement of NUMTs in human biology and pathology. Although information pertaining to NUMTs and numtogenesis is sparse, the role of this aspect of mitochondrial biology to human cancers is apparent. In this review, we present available knowledge about the origin and mechanisms of numtogenesis, with special emphasis on the role of NUMTs in human malignancies. We describe studies undertaken in our laboratory and in others and discuss the influence of NUMTs in tumor initiation and progression and in survival of cancer patients. We describe suppressors of numtogenesis and evolutionary conserved mechanisms underlying numtogenesis in cancer. An understanding the emerging field of numtogenesis should allow comprehension of this process in various malignancies and other diseases and, more generally, in human health.}, }
@article {pmid28503905, year = {2017}, author = {Beresford, J and Elias, M and Pluckrose, L and Sundström, L and Butlin, RK and Pamilo, P and Kulmuni, J}, title = {Widespread hybridization within mound-building wood ants in Southern Finland results in cytonuclear mismatches and potential for sex-specific hybrid breakdown.}, journal = {Molecular ecology}, volume = {26}, number = {15}, pages = {4013-4026}, doi = {10.1111/mec.14183}, pmid = {28503905}, issn = {1365-294X}, mesh = {Animals ; Ants/*genetics ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Female ; Finland ; Gene Flow ; Gene Pool ; *Genetics, Population ; Genome, Insect ; Haplotypes ; Hybrid Vigor ; *Hybridization, Genetic ; Male ; Microsatellite Repeats ; }, abstract = {Hybridization and gene flow between diverging lineages are increasingly recognized as common evolutionary processes, and their consequences can vary from hybrid breakdown to adaptive introgression. We have previously found a population of wood ant hybrids between Formica aquilonia and F. polyctena that shows antagonistic effects of hybridization: females with introgressed alleles show hybrid vigour, whereas males with the same alleles show hybrid breakdown. Here, we investigate whether hybridization is a general phenomenon in this species pair and analyse 647 worker samples from 16 localities in Finland using microsatellite markers and a 1200-bp mitochondrial sequence. Our results show that 27 sampled nests contained parental-like gene pools (six putative F. polyctena and 21 putative F. aquilonia) and all remaining nests (69), from nine localities, contained hybrids of varying degrees. Patterns of genetic variation suggest these hybrids arise from several hybridization events or, instead, have backcrossed to the parental gene pools to varying extents. In contrast to expectations, the mitochondrial haplotypes of the parental species were not randomly distributed among the hybrids. Instead, nests that were closer to parental-like F. aquilonia for nuclear markers preferentially had F. polyctena's mitochondria and vice versa. This systematic pattern suggests there may be underlying selection favouring cytonuclear mismatch and hybridization. We also found a new hybrid locality with strong genetic differences between the sexes similar to those predicted under antagonistic selection on male and female hybrids. Further studies are needed to determine the selective forces that act on male and female genomes in these newly discovered hybrids.}, }
@article {pmid28501977, year = {2017}, author = {Wang, D and Zhao, YQ and Han, YL and Hou, CC and Zhu, JQ}, title = {Characterization of mitochondrial prohibitin from Boleophthalmus pectinirostris and evaluation of its possible role in spermatogenesis.}, journal = {Fish physiology and biochemistry}, volume = {43}, number = {5}, pages = {1299-1313}, pmid = {28501977}, issn = {1573-5168}, support = {Nos. 31272642//National Natural Science Foundation of China/ ; Nos. 2015C110005//Scientific and Technical Project of Ningbo/ ; No.2016A610081//Natural Science Foundation of Ningbo/ ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Fishes/*metabolism ; Male ; Mitochondria/*metabolism ; Phylogeny ; Prohibitins ; RNA, Messenger/genetics/metabolism ; Repressor Proteins/chemistry/genetics/*metabolism ; Spermatogenesis/*physiology ; Testis/metabolism ; }, abstract = {Prohibitin (PHB) is an evolutionarily conserved mitochondrial membrane protein. It plays a vital role in cell proteolysis, senescence, and apoptosis and is associated with spermatogenesis and sperm quality control in mammals. To study the characteristics of the PHB gene and its potential roles during spermatogenesis in Boleophthalmus pectinirostris, we cloned a 1153-bp full-length cDNA from the testis of B. pectinirostris with an open reading frame of 816 bp, which encodes 272 amino acid residues. Real-time quantitative PCR (qPCR) analysis revealed the presence of phb mRNA in all the tissues examined, with higher expression levels found in the testis, kidney, intestine, and muscle tissues. We examined the localization of phb mRNA during spermatogenesis by in situ hybridization (ISH), showing that phb mRNA was distributed in the periphery of the nucleus in primary and secondary spermatocytes. In spermatid and mature sperm, the phb mRNA gradually moved toward one side, where the flagellum is formed. Immunofluorescence (IF) results showed co-localization of the PHB and mitochondria at different stages during spermatogenesis of B. pectinirostris. The signals obtained for PHB decreased as spermatogenesis proceeded; the strongest detection signal was found in secondary spermatocytes, with lower levels of staining in other stages. Additionally, in the mature germ cells, the PHB signals were weak and aggregate in the midpiece of the flagellum.}, }
@article {pmid28501637, year = {2017}, author = {Lane, N}, title = {Serial endosymbiosis or singular event at the origin of eukaryotes?.}, journal = {Journal of theoretical biology}, volume = {434}, number = {}, pages = {58-67}, doi = {10.1016/j.jtbi.2017.04.031}, pmid = {28501637}, issn = {1095-8541}, mesh = {*Biological Evolution ; Energy Metabolism ; Eukaryota/*cytology ; Genomics ; Membranes/metabolism ; Organelles ; Organogenesis/*genetics ; Symbiosis/*genetics ; }, abstract = {'On the Origin of Mitosing Cells' heralded a new way of seeing cellular evolution, with symbiosis at its heart. Lynn Margulis (then Sagan) marshalled an impressive array of evidence for endosymbiosis, from cell biology to atmospheric chemistry and Earth history. Despite her emphasis on symbiosis, she saw plenty of evidence for gradualism in eukaryotic evolution, with multiple origins of mitosis and sex, repeated acquisitions of plastids, and putative evolutionary intermediates throughout the microbial world. Later on, Margulis maintained her view of multiple endosymbioses giving rise to other organelles such as hydrogenosomes, in keeping with the polyphyletic assumptions of the serial endosymbiosis theory. She stood at the threshold of the phylogenetic era, and anticipated its potential. Yet while predicting that the nucleotide sequences of genes would enable a detailed reconstruction of eukaryotic evolution, Margulis did not, and could not, imagine the radically different story that would eventually emerge from comparative genomics. The last eukaryotic common ancestor now seems to have been essentially a modern eukaryotic cell that had already evolved mitosis, meiotic sex, organelles and endomembrane systems. The long search for missing evolutionary intermediates has failed to turn up a single example, and those discussed by Margulis turn out to have evolved reductively from more complex ancestors. Strikingly, Margulis argued that all eukaryotes had mitochondria in her 1967 paper (a conclusion that she later disavowed). But she developed her ideas in the context of atmospheric oxygen and aerobic respiration, neither of which is consistent with more recent geological and phylogenetic findings. Instead, a modern synthesis of genomics and bioenergetics points to the endosymbiotic restructuring of eukaryotic genomes in relation to bioenergetic membranes as the singular event that permitted the evolution of morphological complexity.}, }
@article {pmid28500533, year = {2017}, author = {Lindås, AC and Valegård, K and Ettema, TJG}, title = {Archaeal Actin-Family Filament Systems.}, journal = {Sub-cellular biochemistry}, volume = {84}, number = {}, pages = {379-392}, doi = {10.1007/978-3-319-53047-5_13}, pmid = {28500533}, issn = {0306-0225}, mesh = {Actins/genetics/*metabolism ; Archaea/genetics/*metabolism ; Archaeal Proteins/genetics/*metabolism ; Cytoskeleton ; Phylogeny ; Pyrobaculum/genetics/metabolism ; }, abstract = {Actin represents one of the most abundant and conserved eukaryotic proteins over time, and has an important role in many different cellular processes such as cell shape determination, motility, force generation, cytokinesis, amongst many others. Eukaryotic actin has been studied for decades and was for a long time considered a eukaryote-specific trait. However, in the early 2000s a bacterial actin homolog, MreB, was identified, characterized and found to have a cytoskeletal function and group within the superfamily of actin proteins. More recently, an actin cytoskeleton was also identified in archaea. The genome of the hyperthermophilic crenarchaeon Pyrobaculum calidifontis contains a five-gene cluster named Arcade encoding for an actin homolog, Crenactin, polymerizing into helical filaments spanning the whole length of the cell. Phylogenetic and structural studies place Crenactin closer to the eukaryotic actin than to the bacterial homologues. A significant difference, however, is that Crenactin can form single helical filaments in addition to filaments containing two intertwined proto filaments. The genome of the recently discovered Lokiarchaeota encodes several different actin homologues, termed Lokiactins, which are even more closely related to the eukaryotic actin than Crenactin. A primitive, dynamic actin-based cytoskeleton in archaea could have enabled the engulfment of the alphaproteobacterial progenitor of the mitochondria, a key-event in the evolution of eukaryotes.}, }
@article {pmid28500313, year = {2017}, author = {Robertson, HE and Lapraz, F and Egger, B and Telford, MJ and Schiffer, PH}, title = {The mitochondrial genomes of the acoelomorph worms Paratomella rubra, Isodiametra pulchra and Archaphanostoma ylvae.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1847}, pmid = {28500313}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/H006966/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bayes Theorem ; Gene Order ; Gene Rearrangement ; Genes, Mitochondrial ; Genetics, Population ; Genome Size ; *Genome, Mitochondrial ; Genomics/methods ; Nucleic Acid Conformation ; Phylogeny ; Platyhelminths/*genetics ; Sequence Analysis, DNA ; Transcriptome ; }, abstract = {Acoels are small, ubiquitous - but understudied - marine worms with a very simple body plan. Their internal phylogeny is still not fully resolved, and the position of their proposed phylum Xenacoelomorpha remains debated. Here we describe mitochondrial genome sequences from the acoels Paratomella rubra and Isodiametra pulchra, and the complete mitochondrial genome of the acoel Archaphanostoma ylvae. The P. rubra and A. ylvae sequences are typical for metazoans in size and gene content. The larger I. pulchra mitochondrial genome contains both ribosomal genes, 21 tRNAs, but only 11 protein-coding genes. We find evidence suggesting a duplicated sequence in the I. pulchra mitochondrial genome. The P. rubra, I. pulchra and A. ylvae mitochondria have a unique genome organisation in comparison to other metazoan mitochondrial genomes. We found a large degree of protein-coding gene and tRNA overlap with little non-coding sequence in the compact P. rubra genome. Conversely, the A. ylvae and I. pulchra genomes have many long non-coding sequences between genes, likely driving genome size expansion in the latter. Phylogenetic trees inferred from mitochondrial genes retrieve Xenacoelomorpha as an early branching taxon in the deuterostomes. Sequence divergence analysis between P. rubra sampled in England and Spain indicates cryptic diversity.}, }
@article {pmid28499405, year = {2017}, author = {Cooper, C and Thompson, RCA and Botero, A and Kristancic, A and Peacock, C and Kirilak, Y and Clode, PL}, title = {A comparative molecular and 3-dimensional structural investigation into cross-continental and novel avian Trypanosoma spp. in Australia.}, journal = {Parasites &amp; vectors}, volume = {10}, number = {1}, pages = {234}, pmid = {28499405}, issn = {1756-3305}, mesh = {Animals ; Australia/epidemiology ; Bird Diseases/epidemiology/*parasitology ; DNA, Kinetoplast/genetics ; DNA, Protozoan/genetics ; DNA, Ribosomal ; Geography ; Imaging, Three-Dimensional/methods ; Microscopy, Electron, Scanning/methods ; Mitochondria/ultrastructure ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Trypanosoma/classification/*genetics/isolation &amp; purification/*ultrastructure ; Trypanosomiasis/epidemiology/parasitology/*veterinary ; }, abstract = {BACKGROUND: Molecular and structural information on avian Trypanosoma spp. throughout Australia is limited despite their intrinsic value in understanding trypanosomatid evolution, diversity, and structural biology. In Western Australia tissue samples (n = 429) extracted from 93 birds in 25 bird species were screened using generic PCR primers to investigate the diversity of Trypanosoma spp. To investigate avian trypanosome structural biology the first 3-dimensional ultrastructural models of a Trypanosoma spp. (Trypanosoma sp. AAT) isolated from a bird (currawong, Strepera spp.) were generated using focussed ion beam milling combined with scanning electron microscopy (FIB-SEM).<br><br>RESULTS: Here, we confirm four intercontinental species of avian trypanosomes in native Australian birds, and identify a new avian Trypanosoma. Trypanosome infection was identified in 18 birds from 13 different bird species (19%). A single new genotype was isolated and found to be closely related to T. culicavium (Trypanosoma sp. CC2016 B002). Other Trypanosoma spp. identified include T. avium, T. culicavium, T. thomasbancrofti, Trypanosoma sp. TL.AQ.22, Trypanosoma sp. AAT, and an uncharacterised Trypanosoma sp. (group C-III sensu Zidkov&#xe1; et al. (Infect Genet Evol 12:102-112, 2012)), all previously identified in Australia or other continents. Serially-sectioning Trypanosoma sp. AAT epimastigotes using FIB-SEM revealed the disc-shaped kinetoplast pocket attached perpendicular to the branching mitochondrion. Additionally, the universal minicircle sequence within the kinetoplast DNA and the associated binding protein were determined in Trypanosoma sp. AAT.<br><br>CONCLUSIONS: These results indicate that bird trypanosomes are relatively conserved across continents, while being locally diverse, which supports the hypothesis that bird trypanosomes exist as fewer species than described in the literature. Evidence exists that avian Trypanosoma spp. are infecting mammals and could be transmitted by haemadipsid leeches. Trypanosoma sp. AAT is most likely a separate species currently found only in Australia and the first 3-dimentional ultrastructural analysis of an avian trypanosome provides interesting information on their morphology and organelle arrangement.}, }
@article {pmid28497122, year = {2017}, author = {Franco-Obregón, A and Gilbert, JA}, title = {The Microbiome-Mitochondrion Connection: Common Ancestries, Common Mechanisms, Common Goals.}, journal = {mSystems}, volume = {2}, number = {3}, pages = {}, pmid = {28497122}, issn = {2379-5077}, abstract = {Lynn Margulis in the 1960s elegantly proposed a shared phylogenetic history between bacteria and mitochondria; this relationship has since become a cornerstone of modern cellular biology. Yet, an interesting facet of the interaction between the microbiome and mitochondria has been mostly ignored, that of the systems biology relationship that underpins host health and longevity. The mitochondria are descendants of primordial aerobic pleomorphic bacteria (likely genus Rickettsia) that entered (literally and functionally) into a mutualistic partnership with ancient anaerobic microbes (likely Archaea). A stable symbiosis was established, given the metabolic versatility of the early mitochondria, which were capable of providing energy with or without oxygen, whereas nutrient gathering was the assumed responsibility of the host. While microbial relationships with single-cell protists must have occurred in the past, as they occur today, the evolution of multicellular organisms generated a new framework for symbiosis with the microbial world, taking the ancient partnership to an entirely new level. Cell-cell communication between microbes and single-cell protists was augmented through multicellularity to allow distant communication between the host cells and the microbiome, resulting in the development of complex metabolic relationships and an immune system to manage these interactions. Thus, the host is now the body and its resident mitochondria, and the microbiome is an essential supplier of metabolites that act at the level of mitochondria in skeletal muscle to stabilize host metabolism. We humans are caretakers of a profoundly vast and diverse microbiota, the majority of which resides in the gut. Indeed, the microbial genetic diversity of our microbiota outstrips our own by several orders of magnitude, and the cellular abundance is roughly equivalent to our somatic selves. Modern clinical science has elegantly highlighted the importance of the microbiome for metabolic health and well-being. This perspective underscores one fundamental facet of this symbiosis, the ancestral mitochondrion-microbiome axis.}, }
@article {pmid28495966, year = {2017}, author = {Gray, MW}, title = {Lynn Margulis and the endosymbiont hypothesis: 50 years later.}, journal = {Molecular biology of the cell}, volume = {28}, number = {10}, pages = {1285-1287}, pmid = {28495966}, issn = {1939-4586}, mesh = {Bacteria ; *Biological Evolution ; Cilia ; Eukaryotic Cells ; Mitochondria ; Phylogeny ; Plastids ; *Symbiosis ; }, abstract = {The 1967 article "On the Origin of Mitosing Cells" in the Journal of Theoretical Biology by Lynn Margulis (then Lynn Sagan) is widely regarded as stimulating renewed interest in the long-dormant endosymbiont hypothesis of organelle origins. In her article, not only did Margulis champion an endosymbiotic origin of mitochondria and plastids from bacterial ancestors, but she also posited that the eukaryotic flagellum (undulipodium in her usage) and mitotic apparatus originated from an endosymbiotic, spirochete-like organism. In essence, she presented a comprehensive symbiotic view of eukaryotic cell evolution (eukaryogenesis). Not all of the ideas in her article have been accepted, for want of compelling evidence, but her vigorous promotion of the role of symbiosis in cell evolution unquestionably had a major influence on how subsequent investigators have viewed the origin and evolution of mitochondria and plastids and the eukaryotic cell per se.}, }
@article {pmid28495309, year = {2017}, author = {Ngu, M and Massel, K and Bonen, L}, title = {Group II introns in wheat mitochondria have degenerate structural features and varied splicing pathways.}, journal = {The international journal of biochemistry &amp; cell biology}, volume = {91}, number = {Pt B}, pages = {156-167}, doi = {10.1016/j.biocel.2017.05.014}, pmid = {28495309}, issn = {1878-5875}, mesh = {Base Sequence ; Introns/*genetics ; Mitochondria/*genetics ; RNA Splice Sites/genetics ; *RNA Splicing ; Triticum/*genetics ; }, abstract = {Mitochondrial introns in flowering plant genes are virtually all classified as members of the group II ribozyme family although certain structural features have degenerated to varying degrees over evolutionary time. We are interested in the impact that unconventional intron architecture might have on splicing biochemistry in vivo and we have focused in particular on intronic domains V and VI, which for self-splicing introns provide a key component of the catalytic core and the bulged branchpoint adenosine, respectively. Notably, the two transesterification steps in classical group II splicing are the same as for nuclear spliceosomal introns and release the intron as a lariat. Using RT-PCR and circularized RT-PCR, we had previously demonstrated that several wheat mitochondrial introns which lack a branchpoint adenosine have atypical splicing pathways, and we have now extended this analysis to the full set of wheat introns, namely six trans-splicing and sixteen cis-splicing ones. A number of introns are excised using non-lariat pathways and interestingly, we find that several introns which do have a conventional domain VI also use pathways that appear to exploit other internal or external nucleophiles, with the lariat form being relatively minor. Somewhat surprisingly, several introns with weakly-structured domain V/VI helices still exhibit classical lariat splicing, suggesting that accessory factors aid in restoring a splicing-competent conformation. Our observations illustrate that the loss of conventional group II features during evolution is correlated with altered splicing biochemistry in an intron-distinctive manner.}, }
@article {pmid28493482, year = {2017}, author = {Dibrova, DV and Shalaeva, DN and Galperin, MY and Mulkidjanian, AY}, title = {Emergence of cytochrome bc complexes in the context of photosynthesis.}, journal = {Physiologia plantarum}, volume = {161}, number = {1}, pages = {150-170}, pmid = {28493482}, issn = {1399-3054}, mesh = {Archaea/metabolism ; Bacteria/metabolism ; Cytochromes b/*metabolism ; Cytochromes c/*metabolism ; *Photosynthesis ; Phylogeny ; }, abstract = {The cytochrome bc (cyt bc) complexes are involved in Q-cycling; they oxidize membrane quinols by high-potential electron acceptors, such as cytochromes or plastocyanin, and generate transmembrane proton gradient. In several prokaryotic lineages, and also in plant chloroplasts, the catalytic core of the cyt bc complexes is built of a four-helical cytochrome b (cyt b) that contains three hemes, a three-helical subunit IV, and an iron-sulfur Rieske protein (cytochrome b6 f-type complexes). In other prokaryotic lineages, and also in mitochondria, the cyt b subunit is fused with subunit IV, yielding a seven- or eight-helical cyt b with only two hemes (cyt bc1 -type complexes). Here we present an updated phylogenomic analysis of the cyt b subunits of cyt bc complexes. This analysis provides further support to our earlier suggestion that (1) the ancestral version of cyt bc complex contained a small four-helical cyt b with three hemes similar to the plant cytochrome b6 and (2) independent fusion events led to the formation of large cyts b in several lineages. In the search for a primordial function for the ancestral cyt bc complex, we address the intimate connection between the cyt bc complexes and photosynthesis. Indeed, the Q-cycle turnover in the cyt bc complexes demands high-potential electron acceptors. Before the Great Oxygenation Event, the biosphere had been highly reduced, so high-potential electron acceptors could only be generated upon light-driven charge separation. It appears that an ancestral cyt bc complex capable of Q-cycling has emerged in conjunction with the (bacterio)chlorophyll-based photosynthetic systems that continuously generated electron vacancies at the oxidized (bacterio)chlorophyll molecules.}, }
@article {pmid28487526, year = {2017}, author = {Wang, P and Sha, T and Zhang, Y and Cao, Y and Mi, F and Liu, C and Yang, D and Tang, X and He, X and Dong, J and Wu, J and Yoell, S and Yoell, L and Zhang, KQ and Zhang, Y and Xu, J}, title = {Frequent heteroplasmy and recombination in the mitochondrial genomes of the basidiomycete mushroom Thelephora ganbajun.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1626}, pmid = {28487526}, issn = {2045-2322}, mesh = {Agaricales/*genetics/isolation &amp; purification ; Amino Acid Sequence ; Base Sequence ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Gene Amplification ; Genetic Loci ; *Genome, Mitochondrial ; Geography ; Heterozygote ; Homozygote ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; *Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {In the majority of sexual eukaryotes, the mitochondrial genomes are inherited uniparentally. As a result, individual organisms are homoplasmic, containing mitochondrial DNA (mtDNA) from a single parent. Here we analyzed the mitochondrial genotypes in Clade I of the gourmet mushroom Thelephora ganbajun from its broad geographic distribution range. A total of 299 isolates from 28 geographic locations were sequenced at three mitochondrial loci: the mitochondrial small ribosomal RNA gene, and the cytochrome c oxidase subunits I (COX1) and III (COX3) genes. Quantitative PCR analyses showed that the strains had about 60-160 copies of mitochondrial genomes per cell. Interestingly, while no evidence of heteroplasmy was found at the 12S rRNA gene, 262 of the 299 isolates had clear evidence of heterogeneity at either the COX1 (261 isolates) or COX3 (12 isolates) gene fragments. The COX1 heteroplasmy was characterized by two types of introns residing at different sites of the same region and at different frequencies among the isolates. Allelic association analyses of the observed mitochondrial polymorphic nucleotide sites suggest that mtDNA recombination is common in natural populations of this fungus. Our results contrast the prevailing view that heteroplasmy, if exists, is only transient in basidiomycete fungi.}, }
@article {pmid28487062, year = {2018}, author = {Sandler, N and Kaczmarek, E and Itagaki, K and Zheng, Y and Otterbein, L and Khabbaz, K and Liu, D and Senthilnathan, V and Gruen, RL and Hauser, CJ}, title = {Mitochondrial DAMPs Are Released During Cardiopulmonary Bypass Surgery and Are Associated With Postoperative Atrial Fibrillation.}, journal = {Heart, lung &amp; circulation}, volume = {27}, number = {1}, pages = {122-129}, doi = {10.1016/j.hlc.2017.02.014}, pmid = {28487062}, issn = {1444-2892}, mesh = {Aged ; Atrial Fibrillation/*blood/genetics ; Biomarkers/blood ; Cardiopulmonary Bypass/*adverse effects ; DNA, Mitochondrial/*blood/genetics ; Female ; Heart Diseases/surgery ; Humans ; Male ; Mitochondria/*genetics/metabolism ; Polymerase Chain Reaction ; *Postoperative Complications ; Prospective Studies ; }, abstract = {BACKGROUND: Atrial fibrillation (AF) is the most frequent complication of surgery performed on cardiopulmonary bypass (CPB) and recent work associates CPB with postoperative inflammation. We have shown that all tissue injury releases mitochondrial damage associated molecular patterns (mtDAMPs) including mitochondrial DNA (mtDNA). This can act as a direct, early activator of neutrophils (PMN), eliciting a systemic inflammatory response syndrome (SIRS) while suppressing PMN function. Neutrophil Extracellular Traps (NETs) are crucial to host defence. They carry out NETosis wherein webs of granule proteins and chromatin trap and kill bacteria. We hypothesised that surgery performed on CPB releases mtDAMPs into the circulation. Molecular patterns thus mobilised during CPB might then participate in the pathogenesis of SIRS and predict postoperative complications like AF [1].<br><br>METHODS: We prospectively studied 16 patients undergoing elective operations on CPB. Blood was sampled preoperatively, at the end of CPB and on days 1-2 postoperatively. Plasma samples were analysed for mtDNA. Neutrophil IL-6 gene expression was studied to assess induction of SIRS. Neutrophils were also assayed for the presence of neutrophil extracellular traps (NETs/NETosis). These biologic findings were then correlated to clinical data and compared in patients with and without postoperative AF (POAF).<br><br>RESULTS: Mitochondrial DNA was significantly elevated following CPB (six-fold increase post-CPB, p=0.008 and five-fold increase days 1-2, p=0.02). Patients with POAF showed greater increases in mtDNA post-CPB than those without. Postoperative AF was seen in all patients with a &#x2265;2-fold increase of mtDNA (p=0.037 vs. <2-fold). Neutrophil IL-6 gene transcription increased postoperatively demonstrating SIRS that was greatest days 1-2 (p=0.039). Neutrophil extracellular trap (NET) formation was markedly suppressed in the post-CPB state.<br><br>CONCLUSION: Mitochondrial DNA is released by CPB surgery and is associated with POAF. IL-6 gene expression increases after CPB, demonstrating the evolution of postoperative SIRS. Lastly, cardiac surgery on CPB also suppressed PMN NETosis. Taken together, our data suggest that mtDNA released during surgery on CPB, may be involved in the pathogenesis of SIRS and related postoperative inflammatory events like POAF and infections. Mitochondrial DNA may therefore prove to be an early biomarker for postoperative complications with the degree of association to be determined in appropriately sized studies. If mtDNA is directly involved in cardiac inflammation, mtDNA-induced toll-like receptor-9 (TLR9) signalling could also be targeted therapeutically.}, }
@article {pmid28482903, year = {2017}, author = {Liang, W and Liao, Y and Zhang, J and Huang, Q and Luo, W and Yu, J and Gong, J and Zhou, Y and Li, X and Tang, B and He, S and Yang, J}, title = {Heat shock factor 1 inhibits the mitochondrial apoptosis pathway by regulating second mitochondria-derived activator of caspase to promote pancreatic tumorigenesis.}, journal = {Journal of experimental &amp; clinical cancer research : CR}, volume = {36}, number = {1}, pages = {64}, pmid = {28482903}, issn = {1756-9966}, mesh = {Adult ; Aged ; Animals ; *Apoptosis ; Apoptosis Regulatory Proteins ; Cell Cycle ; Cell Line, Tumor ; Cell Proliferation ; Cell Transformation, Neoplastic/genetics/*metabolism ; Disease Models, Animal ; Female ; Gene Expression ; Heat Shock Transcription Factors/genetics/*metabolism ; Heterografts ; Humans ; Intracellular Signaling Peptides and Proteins/*metabolism ; Male ; Mice ; Middle Aged ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/*metabolism ; Models, Biological ; Neoplasm Grading ; Neoplasm Staging ; Pancreatic Neoplasms/genetics/*metabolism/pathology ; *Signal Transduction ; }, abstract = {BACKGROUND: As a relatively conservative transcriptional regulator in biological evolution, heat shock factor 1 (HSF1) is activated by, and regulates the expression of heat shock proteins (HSPs) in response to a variety of stress conditions. HSF1 also plays a key role in regulating the development of various tumors; however, its role in pancreatic cancer and the specific underlying mechanism are not clear.<br><br>METHODS: We first examined HSF1 expression in pancreatic cancer tissues by immunohistochemistry, and then studied its clinical significance. We then constructed HSF1-siRNA to investigate the potential of HSF1 to regulate apoptosis, proliferation and the cell cycle of pancreatic cancer cells and the underlying mechanism both in vitro and in vivo. Protein chip analysis was used subsequently to explore the molecular regulation pathway. Finally, second mitochondria-derived activator of caspase (SMAC)-siRNA was used to validate the signaling pathway.<br><br>RESULTS: HSF1 was highly expressed in pancreatic cancer tissues and the level of upregulation was found to be closely related to the degree of pancreatic cancer differentiation and poor prognosis. After HSF1-silencing, we found that pancreatic cancer cell proliferation decreased both in vitro and in vivo and the apoptotic cell ratio increased, while the mitochondrial membrane potential decreased, and the cells were arrested at the G0/G1 phase. In terms of the molecular mechanism, we confirmed that HSF1 regulated SMAC to inhibit mitochondrial apoptosis in pancreatic cancer cells, and to promote the occurrence of pancreatic tumors. SMAC silencing reversed the effects of HSF1 silencing.<br><br>CONCLUSION: Our study provides evidence that HSF1 functions as a novel oncogene in pancreatic tumors and is implicated as a target for the diagnosis and treatment of pancreatic cancer.}, }
@article {pmid28478197, year = {2017}, author = {Copilaş-Ciocianu, D and Rutová, T and Pařil, P and Petrusek, A}, title = {Epigean gammarids survived millions of years of severe climatic fluctuations in high latitude refugia throughout the Western Carpathians.}, journal = {Molecular phylogenetics and evolution}, volume = {112}, number = {}, pages = {218-229}, doi = {10.1016/j.ympev.2017.04.027}, pmid = {28478197}, issn = {1095-9513}, mesh = {Altitude ; Amphipoda/genetics/*physiology ; Animals ; Base Sequence ; Bayes Theorem ; *Climate ; Europe ; Genetic Variation ; Geography ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; *Refugium ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Isolated glacial refugia have been documented in Central Europe for a number of taxa, but conclusive evidence for epigean aquatic species has remained elusive. Using molecular data (mitochondrial and nuclear markers), we compared the spatial patterns of lineage diversity of the widely distributed Gammarus fossarum species complex between two adjacent biogeographically and geomorphologically distinct Central European regions: the Bohemian Massif and the Western Carpathians. We investigated if the observed patterns of spatial diversity are more likely to stem from historical or present-day factors. Phylogenetic and phylogeographic analyses revealed eight phylogenetically diverse lineages: two exhibiting local signatures of recent demographic expansion inhabit both regions, while the other six display a relict distributional pattern and are found only in the Western Carpathians. Molecular dating indicates that these lineages are old and probably diverged throughout the Miocene (7-18Ma). Furthermore, their distribution does not seem to be constrained by the present boundaries of river catchments or topography. The contrasting spatial patterns of diversity observed between the two regions thus more likely result from historical rather than contemporaneous or recent factors. Our results indicate that despite the high latitude and proximity to the Pleistocene ice sheets, the Western Carpathians functioned as long-term glacial refugia for permanent freshwater fauna, allowing the uninterrupted survival of ancient lineages through millions of years of drastic climatic fluctuations.}, }
@article {pmid28476317, year = {2017}, author = {Lemire, BD}, title = {Evolution, structure and membrane association of NDUFAF6, an assembly factor for NADH:ubiquinone oxidoreductase (Complex I).}, journal = {Mitochondrion}, volume = {35}, number = {}, pages = {13-22}, doi = {10.1016/j.mito.2017.04.005}, pmid = {28476317}, issn = {1872-8278}, mesh = {Electron Transport Complex I/*metabolism ; Humans ; Mitochondrial Membranes/*chemistry ; Mitochondrial Proteins/chemistry/*genetics/*metabolism ; Models, Molecular ; Phylogeny ; Protein Conformation ; }, abstract = {The NADH:ubiquinone oxidoreductase (complex I) is the largest member of the mitochondrial respiratory chain. Its FMN cofactor accepts two electrons from NADH and transfers them to ubiquinone via a chain of iron-sulphur centers. A central core of 14 highly conserved subunits can couple electron transfer to proton translocation. The mammalian enzyme has an additional ~30 accessory subunits. Complex I has important bioenergetic and metabolic functions and is a known source of reactive oxygen species; these functions link it to a number of hereditary and degenerative diseases. For many complex I deficiencies, the primary defect is not in a subunit-encoding gene, but rather in an assembly factor or chaperone that participates in the biogenesis of newly synthesized complex I from individual subunits and cofactors. NDUFAF6 encodes a complex I assembly factor and mutations result in complex I deficiency, Leigh syndrome or Acadian variant Fanconi syndrome. Human NDUFAF6 is a mitochondria-targeted 333-amino acid protein belonging to the family of squalene and phytoene synthases. Sequence and structural information suggests that NDUFAF6 likely has enzymatic activity, but one that has evolved considerable differences from canonical squalene and phytoene synthases. Most but not all metazoans have an NDUFAF6 ortholog, indicating that in some organisms, complex I biogenesis does not require this protein. NDUFAF6 is a peripheral membrane protein and predictions identify a conserved C-terminal attachment site that have implications for substrate access.}, }
@article {pmid28473298, year = {2017}, author = {Yin, Q and Zhang, Y and Dong, D and Lei, M and Zhang, S and Liao, CC and Pan, YH}, title = {Maintenance of neural activities in torpid Rhinolophus ferrumequinum bats revealed by 2D gel-based proteome analysis.}, journal = {Biochimica et biophysica acta. Proteins and proteomics}, volume = {1865}, number = {8}, pages = {1004-1019}, doi = {10.1016/j.bbapap.2017.04.006}, pmid = {28473298}, issn = {1570-9639}, mesh = {Adaptation, Physiological/physiology ; Animals ; Brain/metabolism/physiology ; Chiroptera/*metabolism/*physiology ; Energy Metabolism/physiology ; Hibernation/physiology ; Mitochondria/metabolism/physiology ; Proteome/*metabolism ; Proteomics/methods ; Seasons ; }, abstract = {Bats are the only mammals capable of self-powered flying. Many bat species hibernate in winter. A reversible control of cerebral activities is critical for bats to accommodate a repeated torpor-arousal cycle during hibernation. Little is known about the molecular mechanisms that regulate neuronal activities in torpid bats. In this study, Rhinolophus ferrumequinum bat brain proteins were fractionated, and their abundance in active and torpid states was compared. Results of 2D gel-based proteomics showed that 38% of identified proteins with a significant change in abundance are involved in synaptic vesicle recycling and cytoskeletal integrity. Changes in the abundance of proteins related to RNA splicing, proteostasis, redox homeostasis, mitochondrial function, and energy metabolism were also detected. In addition, the levels of GNAO1 (guanine nucleotide-binding protein Gαo subunit), an important modulator of neuronal transmembrane signaling, were significantly increased in the insoluble protein fraction of torpid bats; this may be due to GNAO1 palmitoylation making it insoluble. Our data provide molecular evidence for the maintenance of neuronal activities in torpid bats and suggest that a reversible palmitoylation of the G protein plays a role in the regulation of neuronal activities during bat hibernation.}, }
@article {pmid28472937, year = {2017}, author = {Moreira, DA and Buckup, PA and Furtado, C and Val, AL and Schama, R and Parente, TE}, title = {Reducing the information gap on Loricarioidei (Siluriformes) mitochondrial genomics.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {345}, pmid = {28472937}, issn = {1471-2164}, mesh = {Animals ; Base Sequence ; Catfishes/*genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genetic Variation ; *Genome, Mitochondrial ; Genomics ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Phylogeny ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The genetic diversity of Neotropical fish fauna is underrepresented in public databases. This distortion is evident for the order Siluriformes, in which the suborders Siluroidei and Loricarioidei share equivalent proportion of species, although far less is known about the genetics of the latter clade, endemic to the Neotropical Region. Recently, this information gap was evident in a study about the structural diversity of fish mitochondrial genomes, and hampered a precise chronological resolution of Siluriformes. It has also prevented molecular ecology investigations about these catfishes, their interactions with the environment, responses to anthropogenic changes and potential uses.<br><br>RESULTS: Using high-throughput sequencing, we provide the nearly complete mitochondrial genomes for 26 Loricariidae and one Callichthyidae species. Structural features were highly conserved. A notable exception was identified in the monophyletic clade comprising species of the Hemiancistrus, Hypostomini and Peckoltia-clades, a ~60 nucleotide-long deletion encompassing the seven nucleotides at the 3' end of the Conserved Sequence Block (CSB) D of the control region. The expression of mitochondrial genes followed the usual punctuation pattern. Heteroplasmic sites were identified in most species. The retrieved phylogeny strongly corroborates the currently accepted tree, although bringing to debate the relationship between Schizolecis guntheri and Pareiorhaphis garbei, and highlighting the low genetic variability within the Peckoltia-clade, an eco-morphologically diverse and taxonomically problematic group.<br><br>CONCLUSIONS: Herein we have launched the use of high-throughput mitochondrial genomics in the studies of the Loricarioidei species. The new genomic resources reduce the information gap on the molecular diversity of Neotropical fish fauna, impacting the capacity to investigate a variety of aspects of the molecular ecology and evolution of these fishes. Additionally, the species showing the partial CSB-D are candidate models to study the replication and transcription of vertebrate mitochondrial genome.}, }
@article {pmid28463550, year = {2017}, author = {Nakazawa, M and Hayashi, R and Takenaka, S and Inui, H and Ishikawa, T and Ueda, M and Sakamoto, T and Nakano, Y and Miyatake, K}, title = {Physiological functions of pyruvate:NADP[+] oxidoreductase and 2-oxoglutarate decarboxylase in Euglena gracilis under aerobic and anaerobic conditions.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {81}, number = {7}, pages = {1386-1393}, doi = {10.1080/09168451.2017.1318696}, pmid = {28463550}, issn = {1347-6947}, mesh = {Aerobiosis/genetics ; Amino Acid Sequence ; Anaerobiosis/genetics ; Carboxy-Lyases/genetics/*metabolism ; Cloning, Molecular ; Culture Media/chemistry ; Decarboxylation ; Energy Metabolism/*genetics ; Escherichia coli/genetics/metabolism ; Euglena gracilis/*enzymology/genetics ; Fermentation ; Gene Expression ; Gene Expression Regulation ; Glucose/metabolism ; Ketone Oxidoreductases/genetics/*metabolism ; Kinetics ; Mitochondria/genetics/*metabolism ; Oxidation-Reduction ; Protozoan Proteins/genetics/*metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {In Euglena gracilis, pyruvate:NADP[+] oxidoreductase, in addition to the pyruvate dehydrogenase complex, functions for the oxidative decarboxylation of pyruvate in the mitochondria. Furthermore, the 2-oxoglutarate dehydrogenase complex is absent, and instead 2-oxoglutarate decarboxylase is found in the mitochondria. To elucidate the central carbon and energy metabolisms in Euglena under aerobic and anaerobic conditions, physiological significances of these enzymes involved in 2-oxoacid metabolism were examined by gene silencing experiments. The pyruvate dehydrogenase complex was indispensable for aerobic cell growth in a glucose medium, although its activity was less than 1% of that of pyruvate:NADP[+] oxidoreductase. In contrast, pyruvate:NADP[+] oxidoreductase was only involved in the anaerobic energy metabolism (wax ester fermentation). Aerobic cell growth was almost completely suppressed when the 2-oxoglutarate decarboxylase gene was silenced, suggesting that the tricarboxylic acid cycle is modified in Euglena and 2-oxoglutarate decarboxylase takes the place of the 2-oxoglutarate dehydrogenase complex in the aerobic respiratory metabolism.}, }
@article {pmid28461155, year = {2017}, author = {Harish, A and Kurland, CG}, title = {Akaryotes and Eukaryotes are independent descendants of a universal common ancestor.}, journal = {Biochimie}, volume = {138}, number = {}, pages = {168-183}, doi = {10.1016/j.biochi.2017.04.013}, pmid = {28461155}, issn = {1638-6183}, mesh = {Archaea/genetics ; Bacteria/genetics ; Bayes Theorem ; Eukaryota/genetics ; *Evolution, Molecular ; *Genome ; Mitochondria ; *Models, Genetic ; *Phylogeny ; *Proteome ; }, abstract = {We reconstructed a global tree of life (ToL) with non-reversible and non-stationary models of genome evolution that root trees intrinsically. We implemented Bayesian model selection tests and compared the statistical support for four conflicting ToL hypotheses. We show that reconstructions obtained with a Bayesian implementation (Klopfstein et al., 2015) are consistent with reconstructions obtained with an empirical Sankoff parsimony (ESP) implementation (Harish et al., 2013). Both are based on the genome contents of coding sequences for protein domains (superfamilies) from hundreds of genomes. Thus, we conclude that the independent descent of Eukaryotes and Akaryotes (archaea and bacteria) from the universal common ancestor (UCA) is the most probable as well as the most parsimonious hypothesis for the evolutionary origins of extant genomes. Reconstructions of ancestral proteomes by both Bayesian and ESP methods suggest that at least 70% of unique domain-superfamilies known in extant species were present in the UCA. In addition, identification of a vast majority (96%) of the mitochondrial superfamilies in the UCA proteome precludes a symbiotic hypothesis for the origin of eukaryotes. Accordingly, neither the archaeal origin of eukaryotes nor the bacterial origin of mitochondria is supported by the data. The proteomic complexity of the UCA suggests that the evolution of cellular phenotypes in the two primordial lineages, Akaryotes and Eukaryotes, was driven largely by duplication of common superfamilies as well as by loss of unique superfamilies. Finally, innovation of novel superfamilies has played a surprisingly small role in the evolution of Akaryotes and only a marginal role in the evolution of Eukaryotes.}, }
@article {pmid28460111, year = {2017}, author = {Sharbrough, J and Cruise, JL and Beetch, M and Enright, NM and Neiman, M}, title = {Genetic Variation for Mitochondrial Function in the New Zealand Freshwater Snail Potamopyrgus antipodarum.}, journal = {The Journal of heredity}, volume = {108}, number = {7}, pages = {759-768}, doi = {10.1093/jhered/esx041}, pmid = {28460111}, issn = {1465-7333}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Genetic Variation ; *Genome, Mitochondrial ; Hot Temperature ; Mitochondria/genetics/physiology ; New Zealand ; Oxygen Consumption ; Phenotype ; Snails/*genetics ; Stress, Physiological ; }, abstract = {The proteins responsible for mitochondrial function are encoded by 2 different genomes with distinct inheritance regimes, rendering rigorous inference of genotype-phenotype connections intractable for all but a few model systems. Asexual organisms provide a powerful means to address these challenges because offspring produced without recombination inherit both nuclear and mitochondrial genomes from a single parent. As such, these offspring inherit mitonuclear genotypes that are identical to the mitonuclear genotypes of their parents and siblings but different from those of other asexual lineages. Here, we compared mitochondrial function across distinct asexual lineages of Potamopyrgus antipodarum, a New Zealand freshwater snail model for understanding the evolutionary consequences of asexuality. Our analyses revealed substantial phenotypic variation across asexual lineages at 3 levels of biological organization: mitogenomic, organellar, and organismal. These data demonstrate that different asexual lineages have different mitochondrial function phenotypes, likely reflecting heritable variation (i.e., the raw material for evolution) for mitochondrial function in P. antipodarum. The discovery of this variation combined with the methods developed here sets the stage to use P. antipodarum to study central evolutionary questions involving mitochondrial function, including whether mitochondrial mutation accumulation influences the maintenance of sexual reproduction in natural populations.}, }
@article {pmid28460080, year = {2017}, author = {Schiavo, G and Hoffmann, OI and Ribani, A and Utzeri, VJ and Ghionda, MC and Bertolini, F and Geraci, C and Bovo, S and Fontanesi, L}, title = {A genomic landscape of mitochondrial DNA insertions in the pig nuclear genome provides evolutionary signatures of interspecies admixture.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {24}, number = {5}, pages = {487-498}, pmid = {28460080}, issn = {1756-1663}, mesh = {Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial ; *Evolution, Molecular ; *Genome ; *Genomics ; *INDEL Mutation ; Mitochondria/genetics ; Phylogeny ; *Polymorphism, Genetic ; Sequence Analysis, DNA ; Sus scrofa/*genetics ; }, abstract = {Nuclear DNA sequences of mitochondrial origin (numts) are derived by insertion of mitochondrial DNA (mtDNA), into the nuclear genome. In this study, we provide, for the first time, a genome picture of numts inserted in the pig nuclear genome. The Sus scrofa reference nuclear genome (Sscrofa10.2) was aligned with circularized and consensus mtDNA sequences using LAST software. A total of 430 numt sequences that may represent 246 different numt integration events (57 numt regions determined by at least two numt sequences and 189 singletons) were identified, covering about 0.0078% of the nuclear genome. Numt integration events were correlated (0.99) to the chromosome length. The longest numt sequence (about 11 kbp) was located on SSC2. Six numts were sequenced and PCR amplified in pigs of European commercial and local pig breeds, of the Chinese Meishan breed and in European wild boars. Three of them were polymorphic for the presence or absence of the insertion. Surprisingly, the estimated age of insertion of two of the three polymorphic numts was more ancient than that of the speciation time of the Sus scrofa, supporting that these polymorphic sites were originated from interspecies admixture that contributed to shape the pig genome.}, }
@article {pmid28459876, year = {2017}, author = {Araújo Castro, J and Gomes Ferreira, MD and Santana Silva, RJ and Andrade, BS and Micheli, F}, title = {Alternative oxidase (AOX) constitutes a small family of proteins in Citrus clementina and Citrus sinensis L. Osb.}, journal = {PloS one}, volume = {12}, number = {5}, pages = {e0176878}, pmid = {28459876}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Citrus/*enzymology/*genetics ; Conserved Sequence ; Exons ; Gene Expression Regulation, Plant/physiology ; Hydrophobic and Hydrophilic Interactions ; Mitochondria/metabolism ; Mitochondrial Proteins/*genetics/*metabolism ; Molecular Docking Simulation ; Oxidoreductases/*genetics/*metabolism ; Phylogeny ; Plant Proteins/*genetics/*metabolism ; Plant Structures/enzymology/genetics ; Promoter Regions, Genetic ; Protein Processing, Post-Translational ; Protein Structure, Secondary ; Sequence Homology, Amino Acid ; Species Specificity ; Ubiquinone/metabolism ; }, abstract = {The alternative oxidase (AOX) protein is present in plants, fungi, protozoa and some invertebrates. It is involved in the mitochondrial respiratory chain, providing an alternative route for the transport of electrons, leading to the reduction of oxygen to form water. The present study aimed to characterize the family of AOX genes in mandarin (Citrus clementina) and sweet orange (Citrus sinensis) at nucleotide and protein levels, including promoter analysis, phylogenetic analysis and C. sinensis gene expression. This study also aimed to do the homology modeling of one AOX isoform (CcAOXd). Moreover, the molecular docking of the CcAOXd protein with the ubiquinone (UQ) was performed. Four AOX genes were identified in each citrus species. These genes have an open reading frame (ORF) ranging from 852 bp to 1150 bp and a number of exons ranging from 4 to 9. The 1500 bp-upstream region of each AOX gene contained regulatory cis-elements related to internal and external response factors. CsAOX genes showed a differential expression in citrus tissues. All AOX proteins were predicted to be located in mitochondria. They contained the conserved motifs LET, NERMHL, LEEEA and RADE-H as well as several putative post-translational modification sites. The CcAOXd protein was modeled by homology to the AOX of Trypanosona brucei (45% of identity). The 3-D structure of CcAOXd showed the presence of two hydrophobic helices that could be involved in the anchoring of the protein in the inner mitochondrial membrane. The active site of the protein is located in a hydrophobic environment deep inside the AOX structure and contains a diiron center. The molecular docking of CcAOXd with UQ showed that the binding site is a recessed pocket formed by the helices and submerged in the membrane. These data are important for future functional studies of citrus AOX genes and/or proteins, as well as for biotechnological approaches leading to AOX inhibition using UQ homologs.}, }
@article {pmid28456662, year = {2017}, author = {Kinkar, L and Laurimäe, T and Sharbatkhori, M and Mirhendi, H and Kia, EB and Ponce-Gordo, F and Andresiuk, V and Simsek, S and Lavikainen, A and Irshadullah, M and Umhang, G and Oudni-M'rad, M and Acosta-Jamett, G and Rehbein, S and Saarma, U}, title = {New mitogenome and nuclear evidence on the phylogeny and taxonomy of the highly zoonotic tapeworm Echinococcus granulosus sensu stricto.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {52}, number = {}, pages = {52-58}, doi = {10.1016/j.meegid.2017.04.023}, pmid = {28456662}, issn = {1567-7257}, mesh = {Africa, Northern ; Animals ; Asia ; Cell Nucleus/*genetics ; DNA, Helminth/*genetics ; Echinococcus granulosus/*classification/genetics/isolation &amp; purification/metabolism ; Europe ; Genome, Mitochondrial ; Genotype ; Humans ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; South America ; Zoonoses/parasitology ; }, abstract = {Cystic echinococcosis, a zoonotic disease caused by Echinococcus granulosus sensu lato (s. l.), is a significant global public health concern. Echinococcus granulosus s. l. is currently divided into numerous genotypes (G1-G8 and G10) of which G1-G3 are the most frequently implicated genotypes in human infections. Although it has been suggested that G1-G3 could be regarded as a distinct species E. granulosus sensu stricto (s. s.), the evidence to support this is inconclusive. Most importantly, data from nuclear DNA that provide means to investigate the exchange of genetic material between G1-G3 is lacking as none of the published nuclear DNA studies have explicitly included G2 or G3. Moreover, the commonly used relatively short mtDNA sequences, including the complete cox1 gene, have not allowed unequivocal differentiation of genotypes G1-G3. Therefore, significantly longer mtDNA sequences are required to distinguish these genotypes with confidence. The main aim of this study was to evaluate the phylogenetic relations and taxonomy of genotypes G1-G3 using sequences of nearly complete mitogenomes (11,443bp) and three nuclear loci (2984bp). A total of 23 G1-G3 samples were analysed, originating from 5 intermediate host species in 10 countries. The mtDNA data demonstrate that genotypes G1 and G3 are distinct mitochondrial genotypes (separated by 37 mutations), whereas G2 is not a separate genotype or even a monophyletic cluster, but belongs to G3. Nuclear data revealed no genetic separation of G1 and G3, suggesting that these genotypes form a single species due to ongoing gene flow. We conclude that: (a) in the taxonomic sense, genotypes G1 and G3 can be treated as a single species E. granulosus s. s.; (b) genotypes G1 and G3 should be regarded as distinct genotypes only in the context of mitochondrial data; (c) we recommend excluding G2 from the genotype list.}, }
@article {pmid28454930, year = {2017}, author = {Gutiérrez-Rodríguez, J and Barbosa, AM and Martínez-Solano, &#xcd;}, title = {Integrative inference of population history in the Ibero-Maghrebian endemic Pleurodeles waltl (Salamandridae).}, journal = {Molecular phylogenetics and evolution}, volume = {112}, number = {}, pages = {122-137}, doi = {10.1016/j.ympev.2017.04.022}, pmid = {28454930}, issn = {1095-9513}, mesh = {Animal Migration ; Animals ; Calibration ; Climate ; DNA, Mitochondrial/genetics ; Fuzzy Logic ; Genetic Variation ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Morocco ; Phylogeny ; Phylogeography ; Principal Component Analysis ; Salamandridae/*classification ; Spain ; Species Specificity ; Time Factors ; }, abstract = {Inference of population histories from the molecular signatures of past demographic processes is challenging, but recent methodological advances in species distribution models and their integration in time-calibrated phylogeographic studies allow detailed reconstruction of complex biogeographic scenarios. We apply an integrative approach to infer the evolutionary history of the Iberian ribbed newt (Pleurodeles waltl), an Ibero-Maghrebian endemic with populations north and south of the Strait of Gibraltar. We analyzed an extensive multilocus dataset (mitochondrial and nuclear DNA sequences and ten polymorphic microsatellite loci) and found a deep east-west phylogeographic break in Iberian populations dating back to the Plio-Pleistocene. This break is inferred to result from vicariance associated with the formation of the Guadalquivir river basin. In contrast with previous studies, North African populations showed exclusive mtDNA haplotypes, and formed a monophyletic clade within the Eastern Iberian lineage in the mtDNA genealogy. On the other hand, microsatellites failed to recover Moroccan populations as a differentiated genetic cluster. This is interpreted to result from post-divergence gene flow based on the results of IMA2 and Migrate analyses. Thus, Moroccan populations would have originated after overseas dispersal from the Iberian Peninsula in the Pleistocene, with subsequent gene flow in more recent times, implying at least two trans-marine dispersal events. We modeled the distribution of the species and of each lineage, and projected these models back in time to infer climatically favourable areas during the mid-Holocene, the last glacial maximum (LGM) and the last interglacial (LIG), to reconstruct more recent population dynamics. We found minor differences in climatic favourability across lineages, suggesting intraspecific niche conservatism. Genetic diversity was significantly correlated with the intersection of environmental favourability in the LIG and LGM, indicating that populations of P. waltl are genetically more diverse in regions that have remained environmentally favourable through the last glacial cycle, particularly southern Iberia and northern Morocco. This study provides novel insights into the relative roles of geology and climate on the biogeography of a biodiversity hotspot.}, }
@article {pmid28444733, year = {2017}, author = {Du, SNN and Khajali, F and Dawson, NJ and Scott, GR}, title = {Hybridization increases mitochondrial production of reactive oxygen species in sunfish.}, journal = {Evolution; international journal of organic evolution}, volume = {71}, number = {6}, pages = {1643-1652}, doi = {10.1111/evo.13254}, pmid = {28444733}, issn = {1558-5646}, mesh = {Animals ; *Hybridization, Genetic ; Mitochondria/*metabolism ; Oxidative Phosphorylation ; Oxidative Stress ; Perciformes/genetics/*physiology ; *Reactive Oxygen Species ; }, abstract = {Mitochondrial dysfunction and oxidative stress have been suggested to be possible mechanisms underlying hybrid breakdown, as a result of mito-nuclear incompatibilities in respiratory complexes of the electron transport system. However, it remains unclear whether hybridization increases the production of reactive oxygen species (ROS) by mitochondria. We used high-resolution respirometry and fluorometry on isolated liver mitochondria to examine mitochondrial physiology and ROS emission in naturally occurring hybrids of pumpkinseed (Lepomis gibbosus) and bluegill (L. macrochirus). ROS emission was greater in hybrids than in both parent species when respiration was supported by complex I (but not complex II) substrates, and was associated with increases in lipid peroxidation. However, respiratory capacities for oxidative phosphorylation, phosphorylation efficiency, and O2 kinetics in hybrids were intermediate between those in parental species. Flux control ratios of capacities for electron transport (measured in uncoupled mitochondria) relative to oxidative phosphorylation suggested that the limiting influence of the phosphorylation system is reduced in hybrids. This likely helped offset impairments in electron transport capacity and complex III activity, but contributed to augmenting ROS production. Therefore, hybridization can increase mitochondrial ROS production, in support of previous suggestions that mitochondrial dysfunction can induce oxidative stress and thus contribute to hybrid breakdown.}, }
@article {pmid28444372, year = {2017}, author = {Hazkani-Covo, E and Martin, WF}, title = {Quantifying the Number of Independent Organelle DNA Insertions in Genome Evolution and Human Health.}, journal = {Genome biology and evolution}, volume = {9}, number = {5}, pages = {1190-1203}, pmid = {28444372}, issn = {1759-6653}, mesh = {Cell Nucleus/genetics ; Computational Biology/methods ; *DNA Transposable Elements ; DNA, Mitochondrial/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Genome, Mitochondrial ; Genome, Plastid ; Humans ; Mitochondria/genetics ; Mutagenesis, Insertional ; Phylogeny ; Plants ; Plastids/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Fragments of organelle genomes are often found as insertions in nuclear DNA. These fragments of mitochondrial DNA (numts) and plastid DNA (nupts) are ubiquitous components of eukaryotic genomes. They are, however, often edited out during the genome assembly process, leading to systematic underestimation of their frequency. Numts and nupts, once inserted, can become further fragmented through subsequent insertion of mobile elements or other recombinational events that disrupt the continuity of the inserted sequence relative to the genuine organelle DNA copy. Because numts and nupts are typically identified through sequence comparison tools such as BLAST, disruption of insertions into smaller fragments can lead to systematic overestimation of numt and nupt frequencies. Accurate identification of numts and nupts is important, however, both for better understanding of their role during evolution, and for monitoring their increasingly evident role in human disease. Human populations are polymorphic for 141 numt loci, five numts are causal to genetic disease, and cancer genomic studies are revealing an abundance of numts associated with tumor progression. Here, we report investigation of salient parameters involved in obtaining accurate estimates of numt and nupt numbers in genome sequence data. Numts and nupts from 44 sequenced eukaryotic genomes reveal lineage-specific differences in the number, relative age and frequency of insertional events as well as lineage-specific dynamics of their postinsertional fragmentation. Our findings outline the main technical parameters influencing accurate identification and frequency estimation of numts in genomic studies pertinent to both evolution and human health.}, }
@article {pmid28444332, year = {2017}, author = {Leducq, JB and Henault, M and Charron, G and Nielly-Thibault, L and Terrat, Y and Fiumera, HL and Shapiro, BJ and Landry, CR}, title = {Mitochondrial Recombination and Introgression during Speciation by Hybridization.}, journal = {Molecular biology and evolution}, volume = {34}, number = {8}, pages = {1947-1959}, pmid = {28444332}, issn = {1537-1719}, support = {R01 GM101320/GM/NIGMS NIH HHS/United States ; }, mesh = {Chromosome Mapping ; Crosses, Genetic ; Genetic Speciation ; Genome, Mitochondrial/*genetics ; Genotype ; Hybridization, Genetic/*genetics ; Mitochondria/*genetics ; Phenotype ; Recombination, Genetic/genetics ; Saccharomyces/genetics ; }, abstract = {Genome recombination is a major source of genotypic diversity and contributes to adaptation and speciation following interspecies hybridization. The contribution of recombination in these processes has been thought to be largely limited to the nuclear genome because organelles are mostly uniparentally inherited in animals and plants, which prevents recombination. Unicellular eukaryotes such as budding yeasts do, however, transmit mitochondria biparentally, suggesting that during hybridization, both parents could provide alleles that contribute to mitochondrial functions such as respiration and metabolism in hybrid populations or hybrid species. We examined the dynamics of mitochondrial genome transmission and evolution during speciation by hybridization in the natural budding yeast Saccharomyces paradoxus. Using population-scale mitochondrial genome sequencing in two endemic North American incipient species SpB and SpC and their hybrid species SpC*, we found that both parental species contributed to the hybrid mitochondrial genome through recombination. We support our findings by showing that mitochondrial recombination between parental types is frequent in experimental crosses that recreate the early step of this speciation event. In these artificial hybrids, we observed that mitochondrial genome recombination enhances phenotypic variation among diploid hybrids, suggesting that it could play a role in the phenotypic differentiation of hybrid species. Like the nuclear genome, the mitochondrial genome can, therefore, also play a role in hybrid speciation.}, }
@article {pmid28441938, year = {2017}, author = {Marquis, J and Lefebvre, G and Kourmpetis, YAI and Kassam, M and Ronga, F and De Marchi, U and Wiederkehr, A and Descombes, P}, title = {MitoRS, a method for high throughput, sensitive, and accurate detection of mitochondrial DNA heteroplasmy.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {326}, pmid = {28441938}, issn = {1471-2164}, mesh = {DNA, Mitochondrial/*analysis/metabolism ; High-Throughput Nucleotide Sequencing ; Humans ; INDEL Mutation ; Nucleic Acid Amplification Techniques/*methods ; Polymorphism, Single Nucleotide ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Mitochondrial dysfunction is linked to numerous pathological states, in particular related to metabolism, brain health and ageing. Nuclear encoded gene polymorphisms implicated in mitochondrial functions can be analyzed in the context of classical genome wide association studies. By contrast, mitochondrial DNA (mtDNA) variants are more challenging to identify and analyze for several reasons. First, contrary to the diploid nuclear genome, each cell carries several hundred copies of the circular mitochondrial genome. Mutations can therefore be present in only a subset of the mtDNA molecules, resulting in a heterogeneous pool of mtDNA, a situation referred to as heteroplasmy. Consequently, detection and quantification of variants requires extremely accurate tools, especially when this proportion is small. Additionally, the mitochondrial genome has pseudogenized into numerous copies within the nuclear genome over the course of evolution. These nuclear pseudogenes, named NUMTs, must be distinguished from genuine mtDNA sequences and excluded from the analysis.<br><br>RESULTS: Here we describe a novel method, named MitoRS, in which the entire mitochondrial genome is amplified in a single reaction using rolling circle amplification. This approach is easier to setup and of higher throughput when compared to classical PCR amplification. Sequencing libraries are generated at high throughput exploiting a tagmentation-based method. Fine-tuned parameters are finally applied in the analysis to allow detection of variants even of low frequency heteroplasmy. The method was thoroughly benchmarked in a set of experiments designed to demonstrate its robustness, accuracy and sensitivity. The MitoRS method requires 5&#xa0;ng total DNA as starting material. More than 96 samples can be processed in less than a day of laboratory work and sequenced in a single lane of an Illumina HiSeq flow cell. The lower limit for accurate quantification of single nucleotide variants has been measured at 1% frequency.<br><br>CONCLUSIONS: The MitoRS method enables the robust, accurate, and sensitive analysis of a large number of samples. Because it is cost effective and simple to setup, we anticipate this method will promote the analysis of mtDNA variants in large cohorts, and may help assessing the impact of mtDNA heteroplasmy on metabolic health, brain function, cancer progression, or ageing.}, }
@article {pmid28438700, year = {2017}, author = {Wang, P and Wang, Y and Wang, C and Zhang, T and Al-Farraj, SA and Gao, F}, title = {Further consideration on the phylogeny of the Ciliophora: Analyses using both mitochondrial and nuclear data with focus on the extremely confused class Phyllopharyngea.}, journal = {Molecular phylogenetics and evolution}, volume = {112}, number = {}, pages = {96-106}, doi = {10.1016/j.ympev.2017.04.018}, pmid = {28438700}, issn = {1095-9513}, mesh = {Ciliophora/*classification/genetics ; DNA, Protozoan ; DNA, Ribosomal/genetics ; Genome, Protozoan ; Mitochondria/genetics ; Phylogeny ; Ribosome Subunits, Small/genetics ; Sequence Analysis, DNA ; }, abstract = {Most ciliate phylogenetic analyses have largely relied on the nuclear small subunit ribosome DNA (nSSU-rDNA) locus. However, single locus or multi-loci from the same genome or chromosome may not be sufficient enough to elucidate phylogenetic relationships among ciliate taxa. Therefore, in addition to nSSU-rDNA, the mitochondrial small subunit ribosome DNA (mtSSU-rDNA) was applied in this study. We expanded the taxon sampling especially within the class Phyllopharyngea. Phylogenetic analyses based on nSSU-rDNA and mtSSU-rDNA, independently, as well as concatenated were performed and revealed the following: (1) mtSSU-rDNA is more variable than nSSU-rDNA, and is better at elucidating relationships at lower levels, e.g. intra-/inter-specific or generic relationships; (2) the validity of the two genera Mirodysteria and Spirodysteria is challenged based on their similar morphology with Dysteria and the analyses from both mtSSU-rDNA and nSSU-rDNA; (3) Brooklynella is confirmed to be an intermediate taxon between Dysteriidae and Hartmannulidae, and may represent a distinct family; (4) Trithigmostoma should remain in Chilodonellidae; (5) the separation of Paraspathidium from Litostomatea is supported and it groups with prostomateans and plagiopyleans. In summary, results from mtSSU-rDNA corroborated those of nSSU-rDNA for highly supported clades, and the mtSSU-rDNA tree with its secondary structure gave topologies that could be explained by the morphology; therefore it can be useful in some cases towards better resolution of robust phylogenies.}, }
@article {pmid28432817, year = {2017}, author = {Ginzburg, N and Cohen, M and Chipman, AD}, title = {Factors involved in early polarization of the anterior-posterior axis in the milkweed bug Oncopeltus fasciatus.}, journal = {Genesis (New York, N.Y. : 2000)}, volume = {55}, number = {5}, pages = {}, doi = {10.1002/dvg.23027}, pmid = {28432817}, issn = {1526-968X}, mesh = {Animals ; *Body Patterning ; Female ; Gene Expression Regulation, Developmental ; Hemiptera/embryology/*genetics ; Insect Proteins/*genetics/metabolism ; Male ; Transcription Factors/*genetics/metabolism ; Zygote/metabolism ; }, abstract = {The axes of insect embryos are defined early in the blastoderm stage. Genes involved in this polarization are well known in Drosophila, but less so in other insects, such as the milkweed bug Oncopeltus fasciatus. Using quantitative PCR, we looked at differential expression of several candidate genes for early anterior-posterior patterning and found that none of them are expressed asymmetrically in the early blastoderm. We then used an RNA-Seq approach to identify novel candidate genes that might be involved in early polarization in Oncopeltus. We focused on transcription factors (TFs) as these are likely to be central players in developmental processes. Using both homology and domain based identification approaches, we were unable to find any TF encoding transcripts that are expressed asymmetrically along the anterior-posterior axis at early stages. Using a GO-term analysis of all asymmetrically expressed mRNAs, we found an enrichment of genes relating to mitochondrial function in the posterior at the earliest studied time-point. We also found a gradual enrichment of transcription related activities, giving us a putative time frame for the maternal to zygotic transition. Our dataset provides us with a list of new candidate genes in early development, which can be followed up experimentally.}, }
@article {pmid28432484, year = {2017}, author = {Yoon, SH and Kim, J and Shin, D and Cho, S and Kwak, W and Lee, HK and Park, KD and Kim, H}, title = {Complete mitochondrial genome sequences of Korean native horse from Jeju Island: uncovering the spatio-temporal dynamics.}, journal = {Molecular biology reports}, volume = {44}, number = {2}, pages = {233-242}, pmid = {28432484}, issn = {1573-4978}, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Breeding ; DNA, Mitochondrial/genetics ; Genome, Mitochondrial/genetics ; Horses/*genetics ; Korea ; Mitochondria/genetics ; Phylogeny ; Phylogeography/methods ; Sequence Analysis, DNA/methods ; }, abstract = {The Korean native horse (Jeju horse) is one of the most important animals in Korean historical, cultural, and economical viewpoints. In the early 1980s, the Jeju horse was close to extinction. The aim of this study is to explore the phylogenomics of Korean native horse focusing on spatio-temporal dynamics. We determined complete mitochondrial genome sequences for the first Korean native (n = 6) and additional Mongolian (n = 2) horses. Those sequences were analyzed together with 143 published ones using Bayesian coalescent approach as well as three different phylogenetic analysis methods, Bayesian inference, maximum likelihood, and neighbor-joining methods. The phylogenomic trees revealed that the Korean native horses had multiple origins and clustered together with some horses from four European and one Middle Eastern breeds. Our phylogenomic analyses also supported that there was no apparent association between breed or geographic location and the evolution of global horses. Time of the most recent common ancestor of the Korean native horse was approximately 13,200-63,200 years, which was much younger than 0.696 My of modern horses. Additionally, our results showed that all global horse lineages including Korean native horse existed prior to their domestication events occurred in about 6000-10,000 years ago. This is the first study on phylogenomics of the Korean native horse focusing on spatio-temporal dynamics. Our findings increase our understanding of the domestication history of the Korean native horses, and could provide useful information for horse conservation projects as well as for horse genomics, emergence, and the geographical distribution.}, }
@article {pmid28431284, year = {2017}, author = {Nibert, ML}, title = {Mitovirus UGA(Trp) codon usage parallels that of host mitochondria.}, journal = {Virology}, volume = {507}, number = {}, pages = {96-100}, pmid = {28431284}, issn = {1096-0341}, support = {R01 GM033050/GM/NIGMS NIH HHS/United States ; }, mesh = {Codon/*genetics/metabolism ; Fungi/genetics/metabolism/*virology ; Genome, Viral ; Mitochondria/genetics/metabolism/*virology ; Phylogeny ; RNA Viruses/*genetics/physiology ; *Virus Replication ; }, abstract = {Mitoviruses replicate in mitochondria of their host fungi. They have small RNA genomes that encompass a single ORF encoding the viral RdRp. Since UGA codons encode Trp in fungal mitochondria, the RdRp ORF of a typical mitovirus includes multiple UGA codons. In some mitoviruses, however, the ORF has no such codons, suggesting that these particular viruses may be under selective pressure to exclude them. In this report, new evidence is presented that host fungi whose mitoviruses have no or few UGA codons are distinctive in also having no or few UGA codons in their core mitochondrial genes. Thus, the relative exclusion of such codons in a subset of mitoviruses appears to reflect most fundamentally that UGA(Trp) is a rare mitochondrial codon in their particular hosts. The fact that UGA(Trp) is a rare mitochondrial codon in many fungi appears not to have been widely discussed to date.}, }
@article {pmid28429320, year = {2017}, author = {Ebenezer, TE and Carrington, M and Lebert, M and Kelly, S and Field, MC}, title = {Euglena gracilis Genome and Transcriptome: Organelles, Nuclear Genome Assembly Strategies and Initial Features.}, journal = {Advances in experimental medicine and biology}, volume = {979}, number = {}, pages = {125-140}, doi = {10.1007/978-3-319-54910-1_7}, pmid = {28429320}, issn = {0065-2598}, support = {203134/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Cell Nucleus/genetics/metabolism ; *DNA, Protozoan/genetics/metabolism ; Euglena gracilis/*physiology ; Genome, Protozoan/*physiology ; *Mitochondria/genetics/metabolism ; *Plastids/genetics/metabolism ; }, abstract = {Euglena gracilis is a major component of the aquatic ecosystem and together with closely related species, is ubiquitous worldwide. Euglenoids are an important group of protists, possessing a secondarily acquired plastid and are relatives to the Kinetoplastidae, which themselves have global impact as disease agents. To understand the biology of E. gracilis, as well as to provide further insight into the evolution and origins of the Kinetoplastidae, we embarked on sequencing the nuclear genome; the plastid and mitochondrial genomes are already in the public domain. Earlier studies suggested an extensive nuclear DNA content, with likely a high degree of repetitive sequence, together with significant extrachromosomal elements. To produce a list of coding sequences we have combined transcriptome data from both published and new sources, as well as embarked on de novo sequencing using a combination of 454, Illumina paired end libraries and long PacBio reads. Preliminary analysis suggests a surprisingly large genome approaching 2 Gbp, with a highly fragmented architecture and extensive repeat composition. Over 80% of the RNAseq reads from E. gracilis maps to the assembled genome sequence, which is comparable with the well assembled genomes of T. brucei and T. cruzi. In order to achieve this level of assembly we employed multiple informatics pipelines, which are discussed here. Finally, as a preliminary view of the genome architecture, we discuss the tubulin and calmodulin genes, which highlight potential novel splicing mechanisms.}, }
@article {pmid28429315, year = {2017}, author = {Zimorski, V and Rauch, C and van Hellemond, JJ and Tielens, AGM and Martin, WF}, title = {The Mitochondrion of Euglena gracilis.}, journal = {Advances in experimental medicine and biology}, volume = {979}, number = {}, pages = {19-37}, doi = {10.1007/978-3-319-54910-1_2}, pmid = {28429315}, issn = {0065-2598}, mesh = {Anaerobiosis/physiology ; Euglena gracilis/*metabolism ; Fatty Acids/biosynthesis ; Glycolysis/physiology ; Malonyl Coenzyme A/metabolism ; Mitochondria/*physiology ; Oxidation-Reduction ; Pyruvic Acid/metabolism ; }, abstract = {In the presence of oxygen, Euglena gracilis mitochondria function much like mammalian mitochondria. Under anaerobiosis, E. gracilis mitochondria perform a malonyl-CoA independent synthesis of fatty acids leading to accumulation of wax esters, which serve as the sink for electrons stemming from glycolytic ATP synthesis and pyruvate oxidation. Some components (enzymes and cofactors) of Euglena's anaerobic energy metabolism are found among the anaerobic mitochondria of invertebrates, others are found among hydrogenosomes, the H2-producing anaerobic mitochondria of protists.}, }
@article {pmid28420087, year = {2017}, author = {Devarshi, PP and McNabney, SM and Henagan, TM}, title = {Skeletal Muscle Nucleo-Mitochondrial Crosstalk in Obesity and Type 2 Diabetes.}, journal = {International journal of molecular sciences}, volume = {18}, number = {4}, pages = {}, pmid = {28420087}, issn = {1422-0067}, mesh = {Animals ; Cell Nucleus/*metabolism ; Diabetes Mellitus, Type 2/etiology/*metabolism ; Diet, High-Fat ; Energy Metabolism ; Evolution, Molecular ; Glucose/metabolism ; Humans ; Insulin/metabolism ; Insulin Resistance ; Mitochondria, Muscle/genetics/*metabolism ; Muscle, Skeletal/*metabolism ; Obesity/etiology/*metabolism ; Oxidation-Reduction ; *Signal Transduction ; }, abstract = {Skeletal muscle mitochondrial dysfunction, evidenced by incomplete beta oxidation and accumulation of fatty acid intermediates in the form of long and medium chain acylcarnitines, may contribute to ectopic lipid deposition and insulin resistance during high fat diet (HFD)-induced obesity. The present review discusses the roles of anterograde and retrograde communication in nucleo-mitochondrial crosstalk that determines skeletal muscle mitochondrial adaptations, specifically alterations in mitochondrial number and function in relation to obesity and insulin resistance. Special emphasis is placed on the effects of high fat diet (HFD) feeding on expression of nuclear-encoded mitochondrial genes (NEMGs) nuclear receptor factor 1 (NRF-1) and 2 (NRF-2) and peroxisome proliferator receptor gamma coactivator 1 alpha (PGC-1α) in the onset and progression of insulin resistance during obesity and how HFD-induced alterations in NEMG expression affect skeletal muscle mitochondrial adaptations in relation to beta oxidation of fatty acids. Finally, the potential ability of acylcarnitines or fatty acid intermediates resulting from mitochondrial beta oxidation to act as retrograde signals in nucleo-mitochondrial crosstalk is reviewed and discussed.}, }
@article {pmid28419256, year = {2017}, author = {Sablok, G and Chen, TW and Lee, CC and Yang, C and Gan, RC and Wegrzyn, JL and Porta, NL and Nayak, KC and Huang, PJ and Varotto, C and Tang, P}, title = {ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {24}, number = {3}, pages = {327-332}, pmid = {28419256}, issn = {1756-1663}, mesh = {Chloroplasts/genetics ; Codon/analysis/*genetics ; Eukaryota/genetics ; *Evolution, Molecular ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Genomics/*methods ; Mitochondria/genetics ; Software ; }, abstract = {Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/.}, }
@article {pmid28418073, year = {2017}, author = {Mahalingam, S and McClelland, GB and Scott, GR}, title = {Evolved changes in the intracellular distribution and physiology of muscle mitochondria in high-altitude native deer mice.}, journal = {The Journal of physiology}, volume = {595}, number = {14}, pages = {4785-4801}, pmid = {28418073}, issn = {1469-7793}, mesh = {Acclimatization/*physiology ; Altitude ; Animals ; Biological Evolution ; Female ; Hypoxia/*physiopathology ; Male ; Microscopy, Electron, Transmission ; Mitochondria, Muscle/*physiology/ultrastructure ; Muscle, Skeletal/*physiology/ultrastructure ; Oxygen/physiology ; Oxygen Consumption ; Peromyscus/*physiology ; }, abstract = {KEY POINTS: Mitochondrial function changes over time at high altitudes, but the potential benefits of these changes for hypoxia resistance remains unclear. We used high-altitude-adapted populations of deer mice, which exhibit enhanced aerobic performance in hypoxia, to examine whether changes in mitochondrial physiology or intracellular distribution in the muscle contribute to hypoxia resistance. Permeabilized muscle fibres from the gastrocnemius muscle had higher respiratory capacities in high-altitude mice than in low-altitude mice. Highlanders also had higher mitochondrial volume densities, due entirely to an enriched abundance of subsarcolemmal mitochondria, such that more mitochondria were situated near the cell membrane and adjacent to capillaries. There were several effects of hypoxia acclimation on mitochondrial function, some of which were population specific, but they differed from the evolved changes in high-altitude natives, which probably provide a better indication of adaptive traits that improve performance and hypoxia resistance at high altitudes.<br><br>ABSTRACT: High-altitude natives that have evolved to live in hypoxic environments provide a compelling system to understand how animals can overcome impairments in oxygen availability. We examined whether these include changes in mitochondrial physiology or intracellular distribution that contribute to hypoxia resistance in high-altitude deer mice (Peromyscus maniculatus). Mice from populations native to high and low altitudes were born and raised in captivity, and as adults were acclimated to normoxia or hypobaric hypoxia (equivalent to 4300&#xa0;m elevation). We found that highlanders had higher respiratory capacities in the gastrocnemius (but not soleus) muscle than lowlanders (assessed using permeabilized fibres with single or multiple inputs to the electron transport system), due in large part to higher mitochondrial volume densities in the gastrocnemius. The latter was attributed to an increased abundance of subsarcolemmal (but not intermyofibrillar) mitochondria, such that more mitochondria were situated near the cell membrane and adjacent to capillaries. Hypoxia acclimation had no significant effect on these population differences, but it did increase mitochondrial cristae surface densities of mitochondria in both populations. Hypoxia acclimation also altered the physiology of isolated mitochondria by affecting respiratory capacities and cytochrome c oxidase activities in population-specific manners. Chronic hypoxia decreased the release of reactive oxygen species by isolated mitochondria in both populations. There were subtle differences in O2 kinetics between populations, with highlanders exhibiting increased mitochondrial O2 affinity or catalytic efficiency in some conditions. Our results suggest that evolved changes in mitochondrial physiology in high-altitude natives are distinct from the effects of hypoxia acclimation, and probably provide a better indication of adaptive traits that improve performance and hypoxia resistance at high altitudes.}, }
@article {pmid28416382, year = {2017}, author = {Luo, X and Fu, X and Liao, G and Chang, O and Huang, Z and Li, N}, title = {Isolation, pathogenicity and characterization of a novel bacterial pathogen Streptococcus uberis from diseased mandarin fish Siniperca chuatsi.}, journal = {Microbial pathogenesis}, volume = {107}, number = {}, pages = {380-389}, doi = {10.1016/j.micpath.2017.03.049}, pmid = {28416382}, issn = {1096-1208}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Antigens, Bacterial/genetics ; Apoptosis ; Bacterial Proteins/genetics ; Brain/microbiology/pathology ; Carps/microbiology ; China ; DNA, Bacterial ; Disease Models, Animal ; Fish Diseases/*microbiology ; Fishes/*microbiology ; Genome, Microbial ; Heart/microbiology ; Hydrogen-Ion Concentration ; Microbial Sensitivity Tests ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Streptococcal Infections/*microbiology/mortality/*veterinary ; Streptococcus/genetics/*isolation &amp; purification/*pathogenicity/physiology ; Temperature ; Tilapia/microbiology ; Virulence ; }, abstract = {In recent years, mandarin fish had a high mortality rate associated with abnormal swimming, exophthalmia, corneal opacity and eye hemorrhage on a fish farm located at Foshan city, Guangdong province, China. Three isolates of Gram-positive, chain-forming cocci were recovered from moribund fish, and designated as SS131025-1, SS131025-2, and SS131025-3. These isolates were identified as Streptococcus uberis according to their morphologic and physio-biochemical characteristics as well as phylogenetic analysis based on their 16S rRNA and GapC gene sequences. The pathogenicity of S. uberis to mandarin fish was determined by challenge experiments. Results of artificial challenge showed S. uberis infected healthy mandarin fish and lead to death by eyeball injection or immersion route, and the LD50 of SS131025-1 with eyeball injection was 2.0 × 10[6.42] CFU per fish. Moreover extracellular product (ECP) of the isolated S.uberis induced CPB cell apoptosis and cause death of mandarin fish. In addition, these S. uberis strains could also infect tilapia, but not grass carp and crucian carp, and grew in brain-heart infusion broth with an optimal temperature of 37 °C, pH of 7.0, and salinity of 0%. Antibiotic sensitivity testing indicated that these isolates were susceptible to rifampicin and furazolidone but resistant to 20 kinds of antibiotics. Histopathologically, infection with S. uberis could cause serious pathological changes in brain tissues such as vacuoles in matrix, swollen mitochondria with lysis of cristae and disintegration, and lots of coccus was observed both under electron and light microscope. These results shed some light on the pathogenicity of the isolates and how to prevent and control S. uberis infection in mandarin fish.}, }
@article {pmid28412536, year = {2017}, author = {Rivera, JA and Kraus, F and Allison, A and Butler, MA}, title = {Molecular phylogenetics and dating of the problematic New Guinea microhylid frogs (Amphibia: Anura) reveals elevated speciation rates and need for taxonomic reclassification.}, journal = {Molecular phylogenetics and evolution}, volume = {112}, number = {}, pages = {1-11}, doi = {10.1016/j.ympev.2017.04.008}, pmid = {28412536}, issn = {1095-9513}, mesh = {Animals ; Anura/*classification/genetics ; Australia ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; *Genetic Speciation ; Mitochondria/genetics ; Molecular Typing ; New Guinea ; Philippines ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Asterophryinae is a large monophyletic subfamily of Anurans containing over 300 species distributed across one of the world's most geologically active areas - New Guinea and its satellite islands, Australia and the Philippines. The tremendous ecological and morphological diversity of this clade, with apparent specializations for burrowing, terrestrial, semi-aquatic, and arboreal lifestyle, suggests an evolutionary process of adaptive radiation. Despite this spectacular diversity, this and many other questions of evolutionary processes have received little formal study because until now the phylogeny of this spececies-rich clade has remained uncertain. Here we reconstruct a phylogeny for Asterophryinae with greatly increased taxon and genetic sampling relative to prior studies. We use Maximum Likelihood and Bayesian Inference methods to produce the most robust and comprehensive phylogeny to date containing 155 species using 3 nuclear and 2 mitochondrial loci. We also perform a time calibration analysis to estimate the age of the clade. We find support for the monophyly of Asterophryinae as well as need for taxonomic reclassification of several genera. Furthermore, we find increased rates of speciation across the clade supporting the hypothesis of rapid radiation. Lastly, we found that adding taxa to the analysis produced more robust phylogenetic results over adding loci.}, }
@article {pmid28411160, year = {2017}, author = {Maswanganye, KA and Cunningham, MJ and Bennett, NC and Chimimba, CT and Bloomer, P}, title = {Life on the rocks: Multilocus phylogeography of rock hyrax (Procavia capensis) from southern Africa.}, journal = {Molecular phylogenetics and evolution}, volume = {114}, number = {}, pages = {49-62}, doi = {10.1016/j.ympev.2017.04.006}, pmid = {28411160}, issn = {1095-9513}, mesh = {Africa, Southern ; Animals ; Biological Evolution ; Climate Change ; Cytochromes b/classification/genetics ; Gene Flow ; Genetic Variation ; Genotype ; Haplotypes ; Hyraxes/*classification/genetics ; Isoenzymes/classification/genetics ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Protein Kinase C/classification/genetics ; Tartrate-Resistant Acid Phosphatase/classification/genetics ; }, abstract = {Understanding the role of geography and climatic cycles in determining patterns of biodiversity is important in comparative and evolutionary biology and conservation. We studied the phylogeographic pattern and historical demography of a rock-dwelling small mammal species from southern Africa, the rock hyrax Procavia capensis capensis. Using a multilocus coalescent approach, we assessed the influence of strong habitat dependence and fluctuating regional climates on genetic diversity. We sequenced a mitochondrial gene (cytochrome b) and two nuclear introns (AP5, PRKC1) supplemented with microsatellite genotyping, in order to assess evolutionary processes over multiple temporal scales. In addition, distribution modelling was used to investigate the current and predicted distribution of the species under different climatic scenarios. Collectively, the data reveal a complex history of isolation followed by secondary contact shaping the current intraspecific diversity. The cyt b sequences confirmed the presence of two previously proposed geographically and genetically distinct lineages distributed across the southern African Great Escarpment and north-western mountain ranges. Molecular dating suggests Miocene divergence of the lineages, yet there are no discernible extrinsic barriers to gene flow. The nuclear markers reveal incomplete lineage sorting or ongoing mixing of the two lineages. Although the microsatellite data lend some support to the presence of two subpopulations, there is weak structuring within and between lineages. These data indicate the presence of gene flow from the northern into the southern parts of the southern African sub-region likely following the secondary contact. The distribution modelling predictably reveal the species' preference for rocky areas, with stable refugia through time in the northern mountain ranges, the Great Escarpment, as well as restricted areas of the Northern Cape Province and the Cape Fold Mountains of South Africa. Different microclimatic variables appear to determine the distributional range of the species. Despite strong habitat preference, the micro-habitat offered by rocky crevices and unique life history traits likely promoted the adaptability of P. capensis, resulting in the widespread distribution and persistence of the species over a long evolutionary period. Spatio-temporal comparison of the evolutionary histories of other co-distributed species across the rocky landscapes of southern Africa will improve our understanding of the regional patterns of biodiversity and local endemism.}, }
@article {pmid28410432, year = {2017}, author = {Antonini, Y and Machado, CB and Galetti, PM and Oliveira, M and Dirzo, R and Fernandes, GW}, title = {Patterns of orchid bee species diversity and turnover among forested plateaus of central Amazonia.}, journal = {PloS one}, volume = {12}, number = {4}, pages = {e0175884}, pmid = {28410432}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; Bees/classification/genetics/*physiology ; *Biodiversity ; Brazil ; Genetic Loci ; Male ; Mitochondria/genetics ; Phylogeny ; Rainforest ; Temperature ; }, abstract = {The knowledge of spatial pattern and geographic beta-diversity is of great importance for biodiversity conservation and interpreting ecological information. Tropical forests, especially the Amazon Rainforest, are well known for their high species richness and low similarity in species composition between sites, both at local and regional scales. We aimed to determine the effect and relative importance of area, isolation and climate on species richness and turnover in orchid bee assemblages among plateaus in central Brazilian Amazonia. Variance partitioning techniques were applied to assess the relative effects of spatial and environmental variables on bee species richness, phylogeny and composition. We hypothesized that greater abundance and richness of orchid bees would be found on larger plateaus, with a set of core species occurring on all of them. We also hypothesized that smaller plateaus would possess lower phylogenetic diversity. We found 55 bee species distributed along the nine sampling sites (plateaus) with 17 of them being singletons. There was a significant decrease in species richness with decreasing size of plateaus, and a significant decrease in the similarity in species composition with greater distance and climatic variation among sampling sites. Phylogenetic diversity varied among the sampling sites but was directly related to species richness. Although not significantly related to plateau area, smaller or larger PDFaith were observed in the smallest and the largest plateaus, respectively.}, }
@article {pmid28408315, year = {2017}, author = {Allen, JF}, title = {The CoRR hypothesis for genes in organelles.}, journal = {Journal of theoretical biology}, volume = {434}, number = {}, pages = {50-57}, doi = {10.1016/j.jtbi.2017.04.008}, pmid = {28408315}, issn = {1095-8541}, mesh = {*Cell Compartmentation ; Enzymes/genetics ; Organelles/*genetics ; Oxidation-Reduction ; Prokaryotic Cells/*metabolism/ultrastructure ; Symbiosis ; }, abstract = {Chloroplasts and mitochondria perform energy transduction in photosynthesis and respiration. These processes can be described in physico-chemical terms with no obvious requirement for co-located genetic systems, separat from those of the rest of the cell. Accordingly, biochemists once tended to regard endosymbiosis as untestable evolutionary speculation. Lynn Sagan's seminal 1967 paper "On the Origin of Mitosing Cells" outlined the evolution of eukaryotic cells by endosymbiosis of prokaryotes. The endosymbiont hypothesis is consistent with presence of DNA in chloroplasts and mitochondria, but does not assign it a function. Biochemistry and molecular biology now show that Sagan's proposal has an explanatory reach far beyond that originally envisaged. Prokaryotic origins of photosynthetic and respiratory mechanisms are apparent in protein structural insights into energy coupling. Genome sequencing confirms the underlying, prokaryotic architecture of chloroplasts and mitochondria and illustrates the profound influence of the original mergers of their ancestors' genes and proteins with those of their host cells. Peter Mitchell's 1961 chemiosmotic hypothesis applied the concept of vectorial catalysis that underlies biological energy transduction and cell structure, function, and origins. Continuity of electrical charge separation and membrane sidedness requires compartments within compartments, together with intricate mechanisms for transport within and between them. I suggest that the reason for the persistence of distinct genetic systems within bioenergetic organelles is the selective advantage of subcellular co-location of specific genes with their gene products. Co-location for Redox Regulation - CoRR - provides for a dialogue between chemical reduction-oxidation and the action of genes encoding its protein catalysts. These genes and their protein products are in intimate contact, and cannot be isolated from each other without loss of an essential mechanism of adaptation of electron transport to change in the external environment.}, }
@article {pmid28407723, year = {2018}, author = {Huang, Z and Ruan, R}, title = {DNA barcodes and insights into the phylogenetic relationships of Corvidae (Aves: Passeriformes).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {4}, pages = {529-534}, doi = {10.1080/24701394.2017.1315569}, pmid = {28407723}, issn = {2470-1408}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Genome, Mitochondrial ; Mitochondria/*enzymology ; Passeriformes/*classification/*genetics ; *Phylogeny ; }, abstract = {DNA barcoding has become a promising tool for species identification and phylogeny in a wide range of animal taxa using mitochondrial cytochrome c oxidase subunit I (COI). The Corvidae (Aves: Passeriformes) is a species rich and morphologically diverse family. In the present study, we analyzed the COI barcodes of 39 species from 12 genera of Corvidae. COI gene was also used to examine phylogenetic relationships of Corvidae. Every species possessed a barcode distinct from that of other species. Kimura two-parameter distances were calculated between species barcodes. The average genetic distance between the species was 22 times higher compared to the average genetic distance within species. Maximum likelihood method was used to construct a phylogenetic tree. All the species could be discriminated by their distinct clades in the phylogenetic tree. COI gene data provided good evidence for the monophyly of the Corvidae. Members of Cyanopica and Pyrrhocorax were the first to split from the Corvidae lineage. Analysis of COI genes supported the others genera fell into two clades. DNA barcoding is an effective molecular tool for Corvidae species identification and phylogenetic inference.}, }
@article {pmid28397763, year = {2017}, author = {Guzel, E and Arlier, S and Guzeloglu-Kayisli, O and Tabak, MS and Ekiz, T and Semerci, N and Larsen, K and Schatz, F and Lockwood, CJ and Kayisli, UA}, title = {Endoplasmic Reticulum Stress and Homeostasis in Reproductive Physiology and Pathology.}, journal = {International journal of molecular sciences}, volume = {18}, number = {4}, pages = {}, pmid = {28397763}, issn = {1422-0067}, mesh = {Animals ; Endometriosis/*physiopathology ; Endoplasmic Reticulum Stress/*physiology ; Female ; Homeostasis/*physiology ; Humans ; Male ; Models, Biological ; *Reproductive Physiological Phenomena ; Unfolded Protein Response/*physiology ; }, abstract = {The endoplasmic reticulum (ER), comprises 60% of the total cell membrane and interacts directly or indirectly with several cell organelles i.e., Golgi bodies, mitochondria and proteasomes. The ER is usually associated with large numbers of attached ribosomes. During evolution, ER developed as the specific cellular site of synthesis, folding, modification and trafficking of secretory and cell-surface proteins. The ER is also the major intracellular calcium storage compartment that maintains cellular calcium homeostasis. During the production of functionally effective proteins, several ER-specific molecular steps sense quantity and quality of synthesized proteins as well as proper folding into their native structures. During this process, excess accumulation of unfolded/misfolded proteins in the ER lumen results in ER stress, the homeostatic coping mechanism that activates an ER-specific adaptation program, (the unfolded protein response; UPR) to increase ER-associated degradation of structurally and/or functionally defective proteins, thus sustaining ER homeostasis. Impaired ER homeostasis results in aberrant cellular responses, contributing to the pathogenesis of various diseases. Both female and male reproductive tissues undergo highly dynamic cellular, molecular and genetic changes such as oogenesis and spermatogenesis starting in prenatal life, mainly controlled by sex-steroids but also cytokines and growth factors throughout reproductive life. These reproductive changes require ER to provide extensive protein synthesis, folding, maturation and then their trafficking to appropriate cellular location as well as destroying unfolded/misfolded proteins via activating ER-associated degradation mediated proteasomes. Many studies have now shown roles for ER stress/UPR signaling cascades in the endometrial menstrual cycle, ovarian folliculogenesis and oocyte maturation, spermatogenesis, fertilization, pre-implantation embryo development and pregnancy and parturition. Conversely, the contribution of impaired ER homeostasis by severe/prolong ER stress-mediated UPR signaling pathways to several reproductive tissue pathologies including endometriosis, cancers, recurrent pregnancy loss and pregnancy complications associated with pre-term birth have been reported. This review focuses on ER stress and UPR signaling mechanisms, and their potential roles in female and male reproductive physiopathology involving in menstrual cycle changes, gametogenesis, preimplantation embryo development, implantation and placentation, labor, endometriosis, pregnancy complications and preterm birth as well as reproductive system tumorigenesis.}, }
@article {pmid28394399, year = {2017}, author = {Schallenberg-Rüdinger, M and Oldenkott, B and Hiss, M and Trinh, PL and Knoop, V and Rensing, SA}, title = {A Single-Target Mitochondrial RNA Editing Factor of Funaria hygrometrica Can Fully Reconstitute RNA Editing at Two Sites in Physcomitrella patens.}, journal = {Plant &amp; cell physiology}, volume = {58}, number = {3}, pages = {496-507}, doi = {10.1093/pcp/pcw229}, pmid = {28394399}, issn = {1471-9053}, mesh = {Bryopsida/*genetics ; Mitochondria/genetics ; Plant Proteins/genetics ; RNA/*genetics ; RNA Editing/*genetics ; RNA, Mitochondrial ; }, abstract = {Nuclear-encoded pentatricopeptide repeat (PPR) proteins are key factors for site-specific RNA editing, converting cytidines into uridines in plant mitochondria and chloroplasts. All editing factors in the model moss Physcomitrella patens have a C-terminal DYW domain with similarity to cytidine deaminase. However, numerous editing factors in flowering plants lack such a terminal DYW domain, questioning its immediate role in the pyrimidine base conversion process. Here we further investigate the Physcomitrella DYW-type PPR protein PPR_78, responsible for mitochondrial editing sites cox1eU755SL and rps14eU137SL. Complementation assays with truncated proteins demonstrate that the DYW domain is essential for full PPR_78 editing functionality. The DYW domain can be replaced, however, with its counterpart from another editing factor, PPR_79. The PPR_78 ortholog of the related moss Funaria hygrometrica fully complements the Physcomitrella mutant for editing at both sites, although the editing site in rps14 is lacking in Funaria. Editing factor orthologs in different taxa may thus retain editing capacity for multiple sites despite the absence of editing requirement.}, }
@article {pmid28391181, year = {2017}, author = {Meireles, DA and Domingos, RM and Gaiarsa, JW and Ragnoni, EG and Bannitz-Fernandes, R and da Silva Neto, JF and de Souza, RF and Netto, LES}, title = {Functional and evolutionary characterization of Ohr proteins in eukaryotes reveals many active homologs among pathogenic fungi.}, journal = {Redox biology}, volume = {12}, number = {}, pages = {600-609}, pmid = {28391181}, issn = {2213-2317}, mesh = {Amino Acid Sequence ; Animals ; Ascomycota/chemistry/*enzymology/genetics ; Cysteine/genetics ; Eukaryota/genetics/*metabolism ; Evolution, Molecular ; Fungal Proteins/chemistry/genetics/metabolism ; Multigene Family ; Musa/microbiology ; Peroxidases/chemistry/*genetics/*metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {Ohr and OsmC proteins comprise two subfamilies within a large group of proteins that display Cys-based, thiol dependent peroxidase activity. These proteins were previously thought to be restricted to prokaryotes, but we show here, using iterated sequence searches, that Ohr/OsmC homologs are also present in 217 species of eukaryotes with a massive presence in Fungi (186 species). Many of these eukaryotic Ohr proteins possess an N-terminal extension that is predicted to target them to mitochondria. We obtained recombinant proteins for four eukaryotic members of the Ohr/OsmC family and three of them displayed lipoyl peroxidase activity. Further functional and biochemical characterization of the Ohr homologs from the ascomycete fungus Mycosphaerella fijiensis Mf_1 (MfOhr), the causative agent of Black Sigatoka disease in banana plants, was pursued. Similarly to what has been observed for the bacterial proteins, we found that: (i) the peroxidase activity of MfOhr was supported by DTT or dihydrolipoamide (dithiols), but not by β-mercaptoethanol or GSH (monothiols), even in large excess; (ii) MfOhr displayed preference for organic hydroperoxides (CuOOH and tBOOH) over hydrogen peroxide; (iii) MfOhr presented extraordinary reactivity towards linoleic acid hydroperoxides (k=3.18 (±2.13)×10[8]M[-1]s[-1]). Both Cys[87] and Cys[154] were essential to the peroxidase activity, since single mutants for each Cys residue presented no activity and no formation of intramolecular disulfide bond upon treatment with hydroperoxides. The pKa value of the Cysp residue was determined as 5.7±0.1 by a monobromobimane alkylation method. Therefore, eukaryotic Ohr peroxidases share several biochemical features with prokaryotic orthologues and are preferentially located in mitochondria.}, }
@article {pmid28380376, year = {2017}, author = {Anderson, KA and Huynh, FK and Fisher-Wellman, K and Stuart, JD and Peterson, BS and Douros, JD and Wagner, GR and Thompson, JW and Madsen, AS and Green, MF and Sivley, RM and Ilkayeva, OR and Stevens, RD and Backos, DS and Capra, JA and Olsen, CA and Campbell, JE and Muoio, DM and Grimsrud, PA and Hirschey, MD}, title = {SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion.}, journal = {Cell metabolism}, volume = {25}, number = {4}, pages = {838-855.e15}, pmid = {28380376}, issn = {1932-7420}, support = {T32 CA059365/CA/NCI NIH HHS/United States ; F32 DK105665/DK/NIDDK NIH HHS/United States ; R56 AG052568/AG/NIA NIH HHS/United States ; T32 DK007012/DK/NIDDK NIH HHS/United States ; T32 EY021453/EY/NEI NIH HHS/United States ; R24 DK085610/DK/NIDDK NIH HHS/United States ; R01 DK089312/DK/NIDDK NIH HHS/United States ; R01 AG045351/AG/NIA NIH HHS/United States ; UL1 TR001082/TR/NCATS NIH HHS/United States ; P30 AG028716/AG/NIA NIH HHS/United States ; T32 GM007105/GM/NIGMS NIH HHS/United States ; }, mesh = {Amidohydrolases/*metabolism ; Amino Acid Sequence ; Animals ; Carbon-Carbon Ligases/metabolism ; Glucose/metabolism ; HEK293 Cells ; Homeostasis ; Humans ; Insulin/*metabolism ; Insulin Resistance ; Insulin Secretion ; Leucine/*metabolism ; Lysine/*metabolism ; Metabolic Flux Analysis ; Mice, Inbred C57BL ; Mice, Knockout ; Mitochondrial Proteins/chemistry/*metabolism ; Models, Molecular ; Phylogeny ; Sirtuins/chemistry/*metabolism ; }, abstract = {Sirtuins are NAD[+]-dependent protein deacylases that regulate several aspects of metabolism and aging. In contrast to the other mammalian sirtuins, the primary enzymatic activity of mitochondrial sirtuin 4 (SIRT4) and its overall role in metabolic control have remained enigmatic. Using a combination of phylogenetics, structural biology, and enzymology, we show that SIRT4 removes three acyl moieties from lysine residues: methylglutaryl (MG)-, hydroxymethylglutaryl (HMG)-, and 3-methylglutaconyl (MGc)-lysine. The metabolites leading to these post-translational modifications are intermediates in leucine oxidation, and we show a primary role for SIRT4 in controlling this pathway in mice. Furthermore, we find that dysregulated leucine metabolism in SIRT4KO mice leads to elevated basal and stimulated insulin secretion, which progressively develops into glucose intolerance and insulin resistance. These findings identify a robust enzymatic activity for SIRT4, uncover a mechanism controlling branched-chain amino acid flux, and position SIRT4 as a crucial player maintaining insulin secretion and glucose homeostasis during aging.}, }
@article {pmid28373404, year = {2017}, author = {Spira, A and Yurgelun, MB and Alexandrov, L and Rao, A and Bejar, R and Polyak, K and Giannakis, M and Shilatifard, A and Finn, OJ and Dhodapkar, M and Kay, NE and Braggio, E and Vilar, E and Mazzilli, SA and Rebbeck, TR and Garber, JE and Velculescu, VE and Disis, ML and Wallace, DC and Lippman, SM}, title = {Precancer Atlas to Drive Precision Prevention Trials.}, journal = {Cancer research}, volume = {77}, number = {7}, pages = {1510-1541}, pmid = {28373404}, issn = {1538-7445}, support = {R01 AI040127/AI/NIAID NIH HHS/United States ; R01 CA121113/CA/NCI NIH HHS/United States ; U01 CA196408/CA/NCI NIH HHS/United States ; P30 CA023100/CA/NCI NIH HHS/United States ; U01 CA214182/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Cancer Vaccines/immunology ; Cellular Microenvironment ; DNA, Mitochondrial/genetics ; Epigenesis, Genetic ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Germ-Line Mutation ; High-Throughput Nucleotide Sequencing ; Humans ; Mitochondria/physiology ; Neoplasms/etiology/genetics/immunology/*prevention &amp; control ; Precancerous Conditions/*etiology ; *Precision Medicine ; Single-Cell Analysis ; }, abstract = {Cancer development is a complex process driven by inherited and acquired molecular and cellular alterations. Prevention is the holy grail of cancer elimination, but making this a reality will take a fundamental rethinking and deep understanding of premalignant biology. In this Perspective, we propose a national concerted effort to create a Precancer Atlas (PCA), integrating multi-omics and immunity - basic tenets of the neoplastic process. The biology of neoplasia caused by germline mutations has led to paradigm-changing precision prevention efforts, including: tumor testing for mismatch repair (MMR) deficiency in Lynch syndrome establishing a new paradigm, combinatorial chemoprevention efficacy in familial adenomatous polyposis (FAP), signal of benefit from imaging-based early detection research in high-germline risk for pancreatic neoplasia, elucidating early ontogeny in BRCA1-mutation carriers leading to an international breast cancer prevention trial, and insights into the intricate germline-somatic-immunity interaction landscape. Emerging genetic and pharmacologic (metformin) disruption of mitochondrial (mt) respiration increased autophagy to prevent cancer in a Li-Fraumeni mouse model (biology reproduced in clinical pilot) and revealed profound influences of subtle changes in mt DNA background variation on obesity, aging, and cancer risk. The elaborate communication between the immune system and neoplasia includes an increasingly complex cellular microenvironment and dynamic interactions between host genetics, environmental factors, and microbes in shaping the immune response. Cancer vaccines are in early murine and clinical precancer studies, building on the recent successes of immunotherapy and HPV vaccine immune prevention. Molecular monitoring in Barrett's esophagus to avoid overdiagnosis/treatment highlights an important PCA theme. Next generation sequencing (NGS) discovered age-related clonal hematopoiesis of indeterminate potential (CHIP). Ultra-deep NGS reports over the past year have redefined the premalignant landscape remarkably identifying tiny clones in the blood of up to 95% of women in their 50s, suggesting that potentially premalignant clones are ubiquitous. Similar data from eyelid skin and peritoneal and uterine lavage fluid provide unprecedented opportunities to dissect the earliest phases of stem/progenitor clonal (and microenvironment) evolution/diversity with new single-cell and liquid biopsy technologies. Cancer mutational signatures reflect exogenous or endogenous processes imprinted over time in precursors. Accelerating the prevention of cancer will require a large-scale, longitudinal effort, leveraging diverse disciplines (from genetics, biochemistry, and immunology to mathematics, computational biology, and engineering), initiatives, technologies, and models in developing an integrated multi-omics and immunity PCA - an immense national resource to interrogate, target, and intercept events that drive oncogenesis. Cancer Res; 77(7); 1510-41. ©2017 AACR.}, }
@article {pmid28372543, year = {2017}, author = {Voleman, L and Najdrová, V and Ástvaldsson, &#xc1; and Tůmová, P and Einarsson, E and Švindrych, Z and Hagen, GM and Tachezy, J and Svärd, SG and Doležal, P}, title = {Giardia intestinalis mitosomes undergo synchronized fission but not fusion and are constitutively associated with the endoplasmic reticulum.}, journal = {BMC biology}, volume = {15}, number = {1}, pages = {27}, pmid = {28372543}, issn = {1741-7007}, mesh = {Biological Evolution ; Coenzyme A Ligases/metabolism ; Dynamins/metabolism ; Endoplasmic Reticulum/*metabolism ; Giardia lamblia/cytology/*metabolism ; Interphase ; Mitochondria/*metabolism ; *Mitochondrial Dynamics ; }, abstract = {BACKGROUND: Mitochondria of opisthokonts undergo permanent fission and fusion throughout the cell cycle. Here, we investigated the dynamics of the mitosomes, the simplest forms of mitochondria, in the anaerobic protist parasite Giardia intestinalis, a member of the Excavata supergroup of eukaryotes. The mitosomes have abandoned typical mitochondrial traits such as the mitochondrial genome and aerobic respiration and their single role known to date is the formation of iron-sulfur clusters.<br><br>RESULTS: In live experiments, no fusion events were observed between the mitosomes in G. intestinalis. Moreover, the organelles were highly prone to becoming heterogeneous. This suggests that fusion is either much less frequent or even absent in mitosome dynamics. Unlike in mitochondria, division of the mitosomes was absolutely synchronized and limited to mitosis. The association of the nuclear and the mitosomal division persisted during the encystation of the parasite. During the segregation of the divided mitosomes, the subset of the organelles between two G. intestinalis nuclei had a prominent role. Surprisingly, the sole dynamin-related protein of the parasite seemed not to be involved in mitosomal division. However, throughout the cell cycle, mitosomes associated with the endoplasmic reticulum (ER), although none of the known ER-tethering complexes was present. Instead, the ER-mitosome interface was occupied by the lipid metabolism enzyme long-chain acyl-CoA synthetase 4.<br><br>CONCLUSIONS: This study provides the first report on the dynamics of mitosomes. We show that together with the loss of metabolic complexity of mitochondria, mitosomes of G. intestinalis have uniquely streamlined their dynamics by harmonizing their division with mitosis. We propose that this might be a strategy of G. intestinalis to maintain a stable number of organelles during cell propagation. The lack of mitosomal fusion may also be related to the secondary reduction of the organelles. However, as there are currently no reports on mitochondrial fusion in the whole Excavata supergroup, it is possible that the absence of mitochondrial fusion is an ancestral trait common to all excavates.}, }
@article {pmid28369844, year = {2017}, author = {Smith, SRT and Connallon, T}, title = {The contribution of the mitochondrial genome to sex-specific fitness variance.}, journal = {Evolution; international journal of organic evolution}, volume = {71}, number = {5}, pages = {1417-1424}, doi = {10.1111/evo.13238}, pmid = {28369844}, issn = {1558-5646}, mesh = {Animals ; DNA, Mitochondrial ; Female ; Genetic Fitness ; *Genetic Variation ; *Genome, Mitochondrial ; Male ; Mitochondria ; *Selection, Genetic ; }, abstract = {Maternal inheritance of mitochondrial DNA (mtDNA) facilitates the evolutionary accumulation of mutations with sex-biased fitness effects. Whereas maternal inheritance closely aligns mtDNA evolution with natural selection in females, it makes it indifferent to evolutionary changes that exclusively benefit males. The constrained response of mtDNA to selection in males can lead to asymmetries in the relative contributions of mitochondrial genes to female versus male fitness variation. Here, we examine the impact of genetic drift and the distribution of fitness effects (DFE) among mutations-including the correlation of mutant fitness effects between the sexes-on mitochondrial genetic variation for fitness. We show how drift, genetic correlations, and skewness of the DFE determine the relative contributions of mitochondrial genes to male versus female fitness variance. When mutant fitness effects are weakly correlated between the sexes, and the effective population size is large, mitochondrial genes should contribute much more to male than to female fitness variance. In contrast, high fitness correlations and small population sizes tend to equalize the contributions of mitochondrial genes to female versus male variance. We discuss implications of these results for the evolution of mitochondrial genome diversity and the genetic architecture of female and male fitness.}, }
@article {pmid28369657, year = {2017}, author = {Fukasawa, Y and Oda, T and Tomii, K and Imai, K}, title = {Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages.}, journal = {Molecular biology and evolution}, volume = {34}, number = {7}, pages = {1574-1586}, pmid = {28369657}, issn = {1537-1719}, mesh = {Biological Evolution ; Biological Transport ; Carrier Proteins/*genetics/metabolism ; Eukaryota/genetics/metabolism ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Membrane Transport Proteins/genetics/metabolism ; Mitochondria/*genetics/metabolism ; Mitochondrial Membrane Transport Proteins/*genetics/metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/metabolism ; Phylogeny ; Protein Transport/genetics ; Sequence Analysis, Protein/methods ; }, abstract = {Protein transport systems are fundamentally important for maintaining mitochondrial function. Nevertheless, mitochondrial protein translocases such as the kinetoplastid ATOM complex have recently been shown to vary in eukaryotic lineages. Various evolutionary hypotheses have been formulated to explain this diversity. To resolve any contradiction, estimating the primitive state and clarifying changes from that state are necessary. Here, we present more likely primitive models of mitochondrial translocases, specifically the translocase of the outer membrane (TOM) and translocase of the inner membrane (TIM) complexes, using scrutinized phylogenetic profiles. We then analyzed the translocases' evolution in eukaryotic lineages. Based on those results, we propose a novel evolutionary scenario for diversification of the mitochondrial transport system. Our results indicate that presequence transport machinery was mostly established in the last eukaryotic common ancestor, and that primitive translocases already had a pathway for transporting presequence-containing proteins. Moreover, secondary changes including convergent and migrational gains of a presequence receptor in TOM and TIM complexes, respectively, likely resulted from constrained evolution. The nature of a targeting signal can constrain alteration to the protein transport complex.}, }
@article {pmid28366720, year = {2017}, author = {Schönfeld, P and Reiser, G}, title = {Brain energy metabolism spurns fatty acids as fuel due to their inherent mitotoxicity and potential capacity to unleash neurodegeneration.}, journal = {Neurochemistry international}, volume = {109}, number = {}, pages = {68-77}, doi = {10.1016/j.neuint.2017.03.018}, pmid = {28366720}, issn = {1872-9754}, mesh = {Animals ; Brain/*metabolism ; Energy Metabolism/*physiology ; Fatty Acids/*metabolism ; Humans ; Mitochondria/*metabolism ; Neurodegenerative Diseases/*metabolism ; Oxidative Stress/*physiology ; Reactive Oxygen Species/metabolism ; }, abstract = {The brain uses long-chain fatty acids (LCFAs) to a negligible extent as fuel for the mitochondrial energy generation, in contrast to other tissues that also demand high energy. Besides this generally accepted view, some studies using cultured neural cells or whole brain indicate a moderately active mitochondrial β-oxidation. Here, we corroborate the conclusion that brain mitochondria are unable to oxidize fatty acids. In contrast, the combustion of liver-derived ketone bodies by neural cells is long-known. Furthermore, new insights indicate the use of odd-numbered medium-chain fatty acids as valuable source for maintaining the level of intermediates of the citric acid cycle in brain mitochondria. Non-esterified LCFAs or their activated forms exert a large variety of harmful side-effects on mitochondria, such as enhancing the mitochondrial ROS generation in distinct steps of the β-oxidation and therefore potentially increasing oxidative stress. Hence, the question arises: Why do in brain energy metabolism mitochondria selectively spurn LCFAs as energy source? The most likely answer are the relatively higher content of peroxidation-sensitive polyunsaturated fatty acids and the low antioxidative defense in brain tissue. There are two remarkable peroxisomal defects, one relating to α-oxidation of phytanic acid and the other to uptake of very long-chain fatty acids (VLCFAs) which lead to pathologically high tissue levels of such fatty acids. Both, the accumulation of phytanic acid and that of VLCFAs give an enlightening insight into harmful activities of fatty acids on neural cells, which possibly explain why evolution has prevented brain mitochondria from the equipment with significant β-oxidation enzymatic capacity.}, }
@article {pmid28362806, year = {2017}, author = {Baris, TZ and Wagner, DN and Dayan, DI and Du, X and Blier, PU and Pichaud, N and Oleksiak, MF and Crawford, DL}, title = {Evolved genetic and phenotypic differences due to mitochondrial-nuclear interactions.}, journal = {PLoS genetics}, volume = {13}, number = {3}, pages = {e1006517}, pmid = {28362806}, issn = {1553-7404}, mesh = {Active Transport, Cell Nucleus/genetics ; Animals ; Cell Nucleus/*genetics/metabolism ; DNA, Mitochondrial/genetics/metabolism ; *Evolution, Molecular ; Fish Proteins/genetics/metabolism ; Fundulidae/*genetics/metabolism ; Gene Frequency ; Genetics, Population ; Genotype ; Haplotypes ; Linkage Disequilibrium ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Nuclear Proteins/genetics/metabolism ; Oxidative Phosphorylation ; Phenotype ; Polymorphism, Single Nucleotide ; }, abstract = {The oxidative phosphorylation (OxPhos) pathway is responsible for most aerobic ATP production and is the only pathway with both nuclear and mitochondrial encoded proteins. The importance of the interactions between these two genomes has recently received more attention because of their potential evolutionary effects and how they may affect human health and disease. In many different organisms, healthy nuclear and mitochondrial genome hybrids between species or among distant populations within a species affect fitness and OxPhos functions. However, what is less understood is whether these interactions impact individuals within a single natural population. The significance of this impact depends on the strength of selection for mito-nuclear interactions. We examined whether mito-nuclear interactions alter allele frequencies for ~11,000 nuclear SNPs within a single, natural Fundulus heteroclitus population containing two divergent mitochondrial haplotypes (mt-haplotypes). Between the two mt-haplotypes, there are significant nuclear allele frequency differences for 349 SNPs with a p-value of 1% (236 with 10% FDR). Unlike the rest of the genome, these 349 outlier SNPs form two groups associated with each mt-haplotype, with a minority of individuals having mixed ancestry. We use this mixed ancestry in combination with mt-haplotype as a polygenic factor to explain a significant fraction of the individual OxPhos variation. These data suggest that mito-nuclear interactions affect cardiac OxPhos function. The 349 outlier SNPs occur in genes involved in regulating metabolic processes but are not directly associated with the 79 nuclear OxPhos proteins. Therefore, we postulate that the evolution of mito-nuclear interactions affects OxPhos function by acting upstream of OxPhos.}, }
@article {pmid28359943, year = {2017}, author = {Cai, J and Wei, S and Yu, D and Song, R and Lu, Y and Wu, Z and Qin, Q and Jian, J}, title = {BNIP3, a cell pro-apoptotic protein, involved in response to viral infection in orange spotted grouper, Epinephelus coioides.}, journal = {Fish &amp; shellfish immunology}, volume = {64}, number = {}, pages = {407-413}, doi = {10.1016/j.fsi.2017.03.047}, pmid = {28359943}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Apoptosis Regulatory Proteins/chemistry/*genetics/metabolism ; Base Sequence ; *Bass ; Cloning, Molecular ; DNA Virus Infections/genetics/*veterinary/virology ; DNA, Complementary/genetics/metabolism ; Fish Diseases/*genetics/virology ; Fish Proteins/chemistry/*genetics/metabolism ; Phylogeny ; RNA, Messenger/genetics/metabolism ; Ranavirus/*physiology ; Sequence Alignment/veterinary ; Tissue Distribution ; }, abstract = {BNIP3 is a kind of BH3-only protein that induces both cell death and autophagy. Here, a BNIP3 gene (EcBNIP3) was identified from orange spotted grouper, Epinephelus coioides. EcBNIP3 possessed 236 amino acids residues, contained a conservative BNIP3 domain and a transmembrane region. Besides, EcBNIP3 expressed at a relative high level in heart and spleen. EcBNIP3 transcript was up-regulated after SGIV infection in vitro. Subcellular localization analysis revealed that EcBNIP3 was predominantly localized in the cytoplasm and co-localized with mitochondria. In addition, overexpression EcBNIP3 accelerated SGIV infection induced cell death but inhibited viral genes transcription. Taken together, these results provided new evidence that fish BNIP3 might involved in response to virus infection.}, }
@article {pmid28358922, year = {2017}, author = {Tong, C and Tian, F and Zhang, C and Zhao, K}, title = {The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0174534}, pmid = {28358922}, issn = {1932-6203}, mesh = {Adaptation, Physiological/*genetics ; Amino Acid Sequence ; Animals ; Carps/*genetics ; *Evolution, Molecular ; Lakes ; MicroRNAs/classification/*genetics ; Phylogeny ; Tibet ; }, abstract = {Tibetan naked carp Gymnocypris przewalskii is an ideal model system to study highland adaptation of fish, because it evolved specific genetic and phenotypic characteristics to adapt to chronic cold and alkaline environments in Lake Qinghai. MicroRNAs (miRNAs) are small noncoding RNAs that regulating gene expression post-transcriptionally in a wide range of biological processes. In this study, we focus on the role of miRNAs in adaptation of G. przewalskii to extreme conditions in Lake Qinghai. We generate the first miRNAome of G. przewalskii in Schizothoracinae fish. Using several genomic resources, we inferred 341 conserved miRNAs belonged to 152 miRNA families and 43 novel miRNAs in G. przewalskii, and also identified 15 teleost-specific miRNAs. Using a large scale of conserved miRNAs, we constructed a high-confidence phylogenetic tree between teleost and mammals than mitochondria and nuclear genes. In addition, we found that several miRNA family (e.g. miR-10 and let-7) members highly expressed in G. przewalskii, which may function in multiple biological processes. Finally, we predicted a total of 34,258 miRNA targets genes. Conserved miRNAs target genes participating in signal transduction, cell differentiation and biosynthetic process, and showed signature of functional constraint. While novel miRNAs in a species displayed species-specific targets and involved in ion binding, transport and oxidoreductase activity, may affect the expression patterns of targets with signature of gene family expansion or positive selection under extreme environment. Taken together, this study demonstrated that miRNAs may involve into roles of adaptation of G. przewalskii to highland aquatic environment, and also provide insights into miRNA regulatory network in Schizothoracinae fish as a case study.}, }
@article {pmid28358800, year = {2017}, author = {Roberts, RG}, title = {Mitochondria-A billion years of cohabitation.}, journal = {PLoS biology}, volume = {15}, number = {3}, pages = {e2002338}, pmid = {28358800}, issn = {1545-7885}, mesh = {Animals ; Apoptosis ; Archaea/*cytology/*physiology ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Cytophagocytosis ; Endoplasmic Reticulum/physiology ; Energy Metabolism ; Humans ; Mitochondria/genetics/*physiology ; Models, Biological ; *Symbiosis ; }, }
@article {pmid28357316, year = {2016}, author = {Karnkowska, A and Hampl, V}, title = {The curious case of vanishing mitochondria.}, journal = {Microbial cell (Graz, Austria)}, volume = {3}, number = {10}, pages = {491-494}, pmid = {28357316}, issn = {2311-2638}, abstract = {Due to their involvement in the energy metabolism, mitochondria are essential for most eukaryotic cells. Microbial eukaryotes living in low oxygen environments possess reduced forms of mitochondria, namely mitochondrion-related organelles (MROs). These do not produce ATP by oxidative phosphorylation on their membranes and some do not produce ATP at all. Still, they are indispensable because of other essential functions such as iron-sulphur (Fe-S) cluster assembly. Recently, the first microbial eukaryote with neither mitochondrion nor MRO was characterized - Monocercomonoides sp. Genome and transcriptome sequencing of Monocercomonoides revealed that it lacks all hallmark mitochondrial proteins. Crucially, the essential mitochondrial pathway for the Fe-S cluster assembly (ISC) was replaced by a bacterial sulphur mobilization (SUF) system. The discovery of such bona fide amitochondriate eukaryote broadens our knowledge about the diversity and plasticity of eukaryotic cells and provides a substantial contribution to our understanding of eukaryotic cell evolution.}, }
@article {pmid28348231, year = {2017}, author = {Braakman, R and Follows, MJ and Chisholm, SW}, title = {Metabolic evolution and the self-organization of ecosystems.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {15}, pages = {E3091-E3100}, pmid = {28348231}, issn = {1091-6490}, mesh = {*Biological Evolution ; Biomass ; *Ecosystem ; Prochlorococcus/growth &amp; development/*metabolism ; Seawater/*microbiology ; }, abstract = {Metabolism mediates the flow of matter and energy through the biosphere. We examined how metabolic evolution shapes ecosystems by reconstructing it in the globally abundant oceanic phytoplankter Prochlorococcus To understand what drove observed evolutionary patterns, we interpreted them in the context of its population dynamics, growth rate, and light adaptation, and the size and macromolecular and elemental composition of cells. This multilevel view suggests that, over the course of evolution, there was a steady increase in Prochlorococcus' metabolic rate and excretion of organic carbon. We derived a mathematical framework that suggests these adaptations lower the minimal subsistence nutrient concentration of cells, which results in a drawdown of nutrients in oceanic surface waters. This, in turn, increases total ecosystem biomass and promotes the coevolution of all cells in the ecosystem. Additional reconstructions suggest that Prochlorococcus and the dominant cooccurring heterotrophic bacterium SAR11 form a coevolved mutualism that maximizes their collective metabolic rate by recycling organic carbon through complementary excretion and uptake pathways. Moreover, the metabolic codependencies of Prochlorococcus and SAR11 are highly similar to those of chloroplasts and mitochondria within plant cells. These observations lead us to propose a general theory relating metabolic evolution to the self-amplification and self-organization of the biosphere. We discuss the implications of this framework for the evolution of Earth's biogeochemical cycles and the rise of atmospheric oxygen.}, }
@article {pmid28342966, year = {2017}, author = {Hill, RL and Singh, IN and Wang, JA and Hall, ED}, title = {Time courses of post-injury mitochondrial oxidative damage and respiratory dysfunction and neuronal cytoskeletal degradation in a rat model of focal traumatic brain injury.}, journal = {Neurochemistry international}, volume = {111}, number = {}, pages = {45-56}, pmid = {28342966}, issn = {1872-9754}, support = {P30 NS051220/NS/NINDS NIH HHS/United States ; R01 NS083405/NS/NINDS NIH HHS/United States ; R01 NS084857/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Antioxidants/pharmacology ; Brain Injuries, Traumatic/drug therapy/*metabolism ; Cytoskeleton/metabolism ; Disease Models, Animal ; Free Radicals/*metabolism ; Lipid Peroxidation/physiology ; Mitochondria/drug effects/*metabolism ; Oxidative Stress/drug effects ; Rats, Sprague-Dawley ; Reactive Oxygen Species/*metabolism ; Time Factors ; }, abstract = {Traumatic brain injury (TBI) results in rapid reactive oxygen species (ROS) production and oxidative damage to essential brain cellular components leading to neuronal dysfunction and cell death. It is increasingly appreciated that a major player in TBI-induced oxidative damage is the reactive nitrogen species (RNS) peroxynitrite (PN) which is produced in large part in injured brain mitochondria. Once formed, PN decomposes into highly reactive free radicals that trigger membrane lipid peroxidation (LP) of polyunsaturated fatty acids (e.g. arachidonic acid) and protein nitration (3-nitrotyrosine, 3-NT) in mitochondria and other cellular membranes causing various functional impairments to mitochondrial oxidative phosphorylation and calcium (Ca[2+]) buffering capacity. The LP also results in the formation of neurotoxic reactive aldehyde byproducts including 4-hydroxynonenal (4-HNE) and propenal (acrolein) which exacerbates ROS/RNS production and oxidative protein damage in the injured brain. Ultimately, this results in intracellular Ca[2+] overload that activates proteolytic degradation of α-spectrin, a neuronal cytoskeletal protein. Therefore, the aim of this study was to establish the temporal evolution of mitochondrial dysfunction, oxidative damage and cytoskeletal degradation in the brain following a severe controlled cortical impact (CCI) TBI in young male adult rats. In mitochondria isolated from an 8 mm diameter cortical punch including the 5 mm wide impact site and their respiratory function studied ex vivo, we observed an initial decrease in complex I and II mitochondrial bioenergetics within 3 h (h). For complex I bioenergetics, this partially recovered by 12-16 h, whereas for complex II respiration the recovery was complete by 12 h. During the first 24 h, there was no evidence of an injury-induced increase in LP or protein nitration in mitochondrial or cellular homogenates. However, beginning at 24 h, there was a gradual secondary decline in complex I and II respiration that peaked at 72 h. post-TBI that coincided with progressive peroxidation of mitochondrial and cellular lipids, protein nitration and protein modification by 4-HNE and acrolein. The oxidative damage and respiratory failure paralleled an increase in Ca[2+]-induced proteolytic degradation of the neuronal cytoskeletal protein α-spectrin indicating a failure of intracellular Ca[2+] homeostasis. These findings of a surprisingly delayed peak in secondary injury, suggest that the therapeutic window and needed treatment duration for certain antioxidant treatment strategies following CCI-TBI in rodents may be longer than previously believed.}, }
@article {pmid28338960, year = {2017}, author = {Pérez-Zamorano, B and Vallebueno-Estrada, M and Martínez González, J and García Cook, A and Montiel, R and Vielle-Calzada, JP and Delaye, L}, title = {Organellar Genomes from a ∼5,000-Year-Old Archaeological Maize Sample Are Closely Related to NB Genotype.}, journal = {Genome biology and evolution}, volume = {9}, number = {4}, pages = {904-915}, pmid = {28338960}, issn = {1759-6653}, mesh = {Bayes Theorem ; Chloroplasts/genetics ; *Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Genome, Plant ; Genotype ; *Phylogeny ; Zea mays/*genetics ; }, abstract = {The story of how preColumbian civilizations developed goes hand-in-hand with the process of plant domestication by Mesoamerican inhabitants. Here, we present the almost complete sequence of a mitochondrial genome and a partial chloroplast genome from an archaeological maize sample collected at the Valley of Tehuacán, México. Accelerator mass spectrometry dated the maize sample to be 5,040-5,300 years before present (95% probability). Phylogenetic analysis of the mitochondrial genome shows that the archaeological sample branches basal to the other Zea mays genomes, as expected. However, this analysis also indicates that fertile genotype NB is closely related to the archaeological maize sample and evolved before cytoplasmic male sterility genotypes (CMS-S, CMS-T, and CMS-C), thus contradicting previous phylogenetic analysis of mitochondrial genomes from maize. We show that maximum-likelihood infers a tree where CMS genotypes branch at the base of the tree when including sites that have a relative fast rate of evolution thus suggesting long-branch attraction. We also show that Bayesian analysis infer a topology where NB and the archaeological maize sample are at the base of the tree even when including faster sites. We therefore suggest that previous trees suffered from long-branch attraction. We also show that the phylogenetic analysis of the ancient chloroplast is congruent with genotype NB to be more closely related to the archaeological maize sample. As shown here, the inclusion of ancient genomes on phylogenetic trees greatly improves our understanding of the domestication process of maize, one of the most important crops worldwide.}, }
@article {pmid28338801, year = {2017}, author = {Omura, T and Gotoh, O}, title = {Evolutionary origin of mitochondrial cytochrome P450.}, journal = {Journal of biochemistry}, volume = {161}, number = {5}, pages = {399-407}, doi = {10.1093/jb/mvx011}, pmid = {28338801}, issn = {1756-2651}, mesh = {Animals ; Cytochrome P-450 Enzyme System/*metabolism ; Fungi/metabolism ; Mitochondria/enzymology/*metabolism ; Plants/metabolism ; }, abstract = {Different molecular species of cytochrome P450 (P450) are distributed between endoplasmic reticulum (microsomes) and mitochondria in animal cells. Plants and fungi have many microsomal P450s, but no mitochondrial P450 has so far been reported. To elucidate the evolutionary origin of mitochondrial P450s in animal cells, available evidence is examined, and the virtual absence of mitochondrial P450 in plants and fungi is confirmed. It is also suggested that a microsomal P450 is the ancestor of animal mitochondrial P450s. It is likely that the endoplasmic reticulum-targeting sequence at the amino-terminus of a microsomal P450 was converted to a mitochondria-targeting sequence possibly by point mutations of a few amino acid residues or by an exon-shuffling/moving event shortly after animal lineage diverged from plants and fungi in the course of evolution of eukaryotes. It is suggested that the microsome-type P450 first imported into mitochondria utilized the existing ferredoxin in the matrix to receive electrons from NADPH, retained its oxygenase activity in the mitochondria, and gradually diversified to several P450s with different substrate specificities in the course of the evolution of animals.}, }
@article {pmid28338655, year = {2017}, author = {Bell, RAV and Megeney, LA}, title = {Evolution of caspase-mediated cell death and differentiation: twins separated at birth.}, journal = {Cell death and differentiation}, volume = {24}, number = {8}, pages = {1359-1368}, pmid = {28338655}, issn = {1476-5403}, support = {//CIHR/Canada ; }, mesh = {Animals ; Apoptosis/*genetics ; Biological Evolution ; Caspases/*genetics/metabolism ; Cell Differentiation/*genetics ; Cytoskeleton/enzymology/ultrastructure ; DNA Fragmentation ; Eukaryotic Cells/cytology/*enzymology ; Gene Expression Regulation ; Humans ; Mitochondria/enzymology/ultrastructure ; Mitochondrial Membranes/enzymology/ultrastructure ; Proteostasis/*genetics ; Signal Transduction ; }, abstract = {The phenotypic and biochemical similarities between caspase-mediated apoptosis and cellular differentiation are striking. They include such diverse phenomenon as mitochondrial membrane perturbations, cytoskeletal rearrangements and DNA fragmentation. The parallels between the two disparate processes suggest some common ancestry and highlight the paradoxical nature of the death-centric view of caspases. That is, what is the driving selective pressure that sustains death-inducing proteins throughout eukaryotic evolution? Plausibly, caspase function may be rooted in a primordial non-death function, such as cell differentiation, and was co-opted for its role in programmed cell death. This review will delve into the links between caspase-mediated apoptosis and cell differentiation and examine the distinguishing features of these events. More critically, we chronicle the evolutionary origins of caspases and propose that caspases may have held an ancient role in mediating the fidelity of cell division/differentiation through its effects on proteostasis and protein quality control.}, }
@article {pmid28335714, year = {2017}, author = {Sawyer, EM and Brunner, EC and Hwang, Y and Ivey, LE and Brown, O and Bannon, M and Akrobetu, D and Sheaffer, KE and Morgan, O and Field, CO and Suresh, N and Gordon, MG and Gunnell, ET and Regruto, LA and Wood, CG and Fuller, MT and Hales, KG}, title = {Testis-specific ATP synthase peripheral stalk subunits required for tissue-specific mitochondrial morphogenesis in Drosophila.}, journal = {BMC cell biology}, volume = {18}, number = {1}, pages = {16}, pmid = {28335714}, issn = {1471-2121}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Drosophila Proteins/*metabolism ; Drosophila melanogaster/enzymology ; Evolution, Molecular ; Flight, Animal/physiology ; Gene Knockdown Techniques ; Genes, Insect ; Green Fluorescent Proteins/metabolism ; Male ; Mitochondria/*metabolism ; Mitochondrial Proton-Translocating ATPases/chemistry/genetics/*metabolism ; Models, Biological ; *Morphogenesis ; Muscle, Skeletal/metabolism ; Mutation/genetics ; Organ Specificity ; Phenotype ; Phylogeny ; Protein Multimerization ; Protein Subunits/genetics/*metabolism ; Proton-Translocating ATPases/*metabolism ; RNA Interference ; Spermatids/metabolism ; Spermatogenesis ; Testis/*embryology ; }, abstract = {BACKGROUND: In Drosophila early post-meiotic spermatids, mitochondria undergo dramatic shaping into the Nebenkern, a spherical body with complex internal structure that contains two interwrapped giant mitochondrial derivatives. The purpose of this study was to elucidate genetic and molecular mechanisms underlying the shaping of this structure.<br><br>RESULTS: The knotted onions (knon) gene encodes an unconventionally large testis-specific paralog of ATP synthase subunit d and is required for internal structure of the Nebenkern as well as its subsequent disassembly and elongation. Knon localizes to spermatid mitochondria and, when exogenously expressed in flight muscle, alters the ratio of ATP synthase complex dimers to monomers. By RNAi knockdown we uncovered mitochondrial shaping roles for other testis-expressed ATP synthase subunits.<br><br>CONCLUSIONS: We demonstrate the first known instance of a tissue-specific ATP synthase subunit affecting tissue-specific mitochondrial morphogenesis. Since ATP synthase dimerization is known to affect the degree of inner mitochondrial membrane curvature in other systems, the effect of Knon and other testis-specific paralogs of ATP synthase subunits may be to mediate differential membrane curvature within the Nebenkern.}, }
@article {pmid28334892, year = {2017}, author = {Stone, CM and Butt, LE and Bufton, JC and Lourenco, DC and Gowers, DM and Pickford, AR and Cox, PA and Vincent, HA and Callaghan, AJ}, title = {Inhibition of homologous phosphorolytic ribonucleases by citrate may represent an evolutionarily conserved communicative link between RNA degradation and central metabolism.}, journal = {Nucleic acids research}, volume = {45}, number = {8}, pages = {4655-4666}, pmid = {28334892}, issn = {1362-4962}, support = {BB/J016179/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Binding Sites ; Biological Evolution ; Citric Acid/*chemistry/metabolism ; Cloning, Molecular ; Computational Biology ; Conserved Sequence ; Escherichia coli/*enzymology/genetics ; Exosomes/chemistry/enzymology ; Gene Expression ; Humans ; Kinetics ; Mitochondria/chemistry/enzymology ; Molecular Docking Simulation ; Polyribonucleotide Nucleotidyltransferase/*chemistry/genetics/metabolism ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary ; RNA/*chemistry/metabolism ; RNA Stability/genetics ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; Streptomyces antibioticus/*enzymology/genetics ; Structural Homology, Protein ; Substrate Specificity ; Sulfolobus solfataricus/*enzymology/genetics ; Thermodynamics ; }, abstract = {Ribonucleases play essential roles in all aspects of RNA metabolism, including the coordination of post-transcriptional gene regulation that allows organisms to respond to internal changes and environmental stimuli. However, as inherently destructive enzymes, their activity must be carefully controlled. Recent research exemplifies the repertoire of regulatory strategies employed by ribonucleases. The activity of the phosphorolytic exoribonuclease, polynucleotide phosphorylase (PNPase), has previously been shown to be modulated by the Krebs cycle metabolite citrate in Escherichia coli. Here, we provide evidence for the existence of citrate-mediated inhibition of ribonucleases in all three domains of life. In silico molecular docking studies predict that citrate will bind not only to bacterial PNPases from E. coli and Streptomyces antibioticus, but also PNPase from human mitochondria and the structurally and functionally related archaeal exosome complex from Sulfolobus solfataricus. Critically, we show experimentally that citrate also inhibits the exoribonuclease activity of bacterial, eukaryotic and archaeal PNPase homologues in vitro. Furthermore, bioinformatics data, showing key citrate-binding motifs conserved across a broad range of PNPase homologues, suggests that this regulatory mechanism may be widespread. Overall, our data highlight a communicative link between ribonuclease activity and central metabolism that may have been conserved through the course of evolution.}, }
@article {pmid28333349, year = {2017}, author = {Yahalomi, D and Haddas-Sasson, M and Rubinstein, ND and Feldstein, T and Diamant, A and Huchon, D}, title = {The Multipartite Mitochondrial Genome of Enteromyxum leei (Myxozoa): Eight Fast-Evolving Megacircles.}, journal = {Molecular biology and evolution}, volume = {34}, number = {7}, pages = {1551-1556}, doi = {10.1093/molbev/msx072}, pmid = {28333349}, issn = {1537-1719}, mesh = {Animals ; Base Sequence ; Chromosomes/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genome, Mitochondrial/genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Myxozoa/*genetics/metabolism ; Phylogeny ; }, abstract = {Myxozoans are a large group of poorly characterized cnidarian parasites. To gain further insight into their evolution, we sequenced the mitochondrial (mt) genome of Enteromyxum leei and reevaluate the mt genome structure of Kudoa iwatai. Although the typical animal mt genome is a compact, 13-25 kb, circular chromosome, the mt genome of E. leei was found to be fragmented into eight circular chromosomes of ∼23 kb, making it the largest described animal mt genome. Each chromosome was found to harbor a large noncoding region (∼15 kb), nearly identical between chromosomes. The protein coding genes show an unusually high rate of sequence evolution and possess little similarity to their cnidarian homologs. Only five protein coding genes could be identified and no tRNA genes. Surprisingly, the mt genome of K. iwatai was also found to be composed of two chromosomes. These observations confirm the remarkable plasticity of myxozoan mt genomes.}, }
@article {pmid28329425, year = {2017}, author = {Morales, HE and Sunnucks, P and Joseph, L and Pavlova, A}, title = {Perpendicular axes of differentiation generated by mitochondrial introgression.}, journal = {Molecular ecology}, volume = {26}, number = {12}, pages = {3241-3255}, doi = {10.1111/mec.14114}, pmid = {28329425}, issn = {1365-294X}, mesh = {Animals ; Australia ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Gene Flow ; *Genome, Mitochondrial ; *Hybridization, Genetic ; Models, Genetic ; Phylogeny ; Sequence Analysis, DNA ; Songbirds/*genetics ; }, abstract = {Differential introgression of mitochondrial vs. nuclear DNA generates discordant patterns of geographic variation and can promote population divergence and speciation. We examined a potential case of mitochondrial introgression leading to two perpendicular axes of differentiation. The Eastern Yellow Robin Eopsaltria australis, a widespread Australian bird, shows a deep mitochondrial split that is perpendicular to north-south nuclear DNA and plumage colour differentiation. We propose a scenario to explain this pattern: (i) first, both nuclear and mitochondrial genomes differentiated in concert during north-south population divergence; (ii) later, their histories disconnected after two mitochondrial introgression events resulting in a deep mitochondrial split perpendicular to the nuclear DNA structure. We explored this scenario by coalescent modelling of ten mitochondrial genes and 400 nuclear DNA loci. Initial mitochondrial and nuclear genome divergences were estimated to have occurred in the early Pleistocene, consistent with the proposed scenario. Subsequent climatic transitions may have driven later mitochondrial introgression. We consider neutral introgression unlikely and instead propose that the evidence is more consistent with adaptive mitochondrial introgression and selection against incompatible mitochondrial-nuclear combinations. This likely generated an axis of coastal-inland mitochondrial differentiation in the face of nuclear gene flow, perpendicular to the initial north-south axis of differentiation (reflected in genomewide nuclear DNA and colour variation).}, }
@article {pmid28329170, year = {2017}, author = {Cai, H and Rasulova, M and Vandemeulebroucke, L and Meagher, L and Vlaeminck, C and Dhondt, I and Braeckman, BP}, title = {Life-Span Extension by Axenic Dietary Restriction Is Independent of the Mitochondrial Unfolded Protein Response and Mitohormesis in Caenorhabditis elegans.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {72}, number = {10}, pages = {1311-1318}, pmid = {28329170}, issn = {1758-535X}, support = {P40 OD010440/OD/NIH HHS/United States ; }, mesh = {Age Factors ; Animals ; Caenorhabditis elegans/*metabolism ; *Caloric Restriction ; *Life Expectancy ; Mitochondria/*metabolism ; Oxidative Stress ; Phenotype ; Reactive Oxygen Species/metabolism ; Unfolded Protein Response ; }, abstract = {In Caenorhabditis elegans, a broad range of dietary restriction regimens extend life span to different degrees by separate or partially overlapping molecular pathways. One of these regimens, axenic dietary restriction, doubles the worm's life span but currently, almost nothing is known about the underlying molecular mechanism. Previous studies suggest that mitochondrial stress responses such as the mitochondrial unfolded protein response (UPRmt) or mitohormesis may play a vital role in axenic dietary restriction-induced longevity. Here, we provide solid evidence that axenic dietary restriction treatment specifically induces an UPRmt response in C elegans but this induction is not required for axenic dietary restriction-mediated longevity. We also show that reactive oxygen species-mediated mitohormesis is not involved in this phenotype. Hence, changes in mitochondrial physiology and induction of a mitochondrial stress response are not necessarily causal to large increases in life span.}, }
@article {pmid28327596, year = {2017}, author = {Shen, CM and Hu, L and Yang, CH and Yin, CY and Li, ZD and Meng, HT and Guo, YX and Mei, T and Chen, F and Zhu, BF}, title = {Genetic polymorphisms of 54 mitochondrial DNA SNP loci in Chinese Xibe ethnic minority group.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {44407}, pmid = {28327596}, issn = {2045-2322}, mesh = {Alleles ; China ; DNA, Mitochondrial/*genetics ; *Ethnicity ; Gene Frequency ; Genetic Loci ; *Genetics, Population ; Haplotypes ; Humans ; Microsatellite Repeats ; Minority Groups ; Mitochondria/*genetics ; *Phylogeny ; *Polymorphism, Single Nucleotide ; }, abstract = {We analyzed the genetic polymorphisms of 54 mitochondrial DNA (mtDNA) variants in Chinese Xibe ethnic minority group. A total of 137 unrelated healthy volunteers from Chinese Xibe group were the objects of our study. Among the selected loci, there were 51 variable positions including transitions and transversions, and single nucleotide transitions were common (83.93%) versus transversions. These variations defined 64 different mtDNA haplotypes exclusive of (CA)n and 9 bp deletion variation. The haplotype diversity and discrimination power in Xibe population were 0.9800 ± 0.004 and 0.9699, respectively. Besides, we compared Xibe group with 18 other populations and reconstructed a phylogenetic tree using Neighbor-Joining method. The result revealed that Xibe group was a close to Xinjiang Han and Yanbian Korean groups. Our data also indicated that Xibe group has a close relationship with Daur and Ewenki groups, which is reflected by the history that Xibe was influenced by Daur and Ewenki groups during the development of these groups. In conclusion, the variants we studied are polymorphic and could be used as informative genetic markers for forensic and population genetic application.}, }
@article {pmid28323052, year = {2017}, author = {Schmidt, RC and Bart, HL and Nyingi, WD}, title = {Multi-locus phylogeny reveals instances of mitochondrial introgression and unrecognized diversity in Kenyan barbs (Cyprininae: Smiliogastrini).}, journal = {Molecular phylogenetics and evolution}, volume = {111}, number = {}, pages = {35-43}, doi = {10.1016/j.ympev.2017.03.015}, pmid = {28323052}, issn = {1095-9513}, mesh = {Animals ; Cyprinidae/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; *Genetic Loci ; *Genetic Variation ; Geography ; Growth Hormone/metabolism ; Introns/genetics ; Kenya ; Mitochondria/*genetics ; *Phylogeny ; Species Specificity ; }, abstract = {The phylogenetics and taxonomic status of small African barbs (Cyprininae: Smiliogastrini) remains unresolved despite the recent decision to elevate the genus name Enteromius for the group. The main barrier to understanding the origin of African small barbs and evolutionary relationships within the group is the poor resolution of phylogenies published to date. These phylogenies usually rely on mitochondrial markers and have limited taxon sampling. Here we investigate the phylogenetic relationships of small barbs of Kenya utilizing cytochrome b, Growth Hormone (GH) intron 2, and RAG1 markers from multiple populations of many species in the region. This multi-locus study produced well-supported phylogenies and revealed additional issues that complicate understanding the relationships among East African barbs. We observed widespread mtDNA introgression within the Kenyan barbs, highlighting the need to include nuclear markers in phylogenetic studies of the group. The GH intron 2 resolved heterospecific individuals and aided in inferring the species level phylogeny. The study reveals unrecognized diversity within the group, including within species reported to occur throughout East Africa, and it provides the groundwork for future taxonomic work in the region and across Africa.}, }
@article {pmid28321488, year = {2017}, author = {Lee, YH and Chang, CP and Cheng, YJ and Kuo, YY and Lin, YS and Wang, CC}, title = {Evolutionary gain of highly divergent tRNA specificities by two isoforms of human histidyl-tRNA synthetase.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {74}, number = {14}, pages = {2663-2677}, pmid = {28321488}, issn = {1420-9071}, mesh = {Amino Acid Sequence ; Aminoacylation ; Bacillus subtilis/enzymology ; Escherichia coli/enzymology ; *Evolution, Molecular ; Histidine-tRNA Ligase/chemistry/*metabolism ; Humans ; Isoenzymes/chemistry/metabolism ; Mitochondria/metabolism ; Mutant Proteins/metabolism ; Phylogeny ; RNA, Transfer/*metabolism ; Saccharomyces cerevisiae/enzymology ; Substrate Specificity ; }, abstract = {The discriminator base N73 is a key identity element of tRNA[His]. In eukaryotes, N73 is an "A" in cytoplasmic tRNA[His] and a "C" in mitochondrial tRNA[His]. We present evidence herein that yeast histidyl-tRNA synthetase (HisRS) recognizes both A73 and C73, but somewhat prefers A73 even within the context of mitochondrial tRNA[His]. In contrast, humans possess two distinct yet closely related HisRS homologues, with one encoding the cytoplasmic form (with an extra N-terminal WHEP domain) and the other encoding its mitochondrial counterpart (with an extra N-terminal mitochondrial targeting signal). Despite these two isoforms sharing high sequence similarities (81% identity), they strongly preferred different discriminator bases (A73 or C73). Moreover, only the mitochondrial form recognized the anticodon as a strong identity element. Most intriguingly, swapping the discriminator base between the cytoplasmic and mitochondrial tRNA[His] isoacceptors conveniently switched their enzyme preferences. Similarly, swapping seven residues in the active site between the two isoforms readily switched their N73 preferences. This study suggests that the human HisRS genes, while descending from a common ancestor with dual function for both types of tRNA[His], have acquired highly specialized tRNA recognition properties through evolution.}, }
@article {pmid28320321, year = {2017}, author = {Schuster, A and Lopez, JV and Becking, LE and Kelly, M and Pomponi, SA and Wörheide, G and Erpenbeck, D and Cárdenas, P}, title = {Evolution of group I introns in Porifera: new evidence for intron mobility and implications for DNA barcoding.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {82}, pmid = {28320321}, issn = {1471-2148}, mesh = {Animals ; Base Sequence ; Biological Evolution ; *DNA Barcoding, Taxonomic ; Endonucleases/genetics ; *Introns ; Mitochondria/genetics ; Open Reading Frames ; Phylogeny ; Porifera/classification/*genetics ; RNA Splicing ; }, abstract = {BACKGROUND: Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarians, placozoans and one annelid species. Within demosponges, group I and group II introns are present in six families. Based on different insertion sites within the cox1 gene and secondary structures, four types of group I and two types of group II introns are known, which can harbor up to three encoding homing endonuclease genes (HEG) of the LAGLIDADG family (group I) and/or reverse transcriptase (group II). However, only little is known about sponge intron mobility, transmission, and origin due to the lack of a comprehensive dataset. We analyzed the largest dataset on sponge mitochondrial group I introns to date: 95 specimens, from 11 different sponge genera which provided novel insights into the evolution of group I introns.<br><br>RESULTS: For the first time group I introns were detected in four genera of the sponge family Scleritodermidae (Scleritoderma, Microscleroderma, Aciculites, Setidium). We demonstrated that group I introns in sponges aggregate in the most conserved regions of cox1. We showed that co-occurrence of two introns in cox1 is unique among metazoans, but not uncommon in sponges. However, this combination always associates an active intron with a degenerating one. Earlier hypotheses of HGT were confirmed and for the first time VGT and secondary losses of introns conclusively demonstrated.<br><br>CONCLUSION: This study validates the subclass Spirophorina (Tetractinellida) as an intron hotspot in sponges. Our analyses confirm that most sponge group I introns probably originated from fungi. DNA barcoding is discussed and the application of alternative primers suggested.}, }
@article {pmid28318058, year = {2017}, author = {Kollmar, M and Mühlhausen, S}, title = {Nuclear codon reassignments in the genomics era and mechanisms behind their evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {5}, pages = {}, doi = {10.1002/bies.201600221}, pmid = {28318058}, issn = {1521-1878}, mesh = {Amino Acid Sequence ; Ascomycota/classification/genetics ; Cell Nucleus/genetics ; Ciliophora/cytology/genetics ; Codon/*genetics ; *Evolution, Molecular ; *Genetic Code ; Genomics ; Models, Genetic ; Phylogeny ; Protein Biosynthesis ; RNA, Transfer/genetics ; Species Specificity ; }, abstract = {The canonical genetic code ubiquitously translates nucleotide into peptide sequence with several alterations known in viruses, bacteria, mitochondria, plastids, and single-celled eukaryotes. A new hypothesis to explain genetic code changes, termed tRNA loss driven codon reassignment, has been proposed recently when the polyphyly of the yeast codon reassignment events has been uncovered. According to this hypothesis, the driving force for genetic code changes are tRNA or translation termination factor loss-of-function mutations or loss-of-gene events. The free codon can subsequently be captured by all tRNAs that have an appropriately mutated anticodon and are efficiently charged. Thus, codon capture most likely happens by near-cognate tRNAs and tRNAs whose anticodons are not part of the recognition sites of the respective aminoacyl-tRNA-synthetases. This hypothesis comprehensively explains the CTG codon translation as alanine in Pachysolen yeast together with the long known translation of the same codon as serine in Candida albicans and related species, and can also be applied to most other known reassignments.}, }
@article {pmid28314772, year = {2017}, author = {Kong, P and Ufermann, CM and Zimmermann, DLM and Yin, Q and Suo, X and Helms, JB and Brouwers, JF and Gupta, N}, title = {Two phylogenetically and compartmentally distinct CDP-diacylglycerol synthases cooperate for lipid biogenesis in Toxoplasma gondii.}, journal = {The Journal of biological chemistry}, volume = {292}, number = {17}, pages = {7145-7159}, pmid = {28314772}, issn = {1083-351X}, mesh = {Animals ; Animals, Genetically Modified ; Apicoplasts/enzymology ; Diacylglycerol Cholinephosphotransferase/*genetics/metabolism ; Endoplasmic Reticulum/metabolism ; Fibroblasts/metabolism ; Fluorescent Antibody Technique, Indirect ; Gene Deletion ; Glycerophospholipids/*biosynthesis ; Golgi Apparatus/metabolism ; Humans ; Mice ; Mitochondria/metabolism ; Mutation ; Phosphatidylglycerols/chemistry ; Phosphatidylinositols/chemistry ; Phylogeny ; Protein Domains ; Protozoan Proteins/*genetics/metabolism ; Toxoplasma/*enzymology/genetics ; Virulence ; }, abstract = {Toxoplasma gondii is among the most prevalent protozoan parasites, which infects a wide range of organisms, including one-third of the human population. Its rapid intracellular replication within a vacuole requires efficient synthesis of glycerophospholipids. Cytidine diphosphate-diacylglycerol (CDP-DAG) serves as a major precursor for phospholipid synthesis. Given the peculiarities of lipid biogenesis, understanding the mechanism and physiological importance of CDP-DAG synthesis is particularly relevant in T. gondii Here, we report the occurrence of two phylogenetically divergent CDP-DAG synthase (CDS) enzymes in the parasite. The eukaryotic-type TgCDS1 and the prokaryotic-type TgCDS2 reside in the endoplasmic reticulum and apicoplast, respectively. Conditional knockdown of TgCDS1 severely attenuated the parasite growth and resulted in a nearly complete loss of virulence in a mouse model. Moreover, mice infected with the TgCDS1 mutant became fully resistant to challenge infection with a hyper-virulent strain of T. gondii The residual growth of the TgCDS1 mutant was abolished by consecutive deletion of TgCDS2. Lipidomic analyses of the two mutants revealed significant and specific declines in phosphatidylinositol and phosphatidylglycerol levels upon repression of TgCDS1 and after deletion of TgCDS2, respectively. Our data suggest a "division of labor" model of lipid biogenesis in T. gondii in which two discrete CDP-DAG pools produced in the endoplasmic reticulum and apicoplast are subsequently used for the synthesis of phosphatidylinositol in the Golgi bodies and phosphatidylglycerol in the mitochondria. The essential and divergent nature of CDP-DAG synthesis in the parasite apicoplast offers a potential drug target to inhibit the asexual reproduction of T. gondii.}, }
@article {pmid28314749, year = {2017}, author = {Wilby, D and Roberts, NW}, title = {Optical influence of oil droplets on cone photoreceptor sensitivity.}, journal = {The Journal of experimental biology}, volume = {220}, number = {Pt 11}, pages = {1997-2004}, pmid = {28314749}, issn = {1477-9145}, support = {BB/G022917/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Biological Evolution ; Chickens ; Computer Simulation ; Light ; Oils ; *Optics and Photonics ; Retinal Cone Photoreceptor Cells/*cytology/physiology ; Turtles ; Vision, Ocular ; Xenopus laevis ; }, abstract = {Oil droplets are spherical organelles found in the cone photoreceptors of vertebrates. They are generally assumed to focus incident light into the outer segment, and thereby improve light catch because of the droplets' spherical lens-like shape. However, using full-wave optical simulations of physiologically realistic cone photoreceptors from birds, frogs and turtles, we find that pigmented oil droplets actually drastically reduce the transmission of light into the outer segment integrated across the full visible wavelength range of each species. Only transparent oil droplets improve light catch into the outer segments, and any enhancement is critically dependent on the refractive index, diameter of the oil droplet, and diameter and length of the outer segment. Furthermore, oil droplets are not the only optical elements found in cone inner segments. The ellipsoid, a dense aggregation of mitochondria situated immediately prior to the oil droplet, mitigates the loss of light at the oil droplet surface. We describe a framework for integrating these optical phenomena into simple models of receptor sensitivity, and the relevance of these observations to evolutionary appearance and loss of oil droplets is discussed.}, }
@article {pmid28300533, year = {2017}, author = {Lynch, M and Marinov, GK}, title = {Membranes, energetics, and evolution across the prokaryote-eukaryote divide.}, journal = {eLife}, volume = {6}, number = {}, pages = {}, pmid = {28300533}, issn = {2050-084X}, support = {R01 GM036827/GM/NIGMS NIH HHS/United States ; R35 GM122566/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/metabolism ; *Biological Evolution ; *Energy Metabolism ; Eukaryotic Cells/*physiology ; Mitochondria/metabolism ; Prokaryotic Cells/*physiology ; }, abstract = {The evolution of the eukaryotic cell marked a profound moment in Earth's history, with most of the visible biota coming to rely on intracellular membrane-bound organelles. It has been suggested that this evolutionary transition was critically dependent on the movement of ATP synthesis from the cell surface to mitochondrial membranes and the resultant boost to the energetic capacity of eukaryotic cells. However, contrary to this hypothesis, numerous lines of evidence suggest that eukaryotes are no more bioenergetically efficient than prokaryotes. Thus, although the origin of the mitochondrion was a key event in evolutionary history, there is no reason to think membrane bioenergetics played a direct, causal role in the transition from prokaryotes to eukaryotes and the subsequent explosive diversification of cellular and organismal complexity.}, }
@article {pmid28295945, year = {2017}, author = {Sahm, A and Bens, M and Platzer, M and Cellerino, A}, title = {Parallel evolution of genes controlling mitonuclear balance in short-lived annual fishes.}, journal = {Aging cell}, volume = {16}, number = {3}, pages = {488-496}, pmid = {28295945}, issn = {1474-9726}, mesh = {Animals ; Biological Evolution ; Cell Nucleus/genetics/metabolism ; Chiroptera/genetics ; DNA Replication ; Electron Transport Chain Complex Proteins/*genetics/metabolism ; Female ; Fish Proteins/*genetics/metabolism ; Gene Expression Regulation, Developmental ; Genes, Mitochondrial ; *Genome ; Killifishes/classification/*genetics ; Longevity/*genetics ; Male ; Mitochondria/*genetics/metabolism ; Mole Rats/genetics ; Molecular Sequence Annotation ; Phylogeny ; Selection, Genetic ; }, abstract = {The current molecular understanding of the aging process derives almost exclusively from the study of random or targeted single-gene mutations in highly inbred laboratory species, mostly invertebrates. Little information is available as to the genetic mechanisms responsible for natural lifespan variation and the evolution of lifespan, especially in vertebrates. Here, we investigated the pattern of positive selection in annual (i.e., short-lived) and nonannual (i.e., longer-lived) African killifishes to identify a genomic substrate for evolution of annual life history (and reduced lifespan). We identified genes under positive selection in all steps of mitochondrial biogenesis: mitochondrial (mt) DNA replication, transcription from mt promoters, processing and stabilization of mt RNAs, mt translation, assembly of respiratory chain complexes, and electron transport chain. Signs of paralleled evolution (i.e., evolution in more than one branch of Nothobranchius phylogeny) are observed in four out of five steps. Moreover, some genes under positive selection in Nothobranchius are under positive selection also in long-lived mammals such as bats and mole-rats. Complexes of the respiratory chain are formed in a coordinates multistep process where nuclearly and mitochondrially encoded components are assembled and inserted into the inner mitochondrial membrane. The coordination of this process is named mitonuclear balance, and experimental manipulations of mitonuclear balance can increase longevity of laboratory species. Our data strongly indicate that these genes are also casually linked to evolution lifespan in vertebrates.}, }
@article {pmid28288321, year = {2017}, author = {Hrabáková, L and Koloniuk, I and Petrzik, K}, title = {Phomopsis longicolla RNA virus 1 - Novel virus at the edge of myco- and plant viruses.}, journal = {Virology}, volume = {506}, number = {}, pages = {14-18}, doi = {10.1016/j.virol.2017.03.003}, pmid = {28288321}, issn = {1096-0341}, mesh = {Amino Acid Sequence ; Ascomycota/*virology ; Base Sequence ; Fungal Viruses/classification/genetics/*isolation &amp; purification ; Genome, Viral ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Plant Diseases/virology ; Plant Viruses/classification/genetics/*isolation &amp; purification ; RNA Viruses/classification/genetics/*isolation &amp; purification ; RNA, Viral/genetics ; Viral Proteins/genetics ; }, abstract = {The complete nucleotide sequence of a new RNA mycovirus in the KY isolate of Phomopsis longicolla Hobbs 1985 and its protoplasts subcultures p5, p9, and ME711 was discovered. The virus, provisionally named Phomopsis longicolla RNA virus 1 (PlRV1), was localized in mitochondria and was determined to have a genome 2822 nucleotides long. A single open reading frame could be translated in silico by both standard and mitochondrial genetic codes into a product featuring conservative domains for an RNA-dependent RNA polymerase (RdRp). The RdRp of PlRV1 has no counterpart among mycoviruses, but it is about 30% identical with the RdRp of plant ourmiaviruses. Recently, new mycoviruses related to plant ourmiaviruses and forming one clade with PlRV1 have been discovered. This separate clade could represent the crucial link between plant and fungal viruses.}, }
@article {pmid28286223, year = {2017}, author = {Corrigan, S and Maisano Delser, P and Eddy, C and Duffy, C and Yang, L and Li, C and Bazinet, AL and Mona, S and Naylor, GJP}, title = {Historical introgression drives pervasive mitochondrial admixture between two species of pelagic sharks.}, journal = {Molecular phylogenetics and evolution}, volume = {110}, number = {}, pages = {122-126}, doi = {10.1016/j.ympev.2017.03.011}, pmid = {28286223}, issn = {1095-9513}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Ecosystem ; *Gene Pool ; Geography ; Haplotypes/genetics ; Mitochondria/*genetics ; Phylogeny ; Sharks/*genetics ; Species Specificity ; }, abstract = {We use a genomic sampling of both nuclear and mitochondrial DNA markers to examine a pattern of genetic admixture between Carcharhinus galapagensis (Galapagos sharks) and Carcharhinus obscurus (dusky sharks), two well-known and closely related sharks that have been recognized as valid species for more than 100years. We describe widespread mitochondrial-nuclear discordance in which these species are readily distinguishable based on 2152 nuclear single nucleotide polymorphisms from 910 independent autosomal regions, but show pervasive mitochondrial admixture. The species are superficially morphologically cryptic as adults but show marked differences in internal anatomy, as well as niche separation. There was no indication of ongoing hybridization between the species. We conclude that the observed mitochondrial-nuclear discordance is likely due to historical mitochondrial introgression following a range expansion.}, }
@article {pmid28283795, year = {2017}, author = {Hu, YC and Chu, KF and Yang, WK and Lee, TH}, title = {Na[+], K[+]-ATPase β1 subunit associates with α1 subunit modulating a "higher-NKA-in-hyposmotic media" response in gills of euryhaline milkfish, Chanos chanos.}, journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology}, volume = {187}, number = {7}, pages = {995-1007}, pmid = {28283795}, issn = {1432-136X}, support = {103-2311-B-005-004-MY3//Ministry of Science and Technology, Taiwan/ ; }, mesh = {Animals ; Fish Proteins/chemistry/genetics/*metabolism ; Fishes/genetics/*metabolism ; Fresh Water/*chemistry ; Gene Expression Regulation ; Gills/*enzymology ; Models, Molecular ; Osmoregulation ; Phylogeny ; Protein Conformation ; Protein Subunits ; *Salinity ; *Salt Tolerance ; Seawater/*chemistry ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; Sodium-Potassium-Exchanging ATPase/chemistry/genetics/*metabolism ; Structure-Activity Relationship ; Tissue Distribution ; }, abstract = {The euryhaline milkfish (Chanos chanos) is a popular aquaculture species that can be cultured in fresh water, brackish water, or seawater in Southeast Asia. In gills of the milkfish, Na[+], K[+]-ATPase (i.e., NKA; sodium pump) responds to salinity challenges including changes in mRNA abundance, protein amount, and activity. The functional pump is composed of a heterodimeric protein complex composed of α- and β-subunits. Among the NKA genes, α1-β1 isozyme comprises the major form of NKA subunits in mammalian osmoregulatory organs; however, most studies on fish gills have focused on the α1 subunit and did not verify the α1-β1 isozyme. Based on the sequenced milkfish transcriptome, an NKA β1 subunit gene was identified that had the highest amino acid homology to β233, a NKA β1 subunit paralog originally identified in the eel. Despite this high level of homology to β233, phylogenetic analysis and the fact that only a single NKA β1 subunit gene exists in the milkfish suggest that the milkfish gene should be referred to as the NKA β1 subunit gene. The results of accurate domain prediction of the β1 subunit, co-localization of α1 and β1 subunits in epithelial ionocytes, and co-immunoprecipitation of α1 and β1 subunits, indicated the formation of a α1-β1 complex in milkfish gills. Moreover, when transferred to hyposmotic media (fresh water) from seawater, parallel increases in branchial mRNA and protein expression of NKA α1 and β1 subunits suggested their roles in hypo-osmoregulation of euryhaline milkfish. This study molecularly characterized the NKA β1 subunit and provided the first evidence for an NKA α1-β1 association in gill ionocytes of euryhaline teleosts.}, }
@article {pmid28282399, year = {2017}, author = {Wood, LE and De Grave, S and Daniels, SR}, title = {Phylogeographic patterning among two codistributed shrimp species (Crustacea: Decapoda: Palaemonidae) reveals high levels of connectivity across biogeographic regions along the South African coast.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0173356}, pmid = {28282399}, issn = {1932-6203}, mesh = {Animals ; Arthropod Proteins/genetics ; Bayes Theorem ; Biological Evolution ; DNA/chemistry/isolation &amp; purification/metabolism ; Electron Transport Complex IV/genetics ; Genetic Loci ; Genetics, Population ; Mitochondria/enzymology ; Palaemonidae/*classification/genetics ; Phylogeny ; Phylogeography ; Sequence Alignment ; Sequence Analysis, DNA ; South Africa ; }, abstract = {We compare the genetic structuring and demographic history of two sympatric caridean shrimp species with distinct life history traits, one amphidromous species Palaemon capensis and one marine/estuarine species Palaemon peringueyi, in the historical biogeographical context of South Africa. A total of 103 specimens of P. capensis collected from 12 localities and 217 specimens of P. peringueyi collected from 24 localities were sequenced for the mitochondrial cytochrome oxidase one (CO1) locus. Results from analyses of molecular variance (AMOVA), pairwise ΦST comparisons and haplotype networks demonstrate weak to moderate genetic differentiation in P. capensis and P. peringueyi respectively. P. peringueyi exhibits partial isolation between populations associated with distinct biogeographic regions, likely driven by the region's oceanography. However, there is minimal evidence for the occurrence of discrete regional evolutionary lineages. This demonstrated lack of genetic differentiation is consistent with a marine, highly dispersive planktonic phase in both the amphidromous P. capensis and the marine/estuarine P. peringueyi. Bayesian skyline plots, mismatch expansions and time since expansion indicate that both species maintained stable populations during the Last Glacial Maximum (LGM), unlike other southern African aquatic species.}, }
@article {pmid28276011, year = {2017}, author = {Izawa, T and Unger, AK}, title = {Isolation of Mitochondria from Saccharomyces cerevisiae.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1567}, number = {}, pages = {33-42}, doi = {10.1007/978-1-4939-6824-4_3}, pmid = {28276011}, issn = {1940-6029}, mesh = {Cell Fractionation/*methods ; Centrifugation, Density Gradient/methods ; *Mitochondria/metabolism/ultrastructure ; *Saccharomyces cerevisiae/metabolism ; }, abstract = {The budding yeast Saccharomyces cerevisiae is an important model organism to study cellular structure and function. Due to its excellent accessibility to genetics and biochemical and microscopic analyses, studies with yeast have provided fundamental insights into mitochondrial biology. Yeast offers additional advantages because it can grow under fermenting conditions when oxidative phosphorylation is not obligatory and because the majority of mitochondrial structure and function are largely conserved during evolution. Isolation of mitochondria is an important technique for mitochondrial studies. This chapter focuses on procedures for the isolation and purification of intact yeast mitochondria that can be used for numerous functional assays as well as for analyses of mitochondrial ultrastructure.}, }
@article {pmid28274885, year = {2017}, author = {Brenière, SF and Condori, EW and Buitrago, R and Sosa, LF and Macedo, CL and Barnabé, C}, title = {Molecular identification of wild triatomines of the genus Rhodnius in the Bolivian Amazon: Strategy and current difficulties.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {51}, number = {}, pages = {1-9}, doi = {10.1016/j.meegid.2017.03.002}, pmid = {28274885}, issn = {1567-7257}, mesh = {Animals ; Arecaceae ; Bolivia/epidemiology ; Cell Nucleus/genetics ; Chagas Disease/epidemiology/*transmission ; DNA, Mitochondrial/*genetics ; Female ; Haplotypes ; Humans ; Insect Proteins/*genetics ; Insect Vectors/*classification/genetics/parasitology ; Male ; Mitochondria/genetics ; *Phylogeny ; Rhodnius/*classification/genetics/parasitology ; Trypanosoma cruzi/*genetics/isolation &amp; purification ; }, abstract = {The Amazon region has recently been considered as endemic in Latin America. In Bolivia, the vast Amazon region is undergoing considerable human migrations and substantial anthropization of the environment, potentially renewing the danger of establishing the transmission of Chagas disease. The cases of human oral contamination occurring in 2010 in the town of Guayaramerín provided reasons to intensify research. As a result, the goal of this study was to characterize the species of sylvatic triatomines circulating in the surroundings of Yucumo (Beni, Bolivia), a small Amazonian city at the foot of the Andes between the capital (La Paz) and Trinidad the largest city of Beni. The triatomine captures were performed with mice-baited adhesive traps mostly settled in palm trees in forest fragments and pastures. Species were identified by morphological observation, dissection of genitalia, and sequencing of three mitochondrial gene fragments and one nuclear fragment. Molecular analysis was based on (i) the identity score of the haplotypes with GenBank sequences through the BLAST algorithm and (ii) construction of phylogenetic trees. Thirty-four triatomines, all belonging to the Rhodnius genus, of which two were adult males, were captured in palm trees in forest fragments and pastures (overall infestation rate, 12.3%). The morphology of the phallic structures in the two males confirmed the R. stali species. For the other specimens, after molecular sequencing, only one specimen was identified with confidence as belonging to Rhodnius robustus, the others belonged to one of the species of the Rhodnius pictipes complex, probably Rhodnius stali. The two species, R. robustus and R. stali, had previously been reported in the Alto Beni region (edge of the Amazon region), but not yet in the Beni department situated in the Amazon region. Furthermore, the difficulties of molecular characterization of closely related species within the three complexes of the genus Rhodnius are highlighted and discussed.}, }
@article {pmid28274797, year = {2017}, author = {Hall, A and Lächelt, U and Bartek, J and Wagner, E and Moghimi, SM}, title = {Polyplex Evolution: Understanding Biology, Optimizing Performance.}, journal = {Molecular therapy : the journal of the American Society of Gene Therapy}, volume = {25}, number = {7}, pages = {1476-1490}, pmid = {28274797}, issn = {1525-0024}, mesh = {Animals ; Cell Membrane/chemistry/*drug effects/metabolism ; Complement Activation/drug effects ; Complement System Proteins/genetics/metabolism ; Gene Expression Regulation/*drug effects ; *Gene Transfer Techniques ; Genetic Therapy ; Glycolysis ; Humans ; Mitochondria/chemistry/*drug effects/immunology/metabolism ; Oxidation-Reduction ; Polyethyleneimine/chemistry/pharmacokinetics/*toxicity ; Toll-Like Receptors/genetics/immunology ; }, abstract = {Polyethylenimine (PEI) is a gold standard polycationic transfectant. However, the highly efficient transfecting activity of PEI and many of its derivatives is accompanied by serious cytotoxic complications and safety concerns at innate immune levels, which impedes the development of therapeutic polycationic nucleic acid carriers in general and their clinical applications. In recent years, the dilemma between transfection efficacy and adverse PEI activities has been addressed from in-depth investigations of cellular processes during transfection and elucidation of molecular mechanisms of PEI-mediated toxicity and translation of these integrated events to chemical engineering of novel PEI derivatives with an improved benefit-to-risk ratio. This review addresses these perspectives and discusses molecular events pertaining to dynamic and multifaceted PEI-mediated cytotoxicity, including membrane destabilization, mitochondrial dysfunction, and perturbations of glycolytic flux and redox homeostasis as well as chemical strategies for the generation of better tolerated polycations. We further examine the effect of PEI and its derivatives on complement activation and interaction with Toll-like receptors. These perspectives are intended to lay the foundation for an improved understanding of interlinked mechanisms controlling transfection and toxicity and their translation for improved engineering of polycation-based transfectants.}, }
@article {pmid28273082, year = {2017}, author = {Jain, S and Rai, N and Kumar, G and Pruthi, PA and Thangaraj, K and Bajpai, S and Pruthi, V}, title = {Ancient DNA Reveals Late Pleistocene Existence of Ostriches in Indian Sub-Continent.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0164823}, pmid = {28273082}, issn = {1932-6203}, mesh = {Animals ; DNA, Ancient/*analysis ; Egg Shell/metabolism/pathology ; Fossils ; India ; Microscopy, Confocal ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; Struthioniformes/classification/*genetics ; }, abstract = {Ancient DNA (aDNA) analysis of extinct ratite species is of considerable interest as it provides important insights into their origin, evolution, paleogeographical distribution and vicariant speciation in congruence with continental drift theory. In this study, DNA hotspots were detected in fossilized eggshell fragments of ratites (dated ≥25000 years B.P. by radiocarbon dating) using confocal laser scanning microscopy (CLSM). DNA was isolated from five eggshell fragments and a 43 base pair (bp) sequence of a 16S rRNA mitochondrial-conserved region was successfully amplified and sequenced from one of the samples. Phylogenetic analysis of the DNA sequence revealed a 92% identity of the fossil eggshells to Struthio camelus and their position basal to other palaeognaths, consistent with the vicariant speciation model. Our study provides the first molecular evidence for the presence of ostriches in India, complementing the continental drift theory of biogeographical movement of ostriches in India, and opening up a new window into the evolutionary history of ratites.}, }
@article {pmid28273078, year = {2017}, author = {Yan, D and Xiang, G and Chai, X and Qing, J and Shang, H and Zou, B and Mittal, R and Shen, J and Smith, RJ and Fan, YS and Blanton, SH and Tekin, M and Morton, C and Xing, W and Cheng, J and Liu, XZ}, title = {Screening of deafness-causing DNA variants that are common in patients of European ancestry using a microarray-based approach.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0169219}, pmid = {28273078}, issn = {1932-6203}, support = {R01 DC005575/DC/NIDCD NIH HHS/United States ; R01 DC009645/DC/NIDCD NIH HHS/United States ; R01 DC012115/DC/NIDCD NIH HHS/United States ; R01 DC015052/DC/NIDCD NIH HHS/United States ; }, mesh = {Connexin 26 ; Connexin 30 ; Connexins/genetics/metabolism ; DNA/chemistry/genetics/isolation &amp; purification/*metabolism ; DNA, Mitochondrial/chemistry/genetics/metabolism ; Deafness/*genetics/pathology ; Genetic Predisposition to Disease/*genetics ; Genetic Testing/*methods ; Humans ; Membrane Transport Proteins/genetics ; Mitochondria/genetics ; *Oligonucleotide Array Sequence Analysis/instrumentation ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sulfate Transporters ; White People/*genetics ; }, abstract = {The unparalleled heterogeneity in genetic causes of hearing loss along with remarkable differences in prevalence of causative variants among ethnic groups makes single gene tests technically inefficient. Although hundreds of genes have been reported to be associated with nonsyndromic hearing loss (NSHL), GJB2, GJB6, SLC26A4, and mitochondrial (mt) MT-RNR1 and MTTS are the major contributors. In order to provide a faster, more comprehensive and cost effective assay, we constructed a DNA fluidic array, CapitalBioMiamiOtoArray, for the detection of sequence variants in five genes that are common in most populations of European descent. They consist of c.35delG, p.W44C, p.L90P, c.167delT (GJB2); 309kb deletion (GJB6); p.L236P, p.T416P (SLC26A4); and m.1555A>G, m.7444G>A (mtDNA). We have validated our hearing loss array by analyzing a total of 160 DNAs samples. Our results show 100% concordance between the fluidic array biochip-based approach and the established Sanger sequencing method, thus proving its robustness and reliability at a relatively low cost.}, }
@article {pmid28272742, year = {2017}, author = {Höllinger, I and Hermisson, J}, title = {Bounds to parapatric speciation: A Dobzhansky-Muller incompatibility model involving autosomes, X chromosomes, and mitochondria.}, journal = {Evolution; international journal of organic evolution}, volume = {71}, number = {5}, pages = {1366-1380}, doi = {10.1111/evo.13223}, pmid = {28272742}, issn = {1558-5646}, support = {W 1225/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Female ; Gene Dosage ; *Gene Flow ; Genome ; Male ; *Mitochondria ; *Models, Genetic ; *X Chromosome ; }, abstract = {We investigate the conditions for the origin and maintenance of postzygotic isolation barriers, so called (Bateson-)Dobzhansky-Muller incompatibilities or DMIs, among populations that are connected by gene flow. Specifically, we compare the relative stability of pairwise DMIs among autosomes, X chromosomes, and mitochondrial genes. In an analytical approach based on a continent-island framework, we determine how the maximum permissible migration rates depend on the genomic architecture of the DMI, on sex bias in migration rates, and on sex-dependence of allelic and epistatic effects, such as dosage compensation. Our results show that X-linkage of DMIs can enlarge the migration bounds relative to autosomal DMIs or autosome-mitochondrial DMIs, in particular in the presence of dosage compensation. The effect is further strengthened with male-biased migration. This mechanism might contribute to a higher density of DMIs on the X chromosome (large X-effect) that has been observed in several species clades. Furthermore, our results agree with empirical findings of higher introgression rates of autosomal compared to X-linked loci.}, }
@article {pmid28265765, year = {2017}, author = {Martin, WF and Cerff, R}, title = {Physiology, phylogeny, early evolution, and GAPDH.}, journal = {Protoplasma}, volume = {254}, number = {5}, pages = {1823-1834}, pmid = {28265765}, issn = {1615-6102}, support = {666053//European Research Council/International ; }, mesh = {Animals ; Glyceraldehyde-3-Phosphate Dehydrogenases/genetics/*metabolism ; Humans ; Mitochondria/genetics/metabolism ; Phylogeny ; Plastids/enzymology ; Symbiosis/genetics/physiology ; }, abstract = {The chloroplast and cytosol of plant cells harbor a number of parallel biochemical reactions germane to the Calvin cycle and glycolysis, respectively. These reactions are catalyzed by nuclear encoded, compartment-specific isoenzymes that differ in their physiochemical properties. The chloroplast cytosol isoenzymes of D-glyceraldehyde-3-phosphate dehydrogenase (GAPDH) harbor evidence of major events in the history of life: the origin of the first genes, the bacterial-archaeal split, the origin of eukaryotes, the evolution of protein compartmentation during eukaryote evolution, the origin of plastids, and the secondary endosymbiosis among the algae with complex plastids. The reaction mechanism of GAPDH entails phosphorolysis of a thioester to yield an energy-rich acyl phosphate bond, a chemistry that points to primitive pathways of energy conservation that existed even before the origin of the first free-living cells. Here, we recount the main insights that chloroplast and cytosolic GAPDH provided into endosymbiosis and physiological evolution.}, }
@article {pmid28264444, year = {2017}, author = {Gershgorin, RA and Gorbunov, KY and Zverkov, OA and Rubanov, LI and Seliverstov, AV and Lyubetsky, VA}, title = {Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates.}, journal = {Life (Basel, Switzerland)}, volume = {7}, number = {1}, pages = {}, pmid = {28264444}, issn = {2075-1729}, abstract = {Recent phylogenetic analyses are incorporating ultraconserved elements (UCEs) and highly conserved elements (HCEs). Models of evolution of the genome structure and HCEs initially faced considerable algorithmic challenges, which gave rise to (often unnatural) constraints on these models, even for conceptually simple tasks such as the calculation of distance between two structures or the identification of UCEs. In our recent works, these constraints have been addressed with fast and efficient solutions with no constraints on the underlying models. These approaches have led us to an unexpected result: for some organelles and taxa, the genome structure and HCE set, despite themselves containing relatively little information, still adequately resolve the evolution of species. We also used the HCE identification to search for promoters and regulatory elements that characterize the functional evolution of the genome.}, }
@article {pmid28262720, year = {2017}, author = {Gandini, CL and Sanchez-Puerta, MV}, title = {Foreign Plastid Sequences in Plant Mitochondria are Frequently Acquired Via Mitochondrion-to-Mitochondrion Horizontal Transfer.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43402}, pmid = {28262720}, issn = {2045-2322}, mesh = {Arecaceae/classification/genetics ; Base Sequence ; DNA, Mitochondrial ; Evolution, Molecular ; Fagaceae/classification/genetics ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Genome, Plastid ; Lamiaceae/classification/genetics ; Magnoliopsida/classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; Plastids/*genetics ; Rosaceae/classification/genetics ; }, abstract = {Angiosperm mitochondrial genomes (mtDNA) exhibit variable quantities of alien sequences. Many of these sequences are acquired by intracellular gene transfer (IGT) from the plastid. In addition, frequent events of horizontal gene transfer (HGT) between mitochondria of different species also contribute to their expanded genomes. In contrast, alien sequences are rarely found in plastid genomes. Most of the plant-to-plant HGT events involve mitochondrion-to-mitochondrion transfers. Occasionally, foreign sequences in mtDNAs are plastid-derived (MTPT), raising questions about their origin, frequency, and mechanism of transfer. The rising number of complete mtDNAs allowed us to address these questions. We identified 15 new foreign MTPTs, increasing significantly the number of those previously reported. One out of five of the angiosperm species analyzed contained at least one foreign MTPT, suggesting a remarkable frequency of HGT among plants. By analyzing the flanking regions of the foreign MTPTs, we found strong evidence for mt-to-mt transfers in 65% of the cases. We hypothesize that plastid sequences were initially acquired by the native mtDNA via IGT and then transferred to a distantly-related plant via mitochondrial HGT, rather than directly from a foreign plastid to the mitochondrial genome. Finally, we describe three novel putative cases of mitochondrial-derived sequences among angiosperm plastomes.}, }
@article {pmid28259117, year = {2016}, author = {Zinovkin, RA and Skulachev, MV and Skulachev, VP}, title = {Mitochondrial Genome and Longevity.}, journal = {Biochemistry. Biokhimiia}, volume = {81}, number = {12}, pages = {1401-1405}, doi = {10.1134/S0006297916120014}, pmid = {28259117}, issn = {1608-3040}, mesh = {Aging ; Animals ; DNA, Mitochondrial ; Evolution, Molecular ; Genetic Association Studies ; *Genome, Mitochondrial ; Humans ; Longevity/*genetics ; Reactive Oxygen Species ; }, abstract = {The mitochondrial genome provides not only respiratory chain function, but it also ensures the impact of mitochondria on nearly all crucial metabolic processes. It is well known that mitochondria regulate aging and lifespan. However, until now there were no direct experimental data concerning the influence of various mitochondrial DNA variants on lifespan of animals with identical nuclear genome. In a recent paper of J. A. Enríquez and coworkers (Latorre-Pellicer, A., et al. (2016) Nature, 535, 561-565), it was shown that mice carrying nuclear DNA from one strain and mitochondrial DNA from another had longer median lifespan and retarded development of various aging traits. This review critically analyzes that paper and considers some aspects of the crosstalk between the nuclear and mitochondrial genomes. We also discuss new perspectives of gerontology in the light of the discovery made by Enríquez's group.}, }
@article {pmid28258572, year = {2017}, author = {Cerdà, J and Chauvigné, F and Finn, RN}, title = {The Physiological Role and Regulation of Aquaporins in Teleost Germ Cells.}, journal = {Advances in experimental medicine and biology}, volume = {969}, number = {}, pages = {149-171}, doi = {10.1007/978-94-024-1057-0_10}, pmid = {28258572}, issn = {0065-2598}, mesh = {*Adaptation, Physiological ; Animals ; Aquaporins/genetics/*metabolism ; Aquatic Organisms ; Biological Transport ; Cypriniformes/classification/genetics/growth &amp; development/*metabolism ; Female ; Fish Proteins/genetics/*metabolism ; Gene Expression Regulation ; Male ; Oocytes/growth &amp; development/*metabolism ; Osmotic Pressure ; Oxidative Stress ; Perciformes/classification/genetics/growth &amp; development/*metabolism ; Phylogeny ; Protein Isoforms/genetics/metabolism ; Salinity ; Spermatozoa/growth &amp; development/*metabolism ; }, abstract = {The unicellular germ cells and gametes of oviparous teleosts lack the osmoregulatory organs present in juveniles and adults, yet during development and particularly at spawning, they face tremendous osmotic challenges when released into the external aquatic environment. Increasing evidence suggests that transmembrane water channels (aquaporins) evolved to play vital adaptive roles that mitigate the osmotic and oxidative stress problems of the developing oocytes , embryos and spermatozoa. In this chapter, we provide a short overview of the diversity of the aquaporin superfamily in teleosts, and summarize the findings that uncovered a highly specific molecular regulation of aquaporins during oogenesis and spermatogenesis. We further review the multiple functions that these channels play during the establishment of egg buoyancy and the activation and detoxification of spermatozoa in the marine environment.}, }
@article {pmid28257510, year = {2017}, author = {Gao, YS and Jia, XX and Tang, XJ and Fan, YF and Lu, JX and Huang, SH and Tang, MJ}, title = {The genetic diversity of chicken breeds from Jiangxi, assessed with BCDO2 and the complete mitochondrial DNA D-loop region.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0173192}, pmid = {28257510}, issn = {1932-6203}, mesh = {Animals ; Animals, Domestic/genetics ; Avian Proteins/*genetics ; Breeding ; Chickens/genetics ; China ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; Haplotypes ; Mitochondria/genetics ; *Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; beta Carotene/genetics ; beta-Carotene 15,15'-Monooxygenase/*genetics ; }, abstract = {The Jiangxi Province of China has numerous native domestic chicken breeds, including some black skin breeds. The genetic diversity of Jiangxi native chickens is largely unknown, and specifically, the genetic contribution of the grey junglefowl to black skin chickens is not well understood. To address these questions, the complete D-loop region of the mitochondrial DNA (mtDNA) and beta-carotene dioxygenase 2(BCDO2)gene was sequenced in a total of 209 chickens representing seven Jiangxi native breeds. Thirty-one polymorphic sites were identified across the complete mtDNA D-loop region sequence. Twenty-three haplotypes were observed in the seven breeds, which belonged to four distinct mitochondrial clades (A, B, C and E). Clade A and B were dominant in the chickens with a frequency of approximately 67.9%. There were five SNPs that defined two haplotypes, W and Y in BCDO2. Four breeds had one haplotype and three breeds had two. We conclude that Jiangxi native chicken breeds have relatively low genetic diversity and likely share four common maternal lineages from two different maternal ancestors of junglefowl. Furthermore, some Jiangxi chicken populations may have been mixed with chickens with exotic lineage. Further research should be established to protect these domestic chicken resources.}, }
@article {pmid28256554, year = {2017}, author = {Tong, W and He, Q and Park, YJ}, title = {Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43327}, pmid = {28256554}, issn = {2045-2322}, mesh = {Biological Evolution ; DNA, Plant/*genetics ; Genetic Variation ; Genetics, Population ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Oryza/classification/*genetics ; *Phylogeny ; Plant Breeding/methods ; Plant Weeds/classification/*genetics ; Polymorphism, Single Nucleotide ; Republic of Korea ; Sequence Analysis, DNA ; }, abstract = {Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level.}, }
@article {pmid28254477, year = {2017}, author = {López-García, P and Eme, L and Moreira, D}, title = {Symbiosis in eukaryotic evolution.}, journal = {Journal of theoretical biology}, volume = {434}, number = {}, pages = {20-33}, pmid = {28254477}, issn = {1095-8541}, support = {322669/ERC_/European Research Council/International ; }, mesh = {*Biological Evolution ; Ecosystem ; Eukaryota/*cytology/ultrastructure ; Eukaryotic Cells/ultrastructure ; Microbiota ; *Symbiosis ; }, abstract = {Fifty years ago, Lynn Margulis, inspiring in early twentieth-century ideas that put forward a symbiotic origin for some eukaryotic organelles, proposed a unified theory for the origin of the eukaryotic cell based on symbiosis as evolutionary mechanism. Margulis was profoundly aware of the importance of symbiosis in the natural microbial world and anticipated the evolutionary significance that integrated cooperative interactions might have as mechanism to increase cellular complexity. Today, we have started fully appreciating the vast extent of microbial diversity and the importance of syntrophic metabolic cooperation in natural ecosystems, especially in sediments and microbial mats. Also, not only the symbiogenetic origin of mitochondria and chloroplasts has been clearly demonstrated, but improvement in phylogenomic methods combined with recent discoveries of archaeal lineages more closely related to eukaryotes further support the symbiogenetic origin of the eukaryotic cell. Margulis left us in legacy the idea of 'eukaryogenesis by symbiogenesis'. Although this has been largely verified, when, where, and specifically how eukaryotic cells evolved are yet unclear. Here, we shortly review current knowledge about symbiotic interactions in the microbial world and their evolutionary impact, the status of eukaryogenetic models and the current challenges and perspectives ahead to reconstruct the evolutionary path to eukaryotes.}, }
@article {pmid28253086, year = {2017}, author = {Biase, FH}, title = {Oocyte Developmental Competence: Insights from Cross-Species Differential Gene Expression and Human Oocyte-Specific Functional Gene Networks.}, journal = {Omics : a journal of integrative biology}, volume = {21}, number = {3}, pages = {156-168}, doi = {10.1089/omi.2016.0177}, pmid = {28253086}, issn = {1557-8100}, mesh = {Female ; Gene Ontology ; Gene Regulatory Networks/*genetics ; Humans ; Mitochondria/metabolism ; Oocytes/metabolism/*physiology ; }, abstract = {Understanding oocyte developmental competence remains a key challenge for reproductive biology and systems sciences. The transcriptome of oocytes in eutherians is highly complex and is associated with the success of embryo development. Due to sample limitations from humans, animal models are used for investigation of the oocyte transcriptome. Nonetheless, little is known about the diversity of the oocyte transcriptome across eutherians. In this report, comprehensive investigation of 7 public data sets in 4 species, human, macaque, mice, and cattle, shows that 16,572 genes are expressed in oocytes. Approximately 26% of the genes were expressed in all four species. There were 1390, 489, and 187 genes specifically expressed in human, mice, and cattle oocytes, respectively. Coexpression clustering of the genes specifically expressed in human oocytes revealed functional enrichment (FDR <0.05) of Gene Ontology (GO) terms important for oocyte physiology (i.e., "cellular response to metal ion," "negative regulation of growth," "hormone activity," and "receptor activity"). Interrogation of 4 data sets revealed 26 genes whose expressions were significantly (FDR ≤0.1) associated with oocyte developmental competence and concordant fold change in 2 studies. The genes AK2, AKAP1, ECHS1, MRPL10, MRPL24, PTRH2, STX17, SUCLG1, SUOX, and TOMM34 were associated with the GO term "mitochondrion" (FDR <0.01). Collectively, the results offer new insights on gene transcript levels associated with oocyte developmental competence and the central role of mitochondrion for oocyte's health among eutherians. Caution should be exercised, however, when extending the inferences related to gene expression associated with oocyte quality across eutherians.}, }
@article {pmid28251677, year = {2017}, author = {Giannoccaro, MP and La Morgia, C and Rizzo, G and Carelli, V}, title = {Mitochondrial DNA and primary mitochondrial dysfunction in Parkinson's disease.}, journal = {Movement disorders : official journal of the Movement Disorder Society}, volume = {32}, number = {3}, pages = {346-363}, doi = {10.1002/mds.26966}, pmid = {28251677}, issn = {1531-8257}, mesh = {DNA, Mitochondrial/*genetics ; Humans ; Mitochondrial Diseases/genetics/*metabolism ; Parkinson Disease/genetics/*metabolism ; }, abstract = {In 1979, it was observed that parkinsonism could be induced by a toxin inhibiting mitochondrial respiratory complex I. This initiated the long-standing hypothesis that mitochondrial dysfunction may play a key role in the pathogenesis of Parkinson's disease (PD). This hypothesis evolved, with accumulating evidence pointing to complex I dysfunction, which could be caused by environmental or genetic factors. Attention was focused on the mitochondrial DNA, considering the occurrence of mutations, polymorphic haplogroup-specific variants, and defective mitochondrial DNA maintenance with the accumulation of multiple deletions and a reduction of copy number. Genetically determined diseases of mitochondrial DNA maintenance frequently manifest with parkinsonism, but the age-related accumulation of somatic mitochondrial DNA errors also represents a major driving mechanism for PD. Recently, the discovery of the genetic cause of rare inherited forms of PD highlighted an extremely complex homeostatic control over mitochondria, involving their dynamic fission/fusion cycle, the balancing of mitobiogenesis and mitophagy, and consequently the quality control surveillance that corrects faulty mitochondrial DNA maintenance. Many genes came into play, including the PINK1/parkin axis, but also OPA1, as pieces of the same puzzle, together with mitochondrial DNA damage, complex I deficiency and increased oxidative stress. The search for answers will drive future research to reach the understanding necessary to provide therapeutic options directed not only at limiting the clinical evolution of symptoms but also finally addressing the pathogenic mechanisms of neurodegeneration in PD. © 2017 International Parkinson and Movement Disorder Society.}, }
@article {pmid28249161, year = {2017}, author = {Tanaka, H and Takebayashi, SI and Sakamoto, A and Igata, T and Nakatsu, Y and Saitoh, N and Hino, S and Nakao, M}, title = {The SETD8/PR-Set7 Methyltransferase Functions as a Barrier to Prevent Senescence-Associated Metabolic Remodeling.}, journal = {Cell reports}, volume = {18}, number = {9}, pages = {2148-2161}, doi = {10.1016/j.celrep.2017.02.021}, pmid = {28249161}, issn = {2211-1247}, mesh = {Cell Line ; Cell Nucleolus/metabolism ; Cellular Senescence/*physiology ; Chromatin/metabolism ; Cyclin-Dependent Kinase Inhibitor p16/metabolism ; DNA Replication/physiology ; Down-Regulation/physiology ; Gene Expression Regulation/physiology ; Histone-Lysine N-Methyltransferase/*metabolism ; Histones/metabolism ; Humans ; Lysine/metabolism ; Methylation ; Methyltransferases/*metabolism ; Mitochondria/metabolism ; RNA, Ribosomal/metabolism ; Ribosomal Proteins/metabolism ; }, abstract = {Cellular senescence is an irreversible growth arrest that contributes to development, tumor suppression, and age-related conditions. Senescent cells show active metabolism compared with proliferating cells, but the underlying mechanisms remain unclear. Here we show that the SETD8/PR-Set7 methyltransferase, which catalyzes mono-methylation of histone H4 at lysine 20 (H4K20me1), suppresses nucleolar and mitochondrial activities to prevent cellular senescence. SETD8 protein was selectively downregulated in both oncogene-induced and replicative senescence. Inhibition of SETD8 alone was sufficient to trigger senescence. Under these states, the expression of genes encoding ribosomal proteins (RPs) and ribosomal RNAs as well as the cyclin-dependent kinase (CDK) inhibitor p16[INK4A] was increased, with a corresponding reduction of H4K20me1 at each locus. As a result, the loss of SETD8 concurrently stimulated nucleolar function and retinoblastoma protein-mediated mitochondrial metabolism. In conclusion, our data demonstrate that SETD8 acts as a barrier to prevent cellular senescence through chromatin-mediated regulation of senescence-associated metabolic remodeling.}, }
@article {pmid28242298, year = {2017}, author = {Larsen, PA and Lutz, MW and Hunnicutt, KE and Mihovilovic, M and Saunders, AM and Yoder, AD and Roses, AD}, title = {The Alu neurodegeneration hypothesis: A primate-specific mechanism for neuronal transcription noise, mitochondrial dysfunction, and manifestation of neurodegenerative disease.}, journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association}, volume = {13}, number = {7}, pages = {828-838}, pmid = {28242298}, issn = {1552-5279}, support = {S10 OD018164/OD/NIH HHS/United States ; }, mesh = {*Alu Elements ; Animals ; Humans ; Introns ; Membrane Transport Proteins/genetics ; Mitochondria/*genetics ; Mitochondrial Precursor Protein Import Complex Proteins ; Neurodegenerative Diseases/*physiopathology ; *Primates ; }, abstract = {It is hypothesized that retrotransposons have played a fundamental role in primate evolution and that enhanced neurologic retrotransposon activity in humans may underlie the origin of higher cognitive function. As a potential consequence of this enhanced activity, it is likely that neurons are susceptible to deleterious retrotransposon pathways that can disrupt mitochondrial function. An example is observed in the TOMM40 gene, encoding a β-barrel protein critical for mitochondrial preprotein transport. Primate-specific Alu retrotransposons have repeatedly inserted into TOMM40 introns, and at least one variant associated with late-onset Alzheimer's disease originated from an Alu insertion event. We provide evidence of enriched Alu content in mitochondrial genes and postulate that Alus can disrupt mitochondrial populations in neurons, thereby setting the stage for progressive neurologic dysfunction. This Alu neurodegeneration hypothesis is compatible with decades of research and offers a plausible mechanism for the disruption of neuronal mitochondrial homeostasis, ultimately cascading into neurodegenerative disease.}, }
@article {pmid28232454, year = {2017}, author = {Krishnan, A and Abdullah, TS and Mounajjed, T and Hartono, S and McConico, A and White, T and LeBrasseur, N and Lanza, I and Nair, S and Gores, G and Charlton, M}, title = {A longitudinal study of whole body, tissue, and cellular physiology in a mouse model of fibrosing NASH with high fidelity to the human condition.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {312}, number = {6}, pages = {G666-G680}, pmid = {28232454}, issn = {1522-1547}, support = {F30 DK102232/DK/NIDDK NIH HHS/United States ; R01 DK041876/DK/NIDDK NIH HHS/United States ; }, mesh = {Adiposity ; Animals ; Biomarkers/blood ; Blood Glucose/metabolism ; Diet, High-Fat ; Disease Models, Animal ; Disease Progression ; Energy Metabolism ; Humans ; Inflammation Mediators/blood ; Insulin/blood ; Insulin Resistance ; Lipids/blood ; Liver/*metabolism/physiology/physiopathology ; Liver Cirrhosis/genetics/*metabolism/pathology/physiopathology ; Male ; Mice, Inbred C57BL ; Mitochondria, Liver/metabolism/pathology ; Non-alcoholic Fatty Liver Disease/genetics/*metabolism/pathology/physiopathology ; Organ Size ; Species Specificity ; Time Factors ; Weight Gain ; }, abstract = {The sequence of events that lead to inflammation and fibrosing nonalcoholic steatohepatitis (NASH) is incompletely understood. Hence, we investigated the chronology of whole body, tissue, and cellular events that occur during the evolution of diet-induced NASH. Male C57Bl/6 mice were assigned to a fast-food (FF; high calorie, high cholesterol, high fructose) or standard-chow (SC) diet over a period of 36 wk. Liver histology, body composition, mitochondrial respiration, metabolic rate, gene expression, and hepatic lipid content were analyzed. Insulin resistance [homeostasis model assessment-insulin resistance (HOMA-IR)] increased 10-fold after 4 wk. Fibrosing NASH was fully established by 16 wk. Total hepatic lipids increased by 4 wk and remained two- to threefold increased throughout. Hepatic triglycerides declined from sixfold increase at 8 wk to threefold increase by 36 wk. In contrast, hepatic cholesterol levels steadily increased from baseline at 8 wk to twofold by 36 wk. The hepatic immune cell population altered over time with macrophages persisting beyond 16 wk. Mitochondrial oxygen flux rates of FF mice diet were uniformly lower with all the tested substrates (13-276 pmol·s[-1]·ml[-1] per unit citrate synthase) than SC mice (17-394 pmol·s[-1]·ml[-1] per unit citrate synthase) and was accompanied by decreased mitochondrial:nuclear gene copy number ratios after 4 wk. Metabolic rate was lower in FF mice. Mitochondrial glutathione was significantly decreased at 24 wk in FF mice. Expression of dismutases and catalase was also decreased in FF mice. The evolution of NASH in the FF diet-induced model is multiphasic, particularly in terms of hepatic lipid composition. Insulin resistance precedes hepatic inflammation and fibrosis. Mitochondrial dysfunction and depletion occur after the histological features of NASH are apparent. Collectively, these observations provide a unique overview of the sequence of changes that coevolve with the histological evolution of NASH.NEW &amp; NOTEWORTHY This study demonstrates in a first of kind longitudinal analysis, the evolution of nonalcoholic steatohepatitis (NASH) on a fast-food diet-induced model. Key findings include 1) hepatic lipid composition changes in a multiphasic fashion as NASH evolves; 2) insulin resistance precedes hepatic inflammation and fibrosis, answering a longstanding chicken-and-egg question regarding the relationship of insulin resistance to liver histology in NASH; and 3) mitochondrial dysfunction and depletion occur after the histological features of NASH are apparent.}, }
@article {pmid28228475, year = {2017}, author = {Arab, DA and Namyatova, A and Evans, TA and Cameron, SL and Yeates, DK and Ho, SY and Lo, N}, title = {Parallel evolution of mound-building and grass-feeding in Australian nasute termites.}, journal = {Biology letters}, volume = {13}, number = {2}, pages = {}, pmid = {28228475}, issn = {1744-957X}, mesh = {Animals ; Australia ; *Biological Evolution ; Feeding Behavior ; Isoptera/genetics/*physiology ; Mitochondria/genetics ; Nesting Behavior ; Phylogeny ; Poaceae ; Trees ; Wood ; }, abstract = {Termite mounds built by representatives of the family Termitidae are among the most spectacular constructions in the animal kingdom, reaching 6-8 m in height and housing millions of individuals. Although functional aspects of these structures are well studied, their evolutionary origins remain poorly understood. Australian representatives of the termitid subfamily Nasutitermitinae display a wide variety of nesting habits, making them an ideal group for investigating the evolution of mound building. Because they feed on a variety of substrates, they also provide an opportunity to illuminate the evolution of termite diets. Here, we investigate the evolution of termitid mound building and diet, through a comprehensive molecular phylogenetic analysis of Australian Nasutitermitinae. Molecular dating analysis indicates that the subfamily has colonized Australia on three occasions over the past approximately 20 Myr. Ancestral-state reconstruction showed that mound building arose on multiple occasions and from diverse ancestral nesting habits, including arboreal and wood or soil nesting. Grass feeding appears to have evolved from wood feeding via ancestors that fed on both wood and leaf litter. Our results underscore the adaptability of termites to ancient environmental change, and provide novel examples of parallel evolution of extended phenotypes.}, }
@article {pmid28226235, year = {2017}, author = {Gualberto, JM and Newton, KJ}, title = {Plant Mitochondrial Genomes: Dynamics and Mechanisms of Mutation.}, journal = {Annual review of plant biology}, volume = {68}, number = {}, pages = {225-252}, doi = {10.1146/annurev-arplant-043015-112232}, pmid = {28226235}, issn = {1545-2123}, mesh = {DNA Repair ; *DNA, Mitochondrial ; DNA, Plant/metabolism ; Genome Size ; *Genome, Mitochondrial ; Homologous Recombination ; Magnoliopsida/*genetics ; Mitochondria/genetics/metabolism ; Models, Genetic ; Mutation ; }, abstract = {The large mitochondrial genomes of angiosperms are unusually dynamic because of recombination activities involving repeated sequences. These activities generate subgenomic forms and extensive genomic variation even within the same species. Such changes in genome structure are responsible for the rapid evolution of plant mitochondrial DNA and for the variants associated with cytoplasmic male sterility and abnormal growth phenotypes. Nuclear genes modulate these processes, and over the past decade, several of these genes have been identified. They are involved mainly in pathways of DNA repair by homologous recombination and mismatch repair, which appear to be essential for the faithful replication of the mitogenome. Mutations leading to the loss of any of these activities release error-prone repair pathways, resulting in increased ectopic recombination, genome instability, and heteroplasmy. We review the present state of knowledge of the genes and pathways underlying mitochondrial genome stability.}, }
@article {pmid28219344, year = {2017}, author = {Osei-Amponsah, R and Skinner, BM and Adjei, DO and Bauer, J and Larson, G and Affara, NA and Sargent, CA}, title = {Origin and phylogenetic status of the local Ashanti Dwarf pig (ADP) of Ghana based on genetic analysis.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {193}, pmid = {28219344}, issn = {1471-2164}, support = {BB/N000129/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Genotyping Techniques ; Ghana ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeny ; Pigmentation/genetics ; Swine/*genetics ; Y Chromosome/genetics ; }, abstract = {BACKGROUND: The Ashanti Dwarf Pig (ADP) of Ghana is an endangered pig breed with hardy and disease resistant traits. Characterisation of animal genetic resources provides relevant data for their conservation and sustainable use for food security and economic development. We investigated the origin and phylogenetic status of the local ADP of Ghana and their crosses with modern commercial breeds based on mtDNA, MC1R, Y-chromosome sequence polymorphisms, and genome-wide SNP genotyping.<br><br>RESULTS: The study involved 164 local pigs sampled from the three agro-ecological zones of Ghana. Analyses of the mitochondrial D-loop region and Y-chromosome sequences revealed both European and Asian genetic signatures, with differences between the geographical zones. Black coat colour is the most predominant within the breed, with black MC1R alleles of both Asian and European origin. European alleles for spotting are present at a low frequency in the sample set, and may account for the occurrence of spotted piglets in some APD litters. PCA analysis of SNP data revealed a strong location and breed effect on clustering of local Ghanaian pigs. On a global level, Ghanaian local pigs cluster closely with European pigs of commercial origin, but we identified intervals via FST analyses that may elucidate loci for ADP specific traits.<br><br>CONCLUSIONS: The presence of both European and Asian contributions, with differences between geographical zones probably reflects trading and colonial influences. Understanding the effects of admixture on important adaptive and economic traits of the ADP and other local breeds in Africa is critical for developing sustainable conservation programmes to prevent the decline of these genetic resources.}, }
@article {pmid28212874, year = {2017}, author = {Leavitt, DH and Marion, AB and Hollingsworth, BD and Reeder, TW}, title = {Multilocus phylogeny of alligator lizards (Elgaria, Anguidae): Testing mtDNA introgression as the source of discordant molecular phylogenetic hypotheses.}, journal = {Molecular phylogenetics and evolution}, volume = {110}, number = {}, pages = {104-121}, doi = {10.1016/j.ympev.2017.02.010}, pmid = {28212874}, issn = {1095-9513}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Genetic Loci ; Geography ; Lizards/*genetics ; Mitochondria/genetics ; *Models, Genetic ; North America ; *Phylogeny ; Time Factors ; }, abstract = {The increased availability of nuclear DNA sequence data has led to a better appreciation of the role and frequency of introgressive hybridization and subsequent mitochondrial capture in misleading phylogenetic hypotheses based on mtDNA sequence data alone. Relationships among members of the alligator lizard genus Elgaria have been addressed with morphology, allozyme and mtDNA sequence data with discordant results. In this study, we use seven nuclear loci (total of 5.9kb) and ∼3kb of mtDNA to infer the phylogenetic relationships among Elgaria species and test whether the discordance among previous phylogenetic hypotheses is due to introgression and mtDNA capture. While gene tree topologies varied among the different loci, we recovered a well-resolved coalescent-based species tree. Contrary to our expectations, the nDNA-only species tree does not support the sister relationship between E. kingii and E. panamintina inferred from the previous allozyme study. Nevertheless, we found evidence for possible mitochondrial capture in two unexpected situations. The first instance of mtDNA capture involves E. paucicarinata from the Cape Region of Baja California. MtDNA recovered a clade comprising E. paucicarinata and the other two peninsular endemics, while the nDNA-only species tree recovered E. paucicarinata as sister to the continental E. kingii. We hypothesize that this discordance is the result of ancient mitochondrial capture rather than incomplete lineage sorting. Additionally, analyses of nDNA recovered E. panamintina as sister to an E. multicarinata North lineage, whereas the mtDNA gene tree recovers E. panamintina nested within a southern E. multicarinata clade. We hypothesize that this discordance also may be due to mitochondrial capture. Additionally, hybridization between these two lineages may have resulted in geographically limited nuclear introgression. Divergence dating analyses suggest that oviparous Elgaria species diverged within a relatively narrow timeframe from the late Miocene to early Pliocene. We find that accounting for introgressed alleles is important when inferring phylogenetic relationships when using coalescent-based approaches.}, }
@article {pmid28208702, year = {2017}, author = {Plaitakis, A and Kalef-Ezra, E and Kotzamani, D and Zaganas, I and Spanaki, C}, title = {The Glutamate Dehydrogenase Pathway and Its Roles in Cell and Tissue Biology in Health and Disease.}, journal = {Biology}, volume = {6}, number = {1}, pages = {}, pmid = {28208702}, issn = {2079-7737}, abstract = {Glutamate dehydrogenase (GDH) is a hexameric enzyme that catalyzes the reversible conversion of glutamate to α-ketoglutarate and ammonia while reducing NAD(P)[+] to NAD(P)H. It is found in all living organisms serving both catabolic and anabolic reactions. In mammalian tissues, oxidative deamination of glutamate via GDH generates α-ketoglutarate, which is metabolized by the Krebs cycle, leading to the synthesis of ATP. In addition, the GDH pathway is linked to diverse cellular processes, including ammonia metabolism, acid-base equilibrium, redox homeostasis (via formation of fumarate), lipid biosynthesis (via oxidative generation of citrate), and lactate production. While most mammals possess a single GDH1 protein (hGDH1 in the human) that is highly expressed in the liver, humans and other primates have acquired, via duplication, an hGDH2 isoenzyme with distinct functional properties and tissue expression profile. The novel hGDH2 underwent rapid evolutionary adaptation, acquiring unique properties that enable enhanced enzyme function under conditions inhibitory to its ancestor hGDH1. These are thought to provide a biological advantage to humans with hGDH2 evolution occurring concomitantly with human brain development. hGDH2 is co-expressed with hGDH1 in human brain, kidney, testis and steroidogenic organs, but not in the liver. In human cerebral cortex, hGDH1 and hGDH2 are expressed in astrocytes, the cells responsible for removing and metabolizing transmitter glutamate, and for supplying neurons with glutamine and lactate. In human testis, hGDH2 (but not hGDH1) is densely expressed in the Sertoli cells, known to provide the spermatids with lactate and other nutrients. In steroid producing cells, hGDH1/2 is thought to generate reducing equivalents (NADPH) in the mitochondria for the biosynthesis of steroidal hormones. Lastly, up-regulation of hGDH1/2 expression occurs in cancer, permitting neoplastic cells to utilize glutamine/glutamate for their growth. In addition, deregulation of hGDH1/2 is implicated in the pathogenesis of several human disorders.}, }
@article {pmid28202452, year = {2017}, author = {Spooner, DM and Ruess, H and Iorizzo, M and Senalik, D and Simon, P}, title = {Entire plastid phylogeny of the carrot genus (Daucus, Apiaceae): Concordance with nuclear data and mitochondrial and nuclear DNA insertions to the plastid.}, journal = {American journal of botany}, volume = {104}, number = {2}, pages = {296-312}, doi = {10.3732/ajb.1600415}, pmid = {28202452}, issn = {1537-2197}, mesh = {Cell Nucleus/*genetics ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/chemistry/classification/genetics ; Daucus carota/classification/*genetics ; Genes, Plant/genetics ; Genome, Mitochondrial/*genetics ; Genome, Plant/*genetics ; Genome, Plastid/*genetics ; Mutagenesis, Insertional ; *Phylogeny ; Plant Proteins/genetics ; Plastids/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {PREMISE OF THE STUDY: We explored the phylogenetic utility of entire plastid DNA sequences in Daucus and compared the results with prior phylogenetic results using plastid and nuclear DNA sequences.<br><br>METHODS: We used Illumina sequencing to obtain full plastid sequences of 37 accessions of 20 Daucus taxa and outgroups, analyzed the data with phylogenetic methods, and examined evidence for mitochondrial DNA transfer to the plastid (DcMP).<br><br>KEY RESULTS: Our phylogenetic trees of the entire data set were highly resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. Subsets of the data, including regions traditionally used as phylogenetically informative regions, provide various degrees of soft congruence with the entire data set. There are areas of hard incongruence, however, with phylogenies using nuclear data. We extended knowledge of a mitochondrial to plastid DNA insertion sequence previously named DcMP and identified the first instance in flowering plants of a sequence of potential nuclear genome origin inserted into the plastid genome. There is a relationship of inverted repeat junction classes and repeat DNA to phylogeny, but no such relationship with nonsynonymous mutations.<br><br>CONCLUSIONS: Our data have allowed us to (1) produce a well-resolved plastid phylogeny of Daucus, (2) evaluate subsets of the entire plastid data for phylogeny, (3) examine evidence for plastid and nuclear DNA phylogenetic incongruence, and (4) examine mitochondrial and nuclear DNA insertion into the plastid.}, }
@article {pmid28201740, year = {2017}, author = {Bailly-Bechet, M and Martins-Simões, P and Szöllosi, GJ and Mialdea, G and Sagot, MF and Charlat, S}, title = {How Long Does Wolbachia Remain on Board?.}, journal = {Molecular biology and evolution}, volume = {34}, number = {5}, pages = {1183-1193}, doi = {10.1093/molbev/msx073}, pmid = {28201740}, issn = {1537-1719}, mesh = {Animals ; Arthropods/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Haplotypes ; Phylogeny ; Symbiosis/genetics ; Wolbachia/*genetics ; }, abstract = {Wolbachia bacteria infect about half of all arthropods, with diverse and extreme consequences ranging from sex-ratio distortion and mating incompatibilities to protection against viruses. These phenotypic effects, combined with efficient vertical transmission from mothers to offspring, satisfactorily explain the invasion dynamics of Wolbachia within species. However, beyond the species level, the lack of congruence between the host and symbiont phylogenetic trees indicates that Wolbachia horizontal transfers and extinctions do happen and underlie its global distribution. But how often do they occur? And has the Wolbachia pandemic reached its equilibrium? Here, we address these questions by inferring recent acquisition/loss events from the distribution of Wolbachia lineages across the mitochondrial DNA tree of 3,600 arthropod specimens, spanning 1,100 species from Tahiti and surrounding islands. We show that most events occurred within the last million years, but are likely attributable to individual level variation (e.g., imperfect maternal transmission) rather than population level variation (e.g., Wolbachia extinction). At the population level, we estimate that mitochondria typically accumulate 4.7% substitutions per site during an infected episode, and 7.1% substitutions per site during the uninfected phase. Using a Bayesian time calibration of the mitochondrial tree, these numbers translate into infected and uninfected phases of approximately 7 and 9 million years. Infected species thus lose Wolbachia slightly more often than uninfected species acquire it, supporting the view that its present incidence, estimated here slightly below 0.5, represents an epidemiological equilibrium.}, }
@article {pmid28199635, year = {2017}, author = {Martin, WF and Roettger, M and Ku, C and Garg, SG and Nelson-Sathi, S and Landan, G}, title = {Late Mitochondrial Origin Is an Artifact.}, journal = {Genome biology and evolution}, volume = {9}, number = {2}, pages = {373-379}, pmid = {28199635}, issn = {1759-6653}, support = {281357/ERC_/European Research Council/International ; }, mesh = {*Artifacts ; Genes, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; *Symbiosis ; }, abstract = {The origin of mitochondria was a crucial event in eukaryote evolution. A recent report claimed to provide evidence, based on branch length variation in phylogenetic trees, that the mitochondrion came late in eukaryotic evolution. Here, we reinvestigate their claim with a reanalysis of the published data. We show that the analyses underpinning a late mitochondrial origin suffer from multiple fatal flaws founded in inappropriate statistical methods and analyses, in addition to erroneous interpretations.}, }
@article {pmid28193450, year = {2017}, author = {Yuan, K and Yuan, FH and He, HH and Bi, HT and Weng, SP and He, JG and Chen, YH}, title = {Heat shock 70 kDa protein cognate 5 involved in WSSV toleration of Litopenaeus vannamei.}, journal = {Developmental and comparative immunology}, volume = {72}, number = {}, pages = {9-20}, doi = {10.1016/j.dci.2017.02.003}, pmid = {28193450}, issn = {1879-0089}, mesh = {Animals ; Arthropod Proteins/genetics/*metabolism ; Cloning, Molecular ; DNA Virus Infections/*immunology ; HSP70 Heat-Shock Proteins/genetics/*metabolism ; Heat-Shock Response ; Hemocytes/*immunology ; Hot Temperature/adverse effects ; Mitochondria/*metabolism ; Muscles/*virology ; Penaeidae/*immunology ; Phylogeny ; Transcription Factor 4/genetics/metabolism ; Transcriptional Activation ; Unfolded Protein Response ; Up-Regulation ; Viral Load ; White spot syndrome virus 1/*physiology ; }, abstract = {The expression levels of 97 unigenes encoding heat shock proteins of Litopenaeus vannamei was scanned, and ten of them were significantly induced by white spot syndrome virus (WSSV). Among these genes, heat shock 70 kDa protein cognate 5 (LvHSC70-5) was upregulated to the highest extent and subjected to further studies. Subcellular localization assay revealed that LvHSC70-5 was located in the mitochondria. Aside from WSSV infection, unfolded protein response activation and thermal stress could also upregulate LvHSC70-5. Results of reporter gene assay demonstrated that promoter of LvHSC70-5 was activated by L. vannamei heat shock factor protein 1, activating transcription factor 4 and thermal stress. A decrease in the expression of LvHSC70-5 could reduce the aggregation of proteins in hemocytes and the cumulative mortality of WSSV-infected L. vannamei. LvHSC70-5 in L. vannamei hemocytes was upregulated by mild thermal stress. In addition, mild thermal stress, decreased the copy number of WSSV in shrimp muscle and the cumulative mortality of WSSV-infected L. vannamei. Therefore, collecting results suggested that LvHSC70-5 should be involved in WSSV toleration of shrimp L. vannamei.}, }
@article {pmid28191642, year = {2017}, author = {Satjarak, A and Burns, JA and Kim, E and Graham, LE}, title = {Complete mitochondrial genomes of prasinophyte algae Pyramimonas parkeae and Cymbomonas tetramitiformis.}, journal = {Journal of phycology}, volume = {53}, number = {3}, pages = {601-615}, doi = {10.1111/jpy.12521}, pmid = {28191642}, issn = {1529-8817}, mesh = {Chlorophyta/classification/*genetics ; DNA, Algal/*genetics ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Mitochondria are archetypal eukaryotic organelles that were acquired by endosymbiosis of an ancient species of alpha-proteobacteria by the last eukaryotic common ancestor. The genetic information contained within the mitochondrial genome has been an important source of information for resolving relationships among eukaryotic taxa. In this study, we utilized mitochondrial and chloroplast genomes to explore relationships among prasinophytes. Prasinophytes are represented by diverse early-diverging green algae whose physical structures and genomes have the potential to elucidate the traits of the last common ancestor of the Viridiplantae (or Chloroplastida). We constructed de novo mitochondrial genomes for two prasinophyte algal species, Pyramimonas parkeae and Cymbomonas tetramitiformis, representing the prasinophyte clade. Comparisons of genome structure and gene order between these species and to those of other prasinophytes revealed that the mitochondrial genomes of P. parkeae and C. tetramitiformis are more similar to each other than to other prasinophytes, consistent with other molecular inferences of the close relationship between these two species. Phylogenetic analyses using the inferred amino acid sequences of mitochondrial and chloroplast protein-coding genes resolved a clade consisting of P. parkeae and C. tetramitiformis; and this group (representing the prasinophyte clade I) branched with the clade II, consistent with previous studies based on the use of nuclear gene markers.}, }
@article {pmid28189637, year = {2017}, author = {Sieber, KB and Bromley, RE and Dunning Hotopp, JC}, title = {Lateral gene transfer between prokaryotes and eukaryotes.}, journal = {Experimental cell research}, volume = {358}, number = {2}, pages = {421-426}, pmid = {28189637}, issn = {1090-2422}, support = {DP2 OD007372/OD/NIH HHS/United States ; R01 CA206188/CA/NCI NIH HHS/United States ; T32 DK067872/DK/NIDDK NIH HHS/United States ; 1-R01-CA206188/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics/physiology ; Humans ; Mitochondria/metabolism ; Prokaryotic Cells/*cytology ; }, abstract = {Lateral gene transfer (LGT) is an all-encompassing term for the movement of DNA between diverse organisms. LGT is synonymous with horizontal gene transfer, and the terms are used interchangeably throughout the scientific literature. While LGT has been recognized within the bacteria domain of life for decades, inter-domain LGTs are being increasingly described. LGTs between bacteria and complex multicellular organisms are of interest because they challenge the long-held dogma that such transfers could only occur in closely-related, single-celled organisms. Scientists will continue to challenge our understanding of LGT as we sequence more, diverse organisms, as we sequence more endosymbiont-colonized arthropods, and as we continue to appreciate LGT events, both young and old.}, }
@article {pmid28189617, year = {2017}, author = {Peris, D and Arias, A and Orlić, S and Belloch, C and Pérez-Través, L and Querol, A and Barrio, E}, title = {Mitochondrial introgression suggests extensive ancestral hybridization events among Saccharomyces species.}, journal = {Molecular phylogenetics and evolution}, volume = {108}, number = {}, pages = {49-60}, doi = {10.1016/j.ympev.2017.02.008}, pmid = {28189617}, issn = {1095-9513}, mesh = {Base Sequence ; Electron Transport Complex IV/genetics ; Genome, Mitochondrial ; Geography ; Haplotypes/genetics ; *Hybridization, Genetic ; Mitochondria/*genetics ; Open Reading Frames/genetics ; Phylogeny ; Saccharomyces/*genetics ; Sequence Alignment ; Species Specificity ; }, abstract = {Horizontal gene transfer (HGT) in eukaryotic plastids and mitochondrial genomes is common, and plays an important role in organism evolution. In yeasts, recent mitochondrial HGT has been suggested between S. cerevisiae and S. paradoxus. However, few strains have been explored given the lack of accurate mitochondrial genome annotations. Mitochondrial genome sequences are important to understand how frequent these introgressions occur, and their role in cytonuclear incompatibilities and fitness. Indeed, most of the Bateson-Dobzhansky-Muller genetic incompatibilities described in yeasts are driven by cytonuclear incompatibilities. We herein explored the mitochondrial inheritance of several worldwide distributed wild Saccharomyces species and their hybrids isolated from different sources and geographic origins. We demonstrated the existence of several recombination points in mitochondrial region COX2-ORF1, likely mediated by either the activity of the protein encoded by the ORF1 (F-SceIII) gene, a free-standing homing endonuclease, or mostly facilitated by A+T tandem repeats and regions of integration of GC clusters. These introgressions were shown to occur among strains of the same species and among strains of different species, which suggests a complex model of Saccharomyces evolution that involves several ancestral hybridization events in wild environments.}, }
@article {pmid28179510, year = {2017}, author = {Cong, Q and Shen, J and Borek, D and Robbins, RK and Opler, PA and Otwinowski, Z and Grishin, NV}, title = {When COI barcodes deceive: complete genomes reveal introgression in hairstreaks.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1848}, pages = {}, pmid = {28179510}, issn = {1471-2954}, mesh = {Animals ; Butterflies/*growth &amp; development ; Central America ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/genetics ; *Genome, Insect ; *Genome, Mitochondrial ; Phylogeny ; United States ; }, abstract = {Two species of hairstreak butterflies from the genus Calycopis are known in the United States: C. cecrops and C. isobeon Analysis of mitochondrial COI barcodes of Calycopis revealed cecrops-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central American Calycopis species. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27 Calycopis specimens of four species: C. cecrops, C. isobeon, C. quintana and C. bactra Some of these specimens were collected up to 60 years ago and preserved dry in museum collections, but nonetheless produced genomes as complete as fresh samples. Phylogenetic trees reconstructed using the whole mitochondrial and nuclear genomes were incongruent. While USA Calycopis with atypical barcodes grouped with Central American species C. quintana by mitochondria, nuclear genome trees placed them within typical USA C. cecrops in agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially between C. cecrops and C. isobeon About 2.3% of each C. cecrops genome has probably (p-value < 0.01, FDR < 0.1) introgressed from C. isobeon and about 3.4% of each C. isobeon genome may have come from C. cecrops. The introgressed regions are enriched in genes encoding transmembrane proteins, mitochondria-targeting proteins and components of the larval cuticle. This study provides the first example of mitochondrial introgression in Lepidoptera supported by complete genome sequencing. Our results caution about relying solely on COI barcodes and mitochondrial DNA for species identification or discovery.}, }
@article {pmid28178941, year = {2017}, author = {Rishishwar, L and Jordan, IK}, title = {Implications of human evolution and admixture for mitochondrial replacement therapy.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {140}, pmid = {28178941}, issn = {1471-2164}, mesh = {DNA/chemistry/*metabolism ; DNA, Mitochondrial/chemistry/classification/*metabolism ; *Evolution, Molecular ; Gene Frequency ; Genetic Variation ; Genome, Human ; Genotype ; Haplotypes ; Human Genome Project ; Humans ; Mitochondrial Diseases/genetics/therapy ; Mitochondrial Replacement Therapy ; Phylogeny ; }, abstract = {BACKGROUND: Mitochondrial replacement (MR) therapy is a new assisted reproductive technology that allows women with mitochondrial disorders to give birth to healthy children by combining their nuclei with mitochondria from unaffected egg donors. Evolutionary biologists have raised concerns about the safety of MR therapy based on the extent to which nuclear and mitochondrial genomes are observed to co-evolve within natural populations, i.e. the nuclear-mitochondrial mismatch hypothesis. In support of this hypothesis, a number of previous studies on model organisms have provided evidence for incompatibility between nuclear and mitochondrial genomes from divergent populations of the same species.<br><br>RESULTS: We tested the nuclear-mitochondrial mismatch hypothesis for humans by observing the extent of naturally occurring nuclear-mitochondrial mismatch seen for 2,504 individuals across 26 populations, from 5 continental populations groups, characterized as part of the 1000 Genomes Project (1KGP). We also&#xa0;performed a replication analysis on mitochondrial DNA (mtDNA) haplotypes for 1,043 individuals from 58 populations, characterized as part of the Human Genome Diversity Project&#xa0;(HGDP). Nuclear DNA (nDNA) and mtDNA sequences from the 1KGP were directly compared within and between populations, and the population distributions of mtDNA haplotypes derived from both sequence (1KGP) and genotype (HGDP) data were evaluated. Levels of nDNA and mtDNA pairwise sequence divergence are highly correlated, consistent with their co-evolution among human populations. However, there are numerous cases of co-occurrence of nuclear and mitochondrial genomes from divergent populations within individual humans. Furthermore, pairs of individuals with closely related nuclear genomes can have highly divergent mtDNA haplotypes. Supposedly mismatched nuclear-mitochondrial genome combinations are found not only within individuals from populations known to be admixed, where they may be expected, but also from populations with low overall levels of observed admixture.<br><br>CONCLUSIONS: These results show that mitochondrial and nuclear genomes from divergent human populations can co-exist within healthy individuals, indicating that mismatched nDNA-mtDNA combinations are not deleterious or subject to purifying selection. Accordingly, human nuclear-mitochondrial mismatches are not likely to jeopardize the safety of MR therapy.}, }
@article {pmid28176810, year = {2017}, author = {Moodley, Y and Russo, IM and Dalton, DL and Kotzé, A and Muya, S and Haubensak, P and Bálint, B and Munimanda, GK and Deimel, C and Setzer, A and Dicks, K and Herzig-Straschil, B and Kalthoff, DC and Siegismund, HR and Robovský, J and O'Donoghue, P and Bruford, MW}, title = {Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis).}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {41417}, pmid = {28176810}, issn = {2045-2322}, mesh = {Africa South of the Sahara ; Animals ; Base Sequence ; Bayes Theorem ; *Biological Evolution ; Cell Nucleus/genetics ; *Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Genetic Variation ; Haplotypes/genetics ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Perissodactyla/*genetics ; Phylogeny ; Species Specificity ; }, abstract = {The black rhinoceros is again on the verge of extinction due to unsustainable poaching in its native range. Despite a wide historic distribution, the black rhinoceros was traditionally thought of as depauperate in genetic variation, and with very little known about its evolutionary history. This knowledge gap has hampered conservation efforts because hunting has dramatically reduced the species' once continuous distribution, leaving five surviving gene pools of unknown genetic affinity. Here we examined the range-wide genetic structure of historic and modern populations using the largest and most geographically representative sample of black rhinoceroses ever assembled. Using both mitochondrial and nuclear datasets, we described a staggering loss of 69% of the species' mitochondrial genetic variation, including the most ancestral lineages that are now absent from modern populations. Genetically unique populations in countries such as Nigeria, Cameroon, Chad, Eritrea, Ethiopia, Somalia, Mozambique, Malawi and Angola no longer exist. We found that the historic range of the West African subspecies (D. b. longipes), declared extinct in 2011, extends into southern Kenya, where a handful of individuals survive in the Masai Mara. We also identify conservation units that will help maintain evolutionary potential. Our results suggest a complete re-evaluation of current conservation management paradigms for the black rhinoceros.}, }
@article {pmid28175279, year = {2017}, author = {Salomaki, ED and Lane, CE}, title = {Red Algal Mitochondrial Genomes Are More Complete than Previously Reported.}, journal = {Genome biology and evolution}, volume = {9}, number = {1}, pages = {48-63}, pmid = {28175279}, issn = {1759-6653}, mesh = {Evolution, Molecular ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Molecular Sequence Annotation ; Rhodophyta/*classification/cytology/*genetics ; }, abstract = {The enslavement of an alpha-proteobacterial endosymbiont by the last common eukaryotic ancestor resulted in large-scale gene transfer of endosymbiont genes to the host nucleus as the endosymbiont transitioned into the mitochondrion. Mitochondrial genomes have experienced widespread gene loss and genome reduction within eukaryotes and DNA sequencing has revealed that most of these gene losses occurred early in eukaryotic lineage diversification. On a broad scale, more recent modifications to organelle genomes appear to be conserved and phylogenetically informative. The first red algal mitochondrial genome was sequenced more than 20 years ago, and an additional 29 Florideophyceae mitochondria have been added over the past decade. A total of 32 genes have been described to have been missing or considered non-functional pseudogenes from these Florideophyceae mitochondria. These losses have been attributed to endosymbiotic gene transfer or the evolution of a parasitic life strategy. Here we sequenced the mitochondrial genomes from the red algal parasite Choreocolax polysiphoniae and its host Vertebrata lanosa and found them to be complete and conserved in structure with other Florideophyceae mitochondria. This result led us to resequence the previously published parasite Gracilariophila oryzoides and its host Gracilariopsis andersonii, as well as reevaluate reported gene losses from published Florideophyceae mitochondria. Multiple independent losses of rpl20 and a single loss of rps11 can be verified. However by reannotating published data and resequencing specimens when possible, we were able to identify the majority of genes that have been reported as lost or pseudogenes from Florideophyceae mitochondria.}, }
@article {pmid28173693, year = {2017}, author = {Lee, JY and Jun, DY and Park, JE and Kwon, GH and Kim, JS and Kim, YH}, title = {Pro-Apoptotic Role of the Human YPEL5 Gene Identified by Functional Complementation of a Yeast moh1Δ Mutation.}, journal = {Journal of microbiology and biotechnology}, volume = {27}, number = {3}, pages = {633-643}, doi = {10.4014/jmb.1610.10045}, pmid = {28173693}, issn = {1738-8872}, mesh = {Amino Acid Sequence ; Apoptosis/*genetics ; Cell Cycle Proteins/chemistry/*genetics ; Fungal Proteins/chemistry/*genetics/metabolism ; Genetic Complementation Test ; Humans ; Multigene Family ; *Mutation ; Phylogeny ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism ; Yeasts/*genetics/metabolism ; }, abstract = {To examine the pro-apoptotic role of the human ortholog (YPEL5) of the Drosophila Yippee protein, the cell viability of Saccharomyces cerevisiae mutant strain with deleted MOH1, the yeast ortholog, was compared with that of the wild-type (WT)-MOH1 strain after exposure to different apoptogenic stimulants, including UV irradiation, methyl methanesulfonate (MMS), camptothecin (CPT), heat shock, and hyperosmotic shock. The moh1Δ mutant exhibited enhanced cell viability compared with the WT-MOH1 strain when treated with lethal UV irradiation, 1.8 mM MMS, 100 µ CPT, heat shock at 50°C, or 1.2 M KCl. At the same time, the level of Moh1 protein was commonly up-regulated in the WT-MOH1 strain as was that of Ynk1 protein, which is known as a marker for DNA damage. Although the enhanced UV resistance of the moh1Δ mutant largely disappeared following transformation with the yeast MOH1 gene or one of the human YPEL1-YPEL5 genes, the transformant bearing pYES2-YPEL5 was more sensitive to lethal UV irradiation and its UV sensitivity was similar to that of the WT-MOH1 strain. Under these conditions, the UV irradiation-induced apoptotic events, such as FITC-Annexin V stainability, mitochondrial membrane potential (ΔΨm) loss, and metacaspase activation, occurred to a much lesser extent in the moh1Δ mutant compared with the WT-MOH1 strain and the mutant strain bearing pYES2-MOH1 or pYES2-YPEL5. These results demonstrate the functional conservation between yeast Moh1 and human YPEL5, and their involvement in mitochondria-dependent apoptosis induced by DNA damage.}, }
@article {pmid28172670, year = {2017}, author = {Sarver, BA and Demboski, JR and Good, JM and Forshee, N and Hunter, SS and Sullivan, J}, title = {Comparative Phylogenomic Assessment of Mitochondrial Introgression among Several Species of Chipmunks (Tamias).}, journal = {Genome biology and evolution}, volume = {9}, number = {1}, pages = {7-19}, pmid = {28172670}, issn = {1759-6653}, support = {P20 RR016448/RR/NCRR NIH HHS/United States ; P20 RR016454/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial ; Gene Flow ; Genome, Mitochondrial ; Hybridization, Genetic ; Mitochondria/*genetics ; Phylogeny ; Sciuridae/*classification/*genetics ; Selection, Genetic ; United States ; }, abstract = {Many species are not completely reproductively isolated, resulting in hybridization and genetic introgression. Organellar genomes, such as those derived from mitochondria (mtDNA) and chloroplasts, introgress frequently in natural systems; however, the forces shaping patterns of introgression are not always clear. Here, we investigate extensive mtDNA introgression in western chipmunks, focusing on species in the Tamias quadrivittatus group from the central and southern Rocky Mountains. Specifically, we investigate the role of selection in driving patterns of introgression. We sequenced 51 mtDNA genomes from six species and combine these sequences with other published genomic data to yield annotated mitochondrial reference genomes for nine species of chipmunks. Genomic characterization was performed using a series of molecular evolutionary and phylogenetic analyses to test protein-coding genes for positive selection. We fit a series of maximum likelihood models using a model-averaging approach, assessed deviations from neutral expectations, and performed additional tests to search for codons under the influence of selection. We found no evidence for positive selection among these genomes, suggesting that selection has not been the driving force of introgression in these species. Thus, extensive mtDNA introgression among several species of chipmunks likely reflects genetic drift of introgressed alleles in historically fluctuating populations.}, }
@article {pmid28161373, year = {2017}, author = {Felici, R and Buonvicino, D and Muzzi, M and Cavone, L and Guasti, D and Lapucci, A and Pratesi, S and De Cesaris, F and Luceri, F and Chiarugi, A}, title = {Post onset, oral rapamycin treatment delays development of mitochondrial encephalopathy only at supramaximal doses.}, journal = {Neuropharmacology}, volume = {117}, number = {}, pages = {74-84}, doi = {10.1016/j.neuropharm.2017.01.039}, pmid = {28161373}, issn = {1873-7064}, mesh = {Administration, Oral ; Animals ; Cerebellum/metabolism/pathology ; DNA, Mitochondrial/metabolism ; Disease Progression ; Dose-Response Relationship, Drug ; Electron Transport Chain Complex Proteins/metabolism ; Electron Transport Complex I/genetics ; Female ; Male ; Mice ; Mice, Knockout ; Mitochondria/ultrastructure ; Mitochondrial Encephalomyopathies/*drug therapy/*pathology ; Motor Cortex/metabolism/pathology ; Muscle, Skeletal/metabolism ; Sirolimus/administration &amp; dosage/blood/pharmacokinetics/*therapeutic use ; Survival Analysis ; TOR Serine-Threonine Kinases/metabolism ; }, abstract = {Mitochondrial encephalopathies are fatal, infantile neurodegenerative disorders caused by a deficit of mitochondrial functioning, for which there is urgent need to identify efficacious pharmacological treatments. Recent evidence shows that rapamycin administered both intraperitoneally or in the diet delays disease onset and enhances survival in the Ndufs4 null mouse model of mitochondrial encephalopathy. To delineate the clinical translatability of rapamycin in treatment of mitochondrial encephalopathy, we evaluated the drug's effects on disease evolution and mitochondrial parameters adopting treatment paradigms with fixed daily, oral doses starting at symptom onset in Ndufs4 knockout mice. Molecular mechanisms responsible for the pharmacodynamic effects of rapamycin were also evaluated. We found that rapamycin did not affect disease development at clinically-relevant doses (0.5 mg kg[-1]). Conversely, an oral dose previously adopted for intraperitoneal administration (8 mg kg[-1]) delayed development of neurological symptoms and increased median survival by 25%. Neurological improvement and lifespan were not further increased when the dose raised to 20 mg kg[-1]. Notably, rapamycin at 8 mg kg[-1] did not affect the reduced expression of respiratory complex subunits, as well as mitochondrial number and mtDNA content. This treatment regimen however significantly ameliorated architecture of mitochondria cristae in motor cortex and cerebellum. However, reduction of mTOR activity by rapamycin was not consistently found within the brain of knockout mice. Overall, data show the ability of rapamycin to improve ultrastructure of dysfunctional mitochondria and corroborate its therapeutic potential in mitochondrial disorders. The non-clinical standard doses required, however, raise concerns about its rapid and safe clinical transferability.}, }
@article {pmid28160496, year = {2018}, author = {Zhang, Z and Cheng, X and Yue, L and Cui, W and Zhou, W and Gao, J and Yao, H}, title = {Molecular pathogenesis in chronic obstructive pulmonary disease and therapeutic potential by targeting AMP-activated protein kinase.}, journal = {Journal of cellular physiology}, volume = {233}, number = {3}, pages = {1999-2006}, doi = {10.1002/jcp.25844}, pmid = {28160496}, issn = {1097-4652}, mesh = {AMP-Activated Protein Kinases/*metabolism ; Air Pollutants/*adverse effects ; Cellular Senescence/*drug effects ; Humans ; Inflammation/pathology ; Lung/*pathology ; Mitochondria/pathology ; Pulmonary Disease, Chronic Obstructive/*pathology/therapy ; Smoke/*adverse effects ; Smoking ; }, abstract = {Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide, which is characterized by a persistent airflow limitation caused by chronic inflammatory responses to noxious particles or gases. Cigarette smoke and environmental pollutions are major etiological factors for causing COPD. It has been shown that cigarette smoking causes abnormal inflammatory responses, cellular senescence, mitochondrial dysfunction and metabolic dysregulation, suggesting their involvement in the development of COPD. Although the medical care and treatment have advanced, there are no effective therapies to stop or reverse lung destruction in COPD/emphysema. AMP-activated protein kinase (AMPK) is a serine threonine kinase with α, β, and γ subunits that are highly conserved through evolution. AMPK has been shown to regulate bioenergetics, inflammatory responses, senescence, and metabolism. This review focused on the updated understanding of molecular pathogenesis of COPD, and highlighted the crucial roles of AMPK in lung abnormalities as well as discussed the potential therapeutics of AMPK activators in preventing and halting the progression of COPD.}, }
@article {pmid28154081, year = {2017}, author = {Desai, N and Brown, A and Amunts, A and Ramakrishnan, V}, title = {The structure of the yeast mitochondrial ribosome.}, journal = {Science (New York, N.Y.)}, volume = {355}, number = {6324}, pages = {528-531}, pmid = {28154081}, issn = {1095-9203}, support = {/WT_/Wellcome Trust/United Kingdom ; MC_U105184332/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Cryoelectron Microscopy ; Evolution, Molecular ; Mitochondrial Ribosomes/*chemistry/ultrastructure ; Nucleic Acid Conformation ; Protein Biosynthesis ; Protein Conformation ; RNA, Messenger/chemistry/ultrastructure ; RNA, Ribosomal/chemistry/ultrastructure ; Saccharomyces cerevisiae/*ultrastructure ; }, abstract = {Mitochondria have specialized ribosomes (mitoribosomes) dedicated to the expression of the genetic information encoded by their genomes. Here, using electron cryomicroscopy, we have determined the structure of the 75-component yeast mitoribosome to an overall resolution of 3.3 angstroms. The mitoribosomal small subunit has been built de novo and includes 15S ribosomal RNA (rRNA) and 34 proteins, including 14 without homologs in the evolutionarily related bacterial ribosome. Yeast-specific rRNA and protein elements, including the acquisition of a putatively active enzyme, give the mitoribosome a distinct architecture compared to the mammalian mitoribosome. At an expanded messenger RNA channel exit, there is a binding platform for translational activators that regulate translation in yeast but not mammalian mitochondria. The structure provides insights into the evolution and species-specific specialization of mitochondrial translation.}, }
@article {pmid28153100, year = {2017}, author = {Karageorgis, A and Claron, M and Jugé, R and Aspord, C and Thoreau, F and Leloup, C and Kucharczak, J and Plumas, J and Henry, M and Hurbin, A and Verdié, P and Martinez, J and Subra, G and Dumy, P and Boturyn, D and Aouacheria, A and Coll, JL}, title = {Systemic Delivery of Tumor-Targeted Bax-Derived Membrane-Active Peptides for the Treatment of Melanoma Tumors in a Humanized SCID Mouse Model.}, journal = {Molecular therapy : the journal of the American Society of Gene Therapy}, volume = {25}, number = {2}, pages = {534-546}, pmid = {28153100}, issn = {1525-0024}, mesh = {Animals ; Antineoplastic Agents/chemical synthesis/pharmacology ; Apoptosis/drug effects ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Disease Models, Animal ; Humans ; Melanoma/drug therapy/*metabolism/*pathology ; Mice ; Mice, Knockout ; Neovascularization, Pathologic/drug therapy/metabolism/pathology ; Peptide Fragments/administration &amp; dosage/chemical synthesis/*pharmacology ; Tumor Burden/drug effects ; Xenograft Model Antitumor Assays ; bcl-2-Associated X Protein/*chemistry ; }, abstract = {Melanoma is a highly metastatic and deadly form of cancer. Invasive melanoma cells overexpress integrin αvβ3, which is a well-known target for Arg-Gly-Asp-based (RGD) peptides. We developed a sophisticated method to synthetize milligram amounts of a targeted vector that allows the RGD-mediated targeting, internalization, and release of a mitochondria-disruptive peptide derived from the pro-apoptotic Bax protein. We found that 2.5 μM Bax[109-127] was sufficient to destabilize the mitochondria in ten different tumor cell lines, even in the presence of the anti-apoptotic Bcl2 protein, which is often involved in tumor resistance. This pore-forming peptide displayed antitumor activity when it was covalently linked by a disulfide bridge to the tetrameric RAFT-c[RGD]4-platform and after intravenous injection in a human melanoma tumor model established in humanized immuno-competent mice. In addition to its direct toxic effect, treatment with this combination induced the release of the immuno-stimulating factor monocyte chimoattractant protein 1 (MCP1) in the blood and a decrease in the level of the pro-angiogenic factor FGF2. Our novel multifunctional, apoptosis-inducing agent could be further customized and assayed for potential use in tumor-targeted therapy.}, }
@article {pmid28145561, year = {2017}, author = {Blackburn, DG and Anderson, KE and Lo, AR and Marquez, EC and Callard, IP}, title = {Placentation in watersnakes II: Placental ultrastructure in Nerodia erythrogaster (Colubridae: Natricinae).}, journal = {Journal of morphology}, volume = {278}, number = {5}, pages = {675-688}, doi = {10.1002/jmor.20662}, pmid = {28145561}, issn = {1097-4687}, mesh = {Allantois/embryology/ultrastructure ; Animals ; Biological Evolution ; Chorion/embryology/ultrastructure ; Colubridae/*embryology ; Female ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Placenta/*ultrastructure ; Placentation/*physiology ; Pregnancy ; Yolk Sac/embryology/ultrastructure ; }, abstract = {Ultrastructure of the placental tissues from redbelly watersnakes (Nerodia erythrogaster) was analyzed during late pregnancy to provide insight into placental development and function. Examination of the chorioallantoic placenta with transmission electron microscopy reveals that chorionic and uterine epithelia are extremely attenuated but intact and that the eggshell membrane is vestigial and lacks a calcareous layer. These features minimize the interhemal diffusion distance across the placenta. Scanning electron microscopy reveals that fetal and maternal components of the placentas are richly vascularized by dense networks of capillaries. Although the yolk sac omphalopleure has largely been replaced by chorioallantois by late gestation, it retains patches of yolk droplets and regions of absorptive cells with microvilli and abundant mitochondria. Transmission electron microscopy reveals that yolk material is taken up for digestion by endodermal cells. As yolk is removed, allantoic capillaries invade to occupy positions just beneath the epithelium, forming regions of chorioallantoic placentation. Ultrastructural features indicate that the chorioallantoic placenta is specialized for gas exchange, while the omphalallantoic ("yolk sac") placenta shows evidence of functions in yolk digestion and maternal-fetal nutrient transfer. Placental features of this species are consistent with those of other thamnophines, and are evolutionarily convergent on snakes of other viviparous clades.}, }
@article {pmid28132522, year = {2017}, author = {Wen, JJ and Porter, C and Garg, NJ}, title = {Inhibition of NFE2L2-Antioxidant Response Element Pathway by Mitochondrial Reactive Oxygen Species Contributes to Development of Cardiomyopathy and Left Ventricular Dysfunction in Chagas Disease.}, journal = {Antioxidants &amp; redox signaling}, volume = {27}, number = {9}, pages = {550-566}, pmid = {28132522}, issn = {1557-7716}, mesh = {Animals ; Antioxidant Response Elements ; Antioxidants/metabolism ; Cardiomyopathies/genetics/*physiopathology ; Chagas Disease/*complications/genetics ; Disease Models, Animal ; *Down-Regulation ; HeLa Cells ; Humans ; Mice ; Mice, Inbred C57BL ; Mitochondria, Heart/metabolism ; NF-E2-Related Factor 2/*genetics ; Reactive Oxygen Species/*metabolism ; Superoxide Dismutase/metabolism ; Ventricular Dysfunction, Left/genetics/*physiopathology ; }, abstract = {AIMS: We investigated the effects of mitochondrial reactive oxygen species (mtROS) on nuclear factor (erythroid 2)-like 2 (NFE2L2) transcription factor activity during Trypanosoma cruzi (Tc) infection and determined whether enhancing the mtROS scavenging capacity preserved the heart function in Chagas disease.<br><br>RESULTS: C57BL/6 wild type (WT, female) mice infected with Tc exhibited myocardial loss of mitochondrial membrane potential, complex II (CII)-driven coupled respiration, and ninefold increase in mtROS production. In vitro and in vivo studies showed that Tc infection resulted in an ROS-dependent decline in the expression, nuclear translocation, antioxidant response element (ARE) binding, and activity of NFE2L2, and 35-99% decline in antioxidants' (gamma-glutamyl cysteine synthase [&#x3b3;GCS], heme oxygenase-1 [HO1], glutamate-cysteine ligase modifier subunit [GCLM], thioredoxin (Trx), glutathione S transferase [GST], and NAD(P)H dehydrogenase, quinone 1 [NQO1]) expression. An increase in myocardial and mitochondrial oxidative adducts, myocardial interventricular septum thickness, and left ventricle (LV) mass, a decline in LV posterior wall thickness, and disproportionate synthesis of collagens (COLI/COLIII), &#x3b1;SMA, and SM22&#x3b1; were noted in WT.Tc mice. Overexpression of manganese superoxide dismutase (MnSOD) in cultured cells (HeLa or cardiomyocytes) and MnSOD[tg] mice preserved the NFE2L2 transcriptional activity and antioxidant/oxidant balance, and cardiac oxidative and fibrotic pathology were significantly decreased in MnSOD[tg].Tc mice. Importantly, echocardiography finding of a decline in LV systolic (stroke volume, cardiac output, ejection fraction) and diastolic (early/late peak filling ratio, myocardial performance index) function in WT.Tc mice was abolished in MnSOD[tg].Tc mice. Innovation and Conclusion: The mtROS inhibition of NFE2L2/ARE pathway constitutes a key mechanism in signaling the fibrotic gene expression and evolution of chronic cardiomyopathy. Preserving the NFE2L2 activity arrested the mitochondrial and cardiac oxidative stress, cardiac fibrosis, and heart failure in Chagas disease. Antioxid. Redox Signal. 27, 550-566.}, }
@article {pmid28132461, year = {2016}, author = {Wojtkowska, M and Kmita, H}, title = {[Mitochondrial protein import complexes - a phylogenetic perspective].}, journal = {Postepy biochemii}, volume = {62}, number = {2}, pages = {103-110}, pmid = {28132461}, issn = {0032-5422}, mesh = {Carrier Proteins/genetics/*metabolism ; Eukaryota/genetics/*metabolism ; Evolution, Molecular ; Humans ; Mitochondria/genetics/*metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/*metabolism ; Phylogeny ; Protein Transport ; }, abstract = {The proper functioning of mitochondria and consequently of eukaryotic cells requires protein import into mitochondria. The import proceeds due to the presence of different pathways formed by sophisticated complexes known as the import complexes. The complexes are located in all mitochondrial compartments including the both mitochondrial membranes. Here we collect data concerning the organization of the import complexes and available for representatives of currently distinguished eukaryotic lineages. Despite the lack of many data, the emerging picture indicates at differentiation of the complex organization, particularly observed for the TOM complex. This, in turn, implicates interesting issues for further discussion concerning mitochondria evolution and the knowledge practical application.}, }
@article {pmid28132457, year = {2016}, author = {Marszalek, J}, title = {[Mitochondrial Hsp70 - function and evolution].}, journal = {Postepy biochemii}, volume = {62}, number = {2}, pages = {69-76}, pmid = {28132457}, issn = {0032-5422}, mesh = {*Evolution, Molecular ; Genes ; HSP70 Heat-Shock Proteins/genetics/*metabolism/physiology ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Protein Conformation ; Protein Folding ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/*metabolism ; }, abstract = {Hsp70 molecular chaperones function in variety of critical cellular processes, including protein folding, translocation of proteins across membranes and assembly/disassembly of protein complexes. Hsp70 systems consist of a core Hsp70 protein and its co-chaperones: J-protein and nucleotide release factor NRF. These co-chaperones regulate the cycle of interaction with protein substrate via stimulating the ATPase activity of Hsp70 (J-protein) and promoting nucleotide exchange (NRF). Compartments within the eukaryotic cell often contain multiple Hsp70s, J-proteins and NRFs. The capabilities of these systems to carry out diverse cellular functions results from either specialization of an Hsp70 or by interaction of multifunctional Hsp70 with an array of specialized J-proteins. The well-studied Hsp70 systems of yeast mitochondria provide an excellent example of functional divergence and evolution of Hsp70 machineries.}, }
@article {pmid28130668, year = {2017}, author = {Lumme, J and Ziętara, MS and Lebedeva, D}, title = {Ancient and modern genome shuffling: Reticulate mito-nuclear phylogeny of four related allopatric species of Gyrodactylus von Nordmann, 1832 (Monogenea: Gyrodactylidae), ectoparasites on the Eurasian minnow Phoxinus phoxinus (L.) (Cyprinidae).}, journal = {Systematic parasitology}, volume = {94}, number = {2}, pages = {183-200}, pmid = {28130668}, issn = {1573-5192}, mesh = {Animals ; Cyprinidae/parasitology ; *DNA Shuffling ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; *Phylogeny ; Species Specificity ; Trematoda/*classification/*genetics ; }, abstract = {Phylogenetic analyses including four allopatric species of Gyrodactylus von Nordmann, 1832 on the Eurasian minnow Phoxinus phoxinus (L.) (Cyprinidae) revealed incongruence between the nuclear ITS1-5.8S-ITS2 and mitochondrial cox1 phylogenies due to ancient hybridisation. Gyrodactylus pannonicus Molnár, 1968 was sampled close to its type-locality, the upper reaches of River Tisza, tributary of Danube in the Black Sea Basin. Faunistic search detected three new related species with maximum composite likelihood distances in cox1 between 16.8-23.2% (tentatively 1.3 to 1.8 My of divergence). Gyrodactylus albolacustris n. sp. recorded in the White Sea Basin, eastern Baltic Basin and Mongolia was close to G. pannonicus in the nuclear ITS (divergence of 0.9%), but diverged in cox1 by 19.8%. The Mongolian isolate of G. albolacustris n. sp. diverged from the European isolates in cox1 by 8.9%, suggesting 0.7 My of isolation. The two other new species differed from G. pannonicus by >4% in ITS and some large indels in ITS1, and by >20% in cox1. Gyrodactylus danastriae n. sp. was found in River Strwiąż, a tributary of the River Dniester (Black Sea Basin) and was characterised by smaller size of anchors and by 29-41 bp dimorphic insertion in ITS1. Gyrodactylus botnicus n. sp. is considered endemic in the Baltic Basin, but was also found in the White Sea Basin as a postglacial immigrant, where it had hybridised with G. albolacustris n. sp. in spite of the high divergence in ITS (3.9%) and cox1 (22%). The discordant nuclear and mitochondrial phylogenies revealed an ancient mitochondrial introgression: G. albolacustris n. sp. was derived from a hybridisation combining proto-pannonicus ITS with proto-danastriae mitochondria, perhaps 1.3 My ago. The postglacial hybridisation of G. albolacustris n. sp. (as the donor of mtDNA[alb] and ITS[alb]) and G. botnicus n. sp. (donor of the ITS[bot]) offered a model of shuffling of the genomic components: the process of the homogenisation and stabilisation of nuclear ITS (concerted evolution) and the lineage sorting has hardly begun.}, }
@article {pmid28130490, year = {2017}, author = {Sato, A and Suematsu, T and Aihara, KK and Kita, K and Suzuki, T and Watanabe, K and Ohtsuki, T and Watanabe, YI}, title = {Duplication of Drosophila melanogaster mitochondrial EF-Tu: pre-adaptation to T-arm truncation and exclusion of bulky aminoacyl residues.}, journal = {The Biochemical journal}, volume = {474}, number = {6}, pages = {957-969}, doi = {10.1042/BCJ20160929}, pmid = {28130490}, issn = {1470-8728}, mesh = {Amino Acid Sequence ; Animals ; Biological Evolution ; Caenorhabditis elegans/genetics/metabolism ; Cloning, Molecular ; Drosophila Proteins/*chemistry/genetics/metabolism ; Drosophila melanogaster/*genetics/metabolism ; Escherichia coli/genetics/metabolism ; Gene Expression Regulation ; Kinetics ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/*chemistry/genetics/metabolism ; Nucleic Acid Conformation ; Peptide Elongation Factor Tu/*chemistry/genetics/metabolism ; *Protein Biosynthesis ; Protein Isoforms/chemistry/genetics/metabolism ; RNA, Transfer, Amino Acyl/*chemistry/genetics/metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Trichinella/genetics/metabolism ; }, abstract = {Translation elongation factor Tu (EF-Tu) delivers aminoacyl-tRNA (aa-tRNA) to ribosomes in protein synthesis. EF-Tu generally recognizes aminoacyl moieties and acceptor- and T-stems of aa-tRNAs. However, nematode mitochondrial (mt) tRNAs frequently lack all or part of the T-arm that is recognized by canonical EF-Tu. We previously reported that two distinct EF-Tu species, EF-Tu1 and EF-Tu2, respectively, recognize mt tRNAs lacking T-arms and D-arms in the mitochondria of the chromadorean nematode Caenorhabditis elegansC. elegans EF-Tu2 specifically recognizes the seryl moiety of serylated D-armless tRNAs. Mitochondria of the enoplean nematode Trichinella possess three structural types of tRNAs: T-armless tRNAs, D-armless tRNAs, and cloverleaf tRNAs with a short T-arm. Trichinella mt EF-Tu1 binds to all three types and EF-Tu2 binds only to D-armless Ser-tRNAs, showing an evolutionary intermediate state from canonical EF-Tu to chromadorean nematode (e.g. C. elegans) EF-Tu species. We report here that two EF-Tu species also participate in Drosophila melanogaster mitochondria. Both D. melanogaster EF-Tu1 and EF-Tu2 bound to cloverleaf and D-armless tRNAs. D. melanogaster EF-Tu1 has the ability to recognize T-armless tRNAs that do not evidently exist in D. melanogaster mitochondria, but do exist in related arthropod species. In addition, D. melanogaster EF-Tu2 preferentially bound to aa-tRNAs carrying small amino acids, but not to aa-tRNAs carrying bulky amino acids. These results suggest that the Drosophila mt translation system could be another intermediate state between the canonical and nematode mitochondria-type translation systems.}, }
@article {pmid28129888, year = {2017}, author = {VanItallie, TB}, title = {Alzheimer's disease: Innate immunity gone awry?.}, journal = {Metabolism: clinical and experimental}, volume = {69S}, number = {}, pages = {S41-S49}, doi = {10.1016/j.metabol.2017.01.014}, pmid = {28129888}, issn = {1532-8600}, mesh = {Acetylation ; Adaptive Immunity ; Aged ; Aged, 80 and over ; Alzheimer Disease/*immunology/metabolism/physiopathology/prevention &amp; control ; Animals ; Astrocytes/*immunology/metabolism ; Blood-Brain Barrier/immunology/metabolism/physiopathology ; Disease Progression ; Exercise ; Hippocampus/*immunology/metabolism/physiopathology ; Histones/metabolism ; Humans ; *Immunity, Innate ; Inflammasomes/immunology/metabolism ; Microglia/*immunology/metabolism ; Mitochondria/immunology/metabolism ; *Neuroimmunomodulation ; Protein Processing, Post-Translational ; Synapses/immunology/metabolism ; }, abstract = {Inflammation is an immune activity designed to protect the host from pathogens and noxious agents. In its low-intensity form, presence of an inflammatory process must be inferred from appropriate biomarkers. Occult neuroinflammation is not just secondary to Alzheimer's disease (AD) but may contribute to its pathogenesis and promote its progression. A leaky blood-brain barrier (BBB) has been observed in early AD and may play a role in its initiation and development. Studies of the temporal evolution of AD's biomarkers have shown that, in AD, the brain's amyloid burden correlates poorly with cognitive decline. In contrast, cognitive deficits in AD correlate well with synapse loss. Oligomeric forms of amyloid-beta (oAβs) can be synaptotoxic and evidence of their deposition inside synaptic terminals of cognition-associated neurons explains early memory loss in AD better than formation of extracellular Aβ plaques. Among innate immune cells that reside in the brain, microglia sense danger signals represented by proteins like oAβ and become activated by neuronal damage such as that caused by bacterial endotoxins. The resulting reactive microgliosis has been implicated in generating the chronic form of microglial activation believed to promote AD's development. Genome-wide association studies (GWASs) have yielded data from patients with sporadic AD indicating that its causes include genetic variation in the innate immune system. Recent preclinical studies have reported that β-hydroxybutyrate (βOHB) may protect the brain from the adverse effects of both the nucleotide-binding oligomerization domain (NOD)-like receptor protein 3 (NLRP3) inflammasome and the deacetylation of histone. Consequently, there is an urgent need for clinical investigations designed to test whether an orally administered βOHB preparation, such as a ketone ester, can have a similar beneficial effect in human subjects.}, }
@article {pmid28129733, year = {2018}, author = {Li, GL and Xu, YJ and Huang, XM and Xiao, J and Nong, S and Li, CG}, title = {MeDIP-seq reveals the features of mitochondrial genomic methylation in immature testis of Chinese mitten crab Eriocheir sinensis.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {3}, pages = {335-339}, doi = {10.1080/24701394.2016.1278537}, pmid = {28129733}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Brachyura/classification/*genetics ; *DNA Methylation ; Genetic Variation ; *Genome, Mitochondrial ; Male ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {In this study, the methylation of mitochondrial genome in the immature testis of Chinese mitten crab Eriocheir sinensis of the Yangtze River system was determined for the first time using MeDIP-seq. Our methylated DNA fragments covered more than 99% of the mitochondrial genome in E. sinensis loaded from GenBank. There were 8 mutated bases and 42 SNPs in the crab mitochondrial genome. The methylation presented in all genes as well as in an A + T region, but less in intergenic regions in the mitochondrial genome. However, the level of methylation of most genes coding proteins and the A + T region were high. But, the majority of genes encoding tRNAs were hypomethylated, and both the rRNA genes also showed methylation of low or median frequency. Especially, the level of methylation of the intergenic regions is the lowest. Those features indicated that the methylation of DNA may play an important role in gene expressing regulation in the mitochondrial genome of immature testis in E. sinensis.}, }
@article {pmid28129732, year = {2018}, author = {Ruiz-García, M and Chacón, D and Plese, T and Schuler, I and Shostell, JM}, title = {Mitogenomics phylogenetic relationships of the current sloth's genera and species (Bradypodidae and Megalonychidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {2}, pages = {281-299}, doi = {10.1080/24701394.2016.1275602}, pmid = {28129732}, issn = {2470-1408}, mesh = {Animals ; Bayes Theorem ; Evolution, Molecular ; Genetic Variation ; Genome, Mitochondrial ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Sloths/*classification/genetics ; }, abstract = {We sequenced the complete mitogenome of 39 sloths (19 Bradypus variegatus, 4 B. tridactylus, 1 B. pygmaeus, 1 B. torquatus, 4 Choloepus didactylus, and 10 C. hoffmanni). A Bayesian tree (BI) indicated a temporal split between Bradypus and Choloepus around 31 million years ago (MYA, Oligocene) and the other major splits within each genera during the Miocene and Pliocene. A haplotype network (MJN) estimated a lower temporal split between the sloth genera (around 23.5 MYA). Both methods detected the ancestor of B. torquatus as the first to diverge within Bradypus (21 for BI and 19 MJN), followed by that of the ancestor of B. tridactylus. The split of B. pygmaeus from the common ancestor with B. variegatus was around 12 MYA (BI) or 4.3 MYA (MJN). The splits among the previous populations of B. variegatus began around 8 MYA (BI) or 3.6 MYA (MJN). The trans-Andean population was the first to diverge from the remaining cis-Andean populations of B. variegatus. The genetic differentiation of the trans-Andean B. variegatus population relative to the cis-Andean B. variegatus is similar to that found for different species of sloths. The mitogenomic analysis resolved the differentiation of C. hoffmanni from the C. didactylus individuals of the Guiana Shield. However, one C. didactylus from the Colombian Amazon specimen was inside the C. hoffmanni clade. This could be the first example of possible natural hybridization in the Amazon of both Choloepus taxa or the existence of un-differentiable phenotypes of these two species in some Amazonian areas.}, }
@article {pmid28129729, year = {2018}, author = {Lin, X and Zheng, HX and Davie, A and Zhou, S and Wen, L and Meng, J and Zhang, Y and Aladaer, Q and Liu, B and Liu, WJ and Yao, XK}, title = {Association of low race performance with mtDNA haplogroup L3b of Australian thoroughbred horses.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {2}, pages = {323-330}, doi = {10.1080/24701394.2016.1278535}, pmid = {28129729}, issn = {2470-1408}, mesh = {Animals ; Australia ; DNA, Mitochondrial/*genetics ; Female ; Genetic Association Studies/*methods ; Haplotypes ; Horses/*classification/genetics/physiology ; Male ; Mutation ; Phylogeny ; Point Mutation ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; RNA, Ribosomal, 16S/chemistry/genetics ; *Running ; Sequence Analysis, DNA/*methods ; }, abstract = {Mitochondrial DNA (mtDNA) encodes the genes for respiratory chain sub-units that determine the efficiency of oxidative phosphorylation in mitochondria. The aim of this study was to determine if there were any haplogroups and variants in mtDNA that could be associated with athletic performance of Thoroughbred horses. The whole mitochondrial genomes of 53 maternally unrelated Australian Thoroughbred horses were sequenced and an association study was performed with the competition histories of 1123 horses within their maternal lineages. A horse mtDNA phylogenetic tree was constructed based on a total of 195 sequences (including 142 from previous reports). The association analysis showed that the sample groups with poor racing performance history were enriched in haplogroup L3b (p = .0003) and its sub-haplogroup L3b1a (p = .0007), while those that had elite performance appeared to be not significantly associated with haplogroups G2 and L3a1a1a (p > .05). Haplogroup L3b and L3b1a bear two and five specific variants of which variant T1458C (site 345 in 16s rRNA) is the only potential functional variant. Furthermore, secondary reconstruction of 16s RNA showed considerable differences between two types of 16s RNA molecules (with and without T1458C), indicating a potential functional effect. The results suggested that haplogroup L3b, could have a negative association with elite performance. The T1458C mutation harboured in haplogroup L3b could have a functional effect that is related to poor athletic performance.}, }
@article {pmid28129726, year = {2018}, author = {Barroso Lima, NC and Prosdocimi, F}, title = {The heavy strand dilemma of vertebrate mitochondria on genome sequencing age: number of encoded genes or G + T content?.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {2}, pages = {300-302}, doi = {10.1080/24701394.2016.1275603}, pmid = {28129726}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Mitochondrial/genetics ; DNA, Single-Stranded/*genetics ; Genes, Mitochondrial ; Genome Size ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Vertebrates/*genetics ; }, }
@article {pmid28128409, year = {2017}, author = {Ling, SS and Zhu, Y and Lan, D and Li, DS and Pang, HZ and Wang, Y and Li, DY and Wei, RP and Zhang, HM and Wang, CD and Hu, YD}, title = {Analysis of the cytochrome c oxidase subunit II (COX2) gene in giant panda, Ailuropoda melanoleuca.}, journal = {Genetics and molecular research : GMR}, volume = {16}, number = {1}, pages = {}, doi = {10.4238/gmr16019158}, pmid = {28128409}, issn = {1676-5680}, mesh = {Animals ; Electron Transport Complex IV/*genetics ; Energy Metabolism/genetics ; Mitochondria/genetics/metabolism ; Ursidae/*genetics/metabolism ; }, abstract = {The giant panda, Ailuropoda melanoleuca (Ursidae), has a unique bamboo-based diet; however, this low-energy intake has been sufficient to maintain the metabolic processes of this species since the fourth ice age. As mitochondria are the main sites for energy metabolism in animals, the protein-coding genes involved in mitochondrial respiratory chains, particularly cytochrome c oxidase subunit II (COX2), which is the rate-limiting enzyme in electron transfer, could play an important role in giant panda metabolism. Therefore, the present study aimed to isolate, sequence, and analyze the COX2 DNA from individuals kept at the Giant Panda Protection and Research Center, China, and compare these sequences with those of the other Ursidae family members. Multiple sequence alignment showed that the COX2 gene had three point mutations that defined three haplotypes, with 60% of the sequences corresponding to haplotype I. The neutrality tests revealed that the COX2 gene was conserved throughout evolution, and the maximum likelihood phylogenetic analysis, using homologous sequences from other Ursidae species, showed clustering of the COX2 sequences of giant pandas, suggesting that this gene evolved differently in them.}, }
@article {pmid28122942, year = {2017}, author = {Calvo, SE and Julien, O and Clauser, KR and Shen, H and Kamer, KJ and Wells, JA and Mootha, VK}, title = {Comparative Analysis of Mitochondrial N-Termini from Mouse, Human, and Yeast.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {16}, number = {4}, pages = {512-523}, pmid = {28122942}, issn = {1535-9484}, support = {F32 GM114905/GM/NIGMS NIH HHS/United States ; R01 GM081051/GM/NIGMS NIH HHS/United States ; R01 GM097316/GM/NIGMS NIH HHS/United States ; R01 CA154802/CA/NCI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; //CIHR/Canada ; R01 GM077465/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cell Line ; Conserved Sequence ; Evolution, Molecular ; Humans ; Kidney/metabolism ; Liver/metabolism ; Mice ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/*chemistry/genetics/*metabolism ; Proteomics/*methods ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism ; }, abstract = {The majority of mitochondrial proteins are encoded in the nuclear genome, translated in the cytoplasm, and directed to the mitochondria by an N-terminal presequence that is cleaved upon import. Recently, N-proteome catalogs have been generated for mitochondria from yeast and from human U937 cells. Here, we applied the subtiligase method to determine N-termini for 327 proteins in mitochondria isolated from mouse liver and kidney. Comparative analysis between mitochondrial N-termini from mouse, human, and yeast proteins shows that whereas presequences are poorly conserved at the sequence level, other presequence properties are extremely conserved, including a length of ∼20-60 amino acids, a net charge between +3 to +6, and the presence of stabilizing amino acids at the N-terminus of mature proteins that follow the N-end rule from bacteria. As in yeast, ∼80% of mouse presequence cleavage sites match canonical motifs for three mitochondrial peptidases (MPP, Icp55, and Oct1), whereas the remainder do not match any known peptidase motifs. We show that mature mitochondrial proteins often exist with a spectrum of N-termini, consistent with a model of multiple cleavage events by MPP and Icp55. In addition to analysis of canonical targeting presequences, our N-terminal dataset allows the exploration of other cleavage events and provides support for polypeptide cleavage into two distinct enzymes (Hsd17b4), protein cleavages key for signaling (Oma1, Opa1, Htra2, Mavs, and Bcs2l13), and in several cases suggests novel protein isoforms (Scp2, Acadm, Adck3, Hsdl2, Dlst, and Ogdh). We present an integrated catalog of mammalian mitochondrial N-termini that can be used as a community resource to investigate individual proteins, to elucidate mechanisms of mammalian mitochondrial processing, and to allow researchers to engineer tags distally to the presequence cleavage.}, }
@article {pmid28122497, year = {2017}, author = {Martins, RF and Fickel, J and Le, M and van Nguyen, T and Nguyen, HM and Timmins, R and Gan, HM and Rovie-Ryan, JJ and Lenz, D and Förster, DW and Wilting, A}, title = {Phylogeography of red muntjacs reveals three distinct mitochondrial lineages.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {34}, pmid = {28122497}, issn = {1471-2148}, mesh = {Animals ; Asia, Southeastern ; DNA, Mitochondrial ; Evolution, Molecular ; India ; Karyotyping ; Mitochondria/*genetics ; Molecular Typing ; Muntjacs/*classification/genetics ; Phylogeny ; Phylogeography ; }, abstract = {BACKGROUND: The members of the genus Muntiacus are of particular interest to evolutionary biologists due to their extreme chromosomal rearrangements and the ongoing discussions about the number of living species. Red muntjacs have the largest distribution of all muntjacs and were formerly considered as one species. Karyotype differences led to the provisional split between the Southern Red Muntjac (Muntiacus muntjak) and the Northern Red Muntjac (M. vaginalis), but uncertainties remain as, so far, no phylogenetic study has been conducted. Here, we analysed whole mitochondrial genomes of 59 archival and 16 contemporaneous samples to resolve uncertainties about their taxonomy and used red muntjacs as model for understanding the evolutionary history of other species in Southeast Asia.<br><br>RESULTS: We found three distinct matrilineal groups of red muntjacs: Sri Lankan red muntjacs (including the Western Ghats) diverged first from other muntjacs about 1.5 Mya; later northern red muntjacs (including North India and Indochina) and southern red muntjacs (Sundaland) split around 1.12 Mya. The diversification of red muntjacs into these three main lineages was likely promoted by two Pleistocene barriers: one through the Indian subcontinent and one separating the Indochinese and Sundaic red muntjacs. Interestingly, we found a high level of gene flow within the populations of northern and southern red muntjacs, indicating gene flow between populations in Indochina and dispersal of red muntjacs over the exposed Sunda Shelf during the Last Glacial Maximum.<br><br>CONCLUSIONS: Our results provide new insights into the evolution of species in South and Southeast Asia as we found clear genetic differentiation in a widespread and generalist species, corresponding to two known biogeographical barriers: The Isthmus of Kra and the central Indian dry zone. In addition, our molecular data support either the delineation of three monotypic species or three subspecies, but more importantly these data highlight the conservation importance of the Sri Lankan/South Indian red muntjac.}, }
@article {pmid28122260, year = {2017}, author = {Schwartz, L and Seyfried, T and Alfarouk, KO and Da Veiga Moreira, J and Fais, S}, title = {Out of Warburg effect: An effective cancer treatment targeting the tumor specific metabolism and dysregulated pH.}, journal = {Seminars in cancer biology}, volume = {43}, number = {}, pages = {134-138}, doi = {10.1016/j.semcancer.2017.01.005}, pmid = {28122260}, issn = {1096-3650}, mesh = {Animals ; Citrates/administration &amp; dosage ; Humans ; Hydrogen-Ion Concentration ; Neoplasms/metabolism/*therapy ; Oxidative Phosphorylation ; Oxygen/*metabolism ; Thioctic Acid/administration &amp; dosage ; }, abstract = {As stated by Otto Warburg nearly a century ago, cancer is a metabolic disease, a fermentation caused by malfunctioning mitochondria, resulting in increased anabolism and decreased catabolism. Treatment should, therefore, aim at restoring the energy yield. To decrease anabolism, glucose uptake should be reduced (ketogenic diet). To increase catabolism, the oxidative phosphorylation should be restored. Treatment with a combination of α-lipoic acid and hydroxycitrate has been shown to be effective in multiple animal models. This treatment, in combination with conventional chemotherapy, has yielded extremely encouraging results in glioblastoma, brain metastasis and lung cancer. Randomized trials are necessary to confirm these preliminary data. The major limitation is the fact that the combination of α-lipoic acid and hydroxycitrate can only be effective if the mitochondria are still present and/or functional. That may not be the case in the most aggressive tumors. The increased intracellular alkalosis is a strong mitogenic signal, which bypasses most inhibitory signals. Concomitant correction of this alkalosis may be a very effective treatment in case of mitochondrial failure.}, }
@article {pmid28122084, year = {2017}, author = {Lyon, J}, title = {Sanctioned UK Trial of Mitochondrial Transfer Nears.}, journal = {JAMA}, volume = {317}, number = {5}, pages = {462-464}, doi = {10.1001/jama.2016.18680}, pmid = {28122084}, issn = {1538-3598}, mesh = {Bioethical Issues ; Biomedical Research ; DNA, Mitochondrial/*therapeutic use ; Embryo Research/ethics/*legislation &amp; jurisprudence ; Female ; Genetic Drift ; Genetic Therapy/ethics/*legislation &amp; jurisprudence/methods ; Humans ; In Vitro Techniques/ethics ; Male ; Mitochondria/*transplantation ; Mitochondrial Diseases/genetics/*therapy ; Politics ; Sex Factors ; United Kingdom ; United States ; }, }
@article {pmid28120863, year = {2017}, author = {Marques, JP and Farelo, L and Vilela, J and Vanderpool, D and Alves, PC and Good, JM and Boursot, P and Melo-Ferreira, J}, title = {Range expansion underlies historical introgressive hybridization in the Iberian hare.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {40788}, pmid = {28120863}, issn = {2045-2322}, support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/methods ; DNA, Mitochondrial ; *Evolution, Molecular ; Gene Library ; Genetics, Population ; Genotype ; Hares/*genetics ; High-Throughput Nucleotide Sequencing ; *Hybridization, Genetic ; Molecular Sequence Annotation ; Polymorphism, Single Nucleotide ; Selection, Genetic ; Transcriptome ; }, abstract = {Introgressive hybridization is an important and widespread evolutionary process, but the relative roles of neutral demography and natural selection in promoting massive introgression are difficult to assess and an important matter of debate. Hares from the Iberian Peninsula provide an appropriate system to study this question. In its northern range, the Iberian hare, Lepus granatensis, shows a northwards gradient of increasing mitochondrial DNA (mtDNA) introgression from the arctic/boreal L. timidus, which it presumably replaced after the last glacial maximum. Here, we asked whether a south-north expansion wave of L. granatensis into L. timidus territory could underlie mtDNA introgression, and whether nuclear genes interacting with mitochondria ("mitonuc" genes) were affected. We extended previous RNA-sequencing and produced a comprehensive annotated transcriptome assembly for L. granatensis. We then genotyped 100 discovered nuclear SNPs in 317 specimens spanning the species range. The distribution of allele frequencies across populations suggests a northwards range expansion, particularly in the region of mtDNA introgression. We found no correlation between variants at 39 mitonuc genes and mtDNA introgression frequency. Whether the nuclear and mitochondrial genomes coevolved will need a thorough investigation of the hundreds of mitonuc genes, but range expansion and species replacement likely promoted massive mtDNA introgression.}, }
@article {pmid28116945, year = {2018}, author = {Kranthi, S and Ghodke, AB and Puttuswamy, RK and Mandle, M and Nandanwar, R and Satija, U and Pareek, RK and Desai, H and Udikeri, SS and Balakrishna, DJ and Hugar, BM and Monga, D and Kranthi, KR}, title = {Mitochondria COI-based genetic diversity of the cotton leafhopper Amrasca biguttula biguttula (Ishida) populations from India.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {2}, pages = {228-235}, doi = {10.1080/24701394.2016.1275595}, pmid = {28116945}, issn = {2470-1408}, mesh = {Animals ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Gene Flow ; *Genetic Variation ; Genetics, Population ; Haplotypes ; Hemiptera/*classification/genetics ; India ; Insect Proteins/genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {Amrasca biguttula biguttula (Ishida), the cotton leafhopper, is a polyphagous insect pest of Asia and Southeast Asian countries. We sequenced a mitochondrial COI gene fragment from 67 individuals of cotton leafhopper collected from 7 major cotton growing states of North, Central, and South India. Genetic divergence analysis of leaf hopper population across India confirmed the presence of single species. Thirty haplotypes, in total, were determined across different regions of India. While population from North India was dominated by single haplotype, the south and central Indian populations show dispersion of different haplotypes across the region. The neutrality test rejection for the north Indian population also suggests population expansion. The genetic differentiation and gene flow analysis together confirmed the phylogeographic structure of the A. biguttula biguttula Ishida as isolated by distance.}, }
@article {pmid28115024, year = {2017}, author = {Hornok, S and Sándor, AD and Tomanović, S and Beck, R and D'Amico, G and Kontschán, J and Takács, N and Görföl, T and Bendjeddou, ML and Földvári, G and Farkas, R}, title = {East and west separation of Rhipicephalus sanguineus mitochondrial lineages in the Mediterranean Basin.}, journal = {Parasites &amp; vectors}, volume = {10}, number = {1}, pages = {39}, pmid = {28115024}, issn = {1756-3305}, mesh = {Animals ; Arthropod Proteins/genetics ; Dog Diseases/*parasitology ; Dogs ; Female ; Genetic Variation ; Male ; Mediterranean Region ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rhipicephalus sanguineus/*classification/*genetics ; }, abstract = {BACKGROUND: Rhipicephalus sanguineus belongs to a complex of hard tick species with high veterinary-medical significance. Recently, new phylogenetic units have been discovered within R. sanguineus, which therefore needs taxonomic revision. The present study was initiated to provide new information on the phylogeography of relevant haplotypes from less studied regions of Europe and Africa. With this aim, molecular-phylogenetic analyses of two mitochondrial markers were performed on 50 ticks collected in Hungary, the Balkans, countries along the Mediterranean Sea, Kenya and Ivory Coast.<br><br>RESULTS: In the "temperate lineage" of R. sanguineus, based on cytochrome c oxidase subunit 1 (cox1) and 16S rRNA genes, Rhipicephalus sp. I was only found in the eastern part of the Mediterranean Basin (with relatively homogenous haplotypes), whereas Rhipicephalus sp. II occurred in the middle-to-western part of this region (with phylogenetically dichotomous haplotypes). Ticks identified as R. leporis (based on morphology and cox1 gene) were found in Kenya and Ivory Coast. These clustered phylogenetically within R. sanguineus (s.l.) ("tropical lineage").<br><br>CONCLUSIONS: In the Mediterranean Basin two mitochondrial lineages of R. sanguineus, i.e. Rhipicephalus sp. I and Rhipicephalus sp. II exist, which show different geographical distribution. Therefore, data from this study confirm limited gene flow between Rhipicephalus sp. I and Rhipicephalus sp. II, but more evidence (analyses of nuclear markers, extensive morphological and biological comparison etc.) are necessary to infer if they belong to different species or not. The phylogenetic relationships of eastern and western African ticks, which align with R. leporis, need to be studied further within R. sanguineus (s.l.) ("tropical lineage").}, }
@article {pmid28110272, year = {2017}, author = {Mossman, JA and Tross, JG and Jourjine, NA and Li, N and Wu, Z and Rand, DM}, title = {Mitonuclear Interactions Mediate Transcriptional Responses to Hypoxia in Drosophila.}, journal = {Molecular biology and evolution}, volume = {34}, number = {2}, pages = {447-466}, pmid = {28110272}, issn = {1537-1719}, support = {R01 AG027849/AG/NIA NIH HHS/United States ; R01 GM067862/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Drosophila melanogaster/*genetics/metabolism ; Epistasis, Genetic ; Female ; Gene Expression Regulation ; Genotype ; Haplotypes ; Hypoxia/*genetics/metabolism ; Male ; Mitochondria/genetics/metabolism ; Polymorphism, Genetic ; Transcriptional Activation ; Transcriptome ; }, abstract = {Among the major challenges in quantitative genetics and personalized medicine is to understand how gene × gene interactions (G × G: epistasis) and gene × environment interactions (G × E) underlie phenotypic variation. Here, we use the intimate relationship between mitochondria and oxygen availability to dissect the roles of nuclear DNA (nDNA) variation, mitochondrial DNA (mtDNA) variation, hypoxia, and their interactions on gene expression in Drosophila melanogaster. Mitochondria provide an important evolutionary and medical context for understanding G × G and G × E given their central role in integrating cellular signals. We hypothesized that hypoxia would alter mitonuclear communication and gene expression patterns. We show that first order nDNA, mtDNA, and hypoxia effects vary between the sexes, along with mitonuclear epistasis and G × G × E effects. Females were generally more sensitive to genetic and environmental perturbation. While dozens to hundreds of genes are altered by hypoxia in individual genotypes, we found very little overlap among mitonuclear genotypes for genes that were significantly differentially expressed as a consequence of hypoxia; excluding the gene hairy. Oxidative phosphorylation genes were among the most influenced by hypoxia and mtDNA, and exposure to hypoxia increased the signature of mtDNA effects, suggesting retrograde signaling between mtDNA and nDNA. We identified nDNA-encoded genes in the electron transport chain (succinate dehydrogenase) that exhibit female-specific mtDNA effects. Our findings have important implications for personalized medicine, the sex-specific nature of mitonuclear communication, and gene × gene coevolution under variable or changing environments.}, }
@article {pmid28105930, year = {2016}, author = {Kononov, A and Ustyantsev, K and Wang, B and Mastro, VC and Fet, V and Blinov, A and Baranchikov, Y}, title = {Genetic diversity among eight Dendrolimus species in Eurasia (Lepidoptera: Lasiocampidae) inferred from mitochondrial COI and COII, and nuclear ITS2 markers.}, journal = {BMC genetics}, volume = {17}, number = {Suppl 3}, pages = {157}, pmid = {28105930}, issn = {1471-2156}, mesh = {Animals ; Electron Transport Complex IV/*genetics ; Genetic Markers/*genetics ; Genetic Variation ; Insect Proteins/*genetics ; Mitochondria/*genetics ; Moths/classification/*genetics ; Phylogeny ; }, abstract = {BACKGROUND: Moths of genus Dendrolimus (Lepidoptera: Lasiocampidae) are among the major pests of coniferous forests worldwide. Taxonomy and nomenclature of this genus are not entirely established, and there are many species with a controversial taxonomic position. We present a comparative evolutionary analysis of the most economically important Dendrolimus species in Eurasia.<br><br>RESULTS: Our analysis was based on the nucleotide sequences of COI and COII mitochondrial genes and ITS2 spacer of nuclear ribosomal genes. All known sequences were extracted from GenBank. Additional 112 new sequences were identified for 28 specimens of D. sibiricus, D. pini, and D. superans from five regions of Siberia and the Russian Far East to be able to compare the disparate data from all previous studies. In total, 528 sequences were used in phylogenetic analysis. Two clusters of closely related species in Dendrolimus were found. The first cluster includes D. pini, D. sibiricus, and D. superans; and the second, D. spectabilis, D. punctatus, and D. tabulaeformis. Species D. houi and D. kikuchii appear to be the most basal in the genus.<br><br>CONCLUSION: Genetic difference among the second cluster species is very low in contrast to the first cluster species. Phylogenetic position D. tabulaeformis as a subspecies was supported. It was found that D. sibiricus recently separated from D. superans. Integration of D. sibiricus mitochondrial DNA sequences and the spread of this species to the west of Eurasia have been established as the cause of the unjustified allocation of a new species: D. kilmez. Our study further clarifies taxonomic problems in the genus and gives more complete information on the genetic structure of D. pini, D. sibiricus, and D. superans.}, }
@article {pmid28105800, year = {2016}, author = {O Otecko, N and Peng, MS and Yang, HC and Zhang, YP and Wang, GD}, title = {Re-evaluating data quality of dog mitochondrial, Y chromosomal, and autosomal SNPs genotyped by SNP array.}, journal = {Zoological research}, volume = {37}, number = {6}, pages = {356-360}, pmid = {28105800}, issn = {2095-8137}, mesh = {Animals ; Dogs ; Genotype ; Mitochondria/*genetics ; Polymorphism, Single Nucleotide/genetics ; Y Chromosome/*genetics ; }, abstract = {Quality deficiencies in single nucleotide polymorphism (SNP) analyses have important implications. We used missingness rates to investigate the quality of a recently published dataset containing 424 mitochondrial, 211 Y chromosomal, and 160 432 autosomal SNPs generated by a semicustom Illumina SNP array from 5 392 dogs and 14 grey wolves. Overall, the individual missingness rate for mitochondrial SNPs was ~43.8%, with 980 (18.1%) individuals completely missing mitochondrial SNP genotyping (missingness rate=1). In males, the genotype missingness rate was ~28.8% for Y chromosomal SNPs, with 374 males recording rates above 0.96. These 374 males also exhibited completely failed mitochondrial SNPs genotyping, indicative of a batch effect. Individual missingness rates for autosomal markers were greater than zero, but less than 0.5. Neither mitochondrial nor Y chromosomal SNPs achieved complete genotyping (locus missingness rate=0), whereas 5.9% of autosomal SNPs had a locus missingness rate=1. The high missingness rates and possible batch effect show that caution and rigorous measures are vital when genotyping and analyzing SNP array data for domestic animals. Further improvements of these arrays will be helpful to future studies.}, }
@article {pmid28104538, year = {2017}, author = {Davis, A and Abbriano, R and Smith, SR and Hildebrand, M}, title = {Clarification of Photorespiratory Processes and the Role of Malic Enzyme in Diatoms.}, journal = {Protist}, volume = {168}, number = {1}, pages = {134-153}, doi = {10.1016/j.protis.2016.10.005}, pmid = {28104538}, issn = {1618-0941}, mesh = {Algal Proteins/genetics ; Diatoms/enzymology/*metabolism ; Malate Dehydrogenase/*metabolism ; Mitochondria/metabolism ; Oxidation-Reduction ; *Photosynthesis ; Phylogeny ; }, abstract = {Evidence suggests that diatom photorespiratory metabolism is distinct from other photosynthetic eukaryotes in that there may be at least two routes for the metabolism of the photorespiratory metabolite glycolate. One occurs primarily in the mitochondria and is similar to the C2 photorespiratory pathway, and the other processes glycolate through the peroxisomal glyoxylate cycle. Genomic analysis has identified the presence of key genes required for glycolate oxidation, the glyoxylate cycle, and malate metabolism, however, predictions of intracellular localization can be ambiguous and require verification. This knowledge gap leads to uncertainties surrounding how these individual pathways operate, either together or independently, to process photorespiratory intermediates under different environmental conditions. Here, we combine in silico sequence analysis, in vivo protein localization techniques and gene expression patterns to investigate key enzymes potentially involved in photorespiratory metabolism in the model diatom Thalassiosira pseudonana. We demonstrate the peroxisomal localization of isocitrate lyase and the mitochondrial localization of malic enzyme and a glycolate oxidase. Based on these analyses, we propose an updated model for photorespiratory metabolism in T. pseudonana, as well as a mechanism by which C2 photorespiratory metabolism and its associated pathways may operate during silicon starvation and growth arrest.}, }
@article {pmid28102911, year = {2017}, author = {Attacha, S and Solbach, D and Bela, K and Moseler, A and Wagner, S and Schwarzländer, M and Aller, I and Müller, SJ and Meyer, AJ}, title = {Glutathione peroxidase-like enzymes cover five distinct cell compartments and membrane surfaces in Arabidopsis thaliana.}, journal = {Plant, cell &amp; environment}, volume = {40}, number = {8}, pages = {1281-1295}, doi = {10.1111/pce.12919}, pmid = {28102911}, issn = {1365-3040}, mesh = {Amino Acid Sequence ; Arabidopsis/*cytology/*enzymology ; *Cell Compartmentation ; Cell Membrane/*enzymology ; Cytosol/metabolism ; Endoplasmic Reticulum/metabolism ; Glutathione Peroxidase/chemistry/*metabolism ; Green Fluorescent Proteins/metabolism ; Membrane Proteins/chemistry/metabolism ; Mitochondria/metabolism ; Mutation/genetics ; Nuclear Proteins/metabolism ; Phylogeny ; Plastids/metabolism ; Recombinant Fusion Proteins/metabolism ; Secretory Pathway ; Solubility ; Subcellular Fractions/enzymology ; }, abstract = {Glutathione peroxidase-like enzymes (GPXLs) constitute a family of eight peroxidases in Arabidopsis thaliana. In contrast to the eponymous selenocysteine glutathione peroxidases in mammalian cells that use glutathione as electron donor, GPXLs rely on cysteine instead of selenocysteine for activity and depend on the thioredoxin system for reduction. Although plant GPXLs have been implicated in important agronomic traits such as drought tolerance, photooxidative tolerance and immune responses, there remain major ambiguities regarding their subcellular localization. Because their site of action is a prerequisite for an understanding of their function, we investigated the localization of all eight GPXLs in stable Arabidopsis lines expressing N-terminal and C-terminal fusions with redox-sensitive green fluorescent protein 2 (roGFP2) using confocal microscopy. GPXL1 and GPXL7 were found in plastids, while GPXL2 and GPXL8 are cytosolic nuclear. The N-terminal target peptide of GPXL6 is sufficient to direct roGFP2 into mitochondria. Interestingly, GPXL3, GPXL4 and GPXL5 all appear to be membrane bound. GPXL3 was found exclusively in the secretory pathway where it is anchored by a single N-terminal transmembrane domain. GPXL4 and GPXL5 are anchored to the plasma membrane. Presence of an N-terminal myristoylation motif and genetic disruption of membrane association through targeted mutagenesis point to myristoylation as essential for membrane localization.}, }
@article {pmid28100781, year = {2017}, author = {Bruggisser, J and Käser, S and Mani, J and Schneider, A}, title = {Biogenesis of a Mitochondrial Outer Membrane Protein in Trypanosoma brucei: TARGETING SIGNAL AND DEPENDENCE ON A UNIQUE BIOGENESIS FACTOR.}, journal = {The Journal of biological chemistry}, volume = {292}, number = {8}, pages = {3400-3410}, pmid = {28100781}, issn = {1083-351X}, mesh = {Mitochondria/metabolism/ultrastructure ; Mitochondrial Membranes/*metabolism/ultrastructure ; Mitochondrial Proteins/analysis/*metabolism ; Protein Domains ; Protozoan Proteins/analysis/*metabolism ; Trypanosoma brucei brucei/cytology/*metabolism ; }, abstract = {The mitochondrial outer membrane (OM) contains single and multiple membrane-spanning proteins that need to contain signals that ensure correct targeting and insertion into the OM. The biogenesis of such proteins has so far essentially only been studied in yeast and related organisms. Here we show that POMP10, an OM protein of the early diverging protozoan Trypanosoma brucei, is signal-anchored. Transgenic cells expressing variants of POMP10 fused to GFP demonstrate that the N-terminal membrane-spanning domain flanked by a few positively charged or neutral residues is both necessary and sufficient for mitochondrial targeting. Carbonate extraction experiments indicate that although the presence of neutral instead of positively charged residues did not interfere with POMP10 localization, it weakened its interaction with the OM. Expression of GFP-tagged POMP10 in inducible RNAi cell lines shows that its mitochondrial localization depends on pATOM36 but does not require Sam50 or ATOM40, the trypanosomal analogue of the Tom40 import pore. pATOM36 is a kinetoplastid-specific OM protein that has previously been implicated in the assembly of OM proteins and in mitochondrial DNA inheritance. In summary, our results show that although the features of the targeting signal in signal-anchored proteins are widely conserved, the protein machinery that mediates their biogenesis is not.}, }
@article {pmid28096380, year = {2017}, author = {Mühleip, AW and Dewar, CE and Schnaufer, A and Kühlbrandt, W and Davies, KM}, title = {In situ structure of trypanosomal ATP synthase dimer reveals a unique arrangement of catalytic subunits.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {5}, pages = {992-997}, pmid = {28096380}, issn = {1091-6490}, support = {G0600129/MRC_/Medical Research Council/United Kingdom ; MR/L019701/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adenosine Triphosphate/biosynthesis ; Amino Acid Sequence ; Animals ; Catalysis ; Catalytic Domain ; Consensus Sequence ; Dimerization ; Euglena gracilis/*enzymology ; Mitochondria/enzymology ; Models, Molecular ; Protein Conformation ; Proton-Translocating ATPases/*chemistry/metabolism ; Protozoan Proteins/*chemistry/metabolism ; Rotation ; Sequence Alignment ; Sequence Homology, Amino Acid ; Trypanosoma brucei brucei/*enzymology ; }, abstract = {We used electron cryotomography and subtomogram averaging to determine the in situ structures of mitochondrial ATP synthase dimers from two organisms belonging to the phylum euglenozoa: Trypanosoma brucei, a lethal human parasite, and Euglena gracilis, a photosynthetic protist. At a resolution of 32.5 Å and 27.5 Å, respectively, the two structures clearly exhibit a noncanonical F1 head, in which the catalytic (αβ)3 assembly forms a triangular pyramid rather than the pseudo-sixfold ring arrangement typical of all other ATP synthases investigated so far. Fitting of known X-ray structures reveals that this unusual geometry results from a phylum-specific cleavage of the α subunit, in which the C-terminal αC fragments are displaced by ∼20 Å and rotated by ∼30° from their expected positions. In this location, the αC fragment is unable to form the conserved catalytic interface that was thought to be essential for ATP synthesis, and cannot convert γ-subunit rotation into the conformational changes implicit in rotary catalysis. The new arrangement of catalytic subunits suggests that the mechanism of ATP generation by rotary ATPases is less strictly conserved than has been generally assumed. The ATP synthases of these organisms present a unique model system for discerning the individual contributions of the α and β subunits to the fundamental process of ATP synthesis.}, }
@article {pmid28089840, year = {2017}, author = {Fuchs, J and Pons, JM and Bowie, RC}, title = {Biogeography and diversification dynamics of the African woodpeckers.}, journal = {Molecular phylogenetics and evolution}, volume = {108}, number = {}, pages = {88-100}, doi = {10.1016/j.ympev.2017.01.007}, pmid = {28089840}, issn = {1095-9513}, mesh = {Africa ; Animals ; *Biodiversity ; Birds/*classification ; Cell Nucleus/genetics ; Genetic Loci ; Mitochondria/genetics ; Models, Theoretical ; Phylogeny ; *Phylogeography ; Species Specificity ; Time Factors ; }, abstract = {The dynamics of species accumulation of African terrestrial vertebrates over time remains underexplored in comparison with those in the New World, despite Africa hosting about 25% of the world's avian diversity. This lack of knowledge hampers our understanding of the fundamental processes that drive biodiversity and the dynamics of speciation. To begin to address this gap, we reconstructed species-level phylogenies of two unrelated clades of African woodpeckers (12 species of Geocolaptes/Campethera and 13 species of Chloropicus/Mesopicos/Dendropicos/Ipophilus) that diverged from their closest Indo-Malayan relatives at similar times. Our results demonstrate that the current taxonomy is misleading: three (Campethera, Dendropicos and Mesopicos) out of four polytpic genera/subgenera are not monophyletic. Our results also show that current estimates of diversity at the species level are significantly understated, as up to 18 species for the 'Campethera clade' and 19 for the 'Dendropicos clade' could be recognized. The first splits within both clades involve species that are largely restricted to the Guineo-Congolian biogeographic regions, followed by later adaptations to particular habitats (forest versus savannah) and colonization of other regions (e.g. Southern Africa), each of which occurred multiple times in both clades. Assuming a conservative species delimitation scheme, our results indicate that diversification rates are decreasing through time for both clades. Applying a more extreme species recognition scheme (18 and 19 species for the Campethera and Dendropicos clades, respectively), our results support a decrease in diversification rates only for the Dendropicos clade and thus underline the importance of the number of species included in our diversification analyses. Greater ecological diversity of the Campethera clade where multiple species exhibit either an arboreal or terrestrial foraging strategy might explain the constant diversification rates through time we found under the eighteen species scheme.}, }
@article {pmid28088649, year = {2017}, author = {Jardim-Messeder, D and Cabreira-Cagliari, C and Rauber, R and Turchetto-Zolet, AC and Margis, R and Margis-Pinheiro, M}, title = {Fumarate reductase superfamily: A diverse group of enzymes whose evolution is correlated to the establishment of different metabolic pathways.}, journal = {Mitochondrion}, volume = {34}, number = {}, pages = {56-66}, doi = {10.1016/j.mito.2017.01.002}, pmid = {28088649}, issn = {1872-8278}, mesh = {*Biological Evolution ; Biotransformation ; Fumarates/metabolism ; Metabolic Networks and Pathways/*genetics ; Succinate Dehydrogenase/*genetics/*metabolism ; Succinates/metabolism ; }, abstract = {Fumarate and succinate are known to be present in prebiotic systems essential for the origin of life. The fumarate and succinate interconversion reactions have been conserved throughout evolution and are found in all living organisms. The fumarate and succinate interconversion is catalyzed by the enzymes succinate dehydrogenase (SDH) and fumarate reductase (FRD). In this work we show that SDH and FRD are part of a group of enzymes that we propose to designate "fumarate reductase superfamily". Our results demonstrate that these enzymes emerged from a common ancestor and were essential in the development of metabolic pathways involved in energy transduction.}, }
@article {pmid28088333, year = {2017}, author = {Baffy, G}, title = {Mitochondrial uncoupling in cancer cells: Liabilities and opportunities.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1858}, number = {8}, pages = {655-664}, doi = {10.1016/j.bbabio.2017.01.005}, pmid = {28088333}, issn = {0005-2728}, mesh = {Animals ; Antineoplastic Agents/pharmacokinetics ; Cell Hypoxia ; Cell Line, Tumor ; Cellular Reprogramming ; Drug Resistance, Neoplasm/physiology ; Drug Synergism ; Energy Metabolism ; Humans ; Mitochondria/drug effects/*metabolism ; Mitochondrial Uncoupling Proteins/*physiology ; Models, Biological ; Neoplasm Proteins/physiology ; Neoplasms/drug therapy/*metabolism ; Oxidative Phosphorylation/drug effects ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; Symbiosis ; Uncoupling Agents/pharmacology/therapeutic use ; }, abstract = {Acquisition of the endosymbiotic ancestor of mitochondria was a critical event in eukaryote evolution. Mitochondria offered an unparalleled source of metabolic energy through oxidative phosphorylation and allowed the development of multicellular life. However, as molecular oxygen had become the terminal electron acceptor in most eukaryotic cells, the electron transport chain proved to be the largest intracellular source of superoxide, contributing to macromolecular injury, aging, and cancer. Hence, the 'contract of endosymbiosis' represents a compromise between the possibilities and perils of multicellular life. Uncoupling proteins (UCPs), a group of the solute carrier family of transporters, may remove some of the physiologic constraints that link mitochondrial respiration and ATP synthesis by mediating inducible proton leak and limiting oxidative cell injury. This important property makes UCPs an ancient partner in the metabolic adaptation of cancer cells. Efforts are underway to explore the therapeutic opportunities stemming from the intriguing relationship of UCPs and cancer. This article is part of a Special Issue entitled Mitochondria in Cancer, edited by Giuseppe Gasparre, Rodrigue Rossignol and Pierre Sonveaux.}, }
@article {pmid28087774, year = {2017}, author = {Muñoz-Gómez, SA and Wideman, JG and Roger, AJ and Slamovits, CH}, title = {The Origin of Mitochondrial Cristae from Alphaproteobacteria.}, journal = {Molecular biology and evolution}, volume = {34}, number = {4}, pages = {943-956}, doi = {10.1093/molbev/msw298}, pmid = {28087774}, issn = {1537-1719}, mesh = {Alphaproteobacteria/*genetics/metabolism ; Biological Evolution ; Evolution, Molecular ; Membrane Proteins/genetics ; Mitochondria/*genetics/metabolism/*ultrastructure ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/genetics ; Phylogeny ; Protein Binding ; Symbiosis/genetics ; }, abstract = {Mitochondria are the respiratory organelles of eukaryotes and their evolutionary history is deeply intertwined with that of eukaryotes. The compartmentalization of respiration in mitochondria occurs within cristae, whose evolutionary origin has remained unclear. Recent discoveries, however, have revived the old notion that mitochondrial cristae could have had a pre-endosymbiotic origin. Mitochondrial cristae are likely homologous to the intracytoplasmic membranes (ICMs) used by diverse alphaproteobacteria for harnessing energy. Because the Mitochondrial Contact site and Cristae Organizing System (MICOS) that controls the development of cristae evolved from a simplified version that is phylogenetically restricted to Alphaproteobacteria (alphaMICOS), ICMs most probably transformed into cristae during the endosymbiotic origin of mitochondria. This inference is supported by the sequence and structural similarities between MICOS and alphaMICOS, and the expression pattern and cellular localization of alphaMICOS. Given that cristae and ICMs develop similarly, alphaMICOS likely functions analogously to mitochondrial MICOS by culminating ICM development with the creation of tubular connections and membrane contact sites at the alphaproteobacterial envelope. Mitochondria thus inherited a pre-existing ultrastructure adapted to efficient energy transduction from their alphaproteobacterial ancestors. The widespread nature of purple bacteria among alphaproteobacteria raises the possibility that cristae evolved from photosynthetic ICMs.}, }
@article {pmid28087770, year = {2017}, author = {Konrad, A and Thompson, O and Waterston, RH and Moerman, DG and Keightley, PD and Bergthorsson, U and Katju, V}, title = {Mitochondrial Mutation Rate, Spectrum and Heteroplasmy in Caenorhabditis elegans Spontaneous Mutation Accumulation Lines of Differing Population Size.}, journal = {Molecular biology and evolution}, volume = {34}, number = {6}, pages = {1319-1334}, pmid = {28087770}, issn = {1537-1719}, mesh = {Animals ; Biological Evolution ; Caenorhabditis elegans/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Mutation ; Mutation Accumulation ; Mutation Rate ; Phylogeny ; Phylogeography ; Population Density ; Selection, Genetic/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Mitochondrial genomes of metazoans, given their elevated rates of evolution, have served as pivotal markers for phylogeographic studies and recent phylogenetic events. In order to determine the dynamics of spontaneous mitochondrial mutations in small populations in the absence and presence of selection, we evolved mutation accumulation (MA) lines of Caenorhabditis elegans in parallel over 409 consecutive generations at three varying population sizes of N = 1, 10, and 100 hermaphrodites. The N =1 populations should have a minimal influence of natural selection to provide the spontaneous mutation rate and the expected rate of neutral evolution, whereas larger population sizes should experience increasing intensity of selection. New mutations were identified by Illumina paired-end sequencing of 86 mtDNA genomes across 35 experimental lines and compared with published genomes of natural isolates. The spontaneous mitochondrial mutation rate was estimated at 1.05 × 10-7/site/generation. A strong G/C→A/T mutational bias was observed in both the MA lines and the natural isolates. This suggests that the low G + C content at synonymous sites is the product of mutation bias rather than selection as previously proposed. The mitochondrial effective population size per worm generation was estimated to be 62. Although it was previously concluded that heteroplasmy was rare in C. elegans, the vast majority of mutations in this study were heteroplasmic despite an experimental regime exceeding 400 generations. The frequencies of frameshift and nonsynonymous mutations were negatively correlated with population size, which suggests their deleterious effects on fitness and a potent role for selection in their eradication.}, }
@article {pmid28087421, year = {2017}, author = {Martin, WF}, title = {Physiology, anaerobes, and the origin of mitosing cells 50 years on.}, journal = {Journal of theoretical biology}, volume = {434}, number = {}, pages = {2-10}, doi = {10.1016/j.jtbi.2017.01.004}, pmid = {28087421}, issn = {1095-8541}, mesh = {*Biological Evolution ; Eukaryotic Cells/*cytology/ultrastructure ; Flagella ; Mitochondria ; *Origin of Life ; Prokaryotic Cells ; *Symbiosis ; }, abstract = {Endosymbiotic theory posits that some organelles or structures of eukaryotic cells stem from free-living prokaryotes that became endosymbionts within a host cell. Endosymbiosis has a long and turbulent history of controversy and debate going back over 100 years. The 1967 paper by Lynn Sagan (later Lynn Margulis) forced a reluctant field to take endosymbiotic theory seriously and to incorporate it into the fabric of evolutionary thinking. Margulis envisaged three cellular partners associating in series at eukaryotic origin: the host (an engulfing bacterium), the mitochondrion (a respiring bacterium), and the flagellum (a spirochaete), with lineages descended from that flagellated eukaryote subsequently acquiring plastids from cyanobacteria, but on multiple different occasions in her 1967 account. Today, the endosymbiotic origin of mitochondria and plastids (each single events, the data now say) is uncontested textbook knowledge. The host has been more elusive, recent findings identifying it as a member of the archaea, not as a sister group of the archaea. Margulis's proposal for a spirochaete origin of flagellae was abandoned by everyone except her, because no data ever came around to support the idea. Her 1967 proposal that mitochondria and plastids arose from different endosymbionts was novel. The paper presented an appealing narrative that linked the origin of mitochondria with oxygen in Earth history: cyanobacteria make oxygen, oxygen starts accumulating in the atmosphere about 2.4 billion years ago, oxygen begets oxygen-respiring bacteria that become mitochondria via symbiosis, followed by later (numerous) multiple, independent symbioses involving cyanobacteria that brought photosynthesis to eukaryotes. With the focus on oxygen, Margulis's account of eukaryote origin was however unprepared to accommodate the discovery of mitochondria in eukaryotic anaerobes. Today's oxygen narrative has it that the oceans were anoxic up until about 580 million years ago, while the atmosphere attained modern oxygen levels only about 400 million years ago. Since eukaryotes are roughly 1.6 billion years old, much of eukaryotic evolution took place in low oxygen environments, readily explaining the persistence across eukaryotic supergroups of eukaryotic anaerobes and anaerobic mitochondria at the focus of endosymbiotic theories that came after the 1967 paper.}, }
@article {pmid28087256, year = {2017}, author = {Ekoue, DN and He, C and Diamond, AM and Bonini, MG}, title = {Manganese superoxide dismutase and glutathione peroxidase-1 contribute to the rise and fall of mitochondrial reactive oxygen species which drive oncogenesis.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1858}, number = {8}, pages = {628-632}, pmid = {28087256}, issn = {0005-2728}, support = {R21 CA182103/CA/NCI NIH HHS/United States ; 1R01HL125356/NH/NIH HHS/United States ; R01 HL125356/HL/NHLBI NIH HHS/United States ; R01 CA127943/CA/NCI NIH HHS/United States ; R01 CA101053/CA/NCI NIH HHS/United States ; R01 CA193497/CA/NCI NIH HHS/United States ; }, mesh = {Alleles ; *Cell Transformation, Neoplastic ; Disease Progression ; Glutathione Peroxidase/genetics/*physiology ; Humans ; Hydrogen Peroxide/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/genetics/*physiology ; Neoplasm Proteins/genetics/physiology ; Neoplasms/*enzymology/epidemiology ; Oxidation-Reduction ; Reactive Oxygen Species/*metabolism ; Superoxide Dismutase/genetics/*physiology ; Glutathione Peroxidase GPX1 ; }, abstract = {Reactive oxygen species (ROS) largely originating in the mitochondria play essential roles in the metabolic and (epi)genetic reprogramming of cancer cell evolution towards more aggressive phenotypes. Recent studies have indicated that the activity of superoxide dismutase (SOD2) may promote tumor progression by serving as a source of hydrogen peroxide (H2O2). H2O2 is a form of ROS that is particularly active as a redox agent affecting cell signaling due to its ability to freely diffuse out of the mitochondria and alter redox active amino acid residues on regulatory proteins. Therefore, there is likely a dichotomy whereas SOD2 can be considered a protective antioxidant, as well as a pro-oxidant during cancer progression, with these effects depending on the accumulation and detoxification of H2O2. Glutathione peroxidase-1 GPX1, is a selenium-dependent scavenger of H2O2 which partitions between the mitochondria and the cytosol. Epidemiologic studies indicated that allelic variations in the SOD2 and GPX1 genes alter the distribution and relative concentrations of SOD2 and GPX1 in mitochondria, thereby affecting the dynamic between the production and elimination of H2O2. Experimental and epidemiological evidence supporting a conflicting role of SOD2 in tumor biology, and epidemiological evidence that SOD2 and GPX1 can interact to affect cancer risk and progression indicated that it is the net accumulation of mitochondrial H2O2 (mtH2O2) resulting from of the balance between the activities SOD2 and anti-oxidants such as GPX1 that determines whether SOD2 prevents or promotes oncogenesis. In this review, research supporting the idea that GPX1 is a gatekeeper restraining the oncogenic power of mitochondrial ROS generated by SOD2 is presented. This article is part of a Special Issue entitled Mitochondria in Cancer, edited by Giuseppe Gasparre, Rodrigue Rossignol and Pierre Sonveaux.}, }
@article {pmid28081268, year = {2017}, author = {Li, Z and Ding, B and Zhou, X and Wang, GL}, title = {The Rice Dynamin-Related Protein OsDRP1E Negatively Regulates Programmed Cell Death by Controlling the Release of Cytochrome c from Mitochondria.}, journal = {PLoS pathogens}, volume = {13}, number = {1}, pages = {e1006157}, pmid = {28081268}, issn = {1553-7374}, mesh = {*Apoptosis ; Chromosome Mapping ; Cytochromes c/genetics/*metabolism ; Cytoplasm/metabolism ; Cytosol/metabolism ; Dynamins/genetics/*metabolism ; Gene Expression ; Genes, Reporter ; Mitochondria/enzymology/ultrastructure ; Mutation ; Oryza/genetics/*physiology/ultrastructure ; Phenotype ; Phylogeny ; Plant Leaves/genetics/physiology ; Plant Proteins/genetics/metabolism ; Recombinant Fusion Proteins ; Two-Hybrid System Techniques ; }, abstract = {Programmed cell death (PCD) mediated by mitochondrial processes has emerged as an important mechanism for plant development and responses to abiotic and biotic stresses. However, the role of translocation of cytochrome c from the mitochondria to the cytosol during PCD remains unclear. Here, we demonstrate that the rice dynamin-related protein 1E (OsDRP1E) negatively regulates PCD by controlling mitochondrial structure and cytochrome c release. We used a map-based cloning strategy to isolate OsDRP1E from the lesion mimic mutant dj-lm and confirmed that the E409V mutation in OsDRP1E causes spontaneous cell death in rice. Pathogen inoculation showed that dj-lm significantly enhances resistance to fungal and bacterial pathogens. Functional analysis of the E409V mutation showed that the mutant protein impairs OsDRP1E self-association and formation of a higher-order complex; this in turn reduces the GTPase activity of OsDRP1E. Furthermore, confocal microscopy showed that the E409V mutation impairs localization of OsDRP1E to the mitochondria. The E409V mutation significantly affects the morphogenesis of cristae in mitochondria and causes the abnormal release of cytochrome c from mitochondria into cytoplasm. Taken together, our results demonstrate that the mitochondria-localized protein OsDRP1E functions as a negative regulator of cytochrome c release and PCD in plants.}, }
@article {pmid28076891, year = {2017}, author = {Uehling, J and Gryganskyi, A and Hameed, K and Tschaplinski, T and Misztal, PK and Wu, S and Desirò, A and Vande Pol, N and Du, Z and Zienkiewicz, A and Zienkiewicz, K and Morin, E and Tisserant, E and Splivallo, R and Hainaut, M and Henrissat, B and Ohm, R and Kuo, A and Yan, J and Lipzen, A and Nolan, M and LaButti, K and Barry, K and Goldstein, AH and Labbé, J and Schadt, C and Tuskan, G and Grigoriev, I and Martin, F and Vilgalys, R and Bonito, G}, title = {Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {2964-2983}, doi = {10.1111/1462-2920.13669}, pmid = {28076891}, issn = {1462-2920}, mesh = {Animals ; Base Sequence ; Burkholderiaceae/*genetics/metabolism/physiology ; Carbohydrate Metabolism/*genetics ; Evolution, Molecular ; Genome, Bacterial/*genetics ; Genome, Fungal/*genetics ; Lipid Metabolism/*genetics ; Metabolic Networks and Pathways/genetics ; Metagenome/genetics ; Mortierella/*genetics/isolation &amp; purification/physiology ; Phylogeny ; Sequence Analysis, DNA ; Symbiosis/*genetics ; }, abstract = {Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well-known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. We sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within a lineage of endofungal symbionts that are sister clade to Burkholderia. The genome of M. elongata strain AG77 features a core set of primary metabolic pathways for degradation of simple carbohydrates and lipid biosynthesis, while the M. cysteinexigens (AG77) genome is reduced in size and function. Experiments using antibiotics to cure the endobacterium from the host demonstrate that the fungal host metabolism is highly modulated by presence/absence of M. cysteinexigens. Independent comparative phylogenomic analyses of fungal and bacterial genomes are consistent with an ancient origin for M. elongata - M. cysteinexigens symbiosis, most likely over 350 million years ago and concomitant with the terrestrialization of Earth and diversification of land fungi and plants.}, }
@article {pmid28072865, year = {2017}, author = {Mier, P and Pérez-Pulido, AJ and Reynaud, EG and Andrade-Navarro, MA}, title = {Reading the Evolution of Compartmentalization in the Ribosome Assembly Toolbox: The YRG Protein Family.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0169750}, pmid = {28072865}, issn = {1932-6203}, mesh = {Animals ; Archaeal Proteins/chemistry/genetics/metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Cell Compartmentation/*genetics ; *Evolution, Molecular ; Fungal Proteins/chemistry/genetics/metabolism ; GTP Phosphohydrolases/chemistry/*genetics/metabolism ; Protein Transport ; Ribosomes/genetics/*metabolism ; }, abstract = {Reconstructing the transition from a single compartment bacterium to a highly compartmentalized eukaryotic cell is one of the most studied problems of evolutionary cell biology. However, timing and details of the establishment of compartmentalization are unclear and difficult to assess. Here, we propose the use of molecular markers specific to cellular compartments to set up a framework to advance the understanding of this complex intracellular process. Specifically, we use a protein family related to ribosome biogenesis, YRG (YlqF related GTPases), whose evolution is linked to the establishment of cellular compartments, leveraging the current genomic data. We analyzed orthologous proteins of the YRG family in a set of 171 proteomes for a total of 370 proteins. We identified ten YRG protein subfamilies that can be associated to six subcellular compartments (nuclear bodies, nucleolus, nucleus, cytosol, mitochondria, and chloroplast), and which were found in archaeal, bacterial and eukaryotic proteomes. Our analysis reveals organism streamlining related events in specific taxonomic groups such as Fungi. We conclude that the YRG family could be used as a compartmentalization marker, which could help to trace the evolutionary path relating cellular compartments with ribosome biogenesis.}, }
@article {pmid28065928, year = {2017}, author = {Gonçalves-Souza, P and Schlindwein, C and Dötterl, S and Paiva, EA}, title = {Unveiling the osmophores of Philodendron adamantinum (Araceae) as a means to understanding interactions with pollinators.}, journal = {Annals of botany}, volume = {119}, number = {4}, pages = {533-543}, pmid = {28065928}, issn = {1095-8290}, mesh = {Animals ; Coleoptera ; Flowers/anatomy &amp; histology/metabolism/physiology/ultrastructure ; Gas Chromatography-Mass Spectrometry ; Microscopy, Electron ; Philodendron/*anatomy &amp; histology/physiology ; *Pollination/physiology ; Volatile Organic Compounds/analysis/metabolism ; }, abstract = {BACKGROUND AND AIMS: Araceae species pollinated by nocturnal Cyclocephalini beetles attract their pollinators by inflorescence scents. In Philodendron , despite the intense odour, the osmophores exhibit no definite morphological identity, making them difficult to locate. This may explain why structural studies of the scent-releasing tissue are not available so far.<br><br>METHODS: Several approaches were employed for locating and understanding the osmophores of Philodendron adamantinum . A sensory test allowed other analyses to be restricted to fertile and sterile stamens as odour production sites. Stamens were studied under light and electron microscopy. Dynamic headspace and gas chromatography-mass spectrometry were used to collect and analyse scents from different zones of the inflorescence.<br><br>KEY RESULTS: The epidermal cells of the distal portion of fertile stamens and staminodes are papillose and, similar to the parenchyma cells of this region, have dense cytoplasm and large nuclei. In these cells, the composition of organelles is compatible with secretory activity, especially the great number of mitochondria and plastids. In this portion, lipid droplets that are consumed concomitantly with the release of odour were observed. Quantitative scent analyses revealed that the scent, with a predominance of dihydro-&#x3b2;-ionone, is mainly emitted by the fertile and sterile staminate zones of the spadix. An amorphous substance in the stomata pores indicates that the components are secreted and volatilized outside of the osmophore under thermogenic heat.<br><br>CONCLUSIONS: Despite the difficulty in locating osmophores in the absence of morphological identity and inefficiency of neutral red staining, the osmophores of P. adamantinum have some features expected for these structures. The results indicate a functional link between thermogenesis and volatilization of osmophore secretions to produce olfactory signals for attracting specialized beetle pollinators. These first experimental data about the precise location of osmophores in Philodendron will stimulate studies in related species that will allow future comparison and the establishment of patterns of functional morphology.}, }
@article {pmid28059116, year = {2017}, author = {Wang, Q and Zhang, C and Wang, C and Qian, Y and Li, Z and Hong, J and Zhou, X}, title = {Further characterization of Maize chlorotic mottle virus and its synergistic interaction with Sugarcane mosaic virus in maize.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {39960}, pmid = {28059116}, issn = {2045-2322}, mesh = {China ; Chloroplasts/physiology/virology ; Gammaherpesvirinae/classification/genetics/isolation &amp; purification/*pathogenicity ; Mitochondria/virology ; Photosynthesis ; Phylogeny ; Plant Diseases/*virology ; Potyvirus/classification/genetics/isolation &amp; purification/*pathogenicity ; Zea mays/*virology ; }, abstract = {Maize chlorotic mottle virus (MCMV) was first reported in maize in China in 2009. In this study we further analyzed the epidemiology of MCMV and corn lethal necrosis disease (CLND) in China. We determined that CLND observed in China was caused by co-infection of MCMV and sugarcane mosaic virus (SCMV). Phylogenetic analysis using four full-length MCMV cDNA sequences obtained in this study and the available MCMV sequences retrieved from GenBank indicated that Chinese MCMV isolates were derived from the same source. To screen for maize germplasm resistance against MCMV infection, we constructed an infectious clone of MCMV isolate YN2 (pMCMV) and developed an Agrobacterium-mediated injection procedure to allow high throughput inoculations of maize with the MCMV infectious clone. Electron microscopy showed that chloroplast photosynthesis in leaves was significantly impeded by the co-infection of MCMV and SCMV. Mitochondria in the MCMV and SCMV co-infected cells were more severely damaged than in MCMV-infected cells. The results of this study provide further insight into the epidemiology of MCMV in China and shed new light on physiological and cytopathological changes related to CLND in maize.}, }
@article {pmid28057823, year = {2017}, author = {McLaughlin, RN and Malik, HS}, title = {Genetic conflicts: the usual suspects and beyond.}, journal = {The Journal of experimental biology}, volume = {220}, number = {Pt 1}, pages = {6-17}, pmid = {28057823}, issn = {1477-9145}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 GM074108/GM/NIGMS NIH HHS/United States ; K99 GM112941/GM/NIGMS NIH HHS/United States ; P50 GM107632/GM/NIGMS NIH HHS/United States ; R00 GM112941/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Animals ; Biological Evolution ; DNA Transposable Elements ; *Evolution, Molecular ; Gene-Environment Interaction ; *Genome ; Host-Pathogen Interactions ; Humans ; Meiosis ; Models, Genetic ; Selection, Genetic ; }, abstract = {Selfishness is pervasive and manifests at all scales of biology, from societies, to individuals, to genetic elements within a genome. The relentless struggle to seek evolutionary advantages drives perpetual cycles of adaptation and counter-adaptation, commonly referred to as Red Queen interactions. In this review, we explore insights gleaned from molecular and genetic studies of such genetic conflicts, both extrinsic (between genomes) and intrinsic (within genomes or cells). We argue that many different characteristics of selfish genetic elements can be distilled into two types of advantages: an over-replication advantage (e.g. mobile genetic elements in genomes) and a transmission distortion advantage (e.g. meiotic drivers in populations). These two general categories may help classify disparate types of selfish genetic elements.}, }
@article {pmid28054713, year = {2017}, author = {Speijer, D}, title = {Alternating terminal electron-acceptors at the basis of symbiogenesis: How oxygen ignited eukaryotic evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {2}, pages = {}, doi = {10.1002/bies.201600174}, pmid = {28054713}, issn = {1521-1878}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; *Electron Transport ; Energy Metabolism ; Eukaryota/genetics/*metabolism ; Mitochondria/genetics/metabolism ; Oxygen/*metabolism ; *Symbiosis ; }, abstract = {What kind of symbiosis between archaeon and bacterium gave rise to their eventual merger at the origin of the eukaryotes? I hypothesize that conditions favouring bacterial uptake were based on exchange of intermediate carbohydrate metabolites required by recurring changes in availability and use of the two different terminal electron chain acceptors, the bacterial one being oxygen. Oxygen won, and definitive loss of the archaeal membrane potential allowed permanent establishment of the bacterial partner as the proto-mitochondrion, further metabolic integration and highly efficient ATP production. This represents initial symbiogenesis, when crucial eukaryotic traits arose in response to the archaeon-bacterium merger. The attendant generation of internal reactive oxygen species (ROS) gave rise to a myriad of further eukaryotic adaptations, such as extreme mitochondrial genome reduction, nuclei, peroxisomes and meiotic sex. Eukaryotic origins could have started with shuffling intermediate metabolites as is still essential today.}, }
@article {pmid28052087, year = {2017}, author = {Grange, LJ and Smith, CR and Lindsay, DJ and Bentlage, B and Youngbluth, MJ}, title = {High Abundance of the Epibenthic Trachymedusa Ptychogastria polaris Allman, 1878 (Hydrozoa, Trachylina) in Subpolar Fjords along the West Antarctic Peninsula.}, journal = {PloS one}, volume = {12}, number = {1}, pages = {e0168648}, pmid = {28052087}, issn = {1932-6203}, mesh = {Animals ; Antarctic Regions ; Bayes Theorem ; Bays ; Body Size ; *Ecosystem ; Electron Transport Complex IV/metabolism ; *Estuaries ; Geography ; Hydrozoa/anatomy &amp; histology/classification/*physiology ; Image Processing, Computer-Assisted ; Mitochondria/enzymology ; Oceans and Seas ; Phylogeny ; }, abstract = {Medusae can be conspicuous and abundant members of seafloor communities in deep-sea benthic boundary layers. The epibenthic trachymedusa, Ptychogastria polaris Allman, 1878 (Hydrozoa: Trachylina: Ptychogastriidae) occurs in the cold, high latitude systems of both the northern and southern hemispheres, with a circumpolar distribution in Arctic and sub-Arctic areas, and disjunct reports of a few individuals from Antarctica. In January-February 2010, during benthic megafaunal photosurveys in three subpolar fjords along the West Antarctic Peninsula (Andvord, Flandres and Barilari Bays), P. polaris was recorded in Antarctic Peninsula waters. The trachymedusa, identified from megacore-collected specimens, was a common component of the epifauna in the sediment floored basins at 436-725 m depths in Andvord and Flandres Bays, reaching densities up to 13 m-2, with mean densities in individual basins ranging from 0.06 to 4.19 m-2. These densities are 2 to 400-fold higher than previously reported for P. polaris in either the Arctic or Antarctic. This trachymedusa had an aggregated distribution, occurring frequently in Andvord Bay, but was often solitary in Flandres Bay, with a distribution not significantly different from random. Epibenthic individuals were similar in size, typically measuring 15-25 mm in bell diameter. A morphologically similar trachymedusa, presumably the same species, was also observed in the water column near the bottom in all three fjords. This benthopelagic form attained abundances of up to 7 m-2 of seafloor; however, most P. polaris (~ 80%), were observed on soft sediments. Our findings indicate that fjords provide a prime habitat for the development of dense populations of P. polaris, potentially resulting from high and varied food inputs to the fjord floors. Because P. polaris resides in the water column and at the seafloor, large P. polaris populations may contribute significantly to pelagic-benthic coupling in the WAP fjord ecosystems.}, }
@article {pmid28051091, year = {2017}, author = {Freibert, SA and Goldberg, AV and Hacker, C and Molik, S and Dean, P and Williams, TA and Nakjang, S and Long, S and Sendra, K and Bill, E and Heinz, E and Hirt, RP and Lucocq, JM and Embley, TM and Lill, R}, title = {Evolutionary conservation and in vitro reconstitution of microsporidian iron-sulfur cluster biosynthesis.}, journal = {Nature communications}, volume = {8}, number = {}, pages = {13932}, pmid = {28051091}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; 268701/ERC_/European Research Council/International ; }, mesh = {*Biological Evolution ; Cell Nucleus/metabolism ; Cytosol/metabolism ; Fungal Proteins/*biosynthesis/genetics ; Iron-Sulfur Proteins/*biosynthesis/genetics ; Mitochondria/*metabolism ; Pansporablastina/genetics/*metabolism ; Phylogeny ; }, abstract = {Microsporidians are obligate intracellular parasites that have minimized their genome content and sub-cellular structures by reductive evolution. Here, we demonstrate that cristae-deficient mitochondria (mitosomes) of Trachipleistophora hominis are the functional site of iron-sulfur cluster (ISC) assembly, which we suggest is the essential task of these organelles. Cell fractionation, fluorescence imaging and immunoelectron microscopy demonstrate that mitosomes contain a complete pathway for [2Fe-2S] cluster biosynthesis that we biochemically reconstituted using purified mitosomal ISC proteins. The T. hominis cytosolic iron-sulfur protein assembly (CIA) pathway includes the essential Cfd1-Nbp35 scaffold complex that assembles a [4Fe-4S] cluster as shown by spectroscopic methods in vitro. Phylogenetic analyses reveal that the ISC and CIA pathways are predominantly bacterial, but their cytosolic and nuclear target Fe/S proteins are mainly archaeal. This mixed evolutionary history of Fe/S-related proteins and pathways, and their strong conservation among highly reduced parasites, provides compelling evidence for the ancient chimeric ancestry of eukaryotes.}, }
@article {pmid29594864, year = {2017}, author = {Enomoto, M and Nishikawa, T and Siddiqui, N and Chung, S and Ikura, M and Stathopulos, PB}, title = {From Stores to Sinks: Structural Mechanisms of Cytosolic Calcium Regulation.}, journal = {Advances in experimental medicine and biology}, volume = {981}, number = {}, pages = {215-251}, doi = {10.1007/978-3-319-55858-5_10}, pmid = {29594864}, issn = {0065-2598}, support = {MOP-13552//CIHR/Canada ; }, mesh = {Animals ; Calcium/chemistry/*metabolism ; Calcium Channels/chemistry/metabolism ; Calcium Signaling/*physiology ; Cytosol/chemistry/*metabolism ; Endoplasmic Reticulum/chemistry/*metabolism ; Humans ; Inositol 1,4,5-Trisphosphate Receptors/chemistry/metabolism ; Mitochondria, Muscle/chemistry/*metabolism ; Muscle, Skeletal/chemistry/metabolism ; Neoplasm Proteins/chemistry/metabolism ; ORAI1 Protein/chemistry/metabolism ; Stromal Interaction Molecule 1/chemistry/metabolism ; }, abstract = {All eukaryotic cells have adapted the use of the calcium ion (Ca[2+]) as a universal signaling element through the evolution of a toolkit of Ca[2+] sensor, buffer and effector proteins. Among these toolkit components, integral and peripheral proteins decorate biomembranes and coordinate the movement of Ca[2+] between compartments, sense these concentration changes and elicit physiological signals. These changes in compartmentalized Ca[2+] levels are not mutually exclusive as signals propagate between compartments. For example, agonist induced surface receptor stimulation can lead to transient increases in cytosolic Ca[2+] sourced from endoplasmic reticulum (ER) stores; the decrease in ER luminal Ca[2+] can subsequently signal the opening surface channels which permit the movement of Ca[2+] from the extracellular space to the cytosol. Remarkably, the minuscule compartments of mitochondria can function as significant cytosolic Ca[2+] sinks by taking up Ca[2+] in a coordinated manner. In non-excitable cells, inositol 1,4,5 trisphosphate receptors (IP3Rs) on the ER respond to surface receptor stimulation; stromal interaction molecules (STIMs) sense the ER luminal Ca[2+] depletion and activate surface Orai1 channels; surface Orai1 channels selectively permit the movement of Ca[2+] from the extracellular space to the cytosol; uptake of Ca[2+] into the matrix through the mitochondrial Ca[2+] uniporter (MCU) further shapes the cytosolic Ca[2+] levels. Recent structural elucidations of these key Ca[2+] toolkit components have improved our understanding of how they function to orchestrate precise cytosolic Ca[2+] levels for specific physiological responses. This chapter reviews the atomic-resolution structures of IP3R, STIM1, Orai1 and MCU elucidated by X-ray crystallography, electron microscopy and NMR and discusses the mechanisms underlying their biological functions in their respective compartments within the cell.}, }
@article {pmid28034779, year = {2017}, author = {Huang, HJ and Liu, CW and Zhou, X and Zhang, CX and Bao, YY}, title = {A mitochondrial membrane protein is a target for rice ragged stunt virus in its insect vector.}, journal = {Virus research}, volume = {229}, number = {}, pages = {48-56}, doi = {10.1016/j.virusres.2016.12.016}, pmid = {28034779}, issn = {1872-7492}, mesh = {Adenosine Triphosphatases/*genetics/metabolism ; Amino Acid Sequence ; Animals ; Carrier Proteins/*genetics/metabolism ; Gene Expression Regulation ; Glutathione Transferase/genetics/metabolism ; Hemiptera/classification/metabolism/ultrastructure/*virology ; Insect Proteins/*genetics/metabolism ; Insect Vectors/metabolism/ultrastructure/virology ; Membrane Proteins/*genetics/metabolism ; Mitochondria/metabolism/ultrastructure/*virology ; Mitochondrial Proton-Translocating ATPases ; Oryza/parasitology/*virology ; Phylogeny ; Plant Diseases/parasitology/virology ; Protein Binding ; RNA, Small Interfering/genetics/metabolism ; RNA, Viral/genetics/metabolism ; Reoviridae/*genetics/growth &amp; development/metabolism ; Salivary Glands/metabolism/ultrastructure/virology ; Sequence Alignment ; Two-Hybrid System Techniques ; Viral Load ; Viral Nonstructural Proteins/*genetics/metabolism ; Virion/genetics/growth &amp; development/metabolism ; }, abstract = {Rice ragged stunt virus (RRSV; Reoviridae) is exclusively transmitted by the brown planthopper Nilaparvata lugens in a persistent-propagative manner. It is understood that RNA viral proliferation is associated with the intracellular membranes of the insect host cells. However, the molecular mechanisms of the interaction between the RRSV proliferation and the intracellular membranes remain essentially unknown. It will be of great interest to determine whether RRSV protein(s) directly interact with intracellular membrane components of its host cells. In this study, we identified a RRSV nonstructural protein Pns10 interacting with a host oligomycin-sensitivity conferral protein (OSCP) using yeast two-hybrid system. The interaction between RRSV Pns10 and N. lugens OSCP was verified by a glutathione S-transferase pull-down assay. Confocal miscopy revealed colocalization of these two proteins in the cytoplasm of the salivary gland cells during the viral infection. The virions were further detected in the mitochondria under confocal miscopy and transmission electron microscopy combined with western blotting assay. This is the first observation that RRSV protein has a direct link with mitochondria. Suppressing OSCP gene expression by RNA interference notably decreased the viral loads in RRSV-infected insects. These findings revealed novel aspects of a viral protein in targeting the host mitochondrial membrane and provide insights concerning the mitochondrial membrane protein-based virus proliferation mode in the insect vector.}, }
@article {pmid28034628, year = {2017}, author = {Seixas, VC and Russo, CA and Paiva, PC}, title = {Mitochondrial genome of the Christmas tree worm Spirobranchus giganteus (Annelida: Serpulidae) reveals a high substitution rate among annelids.}, journal = {Gene}, volume = {605}, number = {}, pages = {43-53}, doi = {10.1016/j.gene.2016.12.024}, pmid = {28034628}, issn = {1879-0038}, mesh = {Animals ; Annelida/classification/*genetics ; Base Composition ; Biological Evolution ; Chromosome Mapping ; DNA, Mitochondrial/*genetics ; Gene Order ; Gene Rearrangement ; *Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Here we describe, for the first time, the mitochondrial genome of Spirobranchus giganteus (Annelida: Serpulidae) and compare it with all available annelid mitogenomes. The entire mitogenome has 22,058bp in length and bears 12 protein-coding genes (the ATP8 gene is missing), two rRNA, and 24 tRNA genes. The nucleotide composition and GC-skew are surprisingly different from those reported for other annelids. In addition, the pairwise genetic distances between the mitogenomes of S. giganteus and other annelids are higher than the distances for all annelid taxa analyzed. This result is consistent with a faster rate of mitochondrial sequence evolution in S. giganteus, which may explain the difficulty in obtaining PCR products with the available primers. The mitochondrial gene order of S. giganteus was remarkably different not only from that of the Sedentaria lineage, which includes S. giganteus, but also from the mitochondrial gene order of other major annelid lineages. The mitogenome of S. giganteus has no repetitive motifs despite its long control region (4769bp), but genes are shorter and have a lower AT content than other members of Annelida. Finally, we show that mitochondrial gene order rearrangements can directly correlate to variations in gene length.}, }
@article {pmid28033407, year = {2016}, author = {Vogler, RE and Beltramino, AA and Strong, EE and Rumi, A and Peso, JG}, title = {Insights into the Evolutionary History of an Extinct South American Freshwater Snail Based on Historical DNA.}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0169191}, pmid = {28033407}, issn = {1932-6203}, mesh = {Animals ; DNA/*genetics ; *Evolution, Molecular ; *Extinction, Biological ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; Snails/*genetics ; }, abstract = {Highly oxygenated freshwater habitats in the High Paraná River (Argentina-Paraguay) were home to highly endemic snails of the genus Aylacostoma, which face extinction owing to the impoundment of the Yacyretá Reservoir in the 1990s. Two species, A. chloroticum and A. brunneum, are currently included in an ongoing ex situ conservation programme, whereas A. guaraniticum and A. stigmaticum are presumed extinct. Consequently, the validity and affinities of the latter two have remained enigmatic. Here, we provide the first molecular data on the extinct A. stigmaticum by means of historical DNA analysis. We describe patterns of molecular evolution based on partial sequences of the mitochondrial 12S ribosomal RNA gene from the extinct species and from those being bred within the ex situ programme. We further use this gene to derive a secondary structure model, to examine the specific status of A. stigmaticum and to explore the evolutionary history of these snails. The secondary structure model based on A. stigmaticum revealed that most polymorphic sites are located in unpaired regions. Our results support the view that the mitochondrial 12S region is an efficient marker for the discrimination of species, and the extinct A. stigmaticum is recognized here as a distinct evolutionary genetic species. Molecular phylogenetic analyses revealed a sister group relationship between A. chloroticum and A. brunneum, and estimated divergence times suggest that diversification of Aylacostoma in the High Paraná River might have started in the late Miocene via intra-basin speciation due to a past marine transgression. Finally, our findings reveal that DNA may be obtained from dried specimens at least 80 years after their collection, and confirms the feasibility of extracting historical DNA from museum collections for elucidating evolutionary patterns and processes in gastropods.}, }
@article {pmid28031475, year = {2017}, author = {Teardo, E and Carraretto, L and Wagner, S and Formentin, E and Behera, S and De Bortoli, S and Larosa, V and Fuchs, P and Lo Schiavo, F and Raffaello, A and Rizzuto, R and Costa, A and Schwarzländer, M and Szabò, I}, title = {Physiological Characterization of a Plant Mitochondrial Calcium Uniporter in Vitro and in Vivo.}, journal = {Plant physiology}, volume = {173}, number = {2}, pages = {1355-1370}, pmid = {28031475}, issn = {1532-2548}, mesh = {Arabidopsis/cytology/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Calcium/metabolism ; Calcium Channels/genetics/*metabolism ; Calcium-Binding Proteins/metabolism ; Gene Expression Regulation, Plant ; Mitochondria/genetics/metabolism/ultrastructure ; Mutation ; Phylogeny ; Plant Proteins/genetics ; Plant Roots/genetics/metabolism ; }, abstract = {Over the recent years, several proteins that make up the mitochondrial calcium uniporter complex (MCUC) mediating Ca[2+]uptake into the mitochondrial matrix have been identified in mammals, including the channel-forming protein MCU. Although six MCU gene homologs are conserved in the model plant Arabidopsis (Arabidopsis thaliana) in which mitochondria can accumulate Ca[2+], a functional characterization of plant MCU homologs has been lacking. Using electrophysiology, we show that one isoform, AtMCU1, gives rise to a Ca[2+]-permeable channel activity that can be observed even in the absence of accessory proteins implicated in the formation of the active mammalian channel. Furthermore, we provide direct evidence that AtMCU1 activity is sensitive to the mitochondrial calcium uniporter inhibitors Ruthenium Red and Gd[3+], as well as to the Arabidopsis protein MICU, a regulatory MCUC component. AtMCU1 is prevalently expressed in roots, localizes to mitochondria, and its absence causes mild changes in Ca[2+] dynamics as assessed by in vivo measurements in Arabidopsis root tips. Plants either lacking or overexpressing AtMCU1 display root mitochondria with altered ultrastructure and show shorter primary roots under restrictive growth conditions. In summary, our work adds evolutionary depth to the investigation of mitochondrial Ca[2+] transport, indicates that AtMCU1, together with MICU as a regulator, represents a functional configuration of the plant mitochondrial Ca[2+] uptake complex with differences to the mammalian MCUC, and identifies a new player of the intracellular Ca[2+] regulation network in plants.}, }
@article {pmid28029387, year = {2016}, author = {Gracielle, IM and Tidon, R and Báo, SN}, title = {Structure and ultrastructure of spermatozoon in six species of Drosophilidae (Diptera).}, journal = {Tissue &amp; cell}, volume = {48}, number = {6}, pages = {596-604}, doi = {10.1016/j.tice.2016.10.001}, pmid = {28029387}, issn = {1532-3072}, mesh = {Acrosome/ultrastructure ; Animals ; Axoneme/*ultrastructure ; Cell Nucleus/genetics/ultrastructure ; Drosophila/genetics/*ultrastructure ; Male ; Mitochondria/ultrastructure ; *Phylogeny ; Spermatozoa/*ultrastructure ; Testis/ultrastructure ; }, abstract = {The Drosophilidae family is formed by Brachycera Diptera distributed widely across different regions of the planet. It is composed of about 4000 species, 304 of which are found in Brazil. The objective of this work was to characterize morphologically the structure of the male internal reproductive apparatus and the ultrastructure of the spermatozoon in four Neotropical (Drosophila cardini, D. mercatorum, D. nebulosa and D. sturtevanti) and two invasive (D. simulans and Zaprionus indianus) species of drosophilids. The structural aspect of the internal reproductive apparatus corresponds with that described for other drosophilids; however, there are differences in the size and coloration of the structures, such as the testes, in each species analyzed. The spermatozoon of these species was seen to be long and fine, presenting morphological variation. The ultrastructure of the spermatozoon revealed that the morphological pattern is similar to that found in the majority of insects. The head region presents a nucleus with condensed chromatin and the acrosome positioned laterally to the nucleus. In the tail region, the axoneme presents the 9+9+2 pattern commonly described for other species of Diptera. The species presented differences regarding the shape and size of the mitochondrial derivatives. Cytochemical analysis using EPTA also revealed differences in terms of the location of the basic proteins in the mitochondrial derivates. The results obtained contribute to expanding the database for the Drosophilidae family, providing information that may contribute to intra- and inter-specific identification and supplying phylogenetic analyses.}, }
@article {pmid28027966, year = {2017}, author = {Robicheau, BM and Breton, S and Stewart, DT}, title = {Sequence motifs associated with paternal transmission of mitochondrial DNA in the horse mussel, Modiolus modiolus (Bivalvia: Mytilidae).}, journal = {Gene}, volume = {605}, number = {}, pages = {32-42}, doi = {10.1016/j.gene.2016.12.025}, pmid = {28027966}, issn = {1879-0038}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Female ; *Genome, Mitochondrial ; *Inheritance Patterns ; Male ; Mitochondria/genetics ; Mytilidae/classification/*genetics ; Nucleic Acid Conformation ; *Nucleotide Motifs ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Spermatozoa/metabolism ; }, abstract = {In the majority of metazoans paternal mitochondria represent evolutionary dead-ends. In many bivalves, however, this paradigm does not hold true; both maternal and paternal mitochondria are inherited. Herein, we characterize maternal and paternal mitochondrial control regions of the horse mussel, Modiolus modiolus (Bivalvia: Mytilidae). The maternal control region is 808bp long, while the paternal control region is longer at 2.3kb. We hypothesize that the size difference is due to a combination of repeated duplications within the control region of the paternal mtDNA genome, as well as an evolutionarily ancient recombination event between two sex-associated mtDNA genomes that led to the insertion of a second control region sequence in the genome that is now transmitted via males. In a comparison to other mytilid male control regions, we identified two evolutionarily Conserved Motifs, CMA and CMB, associated with paternal transmission of mitochondrial DNA. CMA is characterized by a conserved purine/pyrimidine pattern, while CMB exhibits a specific 13bp nucleotide string within a stem and loop structure. The identification of motifs CMA and CMB in M. modiolus extends our understanding of Sperm Transmission Elements (STEs) that have recently been identified as being associated with the paternal transmission of mitochondria in marine bivalves.}, }
@article {pmid28025543, year = {2016}, author = {Ichinose, M and Sugita, M}, title = {RNA Editing and Its Molecular Mechanism in Plant Organelles.}, journal = {Genes}, volume = {8}, number = {1}, pages = {}, pmid = {28025543}, issn = {2073-4425}, abstract = {RNA editing by cytidine (C) to uridine (U) conversions is widespread in plant mitochondria and chloroplasts. In some plant taxa, "reverse" U-to-C editing also occurs. However, to date, no instance of RNA editing has yet been reported in green algae and the complex thalloid liverworts. RNA editing may have evolved in early land plants 450 million years ago. However, in some plant species, including the liverwort, Marchantia polymorpha, editing may have been lost during evolution. Most RNA editing events can restore the evolutionarily conserved amino acid residues in mRNAs or create translation start and stop codons. Therefore, RNA editing is an essential process to maintain genetic information at the RNA level. Individual RNA editing sites are recognized by plant-specific pentatricopeptide repeat (PPR) proteins that are encoded in the nuclear genome. These PPR proteins are characterized by repeat elements that bind specifically to RNA sequences upstream of target editing sites. In flowering plants, non-PPR proteins also participate in multiple RNA editing events as auxiliary factors. C-to-U editing can be explained by cytidine deamination. The proteins discovered to date are important factors for RNA editing but a bona fide RNA editing enzyme has yet to be identified.}, }
@article {pmid28025278, year = {2017}, author = {Fabre, PH and Upham, NS and Emmons, LH and Justy, F and Leite, YL and Carolina Loss, A and Orlando, L and Tilak, MK and Patterson, BD and Douzery, EJ}, title = {Mitogenomic Phylogeny, Diversification, and Biogeography of South American Spiny Rats.}, journal = {Molecular biology and evolution}, volume = {34}, number = {3}, pages = {613-633}, doi = {10.1093/molbev/msw261}, pmid = {28025278}, issn = {1537-1719}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Biological Evolution ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Phylogeography/methods ; Rats ; Rodentia/*genetics ; Sequence Analysis, DNA/methods ; South America ; }, abstract = {Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorinae), and 5 genera of West Indian hutias (Capromyidae) relatives. Here, we used Illumina shotgun sequencing to assemble 38 new complete mitogenomes, establishing Echimyidae, and Capromyidae as the first major rodent families to be completely sequenced at the genus-level for their mitochondrial DNA. Combining mitogenomes and nuclear exons, we inferred a robust phylogenetic framework that reveals several newly supported nodes as well as the tempo of the higher level diversification of these rodents. Incorporating the full generic diversity of extant echimyids leads us to propose a new higher level classification of two subfamilies: Euryzygomatomyinae and Echimyinae. Of note, the enigmatic Carterodon displays fast-evolving mitochondrial and nuclear sequences, with a long branch that destabilizes the deepest divergences of the echimyid tree, thereby challenging the sister-group relationship between Capromyidae and Euryzygomatomyinae. Biogeographical analyses involving higher level taxa show that several vicariant and dispersal events impacted the evolutionary history of echimyids. The diversification history of Echimyidae seems to have been influenced by two major historical factors, namely (1) recurrent connections between Atlantic and Amazonian Forests and (2) the Northern uplift of the Andes.}, }
@article {pmid28025277, year = {2017}, author = {Christie, JR and Beekman, M}, title = {Uniparental Inheritance Promotes Adaptive Evolution in Cytoplasmic Genomes.}, journal = {Molecular biology and evolution}, volume = {34}, number = {3}, pages = {677-691}, pmid = {28025277}, issn = {1537-1719}, mesh = {Adaptation, Biological/*genetics ; Biological Evolution ; Computer Simulation ; DNA, Mitochondrial/*genetics ; Eukaryota/genetics ; Evolution, Molecular ; Genome ; Mitochondria/genetics ; *Models, Genetic ; Mutation ; *Mutation Rate ; Plastids/genetics ; Reproduction/genetics ; }, abstract = {Eukaryotes carry numerous asexual cytoplasmic genomes (mitochondria and plastids). Lacking recombination, asexual genomes should theoretically suffer from impaired adaptive evolution. Yet, empirical evidence indicates that cytoplasmic genomes experience higher levels of adaptive evolution than predicted by theory. In this study, we use a computational model to show that the unique biology of cytoplasmic genomes-specifically their organization into host cells and their uniparental (maternal) inheritance-enable them to undergo effective adaptive evolution. Uniparental inheritance of cytoplasmic genomes decreases competition between different beneficial substitutions (clonal interference), promoting the accumulation of beneficial substitutions. Uniparental inheritance also facilitates selection against deleterious cytoplasmic substitutions, slowing Muller's ratchet. In addition, uniparental inheritance generally reduces genetic hitchhiking of deleterious substitutions during selective sweeps. Overall, uniparental inheritance promotes adaptive evolution by increasing the level of beneficial substitutions relative to deleterious substitutions. When we assume that cytoplasmic genome inheritance is biparental, decreasing the number of genomes transmitted during gametogenesis (bottleneck) aids adaptive evolution. Nevertheless, adaptive evolution is always more efficient when inheritance is uniparental. Our findings explain empirical observations that cytoplasmic genomes-despite their asexual mode of reproduction-can readily undergo adaptive evolution.}, }
@article {pmid28025274, year = {2017}, author = {Bourguignon, T and Lo, N and Šobotník, J and Ho, SY and Iqbal, N and Coissac, E and Lee, M and Jendryka, MM and Sillam-Dussès, D and Krížková, B and Roisin, Y and Evans, TA}, title = {Mitochondrial Phylogenomics Resolves the Global Spread of Higher Termites, Ecosystem Engineers of the Tropics.}, journal = {Molecular biology and evolution}, volume = {34}, number = {3}, pages = {589-597}, doi = {10.1093/molbev/msw253}, pmid = {28025274}, issn = {1537-1719}, mesh = {Animal Distribution ; Animals ; DNA, Mitochondrial/genetics ; Ecosystem ; Genome, Mitochondrial ; Introduced Species ; Isoptera/*genetics/growth &amp; development ; Mitochondria/genetics ; Phylogeny ; Phylogeography/methods ; Rainforest ; }, abstract = {The higher termites (Termitidae) are keystone species and ecosystem engineers. They have exceptional biomass and play important roles in decomposition of dead plant matter, in soil manipulation, and as the primary food for many animals, especially in the tropics. Higher termites are most diverse in rainforests, with estimated origins in the late Eocene (∼54 Ma), postdating the breakup of Pangaea and Gondwana when most continents became separated. Since termites are poor fliers, their origin and spread across the globe requires alternative explanation. Here, we show that higher termites originated 42-54 Ma in Africa and subsequently underwent at least 24 dispersal events between the continents in two main periods. Using phylogenetic analyses of mitochondrial genomes from 415 species, including all higher termite taxonomic and feeding groups, we inferred 10 dispersal events to South America and Asia 35-23 Ma, coinciding with the sharp decrease in global temperature, sea level, and rainforest cover in the Oligocene. After global temperatures increased, 23-5 Ma, there was only one more dispersal to South America but 11 to Asia and Australia, and one dispersal back to Africa. Most of these dispersal events were transoceanic and might have occurred via floating logs. The spread of higher termites across oceans was helped by the novel ecological opportunities brought about by environmental and ecosystem change, and led termites to become one of the few insect groups with specialized mammal predators. This has parallels with modern invasive species that have been able to thrive in human-impacted ecosystems.}, }
@article {pmid28017858, year = {2017}, author = {Podsiadlowski, L and Gamauf, A and Töpfer, T}, title = {Revising the phylogenetic position of the extinct Mascarene Parrot Mascarinus mascarin (Linnaeus 1771) (Aves: Psittaciformes: Psittacidae).}, journal = {Molecular phylogenetics and evolution}, volume = {107}, number = {}, pages = {499-502}, doi = {10.1016/j.ympev.2016.12.022}, pmid = {28017858}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Cytochromes b/genetics ; Genetic Loci ; Mitochondria/genetics ; Parrots/*classification ; *Phylogeny ; Polymorphism, Genetic ; Sequence Alignment ; Species Specificity ; }, abstract = {The phylogenetic position of the extinct Mascarene Parrot Mascarinus mascarin from La Réunion has been unresolved for centuries. A recent molecular study unexpectedly placed M. mascarin within the clade of phenotypically very different Vasa parrots Coracopsis. Based on DNA extracted from the only other preserved Mascarinus specimen, we show that the previously obtained cytb sequence is probably an artificial composite of partial sequences from two other parrot species and that M. mascarin is indeed a part of the Psittacula diversification, placed close to P. eupatria and P. wardi.}, }
@article {pmid28012957, year = {2017}, author = {De Silva, TN and Peterson, AT and Bates, JM and Fernando, SW and Girard, MG}, title = {Phylogenetic relationships of weaverbirds (Aves: Ploceidae): A first robust phylogeny based on mitochondrial and nuclear markers.}, journal = {Molecular phylogenetics and evolution}, volume = {109}, number = {}, pages = {21-32}, doi = {10.1016/j.ympev.2016.12.013}, pmid = {28012957}, issn = {1095-9513}, mesh = {Animals ; Avian Proteins/genetics ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genetic Markers ; Genetic Speciation ; Mitochondria/genetics ; Multilocus Sequence Typing ; Passeriformes/*genetics ; Phylogeny ; }, abstract = {Weaverbirds are a diverse passerine group with species diversity concentrated in sub-Saharan Africa. No comprehensive phylogenetic hypothesis regarding relationships of weaverbirds has been produced, however, so we developed a first extensive phylogeny for the family Ploceidae, based on a multilocus dataset of three mitochondrial loci and four nuclear markers. Analysis of these data offered strong support for monophyly of the family and revealed seven distinct clades within Ploceidae. A major feature of our results is broad polyphyly of Ploceus: Asian Ploceus species should retain the generic name, whereas African Ploceus, together with Anaplectes, should be placed in Malimbus. In light of deep divergence, we assign the Malagasy Ploceus species to their own genus, Nelicurvius. Divergence time analysis based on DNA substitution rates suggests a mid-Miocene origin of the family. This study lays a foundation for an array of future studies of character evolution, biogeography, and evolutionary history of the family.}, }
@article {pmid28009453, year = {2017}, author = {Alkalaeva, E and Mikhailova, T}, title = {Reassigning stop codons via translation termination: How a few eukaryotes broke the dogma.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {39}, number = {3}, pages = {}, doi = {10.1002/bies.201600213}, pmid = {28009453}, issn = {1521-1878}, mesh = {3' Untranslated Regions ; Animals ; *Codon, Terminator ; Eukaryota/genetics ; Evolution, Molecular ; Humans ; *Peptide Chain Termination, Translational ; Peptide Termination Factors/physiology ; }, abstract = {The genetic code determines how amino acids are encoded within mRNA. It is universal among the vast majority of organisms, although several exceptions are known. Variant genetic codes are found in ciliates, mitochondria, and numerous other organisms. All revealed genetic codes (standard and variant) have at least one codon encoding a translation stop signal. However, recently two new genetic codes with a reassignment of all three stop codons were revealed in studies examining the protozoa transcriptomes. Here, we discuss this finding and the recent studies of variant genetic codes in eukaryotes. We consider the possible molecular mechanisms allowing the use of certain codons as sense and stop signals simultaneously. The results obtained by studying these amazing organisms represent a new and exciting insight into the mechanism of stop codon decoding in eukaryotes. Also see the video abstract here.}, }
@article {pmid28007567, year = {2017}, author = {Cornils, A and Wend-Heckmann, B and Held, C}, title = {Global phylogeography of Oithona similis s.l. (Crustacea, Copepoda, Oithonidae) - A cosmopolitan plankton species or a complex of cryptic lineages?.}, journal = {Molecular phylogenetics and evolution}, volume = {107}, number = {}, pages = {473-485}, doi = {10.1016/j.ympev.2016.12.019}, pmid = {28007567}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Copepoda/*classification ; Electron Transport Complex IV/genetics ; Genetic Variation ; Haplotypes/genetics ; *Internationality ; Mitochondria/genetics ; *Phylogeny ; *Phylogeography ; Plankton/*classification ; Species Specificity ; Time Factors ; }, abstract = {Traditionally, many small-sized copepod species are considered to be widespread, bipolar or cosmopolitan. However, these large-scale distribution patterns need to be re-examined in view of increasing evidence of cryptic and pseudo-cryptic speciation in pelagic copepods. Here, we present a phylogeographic study of Oithona similis s.l. populations from the Arctic Ocean, the Southern Ocean and its northern boundaries, the North Atlantic and the Mediterrranean Sea. O. similis s.l. is considered as one of the most abundant species in temperate to polar oceans and acts as an important link in the trophic network between the microbial loop and higher trophic levels such as fish larvae. Two gene fragments were analysed: the mitochondrial cytochrome oxidase c subunit I (COI), and the nuclear ribosomal 28 S genetic marker. Seven distinct, geographically delimitated, mitochondrial lineages could be identified, with divergences among the lineages ranging from 8 to 24%, thus representing most likely cryptic or pseudocryptic species within O. similis s.l. Four lineages were identified within or close to the borders of the Southern Ocean, one lineage in the Arctic Ocean and two lineages in the temperate Northern hemisphere. Surprisingly the Arctic lineage was more closely related to lineages from the Southern hemisphere than to the other lineages from the Northern hemisphere, suggesting that geographic proximity is a rather poor predictor of how closely related the clades are on a genetic level.}, }
@article {pmid27997751, year = {2017}, author = {Jackrel, SL and Owens, SM and Gilbert, JA and Pfister, CA}, title = {Identifying the plant-associated microbiome across aquatic and terrestrial environments: the effects of amplification method on taxa discovery.}, journal = {Molecular ecology resources}, volume = {17}, number = {5}, pages = {931-942}, doi = {10.1111/1755-0998.12645}, pmid = {27997751}, issn = {1755-0998}, mesh = {Bacteria/*classification/*genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenomics/*methods ; *Microbiota ; Plants/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Plants in terrestrial and aquatic environments contain a diverse microbiome. Yet, the chloroplast and mitochondria organelles of the plant eukaryotic cell originate from free-living cyanobacteria and Rickettsiales. This represents a challenge for sequencing the plant microbiome with universal primers, as ~99% of 16S rRNA sequences may consist of chloroplast and mitochondrial sequences. Peptide nucleic acid clamps offer a potential solution by blocking amplification of host-associated sequences. We assessed the efficacy of chloroplast and mitochondria-blocking clamps against a range of microbial taxa from soil, freshwater and marine environments. While we found that the mitochondrial blocking clamps appear to be a robust method for assessing animal-associated microbiota, Proteobacterial 16S rRNA binds to the chloroplast-blocking clamp, resulting in a strong sequencing bias against this group. We attribute this bias to a conserved 14-bp sequence in the Proteobacteria that matches the 17-bp chloroplast-blocking clamp sequence. By scanning the Greengenes database, we provide a reference list of nearly 1500 taxa that contain this 14-bp sequence, including 48 families such as the Rhodobacteraceae, Phyllobacteriaceae, Rhizobiaceae, Kiloniellaceae and Caulobacteraceae. To determine where these taxa are found in nature, we mapped this taxa reference list against the Earth Microbiome Project database. These taxa are abundant in a variety of environments, particularly aquatic and semiaquatic freshwater and marine habitats. To facilitate informed decisions on effective use of organelle-blocking clamps, we provide a searchable database of microbial taxa in the Greengenes and Silva databases matching various n-mer oligonucleotides of each PNA sequence.}, }
@article {pmid27997535, year = {2016}, author = {Radzvilavicius, AL and Hadjivasiliou, Z and Pomiankowski, A and Lane, N}, title = {Selection for Mitochondrial Quality Drives Evolution of the Germline.}, journal = {PLoS biology}, volume = {14}, number = {12}, pages = {e2000410}, pmid = {27997535}, issn = {1545-7885}, mesh = {Animals ; *Biological Evolution ; Female ; *Germ Cells ; Mitochondria/*genetics ; Oocytes ; *Selection, Genetic ; }, abstract = {The origin of the germline-soma distinction is a fundamental unsolved question. Plants and basal metazoans do not have a germline but generate gametes from pluripotent stem cells in somatic tissues (somatic gametogenesis). In contrast, most bilaterians sequester a dedicated germline early in development. We develop an evolutionary model which shows that selection for mitochondrial quality drives germline evolution. In organisms with low mitochondrial replication error rates, segregation of mutations over multiple cell divisions generates variation, allowing selection to optimize gamete quality through somatic gametogenesis. Higher mutation rates promote early germline sequestration. We also consider how oogamy (a large female gamete packed with mitochondria) alters selection on the germline. Oogamy is beneficial as it reduces mitochondrial segregation in early development, improving adult fitness by restricting variation between tissues. But it also limits variation between early-sequestered oocytes, undermining gamete quality. Oocyte variation is restored through proliferation of germline cells, producing more germ cells than strictly needed, explaining the random culling (atresia) of precursor cells in bilaterians. Unlike other models of germline evolution, selection for mitochondrial quality can explain the stability of somatic gametogenesis in plants and basal metazoans, the evolution of oogamy in all plants and animals with tissue differentiation, and the mutational forces driving early germline sequestration in active bilaterians. The origins of predation in motile bilaterians in the Cambrian explosion is likely to have increased rates of tissue turnover and mitochondrial replication errors, in turn driving germline evolution and the emergence of complex developmental processes.}, }
@article {pmid27989936, year = {2017}, author = {Bolotin-Fukuhara, M}, title = {Thirty years of the HAP2/3/4/5 complex.}, journal = {Biochimica et biophysica acta. Gene regulatory mechanisms}, volume = {1860}, number = {5}, pages = {543-559}, doi = {10.1016/j.bbagrm.2016.10.011}, pmid = {27989936}, issn = {1874-9399}, mesh = {Animals ; History, 20th Century ; History, 21st Century ; Humans ; Mitochondria/genetics/*metabolism ; Multiprotein Complexes/genetics/history/*metabolism ; Trans-Activators/genetics/history/*metabolism ; }, }
@article {pmid27989883, year = {2017}, author = {Saikia, BB and Dubey, SK and Shanmugam, MK and Sundaresan, P}, title = {Whole mitochondrial genome analysis in South Indian patients with Leber's hereditary optic neuropathy.}, journal = {Mitochondrion}, volume = {36}, number = {}, pages = {21-28}, doi = {10.1016/j.mito.2016.10.006}, pmid = {27989883}, issn = {1872-8278}, mesh = {Adolescent ; Adult ; DNA, Mitochondrial/*genetics ; Female ; *Genome, Mitochondrial ; Haplotypes ; Humans ; India ; Male ; Mutation Rate ; Optic Atrophy, Hereditary, Leber/*genetics/*pathology ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Leber's hereditary optic neuropathy (LHON) is a mitochondrial DNA (mtDNA) associated neurodegenerative disorder of retinal ganglion cells. In this study, whole mitochondrial genome sequencing of 75 LHON patients and 40 controls was performed to identify the mutation frequency and haplogroup background of South Indian population. Analysis of mtDNA revealed 559 different variants in LHON patients, including 7 pathogenic mutations, 30 private, and 22 other disease associated variants. A significantly higher (p=0.0008) overall variation load per individual was noted among LHON patients versus controls. We reported for the first time, the association of M haplogroup (p=0.028) with LHON in this cohort.}, }
@article {pmid27989633, year = {2017}, author = {Kyei-Poku, G and Sokolova, YY}, title = {The microsporidium Nosema disstriae (Thomson 1959): Fine structure and phylogenetic position within the N. bombycis clade.}, journal = {Journal of invertebrate pathology}, volume = {143}, number = {}, pages = {90-103}, doi = {10.1016/j.jip.2016.12.003}, pmid = {27989633}, issn = {1096-0805}, mesh = {Animals ; Lepidoptera/parasitology ; Microscopy, Electron ; Microsporidiosis/veterinary ; Nosema/*genetics/*ultrastructure ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {A microsporidium Nosema disstriae (Thomson) is a parasite of the forest tent caterpillar Malacasoma disstria (Lepidoptera: Lasiocampidae), a notable defoliator of deciduous trees in North America. The goal of this paper was to demonstrate the ultrastructure of N. disstriae and to determine the position of this microsporidium within the N. bombycis clade (NBC) using comparative morphology and multiple molecular phylogenetic markers: RPB1, LSU-, ITS- and SSU-rDNA. As a part of this goal, the revision of the described members of the NBC has been performed. The ultrastructure of proliferating stages and spores of N. disstriae were similar to previously described Nosema spp. parasitizing lepidopteran species. Meronts produced tubular-like structures on their surfaces and exhibited a tight association with host mitochondria. All stages were diplokaryotic and developed without interfacial envelopes. Disporoblastic sporogony produced typical Nosema-type spores with 9-12 polar filament coils. A vesicle with immature spores was once recognized on sections, concordant with the previous record of octosporous sporogony in the N. disstriae life cycle. Rarely, spores with thinner envelopes and large posterior vacuoles were seen in the midgut. Tracheae were most heavily infected. Midgut, surrounding muscles, haemocytes and fat body also contained microsporidia. SSUrRNA-inferred phylogenies were consistent with previously published articles and did not resolve the relation within the NBC clade. The RPB1-inferred trees and concatenated RPB1 and LSU-ITS-SSUrDNA-based trees demonstrated clustering of N. disstriae with N. antheraeae as early divergent species within the NBC.}, }
@article {pmid27988283, year = {2017}, author = {Guerrero-Castillo, S and Cabrera-Orefice, A and Huynen, MA and Arnold, S}, title = {Identification and evolutionary analysis of tissue-specific isoforms of mitochondrial complex I subunit NDUFV3.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1858}, number = {3}, pages = {208-217}, doi = {10.1016/j.bbabio.2016.12.004}, pmid = {27988283}, issn = {0005-2728}, mesh = {Alternative Splicing/genetics ; Amino Acid Sequence/genetics ; Animals ; Cattle ; Electron Transport Complex I/chemistry/*genetics ; *Evolution, Molecular ; Exons/genetics ; Gene Expression Regulation ; Humans ; Mice ; Mitochondria, Heart/chemistry/*genetics ; Muscle, Skeletal/chemistry/metabolism ; Organ Specificity ; Protein Isoforms/chemistry/*genetics ; }, abstract = {Mitochondrial complex I is the largest respiratory chain complex. Despite the enormous progress made studying its structure and function in recent years, potential regulatory roles of its accessory subunits remained largely unresolved. Complex I gene NDUFV3, which occurs in metazoa, contains an extra exon that is only present in vertebrates and thereby evolutionary even younger than the rest of the gene. Alternative splicing of this extra exon gives rise to a short NDUFV3-S and a long NDUFV3-L protein isoform. Complexome profiling revealed that the two NDUFV3 isoforms are constituents of the multi-subunit complex I. Further mass spectrometric analyses of complex I from different murine and bovine tissues showed a tissue-specific expression pattern of NDUFV3-S and NDUFV3-L. Hence, NDUFV3-S was identified as the only isoform in heart and skeletal muscle, whereas in liver, brain, and lung NDUFV3-L was expressed as the dominant isoform, together with NDUFV3-S present in all tissues analyzed. Thus, we identified NDUFV3 as the first out of 30 accessory subunits of complex I present in vertebrate- and tissue-specific isoforms. Interestingly, the tissue-specific expression pattern of NDUFV3-S and NDUFV3-L isoforms was paralleled by changes in kinetic parameters, especially the substrate affinity of complex I. This may indicate a regulatory role of the NDUFV3 isoforms in different vertebrate tissues.}, }
@article {pmid27986857, year = {2017}, author = {Graf, M and Arenz, S and Huter, P and Dönhöfer, A and Novácek, J and Wilson, DN}, title = {Cryo-EM structure of the spinach chloroplast ribosome reveals the location of plastid-specific ribosomal proteins and extensions.}, journal = {Nucleic acids research}, volume = {45}, number = {5}, pages = {2887-2896}, pmid = {27986857}, issn = {1362-4962}, mesh = {Binding Sites ; Chloroplast Proteins/*chemistry/metabolism ; Chloroplasts/*chemistry ; Cryoelectron Microscopy ; Models, Molecular ; RNA Stability ; RNA, Ribosomal/chemistry ; Ribosomal Proteins/*chemistry/metabolism ; Ribosome Subunits, Large, Eukaryotic/*chemistry/metabolism ; Ribosome Subunits, Small, Eukaryotic/*chemistry ; Spinacia oleracea/*chemistry ; }, abstract = {Ribosomes are the protein synthesizing machines of the cell. Recent advances in cryo-EM have led to the determination of structures from a variety of species, including bacterial 70S and eukaryotic 80S ribosomes as well as mitoribosomes from eukaryotic mitochondria, however, to date high resolution structures of plastid 70S ribosomes have been lacking. Here we present a cryo-EM structure of the spinach chloroplast 70S ribosome, with an average resolution of 5.4 Å for the small 30S subunit and 3.6 Å for the large 50S ribosomal subunit. The structure reveals the location of the plastid-specific ribosomal proteins (RPs) PSRP1, PSRP4, PSRP5 and PSRP6 as well as the numerous plastid-specific extensions of the RPs. We discover many features by which the plastid-specific extensions stabilize the ribosome via establishing additional interactions with surrounding ribosomal RNA and RPs. Moreover, we identify a large conglomerate of plastid-specific protein mass adjacent to the tunnel exit site that could facilitate interaction of the chloroplast ribosome with the thylakoid membrane and the protein-targeting machinery. Comparing the Escherichia coli 70S ribosome with that of the spinach chloroplast ribosome provides detailed insight into the co-evolution of RP and rRNA.}, }
@article {pmid27986845, year = {2017}, author = {Voznesenskaya, EV and Koteyeva, NK and Edwards, GE and Ocampo, G}, title = {Unique photosynthetic phenotypes in Portulaca (Portulacaceae): C3-C4 intermediates and NAD-ME C4 species with Pilosoid-type Kranz anatomy.}, journal = {Journal of experimental botany}, volume = {68}, number = {2}, pages = {225-239}, pmid = {27986845}, issn = {1460-2431}, mesh = {*Biological Evolution ; Blotting, Western ; Carbon Dioxide/metabolism ; Carbon Isotopes/metabolism ; Cotyledon/anatomy &amp; histology ; Glycine Dehydrogenase (Decarboxylating)/metabolism ; Malate Dehydrogenase/metabolism ; Microscopy, Electron, Transmission ; NAD/metabolism ; Phenotype ; *Photosynthesis ; Plant Leaves/*metabolism/ultrastructure ; Portulaca/*metabolism/ultrastructure ; }, abstract = {Portulacaceae is a family that has considerable diversity in photosynthetic phenotypes. It is one of 19 families of terrestrial plants where species having C4 photosynthesis have been found. Most species in Portulaca are in the alternate-leaved (AL) lineage, which includes one clade (Cryptopetala) with taxa lacking C4 photosynthesis and three clades having C4 species (Oleracea, Umbraticola and Pilosa). All three species in the Cryptopetala clade lack Kranz anatomy, the leaves have C3-like carbon isotope composition and they have low levels of C4 cycle enzymes. Anatomical, biochemical and physiological analyses show they are all C3-C4 intermediates. They have intermediate CO2 compensation points, enrichment of organelles in the centripetal position in bundle sheath (BS) cells, with selective localization of glycine decarboxylase in BS mitochondria. In the three C4 clades there are differences in Kranz anatomy types and form of malic enzyme (ME) reported to function in C4 (NAD-ME versus NADP-ME): Oleracea (Atriplicoid, NAD-ME), Umbraticola (Atriplicoid, NADP-ME) and Pilosa (Pilosoid, NADP-ME). Structural and biochemical analyses were performed on Pilosa clade representatives having Pilosoid-type leaf anatomy with Kranz tissue enclosing individual peripheral vascular bundles and water storage in the center of the leaf. In this clade, all species except P. elatior are NADP-ME-type C4 species with grana-deficient BS chloroplasts and grana-enriched M chloroplasts. Surprisingly, P. elatior has BS chloroplasts enriched in grana and NAD-ME-type photosynthesis. The results suggest photosynthetic phenotypes were probably derived from an ancestor with NADP-ME-type C4, with two independent switches to NAD-ME type.}, }
@article {pmid27982067, year = {2016}, author = {Wu, NN and Zhang, CH and Lee, HJ and Ma, Y and Wang, X and Ma, XJ and Ma, W and Zhao, D and Feng, YM}, title = {Brown adipogenic potential of brown adipocytes and peri-renal adipocytes from human embryo.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {39193}, pmid = {27982067}, issn = {2045-2322}, mesh = {Adipocytes, Brown/cytology/*metabolism ; Adipocytes, White/cytology/metabolism ; Adipogenesis ; Cells, Cultured ; DNA-Binding Proteins/genetics/metabolism ; Embryo, Mammalian/*cytology ; Humans ; Membrane Proteins/genetics/metabolism ; Mitochondria/metabolism ; RNA/chemistry/isolation &amp; purification/metabolism ; Sequence Analysis, RNA ; Stem Cells/cytology/metabolism ; T-Box Domain Proteins/genetics/metabolism ; Transcription Factors/genetics/metabolism ; Transcriptome ; Tumor Necrosis Factor Receptor Superfamily, Member 9/genetics/metabolism ; Uncoupling Protein 1/genetics/metabolism ; }, abstract = {Both brown adipocytes (BAC) and beige cells hold therapeutic potential for the treatment of metabolic disorders. Unfortunately, the amount and activity of these cells are limited in adults. Although BAC marker expression has been shown in peri-renal adipose tissues in children and adults, functional assessment is lacking. Furthermore, it is entirely unknown whether adipose progenitors are present in human embryo and able to give rise to BAC in situ during evolution. Therefore, adipose tissues in the interscapular and peri-renal regions were dissected from human embryo and subcutaneous white adipose tissues (sWAT) were obtained from an adult. After subjected to differentiation in vitro, adipocyte progenitors were detected present in all these adipose tissues. When stimulated for adipogenesis, differentiated adipocytes in the intercapular and peri-renal regions showed similar features: (1) induced BAC and beige cell marker expression including UCP1 and PRDM16 and comparable mitochondrion copy number; (2) similar gene expression patterns by RNA-Seq analysis; and (3) similar maximal oxygen consumption rates examined by respirometry. Nevertheless, stimulation of adipocyte progenitors in sWAT induces neither BAC and beige cell marker expression nor any change of oxygen consumption. In conclusion, peri-renal adipocyte progenitors in human embryo hold browning potential for BAC production.}, }
@article {pmid27982054, year = {2016}, author = {Pfitzner, AK and Steblau, N and Ulrich, T and Oberhettinger, P and Autenrieth, IB and Schütz, M and Rapaport, D}, title = {Mitochondrial-bacterial hybrids of BamA/Tob55 suggest variable requirements for the membrane integration of β-barrel proteins.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {39053}, pmid = {27982054}, issn = {2045-2322}, mesh = {Bacterial Outer Membrane Proteins/chemistry/genetics/*metabolism ; Escherichia coli/chemistry/*metabolism ; Escherichia coli Proteins/chemistry/genetics/*metabolism ; Evolution, Molecular ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Protein Domains ; Recombinant Proteins/chemistry/metabolism ; Saccharomyces cerevisiae/chemistry/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Sequence Homology ; Species Specificity ; }, abstract = {β-Barrel proteins are found in the outer membrane (OM) of Gram-negative bacteria, chloroplasts and mitochondria. The assembly of these proteins into the corresponding OM is facilitated by a dedicated protein complex that contains a central conserved β-barrel protein termed BamA in bacteria and Tob55/Sam50 in mitochondria. BamA and Tob55 consist of a membrane-integral C-terminal domain that forms a β-barrel pore and a soluble N-terminal portion comprised of one (in Tob55) or five (in BamA) polypeptide transport-associated (POTRA) domains. Currently the functional significance of this difference and whether the homology between BamA and Tob55 can allow them to replace each other are unclear. To address these issues we constructed hybrid Tob55/BamA proteins with differently configured N-terminal POTRA domains. We observed that constructs harboring a heterologous C-terminal domain could not functionally replace the bacterial BamA or the mitochondrial Tob55 demonstrating species-specific requirements. Interestingly, the various hybrid proteins in combination with the bacterial chaperones Skp or SurA supported to a variable extent the assembly of bacterial β-barrel proteins into the mitochondrial OM. Collectively, our findings suggest that the membrane assembly of various β-barrel proteins depends to a different extent on POTRA domains and periplasmic chaperones.}, }
@article {pmid27976830, year = {2017}, author = {Harsman, A and Schneider, A}, title = {Mitochondrial protein import in trypanosomes: Expect the unexpected.}, journal = {Traffic (Copenhagen, Denmark)}, volume = {18}, number = {2}, pages = {96-109}, doi = {10.1111/tra.12463}, pmid = {27976830}, issn = {1600-0854}, mesh = {Cytosol/metabolism ; Humans ; Membrane Transport Proteins/metabolism ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/*metabolism ; Protein Transport/*physiology ; Trypanosoma brucei brucei/*metabolism ; }, abstract = {Mitochondria have many different functions, the most important one of which is oxidative phosphorylation. They originated from an endosymbiotic event between a bacterium and an archaeal host cell. It was the evolution of a protein import system that marked the boundary between the endosymbiotic ancestor of the mitochondrion and a true organelle that is under the control of the nucleus. In present day mitochondria more than 95% of all proteins are imported from the cytosol in a proces mediated by hetero-oligomeric protein complexes in the outer and inner mitochondrial membranes. In this review we compare mitochondrial protein import in the best studied model system yeast and the parasitic protozoan Trypanosoma brucei. The 2 organisms are phylogenetically only remotely related. Despite the fact that mitochondrial protein import has the same function in both species, only very few subunits of their import machineries are conserved. Moreover, while yeast has 2 inner membrane protein translocases, one specialized for presequence-containing and one for mitochondrial carrier proteins, T. brucei has a single inner membrane translocase only, that mediates import of both types of substrates. The evolutionary implications of these findings are discussed.}, }
@article {pmid27956259, year = {2017}, author = {Burzyński, A and Soroka, M and Mioduchowska, M and Kaczmarczyk, A and Sell, J}, title = {The complete maternal and paternal mitochondrial genomes of Unio crassus: Mitochondrial molecular clock and the overconfidence of molecular dating.}, journal = {Molecular phylogenetics and evolution}, volume = {107}, number = {}, pages = {605-608}, doi = {10.1016/j.ympev.2016.12.007}, pmid = {27956259}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; Female ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Time Factors ; Unio/*genetics ; }, abstract = {The availability of a rapidly growing number of complete mitochondrial genome sequences provokes high confidence dating approaches. However, even if the congruence between mitochondrial and nuclear markers is reasonable, the resulting topologies are frequently questionable. The unique opportunity to study the evolutionary history of two independent mitochondrial genomes in one phylogenetic context exists in the freshwater mussels family Unionidae. The two lineages function under doubly uniparental inheritance since well before the emergence of the family. Despite the relatively high number of available complete sequences of maternally inherited genomes, comparative analyses are limited by the small number of sequences of counterpart paternally inherited genomes. We have sequenced for the first time the representative set of five sequences (two maternal and three paternal) from the species Unio crassus. Comparative analysis of the phylogenies reconstructed using relevant mitogenomic data available in GenBank (13 species in total) reveal that single - genome inferences are congruent only if the relaxed clock is assumed.}, }
@article {pmid27940540, year = {2017}, author = {Rodríguez-Cousiño, N and Esteban, R}, title = {Relationships and Evolution of Double-Stranded RNA Totiviruses of Yeasts Inferred from Analysis of L-A-2 and L-BC Variants in Wine Yeast Strain Populations.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {4}, pages = {}, pmid = {27940540}, issn = {1098-5336}, mesh = {Antifungal Agents/*metabolism ; Capsid/metabolism ; Fusion Proteins, gag-pol/genetics ; Gene Products, gag/genetics ; Helper Viruses/*genetics ; Mitochondria/genetics ; Saccharomyces cerevisiae/metabolism/*virology ; Satellite Viruses/genetics ; Totivirus/*genetics ; }, abstract = {UNLABELLED: Saccharomyces cerevisiae killer strains secrete a protein toxin active on nonkiller strains of the same (or other) yeast species. Different killer toxins, K1, K2, K28, and Klus, have been described. Each toxin is encoded by a medium-size (1.5- to 2.3-kb) M double-stranded RNA (dsRNA) located in the cytoplasm. M dsRNAs require L-A helper virus for maintenance. L-A belongs to the Totiviridae family, and its dsRNA genome of 4.6 kb codes for the major capsid protein Gag and a minor Gag-Pol protein, which form the virions that separately encapsidate L-A or the M satellites. Different L-A variants exist in nature; on average, 24% of their nucleotides are different. Previously, we reported that L-A-lus was specifically associated with Mlus, suggesting coevolution, and proposed a role of the toxin-encoding M dsRNAs in the appearance of new L-A variants. Here we confirm this by analyzing the helper virus in K2 killer wine strains, which we named L-A-2. L-A-2 is required for M2 maintenance, and neither L-A nor L-A-lus shows helper activity for M2 in the same genetic background. This requirement is overcome when coat proteins are provided in large amounts by a vector or in ski mutants. The genome of another totivirus, L-BC, frequently accompanying L-A in the same cells shows a lower degree of variation than does L-A (about 10% of nucleotides are different). Although L-BC has no helper activity for M dsRNAs, distinct L-BC variants are associated with a particular killer strain. The so-called L-BC-lus (in Klus strains) and L-BC-2 (in K2 strains) are analyzed.<br><br>IMPORTANCE: Killer strains of S. cerevisiae secrete protein toxins that kill nonkiller yeasts. The "killer phenomenon" depends on two dsRNA viruses: L-A and M. M encodes the toxin, and L-A, the helper virus, provides the capsids for both viruses. Different killer toxins exist: K1, K2, K28, and Klus, encoded on different M viruses. Our data indicate that each M dsRNA depends on a specific helper virus; these helper viruses have nucleotide sequences that may be as much as 26% different, suggesting coevolution. In wine environments, K2 and Klus strains frequently coexist. We have previously characterized the association of Mlus and L-A-lus. Here we sequence and characterize L-A-2, the helper virus of M2, establishing the helper virus requirements of M2, which had not been completely elucidated. We also report the existence of two specific L-BC totiviruses in Klus and K2 strains with about 10% of their nucleotides different, suggesting different evolutionary histories from those of L-A viruses.}, }
@article {pmid27931183, year = {2016}, author = {Liu, S and Roellig, DM and Guo, Y and Li, N and Frace, MA and Tang, K and Zhang, L and Feng, Y and Xiao, L}, title = {Evolution of mitosome metabolism and invasion-related proteins in Cryptosporidium.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {1006}, pmid = {27931183}, issn = {1471-2164}, mesh = {Citric Acid Cycle/genetics ; Contig Mapping ; Cryptosporidium/classification/*genetics ; Electron Transport Chain Complex Proteins/metabolism ; Energy Metabolism/genetics ; Evolution, Molecular ; Genome ; Metabolic Networks and Pathways/genetics ; Mitochondria/genetics/*metabolism ; Phylogeny ; Protozoan Proteins/metabolism ; }, abstract = {BACKGROUND: The switch from photosynthetic or predatory to parasitic life strategies by apicomplexans is accompanied with a reductive evolution of genomes and losses of metabolic capabilities. Cryptosporidium is an extreme example of reductive evolution among apicomplexans, with losses of both the mitosome genome and many metabolic pathways. Previous observations on reductive evolution were largely based on comparative studies of various groups of apicomplexans. In this study, we sequenced two divergent Cryptosporidium species and conducted a comparative genomic analysis to infer the reductive evolution of metabolic pathways and differential evolution of invasion-related proteins within the Cryptosporidium lineage.<br><br>RESULTS: In energy metabolism, Cryptosporidium species differ from each other mostly in mitosome metabolic pathways. Compared with C. parvum and C. hominis, C. andersoni possesses more aerobic metabolism and a conventional electron transport chain, whereas C. ubiquitum has further reductions in ubiquinone and polyisprenoid biosynthesis and has lost both the conventional and alternative electron transport systems. For invasion-associated proteins, similar to C. hominis, a reduction in the number of genes encoding secreted MEDLE and insulinase-like proteins in the subtelomeric regions of chromosomes 5 and 6 was also observed in C. ubiquitum and C. andersoni, whereas mucin-type glycoproteins are highly divergent between the gastric C. andersoni and intestinal Cryptosporidium species.<br><br>CONCLUSIONS: Results of the study suggest that rapidly evolving mitosome metabolism and secreted invasion-related proteins could be involved in tissue tropism and host specificity in Cryptosporidium spp. The finding of progressive reduction in mitosome metabolism among Cryptosporidium species improves our knowledge of organelle evolution within apicomplexans.}, }
@article {pmid27928819, year = {2017}, author = {Björkholm, P and Ernst, AM and Hagström, E and Andersson, SG}, title = {Why mitochondria need a genome revisited.}, journal = {FEBS letters}, volume = {591}, number = {1}, pages = {65-75}, doi = {10.1002/1873-3468.12510}, pmid = {27928819}, issn = {1873-3468}, mesh = {Endoplasmic Reticulum/metabolism ; Genes, Mitochondrial ; Genetic Engineering ; *Genome, Mitochondrial ; HeLa Cells ; Humans ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics/metabolism ; Models, Biological ; Recombinant Proteins/metabolism ; Transfection ; }, abstract = {In this paper, we experimentally address the debate about why functional transfer of mitochondrial genes to the nucleus has been halted in some organismal groups and why cytosolic expression of mitochondrial proteins has proven remarkably difficult. By expressing all 13 human mitochondrial-encoded genes with strong mitochondrial-targeting sequences in the cytosol of human cells, we show that all proteins, except ATP8, are transported to the endoplasmic reticulum (ER). These results confirm and extend previous findings based on three mitochondrial genes lacking mitochondrial-targeting sequences that also were relocated to the ER during cytosolic expression. We conclude that subcellular protein targeting constitutes a major barrier to functional transfer of mitochondrial genes to the nuclear genome.}, }
@article {pmid27920033, year = {2017}, author = {Jhuang, HY and Lee, HY and Leu, JY}, title = {Mitochondrial-nuclear co-evolution leads to hybrid incompatibility through pentatricopeptide repeat proteins.}, journal = {EMBO reports}, volume = {18}, number = {1}, pages = {87-101}, pmid = {27920033}, issn = {1469-3178}, mesh = {Amino Acid Sequence ; Cell Nucleus/genetics/*metabolism ; Chromosomes, Fungal ; Fungal Proteins/chemistry/genetics/*metabolism ; Genome, Fungal ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Models, Molecular ; Mutation ; Peptides ; Protein Binding ; Protein Conformation ; Protein Interaction Domains and Motifs ; RNA ; RNA, Mitochondrial ; RNA, Ribosomal ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Mitochondrial-nuclear incompatibility has a major role in reproductive isolation between species. However, the underlying mechanism and driving force of mitochondrial-nuclear incompatibility remain elusive. Here, we report a pentatricopeptide repeat-containing (PPR) protein, Ccm1, and its interacting partner, 15S rRNA, to be involved in hybrid incompatibility between two yeast species, Saccharomyces cerevisiae and Saccharomyces bayanus S. bayanus-Ccm1 has reduced binding affinity for S. cerevisiae-15S rRNA, leading to respiratory defects in hybrid cells. This incompatibility can be rescued by single mutations on several individual PPR motifs, demonstrating the highly evolvable nature of PPR proteins. When we examined other PPR proteins in the closely related Saccharomyces sensu stricto yeasts, about two-thirds of them showed detectable incompatibility. Our results suggest that fast co-evolution between flexible PPR proteins and their mitochondrial RNA substrates may be a common driving force in the development of mitochondrial-nuclear hybrid incompatibility.}, }
@article {pmid27918601, year = {2016}, author = {Malecki, M and Bähler, J}, title = {Identifying genes required for respiratory growth of fission yeast.}, journal = {Wellcome open research}, volume = {1}, number = {}, pages = {12}, pmid = {27918601}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; 095598/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We have used both auxotroph and prototroph versions of the latest deletion-mutant library to identify genes required for respiratory growth on solid glycerol medium in fission yeast. This data set complements and enhances our recent study on functional and regulatory aspects of energy metabolism by providing additional proteins that are involved in respiration. Most proteins identified in this mutant screen have not been implicated in respiration in budding yeast. We also provide a protocol to generate a prototrophic mutant library, and data on technical and biological reproducibility of colony-based high-throughput screens.}, }
@article {pmid27908782, year = {2017}, author = {Raefsky, SM and Mattson, MP}, title = {Adaptive responses of neuronal mitochondria to bioenergetic challenges: Roles in neuroplasticity and disease resistance.}, journal = {Free radical biology &amp; medicine}, volume = {102}, number = {}, pages = {203-216}, pmid = {27908782}, issn = {1873-4596}, support = {ZIA AG000312-16//Intramural NIH HHS/United States ; ZIA AG000317-16//Intramural NIH HHS/United States ; ZIA AG000315-16//Intramural NIH HHS/United States ; ZIA AG000314-16//Intramural NIH HHS/United States ; ZIA AG000317-15//Intramural NIH HHS/United States ; ZIA AG000314-15//Intramural NIH HHS/United States ; ZIA AG000315-15//Intramural NIH HHS/United States ; ZIA AG000312-15//Intramural NIH HHS/United States ; }, mesh = {DNA Repair/genetics ; Disease Resistance/genetics ; Energy Metabolism ; Humans ; Mitochondria/*metabolism/pathology ; Neurodegenerative Diseases/*genetics/pathology ; Neuronal Plasticity/genetics ; Neurons/*metabolism/pathology ; *Organelle Biogenesis ; Signal Transduction ; }, abstract = {An important concept in neurobiology is "neurons that fire together, wire together" which means that the formation and maintenance of synapses is promoted by activation of those synapses. Very similar to the effects of the stress of exercise on muscle cells, emerging findings suggest that neurons respond to activity by activating signaling pathways (e.g., Ca[2+], CREB, PGC-1α, NF-κB) that stimulate mitochondrial biogenesis and cellular stress resistance. These pathways are also activated by aerobic exercise and food deprivation, two bioenergetic challenges of fundamental importance in the evolution of the brains of all mammals, including humans. The metabolic 'switch' in fuel source from liver glycogen store-derived glucose to adipose cell-derived fatty acids and their ketone metabolites during fasting and sustained exercise, appears to be a pivotal trigger of both brain-intrinsic and peripheral organ-derived signals that enhance learning and memory and underlying synaptic plasticity and neurogenesis. Brain-intrinsic extracellular signals include the excitatory neurotransmitter glutamate and the neurotrophic factor BDNF, and peripheral signals may include the liver-derived ketone 3-hydroxybutyrate and the muscle cell-derived protein irisin. Emerging findings suggest that fasting, exercise and an intellectually challenging lifestyle can protect neurons against the dysfunction and degeneration that they would otherwise suffer in acute brain injuries (stroke and head trauma) and neurodegenerative disorders including Alzheimer's, Parkinson's and Huntington's disease. Among the prominent intracellular responses of neurons to these bioenergetic challenges are up-regulation of antioxidant defenses, autophagy/mitophagy and DNA repair. A better understanding of such fundamental hormesis-based adaptive neuronal response mechanisms is expected to result in the development and implementation of novel interventions to promote optimal brain function and healthy brain aging.}, }
@article {pmid27907107, year = {2016}, author = {Kappas, I and Vittas, S and Pantzartzi, CN and Drosopoulou, E and Scouras, ZG}, title = {A Time-Calibrated Mitogenome Phylogeny of Catfish (Teleostei: Siluriformes).}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0166988}, pmid = {27907107}, issn = {1932-6203}, mesh = {Africa ; Animals ; Bayes Theorem ; Biological Evolution ; Catfishes/*classification/genetics ; Cypriniformes/*classification/genetics ; Fossils ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Models, Genetic ; North America ; *Phylogeny ; Phylogeography ; South America ; }, abstract = {A very significant part of the world's freshwater ichthyofauna is represented by ancient, exceptionally diverse and cosmopolitan ray-finned teleosts of the order Siluriformes. Over the years, catfish have been established as an exemplary model for probing historical biogeography at various scales. Yet, several tantalizing gaps still exist in their phylogenetic history, timeline and mode of diversification. Here, we re-examine the phylogeny of catfish by assembling and analyzing almost all publicly available mitogenome data. We constructed an ingroup matrix of 62 full-length mitogenome sequences from 20 catfish families together with four cypriniform outgroups, spanning 15,557 positions in total. Partitioned maximum likelihood analyses and Bayesian relaxed clock dating using fossil age constraints provide some useful and novel insights into the evolutionary history of this group. Loricarioidei are recovered as the first siluriform group to diversify, rendering Neotropics the cradle of the order. The next deepest clade is the South American Diplomystoidei placed as a sister group to all the remaining Siluroidei. The two multifamilial clades of "Big Asia" and "Big Africa" are also recovered, albeit nodal support for the latter is poor. Within "Big Asia", Bagridae are clearly polyphyletic. Other interfamilial relationships, including Clariidae + Heteropneustidae, Doradidae + Auchenipteridae and Ictaluridae + Cranoglanididae are robustly resolved. Our chronogram shows that siluriforms have a Pangaean origin, at least as far back as the Early Cretaceous. The inferred timeline of the basal splits corroborates the "Out-of-South America" hypothesis and accords well with the fossil record. The divergence of Siluroidei most likely postdated the final separation of Africa and South America. An appealing case of phylogenetic affinity elaborated by biogeographic dispersal is exemplified by the Early Paleogene split between the Southeast Asian Cranoglanididae and Ictaluridae, with the latter radiating into North America's freshwater realm by Eocene. The end of Cretaceous probably concludes the major bout of diversification at the family level while with the dawn of the Cenozoic a prolific radiation is evident at the generic level.}, }
@article {pmid27906993, year = {2016}, author = {Perea, S and Vukić, J and Šanda, R and Doadrio, I}, title = {Ancient Mitochondrial Capture as Factor Promoting Mitonuclear Discordance in Freshwater Fishes: A Case Study in the Genus Squalius (Actinopterygii, Cyprinidae) in Greece.}, journal = {PloS one}, volume = {11}, number = {12}, pages = {e0166292}, pmid = {27906993}, issn = {1932-6203}, mesh = {Animals ; Cyprinidae/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genome, Mitochondrial ; Hybridization, Genetic ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; }, abstract = {Hybridization and incomplete lineage sorting are common confounding factors in phylogeny and speciation resulting in mitonuclear disparity. Mitochondrial introgression, a particular case of hybridization, may, in extreme cases, lead to replacement of the mitochondrial genome of one species with that of another (mitochondrial capture). We investigated mitochondrial introgression involving two species of the cyprinid genus Squalius in the western Peloponnese region of Greece using molecular and morphological data. We found evidence of complete mitochondrial introgression of Squalius keadicus into two populations recognized as Squalius peloponensis from the Miras and Pamissos River basins and a divergence of mitochondrial genomes of S. keadicus from the Evrotas basin from that of the introgressed populations dating from the Pleistocene. Secondary contact among basins is a possible factor in connection of the species and the introgression event. Morphological analyses support the hypothesis of mitochondrial introgression, as S. keadicus was different from the other three populations recognized as S. peloponensis, although significant differences were found among the four populations. Isolation by geographical barriers arose during Pleistocene in the western Peloponnese were the source of the evolution of the two reciprocally monophyletic subclades found in the S. keadicus mitochondrial clade, and the morphological differences found among the four populations. Along with the lack of structure in the nuclear genome in the three populations ascribed to S. peloponensis, this suggests an incipient speciation process occurring in these Squalius species in the western Peloponnese.}, }
@article {pmid27906638, year = {2016}, author = {Mutahir, Z and Christiansen, LS and Clausen, AR and Berchtold, MW and Gojkovic, Z and Munch-Petersen, B and Knecht, W and Piškur, J}, title = {Gene duplications and losses among vertebrate deoxyribonucleoside kinases of the non-TK1 Family.}, journal = {Nucleosides, nucleotides &amp; nucleic acids}, volume = {35}, number = {10-12}, pages = {677-690}, doi = {10.1080/15257770.2016.1143557}, pmid = {27906638}, issn = {1532-2335}, mesh = {Animals ; Avian Proteins/chemistry/*genetics ; Chickens ; Evolution, Molecular ; Gene Deletion ; Gene Duplication ; Kinetics ; Organ Specificity ; Thymidine Kinase/chemistry/*genetics ; Xenopus Proteins/chemistry/*genetics ; Xenopus laevis ; }, abstract = {Deoxyribonucleoside kinases (dNKs) salvage deoxyribonucleosides (dNs) and catalyze the rate limiting step of this salvage pathway by converting dNs into corresponding monophosphate forms. These enzymes serve as an excellent model to study duplicated genes and their evolutionary history. So far, among vertebrates only four mammalian dNKs have been studied for their substrate specificity and kinetic properties. However, some vertebrates, such as fish, frogs, and birds, apparently possess a duplicated homolog of deoxycytidine kinase (dCK). In this study, we characterized a family of dCK/deoxyguanosine kinase (dGK)-like enzymes from a frog Xenopus laevis and a bird Gallus gallus. We showed that X. laevis has a duplicated dCK gene and a dGK gene, whereas G. gallus has a duplicated dCK gene but has lost the dGK gene. We cloned, expressed, purified, and subsequently determined the kinetic parameters of the dCK/dGK enzymes encoded by these genes. The two dCK enzymes in G. gallus have broader substrate specificity than their human or X. laevis counterparts. Additionally, the duplicated dCK enzyme in G. gallus might have become mitochondria. Based on our study we postulate that changing and adapting substrate specificities and subcellular localization are likely the drivers behind the evolution of vertebrate dNKs.}, }
@article {pmid27905886, year = {2016}, author = {Zhang, B and He, K and Wan, T and Chen, P and Sun, G and Liu, S and Nguyen, TS and Lin, L and Jiang, X}, title = {Multi-locus phylogeny using topotype specimens sheds light on the systematics of Niviventer (Rodentia, Muridae) in China.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {261}, pmid = {27905886}, issn = {1471-2148}, mesh = {Animals ; Bayes Theorem ; China ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; Mitochondria/genetics ; Murinae/classification/*genetics ; Phylogeny ; Phylogeography ; }, abstract = {BACKGROUND: Niviventer is a genus of white-bellied rats that are among the most common rodents in the Indo-Sundaic region. The taxonomy of the genus has undergone extensive revisions and remains controversial. The current phylogeny is unresolved and was developed primarily on the basis of mitochondrial genes. Identification is extremely difficult, and a large number of GenBank sequences seem to be problematic. We extensively sampled specimens of Niviventer in China and neighboring northern Vietnam, including topotypes of the most reported species (n = 6), subspecies (n = 8), and synonyms (n = 4). We estimated phylogenetic relationships on the basis of one mitochondrial and three nuclear genes, using concatenation and coalescent-based approaches. We also employed molecular species delimitation approaches to test the existence of cryptic and putative new species.<br><br>RESULTS: Our phylogeny was finely resolved, especially for the N. confucianus-like species. Our data provided the first support for N. brahma and N. eha as sister species, an assignment that is congruent with their morphological similarities. Species delimitation analyses provided new insight into species diversity and systematics. Three geographic populations of N. confucianus and one of N. fulvescens were supported as genetically distinct in our species delimitation analyses, while three recognized species (N. coninga, N. huang, and N. lotipes) were not strongly supported as distinct.<br><br>CONCLUSIONS: Our results suggested that several genetically distinct species may be contained within the species currently known as N. confucianus and N. fulvescens. In addition, the results of Bayesian Phylogenetics and Phylogeography (BPP) for N. coninga, N. huang, and N. lotipes indicated that either inter-specific gene flow had occurred or imperfect taxonomy was present. Morphological examinations and morphometric analyses are warranted to examine the molecular results.}, }
@article {pmid27905446, year = {2016}, author = {Taylor-Weiner, A and Zack, T and O'Donnell, E and Guerriero, JL and Bernard, B and Reddy, A and Han, GC and AlDubayan, S and Amin-Mansour, A and Schumacher, SE and Litchfield, K and Turnbull, C and Gabriel, S and Beroukhim, R and Getz, G and Carter, SL and Hirsch, MS and Letai, A and Sweeney, C and Van Allen, EM}, title = {Genomic evolution and chemoresistance in germ-cell tumours.}, journal = {Nature}, volume = {540}, number = {7631}, pages = {114-118}, pmid = {27905446}, issn = {1476-4687}, support = {K08 CA188615/CA/NCI NIH HHS/United States ; T32 HG002295/HG/NHGRI NIH HHS/United States ; U54 HG003067/HG/NHGRI NIH HHS/United States ; }, mesh = {Apoptosis ; Disease Progression ; *Drug Resistance, Neoplasm ; Evolution, Molecular ; Exome/genetics ; Genome, Human/*genetics ; Genomics ; Humans ; Loss of Heterozygosity ; Male ; Mitochondria/metabolism ; Mutation ; Nanog Homeobox Protein/deficiency ; Neoplasm Metastasis/genetics/pathology ; Neoplasms, Germ Cell and Embryonal/*drug therapy/*genetics/metabolism/pathology ; Octamer Transcription Factor-3/deficiency ; Phylogeny ; Proto-Oncogene Proteins p21(ras)/genetics ; Teratoma/genetics ; Testicular Neoplasms/drug therapy/genetics/metabolism/pathology ; Transcriptome/genetics ; Tumor Suppressor Protein p53/genetics ; }, abstract = {Germ-cell tumours (GCTs) are derived from germ cells and occur most frequently in the testes. GCTs are histologically heterogeneous and distinctly curable with chemotherapy. Gains of chromosome arm 12p and aneuploidy are nearly universal in GCTs, but specific somatic genomic features driving tumour initiation, chemosensitivity and progression are incompletely characterized. Here, using clinical whole-exome and transcriptome sequencing of precursor, primary (testicular and mediastinal) and chemoresistant metastatic human GCTs, we show that the primary somatic feature of GCTs is highly recurrent chromosome arm level amplifications and reciprocal deletions (reciprocal loss of heterozygosity), variations that are significantly enriched in GCTs compared to 19 other cancer types. These tumours also acquire KRAS mutations during the development from precursor to primary disease, and primary testicular GCTs (TGCTs) are uniformly wild type for TP53. In addition, by functional measurement of apoptotic signalling (BH3 profiling) of fresh tumour and adjacent tissue, we find that primary TGCTs have high mitochondrial priming that facilitates chemotherapy-induced apoptosis. Finally, by phylogenetic analysis of serial TGCTs that emerge with chemotherapy resistance, we show how TGCTs gain additional reciprocal loss of heterozygosity and that this is associated with loss of pluripotency markers (NANOG and POU5F1) in chemoresistant teratomas or transformed carcinomas. Our results demonstrate the distinct genomic features underlying the origins of this disease and associated with the chemosensitivity phenotype, as well as the rare progression to chemoresistance. These results identify the convergence of cancer genomics, mitochondrial priming and GCT evolution, and may provide insights into chemosensitivity and resistance in other cancers.}, }
@article {pmid27905116, year = {2017}, author = {Sanchez-Puerta, MV and García, LE and Wohlfeiler, J and Ceriotti, LF}, title = {Unparalleled replacement of native mitochondrial genes by foreign homologs in a holoparasitic plant.}, journal = {The New phytologist}, volume = {214}, number = {1}, pages = {376-387}, doi = {10.1111/nph.14361}, pmid = {27905116}, issn = {1469-8137}, mesh = {Base Sequence ; Chromosome Mapping ; DNA, Mitochondrial/genetics ; Fatty Acids, Unsaturated/genetics ; Gene Transfer, Horizontal ; *Genes, Mitochondrial ; Genes, Plant ; Genetic Speciation ; Genome, Mitochondrial ; Open Reading Frames/genetics ; Phylogeny ; Plants/*genetics ; Selection, Genetic ; *Sequence Homology, Nucleic Acid ; }, abstract = {Horizontal gene transfer (HGT) among flowering plant mitochondria occurs frequently and, in most cases, leads to nonfunctional transgenes in the recipient genome. Parasitic plants are particularly prone to this phenomenon, but their mitochondrial genomes (mtDNA) have been largely unexplored. We undertook a large-scale mitochondrial genomic study of the holoparasitic plant Lophophytum mirabile (Balanophoraceae). Comprehensive phylogenetic analyses were performed to address the frequency, origin, and impact of HGT. The sequencing of the complete mtDNA of L. mirabile revealed the unprecedented acquisition of host-derived mitochondrial genes, representing 80% of the protein-coding gene content. All but two of these foreign genes replaced the native homologs and are probably functional in energy metabolism. The genome consists of 54 circular-mapping chromosomes, 25 of which carry no intact genes. The likely functional replacement of up to 26 genes in L. mirabile represents a stunning example of the potential effect of rampant HGT on plant mitochondria. The use of host-derived genes may have a positive effect on the host-parasite relationship, but could also be the result of nonadaptive forces.}, }
@article {pmid27903701, year = {2017}, author = {Gibbin, EM and Chakravarti, LJ and Jarrold, MD and Christen, F and Turpin, V and Massamba N'Siala, G and Blier, PU and Calosi, P}, title = {Can multi-generational exposure to ocean warming and acidification lead to the adaptation of life history and physiology in a marine metazoan?.}, journal = {The Journal of experimental biology}, volume = {220}, number = {Pt 4}, pages = {551-563}, doi = {10.1242/jeb.149989}, pmid = {27903701}, issn = {1477-9145}, mesh = {*Acclimatization ; Acids/analysis ; Animals ; Aquatic Organisms/growth &amp; development/physiology ; Biological Evolution ; Body Size ; Female ; Fertility ; *Global Warming ; Hydrogen-Ion Concentration ; Male ; Mitochondria/metabolism ; Polychaeta/growth &amp; development/*physiology ; Reactive Oxygen Species/metabolism ; Reproduction ; Seawater/analysis ; }, abstract = {Ocean warming and acidification are concomitant global drivers that are currently threatening the survival of marine organisms. How species will respond to these changes depends on their capacity for plastic and adaptive responses. Little is known about the mechanisms that govern plasticity and adaptability or how global changes will influence these relationships across multiple generations. Here, we exposed the emerging model marine polychaete Ophryotrocha labronica to conditions simulating ocean warming and acidification, in isolation and in combination over five generations to identify: (i) how multiple versus single global change drivers alter both juvenile and adult life-history traits; (ii) the mechanistic link between adult physiological and fitness-related life-history traits; and (iii) whether the phenotypic changes observed over multiple generations are of plastic and/or adaptive origin. Two juvenile (developmental rate; survival to sexual maturity) and two adult (average reproductive body size; fecundity) life-history traits were measured in each generation, in addition to three physiological (cellular reactive oxygen species content, mitochondrial density, mitochondrial capacity) traits. We found that multi-generational exposure to warming alone caused an increase in juvenile developmental rate, reactive oxygen species production and mitochondrial density, decreases in average reproductive body size and fecundity, and fluctuations in mitochondrial capacity, relative to control conditions. Exposure to ocean acidification alone had only minor effects on juvenile developmental rate. Remarkably, when both drivers of global change were present, only mitochondrial capacity was significantly affected, suggesting that ocean warming and acidification act as opposing vectors of stress across multiple generations.}, }
@article {pmid27899581, year = {2017}, author = {Clima, R and Preste, R and Calabrese, C and Diroma, MA and Santorsola, M and Scioscia, G and Simone, D and Shen, L and Gasparre, G and Attimonelli, M}, title = {HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor.}, journal = {Nucleic acids research}, volume = {45}, number = {D1}, pages = {D698-D706}, pmid = {27899581}, issn = {1362-4962}, support = {15-1144/AICR_/Worldwide Cancer Research/United Kingdom ; }, mesh = {*DNA, Mitochondrial ; *Databases, Nucleic Acid ; *Genome, Mitochondrial ; Genomics/*methods ; *Haplotypes ; Humans ; Mitochondria/*genetics ; Search Engine ; Software ; Web Browser ; }, abstract = {The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. The database is intended to support both population geneticists as well as clinicians undertaking the task to assess the pathogenicity of specific mtDNA mutations. The wide application of next-generation sequencing (NGS) has provided an enormous volume of high-resolution data at a low price, increasing the availability of human mitochondrial sequencing data, which called for a cogent and significant expansion of HmtDB data content that has more than tripled in the current release. We here describe additional novel features, including: (i) a complete, user-friendly restyling of the web interface, (ii) links to the command-line stand-alone and web versions of the MToolBox package, an up-to-date tool to reconstruct and analyze human mitochondrial DNA from NGS data and (iii) the implementation of the Reconstructed Sapiens Reference Sequence (RSRS) as mitochondrial reference sequence. The overall update renders HmtDB an even more handy and useful resource as it enables a more rapid data access, processing and analysis. HmtDB is accessible at http://www.hmtdb.uniba.it/.}, }
@article {pmid29491956, year = {2016}, author = {Milani, L and Ghiselli, F and Passamonti, M}, title = {Mitochondrial selfish elements and the evolution of biological novelties.}, journal = {Current zoology}, volume = {62}, number = {6}, pages = {687-697}, pmid = {29491956}, issn = {1674-5507}, abstract = {We report the present knowledge about RPHM21, a novel male-specific mitochondrial protein with a putative role in the paternal inheritance of sperm mitochondria in the Manila clam Ruditapes philippinarum, a species with doubly uniparental inheritance of mitochondria (DUI). We review all the available data on rphm21 transcription and translation, analyze in detail its female counterpart, RPHF22, discuss the homology with RPHM21, the putative function and origin, and analyze their polymorphism. The available evidence is compatible with a viral origin of RPHM21 and supports its activity during spermatogenesis. RPHM21 is progressively accumulated in mitochondria and nuclei of spermatogenic cells, and we hypothesize it can influence mitochondrial inheritance and sexual differentiation. We propose a testable model that describes how the acquisition of selfish features by a mitochondrial lineage might have been responsible for the emergence of DUI, and for the evolution of separate sexes (gonochorism) from hermaphroditism. The appearance of DUI most likely entailed the invasion of at least 1 selfish element, and the extant DUI systems can be seen as resolved conflicts. It was proposed that hermaphroditism was the ancestral condition of bivalves, and a correlation between DUI and gonochorism was documented. We hypothesize that DUI might have driven the shift from hermaphroditism to gonochorism, with androdioecy as transition state. The invasion of sex-ratio distorters and the evolution of suppressors can prompt rapid changes among sex-determination mechanisms, and DUI might have been responsible for one of such changes in some bivalve species. If true, DUI would represent the first animal sex-determination system involving mtDNA-encoded proteins.}, }
@article {pmid27887640, year = {2016}, author = {Malecki, M and Bitton, DA and Rodríguez-López, M and Rallis, C and Calavia, NG and Smith, GC and Bähler, J}, title = {Functional and regulatory profiling of energy metabolism in fission yeast.}, journal = {Genome biology}, volume = {17}, number = {1}, pages = {240}, pmid = {27887640}, issn = {1474-760X}, support = {095598/Z/11/Z//Wellcome Trust/United Kingdom ; }, mesh = {Acetyl Coenzyme A/metabolism ; Adaptation, Biological ; Cell Nucleus/genetics/metabolism ; Energy Metabolism/*genetics ; Fermentation ; *Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; Glucose/metabolism ; High-Throughput Nucleotide Sequencing ; Mitochondria/genetics/metabolism ; Mutation ; Schizosaccharomyces/*genetics/*metabolism ; Signal Transduction ; *Transcriptome ; }, abstract = {BACKGROUND: The control of energy metabolism is fundamental for cell growth and function and anomalies in it are implicated in complex diseases and ageing. Metabolism in yeast cells can be manipulated by supplying different carbon sources: yeast grown on glucose rapidly proliferates by fermentation, analogous to tumour cells growing by aerobic glycolysis, whereas on non-fermentable carbon sources metabolism shifts towards respiration.<br><br>RESULTS: We screened deletion libraries of fission yeast to identify over 200 genes required for respiratory growth. Growth media and auxotrophic mutants strongly influenced respiratory metabolism. Most genes uncovered in the mutant screens have not been implicated in respiration in budding yeast. We applied gene-expression profiling approaches to compare steady-state fermentative and respiratory growth and to analyse the dynamic adaptation to respiratory growth. The transcript levels of most genes functioning in energy metabolism pathways are coherently tuned, reflecting anticipated differences in metabolic flows between fermenting and respiring cells. We show that acetyl-CoA synthase, rather than citrate lyase, is essential for acetyl-CoA synthesis in fission yeast. We also investigated the transcriptional response to mitochondrial damage by genetic or chemical perturbations, defining a retrograde response that involves the concerted regulation of distinct groups of nuclear genes that may avert harm from mitochondrial malfunction.<br><br>CONCLUSIONS: This study provides a rich framework of the genetic and regulatory basis of energy metabolism in fission yeast and beyond, and it pinpoints weaknesses of commonly used auxotroph mutants for investigating metabolism. As a model for cellular energy regulation, fission yeast provides an attractive and complementary system to budding yeast.}, }
@article {pmid27880778, year = {2016}, author = {Kvie, KS and Heggenes, J and Anderson, DG and Kholodova, MV and Sipko, T and Mizin, I and Røed, KH}, title = {Colonizing the High Arctic: Mitochondrial DNA Reveals Common Origin of Eurasian Archipelagic Reindeer (Rangifer tarandus).}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0165237}, pmid = {27880778}, issn = {1932-6203}, mesh = {Animals ; Arctic Regions ; DNA/chemistry/isolation &amp; purification/metabolism ; DNA, Mitochondrial/chemistry/genetics/*metabolism ; Genetic Variation ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; Reindeer/classification/*genetics ; }, abstract = {In light of current debates on global climate change it has become important to know more on how large, roaming species have responded to environmental change in the past. Using the highly variable mitochondrial control region, we revisit theories of Rangifer colonization and propose that the High Arctic archipelagos of Svalbard, Franz Josef Land, and Novaia Zemlia were colonized by reindeer from the Eurasian mainland after the last glacial maximum. Comparing mtDNA control region sequences from the three Arctic archipelagos showed a strong genetic connection between the populations, supporting a common origin in the past. A genetic connection between the three archipelagos and two Russian mainland populations was also found, suggesting colonization of the Eurasian high Arctic archipelagos from the Eurasian mainland. The age of the Franz Josef Land material (>2000 years before present) implies that Arctic indigenous reindeer colonized the Eurasian Arctic archipelagos through natural dispersal, before humans approached this region.}, }
@article {pmid27876802, year = {2016}, author = {Mottawea, W and Chiang, CK and Mühlbauer, M and Starr, AE and Butcher, J and Abujamel, T and Deeke, SA and Brandel, A and Zhou, H and Shokralla, S and Hajibabaei, M and Singleton, R and Benchimol, EI and Jobin, C and Mack, DR and Figeys, D and Stintzi, A}, title = {Altered intestinal microbiota-host mitochondria crosstalk in new onset Crohn's disease.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {13419}, pmid = {27876802}, issn = {2041-1723}, support = {R01 DK073338/DK/NIDDK NIH HHS/United States ; P40 OD010995/OD/NIH HHS/United States ; R01 DK047700/DK/NIDDK NIH HHS/United States ; R21 CA195226/CA/NCI NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; }, mesh = {Adolescent ; Animals ; Bacteria/classification/*genetics/isolation &amp; purification ; Child ; Child, Preschool ; Crohn Disease/*microbiology ; Female ; *Gastrointestinal Microbiome ; Germ-Free Life ; Humans ; Interleukin-10/genetics/metabolism ; Male ; Mice ; Mice, Knockout ; Phylogeny ; }, abstract = {Intestinal microbial dysbiosis is associated with Crohn's disease (CD). However, the mechanisms leading to the chronic mucosal inflammation that characterizes this disease remain unclear. In this report, we use systems-level approaches to study the interactions between the gut microbiota and host in new-onset paediatric patients to evaluate causality and mechanisms of disease. We report an altered host proteome in CD patients indicative of impaired mitochondrial functions. In particular, mitochondrial proteins implicated in H2S detoxification are downregulated, while the relative abundance of H2S microbial producers is increased. Network correlation analysis reveals that Atopobium parvulum controls the central hub of H2S producers. A. parvulum induces pancolitis in colitis-susceptible interleukin-10-deficient mice and this phenotype requires the presence of the intestinal microbiota. Administrating the H2S scavenger bismuth mitigates A. parvulum-induced colitis in vivo. This study reveals that host-microbiota interactions are disturbed in CD and thus provides mechanistic insights into CD pathogenesis.}, }
@article {pmid27864892, year = {2017}, author = {Haenel, GJ}, title = {Introgression of mtDNA in Urosaurus lizards: historical and ecological processes.}, journal = {Molecular ecology}, volume = {26}, number = {2}, pages = {606-623}, doi = {10.1111/mec.13930}, pmid = {27864892}, issn = {1365-294X}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/*genetics ; Female ; *Genetics, Population ; Genome, Mitochondrial ; *Hybridization, Genetic ; Lizards/*genetics ; Male ; Microsatellite Repeats ; Phylogeny ; }, abstract = {Introgression of mtDNA appears common in animals, but the implications of acquiring a novel mitochondrial genome are not well known. This study investigates mito-genome introgression between the lizard species Urosaurus graciosus, a thermal specialist, and U. ornatus, a species that occupies a wider range of thermal environments. As ectotherms, their metabolic rate is strongly influenced by the thermal environment; with mitochondria being linked to metabolic rates, overall energy budgets could be impacted by introgression. I use mitochondrial gene trees, inferred from Bayesian analyses of Cyt-B and ND1 gene sequences, along with morphology and microsatellites from nineteen populations of these two species to address if the direction and location of mito-nuclear discordance match predictions of introgression resulting from past population expansions. MtDNA is expected to move from resident species into expanding or invading species. Second, does having a heterospecific form of mitochondria impact body size, a trait strongly associated with fitness? Multiple independent introgression events of historic origin were detected. All introgression was unidirectional with U. ornatus-type mtDNA found in U. graciosus parental type individuals. This result was consistent with population expansions detected in U. graciosus but not U. ornatus. Females with heterospecific mtDNA were significantly smaller than homospecific forms, and heterospecific males had a different relationship of body mass to body length than those with homospecific mtDNA. These changes indicate a potential selective disadvantage for individuals with heterospecific mitochondria and are consistent with the theoretical expectation that deleterious alleles are more likely to persist in expanding populations.}, }
@article {pmid27861795, year = {2017}, author = {Đorđević, M and Stojković, B and Savković, U and Immonen, E and Tucić, N and Lazarević, J and Arnqvist, G}, title = {Sex-specific mitonuclear epistasis and the evolution of mitochondrial bioenergetics, ageing, and life history in seed beetles.}, journal = {Evolution; international journal of organic evolution}, volume = {71}, number = {2}, pages = {274-288}, doi = {10.1111/evo.13109}, pmid = {27861795}, issn = {1558-5646}, mesh = {*Aging ; Animals ; Coleoptera/genetics/*physiology ; Electron Transport Chain Complex Proteins/genetics/metabolism ; *Energy Metabolism ; *Epistasis, Genetic ; Female ; Insect Proteins/genetics/metabolism ; *Life History Traits ; Male ; Mitochondria/*genetics ; Selection, Genetic ; }, abstract = {The role of mitochondrial DNA for the evolution of life-history traits remains debated. We examined mitonuclear effects on the activity of the multisubunit complex of the electron transport chain (ETC) involved in oxidative phosphorylation (OXPHOS) across lines of the seed beetle Acanthoscelides obtectus selected for a short (E) or a long (L) life for more than >160 generations. We constructed and phenotyped mitonuclear introgression lines, which allowed us to assess the independent effects of the evolutionary history of the nuclear and the mitochondrial genome. The nuclear genome was responsible for the largest share of divergence seen in ageing. However, the mitochondrial genome also had sizeable effects, which were sex-specific and expressed primarily as epistatic interactions with the nuclear genome. The effects of mitonuclear disruption were largely consistent with mitonuclear coadaptation. Variation in ETC activity explained a large proportion of variance in ageing and life-history traits and this multivariate relationship differed somewhat between the sexes. In conclusion, mitonuclear epistasis has played an important role in the laboratory evolution of ETC complex activity, ageing, and life histories and these are closely associated. The mitonuclear architecture of evolved differences in life-history traits and mitochondrial bioenergetics was sex-specific.}, }
@article {pmid27856328, year = {2017}, author = {Chitambar, CR}, title = {The therapeutic potential of iron-targeting gallium compounds in human disease: From basic research to clinical application.}, journal = {Pharmacological research}, volume = {115}, number = {}, pages = {56-64}, doi = {10.1016/j.phrs.2016.11.009}, pmid = {27856328}, issn = {1096-1186}, mesh = {Animals ; Antineoplastic Agents/pharmacology/therapeutic use ; Gallium/*pharmacology/*therapeutic use ; Humans ; Iron/*metabolism ; Ligands ; Mitochondria/drug effects/metabolism ; }, abstract = {Gallium, group IIIa metal, shares certain chemical characteristics with iron which enable it to function as an iron mimetic that can disrupt iron-dependent tumor cell growth. Gallium may also display antimicrobial activity by disrupting iron homeostasis in certain bacteria and fungi. Gallium's action on iron homeostasis leads to inhibition of ribonucleotide reductase, mitochondrial function, and changes in proteins of iron transport and storage. In addition, gallium induces an increase in mitochondrial reactive oxygen species in cells which triggers downstream upregulation of metallothionein and hemoxygenase-1. Early clinical trials evaluated the efficacy of the simple gallium salts, gallium nitrate and gallium chloride. However, newer gallium-ligands such as Tris(8-quinolinolato)gallium(III) (KP46) and gallium maltolate have been developed and are undergoing clinical evaluation. Additional gallium-ligands that demonstrate antitumor activity in preclinical studies have emerged. Their mechanisms of action and their spectrum of antitumor activity may extend beyond the earlier generations of gallium compounds and warrant further investigation. This review will focus on the evolution and potential of gallium-based therapeutics.}, }
@article {pmid27849155, year = {2016}, author = {Harner, ME and Unger, AK and Geerts, WJ and Mari, M and Izawa, T and Stenger, M and Geimer, S and Reggiori, F and Westermann, B and Neupert, W}, title = {An evidence based hypothesis on the existence of two pathways of mitochondrial crista formation.}, journal = {eLife}, volume = {5}, number = {}, pages = {}, pmid = {27849155}, issn = {2050-084X}, mesh = {GTP Phosphohydrolases/*genetics/metabolism ; GTP-Binding Proteins/*genetics/metabolism ; Gene Expression ; Mitochondria/*genetics/metabolism/ultrastructure ; Mitochondrial Dynamics/physiology ; Mitochondrial Membranes/*metabolism/ultrastructure ; Mitochondrial Proteins/*genetics/metabolism ; Mitochondrial Proton-Translocating ATPases/*genetics/metabolism ; Organelle Biogenesis ; Protein Multimerization ; Saccharomyces cerevisiae/*genetics/metabolism/ultrastructure ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; }, abstract = {Metabolic function and architecture of mitochondria are intimately linked. More than 60 years ago, cristae were discovered as characteristic elements of mitochondria that harbor the protein complexes of oxidative phosphorylation, but how cristae are formed, remained an open question. Here we present experimental results obtained with yeast that support a novel hypothesis on the existence of two molecular pathways that lead to the generation of lamellar and tubular cristae. Formation of lamellar cristae depends on the mitochondrial fusion machinery through a pathway that is required also for homeostasis of mitochondria and mitochondrial DNA. Tubular cristae are formed via invaginations of the inner boundary membrane by a pathway independent of the fusion machinery. Dimerization of the F1FO-ATP synthase and the presence of the MICOS complex are necessary for both pathways. The proposed hypothesis is suggested to apply also to higher eukaryotes, since the key components are conserved in structure and function throughout evolution.}, }
@article {pmid27847816, year = {2016}, author = {Bi, C and Paterson, AH and Wang, X and Xu, Y and Wu, D and Qu, Y and Jiang, A and Ye, Q and Ye, N}, title = {Analysis of the Complete Mitochondrial Genome Sequence of the Diploid Cotton Gossypium raimondii by Comparative Genomics Approaches.}, journal = {BioMed research international}, volume = {2016}, number = {}, pages = {5040598}, pmid = {27847816}, issn = {2314-6141}, mesh = {Base Sequence ; Cell Nucleus/genetics ; DNA, Circular/genetics ; DNA, Plant/genetics ; *Diploidy ; Genes, Plant ; Genetic Variation ; Genome, Chloroplast/genetics ; *Genome, Mitochondrial ; *Genome, Plant ; Genomics/*methods ; Gossypium/*genetics ; Introns/genetics ; Likelihood Functions ; Microsatellite Repeats/genetics ; Multigene Family ; Open Reading Frames/genetics ; Phylogeny ; RNA Editing/genetics ; RNA, Transfer/genetics ; Trans-Splicing/genetics ; }, abstract = {Cotton is one of the most important economic crops and the primary source of natural fiber and is an important protein source for animal feed. The complete nuclear and chloroplast (cp) genome sequences of G. raimondii are already available but not mitochondria. Here, we assembled the complete mitochondrial (mt) DNA sequence of G. raimondii into a circular genome of length of 676,078 bp and performed comparative analyses with other higher plants. The genome contains 39 protein-coding genes, 6 rRNA genes, and 25 tRNA genes. We also identified four larger repeats (63.9 kb, 10.6 kb, 9.1 kb, and 2.5 kb) in this mt genome, which may be active in intramolecular recombination in the evolution of cotton. Strikingly, nearly all of the G. raimondii mt genome has been transferred to nucleus on Chr1, and the transfer event must be very recent. Phylogenetic analysis reveals that G. raimondii, as a member of Malvaceae, is much closer to another cotton (G. barbadense) than other rosids, and the clade formed by two Gossypium species is sister to Brassicales. The G. raimondii mt genome may provide a crucial foundation for evolutionary analysis, molecular biology, and cytoplasmic male sterility in cotton and other higher plants.}, }
@article {pmid27843124, year = {2016}, author = {Johnston, IG and Jones, NS}, title = {Evolution of Cell-to-Cell Variability in Stochastic, Controlled, Heteroplasmic mtDNA Populations.}, journal = {American journal of human genetics}, volume = {99}, number = {5}, pages = {1150-1162}, pmid = {27843124}, issn = {1537-6605}, support = {MR/J013617/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {DNA Copy Number Variations ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Databases, Genetic ; *Evolution, Molecular ; Humans ; Mitochondria/*genetics/metabolism ; Models, Theoretical ; Mutation ; Reproducibility of Results ; }, abstract = {Populations of physiologically vital mitochondrial DNA (mtDNA) molecules evolve in cells under control from the nucleus. The evolution of populations of mixed mtDNA types is complicated and poorly understood, and variability of these controlled admixtures plays a central role in the inheritance and onset of genetic disease. Here, we develop a mathematical theory describing the evolution of, and variability in, these stochastic populations for any type of cellular control, showing that cell-to-cell variability in mtDNA and mutant load inevitably increases with time, according to rates that we derive and which are notably independent of the mechanistic details of feedback signaling. We show with a set of experimental case studies that this theory explains disparate quantitative results from classical and modern experimental and computational research on heteroplasmy variance in different species. We demonstrate that our general model provides a host of specific insights, including a modification of the often-used but hard-to-interpret Wright formula to correspond directly to biological observables, the ability to quantify selective and mutational pressure in mtDNA populations, and characterization of the pronounced variability inevitably arising from the action of possible mtDNA quality-control mechanisms. Our general theoretical framework, supported by existing experimental results, thus helps us to understand and predict the evolution of stochastic mtDNA populations in cell biology.}, }
@article {pmid27841052, year = {2018}, author = {E, GX and Zhao, YJ and Huang, YF}, title = {Sheep mitochondrial heteroplasmy arises from tandem motifs and unspecific PCR amplification.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {29}, number = {1}, pages = {91-95}, doi = {10.1080/24701394.2016.1242582}, pmid = {27841052}, issn = {2470-1408}, mesh = {Animals ; *Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Regulatory Sequences, Nucleic Acid ; Sheep/*genetics ; *Tandem Repeat Sequences ; }, abstract = {The mitochondrial DNA control region (D-loop) is a widely used molecular marker in evolutionary and phylogeographic research. However, the occurrence of heteroplasmy of the D-loop region within individuals has rarely been investigated. In this study, a total of 85 Chinese sheep were used to amplify a partial D-loop region, and 15 heteroplasmic animals (17.64%) were identified. A comparative analysis of the PCR amplification and cloning of the D-loop sequences from the heteroplasmic samples revealed most of the sequencing profile from the heteroplasmic regions started at the beginning of a 75-bp random repeat motif. In addition, a total of 22 nonsyngeneic sequences with a D-loop were found in 61 of the clones obtained from the 4 random heteroplasmic and 3 homozygote animals, and their genomic locations were compared for homology. In summary, the D-Loop sequencing profiles appear to be heteroplasmic and could arise from tandem repeat motifs and unspecific replication during PCR amplification; however, they are not likely due to the presence of multiple mitochondrial genomes within an individual.}, }
@article {pmid27840392, year = {2016}, author = {Osawa, S and Su, ZH and Nishikawa, M and Tominaga, O}, title = {Silent evolution.}, journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences}, volume = {92}, number = {9}, pages = {455-461}, pmid = {27840392}, issn = {1349-2896}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Coleoptera/genetics/*physiology ; Electron Transport Complex IV/genetics ; Genes, Insect ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Phylogenetic analyses using mitochondrial DNA sequences of several kinds of beetles have shown that their evolution included a silent stage in which no morphological changes took place. We thus propose a new category of evolutionary process called "silent evolution".}, }
@article {pmid27837088, year = {2017}, author = {Garibay-Hernández, A and Barkla, BJ and Vera-Estrella, R and Martinez, A and Pantoja, O}, title = {Membrane Proteomic Insights into the Physiology and Taxonomy of an Oleaginous Green Microalga.}, journal = {Plant physiology}, volume = {173}, number = {1}, pages = {390-416}, pmid = {27837088}, issn = {1532-2548}, mesh = {Algal Proteins/*metabolism ; Base Sequence ; Carbon/metabolism ; Cell Membrane/*metabolism ; Electron Transport ; Electrophoresis ; Lipid Metabolism ; Mass Spectrometry ; Membrane Proteins/chemistry/*metabolism ; Microalgae/*classification/metabolism/*physiology ; Mitochondria/metabolism ; Oxidative Phosphorylation ; Photosynthesis ; Phylogeny ; Protein Domains ; Proteome/*metabolism ; Proteomics/*methods ; Subcellular Fractions/metabolism ; }, abstract = {Ettlia oleoabundans is a nonsequenced oleaginous green microalga. Despite the significant biotechnological interest in producing value-added compounds from the acyl lipids of this microalga, a basic understanding of the physiology and biochemistry of oleaginous microalgae is lacking, especially under nitrogen deprivation conditions known to trigger lipid accumulation. Using an RNA sequencing-based proteomics approach together with manual annotation, we are able to provide, to our knowledge, the first membrane proteome of an oleaginous microalga. This approach allowed the identification of novel proteins in E. oleoabundans, including two photoprotection-related proteins, Photosystem II Subunit S and Maintenance of Photosystem II under High Light1, which were considered exclusive to higher photosynthetic organisms, as well as Retinitis Pigmentosa Type 2-Clathrin Light Chain, a membrane protein with a novel domain architecture. Free-flow zonal electrophoresis of microalgal membranes coupled to liquid chromatography-tandem mass spectrometry proved to be a useful technique for determining the intracellular location of proteins of interest. Carbon-flow compartmentalization in E. oleoabundans was modeled using this information. Molecular phylogenetic analyses of protein markers and 18S ribosomal DNA support the reclassification of E. oleoabundans within the trebouxiophycean microalgae, rather than with the Chlorophyceae class, in which it is currently classified, indicating that it may not be closely related to the model green alga Chlamydomonas reinhardtii A detailed survey of biological processes taking place in the membranes of nitrogen-deprived E. oleoabundans, including lipid metabolism, provides insights into the basic biology of this nonmodel organism.}, }
@article {pmid27836782, year = {2016}, author = {Katz, ME and Braunberger, KS and Kelly, JM}, title = {Role of HxkC, a mitochondrial hexokinase-like protein, in fungal programmed cell death.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {97}, number = {}, pages = {36-45}, doi = {10.1016/j.fgb.2016.11.002}, pmid = {27836782}, issn = {1096-0937}, mesh = {Acetylglucosamine/genetics/metabolism ; Animals ; Apoptosis/*genetics ; Aspergillus nidulans/*genetics ; DNA Fragmentation ; Fungal Proteins/*genetics ; Gene Expression Regulation, Fungal/genetics ; Hexokinase/*genetics ; Mammals ; Mitochondria/genetics ; Tumor Suppressor Protein p53/genetics ; }, abstract = {Apoptosis is a form of programmed cell death (PCD) that occurs during animal development and is also triggered by a variety of signals including nutrient or oxidative stress, hypoxia, DNA damage, viral infection and oncogenic transformation. Though apoptotic-like PCD also occurs in plants and fungi, genes encoding several of the key players in mammalian apoptosis (p53 and BH-domain proteins) have not been identified in these kingdoms. In this report we investigated whether HxkC, a mitochondrial hexokinase-like protein, and XprG, a putative p53-like transcription factor similar to Ndt80, play a role in programmed cell death in the filamentous fungus Aspergillus nidulans. We show that a mutant lacking HxkC is more sensitive to oxidative stress. Autolysis, a form of fungal programmed cell death triggered by carbon starvation, is accelerated in the hxkCΔ1 mutant but not the hxkCΔ1 xprGΔ1 double mutant. In the absence of nutrient stress, the hxkCΔ1 mutant displays XprG-dependent DNA fragmentation typical of apoptosis and elevated levels of intracellular protease. HxkC and XprG are required for catabolism of N-acetylglucosamine, as in Trichoderma reesei. We show that XprG is present in the nucleus. We conclude that, like mammalian mitochondrial hexokinase, HxkC has anti-apoptotic activity and the XprG transcription factor has a pro-apoptotic role in filamentous fungi.}, }
@article {pmid27836743, year = {2017}, author = {Keenan, KA and Grove, TJ and Oldham, CA and O'Brien, KM}, title = {Characterization of mitochondrial glycerol-3-phosphate acyltransferase in notothenioid fishes.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {204}, number = {}, pages = {9-26}, doi = {10.1016/j.cbpb.2016.11.001}, pmid = {27836743}, issn = {1879-1107}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cold Temperature ; Evolution, Molecular ; Glycerol-3-Phosphate O-Acyltransferase/chemistry/*genetics ; Mitochondria/*enzymology ; Perciformes/*genetics/physiology ; RNA, Messenger/genetics/metabolism ; }, abstract = {Hearts of Antarctic icefishes (suborder Notothenioidei, family Channichthyidae) have higher densities of mitochondria, and mitochondria have higher densities of phospholipids, compared to red-blooded notothenioids. Glycerol-3-phosphate acyltransferase (GPAT) catalyzes the rate-limiting step in glycerolipid biosynthesis. There are four isoforms of GPAT in vertebrates; GPAT1 and GPAT2 are localized to the outer mitochondrial membrane, whereas GPAT3 and GPAT4 are localized to the endoplasmic reticulum membrane. We hypothesized that transcript levels of GPAT1 and/or GPAT2 would mirror densities of mitochondrial phospholipids and be higher in the icefish Chaenocephalus aceratus compared to the red-blooded species Notothenia coriiceps. Transcript levels of GPAT1 were quantified in heart ventricles and liver using qRT-PCR. Additionally, GPAT1 cDNA was sequenced in the Antarctic notothenioids, C. aceratus and N. coriiceps, and in the sub-Antarctic notothenioid, Eleginops maclovinus, to identify amino acid substitutions that may maintain GPAT1 function at cold temperature. Transcript levels of GPAT1 were higher in liver compared to heart ventricles but were not significantly different between the two species. In contrast, transcripts of GPAT2 were only detected in ventricle where they were 6.6-fold higher in C. aceratus compared to N. coriiceps. These data suggest GPAT1 may be more important for synthesizing triacylglycerol, whereas GPAT2 may regulate synthesis of phospholipids. GPAT1 amino acid sequences are highly conserved among the three notothenioids with 97.9-98.7% identity. Four amino acid substitutions within the cytosolic region of Antarctic notothenioid GPAT1 may maintain conformational changes necessary for binding and catalysis at cold temperature.}, }
@article {pmid27834740, year = {2016}, author = {Speijer, D}, title = {Being right on Q: shaping eukaryotic evolution.}, journal = {The Biochemical journal}, volume = {473}, number = {22}, pages = {4103-4127}, pmid = {27834740}, issn = {1470-8728}, mesh = {Animals ; Biological Evolution ; Electron Transport Complex I/metabolism ; Eukaryota/*metabolism ; Mitochondria/metabolism ; Peroxisomes/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {Reactive oxygen species (ROS) formation by mitochondria is an incompletely understood eukaryotic process. I proposed a kinetic model [BioEssays (2011) 33: , 88-94] in which the ratio between electrons entering the respiratory chain via FADH2 or NADH (the F/N ratio) is a crucial determinant of ROS formation. During glucose breakdown, the ratio is low, while during fatty acid breakdown, the ratio is high (the longer the fatty acid, the higher is the ratio), leading to higher ROS levels. Thus, breakdown of (very-long-chain) fatty acids should occur without generating extra FADH2 in mitochondria. This explains peroxisome evolution. A potential ROS increase could also explain the absence of fatty acid oxidation in long-lived cells (neurons) as well as other eukaryotic adaptations, such as dynamic supercomplex formation. Effective combinations of metabolic pathways from the host and the endosymbiont (mitochondrion) allowed larger varieties of substrates (with different F/N ratios) to be oxidized, but high F/N ratios increase ROS formation. This might have led to carnitine shuttles, uncoupling proteins, and multiple antioxidant mechanisms, especially linked to fatty acid oxidation [BioEssays (2014) 36: , 634-643]. Recent data regarding peroxisome evolution and their relationships with mitochondria, ROS formation by Complex I during ischaemia/reperfusion injury, and supercomplex formation adjustment to F/N ratios strongly support the model. I will further discuss the model in the light of experimental findings regarding mitochondrial ROS formation.}, }
@article {pmid27833995, year = {2017}, author = {Thomas, P and Sekhar, AC}, title = {Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {885-899}, pmid = {27833995}, issn = {1432-184X}, mesh = {Bacteria/*classification/*genetics/isolation &amp; purification ; Biodiversity ; Chloroplasts/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics ; Ecosystem ; Endophytes/*classification/*genetics/isolation &amp; purification ; India ; Metagenome ; Metagenomics/methods ; Microbiota ; Mitochondria/genetics ; Musa/*microbiology ; *Phylogeny ; Plant Shoots/*growth &amp; development/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {The interior of plants constitutes a unique environment for microorganisms with various organisms inhabiting as endophytes. Unlike subterranean plant parts, aboveground parts are relatively less explored for endophytic microbial diversity. We employed a combination of cultivation and molecular approaches to study the endophytic bacterial diversity in banana shoot-tips. Cultivable bacteria from 20 sucker shoot-tips of cv. Grand Naine included 37 strains under 16 genera and three phyla (Proteobacteria, Actinobacteria, Firmicutes). 16S rRNA gene-ribotyping approach on 799f and 1492r PCR-amplicons to avoid plant organelle sequences was ineffective showing limited bacterial diversity. 16S rRNA metagene profiling targeting the V3-V4 hypervariable region after filtering out the chloroplast (74.2 %), mitochondrial (22.9 %), and unknown sequences (1.1 %) revealed enormous bacterial diversity. Proteobacteria formed the predominant phylum (64 %) succeeded by Firmicutes (12.1 %), Actinobacteria (9.5 %), Bacteroidetes (6.4 %), Planctomycetes, Cyanobacteria, and minor shares (<1 %) of 14 phyla including several candidate phyla besides the domain Euryarchaeota (0.2 %). Microbiome analysis of single shoot-tips through 16S rRNA V3 region profiling showed similar taxonomic richness and diversity and was less affected by plant sequence interferences. DNA extraction kit ominously influenced the phylogenetic diversity. The study has revealed vast diversity of normally uncultivable endophytic bacteria prevailing in banana shoot-tips (20 phyla, 46 classes) with about 2.6 % of the deciphered 269 genera and 1.5 % of the 656 observed species from the same source of shoot-tips attained through cultivation. The predominant genera included several agriculturally important bacteria. The study reveals an immense ecosystem of endophytic bacteria in banana shoot tissues endorsing the earlier documentation of intracellular "Cytobacts" and "Peribacts" with possible roles in plant holobiome and hologenome.}, }
@article {pmid27833437, year = {2016}, author = {Minton, RL and Cruz, MA and Farman, ML and Perez, KE}, title = {Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda).}, journal = {ZooKeys}, volume = {}, number = {626}, pages = {137-154}, pmid = {27833437}, issn = {1313-2989}, abstract = {Helicoidea is a diverse group of land snails with a global distribution. While much is known regarding the relationships of helicoid taxa, comparatively little is known about the evolution of the mitochondrial genome in the superfamily. We sequenced two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 representing the first such data from the helicoid family Polygyridae, and used them in an evolutionary analysis of mitogenomic gene order. We found the mitochondrial genome of Praticolella mexicana to be 14,008 bp in size, possessing the typical 37 metazoan genes. Multiple alternate stop codons are used, as are incomplete stop codons. Mitogenome size and nucleotide content is consistent with other helicoid species. Our analysis of gene order suggested that Helicoidea has undergone four mitochondrial rearrangements in the past. Two rearrangements were limited to tRNA genes only, and two involved protein coding genes.}, }
@article {pmid27825872, year = {2017}, author = {Reem, E and Douek, J and Paz, G and Katzir, G and Rinkevich, B}, title = {Phylogenetics, biogeography and population genetics of the ascidian Botryllus schlosseri in the Mediterranean Sea and beyond.}, journal = {Molecular phylogenetics and evolution}, volume = {107}, number = {}, pages = {221-231}, doi = {10.1016/j.ympev.2016.10.005}, pmid = {27825872}, issn = {1095-9513}, mesh = {Alleles ; Animals ; Base Sequence ; Bayes Theorem ; Electron Transport Complex IV/genetics ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Mediterranean Sea ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; *Phylogeny ; *Phylogeography ; Principal Component Analysis ; Urochordata/*classification/*genetics ; }, abstract = {The wide distribution of the ascidian Botryllus schlosseri along the Mediterranean coasts has been documented since the eighteenth century. However, despite copious documentation, analyses of dispersal modes and genetic profiles were limited to local populations or restricted regions. In order to get a pan-Mediterranean overview, 288 specimens from 11 populations of B. schlosseri from the western and eastern Mediterranean basins were sampled and analyzed using five microsatellite loci and COI sequences. Both molecular markers revealed high polymorphisms, with 182 microsatellites alleles and 54 COI haplotypes. Overall, Fst, Dest, and COI Фpt values were 0.146, 0.635 and 0.322, respectively, reflecting a high genetic diversity and a significant genetic structure as compared to other B. schlosseri populations worldwide, reflected by substantially higher values for effective number of alleles (Ne) in the Mediterranean. A phylogenetic analysis of the COI sequences resulted in four distinct clades and two molecular operational taxonomic units (OTUs). We recorded a stronger genetic structure among the populations of the eastern basin compared to the western basin (microsatellites Fst=0.217 versus 0.082; COI Фpt=0.416 versus 0.171), suggesting either a restricted connectivity between the basins or a stronger genetic drift in each basin. The occurrence of two OTUs and different ecological conditions may also contribute to this finding. Mean Nei's genetic distance in the eastern Mediterranean populations was more than three times higher compared to the western basin. No correlation was observed between geographic and genetic distances (Mantel test), suggesting that maritime transport is the main dispersal vector of B. schlosseri colonies. The possibility that the Mediterranean is a center of diversity for B. schlosseri, and probably its site of origin, is further discussed.}, }
@article {pmid27821209, year = {2017}, author = {Adriano, EA and Okamura, B}, title = {Motility, morphology and phylogeny of the plasmodial worm, Ceratomyxa vermiformis n. sp. (Cnidaria: Myxozoa: Myxosporea).}, journal = {Parasitology}, volume = {144}, number = {2}, pages = {158-168}, doi = {10.1017/S0031182016001852}, pmid = {27821209}, issn = {1469-8161}, mesh = {Animals ; Brazil ; Fish Diseases/epidemiology/parasitology ; Fishes ; Motor Activity/*physiology ; Myxozoa/*genetics/*physiology/ultrastructure ; *Phylogeny ; Rivers ; Species Specificity ; Spores ; }, abstract = {The Myxozoa demonstrate extensive morphological simplification and miniaturization relative to their free-living cnidarian ancestors. This is particularly pronounced in the highly derived myxosporeans, which develop as plasmodia and pseudoplasmodia. To date, motility in these stages has been linked with membrane deformation (e.g. as pseudopodia and mobile folds). Here we illustrate a motile, elongate plasmodium that undergoes coordinated undulatory locomotion, revealing remarkable convergence to a functional worm at the cellular level. Ultrastructural and confocal analyses of these plasmodia identify a highly differentiated external layer containing an actin-rich network, long tubular mitochondria, abundant microtubules, a secreted glycocalyx layer, and an internal region where sporogony occurs and which contains homogeneously distributed granular/fibrillar material. We consider how some of these features may support motility. We also describe the species based on spore morphology and SSU rDNA sequence data, undertake molecular phylogenetic analysis to place it within an early-diverging clade of the ceratomyxids, and evaluate the resultant implications for classification (validity of the genus Meglitschia) and for inferring early host environments (freshwater) of ceratomyxids.}, }
@article {pmid27816016, year = {2016}, author = {Yubuki, N and Huang, SS and Leander, BS}, title = {Comparative Ultrastructure of Fornicate Excavates, Including a Novel Free-living Relative of Diplomonads: Aduncisulcus paluster gen. et sp. nov.}, journal = {Protist}, volume = {167}, number = {6}, pages = {584-596}, doi = {10.1016/j.protis.2016.10.001}, pmid = {27816016}, issn = {1618-0941}, mesh = {Diplomonadida/*classification/*ultrastructure ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; }, abstract = {The Fornicata (Excavata) is a group of microbial eukaryotes consisting of both free-living lineages (e.g., Carpediemonas) and parasitic lineages (e.g. Giardia and Retortamonas) that share several molecular and ultrastructural traits. Carpediemonas-like organisms (CLOs) are free-living lineages that diverged early within the Fornicata, making them important for inferring the early evolutionary history of the group. Molecular phylogenetic analyses of free-living fornicates, including sequences from environmental PCR surveys, have demonstrated that CLOs form six different lineages. Representatives from five of these lineages have been studied at the ultrastructural level. The sixth lineage has been labeled "CL2" but has yet to be described with ultrastructural data. Improved understanding of CL2 is expected to help elucidate character evolution within the Fornicata. Therefore, we comprehensively characterized CL2 (NY0171) in order to understand the ultrastructural traits in this lineage, especially the organization of the microtubular root system (i.e., the flagellar apparatus). CL2 shared several morphological features with other fornicates, including reduced mitochondria and an arched B fiber bridging flagellar roots 1 and 2. The molecular phylogenetic position combined with some distinctive ultrastructural traits (e.g., a curved ventral groove) in CL2 required us to establish a new genus and species, Aduncisulcus paluster gen. et sp. nov.}, }
@article {pmid27814661, year = {2017}, author = {Morley, SA and Nielsen, BL}, title = {Plant mitochondrial DNA.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {22}, number = {6}, pages = {1023-1032}, doi = {10.2741/4531}, pmid = {27814661}, issn = {2768-6698}, support = {R15 GM066787/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA Replication ; DNA, Mitochondrial/*genetics/metabolism ; DNA, Plant/*genetics/metabolism ; Genome, Mitochondrial ; Genome, Plant ; Mitochondria/genetics/metabolism ; Phylogeny ; }, abstract = {Plants possess mitochondrial genomes that are large and complex compared to animals. Nearly all animal mitochondrial genomes are about 16.5. kbp in length, whereas plant mitochondrial genomes range between 200-2,000 kbp. This is curious if we assume modern mitochondria originated from a common alpha-proteobacterial ancestor. Despite their size, plant mitochondrial genomes do not contain significantly more genes than their animal counterparts. Most of the additional DNA found in plant mitochondrial genomes consists of large introns, repeats and non-coding regions. Furthermore, plant mtDNA does not exist as large circular DNA molecules but mostly as a collection of linear DNA with combinations of smaller circular and branched molecules. Studies into these highly fragmented genomes heavily imply that recombination is the main mechanism driving replication of plant mtDNA.}, }
@article {pmid27814642, year = {2017}, author = {Degli Esposti, M}, title = {The long story of mitochondrial DNA and respiratory complex I.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {22}, number = {4}, pages = {722-731}, doi = {10.2741/4512}, pmid = {27814642}, issn = {2768-6698}, mesh = {Animals ; DNA, Mitochondrial/*genetics/*metabolism ; Electron Transport Complex I/chemistry/*genetics/*metabolism ; Evolution, Molecular ; Genes, Mitochondrial ; Humans ; Mitochondrial Proteins/chemistry/genetics/metabolism ; Phylogeny ; Protein Subunits ; }, abstract = {This article examines the long story of the relationship between mitochondrial DNA (mtDNA) and respiratory complex I, NADH:Ubiquinone Oxidoreductase, from its beginning in the genome of the bacterial endosymbiont which then evolved into the mitochondria of our cells. The story begins with the evolution of ancient forms of bacterial complex I into the Nuo14 complex I that was present in the alpha proteobacterial ancestor of mitochondria. The story then becomes complicated in the diversity of eukaryotic organisms that are currently recognized. Therefore, it does not have a clear end, because currently available information shows different situations of metabolic adaptation and gene loss, indicating cases of de-evolution of the original protonmotive complex into a system that may fundamentally assist [FeFe]-hydrogenases in re-oxidising metabolically produced NADH under anaerobic conditions. The history of complex I is thus a never ending story of molecular and physiological evolution producing new perspectives for studying the enzyme complex that occupies the largest proportion of mitochondrial DNA.}, }
@article {pmid27812979, year = {2016}, author = {Bullon, P and Marin-Aguilar, F and Roman-Malo, L}, title = {AMPK/Mitochondria in Metabolic Diseases.}, journal = {Experientia supplementum (2012)}, volume = {107}, number = {}, pages = {129-152}, doi = {10.1007/978-3-319-43589-3_6}, pmid = {27812979}, issn = {1664-431X}, mesh = {AMP-Activated Protein Kinases/*genetics/metabolism ; Autophagy/genetics ; Diabetes Mellitus/drug therapy/enzymology/*genetics/pathology ; Energy Metabolism/genetics ; Gene Expression Regulation ; Homeostasis/genetics ; Humans ; Hypoglycemic Agents/therapeutic use ; Inflammation ; Insulin Resistance/genetics ; Metabolic Syndrome/drug therapy/enzymology/*genetics/pathology ; Metformin/therapeutic use ; Mitochondria/*enzymology/pathology ; Obesity/drug therapy/enzymology/*genetics/pathology ; Protein Subunits/genetics/metabolism ; Signal Transduction ; Thiazolidinediones/therapeutic use ; }, abstract = {The obtaining of nutrients is the most important task in our lives. Energy is central to life's evolutions; this was one of the aspect that induced the selection of the more adaptable and more energetically profitable species. Nowadays things have changed in our modern society. A high proportion of people has access to plenty amount of food and the obesity appear as one of the pathological characteristics of our society. Energy is obtained essentially in the mitochondria with the transfer of protons across the inner membrane that produce ATP. The exactly regulation of the synthesis and degradation of ATP (ATP ↔ ADP + phosphate) is essential to all form of life. This task is performed by the 5' adenosine monophosphate-activated protein kinase (AMPK). mtDNA is highly exposed to oxidative damage and could play a central role in human health and disease. This high potential rate of abnormalities is controlled by one of the most complex mechanism: the autophagy. AMPK appears to be the key cellular energy sensor involved in multiple cellular mechanisms and is essential to have a good metabolic homeostasis to face all the aggression and start the inflammatory reaction. Therefore its disturbances have been related with multiple diseases. Recent findings support the role of AMPK in inflammation and immunity such as Metabolic Syndrome, Obesity and Diabetes. All these Metabolic Disorders are considered pandemics and they need an adequate control and prevention. One important way to achieve it is deepen in the pathogenic mechanisms. Mitochondria and AMPK are the key elements through which it happen, their knowledge and research allow us to a better management. The discovery and use of drugs that can modulate them is imperative to improve our way of manage the metabolic disorders.}, }
@article {pmid27812116, year = {2016}, author = {Cohen, T and Levin, L and Mishmar, D}, title = {Ancient Out-of-Africa Mitochondrial DNA Variants Associate with Distinct Mitochondrial Gene Expression Patterns.}, journal = {PLoS genetics}, volume = {12}, number = {11}, pages = {e1006407}, pmid = {27812116}, issn = {1553-7404}, mesh = {Base Sequence/genetics ; Black People ; DNA Copy Number Variations/genetics ; DNA, Mitochondrial/*biosynthesis/genetics ; *Evolution, Molecular ; Gene Expression Profiling ; Haplotypes ; Human Genome Project ; Humans ; Mitochondria/*genetics ; Mitochondrial Proteins/*biosynthesis/genetics ; Polymorphism, Single Nucleotide ; RNA-Binding Proteins/biosynthesis/genetics ; Ribosomal Proteins/biosynthesis/genetics ; }, abstract = {Mitochondrial DNA (mtDNA) variants have been traditionally used as markers to trace ancient population migrations. Although experiments relying on model organisms and cytoplasmic hybrids, as well as disease association studies, have served to underline the functionality of certain mtDNA SNPs, only little is known of the regulatory impact of ancient mtDNA variants, especially in terms of gene expression. By analyzing RNA-seq data of 454 lymphoblast cell lines from the 1000 Genomes Project, we found that mtDNA variants defining the most common African genetic background, the L haplogroup, exhibit a distinct overall mtDNA gene expression pattern, which was independent of mtDNA copy numbers. Secondly, intra-population analysis revealed subtle, yet significant, expression differences in four tRNA genes. Strikingly, the more prominent African mtDNA gene expression pattern best correlated with the expression of nuclear DNA-encoded RNA-binding proteins, and with SNPs within the mitochondrial RNA-binding proteins PTCD1 and MRPS7. Our results thus support the concept of an ancient regulatory transition of mtDNA-encoded genes as humans left Africa to populate the rest of the world.}, }
@article {pmid27812024, year = {2016}, author = {Jiang, F and Pan, X and Li, X and Yu, Y and Zhang, J and Jiang, H and Dou, L and Zhu, S}, title = {The first complete mitochondrial genome of Dacus longicornis (Diptera: Tephritidae) using next-generation sequencing and mitochondrial genome phylogeny of Dacini tribe.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {36426}, pmid = {27812024}, issn = {2045-2322}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Codon, Terminator ; DNA, Mitochondrial/chemistry/isolation &amp; purification/metabolism ; Electron Transport Complex IV/chemistry/genetics ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/chemistry/genetics ; RNA, Transfer/chemistry/genetics ; Sequence Analysis, DNA ; Tephritidae/classification/*genetics ; }, abstract = {The genus Dacus is one of the most economically important tephritid fruit flies. The first complete mitochondrial genome (mitogenome) of Dacus species - D. longicornis was sequenced by next-generation sequencing in order to develop the mitogenome data for this genus. The circular 16,253 bp mitogenome is the typical set and arrangement of 37 genes present in the ancestral insect. The mitogenome data of D. longicornis was compared to all the published homologous sequences of other tephritid species. We discovered the subgenera Bactrocera, Daculus and Tetradacus differed from the subgenus Zeugodacus, the genera Dacus, Ceratitis and Procecidochares in the possession of TA instead of TAA stop codon for COI gene. There is a possibility that the TA stop codon in COI is the synapomorphy in Bactrocera group in the genus Bactrocera comparing with other Tephritidae species. Phylogenetic analyses based on the mitogenome data from Tephritidae were inferred by Bayesian and Maximum-likelihood methods, strongly supported the sister relationship between Zeugodacus and Dacus.}, }
@article {pmid27717801, year = {2017}, author = {Surve, SV and Jensen, BC and Heestand, M and Mazet, M and Smith, TK and Bringaud, F and Parsons, M and Schnaufer, A}, title = {NADH dehydrogenase of Trypanosoma brucei is important for efficient acetate production in bloodstream forms.}, journal = {Molecular and biochemical parasitology}, volume = {211}, number = {}, pages = {57-61}, pmid = {27717801}, issn = {1872-9428}, support = {MR/L019701/1/MRC_/Medical Research Council/United Kingdom ; R01 AI069057/AI/NIAID NIH HHS/United States ; G0600129/MRC_/Medical Research Council/United Kingdom ; 093228/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Acetates/*metabolism ; Electron Transport Complex I/chemistry/metabolism ; Life Cycle Stages ; Mitochondria/metabolism ; Mutation ; NADH Dehydrogenase/genetics/*metabolism ; Protein Subunits/genetics/metabolism ; Protein Transport ; Trypanosoma brucei brucei/genetics/*growth &amp; development/*metabolism ; }, abstract = {In the slender bloodstream form, Trypanosoma brucei mitochondria are repressed for many functions. Multiple components of mitochondrial complex I, NADH:ubiquinone oxidoreductase, are expressed in this stage, but electron transfer through complex I is not essential. Here we investigate the role of the parasite's second NADH:ubiquinone oxidoreductase, NDH2, which is composed of a single subunit that also localizes to the mitochondrion. While inducible knockdown of NDH2 had a modest growth effect in bloodstream forms, NDH2 null mutants, as well as inducible knockdowns in a complex I deficient background, showed a greater reduction in growth. Altering the NAD[+]/NADH balance would affect numerous processes directly and indirectly, including acetate production. Indeed, loss of NDH2 led to reduced levels of acetate, which is required for several essential pathways in bloodstream form T. brucei and which may have contributed to the observed growth defect. In conclusion our study shows that NDH2 is important, but not essential, in proliferating bloodstream forms of T. brucei, arguing that the mitochondrial NAD[+]/NADH balance is important in this stage, even though the mitochondrion itself is not actively engaged in the generation of ATP.}, }
@article {pmid27449222, year = {2016}, author = {Han, Z and Qin, Y and Kong, F and Deng, Y and Wang, Z and Shen, G and Wang, J and Duan, B and Li, R}, title = {Cloning and Expression Analysis of Eight Upland Cotton Pentatricopeptide Repeat Family Genes.}, journal = {Applied biochemistry and biotechnology}, volume = {180}, number = {6}, pages = {1243-1255}, doi = {10.1007/s12010-016-2164-y}, pmid = {27449222}, issn = {1559-0291}, mesh = {Amino Acid Sequence ; Cloning, Molecular ; *Gene Expression Regulation, Plant/drug effects ; *Genes, Plant ; Gossypium/drug effects/*genetics/physiology ; *Multigene Family ; Phylogeny ; Plant Proteins/chemistry/*genetics/metabolism ; *Repetitive Sequences, Amino Acid ; Sodium Chloride/pharmacology ; Stress, Physiological/drug effects/genetics ; Subcellular Fractions/metabolism ; Time Factors ; }, abstract = {The pentatricopeptide repeat (PPR) gene family is one of the largest gene families in plants. Most PPR genes are localized in mitochondria and chloroplasts functioning in regulation of plant growth and development, fertility restoration for cytoplasmic male sterility (CMS), and stress defense. In this study, using in silico cloning and PCR amplification with degenerate primers based on Arabidopsis PPR genes, we cloned eight new full-length PPR genes encoding protein sequences ranging from 458 to 875 amino acids, with 8 to 16 repetitive PPR elements in upland cotton and all of them lack introns. Expression analysis revealed that eight PPR genes were differently expressed in roots, stems, leaves, and floral buds. As for GhI12, its expression in floral buds at days 3-5 was significantly higher in line 777R (restorer line) than in line 777A (CMS line). Further tests with real-time PCR showed that GhI12 expression peaked at day 3 in 777R, followed by a gradual decline, while its expression fluctuated in 777A, peaking at day 5 and day 13. In addition, Gh155c17 and GhI12 were upregulated under salt stress. This is the first report of upland cotton PPR genes involved in salt stress response.}, }
@article {pmid27806045, year = {2016}, author = {Schröder, MS and Martinez de San Vicente, K and Prandini, TH and Hammel, S and Higgins, DG and Bagagli, E and Wolfe, KH and Butler, G}, title = {Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species.}, journal = {PLoS genetics}, volume = {12}, number = {11}, pages = {e1006404}, pmid = {27806045}, issn = {1553-7404}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Candida/*genetics/growth &amp; development ; Diploidy ; *Genetic Speciation ; Genome, Fungal ; Haplotypes ; Heterozygote ; *Hybridization, Genetic ; Larva/genetics ; Mitochondria/genetics ; *Phylogeny ; Polymorphism, Single Nucleotide ; Saccharomyces cerevisiae/genetics ; }, abstract = {Mating between different species produces hybrids that are usually asexual and stuck as diploids, but can also lead to the formation of new species. Here, we report the genome sequences of 27 isolates of the pathogenic yeast Candida orthopsilosis. We find that most isolates are diploid hybrids, products of mating between two unknown parental species (A and B) that are 5% divergent in sequence. Isolates vary greatly in the extent of homogenization between A and B, making their genomes a mosaic of highly heterozygous regions interspersed with homozygous regions. Separate phylogenetic analyses of SNPs in the A- and B-derived portions of the genome produces almost identical trees of the isolates with four major clades. However, the presence of two mutually exclusive genotype combinations at the mating type locus, and recombinant mitochondrial genomes diagnostic of inter-clade mating, shows that the species C. orthopsilosis does not have a single evolutionary origin but was created at least four times by separate interspecies hybridizations between parents A and B. Older hybrids have lost more heterozygosity. We also identify two isolates with homozygous genomes derived exclusively from parent A, which are pure non-hybrid strains. The parallel emergence of the same hybrid species from multiple independent hybridization events is common in plant evolution, but is much less documented in pathogenic fungi.}, }
@article {pmid27804847, year = {2017}, author = {Schwartz, L and Supuran, CT and Alfarouk, KO}, title = {The Warburg Effect and the Hallmarks of Cancer.}, journal = {Anti-cancer agents in medicinal chemistry}, volume = {17}, number = {2}, pages = {164-170}, doi = {10.2174/1871520616666161031143301}, pmid = {27804847}, issn = {1875-5992}, mesh = {Acidosis/metabolism ; Adenosine Triphosphate/*metabolism ; Alkalosis/metabolism ; Animals ; Carbon Dioxide/metabolism ; Cell Proliferation ; Citrates/metabolism ; Glucose/*metabolism ; Glycolysis ; Humans ; Mitochondria/metabolism/pathology ; Neoplasms/*metabolism/pathology ; *Oxidative Phosphorylation ; Pentose Phosphate Pathway ; Thioctic Acid/metabolism ; }, abstract = {It is a longstanding debate whether cancer is one disease or a set of very diverse diseases. The goal of this paper is to suggest strongly that most of (if not all) the hallmarks of cancer could be the consequence of the Warburg's effect. As a result of the metabolic impairment of the oxidative phosphorylation, there is a decrease in ATP concentration. To compensate the reduced energy yield, there is massive glucose uptake, anaerobic glycolysis, with an up-regulation of the Pentose Phosphate Pathway resulting in increased biosynthesis leading to increased cell division and local pressure. This increased pressure is responsible for the fractal shape of the tumor, the secretion of collagen by the fibroblasts and plays a critical role in metastatic spread. The massive extrusion of lactic acid contributes to the extracellular acidity and the activation of the immune system. The decreased oxidative phosphorylation leads to impairment in CO2 levels inside and outside the cell, with increased intracellular alkalosis and contribution of carbonic acid to extracellular acidosis-mediated by at least two cancer-associated carbonic anhydrase isoforms. The increased intracellular alkalosis is a strong mitogenic signal, which bypasses most inhibitory signals. Mitochondrial disappearance (such as seen in very aggressive tumors) is a consequence of mitochondrial swelling, itself a result of decreased ATP concentration. The transmembrane pumps, which extrude, from the mitochondria, ions, and water, are ATP-dependant. Therapy aiming at increasing both the number and the efficacy of mitochondria could be very useful.}, }
@article {pmid27802314, year = {2016}, author = {Sastre, N and Francino, O and Curti, JN and Armenta, TC and Fraser, DL and Kelly, RM and Hunt, E and Silbermayr, K and Zewe, C and Sánchez, A and Ferrer, L}, title = {Detection, Prevalence and Phylogenetic Relationships of Demodex spp and further Skin Prostigmata Mites (Acari, Arachnida) in Wild and Domestic Mammals.}, journal = {PloS one}, volume = {11}, number = {11}, pages = {e0165765}, pmid = {27802314}, issn = {1932-6203}, mesh = {Animals ; Animals, Wild/*parasitology ; Cell Nucleus/genetics ; Dogs ; Genetic Variation ; Humans ; Mites/*classification/genetics/*physiology ; Mitochondria/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Skin/*parasitology ; }, abstract = {This study was conceived to detect skin mites in social mammals through real-time qPCR, and to estimate taxonomic Demodex and further Prostigmata mite relationships in different host species by comparing sequences from two genes: mitochondrial 16S rRNA and nuclear 18S rRNA. We determined the mite prevalence in the hair follicles of marmots (13%) and bats (17%). The high prevalence found in marmots and bats by sampling only one site on the body may indicate that mites are common inhabitants of their skin. Since we found three different mites (Neuchelacheles sp, Myobia sp and Penthaleus sp) in three bat species (Miotis yumanensis, Miotis californicus and Corynorhinus townsendii) and two different mites (both inferred to be members of the Prostigmata order) in one marmot species (Marmota flaviventris), we tentatively concluded that these skin mites 1) cannot be assigned to the same genus based only on a common host, and 2) seem to evolve according to the specific habitat and/or specific hair and sebaceous gland of the mammalian host. Moreover, two M. yumanensis bats harbored identical Neuchelacheles mites, indicating the possibility of interspecific cross-infection within a colony. However, some skin mites species are less restricted by host species than previously thought. Specifically, Demodex canis seems to be more transmissible across species than other skin mites. D. canis have been found mostly in dogs but also in cats and captive bats. In addition, we report the first case of D. canis infestation in a domestic ferret (Mustela putorius). All these mammalian hosts are related to human activities, and D. canis evolution may be a consequence of this relationship. The monophyletic Demodex clade showing closely related dog and human Demodex sequences also supports this likely hypothesis.}, }
@article {pmid27796771, year = {2016}, author = {Camberos, MD and Pérez, AA and Passicot, GA and Martucci, LC and Wanderley, MI and Udrisar, DP and Cresto, JC}, title = {II - Insulin processing in mitochondria.}, journal = {Journal of bioenergetics and biomembranes}, volume = {48}, number = {5}, pages = {469-482}, pmid = {27796771}, issn = {1573-6881}, mesh = {Adenosine Triphosphate/pharmacology ; Animals ; Diet Therapy ; Insulin/*metabolism/pharmacology ; Insulysin/*metabolism ; Mitochondria/*metabolism ; Mitophagy/drug effects ; Rats ; }, abstract = {Our objective was to know how insulin is processing in mitochondria; if IDE is the only participant in mitochondrial insulin degradation and the role of insulin degradation on IDE accumulation in mitoplasts. Mitochondria and its fractions were isolated as described by Greenwalt. IDE was purified and detected in immunoblot with specific antibodies. High insulin degradation was obtained through addition to rat's diet of 25 g/rat of apple and 10 g/rat of hard-boiled eggs, 3 days a week. Mitochondrial insulin degradation was assayed with 5 % TCA, insulin antibody or Sephadex G50 chromatography. Degradation was also assayed 60 min at 37 °C in mitochondrial fractions (IMS and Mx) with diet or not and without IDE. Degradation in fractions precipitated with ammonium sulfates (60-80 %) were studied after mitochondrial insulin incubation (1 ng. insulin during 15 min, at 30 °C) or with addition of 2.5 mM ATP. Supplementary diet increased insulin degradation. High insulin did not increase mitoplasts accumulation and did not decrease mitochondrial degradation. High insulin and inhibition of degradation evidence insulin competition for a putative transport system. Mitochondrial incubation with insulin increased IDE in matrix as observed in immunoblot. ATP decreased degradation in Mx and increased it in IMS. Chromatography of IMS demonstrated an ATP-dependent protease that degraded insulin, similar to described by Sitte et al. Mitochondria participate in insulin degradation and the diet increased it. High insulin did not accomplish mitochondrial decrease of degradation or its accumulation in mitoplasts. Mitochondrial incubation with insulin increased IDE in matrix. ATP suggested being a regulator of mitochondrial insulin degradation.}, }
@article {pmid27796558, year = {2017}, author = {Yoneva, A and Kuchta, R and Mariaux, J and Georgiev, BB}, title = {The first data on the vitellogenesis of paruterinid tapeworms: an ultrastructural study of Dictyterina cholodkowskii (Cestoda: Cyclophyllidea).}, journal = {Parasitology research}, volume = {116}, number = {1}, pages = {327-334}, pmid = {27796558}, issn = {1432-1955}, mesh = {Animals ; Cestoda/physiology/*ultrastructure ; Cytoplasm/ultrastructure ; Female ; Ovarian Follicle/physiology/ultrastructure ; *Phylogeny ; Vitelline Membrane/physiology ; Vitellogenesis/*physiology ; }, abstract = {The present study provides the first ultrastructural data of the vitellogenesis in a cestode species of the cyclophyllidean family Paruterinidae, aiming to expand the limited data on the vitellogenesis in cyclophyllidean cestodes and to explore the potential of ultrastructural characters associated with vitellogenesis for phylogenetic and taxonomic studies of this order. The process of vitellocyte formation in Dictyterina cholodkowskii follows the general pattern observed in other tapeworms but exhibits several specific differences in the ultrastructure of vitelline cells. The vitellarium contains vitellocytes at various stages of maturation. The periphery of the vitellarium and the space between maturing vitellocytes are occupied by interstitial cells. Differentiation into mature vitellocytes is characterized by high secretory activity, which involves the development of granular endoplasmic reticulum, Golgi complexes, mitochondria and vitelline globules of various sizes. During vitellogenesis, the progressive fusion of these globules results in the formation of two large membrane-limited vitelline vesicles that eventually fuse into a single large vesicle. Mature vitellocytes are composed of a single vitelline vesicle, a high content of cytoplasmic organelles and have no nucleus. No traces of lipid droplets and glycogen granules are detected in the cytoplasm of mature vitellocytes, which might be related to biological peculiarities of this family, i.e. the release of eggs into environment within the tissues of the paruterine organ, which may serve as a source of nutrients for embryos.}, }
@article {pmid27664178, year = {2016}, author = {Grewe, F and Zhu, A and Mower, JP}, title = {Loss of a Trans-Splicing nad1 Intron from Geraniaceae and Transfer of the Maturase Gene matR to the Nucleus in Pelargonium.}, journal = {Genome biology and evolution}, volume = {8}, number = {10}, pages = {3193-3201}, pmid = {27664178}, issn = {1759-6653}, mesh = {Cell Nucleus/metabolism ; Endoribonucleases/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Introns ; NADH Dehydrogenase/*genetics ; Nucleotidyltransferases/*genetics ; Pelargonium/*genetics ; Plant Proteins/*genetics ; Sequence Deletion ; Trans-Splicing ; }, abstract = {The mitochondrial nad1 gene of seed plants has a complex structure, including four introns in cis or trans configurations and a maturase gene (matR) hosted within the final intron. In the geranium family (Geraniaceae), however, sequencing of representative species revealed that three of the four introns, including one in a trans configuration and another that hosts matR, were lost from the nad1 gene in their common ancestor. Despite the loss of the host intron, matR has been retained as a freestanding gene in most genera of the family, indicating that this maturase has additional functions beyond the splicing of its host intron. In the common ancestor of Pelargonium, matR was transferred to the nuclear genome, where it was split into two unlinked genes that encode either its reverse transcriptase or maturase domain. Both nuclear genes are transcribed and contain predicted mitochondrial targeting signals, suggesting that they express functional proteins that are imported into mitochondria. The nuclear localization and split domain structure of matR in the Pelargonium nuclear genome offers a unique opportunity to assess the function of these two domains using transgenic approaches.}, }
@article {pmid27794464, year = {2017}, author = {Uribe, JE and Puillandre, N and Zardoya, R}, title = {Beyond Conus: Phylogenetic relationships of Conidae based on complete mitochondrial genomes.}, journal = {Molecular phylogenetics and evolution}, volume = {107}, number = {}, pages = {142-151}, doi = {10.1016/j.ympev.2016.10.008}, pmid = {27794464}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Conus Snail/*classification/*genetics ; DNA, Mitochondrial/genetics ; Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Understanding how the extraordinary taxonomic and ecological diversity of cone snails (Caenogastropoda: Conidae) evolved requires a statistically robust phylogenetic framework, which thus far is not available. While recent molecular phylogenies have been able to distinguish several deep lineages within the family Conidae, including the genera Profundiconus, Californiconus, Conasprella, and Conus (and within this one, several subgenera), phylogenetic relationships among these genera remain elusive. Moreover, the possibility that additional deep lineages may exist within the family is open. Here, we reconstructed with probabilistic methods a molecular phylogeny of Conidae using the newly sequenced complete or nearly complete mitochondrial (mt) genomes of the following nine species that represent all main Conidae lineages and potentially new ones: Profundiconus teramachii, Californiconus californicus, Conasprella wakayamaensis, Lilliconus sagei, Pseudolilliconus traillii, Conus (Kalloconus) venulatus, Conus (Lautoconus) ventricosus, Conus (Lautoconus) hybridus, and Conus (Eugeniconus) nobilis. To test the monophyly of the family, we also sequenced the nearly complete mt genomes of the following three species representing closely related conoidean families: Benthomangelia sp. (Mangeliidae), Tomopleura sp. (Borsoniidae), and Glyphostoma sp. (Clathurellidae). All newly sequenced conoidean mt genomes shared a relatively constant gene order with rearrangements limited to tRNA genes. The reconstructed phylogeny recovered with high statistical support the monophyly of Conidae and phylogenetic relationships within the family. The genus Profundiconus was placed as sister to the remaining genera. Within these, a clade including Californiconus and Lilliconus+Pseudolilliconus was the sister group of Conasprella to the exclusion of Conus. The phylogeny included a new lineage whose relative phylogenetic position was unknown (Lilliconus) and uncovered thus far hidden diversity within the family (Pseudolilliconus). Moreover, reconstructed phylogenetic relationships allowed inferring that the peculiar diet of Californiconus based on worms, mollusks, crustaceans and fish is derived, and reinforce the hypothesis that the ancestor of Conidae was a worm hunter. A chronogram was reconstructed under an uncorrelated relaxed molecular clock, which dated the origin of the family shortly after the Cretaceous-Tertiary boundary (about 59million years ago) and the divergence among main lineages during the Paleocene and the Eocene (56-30million years ago).}, }
@article {pmid27491516, year = {2016}, author = {Sun, T and Bentolila, S and Hanson, MR}, title = {The Unexpected Diversity of Plant Organelle RNA Editosomes.}, journal = {Trends in plant science}, volume = {21}, number = {11}, pages = {962-973}, doi = {10.1016/j.tplants.2016.07.005}, pmid = {27491516}, issn = {1878-4372}, mesh = {Chloroplasts/genetics ; Organelles/*genetics ; Plant Proteins/chemistry/*genetics/metabolism ; RNA Editing/*genetics ; RNA, Plant/*genetics ; }, abstract = {Flowering plants convert many hundreds of organelle cytidines (Cs) to uridines (Us) during post-transcriptional RNA editing. Pentatricopeptide repeat (PPR) proteins dictate specificity by recognizing RNA sequences near C targets. However, the complete mechanism of the editing machinery is not yet understood. Recently, non-PPR editing factors [RNA editing factor interacting proteins (RIPs)/multiple organellar RNA editing factors (MORFs), organelle RNA recognition motif (ORRM) proteins, organelle zinc-finger (OZ) proteins, and protoporphyrinogen oxidase 1 (PPO1)] have been identified as components of the plant RNA editosome, which is a small RNA-protein complex. Surprisingly, plant editosomes are highly diverse not only with regard to the PPR proteins they contain but also in the non-PPR components that are present. Here we review the most recent progress in the field and discuss the implications of the diversity of plant editosomes for the evolution of RNA editing and for possible future applications.}, }
@article {pmid27793078, year = {2016}, author = {Liu, JM and Xu, ZS and Lu, PP and Li, WW and Chen, M and Guo, CH and Ma, YZ}, title = {Genome-wide investigation and expression analyses of the pentatricopeptide repeat protein gene family in foxtail millet.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {840}, pmid = {27793078}, issn = {1471-2164}, mesh = {Chromosome Mapping ; Chromosomes, Plant ; Computational Biology/methods ; Evolution, Molecular ; *Gene Expression Regulation, Plant ; Gene Ontology ; *Genome, Plant ; Mitochondrial Proteins/*genetics ; Molecular Sequence Annotation ; *Multigene Family ; Phenotype ; Protein Transport ; Setaria Plant/*genetics/metabolism ; }, abstract = {BACKGROUND: Pentatricopeptide repeat (PPR) proteins are encoded by a large gene family of approximately 450 members in Arabidopsis and 477 in rice, which characterized by tandem repetitions of a degenerate 35 amino acid characteristic sequence motifs. A large majority of the PPR genes in the higher plants are localized in organelles. Their functions remain as yet largely unknown. The majority of characterized PPR proteins have been found to function in modulating the expression plastid and mitochondrial genes in plants.<br><br>RESULTS: Here, a genome-wide identification and comparison of the PPR genes from 5 organisms was performed, including the moss Physcomitrella patens, the lycophyte Selaginella moellendorffii, the eudicot Arabidopsis, and the monocots rice and foxtail millet. It appears that the expansion of this gene family prior to the divergence of the euphyllophytes and the lycophytes in land plants. The duplication and divergence rates of the foxtail millet PPR genes (SiPPRs) showed that the expansion period of this gene family around 400 Mya, and indicated that genome segmental duplication was very likely the primary mechanism underlying the expansion of the PPR gene family in vascular plants. An analysis of a complete set of SiPPR genes/proteins that included classification, chromosomal location, orthologous relationships, duplication analysis, and auxiliary motifs is presented. Expression analysis of the SiPPR genes under stress conditions revealed that the expression of 24 SiPPR genes was responsive to abiotic stress. Subcellular localization analysis of 11 PPR proteins indicated that 5 proteins were localized to chloroplasts, that 4 were localized to mitochondria, and that 2 were localized to the cytoplasm.<br><br>CONCLUSIONS: Our results contribute to a more comprehensive understanding the roles of PPR proteins and will be useful in the prioritization of particular PPR proteins for subsequent functional validation studies in foxtail millet.}, }
@article {pmid27661287, year = {2016}, author = {Rammelt, C and Rossmanith, W}, title = {Repairing tRNA termini: News from the 3' end.}, journal = {RNA biology}, volume = {13}, number = {12}, pages = {1182-1188}, pmid = {27661287}, issn = {1555-8584}, mesh = {Animals ; Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Evolution, Molecular ; RNA Editing ; RNA Processing, Post-Transcriptional ; RNA, Archaeal/genetics/metabolism ; RNA, Bacterial/genetics/metabolism ; RNA, Transfer/chemistry/genetics/*metabolism ; }, abstract = {The removal of transcriptional 5' and 3' extensions is an essential step in tRNA biogenesis. In some bacteria, tRNA 5'- and 3'-end maturation require no further steps, because all their genes encode the full tRNA sequence. Often however, the ends are incomplete, and additional maturation, repair or editing steps are needed. In all Eukarya, but also many Archaea and Bacteria, e.g., the universal 3'-terminal CCA is not encoded and has to be added by the CCA-adding enzyme. Apart from such widespread "repair/maturation" processes, tRNA genes in some cases apparently cannot give rise to intact, functional tRNA molecules without further, more specific end repair or editing. Interestingly, the responsible enzymes as far as identified appear to be polymerases usually involved in regular tRNA repair after damage. Alternatively, enzymes are recruited from other non-tRNA pathways; e.g., in animal mitochondria, poly(A) polymerase plays a crucial role in the 3'-end repair/editing of tRNAs. While these repair/editing pathways apparently allowed peculiar tRNA-gene overlaps or mismatching mutations in the acceptor stem to become genetically fixed in some present-day organisms, they may have also driven some global changes in tRNA maturation on a greater evolutionary scale.}, }
@article {pmid27609637, year = {2016}, author = {Torres-Gutierrez, C and Bergo, ES and Emerson, KJ and de Oliveira, TMP and Greni, S and Sallum, MAM}, title = {Mitochondrial COI gene as a tool in the taxonomy of mosquitoes Culex subgenus Melanoconion.}, journal = {Acta tropica}, volume = {164}, number = {}, pages = {137-149}, doi = {10.1016/j.actatropica.2016.09.007}, pmid = {27609637}, issn = {1873-6254}, mesh = {Animals ; Bayes Theorem ; Brazil ; Cluster Analysis ; Culex/classification/*genetics ; Cyclooxygenase 1/*genetics ; DNA Barcoding, Taxonomic ; Insect Proteins/*analysis ; Insect Vectors/classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {The subgenus Melanoconion is the second largest subgenus within the genus Culex, with 160 described species. Several of the species are proven vectors of arboviruses, including West Nile virus, Venezuelan equine encephalitis virus complex and Eastern equine encephalomyelitis virus. Species of Melanoconion are well distributed from southern North America to most countries of South America and display the highest species diversity in tropical regions. Taxonomical identification within this group has been primarily based on morphological characters, with the male genitalia as the source of the most solid diagnostic features. The difficulty in reaching accurate species determinations when studying specimens of Culex (Melanoconion) has been extensively documented as a real limitation to expand knowledge of these insects. We tested the utility of the mitochondrial gene COI as a complementary tool in the taxonomy of Melanoconion. Using a data set of 120 COI sequences from Culex specimen captured in several localities in Brazil, the utility of COI barcodes for species delimitation is discussed through the evaluation of genetic divergences among specimens and the clustering patterns of species in three topologies obtained with Neighbor Joining, Maximum Likelihood and Bayesian phylogenetic inference. For all specimens included in this study a previous morphological examination was performed, and most of the taxonomical determinations were corroborated using the COI barcode. We generated COI sequences that belong to 48 species of Melanoconion, with a mean intraspecific K2P genetic divergence of 3%; and all interspecific divergence values higher than the intraspecific divergence values. This is the first comprehensive study of subgenus Melanoconion, with evidence of COI as a useful and accessible DNA barcode.}, }
@article {pmid27787743, year = {2016}, author = {Da Costa, B and Dumon, E and Le Moigno, L and Bodard, S and Castelnau, P and Letellier, T and Rocher, C}, title = {Respiratory chain inhibition: one more feature to propose MPTP intoxication as a Leigh syndrome model.}, journal = {Journal of bioenergetics and biomembranes}, volume = {48}, number = {5}, pages = {483-491}, pmid = {27787743}, issn = {1573-6881}, mesh = {1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine/administration &amp; dosage/*adverse effects ; Animals ; *Disease Models, Animal ; Electron Transport/*drug effects ; Electron Transport Complex IV/drug effects ; Leigh Disease/*chemically induced ; MPTP Poisoning ; Mice ; Mitochondria/metabolism ; }, abstract = {1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) intoxicated mice have been widely used to model the loss of dopaminergic neurons. As this treatment leads to basal ganglia degeneration, it was proposed that MPTP mice could be used as a model of Leigh syndrome. However, this mitochondrial pathology is biochemically characterized by a respiratory chain dysfunction. To determine if MPTP can affect in vivo mitochondria function, we measured the activities of mitochondrial respiratory chain complexes in several tissues. Our results show that MPTP affects mainly mitochondrial respiratory chain complex IV, as found in Leigh Syndrome, confirming that acute MPTP intoxicated mice are a good model of Leigh Syndrome.}, }
@article {pmid27567984, year = {2016}, author = {Dos Santos, PF and Moreira, DS and Baba, EH and Volpe, CMO and Ruiz, JC and Romanha, AJ and Murta, SMF}, title = {Molecular characterization of lipoamide dehydrogenase gene in Trypanosoma cruzi populations susceptible and resistant to benznidazole.}, journal = {Experimental parasitology}, volume = {170}, number = {}, pages = {1-9}, doi = {10.1016/j.exppara.2016.08.006}, pmid = {27567984}, issn = {1090-2449}, mesh = {Alleles ; Amino Acid Sequence ; Animals ; Blotting, Northern ; Blotting, Southern ; Cloning, Molecular ; DNA, Protozoan/chemistry/isolation &amp; purification ; Dihydrolipoamide Dehydrogenase/chemistry/*genetics ; *Drug Resistance/genetics ; Gene Dosage ; Gene Expression Regulation, Enzymologic ; Mice ; Mitochondria/enzymology ; Nitroimidazoles/*pharmacology ; Phylogeny ; RNA, Messenger/metabolism ; RNA, Protozoan/chemistry/isolation &amp; purification ; Real-Time Polymerase Chain Reaction ; Recombinant Proteins/chemistry/genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Trypanocidal Agents/*pharmacology ; Trypanosoma cruzi/*drug effects/*enzymology/genetics ; }, abstract = {Lipoamide dehydrogenase (LipDH) is a flavin-containing disulfide oxidoreductase from the same group of thioredoxin reductase, glutathione reductase and trypanothione reductase. This enzyme is found in the mitochondria of all aerobic organisms where it takes part in at least three important multienzyme complexes from the citric acid cycle. In this study, we performed a phylogenetic analysis comparing the amino acid sequence of the LipDH from Trypanosoma cruzi (TcLipDH) with the LipDH from other organisms. Subsequently, the copy number of the TcLipDH gene, the mRNA and protein levels, and the enzymatic activity of the LipDH were determined in populations and strains of T. cruzi that were either resistant or susceptible to benznidazole (BZ). In silico analysis showed the presence of two TcLipDH alleles in the T. cruzi genome. It also showed that TcLipDH protein has less than 55% of identity in comparison to the human LipDH, but the active site is conserved in both of them. Southern blot results suggest that the TcLipDH is a single copy gene in the genome of the T. cruzi samples analyzed. Northern blot assays showed one transcript of 2.4 kb in all T. cruzi populations. Northern blot and Real Time RT-PCR data revealed that the TcLipDH mRNA levels were 2-fold more expressed in the BZ-resistant T. cruzi population (17LER) than in its susceptible pair (17WTS). Western blot results revealed that the TcLipDH protein level is 2-fold higher in 17LER sample in comparison to 17WTS sample. In addition, LipDH activity was higher in the 17LER population than in the 17WTS. Sequencing analysis revealed that the amino acid sequences of the TcLipDH from 17WTS and 17LER populations are identical. Our findings show that one of the mechanisms associated with in vitro-induced BZ resistance to T. cruzi correlates with upregulation of LipDH enzyme.}, }
@article {pmid27115713, year = {2016}, author = {Liu, M and Fan, X and Gao, F and Gao, S and Yu, Y and Warren, A and Huang, J}, title = {Tetrahymena australis (Protozoa, Ciliophora): A Well-Known But "Non-Existing" Taxon - Consideration of Its Identification, Definition and Systematic Position.}, journal = {The Journal of eukaryotic microbiology}, volume = {63}, number = {6}, pages = {760-770}, doi = {10.1111/jeu.12323}, pmid = {27115713}, issn = {1550-7408}, mesh = {Base Sequence ; DNA, Mitochondrial/genetics ; DNA, Protozoan/genetics ; Fresh Water/parasitology ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Tetrahymena/*classification/genetics/*isolation &amp; purification ; }, abstract = {A cryptic species of the Tetrahymena pyriformis complex, Tetrahymena australis, has been known for a long time but never properly diagnosed based on taxonomic methods. The species name is thus invalid according to the International Code of Zoological Nomenclature. Recently, a population isolated from a freshwater lake in Wuhan, China was investigated using live observations, silver staining methods and gene sequence data. This organism can be separated from other described species of the T. pyriformis complex by its relatively small body size, the number of somatic kineties and differences in sequences of two genes, namely the small subunit ribosomal RNA (SSU rRNA) and the mitochondrial cytochrome c oxidase subunit I (cox1). We compared the SSU rRNA gene sequences of all available Tetrahymena species to reveal the nucleotide differences within this genus. The sequence of the Wuhan population is identical to two sequences of a previously isolated strain of T. australis (ATCC #30831). Phylogenetic analyses indicate that these three sequences (X56167, M98015, KT334373) cluster with Tetrahymena shanghaiensis (EF070256) in a polytomy. However, sequence divergence of the cox1 gene between the Wuhan population and another strain of T. australis (ATCC #30271) is 1.4%, suggesting that these may represent different subspecies.}, }
@article {pmid27061962, year = {2016}, author = {Shiratori, T and Ishida, KI}, title = {Trachyrhizium urniformis n. g., n. sp., a Novel Marine Filose Thecate Amoeba Related to a Cercozoan Environmental Clade (Novel Clade 4).}, journal = {The Journal of eukaryotic microbiology}, volume = {63}, number = {6}, pages = {722-731}, doi = {10.1111/jeu.12319}, pmid = {27061962}, issn = {1550-7408}, mesh = {Amoeba/*classification/genetics/*isolation &amp; purification/ultrastructure ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Geologic Sediments/*parasitology ; Microscopy, Electron, Transmission ; Phylogeny ; }, abstract = {A novel cercozoan filose thecate amoeba, Trachyrhizium urniformis n. g., n. sp., was isolated from a marine sediment sample collected at Agenashiku Island, Okinawa, Japan. We performed light and electron microscopic observations, and a molecular phylogenetic analysis using the small subunit ribosomal RNA gene of the isolate. Cells of T. urniformis are spherical in shape and are covered by a thin theca possessing a wide rounded aperture. Branching and occasionally anastomosing filopodia with small granules emerge from the aperture. The granules are transported in the filopodia bidirectionally. Transmission electron microscopy showed that cells of T. urniformis possess nucleus with permanently condensed chromatin, Golgi apparatuses, microbodies, mitochondria with tubular cristae, and extrusomes. Several morphological and ultrastructural features of T. urniformis (the presence of thecae and nucleus with permanently condensed chromatin) show similarities with those of Thecofilosea. In a phylogenetic analysis, T. urniformis included in Thecofilosea with weak statistical supports and formed a clade with two sequences that constitutes a cercozoan environmental clade, novel clade 4. On the basis of morphological and ultrastructural information and the results of the phylogenetic analysis, we propose T. urniformis as a new member of class Thecofilosea.}, }
@article {pmid27780056, year = {2016}, author = {van der Giezen, M}, title = {Evolution: Organelles Caught in the Act.}, journal = {Current biology : CB}, volume = {26}, number = {20}, pages = {R913-R915}, doi = {10.1016/j.cub.2016.08.002}, pmid = {27780056}, issn = {1879-0445}, mesh = {Biological Evolution ; *Cercozoa ; Mitochondria ; Organelles ; *Oxygen ; }, abstract = {Mitochondria in the protist Brevimastigomonas motovehiculus are in the process of dismantling their mitochondrial electron transport chain complexes as they adapt to anaerobic environments. Novel protein interactions suggest a highly complicated process rather than the simple removal of unnecessary genes.}, }
@article {pmid27778315, year = {2017}, author = {Stojković, B and Sayadi, A and Đorđević, M and Jović, J and Savković, U and Arnqvist, G}, title = {Divergent evolution of life span associated with mitochondrial DNA evolution.}, journal = {Evolution; international journal of organic evolution}, volume = {71}, number = {1}, pages = {160-166}, doi = {10.1111/evo.13102}, pmid = {27778315}, issn = {1558-5646}, mesh = {*Aging ; Animals ; Cell Nucleus ; Coleoptera/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Haplotypes ; *Longevity ; Microsatellite Repeats ; }, abstract = {Mitochondria play a key role in ageing. The pursuit of genes that regulate variation in life span and ageing have shown that several nuclear-encoded mitochondrial genes are important. However, the role of mitochondrial encoded genes (mtDNA) is more controversial and our appreciation of the role of mtDNA for the evolution of life span is limited. We use replicated lines of seed beetles that have been artificially selected for long or short life for >190 generations, now showing dramatic phenotypic differences, to test for a possible role of mtDNA in the divergent evolution of ageing and life span. We show that these divergent selection regimes led to the evolution of significantly different mtDNA haplotype frequencies. Selection for a long life and late reproduction generated positive selection for one specific haplotype, which was fixed in most such lines. In contrast, selection for reproduction early in life led to both positive selection as well as negative frequency-dependent selection on two different haplotypes, which were both present in all such lines. Our findings suggest that the evolution of life span was in part mediated by mtDNA, providing support for the emerging general tenet that adaptive evolution of life-history syndromes may involve mtDNA.}, }
@article {pmid27725303, year = {2017}, author = {Debard, S and Bader, G and De Craene, JO and Enkler, L and Bär, S and Laporte, D and Hammann, P and Myslinski, E and Senger, B and Friant, S and Becker, HD}, title = {Nonconventional localizations of cytosolic aminoacyl-tRNA synthetases in yeast and human cells.}, journal = {Methods (San Diego, Calif.)}, volume = {113}, number = {}, pages = {91-104}, doi = {10.1016/j.ymeth.2016.09.017}, pmid = {27725303}, issn = {1095-9130}, mesh = {Amino Acyl-tRNA Synthetases/classification/genetics/*metabolism ; Antibodies/chemistry ; Blotting, Western/methods ; Cell Compartmentation ; Cell Fractionation/methods ; Cell Line ; Cell Nucleus/*enzymology/ultrastructure ; Cytosol/*enzymology/ultrastructure ; Fluorescent Antibody Technique/methods ; Gene Expression ; Humans ; Mitochondria/*enzymology/ultrastructure ; Protein Transport ; Ribosomes/*enzymology/ultrastructure ; Saccharomyces cerevisiae/*enzymology/genetics/ultrastructure ; }, abstract = {By definition, cytosolic aminoacyl-tRNA synthetases (aaRSs) should be restricted to the cytosol of eukaryotic cells where they supply translating ribosomes with their aminoacyl-tRNA substrates. However, it has been shown that other translationally-active compartments like mitochondria and plastids can simultaneously contain the cytosolic aaRS and its corresponding organellar ortholog suggesting that both forms do not share the same organellar function. In addition, a fair number of cytosolic aaRSs have also been found in the nucleus of cells from several species. Hence, these supposedly cytosolic-restricted enzymes have instead the potential to be multi-localized. As expected, in all examples that were studied so far, when the cytosolic aaRS is imported inside an organelle that already contains its bona fide corresponding organellar-restricted aaRSs, the cytosolic form was proven to exert a nonconventional and essential function. Some of these essential functions include regulating homeostasis and protecting against various stresses. It thus becomes critical to assess meticulously the subcellular localization of each of these cytosolic aaRSs to unravel their additional roles. With this objective in mind, we provide here a review on what is currently known about cytosolic aaRSs multi-compartmentalization and we describe all commonly used protocols and procedures for identifying the compartments in which cytosolic aaRSs relocalize in yeast and human cells.}, }
@article {pmid27666965, year = {2016}, author = {Gawryluk, RMR and Kamikawa, R and Stairs, CW and Silberman, JD and Brown, MW and Roger, AJ}, title = {The Earliest Stages of Mitochondrial Adaptation to Low Oxygen Revealed in a Novel Rhizarian.}, journal = {Current biology : CB}, volume = {26}, number = {20}, pages = {2729-2738}, doi = {10.1016/j.cub.2016.08.025}, pmid = {27666965}, issn = {1879-0445}, support = {MOP-142349//CIHR/Canada ; }, mesh = {Adaptation, Biological ; Amino Acid Sequence ; Anaerobiosis ; *Biological Evolution ; Cercozoa/classification/genetics/*physiology ; Mitochondria/*physiology ; Oxygen/metabolism ; Phylogeny ; Protozoan Proteins/chemistry/*genetics/metabolism ; Sequence Alignment ; }, abstract = {Mitochondria exist on a functional and evolutionary continuum that includes anaerobic mitochondrion-related organelles (MROs), such as hydrogenosomes. Hydrogenosomes lack many classical mitochondrial features, including conspicuous cristae, mtDNA, the tricarboxylic acid (TCA) cycle, and ATP synthesis powered by an electron transport chain (ETC); instead, they produce ATP anaerobically, liberating H2 and CO2 gas in the process. However, our understanding of the evolutionary transformation from aerobic mitochondria to various MRO types remains incomplete. Here we describe a novel MRO from a cercomonad (Brevimastigomonas motovehiculus n. sp.; Rhizaria). We have sequenced its 30,608-bp mtDNA and characterized organelle function through a combination of transcriptomic, genomic, and cell biological approaches. B. motovehiculus MROs are metabolically versatile, retaining mitochondrial metabolic pathways, such as a TCA cycle and ETC-driven ATP synthesis, but also possessing hydrogenosomal-type pyruvate metabolism and substrate-level phosphorylation. Notably, the B. motovehiculus ETC is degenerate and appears to be losing cytochrome-based electron transport (complexes III and IV). Furthermore, the F1Fo ATP synthase (complex V) is unique, with the highly conserved Atpα subunit fragmented into four separate pieces. The B. motovehiculus MRO appears to be in the process of losing aerobic metabolic capacities. Our findings shed light on the transition between organelle types, specifically the early stages of mitochondrial adaptation to anaerobiosis.}, }
@article {pmid27081924, year = {2016}, author = {Leung, J and Witt, JD and Norwood, W and Dixon, DG}, title = {Implications of Cu and Ni toxicity in two members of the Hyalella azteca cryptic species complex: Mortality, growth, and bioaccumulation parameters.}, journal = {Environmental toxicology and chemistry}, volume = {35}, number = {11}, pages = {2817-2826}, doi = {10.1002/etc.3457}, pmid = {27081924}, issn = {1552-8618}, mesh = {Amphipoda/*drug effects/genetics/growth &amp; development/metabolism ; Animals ; Copper/metabolism/*toxicity ; Electron Transport Complex IV/genetics ; Fresh Water ; Lethal Dose 50 ; Mitochondria/drug effects/enzymology/genetics ; Nickel/metabolism/*toxicity ; North America ; Phylogeny ; Species Specificity ; Survival Analysis ; Toxicity Tests ; Water Pollutants, Chemical/metabolism/*toxicity ; }, abstract = {Hyalella azteca, an amphipod crustacean, is frequently used in freshwater toxicity tests. Since the mid-1980s, numerous organizations have collected and established cultures of H. azteca originating from localities across North America. However, H. azteca is actually a large cryptic species complex whose members satisfy both the biological and the phylogenetic species concepts. Genetic analysis at the mitochondrial COI gene has revealed that only 2 clades are cultured in 17 North American laboratories; however, there are 85 genetically divergent lineages within this complex in the wild. In the present study, 2 members (clades 1 and 8) of the H. azteca species complex were identified using the mitochondrial COI gene. These 2 clades were exposed to Cu or Ni for 14 d. A saturation-based mortality model and the general growth model were used to determine mortality (lethal concentration, 25% and 50% [LC25 and LC50], lethal body concentration, 25% and 50% [LBC25 and LBC50]) and growth (inhibitory concentration, 25% [IC25, IBC25]) endpoints, respectively. A modified saturation-based model was used to estimate metal bioaccumulation parameters. Clade 8 was significantly more tolerant than clade 1, with differences in LC50s. However, the effects of the metals on growth were not significantly different between clades, even though clade 1 was significantly larger than then clade 8. Differences in Cu or Ni bioaccumulation were not observed between clades 1 and 8. The differences in Cu and Ni LC50s may have implications for risk assessments, and it is recommended that toxicity experiments should only be performed with properly identified members of the H. azteca complex to maintain consistency among laboratories. Environ Toxicol Chem 2016;35:2817-2826. © 2016 SETAC.}, }
@article {pmid27775167, year = {2017}, author = {Ming, L and Yi, L and Sa, R and Wang, ZX and Wang, Z and Ji, R}, title = {Genetic diversity and phylogeographic structure of Bactrian camels shown by mitochondrial sequence variations.}, journal = {Animal genetics}, volume = {48}, number = {2}, pages = {217-220}, pmid = {27775167}, issn = {1365-2052}, mesh = {Animals ; Animals, Domestic ; Animals, Wild ; Biological Evolution ; Camelus/blood/classification/*genetics ; Genetic Variation ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; }, abstract = {The Bactrian camel includes various domestic (Camelus bactrianus) and wild (Camelus ferus) breeds that are important for transportation and for their nutritional value. However, there is a lack of extensive information on their genetic diversity and phylogeographic structure. Here, we studied these parameters by examining an 809-bp mtDNA fragment from 113 individuals, representing 11 domestic breeds, one wild breed and two hybrid individuals. We found 15 different haplotypes, and the phylogenetic analysis suggests that domestic and wild Bactrian camels have two distinct lineages. The analysis of molecular variance placed most of the genetic variance (90.14%, P < 0.01) between wild and domestic camel lineages, suggesting that domestic and wild Bactrian camel do not have the same maternal origin. The analysis of domestic Bactrian camels from different geographical locations found there was no significant genetic divergence in China, Russia and Mongolia. This suggests a strong gene flow due to wide movement of domestic Bactrian camels.}, }
@article {pmid27751905, year = {2017}, author = {Woyda-Ploszczyca, AM and Jarmuszkiewicz, W}, title = {The conserved regulation of mitochondrial uncoupling proteins: From unicellular eukaryotes to mammals.}, journal = {Biochimica et biophysica acta. Bioenergetics}, volume = {1858}, number = {1}, pages = {21-33}, doi = {10.1016/j.bbabio.2016.10.003}, pmid = {27751905}, issn = {0005-2728}, mesh = {Aldehydes/*metabolism ; Animals ; Eukaryota/*metabolism ; Fatty Acids, Nonesterified/*metabolism ; Mammals/*metabolism ; Mitochondrial Uncoupling Proteins/*metabolism ; Purine Nucleotides/*metabolism ; Ubiquinone/*metabolism ; }, abstract = {Uncoupling proteins (UCPs) belong to the mitochondrial anion carrier protein family and mediate regulated proton leak across the inner mitochondrial membrane. Free fatty acids, aldehydes such as hydroxynonenal, and retinoids activate UCPs. However, there are some controversies about the effective action of retinoids and aldehydes alone; thus, only free fatty acids are commonly accepted positive effectors of UCPs. Purine nucleotides such as GTP inhibit UCP-mediated mitochondrial proton leak. In turn, membranous coenzyme Q may play a role as a redox state-dependent metabolic sensor that modulates the complete activation/inhibition of UCPs. Such regulation has been observed for UCPs in microorganisms, plant and animal UCP1 homologues, and UCP1 in mammalian brown adipose tissue. The origin of UCPs is still under debate, but UCP homologues have been identified in all systematic groups of eukaryotes. Despite the differing levels of amino acid/DNA sequence similarities, functional studies in unicellular and multicellular organisms, from amoebae to mammals, suggest that the mechanistic regulation of UCP activity is evolutionarily well conserved. This review focuses on the regulatory feedback loops of UCPs involving free fatty acids, aldehydes, retinoids, purine nucleotides, and coenzyme Q (particularly its reduction level), which may derive from the early stages of evolution as UCP first emerged.}, }
@article {pmid27451385, year = {2016}, author = {Agostini, M and Fasolato, C}, title = {When, where and how? Focus on neuronal calcium dysfunctions in Alzheimer's Disease.}, journal = {Cell calcium}, volume = {60}, number = {5}, pages = {289-298}, doi = {10.1016/j.ceca.2016.06.008}, pmid = {27451385}, issn = {1532-1991}, mesh = {Alzheimer Disease/*metabolism/pathology ; Animals ; Calcium/*metabolism ; Humans ; Neurons/*metabolism/pathology ; }, abstract = {Alzheimer's disease (AD), since its characterization as a precise form of dementia with its own pathological hallmarks, has captured scientists' attention because of its complexity. The last 30 years have been filled with discoveries regarding the elusive aetiology of this disease and, thanks to advances in molecular biology and live imaging techniques, we now know that an important role is played by calcium (Ca[2+]). Ca[2+], as ubiquitous second messenger, regulates a vast variety of cellular processes, from neuronal excitation and communication, to muscle fibre contraction and hormone secretion, with its action spanning a temporal scale that goes from microseconds to hours. It is therefore very challenging to conceive a single hypothesis that can integrate the numerous findings on this issue with those coming from the classical fields of AD research such as amyloid-beta (Aβ) and tau pathology. In this contribution, we will focus our attention on the Ca[2+] hypothesis of AD, dissecting it, as much as possible, in its subcellular localization, where the Ca[2+] signal meets its specificity. We will also follow the temporal evolution of the Ca[2+] hypothesis, providing some of the most updated discoveries. Whenever possible, we will link the findings regarding Ca[2+] dysfunction to the other players involved in AD pathogenesis, hoping to provide a crossover body of evidence, useful to amplify the knowledge that will lead towards the discovery of an effective therapy.}, }
@article {pmid27663234, year = {2017}, author = {Kadam, AA and Jubin, T and Mir, HA and Begum, R}, title = {Potential role of Apoptosis Inducing Factor in evolutionarily significant eukaryote, Dictyostelium discoideum survival.}, journal = {Biochimica et biophysica acta. General subjects}, volume = {1861}, number = {1 Pt A}, pages = {2942-2955}, doi = {10.1016/j.bbagen.2016.09.021}, pmid = {27663234}, issn = {0304-4165}, mesh = {Adenosine Triphosphate/metabolism ; Annexin A5/metabolism ; Apoptosis Inducing Factor/*metabolism ; *Biological Evolution ; Calcium/metabolism ; Cell Cycle/drug effects ; Cell Death/drug effects ; Cell Shape/drug effects ; Cytosol/drug effects/metabolism ; Dictyostelium/*cytology/growth &amp; development/*metabolism/ultrastructure ; Down-Regulation/drug effects ; Flow Cytometry ; Fluorescein-5-isothiocyanate/metabolism ; Fluorometry ; Glucose/pharmacology ; Membrane Potential, Mitochondrial/drug effects ; Mitochondria/drug effects/metabolism ; Models, Biological ; NAD/metabolism ; Oxidative Stress/drug effects ; Propidium/metabolism ; Protein Transport/drug effects ; RNA, Antisense/metabolism ; Reactive Oxygen Species/metabolism ; Staining and Labeling ; }, abstract = {Apoptosis Inducing Factor (AIF), a phylogenetically conserved mitochondrial inter-membrane space flavoprotein has an important role in caspase independent cell death. Nevertheless, AIF is also essential for cell survival. It is required for mitochondrial organization and energy metabolism. Upon apoptotic stimulation, AIF induces DNA fragmentation after its mitochondrio-nuclear translocation. Although it executes critical cellular functions in a coordinated manner, the exact mechanism still remains obscure. The present study aims to understand AIF's role in cell survival, growth and development by its down-regulation in an interesting unicellular eukaryote, D. discoideum which exhibits multicellularity upon starvation. Constitutive AIF down-regulated (dR) cells exhibited slower growth and delayed developmental morphogenesis. Also, constitutive AIF dR cells manifested high intracellular ROS, oxidative DNA damage and calcium levels with lower ATP content. Interestingly, constitutive AIF dR cells showed amelioration in cell growth upon antioxidant treatment, strengthening its role as ROS regulator. Under oxidative stress, AIF dR cells showed early mitochondrial membrane depolarization followed by AIF translocation from mitochondria to nucleus and exhibited necrotic cell death as compared to paraptoptic cell death of control cells. Thus, the results of this study provide an exemplar where AIF is involved in growth and development by regulating ROS levels and maintaining mitochondrial function in D. discoideum, an evolutionarily significant model organism exhibiting caspase independent apoptosis.}, }
@article {pmid27767210, year = {2017}, author = {Nakada, T and Tomita, M}, title = {Morphology and phylogeny of a new wall-less freshwater volvocalean flagellate, Hapalochloris nozakii gen. et sp. nov. (Volvocales, Chlorophyceae).}, journal = {Journal of phycology}, volume = {53}, number = {1}, pages = {108-117}, doi = {10.1111/jpy.12484}, pmid = {27767210}, issn = {1529-8817}, mesh = {Algal Proteins/genetics ; Amino Acid Sequence ; Japan ; Microscopy, Electron, Transmission ; *Phylogeny ; Sequence Alignment ; Species Specificity ; Volvocida/*classification/cytology/genetics/*ultrastructure ; }, abstract = {New strains of a wall-less unicellular volvocalean flagellate were isolated from a freshwater environment in Japan. Observations of the alga, described here as Hapalochloris nozakii Nakada, gen. et sp. nov., were made using light, fluorescence, and electron microscopy. Each vegetative cell had two flagella, four contractile vacuoles, and a spirally furrowed cup-shaped chloroplast with an axial pyrenoid, and mitochondria located in the furrows. Based on the morphology, H. nozakii was distinguished from other known wall-less volvocalean flagellates. Under electron microscopy, fibrous material, instead of a cell wall and dense cortical microtubules, was observed outside and inside the cell membrane, respectively. Based on the phylogenetic analyses of 18S rRNA gene sequences, H. nozakii was found to be closely related to Asterococcus, Oogamochlamys, Rhysamphichloris, and "Dunaliella" lateralis and was separated from other known wall-less flagellate volvocaleans, indicating independent secondary loss of the cell wall in H. nozakii. In the combined 18S rRNA and chloroplast gene tree, H. nozakii was sister to Lobochlamys.}, }
@article {pmid27766474, year = {2016}, author = {Hausenloy, DJ and Barrabes, JA and Bøtker, HE and Davidson, SM and Di Lisa, F and Downey, J and Engstrom, T and Ferdinandy, P and Carbrera-Fuentes, HA and Heusch, G and Ibanez, B and Iliodromitis, EK and Inserte, J and Jennings, R and Kalia, N and Kharbanda, R and Lecour, S and Marber, M and Miura, T and Ovize, M and Perez-Pinzon, MA and Piper, HM and Przyklenk, K and Schmidt, MR and Redington, A and Ruiz-Meana, M and Vilahur, G and Vinten-Johansen, J and Yellon, DM and Garcia-Dorado, D}, title = {Ischaemic conditioning and targeting reperfusion injury: a 30 year voyage of discovery.}, journal = {Basic research in cardiology}, volume = {111}, number = {6}, pages = {70}, pmid = {27766474}, issn = {1435-1803}, support = {CS/14/3/31002/BHF_/British Heart Foundation/United Kingdom ; FS/10/39/28270/BHF_/British Heart Foundation/United Kingdom ; PG/14/92/31234/BHF_/British Heart Foundation/United Kingdom ; PG/15/52/31598/BHF_/British Heart Foundation/United Kingdom ; }, mesh = {Animals ; Humans ; *Ischemic Preconditioning, Myocardial ; *Myocardial Reperfusion Injury ; }, abstract = {To commemorate the auspicious occasion of the 30th anniversary of IPC, leading pioneers in the field of cardioprotection gathered in Barcelona in May 2016 to review and discuss the history of IPC, its evolution to IPost and RIC, myocardial reperfusion injury as a therapeutic target, and future targets and strategies for cardioprotection. This article provides an overview of the major topics discussed at this special meeting and underscores the huge importance and impact, the discovery of IPC has made in the field of cardiovascular research.}, }
@article {pmid27765655, year = {2016}, author = {Rajvanshi, S and Choudhary, K and Agrawal, N}, title = {Threading: A novel insilico indagation method for genetic characterization of some diplostomoid metacercariae (Digenea:Diplostomidae Poirier, 1886).}, journal = {Experimental parasitology}, volume = {171}, number = {}, pages = {71-76}, doi = {10.1016/j.exppara.2016.10.013}, pmid = {27765655}, issn = {1090-2449}, mesh = {Amino Acid Sequence ; Amino Acids/analysis ; Animals ; Cyclooxygenase 1/genetics ; DNA, Mitochondrial/chemistry ; Fish Diseases/parasitology ; Fishes ; Helminth Proteins/*chemistry/genetics ; Imaging, Three-Dimensional ; Metacercariae/chemistry/classification/genetics ; Mitochondria/enzymology ; Models, Biological ; Models, Structural ; Molecular Conformation ; Phylogeny ; Protein Conformation ; Proteomics ; Trematoda/chemistry/classification/*genetics ; Trematode Infections/parasitology/veterinary ; }, abstract = {The protein encoding zone of Mitochondrial DNA region (inherited from single lineage) seems most suitable and effective for taxonomic, systematic, ecological, evolutionary, DNA barcoding, cryptic species and population studies, exploiting nucleotide/amino acid datasets (1D/2D/3D conformational level). Nowadays, expeditious computerized methods are in trend for analyzing genetic material to demonstrate variations at various levels of protein structures. Structural proteomics have implemented here for genetic identification, differentiation and relationship of species from information rich data of mt COI gene of the family Diplostomidae with inclusion of molecular tools. Various aspects have been utilized herein for re-validation and infallible discrimination of Trematode diplostomoid metacercariae (Tetracotyle lucknowensis Pandey, 1971; T. xenentodoni Chakrabarti, 1970; T. fausti Rai and Pande, 1969; T. muscularius Chakrabarti, 1970 and Diplostomulum minutum Pandey, 1968), the infective stage in the life cycle, causing severe damage to fish host, whose adults are found mainly in fish eating birds and mammals.}, }
@article {pmid27707801, year = {2016}, author = {Zeman, I and Neboháčová, M and Gérecová, G and Katonová, K and Jánošíková, E and Jakúbková, M and Centárová, I and Dunčková, I and Tomáška, L and Pryszcz, LP and Gabaldón, T and Nosek, J}, title = {Mitochondrial Carriers Link the Catabolism of Hydroxyaromatic Compounds to the Central Metabolism in Candida parapsilosis.}, journal = {G3 (Bethesda, Md.)}, volume = {6}, number = {12}, pages = {4047-4058}, pmid = {27707801}, issn = {2160-1836}, support = {310325/ERC_/European Research Council/International ; }, mesh = {Acetyl-CoA C-Acyltransferase/genetics/metabolism ; Ascomycota/classification/genetics/*metabolism ; Biological Evolution ; Coenzyme A-Transferases/genetics/metabolism ; Fungal Proteins/genetics/metabolism ; Gene Expression Regulation, Fungal ; Hydrocarbons, Aromatic/*metabolism ; Metabolic Networks and Pathways ; Mitochondria/genetics/*metabolism ; Mutation ; Phylogeny ; Protein Transport ; Saccharomyces cerevisiae/genetics/metabolism ; Substrate Specificity ; }, abstract = {The pathogenic yeast Candida parapsilosis metabolizes hydroxyderivatives of benzene and benzoic acid to compounds channeled into central metabolism, including the mitochondrially localized tricarboxylic acid cycle, via the 3-oxoadipate and gentisate pathways. The orchestration of both catabolic pathways with mitochondrial metabolism as well as their evolutionary origin is not fully understood. Our results show that the enzymes involved in these two pathways operate in the cytoplasm with the exception of the mitochondrially targeted 3-oxoadipate CoA-transferase (Osc1p) and 3-oxoadipyl-CoA thiolase (Oct1p) catalyzing the last two reactions of the 3-oxoadipate pathway. The cellular localization of the enzymes indicates that degradation of hydroxyaromatic compounds requires a shuttling of intermediates, cofactors, and products of the corresponding biochemical reactions between cytosol and mitochondria. Indeed, we found that yeast cells assimilating hydroxybenzoates increase the expression of genes SFC1, LEU5, YHM2, and MPC1 coding for succinate/fumarate carrier, coenzyme A carrier, oxoglutarate/citrate carrier, and the subunit of pyruvate carrier, respectively. A phylogenetic analysis uncovered distinct evolutionary trajectories for sparsely distributed gene clusters coding for enzymes of both pathways. Whereas the 3-oxoadipate pathway appears to have evolved by vertical descent combined with multiple losses, the gentisate pathway shows a striking pattern suggestive of horizontal gene transfer to the evolutionarily distant Mucorales.}, }
@article {pmid27760563, year = {2016}, author = {Žárský, V and Doležal, P}, title = {Evolution of the Tim17 protein family.}, journal = {Biology direct}, volume = {11}, number = {1}, pages = {54}, pmid = {27760563}, issn = {1745-6150}, mesh = {Amino Acid Sequence ; *Evolution, Molecular ; Mitochondrial Membrane Transport Proteins/chemistry/*genetics/metabolism ; Phylogeny ; Sequence Alignment ; }, abstract = {BACKGROUND: The Tim17 family of proteins plays a fundamental role in the biogenesis of mitochondria. Three Tim17 family proteins, Tim17, Tim22, and Tim23, are the central components of the widely conserved multi-subunit protein translocases, TIM23 and TIM22, which mediate protein transport across and into the inner mitochondrial membrane, respectively. In addition, several Tim17 family proteins occupy the inner and outer membranes of plastids.<br><br>RESULTS: We have performed comprehensive sequence analyses on 5631 proteomes from all domains of life deposited in the Uniprot database. The analyses showed that the Tim17 family of proteins is much more diverse than previously thought and involves at least ten functionally and phylogenetically distinct groups of proteins. As previously shown, mitochondrial inner membrane accommodates prototypical Tim17, Tim22 and Tim23 and two Tim17 proteins, TIMMDC1 and NDUFA11, which participate in the assembly of complex I of the respiratory chain. In addition, we have identified Romo1/Mgr2 as Tim17 family member. The protein has been shown to control lateral release of substrates fromTIM23 complex in yeast and to participate in the production of reactive oxygen species in mammalian cells. Two peroxisomal proteins, Pmp24 and Tmem135, of so far unknown function also belong to Tim17 protein family. Additionally, a new group of Tim17 family proteins carrying a C-terminal coiled-coil domain has been identified predominantly in fungi.<br><br>CONCLUSIONS: We have mapped the distribution of Tim17 family members in the eukaryotic supergroups and found that the mitochondrial Tim17, Tim22 and Tim23 proteins, as well as the peroxisomal Tim17 family proteins, were all likely to be present in the last eukaryotic common ancestor (LECA). Thus, kinetoplastid mitochondria previously identified as carrying a single Tim17protein family homologue are likely to be the outcome of a secondary reduction. The eukaryotic cell has modified mitochondrial Tim17 family proteins to mediate different functions in multiple cellular compartments including mitochondria, plastids and peroxisomes. Concerning the origin of Tim17 protein family, our analyses do not support the affiliation of the protein family and the component of bacterial amino acid permease. Thus, it is likely that Tim17 protein family is exclusive to eukaryotes.<br><br>REVIEWERS: The article was reviewed by Michael Gray, Martijn Huynen and Kira Makarova.}, }
@article {pmid27614431, year = {2016}, author = {Tardu, M and Dikbas, UM and Baris, I and Kavakli, IH}, title = {RNA-seq analysis of the transcriptional response to blue and red light in the extremophilic red alga, Cyanidioschyzon merolae.}, journal = {Functional &amp; integrative genomics}, volume = {16}, number = {6}, pages = {657-669}, pmid = {27614431}, issn = {1438-7948}, mesh = {Carbon/metabolism ; Chloroplasts/genetics/radiation effects ; Extremophiles/genetics/radiation effects ; Genome, Plant/radiation effects ; High-Throughput Nucleotide Sequencing ; Light ; Mitochondria/genetics ; Photosynthesis/*genetics/radiation effects ; *Phylogeny ; Pigments, Biological/biosynthesis ; Rhodophyta/*genetics/radiation effects ; Transcriptome/*genetics/radiation effects ; }, abstract = {Light is one of the main environmental cues that affects the physiology and behavior of many organisms. The effect of light on genome-wide transcriptional regulation has been well-studied in green algae and plants, but not in red algae. Cyanidioschyzon merolae is used as a model red algae, and is suitable for studies on transcriptomics because of its compact genome with a relatively small number of genes. In addition, complete genome sequences of the nucleus, mitochondrion, and chloroplast of this organism have been determined. Together, these attributes make C. merolae an ideal model organism to study the response to light stimuli at the transcriptional and the systems biology levels. Previous studies have shown that light significantly affects cell signaling in this organism, but there are no reports on its blue light- and red light-mediated transcriptional responses. We investigated the direct effects of blue and red light at the transcriptional level using RNA-seq. Blue and red lights were found to regulate 35 % of the total genes in C. merolae. Blue light affected the transcription of genes involved in protein synthesis while red light specifically regulated the transcription of genes involved in photosynthesis and DNA repair. Blue or red light regulated genes involved in carbon metabolism and pigment biosynthesis. Overall, our data showed that red and blue light regulate the majority of the cellular, cell division, and repair processes in C. merolae.}, }
@article {pmid27751184, year = {2016}, author = {Ku, C and Martin, WF}, title = {A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70 % rule.}, journal = {BMC biology}, volume = {14}, number = {1}, pages = {89}, pmid = {27751184}, issn = {1741-7007}, mesh = {Eukaryotic Cells/*metabolism ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/genetics ; Prokaryotic Cells/*metabolism ; }, abstract = {BACKGROUND: The literature harbors many claims for lateral gene transfer (LGT) from prokaryotes to eukaryotes. Such claims are typically founded in analyses of genome sequences. It is undisputed that many genes entered the eukaryotic lineage via the origin of mitochondria and the origin of plastids. Claims for lineage-specific LGT to eukaryotes outside the context of organelle origins and claims of continuous LGT to eukaryotic lineages are more problematic. If eukaryotes acquire genes from prokaryotes continuously during evolution, then sequenced eukaryote genomes should harbor evidence for recent LGT, like prokaryotic genomes do.<br><br>RESULTS: Here we devise an approach to investigate 30,358 eukaryotic sequences in the context of 1,035,375 prokaryotic homologs among 2585 phylogenetic trees containing homologs from prokaryotes and eukaryotes. Prokaryote genomes reflect a continuous process of gene acquisition and inheritance, with abundant recent acquisitions showing 80-100&#xa0;% amino acid sequence identity to their phylogenetic sister-group homologs from other phyla. By contrast, eukaryote genomes show no evidence for either continuous or recent gene acquisitions from prokaryotes. We find that, in general, genes in eukaryotic genomes that share &#x2265;70&#xa0;% amino acid identity to prokaryotic homologs are genome-specific; that is, they are not found outside individual genome assemblies.<br><br>CONCLUSIONS: Our analyses indicate that eukaryotes do not acquire genes through continual LGT like prokaryotes do. We propose a 70&#xa0;% rule: Coding sequences in eukaryotic genomes that share more than 70&#xa0;% amino acid sequence identity to prokaryotic homologs are most likely assembly or annotation artifacts. The findings further uncover that the role of differential loss in eukaryote genome evolution has been vastly underestimated.}, }
@article {pmid27577682, year = {2016}, author = {Sookoian, S and Flichman, D and Scian, R and Rohr, C and Dopazo, H and Gianotti, TF and Martino, JS and Castaño, GO and Pirola, CJ}, title = {Mitochondrial genome architecture in non-alcoholic fatty liver disease.}, journal = {The Journal of pathology}, volume = {240}, number = {4}, pages = {437-449}, doi = {10.1002/path.4803}, pmid = {27577682}, issn = {1096-9896}, mesh = {Adult ; Case-Control Studies ; DNA, Mitochondrial/genetics ; Female ; Genetic Predisposition to Disease ; *Genome, Mitochondrial ; Germ-Line Mutation ; Haplotypes ; Humans ; Liver Cirrhosis/genetics ; Male ; Middle Aged ; Mitochondria, Liver/genetics ; Mutation ; Mutation, Missense/genetics ; Non-alcoholic Fatty Liver Disease/*genetics ; Oxidative Phosphorylation ; Polymorphism, Genetic ; Severity of Illness Index ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD) is associated with mitochondrial dysfunction, a decreased liver mitochondrial DNA (mtDNA) content, and impaired energy metabolism. To understand the clinical implications of mtDNA diversity in the biology of NAFLD, we applied deep-coverage whole sequencing of the liver mitochondrial genomes. We used a multistage study design, including a discovery phase, a phenotype-oriented study to assess the mutational burden in patients with steatohepatitis at different stages of liver fibrosis, and a replication study to validate findings in loci of interest. We also assessed the potential protein-level impact of the observed mutations. To determine whether the observed changes are tissue-specific, we compared the liver and the corresponding peripheral blood entire mitochondrial genomes. The nuclear genes POLG and POLG2 (mitochondrial DNA polymerase-γ) were also sequenced. We observed that the liver mtDNA of patients with NAFLD harbours complex genomes with a significantly higher mutational (1.28-fold) rate and degree of heteroplasmy than in controls. The analysis of liver mitochondrial genomes of patients with different degrees of fibrosis revealed that the disease severity is associated with an overall 1.4-fold increase in mutation rate, including mutations in genes of the oxidative phosphorylation (OXPHOS) chain. Significant differences in gene and protein expression patterns were observed in association with the cumulative number of OXPHOS polymorphic sites. We observed a high degree of homology (∼98%) between the blood and liver mitochondrial genomes. A missense POLG p.Gln1236His variant was associated with liver mtDNA copy number. In conclusion, we have demonstrated that OXPHOS genes contain the highest number of hotspot positions associated with a more severe phenotype. The variability of the mitochondrial genomes probably originates from a common germline source; hence, it may explain a fraction of the 'missing heritability' of NAFLD. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley &amp; Sons, Ltd.}, }
@article {pmid27749017, year = {2017}, author = {Yubuki, N and Zadrobílková, E and Čepička, I}, title = {Ultrastructure and Molecular Phylogeny of Iotanema spirale gen. nov. et sp. nov., a New Lineage of Endobiotic Fornicata with Strikingly Simplified Ultrastructure.}, journal = {The Journal of eukaryotic microbiology}, volume = {64}, number = {4}, pages = {422-433}, doi = {10.1111/jeu.12376}, pmid = {27749017}, issn = {1550-7408}, mesh = {Animals ; Cytoskeleton/ultrastructure ; DNA, Ribosomal/genetics ; Eukaryota/*classification/genetics/*ultrastructure ; Evolution, Molecular ; Feces/parasitology ; Lizards/*parasitology ; Microscopy, Electron, Transmission ; Phylogeny ; RNA, Ribosomal/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Fornicata (Metamonada) is a group of Excavata living in low-oxygen environments and lacking conventional mitochondria. It includes free-living Carpediemonas-like organisms from marine habitats and predominantly parasitic/commensal retortamonads and diplomonads. Current modest knowledge of biodiversity of Fornicata limits our ability to draw a complete picture of the evolutionary history in this group. Here, we report the discovery of a novel fornicate, Iotanema spirale gen. nov. et sp. nov., obtained from fresh feces of the gecko Phelsuma madagascariensis. Our phylogenetic analyses of the small subunit ribosomal RNA gene demonstrate that I. spirale is closely related to the free-living, marine strain PCS and the Carpediemonas-like organism Hicanonectes teleskopos within Fornicata. Iotanema spirale exhibits several features uncommon to fornicates, such as a single flagellum, a highly reduced cytoskeletal system, and the lack of the excavate ventral groove, but shares these characters with the poorly known genus Caviomonas. Therefore, I. spirale is accommodated within the family Caviomonadidae, which represents the third known endobiotic lineage of Fornicata. This study improves our understanding of character evolution within Fornicata when placed within the molecular phylogenetic context.}, }
@article {pmid27748992, year = {2017}, author = {Hunter, MS and Asiimwe, P and Himler, AG and Kelly, SE}, title = {Host nuclear genotype influences phenotype of a conditional mutualist symbiont.}, journal = {Journal of evolutionary biology}, volume = {30}, number = {1}, pages = {141-149}, doi = {10.1111/jeb.12993}, pmid = {27748992}, issn = {1420-9101}, mesh = {Animals ; Female ; Genetic Variation ; *Genotype ; *Hemiptera ; *Phenotype ; *Rickettsia ; *Symbiosis ; }, abstract = {Arthropods commonly carry maternally inherited intracellular bacterial symbionts that may profoundly influence host biology and evolution. The intracellular symbiont Rickettsia sp. nr. bellii swept rapidly into populations of the sweetpotato whitefly Bemisia tabaci in the south-western USA. Previous laboratory experiments showed female-bias and fitness benefits were associated with Rickettsia infection, potentially explaining the high frequencies of infection observed in field populations, but the effects varied with whitefly genetic line. Here, we explored whether host extranuclear or nuclear genes influenced the variation in the Rickettsia-host phenotype in two genetic lines of the whitefly host, each with Rickettsia-infected and uninfected sublines. Introgression between the Rickettsia-infected subline of one genetic line and the Rickettsia-uninfected subline of the other was used to create two new sublines, each with the maternally inherited extranuclear genetic lineages of one line (Rickettsia, two other symbionts and the mitochondria) and the nuclear genotype of the other. Performance assays comparing the original and new lines showed that in addition to Rickettsia, the interaction of Rickettsia infection with host nuclear genotype influenced development time and the sex ratio of the progeny, whereas the extranuclear genotype did not. Host nuclear genotype, but not extranuclear genotype, also influenced the titre of Rickettsia. Our results support the hypothesis that differences in host nuclear genotype alone may explain considerable within-population variation in host-symbiont phenotype and may contribute to the observed variation in Rickettsia-whitefly interactions worldwide.}, }
@article {pmid27748512, year = {2017}, author = {Demain, LA and Conway, GS and Newman, WG}, title = {Genetics of mitochondrial dysfunction and infertility.}, journal = {Clinical genetics}, volume = {91}, number = {2}, pages = {199-207}, doi = {10.1111/cge.12896}, pmid = {27748512}, issn = {1399-0004}, support = {S35/ACT_/Action on Hearing Loss/United Kingdom ; }, mesh = {DNA Polymerase gamma ; DNA-Directed DNA Polymerase/*genetics ; Female ; Humans ; Infertility, Female/*genetics/pathology ; Infertility, Male/*genetics/pathology ; Male ; Mitochondria/*genetics ; Oocytes/metabolism/pathology ; Reproductive Techniques, Assisted ; Spermatozoa/metabolism/pathology ; }, abstract = {Increasingly, mitochondria are being recognized as having an important role in fertility. Indeed in assisted reproductive technologies mitochondrial function is a key indicator of sperm and oocyte quality. Here, we review the literature regarding mitochondrial genetics and infertility. In many multisystem disorders caused by mitochondrial dysfunction death occurs prior to sexual maturity, or the clinical features are so severe that infertility may be underreported. Interestingly, many of the genes linked to mitochondrial dysfunction and infertility have roles in the maintenance of mitochondrial DNA or in mitochondrial translation. Studies on populations with genetically uncharacterized infertility have highlighted an association with mitochondrial DNA deletions, whether this is causative or indicative of poor functioning mitochondria requires further examination. Studies on the impact of mitochondrial DNA variants present conflicting data but highlight POLG as a particularly interesting candidate gene for both male and female infertility.}, }
@article {pmid27737633, year = {2016}, author = {Lumsden, AL and Young, RL and Pezos, N and Keating, DJ}, title = {Huntingtin-associated protein 1: Eutherian adaptation from a TRAK-like protein, conserved gene promoter elements, and localization in the human intestine.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {214}, pmid = {27737633}, issn = {1471-2148}, mesh = {Animals ; Base Sequence ; Binding Sites ; Caenorhabditis elegans/genetics ; Conserved Sequence/*genetics ; Humans ; Intestinal Mucosa/*metabolism ; Mammals/*genetics ; Mitochondria/genetics ; Multigene Family ; Nerve Tissue Proteins/*metabolism ; Nucleotide Motifs/genetics ; Phylogeny ; *Promoter Regions, Genetic ; Protein Binding/genetics ; Protein Domains ; Protein Transport ; Reproducibility of Results ; Sequence Homology, Nucleic Acid ; Serotonin/metabolism ; Transcription Factors/genetics ; }, abstract = {BACKGROUND: Huntingtin-associated Protein 1 (HAP1) is expressed in neurons and endocrine cells, and is critical for postnatal survival in mice. HAP1 shares a conserved "HAP1_N" domain with TRAfficking Kinesin proteins TRAK1 and TRAK2 (vertebrate), Milton (Drosophila) and T27A3.1 (C. elegans). HAP1, TRAK1 and TRAK2 have a degree of common function, particularly regarding intracellular receptor trafficking. However, TRAK1, TRAK2 and Milton (which have a "Milt/TRAK" domain that is absent in human and rodent HAP1) differ in function to HAP1 in that they are mitochondrial transport proteins, while HAP1 has emerging roles in starvation response. We have investigated HAP1 function by examining its evolution, and upstream gene promoter sequences. We performed phylogenetic analyses of the HAP1_N domain family of proteins, incorporating HAP1 orthologues (identified by genomic synteny) from 5 vertebrate classes, and also searched the Dictyostelium proteome for a common ancestor. Computational analyses of mammalian HAP1 gene promoters were performed to identify phylogenetically conserved regulatory motifs.<br><br>RESULTS: We found that as recently as marsupials, HAP1 contained a Milt/TRAK domain and was more similar to TRAK1 and TRAK2 than to eutherian HAP1. The Milt/TRAK domain likely arose post multicellularity, as it was absent in the Dictyostelium proteome. It was lost from HAP1 in the eutherian lineage, and also from T27A3.1 in C. elegans. The HAP1 promoter from human, mouse, rat, rabbit, horse, dog, Tasmanian devil and opossum contained common sites for transcription factors involved in cell cycle, growth, differentiation, and stress response. A conserved arrangement of regulatory elements was identified, including sites for caudal-related homeobox transcription factors (CDX1 and CDX2), and myc-associated factor X (MAX) in the region of the TATA box. CDX1 and CDX2 are intestine-enriched factors, prompting investigation of HAP1 protein expression in the human duodenum. HAP1 was localized to singly dispersed mucosal cells, including a subset of serotonin-positive enterochromaffin cells.<br><br>CONCLUSION: We have identified eutherian HAP1 as an evolutionarily recent adaptation of a vertebrate TRAK protein-like ancestor, and found conserved CDX1/CDX2 and MAX transcription factor binding sites near the TATA box in mammalian HAP1 gene promoters. We also demonstrated that HAP1 is expressed in endocrine cells of the human gut.}, }
@article {pmid27736028, year = {2017}, author = {Dominguez-Rodriguez, A and Abreu-Gonzalez, P and de la Torre-Hernandez, JM and Gonzalez-Gonzalez, J and Garcia-Camarero, T and Consuegra-Sanchez, L and Garcia-Saiz, MD and Aldea-Perona, A and Virgos-Aller, T and Azpeitia, A and Reiter, RJ and , }, title = {Effect of intravenous and intracoronary melatonin as an adjunct to primary percutaneous coronary intervention for acute ST-elevation myocardial infarction: Results of the Melatonin Adjunct in the acute myocaRdial Infarction treated with Angioplasty trial.}, journal = {Journal of pineal research}, volume = {62}, number = {1}, pages = {}, doi = {10.1111/jpi.12374}, pmid = {27736028}, issn = {1600-079X}, mesh = {Angioplasty, Balloon, Coronary ; Female ; Humans ; Male ; Melatonin/*administration &amp; dosage/adverse effects ; Middle Aged ; Myocardial Reperfusion Injury/*prevention &amp; control ; ST Elevation Myocardial Infarction/*therapy ; }, abstract = {The MARIA randomized trial evaluated the efficacy and safety of melatonin for the reduction of reperfusion injury in patients undergoing revascularization for ST-elevation myocardial infarction (STEMI). This was a prespecified interim analysis. A total of 146 patients presenting with STEMI within 6 hours of chest pain onset were randomized to receive intravenous and intracoronary melatonin (n=73) or placebo (n=73) during primary percutaneous coronary intervention (PPCI). Primary endpoint was myocardial infarct size as assessed by magnetic resonance imaging (MRI) at 6 ± 2 days. Secondary endpoints were changes in left ventricular volumes and ejection fraction (LVEF) at 130 ± 10 days post-PPCI and adverse events during the first year. No significant differences in baseline characteristics were observed between groups. MRI was performed in 108 patients (86.4%). Myocardial infarct size by MRI evaluated 6 ± 2 days post-PPCI, did not differ between melatonin and placebo groups (P=.63). Infarct size assessed by MRI at 130 ± 10 days post-PPCI, performed in 91 patients (72.8%), did not show statistically significant differences between groups (P=.27). The recovery of LVEF from 6 ± 2 to 130 ± 10 days post-PPCI was greater in the placebo group (60.0 ± 10.4% vs 53.1 ± 12.5%, P=.008). Both left ventricular end-diastolic and end-systolic volumes were lower in the placebo group (P=.01). The incidence of adverse events at 1 year was comparable in both groups (P=.150). Thus, in a nonrestricted STEMI population, intravenous and intracoronary melatonin was not associated with a reduction in infarct size and has an unfavourable effect on the ventricular volumes and LVEF evolution. Likewise, there is lack of toxicity of melatonin with the doses used.}, }
@article {pmid27732668, year = {2016}, author = {Rannamäe, E and Lõugas, L and Speller, CF and Valk, H and Maldre, L and Wilczyński, J and Mikhailov, A and Saarma, U}, title = {Three Thousand Years of Continuity in the Maternal Lineages of Ancient Sheep (Ovis aries) in Estonia.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0163676}, pmid = {27732668}, issn = {1932-6203}, mesh = {Animals ; Archaeology ; Breeding/history ; DNA, Mitochondrial/isolation &amp; purification/metabolism ; Estonia ; Fossils ; *Genetic Variation ; Haplotypes ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, Ancient ; History, Medieval ; Mitochondria/genetics ; Sequence Analysis, DNA ; Sheep ; Sheep, Domestic/*genetics ; }, abstract = {Although sheep (Ovis aries) have been one of the most exploited domestic animals in Estonia since the Late Bronze Age, relatively little is known about their genetic history. Here, we explore temporal changes in Estonian sheep populations and their mitochondrial genetic diversity over the last 3000 years. We target a 558 base pair fragment of the mitochondrial hypervariable region in 115 ancient sheep from 71 sites in Estonia (c. 1200 BC-AD 1900s), 19 ancient samples from Latvia, Russia, Poland and Greece (6800 BC-AD 1700), as well as 44 samples of modern Kihnu native sheep breed. Our analyses revealed: (1) 49 mitochondrial haplotypes, associated with sheep haplogroups A and B; (2) high haplotype diversity in Estonian ancient sheep; (3) continuity in mtDNA haplotypes through time; (4) possible population expansion during the first centuries of the Middle Ages (associated with the establishment of the new power regime related to 13th century crusades); (5) significant difference in genetic diversity between ancient populations and modern native sheep, in agreement with the beginning of large-scale breeding in the 19th century and population decline in local sheep. Overall, our results suggest that in spite of the observed fluctuations in ancient sheep populations, and changes in the natural and historical conditions, the utilisation of local sheep has been constant in the territory of Estonia, displaying matrilineal continuity from the Middle Bronze Age through the Modern Period, and into modern native sheep.}, }
@article {pmid27732624, year = {2016}, author = {Gollner, S and Stuckas, H and Kihara, TC and Laurent, S and Kodami, S and Martinez Arbizu, P}, title = {Mitochondrial DNA Analyses Indicate High Diversity, Expansive Population Growth and High Genetic Connectivity of Vent Copepods (Dirivultidae) across Different Oceans.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0163776}, pmid = {27732624}, issn = {1932-6203}, mesh = {Animals ; Copepoda/classification/*genetics ; DNA, Mitochondrial/chemistry/isolation &amp; purification/*metabolism ; Electron Transport Complex IV/genetics ; Genetic Variation ; Genetics, Population ; Haplotypes ; Microscopy, Confocal ; Mitochondria/*genetics ; Oceans and Seas ; Phylogeny ; Population Growth ; Sequence Analysis, DNA ; }, abstract = {Communities in spatially fragmented deep-sea hydrothermal vents rich in polymetallic sulfides could soon face major disturbance events due to deep-sea mineral mining, such that unraveling patterns of gene flow between hydrothermal vent populations will be an important step in the development of conservation policies. Indeed, the time required by deep-sea populations to recover following habitat perturbations depends both on the direction of gene flow and the number of migrants available for re-colonization after disturbance. In this study we compare nine dirivultid copepod species across various geological settings. We analyze partial nucleotide sequences of the mtCOI gene and use divergence estimates (FST) and haplotype networks to infer intraspecific population connectivity between vent sites. Furthermore, we evaluate contrasting scenarios of demographic population expansion/decline versus constant population size (using, for example, Tajima's D). Our results indicate high diversity, population expansion and high connectivity of all copepod populations in all oceans. For example, haplotype diversity values range from 0.89 to 1 and FST values range from 0.001 to 0.11 for Stygiopontius species from the Central Indian Ridge, Mid Atlantic Ridge, East Pacific Rise, and Eastern Lau Spreading Center. We suggest that great abundance and high site occupancy by these species favor high genetic diversity. Two scenarios both showed similarly high connectivity: fast spreading centers with little distance between vent fields and slow spreading centers with greater distance between fields. This unexpected result may be due to some distinct frequency of natural disturbance events, or to aspects of individual life histories that affect realized rates of dispersal. However, our statistical performance analyses showed that at least 100 genomic regions should be sequenced to ensure accurate estimates of migration rate. Our demography parameters demonstrate that dirivultid populations are generally large and continuously undergoing population growth. Benthic and pelagic species abundance data support these findings.}, }
@article {pmid27731355, year = {2016}, author = {Jugé, R and Breugnot, J and Da Silva, C and Bordes, S and Closs, B and Aouacheria, A}, title = {Quantification and Characterization of UVB-Induced Mitochondrial Fragmentation in Normal Primary Human Keratinocytes.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {35065}, pmid = {27731355}, issn = {2045-2322}, mesh = {Apoptosis ; Cell Survival/radiation effects ; Cells, Cultured ; Computational Biology/methods ; DNA Damage ; Dynamins ; GTP Phosphohydrolases/*genetics ; Gene Knockdown Techniques ; Healthy Volunteers ; Humans ; Keratinocytes/cytology/*radiation effects ; Microscopy, Confocal ; Microtubule-Associated Proteins/*genetics ; Mitochondria/genetics/*radiation effects ; Mitochondrial Dynamics/*radiation effects ; Mitochondrial Proteins/*genetics ; Reactive Oxygen Species/metabolism ; }, abstract = {UV irradiation is a major environmental factor causing skin dryness, aging and cancer. UVB in particular triggers cumulative DNA damage, oxidative stress and mitochondrial dysfunction. The objective of our study was to provide both qualitative and quantitative analysis of how mitochondria respond to UVB irradiation in normal human epidermal keratinocytes (NHEK) of healthy donors, with the rationale that monitoring mitochondrial shape will give an indication of cell population fitness and enable the screening of bioactive agents with UVB-protective properties. Our results show that NHEK undergo dose-dependent mitochondrial fragmentation after exposure to UVB. In order to obtain a quantitative measure of this phenomenon, we implemented a novel tool for automated quantification of mitochondrial morphology in live cells based on confocal microscopy and computational calculations of mitochondrial shape descriptors. This method was used to substantiate the effects on mitochondrial morphology of UVB irradiation and of knocking-down the mitochondrial fission-mediating GTPase Dynamin-related protein 1 (DRP1). Our data further indicate that all the major mitochondrial dynamic proteins are expressed in NHEK but that their level changes were stronger after mitochondrial uncoupler treatment than following UVB irradiation or DRP1 knock-down. Our system and procedures might be of interest for the identification of cosmetic or dermatologic UVB-protective agents.}, }
@article {pmid27731328, year = {2017}, author = {Branco, AT and Schilling, L and Silkaitis, K and Dowling, DK and Lemos, B}, title = {Reproductive activity triggers accelerated male mortality and decreases lifespan: genetic and gene expression determinants in Drosophila.}, journal = {Heredity}, volume = {118}, number = {3}, pages = {221-228}, pmid = {27731328}, issn = {1365-2540}, mesh = {Animals ; Down-Regulation ; Drosophila melanogaster/*genetics ; *Gene Expression ; Genotype ; Longevity/*genetics ; Male ; Reproduction/genetics ; Sexual Behavior, Animal ; Testis/physiology ; Up-Regulation ; }, abstract = {Reproduction and aging evolved to be intimately associated. Experimental selection for early-life reproduction drives the evolution of decreased longevity in Drosophila whereas experimental selection for increased longevity leads to changes in reproduction. Although life history theory offers hypotheses to explain these relationships, the genetic architecture and molecular mechanisms underlying reproduction-longevity associations remain a matter of debate. Here we show that mating triggers accelerated mortality in males and identify hundreds of genes that are modulated upon mating in the fruit fly Drosophila melanogaster. Interrogation of genome-wide gene expression in virgin and recently mated males revealed coherent responses, with biological processes that are upregulated (testis-specific gene expression) or downregulated (metabolism and mitochondria-related functions) upon mating. Furthermore, using a panel of genotypes from the Drosophila Synthetic Population Resource (DSPR) as a source of naturally occurring genetic perturbation, we uncover abundant variation in longevity and reproduction-induced mortality among genotypes. Genotypes displayed more than fourfold variation in longevity and reproduction-induced mortality that can be traced to variation in specific segments of the genome. The data reveal individual variation in sensitivity to reproduction and physiological processes that are enhanced and suppressed upon mating. These results raise the prospect that variation in longevity and age-related traits could be traced to processes that coordinate germline and somatic function.}, }
@article {pmid27708261, year = {2016}, author = {Schmitz, J and Noll, A and Raabe, CA and Churakov, G and Voss, R and Kiefmann, M and Rozhdestvensky, T and Brosius, J and Baertsch, R and Clawson, H and Roos, C and Zimin, A and Minx, P and Montague, MJ and Wilson, RK and Warren, WC}, title = {Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {12997}, pmid = {27708261}, issn = {2041-1723}, mesh = {Animals ; Brain/metabolism ; Cell Nucleus/metabolism ; DNA Transposable Elements ; Female ; *Gene Silencing ; *Genome ; *Genome, Mitochondrial ; *Long Interspersed Nucleotide Elements ; Markov Chains ; MicroRNAs/metabolism ; Mitochondria/metabolism ; Muscles/metabolism ; Phylogeny ; RNA, Small Nucleolar/metabolism ; Tarsiidae/*genetics ; }, abstract = {Tarsiers are phylogenetically located between the most basal strepsirrhines and the most derived anthropoid primates. While they share morphological features with both groups, they also possess uncommon primate characteristics, rendering their evolutionary history somewhat obscure. To investigate the molecular basis of such attributes, we present here a new genome assembly of the Philippine tarsier (Tarsius syrichta), and provide extended analyses of the genome and detailed history of transposable element insertion events. We describe the silencing of Alu monomers on the lineage leading to anthropoids, and recognize an unexpected abundance of long terminal repeat-derived and LINE1-mobilized transposed elements (Tarsius interspersed elements; TINEs). For the first time in mammals, we identify a complete mitochondrial genome insertion within the nuclear genome, then reveal tarsier-specific, positive gene selection and posit population size changes over time. The genomic resources and analyses presented here will aid efforts to more fully understand the ancient characteristics of primate genomes.}, }
@article {pmid27708147, year = {2016}, author = {Hofstatter, PG and Tice, AK and Kang, S and Brown, MW and Lahr, DJ}, title = {Evolution of bacterial recombinase A (recA) in eukaryotes explained by addition of genomic data of key microbial lineages.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1840}, pages = {}, pmid = {27708147}, issn = {1471-2954}, support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; }, mesh = {Amoebozoa/enzymology/genetics ; Bacterial Proteins/*genetics ; Dictyostelium/enzymology/genetics ; Eukaryota/enzymology/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; Phylogeny ; Rec A Recombinases/*genetics ; }, abstract = {Recombinase enzymes promote DNA repair by homologous recombination. The genes that encode them are ancestral to life, occurring in all known dominions: viruses, Eubacteria, Archaea and Eukaryota. Bacterial recombinases are also present in viruses and eukaryotic groups (supergroups), presumably via ancestral events of lateral gene transfer. The eukaryotic recA genes have two distinct origins (mitochondrial and plastidial), whose acquisition by eukaryotes was possible via primary (bacteria-eukaryote) and/or secondary (eukaryote-eukaryote) endosymbiotic gene transfers (EGTs). Here we present a comprehensive phylogenetic analysis of the recA genealogy, with substantially increased taxonomic sampling in the bacteria, viruses, eukaryotes and a special focus on the key eukaryotic supergroup Amoebozoa, earlier represented only by Dictyostelium We demonstrate that several major eukaryotic lineages have lost the bacterial recombinases (including Opisthokonta and Excavata), whereas others have retained them (Amoebozoa, Archaeplastida and the SAR-supergroups). When absent, the bacterial recA homologues may have been lost entirely (secondary loss of canonical mitochondria) or replaced by other eukaryotic recombinases. RecA proteins have a transit peptide for organellar import, where they act. The reconstruction of the RecA phylogeny with its EGT events presented here retells the intertwined evolutionary history of eukaryotes and bacteria, while further illuminating the events of endosymbiosis in eukaryotes by expanding the collection of widespread genes that provide insight to this deep history.}, }
@article {pmid27706654, year = {2016}, author = {Ma, HY and Ma, CY and Zhu, JJ and Ren, GJ and Wang, W and Chen, W and Lu, JX and Ma, LB}, title = {Characterization of the complete mitochondrial genome and phylogenetic relationships of the three-spot swimming crab (Portunus sanguinolentus).}, journal = {Genetics and molecular research : GMR}, volume = {15}, number = {3}, pages = {}, doi = {10.4238/gmr.15038580}, pmid = {27706654}, issn = {1676-5680}, mesh = {Animals ; Arthropod Proteins/*genetics ; Brachyura/classification/*genetics ; Codon, Initiator ; Codon, Terminator ; DNA, Mitochondrial/*genetics ; Genome Size ; *Genome, Mitochondrial ; Male ; Mitochondria/genetics ; Molecular Sequence Annotation ; Nucleic Acid Conformation ; Open Reading Frames ; *Phylogeny ; RNA, Transfer/chemistry/genetics ; }, abstract = {In this study, we determined the whole mitochondrial genome profile of the three-spot swimming crab (Portunus sanguinolentus) and elucidated phylogenetic relationships between representative species in the order Decapoda. The mitochondrial genome was 16,024 bp in length and consisted of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Of the 37 genes, 23 were encoded by the heavy strand while 14 were encoded by the light strand. Four types of start codons were identified; ATG initiated nine genes, ATT initiated two genes, and ATC and GTG each started one gene. Nine protein-coding genes ended with a complete TAA or TAG stop codon, and four genes ended with an incomplete T or TA codon. Fourteen non-coding regions were found, which ranged from 1 to 34 bp in length. Nine overlaps were observed, with lengths between 1 and 7 bp. Phylogenetic analysis suggested that P. sanguinolentus is genetically closest to P. trituberculatus and P. pelagicus. Charybdis feriata, C. japonica, and Thalamita crenata formed a single cluster, and were close to the genera Callinectes and Portunus. Therefore, the genera Charybdis and Thalamita should be classified into the subfamily Portuninae.}, }
@article {pmid27706641, year = {2016}, author = {Cao, YY and Li, ZB}, title = {Genetic diversity and population structure of Fenneropenaeus penicillatus determined by mitochondrial DNA analyses.}, journal = {Genetics and molecular research : GMR}, volume = {15}, number = {3}, pages = {}, doi = {10.4238/gmr.15038503}, pmid = {27706641}, issn = {1676-5680}, mesh = {Animals ; China ; DNA, Mitochondrial/*genetics ; Endangered Species ; Genetic Drift ; Genetic Variation ; *Genetics, Population ; Haplotypes ; *Microsatellite Repeats ; Mitochondria/genetics ; Penaeidae/classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Fenneropenaeus penicillatus is a widely distributed economically and ecologically important shrimp species, which is endangered in China. Sequence analysis of 16s rRNA and control region (CR) fragments from mitochondrial DNA was conducted to obtain information on genetic diversity and population structure. Individuals from 12 wild F. penicillatus populations located along the southeast coast of China were used. Polymerase chain reaction (PCR) fragments of the CR gene revealed high genetic diversity among the 12 populations; however, PCR fragments of the 16s rRNA gene revealed very low genetic diversity in the Hainan (HN) and Ningde (ND) populations and high genetic diversity in the DS, BH, PT, XM, and SZ populations. Data obtained from the CR and 16s rRNA genes suggested that high genetic differentiation exists among the 12 populations, which is mainly due to the high genetic differentiation between HN and all other 11 populations. These results may be useful for further sustainable management and utilization of this species.}, }
@article {pmid27706640, year = {2016}, author = {Huang, ZH and Tu, FY}, title = {Characterization and evolution of the mitochondrial DNA control region in Ranidae and their phylogenetic relationship.}, journal = {Genetics and molecular research : GMR}, volume = {15}, number = {3}, pages = {}, doi = {10.4238/gmr.15038491}, pmid = {27706640}, issn = {1676-5680}, mesh = {Animals ; Base Composition ; Conserved Sequence ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; RNA, Transfer, Leu/genetics ; Ranidae/classification/*genetics ; }, abstract = {The control region is considered to be one of the most variable parts of animal mitochondrial DNA (mtDNA). We compared the mtDNA control region from 37 species representing 14 genera and 4 subfamilies of Ranidae, to analyze the evolution of the control region and to determine their phylogenetic relationship. All the Ranidae species had a single control region, except four species that had two repeat regions. The control region spanned the region between the Cyt b and tRNAleu genes in most of the Ranidae species. The length of the control region sequences ranged from 1186 bp (Limnonectes bannaensis) to 6746 bp (Rana kunyuensis). The average genetic distances among the species varied from 1.94% (between R. chosenica and R. plancyi) to 113.25% (between Amolops ricketti and Euphlyctis hexadactylus). The alignment of three conserved sequence blocks was identified. However, conserved sequence boxes F to A were not found in Ranidae. A maximum likelihood method was used to reconstruct the phylogenetic relationship based on a general time reversible + gamma distribution model. The amount of A+T was higher than G+C across the whole control region. The phylogenetic tree grouped members of the respective subfamilies into separate clades, with the exception of Raninae. Our analysis supported that some genera, including Rana and Amolops, may be polyphyletic. Control region sequence is an effective molecular mark for Ranidae phylogenetic inference.}, }
@article {pmid27706563, year = {2016}, author = {Ma, CY and Ma, HY and Ren, GJ and Wang, W and Chen, W and Lu, JX and Zou, X and Ma, LB}, title = {Characterization of the complete mitochondrial genome of Portunus pelagicus with implications for phylogenomics.}, journal = {Genetics and molecular research : GMR}, volume = {15}, number = {3}, pages = {}, doi = {10.4238/gmr.15038719}, pmid = {27706563}, issn = {1676-5680}, mesh = {Animals ; Brachyura/*genetics ; Chromosome Mapping ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; RNA, Untranslated/genetics ; Sequence Analysis, DNA ; }, abstract = {This study determined the mitochondrial genome structure of the blue swimming crab (Portunus pelagicus), and elucidated its phylogenetic relationships among the species within the order Decapoda. The complete mitochondrial genome was 16,155 bp long, and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 DNA control region. The gene order of the genome was the same as that found within the family Portunidae. Twenty-three genes were on the heavy strand and 14 were on the light strand. Almost all of the protein-coding genes were initiated by an ATG codon, except for three genes (ATP6, ND1, and ND3) that started with a rare ATT codon. Of the 13 protein-coding genes, 10 ended with complete TAA or TAG stop codons and three ended with an incomplete T codon. Thirteen non-coding regions were identified that ranged from 1 to 30 bp in length. Nine overlaps were found, which ranged 1 to 7 bp in length. Phylogenetic analyses based on 12 concatenated protein-coding genes revealed that P. pelagicus formed a monophyletic group with Portunus trituberculatus, which were in a larger group with Callinectes sapidus, while the genera Charybdis and Thalamita formed another group. These two groups clustered together and grouped with the genus Scylla. The phylogenetic analysis supported the inclusion of Charybdis in subfamily Portuninae of the family Portunidae, and revealed a close relationship between Charybdis and Thalamita. We suggest that Thalamita should also be classified into the subfamily Portuninae. The results can be used in the study of phylogenetic, population genetic and conservation genetics of P. pelagicus.}, }
@article {pmid27706168, year = {2016}, author = {Chaverri, G and Garin, I and Alberdi, A and Jimenez, L and Castillo-Salazar, C and Aihartza, J}, title = {Unveiling the Hidden Bat Diversity of a Neotropical Montane Forest.}, journal = {PloS one}, volume = {11}, number = {10}, pages = {e0162712}, pmid = {27706168}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; *Biodiversity ; Central America ; Chiroptera/classification/genetics/*metabolism ; DNA/chemistry/isolation &amp; purification/metabolism ; Electron Transport Complex IV/chemistry/genetics/metabolism ; Forests ; Haplotypes ; Likelihood Functions ; Mitochondria/enzymology ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Mountain environments, characterized by high levels of endemism, are at risk of experiencing significant biodiversity loss due to current trends in global warming. While many acknowledge their importance and vulnerability, these ecosystems still remain poorly studied, particularly for taxa that are difficult to sample such as bats. Aiming to estimate the amount of cryptic diversity among bats of a Neotropical montane cloud forest in Talamanca Range-south-east Central America-, we performed a 15-night sampling campaign, which resulted in 90 captured bats belonging to 8 species. We sequenced their mitochondrial cytochrome c oxidase subunit I (COI) and screened their inter- and intraspecific genetic variation. Phylogenetic relations with conspecifics and closely related species from other geographic regions were established using Maximum Likelihood and Bayesian inference methods, as well as median-joining haplotype networks. Mitochondrial lineages highly divergent from hitherto characterized populations (> 9% COI dissimilarity) were found in Myotis oxyotus and Hylonycteris underwoodi. Sturnira burtonlimi and M. keaysi also showed distinct mitochondrial structure with sibling species and/or populations. These results suggest that mountains in the region hold a high degree of endemicity potential that has previously been ignored in bats. They also warn of the high extinction risk montane bats may be facing due to climatic change, particularly in isolated mountain systems like Talamanca Range.}, }
@article {pmid27701310, year = {2016}, author = {Faille, A and Ribera, I and Fresneda, J}, title = {On the genus Aphaobius Abeille de Perrin, 1878, with description of a new species from the mesovoid shallow substratum (MSS) of Austria (Coleoptera: Leiodidae: Cholevinae: Leptodirini).}, journal = {Zootaxa}, volume = {4169}, number = {1}, pages = {44-56}, doi = {10.11646/zootaxa.4169.1.2}, pmid = {27701310}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Austria ; Body Size ; Coleoptera/*anatomy &amp; histology/*classification/genetics/growth &amp; development ; Female ; Male ; Mitochondria/genetics ; Organ Size ; Phylogeny ; }, abstract = {Aphaobius haraldi sp. n. from the mesovoid shallow substratum (MSS) of the Austrian Alps is described, illustrated, and compared with the closest species of the genus. The new species belongs to the A. kraussi species group, formerly including five species. It can be readily separated from other species of the genus by the large parameres, with an enlarged apical part, a unique feature among species of Aphaobius. The phylogenetic position of the new species is clarified using mitochondrial and nuclear data of four related species of Aphaobius, plus some representatives of related genera from the same geographic area. The diversification of the group was estimated to be recent, dating from the Pleistocene. New records and molecular data are provided regarding the enigmatic monospecific genus of the Austrian Alps, Lotharia Mandl, 1944, which was found to be sister to the studied species of Aphaobius.}, }
@article {pmid27701290, year = {2016}, author = {Hiruta, SF and Kakui, K}, title = {Three new brackish-water thalassocypridine species (Crustacea: Ostracoda: Paracyprididae) from the Ryukyu Islands, southwestern Japan.}, journal = {Zootaxa}, volume = {4169}, number = {3}, pages = {515-539}, doi = {10.11646/zootaxa.4169.3.6}, pmid = {27701290}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Crustacea/anatomy &amp; histology/*classification/genetics/growth &amp; development ; Ecosystem ; Female ; Islands ; Japan ; Male ; Mitochondria/genetics ; Organ Size ; Phylogeny ; }, abstract = {We describe three new species of brackish-water ostracods representing two genera in the ostracod tribe Thalassocypridini from mangrove forests in the Ryukyu Islands, subtropical southwestern Japan, and provide their barcoding sequences for the mitochondrial cytochrome c oxidase subunit I (COI) gene. Mangalocypria ryukyuensis sp. nov. was found on Okinawa Island. We also found a Mangalocypria population on Ishigaki Island that was morphologically identical to M. ryukyuensis on Okinawa, but an individual differed by 4.7% in COI sequence (K2P distance) from an individual from Okinawa. This is the first record for Japan of a species in Mangalocypria. Paracypria longiseta sp. nov., obtained from Okinawa Island, is similar to Pontoparta hartmanni. Paracypria plumosa sp. nov. from Ishigaki Island is similar to Pa. adnata described from Yakushima Island, Japan. The COI genetic distance between individuals of Pa. longiseta and Pa. plumosa was roughly as large as that between either of these species and individuals in the Mangalocypria populations. Our study underscores that genera in Thalassocypridini may not represent natural groups, and that this tribe needs taxonomic revision.}, }
@article {pmid27688980, year = {2016}, author = {Quilichini, Y and Bakhoum, AJ and Justine, JL and Bray, RA and Bâ, CT and Marchand, B}, title = {Spermatozoon ultrastructure in two monorchiid digeneans.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e2488}, pmid = {27688980}, issn = {2167-8359}, abstract = {Spermatological characteristics of species from two monorchiid genera, Opisthomonorchis and Paramonorcheides, have been investigated, for the first time, by means of transmission electron microscopy. The ultrastructural study reveals that the mature spermatozoon of Opisthomonorchis dinema and Paramonorcheides selaris share several characters such as the presence of two axonemes of different lengths showing the 9+"1" pattern of the Trepaxonemata, a nucleus, two mitochondria, two bundles of parallel cortical microtubules, external ornamentation of the plasma membrane, spine-like bodies, granules of glycogen and similar morphologies of the anterior and posterior extremities. The slight differences between the male gamete of O. dinema and P. selaris are the length of the first axoneme and the position of the second mitochondrion. This study also elucidates the general morphology of the spermatozoon in all monorchiid species described so far, which corresponds to a unique spermatozoon type. Other interesting finds concern the spermatological similarities between monorchiid spermatozoa and the mature spermatozoon reported in the apocreadiid Neoapocreadium chabaudi. These similarities allow us to suggest a close phylogenetical relationship between the Monorchiidae and the Apocreadiidae, although more studies are needed, especially in the unexplored taxa.}, }
@article {pmid27687288, year = {2016}, author = {Barasa, JE and Abila, R and Grobler, JP and Agaba, M and Chemoiwa, EJ and Kaunda-Arara, B}, title = {High genetic diversity and population differentiation in Clarias gariepinus of Yala Swamp: evidence from mitochondrial DNA sequences.}, journal = {Journal of fish biology}, volume = {89}, number = {6}, pages = {2557-2570}, doi = {10.1111/jfb.13150}, pmid = {27687288}, issn = {1095-8649}, mesh = {Animals ; Catfishes/*genetics ; DNA, Mitochondrial/*chemistry ; *Genetic Variation ; Haplotypes ; Kenya ; Mitochondria/genetics ; *Phylogeny ; Wetlands ; }, abstract = {In order to improve the conservation and sustainable utilization of the African catfish Clarias gariepinus of the Yala Swamp in Kenya, genetic diversity and population structure of Lakes Kanyaboli and Namboyo populations of the species were studied using DNA sequences of the mitochondrial D-loop control region. Genetic diversity inferred as haplotype and nucleotide diversities and number of singletons and shared haplotypes was higher in the Lake Kanyaboli population (LKG) than the Lake Namboyo population (LNG) of C. gariepinus. Thirty-one haplotypes were inferred, of which 25 (80·6%) were private or singletons, while only six (19·4%) haplotypes were shared between LKG and LNG. Both populations were differentiated, with FST value that was significantly different from zero (P < 0·05). Two clusters were inferred both from the maximum likelihood tree and the spanning networks of phylogenetic relationships of haplotypes. Mismatch distribution for total sample was multi-modal but individually, distributions were uni-modal in LKG, but multimodal in LNG. The mean ± s.d. raggedness index for both populations was 0·085 ± 0·098 and not significantly different from zero (P > 0·05). Individual raggedness indices were 0·015 and 0·154 for LKG and LNG respectively. Fu's Fs was negative for both populations, with LKG recording -14·871, while LNG had -2·565, significantly different from zero for LKG (P < 0·05), but the value for LNG was not significant (P > 0·05). Tajima's D was negative for both populations, with LKG recording -1·734, while LNG had -1·136. Standardized square differences (SSD) were 0·001 for LKG and 0·048 for LNG and non-significant between them (P > 0·05). Values between all populations were also not significantly different (P > 0·05), mean ± s.d. SSD 0·025 ± 0·033.}, }
@article {pmid27686791, year = {2016}, author = {Li, XF and Han, C and Zhong, CR and Xu, JQ and Huang, JR}, title = {Identification of Sphaeroma terebrans via morphology and the mitochondrial cytochrome c oxidase subunit I (COI) gene.}, journal = {Zoological research}, volume = {37}, number = {5}, pages = {307-312}, pmid = {27686791}, issn = {2095-8137}, mesh = {Animals ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Genetic Variation ; Haplotypes ; Isopoda/*anatomy &amp; histology/enzymology/*genetics ; Mitochondria/*enzymology ; Phylogeny ; }, abstract = {Sphaeroma terebrans, a wood-boring isopoda, is distributed worldwide in tropical and subtropical mangroves. The taxonomy of S. terebrans is usually based on morphological characteristics, with its molecular identification still poorly understood. The number of teeth on the uropodal exopod and the length of the propodus of the seventh pereopod are considered as the major morphological characteristics in S. terebrans, which can cause difficulty in regards to accurate identification. In this study, we identified S. terebrans via molecular and morphological data. Furthermore, the validity of the mitochondrial cytochrome c oxidase subunit I (COI) gene as a DNA barcode for the identification of genus Sphaeroma, including species S. terebrans, S. retrolaeve, and S. serratum, was examined. The mitochondrial COI gene sequences of all specimens were sequenced and analysed. The interspecific Kimura 2-parameter distances were higher than intraspecific distances and no intraspecific-interspecific distance overlaps were observed. In addition, genetic distance and nucleotide diversity (π) exhibited no differences within S. terebrans. Our results revealed that the mitochondrial COI gene can serve as a valid DNA barcode for the identification of S. terebrans. Furthermore, the number of teeth on the uropodal exopod and the length of the propodus of the seventh pereopod were found to be unreliable taxonomic characteristics for S. terebrans.}, }
@article {pmid27679668, year = {2016}, author = {Thompson, OA and Hawkins, GM and Gorsich, SW and Doran-Peterson, J}, title = {Phenotypic characterization and comparative transcriptomics of evolved Saccharomyces cerevisiae strains with improved tolerance to lignocellulosic derived inhibitors.}, journal = {Biotechnology for biofuels}, volume = {9}, number = {}, pages = {200}, pmid = {27679668}, issn = {1754-6834}, abstract = {BACKGROUND: Lignocellulosic biomass continues to be investigated as a viable source for bioethanol production. However, the pretreatment process generates inhibitory compounds that impair the growth and fermentation performance of microorganisms such as Saccharomyces cerevisiae. Pinewood specifically has been shown to be challenging in obtaining industrially relevant ethanol titers. An industrial S. cerevisiae strain was subjected to directed evolution and adaptation in pretreated pine biomass and resultant strains, GHP1 and GHP4, exhibited improved growth and fermentative ability on pretreated pine in the presence of related inhibitory compounds. A comparative transcriptomic approach was applied to identify and characterize differences in phenotypic stability of evolved strains.<br><br>RESULTS: Evolved strains displayed different fermentative capabilities with pretreated pine that appear to be influenced by the addition or absence of 13 inhibitory compounds during pre-culturing. GHP4 performance was consistent independent of culturing conditions, while GHP1 performance was dependent on culturing with inhibitors. Comparative transcriptomics revealed 52 genes potentially associated with stress responses to multiple inhibitors simultaneously. Fluorescence microscopy revealed improved cellular integrity of both strains with mitochondria exhibiting resistance to the damaging effects of inhibitors in contrast to the parent.<br><br>CONCLUSIONS: Multiple potentially novel genetic targets have been discovered for understanding stress tolerance through the characterization of our evolved strains. This study specifically examines the synergistic effects of multiple inhibitors and identified targets will guide future studies in remediating effects of inhibitors and further development of robust yeast strains for multiple industrial applications.}, }
@article {pmid27666011, year = {2016}, author = {Zambetti, NA and Ping, Z and Chen, S and Kenswil, KJG and Mylona, MA and Sanders, MA and Hoogenboezem, RM and Bindels, EMJ and Adisty, MN and Van Strien, PMH and van der Leije, CS and Westers, TM and Cremers, EMP and Milanese, C and Mastroberardino, PG and van Leeuwen, JPTM and van der Eerden, BCJ and Touw, IP and Kuijpers, TW and Kanaar, R and van de Loosdrecht, AA and Vogl, T and Raaijmakers, MHGP}, title = {Mesenchymal Inflammation Drives Genotoxic Stress in Hematopoietic Stem Cells and Predicts Disease Evolution in Human Pre-leukemia.}, journal = {Cell stem cell}, volume = {19}, number = {5}, pages = {613-627}, doi = {10.1016/j.stem.2016.08.021}, pmid = {27666011}, issn = {1875-9777}, mesh = {Animals ; Bone Marrow Diseases/pathology ; Bone and Bones/abnormalities/pathology ; *DNA Damage ; DNA Repair ; *Disease Progression ; Exocrine Pancreatic Insufficiency/pathology ; Gene Deletion ; Hematopoietic Stem Cells/metabolism/*pathology ; Humans ; Inflammation/*pathology ; Integrases/metabolism ; Leukemia/metabolism/*pathology ; Lipomatosis/pathology ; Mesenchymal Stem Cells/metabolism/*pathology ; Mice ; Mitochondria/metabolism ; Oxidative Stress ; Pathogen-Associated Molecular Pattern Molecules/metabolism ; Precancerous Conditions/metabolism/*pathology ; Proteins/metabolism ; Risk Factors ; S100 Proteins/genetics/metabolism ; Shwachman-Diamond Syndrome ; Signal Transduction ; Sp7 Transcription Factor ; Stem Cell Niche ; Toll-Like Receptors/metabolism ; Transcription Factors/metabolism ; Treatment Outcome ; Tumor Suppressor Protein p53/metabolism ; }, abstract = {Mesenchymal niche cells may drive tissue failure and malignant transformation in the hematopoietic system, but the underlying molecular mechanisms and relevance to human disease remain poorly defined. Here, we show that perturbation of mesenchymal cells in a mouse model of the pre-leukemic disorder Shwachman-Diamond syndrome (SDS) induces mitochondrial dysfunction, oxidative stress, and activation of DNA damage responses in hematopoietic stem and progenitor cells. Massive parallel RNA sequencing of highly purified mesenchymal cells in the SDS mouse model and a range of human pre-leukemic syndromes identified p53-S100A8/9-TLR inflammatory signaling as a common driving mechanism of genotoxic stress. Transcriptional activation of this signaling axis in the mesenchymal niche predicted leukemic evolution and progression-free survival in myelodysplastic syndrome (MDS), the principal leukemia predisposition syndrome. Collectively, our findings identify mesenchymal niche-induced genotoxic stress in heterotypic stem and progenitor cells through inflammatory signaling as a targetable determinant of disease outcome in human pre-leukemia.}, }
@article {pmid27652040, year = {2016}, author = {Gong, M and Zhu, Q and Tan, Q}, title = {Evolutionary analyses of mitochondrial carrier family of dictyostelids.}, journal = {SpringerPlus}, volume = {5}, number = {1}, pages = {1465}, pmid = {27652040}, issn = {2193-1801}, abstract = {The transportation of solutes across the inner membrane of the mitochondria is catalyzed by a nuclear-coded family of transport proteins called mitochondrial carriers (MCs). Sequences from dictyostelid genome projects have facilitated analysis of the evolution of the dictyostelid mitochondrial carrier family (MCF). The average evolutionary distances between various regions in the MCF shows that the transmembrane region (TR) and conical pit region (CPR) are the only two conserved structural regions. A phylogenetic tree built using the concatenated orthologous TR and CPR sequences of 7 MCs showed that dictyostelids are similar to metazoans in this way. A close evolutionary relationship was observed between dictyostelids and metazoans in 4 MCs known to be related to ADP/ATP transport (MAA). This was further evidenced by the fact that dictyostelids have undergone gene expansion similar to that of metazoans during the evolution of MAA. Sequence logo analysis of CPR in MAA showed that dictyostelids have motifs similar to those of Metazoa. Combined with the conserved substrate binding site of 7 MCs in eukaryotes, it is postulated that dictyostelids are closely related to Metazoa with respect to the evolution of MAA.}, }
@article {pmid27646307, year = {2017}, author = {DiMario, RJ and Clayton, H and Mukherjee, A and Ludwig, M and Moroney, JV}, title = {Plant Carbonic Anhydrases: Structures, Locations, Evolution, and Physiological Roles.}, journal = {Molecular plant}, volume = {10}, number = {1}, pages = {30-46}, pmid = {27646307}, issn = {1752-9867}, mesh = {Carbonic Anhydrases/*genetics/*physiology ; Plants/*enzymology ; Protein Isoforms/genetics ; }, abstract = {Carbonic anhydrases (CAs) are zinc metalloenzymes that catalyze the interconversion of CO2 and HCO3[-] and are ubiquitous in nature. Higher plants contain three evolutionarily distinct CA families, αCAs, βCAs, and γCAs, where each family is represented by multiple isoforms in all species. Alternative splicing of CA transcripts appears common; consequently, the number of functional CA isoforms in a species may exceed the number of genes. CAs are expressed in numerous plant tissues and in different cellular locations. The most prevalent CAs are those in the chloroplast, cytosol, and mitochondria. This diversity in location is paralleled in the many physiological and biochemical roles that CAs play in plants. In this review, the number and types of CAs in C3, C4, and crassulacean acid metabolism (CAM) plants are considered, and the roles of the α and γCAs are briefly discussed. The remainder of the review focuses on plant βCAs and includes the identification of homologs between species using phylogenetic approaches, a consideration of the inter- and intracellular localization of the proteins, along with the evidence for alternative splice forms. Current understanding of βCA tissue-specific expression patterns and what controls them are reviewed, and the physiological roles for which βCAs have been implicated are presented.}, }
@article {pmid27631278, year = {2016}, author = {Klimov, VI and Zlatogursky, VV}, title = {Light- and Electron-microscopical Study of Belonocystis marina sp. nov. (Eukaryota: incertae sedis).}, journal = {Protist}, volume = {167}, number = {5}, pages = {479-489}, doi = {10.1016/j.protis.2016.07.003}, pmid = {27631278}, issn = {1618-0941}, mesh = {Eukaryota/classification/*ultrastructure ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Phylogeny ; Species Specificity ; }, abstract = {BelonocystisRainer, 1968 is an enigmatic protist genus, which currently lacks any supergroup affiliation. The spherical cells of this organism move on the substratum using fine non-branching pseudopodia. The cell surface is surrounded with a spiky covering. Belonocystis marina sp. nov. was studied using light- and electron microscopy. It was clearly shown that the surface structures of Belonocystis were scales, not a capsule. The new species could be distinguished by the morphology of the scales, which had a bulbous base with three "skirts" (circular latticed structures) and a spike consisting of many twisted fibrils. Each scale was associated with a short cytoplasmic outgrowth. The organic nature of these scales was confirmed by energy-dispersive X-ray microanalysis. Large multinucleated stages were discovered in the life-cycle of this organism. A survey of the cell ultrastructure revealed all the common eukaryotic organelles, including mitochondria with tubular cristae. No microtubules were detected in ultrathin sections of pseudopodia. Examination of food vacuole contents confirmed that this organism was bacterivorous. The finding of Belonocystis marina is the first record of the genus in a marine habitat. Many similarities in the scale structure and fine structure of the cell between Belonocystis and Luffisphaera were discussed.}, }
@article {pmid27630671, year = {2016}, author = {Bittner, GD and Spaeth, CS and Poon, AD and Burgess, ZS and McGill, CH}, title = {Repair of traumatic plasmalemmal damage to neurons and other eukaryotic cells.}, journal = {Neural regeneration research}, volume = {11}, number = {7}, pages = {1033-1042}, pmid = {27630671}, issn = {1673-5374}, support = {R01 NS081063/NS/NINDS NIH HHS/United States ; }, abstract = {The repair (sealing) of plasmalemmal damage, consisting of small holes to complete transections, is critical for cell survival, especially for neurons that rarely regenerate cell bodies. We first describe and evaluate different measures of cell sealing. Some measures, including morphological/ultra-structural observations, membrane potential, and input resistance, provide very ambiguous assessments of plasmalemmal sealing. In contrast, measures of ionic current flow and dye barriers can, if appropriately used, provide more accurate assessments. We describe the effects of various substances (calcium, calpains, cytoskeletal proteins, ESCRT proteins, mUNC-13, NSF, PEG) and biochemical pathways (PKA, PKC, PLC, Epac, cytosolic oxidation) on plasmalemmal sealing probability, and suggest that substances, pathways, and cellular events associated with plasmalemmal sealing have undergone a very conservative evolution. During sealing, calcium ion influx mobilizes vesicles and other membranous structures (lysosomes, mitochondria, etc.) in a continuous fashion to form a vesicular plug that gradually restricts diffusion of increasingly smaller molecules and ions over a period of seconds to minutes. Furthermore, we find no direct evidence that sealing occurs through the collapse and fusion of severed plasmalemmal leaflets, or in a single step involving the fusion of one large wound vesicle with the nearby, undamaged plasmalemma. We describe how increases in perikaryal calcium levels following axonal transection account for observations that cell body survival decreases the closer an axon is transected to the perikaryon. Finally, we speculate on relationships between plasmalemmal sealing, Wallerian degeneration, and the ability of polyethylene glycol (PEG) to seal cell membranes and rejoin severed axonal ends - an important consideration for the future treatment of trauma to peripheral nerves. A better knowledge of biochemical pathways and cytoplasmic structures involved in plasmalemmal sealing might provide insights to develop treatments for traumatic nerve injuries, stroke, muscular dystrophy, and other pathologies.}, }
@article {pmid27630103, year = {2016}, author = {Christodoulopoulos, G and Dinkel, A and Romig, T and Ebi, D and Mackenstedt, U and Loos-Frank, B}, title = {Cerebral and non-cerebral coenurosis: on the genotypic and phenotypic diversity of Taenia multiceps.}, journal = {Parasitology research}, volume = {115}, number = {12}, pages = {4543-4558}, pmid = {27630103}, issn = {1432-1955}, mesh = {Africa ; Animals ; *Biodiversity ; Brain/*parasitology ; Dog Diseases/*parasitology ; Dogs ; Europe ; Genotype ; Goat Diseases/*parasitology ; Goats ; Haplotypes ; Mitochondria/*genetics ; Phenotype ; Phylogeny ; Sheep ; Sheep Diseases/*parasitology ; Taenia/classification/genetics/*isolation &amp; purification ; Taeniasis/parasitology/*veterinary ; }, abstract = {We characterised the causative agents of cerebral and non-cerebral coenurosis in livestock by determining the mitochondrial genotypes and morphological phenotypes of 52 Taenia multiceps isolates from a wide geographical range in Europe, Africa, and western Asia. Three studies were conducted: (1) a morphological comparison of the rostellar hooks of cerebral and non-cerebral cysts of sheep and goats, (2) a morphological comparison of adult worms experimentally produced in dogs, and (3) a molecular analysis of three partial mitochondrial genes (nad1, cox1, and 12S rRNA) of the same isolates. No significant morphological or genetic differences were associated with the species of the intermediate host. Adult parasites originating from cerebral and non-cerebral cysts differed morphologically, e.g. the shape of the small hooks and the distribution of the testes in the mature proglottids. The phylogenetic analysis of the mitochondrial haplotypes produced three distinct clusters: one cluster including both cerebral isolates from Greece and non-cerebral isolates from tropical and subtropical countries, and two clusters including cerebral isolates from Greece. The majority of the non-cerebral specimens clustered together but did not form a monophyletic group. No monophyletic groups were observed based on geography, although specimens from the same region tended to cluster. The clustering indicates high intraspecific diversity. The phylogenetic analysis suggests that all variants of T. multiceps can cause cerebral coenurosis in sheep (which may be the ancestral phenotype), and some variants, predominantly from one genetic cluster, acquired the additional capacity to produce non-cerebral forms in goats and more rarely in sheep.}, }
@article {pmid27630022, year = {2017}, author = {Niedźwiecka, N and Gronczewska, J and Skorkowski, EF}, title = {NAD-preferring malic enzyme: localization, regulation and its potential role in herring (Clupea harengus) sperm cells.}, journal = {Fish physiology and biochemistry}, volume = {43}, number = {2}, pages = {351-360}, pmid = {27630022}, issn = {1573-5168}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Fish Proteins/*metabolism ; Fishes/*metabolism ; Fumarates/metabolism ; Hydrogen-Ion Concentration ; Malate Dehydrogenase/*metabolism ; Male ; Mitochondria/metabolism ; Muscle, Skeletal/metabolism ; Phosphocreatine/metabolism ; Spermatozoa/*metabolism ; }, abstract = {Herring spermatozoa exhibit a high activity of NAD-preferring malic enzyme (NAD-ME). This enzyme is involved in the generation of NADH or NADPH in the decarboxylation of malate to form pyruvate and requires some divalent cations to express its activity. In order to confirm that NAD-ME isolated from herring sperm cells is localized in mitochondria, we performed immunofluorescent analysis and assayed spectrophotometrically the malic enzyme reaction. Production of polyclonal rabbit antibodies against NAD-ME from herring spermatozoa enabled identification of mitochondrial localization of this enzyme inside herring spermatozoa. The kinetic studies revealed that NAD-ME was competitively inhibited by ATP up to tenfold. Addition of fumarate reversed ATP-dependent inhibition of NAD-ME to 55 % of its maximum activity. The pH-dependent regulation of malic enzyme activity was also examined. Malic enzyme showed maximum activity at pH near 7.0 in all studied conditions. Finally, the role of malic enzyme activity regulation in mitochondria of herring sperm cells was discussed.}, }
@article {pmid27626670, year = {2016}, author = {Dhondt, I and Petyuk, VA and Cai, H and Vandemeulebroucke, L and Vierstraete, A and Smith, RD and Depuydt, G and Braeckman, BP}, title = {FOXO/DAF-16 Activation Slows Down Turnover of the Majority of Proteins in C. elegans.}, journal = {Cell reports}, volume = {16}, number = {11}, pages = {3028-3040}, pmid = {27626670}, issn = {2211-1247}, support = {P41 GM103493/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/*metabolism ; Caenorhabditis elegans Proteins/*metabolism ; Cytoskeletal Proteins/metabolism ; Forkhead Transcription Factors/*metabolism ; Half-Life ; Intracellular Membranes/metabolism ; Isotope Labeling ; Lysosomes/metabolism ; Mitochondria/metabolism ; Muscle Proteins/metabolism ; Protein Biosynthesis ; Proteomics ; Reproducibility of Results ; Stress, Physiological ; Subcellular Fractions/metabolism ; }, abstract = {Most aging hypotheses assume the accumulation of damage, resulting in gradual physiological decline and, ultimately, death. Avoiding protein damage accumulation by enhanced turnover should slow down the aging process and extend the lifespan. However, lowering translational efficiency extends rather than shortens the lifespan in C. elegans. We studied turnover of individual proteins in the long-lived daf-2 mutant by combining SILeNCe (stable isotope labeling by nitrogen in Caenorhabditiselegans) and mass spectrometry. Intriguingly, the majority of proteins displayed prolonged half-lives in daf-2, whereas others remained unchanged, signifying that longevity is not supported by high protein turnover. This slowdown was most prominent for translation-related and mitochondrial proteins. In contrast, the high turnover of lysosomal hydrolases and very low turnover of cytoskeletal proteins remained largely unchanged. The slowdown of protein dynamics and decreased abundance of the translational machinery may point to the importance of anabolic attenuation in lifespan extension, as suggested by the hyperfunction theory.}, }
@article {pmid27620857, year = {2016}, author = {Wollman, FA}, title = {An antimicrobial origin of transit peptides accounts for early endosymbiotic events.}, journal = {Traffic (Copenhagen, Denmark)}, volume = {17}, number = {12}, pages = {1322-1328}, doi = {10.1111/tra.12446}, pmid = {27620857}, issn = {1600-0854}, mesh = {Animals ; Antimicrobial Cationic Peptides/chemistry/genetics/*metabolism ; Chloroplast Proteins/chemistry/genetics/*metabolism ; Chloroplasts/genetics/*metabolism ; Cytosol/chemistry/metabolism ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Host-Pathogen Interactions ; Mitochondria/genetics/*metabolism ; Mitochondrial Membranes ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Prokaryotic Cells/metabolism ; Protein Transport ; Symbiosis ; }, abstract = {Primary endosymbiosis, which gave rise to mitochondria or chloroplasts, required successful targeting of a number of proteins from the host cytosol to the endosymbiotic organelles. A survey of studies published in separate fields of biological research over the past 40 years argues for an antimicrobial origin of targeting peptides. It is proposed that mitochondria and chloroplast derive from microbes that developed a resistance strategy to antimicrobial peptides that consisted in their rapid internalization and proteolytic disposal by microbial peptidases.}, }
@article {pmid27614586, year = {2016}, author = {Sihali-Beloui, O and El-Aoufi, S and Maouche, B and Marco, S}, title = {Psammomys obesus, a unique model of metabolic syndrome, inflammation and autophagy in the pathologic development of hepatic steatosis.}, journal = {Comptes rendus biologies}, volume = {339}, number = {11-12}, pages = {475-486}, doi = {10.1016/j.crvi.2016.08.001}, pmid = {27614586}, issn = {1768-3238}, mesh = {Animals ; *Autophagy ; Body Weight ; Endoplasmic Reticulum Stress/drug effects ; Fatty Liver/*metabolism/*pathology ; Gerbillinae/*metabolism ; Hepatic Stellate Cells/metabolism/pathology ; Hepatocytes/pathology ; Inflammation/*metabolism/*pathology ; Intra-Abdominal Fat/metabolism/pathology ; Liver/pathology ; Male ; Metabolic Syndrome/*metabolism/*pathology ; Necrosis ; Obesity/genetics/pathology ; Organ Size ; }, abstract = {The aim of our transmission electron microscope study was to show, for the first time, the alteration of liver cells involved in the evolution of steatosis to steatohepatitis on a murine model of the diet-induced metabolic syndrome, Psammomys obesus. This pathologic evolution was induced by using the standard laboratory diet during 10 months, and analyzed with metabolic studies and the immunohistochemistry technique. Four months later, hepatocytes charged with lipid vacuoles were involved in autophagy. Furthermore, in the sinusoids, we observed Kupffer cells, neutrophils and macrophages. All those cells were associated with necrotic hepatocytes inducing hepatocellular necrosis. We also noticed a synthesis of extracellular matrix in excess, caused by proliferation and activation of hepatic stellate cells in necrotic areas. We observed as well a fragmentation of the endoplasmic reticulum, which formed isolated membranes (phagophores) surrounding mitochondria. The complex membrane-mitochondria formed like an autophagosome. Thus, a defect in autophagy favored the development and progression of steatohepatitis. In conclusion, our results suggest that P. obesus is very well adapted for experimental research, and could help improve the early therapeutic management of patients and the prevention of autophagic risks in the liver.}, }
@article {pmid27613821, year = {2016}, author = {Ross, JA and Howe, DK and Coleman-Hulbert, A and Denver, DR and Estes, S}, title = {Paternal Mitochondrial Transmission in Intra-Species Caenorhabditis briggsae Hybrids.}, journal = {Molecular biology and evolution}, volume = {33}, number = {12}, pages = {3158-3160}, pmid = {27613821}, issn = {1537-1719}, support = {F32 GM090492/GM/NIGMS NIH HHS/United States ; R01 GM087628/GM/NIGMS NIH HHS/United States ; SC2 GM113727/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis/*genetics ; DNA, Mitochondrial/genetics ; Epistasis, Genetic ; Evolution, Molecular ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Genotype ; Hybrid Cells/physiology ; Male ; Mitochondria/*genetics ; Paternal Inheritance/*genetics ; }, abstract = {To study mitochondrial-nuclear genetic interactions in the nematode Caenorhabditis briggsae, our three laboratories independently created 38 intra-species cytoplasmic-nuclear hybrid (cybrid) lines. Although the cross design combines maternal mitotypes with paternal nuclear genotypes, eight lines (21%) unexpectedly contained paternal mitotypes. All eight share in common ancestry of one of two genetically related strains. This unexpected parallel observation of paternal mitochondrial transmission, undesirable given our intent of creating cybrids, provides a serendipitous experimental model and framework to study the molecular and evolutionary basis of uniparental mitochondrial inheritance.}, }
@article {pmid27613221, year = {2017}, author = {Pitsch, G and Adamec, L and Dirren, S and Nitsche, F and Šimek, K and Sirová, D and Posch, T}, title = {The Green Tetrahymena utriculariae n. sp. (Ciliophora, Oligohymenophorea) with Its Endosymbiotic Algae (Micractinium sp.), Living in Traps of a Carnivorous Aquatic Plant.}, journal = {The Journal of eukaryotic microbiology}, volume = {64}, number = {3}, pages = {322-335}, doi = {10.1111/jeu.12369}, pmid = {27613221}, issn = {1550-7408}, mesh = {Animals ; Base Sequence ; Chlorophyta/*parasitology ; Ciliophora/*classification/metabolism/physiology ; DNA, Protozoan ; Ecology ; Ecosystem ; Life Cycle Stages ; Mitochondria/genetics ; Oligohymenophorea/*classification ; Oxygen/metabolism ; *Phylogeny ; Plants/*parasitology ; RNA, Ribosomal, 18S/genetics ; Symbiosis/*physiology ; Tetrahymena/*classification/cytology/isolation &amp; purification/metabolism ; Tetrahymena thermophila/classification/genetics ; Tracheophyta/parasitology ; }, abstract = {The genus Tetrahymena (Ciliophora, Oligohymenophorea) probably represents the best studied ciliate genus. At present, more than forty species have been described. All are colorless, i.e. they do not harbor symbiotic algae, and as aerobes they need at least microaerobic habitats. Here, we present the morphological and molecular description of the first green representative, Tetrahymena utriculariae n. sp., living in symbiosis with endosymbiotic algae identified as Micractinium sp. (Chlorophyta). The full life cycle of the ciliate species is documented, including trophonts and theronts, conjugating cells, resting cysts and dividers. This species has been discovered in an exotic habitat, namely in traps of the carnivorous aquatic plant Utricularia reflexa (originating from Okavango Delta, Botswana). Green ciliates live as commensals of the plant in this anoxic habitat. Ciliates are bacterivorous, however, symbiosis with algae is needed to satisfy cell metabolism but also to gain oxygen from symbionts. When ciliates are cultivated outside their natural habitat under aerobic conditions and fed with saturating bacterial food, they gradually become aposymbiotic. Based on phylogenetic analyses of 18S rRNA and mitochondrial cox1 genes T. utriculariae forms a sister group to Tetrahymena thermophila.}, }
@article {pmid27612998, year = {2017}, author = {Melis, N and Rubera, I and Cougnon, M and Giraud, S and Mograbi, B and Belaid, A and Pisani, DF and Huber, SM and Lacas-Gervais, S and Fragaki, K and Blondeau, N and Vigne, P and Frelin, C and Hauet, T and Duranton, C and Tauc, M}, title = {Targeting eIF5A Hypusination Prevents Anoxic Cell Death through Mitochondrial Silencing and Improves Kidney Transplant Outcome.}, journal = {Journal of the American Society of Nephrology : JASN}, volume = {28}, number = {3}, pages = {811-822}, pmid = {27612998}, issn = {1533-3450}, mesh = {Animals ; Cell Death/*drug effects ; Cell Hypoxia/drug effects ; Cells, Cultured ; Female ; *Kidney Transplantation ; Lysine/*analogs &amp; derivatives/pharmacology ; Male ; Mice ; Mice, Inbred C57BL ; Mitochondria/*drug effects/*physiology ; Mixed Function Oxygenases ; Peptide Initiation Factors/*drug effects ; RNA-Binding Proteins/*drug effects ; Rats ; Rats, Wistar ; Swine ; Treatment Outcome ; Eukaryotic Translation Initiation Factor 5A ; }, abstract = {The eukaryotic initiation factor 5A (eIF5A), which is highly conserved throughout evolution, has the unique characteristic of post-translational activation through hypusination. This modification is catalyzed by two enzymatic steps involving deoxyhypusine synthase (DHPS) and deoxyhypusine hydroxylase (DOHH). Notably, eIF5A may be involved in regulating the lifespan of Drosophila during long-term hypoxia. Therefore, we investigated the possibility of a link between eIF5A hypusination and cellular resistance to hypoxia/anoxia. Pharmacologic targeting of DHPS by N1-guanyl-1,7-diaminoheptane (GC7) or RNA interference-mediated inhibition of DHPS or DOHH induced tolerance to anoxia in immortalized mouse renal proximal cells. Furthermore, GC7 treatment of cells reversibly induced a metabolic shift toward glycolysis as well as mitochondrial remodeling and led to downregulated expression and activity of respiratory chain complexes, features characteristic of mitochondrial silencing. GC7 treatment also attenuated anoxia-induced generation of reactive oxygen species in these cells and in normoxic conditions, decreased the mitochondrial oxygen consumption rate of cultured cells and mice. In rats, intraperitoneal injection of GC7 substantially reduced renal levels of hypusinated eIF5A and protected against ischemia-reperfusion-induced renal injury. Finally, in the preclinical pig kidney transplant model, intravenous injection of GC7 before kidney removal significantly improved graft function recovery and late graft function and reduced interstitial fibrosis after transplant. This unconventional signaling pathway offers an innovative therapeutic target for treating hypoxic-ischemic human diseases and organ transplantation.}, }
@article {pmid27612012, year = {2017}, author = {Tak, H and Eun, JW and Kim, J and Park, SJ and Kim, C and Ji, E and Lee, H and Kang, H and Cho, DH and Lee, K and Kim, W and Nam, SW and Lee, EK}, title = {T-cell-restricted intracellular antigen 1 facilitates mitochondrial fragmentation by enhancing the expression of mitochondrial fission factor.}, journal = {Cell death and differentiation}, volume = {24}, number = {1}, pages = {49-58}, pmid = {27612012}, issn = {1476-5403}, mesh = {3' Untranslated Regions ; Adenosine Triphosphate/biosynthesis ; Animals ; Bacterial Proteins/genetics/metabolism ; Cell Line ; Dynamins ; GTP Phosphohydrolases/genetics/metabolism ; Humans ; Luminescent Proteins/genetics/metabolism ; Membrane Proteins/antagonists &amp; inhibitors/genetics/*metabolism ; Mice ; MicroRNAs/metabolism ; Microscopy, Fluorescence ; Microtubule-Associated Proteins/genetics/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/antagonists &amp; inhibitors/genetics/*metabolism ; Oxygen Consumption ; Plasmids/genetics/metabolism ; RNA Interference ; RNA, Messenger/metabolism ; RNA, Small Interfering/metabolism ; T-Cell Intracellular Antigen-1/antagonists &amp; inhibitors/genetics/*metabolism ; }, abstract = {Mitochondrial morphology is dynamically regulated by the formation of small fragmented units or interconnected mitochondrial networks, and this dynamic morphological change is a pivotal process in normal mitochondrial function. In the present study, we identified a novel regulator responsible for the regulation of mitochondrial dynamics. An assay using CHANG liver cells stably expressing mitochondrial-targeted yellow fluorescent protein (mtYFP) and a group of siRNAs revealed that T-cell intracellular antigen protein-1 (TIA-1) affects mitochondrial morphology by enhancing mitochondrial fission. The function of TIA-1 in mitochondrial dynamics was investigated through various biological approaches and expression analysis in human specimen. Downregulation of TIA-1-enhanced mitochondrial elongation, whereas ectopic expression of TIA-1 resulted in mitochondria fragmentation. In addition, TIA-1 increased mitochondrial activity, including the rate of ATP synthesis and oxygen consumption. Further, we identified mitochondrial fission factor (MFF) as a direct target of TIA-1, and showed that TIA-1 promotes mitochondrial fragmentation by enhancing MFF translation. TIA-1 null cells had a decreased level of MFF and less mitochondrial Drp1, a critical factor for mitochondrial fragmentation, thereby enhancing mitochondrial elongation. Taken together, our results indicate that TIA-1 is a novel factor that facilitates mitochondrial dynamics by enhancing MFF expression and contributes to mitochondrial dysfunction.}, }
@article {pmid27609835, year = {2016}, author = {Carrie, C and Weißenberger, S and Soll, J}, title = {Plant mitochondria contain the protein translocase subunits TatB and TatC.}, journal = {Journal of cell science}, volume = {129}, number = {20}, pages = {3935-3947}, doi = {10.1242/jcs.190975}, pmid = {27609835}, issn = {1477-9137}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Escherichia coli Proteins/chemistry ; Genes, Essential ; Genes, Plant ; Genome, Mitochondrial ; Green Fluorescent Proteins/metabolism ; Hydrogen-Ion Concentration ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/chemistry/genetics/metabolism ; Molecular Weight ; Peptidyl Transferases/chemistry/genetics/*metabolism ; Phylogeny ; Protein Subunits/chemistry/genetics/*metabolism ; Sequence Alignment ; }, abstract = {Twin-arginine translocation (Tat) pathways have been well-characterized in bacteria and chloroplasts. Genes encoding a TatC protein are found in almost all plant mitochondrial genomes but to date these have not been extensively investigated. For the first time it could be demonstrated that this mitochondrial-encoded TatC is a functional gene that is translated into a protein in the model plant Arabidopsis thaliana A TatB--like subunit localized to the inner membrane was also identified that is nuclear-encoded and is essential for plant growth and development, indicating that plants potentially require a Tat pathway for mitochondrial biogenesis.}, }
@article {pmid27607916, year = {2017}, author = {Sarower, MG and Shahriar, SIM and Nakamura, H and Rouf, MA and Okada, S}, title = {Taxonomic confirmation of mud crab species (genus Scylla) in Bangladesh by nuclear and mitochondrial DNA markers.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {6}, pages = {935-940}, doi = {10.1080/24701394.2016.1214726}, pmid = {27607916}, issn = {2470-1408}, mesh = {Animals ; Bangladesh ; Brachyura/classification/*genetics ; Cell Nucleus/genetics ; Genetic Markers ; Mitochondria/genetics ; *Phylogeny ; Polymerase Chain Reaction ; }, abstract = {Taxonomy of mud crabs genus Scylla has been misidentified for several years due to their high morphological plasticity. Several reports concerning mud crab have been published with misleading identification in Bangladesh. In this study, partial fragments of nuclear and mitochondrial DNA of Scylla species obtained from four locations along the Bangladesh coast were used to resolve taxonomical ambiguity of mud crab species. A single PCR product from the nuclear first internal transcribed spacer (ITS-1) marker and phylogenetic trees constructed based on 16S rDNA sequences indicated that all Scylla species obtained in this study were S. olivacea. Both molecular data and morphological characters revealed that S. olivacea is the only major species in Bangladesh coastal waters. Further, the 16S rDNA haplotypes significantly differed with known S. serrata by 33%. From this study it is clear that 'S. serrata' commonly reported from Bangladesh should be S. olivacea.}, }
@article {pmid27604148, year = {2016}, author = {Satoh, TP and Miya, M and Mabuchi, K and Nishida, M}, title = {Structure and variation of the mitochondrial genome of fishes.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {719}, pmid = {27604148}, issn = {1471-2164}, mesh = {Animals ; Databases, Genetic ; Evolution, Molecular ; Fish Proteins/chemistry/genetics ; Fishes/*classification/*genetics ; Gene Order ; Gene Rearrangement ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Mitochondrial Proteins/chemistry/genetics ; Models, Molecular ; Molecular Conformation ; Phylogeny ; RNA/chemistry/genetics ; RNA, Mitochondrial ; RNA, Ribosomal/chemistry/genetics ; RNA, Ribosomal, 16S/chemistry/genetics ; RNA, Transfer/chemistry/genetics ; }, abstract = {BACKGROUND: The mitochondrial (mt) genome has been used as an effective tool for phylogenetic and population genetic analyses in vertebrates. However, the structure and variability of the vertebrate mt genome are not well understood. A potential strategy for improving our understanding is to conduct a comprehensive comparative study of large mt genome data. The aim of this study was to characterize the structure and variability of the fish mt genome through comparative analysis of large datasets.<br><br>RESULTS: An analysis of the secondary structure of proteins for 250 fish species (248 ray-finned and 2 cartilaginous fishes) illustrated that cytochrome c oxidase subunits (COI, COII, and COIII) and a cytochrome bc1 complex subunit (Cyt b) had substantial amino acid conservation. Among the four proteins, COI was the most conserved, as more than half of all amino acid sites were invariable among the 250 species. Our models identified 43 and 58 stems within 12S rRNA and 16S rRNA, respectively, with larger numbers than proposed previously for vertebrates. The models also identified 149 and 319 invariable sites in 12S rRNA and 16S rRNA, respectively, in all fishes. In particular, the present result verified that a region corresponding to the peptidyl transferase center in prokaryotic 23S rRNA, which is homologous to mt 16S rRNA, is also conserved in fish mt 16S rRNA. Concerning the gene order, we found 35 variations (in 32 families) that deviated from the common gene order in vertebrates. These gene rearrangements were mostly observed in the area spanning the ND5 gene to the control region as well as two tRNA gene cluster regions (IQM and WANCY regions). Although many of such gene rearrangements were unique to a specific taxon, some were shared polyphyletically between distantly related species.<br><br>CONCLUSIONS: Through a large-scale comparative analysis of 250 fish species mt genomes, we elucidated various structural aspects of the fish mt genome and the encoded genes. The present results will be important for understanding functions of the mt genome and developing programs for nucleotide sequence analysis. This study demonstrated the significance of extensive comparisons for understanding the structure of the mt genome.}, }
@article {pmid27593700, year = {2016}, author = {Qin, Y and Man, B and Kosakyan, A and Lara, E and Gu, Y and Wang, H and Mitchell, EA}, title = {Nebela jiuhuensis nov. sp. (Amoebozoa; Arcellinida; Hyalospheniidae): A New Member of the Nebela saccifera - equicalceus - ansata Group Described from Sphagnum Peatlands in South-Central China.}, journal = {The Journal of eukaryotic microbiology}, volume = {63}, number = {5}, pages = {558-566}, doi = {10.1111/jeu.12300}, pmid = {27593700}, issn = {1550-7408}, mesh = {Amoeba/classification ; Amoebozoa/*classification/cytology/genetics/*isolation &amp; purification ; Animals ; Biodiversity ; China ; Classification ; DNA, Protozoan ; Ecology ; Ecosystem ; Electron Transport Complex IV/genetics ; Environmental Pollution ; Lobosea/*classification/cytology/genetics/*isolation &amp; purification ; Microscopy, Electron, Scanning ; Mitochondria/enzymology ; *Phylogeny ; Phylogeography ; Soil/parasitology ; Species Specificity ; Sphagnopsida/*parasitology ; }, abstract = {Hyalospheniids are among the most common and conspicuous testate amoebae in high-latitude peatlands and forest humus. These testate amoebae were widely studied as bioindicators and are increasingly used as models in microbial biogeography. However, data on their diversity and ecology are still very unevenly distributed geographically: notably, data are lacking for low-latitude peatlands. We describe here a new species, Nebela jiuhuensis, from peatlands near the Middle Yangtze River reach of south-central China with characteristic morphology. The test (shell) has hollow horn-like lateral extensions also found in N. saccifera, N. equicalceus (=N. hippocrepis), and N. ansata, three large species restricted mostly to Sphagnum peatlands of Eastern North America. Mitochondrial cytochrome oxidase (COI) data confirm that N. jiuhuensis is closely related to the morphologically very similar North American species N. saccifera and more distantly to N. ansata within the N. penardiana group. These species are all found in wet mosses growing in poor fens. Earlier reports of morphologically similar specimens found in South Korea peatlands suggest that N. jiuhuensis may be distributed in comparable peatlands in Eastern Asia (China and Korea). The discovery of such a conspicuous new species in Chinese peatlands suggests that many new testate amoebae species are yet to be discovered, including potential regional endemics. Furthermore, human activities (e.g., drainage, agriculture, and pollution) have reduced the known habitat of N. jiuhuensis, which can thus be considered as locally endangered. We, therefore, suggest that this very conspicuous micro-organism with a probably limited geographical distribution and specific habitat requirement should be considered as a flagship species for microbial biogeography as well as local environmental conservation and management.}, }
@article {pmid27591564, year = {2016}, author = {Dumas, E and Atyame, CM and Malcolm, CA and Le Goff, G and Unal, S and Makoundou, P and Pasteur, N and Weill, M and Duron, O}, title = {Molecular data reveal a cryptic species within the Culex pipiens mosquito complex.}, journal = {Insect molecular biology}, volume = {25}, number = {6}, pages = {800-809}, doi = {10.1111/imb.12264}, pmid = {27591564}, issn = {1365-2583}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/genetics ; Culex/*classification/*genetics/growth &amp; development/microbiology ; DNA/genetics ; DNA, Mitochondrial/genetics ; Haplotypes ; Larva/classification/genetics ; Multilocus Sequence Typing ; Phylogeny ; Pupa/classification/genetics ; Symbiosis ; Wolbachia/physiology ; }, abstract = {The Culex pipiens mosquito complex is a group of evolutionarily closely related species including C. pipiens and Culex quinquefasciatus, both infected by the cytoplasmically inherited Wolbachia symbiont. A Wolbachia-uninfected population of C. pipiens was however described in South Africa and was recently proposed to represent a cryptic species. In this study, we reconsidered the existence of this species by undertaking an extensive screening for the presence of Wolbachia-uninfected C. pipiens specimens and by characterizing their genetic relatedness with known members of the complex. We first report on the presence of Wolbachia-uninfected specimens in several breeding sites. We next confirm that these uninfected specimens unambiguously belong to the C. pipiens complex. Remarkably, all uninfected specimens harbour mitochondrial haplotypes that are either novel or identical to those previously found in South Africa. In all cases, these mitochondrial haplotypes are closely related, but different, to those found in other C. pipiens complex members known to be infected by Wolbachia. Altogether, these results corroborate the presence of a widespread cryptic species within the C. pipiens species complex. The potential role of this cryptic C. pipiens species in the transmission of pathogens remains however to be determined. The designation 'Culex juppi nov. sp.' is proposed for this mosquito species.}, }
@article {pmid27591172, year = {2016}, author = {Eyer, PA and Leniaud, L and Tinaut, A and Aron, S}, title = {Combined hybridization and mitochondrial capture shape complex phylogeographic patterns in hybridogenetic Cataglyphis desert ants.}, journal = {Molecular phylogenetics and evolution}, volume = {105}, number = {}, pages = {251-262}, doi = {10.1016/j.ympev.2016.08.020}, pmid = {27591172}, issn = {1095-9513}, mesh = {Animals ; Ants/*genetics ; DNA, Mitochondrial ; Female ; Haplotypes ; *Hybridization, Genetic ; Male ; Mitochondria/genetics ; Parthenogenesis/genetics ; Phylogeny ; Phylogeography ; }, abstract = {Some species of Cataglyphis desert ants have evolved a hybridogenetic mode of reproduction at the social scale. In hybridogenetic populations, two distinct genetic lineages coexist. Non-reproductive offspring (workers) are hybrids of the two lineages, whereas sexual offspring (males and new queens) are produced by parthenogenesis and belong to the mother queen lineage. How this unusual reproductive system affects phylogeographic patterns and speciation processes remains completely unknown to date. Using one mitochondrial and four nuclear genes, we examined the phylogenetic relationships between three species of Cataglyphis (C. hispanica, C. humeya and C. velox) where complex DNA inheritance through social hybridogenesis may challenge phylogenetic inference. Our results bring two important insights. First, our data confirm a hybridogenetic mode of reproduction across the whole distribution range of the species C. hispanica. In contrast, they do not provide support for hybridogenesis in the populations sampled of C. humeya and C. velox. This suggests that these populations are not hybridogenetic, or that hybridogenesis is too recent to result in reciprocally monophyletic lineages on nuclear genes. Second, due to mitochondrial introgression between lineages (Darras and Aron, 2015), the faster-evolving COI marker is not lineage specific, hence, unsuitable to further investigate the segregation of lineages in the species studied. Different mitochondrial haplotypes occur in each locality sampled, resulting in strongly structured populations. This micro-allopatric structure leads to over-splitting species delimitation on mitochondrial gene, as every locality could potentially be considered a putative species; haploweb analyses of nuclear markers, however, yield species delimitations that are consistent with morphology. Overall, this study highlights how social hybridogenesis varies across species and shapes complex phylogeographic patterns.}, }
@article {pmid27588285, year = {2016}, author = {Cole, LW}, title = {The Evolution of Per-cell Organelle Number.}, journal = {Frontiers in cell and developmental biology}, volume = {4}, number = {}, pages = {85}, pmid = {27588285}, issn = {2296-634X}, abstract = {Organelles with their own distinct genomes, such as plastids and mitochondria, are found in most eukaryotic cells. As these organelles and their host cells have evolved, the partitioning of metabolic processes and the encoding of interacting gene products have created an obligate codependence. This relationship has played a role in shaping the number of organelles in cells through evolution. Factors such as stochastic evolutionary forces acting on genes involved in organelle biogenesis, organelle-nuclear gene interactions, and physical limitations may, to varying degrees, dictate the selective constraint that per-cell organelle number is under. In particular, coordination between nuclear and organellar gene expression may be important in maintaining gene product stoichiometry, which may have a significant role in constraining the evolution of this trait.}, }
@article {pmid27586818, year = {2016}, author = {De Bortoli, S and Teardo, E and Szabò, I and Morosinotto, T and Alboresi, A}, title = {Evolutionary insight into the ionotropic glutamate receptor superfamily of photosynthetic organisms.}, journal = {Biophysical chemistry}, volume = {218}, number = {}, pages = {14-26}, doi = {10.1016/j.bpc.2016.07.004}, pmid = {27586818}, issn = {1873-4200}, mesh = {Amino Acid Sequence ; Animals ; Chlorophyta/chemistry ; Chloroplasts/chemistry ; Embryophyta/chemistry ; *Evolution, Molecular ; Mitochondria/chemistry ; Photosynthesis/genetics ; *Phylogeny ; Receptors, Ionotropic Glutamate/*genetics ; Sequence Alignment ; }, abstract = {Photosynthetic eukaryotes have a complex evolutionary history shaped by multiple endosymbiosis events that required a tight coordination between the organelles and the rest of the cell. Plant ionotropic glutamate receptors (iGLRs) form a large superfamily of proteins with a predicted or proven non-selective cation channel activity regulated by a broad range of amino acids. They are involved in different physiological processes such as C/N sensing, resistance against fungal infection, root and pollen tube growth and response to wounding and pathogens. Most of the present knowledge is limited to iGLRs located in plasma membranes. However, recent studies localized different iGLR isoforms to mitochondria and/or chloroplasts, suggesting the possibility that they play a specific role in bioenergetic processes. In this work, we performed a comparative analysis of GLR sequences from bacteria and various photosynthetic eukaryotes. In particular, novel types of selectivity filters of bacteria are reported adding new examples of the great diversity of the GLR superfamily. The highest variability in GLR sequences was found among the algal sequences (cryptophytes, diatoms, brown and green algae). GLRs of land plants are not closely related to the GLRs of green algae analyzed in this work. The GLR family underwent a great expansion in vascular plants. Among plant GLRs, Clade III includes sequences from Physcomitrella patens, Marchantia polymorpha and gymnosperms and can be considered the most ancient, while other clades likely emerged later. In silico analysis allowed the identification of sequences with a putative target to organelles. Sequences with a predicted localization to mitochondria and chloroplasts are randomly distributed among different type of GLRs, suggesting that no compartment-related specific function has been maintained across the species.}, }
@article {pmid27572896, year = {2016}, author = {Delhaye, J and Salamin, N and Roulin, A and Criscuolo, F and Bize, P and Christe, P}, title = {Interspecific correlation between red blood cell mitochondrial ROS production, cardiolipin content and longevity in birds.}, journal = {Age (Dordrecht, Netherlands)}, volume = {38}, number = {5-6}, pages = {433-443}, pmid = {27572896}, issn = {1574-4647}, mesh = {Aging/metabolism ; Animals ; Birds/blood/*metabolism ; Body Weight ; Cardiolipins/analysis/*metabolism ; Erythrocytes/chemistry/*metabolism ; *Longevity ; Mitochondria/*metabolism ; Mitochondrial Membranes/chemistry ; Oxidative Stress ; Oxygen Consumption ; Phylogeny ; Reactive Oxygen Species/analysis/*chemistry ; }, abstract = {Mitochondrial respiration releases reactive oxygen species (ROS) as by-products that can damage the soma and may in turn accelerate ageing. Hence, according to "the oxidative stress theory of ageing", longer-lived organisms may have evolved mechanisms that improve mitochondrial function, reduce ROS production and/or increase cell resistance to oxidative damage. Cardiolipin, an important mitochondrial inner-membrane phospholipid, has these properties by binding and stabilizing mitochondrial inner-membrane proteins. Here, we investigated whether ROS production, cardiolipin content and cell membrane resistance to oxidative attack in freshly collected red blood cells (RBCs) are associated with longevity (range 5-35 years) in 21 bird species belonging to seven Orders. After controlling for phylogeny, body size and oxygen consumption, variation in maximum longevity was significantly explained by mitochondrial ROS production and cardiolipin content, but not by membrane resistance to oxidative attack. RBCs of longer-lived species produced less ROS and contained more cardiolipin than RBCs of shorter-lived species did. These results support the oxidative stress theory of ageing and shed light on mitochondrial cardiolipin as an important factor linking ROS production to longevity.}, }
@article {pmid27567714, year = {2016}, author = {Hernández-Martínez, F and Briones-Roblero, CI and Nelson, DR and Rivera-Orduña, FN and Zúñiga, G}, title = {Cytochrome P450 complement (CYPome) of Candida oregonensis, a gut-associated yeast of bark beetle, Dendroctonus rhizophagus.}, journal = {Fungal biology}, volume = {120}, number = {9}, pages = {1077-1089}, doi = {10.1016/j.funbio.2016.06.005}, pmid = {27567714}, issn = {1878-6146}, mesh = {Animals ; Candida/*classification/*enzymology/genetics/isolation &amp; purification ; Cell Membrane/enzymology ; Cytochrome P-450 Enzyme System/*genetics ; Gastrointestinal Tract/microbiology ; Intracellular Membranes/enzymology ; *Phylogeny ; Sequence Homology ; Weevils/*microbiology ; }, abstract = {Bark beetles (Curculionidae: Scolytinae) and associated microorganisms must overcome a complex tree's defence system, which includes toxic monoterpenes, to successfully complete their life cycle. A number of studies have suggested these microorganisms could have ecological roles related with the nutrition, detoxification, and semiochemical production. In particular, in filamentous fungi symbionts, cytochrome P450 (CYP) have been involved with terpenoid detoxification and biotransformation processes. Candida oregonensis has been isolated from the gut, ovaries, and frass of different bark beetle species, and it is a dominant species in the Dendroctonus rhizophagus gut. In this study, we identify, characterise, and infer the phylogenetic relationships of C. oregonensis CYP genes. The results indicate that the cytochrome P450 complement (CYPome) is composed of nine genes (CYP51F1, CYP61A1, CYP56D1, CYP52A59, CYP52A60, CYP52A61, CYP52A62, CYP5217A8, and CYP5217B1), which might participate in primary metabolic reactions such as sterol biosynthesis, biodegradation of xenobiotic, and resistance to environmental stress. The prediction of the cellular location suggests that these CYPs to be anchored to the plasma membrane, membranes of the endoplasmic reticulum, mitochondria, and peroxisomes. These findings lay the foundation for future studies about the functional role of P450s, not only for yeasts, but also for the insects with which they interact.}, }
@article {pmid27565702, year = {2016}, author = {Zhang, XC and Li, W and Zhao, J and Chen, HG and Zhu, XP}, title = {Novel duplication pattern of the mitochondrial control region in Cantor's Giant softshell turtle Pelochelys cantorii.}, journal = {Gene}, volume = {593}, number = {1}, pages = {242-248}, doi = {10.1016/j.gene.2016.08.036}, pmid = {27565702}, issn = {1879-0038}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genome, Mitochondrial/*physiology ; Repetitive Sequences, Nucleic Acid/*physiology ; Turtles/*genetics ; }, abstract = {Cantor's Giant Softshell Turtle, Pelochelys cantorii has become one of the most critically endangered species in the world. When comparative analyses of the P. cantorii complete mitochondrial genome sequences were conducted, we discovered a duplication of a segment of the control region in the mitochondrial genome of P. cantorii. The duplication is characterized by two copies of conserved sequence box 2 (CSB2) and CSB3 in a single control region. In contrast to previous reports of duplications involving the control regions of other animals, this particular pattern of duplications appears to be unique to P. cantorii. Copies of the CSB2 and CSB3 show many of the conserved sequence features typically found in mitochondrial control regions, and rare differences were found between the paralogous copies. Using the primer design principle of simple sequence repeats (SSR) and the reference sequence of the duplicated CSBs, specific primers were designed to amplify the duplicated CSBs. These primers were validated among different individuals and populations of P. cantorii. This unique duplication structure suggests the two copies of the CSB2 and CSB3 may have arisen through occasional tandem duplication and subsequent concerted evolution.}, }
@article {pmid27563053, year = {2016}, author = {Havird, JC and Sloan, DB}, title = {The Roles of Mutation, Selection, and Expression in Determining Relative Rates of Evolution in Mitochondrial versus Nuclear Genomes.}, journal = {Molecular biology and evolution}, volume = {33}, number = {12}, pages = {3042-3053}, pmid = {27563053}, issn = {1537-1719}, support = {F32 GM116361/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Cell Nucleus/*genetics/metabolism ; DNA, Mitochondrial/genetics ; Eukaryota/*genetics ; Gene Expression Regulation ; Genes, Mitochondrial ; Genome, Mitochondrial ; Mitochondria/*genetics/metabolism ; *Mutation Rate ; Oxidative Phosphorylation ; Phylogeny ; }, abstract = {Eukaryotes rely on proteins encoded by the nuclear and mitochondrial (mt) genomes, which interact within multisubunit complexes such as oxidative-phosphorylation enzymes. Although selection is thought to be less efficient on the asexual mt genome, in bilaterian animals the ratio of nonsynonymous to synonymous substitutions (ω) is lower in mt- compared with nuclear-encoded OXPHOS subunits, suggesting stronger effects of purifying selection in the mt genome. Because high levels of gene expression constrain protein sequence evolution, one proposed resolution to this paradox is that mt genes are expressed more highly than nuclear genes. To test this hypothesis, we investigated expression and sequence evolution of mt and nuclear genes from 84 diverse eukaryotes that vary in mt gene content and mutation rate. We found that the relationship between mt and nuclear ω values varied dramatically across eukaryotes. In contrast, transcript abundance is consistently higher for mt genes than nuclear genes, regardless of which genes happen to be in the mt genome. Consequently, expression levels cannot be responsible for the differences in ω Rather, 84% of the variance in the ratio of ω values between mt and nuclear genes could be explained by differences in mutation rate between the two genomes. We relate these findings to the hypothesis that high rates of mt mutation select for compensatory changes in the nuclear genome. We also propose an explanation for why mt transcripts consistently outnumber their nuclear counterparts, with implications for mitonuclear protein imbalance and aging.}, }
@article {pmid27547358, year = {2016}, author = {Hill, GE}, title = {Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap.}, journal = {Ecology and evolution}, volume = {6}, number = {16}, pages = {5831-5842}, pmid = {27547358}, issn = {2045-7758}, abstract = {Mitochondrial genes are widely used in taxonomy and systematics because high mutation rates lead to rapid sequence divergence and because such changes have long been assumed to be neutral with respect to function. In particular, the nucleotide sequence of the mitochondrial gene cytochrome c oxidase subunit 1 has been established as a highly effective DNA barcode for diagnosing the species boundaries of animals. Rarely considered in discussions of mitochondrial evolution in the context of systematics, speciation, or DNA barcodes, however, is the genomic architecture of the eukaryotes: Mitochondrial and nuclear genes must function in tight coordination to produce the complexes of the electron transport chain and enable cellular respiration. Coadaptation of these interacting gene products is essential for organism function. I extend the hypothesis that mitonuclear interactions are integral to the process of speciation. To maintain mitonuclear coadaptation, nuclear genes, which code for proteins in mitochondria that cofunction with the products of mitochondrial genes, must coevolve with rapidly changing mitochondrial genes. Mitonuclear coevolution in isolated populations leads to speciation because population-specific mitonuclear coadaptations create between-population mitonuclear incompatibilities and hence barriers to gene flow between populations. In addition, selection for adaptive divergence of products of mitochondrial genes, particularly in response to climate or altitude, can lead to rapid fixation of novel mitochondrial genotypes between populations and consequently to disruption in gene flow between populations as the initiating step in animal speciation. By this model, the defining characteristic of a metazoan species is a coadapted mitonuclear genotype that is incompatible with the coadapted mitochondrial and nuclear genotype of any other population.}, }
@article {pmid27547212, year = {2016}, author = {Bashir, K and Rasheed, S and Kobayashi, T and Seki, M and Nishizawa, NK}, title = {Regulating Subcellular Metal Homeostasis: The Key to Crop Improvement.}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {1192}, pmid = {27547212}, issn = {1664-462X}, abstract = {Iron (Fe), zinc (Zn), manganese (Mn), and copper (Cu) are essential micronutrient mineral elements for living organisms, as they regulate essential cellular processes, such as chlorophyll synthesis and photosynthesis (Fe, Cu, and Mn), respiration (Fe and Cu), and transcription (Zn). The storage and distribution of these minerals in various cellular organelles is strictly regulated to ensure optimal metabolic rates. Alteration of the balance in uptake, distribution, and/or storage of these minerals severely impairs cellular metabolism and significantly affects plant growth and development. Thus, any change in the metal profile of a cellular compartment significantly affects metabolism. Different subcellular compartments are suggested to be linked through complex retrograde signaling networks to regulate cellular metal homeostasis. Various genes regulating cellular and subcellular metal distribution have been identified and characterized. Understanding the role of these transporters is extremely important to elaborate the signaling between various subcellular compartments. Moreover, modulation of the proteins involved in cellular metal homeostasis may help in the regulation of metabolism, adaptability to a diverse range of environmental conditions, and biofortification. Here, we review progress in the understanding of different subcellular metal transport components in plants and discuss the prospects of regulating cellular metabolism and strategies to develop biofortified crop plants.}, }
@article {pmid27544295, year = {2016}, author = {Xue, L and Wang, M and Li, H and Wang, H and Jiang, F and Hou, L and Geng, J and Lin, Z and Peng, Y and Zhou, H and Yu, H and Jiang, P and Mo, JQ and Guan, MX}, title = {Mitochondrial tRNA mutations in 2070 Chinese Han subjects with hypertension.}, journal = {Mitochondrion}, volume = {30}, number = {}, pages = {208-221}, doi = {10.1016/j.mito.2016.08.008}, pmid = {27544295}, issn = {1872-8278}, mesh = {Adult ; Aged ; Aged, 80 and over ; Asian People ; Case-Control Studies ; China ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Chain Complex Proteins/analysis ; Female ; Gene Expression Profiling ; Gene Frequency ; Humans ; Hypertension/*pathology ; Male ; Middle Aged ; *Mutation ; RNA, Transfer/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Mitochondria have the profound impact on vascular function in both health and disease. However, mitochondrial genetic determinants for the development of hypertension remain poorly explored.<br><br>METHODS AND RESULTS: The Sanger sequence analysis of 22 mitochondrial tRNA genes were performed in a cohort of 2070 Han Chinese hypertensive and 512 control subjects. This analysis identified 165 variants among 22 tRNA genes. These variants were evaluated for the pathogenicity using the following criteria: (1) present in <1% of the controls; (2) evolutional conservation; (3) potential structural and functional alterations. We identified 47 (5 known and 42 novel/putative) hypertension-associated tRNA variants in 80 hypertensive subjects. These variants could have potential structural alterations and functional significance of tRNAs. By using lymphoblastoid cell lines derived from 6 probands carrying one of 6 represented variants (tRNA(Ala) 5655T>C, tRNA(Gly) 10003T>C, tRNA(Leu(UUR)) 3253T>C, tRNA(Asp) 7551A>G, tRNA(Glu) 14692A>G, tRNA(Thr) 15909A>G) and 6 control subjects lacking these variants, we showed marked reductions in the steady-state level of corresponding 5 tRNAs, but not tRNA(Thr), in mutant cell lines, compared with control cells lines. The various decreases in the activities of complexes I, III and IV were observed in mutant cells carrying one of five tRNA variants, except tRNA(Thr) 15909A>G variant. The deficient respirations were responsible for the decrease in the mitochondrial ATP production and increasing production of reactive oxygen species in mutant cell lines carrying one of five tRNA variants.<br><br>CONCLUSION: Mitochondrial tRNA variants are the important causes of hypertension, accounting for 3.9% cases of 2070 Han Chinese hypertensive subjects. Our findings may provide new insights into the pathophysiology of hypertension that were manifested by mitochondrial dysfunction.}, }
@article {pmid27543138, year = {2016}, author = {Borsa, P and Shen, KN and Arlyza, IS and Hoareau, TB}, title = {Multiple cryptic species in the blue-spotted maskray (Myliobatoidei: Dasyatidae: Neotrygon spp.): An update.}, journal = {Comptes rendus biologies}, volume = {339}, number = {9-10}, pages = {417-426}, doi = {10.1016/j.crvi.2016.07.004}, pmid = {27543138}, issn = {1768-3238}, mesh = {Algorithms ; Animals ; Base Sequence ; Cytochromes b/genetics ; Cytochromes c/genetics ; DNA/genetics ; Furans ; Genetic Markers/genetics ; Indian Ocean ; Mitochondria/genetics ; Pentanoic Acids ; Phylogeny ; Skates, Fish/classification/*genetics ; Species Specificity ; }, abstract = {Previous investigations have uncovered divergent mitochondrial clades within the blue-spotted maskray, previously Neotrygon kuhlii (Müller and Henle). The hypothesis that the blue-spotted maskray may consist of a complex of multiple cryptic species has been proposed, and four species have been recently described or resurrected. To test the multiple cryptic species hypothesis, we investigated the phylogenetic relationships and coalescence patterns of mitochondrial sequences in a sample of 127 new individuals from the Indian Ocean and the Coral Triangle region, sequenced at both the CO1 and cytochrome b loci. The maximum-likelihood (ML) tree of concatenated CO1+cytochrome b gene sequences, rooted by the New Caledonian maskray N. trigonoides, yielded 9 strongly supported, main clades. Puillandre's ABGD algorithm detected gaps in nucleotide distance consistent with the ML phylogeny. The general mixed Yule-coalescent algorithm partitioned the dataset into putative species generally consistent with the ML phylogeny. Nuclear markers generally confirmed that distinct mitochondrial clades correspond to genetically isolated lineages. The nine main lineages identified by ML analysis were geographically distributed in a parapatric fashion, indicating reproductive isolation. The hypothesis of multiple cryptic species is thus validated.}, }
@article {pmid27539928, year = {2017}, author = {Guo, W and Zhu, A and Fan, W and Mower, JP}, title = {Complete mitochondrial genomes from the ferns Ophioglossum californicum and Psilotum nudum are highly repetitive with the largest organellar introns.}, journal = {The New phytologist}, volume = {213}, number = {1}, pages = {391-403}, doi = {10.1111/nph.14135}, pmid = {27539928}, issn = {1469-8137}, mesh = {Base Composition/genetics ; DNA, Plant/genetics ; Ferns/*genetics ; Genome Size ; *Genome, Mitochondrial ; Genome, Plant ; Introns/*genetics ; Mitochondria/genetics ; Open Reading Frames/genetics ; Organelles/*genetics ; Phylogeny ; RNA/genetics ; RNA Editing/genetics ; RNA, Mitochondrial ; Repetitive Sequences, Nucleic Acid/*genetics ; }, abstract = {Currently, complete mitochondrial genomes (mitogenomes) are available from all major land plant lineages except ferns. Sequencing of fern mitogenomes could shed light on the major evolutionary transitions that established mitogenomic diversity among extant lineages. In this study, we generated complete mitogenomes from the adder's tongue fern (Ophioglossum californicum) and the whisk fern (Psilotum nudum). The Psilotum mitogenome (628 kb) contains a rich complement of genes and introns, some of which are the largest of any green plant organellar genome. In the Ophioglossum mitogenome (372 kb), gene and intron content is slightly reduced, including the loss of all four mitochondrial ccm genes. Transcripts of nuclear Ccm genes also were not detected, suggesting loss of the entire mitochondrial cytochrome c maturation pathway from Ophioglossum. Both fern mitogenomes are highly repetitive, yet they show extremely low levels of active recombination. Transcriptomic sequencing uncovered ˜1000 sites of C-to-U RNA editing in both species, plus a small number (< 60) of U-to-C edit sites. Overall, the first mitochondrial genomes of ferns show a mix of features shared with lycophytes and/or seed plants and several novel genomic features, enabling a robust reconstruction of the mitogenome in the common ancestor of vascular plants.}, }
@article {pmid27537861, year = {2016}, author = {O'Sullivan, NJ and Teasdale, MD and Mattiangeli, V and Maixner, F and Pinhasi, R and Bradley, DG and Zink, A}, title = {A whole mitochondria analysis of the Tyrolean Iceman's leather provides insights into the animal sources of Copper Age clothing.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {31279}, pmid = {27537861}, issn = {2045-2322}, mesh = {Animals ; Animals, Domestic/classification/*genetics ; Animals, Wild/classification/*genetics ; Cattle ; Clothing ; Deer ; Genome, Mitochondrial ; Goats ; Mitochondria/*genetics ; Mummies ; Phylogeny ; Sequence Analysis, DNA/*methods ; Sheep ; Ursidae ; Whole Genome Sequencing/*methods ; }, abstract = {The attire of the Tyrolean Iceman, a 5,300-year-old natural mummy from the Ötzal Italian Alps, provides a surviving example of ancient manufacturing technologies. Research into his garments has however, been limited by ambiguity surrounding their source species. Here we present a targeted enrichment and sequencing of full mitochondrial genomes sampled from his clothes and quiver, which elucidates the species of production for nine fragments. Results indicate that the majority of the samples originate from domestic ungulate species (cattle, sheep and goat), whose recovered haplogroups are now at high frequency in today's domestic populations. Intriguingly, the hat and quiver samples were produced from wild species, brown bear and roe deer respectively. Combined, these results suggest that Copper Age populations made considered choices of clothing material from both the wild and domestic populations available to them. Moreover, these results show the potential for the recovery of complete mitochondrial genomes from degraded prehistoric artefacts.}, }
@article {pmid27532618, year = {2016}, author = {Šašić, L and Ačanski, J and Vujić, A and Ståhls, G and Radenković, S and Milić, D and Obreht Vidaković, D and Đan, M}, title = {Molecular and Morphological Inference of Three Cryptic Species within the Merodon aureus Species Group (Diptera: Syrphidae).}, journal = {PloS one}, volume = {11}, number = {8}, pages = {e0160001}, pmid = {27532618}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Diptera/anatomy &amp; histology/*classification/genetics ; Electron Transport Complex IV/*genetics ; Eye/anatomy &amp; histology ; Female ; Genes, Mitochondrial/*genetics ; Male ; Mitochondria/enzymology ; Phylogeny ; Sequence Analysis, DNA ; Wings, Animal/*anatomy &amp; histology ; }, abstract = {The Merodon aureus species group (Diptera: Syrphidae: Eristalinae) comprises a number of different sub-groups and species complexes. In this study we focus on resolving the taxonomic status of the entity previously identified as M. cinereus B, here identified as M. atratus species complex. We used an integrative approach based on morphological descriptions, combined with supporting characters that were obtained from molecular analyses of the mitochondrial cytochrome c oxidase I gene as well as from geometric morphometry of wing and surstylus shapes and environmental niche comparisons. All applied data and methods distinguished and supported three morphologically cryptic species: M. atratus stat. nov., M. virgatus sp. nov. and M. balkanicus sp. nov., which constitute the M. atratus species complex. We present an identification key for the sub-groups and species complexes of the M. aureus species group occurring in Europe, describe the taxa and discuss the utility of the applied methods for species delimitation. The estimated divergence times for the species splits of these taxa coincide with the Pleistocene Günz-Mindel interglaciation and the Great interglaciation (between the Ris and Mindel glacial periods).}, }
@article {pmid27528758, year = {2016}, author = {Nunn, AV and Guy, GW and Bell, JD}, title = {The quantum mitochondrion and optimal health.}, journal = {Biochemical Society transactions}, volume = {44}, number = {4}, pages = {1101-1110}, pmid = {27528758}, issn = {1470-8752}, support = {MC_U120061305/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adaptation, Physiological ; Adenosine Triphosphate/metabolism ; Aging ; Animals ; Biological Evolution ; *Energy Metabolism ; *Health Status ; Hormesis ; Humans ; Inflammation/metabolism ; *Longevity ; Mitochondria/*metabolism ; Models, Biological ; Reactive Oxygen Species/metabolism ; }, abstract = {A sufficiently complex set of molecules, if subject to perturbation, will self-organize and show emergent behaviour. If such a system can take on information it will become subject to natural selection. This could explain how self-replicating molecules evolved into life and how intelligence arose. A pivotal step in this evolutionary process was of course the emergence of the eukaryote and the advent of the mitochondrion, which both enhanced energy production per cell and increased the ability to process, store and utilize information. Recent research suggest that from its inception life embraced quantum effects such as 'tunnelling' and 'coherence' while competition and stressful conditions provided a constant driver for natural selection. We believe that the biphasic adaptive response to stress described by hormesis-a process that captures information to enable adaptability, is central to this whole process. Critically, hormesis could improve mitochondrial quantum efficiency, improving the ATP/ROS ratio, whereas inflammation, which is tightly associated with the aging process, might do the opposite. This all suggests that to achieve optimal health and healthy aging, one has to sufficiently stress the system to ensure peak mitochondrial function, which itself could reflect selection of optimum efficiency at the quantum level.}, }
@article {pmid27528689, year = {2016}, author = {Karadjian, G and Hassanin, A and Saintpierre, B and Gembu Tungaluna, GC and Ariey, F and Ayala, FJ and Landau, I and Duval, L}, title = {Highly rearranged mitochondrial genome in Nycteria parasites (Haemosporidia) from bats.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {35}, pages = {9834-9839}, pmid = {27528689}, issn = {1091-6490}, mesh = {Animals ; Cambodia ; Chiroptera/*parasitology ; Democratic Republic of the Congo ; *Genome, Mitochondrial ; *Genome, Protozoan ; Haemosporida/classification/*genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; Mitochondrial Proteins/*genetics ; Phylogeny ; Protozoan Proteins/*genetics ; }, abstract = {Haemosporidia parasites have mostly and abundantly been described using mitochondrial genes, and in particular cytochrome b (cytb). Failure to amplify the mitochondrial cytb gene of Nycteria parasites isolated from Nycteridae bats has been recently reported. Bats are hosts to a diverse and profuse array of Haemosporidia parasites that remain largely unstudied. There is a need to obtain more molecular data from chiropteran parasites. Such data would help to better understand the evolutionary history of Haemosporidia, which notably include the Plasmodium parasites, malaria's agents. We use next-generation sequencing to obtain the complete mitochondrial genome of Nycteria parasites from African Nycteris grandis (Nycteridae) and Rhinolophus alcyone (Rhinolophidae) and Asian Megaderma spasma (Megadermatidae). We report four complete mitochondrial genomes, including two rearranged mitochondrial genomes within Haemosporidia. Our results open outlooks into potentially undiscovered Haemosporidian diversity.}, }
@article {pmid27524662, year = {2016}, author = {Garg, SG and Gould, SB}, title = {The Role of Charge in Protein Targeting Evolution.}, journal = {Trends in cell biology}, volume = {26}, number = {12}, pages = {894-905}, doi = {10.1016/j.tcb.2016.07.001}, pmid = {27524662}, issn = {1879-3088}, mesh = {Amino Acid Sequence ; Amino Acids/*metabolism ; Animals ; Cell Compartmentation ; Eukaryotic Cells/metabolism ; Humans ; Organelles/metabolism ; Protein Transport ; Symbiosis ; }, abstract = {Two eukaryotic compartments are of endosymbiotic origin, the mitochondrion and plastid. These organelles need to import hundreds of proteins from the cytosol. The import machineries of both are of independent origin, but function in a similar fashion and recognize N-terminal targeting sequences that also share similarities. Targeting, however, is generally specific, even though plastid targeting evolved in the presence of established mitochondrial targeting. Here we review current advances on protein import into mitochondria and plastids from diverse eukaryotic lineages and highlight the impact of charged amino acids in targeting. Their presence or absence alone can determine localization, and comparisons across diverse eukaryotes, and their different types of mitochondria and plastids, uncover unexplored avenues of protein import research.}, }
@article {pmid27518222, year = {2016}, author = {Boonrueng, C and Tangpranomkorn, S and Yazhisai, U and Sirikantaramas, S}, title = {Molecular cloning, subcellular localization and characterization of two adenylate kinases from cassava, Manihot esculenta Crantz cv. KU50.}, journal = {Journal of plant physiology}, volume = {204}, number = {}, pages = {66-73}, doi = {10.1016/j.jplph.2016.08.001}, pmid = {27518222}, issn = {1618-1328}, mesh = {Adenylate Kinase/*genetics ; Cloning, Molecular ; Computer Simulation ; Fluorescence ; Gene Expression Regulation, Plant ; Manihot/*enzymology/*genetics ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Recombinant Proteins/isolation &amp; purification ; Subcellular Fractions/enzymology ; }, abstract = {Adenylate kinase (ADK) is a phosphotransferase that plays an important role in cellular energy homeostasis. Many isozymes located in different subcellular compartments have been reported. In this study, we focus on the characterization of cassava (Manihot esculenta) ADKs. We found 15 ADKs that are publicly available in the African cassava genome database. We cloned two ADKs, namely MeADK1 and MeADK2, which are phylogenetically grouped together with the plastidial ADK in potato. Both MeADK1 and MeADK2 showed 66% identity in the amino acid sequences with plastidial ADK in potato. However, we demonstrated that they are localized to mitochondria using GFP fusions of MeADK1 and MeADK2. The Escherichia coli-produced recombinant MeADK1 and MeADK2 preferred forward reactions that produce ATP. They exhibited similar specific activities. The semi-quantitative RT-PCR analysis showed that MeADK1 and MeADK2 in 2-month-old leaves have similar expression patterns under a diurnal light-dark cycle. However, MeADK2 transcripts were expressed at much higher levels than MeADK1 in 5-month-old leaves and roots. Thus, we conclude that MeADK2 might play a vital role in energy homeostasis in cassava mitochondria.}, }
@article {pmid27507266, year = {2016}, author = {Mitchell, A and Guerra, D and Stewart, D and Breton, S}, title = {In silico analyses of mitochondrial ORFans in freshwater mussels (Bivalvia: Unionoida) provide a framework for future studies of their origin and function.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {597}, pmid = {27507266}, issn = {1471-2164}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Bivalvia/classification/*genetics ; Computational Biology/methods ; Computer Simulation ; DNA, Mitochondrial ; Evolution, Molecular ; Fresh Water ; *Genes, Mitochondrial ; *Genome, Mitochondrial ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Hydrophobic and Hydrophilic Interactions ; Ligands ; Mitochondrial Proteins/chemistry/genetics ; *Open Reading Frames ; Phylogeny ; Protein Binding ; Protein Interaction Domains and Motifs ; Structure-Activity Relationship ; }, abstract = {BACKGROUND: Many species of bivalves exhibit a unique system of mtDNA transmission named Doubly Uniparental Inheritance (DUI). Under this system, species have two distinct, sex-linked mitochondrial genomes: the M-type mtDNA, which is transmitted by males to male offspring and found in spermatozoa, and the F-type mtDNA, which is transmitted by females to all offspring, and found in all tissues of females and in somatic tissues of males. Bivalves with DUI also have sex-specific mitochondrial ORFan genes, (M-orf in the M mtDNA, F-orf in the F mtDNA), which are open reading frames having no detectable homology and no known function. DUI ORFan proteins have previously been characterized in silico in a taxonomically broad array of bivalves including four mytiloid, one veneroid and one unionoid species. However, the large evolutionary distance among these taxa prevented a meaningful comparison of ORFan properties among these divergent lineages. The present in silico study focuses on a suite of more closely-related Unionoid freshwater mussel species to provide more reliably interpretable information on patterns of conservation and properties of DUI ORFans. Unionoid species typically have separate sexes, but hermaphroditism also occurs, and hermaphroditic species lack the M-type mtDNA and possess a highly mutated version of the F-orf in their maternally transmitted mtDNA (named H-orf in these taxa). In this study, H-orfs and their respective proteins are analysed for the first time.<br><br>RESULTS: Despite a rapid rate of evolution, strong structural and functional similarities were found for M-ORF proteins compared among species, and among the F-ORF and H-ORF proteins across the studied species. In silico analyses suggest that M-ORFs have a role in transport and cellular processes such as signalling, cell cycle and division, and cytoskeleton organisation, and that F-ORFs may be involved in cellular traffic and transport, and in immune response. H-ORFs appear to be structural glycoproteins, which may be involved in signalling, transport and transcription. Our results also support either a viral or a mitochondrial origin for the ORFans.<br><br>CONCLUSIONS: Our findings reveal striking structural and functional similarities among proteins encoded by mitochondrial ORFans in freshwater mussels, and strongly support a role for these genes in the DUI mechanism. Our analyses also support the possibility of DUI systems with elements of different sources/origins and different mechanisms of action in the distantly-related DUI taxa. Parallel situations to the novel mitochondrially-encoded functions of freshwater mussel ORFans present in some other eukaryotes are also discussed.}, }
@article {pmid27498855, year = {2016}, author = {Kang, L and Zheng, HX and Zhang, M and Yan, S and Li, L and Liu, L and Liu, K and Hu, K and Chen, F and Ma, L and Qin, Z and Wang, Y and Wang, X and Jin, L}, title = {MtDNA analysis reveals enriched pathogenic mutations in Tibetan highlanders.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {31083}, pmid = {27498855}, issn = {2045-2322}, mesh = {Adaptation, Physiological ; Asian People/genetics ; DNA Mutational Analysis ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Founder Effect ; Genetic Variation ; Haplotypes ; Human Migration ; Humans ; Mitochondria/genetics ; Mutation ; Phylogeny ; Tibet ; }, abstract = {Tibetan highlanders, including Tibetans, Monpas, Lhobas, Dengs and Sherpas, are considered highly adaptive to severe hypoxic environments. Mitochondrial DNA (mtDNA) might be important in hypoxia adaptation given its role in coding core subunits of oxidative phosphorylation. In this study, we employed 549 complete highlander mtDNA sequences (including 432 random samples) to obtain a comprehensive view of highlander mtDNA profile. In the phylogeny of a total of 36,914 sequences, we identified 21 major haplogroups representing founding events of highlanders, most of which were coalesced in 10 kya. Through founder analysis, we proposed a three-phase model of colonizing the plateau, i.e., pre-LGM Time (30 kya, 4.68%), post-LGM Paleolithic Time (16.8 kya, 29.31%) and Neolithic Time (after 8 kya, 66.01% in total). We observed that pathogenic mutations occurred far more frequently in 22 highlander-specific lineages (five lineages carrying two pathogenic mutations and six carrying one) than in the 6,857 haplogroups of all the 36,914 sequences (P = 4.87 × 10(-8)). Furthermore, the number of possible pathogenic mutations carried by highlanders (in average 3.18 ± 1.27) were significantly higher than that in controls (2.82 ± 1.40) (P = 1.89 × 10(-4)). Considering that function-altering and pathogenic mutations are enriched in highlanders, we therefore hypothesize that they may have played a role in hypoxia adaptation.}, }
@article {pmid27497992, year = {2016}, author = {Bohne, AV and Teubner, M and Liere, K and Weihe, A and Börner, T}, title = {In vitro promoter recognition by the catalytic subunit of plant phage-type RNA polymerases.}, journal = {Plant molecular biology}, volume = {92}, number = {3}, pages = {357-369}, pmid = {27497992}, issn = {1573-5028}, mesh = {Arabidopsis/*genetics/*virology ; Catalytic Domain/genetics ; DNA-Directed RNA Polymerases/genetics/*metabolism ; Mitochondria/enzymology/genetics ; Promoter Regions, Genetic/*genetics ; RNA/metabolism ; RNA, Mitochondrial ; }, abstract = {We identified sequence motifs, which enhance or reduce the ability of the Arabidopsis phage-type RNA polymerases RPOTm (mitochondrial RNAP), RPOTp (plastidial RNAP), and RPOTmp (active in both organelles) to recognize their promoters in vitro with help of a 'specificity loop'. The importance of this data for the evolution and function of the organellar RNA polymerases is discussed. The single-subunit RNA polymerase (RNAP) of bacteriophage T7 is able to perform all steps of transcription without additional transcription factors. Dicotyledonous plants possess three phage-type RNAPs, RPOTm-the mitochondrial RNAP, RPOTp-the plastidial RNAP, and RPOTmp-an RNAP active in both organelles. RPOTm and RPOTp, like the T7 polymerase, are able to recognize promoters, while RPOTmp displays no significant promoter specificity in vitro. To find out which promoter motifs are crucial for recognition by the polymerases we performed in vitro transcription assays with recombinant Arabidopsis RPOTm and RPOTp enzymes. By comparing different truncated and mutagenized promoter constructs, we observed the same minimal promoter sequence supposed to be needed in vivo for transcription initiation. Moreover, we identified elements of core and flanking sequences, which are of critical importance for promoter recognition and activity in vitro. We further intended to reveal why RPOTmp does not efficiently recognize promoters in vitro and if promoter recognition is based on a structurally defined specificity loop of the plant enzymes as described for the yeast and T7 RNAPs. Interestingly, the exchange of only three amino acids within the putative specificity loop of RPOTmp enabled the enzyme for specific promoter transcription in vitro. Thus, also in plant phage-type RNAPs the specificity loop is engaged in promoter recognition. The results are discussed with respect to their relevance for transcription in organello and to the evolution of RPOT enzymes including the divergence of their functions.}, }
@article {pmid27494995, year = {2016}, author = {Kikuchi, T and Afrin, T and Yoshida, M}, title = {Complete mitochondrial genomes of four entomopathogenic nematode species of the genus Steinernema.}, journal = {Parasites &amp; vectors}, volume = {9}, number = {1}, pages = {430}, pmid = {27494995}, issn = {1756-3305}, mesh = {Animals ; Base Sequence ; Codon ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genome, Helminth ; *Genome, Mitochondrial ; Helminth Proteins/genetics ; Insecta/*parasitology ; Molecular Sequence Data ; Nematoda/classification/*genetics/isolation &amp; purification ; Phylogeny ; }, abstract = {BACKGROUND: Nematodes belonging to the genus Steinernema are insect parasites and are used as effective biological agents against soil-dwelling insect pests. Although the full nuclear genomes of multiple Steinernema species have become available recently, mitochondrial genome information for the genus is limited. In this study, we sequenced the complete mitochondrial genomes of four species of Steinernema and analysed their structure, codon usage and phylogenetic relationships.<br><br>RESULTS: Mitochondrial genomes of Steinernema carpocapsae, S. glaseri, S. kushidai and S. litorale comprised 13,924, 13,851, 15,182 and 21,403&#xa0;bp, respectively, with highly AT-rich nucleotide contents (AT ratio of 71.05-76.76&#xa0;%). All the expected genes, including 12 protein-coding genes (encoding ATP6, CYTB, COX1-3, ND1-6 and ND4L), two rRNA genes and 22 tRNA genes were identified in the four genomes. Phylogenetic analyses based on the amino acid sequences of the 12 protein-coding genes identified the Steinernema species as monophyletic, representing a sister clade of Rhabditina and Ascaridida. In addition, they were more closely positioned to other Clade 10 nematodes, including Bursaphelenchus xylophilus, Aphelenchoides besseyi and Panagrellus redivivus, than to Strongyloides species. Gene arrangements and codon usage analyses supported this relationship. Mitochondrial genome comparison of two distinct strains of S. carpocapsae detected high intra-specific diversity.<br><br>CONCLUSIONS: The mitochondrial genomes of four species of Steinernema determined in this study revealed inter- and intra-species divergences/diversities of mitochondrial genomes in this genus. This information provides useful insights into the phylogenetic position of the genus Steinernema within the Nematoda and represents a useful resource for selecting molecular markers for diagnosis and population studies. These data will increase our understanding of the interesting biology of insect parasites.}, }
@article {pmid27487286, year = {2017}, author = {Karpov, SA and Tcvetkova, VS and Mamkaeva, MA and Torruella, G and Timpano, H and Moreira, D and Mamanazarova, KS and López-García, P}, title = {Morphological and Genetic Diversity of Opisthosporidia: New Aphelid Paraphelidium tribonemae gen. et sp. nov.}, journal = {The Journal of eukaryotic microbiology}, volume = {64}, number = {2}, pages = {204-212}, pmid = {27487286}, issn = {1550-7408}, support = {322669/ERC_/European Research Council/International ; }, mesh = {Amoeba/genetics ; Cysts/ultrastructure ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Ecology ; Eukaryota/*classification/*genetics/physiology/*ultrastructure ; *Genetic Variation ; Life Cycle Stages ; Microscopy, Electron, Transmission ; Organelles/ultrastructure ; *Phylogeny ; Plasmodium/ultrastructure ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Spores/ultrastructure ; }, abstract = {Aphelids are a poorly known group of parasitoids of algae that have raised considerable interest due to their pivotal phylogenetic position. Together with Cryptomycota and the highly derived Microsporidia, they have been recently re-classified as the Opisthosporidia, which constitute the sister group to the fungi within the Holomycota. Despite their huge diversity, as revealed by molecular environmental studies, and their phylogenetic interest, only three genera have been described (Aphelidium, Amoeboaphelidium, and Pseudaphelidium), from which 18S rRNA gene sequences exist only for Amoeboaphelidium and Aphelidium species. Here, we describe the life cycle and ultrastructure of a new representative of Aphelida, Paraphelidium tribonemae gen. et sp. nov., and provide the first 18S rRNA gene sequence obtained for this genus. Molecular phylogenetic analysis indicates that Paraphelidium is distantly related to both Aphelidium and Amoebaphelidium, highlighting the wide genetic diversity of aphelids. Paraphelidium tribonemae has amoeboflagellate zoospores containing a lipid-microbody complex, dictyosomes, and mitochondria with rhomboid cristae, which are also present in trophonts and plasmodia. The amoeboid trophont uses pseudopodia to feed from the host cytoplasm. Although genetically distinct, the genus Paraphelidium is morphologically indistinguishable from other aphelid genera and has zoospores able to produce lamellipodia with subfilopodia like those of Amoeboaphelidium.}, }
@article {pmid27486242, year = {2016}, author = {Burger, PA and Peters, J and Magee, P and Hanotte, O}, title = {Reply to Marom et al.: Mitochondrial panmixia in dromedaries predates ancient caravan trading.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {32}, pages = {E4583-4}, pmid = {27486242}, issn = {1091-6490}, support = {P 24706/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; *Camelus ; Humans ; *Mitochondria ; Prednisolone ; }, }
@article {pmid27473689, year = {2016}, author = {Degli Esposti, M and Cortez, D and Lozano, L and Rasmussen, S and Nielsen, HB and Martinez Romero, E}, title = {Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes.}, journal = {Biology direct}, volume = {11}, number = {}, pages = {34}, pmid = {27473689}, issn = {1745-6150}, mesh = {Alphaproteobacteria/*genetics ; Amino Acid Sequence ; Bacterial Proteins/*genetics ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics ; Humans ; Hydrogenase/*genetics ; Phylogeny ; Rhodospirillaceae/genetics ; }, abstract = {UNLABELLED: Eukaryogenesis, a major transition in evolution of life, originated from the symbiogenic fusion of an archaea with a metabolically versatile bacterium. By general consensus, the latter organism belonged to α proteobacteria, subsequently evolving into the mitochondrial organelle of our cells. The consensus is based upon genetic and metabolic similarities between mitochondria and aerobic α proteobacteria but fails to explain the origin of several enzymes found in the mitochondria-derived organelles of anaerobic eukaryotes such as Trichomonas and Entamoeba. These enzymes are thought to derive from bacterial lineages other than α proteobacteria, e.g., Clostridium - an obligate anaerobe. [FeFe]-hydrogenase constitues the characteristic enzyme of this anaerobic metabolism and is present in different types also in Entamoeba and other anaerobic eukaryotes. Here we show that α proteobacteria derived from metagenomic studies possess both the cytosolic and organellar type of [FeFe]-hydrogenase, as well as all the proteins required for hydrogenase maturation. These organisms are related to cultivated members of the Rhodospirillales order previously suggested to be close relatives of mitochondrial ancestors. For the first time, our evidence supports an α proteobacterial ancestry for both the anaerobic and the aerobic metabolism of eukaryotes.<br><br>REVIEWERS: This article was reviewed by William Martin and Nick Lane, both suggested by the Authors.}, }
@article {pmid27473417, year = {2016}, author = {Goldman, SA}, title = {Causality Assessment in Premarketing Drug Clinical Trials: Regulatory Evolution in the USA and Ongoing Concerns.}, journal = {Drug safety}, volume = {39}, number = {10}, pages = {895-901}, pmid = {27473417}, issn = {1179-1942}, mesh = {Adverse Drug Reaction Reporting Systems/*legislation &amp; jurisprudence ; Clinical Trials as Topic/*legislation &amp; jurisprudence/standards ; Drug Approval/legislation &amp; jurisprudence ; Drugs, Investigational/administration &amp; dosage/*adverse effects ; Humans ; United States ; United States Food and Drug Administration ; }, abstract = {Since 1993, how to assess the causality of serious adverse events in premarketing drug clinical trials has undergone sustained regulatory evolution in the USA. In that year, an investigational drug study for chronic hepatitis B virus infection was emergently stopped after a patient suddenly exhibited hepatic failure and lactic acidosis, which later developed, along with pancreatitis and peripheral neuropathy, in several others after drug discontinuation. Five patients eventually died, including three despite emergency liver transplantation. The drug's multisystem toxicity was not predicted by preclinical animal studies, with grave injury to human mitochondria subsequently implicated. A concerned US Food and Drug Administration (FDA) created a task force whose findings would have a lasting impact on the agency's thinking. In 1994, the FDA proposed to amend its investigational new drug reporting requirements largely based on task force recommendations for ways to enhance the likelihood that sponsors and investigators would consider investigational agents as a possible cause of serious adverse events mimicking the underlying disease or concomitant drug toxicity. Then, in its 1997 final rule for expedited safety reporting requirements for drugs and biologics, the FDA advised sponsors that such reporting of serious, unexpected clinical trial cases would be expected when "there is a reasonable suspected causal relationship between the investigational product and the adverse event (i.e., the causal relationship cannot be ruled out)." This last clause was codified into the suspected adverse drug reaction definition in the FDA's 2003 safety reporting requirements for drugs and biologics proposed rule. The negatively received suspected adverse drug reaction and proposed causality standard were not adopted in the FDA's 2010 finalized investigational new drug safety reporting regulations, the agency stating that "'reasonable possibility' means there is evidence to suggest a causal relationship between the drug and the adverse event." However, such new requirements as aggregate analysis of specific events and expedited reporting of animal or in vitro data suggesting significant harm to humans, and subsequent guidance that sponsors develop "a systematic approach" to premarketing safety assessment, are among the components of the FDA's efforts to enhance determination of a "reasonable possibility" of causality. They are also philosophically consistent with the 1993 task force recommendations, and a reminder of the inherent hazards associated with the use of investigational drugs, particularly in the early stages of human study.}, }
@article {pmid27468745, year = {2016}, author = {Takahashi, Y and Yoshida, M and Inouye, I and Watanabe, MM}, title = {Fibrophrys columna gen. nov., sp. nov: A member of the family Amphifilidae.}, journal = {European journal of protistology}, volume = {56}, number = {}, pages = {41-50}, doi = {10.1016/j.ejop.2016.06.003}, pmid = {27468745}, issn = {1618-0429}, mesh = {Japan ; Microscopy, Electron, Transmission ; Phylogeny ; Ponds/*parasitology ; RNA, Ribosomal, 18S/genetics ; Species Specificity ; Stramenopiles/*classification/cytology/genetics/ultrastructure ; }, abstract = {A novel Diplophrys-like organism, Fibrophrys columna, was isolated from Hiuchigaike Pond in Japan. F. columna showed a nearly orbicular or broadly elliptical cell shape and has fine filamentous, branching ectoplasmic elements emanating from both polar ends of the cell. Cells also contain orange, amber, or colorless lipid bodies. Although its whole cell morphology resembles that of the genus Diplophrys, Fibrophrys is clearly distinct from Diplophrys on the basis of 18S rDNA sequences. Molecular phylogenetic analysis showed a close relationship of F. columna with Amphifila marina, and its sequence is similar to many environmental stramenopile sequences. The cells of F. columna measured 5.0-8.3×5.6-10.3μm and sometimes possessed hernia-like prongs instead of filamentous ectoplasmic elements. An axis-like electron-dense body was observed in the mitochondria. We also studied the ultrastructure of another Fibrophrys strain, Fibrophrys sp. E-1, which is different from the type strain of F. columna. A ladder-like pattern was recognized in the outer part of unidentified cytoplasmic membranes connected with the mitochondria. The unidentified cytoplasmic membranes were connected to the nuclear, lipid body, and mitochondrial outer membranes. We propose a new genus, Fibrophrys, and a new species, F. columna, based on these ultrastructural and molecular features.}, }
@article {pmid27463803, year = {2016}, author = {Fan, X and Chiba, H and Huang, Z and Fei, W and Wang, M and Sáfián, S}, title = {Clarification of the Phylogenetic Framework of the Tribe Baorini (Lepidoptera: Hesperiidae: Hesperiinae) Inferred from Multiple Gene Sequences.}, journal = {PloS one}, volume = {11}, number = {7}, pages = {e0156861}, pmid = {27463803}, issn = {1932-6203}, mesh = {Animals ; Lepidoptera/*classification/genetics ; Mitochondria/genetics ; Peptide Elongation Factor 1/genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; }, abstract = {Members of the skipper tribe Baorini generally resemble each other and are characterized by dark brown wings with hyaline white spots. These shared characteristics have caused difficulties with revealing the relationships among genera and species in the group, and some conflicting taxonomic views remain unresolved. The present study aims to infer a more comprehensive phylogeny of the tribe using molecular data, to test the monophyly of the tribe as well as the genera it includes in order to clarify their taxonomic status, and finally to revise the current classification of the group. In order to reconstruct a phylogenetic tree, the mitochondrial COI-COII and 16S genes as well as the nuclear EF-1α and 28S genes were analyzed using parsimony, maximum likelihood, and Bayesian inference. The analysis included 67 specimens of 41 species, and we confirmed the monophyly of Baorini, and revealed that 14 genera are well supported. The genus Borbo is separated into three clades: Borbo, Pseudoborbo, and Larsenia gen. nov. We confirmed that Polytremis is polyphyletic and separated into three genera: Polytremis, Zinaida, and Zenonoida gen. nov., and also confirmed that the genus Prusiana is a member of the tribe. Relationships among some genera were strongly supported. For example, Zenonia and Zenonoida were found to be sister taxa, closely related to Zinaida and Iton, while Pelopidas and Baoris were also found to cluster together.}, }
@article {pmid27463732, year = {2017}, author = {Kostka, M and Lares-Jiménez, LF and Tyml, T and Dyková, I}, title = {Copromyxa laresi n. sp. (Amoebozoa: Tubulinea) and Transfer of Cashia limacoides (Page, 1967) to Copromyxa Zopf, 1885.}, journal = {The Journal of eukaryotic microbiology}, volume = {64}, number = {2}, pages = {173-182}, doi = {10.1111/jeu.12349}, pmid = {27463732}, issn = {1550-7408}, mesh = {Actins/genetics ; Amoeba ; Amoebozoa/*classification/*genetics/isolation &amp; purification/*ultrastructure ; Animals ; Base Sequence ; Czech Republic ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Elongation Factor 2 Kinase/genetics ; Gills/parasitology ; Lobosea/*classification/*genetics/isolation &amp; purification/*ultrastructure ; Microscopy, Electron ; Mitochondria/parasitology/ultrastructure ; Oligochaeta/parasitology ; Organelles/parasitology/ultrastructure ; *Phylogeny ; Protozoan Proteins/genetics ; Sequence Alignment ; Soil/parasitology ; Spain ; Species Specificity ; Zebrafish/parasitology ; }, abstract = {Five amoeboid organisms of different origin (isolated from fish organs, soil and digestive tract of earthworm) that shared light microscopical and ultrastructural features including type and arrangement of mitochondrial cristae were subjected to phylogenetic analyses based on sequences of SSU rDNA and protein coding genes (actin, cytochrome oxidase I, and eukaryotic elongation factor 2). The reconstruction of multigene phylogeny of the strains studied (i) revealed that they belong to the same single-genus Copromyxa clade; (ii) strongly supported position of Copromyxa cantabrigiensis (syn. Hartmannella cantabrigiensis) within the genus; (iii) together with comparisons of light and electron microscopy data justified reclassification of Cashia limacoides (syn. Vexillifera expectata) to Copromyxa limacoides n. comb., and (iv) justified description of a new species, Copromyxa laresi n. sp.}, }
@article {pmid27463650, year = {2016}, author = {Pennisi, E}, title = {EVOLUTIONARY BIOLOGY. Do genomic conflicts drive evolution?.}, journal = {Science (New York, N.Y.)}, volume = {353}, number = {6297}, pages = {334-335}, doi = {10.1126/science.353.6297.334}, pmid = {27463650}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; Birds/genetics ; Cell Nucleus/*genetics ; Energy Metabolism/*genetics ; Female ; *Genetic Fitness ; *Genome, Mitochondrial ; Genomics ; Male ; *Mating Preference, Animal ; Mitochondria/genetics/metabolism ; Pigmentation ; Plants/genetics ; }, }
@article {pmid27458014, year = {2016}, author = {van Dooren, GG and Yeoh, LM and Striepen, B and McFadden, GI}, title = {The Import of Proteins into the Mitochondrion of Toxoplasma gondii.}, journal = {The Journal of biological chemistry}, volume = {291}, number = {37}, pages = {19335-19350}, pmid = {27458014}, issn = {1083-351X}, support = {R01 AI064671/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Male ; Membrane Transport Proteins/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Protein Transport/physiology ; Protozoan Proteins/*metabolism ; Toxoplasma/*metabolism ; }, abstract = {Outside of well characterized model eukaryotes, relatively little is known about the translocons that transport proteins across the two membranes that surround the mitochondrion. Apicomplexans are a phylum of intracellular parasites that cause major diseases in humans and animals and are evolutionarily distant from model eukaryotes such as yeast. Apicomplexans harbor a mitochondrion that is essential for parasite survival and is a validated drug target. Here, we demonstrate that the apicomplexan Toxoplasma gondii harbors homologues of proteins from all the major mitochondrial protein translocons present in yeast, suggesting these arose early in eukaryotic evolution. We demonstrate that a T. gondii homologue of Tom22 (TgTom22), a central component of the translocon of the outer mitochondrial membrane (TOM) complex, is essential for parasite survival, mitochondrial protein import, and assembly of the TOM complex. We also identify and characterize a T. gondii homologue of Tom7 (TgTom7) that is important for parasite survival and mitochondrial protein import. Contrary to the role of Tom7 in yeast, TgTom7 is important for TOM complex stability, suggesting the role of this protein has diverged during eukaryotic evolution. Together, our study identifies conserved and modified features of mitochondrial protein import in apicomplexan parasites.}, }
@article {pmid27455896, year = {2017}, author = {Koch, RE and Josefson, CC and Hill, GE}, title = {Mitochondrial function, ornamentation, and immunocompetence.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {92}, number = {3}, pages = {1459-1474}, doi = {10.1111/brv.12291}, pmid = {27455896}, issn = {1469-185X}, mesh = {Animals ; *Immunocompetence ; Mitochondria/immunology/*physiology ; Phenotype ; }, abstract = {Understanding the mechanisms that link ornamental displays and individual condition is key to understanding the evolution and function of ornaments. Immune function is an aspect of individual quality that is often associated with the expression of ornamentation, but a general explanation for why the expression of some ornaments seems to be consistently linked to immunocompetence remains elusive. We propose that condition-dependent ornaments may be linked to key aspects of immunocompetence through co-dependence on mitochondrial function. Mitochondrial involvement in immune function is rarely considered outside of the biomedical literature, but the role of mitochondria as the primary energy producers of the cell and the centres of biosynthesis, the oxidative stress response, and cellular signalling place them at the hub of a variety of immune pathways. A promising new mechanistic explanation for correlations between a wide range of ornamental traits and the properties of individual quality is that mitochondrial function may be the 'shared pathway' responsible for links between ornament production and individual condition. Herein, we first review the role of mitochondria as both signal transducers and metabolic regulators of immune function. We then describe connections between hormonal pathways and mitochondria, with implications for both immune function and the expression of ornamentation. Finally, we explore the possibility that ornament expression may link directly to mitochondrial function. Considering condition-dependent traits within the framework of mitochondrial function has the potential to unify central tenets within the study of sexual selection, eco-immunology, oxidative stress ecology, stress and reproductive hormone biology, and animal physiology.}, }
@article {pmid27451341, year = {2016}, author = {He, YH and Lu, X and Tian, JY and Yan, DJ and Li, YC and Lin, R and Perry, B and Chen, XQ and Yu, Q and Cai, WW and Kong, QP}, title = {Mitochondrial DNA plays an equal role in influencing female and male longevity in centenarians.}, journal = {Experimental gerontology}, volume = {83}, number = {}, pages = {94-96}, doi = {10.1016/j.exger.2016.07.010}, pmid = {27451341}, issn = {1873-6815}, mesh = {Adult ; Aged ; Aged, 80 and over ; China ; DNA, Mitochondrial/*genetics ; Female ; Genetic Variation ; Genome, Mitochondrial ; Haplotypes ; Humans ; Longevity/*genetics ; Male ; Middle Aged ; Mitochondria/*genetics ; *Sex Factors ; }, abstract = {The mitochondrion is a double membrane-bound organelle which plays important functional roles in aging and many other complex phenotypes. Transmission of the mitochondrial genome in the matrilineal line causes the evolutionary selection sieve only in females. Theoretically, beneficial or neutral variations are more likely to accumulate and be retained in the female mitochondrial genome during evolution, which may be an initial trigger of gender dimorphism in aging. The asymmetry of evolutionary processes between gender could lead to males and females aging in different ways. If so, gender specific variation loads could be an evolutionary result of maternal heritage of mitochondrial genomes, especially in centenarians who live to an extreme age and are considered as good models for healthy aging. Here, we tested whether the mitochondrial variation loads were associated with altered aging patterns by investigating the mtDNA haplogroup distribution and genetic diversity between female and male centenarians. We found no evidence of differences in aging patterns between genders in centenarians. Our results indicate that the evolutionary consequence of gender dimorphism in mitochondrial genomes is not a factor in the altered aging patterns in human, and that mitochondrial DNA contributes equally to longevity in males and females.}, }
@article {pmid27450107, year = {2017}, author = {Mueller, SJ and Hoernstein, SN and Reski, R}, title = {The mitochondrial proteome of the moss Physcomitrella patens.}, journal = {Mitochondrion}, volume = {33}, number = {}, pages = {38-44}, doi = {10.1016/j.mito.2016.07.007}, pmid = {27450107}, issn = {1872-8278}, mesh = {Bryopsida/*chemistry ; Computational Biology ; Gene Targeting ; Mass Spectrometry ; Microscopy, Fluorescence ; Mitochondria/*chemistry ; Plant Proteins/*analysis ; Proteome/*analysis ; *Proteomics ; }, abstract = {Extant basal land plants are routinely used to trace plant evolution and to track strategies for high abiotic stress resistance. Whereas the structure of mitochondrial genomes and RNA editing are already well studied, mitochondrial proteome research is restricted to a few data sets. While the mitochondrial proteome of the model moss Physcomitrella patens is covered to an estimated 15-25% by proteomic evidence to date, the available data have already provided insights into the evolution of metabolic compartmentation, dual targeting and mitochondrial heterogeneity. This review summarizes the current knowledge about the mitochondrial proteome of P. patens, and gives a perspective on its use as a mitochondrial model system. Its amenability to gene editing, metabolic labelling as well as fluorescence microscopy provides a unique platform to study open questions in mitochondrial biology, such as regulation of protein stability, responses to stress and connectivity to other organelles. Future challenges will include improving the proteomic resources for P. patens, and to link protein inventories and modifications as well as evolutionary differences to the functional level.}, }
@article {pmid27449544, year = {2016}, author = {Rey, B and Dégletagne, C and Bodennec, J and Monternier, PA and Mortz, M and Roussel, D and Romestaing, C and Rouanet, JL and Tornos, J and Duchamp, C}, title = {Hormetic response triggers multifaceted anti-oxidant strategies in immature king penguins (Aptenodytes patagonicus).}, journal = {Free radical biology &amp; medicine}, volume = {97}, number = {}, pages = {577-587}, doi = {10.1016/j.freeradbiomed.2016.07.015}, pmid = {27449544}, issn = {1873-4596}, mesh = {Animals ; Antioxidants/*metabolism ; Basal Metabolism ; Energy Metabolism ; *Hormesis ; Hydrogen Peroxide/metabolism ; Mitochondria, Muscle/metabolism ; Oxidation-Reduction ; Spheniscidae/*physiology ; *Thermotolerance ; }, abstract = {Repeated deep dives are highly pro-oxidative events for air-breathing aquatic foragers such as penguins. At fledging, the transition from a strictly terrestrial to a marine lifestyle may therefore trigger a complex set of anti-oxidant responses to prevent chronic oxidative stress in immature penguins but these processes are still undefined. By combining in vivo and in vitro approaches with transcriptome analysis, we investigated the adaptive responses of sea-acclimatized (SA) immature king penguins (Aptenodytes patagonicus) compared with pre-fledging never-immersed (NI) birds. In vivo, experimental immersion into cold water stimulated a higher thermogenic response in SA penguins than in NI birds, but both groups exhibited hypothermia, a condition favouring oxidative stress. In vitro, the pectoralis muscles of SA birds displayed increased oxidative capacity and mitochondrial protein abundance but unchanged reactive oxygen species (ROS) generation per g tissue because ROS production per mitochondria was reduced. The genes encoding oxidant-generating proteins were down-regulated in SA birds while mRNA abundance and activity of the main antioxidant enzymes were up-regulated. Genes encoding proteins involved in repair mechanisms of oxidized DNA or proteins and in degradation processes were also up-regulated in SA birds. Sea life also increased the degree of fatty acid unsaturation in muscle mitochondrial membranes resulting in higher intrinsic susceptibility to ROS. Oxidative damages to protein or DNA were reduced in SA birds. Repeated experimental immersions of NI penguins in cold-water partially mimicked the effects of acclimatization to marine life, modified the expression of fewer genes related to oxidative stress but in a similar way as in SA birds and increased oxidative damages to DNA. It is concluded that the multifaceted plasticity observed after marine life may be crucial to maintain redox homeostasis in active tissues subjected to high pro-oxidative pressure in diving birds. Initial immersions in cold-water may initiate an hormetic response triggering essential changes in the adaptive antioxidant response to marine life.}, }
@article {pmid27444405, year = {2016}, author = {Gui, S and Wu, Z and Zhang, H and Zheng, Y and Zhu, Z and Liang, D and Ding, Y}, title = {The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {30158}, pmid = {27444405}, issn = {2045-2322}, mesh = {Base Sequence ; Chloroplasts/genetics ; Chromosome Mapping/methods ; Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Genome, Plant/*genetics ; Mitochondria/*genetics ; Multigene Family/genetics ; Nelumbo/*genetics ; Phylogeny ; RNA Editing/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {Nelumbo nucifera is an evolutionary relic from the Late Cretaceous period. Sequencing the N. nucifera mitochondrial genome is important for elucidating the evolutionary characteristics of basal eudicots. Here, the N. nucifera mitochondrial genome was sequenced using single molecule real-time sequencing technology (SMRT), and the mitochondrial genome map was constructed after de novo assembly and annotation. The results showed that the 524,797-bp N. nucifera mitochondrial genome has a total of 63 genes, including 40 protein-coding genes, three rRNA genes and 20 tRNA genes. Fifteen collinear gene clusters were conserved across different plant species. Approximately 700 RNA editing sites in the protein-coding genes were identified. Positively selected genes were identified with selection pressure analysis. Nineteen chloroplast-derived fragments were identified, and seven tRNAs were derived from the chloroplast. These results suggest that the N. nucifera mitochondrial genome retains evolutionarily conserved characteristics, including ancient gene content and gene clusters, high levels of RNA editing, and low levels of chloroplast-derived fragment insertions. As the first publicly available basal eudicot mitochondrial genome, the N. nucifera mitochondrial genome facilitates further analysis of the characteristics of basal eudicots and provides clues of the evolutionary trajectory from basal angiosperms to advanced eudicots.}, }
@article {pmid27436903, year = {2016}, author = {Käser, S and Oeljeklaus, S and Týč, J and Vaughan, S and Warscheid, B and Schneider, A}, title = {Outer membrane protein functions as integrator of protein import and DNA inheritance in mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {31}, pages = {E4467-75}, pmid = {27436903}, issn = {1091-6490}, mesh = {Amino Acid Sequence ; Carrier Proteins/genetics/metabolism ; Cell Line ; DNA, Mitochondrial/genetics/*metabolism ; DNA, Protozoan/genetics/metabolism ; Flagella/metabolism ; Genome, Mitochondrial/genetics ; Mitochondrial Membrane Transport Proteins/genetics/*metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/genetics/*metabolism ; Protein Transport/genetics ; Protozoan Proteins/genetics/*metabolism ; RNA Interference ; Sequence Homology, Amino Acid ; Trypanosoma brucei brucei/cytology/genetics/*metabolism ; }, abstract = {Trypanosomatids are one of the earliest diverging eukaryotes that have fully functional mitochondria. pATOM36 is a trypanosomatid-specific essential mitochondrial outer membrane protein that has been implicated in protein import. Changes in the mitochondrial proteome induced by ablation of pATOM36 and in vitro assays show that pATOM36 is required for the assembly of the archaic translocase of the outer membrane (ATOM), the functional analog of the TOM complex in other organisms. Reciprocal pull-down experiments and immunofluorescence analyses demonstrate that a fraction of pATOM36 interacts and colocalizes with TAC65, a previously uncharacterized essential component of the tripartite attachment complex (TAC). The TAC links the single-unit mitochondrial genome to the basal body of the flagellum and mediates the segregation of the replicated mitochondrial genomes. RNAi experiments show that pATOM36, in line with its dual localization, is not only essential for ATOM complex assembly but also for segregation of the replicated mitochondrial genomes. However, the two functions are distinct, as a truncated version of pATOM36 lacking the 75 C-terminal amino acids can rescue kinetoplast DNA missegregation but not the lack of ATOM complex assembly. Thus, pATOM36 has a dual function and integrates mitochondrial protein import with mitochondrial DNA inheritance.}, }
@article {pmid27436151, year = {2016}, author = {Leeder, WM and Hummel, NF and Göringer, HU}, title = {Multiple G-quartet structures in pre-edited mRNAs suggest evolutionary driving force for RNA editing in trypanosomes.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {29810}, pmid = {27436151}, issn = {2045-2322}, mesh = {Base Sequence ; DNA Replication ; Evolution, Molecular ; *G-Quadruplexes ; Gene Expression Regulation ; Mitochondria/genetics/metabolism ; Models, Molecular ; *RNA Editing ; RNA Precursors/*chemistry/genetics ; RNA, Protozoan/*chemistry/genetics ; Trypanosoma/classification/*genetics ; Trypanosoma brucei brucei/genetics ; }, abstract = {Mitochondrial transcript maturation in African trypanosomes requires a U-nucleotide specific RNA editing reaction. In its most extreme form hundreds of U's are inserted into and deleted from primary transcripts to generate functional mRNAs. Unfortunately, both origin and biological role of the process have remained enigmatic. Here we report a so far unrecognized structural feature of pre-edited mRNAs. We demonstrate that the cryptic pre-mRNAs contain numerous clustered G-nt, which fold into G-quadruplex (GQ) structures. We identified 27 GQ's in the different pre-mRNAs and demonstrate a positive correlation between the steady state abundance of guide (g)RNAs and the sequence position of GQ-elements. We postulate that the driving force for selecting G-rich sequences lies in the formation of DNA/RNA hybrid G-quadruplex (HQ) structures between the pre-edited transcripts and the non-template strands of mitochondrial DNA. HQ's are transcription termination/replication initiation sites and thus guarantee an unperturbed replication of the mt-genome. This is of special importance in the insect-stage of the parasite. In the transcription-on state, the identified GQ's require editing as a GQ-resolving activity indicating a link between replication, transcription and RNA editing. We propose that the different processes have coevolved and suggest the parasite life-cycle and the single mitochondrion as evolutionary driving forces.}, }
@article {pmid27427438, year = {2016}, author = {Patil, TS and Tamboli, AS and Patil, SM and Bhosale, AR and Govindwar, SP and Muley, DV}, title = {Relative profile analysis of molecular markers for identification and genetic discrimination of loaches (Pisces, Nemacheilidae).}, journal = {Comptes rendus biologies}, volume = {339}, number = {9-10}, pages = {364-370}, doi = {10.1016/j.crvi.2016.06.001}, pmid = {27427438}, issn = {1768-3238}, mesh = {Alleles ; Animals ; Classification ; Cypriniformes/*genetics ; DNA/genetics ; DNA Barcoding, Taxonomic ; Gene Frequency ; Genetic Markers/*genetics ; Genetic Variation ; Heterozygote ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic/genetics ; Polymorphism, Restriction Fragment Length ; Species Specificity ; }, abstract = {Genus Nemacheilus, Nemachilichthys and Schistura belong to the family Nemacheilidae of the order Cypriniformes. The present investigation was undertaken to observe genetic diversity, phylogenetic relationship and to develop a molecular-based tool for taxonomic identification. For this purpose, four different types of molecular markers were utilized in which 29 random amplified polymorphic DNA (RAPD), 25 inter-simple sequence repeat (ISSR) markers, and 10 amplified fragment length polymorphism (AFLP) marker sets were screened and mitochondrial COI gene was sequenced. This study added COI barcodes for the identification of Nemacheilus anguilla, Nemachilichthys rueppelli and Schistura denisoni. RAPD showed higher polymorphism (100%) than the ISSR (93.75-100%) and AFLP (93.86-98.96%). The polymorphic information content (PIC), heterozygosity, multiplex ratio, and gene diversity was observed highest for AFLP primers, whereas the major allele frequency was observed higher for RAPD (0.5556) and lowest for AFLP (0.1667). The COI region of all individuals was successfully amplified and sequenced, which gave a 100% species resolution.}, }
@article {pmid27418428, year = {2016}, author = {Manunza, A and Amills, M and Noce, A and Cabrera, B and Zidi, A and Eghbalsaied, S and de Albornoz, EC and Portell, M and Mercadé, A and Sànchez, A and Balteanu, V}, title = {Romanian wild boars and Mangalitza pigs have a European ancestry and harbour genetic signatures compatible with past population bottlenecks.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {29913}, pmid = {27418428}, issn = {2045-2322}, mesh = {Animals ; Genetic Variation ; *Genetics, Population ; Genome ; Heterozygote ; Homozygote ; Mitochondria/genetics ; *Phylogeny ; Romania ; Sus scrofa/*genetics ; }, abstract = {We aimed to analyse the genetic diversity of Romanian wild boars and to compare it with that from other wild boar and pig populations from Europe and Asia. Partial sequencing of the mitochondrial encoded cytochrome b (MT-CYB) gene from 36 Romanian wild boars and 36 domestic pigs (Mangalitza, Bazna and Vietnamese breeds) showed that the diversity of Romanian wild boars and Mangalitza pigs is fairly reduced, and that most of the members of these two populations share a common MT-CYB haplotype. Besides, in strong contrast with the Bazna animals, Romanian wild boars and Mangalitza swine did not carry Asian variants at the MT-CYB locus. The autosomal genotyping of 18 Romanian wild boars with the Illumina Porcine SNP60 BeadChip revealed that their genetic background is fundamentally European, even though signs of a potential Near Eastern ancestry (~25%) were detectable at K = 4 (the most significant number of clusters), but not at higher K-values. Admixture analysis also showed that two wild boars are of a hybrid origin, which could be explained by the mating of feral animals with domestic pigs. Finally, a number of Romanian wild boars displayed long runs of homozygosity, an observation that is consistent with the occurrence of past population bottlenecks and the raise of inbreeding possibly due to overhunting or to the outbreak of infectious diseases.}, }
@article {pmid27412285, year = {2016}, author = {Teulier, L and Weber, JM and Crevier, J and Darveau, CA}, title = {Proline as a fuel for insect flight: enhancing carbohydrate oxidation in hymenopterans.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1834}, pages = {}, pmid = {27412285}, issn = {1471-2954}, mesh = {Animals ; Bees/*physiology ; *Carbohydrate Metabolism ; *Flight, Animal ; Hemolymph/chemistry ; Oxidation-Reduction ; Proline/*chemistry ; Wasps/*physiology ; }, abstract = {Bees are thought to be strict users of carbohydrates as metabolic fuel for flight. Many insects, however, have the ability to oxidize the amino acid proline at a high rate, which is a unique feature of this group of animals. The presence of proline in the haemolymph of bees and in the nectar of plants led to the hypothesis that plants may produce proline as a metabolic reward for pollinators. We investigated flight muscle metabolism of hymenopteran species using high-resolution respirometry performed on permeabilized muscle fibres. The muscle fibres of the honeybee, Apis mellifera, do not have a detectable capacity to oxidize proline, as those from the migratory locust, Locusta migratoria, used here as an outgroup representative. The closely related bumblebee, Bombus impatiens, can oxidize proline alone and more than doubles its respiratory capacity when proline is combined with carbohydrate-derived substrates. A distant wasp species, Vespula vulgaris, exhibits the same metabolic phenotype as the bumblebee, suggesting that proline oxidation is common in hymenopterans. Using a combination of mitochondrial substrates and inhibitors, we further show that in B. impatiens, proline oxidation provides reducing equivalents and electrons directly to the electron transport system. Together, these findings demonstrate that some bee and wasp species can greatly enhance the oxidation of carbohydrates using proline as fuel for flight.}, }
@article {pmid27395200, year = {2016}, author = {Fu, Z and Toda, MJ and Li, NN and Zhang, YP and Gao, JJ}, title = {A new genus of anthophilous drosophilids, Impatiophila (Diptera, Drosophilidae): morphology, DNA barcoding and molecular phylogeny, with descriptions of thirty-nine new species.}, journal = {Zootaxa}, volume = {4120}, number = {1}, pages = {1-100}, doi = {10.11646/zootaxa.4120.1.1}, pmid = {27395200}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; China ; DNA Barcoding, Taxonomic ; Drosophilidae/*anatomy &amp; histology/*classification/genetics/growth &amp; development ; Ecosystem ; Female ; Larva/anatomy &amp; histology/classification/genetics/growth &amp; development ; Male ; Mitochondria/genetics ; Organ Size ; *Phylogeny ; }, abstract = {Breeding habits of essential dependence on flowers for larval food resources have evolved repeatedly in separate lineages of the Drosophilidae. However, flowers of Impatiens L. have never been recognized as hosts for drosophilid flies until recently: two Hirtodrosophila species, H. actinia (Okada) and H. yapingi Gao, were found feeding and breeding on Impatiens flowers. During our recent field surveys in central and southern China, a great number of drosophilid flies morphologically resembling the two species were collected, almost exclusively from flowers of Impatiens (family Balsaminaceae) and the family Gesneriaceae. In the present study, these specimens were identified on the basis of morphological characters and/or partial DNA sequences of the mitochondrial COI (cytochrome c oxidase subunit I gene, used as a barcoding marker). As a result, 39 new species were recognized. We then reconstructed the phylogenetic relationships among most of them, based on concatenated DNA sequences (3047 nucleotide sites) of two mitochondrial (COI and COII, i.e., cytochrome c oxidase subunits I and II, respectively) and three nuclear genes (ATPsyn-alpha, alphaTub84B and Hsc70cb, i.e., ATP synthase alpha, alpha-Tubulin at 84B and Hsc70Cb isoform H, respectively). In the resulting Bayesian and ML (maximum likelihood) trees, three well-supported clades were recognized, with a few species having remained uncertain for their phylogenetic positions. We also conducted a cladistic analysis with data of adult morphological characters to investigate the phylogenetic positions of a few species of which DNA sequence data were not available, and to investigate the classification of species groups with definition of their diagnoses. In consequence, we established a new genus, Impatiophila, for the species visiting flowers of Impatiens and Gesneriaceae, described all the new species, and revised the taxonomy of some known species.}, }
@article {pmid27385510, year = {2016}, author = {Slocinska, M and Barylski, J and Jarmuszkiewicz, W}, title = {Uncoupling proteins of invertebrates: A review.}, journal = {IUBMB life}, volume = {68}, number = {9}, pages = {691-699}, doi = {10.1002/iub.1535}, pmid = {27385510}, issn = {1521-6551}, mesh = {Amino Acid Sequence/genetics ; Animals ; Invertebrates/*genetics/metabolism ; Mitochondrial Membranes/*metabolism ; Mitochondrial Uncoupling Proteins/*genetics/metabolism ; Oxidative Stress/genetics ; Phylogeny ; }, abstract = {Uncoupling proteins (UCPs) mediate inducible proton conductance in the mitochondrial inner membrane. Herein, we summarize our knowledge regarding UCPs in invertebrates. Since 2001, the presence of UCPs has been demonstrated in nematodes, mollusks, amphioxi, and insects. We discuss the following important issues concerning invertebrate UCPs: their evolutionary relationships, molecular and functional properties, and physiological impact. Evolutionary analysis indicates that the branch of vertebrate and invertebrate UCP4-5 diverged early in the evolutionary process prior to the divergence of the animal groups. Several proposed physiological roles of invertebrate UCPs are energy control, metabolic balance, and preventive action against oxidative stress. © 2016 IUBMB Life, 68(9):691-699, 2016.}, }
@article {pmid27383787, year = {2016}, author = {Wallace, DC}, title = {Genetics: Mitochondrial DNA in evolution and disease.}, journal = {Nature}, volume = {535}, number = {7613}, pages = {498-500}, pmid = {27383787}, issn = {1476-4687}, support = {R01 NS021328/NS/NINDS NIH HHS/United States ; R01 NS070298/NS/NINDS NIH HHS/United States ; R01 OD010944/OD/NIH HHS/United States ; }, mesh = {*Biological Evolution ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genetics, Population ; Humans ; Mitochondria/genetics ; }, }
@article {pmid27376282, year = {2016}, author = {Deng, Y and Zhang, Q and Ming, R and Lin, L and Lin, X and Lin, Y and Li, X and Xie, B and Wen, Z}, title = {Analysis of the Mitochondrial Genome in Hypomyces aurantius Reveals a Novel Twintron Complex in Fungi.}, journal = {International journal of molecular sciences}, volume = {17}, number = {7}, pages = {}, pmid = {27376282}, issn = {1422-0067}, mesh = {*Genome, Mitochondrial ; Hypocreales/*genetics ; Introns ; Mitochondria/genetics ; Mitochondrial Proteins/classification/metabolism ; Nucleic Acid Conformation ; Open Reading Frames ; Phylogeny ; RNA, Transfer/chemistry/genetics/metabolism ; }, abstract = {Hypomyces aurantius is a mycoparasite that causes cobweb disease, a most serious disease of cultivated mushrooms. Intra-species identification is vital for disease control, however the lack of genomic data makes development of molecular markers challenging. Small size, high copy number, and high mutation rate of fungal mitochondrial genome makes it a good candidate for intra and inter species differentiation. In this study, the mitochondrial genome of H. H.a0001 was determined from genomic DNA using Illumina sequencing. The roughly 72 kb genome shows all major features found in other Hypocreales: 14 common protein genes, large and small subunit rRNAs genes and 27 tRNAs genes. Gene arrangement comparison showed conserved gene orders in Hypocreales mitochondria are relatively conserved, with the exception of Acremonium chrysogenum and Acremonium implicatum. Mitochondrial genome comparison also revealed that intron length primarily contributes to mitogenome size variation. Seventeen introns were detected in six conserved genes: five in cox1, four in rnl, three in cob, two each in atp6 and cox3, and one in cox2. Four introns were found to contain two introns or open reading frames: cox3-i2 is a twintron containing two group IA type introns; cox2-i1 is a group IB intron encoding two homing endonucleases; and cox1-i4 and cox1-i3 both contain two open reading frame (ORFs). Analyses combining secondary intronic structures, insertion sites, and similarities of homing endonuclease genes reveal two group IA introns arranged side by side within cox3-i2. Mitochondrial data for H. aurantius provides the basis for further studies relating to population genetics and species identification.}, }
@article {pmid27372872, year = {2016}, author = {Mazzocca, A and Ferraro, G and Misciagna, G and Carr, BI}, title = {A systemic evolutionary approach to cancer: Hepatocarcinogenesis as a paradigm.}, journal = {Medical hypotheses}, volume = {93}, number = {}, pages = {132-137}, doi = {10.1016/j.mehy.2016.05.027}, pmid = {27372872}, issn = {1532-2777}, mesh = {Animals ; *Biological Evolution ; Carcinogenesis ; Carcinoma, Hepatocellular/*pathology ; Cell Differentiation ; Cell Nucleus/metabolism ; Cell Proliferation ; DNA, Mitochondrial/metabolism ; Evolution, Molecular ; Fibrosis ; Glycolysis ; Humans ; Inflammation ; Liver/pathology ; Liver Neoplasms/*pathology ; Mitochondria/metabolism ; Models, Theoretical ; Mutation ; Phenotype ; Systems Biology ; Thermodynamics ; }, abstract = {The systemic evolutionary theory of cancer pathogenesis posits that cancer is generated by the de-emergence of the eukaryotic cell system and by the re-emergence of its archaea (genetic material and cytoplasm) and prokaryotic (mitochondria) subsystems with an uncoordinated behavior. This decreased coordination can be caused by a change in the organization of the eukaryote environment (mainly chronic inflammation), damage to mitochondrial DNA and/or to its membrane composition by many agents (e.g. viruses, chemicals, hydrogenated fatty acids in foods) or damage to nuclear DNA that controls mitochondrial energy production or metabolic pathways, including glycolysis. Here, we postulate that the two subsystems (the evolutionarily inherited archaea and the prokaryote) in a eukaryotic differentiated cell are well integrated, and produce the amount of clean energy that is constantly required to maintain the differentiated status. Conversely, when protracted injuries impair cell or tissue organization, the amount of energy necessary to maintain cell differentiation can be restricted, and this may cause gradual de-differentiation of the eukaryotic cell over time. In cirrhotic liver, for example, this process can be favored by reduced oxygen availability to the organ due to an altered vasculature and the fibrotic barrier caused by the disease. Thus, hepatocarcinogenesis is an ideal example to support our hypothesis. When cancer arises, the pre-eukaryote subsystems become predominant, as shown by the metabolic alterations of cancer cells (anaerobic glycolysis and glutamine utilization), and by their capacity for proliferation and invasion, resembling the primitive symbiotic components of the eukaryotic cell.}, }
@article {pmid27371858, year = {2016}, author = {Okamoto, S and Inai, T and Miyakawa, I}, title = {Morphology of mitochondrial nucleoids in respiratory-deficient yeast cells varies depending on the unit length of the mitochondrial DNA sequence.}, journal = {FEMS yeast research}, volume = {16}, number = {5}, pages = {}, doi = {10.1093/femsyr/fow055}, pmid = {27371858}, issn = {1567-1364}, mesh = {DNA, Mitochondrial/genetics/*ultrastructure ; *Electron Transport ; Green Fluorescent Proteins/analysis ; Indoles/analysis ; Microscopy, Fluorescence ; Mitochondria/*ultrastructure ; Saccharomyces cerevisiae/*metabolism/*ultrastructure ; Staining and Labeling ; }, abstract = {We investigated the morphology of mitochondrial nucleoids (mt-nucleoids) and mitochondria in Saccharomyces cerevisiae rho(+) and rho(-) cells with DAPI staining and mitochondria-targeted GFP. Whereas the mt-nucleoids appeared as strings of beads in wild-type rho(+) cells at log phase, the mt-nucleoids in hypersuppressive rho(-) cells (HS40 rho(-) cells) appeared as distinct punctate structures. In order to elucidate whether the punctate mt-nucleoids are common to other rho(-) cells, we observed the mt-nucleoids in rho(-) strains that retain different unit lengths of the mitochondrial DNA (mtDNA) sequence. As a result, rho(-) cells that have long mtDNA sequences, of more than 30 kb, had mt-nucleoids with a strings-of-beads appearance in tubular mitochondria. In contrast, rho(-) cells that have short mtDNA sequences, of <1 kb, had punctate mt-nucleoids in tubular mitochondria. This indicates that the morphology of mt-nucleoids in rho(-) cells significantly varies depending on the unit length of their mtDNA sequence. Analyses of mt-nucleoids suggest that the punctate mt-nucleoids in HS40 rho(-) cells consist of concatemeric mtDNAs and oligomeric circular mtDNAs associated with Abf2p and other nucleoid proteins.}, }
@article {pmid27369454, year = {2016}, author = {Hosner, PA and Braun, EL and Kimball, RT}, title = {Rapid and recent diversification of curassows, guans, and chachalacas (Galliformes: Cracidae) out of Mesoamerica: Phylogeny inferred from mitochondrial, intron, and ultraconserved element sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {102}, number = {}, pages = {320-330}, doi = {10.1016/j.ympev.2016.06.006}, pmid = {27369454}, issn = {1095-9513}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/chemistry/genetics/metabolism ; Eukaryotic Initiation Factor-2/chemistry/genetics/metabolism ; Fossils/history ; Galliformes/*classification/genetics ; Genetic Loci ; History, Ancient ; Introns ; Mitochondria/*genetics ; Mitochondrial Proton-Translocating ATPases/chemistry/genetics/metabolism ; NADH Dehydrogenase/chemistry/genetics/metabolism ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The Cracidae (curassows, guans, and chachalacas) include some of the most spectacular and endangered Neotropical bird species. They lack a comprehensive phylogenetic hypothesis, hence their geographic origin and the history of their diversification remain unclear. We present a species-level phylogeny of Cracidae inferred from a matrix of 430 ultraconserved elements (UCEs; at least one species sampled per genus) and eight more variable loci (introns and mtDNA; all available species). We use this phylogeny along with probabilistic biogeographic modeling to test whether Gondwanan vicariance, ancient dispersal to South America, ancient dispersal from South America, or massive global cooling isolated cracids in the Neotropics. Contrary to previous estimates that extant cracids diversified in the Cretaceous, our fossil-calibrated divergence time estimates instead support that crown Cracidae originated in the late Miocene. Species-rich genera Crax, Penelope, and Ortalis began diversifying as recently as 3Mya. Biogeographic reconstructions indicate that modern cracids originated in Mesoamerica and were isolated from a widespread Laurasian ancestor, consistent with the massive global cooling hypothesis. Current South American diversity is the result of multiple colonization events following uplift of the Panamanian Isthmus, coupled with rapid diversification and evolution of secondary sympatry. Of the four major cracid lineages (curassows, chachalacas, typical guans, horned guan), the only lineage that has failed to colonize and diversify South America is the unique horned guan (Oreophasis derbianus), which is sister to curassows and chachalacas rather than typical guans.}, }
@article {pmid27350685, year = {2016}, author = {Rudra, M and Chatterjee, B and Bahadur, M}, title = {Phylogenetic relationship and time of divergence of Mus terricolor with reference to other Mus species.}, journal = {Journal of genetics}, volume = {95}, number = {2}, pages = {399-409}, pmid = {27350685}, issn = {0973-7731}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; Female ; *Genetic Speciation ; Genetic Variation ; Haplotypes ; Male ; Mice/classification/*genetics ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Mitochondrial DNA control region of Mus terricolor, three aboriginal species M. spretus, M. macedonicus, M. spicilegus; the Asian lineage M. caroli, M. cervicolor, M. cookii; and the two house mice, M. musculus domesticus and M. m. castaneus were analysed to estimate the substitution rate, phylogenetic relationship and the probable time of divergence. Results showed that M. spretus, M. caroli and M. terricolor are highly diverged from each other (caroli/terricolor = 0.146, caroli/spretus = 0.147 and terricolor/spretus = 0.122), whereas M. spretus showed less divergence with two house mice species (0.070 and 0.071). Sequence divergence between M. terricolor and the Palearctic group were found to be ranging from 0.121 to 0.134. Phylogenetic analysis by minimum evolution, neighbour-joining, unweighed pair group method with arithmetic mean and maximum parsimony showed almost similar topology. Two major clusters were found, one included the Asian lineage, M. caroli, M. cookii and M. cervicolor and the other included the house mice M. m. domesticus, M. m. castaneus and the aboriginal mice M. macedonicus and M. spicilegus along with M. spretus, forming the Palearctic clade. M. terricolor was positioned between the Palearctic and Asian clades. Results showed that Palearctic-terricolor and the Asian lineages diverged 5.47 million years ago (Mya), while M. terricolor had split around 4.63 Mya from their ancestor. M. cervicolor, M. cookii and M. caroli diverged between 4.70 and 3.36 Mya, which indicates that M. terricolor and the Asian lineages evolved simultaneously. M. spretus is expected to have diverged nearly 2.9 Mya from their most recent common ancestor.}, }
@article {pmid27350680, year = {2016}, author = {Sarswat, M and Dewan, S and Fartyal, RS}, title = {Mitochondrial DNA sequence variation in Drosophilid species (Diptera: Drosophilidae) along altitudinal gradient from Central Himalayan region of India.}, journal = {Journal of genetics}, volume = {95}, number = {2}, pages = {357-367}, pmid = {27350680}, issn = {0973-7731}, mesh = {Altitude ; Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; Drosophilidae/classification/*genetics ; Ecosystem ; Electron Transport Complex IV/*genetics ; Female ; Genetic Speciation ; Genetic Variation ; Haplotypes ; India ; Insect Proteins/*genetics ; Isoenzymes/genetics ; Male ; Mitochondria/enzymology/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Central Himalayan region of India encompasses varied ecological habitats ranging from near tropics to the mid-elevation forests dominated by cool-temperate taxa. In past, we have reported several new records and novel species from Uttarakhand state of India. Here, we assessed genetic variations in three mitochondrial genes, namely, 16S rRNA, cytochrome c oxidase subunit I and cytochrome c oxidase subunit II (COI and COII) in 26 drosophilid species collected along altitudinal transect from 550 to 2700 m above mean sea level. In the present study, overall 543 sequences were generated, 82 for 16S rRNA, 238 for COI, 223 for COII with 21, 47 and 45 mitochondrial haplotypes for 16S rRNA, COI and COII genes, respectively. Almost all species were represented by 2-3 unique mitochondrial haplotypes, depicting a significant impact of environmental heterogeneity along altitudinal gradient on genetic diversity. Also for the first time, molecular data of some rare species like Drosophila mukteshwarensis, Liodrosophila nitida, Lordiphosa parantillaria, Lordiphosa ayarpathaensis, Scaptomyza himalayana, Scaptomyza tistai, Zaprionus grandis and Stegana minuta are provided to public domains through this study.}, }
@article {pmid27349964, year = {2016}, author = {Rensch, T and Villar, D and Horvath, J and Odom, DT and Flicek, P}, title = {Mitochondrial heteroplasmy in vertebrates using ChIP-sequencing data.}, journal = {Genome biology}, volume = {17}, number = {1}, pages = {139}, pmid = {27349964}, issn = {1474-760X}, support = {WT095908//Wellcome Trust/United Kingdom ; WT098051//Wellcome Trust/United Kingdom ; //Cancer Research UK/United Kingdom ; }, mesh = {Animals ; Chromatin Immunoprecipitation ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; High-Throughput Nucleotide Sequencing ; Humans ; Mitochondria/*genetics/pathology ; Mitochondrial Diseases/*genetics/pathology ; Sequence Analysis, DNA ; Vertebrates/genetics ; }, abstract = {BACKGROUND: Mitochondrial heteroplasmy, the presence of more than one mitochondrial DNA (mtDNA) variant in a cell or individual, is not as uncommon as previously thought. It is mostly due to the high mutation rate of the mtDNA and limited repair mechanisms present in the mitochondrion. Motivated by mitochondrial diseases, much focus has been placed into studying this phenomenon in human samples and in medical contexts. To place these results in an evolutionary context and to explore general principles of heteroplasmy, we describe an integrated cross-species evaluation of heteroplasmy in mammals that exploits previously reported NGS data. Focusing on ChIP-seq experiments, we developed a novel approach to detect heteroplasmy from the concomitant mitochondrial DNA fraction sequenced in these experiments.<br><br>RESULTS: We first demonstrate that the sequencing coverage of mtDNA in ChIP-seq experiments is sufficient for heteroplasmy detection. We then describe a novel detection method for accurate detection of heteroplasmies, which also accounts for the error rate of NGS technology. Applying this method to 79 individuals from 16 species resulted in 107 heteroplasmic positions present in a total of 45 individuals. Further analysis revealed that the majority of detected heteroplasmies occur in intergenic regions.<br><br>CONCLUSION: In addition to documenting the prevalence of mtDNA in ChIP-seq data, the results of our mitochondrial heteroplasmy detection method suggest that mitochondrial heteroplasmies identified across vertebrates share similar characteristics as found for human heteroplasmies. Although largely consistent with previous studies in individual vertebrates, our integrated cross-species analysis provides valuable insights into the evolutionary dynamics of mitochondrial heteroplasmy.}, }
@article {pmid27346342, year = {2016}, author = {Lin, JLJ and Nakagawa, A and Skeen-Gaar, R and Yang, WZ and Zhao, P and Zhang, Z and Ge, X and Mitani, S and Xue, D and Yuan, HS}, title = {Oxidative Stress Impairs Cell Death by Repressing the Nuclease Activity of Mitochondrial Endonuclease G.}, journal = {Cell reports}, volume = {16}, number = {2}, pages = {279-287}, pmid = {27346342}, issn = {2211-1247}, support = {R01 GM059083/GM/NIGMS NIH HHS/United States ; R01 GM079097/GM/NIGMS NIH HHS/United States ; R35 GM118188/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Apoptosis ; Caenorhabditis elegans/cytology/*enzymology ; Caenorhabditis elegans Proteins/chemistry/*metabolism ; Crystallography, X-Ray ; Down-Regulation ; Endodeoxyribonucleases/chemistry/*metabolism ; Enzyme Stability ; Mitochondrial Proteins/chemistry/*metabolism ; Models, Molecular ; Oxidation-Reduction ; *Oxidative Stress ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Protein Structure, Quaternary ; }, abstract = {Endonuclease G (EndoG) is a mitochondrial protein that is released from mitochondria and relocated into the nucleus to promote chromosomal DNA fragmentation during apoptosis. Here, we show that oxidative stress causes cell-death defects in C. elegans through an EndoG-mediated cell-death pathway. In response to high reactive oxygen species (ROS) levels, homodimeric CPS-6-the C. elegans homolog of EndoG-is dissociated into monomers with diminished nuclease activity. Conversely, the nuclease activity of CPS-6 is enhanced, and its dimeric structure is stabilized by its interaction with the worm AIF homolog, WAH-1, which shifts to disulfide cross-linked dimers under high ROS levels. CPS-6 thus acts as a ROS sensor to regulate the life and death of cells. Modulation of the EndoG dimer conformation could present an avenue for prevention and treatment of diseases resulting from oxidative stress.}, }
@article {pmid27345956, year = {2016}, author = {Garg, SG and Martin, WF}, title = {Mitochondria, the Cell Cycle, and the Origin of Sex via a Syncytial Eukaryote Common Ancestor.}, journal = {Genome biology and evolution}, volume = {8}, number = {6}, pages = {1950-1970}, pmid = {27345956}, issn = {1759-6653}, mesh = {Adenosine Triphosphate/*genetics/metabolism ; Archaea/genetics/physiology ; Biological Evolution ; Cell Cycle/genetics ; Cytosol/physiology ; Eukaryotic Cells/physiology ; *Evolution, Molecular ; Meiosis/genetics ; Mitochondria/*genetics ; Mitosis/genetics ; Prokaryotic Cells/physiology ; Protein Interaction Maps/genetics ; *Recombination, Genetic ; }, abstract = {Theories for the origin of sex traditionally start with an asexual mitosing cell and add recombination, thereby deriving meiosis from mitosis. Though sex was clearly present in the eukaryote common ancestor, the order of events linking the origin of sex and the origin of mitosis is unknown. Here, we present an evolutionary inference for the origin of sex starting with a bacterial ancestor of mitochondria in the cytosol of its archaeal host. We posit that symbiotic association led to the origin of mitochondria and gene transfer to host's genome, generating a nucleus and a dedicated translational compartment, the eukaryotic cytosol, in which-by virtue of mitochondria-metabolic energy was not limiting. Spontaneous protein aggregation (monomer polymerization) and Adenosine Tri-phosphate (ATP)-dependent macromolecular movement in the cytosol thereby became selectable, giving rise to continuous microtubule-dependent chromosome separation (reduction division). We propose that eukaryotic chromosome division arose in a filamentous, syncytial, multinucleated ancestor, in which nuclei with insufficient chromosome numbers could complement each other through mRNA in the cytosol and generate new chromosome combinations through karyogamy. A syncytial (or coenocytic, a synonym) eukaryote ancestor, or Coeca, would account for the observation that the process of eukaryotic chromosome separation is more conserved than the process of eukaryotic cell division. The first progeny of such a syncytial ancestor were likely equivalent to meiospores, released into the environment by the host's vesicle secretion machinery. The natural ability of archaea (the host) to fuse and recombine brought forth reciprocal recombination among fusing (syngamy and karyogamy) progeny-sex-in an ancestrally meiotic cell cycle, from which the simpler haploid and diploid mitotic cell cycles arose. The origin of eukaryotes was the origin of vertical lineage inheritance, and sex was required to keep vertically evolving lineages viable by rescuing the incipient eukaryotic lineage from Muller's ratchet. The origin of mitochondria was, in this view, the decisive incident that precipitated symbiosis-specific cell biological problems, the solutions to which were the salient features that distinguish eukaryotes from prokaryotes: A nuclear membrane, energetically affordable ATP-dependent protein-protein interactions in the cytosol, and a cell cycle involving reduction division and reciprocal recombination (sex).}, }
@article {pmid27339178, year = {2016}, author = {Martin, WF and Neukirchen, S and Zimorski, V and Gould, SB and Sousa, FL}, title = {Energy for two: New archaeal lineages and the origin of mitochondria.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {38}, number = {9}, pages = {850-856}, doi = {10.1002/bies.201600089}, pmid = {27339178}, issn = {1521-1878}, mesh = {Archaea/*genetics ; *Energy Metabolism ; Eukaryota/*genetics/metabolism ; *Metagenomics ; *Mitochondria ; *Phylogeny ; }, abstract = {Metagenomics bears upon all aspects of microbiology, including our understanding of mitochondrial and eukaryote origin. Recently, ribosomal protein phylogenies show the eukaryote host lineage - the archaeal lineage that acquired the mitochondrion - to branch within the archaea. Metagenomic studies are now uncovering new archaeal lineages that branch more closely to the host than any cultivated archaea do. But how do they grow? Carbon and energy metabolism as pieced together from metagenome assemblies of these new archaeal lineages, such as the Deep Sea Archaeal Group (including Lokiarchaeota) and Bathyarchaeota, do not match the physiology of any cultivated microbes. Understanding how these new lineages live in their environment is important, and might hold clues about how mitochondria arose and how the eukaryotic lineage got started. Here we look at these exciting new metagenomic studies, what they say about archaeal physiology in modern environments, how they impact views on host-mitochondrion physiological interactions at eukaryote origin.}, }
@article {pmid27332545, year = {2016}, author = {Chiaverano, LM and Bayha, KW and Graham, WM}, title = {Local versus Generalized Phenotypes in Two Sympatric Aurelia Species: Understanding Jellyfish Ecology Using Genetics and Morphometrics.}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0156588}, pmid = {27332545}, issn = {1932-6203}, mesh = {Animals ; DNA, Intergenic/genetics ; *Ecosystem ; Electron Transport Complex IV/metabolism ; Gulf of Mexico ; Imaging, Three-Dimensional ; Mitochondria/metabolism ; Phenotype ; Phylogeny ; Protein Subunits/metabolism ; Scyphozoa/*anatomy &amp; histology/*genetics ; Spectrum Analysis ; Surface Properties ; *Sympatry ; Temperature ; }, abstract = {For individuals living in environmentally heterogeneous environments, a key component for adaptation and persistence is the extent of phenotypic differentiation in response to local environmental conditions. In order to determine the extent of environmentally induced morphological variation in a natural population distributed along environmental gradients, it is necessary to account for potential genetic differences contributing to morphological differentiation. In this study, we set out to quantify geographic morphological variation in the moon jellyfish Aurelia exposed at the extremes of a latitudinal environmental gradient in the Gulf of Mexico (GoM). We used morphological data based on 28 characters, and genetic data taken from mitochondrial cytochrome oxidase I (COI) and nuclear internal transcribed spacer 1 (ITS-1). Molecular analyses revealed the presence of two genetically distinct species of Aurelia co-occurring in the GoM: Aurelia sp. 9 and Aurelia c.f. sp. 2, named for its divergence from (for COI) and similarity to (for ITS-1) Aurelia sp. 2 (Brazil). Neither species exhibited significant population genetic structure between the Northern and the Southeastern Gulf of Mexico; however, they differed greatly in the degree of geographic morphological variation. The morphology of Aurelia sp. 9 exhibited ecophenotypic plasticity and varied significantly between locations, while morphology of Aurelia c.f. sp. 2 was geographically invariant (i.e., canalized). The plastic, generalist medusae of Aurelia sp. 9 are likely able to produce environmentally-induced, "optimal" phenotypes that confer high relative fitness in different environments. In contrast, the non-plastic generalist individuals of Aurelia c.f. sp. 2 likely produce environmentally-independent phenotypes that provide the highest fitness across environments. These findings suggest the two Aurelia lineages co-occurring in the GoM were likely exposed to different past environmental conditions (i.e., different selective pressures) and evolved different strategies to cope with environmental variation. This study highlights the importance of using genetics and morphometric data to understand jellyfish ecology, evolution and systematics.}, }
@article {pmid27329857, year = {2016}, author = {Knie, N and Grewe, F and Fischer, S and Knoop, V}, title = {Reverse U-to-C editing exceeds C-to-U RNA editing in some ferns - a monilophyte-wide comparison of chloroplast and mitochondrial RNA editing suggests independent evolution of the two processes in both organelles.}, journal = {BMC evolutionary biology}, volume = {16}, number = {1}, pages = {134}, pmid = {27329857}, issn = {1471-2148}, mesh = {Biological Evolution ; Chloroplasts/*genetics ; Cytosine ; Equisetum/classification ; Ferns/*genetics ; Magnoliopsida/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA/metabolism ; RNA Editing ; RNA, Chloroplast/genetics ; RNA, Mitochondrial ; RNA, Plant/*metabolism ; RNA, Small Nuclear/metabolism ; Uracil ; }, abstract = {BACKGROUND: RNA editing by C-to-U conversions is nearly omnipresent in land plant chloroplasts and mitochondria, where it mainly serves to reconstitute conserved codon identities in the organelle mRNAs. Reverse U-to-C RNA editing in contrast appears to be restricted to hornworts, some lycophytes, and ferns (monilophytes). A well-resolved monilophyte phylogeny has recently emerged and now allows to trace the side-by-side evolution of both types of pyrimidine exchange editing in the two endosymbiotic organelles.<br><br>RESULTS: Our study of RNA editing in four selected mitochondrial genes show a wide spectrum of divergent RNA editing frequencies including a dominance of U-to-C over the canonical C-to-U editing in some taxa like the order Schizaeales. We find that silent RNA editing leaving encoded amino acids unchanged is highly biased with more than ten-fold amounts of silent C-to-U over U-to-C edits. In full contrast to flowering plants, RNA editing frequencies are low in early-branching monilophyte lineages but increase in later emerging clades. Moreover, while editing rates in the two organelles are usually correlated, we observe uncoupled evolution of editing frequencies in fern mitochondria and chloroplasts. Most mitochondrial RNA editing sites are shared between the recently emerging fern orders whereas chloroplast editing sites are mostly clade-specific. Finally, we observe that chloroplast RNA editing appears to be completely absent in horsetails (Equisetales), the sister clade of all other monilophytes.<br><br>CONCLUSIONS: C-to-U and U-to-C RNA editing in fern chloroplasts and mitochondria follow disinct evolutionary pathways that are surprisingly different from what has previously been found in flowering plants. The results call for careful differentiation of the two types of RNA editing in the two endosymbiotic organelles in comparative evolutionary studies.}, }
@article {pmid27327899, year = {2016}, author = {Cardoso, S and Carvalho, C and Correia, SC and Seiça, RM and Moreira, PI}, title = {Alzheimer's Disease: From Mitochondrial Perturbations to Mitochondrial Medicine.}, journal = {Brain pathology (Zurich, Switzerland)}, volume = {26}, number = {5}, pages = {632-647}, pmid = {27327899}, issn = {1750-3639}, mesh = {Aging ; *Alzheimer Disease/complications/drug therapy/pathology ; Animals ; Antioxidants/*therapeutic use ; Autophagy/drug effects/physiology ; Energy Metabolism/drug effects ; *Healthy Lifestyle ; Humans ; Mitochondria/*drug effects ; Mitochondrial Diseases/metabolism/*therapy ; Oxidative Stress/drug effects ; }, abstract = {Age-related neurodegenerative diseases such as Alzheimer's disease (AD) are distressing conditions causing countless levels of suffering for which treatment is often insufficient or inexistent. Considered to be the most common cause of dementia and an incurable, progressive neurodegenerative disorder, the intricate pathogenic mechanisms of AD continue to be revealed and, consequently, an effective treatment needs to be developed. Among the diverse hypothesis that have been proposed to explain AD pathogenesis, the one concerning mitochondrial dysfunction has raised as one of the most discussed with an actual acceptance in the field. It posits that manipulating mitochondrial function and understanding the deficits that result in mitochondrial injury may help to control and/or limit the development of AD. To achieve such goal, the concept of mitochondrial medicine places itself as a promising gathering of strategies to directly manage the major insidious disturbances of mitochondrial homeostasis as well as attempts to directly or indirectly manage its consequences in the context of AD. The aim of this review is to summarize the evolution that occurred from the establishment of mitochondrial homeostasis perturbation as masterpieces in AD pathogenesis up until the development of mitochondrial medicine. Following a brief glimpse in the past and current hypothesis regarding the triad of aging, mitochondria and AD, this manuscript will address the major mechanisms currently believed to participate in above mentioned events. Both pharmacological and lifestyle interventions will also be reviewed as AD-related mitochondrial therapeutics.}, }
@article {pmid27326927, year = {2016}, author = {St-Pierre, J and Topisirovic, I}, title = {Nucleus to Mitochondria: Lost in Transcription, Found in Translation.}, journal = {Developmental cell}, volume = {37}, number = {6}, pages = {490-492}, doi = {10.1016/j.devcel.2016.06.003}, pmid = {27326927}, issn = {1878-1551}, mesh = {Animals ; Biological Evolution ; Cell Nucleus/*metabolism ; Humans ; Mitochondria/*metabolism ; Models, Biological ; *Protein Biosynthesis ; *Transcription, Genetic ; }, abstract = {Mitochondrial genes reside in the nucleus and mitochondria. In a recent paper in Nature, Couvillion et al. (2016) describe their development of a "mitoribosome profiling" approach and demonstrate that changes in expression of nuclear- and mitochondrial-encoded genes are coordinated at the level of translation during metabolic adaptation to fuel source changes.}, }
@article {pmid27306456, year = {2016}, author = {Hwang, ST and Choi, D}, title = {A novel rice protein family of OsHIGDs may be involved in early signalling of hypoxia-promoted stem growth in deepwater rice.}, journal = {Plant cell reports}, volume = {35}, number = {10}, pages = {2021-2031}, pmid = {27306456}, issn = {1432-203X}, mesh = {Amino Acid Sequence ; Cell Hypoxia/drug effects/genetics ; Ethylenes/pharmacology ; Gene Expression Regulation, Plant/drug effects ; Gene Regulatory Networks/drug effects ; Green Fluorescent Proteins/metabolism ; *Multigene Family ; Organ Specificity/drug effects/genetics ; Oryza/drug effects/genetics/*growth &amp; development/*metabolism ; Phylogeny ; Plant Proteins/chemistry/genetics/*metabolism ; Plant Stems/drug effects/*growth &amp; development/*metabolism ; Protein Binding/drug effects ; *Signal Transduction/drug effects/genetics ; Subcellular Fractions/metabolism ; Two-Hybrid System Techniques ; Water ; }, abstract = {OsHIGDs was identified as a novel hypoxia-responsive protein family. Among them, OsHIGD2 is characterized as a mitochondrial protein and is related to hypoxia signalling through interacting with mitochondrial proteins of critical functions in reducing cell damages caused by hypoxia. Recent evidence supports ethylene as a key factor in modulating plant responses to submergence stress. Meanwhile, there has been general consent that ethylene is not the only signal for the submergence-induced stem growth. In this study, we confirmed that hypoxia also promotes stem elongation in deepwater rice even in the absence of ethylene. As components of ethylene-independent hypoxia signalling, five HIGD (hypoxia-induced gene domain) protein genes were identified. Among the genes, OsHIGD2 showed the fastest and strongest induction by hypoxia as well as submergence. Co-expression analysis indicated that OsHIGD2 had a simultaneous expression pattern with fermentation-related genes, such as ADH1 (alcohol dehydrogenase 1) and PDC2 (pyruvate decarboxylase 2). Transient expression of OsHIGD2 in leaf epidermal cells of Nicotiana benthamiana provided evidence that the protein is localized to mitochondria. We further identified OsHIGD2-interacting proteins through the yeast two-hybrid assay using OsHIGD2 as bait. As a result, three mitochondrial proteins were discovered that function in the regulation of redox potential or reduction of protein damages caused by reactive oxygen species. In this report, we propose that OsHIGD2 is a mitochondrial protein which takes part in the early stage of hypoxia signalling by interacting with proteins that are related to oxygen utilization.}, }
@article {pmid27306450, year = {2016}, author = {Wang, W and Wu, Y and Messing, J}, title = {Genome-wide analysis of pentatricopeptide-repeat proteins of an aquatic plant.}, journal = {Planta}, volume = {244}, number = {4}, pages = {893-899}, pmid = {27306450}, issn = {1432-2048}, mesh = {Aquatic Organisms/*genetics/metabolism ; Araceae/*genetics/metabolism ; Cell Nucleus/genetics ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Genome, Plant/*genetics ; Magnoliopsida/classification/genetics/metabolism ; Multigene Family ; Plant Proteins/*genetics/metabolism ; Repetitive Sequences, Amino Acid/*genetics ; }, abstract = {A large proportion of genes in plant genomes are organized as gene families. Whereas most gene families in the aquative plant Spirodela are reduced in their copy number, the PPR gene family is expanded, which match the RNA editing sites in organelles, providing us with new insights in the evolution of flowering plants. Pentatricopeptide-repeat proteins (PPRs) are nuclear-encoded proteins that are targeted to mitochondria and plastids to stabilize and edit mRNA transcribed from organellar genomes. They have been described for many terrestrial plant species from a diverse spectrum of sequenced genomes. To further increase our understanding of the evolution of this gene family across angiosperms, we analyzed the PPR genes in the aquatic species Spirodela polyrhiza in the order of the Alismatales (monocotyledonous plants). Because we had generated next generation sequencing data from transcripts and had sequenced the genome of Spirodela polyrhiza, we were able to identify its PPR genes and determine the level of their expression. In total, we could identify 556 PPR proteins, of which 238 members belong to the P (P motif) subfamily that is mainly involved in RNA stabilization and 318 ones to the PLS (P, Longer P, shorter P motif) subfamily responsible for RNA editing. Compared to other angiosperms, this is a large increase in the copy number of the PLS-PPRs subfamily and the expansion correlates with the increase of the number of RNA editing sites of organellar transcripts. Expression of PPR was generally stable even during growing and dormant stages, indicating that their function was critical throughout development. However, PPRs, especially those of the PLS subfamily, were expressed at relatively low levels, suggesting a delicate fine-tuning of its trans-acting function in the post-transcriptional regulation of gene expression. Thus, understanding PPR evolution and expression will help decipher the PPR code for their binding sites, which could genetically engineer RNA-binding proteins toward desired sequence.}, }
@article {pmid27301885, year = {2016}, author = {Preston, JL and Royall, AE and Randel, MA and Sikkink, KL and Phillips, PC and Johnson, EA}, title = {High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq).}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {464}, pmid = {27301885}, issn = {1471-2164}, support = {P50 GM098911/GM/NIGMS NIH HHS/United States ; T32 GM007413/GM/NIGMS NIH HHS/United States ; }, mesh = {*Alleles ; Escherichia coli/genetics ; Gene Frequency ; Gene Library ; High-Throughput Nucleotide Sequencing/*methods/standards ; Mutation ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Analysis, DNA/methods/standards ; }, abstract = {BACKGROUND: Polymorphic loci exist throughout the genomes of a population and provide the raw genetic material needed for a species to adapt to changes in the environment. The minor allele frequencies of rare Single Nucleotide Polymorphisms (SNPs) within a population have been difficult to track with Next-Generation Sequencing (NGS), due to the high error rate of standard methods such as Illumina sequencing.<br><br>RESULTS: We have developed a wet-lab protocol and variant-calling method that identifies both sequencing and PCR errors, called Paired-End Low Error Sequencing (PELE-Seq). To test the specificity and sensitivity of the PELE-Seq method, we sequenced control E. coli DNA libraries containing known rare alleles present at frequencies ranging from 0.2-0.4&#xa0;% of the total reads. PELE-Seq had higher specificity and sensitivity than standard libraries. We then used PELE-Seq to characterize rare alleles in a Caenorhabditis remanei nematode worm population before and after laboratory adaptation, and found that minor and rare alleles can undergo large changes in frequency during lab-adaptation.<br><br>CONCLUSION: We have developed a method of rare allele detection that mitigates both sequencing and PCR errors, called PELE-Seq. PELE-Seq was evaluated using control E. coli populations and was then used to compare a wild C. remanei population to a lab-adapted population. The PELE-Seq method is ideal for investigating the dynamics of rare alleles in a broad range of reduced-representation sequencing methods, including targeted amplicon sequencing, RAD-Seq, ddRAD, and GBS. PELE-Seq is also well-suited for whole genome sequencing of mitochondria and viruses, and for high-throughput rare mutation screens.}, }
@article {pmid27297032, year = {2016}, author = {Safari, R and Salimi, R and Tunca, Z and Ozerdem, A and Ceylan, D and Sakizli, M}, title = {Mutation/SNP analysis in EF-hand calcium binding domain of mitochondrial Ca[Formula: see text] uptake 1 gene in bipolar disorder patients.}, journal = {Journal of integrative neuroscience}, volume = {15}, number = {2}, pages = {163-173}, doi = {10.1142/S0219635216500096}, pmid = {27297032}, issn = {0219-6352}, mesh = {Adult ; Bipolar Disorder/*genetics ; Calcium-Binding Proteins/*genetics ; Cation Transport Proteins/*genetics ; Family ; Female ; Genetic Association Studies ; Genetic Predisposition to Disease ; Humans ; Male ; Mitochondrial Membrane Transport Proteins/*genetics ; *Mutation ; Phylogeny ; *Polymorphism, Single Nucleotide ; Sequence Homology, Amino Acid ; }, abstract = {Calcium signaling is important for synaptic plasticity, generation of brain rhythms, regulating neuronal excitability, data processing and cognition. Impairment in calcium homeostasis contributed to the development of psychiatric disorders such as bipolar disorder (BP). MCU is the most important calcium transporter in mitochondria inner membrane responsible for influx of Ca[Formula: see text]. MICU1 is linked with MCU and has two canonical EF hands that are vital for its activity and regulates MCU-mediated Ca[Formula: see text] influx. In the current study, we aimed to investigate the role of genetic alteration of EF hand calcium binding motifs of MICU1 on the development of BP. We examined patients with BP, first degree relatives of these patients and healthy volunteers for mutations and polymorphisms in EF hand calcium binding motifs of MICU1. The result showed no SNP/mutation in BP patients, in healthy subjects and in first degree relatives. Additionally, alignment of the EF hand calcium binding regions among species (Gallus-gallus, Canis-lupus-familiaris, Bos-taurus, Mus-musculus, Rattus-norvegicus, Pan-troglodytes, Homosapiens and Danio-rerio) showed exactly the same amino acids (DLNGDGEVDMEE and DCDGNGELSNKE) except in one of the calcium binding domain of Danio-rerio that there was only one difference; leucine instead of Methionine. Our results showed that the SNP on EF-hand Ca[Formula: see text] binding domains of MICU1 gene had no effect in phenotypic characters of BP patients.}, }
@article {pmid27289532, year = {2016}, author = {Hu, JJ and Liu, TT and Liu, Q and Esch, GW and Chen, JQ and Huang, S and Wen, T}, title = {Prevalence, morphology, and molecular characteristics of Sarcocystis spp. in domestic goats (Capra hircus) from Kunming, China.}, journal = {Parasitology research}, volume = {115}, number = {10}, pages = {3973-3981}, pmid = {27289532}, issn = {1432-1955}, mesh = {Animals ; China/epidemiology ; Cyclooxygenase 1/genetics ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Genetic Variation ; Goat Diseases/*epidemiology/parasitology ; Goats ; Mitochondria/enzymology ; Muscles/parasitology ; Phylogeny ; Prevalence ; Protozoan Proteins/genetics ; Sarcocystis/*classification/enzymology/genetics/ultrastructure ; Sarcocystosis/epidemiology/parasitology/*veterinary ; Sequence Analysis, DNA/veterinary ; }, abstract = {Despite the importance of worldwide goat production, little is known about the prevalence of Sarcocystis spp. in domestic goats (Capra hircus) in China. The aims of the present study were to determine prevalence of Sarcocystis spp. in domestic goats in Kunming, China, as well as to identify parasite species based on morphological characteristics and DNA sequence analysis. Only microscopic sarcocysts of Sarcocystis spp. were detected in 174 of 225 goats (77.3 %). By light and transmission electron microscopy, two species, i.e., Sarcocystis capracanis and Sarcocystis hircicanis, were identified. Two sarcocysts from each of the two species were randomly selected for DNA extraction; the 18S rRNA gene (18S rRNA), the 28S rRNA gene (28S rRNA), and the mitochondrial cytochrome c oxidase subunit 1 (cox1) were amplified by the polymerase chain reaction (PCR) and subsequently sequenced. The results were compared with other previously sequenced Sarcocystis species retrieved from GenBank. There was little sequence variation between two isolates of the same species. S. capracanis was most closely related with Sarcocystis tenella; 18S rRNA, 28S rRNA, and mitochondrial cox1 sequences shared identities of 95.7-99.1, 95.3, and 92.3-93.2 % with those of S. tenella, respectively. Thus, mitochondrial cox1 sequences seem to perform better than 18S rRNA sequences or 28S rRNA sequences for identification of the two species. S. hircicanis was most closely related to Sarcocystis arieticanis, i.e., 18S rRNA and 28S rRNA sequences of the former species shared 97.2-97.4 and 95.6-96.1 % identities with those of latter, respectively. Phylogenetic analysis inferred from the three genetic markers yielded similar results and indicated the two species were within a group of Sarcocystis species with canines as known, or presumed, definitive hosts.}, }
@article {pmid27289097, year = {2016}, author = {Degli Esposti, M}, title = {Late Mitochondrial Acquisition, Really?.}, journal = {Genome biology and evolution}, volume = {8}, number = {6}, pages = {2031-2035}, pmid = {27289097}, issn = {1759-6653}, mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; Mitochondria/*genetics ; Proteobacteria/genetics ; }, abstract = {This article provides a timely critique of a recent Nature paper by Pittis and Gabaldón that has suggested a late origin of mitochondria in eukaryote evolution. It shows that the inferred ancestry of many mitochondrial proteins has been incorrectly assigned by Pittis and Gabaldón to bacteria other than the aerobic proteobacteria from which the ancestor of mitochondria originates, thereby questioning the validity of their suggestion that mitochondrial acquisition may be a late event in eukaryote evolution. The analysis and approach presented here may guide future studies to resolve the true ancestry of mitochondria.}, }
@article {pmid27280585, year = {2016}, author = {Leger, MM and Eme, L and Hug, LA and Roger, AJ}, title = {Novel Hydrogenosomes in the Microaerophilic Jakobid Stygiella incarcerata.}, journal = {Molecular biology and evolution}, volume = {33}, number = {9}, pages = {2318-2336}, pmid = {27280585}, issn = {1537-1719}, support = {MOP-142349//CIHR/Canada ; }, mesh = {Anaerobiosis ; Biological Evolution ; Eukaryota/*genetics/metabolism ; Evolution, Molecular ; Intracellular Membranes/metabolism ; Mitochondria/metabolism ; Organelles/*metabolism ; Phylogeny ; Proteome ; Protozoan Proteins/genetics ; Sequence Analysis, RNA/methods ; Sulfolobaceae/genetics ; }, abstract = {Mitochondrion-related organelles (MROs) have arisen independently in a wide range of anaerobic protist lineages. Only a few of these organelles and their functions have been investigated in detail, and most of what is known about MROs comes from studies of parasitic organisms such as the parabasalid Trichomonas vaginalis Here, we describe the MRO of a free-living anaerobic jakobid excavate, Stygiella incarcerata We report an RNAseq-based reconstruction of S. incarcerata's MRO proteome, with an associated biochemical map of the pathways predicted to be present in this organelle. The pyruvate metabolism and oxidative stress response pathways are strikingly similar to those found in the MROs of other anaerobic protists, such as Pygsuia and Trichomonas This elegant example of convergent evolution is suggestive of an anaerobic biochemical 'module' of prokaryotic origins that has been laterally transferred among eukaryotes, enabling them to adapt rapidly to anaerobiosis. We also identified genes corresponding to a variety of mitochondrial processes not found in Trichomonas, including intermembrane space components of the mitochondrial protein import apparatus, and enzymes involved in amino acid metabolism and cardiolipin biosynthesis. In this respect, the MROs of S. incarcerata more closely resemble those of the much more distantly related free-living organisms Pygsuia biforma and Cantina marsupialis, likely reflecting these organisms' shared lifestyle as free-living anaerobes.}, }
@article {pmid27271616, year = {2016}, author = {Veenman, L and Vainshtein, A and Yasin, N and Azrad, M and Gavish, M}, title = {Tetrapyrroles as Endogenous TSPO Ligands in Eukaryotes and Prokaryotes: Comparisons with Synthetic Ligands.}, journal = {International journal of molecular sciences}, volume = {17}, number = {6}, pages = {}, pmid = {27271616}, issn = {1422-0067}, mesh = {Animals ; Binding Sites ; Biological Evolution ; Biological Transport ; Brain Diseases/metabolism ; Eukaryota/*metabolism ; Humans ; Insecta/metabolism ; Ligands ; Plants/metabolism ; Prokaryotic Cells/*metabolism ; Protein Binding ; Protoporphyrins/chemistry/metabolism ; Receptors, GABA/chemistry/genetics/*metabolism ; Structure-Activity Relationship ; Tetrapyrroles/chemistry/*metabolism ; }, abstract = {The 18 kDa translocator protein (TSPO) is highly 0conserved in eukaryotes and prokaryotes. Since its discovery in 1977, numerous studies established the TSPO's importance for life essential functions. For these studies, synthetic TSPO ligands typically are applied. Tetrapyrroles present endogenous ligands for the TSPO. Tetrapyrroles are also evolutionarily conserved and regulate multiple functions. TSPO and tetrapyrroles regulate each other. In animals TSPO-tetrapyrrole interactions range from effects on embryonic development to metabolism, programmed cell death, response to stress, injury and disease, and even to life span extension. In animals TSPOs are primarily located in mitochondria. In plants TSPOs are also present in plastids, the nuclear fraction, the endoplasmic reticulum, and Golgi stacks. This may contribute to translocation of tetrapyrrole intermediates across organelles' membranes. As in animals, plant TSPO binds heme and protoporphyrin IX. TSPO-tetrapyrrole interactions in plants appear to relate to development as well as stress conditions, including salt tolerance, abscisic acid-induced stress, reactive oxygen species homeostasis, and finally cell death regulation. In bacteria, TSPO is important for switching from aerobic to anaerobic metabolism, including the regulation of photosynthesis. As in mitochondria, in bacteria TSPO is located in the outer membrane. TSPO-tetrapyrrole interactions may be part of the establishment of the bacterial-eukaryote relationships, i.e., mitochondrial-eukaryote and plastid-plant endosymbiotic relationships.}, }
@article {pmid27270999, year = {2016}, author = {Roustan, V and Jain, A and Teige, M and Ebersberger, I and Weckwerth, W}, title = {An evolutionary perspective of AMPK-TOR signaling in the three domains of life.}, journal = {Journal of experimental botany}, volume = {67}, number = {13}, pages = {3897-3907}, doi = {10.1093/jxb/erw211}, pmid = {27270999}, issn = {1460-2431}, support = {P 28491/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {AMP-Activated Protein Kinases/*genetics/metabolism ; Archaea/*genetics ; Bacteria/*genetics ; Biological Evolution ; Eukaryota/*genetics ; *Evolution, Molecular ; *Signal Transduction ; TOR Serine-Threonine Kinases/*genetics/metabolism ; }, abstract = {AMPK and TOR protein kinases are the major control points of energy signaling in eukaryotic cells and organisms. They form the core of a complex regulatory network to co-ordinate metabolic activities in the cytosol with those in the mitochondria and plastids. Despite its relevance, it is still unclear when and how this regulatory pathway was formed during evolution, and to what extent its representations in the major eukaryotic lineages resemble each other. Here we have traced 153 essential proteins forming the human AMPK-TOR pathways across 412 species representing all three domains of life-prokaryotes (bacteria, archaea) and eukaryotes-and reconstructed their evolutionary history. The resulting phylogenetic profiles indicate the presence of primordial core pathways including seven proto-kinases in the last eukaryotic common ancestor. The evolutionary origins of the oldest components of the AMPK pathway, however, extend into the pre-eukaryotic era, and descendants of these ancient proteins can still be found in contemporary prokaryotes. The TOR complex in turn appears as a eukaryotic invention, possibly to aid in retrograde signaling between the mitochondria and the remainder of the cell. Within the eukaryotes, AMPK/TOR showed both a highly conserved core structure and a considerable plasticity. Most notably, KING1, a protein originally assigned as the γ subunit of AMPK in plants, is more closely related to the yeast SDS23 gene family than to the γ subunits in animals or fungi. This suggests its functional difference from a canonical AMPK γ subunit.}, }
@article {pmid27267617, year = {2016}, author = {McCutcheon, JP}, title = {From microbiology to cell biology: when an intracellular bacterium becomes part of its host cell.}, journal = {Current opinion in cell biology}, volume = {41}, number = {}, pages = {132-136}, pmid = {27267617}, issn = {1879-0410}, support = {NNA17BB05A//Intramural NASA/United States ; }, mesh = {Animals ; Bacteria/*metabolism ; Biological Evolution ; Eukaryotic Cells/*microbiology ; Intracellular Space/*microbiology ; Organelles/microbiology ; Symbiosis ; }, abstract = {Mitochondria and chloroplasts are now called organelles, but they used to be bacteria. As they transitioned from endosymbionts to organelles, they became more and more integrated into the biochemistry and cell biology of their hosts. Work over the last 15 years has shown that other symbioses show striking similarities to mitochondria and chloroplasts. In particular, many sap-feeding insects house intracellular bacteria that have genomes that overlap mitochondria and chloroplasts in terms of size and coding capacity. The massive levels of gene loss in some of these bacteria suggest that they, too, are becoming highly integrated with their host cells. Understanding these bacteria will require inspiration from eukaryotic cell biology, because a traditional microbiological framework is insufficient for understanding how they work.}, }
@article {pmid27266671, year = {2016}, author = {Radzvilavicius, AL}, title = {Evolutionary dynamics of cytoplasmic segregation and fusion: Mitochondrial mixing facilitated the evolution of sex at the origin of eukaryotes.}, journal = {Journal of theoretical biology}, volume = {404}, number = {}, pages = {160-168}, doi = {10.1016/j.jtbi.2016.05.037}, pmid = {27266671}, issn = {1095-8541}, mesh = {Alleles ; Animals ; *Biological Evolution ; Cell Fusion ; Cell Nucleus/metabolism ; Eukaryota/*metabolism ; Female ; Genetic Fitness ; Male ; Mitochondria/*metabolism ; Models, Biological ; Mutation/genetics ; *Sex Characteristics ; }, abstract = {Sexual reproduction is a trait shared by all complex life, but the complete account of its origin is missing. Virtually all theoretical work on the evolution of sex has been centered around the benefits of reciprocal recombination among nuclear genes, paying little attention to the evolutionary dynamics of multi-copy mitochondrial genomes. Here I develop a mathematical model to study the evolution of nuclear alleles inducing cell fusion in an ancestral population of clonal proto-eukaryotes. Segregational drift maintains high mitochondrial variance between clonally reproducing hosts, but the effect of segregation is opposed by cytoplasmic mixing which tends to reduce variation between cells in favor of higher heterogeneity within the cell. Despite the reduced long-term population fitness, alleles responsible for sexual cell fusion can spread to fixation. The evolution of sex requires negative epistatic interactions between mitochondrial mutations under strong purifying selection, low mutation load and weak mitochondrial-nuclear associations. I argue that similar conditions could have been maintained during the late stages of eukaryogenesis, facilitating the evolution of sexual cell fusion and meiotic recombination without compromising the stability of the emerging complex cell.}, }
@article {pmid27265872, year = {2016}, author = {Wrobel, L and Sokol, AM and Chojnacka, M and Chacinska, A}, title = {The presence of disulfide bonds reveals an evolutionarily conserved mechanism involved in mitochondrial protein translocase assembly.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {27484}, pmid = {27265872}, issn = {2045-2322}, mesh = {*Biological Evolution ; Disulfides/*chemistry ; Humans ; Membrane Transport Proteins/*metabolism ; Mitochondrial Proteins/*metabolism ; Oxidation-Reduction ; Saccharomyces cerevisiae/metabolism ; }, abstract = {Disulfide bond formation is crucial for the biogenesis and structure of many proteins that are localized in the intermembrane space of mitochondria. The importance of disulfide bond formation within mitochondrial proteins was extended beyond soluble intermembrane space proteins. Tim22, a membrane protein and core component of the mitochondrial translocase TIM22, forms an intramolecular disulfide bond in yeast. Tim22 belongs to the Tim17/Tim22/Tim23 family of protein translocases. Here, we present evidence of the high evolutionary conservation of disulfide bond formation in Tim17 and Tim22 among fungi and metazoa. Topological models are proposed that include the location of disulfide bonds relative to the predicted transmembrane regions. Yeast and human Tim22 variants that are not oxidized do not properly integrate into the membrane complex. Moreover, the lack of Tim17 oxidation disrupts the TIM23 translocase complex. This underlines the importance of disulfide bond formation for mature translocase assembly through membrane stabilization of weak transmembrane domains.}, }
@article {pmid27262428, year = {2016}, author = {Melo, BF and Sidlauskas, BL and Hoekzema, K and Frable, BW and Vari, RP and Oliveira, C}, title = {Molecular phylogenetics of the Neotropical fish family Prochilodontidae (Teleostei: Characiformes).}, journal = {Molecular phylogenetics and evolution}, volume = {102}, number = {}, pages = {189-201}, doi = {10.1016/j.ympev.2016.05.037}, pmid = {27262428}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/genetics ; Characiformes/*classification/genetics ; DNA/chemistry/isolation &amp; purification/metabolism ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; South America ; }, abstract = {Migratory detritivores of the characiform family Prochilodontidae occur throughout the freshwaters of much of South America. Prochilodontids often form massive populations and many species achieve substantial body sizes; a combination that makes them one of the most commercially important fish groups on the continent. Their economic significance notwithstanding, prochilodontids have never been the subject of a comprehensive molecular phylogenetic analysis. Using three mitochondrial and three nuclear loci spanning all prochilodontid species, we generated a novel phylogenetic hypothesis for the family. Our results strongly support monophyly of the family and the three included genera. A novel, highly supported placement of Ichthyoelephas sister to the clade containing Prochilodus and Semaprochilodus diverges from a previous morphological hypothesis. Most previously hypothesized interspecific relationships are corroborated and some longstanding polytomies within Prochilodus and Semaprochilodus are resolved. The morphologically similar P. brevis, P. lacustris, P. nigricans and P. rubrotaeniatus are embedded within what is herein designated as the P. nigricans group. Species limits and distributions of these species are problematic and the group clearly merits taxonomic revision.}, }
@article {pmid27260204, year = {2016}, author = {Ebrahimi, S and Bordbar, A and Parvizi, P}, title = {Genetic dynamics in the sand fly (Diptera: Psychodidae) nuclear and mitochondrial genotypes: evidence for vector adaptation at the border of Iran with Iraq.}, journal = {Parasites &amp; vectors}, volume = {9}, number = {1}, pages = {319}, pmid = {27260204}, issn = {1756-3305}, mesh = {Adaptation, Biological ; Animals ; Cell Nucleus/genetics ; Cytochromes b/genetics ; Female ; *Genetic Variation ; Genotype ; Geography ; Humans ; Insect Vectors/*genetics/physiology ; Iran/epidemiology ; Iraq/epidemiology ; Leishmaniasis, Cutaneous/epidemiology/*transmission ; Male ; Mitochondria/genetics ; Peptide Elongation Factor 1/genetics ; Phlebotomus/genetics/physiology ; Phylogeny ; Psychodidae/*genetics/physiology ; }, abstract = {BACKGROUND: Our investigation uses nucleotide variations of the genera Phlebotomus and Sergentomyia using the EF-1α and Cyt b genotype regions to describe the sand fly fauna and genetic aspects collected at war-torn sites of the Khuzestan boundary between Iraq and Iran.<br><br>METHODS: All sand fly species were characterized using molecular genetics. The field work was conducted in six districts including 24 locations in remote areas for three&#xa0;years at the peak of sand fly activity during cutaneous leishmaniasis (CL) transmission seasons. The distribution of CL vectors was determined based on the climatic regionalization using the kriging method in ArcGIS model. DNA of sand fly pools were screened via polymerase chain reaction (PCR) using neutrality (Tajima's D) and neutral allele frequency (Fu's F s) tests to measure the effect of randomly evolving DNA sequence on the genetic diversity of sand fly populations in response to habitat fragmentation and landscape modification.<br><br>RESULTS: Among the 1213 specimens, ten species were identified&#xa0;based on morphology. The non-native species Phlebotomus sergenti was unequivocally found for the first time in the studied regions. Nucleotide substitutions of sand fly sequences varied most in the most disrupted districts (Dashte-Azadegan and Abadan; disparity index test: P&#x2009;<&#x2009;0.05). The haplotypes of Cyt b from the subgenus Sergentomyia and P. papatasi revealed more heterogeneity (Tajima's D&#x2009;>&#x2009;+2) than P. alexandri (D&#x2009;>&#x2009;+1), which suggests widespread heteroplasmic mitochondrial DNA mutations in the same mtDNA gene among different sand fly species. Subgenus&#xa0; Sintonius exhibited greater fitness (D&#x2009;=&#x2009;0) and (neutrality test; P&#x2009;>&#x2009;0.05) no evidence of selection. The sequence of the nuclear gene EF-1&#x3b1; indicated similar nucleotide differences, as observed for the Cyt b gene, in all sand fly species, but lower levels of polymorphisms (D&#x2009;>&#x2009;+1) were observed compared with the mitochondrial Cyt b gene (D&#x2009;>&#x2009;+2) in the&#xa0;subgenus&#xa0; Sergentomyia.<br><br>CONCLUSION: Our findings describe random nucleotide diversity in the Phlebotomus and Sergentomyia population gene pools due to recent anthropogenic influence. A phylogenetic analysis showed that the closely related species are positioned in monophyletic clades, except for the&#xa0;subgenus Sergentomyia and P. sergenti, and highlights the importance of haplotype variations for the development of adaptability.}, }
@article {pmid27258256, year = {2016}, author = {Zhang, HL and Liu, BB and Wang, XY and Han, ZP and Zhang, DX and Su, CN}, title = {Comparative Mitogenomic Analysis of Species Representing Six Subfamilies in the Family Tenebrionidae.}, journal = {International journal of molecular sciences}, volume = {17}, number = {6}, pages = {}, pmid = {27258256}, issn = {1422-0067}, mesh = {Animals ; Base Composition ; Evolution, Molecular ; Gene Order ; Genome, Mitochondrial ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA/*chemistry ; RNA, Mitochondrial ; Selection, Genetic ; Tenebrio/*classification/*genetics ; }, abstract = {To better understand the architecture and evolution of the mitochondrial genome (mitogenome), mitogenomes of ten specimens representing six subfamilies in Tenebrionidae were selected, and comparative analysis of these mitogenomes was carried out in this study. Ten mitogenomes in this family share a similar gene composition, gene order, nucleotide composition, and codon usage. In addition, our results show that nucleotide bias was strongly influenced by the preference of codon usage for A/T rich codons which significantly correlated with the G + C content of protein coding genes (PCGs). Evolutionary rate analyses reveal that all PCGs have been subjected to a purifying selection, whereas 13 PCGs displayed different evolution rates, among which ATPase subunit 8 (ATP8) showed the highest evolutionary rate. We inferred the secondary structure for all RNA genes of Tenebrio molitor (Te2) and used this as the basis for comparison with the same genes from other Tenebrionidae mitogenomes. Some conserved helices (stems) and loops of RNA structures were found in different domains of ribosomal RNAs (rRNAs) and the cloverleaf structure of transfer RNAs (tRNAs). With regard to the AT-rich region, we analyzed tandem repeat sequences located in this region and identified some essential elements including T stretches, the consensus motif at the flanking regions of T stretch, and the secondary structure formed by the motif at the 3' end of T stretch in major strand, which are highly conserved in these species. Furthermore, phylogenetic analyses using mitogenomic data strongly support the relationships among six subfamilies: ((Tenebrionidae incertae sedis + (Diaperinae + Tenebrioninae)) + (Pimeliinae + Lagriinae)), which is consistent with phylogenetic results based on morphological traits.}, }
@article {pmid27257807, year = {2016}, author = {Matsunami, M and Igawa, T and Michimae, H and Miura, T and Nishimura, K}, title = {Population Structure and Evolution after Speciation of the Hokkaido Salamander (Hynobius retardatus).}, journal = {PloS one}, volume = {11}, number = {6}, pages = {e0156815}, pmid = {27257807}, issn = {1932-6203}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Gene Flow/genetics ; Genotype ; Japan ; Phylogeny ; Sequence Analysis, DNA/methods ; Urodela/classification/*genetics ; }, abstract = {The Hokkaido salamander (Hynobius retardatus) is endemic to Hokkaido Island, Japan, and shows intriguing flexible phenotypic plasticity and regional morphological diversity. However, to date, allozymes and partial mitochondria DNA sequences have provided only an outline of its demographic histories and the pattern of its genetic diversification. To understand the finer details of the population structure of this species and its evolution since speciation, we genotyped five regional populations by using 12 recently developed microsatellite polymorphic markers. We found a clear population structure with low gene flow among the five populations, but a close genetic relationship between the Teshio and Kitami populations. Our demographic analysis suggested that Teshio and Erimo had the largest effective population sizes among the five populations. These findings regarding the population structure and demography of H. retardatus improve our understanding of the faunal phylogeography on Hokkaido Island and also provide fundamental genetic information that will be useful for future studies.}, }
@article {pmid27241629, year = {2016}, author = {Card, DC and Schield, DR and Adams, RH and Corbin, AB and Perry, BW and Andrew, AL and Pasquesi, GI and Smith, EN and Jezkova, T and Boback, SM and Booth, W and Castoe, TA}, title = {Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.}, journal = {Molecular phylogenetics and evolution}, volume = {102}, number = {}, pages = {104-116}, pmid = {27241629}, issn = {1095-9513}, support = {K12 GM000708/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Boidae/classification/*genetics/physiology ; DNA/chemistry/isolation &amp; purification/metabolism ; DNA, Mitochondrial/chemistry/genetics/metabolism ; Dwarfism/pathology/veterinary ; Gene Frequency ; Genetic Variation ; *Genetics, Population ; Haplotypes ; Mitochondria/genetics/metabolism ; Phylogeny ; Phylogeography ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras.}, }
@article {pmid27235550, year = {2016}, author = {Stervander, M and Alström, P and Olsson, U and Ottosson, U and Hansson, B and Bensch, S}, title = {Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae).}, journal = {Molecular phylogenetics and evolution}, volume = {102}, number = {}, pages = {233-245}, doi = {10.1016/j.ympev.2016.05.032}, pmid = {27235550}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/*genetics ; Cytochromes b/chemistry/genetics/metabolism ; DNA/chemistry/isolation &amp; purification/metabolism ; DNA, Mitochondrial/chemistry/genetics/metabolism ; Databases, Genetic ; Genetic Variation ; Mitochondria/*genetics/metabolism ; Passeriformes/*classification/genetics ; Phylogeny ; Phylogeography ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {The avian genus Calandrella (larks) was recently suggested to be non-monophyletic, and was divided into two genera, of which Calandrella sensu stricto comprises 4-5 species in Eurasia and Africa. We analysed mitochondrial cytochrome b (cytb) and nuclear Restriction-site Associated DNA (RAD) sequences from all species, and for cytb we studied 21 of the 22 recognised subspecies, with the aim to clarify the phylogenetic relationships within the genus and to compare large-scale nuclear sequence patterns with a widely used mitochondrial marker. Cytb indicated deep splits among the currently recognised species, although it failed to support the interrelationships among most of these. It also revealed unexpected deep divergences within C. brachydactyla, C. blanfordi/C. erlangeri, C. cinerea, and C. acutirostris. It also suggested that both C. brachydactyla and C. blanfordi, as presently circumscribed, are paraphyletic. In contrast, most of the many subspecies of C. brachydactyla and C. cinerea were unsupported by cytb, although two populations of C. cinerea were found to be genetically distinct. The RAD data corroborated the cytb tree (for the smaller number of taxa analysed) and recovered strongly supported interspecific relationships. However, coalescence analyses of the RAD data, analysed in SNAPP both with and without an outgroup, received equally strong support for two conflicting topologies. We suggest that the tree rooted with an outgroup - which is not recommended for SNAPP - is more trustworthy, and suggest that the reliability of analyses performed without any outgroup species should be thoroughly evaluated. We also demonstrate that degraded museum samples can be phylogenetically informative in RAD analyses following careful bioinformatic treatment. We note that the genus Calandrella is in need of taxonomic revision.}, }
@article {pmid27233443, year = {2016}, author = {Carmi, O and Witt, CC and Jaramillo, A and Dumbacher, JP}, title = {Phylogeography of the Vermilion Flycatcher species complex: Multiple speciation events, shifts in migratory behavior, and an apparent extinction of a Galápagos-endemic bird species.}, journal = {Molecular phylogenetics and evolution}, volume = {102}, number = {}, pages = {152-173}, doi = {10.1016/j.ympev.2016.05.029}, pmid = {27233443}, issn = {1095-9513}, mesh = {Alleles ; Animal Migration/*physiology ; Animals ; Cytochromes b/classification/genetics ; DNA, Mitochondrial/chemistry/genetics/metabolism ; Genetic Variation ; Haplotypes ; Mitochondria/enzymology/metabolism ; NADH Dehydrogenase/classification/genetics ; North America ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Songbirds/*classification/genetics ; South America ; }, abstract = {The Vermilion Flycatcher (Pyrocephalus rubinus) is a widespread species found in North and South America and the Galápagos. Its 12 recognized subspecies vary in degree of geographic isolation, phenotypic distinctness, and migratory status. Some authors suggest that Galápagos subspecies nanus and dubius constitute one or more separate species. Observational reports of distinct differences in song also suggest separate species status for the austral migrant subspecies rubinus. To evaluate geographical patterns of diversification and taxonomic limits within this species complex, we carried out a molecular phylogenetic analysis encompassing 10 subspecies and three outgroup taxa using mitochondrial (ND2, Cyt b) and nuclear loci (ODC introns 6 through 7, FGB intron 5). We used samples of preserved tissues from museum collections as well as toe pad samples from museum skins. Galápagos and continental clades were recovered as sister groups, with initial divergence at ∼1mya. Within the continental clade, North and South American populations were sister groups. Three geographically distinct clades were recovered within South America. We detected no genetic differences between two broadly intergrading North American subspecies, mexicanus and flammeus, suggesting they should not be recognized as separate taxa. Four western South American subspecies were also indistinguishable on the basis of loci that we sampled, but occur in a region with patchy habitat, and may represent recently isolated populations. The austral migrant subspecies, rubinus, comprised a monophyletic mitochondrial clade and had many unique nuclear DNA alleles. In combination with its distinct song, exclusive song recognition behavior, different phenology, and an isolated breeding range, our data suggests that this taxon represents a separate species from other continental populations. Mitochondrial and nuclear genetic data, morphology, and behavior suggest that Galápagos forms should be elevated to two full species corresponding to the two currently recognized subspecies, nanus and dubius. The population of dubius is presumed to be extinct, and thus would represent the first documented extinction of a Galápagos-endemic bird species. Two strongly supported mitochondrial clades divide Galápagos subspecies nanus in a geographic pattern that conflicts with previous hypotheses that were based on plumage color. Several populations of nanus have recently become extinct or are in serious decline. Urgent conservation measures should seek to preserve the deep mitochondrial DNA diversity within nanus, and further work should explore whether additional forms should be recognized within nanus. Ancestral states analysis based on our phylogeny revealed that the most recent common ancestor of extant Vermilion Flycatcher populations was migratory, and that migratory behavior was lost more often than gained within Pyrocephalus and close relatives, as has been shown to be the case within Tyrannidae as a whole.}, }
@article {pmid27230371, year = {2016}, author = {Ball, SG and Bhattacharya, D and Weber, AP}, title = {Infection and the first eukaryotes--Response.}, journal = {Science (New York, N.Y.)}, volume = {352}, number = {6289}, pages = {1065-1066}, doi = {10.1126/science.aaf6733}, pmid = {27230371}, issn = {1095-9203}, mesh = {Alphaproteobacteria/*genetics ; Animals ; *Biological Evolution ; *Host-Pathogen Interactions ; Humans ; Mitochondria/*genetics ; Plastids/*genetics ; Symbiosis/*genetics ; }, }
@article {pmid27230370, year = {2016}, author = {Gould, SB}, title = {Infection and the first eukaryotes.}, journal = {Science (New York, N.Y.)}, volume = {352}, number = {6289}, pages = {1065}, doi = {10.1126/science.aaf6478}, pmid = {27230370}, issn = {1095-9203}, mesh = {Alphaproteobacteria/*genetics ; Animals ; *Biological Evolution ; *Host-Pathogen Interactions ; Humans ; Mitochondria/*genetics ; Plastids/*genetics ; Symbiosis/*genetics ; }, }
@article {pmid27228550, year = {2016}, author = {Yasueda, Y and Tamura, T and Fujisawa, A and Kuwata, K and Tsukiji, S and Kiyonaka, S and Hamachi, I}, title = {A Set of Organelle-Localizable Reactive Molecules for Mitochondrial Chemical Proteomics in Living Cells and Brain Tissues.}, journal = {Journal of the American Chemical Society}, volume = {138}, number = {24}, pages = {7592-7602}, doi = {10.1021/jacs.6b02254}, pmid = {27228550}, issn = {1520-5126}, mesh = {Binding Sites ; Brain/*metabolism ; Cell Culture Techniques ; Chromatography, High Pressure Liquid ; HeLa Cells ; Humans ; Isotope Labeling ; Microscopy, Confocal ; Mitochondria/*metabolism ; Mitochondrial Proteins/*chemistry ; Models, Molecular ; Proteome/*metabolism ; Proteomics/*methods ; Rhodamines/chemistry ; Tandem Mass Spectrometry ; }, abstract = {Protein functions are tightly regulated by their subcellular localization in live cells, and quantitative evaluation of dynamically altered proteomes in each organelle should provide valuable information. Here, we describe a novel method for organelle-focused chemical proteomics using spatially limited reactions. In this work, mitochondria-localizable reactive molecules (MRMs) were designed that penetrate biomembranes and spontaneously concentrate in mitochondria, where protein labeling is facilitated by the condensation effect. The combination of this selective labeling and liquid chromatography-mass spectrometry (LC-MS) based proteomics technology facilitated identification of mitochondrial proteomes and the profile of the intrinsic reactivity of amino acids tethered to proteins expressed in live cultured cells, primary neurons and brain slices. Furthermore, quantitative profiling of mitochondrial proteins whose expression levels change significantly during an oxidant-induced apoptotic process was performed by combination of this MRMs-based method with a standard quantitative MS technique (SILAC: stable isotope labeling by amino acids in cell culture). The use of a set of MRMs represents a powerful tool for chemical proteomics to elucidate mitochondria-associated biological events and diseases.}, }
@article {pmid27226308, year = {2016}, author = {Gütle, DD and Roret, T and Müller, SJ and Couturier, J and Lemaire, SD and Hecker, A and Dhalleine, T and Buchanan, BB and Reski, R and Einsle, O and Jacquot, JP}, title = {Chloroplast FBPase and SBPase are thioredoxin-linked enzymes with similar architecture but different evolutionary histories.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {24}, pages = {6779-6784}, pmid = {27226308}, issn = {1091-6490}, mesh = {*Bryopsida/enzymology/genetics ; *Chloroplast Proteins/genetics/metabolism ; *Evolution, Molecular ; *Fructose-Bisphosphatase/genetics/metabolism ; *Phosphoric Monoester Hydrolases/genetics/metabolism ; *Thioredoxins/genetics/metabolism ; }, abstract = {The Calvin-Benson cycle of carbon dioxide fixation in chloroplasts is controlled by light-dependent redox reactions that target specific enzymes. Of the regulatory members of the cycle, our knowledge of sedoheptulose-1,7-bisphosphatase (SBPase) is particularly scanty, despite growing evidence for its importance and link to plant productivity. To help fill this gap, we have purified, crystallized, and characterized the recombinant form of the enzyme together with the better studied fructose-1,6-bisphosphatase (FBPase), in both cases from the moss Physcomitrella patens (Pp). Overall, the moss enzymes resembled their counterparts from seed plants, including oligomeric organization-PpSBPase is a dimer, and PpFBPase is a tetramer. The two phosphatases showed striking structural homology to each other, differing primarily in their solvent-exposed surface areas in a manner accounting for their specificity for seven-carbon (sedoheptulose) and six-carbon (fructose) sugar bisphosphate substrates. The two enzymes had a similar redox potential for their regulatory redox-active disulfides (-310 mV for PpSBPase vs. -290 mV for PpFBPase), requirement for Mg(2+) and thioredoxin (TRX) specificity (TRX f > TRX m). Previously known to differ in the position and sequence of their regulatory cysteines, the enzymes unexpectedly showed unique evolutionary histories. The FBPase gene originated in bacteria in conjunction with the endosymbiotic event giving rise to mitochondria, whereas SBPase arose from an archaeal gene resident in the eukaryotic host. These findings raise the question of how enzymes with such different evolutionary origins achieved structural similarity and adapted to control by the same light-dependent photosynthetic mechanism-namely ferredoxin, ferredoxin-thioredoxin reductase, and thioredoxin.}, }
@article {pmid27226058, year = {2016}, author = {Morgan, DJ and Poolman, TM and Williamson, AJ and Wang, Z and Clark, NR and Ma'ayan, A and Whetton, AD and Brass, A and Matthews, LC and Ray, DW}, title = {Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {26419}, pmid = {27226058}, issn = {2045-2322}, support = {U54 HL127624/HL/NHLBI NIH HHS/United States ; MR/M008959/1/MRC_/Medical Research Council/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 107851/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; MR/N00583X/1/MRC_/Medical Research Council/United Kingdom ; R01 GM098316/GM/NIGMS NIH HHS/United States ; U54 CA189201/CA/NCI NIH HHS/United States ; MR/M008908/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {A549 Cells ; Adenosine Triphosphate/*metabolism ; Cell Nucleus/metabolism ; Cytoplasm ; Evolution, Molecular ; Gene Expression Profiling ; Gene Regulatory Networks ; HEK293 Cells ; Humans ; Mitochondria/*genetics/*metabolism ; Models, Molecular ; Protein Binding ; Proteomics ; Receptors, Glucocorticoid/chemistry/*metabolism ; }, abstract = {The glucocorticoid receptor (GR), a nuclear receptor and major drug target, has a highly conserved minor splice variant, GRγ, which differs by a single arginine within the DNA binding domain. GRγ, which comprises 10% of all GR transcripts, is constitutively expressed and tightly conserved through mammalian evolution, suggesting an important non-redundant role. However, to date no specific role for GRγ has been reported. We discovered significant differences in subcellular localisation, and nuclear-cytoplasmic shuttling in response to ligand. In addition the GRγ transcriptome and protein interactome was distinct, and with a gene ontology signal for mitochondrial regulation which was confirmed using Seahorse technology. We propose that evolutionary conservation of the single additional arginine in GRγ is driven by a distinct, non-redundant functional profile, including regulation of mitochondrial function.}, }
@article {pmid27223999, year = {2016}, author = {Boo, GH and Le Gall, L and Miller, KA and Freshwater, DW and Wernberg, T and Terada, R and Yoon, KJ and Boo, SM}, title = {A novel phylogeny of the Gelidiales (Rhodophyta) based on five genes including the nuclear CesA, with descriptions of Orthogonacladia gen. nov. and Orthogonacladiaceae fam. nov.}, journal = {Molecular phylogenetics and evolution}, volume = {101}, number = {}, pages = {359-372}, doi = {10.1016/j.ympev.2016.05.018}, pmid = {27223999}, issn = {1095-9513}, mesh = {Cell Nucleus/*genetics ; Genetic Markers ; Likelihood Functions ; *Phylogeny ; Rhodophyta/anatomy &amp; histology/*classification/*genetics ; }, abstract = {Although the Gelidiales are economically important marine red algae producing agar and agarose, the phylogeny of this order remains poorly resolved. The present study provides a molecular phylogeny based on a novel marker, nuclear-encoded CesA, plus plastid-encoded psaA, psbA, rbcL, and mitochondria-encoded cox1 from subsets of 107 species from all ten genera within the Gelidiales. Analyses of individual and combined datasets support the monophyly of three currently recognized families, and reveal a new clade. On the basis of these results, the new family Orthogonacladiaceae is described to accommodate Aphanta and a new genus Orthogonacladia that includes species previously classified as Gelidium madagascariense and Pterocladia rectangularis. Acanthopeltis is merged with Gelidium, which has nomenclatural priority. Nuclear-encoded CesA was found to be useful for improving the resolution of phylogenetic relationships within the Gelidiales and is likely to be valuable for the inference of phylogenetic relationship among other red algal taxa.}, }
@article {pmid27218846, year = {2016}, author = {Burki, F}, title = {Mitochondrial Evolution: Going, Going, Gone.}, journal = {Current biology : CB}, volume = {26}, number = {10}, pages = {R410-2}, doi = {10.1016/j.cub.2016.04.032}, pmid = {27218846}, issn = {1879-0445}, mesh = {*Biological Evolution ; Eukaryota ; Eukaryotic Cells ; *Mitochondria ; Organelles ; }, abstract = {Monocercomonoides is the first example of a eukaryote lacking even the most reduced form of a mitochondrion-related organelle. This has important implications for cellular processes and our understanding of reductive mitochondrial evolution across the eukaryotic tree of life.}, }
@article {pmid27215606, year = {2016}, author = {Pagliuso, A and Tham, TN and Stevens, JK and Lagache, T and Persson, R and Salles, A and Olivo-Marin, JC and Oddos, S and Spang, A and Cossart, P and Stavru, F}, title = {A role for septin 2 in Drp1-mediated mitochondrial fission.}, journal = {EMBO reports}, volume = {17}, number = {6}, pages = {858-873}, pmid = {27215606}, issn = {1469-3178}, support = {670823/ERC_/European Research Council/International ; }, mesh = {Actomyosin/metabolism ; Biological Evolution ; Caenorhabditis elegans Proteins/genetics/metabolism ; Dynamins ; GTP Phosphohydrolases/*metabolism ; Gene Knockdown Techniques ; Gene Silencing ; HeLa Cells ; Humans ; Microtubule-Associated Proteins/*metabolism ; Mitochondria/genetics/*metabolism ; *Mitochondrial Dynamics ; Mitochondrial Proteins/genetics/*metabolism ; Septins/genetics/*metabolism ; }, abstract = {Mitochondria are essential eukaryotic organelles often forming intricate networks. The overall network morphology is determined by mitochondrial fusion and fission. Among the multiple mechanisms that appear to regulate mitochondrial fission, the ER and actin have recently been shown to play an important role by mediating mitochondrial constriction and promoting the action of a key fission factor, the dynamin-like protein Drp1. Here, we report that the cytoskeletal component septin 2 is involved in Drp1-dependent mitochondrial fission in mammalian cells. Septin 2 localizes to a subset of mitochondrial constrictions and directly binds Drp1, as shown by immunoprecipitation of the endogenous proteins and by pulldown assays with recombinant proteins. Depletion of septin 2 reduces Drp1 recruitment to mitochondria and results in hyperfused mitochondria and delayed FCCP-induced fission. Strikingly, septin depletion also affects mitochondrial morphology in Caenorhabditis elegans, strongly suggesting that the role of septins in mitochondrial dynamics is evolutionarily conserved.}, }
@article {pmid27212703, year = {2016}, author = {Yamada, M and Emmanuele, V and Sanchez-Quintero, MJ and Sun, B and Lallos, G and Paull, D and Zimmer, M and Pagett, S and Prosser, RW and Sauer, MV and Hirano, M and Egli, D}, title = {Genetic Drift Can Compromise Mitochondrial Replacement by Nuclear Transfer in Human Oocytes.}, journal = {Cell stem cell}, volume = {18}, number = {6}, pages = {749-754}, pmid = {27212703}, issn = {1875-9777}, support = {P01 HD080642/HD/NICHD NIH HHS/United States ; U54 NS078059/NS/NINDS NIH HHS/United States ; }, mesh = {Cell Line ; Cell Nucleus/metabolism ; DNA, Mitochondrial/genetics ; *Genetic Drift ; Genotype ; Humans ; Mitochondria/*genetics ; *Nuclear Transfer Techniques ; Oocytes/*metabolism ; }, abstract = {Replacement of mitochondria through nuclear transfer between oocytes of two different women has emerged recently as a strategy for preventing inheritance of mtDNA diseases. Although experiments in human oocytes have shown effective replacement, the consequences of small amounts of mtDNA carryover have not been studied sufficiently. Using human mitochondrial replacement stem cell lines, we show that, even though the low levels of heteroplasmy introduced into human oocytes by mitochondrial carryover during nuclear transfer often vanish, they can sometimes instead result in mtDNA genotypic drift and reversion to the original genotype. Comparison of cells with identical oocyte-derived nuclear DNA but different mtDNA shows that either mtDNA genotype is compatible with the nucleus and that drift is independent of mitochondrial function. Thus, although functional replacement of the mitochondrial genome is possible, even low levels of heteroplasmy can affect the stability of the mtDNA genotype and compromise the efficacy of mitochondrial replacement.}, }
@article {pmid27211112, year = {2017}, author = {Cheng, Y and Liu, D and Tang, W}, title = {The complete mitochondrial genome of the Neophocaena asiaeorientails sunamrei (Phocaenidae: Neophocaena).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {2}, pages = {248-249}, doi = {10.3109/19401736.2015.1115863}, pmid = {27211112}, issn = {2470-1408}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Molecular Sequence Annotation ; Phylogeny ; Porpoises/*genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {The complete sequence of the mitochondrial DNA (mtDNA) of the East Asian finless porpoise (Neophocaena asiaeorientails sunamrei) has been completed and annotated in this study. The circular genome is 16 385 bp in length, consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 2 non-coding areas. Ten protein-coding genes use ATG as the initiation codon, except that ND2 started with ATT, and ND3 and ND5 started with ATA. Canonical TAA and TAG termination codons are found in seven protein-coding genes, the remaining four (ND4, ND2, ND3, and COIII) have incomplete termination codons (T or TA), in addition, the COI ends with AGG, and the Cyt b ends with AGA. On the neighbor-joining phylogenetic tree, these results show that the relationship of Phocoenidae is closer with Delphinidae.}, }
@article {pmid27207227, year = {2016}, author = {Wang, CX and Xu, HS and Li, XF and Lu, J and Hu, XX and Liu, X}, title = {The complete mitochondrial genome of the white-tailed tropicbird, Phaethon lepturus.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4259-4260}, doi = {10.3109/19401736.2015.1053076}, pmid = {27207227}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Birds/*genetics ; Codon, Initiator/genetics ; Codon, Terminator/genetics ; DNA, Mitochondrial/genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; Phylogeny ; RNA, Transfer/genetics ; }, abstract = {The white-tailed tropicbird, Phaethon lepturus (Pelecaniformes, Phaethontidae) is a tropicbird, smallest of three closely related seabirds of the tropical oceans and smallest member of the order Pelecaniformes. Here, we first determined the complete mitochondrial genome of while-tailed tropicbird. The mitogenome (17,773 bp) was composed of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 putative control region. Most protein-coding genes started with a traditional ATG codon except for COX1, COX2, and ND3, which initiated with non-typical start codon GTG, GTG, and ATA instead, respectively, and terminated with the mitochondria stop codon (TAA/TCC/AGG/AGA). The mitogenome structural organization was identical to the same genus species Phaethon rubricauda. The overall AT content was 52.04%, which was higher than GC. To obtain the phylogenetic status of Phaethon lepturus, we constructed the species phylogenetic tree together with the 12 protein-coding genes of nine other closely species. We expected that the complete mitogenome of while-tailed tropicbird would contribute to address taxonomic issues and study the related evolution events.}, }
@article {pmid27207080, year = {2016}, author = {Yuan, S and Lu, Z and Wu, X and Fu, H and Bao, D and Malqin, H and Yang, S}, title = {Complete mitochondrial genome of Myospalax aspalax (Rodentia, Spalacidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4250-4251}, doi = {10.3109/19401736.2015.1043532}, pmid = {27207080}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; DNA, Mitochondrial/genetics ; Asia, Eastern ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Rodentia/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {False zokor (Myospalax aspalax) is one of the subterranean rodents distributed in East Asia. Molecular data and demography of M. aspalax are unknown, and the population management is difficult, because it is specialized for underground life. In this study, the complete mitochondrial DNA genome of M. aspalax was determined. The results suggested that the mitogenome was 16,436 bp in length, and consisted of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one displacement loop. The overall base composition of the heavy strand was A 33.40%, T 29.34%, C 24.90%, and G 12.36%, with A + T > C + G. Myospalax aspalax is a sister to the genus Myospalax, and have a most closely relationship with M. psilurus. The mitogenome data are potentially important for population management of M. aspalax and should contribute to the interspecies comparative analyses of genus Myospalax.}, }
@article {pmid27206788, year = {2016}, author = {Gomes, C and Rodrigues-Filho, LF and Sodré, D and Neckel-Oliveira, S and Gordo, M and Gallati, U and Sequeira, F and Vallinoto, M}, title = {Concerted evolution in the mitochondrial control region of the Amazon small-bodied frog Pseudopaludicola canga (Anura, Leiuperidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4270-4273}, doi = {10.3109/19401736.2015.1060477}, pmid = {27206788}, issn = {2470-1408}, mesh = {Animals ; Anura/*genetics ; Base Sequence ; DNA, Mitochondrial/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {This study presents evidence of concerted evolution in the mitochondrial control region of the frog Pseudopaludicola canga. Four repeat units of 88 bp (as well as a fifth, incomplete unit) were observed in the 5' domain, with the duplicated segments of the same specimen being more related to one another than to the equivalent regions in other specimens, as a result of concerted evolution. We highlight that drawing conclusions from phylogeographical analysis using the control region containing VNTRs must be interpreted with caution, because it violated a basic assumption of phylogeny, since the regions cannot be treated as independent characters.}, }
@article {pmid27206536, year = {2016}, author = {Chunnian, L and Wu, X and Ding, X and Wang, H and Guo, X and Chu, M and Bao, P and Yan, P}, title = {Characterization of the complete mitochondrial genome sequence of wild yak (Bos mutus).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4266-4267}, doi = {10.3109/19401736.2015.1060420}, pmid = {27206536}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Cattle/*genetics ; China ; Codon, Initiator/genetics ; DNA, Mitochondrial/genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; }, abstract = {Wild yak is a special breed in China and it is regarded as an important genetic resource for sustainably developing the animal husbandry in Tibetan area and enriching region's biodiversity. The complete mitochondrial genome of wild yak (16,322 bp in length) displayed 37 typical animal mitochondrial genes and A + T-rich (61.01%), with an overall G + C content of only 38.99%. It contained a non-coding control region (D-loop), 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. Most of the genes have ATG initiation codons, whereas ND2, ND3, and ND5 genes start with ATA and were encoded on H-strand. The gene order of wild yak mitogenome is identical to that observed in most other vertebrates. The complete mitochondrial genome sequence of wild yak reported here could provide valuable information for developing genetic markers and phylogenetic analysis in yak.}, }
@article {pmid27198783, year = {2016}, author = {Li, K and Luo, H and Zhang, H and Lan, Y and Han, Z and Shahzad, M and Wang, X and Qiu, G and Huang, S and Jiang, W and Li, J}, title = {First report of Metastrongylus pudendotectus by the genetic characterization of mitochondria genome of cox1 in pigs from Tibet, China.}, journal = {Veterinary parasitology}, volume = {223}, number = {}, pages = {91-95}, doi = {10.1016/j.vetpar.2016.04.036}, pmid = {27198783}, issn = {1873-2550}, mesh = {Animals ; Base Sequence ; DNA, Helminth/genetics ; Electron Transport Complex IV/*genetics ; Genome, Mitochondrial/*genetics ; Metastrongyloidea/genetics/*isolation &amp; purification ; Phylogeny ; Strongylida Infections/epidemiology/parasitology/*veterinary ; Swine ; Swine Diseases/epidemiology/*parasitology ; Tibet/epidemiology ; }, abstract = {Lungworms, a world wild distributed parasites cause serious respiratory diseases to the pigs. A high infection rate of Metastrongylus lungworms has been found in Tibetan pigs being slaughtered in different slaughter houses of Tibet autonomous region. The main aim of our study was to detect and confirm the lungworm parasite by the genetic characterization of mitochondrial cox1genome isolated from the lungs of Tibetan pig. The adult lungworms were collected from the lungs of slaughtered pigs and identification was done through morphological examinations. Total genomic DNA of the extracted worms was performed and a fragment (∼450bp) of the cox1 of mitochondrial (mt) gene was amplified. Amplicons were cloned into PGEM(®)-T Easy vector and the positive clones were sequenced from a commercial company. Sequence and phylogenetic analysis were performed by software of DNAMAN and MEGA respectively. The results revealed that the lungworms infecting the Tibetan pigs were Metastrongylus pudendotectus (M. pudendotectus). To our knowledge, this is the first report for the isolation and identification for the genetic characterization of mitochondria (mt) genome of cox1 of M. pudendotectus derived from Tibetan pigs in Tibet, China.}, }
@article {pmid27197221, year = {2016}, author = {Mühlhausen, S and Findeisen, P and Plessmann, U and Urlaub, H and Kollmar, M}, title = {A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes.}, journal = {Genome research}, volume = {26}, number = {7}, pages = {945-955}, pmid = {27197221}, issn = {1549-5469}, mesh = {Base Sequence ; Cell Nucleus/genetics ; *Codon ; *Evolution, Molecular ; Genetic Code ; Molecular Sequence Annotation ; RNA, Transfer/genetics ; Saccharomycetales/*genetics ; Sequence Analysis, RNA ; }, abstract = {The genetic code is the cellular translation table for the conversion of nucleotide sequences into amino acid sequences. Changes to the meaning of sense codons would introduce errors into almost every translated message and are expected to be highly detrimental. However, reassignment of single or multiple codons in mitochondria and nuclear genomes, although extremely rare, demonstrates that the code can evolve. Several models for the mechanism of alteration of nuclear genetic codes have been proposed (including "codon capture," "genome streamlining," and "ambiguous intermediate" theories), but with little resolution. Here, we report a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons, we show that Pachysolen translates CUG codons as alanine and not as the more usual leucine. The Pachysolen tRNACAG is an anticodon-mutated tRNA(Ala) containing all major alanine tRNA recognition sites. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is not part of the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects.}, }
@article {pmid27194764, year = {2016}, author = {Marzano, SL and Nelson, BD and Ajayi-Oyetunde, O and Bradley, CA and Hughes, TJ and Hartman, GL and Eastburn, DM and Domier, LL}, title = {Identification of Diverse Mycoviruses through Metatranscriptomics Characterization of the Viromes of Five Major Fungal Plant Pathogens.}, journal = {Journal of virology}, volume = {90}, number = {15}, pages = {6846-6863}, pmid = {27194764}, issn = {1098-5514}, mesh = {Ascomycota/*virology ; Fungal Viruses/*classification/*genetics/isolation &amp; purification ; *Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics ; Mycelium/virology ; Phylogeny ; Plant Diseases/*virology ; Plants/*virology ; RNA, Viral/genetics ; *Transcriptome ; }, abstract = {UNLABELLED: Mycoviruses can have a marked effect on natural fungal communities and influence plant health and productivity. However, a comprehensive picture of mycoviral diversity is still lacking. To characterize the viromes of five widely dispersed plant-pathogenic fungi, Colletotrichum truncatum, Macrophomina phaseolina, Diaporthe longicolla, Rhizoctonia solani, and Sclerotinia sclerotiorum, a high-throughput sequencing-based metatranscriptomic approach was used to detect viral sequences. Total RNA and double-stranded RNA (dsRNA) from mycelia and RNA from samples enriched for virus particles were sequenced. Sequence data were assembled de novo, and contigs with predicted amino acid sequence similarities to viruses in the nonredundant protein database were selected. The analysis identified 72 partial or complete genome segments representing 66 previously undescribed mycoviruses. Using primers specific for each viral contig, at least one fungal isolate was identified that contained each virus. The novel mycoviruses showed affinity with 15 distinct lineages: Barnaviridae, Benyviridae, Chrysoviridae, Endornaviridae, Fusariviridae, Hypoviridae, Mononegavirales, Narnaviridae, Ophioviridae, Ourmiavirus, Partitiviridae, Tombusviridae, Totiviridae, Tymoviridae, and Virgaviridae More than half of the viral sequences were predicted to be members of the Mitovirus genus in the family Narnaviridae, which replicate within mitochondria. Five viral sequences showed strong affinity with three families (Benyviridae, Ophioviridae, and Virgaviridae) that previously contained no mycovirus species. The genomic information provides insight into the diversity and taxonomy of mycoviruses and coevolution of mycoviruses and their fungal hosts.<br><br>IMPORTANCE: Plant-pathogenic fungi reduce crop yields, which affects food security worldwide. Plant host resistance is considered a sustainable disease management option but may often be incomplete or lacking for some crops to certain fungal pathogens or strains. In addition, the rising issues of fungicide resistance demand alternative strategies to reduce the negative impacts of fungal pathogens. Those fungus-infecting viruses (mycoviruses) that attenuate fungal virulence may be welcome additions for mitigation of plant diseases. By high-throughput sequencing of the RNAs from 275 isolates of five fungal plant pathogens, 66 previously undescribed mycoviruses were identified. In addition to identifying new potential biological control agents, these results expand the grand view of the diversity of mycoviruses and provide possible insights into the importance of intracellular and extracellular transmission in fungus-virus coevolution.}, }
@article {pmid27194700, year = {2016}, author = {Okie, JG and Smith, VH and Martin-Cereceda, M}, title = {Major evolutionary transitions of life, metabolic scaling and the number and size of mitochondria and chloroplasts.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1831}, pages = {}, pmid = {27194700}, issn = {1471-2954}, mesh = {*Biological Evolution ; Chloroplasts/*metabolism ; Eukaryota/*physiology ; Mitochondria/*metabolism ; Models, Biological ; *Symbiosis ; }, abstract = {We investigate the effects of trophic lifestyle and two types of major evolutionary transitions in individuality-the endosymbiotic acquisition of organelles and development of multicellularity-on organellar and cellular metabolism and allometry. We develop a quantitative framework linking the size and metabolic scaling of eukaryotic cells to the abundance, size and metabolic scaling of mitochondria and chloroplasts and analyse a newly compiled, unprecedented database representing unicellular and multicellular cells covering diverse phyla and tissues. Irrespective of cellularity, numbers and total volumes of mitochondria scale linearly with cell volume, whereas chloroplasts scale sublinearly and sizes of both organelles remain largely invariant with cell size. Our framework allows us to estimate the metabolic scaling exponents of organelles and cells. Photoautotrophic cells and organelles exhibit photosynthetic scaling exponents always less than one, whereas chemoheterotrophic cells and organelles have steeper respiratory scaling exponents close to one. Multicellularity has no discernible effect on the metabolic scaling of organelles and cells. In contrast, trophic lifestyle has a profound and uniform effect, and our results suggest that endosymbiosis fundamentally altered the metabolic scaling of free-living bacterial ancestors of mitochondria and chloroplasts, from steep ancestral scaling to a shallower scaling in their endosymbiotic descendants.}, }
@article {pmid27190001, year = {2016}, author = {Weng, ML and Ruhlman, TA and Jansen, RK}, title = {Plastid-Nuclear Interaction and Accelerated Coevolution in Plastid Ribosomal Genes in Geraniaceae.}, journal = {Genome biology and evolution}, volume = {8}, number = {6}, pages = {1824-1838}, pmid = {27190001}, issn = {1759-6653}, mesh = {Cell Nucleus/*genetics ; Cytosol ; *Evolution, Molecular ; Genome, Plant ; Geraniaceae/*genetics ; Mitochondria/genetics ; Phylogeny ; Plastids/genetics ; Ribosomal Proteins/*genetics ; Ribosomes/genetics ; }, abstract = {Plastids and mitochondria have many protein complexes that include subunits encoded by organelle and nuclear genomes. In animal cells, compensatory evolution between mitochondrial and nuclear-encoded subunits was identified and the high mitochondrial mutation rates were hypothesized to drive compensatory evolution in nuclear genomes. In plant cells, compensatory evolution between plastid and nucleus has rarely been investigated in a phylogenetic framework. To investigate plastid-nuclear coevolution, we focused on plastid ribosomal protein genes that are encoded by plastid and nuclear genomes from 27 Geraniales species. Substitution rates were compared for five sets of genes representing plastid- and nuclear-encoded ribosomal subunit proteins targeted to the cytosol or the plastid as well as nonribosomal protein controls. We found that nonsynonymous substitution rates (dN) and the ratios of nonsynonymous to synonymous substitution rates (ω) were accelerated in both plastid- (CpRP) and nuclear-encoded subunits (NuCpRP) of the plastid ribosome relative to control sequences. Our analyses revealed strong signals of cytonuclear coevolution between plastid- and nuclear-encoded subunits, in which nonsynonymous substitutions in CpRP and NuCpRP tend to occur along the same branches in the Geraniaceae phylogeny. This coevolution pattern cannot be explained by physical interaction between amino acid residues. The forces driving accelerated coevolution varied with cellular compartment of the sequence. Increased ω in CpRP was mainly due to intensified positive selection whereas increased ω in NuCpRP was caused by relaxed purifying selection. In addition, the many indels identified in plastid rRNA genes in Geraniaceae may have contributed to changes in plastid subunits.}, }
@article {pmid27189999, year = {2016}, author = {Song, F and Li, H and Jiang, P and Zhou, X and Liu, J and Sun, C and Vogler, AP and Cai, W}, title = {Capturing the Phylogeny of Holometabola with Mitochondrial Genome Data and Bayesian Site-Heterogeneous Mixture Models.}, journal = {Genome biology and evolution}, volume = {8}, number = {5}, pages = {1411-1426}, pmid = {27189999}, issn = {1759-6653}, mesh = {Animals ; *Evolution, Molecular ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing ; Insecta/genetics ; Mitochondria/genetics ; Molecular Sequence Annotation ; Mutation ; *Phylogeny ; }, abstract = {After decades of debate, a mostly satisfactory resolution of relationships among the 11 recognized holometabolan orders of insects has been reached based on nuclear genes, resolving one of the most substantial branches of the tree-of-life, but the relationships are still not well established with mitochondrial genome data. The main reasons have been the absence of sufficient data in several orders and lack of appropriate phylogenetic methods that avoid the systematic errors from compositional and mutational biases in insect mitochondrial genomes. In this study, we assembled the richest taxon sampling of Holometabola to date (199 species in 11 orders), and analyzed both nucleotide and amino acid data sets using several methods. We find the standard Bayesian inference and maximum-likelihood analyses were strongly affected by systematic biases, but the site-heterogeneous mixture model implemented in PhyloBayes avoided the false grouping of unrelated taxa exhibiting similar base composition and accelerated evolutionary rate. The inclusion of rRNA genes and removal of fast-evolving sites with the observed variability sorting method for identifying sites deviating from the mean rates improved the phylogenetic inferences under a site-heterogeneous model, correctly recovering most deep branches of the Holometabola phylogeny. We suggest that the use of mitochondrial genome data for resolving deep phylogenetic relationships requires an assessment of the potential impact of substitutional saturation and compositional biases through data deletion strategies and by using site-heterogeneous mixture models. Our study suggests a practical approach for how to use densely sampled mitochondrial genome data in phylogenetic analyses.}, }
@article {pmid27189567, year = {2016}, author = {Wisecaver, JH and Alexander, WG and King, SB and Hittinger, CT and Rokas, A}, title = {Dynamic Evolution of Nitric Oxide Detoxifying Flavohemoglobins, a Family of Single-Protein Metabolic Modules in Bacteria and Eukaryotes.}, journal = {Molecular biology and evolution}, volume = {33}, number = {8}, pages = {1979-1987}, doi = {10.1093/molbev/msw073}, pmid = {27189567}, issn = {1537-1719}, mesh = {Adaptation, Biological/genetics ; Amino Acid Sequence ; Bacteria/*genetics/*metabolism ; Bacterial Proteins/*genetics/*metabolism ; Biological Evolution ; Computational Biology ; Databases, Nucleic Acid ; Dihydropteridine Reductase/genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; Eukaryota/*genetics/*metabolism ; Evolution, Molecular ; Fungi/genetics ; Gene Duplication ; Gene Transfer, Horizontal ; Hemeproteins/*genetics/*metabolism ; NADH, NADPH Oxidoreductases/genetics/metabolism ; Nitric Oxide/*metabolism ; Phylogeny ; }, abstract = {Due to their functional independence, proteins that comprise standalone metabolic units, which we name single-protein metabolic modules, may be particularly prone to gene duplication (GD) and horizontal gene transfer (HGT). Flavohemoglobins (flavoHbs) are prime examples of single-protein metabolic modules, detoxifying nitric oxide (NO), a ubiquitous toxin whose antimicrobial properties many life forms exploit, to nitrate, a common source of nitrogen for organisms. FlavoHbs appear widespread in bacteria and have been identified in a handful of microbial eukaryotes, but how the distribution of this ecologically and biomedically important protein family evolved remains unknown. Reconstruction of the evolutionary history of 3,318 flavoHb protein sequences covering the family's known diversity showed evidence of recurrent HGT at multiple evolutionary scales including intrabacterial HGT, as well as HGT from bacteria to eukaryotes. One of the most striking examples of HGT is the acquisition of a flavoHb by the dandruff- and eczema-causing fungus Malassezia from Corynebacterium Actinobacteria, a transfer that growth experiments show is capable of mediating NO resistance in fungi. Other flavoHbs arose via GD; for example, many filamentous fungi possess two flavoHbs that are differentially targeted to the cytosol and mitochondria, likely conferring protection against external and internal sources of NO, respectively. Because single-protein metabolic modules such as flavoHb function independently, readily undergo GD and HGT, and are frequently involved in organismal defense and competition, we suggest that they represent "plug-and-play" proteins for ecological arms races.}, }
@article {pmid27185558, year = {2016}, author = {Karnkowska, A and Vacek, V and Zubáčová, Z and Treitli, SC and Petrželková, R and Eme, L and Novák, L and Žárský, V and Barlow, LD and Herman, EK and Soukal, P and Hroudová, M and Doležal, P and Stairs, CW and Roger, AJ and Eliáš, M and Dacks, JB and Vlček, &#x10c; and Hampl, V}, title = {A Eukaryote without a Mitochondrial Organelle.}, journal = {Current biology : CB}, volume = {26}, number = {10}, pages = {1274-1284}, doi = {10.1016/j.cub.2016.03.053}, pmid = {27185558}, issn = {1879-0445}, support = {62809//CIHR/Canada ; }, mesh = {Biological Evolution ; Cytosol/metabolism ; Mitochondria/*physiology ; Oxymonadida/*cytology/genetics/*physiology ; Phylogeny ; Sulfur/*metabolism ; Transcriptome ; }, abstract = {The presence of mitochondria and related organelles in every studied eukaryote supports the view that mitochondria are essential cellular components. Here, we report the genome sequence of a microbial eukaryote, the oxymonad Monocercomonoides sp., which revealed that this organism lacks all hallmark mitochondrial proteins. Crucially, the mitochondrial iron-sulfur cluster assembly pathway, thought to be conserved in virtually all eukaryotic cells, has been replaced by a cytosolic sulfur mobilization system (SUF) acquired by lateral gene transfer from bacteria. In the context of eukaryotic phylogeny, our data suggest that Monocercomonoides is not primitively amitochondrial but has lost the mitochondrion secondarily. This is the first example of a eukaryote lacking any form of a mitochondrion, demonstrating that this organelle is not absolutely essential for the viability of a eukaryotic cell.}, }
@article {pmid27185408, year = {2016}, author = {Strakova, A and Ní Leathlobhair, M and Wang, GD and Yin, TT and Airikkala-Otter, I and Allen, JL and Allum, KM and Bansse-Issa, L and Bisson, JL and Castillo Domracheva, A and de Castro, KF and Corrigan, AM and Cran, HR and Crawford, JT and Cutter, SM and Delgadillo Keenan, L and Donelan, EM and Faramade, IA and Flores Reynoso, E and Fotopoulou, E and Fruean, SN and Gallardo-Arrieta, F and Glebova, O and Häfelin Manrique, RF and Henriques, JJ and Ignatenko, N and Koenig, D and Lanza-Perea, M and Lobetti, R and Lopez Quintana, AM and Losfelt, T and Marino, G and Martincorena, I and Martínez Castañeda, S and Martínez-López, MF and Meyer, M and Nakanwagi, B and De Nardi, AB and Neunzig, W and Nixon, SJ and Onsare, MM and Ortega-Pacheco, A and Peleteiro, MC and Pye, RJ and Reece, JF and Rojas Gutierrez, J and Sadia, H and Schmeling, SK and Shamanova, O and Ssuna, RK and Steenland-Smit, AE and Svitich, A and Thoya Ngoka, I and Vițălaru, BA and de Vos, AP and de Vos, JP and Walkinton, O and Wedge, DC and Wehrle-Martinez, AS and van der Wel, MG and Widdowson, SA and Murchison, EP}, title = {Mitochondrial genetic diversity, selection and recombination in a canine transmissible cancer.}, journal = {eLife}, volume = {5}, number = {}, pages = {}, pmid = {27185408}, issn = {2050-084X}, support = {//Wellcome Trust/United Kingdom ; 102942/Z/13/A//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; DNA, Mitochondrial/chemistry/genetics ; Dog Diseases/*genetics ; Dogs ; *Genetic Variation ; Mitochondria/*genetics ; *Recombination, Genetic ; *Selection, Genetic ; Sequence Analysis, DNA ; Venereal Tumors, Veterinary/*genetics ; }, abstract = {Canine transmissible venereal tumour (CTVT) is a clonally transmissible cancer that originated approximately 11,000 years ago and affects dogs worldwide. Despite the clonal origin of the CTVT nuclear genome, CTVT mitochondrial genomes (mtDNAs) have been acquired by periodic capture from transient hosts. We sequenced 449 complete mtDNAs from a global population of CTVTs, and show that mtDNA horizontal transfer has occurred at least five times, delineating five tumour clades whose distributions track two millennia of dog global migration. Negative selection has operated to prevent accumulation of deleterious mutations in captured mtDNA, and recombination has caused occasional mtDNA re-assortment. These findings implicate functional mtDNA as a driver of CTVT global metastatic spread, further highlighting the important role of mtDNA in cancer evolution.}, }
@article {pmid27183727, year = {2016}, author = {Titov, VN}, title = {[THE OPTIMIZATION OF NUTRITION FUNCTION UNDER SYNDROME OF RESISTANCE TO INSULIN, DISORDER OF FATTY ACIDS' METABOLISM AND ABSORPTION OF GLUCOSE BY CELLS (A LECTURE)].}, journal = {Klinicheskaia laboratornaia diagnostika}, volume = {61}, number = {1}, pages = {27-38}, pmid = {27183727}, issn = {0869-2084}, mesh = {Atherosclerosis/*metabolism/pathology/prevention &amp; control ; Biological Evolution ; Biological Transport ; Diet/*methods ; Fatty Acids/metabolism ; Glucose/metabolism ; Humans ; Hypertension/*metabolism/pathology/prevention &amp; control ; Insulin/metabolism ; *Insulin Resistance ; Lipid Metabolism ; Metabolic Syndrome/*metabolism/pathology/prevention &amp; control ; Obesity/*metabolism/pathology/prevention &amp; control ; Recommended Dietary Allowances ; Triglycerides/metabolism ; }, abstract = {The phylogenetic processes continue to proceed in Homo Sapiens. At the very early stages ofphylogenesis, the ancient Archaea that formed mitochondria under symbiotic interaction with later bacterial cells conjointly formed yet another system. In this system, there are no cells' absorption of glucose if it is possible to absorb fatty acids from intercellular medium in the form of unesterfied fatty acids or ketonic bodies--metabolites of fatty acids. This is caused by objectively existed conditions and subsequent availability of substrates at the stages ofphylogenesis: acetate, ketonic bodies, fatty acids and only later glucose. The phylogenetically late insulin used after billions years the same dependencies at formation of regulation ofmetabolism offatty acids and cells' absorption of glucose. In order that syndrome ofresistance ceased to exist as afoundation of metabolic pandemic Homo Sapiens has to understand the following. After successful function ofArchaea+bacterial cells and considered by biology action of insulin for the third time in phylogenesis and using biological function of intelligence the content ofphylogenetically earlier palmitic saturated fatty acid infood can't to exceed possibilities of phylogenetically late lipoproteins to transfer it in intercellular medium and blood and cells to absorb it. It is supposed that at early stages of phylogenesis biological function of intelligence is primarily formed to bring into line "unconformities" of regulation of metabolism against the background of seeming relative biological "perfection". These unconformities were subsequently and separately formed at the level of cells in paracrin regulated cenosises of cells and organs and at the level of organism. The prevention of resistance to insulin basically requires biological function of intelligence, principle of self-restraint, bringing into line multiple desires of Homo Sapiens with much less extensive biological possibilities. The "unconformities" of regulation of metabolism in vivo are etiological factors of all metabolic pandemics including atherosclerosis, metabolic arterial hypertension, obesity and metabolic syndrome Tertiannondatum.}, }
@article {pmid27181928, year = {2016}, author = {Benz, C and Kovářová, J and Králová-Hromadová, I and Pierik, AJ and Lukeš, J}, title = {Roles of the Nfu Fe-S targeting factors in the trypanosome mitochondrion.}, journal = {International journal for parasitology}, volume = {46}, number = {10}, pages = {641-651}, doi = {10.1016/j.ijpara.2016.04.006}, pmid = {27181928}, issn = {1879-0135}, mesh = {Antibodies, Protozoan/biosynthesis ; Blotting, Western ; Cells, Cultured ; Chemical Fractionation ; Computational Biology ; Down-Regulation ; Electroporation ; HSP70 Heat-Shock Proteins/metabolism ; Iron-Sulfur Proteins/genetics/immunology/*physiology ; Mitochondria/chemistry/*physiology ; Mitochondrial Proteins/*physiology ; Phylogeny ; Plasmids ; Protozoan Proteins/genetics/immunology/*physiology ; RNA Interference ; Trypanosoma brucei brucei/chemistry/classification/genetics/*physiology ; }, abstract = {Iron-sulphur clusters (ISCs) are protein co-factors essential for a wide range of cellular functions. The core iron-sulphur cluster assembly machinery resides in the mitochondrion, yet due to export of an essential precursor from the organelle, it is also needed for cytosolic and nuclear iron-sulphur cluster assembly. In mitochondria all [4Fe-4S] iron-sulphur clusters are synthesised and transferred to specific apoproteins by so-called iron-sulphur cluster targeting factors. One of these factors is the universally present mitochondrial Nfu1, which in humans is required for the proper assembly of a subset of mitochondrial [4Fe-4S] proteins. Although most eukaryotes harbour a single Nfu1, the genomes of Trypanosoma brucei and related flagellates encode three Nfu genes. All three Nfu proteins localise to the mitochondrion in the procyclic form of T. brucei, and TbNfu2 and TbNfu3 are both individually essential for growth in bloodstream and procyclic forms, suggesting highly specific functions for each of these proteins in the trypanosome cell. Moreover, these two proteins are functional in the iron-sulphur cluster assembly in a heterologous system and rescue the growth defect of a yeast deletion mutant.}, }
@article {pmid27180575, year = {2016}, author = {Liu, ZX and Zhang, Y and Liu, YT and Chang, QC and Su, X and Fu, X and Yue, DM and Gao, Y and Wang, CR}, title = {Complete Mitochondrial Genome of Echinostoma hortense (Digenea: Echinostomatidae).}, journal = {The Korean journal of parasitology}, volume = {54}, number = {2}, pages = {173-179}, pmid = {27180575}, issn = {1738-0006}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; DNA, Protozoan/*genetics ; Dogs ; Echinostoma/*genetics ; Genetic Markers ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Echinostoma hortense (Digenea: Echinostomatidae) is one of the intestinal flukes with medical importance in humans. However, the mitochondrial (mt) genome of this fluke has not been known yet. The present study has determined the complete mt genome sequences of E. hortense and assessed the phylogenetic relationships with other digenean species for which the complete mt genome sequences are available in GenBank using concatenated amino acid sequences inferred from 12 protein-coding genes. The mt genome of E. hortense contained 12 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 non-coding region. The length of the mt genome of E. hortense was 14,994 bp, which was somewhat smaller than those of other trematode species. Phylogenetic analyses based on concatenated nucleotide sequence datasets for all 12 protein-coding genes using maximum parsimony (MP) method showed that E. hortense and Hypoderaeum conoideum gathered together, and they were closer to each other than to Fasciolidae and other echinostomatid trematodes. The availability of the complete mt genome sequences of E. hortense provides important genetic markers for diagnostics, population genetics, and evolutionary studies of digeneans.}, }
@article {pmid27179700, year = {2016}, author = {Kittel, RN and Austin, AD and Klopfstein, S}, title = {Molecular and morphological phylogenetics of chelonine parasitoid wasps (Hymenoptera: Braconidae), with a critical assessment of divergence time estimations.}, journal = {Molecular phylogenetics and evolution}, volume = {101}, number = {}, pages = {224-241}, doi = {10.1016/j.ympev.2016.05.016}, pmid = {27179700}, issn = {1095-9513}, mesh = {Animals ; Biological Evolution ; DNA/chemistry/isolation &amp; purification/metabolism ; DNA-Binding Proteins/genetics ; Fossils ; Male ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; Wasps/*classification/genetics ; }, abstract = {Parasitoid wasps of the subfamily Cheloninae are both species rich and poorly known. Although the taxonomy of Cheloninae appears to be relatively stable, there is no clear understanding of relationships among higher-level taxa. We here applied molecular phylogenetic analyses using three markers (COI, EF1α, 28S) and 37 morphological characters to elucidate the evolution and systematics of these wasps. Analyses were based on 83 specimens representing 13 genera. All genera except Ascogaster, Phanerotoma, and Pseudophanerotoma formed monophyletic groups; Furcidentia (stat. rev.) is raised to generic rank. Neither Chelonus (Chelonus) nor Chelonus (Microchelonus) were recovered as monophyletic, but together formed a monophyletic lineage. The tribes Chelonini and Odontosphaeropygini formed monophyletic groups, but the Phanerotomini sensu Zettel and Pseudophanerotomini were retrieved as either para- or polyphyletic. The genera comprising the former subfamily Adeliinae were confirmed as being nested within the Cheloninae. To estimate the age of the subfamily, we used 16 fossil taxa. Three approaches were compared: fixed-rate dating, node dating, and total-evidence dating, with age estimates differing greatly between the three methods. Shortcomings of each approach in relation to our dataset are discussed, and none of the age estimates is deemed sufficiently reliable. Given that most dating studies use a single method only, in most cases without presenting analyses on the sensitivity to priors, it is likely that numerous age estimates in the literature suffer from a similar lack of robustness. We argue for a more rigorous approach to dating analyses and for a faithful presentation of uncertainties in divergence time estimates. Given the results of the phylogenetic analysis the following taxonomic changes are proposed: Furcidentia Zettel (stat. rev.), previously treated as a subgenus of Pseudophanerotoma Zettel is raised to generic rank; Microchelonus Szépligeti (syn. nov.), variously treated by previous authors, is proposed as a junior synonym of Chelonus Jurine; the following subgenera of Microchelonus - Baculonus Braet &amp; van Achterberg (syn. nov.), Carinichelonus Tobias (syn. nov.) and Scabrichelonus He, Chen &amp; van Achterberg (syn. nov.), are proposed as junior synonyms of Chelonus; a number of new species names are proposed due to homonyms resulting from the above changes and these are listed in the paper.}, }
@article {pmid27179589, year = {2016}, author = {Mesa-Torres, N and Calvo, AC and Oppici, E and Titelbaum, N and Montioli, R and Miranda-Vizuete, A and Cellini, B and Salido, E and Pey, AL}, title = {Caenorhabditis elegans AGXT-1 is a mitochondrial and temperature-adapted ortholog of peroxisomal human AGT1: New insights into between-species divergence in glyoxylate metabolism.}, journal = {Biochimica et biophysica acta}, volume = {1864}, number = {9}, pages = {1195-1205}, doi = {10.1016/j.bbapap.2016.05.004}, pmid = {27179589}, issn = {0006-3002}, mesh = {Adaptation, Biological ; Alanine/chemistry/metabolism ; Amino Acid Sequence ; Animals ; Biological Evolution ; Caenorhabditis elegans/genetics/*metabolism ; Caenorhabditis elegans Proteins/*chemistry/genetics/metabolism ; Cloning, Molecular ; Dimerization ; Energy Metabolism ; Enzyme Stability ; Escherichia coli/genetics/metabolism ; Gene Expression ; Glyoxylates/chemistry/*metabolism ; Humans ; Mitochondria/*metabolism ; Mutation ; Peroxisomes/*metabolism ; Protein Structure, Secondary ; Pyridoxal Phosphate/chemistry/metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; Species Specificity ; Structural Homology, Protein ; Temperature ; Transaminases/*chemistry/genetics/metabolism ; }, abstract = {In humans, glyoxylate is an intermediary product of metabolism, whose concentration is finely balanced. Mutations in peroxisomal alanine:glyoxylate aminotransferase (hAGT1) cause primary hyperoxaluria type 1 (PH1), which results in glyoxylate accumulation that is converted to toxic oxalate. In contrast, glyoxylate is used by the nematode Caenorhabditis elegans through a glyoxylate cycle to by-pass the decarboxylation steps of the tricarboxylic acid cycle and thus contributing to energy production and gluconeogenesis from stored lipids. To investigate the differences in glyoxylate metabolism between humans and C. elegans and to determine whether the nematode might be a suitable model for PH1, we have characterized here the predicted nematode ortholog of hAGT1 (AGXT-1) and compared its molecular properties with those of the human enzyme. Both enzymes form active PLP-dependent dimers with high specificity towards alanine and glyoxylate, and display similar three-dimensional structures. Interestingly, AGXT-1 shows 5-fold higher activity towards the alanine/glyoxylate pair than hAGT1. Thermal and chemical stability of AGXT-1 is lower than that of hAGT1, suggesting temperature-adaptation of the nematode enzyme linked to the lower optimal growth temperature of C. elegans. Remarkably, in vivo experiments demonstrate the mitochondrial localization of AGXT-1 in contrast to the peroxisomal compartmentalization of hAGT1. Our results support the view that the different glyoxylate metabolism in the nematode is associated with the divergent molecular properties and subcellular localization of the alanine:glyoxylate aminotransferase activity.}, }
@article {pmid27173914, year = {2016}, author = {Noguchi, F and Tanifuji, G and Brown, MW and Fujikura, K and Takishita, K}, title = {Complex evolution of two types of cardiolipin synthase in the eukaryotic lineage stramenopiles.}, journal = {Molecular phylogenetics and evolution}, volume = {101}, number = {}, pages = {133-141}, doi = {10.1016/j.ympev.2016.05.011}, pmid = {27173914}, issn = {1095-9513}, mesh = {DNA, Complementary/chemistry/metabolism ; *Evolution, Molecular ; Membrane Proteins/classification/genetics/metabolism ; Mitochondria ; Phylogeny ; RNA/isolation &amp; purification/metabolism ; Sequence Analysis, DNA ; Stramenopiles/*enzymology ; Transferases (Other Substituted Phosphate Groups)/classification/genetics/metabolism ; }, abstract = {The phospholipid cardiolipin is indispensable for eukaryotes to activate mitochondria, and it was previously reported that two phylogenetically distinct types of enzyme synthesizing cardiolipin, one with two phospholipase D domains (CLS_pld) and the other with a CDP-alcohol phosphatidyltransferase domain (CLS_cap), are patchily and complementarily distributed at higher taxonomic (e.g., supergroup) levels of eukaryotes. Stramenopiles, one of the major eukaryotic clades, were considered to exclusively possess CLS_cap. However, through our present surveys with genome or transcriptome data from a broad range of stramenopile taxa, species with both CLS_cap and CLS_pld and species with only CLS_pld or CLS_cap were discovered among this group. Because these homologues of CLS_cap and CLS_pld retrieved from stramenopiles were likely inherited from the last eukaryotic common ancestor, it is reasonable to assume that a common ancestor of all stramenopiles harbored both CLS_cap and CLS_pld. Furthermore, based on the robust organismal phylogeny of stramenopiles unveiled with large-scale phylogenetic analyses, the earliest diverging lineage of stramenopiles (including bicosoecids, placidids, etc.) was found to comprise species with both CLS_cap and CLS_pld along with species with only either CLS_cap or CLS_pld. These findings suggest that a common ancestor of the most basal stramenopile lineage retained these two vertically inherited enzymes and that differential losses of either CLS_cap or CLS_pld occurred in this lineage. On the other hand, in the other stramenopile lineage composed of Ochrophyta, Pseudofungi, and Labyrinthulomycetes (to the exclusion of the most basal lineage), only CLS_cap was found, and therefore a common ancestor of these three groups likely lost CLS_pld. Based on our findings, the evolution of CLS_cap/CLS_pld in stramenopiles appears to be more complex than previously thought.}, }
@article {pmid27172135, year = {2016}, author = {Kaczanowski, S}, title = {Apoptosis: its origin, history, maintenance and the medical implications for cancer and aging.}, journal = {Physical biology}, volume = {13}, number = {3}, pages = {031001}, doi = {10.1088/1478-3975/13/3/031001}, pmid = {27172135}, issn = {1478-3975}, mesh = {Animals ; Antineoplastic Agents/pharmacology ; Apoptosis/drug effects/*physiology ; Biological Evolution ; Cell Respiration ; Cellular Senescence/*physiology ; Humans ; Mitochondria/*metabolism/pathology ; Neoplasms/drug therapy/*pathology ; Neurodegenerative Diseases/pathology ; Phylogeny ; }, abstract = {Programmed cell death is a basic cellular mechanism. Apoptotic-like programmed cell death (called apoptosis in animals) occurs in both unicellular and multicellular eukaryotes, and some apoptotic mechanisms are observed in bacteria. Endosymbiosis between mitochondria and eukaryotic cells took place early in the eukaryotic evolution, and some of the apoptotic-like mechanisms of mitochondria that were retained after this event now serve as parts of the eukaryotic apoptotic machinery. Apoptotic mechanisms have several functions in unicellular organisms: they include kin-selected altruistic suicide that controls population size, sharing common goods, and responding to viral infection. Apoptotic factors also have non-apoptotic functions. Apoptosis is involved in the cellular aging of eukaryotes, including humans. In addition, apoptosis is a key part of the innate tumor-suppression mechanism. Several anticancer drugs induce apoptosis, because apoptotic mechanisms are inactivated during oncogenesis. Because of the ancient history of apoptosis, I hypothesize that there is a deep relationship between mitochondrial metabolism, its role in aerobic versus anaerobic respiration, and the connection between apoptosis and cancer. Whereas normal cells rely primarily on oxidative mitochondrial respiration, most cancer cells use anaerobic metabolism. According to the Warburg hypothesis, the remodeling of the metabolism is one of the processes that leads to cancer. Recent studies indicate that anaerobic, non-mitochondrial respiration is particularly active in embryonic cells, stem cells, and aggressive stem-like cancer cells. Mitochondrial respiration is particularly active during the pathological aging of human cells in neurodegenerative diseases. According to the reversed Warburg hypothesis formulated by Demetrius, pathological aging is induced by mitochondrial respiration. Here, I advance the hypothesis that the stimulation of mitochondrial metabolism leads to pathological aging.}, }
@article {pmid27165939, year = {2016}, author = {Fu, YB and Dong, Y and Yang, MH}, title = {Multiplexed shotgun sequencing reveals congruent three-genome phylogenetic signals for four botanical sections of the flax genus Linum.}, journal = {Molecular phylogenetics and evolution}, volume = {101}, number = {}, pages = {122-132}, doi = {10.1016/j.ympev.2016.05.010}, pmid = {27165939}, issn = {1095-9513}, mesh = {Biological Evolution ; Chloroplasts/genetics ; DNA, Plant/chemistry/isolation &amp; purification/metabolism ; Flax/classification/*genetics ; *Genome, Plant ; Genomics ; High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {A genome-wide detection of phylogenetic signals by next generation sequencing (NGS) has recently emerged as a promising genomic approach for phylogenetic analysis of non-model organisms. Here we explored the use of a multiplexed shotgun sequencing method to assess the phylogenetic relationships of 18 Linum samples representing 16 species within four botanical sections of the flax genus Linum. The whole genome DNAs of 18 Linum samples were fragmented, tagged, and sequenced using an Illumina MiSeq. Acquired sequencing reads per sample were further separated into chloroplast, mitochondrial and nuclear sequence reads. SNP calls upon genome-specific sequence data sets revealed 6143 chloroplast, 2673 mitochondrial, and 19,562 nuclear SNPs. Phylogenetic analyses based on three-genome SNP data sets with and without missing observations showed congruent three-genome phylogenetic signals for four botanical sections of the Linum genus. Specifically, two major lineages showing a separation of Linum-Dasylinum sections and Linastrum-Syllinum sections were confirmed. The Linum section displayed three major branches representing two major evolutionary stages leading to cultivated flax. Cultivated flax and its immediate progenitor were formed as its own branch, genetically more closely related to L. decumbens and L. grandiflorum with chromosome count of eight, and distantly apart from six other species with chromosome count of nine. Five species of the Linastrum and Syllinum sections were genetically more distant from cultivated flax, but they appeared to be more closely related to each other, even with variable chromosome counts. These findings not only provide the first evidence of congruent three-genome phylogenetic pathways within the Linum genus, but also demonstrate the utility of the multiplexed shotgun sequencing in acquisition of three-genome phylogenetic signals of non-model organisms.}, }
@article {pmid27159731, year = {2017}, author = {Ren, G and Ma, H and Ma, C and Wang, W and Chen, W and Ma, L}, title = {Genetic diversity and population structure of Portunus sanguinolentus (Herbst, 1783) revealed by mtDNA COI sequences.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {5}, pages = {740-746}, doi = {10.1080/24701394.2016.1177040}, pmid = {27159731}, issn = {2470-1408}, mesh = {Animals ; Brachyura/*classification/genetics ; China ; Electron Transport Complex IV/*genetics ; Gene Flow ; Genetic Variation ; Genetics, Population ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*methods ; }, abstract = {In this paper, population genetic diversity and genetic structure of Portunus sanguinolentus distributed along China coast was investigated based on mitochondrial DNA cytochrome c oxidase subunit I (COI) gene. Sixty-eight haplotypes and 71 polymorphic sites were detected in 110 individuals sampled from four localities. The average haplotype diversity (h) and nucleotide diversity (π) were 0.9576 and 0.0051, respectively. Pairwise FST statistics among different localities were negative or low and insignificant, suggesting a widespread gene flow. The AMOVA analysis also indicated a broad genetic exchange among four localities (FST= -0.0039, p = 0.559). The high dispersal capabilities of larvae of P. sanguinolentus coupled with the limited physical barriers in marine environment may be responsible for the high gene flow among P. sanguinolentus populations along southeastern coast of China. Moreover, neutrality test and mismatch analysis implied that P. sanguinolentus population might have undergone a rapid population expansion event. The time of population expansion was estimated to occur about 229,000-321,000 years ago.}, }
@article {pmid27159728, year = {2017}, author = {Ahmed, S and Grobler, P and Madisha, T and Kotze, A}, title = {Mitochondrial D-loop sequences reveal a mixture of endemism and immigration in Egyptian goat populations.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {5}, pages = {711-716}, doi = {10.3109/24701394.2016.1174225}, pmid = {27159728}, issn = {2470-1408}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Egypt ; Genetic Variation ; Goats/*classification/genetics ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; Population Dynamics ; Sequence Analysis, DNA/*methods ; }, abstract = {The mitochondrial D-loop region was used to investigate genetic diversity within and between populations of Egyptian goats, to elucidate processes that explain present patterns of diversity and differentiation and to characterize Egyptian goats relative to international breeds. A total of 120 animals from six populations were sampled. Results confirm the main trend from previous studies of mtDNA diversity in goats, with high levels of diversity within populations, but with a comparative lack of genetic structure supporting geographic distribution. Haplotype diversity varied in a narrow range whereas nucleotide diversity values were more informative in showing differences between populations. The majority of goats analyzed (93.2%) displayed haplotypes that group with Haplogroup A, the most common type found in global goat populations. The remaining animals grouped with the less common Haplogroup G. Population differentiation analysis showed some uniqueness in the Aswan and Sharkawi populations from the South and East of Egypt. Overall, the structure of the Egyptian goat population is characterized by a high degree of homogeneity among populations from the north-western coastal region, the Nile Delta and the upper and middle regions of the Nile valley, but with possible introgression of rarer haplotypes into populations at the southern and eastern extremities of the country.}, }
@article {pmid27159725, year = {2017}, author = {Amaral, DT and Mitani, Y and Oliveira, G and Ohmiya, Y and Viviani, VR}, title = {Revisiting Coleoptera a + T-rich region: structural conservation, phylogenetic and phylogeographic approaches in mitochondrial control region of bioluminescent Elateridae species (Coleoptera).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {5}, pages = {671-680}, doi = {10.3109/24701394.2016.1174220}, pmid = {27159725}, issn = {2470-1408}, mesh = {Animals ; Base Sequence ; Coleoptera/*classification/genetics ; Conserved Sequence ; DNA, Mitochondrial/*chemistry/genetics ; Evolution, Molecular ; Genetic Variation ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*methods ; }, abstract = {The control region (CR) or A + T-rich region in Coleoptera mt genome is poorly characterized, including the Elateroidea bioluminescent species. Here, we provided the first attempt to characterize and compare the structure and organization of the CR of different species within Elateridae. We also revisited some sequenced Coleoptera CR and observed consensus T-stretches, non-conserved sequences near the stem-loop and unusual inner tRNAs-like sequences. All these features are probably involved in the replication start of the mt genome. The phylogenetic relationships in Elateridae bioluminescent groups using partial sequence of CR showed the monophyly of Pyrearinus pumilus group and Pyrearinus as a polyphyletic genus, corroborating our previous results. The wider genetic variation obtained by CR analysis could separate two different lineages that occur within P. termitilluminans populations. In Elateridae, the CR exhibited high polymorphism within and between populations, which was also observed in other Coleoptera species, suggesting that the CR could be described as a suitable molecular marker to be applied in phylogenetic and phylogeographic studies.}, }
@article {pmid27159724, year = {2017}, author = {Brandt, AL and Grigorev, K and Afanador-Hernández, YM and Paulino, LA and Murphy, WJ and Núñez, A and Komissarov, A and Brandt, JR and Dobrynin, P and Hernández-Martich, JD and María, R and O'Brien, SJ and Rodríguez, LE and Martínez-Cruzado, JC and Oleksyk, TK and Roca, AL}, title = {Mitogenomic sequences support a north-south subspecies subdivision within Solenodon paradoxus.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {5}, pages = {662-670}, doi = {10.3109/24701394.2016.1167891}, pmid = {27159724}, issn = {2470-1408}, mesh = {Animals ; Eulipotyphla/*classification/genetics ; Evolution, Molecular ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {Solenodons are insectivores found only in Hispaniola and Cuba, with a Mesozoic divergence date versus extant mainland mammals. Solenodons are the oldest lineage of living eutherian mammal for which a mitogenome sequence has not been reported. We determined complete mitogenome sequences for six Hispaniolan solenodons (Solenodon paradoxus) using next-generation sequencing. The solenodon mitogenomes were 16,454-16,457 bp long and carried the expected repertoire of genes. A mitogenomic phylogeny confirmed the basal position of solenodons relative to shrews and moles, with solenodon mitogenomes estimated to have diverged from those of other mammals ca. 78 Mya. Control region sequences of solenodons from the northern (n = 3) and southern (n = 5) Dominican Republic grouped separately in a network, with FST = 0.72 (p = 0.036) between north and south. This regional genetic divergence supports previous morphological and genetic reports recognizing northern (S. p. paradoxus) and southern (S. p. woodi) subspecies in need of separate conservation plans.}, }
@article {pmid27159697, year = {2017}, author = {Muangkram, Y and Amano, A and Wajjwalku, W and Pinyopummintr, T and Thongtip, N and Kaolim, N and Sukmak, M and Kamolnorranath, S and Siriaroonrat, B and Tipkantha, W and Maikaew, U and Thomas, W and Polsrila, K and Dongsaard, K and Sanannu, S and Wattananorrasate, A}, title = {Genetic diversity of the captive Asian tapir population in Thailand, based on mitochondrial control region sequence data and the comparison of its nucleotide structure with Brazilian tapir.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {4}, pages = {597-601}, doi = {10.3109/24701394.2016.1149828}, pmid = {27159697}, issn = {2470-1408}, mesh = {Animals ; Brazil ; DNA, Mitochondrial/*genetics ; Endangered Species ; Genetic Variation ; Mitochondria/genetics ; Perissodactyla/*classification/genetics ; Phylogeny ; *Polymorphism, Genetic ; Sequence Analysis, DNA/*methods ; Thailand ; }, abstract = {The Asian tapir (Tapirus indicus) has been classified as Endangered on the IUCN Red List of Threatened Species (2008). Genetic diversity data provide important information for the management of captive breeding and conservation of this species. We analyzed mitochondrial control region (CR) sequences from 37 captive Asian tapirs in Thailand. Multiple alignments of the full-length CR sequences sized 1268 bp comprised three domains as described in other mammal species. Analysis of 16 parsimony-informative variable sites revealed 11 haplotypes. Furthermore, the phylogenetic analysis using median-joining network clearly showed three clades correlated with our earlier cytochrome b gene study in this endangered species. The repetitive motif is located between first and second conserved sequence blocks, similar to the Brazilian tapir. The highest polymorphic site was located in the extended termination associated sequences domain. The results could be applied for future genetic management based in captivity and wild that shows stable populations.}, }
@article {pmid27159687, year = {2017}, author = {Basheer, VS and Vineesh, N and Bineesh, KK and Kumar, RG and Mohitha, C and Venu, S and Kathirvelpandian, A and Gopalakrishnan, A and Jena, JK}, title = {Mitochondrial signatures for identification of grouper species from Indian waters.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {4}, pages = {451-457}, doi = {10.3109/19401736.2015.1137899}, pmid = {27159687}, issn = {2470-1408}, mesh = {Animals ; Bass/*classification/genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Fish Proteins/genetics ; India ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; }, abstract = {Groupers are important commercial fish in many parts of the world. Accurate identification is critical for effective conservation assessment and fisheries management. Genetic barcodes provide a simple and reproducible method for the identification of species even in the absence of taxonomic expertise. The generation of reference barcodes from properly identified specimens is an important first step in this direction. Here, 36 species belonging to the subfamily Epinephelinae (Family: Serranidae) were collected from landings on the west coast of India and Port Blair, Andaman, and partial nucleotide sequence data of the mitochondrial cytochrome C oxidase subunit I (COI) gene was generated. Barcodes for 13 species were developed from Indian waters for the first time. Analysis using the COI gene produced phylogenetic trees in concurrence with other multi-gene studies. Epinephelus fasciatus and E. areolatus were found to be a species complex, as hypothesized in other studies. The DNA barcodes developed in the study can be used for identifying species within Epinehelinae, where taxonomic ambiguity still exists.}, }
@article {pmid27158872, year = {2016}, author = {Froufe, E and Gan, HM and Lee, YP and Carneiro, J and Varandas, S and Teixeira, A and Zieritz, A and Sousa, R and Lopes-Lima, M}, title = {The male and female complete mitochondrial genome sequences of the Endangered freshwater mussel Potomida littoralis (Cuvier, 1798) (Bivalvia: Unionidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3571-3572}, doi = {10.3109/19401736.2015.1074223}, pmid = {27158872}, issn = {2470-1408}, mesh = {Animals ; Bivalvia/*genetics ; DNA, Mitochondrial/genetics/isolation &amp; purification ; *Endangered Species ; Female ; Fresh Water ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Male ; Mitochondria/genetics ; Open Reading Frames ; Phylogeny ; RNA, Transfer/genetics ; Whole Genome Sequencing ; }, abstract = {Freshwater mussels of the family Unionidae exhibit a particular form of mitochondria inheritance called double uniparental inheritance (DUI), in which the mitochondria are inherited by both male and female parents. The (M)ale and (F)emale mitogenomes are highly divergent within species. In the present study, we determine and describe the complete M and F mitogenomes of the Endangered freshwater mussel Potomida littoralis (Cuvier, 1798). The complete M and F mitogenomes sequences are 16 451 bp and 15 787 bp in length, respectively. Both F and M have the same gene content: 13 protein-coding genes (PCGs), 22 transfer RNA (trn) and 2 ribosomal RNA (rrn) genes. Bayesian analyses based on the concatenated nucleotide sequences of 12 PCGs and 2 rrn genes of both genomes, including mitogenome sequences available from related species, were performed. Male and Female lineages are monophyletic within the family, but reveal distinct phylogenetic relationships.}, }
@article {pmid27158871, year = {2016}, author = {Sung, CH and Tseng, CT and Wang, LJ and Li, YC and Lu, JK}, title = {The complete mitochondrial genome of Babylonia borneensis (Gastropoda: Neogastropoda: Buccinidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3534-3535}, doi = {10.3109/19401736.2015.1074205}, pmid = {27158871}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Gastropoda/*genetics ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitochondrial genome sequence of the Babylonia borneensis is reported for the first time in this study. The length of genome was 15 556 bp, including 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. The nucleotide composition of the mitogenome showed AT-rich feature, with the AT content of 68.2%. Comparison of the identity of the B. borneensis mitogenome with B. areolata, B. lani and B. lutosa was 87.5%, 87.4% and 86.9%, respectively. The construction of phylogenetic tree showed high bootstrap support value. Babylonia borneensis grouped together with other Babylons and the lineages of Buccinidae was strongly supported. In this study, our results could provide a further understanding in the phylogenetic relationships of the Neogastropoda.}, }
@article {pmid27158870, year = {2016}, author = {Xia, Y and Dang, X and Xu, Q and Zhang, D}, title = {The first complete mitochondrial genome of the Maylandia zebra.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3521-3522}, doi = {10.3109/19401736.2015.1074199}, pmid = {27158870}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Equidae/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Maylandia zebra, a member of the family cichlid living in individual African lakes, are regarded as a significant evolution model. Recently the genome sequencing had been done, but there is no sufficient information about its mitochondria. Herein, we first assembled the complete mitochondrial genome sequence of Maylandia zebra. It is a 16 582 bp long sequence with most mitogenome's characteristic structure, 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 putative control region. The GC-content of our fresh sequence is 45.86%, similar to closely related species Oreochromis niloticus. The accuracy and utility of new determined mitogenome sequences can be verified by the phylogenetic analysis, based on whole mitogenome alignment with Neolamprologus brichardi, Pseudotropheus crabro, Oreochromis niloticu, which is closest relative to Maylandia zebra, and 6 others. Using the full mitogenome, we expect to address taxonomic issues and study the related evolution events. Moreover, this is the first report of the mitogenome of genus Maylandia.}, }
@article {pmid27158869, year = {2016}, author = {Lecompte, E and Crouau-Roy, B and Aujard, F and Holota, H and Murienne, J}, title = {Complete mitochondrial genome of the gray mouse lemur, Microcebus murinus (Primates, Cheirogaleidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3514-3516}, doi = {10.3109/19401736.2015.1074196}, pmid = {27158869}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Cheirogaleidae/*genetics ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {We report the high-coverage complete mitochondrial genome sequence of the gray mouse lemur Microcebus murinus. The sequencing has been performed on an Illumina Hiseq 2500 platform, with a genome skimming strategy. The total length of this mitogenome is 16 963 bp, containing 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 non-coding region (D-loop region). The genome organization, nucleotide composition and codon usage are similar to those reported from other primate's mitochondrial genomes. The complete mitochondrial genome sequence reported here will be useful for comparative genomics studies in primates.}, }
@article {pmid27158791, year = {2016}, author = {Cavaleiro, NP and Solé-Cava, AM and Melo, CM and de Almeida, LG and Lazoski, C and Vasconcelos, AT}, title = {The complete mitochondrial genome of Crassostrea gasar (Bivalvia: Ostreidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {4}, pages = {2939-2940}, doi = {10.3109/19401736.2015.1060450}, pmid = {27158791}, issn = {2470-1408}, mesh = {Animals ; Crassostrea/*classification/*genetics ; Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; Whole Genome Sequencing ; }, abstract = {The complete mitochondrial genome of Crassostrea gasar was sequenced using the Ion Proton technology in combination with 454 Roche GS-FLX plataform data. We assembled a 17,686 bp complete circular mitochondrial genome, containing 13 protein-coding genes, a major non-coding region (MNR), two ribosomal RNA genes and 24 transfer RNA genes. Phylogenetic analysis of concatenated amino acid sequences from mitochondria showed monophyletic clades formed with high bootstrap values. This is the first complete mitochondrial sequence of an oyster from South America. Mitogenome sequence was deposited in GenBank under the accession number KR856227.}, }
@article {pmid27158130, year = {2016}, author = {Baruselli, PS and Vieira, LM and Sá Filho, MF and Mingoti, RD and Ferreira, RM and Chiaratti, MR and Oliveira, LH and Sales, JN and Sartori, R}, title = {Associations of insulin resistance later in lactation on fertility of dairy cows.}, journal = {Theriogenology}, volume = {86}, number = {1}, pages = {263-269}, doi = {10.1016/j.theriogenology.2016.04.039}, pmid = {27158130}, issn = {1879-3231}, mesh = {Animals ; Cattle/*physiology ; Female ; Fertility/*physiology ; Insulin Resistance/*physiology ; Lactation/*physiology ; Pregnancy ; }, abstract = {The challenge of getting dairy cows pregnant during early lactation is a well-described, worldwide problem. However, specifically in farms with poor reproductive, nutritional, and environmental conditions/management, a low pregnancy rate during early lactation is followed inevitably by an increased number of nonpregnant cows after 150 days in milk, with even more difficulties to achieve pregnancy. Therefore, several studies were designed to understand and develop strategies to mitigate reduced fertility of cows during late lactation. Experiments were performed under tropical regions to determine metabolic status during lactation and association of stage of lactation on oocyte quality and fertility. Lactating cows with extended days not pregnant (e.g.,>150 days in milk) often had systemic metabolic alterations, including development of peripheral insulin resistance and various oocyte alterations, including reduced expression of genes encoding glucose transport proteins, reduced amounts of mtDNA, increased expression of mitochondria-related genes, and increased expression of apoptosis-related genes. Additionally, in vitro embryo production and pregnancy per AI were lower in late- versus early-lactation cows in some but not all studies. Notwithstanding, when a normal embryo was transferred to a cow in late lactation, the pregnancy per transfer was reasonable, reinforcing the assertion that fertility problems in late-lactation cows may be associated with oocyte quality, fertilization, and/or failure of early embryo development. In conclusion, insulin resistance may reduce oocyte competence and consequently fertility in late-lactation dairy cows.}, }
@article {pmid27151937, year = {2016}, author = {Cruz, JC and Ferraro, DP and Farías, A and Santos, JS and Recco-Pimentel, SM and Faivovich, J and Hermida, GN}, title = {A comparative ultrastructural analysis of spermatozoa in Pleurodema (Anura, Leptodactylidae, Leiuperinae).}, journal = {Journal of morphology}, volume = {277}, number = {7}, pages = {957-977}, doi = {10.1002/jmor.20550}, pmid = {27151937}, issn = {1097-4687}, mesh = {Animals ; Anura/*anatomy &amp; histology/classification ; Biological Evolution ; Male ; Mitochondria/ultrastructure ; *Phylogeny ; Spermatozoa/*ultrastructure ; }, abstract = {This study describes the spermatozoa of 10 of the 15 species of the Neotropical frog genus Pleurodema through transmission electron microscopy. The diversity of oviposition modes coupled with a recent phylogenetic hypothesis of Pleurodema makes it an interesting group for the study of ultrastructural sperm evolution in relation to fertilization environment and egg-clutch structure. We found that Pleurodema has an unusual variability in sperm morphology. The more variable structures were the acrosomal complex, the midpiece, and the tail. The acrosomal complex has all the structures commonly reported in hyloid frogs but with different degree of development of the subacrosomal cone. Regarding the midpiece, the variability is given by the presence or absence of the mitochondrial collar. Finally, the tail is the most variable structure, ranging from single (only axoneme) to more complex (presence of paraxonemal rod, cytoplasmic sheath, and undulating membrane), with the absence of the typical axial fiber present in hyloid frogs, also shared with some other genera of Leiuperinae. J. Morphol. 277:957-977, 2016. © 2016 Wiley Periodicals, Inc.}, }
@article {pmid27150350, year = {2016}, author = {Ortiz, D and Francke, OF}, title = {Two DNA barcodes and morphology for multi-method species delimitation in Bonnetina tarantulas (Araneae: Theraphosidae).}, journal = {Molecular phylogenetics and evolution}, volume = {101}, number = {}, pages = {176-193}, doi = {10.1016/j.ympev.2016.05.003}, pmid = {27150350}, issn = {1095-9513}, mesh = {Animals ; DNA/chemistry/isolation &amp; purification/metabolism ; DNA Barcoding, Taxonomic ; Female ; Male ; Mexico ; Mitochondria/genetics ; Phylogeny ; Spiders/*classification/genetics ; }, abstract = {Determining species boundaries is a central debate in biology. Several recently developed molecular delimitation methods have highlighted extensive inconsistency in classical morphological taxonomy. However, choosing between them is contentious. Molecular studies on theraphosid spiders have found considerable cryptic diversity and many species redundantly described. Most of these studies have relied only on COI, a mitochondrial marker that has proven its efficacy in animal studies, but which also might lead to an over-estimation of diversity. Here we present an integrative approach to species delimitation in Bonnetina, a poorly known group of tarantulas endemic to Mexico. We employed morphological evidence, as well as different setups with distance-based (Hard-Gap barcoding and ABGD) and tree-based (GMYC, PTP and BPP) molecular barcoding approaches, using one mitochondrial (COI) and one nuclear (ITS1) rapidly evolving loci. BPP is also used as a multi-locus method. We also explored the influence of ambiguous alignment choice and of coding gaps as characters in phylogenetic inference and in species delimitation with that marker. Different delimitation methods with COI gave moderately variable results and this gene exhibited a universal barcode gap. The ITS1 gene tree was well supported and robust to alignment choice; with this locus, coding gaps improved branch support and species delimitation with PTP. No universal barcode gap was found with ITS1, and single locus delimitations returned disparate results. However, this locus helped to highlight cases of under- and overestimations by COI. BPP gave solutions with many lineages, in single locus and combined analyses, especially with the recently implemented unguided methodology. We recognize 12 robustly supported species in our data set, of which seven remain undescribed, and three are morphologically cryptic. For COI Bonnetina species identification, we propose intra- and inter-specific thresholds of 2% and 6% sequence divergence, respectively. We conclude that morphological signal for species delimitation in Bonnetina is higher than for other studied tarantulas, but it fails to recognize several lineages in the genus. COI is a functional barcoding marker, and the most reliable source of evidence that we used, but it may also lead to inaccurate delimitations. ITS1 is a highly informative locus for species delimitation and species-level phylogeny, but it performs poorly as a barcoding marker. Due to variability between delimitation methods, we suggest combining evidence from multiple approaches to get better-supported results.}, }
@article {pmid27148492, year = {2016}, author = {Ball, SG and Bhattacharya, D and Qiu, H and Weber, AP}, title = {Commentary: Plastid establishment did not require a chlamydial partner.}, journal = {Frontiers in cellular and infection microbiology}, volume = {6}, number = {}, pages = {43}, pmid = {27148492}, issn = {2235-2988}, mesh = {Carbohydrate Metabolism/*physiology ; Chlamydia/*genetics ; Cyanobacteria/*genetics ; Cyanophora/*genetics ; Plastids/*metabolism ; }, }
@article {pmid27143389, year = {2016}, author = {van Rossum, HM and Kozak, BU and Niemeijer, MS and Dykstra, JC and Luttik, MA and Daran, JM and van Maris, AJ and Pronk, JT}, title = {Requirements for Carnitine Shuttle-Mediated Translocation of Mitochondrial Acetyl Moieties to the Yeast Cytosol.}, journal = {mBio}, volume = {7}, number = {3}, pages = {}, pmid = {27143389}, issn = {2150-7511}, mesh = {Acetyl Coenzyme A/*metabolism ; Biological Transport ; Carnitine/*metabolism ; Culture Media/chemistry ; Cytosol/chemistry ; Glucose/metabolism ; Metabolic Engineering ; Mitochondria/*metabolism ; Saccharomyces cerevisiae/genetics/growth &amp; development/*metabolism ; }, abstract = {UNLABELLED: In many eukaryotes, the carnitine shuttle plays a key role in intracellular transport of acyl moieties. Fatty acid-grown Saccharomyces cerevisiae cells employ this shuttle to translocate acetyl units into their mitochondria. Mechanistically, the carnitine shuttle should be reversible, but previous studies indicate that carnitine shuttle-mediated export of mitochondrial acetyl units to the yeast cytosol does not occur in vivo This apparent unidirectionality was investigated by constitutively expressing genes encoding carnitine shuttle-related proteins in an engineered S. cerevisiae strain, in which cytosolic acetyl coenzyme A (acetyl-CoA) synthesis could be switched off by omitting lipoic acid from growth media. Laboratory evolution of this strain yielded mutants whose growth on glucose, in the absence of lipoic acid, was l-carnitine dependent, indicating that in vivo export of mitochondrial acetyl units to the cytosol occurred via the carnitine shuttle. The mitochondrial pyruvate dehydrogenase complex was identified as the predominant source of acetyl-CoA in the evolved strains. Whole-genome sequencing revealed mutations in genes involved in mitochondrial fatty acid synthesis (MCT1), nuclear-mitochondrial communication (RTG2), and encoding a carnitine acetyltransferase (YAT2). Introduction of these mutations into the nonevolved parental strain enabled l-carnitine-dependent growth on glucose. This study indicates intramitochondrial acetyl-CoA concentration and constitutive expression of carnitine shuttle genes as key factors in enabling in vivo export of mitochondrial acetyl units via the carnitine shuttle.<br><br>IMPORTANCE: This study demonstrates, for the first time, that Saccharomyces cerevisiae can be engineered to employ the carnitine shuttle for export of acetyl moieties from the mitochondria and, thereby, to act as the sole source of cytosolic acetyl-CoA. Further optimization of this ATP-independent mechanism for cytosolic acetyl-CoA provision can contribute to efficient, yeast-based production of industrially relevant compounds derived from this precursor. The strains constructed in this study, whose growth on glucose depends on a functional carnitine shuttle, provide valuable models for further functional analysis and engineering of this shuttle in yeast and other eukaryotes.}, }
@article {pmid27143241, year = {2016}, author = {DiBattista, JD and Whitney, J and Craig, MT and Hobbs, JA and Rocha, LA and Feldheim, KA and Berumen, ML and Bowen, BW}, title = {Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes.}, journal = {Molecular phylogenetics and evolution}, volume = {101}, number = {}, pages = {203-215}, doi = {10.1016/j.ympev.2016.04.036}, pmid = {27143241}, issn = {1095-9513}, mesh = {Animals ; *Biological Evolution ; Cytochromes b/genetics ; DNA, Mitochondrial/chemistry/isolation &amp; purification/metabolism ; *Hybridization, Genetic ; Indian Ocean ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Pacific Ocean ; Perciformes/classification/*genetics ; Phylogeny ; }, abstract = {Closely related species can provide valuable insights into evolutionary processes through comparison of their ecology, geographic distribution and the history recorded in their genomes. In the Indo-Pacific, many reef fishes are divided into sister species that come into secondary contact at biogeographic borders, most prominently where Indian Ocean and Pacific Ocean faunas meet. It is unclear whether hybridization in this contact zone represents incomplete speciation, secondary contact, an evolutionary dead-end (for hybrids) or some combination of the above. To address these issues, we conducted comprehensive surveys of two widely-distributed surgeonfish species, Acanthurus leucosternon (N=141) and A. nigricans (N=412), with mtDNA cytochrome b sequences and ten microsatellite loci. These surgeonfishes are found primarily in the Indian and Pacific Oceans, respectively, but overlap at the Christmas and Cocos-Keeling Islands hybrid zone in the eastern Indian Ocean. We also sampled the two other Pacific members of this species complex, A. achilles (N=54) and A. japonicus (N=49), which are known to hybridize with A. nigricans where their ranges overlap. Our results indicate separation between the four species that range from the recent Pleistocene to late Pliocene (235,000-2.25million years ago). The Pacific A. achilles is the most divergent (and possibly ancestral) species with mtDNA dcorr≈0.04, whereas the other two Pacific species (A. japonicus and A. nigricans) are distinguishable only at a population or subspecies level (ΦST=0.6533, P<0.001). Little population structure was observed within species, with evidence of recent population expansion across all four geographic ranges. We detected sharing of mtDNA haplotypes between species and extensive hybridization based on microsatellites, consistent with later generation hybrids but also the effects of allele homoplasy. Despite extensive introgression, 98% of specimens had concordance between mtDNA lineage and species identification based on external morphology, indicating that species integrity may not be eroding. The A. nigricans complex demonstrates a range of outcomes from incomplete speciation to secondary contact to decreasing hybridization with increasing evolutionary depth.}, }
@article {pmid27135164, year = {2016}, author = {Johnston, IG and Williams, BP}, title = {Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention.}, journal = {Cell systems}, volume = {2}, number = {2}, pages = {101-111}, doi = {10.1016/j.cels.2016.01.013}, pmid = {27135164}, issn = {2405-4712}, mesh = {Bayes Theorem ; DNA, Mitochondrial ; *Eukaryota ; Evolution, Molecular ; Genes, Mitochondrial ; Genome, Mitochondrial ; Mitochondria ; Phylogeny ; }, abstract = {Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modeling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins comprising the structural cores of the electron transport chain are preferentially encoded within mitochondrial genomes across eukaryotes. A combination of high GC content and high protein hydrophobicity is required to explain patterns of mtDNA gene retention; a model that accounts for these selective pressures can also predict the success of artificial gene transfer experiments in vivo. This work provides a general method for data-driven inference of the ordering of evolutionary and progressive events, here identifying the distinct features shaping mitochondrial genomes of present-day species.}, }
@article {pmid27135161, year = {2016}, author = {Allen, JF and Martin, WF}, title = {Why Have Organelles Retained Genomes?.}, journal = {Cell systems}, volume = {2}, number = {2}, pages = {70-72}, doi = {10.1016/j.cels.2016.02.007}, pmid = {27135161}, issn = {2405-4712}, mesh = {Cell Nucleus ; *Chloroplasts ; Electron Transport ; Genome ; Mitochondria/genetics ; *Organelles ; Plants/genetics ; Protein Transport ; }, abstract = {Genes in mitochondria and chloroplasts are co-located with their gene products to permit regulation of trans-membrane electron transport at the energetic boundary of the cell.}, }
@article {pmid27133210, year = {2016}, author = {Bonnard, G and Gobert, A and Arrivé, M and Pinker, F and Salinas-Giegé, T and Giegé, P}, title = {Transfer RNA maturation in Chlamydomonas mitochondria, chloroplast and the nucleus by a single RNase P protein.}, journal = {The Plant journal : for cell and molecular biology}, volume = {87}, number = {3}, pages = {270-280}, doi = {10.1111/tpj.13198}, pmid = {27133210}, issn = {1365-313X}, mesh = {Cell Nucleus/*metabolism ; Chlamydomonas/genetics/*metabolism ; Chloroplasts/*metabolism ; Mitochondria/*metabolism ; RNA, Transfer/genetics/*metabolism ; Ribonuclease P/genetics/*metabolism ; }, abstract = {The maturation of tRNA precursors involves the 5' cleavage of leader sequences by an essential endonuclease called RNase P. Beyond the ancestral ribonucleoprotein (RNP) RNase P, a second type of RNase P called PRORP (protein-only RNase P) evolved in eukaryotes. The current view on the distribution of RNase P in cells is that multiple RNPs, multiple PRORPs or a combination of both, perform specialised RNase P activities in the different compartments where gene expression occurs. Here, we identify a single gene encoding PRORP in the green alga Chlamydomonas reinhardtii while no RNP is found. We show that its product, CrPRORP, is triple-localised to mitochondria, the chloroplast and the nucleus. Its downregulation results in impaired tRNA biogenesis in both organelles and the nucleus. CrPRORP, as a single-subunit RNase P for an entire organism, makes up the most compact and versatile RNase P machinery described in either prokaryotes or eukaryotes.}, }
@article {pmid27132943, year = {2016}, author = {Shibata, H and Chijiwa, T and Hattori, S and Terada, K and Ohno, M and Fukumaki, Y}, title = {The taxonomic position and the unexpected divergence of the Habu viper, Protobothrops among Japanese subtropical islands.}, journal = {Molecular phylogenetics and evolution}, volume = {101}, number = {}, pages = {91-100}, doi = {10.1016/j.ympev.2016.04.027}, pmid = {27132943}, issn = {1095-9513}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Genetic Variation ; Genome, Mitochondrial ; Geography ; *Islands ; Japan ; Likelihood Functions ; Markov Chains ; Monte Carlo Method ; Phylogeny ; Sequence Analysis, DNA ; Time Factors ; Trimeresurus/*classification/*genetics ; *Tropical Climate ; }, abstract = {There are four Habu species currently recognized in Japan: Protobothrops flavoviridis from the Amami Islands and the Okinawa Islands, P. tokarensis from the Tokara Islands, P. elegans from the Yaeyama Islands and Ovophis okinabvensis from the Amami Islands and the Okinawa Islands. To clarify their taxonomic positions, we determined the complete mitochondria genome sequence (approx. 17kb) from two specimens from two different islands each for P. flavoviridis, P. tokarensis and P. elegans as well as one specimen of O. okinavensis and reconstructed the molecular phylogeny of Protobothrops using the published sequences of related species. The maximum likelihood tree showed four major species groups within Protbothrops: Group I consisting of P. cornutus, P. dabieshanensis, P. jerdonii and P. xiangchengensis; Group II consisting of P. flavoviridis and P. tokarensis; Group III consisting of P. maolensis, P. mucrosquamatus and P. elegans; Group IV consisting of P. himalayanus and P. kaubacki. Since we observed an unexpected divergence and the paraphyly of the two samples of P. flavoviridis collected from different islands, Amami-Oshima and Okinawajima within the Group II, we expanded the analysis by increasing the number of P. flavoviridis and P. tokarensis collected from 10 islands: Amami-Oshima (5 specimens), Kakeromajima (4) and Tokunoshima (4) from the Amami Islands, Okinawajima (4), Iheyajima (4), Iejima (4), Tokashikijima (4) and Kumejima (4) from the Okinawa Islands, Kodakarajima (P. tokarensis) (4) and Takarajima (P. tokarensis) (4) from the Tokara Islands. The maximum likelihood tree of the 44 samples replicated the significant divergence of P. flavoviridis between the Amami Clade including Amami-Oshima, Kakeromajima and Tokunoshima and the Okinawa Clade including Okinawajima, Iheyajima, Iejima, Tokashikijima and Kumejima. The Amami Clade also include all specimens from the Tokara Islands currently known as an independent species, P. tokarensis, suggesting the paraphyly of the taxon, P. flavoviridis. In contrast, we observed a distinct lineage of the two specimens from the Yaeyama Islands, supporting the validity of the taxon, P. elegans as an independent species. By MCMC method, we estimated the divergence time between the Amami Clade and the Okinawa Clade to be 6.51MYA, suggesting that the vicariance of the two clades preceded the geological separation of the Amami Islands and the Okinawa Islands (∼1.5MYA). As expected from the limited mobility of terrestrial reptiles including snakes, we observed high genetic divergence in Habu mtDNA among Japanese subtropical island populations.}, }
@article {pmid27132143, year = {2016}, author = {Kobori, Y and Mizuta, S}, title = {Similarity Estimation Between DNA Sequences Based on Local Pattern Histograms of Binary Images.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {14}, number = {2}, pages = {103-112}, pmid = {27132143}, issn = {2210-3244}, mesh = {*Algorithms ; Animals ; Base Sequence ; Genome, Mitochondrial/genetics ; Humans ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Graphical representation of DNA sequences is one of the most popular techniques for alignment-free sequence comparison. Here, we propose a new method for the feature extraction of DNA sequences represented by binary images, by estimating the similarity between DNA sequences using the frequency histograms of local bitmap patterns of images. Our method shows linear time complexity for the length of DNA sequences, which is practical even when long sequences, such as whole genome sequences, are compared. We tested five distance measures for the estimation of sequence similarities, and found that the histogram intersection and Manhattan distance are the most appropriate ones for phylogenetic analyses.}, }
@article {pmid27129899, year = {2016}, author = {Ho, ALFC and Pruett, CL and Lin, J}, title = {Phylogeny and biogeography of Poecilia (Cyprinodontiformes: Poeciliinae) across Central and South America based on mitochondrial and nuclear DNA markers.}, journal = {Molecular phylogenetics and evolution}, volume = {101}, number = {}, pages = {32-45}, doi = {10.1016/j.ympev.2016.04.032}, pmid = {27129899}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/*genetics ; Central America ; DNA, Mitochondrial/*genetics ; Genetic Markers ; Geography ; Mitochondria/genetics ; *Phylogeny ; Poecilia/*classification/*genetics ; South America ; Time Factors ; }, abstract = {Poeciliids are a diverse group of small Neotropical fishes, and despite considerable research attention as models in ecology and evolutionary biology, our understanding of their biogeographic and phylogenetic relationships is still limited. We investigated the phylogenetic relationships of South and Central American Poecilia, by examining 2395 base pairs of mitochondrial DNA (ATPase 8/6, COI) and nuclear DNA (S7) for 18 species across six subgenera. Fifty-eight novel sequences were acquired from newly collected specimens and 20 sequences were obtained from previously published material. Analyses of concatenated and partitioned mitochondrial DNA and nuclear DNA sets resulted in a well-supported phylogeny that resolved several monophyletic groups corresponding to previously hypothesized subgenera and species complexes. A divergence-dating analysis supported the hypothesis of the genus Poecilia dispersing into Central America in the early Pliocene (ancestors of Psychropoecilia+Allopoecilia+Mollienesia: 7.3-2.0Mya) from predominantly South America. Subsequently, one lineage (subgenus Allopoecilia: 5.1-1.3Mya) expanded deeper into South America from Lower-Central America, and one lineage expanded from Nuclear-Central America into South America (subgenus Mollienesia: 0.71-0.14Mya). The subgenus Mollienesia diverged into three monophyletic groups that can be identified by nuptial male dorsal fin morphology and inner jaw dentition. A subclade of the unicuspid short-fins (subgenus Mollienesia) was the lineage that expanded into South America during the middle Pleistocene. Species in this subclade are now distributed across northern South America, where they are partially sympatric with Allopoecilia. However the P. (A.) caucana complex was not monophyletic, with P. (A.) wandae clustering in the Mollienesia subclade that expanded into South America. It is apparent that characters (body size, scale count, pigmentation, and gonopodium morphology) used to define the P. (A.) caucana complex are homoplastic and suggestive of rapid convergence in northern South America. Our improved taxon sampling and divergence-time calibration allowed for insights into the timing and direction of dispersals, and provides an improved understanding of the biogeographic history of an enigmatic group of fishes. Furthermore, we provided strong evidence for the monophyly of the subgenus Mollienesia and further substantiated its species complexes; therefore, we advise a taxonomic re-evaluation for the P. (A.) caucana complex to maintain monophyly of both Mollienesia and Allopoecilia.}, }
@article {pmid27129311, year = {2016}, author = {Zugasti, O and Thakur, N and Belougne, J and Squiban, B and Kurz, CL and Soulé, J and Omi, S and Tichit, L and Pujol, N and Ewbank, JJ}, title = {A quantitative genome-wide RNAi screen in C. elegans for antifungal innate immunity genes.}, journal = {BMC biology}, volume = {14}, number = {}, pages = {35}, pmid = {27129311}, issn = {1741-7007}, support = {P40 OD010440/OD/NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/*genetics/*immunology/microbiology ; Caenorhabditis elegans Proteins/*genetics/*immunology ; Cloning, Molecular ; Epidermis/immunology ; Genetic Association Studies ; Genome, Helminth ; Host-Pathogen Interactions ; Hypocreales ; Immunity, Innate/*genetics ; Mitochondria/pathology ; Mitogen-Activated Protein Kinase Kinases/genetics/metabolism ; RNA Interference ; Signal Transduction ; Up-Regulation ; }, abstract = {BACKGROUND: Caenorhabditis elegans has emerged over the last decade as a useful model for the study of innate immunity. Its infection with the pathogenic fungus Drechmeria coniospora leads to the rapid up-regulation in the epidermis of genes encoding antimicrobial peptides. The molecular basis of antimicrobial peptide gene regulation has been previously characterized through forward genetic screens. Reverse genetics, based on RNAi, provide a complementary approach to dissect the worm's immune defenses.<br><br>RESULTS: We report here the full results of a quantitative whole-genome RNAi screen in C. elegans for genes involved in regulating antimicrobial peptide gene expression. The results will be a valuable resource for those contemplating similar RNAi-based screens and also reveal the limitations of such an approach. We present several strategies, including a comprehensive class clustering method, to overcome these limitations and which allowed us to characterize the different steps of the interaction between C. elegans and the fungus D. coniospora, leading to a complete description of the MAPK pathway central to innate immunity in C. elegans. The results further revealed a cross-tissue signaling, triggered by mitochondrial dysfunction in the intestine, that suppresses antimicrobial peptide gene expression in the nematode epidermis.<br><br>CONCLUSIONS: Overall, our results provide an unprecedented system's level insight into the regulation of C. elegans innate immunity. They represent a significant contribution to our understanding of host defenses and will lead to a better comprehension of the function and evolution of animal innate immunity.}, }
@article {pmid27128953, year = {2016}, author = {Blackstone, NW}, title = {An Evolutionary Framework for Understanding the Origin of Eukaryotes.}, journal = {Biology}, volume = {5}, number = {2}, pages = {}, pmid = {27128953}, issn = {2079-7737}, abstract = {Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real-the endosymbiosis that led to the mitochondrion is often described as "non-Darwinian" because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious-all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.}, }
@article {pmid27122350, year = {2016}, author = {Fujii, S and Suzuki, T and Giegé, P and Higashiyama, T and Koizuka, N and Shikanai, T}, title = {The Restorer-of-fertility-like 2 pentatricopeptide repeat protein and RNase P are required for the processing of mitochondrial orf291 RNA in Arabidopsis.}, journal = {The Plant journal : for cell and molecular biology}, volume = {86}, number = {6}, pages = {504-513}, doi = {10.1111/tpj.13185}, pmid = {27122350}, issn = {1365-313X}, mesh = {Arabidopsis/genetics/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Mitochondria/*genetics/*metabolism ; RNA, Plant/genetics/*metabolism ; Ribonuclease P/genetics/*metabolism ; }, abstract = {Eukaryotes harbor mitochondria obtained via ancient symbiosis events. The successful evolution of energy production in mitochondria has been dependent on the control of mitochondrial gene expression by the nucleus. In flowering plants, the nuclear-encoded pentatricopeptide repeat (PPR) superfamily proteins are widely involved in mitochondrial RNA metabolism. Here, we show that an Arabidopsis nuclear-encoded RNA-binding protein, Restorer-of-fertility-like PPR protein 2 (RFL2), is required for RNA degradation of the mitochondrial orf291 transcript via endonucleolytic cleavage of the transcript in the middle of its reading frame. Both in vivo and in vitro, this RNA cleavage requires the activity of mitochondrial proteinaceous RNase P, which is possibly recruited to the site by RFL2. The site of RNase P cleavage likely forms a tRNA-like structure in the orf291 transcript. This study presents an example of functional collaboration between a PPR protein and an endonuclease in RNA cleavage. Furthermore, we show that the RFL2-binding region within the orf291 gene is hypervariable in the family Brassicaceae, possibly correlated with the rapid evolution of the RNA-recognition interfaces of the RFL proteins.}, }
@article {pmid27121492, year = {2016}, author = {Uto, T and Toyama, M and Yoshinaga, K and Baba, M}, title = {Cepharanthine induces apoptosis through the mitochondria/caspase pathway in murine dendritic cells.}, journal = {Immunopharmacology and immunotoxicology}, volume = {38}, number = {3}, pages = {238-243}, doi = {10.3109/08923973.2016.1173059}, pmid = {27121492}, issn = {1532-2513}, mesh = {Animals ; Apoptosis/*drug effects ; Benzylisoquinolines/*pharmacology ; Caspases/*immunology ; DNA Fragmentation/drug effects ; Female ; Membrane Potential, Mitochondrial/*drug effects ; Mice ; Mitochondria/*immunology ; }, abstract = {CONTEXT: Cepharanthine (CEP) is a biscoclaurine amphipathic alkaloid isolated from the plant Stephania cepharantha Hayata. Although the effects of CEP on several types of cells have been investigated, those on dendritic cells (DCs) are poorly understood.<br><br>OBJECTIVE: To investigate the effect of CEP on the induction of apoptosis in murine DCs.<br><br>MATERIALS AND METHODS: The induction of Annexin V/propidium iodide-positive cells and permeability of mitochondrial membrane potential were evaluated in DCs treated with CEP. Cell-associated caspase activity and DNA fragmentation were analyzed by Dual Sensor: MitoCasp&#x2122; and agarose gel electrophoresis, respectively.<br><br>RESULTS: The number of dead cells was increased by CEP treatment at concentrations more than 10&#x2009;&#x3bc;g/ml. Flow cytometric analysis revealed that the cell death was found to be apoptosis, CEP treatment reduced mitochondrial membrane potential and upregulated the level of cleaved caspases, including caspase-9 and caspase-3/7, in a dose-dependent fashion. Furthermore, DNA fragmentation was observed in CEP-treated DCs.<br><br>CONCLUSION: CEP is capable of inducing apoptosis and may be a potential agent against DC-mediated and allergic diseases.}, }
@article {pmid27121326, year = {2016}, author = {Ma, F and Zhang, Y and Wang, Y and Wan, Y and Miao, Y and Ma, T and Yu, Q and Li, M}, title = {Role of Aif1 in regulation of cell death under environmental stress in Candida albicans.}, journal = {Yeast (Chichester, England)}, volume = {33}, number = {9}, pages = {493-506}, doi = {10.1002/yea.3167}, pmid = {27121326}, issn = {1097-0061}, mesh = {Acetic Acid/pharmacology ; Antifungal Agents/pharmacology ; Apoptosis ; Candida albicans/*enzymology/genetics/pathogenicity ; Caspofungin ; Cell Death/*physiology ; Echinocandins/pharmacology ; Fungal Proteins/genetics/*metabolism ; Gene Deletion ; Gene Expression Regulation, Enzymologic/physiology ; Gene Expression Regulation, Fungal/physiology ; Hydrogen Peroxide/pharmacology ; Lipopeptides/pharmacology ; Membrane Potential, Mitochondrial/drug effects/physiology ; NADH, NADPH Oxidoreductases/genetics/*metabolism ; Phylogeny ; Reactive Oxygen Species ; *Stress, Physiological ; Virulence ; }, abstract = {Apoptosis-inducing factor (AIF) is a conserved flavoprotein localized in the mitochondria, inducing apoptosis after translocation into the nucleus. However, its role in the important fungal pathogen, Candida albicans, remains to be investigated. In this study, we find that the C. albicans AIF protein Aif1, similar to its homologues in other organisms, is localized at the mitochondria and translocated into the nucleus under apoptosis-inducing conditions. Moreover, deletion of AIF1 causes attenuated apoptosis in this pathogen under apoptosis-inducing conditions, such as the treatment of 2 mm H2 O2 , 10 mm acetic acid or 0.08 mg/l caspofungin, and its overexpression enhances this process. Interestingly, treatment with high levels of these agents leads to reversed sensitivity of aif1Δ/Δ and the overexpression strain AIF1ov. In addition, the virulence of C. albicans is not affected by deletion or overexpression of AIF1. Hence, C. albicans Aif1, as a mitochondria-localized protein, plays a dual role in the regulation of cell death under different concentrations of the stress-caused agents. Copyright © 2016 John Wiley &amp; Sons, Ltd.}, }
@article {pmid27116927, year = {2016}, author = {Naghdi, S and Hajnóczky, G}, title = {VDAC2-specific cellular functions and the underlying structure.}, journal = {Biochimica et biophysica acta}, volume = {1863}, number = {10}, pages = {2503-2514}, pmid = {27116927}, issn = {0006-3002}, support = {R01 GM059419/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Apoptosis ; Calcium Signaling ; Conserved Sequence ; Evolution, Molecular ; Gene Expression Regulation ; Humans ; Ion Transport ; Mammals/metabolism ; Mitochondrial Membrane Transport Proteins/metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Permeability Transition Pore ; Models, Molecular ; Neoplasm Proteins/metabolism ; Neoplasms/metabolism ; Protein Conformation ; Protein Isoforms/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Steroids/metabolism ; Structure-Activity Relationship ; Voltage-Dependent Anion Channel 2/chemistry/genetics/*physiology ; }, abstract = {Voltage Dependent Anion-selective Channel 2 (VDAC2) contributes to oxidative metabolism by sharing a role in solute transport across the outer mitochondrial membrane (OMM) with other isoforms of the VDAC family, VDAC1 and VDAC3. Recent studies revealed that VDAC2 also has a distinctive role in mediating sarcoplasmic reticulum to mitochondria local Ca(2+) transport at least in cardiomyocytes, which is unlikely to be explained simply by the expression level of VDAC2. Furthermore, a strictly isoform-dependent VDAC2 function was revealed in the mitochondrial import and OMM-permeabilizing function of pro-apoptotic Bcl-2 family proteins, primarily Bak in many cell types. In addition, emerging evidence indicates a variety of other isoform-specific engagements for VDAC2. Since VDAC isoforms display 75% sequence similarity, the distinctive structure underlying VDAC2-specific functions is an intriguing problem. In this paper we summarize studies of VDAC2 structure and functions, which suggest a fundamental and exclusive role for VDAC2 in health and disease. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou.}, }
@article {pmid27107929, year = {2016}, author = {Yang, R and Brice, B and Ryan, U}, title = {Morphological and molecular characterization of Isospora neochmiae n. sp. in a captive-bred red-browed finch (Neochmia temporalis) (Latham, 1802).}, journal = {Experimental parasitology}, volume = {166}, number = {}, pages = {181-188}, doi = {10.1016/j.exppara.2016.04.011}, pmid = {27107929}, issn = {1090-2449}, mesh = {Animals ; Australia/epidemiology ; Base Sequence ; Bird Diseases/epidemiology/*parasitology ; DNA, Protozoan/chemistry/isolation &amp; purification ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Finches/*parasitology ; HSP70 Heat-Shock Proteins/genetics ; Isospora/classification/*genetics/*ultrastructure ; Isosporiasis/epidemiology/parasitology/*veterinary ; Jejunum/parasitology ; Mitochondria/enzymology ; Oocysts/ultrastructure ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Alignment/veterinary ; }, abstract = {A new Isospora (Apicomplexa: Eimeriidae) species is described from a single red-browed finch (Neochmia temporalis) (subspecies N. temporalis temporalis), that was part of a captive population in Western Australia. Sporulated oocysts of this isolate are spherical, 18.3 (18.2-18.9) × 18.2 (18.2-18.6) μm, with a shape index (length/width) of 1.0; and a smooth and bilayered oocyst wall, 1.2 μm thick (outer layer 0.9 μm, inner 0.3 μm). A polar granule is present, but the oocyst residuum and a micropyle are absent. The sporocysts are ovoid-shaped, 13.3 (9.5-16.4) × 8.6 (6.8-10.0) μm, with a shape index of 1.5. An indistinct Stieda body is present, but the substieda body is absent. A sporocyst residuum is present and composed of numerous granules of different size scattered among the sporozoites. Morphologically, the oocysts from this isolate are different from those of all known valid Isospora spp. Molecular analysis was conducted at 4 loci; the 18S and 28S ribosomal RNA (rRNA), the mitochondrial cytochrome oxidase (COI) gene and the heat shock protein 70 (hsp70) gene. At the 18S locus, this new isolate exhibited 99.9%, 99.8%, 99.7%, and 99.5% similarity to I. sp. MAH-2013a from a superb starling (Lamprotornis superbus), I. MS-2003 from a Southern cape sparrow (Passer melanurus), I. sp. Tokyo from a domestic pigeon (Columba livia domestica) and I. MS-2003 from a Surinam crested oropendula (Psarocolius decumanus). At the 28S locus, this new isolate exhibited 99.7% similarity to both an Isospora sp (MS-2003) from a Northern house sparrow (Passer domesticus) and an Isospora sp. (MS-2003) from a Southern cape sparrow. At the COI locus, this new isolate exhibited 98.9% similarity to an Isospora sp. ex Apodemus flavicollis. At the hsp70 locus, this new isolate exhibited 99% similarity to isolate MS-2003 (AY283879) from a wattled starling (Creatophora cinerea). Based on morphological and molecular data, this isolate is a new species of Isospora, which is named Isospora neochmiae n. sp. after its host, the red-browed finch (Neochmia temporalis).}, }
@article {pmid27100569, year = {2016}, author = {Kmiec, B and Teixeira, PF and Murcha, MW and Glaser, E}, title = {Divergent evolution of the M3A family of metallopeptidases in plants.}, journal = {Physiologia plantarum}, volume = {157}, number = {3}, pages = {380-388}, doi = {10.1111/ppl.12457}, pmid = {27100569}, issn = {1399-3054}, mesh = {Amino Acid Sequence ; Arabidopsis/enzymology/genetics ; Biological Evolution ; Chloroplasts/metabolism ; Cytosol/metabolism ; Metalloproteases/*genetics/metabolism ; Mitochondria/metabolism ; Models, Molecular ; Peptide Hydrolases/*genetics/metabolism ; Phylogeny ; Plant Proteins/genetics/metabolism ; Plants/*enzymology/genetics ; Protein Domains ; *Proteome ; Sequence Analysis, DNA ; }, abstract = {Plants, as stationary organisms, have developed mechanisms allowing them efficient resource reallocation and a response to changing environmental conditions. One of these mechanisms is proteome remodeling via a broad peptidase network present in various cellular compartments including mitochondria and chloroplasts. The genome of the model plant Arabidopsis thaliana encodes as many as 616 putative peptidase-coding genes organized in 55 peptidase families. In this study, we describe the M3A family of peptidases, which comprises four members: mitochondrial and chloroplastic oligopeptidase (OOP), cytosolic oligopeptidase (CyOP), mitochondrial octapeptidyl aminopeptidase 1 (Oct1) and plant-specific protein of M3 family (PSPM3) of unknown function. We have analyzed the evolutionary conservation of M3A peptidases across plant species and the functional specialization of the three distinct subfamilies. We found that the subfamily-containing OOP and CyOP-like peptidases, responsible for oligopeptide degradation in the endosymbiotic organelles (OOP) or in the cytosol (CyOP), are highly conserved in all kingdoms of life. The Oct1-like peptidase subfamily involved in pre-protein maturation in mitochondria is conserved in all eukaryotes, whereas the PSPM3-like protein subfamily is strictly conserved in higher plants only and is of unknown function. Specific characteristics within PSPM3 sequences, i.e. occurrence of a N-terminal transmembrane domain and amino acid changes in distal substrate-binding motif, distinguish PSPM3 proteins from other members of M3A family. We performed peptidase activity measurements to analyze the role of substrate-binding residues in the different Arabidopsis M3A paralogs.}, }
@article {pmid27091756, year = {2016}, author = {Tajima, N and Saitoh, K and Sato, S and Maruyama, F and Ichinomiya, M and Yoshikawa, S and Kurokawa, K and Ohta, H and Tabata, S and Kuwata, A and Sato, N}, title = {Sequencing and analysis of the complete organellar genomes of Parmales, a closely related group to Bacillariophyta (diatoms).}, journal = {Current genetics}, volume = {62}, number = {4}, pages = {887-896}, pmid = {27091756}, issn = {1432-0983}, mesh = {Computational Biology/methods ; Diatoms/*classification/*genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; Genomics ; Molecular Sequence Annotation ; Open Reading Frames ; Phylogeny ; Plastids/*genetics ; *Sequence Analysis, DNA ; }, abstract = {We sequenced the complete plastid and mitochondrial genomes of the unicellular marine phytoplankton Triparma laevis, belonging to the order Parmales (Heterokonta). The cells of Parmales are surrounded by silicified cell walls, similar to Bacillariophyta (diatoms). T. laevis was recognized as a sister group of Bacillariophyta using a molecular phylogenetic analysis based on SSU rDNA and rbcL sequences. Bacillariophyta are the most successful group of phytoplankton in the modern ocean, but the origin and early evolution of them have not been clearly established. Detailed molecular analyses of T. laevis may increase our understanding of the evolutionary relationships among Parmales and Bacillariophyta. The gene contents of the plastid and mitochondrial genomes are similar between T. laevis and Bacillariophyta. The gene order of the plastid genome is also similar to Bacillariophyta, whereas the gene order of the mitochondrial genome is not conserved in Bacillariophyta, but the structure is more compact than Bacillariophyta. Phylogenetic analyses, using plastid-encoded concatenated amino acid datasets and mitochondria-encoded concatenated amino acid datasets suggest that T. laevis is a sister group of Bacillariophyta. These results suggest that the characteristics of the organellar genomes of T. laevis are similar and conserve ancestral characteristics more than Bacillariophyta.}, }
@article {pmid27084951, year = {2016}, author = {Weissensteiner, H and Pacher, D and Kloss-Brandstätter, A and Forer, L and Specht, G and Bandelt, HJ and Kronenberg, F and Salas, A and Schönherr, S}, title = {HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing.}, journal = {Nucleic acids research}, volume = {44}, number = {W1}, pages = {W58-63}, pmid = {27084951}, issn = {1362-4962}, mesh = {Algorithms ; Biological Evolution ; DNA, Mitochondrial/classification/*genetics ; Genetic Variation ; *Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; Mitochondria/genetics ; *Phylogeny ; Quality Control ; Sequence Alignment ; Sequence Analysis, DNA ; *User-Computer Interface ; }, abstract = {Mitochondrial DNA (mtDNA) profiles can be classified into phylogenetic clusters (haplogroups), which is of great relevance for evolutionary, forensic and medical genetics. With the extensive growth of the underlying phylogenetic tree summarizing the published mtDNA sequences, the manual process of haplogroup classification would be too time-consuming. The previously published classification tool HaploGrep provided an automatic way to address this issue. Here, we present the completely updated version HaploGrep 2 offering several advanced features, including a generic rule-based system for immediate quality control (QC). This allows detecting artificial recombinants and missing variants as well as annotating rare and phantom mutations. Furthermore, the handling of high-throughput data in form of VCF files is now directly supported. For data output, several graphical reports are generated in real time, such as a multiple sequence alignment format, a VCF format and extended haplogroup QC reports, all viewable directly within the application. In addition, HaploGrep 2 generates a publication-ready phylogenetic tree of all input samples encoded relative to the revised Cambridge Reference Sequence. Finally, new distance measures and optimizations of the algorithm increase accuracy and speed-up the application. HaploGrep 2 can be accessed freely and without any registration at http://haplogrep.uibk.ac.at.}, }
@article {pmid27082488, year = {2016}, author = {Shi, X and Bentolila, S and Hanson, MR}, title = {Organelle RNA recognition motif-containing (ORRM) proteins are plastid and mitochondrial editing factors in Arabidopsis.}, journal = {Plant signaling &amp; behavior}, volume = {11}, number = {5}, pages = {e1167299}, pmid = {27082488}, issn = {1559-2324}, mesh = {Arabidopsis/*metabolism ; Arabidopsis Proteins/chemistry/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/metabolism ; Organelles/*metabolism ; Phylogeny ; Plastids/*metabolism ; Protein Binding ; Protein Domains ; *RNA Editing ; RNA Recognition Motif Proteins/chemistry/*metabolism ; }, abstract = {Post-transcriptional C-to-U RNA editing occurs at specific sites in plastid and plant mitochondrial transcripts. Members of the Arabidopsis pentatricopeptide repeat (PPR) motif-containing protein family and RNA-editing factor Interacting Protein (RIP, also known as MORF) family have been characterized as essential components of the RNA editing apparatus. Recent studies reveal that several organelle-targeted RNA recognition motif (RRM)-containing proteins are involved in either plastid or mitochondrial RNA editing. ORRM1 (Organelle RRM protein 1) is essential for plastid editing, whereas ORRM2, ORRM3 and ORRM4 are involved in mitochondrial RNA editing. The RRM domain of ORRM1, ORRM3 and ORRM4 is required for editing activity, whereas the auxiliary RIP and Glycine-Rich (GR) domains mediate the ORRM proteins' interactions with other editing factors. The identification of the ORRM proteins as RNA editing factors further expands our knowledge of the composition of the editosome.}, }
@article {pmid27079962, year = {2016}, author = {Yang, J and Liu, G and Zhao, N and Chen, S and Liu, D and Ma, W and Hu, Z and Zhang, M}, title = {Comparative mitochondrial genome analysis reveals the evolutionary rearrangement mechanism in Brassica.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {18}, number = {3}, pages = {527-536}, doi = {10.1111/plb.12414}, pmid = {27079962}, issn = {1438-8677}, mesh = {Biological Evolution ; Brassica/*genetics ; Brassica napus/genetics ; Breeding ; Diploidy ; Gene Rearrangement ; Genome, Mitochondrial/*genetics ; Genome, Plant/*genetics ; Mitochondria/genetics ; Mustard Plant/genetics ; Phylogeny ; Synteny ; }, abstract = {The genus Brassica has many species that are important for oil, vegetable and other food products. Three mitochondrial genome types (mitotype) originated from its common ancestor. In this paper, a B. nigra mitochondrial main circle genome with 232,407 bp was generated through de novo assembly. Synteny analysis showed that the mitochondrial genomes of B. rapa and B. oleracea had a better syntenic relationship than B. nigra. Principal components analysis and development of a phylogenetic tree indicated maternal ancestors of three allotetraploid species in Us triangle of Brassica. Diversified mitotypes were found in allotetraploid B. napus, in which napus-type B. napus was derived from B. oleracea, while polima-type B. napus was inherited from B. rapa. In addition, the mitochondrial genome of napus-type B. napus was closer to botrytis-type than capitata-type B. oleracea. The sub-stoichiometric shifting of several mitochondrial genes suggested that mitochondrial genome rearrangement underwent evolutionary selection during domestication and/or plant breeding. Our findings clarify the role of diploid species in the maternal origin of allotetraploid species in Brassica and suggest the possibility of breeding selection of the mitochondrial genome.}, }
@article {pmid27077367, year = {2016}, author = {Sun, X and Wang, Z and Guo, X and Li, H and Gu, Z}, title = {Coordinated Evolution of Transcriptional and Post-Transcriptional Regulation for Mitochondrial Functions in Yeast Strains.}, journal = {PloS one}, volume = {11}, number = {4}, pages = {e0153523}, pmid = {27077367}, issn = {1932-6203}, support = {R01 AI085286/AI/NIAID NIH HHS/United States ; 1R01AI085286/AI/NIAID NIH HHS/United States ; }, mesh = {Cell Nucleus/genetics ; Electron Transport Chain Complex Proteins/metabolism ; *Evolution, Molecular ; *Gene Expression Profiling ; Genome, Mitochondrial/genetics ; Heme/metabolism ; Mitochondria/*genetics/*metabolism ; Protein Biosynthesis ; RNA, Messenger/genetics/metabolism ; RNA-Binding Proteins/metabolism ; Ribosomes/genetics ; Saccharomyces cerevisiae/*cytology/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Species Specificity ; *Transcription, Genetic ; }, abstract = {Evolution of gene regulation has been proposed to play an important role in environmental adaptation. Exploring mechanisms underlying coordinated evolutionary changes at various levels of gene regulation could shed new light on how organism adapt in nature. In this study, we focused on regulatory differences between a laboratory Saccharomyces cerevisiae strain BY4742 and a pathogenic S. cerevisiae strain, YJM789. The two strains diverge in many features, including growth rate, morphology, high temperature tolerance, and pathogenicity. Our RNA-Seq and ribosomal footprint profiling data showed that gene expression differences are pervasive, and genes functioning in mitochondria are mostly divergent between the two strains at both transcriptional and translational levels. Combining functional genomics data from other yeast strains, we further demonstrated that significant divergence of expression for genes functioning in the electron transport chain (ETC) was likely caused by differential expression of a transcriptional factor, HAP4, and that post-transcriptional regulation mediated by an RNA-binding protein, PUF3, likely led to expression divergence for genes involved in mitochondrial translation. We also explored mito-nuclear interactions via mitochondrial DNA replacement between strains. Although the two mitochondrial genomes harbor substantial sequence divergence, neither growth nor gene expression were affected by mitochondrial DNA replacement in both fermentative and respiratory growth media, indicating compatible mitochondrial and nuclear genomes between these two strains in the tested conditions. Collectively, we used mitochondrial functions as an example to demonstrate for the first time that evolution at both transcriptional and post-transcriptional levels could lead to coordinated regulatory changes underlying strain specific functional variations.}, }
@article {pmid27075887, year = {2016}, author = {Hawkins, MT and Leonard, JA and Helgen, KM and McDonough, MM and Rockwood, LL and Maldonado, JE}, title = {Evolutionary history of endemic Sulawesi squirrels constructed from UCEs and mitogenomes sequenced from museum specimens.}, journal = {BMC evolutionary biology}, volume = {16}, number = {}, pages = {80}, pmid = {27075887}, issn = {1471-2148}, mesh = {Animals ; Biodiversity ; Biological Evolution ; Conserved Sequence ; Genome, Mitochondrial ; Indonesia ; Mitochondria/genetics ; Museums ; Phylogeny ; Sciuridae/*classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The Indonesian island of Sulawesi has a complex geological history. It is composed of several landmasses that have arrived at a near modern configuration only in the past few million years. It is the largest island in the biodiversity hotspot of Wallacea-an area demarcated by the biogeographic breaks between Wallace's and Lydekker's lines. The mammal fauna of Sulawesi is transitional between Asian and Australian faunas. Sulawesi's three genera of squirrels, all endemic (subfamily Nannosciurinae: Hyosciurus, Rubrisciurus and Prosciurillus), are of Asian origin and have evolved a variety of phenotypes that allow a range of ecological niche specializations. Here we present a molecular phylogeny of this radiation using data from museum specimens. High throughput sequencing technology was used to generate whole mitochondrial genomes and a panel of nuclear ultraconserved elements providing a large genome-wide dataset for inferring phylogenetic relationships.<br><br>RESULTS: Our analysis confirmed monophyly of the Sulawesi taxa with deep divergences between the three endemic genera, which predate the amalgamation of the current island of Sulawesi. This suggests lineages may have evolved in allopatry after crossing Wallace's line. Nuclear and mitochondrial analyses were largely congruent and well supported, except for the placement of Prosciurillus murinus. Mitochondrial analysis revealed paraphyly for Prosciurillus, with P. murinus between or outside of Hyosciurus and Rubrisciurus, separate from other species of Prosciurillus. A deep but monophyletic history for the four included species of Prosciurillus was recovered with the nuclear data.<br><br>CONCLUSIONS: The divergence of the Sulawesi squirrels from their closest relatives dated to ~9.7-12.5 million years ago (MYA), pushing back the age estimate of this ancient adaptive radiation prior to the formation of the current conformation of Sulawesi. Generic level diversification took place around 9.7 MYA, opening the possibility that the genera represent allopatric lineages that evolved in isolation in an ancient proto-Sulawesian archipelago. We propose that incongruence between phylogenies based on nuclear and mitochondrial sequences may have resulted from biogeographic discordance, when two allopatric lineages come into secondary contact, with complete replacement of the mitochondria in one species.}, }
@article {pmid27073202, year = {2016}, author = {Khoshravesh, R and Stinson, CR and Stata, M and Busch, FA and Sage, RF and Ludwig, M and Sage, TL}, title = {C3-C4 intermediacy in grasses: organelle enrichment and distribution, glycine decarboxylase expression, and the rise of C2 photosynthesis.}, journal = {Journal of experimental botany}, volume = {67}, number = {10}, pages = {3065-3078}, pmid = {27073202}, issn = {1460-2431}, mesh = {Biological Evolution ; Genes, Plant/genetics/physiology ; Glycine Dehydrogenase (Decarboxylating)/genetics/*metabolism ; Photosynthesis/*physiology ; Phylogeny ; Plant Leaves/anatomy &amp; histology/cytology/physiology ; Poaceae/cytology/enzymology/metabolism/*physiology ; Ribulose-Bisphosphate Carboxylase/metabolism ; }, abstract = {Photorespiratory glycine shuttling and decarboxylation in bundle sheath (BS) cells exhibited by C2 species is proposed to be the evolutionary bridge to C4 photosynthesis in eudicots. To evaluate this in grasses, we compare anatomy, cellular localization of glycine decarboxylase (GDC), and photosynthetic physiology of a suspected C2 grass, Homolepis aturensis, with these traits in known C2 grasses, Neurachne minor and Steinchisma hians, and C3 S laxum that is sister to S hians We also use publicly available genome and RNA-sequencing data to examine the evolution of GDC subunits and enhance our understanding of the evolution of BS-specific GDC expression in C2 and C4 grasses. Our results confirm the identity of H aturensis as a C2 species; GDC is confined predominantly to the organelle-enriched BS cells in H aturensis and S hians and to mestome sheath cells of N minor Phylogenetic analyses and data obtained from immunodetection of the P-subunit of GDC are consistent with the hypothesis that the BS dominant levels of GDC in C2 and C4 species are due to changes in expression of a single GLDP gene in M and BS cells. All BS mitochondria and peroxisomes and most chloroplasts in H aturensis and S hians are situated centripetally in a pattern identical to C2 eudicots. In S laxum, which has C3-like gas exchange patterns, mitochondria and peroxisomes are positioned centripetally as they are in S hians This subcellular phenotype, also present in eudicots, is posited to initiate a facilitation cascade leading to C2 and C4 photosynthesis.}, }
@article {pmid27072803, year = {2016}, author = {Im, CN}, title = {Past, present, and emerging roles of mitochondrial heat shock protein TRAP1 in the metabolism and regulation of cancer stem cells.}, journal = {Cell stress &amp; chaperones}, volume = {21}, number = {4}, pages = {553-562}, pmid = {27072803}, issn = {1466-1268}, mesh = {Animals ; Apoptosis/physiology ; Cell Proliferation ; Cellular Senescence/physiology ; Glycolysis/physiology ; HSP90 Heat-Shock Proteins/*metabolism ; Humans ; Liver Regeneration/physiology ; Mice ; Mitochondria/*metabolism ; Neoplastic Stem Cells/*metabolism ; }, abstract = {Tumor necrosis factor receptor-associated protein 1 (TRAP1), a member of the HSP90 family, controls a variety of physiological functions, including cell proliferation, differentiation, and survival. Most studies have been devoted to understanding the anti-apoptotic roles of TRAP1 in cancer and targeting it for tumor control in clinical settings. Additionally, we have identified a new role for TRAP1 in regulation of liver regeneration after partial hepatectomy in TRAP1 transgenic mice and cellular proliferation in TRAP1-overexpressing cells, via mitochondrial alterations. Moreover, recent works have indicated a role for TRAP1 in the regulation of cancer stem cells (CSCs) as well as a metabolic switch between mitochondrial respiration and aerobic glycolysis called as "Warburg effect." This review discusses the implications of TRAP1 action for both metabolism and the regulation of CSCs.}, }
@article {pmid27068958, year = {2016}, author = {Miliara, X and Matthews, S}, title = {Structural comparison of yeast and human intra-mitochondrial lipid transport systems.}, journal = {Biochemical Society transactions}, volume = {44}, number = {2}, pages = {479-485}, doi = {10.1042/BST20150264}, pmid = {27068958}, issn = {1470-8752}, support = {MRC-M019403//Wellcome Trust/United Kingdom ; 104933//Wellcome Trust/United Kingdom ; MR/J006874/1/MRC_/Medical Research Council/United Kingdom ; 100280//Wellcome Trust/United Kingdom ; MR/M019403/1/MRC_/Medical Research Council/United Kingdom ; WT-100280//Wellcome Trust/United Kingdom ; }, mesh = {Adaptor Proteins, Signal Transducing/chemistry/metabolism ; Amino Acid Sequence ; Biological Transport ; Crystallography, X-Ray ; Humans ; *Lipids ; Membrane Proteins/chemistry/metabolism ; Mitochondria/*metabolism ; Models, Molecular ; Phylogeny ; Protein Conformation ; Sequence Homology, Amino Acid ; Yeasts/*metabolism ; }, abstract = {Mitochondria depend on a tightly regulated supply of phospholipids. The protein of relevant evolutionary and lymphoid interest (PRELI)/Ups1 family together with its mitochondrial chaperones [TP53-regulated inhibitor of apoptosis 1 (TRIAP1)/Mdm35] represents a unique heterodimeric lipid-transfer system that is evolutionary conserved from yeast to man. Recent X-ray crystal structures of the human and yeast systems are compared and discuss here and shed new insight into the mechanism of the PRELI/Ups1 system.}, }
@article {pmid27068356, year = {2016}, author = {Yang, JQ and Hsu, KC and Liu, ZZ and Su, LW and Kuo, PH and Tang, WQ and Zhou, ZC and Liu, D and Bao, BL and Lin, HD}, title = {The population history of Garra orientalis (Teleostei: Cyprinidae) using mitochondrial DNA and microsatellite data with approximate Bayesian computation.}, journal = {BMC evolutionary biology}, volume = {16}, number = {}, pages = {73}, pmid = {27068356}, issn = {1471-2148}, mesh = {Animals ; Bayes Theorem ; China ; Cyprinidae/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Genetics, Population ; Microsatellite Repeats ; Molecular Sequence Data ; Phylogeny ; Phylogeography ; Polymorphism, Genetic ; }, abstract = {BACKGROUND: The South China landmass has been characterized by a complex geological history, including mountain lifting, climate changes, and river capture/reversal events. To determine how this complexity has influenced the landmass's phylogeography, our study examined the phylogeography of Garra orientalis, a cyprinid widely distributed in South China, using sequences from the mitochondrial DNA control region and cytochrome b gene (1887 bp) and polymorphisms of thirteen microsatellite loci.<br><br>RESULTS: In total, 157 specimens were collected from eight populations. All 88 mtDNA haplotypes were identified as belonging to three major lineages, and these lineages were almost allopatric in their distributions. The results of a statistical dispersal-vicariance analysis suggested that the ancestral populations of G. orientalis were distributed south of the Yunkai Mountains, including on Hainan Island. The mtDNA data revealed a strong relationship between phylogeny and geography. In the microsatellite analysis, a total of 339 alleles with an average of 26 alleles per locus were observed across thirteen microsatellite loci. A clustering algorithm for microsatellite data revealed an admixture-like genetic structure. Although the mtDNA and microsatellite data sets displayed a discordant population structure, the results of an approximate Bayesian computation approach showed that these two markers revealed congruent historical signals. The population history of G. orientalis reflects vicariance events and dispersal related to the complex geological history of South China.<br><br>CONCLUSION: Our results (i) found that the discordances between mtDNA and microsatellite markers were accounted for by admixtures; (ii) showed that the Wuzhishan and Yinggeling mountain ranges and Qiongzhou Strait were important barriers limiting gene exchange between populations on both sides; (iii) indicated that during glaciation and inter-glacial periods, the strait and continental shelves were exposed and sank, which contributed with the dispersion and differentiation of populations; and (iv) displayed that the admixtures between lineages took place in coastal populations and then colonized the tributaries of the Pearl River.}, }
@article {pmid27065197, year = {2016}, author = {Gao, Y and Bai, X and Zhang, D and Han, C and Yuan, J and Liu, W and Cao, X and Chen, Z and Shangguan, F and Zhu, Z and Gao, F and Qin, Y}, title = {Mammalian elongation factor 4 regulates mitochondrial translation essential for spermatogenesis.}, journal = {Nature structural &amp; molecular biology}, volume = {23}, number = {5}, pages = {441-449}, pmid = {27065197}, issn = {1545-9985}, mesh = {3T3 Cells ; Animals ; Female ; Gene Expression Regulation ; Infertility, Male/enzymology ; Male ; Mice ; Mice, Knockout ; Mitochondria/*enzymology ; Oxidative Phosphorylation ; Peptide Initiation Factors/chemistry/*physiology ; *Protein Biosynthesis ; Protein Transport ; Ribosomes/enzymology ; *Spermatogenesis ; Testis/enzymology/pathology ; }, abstract = {Elongation factor 4 (EF4) is a key quality-control factor in translation. Despite its high conservation throughout evolution, EF4 deletion in various organisms has not yielded a distinct phenotype. Here we report that genetic ablation of mitochondrial EF4 (mtEF4) in mice causes testis-specific dysfunction in oxidative phosphorylation, leading to male infertility. Deletion of mtEF4 accelerated mitochondrial translation at the cost of producing unstable proteins. Somatic tissues overcame this defect by activating mechanistic (mammalian) target of rapamycin (mTOR), thereby increasing rates of cytoplasmic translation to match rates of mitochondrial translation. However, in spermatogenic cells, the mTOR pathway was downregulated as part of the developmental program, and the resulting inability to compensate for accelerated mitochondrial translation caused cell-cycle arrest and apoptosis. We detected the same phenotype and molecular defects in germline-specific mtEF4-knockout mice. Thus, our study demonstrates cross-talk between mtEF4-dependent quality control in mitochondria and cytoplasmic mTOR signaling.}, }
@article {pmid27062292, year = {2016}, author = {Haig, D}, title = {Intracellular evolution of mitochondrial DNA (mtDNA) and the tragedy of the cytoplasmic commons.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {38}, number = {6}, pages = {549-555}, doi = {10.1002/bies.201600003}, pmid = {27062292}, issn = {1521-1878}, mesh = {Aging ; Animals ; Apoptosis ; *Biological Evolution ; *DNA, Mitochondrial ; Female ; Humans ; Mitochondria/*genetics/physiology ; Mitophagy ; Mutation ; Ovum ; }, abstract = {Mitochondria exist in large numbers per cell. Therefore, the strength of natural selection on individual mtDNAs for their contribution to cellular fitness is weak whereas the strength of selection in favor of mtDNAs that increase their own replication without regard for cellular functions is strong. This problem has been solved for most mitochondrial genes by their transfer to the nucleus but a few critical genes remain encoded by mtDNA. Organisms manage the evolution of mtDNA to prevent mutational decay of essential services mitochondria provide to their hosts. Bottlenecks of mitochondrial numbers in female germlines increase the homogeneity of mtDNAs within cells and allow intraorganismal selection to eliminate cells with low quality mitochondria. Mechanisms of intracellular "quality control" allow direct selection on the competence of individual mtDNAs. These processes maintain the integrity of mtDNAs within the germline but are inadequate to indefinitely maintain mitochondrial function in somatic cells.}, }
@article {pmid27058308, year = {2016}, author = {Neupert, W}, title = {Mitochondrial Gene Expression: A Playground of Evolutionary Tinkering.}, journal = {Annual review of biochemistry}, volume = {85}, number = {}, pages = {65-76}, doi = {10.1146/annurev-biochem-011116-110824}, pmid = {27058308}, issn = {1545-4509}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/*genetics/metabolism ; Electron Transport/*genetics ; Gene Expression Regulation ; *Genome, Mitochondrial ; Humans ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/*genetics/metabolism ; Mitochondrial Ribosomes/chemistry/metabolism ; Organelle Biogenesis ; Protein Biosynthesis ; Signal Transduction ; }, abstract = {This article introduces the Mitochondria theme of the Annual Review of Biochemistry, Volume 85.}, }
@article {pmid27058122, year = {2016}, author = {Ji, Y and Sun, Y and Gao, W and Chu, K and Wang, R and Zhao, Q and Sun, H}, title = {Out of the Sichuan Basin: Rapid species diversification of the freshwater crabs in Sinopotamon (Decapoda: Brachyura: Potamidae) endemic to China.}, journal = {Molecular phylogenetics and evolution}, volume = {100}, number = {}, pages = {80-94}, doi = {10.1016/j.ympev.2016.04.003}, pmid = {27058122}, issn = {1095-9513}, mesh = {Animals ; Brachyura/*classification ; Cell Nucleus/genetics ; China ; *Fresh Water ; Genetic Variation ; Geography ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Species Specificity ; Time Factors ; }, abstract = {Sinopotamon Bott, 1967 is the most speciose and widely distributed freshwater crab genus in East Asia. Our extensive sampling includes about 76% of the known Sinopotamon taxa, and nearly covers its entire distribution area. Based on mitochondrial cytochrome oxidase I (COI) and 16S rRNA, as well as nuclear 28S rRNA and histone H3, we reconstructed the Sinopotamon phylogeny using maximum likelihood and Bayesian approaches. The divergence time was estimated and multiple methods were used to conduct diversification analyses. The ancestral geographic distribution and character state were reconstructed. Three main clades (Clades I, II and III) that roughly correspond to their main geographic distribution ranges were recovered. Our results challenge the current view of the four major species groups based on the morphological differences in the male first gonopod (G1). The most recent common ancestor of Sinopotamon most likely originated from the Sichuan Basin and surrounding mountains (SBSM) and subsequently dispersed throughout central and eastern China. The exceptionally rapid, recent diversification was detected in Clade II. The high incidence of species-level non-monophyly found in Clade II can be explained by recent rapid radiation. Climatic changes, morphological innovations, range expansion and geographical heterogeneity may all contribute to the diversification in Sinopotamon. This study contributes to our knowledge on diversification of freshwater benthic macro-invertebrates in the East Asian inland ecosystem.}, }
@article {pmid27053680, year = {2016}, author = {Klug, D and Mair, GR and Frischknecht, F and Douglas, RG}, title = {A small mitochondrial protein present in myzozoans is essential for malaria transmission.}, journal = {Open biology}, volume = {6}, number = {4}, pages = {160034}, pmid = {27053680}, issn = {2046-2441}, mesh = {Amino Acid Sequence ; Animals ; Conserved Sequence ; Culicidae/parasitology ; Evolution, Molecular ; Humans ; Life Cycle Stages ; Malaria/parasitology/*transmission ; Membrane Proteins/chemistry/metabolism ; Mice ; Mitochondria/metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; Parasites/growth &amp; development/metabolism ; Plasmodium berghei/growth &amp; development/*metabolism ; Protozoan Proteins/chemistry/metabolism ; }, abstract = {Myzozoans (which include dinoflagellates, chromerids and apicomplexans) display notable divergence from their ciliate sister group, including a reduced mitochondrial genome and divergent metabolic processes. The factors contributing to these divergent processes are still poorly understood and could serve as potential drug targets in disease-causing protists. Here, we report the identification and characterization of a small mitochondrial protein from the rodent-infecting apicomplexan parasite Plasmodium berghei that is essential for development in its mosquito host. Parasites lacking the gene mitochondrial protein ookinete developmental defect (mpodd) showed malformed parasites that were unable to transmit to mosquitoes. Knockout parasites displayed reduced mitochondrial mass without affecting organelle integrity, indicating no role of the protein in mitochondrial biogenesis or morphology maintenance but a likely role in mitochondrial import or metabolism. Using genetic complementation experiments, we identified a previously unrecognized Plasmodium falciparum homologue that can rescue the mpodd(-) phenotype, thereby showing that the gene is functionally conserved. As far as can be detected, mpodd is found in myzozoans, has homologues in the phylum Apicomplexa and appears to have arisen in free-living dinoflagellates. This suggests that the MPODD protein has a conserved mitochondrial role that is important for myzozoans. While previous studies identified a number of essential proteins which are generally highly conserved evolutionarily, our study identifies, for the first time, a non-canonical protein fulfilling a crucial function in the mitochondrion during parasite transmission.}, }
@article {pmid27050471, year = {2016}, author = {Shenkar, N and Koplovitz, G and Dray, L and Gissi, C and Huchon, D}, title = {Back to solitude: Solving the phylogenetic position of the Diazonidae using molecular and developmental characters.}, journal = {Molecular phylogenetics and evolution}, volume = {100}, number = {}, pages = {51-56}, doi = {10.1016/j.ympev.2016.04.001}, pmid = {27050471}, issn = {1095-9513}, mesh = {Animals ; Genome, Mitochondrial ; Mitochondria/genetics ; *Phylogeny ; Regeneration/genetics ; Urochordata/*classification/embryology/*genetics ; }, abstract = {The order Aplousobranchia (Chordata, Ascidiacea) contains approximately 1500 species distributed worldwide. Their phylogeny, however, remains unclear, with unresolved family relationships. While most Aplousobranchia are colonial, debates exist concerning the phylogenetic position of families such as the Diazonidae and Cionidae, which exhibit a solitary lifestyle and share morphological characteristics with both Aplousobranchia and Phlebobranchia orders. To clarify the phylogenetic position of the Diazonidae and Cionidae, we determined the complete mitochondrial sequence of the solitary diazonid Rhopalaea idoneta. The phylogenetic reconstruction based on the 13 mitochondrial protein coding genes strongly supports a positioning of Diazonidae well-nested within the Aplousobranchia rather than a positioning as a sister clade of the Aplousobranchia. In addition, we examined the regenerative ability of R. idoneta. Similar to colonial Aplousobranchia, R. idoneta was found to be able to completely regenerate its thorax. Ciona, also known to possess high regenerative abilities, is the Aplousobranchia sister clade rather than a member of the Phlebobranchia. Our results thus indicate that the colonial lifestyle was acquired in the Aplousobranchia, starting from a Ciona-like solitary ancestor and secondarily lost in Diazonidae representatives such as Rhopalaea. The solitary lifestyle of Rhopalaea is thus a derived characteristic rather than an ancestral trait.}, }
@article {pmid27040918, year = {2016}, author = {Gould, SB and Garg, SG and Martin, WF}, title = {Bacterial Vesicle Secretion and the Evolutionary Origin of the Eukaryotic Endomembrane System.}, journal = {Trends in microbiology}, volume = {24}, number = {7}, pages = {525-534}, doi = {10.1016/j.tim.2016.03.005}, pmid = {27040918}, issn = {1878-4380}, mesh = {Archaea/physiology ; Bacteria ; *Biological Evolution ; Endoplasmic Reticulum/*physiology ; Eukaryota/*physiology ; Eukaryotic Cells/cytology ; Golgi Apparatus/*physiology ; Mitochondria/physiology ; Mitochondrial Membranes/*physiology ; Multivesicular Bodies/*physiology ; Nuclear Envelope/physiology ; }, abstract = {Eukaryotes possess an elaborate endomembrane system with endoplasmic reticulum, nucleus, Golgi, lysosomes, peroxisomes, autophagosomes, and dynamic vesicle traffic. Theories addressing the evolutionary origin of eukaryotic endomembranes have overlooked the outer membrane vesicles (OMVs) that bacteria, archaea, and mitochondria secrete into their surroundings. We propose that the eukaryotic endomembrane system originated from bacterial OMVs released by the mitochondrial ancestor within the cytosol of its archaeal host at eukaryote origin. Confined within the host's cytosol, OMVs accumulated naturally, fusing either with each other or with the host's plasma membrane. This matched the host's archaeal secretory pathway for cotranslational protein insertion with outward bound mitochondrial-derived vesicles consisting of bacterial lipids, forging a primordial, secretory endoplasmic reticulum as the cornerstone of the eukaryotic endomembrane system. VIDEO ABSTRACT.}, }
@article {pmid27038285, year = {2016}, author = {Schulze, S and Westhoff, P and Gowik, U}, title = {Glycine decarboxylase in C3, C4 and C3-C4 intermediate species.}, journal = {Current opinion in plant biology}, volume = {31}, number = {}, pages = {29-35}, doi = {10.1016/j.pbi.2016.03.011}, pmid = {27038285}, issn = {1879-0356}, mesh = {Arabidopsis/enzymology/genetics/metabolism ; Arabidopsis Proteins/genetics/metabolism ; Glycine Dehydrogenase (Decarboxylating)/genetics/*metabolism ; Glycine Hydroxymethyltransferase/genetics/metabolism ; Photosynthesis/genetics/physiology ; Plants, Genetically Modified/enzymology/genetics/metabolism ; }, abstract = {The glycine decarboxylase complex (GDC) plays a central role in photorespiration. GDC is localized in the mitochondria and together with serine hydroxymethyltransferase it converts two molecules of glycine to one molecule of serine, CO2 and NH3. Overexpression of GDC subunits in the C3 species Arabidopsis thaliana can increase the metabolic flux through the photorespiratory pathway leading to enhanced photosynthetic efficiency and consequently to an enhanced biomass production of the transgenic plants. Changing the spatial expression patterns of GDC subunits was an important step during the evolution of C3-C4 intermediate and likely also C4 plants. Restriction of the GDC activity to the bundle sheath cells led to the establishment of a photorespiratory CO2 pump.}, }
@article {pmid27037593, year = {2016}, author = {Nakada, T and Tomita, M and Wu, JT and Nozaki, H}, title = {Taxonomic revision of Chlamydomonas subg. Amphichloris (Volvocales, Chlorophyceae), with resurrection of the genus Dangeardinia and descriptions of Ixipapillifera gen. nov. and Rhysamphichloris gen. nov.}, journal = {Journal of phycology}, volume = {52}, number = {2}, pages = {283-304}, doi = {10.1111/jpy.12397}, pmid = {27037593}, issn = {1529-8817}, mesh = {Base Sequence ; Bayes Theorem ; Chlamydomonas/*classification/cytology/genetics ; Microscopy, Fluorescence ; Mitochondria/metabolism ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Chlamydomonas (Cd.) is one of the largest but most polyphyletic genera of freshwater unicellular green algae. It consists of 400-600 morphological species and requires taxonomic revision. Toward reclassification, each morphologically defined classical subgenus (or subgroup) should be examined using culture strains. Chlamydomonas subg. Amphichloris is characterized by a central nucleus between two axial pyrenoids, however, the phylogenetic structure of this subgenus has yet to be examined using molecular data. Here, we examined 12 strains including six newly isolated strains, morphologically identified as Chlamydomonas subg. Amphichloris, using 18S rRNA gene phylogeny, light microscopy, and mitochondria fluorescent microscopy. Molecular phylogenetic analyses revealed three independent lineages of the subgenus, separated from the type species of Chlamydomonas, Cd. reinhardtii. These three lineages were further distinguished from each other by light and fluorescent microscopy-in particular by the morphology of the papillae, chloroplast surface, stigmata, and mitochondria-and are here assigned to three genera: Dangeardinia emend., Ixipapillifera gen. nov., and Rhysamphichloris gen. nov. Based on the molecular and morphological data, two to three species were recognized in each genus, including one new species, I. pauromitos. In addition, Cd. deasonii, which was previously assigned to subgroup "Pleiochloris," was included in the genus Ixipapillifera as I. deasonii comb. nov.}, }
@article {pmid27036943, year = {2016}, author = {Lamech, LT and Saoji, M and Paukstelis, PJ and Lambowitz, AM}, title = {Structural Divergence of the Group I Intron Binding Surface in Fungal Mitochondrial Tyrosyl-tRNA Synthetases That Function in RNA Splicing.}, journal = {The Journal of biological chemistry}, volume = {291}, number = {22}, pages = {11911-11927}, pmid = {27036943}, issn = {1083-351X}, support = {R01 GM037949/GM/NIGMS NIH HHS/United States ; R01 GM037951/GM/NIGMS NIH HHS/United States ; R37 GM037951/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Aspergillus nidulans/*enzymology/genetics/growth &amp; development ; Catalytic Domain ; Coccidioides/*enzymology/genetics/growth &amp; development ; Crystallography, X-Ray ; Introns/*genetics ; Mitochondria/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Neurospora crassa/enzymology ; Protein Binding ; Protein Conformation ; RNA Splicing/*genetics ; Sequence Homology, Amino Acid ; Tyrosine-tRNA Ligase/*chemistry/genetics/*metabolism ; }, abstract = {The mitochondrial tyrosyl-tRNA synthetases (mtTyrRSs) of Pezizomycotina fungi, a subphylum that includes many pathogenic species, are bifunctional proteins that both charge mitochondrial tRNA(Tyr) and act as splicing cofactors for autocatalytic group I introns. Previous studies showed that one of these proteins, Neurospora crassa CYT-18, binds group I introns by using both its N-terminal catalytic and C-terminal anticodon binding domains and that the catalytic domain uses a newly evolved group I intron binding surface that includes an N-terminal extension and two small insertions (insertions 1 and 2) with distinctive features not found in non-splicing mtTyrRSs. To explore how this RNA binding surface diverged to accommodate different group I introns in other Pezizomycotina fungi, we determined x-ray crystal structures of C-terminally truncated Aspergillus nidulans and Coccidioides posadasii mtTyrRSs. Comparisons with previous N. crassa CYT-18 structures and a structural model of the Aspergillus fumigatus mtTyrRS showed that the overall topology of the group I intron binding surface is conserved but with variations in key intron binding regions, particularly the Pezizomycotina-specific insertions. These insertions, which arose by expansion of flexible termini or internal loops, show greater variation in structure and amino acids potentially involved in group I intron binding than do neighboring protein core regions, which also function in intron binding but may be more constrained to preserve mtTyrRS activity. Our results suggest a structural basis for the intron specificity of different Pezizomycotina mtTyrRSs, highlight flexible terminal and loop regions as major sites for enzyme diversification, and identify targets for therapeutic intervention by disrupting an essential RNA-protein interaction in pathogenic fungi.}, }
@article {pmid27034743, year = {2016}, author = {Keller, AC and Knaub, LA and McClatchey, PM and Connon, CA and Bouchard, R and Miller, MW and Geary, KE and Walker, LA and Klemm, DJ and Reusch, JE}, title = {Differential Mitochondrial Adaptation in Primary Vascular Smooth Muscle Cells from a Diabetic Rat Model.}, journal = {Oxidative medicine and cellular longevity}, volume = {2016}, number = {}, pages = {8524267}, pmid = {27034743}, issn = {1942-0994}, support = {T32 HL007171/HL/NHLBI NIH HHS/United States ; 5P01HL014985/HL/NHLBI NIH HHS/United States ; P30 CA046934/CA/NCI NIH HHS/United States ; P01 HL014985/HL/NHLBI NIH HHS/United States ; I01 BX002046/BX/BLRD VA/United States ; P30CA046934/CA/NCI NIH HHS/United States ; UL1 RR025780/RR/NCRR NIH HHS/United States ; 5T32HL007171/HL/NHLBI NIH HHS/United States ; UL1RR025780/RR/NCRR NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Animals ; Diabetes Mellitus, Experimental/*metabolism/pathology ; Male ; Mitochondria, Muscle/*metabolism/pathology ; Muscle, Smooth, Vascular/*metabolism/pathology ; Myocytes, Smooth Muscle/*metabolism/pathology ; Nitric Oxide/metabolism ; Rats ; Rats, Wistar ; Superoxides/metabolism ; }, abstract = {Diabetes affects more than 330 million people worldwide and causes elevated cardiovascular disease risk. Mitochondria are critical for vascular function, generate cellular reactive oxygen species (ROS), and are perturbed by diabetes, representing a novel target for therapeutics. We hypothesized that adaptive mitochondrial plasticity in response to nutrient stress would be impaired in diabetes cellular physiology via a nitric oxide synthase- (NOS-) mediated decrease in mitochondrial function. Primary smooth muscle cells (SMCs) from aorta of the nonobese, insulin resistant rat diabetes model Goto-Kakizaki (GK) and the Wistar control rat were exposed to high glucose (25 mM). At baseline, significantly greater nitric oxide evolution, ROS production, and respiratory control ratio (RCR) were observed in GK SMCs. Upon exposure to high glucose, expression of phosphorylated eNOS, uncoupled respiration, and expression of mitochondrial complexes I, II, III, and V were significantly decreased in GK SMCs (p < 0.05). Mitochondrial superoxide increased with high glucose in Wistar SMCs (p < 0.05) with no change in the GK beyond elevated baseline concentrations. Baseline comparisons show persistent metabolic perturbations in a diabetes phenotype. Overall, nutrient stress in GK SMCs caused a persistent decline in eNOS and mitochondrial function and disrupted mitochondrial plasticity, illustrating eNOS and mitochondria as potential therapeutic targets.}, }
@article {pmid27033304, year = {2016}, author = {Pinti, M and Gibellini, L and Nasi, M and De Biasi, S and Bortolotti, CA and Iannone, A and Cossarizza, A}, title = {Emerging role of Lon protease as a master regulator of mitochondrial functions.}, journal = {Biochimica et biophysica acta}, volume = {1857}, number = {8}, pages = {1300-1306}, doi = {10.1016/j.bbabio.2016.03.025}, pmid = {27033304}, issn = {0006-3002}, mesh = {Cellular Reprogramming ; Craniofacial Abnormalities/enzymology/*genetics/pathology ; DNA, Mitochondrial/*genetics/metabolism ; Eye Abnormalities/enzymology/*genetics/pathology ; Growth Disorders/enzymology/*genetics/pathology ; Hip Dislocation, Congenital/enzymology/*genetics/pathology ; Homeostasis ; Humans ; Mitochondria/*enzymology/pathology ; Models, Molecular ; Molecular Chaperones/*chemistry/genetics/metabolism ; *Mutation ; Osteochondrodysplasias/enzymology/*genetics/pathology ; Protease La/*chemistry/genetics/metabolism ; Protein Folding ; Tooth Abnormalities/enzymology/*genetics/pathology ; }, abstract = {Lon protease is a nuclear-encoded, mitochondrial ATP-dependent protease highly conserved throughout the evolution, crucial for the maintenance of mitochondrial homeostasis. Lon acts as a chaperone of misfolded proteins, and is necessary for maintaining mitochondrial DNA. The impairment of these functions has a deep impact on mitochondrial functionality and morphology. An altered expression of Lon leads to a profound reprogramming of cell metabolism, with a switch from respiration to glycolysis, which is often observed in cancer cells. Mutations of Lon, which likely impair its chaperone properties, are at the basis of a genetic inherited disease named of the cerebral, ocular, dental, auricular, skeletal (CODAS) syndrome. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.}, }
@article {pmid27032679, year = {2016}, author = {Sugita, N and Kawakami, K and Nishiumi, I}, title = {Origin of Japanese White-Eyes and Brown-Eared Bulbuls on the Volcano Islands.}, journal = {Zoological science}, volume = {33}, number = {2}, pages = {146-153}, doi = {10.2108/zs150146}, pmid = {27032679}, issn = {0289-0003}, mesh = {Animals ; Electron Transport Complex IV/genetics/metabolism ; Genetic Variation ; Haplotypes ; Islands ; Japan ; Passeriformes/*genetics/physiology ; Phylogeny ; }, abstract = {The Ogasawara Archipelago comprises two groups of oceanic islands: the Bonin Islands, formed in the Paleogene, and the Volcano Islands, formed in the Quaternary. These groups are located within a moderate distance (ca. 160-270 km) of one another; thus, most land bird species are not distinguished as different subspecies. Two land birds, however, show unusual distribution. The Japanese white-eyes Zosterops japonicus originally inhabited only the Volcano Islands, but has been introduced to the Bonin Islands. The brown-eared bulbuls Hypsipetes amaurotis are distributed as a different subspecies. We investigated their genetic differences and divergences in the Ogasawara Archipelago using mitochondria DNA. The Volcano population of white-eyes had four endemic haplotypes that were divergent from one another, except for the Bonin population, which shared three haplotypes with the Volcano, Izu, and Ryukyu Islands and did not have any endemic haplotype. This is the first genetic suggestion that the Bonin population is a hybrid of introduced populations. With respect to bulbuls, the Volcano and Bonin Islands each had a single endemic haplotype. The Volcano haplotype is closest to a haplotype shared with Izu, the Japanese mainland, Daito and Ryukyu, whereas the Bonin haplotype is closest to one endemic to the south Ryukyu Islands. This indicates that the sources of the two bulbul populations can be geologically and temporally distinguished. The populations of the two species in the Ogasawara Archipelago are irreplaceable, owing to their genetic differences and should be regarded as evolutionarily significant units. In order to prevent introgression between the two populations, we must restrict interisland transfers.}, }
@article {pmid27026114, year = {2016}, author = {Andújar, C and Faille, A and Pérez-González, S and Zaballos, JP and Vogler, AP and Ribera, I}, title = {Gondwanian relicts and oceanic dispersal in a cosmopolitan radiation of euedaphic ground beetles.}, journal = {Molecular phylogenetics and evolution}, volume = {99}, number = {}, pages = {235-246}, doi = {10.1016/j.ympev.2016.03.013}, pmid = {27026114}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Biodiversity ; Biological Evolution ; Coleoptera/*classification/genetics ; Cyclooxygenase 1/genetics ; DNA/chemistry/isolation &amp; purification/metabolism ; Mitochondria/genetics ; New Caledonia ; New Zealand ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Anillini are a tribe of minute, euedaphic ground beetles (Carabidae) characterized by the loss of eyes, loss of wings and high levels of local endemism. Despite their presumed low dispersal, they have a nearly cosmopolitan distribution, including isolated islands such as New Zealand and New Caledonia. We used a time calibrated molecular phylogeny to test, first, if the tribe as currently understood is monophyletic and, second, whether the time of divergence is compatible with an early vicariant diversification after the breakup of Gondwana. We sequenced portions of 6 mitochondrial and 3 nuclear genes for 66 specimens in 17 genera of Anillini plus 39 outgroups. The resulting phylogenetic tree was used to estimate the time of diversification using two independent calibration schemes, by applying molecular rates for the related genus Carabus or by dating the tree with fossil and geological information. Rates of molecular evolution and lineage ages were mostly concordant between both calibration schemes. The monophyly of Anillini was well-supported, and its age was consistent with a Gondwanian origin of the main lineages and an initial diversification at ca. 100Ma representing the split between the eyed Nesamblyops (New Zealand) and the remaining Anillini. The subsequent diversification, including the split of the Nearctic Anillinus and the subsequent splits of Palaearctic lineages, was dated to between 80 and 100Ma and thus was also compatible with a tectonic vicariant origin. On the contrary, the estimated age of the New Caledonian blind Orthotyphlus at ca. 30±20Ma was incompatible with a vicariant origin, suggesting the possibility of trans-oceanic dispersal in these endogean beetles.}, }
@article {pmid27025488, year = {2016}, author = {Spiridonova, LN and Red'kin, YA and Valchuk, OP}, title = {Nuclear mtDNA pseudogenes as a source of new variants of mitochondrial genes: A case study of Siberian rubythroat Luscinia calliope (muscicapidae, aves).}, journal = {Doklady. Biochemistry and biophysics}, volume = {466}, number = {}, pages = {52-56}, pmid = {27025488}, issn = {1608-3091}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Founder Effect ; Haplotypes ; Passeriformes/*genetics ; *Polymorphism, Genetic ; *Pseudogenes ; Recombination, Genetic ; }, abstract = {First evidence for the presence of copies of mitochondrial cytochrome b gene of the subspecies group Luscinia calliope anadyrensis-L. c. camtschatkensis in the nuclear genome of nominative L. c. calliope was obtained, which indirectly indicates the nuclear origin of the subspecies-specific mitochondrial haplotypes in Siberian rubythroat. This fact clarifies the appearance of mitochondrial haplotypes of eastern subspecies by exchange between the homologous regions of the nuclear and mitochondrial genomes followed by fixation by the founder effect. This is the first study to propose a mechanism of DNA fragment exchange between the nucleus and mitochondria (intergenomic recombination) and to show the role of nuclear copies of mtDNA as a source of new taxon-specific mitochondrial haplotypes, which implies their involvement in the microevolutionary processes and morphogenesis.}, }
@article {pmid27023847, year = {2016}, author = {Gustafsson, CM and Falkenberg, M and Larsson, NG}, title = {Maintenance and Expression of Mammalian Mitochondrial DNA.}, journal = {Annual review of biochemistry}, volume = {85}, number = {}, pages = {133-160}, doi = {10.1146/annurev-biochem-060815-014402}, pmid = {27023847}, issn = {1545-4509}, mesh = {Animals ; Biological Evolution ; Cell Nucleus/genetics/metabolism ; DNA Replication ; DNA, Mitochondrial/*genetics/metabolism ; Electron Transport/genetics ; Gene Expression Regulation ; Mammals ; Mitochondria/*genetics/metabolism/ultrastructure ; Mitochondrial Proteins/*genetics/metabolism ; Mitochondrial Ribosomes/chemistry/metabolism ; Models, Molecular ; Oxidative Phosphorylation ; *Protein Biosynthesis ; Protein Transport ; Signal Transduction ; *Transcription, Genetic ; }, abstract = {Mammalian mitochondrial DNA (mtDNA) encodes 13 proteins that are essential for the function of the oxidative phosphorylation system, which is composed of four respiratory-chain complexes and adenosine triphosphate (ATP) synthase. Remarkably, the maintenance and expression of mtDNA depend on the mitochondrial import of hundreds of nuclear-encoded proteins that control genome maintenance, replication, transcription, RNA maturation, and mitochondrial translation. The importance of this complex regulatory system is underscored by the identification of numerous mutations of nuclear genes that impair mtDNA maintenance and expression at different levels, causing human mitochondrial diseases with pleiotropic clinical manifestations. The basic scientific understanding of the mechanisms controlling mtDNA function has progressed considerably during the past few years, thanks to advances in biochemistry, genetics, and structural biology. The challenges for the future will be to understand how mtDNA maintenance and expression are regulated and to what extent direct intramitochondrial cross talk between different processes, such as transcription and translation, is important.}, }
@article {pmid27441209, year = {2015}, author = {Lu, Y and Tucker, D and Dong, Y and Zhao, N and Zhuo, X and Zhang, Q}, title = {Role of Mitochondria in Neonatal Hypoxic-Ischemic Brain Injury.}, journal = {Journal of neuroscience and rehabilitation}, volume = {2}, number = {1}, pages = {1-14}, pmid = {27441209}, issn = {2374-9091}, support = {R01 NS086929/NS/NINDS NIH HHS/United States ; }, abstract = {Hypoxic-ischemia (HI) causes severe brain injury in neonates. It's one of the leading causes to neonatal death and pediatric disability, resulting in devastating consequences, emotionally and economically, to their families. A series of events happens in this process, e.g. excitatory transmitter release, extracelluar Ca[2+] influxing, mitochondrial dysfunction, energy failure, and neuron death. There are two forms of neuron death after HI insult: necrosis and apoptosis, apoptosis being the more prevalent form. Mitochondria handle a series of oxidative reactions, and yield energy for various cellular activities including the maintainance of membrane potential and preservation of intracellular ionic homeostasis. Therefore mitochondria play a critical role in neonatal neurodegeneration following HI, and mitochondrial dysfunction is the key point in neurodegenerative evolution. Because of this, exploring effective mitochondria-based clinical strategies is crucial. Today the only efficacious clinic treatment is hypothermia. However, due to its complex management, clinical complication and autoimmune decrease, its clinical application is limited. So far, many mitochondria-based strategies have been reported neuroprotective in animal models, which offers promise on neonatal therapy. However, since their clinical effectiveness are still unclear, plenty of studies need to be continued in the future. According to recent reports, two novel strategies have been proposed: methylene blue (MB) and melatonin. Although they are still in primary stage, the underlying mechanisms indicate promising clinical applications. Every neurological therapeutic strategy has its intrinsic deficit and limited efficacy, therefore in the long run, the perfect clinical therapy for hypoxic-ischemic neonatal brain injury will be based on the combination of multiple strategies.}, }
@article {pmid27048095, year = {2015}, author = {Zapisek, B and Piątkowski, J}, title = {[PPR proteins--modular factors regulating expression of organellar genomes].}, journal = {Postepy biochemii}, volume = {61}, number = {4}, pages = {403-415}, pmid = {27048095}, issn = {0032-5422}, mesh = {Amino Acid Motifs ; Arabidopsis Proteins/genetics/*metabolism ; Eukaryota/genetics/*metabolism ; Evolution, Molecular ; Fungal Proteins/metabolism ; *Gene Expression Regulation ; *Genome, Mitochondrial ; *Genome, Plastid ; Humans ; Mitochondria/genetics/metabolism ; Plant Proteins/metabolism ; Plastids/genetics/metabolism ; RNA-Binding Proteins/genetics/*metabolism ; }, abstract = {PPR proteins make up the most numerous family of RNA-binding proteins identified to date. They localize almost exclusively to plastids and mitochondria of eukaryotic organisms. The most striking feature of this family is the expansion of PPR protein-encoding genes in vascular plants, which likely coincided with plants colonizing land. PPR proteins participate in stabilizing, editing, splicing, degradation and processing of policistronic transcripts, as well as translation activation in mitochondria and plastids. Although the number of PPR proteins in non-plant organisms is significantly smaller than in plants, they still play a crucial role in regulating the expression of mtDNA. Disruptions of PPR protein-encoding genes usually result in severe phenotypic consequences. Plant PPR proteins bind RNA in a sequence-specific manner, where a single PPR motif recognizes an individual nucleotide in a given sequence. This opens up possibilities for engineering de novo synthetic protein sequences that would interact with precisely determined organellar sequences, thus enabling modulation of mtDNA and ctDNA expression.}, }
@article {pmid27034038, year = {2009}, author = {Hoarau, G and Coyer, JA and Olsen, JL}, title = {PATERNAL LEAKAGE OF MITOCHONDRIAL DNA IN A FUCUS (PHAEOPHYCEAE) HYBRID ZONE(1).}, journal = {Journal of phycology}, volume = {45}, number = {3}, pages = {621-624}, doi = {10.1111/j.1529-8817.2009.00679.x}, pmid = {27034038}, issn = {0022-3646}, abstract = {Eukaryotic mitochondria are mostly uniparentally (maternally) inherited, although mtDNA heteroplasmy has been reported in all major lineages. Heteroplasmy, the presence of more than one mitochondrial genome in an individual, can arise from recombination, point mutations, or by occasional transmission of the paternal mtDNA (=paternal leakage). Here, we report the first evidence of mtDNA paternal leakage in brown algae. In Denmark, where Fucus serratus L. and Fucus evanescens C. Agardh have hybridized for years, we found eight introgressed individuals that possessed the very distinct haplotypes of each parental species. The finding of heteroplasmy in individuals resulting from several generations of backcrosses suggests that paternal leakage occurred in earlier generations and has persisted through several meiotic bottlenecks.}, }
@article {pmid27041620, year = {2008}, author = {Kawai, H and Hanyuda, T and Lindeberg, M and Lindstrom, SC}, title = {MORPHOLOGY AND MOLECULAR PHYLOGENY OF AUREOPHYCUS ALEUTICUS GEN. ET SP. NOV. (LAMINARIALES, PHAEOPHYCEAE) FROM THE ALEUTIAN ISLANDS(1).}, journal = {Journal of phycology}, volume = {44}, number = {4}, pages = {1013-1021}, doi = {10.1111/j.1529-8817.2008.00548.x}, pmid = {27041620}, issn = {0022-3646}, abstract = {A previously unknown species of kelp was collected on Kagamil Island, Aleutian Islands. The species can be easily distinguished from any known laminarialean alga: the erect sporophytic thallus is composed of a thin lanceolate blade attaining ∼2 m in height and ∼0.50 m in width, without midrib, and the edge of the blade at the transition zone is thickened to form a V-shape; the stipe is solid and flattened, slightly translucent, attaining ∼1 m in length; the holdfast is semidiscoidal and up to 0.15 m in diameter. Anatomically, the blade has the typical trumpet-shaped hyphae characteristic of the Chordaceae and derived foliose laminarialean species (i.e., Alariaceae/Laminariaceae/Lessoniaceae). No hair pits or mucilaginous structures were observed on the blade or stipe. No fertile sporophytes were collected, but abundant juvenile sporophytes were observed in the field. In the molecular phylogenetic analyses using chloroplast rbcL gene, nuclear ITS1-5.8S-ITS2 rDNA, and mitochondria nad6 DNA sequences, the new species (Aureophycus aleuticus gen. et sp. nov.) showed a closer relationship with Alariaceae of conventional taxonomy, or the "Group 1" clade of Lane et al. (2006) including Alaria and related taxa than with other groups, although the species was not clearly included in the group. Aureophycus may be a key species in elucidating the evolution of the Alariaceae within the Laminariales. Because of the lack of information on reproductive organs and insufficient resolution of the molecular analyses, we refrain from assigning the new species to a family, but we place the new species in a new genus in the Laminariales.}, }
@article {pmid27041035, year = {2008}, author = {Boore, JL}, title = {DETECTING EVOLUTIONARY TRANSFER OF GENES USING PhIGs(1).}, journal = {Journal of phycology}, volume = {44}, number = {1}, pages = {19-22}, doi = {10.1111/j.1529-8817.2007.00436.x}, pmid = {27041035}, issn = {0022-3646}, abstract = {Organisms have acquired plastids by convoluted paths that have provided multiple opportunities for gene transfer into a host nucleus from intracellular organisms, including the cyanobacterial ancestor of plastids, the proteobacterial ancestor of mitochondria, and both green and red algae whose engulfment has led to secondary acquisition of plastids. These gene movements are most accurately demonstrated by building phylogenetic trees that identify the evolutionary origin of each gene, and one effective tool for this is "PhIGs" (Phylogenetically Inferred Groups; http://PhIGs.org), a set of databases and computer tools with a Web interface for whole-genome evolutionary analysis. PhIGs takes as input gene sets of completely sequenced genomes, builds clusters of genes using a novel, graph-based approach, and reconstructs the evolutionary relationships among all gene families. The user can view and download the sequence alignments, compare intron-exon structures, and follow links to functional genomic databases. Currently, PhIGs contains 652,756 genes from 45 genomes grouped into 61,059 gene families. Graphical displays show the relative positions of these genes among genomes. PhIGs has been used to detect the evolutionary transfer of hundreds of genes from cyanobacteria and red algae into oömycete nuclear genomes, revealing that even though they have no plastids, their ancestors did, having secondarily acquired them from an intracellular red alga. A great number of genomes are soon to become available that are relevant to our broader understanding of the movement of genes among intracellular compartments after engulfing other organisms, and PhIGs will be an effective tool to interpret these gene movements.}, }
@article {pmid28297609, year = {1998}, author = {Ellington, WR and Kinsey, ST}, title = {Functional and Evolutionary Implications of the Distribution of Phosphagens in Primitive-Type Spermatozoa.}, journal = {The Biological bulletin}, volume = {195}, number = {3}, pages = {264-272}, doi = {10.2307/1543138}, pmid = {28297609}, issn = {1939-8697}, abstract = {External fertilization is considered to be the primitive condition in metazoans. The spermatozoa of such organisms typically display a common primitive-type morphology that is present in a range of phyla. These spermatozoa are extremely polarized cells in that the site of ATP synthesis (mitochondria in midpiece) is located at large diffusion distances from the ATP sink (dynein ATPases in the flagellum). Spermatozoa of polychaetes, sipunculids, echiuroids, echinoderms, and tunicates contain the phosphagen creatine phosphate or express the corresponding phosphagen kinase creatine kinase (or both), even when other phosphagens/phosphagen kinases are present in somatic tissues and eggs. The selective expression of the creatine kinase system in these spermatozoa may be related to potential advantages in the cellular transport of energy. To evaluate this possibility, we compared the efficacy of the major phosphagen systems for cellular transport of energy. We used a facilitated diffusion model for spatial ATP buffering, taking into account relative differences in diffusivity and thermodynamic poise. At low ratios of [total phosphagen pool]/ [total adenine nucleotide pool] (CG+P/CAd ratio), creatine phosphate carried a higher fraction of total high-energy phosphate (J) than the other phosphagens. However, J values for all phosphagens were greater than 0.9, and these differences disappeared as the CG+P/CAd ratio was increased. Thus, the functional benefit of using CP, rather than other phosphagens, in energy transport is quite limited. The creatine kinase system became associated with primitive-type spermatozoa early in metazoan evolution. This association is not necessarily related to inherent advantages of this phosphagen system for buffering of ATP, but may be linked to historical events in the evolution of the cell phenotype.}, }
@article {pmid28565202, year = {1998}, author = {Tsumura, Y and Suyama, Y}, title = {DIFFERENTIATION OF MITOCHONDRIAL DNA POLYMORPHISMS IN POPULATIONS OF FIVE JAPANESE ABIES SPECIES.}, journal = {Evolution; international journal of organic evolution}, volume = {52}, number = {4}, pages = {1031-1042}, doi = {10.1111/j.1558-5646.1998.tb01831.x}, pmid = {28565202}, issn = {1558-5646}, abstract = {Mitochondrial DNA polymorphism of 40 populations of five Abies species was investigated using PCR-amplified coxI and coxIII gene probes. Using four combinations of probe and restriction enzyme, we detected three major haplotypes and 15 total haplotypes. We also found varied levels of gene diversity for the different species: 0.741, 0.604, 0.039, 0.000, and 0.292 for A. firma, A. homolepis, A. veitchii, A. mariesii, and A. sachalinensis, respectively. The marginal and southern populations of A. firma and A. homolepis have unique haplotypes, especially the Kyushu, Shikoku, and Kii Peninsula populations, which inhabit areas coinciding with probable refugia of the last glacial period and possess high levels of mtDNA genetic diversity. The haplotypes in some populations suggested mtDNA capture also occurred between species through introgression/hybridization. The strong mtDNA population differentiation in Abies is most likely due to the maternal inheritance of mitochondria and restricted seed dispersal. A phenetic tree based on the genetic similarity of the mtDNA suggests that some species are polyphyletic. Based on mtDNA variation, the five Abies species could be divided roughly into three groups: (1) A. firma and A. homolepis, (2) A. veitchii and A. sachalinensis, and (3) A. mariesii. However, we found that all these Abies species, except A. mariesii, are genetically very closely related according to an analysis of their cpDNA sequences. This showed that the chloroplast rbcL gene differed by only one base substitutions among the four species. We believe that the mtDNA variation and cpDNA similarity clearly reflect relationships among, and the dissemination processes affecting these Abies species since the last glacial period.}, }
@article {pmid29852663, year = {1998}, author = {Tudge, CC and Scheltinga, DM and Jamieson, BGM}, title = {Spermatozoal ultrastructure in the spiny lobster Jasus novaehollandiae Holthuis, 1963 (Palinuridae, Palinura, Decapoda).}, journal = {Journal of morphology}, volume = {236}, number = {2}, pages = {117-126}, doi = {10.1002/(SICI)1097-4687(199805)236:2&lt;117::AID-JMOR3&gt;3.0.CO;2-2}, pmid = {29852663}, issn = {1097-4687}, abstract = {The spermatozoal ultrastructure of the spiny lobster Jasus novaehollandiae is most similar to that in other investigated palinurans and, in particular, to the spermatozoa of Panulirus species. Shared characters include the globular nucleus penetrated by the bases of three or more microtubular arms; an anteriorly situated cytoplasmic zone with mitochondria and conspicuous lamellar bodies; a complex, four-zoned acrosomal vesicle (however, lacking the crystalline region present in Panulirus) with a homogeneous region; a scroll region; a flocculent region; and a region of periacrosomal material that forms finger-like involutions into the flocculent region. The related scyllarid slipper lobsters (Scyllarus and Thenus) possess spermatozoa with acrosome morphology similar to that of Jasus, but the sperm is generally more flattened, numerous radiating acrosome fins are present, and the microtubular arms (in Scyllarus) are cytoplasmic in origin and not nuclear. Sperm morphology provides preliminary evidence in support of the hypothesis of two independent lines of evolution in the Palinuridae but investigation into additional taxa within this group is required. J. Morphol. 236:117-126, 1998. © 1998 Wiley-Liss, Inc.}, }
@article {pmid28564863, year = {1995}, author = {Blackstone, NW}, title = {PERSPECTIVE A UNITS-OF-EVOLUTION PERSPECTIVE ON THE ENDOSYMBIONT THEORY OF THE ORIGIN OF THE MITOCHONDRION.}, journal = {Evolution; international journal of organic evolution}, volume = {49}, number = {5}, pages = {785-796}, doi = {10.1111/j.1558-5646.1995.tb02315.x}, pmid = {28564863}, issn = {1558-5646}, abstract = {Discussions of mitochondria and their hosts often conceptualize this relationship in a more or less modern form, focusing on the metabolic benefits of mitochondria to the host cell or on the possibility of intragenomic conflict. A more inclusive units-of-evolution perspective recognizes that both costs and benefits must be viewed from the level of the cells that initiated this interaction, the protomitochondrion and the primitive host cell. From this perspective, ecological and physiological considerations become central to the characterization of initial and subsequent host-mitochondria associations. Foremost among these considerations is the generation of superoxide radicals by modern mitochondria and the deleterious effects of these endogenous oxidants on modern eukaryotic cells. Because of their photosynthetic and aerobic ecologies, protomitochondria likely were relatively tolerant of such oxidants; anaerobic, heterotrophic, primitive host cells, on the other hand, likely were not. In the initial association of host and symbiont, the latter may have manipulated the former's life history by means of both endogenous oxidants and a superabundance of ATP. A resolution of this units-of-evolution conflict was necessary to continue this association, and this resolution, in a ritualized form, may have shaped the evolution of many features of modern eukaryotic cells and mitochondria, for example, the messenger functions of calcium ions, the regulatory role of phosphorylation cascades in cell-division cycles, the absence from the mitochondrial genome of replication factors, transcription factors, and adenine nucleotide carrier genes. The initial host-mitochondria interaction may have further channeled the evolution of multicellular eukaryotes, particularly animals, resulting in the association of mitochondria and the germinal plasm and in the use of extracellular ATP and endogenous oxidants as developmental signals. Evolutionary explanations for "free-radical" theories of development and aging are thus suggested.}, }
@article {pmid28565002, year = {1995}, author = {Van Horn, R and Clay, K}, title = {MITOCHONDRIAL DNA VARIATION IN THE FUNGUS ATKINSONELLA HYPOXYLON INFECTING SYMPATRIC DANTHONIA GRASSES.}, journal = {Evolution; international journal of organic evolution}, volume = {49}, number = {2}, pages = {360-371}, doi = {10.1111/j.1558-5646.1995.tb02248.x}, pmid = {28565002}, issn = {1558-5646}, abstract = {The purpose of this study was to determine how host identity and geographic proximity were related to genetic variation in the fungus Atkinsonella hypoxylon infecting four sympatric Danthonia grasses. We analyzed 192 A. hypoxylon isolates from 48 geographic sites for mitochondrial DNA (mtDNA) variation by restriction digestion of total DNA with EcoRI, BamHI, and PstI, and subsequent hybridization with purified A. hypoxylon mtDNA. Thirtynine haplotypes were identified. UPGMA cluster analysis showed that mtDNA type is highly correlated with host-species group; isolates from Danthonia compressa and D. spicata formed one branch of the phenogram, and isolates from D. epilis and D. sericea formed the other. Restriction maps of the most common mtDNA haplotypes infecting each host-species pair revealed a 30-kb size difference and a minimum of eight length changes and one restrictionsite change between them. Mapping of the mutation differences among all haplotypes occurring at North Carolina sites resulted in two distinct gene trees corresponding to the two Danthonia species groups, corroborating the phenetic analysis. The results indicate a high degree of host-dependent isolation and establish the existence of host races in A. hypoxylon. Possible mechanisms responsible for this isolation are discussed. Little differentiation existed between isolates from within a Danthonia species pair, and some variation was explained by geographic origin. Analysis of progeny from a natural sexual cross revealed that mitochondria are maternally inherited in A. hypoxylon.}, }
@article {pmid28563817, year = {1991}, author = {Paige, KN and Capman, WC and Jennetten, P}, title = {MITOCHONDRIAL INHERITANCE PATTERNS ACROSS A COTTONWOOD HYBRID ZONE: CYTONUCLEAR DISEQUILIBRIA AND HYBRID ZONE DYNAMICS.}, journal = {Evolution; international journal of organic evolution}, volume = {45}, number = {6}, pages = {1360-1369}, doi = {10.1111/j.1558-5646.1991.tb02641.x}, pmid = {28563817}, issn = {1558-5646}, abstract = {In this study we examine the cytoplasmic inheritance patterns of an interspecific hybridizing population of Fremont and narrowleaf cottonwoods, using mitochondrial DNA. Three mitochondrial probes showing polymorphisms were used to distinguish between trees of known nuclear inheritance. Every tree screened had only one cytoplasmic genotype, either Fremont or narrowleaf. Thus, these results demonstrate that mitochondria are uniparentally inherited in these trees. Previous studies of the nuclear inheritance of this interspecific hybridizing population of cottonwood trees indicated an asymmetry in the frequency of parental genes. Using mitochondrial markers we tested one hypothesis potentially responsible for this asymmetric distribution (i.e., trees of mixed genotypes will be sterile or will not survive if their cytoplasm is derived from one or the other parent). Our results, however, show that both Fremont and narrowleaf mitochondrial markers are found in trees with mixed nuclear genotypes. Thus, nuclear-cytoplasmic incompatibilities do not appear to account for the asymmetric distribution of nuclear genotypes within the hybrid swarm. An alternative explanation for the observed asymmetric distribution of nuclear genotypes is advanced. Although nuclear-cytoplasmic incompatibilities do not appear to explain the asymmetric distribution of nuclear alleles within the hybrid zone, nonrandom associations between nuclear and cytoplasmic genotypes do exist. For example, all F1 hybrids had Fremont mitochondrial genotypes. Furthermore, backcrosses between F1 hybrid and narrowleaf trees have a higher than expected proportion of heterozygous loci and a higher than expected proportion of Fremont mitochondria. We propose that seeds, seedlings, or trees with high proportions of heterozygous loci are at a disadvantage unless they also have the Fremont mitochondrial genotype. While it is generally difficult to infer dynamic processes from static patterns, studies such as ours enable one to gain new insights to the dynamics of plant hybrid zones. A hybridization pattern of decreasingly complex backcrosses as one proceeds from higher to lower elevation within the hybrid swarm, a residue of Fremont cytoplasmic DNA within the pure narrowleaf population, and the unidirectional nature of these crosses suggest that the narrowleaf population may be spreading down the canyon and the Fremont population receding. The eventual fate of the hybrid zone, in relation to these processes, is discussed.}, }
@article {pmid28568820, year = {1991}, author = {Pollak, PE}, title = {CYTOPLASMIC EFFECTS ON COMPONENTS OF FITNESS IN TOBACCO CYBRIDS.}, journal = {Evolution; international journal of organic evolution}, volume = {45}, number = {3}, pages = {785-791}, doi = {10.1111/j.1558-5646.1991.tb04349.x}, pmid = {28568820}, issn = {1558-5646}, }
@article {pmid29517737, year = {1986}, author = {Koll, F}, title = {Does nuclear integration of mitochondrial sequences occur during senescence in Podospora?.}, journal = {Nature}, volume = {324}, number = {6097}, pages = {597-599}, doi = {10.1038/324597a0}, pmid = {29517737}, issn = {1476-4687}, abstract = {Observations in various organisms[1-3] suggest that the transfer of mitochondrial DNA sequences to the nucleus has occurred in the course of evolution. Wright and Cummings have reported[4], on the basis of hybridization experiments, that there is such a transposition in the fungus Podospora anserina during senescence[5] (arrest of vegetative growth) which is accompanied by amplification of specific mitochondrial sequences[6-9]. They suggested that this transposition could explain senescence, and, as it could be regularly observed under laboratory conditions, senescence in Podospora could constitute a model system to study the molecular mechanisms of the transfer of DNA sequences from mitochondria to the nucleus. We report here experiments similar to those of Wright and Cummings[4] but include additional critical controls. Our results do not confirm the data of Wright and Cummings; the only positive signals we observed after hybridization of mitochondrial DNA sequences on nuclear DNAs can be attributed to contaminating DNA from mitochondria or plasmids.}, }
@article {pmid30060640, year = {1983}, author = {Ruppert, EE and Travis, PB}, title = {Hemoglobin-containing cells of Neodasys (Gastrotricha, Chaetonotida). I. Morphology and ultrastructure.}, journal = {Journal of morphology}, volume = {175}, number = {1}, pages = {57-64}, doi = {10.1002/jmor.1051750106}, pmid = {30060640}, issn = {1097-4687}, abstract = {The overall anatomy of Neodasys as well as data for hemoglobin-containing cells are described. Hemoglobin-containing cells are shown to be mesodermal specializations constituting approximately 14% of the animal's total body volume (4.87 ± 10[4] μl). These globular cells (10-14 μm) are situated in two longitudinal rows, each dorsolateral to the straight gut. Branches from the cells enwrap perikarya of muscle and nerve cells whose mitochondria are found just below their respective plasmalemmata in intimate association with the hemoglobin-containing cells. The ground substance of the cytoplasm and nucleoplasm of these nearly organelle-free cells is extremely electron-dense and is presumed to represent the hemoglobin molecules. Locomotion analyses indicate that the cells can undergo a threefold change in linear dimension in 0.25 seconds, raising the possibility of convective mixing in these cells. Structural and ultrastructural comparisons with similar cells in adults of other species of Gastrotricha indicate that the hemoglobin-containing cells of Neodasys may be homologous to the socalled Y cells of other species, some of which contain myofilaments. A muscle-cell origin is considered for the evolution of hemoglobin-containing cells of Neodasys.}, }
@article {pmid28305138, year = {1977}, author = {Wissocq, JC}, title = {[Evolution of muscles inNereidae (Annelida polychaeta) during Epitoky. III. Dedifferentiation of the longitudinal fibres].}, journal = {Wilhelm Roux's archives of developmental biology}, volume = {182}, number = {3}, pages = {227-253}, pmid = {28305138}, issn = {0340-0794}, abstract = {During epitoky inNereidae, the longitudinal muscle fibres are not formedde novo from undifferentiated cells or myoblasts, but arise from the old atokous fibres. These undergo a true dedifferentiation more or less synchronously with a redifferentiation. The two processes are not successive but simultaneous and there is no complete dedifferentiation.The first cells that develop are in the outside muscle layer; then the fibres of the inside layers are transformed in their turn.The transformations consist of: 1) Dedifferentiation of the edge of the inner or coelomic fibre. The contractile structures disappear in this part and numerous glycogen particles differentiate, unrelated to endoplasmic reticulum or ribosomes. No lysosomes or precursory markings are observed before the disappearance of contractile filaments and Z rods. 2) The coelomic edge becomes enlarged. In the axial region of the fibre, numerous mitochondria and α and β glycogen particles take the place of the contractile material. Consequently, the thickness of A and I bands decreases. 3) The heteronereid or epitokous fibre is formed and shows two parts: a myoplasmic cortex and a sarcoplasmic medulla, filled with mitochondria and glycogen. The nucleus with a voluminous nucleolus settles inside a lateral sarcoplasmic swelling.}, }
@article {pmid28304723, year = {1972}, author = {Herbaut, C}, title = {[Cytochemical and ultrastructural study of oogenesis inLithobius forficatus L. (Myriapoda, Chilopoda). Evolution of cellular components].}, journal = {Wilhelm Roux' Archiv fur Entwicklungsmechanik der Organismen}, volume = {170}, number = {2}, pages = {115-134}, pmid = {28304723}, issn = {0043-5546}, abstract = {The development of the oocyte takes place in four classical phases: premeiosis, previtellogenesis, vitellogenesis and maturation.During previtellogenesis, nucleus and cytoplasm grow considerably. The nucleolar material breaks up into numerous masses and laminae and nuclear extrusions are very frequent. The number of ribosomes and mitochondria increases markedly; the mitochondria show pronounced morphological modifications: stacking, honeycomb-like figures. Lysosomal formations are numerous.During vitellogenesis, the nucleus shows little activity and yolk accumulates in the cytoplasm. The number of ribosomes and mitochondria decreases. During maturation, the Golgi apparatus seems to bud off vacuoles in the cortical cytoplasm.Cytological and cytochemical modifications are discussed in relation to the physiological development of the oocyte.}, }
@article {pmid27018240, year = {2016}, author = {Faktorová, D and Dobáková, E and Peña-Diaz, P and Lukeš, J}, title = {From simple to supercomplex: mitochondrial genomes of euglenozoan protists.}, journal = {F1000Research}, volume = {5}, number = {}, pages = {}, pmid = {27018240}, issn = {2046-1402}, abstract = {Mitochondria are double membrane organelles of endosymbiotic origin, best known for constituting the centre of energetics of a eukaryotic cell. They contain their own mitochondrial genome, which as a consequence of gradual reduction during evolution typically contains less than two dozens of genes. In this review, we highlight the extremely diverse architecture of mitochondrial genomes and mechanisms of gene expression between the three sister groups constituting the phylum Euglenozoa - Euglenida, Diplonemea and Kinetoplastea. The earliest diverging euglenids possess a simplified mitochondrial genome and a conventional gene expression, whereas both are highly complex in the two other groups. The expression of their mitochondrial-encoded proteins requires extensive post-transcriptional modifications guided by complex protein machineries and multiple small RNA molecules. Moreover, the least studied diplonemids, which have been recently discovered as a highly abundant component of the world ocean plankton, possess one of the most complicated mitochondrial genome organisations known to date.}, }
@article {pmid27023846, year = {2016}, author = {Greber, BJ and Ban, N}, title = {Structure and Function of the Mitochondrial Ribosome.}, journal = {Annual review of biochemistry}, volume = {85}, number = {}, pages = {103-132}, doi = {10.1146/annurev-biochem-060815-014343}, pmid = {27023846}, issn = {1545-4509}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Biological Evolution ; Carboxylic Ester Hydrolases/genetics/metabolism ; DNA, Mitochondrial/*genetics/metabolism ; Mammals ; Mitochondria/*genetics/metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/*genetics/metabolism ; Mitochondrial Ribosomes/chemistry/metabolism/*ultrastructure ; Models, Molecular ; *Protein Biosynthesis ; RNA, Messenger/genetics/metabolism ; RNA, Transfer/genetics/metabolism ; Ribosome Subunits/chemistry/metabolism/*ultrastructure ; Saccharomyces cerevisiae/genetics/metabolism ; }, abstract = {Mitochondrial ribosomes (mitoribosomes) perform protein synthesis inside mitochondria, the organelles responsible for energy conversion and adenosine triphosphate production in eukaryotic cells. Throughout evolution, mitoribosomes have become functionally specialized for synthesizing mitochondrial membrane proteins, and this has been accompanied by large changes to their structure and composition. We review recent high-resolution structural data that have provided unprecedented insight into the structure and function of mitoribosomes in mammals and fungi.}, }
@article {pmid27021180, year = {2016}, author = {Yang, X and Wang, L and Chen, H and Feng, H and Shen, B and Hu, M and Fang, R}, title = {The complete mitochondrial genome of Gastrothylax crumenifer (Gastrothylacidae, Trematoda) and comparative analyses with selected trematodes.}, journal = {Parasitology research}, volume = {115}, number = {6}, pages = {2489-2497}, pmid = {27021180}, issn = {1432-1955}, mesh = {Animals ; Base Sequence ; Cattle/parasitology ; Cattle Diseases/parasitology ; DNA, Mitochondrial/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Paramphistomatidae/*classification/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {In the present study, we sequenced and analyzed the mitochondrial (mt) genome of Gastrothylax crumenifer and compared it with other selected trematodes. The full mt genome of G. crumenifer was amplified, sequenced, assembled, analyzed and then subjected to phylogenetic analysis. The complete mt genome of G. crumenifer is 14,801 bp in length and contains two rRNA genes, two non-coding regions (LNR and SNR), 12 protein-coding genes, and 22 transfer RNA genes. The gene organization of the G. crumenifer mt genome is the same as that of other trematodes, except for Schistosoma haematobium and Schistosoma spindale. All the genes are transcribed in the same direction and rich in "A + T", which is in accordance with other trematodes, such as Fasciola hepatica, Paramphistomum cervi, and Fischoederius elongatus. Phylogenetic analysis using concatenated amino acid sequences of the 12 protein-coding genes showed that G. crumenifer is closely related to F. elongatus. The availability of mt genome sequence of G. crumenifer can provide useful DNA markers for studying the molecular epidemiology and population genetics of this parasite and other paramphistomes.}, }
@article {pmid27020329, year = {2016}, author = {Umeda, T and Ono, K and Sakai, A and Yamashita, M and Mizuguchi, M and Klein, WL and Yamada, M and Mori, H and Tomiyama, T}, title = {Rifampicin is a candidate preventive medicine against amyloid-β and tau oligomers.}, journal = {Brain : a journal of neurology}, volume = {139}, number = {Pt 5}, pages = {1568-1586}, doi = {10.1093/brain/aww042}, pmid = {27020329}, issn = {1460-2156}, mesh = {Alzheimer Disease/complications/metabolism/*prevention &amp; control ; Amyloid beta-Peptides/*drug effects/metabolism ; Animals ; Caspase 3/metabolism ; Cells, Cultured ; Cytochromes c/metabolism ; Dose-Response Relationship, Drug ; Female ; Hippocampus/metabolism ; Maze Learning/drug effects ; Memory Disorders/complications/drug therapy ; Mice ; Mice, Transgenic ; Microglia/drug effects ; Microtubule-Associated Proteins/metabolism ; Neuroprotective Agents/pharmacology/therapeutic use ; Phosphorylation/drug effects ; Rifampin/*pharmacology/*therapeutic use ; Sequestosome-1 Protein/metabolism ; Synapses/drug effects ; Synucleins/drug effects/metabolism ; Tauopathies/complications/metabolism/*prevention &amp; control ; tau Proteins/*drug effects/metabolism ; }, abstract = {Amyloid-β, tau, and α-synuclein, or more specifically their soluble oligomers, are the aetiologic molecules in Alzheimer's disease, tauopathies, and α-synucleinopathies, respectively. These proteins have been shown to interact to accelerate each other's pathology. Clinical studies of amyloid-β-targeting therapies in Alzheimer's disease have revealed that the treatments after disease onset have little benefit on patient cognition. These findings prompted us to explore a preventive medicine which is orally available, has few adverse effects, and is effective at reducing neurotoxic oligomers with a broad spectrum. We initially tested five candidate compounds: rifampicin, curcumin, epigallocatechin-3-gallate, myricetin, and scyllo-inositol, in cells expressing amyloid precursor protein (APP) with the Osaka (E693Δ) mutation, which promotes amyloid-β oligomerization. Among these compounds, rifampicin, a well-known antibiotic, showed the strongest activities against the accumulation and toxicity (i.e. cytochrome c release from mitochondria) of intracellular amyloid-β oligomers. Under cell-free conditions, rifampicin inhibited oligomer formation of amyloid-β, tau, and α-synuclein, indicating its broad spectrum. The inhibitory effects of rifampicin against amyloid-β and tau oligomers were evaluated in APPOSK mice (amyloid-β oligomer model), Tg2576 mice (Alzheimer's disease model), and tau609 mice (tauopathy model). When orally administered to 17-month-old APPOSK mice at 0.5 and 1 mg/day for 1 month, rifampicin reduced the accumulation of amyloid-β oligomers as well as tau hyperphosphorylation, synapse loss, and microglial activation in a dose-dependent manner. In the Morris water maze, rifampicin at 1 mg/day improved memory of the mice to a level similar to that in non-transgenic littermates. Rifampicin also inhibited cytochrome c release from the mitochondria and caspase 3 activation in the hippocampus. In 13-month-old Tg2576 mice, oral rifampicin at 0.5 mg/day for 1 month decreased amyloid-β oligomer accumulation, tau hyperphosphorylation, synapse loss, and microglial activation, but not amyloid deposition. Rifampicin treatment to 14-15-month-old tau609 mice at 0.5 and 1 mg/day for 1 month also reduced tau oligomer accumulation, tau hyperphosphorylation, synapse loss, and microglial activation in a dose-dependent fashion, and improved the memory almost completely at 1 mg/day. In addition, rifampicin decreased the level of p62/sequestosome-1 in the brain without affecting the increased levels of LC3 (microtubule-associated protein light chain 3) conversion, suggesting the restoration of autophagy-lysosomal function. Considering its prescribed dose and safety in humans, these results indicate that rifampicin could be a promising, ready-to-use medicine for the prevention of Alzheimer's disease and other neurodegenerative diseases.}, }
@article {pmid27018673, year = {2016}, author = {Prantl, L and Schreml, J and Gehmert, S and Klein, S and Bai, X and Zeitler, K and Schreml, S and Alt, E and Gehmert, S and Felthaus, O}, title = {Transcription Profile in Sporadic Multiple Symmetric Lipomatosis Reveals Differential Expression at the Level of Adipose Tissue-Derived Stem Cells.}, journal = {Plastic and reconstructive surgery}, volume = {137}, number = {4}, pages = {1181-1190}, doi = {10.1097/PRS.0000000000002013}, pmid = {27018673}, issn = {1529-4242}, mesh = {Aged ; Cell Differentiation ; Cell Proliferation ; Cells, Cultured ; Female ; Gene Expression Profiling ; Humans ; Lipomatosis, Multiple Symmetrical/*genetics/pathology/physiopathology ; Male ; Mesenchymal Stem Cells/pathology/*physiology ; Middle Aged ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Subcutaneous Fat/pathology/*physiopathology ; *Transcriptome ; }, abstract = {BACKGROUND: The cause of the rare fat distribution disorder multiple symmetric lipomatosis is unknown. Independent reports suggest a higher proliferative activity, hormone resistance, and involvement of mitochondrial function in the disease.<br><br>METHODS: The authors performed morphologic comparison of affected and unaffected tissues in five unrelated patients and generated adipose-derived stem cell cultures from the tissue samples and characterized them as a possible cellular model of multiple symmetric lipomatosis evolution. The authors investigated proliferative activity and the expression of genes relevant to disease processes.<br><br>RESULTS: There was no difference in the morphologic appearance and the surface marker profile. Stem cells from lipomatous tissue showed significantly higher proliferative activity. Polymerase chain reaction arrays showed marked changes in genes associated with proliferation, hormonal regulation, and mitochondria. The authors show that multiple symmetric lipomatosis tissue is morphologically and histologically different from regular subcutaneous fat.<br><br>CONCLUSIONS: This study indicates an involvement of mesenchymal stem cells in the pathogenesis of multiple symmetric lipomatosis and that the evolution of multiple symmetric lipomatosis tissue is a process driven by an inherent defect of the respective cell clone(s). Further molecular genetics and functional analysis will be required to unravel the pathogenetic mechanism underlying the derailment in fat cell metabolism and proliferation. Here, the authors show for the first time that adipose-derived stem cells exhibit many characteristics previously described for native multiple symmetric lipomatosis fat tissue and propose that they are therefore an excellent tool for further functional investigations in multiple symmetric lipomatosis and other disorders of the fat tissue.<br><br>Risk, V.}, }
@article {pmid27014281, year = {2016}, author = {López-Millán, AF and Duy, D and Philippar, K}, title = {Chloroplast Iron Transport Proteins - Function and Impact on Plant Physiology.}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {178}, pmid = {27014281}, issn = {1664-462X}, abstract = {Chloroplasts originated about three billion years ago by endosymbiosis of an ancestor of today's cyanobacteria with a mitochondria-containing host cell. During evolution chloroplasts of higher plants established as the site for photosynthesis and thus became the basis for all life dependent on oxygen and carbohydrate supply. To fulfill this task, plastid organelles are loaded with the transition metals iron, copper, and manganese, which due to their redox properties are essential for photosynthetic electron transport. In consequence, chloroplasts for example represent the iron-richest system in plant cells. However, improvement of oxygenic photosynthesis in turn required adaptation of metal transport and homeostasis since metal-catalyzed generation of reactive oxygen species (ROS) causes oxidative damage. This is most acute in chloroplasts, where radicals and transition metals are side by side and ROS-production is a usual feature of photosynthetic electron transport. Thus, on the one hand when bound by proteins, chloroplast-intrinsic metals are a prerequisite for photoautotrophic life, but on the other hand become toxic when present in their highly reactive, radical generating, free ionic forms. In consequence, transport, storage and cofactor-assembly of metal ions in plastids have to be tightly controlled and are crucial throughout plant growth and development. In the recent years, proteins for iron transport have been isolated from chloroplast envelope membranes. Here, we discuss their putative functions and impact on cellular metal homeostasis as well as photosynthetic performance and plant metabolism. We further consider the potential of proteomic analyses to identify new players in the field.}, }
@article {pmid27011011, year = {2016}, author = {Pingitore, A and Nicolini, G and Kusmic, C and Iervasi, G and Grigolini, P and Forini, F}, title = {Cardioprotection and thyroid hormones.}, journal = {Heart failure reviews}, volume = {21}, number = {4}, pages = {391-399}, pmid = {27011011}, issn = {1573-7322}, mesh = {Animals ; Cardiotonic Agents/*pharmacology ; Disease Models, Animal ; Heart/drug effects/*physiopathology ; Hormone Replacement Therapy ; Humans ; Mitochondria, Heart/drug effects ; Myocardial Ischemia/*physiopathology/*prevention &amp; control ; Rats ; Regeneration/drug effects ; Thyroid Hormones/*pharmacology/physiology ; }, abstract = {The evolution of cardiac disease after an acute ischemic event depends on a complex and dynamic network of mechanisms alternating from ischemic damage due to acute coronary occlusion to reperfusion injury due to the adverse effects of coronary revascularization till post-ischemic remodeling. Cardioprotection is a new purpose of the therapeutic interventions in cardiology with the goal to reduce infarct size and thus prevent the progression toward heart failure after an acute ischemic event. In a complex biological system such as the human one, an effective cardioprotective strategy should diachronically target the network of cross-talking pathways underlying the disease progression. Thyroid system is strictly interconnected with heart homeostasis, and recent studies highlighted its role in cardioprotection, in particular through the preservation of mitochondrial function and morphology, the antifibrotic and proangiogenetic effect and also to the potential induction of cell regeneration and growth. The objective of this review was to highlight the cardioprotective role of triiodothyronine in the complexity of post-ischemic disease evolution.}, }
@article {pmid27009201, year = {2016}, author = {Ling, F and Niu, R and Hatakeyama, H and Goto, Y and Shibata, T and Yoshida, M}, title = {Reactive oxygen species stimulate mitochondrial allele segregation toward homoplasmy in human cells.}, journal = {Molecular biology of the cell}, volume = {27}, number = {10}, pages = {1684-1693}, pmid = {27009201}, issn = {1939-4586}, mesh = {*Alleles ; Chromosome Segregation ; DNA Replication/physiology ; DNA, Mitochondrial/*genetics/*metabolism ; Fibroblasts/metabolism ; Genes, Mitochondrial ; Genome, Mitochondrial ; Humans ; MELAS Syndrome/genetics/metabolism ; Mitochondria/*genetics/*metabolism ; Mutation ; Primary Cell Culture ; Reactive Oxygen Species/*metabolism ; }, abstract = {Mitochondria that contain a mixture of mutant and wild-type mitochondrial (mt) DNA copies are heteroplasmic. In humans, homoplasmy is restored during early oogenesis and reprogramming of somatic cells, but the mechanism of mt-allele segregation remains unknown. In budding yeast, homoplasmy is restored by head-to-tail concatemer formation in mother cells by reactive oxygen species (ROS)-induced rolling-circle replication and selective transmission of concatemers to daughter cells, but this mechanism is not obvious in higher eukaryotes. Here, using heteroplasmic m.3243A > G primary fibroblast cells derived from MELAS patients treated with hydrogen peroxide (H2O2), we show that an optimal ROS level promotes mt-allele segregation toward wild-type and mutant mtDNA homoplasmy. Enhanced ROS level reduced the amount of intact mtDNA replication templates but increased linear tandem multimers linked by head-to-tail unit-sized mtDNA (mtDNA concatemers). ROS-triggered mt-allele segregation correlated with mtDNA-concatemer production and enabled transmission of multiple identical mt-genome copies as a single unit. Our results support a mechanism by which mt-allele segregation toward mt-homoplasmy is mediated by concatemers.}, }
@article {pmid27001515, year = {2016}, author = {Moreira, S and Valach, M and Aoulad-Aissa, M and Otto, C and Burger, G}, title = {Novel modes of RNA editing in mitochondria.}, journal = {Nucleic acids research}, volume = {44}, number = {10}, pages = {4907-4919}, pmid = {27001515}, issn = {1362-4962}, support = {MOP-79309//CIHR/Canada ; }, mesh = {Adenosine/metabolism ; Deamination ; Euglenozoa/*genetics/metabolism ; Genes, Mitochondrial ; Genes, rRNA ; Inosine/metabolism ; Mitochondria/*genetics ; RNA/chemistry/*metabolism ; *RNA Editing ; RNA, Mitochondrial ; Trans-Splicing ; Transcriptome ; }, abstract = {Gene structure and expression in diplonemid mitochondria are unparalleled. Genes are fragmented in pieces (modules) that are separately transcribed, followed by the joining of module transcripts to contiguous RNAs. Some instances of unique uridine insertion RNA editing at module boundaries were noted, but the extent and potential occurrence of other editing types remained unknown. Comparative analysis of deep transcriptome and genome data from Diplonema papillatum mitochondria reveals ∼220 post-transcriptional insertions of uridines, but no insertions of other nucleotides nor deletions. In addition, we detect in total 114 substitutions of cytosine by uridine and adenosine by inosine, amassed into unusually compact clusters. Inosines in transcripts were confirmed experimentally. This is the first report of adenosine-to-inosine editing of mRNAs and ribosomal RNAs in mitochondria. In mRNAs, editing causes mostly amino-acid additions and non-synonymous substitutions; in ribosomal RNAs, it permits formation of canonical secondary structures. Two extensively edited transcripts were compared across four diplonemids. The pattern of uridine-insertion editing is strictly conserved, whereas substitution editing has diverged dramatically, but still rendering diplonemid proteins more similar to other eukaryotic orthologs. We posit that RNA editing not only compensates but also sustains, or even accelerates, ultra-rapid evolution of genome structure and sequence in diplonemid mitochondria.}, }
@article {pmid26998815, year = {2016}, author = {Wang, ZG and Liu, SL and Hu, YJ and Tian, ZQ and Hu, B and Zhang, ZL and Pang, DW}, title = {Dissecting the Factors Affecting the Fluorescence Stability of Quantum Dots in Live Cells.}, journal = {ACS applied materials &amp; interfaces}, volume = {8}, number = {13}, pages = {8401-8408}, doi = {10.1021/acsami.6b01742}, pmid = {26998815}, issn = {1944-8252}, mesh = {Cell Proliferation/drug effects ; *Cell Tracking ; Cell-Penetrating Peptides/chemistry/*pharmacology ; Endocytosis/drug effects ; Fluorescence ; Lysosomes/drug effects ; Microscopy, Confocal ; Microscopy, Fluorescence ; *Molecular Imaging ; Quantum Dots/administration &amp; dosage/*chemistry ; Staining and Labeling ; }, abstract = {Labeling and imaging of live cells with quantum dots (QDs) has attracted great attention in the biomedical field over the past two decades. Maintenance of the fluorescence of QDs in a biological environment is crucial for performing long-term cell tracking to investigate the proliferation and functional evolution of cells. The cell-penetrating peptide transactivator of transcription (TAT) is a well-studied peptide to efficiently enhance the transmembrane delivery. Here, we used TAT peptide-conjugated QDs (TAT-QDs) as a model system to examine the fluorescence stability of QDs in live cells. By confocal microscopy, we found that TAT-QDs were internalized into cells by endocytosis, and transported into the cytoplasm via the mitochondria, Golgi apparatus, and lysosomes. More importantly, the fluorescence of TAT-QDs in live cells was decreased mainly by cell proliferation, and the low pH value in the lysosomes could also lower the fluorescence intensity of intracellular QDs. Quantitative analysis of the amount of QDs in the extracellular region and whole cells indicated that the exocytosis was not the primary cause of fluorescence decay of intracellular QDs. This work facilitates a better understanding of the fluorescence stability of QDs for cell imaging and long-term tracking in live cells. Also, it provides insights into the utility of TAT for transmembrane transportation, and the preparation and modification of QDs for cell imaging and tracking.}, }
@article {pmid26998248, year = {2016}, author = {Leister, D}, title = {Towards understanding the evolution and functional diversification of DNA-containing plant organelles.}, journal = {F1000Research}, volume = {5}, number = {}, pages = {}, pmid = {26998248}, issn = {2046-1402}, abstract = {Plastids and mitochondria derive from prokaryotic symbionts that lost most of their genes after the establishment of endosymbiosis. In consequence, relatively few of the thousands of different proteins in these organelles are actually encoded there. Most are now specified by nuclear genes. The most direct way to reconstruct the evolutionary history of plastids and mitochondria is to sequence and analyze their relatively small genomes. However, understanding the functional diversification of these organelles requires the identification of their complete protein repertoires - which is the ultimate goal of organellar proteomics. In the meantime, judicious combination of proteomics-based data with analyses of nuclear genes that include interspecies comparisons and/or predictions of subcellular location is the method of choice. Such genome-wide approaches can now make use of the entire sequences of plant nuclear genomes that have emerged since 2000. Here I review the results of these attempts to reconstruct the evolution and functions of plant DNA-containing organelles, focusing in particular on data from nuclear genomes. In addition, I discuss proteomic approaches to the direct identification of organellar proteins and briefly refer to ongoing research on non-coding nuclear DNAs of organellar origin (specifically, nuclear mitochondrial DNA and nuclear plastid DNA).}, }
@article {pmid26996128, year = {2016}, author = {Lehmann, G and Udasin, RG and Ciechanover, A}, title = {On the linkage between the ubiquitin-proteasome system and the mitochondria.}, journal = {Biochemical and biophysical research communications}, volume = {473}, number = {1}, pages = {80-86}, doi = {10.1016/j.bbrc.2016.03.055}, pmid = {26996128}, issn = {1090-2104}, mesh = {Cytosol/metabolism ; Homeostasis ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Proteasome Endopeptidase Complex/*metabolism ; Protein Interaction Mapping ; Proteome ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins/metabolism ; Ubiquitin/*metabolism ; Ubiquitination ; }, abstract = {Several metabolic pathways critical for cellular homeostasis occur in the mitochondria. Because of the evolution of mitochondria and their physical separation, these pathways have traditionally been thought to be free from regulation by the ubiquitin-proteasome system. This perception has recently been challenged by evidence for the presence of ubiquitin system components in the mitochondria. Furthermore, it has been shown that certain mitochondrial proteins are conjugated by ubiquitin, and some of them are degraded by the proteasome. Of particular interest is the finding that some of these proteins are localized to the inner membrane and matrix, which rules out that their targeting is mediated by the cytosolic ubiquitin system. However, the extent of the involvement of the ubiquitin system in mitochondrial regulation is not known. The present study addresses this surprising finding, employing several independent approaches. First, we identified reported ubiquitin conjugates in human and yeast mitochondria and found that a large fraction of the mitochondrial proteome (62% in human) is ubiquitinated, with most proteins localized to the inner membrane and matrix. Next, we searched the literature and found that numerous ubiquitin system components localize to the mitochondria and/or contain mitochondrial targeting sequences. Finally, we identified reported protein-protein interactions between ubiquitin system components and mitochondrial proteins. These unexpected findings suggest that mitochondrial regulation by the ubiquitin system is fundamental and may have broad biomedical implications.}, }
@article {pmid26993764, year = {2016}, author = {Herrera, S and Shank, TM}, title = {RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa.}, journal = {Molecular phylogenetics and evolution}, volume = {100}, number = {}, pages = {70-79}, doi = {10.1016/j.ympev.2016.03.010}, pmid = {26993764}, issn = {1095-9513}, mesh = {Animals ; Anthozoa/*classification/*genetics ; Base Sequence ; Bayes Theorem ; Genetic Loci ; Genetic Markers ; Mitochondria/genetics ; *Phylogeny ; Restriction Mapping/*methods ; Sequence Analysis, DNA/*methods ; Species Specificity ; }, abstract = {Species delimitations is problematic in many cases due to the difficulty of evaluating predictions from species hypotheses. In many cases delimitations rely on subjective interpretations of morphological and/or DNA data. Species with inadequate genetic resources needed to answer questions regarding evolutionary relatedness and genetic uniqueness are particularly problematic. In this study, we demonstrate the utility of restriction site associated DNA sequencing (RAD-seq) to objectively resolve unambiguous phylogenetic relationships in a recalcitrant group of deep-sea corals with divergences >80 million years. We infer robust species boundaries in the genus Paragorgia by testing alternative delimitation hypotheses using a Bayes Factors delimitation method. We present substantial evidence rejecting the current morphological species delimitation model for the genus and infer the presence of cryptic species associated with environmental variables. We argue that the suitability limits of RAD-seq for phylogenetic inferences cannot be assessed in terms of absolute time, but are contingent on taxon-specific factors. We show that classical taxonomy can greatly benefit from integrative approaches that provide objective tests to species delimitation hypotheses. Our results lead the way for addressing further questions in marine biogeography, community ecology, population dynamics, conservation, and evolution.}, }
@article {pmid26993763, year = {2016}, author = {Cardinal-McTeague, WM and Sytsma, KJ and Hall, JC}, title = {Biogeography and diversification of Brassicales: A 103million year tale.}, journal = {Molecular phylogenetics and evolution}, volume = {99}, number = {}, pages = {204-224}, doi = {10.1016/j.ympev.2016.02.021}, pmid = {26993763}, issn = {1095-9513}, mesh = {Africa ; Americas ; Arabidopsis/classification/genetics ; Asia ; Australia ; Bayes Theorem ; Biodiversity ; Brassicaceae/*classification/genetics ; DNA, Mitochondrial/isolation &amp; purification/metabolism ; DNA, Plant/isolation &amp; purification/metabolism ; Europe ; *Fossils ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Plastids/genetics ; }, abstract = {Brassicales is a diverse order perhaps most famous because it houses Brassicaceae and, its premier member, Arabidopsis thaliana. This widely distributed and species-rich lineage has been overlooked as a promising system to investigate patterns of disjunct distributions and diversification rates. We analyzed plastid and mitochondrial sequence data from five gene regions (>8000bp) across 151 taxa to: (1) produce a chronogram for major lineages in Brassicales, including Brassicaceae and Arabidopsis, based on greater taxon sampling across the order and previously overlooked fossil evidence, (2) examine biogeographical ancestral range estimations and disjunct distributions in BioGeoBEARS, and (3) determine where shifts in species diversification occur using BAMM. The evolution and radiation of the Brassicales began 103Mya and was linked to a series of inter-continental vicariant, long-distance dispersal, and land bridge migration events. North America appears to be a significant area for early stem lineages in the order. Shifts to Australia then African are evident at nodes near the core Brassicales, which diverged 68.5Mya (HPD=75.6-62.0). This estimated age combined with fossil evidence, indicates that some New World clades embedded amongst Old World relatives (e.g., New World capparoids) are the result of different long distance dispersal events, whereas others may be best explained by land bridge migration (e.g., Forchhammeria). Based on these analyses, the Brassicaceae crown group diverged in Europe/Northern Africa in the Eocene, circa 43.4Mya (HPD=46.6-40.3) and Arabidopsis separated from close congeners circa 10.4Mya. These ages fall between divergent dates that were previously published, suggesting we are slowly converging on a robust age estimate for the family. Three significant shifts in species diversification are observed in the order: (1) 58Mya at the crown of Capparaceae, Cleomaceae and Brassicaceae, (2) 38Mya at the crown of Resedaceae+Stixis clade, and (3) 21Mya at the crown of the tribes Brassiceae and Sisymbrieae within Brassicaceae.}, }
@article {pmid26992928, year = {2016}, author = {Kadlec, AO and Beyer, AM and Ait-Aissa, K and Gutterman, DD}, title = {Mitochondrial signaling in the vascular endothelium: beyond reactive oxygen species.}, journal = {Basic research in cardiology}, volume = {111}, number = {3}, pages = {26}, pmid = {26992928}, issn = {1435-1803}, support = {R01 HL113612/HL/NHLBI NIH HHS/United States ; R21 OD018306/OD/NIH HHS/United States ; T32 GM080202/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Endothelium, Vascular/*metabolism ; Humans ; Mitochondria/*metabolism ; Reactive Oxygen Species/metabolism ; Signal Transduction/*physiology ; }, abstract = {Traditionally, the mitochondria have been viewed as the cell's powerhouse, producing energy in the form of ATP. As a byproduct of ATP formation, the mitochondrial electron transport chain produces substantial amounts of reactive oxygen species (ROS). First thought to be toxic, recent literature indicates an important signaling function for mitochondria-derived ROS, especially in relation to cardiovascular disease pathogenesis. This has spawned an evolution to a more contemporary view of mitochondrial function as a dynamic organelle involved in key regulatory and cell survival processes. Beyond ROS, recent studies have identified a host of mitochondria-linked factors that influence the cellular and extracellular environments, including mitochondria-derived peptides, mitochondria-localized proteins, and the mitochondrial genome itself. Interestingly, many of these factors help orchestrate ROS homeostasis and ROS-related signaling. The paradigm defining the role of mitochondria in the vasculature needs to be updated yet again to include these key signaling factors, which serves as the focus of the current review. In describing these novel signaling factors, we pay specific attention to their influence on endothelial homeostasis. Therapies targeting these pathways are discussed, as are emerging research directions.}, }
@article {pmid26988412, year = {2016}, author = {Maldonado-Sánchez, D and Gutiérrez-Rodríguez, C and Ornelas, JF}, title = {Genetic divergence in the common bush-tanager Chlorospingus ophthalmicus (Aves: Emberizidae) throughout Mexican cloud forests: The role of geography, ecology and Pleistocene climatic fluctuations.}, journal = {Molecular phylogenetics and evolution}, volume = {99}, number = {}, pages = {76-88}, doi = {10.1016/j.ympev.2016.03.014}, pmid = {26988412}, issn = {1095-9513}, mesh = {Animal Migration ; Animals ; Bayes Theorem ; *Climate ; DNA, Mitochondrial/genetics ; *Ecosystem ; *Forests ; *Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Mexico ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Passeriformes/*genetics ; Phylogeny ; *Phylogeography ; Time Factors ; }, abstract = {By integrating mitochondrial DNA (mtDNA), microsatellites and ecological niche modelling (ENM), we investigated the phylogeography of Mexican populations of the common bush-tanager Chlorospingus ophthalmicus to examine the relative role of geographical and ecological features, as well as Pleistocene climatic oscillations in driving the diversification. We sequenced mtDNA of individuals collected throughout the species range in Mexico and genotyped them at seven microsatellite loci. Phylogeographic, population genetics and coalescent methods were used to assess patterns of genetic structure, gene flow and demographic history. ENM was used to infer contractions and expansions at different time periods as well as differences in climatic conditions among lineages. The retrieved mitochondrial and microsatellite groups correspond with the fragmented cloud forest distribution in mountain ranges and morphotectonic provinces. Differing climatic conditions between mountain ranges were detected, and palaeodistribution modelling as well as demographic history analyses, indicated recent population expansions throughout the Sierra Madre Oriental (SMO). The marked genetic structure of C. ophthalmicus was promoted by the presence of ecological and geographical barriers that restricted the movement of individuals among mountain ranges. The SMO was mainly affected by Pleistocene climatic oscillations, with the moist forests model best fitting the displayed genetic patterns of populations in this mountain range.}, }
@article {pmid26986660, year = {2015}, author = {McDowell, RE and Amsler, MO and Li, Q and Lancaster, JR and Amsler, CD}, title = {The immediate wound-induced oxidative burst of Saccharina latissima depends on light via photosynthetic electron transport.}, journal = {Journal of phycology}, volume = {51}, number = {3}, pages = {431-441}, doi = {10.1111/jpy.12302}, pmid = {26986660}, issn = {1529-8817}, abstract = {Reactive oxygen species (ROS) produced by an oxidative burst are an important component of the wound response in algae, vascular plants, and animals. In all taxa, ROS production is usually attributed solely to a defense-related enzyme like NADPH-oxidase (Nox). However, here we show that the initial, wound-induced oxidative burst of the kelp Saccharina latissima depends on light and photosynthetic electron transport. We measured oxygen evolution and ROS production at different light levels and in the presence of a photosynthetic inhibitor, and we used spin trapping and electron paramagnetic resonance as an orthogonal method. Using an in vivo chemical probe, we provide data suggesting that wound-induced ROS production in two distantly related and geographically isolated species of Antarctic macroalgae may be light dependent as well. We propose that electron transport chains are an important and as yet unaddressed component of the wound response, not just for photosynthetic organisms, but for animals via mitochondria as well. This component may have been obscured by the historic use of diphenylene iodonium, which inhibits not only Noxes but also photosynthetic and respiratory electron transport as well. Finally, we anticipate physiological and/or ecological consequences of the light dependence of macroalgal wound-induced ROS since pathogens and grazers do not disappear in the dark.}, }
@article {pmid26982388, year = {2016}, author = {Olayemi, A and Obadare, A and Oyeyiola, A and Igbokwe, J and Fasogbon, A and Igbahenah, F and Ortsega, D and Asogun, D and Umeh, P and Vakkai, I and Abejegah, C and Pahlman, M and Becker-Ziaja, B and Günther, S and Fichet-Calvet, E}, title = {Arenavirus Diversity and Phylogeography of Mastomys natalensis Rodents, Nigeria.}, journal = {Emerging infectious diseases}, volume = {22}, number = {4}, pages = {694-697}, pmid = {26982388}, issn = {1080-6059}, mesh = {Animals ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Disease Reservoirs ; Genetic Variation ; Host-Pathogen Interactions ; Humans ; Lassa Fever/epidemiology/transmission/*veterinary/virology ; Lassa virus/*classification/genetics/isolation &amp; purification ; Mitochondria/chemistry/genetics ; Murinae/classification/genetics/*virology ; Nigeria/epidemiology ; *Phylogeny ; Phylogeography ; RNA, Viral/*genetics ; Rodent Diseases/epidemiology/virology ; Zoonoses ; }, abstract = {Mastomys natalensis rodents are natural hosts for Lassa virus (LASV). Detection of LASV in 2 mitochondrial phylogroups of the rodent near the Niger and Benue Rivers in Nigeria underlines the potential for LASV emergence in fresh phylogroups of this rodent. A Mobala-like sequence was also detected in eastern Nigeria.}, }
@article {pmid26970277, year = {2016}, author = {Massel, K and Silke, JR and Bonen, L}, title = {Multiple splicing pathways of group II trans-splicing introns in wheat mitochondria.}, journal = {Mitochondrion}, volume = {28}, number = {}, pages = {23-32}, doi = {10.1016/j.mito.2016.03.002}, pmid = {26970277}, issn = {1872-8278}, mesh = {Cold Temperature ; *Introns ; Mitochondria/*genetics ; Nucleic Acid Conformation ; RNA Precursors/chemistry/metabolism/radiation effects ; *Trans-Splicing ; Triticum/*genetics ; }, abstract = {Trans-splicing of discontinuous introns in plant mitochondria requires the assembly of independently-transcribed precursor RNAs into splicing-competent structures, and they are expected to be excised as Y-branched molecules ("broken lariats") because these introns belong to the group II ribozyme family. We now demonstrate that this is just one of several trans-splicing pathways for wheat mitochondrial nad1 intron 4 and nad5 intron 2; they also use a hydrolytic pathway and the liberated 5'-half-intron linear molecules are unexpectedly abundant in the RNA population. We also observe a third productive splicing pathway for nad5 intron 2 that yields full-length excised introns in which the termini are joined in vivo and possess non-encoded nucleotides. In the case of trans-splicing nad1 intron 1, which has a weakly-structured and poorly-conserved core sequence, excision appears to be solely through a hydrolytic pathway. When wheat embryos are germinated in the cold rather than at room temperature, an increased complexity in trans-splicing products is seen for nad1 intron 4, suggesting that there can be environmental effects on the RNA folding of bipartite introns. Our observations provide insights into intron evolution and the complexity of RNA processing events in plant mitochondria.}, }
@article {pmid26968896, year = {2016}, author = {Gerle, C}, title = {On the structural possibility of pore-forming mitochondrial FoF1 ATP synthase.}, journal = {Biochimica et biophysica acta}, volume = {1857}, number = {8}, pages = {1191-1196}, doi = {10.1016/j.bbabio.2016.03.008}, pmid = {26968896}, issn = {0006-3002}, mesh = {Animals ; Artemia/chemistry/enzymology ; Catalytic Domain ; Peptidyl-Prolyl Isomerase F ; Cyclophilins/chemistry ; Cyclosporine/chemistry ; Drosophila melanogaster/chemistry/enzymology ; Humans ; Mitochondria/*chemistry/enzymology ; Mitochondrial Membrane Transport Proteins/antagonists &amp; inhibitors/*chemistry/metabolism ; Mitochondrial Permeability Transition Pore ; Mitochondrial Proton-Translocating ATPases/antagonists &amp; inhibitors/*chemistry/metabolism ; Models, Molecular ; Molecular Mimicry ; Protein Multimerization ; Saccharomyces cerevisiae/chemistry/enzymology ; }, abstract = {The mitochondrial permeability transition is an inner mitochondrial membrane event involving the opening of the permeability transition pore concomitant with a sudden efflux of matrix solutes and breakdown of membrane potential. The mitochondrial F(o)F(1) ATP synthase has been proposed as the molecular identity of the permeability transition pore. The likeliness of potential pore-forming sites in the mitochondrial F(o)F(1) ATP synthase is discussed and a new model, the death finger model, is described. In this model, movement of a p-side density that connects the lipid-plug of the c-ring with the distal membrane bending Fo domain allows reversible opening of the c-ring and structural cross-talk with OSCP and the catalytic (αβ)(3) hexamer. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.}, }
@article {pmid26968366, year = {2016}, author = {Palmieri, F and Monné, M}, title = {Discoveries, metabolic roles and diseases of mitochondrial carriers: A review.}, journal = {Biochimica et biophysica acta}, volume = {1863}, number = {10}, pages = {2362-2378}, doi = {10.1016/j.bbamcr.2016.03.007}, pmid = {26968366}, issn = {0006-3002}, mesh = {Animals ; Arabidopsis Proteins/metabolism ; Biological Transport ; Gene Expression ; Humans ; Mitochondria/*metabolism ; Mitochondrial Diseases/genetics/metabolism ; Mitochondrial Membrane Transport Proteins/deficiency/genetics/*physiology ; Mitochondrial Membranes/metabolism ; Phylogeny ; Protein Domains ; Recombinant Proteins/isolation &amp; purification/metabolism ; Saccharomyces cerevisiae Proteins/physiology ; }, abstract = {Mitochondrial carriers (MCs) are a superfamily of nuclear-encoded proteins that are mostly localized in the inner mitochondrial membrane and transport numerous metabolites, nucleotides, cofactors and inorganic anions. Their unique sequence features, i.e., a tripartite structure, six transmembrane α-helices and a three-fold repeated signature motif, allow MCs to be easily recognized. This review describes how the functions of MCs from Saccharomyces cerevisiae, Homo sapiens and Arabidopsis thaliana (listed in the first table) were discovered after the genome sequence of S. cerevisiae was determined in 1996. In the genomic era, more than 50 previously unknown MCs from these organisms have been identified and characterized biochemically using a method consisting of gene expression, purification of the recombinant proteins, their reconstitution into liposomes and transport assays (EPRA). Information derived from studies with intact mitochondria, genetic and metabolic evidence, sequence similarity, phylogenetic analysis and complementation of knockout phenotypes have guided the choice of substrates that were tested in the transport assays. In addition, the diseases associated to defects of human MCs have been briefly reviewed. This article is part of a Special Issue entitled: Mitochondrial Channels edited by Pierre Sonveaux, Pierre Maechler and Jean-Claude Martinou.}, }
@article {pmid26956565, year = {2016}, author = {Levsen, N and Bergero, R and Charlesworth, D and Wolff, K}, title = {Frequent, geographically structured heteroplasmy in the mitochondria of a flowering plant, ribwort plantain (Plantago lanceolata).}, journal = {Heredity}, volume = {117}, number = {1}, pages = {1-7}, pmid = {26956565}, issn = {1365-2540}, support = {MR/K001744/1/MRC_/Medical Research Council/United Kingdom ; BB/J004243/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Alleles ; Crosses, Genetic ; Gene Frequency ; Genes, Mitochondrial ; Genetic Association Studies ; Genetics, Population ; Genotype ; Geography ; Inheritance Patterns ; Mitochondria/*genetics ; Phenotype ; Plantago/*genetics ; Polymorphism, Single Nucleotide ; Recombination, Genetic ; Sequence Analysis, DNA ; }, abstract = {Recent research has convincingly documented cases of mitochondrial heteroplasmy in a small set of wild and cultivated plant species. Heteroplasmy is suspected to be common in flowering plants and investigations of additional taxa may help understand the mechanisms generating heteroplasmy as well as its effects on plant phenotypes. The role of mitochondrial heteroplasmy is of particular interest in plants as cytoplasmic male sterility is controlled by mitochondrial genotypes, sometimes leading to co-occurring female and hermaphroditic individuals (gynodioecy). Paternal leakage may be important in the evolution of mating systems in such populations. We conducted a genetic survey of the gynodioecious plant Plantago lanceolata, in which heteroplasmy has not previously been reported, and estimated the frequencies of mitochondrial genotypes and heteroplasmy. Sanger sequence genotyping of 179 individuals from 15 European populations for two polymorphic mitochondrial loci, atp6 and rps12, identified 15 heteroplasmic individuals. These were distributed among 6 of the 10 populations that had polymorphisms in the target loci and represented 8% of all sampled individuals and 15% of the individuals in those 6 populations. The incidence was highest in Northern England and Scotland. Our results are consistent with geographic differences in the incidence of paternal leakage and/or the rates of nuclear restoration of male fertility.}, }
@article {pmid26956194, year = {2016}, author = {Quirós, PM and Mottis, A and Auwerx, J}, title = {Mitonuclear communication in homeostasis and stress.}, journal = {Nature reviews. Molecular cell biology}, volume = {17}, number = {4}, pages = {213-226}, pmid = {26956194}, issn = {1471-0080}, support = {R01AG043930/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Cell Communication ; Cell Nucleus/*physiology ; *Homeostasis ; Mitochondria/*physiology ; Mitochondrial Proteins/metabolism ; Models, Biological ; Signal Transduction ; *Stress, Physiological ; }, abstract = {Mitochondria participate in crucial cellular processes such as energy harvesting and intermediate metabolism. Although mitochondria possess their own genome--a vestige of their bacterial origins and endosymbiotic evolution--most mitochondrial proteins are encoded in the nucleus. The expression of the mitochondrial proteome hence requires tight coordination between the two genomes to adapt mitochondrial function to the ever-changing cellular milieu. In this Review, we focus on the pathways that coordinate the communication between mitochondria and the nucleus during homeostasis and mitochondrial stress. These pathways include nucleus-to-mitochondria (anterograde) and mitochondria-to-nucleus (retrograde) communication, mitonuclear feedback signalling and proteostasis regulation, the integrated stress response and non-cell-autonomous communication. We discuss how mitonuclear communication safeguards cellular and organismal fitness and regulates lifespan.}, }
@article {pmid26956060, year = {2016}, author = {Lavikainen, A and Iwaki, T and Haukisalmi, V and Konyaev, SV and Casiraghi, M and Dokuchaev, NE and Galimberti, A and Halajian, A and Henttonen, H and Ichikawa-Seki, M and Itagaki, T and Krivopalov, AV and Meri, S and Morand, S and Näreaho, A and Olsson, GE and Ribas, A and Terefe, Y and Nakao, M}, title = {Reappraisal of Hydatigera taeniaeformis (Batsch, 1786) (Cestoda: Taeniidae) sensu lato with description of Hydatigera kamiyai n. sp.}, journal = {International journal for parasitology}, volume = {46}, number = {5-6}, pages = {361-374}, doi = {10.1016/j.ijpara.2016.01.009}, pmid = {26956060}, issn = {1879-0135}, mesh = {Africa ; Animals ; Arvicolinae ; Asia ; Australia ; Bayes Theorem ; Cat Diseases/*parasitology ; Cats ; Cestoda/anatomy &amp; histology/*classification/genetics ; Cestode Infections/parasitology/*veterinary ; DNA Barcoding, Taxonomic/veterinary ; DNA, Helminth/chemistry ; Electron Transport Complex IV/genetics ; Europe ; Felidae/*parasitology ; Mice ; Mitochondria/enzymology/genetics ; Murinae ; Phylogeny ; Phylogeography ; Rats ; Rodent Diseases/*parasitology ; }, abstract = {The common cat tapeworm Hydatigera taeniaeformis is a complex of three morphologically cryptic entities, which can be differentiated genetically. To clarify the biogeography and the host spectrum of the cryptic lineages, 150 specimens of H. taeniaeformis in various definitive and intermediate hosts from Eurasia, Africa and Australia were identified with DNA barcoding using partial mitochondrial cytochrome c oxidase subunit 1 gene sequences and compared with previously published data. Additional phylogenetic analyses of selected isolates were performed using nuclear DNA and mitochondrial genome sequences. Based on molecular data and morphological analysis, Hydatigera kamiyai n. sp. Iwaki is proposed for a cryptic lineage, which is predominantly northern Eurasian and uses mainly arvicoline rodents (voles) and mice of the genus Apodemus as intermediate hosts. Hydatigera taeniaeformis sensu stricto (s.s.) is restricted to murine rodents (rats and mice) as intermediate hosts. It probably originates from Asia but has spread worldwide. Despite remarkable genetic divergence between H. taeniaeformis s.s. and H. kamiyai, interspecific morphological differences are evident only in dimensions of rostellar hooks. The third cryptic lineage is closely related to H. kamiyai, but its taxonomic status remains unresolved due to limited morphological, molecular, biogeographical and ecological data. This Hydatigera sp. is confined to the Mediterranean and its intermediate hosts are unknown. Further studies are needed to classify Hydatigera sp. either as a distinct species or a variant of H. kamiyai. According to previously published limited data, all three entities occur in the Americas, probably due to human-mediated introductions.}, }
@article {pmid26954225, year = {2016}, author = {Ajibike, AB and Ilori, BM and Awotunde, EO and Adegboyega, AR and Osinbowale, AD and Bemji, MN and Durosaro, SO and Adebambo, AO}, title = {WITHDRAWN:Genetic diversity and effect of selection at the mitochondrial hypervariable region in major Nigerian indigenous goat breeds.}, journal = {Asian-Australasian journal of animal sciences}, volume = {}, number = {}, pages = {}, doi = {10.5713/ajas.15.0775}, pmid = {26954225}, issn = {1011-2367}, abstract = {Mitochondrial DNA (mtDNA) hypervariable region 1 (HV1) sequences of three Nigerian indigenous goat breeds; West African Dwarf (WAD), Red Sokoto (RS) and Sahel were used to investigate the genetic diversity and effect of selection between and among these populations. Deoxyribonucleic acid (DNA) of Nigerian indigenous chicken was extracted from blood samples collected and preserved on Fast Technology for Analysis (FTA) paper. The extracted DNA were amplified and sequenced with predefined mitochondria (mtDNA) primer sets for HV1. Eighty-seven (87) polymorphic sites were found in 115 sequences which were grouped into 92 haplotypes. The mean haplotypic and nucleotide diversity were found to be 0.996±0.002 and 0.092±0.04 respectively. Genetic variation within population and between populations accounted for 97.26% and 2.74% of the total maternal variation respectively, with FST value of 0.0274. The Tajima's (D) and Fu's (F) test of neutrality were significant (P<0.05) and negative with the mean value of -1.12 and -21.34 respectively which is an indication of population expansion. The result further revealed that the WAD and RS goats are closely related with less genetic distance value of 0.01, and high genetic distance value (0.02) was observed between RS and Sahel goats and WAD and Sahel goats. Selection analysis result shows that there is more positive selection site (6 sites) to negative site (5 sites) among the Nigerian goats, which signifies how diverse they are as well as how nature has being trying to confer genetic fitness to these breeds.}, }
@article {pmid26953603, year = {2016}, author = {de Barsy, M and Frandi, A and Panis, G and Théraulaz, L and Pillonel, T and Greub, G and Viollier, PH}, title = {Regulatory (pan-)genome of an obligate intracellular pathogen in the PVC superphylum.}, journal = {The ISME journal}, volume = {10}, number = {9}, pages = {2129-2144}, pmid = {26953603}, issn = {1751-7370}, mesh = {Animals ; Bacterial Proteins/genetics ; Chlamydiales/*genetics ; Chlorocebus aethiops ; Chromatin Immunoprecipitation ; Genome, Bacterial/*genetics ; Genomics ; Phylogeny ; Reproducibility of Results ; Transcription Factors/*genetics ; Vero Cells ; Verrucomicrobia/*genetics ; }, abstract = {Like other obligate intracellular bacteria, the Chlamydiae feature a compact regulatory genome that remains uncharted owing to poor genetic tractability. Exploiting the reduced number of transcription factors (TFs) encoded in the chlamydial (pan-)genome as a model for TF control supporting the intracellular lifestyle, we determined the conserved landscape of TF specificities by ChIP-Seq (chromatin immunoprecipitation-sequencing) in the chlamydial pathogen Waddlia chondrophila. Among 10 conserved TFs, Euo emerged as a master TF targeting >100 promoters through conserved residues in a DNA excisionase-like winged helix-turn-helix-like (wHTH) fold. Minimal target (Euo) boxes were found in conserved developmentally-regulated genes governing vertical genome transmission (cytokinesis and DNA replication) and genome plasticity (transposases). Our ChIP-Seq analysis with intracellular bacteria not only reveals that global TF regulation is maintained in the reduced regulatory genomes of Chlamydiae, but also predicts that master TFs interpret genomic information in the obligate intracellular α-proteobacteria, including the rickettsiae, from which modern day mitochondria evolved.}, }
@article {pmid26947058, year = {2016}, author = {De Pinto, V and Reina, S and Gupta, A and Messina, A and Mahalakshmi, R}, title = {Role of cysteines in mammalian VDAC isoforms' function.}, journal = {Biochimica et biophysica acta}, volume = {1857}, number = {8}, pages = {1219-1227}, pmid = {26947058}, issn = {0006-3002}, support = {//Wellcome Trust/United Kingdom ; IA/I/14/1/501305/WTDBT_/DBT-Wellcome Trust India Alliance/India ; }, mesh = {Animals ; Conserved Sequence ; Cysteine/*metabolism ; Evolution, Molecular ; Gene Expression ; Humans ; Ion Transport ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins/*chemistry/genetics/metabolism ; Mitochondrial Membranes/*metabolism ; Models, Molecular ; Mutation ; Protein Multimerization ; Saccharomyces cerevisiae/genetics/metabolism ; Voltage-Dependent Anion Channel 1/*chemistry/genetics/metabolism ; Voltage-Dependent Anion Channel 2/*chemistry/genetics/metabolism ; Voltage-Dependent Anion Channels/*chemistry/genetics/metabolism ; }, abstract = {In this mini-review, we analyze the influence of cysteines in the structure and activity of mitochondrial outer membrane mammalian VDAC isoforms. The three VDAC isoforms show conserved sequences, similar structures and the same gene organization. The meaning of three proteins encoded in different chromosomes must thus be searched for subtle differences at the amino acid level. Among others, cysteine content is noticeable. In humans, VDAC1 has 2, VDAC2 has 9 and VDAC3 has 6 cysteines. Recent works have shown that, at variance from VDAC1, VDAC2 and VDAC3 exhibit cysteines predicted to protrude towards the intermembrane space, making them a preferred target for oxidation by ROS. Mass spectrometry in VDAC3 revealed that a disulfide bridge can be formed and other cysteine oxidations are also detectable. Both VDAC2 and VDAC3 cysteines were mutagenized to highlight their role in vitro and in complementation assays in Δporin1 yeast. Chemico-physical techniques revealed an important function of cysteines in the structural stabilization of the pore. In conclusion, the works available on VDAC cysteines support the notion that the three proteins are paralogs with a similar pore-function and slightly different, but important, ancillary biological functions. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.}, }
@article {pmid26946968, year = {2016}, author = {Chetoui, I and Denis, F and Boussaid, M and Telahigue, K and El Cafsi, M}, title = {Genetic diversity and phylogenetic analysis of two Tunisian bivalves (Mactridae) Mactra corallina (Linnaeus, 1758) and Eastonia rugosa (Helbling, 1799) based on COI gene sequences.}, journal = {Comptes rendus biologies}, volume = {339}, number = {3-4}, pages = {115-122}, doi = {10.1016/j.crvi.2016.02.001}, pmid = {26946968}, issn = {1768-3238}, mesh = {Animals ; Bivalvia/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Tunisia ; }, abstract = {A partial sequence of mitochondrial cytochrome c oxidase subunit I (COI) was used as a genetic marker for a genetic diversity and phylogenetic analysis (DNA barcoding) of two Mactridae species, Mactra corallina and Eastonia rugosa, collected from the Tunisian coast. These Mactridae species could be distinguished by DNA barcoding techniques and they will be considered as monophyletic clades with the Neighbor-Joining (NJ) tree. The genetic structure detected that E. rugosa presents three haplotypes with a high frequency of HER1 (0.89). However, M. corralina shared 14 haplotypes. The haplotypic diversity (H) was equal to 0.205 and 0.954, respectively, for E. rugosa and M. corallina. While the nucleotide diversity (π) was higher for M. corallina (π=0.0818), the mismatch distribution showed a unimodal curve for E. rugosa (a recent sudden demographic expansion) and a multimodal distribution for M. corallina (size stability).}, }
@article {pmid26946085, year = {2016}, author = {Yoshida, K and Hisabori, T}, title = {Adenine nucleotide-dependent and redox-independent control of mitochondrial malate dehydrogenase activity in Arabidopsis thaliana.}, journal = {Biochimica et biophysica acta}, volume = {1857}, number = {6}, pages = {810-818}, doi = {10.1016/j.bbabio.2016.03.001}, pmid = {26946085}, issn = {0006-3002}, mesh = {Adenine Nucleotides/metabolism/*pharmacology ; Adenosine Diphosphate/metabolism/pharmacology ; Adenosine Monophosphate/metabolism/pharmacology ; Adenosine Triphosphate/metabolism/pharmacology ; Amino Acid Sequence ; Arabidopsis/*enzymology/genetics ; Arabidopsis Proteins/genetics/*metabolism ; Biocatalysis/drug effects ; Gene Expression Regulation, Enzymologic/drug effects ; Gene Expression Regulation, Plant/drug effects ; Immunoblotting ; Malate Dehydrogenase/genetics/*metabolism ; Mitochondria/drug effects/genetics/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Recombinant Proteins/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {Mitochondrial metabolism is important for sustaining cellular growth and maintenance; however, the regulatory mechanisms underlying individual processes in plant mitochondria remain largely uncharacterized. Previous redox-proteomics studies have suggested that mitochondrial malate dehydrogenase (mMDH), a key enzyme in the tricarboxylic acid (TCA) cycle and redox shuttling, is under thiol-based redox regulation as a target candidate of thioredoxin (Trx). In addition, the adenine nucleotide status may be another factor controlling mitochondrial metabolism, as respiratory ATP production in mitochondria is believed to be influenced by several environmental stimuli. Using biochemical and reverse-genetic approaches, we addressed the redox- and adenine nucleotide-dependent regulation of mMDH in Arabidopsis thaliana. Recombinant mMDH protein formed intramolecular disulfide bonds under oxidative conditions, but these bonds did not have a considerable effect on mMDH activity. Mitochondria-localized o-type Trx (Trx-o) did not facilitate re-reduction of oxidized mMDH. Determination of the in vivo redox state revealed that mMDH was stably present in the reduced form even in Trx-o-deficient plants. Accordingly, we concluded that mMDH is not in the class of redox-regulated enzymes. By contrast, mMDH activity was lowered by adenine nucleotides (AMP, ADP, and ATP). Each adenine nucleotide suppressed mMDH activity with different potencies and ATP exerted the largest inhibitory effect with a significantly lower K(I). Correspondingly, mMDH activity was inhibited by the increase in ATP/ADP ratio within the physiological range. These results suggest that mMDH activity is finely controlled in response to variations in mitochondrial adenine nucleotide balance.}, }
@article {pmid26931168, year = {2016}, author = {Hagemann, M and Kern, R and Maurino, VG and Hanson, DT and Weber, AP and Sage, RF and Bauwe, H}, title = {Evolution of photorespiration from cyanobacteria to land plants, considering protein phylogenies and acquisition of carbon concentrating mechanisms.}, journal = {Journal of experimental botany}, volume = {67}, number = {10}, pages = {2963-2976}, doi = {10.1093/jxb/erw063}, pmid = {26931168}, issn = {1460-2431}, mesh = {*Biological Evolution ; Carbon/metabolism ; Cyanobacteria/metabolism/*physiology ; Photosynthesis/*physiology ; Phylogeny ; Plant Physiological Phenomena ; Plants/*metabolism ; }, abstract = {Photorespiration and oxygenic photosynthesis are intimately linked processes. It has been shown that under the present day atmospheric conditions cyanobacteria and all eukaryotic phototrophs need functional photorespiration to grow autotrophically. The question arises as to when this essential partnership evolved, i.e. can we assume a coevolution of both processes from the beginning or did photorespiration evolve later to compensate for the generation of 2-phosphoglycolate (2PG) due to Rubisco's oxygenase reaction? This question is mainly discussed here using phylogenetic analysis of proteins involved in the 2PG metabolism and the acquisition of different carbon concentrating mechanisms (CCMs). The phylogenies revealed that the enzymes involved in the photorespiration of vascular plants have diverse origins, with some proteins acquired from cyanobacteria as ancestors of the chloroplasts and others from heterotrophic bacteria as ancestors of mitochondria in the plant cell. Only phosphoglycolate phosphatase was found to originate from Archaea. Notably glaucophyte algae, the earliest branching lineage of Archaeplastida, contain more photorespiratory enzymes of cyanobacterial origin than other algal lineages or land plants indicating a larger initial contribution of cyanobacterial-derived proteins to eukaryotic photorespiration. The acquisition of CCMs is discussed as a proxy for assessing the timing of periods when photorespiratory activity may have been enhanced. The existence of CCMs also had marked influence on the structure and function of photorespiration. Here, we discuss evidence for an early and continuous coevolution of photorespiration, CCMs and photosynthesis starting from cyanobacteria via algae, to land plants.}, }
@article {pmid26930860, year = {2016}, author = {Banta, G and Jindal, V and Mohindru, B and Sharma, S and Kaur, J and Gupta, VK}, title = {Molecular phylogenetic analysis of mango mealybug, Drosicha mangiferae from Punjab.}, journal = {Journal of environmental biology}, volume = {37}, number = {1}, pages = {49-55}, pmid = {26930860}, issn = {0254-8704}, mesh = {Animals ; Base Sequence ; Electron Transport Complex IV/genetics/metabolism ; Gene Expression Regulation, Enzymologic ; Hemiptera/*genetics/physiology ; India ; Litchi ; Mangifera ; Mitochondria/enzymology ; Phylogeny ; Psidium ; }, abstract = {Mealybugs (Hemiptera: Pseudococcidae) are major pests of a wide range of crops and ornamental plants worldwide. Their high degree of morphological similarity makes them difficult to identify and limits their study and management. In the present study, four Indian populations of mango mealybug (mango, litchi, guava from Gurdaspur and mango from Jalandhar) were analyzed. The mtCOI region was amplified, cloned, the nucleotide sequences were determined and analysed. All the four species were found to be D. mangiferae. The population from Litchi and Mango from Gurdaspur showed 100% homologus sequence. The population of Guava-Gurdaspur and Mango-Jalandhar showed a single mutation of 'C' instead of 'T' at 18th and 196th position, respectively. Indian populations were compared with populations from Pakistan (21) and Japan (1). The phylogenetic tree resulted in two main clusters. Cluster1 represent all the 4 populations of Punjab, India, 20 of Pakistan (Punjab, Sind, Lahore, Multan, Faisalabad and Karak districts) with homologous sequences. The two population collected from Faisalabad district of Pakistan and Japan made a separate cluster 2 because the gene sequence used in analysis was from the COI-3p region. However, all the other sequence of D. mangiferae samples under study showed a low nucleotide divergence. The homologus mtCO1 sequence of Indian and Pakistan population concluded that the genetic diversity in mealybug population was quite less over a large geographical area.}, }
@article {pmid26927810, year = {2016}, author = {Byrne, S and Dionisi-Vici, C and Smith, L and Gautel, M and Jungbluth, H}, title = {Vici syndrome: a review.}, journal = {Orphanet journal of rare diseases}, volume = {11}, number = {}, pages = {21}, pmid = {26927810}, issn = {1750-1172}, mesh = {Agenesis of Corpus Callosum/*genetics ; Autophagy-Related Proteins ; Cataract/*genetics ; Chromosomes, Human, Pair 18/genetics ; Humans ; Lysosomal Membrane Proteins ; Mutation/genetics ; Proteins/genetics ; Vesicular Transport Proteins ; }, abstract = {Vici syndrome [OMIM242840] is a severe, recessively inherited congenital disorder characterized by the principal features of callosal agenesis, cataracts, oculocutaneous hypopigmentation, cardiomyopathy, and a combined immunodeficiency. Profound developmental delay, progressive failure to thrive and acquired microcephaly are almost universal, suggesting an evolving (neuro) degenerative component. In most patients there is additional variable multisystem involvement that may affect virtually any organ system, including lungs, thyroid, liver and kidneys. A skeletal myopathy is consistently associated, and characterized by marked fibre type disproportion, increase in internal nuclei, numerous vacuoles, abnormal mitochondria and glycogen storage. Life expectancy is markedly reduced.Vici syndrome is due to recessive mutations in EPG5 on chromosome 18q12.3, encoding ectopic P granules protein 5 (EPG5), a key autophagy regulator in higher organisms. Autophagy is a fundamental cellular degradative pathway conserved throughout evolution with important roles in the removal of defective proteins and organelles, defence against infections and adaptation to changing metabolic demands. Almost 40 EPG mutations have been identified to date, most of them truncating and private to individual families.The differential diagnosis of Vici syndrome includes a number of syndromes with overlapping clinical features, neurological and metabolic disorders with shared CNS abnormalities (in particular callosal agenesis), and primary neuromuscular disorders with a similar muscle biopsy appearance. Vici syndrome is also the most typical example of a novel group of inherited neurometabolic conditions, congenital disorders of autophagy.Management is currently largely supportive and symptomatic but better understanding of the underlying autophagy defect will hopefully inform the development of targeted therapies in future.}, }
@article {pmid26926944, year = {2016}, author = {Fiorentino, V and Manganelli, G and Giusti, F and Ketmaier, V}, title = {Recent expansion and relic survival: Phylogeography of the land snail genus Helix (Mollusca, Gastropoda) from south to north Europe.}, journal = {Molecular phylogenetics and evolution}, volume = {98}, number = {}, pages = {358-372}, doi = {10.1016/j.ympev.2016.02.017}, pmid = {26926944}, issn = {1095-9513}, mesh = {Animal Shells/anatomy &amp; histology ; Animals ; Cell Nucleus/genetics ; Italy ; Mediterranean Region ; Mitochondria/genetics ; Phenotype ; *Phylogeny ; Phylogeography ; Snails/anatomy &amp; histology/*classification/genetics ; }, abstract = {Little is known about the evolutionary history of Helix, despite the fact that it includes the largest land snails in the western Palaearctic, some of which (e.g. H. pomatia Linnaeus, 1758) are valuable human food. We compared two groups of Helix with apparently contrasting evolutionary histories: the widespread species H. pomatia and the group distributed along the Italian Apennine chain, a relatively unknown set of species with a restricted distribution over a range of altitudes. To reconstruct the evolutionary trajectories of these two groups, we analysed morphological (shell and genitalia) and molecular characters (mitochondrial and nuclear markers) in a total of 59 populations from northern and central Europe (H. pomatia) and along the Apennine chain (various species). We also reconstructed the phylogeny and the evolutionary history of the genus by combining our data with that currently available in the literature. We found that spatial changes did not merely imply fragmentation of populations, but also implied environmental changes (woodlands vs. grasslands) that may have triggered the observed phenotypic diversification. We also found that Anatolia is the ancestral range of Helix and is therefore an important area for the Palaearctic diversity. The results provide insights into the evolutionary history of species richness and more generally into the processes that may have shaped the distribution and diversification of these organisms across Europe and the peri-Mediterranean area.}, }
@article {pmid26924130, year = {2016}, author = {Teulier, L and Rey, B and Tornos, J and Le Coadic, M and Monternier, PA and Bourguignon, A and Dolmazon, V and Romestaing, C and Rouanet, JL and Duchamp, C and Roussel, D}, title = {Lipid-induced thermogenesis is up-regulated by the first cold-water immersions in juvenile penguins.}, journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology}, volume = {186}, number = {5}, pages = {639-650}, pmid = {26924130}, issn = {1432-136X}, mesh = {Acclimatization/*physiology ; Animals ; Cold Temperature ; Female ; Lipid Metabolism/*physiology ; Lipids/blood ; Male ; Mitochondria, Muscle/metabolism ; Spheniscidae/*physiology ; Thermogenesis/*physiology ; Water ; }, abstract = {The passage from shore to marine life is a critical step in the development of juvenile penguins and is characterized by a fuel selection towards lipid oxidation concomitant to an enhancement of lipid-induced thermogenesis. However, mechanisms of such thermogenic improvement at fledging remain undefined. We used two different groups of pre-fledging king penguins (Aptenodytes patagonicus) to investigate the specific contribution of cold exposure during water immersion to lipid metabolism. Terrestrial penguins that had never been immersed in cold water were compared with experimentally cold-water immersed juveniles. Experimentally immersed penguins underwent ten successive immersions at approximately 9-10 °C for 5 h over 3 weeks. We evaluated adaptive thermogenesis by measuring body temperature, metabolic rate and shivering activity in fully immersed penguins exposed to water temperatures ranging from 12 to 29 °C. Both never-immersed and experimentally immersed penguins were able to maintain their homeothermy in cold water, exhibiting similar thermogenic activity. In vivo, perfusion of lipid emulsion at thermoneutrality induced a twofold larger calorigenic response in experimentally immersed than in never-immersed birds. In vitro, the respiratory rates and the oxidative phosphorylation efficiency of isolated muscle mitochondria were not improved with cold-water immersions. The present study shows that acclimation to cold water only partially reproduced the fuel selection towards lipid oxidation that characterizes penguin acclimatization to marine life.}, }
@article {pmid26921295, year = {2016}, author = {Ross, E and Blair, D and Guerrero-Hernández, C and Sánchez Alvarado, A}, title = {Comparative and Transcriptome Analyses Uncover Key Aspects of Coding- and Long Noncoding RNAs in Flatworm Mitochondrial Genomes.}, journal = {G3 (Bethesda, Md.)}, volume = {6}, number = {5}, pages = {1191-1200}, pmid = {26921295}, issn = {2160-1836}, support = {R01 GM057260/GM/NIGMS NIH HHS/United States ; R37 GM057260/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/methods ; Evolution, Molecular ; Gene Expression Profiling ; Gene Order ; Genes, Mitochondrial ; *Genome, Mitochondrial ; *Genomics/methods ; Molecular Sequence Annotation ; *Open Reading Frames ; Phylogeny ; Platyhelminths/*genetics ; *RNA, Long Noncoding ; *Transcriptome ; }, abstract = {Exploiting the conservation of various features of mitochondrial genomes has been instrumental in resolving phylogenetic relationships. Despite extensive sequence evidence, it has not previously been possible to conclusively resolve some key aspects of flatworm mitochondrial genomes, including generally conserved traits, such as start codons, noncoding regions, the full complement of tRNAs, and whether ATP8 is, or is not, encoded by this extranuclear genome. In an effort to address these difficulties, we sought to determine the mitochondrial transcriptomes and genomes of sexual and asexual taxa of freshwater triclads, a group previously poorly represented in flatworm mitogenomic studies. We have discovered evidence for an alternative start codon, an extended cox1 gene, a previously undescribed conserved open reading frame, long noncoding RNAs, and a highly conserved gene order across the large evolutionary distances represented within the triclads. Our findings contribute to the expansion and refinement of mitogenomics to address evolutionary issues in this diverse group of animals.}, }
@article {pmid26918168, year = {2016}, author = {Leitsch, D}, title = {Recent Advances in the Trichomonas vaginalis Field.}, journal = {F1000Research}, volume = {5}, number = {}, pages = {}, pmid = {26918168}, issn = {2046-1402}, support = {J 3492/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {The microaerophilic protist parasite Trichomonas vaginalis is occurring globally and causes infections in the urogenital tract in humans, a condition termed trichomoniasis. In fact, trichomoniasis is the most prevalent non-viral sexually transmitted disease with more than 250 million people infected every year. Although trichomoniasis is not life threatening in itself, it can be debilitating and increases the risk of adverse pregnancy outcomes, HIV infection, and, possibly, neoplasias in the prostate and the cervix. Apart from its role as a pathogen, T. vaginalis is also a fascinating organism with a surprisingly large genome for a parasite, i. e. larger than 160 Mb, and a physiology adapted to its microaerophilic lifestyle. In particular, the hydrogenosome, a mitochondria-derived organelle that produces hydrogen, has attracted much interest in the last few decades and rendered T. vaginalis a model organism for eukaryotic evolution. This review will give a succinct overview of the major advances in the T. vaginalis field in the last few years.}, }
@article {pmid26917748, year = {2016}, author = {Hamers, L}, title = {EVOLUTION. Why do cells' power plants hang on to their own genomes?.}, journal = {Science (New York, N.Y.)}, volume = {351}, number = {6276}, pages = {903}, doi = {10.1126/science.351.6276.903}, pmid = {26917748}, issn = {1095-9203}, mesh = {Animals ; Chiroptera ; Energy Metabolism/*genetics ; *Evolution, Molecular ; *Genes, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Mitochondria, Liver/ultrastructure ; Symbiosis/genetics ; }, }
@article {pmid26914395, year = {2016}, author = {Kosuda, S and Sasakawa, K and Ikeda, H}, title = {Directional mitochondrial introgression and character displacement due to reproductive interference in two closely related Pterostichus ground beetle species.}, journal = {Journal of evolutionary biology}, volume = {29}, number = {6}, pages = {1121-1130}, doi = {10.1111/jeb.12852}, pmid = {26914395}, issn = {1420-9101}, mesh = {Animals ; *Coleoptera ; Female ; Hybridization, Genetic ; Male ; Mitochondria ; *Phylogeny ; *Reproduction ; Sympatry ; }, abstract = {Reproductive interference due to interspecific hybridization can lead to character displacement among related species with overlapping ranges. However, no studies have examined which reproductive traits are most important in reducing reproductive interference. We conducted molecular analyses of two nuclear genes (28S and Wingless) and a mitochondrial gene (COI) from two closely related ground beetle species, Pterostichus thunbergi and Pterostichus habui (Coleoptera: Carabidae), with overlapping distributions. In addition, we examined four reproductive traits (body size, organ morphologies of intromittent and non-intromittent male genital organs, and female reproductive period) in sympatric and allopatric habitats. We compared male genital morphology using geometric morphometric analysis. The species determined by morphology were classified into separate groups based on the phylogenetic tree constructed by the nuclear gene (Wingless). However, according to the mitochondrial genes examined, P. thunbergi was not monophyletic, whereas at the sympatric sites, these species formed a monophyletic clade. This incongruence suggests that interspecific hybridization and subsequent mitochondrial introgression from P. habui to P. thunbergi have occurred. Concerning genital morphology, both of the intromittent and nonintromittent organs of P. thunbergi differed more from P. habui at the sympatric sites than between allopatric sites, suggesting reproductive character displacement. Pterostichus thunbergi, which likely arrived in P. habui habitat in small numbers, would have experienced stronger selection pressures than P. habui.}, }
@article {pmid26912842, year = {2016}, author = {Ball, SG and Bhattacharya, D and Weber, AP}, title = {EVOLUTION. Pathogen to powerhouse.}, journal = {Science (New York, N.Y.)}, volume = {351}, number = {6274}, pages = {659-660}, doi = {10.1126/science.aad8864}, pmid = {26912842}, issn = {1095-9203}, mesh = {Alphaproteobacteria/*genetics/pathogenicity ; Animals ; Archaea/metabolism ; *Biological Evolution ; Endocytosis ; Energy Metabolism/genetics ; Eukaryota/genetics ; *Host-Pathogen Interactions ; Humans ; Mitochondria/*genetics ; Plastids/*genetics ; Rickettsia/genetics/pathogenicity ; Symbiosis/*genetics ; }, }
@article {pmid26910434, year = {2016}, author = {Vinnakota, KC and Bazil, JN and Van den Bergh, F and Wiseman, RW and Beard, DA}, title = {Feedback Regulation and Time Hierarchy of Oxidative Phosphorylation in Cardiac Mitochondria.}, journal = {Biophysical journal}, volume = {110}, number = {4}, pages = {972-980}, pmid = {26910434}, issn = {1542-0086}, support = {U01 HL122199/HL/NHLBI NIH HHS/United States ; R01 DK095210/DK/NIDDK NIH HHS/United States ; R00 HL121160/HL/NHLBI NIH HHS/United States ; R01 HL072011/HL/NHLBI NIH HHS/United States ; K99 HL121160/HL/NHLBI NIH HHS/United States ; }, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/*metabolism ; Animals ; Cell Respiration ; *Feedback, Physiological ; Kinetics ; Mitochondria, Heart/*metabolism ; *Oxidative Phosphorylation ; Phosphates/metabolism ; Proton-Translocating ATPases/metabolism ; Rats ; Rats, Wistar ; Succinate-CoA Ligases/metabolism ; Temperature ; }, abstract = {To determine how oxidative ATP synthesis is regulated in the heart, the responses of cardiac mitochondria oxidizing pyruvate to alterations in [ATP], [ADP], and inorganic phosphate ([Pi]) were characterized over a range of steady-state levels of extramitochondrial [ATP], [ADP], and [Pi]. Evolution of the steady states of the measured variables with the flux of respiration shows that: (1) a higher phosphorylation potential is achieved by mitochondria at higher [Pi] for a given flux of respiration; (2) the time hierarchy of oxidative phosphorylation is given by phosphorylation subsystem, electron transport chain, and substrate dehydrogenation subsystems listed in increasing order of their response times; (3) the matrix ATP hydrolysis mass action ratio [ADP] × [Pi]/[ATP] provides feedback to the substrate dehydrogenation flux over the entire range of respiratory flux examined in this study; and finally, (4) contrary to previous models of regulation of oxidative phosphorylation, [Pi] does not modulate the activity of complex III.}, }
@article {pmid26893300, year = {2016}, author = {Klinger, CM and Spang, A and Dacks, JB and Ettema, TJ}, title = {Tracing the Archaeal Origins of Eukaryotic Membrane-Trafficking System Building Blocks.}, journal = {Molecular biology and evolution}, volume = {33}, number = {6}, pages = {1528-1541}, doi = {10.1093/molbev/msw034}, pmid = {26893300}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Archaea/*genetics/*metabolism ; Biological Evolution ; Eukaryota/*genetics/*metabolism ; Evolution, Molecular ; Genes, Archaeal ; Membrane Transport Proteins/*genetics/*metabolism ; Monomeric GTP-Binding Proteins/genetics/metabolism ; Phylogeny ; Protein Transport ; Sequence Analysis, Protein/methods ; }, abstract = {In contrast to prokaryotes, eukaryotic cells are characterized by a complex set of internal membrane-bound compartments. A subset of these, and the protein machineries that move material between them, define the membrane-trafficking system (MTS), the emergence of which represents a landmark in eukaryotic evolution. Unlike mitochondria and plastids, MTS organelles have autogenous origins. Much of the MTS machinery is composed of building blocks, including small GTPase, coiled-coil, beta-propeller + alpha-solenoid, and longin domains. Despite the identification of prokaryotic proteins containing these domains, only few represent direct orthologues, leaving the origins and early evolution of the MTS poorly understood. Here, we present an in-depth analysis of MTS building block homologues in the composite genome of Lokiarchaeum, the recently discovered archaeal sister clade of eukaryotes, yielding several key insights. We identify two previously unreported Eukaryotic Signature Proteins; orthologues of the Gtr/Rag family GTPases, involved in target of rapamycin complex signaling, and of the RLC7 dynein component. We could not identify golgin or SNARE (coiled-coil) or beta-propeller + alpha-solenoid orthologues, nor typical MTS domain fusions, suggesting that these either were lost from Lokiarchaeum or emerged later in eukaryotic evolution. Furthermore, our phylogenetic analyses of lokiarchaeal GTPases support a split into Ras-like and Arf-like superfamilies, with different prokaryotic antecedents, before the advent of eukaryotes. While no GTPase activating proteins or exchange factors were identified, we show that Lokiarchaeum encodes numerous roadblock domain proteins and putative longin domain proteins, confirming the latter's origin from Archaea. Altogether, our study provides new insights into the emergence and early evolution of the eukaryotic membrane-trafficking system.}, }
@article {pmid26889782, year = {2016}, author = {Andreini, C and Banci, L and Rosato, A}, title = {Exploiting Bacterial Operons To Illuminate Human Iron-Sulfur Proteins.}, journal = {Journal of proteome research}, volume = {15}, number = {4}, pages = {1308-1322}, doi = {10.1021/acs.jproteome.6b00045}, pmid = {26889782}, issn = {1535-3907}, mesh = {Apoptosis/genetics ; Arabidopsis/genetics/metabolism ; Archaea/genetics/metabolism ; Bacteria/genetics/*metabolism ; Bacterial Proteins/*chemistry/classification/genetics/metabolism ; Biological Evolution ; Cell Nucleus/metabolism ; Computational Biology ; Cytoplasm/metabolism ; Electron Transport/*genetics ; Gene Expression ; Humans ; Iron-Sulfur Proteins/*chemistry/classification/genetics/metabolism ; Mitochondria/metabolism ; *Operon ; Protein Structure, Secondary ; Reactive Oxygen Species/metabolism ; Ribosomes/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Species Specificity ; Structural Homology, Protein ; User-Computer Interface ; }, abstract = {Organisms from all kingdoms of life use iron-sulfur proteins (FeS-Ps) in a multitude of functional processes. We applied a bioinformatics approach to investigate the human portfolio of FeS-Ps. Sixty-one percent of human FeS-Ps bind Fe4S4 clusters, whereas 39% bind Fe2S2 clusters. However, this relative ratio varies significantly depending on the specific cellular compartment. We compared the portfolio of human FeS-Ps to 12 other eukaryotes and to about 700 prokaryotes. The comparative analysis of the organization of the prokaryotic homologues of human FeS-Ps within operons allowed us to reconstruct the human functional networks involving the conserved FeS-Ps common to prokaryotes and eukaryotes. These functional networks have been maintained during evolution and thus presumably represent fundamental cellular processes. The respiratory chain and the ISC machinery for FeS-P biogenesis are the two conserved processes that involve the majority of human FeS-Ps. Purine metabolism is another process including several FeS-Ps, in which BOLA proteins possibly have a regulatory role. The analysis of the co-occurrence of human FeS-Ps with other proteins highlighted numerous links between the iron-sulfur cluster machinery and the response mechanisms to cell damage, from repair to apoptosis. This relationship probably relates to the production of reactive oxygen species within the biogenesis and degradation of FeS-Ps.}, }
@article {pmid26887409, year = {2016}, author = {Strassert, JF and Tikhonenkov, DV and Pombert, JF and Kolisko, M and Tai, V and Mylnikov, AP and Keeling, PJ}, title = {Moramonas marocensis gen. nov., sp. nov.: a jakobid flagellate isolated from desert soil with a bacteria-like, but bloated mitochondrial genome.}, journal = {Open biology}, volume = {6}, number = {2}, pages = {150239}, pmid = {26887409}, issn = {2046-2441}, mesh = {Base Sequence ; DNA, Ribosomal/genetics ; *Desert Climate ; Eukaryota/*classification/*genetics/isolation &amp; purification/ultrastructure ; Flagella/ultrastructure ; Gene Order ; *Genome, Mitochondrial ; Nucleotide Motifs ; Phylogeny ; *Soil Microbiology ; }, abstract = {A new jakobid genus has been isolated from Moroccan desert soil. The cyst-forming protist Moramonas marocensis gen. nov., sp. nov. has two anteriorly inserted flagella of which one points to the posterior cell pole accompanying the ventral feeding groove and is equipped with a dorsal vane-a feature typical for the Jakobida. It further shows a flagellar root system consisting of singlet microtubular root, left root (R1), right root (R2) and typical fibres associated with R1 and R2. The affiliation of M. marocensis to the Jakobida was confirmed by molecular phylogenetic analyses of the SSU rRNA gene, five nuclear genes and 66 mitochondrial protein-coding genes. The mitochondrial genome has the high number of genes typical for jakobids, and bacterial features, such as the four-subunit RNA polymerase and Shine-Dalgarno sequences upstream of the coding regions of several genes. The M. marocensis mitochondrial genome encodes a similar number of genes as other jakobids, but is unique in its very large genome size (greater than 264 kbp), which is three to four times higher than that of any other jakobid species investigated yet. This increase seems to be due to a massive expansion in non-coding DNA, creating a bloated genome like those of plant mitochondria.}, }
@article {pmid26876639, year = {2016}, author = {Kornilios, P and Thanou, E and Kapli, P and Parmakelis, A and Chatzaki, M}, title = {Peeking through the trapdoor: Historical biogeography of the Aegean endemic spider Cyrtocarenum Ausserer, 1871 with an estimation of mtDNA substitution rates for Mygalomorphae.}, journal = {Molecular phylogenetics and evolution}, volume = {98}, number = {}, pages = {300-313}, doi = {10.1016/j.ympev.2016.01.021}, pmid = {26876639}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; Climate ; DNA, Mitochondrial/*genetics ; Greece ; Mitochondria/genetics ; *Mutation Rate ; *Phylogeny ; Phylogeography ; Spiders/*genetics ; Turkey ; }, abstract = {The Aegean region, located in the Eastern Mediterranean, is an area of rich biodiversity and endemism. Its position, geographical configuration and complex geological history have shaped the diversification history of many animal taxa. Mygalomorph spiders have drawn the attention of researchers, as excellent model systems for phylogeographical investigations. However, phylogeographic studies of spiders in the Aegean region are scarce. In this study, we focused on the phylogeography of the endemic ctenizid trap-door spider Cyrtocarenum Ausserer, 1871. The genus includes two morphologically described species: C. grajum (C.L. Koch, 1836) and C. cunicularium (Olivier, 1811). We sampled 60 specimens from the distributions of both species and analyzed four mitochondrial and two nuclear markers. Cyrtocarenum served as an example to demonstrate the importance of natural history traits in the inference of phylogeographic scenarios. The mtDNA substitution rates inferred for the genus are profoundly higher compared to araneomorph spiders and other arthropods, which seems tightly associated with their biology. We evaluate published mtDNA substitution rates followed in the literature for mygalomorph spiders and discuss potential pitfalls. Following gene tree (maximum likelihood, Bayesian inference) and species tree approaches ((*)BEAST), we reconstructed a time-calibrated phylogeny of the genus. These results, combined with a biogeographical ancestral-area analysis, helped build a biogeographic scenario that describes how the major palaeogeographic and palaeoclimatic events of the Aegean may have affected the distribution of Cyrtocarenum lineages. The diversification of the genus seems to have begun in the Middle Miocene in the present west Aegean area, while major phylogenetic events occurred at the Miocene-Pliocene boundary for C. cunicularium, probably related to the Messinian Salinity Crisis. Our results also demonstrate the clear molecular distinction of the two morphologically described species, but possible cryptic lineages may exist within C. cunicularium.}, }
@article {pmid26874458, year = {2016}, author = {Brahimi, A and Tarai, N and Benhassane, A and Henrard, A and Libois, R}, title = {Genetic and morphological consequences of Quaternary glaciations: A relic barbel lineage (Luciobarbus pallaryi, Cyprinidae) of Guir Basin (Algeria).}, journal = {Comptes rendus biologies}, volume = {339}, number = {2}, pages = {83-98}, doi = {10.1016/j.crvi.2015.12.003}, pmid = {26874458}, issn = {1768-3238}, mesh = {Algeria ; Animals ; *Biological Evolution ; Climate Change/*history ; Cyprinidae/*anatomy &amp; histology/*genetics ; Cytochromes b/genetics ; Genetic Markers ; Genetic Variation ; History, Ancient ; *Ice Cover ; Mitochondria/genetics ; }, abstract = {Climatic variations during the Quaternary period had a considerable impact on landscapes and habitat fragmentation (rivers) in North Africa. These historical events can have significant consequences on the genetic structure of the populations. Indeed, geographically separated and genetically isolated populations tend to differentiate themselves through time, eventually becoming distinct lineages, allowing new species to emerge in later generations. The aim of the present study is to use genetic and morphological techniques to evaluate the major role of the Saalian glaciation (Middle Quaternary) in the establishment of the geographic space and in the evolution of the intraspecific genetic diversity, by tracing the demographic history of barbels belonging to the Luciobarbus pallaryi (Cyprinidae) species in the Guir Basin (Algeria). In this context, two populations, from two distinct and isolated sites, were studied. Analysis of the cytochrome b (cyt b) mitochondrial markers and of the "D-loop" control region has shown that the "upstream" and "downstream" Guir populations are genetically differentiated. The molecular analyses suggest that the upstream population was disconnected from this hydrographic system during the Saalian glaciation period of the Quaternary. Subsequently, it was isolated in the foggaras underground waters in the Great Western Erg, at approximately 320 000 years BP, creating, through a bottleneck effect, a new allopatric lineage referred to as "Adrar". Conversely, the high genetic diversity in the upstream Guir (Bechar) population suggests that the stock is globally in expansion. These barbels (n=52) were also examined with meristic, morphometric, osteological, and biological features. These data also reveal a complete discrimination between the two populations, with a remarkable and distinctive behavioural adaptation for the Adrar specimens: neoteny.}, }
@article {pmid26872774, year = {2016}, author = {Ševčíková, T and Klimeš, V and Zbránková, V and Strnad, H and Hroudová, M and Vlček, &#x10c; and Eliáš, M}, title = {A Comparative Analysis of Mitochondrial Genomes in Eustigmatophyte Algae.}, journal = {Genome biology and evolution}, volume = {8}, number = {3}, pages = {705-722}, pmid = {26872774}, issn = {1759-6653}, mesh = {*Evolution, Molecular ; Genome, Mitochondrial ; Genomics ; *Phylogeny ; Stramenopiles/*genetics ; }, abstract = {Eustigmatophyceae (Ochrophyta, Stramenopiles) is a small algal group with species of the genus Nannochloropsis being its best studied representatives. Nuclear and organellar genomes have been recently sequenced for several Nannochloropsis spp., but phylogenetically wider genomic studies are missing for eustigmatophytes. We sequenced mitochondrial genomes (mitogenomes) of three species representing most major eustigmatophyte lineages, Monodopsis sp. MarTras21, Vischeria sp. CAUP Q 202 and Trachydiscus minutus, and carried out their comparative analysis in the context of available data from Nannochloropsis and other stramenopiles, revealing a number of noticeable findings. First, mitogenomes of most eustigmatophytes are highly collinear and similar in the gene content, but extensive rearrangements and loss of three otherwise ubiquitous genes happened in the Vischeria lineage; this correlates with an accelerated evolution of mitochondrial gene sequences in this lineage. Second, eustigmatophytes appear to be the only ochrophyte group with the Atp1 protein encoded by the mitogenome. Third, eustigmatophyte mitogenomes uniquely share a truncated nad11 gene encoding only the C-terminal part of the Nad11 protein, while the N-terminal part is encoded by a separate gene in the nuclear genome. Fourth, UGA as a termination codon and the cognate release factor mRF2 were lost from mitochondria independently by the Nannochloropsis and T. minutus lineages. Finally, the rps3 gene in the mitogenome of Vischeria sp. is interrupted by the UAG codon, but the genome includes a gene for an unusual tRNA with an extended anticodon loop that we speculate may serve as a suppressor tRNA to properly decode the rps3 gene.}, }
@article {pmid26872675, year = {2016}, author = {Moe, GW and Marín-García, J}, title = {Role of cell death in the progression of heart failure.}, journal = {Heart failure reviews}, volume = {21}, number = {2}, pages = {157-167}, pmid = {26872675}, issn = {1573-7322}, mesh = {*Cell Death ; *Disease Progression ; Heart Failure/*physiopathology ; Humans ; Mitochondria, Heart/*metabolism ; Myocytes, Cardiac/*pathology ; Signal Transduction/physiology ; }, abstract = {All multicellular organisms develop during evolution the highly regulated and interconnected pathways of cell death. This complex network contributes to the pathogenesis of various cardiovascular disorders including ischemia/reperfusion injury, myocardial infarction, heart failure, dysrhythmias and atherosclerosis. Chronic cardiac remodeling response and transition to overt HF have been associated with modestly increased apoptosis, although the actual burden of chronic cell loss attributable to apoptosis is not clear. Central mediators of cardiomyocyte survival and death are the mitochondrial organelles. Based on its morphological characteristics, cell death can be classified into three major types: apoptosis, necrosis and autophagy. Recently, a new pathway of regulated necrosis, necroptosis, has also been reported in the failing heart. The mitochondrial (intrinsic) and the death-receptor-mediated (extrinsic) converge at mitochondria inducing release of mitochondrial apoptogens to initiate the caspase cascade and eventually degradation of the doomed cardiomyocyte. Activation of death receptors can initiate not only extrinsic apoptotic pathway, but also necrosis. On the other hand, autophagy, which is characterized by the massive formation of lysosomal-derived vesicles, containing degenerating cytoplasmic contents, is primarily a survival response to nutrient deprivation, and a selective form of autophagy, mitophagy, is also a protective mechanism that allows to eliminate damaged mitochondria and thereby to attenuate mitochondria-mediated apoptosis and necrosis in the myocardium. Further insight into the molecular mechanisms underlying cell death will increase the efficiency and repertoire of therapeutic interventions available in cardiovascular disease.}, }
@article {pmid26868331, year = {2016}, author = {Nadimi, M and Daubois, L and Hijri, M}, title = {Mitochondrial comparative genomics and phylogenetic signal assessment of mtDNA among arbuscular mycorrhizal fungi.}, journal = {Molecular phylogenetics and evolution}, volume = {98}, number = {}, pages = {74-83}, doi = {10.1016/j.ympev.2016.01.009}, pmid = {26868331}, issn = {1095-9513}, mesh = {DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; *Genomics ; Glomeromycota/classification/*genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Mycorrhizae/classification/*genetics ; *Phylogeny ; }, abstract = {Mitochondrial (mt) genes, such as cytochrome C oxidase genes (cox), have been widely used for barcoding in many groups of organisms, although this approach has been less powerful in the fungal kingdom due to the rapid evolution of their mt genomes. The use of mt genes in phylogenetic studies of Dikarya has been met with success, while early diverging fungal lineages remain less studied, particularly the arbuscular mycorrhizal fungi (AMF). Advances in next-generation sequencing have substantially increased the number of publically available mtDNA sequences for the Glomeromycota. As a result, comparison of mtDNA across key AMF taxa can now be applied to assess the phylogenetic signal of individual mt coding genes, as well as concatenated subsets of coding genes. Here we show comparative analyses of publically available mt genomes of Glomeromycota, augmented with two mtDNA genomes that were newly sequenced for this study (Rhizophagus irregularis DAOM240159 and Glomus aggregatum DAOM240163), resulting in 16 complete mtDNA datasets. R. irregularis isolate DAOM240159 and G. aggregatum isolate DAOM240163 showed mt genomes measuring 72,293bp and 69,505bp with G+C contents of 37.1% and 37.3%, respectively. We assessed the phylogenies inferred from single mt genes and complete sets of coding genes, which are referred to as "supergenes" (16 concatenated coding genes), using Shimodaira-Hasegawa tests, in order to identify genes that best described AMF phylogeny. We found that rnl, nad5, cox1, and nad2 genes, as well as concatenated subset of these genes, provided phylogenies that were similar to the supergene set. This mitochondrial genomic analysis was also combined with principal coordinate and partitioning analyses, which helped to unravel certain evolutionary relationships in the Rhizophagus genus and for G. aggregatum within the Glomeromycota. We showed evidence to support the position of G. aggregatum within the R. irregularis 'species complex'.}, }
@article {pmid26861137, year = {2016}, author = {Kelley, JL and Arias-Rodriguez, L and Patacsil Martin, D and Yee, MC and Bustamante, CD and Tobler, M}, title = {Mechanisms Underlying Adaptation to Life in Hydrogen Sulfide-Rich Environments.}, journal = {Molecular biology and evolution}, volume = {33}, number = {6}, pages = {1419-1434}, pmid = {26861137}, issn = {1537-1719}, mesh = {Acclimatization/genetics/physiology ; Adaptation, Physiological/genetics/*physiology ; Animals ; Biological Evolution ; Ecosystem ; Environment ; Evolution, Molecular ; Gene Flow ; Genetics, Population/methods ; Genome ; Hydrogen Sulfide/*metabolism ; Poecilia/genetics/metabolism/*physiology ; Selection, Genetic ; Sequence Alignment/methods ; Sequence Analysis, RNA/methods ; Transcriptome ; }, abstract = {Hydrogen sulfide (H2S) is a potent toxicant interfering with oxidative phosphorylation in mitochondria and creating extreme environmental conditions in aquatic ecosystems. The mechanistic basis of adaptation to perpetual exposure to H2S remains poorly understood. We investigated evolutionarily independent lineages of livebearing fishes that have colonized and adapted to springs rich in H2S and compared their genome-wide gene expression patterns with closely related lineages from adjacent, nonsulfidic streams. Significant differences in gene expression were uncovered between all sulfidic and nonsulfidic population pairs. Variation in the number of differentially expressed genes among population pairs corresponded to differences in divergence times and rates of gene flow, which is consistent with neutral drift driving a substantial portion of gene expression variation among populations. Accordingly, there was little evidence for convergent evolution shaping large-scale gene expression patterns among independent sulfide spring populations. Nonetheless, we identified a small number of genes that was consistently differentially expressed in the same direction in all sulfidic and nonsulfidic population pairs. Functional annotation of shared differentially expressed genes indicated upregulation of genes associated with enzymatic H2S detoxification and transport of oxidized sulfur species, oxidative phosphorylation, energy metabolism, and pathways involved in responses to oxidative stress. Overall, our results suggest that modification of processes associated with H2S detoxification and toxicity likely complement each other to mediate elevated H2S tolerance in sulfide spring fishes. Our analyses allow for the development of novel hypotheses about biochemical and physiological mechanisms of adaptation to extreme environments.}, }
@article {pmid26852331, year = {2016}, author = {Buczek, D and Wojtkowska, M and Suzuki, Y and Sonobe, S and Nishigami, Y and Antoniewicz, M and Kmita, H and Makałowski, W}, title = {Protein import complexes in the mitochondrial outer membrane of Amoebozoa representatives.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {99}, pmid = {26852331}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Amoebozoa/classification/genetics/*metabolism ; Carrier Proteins/metabolism ; Conserved Sequence ; Exons ; Genetic Variation ; Genome, Protozoan ; Introns ; Mitochondrial Membranes/*metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Multiprotein Complexes/*metabolism ; Phylogeny ; Protein Subunits ; Protein Transport ; Protozoan Proteins/chemistry/*metabolism ; Transcriptome ; }, abstract = {BACKGROUND: An ancestral trait of eukaryotic cells is the presence of mitochondria as an essential element for function and survival. Proper functioning of mitochondria depends on the import of nearly all proteins that is performed by complexes located in both mitochondrial membranes. The complexes have been proposed to contain subunits formed by proteins common to all eukaryotes and additional subunits regarded as lineage specific. Since Amoebozoa is poorly sampled for the complexes we investigated the outer membrane complexes, namely TOM, TOB/SAM and ERMES complexes, using available genome and transcriptome sequences, including transcriptomes assembled by us.<br><br>RESULTS: The results indicate differences in the organization of the Amoebozoa TOM, TOB/SAM and ERMES complexes, with the TOM complex appearing to be the most diverse. This is reflected by differences in the number of involved subunits and in similarities to the cognate proteins of representatives from different supergroups of eukaryotes.<br><br>CONCLUSIONS: The obtained results clearly demonstrate structural variability/diversity of these complexes in the Amoebozoa lineage and the reduction of their complexity as compared with the same complexes of model organisms.}, }
@article {pmid26850834, year = {2016}, author = {Pereira, RJ and Martínez-Solano, I and Buckley, D}, title = {Hybridization during altitudinal range shifts: nuclear introgression leads to extensive cyto-nuclear discordance in the fire salamander.}, journal = {Molecular ecology}, volume = {25}, number = {7}, pages = {1551-1565}, doi = {10.1111/mec.13575}, pmid = {26850834}, issn = {1365-294X}, mesh = {*Altitude ; Animals ; Biological Evolution ; Climate Change ; DNA, Mitochondrial/genetics ; *Gene Flow ; *Genetics, Population ; Haplotypes ; *Hybridization, Genetic ; Models, Genetic ; Phylogeography ; Salamandra/*genetics ; Sequence Analysis, DNA ; }, abstract = {Ecological models predict that, in the face of climate change, taxa occupying steep altitudinal gradients will shift their distributions, leading to the contraction or extinction of the high-elevation (cold-adapted) taxa. However, hybridization between ecomorphologically divergent taxa commonly occurs in nature and may lead to alternative evolutionary outcomes, such as genetic merger or gene flow at specific genes. We evaluate this hypothesis by studying patterns of divergence and gene flow across three replicate contact zones between high- and low-elevation ecomorphs of the fire salamander (Salamandra salamandra) that have experienced altitudinal range shifts over the current postglacial period. Strong population structure with high genetic divergence in mitochondrial DNA suggests that vicariant evolution has occurred over several glacial-interglacial cycles and that it has led to cryptic differentiation within ecomorphs. In current parapatric boundaries, we do not find evidence for local extinction and replacement upon postglacial expansion. Instead, parapatric taxa recurrently show discordance between mitochondrial and nuclear markers, suggesting nuclear-mediated gene flow across contact zones. Isolation with migration models support this hypothesis by showing significant gene flow across all five parapatric boundaries. Together, our results suggest that, while some genomic regions, such as the mitochondria, may follow morphologic species traits and retreat to isolated mountain tops, other genomic regions, such as nuclear markers, may flow across parapatric boundaries, sometimes leading to a complete genetic merger. We show that despite high ecologic and morphologic divergence over prolonged periods of time, hybridization allows for evolutionary outcomes alternative to extinction and replacement of taxa in response to climate change.}, }
@article {pmid26846713, year = {2016}, author = {Schuler, H and Köppler, K and Daxböck-Horvath, S and Rasool, B and Krumböck, S and Schwarz, D and Hoffmeister, TS and Schlick-Steiner, BC and Steiner, FM and Telschow, A and Stauffer, C and Arthofer, W and Riegler, M}, title = {The hitchhiker's guide to Europe: the infection dynamics of an ongoing Wolbachia invasion and mitochondrial selective sweep in Rhagoletis cerasi.}, journal = {Molecular ecology}, volume = {25}, number = {7}, pages = {1595-1609}, pmid = {26846713}, issn = {1365-294X}, support = {I 2604/FWF_/Austrian Science Fund FWF/Austria ; J 3527/FWF_/Austrian Science Fund FWF/Austria ; P 26749/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/*genetics ; Disease Transmission, Infectious ; Europe ; *Evolution, Molecular ; Gene Frequency ; *Genetics, Population ; Genome, Insect ; Genotype ; Germany ; Haplotypes ; Microsatellite Repeats ; Models, Genetic ; Selection, Genetic ; Sequence Analysis, DNA ; Spatio-Temporal Analysis ; Tephritidae/*genetics/*microbiology ; Wolbachia/*genetics ; }, abstract = {Wolbachia is a maternally inherited and ubiquitous endosymbiont of insects. It can hijack host reproduction by manipulations such as cytoplasmic incompatibility (CI) to enhance vertical transmission. Horizontal transmission of Wolbachia can also result in the colonization of new mitochondrial lineages. In this study, we present a 15-year-long survey of Wolbachia in the cherry fruit fly Rhagoletis cerasi across Europe and the spatiotemporal distribution of two prevalent strains, wCer1 and wCer2, and associated mitochondrial haplotypes in Germany. Across most of Europe, populations consisted of either 100% singly (wCer1) infected individuals with haplotype HT1, or 100% doubly (wCer1&amp;2) infected individuals with haplotype HT2, differentiated only by a single nucleotide polymorphism. In central Germany, singly infected populations were surrounded by transitional populations, consisting of both singly and doubly infected individuals, sandwiched between populations fixed for wCer1&amp;2. Populations with fixed infection status showed perfect association of infection and mitochondria, suggesting a recent CI-driven selective sweep of wCer2 linked with HT2. Spatial analysis revealed a range expansion for wCer2 and a large transition zone in which wCer2 splashes appeared to coalesce into doubly infected populations. Unexpectedly, the transition zone contained a large proportion (22%) of wCer1&amp;2 individuals with HT1, suggesting frequent intraspecific horizontal transmission. However, this horizontal transmission did not break the strict association between infection types and haplotypes in populations outside the transition zone, suggesting that this horizontally acquired Wolbachia infection may be transient. Our study provides new insights into the rarely studied Wolbachia invasion dynamics in field populations.}, }
@article {pmid26846524, year = {2016}, author = {Ren, J and Hou, Z and Wang, H and Sun, MA and Liu, X and Liu, B and Guo, X}, title = {Intraspecific Variation in Mitogenomes of Five Crassostrea Species Provides Insight into Oyster Diversification and Speciation.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {18}, number = {2}, pages = {242-254}, pmid = {26846524}, issn = {1436-2236}, mesh = {Animals ; Base Sequence ; China ; Crassostrea/classification/*genetics ; Gene Flow ; Genetic Speciation ; *Genome, Mitochondrial ; Mitochondria/genetics ; *Mutagenesis, Insertional ; *Phylogeny ; Phylogeography ; *Polymorphism, Single Nucleotide ; Reproductive Isolation ; Sequence Analysis, DNA ; *Sequence Deletion ; }, abstract = {A large number of Crassostrea oysters are found in Asia-Pacific. While analyses of interspecific variation have helped to establish historical relationships among these species, studies on intraspecific variation are necessary to understand their recent evolutionary history and current forces driving population biology. We resequenced 18 and analyzed 31 mitogenomes of five Crassostrea species from China: Crassostrea gigas, Crassostrea angulata, Crassostrea sikamea, Crassostrea ariakensis, and Crassostrea hongkongensis. Our analysis finds abundant insertions, deletions, and single-nucleotide polymorphisms in all species. Intraspecific variation varies greatly among species with polymorphic sites ranging from 54 to 293 and nucleotide diversity ranging from 0.00106 to 0.00683. In all measurements, C. hongkongensis that has the narrowest geographic distribution exhibits the least sequence diversity; C. ariakensis that has the widest distribution shows the highest diversity, and species with intermediate distribution show intermediate levels of diversity. Low sequence diversity in C. hongkongensis may reflect recent bottlenecks that are probably exacerbated by human transplantation. High diversity in C. ariakensis is likely due to divergence of northern and southern China populations that have been separated without gene flow. The significant differences in mitogenome diversity suggest that the five sister species of Crassostrea have experienced different evolutionary forces since their divergence. The recent divergence of two C. ariakensis populations and the C. gigas/angulata species complex provides evidence for continued diversification and speciation of Crassostrea species along China's coast, which are shaped by unknown mechanisms in a north-south divide.}, }
@article {pmid26840490, year = {2016}, author = {Pittis, AA and Gabaldón, T}, title = {Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry.}, journal = {Nature}, volume = {531}, number = {7592}, pages = {101-104}, pmid = {26840490}, issn = {1476-4687}, support = {310325/ERC_/European Research Council/International ; }, mesh = {Eukaryotic Cells/*cytology/metabolism ; Genes, Bacterial/*genetics ; Genes, Mitochondrial/*genetics ; Genomics ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Models, Biological ; *Phylogeny ; Prokaryotic Cells/*cytology/metabolism ; Symbiosis/*genetics ; }, abstract = {The origin of eukaryotes stands as a major conundrum in biology. Current evidence indicates that the last eukaryotic common ancestor already possessed many eukaryotic hallmarks, including a complex subcellular organization. In addition, the lack of evolutionary intermediates challenges the elucidation of the relative order of emergence of eukaryotic traits. Mitochondria are ubiquitous organelles derived from an alphaproteobacterial endosymbiont. Different hypotheses disagree on whether mitochondria were acquired early or late during eukaryogenesis. Similarly, the nature and complexity of the receiving host are debated, with models ranging from a simple prokaryotic host to an already complex proto-eukaryote. Most competing scenarios can be roughly grouped into either mito-early, which consider the driving force of eukaryogenesis to be mitochondrial endosymbiosis into a simple host, or mito-late, which postulate that a significant complexity predated mitochondrial endosymbiosis. Here we provide evidence for late mitochondrial endosymbiosis. We use phylogenomics to directly test whether proto-mitochondrial proteins were acquired earlier or later than other proteins of the last eukaryotic common ancestor. We find that last eukaryotic common ancestor protein families of alphaproteobacterial ancestry and of mitochondrial localization show the shortest phylogenetic distances to their closest prokaryotic relatives, compared with proteins of different prokaryotic origin or cellular localization. Altogether, our results shed new light on a long-standing question and provide compelling support for the late acquisition of mitochondria into a host that already had a proteome of chimaeric phylogenetic origin. We argue that mitochondrial endosymbiosis was one of the ultimate steps in eukaryogenesis and that it provided the definitive selective advantage to mitochondria-bearing eukaryotes over less complex forms.}, }
@article {pmid26840482, year = {2016}, author = {Ettema, TJ}, title = {Evolution: Mitochondria in the second act.}, journal = {Nature}, volume = {531}, number = {7592}, pages = {39-40}, pmid = {26840482}, issn = {1476-4687}, mesh = {Eukaryotic Cells/*cytology ; Genes, Bacterial/*genetics ; Genes, Mitochondrial/*genetics ; Mitochondria/*genetics ; *Phylogeny ; Prokaryotic Cells/*cytology ; Symbiosis/*genetics ; }, }
@article {pmid26833505, year = {2016}, author = {Kamikawa, R and Shiratori, T and Ishida, K and Miyashita, H and Roger, AJ}, title = {Group II Intron-Mediated Trans-Splicing in the Gene-Rich Mitochondrial Genome of an Enigmatic Eukaryote, Diphylleia rotans.}, journal = {Genome biology and evolution}, volume = {8}, number = {2}, pages = {458-466}, pmid = {26833505}, issn = {1759-6653}, mesh = {Electron Transport Complex IV/genetics ; Eukaryota/classification/*genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; *Introns ; Open Reading Frames ; Phylogeny ; *RNA Splicing ; }, abstract = {Although mitochondria have evolved from a single endosymbiotic event, present day mitochondria of diverse eukaryotes display a great range of genome structures, content and features. Group I and group II introns are two features that are distributed broadly but patchily in mitochondrial genomes across branches of the tree of eukaryotes. While group I intron-mediated trans-splicing has been reported from some lineages distantly related to each other, findings of group II intron-mediated trans-splicing has been restricted to members of the Chloroplastida. In this study, we found the mitochondrial genome of the unicellular eukaryote Diphylleia rotans possesses currently the second largest gene repertoire. On the basis of a probable phylogenetic position of Diphylleia, which is located within Amorphea, current mosaic gene distribution in Amorphea must invoke parallel gene losses from mitochondrial genomes during evolution. Most notably, although the cytochrome c oxidase subunit (cox) 1 gene was split into four pieces which located at a distance to each other, we confirmed that a single mature mRNA that covered the entire coding region could be generated by group II intron-mediated trans-splicing. This is the first example of group II intron-mediated trans-splicing outside Chloroplastida. Similar trans-splicing mechanisms likely work for bipartitely split cox2 and nad3 genes to generate single mature mRNAs. We finally discuss origin and evolution of this type of trans-splicing in D. rotans as well as in eukaryotes.}, }
@article {pmid26831941, year = {2016}, author = {Guo, W and Grewe, F and Fan, W and Young, GJ and Knoop, V and Palmer, JD and Mower, JP}, title = {Ginkgo and Welwitschia Mitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution.}, journal = {Molecular biology and evolution}, volume = {33}, number = {6}, pages = {1448-1460}, doi = {10.1093/molbev/msw024}, pmid = {26831941}, issn = {1537-1719}, mesh = {Base Sequence ; *Biological Evolution ; Chromosome Mapping ; Evolution, Molecular ; Genes, Plant ; *Genome, Mitochondrial ; Genome, Plant ; Ginkgo biloba/*genetics ; Gnetophyta/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA Editing ; }, abstract = {Mitochondrial genomes (mitogenomes) of flowering plants are well known for their extreme diversity in size, structure, gene content, and rates of sequence evolution and recombination. In contrast, little is known about mitogenomic diversity and evolution within gymnosperms. Only a single complete genome sequence is available, from the cycad Cycas taitungensis, while limited information is available for the one draft sequence, from Norway spruce (Picea abies). To examine mitogenomic evolution in gymnosperms, we generated complete genome sequences for the ginkgo tree (Ginkgo biloba) and a gnetophyte (Welwitschia mirabilis). There is great disparity in size, sequence conservation, levels of shared DNA, and functional content among gymnosperm mitogenomes. The Cycas and Ginkgo mitogenomes are relatively small, have low substitution rates, and possess numerous genes, introns, and edit sites; we infer that these properties were present in the ancestral seed plant. By contrast, the Welwitschia mitogenome has an expanded size coupled with accelerated substitution rates and extensive loss of these functional features. The Picea genome has expanded further, to more than 4 Mb. With regard to structural evolution, the Cycas and Ginkgo mitogenomes share a remarkable amount of intergenic DNA, which may be related to the limited recombinational activity detected at repeats in Ginkgo Conversely, the Welwitschia mitogenome shares almost no intergenic DNA with any other seed plant. By conducting the first measurements of rates of DNA turnover in seed plant mitogenomes, we discovered that turnover rates vary by orders of magnitude among species.}, }
@article {pmid26829901, year = {2016}, author = {Fromm, S and Senkler, J and Zabaleta, E and Peterhänsel, C and Braun, HP}, title = {The carbonic anhydrase domain of plant mitochondrial complex I.}, journal = {Physiologia plantarum}, volume = {157}, number = {3}, pages = {289-296}, doi = {10.1111/ppl.12424}, pmid = {26829901}, issn = {1399-3054}, mesh = {Arabidopsis/*enzymology/genetics ; Arabidopsis Proteins/metabolism ; Carbonic Anhydrases/chemistry/genetics/*metabolism ; Electron Transport Complex I/chemistry/genetics/*metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins/chemistry/genetics/metabolism ; Mutation ; }, abstract = {The mitochondrial NADH dehydrogenase complex (complex I) consists of several functional domains which independently arose during evolution. In higher plants, it contains an additional domain which includes proteins resembling gamma-type carbonic anhydrases. The Arabidopsis genome codes for five complex I-integrated gamma-type carbonic anhydrases (γCA1, γCA2, γCA3, γCAL1, γCAL2), but only three copies of this group of proteins form an individual extra domain. Biochemical analyses revealed that the domain is composed of one copy of either γCAL1 or γCAL2 plus two copies of the γCA1/γCA2 proteins. Thus, the carbonic anhydrase domain can have six distinct subunit configurations. Single and double mutants with respect to the γCA/γCAL proteins were employed to genetically dissect the function of the domain. New insights into complex I biology in plants will be reviewed and discussed.}, }
@article {pmid26826602, year = {2016}, author = {Pánek, T and Zadrobílková, E and Walker, G and Brown, MW and Gentekaki, E and Hroudová, M and Kang, S and Roger, AJ and Tice, AK and Vlček, &#x10c; and Čepička, I}, title = {First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group.}, journal = {Molecular phylogenetics and evolution}, volume = {98}, number = {}, pages = {41-51}, doi = {10.1016/j.ympev.2016.01.011}, pmid = {26826602}, issn = {1095-9513}, mesh = {Archamoebae/*classification/*genetics/metabolism/ultrastructure ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Mitochondria/metabolism ; Multigene Family/*genetics ; Nitrogen Fixation/genetics ; *Phylogeny ; Sulfates/metabolism ; }, abstract = {Archamoebae is an understudied group of anaerobic free-living or endobiotic protists that constitutes the major anaerobic lineage of the supergroup Amoebozoa. Hitherto, the phylogeny of Archamoebae was based solely on SSU rRNA and actin genes, which did not resolve relationships among the main lineages of the group. Because of this uncertainty, several different scenarios had been proposed for the phylogeny of the Archamoebae. In this study, we present the first multigene phylogenetic analysis that includes members of Pelomyxidae, and Rhizomastixidae. The analysis clearly shows that Mastigamoebidae, Pelomyxidae and Rhizomastixidae form a clade of mostly free-living, amoeboid flagellates, here called Pelobiontida. The predominantly endobiotic and aflagellated Entamoebidae represents a separate, deep-branching lineage, Entamoebida. Therefore, two unique evolutionary events, horizontal transfer of the nitrogen fixation system from bacteria and transfer of the sulfate activation pathway to mitochondrial derivatives, predate the radiation of recent lineages of Archamoebae. The endobiotic lifestyle has arisen at least three times independently during the evolution of the group. We also present new ultrastructural data that clarifies the primary divergence among the family Mastigamoebidae which had previously been inferred from phylogenetic analyses based on SSU rDNA.}, }
@article {pmid26825688, year = {2016}, author = {Wideman, JG and Muñoz-Gómez, SA}, title = {The evolution of ERMIONE in mitochondrial biogenesis and lipid homeostasis: An evolutionary view from comparative cell biology.}, journal = {Biochimica et biophysica acta}, volume = {1861}, number = {8 Pt B}, pages = {900-912}, doi = {10.1016/j.bbalip.2016.01.015}, pmid = {26825688}, issn = {0006-3002}, mesh = {Animals ; *Biological Evolution ; Endoplasmic Reticulum/*metabolism ; Homeostasis/physiology ; Humans ; Lipid Metabolism/*physiology ; Mitochondria/metabolism/*physiology ; Mitochondrial Membranes/metabolism ; *Organelle Biogenesis ; Phylogeny ; }, abstract = {The ER-mitochondria organizing network (ERMIONE) in Saccharomyces cerevisiae is involved in maintaining mitochondrial morphology and lipid homeostasis. ERMES and MICOS are two scaffolding complexes of ERMIONE that contribute to these processes. ERMES is ancient but has been lost in several lineages including animals, plants, and SAR (stramenopiles, alveolates and rhizaria). On the other hand, MICOS is ancient and has remained present in all organisms bearing mitochondrial cristae. The ERMIONE precursor evolved in the α-proteobacterial ancestor of mitochondria which had the central subunit of MICOS, Mic60. The subsequent evolution of ERMIONE and its interactors in eukaryotes reflects the integrative co-evolution of mitochondria and their hosts and the adaptive paths that some lineages have followed in their specialization to certain environments. By approaching the ERMIONE from a perspective of comparative evolutionary cell biology, we hope to shed light on not only its evolutionary history, but also how ERMIONE components may function in organisms other than S. cerevisiae. This article is part of a Special Issue entitled: The cellular lipid landscape edited by Tim P. Levine and Anant K. Menon.}, }
@article {pmid26821297, year = {2016}, author = {Yang, R and Brice, B and Jian, F and Ryan, U}, title = {Morphological and molecular characterization of Isospora manorinae n. sp. in a yellow-throated miner (Manorina flavigula wayensis) (Gould, 1840).}, journal = {Experimental parasitology}, volume = {163}, number = {}, pages = {16-23}, doi = {10.1016/j.exppara.2016.01.013}, pmid = {26821297}, issn = {1090-2449}, mesh = {Animals ; Bird Diseases/epidemiology/*parasitology ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Feces/parasitology ; Isospora/*classification/genetics/ultrastructure ; Isosporiasis/epidemiology/parasitology/*veterinary ; Mitochondria/enzymology ; Oocysts/ultrastructure ; Passeriformes/*parasitology ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Alignment ; Western Australia/epidemiology ; }, abstract = {A new Isospora (Apicomplexa:Eimeriidae) species is described from a single yellow-throated miner bird (Manorina flavigula) (subspecies M. f. wayensis) in Western Australia. Sporulated oocysts (n = 32) of this isolate are spherical to subspherical, 22.8 (20.3-23.8) × 18.3 (17.7-18.7) μm, with a shape index (length/width) of 1.25 (1.2-1.3); and a smooth and bilayered oocyst wall, 1.3 μm thick (outer layer 0.9 μm, inner 0.4 μm). A polar granule is present, but the micropyle and oocyst residuum are absent. The sporocysts are lemon-shaped, 15.5 (14.6-15.8) × 9.5 (9.5-10.2) μm, with a shape index of 1.6. Stieda and substieda bodies are present, the Stieda body being knob-like and the substieda body being subspherical-shaped. A sporocyst residuum is present and composed of numerous granules of different size scattered among the sporozoites, a spheroid or subspheroid refractile body is present in the sporozoite. Morphologically, the oocysts from this isolate are different from those of all known valid Isospora spp. Molecular analysis was conducted at 3 loci; the 18S and 28S ribosomal RNA and the mitochondrial cytochrome oxidase (COI) gene. At the 18S locus, this new isolate exhibited 99.2% similarity to Isospora gryphoni and three other Isospora spp. Further analysis of a subgroup of 300 bp long 18S sequences (8), including Isospora anthochaerae was conducted. This new isolate grouped in a clade with I. anthochaerae and exhibited 99.3% similarity. At the 28S locus, this new isolate grouped with I. anthochaerae with which it shared 99.1% similarity. At the COI locus, this new isolate exhibited 96.8% similarity to Isospora sp. JCI-2015 from a spectacled warbler (Sylvia conspicillata) in Spain. Further analysis from a subgroup of shorter COI sequences (n = 13) was performed and this new isolate exhibited 99.1% similarity to I. anthochaerae. Based on morphological and molecular data, this isolate is a new species of Isospora, which is named Isospora manorinae n. sp. after its host, the yellow-throated miner (Manorina flavigula wayensis).}, }
@article {pmid26812134, year = {2016}, author = {Alam, MM and Lal, S and FitzGerald, KE and Zhang, L}, title = {A holistic view of cancer bioenergetics: mitochondrial function and respiration play fundamental roles in the development and progression of diverse tumors.}, journal = {Clinical and translational medicine}, volume = {5}, number = {1}, pages = {3}, pmid = {26812134}, issn = {2001-1326}, abstract = {Since Otto Warburg made the first observation that tumor cells exhibit altered metabolism and bioenergetics in the 1920s, many scientists have tried to further the understanding of tumor bioenergetics. Particularly, in the past decade, the application of the state-of the-art metabolomics and genomics technologies has revealed the remarkable plasticity of tumor metabolism and bioenergetics. Firstly, a wide array of tumor cells have been shown to be able to use not only glucose, but also glutamine for generating cellular energy, reducing power, and metabolic building blocks for biosynthesis. Secondly, many types of cancer cells generate most of their cellular energy via mitochondrial respiration and oxidative phosphorylation. Glutamine is the preferred substrate for oxidative phosphorylation in tumor cells. Thirdly, tumor cells exhibit remarkable versatility in using bioenergetics substrates. Notably, tumor cells can use metabolic substrates donated by stromal cells for cellular energy generation via oxidative phosphorylation. Further, it has been shown that mitochondrial transfer is a critical mechanism for tumor cells with defective mitochondria to restore oxidative phosphorylation. The restoration is necessary for tumor cells to gain tumorigenic and metastatic potential. It is also worth noting that heme is essential for the biogenesis and proper functioning of mitochondrial respiratory chain complexes. Hence, it is not surprising that recent experimental data showed that heme flux and function are elevated in non-small cell lung cancer (NSCLC) cells and that elevated heme function promotes intensified oxygen consumption, thereby fueling tumor cell proliferation and function. Finally, emerging evidence increasingly suggests that clonal evolution and tumor genetic heterogeneity contribute to bioenergetic versatility of tumor cells, as well as tumor recurrence and drug resistance. Although mutations are found only in several metabolic enzymes in tumors, diverse mutations in signaling pathways and networks can cause changes in the expression and activity of metabolic enzymes, which likely enable tumor cells to gain their bioenergetic versatility. A better understanding of tumor bioenergetics should provide a more holistic approach to investigate cancer biology and therapeutics. This review therefore attempts to comprehensively consider and summarize the experimental data supporting our latest view of cancer bioenergetics.}, }
@article {pmid26812112, year = {2016}, author = {Subbarayan, S and Marimuthu, SK and Nachimuthu, SK and Zhang, W and Subramanian, S}, title = {Characterization and cytotoxic activity of apoptosis-inducing pierisin-5 protein from white cabbage butterfly.}, journal = {International journal of biological macromolecules}, volume = {87}, number = {}, pages = {16-27}, doi = {10.1016/j.ijbiomac.2016.01.072}, pmid = {26812112}, issn = {1879-0003}, mesh = {ADP Ribose Transferases/*genetics/isolation &amp; purification/*toxicity ; Animals ; Apoptosis/*drug effects ; Butterflies/*genetics/growth &amp; development ; Cell Cycle/drug effects ; Cell Proliferation/drug effects ; Conserved Sequence ; DNA Fragmentation/drug effects ; Evolution, Molecular ; Gene Dosage ; Gene Expression Regulation, Developmental ; HeLa Cells ; Hep G2 Cells ; Humans ; Insect Proteins/*genetics/isolation &amp; purification/*toxicity ; Mice ; Mitochondria/drug effects ; Rats ; Sequence Analysis ; }, abstract = {In this study, caspase-dependent apoptosis-inducing pierisin-5 gene was identified and characterized from cabbage white butterfly, Pieris canidia. A thousand-fold increase in expression of pierisin-5 gene was observed from second to third instar larvae, gradually decreasing before pupation. Pierisin-5 was purified from the fifth-instar larvae and was found to exhibit cytotoxicity against HeLa and HepG2 human cancer cell lines. Pierisin-5 showed growth inhibition and several morphological changes such as cell shrinkage, chromatin condensation and apoptotic body formation with programmed cell death in HeLa and HepG2 cells. Moreover, DNA fragmentation was observed after gel electrophoresis analysis. Caspase substrate assay showed further cleavage of Ac-DEVD-pNA, suggesting the activation of Caspase-3. Flow cytometry analysis revealed the cell cycle arrest at G1 phase and increased the percentage of apoptotic cells in cancer cell lines treated with pierisin-5. These findings suggest that pierisin-5 could significantly induce apoptosis in cancer cell lines and is mediated by activation of caspase-3 in the mitochondrial pathway. Phylogenetic analysis using pierisin proteins from Pierid butterflies, ADP-ribosylating toxins from bacteria, human, rat, and mouse indicated the possibility of horizontal transfer of pierisin genes from bacteria to butterflies. The single copy of pierisin gene unlike other insect toxin genes also supports lateral transfer.}, }
@article {pmid26811484, year = {2016}, author = {Lane, N and Martin, WF}, title = {Mitochondria, complexity, and evolutionary deficit spending.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {113}, number = {6}, pages = {E666}, pmid = {26811484}, issn = {1091-6490}, mesh = {Animals ; *Energy Metabolism ; Eukaryotic Cells/*cytology/*metabolism ; *Evolution, Molecular ; Genome/*genetics ; Humans ; *Models, Biological ; Prokaryotic Cells/*cytology/*metabolism ; }, }
@article {pmid26810560, year = {2016}, author = {Ma, L and Dong, WW and Jiang, GF and Wang, X}, title = {The Complete Mitochondrial Genome of Brachmia macroscopa (Lepidoptera: Gelechiidae) and Its Related Phylogenetic Analysis.}, journal = {Journal of insect science (Online)}, volume = {16}, number = {1}, pages = {}, pmid = {26810560}, issn = {1536-2442}, mesh = {Animals ; Genome, Insect/*genetics ; Mitochondria/*genetics ; Moths/*genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; }, abstract = {The sweet potato leaf folder, Brachmia macroscopa, is an important pest in China. The complete mitogenome, which consists of 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and an A + T-rich region, was sequenced and found to be 15,394 bp in length (GeneBank no. KT354968). The gene order and orientation of the B. macroscopa mitogenome were similar to those of other sequenced lepidopteran species. All of the PCGs started with ATN as the canonical start codon except for cox1, which started with CGA. In regard to stop codons, most PCGs stopped at TAA except for cox2, which stopped at TA, and nad4, which stopped at a single T. Thirteen PCGs of the available species (33 taxa) were used to demonstrate phylogenetic relationships. The ditrysian cluster was supported as a monophyletic clade at high levels by using maximum likelihood and Bayesian methods. The apoditrysian group, covering the Gelechioidea, formed a monophyletic clade with a bootstrap value of 88% and a posterior probability of 1.00. The superfamily Gelechioidea was supported as a monophyletic lineage by a posterior probability of 1.00.}, }
@article {pmid26809915, year = {2015}, author = {Esmaelizad, M and Zeinedin, H and Razmaraii, N and Mirjalili, A}, title = {Molecular Study of the G1 Haplotypes of Echinococcus granulosus from Iran Based on Cytochrome C Oxidase (Subunit 1) Sequence.}, journal = {Turkiye parazitolojii dergisi}, volume = {39}, number = {4}, pages = {286-290}, doi = {10.5152/tpd.2015.4292}, pmid = {26809915}, issn = {2146-3077}, mesh = {Animals ; Base Sequence ; Cytochromes c1/chemistry/*genetics ; DNA, Helminth/chemistry/isolation &amp; purification ; Echinococcosis, Hepatic/parasitology/*veterinary ; Echinococcus granulosus/*classification/genetics/isolation &amp; purification ; Electron Transport Complex IV/*genetics ; Genotype ; Genotyping Techniques ; Goat Diseases/*parasitology ; Goats ; Haplotypes ; Iran ; Mitochondria/enzymology ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Sequence Alignment ; Sheep ; Sheep Diseases/*parasitology ; }, abstract = {OBJECTIVE: In this study, we attempted to identify new Echinococcus granulosus isolates in the North West provinces of Iran based on the mitochondrial cytochrome c oxidase subunit 1 (CO1) sequence.<br><br>METHODS: Twenty-nine hydatid cysts from sheep and goats were collected. Genomic DNAs were extracted, and a partial sequence of the CO1 gene was amplified. Polymerase chain reaction products were cloned and sequenced with M13 primers in both directions.<br><br>RESULTS: All Iranian isolates were located in G1 and G3 genotypes. For the first time, a new G1 haplotype in two Iranian isolates were identified.<br><br>CONCLUSION: It seems that this new haplotype was transmitted from Jordan to Iran or vice versa.}, }
@article {pmid26809101, year = {2016}, author = {Shi, H and Dong, J and Irwin, DM and Zhang, S and Mao, X}, title = {Repetitive transpositions of mitochondrial DNA sequences to the nucleus during the radiation of horseshoe bats (Rhinolophus, Chiroptera).}, journal = {Gene}, volume = {581}, number = {2}, pages = {161-169}, doi = {10.1016/j.gene.2016.01.035}, pmid = {26809101}, issn = {1879-0038}, mesh = {Active Transport, Cell Nucleus ; Animals ; Cell Nucleus/*metabolism ; Chiroptera/*genetics ; DNA, Mitochondrial/*genetics/*metabolism ; Evolution, Molecular ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Transposition of mitochondrial DNA into the nucleus, which gives rise to nuclear mitochondrial DNAs (NUMTs), has been well documented in eukaryotes. However, very few studies have assessed the frequency of these transpositions during the evolutionary history of a specific taxonomic group. Here we used the horseshoe bats (Rhinolophus) as a case study to determine the frequency and relative timing of nuclear transfers of mitochondrial control region sequences. For this, phylogenetic and coalescent analyzes were performed on NUMTs and authentic mtDNA sequences generated from eight horseshoe bat species. Our results suggest at least three independent transpositions, including two ancient and one more recent, during the evolutionary history of Rhinolophus. The two ancient transpositions are represented by the NUMT-1 and -2 clades, with each clade consisting of NUMTs from almost all studied species but originating from different portions of the mtDNA genome. Furthermore, estimates of the most recent common ancestor for each clade corresponded to the time of the initial diversification of this genus. The recent transposition is represented by NUMT-3, which was discovered only in a specific subgroup of Rhinolophus and exhibited a close relationship to its mitochondrial counterpart. Our similarity searches of mtDNA in the R. ferrumequinum genome confirmed the presence of NUMT-1 and NUMT-2 clade sequences and, for the first time, assessed the extent of NUMTs in a bat genome. To our knowledge, this is the first study to report on the frequency of transpositions of mtDNA occurring before the common ancestry of a genus.}, }
@article {pmid26800442, year = {2016}, author = {Graham, NR and Fisher, BL and Girman, DJ}, title = {Phylogeography in Response to Reproductive Strategies and Ecogeographic Isolation in Ant Species on Madagascar: Genus Mystrium (Formicidae: Amblyoponinae).}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0146170}, pmid = {26800442}, issn = {1932-6203}, mesh = {Animals ; Ants/*classification/*genetics ; Base Sequence ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Ecosystem ; Genetic Variation/genetics ; Geography ; Madagascar ; Mitochondria/*genetics ; Phylogeography ; Reproduction ; Sequence Analysis, DNA ; *Social Isolation ; }, abstract = {The bulk of models used to understand the species diversification on Madagascar have been constructed using vertebrate taxa. It is not clear how these models affect less vagile species that may interact at a variety of spatial scales. Several studies on vertebrates have divided Madagascar into east-west bioclimatic regions, suggesting there is a fundamental division between eastern wet-adapted and western dry-adapted taxa. An alternative model of ecogeographic constraints shows a north-south division. We test whether the diversification in a small arthropod with variable degrees of dispersal conform to either model of ecogeographic constraints proposed for vertebrate taxa. We employ a molecular taxonomic dataset using ~2 kilobases nuDNA (Wg, LW Rh, Abd-A, 28s) and 790 basepairs mtDNA (CO1), along with geographic and habitat data, to examine the diversification patterns of the ant genus Mystrium Roger, 1862, (Subfamily Amblyoponinae) from Madagascar. The nuclear and mitochondrial phylogenies were both congruent with morphospecies as indicated in a recent revision of the genus. Species of Mystrium practice different colony reproductive strategies (winged queens vs non-winged queens). Alternate reproductive strategies led to inequalities in female dispersal ability among species, providing an additional layer for examination of the impacts of vagility on divergence, especially when measured using a maternally inherited locus. Mystrium species distribution patterns support these models of ecogeographic constraints. Reproductive strategy effected how Mystrium mtDNA lineages were associated with large-scale habitat distinctions and various topographical features. Furthermore, in some cases we find microgeographic population structure which appears to have been impacted by localized habitat differences (tsingy limestone formations, littoral forest) on a scale much smaller than that found in vertebrates. The current system offers a finer scale look at species diversification on the island, and helps achieve a more universal understanding of the generation of biodiversity on Madagascar.}, }
@article {pmid26800039, year = {2016}, author = {Kersten, B and Faivre Rampant, P and Mader, M and Le Paslier, MC and Bounon, R and Berard, A and Vettori, C and Schroeder, H and Leplé, JC and Fladung, M}, title = {Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding.}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0147209}, pmid = {26800039}, issn = {1932-6203}, mesh = {Chloroplasts/*genetics ; *Genome, Plant ; Mitochondria/*genetics ; Phylogeny ; *Plant Breeding ; Populus/classification/*genetics ; }, abstract = {Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organization of the chloroplast genomes of both Populus clones is described. A phylogenetic tree constructed from all available complete chloroplast DNA sequences of Populus was not congruent with the assignment of the related species to different Populus sections. In total, 3,024 variable nucleotide positions were identified among all compared Populus chloroplast DNA sequences. The 5-prime part of the LSC from trnH to atpA showed the highest frequency of variations. The variable positions included 163 positions with SNPs allowing for differentiating the two clones with P. tremula chloroplast genomes (W52, 717-1B4) from the other seven Populus individuals. These potential P. tremula-specific SNPs were displayed as a whole-plastome barcode on the P. tremula W52 chloroplast DNA sequence. Three of these SNPs and one InDel in the trnH-psbA linker were successfully validated by Sanger sequencing in an extended set of Populus individuals. The complete mitochondrial genome sequence of P. tremula is the first in the family of Salicaceae. The mitochondrial genomes of the two clones are 783,442 bp (W52) and 783,513 bp (717-1B4) in size, structurally very similar and organized as single circles. DNA sequence regions with high similarity to the W52 chloroplast sequence account for about 2% of the W52 mitochondrial genome. The mean SNP frequency was found to be nearly six fold higher in the chloroplast than in the mitochondrial genome when comparing 717-1B4 with W52. The availability of the genomic information of all three DNA-containing cell organelles will allow a holistic approach in poplar molecular breeding in the future.}, }
@article {pmid26794804, year = {2016}, author = {Nývltová, E and Smutná, T and Tachezy, J and Hrdý, I}, title = {OsmC and incomplete glycine decarboxylase complex mediate reductive detoxification of peroxides in hydrogenosomes of Trichomonas vaginalis.}, journal = {Molecular and biochemical parasitology}, volume = {206}, number = {1-2}, pages = {29-38}, doi = {10.1016/j.molbiopara.2016.01.006}, pmid = {26794804}, issn = {1872-9428}, mesh = {Amino Acid Sequence ; Axenic Culture ; Cloning, Molecular ; Escherichia coli/genetics/metabolism ; Gene Expression ; Glycine Decarboxylase Complex/genetics/*metabolism ; Hydrogen Peroxide/*metabolism ; Kinetics ; Metabolic Detoxication, Phase I/genetics ; Mitochondria/*metabolism/ultrastructure ; Oxidation-Reduction ; Peroxidases/genetics/*metabolism ; Phylogeny ; Protein Binding ; Protozoan Proteins/genetics/*metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/genetics/*metabolism/ultrastructure ; }, abstract = {Osmotically inducible protein (OsmC) and organic hydroperoxide resistance protein (Ohr) are small, thiol-dependent peroxidases that comprise a family of prokaryotic protective proteins central to the defense against deleterious effects of organic hydroperoxides, which are reactive molecules that are formed during interactions between the host immune system and pathogens. Trichomonas vaginalis, a sexually transmitted parasite of humans, possesses OsmC homologues in its hydrogenosomes, anaerobic mitochondrial organelles that harbor enzymes and pathways that are sensitive to oxidative damage. The glycine decarboxylase complex (GDC), which consists of four proteins (i.e., L, H, P and T), is in eukaryotes exclusively mitochondrial enzymatic system that catalyzes oxidative decarboxylation and deamination of glycine. However, trichomonad hydrogenosomes contain only the L and H proteins, whose physiological functions are unknown. Here, we found that the hydrogenosomal L and H proteins constitute a lipoate-dependent redox system that delivers electrons from reduced nicotinamide adenine dinucleotide (NADH) to OsmC for the reductive detoxification of peroxides. Our searches of genome databases revealed that, in addition to prokaryotes, homologues of OsmC/Ohr family proteins with predicted mitochondrial localization are present in various eukaryotic lineages. Therefore, we propose that the novel OsmC-GDC-based redox system may not be limited to T. vaginalis.}, }
@article {pmid26792249, year = {2016}, author = {Santos, HJ and Imai, K and Hanadate, Y and Fukasawa, Y and Oda, T and Mi-Ichi, F and Nozaki, T}, title = {Screening and discovery of lineage-specific mitosomal membrane proteins in Entamoeba histolytica.}, journal = {Molecular and biochemical parasitology}, volume = {209}, number = {1-2}, pages = {10-17}, doi = {10.1016/j.molbiopara.2016.01.001}, pmid = {26792249}, issn = {1872-9428}, mesh = {Amino Acid Sequence ; Biological Evolution ; Datasets as Topic ; Entamoeba histolytica/*metabolism ; Humans ; Membrane Proteins/chemistry/*metabolism ; Mitochondria/metabolism ; Mitochondrial Membranes/chemistry/*metabolism ; Protein Transport ; Protozoan Proteins/chemistry/*metabolism ; }, abstract = {Entamoeba histolytica, an anaerobic intestinal parasite causing dysentery and extra-intestinal abscesses in humans, possesses highly reduced and divergent mitochondrion-related organelles (MROs) called mitosomes. This organelle lacks many features associated with canonical aerobic mitochondria and even other MROs such as hydrogenosomes. The Entamoeba mitosome has been found to have a compartmentalized sulfate activation pathway, which was recently implicated to have a role in amebic stage conversion. It also features a unique shuttle system via Tom60, which delivers proteins from the cytosol to the mitosome. In addition, only Entamoeba mitosomes possess a novel subclass of β-barrel outer membrane protein called MBOMP30. With the discoveries of such unique features of mitosomes of Entamoeba, there still remain a number of significant unanswered issues pertaining to this organelle. Particularly, the present understanding of the inner mitosomal membrane of Entamoeba is extremely limited. So far, only a few homologs for transporters of various substrates have been confirmed, while the components of the protein translocation complexes appear to be absent or are yet to be discovered. Employing a similar strategy as in our previous work, we collaborated to screen and discover mitosomal membrane proteins. Using a specialized prediction pipeline, we searched for proteins possessing α-helical transmembrane domains, which are unique to E. histolytica mitosomes. From the prediction algorithm, 25 proteins emerged as candidates, two of which were initially observed to be localized to the mitosomes. Further screening and analysis of the predicted proteins may provide clues to answer key questions on mitosomal evolution, biogenesis, dynamics, and biochemical processes.}, }
@article {pmid26792248, year = {2016}, author = {Bae, YA and Kim, JG and Kong, Y}, title = {Phylogenetic characterization of Clonorchis sinensis proteins homologous to the sigma-class glutathione transferase and their differential expression profiles.}, journal = {Molecular and biochemical parasitology}, volume = {206}, number = {1-2}, pages = {46-55}, doi = {10.1016/j.molbiopara.2016.01.002}, pmid = {26792248}, issn = {1872-9428}, mesh = {Amino Acid Sequence ; Animals ; Clonorchis sinensis/classification/drug effects/enzymology/*genetics ; Cytosol/drug effects/enzymology ; Eicosanoids/metabolism ; Evolution, Molecular ; Gene Expression Regulation ; *Genome, Protozoan ; Glutathione/metabolism ; Glutathione Transferase/*genetics/metabolism ; Helminth Proteins/*genetics/metabolism ; Hydrogen Peroxide/pharmacology ; Intramolecular Oxidoreductases/*genetics/metabolism ; Isoenzymes/genetics/metabolism ; Lipocalins/*genetics/metabolism ; Microsomes/drug effects/enzymology ; Mitochondria/drug effects/enzymology ; Oxidation-Reduction ; Oxidative Stress ; *Phylogeny ; Piperonyl Butoxide/pharmacology ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Glutathione transferase (GST) is one of the major antioxidant proteins with diverse supplemental activities including peroxidase, isomerase, and thiol transferase. GSTs are classified into multiple classes on the basis of their primary structures and substrate/inhibitor specificity. However, the evolutionary routes and physiological environments specific to each of the closely related bioactive enzymes remain elusive. The sigma-like GSTs exhibit amino acid conservation patterns similar to the prostaglandin D synthases (PGDSs). In this study, we analyzed the phylogenetic position of the GSTs of the biocarcinogenic liver fluke, Clonorchis sinensis. We also observed induction profile of the GSTs in association with the parasite's maturation and in response to exogenous oxidative stresses, with special attention to sigma-class GSTs and PGDSs. The C. sinensis genome encoded 12 GST protein species, which were separately assigned to cytosolic (two omega-, one zeta-, two mu-, and five sigma-class), mitochondrial (one kappa-class), and microsomal (one membrane-associated proteins in eicosanoid and glutathione metabolism-like protein) GST families. Multiple sigma GST (or PGDS) orthologs were also detected in Opisthorchis viverrini. Other trematode species possessed only a single sigma-like GST gene. A phylogenetic analysis demonstrated that one of the sigma GST lineages duplicated in the common ancestor of trematodes were specifically expanded in the opisthorchiids, but deleted in other trematodes. The induction profiles of these sigma GST genes along with the development and aging of C. sinensis, and against various exogenous chemical stimuli strongly suggest that the paralogous sigma GST genes might be undergone specialized evolution to cope with the diverse hostile biochemical environments within the mammalian hepatobiliary ductal system.}, }
@article {pmid26789594, year = {2016}, author = {Ott, M and Amunts, A and Brown, A}, title = {Organization and Regulation of Mitochondrial Protein Synthesis.}, journal = {Annual review of biochemistry}, volume = {85}, number = {}, pages = {77-101}, doi = {10.1146/annurev-biochem-060815-014334}, pmid = {26789594}, issn = {1545-4509}, support = {MC_U105184332/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/*genetics/metabolism ; Gene Expression Regulation ; *Genome, Mitochondrial ; Humans ; Mitochondria/*genetics/metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/*genetics/metabolism ; Mitochondrial Ribosomes/chemistry/metabolism ; Models, Molecular ; Organelle Biogenesis ; Oxidative Phosphorylation ; *Protein Biosynthesis ; Signal Transduction ; }, abstract = {Mitochondria are essential organelles of endosymbiotic origin that are responsible for oxidative phosphorylation within eukaryotic cells. Independent evolution between species has generated mitochondrial genomes that are extremely diverse, with the composition of the vestigial genome determining their translational requirements. Typically, translation within mitochondria is restricted to a few key subunits of the oxidative phosphorylation complexes that are synthesized by dedicated ribosomes (mitoribosomes). The dramatically rearranged mitochondrial genomes, the limited set of transcripts, and the need for the synthesized proteins to coassemble with nuclear-encoded subunits have had substantial consequences for the translation machinery. Recent high-resolution cryo-electron microscopy has revealed the effect of coevolution on the mitoribosome with the mitochondrial genome. In this review, we place the new structural information in the context of the molecular mechanisms of mitochondrial translation and focus on the novel ways protein synthesis is organized and regulated in mitochondria.}, }
@article {pmid26787157, year = {2016}, author = {Teves, SC and Gardim, S and Carbajal de la Fuente, AL and Lopes, CM and Gonçalves, TC and dos Santos Mallet, JR and da Rosa, JA and Almeida, CE}, title = {Mitochondrial Genes Reveal Triatoma jatai as a Sister Species to Triatoma costalimai (Reduviidae: Triatominae).}, journal = {The American journal of tropical medicine and hygiene}, volume = {94}, number = {3}, pages = {686-688}, pmid = {26787157}, issn = {1476-1645}, mesh = {Animals ; Bayes Theorem ; Genetic Speciation ; Mitochondria/*genetics ; Phylogeny ; Species Specificity ; Triatoma/*genetics ; }, abstract = {Triatoma jatai was described using a set of morphological structures from specimens collected in Paranã municipality of Tocantins State, Brazil. Under a Bayesian framework and using two mitochondrial genes (16S and COI), phylogenetic analysis recovered T. jatai as a sister species to Triatoma costalimai with higher genetic distances than between other well-recognized species. Our results agree with previous suggestions based on morphometric analysis. In the light of the non-monophyly of Matogrossensis subcomplex, the inclusion of T. jatai shall be considered for reevaluating this group.}, }
@article {pmid26782414, year = {2015}, author = {Yin, SL and Lan, C and Pei, H and Zhu, ZQ}, title = {Mitochondrial transfer RNA mutations and hypertension.}, journal = {Genetics and molecular research : GMR}, volume = {14}, number = {4}, pages = {17692-17698}, doi = {10.4238/2015.December.21.42}, pmid = {26782414}, issn = {1676-5680}, mesh = {DNA, Mitochondrial/*genetics ; Humans ; Hypertension/*genetics/pathology ; Mitochondria/genetics ; Mutation ; *Phylogeny ; Polymorphism, Genetic ; RNA, Transfer/*genetics ; }, abstract = {Mutations in mitochondrial DNA have been found to be associated with hypertension. Of these, mitochondrial transfer RNA (mt-tRNA) is a hot spot for these pathogenic mutations. It is generally believed that these mutations may result in the failure of mt-tRNA metabolism, thereby worsening mitochondrial dysfunction and resulting in hypertension. mt-tRNA is known for its high frequency of polymorphisms and mutations, and the number of reports regarding mt-tRNA mutations and hypertension is increasing significantly. To better understand the molecular basis of maternally inherited hypertension, we reassessed the link between four mt-tRNA mutations (G15927A in tRNA(Thr), C7492T in tRNA(Ser(UCN)), A4386G in tRNA(Gln), and C14686T in tRNA(Glu)) and hypertension. We first used the phylogenetic approach to investigate the deleterious roles of these mutations, then we used RNA Fold Web Server to predict the minimum free energy of these mt-tRNAs with and without mutations. Using the pathogenicity scoring system, we found that the G15927A and C7492T mutations are classified as pathogenic while all other studied mutations are neutral polymorphisms. Our study provides valuable information for the detection of pathogenic mt-tRNA mutations in hypertension.}, }
@article {pmid26781919, year = {2016}, author = {Quesada, V}, title = {The roles of mitochondrial transcription termination factors (MTERFs) in plants.}, journal = {Physiologia plantarum}, volume = {157}, number = {3}, pages = {389-399}, doi = {10.1111/ppl.12416}, pmid = {26781919}, issn = {1399-3054}, mesh = {Cell Nucleus/metabolism ; Chloroplast Proteins/genetics/*metabolism ; Chloroplasts/metabolism ; Gene Expression Regulation, Plant ; Genome, Plant/*genetics ; Mitochondria/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Mutation ; Phenotype ; Plant Proteins/genetics/metabolism ; Plants/genetics/*metabolism ; Stress, Physiological ; Transcription Termination, Genetic ; }, abstract = {Stress such as salinity, cold, heat or drought affect plant growth and development, and frequently result in diminished productivity. Unlike animals, plants are sedentary organisms that must withstand and cope with environmental stresses. During evolution, plants have developed strategies to successfully adapt to or tolerate such stresses, which might have led to the expansion and functional diversification of gene families. Some new genes may have acquired functions that could differ from those of their animal homologues, e.g. in response to abiotic stress. The mitochondrial transcription termination factor (MTERF) family could be a good example of this. Originally identified and characterized in metazoans, MTERFs regulate transcription, translation and DNA replication in vertebrate mitochondria. Plant genomes harbor a considerably larger number of MTERFs than animals. Nonetheless, only eight plant MTERFs have been characterized, which encode chloroplast or mitochondrial proteins. Mutations in MTERFs alter the expression of organelle genes and impair chloroplast or mitochondria development. This information is transmitted to the nucleus, probably through retrograde signaling, because mterf plants often exhibit changes in nuclear gene expression. This study summarizes the recent findings, mainly from the analysis of mterf mutants, which support an emerging role for plant MTERFs in response to abiotic stress.}, }
@article {pmid26776396, year = {2016}, author = {Patra, AK and Kwon, YM and Kang, SG and Fujiwara, Y and Kim, SJ}, title = {The complete mitochondrial genome sequence of the tubeworm Lamellibrachia satsuma and structural conservation in the mitochondrial genome control regions of Order Sabellida.}, journal = {Marine genomics}, volume = {26}, number = {}, pages = {63-71}, doi = {10.1016/j.margen.2015.12.010}, pmid = {26776396}, issn = {1876-7478}, mesh = {Animals ; Base Sequence ; Codon ; DNA/genetics ; Gene Expression Regulation/*physiology ; Genome, Mitochondrial/*genetics ; Phylogeny ; Polychaeta/classification/*genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {The control region of the mitochondrial genomes shows high variation in conserved sequence organizations, which follow distinct evolutionary patterns in different species or taxa. In this study, we sequenced the complete mitochondrial genome of Lamellibrachia satsuma from the cold-seep region of Kagoshima Bay, as a part of whole genome study and extensively studied the structural features and patterns of the control region sequences. We obtained 15,037 bp of mitochondrial genome using Illumina sequencing and identified the non-coding AT-rich region or control region (354 bp, AT=83.9%) located between trnH and trnR. We found 7 conserved sequence blocks (CSB), scattered throughout the control region of L. satsuma and other taxa of Annelida. The poly-TA stretches, which commonly form the stem of multiple stem-loop structures, are most conserved in the CSB-I and CSB-II regions. The mitochondrial genome of L. satsuma encodes a unique repetitive sequence in the control region, which forms a unique secondary structure in comparison to Lamellibrachia luymesi. Phylogenetic analyses of all protein-coding genes indicate that L. satsuma forms a monophyletic clade with L. luymesi along with other tubeworms found in cold-seep regions (genera: Lamellibrachia, Escarpia, and Seepiophila). In general, the control region sequences of Annelida could be aligned with certainty within each genus, and to some extent within the family, but with a higher rate of variation in conserved regions.}, }
@article {pmid26771520, year = {2016}, author = {Ray, S and Kassan, A and Busija, AR and Rangamani, P and Patel, HH}, title = {The plasma membrane as a capacitor for energy and metabolism.}, journal = {American journal of physiology. Cell physiology}, volume = {310}, number = {3}, pages = {C181-92}, pmid = {26771520}, issn = {1522-1563}, support = {HL-091071/HL/NHLBI NIH HHS/United States ; HL-107200/HL/NHLBI NIH HHS/United States ; P01 HL066941/HL/NHLBI NIH HHS/United States ; T32 GM007752/GM/NIGMS NIH HHS/United States ; I01 BX001963/BX/BLRD VA/United States ; HL-066941/HL/NHLBI NIH HHS/United States ; R01 HL091071/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Cell Membrane/*metabolism ; Elasticity ; *Electric Capacitance ; *Energy Metabolism ; Humans ; Membrane Fluidity ; Membrane Lipids/metabolism ; Membrane Microdomains/metabolism ; Membrane Proteins/metabolism ; Models, Biological ; Oxidation-Reduction ; Oxygen/metabolism ; Signal Transduction ; }, abstract = {When considering which components of the cell are the most critical to function and physiology, we naturally focus on the nucleus, the mitochondria that regulate energy and apoptotic signaling, or other organelles such as the endoplasmic reticulum, Golgi, ribosomes, etc. Few people will suggest that the membrane is the most critical element of a cell in terms of function and physiology. Those that consider the membrane critical will point to its obvious barrier function regulated by the lipid bilayer and numerous ion channels that regulate homeostatic gradients. What becomes evident upon closer inspection is that not all membranes are created equal and that there are lipid-rich microdomains that serve as platforms of signaling and a means of communication with the intracellular environment. In this review, we explore the evolution of membranes, focus on lipid-rich microdomains, and advance the novel concept that membranes serve as "capacitors for energy and metabolism." Within this framework, the membrane then is the primary and critical regulator of stress and disease adaptation of the cell.}, }
@article {pmid26759362, year = {2016}, author = {Warren, JM and Simmons, MP and Wu, Z and Sloan, DB}, title = {Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes.}, journal = {Genome biology and evolution}, volume = {8}, number = {2}, pages = {364-374}, pmid = {26759362}, issn = {1759-6653}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Genome, Plant ; Magnoliopsida/classification/*genetics ; Mutagenesis, Insertional ; Mutation Rate ; Plasmids/*genetics ; }, abstract = {The mitochondrial genomes of flowering plants experience frequent insertions of foreign sequences, including linear plasmids that also exist in standalone forms within mitochondria, but the history and phylogenetic distribution of plasmid insertions is not well known. Taking advantage of the increased availability of plant mitochondrial genome sequences, we performed phylogenetic analyses to reconstruct the evolutionary history of these plasmids and plasmid-derived insertions. Mitochondrial genomes from multiple land plant lineages (including liverworts, lycophytes, ferns, and gymnosperms) include fragmented remnants from ancient plasmid insertions. Such insertions are much more recent and widespread in angiosperms, in which approximately 75% of sequenced mitochondrial genomes contain identifiable plasmid insertions. Although conflicts between plasmid and angiosperm phylogenies provide clear evidence of repeated horizontal transfers, we were still able to detect significant phylogenetic concordance, indicating that mitochondrial plasmids have also experienced sustained periods of (effectively) vertical transmission in angiosperms. The observed levels of sequence divergence in plasmid-derived genes suggest that nucleotide substitution rates in these plasmids, which often encode their own viral-like DNA polymerases, are orders of magnitude higher than in mitochondrial chromosomes. Based on these results, we hypothesize that the periodic incorporation of mitochondrial genes into plasmids contributes to the remarkable heterogeneity in substitution rates among genes that has recently been discovered in some angiosperm mitochondrial genomes. In support of this hypothesis, we show that the recently acquired ψtrnP-trnW gene region in a maize linear plasmid is evolving significantly faster than homologous sequences that have been retained in the mitochondrial chromosome in closely related grasses.}, }
@article {pmid26756186, year = {2015}, author = {Yurkiv, B and Wasser, SP and Nevo, E and Sybirna, NO}, title = {Antioxidant Effects of Medicinal Mushrooms Agaricus brasiliensis and Ganoderma lucidum (Higher Basidiomycetes): Evidence from Animal Studies.}, journal = {International journal of medicinal mushrooms}, volume = {17}, number = {10}, pages = {943-955}, doi = {10.1615/intjmedmushrooms.v17.i10.40}, pmid = {26756186}, issn = {1940-4344}, mesh = {*Agaricus ; Animals ; Antioxidants/*pharmacology ; Catalase/metabolism ; Diabetes Mellitus, Experimental/therapy ; Glutathione Reductase/metabolism ; Glycoproteins/metabolism ; Leukocytes/enzymology ; Lipid Peroxidation ; Male ; Oxidative Stress ; Rats ; Rats, Wistar ; *Reishi ; Superoxide Dismutase/metabolism ; Thiobarbituric Acid Reactive Substances/metabolism ; }, abstract = {With diabetes mellitus and increased glucose concentrations, the mitochondria electron transport chain is disrupted, superoxide anions are overproduced, and oxidative stress develops in cells. Thus, preventing oxidative stress can produce a decrease in the antioxidant system activity and an increase in apoptosis in immune cells. The application of medicinal mushrooms is a new possible approach to diabetes mellitus treatment. Therefore, the aim of this work was to investigate the influence of administration of the medicinal mushrooms Agaricus brasiliensis and Ganoderma lucidum on antioxidant enzyme activity in rat leukocytes. Wistar outbred white rats were used in the study. Streptozotocin was intraperitoneally injected once at a dose of 50 mg/kg body weight. Mushroom preparations were orally administered at a dose of 1 g/kg/day for 2 weeks. This revealed that in diabetes mellitus, the level of antioxidant enzyme activity is significantly decreased compared with control values, whereas the levels of lipid peroxidation is increased; this manifested in an increase in the amount of thiobarbituric acid reactive substances (TBARS). The medicinal mushrooms' administration is accompanied by an increase in antioxidant enzyme activity to control values and is even higher in the case of A. brasiliensis administration when compared with the diabetic group. As for the indicators of lipid peroxidation under mushroom administration of A. brasiliensis and G. lucidum, we observed a significant decrease of TBARS levels compared with the diabetic group. Increased activity of antioxidant enzymes and reduction of TBARS level indicate pronounced antioxidant properties of studied mushrooms.}, }
@article {pmid26754561, year = {2016}, author = {Osuda, Y and Shinzawa-Itoh, K and Tani, K and Maeda, S and Yoshikawa, S and Tsukihara, T and Gerle, C}, title = {Two-dimensional crystallization of monomeric bovine cytochrome c oxidase with bound cytochrome c in reconstituted lipid membranes.}, journal = {Microscopy (Oxford, England)}, volume = {65}, number = {3}, pages = {263-267}, pmid = {26754561}, issn = {2050-5701}, mesh = {Animals ; Cattle ; Crystallization ; Crystallography, X-Ray ; Cytochromes c/*chemistry ; Electron Transport Complex IV/*chemistry ; Membrane Proteins/*metabolism ; Mitochondria/metabolism ; Mitochondrial Membranes/*metabolism ; }, abstract = {Mitochondrial cytochrome c oxidase utilizes electrons provided by cytochrome c for the active vectorial transport of protons across the inner mitochondrial membrane through the reduction of molecular oxygen to water. Direct structural evidence on the transient cytochrome c oxidase-cytochrome c complex thus far, however, remains elusive and its physiological relevant oligomeric form is unclear. Here, we report on the 2D crystallization of monomeric bovine cytochrome c oxidase with tightly bound cytochrome c at a molar ratio of 1:1 in reconstituted lipid membranes at the basic pH of 8.5 and low ionic strength.}, }
@article {pmid26752183, year = {2016}, author = {Mallela, SK and Almeida, R and Ejsing, CS and Conzelmann, A}, title = {Functions of Ceramide Synthase Paralogs YPR114w and YJR116w of Saccharomyces cerevisiae.}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0145831}, pmid = {26752183}, issn = {1932-6203}, mesh = {Acetylcysteine/pharmacology ; Alkaline Ceramidase/genetics/metabolism ; Amidohydrolases/genetics/metabolism ; Antifungal Agents/pharmacology ; Antioxidants/pharmacology ; Cations, Divalent ; Ceramides/*biosynthesis ; Copper/toxicity ; Fatty Acids, Monounsaturated/pharmacology ; Gene Deletion ; *Gene Expression Regulation, Fungal ; Membrane Proteins/genetics/metabolism ; Mitochondria/metabolism ; Oxidoreductases/genetics/metabolism ; Oxygen/pharmacology ; Phylogeny ; Reactive Oxygen Species/metabolism ; Saccharomyces cerevisiae/classification/drug effects/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; Vacuoles/metabolism ; }, abstract = {Ceramide is synthesized in yeast by two redundant acyl-CoA dependent synthases, Lag1 and Lac1. In lag1∆ lac1∆ cells, free fatty acids and sphingoid bases are elevated, and ceramides are produced through the redundant alkaline ceramidases Ypc1 and Ydc1, working backwards. Even with all four of these genes deleted, cells are surviving and continue to contain small amounts of complex sphingolipids. Here we show that these residual sphingolipids are not synthesized by YPR114w or YJR116w, proteins of unknown function showing a high degree of homology to Lag1 and Lac1. Indeed, the hextuple lag1∆ lac1∆ ypc1∆ ydc1∆ ypr114w∆ yjr116w∆ mutant still contains ceramides and complex sphingolipids. Yjr116w∆ exhibit an oxygen-dependent hypersensitivity to Cu2+ due to an increased mitochondrial production of reactive oxygen species (ROS) and a mitochondrially orchestrated programmed cell death in presence of copper, but also a general copper hypersensitivity that cannot be counteracted by the antioxidant N-acetyl-cysteine (NAC). Myriocin efficiently represses the synthesis of sphingoid bases of ypr114w∆, but not its growth. Both yjr116w∆ and ypr114w∆ have fragmented vacuoles and produce less ROS than wild type, before and after diauxic shift. Ypr114w∆/ypr114w∆ have an increased chronological life span. Thus, Yjr116w and Ypr114w are related, but not functionally redundant.}, }
@article {pmid26751688, year = {2016}, author = {Wang, J and Lu, B and Zan, R and Chai, J and Ma, W and Jin, W and Duan, R and Luo, J and Murphy, RW and Xiao, H and Chen, Z}, title = {Phylogenetic Relationships of Five Asian Schilbid Genera Including Clupisoma (Siluriformes: Schilbeidae).}, journal = {PloS one}, volume = {11}, number = {1}, pages = {e0145675}, pmid = {26751688}, issn = {1932-6203}, mesh = {Animals ; Catfishes/classification/*genetics ; Cell Nucleus/chemistry ; Cytochromes b/genetics ; Electron Transport Complex IV/*genetics ; Fish Proteins/*genetics ; Homeodomain Proteins/genetics ; Mitochondria/chemistry ; Mitochondrial Proteins/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {The phylogenetic relationships of Asian schilbid catfishes of the genera Clupisoma, Ailia, Horabagrus, Laides and Pseudeutropius are poorly understood, especially those of Clupisoma. Herein, we reconstruct the phylogeny of 38 species of catfishes belonging to 28 genera and 14 families using the concatenated mitochondrial genes COI, cytb, and 16S rRNA, as well as the nuclear genes RAG1 and RAG2. The resulting phylogenetic trees consistently place Clupisoma as the sister taxon of Laides, and the five representative Asian schilbid genera form two monophyletic groups with the relationships (Ailia (Laides, Clupisoma)) and (Horabagrus, Pseudeutropius). The so-called "Big Asia" lineage relates distantly to African schilbids. Independent analyses of the mitochondrial and nuclear DNA data yield differing trees for the two Asian schilbid groups. Analyses of the mitochondrial gene data support a sister-group relationship for (Ailia (Laides, Clupisoma)) and the Sisoroidea and a sister-taxon association of (Horabagrus, Pseudeutropius) and the Bagridae. In contrast, analyses of the combined nuclear data indicate (Ailia (Laides, Clupisoma)) to be the sister group to (Horabagrus, Pseudeutropius). Our results indicate that the Horabagridae, recognized by some authors as consisting of Horabagrus, Pseudeutropius and Clupisoma does not include the latter genus. We formally erect a new family, Ailiidae fam. nov. for a monophyletic Asian group comprised of the genera Ailia, Laides and Clupisoma.}, }
@article {pmid26739881, year = {2016}, author = {Rollins, LA and Woolnough, AP and Fanson, BG and Cummins, ML and Crowley, TM and Wilton, AN and Sinclair, R and Butler, A and Sherwin, WB}, title = {Selection on Mitochondrial Variants Occurs between and within Individuals in an Expanding Invasion.}, journal = {Molecular biology and evolution}, volume = {33}, number = {4}, pages = {995-1007}, doi = {10.1093/molbev/msv343}, pmid = {26739881}, issn = {1537-1719}, mesh = {Animals ; Birds/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genetic Variation ; Genome, Mitochondrial/*genetics ; Genotype ; Introduced Species ; Mitochondria/genetics ; Mutation ; Selection, Genetic/*genetics ; }, abstract = {Mitochondria are critical for life, yet their underlying evolutionary biology is poorly understood. In particular, little is known about interaction between two levels of evolution: between individuals and within individuals (competition between cells, mitochondria or mitochondrial DNA molecules). Rapid evolution is suspected to occur frequently in mitochondrial DNA, whose maternal inheritance predisposes advantageous mutations to sweep rapidly though populations. Rapid evolution is also predicted in response to changed selection regimes after species invasion or removal of pathogens or competitors. Here, using empirical and simulated data from a model invasive bird species, we provide the first demonstration of rapid selection on the mitochondrial genome within individuals in the wild. Further, we show differences in mitochondrial DNA copy number associated with competing genetic variants, which may provide a mechanism for selection. We provide evidence for three rarely documented phenomena: selection associated with mitochondrial DNA abundance, selection on the mitochondrial control region, and contemporary selection during invasion.}, }
@article {pmid26734886, year = {2016}, author = {Enríquez, JA}, title = {Supramolecular Organization of Respiratory Complexes.}, journal = {Annual review of physiology}, volume = {78}, number = {}, pages = {533-561}, doi = {10.1146/annurev-physiol-021115-105031}, pmid = {26734886}, issn = {1545-1585}, mesh = {Animals ; Electron Transport/*physiology ; Electron-Transferring Flavoproteins/*metabolism ; Humans ; Mitochondria/metabolism/physiology ; Mitochondrial Membranes/metabolism/physiology ; }, abstract = {Since the discovery of the existence of superassemblies between mitochondrial respiratory complexes, such superassemblies have been the object of a passionate debate. It is accepted that respiratory supercomplexes are structures that occur in vivo, although which superstructures are naturally occurring and what could be their functional role remain open questions. The main difficulty is to make compatible the existence of superassemblies with the corpus of data that drove the field to abandon the early understanding of the physical arrangement of the mitochondrial respiratory chain as a compact physical entity (the solid model). This review provides a nonexhaustive overview of the evolution of our understanding of the structural organization of the electron transport chain from the original idea of a compact organization to a view of freely moving complexes connected by electron carriers. Today supercomplexes are viewed not as a revival of the old solid model but rather as a refined revision of the fluid model, which incorporates a new layer of structural and functional complexity.}, }
@article {pmid26732015, year = {2016}, author = {Immonen, E and Collet, M and Goenaga, J and Arnqvist, G}, title = {Direct and indirect genetic effects of sex-specific mitonuclear epistasis on reproductive ageing.}, journal = {Heredity}, volume = {116}, number = {3}, pages = {338-347}, pmid = {26732015}, issn = {1365-2540}, support = {294333/ERC_/European Research Council/International ; }, mesh = {*Aging ; Animals ; Biological Evolution ; Cell Nucleus/genetics ; Coleoptera/*genetics ; DNA, Mitochondrial/genetics ; *Epistasis, Genetic ; Female ; Fertility ; Genotype ; Haplotypes ; Linear Models ; Longevity/genetics ; Male ; Mitochondria/genetics ; Models, Genetic ; Reproduction ; *Sex Characteristics ; }, abstract = {Mitochondria are involved in ageing and their function requires coordinated action of both mitochondrial and nuclear genes. Epistasis between the two genomes can influence lifespan but whether this also holds for reproductive senescence is unclear. Maternal inheritance of mitochondria predicts sex differences in the efficacy of selection on mitonuclear genotypes that should result in differences between females and males in mitochondrial genetic effects. Mitonuclear genotype of a focal individual may also indirectly affect trait expression in the mating partner. We tested these predictions in the seed beetle Callosobruchus maculatus, using introgression lines harbouring distinct mitonuclear genotypes. Our results reveal both direct and indirect sex-specific effects of mitonuclear epistasis on reproductive ageing. Females harbouring coadapted mitonuclear genotypes showed higher lifetime fecundity due to slower senescence relative to novel mitonuclear combinations. We found no evidence for mitonuclear coadaptation in males. Mitonuclear epistasis not only affected age-specific ejaculate weight, but also influenced male age-dependent indirect effects on traits expressed by their female partners (fecundity, egg size, longevity). These results demonstrate important consequences of sex-specific mitonuclear epistasis for both mating partners, consistent with a role for mitonuclear genetic constraints upon sex-specific adaptive evolution.}, }
@article {pmid26728607, year = {2016}, author = {Wolff, JN and Pichaud, N and Camus, MF and Côté, G and Blier, PU and Dowling, DK}, title = {Evolutionary implications of mitochondrial genetic variation: mitochondrial genetic effects on OXPHOS respiration and mitochondrial quantity change with age and sex in fruit flies.}, journal = {Journal of evolutionary biology}, volume = {29}, number = {4}, pages = {736-747}, doi = {10.1111/jeb.12822}, pmid = {26728607}, issn = {1420-9101}, mesh = {Aging/*genetics ; Animals ; *Biological Evolution ; Drosophila/*genetics ; Female ; Genes, Mitochondrial/*genetics ; *Genetic Variation ; Male ; Mitochondria/genetics ; *Oxidative Phosphorylation ; Sex Factors ; }, abstract = {The ancient acquisition of the mitochondrion into the ancestor of modern-day eukaryotes is thought to have been pivotal in facilitating the evolution of complex life. Mitochondria retain their own diminutive genome, with mitochondrial genes encoding core subunits involved in oxidative phosphorylation. Traditionally, it was assumed that there was little scope for genetic variation to accumulate and be maintained within the mitochondrial genome. However, in the past decade, mitochondrial genetic variation has been routinely tied to the expression of life-history traits such as fertility, development and longevity. To examine whether these broad-scale effects on life-history trait expression might ultimately find their root in mitochondrially mediated effects on core bioenergetic function, we measured the effects of genetic variation across twelve different mitochondrial haplotypes on respiratory capacity and mitochondrial quantity in the fruit fly, Drosophila melanogaster. We used strains of flies that differed only in their mitochondrial haplotype, and tested each sex separately at two different adult ages. Mitochondrial haplotypes affected both respiratory capacity and mitochondrial quantity. However, these effects were highly context-dependent, with the genetic effects contingent on both the sex and the age of the flies. These sex- and age-specific genetic effects are likely to resonate across the entire organismal life-history, providing insights into how mitochondrial genetic variation may contribute to sex-specific trajectories of life-history evolution.}, }
@article {pmid26725199, year = {2016}, author = {Lavrov, DV and Adamski, M and Chevaldonné, P and Adamska, M}, title = {Extensive Mitochondrial mRNA Editing and Unusual Mitochondrial Genome Organization in Calcaronean Sponges.}, journal = {Current biology : CB}, volume = {26}, number = {1}, pages = {86-92}, doi = {10.1016/j.cub.2015.11.043}, pmid = {26725199}, issn = {1879-0445}, mesh = {Animals ; Base Sequence ; Biological Evolution ; DNA, Mitochondrial/*genetics/metabolism ; Genome, Mitochondrial ; Mitochondria/*genetics/*metabolism ; Molecular Sequence Data ; Mutation Rate ; Phylogeny ; Porifera/*genetics ; RNA/genetics/metabolism ; *RNA Editing ; RNA, Messenger/genetics/metabolism ; }, abstract = {One of the unusual features of DNA-containing organelles in general and mitochondria in particular is the frequent occurrence of RNA editing [1]. The term "RNA editing" refers to a variety of mechanistically unrelated biochemical processes that alter RNA sequence during or after transcription [2]. The editing can be insertional, deletional, or substitutional and has been found in all major types of RNAs [3, 4]. Although mitochondrial mRNA editing is widespread in some eukaryotic lineages [5-7], it is rare in animals, with reported cases limited both in their scope and in phylogenetic distribution [8-11] (see also [12]). While analyzing genomic data from calcaronean sponges Sycon ciliatum and Leucosolenia complicata, we were perplexed by the lack of recognizable mitochondrial coding sequences. Comparison of genomic and transcriptomic data from these species revealed the presence of mitochondrial cryptogenes whose transcripts undergo extensive editing. This editing consisted of single or double uridylate (U) insertions in pre-existing short poly(U) tracts. Subsequent analysis revealed the presence of similar editing in Sycon coactum and the loss of editing in Petrobiona massiliana, a hypercalcified calcaronean sponge. In addition, mitochondrial genomes of at least some calcaronean sponges were found to have a highly unusual architecture, with nearly all genes located on individual and likely linear chromosomes. Phylogenetic analysis of mitochondrial coding sequences revealed accelerated rates of sequence evolution in this group. The latter observation presents a challenge for the mutational-hazard hypothesis [13], which posits that mRNA editing should not occur in lineages with an elevated mutation rate.}, }
@article {pmid26720602, year = {2015}, author = {Ye, YY and Wu, CW and Li, JJ}, title = {Genetic Population Structure of Macridiscus multifarius (Mollusca: Bivalvia) on the Basis of Mitochondrial Markers: Strong Population Structure in a Species with a Short Planktonic Larval Stage.}, journal = {PloS one}, volume = {10}, number = {12}, pages = {e0146260}, pmid = {26720602}, issn = {1932-6203}, mesh = {Animals ; Bivalvia/*genetics ; China ; DNA, Mitochondrial/genetics ; Demography/methods ; Fisheries ; Genetic Drift ; Genetic Markers/*genetics/*immunology/*physiology ; Genetic Variation/genetics ; Genetics, Population/methods ; Geography/methods ; Haplotypes/genetics ; Larva/*genetics ; Mitochondria/*genetics ; Mollusca/*genetics ; Plankton/*genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The clam Macridiscus multifarius with a planktonic larval stage of about 10 days is an ecologically and economically important species in the coastal regions of China. In this study, 3 mt-DNA markers (COI, 12S rRNA, and ND1) were used to investigate the population structure and demography of wild M. multifarius populations in 3 coastal localities of the East China Sea (ZS and ZP populations) and Beibu Gulf in the South China Sea (BH population). Sequences of 685 bp in COI, 350 bp in 12S rRNA, and 496 bp in ND1 were determined. High level and significant FST values were obtained among the different localities on the basis of either COI (FST = 0.100-0.444, p < 0.05) or 12S rRNA (FST = 0.199-0.742, p < 0.05) gene, indicating a high degree of genetic differentiation among the populations. FST values were significant but weak for the ND1 gene because it is highly conservative. The median-joining network suggested an obvious genetic differentiation between ZS and BH populations, and the finding is consistent with the results of our demographic analyses using the unweighted pair group method with arithmetic mean. Our study unraveled the extant population genetic structure of M. multifarius and explained the strong population structure of a species with a short planktonic larval stage species; this information could be useful for fishery management measures, including artificial breeding and conservation.}, }
@article {pmid26714105, year = {2015}, author = {Shou, W}, title = {Acknowledging selection at sub-organismal levels resolves controversy on pro-cooperation mechanisms.}, journal = {eLife}, volume = {4}, number = {}, pages = {}, pmid = {26714105}, issn = {2050-084X}, mesh = {*Biological Evolution ; Eukaryota ; *Symbiosis ; }, abstract = {Cooperators who pay a cost to produce publically-available benefits can be exploited by cheaters who do not contribute fairly. How might cooperation persist against cheaters? Two classes of mechanisms are known to promote cooperation: 'partner choice', where a cooperator preferentially interacts with cooperative over cheating partners; and 'partner fidelity feedback', where repeated interactions between individuals ensure that cheaters suffer as their cooperative partners languish (see, for example, Momeni et al., 2013). However when both mechanisms can act, differentiating them has generated controversy. Here, I resolve this controversy by noting that selection can operate on organismal and sub-organismal 'entities' such that partner fidelity feedback at sub-organismal level can appear as partner choice at organismal level. I also show that cooperation between multicellular eukaryotes and mitochondria is promoted by partner fidelity feedback and partner choice between sub-organismal entities, in addition to being promoted by partner fidelity feedback between hosts and symbionts, as was previously known.}, }
@article {pmid26713817, year = {2017}, author = {Yang, C and Li, L and Zhong, T and Wang, L and Zhang, H}, title = {Characterization of the complete mitochondrial genome sequence of Ujumuqin sheep (Ovis aries).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {3}, pages = {315-316}, doi = {10.3109/19401736.2015.1122761}, pmid = {26713817}, issn = {2470-1408}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Genetic Variation/genetics ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Transfer/genetics ; Sheep ; Sheep, Domestic ; }, abstract = {Sheep is one of the most important and widespread domestic animals. Nevertheless, the origins of most sheep breeds are poorly understood, specifically the fat-tailed sheep that maternally originates from a specific group. Here, we reported the whole mitochondrial DNA of Ujumuqin sheep (Ovis aries), derived from one of the oldest fat-tailed sheep breed-Mongolian sheep in China. It harbors 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and a D-Loop region. The mitogenome is 16 617 bp in length, with a homology of 50% between the mitogenome of Ujumuqin sheep and that of Texel sheep. The unveiling of the mitochondrial DNA sequence of Ujumuqin sheep will have a significant role to play in the further studies on sheep evolution and domestication.}, }
@article {pmid26713762, year = {2015}, author = {Halley, YA and Oldeschulte, DL and Bhattarai, EK and Hill, J and Metz, RP and Johnson, CD and Presley, SM and Ruzicka, RE and Rollins, D and Peterson, MJ and Murphy, WJ and Seabury, CM}, title = {Northern Bobwhite (Colinus virginianus) Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy.}, journal = {PloS one}, volume = {10}, number = {12}, pages = {e0144913}, pmid = {26713762}, issn = {1932-6203}, mesh = {Animals ; Colinus ; Evolution, Molecular ; Female ; Gene Frequency ; Genetic Speciation ; Genome, Mitochondrial ; Haplotypes ; Male ; Metagenomics ; Mitochondria/*genetics ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {Herein, we evaluated the concordance of population inferences and conclusions resulting from the analysis of short mitochondrial fragments (i.e., partial or complete D-Loop nucleotide sequences) versus complete mitogenome sequences for 53 bobwhites representing six ecoregions across TX and OK (USA). Median joining (MJ) haplotype networks demonstrated that analyses performed using small mitochondrial fragments were insufficient for estimating the true (i.e., complete) mitogenome haplotype structure, corresponding levels of divergence, and maternal population history of our samples. Notably, discordant demographic inferences were observed when mismatch distributions of partial (i.e., partial D-Loop) versus complete mitogenome sequences were compared, with the reduction in mitochondrial genomic information content observed to encourage spurious inferences in our samples. A probabilistic approach to variant prediction for the complete bobwhite mitogenomes revealed 344 segregating sites corresponding to 347 total mutations, including 49 putative nonsynonymous single nucleotide variants (SNVs) distributed across 12 protein coding genes. Evidence of gross heteroplasmy was observed for 13 bobwhites, with 10 of the 13 heteroplasmies involving one moderate to high frequency SNV. Haplotype network and phylogenetic analyses for the complete bobwhite mitogenome sequences revealed two divergent maternal lineages (dXY = 0.00731; FST = 0.849; P < 0.05), thereby supporting the potential for two putative subspecies. However, the diverged lineage (n = 103 variants) almost exclusively involved bobwhites geographically classified as Colinus virginianus texanus, which is discordant with the expectations of previous geographic subspecies designations. Tests of adaptive evolution for functional divergence (MKT), frequency distribution tests (D, FS) and phylogenetic analyses (RAxML) provide no evidence for positive selection or hybridization with the sympatric scaled quail (Callipepla squamata) as being explanatory factors for the two bobwhite maternal lineages observed. Instead, our analyses support the supposition that two diverged maternal lineages have survived from pre-expansion to post-expansion population(s), with the segregation of some slightly deleterious nonsynonymous mutations.}, }
@article {pmid26713722, year = {2017}, author = {Jebb, D and Foley, NM and Puechmaille, SJ and Teeling, EC}, title = {The complete mitochondrial genome of the Greater Mouse-Eared bat, Myotis myotis (Chiroptera: Vespertilionidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {3}, pages = {347-349}, doi = {10.3109/19401736.2015.1122775}, pmid = {26713722}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Base Sequence ; Chiroptera/*genetics ; DNA, Mitochondrial ; *Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {In this study, we report the complete mitochondrial genome of the Greater Mouse-Eared Bat, Myotis myotis. The mitogenome is 17 213 bp with base composition A (34.2%), G (13%), C (22.4%), and T (30.5%). The genome shows conserved synteny with other mammalian mitogenomes, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region (D-Loop). The majority of the genes are encoded on the H-Strand, except for ND6 and eight tRNAs. All protein-coding genes start with the ATG start codon, except for ND2, ND3, and ND5 which begin with ATT or ATA. Seven protein-coding genes terminated in a canonical stop codon, TAA or TAG, five contain incomplete stop codons, T or TA. Cytochrome b terminates in the mitochondria specific stop codon AGA. This mitogenome provides a valuable resource for future studies of M. myotis and other bat and mammal species.}, }
@article {pmid26713710, year = {2017}, author = {Urantowka, AD and Mackiewicz, P}, title = {Complete mitochondrial genome of Blue-winged Macaw (Primolius maracana).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {2}, pages = {275-276}, doi = {10.3109/19401736.2015.1118077}, pmid = {26713710}, issn = {2470-1408}, mesh = {Animals ; Body Size ; *Genome, Mitochondrial ; Mitochondria/genetics ; Parrots/anatomy &amp; histology/*genetics ; *Phylogeny ; }, abstract = {abtract The presence of bare facial area distinguishes Macaws from other members of the Arini tribe. Genera and species of the Macaw group differ in pattern of this bare skin as well as in body size. Individuals of the genera: Diopsittaca, Orthopsittaca, and Primolius are significantly smaller than the members of the genera: Anodorhynchus, Cyanopsitta, and the most species of the genus Ara. The genus Primolius contains three species: P. auricollis, P. couloni, and P. maracana, which are classified as medium-sized Macaws. So far, mitochondrial genome representative for the genus was sequenced only for Primolius couloni species. Primolius maracana mitogenome, which was sequenced in this study, will be indispensable to refine the phylogenetic relationships between Primolius species, as results of molecular researches seems to be inconsistent with Primolius species morphology.}, }
@article {pmid26713709, year = {2017}, author = {Wang, P and Chen, S and Ou, Y and Wen, J and Li, J}, title = {Complete mitochondrial genome of Toxabramis houdemeri (Cypriniformes; Cyprinidae) and its phylogenetic analysis.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {2}, pages = {292-293}, doi = {10.3109/19401736.2015.1118085}, pmid = {26713709}, issn = {2470-1408}, mesh = {Animals ; Cyprinidae/*genetics ; Fish Proteins/genetics ; Genes, Mitochondrial ; Genes, rRNA ; *Genome, Mitochondrial ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; *Phylogeny ; RNA, Transfer/genetics ; }, abstract = {Toxabramis houdemeri belongs to the genus Toxabramis in the subfamily of Cultrinae (Cyprinidae). We first determine the complete mitochondrial genome of T. houdemeri in this study. It is 16 618 bp in length, with the base composition on the heavy strand: 30.79% A, 16.61% G, 27.29% C, and 25.31% T. It has the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a D-loop region. Phylogenetic analysis showed that T. houdemeri was clustered into one branch of the subfamily of Cultrinae, and closely related to Hemiculter leucisculus. The present study will contribute to genetic resources conservation of T. houdemeri and studying its population genetic structure and phylogenetic relationships.}, }
@article {pmid26713463, year = {2017}, author = {Hu, Y and Bao, B and Gong, X}, title = {The complete mitochondrial genome sequence of Yongeichthys criniger and phylogenetic studies of Gobiidae.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {2}, pages = {281-282}, doi = {10.3109/19401736.2015.1118080}, pmid = {26713463}, issn = {2470-1408}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Fish Proteins/genetics ; Genes, rRNA ; *Genome, Mitochondrial ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {Yongeichthys criniger belongs to Gobiidae, Gobioidei, and Perciformes in taxonomy. Its mitochondrial genome was first determined, which consists of 13 typical vertebrate protein-coding genes, 22 tRNA, 2 rRNA genes, and 1 control region. The mitogenome base's composition is 27.28% for A, 26.12% for T, 28.98% for C, and 17.62% for G. The phylogenic analysis involves 32 Gobiidae species in GenBank database. The results will provide more molecular information for the further studies on species identification and phylogenic evolution of Gobiidae.}, }
@article {pmid26712463, year = {2016}, author = {Logan, A and Pell, VR and Shaffer, KJ and Evans, C and Stanley, NJ and Robb, EL and Prime, TA and Chouchani, ET and Cochemé, HM and Fearnley, IM and Vidoni, S and James, AM and Porteous, CM and Partridge, L and Krieg, T and Smith, RA and Murphy, MP}, title = {Assessing the Mitochondrial Membrane Potential in Cells and In Vivo using Targeted Click Chemistry and Mass Spectrometry.}, journal = {Cell metabolism}, volume = {23}, number = {2}, pages = {379-385}, pmid = {26712463}, issn = {1932-7420}, support = {MC_U105663142/MRC_/Medical Research Council/United Kingdom ; MC-A070-5PS30/MRC_/Medical Research Council/United Kingdom ; MC_UP_1102/10/MRC_/Medical Research Council/United Kingdom ; PG/12/42/29655/BHF_/British Heart Foundation/United Kingdom ; BHF-PG12/42/29655/BHF_/British Heart Foundation/United Kingdom ; BB/D020786/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 098565/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Cell Line ; Click Chemistry/*methods ; *Membrane Potential, Mitochondrial ; Mice, Inbred C57BL ; Molecular Probes/metabolism ; Tandem Mass Spectrometry/*methods ; }, abstract = {The mitochondrial membrane potential (Δψm) is a major determinant and indicator of cell fate, but it is not possible to assess small changes in Δψm within cells or in vivo. To overcome this, we developed an approach that utilizes two mitochondria-targeted probes each containing a triphenylphosphonium (TPP) lipophilic cation that drives their accumulation in response to Δψm and the plasma membrane potential (Δψp). One probe contains an azido moiety and the other a cyclooctyne, which react together in a concentration-dependent manner by "click" chemistry to form MitoClick. As the mitochondrial accumulation of both probes depends exponentially on Δψm and Δψp, the rate of MitoClick formation is exquisitely sensitive to small changes in these potentials. MitoClick accumulation can then be quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS). This approach enables assessment of subtle changes in membrane potentials within cells and in the mouse heart in vivo.}, }
@article {pmid26710999, year = {2017}, author = {Jiang, L and Zhao, L and Liu, Y and Leng, Z and Zhao, L and Ruan, Q}, title = {The complete mitochondrial genome sequence of the Dark-spotted frog Pelophylax nigromaculatus (Amphibia, Anura, Ranidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {2}, pages = {236-237}, doi = {10.3109/19401736.2015.1115857}, pmid = {26710999}, issn = {2470-1408}, mesh = {Amphibian Proteins/genetics ; Animals ; China ; DNA, Mitochondrial/genetics ; Asia, Eastern ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; Phylogeography ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Ranidae/*genetics ; Russia ; }, abstract = {The dark-spotted frog (Pelophylax nigromaculatus) belongs to Ranidae. This species is known from the Russian Far East, central, northern and north-eastern China, the Democratic People's Republic of Korea, the Republic of Korea, and Japan. In this study, the complete mitochondrial genome of P. nigromaculatus was sequenced. The mitogenome was 17 567 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a non-coding control region. As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the P. nigromaculatus is 29.2% A, 27.4% T, 28.4% C, and 15.0% G. Phylogenetic analysis showed P. nigromaculatus was closely related to P. plancyi and P. chosenicus. The complete mitogenome of P. nigromaculatus can provide important data for the studies on phylogenetic relationship and population genetics to further explore the taxonomic status of this species.}, }
@article {pmid26710828, year = {2017}, author = {Liu, Y and Jiang, L}, title = {The complete mitochondrial genome sequence of the Himalayan goral, Naemorhedus goral (Cetartiodactyla: Caprinae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {2}, pages = {233-235}, doi = {10.3109/19401736.2015.1115856}, pmid = {26710828}, issn = {2470-1408}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Ruminants/*genetics ; }, abstract = {The Himalayan goral (Naemorhedus goral) belongs to the subfamily Caprinae, which is distributed across the Himalayas including Bhutan, northern India including Sikkim and Arunachal Pradesh, Nepal, southern Tibet, and possibly western Myanmar. In this study, the complete mitochondrial genome of N. goral was sequenced. The mitogenome was 16 533 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a non-coding control region. As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the N. goral is 33.7% A, 27.2% T, 26.0% C, and 13.1% G. Phylogenetic analysis based on the mitogenome sequences using the Bayesian inferences method showed that Naemorhedus and Capricornis formed a monophyletic group and the N. goral was closely related to N. griseus. We expect that the present results will facilitate further investigation of the phylogenetic relationships and population genetics of genus Naemorhedus.}, }
@article {pmid26710601, year = {2015}, author = {Zhang, Y and Guo, L and Zhang, S and Liu, X}, title = {[Determining mitochondrial molecular markers suitable for genetic diversity analysis of Cordyceps militaris].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {55}, number = {7}, pages = {826-833}, pmid = {26710601}, issn = {0001-6209}, mesh = {Biomarkers/analysis ; Cordyceps/classification/*genetics/isolation &amp; purification ; Fungal Proteins/genetics ; *Genetic Variation ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {OBJECTIVE: To screen efficient molecular markers suitable for genetic diversity analysis of Cordyceps militaris from mitochondrial DNA.<br><br>METHODS: We amplified 12 mitochondrial DNA fragments and 3 nuclear DNA fragments from each of 20 C. militaris isolates and analyzed nucleotide variations on these DNA fragments.<br><br>RESULTS: We revealed a greatly higher genetic variation in mitochondrial DNA fragments than in nuclear DNA fragments. Specifically, C. militaris isolates exhibited intron presence/absence diversity in some mitochondrial fragments, and more variable sites were found in mitochondrial fragments than in nuclear fragments. The extent of nucleotide variations also varied by mitochondrial fragment, and intronic proteins seemed to be more vulnerable to amino acid changes than exonic proteins. Genetic diversity increased with the number of molecular markers used.<br><br>CONCLUSION: We recommended using (in order) nad3-cox2. cox2-nad5, cox2, cox3, cob, and cox1 for future genetic diversity and population genetic studies of C. militaris.}, }
@article {pmid26709737, year = {2017}, author = {Guo, C and Zhang, Q and Huang, Y}, title = {The complete mitochondrial genome of the Oedaleus infernalis sauss (Orthoptera: Oedipodidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {1}, pages = {89-90}, doi = {10.3109/19401736.2015.1110812}, pmid = {26709737}, issn = {2470-1408}, mesh = {Animals ; Base Sequence ; China ; Codon ; DNA, Mitochondrial ; Gene Order ; *Genes, Mitochondrial ; Genome Size ; Genome, Insect ; *Genome, Mitochondrial ; Genomics ; Grasshoppers/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The Oedaleus infernalis sauss (Orthoptera: Oedipodidae) is one of the main pests at the rice production area in China, and they mainly feed on leaves and grain of rice. The mitogenome was 15 898 bp long and composed of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one putative control region. Most protein-coding genes started with a traditional ATN codon, and terminated with the mitochondria stop codon (TAA/TAG) or a single T-- base. The average A + T content of the O. infernalis sauss mitochondrial genome protein-coding sequence, rRNA, tRNA gene, and A + T-rich region was corresponding well to the A + T bias generally observed in insect mitochondrial genomes. Using the 12 protein-coding genes of O. infernalis sauss in this study, together with 15 other closely species, a preliminary phylogenetic analysis has been carried out.}, }
@article {pmid26708415, year = {2016}, author = {Lütz-Meindl, U and Luckner, M and Andosch, A and Wanner, G}, title = {Structural stress responses and degradation of dictyosomes in algae analysed by TEM and FIB-SEM tomography.}, journal = {Journal of microscopy}, volume = {263}, number = {2}, pages = {129-141}, doi = {10.1111/jmi.12369}, pmid = {26708415}, issn = {1365-2818}, mesh = {Endoplasmic Reticulum/metabolism ; Golgi Apparatus/*metabolism ; Imaging, Three-Dimensional ; Micrasterias/*cytology/metabolism/*ultrastructure ; Microscopy, Electron ; Phylogeny ; Tomography, X-Ray Computed ; }, abstract = {Stress-induced physiological deficiencies in cells are reflected in structural, morphological and functional reactions of organelles. Although numerous investigations have focused on chloroplasts and mitochondria as main targets of different stressors in plant cells, there is insufficient information on the plant Golgi apparatus as stress sensor. By using the advantages of field emission scanning electron microscopy tomography in combination with classical ultrathin sectioning and transmission electron microscopic analyses, we provide structural evidence for common stress responses of the large and highly stable dictyosomes in the algal model system Micrasterias. Stress is induced by different metals such as manganese and lead, by starvation in 9 weeks of darkness or by inhibiting photosynthesis or glycolysis and by disturbing ionic homeostasis via KCl. For the first time a stress-induced degradation pathway of dictyosomes is described that does not follow "classical" autophagy but occurs by disintegration of cisternae into single membrane balls that seem to be finally absorbed by the endoplasmic reticulum (ER). Comparison of the morphological features that accompany dictyosomal degradation in Micrasterias to similar reactions observed during the same stress application in Nitella indicates an ubiquitous degradation process at least in algae. As the algae investigated belong to the closest relatives of higher land plants these results may also be relevant for understanding dictyosomal stress and degradation responses in the latter phylogenetic group. In addition, this study shows that two-dimensional transmission electron microscopy is insufficient for elucidating complex processes such as organelle degradation, and that information from three-dimensional reconstructions as provided by field emission scanning electron microscopy tomography is absolutely required for a comprehensive understanding of the phenomenon.}, }
@article {pmid26703096, year = {2016}, author = {Konovalova, O and Logacheva, M}, title = {Mitochondrial genome of two marine fungal species.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4280-4281}, doi = {10.3109/19401736.2015.1082094}, pmid = {26703096}, issn = {2470-1408}, mesh = {Acremonium/*genetics ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; DNA, Mitochondrial/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome ; Genome, Fungal/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Here is a first record for a mitochondrial genome of marine fungus Acremonium fuci and closely related species Emericellopsis sp. One strain for each species, differentiated by morphological features was studied. Complete mitochondrial sequences are 24 565 and 24 951 bp in length. The circular molecule encodes all genes typical for fungal mitochondrial genomes: 15 protein-coding genes, 28 tRNAs, and large and small subunits of RNA. All structural genes are located on one strand and transcribed in one direction. Mitogenomes of species have 99% identity in protein-coding genes, but differ in some structural features: one of them has additional ORF with a similarity to cox1 gene, and another one has an intron in nad5 gene.}, }
@article {pmid26701877, year = {2016}, author = {Lavery, DL and Martinez, P and Gay, LJ and Cereser, B and Novelli, MR and Rodriguez-Justo, M and Meijer, SL and Graham, TA and McDonald, SA and Wright, NA and Jansen, M}, title = {Evolution of oesophageal adenocarcinoma from metaplastic columnar epithelium without goblet cells in Barrett's oesophagus.}, journal = {Gut}, volume = {65}, number = {6}, pages = {907-913}, pmid = {26701877}, issn = {1468-3288}, support = {A14895//Cancer Research UK/United Kingdom ; }, mesh = {Adenocarcinoma/*pathology ; Barrett Esophagus/*complications ; Biopsy ; Electron Transport Complex IV ; Epithelium/pathology ; Esophageal Neoplasms/*pathology ; Exome ; Female ; Goblet Cells/*pathology ; Humans ; Metaplasia/pathology ; Middle Aged ; Mitochondria ; Mutation ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVE: Barrett's oesophagus commonly presents as a patchwork of columnar metaplasia with and without goblet cells in the distal oesophagus. The presence of metaplastic columnar epithelium with goblet cells on oesophageal biopsy is a marker of cancer progression risk, but it is unclear whether clonal expansion and progression in Barrett's oesophagus is exclusive to columnar epithelium with goblet cells.<br><br>DESIGN: We developed a novel method to trace the clonal ancestry of an oesophageal adenocarcinoma across an entire Barrett's segment. Clonal expansions in Barrett's mucosa were identified using cytochrome c oxidase enzyme histochemistry. Somatic mutations were identified through mitochondrial DNA sequencing and single gland whole exome sequencing.<br><br>RESULTS: By tracing the clonal origin of an oesophageal adenocarcinoma across an entire Barrett's segment through a combination of histopathological spatial mapping and clonal ordering, we find that this cancer developed from a premalignant clonal expansion in non-dysplastic ('cardia-type') columnar metaplasia without goblet cells.<br><br>CONCLUSION: Our data demonstrate the premalignant potential of metaplastic columnar epithelium without goblet cells in the context of Barrett's oesophagus.}, }
@article {pmid26700193, year = {2016}, author = {Waqas, MY and Liu, T and Yang, P and Ahmed, N and Zhang, Q and Hu, L and Hong, C and Chen, Q}, title = {Morphological and ultrastructural study of the efferent ductules in the Chinese soft-shelled turtle Pelodiscus sinensis.}, journal = {Journal of experimental zoology. Part A, Ecological genetics and physiology}, volume = {325}, number = {2}, pages = {122-131}, doi = {10.1002/jez.2002}, pmid = {26700193}, issn = {1932-5231}, mesh = {Animals ; Epididymis/*anatomy &amp; histology/ultrastructure ; Epithelium/ultrastructure ; Male ; Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; Turtles/*anatomy &amp; histology ; }, abstract = {Comparative study of the turtle excurrent duct system increases our understanding the evolution of sperm motility and fertility maintenance in higher vertebrates. Therefore, in this study we observed the histology and ultrastructure organization of efferent ductules in the Pelodiscus sinensis using light and transmission electron microscopy. The efferent ductules are extra- testicular and 22-28 in number originate from rete testis. The epithelium is entirely composed of two types of cells, the predominant non-ciliated and ciliated cells. The ciliated cells have long cilia that protrude into the lumen to form a meshwork. These cells associated with clusters of mitochondria in the supranuclear cytoplasm and possess coated vesicles, vacuole, intracellular spaces, and junction complexes. Ciliated cells in the proximal portion of the ductules contain an endocytic apparatus with coated pits and tubules in the apical cytoplasm. Interdigitations and lipid droplets are predominantly present around the nuclei of these cells. The non-ciliated cells have clusters of mitochondria present in both the supranuclear and perinuclear cytoplasm whereas, the nuclei of these cells are lightly stained. Moreover, the contour of the epithelium towards lumen is irregular as it has a deep indentation. The apical cytoplasm goes deep into the lumen to form cytoplasmic processes. This is the first study to describe the detailed features of efferent ductules in Pelodiscus sinensis with, special focus on the morphology of ciliated cells, as these cells are involved in the mixing of luminal fluid and transport of spermatozoa towards the distal region.}, }
@article {pmid26698328, year = {2016}, author = {Shinzawa-Itoh, K and Shimomura, H and Yanagisawa, S and Shimada, S and Takahashi, R and Oosaki, M and Ogura, T and Tsukihara, T}, title = {Purification of Active Respiratory Supercomplex from Bovine Heart Mitochondria Enables Functional Studies.}, journal = {The Journal of biological chemistry}, volume = {291}, number = {8}, pages = {4178-4184}, pmid = {26698328}, issn = {1083-351X}, mesh = {Animals ; Cattle ; Digitonin/*chemistry ; Electron Transport Chain Complex Proteins/chemistry/*isolation &amp; purification ; Mitochondria, Heart/*enzymology ; Muscle Proteins/chemistry/*isolation &amp; purification ; Myocardium/*enzymology ; Polymers/*chemistry ; Propylamines/*chemistry ; }, abstract = {To understand the roles of mitochondrial respiratory chain supercomplexes, methods for consistently separating and preparing supercomplexes must be established. To this end, we solubilized supercomplexes from bovine heart mitochondria with digitonin and then replaced digitonin with amphipol (A8-35), an amphiphilic polymer. Afterward, supercomplexes were separated from other complexes by sucrose density gradient centrifugation. Twenty-six grams of bovine myocardium yielded 3.2 mg of amphipol-stabilized supercomplex. The purified supercomplexes were analyzed based on their absorption spectra as well as Q10 (ubiquinone with ten isoprene units) and lipid assays. The supercomplex sample did not contain cytochrome c but did contain complexes I, III, and IV at a ratio of 1:2:1, 6 molecules of Q10, and 623 atoms of phosphorus. When cytochrome c was added, the supercomplex exhibited KCN-sensitive NADH oxidation; thus, the purified supercomplex was active. Reduced complex IV absorbs at 444 nm, so we measured the resonance Raman spectrum of the reduced amphipol-solubilized supercomplex and the mixture of amphipol-solubilized complexes I1, III2, and IV1 using an excitation wavelength of 441.6 nm, allowing measurement precision comparable with that obtained for complex IV alone. Use of the purified active sample provides insights into the effects of supercomplex formation.}, }
@article {pmid26685167, year = {2016}, author = {Jaromin, E and Wyszkowska, J and Labecka, AM and Sadowska, ET and Koteja, P}, title = {Hindlimb muscle fibre size and glycogen stores in bank voles with increased aerobic exercise metabolism.}, journal = {The Journal of experimental biology}, volume = {219}, number = {Pt 4}, pages = {470-473}, doi = {10.1242/jeb.130476}, pmid = {26685167}, issn = {1477-9145}, mesh = {Animals ; Arvicolinae/genetics/*metabolism ; Energy Metabolism/*genetics ; Glycogen/*metabolism ; Hindlimb ; Muscle Fibers, Skeletal/*physiology ; Muscle, Skeletal/chemistry/*metabolism ; *Physical Conditioning, Animal ; Swimming ; }, abstract = {To test hypotheses concerning physiological factors limiting the rate of aerobic exercise metabolism, we used a unique experimental evolution model: lines of bank voles selected for high swim-induced aerobic metabolism (A) and unselected, control lines (C). We investigated putative adaptations that result in the increased performance of the hindlimb muscle (gastrocnemius joined with plantaris). The body mass-adjusted muscle mass was higher in A-lines (0.093 g) than in C-lines (0.083 g; P=0.01). However, selection did not affect mean muscle fibre cross-sectional area (P=0.34) or glycogen content assessed with a histochemical periodic acid-Schiff reaction (PAS; P=0.82). The results suggest that the increased aerobic performance is achieved by an increase of total muscle mass, without major qualitative changes in the muscle fibre architecture. However, such a conclusion should be treated with caution, because other modifications, such as increased density of capillaries or mitochondria, could occur.}, }
@article {pmid26683828, year = {2015}, author = {Mynhardt, S and Maree, S and Pelser, I and Bennett, NC and Bronner, GN and Wilson, JW and Bloomer, P}, title = {Phylogeography of a Morphologically Cryptic Golden Mole Assemblage from South-Eastern Africa.}, journal = {PloS one}, volume = {10}, number = {12}, pages = {e0144995}, pmid = {26683828}, issn = {1932-6203}, mesh = {Africa, Eastern ; Africa, Southern ; Animals ; Biological Evolution ; DNA, Mitochondrial/*analysis ; Genetic Variation ; Mitochondria/*genetics ; Molecular Sequence Data ; Moles/*classification/*genetics ; Phylogeny ; Phylogeography ; }, abstract = {The Greater Maputaland-Pondoland-Albany (GMPA) region of southern Africa was recently designated as a centre of vertebrate endemism. The phylogeography of the vertebrate taxa occupying this region may provide insights into the evolution of faunal endemism in south-eastern Africa. Here we investigate the phylogeographic patterns of an understudied small mammal species assemblage (Amblysomus) endemic to the GMPA, to test for cryptic diversity within the genus, and to better understand diversification across the region. We sampled specimens from 50 sites across the distributional range of Amblysomus, with emphasis on the widespread A. hottentotus, to analyse geographic patterns of genetic diversity using mitochondrial DNA (mtDNA) and nuclear intron data. Molecular dating was used to elucidate the evolutionary and phylogeographic history of Amblysomus. Our phylogenetic reconstructions show that A. hottentotus comprises several distinct lineages, or evolutionarily significant units (ESUs), some with restricted geographic ranges and thus worthy of conservation attention. Divergence of the major lineages dated to the early Pliocene, with later radiations in the GMPA during the late-Pliocene to early-Pleistocene. Evolutionary diversification within Amblysomus may have been driven by uplift of the Great Escarpment c. 5-3 million years ago (Ma), habitat changes associated with intensification of the east-west rainfall gradient across South Africa and the influence of subsequent global climatic cycles. These drivers possibly facilitated geographic spread of ancestral lineages, local adaptation and vicariant isolation. Our study adds to growing empirical evidence identifying East and southern Africa as cradles of vertebrate diversity.}, }
@article {pmid26681479, year = {2017}, author = {Chen, X and Chen, Y and Yu, M and Sha, Z and Shan, X}, title = {The complete mitochondrial genome of the Azuma emmnion.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {1}, pages = {77-78}, doi = {10.3109/19401736.2015.1110806}, pmid = {26681479}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Base Sequence ; DNA, Mitochondrial ; *Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; Genomics ; Perciformes/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The complete mitochondrial genome of the Azuma emmnion has been determined. The total length of a complete nucleotide sequence of the mitochondria is 16 522 bp, which contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and one D-loop region. Its nucleotide sequence and composition of A. emmnion mitochondrion was similar to most other vertebrates. Nucleotide base composition of mitochondrial genome was the following: 25.58% for A, 18.22% for G, 27.67% for C, 28.53% for T. The phylogenetic analysis result, which based on the complete mitogenomes of of A. emmnion and other 11 fish species, indicated that A. emmnion and Pholis crassispina clustered into one branch.}, }
@article {pmid26680506, year = {2017}, author = {Lan, D and Hu, Y and Zhu, Q and Liu, Y}, title = {Mitochondrial DNA study in domestic chicken.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {28}, number = {1}, pages = {25-29}, doi = {10.3109/19401736.2015.1106526}, pmid = {26680506}, issn = {2470-1408}, mesh = {Animals ; Animals, Domestic/genetics ; Avian Proteins/genetics ; Chickens/*genetics ; DNA, Mitochondrial/*genetics/metabolism ; Promoter Regions, Genetic ; }, abstract = {Mitochondrial DNA has the characteristic of quick evolution, matrilineal inheritance, and simple molecular structure, and it serves as the most used marker for molecular study. As an important role of genomics, studying it can help understand the origins, history, and adaptation of domestication. Because of its wide spread popularity, chicken is one of the important domestic animals, which provides humans with a stable source of protein, including both meat and eggs. This article reviews recent studies of chicken mitochondrial DNA. Mitochondrial D-loop and mitochondrial genomics pinpoint the geographic origins of the domestic chicken which was multiple origins; moreover, the mitochondria gene mutation has an association with high-altitude adaptation and the mitochondria-associated diseases' study in poultry is not performed.}, }
@article {pmid26678550, year = {2016}, author = {Huang, R and Zhou, Y and Yao, Y and Zhao, B and Zhang, Y and Xu, HL}, title = {Complete mitochondrial genome and phylogenetic relationship analysis of Garrulax affinis (Passeriformes, Timaliidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3502-3503}, doi = {10.3109/19401736.2015.1066368}, pmid = {26678550}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Passeriformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Garrulax affinis was a medium-sized bird of Timaliidae, and we got its complete mitochondrial genome by the polymerase chain reaction method (PCR). The genome (17 856 in length), it contained 13 protein-coding genes, 2 rRNA (12S and 16S) genes, 2 tRNA genes, 2 control regions (D-loop). All protein-coding, rRNA, and tRNA genes were similar to other Passeriformes in gene arrangement and composition. In 13 PCGs, 12 were initiated with ATG, only COI was GTG, and stopped by five types of stop codons. We constructed a phylogenetic tree based on 13 PCGs of G. affinis and other nine Timaliidae species, found that the species belong to the same Passeriformes all cluster together.}, }
@article {pmid26671255, year = {2016}, author = {Cusimano, N and Wicke, S}, title = {Massive intracellular gene transfer during plastid genome reduction in nongreen Orobanchaceae.}, journal = {The New phytologist}, volume = {210}, number = {2}, pages = {680-693}, doi = {10.1111/nph.13784}, pmid = {26671255}, issn = {1469-8137}, mesh = {Bayes Theorem ; Biological Evolution ; Cell Nucleus/genetics ; *Gene Transfer Techniques ; Genes, Plant ; *Genome, Plastid ; Intracellular Space/*metabolism ; Mitochondria/genetics ; Nucleotides/genetics ; Orobanchaceae/*genetics ; Phylogeny ; Probability ; Pseudogenes ; Selection, Genetic ; }, abstract = {Plastid genomes (plastomes) of nonphotosynthetic plants experience extensive gene losses and an acceleration of molecular evolutionary rates. Here, we inferred the mechanisms and timing of reductive genome evolution under relaxed selection in the broomrape family (Orobanchaceae). We analyzed the plastomes of several parasites with a major focus on the genus Orobanche using genome-descriptive and Bayesian phylogenetic-comparative methods. Besides this, we scanned the parasites' other cellular genomes to trace the fate of all genes that were purged from their plastomes. Our analyses indicate that the first functional gene losses occurred within 10 Myr of the transition to obligate parasitism in Orobanchaceae, and that the physical plastome reduction proceeds by small deletions that accumulate over time. Evolutionary rate shifts coincide with the genomic reduction process in broomrapes, suggesting that the shift of selectional constraints away from photosynthesis to other molecular processes alters the plastid rate equilibrium. Most of the photosynthesis-related genes or fragments of genes lost from the plastomes of broomrapes have survived in their nuclear or mitochondrial genomes as the results of multiple intracellular transfers and subsequent fragmentation. Our findings indicate that nonessential DNA is eliminated much faster in the plastomes of nonphotosynthetic parasites than in their other cellular genomes.}, }
@article {pmid26668171, year = {2015}, author = {Richardson, E and Zerr, K and Tsaousis, A and Dorrell, RG and Dacks, JB}, title = {Evolutionary cell biology: functional insight from "endless forms most beautiful".}, journal = {Molecular biology of the cell}, volume = {26}, number = {25}, pages = {4532-4538}, pmid = {26668171}, issn = {1939-4586}, support = {BB/M009971/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biological Evolution ; *Cell Biology ; *Eukaryotic Cells ; *Genetic Variation ; Mitochondria/genetics ; Phylogeny ; Plastids/genetics ; }, abstract = {In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking.}, }
@article {pmid26659590, year = {2015}, author = {Baeta, M and Núñez, C and Cardoso, S and Palencia-Madrid, L and Piñeiro-Hermida, S and Arriba-Barredo, M and Villanueva-Millán, MJ and M de Pancorbo, M}, title = {Different Evolutionary History for Basque Diaspora Populations in USA and Argentina Unveiled by Mitochondrial DNA Analysis.}, journal = {PloS one}, volume = {10}, number = {12}, pages = {e0144919}, pmid = {26659590}, issn = {1932-6203}, mesh = {Argentina ; Biological Evolution ; DNA, Mitochondrial/*chemistry/classification ; Emigration and Immigration ; Genetic Linkage ; Genetic Variation ; Genetics, Population ; Haplotypes ; Humans ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; United States ; White People/genetics ; }, abstract = {The Basque Diaspora in Western USA and Argentina represents two populations which have maintained strong Basque cultural and social roots in a completely different geographic context. Hence, they provide an exceptional opportunity to study the maternal genetic legacy from the ancestral Basque population and assess the degree of genetic introgression from the host populations in two of the largest Basque communities outside the Basque Country. For this purpose, we analyzed the complete mitochondrial DNA control region of Basque descendants living in Western USA (n = 175) and in Argentina (n = 194). The Diaspora populations studied here displayed a genetic diversity in their European maternal input which was similar to that of the Basque source populations, indicating that not important founder effects would have occurred. Actually, the genetic legacy of the Basque population still prevailed in their present-day maternal pools, by means of a haplogroup distribution similar to the source population characterized by the presence of autochthonous Basque lineages, such as U5b1f1a and J1c5c1. However, introgression of non-Basque lineages, mostly Native American, has been observed in the Diaspora populations, particularly in Argentina, where the quick assimilation of the newcomers would have favored a wider admixture with host populations. In contrast, a longer isolation of the Diaspora groups in USA, because of language and cultural differences, would have limited the introgression of local lineages. This study reveals important differences in the maternal evolutionary histories of these Basque Diaspora populations, which have to be taken into consideration in forensic and medical genetic studies.}, }
@article {pmid26653218, year = {2015}, author = {Huchon, D and Szitenberg, A and Shefer, S and Ilan, M and Feldstein, T}, title = {Mitochondrial group I and group II introns in the sponge orders Agelasida and Axinellida.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {278}, pmid = {26653218}, issn = {1471-2148}, mesh = {Animals ; Base Sequence ; Electron Transport Complex IV/genetics ; Gene Transfer, Horizontal ; Genome, Mitochondrial ; *Introns ; Molecular Sequence Data ; Phylogeny ; Porifera/*classification/*genetics ; RNA Splicing ; }, abstract = {BACKGROUND: Self-splicing introns are present in the mitochondria of members of most eukaryotic lineages. They are divided into Group I and Group II introns, according to their secondary structure and splicing mechanism. Being rare in animals, self-splicing introns were only described in a few sponges, cnidarians, placozoans and one annelid species. In sponges, three types of mitochondrial Group I introns were previously described in two demosponge families (Tetillidae, and Aplysinellidae) and in the homoscleromorph family Plakinidae. These three introns differ in their insertion site, secondary structure and in the sequence of the LAGLIDADG gene they encode. Notably, no group II introns have been previously described in sponges.<br><br>RESULTS: We report here the presence of mitochondrial introns in the cytochrome oxidase subunit 1 (COI) gene of three additional sponge species from three different families: Agelas oroides (Agelasidae, Agelasida), Cymbaxinella (p) verrucosa (Hymerhabdiidae, Agelasida) and Axinella polypoides (Axinellidae, Axinellida). We show, for the first time, that sponges can also harbour Group II introns in their COI gene, whose presence in animals' mitochondria has so far been described in only two phyla, Placozoa and Annelida. Surprisingly, two different Group II introns were discovered in the COI gene of C. verrucosa. Phylogenetic analysis indicates that the Group II introns present in C. verrucosa are related to red algae (Rhodophyta) introns.<br><br>CONCLUSIONS: The differences found among intron secondary structures and the phylogenetic inferences support the hypothesis that the introns originated from independent horizontal gene transfer events. Our results thus suggest that self-splicing introns are more diverse in the mitochondrial genome of sponges than previously anticipated.}, }
@article {pmid26649810, year = {2016}, author = {Bull, L}, title = {On Cellular Darwinism: Mitochondria.}, journal = {Artificial life}, volume = {22}, number = {1}, pages = {112-118}, doi = {10.1162/ARTL_a_00182}, pmid = {26649810}, issn = {1064-5462}, mesh = {*Biological Coevolution ; *Cell Nucleus ; *Mitochondria ; Selection, Genetic ; Symbiosis ; }, abstract = {The significant role of mitochondria within cells is becoming increasingly clear. This letter uses the NKCS model of coupled fitness landscapes to explore aspects of organelle-nucleus coevolution. The phenomenon of mitochondrial diversity is allowed to emerge under a simple intracellular evolutionary process, including varying the relative rate of evolution by the organelle. It is shown how the conditions for the maintenance of more than one genetic variant of mitochondria are similar to those previously suggested as needed for the original symbiotic origins of the relationship using the NKCS model.}, }
@article {pmid26643887, year = {2015}, author = {Baum, DA}, title = {A comparison of autogenous theories for the origin of eukaryotic cells.}, journal = {American journal of botany}, volume = {102}, number = {12}, pages = {1954-1965}, doi = {10.3732/ajb.1500196}, pmid = {26643887}, issn = {1537-2197}, mesh = {*Biological Evolution ; Eukaryotic Cells/*cytology/*physiology ; Models, Biological ; }, abstract = {PREMISE: Eukaryotic cells have many unique features that all evolved on the stem lineage of living eukaryotes, making it difficult to reconstruct the order in which they accumulated. Nuclear endosymbiotic theories hold that three prokaryotes (nucleus, cytoplasm, and mitochondrion) came together to form a eukaryotic cell, whereas autogenous models hold that the nucleus and cytoplasm formed through evolutionary changes in a single prokaryotic lineage. Given several problems with nuclear endosymbiotic theories, this review focuses on autogenous models.<br><br>KEY INSIGHTS: Until recently all autogenous models assumed an outside-in (OI) topology, proposing that the nuclear envelope was formed from membrane-bound vesicles within the original cell body. Buzz Baum and I recently proposed an inside-out (IO) alternative, suggesting that the nucleus corresponds to the original cell body, with the cytoplasmic compartment deriving from extracellular protrusions. In this review, I show that OI and IO models are compatible with both mitochondria early (ME) or mitochondria late (ML) formulations. Whereas ME models allow that the relationship between mitochondria and host was mutualistic from the outset, ML models imply that the association began with predation or parasitism, becoming mutualistic later. In either case, the mutualistic interaction that eventually formed was probably syntrophic.<br><br>CONCLUSIONS: Diverse features of eukaryotic cell biology align well with the IOME model, but it would be premature to rule out the OIME model. ML models require that phagocytosis, a complex and energy expensive process, evolved before mitochondria, which seems unlikely. Nonetheless, further research is needed, especially resolution of the phylogenetic affinities of mitochondria.}, }
@article {pmid26642812, year = {2016}, author = {Kim, S and Kim, H and Shin, SC}, title = {Complete mitochondrial genome of the Antarctic midge Parochlus steinenii (Diptera: Chironomidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3475-3476}, doi = {10.3109/19401736.2015.1066355}, pmid = {26642812}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Diptera/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Parochlus steinenii is a winged midge found in the Antarctic Peninsula and its offshore islands. We determined the complete mitochondrial genome sequence of P. steinenii, which is comprised of 16 803 nucleotides and contains 13 protein-coding genes (PCGs), 22 tRNA genes, and the large (rrnL) and small (rrnS) rRNA genes. Its total A + T content is 72.5%. The PCG arrangement of P. steinenii is identical to that of the ancestral Diptera ground pattern. This is the first report on the mitogenome sequence of an Antarctic midge, and provides insights into the evolution of dipterans in Antarctica.}, }
@article {pmid26642375, year = {2016}, author = {Liao, H and Yang, X and Li, Z and Ding, Y and Guo, Y}, title = {The complete mitochondria genome of Parasarcophaga albiceps (Diptera: Sarcophagidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4696-4698}, doi = {10.3109/19401736.2015.1106507}, pmid = {26642375}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Evolution, Molecular ; Genes, Insect ; *Genes, Mitochondrial ; *Genome, Mitochondrial ; Phylogeny ; Sarcophagidae/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {Parasarcophaga albiceps is one of the forensically important fly species which belongs to the family Sarcophagidae. In this study, we report the complete mitochondrial genome of P. albiceps to provide a supplemental data for species identification. The 14 935 bp-long mitogenome is composed of 13 protein-encoding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding AT-rich region. The permutation of the genes is in conformity with that observed in the ancestral arthropod. The overall base compositions of A, G, C and T are 39.24%, 9.70%, 14.44%, and 36.62%, respectively. Phylogenetic analysis shows the composition of the P. albiceps mitochondrial genome, which is very similar to that of another eight species of Sarcophagidae. The monophyletic branches of the phylogenetic tree reveal that complete mitochondrial genome is suitable for discrimination between these species, providing high support for separation on congeneric species. Therefore, the molecular method applied to the sarcophagid species identification is feasible. The complete mitochondrial genome of P. albiceps is supposed to make contributions to enriching the dipteran mitochondrial genomes and provide a potential tool for species identification.}, }
@article {pmid26639990, year = {2016}, author = {Uliano-Silva, M and Americo, JA and Costa, I and Schomaker-Bastos, A and de Freitas Rebelo, M and Prosdocimi, F}, title = {The complete mitochondrial genome of the golden mussel Limnoperna fortunei and comparative mitogenomics of Mytilidae.}, journal = {Gene}, volume = {577}, number = {2}, pages = {202-208}, doi = {10.1016/j.gene.2015.11.043}, pmid = {26639990}, issn = {1879-0038}, mesh = {Animals ; Base Sequence ; Evolution, Molecular ; *Genome, Mitochondrial ; Mitochondrial Proton-Translocating ATPases/genetics ; Molecular Sequence Data ; Mytilidae/classification/*genetics ; *Phylogeny ; Pseudogenes ; RNA, Transfer/genetics ; Sequence Alignment ; }, abstract = {Here we describe the mitochondrial genome of the golden mussel Limnoperna fortunei, an Asian bivalve which has become one of the most aggressive invasive species in Japan and South America. The mitochondrial genome of L. fortunei does not present conserved gene arrangement when compared to the other Mytilidae species suggesting a high degree of gene recombination in the mitochondria of this clade. In addition, the golden mussel mitogenome encodes two copies of tRNA(Lys) and presents a putative pseudogene for the atp8 gene sequence that encodes a 27 amino acid peptide containing an in-frame stop codon. The presence of this pseudogene raises the question as to whether atp8 is encoded in some bivalve mitochondrial genomes or not. The phylogenetic analysis of all complete mitochondrial genomes available from Mytilidae mussels confirmed the close evolutionary relationships among bivalves from the genus Mytilys and placed L. fortunei coming from a more ancestral branch on the family. The supermatrix phylogeny described used the concatenation of all 12 genes from the mitochondria and disputed the monophyly of the genus Perna, as Perna perna was shown to be more closely related to Brachidontes exustus than to Perna viridis. The comparative analysis of mitogenome synteny also confirmed the polyphyly of the genus Perna. The complete and annotated mitogenome has been published in GenBank under the accession number KP756905.}, }
@article {pmid26634536, year = {2015}, author = {Xu, X and Tan, YP and Cheng, G and Liu, XQ and Xia, CJ and Luo, FY and Wang, CT}, title = {Genomic survey and gene expression analysis of the VDAC gene family in rice.}, journal = {Genetics and molecular research : GMR}, volume = {14}, number = {4}, pages = {15683-15696}, doi = {10.4238/2015.December.1.20}, pmid = {26634536}, issn = {1676-5680}, mesh = {Chromosome Mapping ; Cluster Analysis ; Computational Biology/methods ; Gene Duplication ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Order ; Gene Regulatory Networks ; Genetic Loci ; Genome, Plant ; *Genomics ; *Multigene Family ; Oryza/classification/*genetics/metabolism ; Phylogeny ; Voltage-Dependent Anion Channels/*genetics/metabolism ; }, abstract = {The voltage-dependent anion channel (VDAC), also known as a mitochondrial porin, plays an important role in the regulation of metabolic and energetic functions of mitochondria, as well as in mitochondria-mediated apoptosis. Cytoplasmic male sterility (CMS) is of major economic importance for commercial hybrid production and a research model for the interaction be-tween nuclear and cytoplasmic genomes. Recent research has revealed that CMS is associated with programmed cell death. Here, we used the Honglian (HL)-CMS line of rice (Oryza sativa) as material to investigate the association of O. sativa VDAC (OsVDAC) expression to CMS. Eight VDACs were extracted from rice in this study. Bioinformatic analysis of the rice VDACs was conducted at the DNA, cDNA, and protein level. Expression patterns of OsVDACs were analyzed in different organs and during different stages of pollen development using sterile line YuetaiA (YTA), and its maintainer line YuetaiB (YTB). Differential expression of OsVDACs between YTA and YTB was observed, suggesting that VDACs may be involved in the formation of HL-CMS.}, }
@article {pmid26627655, year = {2015}, author = {Janardan, N and Harijan, RK and Kiema, TR and Wierenga, RK and Murthy, MR}, title = {Structural characterization of a mitochondrial 3-ketoacyl-CoA (T1)-like thiolase from Mycobacterium smegmatis.}, journal = {Acta crystallographica. Section D, Biological crystallography}, volume = {71}, number = {Pt 12}, pages = {2479-2493}, doi = {10.1107/S1399004715019331}, pmid = {26627655}, issn = {1399-0047}, mesh = {Acetyl-CoA C-Acyltransferase/*chemistry/genetics/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/genetics/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Escherichia coli/genetics/metabolism ; Gene Expression ; Kinetics ; Mitochondria/*chemistry/enzymology ; Mitochondrial Proteins/*chemistry/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mycobacterium smegmatis/*chemistry/classification/enzymology ; Phylogeny ; Protein Binding ; Protein Multimerization ; Protein Structure, Secondary ; Protein Subunits/*chemistry/genetics/metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; Substrate Specificity ; }, abstract = {Thiolases catalyze the degradation and synthesis of 3-ketoacyl-CoA molecules. Here, the crystal structures of a T1-like thiolase (MSM-13 thiolase) from Mycobacterium smegmatis in apo and liganded forms are described. Systematic comparisons of six crystallographically independent unliganded MSM-13 thiolase tetramers (dimers of tight dimers) from three different crystal forms revealed that the two tight dimers are connected to a rigid tetramerization domain via flexible hinge regions, generating an asymmetric tetramer. In the liganded structure, CoA is bound to those subunits that are rotated towards the tip of the tetramerization loop of the opposing dimer, suggesting that this loop is important for substrate binding. The hinge regions responsible for this rotation occur near Val123 and Arg149. The Lα1-covering loop-Lα2 region, together with the Nβ2-Nα2 loop of the adjacent subunit, defines a specificity pocket that is larger and more polar than those of other tetrameric thiolases, suggesting that MSM-13 thiolase has a distinct substrate specificity. Consistent with this finding, only residual activity was detected with acetoacetyl-CoA as the substrate in the degradative direction. No activity was observed with acetyl-CoA in the synthetic direction. Structural comparisons with other well characterized thiolases suggest that MSM-13 thiolase is probably a degradative thiolase that is specific for 3-ketoacyl-CoA molecules with polar, bulky acyl chains.}, }
@article {pmid26620805, year = {2016}, author = {Sherrard-Smith, E and Stanton, DW and Cable, J and Orozco-terWengel, P and Simpson, VR and Elmeros, M and van Dijk, J and Simonnet, F and Roos, A and Lemarchand, C and Poledník, L and Heneberg, P and Chadwick, EA}, title = {Distribution and molecular phylogeny of biliary trematodes (Opisthorchiidae) infecting native Lutra lutra and alien Neovison vison across Europe.}, journal = {Parasitology international}, volume = {65}, number = {2}, pages = {163-170}, doi = {10.1016/j.parint.2015.11.007}, pmid = {26620805}, issn = {1873-0329}, mesh = {Animals ; Europe/epidemiology ; France/epidemiology ; Gene Flow ; Germany/epidemiology ; Haplotypes ; Introduced Species ; Mink/*parasitology ; Mitochondria/genetics ; Otters/*parasitology ; Phylogeny ; Poland/epidemiology ; Trematoda/classification/*genetics/*isolation &amp; purification ; Trematode Infections/epidemiology/parasitology/*veterinary ; United Kingdom ; }, abstract = {The recent identification of Pseudamphistomum truncatum, (Rudolphi, 1819) (Trematoda: Opisthorchiidae) and Metorchis bilis (Braun, 1790) Odening, 1962 (synonymous with Metorchis albidus (Braun, 1893) Loos, 1899 and Metorchis crassiusculus (Rudolphi, 1809) Looss, 1899 (Trematoda: Opisthorchiidae)) in otters from Britain caused concern because of associated biliary damage, coupled with speculation over their alien status. Here, we investigate the presence, intensity and phylogeny of these trematodes in mustelids (principally otters) across Europe (Czech Republic, Denmark, France, Germany, Norway, Poland and Sweden and Britain). The trematodes were identified to species using the internal transcribed spacer II (ITS2) locus. Both parasites were found across Europe but at unequal frequency. In the German state of Saxony, eight out of eleven (73%) otters examined were infected with P. truncatum whilst this parasite was not found in either mink from Scotland (n=40) or otters from Norway (n=21). Differences in the phylogenies between the two species suggest divergent demographic histories possibly reflecting contrasting host diet or competitive exclusion, with M. bilis exhibiting greater mitochondrial diversity than P. truncatum. Shared haplotypes within the ranges of both parasite species probably reflect relatively unrestricted movements (both natural and anthropogenic) of intermediate and definitive hosts across Europe.}, }
@article {pmid26615986, year = {2016}, author = {Kaguni, LS and Oliveira, MT}, title = {Structure, function and evolution of the animal mitochondrial replicative DNA helicase.}, journal = {Critical reviews in biochemistry and molecular biology}, volume = {51}, number = {1}, pages = {53-64}, pmid = {26615986}, issn = {1549-7798}, support = {R01 GM045295/GM/NIGMS NIH HHS/United States ; GM45295/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; DNA Helicases/chemistry/*metabolism ; Evolution, Molecular ; Humans ; Mitochondria/*enzymology ; Models, Animal ; Molecular Sequence Data ; Mutation ; Sequence Homology, Amino Acid ; }, abstract = {The mitochondrial replicative DNA helicase is essential for animal mitochondrial DNA (mtDNA) maintenance. Deleterious mutations in the gene that encodes it cause mitochondrial dysfunction manifested in developmental delays, defects and arrest, limited life span, and a number of human pathogenic phenotypes that are recapitulated in animals across taxa. In fact, the replicative mtDNA helicase was discovered with the identification of human disease mutations in its nuclear gene, and based upon its deduced amino acid sequence homology with bacteriophage T7 gene 4 protein (T7 gp4), a bi-functional primase-helicase. Since that time, numerous investigations of its structure, mechanism, and physiological relevance have been reported, and human disease alleles have been modeled in the human, mouse, and Drosophila systems. Here, we review this literature and draw evolutionary comparisons that serve to shed light on its divergent features.}, }
@article {pmid26615219, year = {2015}, author = {Degli Esposti, M}, title = {Genome Analysis of Structure-Function Relationships in Respiratory Complex I, an Ancient Bioenergetic Enzyme.}, journal = {Genome biology and evolution}, volume = {8}, number = {1}, pages = {126-147}, pmid = {26615219}, issn = {1759-6653}, mesh = {Amino Acid Sequence ; Bacteria/enzymology/genetics ; Bacterial Proteins/chemistry/*genetics/metabolism ; Conserved Sequence ; Electron Transport Complex I/chemistry/*genetics/metabolism ; *Evolution, Molecular ; *Genome, Bacterial ; Molecular Sequence Data ; }, abstract = {Respiratory complex I (NADH:ubiquinone oxidoreductase) is a ubiquitous bioenergetic enzyme formed by over 40 subunits in eukaryotes and a minimum of 11 subunits in bacteria. Recently, crystal structures have greatly advanced our knowledge of complex I but have not clarified the details of its reaction with ubiquinone (Q). This reaction is essential for bioenergy production and takes place in a large cavity embedded within a conserved module that is homologous to the catalytic core of Ni-Fe hydrogenases. However, how a hydrogenase core has evolved into the protonmotive Q reductase module of complex I has remained unclear. This work has exploited the abundant genomic information that is currently available to deduce structure-function relationships in complex I that indicate the evolutionary steps of Q reactivity and its adaptation to natural Q substrates. The results provide answers to fundamental questions regarding various aspects of complex I reaction with Q and help re-defining the old concept that this reaction may involve two Q or inhibitor sites. The re-definition leads to a simplified classification of the plethora of complex I inhibitors while throwing a new light on the evolution of the enzyme function.}, }
@article {pmid26613727, year = {2016}, author = {Wagener, J}, title = {Regulation of mitochondrial inner membrane fusion: divergent evolution with similar solutions?.}, journal = {Current genetics}, volume = {62}, number = {2}, pages = {291-294}, pmid = {26613727}, issn = {1432-0983}, mesh = {Animals ; *Biological Evolution ; *Membrane Fusion ; *Mitochondria ; *Mitochondrial Membranes ; Proteolysis ; }, abstract = {Continuous mitochondrial fusion and fission define the dynamic shape of mitochondria. One essential player of mitochondrial fusion is the conserved inner membrane dynamin-like GTPase Mgm1/OPA1. Limited proteolysis of this protein has been proposed as a mechanism to separate and subsequently eliminate dysfunctional parts from the mitochondrial network. Here, I briefly summarize our current knowledge about the underlying proteolytic processing steps in mammals, baker's yeast, Schizosaccharomyces pombe, Drosophila melanogaster and Aspergillus fumigatus. The apparent great diversity in Mgm1/OPA1 processing among the analyzed species indicates a surprising mechanistic heterogeneity in the regulation of mitochondrial inner membrane fusion.}, }
@article {pmid26601776, year = {2016}, author = {Jung, J and Uesugi, N and Jeong, NY and Park, BS and Konishi, H and Kiyama, H}, title = {Increase of transcription factor EB (TFEB) and lysosomes in rat DRG neurons and their transportation to the central nerve terminal in dorsal horn after nerve injury.}, journal = {Neuroscience}, volume = {313}, number = {}, pages = {10-22}, doi = {10.1016/j.neuroscience.2015.11.028}, pmid = {26601776}, issn = {1873-7544}, mesh = {Adenosine Triphosphate/metabolism ; Adenoviridae/genetics ; Animals ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/*metabolism ; Disease Models, Animal ; Exocytosis/physiology ; Ganglia, Spinal/*metabolism/pathology ; Genetic Vectors ; Glycoproteins/metabolism ; Lectins/metabolism ; Lumbar Vertebrae ; Luminescent Proteins/genetics/metabolism ; Lysosomal Membrane Proteins/genetics/metabolism ; Lysosomes/*metabolism ; Male ; Microglia/metabolism ; Neurons/*metabolism/pathology ; Nucleotide Transport Proteins/genetics/metabolism ; RNA, Messenger/metabolism ; Rats, Wistar ; Spinal Nerves/*injuries/metabolism ; Versicans ; Red Fluorescent Protein ; }, abstract = {In the spinal dorsal horn (DH), nerve injury activates microglia and induces neuropathic pain. Several studies clarified an involvement of adenosine triphosphate (ATP) in the microglial activation. However, the origin of ATP together with the release mechanism is unclear. Recent in vitro study revealed that an ATP marker, quinacrine, in lysosomes was released from neurite terminal of dorsal root ganglion (DRG) neurons to extracellular space via lysosomal exocytosis. Here, we demonstrate a possibility that the lysosomal ingredient including ATP released from DRG neurons by lysosomal-exocytosis is an additional source of the glial activation in DH after nerve injury. After rat L5 spinal nerve ligation (SNL), mRNA for transcription factor EB (TFEB), a transcription factor controlling lysosomal activation and exocytosis, was induced in the DRG. Simultaneously both lysosomal protein, LAMP1- and vesicular nuclear transporter (VNUT)-positive vesicles were increased in L5 DRG neurons and ipsilateral DH. The quinacrine staining in DH was increased and co-localized with LAMP1 immunoreactivity after nerve injury. In DH, LAMP1-positive vesicles were also co-localized with a peripheral nerve marker, Isolectin B4 (IB4) lectin. Injection of the adenovirus encoding mCherry-LAMP1 into DRG showed that mCherry-positive lysosomes are transported to the central nerve terminal in DH. These findings suggest that activation of lysosome synthesis including ATP packaging in DRG, the central transportation of the lysosome, and subsequent its exocytosis from the central nerve terminal of DRG neurons in response to nerve injury could be a partial mechanism for activation of microglia in DH. This lysosome-mediated microglia activation mechanism may provide another clue to control nociception and pain.}, }
@article {pmid26596041, year = {2015}, author = {Titov, VN}, title = {[THE BIOLOGICAL FUNCTION OF NUTRITION, BIOLOGICAL REACTION OF EXOTROPHY, DEPOSITING AND ENDOTROPHY. THE VISCERAL FATTY CELLS AND ADIPOCYTES - PHYLOGENETICALLY, FUNCTIONALLY AND REGULATORY DIFFERENT POOLS OF FATTY TISSUE].}, journal = {Klinicheskaia laboratornaia diagnostika}, volume = {60}, number = {8}, pages = {14-23}, pmid = {26596041}, issn = {0869-2084}, mesh = {Adipocytes/classification/*metabolism/pathology ; Adiponectin/genetics/metabolism ; Adipose Tissue, Brown/*metabolism/pathology ; Autocrine Communication ; Fatty Acids/metabolism ; Gene Expression Regulation ; Humans ; Intra-Abdominal Fat/*metabolism/pathology ; Leptin/genetics/metabolism ; Lipid Metabolism ; Metabolic Syndrome/genetics/*metabolism/pathology ; Mitochondria/metabolism ; Paracrine Communication ; Phylogeny ; Signal Transduction ; }, abstract = {For billions years, two phylogenetically, functionally and regulatory different pools of fatty cells - visceral fatty acids and adipocytes coexist in vivo. Their becoming occurred at different degrees of phylogenesis. The phylogenetically earlier pool of visceral fatty acids is meant to supply with fatty acids-substrates for gaining energy by those cells which implement biological function of nutrition (trophology), homeostasis, endoecology biological function of adaptation and continuation of species. They have no receptors to phylogenetically later insulin. The adipocytes, later in phylogenesis, implement one biological function - the function of locomotion and they are as insulin-dependent as skeletal myocytes, cardiomyocytes, adipocytes and periportal hepatocytes. The difference in regulation is traced on all levels of "biological perfection " - autocrine (cellular) level, in humoral regulated paracrin cenosises of cells and on the level of organism. In biological function of trophology, paracrin cenosises of visceral fatty acids and adipocytes implement subsequently three biological reactions: exotrophy, deposit of fatty acids and endotrophy. In conditions of humoral regulation of three functionally different biological reactions in paracrin cenosises synthesis of so many humoral mediators is required. The humoral mediators of mechanism of feedback at autocrine level, in paracrin cenosises and at the level of organism are leptin of visceral fatty acids and adiponectin of adipocytes. At the level of organism, phylogenetically earlier paracrin cenosises of fatty cells are regulated by endocrine system. The phylogenetically later paracrin cenosises are regulated by insulin and nuclei of hypothalamus. The metabolic syndrome is a pathology of phylogenetically earlier insulin-independent visceral fatty acids. The obesity is a pathology of phylogenetically later pool of insulin-dependent adipocytes.}, }
@article {pmid26589126, year = {2015}, author = {Gnaiger, E and Boushel, R and Søndergaard, H and Munch-Andersen, T and Damsgaard, R and Hagen, C and Díez-Sánchez, C and Ara, I and Wright-Paradis, C and Schrauwen, P and Hesselink, M and Calbet, JA and Christiansen, M and Helge, JW and Saltin, B}, title = {Mitochondrial coupling and capacity of oxidative phosphorylation in skeletal muscle of Inuit and Caucasians in the arctic winter.}, journal = {Scandinavian journal of medicine &amp; science in sports}, volume = {25 Suppl 4}, number = {}, pages = {126-134}, doi = {10.1111/sms.12612}, pmid = {26589126}, issn = {1600-0838}, mesh = {Adenosine Triphosphate/biosynthesis ; Adult ; Cell Respiration ; Cold Temperature ; DNA, Mitochondrial ; Deltoid Muscle/cytology/*metabolism ; Denmark/ethnology ; Fatty Acids/metabolism ; Female ; Greenland/ethnology ; Haplotypes ; Humans ; *Inuit/genetics ; Ion Channels/metabolism ; Male ; Mitochondria, Muscle/*metabolism ; Mitochondrial Proteins/metabolism ; Oxidation-Reduction ; *Oxidative Phosphorylation ; Oxygen Consumption ; Quadriceps Muscle/cytology/*metabolism ; Seasons ; Skiing/physiology ; Thermogenesis ; Uncoupling Protein 3 ; *White People/genetics ; }, abstract = {During evolution, mitochondrial DNA haplogroups of arctic populations may have been selected for lower coupling of mitochondrial respiration to ATP production in favor of higher heat production. We show that mitochondrial coupling in skeletal muscle of traditional and westernized Inuit habituating northern Greenland is identical to Danes of western Europe haplogroups. Biochemical coupling efficiency was preserved across variations in diet, muscle fiber type, and uncoupling protein-3 content. Mitochondrial phenotype displayed plasticity in relation to lifestyle and environment. Untrained Inuit and Danes had identical capacities to oxidize fat substrate in arm muscle, which increased in Danes during the 42 days of acclimation to exercise, approaching the higher level of the Inuit hunters. A common pattern emerges of mitochondrial acclimatization and evolutionary adaptation in humans at high latitude and high altitude where economy of locomotion may be optimized by preservation of biochemical coupling efficiency at modest mitochondrial density, when submaximum performance is uncoupled from VO2max and maximum capacities of oxidative phosphorylation.}, }
@article {pmid26583150, year = {2015}, author = {Roussel, E and Drolet, MC and Walsh-Wilkinson, E and Dhahri, W and Lachance, D and Gascon, S and Sarrhini, O and Rousseau, JA and Lecomte, R and Couet, J and Arsenault, M}, title = {Transcriptional Changes Associated with Long-Term Left Ventricle Volume Overload in Rats: Impact on Enzymes Related to Myocardial Energy Metabolism.}, journal = {BioMed research international}, volume = {2015}, number = {}, pages = {949624}, pmid = {26583150}, issn = {2314-6141}, support = {MOP-106479//Canadian Institutes of Health Research/Canada ; MOP-61818//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Aortic Valve Insufficiency/drug therapy/*genetics/physiopathology ; Cardiac Volume/genetics ; Disease Models, Animal ; Energy Metabolism/*genetics ; Fenofibrate/administration &amp; dosage ; Heart Failure/drug therapy/*genetics/physiopathology ; Heart Ventricles/drug effects/metabolism/physiopathology ; Humans ; Hypertrophy, Left Ventricular/*genetics/metabolism/physiopathology ; Mitochondria, Heart/genetics ; Oxidation-Reduction ; PPAR alpha/genetics ; Rats ; Transcriptome ; Ventricular Function, Left/drug effects/genetics ; }, abstract = {Patients with left ventricle (LV) volume overload (VO) remain in a compensated state for many years although severe dilation is present. The myocardial capacity to fulfill its energetic demand may delay decompensation. We performed a gene expression profile, a model of chronic VO in rat LV with severe aortic valve regurgitation (AR) for 9 months, and focused on the study of genes associated with myocardial energetics. Methods. LV gene expression profile was performed in rats after 9 months of AR and compared to sham-operated controls. LV glucose and fatty acid (FA) uptake was also evaluated in vivo by positron emission tomography in 8-week AR rats treated or not with fenofibrate, an activator of FA oxidation (FAO). Results. Many LV genes associated with mitochondrial function and metabolism were downregulated in AR rats. FA β-oxidation capacity was significantly impaired as early as two weeks after AR. Treatment with fenofibrate, a PPARα agonist, normalized both FA and glucose uptake while reducing LV dilation caused by AR. Conclusion. Myocardial energy substrate preference is affected early in the evolution of LV-VO cardiomyopathy. Maintaining a relatively normal FA utilization in the myocardium could translate into less glucose uptake and possibly lesser LV remodeling.}, }
@article {pmid26578312, year = {2016}, author = {James, JE and Piganeau, G and Eyre-Walker, A}, title = {The rate of adaptive evolution in animal mitochondria.}, journal = {Molecular ecology}, volume = {25}, number = {1}, pages = {67-78}, pmid = {26578312}, issn = {1365-294X}, mesh = {Adaptation, Biological/*genetics ; Animals ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Mitochondria/*genetics ; Models, Genetic ; Mutation Rate ; Polymorphism, Genetic ; }, abstract = {We have investigated whether there is adaptive evolution in mitochondrial DNA, using an extensive data set containing over 500 animal species from a wide range of taxonomic groups. We apply a variety of McDonald-Kreitman style methods to the data. We find that the evolution of mitochondrial DNA is dominated by slightly deleterious mutations, a finding which is supported by a number of previous studies. However, when we control for the presence of deleterious mutations using a new method, we find that mitochondria undergo a significant amount of adaptive evolution, with an estimated 26% (95% confidence intervals: 5.7-45%) of nonsynonymous substitutions fixed by adaptive evolution. We further find some weak evidence that the rate of adaptive evolution is correlated to synonymous diversity. We interpret this as evidence that at least some adaptive evolution is limited by the supply of mutations.}, }
@article {pmid26577075, year = {2015}, author = {Speijer, D}, title = {Birth of the eukaryotes by a set of reactive innovations: New insights force us to relinquish gradual models.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {37}, number = {12}, pages = {1268-1276}, doi = {10.1002/bies.201500107}, pmid = {26577075}, issn = {1521-1878}, mesh = {Adenosine Triphosphate/metabolism ; Archaea/metabolism ; Eukaryota/*metabolism/*physiology ; Mitochondria/metabolism ; Proteome/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {Of two contending models for eukaryotic evolution the "archezoan" has an amitochondriate eukaryote take up an endosymbiont, while "symbiogenesis" states that an Archaeon became a eukaryote as the result of this uptake. If so, organelle formation resulting from new engulfments is simplified by the primordial symbiogenesis, and less informative regarding the bacterium-to-mitochondrion conversion. Gradualist archezoan visions still permeate evolutionary thinking, but are much less likely than symbiogenesis. Genuine amitochondriate eukaryotes have never been found and rapid, explosive adaptive periods characteristic of symbiogenetic models explain this. Mitochondrial proteomes, encoded by genes of "eukaryotic origin" not easily linked to host or endosymbiont, can be understood in light of rapid adjustments to new evolutionary pressures. Symbiogenesis allows "expensive" eukaryotic inventions via efficient ATP generation by nascent mitochondria. However, efficient ATP production equals enhanced toxic internal ROS formation. The synergistic combination of these two driving forces gave rise to the rapid evolution of eukaryotes. Also watch the Video Abstract.}, }
@article {pmid26558285, year = {2015}, author = {Kwon, DN and Choi, YJ and Cho, SG and Park, C and Seo, HG and Song, H and Kim, JH}, title = {CMP-Neu5Ac Hydroxylase Null Mice as a Model for Studying Metabolic Disorders Caused by the Evolutionary Loss of Neu5Gc in Humans.}, journal = {BioMed research international}, volume = {2015}, number = {}, pages = {830315}, pmid = {26558285}, issn = {2314-6141}, mesh = {Animals ; Cluster Analysis ; Disease Models, Animal ; Evolution, Molecular ; Gene Regulatory Networks/genetics ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Mitochondria, Liver/*genetics/*metabolism ; Mixed Function Oxygenases/*deficiency/*genetics/metabolism ; Neuraminic Acids/*metabolism ; Oxidative Stress/genetics ; }, abstract = {The purpose of this study was to identify the modification/turnover of gene products that are altered in humans due to evolutionary loss of Neu5Gc. CMP-Neu5Ac hydroxylase- (Cmah-) deficient mice show the infiltration of Kupffer cells within liver sinusoids, whereas body and liver weight develop normally. Pathway analysis by use of Illumina MouseRef-8 v2 Expression BeadChip provided evidence that a number of biological pathways, including the glycolysis, gluconeogenesis, TCA cycle, and pentose phosphate pathways, as well as glycogen metabolism-related gene expression, were significantly upregulated in Cmah-null mice. The intracellular glucose supply in Cmah-null mice resulted in mitochondrial dysfunction, oxidative stress, and the advanced glycation end products accumulation that could further induce oxidative stress. Finally, low sirtuin-1 and sirtuin-3 gene expressions due to higher NADH/NAD in Cmah-null mice decreased Foxo-1 and MnSOD gene expression, suggesting that oxidative stress may result in mitochondrial dysfunction in Cmah-null mouse. The present study suggests that mice with CMAH deficiency can be taken as an important model for studying metabolic disorders in humans.}, }
@article {pmid26555471, year = {2015}, author = {Tereshina, EV and Laskavy, VN and Ivanenko, SI}, title = {Four Components of the Conjugated Redox System in Organisms: Carbon, Nitrogen, Sulfur, Oxygen.}, journal = {Biochemistry. Biokhimiia}, volume = {80}, number = {9}, pages = {1186-1200}, doi = {10.1134/S0006297915090096}, pmid = {26555471}, issn = {1608-3040}, mesh = {Animals ; Arginine/*chemistry/*metabolism ; Bacteria/classification/metabolism ; Formaldehyde/*chemistry ; Glutathione/*metabolism ; Homeostasis ; Humans ; Nitric Oxide/*metabolism ; Oxidation-Reduction ; Plants/metabolism ; Urea/*metabolism ; }, abstract = {C1 compounds participate in various metabolic processes and regulations including DNA methylation. Formaldehyde (FA), a product of methyl group oxidation, is highly cytotoxic. In the cell, there are two pathways of its utilization: assimilation and oxidation. Formaldehyde displays cytotoxicity, and therefore its oxidation is considered as detoxification. The sensitivity to the threshold concentration of FA we regard as an indication of its major role in biosystem functioning. A model of a three-component conjugated redox system is proposed in which the methyl group oxidation pathway is an archaic and conservative donor of protons and electrons, the reduction of O2 serves as an acceptor, and the arginine amino group is used for production of both urea and nitric oxide (the donor and acceptor, respectively). The fourth component of the redox system is glutathione, which maintains redox balance. The three-level system of proton donors includes the oxidation of a methyl group (first level), the oxidation of acetate in mitochondria (second level), and glucose catabolism in the pentose phosphate pathway (third level). The whole redox system is united by the sulfhydryl groups of cysteines, glutathione, thioredoxin, and α-lipoic acid. The central regulatory role in this redox system belongs to glutathione-dependent formaldehyde dehydrogenase, which controls FA binding with tetrahydrofolic acid, arginine methylation, and denitrosation of sulfhydryl groups. The conjugated redox system was formed during evolution as a union of separate redox cycles of carbon, nitrogen, sulfur, and oxygen.}, }
@article {pmid26545917, year = {2016}, author = {Delewski, W and Paterkiewicz, B and Manicki, M and Schilke, B and Tomiczek, B and Ciesielski, SJ and Nierzwicki, L and Czub, J and Dutkiewicz, R and Craig, EA and Marszalek, J}, title = {Iron-Sulfur Cluster Biogenesis Chaperones: Evidence for Emergence of Mutational Robustness of a Highly Specific Protein-Protein Interaction.}, journal = {Molecular biology and evolution}, volume = {33}, number = {3}, pages = {643-656}, pmid = {26545917}, issn = {1537-1719}, support = {R01 GM027870/GM/NIGMS NIH HHS/United States ; GM27870/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Motifs ; Amino Acid Substitution ; Evolution, Molecular ; Fungal Proteins/genetics/metabolism ; HSP70 Heat-Shock Proteins/chemistry/genetics/metabolism ; Iron/*metabolism ; Microbial Viability/genetics ; Models, Molecular ; Molecular Chaperones/chemistry/*genetics/*metabolism ; *Mutation ; Protein Binding ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Interaction Mapping ; Protein Interaction Maps ; Saccharomyces cerevisiae/genetics/metabolism ; Schizosaccharomyces/genetics/metabolism ; *Sulfur ; }, abstract = {Biogenesis of iron-sulfur clusters (FeS) is a highly conserved process involving Hsp70 and J-protein chaperones. However, Hsp70 specialization differs among species. In most eukaryotes, including Schizosaccharomyces pombe, FeS biogenesis involves interaction between the J-protein Jac1 and the multifunctional Hsp70 Ssc1. But, in Saccharomyces cerevisiae and closely related species, Jac1 interacts with the specialized Hsp70 Ssq1, which emerged through duplication of SSC1. As little is known about how gene duplicates affect the robustness of their protein interaction partners, we analyzed the functional and evolutionary consequences of Ssq1 specialization on the ubiquitous J-protein cochaperone Jac1, by comparing S. cerevisiae and S. pombe. Although deletion of JAC1 is lethal in both species, alanine substitutions within the conserved His-Pro-Asp (HPD) motif, which is critical for Jac1:Hsp70 interaction, have species-specific effects. They are lethal in S. pombe, but not in S. cerevisiae. These in vivo differences correlated with in vitro biochemical measurements. Charged residues present in the J-domain of S. cerevisiae Jac1, but absent in S. pombe Jac1, are important for tolerance of S. cerevisiae Jac1 to HPD alterations. Moreover, Jac1 orthologs from species that encode Ssq1 have a higher sequence divergence. The simplest interpretation of our results is that Ssq1's coevolution with Jac1 resulted in expansion of their binding interface, thus increasing the efficiency of their interaction. Such an expansion could in turn compensate for negative effects of HPD substitutions. Thus, our results support the idea that the robustness of Jac1 emerged as consequence of its highly efficient and specific interaction with Ssq1.}, }
@article {pmid26545175, year = {2016}, author = {Wang, C and Zhao, S and Du, Y and Guo, Z}, title = {Single nucleotide polymorphisms in the D-loop region of mitochondrial DNA is associated with colorectal cancer outcome.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4361-4363}, doi = {10.3109/19401736.2015.1089502}, pmid = {26545175}, issn = {2470-1408}, mesh = {Biological Evolution ; Colorectal Neoplasms/genetics ; DNA, Mitochondrial/*genetics ; Gene Order ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Humans ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Prognosis ; Sequence Analysis, DNA/methods ; }, abstract = {Single nucleotide polymorphisms (SNPs) in the displacement loop (D-Loop) of mitochondrial DNA (mtDNA) has been identified for their association with the risk and outcome in many cancers. We have identified risk associated D-loop SNPs for colorectal cancer previously, in the present study, we evaluate their prognostic value for postoperative survival of colorectal cancer (CRC). The minor haplotype of nucleotides 16290T and frequent haplotype of nucleotide 16298T in the hypervariable segment 1 (HV1) region of the D-loop were identified for their association with high survival rate of CRC. After adjusted with COX proportional hazard model, the nucleotide site of 16290 was identified as independent predictor for CRC (RR, 0.379; 95% CI, 0.171-0.839; p = 0.017). In conclusion, SNPs in the mtDNA D-Loop were found to be valuable markers for colorectal cancer outcome evaluation.}, }
@article {pmid26544530, year = {2016}, author = {Zhou, T and Li, D and Dujsebayeva, TN and Liu, J and Guo, X}, title = {Complete mitochondrial genome of Stummer's Racerunner (Eremias stummeri) from Kazakhstan.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4340-4341}, doi = {10.3109/19401736.2015.1089491}, pmid = {26544530}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Kazakhstan ; Lizards/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The whole mitochondrial genome was determined from a viviparous racerunner, Eremias stummeri, which was collected from southeast Kazakhstan. The mitogenome sequence was 19 602 bp in size, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region, which is similar to the typical mtDNA of vertebrates. Mitochondrial genomes analyses using maximum parsimony and Bayesian analyses yielded identical phylogenetic trees, indicating a close phylogenetic affinity of the sampled taxa in genus Eremias. Monophyly of both Eremias and its viviparous group is recovered. The complete mitogenome sequence of E. stummeri provides fundamental data for resolving phylogeneitc and genetic problems related to Eremias viviparity.}, }
@article {pmid26544023, year = {2016}, author = {Shi, X and Zhu, Q and Wu, N and Tu, J and Yang, D and Xu, H and Yao, Y and Yang, M and Li, D}, title = {The complete nucleotide sequence of the mitochondrial genome of Drosophila formosana (Diptera: Drosophilidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4316-4317}, doi = {10.3109/19401736.2015.1089480}, pmid = {26544023}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; DNA, Mitochondrial/*genetics ; Drosophila/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Nucleotides ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Drosophila formosana (Diptera: Drosophilidae) belongs to the Drosophilidae group of Drosophila. The mitochondrial genome sequence of Drosophila formosana is determined in this study. Mitochondrion of D. formosana is a circular DNA molecule of the 16 100 nucleotide pairs (bp) that contains one encoding region including 37 genes and 1 non-coding A + T-rich region. The similarity and typicality have been showed by the structure and organization analysis. All genes are arranged in the circular DNA molecule. In addition to DN5 that use GTG start codon, all other protein-coding genes (PCGs) start with an ATN start codon. Ten protein-coding genes stop with the termination codon TAN, while other protein-coding genes (PCGs) used incomplete termination codon TA- (cox2, nad5, nad1). The A + T-rich region with a length of 1088 bp is located between rrnS and trnI. The mitochondrial genome of D. formosana has been completely sequenced for the first time in this study.}, }
@article {pmid26540489, year = {2016}, author = {Çolak, R and Olgun Karacan, G and Kandemir, I and Çolak, E and Kankiliç, T and Yigit, N and Michaux, J}, title = {Genetic variations of Turkish bank vole, Myodes glareolus (Mammalia: Rodentia) inferred from mtDNA.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4372-4379}, doi = {10.3109/19401736.2015.1089537}, pmid = {26540489}, issn = {2470-1408}, mesh = {Animals ; Arvicolinae/*genetics ; Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Gene Order ; Genes, Mitochondrial/genetics ; Genetic Variation ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Rodentia/genetics ; Sequence Analysis, DNA/methods ; Turkey ; }, abstract = {The bank vole, Myodes glareolus, lives in deciduous forests throughout the Palearctic region. In Turkey, this species is distributed only in northern Anatolia (the Black Sea region) where these forests exist. This study reveals genetic differentiation among bank vole populations based on two regions of mitochondrial DNA (cytochrome b and D-loop). Populations in northern Anatolia are divided into two genetic lineages (the "eastern" and "western Black Sea" lineages) by the Kızılırmak Valley. While the western Black Sea lineage is close to the Balkan lineage, in accordance with their geographical proximities, surprisingly, the Uludag lineage, also situated in Western Turkey appears related to the eastern Black Sea population. The divergence time analyses suggest a separation between the Balkan and Turkish groups around 0.26 Mya, whereas the split between the eastern and western Black sea lineages appeared a little bit later (0.20 Mya). Our results suggest that regional refuges existed for this species in Turkey and that small-scale habitat fragmentations led to genetic differentiations between Myodes populations.}, }
@article {pmid26539745, year = {2016}, author = {He, S and Lu, J and Jiang, W and Yang, S and Yang, J and Shi, Q}, title = {The complete mitochondrial genome sequence of a cavefish Sinocyclocheilus anshuiensis (Cypriniformes: Cyprinidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4256-4258}, doi = {10.3109/19401736.2015.1046127}, pmid = {26539745}, issn = {2470-1408}, mesh = {Animals ; China ; Cyprinidae/*genetics ; Cypriniformes/*genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Open Reading Frames/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; }, abstract = {Sinocyclocheilus anshuiensis is a special cavefish that lives in the Southwestern China with many specific regressive features, such as rudimentary eyes and scales, and loss of pigmentation. In this study, we performed sequencing and assembly of its complete mitochondrial genome. We confirmed that total length of the mitochondrion is 16 618 bp with an AT ratio of 55.4%. The complete mitochondrial genome contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and a 963 bp control region. Our current data provide important resources for the research of cavefish mitochondrial evolution and energy metabolism.}, }
@article {pmid26538459, year = {2015}, author = {Bhandari, S and Zhang, X and Cui, C and Bianba,  and Liao, S and Peng, Y and Zhang, H and Xiang, K and Shi, H and Ouzhuluobu,  and Baimakongzhuo,  and Gonggalanzi,  and Liu, S and Gengdeng,  and Wu, T and Qi, X and Su, B}, title = {Genetic evidence of a recent Tibetan ancestry to Sherpas in the Himalayan region.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {16249}, pmid = {26538459}, issn = {2045-2322}, mesh = {Adaptation, Physiological/genetics ; Asian People/*genetics ; Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/genetics ; Ethnicity/*genetics ; Genetic Linkage/*genetics ; Genetic Variation/*genetics ; Genetics, Population/methods ; Haplotypes/genetics ; Humans ; Mitochondria/genetics ; Nepal ; Phylogeny ; Tibet ; }, abstract = {Sherpas living around the Himalayas are renowned as high-altitude mountain climbers but when and where the Sherpa people originated from remains contentious. In this study, we collected DNA samples from 582 Sherpas living in Nepal and Tibet Autonomous Region of China to study the genetic diversity of both their maternal (mitochondrial DNA) and paternal (Y chromosome) lineages. Analysis showed that Sherpas share most of their paternal and maternal lineages with indigenous Tibetans, representing a recently derived sub-lineage. The estimated ages of two Sherpa-specific mtDNA sub-haplogroups (C4a3b1 and A15c1) indicate a shallow genetic divergence between Sherpas and Tibetans less than 1,500 years ago. These findings reject the previous theory that Sherpa and Han Chinese served as dual ancestral populations of Tibetans, and conversely suggest that Tibetans are the ancestral populations of the Sherpas, whose adaptive traits for high altitude were recently inherited from their ancestors in Tibet.}, }
@article {pmid26535725, year = {2015}, author = {Andrade, BS and Góes-Neto, A}, title = {Phylogenetic analysis of DNA and RNA polymerases from a Moniliophthora perniciosa mitochondrial plasmid reveals probable lateral gene transfer.}, journal = {Genetics and molecular research : GMR}, volume = {14}, number = {4}, pages = {14105-14114}, doi = {10.4238/2015.October.29.30}, pmid = {26535725}, issn = {1676-5680}, mesh = {Agaricales/*enzymology/*genetics ; Cacao/microbiology ; DNA-Directed DNA Polymerase/*genetics ; DNA-Directed RNA Polymerases/*genetics ; *Gene Transfer, Horizontal ; Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Plant Diseases/microbiology ; Plasmids/genetics ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; }, abstract = {The filamentous fungus Moniliophthora perniciosa is a hemibiotrophic basidiomycete that causes witches' broom disease of cacao (Theobroma cacao L.). Many fungal mitochondrial plasmids are DNA and RNA polymerase-encoding invertrons with terminal inverted repeats and 5'-linked proteins. The aim of this study was to carry out comparative and phylogenetic analyses of DNA and RNA polymerases for all known linear mitochondrial plasmids in fungi. We performed these analyses at both gene and protein levels and assessed differences between fungal and viral polymerases in order to test the lateral gene transfer (LGT) hypothesis. We analyzed all mitochondrial plasmids of the invertron type within the fungal clade, including five from Ascomycota, seven from Basidiomycota, and one from Chytridiomycota. All phylogenetic analyses generated similar tree topologies regardless of the methods and datasets used. It is likely that DNA and RNA polymerase genes were inserted into the mitochondrial genomes of the 13 fungal species examined in our study as a result of different LGT events. These findings are important for a better understanding of the evolutionary relationships between fungal mitochondrial plasmids.}, }
@article {pmid26530087, year = {2015}, author = {Wagner, S and Behera, S and De Bortoli, S and Logan, DC and Fuchs, P and Carraretto, L and Teardo, E and Cendron, L and Nietzel, T and Füßl, M and Doccula, FG and Navazio, L and Fricker, MD and Van Aken, O and Finkemeier, I and Meyer, AJ and Szabò, I and Costa, A and Schwarzländer, M}, title = {The EF-Hand Ca2+ Binding Protein MICU Choreographs Mitochondrial Ca2+ Dynamics in Arabidopsis.}, journal = {The Plant cell}, volume = {27}, number = {11}, pages = {3190-3212}, pmid = {26530087}, issn = {1532-298X}, mesh = {Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/*metabolism ; Calcium ; Calcium Signaling ; Calcium-Binding Proteins/*metabolism ; Cell Respiration ; Cytosol/metabolism ; DNA, Bacterial/genetics ; *EF Hand Motifs ; Mitochondria/*metabolism/ultrastructure ; Mutagenesis, Insertional/genetics ; Phylogeny ; Plant Roots/metabolism/ultrastructure ; Protein Binding ; Protein Transport ; Seedlings/metabolism ; Sequence Homology, Amino Acid ; Subcellular Fractions/metabolism ; }, abstract = {Plant organelle function must constantly adjust to environmental conditions, which requires dynamic coordination. Ca(2+) signaling may play a central role in this process. Free Ca(2+) dynamics are tightly regulated and differ markedly between the cytosol, plastid stroma, and mitochondrial matrix. The mechanistic basis of compartment-specific Ca(2+) dynamics is poorly understood. Here, we studied the function of At-MICU, an EF-hand protein of Arabidopsis thaliana with homology to constituents of the mitochondrial Ca(2+) uniporter machinery in mammals. MICU binds Ca(2+) and localizes to the mitochondria in Arabidopsis. In vivo imaging of roots expressing a genetically encoded Ca(2+) sensor in the mitochondrial matrix revealed that lack of MICU increased resting concentrations of free Ca(2+) in the matrix. Furthermore, Ca(2+) elevations triggered by auxin and extracellular ATP occurred more rapidly and reached higher maximal concentrations in the mitochondria of micu mutants, whereas cytosolic Ca(2+) signatures remained unchanged. These findings support the idea that a conserved uniporter system, with composition and regulation distinct from the mammalian machinery, mediates mitochondrial Ca(2+) uptake in plants under in vivo conditions. They further suggest that MICU acts as a throttle that controls Ca(2+) uptake by moderating influx, thereby shaping Ca(2+) signatures in the matrix and preserving mitochondrial homeostasis. Our results open the door to genetic dissection of mitochondrial Ca(2+) signaling in plants.}, }
@article {pmid26524115, year = {2016}, author = {Denning, C and Borgdorff, V and Crutchley, J and Firth, KS and George, V and Kalra, S and Kondrashov, A and Hoang, MD and Mosqueira, D and Patel, A and Prodanov, L and Rajamohan, D and Skarnes, WC and Smith, JG and Young, LE}, title = {Cardiomyocytes from human pluripotent stem cells: From laboratory curiosity to industrial biomedical platform.}, journal = {Biochimica et biophysica acta}, volume = {1863}, number = {7 Pt B}, pages = {1728-1748}, pmid = {26524115}, issn = {0006-3002}, support = {BB/G021821/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; PG/09/027/27141/BHF_/British Heart Foundation/United Kingdom ; NC/K000225/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; NC/C013105/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; G0801098/MRC_/Medical Research Council/United Kingdom ; PG/14/59/31000/BHF_/British Heart Foundation/United Kingdom ; G113/30/MRC_/Medical Research Council/United Kingdom ; BBS/B/06164/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RG/14/1/30588/BHF_/British Heart Foundation/United Kingdom ; MR/M017354/1/MRC_/Medical Research Council/United Kingdom ; RG/11/19/29264/BHF_/British Heart Foundation/United Kingdom ; BB/G010390/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/E006159/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L012618/1/MRC_/Medical Research Council/United Kingdom ; NC/C013202/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; }, mesh = {Biomedical Research/*methods ; Cardiovascular Agents/*pharmacology/toxicity ; Cell Differentiation ; *Cell Lineage ; Cell Proliferation ; Cells, Cultured ; Drug Discovery/*methods ; Genotype ; Heart Diseases/chemically induced/*drug therapy/metabolism/pathology/physiopathology ; *High-Throughput Screening Assays ; Humans ; Induced Pluripotent Stem Cells/drug effects/metabolism/*physiology ; Myocytes, Cardiac/drug effects/metabolism/*physiology ; Phenotype ; Risk Assessment ; Toxicity Tests/*methods ; }, abstract = {Cardiomyocytes from human pluripotent stem cells (hPSCs-CMs) could revolutionise biomedicine. Global burden of heart failure will soon reach USD $90bn, while unexpected cardiotoxicity underlies 28% of drug withdrawals. Advances in hPSC isolation, Cas9/CRISPR genome engineering and hPSC-CM differentiation have improved patient care, progressed drugs to clinic and opened a new era in safety pharmacology. Nevertheless, predictive cardiotoxicity using hPSC-CMs contrasts from failure to almost total success. Since this likely relates to cell immaturity, efforts are underway to use biochemical and biophysical cues to improve many of the ~30 structural and functional properties of hPSC-CMs towards those seen in adult CMs. Other developments needed for widespread hPSC-CM utility include subtype specification, cost reduction of large scale differentiation and elimination of the phenotyping bottleneck. This review will consider these factors in the evolution of hPSC-CM technologies, as well as their integration into high content industrial platforms that assess structure, mitochondrial function, electrophysiology, calcium transients and contractility. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Integration of Developmental and Environmental Cues in the Heart edited by Marcus Schaub and Hughes Abriel.}, }
@article {pmid26518739, year = {2016}, author = {Lam, DW and Verbruggen, H and Saunders, GW and Vis, ML}, title = {Multigene phylogeny of the red algal subclass Nemaliophycidae.}, journal = {Molecular phylogenetics and evolution}, volume = {94}, number = {Pt B}, pages = {730-736}, doi = {10.1016/j.ympev.2015.10.015}, pmid = {26518739}, issn = {1095-9513}, mesh = {Bayes Theorem ; *Genes, Plant ; Genetic Markers ; Mitochondria/genetics ; Molecular Typing ; Phylogeny ; Plastids/genetics ; Rhodophyta/*classification ; }, abstract = {The red algae (Rhodophyta) are a lineage of primary endosymbionts whose ancestors represent some of the first photosynthetic eukaryotes on the planet. They primarily inhabit marine ecosystems, with only ∼5% of species found in freshwater systems. The subclass Nemaliophycidae is very diverse in ecological and life history features and therefore a useful model to study these traits, but the phylogenetic relationships among the orders are, for the most part, poorly resolved. To elucidate the phylogeny of the Nemaliophycidae, we constructed a nine-gene dataset comprised of nuclear, plastid, and mitochondrial markers for 67 red algal specimens. The resulting maximum likelihood (ML) phylogeny confirmed the monophyly of all orders. The sister relationship of the Acrochaetiales and Palmariales received high support and the relationship of the Balliales with Balbianiales and Entwisleiales with Colaconematales was moderately supported. The Nemaliales, Entwisleiales, Colaconematales, Palmariales and Acrochaetiales formed a highly supported clade. Unfortunately, all other relationships among the orders had low bootstrap support. Although the ML analysis did not resolve many of the relationships, further analyses suggested that a resolution is possible. A Phycas analysis supported a dichotomously branching tree and Bayesian analysis showed a similar topology with all relationships highly supported. Simulations extrapolating the number of nucleotide characters beyond the current size of the dataset suggested that most nodes in the phylogeny would be resolved if more data become available. Phylogenomic approaches will be necessary to provide a well-supported phylogeny of this subclass with all relationships resolved such that the evolution of freshwater species from marine ancestors as well as reproductive traits can be explored.}, }
@article {pmid26517908, year = {2015}, author = {Schaedler, TA and Faust, B and Shintre, CA and Carpenter, EP and Srinivasan, V and van Veen, HW and Balk, J}, title = {Structures and functions of mitochondrial ABC transporters.}, journal = {Biochemical Society transactions}, volume = {43}, number = {5}, pages = {943-951}, doi = {10.1042/BST20150118}, pmid = {26517908}, issn = {1470-8752}, support = {106169//Wellcome Trust/United Kingdom ; BB/H00288X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {ATP-Binding Cassette Transporters/classification/genetics/*metabolism ; Animals ; Crystallography, X-Ray ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Mutation ; Phylogeny ; Plant Proteins/chemistry/genetics/metabolism ; Saccharomyces cerevisiae/chemistry/genetics/metabolism ; }, abstract = {A small number of physiologically important ATP-binding cassette (ABC) transporters are found in mitochondria. Most are half transporters of the B group forming homodimers and their topology suggests they function as exporters. The results of mutant studies point towards involvement in iron cofactor biosynthesis. In particular, ABC subfamily B member 7 (ABCB7) and its homologues in yeast and plants are required for iron-sulfur (Fe-S) cluster biosynthesis outside of the mitochondria, whereas ABCB10 is involved in haem biosynthesis. They also play a role in preventing oxidative stress. Mutations in ABCB6 and ABCB7 have been linked to human disease. Recent crystal structures of yeast Atm1 and human ABCB10 have been key to identifying substrate-binding sites and transport mechanisms. Combined with in vitro and in vivo studies, progress is being made to find the physiological substrates of the different mitochondrial ABC transporters.}, }
@article {pmid26512981, year = {2016}, author = {Zheng, F and Liu, H and Zhang, Y and Wang, Q and Wang, B}, title = {Complete mitochondrial genome of the Pseudopleuronectes yokohamae (Pleuronectiforll: Pleuronectidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4347-4348}, doi = {10.3109/19401736.2015.1089494}, pmid = {26512981}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Flatfishes/genetics ; Flounder/*genetics ; Gene Order ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {In this study, the complete mitochondrial genome of the Pseudopleuronectes yokohamae was sequenced. The mitochondrial genome is 17 383 bp in length, consisting of 13 protein-coding genes, 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs) and a control region (D-loop). The gene order and composition of P. yokohamae mitochondrial genome was similar to that of most other vertebrates. Two rRNA genes for 12S rRNA (949 bases) and 16S rRNA (1716 bases) are located between tRNA-Phe (GAA) and tRNA-Leu (TAA) and separated by the tRNA-Val. The control region of P. yokohamae, is located after tRNA-Pro and found to be 1679 bp. The overall nucleotides base composition of the heavy strand is A (27.55%), T (26.45%), G (28.75%), C (17.26%). With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The 22 tRNA genes could be folded into a typical clover-leaf secondary structure. The phylogenetic trees consistently show that P. yokohama, Kareius bicoloratus and Platichthys stellatus from the same genus clustered into one branch. The complete mitogenome sequence information of P. yokohamae would provide useful data for further studies on population genetics and molecular systematics.}, }
@article {pmid26512320, year = {2015}, author = {Wideman, JG}, title = {The ubiquitous and ancient ER membrane protein complex (EMC): tether or not?.}, journal = {F1000Research}, volume = {4}, number = {}, pages = {624}, pmid = {26512320}, issn = {2046-1402}, abstract = {The recently discovered endoplasmic reticulum (ER) membrane protein complex (EMC) has been implicated in ER-associated degradation (ERAD), lipid transport and tethering between the ER and mitochondrial outer membranes, and assembly of multipass ER-membrane proteins. The EMC has been studied in both animals and fungi but its presence outside the Opisthokont clade (animals + fungi + related protists) has not been demonstrated. Here, using homology-searching algorithms, I show that the EMC is truly an ancient and conserved protein complex, present in every major eukaryotic lineage. Very few organisms have completely lost the EMC, and most, even over 2 billion years of eukaryote evolution, have retained a majority of the complex members. I identify Sop4 and YDR056C in Saccharomyces cerevisiae as Emc7 and Emc10, respectively, subunits previously thought to be specific to animals. This study demonstrates that the EMC was present in the last eukaryote common ancestor (LECA) and is an extremely important component of eukaryotic cells even though its primary function remains elusive.}, }
@article {pmid26510672, year = {2015}, author = {Alexander, M and Ho, SY and Molak, M and Barnett, R and Carlborg, &#xd6; and Dorshorst, B and Honaker, C and Besnier, F and Wahlberg, P and Dobney, K and Siegel, P and Andersson, L and Larson, G}, title = {Mitogenomic analysis of a 50-generation chicken pedigree reveals a rapid rate of mitochondrial evolution and evidence for paternal mtDNA inheritance.}, journal = {Biology letters}, volume = {11}, number = {10}, pages = {}, pmid = {26510672}, issn = {1744-957X}, support = {337574/ERC_/European Research Council/International ; }, mesh = {Animals ; Animals, Newborn ; *Biological Evolution ; Body Weight ; Chickens/*genetics ; DNA, Mitochondrial/*genetics ; Female ; Genome, Mitochondrial ; Male ; Mitochondria/*genetics ; Mutation Rate ; Pedigree ; Time Factors ; }, abstract = {Mitochondrial genomes represent a valuable source of data for evolutionary research, but studies of their short-term evolution have typically been limited to invertebrates, humans and laboratory organisms. Here we present a detailed study of 12 mitochondrial genomes that span a total of 385 transmissions in a well-documented 50-generation pedigree in which two lineages of chickens were selected for low and high juvenile body weight. These data allowed us to test the hypothesis of time-dependent evolutionary rates and the assumption of strict maternal mitochondrial transmission, and to investigate the role of mitochondrial mutations in determining phenotype. The identification of a non-synonymous mutation in ND4L and a synonymous mutation in CYTB, both novel mutations in Gallus, allowed us to estimate a molecular rate of 3.13 × 10(-7) mutations/site/year (95% confidence interval 3.75 × 10(-8)-1.12 × 10(-6)). This is substantially higher than avian rate estimates based upon fossil calibrations. Ascertaining which of the two novel mutations was present in an additional 49 individuals also revealed an instance of paternal inheritance of mtDNA. Lastly, an association analysis demonstrated that neither of the point mutations was strongly associated with the phenotypic differences between the two selection lines. Together, these observations reveal the highly dynamic nature of mitochondrial evolution over short time periods.}, }
@article {pmid26510618, year = {2016}, author = {Yu, P and Yang, QC and Ding, SQ and Zhang, J and Li, XL and Bi, ZH and Wan, Q}, title = {The complete sequence of mitochondrial genome of Sinibotia pulchra (Cypriniformes: Cobitidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4318-4319}, doi = {10.3109/19401736.2015.1089481}, pmid = {26510618}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; Cyprinidae/genetics ; Cypriniformes/*genetics ; DNA, Mitochondrial/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Sinibotia pulchra (Cypriniformes: Cobitidae) is a small cyprinid fish. In this study, the complete mitochondrial genome sequence of S. pulchra is sequenced. The S. pulchra complete mitochondrial genome (GenBank accession no. KT362179) was a circular molecule of 16 568 bp in length, with 13 protein-coding genes (PCGs), 2 ribosome RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, an L-strand replication origin (OL) and a control region (D-loop). The nucleotide acid composition of the entire mitogenome was 31.69% for A, 25.63% for T, 26.94% for C and 15.74% for G, with an AT content of 57.32%. The AT content of 12S rRNA, 16S rRNA and D-loop was 50.21%, 56.86% and 66.74%, respectively.}, }
@article {pmid26507459, year = {2016}, author = {Ogata, T and Senoo, T and Kawano, S and Ikeda, S}, title = {Mitochondrial superoxide dismutase deficiency accelerates chronological aging in the fission yeast Schizosaccharomyces pombe.}, journal = {Cell biology international}, volume = {40}, number = {1}, pages = {100-106}, doi = {10.1002/cbin.10556}, pmid = {26507459}, issn = {1095-8355}, mesh = {Aging/*metabolism ; Antioxidants/metabolism ; DNA, Fungal/genetics ; Mitochondria/metabolism ; Mutation ; Mutation Rate ; Oxidative Stress/physiology ; Reactive Oxygen Species/metabolism ; Schizosaccharomyces/cytology/*enzymology/genetics ; Schizosaccharomyces pombe Proteins/genetics/*metabolism ; Superoxide Dismutase/*deficiency/genetics/metabolism ; Superoxides/metabolism ; }, abstract = {A mitochondrial superoxide dismutase (SOD2) is the first line of antioxidant defense against mitochondrial superoxide. Even though the involvement of SOD2 in lifespan has been studied extensively in several organisms, characterization of the aging process has not been performed for the sod2 mutant (sod2Δ) of a prominent model Schizosaccharomyces pombe. In this study, we measured the chronological lifespan of sod2Δ cells by their ability to survive in long-term culture. SOD2 deficiency drastically decreased cell viability in the stationary phase. The mutation frequency of nuclear DNA in sod2Δ was elevated in the stationary phase, and cellular proteins and nuclear DNA were extensively degraded, concurrent with cell death. The sod2 gene in wild-type cells could be induced by an increase in endogenous oxidative stresses, after which, SOD2 activity was substantially elevated during the stationary phase. Culture in a lower glucose concentration (calorie restriction) prominently extended the sod2Δ lifespan. Therefore, S. pombe SOD2 plays a critical role in longevity through its upregulation in the non-dividing phase.}, }
@article {pmid26505536, year = {2016}, author = {Brennan, IG and Bauer, AM and Jackman, TR}, title = {Mitochondrial introgression via ancient hybridization, and systematics of the Australian endemic pygopodid gecko genus Delma.}, journal = {Molecular phylogenetics and evolution}, volume = {94}, number = {Pt B}, pages = {577-590}, doi = {10.1016/j.ympev.2015.10.005}, pmid = {26505536}, issn = {1095-9513}, mesh = {Animals ; Australia ; DNA Primers ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; *Genetic Speciation ; Hybridization, Genetic ; Lizards/classification/*genetics ; Mitochondria/genetics ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Hybridization ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Of the more than 1500 species of geckos found across six continents, few remain as unfamiliar as the pygopodids - Family Pygopodidae (Gray, 1845). These gekkotans are limited to Australia (44 species) and New Guinea (2 species), but have diverged extensively into the most ecologically diverse limbless radiation save Serpentes. Current phylogenetic understanding of the family has relied almost exclusively on two works, which have produced and synthesized an immense amount of morphological, geographical, and molecular data. However, current interspecific relationships within the largest genus Delma Gray 1831 are based chiefly upon data from two mitochondrial loci (16s, ND2). Here, we reevaluate the interspecific relationships within the genus Delma using two mitochondrial and four nuclear loci (RAG1, MXRA5, MOS, DYNLL1), and identify points of strong conflict between nuclear and mitochondrial genomic data. We address mito-nuclear discordance, and remedy this conflict by recognizing several points of mitochondrial introgression as the result of ancient hybridization events. Owing to the legacy value and intraspecific informativeness, we suggest the continued use of ND2 as a phylogenetic marker. Results identify strong support for species groups, but relationships among these clades, and the placement of several enigmatic taxa remain uncertain. We suggest a more careful review of Delma australis and the 'northwest Australia' clade. Accurately assessing and addressing species richness and relationships within this endemic Australian Gekkotan genus is relevant for understanding patterns of squamate speciation across the region.}, }
@article {pmid26505145, year = {2016}, author = {Villarreal A, JC and Crandall-Stotler, BJ and Hart, ML and Long, DG and Forrest, LL}, title = {Divergence times and the evolution of morphological complexity in an early land plant lineage (Marchantiopsida) with a slow molecular rate.}, journal = {The New phytologist}, volume = {209}, number = {4}, pages = {1734-1746}, doi = {10.1111/nph.13716}, pmid = {26505145}, issn = {1469-8137}, mesh = {Base Sequence ; Likelihood Functions ; Marchantia/*anatomy &amp; histology ; Mitochondria/genetics ; *Phylogeny ; Plastids/genetics ; Time Factors ; }, abstract = {We present a complete generic-level phylogeny of the complex thalloid liverworts, a lineage that includes the model system Marchantia polymorpha. The complex thalloids are remarkable for their slow rate of molecular evolution and for being the only extant plant lineage to differentiate gas exchange tissues in the gametophyte generation. We estimated the divergence times and analyzed the evolutionary trends of morphological traits, including air chambers, rhizoids and specialized reproductive structures. A multilocus dataset was analyzed using maximum likelihood and Bayesian approaches. Relative rates were estimated using local clocks. Our phylogeny cements the early branching in complex thalloids. Marchantia is supported in one of the earliest divergent lineages. The rate of evolution in organellar loci is slower than for other liverwort lineages, except for two annual lineages. Most genera diverged in the Cretaceous. Marchantia polymorpha diversified in the Late Miocene, giving a minimum age estimate for the evolution of its sex chromosomes. The complex thalloid ancestor, excluding Blasiales, is reconstructed as a plant with a carpocephalum, with filament-less air chambers opening via compound pores, and without pegged rhizoids. Our comprehensive study of the group provides a temporal framework for the analysis of the evolution of critical traits essential for plants during land colonization.}, }
@article {pmid26503662, year = {2016}, author = {Nuralitha, S and Siregar, JE and Syafruddin, D and Roelands, J and Verhoef, J and Hoepelman, AI and Marzuki, S}, title = {Within-Host Selection of Drug Resistance in a Mouse Model of Repeated Incomplete Malaria Treatment: Comparison between Atovaquone and Pyrimethamine.}, journal = {Antimicrobial agents and chemotherapy}, volume = {60}, number = {1}, pages = {258-263}, pmid = {26503662}, issn = {1098-6596}, mesh = {Amino Acid Substitution ; Animals ; Antimalarials/*pharmacology ; Atovaquone/*pharmacology ; Cell Nucleus/drug effects/enzymology/genetics ; Cytochromes b/*genetics/metabolism ; Drug Resistance/drug effects/*genetics ; Gene Expression ; Host-Parasite Interactions ; Malaria/drug therapy/parasitology ; Mice ; Mice, Inbred BALB C ; Mitochondria/drug effects/enzymology/genetics ; Mutation Rate ; Parasitic Sensitivity Tests ; Plasmodium berghei/*drug effects/enzymology/genetics ; Protozoan Proteins/genetics/metabolism ; Pyrimethamine/*pharmacology ; Selection, Genetic ; Tetrahydrofolate Dehydrogenase/*genetics/metabolism ; Treatment Failure ; }, abstract = {The evolutionary selection of malaria parasites within individual hosts is an important factor in the emergence of drug resistance but is still not well understood. We have examined the selection process for drug resistance in the mouse malaria agent Plasmodium berghei and compared the dynamics of the selection for atovaquone and pyrimethamine. Resistance to these drugs has been shown to be associated with genetic lesions in the dihydrofolate reductase gene in the case of pyrimethamine and in the mitochondrial cytochrome b gene for atovaquone. A mouse malaria model for the selection of drug resistance, based on repeated incomplete treatment (RICT) with a therapeutic dose of antimalarial drugs, was established. The number of treatment cycles for the development of stable resistance to atovaquone (2.47 ± 0.70; n = 19) was found to be significantly lower than for pyrimethamine (5.44 ± 1.46; n = 16; P < 0.0001), even when the parental P. berghei Leiden strain was cloned prior to the resistance selection. Similar results were obtained with P. berghei Edinburgh. Mutational changes underlying the resistance were identified to be S110N in dihydrofolate reductase for pyrimethamine and Y268N, Y268C, Y268S, L271V-K272R, and G280D in cytochrome b for atovaquone. These results are consistent with the rate of mitochondrial DNA mutation being higher than that in the nucleus and suggest that mutation leading to pyrimethamine resistance is not a rare event.}, }
@article {pmid26501689, year = {2015}, author = {Breton, S and Stewart, DT}, title = {Atypical mitochondrial inheritance patterns in eukaryotes.}, journal = {Genome}, volume = {58}, number = {10}, pages = {423-431}, doi = {10.1139/gen-2015-0090}, pmid = {26501689}, issn = {1480-3321}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Eukaryota/*genetics ; Evolution, Molecular ; Female ; Genes, Dominant ; *Genes, Mitochondrial ; Genetic Variation ; Genome, Mitochondrial ; Humans ; Inheritance Patterns/*genetics ; Male ; Mitochondria/*genetics ; Sex Determination Processes ; }, abstract = {Mitochondrial DNA (mtDNA) is predominantly maternally inherited in eukaryotes. Diverse molecular mechanisms underlying the phenomenon of strict maternal inheritance (SMI) of mtDNA have been described, but the evolutionary forces responsible for its predominance in eukaryotes remain to be elucidated. Exceptions to SMI have been reported in diverse eukaryotic taxa, leading to the prediction that several distinct molecular mechanisms controlling mtDNA transmission are present among the eukaryotes. We propose that these mechanisms will be better understood by studying the deviations from the predominating pattern of SMI. This minireview summarizes studies on eukaryote species with unusual or rare mitochondrial inheritance patterns, i.e., other than the predominant SMI pattern, such as maternal inheritance of stable heteroplasmy, paternal leakage of mtDNA, biparental and strictly paternal inheritance, and doubly uniparental inheritance of mtDNA. The potential genes and mechanisms involved in controlling mitochondrial inheritance in these organisms are discussed. The linkage between mitochondrial inheritance and sex determination is also discussed, given that the atypical systems of mtDNA inheritance examined in this minireview are frequently found in organisms with uncommon sexual systems such as gynodioecy, monoecy, or andromonoecy. The potential of deviations from SMI for facilitating a better understanding of a number of fundamental questions in biology, such as the evolution of mtDNA inheritance, the coevolution of nuclear and mitochondrial genomes, and, perhaps, the role of mitochondria in sex determination, is considerable.}, }
@article {pmid26497252, year = {2017}, author = {Long, Z and Zhang, X and Sun, Q and Liu, Y and Liao, N and Wu, H and Wang, X and Hai, C}, title = {Evolution of metabolic disorder in rats fed high sucrose or high fat diet: Focus on redox state and mitochondrial function.}, journal = {General and comparative endocrinology}, volume = {242}, number = {}, pages = {92-100}, doi = {10.1016/j.ygcen.2015.10.012}, pmid = {26497252}, issn = {1095-6840}, mesh = {Animals ; Diet, High-Fat/*adverse effects ; Dietary Sucrose/administration &amp; dosage/*adverse effects ; Energy Metabolism ; Glucose/metabolism ; Glucose Intolerance/metabolism ; Insulin/metabolism ; Insulin Resistance ; Male ; Metabolic Diseases ; Mitochondria/*drug effects/physiology ; Oxidation-Reduction ; Oxidative Stress ; Rats ; }, abstract = {Glucotoxicity and lipotoxicity are major hallmarks of metabolic disorder. High consumption of fat or carbohydrate rich food is a major risk of metabolic disorder. However, the evolution of high fat or high carbohydrate diet-induced metabolic disorder is not clear. In the study, we tried to find distinguished and common ways involved in the pathogenesis of insulin resistance induced by high fat (HF) and high sucrose (HS) diet. We found that HS diet induced mild glucose intolerance (2month), followed by a "temporary non-symptom phase" (3month), and then induced significant metabolic abnormality (4month). HF diet induced an early "responsive enhancement phase" (2month), and then gradually caused severe metabolic dysfunction (3-4month). After a mild induction of mitochondrial ROS generation (2month), HS diet resulted in a "temporary non-symptom phase" (3month), and then induced a more significant mitochondrial ROS production (4month). The impairment of mitochondrial function induced by HS diet was progressive (2-4month). HF diet induced gradual mitochondrial ROS generation and hyperpolarization. HF diet induced an early "responsive enhancement" of mitochondrial function (2month), and then gradually resulted in severe decrease of mitochondrial function (3-4month). Despite the patterns of HS and HF diet-induced insulin resistance were differential, final mitochondrial ROS generation combined with mitochondrial dysfunction may be the common pathway. These findings demonstrate a novel understanding of the mechanism of insulin resistance and highlight the pivotal role of mitochondrial ROS generation and mitochondrial dysfunction in the pathogenesis of metabolic disorder.}, }
@article {pmid26488305, year = {2016}, author = {Liu, JB and Zeng, YF and Yuan, C and Yue, YJ and Ding, XZ and Guo, TT and Han, JL and Feng, RL and Sun, XP and Niu, CE and Yang, BH and Guo, J}, title = {The complete mitochondrial genome sequence of the dwarf blue sheep, Pseudois schaeferi haltenorth in China.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4411-4413}, doi = {10.3109/19401736.2015.1089548}, pmid = {26488305}, issn = {2470-1408}, mesh = {Animals ; China ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial/genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; Sheep/*genetics ; Whole Genome Sequencing/methods ; }, abstract = {The dwarf blue sheep (Pseudois schaeferi haltenorth) belongs the subfamily Caprinae, which is distributed in Sichuan, Tibet, Yunnan, and Qinghai in China. In this study, the complete mitochondrial genome of Pseudois schaeferi haltenorth was sequenced. The mitogenome was 16 741 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a non-coding control region (D-loop region). As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the Pseudois schaeferi haltenorth is 33.54% A, 26.37% T, 26.91% C, and 13.18% G, A + T (59.91%) was higher than G + C (40.09%). The phylogenetic relationships was analyzed using the complete mitogenome sequence, results show that P. schaeferi haltenorth should be a different species differ from the Genus pseudois hodgson. These information provide useful data for further study on the protection of genetic resources and the taxonomy of Caprinae.}, }
@article {pmid26487483, year = {2016}, author = {Liu, J and Jin, W and Wu, C}, title = {The first complete mitochondrial genome of Serranidae sp. (Percoidea, Serranidae) and phylogenetic analysis based on Bayesian.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4436-4438}, doi = {10.3109/19401736.2015.1089560}, pmid = {26487483}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Bayes Theorem ; Conserved Sequence/genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; }, abstract = {In the present study, the complete mitochondrial genome of Serranidae sp. was determined first. The entire mitochondrial genome of Serranidae sp. is 16 512 bp in length, containing 13 protein-coding genes and 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA) and 2 main non-coding regions (the control region and the origin of the light-strand replication). The gene arrangement, base composition and tRNA structures of Serranidae sp. are similar to most of the bony fishes. The central conserved sequence blocks (CSB-1, CSB-2, and CSB-3) and the core sequence (ACATATATGT) of terminal-associated sequences were recognized in the control region. Meanwhile, the conserved motif 5'-GCCGG-3' was identified in the origin of light-strand replication of Serranidae sp. Phylogenetic tree, which is constructed based on the complete mitochondrial genome sequences of Serranidae sp., shows that Serranidae sp. is clustered with the fishes of the family Pentacerotidae. We expect that the mitochondrial genome of Serranidae sp. would play a key role in phylogenetic analysis of Serranidae.}, }
@article {pmid26487099, year = {2015}, author = {Kolondra, A and Labedzka-Dmoch, K and Wenda, JM and Drzewicka, K and Golik, P}, title = {The transcriptome of Candida albicans mitochondria and the evolution of organellar transcription units in yeasts.}, journal = {BMC genomics}, volume = {16}, number = {}, pages = {827}, pmid = {26487099}, issn = {1471-2164}, mesh = {Amino Acid Sequence/genetics ; Base Sequence ; Candida albicans/*genetics ; DNA, Mitochondrial/genetics ; Gene Expression ; Gene Expression Regulation, Fungal ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Introns/genetics ; Mitochondria/genetics ; Organelles/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Saccharomyces cerevisiae/genetics ; Schizosaccharomyces/genetics ; *Transcription, Genetic ; Transcriptome/*genetics ; }, abstract = {BACKGROUND: Yeasts show remarkable variation in the organization of their mitochondrial genomes, yet there is little experimental data on organellar gene expression outside few model species. Candida albicans is interesting as a human pathogen, and as a representative of a clade that is distant from the model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. Unlike them, it encodes seven Complex I subunits in its mtDNA. No experimental data regarding organellar expression were available prior to this study.<br><br>METHODS: We used high-throughput RNA sequencing and traditional RNA biology techniques to study the mitochondrial transcriptome of C. albicans strains BWP17 and SN148.<br><br>RESULTS: The 14 protein-coding genes, two ribosomal RNA genes, and 24 tRNA genes are expressed as eight primary polycistronic transcription units. We also found transcriptional activity in the noncoding regions, and antisense transcripts that could be a part of a regulatory mechanism. The promoter sequence is a variant of the nonanucleotide identified in other yeast mtDNAs, but some of the active promoters show significant departures from the consensus. The primary transcripts are processed by a tRNA punctuation mechanism into the monocistronic and bicistronic mature RNAs. The steady state levels of various mature transcripts exhibit large differences that are a result of posttranscriptional regulation. Transcriptome analysis allowed to precisely annotate the positions of introns in the RNL (2), COB (2) and COX1 (4) genes, as well as to refine the annotation of tRNAs and rRNAs. Comparative study of the mitochondrial genome organization in various Candida species indicates that they undergo shuffling in blocks usually containing 2-3 genes, and that their arrangement in primary transcripts is not conserved. tRNA genes with their associated promoters, as well as GC-rich sequence elements play an important role in these evolutionary events.<br><br>CONCLUSIONS: The main evolutionary force shaping the mitochondrial genomes of yeasts is the frequent recombination, constantly breaking apart and joining genes into novel primary transcription units. The mitochondrial transcription units are constantly rearranged in evolution shaping the features of gene expression, such as the presence of secondary promoter sites that are inactive, or act as "booster" promoters, simplified transcriptional regulation and reliance on posttranscriptional mechanisms.}, }
@article {pmid26487090, year = {2016}, author = {Li, Z and Chen, Z and Gao, J and Wang, L and Chen, X and Zhao, Y}, title = {The complete mitochondrial genome of the Symphysodon aequifasciatus (Pellegrin, 1904).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4425-4426}, doi = {10.3109/19401736.2015.1089555}, pmid = {26487090}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Cichlids/*genetics ; DNA, Mitochondrial/*genetics ; Gene Order/genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {In this study, the complete mitogenome sequence of the Symphysodon aequifasciatus has been sequenced by next-generation sequencing method. The mitogenome consists of 16 545 bp, including 13 protein-coding genes, 22 transfer RNAs and 2 ribosomal RNAs genes. The overall base composition of the fish is 28.8% for A, 30.1% for C, 15.0% for G, and 26.1% for T, suggesting a 99% identity to S. discus Heckel and a 98% identity to S. haraldi. It provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for Symphysodon phylogeny.}, }
@article {pmid26486988, year = {2016}, author = {Yang, H and Bao, X and Wang, B and Liu, W}, title = {The complete mitochondrial genome of Chirolophis japonicus (Perciformes: Stichaeidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4419-4420}, doi = {10.3109/19401736.2015.1089552}, pmid = {26486988}, issn = {2470-1408}, mesh = {Amino Acid Sequence/genetics ; Animals ; Base Composition/genetics ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial/genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The complete mitochondrial genome of Chirolophis japonicus was sequenced for the first time in this study. It is a closed-circular molecule of 16 521 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, an origin of light strand replication (OL), and a control region (CR). The overall base composition of the heavy-strand is 25.5% A, 28.6% T, 18.3% G, and 27.6% C, and the lengths of 2 rRNA genes are 946 and 1692 bp, respectively. Maximum likelihood tree based on all the amino acid sequences of 13 mitochondrial PCGs was constructed, in which C. japonicus is close to three species of infraorder Zoarcales. These results are expected to provide useful molecular data for species identification and further phylogenetic studies of genus Chirolophis.}, }
@article {pmid26486753, year = {2016}, author = {Chen, D and Zhang, K and Liu, S and Chen, F}, title = {The complete mitochondrial genome of the Dipodomys ordii (Ord's kangaroo rat).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4322-4323}, doi = {10.3109/19401736.2015.1089483}, pmid = {26486753}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; DNA, Mitochondrial/*genetics ; Dipodomys/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Ord's kangaroo rat is a kangaroo rat native to western North America. In this study, we first reported the complete mitochondrial genome of Dipodomys ordii that the first has the complete mitochondrial genome in the genus of Heteromyidae. The mitogenome is a circular molecule of 16 257 bp in length, containing 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a putative displacement loop region. All protein-coding genes started with a traditional ATN codon and terminated with the mitochondria stop codon (TAA/TAG/AGA) or a single T base. The gene order and composition of mitogenome was similar to that of most other Sciurognathi species and its GC content was 36.73%. Thirteen protein-coding genes of D. ordii together with eight other closely species were used to construct the species phylogenetic tree for verification of the accuracy of new determined mitogenome sequences.}, }
@article {pmid26486169, year = {2016}, author = {Liu, J and Jin, W and Wu, C}, title = {Complete mitochondrial genome of banjofish (Banjos banjos): genome characterization and phylogenetic analysis.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4433-4435}, doi = {10.3109/19401736.2015.1089559}, pmid = {26486169}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Conserved Sequence/genetics ; DNA, Mitochondrial/genetics ; Fishes/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The banjofish (Banjos banjos) is the only species in the monotypic genus Banjos and in the family Banjosidae. To understand the phylogenetic relationship of banjofish in teleost, we firstly determined the complete mitochondrial genome of banjofish. The entire mitochondrial genome of banjofish is 16 485 bp in length, including 13 protein-coding genes and 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA) and a control region (CR). The overall base composition is T, 26.2%; C, 29.2%; A, 28.6% and G, 16.0%. The central conserved sequence blocks (CSB) were identified and the core sequence (ACATATATGT) of terminal-associated sequences was recognized in the control region. The gene arrangement, base composition, and tRNA structures of the complete mitochondrial genome of banjofish is consistent with those of other teleost. The complete mitochondrial genome of banjofish was used to construct phylogenetic tree, which shows that banjofish is clustered with the fishes of the family Histiopteridae. We expect that the availability of mitochondrial genome of banjofish will facilitate the further investigations of the taxonomic resolution, biogeography and molecular systematic.}, }
@article {pmid26484802, year = {2015}, author = {Granger, DN and Kvietys, PR}, title = {Reperfusion injury and reactive oxygen species: The evolution of a concept.}, journal = {Redox biology}, volume = {6}, number = {}, pages = {524-551}, pmid = {26484802}, issn = {2213-2317}, support = {R01 HL026441/HL/NHLBI NIH HHS/United States ; HL26441-32/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Cell Hypoxia ; Humans ; Oxidation-Reduction ; Oxidative Stress ; Reactive Oxygen Species/*metabolism ; Reperfusion Injury/*metabolism ; }, abstract = {Reperfusion injury, the paradoxical tissue response that is manifested by blood flow-deprived and oxygen-starved organs following the restoration of blood flow and tissue oxygenation, has been a focus of basic and clinical research for over 4-decades. While a variety of molecular mechanisms have been proposed to explain this phenomenon, excess production of reactive oxygen species (ROS) continues to receive much attention as a critical factor in the genesis of reperfusion injury. As a consequence, considerable effort has been devoted to identifying the dominant cellular and enzymatic sources of excess ROS production following ischemia-reperfusion (I/R). Of the potential ROS sources described to date, xanthine oxidase, NADPH oxidase (Nox), mitochondria, and uncoupled nitric oxide synthase have gained a status as the most likely contributors to reperfusion-induced oxidative stress and represent priority targets for therapeutic intervention against reperfusion-induced organ dysfunction and tissue damage. Although all four enzymatic sources are present in most tissues and are likely to play some role in reperfusion injury, priority and emphasis has been given to specific ROS sources that are enriched in certain tissues, such as xanthine oxidase in the gastrointestinal tract and mitochondria in the metabolically active heart and brain. The possibility that multiple ROS sources contribute to reperfusion injury in most tissues is supported by evidence demonstrating that redox-signaling enables ROS produced by one enzymatic source (e.g., Nox) to activate and enhance ROS production by a second source (e.g., mitochondria). This review provides a synopsis of the evidence implicating ROS in reperfusion injury, the clinical implications of this phenomenon, and summarizes current understanding of the four most frequently invoked enzymatic sources of ROS production in post-ischemic tissue.}, }
@article {pmid26481237, year = {2016}, author = {Liu, GX and Ma, HM and Xie, HY and Xuan, N and Picimbon, JF}, title = {Sequence variation of Bemisia tabaci Chemosensory Protein 2 in cryptic species B and Q: New DNA markers for whitefly recognition.}, journal = {Gene}, volume = {576}, number = {1 Pt 2}, pages = {284-291}, doi = {10.1016/j.gene.2015.10.036}, pmid = {26481237}, issn = {1879-0038}, mesh = {Animals ; Base Sequence ; China ; Deoxyribonucleases, Type II Site-Specific/genetics/metabolism ; Electron Transport Complex IV/genetics ; Gene Transfer, Horizontal ; *Genetic Markers ; Genetic Variation ; Genetics, Population ; Hemiptera/*genetics ; Insect Proteins/*genetics ; Introns ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Bemisia tabaci Gennadius biotypes B and Q are two of the most important worldwide agricultural insect pests. Genomic sequences of Type-2 B. tabaci chemosensory protein (BtabCSP2) were cloned and sequenced in B and Q biotypes, revealing key biotype-specific variations in the intron sequence. A Q260 sequence was found specifically in Q-BtabCSP2 and Cucumis melo LN692399, suggesting ancestral horizontal transfer of gene between the insect and the plant through bacteria. A cleaved amplified polymorphic sequences (CAPS) method was then developed to differentiate B and Q based on the sequence variation in exon of BtabCSP2 gene. The performances of CSP2-based CAPS for whitefly recognition were assessed using B. tabaci field collections from Shandong Province (P.R. China). Our SacII based CAPS method led to the same result compared to mitochondrial cytochrome oxidase-based CAPS method in the field collections. We therefore propose an explanation for CSP origin and a new rapid simple molecular method based on genomic DNA and chemosensory gene to differentiate accurately the B and Q whiteflies of the Bemisia complex around the world.}, }
@article {pmid26477565, year = {2016}, author = {Huynen, MA and Mühlmeister, M and Gotthardt, K and Guerrero-Castillo, S and Brandt, U}, title = {Evolution and structural organization of the mitochondrial contact site (MICOS) complex and the mitochondrial intermembrane space bridging (MIB) complex.}, journal = {Biochimica et biophysica acta}, volume = {1863}, number = {1}, pages = {91-101}, doi = {10.1016/j.bbamcr.2015.10.009}, pmid = {26477565}, issn = {0006-3002}, mesh = {Cell Line, Tumor ; *Evolution, Molecular ; Humans ; Mitochondrial Proteins/*genetics ; Multiprotein Complexes/*genetics ; }, abstract = {We have analyzed the distribution of mitochondrial contact site and cristae organizing system (MICOS) complex proteins and mitochondrial intermembrane space bridging complex (MIB) proteins over (sub)complexes and over species. The MICOS proteins are associated with the formation and maintenance of mitochondrial cristae. Indeed, the presence of MICOS genes in genomes correlates well with the presence of cristae: all cristae containing species have at least one MICOS gene and cristae-less species have none. Mic10 is the most widespread MICOS gene, while Mic60 appears be the oldest one, as it originates in the ancestors of mitochondria, the proteobacteria. In proteobacteria the gene occurs in clusters with genes involved in heme synthesis while the protein has been observed in intracellular membranes of the alphaproteobacterium Rhodobacter sphaeroides. In contrast, Mic23 and Mic27 appear to be the youngest MICOS proteins, as they only occur in opisthokonts. The remaining MICOS proteins, Mic10, Mic19, Mic25 and Mic12, the latter we show to be orthologous to human C19orf70/QIL1, trace back to the root of the eukaryotes. Of the remaining MIB proteins, also DNAJC11 shows a high correlation with the presence of cristae. In mitochondrial protein complexome profiles, the MIB complex occurs as a defined complex and as separate subcomplexes, potentially reflecting various assembly stages. We find three main forms of the complex: A) The MICOS complex, containing all the MICOS proteins, B) a membrane bridging subcomplex, containing in addition SAMM50, MTX2 and the previously uncharacterized MTX3, and C) the complete MIB complex containing in addition DNAJC11 and MTX1.}, }
@article {pmid26478175, year = {2016}, author = {Song, N and Li, H and Cai, W and Yan, F and Wang, J and Song, F}, title = {Phylogenetic relationships of Hemiptera inferred from mitochondrial and nuclear genes.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4380-4389}, doi = {10.3109/19401736.2015.1089538}, pmid = {26478175}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Gene Order ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Hemiptera/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Here, we reconstructed the Hemiptera phylogeny based on the expanded mitochondrial protein-coding genes and the nuclear 18S rRNA gene, separately. The differential rates of change across lineages may associate with long-branch attraction (LBA) effect and result in conflicting estimates of phylogeny from different types of data. To reduce the potential effects of systematic biases on inferences of topology, various data coding schemes, site removal method, and different algorithms were utilized in phylogenetic reconstruction. We show that the outgroups Phthiraptera, Thysanoptera, and the ingroup Sternorrhyncha share similar base composition, and exhibit "long branches" relative to other hemipterans. Thus, the long-branch attraction between these groups is suspected to cause the failure of recovering Hemiptera under the homogeneous model. In contrast, a monophyletic Hemiptera is supported when heterogeneous model is utilized in the analysis. Although higher level phylogenetic relationships within Hemiptera remain to be answered, consensus between analyses is beginning to converge on a stable phylogeny.}, }
@article {pmid26477802, year = {2016}, author = {Flynn, T and Signal, B and Johnson, SL and Gemmell, NJ}, title = {Mitochondrial genome diversity among six laboratory zebrafish (Danio rerio) strains.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4364-4371}, doi = {10.3109/19401736.2015.1089536}, pmid = {26477802}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Gene Order ; Genes, Mitochondrial/genetics ; Genetic Variation/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Mutation ; Phylogeny ; Sequence Analysis, DNA/methods ; Zebrafish/*genetics ; }, abstract = {The mitochondrial genome (mtDNA) is distinct from the nuclear genome and is known to play a significant role in several disease phenotypes, such as longevity and fertility. Here we characterize the complete mitochondrial genomes (∼16 590 bp), and the extent of within and between strain variation for 27 adult zebrafish, representing five commonly used laboratory strains (AB, TL, HL, WIK, and SJD) and one line acquired from a local pet shop. These data were subsequently analyzed to determine the phylogenetic relationships between strains and ascertain if positive selection might be operating on any mtDNA genes. Relationships between strains are not entirely consistent with those observed previously using nuclear DNA. Further there is a substantial body of variation within current zebrafish lines, with 172 variants described across lines. Of these, 27 changes are non-synonymous and there is nominal evidence for positive selection in the mtDNA sequences at some of these sites. We further identify novel frameshift mutations in eight genes, which are all predicted to have functional consequences. Our study provides the first information on mtDNA diversity in zebrafish, identifies multiple non-synonymous substitutions and other mutations expected to have functional effects, and represents an important first step in establishing zebrafish as a model for investigating the phenotypic effects of mtDNA mutations.}, }
@article {pmid26477699, year = {2016}, author = {Starostová, Z and Musilová, Z}, title = {The complete mitochondrial genome of the Madagascar ground gecko Paroedura picta (Squamata: Gekkonidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4397-4398}, doi = {10.3109/19401736.2015.1089540}, pmid = {26477699}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Gene Order ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Lizards/*genetics ; Madagascar ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {We sequenced the complete mitochondrial genome of the Madagascar ground gecko Paroedura picta (Squamata: Gekkonidae). The mitogenome is 17 220 base pairs long and conforms to the typical vertebrate gene composition and arrangement, i.e. 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and 1919 bp long control region. We reconstructed phylogenetic relationships of P. picta and representatives of nine other genera from the family Gekkonidae and calculated mean p-distances for all 13 protein-coding mitochondrial genes. The lowest mean p-distances were found in cytochrome oxidase subunit I and III genes (COI and COIII) indicating their usefulness for elucidating deeper phylogenetic relationships.}, }
@article {pmid26475939, year = {2016}, author = {Akihito,  and Akishinonomiya, F and Ikeda, Y and Aizawa, M and Nakagawa, S and Umehara, Y and Yonezawa, T and Mano, S and Hasegawa, M and Nakabo, T and Gojobori, T}, title = {Speciation of two gobioid species, Pterogobius elapoides and Pterogobius zonoleucus revealed by multi-locus nuclear and mitochondrial DNA analyses.}, journal = {Gene}, volume = {576}, number = {2 Pt 1}, pages = {593-602}, doi = {10.1016/j.gene.2015.10.014}, pmid = {26475939}, issn = {1879-0038}, mesh = {Animals ; Base Sequence ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Fishes/*classification/genetics ; Molecular Sequence Data ; Sequence Homology, Nucleic Acid ; }, abstract = {To understand how geographical differentiation of gobioid fish species led to speciation, two populations of the Pacific Ocean and the Sea of Japan for each of the two gobioid species, Pterogobius elapoides and Pterogobius zonoleucus, were studied in both morphological and molecular features. Analyzing mitochondrial genes, Akihito et al. (2008) suggested that P. zonoleucus does not form a monophyletic clade relative to P. elapoides, indicating that "Sea of Japan P. zonoleucus" and P. elapoides form a clade excluding "Pacific P. zonoleucus" as an outgroup. Because morphological classification clearly distinguish these two species and a gene tree may differ from a population tree, we examined three nuclear genes, S7RP, RAG1, and TBR1, in this work, in order to determine whether nuclear and mitochondrial trees are concordant, thus shedding light on the evolutionary history of this group of fishes. Importantly, nuclear trees were based on exactly the same individuals that were used for the previously published mtDNA trees. The tree based on RAG1 exon sequences suggested a closer relationship of P. elapoides with "Sea of Japan P. zonoleucus", which was in agreement with the mitochondrial tree. In contrast, S7RP and TBR1 introns recovered a monophyletic P. zonoleucus. If the mitochondrial tree represents the population tree in which P. elapoides evolved from "Sea of Japan P. zonoleucus", the population size of P. elapoides is expected to be smaller than that of "Sea of Japan P. zonoleucus". This is because a smaller population of the new species is usually differentiated from a larger population of the ancestral species when the speciation occurred. However, we found no evidence of such a small population size during the evolution of P. elapoides. Therefore, we conclude that the monophyletic P. zonoleucus as suggested by S7RP and TBR1 most likely represents the population tree, which is consistent with the morphological classification. In this case, it is possible that the incongruent mitochondrial and RAG1 trees are either due to incomplete lineage sorting of ancestral polymorphisms or to introgression by hybridization. Because of a smaller effective population size of mitochondria compared with nuclear genes, the introgression might be a more likely scenario in explaining the incongruent mitochondrial tree than the incomplete lineage sorting. Because of smaller effective population size of "Sea of Japan P. zonoleucus" than that of P. elapoides, the direction of the introgression was likely to be from the latter to the former. This evolutionary work of the two gobioid species highlights the need of analyzing multiple gene trees for both nuclear and mitochondrial genes as well as scrutinization of morphological characteristics to obtain a population tree representing the organismal evolutionary history.}, }
@article {pmid26475645, year = {2015}, author = {Bakhoum, AJ and Quilichini, Y and Justine, JL and Bray, RA and Miquel, J and Feliu, C and Bâ, CT and Marchand, B}, title = {First spermatological study in the Atractotrematidae (Digenea, Haploporoidea): the case of Atractotrema sigani, intestinal parasite of Siganus lineatus.}, journal = {Parasite (Paris, France)}, volume = {22}, number = {}, pages = {26}, pmid = {26475645}, issn = {1776-1042}, mesh = {Animals ; Axoneme/ultrastructure ; Fish Diseases/parasitology ; Intestinal Diseases, Parasitic/parasitology/veterinary ; Male ; Microscopy, Electron ; Microtubules/ultrastructure ; Organelles/ultrastructure ; Pacific Ocean ; Phylogeny ; Species Specificity ; Spermatozoa/*ultrastructure ; Trematoda/classification/*cytology ; Trematode Infections/parasitology/veterinary ; }, abstract = {The ultrastructural organization of the mature spermatozoon of the digenean Atractotrema sigani (from Siganus lineatus off New Caledonia) was investigated by transmission electron microscopy. The male gamete of A. sigani exhibits the general morphology described in digeneans with the presence of two axonemes of different lengths showing the 9 + "1" pattern of the Trepaxonemata, a nucleus, two mitochondria, two bundles of parallel cortical microtubules, external ornamentation, spine-like bodies and granules of glycogen. However, the mature spermatozoon of A. sigani has some specific characters such as the morphology of its anterior region and the submembranous electron-dense material. Although similar structures have been reported in some digenean species, the presence of a submembranous electron-dense material describing a complete ring is reported here for the first time in the mature spermatozoon of A. sigani. In addition, sperm characteristics are compared between the Haploporoidea and their supposed close superfamilies, and possible phylogenetic implications of these findings for the Digenea are discussed.}, }
@article {pmid26475173, year = {2015}, author = {Rada, P and Makki, AR and Zimorski, V and Garg, S and Hampl, V and Hrdý, I and Gould, SB and Tachezy, J}, title = {N-Terminal Presequence-Independent Import of Phosphofructokinase into Hydrogenosomes of Trichomonas vaginalis.}, journal = {Eukaryotic cell}, volume = {14}, number = {12}, pages = {1264-1275}, pmid = {26475173}, issn = {1535-9786}, mesh = {Adenosine Triphosphate/pharmacology ; Amino Acid Sequence ; Diphosphates/metabolism ; Ferredoxins/metabolism ; Hydrogen/*metabolism ; Mitochondria/drug effects/metabolism ; Molecular Sequence Data ; Organelles/drug effects/*metabolism ; Phosphofructokinases/*chemistry/*metabolism ; Phylogeny ; Promoter Regions, Genetic/genetics ; Protein Transport/drug effects ; Saccharomyces cerevisiae/drug effects/metabolism ; Sequence Alignment ; Trichomonas vaginalis/drug effects/*enzymology ; }, abstract = {Mitochondrial evolution entailed the origin of protein import machinery that allows nuclear-encoded proteins to be targeted to the organelle, as well as the origin of cleavable N-terminal targeting sequences (NTS) that allow efficient sorting and import of matrix proteins. In hydrogenosomes and mitosomes, reduced forms of mitochondria with reduced proteomes, NTS-independent targeting of matrix proteins is known. Here, we studied the cellular localization of two glycolytic enzymes in the anaerobic pathogen Trichomonas vaginalis: PPi-dependent phosphofructokinase (TvPPi-PFK), which is the main glycolytic PFK activity of the protist, and ATP-dependent PFK (TvATP-PFK), the function of which is less clear. TvPPi-PFK was detected predominantly in the cytosol, as expected, while all four TvATP-PFK paralogues were imported into T. vaginalis hydrogenosomes, although none of them possesses an NTS. The heterologous expression of TvATP-PFK in Saccharomyces cerevisiae revealed an intrinsic capability of the protein to be recognized and imported into yeast mitochondria, whereas yeast ATP-PFK resides in the cytosol. TvATP-PFK consists of only a catalytic domain, similarly to "short" bacterial enzymes, while ScATP-PFK includes an N-terminal extension, a catalytic domain, and a C-terminal regulatory domain. Expression of the catalytic domain of ScATP-PFK and short Escherichia coli ATP-PFK in T. vaginalis resulted in their partial delivery to hydrogenosomes. These results indicate that TvATP-PFK and the homologous ATP-PFKs possess internal structural targeting information that is recognized by the hydrogenosomal import machinery. From an evolutionary perspective, the predisposition of ancient ATP-PFK to be recognized and imported into hydrogenosomes might be a relict from the early phases of organelle evolution.}, }
@article {pmid26474847, year = {2016}, author = {Mani, J and Meisinger, C and Schneider, A}, title = {Peeping at TOMs-Diverse Entry Gates to Mitochondria Provide Insights into the Evolution of Eukaryotes.}, journal = {Molecular biology and evolution}, volume = {33}, number = {2}, pages = {337-351}, doi = {10.1093/molbev/msv219}, pmid = {26474847}, issn = {1537-1719}, mesh = {*Biological Evolution ; Eukaryota/classification/*genetics ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/chemistry/*metabolism ; Mitochondrial Proteins/metabolism ; Multigene Family ; Multiprotein Complexes ; Plants/metabolism ; Porins/chemistry/metabolism ; Protein Binding ; Protein Subunits/metabolism ; Protein Transport ; Receptors, Cell Surface/chemistry/metabolism ; Symbiosis ; Trypanosoma/metabolism ; Yeasts/metabolism ; }, abstract = {Mitochondria are essential for eukaryotic life and more than 95% of their proteins are imported as precursors from the cytosol. The targeting signals for this posttranslational import are conserved in all eukaryotes. However, this conservation does not hold true for the protein translocase of the mitochondrial outer membrane that serves as entry gate for essentially all precursor proteins. Only two of its subunits, Tom40 and Tom22, are conserved and thus likely were present in the last eukaryotic common ancestor. Tom7 is found in representatives of all supergroups except the Excavates. This suggests that it was added to the core of the translocase after the Excavates segregated from all other eukaryotes. A comparative analysis of the biochemically and functionally characterized outer membrane translocases of yeast, plants, and trypanosomes, which represent three eukaryotic supergroups, shows that the receptors that recognize the conserved import signals differ strongly between the different systems. They present a remarkable example of convergent evolution at the molecular level. The structural diversity of the functionally conserved import receptors therefore provides insight into the early evolutionary history of mitochondria.}, }
@article {pmid26471207, year = {2016}, author = {Wang, S and Cong, H and Kong, L and Motokawa, M and Li, Y}, title = {Complete mitochondrial genome of the greater bandicoot rat Bandicota indica (Rodentia: Muridae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4349-4350}, doi = {10.3109/19401736.2015.1089495}, pmid = {26471207}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Gene Order ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Murinae/*genetics ; Phylogeny ; Rodentia/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The complete mitochondrial genome of the greater bandicoot rat (Bandicota indica) was first sequenced and characterized. The genome was 16 326 bp in length, the composition and arrangement of its genes were analogous to other rodents. To confirm the phylogenetic position of B. indica, the mitochondrial nucleotide sequence data of other 20 Rodentia species were used to construct phylogenetic tree by maximum likelihood. Phylogenetic analysis demonstrated that genera Bandicota and Rattus were sister taxa, and B. indica was closer to the genus Rattus than to genera Niviventer and Leopoldamys. The mitochondrial genome of B. indica presented in this study can provide useful information for species delimitation, taxonomic and phylogenetic analyses as well as other studies of the species.}, }
@article {pmid26470830, year = {2016}, author = {Cao, W and Xia, Y}, title = {The complete mitochondrial genome of the Cavia aperea.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4429-4430}, doi = {10.3109/19401736.2015.1089557}, pmid = {26470830}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Brazil ; DNA, Mitochondrial/genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; Guinea Pigs/*genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Cavia aperea which is a Brazilian guinea pig is found in the South America. Recently the genome sequencing of C. aperea was done, but no more information of its mitochondrial had been reported. Herein, we assembled the complete mitochondrial genome sequence of C. aperea. It is a 16 835 bp long sequence with most mitogenome's characteristic structure; 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, 1 D-loop region, 1 repeat region and 3 STS regions. The GC-content of our fresh sequence is 39%. It can verify the accuracy and utility of newly determined mitogenome sequences by the phylogenetic analysis, based on whole mitogenome alignment with C. porcellus, which is the closest relative to C. aperea. We expect that using the full mitogenome we can address the taxonomic issues and study the related the evolution events.}, }
@article {pmid26470640, year = {2016}, author = {Kozhukhar, N and Spadafora, D and Fayzulin, R and Shokolenko, IN and Alexeyev, M}, title = {The efficiency of the translesion synthesis across abasic sites by mitochondrial DNA polymerase is low in mitochondria of 3T3 cells.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4390-4396}, pmid = {26470640}, issn = {2470-1408}, support = {P01 HL066299/HL/NHLBI NIH HHS/United States ; R01 OD010944/OD/NIH HHS/United States ; }, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; DNA Damage ; DNA Glycosylases/metabolism ; DNA Polymerase gamma/metabolism ; DNA Repair/*genetics ; DNA, Mitochondrial/*genetics ; DNA-Directed DNA Polymerase ; Gene Order ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mice/*genetics ; Mitochondria/genetics ; NIH 3T3 Cells ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Translesion synthesis by specialized DNA polymerases is an important strategy for mitigating DNA damage that cannot be otherwise repaired either due to the chemical nature of the lesion. Apurinic/Apyrimidinic (abasic, AP) sites represent a block to both transcription and replication, and are normally repaired by the base excision repair (BER) pathway. However, when the number of abasic sites exceeds BER capacity, mitochondrial DNA is targeted for degradation. Here, we used two uracil-N-glycosylase (UNG1) mutants, Y147A or N204D, to generate AP sites directly in the mtDNA of NIH3T3 cells in vivo at sites normally occupied by T or C residues, respectively, and to study repair of these lesions in their native context. We conclude that mitochondrial DNA polymerase γ (Pol γ) is capable of translesion synthesis across AP sites in mitochondria of the NIH3T3 cells, and obeys the A-rule. However, in our system, base excision repair (BER) and mtDNA degradation occur more frequently than translesion bypass of AP sites.}, }
@article {pmid26468067, year = {2015}, author = {Radzvilavicius, AL and Blackstone, NW}, title = {Conflict and cooperation in eukaryogenesis: implications for the timing of endosymbiosis and the evolution of sex.}, journal = {Journal of the Royal Society, Interface}, volume = {12}, number = {111}, pages = {20150584}, pmid = {26468067}, issn = {1742-5662}, mesh = {Adenylyl Cyclases/metabolism ; Alleles ; *Biological Evolution ; Calcium/metabolism ; Cytoplasm/metabolism ; Cytosol/metabolism ; Electron Transport ; Eukaryotic Cells/*physiology ; Genome ; Mitochondrial ADP, ATP Translocases/metabolism ; Models, Biological ; Oxidation-Reduction ; Phylogeny ; *Reproduction ; Signal Transduction ; *Symbiosis ; }, abstract = {Roughly 1.5-2.0 Gya, the eukaryotic cell evolved from an endosymbiosis of an archaeal host and proteobacterial symbionts. The timing of this endosymbiosis relative to the evolution of eukaryotic features remains subject to considerable debate, yet the evolutionary process itself constrains the timing of these events. Endosymbiosis entailed levels-of-selection conflicts, and mechanisms of conflict mediation had to evolve for eukaryogenesis to proceed. The initial mechanisms of conflict mediation (e.g. signalling with calcium and soluble adenylyl cyclase, substrate carriers, adenine nucleotide translocase, uncouplers) led to metabolic homeostasis in the eukaryotic cell. Later mechanisms (e.g. mitochondrial gene loss) contributed to the chimeric eukaryotic genome. These integral features of eukaryotes were derived because of, and therefore subsequent to, endosymbiosis. Perhaps the greatest opportunity for conflict arose with the emergence of eukaryotic sex, involving whole-cell fusion. A simple model demonstrates that competition on the lower level severely hinders the evolution of sex. Cytoplasmic mixing, however, is beneficial for non-cooperative endosymbionts, which could have used their aerobic metabolism to manipulate the life history of the host. While early evolution of sex may have facilitated symbiont acquisition, sex would have also destabilized the subsequent endosymbiosis. More plausibly, the evolution of sex and the true nucleus concluded the transition.}, }
@article {pmid26466198, year = {2016}, author = {Nah, G and Im, JH and Kim, JW and Kim, K and Lim, J and Choi, AY and Choi, IY and Yang, TJ and Park, TS and Lee, D and Kim, DS}, title = {The complete chloroplast genomes of three Korean Echinochloa crus-galli accessions.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4357-4358}, doi = {10.3109/19401736.2015.1089499}, pmid = {26466198}, issn = {2470-1408}, mesh = {Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; Chloroplasts/genetics ; DNA, Chloroplast/genetics ; Echinochloa/*genetics ; Gene Order ; Genes, Mitochondrial/genetics ; Genes, Plant ; Genome/genetics ; Genome, Chloroplast/*genetics ; Genome, Mitochondrial/*genetics ; Genome, Plant/genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The complete chloroplast (cp) genomes of three Echinochloa crus-galli accessions (KR822684, KR822685, and KR822686) are reported in this work. The cp genome size is similar in three accessions, ranging from 139 846 bp to 139 860 bp. All three genomes have two inverted repeats (IR) of 22 748 bp per each IR with a large single copy (LSC) region of 81 833-81 844 bp and a small single copy (SSC) region of 12 517-12 520 bp. The total of 131 genes was identified in individual accession. Phylogenetic analysis revealed three Korean Echinochloa accessions belonged to E. crus-galli, and diverged less than 0.1 million years ago (Mya).}, }
@article {pmid26466017, year = {2016}, author = {Guo, Q and Bianba, D and Zheng, W}, title = {Characterization of the complete chloroplast genome of Juniperus cedrus (Cupressaceae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4355-4356}, doi = {10.3109/19401736.2015.1089498}, pmid = {26466017}, issn = {2470-1408}, mesh = {Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; Cedrus/*genetics ; Chloroplasts/genetics ; Cupressaceae/genetics ; DNA, Chloroplast/genetics ; Evolution, Molecular ; Gene Order ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Chloroplast/*genetics ; Genome, Mitochondrial/*genetics ; Genome, Plant/genetics ; Juniperus/genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The complete chloroplast genome of Juniperus cedrus is a circular molecule of 127 126 bp in length with 115 single copy genes and two duplicated genes (trnI-CAU and trnQ-UUG). The genome contains 82 protein-coding genes, four ribosomal RNA genes and 33 transfer RNA genes. In these genes, eight genes (rpl16, rpl2, rpoC1, petD, petB, ndhB, ndhA and atpF) harbor a single intron and two genes (rps12 and ycf3) harbor two introns. Like other sequenced chloroplast genomes of conifers, this genome does not contain canonical inverted repeats (IRs), and the overall GC content of J. cedrus chloroplast DNA is 35%. The phylogenetic analysis revealed that J. cedrus is more closely related to J. scopulorum and J. bermudiana.}, }
@article {pmid26465980, year = {2016}, author = {Dai, X and Li, W and Tian, S}, title = {Complete mitochondrial genome of Hemiculter bleekeri bleekeri.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4338-4339}, doi = {10.3109/19401736.2015.1089490}, pmid = {26465980}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; China ; Cyprinidae/*genetics ; DNA, Mitochondrial/*genetics ; Fresh Water ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Rivers ; Sequence Analysis, DNA/methods ; }, abstract = {Hemiculter bleekeri bleekeri is a typical freshwater species that are mainly distributed in the river basins in China. The biological information of this species is very limited. In this study, we determined the complete mitogenome sequence of H. bleekeri bleekeri. The complete mitogenome of H. bleekeri bleekeri is 16 6173 bp in length, which contains 22 transfer RNAs, 2 ribosomal RNAs, 13 protein-coding genes and 2 non-coding region, a rep region (33 bp) and a control region (D-loop). This work provides new information which is helpful for comprehending the molecular systematic, taxonomic status and evolutionary biology of this species.}, }
@article {pmid26465834, year = {2016}, author = {Sung, CH and Wu, CC and Tseng, CT and Lu, JK and Lin, HC}, title = {The complete mitochondrial genome of Poecilia formosa (Actinopterygii: Cyprinodontiformes: Poeciliidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4331-4332}, doi = {10.3109/19401736.2015.1089487}, pmid = {26465834}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; Cyprinodontiformes/genetics ; DNA, Mitochondrial/*genetics ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Poecilia/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The complete mitochondrial genome sequence of the Poecilia formosa is first reported in this study. The length of genome is 16 550 bp, including 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. Congeneric mitogenome sequence identity is 87.7% with P. reticulate and 93.1% with P. sphenops. The reconstructed phylogenetic relationships of 16 Cyprinodontiformes species based on 13 protein-coding genes were highly supported and the clade of all Poecilia fishes included had a support value of 100%. Our results shall provide a better understanding in the evolutionary histories of the Cyprinodontiformes.}, }
@article {pmid26465833, year = {2016}, author = {Kim, NR and Kim, K and Lee, SC and Lee, JH and Cho, SH and Yu, Y and Kim, YD and Yang, TJ}, title = {The complete chloroplast genomes of two Wisteria species, W. floribunda and W. sinensis (Fabaceae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4353-4354}, doi = {10.3109/19401736.2015.1089497}, pmid = {26465833}, issn = {2470-1408}, mesh = {Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; Chloroplasts/genetics ; Fabaceae/*genetics ; Gene Order ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Chloroplast/*genetics ; Genome, Mitochondrial/*genetics ; Genome, Plant/genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Wisteria/genetics ; }, abstract = {Wisteria floribunda and Wisteria sinensis are ornamental woody vines in the Fabaceae. The complete chloroplast genome sequences of the two species were generated by de novo assembly using whole genome next generation sequences. The chloroplast genomes of W. floribunda and W. sinensis were 130 960 bp and 130 561 bp long, respectively, and showed inverted repeat (IR)-lacking structures as those reported in IRLC in the Fabaceae. The chloroplast genomes of both species contained same number of protein-coding sequences (77), tRNA genes (30), and rRNA genes (4). The phylogenetic analysis with the reported chloroplast genomes confirmed close taxonomical relationship of W. floribunda and W. sinensis.}, }
@article {pmid26465710, year = {2016}, author = {Nah, G and Im, JH and Lim, SH and Kim, K and Choi, AY and Yook, MJ and Kim, S and Kim, C and Kim, DS}, title = {Complete chloroplast genomes of two Miscanthus species.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4359-4360}, doi = {10.3109/19401736.2015.1089500}, pmid = {26465710}, issn = {2470-1408}, mesh = {Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; Chloroplasts/genetics ; DNA, Chloroplast/genetics ; Gene Order ; Genes, Mitochondrial/genetics ; Genes, Plant/genetics ; Genome/genetics ; Genome, Chloroplast/*genetics ; Genome, Mitochondrial/*genetics ; Genome, Plant/genetics ; Mitochondria/genetics ; Phylogeny ; Poaceae/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The complete chloroplast (cp) genomes of two Miscanthus species, M. sinensis and M. sacchariflorus, were sequenced and investigated for genes, genome size variation, and polymorphisms. There are 170 genes in both cp genomes, consisting of 122 mRNA genes (84 protein-coding genes and 38 hypothetical genes), 40 tRNA genes, and 8 rRNA genes. The cp genome contains two inverted repeat (IR) regions, separated by large single copy (LSC) region and small single copy (SSC) region. Indels were responsible for 40 bp difference in cp genome size in two species. In addition, we established phylogenetic relationship with other monocot cp genomes, and estimated divergence time. The two Miscanthus species clustered together among other C4 monocot species and the divergence time of two Miscanthus species was approximately 0.5 1-0.84 Mya.}, }
@article {pmid26465389, year = {2016}, author = {Teng, XX and Xie, ZH and Zhang, Y}, title = {The complete mitochondrial genome of the common buckeye Junonia coenia (Insecta: Lepidoptera: Nymphalidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4351-4352}, doi = {10.3109/19401736.2015.1089496}, pmid = {26465389}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; Butterflies/genetics ; DNA, Mitochondrial/*genetics ; Gene Order ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Insecta/genetics ; Lepidoptera/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The complete mitochondrial genome of the common buckeye Junonia coenia (Insecta: Lepidoptera: Nymphalidae) was reconstructed from whole-genome Illumina sequencing data with an average coverage of 1213×. The circular genome is 15 222 bp in length, and consists of 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs) and one D-loop region. All PCGs are initiated with ATN codons. Five PCGs (COX1, COX2, CYTB, ND2 &amp; ND4) harbor an incomplete termination codon T--, while all the others are terminated with TAA. The nucleotide composition is highly asymmetric (39.6% A, 11.6% C, 7.7% G &amp; 41.1% T) with an overall GC content of 19.3%. Phylogenetic analysis suggested that J. coenia is phylogenetically closer to its congeners and its consubfamilial counterparts than to the other taxa.}, }
@article {pmid26465267, year = {2016}, author = {Li, X and Jiang, Y and Li, Y and Ni, Q and Yao, Y and Xu, H and Zhang, M}, title = {Complete mitochondrial genome sequence of red-tailed knobby newt (Tylototriton kweichowensis).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4336-4337}, doi = {10.3109/19401736.2015.1089489}, pmid = {26465267}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Perciformes/genetics ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; Salamandridae/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The entire mitogenome of Tylototriton kweichowensis is 16 727 bp in length. It consists of 13 protein-coding genes (PCGS), 2 ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA), and 1 control region (CR). Except for ND6 subunit and 8 tRNA genes are distributed on the L-strand, all the other PCGs and tRNA genes are located on the H-strand. "ATG" and "GTG" are the start codons of the PCGs, "TAA", "AGA", "TA-" and "T--" are the stop codons. Most of the tRNA genes can be folded into typical clover-leaf secondary structure. The genome of T. kweichowensis has two repeat sequences in the cob-noncoding region. Mitogenomic phylogenetic analysis (NJ tree) robustly resolved the genus-level relationship among the three genera Tylototriton, Echinotriton, and Pleurodeles, and which is congruent with the previous molecular phylogeny results.}, }
@article {pmid26465068, year = {2016}, author = {Doña, J and Ruiz-Ruano, FJ and Jovani, R}, title = {DNA barcoding of Iberian Peninsula and North Africa Tawny Owls Strix aluco suggests the Strait of Gibraltar as an important barrier for phylogeography.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4475-4478}, doi = {10.3109/19401736.2015.1089573}, pmid = {26465068}, issn = {2470-1408}, mesh = {Africa, Northern ; Animals ; Bayes Theorem ; DNA/chemistry/isolation &amp; purification/metabolism ; *DNA Barcoding, Taxonomic ; Genetic Variation ; Gibraltar ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Strigiformes/classification/*genetics ; }, abstract = {Eight subspecies have been proposed within the Tawny Owl (Strix aluco) species. However, recent molecular data have challenged this view, encouraging further work in this species complex. Here we reevaluated the taxonomic status between the North-Western African Tawny Owl, S. a. mauritanica, and its closest Iberian Tawny Owl population (from the S. a. sylvatica to S. a. aluco clade) separated by the Strait of Gibraltar. The Tawny Owl is a non-migratory and territorial species, and juvenile dispersal is restricted to a few kilometers around the natal site. This limited dispersal and the barrier imposed by the Strait of Gibraltar predicted a strong differentiation between the two populations. We tested this using DNA barcoding, Bayesian phylogenetic and species delimitation analysis. We found that an 81.1% of variation is due to the intergroups variation. In addition, the inter-intraspecific distances distribution revealed a barcoding gap among the two subspecies. Also, posterior probabilities and the PAB value allowed to reject the hypothesis that observed degree of distinctiveness is due to random coalescence processes. These findings clearly support the Strait of Gibraltar as an isolating barrier for this species. The subspecific status is confirmed and species status is even suggested for S. a. mauritanica.}, }
@article {pmid26463086, year = {2016}, author = {Hao, RC and Wang, GH and Yang, GZ and Zan, LS}, title = {The complete mitochondrial genome sequence of Zebrias crossolepis (pleuronectiformes: soleidae) and Acrossocheilus monticola (cypriniformes: cyprinidae) and phylogenetic studies.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4326-4327}, doi = {10.3109/19401736.2015.1089485}, pmid = {26463086}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; Cyprinidae/genetics ; Cypriniformes/*genetics ; DNA, Mitochondrial/*genetics ; Flatfishes/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing ; }, abstract = {In this study, two complete mitogenome sequences of Zebrias crossolepis and Acrossocheilus monticola were determined and the phylogenetic relationship were constructed based on concatenated nucleotide sequences of 12 mitochondrial protein-coding genes. The length of the complete mitogenome sequence are 16 775 bp and 16 605 bp in Z. crossolepis and A. monticola, respectively, both containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region (CR), and a light-strand replication origin (OL). The overall base composition is 28.3% A, 26.3% T, 30.0% C, 15.5% G, with a slight AT bias (54.6%) in Z. crossolepis, while 31.4% A, 24.5% T, 28.2% C, 15.9% G, with an slight AT bias (55.9%) in A. monticola. All the protein-coding genes use the initiation codon ATG except COI uses GTG. Most of them have TAA or TAG as the stop codon, while ND4 and Cytb in Z. crossolepis and COII, ND4, and Cytb in A. monticola use an incomplete stop codon T. These results are expected to provide useful molecular data for species identification and further phylogenetic studies.}, }
@article {pmid26462964, year = {2016}, author = {Liu, H and Cai, S and Zhang, H and Vrijenhoek, RC}, title = {Complete mitochondrial genome of hydrothermal vent clam Calyptogena magnifica.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4333-4335}, doi = {10.3109/19401736.2015.1089488}, pmid = {26462964}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; Bivalvia/*genetics ; DNA, Mitochondrial/*genetics ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Hydrothermal Vents ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The mitochondrial genome of the hydrothermal vent clam Calyptogena magnifica (Bivalvia, Veneroida, Vesicomyidae) is reported for the first time in this study. The total length of its mitochondrial genome is 19 738 bp with overall GC content of 31.6%. The mitochondrial genome consists of 36 genes, including 13 protein-coding sequences, 2 rRNA and 21 tRNA genes. Two distinct repeat motifs are located between tRNA[Trp] and ND6.}, }
@article {pmid26462909, year = {2015}, author = {Wallet, C and Le Ret, M and Bergdoll, M and Bichara, M and Dietrich, A and Gualberto, JM}, title = {The RECG1 DNA Translocase Is a Key Factor in Recombination Surveillance, Repair, and Segregation of the Mitochondrial DNA in Arabidopsis.}, journal = {The Plant cell}, volume = {27}, number = {10}, pages = {2907-2925}, pmid = {26462909}, issn = {1532-298X}, mesh = {Arabidopsis/cytology/*enzymology/genetics ; Arabidopsis Proteins/genetics/*metabolism ; *DNA Repair ; *DNA Replication ; DNA, Mitochondrial/*genetics ; DNA, Plant/genetics ; DNA-Binding Proteins/genetics/metabolism ; Gene Knockout Techniques ; Membrane Transport Proteins/genetics/*metabolism ; Mitochondria/metabolism ; Models, Molecular ; Mutation ; Phenotype ; Phylogeny ; Plastids/metabolism ; Recombination, Genetic ; }, abstract = {The mitochondria of flowering plants have considerably larger and more complex genomes than the mitochondria of animals or fungi, mostly due to recombination activities that modulate their genomic structures. These activities most probably participate in the repair of mitochondrial DNA (mtDNA) lesions by recombination-dependent processes. Rare ectopic recombination across short repeats generates new genomic configurations that contribute to mtDNA heteroplasmy, which drives rapid evolution of the sequence organization of plant mtDNAs. We found that Arabidopsis thaliana RECG1, an ortholog of the bacterial RecG translocase, is an organellar protein with multiple roles in mtDNA maintenance. RECG1 targets to mitochondria and plastids and can complement a bacterial recG mutant that shows defects in repair and replication control. Characterization of Arabidopsis recG1 mutants showed that RECG1 is required for recombination-dependent repair and for suppression of ectopic recombination in mitochondria, most likely because of its role in recovery of stalled replication forks. The analysis of alternative mitotypes present in a recG1 line and of their segregation following backcross allowed us to build a model to explain how a new stable mtDNA configuration, compatible with normal plant development, can be generated by stoichiometric shift.}, }
@article {pmid26462716, year = {2016}, author = {Lee, JH and Kim, K and Kim, NR and Lee, SC and Yang, TJ and Kim, YD}, title = {The complete chloroplast genome of a medicinal plant Epimedium koreanum Nakai (Berberidaceae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4342-4343}, doi = {10.3109/19401736.2015.1089492}, pmid = {26462716}, issn = {2470-1408}, mesh = {Base Composition/genetics ; Base Sequence/genetics ; Berberidaceae/genetics ; Biological Evolution ; Chloroplasts/genetics ; Epimedium/*genetics ; Genes, Mitochondrial/genetics ; Genes, Plant/genetics ; Genome/genetics ; Genome, Chloroplast/*genetics ; Genome, Mitochondrial/genetics ; Genome, Plant/genetics ; Mitochondria/genetics ; Phylogeny ; Plants, Medicinal/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Epimedium koreanum is a perennial medicinal plant distributed in Eastern Asia. The complete chloroplast genome sequences of E. koreanum was obtained by de novo assembly using whole genome next-generation sequences. The chloroplast genome of E. koreanum was 157 218 bp in length and separated into four distinct regions such as large single copy region (89 600 bp), small single copy region (17 222 bp) and a pair of inverted repeat regions (25 198 bp). The genome contained a total of 112 genes including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis with the reported chloroplast genomes revealed that E. koreanum is most closely related to Berberis bealei, a traditional medicinal plant in the Berberidaceae family.}, }
@article {pmid26462597, year = {2016}, author = {Kinaro, ZO and Xue, L and Nyaundi, KJ and Shen, J}, title = {The mitochondrial genome of an endangered native Singidia tilapia, Oreochromis esculentus: genome organization and control region polymorphism.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4344-4346}, doi = {10.3109/19401736.2015.1089493}, pmid = {26462597}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; Cichlids/genetics ; DNA, Mitochondrial/*genetics ; Genes, Mitochondrial/genetics ; Genetic Variation ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Tilapia/*genetics ; }, abstract = {Singidia tilapia (Oreochromis esculentus) is a native Cichlid fish of important commercial value, distributed in Lake Victoria, East Africa. Due to its declining population levels in its natural habitat, this species has now been classified as a Critically Endangerd by the International Union for the Conservation of nature (IUCN). In the present study the complete nucleotide sequence of the mitochondrial genome (mtDNA) of O. esculentus was determined. In addition, polymorphism analysis based on the mtDNA's control region sequence was investigated on two of its remaining populations of Yala and Borabu as well as a phylogenetic consideration using 16S rRNA mtDNA genes to explore its position and relationship within Cichlidae fish. The length of the complete mitogenome of O. esculentus is 16 622 bp, containing the same order and an identical number of genes and regions with the other reported Cichlid fishes, which consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a putative non-coding region. The phylogenetic analysis shows O. esculentus being clustered within the Oreochromini sub-tribe of the Cichlidae. The high genetic diversity and low genetic differentiation between the two populations indicated the need for conservation of both the refuge ecosystems and the fish species under study.}, }
@article {pmid26462546, year = {2016}, author = {Sun, Z and Wang, B and Sun, X and Yan, L and Pan, T and Zhang, B}, title = {Phylogenetic studies of Anas clypeata (Anatidae: Anas) based on complete mitochondrial DNA sequences.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4320-4321}, doi = {10.3109/19401736.2015.1089482}, pmid = {26462546}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; DNA, Mitochondrial/*genetics ; Ducks/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Northern shoveler (Anas clypeata) is a middle-sized duck living in an extremely geographical range in northern hemisphere. Here, the complete mitochondrial genome of A. clypeata (16 599 bp in length) has been analyzed for building the database. Similar to the typical mtDNA of vertebrates, it contained 37 genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes) and a non-coding region (D-loop). Overall base composition of the complete mitochondrial DNA is A (29.4%), G (15.7%), C (32.5%) and T (22.4%), the percentage of A and T (51.8%) is slightly higher than G and C (48.2%). All the genes in A. clypeata were distributed on the H-strand, except for the ND6 subunit gene and 9 tRNA genes which were encoded on the L-strand. The phylogenetic relationships of 12 Anatidae species were reconstructed based on the complete mtDNA sequences using the Bayesian inference method.}, }
@article {pmid26462363, year = {2015}, author = {Vitetta, L and Palacios, T and Hall, S and Coulson, S}, title = {Gastrointestinal Tract Commensal Bacteria and Probiotics: Influence on End-Organ Physiology.}, journal = {Progress in drug research. Fortschritte der Arzneimittelforschung. Progres des recherches pharmaceutiques}, volume = {70}, number = {}, pages = {1-33}, doi = {10.1007/978-3-0348-0927-6_1}, pmid = {26462363}, issn = {0071-786X}, mesh = {Animals ; Bacteria/*isolation &amp; purification ; Gastrointestinal Tract/*microbiology ; Humans ; Hygiene ; Immune Tolerance ; Microbiota ; Probiotics/*therapeutic use ; }, abstract = {Bacteria represent the earliest form of independent life on this planet. Bacterial development has included cooperative symbiosis with plants (e.g., Leguminosae family and nitrogen fixing bacteria in soil) and animals (e.g., the gut microbiome). It is generally agreed upon that the fusion of two prokaryotes evolutionarily gave rise to the eukaryotic cell in which mitochondria may be envisaged as a genetically functional mosaic, a relic from one of the prokaryotes. This is expressed by the appearance of mitochondria in eukaryotic cells (an alpha-proteobacteria input), a significant endosymbiotic evolutionary event. As such, the evolution of human life has been complexly connected to bacterial activities. Hence, microbial colonization of mammals has been a progressively driven process. The interactions between the human host and the microbiome inhabiting the gastrointestinal tract (GIT) for example, afford the human host the necessary cues for the development of regulated signals that in part are induced by reactive oxygen species (ROS). This regulated activity then promotes immunological tolerance and metabolic regulation and stability, which then helps establish control of local and extraintestinal end-organ (e.g., kidneys) physiology. Pharmacobiotics, the targeted administration of live probiotic cultures, is an advancing area of potential therapeutics, either directly or as adjuvants. Hence the continued scientific understanding of the human microbiome in health and disease may further lead to fine tuning the targeted delivery of probiotics for a therapeutic gain.}, }
@article {pmid26462158, year = {2015}, author = {Garcia-Heredia, JM and Carnero, A}, title = {Decoding Warburg's hypothesis: tumor-related mutations in the mitochondrial respiratory chain.}, journal = {Oncotarget}, volume = {6}, number = {39}, pages = {41582-41599}, pmid = {26462158}, issn = {1949-2553}, mesh = {Animals ; Cell Transformation, Neoplastic/*genetics/metabolism/pathology ; Electron Transport Chain Complex Proteins/*genetics/metabolism ; Energy Metabolism/*genetics ; Genetic Predisposition to Disease ; Glycolysis/genetics ; Humans ; Mitochondria/*metabolism/pathology ; Mitochondrial Proteins/*genetics/metabolism ; *Mutation ; Neoplasms/*genetics/metabolism/pathology ; Oxidative Phosphorylation ; Phenotype ; Risk Factors ; }, abstract = {Otto Warburg observed that cancer cells derived their energy from aerobic glycolysis by converting glucose to lactate. This mechanism is in opposition to the higher energy requirements of cancer cells because oxidative phosphorylation (OxPhos) produces more ATP from glucose. Warburg hypothesized that this phenomenon occurs due to the malfunction of mitochondria in cancer cells. The rediscovery of Warburg's hypothesis coincided with the discovery of mitochondrial tumor suppressor genes that may conform to Warburg's hypothesis along with the demonstrated negative impact of HIF-1 on PDH activity and the activation of HIF-1 by oncogenic signals such as activated AKT. This work summarizes the alterations in mitochondrial respiratory chain proteins that have been identified and their involvement in cancer. Also discussed is the fact that most of the mitochondrial mutations have been found in homoplasmy, indicating a positive selection during tumor evolution, thereby supporting their causal role.}, }
@article {pmid26458992, year = {2015}, author = {Wynn, EL and Christensen, AC}, title = {Are Synonymous Substitutions in Flowering Plant Mitochondria Neutral?.}, journal = {Journal of molecular evolution}, volume = {81}, number = {3-4}, pages = {131-135}, pmid = {26458992}, issn = {1432-1432}, mesh = {Amino Acid Sequence ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genes, Plant/genetics ; Genome, Plant ; Mutation Rate ; Phylogeny ; Plants/*genetics ; Pseudogenes ; *Silent Mutation ; }, abstract = {Angiosperm mitochondrial genes appear to have very low mutation rates, while non-gene regions expand, diverge, and rearrange quickly. One possible explanation for this disparity is that synonymous substitutions in plant mitochondrial genes are not truly neutral and selection keeps their occurrence low. If this were true, the explanation for the disparity in mutation rates in genes and non-genes needs to consider selection as well as mechanisms of DNA repair. Rps14 is co-transcribed with cob and rpl5 in most plant mitochondrial genomes, but in some genomes, rps14 has been duplicated to the nucleus leaving a pseudogene in the mitochondria. This provides an opportunity to compare neutral substitution rates in pseudogenes with synonymous substitution rates in the orthologs. Genes and pseudogenes of rps14 have been aligned among different species and the mutation rates have been calculated. Neutral substitution rates in pseudogenes and synonymous substitution rates in genes are significantly different, providing evidence that synonymous substitutions in plant mitochondrial genes are not completely neutral. The non-neutrality is not sufficient to completely explain the exceptionally low mutation rates in land plant mitochondrial genomes, but selective forces appear to play a small role.}, }
@article {pmid26458552, year = {2015}, author = {Devall, M and Burrage, J and Caswell, R and Johnson, M and Troakes, C and Al-Sarraj, S and Jeffries, AR and Mill, J and Lunnon, K}, title = {A comparison of mitochondrial DNA isolation methods in frozen post-mortem human brain tissue--applications for studies of mitochondrial genetics in brain disorders.}, journal = {BioTechniques}, volume = {59}, number = {4}, pages = {241-2, 244-6}, doi = {10.2144/000114343}, pmid = {26458552}, issn = {1940-9818}, support = {G1100695/MRC_/Medical Research Council/United Kingdom ; G9318379/MRC_/Medical Research Council/United Kingdom ; MR/L016397/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Autopsy ; Brain/*metabolism ; Brain Diseases/*genetics/pathology ; DNA, Mitochondrial/genetics/*isolation &amp; purification ; Evolution, Molecular ; Humans ; Mitochondria/*genetics/metabolism ; Phylogeny ; Pseudogenes ; }, abstract = {Given that many brain disorders are characterized by mitochondrial dysfunction, there is a growing interest in investigating genetic and epigenetic variation in mitochondrial DNA (mtDNA). One major caveat for such studies is the presence of nuclear-mitochondrial pseudogenes (NUMTs), which are regions of the mitochondrial genome that have been inserted into the nuclear genome over evolution and, if not accounted for, can confound genetic studies of mtDNA. Here we provide the first systematic comparison of methods for isolating mtDNA from frozen post-mortem human brain tissue. Our data show that a commercial method from Miltenyi Biotec, which magnetically isolates mitochondria using antibodies raised against the mitochondrial import receptor subunit TOM22, gives significant mtDNA enrichment and should be considered the method of choice for mtDNA studies in frozen brain tissue.}, }
@article {pmid26457491, year = {2016}, author = {Liu, F and Bao, X and Fan, Y and Li, J and Yao, X}, title = {Sequencing and analysis of the complete mitochondrial genome of Brown Shrike, Lanius cristatus (Passeriformes, Laniidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3544-3546}, doi = {10.3109/19401736.2015.1074210}, pmid = {26457491}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Passeriformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitochondrial genome of the Brown Shrike (Lanius cristatus) was 16 821 bp in length. The accession number was KT004451 and the contents of A, T, C, and G were 31.10%(5237 bp), 25.60%(4309 bp), 28.60%(4814 bp), and 14.60%(2461 bp), respectively. Gene organization and length was similar to other species of birds. It comprises of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. All protein-coding genes use the typical initiation codon ATG, except for COX1 which was initiated with GTG. All the complete stop codon was coincident with the Black-headed Gull (Chroicocephalus ridibundus) and the Grey-backed Shrike (Lanius tephronotus), except for ND2, which was terminated with TAG. In addition, the phylogenetic relationships of Passeriformes based on complete mitochondrial genomes showed that the genetic distance of Laniidae and Corvidae was closer than others.}, }
@article {pmid26455774, year = {2015}, author = {López-García, P and Moreira, D}, title = {Open Questions on the Origin of Eukaryotes.}, journal = {Trends in ecology &amp; evolution}, volume = {30}, number = {11}, pages = {697-708}, pmid = {26455774}, issn = {1872-8383}, support = {322669/ERC_/European Research Council/International ; }, mesh = {Archaea ; *Biological Evolution ; Eukaryota/*classification ; Eukaryotic Cells ; Mitochondria ; *Phylogeny ; Symbiosis ; }, abstract = {Despite recent progress, the origin of the eukaryotic cell remains enigmatic. It is now known that the last eukaryotic common ancestor was complex and that endosymbiosis played a crucial role in eukaryogenesis at least via the acquisition of the alphaproteobacterial ancestor of mitochondria. However, the nature of the mitochondrial host is controversial, although the recent discovery of an archaeal lineage phylogenetically close to eukaryotes reinforces models proposing archaea-derived hosts. We argue that, in addition to improved phylogenomic analyses with more comprehensive taxon sampling to pinpoint the closest prokaryotic relatives of eukaryotes, determining plausible mechanisms and selective forces at the origin of key eukaryotic features, such as the nucleus or the bacterial-like eukaryotic membrane system, is essential to constrain existing models.}, }
@article {pmid26454011, year = {2015}, author = {Moog, D and Rensing, SA and Archibald, JM and Maier, UG and Ullrich, KK}, title = {Localization and Evolution of Putative Triose Phosphate Translocators in the Diatom Phaeodactylum tricornutum.}, journal = {Genome biology and evolution}, volume = {7}, number = {11}, pages = {2955-2969}, pmid = {26454011}, issn = {1759-6653}, mesh = {Amino Acid Sequence ; *Biological Evolution ; Chloroplast Proteins/*genetics ; Diatoms/*genetics ; Molecular Sequence Data ; Monosaccharide Transport Proteins/*genetics ; Phosphates/metabolism ; Phylogeny ; Plastids/genetics ; *Symbiosis ; Trioses/metabolism ; }, abstract = {The establishment of a metabolic connection between host and symbiont is a crucial step in the evolution of an obligate endosymbiotic relationship. Such was the case in the evolution of mitochondria and plastids. Whereas the mechanisms of metabolite shuttling between the plastid and host cytosol are relatively well studied in Archaeplastida-organisms that acquired photosynthesis through primary endosymbiosis-little is known about this process in organisms with complex plastids. Here, we focus on the presence, localization, and phylogeny of putative triose phosphate translocators (TPTs) in the complex plastid of diatoms. These proteins are thought to play an essential role in connecting endosymbiont and host metabolism via transport of carbohydrates generated by the photosynthesis machinery of the endosymbiont. We show that the complex plastid localized TPTs are monophyletic and present a model for how the initial metabolic link between host and endosymbiont might have been established in diatoms and other algae with complex red plastids and discuss its implications on the evolution of those lineages.}, }
@article {pmid26453092, year = {2016}, author = {Marangi, M and Hall, MJ and Aitken, A and Ready, PD and Giangaspero, A}, title = {Origins of Wohlfahrtia magnifica in Italy based on the identification of mitochondrial cytochrome b gene haplotypes.}, journal = {Parasitology research}, volume = {115}, number = {2}, pages = {483-487}, pmid = {26453092}, issn = {1432-1955}, mesh = {Animals ; Cytochromes b/*genetics ; Europe ; *Genes, Mitochondrial ; Geography ; Haplotypes ; Italy/epidemiology ; Larva ; Mitochondria ; Myiasis/epidemiology/parasitology/*veterinary ; Phylogeny ; Polymerase Chain Reaction ; Sarcophagidae/*genetics ; Sheep ; Sheep Diseases/epidemiology/*parasitology ; }, abstract = {To identify the geographical origins of larvae of Wohlfahrtia magnifica (Diptera: Sarcophagidae) causing myiasis of sheep in Italy, comparative DNA sequence analysis of the mitochondrial cytochrome b gene was performed, based on gene fragments amplified by PCR from genomic DNA isolated from individual specimens. DNA extractions of 19 larvae from Lazio, Molise, Puglia, and Sicilia generated 17 readable sequences homologous to 2 haplotypes, either CB_magn01 or CB_magn02; DNA extracts from 4 adult flies from Calabria (reared from larvae) produced 4 readable sequences belonging to the haplotype CB_magn01. The two haplotypes found represent both the East and West phylogenetic lineages of W. magnifica, which is consistent with the species' arrival from central/southeast Europe (East lineage) and/or from southwest Europe/northwest Africa (West lineage). This is the first report of the sympatric occurrence of the two lineages, which could have resulted from natural or human-assisted dispersal. Polymorphic nuclear loci will have to be characterized in order to explain the origins and lack of mitochondrial haplotype diversity of this pest in Italy, where it poses increasing veterinary problems.}, }
@article {pmid26444432, year = {2015}, author = {Xu, Q and Tang, B and Zou, Q and Zheng, H and Liu, X and Wang, S}, title = {Effects of Pyriproxyfen on Female Reproduction in the Common Cutworm, Spodoptera litura (F.) (Lepidoptera: Noctuidae).}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0138171}, pmid = {26444432}, issn = {1932-6203}, mesh = {Animals ; Endoplasmic Reticulum/drug effects ; Female ; Fertility/drug effects ; Insecticides/pharmacology ; Juvenile Hormones/*pharmacology ; Larva/drug effects ; Lepidoptera/*drug effects ; Mitochondria/drug effects ; Oocytes/drug effects ; Oviposition/drug effects ; Pyridines/*pharmacology ; Reproduction/*drug effects ; Spodoptera/*drug effects ; }, abstract = {The common cutworm, Spodoptera litura, is a rapidly reproducing pest of numerous agricultural ecosystems worldwide. The use of pesticides remains the primary means for controlling S. litura, despite their negative ecological impact and potential threat to human health. The use of exogenous hormone analogs may represent an alternative to insecticides. Juvenile hormones (JHs) play an important role in the reproductive systems of female insects, but the effects of pyriproxyfen, a JH analog, on reproduction in S. litura were poorly understood. In this paper, we topically treated the newly emerged females with 20, 60, or 100 μg of pyriproxyfen to determine its effects on reproduction. Then, we examined the expression of vitellogenin (Vg) and three hormone receptors, USP, HR3, and EcR, using quantitative reverse transcription and real-time polymerase chain reaction (qRT-PCR), and found that pyriproxyfen up-regulated the expression of Vg, USP, and HR3, whereas the expression of EcR was unaffected. An analysis of fecundity showed that the peak oviposition day, lifespan, and oviposition period were progressively shortened as the pyriproxyfen dosage increased. We also found that pyriproxyfen decreased egg laying amount, whereas the number of mature eggs that remained in the ovarioles of dead females increased as the pyriproxyfen dosage increased. We examined oocytes using transmission electron microscopy and found that treatment with 100 μg of pyriproxyfen increased the metabolism by increasing the amount of rough endoplasmic reticulum and mitochondria in the primary oocytes. Our results suggest that the topical application of pyriproxyfen on newly emerged females can efficiently reduce reproduction in S. litura and may represent an alternative to the use of insecticides for controlling the agricultural pest.}, }
@article {pmid26444283, year = {2015}, author = {Greig, K and Boocock, J and Prost, S and Horsburgh, KA and Jacomb, C and Walter, R and Matisoo-Smith, E}, title = {Complete Mitochondrial Genomes of New Zealand's First Dogs.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0138536}, pmid = {26444283}, issn = {1932-6203}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Dogs/*genetics ; Genetics, Population/methods ; Genome, Mitochondrial/*genetics ; Geography/methods ; Haplotypes/genetics ; Indonesia ; Mitochondria/*genetics ; New Zealand ; Pacific Ocean ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Dogs accompanied people in their migrations across the Pacific Ocean and ultimately reached New Zealand, which is the southern-most point of their oceanic distribution, around the beginning of the fourteenth century AD. Previous ancient DNA analyses of mitochondrial control region sequences indicated the New Zealand dog population included two lineages. We sequenced complete mitochondrial genomes of fourteen dogs from the colonisation era archaeological site of Wairau Bar and found five closely-related haplotypes. The limited number of mitochondrial lineages present at Wairau Bar suggests that the founding population may have comprised only a few dogs; or that the arriving dogs were closely related. For populations such as that at Wairau Bar, which stemmed from relatively recent migration events, control region sequences have insufficient power to address questions about population structure and founding events. Sequencing mitogenomes provided the opportunity to observe sufficient diversity to discriminate between individuals that would otherwise be assigned the same haplotype and to clarify their relationships with each other. Our results also support the proposition that at least one dispersal of dogs into the Pacific was via a south-western route through Indonesia.}, }
@article {pmid26439354, year = {2015}, author = {Archibald, JM}, title = {Endosymbiosis and Eukaryotic Cell Evolution.}, journal = {Current biology : CB}, volume = {25}, number = {19}, pages = {R911-21}, doi = {10.1016/j.cub.2015.07.055}, pmid = {26439354}, issn = {1879-0445}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {*Biological Evolution ; Eukaryota/*physiology ; Eukaryotic Cells/*physiology ; Evolution, Molecular ; Genomics ; Organelles/*physiology ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Understanding the evolution of eukaryotic cellular complexity is one of the grand challenges of modern biology. It has now been firmly established that mitochondria and plastids, the classical membrane-bound organelles of eukaryotic cells, evolved from bacteria by endosymbiosis. In the case of mitochondria, evidence points very clearly to an endosymbiont of α-proteobacterial ancestry. The precise nature of the host cell that partnered with this endosymbiont is, however, very much an open question. And while the host for the cyanobacterial progenitor of the plastid was undoubtedly a fully-fledged eukaryote, how - and how often - plastids moved from one eukaryote to another during algal diversification is vigorously debated. In this article I frame modern views on endosymbiotic theory in a historical context, highlighting the transformative role DNA sequencing played in solving early problems in eukaryotic cell evolution, and posing key unanswered questions emerging from the age of comparative genomics.}, }
@article {pmid26437714, year = {2015}, author = {Jafari, M and Mirzaie, M and Sadeghi, M}, title = {Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms.}, journal = {BMC bioinformatics}, volume = {16}, number = {}, pages = {319}, pmid = {26437714}, issn = {1471-2105}, mesh = {*Algorithms ; Animals ; Benchmarking ; Biological Evolution ; Cluster Analysis ; Humans ; Markov Chains ; Mitochondria/metabolism ; Protein Interaction Maps ; Proteins/chemistry/*metabolism ; }, abstract = {BACKGROUND: In the field of network science, exploring principal and crucial modules or communities is critical in the deduction of relationships and organization of complex networks. This approach expands an arena, and thus allows further study of biological functions in the field of network biology. As the clustering algorithms that are currently employed in finding modules have innate uncertainties, external and internal validations are necessary.<br><br>METHODS: Sequence and network structure alignment, has been used to define the Interlog Protein Network (IPN). This network is an evolutionarily conserved network with communal nodes and less false-positive links. In the current study, the IPN is employed as an evolution-based benchmark in the validation of the module finding methods. The clustering results of five algorithms; Markov Clustering (MCL), Restricted Neighborhood Search Clustering (RNSC), Cartographic Representation (CR), Laplacian Dynamics (LD) and Genetic Algorithm; to find communities in Protein-Protein Interaction networks (GAPPI) are assessed by IPN in four distinct Protein-Protein Interaction Networks (PPINs).<br><br>RESULTS: The MCL shows a more accurate algorithm based on this evolutionary benchmarking approach. Also, the biological relevance of proteins in the IPN modules generated by MCL is compatible with biological standard databases such as Gene Ontology, KEGG and Reactome.<br><br>CONCLUSION: In this study, the IPN shows its potential for validation of clustering algorithms due to its biological logic and straightforward implementation.}, }
@article {pmid26436958, year = {2016}, author = {Wang, FY and Wang, TY and Liao, TY and Liu, MY}, title = {The complete mitochondrial genome sequence of Nemateleotris decora (gobiiformes, gobiidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4274-4275}, doi = {10.3109/19401736.2015.1082091}, pmid = {26436958}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; DNA, Mitochondrial/genetics ; Gene Order/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; }, abstract = {We determined the mitochondrial genome (mitogenome) sequence of Nemateleotris decora by using a long polymerase chain reaction (PCR) method and next-generation sequence (NGS) technology. The total length of N. decora mitogenome is 16 502 bp, consisting of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs genes, and a non-coding control region. The overall base composition of N. decora is 25.22% for A, 25.90% for T, 30.69% for G, and 18.19% for C. Our results showed the complete mitogenome is a good marker for the phylogenetic study.}, }
@article {pmid26436880, year = {2015}, author = {Noguchi, F and Shimamura, S and Nakayama, T and Yazaki, E and Yabuki, A and Hashimoto, T and Inagaki, Y and Fujikura, K and Takishita, K}, title = {Metabolic Capacity of Mitochondrion-related Organelles in the Free-living Anaerobic Stramenopile Cantina marsupialis.}, journal = {Protist}, volume = {166}, number = {5}, pages = {534-550}, doi = {10.1016/j.protis.2015.08.002}, pmid = {26436880}, issn = {1618-0941}, mesh = {Mitochondria/*metabolism ; Phylogeny ; Sequence Analysis, RNA ; Stramenopiles/genetics/*metabolism ; }, abstract = {Functionally and morphologically degenerate mitochondria, so-called mitochondrion-related organelles (MROs), are frequently found in eukaryotes inhabiting hypoxic or anoxic environments. In the last decade, MROs have been discovered from a phylogenetically broad range of eukaryotic lineages and these organelles have been revealed to possess diverse metabolic capacities. In this study, the biochemical characteristics of an MRO in the free-living anaerobic protist Cantina marsupialis, which represents an independent lineage in stramenopiles, were inferred based on RNA-seq data. We found transcripts for proteins known to function in one form of MROs, the hydrogenosome, such as pyruvate:ferredoxin oxidoreductase, iron-hydrogenase, acetate:succinate CoA-transferase, and succinyl-CoA synthase, along with transcripts for acetyl-CoA synthetase (ADP-forming). These proteins possess putative mitochondrial targeting signals at their N-termini, suggesting dual ATP generation systems through anaerobic pyruvate metabolism in Cantina MROs. In addition, MROs in Cantina were also shown to share several features with canonical mitochondria, including amino acid metabolism and an "incomplete" tricarboxylic acid cycle. Transcripts for all four subunits of complex II (CII) of the electron transport chain were detected, while there was no evidence for the presence of complexes I, III, IV, or F1Fo ATPase. Cantina MRO biochemistry challenges the categories of mitochondrial organelles recently proposed.}, }
@article {pmid26435002, year = {2016}, author = {Manna, S and Harman, A}, title = {Horizontal gene transfer of a Chlamydial tRNA-guanine transglycosylase gene to eukaryotic microbes.}, journal = {Molecular phylogenetics and evolution}, volume = {94}, number = {Pt A}, pages = {392-396}, doi = {10.1016/j.ympev.2015.09.022}, pmid = {26435002}, issn = {1095-9513}, mesh = {Acanthamoeba/*genetics ; Amebiasis/genetics/parasitology ; Chlamydia/enzymology/*genetics ; Deltaproteobacteria/enzymology/genetics ; Dysentery, Bacillary/microbiology ; Eukaryota/genetics ; *Gene Transfer, Horizontal ; Pentosyltransferases/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Shigella flexneri/enzymology/genetics ; }, abstract = {tRNA-guanine transglycosylases are found in all domains of life and mediate the base exchange of guanine with queuine in the anticodon loop of tRNAs. They can also regulate virulence in bacteria such as Shigella flexneri, which has prompted the development of drugs that inhibit the function of these enzymes. Here we report a group of tRNA-guanine transglycosylases in eukaryotic microbes (algae and protozoa) which are more similar to their bacterial counterparts than previously characterized eukaryotic tRNA-guanine transglycosylases. We provide evidence demonstrating that the genes encoding these enzymes were acquired by these eukaryotic lineages via horizontal gene transfer from the Chlamydiae group of bacteria. Given that the S. flexneri tRNA-guanine transglycosylase can be targeted by drugs, we propose that the bacterial-like tRNA-guanine transglycosylases could potentially be targeted in a similar fashion in pathogenic amoebae that possess these enzymes such as Acanthamoeba castellanii. This work also presents ancient prokaryote-to-eukaryote horizontal gene transfer events as an untapped resource of potential drug target identification in pathogenic eukaryotes.}, }
@article {pmid26426123, year = {2015}, author = {Fujita, Y and Fujiwara, K and Zenitani, S and Yamashita, T}, title = {Acetylation of NDPK-D Regulates Its Subcellular Localization and Cell Survival.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0139616}, pmid = {26426123}, issn = {1932-6203}, mesh = {Acetylation ; Animals ; *Apoptosis ; Blotting, Western ; Brain/cytology/*metabolism ; Cell Nucleus/*metabolism ; Cell Proliferation ; Cells, Cultured ; Electroporation ; Female ; Fluorescent Antibody Technique ; HEK293 Cells ; Humans ; Immunoenzyme Techniques ; Immunoprecipitation ; In Situ Hybridization ; Mice ; Mice, Inbred C57BL ; Mitochondria/*metabolism ; Neuroblastoma/genetics/*metabolism/*pathology ; Nucleoside Diphosphate Kinase D/genetics/*metabolism ; RNA, Messenger/genetics ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Sirtuin 1/genetics/metabolism ; Subcellular Fractions ; }, abstract = {Nucleoside diphosphate kinases (NDPK) are ubiquitous enzymes that catalyze the reversible phosphotransfer of γ-phosphates between di- and triphosphonucleosides. NDPK-D (Nm23-H4) is the only member of the NDPK family with a mitochondrial targeting sequence. Despite the high expression of NDPK-D in the developing central nervous system, its function remains to be determined. In this study, we show that NDPK-D knockdown induces apoptosis in neuroblastoma cells as well as in mouse cortex, suggesting that NDPK-D is required for neuronal survival. We identified NDPK-D as a binding partner of NAD+-dependent histone deacetylase, SIRT1, by yeast two-hybrid screening. NDPK-D co-localized with SIRT1, and the association of these molecules was confirmed by co-immunoprecipitation. Inhibition of SIRT1 increases the acetylation of NDPK-D. Overexpression of NDPK-D along with SIRT1, or mutation in the acetylated lysine residues in NDPK-D, increases its nuclear accumulation. Furthermore, the NDPK-D acetylation-mimic mutant increased apoptosis in N1E-115 cells. Our data demonstrate that acetylation regulates the shuttling of NDPK-D between nucleus and cytoplasm, and increased acetylation of NDPK-D causes apoptosis.}, }
@article {pmid26425990, year = {2016}, author = {Liu, S and Wang, X and Xie, L and Tan, M and Li, Z and Su, X and Zhang, H and Misof, B and Kjer, KM and Tang, M and Niehuis, O and Jiang, H and Zhou, X}, title = {Mitochondrial capture enriches mito-DNA 100 fold, enabling PCR-free mitogenomics biodiversity analysis.}, journal = {Molecular ecology resources}, volume = {16}, number = {2}, pages = {470-479}, doi = {10.1111/1755-0998.12472}, pmid = {26425990}, issn = {1755-0998}, mesh = {Animals ; *Biodiversity ; DNA, Mitochondrial/chemistry/*genetics/*isolation &amp; purification ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Insecta/genetics ; Mitochondria/*genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Biodiversity analyses based on next-generation sequencing (NGS) platforms have developed by leaps and bounds in recent years. A PCR-free strategy, which can alleviate taxonomic bias, was considered as a promising approach to delivering reliable species compositions of targeted environments. The major impediment of such a method is the lack of appropriate mitochondrial DNA enrichment ways. Because mitochondrial genomes (mitogenomes) make up only a small proportion of total DNA, PCR-free methods will inevitably result in a huge excess of data (>99%). Furthermore, the massive volume of sequence data is highly demanding on computing resources. Here, we present a mitogenome enrichment pipeline via a gene capture chip that was designed by virtue of the mitogenome sequences of the 1000 Insect Transcriptome Evolution project (1KITE, www.1kite.org). A mock sample containing 49 species was used to evaluate the efficiency of the mitogenome capture method. We demonstrate that the proportion of mitochondrial DNA can be increased by approximately 100-fold (from the original 0.47% to 42.52%). Variation in phylogenetic distances of target taxa to the probe set could in principle result in bias in abundance. However, the frequencies of input taxa were largely maintained after capture (R(2) = 0.81). We suggest that our mitogenome capture approach coupled with PCR-free shotgun sequencing could provide ecological researchers an efficient NGS method to deliver reliable biodiversity assessment.}, }
@article {pmid26421611, year = {2015}, author = {Lopes-Marques, M and Delgado, IL and Ruivo, R and Torres, Y and Sainath, SB and Rocha, E and Cunha, I and Santos, MM and Castro, LF}, title = {The Origin and Diversity of Cpt1 Genes in Vertebrate Species.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0138447}, pmid = {26421611}, issn = {1932-6203}, mesh = {Animals ; Carnitine O-Palmitoyltransferase/*genetics ; Energy Metabolism/physiology ; *Evolution, Molecular ; Humans ; *Phylogeny ; }, abstract = {The Carnitine palmitoyltransferase I (Cpt1) gene family plays a crucial role in energy homeostasis since it is required for the occurrence of fatty acid β-oxidation in the mitochondria. The exact gene repertoire in different vertebrate lineages is variable. Presently, four genes are documented: Cpt1a, also known as Cpt1a1, Cpt1a2; Cpt1b and Cpt1c. The later is considered a mammalian innovation resulting from a gene duplication event in the ancestor of mammals, after the divergence of sauropsids. In contrast, Cpt1a2 has been found exclusively in teleosts. Here, we reassess the overall evolutionary relationships of Cpt1 genes using a combination of approaches, including the survey of the gene repertoire in basal gnathostome lineages. Through molecular phylogenetics and synteny studies, we find that Cpt1c is most likely a rapidly evolving orthologue of Cpt1a2. Thus, Cpt1c is present in other lineages such as cartilaginous fish, reptiles, amphibians and the coelacanth. We show that genome duplications (2R) and variable rates of sequence evolution contribute to the history of Cpt1 genes in vertebrates. Finally, we propose that loss of Cpt1b is the likely cause for the unusual energy metabolism of elasmobranch.}, }
@article {pmid26419670, year = {2015}, author = {Nishimura, K and Apitz, J and Friso, G and Kim, J and Ponnala, L and Grimm, B and van Wijk, KJ}, title = {Discovery of a Unique Clp Component, ClpF, in Chloroplasts: A Proposed Binary ClpF-ClpS1 Adaptor Complex Functions in Substrate Recognition and Delivery.}, journal = {The Plant cell}, volume = {27}, number = {10}, pages = {2677-2691}, pmid = {26419670}, issn = {1532-298X}, mesh = {Adaptor Proteins, Signal Transducing/genetics/*metabolism ; Aldehyde Oxidoreductases/genetics/metabolism ; Arabidopsis/*enzymology/genetics ; Arabidopsis Proteins/genetics/*metabolism ; Carrier Proteins/genetics/*metabolism ; Chloroplasts/enzymology ; Endopeptidase Clp/genetics/*metabolism ; *Models, Molecular ; Molecular Chaperones/genetics/metabolism ; Multienzyme Complexes ; Mutation ; Phylogeny ; Protein Interaction Mapping ; *Proteome ; Sequence Analysis, DNA ; Substrate Specificity ; }, abstract = {Clp proteases are found in prokaryotes, mitochondria, and plastids where they play crucial roles in maintaining protein homeostasis (proteostasis). The plant plastid Clp machinery comprises a hetero-oligomeric ClpPRT proteolytic core, ATP-dependent chaperones ClpC and ClpD, and an adaptor protein, ClpS1. ClpS1 selects substrates to the ClpPR protease-ClpC chaperone complex for degradation, but the underlying substrate recognition and delivery mechanisms are currently unclear. Here, we characterize a ClpS1-interacting protein in Arabidopsis thaliana, ClpF, which can interact with the Clp substrate glutamyl-tRNA reductase. ClpF and ClpS1 mutually stimulate their association with ClpC. ClpF, which is only found in photosynthetic eukaryotes, contains bacterial uvrB/C and YccV protein domains and a unique N-terminal domain. We propose a testable model in which ClpS1 and ClpF form a binary adaptor for selective substrate recognition and delivery to ClpC, reflecting an evolutionary adaptation of the Clp system to the plastid proteome.}, }
@article {pmid26416980, year = {2016}, author = {Adrion, JR and White, PS and Montooth, KL}, title = {The Roles of Compensatory Evolution and Constraint in Aminoacyl tRNA Synthetase Evolution.}, journal = {Molecular biology and evolution}, volume = {33}, number = {1}, pages = {152-161}, pmid = {26416980}, issn = {1537-1719}, support = {T32 GM007757/GM/NIGMS NIH HHS/United States ; T32-GM007757/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acyl-tRNA Synthetases/*genetics ; Animals ; Birds/genetics ; Cell Nucleus/genetics ; Drosophila/genetics ; *Evolution, Molecular ; Gene Expression/*genetics ; Genome, Mitochondrial/*genetics ; Humans ; Mitochondria/genetics ; }, abstract = {Mitochondrial protein translation requires interactions between transfer RNAs encoded by the mitochondrial genome (mt-tRNAs) and mitochondrial aminoacyl tRNA synthetase proteins (mt-aaRS) encoded by the nuclear genome. It has been argued that animal mt-tRNAs have higher deleterious substitution rates relative to their nuclear-encoded counterparts, the cytoplasmic tRNAs (cyt-tRNAs). This dynamic predicts elevated rates of compensatory evolution of mt-aaRS that interact with mt-tRNAs, relative to aaRS that interact with cyt-tRNAs (cyt-aaRS). We find that mt-aaRS do evolve at significantly higher rates (exemplified by higher dN and dN/dS) relative to cyt-aaRS, across mammals, birds, and Drosophila. While this pattern supports a model of compensatory evolution, the level at which a gene is expressed is a more general predictor of protein evolutionary rate. We find that gene expression level explains 10-56% of the variance in aaRS dN/dS, and that cyt-aaRS are more highly expressed in addition to having lower dN/dS values relative to mt-aaRS, consistent with more highly expressed genes being more evolutionarily constrained. Furthermore, we find no evidence of positive selection acting on either class of aaRS protein, as would be expected under a model of compensatory evolution. Nevertheless, the signature of faster mt-aaRS evolution persists in mammalian, but not bird or Drosophila, lineages after controlling for gene expression, suggesting some additional effect of compensatory evolution for mammalian mt-aaRS. We conclude that gene expression is the strongest factor governing differential amino acid substitution rates in proteins interacting with mitochondrial versus cytoplasmic factors, with important differences in mt-aaRS molecular evolution among taxonomic groups.}, }
@article {pmid26416383, year = {2015}, author = {Igea, J and Aymerich, P and Bannikova, AA and Gosálbez, J and Castresana, J}, title = {Multilocus species trees and species delimitation in a temporal context: application to the water shrews of the genus Neomys.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {209}, pmid = {26416383}, issn = {1471-2148}, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Cytochromes b/genetics ; Fossils ; Gene Flow ; *Genetic Speciation ; Introns ; Mitochondria/genetics ; Phylogeny ; Shrews/*classification/*genetics ; }, abstract = {BACKGROUND: Multilocus data are becoming increasingly important in determining the phylogeny of closely related species and delimiting species. In species complexes where unequivocal fossil calibrations are not available, rigorous dating of the coalescence-based species trees requires accurate mutation rates of the loci under study but, generally, these rates are unknown. Here, we obtained lineage-specific mutation rates of these loci from a higher-level phylogeny with a reliable fossil record and investigated how different choices of mutation rates and species tree models affected the split time estimates. We implemented this strategy with a genus of water shrews, Neomys, whose taxonomy has been contentious over the last century.<br><br>RESULTS: We sequenced 13 introns and cytochrome b from specimens of the three species currently recognized in this genus including two subspecies of N. anomalus that were originally described as species. A Bayesian multilocus species delimitation method and estimation of gene flow supported that these subspecies are distinct evolutionary lineages that should be treated as distinct species: N. anomalus (sensu stricto), limited to part of the Iberian Peninsula, and N. milleri, with a larger Eurasian range. We then estimated mutation rates from a Bayesian relaxed clock analysis of the mammalian orthologues with several fossil calibrations. Next, using the estimated Neomys-specific rates for each locus in an isolation-with-migration model, the split time for these sister taxa was dated at 0.40 Myr ago (with a 95 % confidence interval of 0.26 - 0.86 Myr), likely coinciding with one of the major glaciations of the Middle Pleistocene. We also showed that the extrapolation of non-specific rates or the use of simpler models would lead to very different split time estimates.<br><br>CONCLUSIONS: We showed that the estimation of rigorous lineage-specific mutation rates for each locus allows the inference of robust split times in a species tree framework. These times, in turn, afford a better understanding of the timeframe required to achieve isolation and, eventually, speciation in sister lineages. The application of species delimitation methods and an accurate dating strategy to the genus Neomys helped to clarify its controversial taxonomy.}, }
@article {pmid26414446, year = {2015}, author = {Suslov, NB and DasGupta, S and Huang, H and Fuller, JR and Lilley, DM and Rice, PA and Piccirilli, JA}, title = {Crystal structure of the Varkud satellite ribozyme.}, journal = {Nature chemical biology}, volume = {11}, number = {11}, pages = {840-846}, pmid = {26414446}, issn = {1552-4469}, support = {R01 GM102489/GM/NIGMS NIH HHS/United States ; P41 GM103403/GM/NIGMS NIH HHS/United States ; R01AI081987/AI/NIAID NIH HHS/United States ; B17092/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 11722/CRUK_/Cancer Research UK/United Kingdom ; R01GM102489/GM/NIGMS NIH HHS/United States ; R01 AI081987/AI/NIAID NIH HHS/United States ; }, mesh = {Adenine/chemistry/metabolism ; Catalytic Domain ; Crystallography, X-Ray ; Endoribonucleases/*chemistry/genetics/metabolism ; Evolution, Molecular ; Fungal Proteins/*chemistry/genetics/metabolism ; Gene Expression ; Guanine/chemistry/metabolism ; Mitochondria/chemistry/enzymology ; Molecular Docking Simulation ; Mutation ; Neurospora/*chemistry/enzymology ; Nucleic Acid Conformation ; Phosphates/chemistry/metabolism ; Plasmids/chemistry/metabolism ; Protein Multimerization ; Protein Structure, Secondary ; RNA/*chemistry/genetics/metabolism ; RNA, Catalytic/*chemistry/genetics/metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; }, abstract = {The Varkud satellite (VS) ribozyme mediates rolling-circle replication of a plasmid found in the Neurospora mitochondrion. We report crystal structures of this ribozyme from Neurospora intermedia at 3.1 Å resolution, which revealed an intertwined dimer formed by an exchange of substrate helices. In each protomer, an arrangement of three-way helical junctions organizes seven helices into a global fold that creates a docking site for the substrate helix of the other protomer, resulting in the formation of two active sites in trans. This mode of RNA-RNA association resembles the process of domain swapping in proteins and has implications for RNA regulation and evolution. Within each active site, adenine and guanine nucleobases abut the scissile phosphate, poised to serve direct roles in catalysis. Similarities to the active sites of the hairpin and hammerhead ribozymes highlight the functional importance of active-site features, underscore the ability of RNA to access functional architectures from distant regions of sequence space, and suggest convergent evolution.}, }
@article {pmid26413404, year = {2014}, author = {Martínez, VH and Monasterio de Gonzo, G and Uribe, MC and Grier, HJ}, title = {Testicular structure in three viviparous species of teleosts in the genus Jenynsia (Anablepidae).}, journal = {Spermatogenesis}, volume = {4}, number = {3}, pages = {e983399}, pmid = {26413404}, issn = {2156-5554}, abstract = {Histological structure of the testes and development of spermatozoa in Jenynsia species is described using light, scanning and transmission electron microscopy. The testis type is restricted spermatogonial, wherein spermatogonia are restricted to the distal ends of lobules, typical of the Atherinomorpha, and spermatogenesis is continuous throughout the year in wild-caught fish. Within the testicular lobes there are lobular germinal compartments wherein the functional units are spermatocysts, whose borders are formed by Sertoli cells. Spermatocysts may contain meiotic primary spermatocytes, secondary spermatocytes, spermatids, undergoing spermiogenesis, or spermatozoa. Spermatocysts with later stages of developing sperm are located proximal to the testicular ducts. During spermiogenesis, spermatid nuclei become elongated. As this occurs, the nucleus develops a deep, central fossa that contains the centriolar complex. As the flagellum grows, enlarging spermatid mitochondria migrate posteriorly alongside the flagellum but remain separated from it by the cytoplasmatic canal, an indentation of the plasma membrane. Between the enlarged mitochondria and plasma membrane, a sub-mitochondrial net develops. In longitudinal sections, the enlarged mitochondria are stacked in a zig-zag fashion, and in transverse sections they appear as a ring surrounding the flagellum, but separated from it by the cytoplasmic canal. Spermatozoa of the 3 jenynsiid species have an introsperm complex composed of a long mid-piece whose flagellum has a single "wing." Within the efferent ducts and the tubular gonopodium, sperm are lightly packed in a side by side fashion which facilitates their transfer into the female reproductive tract. This study presents detailed descriptions of testicular organization and cytological characterization of the stages of spermatozoa differentiation in 3 species of Jenynsia from northwestern Argentina (J. alternimaculata, J. multidentata and J. maculata), in order to contribute to the understanding of testicular structure and development of spermatozoa in the context of evolution of viviparity in this fish lineage.}, }
@article {pmid26410415, year = {2016}, author = {Yang, J and Ye, F and Huang, Y}, title = {Mitochondrial genomes of four katydids (Orthoptera: Phaneropteridae): New gene rearrangements and their phylogenetic implications.}, journal = {Gene}, volume = {575}, number = {2 Pt 3}, pages = {702-711}, doi = {10.1016/j.gene.2015.09.052}, pmid = {26410415}, issn = {1879-0038}, mesh = {Animals ; Bayes Theorem ; Evolution, Molecular ; *Gene Rearrangement ; Genome Size ; Genome, Insect ; *Genome, Mitochondrial ; Likelihood Functions ; Mitochondria/*genetics ; Multigene Family ; Orthoptera/classification/*genetics ; Phylogeny ; }, abstract = {Phaneropteridae is a family of Orthoptera that displays an amazing amount of diversity in terms of both forms and species. We sequenced the mitochondrial genomes (mitogenomes) of two bush katydids: Ruidocollaris obscura and Kuwayamaea brachyptera (Phaneropterinae), and two true katydids: Orophyllus montanus and Phyllomimus detersus (Pseudophyllinae), to obtain further insight into the characteristics of the katydid mitogenomes and to investigate the taxonomic status of subfamily Pseudophyllinae and the diversity of gene arrangements among Phaneropteridae. The following general genomic characteristics were observed in the four katydids: a longer length of the mitogenomes (16,007bp-16,667bp) compared with Caelifera, abundant intergenic spacers, and accepted atypical initiation codons (GTG and TTG, found in cox1, nad1 and nad2). A new orientation of the gene arrangement "trnM-trnI-trnQ" was identified in P. detersus, which is the first representative of Polyneoptera found to carry this gene cluster. Large identical fragments (492bp) were detected in control region 1 (CR1) and control region 2 (CR2) of R. obscura. The high similarity of the duplicated CRs is likely due to a recent gene duplication or concerted evolution. Analyses of the duplicated CRs revealed one conserved stem-loop (on the N-strand) located in the identical sequences of both CRs that might be linked to replication initiation. Phylogenetic analyses based on 13 protein-coding genes and 2 ribosomal RNA genes from 20 Ensiferan species yielded the identical topologies between two different methods (maximum likelihood and bayesian inference). The newly sequenced Pseudophyllinae species was placed as the sister group of Phaneropterinae, and Mecopodinae clustered with Pseudophyllinae+Phaneropterinae. Additionally, we speculate that the species in Ruidocollaris and Sinochlora, as well as their closely related genera, may have undergone numerous rearrangement events.}, }
@article {pmid26408967, year = {2016}, author = {McCord, CL and Westneat, MW}, title = {Phylogenetic relationships and the evolution of BMP4 in triggerfishes and filefishes (Balistoidea).}, journal = {Molecular phylogenetics and evolution}, volume = {94}, number = {Pt A}, pages = {397-409}, doi = {10.1016/j.ympev.2015.09.014}, pmid = {26408967}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Biodiversity ; Bone Morphogenetic Protein 4/*genetics ; *Evolution, Molecular ; *Genetic Speciation ; Mitochondria/genetics ; Oceans and Seas ; Phylogeny ; Sequence Analysis, DNA ; Tetraodontiformes/*classification/*genetics ; }, abstract = {The triggerfishes (family Balistidae) and filefishes (family Monacanthidae) comprise a charismatic superfamily (Balistoidea) within the diverse order Tetraodontiformes. This group of largely marine fishes occupies an impressive ecological range across the world's oceans, and is well known for its locomotor and feeding diversity, unusual body shapes, small genome size, and ecological and economic importance. In order to investigate the evolutionary history of these important fish families, we used multiple phylogenetic methods to analyze molecular data from 86 species spanning the extant biodiversity of Balistidae and Monacanthidae. In addition to three gene regions that have been used extensively in phylogenetic analyses, we include sequence data for two mitochondrial regions, two nuclear markers, and the growth factor gene bmp4, which is involved with cranial development. Phylogenetic analyses strongly support the monophyly of the superfamily Balistoidea, the sister-family relationship of Balistidae and Monacanthidae, as well as three triggerfish and four filefish clades that are well resolved. A new classification for the Balistidae is proposed based on phylogenetic groups. Bayesian topology, as well as the timing of major cladogenesis events, is largely congruent with previous hypotheses of balistid phylogeny. However, we present a novel topology for major clades in the filefish family that illustrate the genera Aluterus and Stephanolepis are more closely related than previously posited. Molecular rates suggest a Miocene and Oligocene origin for the families Balistidae and Monacanthidae, respectively, and significant divergence of species in both families within the past 5 million years. A second key finding of this study is that, relative to the other protein-coding gene regions in our DNA supermatrix, bmp4 shows a rapid accumulation of both synonymous and non-synonymous substitutions, especially within the family Monacanthidae. Overall substitution patterns in bmp4 support the hypothesis of stabilizing selection during the evolutionary history of regulatory genes, with a small number of isolated examples of accelerated non-synonymous changes detected in our phylogeny.}, }
@article {pmid26406276, year = {2016}, author = {Yao, H and Gao, M and Liu, K and Zhao, S}, title = {Sequence characterization and phylogeny analysis of the complete mitochondrial genome of verreaux's sifaka, Propithecus verreauxi (primates: indriidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4431-4432}, doi = {10.3109/19401736.2015.1089558}, pmid = {26406276}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Codon, Initiator/genetics ; Codon, Terminator/genetics ; Gene Order/genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; Primates/*genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; Strepsirhini/*genetics ; }, abstract = {The Verreaux's sifaka, Propithecus verreauxi, is a medium-sized lemur that inhabits in tropical dry lowland and montane forest. Here, we reported the complete mitochondrial genome sequence of this species. The mitogenome of P. verreauxi is 17 106 bp in length and composed of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes and a control region. The structure about gene order and composition is identical to that of the other lemur species and related genera. The overall base composition of the heavy strand in descending order is A (32.84%), T (27.13%), C (26.95%), and G (13.08%). Most of the genes are encoded on the heavy strand except for the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes. With the exception of COX3, which terminates with an incomplete stop codon (T-), all the other PCGs initiates with a traditional ATN start codon and ends with the typical mitochondrial stop codon (TAG/TAA/AGA). The phylogenetic tree constructed using the complete mitochondrial genome sequences of P. verreauxi together with 15 other closely related species with Neighbor-Joining (NJ) method shows that P. verreauxi is closer to P. coquereli in the phylogenetic relationship.}, }
@article {pmid26406120, year = {2016}, author = {Guan, N and Nie, C and Geng, R and Gao, Z and Zhang, X}, title = {The complete mitochondrial genome of the hybrid of Megalobrama amblycephala (♀) × Megalobrama skolkovii (♂).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4294-4295}, doi = {10.3109/19401736.2015.1082102}, pmid = {26406120}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Chimera/genetics ; Conserved Sequence/genetics ; Cyprinidae/*genetics ; DNA, Mitochondrial/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The complete mitochondrial genome of the hybrid of Megalobrama amblycephala (♀) × Megalobrama skolkovii (♂) was characterized first in this study. The total length of the genome was identical to the female parent as 16 623 bp, and the overall base composition was 31.23% A, 24.69% T, 27.89% C, and 16.19% G, with a slight A + T bias. It contained 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions (the control region and the origin of the light-strand replication). This study discovered the 99.88% sequence identity between the hybrid and its female parent, which confirmed the maternal inheritance pattern followed by the mitochondrial genome of the hybrid. However, the sequence alignment of mitochondrial genomes between the hybrid and its female parent revealed a total of 20 variable sites in 10 genes or regions, especially 4 sense mutations in 2 PCGs (COX1 and ATPase6). The complete mitochondrial genome sequence of this hybrid bream may provide an important dataset for further study in mitochondrial inheritance mechanism.}, }
@article {pmid26404767, year = {2016}, author = {Tang, X and Bi, G}, title = {Complete mitochondrial genome of Fistulifera solaris (Bacillariophycidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4405-4406}, doi = {10.3109/19401736.2015.1089545}, pmid = {26404767}, issn = {2470-1408}, mesh = {Base Composition/genetics ; Codon, Initiator/genetics ; DNA, Mitochondrial/genetics ; Diatoms/*genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; Introns/genetics ; Mitochondria/genetics ; Open Reading Frames/genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {The complete mitochondrial DNA of pennate diatom Fistulifera solaris was determined. The circular mitochondrial genome is 39 648 bp in length with 28.1% GC content and contains 63 genes, including 33 protein-coding genes, three conserved open reading frame (ORF154, ORF192 and ORF251), 25 tRNA and 2 rRNA genes. All protein-coding genes have AUG as start codon. A group I intron was found in nad11 gene. Both the gene content and the structure of Fistulifera solaris mitochondrial genome are very similar to Berkeleya fennica mitogenome (KM886611). Phylogeny analysis indicate F. solaris a close genetic relationship with Berkeleya fennica. This new mitogenome will provide more useful information for exploration in diatoms diversity and evolution.}, }
@article {pmid26404517, year = {2016}, author = {Zhao, M and Ma, H and Ma, C and Zhang, H and Zhang, X and Meng, Y and Wei, H and Chen, F and Ma, L}, title = {The complete mitochondrial genome and gene organization of Cubiceps squamiceps (Perciformes: nomeidae) with phylogenetic consideration.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4296-4297}, doi = {10.3109/19401736.2015.1082103}, pmid = {26404517}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; DNA, Mitochondrial/*genetics ; Fishes/genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {In this study, we reported the complete mitochondrial DNA sequence of Cubiceps squamiceps, and its phylogenetic relationship. The full length of this mitogenome was 16 510 bp, including 22 transfer RNA genes, two ribosomal RNA genes, 13 protein-coding genes, and a putative control region. The location of genes in mitochondrial genome was similar to other fish species within family Nomeidae. Twenty-eight genes were located on the heavy strand, while nine genes were located on the light strand. The nucleotide composition of this mitogenome was 27.5% for A, 28.5% for C, 17.5% for G, and 26.5% for T. From the NJ phylogenetic tree, we can find that C. squamiceps was genetically closest to C. pauciradiatus among 20 species within suborder Stromateoidei. This study could lay the basis for the future studies in population genetic diversity, taxonomic status, molecular systematics, and conservation genetics in C. squamiceps.}, }
@article {pmid26403677, year = {2015}, author = {Schwartz, TS and Arendsee, ZW and Bronikowski, AM}, title = {Mitochondrial divergence between slow- and fast-aging garter snakes.}, journal = {Experimental gerontology}, volume = {71}, number = {}, pages = {135-146}, doi = {10.1016/j.exger.2015.09.004}, pmid = {26403677}, issn = {1873-6815}, mesh = {Aging/genetics/*physiology ; Animals ; Base Sequence ; Colubridae/genetics/*physiology ; Ecotype ; Female ; Gene Expression Regulation/physiology ; Gene Regulatory Networks/physiology ; Genome, Mitochondrial ; Haplotypes ; Heat-Shock Response/genetics ; Longevity/genetics/physiology ; Mitochondria/*physiology ; Phenotype ; Sequence Alignment ; Species Specificity ; }, abstract = {Mitochondrial function has long been hypothesized to be intimately involved in aging processes--either directly through declining efficiency of mitochondrial respiration and ATP production with advancing age, or indirectly, e.g., through increased mitochondrial production of damaging free radicals with age. Yet we lack a comprehensive understanding of the evolution of mitochondrial genotypes and phenotypes across diverse animal models, particularly in species that have extremely labile physiology. Here, we measure mitochondrial genome-types and transcription in ecotypes of garter snakes (Thamnophis elegans) that are adapted to disparate habitats and have diverged in aging rates and lifespans despite residing in close proximity. Using two RNA-seq datasets, we (1) reconstruct the garter snake mitochondrial genome sequence and bioinformatically identify regulatory elements, (2) test for divergence of mitochondrial gene expression between the ecotypes and in response to heat stress, and (3) test for sequence divergence in mitochondrial protein-coding regions in these slow-aging (SA) and fast-aging (FA) naturally occurring ecotypes. At the nucleotide sequence level, we confirmed two (duplicated) mitochondrial control regions one of which contains a glucocorticoid response element (GRE). Gene expression of protein-coding genes was higher in FA snakes relative to SA snakes for most genes, but was neither affected by heat stress nor an interaction between heat stress and ecotype. SA and FA ecotypes had unique mitochondrial haplotypes with amino acid substitutions in both CYTB and ND5. The CYTB amino acid change (Isoleucine → Threonine) was highly segregated between ecotypes. This divergence of mitochondrial haplotypes between SA and FA snakes contrasts with nuclear gene-flow estimates, but correlates with previously reported divergence in mitochondrial function (mitochondrial oxygen consumption, ATP production, and reactive oxygen species consequences).}, }
@article {pmid26402847, year = {2015}, author = {Guan, X and Chen, H and Abramson, A and Man, H and Wu, J and Yu, O and Nikolau, BJ}, title = {A phosphopantetheinyl transferase that is essential for mitochondrial fatty acid biosynthesis.}, journal = {The Plant journal : for cell and molecular biology}, volume = {84}, number = {4}, pages = {718-732}, doi = {10.1111/tpj.13034}, pmid = {26402847}, issn = {1365-313X}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/growth &amp; development/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Bacterial Proteins/classification/genetics/*metabolism ; Blotting, Western ; Fatty Acids/*biosynthesis ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Glycine/metabolism ; Glycolates/metabolism ; Green Fluorescent Proteins/genetics/metabolism ; Microscopy, Confocal ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Molecular Sequence Data ; Mutation ; Phylogeny ; Plants, Genetically Modified ; RNA Interference ; Reverse Transcriptase Polymerase Chain Reaction ; Seeds/genetics/growth &amp; development/metabolism ; Sequence Homology, Amino Acid ; Transferases (Other Substituted Phosphate Groups)/classification/genetics/*metabolism ; }, abstract = {In this study we report the molecular genetic characterization of the Arabidopsis mitochondrial phosphopantetheinyl transferase (mtPPT), which catalyzes the phosphopantetheinylation and thus activation of mitochondrial acyl carrier protein (mtACP) of mitochondrial fatty acid synthase (mtFAS). This catalytic capability of the purified mtPPT protein (encoded by AT3G11470) was directly demonstrated in an in vitro assay that phosphopantetheinylated mature Arabidopsis apo-mtACP isoforms. The mitochondrial localization of the AT3G11470-encoded proteins was validated by the ability of their N-terminal 80-residue leader sequence to guide a chimeric GFP protein to this organelle. A T-DNA-tagged null mutant mtppt-1 allele shows an embryo-lethal phenotype, illustrating a crucial role of mtPPT for embryogenesis. Arabidopsis RNAi transgenic lines with reduced mtPPT expression display typical phenotypes associated with a deficiency in the mtFAS system, namely miniaturized plant morphology, slow growth, reduced lipoylation of mitochondrial proteins, and the hyperaccumulation of photorespiratory intermediates, glycine and glycolate. These morphological and metabolic alterations are reversed when these plants are grown in a non-photorespiratory condition (i.e. 1% CO2 atmosphere), demonstrating that they are a consequence of a deficiency in photorespiration due to the reduced lipoylation of the photorespiratory glycine decarboxylase.}, }
@article {pmid26399812, year = {2015}, author = {Hamilton, G}, title = {The hidden risks for 'three-person' babies.}, journal = {Nature}, volume = {525}, number = {7570}, pages = {444-446}, pmid = {26399812}, issn = {1476-4687}, mesh = {Aging/genetics/pathology ; Animals ; Biological Therapy/*adverse effects ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; Drosophila melanogaster/cytology/genetics ; *Evolution, Molecular ; Female ; Genome, Mitochondrial/genetics ; Haplotypes/genetics ; Humans ; Male ; Mice ; Mitochondria/*genetics/pathology/physiology/*transplantation ; Mitochondrial Diseases/genetics/*pathology/*therapy ; Models, Biological ; Neoplasms/genetics/pathology ; Neurodegenerative Diseases/genetics/pathology ; Obesity/genetics/pathology/therapy ; Risk Assessment/ethics/standards ; Symbiosis/genetics ; }, }
@article {pmid26399640, year = {2016}, author = {Spanaki, C and Kotzamani, D and Kleopa, K and Plaitakis, A}, title = {Evolution of GLUD2 Glutamate Dehydrogenase Allows Expression in Human Cortical Neurons.}, journal = {Molecular neurobiology}, volume = {53}, number = {8}, pages = {5140-5148}, pmid = {26399640}, issn = {1559-1182}, mesh = {Adult ; Aged ; Aged, 80 and over ; Antibody Specificity ; Astrocytes/enzymology ; Calnexin/metabolism ; Cell Nucleus/metabolism ; Cerebral Cortex/*cytology ; *Evolution, Molecular ; Glutamate Dehydrogenase/*metabolism ; Humans ; Middle Aged ; Neurons/*enzymology ; }, abstract = {Human hGDH2 arose via duplication in the apes and driven by positive selection acquired enhanced catalytic ability under conditions inhibitory to its precursor hGDH1 (common to all mammals). To explore the biological advantage provided by the novel enzyme, we studied, by immunohistochemistry (IHC) and immunofluorescence (IF), hGDH1 and hGDH2 expression in the human brain. Studies on human cortical tissue using anti-hGDH1-specific antibody revealed that hGDH1 was expressed in glial cells (astrocytes, oligodendrocytes, and oligodendrocyte precursors) with neurons being devoid of hGDH1 staining. In contrast, an hGDH2-specific antiserum labeled both astrocytes and neurons. Specifically, hGDH2 immunoreactivity was found in the cytoplasm of large neuronal cells within coarse structures resembling mitochondria. These were distributed either in the perikaryon or in the cell periphery. Double immunofluorescence (IF) suggested that the latter represented hGDH2-labeled mitochondria of presynaptic nerve terminals. Hence, hGDH2 evolution bestowed large human neurons with enhanced glutamate metabolizing capacity, thus strengthening cortical excitatory transmission.}, }
@article {pmid26396189, year = {2015}, author = {Kassa, T and Jana, S and Strader, MB and Meng, F and Jia, Y and Wilson, MT and Alayash, AI}, title = {Sickle Cell Hemoglobin in the Ferryl State Promotes βCys-93 Oxidation and Mitochondrial Dysfunction in Epithelial Lung Cells (E10).}, journal = {The Journal of biological chemistry}, volume = {290}, number = {46}, pages = {27939-27958}, pmid = {26396189}, issn = {1083-351X}, support = {P01 HL110900/HL/NHLBI NIH HHS/United States ; P01-HL110900/HL/NHLBI NIH HHS/United States ; }, mesh = {Anemia, Hemolytic/enzymology ; Anemia, Sickle Cell/enzymology ; Catalysis ; Cyclic N-Oxides/chemistry ; Cysteine/*chemistry ; Energy Metabolism ; Heme/chemistry ; Heme Oxygenase (Decyclizing)/chemistry ; Hemoglobin, Sickle/*chemistry ; Humans ; Hydrogen Peroxide/chemistry ; Iron/*chemistry ; Lung/enzymology ; Methemoglobin/chemistry ; Mitochondria/*metabolism ; Oxidation-Reduction ; Oxygen Consumption ; Respiratory Mucosa/*enzymology/ultrastructure ; }, abstract = {Polymerization of intraerythrocytic deoxyhemoglobin S (HbS) is the primary molecular event that leads to hemolytic anemia in sickle cell disease (SCD). We reasoned that HbS may contribute to the complex pathophysiology of SCD in part due to its pseudoperoxidase activity. We compared oxidation reactions and the turnover of oxidation intermediates of purified human HbS and HbA. Hydrogen peroxide (H2O2) drives a catalytic cycle that includes the following three distinct steps: 1) initial oxidation of ferrous (oxy) to ferryl Hb; 2) autoreduction of the ferryl intermediate to ferric (metHb); and 3) reaction of metHb with an additional H2O2 molecule to regenerate the ferryl intermediate. Ferrous and ferric forms of both proteins underwent initial oxidation to the ferryl heme in the presence of H2O2 at equal rates. However, the rate of autoreduction of ferryl to the ferric form was slower in the HbS solutions. Using quantitative mass spectrometry and the spin trap, 5,5-dimethyl-1-pyrroline-N-oxide, we found more irreversibly oxidized βCys-93in HbS than in HbA. Incubation of the ferric or ferryl HbS with cultured lung epithelial cells (E10) induced a drop in mitochondrial oxygen consumption rate and impairment of cellular bioenergetics that was related to the redox state of the iron. Ferryl HbS induced a substantial drop in the mitochondrial transmembrane potential and increases in cytosolic heme oxygenase (HO-1) expression and mitochondrial colocalization in E10 cells. Thus, highly oxidizing ferryl Hb and heme, the product of oxidation, may be central to the evolution of vasculopathy in SCD and may suggest therapeutic modalities that interrupt heme-mediated inflammation.}, }
@article {pmid26393435, year = {2016}, author = {Bremer, K and Kocha, KM and Snider, T and Moyes, CD}, title = {Sensing and responding to energetic stress: The role of the AMPK-PGC1α-NRF1 axis in control of mitochondrial biogenesis in fish.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {199}, number = {}, pages = {4-12}, doi = {10.1016/j.cbpb.2015.09.005}, pmid = {26393435}, issn = {1879-1107}, mesh = {AMP-Activated Protein Kinases/*metabolism ; Amino Acid Sequence ; Animals ; Enzyme Activation ; Fishes/*metabolism/physiology ; Humans ; Nuclear Respiratory Factor 1/*metabolism ; *Organelle Biogenesis ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/chemistry/*metabolism ; Rats ; *Stress, Physiological ; }, abstract = {Remodeling the muscle metabolic machinery in mammals in response to energetic challenges depends on the energy sensor AMP-activated protein kinase (AMPK) and its ability to phosphorylate PPAR γ coactivator 1 α (PGC1α), which in turn coactivates metabolic genes through direct and indirect association with DNA-binding proteins such as the nuclear respiratory factor 1 (NRF1) (Wu et al., 1999). The integrity of this axis in fish is uncertain because PGC1α i) lacks the critical Thr177 targeted by AMPK and ii) has mutations that may preclude binding NRF1. In this study we found no evidence that AMPK regulates mitochondrial gene expression through PGC1α in zebrafish and goldfish. AICAR treatment of zebrafish blastula cells increased phosphorylation of AMPK and led to changes in transcript levels of the AMPK targets mTOR and hexokinase 2. However, we saw no increases in mRNA levels for genes associated with mitochondrial biogenesis, including PGC1α, NRF1, and COX7C, a cytochrome c oxidase subunit. Further, AMPK phosphorylated mammalian peptides of PGC1α but not the corresponding region of zebrafish or goldfish in vitro. In vivo cold acclimation of goldfish caused an increase in mitochondrial enzymes, AMP and ADP levels, however AMPK phosphorylation decreased. In fish, the NRF1-PGC1α axis may be disrupted due to insertions in fish PGC1α orthologs within the region that serves as NRF1 binding domain in mammals. Immunocopurification showed that recombinant NRF1 protein binds mammalian but not fish PGC1α. Collectively, our studies suggest that fish have a disruption in the AMPK-PGC1α-NRF1 pathway due to structural differences between fish and mammalian PGC1α.}, }
@article {pmid26390919, year = {2015}, author = {Choo, A and O'Keefe, LV and Lee, CS and Gregory, SL and Shaukat, Z and Colella, A and Lee, K and Denton, D and Richards, RI}, title = {Tumor suppressor WWOX moderates the mitochondrial respiratory complex.}, journal = {Genes, chromosomes &amp; cancer}, volume = {54}, number = {12}, pages = {745-761}, doi = {10.1002/gcc.22286}, pmid = {26390919}, issn = {1098-2264}, support = {NIH/NIGMS R01-GM084947//PHS HHS/United States ; }, mesh = {Animals ; Catalytic Domain ; Cell Proliferation ; *Chromosome Fragile Sites ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster/genetics/metabolism ; Electron Transport Complex I/*metabolism ; Fatty Acid Synthases/genetics/metabolism ; Glycolysis/*genetics ; Homeostasis ; Metabolic Networks and Pathways/genetics ; Mitochondria/genetics/*metabolism ; NADH, NADPH Oxidoreductases/genetics/metabolism ; Neoplasms/genetics/metabolism ; Oxidative Phosphorylation ; Reactive Oxygen Species/metabolism ; Tumor Suppressor Proteins/genetics/*metabolism ; WW Domain-Containing Oxidoreductase ; }, abstract = {Fragile site FRA16D exhibits DNA instability in cancer, resulting in diminished levels of protein from the WWOX gene that spans it. WWOX suppresses tumor growth by an undefined mechanism. WWOX participates in pathways involving aerobic metabolism and reactive oxygen species. WWOX comprises two WW domains as well as a short-chain dehydrogenase/reductase enzyme. Herein is described an in vivo genetic analysis in Drosophila melanogaster to identify functional interactions between WWOX and metabolic pathways. Altered WWOX levels modulate variable cellular outgrowths caused by genetic deficiencies of components of the mitochondrial respiratory complexes. This modulation requires the enzyme active site of WWOX, and the defective respiratory complex-induced cellular outgrowths are mediated by reactive oxygen species, dependent upon the Akt pathway and sensitive to levels of autophagy and hypoxia-inducible factor. WWOX is known to contribute to homeostasis by regulating the balance between oxidative phosphorylation and glycolysis. Reduction of WWOX levels results in diminished ability to respond to metabolic perturbation of normal cell growth. Thus, the ability of WWOX to facilitate escape from mitochondrial damage-induced glycolysis (Warburg effect) is, therefore, a plausible mechanism for its tumor suppressor activity.}, }
@article {pmid26388034, year = {2015}, author = {Zhang, L and Li, H and Li, S and Zhang, A and Kou, F and Xun, H and Wang, P and Wang, Y and Song, F and Cui, J and Cui, J and Gouge, DH and Cai, W}, title = {Phylogeographic structure of cotton pest Adelphocoris suturalis (Hemiptera: Miridae): strong subdivision in China inferred from mtDNA and rDNA ITS markers.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {14009}, pmid = {26388034}, issn = {2045-2322}, mesh = {Animals ; Base Sequence ; China ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex I/genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Genetic Variation/genetics ; Gossypium ; Heteroptera/*genetics/physiology ; Japan ; Mitochondria/*genetics ; Phylogeography ; RNA, Ribosomal, 28S/genetics ; RNA, Ribosomal, 5.8S/genetics ; Sequence Analysis, DNA ; }, abstract = {Phylogeographic patterns of some extant plant and vertebrate species have been well studied; however, they are poorly understood in the majority of insects. The study documents analysis of mitochondrial (COI, CYTB and ND5) and nuclear (5.8S rDNA, ITS2 and 28S rDNA) data from 419 individuals of Adelphocoris suturalis, which is one of the main cotton pests found in the 31 locations in China and Japan involved in the study. Results show that the species is highly differentiated between populations from central China and peripheral China regions. Analysis of molecular variance showed a high level of geographical differentiation at different hierarchical levels. Isolation-by-distance test showed no significant correlation between genetic distance and geographical distance among A. suturalis populations, which suggested gene flow is not restricted by distance. In seven peripheral populations, the high levels of genetic differentiation and the small Nem values implied that geographic barriers were more likely restrict gene flow. Neutrality tests and the Bayesian skyline plot suggested population expansion likely happened during the cooling transition between Last Interglacial and Last Glacial Maximum. All lines of evidence suggest that physical barriers, Pleistocene climatic oscillations and geographical heterogeneity have affected the population structure and distribution of this insect in China.}, }
@article {pmid26384251, year = {2016}, author = {Jin, JM and Hou, CC and Tan, FQ and Yang, WX}, title = {The potential function of prohibitin during spermatogenesis in Chinese fire-bellied newt Cynops orientalis.}, journal = {Cell and tissue research}, volume = {363}, number = {3}, pages = {805-822}, doi = {10.1007/s00441-015-2280-y}, pmid = {26384251}, issn = {1432-0878}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Western ; Cloning, Molecular ; DNA, Complementary/genetics ; Fluorescent Antibody Technique ; Gene Expression Regulation ; In Situ Hybridization ; Male ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Prohibitins ; RNA, Messenger/genetics/metabolism ; Repressor Proteins/genetics/*metabolism ; Salamandridae/genetics/*physiology ; Sequence Alignment ; Sertoli Cells/cytology/metabolism ; *Spermatogenesis/genetics ; Spermatozoa/cytology/metabolism ; Staining and Labeling ; Time Factors ; }, abstract = {Prohibitin proteins are multifunctional proteins located mainly at the inner membrane of mitochondria expressed in universal species. They play a vital role in mitochondria's function, cell proteolysis, senescence, apoptosis and as a substrate for ubiquitination. In this study, we used PCR cloning, protein and nucleotide acids alignment, protein structure prediction, western blot, in situ hybridization and immunofluorescence to study the characteristics of the prohibitin gene and the potential role of prohibitin in spermatogenesis and spermiogenesis processes in the Chinese fire-bellied newt Cynops orientalis. First, we cloned a 1452-bp full-length cDNA from the testis of Cynops orientalis. Second, we found that the 272 amino acids of prohibitin have a SPFH family domain. Thirdly, the western blots showed high expression of prohibitin in testis while the protein size was approximately 32 kDa. Fourthly, the results of in situ hybridization and immunofluorescence experiments showed that most of the prohibitins travelled with the mitochondria's migration in Cynops orientalis. The quantities of mRNA decreased as spermiogenesis proceeded, although the signals of prohibitins existed during the whole period of spermatogenesis and spermiogenesis. In the mature germ cells, the signals of prohibitins were weak and aggregated at the end of the cell. Finally, we discovered that the Sertoli cells had a large quantity of prohibitins and we made several assumptions of prohibitins' potential roles in those cells. This is the first time that the relationship between mitochondria and prohibitin in different stages of the sperm cells in Cynops orientalis has been examined, which also revealed that Sertoli cells have abundant prohibitins.}, }
@article {pmid26381927, year = {2015}, author = {Sheiner, L and Fellows, JD and Ovciarikova, J and Brooks, CF and Agrawal, S and Holmes, ZC and Bietz, I and Flinner, N and Heiny, S and Mirus, O and Przyborski, JM and Striepen, B}, title = {Toxoplasma gondii Toc75 Functions in Import of Stromal but not Peripheral Apicoplast Proteins.}, journal = {Traffic (Copenhagen, Denmark)}, volume = {16}, number = {12}, pages = {1254-1269}, doi = {10.1111/tra.12333}, pmid = {26381927}, issn = {1600-0854}, support = {104111//Wellcome Trust/United Kingdom ; K99 AI103032/AI/NIAID NIH HHS/United States ; R01 AI064671/AI/NIAID NIH HHS/United States ; R01 AI084415/AI/NIAID NIH HHS/United States ; }, mesh = {Apicomplexa/genetics/metabolism ; Apicoplasts/genetics/*metabolism ; Erythrocytes/parasitology ; Fibroblasts/parasitology ; Green Fluorescent Proteins ; Humans ; Intracellular Membranes/*metabolism ; Membrane Proteins/genetics/*metabolism ; Microscopy, Fluorescence ; Mitochondria/metabolism ; Mutagenesis, Site-Directed ; Phenylalanine/genetics ; Phylogeny ; Protein Transport ; Protozoan Proteins/genetics/*metabolism ; Toxoplasma/genetics/*metabolism ; }, abstract = {Apicomplexa are unicellular parasites causing important human and animal diseases, including malaria and toxoplasmosis. Most of these pathogens possess a relict but essential plastid, the apicoplast. The apicoplast was acquired by secondary endosymbiosis between a red alga and a flagellated eukaryotic protist. As a result the apicoplast is surrounded by four membranes. This complex structure necessitates a system of transport signals and translocons allowing nuclear encoded proteins to find their way to specific apicoplast sub-compartments. Previous studies identified translocons traversing two of the four apicoplast membranes. Here we provide functional support for the role of an apicomplexan Toc75 homolog in apicoplast protein transport. We identify two apicomplexan genes encoding Toc75 and Sam50, both members of the Omp85 protein family. We localize the respective proteins to the apicoplast and the mitochondrion of Toxoplasma and Plasmodium. We show that the Toxoplasma Toc75 is essential for parasite growth and that its depletion results in a rapid defect in the import of apicoplast stromal proteins while the import of proteins of the outer compartments is affected only as the secondary consequence of organelle loss. These observations along with the homology to Toc75 suggest a potential role in transport through the second innermost membrane.}, }
@article {pmid26379046, year = {2015}, author = {Taniguchi, T and Manai, D and Shibata, M and Itabashi, Y and Monde, K}, title = {Stereochemical analysis of glycerophospholipids by vibrational circular dichroism.}, journal = {Journal of the American Chemical Society}, volume = {137}, number = {38}, pages = {12191-12194}, doi = {10.1021/jacs.5b05832}, pmid = {26379046}, issn = {1520-5126}, mesh = {*Circular Dichroism ; Glycerophospholipids/*chemistry ; Molecular Structure ; Stereoisomerism ; *Vibration ; }, abstract = {The stereochemistry of glycerophospholipids (GPLs) has been of interest for its roles in the evolution of life and in their biological activity. However, because of their structural complexity, no convenient method to determine their configuration has been reported. In this work, through the first systematic application of vibrational circular dichroism (VCD) spectroscopy to various diacylated GPLs, we have revealed that their chirality can be assigned by the sign of a VCD exciton couplet generated by the interaction of two carbonyl groups. This paper also presents spectroscopic evidence for the stereochemistry of GPLs isolated from bacteria, eukaryotes, and mitochondria.}, }
@article {pmid26378642, year = {2015}, author = {Vacca, M and Allison, M and Griffin, JL and Vidal-Puig, A}, title = {Fatty Acid and Glucose Sensors in Hepatic Lipid Metabolism: Implications in NAFLD.}, journal = {Seminars in liver disease}, volume = {35}, number = {3}, pages = {250-261}, doi = {10.1055/s-0035-1562945}, pmid = {26378642}, issn = {1098-8971}, support = {MC_PC_13030/MRC_/Medical Research Council/United Kingdom ; RG/12/13/29853/BHF_/British Heart Foundation/United Kingdom ; MC_UU_12012/2/MRC_/Medical Research Council/United Kingdom ; G0802051/MRC_/Medical Research Council/United Kingdom ; G0400192/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adipose Tissue/metabolism/physiopathology ; Animals ; Blood Glucose/*metabolism ; Disease Progression ; Fatty Acids/blood/*metabolism ; Humans ; Insulin/blood ; Insulin Resistance ; Liver/*metabolism/physiopathology ; Mitochondria, Liver/metabolism ; Non-alcoholic Fatty Liver Disease/blood/diagnosis/*metabolism/physiopathology ; Prognosis ; Risk Factors ; }, abstract = {The term nonalcoholic fatty liver disease (NAFLD) covers a pathologic spectrum from lipid accumulation alone (simple steatosis) to steatosis with associated inflammation and fibrosis (nonalcoholic steatohepatitis [NASH]). Nonalcoholic steatohepatitis can progress to cirrhosis and potentially to hepatocellular carcinoma. Although a genetic predisposition has been highlighted, NAFLD is strongly associated with an unhealthy lifestyle and hypercaloric diet in the context of obesity and metabolic disease. The dysregulation of specific pathways (insulin signaling, mitochondrial function, fatty acid, and lipoprotein metabolism) have been linked to steatosis, but elucidating the molecular events determining evolution of the disease still requires further research before it can be translated into specific personalized interventional strategies. In this review, the authors focus on the early events of the pathophysiology of NASH, dissecting the metabolic and nutritional pathways involving fatty acids and glucose sensors that can modulate lipid accumulation in the liver, but also condition the progression to cirrhosis and hepatocellular carcinoma.}, }
@article {pmid26378443, year = {2015}, author = {Shrestha, Y and Wirshing, HH and Harasewych, MG}, title = {The Genus Cerion (Gastropoda: Cerionidae) in the Florida Keys.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0137325}, pmid = {26378443}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Florida ; Gastropoda/*classification/*genetics ; Genetic Variation ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Protein Subunits/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The systematic relationships and phylogeography of Cerion incanum, the only species of Cerion native to the Florida Keys, are reviewed based on partial sequences of the mitochondrial COI and 16S genes derived from 18 populations spanning the range of this species and including the type localities of all four described subspecies. Our samples included specimens of Cerion casablancae, a species introduced to Indian Key in 1912, and a population of C. incanum x C. casablancae hybrids descended from a population of C. casablancae introduced onto Bahia Honda Key in the same year. Molecular data did not support the partition of C. incanum into subspecies, nor could populations be apportioned reliably into subspecies based on morphological features used to define the subspecies. Phylogenetic analyses affirmed the derived relationship of C. incanum relative to other cerionids, and indicated a Bahamian origin for the Cerion fauna of southern Florida. Relationships among the populations throughout the Keys indicate that the northernmost populations, closest to the Tomeu paleoislands that had been inhabited by Cerion petuchi during the Calabrian Pleistocene, are the oldest. The range of Cerion incanum expanded as the archipelago that is the Florida Keys was formed since the lower Tarantian Pleistocene by extension from the northeast to the southwest, with new islands populated as they were formed. The faunas of the High Coral Keys in the northeast and the Oölite Keys in the southwest, both with large islands that host multiple discontinuous populations of Cerion, are each composed of well supported clades that are characterized by distinctive haplotypes. In contrast, the fauna of the intervening Low Coral Keys consist of a heterogeneous series of populations, some with haplotypes derived from the High Coral Keys, others from the Oölite Keys. Individuals from the C. incanum x C. casablancae hybrid population inhabiting the southeastern coast of Bahia Honda Key were readily segregated based on their mitogenome lineage, grouping either with C. incanum or with C. casablancae from Indian Key. Hybrids with C. casablancae mitogenomes had haplotypes that were more divergent from their parent mitogenome than were hybrids with C. incanum mitogenomes.}, }
@article {pmid26376423, year = {2015}, author = {Weber-Lotfi, F and Koulintchenko, MV and Ibrahim, N and Hammann, P and Mileshina, DV and Konstantinov, YM and Dietrich, A}, title = {Nucleic acid import into mitochondria: New insights into the translocation pathways.}, journal = {Biochimica et biophysica acta}, volume = {1853}, number = {12}, pages = {3165-3181}, doi = {10.1016/j.bbamcr.2015.09.011}, pmid = {26376423}, issn = {0006-3002}, mesh = {Arabidopsis/metabolism ; Biological Transport ; Mitochondria/*metabolism ; Nucleic Acids/*metabolism ; Saccharomyces cerevisiae/metabolism ; }, abstract = {Mitochondria have retained indispensable but limited genetic information and they import both proteins and nucleic acids from the cytosol. RNA import is essential for gene expression and regulation, whereas competence for DNA uptake is likely to contribute to organellar genome dynamics and evolution. Contrary to protein import mechanisms, the way nucleic acids cross the mitochondrial membranes remains poorly understood. Using proteomic, genetic and biochemical approaches with both plant and yeast organelles, we develop here a model for DNA uptake into mitochondria. The first step includes the voltage-dependent anion channel and an outer membrane-located precursor fraction of a protein normally located in the inner membrane. To proceed, the DNA is then potentially recruited in the intermembrane space by an accessible subunit of one of the respiratory chain complexes. Final translocation through the inner membrane remains the most versatile but points to the components considered to make the mitochondrial permeability transition pore. Depending on the size, DNA and RNA cooperate or compete for mitochondrial uptake, which shows that they share import mechanisms. On the other hand, our results imply the existence of more than one route for nucleic acid translocation into mitochondria.}, }
@article {pmid26367084, year = {2016}, author = {López, K and Angeli, C and Aguilar, C and Loaiza, JR and De León, LF and McMillan, WO and Miller, MJ}, title = {Extreme mitogenomic divergence between two syntopic specimens of Arremon aurantiirostris (Aves: Emberizidae) in central Panama suggests possible cryptic species.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3451-3453}, doi = {10.3109/19401736.2015.1066344}, pmid = {26367084}, issn = {2470-1408}, mesh = {Animals ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; NADH Dehydrogenase/genetics ; Panama ; Phylogeny ; Sequence Analysis, DNA/*methods ; Sparrows/classification/*genetics ; Species Specificity ; }, abstract = {We report the complete mitochondrial genome of two specimens of Orange-billed Sparrow Arremon aurantiirostris from Colón Province, in central Panama. The two specimens were collected on the same day, and at the same locality; however, they showed substantial divergence (6.3% average pairwise divergence among coding genes). A survey of ND2 sequence variation across Panama suggests that this divergence is the result of geographic differentiation and secondary contact. This high level of mitochondrial divergence among co-occurring individuals raises the possibility of multiple biological species in Orange-billed Sparrows. Our results are yet another demonstration that much remains to be discovered regarding avian biodiversity in Panama and throughout the Neotropics.}, }
@article {pmid26365344, year = {2016}, author = {Cao, W and Xia, Y}, title = {The first complete mitochondrial genome of the Pundamilia nyererei.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4292-4293}, doi = {10.3109/19401736.2015.1082101}, pmid = {26365344}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Cichlids/*genetics ; Conserved Sequence/genetics ; DNA, Mitochondrial/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Pundamilia nyererei, a member of the family cichlid lived in individual African lakes, regarded as a significant evolution model. Recently the genome sequencing had been done, but no more information of its mitochondrial reported. Herein, we first assembled the complete mitochondrial genome sequence of Pundamilia nyererei. It is a 16 758 bp long sequence with most mitogenome's characteristic structure, 13 protein-coding genes, 20 of tRNA genes, two of rRNA genes, and one putative control region. The GC-content of our fresh sequence is 45.24%, similar to closely related species Oreochromis niloticus. It can verify the accuracy and the utility of new determined mitogenome sequences by the phylogenetic analysis, based on whole mitogenome alignment with Dimidiochromis compressiceps, which is closest relative to Pundamilia nyererei, and seven others. We expect that using the full mitogenome to address taxonomic issues and study the related evolution events. Moreover, this is the first report of the mitogenome of genus Pundamilia nyererei.}, }
@article {pmid26365128, year = {2016}, author = {Wei, H and Jia, Q and Chen, G and Chen, S}, title = {The complete mitogenome of lesser striped shrew Sorex bedfordiae (soricidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4290-4291}, doi = {10.3109/19401736.2015.1082100}, pmid = {26365128}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Conserved Sequence/genetics ; DNA, Mitochondrial/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Shrews/*genetics ; }, abstract = {The Sorex genus is type genus in Soricidae. Most of them lack comprehensive biological data. In this study, the complete mitochondrial genome sequence of Sorex bedfordiae was determined. The mitogenome is 17 160 base pairs in length and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The nucleotide sequence data of 12 heavy-strand protein-coding genes of Sorex bedfordiae and other 10 species in Soricidae were used for phylogenetic analyses. Tree constructed using Bayesian phylogenetic methods demonstrated Sorex bedfordiae as a sister to Sorex cylindricauda. Phylogenetic analyses further confirmed that Blarinella diverged prior to Sorex and Anourosorex, but Episoriculus differentiated earlier than Neomys and Nectogale within subfamily Soricinae.}, }
@article {pmid26363553, year = {2015}, author = {Pinti, M and Gibellini, L and Liu, Y and Xu, S and Lu, B and Cossarizza, A}, title = {Mitochondrial Lon protease at the crossroads of oxidative stress, ageing and cancer.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {72}, number = {24}, pages = {4807-4824}, pmid = {26363553}, issn = {1420-9071}, mesh = {Aging/*genetics/pathology ; Cell Proliferation ; Cell Survival ; Conserved Sequence ; Evolution, Molecular ; Gene Expression Regulation ; Humans ; Metabolic Networks and Pathways ; Mitochondria/enzymology/metabolism ; Mitochondrial Proteins/genetics/metabolism/*physiology ; Models, Biological ; Neoplasms/*genetics/pathology ; *Oxidative Stress ; Protease La/genetics/metabolism/*physiology ; }, abstract = {Lon protease is a nuclear DNA-encoded mitochondrial enzyme highly conserved throughout evolution, involved in the degradation of damaged and oxidized proteins of the mitochondrial matrix, in the correct folding of proteins imported in mitochondria, and in the maintenance of mitochondrial DNA. Lon expression is induced by various stimuli, including hypoxia and reactive oxygen species, and provides protection against cell stress. Lon down-regulation is associated with ageing and with cell senescence, while up-regulation is observed in tumour cells, and is correlated with a more aggressive phenotype of cancer. Lon up-regulation contributes to metabolic reprogramming observed in cancer, favours the switch from a respiratory to a glycolytic metabolism, helping cancer cell survival in the tumour microenvironment, and contributes to epithelial to mesenchymal transition. Silencing of Lon, or pharmacological inhibition of its activity, causes cell death in various cancer cells. Thus, Lon can be included in the growing class of proteins that are not responsible for oncogenic transformation, but that are essential for survival and proliferation of cancer cells, and that can be considered as a new target for development of anticancer drugs.}, }
@article {pmid26361047, year = {2015}, author = {Kono, Y and Kohn, JR}, title = {Range and Frequency of Africanized Honey Bees in California (USA).}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0137407}, pmid = {26361047}, issn = {1932-6203}, mesh = {Animals ; *Bees/anatomy &amp; histology/genetics ; California ; Genes, Insect ; Genes, Mitochondrial ; Genetics, Population ; Polymorphism, Single Nucleotide ; Population Dynamics ; Sequence Analysis, DNA ; }, abstract = {Africanized honey bees entered California in 1994 but few accounts of their northward expansion or their frequency relative to European honey bees have been published. We used mitochondrial markers and morphometric analyses to determine the prevalence of Africanized honeybees in San Diego County and their current northward progress in California west of the Sierra Nevada crest. The northernmost African mitotypes detected were approximately 40 km south of Sacramento in California's central valley. In San Diego County, 65% of foraging honey bee workers carry African mitochondria and the estimated percentage of Africanized workers using morphological measurements is similar (61%). There was no correlation between mitotype and morphology in San Diego County suggesting Africanized bees result from bidirectional hybridization. Seventy percent of feral hives, but only 13% of managed hives, sampled in San Diego County carried the African mitotype indicating that a large fraction of foraging workers in both urban and rural San Diego County are feral. We also found a single nucleotide polymorphism at the DNA barcode locus COI that distinguishes European and African mitotypes. The utility of this marker was confirmed using 401 georeferenced honey bee sequences from the worldwide Barcode of Life Database. Future censuses can determine whether the current range of the Africanized form is stable, patterns of introgression at nuclear loci, and the environmental factors that may limit the northern range of the Africanized honey bee.}, }
@article {pmid26356709, year = {2015}, author = {Pirola, CJ and Scian, R and Gianotti, TF and Dopazo, H and Rohr, C and Martino, JS and Castaño, GO and Sookoian, S}, title = {Epigenetic Modifications in the Biology of Nonalcoholic Fatty Liver Disease: The Role of DNA Hydroxymethylation and TET Proteins.}, journal = {Medicine}, volume = {94}, number = {36}, pages = {e1480}, pmid = {26356709}, issn = {1536-5964}, mesh = {5-Methylcytosine/analogs &amp; derivatives ; Adult ; Cytosine/*analogs &amp; derivatives/metabolism ; DNA Methylation/genetics ; DNA-Binding Proteins/*genetics ; Epigenesis, Genetic ; Female ; Genetic Predisposition to Disease ; Heat-Shock Proteins/genetics ; Humans ; *Liver/metabolism/pathology ; Male ; Middle Aged ; Mitochondria, Liver/*metabolism ; Mixed Function Oxygenases ; *Non-alcoholic Fatty Liver Disease/epidemiology/genetics/metabolism ; Organelle Biogenesis ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha ; Proto-Oncogene Proteins/*genetics ; Transcription Factors/*genetics ; }, abstract = {The 5-Hydroxymethylcytosine (5-hmC) is an epigenetic modification whose role in the pathogenesis of metabolic-related complex diseases remains unexplored; 5-hmC appears to be prevalent in the mitochondrial genome. The Ten-Eleven-Translocation (TET) family of proteins is responsible for catalyzing the conversion of 5-methylcytosine to 5-hmC. We hypothesized that epigenetic editing by 5-hmC might be a novel mechanism through which nonalcoholic fatty liver disease (NAFLD)-associated molecular traits could be explained.Hence, we performed an observational study to explore global levels of 5-hmC in fresh liver samples of patients with NAFLD and controls (n = 90) using an enzyme-linked-immunosorbent serologic assay and immunohistochemistry. We also screened for genetic variation in TET 1-3 loci by next generation sequencing to explore its contribution to the disease biology. The study was conducted in 2 stages (discovery and replication) and included 476 participants.We observed that the amount of 5-hmC in the liver of both NAFLD patients and controls was relatively low (up to 0.1%); a significant association was found with liver mitochondrial DNA copy number (R = 0.50, P = 0.000382) and PPARGC1A-mRNA levels (R = -0.57, P = 0.04).We did not observe any significant difference in the 5-hmC nuclear immunostaining score between NAFLD patients and controls; nevertheless, we found that patients with NAFLD (0.4 ± 0.5) had significantly lower nonnuclear-5-hmC staining compared with controls (1.8 ± 0.8), means ± standard deviation, P = 0.028. The missense p.Ile1123Met variant (TET1-rs3998860) was significantly associated with serum levels of caspase-generated CK-18 fragment-cell death biomarker in the discovery and replication stage, and the disease severity (odds ratio: 1.47, 95% confidence interval: 1.10-1.97; P = 0.005). The p.Ile1762Val substitution (TET2-rs2454206) was associated with liver PPARGC1A-methylation and transcriptional levels, and Type 2 diabetes.Our results suggest that 5-hmC might be involved in the pathogenesis of NAFLD by regulating liver mitochondrial biogenesis and PPARGC1A expression. Genetic diversity at TET loci suggests an "epigenetic" regulation of programmed liver-cell death and a TET-mediated fine-tuning of the liver PPARGC1A-transcriptional program.}, }
@article {pmid26350462, year = {2015}, author = {Wang, W and McReynolds, MR and Goncalves, JF and Shu, M and Dhondt, I and Braeckman, BP and Lange, SE and Kho, K and Detwiler, AC and Pacella, MJ and Hanna-Rose, W}, title = {Comparative Metabolomic Profiling Reveals That Dysregulated Glycolysis Stemming from Lack of Salvage NAD+ Biosynthesis Impairs Reproductive Development in Caenorhabditis elegans.}, journal = {The Journal of biological chemistry}, volume = {290}, number = {43}, pages = {26163-26179}, pmid = {26350462}, issn = {1083-351X}, support = {P40 OD010440/OD/NIH HHS/United States ; R01 GM086786/GM/NIGMS NIH HHS/United States ; GM086786/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/genetics/metabolism/*physiology ; Glycolysis ; *Metabolomics ; NAD/*biosynthesis ; Reproduction ; }, abstract = {Temporal developmental progression is highly coordinated in Caenorhabditis elegans. However, loss of nicotinamidase PNC-1 activity slows reproductive development, uncoupling it from its typical progression relative to the soma. Using LC/MS we demonstrate that pnc-1 mutants do not salvage the nicotinamide released by NAD(+) consumers to resynthesize NAD(+), resulting in a reduction in global NAD(+) bioavailability. We manipulate NAD(+) levels to demonstrate that a minor deficit in NAD(+) availability is incompatible with a normal pace of gonad development. The NAD(+) deficit compromises NAD(+) consumer activity, but we surprisingly found no functional link between consumer activity and reproductive development. As a result we turned to a comparative metabolomics approach to identify the cause of the developmental phenotype. We reveal widespread metabolic perturbations, and using complementary pharmacological and genetic approaches, we demonstrate that a glycolytic block accounts for the slow pace of reproductive development. Interestingly, mitochondria are protected from both the deficiency in NAD(+) biosynthesis and the effects of reduced glycolytic output. We suggest that compensatory metabolic processes that maintain mitochondrial activity in the absence of efficient glycolysis are incompatible with the requirements for reproductive development, which requires high levels of cell division. In addition to demonstrating metabolic requirements for reproductive development, this work also has implications for understanding the mechanisms behind therapeutic interventions that target NAD(+) salvage biosynthesis for the purposes of inhibiting tumor growth.}, }
@article {pmid26350413, year = {2015}, author = {Stefano, GB and Mantione, KJ and Capellan, L and Casares, FM and Challenger, S and Ramin, R and Samuel, JM and Snyder, C and Kream, RM}, title = {Morphine stimulates nitric oxide release in human mitochondria.}, journal = {Journal of bioenergetics and biomembranes}, volume = {47}, number = {5}, pages = {409-417}, pmid = {26350413}, issn = {1573-6881}, mesh = {Autocrine Communication/*drug effects ; Cell Line ; Energy Metabolism/*drug effects ; Humans ; Mitochondria/*metabolism ; Morphine/*pharmacology ; Nitric Oxide/*biosynthesis ; Paracrine Communication/*drug effects ; }, abstract = {The expression of morphine by plants, invertebrate, and vertebrate cells and organ systems, strongly indicates a high level of evolutionary conservation of morphine and related morphinan alkaloids as required for life. The prototype catecholamine, dopamine, serves as an essential chemical intermediate in morphine biosynthesis, both in plants and animals. We surmise that, before the emergence of specialized plant and animal cells/organ systems, primordial multi-potential cell types required selective mechanisms to limit their responsiveness to environmental cues. Accordingly, cellular systems that emerged with the potential for recruitment of the free radical gas nitric oxide (NO) as a multi-faceted autocrine/paracrine signaling molecule, were provided with extremely positive evolutionary advantages. Endogenous morphinergic signaling, in concert with NO-coupled signaling systems, has evolved as an autocrine/paracrine regulator of metabolic homeostasis, energy metabolism, mitochondrial respiration and energy production. Basic physiological processes involving morphinergic/NO-coupled regulation of mitochondrial function, with special emphasis on the cardiovascular system, are critical to all organismic survival. Key to this concept may be the phenomenon of mitochondrial enslavement in eukaryotic evolution via endogenous morphine.}, }
@article {pmid26347565, year = {2015}, author = {Roussel, D and Salin, K and Dumet, A and Romestaing, C and Rey, B and Voituron, Y}, title = {Oxidative phosphorylation efficiency, proton conductance and reactive oxygen species production of liver mitochondria correlates with body mass in frogs.}, journal = {The Journal of experimental biology}, volume = {218}, number = {Pt 20}, pages = {3222-3228}, doi = {10.1242/jeb.126086}, pmid = {26347565}, issn = {1477-9145}, mesh = {Animals ; Body Weight/*physiology ; Energy Metabolism ; Mitochondria, Liver/chemistry/*metabolism ; Oxidative Phosphorylation ; *Protons ; Ranidae/*metabolism ; Reactive Oxygen Species/*metabolism ; }, abstract = {Body size is a central biological parameter affecting most biological processes (especially energetics) and the mitochondrion is a key organelle controlling metabolism and is also the cell's main source of chemical energy. However, the link between body size and mitochondrial function is still unclear, especially in ectotherms. In this study, we investigated several parameters of mitochondrial bioenergetics in the liver of three closely related species of frog (the common frog Rana temporaria, the marsh frog Pelophylax ridibundus and the bull frog Lithobates catesbeiana). These particular species were chosen because of their differences in adult body mass. We found that mitochondrial coupling efficiency was markedly increased with animal size, which led to a higher ATP production (+70%) in the larger frogs (L. catesbeiana) compared with the smaller frogs (R. temporaria). This was essentially driven by a strong negative dependence of mitochondrial proton conductance on body mass. Liver mitochondria from the larger frogs (L. catesbeiana) displayed 50% of the proton conductance of mitochondria from the smaller frogs (R. temporaria). Contrary to our prediction, the low mitochondrial proton conductance measured in L. catesbeiana was not associated with higher reactive oxygen species production. Instead, liver mitochondria from the larger individuals produced significantly lower levels of radical oxygen species than those from the smaller frogs. Collectively, the data show that key bioenergetics parameters of mitochondria (proton leak, ATP production efficiency and radical oxygen species production) are correlated with body mass in frogs. This research expands our understanding of the relationship between mitochondrial function and the evolution of allometric scaling in ectotherms.}, }
@article {pmid26341299, year = {2015}, author = {Lechner, M and Rossmanith, W and Hartmann, RK and Thölken, C and Gutmann, B and Giegé, P and Gobert, A}, title = {Distribution of Ribonucleoprotein and Protein-Only RNase P in Eukarya.}, journal = {Molecular biology and evolution}, volume = {32}, number = {12}, pages = {3186-3193}, doi = {10.1093/molbev/msv187}, pmid = {26341299}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Base Sequence ; Conserved Sequence ; Eukaryota/enzymology/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Secondary ; RNA/genetics/metabolism ; RNA Precursors/genetics/metabolism ; RNA, Catalytic/genetics/metabolism ; RNA, Transfer/genetics/metabolism ; Ribonuclease P/genetics/*metabolism ; Ribonucleoproteins/genetics/*metabolism ; Sequence Alignment ; }, abstract = {RNase P is the endonuclease that removes 5' leader sequences from tRNA precursors. In Eukarya, separate RNase P activities exist in the nucleus and mitochondria/plastids. Although all RNase P enzymes catalyze the same reaction, the different architectures found in Eukarya range from ribonucleoprotein (RNP) enzymes with a catalytic RNA and up to 10 protein subunits to single-subunit protein-only RNase P (PRORP) enzymes. Here, analysis of the phylogenetic distribution of RNP and PRORP enzymes in Eukarya revealed 1) a wealth of novel P RNAs in previously unexplored phylogenetic branches and 2) that PRORP enzymes are more widespread than previously appreciated, found in four of the five eukaryal supergroups, in the nuclei and/or organelles. Intriguingly, the occurrence of RNP RNase P and PRORP seems mutually exclusive in genetic compartments of modern Eukarya. Our comparative analysis provides a global picture of the evolution and diversification of RNase P throughout Eukarya.}, }
@article {pmid26339998, year = {2015}, author = {Milani, L and Ghiselli, F and Pecci, A and Maurizii, MG and Passamonti, M}, title = {The Expression of a Novel Mitochondrially-Encoded Gene in Gonadic Precursors May Drive Paternal Inheritance of Mitochondria.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0137468}, pmid = {26339998}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Bivalvia/cytology/*genetics/growth &amp; development ; Gene Expression Regulation, Developmental ; *Genes, Mitochondrial ; Genetic Markers ; Gonads/cytology/growth &amp; development/*metabolism ; *Inheritance Patterns ; Male ; Mitochondria/genetics ; Models, Molecular ; Molecular Sequence Data ; Organogenesis/genetics ; Sequence Alignment ; Spermatogenesis/genetics ; Spermatozoa/cytology/growth &amp; development/*metabolism ; }, abstract = {Mitochondria have an active role in germ line development, and their inheritance dynamics are relevant to this process. Recently, a novel protein (RPHM21) was shown to be encoded in sperm by the male-transmitted mtDNA of Ruditapes philippinarum, a species with Doubly Uniparental Inheritance (DUI) of mitochondria. In silico analyses suggested a viral origin of RPHM21, and we hypothesized that the endogenization of a viral element provided sperm mitochondria of R. philippinarum with the ability to invade male germ line, thus being transmitted to the progeny. In this work we investigated the dynamics of germ line development in relation to mitochondrial transcription and expression patterns using qPCR and specific antibodies targeting the germ line marker VASPH (R. philippinarum VASA homolog), and RPHM21. Based on the experimental results we conclude that both targets are localized in the primordial germ cells (PGCs) of males, but while VASPH is detected in all PGCs, RPHM21 appears to be expressed only in a subpopulation of them. Since it has been predicted that RPHM21 might have a role in cell proliferation and migration, we here suggest that PGCs expressing it might gain advantage over others and undertake spermatogenesis, accounting for RPHM21 presence in all spermatozoa. Understanding how foreign sequence endogenization and co-option can modify the biology of an organism is of particular importance to assess the impact of such events on evolution.}, }
@article {pmid26338186, year = {2015}, author = {Garg, S and Stölting, J and Zimorski, V and Rada, P and Tachezy, J and Martin, WF and Gould, SB}, title = {Conservation of Transit Peptide-Independent Protein Import into the Mitochondrial and Hydrogenosomal Matrix.}, journal = {Genome biology and evolution}, volume = {7}, number = {9}, pages = {2716-2726}, pmid = {26338186}, issn = {1759-6653}, mesh = {*Evolution, Molecular ; Mitochondria/*metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; *Protein Sorting Signals ; Protein Transport ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism ; Trichomonas vaginalis/metabolism ; }, abstract = {The origin of protein import was a key step in the endosymbiotic acquisition of mitochondria. Though the main translocon of the mitochondrial outer membrane, TOM40, is ubiquitous among organelles of mitochondrial ancestry, the transit peptides, or N-terminal targeting sequences (NTSs), recognised by the TOM complex, are not. To better understand the nature of evolutionary conservation in mitochondrial protein import, we investigated the targeting behavior of Trichomonas vaginalis hydrogenosomal proteins in Saccharomyces cerevisiae and vice versa. Hydrogenosomes import yeast mitochondrial proteins even in the absence of their native NTSs, but do not import yeast cytosolic proteins. Conversely, yeast mitochondria import hydrogenosomal proteins with and without their short NTSs. Conservation of an NTS-independent mitochondrial import route from excavates to opisthokonts indicates its presence in the eukaryote common ancestor. Mitochondrial protein import is known to entail electrophoresis of positively charged NTSs across the electrochemical gradient of the inner mitochondrial membrane. Our present findings indicate that mitochondrial transit peptides, which readily arise from random sequences, were initially selected as a signal for charge-dependent protein targeting specifically to the mitochondrial matrix. Evolutionary loss of the electron transport chain in hydrogenosomes and mitosomes lifted the selective constraints that maintain positive charge in NTSs, allowing first the NTS charge, and subsequently the NTS itself, to be lost. This resulted in NTS-independent matrix targeting, which is conserved across the evolutionary divide separating trichomonads and yeast, and which we propose is the ancestral state of mitochondrial protein import.}, }
@article {pmid26336107, year = {2015}, author = {Kuszak, AJ and Jacobs, D and Gurnev, PA and Shiota, T and Louis, JM and Lithgow, T and Bezrukov, SM and Rostovtseva, TK and Buchanan, SK}, title = {Evidence of Distinct Channel Conformations and Substrate Binding Affinities for the Mitochondrial Outer Membrane Protein Translocase Pore Tom40.}, journal = {The Journal of biological chemistry}, volume = {290}, number = {43}, pages = {26204-26217}, pmid = {26336107}, issn = {1083-351X}, support = {//Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Candida glabrata/*metabolism ; Fungal Proteins/chemistry/*metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; Molecular Sequence Data ; Protein Structure, Secondary ; Sequence Homology, Amino Acid ; }, abstract = {Nearly all mitochondrial proteins are coded by the nuclear genome and must be transported into mitochondria by the translocase of the outer membrane complex. Tom40 is the central subunit of the translocase complex and forms a pore in the mitochondrial outer membrane. To date, the mechanism it utilizes for protein transport remains unclear. Tom40 is predicted to comprise a membrane-spanning β-barrel domain with conserved α-helical domains at both the N and C termini. To investigate Tom40 function, including the role of the N- and C-terminal domains, recombinant forms of the Tom40 protein from the yeast Candida glabrata, and truncated constructs lacking the N- and/or C-terminal domains, were functionally characterized in planar lipid membranes. Our results demonstrate that each of these Tom40 constructs exhibits at least four distinct conductive levels and that full-length and truncated Tom40 constructs specifically interact with a presequence peptide in a concentration- and voltage-dependent manner. Therefore, neither the first 51 amino acids of the N terminus nor the last 13 amino acids of the C terminus are required for Tom40 channel formation or for the interaction with a presequence peptide. Unexpectedly, substrate binding affinity was dependent upon the Tom40 state corresponding to a particular conductive level. A model where two Tom40 pores act in concert as a dimeric protein complex best accounts for the observed biochemical and electrophysiological data. These results provide the first evidence for structurally distinct Tom40 conformations playing a role in substrate recognition and therefore in transport function.}, }
@article {pmid26336091, year = {2015}, author = {Bosacchi, M and Gurdon, C and Maliga, P}, title = {Plastid Genotyping Reveals the Uniformity of Cytoplasmic Male Sterile-T Maize Cytoplasms.}, journal = {Plant physiology}, volume = {169}, number = {3}, pages = {2129-2137}, pmid = {26336091}, issn = {1532-2548}, mesh = {Cytoplasm/genetics ; *Genetic Variation ; Genome, Mitochondrial/*genetics ; Genome, Plastid/genetics ; Genotype ; Genotyping Techniques ; Mitochondria/genetics ; Phylogeny ; Plant Infertility/*genetics ; Plastids/genetics/metabolism ; Pollen/genetics/physiology ; Sequence Analysis, DNA ; Zea mays/*genetics/physiology ; }, abstract = {Cytoplasmic male-sterile (CMS) lines in maize (Zea mays) have been classified by their response to specific restorer genes into three categories: cms-C, cms-S, and cms-T. A mitochondrial genome representing each of the CMS cytotypes has been sequenced, and male sterility in the cms-S and cms-T cytotypes is linked to chimeric mitochondrial genes. To identify markers for plastid genotyping, we sequenced the plastid genomes of three fertile maize lines (B37, B73, and A188) and the B37 cms-C, cms-S, and cms-T cytoplasmic substitution lines. We found that the plastid genomes of B37 and B73 lines are identical. Furthermore, the fertile and CMS plastid genomes are conserved, differing only by zero to three single-nucleotide polymorphisms (SNPs) in coding regions and by eight to 22 SNPs and 10 to 21 short insertions/deletions in noncoding regions. To gain insight into the origin and transmission of the cms-T trait, we identified three SNPs unique to the cms-T plastids and tested the three diagnostic SNPs in 27 cms-T lines, representing the HA, I, Q, RS, and T male-sterile cytoplasms. We report that each of the tested 27 cms-T group accessions have the same three diagnostic plastid SNPs, indicating a single origin and maternal cotransmission of the cms-T mitochondria and plastids to the seed progeny. Our data exclude exceptional pollen transmission of organelles or multiple horizontal gene transfer events as the source of the mitochondrial urf13-T (unidentified reading frame encoding 13-kD cms-T protein) gene in the cms-T cytoplasms. Plastid genotyping enables a reassessment of the evolutionary relationships of cytoplasms in cultivated maize.}, }
@article {pmid26335041, year = {2016}, author = {Criscione, F and Köhler, F}, title = {Snails in the desert: Assessing the mitochondrial and morphological diversity and the influence of aestivation behavior on lineage differentiation in the Australian endemic Granulomelon Iredale, 1933 (Stylommatophora: Camaenidae).}, journal = {Molecular phylogenetics and evolution}, volume = {94}, number = {Pt A}, pages = {101-112}, doi = {10.1016/j.ympev.2015.08.021}, pmid = {26335041}, issn = {1095-9513}, mesh = {Animals ; Australia ; Biological Evolution ; DNA, Mitochondrial/genetics ; *Desert Climate ; Estivation/*physiology ; Male ; Mitochondria/genetics ; *Phylogeny ; Phylogeography ; Snails/*classification/genetics/*physiology ; }, abstract = {Progressive aridification since the mid-Miocene has had a significant influence on the evolution of the biota in the arid zone of central Australia. Especially moisture sensitive groups, such as snails, are often restricted to topographically complex areas, which have acted as refugia in an otherwise inhospitable environment. This historical fragmentation is deemed to be a potent agent of allopatric lineage diversification. Camaenid land snails are amongst only a few terrestrial gastropods that have managed to survive in the arid zone probably due to their ability to escape desiccation through aestivation. Here, we present the first study of the mitochondrial lineage differentiation in an endemic land snail genus from the Australian 'Red Centre', Granulomelon Iredale, 1933. Exposing significant incongruence between mtDNA phylogeny and morphology-based taxonomy, we completely revise the species and genus level taxonomy of this camaenid group. We demonstrate that this genus contains three species, G. grandituberculatum, G. adcockianum and G. squamulosum, which have so far been assigned to different genera: Granulomelon Iredale, 1933 (junior synonym: Baccalena Iredale, 1937), Basedowena Iredale, 1937 and Pleuroxia Ancey, 1887. Two of these species are widespread comprising multiple divergent mitochondrial lineages. Based on a molecular clock estimate, these lineages diverged approximately during the mid-Pleistocene, a period of particularly severe aridification. The phylogeographic patterns are consistent with an isolation-by-distance model in one species but not the other. We suggest that these differences can be attributed to their distinctive aestivation behavior.}, }
@article {pmid26334392, year = {2015}, author = {Zeng, X and Cheng, N and Zheng, X and Diao, Y and Fang, G and Jin, S and Zhou, F and Hu, Z}, title = {Molecular cloning and characterization of two manganese superoxide dismutases from Miscanthus × giganteus.}, journal = {Plant cell reports}, volume = {34}, number = {12}, pages = {2137-2149}, pmid = {26334392}, issn = {1432-203X}, mesh = {Amino Acid Sequence ; Antioxidants/metabolism ; Base Sequence ; Cloning, Molecular ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Poaceae/*enzymology/genetics ; Sequence Analysis, DNA ; Superoxide Dismutase/*genetics/metabolism ; }, abstract = {Six MnSOD genes were isolated from five Miscanthus species. MgMnSOD1 functions in mitochondria and MgMnSOD1 seems to be the main MnSOD gene involved in stress response of M. × giganteus. Miscanthus × giganteus is a promising biomass energy crop with advantages of vigorous growth, high yield, low fertilizer and pesticide inputs. However, poor overwinter ability limits its widespread cultivation. Moreover, narrow genetic base may increase the risk of susceptibility to diseases and pests. Manganese superoxide dismutase (MnSOD), an important antioxidant enzyme involved in stress tolerance is able to protect plant cells from accumulated reactive oxygen species by converting superoxide to peroxide and oxygen. In many plants, overexpression of MnSOD has shown the ability to enhance the resistance to various stresses. This article describes the studies performed in an attempt to elucidate the molecular and enzymatic properties of MnSODs in M. × giganteus. MnSOD genes from M. × giganteus (MgMnSOD1, MgMnSOD2), M. lutarioriparia (MlMnSOD), M. sacchariflora (MsaMnSOD), M. sinensis (MsiMnSOD), and M. floridulus (MfMnSOD) were cloned and sequenced. The sequence analysis and expression patterns of MgMnSOD1 and MgMnSOD2 suggest that they were orthologous genes which were inherited from the two parents, M. sacchariflora and M. sinensis, respectively. In addition, MgMnSOD1 is predicted to be the main MnSOD gene involved in stress response of M. × giganteus. The activity of purified recombinant MgMnSOD1 was 1854.79 ± 39.98 U mg(-1) (mean ± SD). Further enzymatic assays revealed that the protein exhibited an outstanding thermal stability. MgMnSOD1 is predicted to be targeted to mitochondria and involved in removing the superoxide radical generated by respiration. The presence and sequences of other SOD isozymes transcripts were also investigated in this study.}, }
@article {pmid26332748, year = {2016}, author = {Hwang, JY and Jin, GD and Park, J and Lee, SG and Kim, EB}, title = {Complete sequences of eastern water bat, Myotis petax (Chiroptera; Microchiroptera; Vespertilionidae) mitogenome.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3715-3716}, doi = {10.3109/19401736.2015.1079871}, pmid = {26332748}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Chiroptera/classification/*genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; Phylogeny ; Polymorphism, Genetic ; }, abstract = {Complete mitochondria genome sequences of myotis petax (Chiroptera; Microchiroptera; Vespertilionidae) were first identified in the present study. The sequences were obtained from the four individuals and composition of nucleotide AT and GC was about 64.58% and 35.42%, respectively. The lengths of mitogenomes were ranged from 17 296 to 17 299 bp. Total 51 variable sites were observed in the four mitogenomes and 38 sites were singleton polymorphic sites. Phylogenic study revealed that the species would have relatively closed evolutionary distance with m. macrodactylus rather than other species in the genus, myotis. Present study will provide important genomic materials supporting confirmation of taxon of species called bats, which is included in one of the largest orders among the mammals.}, }
@article {pmid26332127, year = {2015}, author = {Carvalho, DS and Andrade, RF and Pinho, ST and Góes-Neto, A and Lobão, TC and Bomfim, GC and El-Hani, CN}, title = {What are the Evolutionary Origins of Mitochondria? A Complex Network Approach.}, journal = {PloS one}, volume = {10}, number = {9}, pages = {e0134988}, pmid = {26332127}, issn = {1932-6203}, mesh = {Alphaproteobacteria/chemistry/*genetics ; Bacterial Proteins/chemistry/*genetics ; Eukaryotic Cells/*cytology/microbiology ; *Evolution, Molecular ; Mitochondria/chemistry/*genetics ; Mitochondrial Proton-Translocating ATPases/chemistry/*genetics ; Phylogeny ; Protein Subunits/chemistry/genetics ; Rickettsia/chemistry/*genetics ; Sequence Analysis, Protein ; }, abstract = {Mitochondria originated endosymbiotically from an Alphaproteobacteria-like ancestor. However, it is still uncertain which extant group of Alphaproteobacteria is phylogenetically closer to the mitochondrial ancestor. The proposed groups comprise the order Rickettsiales, the family Rhodospirillaceae, and the genus Rickettsia. In this study, we apply a new complex network approach to investigate the evolutionary origins of mitochondria, analyzing protein sequences modules in a critical network obtained through a critical similarity threshold between the studied sequences. The dataset included three ATP synthase subunits (4, 6, and 9) and its alphaproteobacterial homologs (b, a, and c). In all the subunits, the results gave no support to the hypothesis that Rickettsiales are closely related to the mitochondrial ancestor. Our findings support the hypothesis that mitochondria share a common ancestor with a clade containing all Alphaproteobacteria orders, except Rickettsiales.}, }
@article {pmid26331255, year = {2015}, author = {Pandini, A and Kleinjung, J and Taylor, WR and Junge, W and Khan, S}, title = {The Phylogenetic Signature Underlying ATP Synthase c-Ring Compliance.}, journal = {Biophysical journal}, volume = {109}, number = {5}, pages = {975-987}, pmid = {26331255}, issn = {1542-0086}, support = {U117581331//Medical Research Council/United Kingdom ; }, mesh = {Amino Acid Motifs ; Animals ; Cattle ; Evolution, Molecular ; Mitochondria/enzymology ; Molecular Dynamics Simulation ; Movement ; *Phylogeny ; Protein Multimerization ; Protein Structure, Quaternary ; Proton-Translocating ATPases/*chemistry/*metabolism ; }, abstract = {The proton-driven ATP synthase (FOF1) is comprised of two rotary, stepping motors (FO and F1) coupled by an elastic power transmission. The elastic compliance resides in the rotor module that includes the membrane-embedded FO c-ring. Proton transport by FO is firmly coupled to the rotation of the c-ring relative to other FO subunits (ab2). It drives ATP synthesis. We used a computational method to investigate the contribution of the c-ring to the total elastic compliance. We performed principal component analysis of conformational ensembles built using distance constraints from the bovine mitochondrial c-ring x-ray structure. Angular rotary twist, the dominant ring motion, was estimated to show that the c-ring accounted in part for the measured compliance. Ring rotation was entrained to rotation of the external helix within each hairpin-shaped c-subunit in the ring. Ensembles of monomer and dimers extracted from complete c-rings showed that the coupling between collective ring and the individual subunit motions was independent of the size of the c-ring, which varies between organisms. Molecular determinants were identified by covariance analysis of residue coevolution and structural-alphabet-based local dynamics correlations. The residue coevolution gave a readout of subunit architecture. The dynamic couplings revealed that the hinge for both ring and subunit helix rotations was constructed from the proton-binding site and the adjacent glycine motif (IB-GGGG) in the midmembrane plane. IB-GGGG motifs were linked by long-range couplings across the ring, while intrasubunit couplings connected the motif to the conserved cytoplasmic loop and adjacent segments. The correlation with principal collective motions shows that the couplings underlie both ring rotary and bending motions. Noncontact couplings between IB-GGGG motifs matched the coevolution signal as well as contact couplings. The residue coevolution reflects the physiological importance of the dynamics that may link proton transfer to ring compliance.}, }
@article {pmid26330185, year = {2016}, author = {Ren, J and Pu, J and Buchinger, T and Zhu, X and Baker, C and Li, W}, title = {The mitogenomes of the pouched lamprey (Geotria australis) and least brook lamprey (Lampetra aepyptera) with phylogenetic considerations.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3560-3562}, doi = {10.3109/19401736.2015.1074218}, pmid = {26330185}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Gene Dosage ; Gene Order ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Lampreys/*classification/genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {We report the mitogenomes of the pouched lamprey (Geotria australis) and least brook lamprey (Lampetra aepyptera) in the families Geotriidae and Petromyzontidae, respectively. Both of the mitogenomes contain the 37 typical vertebrate genes. Their gene order and contents are identical to those of previously described lamprey mitogenomes. The mitogenome of G. australis (17 080 bp) is the largest among the 10 reported lamprey mitogenomes, owed to two long noncoding regions. The mitogenome of L. aepyptera is 77 bp longer (16 236 bp) than that of the congeneric European river lamprey L. fluviatilis, a size difference mostly due to different copy numbers of tandem repeats in the noncoding regions. The phylogenetic analysis supports that the pouched lamprey (Geotriidae) diverged earlier from the common ancestor of lampreys than the Petromyzonids, and the placement of the least brook lamprey in the genus Lampetra.}, }
@article {pmid26330004, year = {2016}, author = {Bo, Z and Wenping, S and Kefeng, L and Debin, Z and Chao, M and Guangxia, X}, title = {The complete mitochondrial genome of Cleithenes herzenstein and its phylogenetic analysis.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3663-3665}, doi = {10.3109/19401736.2015.1079845}, pmid = {26330004}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Base Sequence ; DNA, Mitochondrial/genetics ; Fishes/*genetics ; Gene Order ; Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Whole Genome Sequencing ; }, abstract = {The complete mitochondrial genome of Stewartia sinensis was obtained with long PCR approach. Amplification primers were designed according to mitogenome sequences of some other fish species. PCR reactions were according to Kong et al. (2009). The complete mitochondria sequence of Cleithenes herzenstein was deposited in GenBank under the accession number KT223828. Structural and evolutionary analyses were also performed. The length of the complete mitochondrial DNA sequence was 17 175 bp, consisting of 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. Other than D-loop, another non-coding region named ''OL'' region was found (Table 1). The ''OL'' region (CTTTTTCCCGCCTAGTTTAACCAGTAAAAGGCGGGAA) is 38 bp and has the potential to fold into a stem-loop secondary structure. Most of the genes were encoded on the heavy strand (H strand) except for ND6 and eight tRNA genes (Table 1). The base composition and gene arrangement of C. herzenstein mitogenome was identical to typical vertebrate. For sequence alignment, the mitogenome sequence of C. herzenstein was 96% and 95% similar to that of Platichthys stellatus and Verasper moseri, respectively.}, }
@article {pmid26323764, year = {2015}, author = {Koonin, EV}, title = {Origin of eukaryotes from within archaea, archaeal eukaryome and bursts of gene gain: eukaryogenesis just made easier?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140333}, pmid = {26323764}, issn = {1471-2970}, mesh = {Archaea/*genetics ; *Biological Evolution ; Eukaryota/genetics ; *Eukaryotic Cells ; *Genome, Archaeal ; }, abstract = {The origin of eukaryotes is a fundamental, forbidding evolutionary puzzle. Comparative genomic analysis clearly shows that the last eukaryotic common ancestor (LECA) possessed most of the signature complex features of modern eukaryotic cells, in particular the mitochondria, the endomembrane system including the nucleus, an advanced cytoskeleton and the ubiquitin network. Numerous duplications of ancestral genes, e.g. DNA polymerases, RNA polymerases and proteasome subunits, also can be traced back to the LECA. Thus, the LECA was not a primitive organism and its emergence must have resulted from extensive evolution towards cellular complexity. However, the scenario of eukaryogenesis, and in particular the relationship between endosymbiosis and the origin of eukaryotes, is far from being clear. Four recent developments provide new clues to the likely routes of eukaryogenesis. First, evolutionary reconstructions suggest complex ancestors for most of the major groups of archaea, with the subsequent evolution dominated by gene loss. Second, homologues of signature eukaryotic proteins, such as actin and tubulin that form the core of the cytoskeleton or the ubiquitin system, have been detected in diverse archaea. The discovery of this 'dispersed eukaryome' implies that the archaeal ancestor of eukaryotes was a complex cell that might have been capable of a primitive form of phagocytosis and thus conducive to endosymbiont capture. Third, phylogenomic analyses converge on the origin of most eukaryotic genes of archaeal descent from within the archaeal evolutionary tree, specifically, the TACK superphylum. Fourth, evidence has been presented that the origin of the major archaeal phyla involved massive acquisition of bacterial genes. Taken together, these findings make the symbiogenetic scenario for the origin of eukaryotes considerably more plausible and the origin of the organizational complexity of eukaryotic cells more readily explainable than they appeared until recently.}, }
@article {pmid26323761, year = {2015}, author = {Martin, WF and Garg, S and Zimorski, V}, title = {Endosymbiotic theories for eukaryote origin.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140330}, pmid = {26323761}, issn = {1471-2970}, mesh = {*Biological Evolution ; Eukaryotic Cells/*classification/*cytology ; Organelles/genetics/physiology ; Symbiosis/*genetics/*physiology ; }, abstract = {For over 100 years, endosymbiotic theories have figured in thoughts about the differences between prokaryotic and eukaryotic cells. More than 20 different versions of endosymbiotic theory have been presented in the literature to explain the origin of eukaryotes and their mitochondria. Very few of those models account for eukaryotic anaerobes. The role of energy and the energetic constraints that prokaryotic cell organization placed on evolutionary innovation in cell history has recently come to bear on endosymbiotic theory. Only cells that possessed mitochondria had the bioenergetic means to attain eukaryotic cell complexity, which is why there are no true intermediates in the prokaryote-to-eukaryote transition. Current versions of endosymbiotic theory have it that the host was an archaeon (an archaebacterium), not a eukaryote. Hence the evolutionary history and biology of archaea increasingly comes to bear on eukaryotic origins, more than ever before. Here, we have compiled a survey of endosymbiotic theories for the origin of eukaryotes and mitochondria, and for the origin of the eukaryotic nucleus, summarizing the essentials of each and contrasting some of their predictions to the observations. A new aspect of endosymbiosis in eukaryote evolution comes into focus from these considerations: the host for the origin of plastids was a facultative anaerobe.}, }
@article {pmid26323757, year = {2015}, author = {Stairs, CW and Leger, MM and Roger, AJ}, title = {Diversity and origins of anaerobic metabolism in mitochondria and related organelles.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140326}, pmid = {26323757}, issn = {1471-2970}, support = {FRN#62809//Canadian Institutes of Health Research/Canada ; }, mesh = {Anaerobiosis ; *Biological Evolution ; Eukaryotic Cells/cytology/*physiology ; Gene Expression Regulation ; Organelles/genetics/*metabolism ; Oxygen Consumption ; }, abstract = {Across the diversity of life, organisms have evolved different strategies to thrive in hypoxic environments, and microbial eukaryotes (protists) are no exception. Protists that experience hypoxia often possess metabolically distinct mitochondria called mitochondrion-related organelles (MROs). While there are some common metabolic features shared between the MROs of distantly related protists, these organelles have evolved independently multiple times across the breadth of eukaryotic diversity. Until recently, much of our knowledge regarding the metabolic potential of different MROs was limited to studies in parasitic lineages. Over the past decade, deep-sequencing studies of free-living anaerobic protists have revealed novel configurations of metabolic pathways that have been co-opted for life in low oxygen environments. Here, we provide recent examples of anaerobic metabolism in the MROs of free-living protists and their parasitic relatives. Additionally, we outline evolutionary scenarios to explain the origins of these anaerobic pathways in eukaryotes.}, }
@article {pmid26323753, year = {2015}, author = {Lake, JA}, title = {Eukaryotic origins.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {370}, number = {1678}, pages = {20140321}, pmid = {26323753}, issn = {1471-2970}, mesh = {Archaea/*genetics ; *Biological Evolution ; *Eukaryotic Cells ; }, abstract = {The origin of the eukaryotes is a fundamental scientific question that for over 30 years has generated a spirited debate between the competing Archaea (or three domains) tree and the eocyte tree. As eukaryotes ourselves, humans have a personal interest in our origins. Eukaryotes contain their defining organelle, the nucleus, after which they are named. They have a complex evolutionary history, over time acquiring multiple organelles, including mitochondria, chloroplasts, smooth and rough endoplasmic reticula, and other organelles all of which may hint at their origins. It is the evolutionary history of the nucleus and their other organelles that have intrigued molecular evolutionists, myself included, for the past 30 years and which continues to hold our interest as increasingly compelling evidence favours the eocyte tree. As with any orthodoxy, it takes time to embrace new concepts and techniques.}, }
@article {pmid26323685, year = {2015}, author = {Lane, N and Powell, K}, title = {Nick Lane: Unearthing the first cellular innovations.}, journal = {The Journal of cell biology}, volume = {210}, number = {5}, pages = {684-685}, pmid = {26323685}, issn = {1540-8140}, mesh = {*Biological Evolution ; *Cell Biology ; Cell Membrane/physiology ; Energy Metabolism/physiology ; Humans ; Hydrothermal Vents ; Mitochondria/pathology/physiology ; Origin of Life ; }, abstract = {Lane’s unorthodox career stalks the origins of complex eukaryotic life.}, }
@article {pmid26321226, year = {2016}, author = {Ojanguren-Affilastro, AA and Mattoni, CI and Ochoa, JA and Ramírez, MJ and Ceccarelli, FS and Prendini, L}, title = {Phylogeny, species delimitation and convergence in the South American bothriurid scorpion genus Brachistosternus Pocock 1893: Integrating morphology, nuclear and mitochondrial DNA.}, journal = {Molecular phylogenetics and evolution}, volume = {94}, number = {Pt A}, pages = {159-170}, doi = {10.1016/j.ympev.2015.08.007}, pmid = {26321226}, issn = {1095-9513}, mesh = {Acclimatization ; Altitude ; Animals ; Base Sequence ; Bayes Theorem ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; Desert Climate ; Electron Transport Complex IV/genetics ; *Genetic Speciation ; Likelihood Functions ; Male ; Mitochondria/genetics ; *Phylogeny ; Scorpions/*anatomy &amp; histology/*genetics ; South America ; }, abstract = {A phylogenetic analysis of the scorpion genus Brachistosternus Pocock, 1893 (Bothriuridae Simon, 1880) is presented, based on a dataset including 41 of the 43 described species and five outgroups, 116 morphological characters and more than 4150 base-pairs of DNA sequence from the nuclear 18S rDNA and 28S rDNA gene loci, and the mitochondrial 12S rDNA, 16S rDNA, and Cytochrome c Oxidase Subunit I gene loci. Analyses conducted using parsimony, Maximum Likelihood and Bayesian Inference were largely congruent with high support for most clades. The results confirmed the monophyly of Brachistosternus, the nominal subgenus, and subgenus Ministernus Francke, 1985, as in previous analyses based only on morphology, but differed in several other respects. Species from the plains of the Atacama Desert diverged basally whereas the high altitude Andean species radiated from a more derived ancestor, presumably as a consequence of Andean uplift and associated changes in climate. Species limits were assessed among species that contain intraspecific variation (e.g., different morphs), are difficult to separate morphologically, and/or exhibit widespread or disjunct distributions. The extent of convergence in morphological adaptation to life on sandy substrata (psammophily) and the complexity of the male genitalia, or hemispermatophores, was investigated. Psammophily evolved on at least four independent occasions. The lobe regions of the hemispermatophore increased in complexity on three independent occasions, and decreased in complexity on another three independent occasions.}, }
@article {pmid26319575, year = {2015}, author = {Rauch, C and Vries, Jd and Rommel, S and Rose, LE and Woehle, C and Christa, G and Laetz, EM and Wägele, H and Tielens, AG and Nickelsen, J and Schumann, T and Jahns, P and Gould, SB}, title = {Why It Is Time to Look Beyond Algal Genes in Photosynthetic Slugs.}, journal = {Genome biology and evolution}, volume = {7}, number = {9}, pages = {2602-2607}, pmid = {26319575}, issn = {1759-6653}, mesh = {Animals ; *Evolution, Molecular ; Gastropoda/*genetics ; Gene Transfer, Horizontal ; Photosynthesis/genetics ; Plastids/*genetics ; }, abstract = {Eukaryotic organelles depend on nuclear genes to perpetuate their biochemical integrity. This is true for mitochondria in all eukaryotes and plastids in plants and algae. Then how do kleptoplasts, plastids that are sequestered by some sacoglossan sea slugs, survive in the animals' digestive gland cells in the absence of the algal nucleus encoding the vast majority of organellar proteins? For almost two decades, lateral gene transfer (LGT) from algae to slugs appeared to offer a solution, but RNA-seq analysis, later supported by genome sequencing of slug DNA, failed to find any evidence for such LGT events. Yet, isolated reports continue to be published and are readily discussed by the popular press and social media, making the data on LGT and its support for kleptoplast longevity appear controversial. However, when we take a sober look at the methods used, we realize that caution is warranted in how the results are interpreted. There is no evidence that the evolution of kleptoplasty in sea slugs involves LGT events. Based on what we know about photosystem maintenance in embryophyte plastids, we assume kleptoplasts depend on nuclear genes. However, studies have shown that some isolated algal plastids are, by nature, more robust than those of land plants. The evolution of kleptoplasty in green sea slugs involves many promising and unexplored phenomena, but there is no evidence that any of these require the expression of slug genes of algal origin.}, }
@article {pmid26318870, year = {2015}, author = {Zhong, Z and Norvienyeku, J and Yu, J and Chen, M and Cai, R and Hong, Y and Chen, L and Zhang, D and Wang, B and Zhou, J and Lu, G and Chen, X and Wang, Z}, title = {Two different subcellular-localized Acetoacetyl-CoA acetyltransferases differentiate diverse functions in Magnaporthe oryzae.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {83}, number = {}, pages = {58-67}, doi = {10.1016/j.fgb.2015.08.008}, pmid = {26318870}, issn = {1096-0937}, mesh = {Acetyl-CoA C-Acetyltransferase/genetics/*metabolism ; Amino Acid Sequence ; Cytoplasm/enzymology ; Gene Deletion ; Gene Expression Regulation, Fungal ; Genes, Fungal ; Homologous Recombination ; Hordeum/microbiology ; Magnaporthe/*enzymology/genetics/pathogenicity ; Mevalonic Acid/metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Morphogenesis ; Mutagenesis ; Mutation ; Oryza/microbiology ; Phylogeny ; Plant Diseases/microbiology ; Virulence ; }, abstract = {The mevalonate pathway is an efficient biosynthesis pathway that yields isoprenoids for promoting different crucial cellular functions, including ergosterol synthesis and growth regulation. Acetoacetyl-CoA acetyltransferase (EC2.3.1.9) is the first major catalytic enzyme constituting the mevalonate pathway and catalyzes the transformation of Acetoacetyl-CoA from two molecules of acetyl-CoA enroute ergosterol production in fungi. We identified two homologous genes encoding Acetoacetyl-CoA acetyltransferase (MoAcat1 and MoAcat2) in Magnaporthe oryzae, the rice blast fungus. Phylogenetic analysis indicates these two genes have different evolutionary history. We subsequently, conducted targeted gene deletion using homologous recombination technology to ascertain the unique roles of the two MoAcat homologues during the fungal morphogenesis and pathogenesis. The findings from our investigations showed that the activity of MoAcat1 promoted virulence in the rice blast fungus as such, the ΔMoacat1 mutants generated exhibited defect in virulence, whilst ΔMoacat1 mutants did not portray growth defects. ΔMoacat2 mutants on the other hand were characterized by reduction in growth and virulence. Furthermore, MoAcat1 and MoAcat2 showed different expression patterns and subcellular localizations in M. oryzae. From our investigations we came to the conclusion that, different subcellular localization contributes to the diverse functions of MoAcat1 and MoAcat2, which helps the successful establishment of blast disease by promoting efficient development of cell morphology and effective colonization of host tissue.}, }
@article {pmid26311176, year = {2015}, author = {Wolf, PG and Sessa, EB and Marchant, DB and Li, FW and Rothfels, CJ and Sigel, EM and Gitzendanner, MA and Visger, CJ and Banks, JA and Soltis, DE and Soltis, PS and Pryer, KM and Der, JP}, title = {An Exploration into Fern Genome Space.}, journal = {Genome biology and evolution}, volume = {7}, number = {9}, pages = {2533-2544}, pmid = {26311176}, issn = {1759-6653}, mesh = {DNA, Plant/chemistry ; Ferns/*genetics ; Genome Size ; Genome, Chloroplast ; Genome, Mitochondrial ; *Genome, Plant ; Genomics ; Plant Proteins/genetics ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.}, }
@article {pmid26305230, year = {2016}, author = {Su, XH and Zhao, S and Wang, K and Xing, LX}, title = {Complete mitochondrial genome of the "floppy-wing" morph reproductive termite, Reticulitermes labralis (Isoptera: Rhinotermitidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3547-3548}, doi = {10.3109/19401736.2015.1074211}, pmid = {26305230}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Isoptera/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitochondrial genome of Reticulitermes labralis (Isoptera: Rhinotermitidae) was determined for its nucleotide sequence of 16 113 bp. Its gene content and organization were identical with other Reticulitermes species. The 13 protein-coding genes (PCGs) have typical ATN initiation codon. But, the stop codons were TAA, TAG and an incomplete termination codon (T) abutting an adjacent tRNA gene. Twenty-two tRNA genes, in addition to tRNASer(AGN) replaced lacking of the DHU stem with a simple loop, showed the typical clover-leaf secondary structure. The A + T-rich region was 1311 bp in length with 65.98% A + T content. In addition to the A + T-rich region, non-coding sequences of the mtDNA genome harbored 17 intergenic spacers. There were three complete repeats of repeat A in CR, which were not discovered in other termite species. Phylogenetic tree based on the 11 complete mitochondrial genome sequences of closely related termite species accords well with morphological phylogenetic analysis.}, }
@article {pmid26304849, year = {2015}, author = {Law, YS and Zhang, R and Guan, X and Cheng, S and Sun, F and Duncan, O and Murcha, MW and Whelan, J and Lim, BL}, title = {Phosphorylation and Dephosphorylation of the Presequence of Precursor MULTIPLE ORGANELLAR RNA EDITING FACTOR3 during Import into Mitochondria from Arabidopsis.}, journal = {Plant physiology}, volume = {169}, number = {2}, pages = {1344-1355}, pmid = {26304849}, issn = {1532-2548}, mesh = {14-3-3 Proteins/metabolism ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; HSP70 Heat-Shock Proteins/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Mutation ; Phosphorylation ; Phylogeny ; Plants, Genetically Modified ; Protein Precursors/metabolism ; Protein Serine-Threonine Kinases/metabolism ; Protein Transport ; Transcription Factors/metabolism ; }, abstract = {The nucleus-encoded mitochondria-targeted proteins, multiple organellar RNA editing factors (MORF3, MORF5, and MORF6), interact with Arabidopsis (Arabidopsis thaliana) PURPLE ACID PHOSPHATASE2 (AtPAP2) located on the chloroplast and mitochondrial outer membranes in a presequence-dependent manner. Phosphorylation of the presequence of the precursor MORF3 (pMORF3) by endogenous kinases in wheat germ translation lysate, leaf extracts, or STY kinases, but not in rabbit reticulocyte translation lysate, resulted in the inhibition of protein import into mitochondria. This inhibition of import could be overcome by altering threonine/serine residues to alanine on the presequence, thus preventing phosphorylation. Phosphorylated pMORF3, but not the phosphorylation-deficient pMORF3, can form a complex with 14-3-3 proteins and HEAT SHOCK PROTEIN70. The phosphorylation-deficient mutant of pMORF3 also displayed faster rates of import when translated in wheat germ lysates. Mitochondria isolated from plants with altered amounts of AtPAP2 displayed altered protein import kinetics. The import rate of pMORF3 synthesized in wheat germ translation lysate into pap2 mitochondria was slower than that into wild-type mitochondria, and this rate disparity was not seen for pMORF3 synthesized in rabbit reticulocyte translation lysate, the latter translation lysate largely deficient in kinase activity. Taken together, these results support a role for the phosphorylation and dephosphorylation of pMORF3 during the import into plant mitochondria. These results suggest that kinases, possibly STY kinases, and AtPAP2 are involved in the import of protein into both mitochondria and chloroplasts and provide a mechanism by which the import of proteins into both organelles may be coordinated.}, }
@article {pmid26300379, year = {2016}, author = {Mai, Q and Li, W and Chen, H and Ai, W and Chen, X}, title = {Complete mitochondrial genome and phylogenetic position of the Sicklefin weasel shark Hemigaleus microstoma.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3491-3492}, doi = {10.3109/19401736.2015.1066363}, pmid = {26300379}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; Sharks/*genetics ; }, abstract = {The complete mitochondrial genome of the Sicklefin weasel shark Hemigaleus microstoma was first presented in this study. It was 16 701 bp in length with the typical gene arrangement in vertebrates. A total of 25 bp short intergenic spaces and 33 bp overlaps located in 12 and 9 gene junctions, respectively. The overall nucleotide composition was 31.0% A, 26.4% C, 13.5% G and 29.1% T. Two start (ATG and GTG) and three stop (TAG, AGG and TAA/T) codons were found in the protein-coding genes. The size of 22 tRNA genes ranged from 67 to 75 bp. In the phylogenetic tree, H. microstoma (Hemigaleidae) was placed as sister to Galeocerdo cuvier (Carcharhinidae).}, }
@article {pmid26299456, year = {2015}, author = {Kuijper, B}, title = {Mitochondria: The Red Queen lies within (comment on DOI 10.1002/bies.201500057).}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {37}, number = {9}, pages = {934}, doi = {10.1002/bies.201500099}, pmid = {26299456}, issn = {1521-1878}, mesh = {Animals ; *Biological Evolution ; Eukaryota/*genetics ; Humans ; Mitochondria/*genetics ; *Models, Biological ; Mutation/*genetics ; *Recombination, Genetic ; *Sex Characteristics ; }, }
@article {pmid26297113, year = {2015}, author = {Bastiaansen, JA and Cheng, T and Lei, H and Gruetter, R and Comment, A}, title = {Direct noninvasive estimation of myocardial tricarboxylic acid cycle flux in vivo using hyperpolarized [13]C magnetic resonance.}, journal = {Journal of molecular and cellular cardiology}, volume = {87}, number = {}, pages = {129-137}, doi = {10.1016/j.yjmcc.2015.08.012}, pmid = {26297113}, issn = {1095-8584}, mesh = {Acetylcarnitine ; Animals ; Carbon Isotopes/administration &amp; dosage ; *Citric Acid Cycle ; Humans ; *Magnetic Resonance Imaging ; Mitochondria, Heart/metabolism/pathology ; Myocardium/*metabolism/pathology ; Rats ; Tricarboxylic Acids/isolation &amp; purification/*metabolism ; }, abstract = {BACKGROUND: The heart relies on continuous energy production and imbalances herein impair cardiac function directly. The tricarboxylic acid (TCA) cycle is the primary means of energy generation in the healthy myocardium, but direct noninvasive quantification of metabolic fluxes is challenging due to the low concentration of most metabolites. Hyperpolarized (13)C magnetic resonance spectroscopy (MRS) provides the opportunity to measure cellular metabolism in real time in vivo. The aim of this work was to noninvasively measure myocardial TCA cycle flux (VTCA) in vivo within a single minute.<br><br>METHODS AND RESULTS: Hyperpolarized [1-(13)C]acetate was administered at different concentrations in healthy rats. (13)C incorporation into [1-(13)C]acetylcarnitine and the TCA cycle intermediate [5-(13)C]citrate was dynamically detected in vivo with a time resolution of 3s. Different kinetic models were established and evaluated to determine the metabolic fluxes by simultaneously fitting the evolution of the (13)C labeling in acetate, acetylcarnitine, and citrate. VTCA was estimated to be 6.7&#xb1;1.7 &#x3bc;mol&#xb7;g(-1)&#xb7;min(-1) (dry weight), and was best estimated with a model using only the labeling in citrate and acetylcarnitine, independent of the precursor. The TCA cycle rate was not linear with the citrate-to-acetate metabolite ratio, and could thus not be quantified using a ratiometric approach. The (13)C signal evolution of citrate, i.e. citrate formation was independent of the amount of injected acetate, while the (13)C signal evolution of acetylcarnitine revealed a dose dependency with the injected acetate. The (13)C labeling of citrate did not correlate to that of acetylcarnitine, leading to the hypothesis that acetylcarnitine formation is not an indication of mitochondrial TCA cycle activity in the heart.<br><br>CONCLUSIONS: Hyperpolarized [1-(13)C]acetate is a metabolic probe independent of pyruvate dehydrogenase (PDH) activity. It allows the direct estimation of VTCA in vivo, which was shown to be neither dependent on the administered acetate dose nor on the (13)C labeling of acetylcarnitine. Dynamic (13)C MRS coupled to the injection of hyperpolarized [1-(13)C]acetate can enable the measurement of metabolic changes during impaired heart function.}, }
@article {pmid26295342, year = {2015}, author = {Mandel, JR and McCauley, DE}, title = {Pervasive Mitochondrial Sequence Heteroplasmy in Natural Populations of Wild Carrot, Daucus carota spp. carota L.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0136303}, pmid = {26295342}, issn = {1932-6203}, mesh = {Biological Evolution ; Daucus carota/classification/*genetics ; Electron Transport Complex IV/*genetics ; *Genome, Mitochondrial ; *Genome, Plant ; Genotype ; Inheritance Patterns ; Linkage Disequilibrium ; Mitochondria/genetics ; *Polymorphism, Single Nucleotide ; Proton-Translocating ATPases/*genetics ; Recombination, Genetic ; }, abstract = {Exceptions to the generally accepted rules that plant mitochondrial genomes are strictly maternally inherited and that within-individual sequence diversity in those genomes, i.e., heteroplasmy, should be minimal are becoming increasingly apparent especially with regard to sequence-level heteroplasmy. These findings raise questions about the potential significance of such heteroplasmy for plant mitochondrial genome evolution. Still studies quantifying the amount and consequences of sequence heteroplasmy in natural populations are rare. In this study, we report pervasive sequence heteroplasmy in natural populations of wild carrot, a close relative of the cultivated crop. In order to assay directly for this heteroplasmy, we implemented a quantitative PCR assay that can detect and quantify intra-individual SNP variation in two mitochondrial genes (Cox1 and Atp9). We found heteroplasmy in > 60% of all wild carrot populations surveyed and in > 30% of the 140 component individuals that were genotyped. Heteroplasmy ranged from a very small proportion of the total genotype (e.g., 0.995:0.005) to near even mixtures (e.g., 0.590:0.410) in some individuals. These results have important implications for the role of intra-genomic recombination in the generation of plant mitochondrial genome genotypic novelty. The consequences of such recombination are evident in the results of this study through analysis of the degree of linkage disequilibrium (LD) between the SNP sites at the two genes studied.}, }
@article {pmid26295156, year = {2015}, author = {Jiang, L and Chen, J and Wang, P and Ren, Q and Yuan, J and Qian, C and Hua, X and Guo, Z and Zhang, L and Yang, J and Wang, Y and Zhang, Q and Ding, H and Bi, D and Zhang, Z and Wang, Q and Chen, D and Kan, X}, title = {The Mitochondrial Genomes of Aquila fasciata and Buteo lagopus (Aves, Accipitriformes): Sequence, Structure and Phylogenetic Analyses.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0136297}, pmid = {26295156}, issn = {1932-6203}, mesh = {Animals ; Base Composition ; Base Sequence ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Falconiformes/classification/*genetics ; Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The family Accipitridae is one of the largest groups of non-passerine birds, including 68 genera and 243 species globally distributed. In the present study, we determined the complete mitochondrial sequences of two species of accipitrid, namely Aquila fasciata and Buteo lagopus, and conducted a comparative mitogenome analysis across the family. The mitogenome length of A. fasciata and B. lagopus are 18,513 and 18,559 bp with an A + T content of 54.2% and 55.0%, respectively. For both the two accipitrid birds mtDNAs, obvious positive AT-skew and negative GC-skew biases were detected for all 12 PCGs encoded by the H strand, whereas the reverse was found in MT-ND6 encoded by the L strand. One extra nucleotide'C'is present at the position 174 of MT-ND3 gene of A. fasciata, which is not observed at that of B. lagopus. Six conserved sequence boxes in the Domain II, named boxes F, E, D, C, CSBa, and CSBb, respectively, were recognized in the CRs of A. fasciata and B. lagopus. Rates and patterns of mitochondrial gene evolution within Accipitridae were also estimated. The highest dN/dS was detected for the MT-ATP8 gene (0.32493) among Accipitridae, while the lowest for the MT-CO1 gene (0.01415). Mitophylogenetic analysis supported the robust monophyly of Accipitriformes, and Cathartidae was basal to the balance of the order. Moreover, we performed phylogenetic analyses using two other data sets (two mitochondrial loci, and combined nuclear and mitochondrial loci). Our results indicate that the subfamily Aquilinae and all currently polytypic genera of this subfamily are monophyletic. These two novel mtDNA data will be useful in refining the phylogenetic relationships and evolutionary processes of Accipitriformes.}, }
@article {pmid26293809, year = {2015}, author = {Umeda, T and Ramser, EM and Yamashita, M and Nakajima, K and Mori, H and Silverman, MA and Tomiyama, T}, title = {Intracellular amyloid β oligomers impair organelle transport and induce dendritic spine loss in primary neurons.}, journal = {Acta neuropathologica communications}, volume = {3}, number = {}, pages = {51}, pmid = {26293809}, issn = {2051-5960}, mesh = {Amyloid beta-Peptides/*metabolism/pharmacology ; Amyloid beta-Protein Precursor/genetics ; Animals ; Brain-Derived Neurotrophic Factor/metabolism ; Cells, Cultured ; Dendritic Spines/*pathology ; Dose-Response Relationship, Drug ; Embryo, Mammalian ; Green Fluorescent Proteins/genetics/metabolism ; Hippocampus/cytology ; Intracellular Fluid/*metabolism ; Mice ; Mice, Transgenic ; Mutation/genetics ; Neurons/*ultrastructure ; Organelles/*metabolism ; Protein Transport/*physiology ; Transfection ; tau Proteins/deficiency/genetics ; }, abstract = {INTRODUCTION: Synaptic dysfunction and intracellular transport defects are early events in Alzheimer's disease (AD). Extracellular amyloid β (Aβ) oligomers cause spine alterations and impede the transport of proteins and organelles such as brain-derived neurotrophic factor (BDNF) and mitochondria that are required for synaptic function. Meanwhile, intraneuronal accumulation of Aβ precedes its extracellular deposition and is also associated with synaptic dysfunction in AD. However, the links between intracellular Aβ, spine alteration, and mechanisms that support synaptic maintenance such as organelle trafficking are poorly understood.<br><br>RESULTS: We compared the effects of wild-type and Osaka (E693&#x394;)-mutant amyloid precursor proteins: the former secretes A&#x3b2; into extracellular space and the latter accumulates A&#x3b2; oligomers within cells. First we investigated the effects of intracellular A&#x3b2; oligomers on dendritic spines in primary neurons and their tau-dependency using tau knockout neurons. We found that intracellular A&#x3b2; oligomers caused a reduction in mushroom, or mature spines, independently of tau. We also found that intracellular A&#x3b2; oligomers significantly impaired the intracellular transport of BDNF, mitochondria, and recycling endosomes: cargoes essential for synaptic maintenance. A reduction in BDNF transport by intracellular A&#x3b2; oligomers was also observed in tau knockout neurons.<br><br>CONCLUSIONS: Our findings indicate that intracellular A&#x3b2; oligomers likely contribute to early synaptic pathology in AD and argue against the consensus that A&#x3b2;-induced spine loss and transport defects require tau.}, }
@article {pmid26292157, year = {2015}, author = {Häfner, S}, title = {How the cell got its mitochondria.}, journal = {Microbes and infection}, volume = {17}, number = {10}, pages = {676-679}, doi = {10.1016/j.micinf.2015.07.003}, pmid = {26292157}, issn = {1769-714X}, mesh = {Biological Evolution ; Cell Line ; Epithelial Cells/*microbiology ; *Host-Pathogen Interactions ; Humans ; Mitochondria/*physiology/*ultrastructure ; Mycobacterium tuberculosis/*physiology ; }, }
@article {pmid26291784, year = {2016}, author = {Park, JS and Simpson, AG}, title = {Characterization of a Deep-Branching Heterolobosean, Pharyngomonas turkanaensis n. sp., Isolated from a Non-Hypersaline Habitat, and Ultrastructural Comparison of Cysts and Amoebae Among Pharyngomonas Strains.}, journal = {The Journal of eukaryotic microbiology}, volume = {63}, number = {1}, pages = {100-111}, doi = {10.1111/jeu.12260}, pmid = {26291784}, issn = {1550-7408}, mesh = {Animals ; Eukaryota/*classification/growth &amp; development/isolation &amp; purification/*ultrastructure ; Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; Phylogeny ; Salinity ; }, abstract = {An unusual heterolobosean amoeba, isolate LO, was isolated recently from a sample with a salinity of ~4‰, from Lake Turkana in East Africa. 18S rDNA phylogenies confirm that isolate LO branches among halophilic amoeboflagellates assigned to Pharyngomonas. We examined the ultrastructure of the amoeba and cyst stages of isolate LO, as well as the amoebae and cysts of Pharyngomonas kirbyi (isolates AS12B and SD1A). The amoebae of all three isolates lacked discrete dictyosomes and had discoidal/flattened mitochondrial cristae, but the mitochondria were not enrobed by rough endoplasmic reticulum. The cysts of all three isolates showed a thick, bipartite cyst wall, and lacked cyst pores. The cysts of isolate LO were distinct in that the ectocyst was very loose-fitting, and could contain "crypts". No flagellate form of isolate LO has been observed to date, and a salinity-for-growth experiment showed that isolate LO can grow at 15-100‰ salinity, indicating that it is halotolerant. By contrast, other studied Pharyngomonas isolates are amoeboflagellates and true halophiles. Therefore, we propose isolate LO as a new species, Pharyngomonas turkanaensis n. sp. It is possible that P. turkanaensis descended from halophilic ancestors, and represents a secondary reestablishment of a physiology adapted for moderate salinity.}, }
@article {pmid26288099, year = {2015}, author = {Wang, X and Liu, N and Zhang, H and Yang, XJ and Huang, Y and Lei, F}, title = {Extreme variation in patterns of tandem repeats in mitochondrial control region of yellow-browed tits (Sylviparus modestus, Paridae).}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {13227}, pmid = {26288099}, issn = {2045-2322}, mesh = {Animals ; Base Sequence ; Databases as Topic ; *Genetic Variation ; Haplotypes/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Passeriformes/*genetics ; Phylogeny ; Sequence Alignment ; Tandem Repeat Sequences/*genetics ; }, abstract = {To investigate the evolutionary pattern and origins of tandem repeats in the mitochondrial control region of the yellow-browed tit (Sylviparus modestus), the control region and another four mitochondrial loci from fifteen individuals were analyzed. A 117-bp tandem repeat unit that repeated once, twice or three times in different individuals was found, and a rarely reported arrangement for this tandem repeats region that a 5' imperfect copy at its downstream and a 3' imperfect copy at its upstream was observed. The haplotype network, phylogenetic trees, and ancestral state reconstruction of the combined dataset of five loci suggested multiple origins of the same repeat number. The turnover model via slipped-strand mispairing was introduced to interpret the results, because mispairing occurred so frequently that multiple origins of certain repeat number were observed. Insertion via recombination should be a better explanation for the origin of this tandem repeat unit, considering characteristics of the combined sequence of the 3' and 5' imperfect copy, including identification of its homolog in other passerines and its predicted secondary structure.}, }
@article {pmid26287583, year = {2016}, author = {Li, G and Li, W and Lv, S and Li, C and Qian, Y and Xu, J and Lu, Y and Lin, Y and Yang, P and Lin, Z and Yang, S}, title = {Identification and phylogenetic analysis of the mitogenome of Sarcocheilichthys parvus Nichols (Cypriniformes: Cyprinidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3542-3543}, doi = {10.3109/19401736.2015.1074209}, pmid = {26287583}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; China ; Cyprinidae/*genetics ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {In the present study, the complete mitogenome sequence of a Sarcocheilichthys parvus Nichols was sequenced and identified. It contained 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and 2 non-coding regions. The phylogenetic analysis showed that the mitogenome sequence could be useful data in the field of systematics and conservation biology for S. parvus Nichols and other aquatic species.}, }
@article {pmid26287458, year = {2015}, author = {Ku, C and Nelson-Sathi, S and Roettger, M and Sousa, FL and Lockhart, PJ and Bryant, D and Hazkani-Covo, E and McInerney, JO and Landan, G and Martin, WF}, title = {Endosymbiotic origin and differential loss of eukaryotic genes.}, journal = {Nature}, volume = {524}, number = {7566}, pages = {427-432}, pmid = {26287458}, issn = {1476-4687}, mesh = {Archaea/genetics ; Bacteria/genetics ; Cluster Analysis ; Eukaryota/classification/*genetics ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome/genetics ; Mitochondria/genetics ; *Models, Genetic ; Organelles/*genetics ; Phylogeny ; Plastids/genetics ; Prokaryotic Cells/metabolism ; Proteome/genetics ; Symbiosis/*genetics ; Time Factors ; }, abstract = {Chloroplasts arose from cyanobacteria, mitochondria arose from proteobacteria. Both organelles have conserved their prokaryotic biochemistry, but their genomes are reduced, and most organelle proteins are encoded in the nucleus. Endosymbiotic theory posits that bacterial genes in eukaryotic genomes entered the eukaryotic lineage via organelle ancestors. It predicts episodic influx of prokaryotic genes into the eukaryotic lineage, with acquisition corresponding to endosymbiotic events. Eukaryotic genome sequences, however, increasingly implicate lateral gene transfer, both from prokaryotes to eukaryotes and among eukaryotes, as a source of gene content variation in eukaryotic genomes, which predicts continuous, lineage-specific acquisition of prokaryotic genes in divergent eukaryotic groups. Here we discriminate between these two alternatives by clustering and phylogenetic analysis of eukaryotic gene families having prokaryotic homologues. Our results indicate (1) that gene transfer from bacteria to eukaryotes is episodic, as revealed by gene distributions, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria; (2) that gene inheritance in eukaryotes is vertical, as revealed by extensive topological comparison, sparse gene distributions stemming from differential loss; and (3) that continuous, lineage-specific lateral gene transfer, although it sometimes occurs, does not contribute to long-term gene content evolution in eukaryotic genomes.}, }
@article {pmid26286985, year = {2015}, author = {Allen, JF}, title = {Why chloroplasts and mitochondria retain their own genomes and genetic systems: Colocation for redox regulation of gene expression.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10231-10238}, pmid = {26286985}, issn = {1091-6490}, mesh = {Chloroplasts/genetics/*physiology ; Cytosol/metabolism ; DNA Replication ; DNA, Plant/genetics ; Electron Transport ; *Gene Expression Regulation, Plant ; Genome, Chloroplast ; Genome, Mitochondrial ; Mitochondria/genetics/*physiology ; *Oxidation-Reduction ; Oxidative Phosphorylation ; Photosynthesis/physiology ; Plants/genetics ; Transcription, Genetic ; }, abstract = {Chloroplasts and mitochondria are subcellular bioenergetic organelles with their own genomes and genetic systems. DNA replication and transmission to daughter organelles produces cytoplasmic inheritance of characters associated with primary events in photosynthesis and respiration. The prokaryotic ancestors of chloroplasts and mitochondria were endosymbionts whose genes became copied to the genomes of their cellular hosts. These copies gave rise to nuclear chromosomal genes that encode cytosolic proteins and precursor proteins that are synthesized in the cytosol for import into the organelle into which the endosymbiont evolved. What accounts for the retention of genes for the complete synthesis within chloroplasts and mitochondria of a tiny minority of their protein subunits? One hypothesis is that expression of genes for protein subunits of energy-transducing enzymes must respond to physical environmental change by means of a direct and unconditional regulatory control--control exerted by change in the redox state of the corresponding gene product. This hypothesis proposes that, to preserve function, an entire redox regulatory system has to be retained within its original membrane-bound compartment. Colocation of gene and gene product for redox regulation of gene expression (CoRR) is a hypothesis in agreement with the results of a variety of experiments designed to test it and which seem to have no other satisfactory explanation. Here, I review evidence relating to CoRR and discuss its development, conclusions, and implications. This overview also identifies predictions concerning the results of experiments that may yet prove the hypothesis to be incorrect.}, }
@article {pmid26286984, year = {2015}, author = {Campbell, MA and Van Leuven, JT and Meister, RC and Carey, KM and Simon, C and McCutcheon, JP}, title = {Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10192-10199}, pmid = {26286984}, issn = {1091-6490}, support = {P20RR017670/RR/NCRR NIH HHS/United States ; }, mesh = {Alphaproteobacteria/*genetics ; Animals ; Evolution, Molecular ; Female ; *Genome, Bacterial ; Genome, Mitochondrial ; Genomics ; Hemiptera/*microbiology ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Open Reading Frames ; Organelles ; Phylogeny ; Plastids/genetics ; Ribosomes/metabolism ; Species Specificity ; *Symbiosis ; }, abstract = {Comparative genomics from mitochondria, plastids, and mutualistic endosymbiotic bacteria has shown that the stable establishment of a bacterium in a host cell results in genome reduction. Although many highly reduced genomes from endosymbiotic bacteria are stable in gene content and genome structure, organelle genomes are sometimes characterized by dramatic structural diversity. Previous results from Candidatus Hodgkinia cicadicola, an endosymbiont of cicadas, revealed that some lineages of this bacterium had split into two new cytologically distinct yet genetically interdependent species. It was hypothesized that the long life cycle of cicadas in part enabled this unusual lineage-splitting event. Here we test this hypothesis by investigating the structure of the Ca. Hodgkinia genome in one of the longest-lived cicadas, Magicicada tredecim. We show that the Ca. Hodgkinia genome from M. tredecim has fragmented into multiple new chromosomes or genomes, with at least some remaining partitioned into discrete cells. We also show that this lineage-splitting process has resulted in a complex of Ca. Hodgkinia genomes that are 1.1-Mb pairs in length when considered together, an almost 10-fold increase in size from the hypothetical single-genome ancestor. These results parallel some examples of genome fragmentation and expansion in organelles, although the mechanisms that give rise to these extreme genome instabilities are likely different.}, }
@article {pmid26286983, year = {2015}, author = {Godfrey-Smith, P}, title = {Reproduction, symbiosis, and the eukaryotic cell.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10120-10125}, pmid = {26286983}, issn = {1091-6490}, mesh = {Animals ; Biological Evolution ; Eukaryotic Cells/*physiology ; Humans ; Mitochondria/physiology ; Models, Biological ; *Reproduction ; Selection, Genetic ; Social Behavior ; *Symbiosis ; }, abstract = {This paper develops a conceptual framework for addressing questions about reproduction, individuality, and the units of selection in symbiotic associations, with special attention to the origin of the eukaryotic cell. Three kinds of reproduction are distinguished, and a possible evolutionary sequence giving rise to a mitochondrion-containing eukaryotic cell from an endosymbiotic partnership is analyzed as a series of transitions between each of the three forms of reproduction. The sequence of changes seen in this "egalitarian" evolutionary transition is compared with those that apply in "fraternal" transitions, such as the evolution of multicellularity in animals.}, }
@article {pmid26285652, year = {2015}, author = {Yu, G and Xiang, H and Tian, J and Yin, J and Pinkert, CA and Li, Q and Zhao, X}, title = {Mitochondrial Haplotypes Influence Metabolic Traits in Porcine Transmitochondrial Cybrids.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {13118}, pmid = {26285652}, issn = {2045-2322}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Base Sequence ; Cell Line ; Genome, Mitochondrial/genetics ; Haplotypes/*genetics ; Hybrid Cells/*metabolism ; Mitochondria/*genetics ; Mutation, Missense/genetics ; Phylogeny ; Reactive Oxygen Species/metabolism ; Reproducibility of Results ; Succinate Dehydrogenase/metabolism ; Sus scrofa/*genetics ; }, abstract = {In farm animals, mitochondrial DNA mutations exist widely across breeds and individuals. In order to identify differences among mtDNA haplotypes, two porcine transmitochondrial cybrids were generated by fusion of a Lantang pig cell line devoid of mitochondrial DNA with enucleated cytoplasm from either a Large White pig or a Xiang pig harboring potentially divergent mitochondrial haplotypes. These cybrid cells were subjected to mitochondrial genome sequencing, copy number detecting and analysis of biochemical traits including succinate dehydrogenase (SDH) activity, ATP content and susceptibility to reactive oxygen species (ROS). The Lantang and Xiang mitochondrial genomes were highly homologous with only 18 polymorphic sites, and differed radically from the Large White with 201 and 198 mutations respectively. The Large White and Xiang cybrids exhibited similar mtDNA copy numbers and different values among biochemical traits, generated greater ROS production (P < 0.05) and less SDH activity (P < 0.05) and a lesser ATP content (P < 0.05). The results show that functional differences exist between cybrid cells which differ in mitochondrial genomic background. In conclusion, transmitochondrial cybrids provide the first direct evidence on pig biochemical traits linking different mitochondrial genome haplotypes.}, }
@article {pmid26285039, year = {2015}, author = {Almeida, D and Maldonado, E and Vasconcelos, V and Antunes, A}, title = {Adaptation of the Mitochondrial Genome in Cephalopods: Enhancing Proton Translocation Channels and the Subunit Interactions.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0135405}, pmid = {26285039}, issn = {1932-6203}, mesh = {Adaptation, Physiological/*genetics ; Amino Acid Sequence ; Animals ; Cephalopoda/*genetics/growth &amp; development/metabolism ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial/*genetics ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Mitochondrial Proton-Translocating ATPases/*genetics ; Molecular Sequence Data ; Oxidative Phosphorylation ; Phylogeny ; Selection, Genetic ; Sequence Homology, Amino Acid ; }, abstract = {Mitochondrial protein-coding genes (mt genes) encode subunits forming complexes of crucial cellular pathways, including those involved in the vital process of oxidative phosphorylation (OXPHOS). Despite the vital role of the mitochondrial genome (mt genome) in the survival of organisms, little is known with respect to its adaptive implications within marine invertebrates. The molluscan Class Cephalopoda is represented by a marine group of species known to occupy contrasting environments ranging from the intertidal to the deep sea, having distinct metabolic requirements, varied body shapes and highly advanced visual and nervous systems that make them highly competitive and successful worldwide predators. Thus, cephalopods are valuable models for testing natural selection acting on their mitochondrial subunits (mt subunits). Here, we used concatenated mt genes from 17 fully sequenced mt genomes of diverse cephalopod species to generate a robust mitochondrial phylogeny for the Class Cephalopoda. We followed an integrative approach considering several branches of interest-covering cephalopods with distinct morphologies, metabolic rates and habitats-to identify sites under positive selection and localize them in the respective protein alignment and/or tridimensional structure of the mt subunits. Our results revealed significant adaptive variation in several mt subunits involved in the energy production pathway of cephalopods: ND5 and ND6 from Complex I, CYTB from Complex III, COX2 and COX3 from Complex IV, and in ATP8 from Complex V. Furthermore, we identified relevant sites involved in protein-interactions, lining proton translocation channels, as well as disease/deficiencies related sites in the aforementioned complexes. A particular case, revealed by this study, is the involvement of some positively selected sites, found in Octopoda lineage in lining proton translocation channels (site 74 from ND5) and in interactions between subunits (site 507 from ND5) of Complex I.}, }
@article {pmid26284102, year = {2015}, author = {Rogalski, M and do Nascimento Vieira, L and Fraga, HP and Guerra, MP}, title = {Plastid genomics in horticultural species: importance and applications for plant population genetics, evolution, and biotechnology.}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {586}, pmid = {26284102}, issn = {1664-462X}, abstract = {During the evolution of the eukaryotic cell, plastids, and mitochondria arose from an endosymbiotic process, which determined the presence of three genetic compartments into the incipient plant cell. After that, these three genetic materials from host and symbiont suffered several rearrangements, bringing on a complex interaction between nuclear and organellar gene products. Nowadays, plastids harbor a small genome with ∼130 genes in a 100-220 kb sequence in higher plants. Plastid genes are mostly highly conserved between plant species, being useful for phylogenetic analysis in higher taxa. However, intergenic spacers have a relatively higher mutation rate and are important markers to phylogeographical and plant population genetics analyses. The predominant uniparental inheritance of plastids is like a highly desirable feature for phylogeny studies. Moreover, the gene content and genome rearrangements are efficient tools to capture and understand evolutionary events between different plant species. Currently, genetic engineering of the plastid genome (plastome) offers a number of attractive advantages as high-level of foreign protein expression, marker gene excision, gene expression in operon and transgene containment because of maternal inheritance of plastid genome in most crops. Therefore, plastid genome can be used for adding new characteristics related to synthesis of metabolic compounds, biopharmaceutical, and tolerance to biotic and abiotic stresses. Here, we describe the importance and applications of plastid genome as tools for genetic and evolutionary studies, and plastid transformation focusing on increasing the performance of horticultural species in the field.}, }
@article {pmid26283405, year = {2015}, author = {Lane, N and Martin, WF}, title = {Eukaryotes really are special, and mitochondria are why.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {35}, pages = {E4823}, pmid = {26283405}, issn = {1091-6490}, mesh = {Animals ; *Biological Evolution ; Eukaryota/*metabolism ; Humans ; *Origin of Life ; }, }
@article {pmid26283342, year = {2015}, author = {Keeling, PJ and McCutcheon, JP and Doolittle, WF}, title = {Symbiosis becoming permanent: Survival of the luckiest.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10101-10103}, pmid = {26283342}, issn = {1091-6490}, mesh = {Animals ; *Biological Evolution ; Canada ; Chloroplasts/physiology ; Genome ; Genotype ; Mitochondria/physiology ; Plastids/physiology ; Symbiosis/*physiology ; United States ; }, }
@article {pmid26281979, year = {2016}, author = {Bonavita, S and Regina, TM}, title = {The evolutionary conservation of rps3 introns and rps19-rps3-rpl16 gene cluster in Adiantum capillus-veneris mitochondria.}, journal = {Current genetics}, volume = {62}, number = {1}, pages = {173-184}, pmid = {26281979}, issn = {1432-0983}, mesh = {Adiantum/*genetics ; Base Sequence ; *Evolution, Molecular ; Gene Expression Regulation, Plant ; *Genes, Mitochondrial ; Genome, Mitochondrial ; *Introns ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Ribosomal Proteins/chemistry/*genetics ; Sequence Alignment ; }, abstract = {Ferns are a large and evolutionarily critical group of vascular land plants for which quite limited mitochondrial gene content and genome organization data are, currently, available. This study reports that the gene for the ribosomal protein S3 (rps3) is preserved and physically clustered to an upstream rps19 and a downstream overlapping rpl16 locus in the mitochondrial DNA of the true fern Adiantum capillus-veneris L. Sequence analysis also revealed that the rps3 gene is interrupted by two cis-splicing group II introns, like the counterpart in lycopod and gymnosperm representatives. A preliminary polymerase chain reaction (PCR) survey confirmed a scattered distribution pattern of both the rps3 introns also in other fern lineages. Northern blot and reverse transcription (RT)-PCR analyses demonstrated that the three ribosomal protein genes are co-transcribed as a polycistronic mRNA and modified by RNA editing. Particularly, the U-to-C type editing amends numerous genomic stop codons in the A. capillus-veneris rps19, rps3 and rpl16 sequences, thus, assuring the synthesis of complete and functional polypeptides. Collectively, the findings from this study further expand our knowledge of the mitochondrial rps3 architecture and evolution, also, bridging the significant molecular data gaps across the so far underrepresented ferns and all land plants.}, }
@article {pmid26280166, year = {2015}, author = {Pan, T and Wang, H and Hu, C and Sun, Z and Zhu, X and Meng, T and Meng, X and Zhang, B}, title = {Species Delimitation in the Genus Moschus (Ruminantia: Moschidae) and Its High-Plateau Origin.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0134183}, pmid = {26280166}, issn = {1932-6203}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; Ruminants/*classification/*genetics ; Sequence Analysis, DNA/methods ; Tibet ; }, abstract = {The authenticity of controversial species is a significant challenge for systematic biologists. Moschidae is a small family of musk deer in the Artiodactyla, composing only one genus, Moschus. Historically, the number of species in the Moschidae family has been debated. Presently, most musk deer species were restricted in the Tibetan Plateau and surrounding/adjacent areas, which implied that the evolution of Moschus might have been punctuated by the uplift of the Tibetan Plateau. In this study, we aimed to determine the evolutionary history and delimit the species in Moschus by exploring the complete mitochondrial genome (mtDNA) and other mitochondrial gene. Our study demonstrated that six species, M. leucogaster, M. fuscus, M. moschiferus, M. berezovskii, M. chrysogaster and M. anhuiensis, were authentic species in the genus Moschus. Phylogenetic analysis and molecular dating showed that the ancestor of the present Moschidae originates from Tibetan Plateau which suggested that the evolution of Moschus was prompted by the most intense orogenic movement of the Tibetan Plateau during the Pliocene age, and alternating glacial-interglacial geological eras.}, }
@article {pmid26280086, year = {2015}, author = {Farhadi, M and Fazaeli, A and Haniloo, A}, title = {Genetic characterization of livestock and human hydatid cyst isolates from northwest Iran, using the mitochondrial cox1 gene sequence.}, journal = {Parasitology research}, volume = {114}, number = {12}, pages = {4363-4370}, pmid = {26280086}, issn = {1432-1955}, mesh = {Animals ; Cattle ; Cattle Diseases/*parasitology ; Cyclooxygenase 1/*genetics ; Echinococcosis/*parasitology/*veterinary ; Echinococcus granulosus/classification/enzymology/genetics/*isolation &amp; purification ; Genotype ; Helminth Proteins/*genetics ; Humans ; Iran ; Livestock ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sheep/parasitology ; Sheep Diseases/*parasitology ; Sheep, Domestic/genetics ; }, abstract = {Cystic echinococcosis (CE), caused by larval stages of the tapeworm Echinococcus granulosus, is one of the most important zoonoses distributed worldwide. Genotype analysis of the parasite isolates from various hosts is required to better understand the host specificity and transmission routes. The aim of this study was to identify the genotypes of E. granulosus isolated from humans and domestic animals from northwest of Iran (Zanjan Province) using the mitochondrial cox1 gene sequence. A total of 86 hydatid cysts including 49 sheep and 28 cattle isolates from the slaughterhouse and nine human isolates from surgical wards of local hospitals were collected. The isolates were subjected to DNA extraction, PCR amplification, and sequence. Eighty-two (95.35 %) isolates, including 47 sheep, 26 cattle, and all nine human isolates, were determined as G1 genotype, and the remaining four (4.65 %), including two sheep and two cattle isolates, were identified as G3 genotype. From the cox1 sequence data, 13 different haplotypes (10 G1s and three G3s) were detected and named as EGH1-EGH13 (GenBank accession numbers, KP859559-KP859571). EGH1 was the major variant among the haplotypes, and it was identified in 46 (53.49 %) isolates (31 sheep, 14 cattle, and one human). Alignment of the partial cox1 sequences showed 12 point mutations including seven (58.3 %) synonymous and five (41.7 %) non-synonymous substitutions. Based on the results, G1 was the major genotype of E. granulosus in northwest of Iran affecting sheep, cattle, and humans. In addition, a minor group of G3 genotype was found to be circulating in this region.}, }
@article {pmid26277108, year = {2015}, author = {Horáková, E and Changmai, P and Paris, Z and Salmon, D and Lukeš, J}, title = {Simultaneous depletion of Atm and Mdl rebalances cytosolic Fe-S cluster assembly but not heme import into the mitochondrion of Trypanosoma brucei.}, journal = {The FEBS journal}, volume = {282}, number = {21}, pages = {4157-4175}, doi = {10.1111/febs.13411}, pmid = {26277108}, issn = {1742-4658}, mesh = {ATP-Binding Cassette Transporters/antagonists &amp; inhibitors/genetics/*metabolism ; Aconitate Hydratase/metabolism ; Cytosol/metabolism ; Fumarate Hydratase/metabolism ; Gene Knockdown Techniques ; Genes, Protozoan ; Genetic Complementation Test ; Heme/metabolism ; Iron-Sulfur Proteins/metabolism ; Mitochondria/metabolism ; Models, Biological ; Multidrug Resistance-Associated Proteins/antagonists &amp; inhibitors/genetics/metabolism ; Phylogeny ; Protozoan Proteins/antagonists &amp; inhibitors/genetics/*metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Trypanosoma brucei brucei/genetics/*metabolism ; }, abstract = {ABC transporter mitochondrial 1 (Atm1) and multidrug resistance-like 1 (Mdl) are mitochondrial ABC transporters. Although Atm1 was recently suggested to transport different forms of glutathione from the mitochondrion, which are used for iron-sulfur (Fe-S) cluster maturation in the cytosol, the function of Mdl remains elusive. In Trypanosoma brucei, we identified one homolog of each of these genes, TbAtm and TbMdl, which were downregulated either separately or simultaneously using RNA interference. Individual depletion of TbAtm and TbMdl led to limited growth defects. In cells downregulated for TbAtm, the enzymatic activities of the Fe-S cluster proteins aconitase and fumarase significantly decreased in the cytosol but not in the mitochondrion. Downregulation of TbMdl did not cause any change in activities of the Fe-S proteins. Unexpectedly, the simultaneous downregulation of TbAtm and TbMdl did not result in any growth defect, nor were the Fe-S cluster protein activities altered in either the cytosolic or mitochondrial compartments. Additionally, TbAtm and TbMdl were able to partially restore the growth of the Saccharomyces cerevisiae Δatm1 and Δmdl2 null mutants, respectively. Because T. brucei completely lost the heme b biosynthesis pathway, this cofactor has to be obtained from the host. Based on our results, TbMdl is a candidate for mitochondrial import of heme b, which was markedly decreased in both TbMdl and TbAtm + TbMdl knockdowns. Moreover, the levels of heme a were strongly decreased in the same knockdowns, suggesting that TbMdl plays a key role in heme a biosynthesis, thus affecting the overall heme homeostasis in T. brucei.}, }
@article {pmid26273922, year = {2016}, author = {Jang, YS and Kim, S and Kim, KY and Park, JH}, title = {Complete mitochondrial genome of Sebastes taczanowskii (Scorpaenidae, Scorpaeniformes) from the East Sea, Korea.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3531-3533}, doi = {10.3109/19401736.2015.1074204}, pmid = {26273922}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Republic of Korea ; Sequence Analysis, DNA/*methods ; }, abstract = {Sebastes taczanowskii is a subarctic species in the north-western Pacific Ocean. To obtain mitochondrial DNA sequences for phylogeny, the complete mitogenome (16 452 bp in length) of S. taczanowskii was constructed using next-generation sequencing. The circular mitogenome contains 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNAs and the control region, for which gene structure and positions were similar to those of other Scorpaenidae. The complete mitogenome composed of 27.8% A, 26.5% T, 17.3% G and 28.5% C, with a slight AT bias (54.3%). All PCGs use a typical start codon, ATG, except COX1 (GTG). The terminal codon of PCGs was mainly TAR, with the exceptions of ND4 (AGA) and Cytb (incomplete codon, T). Sebastes taczanowskii was clearly divided from other Scorpaenidae in the phylogenetic tree using 2 rRNA and 13 PCGs. The mitogenome of S. taczanowskii can be useful for constructing the molecular phylogenetic tree within Scorpaenidae.}, }
@article {pmid26273916, year = {2016}, author = {Chen, X and Song, XL and Chen, LY and Li, Y}, title = {The complete mitochondrial genome of the Metriaclima zebra.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3563-3564}, doi = {10.3109/19401736.2015.1074219}, pmid = {26273916}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Cichlids/*genetics ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Cichlid fish from East Africa are remarkable for phenotypic and behavioral diversity on a backdrop of genomic similarity. Metriaclima zebra is a member of the Cichlidae family. Here, we reported the complete mitogenome sequence of M. zebra, which was 16 582 bp and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 non-coding control region. A phylogenetic tree was constructed based on complete mitogenomes of M. zebra and 11 closely related Cichlidae species to approve the accuracy. The complete mitochondrial genome of the M. zebra would provide more information for the research of M. zebra and the evolution of Cichlidae family.}, }
@article {pmid26272235, year = {2015}, author = {Manchester, LC and Coto-Montes, A and Boga, JA and Andersen, LP and Zhou, Z and Galano, A and Vriend, J and Tan, DX and Reiter, RJ}, title = {Melatonin: an ancient molecule that makes oxygen metabolically tolerable.}, journal = {Journal of pineal research}, volume = {59}, number = {4}, pages = {403-419}, doi = {10.1111/jpi.12267}, pmid = {26272235}, issn = {1600-079X}, mesh = {Animals ; Antioxidants/*metabolism/pharmacology/*physiology ; Chloroplasts/metabolism ; Circadian Rhythm/drug effects/physiology ; Free Radical Scavengers/metabolism ; Humans ; Melatonin/*metabolism/pharmacology/*physiology ; Mitochondria/metabolism ; Oxidative Stress/drug effects ; Oxygen/*metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {Melatonin is remarkably functionally diverse with actions as a free radical scavenger and antioxidant, circadian rhythm regulator, anti-inflammatory and immunoregulating molecule, and as an oncostatic agent. We hypothesize that the initial and primary function of melatonin in photosynthetic cyanobacteria, which appeared on Earth 3.5-3.2 billion years ago, was as an antioxidant. The evolution of melatonin as an antioxidant by this organism was necessary as photosynthesis is associated with the generation of toxic-free radicals. The other secondary functions of melatonin came about much later in evolution. We also surmise that mitochondria and chloroplasts may be primary sites of melatonin synthesis in all eukaryotic cells that possess these organelles. This prediction is made on the basis that mitochondria and chloroplasts of eukaryotes developed from purple nonsulfur bacteria (which also produce melatonin) and cyanobacteria when they were engulfed by early eukaryotes. Thus, we speculate that the melatonin-synthesizing actions of the engulfed bacteria were retained when these organelles became mitochondria and chloroplasts, respectively. That mitochondria are likely sites of melatonin formation is supported by the observation that this organelle contains high levels of melatonin that are not impacted by blood melatonin concentrations. Melatonin has a remarkable array of means by which it thwarts oxidative damage. It, as well as its metabolites, is differentially effective in scavenging a variety of reactive oxygen and reactive nitrogen species. Moreover, melatonin and its metabolites modulate a large number of antioxidative and pro-oxidative enzymes, leading to a reduction in oxidative damage. The actions of melatonin on radical metabolizing/producing enzymes may be mediated by the Keap1-Nrf2-ARE pathway. Beyond its direct free radical scavenging and indirect antioxidant effects, melatonin has a variety of physiological and metabolic advantages that may enhance its ability to limit oxidative stress.}, }
@article {pmid26272083, year = {2015}, author = {Neubauer, M and Zhu, Z and Penka, M and Helmschrott, C and Wagener, N and Wagener, J}, title = {Mitochondrial dynamics in the pathogenic mold Aspergillus fumigatus: therapeutic and evolutionary implications.}, journal = {Molecular microbiology}, volume = {98}, number = {5}, pages = {930-945}, doi = {10.1111/mmi.13167}, pmid = {26272083}, issn = {1365-2958}, mesh = {Aspergillosis/therapy ; Aspergillus fumigatus/enzymology/*genetics/growth &amp; development/*physiology ; Azoles/pharmacology ; DNA, Fungal/metabolism ; DNA, Mitochondrial/metabolism ; Drug Resistance, Fungal/genetics ; *Evolution, Molecular ; Fungal Proteins/genetics/*metabolism ; *Mitochondrial Dynamics/physiology ; Mitochondrial Proteins/genetics/metabolism ; Mutation ; Peptide Hydrolases ; Phenotype ; Spores, Fungal/genetics ; }, abstract = {Mitochondria within eukaryotic cells continuously fuse and divide. This phenomenon is called mitochondrial dynamics and crucial for mitochondrial function and integrity. We performed a comprehensive analysis of mitochondrial dynamics in the pathogenic mold Aspergillus fumigatus. Phenotypic characterization of respective mutants revealed the general essentiality of mitochondrial fusion for mitochondrial genome maintenance and the mold's viability. Surprisingly, it turned out that the mitochondrial rhomboid protease Pcp1 and its processing product, s-Mgm,1 which are crucial for fusion in yeast, are dispensable for fusion, mtDNA maintenance and viability in A. fumigatus. In contrast, mitochondrial fission mutants show drastically reduced growth and sporulation rates and increased heat susceptibility. However, reliable inheritance of mitochondria to newly formed conidia is ensured. Strikingly, mitochondrial fission mutants show a significant and growth condition-dependent increase in azole resistance. Parallel disruption of fusion in a fission mutant partially rescues growth and sporulation defects and further increases the azole resistance phenotype. Taken together, our results indicate an emerging dispensability of the mitochondrial rhomboid protease function in mitochondrial fusion, the suitability of mitochondrial fusion machinery as antifungal target and the involvement of mitochondrial dynamics in azole susceptibility.}, }
@article {pmid26268215, year = {2015}, author = {Burgess, AL and David, R and Searle, IR}, title = {Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae.}, journal = {BMC plant biology}, volume = {15}, number = {}, pages = {199}, pmid = {26268215}, issn = {1471-2229}, mesh = {5-Methylcytosine/*metabolism ; Cell Nucleus/genetics ; Chloroplasts/genetics ; *Evolution, Molecular ; Methylation ; Methyltransferases/genetics ; Mitochondria/genetics ; Phylogeny ; Plants/*genetics/metabolism ; RNA, Transfer/*genetics/metabolism ; RNA, Untranslated/genetics ; Transcriptome ; }, abstract = {BACKGROUND: Post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m(5)C) is an important modification that regulates RNA metabolism and occurs in both eukaryotes and prokaryotes. Yet, to date, no transcriptome-wide identification of m(5)C sites has been undertaken in plants. Plants provide a unique comparative system for investigating the origin and evolution of m(5)C as they contain three different genomes, the nucleus, mitochondria and chloroplast. Here we use bisulfite conversion of RNA combined with high-throughput IIlumina sequencing (RBS-seq) to identify single-nucleotide resolution of m(5)C sites in non-coding ribosomal RNAs and transfer RNAs of all three sub-cellular transcriptomes across six diverse species that included, the single-celled algae Nannochloropsis oculata, the macro algae Caulerpa taxifolia and multi-cellular higher plants Arabidopsis thaliana, Brassica rapa, Triticum durum and Ginkgo biloba.<br><br>RESULTS: Using the plant model Arabidopsis thaliana, we identified a total of 39 highly methylated m(5)C sites in predicted structural positions of nuclear tRNAs and 7 m(5)C sites in rRNAs from nuclear, chloroplast and mitochondrial transcriptomes. Both the nucleotide position and percent methylation of tRNAs and rRNAs m(5)C sites were conserved across all species analysed, from single celled algae N. oculata to multicellular plants. Interestingly the mitochondrial and chloroplast encoded tRNAs were devoid of m(5)C in A. thaliana and this is generally conserved across Plantae. This suggests independent evolution of organelle methylation in animals and plants, as animal mitochondrial tRNAs have m(5)C sites. Here we characterize 5 members of the RNA 5-methylcytosine family in Arabidopsis and extend the functional characterization of TRDMT1 and NOP2A/OLI2. We demonstrate that nuclear tRNA methylation requires two evolutionarily conserved methyltransferases, TRDMT1 and TRM4B. trdmt1 trm4b double mutants are hypersensitive to the antibiotic hygromycin B, demonstrating the function of tRNA methylation in regulating translation. Additionally we demonstrate that nuclear large subunit 25S rRNA methylation requires the conserved RNA methyltransferase NSUN5. Our results also suggest functional redundancy of at least two of the NOP2 paralogs in Arabidopsis.<br><br>CONCLUSIONS: Our data demonstrates widespread occurrence and conservation of non-coding RNA methylation in the kingdom Plantae, suggesting important and highly conserved roles of this post-transcriptional modification.}, }
@article {pmid26267495, year = {2015}, author = {Kumar Singh, M and Janardhan Reddy, PV and Sreedhar, AS and Tiwari, PK}, title = {Molecular characterization and expression analysis of hsp60 gene homologue of sheep blowfly, Lucilia cuprina.}, journal = {Journal of thermal biology}, volume = {52}, number = {}, pages = {24-37}, doi = {10.1016/j.jtherbio.2015.05.001}, pmid = {26267495}, issn = {0306-4565}, mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Cell Nucleus/metabolism/physiology ; Chaperonin 60/biosynthesis/*genetics ; Cloning, Molecular ; Diptera/*physiology ; Gene Expression Regulation/*genetics/*physiology ; Heat-Shock Response/genetics/physiology ; Hot Temperature ; Introns ; Larva/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Temperature ; }, abstract = {The 60kDa heat shock protein (Hsp60) or chaperonin is one among the highly conserved families of heat shock proteins, known to be involved in variety of cellular activities, including protein folding, thermal protection, etc. In this study we sequence characterized hsp60 gene homologue of Lucilia cuprina, isolated and cloned from the genomic library as well as by genomic PCR, followed by RACE- PCR. The L. cuprina hsp60 gene/protein expression pattern was analyzed in various tissues, either at normal temperature (25±1°C) or after exposure to heat stress (42°C). The analysis of nucleotide sequence of Lchsp60 gene revealed absence of intron and the nuclear localizing signal (NLS). The deduced amino acid sequence showed presence of unique conserved sequences, such as those for mitochondrial localization, ATP binding, etc. Unlike Drosophila, Lucilia showed presence of only one isoform, i.e., hsp60A. Phylogenetic analysis of hsp60 gene homologues from different species revealed Lchsp60 to have >88.36% homology with D. melanogaster, 76.86% with L. sericata, 58.31% with mice, 57.99% with rat, and 57.72% with human. Expression analysis using Real Time PCR and fluorescence imaging showed significant enhancement in the expression level of Lchsp60 upon heat stress in a tissue specific manner, indicating its likely role in thermo-tolerance as well as in normal cellular activities.}, }
@article {pmid26260186, year = {2016}, author = {Li, W and Liu, Y and Xu, Q}, title = {Complete mitochondrial genome of Schizothorax nukiangensis Tsao (Cyprinidae: Schizothorax).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3549-3550}, doi = {10.3109/19401736.2015.1074212}, pmid = {26260186}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {In this work, we reported the complete mitochondrial genome sequence of the Schizothorax nukiangensis Tsao for the first time. The complete mtDNA genome sequence of S. nukiangensis Tsao was 16 585 bp in length, which contains 22 transfer RNA genes, 2 rRNA genes, 13 protein-coding genes, an origin of light-strand replication (OL) and a control region (D-Loop). The overall base composition of the mitogenome was calculated to be 29.6% for A, 27.0% for C, 17.9% for G and 25.5% for T. The complete mitogenome of the S. nukiangensis Tsao can provide an important data set for further studies on population history, molecular systematics, phylogeography and stock assessment.}, }
@article {pmid26260185, year = {2016}, author = {Dang, X and Xia, Y and Xu, Q and Zhang, J}, title = {The complete mitochondrial genome of the Poecilia formosa (Amazon molly).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3523-3524}, doi = {10.3109/19401736.2015.1074200}, pmid = {26260185}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Poecilia/*genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The Amazon molly, Poecilia formosa, a member of the Poeciliidae family, is a freshwater fish reproducing through gynogenesis. The complete mitochondrial genome of the P. formosa is determined for the first time in this study. It is a circular molecule of 16 542 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 putative control region. The overall base composition of the genome is A (29.59%), T (27.57%), C (28.27%), and G (14.57%) with 42.84% GC content, which is lower than the content of AT. Most protein-coding genes started with a traditional ATG codon except for COX2, ND5 and ND6, which initiated with ATA, GTG and TTA, respectively. The stop codon was a single T- - base in most of the protein-coding genes, but COX2 and ATP8 both employed TAA and ND2 terminated with AGG codon. Phylogenetic tree was constructed based on the complete mitogenome of P. formosa and closely related 11 chondrichthian species to assess their phylogenic relationship and evolution. The complete mitochondrial genome of the amazon molly would help to study the evolution of Poeciliidae family.}, }
@article {pmid26260184, year = {2016}, author = {Das, SP and Bit, A and Patnaik, S and Sahoo, L and Meher, PK and Jayasankar, P and Saha, TM and Patel, AB and Patel, N and Koringa, P and Joshi, CG and Agarwal, S and Pandey, M and Srivastava, S and Kushwaha, B and Kumar, R and Nagpure, NS and Iquebal, MA and Jaiswal, S and Kumar, D and Jena, JK and Das, P}, title = {Low-depth shotgun sequencing resolves complete mitochondrial genome sequence of Labeo rohita.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3517-3518}, doi = {10.3109/19401736.2015.1074197}, pmid = {26260184}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Labeo rohita, popularly known as rohu, is a widely cultured species in whole Indian subcontinent. In the present study, we used in-silico approach to resolve complete mitochondrial genome of rohu. Low-depth shotgun sequencing using Roche 454 GS FLX (Branford, Connecticut, USA) followed by de novo assembly in CLC Genomics Workbench version 7.0.4 (Aarhus, Denmark) revealed the complete mitogenome of L. rohita to be 16 606 bp long (accession No. KR185963). It comprised of 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 1 putative control region. The gene order and organization are similar to most vertebrates. The mitogenome in the present investigation has 99% similarity with that of previously reported mitogenomes of rohu and this is also evident from the phylogenetic study using maximum-likelihood (ML) tree method. This study was done to determine the feasibility, accuracy and reliability of low-depth sequence data obtained from NGS platform as compared to the Sanger sequencing. Thus, NGS technology has proven to be competent and a rapid in-silico alternative to resolve the complete mitochondrial genome sequence, thereby reducing labors and time.}, }
@article {pmid26260179, year = {2016}, author = {Li, Y and Yao, J and Zhao, X and Li, L and Yan, S}, title = {Complete mitochondrial genome sequence of Chestnut-flanked white-eye (Zosterops erythropleurus).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3529-3530}, doi = {10.3109/19401736.2015.1074203}, pmid = {26260179}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Passeriformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The Chestnut-flanked white-eye (Zosterops erythropleurus) is a species of family Zosteropidae, which is distributed widely in the world. In the present study, the complete mitochondrial genome sequence of Chestnut-flanked white-eye was determined. It has a total length of 17 811 bp, and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes and 2 control regions. The total base composition was 30.2% for A, 31.0% for C, 14.2% for G and 24.6% for T. The phylogenetic tree of Chestnut-flanked white-eye and 13 other species belonging to the order Passeriformes was built. The molecular data presented here will be useful to study the evolutionary relationships and genetic diversity of Chestnut-flanked white-eye.}, }
@article {pmid26260178, year = {2016}, author = {Chen, L and Song, X and Chen, X and Dang, X and Wang, W}, title = {The complete mitochondrial genome of the Pundamilia nyererei (Perciformes, Cichlidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3567-3568}, doi = {10.3109/19401736.2015.1074221}, pmid = {26260178}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Cichlids/*genetics ; Codon, Initiator ; Codon, Terminator ; DNA, Mitochondrial/genetics ; Fish Proteins/genetics ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Whole Genome Sequencing ; }, abstract = {Pundamilia nyererei (Perciformes, Cichlidae) is a member of Cichlid fishes that lives in the Great Lakes of East Africa. Fishes of the Cichlidae family can adapt spectacular trophic radiations and provide good potential examples of vertebrate adaptive radiations. Here, we firstly assembled the complete mitochondrial genome (mitogenome) of Pundamilia nyererei. The mitgenome was 16 761 bp in length, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 putative control region. Most of these protein-coding genes started with a traditional ATG codon except for COX1, which initiated with an infrequent start codon GTG instead, and terminated with the mitochondrial stop codon (TAA/AGG/AGA) or a single T base. The mitogenome structural organization is identical to other Cichlid fish. The overall GC content is 45.25%, which is lower than the AT content. According to these new determined mitogenome sequences and 10 other species under the same family or order, we have constructed the species phylogenetic tree to verify the accuracy of newly assembled mitogenome sequences. We accept that by taking the advantage of full mitogenome, we can address taxonomic issue and study the related evolutionary events. Our current data are going to provide important resources for the research of Cichlid fishes mitochondrial evolution and energy metabolism.}, }
@article {pmid26260177, year = {2016}, author = {Zhang, G and Wang, R and Mao, J and Yin, S and Tao, P and Chen, J and Yu, X and Tang, Z and Chen, S}, title = {The complete mitochondrial genome and phylogenic analysis of Pseudobagrus vachelli.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3551-3552}, doi = {10.3109/19401736.2015.1074213}, pmid = {26260177}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Catfishes/*genetics ; Gene Order ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitochondrial genome of Pseudobagrus vachelli has been sequenced. The mitochondrial genome is 16 529 bp in length, with the base composition of 31.61% A, 26.88% T, 26.55% C, and 14.96% G, containing 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and a major non-coding control region (D-loop region). The gene order and orientation are similar with some typical fish species. The data will provide useful molecular information for phylogenetic studies concerning P. vachelli and its related species.}, }
@article {pmid26260175, year = {2016}, author = {Wilson, JJ and Hefner, M and Walker, CW and Page, ST}, title = {Complete mitochondrial genome of the soft-shell clam Mya arenaria.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3553-3554}, pmid = {26260175}, issn = {2470-1408}, support = {P20 GM103423/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Composition ; Gene Order ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Mya/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {We have sequenced and characterized the complete mitochondrial genome of the soft-shell clam, Mya arenaria, an important organism for environmental toxicology and aquaculture. Mya arenaria is located in the taxonomic order Myoida, which lacks any member with a completely annotated mitogenome. The M. arenaria mitochondrial genome is 17 947 bp in length. Like most marine bivalves, the circular mitogenome codes entirely on the heavy strand, with no introns. As with other bivalves, the gene order of the mitochondrion is highly rearranged. The mitogenome contains 12 protein-coding genes but ATP8 is missing, consistent with about half of all bivalve genera. Twenty-three tRNAs were identified. Phylogenetic analysis shows that M. arenaria is related most closely with the bivalves Sinonovacula constricta, and Moerella iridescens, of the infraclass Euheterodonta (unassigned). This, along with the close grouping of the phylogenetic trees, confirms a close tie between Myoida and Euheterodonta (unassigned).}, }
@article {pmid26260174, year = {2016}, author = {Jiang, L and Chen, B and Feng, J and Mahboob, S and Al-Ghanim, KA}, title = {Intraspecific mitochondrial variations between Rhinogobio typus from the Yellow River and Yangtze River.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3536-3537}, doi = {10.3109/19401736.2015.1074206}, pmid = {26260174}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; China ; Cyprinidae/*classification/genetics ; Evolution, Molecular ; Genes, rRNA ; Genetic Variation ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitochondrial genome of the first individual Rhinogobio typus collected from the Yellow River were sequenced and compared with the previously reported complete mitochondrial sequence of Rhinogobio typus from the Yangtze River. The length of their circular mitochondrial genome was determined to be 16 599 and 16 608 bp respectively. The comparison of two mitochondrial genomes revealed 237 base pair substitutions and 17 insertions or deletions (indels), including 182 base pair substitutions and 2 indels in protein-coding region. Phylogenetic tree was constructed based on complete mitogenomes of the two populations and closely related 13 teleost species to assess their phylogenic relationship and evolution.}, }
@article {pmid26260173, year = {2016}, author = {Yang, X and Xie, GL and Wu, XP and Ouyang, S}, title = {The complete mitochondrial genome of Chinese land snail Aegista aubryana (Gastropoda: Pulmonata: Bradybaenidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3538-3539}, doi = {10.3109/19401736.2015.1074207}, pmid = {26260173}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; China ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; Snails/*genetics ; }, abstract = {Aegista aubryana is an endemic land snail in China. The complete mitochondrial genome of A. aubryana was first determined using long PCR reactions and primer walking method (accession number KT192071). The genome has a length of 14 238 bp, containing 37 typical mitochondrial genes (13 protein-coding genes, 22 tRNA genes and 2 rRNA genes). The base composition of the whole heavy strand is A 31.32%, T 37.86%, C 14.46% and G 16.36%. The results of phylogenetic analyses showed that the A. aubryana is most closely related to Mastigeulota kiangsinensis. This new complete mitochondrial genome can be the basic data for further studies on mitogenome comparison, molecular taxonomy and phylogenetic analyses in bradybaenid snails and Molluscs at large.}, }
@article {pmid26260172, year = {2016}, author = {Park, CE and Park, GS and Kim, MC and Kim, KH and Park, HC and Lee, IJ and Shin, JH}, title = {Complete mitochondrial genome of the Korean endemic species Microphysogobio yaluensis (Teleostei, Cypriniformes, Cyprinidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3557-3559}, doi = {10.3109/19401736.2015.1074217}, pmid = {26260172}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Republic of Korea ; Sequence Analysis, DNA/*methods ; }, abstract = {In this study, we sequenced the complete mitochondrial genome of the Korean endemic species Microphysogobio yaluensis (Teleostei, Cypriniformes, Cyprinidae). The mitogenome, consisted of 16 601 base pairs (bp), encoding 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and 2 non-coding regions. The overall base composition of M. yaluensis was G + C: 43.8%, A + T: 56.2%, apparently with a slight AT bias. Phylogenetic analysis showed that M. yaluensis was close to Hemibarbus mylodon.}, }
@article {pmid26260171, year = {2016}, author = {Bustamante, C and Barría, C and Vargas-Caro, C and Ovenden, JR and Bennett, MB}, title = {The phylogenetic position of the giant devil ray Mobula mobular (Bonnaterre, 1788) (Myliobatiformes, Myliobatidae) inferred from the mitochondrial genome.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3540-3541}, doi = {10.3109/19401736.2015.1074208}, pmid = {26260171}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Evolution, Molecular ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; Skates, Fish/*genetics ; }, abstract = {The giant devil ray, Mobula mobular, is a member of one of the most distinct groups of cartilaginous fishes, the Mobulidae (manta and devil rays), and is the only mobulid assessed as Endangered due its restricted distribution, high bycatch mortality and suspected population decline. The complete mitochondrial genome is 18 913 base pairs in length and comprises 2 rRNAs, 13 protein-coding genes, 22 tRNAs and 2 non-coding regions. Comparison with the partial mitogenome of M. japanica suggests a sister-cryptic species complex and two different taxonomic units. However, the limited divergence within the species (>99.9% genetic identity) may be the result of a geographically and numerically restricted population of M. mobular within the Mediterranean Sea.}, }
@article {pmid26260170, year = {2016}, author = {Luo, X and Kang, X and Zhang, D}, title = {Complete mitochondrial genome of the American flamingo, Phoenicopterus ruber (Phoenicopteriformes, Phoenicopteridae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3519-3520}, doi = {10.3109/19401736.2015.1074198}, pmid = {26260170}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Birds/*genetics ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; United States ; }, abstract = {The American flamingo, Phoenicopterus ruber (P. ruber), is a large species of flamingo closely related to the greater flamingo and Chilean flamingo. In this paper, the complete mitochondrial genome sequence of P. ruber has been assembled for the first time. It was 17 476 bp in length and consisted of 13 typical vertebrate protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 control regions. COI and ND3 genes used GTG and ATC as start codons respectively, but the remaining protein-coding genes were encoded beginning with orthodox ATG codon. Two triplet codons (TAA, AGG) and one single T base were employed as stop codons. The arrangement of the overall genes and noncoding regions was identical to the same genus flamingo Phoenicopterus roseus. The AT content (54.27%) was higher than the GC content. Phylogenetic analysis was performed using 12 protein-coding genes, combined with other 11 species from the same Neognathae, which validated the responsibility and utility of this new mitochondrial genome.}, }
@article {pmid26258519, year = {2016}, author = {Yu, P and Ding, S and Yang, Q and Li, X and Wan, Q}, title = {The complete mitochondrial genome of Sinibotia robusta (Cypriniformes: Cobitidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3471-3472}, doi = {10.3109/19401736.2015.1066353}, pmid = {26258519}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Cypriniformes/*genetics ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The Sinibotia robusta mitochondrial genome (GenBank accession no. KP979711) was a circular molecule of 16 575 bp in length, with two rRNA genes, 13 protein-coding genes, 22 tRNA genes, an l-strand replication origin (OL), and a control region (D-loop). The nucleotide acid composition of the entire mitogenome was 31.91% for A, 26.90% for C, 15.56% for G, and 25.63% for T, with an A + T content of 57.54%. And the A + T content of 12S rRNA, 16S rRNA, and D-loop was 51.26%, 56.17%, and 67.73%, respectively.}, }
@article {pmid26258518, year = {2016}, author = {Wu, Z and Li, X}, title = {Complete mitochondrial genome of the Nemipterus virgatus (Perciformes: Nemipteridae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3485-3486}, doi = {10.3109/19401736.2015.1066360}, pmid = {26258518}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitochondrial genome of the Nemipterus virgatus has been sequenced. The mitochondrial genome is 16 992 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and one control region. The gene order and composition of N. virgatus mitochondrial genome was similar to that of most other vertebrates. The overall nucleotides base composition of the light strand is A (27.89%), G (26.61%), C (16.45%), T (29.05%). With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The tRNA-Ser2 gene lacked DHC arm and could not fold into a typical clover-leaf secondary structure. Seen from the phylogenetic tree, N. virgatus, Nemipterus japonicus, and Nemipterus bathybius from the same genus clustered into one branch.}, }
@article {pmid26258517, year = {2016}, author = {Tian, XX and Pan, WJ and Chen, LL and Xu, YY and Pan, HC}, title = {The complete mitochondrial genome of stretch spider Tetragnatha maxillosa (Araneae: Tetragnathidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3469-3470}, doi = {10.3109/19401736.2015.1066352}, pmid = {26258517}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; Spiders/cytology/*genetics ; }, abstract = {The stretch spider Tetragnatha maxillosa (Araneae: Tetragnathidae) is found all over the world. In the present study, we investigated the complete mitochondrial genome of T. maxillosa and the mitogenome is a circular molecule of 14 414 bp in length, consists of 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a control region. The A + T content of the overall base composition of H-strand is 74.5% (T: 40.4%; C: 9.6%; A: 34.1%; G: 15.9%). COI gene begins with TTT as start codon, COII and COIII genes begin with TTG as start codon, ATP8, Cyt b, ND2, and ND4L genes begin with ATT as start codon, and other six protein-coding genes start with ATA. ATP6, ATP8, COI, COIII, ND1, ND3, and ND6 genes are terminated with TAA as stop codon, Cyt b, ND2, ND4, ND4L, and ND5 end with T, and COII ends with TAG. In addition, the phylogenetic relationships from neighbor-joining analyses based on the 13 concatenated PCGs indicated (Tetragnatha (Nephila (Argiope (Araneus, Neoscona)))).}, }
@article {pmid26258516, year = {2016}, author = {Hu, J and Chen, Y and Zhao, H and Yang, H and Liu, L}, title = {Complete mitochondrial genome of Rhodeus ocellatus (Cypriniformes: Cyprinidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3489-3490}, doi = {10.3109/19401736.2015.1066362}, pmid = {26258516}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitogenome sequence of Rhodeus ocellatus (Kner) was determined using the next-generation sequencing (NGS). The genome was 16 761 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a control region. The overall nucleotide composition was 30.43% A, 27.50% T, 25.94% C, and 16.13% G, with an A + T bias of 57.93%. The gene composition and the arrangement of the R. ocellatus mitochondrial genome were similar to that of most other vertebrates. The complete mitochondrial genome sequence will help to study the evolutionary relationships and population genetics of Rhodeus fish.}, }
@article {pmid26258511, year = {2016}, author = {Li, Y and Lu, J and Wang, Z}, title = {Complete mitochondrial genome of Lasiopodomys mandarinus mandarinus (Arvicolinae, Rodentia).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1459-1460}, doi = {10.3109/19401736.2014.953092}, pmid = {26258511}, issn = {2470-1408}, mesh = {Animals ; Arvicolinae/*genetics ; Base Composition ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Mandarin voles (Lasiopodomys mandarinus) is a subterranean rodent species that are often used as a model for studying subterranean hypoxic stress in mammals. Its subspecies L. m. mandarinus span in cropland in most area of north China and is regarded as an agricultural pest. In this paper, the complete mitochondrial genome of L. m. mandarinus has been determined. Our results showed that the mitochondrial genome of L. m. mandarinus is a circular molecule of 16,367 bp, which contents 13 protein-coding, 22 tRNAs and 2 rRNAs genes. The overall base composition of the heavy strand is 32.47% A, 27.04% T, 27.01% C, and 13.47% G. with an AT content of 59.51%.}, }
@article {pmid26258507, year = {2016}, author = {Wang, Q and Wu, Z and Sun, D and Luo, J}, title = {The complete mitochondrial genome of the Ephippus orbis (Perciformes: Ephippidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3444-3445}, doi = {10.3109/19401736.2015.1063134}, pmid = {26258507}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; NADH Dehydrogenase/genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitochondrial genome of the Ephippus orbis has been sequenced. The mitochondrial genome is 16 670 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and one control region. The gene order and the composition of E. orbis mitochondrial genome were similar to that of most other vertebrates. The overall nucleotides base composition of the heavy strand is A (27.17%), G (16.41%), C (31.46%), and T (24.96%). With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. Seen from the phylogenetic tree (Figure 1), E. orbis, Platax teira, and Platax orbicularis from the same family (Ephippidae) clustered into one branch and were significantly divergent from the other families of closely related fish species.}, }
@article {pmid26258504, year = {2016}, author = {Li, W and Tian, S and Zhu, J and Wu, F and Wang, K and Dai, X}, title = {Characterization of the complete mitochondrial genome of Sickle pomfret Taractichthys steindachneri (Perciformes: Bramidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3481-3482}, doi = {10.3109/19401736.2015.1066358}, pmid = {26258504}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genome Size ; Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/classification/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitogenome sequence of Taractichthys steindachneri was sequenced and analyzed in this study. The complete mitogenome of T. steindachneri is 16 723 bp in length, which contains 22 transfer RNAs, 2 ribosomal RNAs, 13 protein-coding genes and 2 non-coding region, a rep region and a control region (D-loop). This study will be useful for studying on the molecular systematic, taxonomic status and conservation genetics.}, }
@article {pmid26258501, year = {2016}, author = {Liu, QN and Chai, XY and Jiang, SH and Zhou, CL and Xuan, FJ and Tang, BP}, title = {Characterization of the complete mitochondrial genome of the red crayfish, Procambarus clarkii (Decapoda: Cambaridae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3458-3459}, doi = {10.3109/19401736.2015.1066346}, pmid = {26258501}, issn = {2470-1408}, mesh = {Animals ; Astacoidea/*genetics ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Here we present the complete mitochondrial (mt) genome of Procambarus clarkii (Decapoda: Cambaridae) and provide its annotation. The complete mt genome was determined to be 15 929 bp and contains 22 tRNA genes, 13 protein-coding genes (PCGs), two rRNA genes, and a D-loop region. The nucleotide composition was biased toward A + T nucleotides (72.91%) and the AT skew of this mt genome was slightly negative. All the 22 tRNA genes displayed a typical clover-leaf structure, with the exception of trnS1 (AGN). About 13 PCGs were initiated by ATN codons, except for cox1 and nad2 genes which were initiated by ACG and GTG, respectively. Six of the 13 PCGs harbor the incomplete termination codon by T or TA. The D-loop region of the mt genome was 1188 bp in length and the A + T content was 81.08%. Phylogenetic analysis showed that the placement of P. clarkii was within the Cambaridae. This mt genome sequence will provide a better understanding for crayfish evolution in the future.}, }
@article {pmid26256644, year = {2015}, author = {Mokodongan, DF and Yamahira, K}, title = {Origin and intra-island diversification of Sulawesi endemic Adrianichthyidae.}, journal = {Molecular phylogenetics and evolution}, volume = {93}, number = {}, pages = {150-160}, doi = {10.1016/j.ympev.2015.07.024}, pmid = {26256644}, issn = {1095-9513}, mesh = {Animals ; Biodiversity ; Fishes/*genetics ; Genetic Speciation ; Indonesia ; Lakes ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Although the family Adrianichthyidae is broadly distributed throughout East and Southeast Asia, 19 endemic species, over half of the family, are distributed in Sulawesi, which is an island in Wallacea. However, it remains unclear how this Adrianichthyidae biodiversity hotspot was shaped. In this study, we reconstructed molecular phylogenies for the Sulawesi adrianichthyids and estimated the divergence times of major lineages to infer the detailed history of their origin and subsequent intra-island diversification. The mitochondrial and nuclear phylogenies revealed that Sulawesi adrianichthyids are monophyletic, which indicates that they diverged from a single common ancestor. Species in the earliest branching lineages are currently distributed in the central and southeastern parts of the island, indicating that the common ancestor colonized Sula Spur, which is a large promontory that projects from the Australian continental margin, from Asia by oversea dispersal c.a. 20Mya. The first diversification event on Sulawesi, the split of the genus Adrianichthys, occurred c.a. 16Mya, and resulted in the nesting of Adrianichthys within Oryzias. Strong geographic structure was evident in the phylogeny; many species in the lineages branching off early are riverine and widely distributed in the southeastern and southwestern arms of Sulawesi, which suggests that oversea dispersal between tectonic subdivisions of this island during the late Miocene (7-5Mya) contributed to the distributions and diversification of the early branching lineages. In contrast, most species in the lineages branched off later are endemic to a single tectonic lake or lake system in the central Sulawesi, suggesting that habitat fragmentation due to the Pliocene collisions (c.a. 4Mya) among the tectonic subdivisions was the primary factor for diversification of the late branching, lacustrine lineages. Adrianichthys and some Oryzias in a certain late branching lineage are sympatric in Lake Poso, which indicates multiple colonizations of these distinct lineages into this tectonic lake. Thus, the diversification of Sulawesi adrianichthyids largely reflects the complex geological history of this island.}, }
@article {pmid26250483, year = {2015}, author = {Diana, M and Noll, E and Diemunsch, P and Moussallieh, FM and Namer, IJ and Charles, AL and Lindner, V and Agnus, V and Geny, B and Marescaux, J}, title = {Metabolism-Guided Bowel Resection: Potential Role and Accuracy of Instant Capillary Lactates to Identify the Optimal Resection Site.}, journal = {Surgical innovation}, volume = {22}, number = {5}, pages = {453-461}, doi = {10.1177/1553350615598620}, pmid = {26250483}, issn = {1553-3514}, mesh = {Animals ; Biopsy ; Digestive System Surgical Procedures/*methods ; Female ; Intestine, Small/chemistry/*injuries/metabolism/*surgery ; Ischemia/metabolism ; Lactates/*blood/metabolism ; Metabolomics/*methods ; Swine ; }, abstract = {BACKGROUND: Strip-based handheld devices can measure lactatemia on capillary blood obtained by needle puncturing. We aimed to assess the kinetic of bowel capillary lactates, metabolomics profiling, and mitochondria respiratory rate in a prolonged model of bowel hypoperfusion.<br><br>MATERIALS AND METHODS: In 6 pigs, a 3- to 4-cm ischemic segment was created in 6 small bowel loops (total = 36 loops) by clamping the vascular supply, for a duration of 1 to 6 hours. Hourly, 5 blood samples were obtained by puncturing the serosa, and lactates were measured using a handheld analyzer. Samples were made at the following regions of interest (ROIs): center of the ischemic area (1), proximal and distal clinical margins of resection (2a-2b), and vascularized zones (3a-3b). Every hour, surgical biopsies of ROIs were sampled. Activity of bowel mitochondria complexes was measured after 1, 3, and 5 hours of ischemia. Quantification of metabolites was performed on all samples (total N = 180).<br><br>RESULTS: Capillary lactates were significantly higher at ROI 1 versus ROI 3ab at all time points. After 1 hour lactates at the margins were significantly higher than those at vascularized areas (P = .0095), showing a mismatch between visual assessment and actual perfusion status. From 2 to 6 hours, there was no difference in lactates between ROIs 2a-2b and 3a-3b. Maximal tissue respiration decreased significantly after 1 hour (ROI 1 vs ROI 3ab). Seven metabolites (lactate, glucose, aspartate, choline, creatine, taurine, and tyrosine) expressed significantly different evolutions between ROIs.<br><br>CONCLUSIONS: Capillary lactates could help precisely estimate local bowel perfusion status.}, }
@article {pmid26249499, year = {2015}, author = {Crous, M and Roldán, MI}, title = {Characterization of mitochondrial control region in Merlucciidae: sequence variation and molecular phylogeny.}, journal = {Zootaxa}, volume = {3972}, number = {3}, pages = {393-406}, doi = {10.11646/zootaxa.3972.3.5}, pmid = {26249499}, issn = {1175-5326}, mesh = {Animal Distribution ; Animals ; Gadiformes/*classification/*genetics ; *Genetic Variation ; Mitochondria/*genetics ; *Phylogeny ; *Promoter Regions, Genetic ; }, abstract = {In order to describe the structure and evolution of Merlucciidae and related Gadiformes mitochondrial control region we analysed 470 bp of 31 taxa belonging to 28 different species. The general structure and conserved sequence blocks observed in Gadiformes mitochondrial control region are similar to those present in other teleost fishes. The length of this segment is variable among related species due to the presence of numerous indels at domain I. Domain II is the most conserved region with a high G content. The GTGGG-box is absent in all Merluccius and seven other Gadidae species. Several methods of phylogenetic analyses has revealed the monophyly of Gadiformes, Gadinae and Merlucciidae. Merlucciidae is most closely related to Gadidae. Within Merlucciidae, American and Euroafrican clades show similar levels of differentiation to those within Gadinae where Trisopterus and Micromesistius are sister taxa. Genetic distance values for Merluccius subspecies pairs are less than half of those between species, comparable to intra specific differentiation levels in marine fish species.}, }
@article {pmid26248187, year = {2015}, author = {Burgess, TI}, title = {Molecular Characterization of Natural Hybrids Formed between Five Related Indigenous Clade 6 Phytophthora Species.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0134225}, pmid = {26248187}, issn = {1932-6203}, mesh = {Bayes Theorem ; Cell Cycle Proteins/classification/genetics/metabolism ; Genome ; HSP90 Heat-Shock Proteins/genetics/metabolism ; Haplotypes ; *Hybridization, Genetic ; Mitochondria/classification/genetics ; NADH Dehydrogenase/classification/genetics/metabolism ; Phylogeny ; Phytophthora/*genetics ; Polymorphism, Single Nucleotide ; Tubulin/genetics/metabolism ; }, abstract = {Most Phytophthora hybrids characterized to date have emerged from nurseries and managed landscapes, most likely generated as a consequence of biological invasions associated with the movement of living plants and germplasm for ornamental, horticultural and agricultural purposes. Presented here is evidence for natural hybridization among a group of five closely related indigenous clade 6 Phytophthora species isolated from waterways and riparian ecosystems in Western Australia. Molecular characterization of hybrids consisted of cloning and sequencing two nuclear genes (ITS and ASF), sequencing of two further nuclear loci (BT and HSP) and of two mitochondrial loci (COI and NADH). Additionally, phenotypic traits including morphology of sporangia and optima and maxima temperatures for growth were also determined. In most cases the nuclear genes were biparentally and in all cases the mtDNA were uniparentally inherited, indicating hybrid formation through sexual crosses. Some isolates bear the molecular signature of three parents suggesting additional hybrid events, although it cannot be determined from the data if these were sequential or simultaneous. These species and their hybrids co-exist in riparian ecosystems and waterways where their ability for rapid asexual proliferation would enable them to rapidly colonize green plant litter. The apparent ease of hybridization could eventually lead to the merging of species through introgression. However, at this point in time, species integrity has been maintained and a more likely scenario is that the hybrids are not stable evolutionary lineages, but rather transient hybrid clones.}, }
@article {pmid26248000, year = {2016}, author = {Hwang, JY and Han, GG and Park, JY and Kim, EM and An, CM and Kang, JH and Choi, YJ and Kim, EB}, title = {Complete sequence and polymorphisms of female Ruditapes philippinarum (Mollusca: Bivalvia) mitochondria genome.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3462-3463}, doi = {10.3109/19401736.2015.1066348}, pmid = {26248000}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Bivalvia/*genetics ; DNA, Ribosomal/genetics ; Female ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Mitogenome of female Ruditapes philippinarum organism was sequenced, and genomic variation and phylogeny were examined in this study. Length of the mitogenome was 22 089 bp showing 94.28% of sequence identity with previously reported sequence. Total 707 single nucleotide polymorphisms, SNPs, were detected and 50 residues were non-synonymous SNPs among the 202 SNPs in protein-coding genes. Deleted genomic fragments with of 265 bp and 322 bp were observed in non-coding regions, ND2 to ND4L and ND4L to tRNA(Ile), respectively. Phylogenic analysis confirmed that used organisms were female R. philippinarum, and the species has closer evolutionary distance with genus Paphia rather than genus Meretrix. Our finding will be help to set an insight for population and evolutionary genomics of Veneroida clams as well as application to marine industry.}, }
@article {pmid26244691, year = {2016}, author = {Liu, C and Wu, X and Shen, HD}, title = {Complete mitochondrial genome of Vaginulus alte and Homoiodoris japonica.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3454-3457}, doi = {10.3109/19401736.2015.1066345}, pmid = {26244691}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gastropoda/classification/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitochondrial genome sequence of Vaginulus alte and Homoiodoris japonica are described first in the article. The mitogenomes (14 772 bp and 14 601 bp) contain 22 tRNA genes, two ribosomal RNA genes, and 13 protein-coding genes, and one putative control region (CR). CR is not well characterized due to the lack of discrete conserved sequence blocks. This characteristic is similar with CRs of other invertebrate mitochondrial genomes, which is the typical bivalvia mitochondrial gene composition.}, }
@article {pmid26243158, year = {2015}, author = {Matta, CF and Massa, L}, title = {Energy Equivalence of Information in the Mitochondrion and the Thermodynamic Efficiency of ATP Synthase.}, journal = {Biochemistry}, volume = {54}, number = {34}, pages = {5376-5378}, doi = {10.1021/acs.biochem.5b00834}, pmid = {26243158}, issn = {1520-4995}, mesh = {Adenosine Triphosphate/biosynthesis ; Animals ; Energy Metabolism ; Humans ; Kidney/metabolism ; Mitochondria/metabolism ; Mitochondrial Proton-Translocating ATPases/*chemistry/*metabolism ; Models, Biological ; Proton-Motive Force ; Thermodynamics ; }, abstract = {Half a century ago, Johnson and Knudsen resolved the puzzle of the apparent low efficiency of the kidney (∼ 0.5%) compared to most other bodily organs (∼ 40%) by taking into account the entropic cost of ion sorting, the principal function of this organ. Similarly, it is shown that the efficiency of energy transduction of the chemiosmotic proton-motive force by ATP synthase is closer to 90% instead of the oft-quoted textbook value of only 60% when information theoretic considerations are applied to the mitochondrion. This high efficiency is consistent with the mechanical energy transduction of ATP synthase known to be close to the 100% thermodynamic limit. It would have been wasteful for evolution to maximize the mechanical energy transduction to 100% while wasting 40% of the chemiosmotic free energy in the conversion of the proton-motive force into mechanical work before being captured as chemical energy in adenosine 5'-triphosphate.}, }
@article {pmid26242721, year = {2016}, author = {Li, YX and Wang, XG and Ou, J and Yao, FJ and Yang, Y and Wei, ZM}, title = {The complete mitochondrial genome of Coptotermes testaceus (Isoptera: Rhinotermitidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3466-3468}, doi = {10.3109/19401736.2015.1066351}, pmid = {26242721}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Isoptera/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete circular mitochondrial genome (mitogenome) of Coptotermes testaceus is 15 752bp in size, containing 37 typical genes and one non-coding AT-rich region. The AT content of the AT-rich region is 68.3%. All protein coding genes (PCGs) start with standard ATN initiation codons and end with complete termination codons TAA or TAG except for cox2, atp8, and nad5 genes using an incomplete stop codon T. tRNA genes are predicted with a characteristic cloverleaf secondary structure except for trnS1(()(AGN)()), whose dihydrouridine (DHU) arm is replaced by a simple loop. The size of the large and small ribosomal RNA genes are 1315 and 818 bp, respectively. Phylogenetic analysis found that (i) the C. testaceus clade formed the sister group with another clade containing Coptotermes lacteus and Coptotermes formosanus; and (ii) Coptotermes lacteus had a close relationship with Coptotermes clade, but with lower credibility than other clades, the bootstrap value was 97%.}, }
@article {pmid26241330, year = {2015}, author = {Kerk, D and Silver, D and Uhrig, RG and Moorhead, GB}, title = {"PP2C7s", Genes Most Highly Elaborated in Photosynthetic Organisms, Reveal the Bacterial Origin and Stepwise Evolution of PPM/PP2C Protein Phosphatases.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0132863}, pmid = {26241330}, issn = {1932-6203}, mesh = {Archaeal Proteins/chemistry/genetics ; Bacterial Proteins/chemistry/*genetics ; Chlorophyta/*enzymology/genetics ; Chloroplasts/enzymology ; *Evolution, Molecular ; Gene Expression Regulation, Plant ; Gene Regulatory Networks ; *Genes, Plant ; Magnesium/physiology ; Mitochondria/enzymology ; Molecular Structure ; Phosphoprotein Phosphatases/chemistry/*genetics ; Photosynthesis/*genetics ; Phylogeny ; Plant Proteins/chemistry/*genetics ; Plants/*enzymology/genetics ; Protein Phosphatase 2C ; Protein Structure, Secondary ; Sequence Alignment ; Sequence Homology, Amino Acid ; Starch/metabolism ; }, abstract = {Mg+2/Mn+2-dependent type 2C protein phosphatases (PP2Cs) are ubiquitous in eukaryotes, mediating diverse cellular signaling processes through metal ion catalyzed dephosphorylation of target proteins. We have identified a distinct PP2C sequence class ("PP2C7s") which is nearly universally distributed in Eukaryotes, and therefore apparently ancient. PP2C7s are by far most prominent and diverse in plants and green algae. Combining phylogenetic analysis, subcellular localization predictions, and a distillation of publically available gene expression data, we have traced the evolutionary trajectory of this gene family in photosynthetic eukaryotes, demonstrating two major sequence assemblages featuring a succession of increasingly derived sub-clades. These display predominant expression moving from an ancestral pattern in photosynthetic tissues toward non-photosynthetic, specialized and reproductive structures. Gene co-expression network composition strongly suggests a shifting pattern of PP2C7 gene functions, including possible regulation of starch metabolism for one homologue set in Arabidopsis and rice. Distinct plant PP2C7 sub-clades demonstrate novel amino terminal protein sequences upon motif analysis, consistent with a shifting pattern of regulation of protein function. More broadly, neither the major events in PP2C sequence evolution, nor the origin of the diversity of metal binding characteristics currently observed in different PP2C lineages, are clearly understood. Identification of the PP2C7 sequence clade has allowed us to provide a better understanding of both of these issues. Phylogenetic analysis and sequence comparisons using Hidden Markov Models strongly suggest that PP2Cs originated in Bacteria (Group II PP2C sequences), entered Eukaryotes through the ancestral mitochondrial endosymbiosis, elaborated in Eukaryotes, then re-entered Bacteria through an inter-domain gene transfer, ultimately producing bacterial Group I PP2C sequences. A key evolutionary event, occurring first in ancient Eukaryotes, was the acquisition of a conserved aspartate in classic Motif 5. This has been inherited subsequently by PP2C7s, eukaryotic PP2Cs and bacterial Group I PP2Cs, where it is crucial to the formation of a third metal binding pocket, and catalysis.}, }
@article {pmid26240360, year = {2015}, author = {Bauer, D and Merz, DR and Pelz, B and Theisen, KE and Yacyshyn, G and Mokranjac, D and Dima, RI and Rief, M and Žoldák, G}, title = {Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10389-10394}, pmid = {26240360}, issn = {1091-6490}, mesh = {Actins/chemistry ; Adenosine Triphosphatases/chemistry ; Amino Acid Sequence ; Computer Simulation ; Elasticity ; Escherichia coli Proteins/*chemistry ; HSP70 Heat-Shock Proteins/*chemistry ; Lasers ; Mitochondria/metabolism ; Models, Molecular ; Molecular Chaperones ; Molecular Sequence Data ; Nucleotides/*chemistry ; Phylogeny ; Protein Binding ; Protein Denaturation ; Protein Folding ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/*chemistry ; Signal Transduction ; }, abstract = {The regulation of protein function through ligand-induced conformational changes is crucial for many signal transduction processes. The binding of a ligand alters the delicate energy balance within the protein structure, eventually leading to such conformational changes. In this study, we elucidate the energetic and mechanical changes within the subdomains of the nucleotide binding domain (NBD) of the heat shock protein of 70 kDa (Hsp70) chaperone DnaK upon nucleotide binding. In an integrated approach using single molecule optical tweezer experiments, loop insertions, and steered coarse-grained molecular simulations, we find that the C-terminal helix of the NBD is the major determinant of mechanical stability, acting as a glue between the two lobes. After helix unraveling, the relative stability of the two separated lobes is regulated by ATP/ADP binding. We find that the nucleotide stays strongly bound to lobe II, thus reversing the mechanical hierarchy between the two lobes. Our results offer general insights into the nucleotide-induced signal transduction within members of the actin/sugar kinase superfamily.}, }
@article {pmid26237419, year = {2015}, author = {Li, DH and Shi, W and Munroe, TA and Gong, L and Kong, XY}, title = {Concerted Evolution of Duplicate Control Regions in the Mitochondria of Species of the Flatfish Family Bothidae (Teleostei: Pleuronectiformes).}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0134580}, pmid = {26237419}, issn = {1932-6203}, mesh = {Animals ; Conserved Sequence ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Flounder/*genetics ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Mitogenomes of flatfishes (Pleuronectiformes) exhibit the greatest diversity of gene rear-rangements in teleostean fishes. Duplicate control regions (CRs) have been found in the mito-genomes of two flatfishes, Samariscus latus (Samaridae) and Laeops lanceolata (Bothidae), which is rare in teleosts. It has been reported that duplicate CRs have evolved in a concerted fashion in fishes and other animals, however, whether concerted evo-lution exists in flatfishes remains unknown. In this study, based on five newly sequenced and six previously reported mitogenomes of lefteye flounders in the Bothidae, we explored whether duplicate CRs and concerted evolution exist in these species. Results based on the present study and previous reports show that four out of eleven bothid species examined have duplicate CRs of their mitogenomes. The core regions of the duplicate CRs of mitogenomes in the same species have identical, or nearly identical, sequences when compared to each other. This pattern fits the typical characteristics of concerted evolution. Additionally, phylogenetic and ancestral state reconstruction analysis also provided evidence to support the hypothesis that duplicate CRs evolved concertedly. The core region of concerted evolution is situated at the conserved domains of the CR of the mitogenome from the termination associated sequences (TASs) to the conserved sequence blocks (CSBs). Commonly, this region is con-sidered to regulate mitochondrial replication and transcription. Thus, we hypothesize that the cause of concerted evolution of the duplicate CRs in the mtDNAs of these four bothids may be related to some function of the conserved sequences of the CRs during mitochondrial rep-lication and transcription. We hope our results will provide fresh insight into the molecular mechanisms related to replication and evolution of mitogenomes.}, }
@article {pmid26232548, year = {2015}, author = {Ran, JH and Shen, TT and Liu, WJ and Wang, PP and Wang, XQ}, title = {Mitochondrial introgression and complex biogeographic history of the genus Picea.}, journal = {Molecular phylogenetics and evolution}, volume = {93}, number = {}, pages = {63-76}, doi = {10.1016/j.ympev.2015.07.020}, pmid = {26232548}, issn = {1095-9513}, mesh = {Base Sequence ; Cell Nucleus/genetics ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; Gene Regulatory Networks ; Genes, Plant ; Genetic Variation ; Mitochondria/*genetics ; Phylogeny ; *Phylogeography ; Picea/classification/*genetics ; Recombination, Genetic/genetics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Biogeographic history of plants is much more complex in the Northern Hemisphere than in the Southern Hemisphere due to that both the Bering and the North Atlantic land bridges contributed to floristic exchanges in the Cenozoic, which led to hybridization between congeneric species from different continents. It would be interesting to know how intercontinental gene flow and introgression have affected plant phylogenetic reconstruction and biogeographic inference. In this study, we reinvestigated the phylogenetic and biogeographic history of Picea, a main component of the Northern Hemisphere forest with many species that originated from recent radiation, using two chloroplast (cp), one mitochondrial (mt) and three single-copy nuclear gene markers. The generated gene trees are topologically highly discordant and the geographically closely related species generally show a close affinity of mtDNA rather than cp- or nuclear DNA, suggesting that inter- and intra-continental gene flow and mtDNA introgression might have occurred commonly. However, all gene trees resolved Picea breweriana as the basal-most lineage, which, together with fossil evidence, supports the North American origin hypothesis for the genus. Both dispersal and vicariance have played important roles in the evolution of Picea, and the Bering Land Bridge could have mediated the "North America to Eurasia" dispersal at least two times during the Miocene and Pliocene. Our study again demonstrates the importance of applying data from three genomes for a clear understanding of evolutionary histories in the pine family. Any markers from a single genome alone will not reveal a clear picture of the phylogenetic relationships among closely related congeneric species. In particular, mtDNA markers should be cautiously used, considering that introgression of the maternally inherited mtDNA with a lower rate of gene flow (by seeds) could have occurred much more frequently than that of the paternally inherited cpDNA with a higher rate of gene flow (by pollen) in Pinaceae.}, }
@article {pmid26226593, year = {2016}, author = {Yao, J and Zhao, X and Li, Y and Li, L and Yan, S}, title = {The complete sequence of mitochondrial genome of Siberian accentor (Prunella montanella).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3440-3441}, doi = {10.3109/19401736.2015.1063132}, pmid = {26226593}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Passeriformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The Siberian accentor, Prunella montanella (Passeriformes, Prunellidae), is a small passerine bird. In this study, the complete mitochondrial genome sequence of Siberian accentor was determined. It has a total length of 16 832 bp, and contains 13 protein coding genes, 22 tRNA genes, two ribosome RNA genes, and one control region. The nucleotide composition is 30.1% for A, 31.0% for C, 15.0% for G and 23.9% for T, respectively. The overall GC content is lower than AT. The phylogenetic tree of Siberian accentor and 10 other species belonging to order Passeriformes was built. The DNA data presented here will be useful to study the evolutionary relationships and genetic diversity of Siberian accentors.}, }
@article {pmid26226163, year = {2015}, author = {Atray, I and Bentur, JS and Nair, S}, title = {The Asian Rice Gall Midge (Orseolia oryzae) Mitogenome Has Evolved Novel Gene Boundaries and Tandem Repeats That Distinguish Its Biotypes.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0134625}, pmid = {26226163}, issn = {1932-6203}, mesh = {Animals ; Codon, Initiator/genetics ; Codon, Terminator/genetics ; Diptera/*genetics ; Genes, Insect/*genetics ; Genome, Insect/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; RNA, Untranslated/genetics ; Tandem Repeat Sequences/*drug effects ; }, abstract = {The complete mitochondrial genome of the Asian rice gall midge, Orseolia oryzae (Diptera; Cecidomyiidae) was sequenced, annotated and analysed in the present study. The circular genome is 15,286 bp with 13 protein-coding genes, 22 tRNAs and 2 ribosomal RNA genes, and a 578 bp non-coding control region. All protein coding genes used conventional start codons and terminated with a complete stop codon. The genome presented many unusual features: (1) rearrangement in the order of tRNAs as well as protein coding genes; (2) truncation and unusual secondary structures of tRNAs; (3) presence of two different repeat elements in separate non-coding regions; (4) presence of one pseudo-tRNA gene; (5) inversion of the rRNA genes; (6) higher percentage of non-coding regions when compared with other insect mitogenomes. Rearrangements of the tRNAs and protein coding genes are explained on the basis of tandem duplication and random loss model and why intramitochondrial recombination is a better model for explaining rearrangements in the O. oryzae mitochondrial genome is discussed. Furthermore, we evaluated the number of iterations of the tandem repeat elements found in the mitogenome. This led to the identification of genetic markers capable of differentiating rice gall midge biotypes and the two Orseolia species investigated.}, }
@article {pmid26218308, year = {2016}, author = {Wang, HL and Zhang, Z and Bing, XL and Liu, YQ and Liu, SS and Wang, XW}, title = {A complete mitochondrial DNA genome derived from a Chinese population of the Bemisia afer species complex (Hemiptera: Aleyrodidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3500-3501}, doi = {10.3109/19401736.2015.1066367}, pmid = {26218308}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Hemiptera/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {We report here the sequence of a complete mitochondrial genome (mitogenome) of a population of Bemisia afer species complex, which was collected from Abutilonaviecnnae gaerner at LinYi, Shan Dong province of China (hereafter B. afer_China_Ag) (GenBank accession number: KR819174). The mitogenome of B. afer_China_Ag is 15 300 bp and contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and 2 control regions. The content and arrangement of mitochondrial genes of B. afer_China_Ag exhibit remarkable differences from the mitogenome of a B. afer population collected from African cassava (KF734668). Phylogenetic analyses based on 13 protein-coding genes support the close relationship of the two sequenced B. afer mitogenomes and confirm the species status of our specimen.}, }
@article {pmid26216303, year = {2015}, author = {Ivanov, I and Kuhn, H and Heydeck, D}, title = {Structural and functional biology of arachidonic acid 15-lipoxygenase-1 (ALOX15).}, journal = {Gene}, volume = {573}, number = {1}, pages = {1-32}, pmid = {26216303}, issn = {1879-0038}, support = {R01 GM089820/GM/NIGMS NIH HHS/United States ; GM089820/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Arachidonate 15-Lipoxygenase/*chemistry/genetics/*metabolism ; Humans ; Isoenzymes/chemistry/metabolism ; Protein Conformation ; }, abstract = {Lipoxygenases (LOX) form a family of lipid peroxidizing enzymes, which have been implicated in a number of physiological processes and in the pathogenesis of inflammatory, hyperproliferative and neurodegenerative diseases. They occur in two of the three domains of terrestrial life (bacteria, eucarya) and the human genome involves six functional LOX genes, which encode for six different LOX isoforms. One of these isoforms is ALOX15, which has first been described in rabbits in 1974 as enzyme capable of oxidizing membrane phospholipids during the maturational breakdown of mitochondria in immature red blood cells. During the following decades ALOX15 has extensively been characterized and its biological functions have been studied in a number of cellular in vitro systems as well as in various whole animal disease models. This review is aimed at summarizing the current knowledge on the protein-chemical, molecular biological and enzymatic properties of ALOX15 in various species (human, mouse, rabbit, rat) as well as its implication in cellular physiology and in the pathogenesis of various diseases.}, }
@article {pmid26206358, year = {2015}, author = {Boyle, KS and Riepe, S and Bolen, G and Parmentier, E}, title = {Variation in swim bladder drumming sounds from three doradid catfish species with similar sonic morphologies.}, journal = {The Journal of experimental biology}, volume = {218}, number = {Pt 18}, pages = {2881-2891}, doi = {10.1242/jeb.123414}, pmid = {26206358}, issn = {1477-9145}, mesh = {Air Sacs/anatomy &amp; histology/*physiology ; *Animal Communication ; Animals ; Catfishes/anatomy &amp; histology/*physiology ; Muscle Contraction/*physiology ; Muscle Fibers, Skeletal/physiology ; Muscle, Skeletal/anatomy &amp; histology/physiology ; *Sound ; }, abstract = {A variety of teleost fishes produce sounds for communication by vibrating the swim bladder with fast contracting muscles. Doradid catfishes have an elastic spring apparatus (ESA) for sound production. Contractions of the ESA protractor muscle pull the anterior transverse process of the 4th vertebra or Müllerian ramus (MR) to expand the swim bladder and elasticity of the MR returns the swim bladder to the resting state. In this study, we examined the sound characteristics and associated fine structure of the protractor drumming muscles of three doradid species: Acanthodoras cataphractus, Platydoras hancockii and Agamyxis pectinifrons. Despite large variations in size, sounds from all three species had similar mean dominant rates ranging from 91 to 131 Hz and showed frequencies related to muscle contraction speed rather than fish size. Sounds differed among species in terms of waveform shape and their rate of amplitude modulation. In addition, multiple distinguishable sound types were observed from each species: three sound types from A. cataphractus and P. hancockii, and two sound types from A. pectinifrons. Although sounds differed among species, no differences in muscle fiber fine structure were observed at the species level. Drumming muscles from each species bear features associated with fast contractions, including sarcoplasmic cores, thin radial myofibrils, abundant mitochondria and an elaborated sarcoplasmic reticulum. These results indicate that sound differences between doradids are not due to swimbladder size, muscle anatomy, muscle length or Müllerian ramus shape, but instead result from differences in neural activation of sonic muscles.}, }
@article {pmid26205690, year = {2015}, author = {Nagataki, M and Tantrawatpan, C and Agatsuma, T and Sugiura, T and Duenngai, K and Sithithaworn, P and Andrews, RH and Petney, TN and Saijuntha, W}, title = {Mitochondrial DNA sequences of 37 collar-spined echinostomes (Digenea: Echinostomatidae) in Thailand and Lao PDR reveals presence of two species: Echinostoma revolutum and E. miyagawai.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {35}, number = {}, pages = {56-62}, doi = {10.1016/j.meegid.2015.07.022}, pmid = {26205690}, issn = {1567-7257}, mesh = {Animals ; DNA, Helminth/analysis ; DNA, Mitochondrial/*analysis ; Ducks/*parasitology ; Echinostoma/*classification/*genetics ; Electron Transport Complex IV/analysis ; Genetic Variation ; Haplotypes ; Laos ; Mitochondria/*genetics ; NADH Dehydrogenase/analysis ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*methods ; Thailand ; }, abstract = {The "37 collar-spined" or "revolutum" group of echinostomes is recognized as a species complex. The identification of members of this complex by morphological taxonomic characters is difficult and confusing, and hence, molecular analyses are a useful alternative method for molecular systematic studies. The current study examined the genetic diversity of those 37 collar-spined echinostomes which are recognized morphologically as Echinostoma revolutum in Thailand and Lao PDR using the cytochrome c oxidase subunit 1 (CO1) and the NADH dehydrogenase subunit 1 (ND1) sequences. On the basis of molecular investigations, at least two species of 37 collar-spined echinostomes exist in Southeast Asia, namely E. revolutum and Echinostoma miyagawai. The specimens examined in this study, coming from ducks in Thailand and Lao PDR, were compared to isolates from America, Europe and Australia for which DNA sequences are available in public databases. Haplotype analysis detected 6 and 26 haplotypes when comparing the CO1 sequences of E. revolutum and E. miyagawai, respectively, from different geographical isolates from Thailand and Lao PDR. The phylogenetic trees, ND1 haplotype network and genetic differentiation (ɸST) analyses showed that E. revolutum were genetically different on a continental scale, i.e. Eurasian and American lineages.}, }
@article {pmid26203001, year = {2015}, author = {Salin, K and Auer, SK and Rey, B and Selman, C and Metcalfe, NB}, title = {Variation in the link between oxygen consumption and ATP production, and its relevance for animal performance.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1812}, pages = {20151028}, pmid = {26203001}, issn = {1471-2954}, mesh = {Adenosine Triphosphate/*metabolism ; Animals ; Biological Evolution ; *Energy Metabolism ; Invertebrates/metabolism ; Mitochondria/*metabolism ; *Oxygen Consumption ; Vertebrates/metabolism ; }, abstract = {It is often assumed that an animal's metabolic rate can be estimated through measuring the whole-organism oxygen consumption rate. However, oxygen consumption alone is unlikely to be a sufficient marker of energy metabolism in many situations. This is due to the inherent variability in the link between oxidation and phosphorylation; that is, the amount of adenosine triphosphate (ATP) generated per molecule of oxygen consumed by mitochondria (P/O ratio). In this article, we describe how the P/O ratio can vary within and among individuals, and in response to a number of environmental parameters, including diet and temperature. As the P/O ratio affects the efficiency of cellular energy production, its variability may have significant consequences for animal performance, such as growth rate and reproductive output. We explore the adaptive significance of such variability and hypothesize that while a reduction in the P/O ratio is energetically costly, it may be associated with advantages in terms of somatic maintenance through reduced production of reactive oxygen species. Finally, we discuss how considering variation in mitochondrial efficiency, together with whole-organism oxygen consumption, can permit a better understanding of the relationship between energy metabolism and life history for studies in evolutionary ecology.}, }
@article {pmid26202992, year = {2015}, author = {Okamura, T and Kondo, R}, title = {Suigetsumonas clinomigrationis gen. et sp. nov., a Novel Facultative Anaerobic Nanoflagellate Isolated from the Meromictic Lake Suigetsu, Japan.}, journal = {Protist}, volume = {166}, number = {4}, pages = {409-421}, doi = {10.1016/j.protis.2015.06.003}, pmid = {26202992}, issn = {1618-0941}, mesh = {Japan ; Lakes/parasitology ; Microscopy, Electron, Transmission ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; Species Specificity ; Stramenopiles/*classification/genetics/isolation &amp; purification/ultrastructure ; }, abstract = {A novel facultative anaerobic bacterivorous nanoflagellate was isolated from the water just below the permanent oxic-anoxic interface of the meromictic Lake Suigetsu, Japan. We characterized the isolate using light and transmission electron microscopy and molecular phylogenetic analyses inferred from 18S rDNA sequences. The phylogenetic analyses showed that the isolate belonged to class Placididea (stramenopiles). The isolate showed key ultrastructural features of the Placididea, such as flagellar hairs with two unequal terminal filaments, microtubular root 2 changing in shape from an arced to an acute-angled shape, and a lack of an x-fiber in root 2. However, the isolate had a single helix in the flagellar transition region, which is a double helix in the two known placidid nanoflagellates Placidia cafeteriopsis and Wobblia lunata. Moreover, the isolate had different intracellular features compared with these two genera, such as the arrangement of basal bodies, the components of the flagellar apparatus, the number of mitochondria, and the absence (or presence) of paranuclear bodies. The 18S rDNA sequence was also phylogenetically distant from the clades of the known Placididae W. lunata and P. cafeteriopsis. Consequently, the newly isolated nanoflagellate was described as Suigetsumonas clinomigrationis gen. et sp. nov.}, }
@article {pmid26201475, year = {2015}, author = {Havird, JC and Hall, MD and Dowling, DK}, title = {The evolution of sex: A new hypothesis based on mitochondrial mutational erosion: Mitochondrial mutational erosion in ancestral eukaryotes would favor the evolution of sex, harnessing nuclear recombination to optimize compensatory nuclear coadaptation.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {37}, number = {9}, pages = {951-958}, pmid = {26201475}, issn = {1521-1878}, support = {F32 GM116361/GM/NIGMS NIH HHS/United States ; F32GM116361/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; Animals ; *Biological Evolution ; Cell Nucleus/genetics ; Eukaryota/*genetics ; Humans ; Mitochondria/*genetics ; *Models, Biological ; Mutation/*genetics ; *Recombination, Genetic ; *Sex Characteristics ; }, abstract = {The evolution of sex in eukaryotes represents a paradox, given the "twofold" fitness cost it incurs. We hypothesize that the mutational dynamics of the mitochondrial genome would have favored the evolution of sexual reproduction. Mitochondrial DNA (mtDNA) exhibits a high-mutation rate across most eukaryote taxa, and several lines of evidence suggest that this high rate is an ancestral character. This seems inexplicable given that mtDNA-encoded genes underlie the expression of life's most salient functions, including energy conversion. We propose that negative metabolic effects linked to mitochondrial mutation accumulation would have invoked selection for sexual recombination between divergent host nuclear genomes in early eukaryote lineages. This would provide a mechanism by which recombinant host genotypes could be rapidly shuffled and screened for the presence of compensatory modifiers that offset mtDNA-induced harm. Under this hypothesis, recombination provides the genetic variation necessary for compensatory nuclear coadaptation to keep pace with mitochondrial mutation accumulation.}, }
@article {pmid26200853, year = {2015}, author = {Armstrong, CM}, title = {Packaging life: the origin of ion-selective channels.}, journal = {Biophysical journal}, volume = {109}, number = {2}, pages = {173-177}, pmid = {26200853}, issn = {1542-0086}, mesh = {Animals ; Bacteria/metabolism ; Biological Evolution ; Humans ; Ion Channels/*metabolism ; Mitochondria/metabolism ; Osmosis/physiology ; }, }
@article {pmid26196835, year = {2015}, author = {Kosakyan, A and Mulot, M and Mitchell, EA and Lara, E}, title = {Environmental DNA COI barcoding for quantitative analysis of protists communities: A test using the Nebela collaris complex (Amoebozoa; Arcellinida; Hyalospheniidae).}, journal = {European journal of protistology}, volume = {51}, number = {4}, pages = {311-320}, doi = {10.1016/j.ejop.2015.06.005}, pmid = {26196835}, issn = {1618-0429}, mesh = {Amoebozoa/*classification/*genetics ; *Biodiversity ; *DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics ; Mitochondria/genetics ; Phylogeny ; Soil/parasitology ; }, abstract = {Environmental DNA surveys are used for screening eukaryotic diversity. However, it is unclear how quantitative this approach is and to what extent results from environmental DNA studies can be used for ecological studies requiring quantitative data. Mitochondrial cytochrome oxidase (COI) is used for species-level taxonomic studies of testate amoebae and should allow assessing the community composition from environmental samples, thus bypassing biases due to morphological identification. We tested this using a COI clone library approach and focusing on the Nebela collaris complex. Comparisons with direct microscopy counts showed that the COI clone library diversity data matched the morphologically identified taxa, and that community composition estimates using the two approaches were similar. However, this correlation was improved when microscopy counts were corrected for biovolume. Higher correlation with biovolume-corrected community data suggests that COI clone library data matches the ratio of mitochondria and that within closely-related taxa the density of mitochondria per unit biovolume is approximately constant. Further developments of this metabarcoding approach including quantifying the mitochondrial density among closely-related taxa, experiments on other taxonomic groups and using high throughput sequencing should make if possible to quantitatively estimate community composition of different groups, which would be invaluable for microbial food webs studies.}, }
@article {pmid26195779, year = {2015}, author = {Björkholm, P and Harish, A and Hagström, E and Ernst, AM and Andersson, SG}, title = {Mitochondrial genomes are retained by selective constraints on protein targeting.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10154-10161}, pmid = {26195779}, issn = {1091-6490}, mesh = {Bacterial Proteins/metabolism ; Cell Nucleus/genetics ; Chloroplast Proteins/metabolism ; Computational Biology ; Cytochromes b/metabolism ; Cytosol/metabolism ; Endoplasmic Reticulum/metabolism ; Genome, Mitochondrial/*genetics ; HeLa Cells/metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Membrane Proteins/genetics ; Mitochondrial Proteins/*metabolism ; Mitochondrial Proton-Translocating ATPases/metabolism ; Oxidative Phosphorylation ; Phylogeny ; Protein Folding ; Protein Structure, Tertiary ; Signal Recognition Particle/metabolism ; Thermodynamics ; }, abstract = {Mitochondria are energy-producing organelles in eukaryotic cells considered to be of bacterial origin. The mitochondrial genome has evolved under selection for minimization of gene content, yet it is not known why not all mitochondrial genes have been transferred to the nuclear genome. Here, we predict that hydrophobic membrane proteins encoded by the mitochondrial genomes would be recognized by the signal recognition particle and targeted to the endoplasmic reticulum if they were nuclear-encoded and translated in the cytoplasm. Expression of the mitochondrially encoded proteins Cytochrome oxidase subunit 1, Apocytochrome b, and ATP synthase subunit 6 in the cytoplasm of HeLa cells confirms export to the endoplasmic reticulum. To examine the extent to which the mitochondrial proteome is driven by selective constraints within the eukaryotic cell, we investigated the occurrence of mitochondrial protein domains in bacteria and eukaryotes. The accessory protein domains of the oxidative phosphorylation system are unique to mitochondria, indicating the evolution of new protein folds. Most of the identified domains in the accessory proteins of the ribosome are also found in eukaryotic proteins of other functions and locations. Overall, one-third of the protein domains identified in mitochondrial proteins are only rarely found in bacteria. We conclude that the mitochondrial genome has been maintained to ensure the correct localization of highly hydrophobic membrane proteins. Taken together, the results suggest that selective constraints on the eukaryotic cell have played a major role in modulating the evolution of the mitochondrial genome and proteome.}, }
@article {pmid26195746, year = {2015}, author = {Speijer, D and Lukeš, J and Eliáš, M}, title = {Sex is a ubiquitous, ancient, and inherent attribute of eukaryotic life.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {29}, pages = {8827-8834}, pmid = {26195746}, issn = {1091-6490}, mesh = {Cell Fusion ; Eukaryotic Cells/*physiology ; Genome ; Meiosis ; Mitochondria/metabolism ; Molecular Sequence Data ; Reactive Oxygen Species/metabolism ; *Reproduction ; Sequence Analysis, DNA ; }, abstract = {Sexual reproduction and clonality in eukaryotes are mostly seen as exclusive, the latter being rather exceptional. This view might be biased by focusing almost exclusively on metazoans. We analyze and discuss reproduction in the context of extant eukaryotic diversity, paying special attention to protists. We present results of phylogenetically extended searches for homologs of two proteins functioning in cell and nuclear fusion, respectively (HAP2 and GEX1), providing indirect evidence for these processes in several eukaryotic lineages where sex has not been observed yet. We argue that (i) the debate on the relative significance of sex and clonality in eukaryotes is confounded by not appropriately distinguishing multicellular and unicellular organisms; (ii) eukaryotic sex is extremely widespread and already present in the last eukaryotic common ancestor; and (iii) the general mode of existence of eukaryotes is best described by clonally propagating cell lines with episodic sex triggered by external or internal clues. However, important questions concern the relative longevity of true clonal species (i.e., species not able to return to sexual procreation anymore). Long-lived clonal species seem strikingly rare. We analyze their properties in the light of meiotic sex development from existing prokaryotic repair mechanisms. Based on these considerations, we speculate that eukaryotic sex likely developed as a cellular survival strategy, possibly in the context of internal reactive oxygen species stress generated by a (proto) mitochondrion. Thus, in the context of the symbiogenic model of eukaryotic origin, sex might directly result from the very evolutionary mode by which eukaryotic cells arose.}, }
@article {pmid26195217, year = {2016}, author = {Ding, M and Wu, J and Qian, L and Pan, T and Zhang, B}, title = {Complete mitochondrial genome of Lycodon flavozonatum and implications for Colubridae taxonomy.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3473-3474}, doi = {10.3109/19401736.2015.1066354}, pmid = {26195217}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Colubridae/*classification/genetics ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Lycodon flavozonatum, a species of Colubcridae family, is mainly inhabited in hilly region of forest in South China, India, Myanmar, and Vietnam. In this study, the complete mtDNA of L. flavozonatum is 17 172 bp long, which contains 13 protein-coding genes, 22 tRNA genes, two rRNA (12S and 16S rRNA), and two control regions and a stem-loop region. Most of these genes are encoded in the H-strand; only ND6, stem-loop and other nine tRNA genes are on the L-strand. The phylogenetic tree among the 14 Serpentiformes species was divided into three major clade; Lycodon makes up the first clade, which showed a sister relationship to the second clade, Elaphe; Hypsiglena forms the third clade and is sister to Lycodon and Elaphe. And the species of L. flavozonatum which we studied belongs to the first clade.}, }
@article {pmid26195216, year = {2016}, author = {An, M and Zhang, Z and Li, X and Yang, S}, title = {The complete mitochondrial genome of the White-throated Tinamou, Tinamus guttatus (Tinamiformes, Tinamidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {4}, pages = {2800-2801}, doi = {10.3109/19401736.2015.1053073}, pmid = {26195216}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Birds/classification/*genetics ; Codon, Initiator/genetics ; Codon, Terminator/genetics ; Genome, Mitochondrial/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The White-throated Tinamou, Tinamus guttatus (Tinamiformes, Tinamidae) is a species of the family Tinamidae. Herein, we firstly reported the complete mitochondrial genome of White-throated Tinamou. The length of mitogenome was 16 750 bp, and composed of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 putative misc-feature region. Most protein-coding genes started with a traditional ATG codon, but specially, COX1 and COX2 initiated with an infrequent start codon GTG instead, ND3 and ND5 initiated with ATA instead. Protein-coding genes terminated with the mitochondria stop codon (TAA/TAG/AGG/AGA) or a single base(A/T). The mitogenome structural organization was identical to the closely related species Tinamus major. The GC content was 42.66%. To verify the accuracy and utility of new determined mitogenome sequences, we constructed the species phylogenetic tree with the 12 protein-coding genes of Tinamus guttatus together with nine other closely species. We expected that using the full mitogenome to address taxonomic issues and study the related evolution events.}, }
@article {pmid26195214, year = {2016}, author = {Ning, Y and Liu, H and Jiang, G and Ma, J}, title = {Phylogenetic relationship of Eurasian lynx (Lynx lynx) revealed by complete mitochondrial genome.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3477-3478}, doi = {10.3109/19401736.2015.1066356}, pmid = {26195214}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Lynx/classification/*genetics ; Mitochondria/*genetics ; Muscles/chemistry ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The Eurasian lynx (Lynx lynx) is an Endangered species in northeast China. We first obtained muscle sample, extracted the sample DNA and sequenced the whole mtDNA genome of lynx from northeast China. We reconstructed the phylogenetic tree of Eurasian lynx and 10 other most closely related Felidae species. This lynx's complete mitogenome is 17 054bp in length, includes 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. The phylogenetic tree confirmed previous research results.}, }
@article {pmid26192946, year = {2015}, author = {Renaud, S and Dufour, AB and Hardouin, EA and Ledevin, R and Auffray, JC}, title = {Once upon Multivariate Analyses: When They Tell Several Stories about Biological Evolution.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0132801}, pmid = {26192946}, issn = {1932-6203}, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/classification ; Discriminant Analysis ; Genetic Variation ; Mice ; Mitochondria/genetics ; Molar/*anatomy &amp; histology ; Multivariate Analysis ; Phenotype ; Phylogeny ; Principal Component Analysis ; }, abstract = {Geometric morphometrics aims to characterize of the geometry of complex traits. It is therefore by essence multivariate. The most popular methods to investigate patterns of differentiation in this context are (1) the Principal Component Analysis (PCA), which is an eigenvalue decomposition of the total variance-covariance matrix among all specimens; (2) the Canonical Variate Analysis (CVA, a.k.a. linear discriminant analysis (LDA) for more than two groups), which aims at separating the groups by maximizing the between-group to within-group variance ratio; (3) the between-group PCA (bgPCA) which investigates patterns of between-group variation, without standardizing by the within-group variance. Standardizing within-group variance, as performed in the CVA, distorts the relationships among groups, an effect that is particularly strong if the variance is similarly oriented in a comparable way in all groups. Such shared direction of main morphological variance may occur and have a biological meaning, for instance corresponding to the most frequent standing genetic variation in a population. Here we undertake a case study of the evolution of house mouse molar shape across various islands, based on the real dataset and simulations. We investigated how patterns of main variance influence the depiction of among-group differentiation according to the interpretation of the PCA, bgPCA and CVA. Without arguing about a method performing 'better' than another, it rather emerges that working on the total or between-group variance (PCA and bgPCA) will tend to put the focus on the role of direction of main variance as line of least resistance to evolution. Standardizing by the within-group variance (CVA), by dampening the expression of this line of least resistance, has the potential to reveal other relevant patterns of differentiation that may otherwise be blurred.}, }
@article {pmid26190078, year = {2016}, author = {Zhang, Z and An, M and Deng, Y and Zhu, S}, title = {The complete mitochondrial genome of the Downy woodpecker, Picoides pubescens (Piciformes: Picidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3479-3480}, doi = {10.3109/19401736.2015.1066357}, pmid = {26190078}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Birds/*genetics ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The Downy woodpecker (Picoides pubescens) is a species of woodpecker which is the smallest in North America. This present study firstly reported the complete mitochondrial genome of downy woodpecker. We performed assembly of mitogenome structural by SPAdes and the Picidae species Dryocopus pileatus act as a reference. The mitogenome was 16 840 bp in length, which contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and 1 putative misc-feature region. The overall AT content is 52.76% which is higher than GC. To approve the accuracy of new determined mitogenome sequences, a phylogenetic tree of downy woodpecker together with other nine closely species was established by 12 protein-coding genes. This first complete mitogenome of Picoides species will contribute to identify species and study the related evolution events.}, }
@article {pmid26189992, year = {2015}, author = {Williams-Newkirk, AJ and Burroughs, M and Changayil, SS and Dasch, GA}, title = {The mitochondrial genome of the lone star tick (Amblyomma americanum).}, journal = {Ticks and tick-borne diseases}, volume = {6}, number = {6}, pages = {793-801}, doi = {10.1016/j.ttbdis.2015.07.006}, pmid = {26189992}, issn = {1877-9603}, support = {T32AI055404/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Female ; *Genome, Mitochondrial ; Phylogeny ; Polymorphism, Genetic ; Species Specificity ; Ticks/*genetics ; }, abstract = {Amblyomma americanum is an abundant tick in the southeastern, midwestern, and northeastern United States. It is a vector of multiple diseases, but limited genomic resources are available for it. We sequenced the complete mitochondrial genome of a single female A. americanum collected in Georgia using the Illumina platform. The consensus sequence was 14,709 bp long, and the mean coverage across the assembly was >12,000×. All expected tick genomic features were present, including two "Tick-Box" motifs, and in the expected order for the Metastriata. Heteroplasmy rates were low compared to the most closely related tick for which data are available, Amblyomma cajennense. The phylogeny derived from the concatenated protein coding and rRNA genes from the 33 available tick mitochondrial genomes was consistent with those previously proposed for the Acari. This is the first complete mitochondrial sequence for A. americanum, which provides a useful reference for future studies of A. americanum population genetics and tick phylogeny.}, }
@article {pmid26186306, year = {2016}, author = {Lu, WJ and Hu, WG and Wang, GP}, title = {Complete mitochondrial genome of Pseudoperonospora cubensis.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3487-3488}, doi = {10.3109/19401736.2015.1066361}, pmid = {26186306}, issn = {2470-1408}, mesh = {Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Oomycetes/*genetics ; Open Reading Frames ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Pseudoperonospora cubensis is a species of water mould known for causing downy mildew on cucurbits. 454 GS FLX Titanium sequencing data was used to obtain its complete mitochondrial genome (38 553 bp). The mitogenome contains 60 genes, including two ribosomal RNA, 25 transfer RNA, 15 ribosomal proteins, five open reading frames (ORFs). The rps3 and rpl16 overlapped each other by 14 bp. The gene order and composition of P. cubensis was similar to that of most other oomycetes, and its GC content was 22.4%. It is the first report of the complete mitochondrial genome in the genus Pseudoperonospora. Phylogeny analysis indicates that P. cubensis has a close genetic relationship with genus Phytophthora.}, }
@article {pmid26186304, year = {2016}, author = {Chhakchhuak, L and De Mandal, S and Gurusubramanian, G and Nachimuthu, SK}, title = {The near complete mitochondrial genome of the Giant honey bee, Apis dorsata (Hymenoptera: Apidae: Apinae) and its phylogenetic status.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3483-3484}, doi = {10.3109/19401736.2015.1066359}, pmid = {26186304}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Bees/*genetics ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {In this report, we sequenced and characterized the near complete mitochondrial genome of Apis dorsata collected from Mizoram, India. For sequencing of the complete mitochondrial genome, Illumina NextSeq500 platform was used. The near complete mitochondrial genome was assembled to be 15 076 bplong and contains the same gene order as the other honey bees. The assembly contains 13 protein coding genes, 21 transfer RNA, 2 ribosomal RNA and a partial control (A + T-rich) region estimated to be 75 bp. This is the first near complete sequenced mitochondrial genome from the giant honeybee A. dorsata which will benefit future genomics studies for understanding the phylogenetic relationship within the bee family.}, }
@article {pmid26184462, year = {2015}, author = {Stefano, GB and Snyder, C and Kream, RM}, title = {Mitochondria, Chloroplasts in Animal and Plant Cells: Significance of Conformational Matching.}, journal = {Medical science monitor : international medical journal of experimental and clinical research}, volume = {21}, number = {}, pages = {2073-2078}, pmid = {26184462}, issn = {1643-3750}, mesh = {Animals ; Chloroplasts/metabolism/*physiology ; Eukaryotic Cells/*ultrastructure ; Mitochondria/metabolism/*physiology ; Plant Cells/*ultrastructure ; Prokaryotic Cells/ultrastructure ; }, abstract = {Many commonalities between chloroplasts and mitochondria exist, thereby suggesting a common origin via a bacterial ancestor capable of enhanced ATP-dependent energy production functionally linked to cellular respiration and photosynthesis. Accordingly, the molecular evolution/retention of the catalytic Qo quinol oxidation site of cytochrome b complexes as the tetrapeptide PEWY sequence functionally underlies the common retention of a chemiosmotic proton gradient mechanism for ATP synthesis in cellular respiration and photosynthesis. Furthermore, the dual regulatory targeting of mitochondrial and chloroplast gene expression by mitochondrial transcription termination factor (MTERF) proteins to promote optimal energy production and oxygen consumption further advances these evolutionary contentions. As a functional consequence of enhanced oxygen utilization and production, significant levels of reactive oxygen species (ROS) may be generated within mitochondria and chloroplasts, which may effectively compromise cellular energy production following prolonged stress/inflammationary conditions. Interestingly, both types of organelles have been identified in selected animal cells, most notably specialized digestive cells lining the gut of several species of Sacoglossan sea slugs. Termed kleptoplasty or kleptoplastic endosymbiosis, functional chloroplasts from algal food sources are internalized and stored within digestive cells to provide the host with dual energy sources derived from mitochondrial and photosynthetic processes. Recently, the observation of internalized algae within embryonic tissues of the spotted salamander strongly suggest that developmental processes within a vertebrate organism may require photosynthetic endosymbiosis as an internal regulator. The dual presence of mitochondria and functional chloroplasts within specialized animal cells indicates a high degree of biochemical identity, stereoselectivity, and conformational matching that are the likely keys to their functional presence and essential endosymbiotic activities for over 2.5 billion years.}, }
@article {pmid26181210, year = {2016}, author = {Park, CE and Park, GS and Kwak, Y and Hong, SJ and Khan, AR and Jung, BK and Park, YJ and Kim, MC and Kim, KH and Park, HC and Lee, IJ and Shin, JH}, title = {Complete mitochondrial genome of the endemic species Korean aucha perch Coreoperca herzi (Teleostei, Centrarchiformes, Sinipercidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3493-3495}, doi = {10.3109/19401736.2015.1066364}, pmid = {26181210}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perches/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {In this study, we sequenced the complete mitochondrial genome of the endemic species Korean aucha perch Coreoperca herzi (Teleostei, Centrarchiformes, Sinipercidae). The mitogenome, consisting of 16 495 base pairs (bp), encoded 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and 2 non-coding region. The overall base composition of C. herzi is G + C: 46.3%, A + T: 53.7%, apparently with a slight AT bias. Phylogenetic analysis showed that the C. herzi was closed to Coreoperca kawamebari.}, }
@article {pmid26162048, year = {2016}, author = {Wu, Z and Wang, D and Hu, J and Wang, Q}, title = {Complete mitochondrial genome of the Scorpaenopsis cirrhosa (Scorpaeniformes: Scorpaenidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3449-3450}, doi = {10.3109/19401736.2015.1063136}, pmid = {26162048}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitochondrial genome of the Scorpaenopsis cirrhosa has been sequenced. The mitochondrial genome is 16 966 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region. The gene order and composition of S. cirrhosa mitochondrial genome was similar to that of most other vertebrates. The overall nucleotides base composition of the heavy strand is A (27.91%), G (17.71%), C (28.02%), and T (26.35%). With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The tRNA-Ser2 gene lacked DHC arm and could not fold into a typical clover-leaf secondary structure. Seen from the phylogenetic tree, S. cirrhosa, a stonefish and four rockfishes from the same order (Scorpaeniformes) clustered into one branch.}, }
@article {pmid26156582, year = {2015}, author = {Jelić, M and Arnqvist, G and Novičić, ZK and Kenig, B and Tanasković, M and Anđelković, M and Stamenković-Radak, M}, title = {Sex-specific effects of sympatric mitonuclear variation on fitness in Drosophila subobscura.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {135}, pmid = {26156582}, issn = {1471-2148}, support = {294333/ERC_/European Research Council/International ; }, mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; Drosophila/classification/*cytology/*genetics/physiology ; Female ; Linkage Disequilibrium ; Male ; Mitochondria/*genetics ; *Polymorphism, Genetic ; Sex Characteristics ; Sympatry ; }, abstract = {BACKGROUND: A number of recent studies have shown that the pattern of mitochondrial DNA variation and evolution is at odds with a neutral equilibrium model. Theory has suggested that selection on mitonuclear genotypes can act to maintain stable mitonuclear polymorphism within populations. However, this effect largely relies upon selection being either sex-specific or frequency dependent. Here, we use mitonuclear introgression lines to assess differences in a series of key life-history traits (egg-to-adult developmental time, viability, offspring sex-ratio, adult longevity and resistance to desiccation) in Drosophila subobscura fruit flies carrying one of three different sympatric mtDNA haplotypes.<br><br>RESULTS: We found functional differences between these sympatric mtDNA haplotypes, but these effects were contingent upon the nuclear genome with which they were co-expressed. Further, we demonstrate a significant mitonuclear genetic effect on adult sex ratio, as well as a sex&#x2009;&#xd7;&#x2009;mtDNA&#x2009;&#xd7;&#x2009;nuDNA interaction for adult longevity.<br><br>CONCLUSIONS: The observed effects suggest that sex specific mitonuclear selection contributes to the maintenance of mtDNA polymorphism and to mitonuclear linkage disequilibrium in this model system.}, }
@article {pmid26153741, year = {2016}, author = {Tsunashima, T and Yamada, R and Abe, K and Noguchi, S and Itoi, S and Nakai, S and Takai, N and Sugita, H}, title = {Phylogenetic position of Scombropidae within teleostei: the complete mitochondrial genome of the gnomefish, Scombrops gilberti.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3446-3448}, doi = {10.3109/19401736.2015.1063135}, pmid = {26153741}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Ribosomal/genetics ; Fishes/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitochondrial genome of the Japanese gnomefish, Scombrops gilberti, was determined using a PCR-based method. The total length of mitochondrial DNA (mtDNA) is 16 518 bp, which includes 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and one control region. The mitochondrial gene arrangement of S. gilberti was found to be identical to that of other scombropid and indeed, other teleosts as well. Maximum likelihood analysis revealed that Scombropidae forms a sister group to Pempheriformes.}, }
@article {pmid26153738, year = {2016}, author = {Park, CE and Park, GS and Kwak, Y and Hong, SJ and Khan, AR and Jung, BK and Park, YJ and Kim, JG and Park, HC and Shin, JH}, title = {Complete mitochondrial genome of Cygnus olor (Aves, Anseriformes, Anatidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3442-3443}, doi = {10.3109/19401736.2015.1063133}, pmid = {26153738}, issn = {2470-1408}, mesh = {Animals ; Anseriformes/*genetics ; Base Composition ; DNA, Ribosomal/genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitochondrial genome of Cygnus olor (Aves, Anseriformes, Anatidae) was revealed in this study. Total 16 739 base pairs (bp) of this mitogenome encoded genes for 13 protein coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and a D-loop (control region). The 12S rRNA and 16S rRNA genes are located between tRNA-Phe and tRNA-Leu (UUR) and segmentalized by the tRNA-Val. D-loop is located between tRNA-Glu and tRNA-Phe. The overall base composition of C. olor is G + C: 47.8%, A + T: 52.2%, apparently with a slight AT bias. Following the phylogenetic analysis, the C. olor was closed to Anser cygnoides.}, }
@article {pmid26152724, year = {2015}, author = {Tattikota, SG and Rathjen, T and Hausser, J and Khedkar, A and Kabra, UD and Pandey, V and Sury, M and Wessels, HH and Mollet, IG and Eliasson, L and Selbach, M and Zinzen, RP and Zavolan, M and Kadener, S and Tschöp, MH and Jastroch, M and Friedländer, MR and Poy, MN}, title = {miR-184 Regulates Pancreatic β-Cell Function According to Glucose Metabolism.}, journal = {The Journal of biological chemistry}, volume = {290}, number = {33}, pages = {20284-20294}, pmid = {26152724}, issn = {1083-351X}, support = {260744/ERC_/European Research Council/International ; }, mesh = {Animals ; Argonaute Proteins/metabolism ; Cell Line ; Glucose/*metabolism ; Homeostasis/physiology ; Islets of Langerhans/metabolism/*physiology ; Mice ; MicroRNAs/genetics/*physiology ; Mitochondria/metabolism ; }, abstract = {In response to fasting or hyperglycemia, the pancreatic β-cell alters its output of secreted insulin; however, the pathways governing this adaptive response are not entirely established. Although the precise role of microRNAs (miRNAs) is also unclear, a recurring theme emphasizes their function in cellular stress responses. We recently showed that miR-184, an abundant miRNA in the β-cell, regulates compensatory proliferation and secretion during insulin resistance. Consistent with previous studies showing miR-184 suppresses insulin release, expression of this miRNA was increased in islets after fasting, demonstrating an active role in the β-cell as glucose levels lower and the insulin demand ceases. Additionally, miR-184 was negatively regulated upon the administration of a sucrose-rich diet in Drosophila, demonstrating strong conservation of this pathway through evolution. Furthermore, miR-184 and its target Argonaute2 remained inversely correlated as concentrations of extracellular glucose increased, underlining a functional relationship between this miRNA and its targets. Lastly, restoration of Argonaute2 in the presence of miR-184 rescued suppression of miR-375-targeted genes, suggesting these genes act in a coordinated manner during changes in the metabolic context. Together, these results highlight the adaptive role of miR-184 according to glucose metabolism and suggest the regulatory role of this miRNA in energy homeostasis is highly conserved.}, }
@article {pmid26148004, year = {2015}, author = {Takeuchi, F and Sekizuka, T and Ogasawara, Y and Yokoyama, H and Kamikawa, R and Inagaki, Y and Nozaki, T and Sugita-Konishi, Y and Ohnishi, T and Kuroda, M}, title = {The Mitochondrial Genomes of a Myxozoan Genus Kudoa Are Extremely Divergent in Metazoa.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0132030}, pmid = {26148004}, issn = {1932-6203}, mesh = {Animals ; *Base Sequence ; *Genome, Mitochondrial ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Myxozoa/*classification/*genetics ; }, abstract = {The Myxozoa are oligo-cellular parasites with alternate hosts--fish and annelid worms--and some myxozoan species harm farmed fish. The phylum Myxozoa, comprising 2,100 species, was difficult to position in the tree of life, due to its fast evolutionary rate. Recent phylogenomic studies utilizing an extensive number of nuclear-encoded genes have confirmed that Myxozoans belong to Cnidaria. Nevertheless, the evolution of parasitism and extreme body simplification in Myxozoa is not well understood, and no myxozoan mitochondrial DNA sequence has been reported to date. To further elucidate the evolution of Myxozoa, we sequenced the mitochondrial genomes of the myxozoan species Kudoa septempunctata, K. hexapunctata and K. iwatai and compared them with those of other metazoans. The Kudoa mitochondrial genomes code for ribosomal RNAs, transfer RNAs, eight proteins for oxidative phosphorylation and three proteins of unknown function, and they are among the metazoan mitochondrial genomes coding the fewest proteins. The mitochondrial-encoded proteins were extremely divergent, exhibiting the fastest evolutionary rate in Metazoa. Nevertheless, the dN/dS ratios of the protein genes in genus Kudoa were approximately 0.1 and similar to other cnidarians, indicating that the genes are under negative selection. Despite the divergent genetic content, active oxidative phosphorylation was indicated by the transcriptome, metabolism and structure of mitochondria in K. septempunctata. As possible causes, we attributed the divergence to the population genetic characteristics shared between the two most divergent clades, Ctenophora and Myxozoa, and to the parasitic lifestyle of Myxozoa. The fast-evolving, functional mitochondria of the genus Kudoa expanded our understanding of metazoan mitochondrial evolution.}, }
@article {pmid26147677, year = {2015}, author = {Nakajima, Y and Shinzato, C and Satoh, N and Mitarai, S}, title = {Novel Polymorphic Microsatellite Markers Reveal Genetic Differentiation between Two Sympatric Types of Galaxea fascicularis.}, journal = {PloS one}, volume = {10}, number = {7}, pages = {e0130176}, pmid = {26147677}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*genetics ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Genetic Drift ; Genetic Markers/*genetics ; Genetic Variation/*genetics ; Genotype ; High-Throughput Nucleotide Sequencing/methods ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Mutation/genetics ; RNA, Untranslated/genetics ; Sequence Analysis, DNA/methods ; Sympatry/*genetics ; }, abstract = {The reef-building, scleractinian coral, Galaxea fascicularis, is classified into soft and hard types, based on nematocyst morphology. This character is correlated with the length of the mitochondrial non-coding region (mt-Long: soft colony type, and nematocysts with wide capsules and long shafts; mt-Short: hard colony type, and nematocysts with thin capsules and short shafts). We isolated and characterized novel polymorphic microsatellite markers for G. fascicularis using next-generation sequencing. Based upon the mitochondrial non-coding region, 53 of the 97 colonies collected were mt-Long (mt-L) and 44 were mt-Short (mt-S). Among the 53 mt-L colonies, 27 loci were identified as amplifiable, polymorphic microsatellite loci, devoid of somatic mutations and free of scoring errors. Eleven of those 27 loci were also amplifiable and polymorphic in the 44 mt-S colonies; these 11 are cross-type microsatellite loci. The other 16 loci were considered useful only for mt-L colonies. These 27 loci identified 10 multilocus lineages (MLLs) among the 53 mt-L colonies (NMLL/N = 0.189), and the 11 cross-type loci identified 7 MLLs in 44 mt-S colonies (NMLL/N = 0.159). Significant genetic differentiation between the two types was detected based on the genetic differentiation index (FST = 0.080, P = 0.001). Bayesian clustering also indicated that these two types are genetically isolated. While nuclear microsatellite genotypes also showed genetic differentiation between mitochondrial types, the mechanism of divergence is not yet clear. These markers will be useful to estimate genetic diversity, differentiation, and connectivity among populations, and to understand evolutionary processes, including divergence of types in G. fascicularis.}, }
@article {pmid26142878, year = {2016}, author = {Juhász, Z and Fehér, T and Németh, E and Pamjav, H}, title = {mtDNA analysis of 174 Eurasian populations using a new iterative rank correlation method.}, journal = {Molecular genetics and genomics : MGG}, volume = {291}, number = {1}, pages = {493-509}, pmid = {26142878}, issn = {1617-4623}, mesh = {DNA, Mitochondrial/*genetics ; Ethnicity/genetics ; Genetics, Population/methods ; Haplotypes/genetics ; Humans ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {In this study, we analyse 27-dimensional mtDNA haplogroup distributions of 174 Eurasian, North-African and American populations, including numerous ancient data as well. The main contribution of this work was the description of the haplogroup distribution of recent and ancient populations as compounds of certain hypothetic ancient core populations immediately or indirectly determining the migration processes in Eurasia for a long time. To identify these core populations, we developed a new iterative algorithm determining clusters of the 27 mtDNA haplogroups studied having strong rank correlation among each other within a definite subset of the populations. Based on this study, the current Eurasian populations can be considered as compounds of three early core populations regarding to maternal lineages. We wanted to show that a simultaneous analysis of ancient and recent data using a new iterative rank correlation algorithm and the weighted SOC learning technique may reveal the most important and deterministic migration processes in the past. This technique allowed us to determine geographically, historically and linguistically well-interpretable clusters of our dataset having a very specific, hardly classifiable structure. The method was validated using a 2-dimensional stepping stone model.}, }
@article {pmid26139575, year = {2015}, author = {Xu, J and Zhang, L and Yang, DL and Li, Q and He, Z}, title = {Thymidine kinases share a conserved function for nucleotide salvage and play an essential role in Arabidopsis thaliana growth and development.}, journal = {The New phytologist}, volume = {208}, number = {4}, pages = {1089-1103}, doi = {10.1111/nph.13530}, pmid = {26139575}, issn = {1469-8137}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/growth &amp; development/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Cytosol/metabolism ; Escherichia coli ; *Genes, Plant ; Humans ; Mitochondria/metabolism ; Molecular Sequence Data ; Mutation ; Nucleotides/*metabolism ; Oryza/genetics ; *Phylogeny ; Plant Development/*genetics ; Pyrimidine Nucleosides/metabolism ; Sequence Alignment ; Thymidine Kinase/*genetics/metabolism ; }, abstract = {Thymidine kinases (TKs) are important components in the nucleotide salvage pathway. However, knowledge about plant TKs is quite limited. In this study, the molecular function of TKs in Arabidopsis thaliana was investigated. Two TKs were identified and named AtTK1 and AtTK2. Expression of both genes was ubiquitous, but AtTK1 was strongly expressed in high-proliferation tissues. AtTK1 was localized to the cytosol, whereas AtTK2 was localized to the mitochondria. Mutant analysis indicated that the two genes function coordinately to sustain normal plant development. Enzymatic assays showed that the two TK proteins shared similar catalytic specificity for pyrimidine nucleosides. They were able to complement an Escherichia coli strain lacking TK activity. 5'-Fluorodeoxyuridine (FdU) resistance and 5-ethynyl 2'-deoxyuridine (EdU) incorporation assays confirmed their activity in vivo. Furthermore, the tk mutant phenotype could be alleviated by nucleotide feeding, establishing that the biosynthesis of pyrimidine nucleotides was disrupted by the TK deficiency. Finally, both human and rice (Oryza sativa) TKs were able to rescue the tk mutants, demonstrating the functional conservation of TKs across organisms. Taken together, our findings clarify the specialized function of two TKs in A. thaliana and establish that the salvage pathway mediated by the kinases is essential for plant growth and development.}, }
@article {pmid26138253, year = {2015}, author = {Consuegra, S and John, E and Verspoor, E and de Leaniz, CG}, title = {Patterns of natural selection acting on the mitochondrial genome of a locally adapted fish species.}, journal = {Genetics, selection, evolution : GSE}, volume = {47}, number = {1}, pages = {58}, pmid = {26138253}, issn = {1297-9686}, mesh = {Animals ; Animals, Domestic/genetics ; Evolution, Molecular ; Fish Proteins/genetics ; *Genome, Mitochondrial ; Mitochondria/genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; Salmo salar/*genetics/metabolism ; *Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Mitochondrial DNA (mtDNA) is frequently used in population genetic studies and is usually considered as a neutral marker. However, given the functional importance of the proteins encoded by the mitochondrial genome, and the prominent role of mitochondria in cellular energy production, the assumption of neutrality is increasingly being questioned.<br><br>RESULTS: We tested for evidence of selection on the mitochondrial genome of the Atlantic salmon, which is a locally adapted and widely farmed species and is distributed across a large latitudinal cline. We analysed 20 independent regions of the salmon mtDNA that represented nine genes (ND1, ND2, ND3, COX1, COX2, ATP6, ND4, ND5, and CYTB). These 20 mtDNA regions were sequenced using a 454 approach from samples collected across the entire European range of this species. We found evidence of positive selection at the ND1, ND3 and ND4 genes, which is supported by at least two different codon-based methods and also by differences in the chemical properties of the amino acids involved. The geographical distribution of some of the mutations indicated to be under selection was not random, and some mutations were private to artic populations. We discuss the possibility that selection acting on the Atlantic salmon mtDNA genome might be related to the need for increased metabolic efficiency at low temperatures.<br><br>CONCLUSIONS: The analysis of sequences representing nine mitochondrial genes that are involved in the OXPHOS pathway revealed signatures of positive selection in the mitochondrial genome of the Atlantic salmon. The properties of the amino acids involved suggest that some of the mutations that were identified to be under positive selection might have functional implications, possibly in relation to metabolic efficiency. Experimental evidence, and better understanding of regional phylogeographic structuring, are needed to clarify the potential role of selection acting on the mitochondrial genome of Atlantic salmon and other locally adapted fishes.}, }
@article {pmid26135515, year = {2015}, author = {Zhou, G and Song, Z and Yin, Y and Jiang, W and Wang, Z}, title = {Involvement of an alternative oxidase in the regulation of hyphal growth and microsclerotial formation in Nomuraea rileyi CQNr01.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {31}, number = {9}, pages = {1343-1352}, pmid = {26135515}, issn = {1573-0972}, mesh = {Cloning, Molecular ; Fungal Proteins/genetics/metabolism ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Fungal ; Hyphae/enzymology/genetics/*growth &amp; development ; Hypocreales/enzymology/genetics/*growth &amp; development ; Oxidoreductases/*genetics/*metabolism ; Phylogeny ; }, abstract = {Mitochondria of Nomuraea rileyi contain an alternative oxidase (Aox), which reduces oxygen to water by accepting electrons directly from ubiquinol. Furthermore, through a transcriptional analysis, we found that an alternative oxidase (Nraox) was up-regulated during microsclerotial formation. To study the function of NrAox, Nraox was cloned from N. rileyi CQNr01. The full-length cDNA was 1266 bp with an open reading frame of 1068 bp encoding 355 amino acids. A phylogenetic analysis revealed that the NrAox of N. rileyi was closely related to Metarhizium acridum Aox. The relative expression level of the Nraox was up-regulated during microsclerotial (MS) initiation. A salicylhydroxamic acid, a specific alternative oxidase inhibitor, application to the culture media severely decreased MS yields, changed the hyphae morphology and slowed the H2O2 removal. Nraox silencing caused mycelial deformations, reduced the MS yields by 97.3 % and increased MS size compared with those of the control. MS virulence was decreased to 26.2 % after Nraox was silenced. However, the Nraox-silenced strain was sensitive to environmental stress, and the growth rate was reduced under stress conditions. The results obtained suggested that Nraox is required for MS differentiation by regulating the intracellular H2O2 concentration and hypha growth. Additionally, Nraox had a great impact on the virulence of N. rileyi.}, }
@article {pmid26134044, year = {2015}, author = {Li, W and Wen, C and Li, W and Wang, H and Guan, X and Zhang, W and Ye, W and Lu, J}, title = {The tRNA(Gly) T10003C mutation in mitochondrial haplogroup M11b in a Chinese family with diabetes decreases the steady-state level of tRNA(Gly), increases aberrant reactive oxygen species production, and reduces mitochondrial membrane potential.}, journal = {Molecular and cellular biochemistry}, volume = {408}, number = {1-2}, pages = {171-179}, pmid = {26134044}, issn = {1573-4919}, mesh = {Aged ; Asian People/ethnology/*genetics ; China/ethnology ; Diabetes Mellitus, Type 2/ethnology/*genetics ; Female ; Genetic Predisposition to Disease ; Genome, Mitochondrial ; Haplotypes ; Humans ; Male ; Membrane Potential, Mitochondrial ; Middle Aged ; Mitochondria/*genetics ; Mitochondrial Diseases/*genetics ; *Mutation ; Oxygen Consumption ; Pedigree ; Phylogeny ; RNA, Transfer, Gly/*genetics ; Reactive Oxygen Species/metabolism ; }, abstract = {Mitochondrial diabetes originates mainly from mutations located in maternally transmitted, mitochondrial tRNA-coding genes. In a genetic screening program of type 2 diabetes conducted with a Chinese Han population, we found one family with suggestive maternally transmitted diabetes. The proband's mitochondrial genome was analyzed using DNA sequencing. Total 42 known nucleoside changes and 1 novel variant were identified, and the entire mitochondrial DNA sequence was assigned to haplogroup M11b. Phylogenetic analysis showed that a homoplasmic mutation, 10003T>C transition, occurred at the highly conserved site in the gene encoding tRNA(Gly). Using a transmitochondrial cybrid cell line harboring this mutation, we observed that the steady-state level of tRNA(Gly) significantly affected and the amount of tRNA(Gly) decreased by 97%, production of reactive oxygen species was enhanced, and mitochondrial membrane potential, mtDNA copy number and cellular oxygen consumption rate were remarkably decreased compared with wild-type cybrid cells. The homoplasmic 10003T>C mutation in the mitochondrial tRNA(Gly) gene suggested to be as a pathogenesis-related mutation which might contribute to the maternal inherited diabetes in the Han Chinese family.}, }
@article {pmid26122344, year = {2016}, author = {Hwang, JY and Jin, GD and Park, J and Kim, H and Lee, CK and Kwak, W and Nam, BH and An, CM and Park, JY and Park, KH and Huh, CS and Kim, EB}, title = {Complete genome sequence and SNPs of Raja pulchra (Rajiformes, Rajidae) mitochondria.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {4}, pages = {2975-2977}, doi = {10.3109/19401736.2015.1060467}, pmid = {26122344}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Fishes/*classification/*genetics ; Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; Open Reading Frames ; Phylogeny ; *Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; *Whole Genome Sequencing ; }, abstract = {Mitochondrial genomes were sequenced from five Raja pulchra individuals, and single-nucleotide polymorphisms (SNPs) were identified by comparing previously announced sequences in this study. Total 117 SNPs were detected and they were present in 2 rRNA genes, 9 tRNA genes, 13 protein coding genes and non-coding region. One deleted polymorphic site, which was located in 16S rRNA gene, was observed in two individuals. Six polymorphic sites were non-synonymous SNPs, which were distributed in ND1, ND2, ATP6 and ND4 gene. Phylogenic analysis validated current taxa. The genome sequences of R. pulchra mitochondria could be comparable information for understanding species divergence and genomic variation among the populations.}, }
@article {pmid26121931, year = {2016}, author = {Mishra, RC and Grover, A}, title = {ClpB/Hsp100 proteins and heat stress tolerance in plants.}, journal = {Critical reviews in biotechnology}, volume = {36}, number = {5}, pages = {862-874}, doi = {10.3109/07388551.2015.1051942}, pmid = {26121931}, issn = {1549-7801}, mesh = {Endopeptidase Clp/*genetics ; Global Warming ; Heat-Shock Proteins/*genetics ; Molecular Chaperones ; Mutation ; Phylogeny ; Plants, Genetically Modified/*genetics ; Stress, Physiological/genetics ; Thermotolerance/*genetics ; }, abstract = {High-temperature stress can disrupt cellular proteostasis, resulting in the accumulation of insoluble protein aggregates. For survival under stressful conditions, it is important for cells to maintain a pool of native soluble proteins by preventing and/or dissociating these aggregates. Chaperones such as GroEL/GroES (Hsp60/Hsp10) and DnaK/DnaJ/GrpE (Hsp70/Hsp40/nucleotide exchange factor) help cells minimize protein aggregation. Protein disaggregation is accomplished by chaperones belonging to the Caseinolytic Protease (Clp) family of proteins. ClpB/Hsp100 proteins are strikingly ubiquitous and are found in bacteria, yeast and multi-cellular plants. The expression of these proteins is regulated by heat stress (HS) and developmental cues. Bacteria and yeast contain one and two forms of ClpB proteins, respectively. Plants possess multiple forms of these proteins that are localized to different cellular compartments (i.e. cytoplasm/nucleus, chloroplast or mitochondria). Overwhelming evidence suggests that ClpB/Hsp100 proteins play decisive roles in cell adaptation to HS. Mutant bacteria and yeast cells lacking active ClpB/Hsp100 proteins are critically sensitive to high-temperature stress. Likewise, Arabidopsis, maize and rice mutants lacking cytoplasmic ClpB proteins are very sensitive to heat. In this study, we present the structural and functional attributes of plant ClpB forms.}, }
@article {pmid26119842, year = {2016}, author = {Chen, K and Sun, L and Zong, L and Wu, X and Zhan, Y and Dong, C and Cao, H and Tang, H and Jiang, H}, title = {GJB2 and mitochondrial 12S rRNA susceptibility mutations in sudden deafness.}, journal = {European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery}, volume = {273}, number = {6}, pages = {1393-1398}, pmid = {26119842}, issn = {1434-4726}, mesh = {Adult ; Case-Control Studies ; Connexin 26 ; Connexins/*genetics ; DNA Mutational Analysis/methods ; Deafness/genetics ; Female ; Gene Frequency ; Genes, Mitochondrial ; *Genetic Predisposition to Disease ; Hearing Loss, Sudden/*genetics ; Heterozygote ; Homozygote ; Humans ; Male ; Middle Aged ; Mitochondria/*genetics ; *Mutation ; Phylogeny ; Polymorphism, Genetic ; *RNA, Ribosomal ; }, abstract = {Genetic susceptibility may play an important role in the pathogenesis of sudden deafness. However, the specific genes involved are largely unknown. We sought to explore the frequency of GJB2 and mitochondrial 12S rRNA susceptibility mutations in patients with sudden deafness. Between September 2011 and May 2012, 62 consecutive patients with sudden deafness were seen. In 50 of these, no etiological factors for sudden deafness were found. We detected GJB2 and mitochondrial 12S rRNA variants by direct sequencing in these 50 patients and in 53-aged matched controls with normal hearing. In addition, we undertook functional analyses of the mitochondrial mutations which we detected, applying structural and phylogenetic analysis. GJB2 sequencing identified six mutations, including three pathogenic mutations (c.235delC, c.299-300delAT, c.109G>A) and three polymorphisms, in the study participants, giving an allele frequency of 15.0 %. A homozygous c.109G>A mutation was detected in two participants. A total of 16 variants in mitochondrial 12S rRNA gene were identified in the participants. No significant differences were found in GJB2 heterozygosity or in mitochondrial 12S rRNA variants between patients with sudden deafness and in controls. Our results suggest that the homozygous GJB2 c.109G>A mutation may be a cause of sudden deafness involving both ears. This finding should increase awareness of the likely role of genetic factors in the etiology of sudden deafness in general.}, }
@article {pmid26118639, year = {2015}, author = {Good, JM and Vanderpool, D and Keeble, S and Bi, K}, title = {Negligible nuclear introgression despite complete mitochondrial capture between two species of chipmunks.}, journal = {Evolution; international journal of organic evolution}, volume = {69}, number = {8}, pages = {1961-1972}, doi = {10.1111/evo.12712}, pmid = {26118639}, issn = {1558-5646}, support = {S10RR027303/RR/NCRR NIH HHS/United States ; S10RR029668/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Cell Nucleus/genetics ; Exons ; *Gene Flow ; Genetics, Population ; Genome, Mitochondrial ; *Hybridization, Genetic ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; Sciuridae/*genetics ; Sequence Analysis, DNA ; *Transcriptome ; }, abstract = {The idea that species boundaries can be semipermeable to gene flow is now widely accepted but the evolutionary importance of introgressive hybridization remains unclear. Here we examine the genomic contribution of gene flow between two hybridizing chipmunk species, Tamias ruficaudus and T. amoenus. Previous studies have shown that ancient hybridization has resulted in complete fixation of introgressed T. ruficaudus mitochondrial DNA (mtDNA) in some populations of T. amoenus, but the extent of nuclear introgression is not known. We used targeted capture to sequence over 10,500 gene regions from multiple individuals of both species. We found that most of the nuclear genome is sorted between these species and that overall genealogical patterns do not show evidence for introgression. Our analysis rules out all but very minor levels of interspecific gene flow, indicating that introgressive hybridization has had little impact on the overall genetic composition of these species outside of the mitochondrial genome. Given that much of the evidence for introgression in animals has come from mtDNA, our results underscore that unraveling the importance introgressive hybridization during animal speciation will require a genome-wide perspective that is still absent for many species.}, }
@article {pmid26116918, year = {2015}, author = {Pett, W and Lavrov, DV}, title = {Cytonuclear Interactions in the Evolution of Animal Mitochondrial tRNA Metabolism.}, journal = {Genome biology and evolution}, volume = {7}, number = {8}, pages = {2089-2101}, pmid = {26116918}, issn = {1759-6653}, mesh = {Amino Acyl-tRNA Synthetases/*genetics ; Animals ; Cell Nucleus/genetics ; Ctenophora/genetics ; *Evolution, Molecular ; Mitochondria/enzymology/genetics ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA/*genetics/metabolism ; RNA, Mitochondrial ; RNA, Transfer/*genetics/metabolism ; Ribonuclease P/genetics ; }, abstract = {The evolution of mitochondrial information processing pathways, including replication, transcription and translation, is characterized by the gradual replacement of mitochondrial-encoded proteins with nuclear-encoded counterparts of diverse evolutionary origins. Although the ancestral enzymes involved in mitochondrial transcription and replication have been replaced early in eukaryotic evolution, mitochondrial translation is still carried out by an apparatus largely inherited from the α-proteobacterial ancestor. However, variation in the complement of mitochondrial-encoded molecules involved in translation, including transfer RNAs (tRNAs), provides evidence for the ongoing evolution of mitochondrial protein synthesis. Here, we investigate the evolution of the mitochondrial translational machinery using recent genomic and transcriptomic data from animals that have experienced the loss of mt-tRNAs, including phyla Cnidaria and Ctenophora, as well as some representatives of all four classes of Porifera. We focus on four sets of mitochondrial enzymes that directly interact with tRNAs: Aminoacyl-tRNA synthetases, glutamyl-tRNA amidotransferase, tRNA(Ile) lysidine synthetase, and RNase P. Our results support the observation that the fate of nuclear-encoded mitochondrial proteins is influenced by the evolution of molecules encoded in mitochondrial DNA, but in a more complex manner than appreciated previously. The data also suggest that relaxed selection on mitochondrial translation rather than coevolution between mitochondrial and nuclear subunits is responsible for elevated rates of evolution in mitochondrial translational proteins.}, }
@article {pmid26116422, year = {2015}, author = {Mazzoleni, M and Figuet, S and Martin-Laffon, J and Mininno, M and Gilgen, A and Leroux, M and Brugière, S and Tardif, M and Alban, C and Ravanel, S}, title = {Dual Targeting of the Protein Methyltransferase PrmA Contributes to Both Chloroplastic and Mitochondrial Ribosomal Protein L11 Methylation in Arabidopsis.}, journal = {Plant &amp; cell physiology}, volume = {56}, number = {9}, pages = {1697-1710}, doi = {10.1093/pcp/pcv098}, pmid = {26116422}, issn = {1471-9053}, mesh = {Amino Acid Sequence ; Arabidopsis/*enzymology ; Arabidopsis Proteins/*metabolism ; Chloroplasts/*enzymology ; Genetic Complementation Test ; Germination ; Methylation ; Methyltransferases/*metabolism ; Mitochondria/*enzymology ; Mitochondrial Proteins/metabolism ; Molecular Sequence Data ; Mutation/genetics ; Peptides/chemistry/metabolism ; Photosynthesis ; Phylogeny ; Protein Biosynthesis ; Protein Transport ; Ribosomal Proteins/*metabolism ; Subcellular Fractions/metabolism ; }, abstract = {Methylation of ribosomal proteins has long been described in prokaryotes and eukaryotes, but our knowledge about the enzymes responsible for these modifications in plants is scarce. The bacterial protein methyltransferase PrmA catalyzes the trimethylation of ribosomal protein L11 (RPL11) at three distinct sites. The role of these modifications is still unknown. Here, we show that PrmA from Arabidopsis thaliana (AtPrmA) is dually targeted to chloroplasts and mitochondria. Mass spectrometry and enzymatic assays indicated that the enzyme methylates RPL11 in plasto- and mitoribosomes in vivo. We determined that the Arabidopsis and Escherichia coli PrmA enzymes share similar product specificity, making trimethylated residues, but, despite an evolutionary relationship, display a difference in substrate site specificity. In contrast to the bacterial enzyme that trimethylates the ε-amino group of two lysine residues and the N-terminal α-amino group, AtPrmA methylates only one lysine in the MAFCK(D/E)(F/Y)NA motif of plastidial and mitochondrial RPL11. The plant enzyme possibly methylates the N-terminus of plastidial RPL11, whereas mitochondrial RPL11 is N-α-acetylated by an unknown acetyltransferase. Lastly, we found that an Arabidopsis prma-null mutant is viable in standard environmental conditions and no molecular defect could be associated with a lack of RPL11 methylation in leaf chloroplasts or mitochondria. However, the conservation of PrmA during the evolution of photosynthetic eukaryotes together with the location of methylated residues at the binding site of translation factors to ribosomes suggests that RPL11 methylation in plant organelles could be involved, in combination with other post-translational modifications, in optimizing ribosome function.}, }
@article {pmid26110316, year = {2015}, author = {Arakawa, H and Iliakis, G}, title = {Alternative Okazaki Fragment Ligation Pathway by DNA Ligase III.}, journal = {Genes}, volume = {6}, number = {2}, pages = {385-398}, pmid = {26110316}, issn = {2073-4425}, abstract = {Higher eukaryotes have three types of DNA ligases: DNA ligase 1 (Lig1), DNA ligase 3 (Lig3) and DNA ligase 4 (Lig4). While Lig1 and Lig4 are present in all eukaryotes from yeast to human, Lig3 appears sporadically in evolution and is uniformly present only in vertebrates. In the classical, textbook view, Lig1 catalyzes Okazaki-fragment ligation at the DNA replication fork and the ligation steps of long-patch base-excision repair (BER), homologous recombination repair (HRR) and nucleotide excision repair (NER). Lig4 is responsible for DNA ligation at DNA double strand breaks (DSBs) by the classical, DNA-PKcs-dependent pathway of non-homologous end joining (C-NHEJ). Lig3 is implicated in a short-patch base excision repair (BER) pathway, in single strand break repair in the nucleus, and in all ligation requirements of the DNA metabolism in mitochondria. In this scenario, Lig1 and Lig4 feature as the major DNA ligases serving the most essential ligation needs of the cell, while Lig3 serves in the cell nucleus only minor repair roles. Notably, recent systematic studies in the chicken B cell line, DT40, involving constitutive and conditional knockouts of all three DNA ligases individually, as well as of combinations thereof, demonstrate that the current view must be revised. Results demonstrate that Lig1 deficient cells proliferate efficiently. Even Lig1/Lig4 double knockout cells show long-term viability and proliferate actively, demonstrating that, at least in DT40, Lig3 can perform all ligation reactions of the cellular DNA metabolism as sole DNA ligase. Indeed, in the absence of Lig1, Lig3 can efficiently support semi-conservative DNA replication via an alternative Okazaki-fragment ligation pathway. In addition, Lig3 can back up NHEJ in the absence of Lig4, and can support NER and HRR in the absence of Lig1. Supporting observations are available in less elaborate genetic models in mouse cells. Collectively, these observations raise Lig3 from a niche-ligase to a universal DNA ligase, which can potentially substitute or backup the repair and replication functions of all other DNA ligases in the cell nucleus. Thus, the old model of functionally dedicated DNA ligases is now replaced by one in which only Lig4 remains dedicated to C-NHEJ, with Lig1 and Lig3 showing an astounding functional flexibility and interchangeability for practically all nuclear ligation functions. The underlying mechanisms of Lig3 versus Lig1 utilization in DNA repair and replication are expected to be partly different and remain to be elucidated.}, }
@article {pmid26107900, year = {2015}, author = {Gong, L and Shi, W and Si, LZ and Wang, ZM and Kong, XY}, title = {[The complete mitochondrial genome of peacock sole Pardachirus pavoninus (Pleuronectiformes: Soleidae) and comparative analysis of the control region among 13 soles].}, journal = {Molekuliarnaia biologiia}, volume = {49}, number = {3}, pages = {461-471}, doi = {10.7868/S0026898415030064}, pmid = {26107900}, issn = {0026-8984}, mesh = {Animals ; Base Sequence ; Chromosome Mapping ; Conserved Sequence ; Flatfishes/classification/*genetics ; *Genes, Mitochondrial ; Genes, rRNA ; *Genome, Mitochondrial ; *Locus Control Region ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Tandem Repeat Sequences ; }, abstract = {The complete mitogenome of the peacock sole Pardachirus pavoninus (Lacepède, 1802) was determined. The total length is 16 536 bp, containing 13 protein-coding genes, 22 tRNA genes and two rRNA genes, as well as one control region (CR). The L-strand replication origin (OL), which is typically located in the WANCY cluster, is lost in P. pavoninus. The gene arrangement is identical to that in most teleosts. Comparison of the CR sequences among 13 soles reveals that a 211-bp fragment at the 5'-end of the CR is lost in the P. pavoninus mitogenome, responsible for its short sequence with a length of 872 bp. All typical conservative blocks (TAS, CSB-F, E, D, C, B, A, CSB-1, 2, 3) are identified. Seven out of 13 soles contain tandem repeats in the CR and the possible mechanisms of their formation are discussed. These results may provide the consensus sequences of the conserved units in the sole CR as well as molecular data for phylogenetic studies on Soleidae and Pleuronectiformes.}, }
@article {pmid26107249, year = {2015}, author = {Cimmaruta, R and Lucente, D and Nascetti, G}, title = {Persistence, isolation and diversification of a naturally fragmented species in local refugia: the case of Hydromantes strinatii.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0131298}, pmid = {26107249}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; Cell Nucleus/metabolism ; Climate ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Ecosystem ; *Evolution, Molecular ; France ; Gene Frequency ; Genetic Drift ; Genetic Variation ; *Genetics, Population ; Geography ; Haplotypes ; Heterozygote ; Isoenzymes/chemistry ; Italy ; Linkage Disequilibrium ; Mediterranean Sea ; Mitochondria/metabolism ; NADH Dehydrogenase/genetics ; Phylogeny ; *Refugium ; Sequence Analysis, DNA ; Urodela/*genetics ; }, abstract = {The study of the European plethodontid salamander Hydromantes strinatii using allozyme and mitochondrial markers showed a strong geographical genetic structure. This was likely the outcome of different evolutionary mechanisms leaving their signature despite the effects of the genetic drift due to the low population size typical of this species. Two highly divergent clades were identified in the eastern and central-western part of the range, with further geographic sub-structure. Nuclear and mitochondrial markers substantially recovered the same population groups but were conflicting in reconstructing their relationships. This apparent incongruence highlighted the action of different mechanisms such as secondary contacts and incomplete lineage sorting in originating the observed genetic variation. The troglophilic habit of this species provided the opportunity to show the importance of caves as local refugia in maintaining the genetic diversity through the persistence of local populations. Accordingly, high nucleotide and haplotype diversity, strong geographic genetic structuring and lack of expansion were evidenced. This signature was found in the populations from the Ligurian and Maritime Alps, in agreement with the complex orography and paleoclimatic history of this Mediterranean hotspot.}, }
@article {pmid26105995, year = {2015}, author = {Zhang, H and Luo, M and Day, RC and Talbot, MJ and Ivanova, A and Ashton, AR and Chaudhury, AM and Macknight, RC and Hrmova, M and Koltunow, AM}, title = {Developmentally regulated HEART STOPPER, a mitochondrially targeted L18 ribosomal protein gene, is required for cell division, differentiation, and seed development in Arabidopsis.}, journal = {Journal of experimental botany}, volume = {66}, number = {19}, pages = {5867-5880}, pmid = {26105995}, issn = {1460-2431}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/growth &amp; development/metabolism ; Arabidopsis Proteins/chemistry/*genetics/metabolism ; Cell Differentiation ; Cell Division ; Gene Expression Regulation, Developmental ; *Gene Expression Regulation, Plant ; Mutation ; Phylogeny ; Ribosomal Proteins/chemistry/*genetics/metabolism ; Seeds/genetics/growth &amp; development/metabolism ; Sequence Alignment ; }, abstract = {Evidence is presented for the role of a mitochondrial ribosomal (mitoribosomal) L18 protein in cell division, differentiation, and seed development after the characterization of a recessive mutant, heart stopper (hes). The hes mutant produced uncellularized endosperm and embryos arrested at the late globular stage. The mutant embryos differentiated partially on rescue medium with some forming callus. HES (At1g08845) encodes a mitochondrially targeted member of a highly diverged L18 ribosomal protein family. The substitution of a conserved amino residue in the hes mutant potentially perturbs mitoribosomal function via altered binding of 5S rRNA and/or influences the stability of the 50S ribosomal subunit, affecting mRNA binding and translation. Consistent with this, marker genes for mitochondrial dysfunction were up-regulated in the mutant. The slow growth of the endosperm and embryo indicates a defect in cell cycle progression, which is evidenced by the down-regulation of cell cycle genes. The down-regulation of other genes such as EMBRYO DEFECTIVE genes links the mitochondria to the regulation of many aspects of seed development. HES expression is developmentally regulated, being preferentially expressed in tissues with active cell division and differentiation, including developing embryos and the root tips. The divergence of the L18 family, the tissue type restricted expression of HES, and the failure of other L18 members to complement the hes phenotype suggest that the L18 proteins are involved in modulating development. This is likely via heterogeneous mitoribosomes containing different L18 members, which may result in differential mitochondrial functions in response to different physiological situations during development.}, }
@article {pmid26103722, year = {2015}, author = {Chen, B and Lu, YR and Chen, YN and Kang, YJ and Cheng, JQ}, title = {[Endothelium Aging and Oxidative Stress].}, journal = {Sheng li ke xue jin zhan [Progress in physiology]}, volume = {46}, number = {1}, pages = {23-27}, pmid = {26103722}, issn = {0559-7765}, mesh = {Animals ; *Cellular Senescence ; Disease ; Endothelium, Vascular/metabolism/*physiopathology ; Humans ; Mitochondria/metabolism ; Nitric Oxide Synthase Type III/*metabolism ; Oxidation-Reduction ; *Oxidative Stress ; Reactive Oxygen Species/metabolism ; Signal Transduction ; }, abstract = {In the endothelium, ROS mainly derive from mitochondria, endothelial nitric oxide synthases and NADPH oxidases 4. Excessive ROS are a major cause of oxidative stress, the primary stimulus of vascular dysfunction and oxidative stress-related diseases. However, cellular evolution has made possible the development of adaptive antioxidant systems that scavenge excessive ROS, such as Nrf2/Keapl-ARE, PPAR-y, SIRT and FOXO, etc. Among them, the Nrf2/Keapl-ARE signaling pathway is perhaps the most prominent. What is more, there are the "crosstalk" among these antioxidant stress-related signaling pathways aim to alleviate oxidative stress injurys and promote cells survival. The understanding of the relationship between endothelial aging and oxidative stress may serve as a therapeutic clues in the treatment of oxidative stress-related diseases.}, }
@article {pmid26102479, year = {2015}, author = {Bundus, JD and Alaei, R and Cutter, AD}, title = {Gametic selection, developmental trajectories, and extrinsic heterogeneity in Haldane's rule.}, journal = {Evolution; international journal of organic evolution}, volume = {69}, number = {8}, pages = {2005-2017}, doi = {10.1111/evo.12708}, pmid = {26102479}, issn = {1558-5646}, mesh = {Animals ; Caenorhabditis/*embryology/*genetics/growth &amp; development ; Cell Nucleus/genetics ; Embryo, Nonmammalian ; *Hybridization, Genetic ; Infertility/genetics ; Male ; Mitochondria/genetics ; *Reproductive Isolation ; Sex Chromosomes ; Spermatozoa/physiology ; Temperature ; }, abstract = {Deciphering the genetic and developmental causes of the disproportionate rarity, inviability, and sterility of hybrid males, Haldane's rule, is important for understanding the evolution of reproductive isolation between species. Moreover, extrinsic and prezygotic factors can contribute to the magnitude of intrinsic isolation experienced between species with partial reproductive compatibility. Here, we use the nematodes Caenorhabditis briggsae and C. nigoni to quantify the sensitivity of hybrid male viability to extrinsic temperature and developmental timing, and test for a role of mito-nuclear incompatibility as a genetic cause. We demonstrate that hybrid male inviability manifests almost entirely as embryonic, not larval, arrest and is maximal at the lowest rearing temperatures, indicating an intrinsic-by-extrinsic interaction to hybrid inviability. Crosses using mitochondrial substitution strains that have reciprocally introgressed mitochondrial and nuclear genomes show that mito-nuclear incompatibility is not a dominant contributor to postzygotic isolation and does not drive Haldane's rule in this system. Crosses also reveal that competitive superiority of X-bearing sperm provides a novel means by which postmating prezygotic factors exacerbate the rarity of hybrid males. These findings highlight the important roles of gametic, developmental, and extrinsic factors in modulating the manifestation of Haldane's rule.}, }
@article {pmid26099175, year = {2015}, author = {Lill, R and Dutkiewicz, R and Freibert, SA and Heidenreich, T and Mascarenhas, J and Netz, DJ and Paul, VD and Pierik, AJ and Richter, N and Stümpfig, M and Srinivasan, V and Stehling, O and Mühlenhoff, U}, title = {The role of mitochondria and the CIA machinery in the maturation of cytosolic and nuclear iron-sulfur proteins.}, journal = {European journal of cell biology}, volume = {94}, number = {7-9}, pages = {280-291}, doi = {10.1016/j.ejcb.2015.05.002}, pmid = {26099175}, issn = {1618-1298}, mesh = {ATP-Binding Cassette Transporters/*metabolism ; Cell Nucleus/metabolism ; Cytosol/*metabolism ; Humans ; Iron-Sulfur Proteins/*metabolism ; Membrane Transport Proteins/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Protein Transport/physiology ; }, abstract = {Mitochondria have been derived from alpha-bacterial endosymbionts during the evolution of eukaryotes. Numerous bacterial functions have been maintained inside the organelles including fatty acid degradation, citric acid cycle, oxidative phosphorylation, and the synthesis of heme or lipoic acid cofactors. Additionally, mitochondria have inherited the bacterial iron-sulfur cluster assembly (ISC) machinery. Many of the ISC components are essential for cell viability because they generate a still unknown, sulfur-containing compound for the assembly of cytosolic and nuclear Fe/S proteins that perform important functions in, e.g., protein translation, DNA synthesis and repair, and chromosome segregation. The sulfur-containing compound is exported by the mitochondrial ABC transporter Atm1 (human ABCB7) and utilized by components of the cytosolic iron-sulfur protein assembly (CIA) machinery. An appealing minimal model for the striking compartmentation of eukaryotic Fe/S protein biogenesis is provided by organisms that contain mitosomes instead of mitochondria. Mitosomes have been derived from mitochondria by reductive evolution, during which they have lost virtually all classical mitochondrial tasks. Nevertheless, mitosomes harbor all core ISC components which presumably have been maintained for assisting the maturation of cytosolic-nuclear Fe/S proteins. The current review is centered around the Atm1 export process. We present an overview on the mitochondrial requirements for the export reaction, summarize recent insights into the 3D structure and potential mechanism of Atm1, and explain how the CIA machinery uses the mitochondrial export product for the assembly of cytosolic and nuclear Fe/S proteins.}, }
@article {pmid26093476, year = {2015}, author = {Lak, B and Yushin, VV and Slos, D and Claeys, M and Decraemer, W and Bert, W}, title = {High-pressure freezing and freeze-substitution fixation reveal the ultrastructure of immature and mature spermatozoa of the plant-parasitic nematode Trichodorus similis (Nematoda; Triplonchida; Trichodoridae).}, journal = {Micron (Oxford, England : 1993)}, volume = {77}, number = {}, pages = {25-31}, doi = {10.1016/j.micron.2015.05.012}, pmid = {26093476}, issn = {1878-4291}, mesh = {Animals ; Cell Nucleus/ultrastructure ; Freeze Substitution ; *Freezing ; Male ; Microscopy, Electron, Transmission ; Nematoda/*ultrastructure ; Nuclear Envelope/ultrastructure ; Plants/parasitology ; Pseudopodia/ultrastructure ; Sperm Maturation ; Spermatogenesis ; Spermatozoa/*ultrastructure ; }, abstract = {The spermatozoa from testis and spermatheca of the plant-parasitic nematode Trichodorus similis Seinhorst, 1963 (Nematoda; Triplonchida; Trichodoridae) were studied with transmission electron microscopy (TEM), being the first study on spermatogenesis of a representative of the order Triplonchida and important to unravel nematode sperm evolution. Comprehensive results could only be obtained using high-pressure freezing (HPF) and freeze-substitution instead of chemical fixation, demonstrating the importance of cryo-fixation for nematode ultrastructural research. The spermatozoa from the testis (immature spermatozoa) are unpolarized cells covered by numerous filopodia. They contain a centrally-located nucleus without a nuclear envelope, surrounded by mitochondria. Specific fibrous bodies (FB) as long parallel bundles of filaments occupy the peripheral cytoplasm. No structures resembling membranous organelles (MO), as found in the sperm of many other nematodes, were observed in immature spermatozoa of T. similis. The spermatozoa from the uterus (mature or activated spermatozoa) are bipolar cells with an anterior pseudopod and posterior main cell body (MCB), which include a nucleus, mitochondria and MO appearing as large vesicles with finger-like invaginations of the outer cell membrane, or as large vesicles connected to the inner cell membrane. The peripheral MO open to the exterior via pores. In the mature sperm, neither FBs nor filopodia were observed. An important feature of T. similis spermatozoa is the late formation of MO; they first appear in mature spermatozoa. This pattern of MO formation is known for several other orders of the nematode class Enoplea: Enoplida, Mermithida, Dioctophymatida, Trichinellida but has never been observed in the class Chromadorea.}, }
@article {pmid26085518, year = {2015}, author = {Lv, FH and Peng, WF and Yang, J and Zhao, YX and Li, WR and Liu, MJ and Ma, YH and Zhao, QJ and Yang, GL and Wang, F and Li, JQ and Liu, YG and Shen, ZQ and Zhao, SG and Hehua, E and Gorkhali, NA and Farhad Vahidi, SM and Muladno, M and Naqvi, AN and Tabell, J and Iso-Touru, T and Bruford, MW and Kantanen, J and Han, JL and Li, MH}, title = {Mitogenomic Meta-Analysis Identifies Two Phases of Migration in the History of Eastern Eurasian Sheep.}, journal = {Molecular biology and evolution}, volume = {32}, number = {10}, pages = {2515-2533}, pmid = {26085518}, issn = {1537-1719}, mesh = {Animal Migration/*physiology ; Animals ; Animals, Domestic/genetics ; DNA, Mitochondrial/genetics ; Female ; Genetic Variation ; *Genomics ; Geography ; Meta-Analysis as Topic ; Mitochondria/*genetics ; Models, Genetic ; Phylogeny ; Selection, Genetic ; Sheep/*genetics ; Time Factors ; }, abstract = {Despite much attention, history of sheep (Ovis aries) evolution, including its dating, demographic trajectory and geographic spread, remains controversial. To address these questions, we generated 45 complete and 875 partial mitogenomic sequences, and performed a meta-analysis of these and published ovine mitochondrial DNA sequences (n = 3,229) across Eurasia. We inferred that O. orientalis and O. musimon share the most recent female ancestor with O. aries at approximately 0.790 Ma (95% CI: 0.637-0.934 Ma) during the Middle Pleistocene, substantially predating the domestication event (∼8-11 ka). By reconstructing historical variations in effective population size, we found evidence of a rapid population increase approximately 20-60 ka, immediately before the Last Glacial Maximum. Analyses of lineage expansions showed two sheep migratory waves at approximately 4.5-6.8 ka (lineages A and B: ∼6.4-6.8 ka; C: ∼4.5 ka) across eastern Eurasia, which could have been influenced by prehistoric West-East commercial trade and deliberate mating of domestic and wild sheep, respectively. A continent-scale examination of lineage diversity and approximate Bayesian computation analyses indicated that the Mongolian Plateau region was a secondary center of dispersal, acting as a "transportation hub" in eastern Eurasia: Sheep from the Middle Eastern domestication center were inferred to have migrated through the Caucasus and Central Asia, and arrived in North and Southwest China (lineages A, B, and C) and the Indian subcontinent (lineages B and C) through this region. Our results provide new insights into sheep domestication, particularly with respect to origins and migrations to and from eastern Eurasia.}, }
@article {pmid26077836, year = {2015}, author = {Raven, JA}, title = {Implications of mutation of organelle genomes for organelle function and evolution.}, journal = {Journal of experimental botany}, volume = {66}, number = {19}, pages = {5639-5650}, doi = {10.1093/jxb/erv298}, pmid = {26077836}, issn = {1460-2431}, mesh = {*Biological Evolution ; *Mutation ; Organelles/*genetics/metabolism ; Plants/*genetics/metabolism ; Zea mays/genetics/metabolism ; }, abstract = {Organelle genomes undergo more variation, including that resulting from damage, than eukaryotic nuclear genomes, or bacterial genomes, under the same conditions. Recent advances in characterizing the changes to genomes of chloroplasts and mitochondria of Zea mays should, when applied more widely, help our understanding of how damage to organelle genomes relates to how organelle function is maintained through the life of individuals and in succeeding generations. Understanding of the degree of variation in the changes to organelle DNA and its repair among photosynthetic organisms might help to explain the variations in the rate of nucleotide substitution among organelle genomes. Further studies of organelle DNA variation, including that due to damage and its repair might also help us to understand why the extent of DNA turnover in the organelles is so much greater than that in their bacterial (cyanobacteria for chloroplasts, proteobacteria for mitochondria) relatives with similar rates of production of DNA-damaging reactive oxygen species. Finally, from the available data, even the longest-lived organelle-encoded proteins, and the RNAs needed for their synthesis, are unlikely to maintain organelle function for much more than a week after the complete loss of organelle DNA.}, }
@article {pmid26073494, year = {2015}, author = {Chandel, NS}, title = {Evolution of Mitochondria as Signaling Organelles.}, journal = {Cell metabolism}, volume = {22}, number = {2}, pages = {204-206}, doi = {10.1016/j.cmet.2015.05.013}, pmid = {26073494}, issn = {1932-7420}, support = {5P01HL071643/HL/NHLBI NIH HHS/United States ; R01CA123067/CA/NCI NIH HHS/United States ; R01HL12206201/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Energy Metabolism/*physiology ; *Evolution, Molecular ; Humans ; Mitochondria/*physiology ; Signal Transduction/*physiology ; *Stress, Physiological ; }, abstract = {Mitochondria have primarily been viewed as bioenergetic and biosynthetic organelles that autonomously co-exist within the cell. However, the past two decades have provided evidence that mitochondria function as signaling organelles, constantly communicating with the cytosol to initiate biological events under homeostatic and stress conditions. Thus, the signaling function of the mitochondria may have been selected by nature from the inception of the early eukaryote, as discussed in this essay.}, }
@article {pmid26070000, year = {2015}, author = {Hubbard, WJ and Bland, KI and Chaudry, IH}, title = {The ERRor of Our Ways: Estrogen-Related Receptors are About Energy, Not Hormones, and are Potential New Targets for Trauma and Shock.}, journal = {Shock (Augusta, Ga.)}, volume = {44}, number = {1}, pages = {3-15}, doi = {10.1097/SHK.0000000000000364}, pmid = {26070000}, issn = {1540-0514}, mesh = {Animals ; *Energy Metabolism ; *Evolution, Molecular ; Humans ; *Mitochondria/genetics/metabolism ; PPAR gamma/genetics/metabolism ; *Receptors, Estrogen/genetics/metabolism ; *Shock/genetics/metabolism ; Transcription Factors/genetics/metabolism ; *Wounds and Injuries/genetics/metabolism ; }, abstract = {As with sharks and horseshoe crabs, some designs of nature need only minor evolutionary adjustments during the millennia to remain superbly adapted. Such is the case at the molecular level for the nuclear receptors (NRs), which seem to have originated concomitantly with the earliest metazoan lineage of animals. A wide array of NRs persists today throughout all animal phyla with many different functions, yet they share a highly conserved protein structure, a testament to their having evolved through numerous gene duplications. Of particular interest for this readership are the estrogen-related receptors (ERRs), which have significant supportive roles in energy creation and regulation, mitochondrial function and biogenesis, development, tissue repair, hypoxia, and cancer. Thus, placed at the nexus of energetics and homeostasis, ERR (in association with the coregulatory molecules peroxisome proliferator-activated receptor-γ coactivator-1α and -β) can facilitate repair from injury and adaptations to stressful environments. Whereas it is curious that ERRs and some other NRs exist as "orphans" by virtue of having no known cognate ligand, increasing interest in the estrogen receptor has led to the development of synthetic ligands and screening for naturally occurring molecules, either capable of modulating ERR activity. Thus, what is needed now is a nomenclature update for the ERR to focus the mind on energetics and metabolism, the most compromised and crucial systems after trauma and shock.}, }
@article {pmid26067811, year = {2015}, author = {Haliloglu, G and Talim, B and Sel, CG and Topaloglu, H}, title = {Clinical characteristics of megaconial congenital muscular dystrophy due to choline kinase beta gene defects in a series of 15 patients.}, journal = {Journal of inherited metabolic disease}, volume = {38}, number = {6}, pages = {1099-1108}, pmid = {26067811}, issn = {1573-2665}, mesh = {Adolescent ; Child ; Child, Preschool ; Choline Kinase/blood/*genetics ; Female ; Humans ; Infant ; Intellectual Disability/*genetics ; Magnetic Resonance Imaging ; Male ; Microcephaly/genetics ; Mitochondria/*ultrastructure ; Muscle Hypotonia/genetics ; Muscle Weakness/genetics ; Muscle, Skeletal/*pathology ; Muscular Dystrophies/*genetics ; Mutation ; Phenotype ; Tertiary Care Centers ; Turkey ; }, abstract = {A new form of congenital muscular dystrophy (CMD) with multisystem involvement and characteristic mitochondrial structural changes, due to choline kinase beta (CHKB) gene defects has been characterized by intellectual disability, autistic features, ichthyosis-like skin changes, and dilated cardiomyopathy. We define the clinical characteristics in 15 patients, from 14 unrelated families with so-called 'megaconial CMD', all having mutations in CHKB. Core clinical phenotype included global developmental delay prominent in gross-motor and language domains, severe intellectual disability (ID), and/or muscle weakness in all cases. Muscle biopsies were equivocally 'megaconial' in all. Other peculiarities were: ichthyosis-like skin changes (n = 11), increased serum CK levels (n = 12), microcephaly (n = 6), dysmorphic facial features (n = 7), neonatal hypotonia (n = 3), seizures (n = 3), epileptiform activity without clinically overt seizures (n = 2), dilated cardiomyopathy (n = 2), decreased left ventricular systolic function (n = 2), congenital heart defects (n = 3), sensorineural (n = 1), and conductive hearing loss (n = 1). Ten patients had cranial neuroimaging (MRI-MRS) study, which was notably normal in all, other than one patient having a decreased choline: creatine peak. Intra-familial variability in clinical expression of the disease is noted in four families. Two siblings from the same family, one presenting with global developmental delay and dilated cardiomyopathy, and the other with ichthyosis, ID and proximal weakness without cardiomyopathy died at the ages of 2 years 1 month, and 7 years 4 months respectively. Evolution was progressive (n = 13) and static (n = 2).}, }
@article {pmid26066286, year = {2015}, author = {Rodríguez-Fernández, JL and de Lacoba, MG}, title = {Plasma membrane-associated superstructure: Have we overlooked a new type of organelle in eukaryotic cells?.}, journal = {Journal of theoretical biology}, volume = {380}, number = {}, pages = {346-358}, doi = {10.1016/j.jtbi.2015.05.029}, pmid = {26066286}, issn = {1095-8541}, mesh = {Biological Evolution ; Cell Membrane/physiology/*ultrastructure ; Cell Polarity ; Eukaryotic Cells/*ultrastructure ; *Organelles ; }, abstract = {A variety of intriguing plasma membrane-associated regions, including focal adhesions, adherens junctions, tight junctions, immunological synapses, neuromuscular junctions and the primary cilia, among many others, have been described in eukaryotic cells. Emphasizing their importance, alteration in their molecular structures induces or correlates with different pathologies. These regions display surface proteins connected to intracellular molecules, including cytoskeletal component, which maintain their cytoarchitecture, and signalling proteins, which regulate their organization and functions. Based on the molecular similarities and other common features observed, we suggest that, despite differences in external appearances, all these regions are just the same superstructure that appears in different locations and cells. We hypothesize that this superstructure represents an overlooked new type of organelle that we call plasma membrane-associated superstructure (PMAS). Therefore, we suggest that eukaryotic cells include classical organelles (e.g. mitochondria, Golgi and others) and also PMAS. We speculate that this new type of organelle might be an innovation associated to the emergence of eukaryotes. Finally we discuss the implications of the hypothesis proposed.}, }
@article {pmid26059473, year = {2015}, author = {Richter, V and Singh, AP and Kvansakul, M and Ryan, MT and Osellame, LD}, title = {Splitting up the powerhouse: structural insights into the mechanism of mitochondrial fission.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {72}, number = {19}, pages = {3695-3707}, pmid = {26059473}, issn = {1420-9071}, mesh = {Cardiolipins/metabolism ; Dynamins ; Endoplasmic Reticulum/*physiology ; GTP Phosphohydrolases/chemistry/*metabolism ; Homeostasis/*physiology ; Humans ; Microtubule-Associated Proteins/chemistry/*metabolism ; Mitochondrial Dynamics/*physiology ; Mitochondrial Proteins/chemistry/*metabolism ; *Models, Molecular ; Plakins/*metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {Mitochondria are dynamic organelles whose shape is regulated by the opposing processes of fission and fusion, operating in conjunction with organelle distribution along the cytoskeleton. The importance of fission and fusion homeostasis has been highlighted by a number of disease states linked to mutations in proteins involved in regulating mitochondrial morphology, in addition to changes in mitochondrial dynamics in Alzheimer's, Huntington's and Parkinson's diseases. While a number of mitochondrial morphology proteins have been identified, how they co-ordinate to assemble the fission apparatus is not clear. In addition, while the master mediator of mitochondrial fission, dynamin-related protein 1, is conserved throughout evolution, the adaptor proteins involved in its mitochondrial recruitment are not. This review focuses on our current understanding of mitochondrial fission and the proteins that regulate this process in cell homeostasis, with a particular focus on the recent mechanistic insights based on protein structures.}, }
@article {pmid26051128, year = {2015}, author = {Gjerde, B and Hilali, M and Mawgood, SA}, title = {Molecular characterisation of three regions of the nuclear ribosomal DNA unit and the mitochondrial cox1 gene of Sarcocystis fusiformis from water buffaloes (Bubalus bubalis) in Egypt.}, journal = {Parasitology research}, volume = {114}, number = {9}, pages = {3401-3413}, pmid = {26051128}, issn = {1432-1955}, mesh = {Animals ; *Buffaloes ; Cyclooxygenase 1/genetics/*metabolism ; DNA, Ribosomal/genetics ; Egypt/epidemiology ; Gene Expression Regulation, Enzymologic ; Genes, Mitochondrial ; *Genetic Variation ; Mitochondria/enzymology ; Phylogeny ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 28S/genetics/metabolism ; Sarcocystis/*enzymology/genetics/isolation &amp; purification/metabolism ; Sarcocystosis/epidemiology/parasitology/*veterinary ; Sequence Analysis, DNA ; }, abstract = {A total of 33 macroscopically visible (3-11 × 1-5 mm) sarcocysts of Sarcocystis fusiformis were excised from the oesophagus of 12 freshly slaughtered water buffalos in Giza, Egypt. Genomic DNA was extracted from the sarcocysts, and all isolates were characterised at the mitochondrial cytochrome c oxidase subunit I (cox1) gene through PCR amplification and direct sequencing, whereas a few selected isolates were characterised at the 18S and 28S ribosomal (r) RNA genes and the internal transcribed spacer 1 (ITS1) region of the nuclear rDNA unit following cloning. Among the 33 cox1 sequences (1,038-bp long), there was a total of 13 haplotypes, differing from each other by one to seven substitutions and sharing an identity of 99.3-99.9 %. In comparison, the sequence identity was 98.8-99.0 % among eight complete 18S rRNA gene sequences (1,873-1,879-bp long), 98.1-100 % among 28 complete ITS1 sequences (853-864-bp long) and 97.4-99.6 % among five partial 28S rRNA gene sequences (1,607-1,622 bp). At the three nuclear loci, the intraspecific (and intra-isolate) sequence variation was due to both substitutions and indels, which necessitated cloning of the PCR products before sequencing. Some additional clones of the 18S and 28S rRNA genes were highly divergent from the more typical clones, but the true nature of these aberrant clones could not be determined. Sequence comparisons and phylogenetic analyses based on either 18S rRNA gene or cox1 nucleotide sequences, placed S. fusiformis closest to Sarcocystis cafferi from the African buffalo, but only the analyses based on cox1 data separated the two taxa clearly from each other and showed that they were separate species (monophyletic clusters and 93 % sequence identity at cox1 versus interleaved sequences and 98.7-99.1 % sequence identity at the 18S rRNA gene). Two cats experimentally infected with sarcocysts of S. fusiformis started shedding small numbers of sporocysts 8-10 days post-infection (dpi) and were euthanized 15 dpi. Sporocysts isolated from the intestinal mucosa of both cats were identified molecularly as belonging to S. fusiformis through PCR amplification and sequencing of the partial cox1. The two sporocyst-derived cox1 sequences were identical with the most common sarcocyst-derived cox1 haplotype.}, }
@article {pmid26048547, year = {2015}, author = {Hua, X and Cowman, P and Warren, D and Bromham, L}, title = {Longevity Is Linked to Mitochondrial Mutation Rates in Rockfish: A Test Using Poisson Regression.}, journal = {Molecular biology and evolution}, volume = {32}, number = {10}, pages = {2633-2645}, doi = {10.1093/molbev/msv137}, pmid = {26048547}, issn = {1537-1719}, mesh = {Animals ; Computer Simulation ; DNA, Mitochondrial/*genetics ; Fishes/*genetics/*physiology ; Least-Squares Analysis ; Longevity/*genetics ; Mitochondria/*genetics ; *Mutation Rate ; Quantitative Trait, Heritable ; Regression Analysis ; Species Specificity ; }, abstract = {The mitochondrial theory of ageing proposes that the cumulative effect of biochemical damage in mitochondria causes mitochondrial mutations and plays a key role in ageing. Numerous studies have applied comparative approaches to test one of the predictions of the theory: That the rate of mitochondrial mutations is negatively correlated with longevity. Comparative studies face three challenges in detecting correlates of mutation rate: Covariation of mutation rates between species due to ancestry, covariation between life-history traits, and difficulty obtaining accurate estimates of mutation rate. We address these challenges using a novel Poisson regression method to examine the link between mutation rate and lifespan in rockfish (Sebastes). This method has better performance than traditional sister-species comparisons when sister species are too recently diverged to give reliable estimates of mutation rate. Rockfish are an ideal model system: They have long life spans with indeterminate growth and little evidence of senescence, which minimizes the confounding tradeoffs between lifespan and fecundity. We show that lifespan in rockfish is negatively correlated to rate of mitochondrial mutation, but not the rate of nuclear mutation. The life history of rockfish allows us to conclude that this relationship is unlikely to be driven by the tradeoffs between longevity and fecundity, or by the frequency of DNA replications in the germline. Instead, the relationship is compatible with the hypothesis that mutation rates are reduced by selection in long-lived taxa to reduce the chance of mitochondrial damage over its lifespan, consistent with the mitochondrial theory of ageing.}, }
@article {pmid26047467, year = {2015}, author = {Wideman, JG and Moore, BP}, title = {The Evolutionary History of MAPL (Mitochondria-Associated Protein Ligase) and Other Eukaryotic BAM/GIDE Domain Proteins.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0128795}, pmid = {26047467}, issn = {1932-6203}, mesh = {Animals ; Biological Evolution ; Fungal Proteins/chemistry/genetics ; Fungi/chemistry/genetics ; Humans ; *Phylogeny ; Plant Proteins/chemistry/genetics ; Plants/chemistry/genetics ; Protein Structure, Tertiary ; Ubiquitin-Protein Ligases/chemistry/*genetics ; }, abstract = {MAPL (mitochondria-associated protein ligase, also called MULAN/GIDE/MUL1) is a multifunctional mitochondrial outer membrane protein found in human cells that contains a unique BAM (beside a membrane) domain and a C-terminal RING-finger domain. MAPL has been implicated in several processes that occur in animal cells such as NF-kB activation, innate immunity and antiviral signaling, suppression of PINK1/parkin defects, mitophagy in skeletal muscle, and caspase-dependent apoptosis. Previous studies demonstrated that the BAM domain is present in diverse organisms in which most of these processes do not occur, including plants, archaea, and bacteria. Thus the conserved function of MAPL and its BAM domain remains an open question. In order to gain insight into its conserved function, we investigated the evolutionary origins of MAPL by searching for homologues in predicted proteomes of diverse eukaryotes. We show that MAPL proteins with a conserved BAM-RING architecture are present in most animals, protists closely related to animals, a single species of fungus, and several multicellular plants and related green algae. Phylogenetic analysis demonstrated that eukaryotic MAPL proteins originate from a common ancestor and not from independent horizontal gene transfers from bacteria. We also determined that two independent duplications of MAPL occurred, one at the base of multicellular plants and another at the base of vertebrates. Although no other eukaryote genome examined contained a verifiable MAPL orthologue, BAM domain-containing proteins were identified in the protists Bigelowiella natans and Ectocarpus siliculosis. Phylogenetic analyses demonstrated that these proteins are more closely related to prokaryotic BAM proteins and therefore likely arose from independent horizontal gene transfers from bacteria. We conclude that MAPL proteins with BAM-RING architectures have been present in the holozoan and viridiplantae lineages since their very beginnings. Our work paves the way for future studies into MAPL function in alternative model organisms like Capsaspora owczarzaki and Chlamydomonas reinhardtii that will help to answer the question of MAPL's ancestral function in ways that cannot be answered by studying animal cells alone.}, }
@article {pmid26047054, year = {2015}, author = {MacDonald, SM and Lee, RW}, title = {Validation of Polytomella piriformis nomen nudum (Chlamydomonadaceae): a Distinct Lineage Within a Genus of Nonphotosynthetic Green Algae.}, journal = {The Journal of eukaryotic microbiology}, volume = {62}, number = {6}, pages = {840-844}, doi = {10.1111/jeu.12241}, pmid = {26047054}, issn = {1550-7408}, mesh = {Base Sequence ; DNA, Mitochondrial ; DNA, Plant/genetics ; Evolution, Molecular ; Genes, Plant ; Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 18S ; Sequence Analysis, DNA ; Species Specificity ; Volvocida/*classification/*genetics ; }, abstract = {Polytomella strain SAG 63-10 was first described by Pringsheim (1963) as Polytomella piriformis nomen nudum. The current study validates the name Polytomella piriformis following the International Code of Nomenclature for algae, fungi, and plants (ICN). We present 18S rRNA sequences of SAG 63-10 and several other Polytomella strains, which, along with existing mitochondrial DNA sequences, clearly distinguishes P. piriformis n. sp. from other available Polytomella species. The first type material of the species is presented, as well as an illustration and micrographs. Our own observations of P. piriformis SAG 63-10 are compared to Pringsheim's description and to descriptions of other valid Polytomella spp.}, }
@article {pmid26046756, year = {2015}, author = {Snoeck, HW}, title = {Can Metabolic Mechanisms of Stem Cell Maintenance Explain Aging and the Immortal Germline?.}, journal = {Cell stem cell}, volume = {16}, number = {6}, pages = {582-584}, pmid = {26046756}, issn = {1875-9777}, support = {R01 AG029626/AG/NIA NIH HHS/United States ; }, mesh = {Aging/*physiology ; Animals ; Biological Evolution ; Germ Cells/*physiology ; Humans ; Mitochondria/metabolism ; Models, Biological ; Stem Cells/*cytology/*metabolism ; }, abstract = {The mechanisms underlying the aging process are not understood. Even tissues endowed with somatic stem cells age while the germline appears immortal. I propose that this paradox may be explained by the pervasive use of glycolysis by somatic stem cells as opposed to the predominance of mitochondrial respiration in gametes.}, }
@article {pmid26046351, year = {2015}, author = {Vuillaume, B and Valette, V and Lepais, O and Grandjean, F and Breuil, M}, title = {Genetic Evidence of Hybridization between the Endangered Native Species Iguana delicatissima and the Invasive Iguana iguana (Reptilia, Iguanidae) in the Lesser Antilles: Management Implications.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0127575}, pmid = {26046351}, issn = {1932-6203}, mesh = {Animals ; Cluster Analysis ; Discriminant Analysis ; *Endangered Species ; Genetic Variation ; Genotype ; Haplotypes ; *Hybridization, Genetic ; Iguanas/*genetics ; *Introduced Species ; Male ; Markov Chains ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; NADH Dehydrogenase/genetics ; Principal Component Analysis ; }, abstract = {The worldwide increase of hybridization in different groups is thought to have become more important with the loss of isolating barriers and the introduction of invasive species. This phenomenon could result in the extinction of endemic species. This study aims at investigating the hybridization dynamics between the endemic and threatened Lesser Antillean iguana (Iguana delicatissima) and the invasive common green iguana (Iguana iguana) in the Lesser Antilles, as well as assessing the impact of interspecific hybridization on the decline of I. delicatissima. 59 I. delicatissima (5 localities), 47 I. iguana (12 localities) and 27 hybrids (5 localities), who were all identified based on morphological characters, have been genotyped at 15 microsatellites markers. We also sequenced hybrids using ND4 mitochondrial loci to further investigate mitochondrial introgression. The genetic clustering of species and hybrid genetic assignment were performed using a comparative approach, through the implementation of a Discriminant Analysis of Principal Component (DAPC) based on statistics, as well as genetic clustering approaches based on the genetic models of several populations (Structure, NewHybrids and HIest), in order to get full characterization of hybridization patterns and introgression dynamics across the islands. The iguanas identified as hybrids in the wild, thanks to morphological analysis, were all genetically F1, F2, or backcrosses. A high proportion of individuals were also the result of a longer-term admixture. The absence of reproductive barriers between species leads to hybridization when species are in contact. Yet morphological and behavioral differences between species could explain why males I. iguana may dominate I. delicatissima, thus resulting in short-term species displacement and extinction by hybridization and recurrent introgression from I. iguana toward I. delicatissima. As a consequence, I. delicatissima gets eliminated through introgression, as observed in recent population history over several islands. These results have profound implications for species management of the endangered I. delicatissima and practical conservation recommendations are being discussed in the light of these findings.}, }
@article {pmid26044255, year = {2015}, author = {Patil, KD and Halperin, HR and Becker, LB}, title = {Cardiac arrest: resuscitation and reperfusion.}, journal = {Circulation research}, volume = {116}, number = {12}, pages = {2041-2049}, pmid = {26044255}, issn = {1524-4571}, support = {K12 HL109009/HL/NHLBI NIH HHS/United States ; R01 HL067630/HL/NHLBI NIH HHS/United States ; R01 HL071734/HL/NHLBI NIH HHS/United States ; R01 HL126092/HL/NHLBI NIH HHS/United States ; }, mesh = {Calcium Signaling ; Cardiopulmonary Resuscitation/*methods ; Cardiovascular Agents/adverse effects/therapeutic use ; Chest Wall Oscillation ; Combined Modality Therapy ; Defibrillators ; Defibrillators, Implantable ; Drug Therapy, Combination ; Electric Countershock/methods/trends ; Equipment Design ; Heart Arrest/etiology/metabolism/physiopathology/*therapy ; Humans ; Mitochondria, Heart/physiology ; Models, Cardiovascular ; Myocardial Contraction/physiology ; Myocardial Reperfusion/*methods ; Myocardial Reperfusion Injury/etiology/physiopathology/prevention &amp; control ; Survival Rate ; Treatment Outcome ; Ventricular Fibrillation/complications/physiopathology/therapy ; }, abstract = {The modern treatment of cardiac arrest is an increasingly complex medical procedure with a rapidly changing array of therapeutic approaches designed to restore life to victims of sudden death. The 2 primary goals of providing artificial circulation and defibrillation to halt ventricular fibrillation remain of paramount importance for saving lives. They have undergone significant improvements in technology and dissemination into the community subsequent to their establishment 60 years ago. The evolution of artificial circulation includes efforts to optimize manual cardiopulmonary resuscitation, external mechanical cardiopulmonary resuscitation devices designed to augment circulation, and may soon advance further into the rapid deployment of specially designed internal emergency cardiopulmonary bypass devices. The development of defibrillation technologies has progressed from bulky internal defibrillators paddles applied directly to the heart, to manually controlled external defibrillators, to automatic external defibrillators that can now be obtained over-the-counter for widespread use in the community or home. But the modern treatment of cardiac arrest now involves more than merely providing circulation and defibrillation. As suggested by a 3-phase model of treatment, newer approaches targeting patients who have had a more prolonged cardiac arrest include treatment of the metabolic phase of cardiac arrest with therapeutic hypothermia, agents to treat or prevent reperfusion injury, new strategies specifically focused on pulseless electric activity, which is the presenting rhythm in at least one third of cardiac arrests, and aggressive post resuscitation care. There are discoveries at the cellular and molecular level about ischemia and reperfusion pathobiology that may be translated into future new therapies. On the near horizon is the combination of advanced cardiopulmonary bypass plus a cocktail of multiple agents targeted at restoration of normal metabolism and prevention of reperfusion injury, as this holds the promise of restoring life to many patients for whom our current therapies fail.}, }
@article {pmid26042149, year = {2015}, author = {Chou, JY and Leu, JY}, title = {The Red Queen in mitochondria: cyto-nuclear co-evolution, hybrid breakdown and human disease.}, journal = {Frontiers in genetics}, volume = {6}, number = {}, pages = {187}, pmid = {26042149}, issn = {1664-8021}, abstract = {Cyto-nuclear incompatibility, a specific form of Dobzhansky-Muller incompatibility caused by incompatible alleles between mitochondrial and nuclear genomes, has been suggested to play a critical role during speciation. Several features of the mitochondrial genome (mtDNA), including high mutation rate, dynamic genomic structure, and uniparental inheritance, make mtDNA more likely to accumulate mutations in the population. Once mtDNA has changed, the nuclear genome needs to play catch-up due to the intimate interactions between these two genomes. In two populations, if cyto-nuclear co-evolution is driven in different directions, it may eventually lead to hybrid incompatibility. Although cyto-nuclear incompatibility has been observed in a wide range of organisms, it remains unclear what type of mutations drives the co-evolution. Currently, evidence supporting adaptive mutations in mtDNA remains limited. On the other hand, it has been known that some mutations allow mtDNA to propagate more efficiently but compromise the host fitness (described as selfish mtDNA). Arms races between such selfish mtDNA and host nuclear genomes can accelerate cyto-nuclear co-evolution and lead to a phenomenon called the Red Queen Effect. Here, we discuss how the Red Queen Effect may contribute to the frequent observation of cyto-nuclear incompatibility and be the underlying driving force of some human mitochondrial diseases.}, }
@article {pmid26041663, year = {2015}, author = {Virmani, A and Pinto, L and Bauermann, O and Zerelli, S and Diedenhofen, A and Binienda, ZK and Ali, SF and van der Leij, FR}, title = {The Carnitine Palmitoyl Transferase (CPT) System and Possible Relevance for Neuropsychiatric and Neurological Conditions.}, journal = {Molecular neurobiology}, volume = {52}, number = {2}, pages = {826-836}, pmid = {26041663}, issn = {1559-1182}, mesh = {Animals ; Brain/enzymology ; Cardiovascular Diseases/enzymology ; Carnitine/metabolism ; Carnitine O-Palmitoyltransferase/deficiency/genetics/*physiology ; Ceramides/metabolism ; Diabetes Mellitus, Type 2/enzymology ; Disease Progression ; Eating/physiology ; Endocannabinoids/metabolism ; Energy Metabolism/physiology ; Fatty Acids/metabolism ; Humans ; Hypoglycemia ; Insulin/metabolism ; Learning/physiology ; Lipid Metabolism, Inborn Errors ; Malonyl Coenzyme A/metabolism ; Metabolic Syndrome/enzymology ; Mitochondria/*enzymology ; Mitochondria, Liver/enzymology ; Mitochondria, Muscle/enzymology ; Multienzyme Complexes/physiology ; Neurodegenerative Diseases/*enzymology ; Oxidation-Reduction ; Protein Isoforms ; }, abstract = {The carnitine palmitoyl transferase (CPT) system is a multiprotein complex with catalytic activity localized within a core represented by CPT1 and CPT2 in the outer and inner membrane of the mitochondria, respectively. Two proteins, the acyl-CoA synthase and a translocase also form part of this system. This system is crucial for the mitochondrial beta-oxidation of long-chain fatty acids. CPT1 has two well-known isoforms, CPT1a and CPT1b. CPT1a is the hepatic isoform and CPT1b is typically muscular; both are normally utilized by the organism for metabolic processes throughout the body. There is a strong evidence for their involvement in various disease states, e.g., metabolic syndrome, cardiovascular diseases, and in diabetes mellitus type 2. Recently, a new, third isoform of CPT was described, CPT1c. This is a neuronal isoform and is prevalently localized in brain regions such as hypothalamus, amygdala, and hippocampus. These brain regions play an important role in control of food intake and neuropsychiatric and neurological diseases. CPT activity has been implicated in several neurological and social diseases mainly related to the alteration of insulin equilibrium in the brain. These pathologies include Parkinson's disease, Alzheimer's disease, and schizophrenia. Evolution of both Parkinson's disease and Alzheimer's disease is in some way linked to brain insulin and related metabolic dysfunctions with putative links also with the diabetes type 2. Studies show that in the CNS, CPT1c affects ceramide levels, endocannabionoids, and oxidative processes and may play an important role in various brain functions such as learning.}, }
@article {pmid26040695, year = {2015}, author = {Qin, J and Zhang, Y and Zhou, X and Kong, X and Wei, S and Ward, RD and Zhang, AB}, title = {Mitochondrial phylogenomics and genetic relationships of closely related pine moth (Lasiocampidae: Dendrolimus) species in China, using whole mitochondrial genomes.}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {428}, pmid = {26040695}, issn = {1471-2164}, mesh = {Animals ; Base Pair Mismatch ; China ; Codon, Initiator/genetics ; DNA, Mitochondrial/analysis/isolation &amp; purification ; Evolution, Molecular ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics/metabolism ; Moths/classification/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; RNA, Transfer/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Pine moths (Lepidoptera; Bombycoidea; Lasiocampidae: Dendrolimus spp.) are among the most serious insect pests of forests, especially in southern China. Although COI barcodes (a standardized portion of the mitochondrial cytochrome c oxidase subunit I gene) can distinguish some members of this genus, the evolutionary relationships of the three morphospecies Dendrolimus punctatus, D. tabulaeformis and D. spectabilis have remained largely unresolved. We sequenced whole mitochondrial genomes of eight specimens, including D. punctatus wenshanensis. This is an unambiguous subspecies of D. punctatus, and was used as a reference for inferring the relationships of the other two morphospecies of the D. punctatus complex. We constructed phylogenetic trees from this data, including twelve published mitochondrial genomes of other Bombycoidea species, and examined the relationships of the Dendrolimus taxa using these trees and the genomic features of the mitochondrial genome.<br><br>RESULTS: The eight fully sequenced mitochondrial genomes from the three morphospecies displayed similar genome structures as other Bombycoidea species in terms of gene content, base composition, level of overall AT-bias and codon usage. However, the Dendrolimus genomes possess a unique feature in the large ribosomal 16S RNA subunits (rrnL), which are more than 60 bp longer than other members of the superfamily and have a higher AC proportion. The eight mitochondrial genomes of Dendrolimus were highly conservative in many aspects, for example with identical stop codons and overlapping regions. But there were many differences in start codons, intergenic spacers, and numbers of mismatched base pairs of tRNA (transfer RNA genes). Our results, based on phylogenetic trees, genetic distances, species delimitation and genomic features (such as intergenic spacers) of the mitochondrial genome, indicated that D. tabulaeformis is as close to D. punctatus as is D. punctatus wenshanensis, whereas D. spectabilis evolved independently from D. tabulaeformis and D. punctatus. Whole mitochondrial DNA phylogenies showed that D. spectabilis formed a well-supported monophyletic clade, with a clear species boundary separating it from the other congeners examined here. However, D. tabulaeformis often clustered with D. punctatus and with the subspecies D. punctatus wenshanensis. Genetic distance analyses showed that the distance between D. tabulaeformis and D. punctatus is generally less than the intraspecific distance of D. punctatus and its subspecies D. punctatus wenshanensis. In the species delimitation analysis of Poisson Tree Processes (PTP), D. tabulaeformis, D. punctatus and D. punctatus wenshanensis clustered into a putative species separated from D. spectabilis. In comparison with D. spectabilis, D. tabulaeformis and D. punctatus also exhibit a similar structure in intergenic spacer characterization. These different types of evidence suggest that D. tabulaeformis is very close to D. punctatus and its subspecies D. punctatus wenshanensis, and is likely to be another subspecies of D. punctatus.<br><br>CONCLUSIONS: Whole mitochondrial genomes possess relatively rich genetic information compared with the traditional use of single or multiple genes for phylogenetic purposes. They can be used to better infer phylogenetic relationships and degrees of relatedness of taxonomic groups, at least from the aspect of maternal lineage: caution should be taken due to the maternal-only inheritance of this genome. Our results indicate that D. spectabilis is an independent lineage, while D. tabulaeformis shows an extremely close relationship to D. punctatus.}, }
@article {pmid26039239, year = {2015}, author = {Wang, Y and Chen, J and Jiang, LY and Qiao, GX}, title = {Hemipteran mitochondrial genomes: features, structures and implications for phylogeny.}, journal = {International journal of molecular sciences}, volume = {16}, number = {6}, pages = {12382-12404}, pmid = {26039239}, issn = {1422-0067}, mesh = {Animals ; Genes, Insect ; *Genome, Mitochondrial ; Hemiptera/*genetics ; Mitochondria/*genetics ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; }, abstract = {The study of Hemipteran mitochondrial genomes (mitogenomes) began with the Chagas disease vector, Triatoma dimidiata, in 2001. At present, 90 complete Hemipteran mitogenomes have been sequenced and annotated. This review examines the history of Hemipteran mitogenomes research and summarizes the main features of them including genome organization, nucleotide composition, protein-coding genes, tRNAs and rRNAs, and non-coding regions. Special attention is given to the comparative analysis of repeat regions. Gene rearrangements are an additional data type for a few families, and most mitogenomes are arranged in the same order to the proposed ancestral insect. We also discuss and provide insights on the phylogenetic analyses of a variety of taxonomic levels. This review is expected to further expand our understanding of research in this field and serve as a valuable reference resource.}, }
@article {pmid26032732, year = {2015}, author = {Zaidi, A and Singh, KP and Anwar, S and Suman, SS and Equbal, A and Singh, K and Dikhit, MR and Bimal, S and Pandey, K and Das, P and Ali, V}, title = {Interaction of frataxin, an iron binding protein, with IscU of Fe-S clusters biogenesis pathway and its upregulation in AmpB resistant Leishmania donovani.}, journal = {Biochimie}, volume = {115}, number = {}, pages = {120-135}, doi = {10.1016/j.biochi.2015.05.016}, pmid = {26032732}, issn = {1638-6183}, mesh = {Amino Acid Sequence ; Amphotericin B/*pharmacology ; Animals ; Binding Sites ; Carbon-Sulfur Lyases/metabolism ; Cloning, Molecular ; *Drug Resistance ; Female ; Humans ; Iron/metabolism ; Iron-Binding Proteins/chemistry/genetics/isolation &amp; purification/*metabolism ; Iron-Sulfur Proteins/*biosynthesis/*metabolism ; Leishmania donovani/drug effects/*metabolism ; Mice ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Binding ; Protein Conformation ; Protein Transport ; Protozoan Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Sequence Analysis ; *Up-Regulation ; Frataxin ; }, abstract = {Leishmania donovani is a unicellular protozoon parasite that causes visceral leishmaniasis (VL), which is a fatal disease if left untreated. Certain Fe-S proteins of the TCA cycle and respiratory chain have been found in the Leishmania parasite but the precise mechanisms for their biogenesis and the maturation of Fe-S clusters remains unknown. Fe-S clusters are ubiquitous cofactors of proteins that perform critical cellular functions. The clusters are biosynthesized by the mitochondrial Iron-Sulphur Cluster (ISC) machinery with core protein components that include the catalytic cysteine desulphurase IscS, the scaffold proteins IscU and IscA, and frataxin as an iron carrier/donor. However, no information regarding frataxin, its regulation, or its role in drug resistance is available for the Leishmania parasite. In this study, we characterized Ld-frataxin to investigate its role in the ISC machinery of L. donovani. We expressed and purified the recombinant Ld-frataxin protein and observed its interaction with Ld-IscU by co-purification and pull-down assay. Furthermore, we observed that the cysteine desulphurase activity of the purified Ld-IscS protein was stimulated in the presence of Ld-frataxin and Ld-IscU, particularly in the presence of iron; neither Ld-frataxin nor Ld-IscU alone had significant effects on Ld-IscS activity. Interestingly, RT-PCR and western blotting showed that Ld-frataxin is upregulated in AmpB-resistant isolates compared to sensitive strains, which may support higher Fe-S protein activity in AmpB-resistant L. donovani. Additionally, Ld-frataxin was localized in the mitochondria, as revealed by digitonin fractionation and indirect immunofluorescence. Thus, our results suggest the role of Ld-frataxin as an iron binding/carrier protein for Fe-S cluster biogenesis that physically interacts with other core components of the ISC machinery within the mitochondria.}, }
@article {pmid26030866, year = {2015}, author = {Bergamo, LW and Fresia, P and Azeredo-Espin, AM}, title = {Incongruent nuclear and mitochondrial genetic structure of new world screwworm fly populations due to positive selection of mutations associated with dimethyl- and diethyl-organophosphates resistance.}, journal = {PloS one}, volume = {10}, number = {6}, pages = {e0128441}, pmid = {26030866}, issn = {1932-6203}, mesh = {Animals ; Cell Nucleus/*metabolism ; Diptera/genetics/*metabolism ; Insecticide Resistance ; Mitochondria/*metabolism ; Organophosphorus Compounds/*pharmacology ; Selection, Genetic ; }, abstract = {Livestock production is an important economic activity in Brazil, which has been suffering significant losses due to the impact of parasites. The New World screwworm (NWS) fly, Cochliomyia hominivorax, is an ectoparasite and one of the most important myiasis-causing flies endemic to the Americas. The geographic distribution of NWS has been reduced after the implementation of the Sterile Insect Technique (SIT), being eradicated in North America and part of Central America. In South America, C. hominivorax is controlled by chemical insecticides, although indiscriminate use can cause selection of resistant individuals. Previous studies have associated the Gly137Asp and Trp251Leu mutations in the active site of carboxylesterase E3 to resistance of diethyl and dimethyl-organophosphates insecticides, respectively. Here, we have sequenced a fragment of the carboxylesterase E3 gene (ChαE7), comprising part of intron iII, exon eIII, intron iIII and part of exon eIV, and three mitochondrial gene sequences (CR, COI and COII), of NWS flies from 21 locations in South America. These markers were used for population structure analyses and the ChαE7 gene was also investigated to gain insight into the selective pressures that have shaped its evolution. Analysis of molecular variance (AMOVA) and pairwise FST analysis indicated an increased genetic structure between locations in the ChαE7 compared to the concatenated mitochondrial genes. Discriminant analysis of principal components (DAPC) and spatial analysis of molecular variance (SAMOVA) indicated different degrees of genetic structure for all markers, in agreement with the AMOVA results, but with low correlation to geographic data. The NWS fly is considered a panmitic species based on mitochondrial data, while it is structured into three groups considering the ChαE7 gene. A negative association between the two mutations related to organophosphate resistance and Fay &amp; Wu's H significant negative values for the exons, suggest that these mutations evolved under positive selection.}, }
@article {pmid26025518, year = {2015}, author = {Tamaki, S and Maruta, T and Sawa, Y and Shigeoka, S and Ishikawa, T}, title = {Biochemical and physiological analyses of NADPH-dependent thioredoxin reductase isozymes in Euglena gracilis.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {236}, number = {}, pages = {29-36}, doi = {10.1016/j.plantsci.2015.03.016}, pmid = {26025518}, issn = {1873-2259}, mesh = {Algal Proteins/chemistry/*genetics/metabolism ; Amino Acid Sequence ; Cytosol/metabolism ; Euglena gracilis/*genetics/metabolism ; *Gene Expression Regulation ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Plastids/genetics/metabolism ; Protozoan Proteins/chemistry/*genetics/metabolism ; Sequence Alignment ; Thioredoxin-Disulfide Reductase/chemistry/*genetics/metabolism ; }, abstract = {At least four peroxiredoxins that are coupled with the thioredoxin (Trx) system have been shown to play a key role in redox metabolism in the unicellular phytoflagellate Euglena gracilis. In order to clarify Trx-mediated redox regulation in this alga, we herein identified three NADPH-dependent thioredoxin reductases (NTRs) using a homologous search and characterized their enzymatic properties and physiological roles. Each Euglena NTR protein belonged to the small, large, and NTRC types, and were named EgNTR1, EgNTR2, and EgNTRC, respectively. EgNTR2 was phylogenetically different from the known NTRs in eukaryotic algae. EgNTR1 was predicted to be localized in mitochondria, EgNTR2 in the cytosol, and EgNTRC in plastids. The catalytic efficiency of EgNTR2 for NADPH was 30-46-fold higher than those of EgNTR1 and truncated form of EgNTRC, suggested that large type EgNTR2 reduced Trx more efficiently. The silencing of EgNTR2 gene expression resulted in significant growth inhibition and cell hypertrophy in Euglena cells. These results suggest that EgNTRs function in each cellular compartment and are physiologically important, particularly in the cytosol.}, }
@article {pmid26022125, year = {2015}, author = {Tanti, GK and Pandey, S and Goswami, SK}, title = {SG2NA enhances cancer cell survival by stabilizing DJ-1 and thus activating Akt.}, journal = {Biochemical and biophysical research communications}, volume = {463}, number = {4}, pages = {524-531}, doi = {10.1016/j.bbrc.2015.05.069}, pmid = {26022125}, issn = {1090-2104}, mesh = {Animals ; Autoantigens/*physiology ; Calmodulin-Binding Proteins/*physiology ; Cell Line ; Cell Line, Tumor ; Cell Survival/*physiology ; Enzyme Activation ; Humans ; Intracellular Signaling Peptides and Proteins/*metabolism ; Mice ; Neoplasms/enzymology/metabolism/pathology ; Oncogene Proteins/*metabolism ; Peroxiredoxins/*metabolism ; Protein Deglycase DJ-1 ; Proto-Oncogene Proteins c-akt/*metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {SG2NA in association with striatin and zinedin forms a striatin family of WD-40 repeat proteins. This family of proteins functions as scaffold in different signal transduction pathways. They also act as a regulatory subunit of protein phosphatase 2A. We have shown that SG2NA which evolved first in the metazoan evolution among the striatin family members expresses different isoforms generated out of alternative splicing. We have also shown that SG2NA protects cells from oxidative stress by recruiting DJ-1 and Akt to mitochondria and membrane in the post-mitotic neuronal cells. DJ-1 is both cancer and Parkinson's disease related protein. In the present study we have shown that SG2NA protects DJ-1 from proteasomal degradation in cancer cells. Hence, downregulation of SG2NA reduces DJ-1/Akt colocalization in cancer cells resulting in the reduction of anchorage dependent and independent growth. Thus SG2NA enhances cancer cell survival. Reactive oxygen species enhances SG2NA, DJ-1 and Akt trimerization. Removal of the reactive oxygen species by N-acetyl-cysteine thus reduces cancer cell growth.}, }
@article {pmid26016880, year = {2016}, author = {Rider, SD}, title = {The complete mitochondrial genome of the desert darkling beetle Asbolus verrucosus (Coleoptera, Tenebrionidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {4}, pages = {2447-2449}, doi = {10.3109/19401736.2015.1033692}, pmid = {26016880}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Coleoptera/*classification/*genetics ; Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA ; Whole Genome Sequencing ; }, abstract = {The complete mitochondrial genome of the desert darkling beetle Asbolus verrucosus (LeConte, 1851) was sequenced using paired-end technology to an average depth of 42,111× and assembled using De Bruijn graph-based methods. The genome is 15,828 bp in length and conforms to the basal arthropod mitochondrial gene composition with the same gene orders and orientations as other darkling beetle mitochondria. This arrangement includes a control region, 22 tRNA genes, 2 rRNA genes and 13 protein-coding genes. The main coding strand is probably replicated as the lagging strand (GC skew of -0.36 and AT skew of +0.19). Phylogenomics analyses are consistent with taxonomic classifications and indicate that Tenebrio molitor is the closest relative that has a completely sequenced mitochondrial genome available for analysis. This is the first fully assembled mitogenome sequence for a darkling beetle in the subfamily Pimeliinae and will be useful for population studies on members of this ecologically important group of beetles.}, }
@article {pmid26014357, year = {2015}, author = {Shalaeva, DN and Dibrova, DV and Galperin, MY and Mulkidjanian, AY}, title = {Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly.}, journal = {Biology direct}, volume = {10}, number = {}, pages = {29}, pmid = {26014357}, issn = {1745-6150}, mesh = {Animals ; Apoptosis ; *Apoptosomes ; Apoptotic Protease-Activating Factor 1/*chemistry ; Cytochromes c/*chemistry ; Horses ; Humans ; Hydrogen Bonding ; Lysine/chemistry ; Microscopy, Electron ; Molecular Dynamics Simulation ; Phylogeny ; Protein Binding ; Protein Interaction Mapping ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Salts/chemistry ; Static Electricity ; }, abstract = {BACKGROUND: Binding of cytochrome c, released from the damaged mitochondria, to the apoptotic protease activating factor 1 (Apaf-1) is a key event in the apoptotic signaling cascade. The binding triggers a major domain rearrangement in Apaf-1, which leads to oligomerization of Apaf-1/cytochrome c complexes into an apoptosome. Despite the availability of crystal structures of cytochrome c and Apaf-1 and cryo-electron microscopy models of the entire apoptosome, the binding mode of cytochrome c to Apaf-1, as well as the nature of the amino acid residues of Apaf-1 involved remain obscure.<br><br>RESULTS: We investigated the interaction between cytochrome c and Apaf-1 by combining several modeling approaches. We have applied protein-protein docking and energy minimization, evaluated the resulting models of the Apaf-1/cytochrome c complex, and carried out a further analysis by means of molecular dynamics simulations. We ended up with a single model structure where all the lysine residues of cytochrome c that are known as functionally-relevant were involved in forming salt bridges with acidic residues of Apaf-1. This model has revealed three distinctive bifurcated salt bridges, each involving a single lysine residue of cytochrome c and two neighboring acidic resides of Apaf-1. Salt bridge-forming amino acids of Apaf-1 showed a clear evolutionary pattern within Metazoa, with pairs of acidic residues of Apaf-1, involved in bifurcated salt bridges, reaching their highest numbers in the sequences of vertebrates, in which the cytochrome c-mediated mechanism of apoptosome formation seems to be typical.<br><br>CONCLUSIONS: The reported model of an Apaf-1/cytochrome c complex provides insights in the nature of protein-protein interactions which are hard to observe in crystallographic or electron microscopy studies. Bifurcated salt bridges can be expected to be stronger than simple salt bridges, and their formation might promote the conformational change of Apaf-1, leading to the formation of an apoptosome. Combination of structural and sequence analyses provides hints on the evolution of the cytochrome c-mediated apoptosis.}, }
@article {pmid26009982, year = {2015}, author = {Takebayashi, S and Tanaka, H and Hino, S and Nakatsu, Y and Igata, T and Sakamoto, A and Narita, M and Nakao, M}, title = {Retinoblastoma protein promotes oxidative phosphorylation through upregulation of glycolytic genes in oncogene-induced senescent cells.}, journal = {Aging cell}, volume = {14}, number = {4}, pages = {689-697}, pmid = {26009982}, issn = {1474-9726}, mesh = {Cell Line, Tumor ; Cellular Senescence/genetics ; Citric Acid Cycle/genetics ; Epithelial Cells/*metabolism/pathology ; Gene Expression Profiling ; *Gene Expression Regulation, Neoplastic ; *Genes, ras ; Glycolysis/*genetics ; Humans ; Mitochondria/genetics/metabolism/pathology ; *Oxidative Phosphorylation ; Respiratory Mucosa/metabolism/pathology ; Retinoblastoma Protein/deficiency/*genetics ; Signal Transduction ; }, abstract = {Metabolism is closely linked with cellular state and biological processes, but the mechanisms controlling metabolic properties in different contexts remain unclear. Cellular senescence is an irreversible growth arrest induced by various stresses, which exhibits active secretory and metabolic phenotypes. Here, we show that retinoblastoma protein (RB) plays a critical role in promoting the metabolic flow by activating both glycolysis and mitochondrial oxidative phosphorylation (OXPHOS) in cells that have undergone oncogene-induced senescence (OIS). A combination of real-time metabolic monitoring, and metabolome and gene expression analyses showed that OIS-induced fibroblasts developed an accelerated metabolic flow. The loss of RB downregulated a series of glycolytic genes and simultaneously reduced metabolites produced from the glycolytic pathway, indicating that RB upregulates glycolytic genes in OIS cells. Importantly, both mitochondrial OXPHOS and glycolytic activities were abolished in RB-depleted or downstream glycolytic enzyme-depleted OIS cells, suggesting that RB-mediated glycolytic activation induces a metabolic flux into the OXPHOS pathway. Collectively, our findings reveal that RB essentially functions in metabolic remodeling and the maintenance of the active energy production in OIS cells.}, }
@article {pmid26004762, year = {2015}, author = {Muñoz-Gómez, SA and Slamovits, CH and Dacks, JB and Baier, KA and Spencer, KD and Wideman, JG}, title = {Ancient homology of the mitochondrial contact site and cristae organizing system points to an endosymbiotic origin of mitochondrial cristae.}, journal = {Current biology : CB}, volume = {25}, number = {11}, pages = {1489-1495}, doi = {10.1016/j.cub.2015.04.006}, pmid = {26004762}, issn = {1879-0445}, mesh = {*Evolution, Molecular ; Mitochondria/*physiology ; Multiprotein Complexes/*genetics ; *Structural Homology, Protein ; *Symbiosis ; }, abstract = {Mitochondria are eukaryotic organelles that originated from an endosymbiotic α-proteobacterium. As an adaptation to maximize ATP production through oxidative phosphorylation, mitochondria contain inner membrane invaginations called cristae. Recent work has characterized a multi-protein complex in yeast and animal mitochondria called MICOS (mitochondrial contact site and cristae organizing system), responsible for the determination and maintenance of cristae [1-4]. However, the origin and evolution of these characteristic mitochondrial features remain obscure. We therefore conducted a comprehensive search for MICOS components across the major groups that encompass eukaryotic diversity to determine the extent of conservation of this complex. We detected homologs for the majority of MICOS components among opisthokonts (the group containing animals and fungi), but only Mic60 and Mic10 were consistently identified outside this group. The conservation of Mic60 and Mic10 in eukaryotes is consistent with their central role in MICOS function [5-7], indicating that the basic mechanism for cristae determination arose early in evolution and has remained relatively unchanged. We found that eukaryotes with ultrastructurally simplified anaerobic mitochondria that lack cristae have also lost MICOS. We then searched for a prokaryotic MICOS and identified a homolog of Mic60 present only in α-proteobacteria, providing evidence for the endosymbiotic origin of mitochondrial cristae. Our study clarifies the origins of mitochondrial cristae and their subsequent evolutionary history, provides evidence for a general mechanism of cristae formation and maintenance in eukaryotes, and points to a new potential factor involved in membrane differentiation in prokaryotes.}, }
@article {pmid26004364, year = {2015}, author = {Ilkun, O and Wilde, N and Tuinei, J and Pires, KM and Zhu, Y and Bugger, H and Soto, J and Wayment, B and Olsen, C and Litwin, SE and Abel, ED}, title = {Antioxidant treatment normalizes mitochondrial energetics and myocardial insulin sensitivity independently of changes in systemic metabolic homeostasis in a mouse model of the metabolic syndrome.}, journal = {Journal of molecular and cellular cardiology}, volume = {85}, number = {}, pages = {104-116}, pmid = {26004364}, issn = {1095-8584}, support = {R01 HL073167/HL/NHLBI NIH HHS/United States ; T32DK091317/DK/NIDDK NIH HHS/United States ; U54 HL112311/HL/NHLBI NIH HHS/United States ; U01 HL070525/HL/NHLBI NIH HHS/United States ; R01HL73167/HL/NHLBI NIH HHS/United States ; UO1HL70525/HL/NHLBI NIH HHS/United States ; T32 DK091317/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Antioxidants/*pharmacology/therapeutic use ; Drug Evaluation, Preclinical ; Energy Metabolism ; Fatty Acids/metabolism ; Homeostasis ; Insulin/blood ; Insulin Resistance ; Metabolic Syndrome/blood/*drug therapy ; Metalloporphyrins/*pharmacology/therapeutic use ; Mice, Inbred C57BL ; Mice, Obese ; Mitochondria, Heart/*metabolism ; Myocardium/metabolism ; Oxidative Stress ; Signal Transduction ; }, abstract = {Cardiac dysfunction in obesity is associated with mitochondrial dysfunction, oxidative stress and altered insulin sensitivity. Whether oxidative stress directly contributes to myocardial insulin resistance remains to be determined. This study tested the hypothesis that ROS scavenging will improve mitochondrial function and insulin sensitivity in the hearts of rodent models with varying degrees of insulin resistance and hyperglycemia. The catalytic antioxidant MnTBAP was administered to the uncoupling protein-diphtheria toxin A (UCP-DTA) mouse model of insulin resistance (IR) and obesity, at early and late time points in the evolution of IR, and to db/db mice with severe obesity and type-two diabetes. Mitochondrial function was measured in saponin-permeabilized cardiac fibers. Aconitase activity and hydrogen peroxide emission were measured in isolated mitochondria. Insulin-stimulated glucose oxidation, glycolysis and fatty acid oxidation rates were measured in isolated working hearts, and 2-deoxyglucose uptake was measured in isolated cardiomyocytes. Four weeks of MnTBAP attenuated glucose intolerance in 13-week-old UCP-DTA mice but was without effect in 24-week-old UCP-DTA mice and in db/db mice. Despite the absence of improvement in the systemic metabolic milieu, MnTBAP reversed cardiac mitochondrial oxidative stress and improved mitochondrial bioenergetics by increasing ATP generation and reducing mitochondrial uncoupling in all models. MnTBAP also improved myocardial insulin mediated glucose metabolism in 13 and 24-week-old UCP-DTA mice. Pharmacological ROS scavenging improves myocardial energy metabolism and insulin responsiveness in obesity and type 2 diabetes via direct effects that might be independent of changes in systemic metabolism.}, }
@article {pmid26002517, year = {2015}, author = {Zatti, SA and Naldoni, J and Silva, MR and Maia, AA and Adriano, EA}, title = {Morphology, ultrastructure and phylogeny of Myxobolus curimatae n. sp. (Myxozoa: Myxosporea) a parasite of Prochilodus costatus (Teleostei: Prochilodontidae) from the São Francisco River, Brazil.}, journal = {Parasitology international}, volume = {64}, number = {5}, pages = {362-368}, doi = {10.1016/j.parint.2015.05.011}, pmid = {26002517}, issn = {1873-0329}, mesh = {Animals ; Brazil/epidemiology ; Fish Diseases/*parasitology ; Fishes ; Myxozoa/*genetics/*ultrastructure ; Parasitic Diseases, Animal/epidemiology/*parasitology ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Myxobolus curimatae n. sp. has been found infecting the gill filaments of Prochilodus costatus (Prochilodontidae) from the São Francisco River in the state of Minas Gerais, Brazil. The prevalence of the species was 18.7%. Mature spores were rounded from a frontal view, with elongated polar capsules of equal size, and had polar filaments with 9-10 turns. Ultrastructural analysis revealed that sporogenesis patterns followed those of other Myxobolus species. The plasmodium walls had numerous invaginations and protrusions, and few pinocytic channels. Numerous mitochondria, generative cells and young pansporoblasts were observed in the peripherical areas of the plasmodia, and mature spores were found in deeper layers. A layer of collagenic fibrils surrounded the plasmodia. The morphological data and molecular analysis of the 18S rDNA identified this parasite as a new species. The maximum likelihood phylogenetic tree showed M. curimatae n. sp., as a sister species of Thelohanellus marginatus, in a basal branch of the subclade composed by parasites with tropism to different organs and host families.}, }
@article {pmid26001724, year = {2015}, author = {Kinghorn, KJ and Castillo-Quan, JI and Bartolome, F and Angelova, PR and Li, L and Pope, S and Cochemé, HM and Khan, S and Asghari, S and Bhatia, KP and Hardy, J and Abramov, AY and Partridge, L}, title = {Loss of PLA2G6 leads to elevated mitochondrial lipid peroxidation and mitochondrial dysfunction.}, journal = {Brain : a journal of neurology}, volume = {138}, number = {Pt 7}, pages = {1801-1816}, pmid = {26001724}, issn = {1460-2156}, support = {090541/Z/09/Z//Wellcome Trust/United Kingdom ; 089698//Wellcome Trust/United Kingdom ; 098565//Wellcome Trust/United Kingdom ; MC_G1000735/MRC_/Medical Research Council/United Kingdom ; H-1105/PUK_/Parkinson's UK/United Kingdom ; R01 GM084947/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Line ; Drosophila Proteins/*genetics/metabolism ; Drosophila melanogaster ; Fibroblasts/metabolism ; Gene Knockout Techniques ; Group VI Phospholipases A2/*genetics/metabolism ; Group X Phospholipases A2/*genetics/metabolism ; Humans ; Lipid Peroxidation/*genetics ; Mass Spectrometry ; Membrane Potential, Mitochondrial/genetics ; Microscopy, Fluorescence ; Mitochondria/*metabolism/pathology ; Neurodegenerative Diseases/genetics/metabolism/pathology ; Oxidative Stress/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {The PLA2G6 gene encodes a group VIA calcium-independent phospholipase A2 beta enzyme that selectively hydrolyses glycerophospholipids to release free fatty acids. Mutations in PLA2G6 have been associated with disorders such as infantile neuroaxonal dystrophy, neurodegeneration with brain iron accumulation type II and Karak syndrome. More recently, PLA2G6 was identified as the causative gene in a subgroup of patients with autosomal recessive early-onset dystonia-parkinsonism. Neuropathological examination revealed widespread Lewy body pathology and the accumulation of hyperphosphorylated tau, supporting a link between PLA2G6 mutations and parkinsonian disorders. Here we show that knockout of the Drosophila homologue of the PLA2G6 gene, iPLA2-VIA, results in reduced survival, locomotor deficits and organismal hypersensitivity to oxidative stress. Furthermore, we demonstrate that loss of iPLA2-VIA function leads to a number of mitochondrial abnormalities, including mitochondrial respiratory chain dysfunction, reduced ATP synthesis and abnormal mitochondrial morphology. Moreover, we show that loss of iPLA2-VIA is strongly associated with increased lipid peroxidation levels. We confirmed our findings using cultured fibroblasts taken from two patients with mutations in the PLA2G6 gene. Similar abnormalities were seen including elevated mitochondrial lipid peroxidation and mitochondrial membrane defects, as well as raised levels of cytoplasmic and mitochondrial reactive oxygen species. Finally, we demonstrated that deuterated polyunsaturated fatty acids, which inhibit lipid peroxidation, were able to partially rescue the locomotor abnormalities seen in aged flies lacking iPLA2-VIA gene function, and restore mitochondrial membrane potential in fibroblasts from patients with PLA2G6 mutations. Taken together, our findings demonstrate that loss of normal PLA2G6 gene activity leads to lipid peroxidation, mitochondrial dysfunction and subsequent mitochondrial membrane abnormalities. Furthermore we show that the iPLA2-VIA knockout fly model provides a useful platform for the further study of PLA2G6-associated neurodegeneration.}, }
@article {pmid26000947, year = {2016}, author = {Shen, KN and Tsai, SY and Chen, CH and Hsiao, CD and Durand, JD}, title = {Next generation sequencing yields the complete mitochondrial genome of the largescale mullet, Liza macrolepis (Teleostei: Mugilidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4232-4233}, doi = {10.3109/19401736.2015.1022755}, pmid = {26000947}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Biological Evolution ; Cyprinidae/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genes, rRNA/genetics ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Lepidoptera/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {In this study, the complete mitogenome sequence of largescale mullet (Teleostei: Mugilidae) has been sequenced by the next-generation sequencing method. The assembled mitogenome, consisting of 16,832 bp, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs genes, and a non-coding control region of D-loop. D-loop which has a length of 1094 bp is located between tRNA-Pro and tRNA-Phe. The overall base composition of largescale mullet is 27.8% for A, 30.1% for C, 16.2% for G, and 25.9% for T. The complete mitogenome may provide essential and important DNA molecular data for further phylogenetic and evolutionary analysis for Mugilidae.}, }
@article {pmid25999055, year = {2015}, author = {Knie, N and Fischer, S and Grewe, F and Polsakiewicz, M and Knoop, V}, title = {Horsetails are the sister group to all other monilophytes and Marattiales are sister to leptosporangiate ferns.}, journal = {Molecular phylogenetics and evolution}, volume = {90}, number = {}, pages = {140-149}, doi = {10.1016/j.ympev.2015.05.008}, pmid = {25999055}, issn = {1095-9513}, mesh = {Amino Acid Sequence ; Chloroplasts/genetics ; DNA, Mitochondrial/chemistry/genetics ; Equisetum/*classification ; Ferns/*classification/genetics ; Introns ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {The "Monilophyte" clade comprising ferns, horsetails and whisk ferns receives unequivocal support from molecular data as the sister clade to seed plants. However, the branching order of its earliest emerging lineages, the Equisetales (horsetails), the Marattiales, the Ophioglossales/Psilotales and the large group of leptosporangiate ferns has remained dubious. We investigated the mitochondrial nad2 and rpl2 genes as two new, intron-containing loci for a wide sampling of taxa. We found that both group II introns - nad2i542g2 and rpl2i846g2 - are universally present among monilophytes. Both introns have orthologues in seed plants where nad2i542g2 has evolved into a trans-arrangement. In contrast and despite substantial size extensions to more than 5kb in Psilotum, nad2i542g2 remains cis-arranged in the monilophytes. For phylogenetic analyses, we filled taxonomic gaps in previously investigated mitochondrial (atp1, nad5) and chloroplast (atpA, atpB, matK, rbcL, rps4) loci and created a 9-gene matrix that also included the new mitochondrial nad2 and rpl2 loci. We extended the taxon sampling with two taxa each for all land plant outgroups (liverworts, mosses, hornworts, lycophytes and seed plants) to minimize the risk of phylogenetic artefacts. We ultimately obtained a well-supported molecular phylogeny placing Marattiales as sister to leptosporangiate ferns and horsetails as sister to all remaining monilophytes. In addition, an indel in an exon of the here introduced rpl2 locus independently supports the placement of horsetails. We conclude that under dense taxon sampling, phylogenetic information from a prudent choice of loci is currently superior to character-rich phylogenomic approaches at low taxon sampling. As here shown the selective choice of loci and taxa enabled us to resolve the long-enigmatic diversifications of the earliest monilophyte lineages.}, }
@article {pmid25997954, year = {2015}, author = {Stefano, GB and Kream, RM}, title = {Hypoxia defined as a common culprit/initiation factor in mitochondrial-mediated proinflammatory processes.}, journal = {Medical science monitor : international medical journal of experimental and clinical research}, volume = {21}, number = {}, pages = {1478-1484}, pmid = {25997954}, issn = {1643-3750}, mesh = {Adenosine Triphosphate/biosynthesis ; Animals ; Biological Evolution ; Cell Hypoxia/*physiology ; Cellular Microenvironment ; Cellular Senescence ; Cytokines/metabolism ; Energy Metabolism ; Gene Expression Regulation ; Humans ; Immunity, Innate ; Immunocompetence ; Inflammation/*etiology/physiopathology ; Invertebrates/physiology ; Microglia/*physiology ; Mitochondria/*physiology ; *Models, Biological ; Neuroimmunomodulation/*physiology ; Nitric Oxide/*physiology ; Nitrites/metabolism ; Opioid Peptides/metabolism ; Signal Transduction ; Vertebrates/physiology ; }, abstract = {In mammals and invertebrates, the activities of neuro- and immuno-competent cells, e.g., glia, which are present in nervous tissues, are deemed of critical importance to normative neuronal function. The responsiveness of invertebrate and vertebrate immuno-competent glia to a common set of signal molecules, such as nitric oxide and endogenous morphine, is functionally linked to physiologically driven innate immunological and neuronal activities. Importantly, the presence of a common, evolutionarily conserved, set of signal molecules in comparative animal groups strongly suggests an expansive intermediate metabolic profile dependent on high output mitochondrial ATP production and utilization. Normative bidirectional neural-immune communication across invertebrate and vertebrate species requires common anatomical and biochemical substrates and pathways involved in energy production and mitochondrial integrity. Within this closed-loop system, abnormal perturbation of the respective tissue functions will have profound ramifications in functionally altering associated nervous and vascular systems and it is highly likely that the initial trigger to the induction of a physiologically debilitating pro-inflammatory state is a micro-environmental hypoxic event. This is surmised by the need for an unwavering constant oxygen supply. In this case, temporal perturbations of normative oxygen tension may be tolerated for short, but not extended, periods and ischemic/hypoxic perturbations in oxygen delivery represent significant physiological challenges to overall cellular and multiple organ system viability. Hence, hypoxic triggering of multiple pro-inflammatory events, if not corrected, will promote pathophysiological amplification leading to a deleterious cascade of bio-senescent cellular and molecular signaling pathways, which converge to markedly impair mitochondrial energy utilization and ATP production.}, }
@article {pmid25992976, year = {2015}, author = {Niemi, M and Bläuer, A and Iso-Touru, T and Harjula, J and Nyström Edmark, V and Rannamäe, E and Lõugas, L and Sajantila, A and Lidén, K and Taavitsainen, JP}, title = {Temporal fluctuation in North East Baltic Sea region cattle population revealed by mitochondrial and Y-chromosomal DNA analyses.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0123821}, pmid = {25992976}, issn = {1932-6203}, mesh = {Animals ; Animals, Domestic/genetics ; Baltic States ; Base Sequence ; Bone and Bones/cytology ; Breeding ; Cattle/*genetics ; DNA, Mitochondrial/*genetics ; Genetic Variation/*genetics ; Haplotypes/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Radiometric Dating ; Sequence Analysis, DNA/veterinary ; Y Chromosome/*genetics ; }, abstract = {BACKGROUND: Ancient DNA analysis offers a way to detect changes in populations over time. To date, most studies of ancient cattle have focused on their domestication in prehistory, while only a limited number of studies have analysed later periods. Conversely, the genetic structure of modern cattle populations is well known given the undertaking of several molecular and population genetic studies.<br><br>RESULTS: Bones and teeth from ancient cattle populations from the North-East Baltic Sea region dated to the Prehistoric (Late Bronze and Iron Age, 5 samples), Medieval (14), and Post-Medieval (26) periods were investigated by sequencing 667 base pairs (bp) from the mitochondrial DNA (mtDNA) and 155 bp of intron 19 in the Y-chromosomal UTY gene. Comparison of maternal (mtDNA haplotypes) genetic diversity in ancient cattle (45 samples) with modern cattle populations in Europe and Asia (2094 samples) revealed 30 ancient mtDNA haplotypes, 24 of which were shared with modern breeds, while 6 were unique to the ancient samples. Of seven Y-chromosomal sequences determined from ancient samples, six were Y2 and one Y1 haplotype. Combined data including Swedish samples from the same periods (64 samples) was compared with the occurrence of Y-chromosomal haplotypes in modern cattle (1614 samples).<br><br>CONCLUSIONS: The diversity of haplogroups was highest in the Prehistoric samples, where many haplotypes were unique. The Medieval and Post-Medieval samples also show a high diversity with new haplotypes. Some of these haplotypes have become frequent in modern breeds in the Nordic Countries and North-Western Russia while other haplotypes have remained in only a few local breeds or seem to have been lost. A temporal shift in Y-chromosomal haplotypes from Y2 to Y1 was detected that corresponds with the appearance of new mtDNA haplotypes in the Medieval and Post-Medieval period. This suggests a replacement of the Prehistoric mtDNA and Y chromosomal haplotypes by new types of cattle.}, }
@article {pmid25989702, year = {2015}, author = {Park, S and Grewe, F and Zhu, A and Ruhlman, TA and Sabir, J and Mower, JP and Jansen, RK}, title = {Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers.}, journal = {The New phytologist}, volume = {208}, number = {2}, pages = {570-583}, doi = {10.1111/nph.13467}, pmid = {25989702}, issn = {1469-8137}, mesh = {Base Sequence ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Gene Conversion ; *Gene Transfer, Horizontal ; *Genes, Plant ; *Genome, Mitochondrial ; *Genome, Plant ; Geranium/*genetics ; Intracellular Space/*genetics ; Introns/genetics ; Molecular Sequence Data ; Phylogeny ; Time Factors ; }, abstract = {The exchange of genetic material between cellular organelles through intracellular gene transfer (IGT) or between species by horizontal gene transfer (HGT) has played an important role in plant mitochondrial genome evolution. The mitochondrial genomes of Geraniaceae display a number of unusual phenomena including highly accelerated rates of synonymous substitutions, extensive gene loss and reduction in RNA editing. Mitochondrial DNA sequences assembled for 17 species of Geranium revealed substantial reduction in gene and intron content relative to the ancestor of the Geranium lineage. Comparative analyses of nuclear transcriptome data suggest that a number of these sequences have been functionally relocated to the nucleus via IGT. Evidence for rampant HGT was detected in several Geranium species containing foreign organellar DNA from diverse eudicots, including many transfers from parasitic plants. One lineage has experienced multiple, independent HGT episodes, many of which occurred within the past 5.5 Myr. Both duplicative and recapture HGT were documented in Geranium lineages. The mitochondrial genome of Geranium brycei contains at least four independent HGT tracts that are absent in its nearest relative. Furthermore, G. brycei mitochondria carry two copies of the cox1 gene that differ in intron content, providing insight into contrasting hypotheses on cox1 intron evolution.}, }
@article {pmid25986376, year = {2015}, author = {Mi-ichi, F and Miyamoto, T and Takao, S and Jeelani, G and Hashimoto, T and Hara, H and Nozaki, T and Yoshida, H}, title = {Entamoeba mitosomes play an important role in encystation by association with cholesteryl sulfate synthesis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {22}, pages = {E2884-90}, pmid = {25986376}, issn = {1091-6490}, mesh = {Adaptation, Biological/*physiology ; Archamoebae/*physiology ; *Biological Evolution ; Biosynthetic Pathways/*physiology ; Chlorates/pharmacology ; Cholesterol Esters/*biosynthesis/isolation &amp; purification ; Computational Biology ; Dose-Response Relationship, Drug ; Entamoeba/*physiology ; Fluorescent Antibody Technique, Indirect ; Magnetic Resonance Spectroscopy ; Mass Spectrometry ; Mitochondria/metabolism/*physiology ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Species Specificity ; Sulfotransferases/genetics ; }, abstract = {Hydrogenosomes and mitosomes are mitochondrion-related organelles (MROs) that have highly reduced and divergent functions in anaerobic/microaerophilic eukaryotes. Entamoeba histolytica, a microaerophilic, parasitic amoebozoan species, which causes intestinal and extraintestinal amoebiasis in humans, possesses mitosomes, the existence and biological functions of which have been a longstanding enigma in the evolution of mitochondria. We previously demonstrated that sulfate activation, which is not generally compartmentalized to mitochondria, is a major function of E. histolytica mitosomes. However, because the final metabolites of sulfate activation remain unknown, the overall scheme of this metabolism and the role of mitosomes in Entamoeba have not been elucidated. In this study we purified and identified cholesteryl sulfate (CS) as a final metabolite of sulfate activation. We then identified the gene encoding the cholesteryl sulfotransferase responsible for synthesizing CS. Addition of CS to culture media increased the number of cysts, the dormant form that differentiates from proliferative trophozoites. Conversely, chlorate, a selective inhibitor of the first enzyme in the sulfate-activation pathway, inhibited cyst formation in a dose-dependent manner. These results indicate that CS plays an important role in differentiation, an essential process for the transmission of Entamoeba between hosts. Furthermore, we show that Mastigamoeba balamuthi, an anaerobic, free-living amoebozoan species, which is a close relative of E. histolytica, also has the sulfate-activation pathway in MROs but does not possess the capacity for CS production. Hence, we propose that a unique function of MROs in Entamoeba contributes to its adaptation to its parasitic life cycle.}, }
@article {pmid25980602, year = {2015}, author = {Hughes, L and Carton, R and Minguzzi, S and McEntee, G and Deinum, EE and O'Connell, MJ and Parle-McDermott, A}, title = {An active second dihydrofolate reductase enzyme is not a feature of rat and mouse, but they do have activity in their mitochondria.}, journal = {FEBS letters}, volume = {589}, number = {15}, pages = {1855-1862}, doi = {10.1016/j.febslet.2015.05.017}, pmid = {25980602}, issn = {1873-3468}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; DNA Primers ; Mice ; Mitochondria/*enzymology ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Polymerase Chain Reaction ; Rats ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Tetrahydrofolate Dehydrogenase/classification/genetics/*metabolism ; }, abstract = {The identification of a second functional dihydrofolate reductase enzyme in humans, DHFRL1, led us to consider whether this is also a feature of rodents. We demonstrate that dihydrofolate reductase activity is also a feature of the mitochondria in both rat and mouse but this is not due to a second enzyme. While our phylogenetic analysis revealed that RNA-mediated DHFR duplication events did occur across the mammal tree, the duplicates in brown rat and mouse are likely to be processed pseudogenes. Humans have evolved the need for two separate enzymes while laboratory rats and mice have just one.}, }
@article {pmid25979672, year = {2015}, author = {Xu, H and Zhang, DL and Yu, DH and Lv, CH and Luo, HY and Wang, ZY}, title = {Molecular cloning and expression analysis of scd1 gene from large yellow croaker Larimichthys crocea under cold stress.}, journal = {Gene}, volume = {568}, number = {1}, pages = {100-108}, doi = {10.1016/j.gene.2015.05.027}, pmid = {25979672}, issn = {1879-0038}, mesh = {Adaptation, Physiological ; Amino Acid Sequence ; Animals ; Cloning, Molecular ; Cold-Shock Response ; Fish Proteins/*genetics/metabolism ; Gene Expression Profiling ; Molecular Sequence Data ; Organ Specificity ; Perciformes/*genetics/metabolism ; Phylogeny ; Stearoyl-CoA Desaturase/*genetics/metabolism ; Transcriptome ; }, abstract = {Desaturation of fatty acids is an important adaptation mechanism to maintain membrane fluidity under cold stress. To comprehend the mechanism of adaptation to low temperatures in fish, we investigated stearoyl-CoA desaturase 1 (SCD1) endocrine expression in the process of cold acclimation from 15°C to 7°C in Larimichthys crocea. The cDNA and genomic sequences of scd1 were cloned and characterized and named as Lcscd1. The cDNA encoded an iron-containing protein of 337 amino acids with functional motifs. The full-length genome sequence of Lcscd1 was composed of 2556 nucleotides, including five exons and four introns. Tissue expression profiles by qPCR and western blot analysis revealed that Lcscd1 was highly expressed in the liver, followed by the brain. The expression of Lcscd1 mRNA in the liver was firstly down-regulated from 15°C to 11°C, and then up-regulated until the first day of 7°C, followed by a decline until the last day. In the brain, the expression showed no significant change from 15°C to 9°C, but then significantly increased until the last day of 7°C. SCD1 protein expression in the liver decreased from 15°C to the first day of 7°C, and then gradually recovered to the starting level. In the brain, SCD1 protein expression maintained rising trends in the whole process. Immunoelectron microscopic analysis showed that SCD1 was localized in fat granules, mitochondria and granular endoplasmic reticulum of hepatic cells, but only in mitochondria of encephalic cells. The results above suggested that SCD1 expression was responsive to both cold and starvation stresses in the liver, but only to cold stress in the brain. In conclusion, these findings suggested that SCD1 may be involved in fish adaptation to cold stress.}, }
@article {pmid25977472, year = {2015}, author = {Signorovitch, A and Hur, J and Gladyshev, E and Meselson, M}, title = {Allele Sharing and Evidence for Sexuality in a Mitochondrial Clade of Bdelloid Rotifers.}, journal = {Genetics}, volume = {200}, number = {2}, pages = {581-590}, pmid = {25977472}, issn = {1943-2631}, mesh = {*Alleles ; Animals ; Gene Order ; Genes, Mitochondrial ; Genetic Loci ; Meiosis ; Mitochondria/*genetics ; Phylogeny ; Rotifera/classification/*genetics ; *Sexual Behavior ; }, abstract = {Rotifers of Class Bdelloidea are common freshwater invertebrates of ancient origin whose apparent asexuality has posed a challenge to the view that sexual reproduction is essential for long-term evolutionary success in eukaryotes and to hypotheses for the advantage of sex. The possibility nevertheless exists that bdelloids reproduce sexually under unknown or inadequately investigated conditions. Although certain methods of population genetics offer definitive means for detecting infrequent or atypical sex, they have not previously been applied to bdelloid rotifers. We conducted such a test with bdelloids belonging to a mitochondrial clade of Macrotrachela quadricornifera. This revealed a striking pattern of allele sharing consistent with sexual reproduction and with meiosis of an atypical sort, in which segregation occurs without requiring homologous chromosome pairs.}, }
@article {pmid25977255, year = {2015}, author = {Karunadharma, PP and Basisty, N and Chiao, YA and Dai, DF and Drake, R and Levy, N and Koh, WJ and Emond, MJ and Kruse, S and Marcinek, D and Maccoss, MJ and Rabinovitch, PS}, title = {Respiratory chain protein turnover rates in mice are highly heterogeneous but strikingly conserved across tissues, ages, and treatments.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {29}, number = {8}, pages = {3582-3592}, pmid = {25977255}, issn = {1530-6860}, support = {R01 HL101186/HL/NHLBI NIH HHS/United States ; T32 AG000057/AG/NIA NIH HHS/United States ; P30 AG013280/AG/NIA NIH HHS/United States ; R01 AG038550/AG/NIA NIH HHS/United States ; P01 AG001751/AG/NIA NIH HHS/United States ; P30 AG0132280/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Caloric Restriction/methods ; Electron Transport/*physiology ; Female ; Isotope Labeling/methods ; Leucine/metabolism ; Mass Spectrometry/methods ; Mice ; Mice, Inbred C57BL ; Mitochondria/*physiology ; Protein Subunits/metabolism ; Proteins/*metabolism ; Proteolysis ; Ubiquitination/physiology ; }, abstract = {The mitochondrial respiratory chain (RC) produces most of the cellular ATP and requires strict quality-control mechanisms. To examine RC subunit proteostasis in vivo, we measured RC protein half-lives (HLs) in mice by liquid chromatography-tandem mass spectrometry with metabolic [(2)H3]-leucine heavy isotope labeling under divergent conditions. We studied 7 tissues/fractions of young and old mice on control diet or one of 2 diet regimens (caloric restriction or rapamycin) that altered protein turnover (42 conditions in total). We observed a 6.5-fold difference in mean HL across tissues and an 11.5-fold difference across all conditions. Normalization to the mean HL of each condition showed that relative HLs were conserved across conditions (Spearman's ρ = 0.57; P < 10(-4)), but were highly heterogeneous between subunits, with a 7.3-fold mean range overall, and a 2.2- to 4.6-fold range within each complex. To identify factors regulating this conserved distribution, we performed statistical analyses to study the correlation of HLs to the properties of the subunits. HLs significantly correlated with localization within the mitochondria, evolutionary origin, location of protein-encoding, and ubiquitination levels. These findings challenge the notion that all subunits in a complex turnover at comparable rates and suggest that there are common rules governing the differential proteolysis of RC protein subunits under divergent cellular conditions.}, }
@article {pmid25976758, year = {2015}, author = {Otten, AB and Smeets, HJ}, title = {Evolutionary defined role of the mitochondrial DNA in fertility, disease and ageing.}, journal = {Human reproduction update}, volume = {21}, number = {5}, pages = {671-689}, doi = {10.1093/humupd/dmv024}, pmid = {25976758}, issn = {1460-2369}, mesh = {Aging/*genetics ; Animals ; *Biological Evolution ; DNA, Mitochondrial/*genetics/*physiology ; Fertility/*genetics ; Fungi/genetics ; Genome/genetics ; Humans ; Mutation/genetics ; Phylogeny ; Plants/genetics ; Reproduction/genetics ; }, abstract = {BACKGROUND: The endosymbiosis of an alpha-proteobacterium and a eubacterium a billion years ago paved the way for multicellularity and enabled eukaryotes to flourish. The selective advantage for the host was the acquired ability to generate large amounts of intracellular hydrogen-dependent adenosine triphosphate. The price was increased reactive oxygen species (ROS) inside the eukaryotic cell, causing high mutation rates of the mitochondrial DNA (mtDNA). According to the Muller's ratchet theory, this accumulation of mutations in asexually transmitted mtDNA would ultimately lead to reduced reproductive fitness and eventually extinction. However, mitochondria have persisted over the course of evolution, initially due to a rapid, extreme evolutionary reduction of the mtDNA content. After the phylogenetic divergence of eukaryotes into animals, fungi and plants, differences in evolution of the mtDNA occurred with different adaptations for coping with the mutation burden within these clades. As a result, mitochondrial evolutionary mechanisms have had a profound effect on human adaptation, fertility, healthy reproduction, mtDNA disease manifestation and transmission and ageing. An understanding of these mechanisms might elucidate novel approaches for treatment and prevention of mtDNA disease.<br><br>METHODS: The scientific literature was investigated to determine how mtDNA evolved in animals, plants and fungi. Furthermore, the different mechanisms of mtDNA inheritance and of balancing Muller's ratchet in these species were summarized together with the consequences of these mechanisms for human health and reproduction.<br><br>RESULTS: Animal, plant and fungal mtDNA have evolved differently. Animals have compact genomes, little recombination, a stable number of genes and a high mtDNA copy number, whereas plants have larger genomes with variable gene counts, a low mtDNA copy number and many recombination events. Fungal mtDNA is somewhere in between. In plants, the mtDNA mutation rate is kept low by effective ROS defence and efficient recombination-mediated mtDNA repair. In animal mtDNA, these mechanisms are not or less well-developed and the detrimental mutagenesis events are controlled by a high mtDNA copy number in combination with a genetic bottleneck and purifying selection during transmission. The mtDNA mutation rates in animals are higher than in plants, which allow mobile animals to adapt more rapidly to various environmental conditions in terms of energy production, whereas static plants do not have this need. Although at the level of the species, these mechanisms have been extremely successful, they can have adverse effects for the individual, resulting, in humans, in severe or unpredictably segregating mtDNA diseases, as well as fertility problems and unhealthy ageing.<br><br>CONCLUSIONS: Understanding the forces and processes that underlie mtDNA evolution among different species increases our knowledge on the detrimental consequences that individuals can have from these evolutionary end-points. Alternative outcomes in animals, fungi and plants will lead to a better understanding of the inheritance of mtDNA disorders and mtDNA-related fertility problems. These will allow the development of options to ameliorate, cure and/or prevent mtDNA diseases and mtDNA-related fertility problems.}, }
@article {pmid25969454, year = {2015}, author = {Freel, KC and Friedrich, A and Schacherer, J}, title = {Mitochondrial genome evolution in yeasts: an all-encompassing view.}, journal = {FEMS yeast research}, volume = {15}, number = {4}, pages = {fov023}, doi = {10.1093/femsyr/fov023}, pmid = {25969454}, issn = {1567-1364}, mesh = {*Evolution, Molecular ; *Genetic Variation ; *Genome, Mitochondrial ; Genomics ; Yeasts/*genetics ; }, abstract = {Mitochondria are important organelles that harbor their own genomes encoding a key set of proteins that ensure respiration and provide the eukaryotic cell with energy. Recent advances in high-throughput sequencing technologies present a unique opportunity to explore mitochondrial (mt) genome evolution. The Saccharomycotina yeasts have proven to be the leading organisms for mt comparative and population genomics. In fact, the explosion of complete yeast mt genome sequences has allowed for a broader view of the mt diversity across this incredibly diverse subphylum, both within and between closely related species. Here, we summarize the present state of yeast mitogenomics, including the currently available data and what it reveals concerning the diversity of content, organization, structure and evolution of mt genomes.}, }
@article {pmid25968459, year = {2015}, author = {Low, VL and Takaoka, H and Adler, PH and Ya'cob, Z and Norma-Rashid, Y and Chen, CD and Sofian-Azirun, M}, title = {A multi-locus approach resolves the phylogenetic relationships of the Simulium asakoae and Simulium ceylonicum species groups in Malaysia: evidence for distinct evolutionary lineages.}, journal = {Medical and veterinary entomology}, volume = {29}, number = {3}, pages = {330-337}, doi = {10.1111/mve.12120}, pmid = {25968459}, issn = {1365-2915}, mesh = {Animals ; Biological Evolution ; Electron Transport Complex IV/genetics ; Insect Proteins/genetics ; Malaysia ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Simuliidae/*classification/*genetics ; }, abstract = {A multi-locus approach was used to examine the DNA sequences of 10 nominal species of blackfly in the Simulium subgenus Gomphostilbia (Diptera: Simuliidae) in Malaysia. Molecular data were acquired from partial DNA sequences of the mitochondria-encoded cytochrome c oxidase subunit I (COI), 12S rRNA and 16S rRNA genes, and the nuclear-encoded 18S rRNA and 28S rRNA genes. No single gene, nor the concatenated gene set, resolved all species or all relationships. However, all morphologically established species were supported by at least one gene. The multi-locus sequence analysis revealed two distinct evolutionary lineages, conforming to the morphotaxonomically recognized Simulium asakoae and Simulium ceylonicum species groups.}, }
@article {pmid25966796, year = {2015}, author = {Oelkrug, R and Polymeropoulos, ET and Jastroch, M}, title = {Brown adipose tissue: physiological function and evolutionary significance.}, journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology}, volume = {185}, number = {6}, pages = {587-606}, pmid = {25966796}, issn = {1432-136X}, mesh = {Adipose Tissue, Brown/anatomy &amp; histology/cytology/*physiology ; Animals ; Animals, Newborn ; Antioxidants/metabolism ; *Biological Evolution ; Body Weight ; Female ; Humans ; Ion Channels/metabolism ; Mammals/physiology ; Marsupialia/physiology ; Mitochondria/metabolism ; Mitochondrial Proteins/metabolism ; Phylogeny ; Reproduction/physiology ; Rodentia/physiology ; Thermogenesis/*physiology ; Uncoupling Protein 1 ; }, abstract = {In modern eutherian (placental) mammals, brown adipose tissue (BAT) evolved as a specialized thermogenic organ that is responsible for adaptive non-shivering thermogenesis (NST). For NST, energy metabolism of BAT mitochondria is increased by activation of uncoupling protein 1 (UCP1), which dissipates the proton motive force as heat. Despite the presence of UCP1 orthologues prior to the divergence of teleost fish and mammalian lineages, UCP1's significance for thermogenic adipose tissue emerged at later evolutionary stages. Recent studies on the presence of BAT in metatherians (marsupials) and eutherians of the afrotherian clade provide novel insights into the evolution of adaptive NST in mammals. In particular studies on the 'protoendothermic' lesser hedgehog tenrec (Afrotheria) suggest an evolutionary scenario linking BAT to the onset of eutherian endothermy. Here, we review the physiological function and distribution of BAT in an evolutionary context by focusing on the latest research on phylogenetically distinct species.}, }
@article {pmid25962484, year = {2016}, author = {Cai, Y and Zhang, L and Wang, Y and Liu, Q and Shui, Q and Yue, B and Zhang, Z and Li, J}, title = {Identification of deer species (Cervidae, Cetartiodactyla) in China using mitochondrial cytochrome c oxidase subunit I (mtDNA COI).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4240-4243}, doi = {10.3109/19401736.2014.1003919}, pmid = {25962484}, issn = {2470-1408}, mesh = {Animals ; China ; DNA Barcoding, Taxonomic/methods ; DNA, Mitochondrial/*genetics ; Deer/*genetics ; Electron Transport Complex IV/*genetics ; Genome, Mitochondrial/genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {In China, many deer species are threatened and their wild populations are decreasing. In this study, a segment of mitochondrial cytochrome oxidase subunit I (COI) was used as a DNA barcode to identify Cervidae species. COI sequences of 30 individuals from nine species were determined. Together with 148 sequences from BOLD and Genbank, a total of 178 sequences from 21 species of the family Cervidae were analyzed. The results showed that all species had unique COI sequences, and there was no barcode sharing among them. The mean K2P distances within species, genus, and family were 1.3%, 3.4%, and 8.9%, respectively. The neighbor-joining (NJ) tree was in most cases concordant with modern deer classification. Three species showed maximum intraspecific divergences higher than their minimum interspecific divergences. However, all species could be discriminated by their diagnostic characters in BLOG analysis. The present study confirmed that COI barcodes can effectively distinguish Cervidae species in China.}, }
@article {pmid25962482, year = {2016}, author = {Liu, G and Tan, X and Shi, F and Liu, Z}, title = {Complete mitochondrial genome of the Macaca mulatta brevicaudus.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3432-3433}, doi = {10.3109/19401736.2015.1022735}, pmid = {25962482}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Macaca mulatta/*genetics ; Mitochondria/*genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitochondrial sequence of the Macaca mulatta brevicaudus has been determined by mapping the raw data to previously published mitochondrial assemblies of the corresponding species. The total sequence length is 16,561 bp, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one D-loop control region. The base composition of the mtDNA genome is 31.77% A, 25.14% T, 30.33% C, and 12.76% G, with an AT content of 56.90%. The arrangement of genes in M. m. brevicaudus is identical to that of M. mulatta. All genes are encoded on the heavy strand with the exception of ND6 and eight tRNA genes. The mitochondrial genome of M. m. brevicaudus presented here will contribute to a better understanding of the population genetics, help to protect its genetic diversity and resolve phylogenetic relationships within the family.}, }
@article {pmid25957689, year = {2015}, author = {Kardon, JR and Yien, YY and Huston, NC and Branco, DS and Hildick-Smith, GJ and Rhee, KY and Paw, BH and Baker, TA}, title = {Mitochondrial ClpX Activates a Key Enzyme for Heme Biosynthesis and Erythropoiesis.}, journal = {Cell}, volume = {161}, number = {4}, pages = {858-867}, pmid = {25957689}, issn = {1097-4172}, support = {T32 HL007574/HL/NHLBI NIH HHS/United States ; R01 GM049224/GM/NIGMS NIH HHS/United States ; F32DK095726/DK/NIDDK NIH HHS/United States ; F32 DK095726/DK/NIDDK NIH HHS/United States ; P01HL032262/HL/NHLBI NIH HHS/United States ; P01 HL032262/HL/NHLBI NIH HHS/United States ; R01 DK070838/DK/NIDDK NIH HHS/United States ; R01DK070838/DK/NIDDK NIH HHS/United States ; T32HL007574/HL/NHLBI NIH HHS/United States ; F32DK098866/DK/NIDDK NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; F32 DK098866/DK/NIDDK NIH HHS/United States ; }, mesh = {5-Aminolevulinate Synthetase/metabolism ; Amino Acid Sequence ; Aminolevulinic Acid/metabolism ; Animals ; Biological Evolution ; Endopeptidase Clp/chemistry/genetics/*metabolism ; *Erythropoiesis ; Eukaryota/genetics/*metabolism ; Heme/*biosynthesis ; Humans ; Mitochondria/metabolism ; Mitochondrial Proteins/metabolism ; Molecular Chaperones/metabolism ; Molecular Sequence Data ; Saccharomyces cerevisiae/cytology/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Sequence Alignment ; Zebrafish/metabolism ; }, abstract = {The mitochondrion maintains and regulates its proteome with chaperones primarily inherited from its bacterial endosymbiont ancestor. Among these chaperones is the AAA+ unfoldase ClpX, an important regulator of prokaryotic physiology with poorly defined function in the eukaryotic mitochondrion. We observed phenotypic similarity in S. cerevisiae genetic interaction data between mitochondrial ClpX (mtClpX) and genes contributing to heme biosynthesis, an essential mitochondrial function. Metabolomic analysis revealed that 5-aminolevulinic acid (ALA), the first heme precursor, is 5-fold reduced in yeast lacking mtClpX activity and that total heme is reduced by half. mtClpX directly stimulates ALA synthase in vitro by catalyzing incorporation of its cofactor, pyridoxal phosphate. This activity is conserved in mammalian homologs; additionally, mtClpX depletion impairs vertebrate erythropoiesis, which requires massive upregulation of heme biosynthesis to supply hemoglobin. mtClpX, therefore, is a widely conserved stimulator of an essential biosynthetic pathway and uses a previously unrecognized mechanism for AAA+ unfoldases.}, }
@article {pmid25957318, year = {2015}, author = {Crampton-Platt, A and Timmermans, MJ and Gimmel, ML and Kutty, SN and Cockerill, TD and Vun Khen, C and Vogler, AP}, title = {Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample.}, journal = {Molecular biology and evolution}, volume = {32}, number = {9}, pages = {2302-2316}, pmid = {25957318}, issn = {1537-1719}, mesh = {Animals ; Borneo ; Coleoptera/*genetics ; Contig Mapping ; Gene Frequency ; Genes, Insect ; Genetic Variation ; Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Metagenome ; Mitochondria/*genetics ; Phylogeny ; Rainforest ; Sequence Analysis, DNA ; }, abstract = {In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately 500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA "superbarcodes" for testing hypotheses regarding global patterns of diversity.}, }
@article {pmid25953984, year = {2015}, author = {Leslie, M}, title = {Evolution. Deep-ocean microbe is closest living relative of complex cells.}, journal = {Science (New York, N.Y.)}, volume = {348}, number = {6235}, pages = {615-616}, doi = {10.1126/science.348.6235.615}, pmid = {25953984}, issn = {1095-9203}, mesh = {Archaea/enzymology/genetics/ultrastructure ; Bacteria/enzymology/genetics/ultrastructure ; *Biological Evolution ; Chloroplasts ; Eukaryota/*classification/genetics/*ultrastructure ; Mitochondria ; Oceans and Seas ; Seawater/*microbiology ; }, }
@article {pmid25950581, year = {2015}, author = {Pilipenko, AS and Trapezov, RO and Zhuravlev, AA and Molodin, VI and Romaschenko, AG}, title = {MtDNA Haplogroup A10 Lineages in Bronze Age Samples Suggest That Ancient Autochthonous Human Groups Contributed to the Specificity of the Indigenous West Siberian Population.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0127182}, pmid = {25950581}, issn = {1932-6203}, mesh = {Asian People/genetics/history ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Female ; Gene Pool ; Genetic Variation ; Genetics, Population ; Haplotypes ; History, Ancient ; Humans ; Male ; Mitochondria/genetics ; *Paleontology/methods ; Phylogeny ; Phylogeography ; Siberia ; }, abstract = {BACKGROUND: The craniometric specificity of the indigenous West Siberian human populations cannot be completely explained by the genetic interactions of the western and eastern Eurasian groups recorded in the archaeology of the area from the beginning of the 2nd millennium BC. Anthropologists have proposed another probable explanation: contribution to the genetic structure of West Siberian indigenous populations by ancient human groups, which separated from western and eastern Eurasian populations before the final formation of their phenotypic and genetic features and evolved independently in the region over a long period of time. This hypothesis remains untested. From the genetic point of view, it could be confirmed by the presence in the gene pool of indigenous populations of autochthonous components that evolved in the region over long time periods. The detection of such components, particularly in the mtDNA gene pool, is crucial for further clarification of early regional genetic history.<br><br>RESULTS AND CONCLUSION: We present the results of analysis of mtDNA samples (n = 10) belonging to the A10 haplogroup, from Bronze Age populations of West Siberian forest-steppe (V-I millennium BC), that were identified in a screening study of a large diachronic sample (n = 96). A10 lineages, which are very rare in modern Eurasian populations, were found in all the Bronze Age groups under study. Data on the A10 lineages' phylogeny and phylogeography in ancient West Siberian and modern Eurasian populations suggest that A10 haplogroup underwent a long-term evolution in West Siberia or arose there autochthonously; thus, the presence of A10 lineages indicates the possible contribution of early autochthonous human groups to the genetic specificity of modern populations, in addition to contributions of later interactions of western and eastern Eurasian populations.}, }
@article {pmid25948649, year = {2016}, author = {Xavier, JM and Rodrigues, CM and Solá, S}, title = {Mitochondria: Major Regulators of Neural Development.}, journal = {The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry}, volume = {22}, number = {4}, pages = {346-358}, doi = {10.1177/1073858415585472}, pmid = {25948649}, issn = {1089-4098}, mesh = {Animals ; Apoptosis ; Bile Acids and Salts ; Cell Cycle ; DNA, Mitochondrial/metabolism/physiology ; Energy Metabolism ; Humans ; Mitochondria/metabolism/*physiology ; Neural Stem Cells/metabolism/*physiology ; *Neurogenesis ; Neuronal Plasticity ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; }, abstract = {Mitochondria are organelles derived from primitive symbiosis between archeon ancestors and prokaryotic α-proteobacteria species, which lost the capacity of synthetizing most proteins encoded the bacterial DNA, along the evolutionary process of eukaryotes. Nowadays, mitochondria are constituted by small circular mitochondrial DNA of 16 kb, responsible for the control of several proteins, including polypeptides of the electron transport chain. Throughout evolution, these organelles acquired the capacity of regulating energy production and metabolism, thus becoming central modulators of cell fate. In fact, mitochondria are crucial for a variety of cellular processes, including adenosine triphosphate production by oxidative phosphorylation, intracellular Ca(2+) homeostasis, generation of reactive oxygen species, and also cellular specialization in a variety of tissues that ultimately relies on specific mitochondrial specialization and maturation. In this review, we discuss recent evidence extending the importance of mitochondrial function and energy metabolism to the context of neuronal development and adult neurogenesis.}, }
@article {pmid25945801, year = {2015}, author = {Roncalli, V and Cieslak, MC and Passamaneck, Y and Christie, AE and Lenz, PH}, title = {Glutathione S-Transferase (GST) Gene Diversity in the Crustacean Calanus finmarchicus--Contributors to Cellular Detoxification.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0123322}, pmid = {25945801}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Arthropod Proteins/chemistry/*genetics/metabolism ; Crustacea/enzymology/*genetics ; Cytoplasm/enzymology ; *Genetic Variation ; Glutathione Transferase/chemistry/*genetics/metabolism ; Isoenzymes/genetics/metabolism ; Microsomes/enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Transcriptome ; }, abstract = {Detoxification is a fundamental cellular stress defense mechanism, which allows an organism to survive or even thrive in the presence of environmental toxins and/or pollutants. The glutathione S-transferase (GST) superfamily is a set of enzymes involved in the detoxification process. This highly diverse protein superfamily is characterized by multiple gene duplications, with over 40 GST genes reported in some insects. However, less is known about the GST superfamily in marine organisms, including crustaceans. The availability of two de novo transcriptomes for the copepod, Calanus finmarchicus, provided an opportunity for an in depth study of the GST superfamily in a marine crustacean. The transcriptomes were searched for putative GST-encoding transcripts using known GST proteins from three arthropods as queries. The identified transcripts were then translated into proteins, analyzed for structural domains, and annotated using reciprocal BLAST analysis. Mining the two transcriptomes yielded a total of 41 predicted GST proteins belonging to the cytosolic, mitochondrial or microsomal classes. Phylogenetic analysis of the cytosolic GSTs validated their annotation into six different subclasses. The predicted proteins are likely to represent the products of distinct genes, suggesting that the diversity of GSTs in C. finmarchicus exceeds or rivals that described for insects. Analysis of relative gene expression in different developmental stages indicated low levels of GST expression in embryos, and relatively high expression in late copepodites and adult females for several cytosolic GSTs. A diverse diet and complex life history are factors that might be driving the multiplicity of GSTs in C. finmarchicus, as this copepod is commonly exposed to a variety of natural toxins. Hence, diversity in detoxification pathway proteins may well be key to their survival.}, }
@article {pmid25944937, year = {2015}, author = {Wu, Z and Cuthbert, JM and Taylor, DR and Sloan, DB}, title = {The massive mitochondrial genome of the angiosperm Silene noctiflora is evolving by gain or loss of entire chromosomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10185-10191}, pmid = {25944937}, issn = {1091-6490}, mesh = {Chromosomes/*ultrastructure ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Plant ; Genetic Variation ; *Genome, Mitochondrial ; Genome, Plant ; Molecular Sequence Data ; Phylogeny ; Plastids/genetics ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Silene/*genetics ; }, abstract = {Across eukaryotes, mitochondria exhibit staggering diversity in genomic architecture, including the repeated evolution of multichromosomal structures. Unlike in the nucleus, where mitosis and meiosis ensure faithful transmission of chromosomes, the mechanisms of inheritance in fragmented mitochondrial genomes remain mysterious. Multichromosomal mitochondrial genomes have recently been found in multiple species of flowering plants, including Silene noctiflora, which harbors an unusually large and complex mitochondrial genome with more than 50 circular-mapping chromosomes totaling ∼7 Mb in size. To determine the extent to which such genomes are stably maintained, we analyzed intraspecific variation in the mitochondrial genome of S. noctiflora. Complete genomes from two populations revealed a high degree of similarity in the sequence, structure, and relative abundance of mitochondrial chromosomes. For example, there are no inversions between the genomes, and there are only nine SNPs in 25 kb of protein-coding sequence. Remarkably, however, these genomes differ in the presence or absence of 19 entire chromosomes, all of which lack any identifiable genes or contain only duplicate gene copies. Thus, these mitochondrial genomes retain a full gene complement but carry a highly variable set of chromosomes that are filled with presumably dispensable sequence. In S. noctiflora, conventional mechanisms of mitochondrial sequence divergence are being outstripped by an apparently nonadaptive process of whole-chromosome gain/loss, highlighting the inherent challenge in maintaining a fragmented genome. We discuss the implications of these findings in relation to the question of why mitochondria, more so than plastids and bacterial endosymbionts, are prone to the repeated evolution of multichromosomal genomes.}, }
@article {pmid25936970, year = {2015}, author = {Hayashi, K and Ichikawa-Seki, M and Mohanta, UK and Singh, TS and Shoriki, T and Sugiyama, H and Itagaki, T}, title = {Molecular phylogenetic analysis of Fasciola flukes from eastern India.}, journal = {Parasitology international}, volume = {64}, number = {5}, pages = {334-338}, doi = {10.1016/j.parint.2015.04.004}, pmid = {25936970}, issn = {1873-0329}, mesh = {Animals ; Buffaloes/parasitology ; Cattle ; Cattle Diseases/epidemiology/parasitology ; Fasciola/*genetics ; Fascioliasis/genetics/*veterinary ; Haplotypes ; India/epidemiology ; Mitochondria/enzymology ; NADH Dehydrogenase/genetics/metabolism ; Phylogeny ; }, abstract = {Fasciola flukes from eastern India were characterized on the basis of spermatogenesis status and nuclear ITS1. Both Fasciola gigantica and aspermic Fasciola flukes were detected in Imphal, Kohima, and Gantoku districts. The sequences of mitochondrial nad1 were analyzed to infer their phylogenetical relationship with neighboring countries. The haplotypes of aspermic Fasciola flukes were identical or showed a single nucleotide substitution compared to those from populations in the neighboring countries, corroborating the previous reports that categorized them in the same lineage. However, the prevalence of aspermic Fasciola flukes in eastern India was lower than those in the neighboring countries, suggesting that they have not dispersed throughout eastern India. In contrast, F. gigantica was predominant and well diversified, and the species was thought to be distributed in the area for a longer time than the aspermic Fasciola flukes. Fasciola gigantica populations from eastern India were categorized into two distinct haplogroups A and B. The level of their genetic diversity suggests that populations belonging to haplogroup A have dispersed from the west side of the Indian subcontinent to eastern India with the artificial movement of domestic cattle, Bos indicus, whereas populations belonging to haplogroup B might have spread from Myanmar to eastern India with domestic buffaloes, Bubalus bubalis.}, }
@article {pmid25936915, year = {2015}, author = {Zhao, B and Zhang, WD and Duan, YL and Lu, YQ and Cun, YX and Li, CH and Guo, K and Nie, WH and Li, L and Zhang, R and Zheng, P}, title = {Filia Is an ESC-Specific Regulator of DNA Damage Response and Safeguards Genomic Stability.}, journal = {Cell stem cell}, volume = {16}, number = {6}, pages = {684-698}, pmid = {25936915}, issn = {1875-9777}, support = {P30 CA010815/CA/NCI NIH HHS/United States ; R01 CA160331/CA/NCI NIH HHS/United States ; CA010815/CA/NCI NIH HHS/United States ; R01CA160331/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Apoptosis/drug effects ; Ataxia Telangiectasia Mutated Proteins/metabolism ; Cell Cycle Checkpoints/drug effects ; Cell Differentiation/drug effects ; Cell Transformation, Neoplastic/metabolism/pathology ; Centrosome/drug effects/metabolism ; Checkpoint Kinase 2/metabolism ; *DNA Damage ; DNA Repair/drug effects ; *Genomic Instability/drug effects ; Mice ; Mitochondria/drug effects/metabolism ; Mouse Embryonic Stem Cells/cytology/drug effects/*metabolism ; Mutagens/toxicity ; Phosphorylation/drug effects ; Phosphoserine/metabolism ; Poly(ADP-ribose) Polymerases/metabolism ; Protein Binding/drug effects ; Protein Transport/drug effects ; Proteins/*metabolism ; Signal Transduction/drug effects ; Subcellular Fractions/drug effects/metabolism ; Up-Regulation/drug effects ; }, abstract = {Pluripotent stem cells (PSCs) hold great promise in cell-based therapy, but the genomic instability seen in culture hampers their full application. A greater understanding of the factors that regulate genomic stability in PSCs could help address this issue. Here we describe the identification of Filia as a specific regulator of genomic stability in mouse embryonic stem cells (ESCs). Filia expression is induced by genotoxic stress. Filia promotes centrosome integrity and regulates the DNA damage response (DDR) through multiple pathways, including DDR signaling, cell-cycle checkpoints and damage repair, ESC differentiation, and apoptosis. Filia depletion causes ESC genomic instability, induces resistance to apoptosis, and promotes malignant transformation. As part of its role in DDR, Filia interacts with PARP1 and stimulates its enzymatic activity. Filia also constitutively resides on centrosomes and translocates to DNA damage sites and mitochondria, consistent with its multifaceted roles in regulating centrosome integrity, damage repair, and apoptosis.}, }
@article {pmid25936275, year = {2015}, author = {Grosjean, S and Ohler, A and Chuaynkern, Y and Cruaud, C and Hassanin, A}, title = {Improving biodiversity assessment of anuran amphibians using DNA barcoding of tadpoles. Case studies from Southeast Asia.}, journal = {Comptes rendus biologies}, volume = {338}, number = {5}, pages = {351-361}, doi = {10.1016/j.crvi.2015.03.015}, pmid = {25936275}, issn = {1768-3238}, mesh = {Animals ; Anura/classification/*physiology ; Asia, Southeastern ; *Biodiversity ; Classification ; Conservation of Natural Resources ; DNA/*genetics ; DNA Barcoding, Taxonomic ; Environmental Monitoring/*methods ; Genetic Markers ; Larva/*physiology ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Reproducibility of Results ; Species Specificity ; }, abstract = {Amphibian populations are dramatically declining, while their inventory is far from being achieved. Tadpoles are usually overlooked from biodiversity survey, whereas their consideration will optimize species counts and knowledge of their ecological and developmental requirements is essential in conservation planning. Two mitochondrial markers, 16S (397 new sequences obtained) and COI (343 new sequences obtained), are used to test DNA barcoding on a set of larval and adult Asian amphibians represented by 83 recognized species from 65 sites. The advantages and drawbacks of each marker are assessed, COI barcoding being advocated for global DNA barcoding, whereas 16S suits for taxonomically or geographically restricted DNA barcoding. About half of the collected tadpoles were badly identified or incompletely named in the field. All tadpole sequences (except one case of probable introgressive hybridization) were correctly assigned to their respective species. Finally six clusters of tadpole sequences without conspecific adults were revealed, stressing the importance of collecting and taking into account tadpoles in biodiversity survey and conservation planning.}, }
@article {pmid25931514, year = {2015}, author = {Hill, GE}, title = {Mitonuclear Ecology.}, journal = {Molecular biology and evolution}, volume = {32}, number = {8}, pages = {1917-1927}, pmid = {25931514}, issn = {1537-1719}, mesh = {Animals ; Cell Nucleus/*genetics ; *Evolution, Molecular ; Genes, Mitochondrial/*physiology ; Genome, Mitochondrial/*physiology ; Humans ; Mitochondria/*genetics ; }, abstract = {Eukaryotes were born of a chimeric union between two prokaryotes--the progenitors of the mitochondrial and nuclear genomes. Early in eukaryote evolution, most mitochondrial genes were lost or transferred to the nucleus, but a core set of genes that code exclusively for products associated with the electron transport system remained in the mitochondrion. The products of these mitochondrial genes work in intimate association with the products of nuclear genes to enable oxidative phosphorylation and core energy production. The need for coadaptation, the challenge of cotransmission, and the possibility of genomic conflict between mitochondrial and nuclear genes have profound consequences for the ecology and evolution of eukaryotic life. An emerging interdisciplinary field that I call "mitonuclear ecology" is reassessing core concepts in evolutionary ecology including sexual reproduction, two sexes, sexual selection, adaptation, and speciation in light of the interactions of mitochondrial and nuclear genomes.}, }
@article {pmid25925750, year = {2015}, author = {Blein, S and Bardel, C and Danjean, V and McGuffog, L and Healey, S and Barrowdale, D and Lee, A and Dennis, J and Kuchenbaecker, KB and Soucy, P and Terry, MB and Chung, WK and Goldgar, DE and Buys, SS and ,  and Janavicius, R and Tihomirova, L and Tung, N and Dorfling, CM and van Rensburg, EJ and Neuhausen, SL and Ding, YC and Gerdes, AM and Ejlertsen, B and Nielsen, FC and Hansen, TV and Osorio, A and Benitez, J and Conejero, RA and Segota, E and Weitzel, JN and Thelander, M and Peterlongo, P and Radice, P and Pensotti, V and Dolcetti, R and Bonanni, B and Peissel, B and Zaffaroni, D and Scuvera, G and Manoukian, S and Varesco, L and Capone, GL and Papi, L and Ottini, L and Yannoukakos, D and Konstantopoulou, I and Garber, J and Hamann, U and Donaldson, A and Brady, A and Brewer, C and Foo, C and Evans, DG and Frost, D and Eccles, D and ,  and Douglas, F and Cook, J and Adlard, J and Barwell, J and Walker, L and Izatt, L and Side, LE and Kennedy, MJ and Tischkowitz, M and Rogers, MT and Porteous, ME and Morrison, PJ and Platte, R and Eeles, R and Davidson, R and Hodgson, S and Cole, T and Godwin, AK and Isaacs, C and Claes, K and De Leeneer, K and Meindl, A and Gehrig, A and Wappenschmidt, B and Sutter, C and Engel, C and Niederacher, D and Steinemann, D and Plendl, H and Kast, K and Rhiem, K and Ditsch, N and Arnold, N and Varon-Mateeva, R and Schmutzler, RK and Preisler-Adams, S and Markov, NB and Wang-Gohrke, S and de Pauw, A and Lefol, C and Lasset, C and Leroux, D and Rouleau, E and Damiola, F and ,  and Dreyfus, H and Barjhoux, L and Golmard, L and Uhrhammer, N and Bonadona, V and Sornin, V and Bignon, YJ and Carter, J and Van Le, L and Piedmonte, M and DiSilvestro, PA and de la Hoya, M and Caldes, T and Nevanlinna, H and Aittomäki, K and Jager, A and van den Ouweland, AM and Kets, CM and Aalfs, CM and van Leeuwen, FE and Hogervorst, FB and Meijers-Heijboer, HE and ,  and Oosterwijk, JC and van Roozendaal, KE and Rookus, MA and Devilee, P and van der Luijt, RB and Olah, E and Diez, O and Teulé, A and Lazaro, C and Blanco, I and Del Valle, J and Jakubowska, A and Sukiennicki, G and Gronwald, J and Lubinski, J and Durda, K and Jaworska-Bieniek, K and Agnarsson, BA and Maugard, C and Amadori, A and Montagna, M and Teixeira, MR and Spurdle, AB and Foulkes, W and Olswold, C and Lindor, NM and Pankratz, VS and Szabo, CI and Lincoln, A and Jacobs, L and Corines, M and Robson, M and Vijai, J and Berger, A and Fink-Retter, A and Singer, CF and Rappaport, C and Kaulich, DG and Pfeiler, G and Tea, MK and Greene, MH and Mai, PL and Rennert, G and Imyanitov, EN and Mulligan, AM and Glendon, G and Andrulis, IL and Tchatchou, S and Toland, AE and Pedersen, IS and Thomassen, M and Kruse, TA and Jensen, UB and Caligo, MA and Friedman, E and Zidan, J and Laitman, Y and Lindblom, A and Melin, B and Arver, B and Loman, N and Rosenquist, R and Olopade, OI and Nussbaum, RL and Ramus, SJ and Nathanson, KL and Domchek, SM and Rebbeck, TR and Arun, BK and Mitchell, G and Karlan, BY and Lester, J and Orsulic, S and Stoppa-Lyonnet, D and Thomas, G and Simard, J and Couch, FJ and Offit, K and Easton, DF and Chenevix-Trench, G and Antoniou, AC and Mazoyer, S and Phelan, CM and Sinilnikova, OM and Cox, DG}, title = {An original phylogenetic approach identified mitochondrial haplogroup T1a1 as inversely associated with breast cancer risk in BRCA2 mutation carriers.}, journal = {Breast cancer research : BCR}, volume = {17}, number = {1}, pages = {61}, pmid = {25925750}, issn = {1465-542X}, support = {U10 CA180868/CA/NCI NIH HHS/United States ; UG1 CA189867/CA/NCI NIH HHS/United States ; R01 CA176785/CA/NCI NIH HHS/United States ; 11174/CRUK_/Cancer Research UK/United Kingdom ; U10 CA027469/CA/NCI NIH HHS/United States ; U01 CA116167/CA/NCI NIH HHS/United States ; R01 CA083855/CA/NCI NIH HHS/United States ; R01 CA116167/CA/NCI NIH HHS/United States ; U10 CA037517/CA/NCI NIH HHS/United States ; N02CP65504/CP/NCI NIH HHS/United States ; R01 CA102776/CA/NCI NIH HHS/United States ; U24 CA196067/CA/NCI NIH HHS/United States ; N02CP11019/CP/NCI NIH HHS/United States ; R01 CA140323/CA/NCI NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; RC4 CA153828/CA/NCI NIH HHS/United States ; U10 CA101165/CA/NCI NIH HHS/United States ; R01 CA142996/CA/NCI NIH HHS/United States ; P50 CA125183/CA/NCI NIH HHS/United States ; UM1 CA164920/CA/NCI NIH HHS/United States ; P30 CA168524/CA/NCI NIH HHS/United States ; U01 CA161032/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R01 CA128978/CA/NCI NIH HHS/United States ; P50 CA116201/CA/NCI NIH HHS/United States ; U01 CA113916/CA/NCI NIH HHS/United States ; }, mesh = {BRCA1 Protein/genetics ; Breast Neoplasms/*genetics ; Female ; *Genes, BRCA2 ; *Genes, Mitochondrial ; Genetic Predisposition to Disease ; Haplotypes ; *Heterozygote ; Humans ; *Mutation ; Phylogeny ; Risk ; }, abstract = {INTRODUCTION: Individuals carrying pathogenic mutations in the BRCA1 and BRCA2 genes have a high lifetime risk of breast cancer. BRCA1 and BRCA2 are involved in DNA double-strand break repair, DNA alterations that can be caused by exposure to reactive oxygen species, a main source of which are mitochondria. Mitochondrial genome variations affect electron transport chain efficiency and reactive oxygen species production. Individuals with different mitochondrial haplogroups differ in their metabolism and sensitivity to oxidative stress. Variability in mitochondrial genetic background can alter reactive oxygen species production, leading to cancer risk. In the present study, we tested the hypothesis that mitochondrial haplogroups modify breast cancer risk in BRCA1/2 mutation carriers.<br><br>METHODS: We genotyped 22,214 (11,421 affected, 10,793 unaffected) mutation carriers belonging to the Consortium of Investigators of Modifiers of BRCA1/2 for 129 mitochondrial polymorphisms using the iCOGS array. Haplogroup inference and association detection were performed using a phylogenetic approach. ALTree was applied to explore the reference mitochondrial evolutionary tree and detect subclades enriched in affected or unaffected individuals.<br><br>RESULTS: We discovered that subclade T1a1 was depleted in affected BRCA2 mutation carriers compared with the rest of clade T (hazard ratio (HR) = 0.55; 95% confidence interval (CI), 0.34 to 0.88; P = 0.01). Compared with the most frequent haplogroup in the general population (that is, H and T clades), the T1a1 haplogroup has a HR of 0.62 (95% CI, 0.40 to 0.95; P = 0.03). We also identified three potential susceptibility loci, including G13708A/rs28359178, which has demonstrated an inverse association with familial breast cancer risk.<br><br>CONCLUSIONS: This study illustrates how original approaches such as the phylogeny-based method we used can empower classical molecular epidemiological studies aimed at identifying association or risk modification effects.}, }
@article {pmid25917582, year = {2015}, author = {Yeşilöz, H and Yıldırım, A}, title = {[The Molecular Classification Of Blackfly (Diptera: Simuliidae) Species Which Pose a Problem in Nevşehir Part of Central Kızılırmak Basin].}, journal = {Turkiye parazitolojii dergisi}, volume = {39}, number = {1}, pages = {33-40}, doi = {10.5152/tpd.2015.3778}, pmid = {25917582}, issn = {2146-3077}, mesh = {Animals ; DNA/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry ; DNA, Ribosomal Spacer/chemistry ; Electron Transport Complex IV/genetics ; Larva/anatomy &amp; histology/genetics ; Mitochondria/enzymology ; *Phylogeny ; RNA, Ribosomal, 28S/genetics ; Simuliidae/anatomy &amp; histology/*classification/genetics ; Turkey ; }, abstract = {OBJECTIVE: This study was carried out to determine the molecular characterization of simuliid species which cause a problem in the part of Kızılırmak passes from Ürgüp and Gülşehir districts of Nevşehir.<br><br>METHODS: Between May and September 2011, totally 150 simuliid larvae were sampled. Morphological identifications of the collected larvae specimens were done before the molecular analyses. Genomic DNA extractions were utilized on 7 larvae specimens which were selected from morphologically identified samples and the sequence and phylogenetic analyses were performed after the amplification of the partial mitochondrial cytochrome oxidase subunit 1 (mt-COI) and ribosomal complete internal transcript spacer 2 and partial 28S (ITS-2/28S) gene regions.<br><br>RESULTS: Eighty-five, 46 and 19 out of 150 morphologically examined specimens were identified as Simulium (S.) Wilhelmia sp., S. Wilhelmia lineatum and S. Wilhelmia balcanicum, respectively. Among the amplified samples with respect to mt-COI and ITS-2/28S gene regions, sequence analyses were performed on 3 and 2 isolates from S. Wilhelmia sp. and both S. lineatum and S. balcanicum. The isolates were found to be clustered together depending on the species for both gene regions phylogenetically and the sequence heterogeneity was found to be higher in S. lineatum. When comparing with the other species under the Wilhelmia subgenus, S. lineatum and S. balcanicum were determined to be more close to each other.<br><br>CONCLUSION: Scientific data on the molecular characterization and phylogeny of blackfly species under the S. Wilhelima subgenus which pose a problem in the Central K&#x131;z&#x131;l&#x131;rmak Basin were provided with this study.}, }
@article {pmid25916611, year = {2015}, author = {Zhang, T and Li, W and Chen, H and Yu, H}, title = {Full genome sequence of a putative novel mitovirus isolated from Rhizoctonia cerealis.}, journal = {Archives of virology}, volume = {160}, number = {7}, pages = {1815-1818}, doi = {10.1007/s00705-015-2431-1}, pmid = {25916611}, issn = {1432-8798}, mesh = {Base Sequence ; *Genome, Viral ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; RNA Viruses/classification/*genetics/*isolation &amp; purification ; Rhizoctonia/*virology ; Viral Proteins/genetics ; }, abstract = {A putative novel mitovirus was found in isolate R1084 of the fungus Rhizoctonia cerealis, the causal agent of sharp eyespot of wheat in China. The full genome sequence of the virus was determined and analyzed. The complete cDNA sequence is 3149 nucleotides long with 59.7% A+T content. Using either the fungal mitochondrial or universal genetic code, the viral genome was found to contain a single large open reading frame that is predicted to encode a protein of 812 amino acids with an RNA-dependent RNA polymerase (RdRp) domain that is conserved in the mitovirus RdRp superfamily. The amino acid sequence of the RdRp domain is only 50% identical to the corresponding domain in Sclerotinia sclerotiorum mitovirus 11, and therefore, this virus is proposed to be a novel mitovirus, designated as Rhizoctonia cerealis mitovirus 1-R1084 (RcMV1-R1084). The distinct codon usage of RcMV1-R1084 hints that this virus is potentially able to replicate not only in mitochondria but also in the cytoplasm. This is the first report of a full-length genomic sequence of a putative mitovirus in R. cerealis.}, }
@article {pmid25916587, year = {2015}, author = {Levin, L and Mishmar, D}, title = {A genetic view of the mitochondrial role in ageing: killing us softly.}, journal = {Advances in experimental medicine and biology}, volume = {847}, number = {}, pages = {89-106}, doi = {10.1007/978-1-4939-2404-2_4}, pmid = {25916587}, issn = {0065-2598}, mesh = {*Aging/genetics ; Animals ; DNA, Mitochondrial/physiology ; Energy Metabolism ; Humans ; Mitochondria/*physiology ; }, abstract = {In contrast to the nuclear genome, the mitochondrial DNA (mtDNA) is maternally inherited and resides in multiple cellular copies that may vary in sequence (heteroplasmy). Although the interaction between mtDNA and nuclear DNA-encoded factors (mito-nuclear interaction) is vital, the mtDNA accumulates mutations an order of magnitude faster than the nuclear genome both during evolution and during the lifetime of the individual, thus requiring tight mito-nuclear co-evolution. These unique features drew the attention of many to suggest a role for the mitochondria in ageing. Although an excess of mtDNA mutations has been found in aged humans and animal models, most of these mutations had minor functional potential. Moreover, there are mtDNA mutations that recur in aged humans, but do not have any clear functionality. Nevertheless, accumulation of recurrent private mutations with minor functionality in the fast-ageing, mtDNA polymerase mutated mice (Pol-gamma), suggested that these very mtDNA alterations participate in ageing. This introduces a paradox: how would either single or recurrent mutations with negligible functionality play a role in a major chronic phenotype such as ageing?Here, we propose a hypothesis to partially resolve this paradox: accumulation of mitochondrial mutations with subtle functionality, which was overlooked by the mechanisms of selection, supplemented by slightly affected fusion-fission cycles, will hamper mitochondrial functional complementation within cells, disrupt mito-nuclear interactions and lead to ageing. Since certain mito-nuclear genotypes are less functionally compatible than others, and since the mtDNA and the nuclear genome segregate independently among generations, mild functionality of mutations will have differential effect on individuals in the population thus explaining the large variability in the ageing phenotype even within ethnic groups. We emphasize the role of recurrent mtDNA mutations with functional potential during evolution and during the lifetime of the individual.}, }
@article {pmid25910726, year = {2015}, author = {Kubiszewski-Jakubiak, S and Megel, C and Ubrig, E and Salinas, T and Duchêne, AM and Maréchal-Drouard, L}, title = {In vitro RNA uptake studies in plant mitochondria.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1305}, number = {}, pages = {45-60}, doi = {10.1007/978-1-4939-2639-8_4}, pmid = {25910726}, issn = {1940-6029}, mesh = {Arabidopsis/genetics/*metabolism ; Electrophoresis, Polyacrylamide Gel/methods ; Mitochondria/genetics/*metabolism ; RNA Transport ; RNA, Plant/genetics/*metabolism ; RNA, Transfer/genetics/*metabolism ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Solanum tuberosum/genetics/*metabolism ; Transcription, Genetic ; }, abstract = {During evolution, most of the ancestral genes from the endosymbiotic α-proteobacteria at the origin of mitochondria have been either lost or transferred to the nuclear genome. To allow the comeback of proteins and RNAs [in particular transfer RNA (tRNAs)] into the organelle, macromolecule import systems were universally established. While protein import processes have been studied into details, much less is known about tRNA mitochondrial import. In plants, part of the knowledge on the tRNA import process into mitochondria has been acquired thanks to in vitro import assays. Furthermore, the development of in vitro RNA import strategies allowed the study of plant mitochondrial gene expression. The purpose of this chapter is to provide detailed protocols to perform in vitro RNA uptake into potato (Solanum tuberosum) or Arabidopsis (Arabidopsis thaliana) mitochondria as well as approaches to analyze them.}, }
@article {pmid25909565, year = {2015}, author = {Loader, SP and Lawson, LP and Portik, DM and Menegon, M}, title = {Three new species of spiny throated reed frogs (Anura: Hyperoliidae) from evergreen forests of Tanzania.}, journal = {BMC research notes}, volume = {8}, number = {}, pages = {167}, pmid = {25909565}, issn = {1756-0500}, mesh = {Altitude ; Animals ; Anura/*physiology ; Bayes Theorem ; Ecosystem ; Female ; *Forests ; Genetic Variation ; Male ; Mitochondria/metabolism ; Nucleotides/genetics ; Phylogeny ; Species Specificity ; Tanzania ; }, abstract = {BACKGROUND: The East African spiny-throated reed frog complex (Hyperolius spinigularis, H. tanneri, and H. minutissimus) is comprised of morphologically similar species with highly fragmented populations across the Eastern Afromontane Region. Recent genetic evidence has supported the distinctiveness of populations suggesting a number of cryptic species. We analyse newly collected morphological data and evaluate the taxonomic distinctiveness of populations.<br><br>RESULTS: We find three new distinct species on the basis of morphological and molecular evidence. The primary morphological traits distinguishing species within the Hyperolius spinigularis complex include the proportions and degree of spinosity of the gular flap in males and snout-urostyle length in females. Other features allow the three species to be distinguished from each other (genetics). We refine the understanding of H. minutissimus which can be found in both forest and grassland habitats of the Udzungwa Mountains, and provide more details on the call of this species. Further details on ecology are noted for all species where known.<br><br>CONCLUSIONS: Three new species are described and we narrow the definition and distribution of Hyperolius spinigularis and H. minutissimus in East Africa. The spiny-throated reed frogs have highly restricted distributions across the fragmented mountains of the Eastern Afromontane region. Given the newly defined and substantially narrower distributions of these spiny-throated reed frog species, conservation concerns are outlined.}, }
@article {pmid25902514, year = {2015}, author = {Gornik, SG and Febrimarsa,  and Cassin, AM and MacRae, JI and Ramaprasad, A and Rchiad, Z and McConville, MJ and Bacic, A and McFadden, GI and Pain, A and Waller, RF}, title = {Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {18}, pages = {5767-5772}, pmid = {25902514}, issn = {1091-6490}, mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Oxidoreductases/metabolism ; Animals ; Cell Nucleus/metabolism ; Crustacea ; Cytosol/metabolism ; Dinoflagellida/genetics/*physiology ; Fatty Acid Synthases/metabolism ; Fatty Acids/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Parasites ; Photosynthesis ; Phylogeny ; Plasmodium ; Plastids/*genetics ; RNA/metabolism ; Symbiosis/*genetics ; Transcriptome ; }, abstract = {Organelle gain through endosymbiosis has been integral to the origin and diversification of eukaryotes, and, once gained, plastids and mitochondria seem seldom lost. Indeed, discovery of nonphotosynthetic plastids in many eukaryotes--notably, the apicoplast in apicomplexan parasites such as the malaria pathogen Plasmodium--highlights the essential metabolic functions performed by plastids beyond photosynthesis. Once a cell becomes reliant on these ancillary functions, organelle dependence is apparently difficult to overcome. Previous examples of endosymbiotic organelle loss (either mitochondria or plastids), which have been invoked to explain the origin of eukaryotic diversity, have subsequently been recognized as organelle reduction to cryptic forms, such as mitosomes and apicoplasts. Integration of these ancient symbionts with their hosts has been too well developed to reverse. Here, we provide evidence that the dinoflagellate Hematodinium sp., a marine parasite of crustaceans, represents a rare case of endosymbiotic organelle loss by the elimination of the plastid. Extensive RNA and genomic sequencing data provide no evidence for a plastid organelle, but, rather, reveal a metabolic decoupling from known plastid functions that typically impede organelle loss. This independence has been achieved through retention of ancestral anabolic pathways, enzyme relocation from the plastid to the cytosol, and metabolic scavenging from the parasite's host. Hematodinium sp. thus represents a further dimension of endosymbiosis--life after the organelle.}, }
@article {pmid25902071, year = {2015}, author = {He, J and Lu, Y and Xia, H and Liang, Y and Wang, X and Bao, W and Yun, S and Ye, Y and Zheng, C and Liu, Z and Shi, S}, title = {Circulating Mitochondrial DAMPs Are Not Effective Inducers of Proteinuria and Kidney Injury in Rodents.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0124469}, pmid = {25902071}, issn = {1932-6203}, mesh = {Animals ; DNA, Mitochondrial/blood ; Kidney/metabolism/pathology ; Kidney Diseases/*complications/*metabolism ; Kinetics ; Liver/metabolism ; Lung/metabolism/pathology ; Mice, Inbred BALB C ; Mitochondria/*metabolism ; Neutrophils/metabolism ; Proteinuria/blood/*complications/*metabolism ; Rats, Sprague-Dawley ; }, abstract = {Mitochondria in eukaryotic cells are derived from bacteria in evolution. Like bacteria, mitochondria contain DNA with unmethylated CpG motifs and formyl peptides, both of which have recently been shown to be damage associated molecular patterns (DAMPs) and induce immune response and cell injury. Based on the facts that circulating mitochondrial DAMPs (mtDAMPs) are increased in the patients of trauma or burn injury who also have proteinuria, that mtDAMPs can activate immune cells which in turn secrete glomerular permeability factors, that renal intrinsic cells express a variety of DAMP receptors, and that mtDAMPs can directly increase endothelial cell permeability in vitro, we hypothesized that mtDAMPs may be novel circulating factors inducing proteinuria and kidney injury. We tested this hypothesis by directly injecting mtDAMPs into rodents and examining urinary protein and kidney histology. We prepared mtDAMP samples, including mitochondrial DNA (mtDNA) and mitochondrial debris (MTD), from rodent liver. In mice, injection of mtDNA for 20 μg/ml initial concentration in circulation (much higher than the clinical range), did not cause any renal manifestations. However, an increased dose leading to 45 μg/ml initial concentration in circulation resulted in a transient, slight increase in urinary albumin. In rats, MTD injection resulting in 450 μg/ml initial concentration of MTD protein in circulation, which was much higher than the clinical range, caused mild, transient proteinuria and lung lesions. Multiple injections of such large amount of either mtDNA or MTD into rodents on 3 consecutive days also failed in inducing proteinuria and kidney injury. In summary, clinical levels of circulating mtDAMPs do not induce proteinuria and clinically irrelevant high levels of mtDAMPs cause only a transient and slight increase in urinary protein in rodents, suggesting that circulating mtDAMPs may not be responsible for the proteinuria and kidney injury in patients with trauma, burn injury, and other diseases.}, }
@article {pmid25896956, year = {2015}, author = {Zhang, Y and Zhang, S and Zhang, G and Liu, X and Wang, C and Xu, J}, title = {Comparison of mitochondrial genomes provides insights into intron dynamics and evolution in the caterpillar fungus Cordyceps militaris.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {77}, number = {}, pages = {95-107}, doi = {10.1016/j.fgb.2015.04.009}, pmid = {25896956}, issn = {1096-0937}, mesh = {Animals ; Cordyceps/*genetics/pathogenicity/ultrastructure ; *Evolution, Molecular ; Exons ; Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Introns ; Larva/microbiology ; Mitochondrial Proteins/genetics ; Phylogeny ; }, abstract = {Intra-specific comparison of mitochondrial genomes can help elucidate the evolution of a species, however it has not been performed for hypocrealean fungi that form diverse symbiotic associations with other organisms. In this study, comparative analyses of three completely sequenced mitochondrial genomes of a hypocrealean fungus, Cordyceps militaris, the type species of Cordyceps genus, revealed that the introns were the main contributors to mitochondrial genome size variations among strains. Mitochondrial genes in C. militaris have been invaded by group I introns in at least eight positions. PCR assays of various C. militaris isolates showed abundant variations of intron presence/absence among strains at seven of the eight intronic loci. Although the ancestral intron pattern was inferred to contain all eight introns, loss and/or gain events occurred for seven of the eight introns. These introns invaded the C. militaris mitochondrial genome probably by horizontal transfer from other fungi, and intron insertions into intronless genes in C. militaris were accompanied by co-conversions of upstream exon sequences especially for those introns targeting protein-coding genes. We also detected phylogenetic congruence between the intron and exon trees at each individual locus, consistent with the ancestral mitochondria of C. militaris as having all eight introns. This study helps to explain the evolution of C. militaris mitochondrial genomes and will facilitate population genetic studies of this medicinally important fungus.}, }
@article {pmid25893565, year = {2015}, author = {Liu, F and Pang, S}, title = {Mitochondrial genome of Turbinaria ornata (Sargassaceae, Phaeophyceae): comparative mitogenomics of brown algae.}, journal = {Current genetics}, volume = {61}, number = {4}, pages = {621-631}, pmid = {25893565}, issn = {1432-0983}, mesh = {Biological Evolution ; Chromosome Mapping ; Coral Reefs ; DNA, Intergenic/*chemistry ; DNA, Mitochondrial/*genetics ; *Genome, Mitochondrial ; Mitochondria/genetics ; *Open Reading Frames ; Phaeophyceae/classification/*genetics ; Phylogeny ; }, abstract = {Turbinaria ornata (Turner) J. Agardh is a perennial brown alga native to coral reef ecosystems of tropical areas of the Pacific and Indian Ocean. Very little is known about its organellar genome structure. In the present work, the complete mitochondrial genome sequence of T. ornata was determined and compared with other reported brown algal mtDNAs. The circular mitogenome of 34,981 bp contains a basic set of 65 mitochondrial genes. The structure and organization of T. ornata mitogenome is very similar to Sargassum species. Turbinaria ornata genes overlap by a total of 164 bp in 12 different locations from 1 to 66 bp, and the non-coding sequences are 1872 bp, constituting approximate 5.35 % of the genome. The total spacer size has positive correlation with the brown algal mitogenome size with the correlation coefficient of 0.7972. Several regions displaying greater inconsistency (rnl-trnK spacer, cox2 gene, cox3-atp6 spacer, rps14-rns middle region and trnP-rnl spacer) have been identified in brown algal mtDNAs. The observed uncertainty regarding the position and support values of some branches might be closely associated with the heterogeneity of evolutionary rate.}, }
@article {pmid25889953, year = {2015}, author = {Gutiérrez-Aguilar, M and Uribe-Carvajal, S}, title = {The mitochondrial unselective channel in Saccharomyces cerevisiae.}, journal = {Mitochondrion}, volume = {22}, number = {}, pages = {85-90}, doi = {10.1016/j.mito.2015.04.002}, pmid = {25889953}, issn = {1872-8278}, mesh = {Ion Channels/*metabolism ; Mitochondrial Membrane Transport Proteins/*metabolism ; Mitochondrial Membranes/*enzymology/*metabolism ; Mitochondrial Permeability Transition Pore ; Saccharomyces cerevisiae/*enzymology/*metabolism ; }, abstract = {Opening of the mitochondrial permeability transition (MPT) pore mediates the increase in the unselective permeability to ions and small molecules across the inner mitochondrial membrane. MPT results from the opening of channels of unknown identity in mitochondria from plants, animals and yeast. However, the effectors and conditions required for MPT to occur in different species are remarkably disparate. Here we critically review previous and recent findings concerning the mitochondrial unselective channel of the yeast Saccharomyces cerevisiae to determine if it can be considered a counterpart of the mammalian MPT pore.}, }
@article {pmid25885076, year = {2015}, author = {Fanciulli, PP and Mercati, D and Machida, R and Dallai, R}, title = {Spermiogenesis and sperm ultrastructure of Machilontus sp (Insecta: Archaeognatha) with phylogenetic consideration.}, journal = {Micron (Oxford, England : 1993)}, volume = {73}, number = {}, pages = {47-53}, doi = {10.1016/j.micron.2015.03.011}, pmid = {25885076}, issn = {1878-4291}, mesh = {Acrosome/ultrastructure ; Animals ; Axoneme ; Cell Nucleus/ultrastructure ; Insecta/*physiology/*ultrastructure ; Male ; Microscopy, Electron, Transmission/methods ; Microtubules/ultrastructure ; Phylogeny ; Species Specificity ; Sperm Tail/ultrastructure ; Spermatids/ultrastructure ; Spermatogenesis ; Spermatozoa/*ultrastructure ; }, abstract = {The sperm structure of the jumping bristletail Machilontus sp has been described. The species shares several sperm characteristics with other genera of the same order Archaeognatha. During late spermiogenesis the spermatid bends at half of its length with the two limbs closely apposed within the same plasma membrane. The sperm has a helicoidal bi-layered acrosome with a filamentous perforatorium and a long nucleus. The elongated flagellum consists of an axoneme with 9 accessory microtubules external to the 9+2, two rows of conventional mitochondria and two accessory bodies. The accessory bodies are located lateral to the axoneme and are probably responsible for the shifting of the accessory tubules in two opposite groups of 5 and 4 tubules, respectively. These sperm characteristics represent common traits of all Archaeognatha.}, }
@article {pmid25883267, year = {2015}, author = {Booth, A and Doolittle, WF}, title = {Eukaryogenesis, how special really?.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10278-10285}, pmid = {25883267}, issn = {1091-6490}, mesh = {Animals ; *Biological Evolution ; Energy Metabolism ; Escherichia coli/metabolism ; Eukaryota/*metabolism ; Eukaryotic Cells/cytology ; Evolution, Molecular ; Genome, Bacterial ; Humans ; Introns ; Mitochondria/metabolism/physiology ; *Origin of Life ; Phenotype ; Phylogeny ; Plants ; Prokaryotic Cells/cytology ; Spliceosomes/physiology ; }, abstract = {Eukaryogenesis is widely viewed as an improbable evolutionary transition uniquely affecting the evolution of life on this planet. However, scientific and popular rhetoric extolling this event as a singularity lacks rigorous evidential and statistical support. Here, we question several of the usual claims about the specialness of eukaryogenesis, focusing on both eukaryogenesis as a process and its outcome, the eukaryotic cell. We argue in favor of four ideas. First, the criteria by which we judge eukaryogenesis to have required a genuinely unlikely series of events 2 billion years in the making are being eroded by discoveries that fill in the gaps of the prokaryote:eukaryote "discontinuity." Second, eukaryogenesis confronts evolutionary theory in ways not different from other evolutionary transitions in individuality; parallel systems can be found at several hierarchical levels. Third, identifying which of several complex cellular features confer on eukaryotes a putative richer evolutionary potential remains an area of speculation: various keys to success have been proposed and rejected over the five-decade history of research in this area. Fourth, and perhaps most importantly, it is difficult and may be impossible to eliminate eukaryocentric bias from the measures by which eukaryotes as a whole are judged to have achieved greater success than prokaryotes as a whole. Overall, we question whether premises of existing theories about the uniqueness of eukaryogenesis and the greater evolutionary potential of eukaryotes have been objectively formulated and whether, despite widespread acceptance that eukaryogenesis was "special," any such notion has more than rhetorical value.}, }
@article {pmid25882680, year = {2015}, author = {Manna, S}, title = {An overview of pentatricopeptide repeat proteins and their applications.}, journal = {Biochimie}, volume = {113}, number = {}, pages = {93-99}, doi = {10.1016/j.biochi.2015.04.004}, pmid = {25882680}, issn = {1638-6183}, mesh = {Animals ; *Evolution, Molecular ; Humans ; RNA Processing, Post-Transcriptional/*physiology ; RNA-Binding Proteins/*genetics/*metabolism ; }, abstract = {Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. These proteins facilitate processing, splicing, editing, stability and translation of RNAs. While major advances in PPR research have been achieved with plant PPR proteins, the significance of non-plant PPR proteins is becoming of increasing importance. PPR proteins are classified into different subclasses based on their domain architecture, which is often a reflection of their function. This review provides an overview of the significant findings regarding the functions, evolution and applications of PPR proteins. Horizontal gene transfer appears to have played a major role in the sporadic phylogenetic distribution of different PPR subclasses in both eukaryotes and prokaryotes. Additionally, the use of synthetic biology and protein engineering to create designer PPR proteins to control gene expression in vivo is discussed. This review also highlights some of the aspects of PPR research that require more attention particularly in non-plant organisms. This includes the lack of research into the recently discovered PPR-TGM subclass, which is not only the first PPR subclass absent from plants but present in economically and clinically-relevant pathogens. Investigation into the structure and function of PPR-TGM proteins in these pathogens presents a novel opportunity for the exploitation of PPR proteins as drug targets to prevent disease.}, }
@article {pmid25880558, year = {2015}, author = {Christie, JR and Schaerf, TM and Beekman, M}, title = {Selection against heteroplasmy explains the evolution of uniparental inheritance of mitochondria.}, journal = {PLoS genetics}, volume = {11}, number = {4}, pages = {e1005112}, pmid = {25880558}, issn = {1553-7404}, mesh = {Animals ; Evolution, Molecular ; *Genes, Mitochondrial ; *Haplotypes ; Humans ; Mitochondria/*genetics ; *Models, Genetic ; *Selection, Genetic ; }, abstract = {Why are mitochondria almost always inherited from one parent during sexual reproduction? Current explanations for this evolutionary mystery include conflict avoidance between the nuclear and mitochondrial genomes, clearing of deleterious mutations, and optimization of mitochondrial-nuclear coadaptation. Mathematical models, however, fail to show that uniparental inheritance can replace biparental inheritance under any existing hypothesis. Recent empirical evidence indicates that mixing two different but normal mitochondrial haplotypes within a cell (heteroplasmy) can cause cell and organism dysfunction. Using a mathematical model, we test if selection against heteroplasmy can lead to the evolution of uniparental inheritance. When we assume selection against heteroplasmy and mutations are neither advantageous nor deleterious (neutral mutations), uniparental inheritance replaces biparental inheritance for all tested parameter values. When heteroplasmy involves mutations that are advantageous or deleterious (non-neutral mutations), uniparental inheritance can still replace biparental inheritance. We show that uniparental inheritance can evolve with or without pre-existing mating types. Finally, we show that selection against heteroplasmy can explain why some organisms deviate from strict uniparental inheritance. Thus, we suggest that selection against heteroplasmy explains the evolution of uniparental inheritance.}, }
@article {pmid25880387, year = {2015}, author = {Nguyen, DT and Spooner-Hart, RN and Riegler, M}, title = {Polyploidy versus endosymbionts in obligately thelytokous thrips.}, journal = {BMC evolutionary biology}, volume = {15}, number = {}, pages = {23}, pmid = {25880387}, issn = {1471-2148}, mesh = {Animals ; Cell Nucleus/genetics ; Female ; Genetic Variation ; Male ; Mitochondria/genetics ; *Parthenogenesis ; Phylogeny ; Polymerase Chain Reaction ; *Polyploidy ; Symbiosis ; Thysanoptera/classification/*genetics/*microbiology/physiology ; Wolbachia/genetics/*isolation &amp; purification ; }, abstract = {BACKGROUND: Thelytoky, the parthenogenetic development of females, has independently evolved in several insect orders yet the study of its mechanisms has so far mostly focussed on haplodiploid Hymenoptera, while alternative mechanisms of thelytoky such as polyploidy are far less understood. In haplodiploid insects, thelytoky can be encoded in their genomes, or induced by maternally inherited bacteria such as Wolbachia or Cardinium. Microbially facilitated thelytoky usually results in complete homozygosity due to gamete duplication and can be reverted into arrhenotoky, the parthenogenetic development of males, through treatment with antibiotics. In contrast, genetically encoded thelytoky cannot be removed and may result in conservation of heterozygosity due to gamete fusion. We have probed the obligate thelytoky of the greenhouse thrips, Heliothrips haemorrhoidalis (Bouché), a significant cosmopolitan pest and a model species of thelytoky in the haplodiploid insect order Thysanoptera. Earlier studies suggested terminal fusion as a mechanism for thelytoky in this species, while another study reported presence of Wolbachia; later it was speculated that Wolbachia plays a role in this thrips' thelytokous reproduction.<br><br>RESULTS: By using PCR and sequence analysis, we demonstrated that global population samples of H. haemorrhoidalis were not infected with Wolbachia, Cardinium or any other known bacterial reproductive manipulators. Antibiotic treatment of this thrips did also not result in male production. Some individuals carried two different alleles in two nuclear loci, histone 3 and elongation factor 1 alpha, suggesting heterozygosity. However, the majority of individuals had three different alleles suggesting that they were polyploid. Genetic diversity across both nuclear loci was low in all populations, and absent from mitochondrial cytochrome oxidase I, indicating that this species had experienced genetic bottlenecks, perhaps due to its invasion biology or a switch to thelytoky.<br><br>CONCLUSIONS: Geographically broad sampling and experimental manipulation revealed low genetic diversity, absence of Wolbachia but presence of three different alleles of nuclear loci in most analysed individuals of obligately thelytokous H. haemorrhoidalis. This suggests that polyploidy may be involved in the thelytokous reproduction of this thrips species, and polyploidy may be a contributing factor in the reproduction of Thysanoptera and other haplodiploid insect orders.}, }
@article {pmid25878088, year = {2015}, author = {Govindarajulu, R and Parks, M and Tennessen, JA and Liston, A and Ashman, TL}, title = {Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species.}, journal = {American journal of botany}, volume = {102}, number = {4}, pages = {544-554}, doi = {10.3732/ajb.1500026}, pmid = {25878088}, issn = {1537-2197}, mesh = {Cell Nucleus/genetics ; Evolution, Molecular ; Fragaria/*genetics/metabolism ; *Genome, Chloroplast ; *Genome, Mitochondrial ; *Genome, Plant ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {PREMISE OF THE STUDY: Molecular phylogenies derived from all three plant genomes can provide insight into the evolutionary history of plant groups influenced by reticulation. We sought to reconstruct mitochondrial exome, chloroplast, and nuclear genome phylogenies for octoploid Fragaria and their diploid ancestors and to document patterns of incongruence between and within the cytoplasmic genomes and interpret these in the context of evolutionary origin of the octoploid strawberries.<br><br>METHODS: Using a genome-skimming approach, we assembled chloroplast genomes and mitochondrial exomes, and we used the POLiMAPS method to assemble nuclear sequence for octoploid species and constructed phylogenies from all three genomes. We assessed incongruence between and within cytoplasmic genomes using topology-based phylogenetic incongruence tests.<br><br>KEY RESULTS: The incongruent cytoplasmic genome phylogeny with respect to the placement of octoploids suggests potential breakage in linkage disequilibrium of cytoplasmic genomes during allopolyploid origin of the octoploids. Furthermore, a single mitochondrial chimeric gene with a putative role in cytoplasmic male sterility yields a phylogeny that is inconsistent with the rest of the mitochondrial genome but consistent with the chloroplast phylogeny, suggesting intracellular gene transfer between heteroplasmic mitochondria, possibly driven by selection to overcome the effects of mito-nuclear incompatibility in octoploid origins.<br><br>CONCLUSIONS: This work expands on the current understanding of evolutionary history of the octoploid ancestors of cultivated strawberry. It demonstrates phylogenetic incongruence between cytoplasmic genomes in octoploids with respect to diploid ancestors, indicating breakage in linkage disequilibrium of cytoplasmic genomes. We discuss potential organism-level processes that may have contributed to the observed incongruence in Fragaria.}, }
@article {pmid25877339, year = {2015}, author = {Catalano, SR and Whittington, ID and Donnellan, SC and Bertozzi, T and Gillanders, BM}, title = {First comparative insight into the architecture of COI mitochondrial minicircle molecules of dicyemids reveals marked inter-species variation.}, journal = {Parasitology}, volume = {142}, number = {8}, pages = {1066-1079}, doi = {10.1017/S0031182015000384}, pmid = {25877339}, issn = {1469-8161}, mesh = {Animals ; Base Sequence ; Cephalopoda/*parasitology ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Genome, Mitochondrial/*genetics ; Invertebrates/*classification/enzymology/genetics ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Untranslated/genetics ; Sequence Alignment/veterinary ; Sequence Analysis, DNA/veterinary ; Species Specificity ; }, abstract = {Dicyemids, poorly known parasites of benthic cephalopods, are one of the few phyla in which mitochondrial (mt) genome architecture departs from the typical ~16 kb circular metazoan genome. In addition to a putative circular genome, a series of mt minicircles that each comprises the mt encoded units (I-III) of the cytochrome c oxidase complex have been reported. Whether the structure of the mt minicircles is a consistent feature among dicyemid species is unknown. Here we analyse the complete cytochrome c oxidase subunit I (COI) minicircle molecule, containing the COI gene and an associated non-coding region (NCR), for ten dicyemid species, allowing for first time comparisons between species of minicircle architecture, NCR function and inferences of minicircle replication. Divergence in COI nucleotide sequences between dicyemid species was high (average net divergence = 31.6%) while within species diversity was lower (average net divergence = 0.2%). The NCR and putative 5' section of the COI gene were highly divergent between dicyemid species (average net nucleotide divergence of putative 5' COI section = 61.1%). No tRNA genes were found in the NCR, although palindrome sequences with the potential to form stem-loop structures were identified in some species, which may play a role in transcription or other biological processes.}, }
@article {pmid25876460, year = {2015}, author = {Morales, HE and Pavlova, A and Joseph, L and Sunnucks, P}, title = {Positive and purifying selection in mitochondrial genomes of a bird with mitonuclear discordance.}, journal = {Molecular ecology}, volume = {24}, number = {11}, pages = {2820-2837}, doi = {10.1111/mec.13203}, pmid = {25876460}, issn = {1365-294X}, mesh = {Amino Acid Substitution ; Animals ; *Evolution, Molecular ; Female ; Genetic Variation ; *Genetics, Population ; *Genome, Mitochondrial ; Models, Genetic ; Molecular Sequence Data ; Passeriformes/*genetics ; Phylogeny ; *Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {Diversifying selection on metabolic pathways can reduce intraspecific gene flow and promote population divergence. An opportunity to explore this arises from mitonuclear discordance observed in an Australian bird Eopsaltria australis. Across >1500 km, nuclear differentiation is low and latitudinally structured by isolation by distance, whereas two highly divergent, parapatric mitochondrial lineages (>6.6% in ND2) show a discordant longitudinal geographic pattern and experience different climates. Vicariance, incomplete lineage sorting and sex-biased dispersal were shown earlier to be unlikely drivers of the mitonuclear discordance; instead, natural selection on a female-linked trait was the preferred hypothesis. Accordingly, here we tested for signals of positive, divergent selection on mitochondrial genes in E. australis. We used codon models and physicochemical profiles of amino acid replacements to analyse complete mitochondrial genomes of the two mitochondrial lineages in E. australis, its sister species Eopsaltria griseogularis, and outgroups. We found evidence of positive selection on at least five amino acids, encoded by genes of two oxidative phosphorylation pathway complexes NADH dehydrogenase (ND4 and ND4L) and cytochrome bc1 (cyt-b) against a background of widespread purifying selection on all mitochondrial genes. Three of these amino acid replacements were fixed in ND4 of the geographically most widespread E. australis lineage. The other two replacements were fixed in ND4L and cyt-b of the geographically more restricted E. australis lineage. We discuss whether this selection may reflect local environmental adaptation, a by-product of other selective processes, or genetic incompatibilities, and propose how these hypotheses can be tested in future.}, }
@article {pmid25870770, year = {2015}, author = {Bruenn, JA and Warner, BE and Yerramsetty, P}, title = {Widespread mitovirus sequences in plant genomes.}, journal = {PeerJ}, volume = {3}, number = {}, pages = {e876}, pmid = {25870770}, issn = {2167-8359}, abstract = {The exploration of the evolution of RNA viruses has been aided recently by the discovery of copies of fragments or complete genomes of non-retroviral RNA viruses (Non-retroviral Endogenous RNA Viral Elements, or NERVEs) in many eukaryotic nuclear genomes. Among the most prominent NERVEs are partial copies of the RNA dependent RNA polymerase (RdRP) of the mitoviruses in plant mitochondrial genomes. Mitoviruses are in the family Narnaviridae, which are the simplest viruses, encoding only a single protein (the RdRP) in their unencapsidated viral plus strand. Narnaviruses are known only in fungi, and the origin of plant mitochondrial mitovirus NERVEs appears to be horizontal transfer from plant pathogenic fungi. At least one mitochondrial mitovirus NERVE, but not its nuclear copy, is expressed.}, }
@article {pmid25869380, year = {2015}, author = {Smith, DR}, title = {Mutation rates in plastid genomes: they are lower than you might think.}, journal = {Genome biology and evolution}, volume = {7}, number = {5}, pages = {1227-1234}, pmid = {25869380}, issn = {1759-6653}, mesh = {Chlorophyta/genetics ; DNA, Mitochondrial/chemistry ; Genome, Mitochondrial ; *Genome, Plastid ; *Mutation Rate ; Plants/genetics ; Rhodophyta/genetics ; }, abstract = {Within plastid-bearing species, the mutation rate of the plastid genome is often assumed to be greater than that of the mitochondrial genome. This assumption is based on early, pioneering studies of land plant molecular evolution, which uncovered higher rates of synonymous substitution in plastid versus mitochondrial DNAs. However, much of the plastid-containing eukaryotic diversity falls outside of land plants, and the patterns of plastid DNA evolution for embryophytes do not necessarily reflect those of other groups. Recent analyses of plastid and mitochondrial substitution rates in diverse lineages have uncovered very different trends than those recorded for land plants. Here, I explore these new data and argue that for many protists the plastid mutation rate is lower than that of the mitochondrion, including groups with primary or secondary plastids as well as nonphotosynthetic algae. These findings have far-reaching implications for how we view plastid genomes and how their sequences are used for evolutionary analyses, and might ultimately reflect a general tendency toward more efficient DNA repair mechanisms in plastids than in mitochondria.}, }
@article {pmid25869358, year = {2015}, author = {Samuilov, VD and Kiselevsky, DB}, title = {Effect of cationic plastoquinone SkQ1 on electron transfer reactions in chloroplasts and mitochondria from pea seedlings.}, journal = {Biochemistry. Biokhimiia}, volume = {80}, number = {4}, pages = {417-423}, doi = {10.1134/S0006297915040045}, pmid = {25869358}, issn = {1608-3040}, mesh = {Cell Respiration/drug effects ; Chloroplasts/*drug effects/metabolism ; Electron Transport/drug effects ; Mitochondria/*drug effects/metabolism ; Pisum sativum/*drug effects/metabolism ; Photosynthetic Reaction Center Complex Proteins/drug effects ; Plastoquinone/*analogs &amp; derivatives/pharmacology ; Seedlings/*drug effects/metabolism ; }, abstract = {Plastoquinone bound with decyltriphenylphosphonium cation (SkQ1) penetrating through the membrane in nanomolar concentrations inhibited H2O2 generation in cells of epidermis of pea seedling leaves that was detected by the fluorescence of 2',7'-dichlorofluorescein. Photosynthetic electron transfer in chloroplasts isolated from pea leaves is suppressed by SkQ1 at micromolar concentrations: the electron transfer in chloroplasts under the action of photosystem II or I (with silicomolybdate or methyl viologen as electron acceptors, respectively) is more sensitive to SkQ1 than under the action of photosystem II + I (with ferricyanide or p-benzoquinone as electron acceptors). SkQ1 reduced by borohydride is oxidized by ferricyanide, p-benzoquinone, and, to a lesser extent, by silicomolybdate, but not by methyl viologen. SkQ1 is not effective as an electron acceptor supporting O2 evolution from water in illuminated chloroplasts. The data on suppression of photosynthetic O2 evolution or consumption show that SkQ1, similarly to phenazine methosulfate, causes conversion of the chloroplast redox-chain from non-cyclic electron transfer mode to the cyclic mode without O2 evolution. Oxidation of NADH or succinate in mitochondria isolated from pea roots is stimulated by SkQ1.}, }
@article {pmid25868525, year = {2016}, author = {Li, X and Lu, J and Lu, J and Hu, X and Huang, Z}, title = {The complete mitochondrial genome of the American crow, Corvus brachyrhynchos (Passeriformes, Corvidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4213-4214}, doi = {10.3109/19401736.2015.1022745}, pmid = {25868525}, issn = {2470-1408}, mesh = {Animals ; Avian Proteins/genetics ; Crows/*genetics ; *Genome, Mitochondrial ; Mitochondrial Proteins/genetics ; *Phylogeny ; RNA/genetics ; RNA, Mitochondrial ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {The American crow, Corvus brachyrhynchos (Passeriformes, Corvidae), is a large passerine bird species closely related to the raven. Herein, we first published the complete mitochondrial genome of American crows. The mitogenome was 16,917 bp long, and composed of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one putative control region. Most protein-coding genes started with a traditional ATG codon except for COI, which initiated with an infrequent start codon GTG instead, and terminated with the mitochondria stop codon (TAA/AGG/AGA) or a single T base. The mitogenome structural organization is identical to that of the other corvus species and related genera. The overall GC content is 44.25% which is lower than AT. Using the 12 protein-coding genes of Corvus brachyrhynchos in this study, together with 10 other closely species, we constructed the species phylogenetic tree to verify the accuracy and utility of new determined mitogenome sequences. We expect that using the full mitogenome to address taxonomic issues and study the related evolution events. Moreover, this is the first report of bird mitogenomes after 48 avian species genome project achievements released in December 2014.}, }
@article {pmid25865816, year = {2015}, author = {Kake-Guena, SA and Touisse, K and Vergilino, R and Dufresne, F and Blier, PU and Lemieux, H}, title = {Assessment of mitochondrial functions in Daphnia pulex clones using high-resolution respirometry.}, journal = {Journal of experimental zoology. Part A, Ecological genetics and physiology}, volume = {323}, number = {5}, pages = {292-300}, doi = {10.1002/jez.1913}, pmid = {25865816}, issn = {1932-5231}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/genetics/metabolism ; Daphnia/genetics/*metabolism ; Energy Metabolism ; Environment ; Genetic Variation ; Haplotypes ; Mitochondria/genetics/*metabolism ; Oxidative Phosphorylation ; Ploidies ; Sequence Analysis, DNA ; }, abstract = {The objectives of our study were to adapt a method to measure mitochondrial function in intact mitochondria from the small crustacean Daphnia pulex and to validate if this method was sensitive enough to characterize mitochondrial metabolism in clones of the pulex complex differing in ploidy levels, mitochondrial DNA haplotypes, and geographic origins. Daphnia clones belonging to the Daphnia pulex complex represent a powerful model to delineate the link between mitochondrial DNA evolution and mitochondrial phenotypes, as single genotypes with divergent mtDNA can be grown under various experimental conditions. Our study included two diploid clones from temperate environments and two triploid clones from subarctic environments. The whole animal permeabilization and measurement of respiration with high-resolution respirometry enabled the measurement of the functional capacity of specific mitochondrial complexes in four clones. When expressing the activity as ratios, our method detected significant interclonal variations. In the triploid subarctic clone from Kuujjurapik, a higher proportion of the maximal physiological oxidative phosphorylation (OXPHOS) capacity of mitochondria was supported by complex II, and a lower proportion by complex I. The triploid subarctic clone from Churchill (Manitoba) showed the lowest proportion of the maximal OXPHOS supported by complex II. Additional studies are required to determine if these differences in mitochondrial functions are related to differences in mitochondrial haplotypes or ploidy level and if they might be associated with fitness divergences and therefore selective value.}, }
@article {pmid25861990, year = {2015}, author = {Antonenkov, VD and Isomursu, A and Mennerich, D and Vapola, MH and Weiher, H and Kietzmann, T and Hiltunen, JK}, title = {The Human Mitochondrial DNA Depletion Syndrome Gene MPV17 Encodes a Non-selective Channel That Modulates Membrane Potential.}, journal = {The Journal of biological chemistry}, volume = {290}, number = {22}, pages = {13840-13861}, pmid = {25861990}, issn = {1083-351X}, mesh = {Amino Acid Sequence ; Animals ; Autophagy ; Circular Dichroism ; DNA Damage ; DNA, Mitochondrial/*genetics ; Fibroblasts/metabolism ; Fluoresceins/chemistry ; Genotype ; Homeostasis ; Humans ; Hydrogen-Ion Concentration ; Mass Spectrometry ; *Membrane Potential, Mitochondrial ; Membrane Proteins/*genetics ; Mice ; Mice, Transgenic ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Oxidation-Reduction ; Phosphorylation ; Phylogeny ; Pichia/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {The human MPV17-related mitochondrial DNA depletion syndrome is an inherited autosomal recessive disease caused by mutations in the inner mitochondrial membrane protein MPV17. Although more than 30 MPV17 gene mutations were shown to be associated with mitochondrial DNA depletion syndrome, the function of MPV17 is still unknown. Mice deficient in Mpv17 show signs of premature aging. In the present study, we used electrophysiological measurements with recombinant MPV17 to reveal that this protein forms a non-selective channel with a pore diameter of 1.8 nm and located the channel's selectivity filter. The channel was weakly cation-selective and showed several subconductance states. Voltage-dependent gating of the channel was regulated by redox conditions and pH and was affected also in mutants mimicking a phosphorylated state. Likewise, the mitochondrial membrane potential (Δψm) and the cellular production of reactive oxygen species were higher in embryonic fibroblasts from Mpv17(-/-) mice. However, despite the elevated Δψm, the Mpv17-deficient mitochondria showed signs of accelerated fission. Together, these observations uncover the role of MPV17 as a Δψm-modulating channel that apparently contributes to mitochondrial homeostasis under different conditions.}, }
@article {pmid25861818, year = {2015}, author = {van der Sluis, EO and Bauerschmitt, H and Becker, T and Mielke, T and Frauenfeld, J and Berninghausen, O and Neupert, W and Herrmann, JM and Beckmann, R}, title = {Parallel Structural Evolution of Mitochondrial Ribosomes and OXPHOS Complexes.}, journal = {Genome biology and evolution}, volume = {7}, number = {5}, pages = {1235-1251}, pmid = {25861818}, issn = {1759-6653}, mesh = {*Evolution, Molecular ; Genes, Mitochondrial ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Mutation ; Neurospora crassa/genetics ; Oxidative Phosphorylation ; Protein Subunits/genetics ; RNA, Ribosomal/chemistry ; Ribosomal Proteins/chemistry ; Ribosomes/*chemistry/ultrastructure ; }, abstract = {The five macromolecular complexes that jointly mediate oxidative phosphorylation (OXPHOS) in mitochondria consist of many more subunits than those of bacteria, yet, it remains unclear by which evolutionary mechanism(s) these novel subunits were recruited. Even less well understood is the structural evolution of mitochondrial ribosomes (mitoribosomes): while it was long thought that their exceptionally high protein content would physically compensate for their uniquely low amount of ribosomal RNA (rRNA), this hypothesis has been refuted by structural studies. Here, we present a cryo-electron microscopy structure of the 73S mitoribosome from Neurospora crassa, together with genomic and proteomic analyses of mitoribosome composition across the eukaryotic domain. Surprisingly, our findings reveal that both structurally and compositionally, mitoribosomes have evolved very similarly to mitochondrial OXPHOS complexes via two distinct phases: A constructive phase that mainly acted early in eukaryote evolution, resulting in the recruitment of altogether approximately 75 novel subunits, and a reductive phase that acted during metazoan evolution, resulting in gradual length-reduction of mitochondrially encoded rRNAs and OXPHOS proteins. Both phases can be well explained by the accumulation of (slightly) deleterious mutations and deletions, respectively, in mitochondrially encoded rRNAs and OXPHOS proteins. We argue that the main role of the newly recruited (nuclear encoded) ribosomal- and OXPHOS proteins is to provide structural compensation to the mutationally destabilized mitochondrially encoded components. While the newly recruited proteins probably provide a selective advantage owing to their compensatory nature, and while their presence may have opened evolutionary pathways toward novel mitochondrion-specific functions, we emphasize that the initial events that resulted in their recruitment was nonadaptive in nature. Our framework is supported by population genetic studies, and it can explain the complete structural evolution of mitochondrial ribosomes and OXPHOS complexes, as well as many observed functions of individual proteins.}, }
@article {pmid25854186, year = {2015}, author = {Breitenbach, M and Weber, M and Rinnerthaler, M and Karl, T and Breitenbach-Koller, L}, title = {Oxidative stress in fungi: its function in signal transduction, interaction with plant hosts, and lignocellulose degradation.}, journal = {Biomolecules}, volume = {5}, number = {2}, pages = {318-342}, pmid = {25854186}, issn = {2218-273X}, support = {P 26713/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Amino Acid Sequence ; Fungi/enzymology/genetics/*metabolism/pathogenicity ; Lignin/*metabolism ; Molecular Sequence Data ; *Oxidative Stress ; Oxidoreductases/metabolism ; Phylogeny ; Reactive Oxygen Species/metabolism ; *Signal Transduction ; Virulence/genetics ; }, abstract = {In this review article, we want to present an overview of oxidative stress in fungal cells in relation to signal transduction, interaction of fungi with plant hosts, and lignocellulose degradation. We will discuss external oxidative stress which may occur through the interaction with other microorganisms or plant hosts as well as internally generated oxidative stress, which can for instance originate from NADPH oxidases or "leaky" mitochondria and may be modulated by the peroxiredoxin system or by protein disulfide isomerases thus contributing to redox signaling. Analyzing redox signaling in fungi with the tools of molecular genetics is presently only in its beginning. However, it is already clear that redox signaling in fungal cells often is linked to cell differentiation (like the formation of perithecia), virulence (in plant pathogens), hyphal growth and the successful passage through the stationary phase.}, }
@article {pmid25853734, year = {2015}, author = {Field, LD and Delehanty, JB and Chen, Y and Medintz, IL}, title = {Peptides for specifically targeting nanoparticles to cellular organelles: quo vadis?.}, journal = {Accounts of chemical research}, volume = {48}, number = {5}, pages = {1380-1390}, doi = {10.1021/ar500449v}, pmid = {25853734}, issn = {1520-4898}, mesh = {Animals ; COS Cells ; Chlorocebus aethiops ; HeLa Cells ; Humans ; Nanoparticles/*chemistry/*metabolism ; Organelles/*metabolism ; PC12 Cells ; Peptides/*chemistry/*metabolism ; Rats ; }, abstract = {The interfacing of nanomaterials and especially nanoparticles within all aspects of biological research continues to grow at a nearly unabated pace with projected applications focusing on powerful new tools for cellular labeling, imaging, and sensing, theranostic materials, and drug delivery. At the most fundamental level, many of these nanoparticles are meant to target not only very specific cell-types, regardless of whether they are in a culture, tissue, an animal model, or ultimately a patient, but also in many cases a specific subcellular organelle. During this process, these materials will undergo a complex journey that must first find the target cell of interest, then be taken up by those cells across the extracellular membrane, and ultimately localize to a desired subcellular organelle, which may include the nucleus, plasma membrane, endolysosomal system, mitochondria, cytosol, or endoplasmic reticulum. To accomplish these complex tasks in the correct sequence, researchers are increasingly interested in selecting for and exploiting targeting peptides that can impart the requisite capabilities to a given nanoparticle construct. There are also a number of related criteria that need careful consideration for this undertaking centering on the nature and properties of the peptide vector itself, the peptide-nanoparticle conjugate characteristics, and the target cell. Here, we highlight some important issues and key research areas related to this burgeoning field. We begin by providing a brief overview of some criteria for optimal attachment of peptides to nanoparticles, the predominant methods by which nanoparticles enter cells, and some of the peptide sequences that have been utilized to facilitate nanoparticle delivery to cells focusing on those that engender the initial targeting and uptake. Because almost all materials delivered to cells by peptides utilize the endosomal system of vesicular transport and in many cases remain sequestered within the vesicles, we critically evaluate the issue of endosomal escape in the context of some recently reported successes in this regard. Following from this, peptides that have been reported to deliver nanoparticles to specific subcellular compartments are examined with a focus on what they delivered and the putative mechanisms by which they were able to accomplish this. The last section focuses on two areas that are critical to realizing this overall approach in the long term. The first is how to select for peptidyl sequences capable of improved or more specific cellular or subcellular targeting based upon principles commonly associated with drug discovery. The second looks at what has been done to create modular peptides that incorporate multiple desirable functionalities within a single, contiguous sequence. This provides a viable alternative to either the almost insurmountable challenge of finding one sequence capable of all functions or, alternatively, attaching different peptides with different functionalities to the same nanoparticle in different ratios when trying to orchestrate their net effects. Finally, we conclude with a brief perspective on the future evolution and broader impact of this growing area of bionanoscience.}, }
@article {pmid25853038, year = {2015}, author = {Kodaira, M and Hatakeyama, H and Yuasa, S and Seki, T and Egashira, T and Tohyama, S and Kuroda, Y and Tanaka, A and Okata, S and Hashimoto, H and Kusumoto, D and Kunitomi, A and Takei, M and Kashimura, S and Suzuki, T and Yozu, G and Shimojima, M and Motoda, C and Hayashiji, N and Saito, Y and Goto, Y and Fukuda, K}, title = {Impaired respiratory function in MELAS-induced pluripotent stem cells with high heteroplasmy levels.}, journal = {FEBS open bio}, volume = {5}, number = {}, pages = {219-225}, pmid = {25853038}, issn = {2211-5463}, abstract = {Mitochondrial diseases are heterogeneous disorders, caused by mitochondrial dysfunction. Mitochondria are not regulated solely by nuclear genomic DNA but by mitochondrial DNA. It is difficult to develop effective therapies for mitochondrial disease because of the lack of mitochondrial disease models. Mitochondrial myopathy, encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) is one of the major mitochondrial diseases. The aim of this study was to generate MELAS-specific induced pluripotent stem cells (iPSCs) and to demonstrate that MELAS-iPSCs can be models for mitochondrial disease. We successfully established iPSCs from the primary MELAS-fibroblasts carrying 77.7% of m.3243A>G heteroplasmy. MELAS-iPSC lines ranged from 3.6% to 99.4% of m.3243A>G heteroplasmy levels. The enzymatic activities of mitochondrial respiratory complexes indicated that MELAS-iPSC-derived fibroblasts with high heteroplasmy levels showed a deficiency of complex I activity but MELAS-iPSC-derived fibroblasts with low heteroplasmy levels showed normal complex I activity. Our data indicate that MELAS-iPSCs can be models for MELAS but we should carefully select MELAS-iPSCs with appropriate heteroplasmy levels and respiratory functions for mitochondrial disease modeling.}, }
@article {pmid25849196, year = {2015}, author = {Telonis, AG and Kirino, Y and Rigoutsos, I}, title = {Mitochondrial tRNA-lookalikes in nuclear chromosomes: could they be functional?.}, journal = {RNA biology}, volume = {12}, number = {4}, pages = {375-380}, pmid = {25849196}, issn = {1555-8584}, support = {R01 GM106047/GM/NIGMS NIH HHS/United States ; GM106047/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Cell Nucleus/*genetics ; Chromosomes/*metabolism ; Humans ; Invertebrates/metabolism ; Mitochondria/metabolism ; Primates/metabolism ; RNA, Transfer/*genetics/metabolism ; Regulatory Sequences, Nucleic Acid ; Rodentia/metabolism ; }, abstract = {The presence in human nuclear chromosomes of multiple sequences that are highly similar to human mitochondrial tRNAs (tRNA-lookalikes) raises intriguing questions about the possible functionality of these genomic loci. In this perspective, we explore the significance of the mitochondrial tRNA-lookalikes based on a series of properties that argue for their non-accidental nature. We particularly focus on the possibility of transcription as well as on potential functional roles for these sequences that can range from their acting as DNA regulatory elements to forming functional mature tRNAs or tRNA-derived fragments. Extension of our analysis to other simians (chimp, gorilla, rhesus, and squirrel monkey), 2 rodents (mouse and rat), a marsupial (opossum) and 3 invertebrates (fruit-fly, worm, and sponge) revealed that mitochondrial tRNA-lookalikes are prevalent in primates and the opossum but absent from the other analyzed organisms.}, }
@article {pmid25849039, year = {2015}, author = {Drovetski, SV and Semenov, G and Red'kin, YA and Sotnikov, VN and Fadeev, IV and Koblik, EA}, title = {Effects of asymmetric nuclear introgression, introgressive mitochondrial sweep, and purifying selection on phylogenetic reconstruction and divergence estimates in the Pacific clade of Locustella warblers.}, journal = {PloS one}, volume = {10}, number = {4}, pages = {e0122590}, pmid = {25849039}, issn = {1932-6203}, mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Female ; *Gene Flow ; Genetic Loci/genetics ; Mitochondria/*genetics ; *Phylogeny ; *Selection, Genetic ; Songbirds/classification/*genetics ; }, abstract = {When isolated but reproductively compatible populations expand geographically and meet, simulations predict asymmetric introgression of neutral loci from a local to invading taxon. Genetic introgression may affect phylogenetic reconstruction by obscuring topology and divergence estimates. We combined phylogenetic analysis of sequences from one mtDNA and 12 nuDNA loci with analysis of gene flow among 5 species of Pacific Locustella warblers to test for presence of genetic introgression and its effects on tree topology and divergence estimates. Our data showed that nuDNA introgression was substantial and asymmetrical among all members of superspecies groups whereas mtDNA showed no introgression except a single species pair where the invader's mtDNA was swept by mtDNA of the local species. This introgressive sweep of mtDNA had the opposite direction of the nuDNA introgression and resulted in the paraphyly of the local species' mtDNA haplotypes with respect to those of the invader. Тhe multilocus nuDNA species tree resolved all inter- and intraspecific relationships despite substantial introgression. However, the node ages on the species tree may be underestimated as suggested by the differences in node age estimates based on non-introgressing mtDNA and introgressing nuDNA. In turn, the introgressive sweep and strong purifying selection appear to elongate internal branches in the mtDNA gene tree.}, }
@article {pmid25848019, year = {2015}, author = {Gray, MW}, title = {Mosaic nature of the mitochondrial proteome: Implications for the origin and evolution of mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10133-10138}, pmid = {25848019}, issn = {1091-6490}, mesh = {Alphaproteobacteria/*physiology ; Animals ; Biological Evolution ; DNA, Mitochondrial/physiology ; Evolution, Molecular ; Gene Transfer Techniques ; Genome, Mitochondrial ; Humans ; Mice ; Mitochondria/*physiology ; Mitochondrial Proteins/*physiology ; Phylogeny ; *Proteome ; Symbiosis ; Yeasts ; }, abstract = {Comparative studies of the mitochondrial proteome have identified a conserved core of proteins descended from the α-proteobacterial endosymbiont that gave rise to the mitochondrion and was the source of the mitochondrial genome in contemporary eukaryotes. A surprising result of phylogenetic analyses is the relatively small proportion (10-20%) of the mitochondrial proteome displaying a clear α-proteobacterial ancestry. A large fraction of mitochondrial proteins typically has detectable homologs only in other eukaryotes and is presumed to represent proteins that emerged specifically within eukaryotes. A further significant fraction of the mitochondrial proteome consists of proteins with homologs in prokaryotes, but without a robust phylogenetic signal affiliating them with specific prokaryotic lineages. The presumptive evolutionary source of these proteins is quite different in contending models of mitochondrial origin.}, }
@article {pmid25847423, year = {2015}, author = {Greif, G and Rodriguez, M and Reyna-Bello, A and Robello, C and Alvarez-Valin, F}, title = {Kinetoplast adaptations in American strains from Trypanosoma vivax.}, journal = {Mutation research}, volume = {773}, number = {}, pages = {69-82}, doi = {10.1016/j.mrfmmm.2015.01.008}, pmid = {25847423}, issn = {1873-135X}, mesh = {Adaptation, Physiological ; Adenosine Triphosphatases/genetics ; Amino Acid Sequence ; DNA, Kinetoplast/*physiology ; Genome, Protozoan ; Mitochondria/*genetics/metabolism ; Molecular Sequence Data ; RNA Editing ; Trypanosoma vivax/*genetics ; }, abstract = {The mitochondrion role changes during the digenetic life cycle of African trypanosomes. Owing to the low abundance of glucose in the insect vector (tsetse flies) the parasites are dependent upon a fully functional mitochondrion, capable of performing oxidative phosphorylation. Nevertheless, inside the mammalian host (bloodstream forms), which is rich in nutrients, parasite proliferation relies on glycolysis, and the mitochondrion is partially redundant. In this work we perform a comparative study of the mitochondrial genome (kinetoplast) in different strains of Trypanosoma vivax. The comparison was conducted between a West African strain that goes through a complete life cycle and two American strains that are mechanically transmitted (by different vectors) and remain as bloodstream forms only. It was found that while the African strain has a complete and apparently fully functional kinetoplast, the American T. vivax strains have undergone a drastic process of mitochondrial genome degradation, in spite of the recent introduction of these parasites in America. Many of their genes exhibit different types of mutations that are disruptive of function such as major deletions, frameshift causing indels and missense mutations. Moreover, all but three genes (A6-ATPase, RPS12 and MURF2) are not edited in the American strains, whereas editing takes place normally in all (editable) genes from the African strain. Two of these genes, A6-ATPase and RPS12, are known to play an essential function during bloodstream stage. Analysis of the minicircle population shows that its diversity has been greatly reduced, remaining mostly those minicircles that carry guide RNAs necessary for the editing of A6-ATPase and RPS12. The fact that these two genes remain functioning normally, as opposed to that reported in Trypanosoma brucei-like trypanosomes that restrict their life cycle to the bloodstream forms, along with other differences, is indicative that the American T. vivax strains are following a novel evolutionary pathway.}, }
@article {pmid25847086, year = {2015}, author = {Messenger, LA and Garcia, L and Vanhove, M and Huaranca, C and Bustamante, M and Torrico, M and Torrico, F and Miles, MA and Llewellyn, MS}, title = {Ecological host fitting of Trypanosoma cruzi TcI in Bolivia: mosaic population structure, hybridization and a role for humans in Andean parasite dispersal.}, journal = {Molecular ecology}, volume = {24}, number = {10}, pages = {2406-2422}, pmid = {25847086}, issn = {1365-294X}, support = {/WT_/Wellcome Trust/United Kingdom ; 066806/WT_/Wellcome Trust/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bolivia ; Chagas Disease/parasitology ; DNA, Mitochondrial/genetics ; DNA, Protozoan/genetics ; Gene Flow ; Genetic Variation ; *Genetics, Population ; Genotype ; Geography ; Humans ; *Hybridization, Genetic ; Microsatellite Repeats ; Sequence Analysis, DNA ; Trypanosoma cruzi/*genetics ; }, abstract = {An improved understanding of how a parasite species exploits its genetic repertoire to colonize novel hosts and environmental niches is crucial to establish the epidemiological risk associated with emergent pathogenic genotypes. Trypanosoma cruzi, a genetically heterogeneous, multi-host zoonosis, provides an ideal system to examine the sylvatic diversification of parasitic protozoa. In Bolivia, T. cruzi I, the oldest and most widespread genetic lineage, is pervasive across a range of ecological clines. High-resolution nuclear (26 loci) and mitochondrial (10 loci) genotyping of 199 contemporaneous sylvatic TcI clones was undertaken to provide insights into the biogeographical basis of T. cruzi evolution. Three distinct sylvatic parasite transmission cycles were identified: one highland population among terrestrial rodent and triatomine species, composed of genetically homogenous strains (Ar = 2.95; PA/L = 0.61; DAS = 0.151), and two highly diverse, parasite assemblages circulating among predominantly arboreal mammals and vectors in the lowlands (Ar = 3.40 and 3.93; PA/L = 1.12 and 0.60; DAS = 0.425 and 0.311, respectively). Very limited gene flow between neighbouring terrestrial highland and arboreal lowland areas (distance ~220 km; FST = 0.42 and 0.35) but strong connectivity between ecologically similar but geographically disparate terrestrial highland ecotopes (distance >465 km; FST = 0.016-0.084) strongly supports ecological host fitting as the predominant mechanism of parasite diversification. Dissimilar heterozygosity estimates (excess in highlands, deficit in lowlands) and mitochondrial introgression among lowland strains may indicate fundamental differences in mating strategies between populations. Finally, accelerated parasite dissemination between densely populated, highland areas, compared to uninhabited lowland foci, likely reflects passive, long-range anthroponotic dispersal. The impact of humans on the risk of epizootic Chagas disease transmission in Bolivia is discussed.}, }
@article {pmid25838283, year = {2015}, author = {Szathmáry, E}, title = {Toward major evolutionary transitions theory 2.0.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10104-10111}, pmid = {25838283}, issn = {1091-6490}, support = {294332/ERC_/European Research Council/International ; }, mesh = {Animals ; Bacteria/genetics ; *Biological Evolution ; Cultural Characteristics ; Ecosystem ; Eukaryotic Cells/cytology ; Female ; Gene Transfer, Horizontal ; Genetic Code ; Humans ; Language ; Male ; Mitochondria/genetics ; Organelle Biogenesis ; Phagocytosis ; Phylogeny ; Plastids/genetics ; Reproducibility of Results ; Stochastic Processes ; }, abstract = {The impressive body of work on the major evolutionary transitions in the last 20 y calls for a reconstruction of the theory although a 2D account (evolution of informational systems and transitions in individuality) remains. Significant advances include the concept of fraternal and egalitarian transitions (lower-level units like and unlike, respectively). Multilevel selection, first without, then with, the collectives in focus is an important explanatory mechanism. Transitions are decomposed into phases of origin, maintenance, and transformation (i.e., further evolution) of the higher level units, which helps reduce the number of transitions in the revised list by two so that it is less top-heavy. After the transition, units show strong cooperation and very limited realized conflict. The origins of cells, the emergence of the genetic code and translation, the evolution of the eukaryotic cell, multicellularity, and the origin of human groups with language are reconsidered in some detail in the light of new data and considerations. Arguments are given why sex is not in the revised list as a separate transition. Some of the transitions can be recursive (e.g., plastids, multicellularity) or limited (transitions that share the usual features of major transitions without a massive phylogenetic impact, such as the micro- and macronuclei in ciliates). During transitions, new units of reproduction emerge, and establishment of such units requires high fidelity of reproduction (as opposed to mere replication).}, }
@article {pmid25835781, year = {2015}, author = {Báez, AL and Reynoso, MN and Lo Presti, MS and Bazán, PC and Strauss, M and Miler, N and Pons, P and Rivarola, HW and Paglini-Oliva, P}, title = {Mitochondrial dysfunction in skeletal muscle during experimental Chagas disease.}, journal = {Experimental and molecular pathology}, volume = {98}, number = {3}, pages = {467-475}, doi = {10.1016/j.yexmp.2015.03.034}, pmid = {25835781}, issn = {1096-0945}, mesh = {Animals ; Chagas Disease/*metabolism/pathology ; Electron Transport Chain Complex Proteins/metabolism ; Female ; Male ; Mice ; Mitochondria, Muscle/*metabolism/ultrastructure ; Muscle, Skeletal/*metabolism/ultrastructure ; }, abstract = {Trypanosoma cruzi invasion and replication in cardiomyocytes and other tissues induce cellular injuries and cytotoxic reactions, with the production of inflammatory cytokines and nitric oxide, both sources of reactive oxygen species. The myocyte response to oxidative stress involves the progression of cellular changes primarily targeting mitochondria. Similar alterations could be taking place in mitochondria from the skeletal muscle; if that is the case, a simple skeletal muscle biopsy would give information about the cardiac energetic production that could be used as a predictor of the chagasic cardiopathy evolution. Therefore, in the present paper we studied skeletal muscle mitochondrial structure and the enzymatic activity of citrate synthase and respiratory chain complexes I to IV (CI-CIV), in Albino Swiss mice infected with T. cruzi, Tulahuen strain and SGO Z12 and Lucky isolates, along the infection. Changes in the mitochondrial structure were detected in 100% of the mitochondria analyzed from the infected groups: they all presented at least 1 significant abnormality such as increase in their matrix or disorganization of their cristae, which are probably related to the enzymatic dysfunction. When we studied the Krebs cycle functionality through the measurement of the specific citrate synthase activity, we found it to be significantly diminished during the acute phase of the infection in Tulahuen and SGO Z12 infected groups with respect to the control one; citrate synthase activity from the Lucky group was significantly increased (p<0.05). The activity of this enzyme was reduced in all the infected groups during the chronic asymptomatic phase (p<0.001) and return to normal values (Tulahuen and SGO Z12) or increased its activity (Lucky) by day 365 post-infection (p.i.). When the mitochondrial respiratory chain was analyzed from the acute to the chronic phase of the infection through the measurement of the activity of complexes I to IV, the activity of CI remained similar to control in Tulahuen and Lucky groups, but was significantly augmented in the SGO Z12 one in the acute and chronic phases (p<0.05). CII increased its activity in Tulahuen and Lucky groups by day 75 p.i. and in SGO Z12 by day 365 p.i. (p<0.05). CIII showed a similar behavior in the 3 infected groups, remaining similar to control values in the first two stages of the infection and significantly increasing later on (p<0.0001). CIV showed an increase in its activity in Lucky throughout all stages of infection (p<0.0001) and an increase in Tulahuen by day 365days p.i. (p<0.0001); SGO Z12 on the other hand, showed a decreased CIV activity at the same time. The structural changes in skeletal muscle mitochondria and their altered enzyme activity began in the acute phase of infection, probably modifying the ability of mitochondria to generate energy; these changes were not compensated in the rest of the phases of the infection. Chagas is a systemic disease, which produces not only heart damage but also permanent skeletal muscle alterations.}, }
@article {pmid25831547, year = {2015}, author = {Leger, MM and Petrů, M and Žárský, V and Eme, L and Vlček, &#x10c; and Harding, T and Lang, BF and Eliáš, M and Doležal, P and Roger, AJ}, title = {An ancestral bacterial division system is widespread in eukaryotic mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10239-10246}, pmid = {25831547}, issn = {1091-6490}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Adenosine Triphosphatases/metabolism ; Arabidopsis/genetics ; Bacteria/cytology ; Bacterial Proteins/*genetics/metabolism ; Base Sequence ; Cell Cycle Proteins/metabolism ; Cell Division ; Cytoskeletal Proteins/*genetics ; DNA, Bacterial/*genetics ; Databases, Genetic ; Dictyostelium/metabolism ; Escherichia coli Proteins/metabolism ; Evolution, Molecular ; Likelihood Functions ; Mitochondria/*metabolism ; *Mitochondrial Dynamics ; Molecular Sequence Data ; Phylogeny ; Plastids/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; }, abstract = {Bacterial division initiates at the site of a contractile Z-ring composed of polymerized FtsZ. The location of the Z-ring in the cell is controlled by a system of three mutually antagonistic proteins, MinC, MinD, and MinE. Plastid division is also known to be dependent on homologs of these proteins, derived from the ancestral cyanobacterial endosymbiont that gave rise to plastids. In contrast, the mitochondria of model systems such as Saccharomyces cerevisiae, mammals, and Arabidopsis thaliana seem to have replaced the ancestral α-proteobacterial Min-based division machinery with host-derived dynamin-related proteins that form outer contractile rings. Here, we show that the mitochondrial division system of these model organisms is the exception, rather than the rule, for eukaryotes. We describe endosymbiont-derived, bacterial-like division systems comprising FtsZ and Min proteins in diverse less-studied eukaryote protistan lineages, including jakobid and heterolobosean excavates, a malawimonad, stramenopiles, amoebozoans, a breviate, and an apusomonad. For two of these taxa, the amoebozoan Dictyostelium purpureum and the jakobid Andalucia incarcerata, we confirm a mitochondrial localization of these proteins by their heterologous expression in Saccharomyces cerevisiae. The discovery of a proteobacterial-like division system in mitochondria of diverse eukaryotic lineages suggests that it was the ancestral feature of all eukaryotic mitochondria and has been supplanted by a host-derived system multiple times in distinct eukaryote lineages.}, }
@article {pmid25826417, year = {2015}, author = {Kotakis, C}, title = {Non-coding RNAs' partitioning in the evolution of photosynthetic organisms via energy transduction and redox signaling.}, journal = {RNA biology}, volume = {12}, number = {1}, pages = {101-104}, pmid = {25826417}, issn = {1555-8584}, mesh = {*Energy Metabolism ; *Evolution, Molecular ; Oxidation-Reduction ; Photosynthesis ; Plant Cells/*classification/*metabolism ; RNA, Untranslated/*metabolism ; Signal Transduction ; }, abstract = {Ars longa, vita brevis -Hippocrates Chloroplasts and mitochondria are genetically semi-autonomous organelles inside the plant cell. These constructions formed after endosymbiosis and keep evolving throughout the history of life. Experimental evidence is provided for active non-coding RNAs (ncRNAs) in these prokaryote-like structures, and a possible functional imprinting on cellular electrophysiology by those RNA entities is described. Furthermore, updated knowledge on RNA metabolism of organellar genomes uncovers novel inter-communication bridges with the nucleus. This class of RNA molecules is considered as a unique ontogeny which transforms their biological role as a genetic rheostat into a synchronous biochemical one that can affect the energetic charge and redox homeostasis inside cells. A hypothesis is proposed where such modulation by non-coding RNAs is integrated with genetic signals regulating gene transfer. The implications of this working hypothesis are discussed, with particular reference to ncRNAs involvement in the organellar and nuclear genomes evolution since their integrity is functionally coupled with redox signals in photosynthetic organisms.}, }
@article {pmid25814499, year = {2015}, author = {Smith, DR and Keeling, PJ}, title = {Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10177-10184}, pmid = {25814499}, issn = {1091-6490}, mesh = {Animals ; *Biological Evolution ; Cell Lineage ; Cell Nucleus/genetics ; Chromosomes/ultrastructure ; DNA Repair ; DNA, Mitochondrial/genetics ; Genetics, Population ; Genome ; *Genome, Mitochondrial ; Genomics ; Humans ; Mutation ; Nucleotides/genetics ; Plants ; Plastids/*genetics ; RNA Processing, Post-Transcriptional ; Sequence Analysis, DNA ; Symbiosis/genetics ; }, abstract = {Mitochondrial and plastid genomes show a wide array of architectures, varying immensely in size, structure, and content. Some organelle DNAs have even developed elaborate eccentricities, such as scrambled coding regions, nonstandard genetic codes, and convoluted modes of posttranscriptional modification and editing. Here, we compare and contrast the breadth of genomic complexity between mitochondrial and plastid chromosomes. Both organelle genomes have independently evolved many of the same features and taken on similar genomic embellishments, often within the same species or lineage. This trend is most likely because the nuclear-encoded proteins mediating these processes eventually leak from one organelle into the other, leading to a high likelihood of processes appearing in both compartments in parallel. However, the complexity and intensity of genomic embellishments are consistently more pronounced for mitochondria than for plastids, even when they are found in both compartments. We explore the evolutionary forces responsible for these patterns and argue that organelle DNA repair processes, mutation rates, and population genetic landscapes are all important factors leading to the observed convergence and divergence in organelle genome architecture.}, }
@article {pmid25812051, year = {2016}, author = {Wang, HR and Li, YW and Wu, JL and Guo, SL}, title = {Mitochondrial tRNA mutations in patients with myelodysplastic syndromes.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {4}, pages = {2315-2317}, doi = {10.3109/19401736.2015.1022760}, pmid = {25812051}, issn = {2470-1408}, mesh = {Alleles ; Evolution, Molecular ; *Genes, Mitochondrial ; *Genetic Association Studies ; *Genetic Predisposition to Disease ; Genotype ; Humans ; *Mutation ; Myelodysplastic Syndromes/*genetics ; Polymorphism, Single Nucleotide ; RNA, Transfer/*genetics ; }, abstract = {Increasing evidence showed that mitochondria play an important role in the development of myelodysplastic syndromes (MDS). Mitochondrial dysfunctions caused by mitochondrial DNA mutations, especially mitochondrial tRNA mutations, were found to be associated with MDS in many studies. However, the link between a candidate mitochondrial tRNA mutation and MDS was not clear. In this study, we investigated the role of some mitochondrial tRNA mutations, and their deleterious roles were further discussed.}, }
@article {pmid25811639, year = {2015}, author = {González-Sánchez, JC and Costa, R and Devos, DP}, title = {A multi-functional tubulovesicular network as the ancestral eukaryotic endomembrane system.}, journal = {Biology}, volume = {4}, number = {2}, pages = {264-281}, pmid = {25811639}, issn = {2079-7737}, abstract = {The origin of the eukaryotic endomembrane system is still the subject of much speculation. We argue that the combination of two recent hypotheses addressing the eukaryotic endomembrane's early evolution supports the possibility that the ancestral membranes were organised as a multi-functional tubulovesicular network. One of the potential selective advantages provided by this organisation was the capacity to perform endocytosis. This possibility is illustrated by membrane organisations observed in current organisms in the three domains of life. Based on this, we propose a coherent model of autogenous eukaryotic endomembrane system evolution in which mitochondria are involved at a late stage.}, }
@article {pmid25809607, year = {2015}, author = {Forini, F and Nicolini, G and Iervasi, G}, title = {Mitochondria as key targets of cardioprotection in cardiac ischemic disease: role of thyroid hormone triiodothyronine.}, journal = {International journal of molecular sciences}, volume = {16}, number = {3}, pages = {6312-6336}, pmid = {25809607}, issn = {1422-0067}, mesh = {Humans ; Mitochondria/*metabolism/pathology ; Myocardial Ischemia/*metabolism ; Myocardial Reperfusion Injury/*metabolism/pathology ; Triiodothyronine/*metabolism ; }, abstract = {Ischemic heart disease is the major cause of mortality and morbidity worldwide. Early reperfusion after acute myocardial ischemia has reduced short-term mortality, but it is also responsible for additional myocardial damage, which in the long run favors adverse cardiac remodeling and heart failure evolution. A growing body of experimental and clinical evidence show that the mitochondrion is an essential end effector of ischemia/ reperfusion injury and a major trigger of cell death in the acute ischemic phase (up to 48-72 h after the insult), the subacute phase (from 72 h to 7-10 days) and chronic stage (from 10-14 days to one month after the insult). As such, in recent years scientific efforts have focused on mitochondria as a target for cardioprotective strategies in ischemic heart disease and cardiomyopathy. The present review discusses recent advances in this field, with special emphasis on the emerging role of the biologically active thyroid hormone triiodothyronine (T3).}, }
@article {pmid25807984, year = {2015}, author = {Morrow, EH and Reinhardt, K and Wolff, JN and Dowling, DK}, title = {Risks inherent to mitochondrial replacement.}, journal = {EMBO reports}, volume = {16}, number = {5}, pages = {541-544}, pmid = {25807984}, issn = {1469-3178}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Genetic Variation ; Humans ; Mitochondria/*genetics/*metabolism ; Mitochondrial Diseases/epidemiology/*genetics/*metabolism/therapy ; }, }
@article {pmid25807469, year = {2015}, author = {Tomasini, N and Diosque, P}, title = {Evolution of Trypanosoma cruzi: clarifying hybridisations, mitochondrial introgressions and phylogenetic relationships between major lineages.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {110}, number = {3}, pages = {403-413}, pmid = {25807469}, issn = {1678-8060}, mesh = {*Biological Evolution ; DNA, Protozoan/genetics ; Genetic Variation ; Genotype ; Hybridization, Genetic/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Trypanosoma cruzi/classification/*genetics ; }, abstract = {Several different models of Trypanosoma cruzi evolution have been proposed. These models suggest that scarce events of genetic exchange occurred during the evolutionary history of this parasite. In addition, the debate has focused on the existence of one or two hybridisation events during the evolution of T. cruzi lineages. Here, we reviewed the literature and analysed available sequence data to clarify the phylogenetic relationships among these different lineages. We observed that TcI, TcIII and TcIV form a monophyletic group and that TcIII and TcIV are not, as previously suggested, TcI-TcII hybrids. Particularly, TcI and TcIII are sister groups that diverged around the same time that a widely distributed TcIV split into two clades (TcIVS and TcIVN). In addition, we collected evidence that TcIII received TcIVS kDNA by introgression on several occasions. Different demographic hypotheses (surfing and asymmetrical introgression) may explain the origin and expansion of the TcIII group. Considering these hypotheses, genetic exchange should have been relatively frequent between TcIII and TcIVS in the geographic area in which their distributions overlapped. In addition, our results support the hypothesis that two independent hybridisation events gave rise to TcV and TcVI. Consequently, TcIVS kDNA was first transferred to TcIII and later to TcV and TcVI in TcII/TcIII hybridisation events.}, }
@article {pmid25806583, year = {2016}, author = {Hofman, S and Pabijan, M and Osikowski, A and Litvinchuk, SN and Szymura, JM}, title = {Phylogenetic relationships among four new complete mitogenome sequences of Pelophylax (Amphibia: Anura) from the Balkans and Cyprus.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3434-3437}, doi = {10.3109/19401736.2015.1025266}, pmid = {25806583}, issn = {2470-1408}, mesh = {Animals ; Anura/genetics ; Balkan Peninsula ; Base Composition ; Cyprus ; Gene Order ; Genes, rRNA ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {We present the full-length mitogenome sequences of four European water frog species: Pelophylax cypriensis, P. epeiroticus, P. kurtmuelleri and P. shqipericus. The mtDNA size varied from 17,363 to 17,895 bp, and its organization with the LPTF tRNA gene cluster preceding the 12 S rRNA gene displayed the typical Neobatrachian arrangement. Maximum likelihood and Bayesian inference revealed a well-resolved mtDNA phylogeny of seven European Pelophylax species. The uncorrected p-distance for among Pelophylax mitogenomes was 9.6 (range 0.01-0.13). Most divergent was the P. shqipericus mitogenome, clustering with the "P. lessonae" group, in contrast to the other three new Pelophylax mitogenomes related to the "P. bedriagae/ridibundus" lineage. The new mitogenomes resolve ambiguities of the phylogenetic placement of P. cretensis and P. epeiroticus.}, }
@article {pmid25805857, year = {2015}, author = {Collins, RA and Stajich, JE and Field, DJ and Olive, JE and DeAbreu, DM}, title = {The low information content of Neurospora splicing signals: implications for RNA splicing and intron origin.}, journal = {RNA (New York, N.Y.)}, volume = {21}, number = {5}, pages = {997-1004}, pmid = {25805857}, issn = {1469-9001}, support = {MOP-12837//Canadian Institutes of Health Research/Canada ; }, mesh = {Base Sequence ; Evolution, Molecular ; Genetic Speciation ; *Introns/genetics ; Mitochondria/genetics ; Neurospora/*genetics ; Plasmids/genetics ; RNA Splice Sites/*genetics ; RNA Splicing/*genetics ; Species Specificity ; Spliceosomes/genetics/metabolism ; }, abstract = {When we expressed a small (0.9 kb) nonprotein-coding transcript derived from the mitochondrial VS plasmid in the nucleus of Neurospora we found that it was efficiently spliced at one or more of eight 5' splice sites and ten 3' splice sites, which are present apparently by chance in the sequence. Further experimental and bioinformatic analyses of other mitochondrial plasmids, random sequences, and natural nuclear genes in Neurospora and other fungi indicate that fungal spliceosomes recognize a wide range of 5' splice site and branchpoint sequences and predict introns to be present at high frequency in random sequence. In contrast, analysis of intronless fungal nuclear genes indicates that branchpoint, 5' splice site and 3' splice site consensus sequences are underrepresented compared with random sequences. This underrepresentation of splicing signals is sufficient to deplete the nuclear genome of splice sites at locations that do not comprise biologically relevant introns. Thus, the splicing machinery can recognize a wide range of splicing signal sequences, but splicing still occurs with great accuracy, not because the splicing machinery distinguishes correct from incorrect introns, but because incorrect introns are substantially depleted from the genome.}, }
@article {pmid25800739, year = {2015}, author = {Morozov, YI and Parshin, AV and Agaronyan, K and Cheung, AC and Anikin, M and Cramer, P and Temiakov, D}, title = {A model for transcription initiation in human mitochondria.}, journal = {Nucleic acids research}, volume = {43}, number = {7}, pages = {3726-3735}, pmid = {25800739}, issn = {1362-4962}, support = {102535//Wellcome Trust/United Kingdom ; R01 GM104231/GM/NIGMS NIH HHS/United States ; 102535/Z/13/Z//Wellcome Trust/United Kingdom ; R01GM104231/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Mitochondria/*metabolism ; *Models, Biological ; *Transcription, Genetic ; }, abstract = {Regulation of transcription of mtDNA is thought to be crucial for maintenance of redox potential and vitality of the cell but is poorly understood at the molecular level. In this study we mapped the binding sites of the core transcription initiation factors TFAM and TFB2M on human mitochondrial RNA polymerase, and interactions of the latter with promoter DNA. This allowed us to construct a detailed structural model, which displays a remarkable level of interaction between the components of the initiation complex (IC). The architecture of the mitochondrial IC suggests mechanisms of promoter binding and recognition that are distinct from the mechanisms found in RNAPs operating in all domains of life, and illuminates strategies of transcription regulation developed at the very early stages of evolution of gene expression.}, }
@article {pmid25795412, year = {2015}, author = {Nosek, J and Tomaska, L and Burger, G and Lang, BF}, title = {Programmed translational bypassing elements in mitochondria: structure, mobility, and evolutionary origin.}, journal = {Trends in genetics : TIG}, volume = {31}, number = {4}, pages = {187-194}, doi = {10.1016/j.tig.2015.02.010}, pmid = {25795412}, issn = {0168-9525}, support = {MOP-79309//Canadian Institutes of Health Research/Canada ; }, mesh = {Bacteriophage T4/genetics/metabolism ; Frameshifting, Ribosomal ; Mitochondria/*genetics/*metabolism ; Protein Biosynthesis/*genetics ; RNA, Messenger/chemistry/*genetics ; *Regulatory Sequences, Ribonucleic Acid ; Yeasts/genetics/metabolism ; }, abstract = {Programmed translational bypassing enables ribosomes to 'ignore' a precise mRNA interval of several dozen nucleotides. Well-characterized bypassed sequences include hop and byp elements, present in bacteriophage T4 and mitochondria of the yeast Magnusiomyces capitatus, respectively. The bypassing mechanism of byps is probably similar to that of hop, yet the former appears more effective and less constrained as to sequence context. Furthermore, both elements are mobile but hop moves as part of a cassette including a homing endonuclease, whereas byps seem to spread like miniature DNA transposable elements known as GC clusters. Here, we argue that hop and byps arose independently by convergent evolution, and that byps evolved in magnusiomycete mitochondria due to (as yet unknown) alterations of the mitochondrial translation machinery.}, }
@article {pmid25788489, year = {2015}, author = {Jacobsen, MW and Pujolar, JM and Hansen, MM}, title = {Relationship between amino acid changes in mitochondrial ATP6 and life-history variation in anguillid eels.}, journal = {Biology letters}, volume = {11}, number = {3}, pages = {}, pmid = {25788489}, issn = {1744-957X}, mesh = {Adaptation, Biological/genetics ; Amino Acid Sequence ; Anguilla/genetics/*physiology ; Animal Migration/*physiology ; Animals ; DNA, Mitochondrial/genetics ; Genotype ; Larva/*physiology ; Life Cycle Stages ; Mitochondria/*genetics ; Mitochondrial Proton-Translocating ATPases/*metabolism ; Phenotype ; Phylogeny ; Reproduction/physiology ; }, abstract = {Mitochondrial genes are part of the oxidative phosphorylation pathway and important for energy production. Although evidence for positive selection at the mitochondrial level exists, few studies have investigated the link between amino acid changes and phenotype. Here we test the hypothesis that differences in two life-history related traits, migratory distance between spawning and foraging areas and larval phase duration, are associated with divergent selection within the mitochondrial ATP6 gene in anguillid eels. We compare amino acid changes among 18 species with the sequence of the putative ancestral species, believed to have shown short migratory distance and larval phase duration. We find positive correlations between both life-history related traits and (i) the number of amino acid changes and (ii) the strength of the combined physico-chemical and structural changes at positions previously identified as candidates for positive selection. This supports a link between genotype and phenotype driven by positive selection at ATP6.}, }
@article {pmid25788442, year = {2016}, author = {Pandey, N and Rajagopal, R}, title = {Molecular characterization and diversity analysis of bacterial communities associated with Dialeurolonga malleswaramensis (Hemiptera: Aleyrodidae) adults using 16S rDNA amplicon pyrosequencing and FISH.}, journal = {Insect science}, volume = {23}, number = {5}, pages = {704-711}, doi = {10.1111/1744-7917.12220}, pmid = {25788442}, issn = {1744-7917}, mesh = {Animals ; Bacteria/*genetics/isolation &amp; purification ; DNA, Bacterial/*genetics ; Hemiptera/genetics/*microbiology ; In Situ Hybridization, Fluorescence ; India ; Mitochondria/genetics ; Phylogeny ; Polyalthia/parasitology ; RNA, Ribosomal, 16S/*genetics ; Symbiosis ; }, abstract = {Dialeurolonga malleswaramensis Sundararaj (Hemiptera: Aleyrodidae) is a phytophagous sap sucking insect. It infests Polyalthia longifolia, an important avenue tree of India, effective in alleviating noise pollution and having immense medicinal importance. Samples of this insect were collected from Polyalthia longifolia. The cytochrome c oxidase subunit I gene (mtCO1) helped in the molecular characterization of the insect. This study reports the bacterial diversity in D. malleswaramensis adults by high throughput 16S rDNA amplicon pyrosequencing. The major genera identified were Portiera and Arsenophonus. Other bacterial genera detected were uncultured alpha proteobacterium, Sphingopyxis and Methylobacterium. We also employed fluorescence in situ hybridization (FISH) in whole mount samples to confirm the presence of dominant endosymbionts Portiera and Arsenophonus to the bacteriocyte of D. malleswaramensis. This study concludes that combining techniques like 16S rDNA amplicon pyrosequencing and FISH reveal both dominant and rare bacteria. The data also predict the evolutionary position of this pest with respect to other whitefly species using a mitochondrial marker.}, }
@article {pmid25783787, year = {2015}, author = {Huang, CY and Lin, CH and Lin, HC}, title = {Development of gas exchange and ion regulation in two species of air-breathing fish, Betta splendens and Macropodus opercularis.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {185}, number = {}, pages = {24-32}, doi = {10.1016/j.cbpa.2015.03.008}, pmid = {25783787}, issn = {1531-4332}, mesh = {Animals ; Biological Evolution ; Female ; Fish Proteins/metabolism ; Fishes/anatomy &amp; histology/*growth &amp; development ; Gills/growth &amp; development/ultrastructure ; Male ; Oxygen/metabolism ; Respiration ; Sodium-Potassium-Exchanging ATPase/metabolism ; }, abstract = {Aquatic air-breathing anabantoids, a group of fish species characterized by the presence of a labyrinth organ and some gills, exhibit morphological variations. This study aimed to examine whether unequal gill growth begins during the early stages and described the sequence of the early gill developmental events in Betta splendens and Macropodus opercularis. To determine when the ion regulatory and gas exchange abilities first appear in the gills, mitochondria-rich cells (MRCs) and neuroepithelial cells (NECs) were examined in young B. splendens. To evaluate the relative importance of the gills and the labyrinth organ under different levels of oxygen uptake stress, the levels of carbonic anhydrase II (CAII) and Na(+)/K(+)-ATPase (NKA) protein expressions in 2 gills and the labyrinth organ were examined in M. opercularis. We found that the first 3 gills developed earlier than the 4th gill in both species, an indication that the morphological variation begins early in life. In B. splendens, the MRCs and NECs clearly appeared in the first 3 gills at 4 dph and were first found in the 4th gill until 11 dph. The oxygen-sensing ability of the gills was concordant with the ionoregulatory function. In M. opercularis, the hypoxic group had a significantly higher air-breathing frequency. CAII protein expression was higher in the labyrinth organ in the hypoxic group. The gills exhibited increased NKA protein expression in the hypoxic and restricted groups, respectively. Functional plasticity in CAII and NKA protein expressions was found between the gills and the labyrinth organ in adult M. opercularis.}, }
@article {pmid25777063, year = {2015}, author = {Wang, JZ and Wang, ZH}, title = {Senescence may mediate conversion of tau phosphorylation-induced apoptotic escape to neurodegeneration.}, journal = {Experimental gerontology}, volume = {68}, number = {}, pages = {82-86}, doi = {10.1016/j.exger.2015.03.007}, pmid = {25777063}, issn = {1873-6815}, mesh = {Alzheimer Disease/*etiology/physiopathology/therapy ; Animals ; Apoptosis/*physiology ; Cellular Senescence/*physiology ; Disease Models, Animal ; Endoplasmic Reticulum Stress/physiology ; Humans ; Mitochondria/metabolism ; Neurofibrillary Tangles/physiology ; Neurogenesis/physiology ; Neuroglia/physiology ; Phosphorylation/physiology ; Proto-Oncogene Proteins c-akt/physiology ; Tumor Suppressor Protein p53/physiology ; tau Proteins/*metabolism ; }, abstract = {Neurodegeneration is the characteristic pathology in the brains of Alzheimer's disease (AD). However, the nature and molecular mechanism leading to the degeneration are not clarified. Given that only the neurons filled with neurofibrillary tangles survive to the end stage of the disease and the major component of the tangles is the hyperphosphorylated tau proteins, it is conceivable that tau hyperphosphorylation must play a crucial role in AD neurodegeneration. We have demonstrated that tau hyperphosphorylation renders the cells more resistant to the acute apoptosis. The molecular mechanisms involve substrate competition of tau and β-catenin for glycogen synthase kinase 3β (GSK-3β); activation of Akt; preservation of Bcl-2 and suppression of Bax, cytosolic cytochrome-c, and caspase-3 activity; and upregulation of unfolded protein response (UPR), i.e., up-regulating phosphorylation of PERK, eIF2 and IRE1 with an increased cleavage of ATF6 and ATF4. On the other hand, tau hyperphosphorylation promotes its intracellular accumulation and disrupts axonal transport; hyperphosphorylated tau also impairs cholinergic function and inhibits proteasome activity. These findings indicate that tau hyperphosphorylation and its intracellular accumulation play dual role in the evolution of AD. We speculate that transient tau phosphorylation helps cells abort from an acute apoptosis, while persistent tau hyperphosphorylation/accumulation may trigger cell senescence that eventually causes a chronic neurodegeneration. Therefore, the nature of "AD neurodegeneration" may represent a new type of tau-regulated chronic neuron death; and the stage of cell senescence may provide a broad window for the intervention of AD.}, }
@article {pmid25776552, year = {2015}, author = {Mitsopoulos, P and Chang, YH and Wai, T and König, T and Dunn, SD and Langer, T and Madrenas, J}, title = {Stomatin-like protein 2 is required for in vivo mitochondrial respiratory chain supercomplex formation and optimal cell function.}, journal = {Molecular and cellular biology}, volume = {35}, number = {10}, pages = {1838-1847}, pmid = {25776552}, issn = {1098-5549}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Cell Proliferation ; Cells, Cultured ; Electron Transport Chain Complex Proteins/*metabolism ; Membrane Potential, Mitochondrial ; Membrane Proteins/genetics/*metabolism ; Mice ; Mice, Knockout ; Mitochondria/*physiology ; Mitochondrial Proteins/genetics/*metabolism ; Nerve Tissue Proteins/genetics/*metabolism ; Oxidative Phosphorylation ; Phenotype ; T-Lymphocytes/*metabolism ; }, abstract = {Stomatin-like protein 2 (SLP-2) is a mainly mitochondrial protein that is widely expressed and is highly conserved across evolution. We have previously shown that SLP-2 binds the mitochondrial lipid cardiolipin and interacts with prohibitin-1 and -2 to form specialized membrane microdomains in the mitochondrial inner membrane, which are associated with optimal mitochondrial respiration. To determine how SLP-2 functions, we performed bioenergetic analysis of primary T cells from T cell-selective Slp-2 knockout mice under conditions that forced energy production to come almost exclusively from oxidative phosphorylation. These cells had a phenotype characterized by increased uncoupled mitochondrial respiration and decreased mitochondrial membrane potential. Since formation of mitochondrial respiratory chain supercomplexes (RCS) may correlate with more efficient electron transfer during oxidative phosphorylation, we hypothesized that the defect in mitochondrial respiration in SLP-2-deficient T cells was due to deficient RCS formation. We found that in the absence of SLP-2, T cells had decreased levels and activities of complex I-III2 and I-III2-IV(1-3) RCS but no defects in assembly of individual respiratory complexes. Impaired RCS formation in SLP-2-deficient T cells correlated with significantly delayed T cell proliferation in response to activation under conditions of limiting glycolysis. Altogether, our findings identify SLP-2 as a key regulator of the formation of RCS in vivo and show that these supercomplexes are required for optimal cell function.}, }
@article {pmid25774795, year = {2015}, author = {Gómez, GF and Bickersmith, SA and González, R and Conn, JE and Correa, MM}, title = {Molecular taxonomy provides new insights into anopheles species of the neotropical arribalzagia series.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0119488}, pmid = {25774795}, issn = {1932-6203}, support = {R01 AI054139/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anopheles/*classification/genetics ; Colombia ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Female ; Insect Proteins/genetics ; Male ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Phylogenetic analysis of partial mitochondrial cytochrome oxidase c subunit I (COI) and nuclear internal transcribed spacer 2 (ITS2) sequences were used to evaluate initial identification and to investigate phylogenetic relationships of seven Anopheles morphospecies of the Arribalzagia Series from Colombia. Phylogenetic trees recovered highly supported clades for An. punctimaculas.s., An. calderoni, An. malefactor s.l., An. neomaculipalpus, An. apicimacula s.l., An. mattogrossensis and An. peryassui. This study provides the first molecular confirmation of An. malefactorfrom Colombia and discovered conflicting patterns of divergence for the molecular markers among specimens from northeast and northern Colombia suggesting the presence of two previously unrecognized Molecular Operational Taxonomic Units (MOTUs). Furthermore, two highly differentiated An. apicimacula MOTUs previously found in Panama were detected. Overall, the combined molecular dataset facilitated the detection of known and new Colombian evolutionary lineages, and constitutes the baseline for future research on their bionomics, ecology and potential role as malaria vectors.}, }
@article {pmid25760948, year = {2015}, author = {Hadas, L and Hermon, D and Boldo, A and Arieli, G and Gafny, R and King, R and Bar-Gal, GK}, title = {Wild gazelles of the southern Levant: genetic profiling defines new conservation priorities.}, journal = {PloS one}, volume = {10}, number = {3}, pages = {e0116401}, pmid = {25760948}, issn = {1932-6203}, mesh = {Animals ; Antelopes/*classification/*genetics ; Cell Nucleus/genetics ; Conservation of Natural Resources ; DNA/*genetics ; Gene Flow ; Genetic Variation ; Israel ; Microsatellite Repeats ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*methods ; }, abstract = {The mountain gazelle (Gazella gazelle), Dorcas gazelle (Gazella Dorcas) and acacia gazelle (Gazella arabica acacia) were historically abundant in the southern Levant, and more specifically in Israel. Anthropogenic and natural changes have caused a rapid decline in gazelle populations, raising concerns about their conservation status and future survival. The genetic profile of 111 wild gazelles from Israel was determined based on three regions of mitochondrial DNA (control region, Cytochrome b and 12S ribosomal RNA) and nine nuclear microsatellite markers. Genetic analysis of the mountain gazelle population, the largest known population of this rare species, revealed adequate diversity levels and gene flow between subpopulations. Nevertheless, ongoing habitat degradation and other human effects, such as poaching, suggest the need for drastic measures to prevent species extinction. Dorcas gazelles in Israel displayed inbreeding within subpopulations while still maintaining considerable genetic diversity overall. This stable population, represented by a distinctive genetic profile, is fragmented and isolated from its relatives in neighboring localities. Based on the genetic profile of a newly sampled subpopulation in Israel, we provide an alternative hypothesis for the historic dispersal of Dorcas gazelle, from the Southern Levant to northern Africa. The small acacia gazelle population was closest to gazelles from the Farasan Islands of Saudi Arabia, based on mitochondrial markers. The two populations did not share haplotypes, suggesting that these two populations may be the last remnant wild gazelles of this species worldwide. Only a dozen acacia gazelles survive in Israel, and urgent steps are needed to ensure the survival of this genetically distinctive lineage. The genetic assessments of our study recognize new conservation priorities for each gazelle species in the Southern Levant.}, }
@article {pmid25754775, year = {2015}, author = {Lassiter, ES and Russ, C and Nusbaum, C and Zeng, Q and Saville, AC and Olarte, RA and Carbone, I and Hu, CH and Seguin-Orlando, A and Samaniego, JA and Thorne, JL and Ristaino, JB}, title = {Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species.}, journal = {Current genetics}, volume = {61}, number = {4}, pages = {567-577}, pmid = {25754775}, issn = {1432-0983}, support = {R01 GM070806/GM/NIGMS NIH HHS/United States ; GM070806/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Evolution ; Chimera/microbiology ; Colombia ; DNA, Mitochondrial/genetics ; Ecuador ; *Genome, Mitochondrial ; Solanum lycopersicum/microbiology ; Mitochondria/*genetics ; Peru ; *Phylogeny ; Phylogeography ; Phytophthora/classification/*genetics ; Phytophthora infestans/classification/*genetics ; Plant Diseases/microbiology ; Sequence Analysis, DNA ; Solanum tuberosum/microbiology ; }, abstract = {Phytophthora infestans is one of the most destructive plant pathogens of potato and tomato globally. The pathogen is closely related to four other Phytophthora species in the 1c clade including P. phaseoli, P. ipomoeae, P. mirabilis and P. andina that are important pathogens of other wild and domesticated hosts. P. andina is an interspecific hybrid between P. infestans and an unknown Phytophthora species. We have sequenced mitochondrial genomes of the sister species of P. infestans and examined the evolutionary relationships within the clade. Phylogenetic analysis indicates that the P. phaseoli mitochondrial lineage is basal within the clade. P. mirabilis and P. ipomoeae are sister lineages and share a common ancestor with the Ic mitochondrial lineage of P. andina. These lineages in turn are sister to the P. infestans and P. andina Ia mitochondrial lineages. The P. andina Ic lineage diverged much earlier than the P. andina Ia mitochondrial lineage and P. infestans. The presence of two mitochondrial lineages in P. andina supports the hybrid nature of this species. The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests that the origin of this species hybrid in nature may occur there.}, }
@article {pmid25748711, year = {2015}, author = {Bai, X and Kim, TI and Lee, JY and Dai, F and Hong, SJ}, title = {Identification and molecular characterization of Parkin in Clonorchis sinensis.}, journal = {The Korean journal of parasitology}, volume = {53}, number = {1}, pages = {65-75}, pmid = {25748711}, issn = {1738-0006}, mesh = {Amino Acid Sequence ; Animals ; Clonorchis sinensis/*enzymology ; Cluster Analysis ; Conserved Sequence ; DNA, Complementary/genetics ; Energy Metabolism ; Gene Expression Profiling ; Mitochondria/metabolism ; Models, Molecular ; Molecular Weight ; Phylogeny ; Protein Conformation ; Sequence Homology, Amino Acid ; Ubiquitin-Protein Ligases/chemistry/*genetics/*metabolism ; }, abstract = {Clonorchis sinensis habitating in the bile duct of mammals causes clonorchiasis endemic in East Asian countries. Parkin is a RING-between-RING protein and has E3-ubiquitin ligase activity catalyzing ubiquitination and degradation of substrate proteins. A cDNA clone of C. sinensis was predicted to encode a polypeptide homologous to parkin (CsParkin) including 5 domains (Ubl, RING0, RING1, IBR, and RING2). The cysteine and histidine residues binding to Zn(2+) were all conserved and participated in formation of tertiary structural RINGs. Conserved residues were also an E2-binding site in RING1 domain and a catalytic cysteine residue in the RING2 domain. Native CsParkin was determined to have an estimated molecular weight of 45.7 kDa from C. sinensis adults by immunoblotting. CsParkin revealed E3-ubiquitin ligase activity and higher expression in metacercariae than in adults. CsParkin was localized in the locomotive and male reproductive organs of C. sinensis adults, and extensively in metacercariae. Parkin has been found to participate in regulating mitochondrial function and energy metabolism in mammalian cells. From these results, it is suggested that CsParkin play roles in energy metabolism of the locomotive organs, and possibly in protein metabolism of the reproductive organs of C. sinensis.}, }
@article {pmid25746686, year = {2015}, author = {Yin, F and Cadenas, E}, title = {Mitochondria: the cellular hub of the dynamic coordinated network.}, journal = {Antioxidants &amp; redox signaling}, volume = {22}, number = {12}, pages = {961-964}, pmid = {25746686}, issn = {1557-7716}, mesh = {Animals ; *Cytoplasm ; Homeostasis ; Humans ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/*metabolism ; Mitophagy ; Protein Kinases/metabolism ; Sirtuins/metabolism ; }, abstract = {Mitochondria are the powerhouses of the eukaryotic cell. After billions of years of evolution, mitochondria have adaptively integrated into the symbiont. Such integration is not only evidenced by the consolidation of genetic information, that is, the transfer of most mitochondrial genes into the nucleus, but also manifested by the functional recombination by which mitochondria participate seamlessly in various cellular processes. In the past decade, the field of mitochondria biology has been focused on the dynamic and interactive features of these semiautonomous organelles. Aspects of a complex multilayer quality control system coordinating mitochondrial function and environmental changes are being uncovered and refined. This Forum summarizes the recent progress of these critical topics, with a focus on the dynamic quality control of mitochondrial reticulum, including their biogenesis, dynamic remodeling, and degradation, as well as the homeostasis of the mitochondrial proteome. These diverse but interconnected mechanisms are found to be critical in the maintenance of a functional, efficient, and responsive mitochondrial population and could therefore become therapeutic targets in numerous mitochondrion-implicated disorders.}, }
@article {pmid25740821, year = {2015}, author = {Oliveira, MT and Haukka, J and Kaguni, LS}, title = {Evolution of the metazoan mitochondrial replicase.}, journal = {Genome biology and evolution}, volume = {7}, number = {4}, pages = {943-959}, pmid = {25740821}, issn = {1759-6653}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; DNA Polymerase gamma ; DNA-Directed DNA Polymerase/*chemistry/classification/*genetics ; *Evolution, Molecular ; Genome, Mitochondrial ; Humans ; Mitochondria/*enzymology ; Mitochondrial Proteins/*chemistry/classification/*genetics ; Nematoda/genetics ; Phylogeny ; Protein Multimerization ; Protein Subunits/chemistry ; Sequence Deletion ; }, abstract = {The large number of complete mitochondrial DNA (mtDNA) sequences available for metazoan species makes it a good system for studying genome diversity, although little is known about the mechanisms that promote and/or are correlated with the evolution of this organellar genome. By investigating the molecular evolutionary history of the catalytic and accessory subunits of the mtDNA polymerase, pol γ, we sought to develop mechanistic insight into its function that might impact genome structure by exploring the relationships between DNA replication and animal mitochondrial genome diversity. We identified three evolutionary patterns among metazoan pol γs. First, a trend toward stabilization of both sequence and structure occurred in vertebrates, with both subunits evolving distinctly from those of other animal groups, and acquiring at least four novel structural elements, the most important of which is the HLH-3β (helix-loop-helix, 3 β-sheets) domain that allows the accessory subunit to homodimerize. Second, both subunits of arthropods and tunicates have become shorter and evolved approximately twice as rapidly as their vertebrate homologs. And third, nematodes have lost the gene for the accessory subunit, which was accompanied by the loss of its interacting domain in the catalytic subunit of pol γ, and they show the highest rate of molecular evolution among all animal taxa. These findings correlate well with the mtDNA genomic features of each group described above, and with their modes of DNA replication, although a substantive amount of biochemical work is needed to draw conclusive links regarding the latter. Describing the parallels between evolution of pol γ and metazoan mtDNA architecture may also help in understanding the processes that lead to mitochondrial dysfunction and to human disease-related phenotypes.}, }
@article {pmid25736565, year = {2015}, author = {Neumann, S and El Maadidi, S and Faletti, L and Haun, F and Labib, S and Schejtman, A and Maurer, U and Borner, C}, title = {How do viruses control mitochondria-mediated apoptosis?.}, journal = {Virus research}, volume = {209}, number = {}, pages = {45-55}, pmid = {25736565}, issn = {1872-7492}, mesh = {*Apoptosis ; *Host-Pathogen Interactions ; Humans ; *Immunity, Innate ; Mitochondria/*metabolism ; *Virus Replication ; Viruses/*growth &amp; development/*immunology ; }, abstract = {There is no doubt that viruses require cells to successfully reproduce and effectively infect the next host. The question is what is the fate of the infected cells? All eukaryotic cells can "sense" viral infections and exhibit defence strategies to oppose viral replication and spread. This often leads to the elimination of the infected cells by programmed cell death or apoptosis. This "sacrifice" of infected cells represents the most primordial response of multicellular organisms to viruses. Subverting host cell apoptosis, at least for some time, is therefore a crucial strategy of viruses to ensure their replication, the production of essential viral proteins, virus assembly and the spreading to new hosts. For that reason many viruses harbor apoptosis inhibitory genes, which once inside infected cells are expressed to circumvent apoptosis induction during the virus reproduction phase. On the other hand, viruses can take advantage of stimulating apoptosis to (i) facilitate shedding and hence dissemination, (ii) to prevent infected cells from presenting viral antigens to the immune system or (iii) to kill non-infected bystander and immune cells which would limit viral propagation. Hence the decision whether an infected host cell undergoes apoptosis or not depends on virus type and pathogenicity, its capacity to oppose antiviral responses of the infected cells and/or to evade any attack from immune cells. Viral genomes have therefore been adapted throughout evolution to satisfy the need of a particular virus to induce or inhibit apoptosis during its life cycle. Here we review the different strategies used by viruses to interfere with the two major apoptosis as well as with the innate immune signaling pathways in mammalian cells. We will focus on the intrinsic mitochondrial pathway and discuss new ideas about how particular viruses could activately engage mitochondria to induce apoptosis of their host.}, }
@article {pmid25733873, year = {2015}, author = {Ku, C and Nelson-Sathi, S and Roettger, M and Garg, S and Hazkani-Covo, E and Martin, WF}, title = {Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10139-10146}, pmid = {25733873}, issn = {1091-6490}, support = {232975/ERC_/European Research Council/International ; }, mesh = {Alleles ; Animals ; Chloroplasts/genetics ; Computational Biology ; Cyanobacteria/genetics ; DNA, Bacterial/genetics ; Escherichia coli/genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genome ; Genome, Bacterial ; Humans ; Mitochondria/genetics ; Phylogeny ; Plastids/genetics ; Recombination, Genetic ; Symbiosis/*genetics ; }, abstract = {Endosymbiotic theory in eukaryotic-cell evolution rests upon a foundation of three cornerstone partners--the plastid (a cyanobacterium), the mitochondrion (a proteobacterium), and its host (an archaeon)--and carries a corollary that, over time, the majority of genes once present in the organelle genomes were relinquished to the chromosomes of the host (endosymbiotic gene transfer). However, notwithstanding eukaryote-specific gene inventions, single-gene phylogenies have never traced eukaryotic genes to three single prokaryotic sources, an issue that hinges crucially upon factors influencing phylogenetic inference. In the age of genomes, single-gene trees, once used to test the predictions of endosymbiotic theory, now spawn new theories that stand to eventually replace endosymbiotic theory with descriptive, gene tree-based variants featuring supernumerary symbionts: prokaryotic partners distinct from the cornerstone trio and whose existence is inferred solely from single-gene trees. We reason that the endosymbiotic ancestors of mitochondria and chloroplasts brought into the eukaryotic--and plant and algal--lineage a genome-sized sample of genes from the proteobacterial and cyanobacterial pangenomes of their respective day and that, even if molecular phylogeny were artifact-free, sampling prokaryotic pangenomes through endosymbiotic gene transfer would lead to inherited chimerism. Recombination in prokaryotes (transduction, conjugation, transformation) differs from recombination in eukaryotes (sex). Prokaryotic recombination leads to pangenomes, and eukaryotic recombination leads to vertical inheritance. Viewed from the perspective of endosymbiotic theory, the critical transition at the eukaryote origin that allowed escape from Muller's ratchet--the origin of eukaryotic recombination, or sex--might have required surprisingly little evolutionary innovation.}, }
@article {pmid25732537, year = {2015}, author = {Carrie, C and Venne, AS and Zahedi, RP and Soll, J}, title = {Identification of cleavage sites and substrate proteins for two mitochondrial intermediate peptidases in Arabidopsis thaliana.}, journal = {Journal of experimental botany}, volume = {66}, number = {9}, pages = {2691-2708}, pmid = {25732537}, issn = {1460-2431}, mesh = {Arabidopsis/*enzymology/metabolism ; Arabidopsis Proteins/analysis/chemistry/*metabolism ; Binding Sites ; Gene Expression Regulation, Plant ; Peptide Hydrolases/analysis/chemistry/*metabolism ; Substrate Specificity ; }, abstract = {Most mitochondrial proteins contain an N-terminal targeting signal that is removed by specific proteases following import. In plant mitochondria, only mitochondrial processing peptidase (MPP) has been characterized to date. Therefore, we sought to determine the substrates and cleavage sites of the Arabidopsis thaliana homologues to the yeast Icp55 and Oct1 proteins, using the newly developed ChaFRADIC method for N-terminal protein sequencing. We identified 88 and seven putative substrates for Arabidopsis ICP55 and OCT1, respectively. It was determined that the Arabidopsis ICP55 contains an almost identical cleavage site to that of Icp55 from yeast. However, it can also remove a far greater range of amino acids. The OCT1 substrates from Arabidopsis displayed no consensus cleavage motif, and do not contain the classical -10R motif identified in other eukaryotes. Arabidopsis OCT1 can also cleave presequences independently, without the prior cleavage of MPP. It was concluded that while both OCT1 and ICP55 were probably acquired early on in the evolution of mitochondria, their substrate profiles and cleavage sites have either remained very similar or diverged completely.}, }
@article {pmid25729802, year = {2015}, author = {Sloan, DB}, title = {Using plants to elucidate the mechanisms of cytonuclear co-evolution.}, journal = {The New phytologist}, volume = {205}, number = {3}, pages = {1040-1046}, doi = {10.1111/nph.12835}, pmid = {25729802}, issn = {1469-8137}, mesh = {Cell Nucleus/*genetics ; DNA, Mitochondrial ; *DNA, Plant ; *Evolution, Molecular ; Genes, Plant ; *Genome, Mitochondrial ; *Genome, Plant ; Mitochondria/*genetics ; Mutation Rate ; Plants/*genetics ; Silene/genetics ; }, abstract = {The presence of both cytoplasmic and nuclear genomes within eukaryotic cells raises fascinating questions about co-evolution between genomic compartments that experience fundamentally different mutation rates and modes of inheritance. The highly mutagenic environments found in the mitochondria of some eukaryotes have generated interest in the role that mitochondrial mutation accumulation plays in phenomena such as intracellular gene transfer, compensatory evolution in the nucleus and the evolution of reproductive isolation. Although plant systems have played an important historical role in the study of cytonuclear co-evolution, they remain underutilized in many respects. In particular, the enormous natural variation in DNA substitution rates, gene content and genome architecture in plant mitochondria - much of which has even been found within a single genus – provides opportunities to resolve longstanding evolutionary questions about the consequences of mitochondrial mutation accumulation. This review summarizes some of the classic questions about cytonuclear co-evolution that could be addressed by taking advantage of the variation in plants and highlights a recent analysis of the effect of mitochondrial mutation accumulation on rates of molecular evolution in the nucleus.}, }
@article {pmid25726607, year = {2014}, author = {Li, XM and Li, XB and Huang, W}, title = {[Research progress on mitochondrial genome structure in the phylum apicomplexa].}, journal = {Zhongguo ji sheng chong xue yu ji sheng chong bing za zhi = Chinese journal of parasitology &amp; parasitic diseases}, volume = {32}, number = {5}, pages = {388-392}, pmid = {25726607}, issn = {1000-7423}, mesh = {Apicomplexa/*genetics ; DNA, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Plastids ; }, abstract = {Mitochondria are ubiquitous organelles in all eukaryotic cells which are essential for a series of cellular processes and signal transduction. The phylum Apicomplexa includes series of unicellular eukaryotes and some of them are clinically or economically important parasites. Recent studies have demonstrated that apicomplexan parasites' mitochondrial genomes exhibit remarkably diverse structures and they are ideal biological models to comprehend the evolution of mitochondrial genomes. This paper summarizes the mitochondrial genome structure of some representative apicomplexan, highlights their structure characteristics along with evolution process, and briefly describes their nuclear mitochondrial DNA and nuclear plastid DNA.}, }
@article {pmid25724193, year = {2015}, author = {Tang, WG and Song, P and Cao, ZY and Wang, P and Zhu, GP}, title = {A unique homodimeric NAD[+]-linked isocitrate dehydrogenase from the smallest autotrophic eukaryote Ostreococcus tauri.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {29}, number = {6}, pages = {2462-2472}, doi = {10.1096/fj.14-257014}, pmid = {25724193}, issn = {1530-6860}, mesh = {Algal Proteins/*chemistry/genetics/metabolism ; Amino Acid Sequence ; Base Sequence ; Binding Sites/genetics ; Blotting, Western ; Chlorophyta/*enzymology/genetics ; Circular Dichroism ; Isocitrate Dehydrogenase/*chemistry/classification/metabolism ; Isocitrates/metabolism ; Kinetics ; Magnesium/metabolism ; Manganese/metabolism ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Molecular Weight ; Mutation ; NAD/*chemistry/metabolism ; NADP/chemistry/metabolism ; Phylogeny ; Protein Binding ; *Protein Multimerization ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {In eukaryotes, NAD(+)-dependent isocitrate dehydrogenase (IDH) is strictly mitochondrial and is a key enzyme in the Krebs cycle. To date, all known NAD(+)-specific IDHs (NAD-IDHs) in the mitochondria are believed to be heteromeric in solution. Here, a unique homodimeric NAD-IDH from Ostreococcus tauri (OtIDH), the smallest autotrophic picoeukaryote, was unveiled. Active OtIDH has a molecular weight of ∼93 kDa with each subunit of 46.7 kDa. In the presence of Mn(2+) and Mg(2+), OtIDH displayed 42-fold and 51-fold preference for NAD(+) over NADP(+), respectively. Interestingly, OtIDH exhibited a sigmoidal kinetic behavior in response to isocitrate unlike other homodimeric homologs, and a remarkably high affinity for isocitrate (S0.5 < 10 μM) unlike other hetero-oligomeric homologs. Furthermore, its coenzyme specificity can be completely converted from NAD(+) (ancient trait) to NADP(+) (adaptive trait) by rational mutagenesis based on the evolutionary trace. Mutants D344R and D344R/M345H displayed a 15-fold and 72-fold preference for NADP(+) over NAD(+), respectively, indicating that D344 and M345 are the determinants of NAD(+) specificity. These findings also suggest that OtIDH may be an ancestral form of type II IDHs (all reported members are NADP(+)-linked enzymes) and may have evolved into NADP(+)-dependent IDH for adaptation to the increased demand of NADPH under carbon starvation.}, }
@article {pmid25714339, year = {2015}, author = {Nojima, Y and Ito, K and Ono, H and Nakazato, T and Bono, H and Yokoyama, T and Sato, R and Suetsugu, Y and Nakamura, Y and Yamamoto, K and Satoh, J and Tabunoki, H and Fugo, H}, title = {Superoxide dismutases, SOD1 and SOD2, play a distinct role in the fat body during pupation in silkworm Bombyx mori.}, journal = {PloS one}, volume = {10}, number = {2}, pages = {e0116007}, pmid = {25714339}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Bombyx/drug effects/genetics/*metabolism ; Cell Line ; Cloning, Molecular ; DNA, Complementary/genetics ; Fat Body/*metabolism ; Gene Expression Regulation ; Insecticides/pharmacology ; Isosorbide Dinitrate/pharmacology ; Molecular Sequence Data ; Organ Specificity ; Phylogeny ; Reactive Oxygen Species/metabolism ; Rotenone/pharmacology ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Superoxide Dismutase/genetics/*metabolism ; Superoxide Dismutase-1 ; }, abstract = {One way that aerobic biological systems counteract the generation of reactive oxygen species (ROS) is with superoxide dismutase proteins SOD1 and SOD2 that metabolize superoxide radicals to molecular oxygen and hydrogen peroxide or scavenge oxygen radicals produced by the extensive oxidation-reduction and electron-transport reactions that occur in mitochondria. We characterized SOD1 and SOD2 of Bombyx mori isolated from the fat body of larvae. Immunological analysis demonstrated the presence of BmSOD1 and BmSOD2 in the silk gland, midgut, fat body, Malpighian tubules, testis and ovary from larvae to adults. We found that BmSOD2 had a unique expression pattern in the fat body through the fifth instar larval developmental stage. The anti-oxidative functions of BmSOD1 and BmSOD2 were assessed by exposing larvae to insecticide rotenone or vasodilator isosorbide dinitrate, which is an ROS generator in BmN4 cells; however, exposure to these compounds had no effect on the expression levels of either BmSOD protein. Next, we investigated the physiological role of BmSOD1 and BmSOD2 under environmental oxidative stress, applied through whole-body UV irradiation and assayed using quantitative RT-PCR, immunoblotting and microarray analysis. The mRNA expression level of both BmSOD1 and BmSOD2 was markedly increased but protein expression level was increased only slightly. To examine the differences in mRNA and protein level due to UV irradiation intensity, we performed microarray analysis. Gene set enrichment analysis revealed that genes in the insulin signaling pathway and PPAR signaling pathway were significantly up-regulated after 6 and 12 hours of UV irradiation. Taken together, the activities of BmSOD1 and BmSOD2 may be related to the response to UV irradiation stress in B. mori. These results suggest that BmSOD1 and BmSOD2 modulate environmental oxidative stress in the cell and have a specific role in fat body of B. mori during pupation.}, }
@article {pmid25711245, year = {2015}, author = {Yant, L}, title = {When two is a crowd: mitochondrial genome merger and its aftermath.}, journal = {The New phytologist}, volume = {206}, number = {1}, pages = {8-9}, doi = {10.1111/nph.13321}, pmid = {25711245}, issn = {1469-8137}, mesh = {Genome, Mitochondrial/*genetics ; Genome, Plant/*genetics ; *Homologous Recombination ; Magnoliopsida/*genetics ; Solanaceae/*genetics ; }, }
@article {pmid25710177, year = {2015}, author = {Erives, AJ and Fassler, JS}, title = {Metabolic and chaperone gene loss marks the origin of animals: evidence for Hsp104 and Hsp78 chaperones sharing mitochondrial enzymes as clients.}, journal = {PloS one}, volume = {10}, number = {2}, pages = {e0117192}, pmid = {25710177}, issn = {1932-6203}, mesh = {Aconitate Hydratase/classification/genetics ; Animals ; Bayes Theorem ; Choanoflagellata/genetics ; Endopeptidase Clp/classification/genetics ; Heat-Shock Proteins/*genetics/metabolism ; Likelihood Functions ; Mitochondria/*enzymology/metabolism ; Mutation ; Phylogeny ; Promoter Regions, Genetic ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {The evolution of animals involved acquisition of an emergent gene repertoire for gastrulation. Whether loss of genes also co-evolved with this developmental reprogramming has not yet been addressed. Here, we identify twenty-four genetic functions that are retained in fungi and choanoflagellates but undetectable in animals. These lost genes encode: (i) sixteen distinct biosynthetic functions; (ii) the two ancestral eukaryotic ClpB disaggregases, Hsp78 and Hsp104, which function in the mitochondria and cytosol, respectively; and (iii) six other assorted functions. We present computational and experimental data that are consistent with a joint function for the differentially localized ClpB disaggregases, and with the possibility of a shared client/chaperone relationship between the mitochondrial Fe/S homoaconitase encoded by the lost LYS4 gene and the two ClpBs. Our analyses lead to the hypothesis that the evolution of gastrulation-based multicellularity in animals led to efficient extraction of nutrients from dietary sources, loss of natural selection for maintenance of energetically expensive biosynthetic pathways, and subsequent loss of their attendant ClpB chaperones.}, }
@article {pmid25707022, year = {2015}, author = {Cianciulli, A and Calvello, R and Panaro, MA}, title = {Determinism and randomness in the evolution of introns and sine inserts in mouse and human mitochondrial solute carrier and cytokine receptor genes.}, journal = {Computational biology and chemistry}, volume = {55}, number = {}, pages = {49-59}, doi = {10.1016/j.compbiolchem.2015.02.012}, pmid = {25707022}, issn = {1476-928X}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Carrier Proteins/genetics/*metabolism ; Conserved Sequence ; Humans ; Introns/*genetics/*physiology ; Mice ; Mitochondria/genetics/*metabolism ; Receptors, Cytokine/genetics/*metabolism ; }, abstract = {In the homologous genes studied, the exons and introns alternated in the same order in mouse and human. We studied, in both species: corresponding short segments of introns, whole corresponding introns and complete homologous genes. We considered the total number of nucleotides and the number and orientation of the SINE inserts. Comparisons of mouse and human data series showed that at the level of individual relatively short segments of intronic sequences the stochastic variability prevails in the local structuring, but at higher levels of organization a deterministic component emerges, conserved in mouse and human during the divergent evolution, despite the ample re-editing of the intronic sequences and the fact that processes such as SINE spread had taken place in an independent way in the two species. Intron conservation is negatively correlated with the SINE occupancy, suggesting that virus inserts interfere with the conservation of the sequences inherited from the common ancestor.}, }
@article {pmid25706746, year = {2015}, author = {Diaz-Muñoz, MD and Bell, SE and Fairfax, K and Monzon-Casanova, E and Cunningham, AF and Gonzalez-Porta, M and Andrews, SR and Bunik, VI and Zarnack, K and Curk, T and Heggermont, WA and Heymans, S and Gibson, GE and Kontoyiannis, DL and Ule, J and Turner, M}, title = {The RNA-binding protein HuR is essential for the B cell antibody response.}, journal = {Nature immunology}, volume = {16}, number = {4}, pages = {415-425}, pmid = {25706746}, issn = {1529-2916}, support = {BBS/E/B/000C0409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J001457/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L009986/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; P01 AG014930/AG/NIA NIH HHS/United States ; BBS/E/B/000C0407/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J00152X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Acyltransferases/genetics/immunology ; Alternative Splicing/immunology ; Animals ; Antigens/administration &amp; dosage/immunology ; B-Lymphocytes/cytology/drug effects/*immunology ; Cell Death ; Cell Differentiation ; Cell Proliferation ; ELAV Proteins/genetics/*immunology ; Erythrocytes/immunology ; Germinal Center/cytology/drug effects/*immunology ; *Immunity, Humoral ; Immunization ; Immunoglobulin Class Switching ; Immunoglobulins/*biosynthesis ; Lipopolysaccharides/pharmacology ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Mitochondria/genetics/immunology ; RNA, Messenger/genetics/*immunology ; Reactive Oxygen Species/immunology/metabolism ; Sheep ; }, abstract = {Post-transcriptional regulation of mRNA by the RNA-binding protein HuR (encoded by Elavl1) is required in B cells for the germinal center reaction and for the production of class-switched antibodies in response to thymus-independent antigens. Transcriptome-wide examination of RNA isoforms and their abundance and translation in HuR-deficient B cells, together with direct measurements of HuR-RNA interactions, revealed that HuR-dependent splicing of mRNA affected hundreds of transcripts, including that encoding dihydrolipoamide S-succinyltransferase (Dlst), a subunit of the 2-oxoglutarate dehydrogenase (α-KGDH) complex. In the absence of HuR, defective mitochondrial metabolism resulted in large amounts of reactive oxygen species and B cell death. Our study shows how post-transcriptional processes control the balance of energy metabolism required for the proliferation and differentiation of B cells.}, }
@article {pmid25702753, year = {2015}, author = {Kaya, A and Lobanov, AV and Gladyshev, VN}, title = {Evidence that mutation accumulation does not cause aging in Saccharomyces cerevisiae.}, journal = {Aging cell}, volume = {14}, number = {3}, pages = {366-371}, pmid = {25702753}, issn = {1474-9726}, support = {R37 GM065204/GM/NIGMS NIH HHS/United States ; AG038004/AG/NIA NIH HHS/United States ; GM065204/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Mitochondrial/genetics ; Mitochondria/*genetics ; Mutation/*genetics ; *Mutation Accumulation ; Mutation Rate ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/*genetics ; }, abstract = {The concept that mutations cause aging phenotypes could not be directly tested previously due to inability to identify age-related mutations in somatic cells and determine their impact on organismal aging. Here, we subjected Saccharomyces cerevisiae to multiple rounds of replicative aging and assessed de novo mutations in daughters of mothers of different age. Mutations did increase with age, but their low numbers, < 1 per lifespan, excluded their causal role in aging. Structural genome changes also had no role. A mutant lacking thiol peroxidases had the mutation rate well above that of wild-type cells, but this did not correspond to the aging pattern, as old wild-type cells with few or no mutations were dying, whereas young mutant cells with many more mutations continued dividing. In addition, wild-type cells lost mitochondrial DNA during aging, whereas shorter-lived mutant cells preserved it, excluding a causal role of mitochondrial mutations in aging. Thus, DNA mutations do not cause aging in yeast. These findings may apply to other damage types, suggesting a causal role of cumulative damage, as opposed to individual damage types, in organismal aging.}, }
@article {pmid25701603, year = {2015}, author = {Randhawa, R and Sehgal, M and Singh, TR and Duseja, A and Changotra, H}, title = {Unc-51 like kinase 1 (ULK1) in silico analysis for biomarker identification: a vital component of autophagy.}, journal = {Gene}, volume = {562}, number = {1}, pages = {40-49}, doi = {10.1016/j.gene.2015.02.056}, pmid = {25701603}, issn = {1879-0038}, mesh = {Amino Acid Sequence ; Animals ; Autophagy/*genetics ; Autophagy-Related Protein-1 Homolog ; Biomarkers/metabolism ; Computer Simulation ; Humans ; Intracellular Signaling Peptides and Proteins/chemistry/*genetics/metabolism ; Lipoylation ; Mammals/genetics ; Molecular Sequence Data ; Peptide Mapping ; Phosphorylation ; Phylogeny ; Protein Binding ; Protein Interaction Mapping ; Protein Isoforms/chemistry/genetics/metabolism ; *Protein Processing, Post-Translational ; Protein Serine-Threonine Kinases/chemistry/*genetics/metabolism ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Transcription Factors/*genetics/metabolism ; Transcription, Genetic ; Xenopus/genetics ; }, abstract = {Autophagy is a degradation pathway involving lysosomal machinery for degradation of damaged organelles like the endoplasmic reticulum and mitochondria into their building blocks to maintain homeostasis within the cell. ULK1, a serine/threonine kinase, is conserved across species, from yeasts to mammals, and plays a central role in autophagy pathway. It receives signals from upstream modulators such as TIP60, mTOR and AMPK and relays them to its downstream substrates like Ambra1 and ZIP kinase. The activity of this complex is regulated through protein-protein interactions and post-translational modifications. Applying in silico analysis we identified (i) conserved patterns of ULK1 that showed its evolutionary relationship between the species which were closely related in a family compared to others. (ii) A total of 23 TFBS distributed throughout ULK1 and nuclear factor (erythroid-derived) 2 (NFE2) is of utmost significance because of its high importance rate. NEF2 has already been shown experimentally to play a role in the autophagy pathway. Most of these were of zinc coordinating class and we suggest that this information could be utilized to modulate this pathway by modifying interactions of these TFs with ULK1. (iii) CATTT haplotype was prominently found with frequency 0.774 in the studied population and nsSNPs which could have harmful effect on ULK1 protein and these could further be tested. (iv) A total of 83 phosphorylation sites were identified; 26 are already known and 57 are new that include one at tyrosine residue which could further be studied for its involvement in ULK1 regulation and hence autophagy. Furthermore, 4 palmitoylation sites at positions 426, 927, 1003 and 1049 were also found which could further be studied for protein-protein interactions as well as in trafficking.}, }
@article {pmid25699200, year = {2015}, author = {Bakhoum, AJ and Quilichini, Y and Justine, JL and Bray, RA and Bâ, CT and Marchand, B}, title = {Ultrastructural study of sperm cells in Acanthocolpidae: the case of Stephanostomum murielae and Stephanostomoides tenuis (Digenea).}, journal = {PeerJ}, volume = {3}, number = {}, pages = {e744}, pmid = {25699200}, issn = {2167-8359}, support = {U17 CE002013/CE/NCIPC CDC HHS/United States ; }, abstract = {The mature spermatozoa of Stephanostomum murielae and Stephanostomoides tenuis are described by transmission electron microscopy. They present several ultrastructural features previously reported in other digeneans. Their spermatozoa possess two axonemes of different length showing the 9 + '1' trepaxonematan pattern, four attachment zones, two mitochondria (with an anterior moniliform one in S. murielae), a nucleus, two bundles of parallel cortical microtubules, external ornamentation of the plasma membrane, spine-like bodies and granules of glycogen. The main differences between the mature spermatozoon of S. murielae and S. tenuis are the maximum number of cortical microtubules, the morphology of the anterior spermatozoon extremity and the anterior mitochondrion. This study is the first concerning members of the family Acanthocolpidae. The main ultrastructural characteristics discussed are the morphology of the anterior and posterior spermatozoon extremities, antero-lateral electron dense material, external ornamentations, spine-like bodies and number and morphology of mitochondria. In addition, the phylogenetic significance of all these ultrastructural features is discussed and compared to molecular results in order to highlight the complex relationships in the Digenea.}, }
@article {pmid25692999, year = {2014}, author = {Sarin, LP and Leidel, SA}, title = {Modify or die?--RNA modification defects in metazoans.}, journal = {RNA biology}, volume = {11}, number = {12}, pages = {1555-1567}, pmid = {25692999}, issn = {1555-8584}, mesh = {Amyotrophic Lateral Sclerosis/genetics/metabolism/pathology ; Animals ; Dysautonomia, Familial/genetics/metabolism/pathology ; Epilepsy, Rolandic/genetics/metabolism/pathology ; Genome-Wide Association Study ; Humans ; Intellectual Disability/genetics/metabolism/pathology ; Mutation ; Neoplasms/genetics/metabolism/pathology ; Nucleic Acid Conformation ; Phenotype ; RNA/*genetics/*metabolism ; *RNA Processing, Post-Transcriptional ; RNA, Mitochondrial ; RNA, Transfer/genetics/*metabolism ; tRNA Methyltransferases/genetics/*metabolism ; }, abstract = {Chemical RNA modifications are present in all kingdoms of life and many of these post-transcriptional modifications are conserved throughout evolution. However, most of the research has been performed on single cell organisms, whereas little is known about how RNA modifications contribute to the development of metazoans. In recent years, the identification of RNA modification genes in genome wide association studies (GWAS) has sparked new interest in previously neglected genes. In this review, we summarize recent findings that connect RNA modification defects and phenotypes in higher eukaryotes. Furthermore, we discuss the implications of aberrant tRNA modification in various human diseases including metabolic defects, mitochondrial dysfunctions, neurological disorders, and cancer. As the molecular mechanisms of these diseases are being elucidated, we will gain first insights into the functions of RNA modifications in higher eukaryotes and finally understand their roles during development.}, }
@article {pmid25692577, year = {2015}, author = {Vodă, R and Dapporto, L and Dincă, V and Vila, R}, title = {Why do cryptic species tend not to co-occur? A case study on two cryptic pairs of butterflies.}, journal = {PloS one}, volume = {10}, number = {2}, pages = {e0117802}, pmid = {25692577}, issn = {1932-6203}, mesh = {Animal Distribution ; Animals ; Butterflies/*genetics/physiology ; Climate ; Ecosystem ; Evolution, Molecular ; Genetic Markers/genetics ; Haplotypes ; Mitochondria/genetics ; Models, Theoretical ; *Phylogeny ; }, abstract = {As cryptic diversity is being discovered, mostly thanks to advances in molecular techniques, it is becoming evident that many of these taxa display parapatric distributions in mainland and that they rarely coexist on islands. Genetic landscapes, haplotype networks and ecological niche modeling analyses were performed for two pairs of non-sister cryptic butterfly species, Aricia agestis-A. cramera and Polyommatus icarus-P. celina (Lycaenidae), to specifically assess non-coexistence on western Mediterranean islands, and to test potential causes producing such chequered distribution patterns. We show that the morphologically and ecologically equivalent pairs of species do not coexist on any of the studied islands, although nearly all islands are colonized by one of them. According to our models, the cryptic pairs displayed marked climatic preferences and 'precipitation during the driest quarter' was recovered as the most important climatic determinant. However, neither dispersal capacity, nor climatic or ecological factors fully explain the observed distributions across particular sea straits, and the existence of species interactions resulting in mutual exclusion is suggested as a necessary hypothesis. Given that the studied species are habitat generalists, feeding on virtually unlimited resources, we propose that reproductive interference, together with climatic preferences, sustain density-dependent mechanisms like "founder takes all" and impede coexistence on islands. Chequered distributions among cryptic taxa, both sister and non-sister, are common in butterflies, suggesting that the phenomenon revealed here could be important in determining biodiversity patterns.}, }
@article {pmid25691734, year = {2015}, author = {Purkanti, R and Thattai, M}, title = {Ancient dynamin segments capture early stages of host-mitochondrial integration.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {9}, pages = {2800-2805}, pmid = {25691734}, issn = {1091-6490}, support = {/WT_/Wellcome Trust/United Kingdom ; 500103/Z/09/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Arabidopsis ; Caenorhabditis elegans ; Chloroplasts/genetics/metabolism ; Dictyostelium ; Drosophila melanogaster ; *Dynamins/genetics/metabolism ; *Evolution, Molecular ; Humans ; *Mitochondria/genetics/metabolism ; Mitochondrial Dynamics/*physiology ; Saccharomyces cerevisiae ; Schizosaccharomyces ; }, abstract = {Eukaryotic cells use dynamins-mechano-chemical GTPases--to drive the division of endosymbiotic organelles. Here we probe early steps of mitochondrial and chloroplast endosymbiosis by tracing the evolution of dynamins. We develop a parsimony-based phylogenetic method for protein sequence reconstruction, with deep time resolution. Using this, we demonstrate that dynamins diversify through the punctuated transformation of sequence segments on the scale of secondary-structural elements. We find examples of segments that have remained essentially unchanged from the 1.8-billion-y-old last eukaryotic common ancestor to the present day. Stitching these together, we reconstruct three ancestral dynamins: The first is nearly identical to the ubiquitous mitochondrial division dynamins of extant eukaryotes, the second is partially preserved in the myxovirus-resistance--like dynamins of metazoans, and the third gives rise to the cytokinetic dynamins of amoebozoans and plants and to chloroplast division dynamins. The reconstructed sequences, combined with evolutionary models and published functional data, suggest that the ancestral mitochondrial division dynamin also mediated vesicle scission. This bifunctional protein duplicated into specialized mitochondrial and vesicle variants at least three independent times--in alveolates, green algae, and the ancestor of fungi and metazoans-accompanied by the loss of the ancient prokaryotic mitochondrial division protein FtsZ. Remarkably, many extant species that retain FtsZ also retain the predicted ancestral bifunctional dynamin. The mitochondrial division apparatus of such organisms, including amoebozoans, red algae, and stramenopiles, seems preserved in a near-primordial form.}, }
@article {pmid25681241, year = {2015}, author = {Lemire, BD}, title = {Evolution of FOXRED1, an FAD-dependent oxidoreductase necessary for NADH:ubiquinone oxidoreductase (Complex I) assembly.}, journal = {Biochimica et biophysica acta}, volume = {1847}, number = {4-5}, pages = {451-457}, doi = {10.1016/j.bbabio.2015.01.014}, pmid = {25681241}, issn = {0006-3002}, mesh = {*Biological Evolution ; Electron Transport ; Electron Transport Complex I/*metabolism ; Humans ; Molecular Chaperones/chemistry/genetics/*metabolism ; NADH, NADPH Oxidoreductases/*metabolism ; *Phylogeny ; }, abstract = {Complex I (NADH:ubiquinone oxidoreductase) is the major entry point for electrons into the respiratory chains of bacteria and mitochondria. Mammalian complex I is composed of 45 subunits and harbors FMN and iron-sulfur cluster cofactors. A heterogeneous disease profile is associated with complex I deficiency. In a large fraction of complex I deficiencies, the primary defect is not in any of the genes encoding a subunit. The proper assembly and function of complex I require the participation of at least 12 assembly factors or chaperones. FOXRED1 encodes a complex I-specific assembly factor and mutations in this gene result in complex I deficiency, infantile onset encephalomyopathy and Leigh syndrome. The human FOXRED1 protein is a mitochondria-targeted 486-amino acid FAD-dependent oxidoreductase. It is most closely related to N-methyl amino acid dehydrogenases. FOXRED1 orthologs are present in archaea, bacteria and eukaryotes. Fungal FOXRED1 orthologs were likely acquired from alphaproteobacteria by horizontal gene transfer. The phylogenetic profile of FOXRED1 orthologs does not parallel the phylogenetic profile of complex I, strongly suggesting that, at least in some organisms, FOXRED1 has a function unrelated to complex I. The only large clade where all members investigated contain both FOXRED1 and complex I is the metazoans. Some bacterial FOXRED1 genes are present in metabolic operons related to amino acid metabolism. FOXRED1 phylogenetic distribution and gene organization suggest a metabolic role for FOXRED1 in complex I biogenesis should be considered.}, }
@article {pmid25675712, year = {2015}, author = {Shashank, PR and Ojha, R and Venkatesan, T and Jalali, SK and Bhanu, KR}, title = {Molecular characterization of brinjal shoot and fruit borer, Leucinodes orbonalis (Guenée) (Lepidoptera: Crambidae) based on mitochondrial marker cytochrome oxidase I and their phylogenetic relationship.}, journal = {Indian journal of experimental biology}, volume = {53}, number = {1}, pages = {51-55}, pmid = {25675712}, issn = {0019-5189}, mesh = {Animals ; Biomarkers ; DNA Primers ; Electron Transport Complex IV/*genetics ; Lepidoptera/enzymology/*genetics ; Mitochondria/*enzymology ; *Phylogeny ; Polymerase Chain Reaction ; }, abstract = {Shoot and fruit borer, Leucinodes orbonalis is an important insect pest infesting brinjal or eggplant in India. Molecular characterization of nine different populations belonging to various brinjal growing regions was done using Cytochorome C Oxidase I (COI) gene. Nucleotide analysis of genetic diversity and phylogenetic analysis of the COI indicate that the L. orbonalis from different geographical regions are homogenous. The results showed less nucleotide diversity (π = 0.007895) and overall mean distance (0.008 ± 0.003). Topologies of neighbour-joining (NJ) trees indicate all the populations belong to single major clade. Therefore, it is inferred that there was no significant molecular diversity within L. orbonalis of different geographical locations of India with respect to COI.}, }
@article {pmid25660376, year = {2015}, author = {Flegontov, P and Michálek, J and Janouškovec, J and Lai, DH and Jirků, M and Hajdušková, E and Tomčala, A and Otto, TD and Keeling, PJ and Pain, A and Oborník, M and Lukeš, J}, title = {Divergent mitochondrial respiratory chains in phototrophic relatives of apicomplexan parasites.}, journal = {Molecular biology and evolution}, volume = {32}, number = {5}, pages = {1115-1131}, doi = {10.1093/molbev/msv021}, pmid = {25660376}, issn = {1537-1719}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Alveolata/genetics/metabolism ; Animals ; Apicomplexa/genetics ; Cytochromes c/metabolism ; Electron Transport ; Electron Transport Complex I/genetics/metabolism ; *Evolution, Molecular ; *Genetic Variation ; Genome, Mitochondrial ; Lactic Acid/metabolism ; Mitochondria/*genetics/metabolism ; Mitochondrial Proton-Translocating ATPases/genetics/metabolism ; Parasites/genetics/metabolism ; Photosynthesis/genetics ; *Phylogeny ; }, abstract = {Four respiratory complexes and ATP-synthase represent central functional units in mitochondria. In some mitochondria and derived anaerobic organelles, a few or all of these respiratory complexes have been lost during evolution. We show that the respiratory chain of Chromera velia, a phototrophic relative of parasitic apicomplexans, lacks complexes I and III, making it a uniquely reduced aerobic mitochondrion. In Chromera, putative lactate:cytochrome c oxidoreductases are predicted to transfer electrons from lactate to cytochrome c, rendering complex III unnecessary. The mitochondrial genome of Chromera has the smallest known protein-coding capacity of all mitochondria, encoding just cox1 and cox3 on heterogeneous linear molecules. In contrast, another photosynthetic relative of apicomplexans, Vitrella brassicaformis, retains the same set of genes as apicomplexans and dinoflagellates (cox1, cox3, and cob).}, }
@article {pmid25655327, year = {2015}, author = {Zhou, W and Zhou, J and Lv, Y and Qu, Y and Chi, M and Li, J and Feng, H}, title = {Identification and characterization of MAVS from black carp Mylopharyngodon piceus.}, journal = {Fish &amp; shellfish immunology}, volume = {43}, number = {2}, pages = {460-468}, doi = {10.1016/j.fsi.2015.01.016}, pmid = {25655327}, issn = {1095-9947}, mesh = {Adaptor Proteins, Signal Transducing/chemistry/*genetics/metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; *Cyprinidae ; Fish Diseases/genetics/*immunology/virology ; Fish Proteins/chemistry/*genetics/metabolism ; *Gene Expression Regulation ; *Immunity, Innate ; Molecular Sequence Data ; Organ Specificity ; Phylogeny ; Reoviridae/physiology ; Reoviridae Infections/genetics/immunology/veterinary/virology ; Rhabdoviridae/physiology ; Rhabdoviridae Infections/genetics/immunology/veterinary/virology ; }, abstract = {MAVS (mitochondria antiviral signaling protein) plays an important role in the host cellular innate immune response against microbial pathogens. In this study, MAVS has been cloned and characterized from black carp (Mylopharyngodon piceus). The full-length cDNA of black carp MAVS (bcMAVS) consists of 2352 nucleotides and the predicted bcMAVS protein contains 579 amino acids. Structural analysis showed that bcMAVS is composed of functional domains including an N-terminal CARD, a central proline-rich domain, a putative TRAF2-binding motif and a C-terminal TM domain, which is similar to mammalian MAVS. bcMAVS is constitutively transcribed in all the selected tissues including gill, kidney, heart, intestine, liver, muscle, skin and spleen; bcMAVS mRNA level in intestine, liver, muscle increased but decreased in spleen right after GCRV or SVCV infection. Multiple bands of bcMAVS were detected in western blot when it was expressed in tissue culture, which is similar to mammalian MAVS. Immunofluorescence assay determined that bcMAVS is a mitochondria protein and luciferase reporter assay demonstrated that bcMAVS could induce zebrafish IFN and EPC IFN expression in tissue culture. Data generated in this manuscript has built a solid foundation for further elucidating the function of bcMAVS in the innate immune system of black carp.}, }
@article {pmid25653025, year = {2015}, author = {Kuijper, B and Lane, N and Pomiankowski, A}, title = {Can paternal leakage maintain sexually antagonistic polymorphism in the cytoplasm?.}, journal = {Journal of evolutionary biology}, volume = {28}, number = {2}, pages = {468-480}, pmid = {25653025}, issn = {1420-9101}, mesh = {Alleles ; Animals ; Cytoplasm ; DNA, Mitochondrial/genetics ; Epistasis, Genetic ; Female ; Haploidy ; Male ; *Models, Genetic ; Polymorphism, Genetic/*genetics/physiology ; }, abstract = {A growing number of studies in multicellular organisms highlight low or moderate frequencies of paternal transmission of cytoplasmic organelles, including both mitochondria and chloroplasts. It is well established that strict maternal inheritance is selectively blind to cytoplasmic elements that are deleterious to males - 'mother's curse'. But it is not known how sensitive this conclusion is to slight levels of paternal cytoplasmic leakage. We assess the scope for polymorphism when individuals bear multiple cytoplasmic alleles in the presence of paternal leakage, bottlenecks and recurrent mutation. When fitness interactions among cytoplasmic elements within an individual are additive, we find that sexually antagonistic polymorphism is restricted to cases of strong selection on males. However, when fitness interactions among cytoplasmic elements are nonlinear, much more extensive polymorphism can be supported in the cytoplasm. In particular, mitochondrial mutants that have strong beneficial fitness effects in males and weak deleterious fitness effects in females when rare (i.e. 'reverse dominance') are strongly favoured under paternal leakage. We discuss how such epistasis could arise through preferential segregation of mitochondria in sex-specific somatic tissues. Our analysis shows how paternal leakage can dampen the evolution of deleterious male effects associated with predominant maternal inheritance of cytoplasm, potentially explaining why 'mother's curse' is less pervasive than predicted by earlier work.}, }
@article {pmid25652939, year = {2015}, author = {Li, X and Huang, Y and Lei, F}, title = {Comparative mitochondrial genomics and phylogenetic relationships of the Crossoptilon species (Phasianidae, Galliformes).}, journal = {BMC genomics}, volume = {16}, number = {1}, pages = {42}, pmid = {25652939}, issn = {1471-2164}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Galliformes/*genetics ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Quail/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Phasianidae is a family of Galliformes containing 38 genera and approximately 138 species, which is grouped into two tribes based on their morphological features, the Pheasants and Partridges. Several studies have attempted to reconstruct the phylogenetic relationships of the Phasianidae, but many questions still remain unaddressed, such as the taxonomic status and phylogenetic relationships among Crossoptilon species. The mitochondrial genome (mitogenome) has been extensively used to infer avian genetic diversification with reasonable resolution. Here, we sequenced the entire mitogenomes of three Crossoptilon species (C. harmani, C. mantchuricum and C. crossoptilon) to investigate their evolutionary relationship among Crossoptilon species.<br><br>RESULTS: The complete mitogenomes of C. harmani, C. mantchuricum and C. crossoptilon are 16682 bp, 16690 bp and 16680 bp in length, respectively, encoding a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a putative control region. C. auritum and C. mantchuricum are more closely related genetically, whereas C. harmani is more closely related to C. crossoptilon. Crossoptilon has a closer relationship with Lophura, and the following phylogenetic relationship was reconstructed: ((Crossoptilon + Lophura) + (Phasianus + Chrysolophus)). The divergence time between the clades C. harmani-C. crossoptilon and C. mantchuricum-C. auritum is consistent with the uplift of the Tibetan Plateau during the Tertiary Pliocene. The Ka/Ks analysis showed that atp8 gene in the Crossoptilon likely experienced a strong selective pressure in adaptation to the plateau environment.<br><br>CONCLUSIONS: C. auritum with C. mantchuricum and C. harmani with C. crossoptilon form two pairs of sister groups. The genetic distance between C. harmani and C. crossoptilon is far less than the interspecific distance and is close to the intraspecific distance of Crossoptilon, indicating that C. harmani is much more closely related to C. crossoptilon. Our mito-phylogenomic analysis supports the monophyly of Crossoptilon and its closer relationship with Lophura. The uplift of Tibetan Plateau is suggested to impact the divergence between C. harmani-C. crossoptilon clade and C. mantchuricum-C. auritum clade during the Tertiary Pliocene. Atp8 gene in the Crossoptilon species might have experienced a strong selective pressure for adaptation to the plateau environment.}, }
@article {pmid25651039, year = {2015}, author = {Szumiel, I}, title = {From radioresistance to radiosensitivity: In vitro evolution of L5178Y lymphoma.}, journal = {International journal of radiation biology}, volume = {91}, number = {6}, pages = {465-471}, doi = {10.3109/09553002.2014.996263}, pmid = {25651039}, issn = {1362-3095}, mesh = {Animals ; Biological Evolution ; Cell Line, Tumor ; Cell Proliferation ; DNA Damage ; Epigenesis, Genetic/radiation effects ; Genomic Instability/radiation effects ; Leukemia L5178/genetics/pathology/*radiotherapy ; Mice ; Mitochondria/genetics/radiation effects ; Oxidative Stress/radiation effects ; Phenotype ; *Radiation Tolerance/genetics ; Tumor Microenvironment/genetics/radiation effects ; }, abstract = {PURPOSE: To discuss the possible reasons for the loss of tumourigenicity and the acquisition of new phenotypic features (among them, sensitivity to X and UVC radiations) as a result of in vitro cultivation of L5178Y lymphoma cells.<br><br>RESULTS: Ten years ago the phenotypic differences between LY-R (original L5178Y maintained in vivo and examined in vitro) and LY-S lines were reviewed in detail by the author. The loss of tumourigenicity of LY-R cells upon in vitro cultivation accompanying the acquirement of the LY-S phenotype had been described earlier by Beer et al. (1983). In spite of their common origin, the sublines were shown to differ in their relative sensitivity to a number of DNA damaging agents and in numerous other features. Here, selected differences between LY-R and LY-S lines are briefly reviewed. It is proposed that Wallace's concept (2010a) that mitochondria are the interface between environmental conditions and the genome may explain the LY-R-LY-S conversion under prolonged in vitro cultivation.<br><br>CONCLUSION: The differences between the LY lines were probably of epigenetic rather than genetic character. The properties of LY-R cells changed as a result of exposure to an oxic in vitro milieu. The changes could be preconditioned by heteroplasmy and the selection of cells endowed with mitochondria best fitted to a high oxygen-low carbon dioxide environment.}, }
@article {pmid25649769, year = {2015}, author = {Sakamoto, A and Hino, S and Nagaoka, K and Anan, K and Takase, R and Matsumori, H and Ojima, H and Kanai, Y and Arita, K and Nakao, M}, title = {Lysine Demethylase LSD1 Coordinates Glycolytic and Mitochondrial Metabolism in Hepatocellular Carcinoma Cells.}, journal = {Cancer research}, volume = {75}, number = {7}, pages = {1445-1456}, doi = {10.1158/0008-5472.CAN-14-1560}, pmid = {25649769}, issn = {1538-7445}, mesh = {Animals ; Carcinoma, Hepatocellular/*enzymology/pathology ; Gene Expression ; Glucose Transporter Type 1/genetics/metabolism ; Glycolysis ; Hep G2 Cells ; Histone Demethylases/*physiology ; Histones/metabolism ; Humans ; Hypoxia-Inducible Factor 1, alpha Subunit/physiology ; Liver Neoplasms/*enzymology/pathology ; Methylation ; Mice, SCID ; Mitochondria, Liver/*enzymology ; Neoplasm Transplantation ; Protein Processing, Post-Translational ; Tumor Burden ; }, abstract = {The hallmark of most cancer cells is the metabolic shift from mitochondrial to glycolytic metabolism for adapting to the surrounding environment. Although epigenetic modification is intimately linked to cancer, the molecular mechanism, by which epigenetic factors regulate cancer metabolism, is poorly understood. Here, we show that lysine-specific demethylase-1 (LSD1, KDM1A) has an essential role in maintaining the metabolic shift in human hepatocellular carcinoma cells. Inhibition of LSD1 reduced glucose uptake and glycolytic activity, with a concurrent activation of mitochondrial respiration. These metabolic changes coexisted with the inactivation of the hypoxia-inducible factor HIF1α, resulting in a decreased expression of GLUT1 and glycolytic enzymes. In contrast, during LSD1 inhibition, a set of mitochondrial metabolism genes was activated with the concomitant increase of methylated histone H3 at lysine 4 in the promoter regions. Consistently, both LSD1 and GLUT1 were significantly overexpressed in carcinoma tissues. These findings demonstrate the epigenetic plasticity of cancer cell metabolism, which involves an LSD1-mediated mechanism.}, }
@article {pmid25648916, year = {2016}, author = {Gan, HM and Gan, HY and Lee, YP and Grandjean, F and Austin, CM}, title = {The complete mitogenome of the invasive spiny-cheek crayfish Orconectes limosus (Rafinesque, 1817) (Crustacea: Decapoda: Cambaridae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {5}, pages = {3181-3183}, doi = {10.3109/19401736.2015.1007326}, pmid = {25648916}, issn = {2470-1408}, mesh = {AT Rich Sequence ; Animals ; Base Composition ; Decapoda/*genetics ; *Genome, Mitochondrial ; Introduced Species ; Open Reading Frames ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {The invasive freshwater crayfish Orconectes limosus mitogenome was recovered by genome skimming. The mitogenome is 16,223 base pairs in length consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The O. limosus mitogenome has an AT bias of 71.37% and base composition of 39.8% for T, 10.3% for C, 31.5% for A, and 18.4% for G. The mitogene order is identical to two other genera of northern hemisphere crayfish that have been sequenced for this organelle.}, }
@article {pmid25644308, year = {2015}, author = {Bakhoum, AJ and Quilichini, Y and Justine, JL and Bray, RA and Bâ, CT and Marchand, B}, title = {Neomultitestis aspidogastriformis Bray and Cribb, 2003 (Digenea, Lepocreadiidae): mature spermatozoon and sperm morphologies in the Lepocreadioidea.}, journal = {Cell biology international}, volume = {39}, number = {7}, pages = {799-807}, doi = {10.1002/cbin.10449}, pmid = {25644308}, issn = {1095-8355}, mesh = {Animals ; Cell Nucleus/ultrastructure ; Glycogen/analysis ; Male ; Microscopy, Electron, Transmission ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Spermatozoa/*ultrastructure ; Trematoda/*cytology/ultrastructure ; }, abstract = {Spermatological characteristics are described for the first time in the genus Neomultitestis Machida, 1982, belonging to the family Lepocreadiidae Odhner, 1905. Adult Neomultitestis aspidogastriformis were collected from the digestive tract of Platax teira, caught off New Caledonia. The mature spermatozoon of N. aspidogastriformis is described by transmission electron microscopy (TEM). It includes two axonemes with 9 + "1" pattern of Trepaxonemata, an antero-lateral electron-dense material, attachment zones, two mitochondria, a nucleus, two bundles of parallel cortical microtubules, external ornamentation of the plasma membrane, spine-like bodies, and granules of glycogen. Certain ultrastructural characteristics of the spermatozoon, especially the antero-lateral electron-dense material, are shared by N. aspidogastriformis and all species of the superfamily Lepocreadioidea studied so far. The antero-lateral electron-dense material, present in different families of lepocreadioids, supports the monophyletic status of the superfamily. We also list several ultrastructural characteristics which characterize the mature spermatozoon of the Lepocreadioidea.}, }
@article {pmid25644076, year = {2015}, author = {Pontieri, P and De Stefano, M and Massardo, DR and Gunge, N and Miyakawa, I and Sando, N and Pignone, D and Pizzolante, G and Romano, R and Alifano, P and Del Giudice, L}, title = {Tellurium as a valuable tool for studying the prokaryotic origins of mitochondria.}, journal = {Gene}, volume = {559}, number = {2}, pages = {177-183}, doi = {10.1016/j.gene.2015.01.060}, pmid = {25644076}, issn = {1879-0038}, mesh = {Biological Evolution ; DNA, Mitochondrial/metabolism ; Escherichia coli/metabolism/ultrastructure ; Halobacterium salinarum/metabolism/ultrastructure ; Mitochondria/metabolism/ultrastructure ; Mitochondrial Membranes/metabolism ; Neisseria lactamica/metabolism/ultrastructure ; Saccharomyces cerevisiae/growth &amp; development/metabolism/ultrastructure ; Sphingomonas/metabolism/ultrastructure ; Tellurium/*metabolism ; }, abstract = {Mitochondria are eukaryotic organelles which contain the own genetic material and evolved from free-living Eubacteria, namely hydrogen-producing Alphaproteobacteria. Since 1965, biologists provided, by research at molecular level, evidence for the prokaryotic origins of mitochondria. However, determining the precise origins of mitochondria is challenging due to inherent difficulties in phylogenetically reconstructing ancient evolutionary events. The use of new tools to evidence the prokaryotic origin of mitochondria could be useful to gain an insight into the bacterial endosymbiotic event that resulted in the permanent acquisition of bacteria, from the ancestral cell, that through time were transformed into mitochondria. Electron microscopy has shown that both proteobacterial and yeast cells during their growth in the presence of increasing amount of tellurite resulted in dose-dependent blackening of the culture due to elemental tellurium (Te(0)) that formed large deposits either along the proteobacterial membrane or along the yeast cell wall and mitochondria. Since the mitochondrial inner membrane composition is similar to that of proteobacterial membrane, in the present work we evidenced the black tellurium deposits on both, cell wall and mitochondria of ρ(+) and respiratory deficient ρ(-) mutants of yeast. A possible role of tellurite in studying the evolutionary origins of mitochondria will be discussed.}, }
@article {pmid25637223, year = {2015}, author = {Dean, R and Zimmer, F and Mank, JE}, title = {Deficit of mitonuclear genes on the human X chromosome predates sex chromosome formation.}, journal = {Genome biology and evolution}, volume = {7}, number = {2}, pages = {636-641}, pmid = {25637223}, issn = {1759-6653}, support = {260233/ERC_/European Research Council/International ; }, mesh = {Animals ; Cell Nucleus/*genetics ; Chickens/genetics ; Chromosomes, Human, X/*genetics ; Genes, Mitochondrial/*genetics ; Humans ; Molecular Sequence Annotation ; Platypus/genetics ; Synteny/genetics ; }, abstract = {Two taxa studied to date, the therian mammals and Caenorhabditis elegans, display underrepresentations of mitonuclear genes (mt-N genes, nuclear genes whose products are imported to and act within the mitochondria) on their X chromosomes. This pattern has been interpreted as the result of sexual conflict driving mt-N genes off of the X chromosome. However, studies in several other species have failed to detect a convergent biased distribution of sex-linked mt-N genes, leading to questions over the generality of the role of sexual conflict in shaping the distribution of mt-N genes. Here we tested whether mt-N genes moved off of the therian X chromosome following sex chromosome formation, consistent with the role of sexual conflict, or whether the paucity of mt-N genes on the therian X is a chance result of an underrepresentation on the ancestral regions that formed the X chromosome. We used a synteny-based approach to identify the ancestral regions in the platypus and chicken genomes that later formed the therian X chromosome. We then quantified the movement of mt-N genes on and off of the X chromosome and the distribution of mt-N genes on the human X and ancestral X regions. We failed to find an excess of mt-N gene movement off of the X. The bias of mt-N genes on ancestral therian X chromosomes was also not significantly different from the biases on the human X. Together our results suggest that, rather than conflict driving mt-N genes off of the mammalian X, random biases on chromosomes that formed the X chromosome could explain the paucity of mt-N genes in the therian lineage.}, }
@article {pmid25631025, year = {2015}, author = {Cheng, Y and Perocchi, F}, title = {Prediction of mitochondrial protein function by comparative physiology and phylogenetic profiling.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1264}, number = {}, pages = {321-329}, doi = {10.1007/978-1-4939-2257-4_28}, pmid = {25631025}, issn = {1940-6029}, mesh = {Animals ; Biological Evolution ; Computational Biology/methods ; Databases, Genetic ; Humans ; Internet ; Mitochondria/*genetics/*metabolism ; Mitochondrial Proteins/*genetics/*metabolism ; *Models, Biological ; *Phylogeny ; *Physiology, Comparative ; }, abstract = {According to the endosymbiotic theory, mitochondria originate from a free-living alpha-proteobacteria that established an intracellular symbiosis with the ancestor of present-day eukaryotic cells. During the bacterium-to-organelle transformation, the proto-mitochondrial proteome has undergone a massive turnover, whereby less than 20 % of modern mitochondrial proteomes can be traced back to the bacterial ancestor. Moreover, mitochondrial proteomes from several eukaryotic organisms, for example, yeast and human, show a rather modest overlap, reflecting differences in mitochondrial physiology. Those differences may result from the combination of differential gain and loss of genes and retargeting processes among lineages. Therefore, an evolutionary signature, also called "phylogenetic profile", could be generated for every mitochondrial protein. Here, we present two evolutionary biology approaches to study mitochondrial physiology: the first strategy, which we refer to as "comparative physiology," allows the de novo identification of mitochondrial proteins involved in a physiological function; the second, known as "phylogenetic profiling," allows to predict protein functions and functional interactions by comparing phylogenetic profiles of uncharacterized and known components.}, }
@article {pmid25630736, year = {2016}, author = {Zhang, Y and Xie, Z and Deng, X and Xie, Z and Liu, J and Xie, L and Luo, S and Huang, L and Huang, J and Zeng, T and Wang, S}, title = {Mitochondrial genome of the Luchuan pig (Sus scrofa).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4139-4141}, doi = {10.3109/19401736.2014.1003881}, pmid = {25630736}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; DNA, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Open Reading Frames/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; Sus scrofa ; Swine/*genetics ; }, abstract = {The complete mitochondrial genome sequence of the Luchuan pig was measured by PCR-based methods, primer-walking sequencing, and fragment cloning. The entire mitochondrial genome of the Luchuan pig was identified as a circular molecule consisting of 16,730 bp (GenBank accession number: KP126954). The contents of A, T, C, and G in the mitochondrial genome were found to be 34.65%, 25.80%, 26.19%, and 13.36%, respectively. The complete mitochondrial genome of the Luchuan pig contains a typical structure, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region (D-loop region). This complete mitochondrial genome sequence provides essential information in understanding phylogenetic relationships among Sus scrofa domestic mitochondrial genomes.}, }
@article {pmid25629468, year = {2016}, author = {Wu, YP and Xie, JF and He, QS and Xie, JL}, title = {The complete mitochondrial genome sequence of Colossoma macropomum (Characiformes: Serrasalmidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4080-4081}, doi = {10.3109/19401736.2014.1003853}, pmid = {25629468}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Characiformes/*genetics ; Codon, Initiator/genetics ; Codon, Terminator/genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; South America ; Whole Genome Sequencing/methods ; }, abstract = {Colossoma macropomum (Cuvier, 1816) is the largest characin of South America. This species and its congeners mainly feed on zooplankton, insects, snails and decaying plants. In this paper, we sequenced and annotated the complete mitogenome of C. macropomum. The total length is 16,703 bp, and it typically consist of 37 genes, including 13 protein-coding genes, two rRNAs, 22 tRNA, a light-strand replication origin (OL) and a large control region (D-loop). The overall base composition is 29.9%, 24.6%, 29.5% and 15.9% for A, T, C and G, respectively, with a slight bias on AT content (54.6%). All protein-coding genes share the start codon ATG, except for COI, which begins with GTG. Most of them have TAA or TAG as the stop codon, except COII, ND4 use AGA and COI, Cytb use an incomplete stop codon T. This information could provide useful molecular data and contribute to further phylogenetic studies of Characiformes and Serrasalmidae.}, }
@article {pmid25627319, year = {2016}, author = {Uliano-Silva, M and Americo, J and Bastos, AS and Furtado, C and Rebelo, MF and Prosdocimi, F}, title = {Complete mitochondrial genome of the brown mussel Perna perna (Bivalve, Mytilidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {3955-3956}, doi = {10.3109/19401736.2014.989502}, pmid = {25627319}, issn = {2470-1408}, mesh = {Animals ; Evolution, Molecular ; Gene Order ; *Genes, Mitochondrial ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Perna/*genetics ; Sequence Analysis, DNA ; }, abstract = {The complete sequence of the brown mussel Perna perna mitochondrial genome is described in this article. It was sequenced in 1/11 of an Illumina HiSeq lane using Nextera multiplexing kit. The mitogenome was assembled using both (i) de novo assembly and (ii) referenced-based strategies with mitoMaker software. Perna perna mitogenome is a circular molecule of 18,415 bp in size, containing 12 protein-coding genes, 23 transfer RNAs, 2 ribossomal RNAs and several non-coding regions. As shown in the previous studies, Perna perna does not present the doubly uniparental inheritance system (DUI) of mitochondria and does not encode the ATPase8 gene, in accordance with other Mytilidae data.}, }
@article {pmid25626174, year = {2015}, author = {Schmitz-Linneweber, C and Lampe, MK and Sultan, LD and Ostersetzer-Biran, O}, title = {Organellar maturases: A window into the evolution of the spliceosome.}, journal = {Biochimica et biophysica acta}, volume = {1847}, number = {9}, pages = {798-808}, doi = {10.1016/j.bbabio.2015.01.009}, pmid = {25626174}, issn = {0006-3002}, mesh = {Cell Nucleus/enzymology ; Chloroplasts/enzymology ; Endoribonucleases/*physiology ; *Evolution, Molecular ; Introns ; Mitochondria/enzymology ; Nucleotidyltransferases/*physiology ; RNA Splicing ; Spliceosomes/*physiology ; }, abstract = {During the evolution of eukaryotic genomes, many genes have been interrupted by intervening sequences (introns) that must be removed post-transcriptionally from RNA precursors to form mRNAs ready for translation. The origin of nuclear introns is still under debate, but one hypothesis is that the spliceosome and the intron-exon structure of genes have evolved from bacterial-type group II introns that invaded the eukaryotic genomes. The group II introns were most likely introduced into the eukaryotic genome from an α-proteobacterial predecessor of mitochondria early during the endosymbiosis event. These self-splicing and mobile introns spread through the eukaryotic genome and later degenerated. Pieces of introns became part of the general splicing machinery we know today as the spliceosome. In addition, group II introns likely brought intron maturases with them to the nucleus. Maturases are found in most bacterial introns, where they act as highly specific splicing factors for group II introns. In the spliceosome, the core protein Prp8 shows homology to group II intron-encoded maturases. While maturases are entirely intron specific, their descendant of the spliceosomal machinery, the Prp8 protein, is an extremely versatile splicing factor with multiple interacting proteins and RNAs. How could such a general player in spliceosomal splicing evolve from the monospecific bacterial maturases? Analysis of the organellar splicing machinery in plants may give clues on the evolution of nuclear splicing. Plants encode various proteins which are closely related to bacterial maturases. The organellar genomes contain one maturase each, named MatK in chloroplasts and MatR in mitochondria. In addition, several maturase genes have been found in the nucleus as well, which are acting on mitochondrial pre-RNAs. All plant maturases show sequence deviation from their progenitor bacterial maturases, and interestingly are all acting on multiple organellar group II intron targets. Moreover, they seem to function in the splicing of group II introns together with a number of additional nuclear-encoded splicing factors, possibly acting as an organellar proto-spliceosome. Together, this makes them interesting models for the early evolution of nuclear spliceosomal splicing. In this review, we summarize recent advances in our understanding of the role of plant maturases and their accessory factors in plants. This article is part of a Special Issue entitled: Chloroplast Biogenesis.}, }
@article {pmid25624149, year = {2015}, author = {Jung, KH and Kim, SR and Giong, HK and Nguyen, MX and Koh, HJ and An, G}, title = {Genome-wide identification and functional analysis of genes expressed ubiquitously in rice.}, journal = {Molecular plant}, volume = {8}, number = {2}, pages = {276-289}, doi = {10.1016/j.molp.2014.10.013}, pmid = {25624149}, issn = {1752-9867}, mesh = {*Gene Expression Regulation, Plant ; Genome, Plant/*genetics ; Oryza/classification/*genetics ; Phylogeny ; Plant Proteins/genetics/metabolism ; Seedlings/genetics/metabolism ; }, abstract = {Genes that are expressed ubiquitously throughout all developmental stages are thought to be necessary for basic biological or cellular functions. Therefore, determining their biological roles is a great challenge. We identified 4034 of these genes in rice after studying the results of Agilent 44K and Affymetrix meta-anatomical expression profiles. Among 105 genes that were characterized by loss-of-function analysis, 79 were classified as members of gene families, the majority of which were predominantly expressed. Using T-DNA insertional mutants, we examined 43 genes and found that loss of expression of six genes caused developing seed- or seedling-defective phenotypes. Of these, three are singletons without similar family members and defective phenotypes are expected from mutations. Phylogenomic analyses integrating genome-wide transcriptome data revealed the functional dominance of three ubiquitously expressed family genes. Among them, we investigated the function of Os03g19890, which is involved in ATP generation within the mitochondria during endosperm development. We also created and evaluated functional networks associated with this gene to understand the molecular mechanism. Our study provides a useful strategy for pheonome analysis of ubiquitously expressed genes in rice.}, }
@article {pmid25616281, year = {2015}, author = {Gnipová, A and Šubrtová, K and Panicucci, B and Horváth, A and Lukeš, J and Zíková, A}, title = {The ADP/ATP carrier and its relationship to oxidative phosphorylation in ancestral protist trypanosoma brucei.}, journal = {Eukaryotic cell}, volume = {14}, number = {3}, pages = {297-310}, pmid = {25616281}, issn = {1535-9786}, mesh = {*Evolution, Molecular ; Mitochondrial ADP, ATP Translocases/chemistry/genetics/*metabolism ; *Oxidative Phosphorylation ; Protozoan Proteins/chemistry/genetics/*metabolism ; Trypanosoma brucei brucei/*genetics/metabolism ; }, abstract = {The highly conserved ADP/ATP carrier (AAC) is a key energetic link between the mitochondrial (mt) and cytosolic compartments of all aerobic eukaryotic cells, as it exchanges the ATP generated inside the organelle for the cytosolic ADP. Trypanosoma brucei, a parasitic protist of medical and veterinary importance, possesses a single functional AAC protein (TbAAC) that is related to the human and yeast ADP/ATP carriers. However, unlike previous studies performed with these model organisms, this study showed that TbAAC is most likely not a stable component of either the respiratory supercomplex III+IV or the ATP synthasome but rather functions as a physically separate entity in this highly diverged eukaryote. Therefore, TbAAC RNA interference (RNAi) ablation in the insect stage of T. brucei does not impair the activity or arrangement of the respiratory chain complexes. Nevertheless, RNAi silencing of TbAAC caused a severe growth defect that coincides with a significant reduction of mt ATP synthesis by both substrate and oxidative phosphorylation. Furthermore, TbAAC downregulation resulted in a decreased level of cytosolic ATP, a higher mt membrane potential, an elevated amount of reactive oxygen species, and a reduced consumption of oxygen in the mitochondria. Interestingly, while TbAAC has previously been demonstrated to serve as the sole ADP/ATP carrier for ADP influx into the mitochondria, our data suggest that a second carrier for ATP influx may be present and active in the T. brucei mitochondrion. Overall, this study provides more insight into the delicate balance of the functional relationship between TbAAC and the oxidative phosphorylation (OXPHOS) pathway in an early diverged eukaryote.}, }
@article {pmid25611331, year = {2014}, author = {Machnicka, MA and Olchowik, A and Grosjean, H and Bujnicki, JM}, title = {Distribution and frequencies of post-transcriptional modifications in tRNAs.}, journal = {RNA biology}, volume = {11}, number = {12}, pages = {1619-1629}, pmid = {25611331}, issn = {1555-8584}, mesh = {Animals ; Bacteria/classification/genetics/metabolism ; Euryarchaeota/classification/genetics/metabolism ; Fungi/classification/genetics/metabolism ; Mitochondria/genetics/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Phylogeny ; Plastids/genetics/metabolism ; *Protein Biosynthesis ; *RNA Processing, Post-Transcriptional ; RNA, Messenger/genetics/*metabolism ; RNA, Transfer/chemistry/genetics/*metabolism ; *Software ; Viridiplantae/classification/genetics/metabolism ; }, abstract = {Functional tRNA molecules always contain a wide variety of post-transcriptionally modified nucleosides. These modifications stabilize tRNA structure, allow for proper interaction with other macromolecules and fine-tune the decoding of mRNAs during translation. Their presence in functionally important regions of tRNA is conserved in all domains of life. However, the identities of many of these modified residues depend much on the phylogeny of organisms the tRNAs are found in, attesting for domain-specific strategies of tRNA maturation. In this work we present a new tool, tRNAmodviz web server (http://genesilico.pl/trnamodviz) for easy comparative analysis and visualization of modification patterns in individual tRNAs, as well as in groups of selected tRNA sequences. We also present results of comparative analysis of tRNA sequences derived from 7 phylogenetically distinct groups of organisms: Gram-negative bacteria, Gram-positive bacteria, cytosol of eukaryotic single cell organisms, Fungi and Metazoa, cytosol of Viridiplantae, mitochondria, plastids and Euryarchaeota. These data update the study conducted 20 y ago with the tRNA sequences available at that time.}, }
@article {pmid25609566, year = {2015}, author = {Wang, Z and Wu, M}, title = {An integrated phylogenomic approach toward pinpointing the origin of mitochondria.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {7949}, pmid = {25609566}, issn = {2045-2322}, mesh = {Alphaproteobacteria/genetics ; *Evolution, Molecular ; Genomics ; Mitochondria/*genetics ; *Phylogeny ; Rickettsiaceae/*genetics ; Symbiosis/genetics ; }, abstract = {Overwhelming evidence supports the endosymbiosis theory that mitochondria originated once from the Alphaproteobacteria. However, its exact position in the tree of life remains highly debated. This is because systematic errors, including biased taxonomic sampling, high evolutionary rates and sequence composition bias have long plagued the mitochondrial phylogenetics. In this study, we address this issue by 1) increasing the taxonomic representation of alphaproteobacterial genomes by sequencing 18 phylogenetically novel species. They include 5 Rickettsiales and 4 Rhodospirillales, two orders that have shown close affiliations with mitochondria previously, 2) using a set of 29 slowly evolving mitochondria-derived nuclear genes that are less biased than mitochondria-encoded genes as the alternative "well behaved" markers for phylogenetic analysis, 3) applying site heterogeneous mixture models that account for the sequence composition bias. With the integrated phylogenomic approach, we are able to for the first time place mitochondria unequivocally within the Rickettsiales order, as a sister clade to the Rickettsiaceae and Anaplasmataceae families, all subtended by the Holosporaceae family. Our results suggest that mitochondria most likely originated from a Rickettsiales endosymbiont already residing in the host, but not from the distantly related free-living Pelagibacter and Rhodospirillales.}, }
@article {pmid25608613, year = {2015}, author = {Nicolaisen, K and Missbach, S and Hsueh, YC and Ertel, F and Fulgosi, H and Sommer, MS and Schleiff, E}, title = {The Omp85-type outer membrane protein p36 of Arabidopsis thaliana evolved by recent gene duplication.}, journal = {Journal of plant research}, volume = {128}, number = {2}, pages = {317-325}, pmid = {25608613}, issn = {1618-0860}, mesh = {Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Base Sequence ; *Evolution, Molecular ; *Gene Duplication ; Membrane Proteins/*genetics/metabolism ; Plastids/genetics/metabolism ; }, abstract = {Proteins of the Omp85 family are involved in the insertion of β-barrel shaped outer membrane proteins in bacteria and mitochondria, and-at least-in the transfer of preproteins across the chloroplast outer envelope. In general these proteins consist of up to five N-terminal "polypeptide transport associated" (POTRA) domains and a C-terminal, membrane embedded β-barrel domain. In Arabidopsis thaliana two plastidic gene families coding for Omp85-like proteins exist, namely the Toc75-III and the Toc75-V/Oep80 sub-family. The latter is composed of three genes, of which two do not contain POTRA domains. These are annotated as P39 and P36. However, P36 resulted from a very recent gene duplication of P39 and appears to be specific to Arabidopsis thaliana. Furthermore, we show that P39 is specifically expressed in vein tissues, while P36 is expressed at early and late developmental stages. T-DNA insertion in P36 causes a mild phenotype with reduced starch accumulation in chloroplasts of sepals pointing towards a yet to be described plastid function.}, }
@article {pmid25608518, year = {2015}, author = {Walpole, TB and Palmer, DN and Jiang, H and Ding, S and Fearnley, IM and Walker, JE}, title = {Conservation of complete trimethylation of lysine-43 in the rotor ring of c-subunits of metazoan adenosine triphosphate (ATP) synthases.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {14}, number = {4}, pages = {828-840}, pmid = {25608518}, issn = {1535-9484}, support = {MC_U105663148/MRC_/Medical Research Council/United Kingdom ; MC_U105663150/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; *Conserved Sequence ; Humans ; Invertebrates/metabolism ; Lysine/*metabolism ; Methylation ; Molecular Sequence Data ; Molecular Weight ; Peptides/metabolism ; Phylogeny ; Protein Processing, Post-Translational ; Protein Subunits/chemistry/isolation &amp; purification/*metabolism ; Proton-Translocating ATPases/chemistry/*metabolism ; Spectrometry, Mass, Electrospray Ionization ; Tandem Mass Spectrometry ; }, abstract = {The rotors of ATP synthases turn about 100 times every second. One essential component of the rotor is a ring of hydrophobic c-subunits in the membrane domain of the enzyme. The rotation of these c-rings is driven by a transmembrane proton-motive force, and they turn against a surface provided by another membrane protein, known as subunit a. Together, the rotating c-ring and the static subunit a provide a pathway for protons through the membrane in which the c-ring and subunit a are embedded. Vertebrate and invertebrate c-subunits are well conserved. In the structure of the bovine F1-ATPase-c-ring subcomplex, the 75 amino acid c-subunit is folded into two transmembrane α-helices linked by a short loop. Each bovine rotor-ring consists of eight c-subunits with the N- and C-terminal α-helices forming concentric inner and outer rings, with the loop regions exposed to the phospholipid head-group region on the matrix side of the inner membrane. Lysine-43 is in the loop region and its ε-amino group is completely trimethylated. The role of this modification is unknown. If the trimethylated lysine-43 plays some important role in the functioning, assembly or degradation of the c-ring, it would be expected to persist throughout vertebrates and possibly invertebrates also. Therefore, we have carried out a proteomic analysis of c-subunits across representative species from different classes of vertebrates and from invertebrate phyla. In the twenty-nine metazoan species that have been examined, the complete methylation of lysine-43 is conserved, and it is likely to be conserved throughout the more than two million extant metazoan species. In unicellular eukaryotes and prokaryotes, when the lysine is conserved it is unmethylated, and the stoichiometries of c-subunits vary from 9-15. One possible role for the trimethylated residue is to provide a site for the specific binding of cardiolipin, an essential component of ATP synthases in mitochondria.}, }
@article {pmid25605899, year = {2015}, author = {Hayashi, T and Asano, Y and Shintani, Y and Aoyama, H and Kioka, H and Tsukamoto, O and Hikita, M and Shinzawa-Itoh, K and Takafuji, K and Higo, S and Kato, H and Yamazaki, S and Matsuoka, K and Nakano, A and Asanuma, H and Asakura, M and Minamino, T and Goto, Y and Ogura, T and Kitakaze, M and Komuro, I and Sakata, Y and Tsukihara, T and Yoshikawa, S and Takashima, S}, title = {Higd1a is a positive regulator of cytochrome c oxidase.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {5}, pages = {1553-1558}, pmid = {25605899}, issn = {1091-6490}, mesh = {Adenosine Triphosphate/biosynthesis ; Animals ; Cattle ; Electron Transport Complex IV/chemistry/*metabolism ; Fluorescence Resonance Energy Transfer ; Hypoxia/enzymology/metabolism ; Hypoxia-Inducible Factor 1, alpha Subunit/genetics/*physiology ; Mitochondria/enzymology ; Oxidative Phosphorylation ; Protein Conformation ; }, abstract = {Cytochrome c oxidase (CcO) is the only enzyme that uses oxygen to produce a proton gradient for ATP production during mitochondrial oxidative phosphorylation. Although CcO activity increases in response to hypoxia, the underlying regulatory mechanism remains elusive. By screening for hypoxia-inducible genes in cardiomyocytes, we identified hypoxia inducible domain family, member 1A (Higd1a) as a positive regulator of CcO. Recombinant Higd1a directly integrated into highly purified CcO and increased its activity. Resonance Raman analysis revealed that Higd1a caused structural changes around heme a, the active center that drives the proton pump. Using a mitochondria-targeted ATP biosensor, we showed that knockdown of endogenous Higd1a reduced oxygen consumption and subsequent mitochondrial ATP synthesis, leading to increased cell death in response to hypoxia; all of these phenotypes were rescued by exogenous Higd1a. These results suggest that Higd1a is a previously unidentified regulatory component of CcO, and represents a therapeutic target for diseases associated with reduced CcO activity.}, }
@article {pmid25605644, year = {2015}, author = {Wilson, DF}, title = {Programming and regulation of metabolic homeostasis.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {308}, number = {6}, pages = {E506-17}, doi = {10.1152/ajpendo.00544.2014}, pmid = {25605644}, issn = {1522-1555}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Cell Respiration ; Electron Transport Complex IV/metabolism ; Energy Metabolism/*physiology ; Eukaryotic Cells/*metabolism ; Homeostasis/*physiology ; Humans ; Mitochondria/metabolism ; Models, Theoretical ; Oxidative Phosphorylation ; }, abstract = {Evidence is presented that the rate and equilibrium constants in mitochondrial oxidative phosphorylation set and maintain metabolic homeostasis in eukaryotic cells. These internal constants determine the energy state ([ATP]/[ADP][Pi]), and the energy state maintains homeostasis through a bidirectional sensory/signaling control network that reaches every aspect of cellular metabolism. The energy state is maintained with high precision (to ∼1 part in 10(10)), and the control system can respond to transient changes in energy demand (ATP utilization) of more than 100 times the resting rate. Epigenetic and environmental factors are able to "fine-tune" the programmed set point over a narrow range to meet the special needs associated with cell differentiation and chronic changes in metabolic requirements. The result is robust across-platform control of metabolism, which is essential to cellular differentiation and the evolution of complex organisms. A model of oxidative phosphorylation is presented, for which the steady-state rate expression has been derived and computer programmed. The behavior of oxidative phosphorylation predicted by the model is shown to fit the experimental data available for isolated mitochondria as well as for cells and tissues. This includes measurements from several different mammalian tissues as well as from insect flight muscle and plants. The respiratory chain and oxidative phosphorylation is remarkably similar for all higher plants and animals. This is consistent with the efficient synthesis of ATP and precise control of metabolic homeostasis provided by oxidative phosphorylation being a key to cellular differentiation and the evolution of structures with specialized function.}, }
@article {pmid25603118, year = {2014}, author = {Igloi, GL and Leisinger, AK}, title = {Identity elements for the aminoacylation of metazoan mitochondrial tRNA(Arg) have been widely conserved throughout evolution and ensure the fidelity of the AGR codon reassignment.}, journal = {RNA biology}, volume = {11}, number = {10}, pages = {1313-1323}, pmid = {25603118}, issn = {1555-8584}, mesh = {Amino Acyl-tRNA Synthetases/genetics/*metabolism ; Animals ; Anticodon/*genetics ; Base Sequence ; *Biological Evolution ; Caenorhabditis elegans/enzymology/genetics ; Coleoptera ; Genetic Code ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Transfer, Arg/genetics/*metabolism ; Saccharomyces cerevisiae/enzymology/genetics ; Transfer RNA Aminoacylation/*physiology ; }, abstract = {Eumetazoan mitochondrial tRNAs possess structures (identity elements) that require the specific recognition by their cognate nuclear-encoded aminoacyl-tRNA synthetases. The AGA (arginine) codon of the standard genetic code has been reassigned to serine/glycine/termination in eumetazoan organelles and is translated in some organisms by a mitochondrially encoded tRNA(Ser)UCU. One mechanism to prevent mistranslation of the AGA codon as arginine would require a set of tRNA identity elements distinct from those possessed by the cytoplasmic tRNAArg in which the major identity elements permit the arginylation of all 5 encoded isoacceptors. We have performed comparative in vitro aminoacylation using an insect mitochondrial arginyl-tRNA synthetase and tRNAArgUCG structural variants. The established identity elements are sufficient to maintain the fidelity of tRNASerUCU reassignment. tRNAs having a UCU anticodon cannot be arginylated but can be converted to arginine acceptance by identity element transplantation. We have examined the evolutionary distribution and functionality of these tRNA elements within metazoan taxa. We conclude that the identity elements that have evolved for the recognition of mitochondrial tRNAArgUCG by the nuclear encoded mitochondrial arginyl-tRNA synthetases of eumetazoans have been extensively, but not universally conserved, throughout this clade. They ensure that the AGR codon reassignment in eumetazoan mitochondria is not compromised by misaminoacylation. In contrast, in other metazoans, such as Porifera, whose mitochondrial translation is dictated by the universal genetic code, recognition of the 2 encoded tRNAArgUCG/UCU isoacceptors is achieved through structural features that resemble those employed by the yeast cytoplasmic system.}, }
@article {pmid25600751, year = {2016}, author = {Romanova, EV and Mikhailov, KV and Logacheva, MD and Kamaltynov, RM and Aleoshin, VV and Sherbakov, DY}, title = {The complete mitochondrial genome of a deep-water Baikalian amphipoda Brachyuropus grewingkii (Dybowsky, 1874).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4158-4159}, doi = {10.3109/19401736.2014.1003891}, pmid = {25600751}, issn = {2470-1408}, mesh = {Amphipoda/*genetics ; Animals ; Base Composition ; Gene Order ; Genome Size ; Genome, Mitochondrial ; Mitochondria/*genetics ; Open Reading Frames ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {In this study, we present a complete mitochondrial genome of a deep-water amphipoda Brachyuropus grewingkii (Dybowsky, 1874) from Lake Baikal. A circular mitochondrial DNA has 17,118 bp in length and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, a putative control region, and five intergenic spacers. An extended control region and altered positions of some tRNA genes distinguish mitochondrial genome of B. grewingkii from the mitochondrial genomes described for other Baikalian amphipoda species.}, }
@article {pmid25600745, year = {2016}, author = {Lu, J and Li, XF and Yuan, H}, title = {The complete mitochondrial genome of large flying fox, Pteropus vampyrus (Pteropus, Pteropodidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4166-4167}, doi = {10.3109/19401736.2014.1003895}, pmid = {25600745}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Chiroptera/*genetics ; Gene Order ; Genome Size ; Genome, Mitochondrial ; Mitochondria/*genetics ; Open Reading Frames ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The large flying fox (Pteropus vampyrus) is named after its fox-like face and noted for being one of the largest bats. Here, we reported the complete mitogenome sequence of P. vampyrus, which was 16,554 bp and composed of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region, with a base composition of lower G+C content (41.5%). Like other bats, all genes were located on H-strand except for eight tRNA and ND6 genes. Most protein-coding genes started with an ATG codon except for ND2, ND3, and ND5, which initiated with ATA or ATT instead, and terminated with the typical stop codon (TAA/TAG) or a single T or an unexpected codon of AGG. Within the control region, 6 bp repeat (TACGCA) was appeared only nine times, much lower than other published Pteropus species. These results provided basic information for researching Pteropus vampyrus on genetics, phylogeny, and adaptive evolution.}, }
@article {pmid25600726, year = {2016}, author = {Ran, ML and Chen, B and He, CQ and Li, Z and Dong, LH}, title = {The complete mitochondrial genome of Jintang black goat (Capra hircus).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {4151-4152}, doi = {10.3109/19401736.2014.1003887}, pmid = {25600726}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; Genome, Mitochondrial ; Goats/*genetics ; Mitochondria/*genetics ; Open Reading Frames ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Jintang black goat (Capra hircus) is an indigenous breed of Sichuan province of China. It is the first time that the complete mitochondrial genome sequence of Jintang black goat is reported in this work, which is determined through the PCR-based method. The total length of the mitogenome is 16,813 bp, which contains two ribosomal RNA genes, 22 tRNA genes, 13 PCGs, and a control region (D-loop region). The total base composition of Jintang black goat mitochondrial genome is 33.52% A, 13.13% G, 27.35% T, and 26.00% C, and in the order A > T > C > G. The complete mitochondrial genome of Jintang black goat provides an important data in genetic mechanism and the evolution genomes.}, }
@article {pmid25600501, year = {2015}, author = {Seligmann, H}, title = {Phylogeny of genetic codes and punctuation codes within genetic codes.}, journal = {Bio Systems}, volume = {129}, number = {}, pages = {36-43}, doi = {10.1016/j.biosystems.2015.01.003}, pmid = {25600501}, issn = {1872-8324}, mesh = {Amino Acids ; Animals ; Bacteria/genetics ; *Codon, Initiator ; *Codon, Terminator ; Frameshifting, Ribosomal ; *Genetic Code ; Humans ; *Mitochondria ; *Phylogeny ; Principal Component Analysis ; RNA, Transfer ; }, abstract = {Punctuation codons (starts, stops) delimit genes, reflect translation apparatus properties. Most codon reassignments involve punctuation. Here two complementary approaches classify natural genetic codes: (A) properties of amino acids assigned to codons (classical phylogeny), coding stops as X (A1, antitermination/suppressor tRNAs insert unknown residues), or as gaps (A2, no translation, classical stop); and (B) considering only punctuation status (start, stop and other codons coded as -1, 0 and 1 (B1); 0, -1 and 1 (B2, reflects ribosomal translational dynamics); and 1, -1, and 0 (B3, starts/stops as opposites)). All methods separate most mitochondrial codes from most nuclear codes; Gracilibacteria consistently cluster with metazoan mitochondria; mitochondria co-hosted with chloroplasts cluster with nuclear codes. Method A1 clusters the euplotid nuclear code with metazoan mitochondria; A2 separates euplotids from mitochondria. Firmicute bacteria Mycoplasma/Spiroplasma and Protozoan (and lower metazoan) mitochondria share codon-amino acid assignments. A1 clusters them with mitochondria, they cluster with the standard genetic code under A2: constraints on amino acid ambiguity versus punctuation-signaling produced the mitochondrial versus bacterial versions of this genetic code. Punctuation analysis B2 converges best with classical phylogenetic analyses, stressing the need for a unified theory of genetic code punctuation accounting for ribosomal constraints.}, }
@article {pmid25598369, year = {2014}, author = {Yu, X and He, Z and Xiang, H and Zheng, J and Nan, B and Zheng, B and Gao, J and Huang, S and Guan, M and Chen, B}, title = {[Function study of non-syndromic deafness associated mitochondrial 12S rRNA A839G mutation].}, journal = {Zhonghua er bi yan hou tou jing wai ke za zhi = Chinese journal of otorhinolaryngology head and neck surgery}, volume = {49}, number = {11}, pages = {908-915}, pmid = {25598369}, issn = {1673-0860}, mesh = {Aminoglycosides ; Cell Line ; DNA, Mitochondrial ; Deafness/*genetics ; Galactose ; Hearing Tests ; Mitochondria ; Mutation ; Pedigree ; Phylogeny ; RNA, Ribosomal/*genetics ; }, abstract = {OBJECTIVE: To investigate the correlation between nonsyndromic deafness and mitochondrial 12s rRNA A839G mutation.<br><br>METHODS: According to the clinical manifestations of mitochondrial DNA sequencing and analysis to find and determine family containing mitochondrial 12s rRNA A839G mutation. Harvested its family members blood and transferred their lymphocytes into lymphoblastoid cell lines, followed by cells cultured, cell doubling experiment, susceptibility testing, cellular oxygen consumption rate experiment, ROS and mitochondrial membrane potential experimental tests were progressed to explore the correlation between the A839G mutation and nonsyndromic deafness.<br><br>RESULTS: The mitochondrial 12s rRNA A839G mutation pedigrees were determined through the full sequence detections of the Mitochondrial DNA, further phylogenetic analysis showed that 839 point conservative index (CI) up to 78.6%; in RPMI-galactose medium containing A839G gene mutant cell line, the doubling time was significantly longer than the control group, and the difference was significant (P = 0.033). The effect to cell lines containing the A839G mutation of aminoglycoside drugs was not obvious. When compared with the control group, cell lines containing the A839G mutation significantly reduced cellular oxygen consumption rate(P = 0.033); compared with the control group, the ROS levels of cell lines containing the A839G mutation appeared more substantial elevated with significan difference (P < 0.01). The mitochondrial membrane potential of cells of experimental group was significantly reduced than the control group.<br><br>CONCLUSION: The present study proved that the mitochondria 12s rRNA A839G mutations affect the function of the mitochondrial respiratory chain at the cell level, which might reduce the growth rate of the mutant cell lines, result in hearing.}, }
@article {pmid25596888, year = {2015}, author = {Ulrich, T and Rapaport, D}, title = {Biogenesis of beta-barrel proteins in evolutionary context.}, journal = {International journal of medical microbiology : IJMM}, volume = {305}, number = {2}, pages = {259-264}, doi = {10.1016/j.ijmm.2014.12.009}, pmid = {25596888}, issn = {1618-0607}, mesh = {Bacterial Outer Membrane Proteins/chemistry/*metabolism ; Biological Evolution ; Chloroplast Proteins/chemistry/*metabolism ; Chloroplasts/chemistry/metabolism ; Gram-Negative Bacteria/chemistry/metabolism ; Mitochondria/chemistry/metabolism ; Mitochondrial Membranes/chemistry/metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; Models, Biological ; Protein Conformation ; *Protein Multimerization ; }, abstract = {The vast majority of outer membrane (OM) proteins in Gram-negative bacteria belongs to the class of membrane-embedded β-barrel proteins. Besides Gram-negative bacteria, the presence of β-barrel proteins is restricted to the OM of the eukaryotic organelles mitochondria and chloroplasts that were derived from prokaryotic ancestors. The assembly of these proteins into the corresponding OM is in each case facilitated by a dedicated protein complex that contains a highly conserved central β-barrel protein termed BamA/YaeT/Omp85 in Gram-negative bacteria and Tob55/Sam50 in mitochondria. However, little is known about the exact mechanism by which these complexes mediate the integration of β-barrel precursors into the lipid bilayer. Interestingly, previous studies showed that during evolution, these complexes retained the ability to functionally assemble β-barrel proteins from different origins. In this review we summarize the current knowledge on the biogenesis pathway of β-barrel proteins in Gram-negative bacteria, mitochondria and chloroplasts and focus on the commonalities and divergences that evolved between the different β-barrel assembly machineries.}, }
@article {pmid25592976, year = {2015}, author = {Goldberg, J and Bresseel, J and Constant, J and Kneubühler, B and Leubner, F and Michalik, P and Bradler, S}, title = {Extreme convergence in egg-laying strategy across insect orders.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {7825}, pmid = {25592976}, issn = {2045-2322}, mesh = {Animals ; Coleoptera/classification/growth &amp; development ; Female ; Histones/genetics ; Insecta/classification/growth &amp; development/*physiology ; Mantodea/classification/growth &amp; development ; Mitochondria/genetics ; Ovum/growth &amp; development/metabolism ; Phylogeny ; RNA, Ribosomal, 28S/genetics ; Tomography, X-Ray Computed ; }, abstract = {The eggs of stick and leaf insects (Phasmatodea) bear strong resemblance to plant seeds and are commonly dispersed by females dropping them to the litter. Here we report a novel egg-deposition mode for Phasmatodea performed by an undescribed Vietnamese species of the enigmatic subfamily Korinninae that produces a complex egg case (ootheca), containing numerous eggs in a highly ordered arrangement. This novel egg-deposition mode is most reminiscent of egg cases produced by members of unrelated insect orders, e.g. by praying mantises (Mantodea) and tortoise beetles (Coleoptera: Cassidinae). Ootheca production constitutes a striking convergence and major transition in reproductive strategy among stick insects, viz. a shift from dispersal of individual eggs to elaborate egg concentration. Adaptive advantages of ootheca formation on arboreal substrate are likely related to protection against parasitoids and desiccation and to allocation of specific host plants. Our phylogenetic analysis of nuclear (28S, H3) and mitochondrial (COI, COII) genes recovered Korinninae as a subordinate taxon among the species-rich Necrosciinae with Asceles as sister taxon, thus suggesting that placement of single eggs on leaves by host plant specialists might be the evolutionary precursor of ootheca formation within stick insects.}, }
@article {pmid25592231, year = {2015}, author = {Pervaiz, T and Sun, X and Zhang, Y and Tao, R and Zhang, J and Fang, J}, title = {Association between Chloroplast and Mitochondrial DNA sequences in Chinese Prunus genotypes (Prunus persica, Prunus domestica, and Prunus avium).}, journal = {BMC plant biology}, volume = {15}, number = {}, pages = {4}, pmid = {25592231}, issn = {1471-2229}, mesh = {Alleles ; Base Sequence ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; Genetic Markers ; Genotype ; Microsatellite Repeats/genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; Prunus/*genetics ; Prunus avium/genetics ; Prunus domestica/genetics ; Prunus persica/genetics ; Sequence Alignment ; }, abstract = {BACKGROUND: The nuclear DNA is conventionally used to assess the diversity and relatedness among different species, but variations at the DNA genome level has also been used to study the relationship among different organisms. In most species, mitochondrial and chloroplast genomes are inherited maternally; therefore it is anticipated that organelle DNA remains completely associated. Many research studies were conducted simultaneously on organelle genome. The objectives of this study was to analyze the genetic relationship between chloroplast and mitochondrial DNA in three Chinese Prunus genotypes viz., Prunus persica, Prunus domestica, and Prunus avium.<br><br>RESULTS: We investigated the genetic diversity of Prunus genotypes using simple sequence repeat (SSR) markers relevant to the chloroplast and mitochondria. Most of the genotypes were genetically similar as revealed by phylogenetic analysis. The Y2 Wu Xing (Cherry) and L2 Hong Xin Li (Plum) genotypes have a high similarity index (0.89), followed by Zi Ye Li (0.85), whereas; L1 Tai Yang Li (plum) has the lowest genetic similarity (0.35). In case of cpSSR, Hong Tao (Peach) and L1 Tai Yang Li (Plum) genotypes demonstrated similarity index of 0.85 and Huang Tao has the lowest similarity index of 0.50. The mtSSR nucleotide sequence analysis revealed that each genotype has similar amplicon length (509 bp) except M5Y1 i.e., 505 bp with CCB256 primer; while in case of NAD6 primer, all genotypes showed different sizes. The MEHO (Peach), MEY1 (Cherry), MEL2 (Plum) and MEL1 (Plum) have 586 bps; while MEY2 (Cherry), MEZI (Plum) and MEHU (Peach) have 585, 584 and 566 bp, respectively. The CCB256 primer showed highly conserved sequences and minute single polymorphic nucleotides with no deletion or mutation. The cpSSR (ARCP511) microsatellites showed the harmonious amplicon length. The CZI (Plum), CHO (Peach) and CL1 (Plum) showed 182 bp; whileCHU (Peach), CY2 (Cherry), CL2 (Plum) and CY1 (Cherry) showed 181 bp amplicon lengths.<br><br>CONCLUSIONS: These results demonstrated high conservation in chloroplast and mitochondrial genome among Prunus species during the evolutionary process. These findings are valuable to study the organelle DNA diversity in different species and genotypes of Prunus to provide in depth insight in to the mitochondrial and chloroplast genomes.}, }
@article {pmid25590636, year = {2015}, author = {Head, SI and Chan, S and Houweling, PJ and Quinlan, KG and Murphy, R and Wagner, S and Friedrich, O and North, KN}, title = {Altered Ca2+ kinetics associated with α-actinin-3 deficiency may explain positive selection for ACTN3 null allele in human evolution.}, journal = {PLoS genetics}, volume = {11}, number = {2}, pages = {e1004862}, pmid = {25590636}, issn = {1553-7404}, mesh = {Acclimatization/genetics ; Actinin/deficiency/*genetics ; Animals ; *Biological Evolution ; Calcium/*metabolism ; Cold Temperature ; Humans ; Kinetics ; Male ; Mice ; Mice, Knockout ; Mitochondria/genetics/metabolism/pathology ; Muscle Fibers, Fast-Twitch/metabolism/pathology ; Muscle, Skeletal/metabolism/pathology ; Muscular Diseases/*genetics/metabolism/pathology ; Polymorphism, Genetic ; *Selection, Genetic ; Weather ; }, abstract = {Over 1.5 billion people lack the skeletal muscle fast-twitch fibre protein α-actinin-3 due to homozygosity for a common null polymorphism (R577X) in the ACTN3 gene. α-Actinin-3 deficiency is detrimental to sprint performance in elite athletes and beneficial to endurance activities. In the human genome, it is very difficult to find single-gene loss-of-function variants that bear signatures of positive selection, yet intriguingly, the ACTN3 null variant has undergone strong positive selection during recent evolution, appearing to provide a survival advantage where food resources are scarce and climate is cold. We have previously demonstrated that α-actinin-3 deficiency in the Actn3 KO mouse results in a shift in fast-twitch fibres towards oxidative metabolism, which would be more "energy efficient" in famine, and beneficial to endurance performance. Prolonged exposure to cold can also induce changes in skeletal muscle similar to those observed with endurance training, and changes in Ca2+ handling by the sarcoplasmic reticulum (SR) are a key factor underlying these adaptations. On this basis, we explored the effects of α-actinin-3 deficiency on Ca2+ kinetics in single flexor digitorum brevis muscle fibres from Actn3 KO mice, using the Ca2+-sensitive dye fura-2. Compared to wild-type, fibres of Actn3 KO mice showed: (i) an increased rate of decay of the twitch transient; (ii) a fourfold increase in the rate of SR Ca2+ leak; (iii) a threefold increase in the rate of SR Ca2+ pumping; and (iv) enhanced maintenance of tetanic Ca2+ during fatigue. The SR Ca2+ pump, SERCA1, and the Ca2+-binding proteins, calsequestrin and sarcalumenin, showed markedly increased expression in muscles of KO mice. Together, these changes in Ca2+ handling in the absence of α-actinin-3 are consistent with cold acclimatisation and thermogenesis, and offer an additional explanation for the positive selection of the ACTN3 577X null allele in populations living in cold environments during recent evolution.}, }
@article {pmid25590140, year = {2015}, author = {Ivarsson, N and Westerblad, H}, title = {α-Actinin-3: why gene loss is an evolutionary gain.}, journal = {PLoS genetics}, volume = {11}, number = {1}, pages = {e1004908}, pmid = {25590140}, issn = {1553-7404}, mesh = {Actinin/*genetics ; Adaptation, Physiological/*genetics ; Cold Temperature ; *Evolution, Molecular ; Fatigue/genetics/pathology ; Humans ; Mitochondria/genetics ; Muscle Contraction/genetics ; Muscle, Skeletal/metabolism ; *Protein Biosynthesis ; }, }
@article {pmid25573905, year = {2015}, author = {Nývltová, E and Stairs, CW and Hrdý, I and Rídl, J and Mach, J and Pačes, J and Roger, AJ and Tachezy, J}, title = {Lateral gene transfer and gene duplication played a key role in the evolution of Mastigamoeba balamuthi hydrogenosomes.}, journal = {Molecular biology and evolution}, volume = {32}, number = {4}, pages = {1039-1055}, pmid = {25573905}, issn = {1537-1719}, support = {MOP-62809//Canadian Institutes of Health Research/Canada ; }, mesh = {Anaerobiosis/genetics ; Archamoebae/enzymology/*genetics/metabolism ; Cell Membrane Structures/genetics/metabolism ; Energy Metabolism/*genetics ; Enzymes/genetics/isolation &amp; purification ; *Evolution, Molecular ; *Gene Duplication ; *Gene Transfer, Horizontal ; Organelles/enzymology/*genetics/metabolism ; }, abstract = {Lateral gene transfer (LGT) is an important mechanism of evolution for protists adapting to oxygen-poor environments. Specifically, modifications of energy metabolism in anaerobic forms of mitochondria (e.g., hydrogenosomes) are likely to have been associated with gene transfer from prokaryotes. An interesting question is whether the products of transferred genes were directly targeted into the ancestral organelle or initially operated in the cytosol and subsequently acquired organelle-targeting sequences. Here, we identified key enzymes of hydrogenosomal metabolism in the free-living anaerobic amoebozoan Mastigamoeba balamuthi and analyzed their cellular localizations, enzymatic activities, and evolutionary histories. Additionally, we characterized 1) several canonical mitochondrial components including respiratory complex II and the glycine cleavage system, 2) enzymes associated with anaerobic energy metabolism, including an unusual D-lactate dehydrogenase and acetyl CoA synthase, and 3) a sulfate activation pathway. Intriguingly, components of anaerobic energy metabolism are present in at least two gene copies. For each component, one copy possesses an mitochondrial targeting sequence (MTS), whereas the other lacks an MTS, yielding parallel cytosolic and hydrogenosomal extended glycolysis pathways. Experimentally, we confirmed that the organelle targeting of several proteins is fully dependent on the MTS. Phylogenetic analysis of all extended glycolysis components suggested that these components were acquired by LGT. We propose that the transformation from an ancestral organelle to a hydrogenosome in the M. balamuthi lineage involved the lateral acquisition of genes encoding extended glycolysis enzymes that initially operated in the cytosol and that established a parallel hydrogenosomal pathway after gene duplication and MTS acquisition.}, }
@article {pmid25566271, year = {2014}, author = {Suwastika, IN and Denawa, M and Yomogihara, S and Im, CH and Bang, WY and Ohniwa, RL and Bahk, JD and Takeyasu, K and Shiina, T}, title = {Evidence for lateral gene transfer (LGT) in the evolution of eubacteria-derived small GTPases in plant organelles.}, journal = {Frontiers in plant science}, volume = {5}, number = {}, pages = {678}, pmid = {25566271}, issn = {1664-462X}, abstract = {The genomes of free-living bacteria frequently exchange genes via lateral gene transfer (LGT), which has played a major role in bacterial evolution. LGT also played a significant role in the acquisition of genes from non-cyanobacterial bacteria to the lineage of "primary" algae and land plants. Small GTPases are widely distributed among prokaryotes and eukaryotes. In this study, we inferred the evolutionary history of organelle-targeted small GTPases in plants. Arabidopsis thaliana contains at least one ortholog in seven subfamilies of OBG-HflX-like and TrmE-Era-EngA-YihA-Septin-like GTPase superfamilies (together referred to as Era-like GTPases). Subcellular localization analysis of all Era-like GTPases in Arabidopsis revealed that all 30 eubacteria-related GTPases are localized to chloroplasts and/or mitochondria, whereas archaea-related DRG and NOG1 are localized to the cytoplasm and nucleus, respectively, suggesting that chloroplast- and mitochondrion-localized GTPases are derived from the ancestral cyanobacterium and α-proteobacterium, respectively, through endosymbiotic gene transfer (EGT). However, phylogenetic analyses revealed that plant organelle GTPase evolution is rather complex. Among the eubacterium-related GTPases, only four localized to chloroplasts (including one dual targeting GTPase) and two localized to mitochondria were derived from cyanobacteria and α-proteobacteria, respectively. Three other chloroplast-targeted GTPases were related to α-proteobacterial proteins, rather than to cyanobacterial GTPases. Furthermore, we found that four other GTPases showed neither cyanobacterial nor α-proteobacterial affiliation. Instead, these GTPases were closely related to clades from other eubacteria, such as Bacteroides (Era1, EngB-1, and EngB-2) and green non-sulfur bacteria (HflX). This study thus provides novel evidence that LGT significantly contributed to the evolution of organelle-targeted Era-like GTPases in plants.}, }
@article {pmid25564461, year = {2015}, author = {Bongaerts, P and Frade, PR and Hay, KB and Englebert, N and Latijnhouwers, KR and Bak, RP and Vermeij, MJ and Hoegh-Guldberg, O}, title = {Deep down on a Caribbean reef: lower mesophotic depths harbor a specialized coral-endosymbiont community.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {7652}, pmid = {25564461}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/classification/*genetics/growth &amp; development ; Caribbean Region ; Coral Reefs ; Ecosystem ; Genetic Variation ; Genotype ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/chemistry/genetics/metabolism ; Symbiosis/genetics ; Temperature ; }, abstract = {The composition, ecology and environmental conditions of mesophotic coral ecosystems near the lower limits of their bathymetric distributions remain poorly understood. Here we provide the first in-depth assessment of a lower mesophotic coral community (60-100 m) in the Southern Caribbean through visual submersible surveys, genotyping of coral host-endosymbiont assemblages, temperature monitoring and a growth experiment. The lower mesophotic zone harbored a specialized coral community consisting of predominantly Agaricia grahamae, Agaricia undata and a "deep-water" lineage of Madracis pharensis, with large colonies of these species observed close to their lower distribution limit of ~90 m depth. All three species associated with "deep-specialist" photosynthetic endosymbionts (Symbiodinium). Fragments of A. grahamae exhibited growth rates at 60 m similar to those observed for shallow Agaricia colonies (~2-3 cm yr(-1)), but showed bleaching and (partial) mortality when transplanted to 100 m. We propose that the strong reduction of temperature over depth (Δ5°C from 40 to 100 m depth) may play an important contributing role in determining lower depth limits of mesophotic coral communities in this region. Rather than a marginal extension of the reef slope, the lower mesophotic represents a specialized community, and as such warrants specific consideration from science and management.}, }
@article {pmid25557487, year = {2015}, author = {Škodová-Sveráková, I and Verner, Z and Skalický, T and Votýpka, J and Horváth, A and Lukeš, J}, title = {Lineage-specific activities of a multipotent mitochondrion of trypanosomatid flagellates.}, journal = {Molecular microbiology}, volume = {96}, number = {1}, pages = {55-67}, doi = {10.1111/mmi.12920}, pmid = {25557487}, issn = {1365-2958}, mesh = {Electron Transport/genetics/*physiology ; Leishmania/genetics/metabolism ; Mitochondria/genetics/*physiology ; Oxidative Phosphorylation ; Phylogeny ; Trypanosoma brucei brucei/genetics/metabolism ; Trypanosomatina/genetics/*metabolism ; }, abstract = {Trypanosomatids are a very diverse group composed of monoxenous and dixenous parasites belonging to the excavate class Kinetoplastea. Here we studied the respiration of five monoxenous species (Blechomonas ayalai, Herpetomonas muscarum, H. samuelpessoai, Leptomonas pyrrhocoris and Sergeia podlipaevi) introduced into culture, each representing a novel yet globally distributed and/or species-rich clade, and compare them with well-studied flagellates Trypanosoma brucei, Phytomonas serpens, Crithidia fasciculata and Leishmania tarentolae. Differences in structure and activities of respiratory chain complexes, respiration and other biochemical parameters recorded under laboratory conditions reveal their substantial diversity, likely a reflection of different host environments. Phylogenetic relationships of the analysed trypanosomatids do not correlate with their biochemical parameters, with the differences within clades by far exceeding those among clades. As the S. podlipaevi canonical respiratory chain complexes have very low activities, we believe that its mitochondrion is utilised for purposes other than oxidative phosphorylation. Hence, the single reticulated mitochondrion of diverse trypanosomatids seems to retain multipotency, with the capacity to activate its individual components based on the host environment.}, }
@article {pmid26977240, year = {2015}, author = {Mnif, L and Sellami, R and Masmoudi, J}, title = {Schizophrenia and Leigh syndrome, a simple comorbidity or the same etiopathogeny: about a case.}, journal = {The Pan African medical journal}, volume = {22}, number = {}, pages = {333}, pmid = {26977240}, issn = {1937-8688}, mesh = {Humans ; Leigh Disease/*complications/etiology ; Male ; Schizophrenia/*complications/etiology ; Young Adult ; }, abstract = {Leigh syndrome is a mitochondrial encephalomyopathy that occurs due to "cytochrome c oxidase deficiency". Few psychiatric disorders have been defined that are associated with Leigh syndrome. The objective of this work is to study relations between mitochondrial dysfunction and psychiatric disorders. It was a 20 year old male patient, who received Modopar, for severe extra pyramidal symptoms caused by Leigh syndrome. He developed, four months ago, acute psychotic symptoms such as audio-visual hallucinations, persecution and mystic delirium. The cerebral MRI has shown signal abnormalities in central grey nucleus. The EEG recording and blood test were normal. The hypothesis of drug induced psychiatric disorders (Modopar) was possible. The evolution under atypical antipsychotic was only partial. In this case, the cerebrospinal fluid and lactate levels mean that mitochondria were not an overall explanation for these psychiatric disorders but may at least play a partial role. Psychiatric disorders may just be acomorbidity.}, }
@article {pmid25549576, year = {2015}, author = {Krupenko, NI and Holmes, RS and Tsybovsky, Y and Krupenko, SA}, title = {Aldehyde dehydrogenase homologous folate enzymes: Evolutionary switch between cytoplasmic and mitochondrial localization.}, journal = {Chemico-biological interactions}, volume = {234}, number = {}, pages = {12-17}, pmid = {25549576}, issn = {1872-7786}, support = {R01 CA095030/CA/NCI NIH HHS/United States ; R01 DK054388/DK/NIDDK NIH HHS/United States ; CA095030/CA/NCI NIH HHS/United States ; DK054388/DK/NIDDK NIH HHS/United States ; }, mesh = {Aldehyde Dehydrogenase/*metabolism ; Amino Acid Sequence ; Animals ; Cytoplasm/*enzymology/*metabolism ; Evolution, Molecular ; Folic Acid/*metabolism ; Humans ; Invertebrates/enzymology/metabolism ; Mitochondria/*enzymology/*metabolism ; Phylogeny ; Vertebrates/embryology/metabolism ; Zebrafish/metabolism ; }, abstract = {Cytosolic and mitochondrial 10-formyltetrahydrofolate dehydrogenases are products of separate genes in vertebrates but only one such gene is present in invertebrates. There is a significant degree of sequence similarity between the two enzymes due to an apparent origin of the gene for the mitochondrial enzyme (ALDH1L2) from the duplication of the gene for the cytosolic enzyme (ALDH1L1). The primordial ALDH1L gene originated from a natural fusion of three unrelated genes, one of which was an aldehyde dehydrogenase. Such structural organization defined the catalytic mechanism of these enzymes, which is similar to that of aldehyde dehydrogenases. Here we report the analysis of ALDH1L1 and ALDH1L2 genes from different species and their phylogeny and evolution. We also performed sequence and structure comparison of ALDH1L enzymes possessing aldehyde dehydrogenase catalysis to those lacking this feature in an attempt to explain mechanistic differences between cytoplasmic ALDH1L1 and mitochondrial ALDH1L2 enzymes and to better understand their functional roles.}, }
@article {pmid25547918, year = {2016}, author = {Zhao, JL and Wu, YP and Su, TJ and Jiang, GF and Wu, CS and Zhu, CD}, title = {The complete mitochondrial genome of Acleris fimbriana (Lepidoptera: Tortricidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {3}, pages = {2200-2202}, doi = {10.3109/19401736.2014.982625}, pmid = {25547918}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; DNA, Mitochondrial/genetics ; Gene Order/genetics ; Genes, Mitochondrial ; Genome/genetics ; Genome, Insect/genetics ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Lepidoptera/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; }, abstract = {The yellow tortrix, Acleris fimbriana belongs to Tortricidae in Lepidoptera. We described the complete mitogenome of A. fimbriana, which is typical circular duplex molecules and 15,933 bp in length containing the standard metazoan set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and an A + T-rich region with macro-repeat sequences. All the inferred tRNA secondary structures show the common cloverleaf pattern, with the exception of trnS1(AGN) which lacks the DHU arm. The A. fimbriana mitochondrial genome has the same gene order with other lepidopterans.}, }
@article {pmid25544518, year = {2014}, author = {Ito, M and Watanabe, K and Maeto, K}, title = {Revision of the genus Arotes Gravenhorst (Hymenoptera: Ichneumonidae: Acaenitinae) from Japan.}, journal = {Zootaxa}, volume = {3893}, number = {2}, pages = {196-208}, doi = {10.11646/zootaxa.3893.2.2}, pmid = {25544518}, issn = {1175-5334}, mesh = {Animal Distribution ; Animal Structures/anatomy &amp; histology/growth &amp; development ; Animals ; Body Size ; Female ; Islands ; Japan ; Male ; Mitochondria/genetics ; Molecular Sequence Data ; Organ Size ; Phylogeny ; Wasps/anatomy &amp; histology/*classification/genetics/growth &amp; development ; }, abstract = {Three Japanese species of the genus Arotes Gravenhorst, 1829 are revised. A new species, A. japonicus Ito &amp; Watanabe, sp. nov., is described from the four main islands of Japan. This species can easily be distinguished from congeneric species by the black body without yellow markings and the entirely black hind tibia. Arotes sugiharai Uchida, 1934 is newly recorded from the islands of Kyushu and Tsushima, and the males of this species are described for the first time. The synonymy of A. moiwanus (Matsumura, 1912) and its color variant alboannulatus Uchida, 1928 are confirmed by DNA sequence analysis of the mitochondrial COI gene. The key to the world's species of Arotes proposed by Castillo et al. (2011) is updated and a key to the Japanese species is provided.}, }
@article {pmid25540913, year = {2015}, author = {De Loof, A}, title = {The essence of female-male physiological dimorphism: differential Ca2+-homeostasis enabled by the interplay between farnesol-like endogenous sesquiterpenoids and sex-steroids? The Calcigender paradigm.}, journal = {General and comparative endocrinology}, volume = {211}, number = {}, pages = {131-146}, doi = {10.1016/j.ygcen.2014.12.003}, pmid = {25540913}, issn = {1095-6840}, mesh = {Animals ; Calcium/*metabolism ; Farnesol/*metabolism ; Female ; Gonadal Steroid Hormones/*metabolism ; *Homeostasis ; Humans ; Male ; *Models, Biological ; *Sex Characteristics ; }, abstract = {Ca(2+) is the most omnipresent pollutant on earth, in higher concentrations a real threat to all living cells. When [Ca(2+)]i rises above 100 nM (=resting level), excess Ca(2+) needs to be confined in the SER and mitochondria, or extruded by the different Ca(2+)-ATPases. The evolutionary origin of eggs and sperm cells has a crucial, yet often overlooked link with Ca(2+)-homeostasis. Because there is no goal whatsoever in evolution, gametes did neither originate "with the purpose" of generating a progeny nor of increasing fitness by introducing meiosis. The explanation may simply be that females "invented the trick" to extrude eggs from their body as an escape strategy for getting rid of toxic excess Ca(2+) resulting from a sex-hormone driven increased influx into particular cells and tissues. The production of Ca(2+)-rich milk, seminal fluid in males and all secreted proteins by eukaryotic cells may be similarly explained. This view necessitates an upgrade of the role of the RER-Golgi system in extruding Ca(2+). In the context of insect metamorphosis, it has recently been (re)discovered that (some isoforms of) Ca(2+)-ATPases act as membrane receptors for some types of lipophilic ligands, in particular for endogenous farnesol-like sesquiterpenoids (FLS) and, perhaps, for some steroid hormones as well. A novel paradigm, tentatively named "Calcigender" emerges. Its essence is: gender-specific physiotypes ensue from differential Ca(2+)-homeostasis enabled by genetic differences, farnesol/FLS and sex hormones. Apparently the body of reproducing females gets temporarily more poisoned by Ca(2+) than the male one, a selective benefit rather than a disadvantage.}, }
@article {pmid25539161, year = {2016}, author = {Ran, ML and He, J and Tan, JY and Yang, AQ and Li, Z and Chen, B}, title = {The complete sequence of the mitochondrial genome of Luchuan pig (Sus scrofa).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {3}, pages = {1880-1881}, doi = {10.3109/19401736.2014.971269}, pmid = {25539161}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sus scrofa/*genetics ; *Whole Genome Sequencing ; }, abstract = {Luchuan pig is one of the famous native breeds in China. In this study, we report the complete mitochondrial genome sequence of Luchuan pig for the first time, which is determined through the PCR-based method. The total length of the mitogenome is 16,710 bp with the base composition of 34.67% A, 13.33% G, 25.82% T and 26.18% C, and an A + T (60.48%)-rich feature is detected, which contains 1 control region (D-loop region), 2 ribosomal RNA genes, 13 PCGs and 22 tRNA genes. The complete mitochondrial genome of Luchuan pig provides an important data in genetic mechanism and the evolution genomes.}, }
@article {pmid25536042, year = {2014}, author = {Lamech, LT and Mallam, AL and Lambowitz, AM}, title = {Evolution of RNA-protein interactions: non-specific binding led to RNA splicing activity of fungal mitochondrial tyrosyl-tRNA synthetases.}, journal = {PLoS biology}, volume = {12}, number = {12}, pages = {e1002028}, pmid = {25536042}, issn = {1545-7885}, support = {R01 GM037951/GM/NIGMS NIH HHS/United States ; R37 GM037951/GM/NIGMS NIH HHS/United States ; GM037951/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Evolution, Molecular ; Fungal Proteins/chemistry/*metabolism ; Introns/genetics ; Mitochondria/enzymology ; Models, Molecular ; Molecular Sequence Data ; Neurospora crassa/*enzymology ; Protein Binding ; Protein Structure, Tertiary ; RNA Splicing/*genetics ; RNA, Catalytic/metabolism ; RNA, Fungal/chemistry/*metabolism ; Recombinant Proteins/chemistry/metabolism ; Scattering, Small Angle ; Sequence Alignment ; Sequence Deletion ; Tyrosine-tRNA Ligase/*metabolism ; X-Ray Diffraction ; }, abstract = {The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (mtTyrRS; CYT-18 protein) evolved a new function as a group I intron splicing factor by acquiring the ability to bind group I intron RNAs and stabilize their catalytically active RNA structure. Previous studies showed: (i) CYT-18 binds group I introns by using both its N-terminal catalytic domain and flexibly attached C-terminal anticodon-binding domain (CTD); and (ii) the catalytic domain binds group I introns specifically via multiple structural adaptations that occurred during or after the divergence of Peziomycotina and Saccharomycotina. However, the function of the CTD and how it contributed to the evolution of splicing activity have been unclear. Here, small angle X-ray scattering analysis of CYT-18 shows that both CTDs of the homodimeric protein extend outward from the catalytic domain, but move inward to bind opposite ends of a group I intron RNA. Biochemical assays show that the isolated CTD of CYT-18 binds RNAs non-specifically, possibly contributing to its interaction with the structurally different ends of the intron RNA. Finally, we find that the yeast mtTyrRS, which diverged from Pezizomycotina fungal mtTyrRSs prior to the evolution of splicing activity, binds group I intron and other RNAs non-specifically via its CTD, but lacks further adaptations needed for group I intron splicing. Our results suggest a scenario of constructive neutral (i.e., pre-adaptive) evolution in which an initial non-specific interaction between the CTD of an ancestral fungal mtTyrRS and a self-splicing group I intron was "fixed" by an intron RNA mutation that resulted in protein-dependent splicing. Once fixed, this interaction could be elaborated by further adaptive mutations in both the catalytic domain and CTD that enabled specific binding of group I introns. Our results highlight a role for non-specific RNA binding in the evolution of RNA-binding proteins.}, }
@article {pmid25535083, year = {2014}, author = {Betat, H and Long, Y and Jackman, JE and Mörl, M}, title = {From end to end: tRNA editing at 5'- and 3'-terminal positions.}, journal = {International journal of molecular sciences}, volume = {15}, number = {12}, pages = {23975-23998}, pmid = {25535083}, issn = {1422-0067}, support = {R01 GM087543/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Humans ; *RNA Editing ; RNA, Transfer/*genetics/*metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; }, abstract = {During maturation, tRNA molecules undergo a series of individual processing steps, ranging from exo- and endonucleolytic trimming reactions at their 5'- and 3'-ends, specific base modifications and intron removal to the addition of the conserved 3'-terminal CCA sequence. Especially in mitochondria, this plethora of processing steps is completed by various editing events, where base identities at internal positions are changed and/or nucleotides at 5'- and 3'-ends are replaced or incorporated. In this review, we will focus predominantly on the latter reactions, where a growing number of cases indicate that these editing events represent a rather frequent and widespread phenomenon. While the mechanistic basis for 5'- and 3'-end editing differs dramatically, both reactions represent an absolute requirement for generating a functional tRNA. Current in vivo and in vitro model systems support a scenario in which these highly specific maturation reactions might have evolved out of ancient promiscuous RNA polymerization or quality control systems.}, }
@article {pmid25532965, year = {2014}, author = {Xie, Y and Zhou, X and Zhang, Z and Wang, C and Sun, Y and Liu, T and Gu, X and Wang, T and Peng, X and Yang, G}, title = {Absence of genetic structure in Baylisascaris schroederi populations, a giant panda parasite, determined by mitochondrial sequencing.}, journal = {Parasites &amp; vectors}, volume = {7}, number = {}, pages = {606}, pmid = {25532965}, issn = {1756-3305}, mesh = {Animals ; Ascaridida Infections/epidemiology/parasitology/*veterinary ; Ascaridoidea/*genetics/isolation &amp; purification ; Base Sequence ; China/epidemiology ; DNA, Helminth/chemistry/genetics ; DNA, Mitochondrial/chemistry/genetics ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Ursidae/*parasitology ; }, abstract = {BACKGROUND: Infection with the parasitic nematode, Baylisascaris schroederi (Ascaridida: Nematoda), is one of the most important causes of death in giant pandas, and was responsible for half of deaths between 2001 and 2005. Mitochondrial (mt) DNA sequences of parasites can unveil their genetic diversity and depict their likely dynamic evolution and therefore may provide insights into parasite survival and responses to host changes, as well as parasite control.<br><br>METHODS: Based on previous studies, the present study further annotated the genetic variability and structure of B. schroederi populations by combining two different mtDNA markers, ATPase subunit 6 (atp6) and cytochrome c oxidase subunit I (cox1). Both sequences were completely amplified and genetically analyzed among 57 B. schroederi isolates, which were individually collected from ten geographical regions located in three important giant panda habitats in China (Minshan, Qionglai and Qinling mountain ranges).<br><br>RESULTS: For the DNA dataset, we identified 20 haplotypes of atp6, 24 haplotypes of cox1, and 39 haplotypes of atp6&#x2009;+&#x2009;cox1. Further haplotype network and phylogenetic analyses demonstrated that B. schroederi populations were predominantly driven by three common haplotypes, atp6 A1, cox1 C10, and atp6&#x2009;+&#x2009;cox1 H11. However, due to low rates of gene differentiation between the three populations, both the atp6 and cox1 genes appeared not to be significantly associated with geographical divisions. In addition, high gene flow was detected among the B. schroederi populations, consistent with previous studies, suggesting that this parasite may be essentially homogenous across endemic areas. Finally, neutrality tests and mismatch analysis indicated that B. schroederi had undergone earlier demographic expansion.<br><br>CONCLUSIONS: These results confirmed that B. schroederi populations do not follow a pattern of isolation by distance, further revealing the possible existence of physical connections before geographic separation. This study should also contribute to an improved understanding of the population genetics and evolutionary biology of B. schroederi and assist in the control of baylisascariasis in giant pandas.}, }
@article {pmid25527898, year = {2014}, author = {Saunier, A and Garcia, P and Becquet, V and Marsaud, N and Escudié, F and Pante, E}, title = {Mitochondrial genomes of the Baltic clam Macoma balthica (Bivalvia: Tellinidae): setting the stage for studying mito-nuclear incompatibilities.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {259}, pmid = {25527898}, issn = {1471-2148}, mesh = {Animals ; Bivalvia/*cytology/*genetics ; *Cell Nucleus ; DNA, Intergenic ; Evolution, Molecular ; *Genome, Mitochondrial ; Membrane Proteins/genetics ; *Mitochondria ; Molecular Sequence Annotation ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {BACKGROUND: Allopatric divergence across lineages can lead to post-zygotic reproductive isolation upon secondary contact and disrupt coevolution between mitochondrial and nuclear genomes, promoting emergence of genetic incompatibilities. A previous F ST scan on the transcriptome of the Baltic clam Macoma balthica highlighted several genes potentially involved in mito-nuclear incompatibilities (MNIs). As proteins involved in the mitochondrial oxidative phosphorylation (OXPHO) chain are prone to MNIs and can contribute to the maintenance of genetic barriers, the mitochondrial genomes of six Ma. balthica individuals spanning two secondary contact zones were sequenced using the Illumina MiSeq plateform.<br><br>RESULTS: The mitogenome has an approximate length of 16,806&#xa0;bp and encodes 13 protein-coding genes, 2 rRNAs and 22 tRNAs, all located on the same strand. atp8, a gene long reported as rare in bivalves, was detected. It encodes 42 amino acids and is putatively expressed and functional. A large unassigned region was identified between rrnS and tRNA (Met) and could likely correspond to the Control Region. Replacement and synonymous mutations were mapped on the inferred secondary structure of all protein-coding genes of the OXPHO chain. The atp6 and atp8 genes were characterized by background levels of replacement mutations, relative to synonymous mutations. However, most nad genes (notably nad2 and nad5) were characterized by an elevated proportion of replacement mutations.<br><br>CONCLUSIONS: Six nearly complete mitochondrial genomes were successfully assembled and annotated, providing the necessary roadmap to study MNIs at OXPHO loci. Few replacement mutations were mapped on mitochondrial-encoded ATP synthase subunits, which is in contrast with previous data on nuclear-encoded subunits. Conversely, the high population divergence and the prevalence of non-synonymous mutations at nad genes are congruent with previous observations from the nuclear transcriptome. This further suggest that MNIs between subunits of Complex I of the OXPHO chain, coding for NADH dehydrogenase, may play a role in maintaining barriers to gene flow in Ma. balthica.}, }
@article {pmid25527836, year = {2014}, author = {Beaudet, D and de la Providencia, IE and Labridy, M and Roy-Bolduc, A and Daubois, L and Hijri, M}, title = {Intraisolate mitochondrial genetic polymorphism and gene variants coexpression in arbuscular mycorrhizal fungi.}, journal = {Genome biology and evolution}, volume = {7}, number = {1}, pages = {218-227}, pmid = {25527836}, issn = {1759-6653}, mesh = {Alleles ; Cell Nucleolus/*genetics ; *Evolution, Molecular ; Gene Expression Regulation, Fungal ; Genome, Fungal ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; Mycorrhizae/*genetics ; Phylogeny ; Polymorphism, Genetic ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) are multinucleated and coenocytic organisms, in which the extent of the intraisolate nuclear genetic variation has been a source of debate. Conversely, their mitochondrial genomes (mtDNAs) have appeared to be homogeneous within isolates in all next generation sequencing (NGS)-based studies. Although several lines of evidence have challenged mtDNA homogeneity in AMF, extensive survey to investigate intraisolate allelic diversity has not previously been undertaken. In this study, we used a conventional polymerase chain reaction -based approach on selected mitochondrial regions with a high-fidelity DNA polymerase, followed by cloning and Sanger sequencing. Two isolates of Rhizophagus irregularis were used, one cultivated in vitro for several generations (DAOM-197198) and the other recently isolated from the field (DAOM-242422). At different loci in both isolates, we found intraisolate allelic variation within the mtDNA and in a single copy nuclear marker, which highlighted the presence of several nonsynonymous mutations in protein coding genes. We confirmed that some of this variation persisted in the transcriptome, giving rise to at least four distinct nad4 transcripts in DAOM-197198. We also detected the presence of numerous mitochondrial DNA copies within nuclear genomes (numts), providing insights to understand this important evolutionary process in AMF. Our study reveals that genetic variation in Glomeromycota is higher than what had been previously assumed and also suggests that it could have been grossly underestimated in most NGS-based AMF studies, both in mitochondrial and nuclear genomes, due to the presence of low-level mutations.}, }
@article {pmid25519070, year = {2014}, author = {Rogovin, KA and Khrushcheva, AM and Shekarova, ON and Ushakova, MV and Manskikh, VN and Sokolova, OV and Vasilieva, NY}, title = {Effects of mitochondria-targeted plastoquinone derivative antioxidant (SkQ1) on demography of free-breeding Campbell dwarf hamsters (Phodopus campbelli) kept in outdoor conditions. reproduction and lifespan: explanation in the framework of ultimate loads.}, journal = {Biochemistry. Biokhimiia}, volume = {79}, number = {10}, pages = {1117-1129}, doi = {10.1134/S0006297914100137}, pmid = {25519070}, issn = {1608-3040}, mesh = {Aging/drug effects ; Animals ; Antioxidants/*pharmacology ; Body Weight/drug effects ; Cricetinae ; Dermatitis, Allergic Contact/immunology ; Female ; Hydrocortisone/blood ; Immunity, Humoral ; Litter Size ; Longevity/*drug effects ; Male ; Mitochondria/drug effects ; Neutrophils/drug effects/metabolism ; Phodopus ; Plastoquinone/*analogs &amp; derivatives/pharmacology ; Pregnancy ; Reproduction/*drug effects/physiology ; Seasons ; }, abstract = {We studied demographic effects of the mitochondria-targeted antioxidant SkQ1 on free-breeding Campbell dwarf hamsters (Phodopus campbelli, Thomas, 1905, Rodentia, Cricetidae) in an outdoor vivarium with seasonally varying day length and temperatures. The animals were kept in pairs from their young age. We removed litters from parental cages at their age of 25 days. Experimental hamsters received daily 50 nmol/kg SkQ1 with water by oral dosing, whereas control animals received water. SkQ1 had no effect on the lifespan of either males or females in reproductive pairs. Mortality among females was higher than among males irrespective of SkQ1 treatment, this being related to higher costs of reproduction in females. However, SkQ1 accelerated breeding in pairs in the first half of the reproductive period of a year. Although there were no statistical differences in body mass of males and females between experimental and control animals during most of their life, SkQ1-receiving males had higher body mass at the end of their life. The opposite tendency was characteristic for old females. One-year-old males and females of the experimental and control groups showed no difference in intensity of immune response to sheep red blood cells. The dermal hypersensitivity response to phytohemagglutinin (test for T-cell immunity) was significantly higher in SkQ1-treated 1- and 1.5-year-old males. This was not true for females. There was a tendency toward increased density of the neutrophil population in blood in 1-year-old SkQ1-treated males. However, experimental males showed no difference from control males in the activity of the "peroxidase-endogenous hydrogen peroxide system" of neutrophils. The background level of stress estimated by the concentration of cortisol in blood serum was significantly lower in the SkQ1-treated males during autumn adaptive adjustment of the organism. A similar trend was also observed during the January frosts, when the background level of stress was rather high. We observed no differences between cortisol concentration in experimental and control animals during the reproductive period in early spring and mid-summer. We tend to interpret the absence of geroprotective effect of SkQ1 on free-breeding dwarf hamsters by its ability to intensify breeding. We previously demonstrated the ability of SkQ1 to increase the lifespan of non-breeding females.}, }
@article {pmid25519069, year = {2014}, author = {Rogovin, KA and Khrushcheva, AM and Shekarova, ON and Ushakova, MV and Manskikh, VN and Vasilieva, NY}, title = {Mitochondria-targeted antioxidant SkQ1 accelerates maturation in Campbell dwarf hamsters (Phodopus campbelli).}, journal = {Biochemistry. Biokhimiia}, volume = {79}, number = {10}, pages = {1111-1116}, doi = {10.1134/S0006297914100125}, pmid = {25519069}, issn = {1608-3040}, mesh = {Animals ; Antioxidants/*pharmacology ; Cricetinae ; Epididymis/drug effects ; Female ; Male ; Mitochondria/*drug effects ; Organ Size ; Phodopus/*growth &amp; development ; Plastoquinone/*analogs &amp; derivatives/pharmacology ; Pregnancy ; Sexual Maturation/*drug effects ; Uterus/drug effects ; Vagina/drug effects ; }, abstract = {We tested two hypotheses. 1) SkQ1 positively affects postnatal development of hamsters in litters born to parents receiving long-term SkQ1 treatment. 2) SkQ1 accelerates maturation of juvenile females receiving the antioxidant treatment from 10 days of age. Parental pairs were kept in an outdoor vivarium under conditions close to natural. At the age of 25 days, juvenile males in litters born to parents treated daily with SkQ1 (50 nmol/kg per os) had higher epididymis mass. Both the size of a litter and SkQ1 affected epididymis mass in young males. Both the litter size and SkQ1 affected uterus mass in 25-day-old females. Juvenile females who received SkQ1 treatment from 10 days of age demonstrated earlier opening of the vagina. This experiment was replicated with the same result. At the age of 2.5 months, virgin females treated with SkQ1 from the early age demonstrated higher ovary mass.}, }
@article {pmid25519058, year = {2014}, author = {Skulachev, MV and Skulachev, VP}, title = {New data on programmed aging - slow phenoptosis.}, journal = {Biochemistry. Biokhimiia}, volume = {79}, number = {10}, pages = {977-993}, doi = {10.1134/S0006297914100010}, pmid = {25519058}, issn = {1608-3040}, mesh = {Aging/*physiology ; Animals ; Antioxidants/metabolism ; Apoptosis ; *Biological Evolution ; Fertility ; Gene Expression Regulation ; Hyaluronic Acid/*metabolism ; Invertebrates/physiology ; Longevity ; Mitochondria/*metabolism ; Neoplasms/etiology ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; Rodentia/*physiology ; }, abstract = {This review summarizes the latest data on biochemistry and physiology of living organisms. These data suggest that aging, i.e. coordinated age-dependent weakening of many vital functions leading to gradual increase in the probability of dying, is not common to all organisms. Some species have been described whose probability of death does not depend on age or even decreases with age, this being accompanied by constant or increasing fertility. In the case of the naked mole rat (a non-aging mammal), a mechanism has been identified that protects this animal from cancer and the most common age-related diseases. The high molecular weight polysaccharide hyaluronan, a linear polymer composed of multiple repeated disaccharide of glucuronic acid and glucosamine, plays the key role in this mechanism. Hyaluronan is accumulated in the intercellular spaces in the organs and tissues of the naked mole rat. This polysaccharide provides early contact inhibition of cell division (anti-cancer effect). In addition, hyaluronan prevents the development of certain types of apoptosis, in particular, those induced by reactive oxygen species (ROS) (geroprotective effect preventing ROS-induced decrease in cellularity in the organs and tissues of aging organisms). Extraordinary longevity of the naked mole rat (over 30 years, which is long for a rodent the size of a mouse) is connected to its eusocial lifestyle, when only the "queen" and its few "husbands" breed, while the huge army of non-breeding "subordinates" provide the "royal family" with protection from predators, food, and construction and maintenance of an underground labyrinth size of a football field. This way of life removes the pressure of natural selection from the "family" and makes aging - the program that is counterproductive for the individual but increases "evolvability" of its offspring - unnecessary. The example of the naked mole rat demonstrates the optional character of the aging program for the organism. Many facts indicating that aging can be regulated by an organism provide another argument in favor of optionality of aging. Cases have been described when aging as a program useful for the evolution of offspring but counterproductive for the parental individual slows under conditions that threaten the very existence of the individual. These conditions include food restriction (the threat of death from starvation), heavy muscular work, decrease or increase in the environmental temperature, small amounts of poisons (including ROS; here we speak about the paradoxical geroprotective effect of the low doses of prooxidants that inhibit apoptosis). On the other hand, aging can be inhibited (and maybe even cancelled) artificially. This can be done by turning off the genes encoding the proteins participating in the aging program, such as FAT10, p66shc, and some others. In addition, the gene of the antioxidant enzyme catalase can be addressed into mitochondria, where it will split mitochondrial hydrogen peroxide, the level of which increases with age. However, today the simplest way to slow down the aging program is the use of mitochondria-targeted low molecular weight antioxidant compounds of plastoquinonyl decyltriphenylphosphonium-type (SkQ1), which prolong the life of animals, plants, and fungi and inhibit the development of many age-related diseases and symptoms.}, }
@article {pmid25510528, year = {2015}, author = {Tsuchiya, M and Toyofuku, T and Uematsu, K and Brüchert, V and Collen, J and Yamamoto, H and Kitazato, H}, title = {Cytologic and Genetic Characteristics of Endobiotic Bacteria and Kleptoplasts of Virgulinella fragilis (Foraminifera).}, journal = {The Journal of eukaryotic microbiology}, volume = {62}, number = {4}, pages = {454-469}, doi = {10.1111/jeu.12200}, pmid = {25510528}, issn = {1550-7408}, mesh = {Adenosine Triphosphate/biosynthesis ; Animals ; Bacteria/*cytology/*genetics/isolation &amp; purification/metabolism ; Carbon/metabolism ; Cell Membrane/microbiology ; Cytoplasm/microbiology ; Deltaproteobacteria/*cytology/*genetics/isolation &amp; purification ; Foraminifera/*microbiology ; Geologic Sediments/microbiology ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Phylogeny ; *Symbiosis ; }, abstract = {The benthic foraminifer Virgulinella fragilis Grindell and Collen 1976 has multiple putative symbioses with both bacterial and kleptoplast endobionts, possibly aiding its survival in environments from dysoxia (5-45 μmol-O2 /L) to microxia (0-5 μmol-O2 /L) and in the dark. To clarify the origin and function of V. fragilis endobionts, we used genetic analyses and transmission electron microscope observations. Virgulinella fragilis retained δ-proteobacteria concentrated at its cell periphery just beneath the cell membranes. Unlike another foraminifer Stainforthia spp., which retains many bacterial species, V. fragilis has a less variable bacterial community. This suggests that V. fragilis maintains a specific intracellular bacterial flora. Unlike the endobiotic bacteria, V. fragilis klepto-plasts originated from various diatom species and are found in the interior cytoplasm. We found evidence of both retention and digestion of kleptoplasts, and of fragmentation of the kleptoplastid outer membrane that likely facilitates transport of kleptoplastid products to the host. Accumulations of mitochondria were observed encircling endobiotic bacteria. It is likely that the bacteria use host organic material for carbon oxidation. The mitochondria may use oxygen available around the δ-proteobacteria and synthesize adenosine triphosphate, perhaps for sulfide oxidation.}, }
@article {pmid25505488, year = {2014}, author = {Shigeno, S and Ogura, A and Mori, T and Toyohara, H and Yoshida, T and Tsuchida, S and Fujikura, K}, title = {Sensing deep extreme environments: the receptor cell types, brain centers, and multi-layer neural packaging of hydrothermal vent endemic worms.}, journal = {Frontiers in zoology}, volume = {11}, number = {1}, pages = {82}, pmid = {25505488}, issn = {1742-9994}, abstract = {INTRODUCTION: Deep-sea alvinellid worm species endemic to hydrothermal vents, such as Alvinella and Paralvinella, are considered to be among the most thermotolerant animals known with their adaptability to toxic heavy metals, and tolerance of highly reductive and oxidative stressful environments. Despite the number of recent studies focused on their overall transcriptomic, proteomic, and metabolic stabilities, little is known regarding their sensory receptor cells and electrically active neuro-processing centers, and how these can tolerate and function in such harsh conditions.<br><br>RESULTS: We examined the extra- and intracellular organizations of the epidermal ciliated sensory cells and their higher centers in the central nervous system through immunocytochemical, ultrastructural, and neurotracing analyses. We observed that these cells were rich in mitochondria and possessed many electron-dense granules, and identified specialized glial cells and serial myelin-like repeats in the head sensory systems of Paralvinella hessleri. Additionally, we identified the major epidermal sensory pathways, in which a pair of distinct mushroom bodies-like or small interneuron clusters was observed. These sensory learning and memory systems are commonly found in insects and annelids, but the alvinellid inputs are unlikely derived from the sensory ciliary cells of the dorsal head regions.<br><br>CONCLUSIONS: Our evidence provides insight into the cellular and system-wide adaptive structure used to sense, process, and combat the deep-sea hydrothermal vent environment. The alvinellid sensory cells exhibit characteristics of annelid ciliary types, and among the most unique features were the head sensory inputs and structure of the neural cell bodies of the brain, which were surrounded by multiple membranes. We speculated that such enhanced protection is required for the production of normal electrical signals, and to avoid the breakdown of the membrane surrounding metabolically fragile neurons from oxidative stress. Such pivotal acquisition is not broadly found in the all body parts, suggesting the head sensory inputs are specific, and these heterogenetic protection mechanisms may be present in alvinellid worms.}, }
@article {pmid25504421, year = {2015}, author = {Ghoshroy, S and Robertson, DL}, title = {Molecular evolution of nitrogen assimilatory enzymes in marine prasinophytes.}, journal = {Journal of molecular evolution}, volume = {80}, number = {1}, pages = {65-80}, pmid = {25504421}, issn = {1432-1432}, mesh = {Animals ; Chlorophyta/classification/enzymology/*genetics ; *Evolution, Molecular ; Glutamate-Ammonia Ligase/*genetics ; Nitrate Reductase/*genetics ; Nitrogen/*metabolism ; Phylogeny ; }, abstract = {Nitrogen assimilation is a highly regulated process requiring metabolic coordination of enzymes and pathways in the cytosol, chloroplast, and mitochondria. Previous studies of prasinophyte genomes revealed that genes encoding nitrate and ammonium transporters have a complex evolutionary history involving both vertical and horizontal transmission. Here we examine the evolutionary history of well-conserved nitrogen-assimilating enzymes to determine if a similar complex history is observed. Phylogenetic analyses suggest that genes encoding glutamine synthetase (GS) III in the prasinophytes evolved by horizontal gene transfer from a member of the heterokonts. In contrast, genes encoding GSIIE, a canonical vascular plant and green algal enzyme, were found in the Micromonas genomes but have been lost from Ostreococcus. Phylogenetic analyses placed the Micromonas GSIIs in a larger chlorophyte/vascular plant clade; a similar topology was observed for ferredoxin-dependent nitrite reductase (Fd-NiR), indicating the genes encoding GSII and Fd-NiR in these prasinophytes evolved via vertical transmission. Our results show that genes encoding the nitrogen-assimilating enzymes in Micromonas and Ostreococcus have been differentially lost and as well as recruited from different evolutionary lineages, suggesting that the regulation of nitrogen assimilation in prasinophytes will differ from other green algae.}, }
@article {pmid25503745, year = {2014}, author = {Suomi, F and Menger, KE and Monteuuis, G and Naumann, U and Kursu, VA and Shvetsova, A and Kastaniotis, AJ}, title = {Expression and evolution of the non-canonically translated yeast mitochondrial acetyl-CoA carboxylase Hfa1p.}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e114738}, pmid = {25503745}, issn = {1932-6203}, mesh = {5' Untranslated Regions/genetics ; Acetyl-CoA Carboxylase/*biosynthesis/*genetics ; Base Sequence ; Codon, Initiator/genetics ; *Evolution, Molecular ; *Gene Expression Regulation, Fungal ; Kluyveromyces/genetics ; Mitochondria/enzymology/*genetics ; Mitochondrial Proteins/*biosynthesis/*genetics ; Molecular Sequence Data ; Mutation ; *Peptide Chain Initiation, Translational ; Saccharomyces cerevisiae/cytology/enzymology/*genetics ; Saccharomyces cerevisiae Proteins/*biosynthesis/*genetics ; Transcription, Genetic ; }, abstract = {The Saccharomyces cerevisiae genome encodes two sequence related acetyl-CoA carboxylases, the cytosolic Acc1p and the mitochondrial Hfa1p, required for respiratory function. Several aspects of expression of the HFA1 gene and its evolutionary origin have remained unclear. Here, we determined the HFA1 transcription initiation sites by 5' RACE analysis. Using a novel "Stop codon scanning" approach, we mapped the location of the HFA1 translation initiation site to an upstream AUU codon at position -372 relative to the annotated start codon. This upstream initiation leads to production of a mitochondrial targeting sequence preceding the ACC domains of the protein. In silico analyses of fungal ACC genes revealed conserved "cryptic" upstream mitochondrial targeting sequences in yeast species that have not undergone a whole genome duplication. Our Δhfa1 baker's yeast mutant phenotype rescue studies using the protoploid Kluyveromyces lactis ACC confirmed functionality of the cryptic upstream mitochondrial targeting signal. These results lend strong experimental support to the hypothesis that the mitochondrial and cytosolic acetyl-CoA carboxylases in S. cerevisiae have evolved from a single gene encoding both the mitochondrial and cytosolic isoforms. Leaning on a cursory survey of a group of genes of our interest, we propose that cryptic 5' upstream mitochondrial targeting sequences may be more abundant in eukaryotes than anticipated thus far.}, }
@article {pmid25502045, year = {2014}, author = {Hu, J and Jiang, ZL and Nardi, F and Liu, YY and Luo, XR and Li, HX and Zhang, ZK}, title = {Members of Bemisia tabaci (Hemiptera: Aleyrodidae) cryptic species and the status of two invasive alien species in the Yunnan Province (China).}, journal = {Journal of insect science (Online)}, volume = {14}, number = {}, pages = {}, pmid = {25502045}, issn = {1536-2442}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; China ; Electron Transport Complex IV/genetics ; Genetic Speciation ; Hemiptera/*classification/genetics ; Introduced Species ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeography ; Polymerase Chain Reaction ; }, abstract = {Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex that includes some of the most significant pests of agriculture and horticulture worldwide. To understand the diversity and distribution of B. tabaci cryptic species in Yunnan, a famous biodiversity hotspot in China, a large-scale sampling was conducted from year 2010 to 2013 in 10 prefectures. Mitochondrial cytochrome oxidase I gene sequences were used to identify different cryptic species. Phylogenetic analyses were performed using Bayesian methods to assess the position of a new B. tabaci cryptic species in the context of the B. tabaci diversity in Asia. The survey indicates at least eight B. tabaci cryptic species are present in Yunnan, two invasive (MEAM1 and MED) and six indigenous (China 2, China3, China 4, Asia I, Asia II 1, and Asia II 6), MEAM1, MED, and Asia I being the three predominant cryptic species in Yunnan. Compared with MEAM1, MED has a wider distribution. Based on molecular data, a new cryptic species, here named China 4, was identified that appears to be related to China 1, China 2, and China 3. Future efforts should focus on the interactions between predominant B. tabaci cryptic species and begomoviruses and on the development of effective control strategies.}, }
@article {pmid25499696, year = {2015}, author = {Sun, S and Kong, L and Yu, H and Li, Q}, title = {The complete mitochondrial DNA of Tegillarca granosa and comparative mitogenomic analyses of three Arcidae species.}, journal = {Gene}, volume = {557}, number = {1}, pages = {61-70}, doi = {10.1016/j.gene.2014.12.011}, pmid = {25499696}, issn = {1879-0038}, mesh = {Animals ; Arcidae/*genetics ; Base Composition ; Base Sequence ; Chromosome Mapping ; DNA, Mitochondrial/*genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Tandem Repeat Sequences/genetics ; }, abstract = {To better understand the characteristics and the evolutionary dynamics of mt genomes in Arcidae, the complete mitochondrial genome of Tegillarca granosa was firstly determined and compared with other two Arcidae species (Scapharca broughtonii and Scapharca kagoshimensis). The complete mitochondrial genome of T. granosa was 31,589 bp in length, including 12 protein-coding genes, 2 rRNA genes and 23 tRNA genes, and a major non-coding region. Three tandem repeat fragments were identified in the major non-coding region and the tandem repeat motifs of these fragments can be folded into stem-loop structures. The mitochondrial genome of the three species has several common features such as the AT content, the arrangement of the protein-coding genes, the codon usage of the protein-coding genes and AT/GC skew. However, a high level of variability is presented in the size of the genome, the number of tRNA genes and the length of non-coding sequences in the three mitogenomes. According to the phylogenetic analyses, these mitogenome-level characters are correlated with their phylogenetic relationships. It is the absence of the duplicated tRNAs and large non-coding sequences that are responsible for the length divergence of mitogenomes between T. granosa and other two Arcidae species. The phylogenetic analyses were conducted based on 12 partitioned protein genes, which support the relationship at the family level: (((Pectinidae+Ostreidae)+Mytilidae)+Arcidae).}, }
@article {pmid25498759, year = {2014}, author = {Chan, A and Chiang, LP and Hapuarachchi, HC and Tan, CH and Pang, SC and Lee, R and Lee, KS and Ng, LC and Lam-Phua, SG}, title = {DNA barcoding: complementing morphological identification of mosquito species in Singapore.}, journal = {Parasites &amp; vectors}, volume = {7}, number = {}, pages = {569}, pmid = {25498759}, issn = {1756-3305}, mesh = {Animal Distribution ; Animals ; Culicidae/classification/*genetics/physiology ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/genetics/metabolism ; Gene Expression Regulation, Enzymologic ; Mitochondria/enzymology ; Phylogeny ; Singapore ; }, abstract = {BACKGROUND: Taxonomy that utilizes morphological characteristics has been the gold standard method to identify mosquito species. However, morphological identification is challenging when the expertise is limited and external characters are damaged because of improper specimen handling. Therefore, we explored the applicability of mitochondrial cytochrome C oxidase subunit 1 (COI) gene-based DNA barcoding as an alternative tool to identify mosquito species. In the present study, we compared the morphological identification of mosquito specimens with their differentiation based on COI barcode, in order to establish a more reliable identification system for mosquito species found in Singapore.<br><br>METHODS: We analysed 128 adult mosquito specimens, belonging to 45 species of 13 genera. Phylogenetic trees were constructed for Aedes, Anopheles, Culex and other genera of mosquitoes and the distinctive clustering of different species was compared with their taxonomic identity.<br><br>RESULTS: The COI-based DNA barcoding achieved a 100% success rate in identifying the mosquito species. We also report COI barcode sequences of 16 mosquito species which were not available previously in sequence databases.<br><br>CONCLUSIONS: Our study utilised for the first time DNA barcoding to identify mosquito species in Singapore. COI-based DNA barcoding is a useful tool to complement taxonomy-based identification of mosquito species.}, }
@article {pmid25495152, year = {2015}, author = {Yang, LY and Machado, CA and Dang, XD and Peng, YQ and Yang, DR and Zhang, DY and Liao, WJ}, title = {The incidence and pattern of copollinator diversification in dioecious and monoecious figs.}, journal = {Evolution; international journal of organic evolution}, volume = {69}, number = {2}, pages = {294-304}, pmid = {25495152}, issn = {1558-5646}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; *Biological Evolution ; Ficus/*physiology ; Genes, rRNA ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Pollination ; Sequence Alignment ; Symbiosis ; Wasps/*classification/*genetics ; }, abstract = {Differences in breeding system are associated with correlated ecological and morphological changes in plants. In Ficus, dioecy and monoecy are strongly associated with different suites of traits (tree height, population density, fruiting frequency, pollinator dispersal ecology). Although approximately 30% of fig species are pollinated by multiple species of fig-pollinating wasps, it has been suggested that copollinators are rare in dioecious figs. Here, we test whether there is a connection between the fig breeding system and copollinator incidence and diversification by conducting a meta-analysis of molecular data from pollinators of 119 fig species that includes new data from 15 Asian fig species. We find that the incidence of copollinators is not significantly different between monoecious and dioecious Ficus. Surprisingly, while all copollinators in dioecious figs are sister taxa, only 32.1% in monoecious figs are sister taxa. We present hypotheses to explain those patterns and discuss their consequences on the evolution of this mutualism.}, }
@article {pmid25491543, year = {2015}, author = {Matsuoka, S and Sugiyama, S and Matsuoka, D and Hirose, M and Lethu, S and Ano, H and Hara, T and Ichihara, O and Kimura, SR and Murakami, S and Ishida, H and Mizohata, E and Inoue, T and Murata, M}, title = {Water-mediated recognition of simple alkyl chains by heart-type fatty-acid-binding protein.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {54}, number = {5}, pages = {1508-1511}, pmid = {25491543}, issn = {1521-3773}, mesh = {Binding Sites ; Calorimetry ; Crystallography, X-Ray ; Fatty Acid Binding Protein 3 ; Fatty Acid-Binding Proteins/chemistry/*metabolism ; Fatty Acids/chemistry/metabolism ; Humans ; Molecular Dynamics Simulation ; Myocardium/*metabolism ; Protein Structure, Tertiary ; Thermodynamics ; Water/chemistry/*metabolism ; }, abstract = {Long-chain fatty acids (FAs) with low water solubility require fatty-acid-binding proteins (FABPs) to transport them from cytoplasm to the mitochondria for energy production. However, the precise mechanism by which these proteins recognize the various lengths of simple alkyl chains of FAs with similar high affinity remains unknown. To address this question, we employed a newly developed calorimetric method for comprehensively evaluating the affinity of FAs, sub-Angstrom X-ray crystallography to accurately determine their 3D structure, and energy calculations of the coexisting water molecules using the computer program WaterMap. Our results clearly showed that the heart-type FABP (FABP3) preferentially incorporates a U-shaped FA of C10-C18 using a lipid-compatible water cluster, and excludes longer FAs using a chain-length-limiting water cluster. These mechanisms could help us gain a general understanding of how proteins recognize diverse lipids with different chain lengths.}, }
@article {pmid25489773, year = {2016}, author = {Du, LN and Shi, FL and Liu, ZJ and Zhou, QH}, title = {Complete mitochondrial genome of the crested black macaque (Macaca nigra).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {3888-3889}, doi = {10.3109/19401736.2014.987248}, pmid = {25489773}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Mitochondrial/chemistry/genetics ; Genome, Mitochondrial/*genetics ; Macaca/*genetics ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {The complete mitochondrial sequence of the crested black macaque (Macaca nigra) has been determined by mapping the raw data to previously published mitochondrial assemblies of the corresponding species. The total sequence length is 16,564 bp and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 D-loop control region. The base composition of mtDNA genome is 31.76% A, 25.27% T, 30.17% C, and 12.80% G, with an AT content of 57.03%. The arrangement of genes in M. nigra is identical to that of M. mulatta. All genes are encoded on the heavy strand with the exception of ND6 and eight tRNA genes. The mitochondrial genome of M. nigra presented here will contribute to a better understanding of the population genetics, help to protect its genetic diversity and resolve phylogenetic relationships within the family.}, }
@article {pmid25488255, year = {2014}, author = {Wang, SP and Yang, H and Wu, JW and Gauthier, N and Fukao, T and Mitchell, GA}, title = {Metabolism as a tool for understanding human brain evolution: lipid energy metabolism as an example.}, journal = {Journal of human evolution}, volume = {77}, number = {}, pages = {41-49}, doi = {10.1016/j.jhevol.2014.06.013}, pmid = {25488255}, issn = {1095-8606}, support = {178978//Canadian Institutes of Health Research/Canada ; 221920//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; *Biological Evolution ; *Brain/metabolism/physiology ; Humans ; Ketone Bodies ; Lipid Metabolism/*physiology ; Mice ; Mitochondria/physiology ; Triglycerides ; }, abstract = {Genes and the environment both influence the metabolic processes that determine fitness. To illustrate the importance of metabolism for human brain evolution and health, we use the example of lipid energy metabolism, i.e. the use of fat (lipid) to produce energy and the advantages that this metabolic pathway provides for the brain during environmental energy shortage. We briefly describe some features of metabolism in ancestral organisms, which provided a molecular toolkit for later development. In modern humans, lipid energy metabolism is a regulated multi-organ pathway that links triglycerides in fat tissue to the mitochondria of many tissues including the brain. Three important control points are each suppressed by insulin. (1) Lipid reserves in adipose tissue are released by lipolysis during fasting and stress, producing fatty acids (FAs) which circulate in the blood and are taken up by cells. (2) FA oxidation. Mitochondrial entry is controlled by carnitine palmitoyl transferase 1 (CPT1). Inside the mitochondria, FAs undergo beta oxidation and energy production in the Krebs cycle and respiratory chain. (3) In liver mitochondria, the 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) pathway produces ketone bodies for the brain and other organs. Unlike most tissues, the brain does not capture and metabolize circulating FAs for energy production. However, the brain can use ketone bodies for energy. We discuss two examples of genetic metabolic traits that may be advantageous under most conditions but deleterious in others. (1) A CPT1A variant prevalent in Inuit people may allow increased FA oxidation under nonfasting conditions but also predispose to hypoglycemic episodes. (2) The thrifty genotype theory, which holds that energy expenditure is efficient so as to maximize energy stores, predicts that these adaptations may enhance survival in periods of famine but predispose to obesity in modern dietary environments.}, }
@article {pmid25487526, year = {2014}, author = {Liedmann, S and Hrincius, ER and Guy, C and Anhlan, D and Dierkes, R and Carter, R and Wu, G and Staeheli, P and Green, DR and Wolff, T and McCullers, JA and Ludwig, S and Ehrhardt, C}, title = {Viral suppressors of the RIG-I-mediated interferon response are pre-packaged in influenza virions.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {5645}, pmid = {25487526}, issn = {2041-1723}, support = {P30 CA021765/CA/NCI NIH HHS/United States ; R01 AI044828/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Motifs ; Animals ; Cell Line, Tumor ; DEAD Box Protein 58 ; DEAD-box RNA Helicases/*chemistry ; Evolution, Molecular ; Female ; Humans ; Imaging, Three-Dimensional ; Influenza A virus/*pathogenicity ; Interferon Type I/*immunology ; Lung/immunology/virology ; Male ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Mice, Inbred DBA ; Mice, Knockout ; Mitochondria/*virology ; RNA Viruses/pathogenicity ; Receptors, Immunologic ; Viral Load ; Viral Proteins/chemistry ; Virion/*chemistry ; Virulence ; }, abstract = {The type I interferon (IFN) response represents the first line of defence to invading pathogens. Internalized viral ribonucleoproteins (vRNPs) of negative-strand RNA viruses induce an early IFN response by interacting with retinoic acid inducible gene I (RIG-I) and its recruitment to mitochondria. Here we employ three-dimensional stochastic optical reconstruction microscopy (STORM) to visualize incoming influenza A virus (IAV) vRNPs as helical-like structures associated with mitochondria. Unexpectedly, an early IFN induction in response to vRNPs is not detected. A distinct amino-acid motif in the viral polymerases, PB1/PA, suppresses early IFN induction. Mutation of this motif leads to reduced pathogenicity in vivo, whereas restoration increases it. Evolutionary dynamics in these sequences suggest that completion of the motif, combined with viral reassortment can contribute to pandemic risks. In summary, inhibition of the immediate anti-viral response is 'pre-packaged' in IAV in the sequences of vRNP-associated polymerase proteins.}, }
@article {pmid25487023, year = {2015}, author = {Regev-Rudzki, N and Gabriel, K and Bursać, D}, title = {The evolution and function of co-chaperones in mitochondria.}, journal = {Sub-cellular biochemistry}, volume = {78}, number = {}, pages = {201-217}, doi = {10.1007/978-3-319-11731-7_10}, pmid = {25487023}, issn = {0306-0225}, mesh = {Animals ; *Evolution, Molecular ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; Molecular Chaperones/chemistry/*metabolism ; Protein Conformation ; Protein Transport ; Signal Transduction ; Structure-Activity Relationship ; }, abstract = {Mitochondrial chaperones mediate and affect critical organellar processes, essential for cellular function. These chaperone systems have both prokaryotic and eukaryotic features. While some of the mitochondrial co-chaperones have clear homologues in prokaryotes, some are unique to eukaryotes and have no homologues in the chaperone machinery of other cellular compartments. The mitochondrial co-chaperones are required for protein import into the organelle and in enforcing the structure of the main chaperones. In addition to novel types of interaction with their senior partners, unexpected and essential interactions between the co-chaperones themselves have recently been described.}, }
@article {pmid25486052, year = {2014}, author = {Gabriel, F and Accoceberry, I and Bessoule, JJ and Salin, B and Lucas-Guérin, M and Manon, S and Dementhon, K and Noël, T}, title = {A Fox2-dependent fatty acid ß-oxidation pathway coexists both in peroxisomes and mitochondria of the ascomycete yeast Candida lusitaniae.}, journal = {PloS one}, volume = {9}, number = {12}, pages = {e114531}, pmid = {25486052}, issn = {1932-6203}, mesh = {Blotting, Western ; Candida/growth &amp; development/*metabolism ; Candidiasis/metabolism/microbiology ; Carbon/metabolism ; Cells, Cultured ; Enoyl-CoA Hydratase/genetics/*metabolism ; Fatty Acids/*chemistry/*metabolism ; Immunoenzyme Techniques ; Microscopy, Immunoelectron ; Mitochondria/*metabolism ; Mutation/genetics ; Oxidation-Reduction ; Peroxisomes/*metabolism ; RNA, Messenger/genetics ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {It is generally admitted that the ascomycete yeasts of the subphylum Saccharomycotina possess a single fatty acid ß-oxidation pathway located exclusively in peroxisomes, and that they lost mitochondrial ß-oxidation early during evolution. In this work, we showed that mutants of the opportunistic pathogenic yeast Candida lusitaniae which lack the multifunctional enzyme Fox2p, a key enzyme of the ß-oxidation pathway, were still able to grow on fatty acids as the sole carbon source, suggesting that C. lusitaniae harbored an alternative pathway for fatty acid catabolism. By assaying 14Cα-palmitoyl-CoA consumption, we demonstrated that fatty acid catabolism takes place in both peroxisomal and mitochondrial subcellular fractions. We then observed that a fox2Δ null mutant was unable to catabolize fatty acids in the mitochondrial fraction, thus indicating that the mitochondrial pathway was Fox2p-dependent. This finding was confirmed by the immunodetection of Fox2p in protein extracts obtained from purified peroxisomal and mitochondrial fractions. Finally, immunoelectron microscopy provided evidence that Fox2p was localized in both peroxisomes and mitochondria. This work constitutes the first demonstration of the existence of a Fox2p-dependent mitochondrial β-oxidation pathway in an ascomycetous yeast, C. lusitaniae. It also points to the existence of an alternative fatty acid catabolism pathway, probably located in peroxisomes, and functioning in a Fox2p-independent manner.}, }
@article {pmid25485579, year = {2014}, author = {Arlia-Ciommo, A and Piano, A and Leonov, A and Svistkova, V and Titorenko, VI}, title = {Quasi-programmed aging of budding yeast: a trade-off between programmed processes of cell proliferation, differentiation, stress response, survival and death defines yeast lifespan.}, journal = {Cell cycle (Georgetown, Tex.)}, volume = {13}, number = {21}, pages = {3336-3349}, pmid = {25485579}, issn = {1551-4005}, mesh = {Endoplasmic Reticulum/metabolism ; Fungal Proteins/metabolism ; Mitochondria/genetics/metabolism ; Protein Serine-Threonine Kinases/metabolism ; Saccharomycetales/growth &amp; development/*metabolism ; Unfolded Protein Response ; }, abstract = {Recent findings suggest that evolutionarily distant organisms share the key features of the aging process and exhibit similar mechanisms of its modulation by certain genetic, dietary and pharmacological interventions. The scope of this review is to analyze mechanisms that in the yeast Saccharomyces cerevisiae underlie: (1) the replicative and chronological modes of aging; (2) the convergence of these 2 modes of aging into a single aging process; (3) a programmed differentiation of aging cell communities in liquid media and on solid surfaces; and (4) longevity-defining responses of cells to some chemical compounds released to an ecosystem by other organisms populating it. Based on such analysis, we conclude that all these mechanisms are programs for upholding the long-term survival of the entire yeast population inhabiting an ecological niche; however, none of these mechanisms is a "program of aging" - i.e., a program for progressing through consecutive steps of the aging process.}, }
@article {pmid25484174, year = {2016}, author = {Chen, H and Huang, H and Li, J and Zhao, Y and Deng, S and Li, G and Huang, H and Zhu, C}, title = {Characterization of the complete mitochondrial genome of Seriolella porosa (Perciformes: Centrolophidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {3}, pages = {2203-2204}, doi = {10.3109/19401736.2014.982626}, pmid = {25484174}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; DNA, Mitochondrial/genetics ; Fishes/genetics ; Gene Order/genetics ; Genes, Mitochondrial ; Genome/genetics ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; }, abstract = {We have presented the complete mitochondrial genome of the Seriolella porosa in this study. The mitochondrial genome is 16,814 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The gene order and composition of Seriolella porosa mitochondrial genome was similar to those of most vertebrates. The nucleotide compositions of the light strand in descending order is 29.75% of T, 29.39% of G, 24.84% of A and 16.02% of C. With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all the other mitochondrial genes are encoded on the heavy strand.}, }
@article {pmid25484173, year = {2016}, author = {Liang, R and Wang, C and Zou, Q and Zhou, A and Zhou, M}, title = {Molecular phylogenetic relationships of some common sweetlips (Haemulidae: Plectorhynchinae) and the synonyms controversy of two Plectorhinchus species.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {3}, pages = {2209-2214}, doi = {10.3109/19401736.2014.982628}, pmid = {25484173}, issn = {2470-1408}, mesh = {Animals ; Cytochromes b/classification/genetics ; DNA/chemistry/isolation &amp; purification/metabolism ; Electron Transport Complex IV/classification/genetics ; Mitochondria/genetics ; Perciformes/*classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Molecular phylogenetic topologies from 40 individuals of 17 sweetlips were constructed based on the mitochondrial cytochrome b (cyt b) and cytochrome c oxidase subunit I (COI) genes. All phylogenetic results strongly revealed the division of the sweetlips into three morphological distinct groups. Group I: sweetlips with colorful patterns, Group II and Group III: species with uniformly dark patterns. The relationships of those morphologically confused Plectorhinchus species were well-resolved in the phylogenetic results. We also confirmed that the genus Diagramma was placed inside the colorful Plectorhinchus groups, suggesting close relationship of Diagramma within Plectorhinchus. Additionally, we found that two species, P. orientalis and P. vittatus, which were traditionally considered as synonyms for oriental sweetlips, which were suggested to be two distinct species. Sequence divergence also revealed a great genetic variation between P. orientalis and P. vittatus (6.0% in Cyt b and 7.4% in COI), which was largely greater than the species diagnosis divergence value (2%) suggested by Hebert et al. This new finding suggested P. orientalis and P. vittatus might be two distinct species and should not be placed as synonyms.}, }
@article {pmid25482898, year = {2015}, author = {Smith, KF and Abbott, CL and Saito, Y and Fidler, AE}, title = {Comparison of whole mitochondrial genome sequences from two clades of the invasive ascidian, Didemnum vexillum.}, journal = {Marine genomics}, volume = {19}, number = {}, pages = {75-83}, doi = {10.1016/j.margen.2014.11.007}, pmid = {25482898}, issn = {1876-7478}, mesh = {Adaptation, Biological/*genetics ; Animal Distribution ; Animals ; Base Sequence ; Computational Biology ; DNA Primers/genetics ; *Genetic Variation ; Genetics, Population ; Genome, Mitochondrial/*genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; *Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; Species Specificity ; Urochordata/*genetics ; }, abstract = {The mitochondria are the main source of cellular energy production and have an important role in development, fertility, and thermal limitations. Adaptive mitochondrial DNA mutations have the potential to be of great importance in determining aspects of the life history of an organism. Phylogenetic analyses of the globally invasive marine ascidian Didemnum vexillum using the mitochondrial cytochrome c oxidase 1 (COX1) coding region, revealed two distinct clades. Representatives of one clade (denoted by 'B') are geographically restricted to D. vexillum's native region (north-west Pacific Ocean, including Japan), whereas members of the other clade (denoted by 'A') have been introduced and become invasive in temperate coastal areas around the world. Persistence of clade B's restricted distribution may reflect it being inherently less invasive than clade A. To investigate this we sought to determine if the two clades differ significantly in other mitochondrial genes of functional significance, specifically, alterations in amino acids encoded in mitochondrial enzyme subunits. Differences in functional mitochondrial genes could indicate an increased ability for clade A colonies to tolerate a wider range of environmental temperature. Full mitochondrial genomic sequences from D. vexillum clades A and B were obtained and they predict significant sequence differences in genes encoding for enzymes involved in oxidative phosphorylation. Diversity levels were relatively high and showed divergence across almost all genes, with p-distance values between the two clades indicating recent divergence. Both clades showed an excess of rare variants, which is consistent with balancing selection or a recent population expansion. Results presented here will inform future research focusing on examining the functional properties of the corresponding mitochondrial respiration enzymes, of A and B clade enzymes. By comparing closely related taxa that have differing distributions it is possible to identify genes and phenotypes suited to particular environments. The examination of mitochondrial genotypes, and associated enzyme functioning, across populations may aid in our understanding of thermal tolerance and environmental adaptation.}, }
@article {pmid25482773, year = {2014}, author = {Wang, M and Ma, X and Shen, J and Li, C and Zhang, W}, title = {The ongoing story: the mitochondria pyruvate carrier 1 in plant stress response in Arabidopsis.}, journal = {Plant signaling &amp; behavior}, volume = {9}, number = {10}, pages = {e973810}, pmid = {25482773}, issn = {1559-2324}, mesh = {Anion Transport Proteins ; Arabidopsis/genetics/*physiology ; Arabidopsis Proteins ; Gene Expression Regulation, Plant ; Membrane Transport Proteins/genetics/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins ; Monocarboxylic Acid Transporters ; Phylogeny ; Protein Interaction Mapping ; Protein Transport ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins ; *Stress, Physiological ; Subcellular Fractions/metabolism ; }, abstract = {Abscisic acid (ABA) is an important regulator of guard cell ion channels and stomatal movements in response to drought stress. Pyruvate is the final product of glycolysis in the cytosol, and could be transported by mitochondrial pyruvate carriers (MPCs) into mitochondrion for consequent cellular substance and energy metabolism. We recently characterized the first putative mitochondrial pyruvate carrier, NRGA1, in planta, and found that this small protein is involved in the negative regulation of drought and ABA induced guard cell signaling in Arabidopsis thaliana. The findings revealed a probable link between mitochondrial pyruvate transport and guard cell signaling. It has also been shown that NRGA1 protein product was directed to the mitochondria, and co-expression of MPC1 and NRGA1 functionally complement the absence of a native pyruvate transport protein in yeast. Here, we further demonstrated that MPC1 showed similar sub-cellular localization pattern to NRGA1. Quantitative RT-PCR analysis showed that the transcription of both NRGA1 and MPC1 were induced by pyruvate or ABA, and pyruvate strengthened the ABA induced transcription of these 2 genes. The similarity in subcellular localization and gene expression to ABA strongly suggests that MPC1 may associate with NRGA1 for mitochondrial pyruvate transport and is involved in ABA mediated stomatal movements in Arabidopsis.}, }
@article {pmid25481706, year = {2015}, author = {Blackstone, NW}, title = {The impact of mitochondrial endosymbiosis on the evolution of calcium signaling.}, journal = {Cell calcium}, volume = {57}, number = {3}, pages = {133-139}, doi = {10.1016/j.ceca.2014.11.006}, pmid = {25481706}, issn = {1532-1991}, mesh = {Animals ; *Biological Evolution ; Calcium Signaling/*physiology ; Eukaryotic Cells/metabolism ; Humans ; Mitochondria/*metabolism ; Prokaryotic Cells/metabolism ; Symbiosis/*physiology ; }, abstract = {At high concentrations, calcium has detrimental effects on biological systems. Life likely arose in a low calcium environment, and the first cells evolved mechanisms to maintain this environment internally. Bursts of calcium influx followed by efflux or sequestration thus developed in a functional context. For example, in proto-cells with exterior energy-converting membranes, such bursts could be used to depolarize the membrane. In this way, proto-cells could maintain maximal phosphorylation (metabolic state 3) and moderate levels of reactive oxygen species (ROS), while avoiding the resting state (metabolic state 4) and high levels of ROS. This trait is likely a shared primitive characteristic of prokaryotes. When eukaryotes evolved, the α-proteobacteria that gave rise to proto-mitochondria inhabited a novel environment, the interior of the proto-eukaryote that had a low calcium concentration. In this environment, metabolic homeostasis was difficult to maintain, and there were inherent risks from ROS, yet depolarizing the proto-mitochondrial membrane by calcium influx was challenging. To maintain metabolic state 3, proto-mitochondria were required to congregate near calcium influx points in the proto-eukaryotic membrane. This behavior, resulting in embryonic forms of calcium signaling, may have occurred immediately after the initiation of the endosymbiosis. Along with ROS, calcium may have served as one of the key forms of crosstalk among the community of prokaryotes that led to the eukaryotic cell.}, }
@article {pmid25476837, year = {2014}, author = {Datt, M and Sharma, A}, title = {Evolutionary and structural annotation of disease-associated mutations in human aminoacyl-tRNA synthetases.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {1063}, pmid = {25476837}, issn = {1471-2164}, mesh = {Algorithms ; Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/chemistry/*genetics ; Cytoplasm/enzymology ; Disease/*genetics ; *Evolution, Molecular ; Genomics ; Humans ; Models, Molecular ; *Molecular Sequence Annotation ; Molecular Sequence Data ; *Mutation ; Protein Conformation ; }, abstract = {BACKGROUND: Mutation(s) in proteins are a natural byproduct of evolution but can also cause serious diseases. Aminoacyl-tRNA synthetases (aaRSs) are indispensable components of all cellular protein translational machineries, and in humans they drive translation in both cytoplasm and mitochondria. Mutations in aaRSs have been implicated in a plethora of diseases including neurological conditions, metabolic disorders and cancer.<br><br>RESULTS: We have developed an algorithmic approach for genome-wide analyses of sequence substitutions that combines evolutionary, structural and functional information. This pipeline enabled us to super-annotate human aaRS mutations and analyze their linkage to health disorders. Our data suggest that in some but not all cases, aaRS mutations occur in functional and structural sectors where they can manifest their pathological effects by altering enzyme activity or causing structural instability. Further, mutations appear in both solvent exposed and buried regions of aaRSs indicating that these alterations could lead to dysfunctional enzymes resulting in abnormal protein translation routines by affecting inter-molecular interactions or by disruption of non-bonded interactions. Overall, the prevalence of mutations is much higher in mitochondrial aaRSs, and the two most often mutated aaRSs are mitochondrial glutamyl-tRNA synthetase and dual localized glycyl-tRNA synthetase. Out of 63 mutations annotated in this work, only 12 (~20%) were observed in regions that could directly affect aminoacylation activity via either binding to ATP/amino-acid, tRNA or by involvement in dimerization. Mutations in structural cores or at potential biomolecular interfaces account for ~55% mutations while remaining mutations (~25%) remain structurally un-annotated.<br><br>CONCLUSION: This work provides a comprehensive structural framework within which most defective human aaRSs have been structurally analyzed. The methodology described here could be employed to annotate mutations in other protein families in a high-throughput manner.}, }
@article {pmid25475392, year = {2015}, author = {Stapleton, PA and Nichols, CE and Yi, J and McBride, CR and Minarchick, VC and Shepherd, DL and Hollander, JM and Nurkiewicz, TR}, title = {Microvascular and mitochondrial dysfunction in the female F1 generation after gestational TiO2 nanoparticle exposure.}, journal = {Nanotoxicology}, volume = {9}, number = {8}, pages = {941-951}, pmid = {25475392}, issn = {1743-5404}, support = {K99 ES024783/ES/NIEHS NIH HHS/United States ; R01-ES015022/ES/NIEHS NIH HHS/United States ; T32 HL090610/HL/NHLBI NIH HHS/United States ; DP2 DK083095/DK/NIDDK NIH HHS/United States ; DP2DK083095/DK/NIDDK NIH HHS/United States ; T32-HL090610/HL/NHLBI NIH HHS/United States ; F32 ES023435/ES/NIEHS NIH HHS/United States ; R01 ES015022/ES/NIEHS NIH HHS/United States ; F32-ES023435/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Cell Respiration/drug effects ; Coronary Vessels/drug effects ; Female ; Hydrogen Peroxide/metabolism ; Mechanotransduction, Cellular ; Microvessels/*drug effects ; Mitochondria/*drug effects/metabolism/*pathology ; Nanoparticles/administration &amp; dosage/chemistry/*toxicity ; Oxidative Stress/drug effects ; Pregnancy ; Prenatal Exposure Delayed Effects/*metabolism ; Rats ; Titanium/administration &amp; dosage/chemistry/*toxicity ; Uterine Artery/drug effects ; }, abstract = {Due to the ongoing evolution of nanotechnology, there is a growing need to assess the toxicological outcomes in under-studied populations in order to properly consider the potential of engineered nanomaterials (ENM) and fully enhance their safety. Recently, we and others have explored the vascular consequences associated with gestational nanomaterial exposure, reporting microvascular dysfunction within the uterine circulation of pregnant dams and the tail artery of fetal pups. It has been proposed (via work derived by the Barker Hypothesis) that mitochondrial dysfunction and subsequent oxidative stress mechanisms as a possible link between a hostile gestational environment and adult disease. Therefore, in this study, we exposed pregnant Sprague-Dawley rats to nanosized titanium dioxide aerosols after implantation (gestational day 6). Pups were delivered, and the progeny grew into adulthood. Microvascular reactivity, mitochondrial respiration and hydrogen peroxide production of the coronary and uterine circulations of the female offspring were evaluated. While there were no significant differences within the maternal or litter characteristics, endothelium-dependent dilation and active mechanotransduction in both coronary and uterine arterioles were significantly impaired. In addition, there was a significant reduction in maximal mitochondrial respiration (state 3) in the left ventricle and uterus. These studies demonstrate microvascular dysfunction and coincide with mitochondrial inefficiencies in both the cardiac and uterine tissues, which may represent initial evidence that prenatal ENM exposure produces microvascular impairments that persist throughout multiple developmental stages.}, }
@article {pmid25474405, year = {2014}, author = {Heinz, E and Hacker, C and Dean, P and Mifsud, J and Goldberg, AV and Williams, TA and Nakjang, S and Gregory, A and Hirt, RP and Lucocq, JM and Kunji, ER and Embley, TM}, title = {Plasma membrane-located purine nucleotide transport proteins are key components for host exploitation by microsporidian intracellular parasites.}, journal = {PLoS pathogens}, volume = {10}, number = {12}, pages = {e1004547}, pmid = {25474405}, issn = {1553-7374}, support = {/WT_/Wellcome Trust/United Kingdom ; MC_U105663139/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Acquired Immunodeficiency Syndrome/microbiology ; Biological Transport, Active/physiology ; Carrier Proteins/genetics/*metabolism ; DNA, Fungal/biosynthesis/genetics ; Fungal Proteins/genetics/*metabolism ; Humans ; Microsporidia/genetics/isolation &amp; purification/*metabolism ; Purine Nucleotides/*metabolism ; RNA, Fungal/biosynthesis/genetics ; }, abstract = {Microsporidia are obligate intracellular parasites of most animal groups including humans, but despite their significant economic and medical importance there are major gaps in our understanding of how they exploit infected host cells. We have investigated the evolution, cellular locations and substrate specificities of a family of nucleotide transport (NTT) proteins from Trachipleistophora hominis, a microsporidian isolated from an HIV/AIDS patient. Transport proteins are critical to microsporidian success because they compensate for the dramatic loss of metabolic pathways that is a hallmark of the group. Our data demonstrate that the use of plasma membrane-located nucleotide transport proteins (NTT) is a key strategy adopted by microsporidians to exploit host cells. Acquisition of an ancestral transporter gene at the base of the microsporidian radiation was followed by lineage-specific events of gene duplication, which in the case of T. hominis has generated four paralogous NTT transporters. All four T. hominis NTT proteins are located predominantly to the plasma membrane of replicating intracellular cells where they can mediate transport at the host-parasite interface. In contrast to published data for Encephalitozoon cuniculi, we found no evidence for the location for any of the T. hominis NTT transporters to its minimal mitochondria (mitosomes), consistent with lineage-specific differences in transporter and mitosome evolution. All of the T. hominis NTTs transported radiolabelled purine nucleotides (ATP, ADP, GTP and GDP) when expressed in Escherichia coli, but did not transport radiolabelled pyrimidine nucleotides. Genome analysis suggests that imported purine nucleotides could be used by T. hominis to make all of the critical purine-based building-blocks for DNA and RNA biosynthesis during parasite intracellular replication, as well as providing essential energy for parasite cellular metabolism and protein synthesis.}, }
@article {pmid25471441, year = {2016}, author = {Dietrich, C and Brune, A}, title = {The complete mitogenomes of six higher termite species reconstructed from metagenomic datasets (Cornitermes sp., Cubitermes ugandensis, Microcerotermes parvus, Nasutitermes corniger, Neocapritermes taracua, and Termes hospes).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {3903-3904}, doi = {10.3109/19401736.2014.987257}, pmid = {25471441}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA/chemistry/isolation &amp; purification/metabolism ; Databases, Genetic ; Gastrointestinal Tract/metabolism ; *Genome, Mitochondrial ; Isoptera/classification/*genetics ; Likelihood Functions ; Metagenomics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {We reconstructed the complete mitochondrial genomes of six higher termite species from metagenomic datasets of their isolated hindgut compartments. The sequencing reads were retrieved and assembled with the mitochondrial-baiting and iterative-mapping algorithm (MITObim), which yielded closed mitogenomes without additional finishing efforts (average coverage ranging from 2300- to 17,000-fold). The genomes ranged from 16.1 to 17.6 kbp in size and had G+C contents between 32 and 35 mol%; each contained the same 37 genes present also in the mitochondria of other termite species. Our study substantially increases the number of termite mitogenomes available for phylogenetic studies and offers a facile strategy for identifying host species in metagenomic studies of their associated microbiota.}, }
@article {pmid25471440, year = {2016}, author = {Zhang, C and Fu, X and Zhu, Z and Xie, K and Guo, Y}, title = {The complete mitochondrial genome sequence of Helicophagella melanura (Diptera: Sarcophagidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {3905-3906}, doi = {10.3109/19401736.2014.987258}, pmid = {25471440}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Codon, Initiator ; Codon, Terminator ; DNA, Mitochondrial/chemistry/isolation &amp; purification/metabolism ; Diptera/classification/*genetics ; *Genome, Mitochondrial ; Insect Proteins/chemistry/genetics/metabolism ; Open Reading Frames/genetics ; Phylogeny ; RNA, Ribosomal/chemistry/genetics/metabolism ; RNA, Transfer/chemistry/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {The mitochondrial genome of Helicophagella melanura, a representative of the Sarcophagidae family, was completely sequenced for the first time. The genome is a double-stranded circular molecule of 15,190 bp length, including the 37 genes and 1 non-coding AT-rich region. The gene contents of the mtDNA were identical to those observed in the ancestral arthropod. The total base composition of Helicophagella melanura mitochondrial genome is 39.42% for A, 36.22% for T, 14.71% for C and 9.65% for G and in the order A > T > C > G. The mitochondrial genome data of Helicophagella melanura is useful markers for species discrimination in forensic entomology and for phylogenetic analysis.}, }
@article {pmid25470294, year = {2014}, author = {Liu, SJ and Zhang, YP}, title = {Mitochondria in human diseases and animal evolution.}, journal = {Current molecular medicine}, volume = {14}, number = {10}, pages = {1245-1246}, doi = {10.2174/1566524014666141202125126}, pmid = {25470294}, issn = {1875-5666}, mesh = {Animals ; Biological Evolution ; Gene Expression Regulation ; *Genome, Mitochondrial ; Humans ; Mitochondria/*genetics/metabolism/pathology ; Mitochondrial Diseases/*genetics/metabolism/pathology ; Mitochondrial Proteins/*genetics/metabolism ; Mutation ; Oxidative Phosphorylation ; Protein Transport ; }, }
@article {pmid25470290, year = {2014}, author = {Zhong, L and Tang, J and Kong, QP and Sun, C and Zhou, WP and Yang, M and Yao, YG and Zhang, YP}, title = {Reappraising the relationship between mitochondrial DNA variant m.16189T&gt;C and type 2 diabetes mellitus in East Asian populations.}, journal = {Current molecular medicine}, volume = {14}, number = {10}, pages = {1273-1278}, doi = {10.2174/1566524014666141202161326}, pmid = {25470290}, issn = {1875-5666}, mesh = {*Alleles ; Asian People ; Case-Control Studies ; China ; DNA, Mitochondrial/*genetics ; Diabetes Mellitus, Type 2/ethnology/*genetics/pathology ; Gene Frequency ; Genetic Loci ; Genetic Predisposition to Disease ; Haplotypes ; Humans ; Mitochondria/*genetics ; *Polymorphism, Single Nucleotide ; Regression Analysis ; }, abstract = {The role of mitochondrial DNA (mtDNA) variant 16189T>C in type 2 diabetes mellitus (T2DM) remains hotly debated in the past decade. If mutation 16189T>C indeed posed a risk to T2DM, as echoed by some recent studies, correlation between this mutation and disease should be observed when carrying out a systematical study using data and samples collected in a large geographic region in China. To test this hypothesis, we first performed a linear regression analysis between the prevalence of T2DM and the allele frequency of 16189C variant in 10 East Asian populations, and further genotyped this variant in two casecontrol cohorts from west Han Chinese (Kunming and Xining). Linear regression analysis showed that no significant correlation was observed (r(2)=0.211, P=0.181), and the genotyping results indicated that the m.16189T>C frequency difference between case and control was not significant in either populations (P=0.38 and 0.89 for Kunming and Xining, respectively). Matrilineal backgrounds constitution (in terms of haplogroups) analysis generated a similar haplogroup distribution in both populations (P>0.1). All results failed to substantiate that m.16189T>C may play an active role in the development of T2DM in East Asian populations.}, }
@article {pmid25470289, year = {2014}, author = {Chen, D and Li, Y and Li, H and Wang, K and Du, S and Chu, W and Zhang, J}, title = {The genetic diversity of sinipercid fishes based on complete mitochondrial DNA of six sinipercid fishes from different drainages in China.}, journal = {Current molecular medicine}, volume = {14}, number = {10}, pages = {1279-1285}, doi = {10.2174/1566524014666141202162058}, pmid = {25470289}, issn = {1875-5666}, mesh = {Animals ; China ; DNA, Mitochondrial/*genetics ; Genes, Mitochondrial ; *Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Mutation Rate ; Perciformes/classification/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Sinipercids are a group of freshwater perciform fish endemic in East Asia with the majority of species recorded in China. In the present study, we analyzed the organizations of complete mitogenomes of the six sinipercid fish populations from the Yangtze River and the Pearl River systems in China. The proportion of G was relatively low just at 16.2%-16.5% among the fish populations analyzed. The similarity and divergence analysis showed that the populations from different drainages have more sequence similarities than those from different species in the same drainages. The rate of point mutation was 0.39% and a total of 422 variable sites were identified in the 12 protein-coding genes (excluding the ND6) among the four S. scherzeri populations. The analysis of evolutionary relationship showed that the four S. scherzeri populations can be divided into two groups of Yangtze River system and the Pearl River. Overall the data provide significant information for the genetic and evolutionary status of sinipercids upon adapting to different environments, and for genetic conservation and selective breeding of these fish species in fishery and aquaculture.}, }
@article {pmid25470288, year = {2014}, author = {Wang, J and Peng, LY and You, CP and Li, QL and Wen, M and Liu, SJ and Hong, YH}, title = {Minifish mtDNA has abundance of repeat sequences and inefficient replication in vitro.}, journal = {Current molecular medicine}, volume = {14}, number = {10}, pages = {1299-1307}, doi = {10.2174/1566524014666141202163927}, pmid = {25470288}, issn = {1875-5666}, mesh = {Animals ; Base Sequence ; China ; Cypriniformes/classification/*genetics ; DNA Replication ; DNA, Mitochondrial/chemistry/*genetics ; *Genes, Mitochondrial ; Genome Size ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; *Tandem Repeat Sequences ; Wetlands ; }, abstract = {Paedocypris is a newly described minifish genus endemic to Southeast Asia. Besides a tiny adult size of ~8 mm in length, minifish feature fragmentary habitats of acidic peat blackwater swamps, an unusual reproduction mode, truncated development and one of the smallest known genomes. A complete sequence is absent for the minifish mitochondrial DNA (mtDNA). Here we report the complete mtDNA sequence and its unusual feature in the minifish P. progenetica (Pp). We show that the Pp mtDNA is a circular molecule of 17,382 bp in length and has the same number of similarly oriented genes as in other vertebrates. Specifically, it comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 D-loop. Surprisingly, the D-loop is elusive for amplification by standard PCR conditions. The D-loop possesses a 28-bp dinucleotide TA repeat and more intriguingly, up to 25 copies of a 34-bp tandem repeat sequence. These tandem repeats predict the formation of paired regions. Hence, besides a generally conserved mtDNA with other vertebrates, the Pp mtDNA features an unusual D-loop and compromised DNA replication in vitro.}, }
@article {pmid25470287, year = {2014}, author = {Chen, XW and Li, QL and Hu, XJ and Yuan, YM and Wen, M and Peng, LY and Liu, SJ and Hong, YH}, title = {Minifish shows high genetic variation in mtDNA size.}, journal = {Current molecular medicine}, volume = {14}, number = {10}, pages = {1308-1313}, doi = {10.2174/1566524014666141202170144}, pmid = {25470287}, issn = {1875-5666}, mesh = {Animals ; China ; Cypriniformes/*genetics ; *DNA Copy Number Variations ; DNA Primers/chemistry ; DNA Replication ; DNA, Mitochondrial/chemistry/*genetics ; Electrophoresis, Agar Gel ; *Genes, Mitochondrial ; Genetic Speciation ; Genome Size ; Mitochondria/*genetics ; Polymerase Chain Reaction ; *Tandem Repeat Sequences ; }, abstract = {The genus Paedocypris is a newly described taxon of minifish species that are characterized by extensive chromosome evolution and one of the smallest known vertebrate nuclear genomes. Paedocypris features a tiny adult size, a short generation time, low fecundity and fragmented tropical habitats, which are factors that favor rapid speciation. Most recently, we have revealed that P. progenetica (Pp), the type species of the genus Paedocypris, has an unusual mtDNA bearing - within its D-loop - a tandem array of a 34-bp repeat sequence called the minifish repeat, which shows compromised replication efficiency in vitro. Here we report that Pp exhibits high genetic variation in mtDNA size. The efficiency of D-loop amplification was found to depend upon primers. Interestingly, Pp individuals of one and the same population differed drastically in mtDNA size resulting from varying copy numbers of the minifish repeat. We conclude that minifish has a high mutation rate and perhaps represents a rapidly evolving taxon of vertebrates.}, }
@article {pmid25470285, year = {2014}, author = {You, CP and Zhao, RR and Hu, J and Liu, SJ and Tao, M and Zhang, C and Chen, YB and Qin, QB and Xiao, J and Duan, W and Liu, Y}, title = {Inheritance of the complete mitochondrial genomes in three different ploidy fishes.}, journal = {Current molecular medicine}, volume = {14}, number = {10}, pages = {1322-1330}, doi = {10.2174/1566524014666141203100205}, pmid = {25470285}, issn = {1875-5666}, mesh = {Animals ; Biological Evolution ; Cell Nucleus/*genetics ; Chimera ; Cyprinidae/classification/*genetics ; Female ; *Genes, Mitochondrial ; Genome Size ; *Genome, Mitochondrial ; Goldfish/classification/*genetics ; Hybridization, Genetic ; Inheritance Patterns ; Male ; Mitochondria/*genetics ; Phylogeny ; Ploidies ; }, abstract = {Diploid natural gynogenetic goldfish (2nGRCG), triploid hybrids (3nRB) and tetraploid hybrids (4nRB) are generated by distant hybridization of red common goldfish (RCG, Carassius auratus red var.) and blunt snout bream (BSB, Megalobrama amblycephala). In the present study, we obtained the complete mitochondrial DNA (mtDNA) sequences of the hybrid offspring and compared them with the homologous sequences of RCG and BSB. All mtDNA sequences of these hybrids were 16,580bp in length, and the genes number, size, and order were quite similar to that of RCG. Genetic analysis revealed that the mtDNA sequences of these hybrids had high similarity (>99%) and low divergence (<2%) to their maternal RCG, yet lower similarities (84%) and higher divergences (16%) to their paternal BSB. The phylogenetic analysis also showed that the sequences of 2nGRCG, 3nRB and 4nRB were clustered with RCG rather than with BSB. These results indicate that the mitochondrial genomes of 2nGRCG, 3nRB and 4nRB remain maternally inherited after hybridization and polyploidization. Moreover, clade separation of hybrid offspring from their paternal BSB in the phylogenetic tree implies that phylogenetic analysis of mtDNA is incomplete for elucidating the true relationships between different species, particularly when they have undergone hybridization or allopolyploidization. Our study provides significant information for both evolution and genetic studies of mtDNA for hybrid species and allopolyploidization species.}, }
@article {pmid25470284, year = {2014}, author = {Ning, T and Li, J and Lin, K and Xiao, H and Wylie, S and Hua, S and Li, H and Zhang, YP}, title = {Complex evolutionary patterns revealed by mitochondrial genomes of the domestic horse.}, journal = {Current molecular medicine}, volume = {14}, number = {10}, pages = {1286-1298}, doi = {10.2174/1566524014666141203100940}, pmid = {25470284}, issn = {1875-5666}, mesh = {Amino Acid Substitution ; Animals ; Biological Evolution ; *DNA, Mitochondrial ; Female ; Genes, Mitochondrial ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Horses/classification/*genetics ; Inheritance Patterns ; Male ; Mitochondria/*genetics ; *Phylogeny ; Selection, Genetic ; }, abstract = {The domestic horse is the most widely used and important stock and recreational animal, valued for its strength and endurance. The energy required by the domestic horse is mainly supplied by mitochondria via oxidative phosphorylation. Thus, selection may have played an essential role in the evolution of the horse mitochondria. Besides, demographic events also affect the DNA polymorphic pattern on mitochondria. To understand the evolutionary patterns of the mitochondria of the domestic horse, we used a deep sequencing approach to obtain the complete sequences of 15 mitochondrial genomes, and four mitochondrial gene sequences, ND6, ATP8, ATP6 and CYTB, collected from 509, 363, 363 and 409 domestic horses, respectively. Evidence of strong substitution rate heterogeneity was found at nonsynonymous sites across the genomes. Signatures of recent positive selection on mtDNA of domestic horse were detected. Specifically, five amino acids in the four mitochondrial genes were identified as the targets of positive selection. Coalescentbased simulations imply that recent population expansion is the most probable explanation for the matrilineal population history for domestic horse. Our findings reveal a complex pattern of non-neutral evolution of the mitochondrial genome in the domestic horses.}, }
@article {pmid25470283, year = {2014}, author = {Ma, W and Zhu, ZH and Bi, XY and Murphy, RW and Wang, SY and Gao, Y and Xiao, H and Zhang, YP and Luo, J}, title = {Allopolyploidization is not so simple: evidence from the origin of the tribe Cyprinini (Teleostei: Cypriniformes).}, journal = {Current molecular medicine}, volume = {14}, number = {10}, pages = {1331-1338}, doi = {10.2174/1566524014666141203101543}, pmid = {25470283}, issn = {1875-5666}, mesh = {Animals ; Carps/classification/*genetics ; Cell Nucleus/*genetics ; Chimera ; Evolution, Molecular ; Female ; Gene Duplication ; *Genes, Mitochondrial ; Genetic Speciation ; *Genome, Mitochondrial ; Goldfish/classification/*genetics ; Growth Hormone/genetics ; Homeodomain Proteins/genetics ; Hybridization, Genetic ; Inheritance Patterns ; Male ; Mitochondria/*genetics ; *Phylogeny ; Ploidies ; }, abstract = {The identification of allopolyploidization events benefits from molecular dating and divergence assessments of progenitor genomes. Information on gene duplications only, either orthologs or paralogs, provides incomplete information. Analyses of mitochondrial DNA yield insights into matrilineal history, which may differ from patrilineal evolution. Two important food and pet fishes, the common carp (Cyprinus carpio) and goldfish (Carassius sp.), appear to have experienced allotetraploidization sometime from 12 to 20 million years ago (Ma). However, much work is necessary to detail the initial polyploidization event. Herein, we use this group of fishes as a model system to investigate competing scenarios for allopolyploidization. We analyze both the nuclear genes encoding growth hormone (GH), recombination activating protein 1 (RAG1) and HOXA2B gene, and the maternal heredited 12 concatenated mitochondrial protein-coding gene in 19 species of cyprinids and use two species in Balitoridae as outgroup taxa. Our analyses clarify the phylogenetic position of the paternal and maternal ancestors for the common carp and goldfish. The estimation of matrilineal divergence (10.71-12.42 Ma) is significantly younger than the dates of the parental ancestor divergedthat obtained by nuclear genes (16.62-19.64 Ma). Analyses of both genomes date the allopolyploidization event of the common ancestor of Cy. carpio and Ca sp. to about 10.71-12.42 Ma, which is most likely represented by maternal divergent time. The divergence of the two copies of the nuclear genes which was more ancient than the maternal markers might have been included the divergence of the progenitors' genome divergence when the allopolyploidization event occurred. Thus, the scenarios of allopolyploidzation for this group of fish can be suggested as the following: the matrilineal common ancestor of species in tribe Cyprinini might have doubled its genome by mating with a paternal ancestor in the subfamily Cyprininae, which was a sister-group that diverged around 4.20-8.93 Ma. Our work provides new evidence for the divergence dates of allopolyploidization within the Cyprinini, and documents the necessity of considering both matrilineal and patrilineal histories when investigating allopolyploidization.}, }
@article {pmid25463302, year = {2015}, author = {Xiang, Z and Qu, F and Wang, F and Xiao, S and Jun, L and Zhang, Y and Yu, Z}, title = {ChBax/Bak as key regulators of the mitochondrial apoptotic pathway: cloned and characterized in Crassostrea hongkongensis.}, journal = {Fish &amp; shellfish immunology}, volume = {42}, number = {2}, pages = {225-232}, doi = {10.1016/j.fsi.2014.11.013}, pmid = {25463302}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Apoptosis/*genetics ; Base Sequence ; Cloning, Molecular ; Crassostrea/*genetics/metabolism ; DNA, Complementary/genetics/metabolism ; Genes, Reporter ; HEK293 Cells ; Hemocytes/metabolism ; Humans ; Mitochondria/physiology ; Molecular Sequence Data ; Phylogeny ; RNA, Messenger/genetics/metabolism ; Sequence Alignment ; Tumor Suppressor Protein p53/genetics/metabolism ; bcl-2 Homologous Antagonist-Killer Protein/*genetics/metabolism ; bcl-2-Associated X Protein/*genetics/metabolism ; }, abstract = {Apoptosis has been primarily investigated in mammals, and little is known about apoptosis in mollusks. The proteins Bax and Bak play critical roles in the mitochondrial apoptosis pathway and in determining cell fate. In this study, ChBax and ChBak, homologs of the well-known Bax and Bak proteins, were identified from the oyster Crassostrea hongkongensis. The ChBax/Bak proteins consist of 207/232 amino acids with the typical domains found in BCL-2 family members. ChBax and ChBak mRNA expression were detected in all 8 of the selected oyster tissues and at the different stages of development. Fluorescence microscopy revealed that the full-length proteins of ChBax/Bak were located in the cytoplasm and mitochondrial outer membrane, of HEK293T cells, respectively. Furthermore, both of the genes' expression levels were found to increase in the hemocytes of oysters challenged with pathogens. The over-expression of ChBax or ChBak activates the p53-Luc reporter gene in HEK293T cells in a dose-dependent manner. These results indicate that ChBax and ChBak may play important roles in the mitochondrial apoptotic pathway in oysters.}, }
@article {pmid25463290, year = {2015}, author = {Li, T and Wang, Y and Gao, Y and Li, Q}, title = {Identification and characterisation of the anti-oxidative stress properties of the lamprey prohibitin 2 gene.}, journal = {Fish &amp; shellfish immunology}, volume = {42}, number = {2}, pages = {447-456}, doi = {10.1016/j.fsi.2014.11.016}, pmid = {25463290}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; DNA, Complementary/genetics/metabolism ; Female ; Fish Proteins/*genetics/metabolism ; Gene Expression Regulation/*drug effects ; Hydrogen Peroxide/pharmacology ; Lampreys/*genetics/*immunology/metabolism ; Male ; Molecular Sequence Data ; Organ Specificity ; Oxidative Stress/*drug effects ; Phylogeny ; Prohibitins ; RNA, Messenger/genetics/metabolism ; Real-Time Polymerase Chain Reaction/veterinary ; Repressor Proteins/*genetics/metabolism ; Sequence Alignment/veterinary ; }, abstract = {The highly conserved protein prohibitin 2 (PHB2) has been implicated as a cell-surface receptor in the regulation of proliferation, apoptosis, transcription, and mitochondrial protein folding. In the present study, we identified a Lampetra morii homologue of PHB2, Lm-PHB2, showing greater than 61.8% sequence identity with its homologues. Phylogenetic analysis indicated that the position of Lm-PHB2 is consistent with lamprey phylogeny. Expression of the Lm-PHB2 protein was nearly equivalent in the heart, liver, kidneys, intestines, and muscles of normal lampreys. However, the Lm-PHB2 protein was down-regulated in the myocardia of lampreys challenged for 5 days with adriamycin (Adr), followed by a significant up-regulation 10 days after treatment. In vitro, recombinant Lm-PHB2 (rLm-PHB2) protein could significantly enhance the H2O2-induced oxidative stress tolerance in Chang liver (CHL) cells. Further mechanism studies indicated that the nucleus-to-mitochondria translocation of Lm-PHB2 was closely involved in the oxidative stress protection. Our results suggests that the strategies to modulate Lm-PHB2 levels may constitute a novel therapeutic approach for myocardial injury and liver inflammatory diseases, conditions in which oxidative stress plays a critical role in tissue injury and inflammation.}, }
@article {pmid25462333, year = {2014}, author = {Shellman, ER and Chen, Y and Lin, X and Burant, CF and Schnell, S}, title = {Metabolic network motifs can provide novel insights into evolution: The evolutionary origin of Eukaryotic organelles as a case study.}, journal = {Computational biology and chemistry}, volume = {53PB}, number = {}, pages = {242-250}, pmid = {25462333}, issn = {1476-928X}, support = {P30 DK089503/DK/NIDDK NIH HHS/United States ; T32 GM008322/GM/NIGMS NIH HHS/United States ; P30 DK020572/DK/NIDDK NIH HHS/United States ; R01 DK079084/DK/NIDDK NIH HHS/United States ; U24 DK097153/DK/NIDDK NIH HHS/United States ; }, abstract = {Phylogenetic trees are typically constructed using genetic and genomic data, and provide robust evolutionary relationships of species from the genomic point of view. We present an application of network motif mining and analysis of metabolic pathways that when used in combination with phylogenetic trees can provide a more complete picture of evolution. By using distributions of three-node motifs as a proxy for metabolic similarity, we analyze the ancestral origin of Eukaryotic organelles from the metabolic point of view to illustrate the application of our motif mining and analysis network approach. Our analysis suggests that the hypothesis of an early proto-Eukaryote could be valid. It also suggests that a δ- or ϵ-Proteobacteria may have been the endosymbiotic partner that gave rise to modern mitochondria. Our evolutionary analysis needs to be extended by building metabolic network reconstructions of species from the phylum Crenarchaeota, which is considered to be a possible archaeal ancestor of the eukaryotic cell. In this paper, we also propose a methodology for constructing phylogenetic trees that incorporates metabolic network signatures to identify regions of genomically-estimated phylogenies that may be spurious. We find that results generated from our approach are consistent with a parallel phylogenetic analysis using the method of feature frequency profiles.}, }
@article {pmid25460232, year = {2014}, author = {Shiratori, T and Yokoyama, A and Ishida, K}, title = {Phylogeny, ultrastructure, and flagellar apparatus of a new Marimonad flagellate Abollifer globosa sp. nov. (Imbricatea, Cercozoa).}, journal = {Protist}, volume = {165}, number = {6}, pages = {808-824}, doi = {10.1016/j.protis.2014.10.003}, pmid = {25460232}, issn = {1618-0941}, mesh = {Cercozoa/*classification/genetics/*ultrastructure ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Flagella/ultrastructure ; Microscopy, Electron, Transmission ; *Phylogeny ; Phylogeography ; Seawater ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Abollifer is a little-known genus of marine heterotrophic flagellates with no ultrastructural and molecular information, and its taxonomic position remains uncertain. In this study, we report a new species of Abollifer, Abollifer globosa sp. nov., isolated from a seawater sample collected at Tokyo Bay. To reveal the taxonomic position and morphological characteristics of A. globosa, we performed light and electron microscopic observations and a phylogenetic analysis using small subunit ribosomal DNA sequences. A. globosa cells were 29.5 μm in length and 22.4 μm in width, oval or ovoid in shape with an apical projection. Two unequal flagella emerged from a deep subapical flagellar pit. The rim of the flagellar pit except for the ventral side was swollen. Electron microscopic observations showed that A. globosa possessed mitochondria with tubular cristae, a Golgi apparatus, microbodies, extrusomes, and many endosymbiotic bacteria. Basal bodies were arranged in parallel. The flagellar apparatus of A. globosa showed affinity with common gliding cercozoan flagellates. Our phylogenetic tree showed that A. globosa branched as the sister position of order Marimonadida (Imbricatea, Cercozoa). On the basis of the morphological and molecular phylogenetic analysis, we conclude that A. globosa is a new member of the order Marimonadida.}, }
@article {pmid25451744, year = {2015}, author = {Ramakodi, MP and Singh, B and Wells, JD and Guerrero, F and Ray, DA}, title = {A 454 sequencing approach to dipteran mitochondrial genome research.}, journal = {Genomics}, volume = {105}, number = {1}, pages = {53-60}, doi = {10.1016/j.ygeno.2014.10.014}, pmid = {25451744}, issn = {1089-8646}, mesh = {Animals ; Diptera/classification/cytology/*genetics ; Evolution, Molecular ; Genome, Insect ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {The availability of complete mitochondrial genome (mtgenome) data for Diptera, one of the largest metazoan orders, in public databases is limited. The advent of high throughput sequencing technology provides the potential to generate mtgenomes for many species affordably and quickly. However, these technologies need to be validated for dipterans as the members of this clade play important economic and research roles. Illumina and 454 sequencing platforms are widely used in genomic research involving non-model organisms. The Illumina platform has already been utilized for generating mitochondrial genomes without using conventional long range PCR for insects whereas the power of 454 sequencing for generating mitochondrial genome drafts without PCR has not yet been validated for insects. Thus, this study examines the utility of 454 sequencing approach for dipteran mtgenomic research. We generated complete or nearly complete mitochondrial genomes for Cochliomyia hominivorax, Haematobia irritans, Phormia regina and Sarcophaga crassipalpis using a 454 sequencing approach. Comparisons between newly obtained and existing assemblies for C. hominivorax and H. irritans revealed no major discrepancies and verified the utility of 454 sequencing for dipteran mitochondrial genomes. We also report the complete mitochondrial sequences for two forensically important flies, P. regina and S. crassipalpis, which could be used to provide useful information to legal personnel. Comparative analyses revealed that dipterans follow similar codon usage and nucleotide biases that could be due to mutational and selection pressures. This study illustrates the utility of 454 sequencing to obtain complete mitochondrial genomes for dipterans without the aid of conventional molecular techniques such as PCR and cloning and validates this method of mtgenome sequencing in arthropods.}, }
@article {pmid25450980, year = {2015}, author = {Kim, JH and Bothe, JR and Alderson, TR and Markley, JL}, title = {Tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by NMR, SAXS, chemical crosslinking, and functional studies.}, journal = {Biochimica et biophysica acta}, volume = {1853}, number = {6}, pages = {1416-1428}, pmid = {25450980}, issn = {0006-3002}, support = {P41 RR002301/RR/NCRR NIH HHS/United States ; S10RR025062/RR/NCRR NIH HHS/United States ; S10 RR008438-01/RR/NCRR NIH HHS/United States ; U01 GM94622/GM/NIGMS NIH HHS/United States ; P41 GM066326/GM/NIGMS NIH HHS/United States ; S10RR029220/RR/NCRR NIH HHS/United States ; S10 RR025062/RR/NCRR NIH HHS/United States ; U01 GM094622/GM/NIGMS NIH HHS/United States ; S10 RR029220/RR/NCRR NIH HHS/United States ; F32 GM110939/GM/NIGMS NIH HHS/United States ; P41RR02301/RR/NCRR NIH HHS/United States ; P41GM66326/GM/NIGMS NIH HHS/United States ; S10 RR002781-01/RR/NCRR NIH HHS/United States ; S10 RR002781/RR/NCRR NIH HHS/United States ; P41 GM103399/GM/NIGMS NIH HHS/United States ; S10 RR008438/RR/NCRR NIH HHS/United States ; S10 RR023438/RR/NCRR NIH HHS/United States ; S10RR023438/RR/NCRR NIH HHS/United States ; }, mesh = {Cross-Linking Reagents/chemistry ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/*chemistry/genetics/metabolism ; Humans ; Iron-Sulfur Proteins/*chemistry/genetics/metabolism ; Magnetic Resonance Spectroscopy/*methods ; Operon ; Protein Binding ; *Scattering, Small Angle ; X-Ray Diffraction/*methods ; }, abstract = {Proteins containing iron-sulfur (Fe-S) clusters arose early in evolution and are essential to life. Organisms have evolved machinery consisting of specialized proteins that operate together to assemble Fe-S clusters efficiently so as to minimize cellular exposure to their toxic constituents: iron and sulfide ions. To date, the best studied system is the iron-sulfur cluster (isc) operon of Escherichia coli, and the eight ISC proteins it encodes. Our investigations over the past five years have identified two functional conformational states for the scaffold protein (IscU) and have shown that the other ISC proteins that interact with IscU prefer to bind one conformational state or the other. From analyses of the NMR spectroscopy-derived network of interactions of ISC proteins, small-angle X-ray scattering (SAXS) data, chemical crosslinking experiments, and functional assays, we have constructed working models for Fe-S cluster assembly and delivery. Future work is needed to validate and refine what has been learned about the E. coli system and to extend these findings to the homologous Fe-S cluster biosynthetic machinery of yeast and human mitochondria. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.}, }
@article {pmid25445281, year = {2015}, author = {Li, W and Zhang, XC and Zhao, J and Shi, Y and Zhu, XP}, title = {Complete mitochondrial genome of Cuora trifasciata (Chinese three-striped box turtle), and a comparative analysis with other box turtles.}, journal = {Gene}, volume = {555}, number = {2}, pages = {169-177}, doi = {10.1016/j.gene.2014.10.060}, pmid = {25445281}, issn = {1879-0038}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; China ; Codon ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; Genomics ; Likelihood Functions ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; Turtles/classification/*genetics ; Vietnam ; }, abstract = {Cuora trifasciata has become one of the most critically endangered species in the world. The complete mitochondrial genome of C. trifasciata (Chinese three-striped box turtle) was determined in this study. Its mitochondrial genome is a 16,575-bp-long circular molecule that consists of 37 genes that are typically found in other vertebrates. And the basic characteristics of the C. trifasciata mitochondrial genome were also determined. Moreover, a comparison of C. trifasciata with Cuora cyclornata, Cuora pani and Cuora aurocapitata indicated that the four mitogenomics differed in length, codons, overlaps, 13 protein-coding genes (PCGs), ND3, rRNA genes, control region, and other aspects. Phylogenetic analysis with Bayesian inference and maximum likelihood based on 12 protein-coding genes of the genus Cuora indicated the phylogenetic position of C. trifasciata within Cuora. The phylogenetic analysis also showed that C. trifasciata from Vietnam and China formed separate monophyletic clades with different Cuora species. The results of nucleotide base compositions, protein-coding genes and phylogenetic analysis showed that C. trifasciata from these two countries may represent different Cuora species.}, }
@article {pmid25444935, year = {2015}, author = {Krakowetz, CN and Chilton, NB}, title = {Sequence and secondary structure of the mitochondrial 16S ribosomal RNA gene of Ixodes scapularis.}, journal = {Molecular and cellular probes}, volume = {29}, number = {1}, pages = {35-38}, doi = {10.1016/j.mcp.2014.11.001}, pmid = {25444935}, issn = {1096-1194}, mesh = {Animals ; Evolution, Molecular ; Ixodes/*genetics ; Mitochondria/genetics ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeography ; RNA/*chemistry/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal, 16S/*chemistry/*genetics ; Sequence Alignment ; Sequence Analysis, RNA ; }, abstract = {The complete DNA sequences and secondary structure of the mitochondrial (mt) 16S ribosomal (r) RNA gene were determined for six Ixodes scapularis adults. There were 44 variable nucleotide positions in the 1252 bp sequence alignment. Most (95%) nucleotide alterations did not affect the integrity of the secondary structure of the gene because they either occurred at unpaired positions or represented compensatory changes that maintained the base pairing in helices. A large proportion (75%) of the intraspecific variation in DNA sequence occurred within Domains I, II and VI of the 16S gene. Therefore, several regions within this gene may be highly informative for studies of the population genetics and phylogeography of I. scapularis, a major vector of pathogens of humans and domestic animals in North America.}, }
@article {pmid25441621, year = {2015}, author = {Sanchez-Puerta, MV and Zubko, MK and Palmer, JD}, title = {Homologous recombination and retention of a single form of most genes shape the highly chimeric mitochondrial genome of a cybrid plant.}, journal = {The New phytologist}, volume = {206}, number = {1}, pages = {381-396}, pmid = {25441621}, issn = {1469-8137}, support = {R03 TW008353/TW/FIC NIH HHS/United States ; FIRCA-BB-R03-TW008353-01/BB/FDA HHS/United States ; }, mesh = {Base Sequence ; Chimera ; DNA, Mitochondrial/chemistry/genetics ; Genome, Mitochondrial/*genetics ; Genome, Plant/*genetics ; *Homologous Recombination ; Hyoscyamus/genetics ; Magnoliopsida/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; Solanaceae/*genetics ; Nicotiana/genetics ; }, abstract = {The structure and evolution of angiosperm mitochondrial genomes are driven by extremely high rates of recombination and rearrangement. An excellent experimental system for studying these events is offered by cybrid plants, in which parental mitochondria usually fuse and their genomes recombine. Little is known about the extent, nature and consequences of mitochondrial recombination in these plants. We conducted the first study in which the organellar genomes of a cybrid - between Nicotiana tabacum and Hyoscyamus niger - were sequenced and compared to those of its parents. This cybrid mitochondrial genome is highly recombinant, reflecting at least 30 crossovers and five gene conversions between its parental genomes. It is also surprisingly large (41% and 64% larger than the parental genomes), yet contains single alleles for 90% of mitochondrial genes. Recombination produced a remarkably chimeric cybrid mitochondrial genome and occurred entirely via homologous mechanisms involving the double-strand break repair and/or break-induced replication pathways. Retention of a single form of most genes could be advantageous to minimize intracellular incompatibilities and/or reflect neutral forces that preferentially eliminate duplicated regions. We discuss the relevance of these findings to the surprisingly frequent occurrence of horizontal gene - and genome - transfer in angiosperm mitochondrial DNAs.}, }
@article {pmid25435547, year = {2015}, author = {Murcha, MW and Narsai, R and Devenish, J and Kubiszewski-Jakubiak, S and Whelan, J}, title = {MPIC: a mitochondrial protein import components database for plant and non-plant species.}, journal = {Plant &amp; cell physiology}, volume = {56}, number = {1}, pages = {e10}, doi = {10.1093/pcp/pcu186}, pmid = {25435547}, issn = {1471-9053}, mesh = {Base Sequence ; *Databases, Factual ; Fungi/*genetics ; Humans ; Mitochondria/genetics ; Mitochondrial Proteins/*genetics ; Molecular Sequence Annotation ; Phaeophyceae/*genetics ; Phylogeny ; Plants/*genetics ; Protein Transport ; Rhodophyta/*genetics ; }, abstract = {In the 2 billion years since the endosymbiotic event that gave rise to mitochondria, variations in mitochondrial protein import have evolved across different species. With the genomes of an increasing number of plant species sequenced, it is possible to gain novel insights into mitochondrial protein import pathways. We have generated the Mitochondrial Protein Import Components (MPIC) Database (DB; http://www.plantenergy.uwa.edu.au/applications/mpic) providing searchable information on the protein import apparatus of plant and non-plant mitochondria. An in silico analysis was carried out, comparing the mitochondrial protein import apparatus from 24 species representing various lineages from Saccharomyces cerevisiae (yeast) and algae to Homo sapiens (human) and higher plants, including Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice) and other more recently sequenced plant species. Each of these species was extensively searched and manually assembled for analysis in the MPIC DB. The database presents an interactive diagram in a user-friendly manner, allowing users to select their import component of interest. The MPIC DB presents an extensive resource facilitating detailed investigation of the mitochondrial protein import machinery and allowing patterns of conservation and divergence to be recognized that would otherwise have been missed. To demonstrate the usefulness of the MPIC DB, we present a comparative analysis of the mitochondrial protein import machinery in plants and non-plant species, revealing plant-specific features that have evolved.}, }
@article {pmid25433563, year = {2014}, author = {Borsa, P and Sembiring, A and Fauvelot, C and Chen, WJ}, title = {Resurrection of Indian Ocean humbug damselfish, Dascyllus abudafur (Forsskål) from synonymy with its Pacific Ocean sibling, Dascyllus aruanus (L.).}, journal = {Comptes rendus biologies}, volume = {337}, number = {12}, pages = {709-716}, doi = {10.1016/j.crvi.2014.09.001}, pmid = {25433563}, issn = {1768-3238}, mesh = {Animals ; Base Sequence ; Coral Reefs ; DNA, Mitochondrial/genetics ; Indian Ocean ; Mitochondria/genetics ; Molecular Sequence Data ; Pacific Ocean ; Perciformes/classification/*physiology ; Phylogeny ; Pigmentation/genetics ; Species Specificity ; }, abstract = {Previous phylogeographic studies of the humbug damselfish, a widespread Indo-West Pacific coral reef fish, have revealed a split of two main mitochondrial lineages distributed on either side of the Indo-Pacific barrier. This has been interpreted as the result of vicariance. It has been hypothesized that reproductive barriers might currently limit gene flow between humbug damselfish populations from the Indian Ocean and the Pacific Ocean. In this study, we review the published phylogeographic information to update the distribution of the two main mitochondrial lineages of humbug damselfish. The Indian lineage was distributed from the Red Sea to the eastern extremity of the Sunda Shelf while the Pacific lineage, which diverged from the former by 0.6% net nucleotide divergence and diagnostic substitutions at three nucleotide sites at the cytochrome b locus, was distributed east and north of the Sunda Shelf. The two forms, which are also genetically distinct at nuclear loci, were also characterized by distinct pigmentation patterns. We argue that the two forms represent geminate species. Epithet aruanus Linnaeus is maintained for the Pacific Ocean humbug damselfish while epithet abudafur (Forsskål) is here resurrected for the Indian Ocean humbug damselfish. Future studies should focus on the population genetic structure of the transition zone between Dascyllus abudafur and D. aruanus.}, }
@article {pmid25433485, year = {2014}, author = {Han, L and Zhu, S and Ning, C and Cai, D and Wang, K and Chen, Q and Hu, S and Yang, J and Shao, J and Zhu, H and Zhou, H}, title = {Ancient DNA provides new insight into the maternal lineages and domestication of Chinese donkeys.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {246}, pmid = {25433485}, issn = {1471-2148}, mesh = {Animals ; Animals, Domestic ; Archaeology ; China ; Cytochromes b/genetics ; DNA, Mitochondrial/analysis/*genetics ; Equidae/*classification/*genetics ; Horses/genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {BACKGROUND: The donkey (Equus asinus) is an important domestic animal that provides a reliable source of protein and method of transportation for many human populations. However, the process of domestication and the dispersal routes of the Chinese donkey are still unclear, as donkey remains are sparse in the archaeological record and often confused with horse remains. To explore the maternal origins and dispersal route of Chinese donkeys, both mitochondrial DNA D-loop and cytochrome b gene fragments of 21 suspected donkey remains from four archaeological sites in China were amplified and sequenced.<br><br>RESULTS: Molecular methods of species identification show that 17 specimens were donkeys and three samples had the maternal genetic signature of horses. One sample that dates to about 20,000 years before present failed to amplify. In this study, the phylogenetic analysis reveals that ancient Chinese donkeys have high mitochondrial DNA diversity and two distinct mitochondrial maternal lineages, known as the Somali and Nubian lineages. These results indicate that the maternal origin of Chinese domestic donkeys was probably related to the African wild ass, which includes the Nubian wild ass (Equus africanus africanus) and the Somali wild ass (Equus africanus somaliensis). Combined with historical records, the results of this study implied that domestic donkeys spread into west and north China before the emergence of the Han dynasty. The number of Chinese domestic donkeys had increased primarily to meet demand for the expansion of trade, and they were likely used as commodities or for shipping goods along the Silk Road during the Tang Dynasty, when the Silk Road reached its golden age.<br><br>CONCLUSIONS: This study is the first to provide valuable ancient animal DNA evidence for early trade between African and Asian populations. The ancient DNA analysis of Chinese donkeys also sheds light on the dynamic process of the maternal origin, domestication, and dispersal route of ancient Chinese donkeys.}, }
@article {pmid25432941, year = {2014}, author = {Degli Esposti, M}, title = {Bioenergetic evolution in proteobacteria and mitochondria.}, journal = {Genome biology and evolution}, volume = {6}, number = {12}, pages = {3238-3251}, pmid = {25432941}, issn = {1759-6653}, mesh = {*Energy Metabolism ; *Evolution, Molecular ; Methanol/metabolism ; Mitochondria/*genetics/metabolism ; Proteobacteria/*genetics/metabolism/ultrastructure ; Symbiosis ; }, abstract = {Mitochondria are the energy-producing organelles of our cells and derive from bacterial ancestors that became endosymbionts of microorganisms from a different lineage, together with which they formed eukaryotic cells. For a long time it has remained unclear from which bacteria mitochondria actually evolved, even if these organisms in all likelihood originated from the α lineage of proteobacteria. A recent article (Degli Esposti M, et al. 2014. Evolution of mitochondria reconstructed from the energy metabolism of living bacteria. PLoS One 9:e96566) has presented novel evidence indicating that methylotrophic bacteria could be among the closest living relatives of mitochondrial ancestors. Methylotrophs are ubiquitous bacteria that live on single carbon sources such as methanol and methane; in the latter case they are called methanotrophs. In this review, I examine their possible ancestry to mitochondria within a survey of the common features that can be found in the central and terminal bioenergetic systems of proteobacteria and mitochondria. I also discuss previously overlooked information on methanotrophic bacteria, in particular their intracytoplasmic membranes resembling mitochondrial cristae and their capacity of establishing endosymbiotic relationships with invertebrate animals and archaic plants. This information appears to sustain the new idea that mitochondrial ancestors could be related to extant methanotrophic proteobacteria, a possibility that the genomes of methanotrophic endosymbionts will hopefully clarify.}, }
@article {pmid25431826, year = {2015}, author = {Zhou, CL and Turdy, R and Halik, M}, title = {Genetic differentiation between red deer from different sample sites on the Tianshan Mountains (Cervus elaphus), China.}, journal = {Mitochondrial DNA}, volume = {26}, number = {1}, pages = {101-111}, doi = {10.3109/19401736.2014.984165}, pmid = {25431826}, issn = {1940-1744}, mesh = {Animals ; China ; Cytochromes b/genetics ; Deer/classification/*genetics ; Genes, Mitochondrial ; *Genetic Variation ; Geography ; Haplotypes ; Microsatellite Repeats ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; }, abstract = {About 273 individuals were identified from 471 fecal samples from six different red deer populations in China. The genetic structure showed that the red deer from the western and eastern Tianshan Mountains was different. A total number of 12 haplotypes were defined by 97 variable sites by the control region (CR), and 10 haplotypes were defined by 34 variable sites by cytochrome b. There was no haplotype sharing between red deer populations from western and eastern Tianshan Mountains by the CR and the cytochrome b. The red deer populations from west were clade with wapiti from North American and red deer from Siberia, while red deer populations from east were clade with red deer from Crimea in Pleistocene rather than west at present. The result of NETWORK also showed that red deer populations from western and eastern Tianshan Mountains were different. The haplotype and the Fst value between western and eastern Tianshan red deer were significantly different. The AMOVA analysis showed that 97.34% and 1.14% of the total genetic variability were found within populations and among populations within groups, respectively, by microsatellite. AMOVA for mitochondria showed that most of the variance was explained among-group. The Fst, pairwise distance, and phylogenetic relationship result showed that red deer between western and eastern Tianshan were more different than some of the red deer from North-Asia, South-Asia, East-Asia, and wapiti. All data from this study do support that the genetic characteristics of red deer between western and eastern Tianshan Mountains by microsatellite, control region, and cytochrome b were different.}, }
@article {pmid25431021, year = {2014}, author = {Tak, H and Kim, J and Jayabalan, AK and Lee, H and Kang, H and Cho, DH and Ohn, T and Nam, SW and Kim, W and Lee, EK}, title = {miR-27 regulates mitochondrial networks by directly targeting the mitochondrial fission factor.}, journal = {Experimental &amp; molecular medicine}, volume = {46}, number = {11}, pages = {e123}, pmid = {25431021}, issn = {2092-6413}, mesh = {3' Untranslated Regions ; Cell Line ; Gene Expression Regulation ; Humans ; Membrane Potential, Mitochondrial ; Membrane Proteins/*genetics ; MicroRNAs/*metabolism ; Mitochondria/*genetics/*metabolism ; *Mitochondrial Dynamics ; Mitochondrial Proteins/*genetics ; *Protein Biosynthesis ; RNA, Messenger/genetics/metabolism ; }, abstract = {Mitochondrial morphology is dynamically regulated by forming small, fragmented units or interconnected networks, and this is a pivotal process that is used to maintain mitochondrial homeostasis. Although dysregulation of mitochondrial dynamics is related to the pathogenesis of several human diseases, its molecular mechanism is not fully elucidated. In this study, we demonstrate the potential role of miR-27 in the regulation of mitochondrial dynamics. Mitochondrial fission factor (MFF) mRNA is a direct target of miR-27, whose ectopic expression decreases MFF expression through binding to its 3'-untranslated region. Expression of miR-27 results in the elongation of mitochondria as well as an increased mitochondrial membrane potential and mitochondrial ATP level. Our results suggest that miR-27 is a novel regulator affecting morphological mitochondrial changes by targeting MFF.}, }
@article {pmid25427806, year = {2016}, author = {Lin, HY and Chang, CH and Ho, HC and Shao, KT}, title = {The complete mitochondrial genome of Wanieso lizardfish Saurida wanieso Shindo &amp; Yamada, 1972 (Aulopiformes: Synodontidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {3}, pages = {2190-2191}, doi = {10.3109/19401736.2014.982620}, pmid = {25427806}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; DNA, Mitochondrial/genetics ; Fishes/*genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; }, abstract = {The complete mitochondrial genome of the Wanieso lizardfish (Saurida wanieso) was determined by using a PCR-based method. The total length of mitochondrial DNA is 16,552 base pairs including 13 protein-coding genes, 2 ribosomal RNA, 22 transfer RNA genes, 1 replication origin region and 1 control region as other Saurida spp. and bony fish. Base composition of the genome is A (25.7%), T (25.2%), C (31.5%), and G (17.6%) with an A + T-rich hallmark as that of other vertebrate mitochondrial genomes.}, }
@article {pmid25425607, year = {2015}, author = {Burgstaller, JP and Johnston, IG and Poulton, J}, title = {Mitochondrial DNA disease and developmental implications for reproductive strategies.}, journal = {Molecular human reproduction}, volume = {21}, number = {1}, pages = {11-22}, pmid = {25425607}, issn = {1460-2407}, support = {MR/J010448/1/MRC_/Medical Research Council/United Kingdom ; MR/J013617/1/MRC_/Medical Research Council/United Kingdom ; WT0948685MA/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Biological Evolution ; *DNA, Mitochondrial ; Databases, Genetic ; Haplotypes ; Humans ; Mitochondria/*genetics ; Mitochondrial Diseases/*genetics/*prevention &amp; control ; Reproduction ; }, abstract = {Mitochondrial diseases are potentially severe, incurable diseases resulting from dysfunctional mitochondria. Several important mitochondrial diseases are caused by mutations in mitochondrial DNA (mtDNA), the genetic material contained within mitochondria, which is maternally inherited. Classical and modern therapeutic approaches exist to address the inheritance of mtDNA disease, but are potentially complicated by the fact that cellular mtDNA populations evolve according to poorly-understood dynamics during development and organismal lifetimes. We review these therapeutic approaches and models of mtDNA dynamics during development, and discuss the implications of recent results from these models for modern mtDNA therapies. We particularly highlight mtDNA segregation-differences in proliferative rates between different mtDNA haplotypes-as a potential and underexplored issue in such therapies. However, straightforward strategies exist to combat this and other potential therapeutic problems. In particular, we describe haplotype matching as an approach with the power to potentially ameliorate any expected issues from mtDNA incompatibility.}, }
@article {pmid25424737, year = {2015}, author = {Andersen, JC and Gwiazdowski, RA and Gdanetz, K and Gruwell, ME}, title = {Armored scale insect endosymbiont diversity at the species level: genealogical patterns of Uzinura diasipipdicola in the Chionaspis pinifoliae-Chionaspis heterophyllae species complex (Hemiptera: Coccoidea: Diaspididae).}, journal = {Bulletin of entomological research}, volume = {105}, number = {1}, pages = {110-120}, doi = {10.1017/S0007485314000820}, pmid = {25424737}, issn = {1475-2670}, mesh = {Animals ; Bacterial Proteins/genetics ; Bacteroidetes/*classification/*genetics ; Bayes Theorem ; Cell Nucleus/genetics ; Chaperonin 60/genetics ; DNA, Bacterial/genetics ; Evolution, Molecular ; Food Chain ; Hemiptera/*classification/*microbiology ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Pinus/physiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Armored scale insects and their primary bacterial endosymbionts show nearly identical patterns of co-diversification when viewed at the family level, though the persistence of these patterns at the species level has not been explored in this group. Therefore we investigated genealogical patterns of co-diversification near the species level between the primary endosymbiont Uzinura diaspidicola and its hosts in the Chionaspis pinifoliae-Chionaspis heterophyllae species complex. To do this we generated DNA sequence data from three endosymbiont loci (rspB, GroEL, and 16S) and analyzed each locus independently using statistical parsimony network analyses and as a concatenated dataset using Bayesian phylogenetic reconstructions. We found that for two endosymbiont loci, 16S and GroEL, sequences from U. diaspidicola were broadly associated with host species designations, while for rspB this pattern was less clear as C. heterophyllae (species S1) shared haplotypes with several other Chionaspis species. We then compared the topological congruence of the phylogenetic reconstructions generated from a concatenated dataset of endosymbiont loci (including all three loci, above) to that from a concatenated dataset of armored scale hosts, using published data from two nuclear loci (28S and EF1α) and one mitochondrial locus (COI-COII) from the armored scale hosts. We calculated whether the two topologies were congruent using the Shimodaira-Hasegawa test. We found no significant differences (P = 0.4892) between the topologies suggesting that, at least at this level of resolution, co-diversification of U. diaspidicola with its armored scale hosts also occurs near the species level. This is the first such study of co-speciation at the species level between U. diaspidicola and a group of armored scale insects.}, }
@article {pmid25423520, year = {2016}, author = {Landínez-García, RM and Alzate, JF and Márquez, EJ}, title = {Mitochondrial genome of the Neotropical trans-Andean fish Ichthyoelephas longirostris, Steindachner 1879 (Characiformes, Prochilodontidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {3}, pages = {2194-2195}, doi = {10.3109/19401736.2014.982622}, pmid = {25423520}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Characiformes/*genetics ; DNA, Mitochondrial/genetics ; Gene Order/genetics ; Genes, Mitochondrial ; Genome/genetics ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; }, abstract = {Ichthyoelephas longirostris is a trans-Andean migratory species belonging to Prochilodontidae family. In this work, the mitochondrial genome of I. longirostris was sequenced by Illumina technology. The 16,840 bp mitogenome encodes 13 proteins, 22 tRNAs, 2 ribosomal RNAs and present a conserved synteny with others species of the Order Characiformes.}, }
@article {pmid25423519, year = {2016}, author = {Landínez-García, RM and Alzate, JF and Márquez, EJ}, title = {Mitochondrial genome of the Neotropical detritivore fish Curimata mivartii Steindachner 1878 (Characiformes, Curimatidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {3}, pages = {2196-2197}, doi = {10.3109/19401736.2014.982623}, pmid = {25423519}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Characiformes/*genetics ; DNA, Mitochondrial/genetics ; Gene Order/genetics ; Genes, Mitochondrial ; Genome/genetics ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; }, abstract = {Curimata mivartii is a detritivorous species Neotropical, which is of great importance to local fisheries and riverine ecosystems. In this work, the mitochondrial genome of C. mivartii was completely sequenced using a combination of 454 FLX(+) platform and Sanger/capillary sequencing. The mitogenome is 16,705 bp in length, encodes 13 proteins, 22 tRNAs, 2 ribosomal RNAs and exhibit perfect synteny with others Characiformes.}, }
@article {pmid25423518, year = {2016}, author = {Guo, Y and Bai, Q and Yan, T and Wang, Z and Liu, C}, title = {Mitogenomes of genus Pristipomoides, Lutjanus and Pterocaesio confirm Caesionidae nests in Lutjanidae.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {3}, pages = {2198-2199}, doi = {10.3109/19401736.2014.982624}, pmid = {25423518}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; DNA, Mitochondrial/genetics ; Fishes/genetics ; Gene Order/genetics ; Genes, Mitochondrial ; Genome/genetics ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; }, abstract = {In this study, the complete mitochondrial genome of Goldbanded jobfish (Perciformes: Lutjanidae: Etelinae: Pristipomoides multidens) was sequenced using long-PCR amplification (Accession No.: KF430626). The mitochondrial genome is highly homologous to those of other teleosts. Consensus tree based on phylogeny analysis of nucleotide sequences using the protein-coding regions combined sequences (apart from ND6) in 11 species supports the fact that Pristipomoides multidens of Etelinae and the cluster of Subfamily Lutjaninae remain the sister relationship, consistent with the traditional taxonomy, while the fusiliers (Pterocaesio tile) of family Caesionidae nested within the genus Lutjanus of family Lutjanidae and showed more closely relationship with the non-reddish snappers cluster including L. russellii and L. argentimaculatus. Conclusively, this mitogenomic phylogeny indicates that the Caesionidae is a synonym of family Lutjanidae. Given the morphologic and feeding diversity, we hypothesize that the variation of feeding systems of genus Lutjanus may drive the speciation of snappers and fusiliers.}, }
@article {pmid25423515, year = {2016}, author = {Shen, KN and Chen, CH and Hsiao, CD}, title = {Next generation sequencing yields the complete mitochondrial genome of the Hornlip mullet Plicomugil labiosus (Teleostei: Mugilidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {3}, pages = {2192-2193}, doi = {10.3109/19401736.2014.982621}, pmid = {25423515}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; DNA, Mitochondrial/genetics ; Gene Order/genetics ; Genes, Mitochondrial ; Genome/genetics ; Genome, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Smegmamorpha/*genetics ; Whole Genome Sequencing/methods ; }, abstract = {In this study, the complete mitogenome sequence of hornlip mullet Plicomugil labiosus (Teleostei: Mugilidae) has been sequenced by next-generation sequencing method. The assembled mitogenome, consisting of 16,829 bp, had the typical vertebrate mitochondrial gene arrangement, including 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a non-coding control region of D-loop. D-loop contains 1057 bp length is located between tRNA-Pro and tRNA-Phe. The overall base composition of P. labiosus is 28.0% for A, 29.3% for C, 15.5% for G and 27.2% for T. The complete mitogenome may provide essential and important DNA molecular data for further population, phylogenetic and evolutionary analysis for Mugilidae.}, }
@article {pmid25423509, year = {2016}, author = {Li, M and Li, Y and Chen, Z}, title = {Description of the mitochondrial genome of yellowtail scad Atule mate (Perciformes: Carangidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {3}, pages = {2186-2187}, doi = {10.3109/19401736.2014.982618}, pmid = {25423509}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; DNA, Mitochondrial/genetics ; Fishes/genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; }, abstract = {The yellowtail scad Atule mate is an economic fish species distributed throughout the tropical and subtropical oceans of the Indo-Pacific region. In the present study, we assembled the complete mitochondrial genome of A. mate from contiguous, overlapping segments amplified by PCR. The mitogenome sequence was 16,565 bp in length, consisting of 37 typical animal mitochondrial genes and 1 control region, same with the typical vertebrate mitochondrial gene arrangement. The overall base composition of the heavy strand was 28.4% for A, 27.6% for T, 16.3% for G, and 27.7% for C. Phylogenetic analyses using the protein-coding gene sequences reveal that genus Atule was most closely related to Alepes.}, }
@article {pmid25423508, year = {2016}, author = {Mao-Liang, R and Chen, B and Ouyang, X and Li, Z and Dong, LH}, title = {The complete mitochondrial genome of Xiangdong black goat (Capra hircus).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {3}, pages = {2180-2181}, doi = {10.3109/19401736.2014.982615}, pmid = {25423508}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; China ; DNA, Mitochondrial/genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Goats/*genetics ; Mitochondria/genetics ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; }, abstract = {Xiangdong black goat (Capra hircus) is a native breed of Hunan province in China. It is the first time that the complete mitochondrial genome sequence of Xiangdong black goat is reported in this work, which is determined through the PCR-based method. The total length of the mitognome is 16,641 bp, which contains 2 ribosomal RNA genes, 22 tRNA genes, 13 PCGs and 1 conntrol region (D-loop region). The total base composition of Lantang pig mitochondrial genome is 33.53% A, 13.12% G, 27.25% T and 26.09% C, in the order A > T > C > G. The complete mitochondrial genome of Xiangdong black goat provides an important data in genetic mechanism and the evolution genomes.}, }
@article {pmid25423506, year = {2016}, author = {Gong, X and Zhu, W and Bao, B}, title = {Complete mitochondrial DNA sequence of the Eastern keelback mullet Liza affinis.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {3}, pages = {2178-2179}, doi = {10.3109/19401736.2014.982614}, pmid = {25423506}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; DNA, Mitochondrial/genetics ; Fishes/genetics ; Gene Order/genetics ; Genes, Mitochondrial/genetics ; Genome/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Smegmamorpha/*genetics ; Whole Genome Sequencing/methods ; }, abstract = {Eastern keelback mullet (Liza affinis) inhabits inlet waters and estuaries of rivers. In this paper, we initially determined the complete mitochondrial genome of Liza affinis. The entire mtDNA sequence is 16,831 bp in length, including 2 rRNA genes, 22 tRNA genes, 13 protein-coding genes and 1 putative control region. Its order and numbers of genes are similar to most bony fishes.}, }
@article {pmid25421434, year = {2014}, author = {Kannan, S and Rogozin, IB and Koonin, EV}, title = {MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {237}, pmid = {25421434}, issn = {1471-2148}, support = {//Intramural NIH HHS/United States ; }, mesh = {Alphaproteobacteria/genetics/physiology ; Biological Evolution ; Cell Nucleus/genetics ; Eukaryota/*cytology/*genetics/physiology ; *Evolution, Molecular ; Genes, Mitochondrial ; Introns ; Mitochondria/genetics/physiology ; Symbiosis ; }, abstract = {BACKGROUND: Mitochondria are ubiquitous membranous organelles of eukaryotic cells that evolved from an alpha-proteobacterial endosymbiont and possess a small genome that encompasses from 3 to 106 genes. Accumulation of thousands of mitochondrial genomes from diverse groups of eukaryotes provides an opportunity for a comprehensive reconstruction of the evolution of the mitochondrial gene repertoire.<br><br>RESULTS: Clusters of orthologous mitochondrial protein-coding genes (MitoCOGs) were constructed from all available mitochondrial genomes and complemented with nuclear orthologs of mitochondrial genes. With minimal exceptions, the mitochondrial gene complements of eukaryotes are subsets of the superset of 66 genes found in jakobids. Reconstruction of the evolution of mitochondrial genomes indicates that the mitochondrial gene set of the last common ancestor of the extant eukaryotes was slightly larger than that of jakobids. This superset of mitochondrial genes likely represents an intermediate stage following the loss and transfer to the nucleus of most of the endosymbiont genes early in eukaryote evolution. Subsequent evolution in different lineages involved largely parallel transfer of ancestral endosymbiont genes to the nuclear genome. The intron density in nuclear orthologs of mitochondrial genes typically is nearly the same as in the rest of the genes in the respective genomes. However, in land plants, the intron density in nuclear orthologs of mitochondrial genes is almost 1.5-fold lower than the genomic mean, suggestive of ongoing transfer of functional genes from mitochondria to the nucleus.<br><br>CONCLUSIONS: The MitoCOGs are expected to become an important resource for the study of mitochondrial evolution. The nearly complete superset of mitochondrial genes in jakobids likely represents an intermediate stage in the evolution of eukaryotes after the initial, extensive loss and transfer of the endosymbiont genes. In addition, the bacterial multi-subunit RNA polymerase that is encoded in the jakobid mitochondrial genomes was replaced by a single-subunit phage-type RNA polymerase in the rest of the eukaryotes. These results are best compatible with the rooting of the eukaryotic tree between jakobids and the rest of the eukaryotes. The land plants are the only eukaryotic branch in which the gene transfer from the mitochondrial to the nuclear genome appears to be an active, ongoing process.}, }
@article {pmid25419960, year = {2015}, author = {Lam, SS and Martell, JD and Kamer, KJ and Deerinck, TJ and Ellisman, MH and Mootha, VK and Ting, AY}, title = {Directed evolution of APEX2 for electron microscopy and proximity labeling.}, journal = {Nature methods}, volume = {12}, number = {1}, pages = {51-54}, pmid = {25419960}, issn = {1548-7105}, support = {P41 GM103412/GM/NIGMS NIH HHS/United States ; 5R01GM077465-08/GM/NIGMS NIH HHS/United States ; R01GM086197/GM/NIGMS NIH HHS/United States ; //Howard Hughes Medical Institute/United States ; R01 GM077465/GM/NIGMS NIH HHS/United States ; R01 GM086197/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ascorbate Peroxidases/*biosynthesis/genetics ; COS Cells ; Calcium-Binding Proteins/analysis ; Cation Transport Proteins/analysis ; Chlorocebus aethiops ; Directed Molecular Evolution/methods ; HEK293 Cells ; HeLa Cells ; Humans ; Microscopy, Electron, Transmission/*methods ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins/analysis ; Proteomics/*methods ; Saccharomyces cerevisiae/enzymology ; }, abstract = {APEX is an engineered peroxidase that functions as an electron microscopy tag and a promiscuous labeling enzyme for live-cell proteomics. Because limited sensitivity precludes applications requiring low APEX expression, we used yeast-display evolution to improve its catalytic efficiency. APEX2 is far more active in cells, enabling the use of electron microscopy to resolve the submitochondrial localization of calcium uptake regulatory protein MICU1. APEX2 also permits superior enrichment of endogenous mitochondrial and endoplasmic reticulum membrane proteins.}, }
@article {pmid25416619, year = {2014}, author = {Sloan, DB and Wu, Z}, title = {History of plastid DNA insertions reveals weak deletion and at mutation biases in angiosperm mitochondrial genomes.}, journal = {Genome biology and evolution}, volume = {6}, number = {12}, pages = {3210-3221}, pmid = {25416619}, issn = {1759-6653}, mesh = {*Evolution, Molecular ; *Gene Deletion ; *Genome, Mitochondrial ; Genome, Plant ; *Genome, Plastid ; Magnoliopsida/*genetics ; *Mutagenesis, Insertional ; Phylogeny ; }, abstract = {Angiosperm mitochondrial genomes exhibit many unusual properties, including heterogeneous nucleotide composition and exceptionally large and variable genome sizes. Determining the role of nonadaptive mechanisms such as mutation bias in shaping the molecular evolution of these unique genomes has proven challenging because their dynamic structures generally prevent identification of homologous intergenic sequences for comparative analyses. Here, we report an analysis of angiosperm mitochondrial DNA sequences that are derived from inserted plastid DNA (mtpts). The availability of numerous completely sequenced plastid genomes allows us to infer the evolutionary history of these insertions, including the specific nucleotide substitutions and indels that have occurred because their incorporation into the mitochondrial genome. Our analysis confirmed that many mtpts have a complex history, including frequent gene conversion and multiple examples of horizontal transfer between divergent angiosperm lineages. Nevertheless, it is clear that the majority of extant mtpt sequence in angiosperms is the product of recent transfer (or gene conversion) and is subject to rapid loss/deterioration, suggesting that most mtpts are evolving relatively free from functional constraint. The evolution of mtpt sequences reveals a pattern of biased mutational input in angiosperm mitochondrial genomes, including an excess of small deletions over insertions and a skew toward nucleotide substitutions that increase AT content. However, these mutation biases are far weaker than have been observed in many other cellular genomes, providing insight into some of the notable features of angiosperm mitochondrial architecture, including the retention of large intergenic regions and the relatively neutral GC content found in these regions.}, }
@article {pmid25415968, year = {2015}, author = {Knie, N and Polsakiewicz, M and Knoop, V}, title = {Horizontal gene transfer of chlamydial-like tRNA genes into early vascular plant mitochondria.}, journal = {Molecular biology and evolution}, volume = {32}, number = {3}, pages = {629-634}, doi = {10.1093/molbev/msu324}, pmid = {25415968}, issn = {1537-1719}, mesh = {Chlamydiales/*genetics ; Chloroplasts/genetics ; DNA, Plant/*genetics ; Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/*genetics ; Genes, Mitochondrial ; Huperzia/*genetics ; Phylogeny ; Plants/classification/genetics ; RNA, Transfer/*genetics ; }, abstract = {Mitochondrial genomes of lycophytes are surprisingly diverse, including strikingly different transfer RNA (tRNA) gene complements: No mitochondrial tRNA genes are present in the spikemoss Selaginella moellendorffii, whereas 26 tRNAs are encoded in the chondrome of the clubmoss Huperzia squarrosa. Reinvestigating the latter we found that trnL(gag) and trnS(gga) had never before been identified in any other land plant mitochondrial DNA. Sensitive sequence comparisons showed these two tRNAs as well as trnN(guu) and trnS(gcu) to be very similar to their respective counterparts in chlamydial bacteria. We identified homologs of these chlamydial-type tRNAs also in other lycophyte, fern, and gymnosperm DNAs, suggesting horizontal gene transfer (HGT) into mitochondria in the early vascular plant stem lineages. These findings extend plant mitochondrial HGT to affect individual tRNA genes, to include bacterial donors, and suggest that Chlamydiae on top of their recently proposed key role in primary chloroplast establishment may also have participated in early tracheophyte genome evolution.}, }
@article {pmid25415967, year = {2015}, author = {Barreto, FS and Pereira, RJ and Burton, RS}, title = {Hybrid dysfunction and physiological compensation in gene expression.}, journal = {Molecular biology and evolution}, volume = {32}, number = {3}, pages = {613-622}, doi = {10.1093/molbev/msu321}, pmid = {25415967}, issn = {1537-1719}, mesh = {Animals ; Copepoda/genetics ; Female ; Gene Expression/*genetics ; Genetic Fitness/*genetics ; *Genetic Speciation ; Hybridization, Genetic/*genetics ; Male ; Mitochondria/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Sequence Analysis, RNA ; }, abstract = {The formation of new species is often a consequence of genetic incompatibilities accumulated between populations during allopatric divergence. When divergent taxa interbreed, these incompatibilities impact physiology and have a direct cost resulting in reduced hybrid fitness. Recent surveys of gene regulation in interspecific hybrids have revealed anomalous expression across large proportions of the genome, with 30-70% of all genes exhibiting transgressive expression (i.e., higher or lower levels compared with both parental taxa), and these were mostly in the direction of downregulation. However, as most of these studies have focused on pairs of species exhibiting high degrees of reproductive isolation, the association between regulatory disruption and reduced hybrid fitness prior to species formation remains unclear. Within the copepod species Tigriopus californicus, interpopulation hybrids at F2 or later generations show reduced fitness associated with mitochondrial dysfunction. Here we show that in contrast to studies of interspecific hybrids, only 1.2% of the transcriptome is transgressively expressed in F3+ interpopulation hybrids of T. californicus, and nearly 80% of these genes are overexpressed rather than underexpressed; remarkably, none of these genes are among those showing divergent expression between parentals, nor is magnitude of transgressive gene expression in hybrids dependent on levels of protein sequence divergence. Moreover, many genes with transgressive expression are components of functional pathways impacted by mitonuclear incompatibilities in hybrid T. californicus (e.g., oxidative phosphorylation and antioxidant response). Our results suggest that hybrid breakdown at early stages of speciation may result from initial incompatibilities amplified by the cost of compensatory physiological responses.}, }
@article {pmid25414329, year = {2014}, author = {Zhou, XL and Ruan, ZR and Wang, M and Fang, ZP and Wang, Y and Chen, Y and Liu, RJ and Eriani, G and Wang, ED}, title = {A minimalist mitochondrial threonyl-tRNA synthetase exhibits tRNA-isoacceptor specificity during proofreading.}, journal = {Nucleic acids research}, volume = {42}, number = {22}, pages = {13873-13886}, pmid = {25414329}, issn = {1362-4962}, mesh = {Anticodon ; Evolution, Molecular ; Gene Deletion ; Mitochondria/*enzymology ; Protein Structure, Tertiary ; RNA, Transfer, Thr/chemistry/*metabolism ; Saccharomyces cerevisiae/enzymology/genetics ; Threonine-tRNA Ligase/chemistry/genetics/*metabolism ; *Transfer RNA Aminoacylation ; }, abstract = {Yeast mitochondria contain a minimalist threonyl-tRNA synthetase (ThrRS) composed only of the catalytic core and tRNA binding domain but lacking the entire editing domain. Besides the usual tRNA(Thr)2, some budding yeasts, such as Saccharomyces cerevisiae, also contain a non-canonical tRNA(Thr)1 with an enlarged 8-nucleotide anticodon loop, reprograming the usual leucine CUN codons to threonine. This raises interesting questions about the aminoacylation fidelity of such ThrRSs and the possible contribution of the two tRNA(Thr)s during editing. Here, we found that, despite the absence of the editing domain, S. cerevisiae mitochondrial ThrRS (ScmtThrRS) harbors a tRNA-dependent pre-transfer editing activity. Remarkably, only the usual tRNA(Thr)2 stimulated pre-transfer editing, thus, establishing the first example of a synthetase exhibiting tRNA-isoacceptor specificity during pre-transfer editing. We also showed that the failure of tRNA(Thr)1 to stimulate tRNA-dependent pre-transfer editing was due to the lack of an editing domain. Using assays of the complementation of a ScmtThrRS gene knockout strain, we showed that the catalytic core and tRNA binding domain of ScmtThrRS co-evolved to recognize the unusual tRNA(Thr)1. In combination, the results provide insights into the tRNA-dependent editing process and suggest that tRNA-dependent pre-transfer editing takes place in the aminoacylation catalytic core.}, }
@article {pmid25409606, year = {2014}, author = {Sato, Y and Nakamura, T and Yamada, Y and Akita, H and Harashima, H}, title = {Multifunctional enveloped nanodevices (MENDs).}, journal = {Advances in genetics}, volume = {88}, number = {}, pages = {139-204}, doi = {10.1016/B978-0-12-800148-6.00006-7}, pmid = {25409606}, issn = {0065-2660}, mesh = {Adjuvants, Immunologic/chemistry/pharmacology ; DNA-Binding Proteins/chemistry ; Drug Delivery Systems/instrumentation/*methods ; *Gene Transfer Techniques ; Genetic Therapy/*methods ; Genetic Vectors/genetics/pharmacology ; Humans ; Lipids/chemistry ; Liposomes ; Membrane Fusion ; Mitochondria/genetics ; Nanomedicine/*instrumentation/methods ; Nanoparticles ; Nucleic Acids/administration &amp; dosage/chemistry ; Oligodeoxyribonucleotides/administration &amp; dosage/pharmacology ; Oligopeptides/chemistry ; Peptide Nucleic Acids/administration &amp; dosage/pharmacology ; Peptides/chemistry ; RNA, Small Interfering ; Transfection ; }, abstract = {It is anticipated that nucleic acid medicines will be in widespread use in the future, since they have the potential to cure diseases based on molecular mechanisms at the level of gene expression. However, intelligent delivery systems are required to achieve nucleic acid therapy, since they can perform their function only when they reach the intracellular site of action. We have been developing a multifunctional envelope-type nanodevice abbreviated as MEND, which consists of functional nucleic acids as a core and lipid envelope, and can control not only biodistribution but also the intracellular trafficking of nucleic acids. In this chapter, we review the development and evolution of the MEND by providing several successful examples, including the R8-MEND, the KALA-MEND, the MITO-Porter, the YSK-MEND, and the PALM.}, }
@article {pmid25399870, year = {2015}, author = {Stoll, K and Jonietz, C and Binder, S}, title = {In Arabidopsis thaliana two co-adapted cyto-nuclear systems correlate with distinct ccmC transcript sizes.}, journal = {The Plant journal : for cell and molecular biology}, volume = {81}, number = {2}, pages = {247-257}, doi = {10.1111/tpj.12724}, pmid = {25399870}, issn = {1365-313X}, mesh = {Arabidopsis/*genetics ; Arabidopsis Proteins/genetics/metabolism ; Genotype ; Mitochondrial Proteins/genetics/metabolism ; Polymorphism, Genetic/genetics ; }, abstract = {Plant mitochondrial transcripts undergo maturation processes at both termini. Although frequently observed, the post-transcriptional formation of mature 5' ends is still poorly understood. We now analyzed the processing of transcripts derived from the mitochondrial ccmC gene, coding for a component of the cytochrome c maturation system. In Arabidopsis thaliana (Arabidopsis) there are two mitochondrial ccmC configurations, discriminated by a 66-bp sequence segment located approximately 500 bp upstream of the ccmC gene. In Arabidopsis accessions these divergent mitochondrial genotypes correlate with the generation of two different 5' termini that map to positions around -484 in accession Columbia (Col ccmC genotype) or -390 in accession C24 relative to the translation start codon (C24 ccmC genotype). Previously we identified RNA PROCESSING FACTOR 3 (RPF3), a pentatricopeptide repeat (PPR) protein required for the maturation of ccmCmRNAs with -484 5' ends transcribed from the Col ccmC genotype. Now we identified several accessions defective in maturation of ccmC transcripts. Taking advantage of this natural genetic variation we identified RNA PROCESSING FACTOR 6 (RPF6), a PPR protein necessary for the generation of ccmCmRNAs with -390 5' ends transcribed from the C24 ccmC genotype. Both Col-type and C24-type accessions encode RPF3 and RPF6 so that they can process ccmC transcripts derived from the two different mitochondrial genotypes. These factors and their cognate RNA recognition sites in the different ccmC genotypes are an intriguing example for the evolution of two co-adapted cyto-nuclear systems required for the same process i.e. 5' maturation of ccmC transcripts.}, }
@article {pmid25398535, year = {2015}, author = {Kvansakul, M and Hinds, MG}, title = {The Bcl-2 family: structures, interactions and targets for drug discovery.}, journal = {Apoptosis : an international journal on programmed cell death}, volume = {20}, number = {2}, pages = {136-150}, doi = {10.1007/s10495-014-1051-7}, pmid = {25398535}, issn = {1573-675X}, mesh = {Animals ; Antineoplastic Agents/*pharmacology/therapeutic use ; *Apoptosis ; Drug Discovery ; Humans ; Models, Molecular ; Neoplasms/drug therapy ; Protein Interaction Domains and Motifs ; Protein Interaction Mapping ; Proto-Oncogene Proteins c-bcl-2/antagonists &amp; inhibitors/*physiology ; }, abstract = {Two phylogenetically and structurally distinct groups of proteins regulate stress induced intrinsic apoptosis, the programmed disassembly of cells. Together they form the B cell lymphoma-2 (Bcl-2) family. Bcl-2 proteins appeared early in metazoan evolution and are identified by the presence of up to four short conserved sequence blocks known as Bcl-2 homology (BH) motifs, or domains. The simple BH3-only proteins bear only a BH3-motif and are intrinsically disordered proteins and antagonize or activate the other group, the multi-motif Bcl-2 proteins that have up to four BH motifs, BH1-BH4. Multi-motif Bcl-2 proteins are either pro-survival or pro-apoptotic in action and have remarkably similar α-helical bundle structures that provide a binding groove formed from the BH1, BH2, and BH3-motifs for their BH3-bearing antagonists. In mammals a network of interactions between Bcl-2 members regulates mitochondrial outer membrane permeability (MOMP) and efflux of cytochrome c and other death inducing factors from mitochondria to initiate the apoptotic caspase cascade, but the molecular events leading to MOMP are uncertain. Dysregulation of the Bcl-2 family occurs in many diseases and pathogenic viruses have assimilated pro-survival Bcl-2 proteins to evade immune responses. Their role in disease has made the Bcl-2 family the focus of drug design attempts and clinical trials are showing promise for 'BH3-mimics', drugs that mimic the ability of BH3-only proteins to neutralize selected pro-survival proteins to induce cell death in tumor cells. This review focuses on the structural biology of Bcl-2 family proteins, their interactions and attempts to harness them as targets for drug design.}, }
@article {pmid25394329, year = {2015}, author = {Bolte, K and Rensing, SA and Maier, UG}, title = {The evolution of eukaryotic cells from the perspective of peroxisomes: phylogenetic analyses of peroxisomal beta-oxidation enzymes support mitochondria-first models of eukaryotic cell evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {37}, number = {2}, pages = {195-203}, doi = {10.1002/bies.201400151}, pmid = {25394329}, issn = {1521-1878}, mesh = {Eukaryotic Cells/*metabolism ; Fatty Acids/metabolism ; Mitochondria/metabolism ; Oxidation-Reduction ; Peroxisomes/*metabolism ; *Phylogeny ; }, abstract = {Beta-oxidation of fatty acids and detoxification of reactive oxygen species are generally accepted as being fundamental functions of peroxisomes. Additionally, these pathways might have been the driving force favoring the selection of this compartment during eukaryotic evolution. Here we performed phylogenetic analyses of enzymes involved in beta-oxidation of fatty acids in Bacteria, Eukaryota, and Archaea. These imply an alpha-proteobacterial origin for three out of four enzymes. By integrating the enzymes' history into the contrasting models on the origin of eukaryotic cells, we conclude that peroxisomes most likely evolved non-symbiotically and subsequent to the acquisition of mitochondria in an archaeal host cell.}, }
@article {pmid25394323, year = {2014}, author = {Bakhoum, AJ and Quilichini, Y and Miquel, J and Feliu, C and Bâ, CT and Marchand, B}, title = {Collyricloides massanae (Digenea, Collyriclidae): spermatozoon ultrastructure and phylogenetic importance.}, journal = {Parasite (Paris, France)}, volume = {21}, number = {}, pages = {59}, pmid = {25394323}, issn = {1776-1042}, support = {U17 CE002013/CE/NCIPC CDC HHS/United States ; }, mesh = {Animals ; Axoneme/ultrastructure ; France ; Male ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Murinae/parasitology ; Phylogeny ; Rodent Diseases/parasitology ; Spermatozoa/*ultrastructure ; Trematoda/classification/*cytology ; Trematode Infections/parasitology/veterinary ; }, abstract = {The spermatological characteristics of Collyricloides massanae (Digenea: Collyriclidae), a parasite of Apodemus sylvaticus caught in France, were studied by means of transmission electron microscopy. The mature sperm of C. massanae presents two axonemes of different lengths with the 9 + "1" pattern of the Trepaxonemata, two bundles of parallel cortical microtubules, external ornamentation of the plasma membrane, spine-like bodies, one mitochondrion, a nucleus and granules of glycogen. An analysis of spermatological organisation emphasised some differences between the mature spermatozoon of C. massanae and those reported in the Gorgoderoidea species studied to date, specially belonging to the families Dicrocoeliidae, Paragonimidae and Troglotrematidae. The ultrastructural criteria described in C. massanae such as the morphology of both anterior and posterior spermatozoon extremities, the association "external ornamentation+cortical microtubules", the type 2 of external ornamentation and the spine-like bodies would allow us to bring closer the Collyriclidae to Microphalloidea. However, further ultrastructural and molecular studies are needed particularly in the unexplored taxa in order to fully resolve the phylogenetic position of the Collyriclidae.}, }
@article {pmid25393008, year = {2014}, author = {Vasconcellos, Rde S and Mariotini-Moura, C and Gomes, RS and Serafim, TD and Firmino, Rde C and Silva E Bastos, M and Castro, FF and Oliveira, CM and Borges-Pereira, L and de Souza, AC and de Souza, RF and Gómez, GA and Pinheiro, Ada C and Maciel, TE and Silva-Júnior, A and Bressan, GC and Almeida, MR and Baqui, MM and Afonso, LC and Fietto, JL}, title = {Leishmania infantum ecto-nucleoside triphosphate diphosphohydrolase-2 is an apyrase involved in macrophage infection and expressed in infected dogs.}, journal = {PLoS neglected tropical diseases}, volume = {8}, number = {11}, pages = {e3309}, pmid = {25393008}, issn = {1935-2735}, mesh = {Amino Acid Sequence ; Animals ; Apyrase/chemistry/genetics/*metabolism ; Cell Line ; Dogs ; Female ; Leishmania infantum/chemistry/cytology/*enzymology/metabolism ; Leishmaniasis, Visceral/*parasitology ; Lymph Nodes/parasitology ; Macrophages/*parasitology ; Mice ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/chemistry/genetics/*metabolism ; Rabbits ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; }, abstract = {BACKGROUND: Visceral leishmaniasis is an important tropical disease, and Leishmania infantum chagasi (synonym of Leishmania infantum) is the main pathogenic agent of visceral leishmaniasis in the New World. Recently, ecto-nucleoside triphosphate diphosphohydrolases (E-NTPDases) were identified as enablers of infection and virulence factors in many pathogens. Two putative E-NTPDases (∼70 kDa and ∼45 kDa) have been found in the L. infantum genome. Here, we studied the ∼45 kDa E-NTPDase from L. infantum chagasi to describe its natural occurrence, biochemical characteristics and influence on macrophage infection.<br><br>We used live L. infantum chagasi to demonstrate its natural ecto-nucleotidase activity. We then isolated, cloned and expressed recombinant rLicNTPDase-2 in bacterial system. The recombinant rLicNTPDase-2 hydrolyzed a wide variety of triphosphate and diphosphate nucleotides (GTP> GDP &#x200a;=&#x200a; UDP> ADP> UTP &#x200a;=&#x200a; ATP) in the presence of calcium or magnesium. In addition, rLicNTPDase-2 showed stable activity over a pH range of 6.0 to 9.0 and was partially inhibited by ARL67156 and suramin. Microscopic analyses revealed the presence of this protein on cell surfaces, vesicles, flagellae, flagellar pockets, kinetoplasts, mitochondria and nuclei. The blockade of E-NTPDases using antibodies and competition led to lower levels of parasite adhesion and infection of macrophages. Furthermore, immunohistochemistry showed the expression of E-NTPDases in amastigotes in the lymph nodes of naturally infected dogs from an area of endemic visceral leishmaniasis.<br><br>CONCLUSIONS/SIGNIFICANCE: In this work, we cloned, expressed and characterized the NTPDase-2 from L. infantum chagasi and demonstrated that it functions as a genuine enzyme from the E-NTPDase/CD39 family. We showed that E-NTPDases are present on the surface of promastigotes and in other intracellular locations. We showed, for the first time, the broad expression of LicNTPDases in naturally infected dogs. Additionally, the blockade of NTPDases led to lower levels of in vitro adhesion and infection, suggesting that these proteins are possible targets for rational drug design.}, }
@article {pmid25391846, year = {2015}, author = {Erpenbeck, D and Aryasari, R and Hooper, JN and Wörheide, G}, title = {A mitochondrial intron in a verongid sponge.}, journal = {Journal of molecular evolution}, volume = {80}, number = {1}, pages = {13-17}, pmid = {25391846}, issn = {1432-1432}, mesh = {Animals ; Genome, Mitochondrial ; Introns/*genetics ; Mitochondria/*genetics ; Phylogeny ; Porifera/classification/*genetics ; }, abstract = {We discovered for the first time a mitochondrial intron in a non-tetillid demosponge, which sheds new light on the interpretation of mitochondrial intron evolution among non-bilaterian animals and has consequences for phylogenetic and DNA barcoding studies. The newly discovered class 1 intron of Aplysinella rhax (Verongida) CO1 has an ORF for a putative LAGLIDADG-type and resembles other sponge and cnidarian mitochondrial introns. Our analysis of the Aplysinella rhax intron underlines that the patchy distribution of introns in sponges is caused by a combination of horizontal and vertical transmission. Further implications for CO1 phylogenetic and barcoding projects are discussed.}, }
@article {pmid25390889, year = {2014}, author = {Dejong, CA and Wilson, JY}, title = {The Cytochrome P450 superfamily complement (CYPome) in the annelid Capitella teleta.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e107728}, pmid = {25390889}, issn = {1932-6203}, mesh = {Amino Acid Motifs ; Animals ; Annelida/*genetics ; Cytochrome P-450 Enzyme System/chemistry/*genetics ; Mitochondria/metabolism ; Molecular Sequence Annotation ; Phylogeny ; Species Specificity ; Steroids/chemistry ; Sterol 14-Demethylase/chemistry ; Transcription, Genetic ; Xenobiotics/chemistry ; }, abstract = {The Cytochrome P450 super family (CYP) is responsible for a wide range of functions in metazoans, having roles in both exogenous and endogenous substrate metabolism. Annelids are known to metabolize polycyclic aromatic hydrocarbons (PAHs) and produce estrogen. CYPs are postulated to be key enzymes in these processes in annelids. In this study, the CYP complement (CYPome) of the annelid Capitella teleta has been robustly identified and annotated with the genome assembly available. Phylogenetic analyses were performed to understand the evolutionary relationships between CYPs in C. teleta and other species. Predictions of which CYPs are potentially involved in both PAH metabolism and steroidogensis were made based on phylogeny. Annotation of 84 full length and 12 partial CYP sequences predicted a total of 96 functional CYPs in C. teleta. A further 13 CYP fragments were found but these may be pseudogenes. The C. teleta CYPome contained 24 novel CYP families and seven novel CYP subfamilies within existing families. A phylogenetic analysis identified that the C. teleta sequences were found in 9 of the 11 metazoan CYP clans. Two CYPs, CYP3071A1 and CYP3072A1, did not cluster with any metazoan CYP clans. We found xenobiotic response elements (XREs) upstream of C. teleta CYPs related to vertebrate CYP1 (CYP3060A1, CYP3061A1) and from families with reported transcriptional upregulation in response to PAH exposure (CYP4, CYP331). C. teleta had a CYP51A1 with ∼65% identity to vertebrate CYP51A1 sequences and has been predicted to have lanosterol 14 α-demethylase activity. CYP376A1, CYP3068A1, CYP3069A1, and CYP3070A1 were the most appropriate candidates for steroidogenesis genes based on their phylogeny and warrant further analyses, though no specific aromatase (estrogen synthesis) candidates were found. Presence of XREs upstream of C. teleta CYPs may indicate a functional aryl hydrocarbon receptor in C. teleta and candidate CYPs for studies of PAH metabolism.}, }
@article {pmid25389773, year = {2014}, author = {Vahtera, V and Edgecombe, GD}, title = {First molecular data and the phylogenetic position of the millipede-like centipede Edentistoma octosulcatum Tömösváry, 1882 (Chilopoda: Scolopendromorpha: Scolopendridae).}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e112461}, pmid = {25389773}, issn = {1932-6203}, mesh = {Animals ; Arthropods/anatomy &amp; histology/*classification/genetics ; Carnivory/physiology ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Genetic Markers ; Genetic Speciation ; Malaysia ; Mitochondria/genetics ; *Phylogeny ; Phylogeography ; }, abstract = {Edentistoma octosulcatum Tömösváry, 1882, is a rare, superficially millipede-like centipede known only from Borneo and the Philippines. It is unique within the order Scolopendromorpha for its slow gait, robust tergites, and highly modified gizzard and mandible morphology. Not much is known about the biology of the species but it has been speculated to be arboreal with a possibly vegetarian diet. Until now its phylogenetic position within the subfamily Otostigminae has been based only on morphological characters, being variably ranked as a monotypic tribe (Arrhabdotini) or classified with the Southeast Asian genus Sterropristes Attems, 1934. The first molecular data for E. octosulcatum sourced from a newly collected specimen from Sarawak were analysed with and without morphology. Parsimony analysis of 122 morphological characters together with two nuclear and two mitochondrial loci resolves Edentistoma as sister group to three Indo-Australian species of Rhysida, this clade in turn grouping with Ethmostigmus, whereas maximum likelihood and parsimony analyses of the molecular data on their own ally Edentistoma with species of Otostigmus. A position of Edentistoma within Otostigmini (rather than being its sister group as predicted by the Arrhabdotini hypothesis) is consistently retrieved under different analytical conditions, but support values within the subfamily remain low for most nodes. The species exhibits strong pushing behaviour, suggestive of burrowing habits. Evidence against a suggested vegetarian diet is provided by observation of E. octosulcatum feeding on millipedes in the genus Trachelomegalus.}, }
@article {pmid25377452, year = {2014}, author = {Padua, MV and Zeh, DW and Bonilla, MM and Zeh, JA}, title = {Sisters' curse: sexually antagonistic effects constrain the spread of a mitochondrial haplogroup superior in sperm competition.}, journal = {Proceedings. Biological sciences}, volume = {281}, number = {1797}, pages = {}, pmid = {25377452}, issn = {1471-2954}, mesh = {Animals ; Arachnida/*genetics/physiology ; Biological Evolution ; DNA, Mitochondrial/*chemistry ; Female ; *Haplotypes ; Male ; Phylogeny ; Sequence Analysis, DNA ; Sexual Behavior, Animal ; Spermatozoa/*physiology ; }, abstract = {Maternal inheritance of mitochondria creates a sex-specific selective sieve with implications for male longevity, disease susceptibility and infertility. Because males are an evolutionary dead end for mitochondria, mitochondrial mutations that are harmful or beneficial to males but not females cannot respond directly to selection. Although the importance of this male/female asymmetry in evolutionary response depends on the extent to which mitochondrial mutations exert antagonistic effects on male and female fitness, few studies have documented sex-specific selection acting on mitochondria. Here, we exploited the discovery of two highly divergent mitochondrial haplogroups (A and B2) in central Panamanian populations of the pseudoscorpion Cordylochernes scorpioides. Next-generation sequencing and phylogenetic analyses suggest that selection on the ND4 and ND4L mitochondrial genes may partially explain sexually antagonistic mitochondrial effects on reproduction. Males carrying the rare B2 mitochondrial haplogroup enjoy a marked advantage in sperm competition, but B2 females are significantly less sexually receptive at second mating than A females. This reduced propensity for polyandry is likely to significantly reduce female lifetime reproductive success, thereby limiting the spread of the male beneficial B2 haplogroup. Our findings suggest that maternal inheritance of mitochondria and sexually antagonistic selection can constrain male adaptation and sexual selection in nature.}, }
@article {pmid25375139, year = {2014}, author = {Zheng, X and Zhang, X and Ding, L and Lee, JR and Weinberger, PM and Dynan, WS}, title = {Synergistic effect of high charge and energy particle radiation and chronological age on biomarkers of oxidative stress and tissue degeneration: a ground-based study using the vertebrate laboratory model organism Oryzias latipes.}, journal = {PloS one}, volume = {9}, number = {11}, pages = {e111362}, pmid = {25375139}, issn = {1932-6203}, mesh = {Aging/*radiation effects ; Animals ; Biomarkers/metabolism ; *Cosmic Radiation ; Lipid Peroxidation/radiation effects ; Liver/metabolism/*radiation effects ; Mitochondria/metabolism/radiation effects ; Oryzias ; Oxidative Stress/*radiation effects ; Space Flight ; }, abstract = {High charge and energy (HZE) particles are a main hazard of the space radiation environment. Uncertainty regarding their health effects is a limiting factor in the design of human exploration-class space missions, that is, missions beyond low earth orbit. Previous work has shown that HZE exposure increases cancer risk and elicits other aging-like phenomena in animal models. Here, we investigate how a single exposure to HZE particle radiation, early in life, influences the subsequent age-dependent evolution of oxidative stress and appearance of degenerative tissue changes. Embryos of the laboratory model organism, Oryzias latipes (Japanese medaka fish), were exposed to HZE particle radiation at doses overlapping the range of anticipated human exposure. A separate cohort was exposed to reference γ-radiation. Survival was monitored for 750 days, well beyond the median lifespan. The population was also sampled at intervals and liver tissue was subjected to histological and molecular analysis. HZE particle radiation dose and aging contributed synergistically to accumulation of lipid peroxidation products, which are a marker of chronic oxidative stress. This was mirrored by a decline in PPARGC1A mRNA, which encodes a transcriptional co-activator required for expression of oxidative stress defense genes and for mitochondrial maintenance. Consistent with chronic oxidative stress, mitochondria had an elongated and enlarged ultrastructure. Livers also had distinctive, cystic lesions. Depending on the endpoint, effects of γ-rays in the same dose range were either lesser or not detected. Results provide a quantitative and qualitative framework for understanding relative contributions of HZE particle radiation exposure and aging to chronic oxidative stress and tissue degeneration.}, }
@article {pmid25368074, year = {2014}, author = {Hao, JJ and Hao, JS and Sun, XY and Zhang, LL and Yang, Q}, title = {The complete mitochondrial genomes of the Fenton's wood white, Leptidea morsei, and the lemon emigrant, Catopsilia pomona.}, journal = {Journal of insect science (Online)}, volume = {14}, number = {}, pages = {130}, pmid = {25368074}, issn = {1536-2442}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Butterflies/*classification/*genetics ; Codon ; DNA, Intergenic/genetics ; DNA, Mitochondrial/genetics ; *Genome, Insect ; *Genome, Mitochondrial ; Insect Proteins/genetics ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The complete mitochondrial genomes of Leptidea morsei Fenton (Lepidoptera: Pieridae: Dis-morphiinae) and Catopsilia pomona (F.) (Lepidoptera: Pieridae: Coliadinae) were determined to be 15,122 and 15,142 bp in length, respectively, with that of L. morsei being the smallest among all known butterflies. Both mitogenomes contained 37 genes and an A+T-rich region, with the gene order identical to those of other butterflies, except for the presence of a tRNA-like insertion, tRNA(Leu) (UUR), in C. pomona. The nucleotide compositions of both genomes were higher in A and T (80.2% for L. morsei and 81.3% for C. pomona) than C and G; the A+T bias had a significant effect on the codon usage and the amino acid composition. The protein-coding genes utilized the standard mitochondrial start codon ATN, except the COI gene using CGA as the initiation codon, as reported in other butterflies. The intergenic spacer sequence between the tRNA(Ser) (UCN) and ND1 genes contained the ATACTAA motif. The A+T-rich region harbored a poly-T stretch and a conserved ATAGA motif located at the end of the region. In addition, there was a triplicated 23 bp repeat and a microsatellite-like (TA)9(AT)3 element in the A+T-rich region of the L. morsei mitogenome, while in C. pomona, there was a duplicated 24 bp repeat element and a microsatellite-like (TA)9 element. The phylogenetic trees of the main butterfly lineages (Hesperiidae, Papilionidae, Pieridae, Nymphalidae, Lycaenidae, and Riodinidae) were reconstructed with maximum likelihood and Bayesian inference methods based on the 13 concatenated nucleotide sequences of protein-coding genes, and both trees showed that the Pieridae family is sister to Lycaenidae. Although this result contradicts the traditional morphologically based views, it agrees with other recent studies based on mitochondrial genomic data.}, }
@article {pmid25367071, year = {2015}, author = {Avelange-Macherel, MH and Payet, N and Lalanne, D and Neveu, M and Tolleter, D and Burstin, J and Macherel, D}, title = {Variability within a pea core collection of LEAM and HSP22, two mitochondrial seed proteins involved in stress tolerance.}, journal = {Plant, cell &amp; environment}, volume = {38}, number = {7}, pages = {1299-1311}, doi = {10.1111/pce.12480}, pmid = {25367071}, issn = {1365-3040}, mesh = {Amino Acid Sequence ; Genotype ; Heat-Shock Proteins/genetics/*metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Pisum sativum/genetics/growth &amp; development/*physiology ; Plant Proteins/genetics/metabolism ; Protein Isoforms ; Seeds/metabolism ; Sequence Alignment ; Stress, Physiological ; Temperature ; }, abstract = {LEAM, a late embryogenesis abundant protein, and HSP22, a small heat shock protein, were shown to accumulate in the mitochondria during pea (Pisum sativum L.) seed development, where they are expected to contribute to desiccation tolerance. Here, their expression was examined in seeds of 89 pea genotypes by Western blot analysis. All genotypes expressed LEAM and HSP22 in similar amounts. In contrast with HSP22, LEAM displayed different isoforms according to apparent molecular mass. Each of the 89 genotypes harboured a single LEAM isoform. Genomic and RT-PCR analysis revealed four LEAM genes differing by a small variable indel in the coding region. These variations were consistent with the apparent molecular mass of each isoform. Indels, which occurred in repeated domains, did not alter the main properties of LEAM. Structural modelling indicated that the class A α-helix structure, which allows interactions with the mitochondrial inner membrane in the dry state, was preserved in all isoforms, suggesting functionality is maintained. The overall results point out the essential character of LEAM and HSP22 in pea seeds. LEAM variability is discussed in terms of pea breeding history as well as LEA gene evolution mechanisms.}, }
@article {pmid25361999, year = {2015}, author = {Stenvinkel, P}, title = {Obesity--a disease with many aetiologies disguised in the same oversized phenotype: has the overeating theory failed?.}, journal = {Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association}, volume = {30}, number = {10}, pages = {1656-1664}, doi = {10.1093/ndt/gfu338}, pmid = {25361999}, issn = {1460-2385}, mesh = {Diet/*adverse effects ; Humans ; Hyperphagia/*physiopathology ; Metabolic Syndrome/*etiology ; Mitochondria/metabolism ; Obesity/etiology/*physiopathology ; Phenotype ; }, abstract = {Evolution has led to metabolic thrift in humans--a genetic heritage that, when exposed to the modern 'obesogenic' milieu with energy-dense food and a sedentary lifestyle, predisposes to obesity. The current paradigm that overeating of easily digestible carbohydrates and the resulting imbalance between energy in and out as the cause of overweight has recently been challenged. Indeed, studies suggest that the host response to various nutrients contributes to overeating and fat accumulation. Alterations in neurotransmitter functions, changes in the epigenome, dysbiosis of gut microbiota and effects of specific nutrients (or lack of such nutrients) on mitochondrial function and signalling pathways may promote fat accumulation independent of calories. Whereas nutrients that stimulate generation of uric acid (such as fructose and purine-rich food) cause insulin resistance and fat accumulation, other nutrients (such as antioxidants, plant food, probiotics, nuts, soy and omega-3) counteract the negative effects of a calorie-rich diet by salutary effects on mitochondrial biogenesis. Thus, the specific metabolic effects of different nutrients may be more important than its total energy content. By studying the impact of nutrients on mitochondrial health, as well as the trans-generational impact of nutrients during fetal life, and how specific bacterial species correlate with fat mass accumulation, new dietary targets for obesity management may emerge. Overeating and overshooting of calories could to a large extent represent a symptom rather than a cause of obesity; therefore, hypocaloric diets should probably not be the main, and certainly not the only, focus for treatment of the obese patient.}, }
@article {pmid25360420, year = {2014}, author = {Vitetta, L and Hall, S and Linnane, AW}, title = {Live probiotic cultures and the gastrointestinal tract: symbiotic preservation of tolerance whilst attenuating pathogenicity.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {143}, pmid = {25360420}, issn = {2235-2988}, mesh = {Animals ; Bacterial Physiological Phenomena ; Gastrointestinal Tract/*microbiology ; Host-Pathogen Interactions ; Humans ; Intestinal Mucosa/immunology/metabolism ; Mitochondria/metabolism ; *Probiotics ; Signal Transduction ; Symbiosis ; }, abstract = {Bacteria comprise the earliest form of independent life on this planet. Bacterial development has included co-operative symbiosis with plants (e.g., Leguminosae family and nitrogen fixing bacteria in soil) and animals (e.g., the gut microbiome). A fusion event of two prokaryotes evolutionarily gave rise to the eukaryote cell in which mitochondria may be envisaged as a genetically functional mosaic, a relic from one of the prokaryote cells. The discovery of bacterial inhibitors such chloramphenicol and others has been exploited to highlight mitochondria as arising from a bacterial progenitor. As such the evolution of human life has been complexly connected to bacterial activity. This is embodied, by the appearance of mitochondria in eukaryotes (alphaproteobacteria contribution), a significant endosymbiotic evolutionary event. During the twentieth century there was an increasing dependency on anti-microbials as mainline therapy against bacterial infections. It is only comparatively recently that the essential roles played by the gastrointestinal tract (GIT) microbiome in animal health and development has been recognized as opposed to the GIT microbiome being a toxic collection of micro-organisms. It is now well-documented that the GIT microbiome is comprised of a complex cohort of commensal and potentially pathogenic bacteria. Microbial interactions in the GIT provide the necessary cues for the development of regulated signals [in part by reactive oxygen species (ROS)] that promote immunological tolerance, metabolic regulation and stability, and other factors, which may then help control local and extra-intestinal end organ (e.g., kidneys) physiology. Pharmacobiotics, the administration of live probiotic cultures is an exciting growth area of potential therapeutics, developing together with an increased scientific understanding of GIT microbiome symbiosis in health and disease. Hence probiotic bacteria may provide a therapeutic connect with the GIT microbiome that can rescue mitochondrial dysfunction by linking a biologically plausible cellular signaling program (ROS reliant) between the human host and its microbiome cohort for a continued co-operative symbiosis that maintains homeostasis favorable to both.}, }
@article {pmid25359943, year = {2014}, author = {Pennisi, E}, title = {Microbiology. Modern symbionts inside cells mimic organelle evolution.}, journal = {Science (New York, N.Y.)}, volume = {346}, number = {6209}, pages = {532-533}, doi = {10.1126/science.346.6209.532}, pmid = {25359943}, issn = {1095-9203}, mesh = {Animals ; *Bacteria ; *Biological Evolution ; Cells/*microbiology/*ultrastructure ; *Chloroplasts ; Hemiptera/microbiology/ultrastructure ; Humans ; *Mitochondria ; Plants/microbiology/ultrastructure ; *Symbiosis ; }, }
@article {pmid25359921, year = {2014}, author = {Aledo, JC and Valverde, H and Ruíz-Camacho, M and Morilla, I and López, FD}, title = {Protein-protein interfaces from cytochrome c oxidase I evolve faster than nonbinding surfaces, yet negative selection is the driving force.}, journal = {Genome biology and evolution}, volume = {6}, number = {11}, pages = {3064-3076}, pmid = {25359921}, issn = {1759-6653}, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Cattle ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/chemistry/*genetics/metabolism ; *Evolution, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Subunits/chemistry/genetics/metabolism ; *Selection, Genetic ; }, abstract = {Respiratory complexes are encoded by two genomes (mitochondrial DNA [mtDNA] and nuclear DNA [nDNA]). Although the importance of intergenomic coadaptation is acknowledged, the forces and constraints shaping such coevolution are largely unknown. Previous works using cytochrome c oxidase (COX) as a model enzyme have led to the so-called "optimizing interaction" hypothesis. According to this view, mtDNA-encoded residues close to nDNA-encoded residues evolve faster than the rest of positions, favoring the optimization of protein-protein interfaces. Herein, using evolutionary data in combination with structural information of COX, we show that failing to discern the effects of interaction from other structural and functional effects can lead to deceptive conclusions such as the "optimizing hypothesis." Once spurious factors have been accounted for, data analysis shows that mtDNA-encoded residues engaged in contacts are, in general, more constrained than their noncontact counterparts. Nevertheless, noncontact residues from the surface of COX I subunit are a remarkable exception, being subjected to an exceptionally high purifying selection that may be related to the maintenance of a suitable heme environment. We also report that mtDNA-encoded residues involved in contacts with other mtDNA-encoded subunits are more constrained than mtDNA-encoded residues interacting with nDNA-encoded polypeptides. This differential behavior cannot be explained on the basis of predicted thermodynamic stability, as interactions between mtDNA-encoded subunits contribute more weakly to the complex stability than those interactions between subunits encoded by different genomes. Therefore, the higher conservation observed among mtDNA-encoded residues involved in intragenome interactions is likely due to factors other than structural stability.}, }
@article {pmid25359314, year = {2014}, author = {Harl, J and Páll-Gergely, B and Kirchner, S and Sattmann, H and Duda, M and Kruckenhauser, L and Haring, E}, title = {Phylogeography of the land snail genus Orcula (Orculidae, Stylommatophora) with emphasis on the Eastern Alpine taxa: speciation, hybridization and morphological variation.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {223}, pmid = {25359314}, issn = {1471-2148}, mesh = {Animals ; Biodiversity ; *Genetic Speciation ; Hybridization, Genetic ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Snails/*classification/*genetics ; }, abstract = {BACKGROUND: The Central and Southern European mountain ranges represent important biodiversity hotspots and show high levels of endemism. In the land snail genus Orcula Held, 1837 nine species are distributed in the Alps and a few taxa inhabit the Carpathians, the Dinarids and the Western Black Sea region. In order to elucidate the general patterns of temporal and geographic diversification, mitochondrial and nuclear markers were analyzed in all 13 Orcula species. We particularly aimed to clarify whether the Alpine taxa represent a monophyletic group and if the local species diversity is rather the result of isolation in geographically separated Pleistocene glacial refuges or earlier Tertiary and Quaternary palaeogeographic events. In order to test if patterns of molecular genetic and morphological differentiation were congruent and/or if hybridization had occurred, shell morphometric investigations were performed on the Orcula species endemic to the Alps.<br><br>RESULTS: The phylogenetic trees resulting from the analyses of both the mitochondrial (COI, 12S and 16S) and the nuclear (H4/H3) data sets revealed three main groups, which correspond to the three subgenera Orcula, Illyriobanatica and Hausdorfia. The reconstruction of the historic geographic ranges suggested that the genus originated in the Dinarides during the Middle Miocene and first colonized the Alps during the Late Miocene, giving rise to the most diverse subgenus Orcula. Within the latter subgenus (including all Alpine endemics) almost all species were differentiated by both molecular genetic markers and by shell morphometrics, except O. gularis and O. pseudodolium.<br><br>CONCLUSIONS: The present study confirms the importance of the Alps as biodiversity hotspot and origin center of land snail diversity. The species diversity in the subgenus Orcula was likely promoted by Miocene to Pliocene palaeogeographic events and the insular distribution of preferred limestone areas. In some cases, speciation events could be linked to the divergence of populations in glacial refuges during the Pleistocene. Sporadic contact between geographically separated and reproductively not yet isolated populations led to intermixture of haplogroups within species and even hybridization and mitochondrial capture between species.}, }
@article {pmid25352854, year = {2014}, author = {Day, PM and Potter, D and Inoue, K}, title = {Evolution and targeting of Omp85 homologs in the chloroplast outer envelope membrane.}, journal = {Frontiers in plant science}, volume = {5}, number = {}, pages = {535}, pmid = {25352854}, issn = {1664-462X}, abstract = {Translocon at the outer-envelope-membrane of chloroplasts 75 (Toc75) is the core component of the chloroplast protein import machinery. It belongs to the Omp85 family whose members exist in various Gram-negative bacteria, mitochondria, and chloroplasts of eukaryotes. Chloroplasts of Viridiplantae contain another Omp85 homolog called outer envelope protein 80 (OEP80), whose exact function is unknown. In addition, the Arabidopsis thaliana genome encodes truncated forms of Toc75 and OEP80. Multiple studies have shown a common origin of the Omp85 homologs of cyanobacteria and chloroplasts but their results about evolutionary relationships among cyanobacterial Omp85 (cyanoOmp85), Toc75, and OEP80 are inconsistent. The bipartite targeting sequence-dependent sorting of Toc75 has been demonstrated but the targeting mechanisms of other chloroplast Omp85 homologs remain largely unexplored. This study was aimed to address these unresolved issues in order to further our understanding of chloroplast evolution. Sequence alignments and recently determined structures of bacterial Omp85 homologs were used to predict structures of chloroplast Omp85 homologs. The results enabled us to identify amino acid residues that may indicate functional divergence of Toc75 from cyanoOmp85 and OEP80. Phylogenetic analyses using Omp85 homologs from various cyanobacteria and chloroplasts provided strong support for the grouping of Toc75 and OEP80 sister to cyanoOmp85. However, this support was diminished when the analysis included Omp85 homologs from other bacteria and mitochondria. Finally, results of import assays using isolated chloroplasts support outer membrane localization of OEP80tr and indicate that OEP80 may carry a cleavable targeting sequence.}, }
@article {pmid25350791, year = {2014}, author = {Baum, DA and Baum, B}, title = {An inside-out origin for the eukaryotic cell.}, journal = {BMC biology}, volume = {12}, number = {}, pages = {76}, pmid = {25350791}, issn = {1741-7007}, mesh = {*Biological Evolution ; Cell Nucleus/ultrastructure ; Cell Wall/ultrastructure ; Eukaryotic Cells/*metabolism ; Models, Biological ; Phylogeny ; Prokaryotic Cells/*metabolism ; }, abstract = {BACKGROUND: Although the origin of the eukaryotic cell has long been recognized as the single most profound change in cellular organization during the evolution of life on earth, this transition remains poorly understood. Models have always assumed that the nucleus and endomembrane system evolved within the cytoplasm of a prokaryotic cell.<br><br>RESULTS: Drawing on diverse aspects of cell biology and phylogenetic data, we invert the traditional interpretation of eukaryotic cell evolution. We propose that an ancestral prokaryotic cell, homologous to the modern-day nucleus, extruded membrane-bound blebs beyond its cell wall. These blebs functioned to facilitate material exchange with ectosymbiotic proto-mitochondria. The cytoplasm was then formed through the expansion of blebs around proto-mitochondria, with continuous spaces between the blebs giving rise to the endoplasmic reticulum, which later evolved into the eukaryotic secretory system. Further bleb-fusion steps yielded a continuous plasma membrane, which served to isolate the endoplasmic reticulum from the environment.<br><br>CONCLUSIONS: The inside-out theory is consistent with diverse kinds of data and provides an alternative framework by which to explore and understand the dynamic organization of modern eukaryotic cells. It also helps to explain a number of previously enigmatic features of cell biology, including the autonomy of nuclei in syncytia and the subcellular localization of protein N-glycosylation, and makes many predictions, including a novel mechanism of interphase nuclear pore insertion.}, }
@article {pmid25350281, year = {2014}, author = {Li, M and Pang, Z and Xiao, W and Liu, X and Zhang, Y and Yu, D and Yang, M and Yang, Y and Hu, J and Luo, K}, title = {A transcriptome analysis suggests apoptosis-related signaling pathways in hemocytes of Spodoptera litura after parasitization by Microplitis bicoloratus.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e110967}, pmid = {25350281}, issn = {1932-6203}, mesh = {Animals ; *Apoptosis ; Cell Membrane Permeability ; DNA Fragmentation ; Gene Expression Profiling ; *Gene Expression Regulation ; Hemocytes/cytology/*metabolism/parasitology ; Host-Parasite Interactions ; Immunosuppression Therapy ; Lectins, C-Type/chemistry ; Mitochondrial Membrane Transport Proteins/metabolism ; Mitochondrial Membranes ; Mitochondrial Permeability Transition Pore ; NF-kappa B/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Signal Transduction ; Spodoptera/*metabolism/parasitology ; Transcription, Genetic ; *Transcriptome ; *Wasps ; }, abstract = {Microplitis bicoloratus parasitism induction of apoptotic DNA fragmentation of host Spodoptera litura hemocytes has been reported. However, how M. bicoloratus parasitism regulates the host signaling pathways to induce DNA fragmentation during apoptosis remains unclear. To address this question, we performed a new RNAseq-based comparative analysis of the hemocytes transcriptomes of non-parasitized and parasitized S. litura. We were able to assemble a total of more than 11.63 Gbp sequence, to yield 20,571 unigenes. At least six main protein families encoded by M. bicoloratus bracovirus are expressed in the parasitized host hemocytes: Ankyrin-repeat, Ben domain, C-type lectin, Egf-like and Mucin-like, protein tyrosine phosphatase. The analysis indicated that during DNA fragmentation and cell death, 299 genes were up-regulated and 2,441 genes were down-regulated. Data on five signaling pathways related with cell death, the gap junctions, Ca2+, PI3K/Akt, NF-κB, ATM/p53 revealed that CypD, which is involved in forming a Permeability Transition Pore Complex (PTPC) to alter mitochondrial membrane permeabilization (MMP), was dramatically up-regulated. The qRT-PCR also provided that the key genes for cell survival were down-regulated under M. bicoloratus parasitism, including those encoding Inx1, Inx2 and Inx3 of the gap junction signaling pathway, p110 subunit of the PI3K/Akt signaling pathway, and the p50 and p65 subunit of the NF-κB signaling pathway. These findings suggest that M. bicoloratus parasitism may regulate host mitochondria to trigger internucleosomal DNA fragmentation. This study will facilitate the identification of immunosuppression-related genes and also improves our understanding of molecular mechanisms underlying polydnavirus-parasitoid-host interaction.}, }
@article {pmid25342463, year = {2015}, author = {Binkienė, R and Kornienko, SA and Tkach, VV}, title = {Soricinia genovi n. sp. from Neomys fodiens in Bulgaria, with redescription of Soricinia globosa (Baer, 1931) (Cyclophyllidea: Hymenolepididae).}, journal = {Parasitology research}, volume = {114}, number = {1}, pages = {209-218}, pmid = {25342463}, issn = {1432-1955}, mesh = {Animals ; Bulgaria/epidemiology ; Cestoda/*anatomy &amp; histology/*classification/genetics/isolation &amp; purification ; Cestode Infections/epidemiology/parasitology/*veterinary ; DNA, Ribosomal/genetics ; Female ; Mitochondria/genetics ; Phylogeny ; *Shrews ; }, abstract = {Examination of specimens collected from water shrews Neomys fodiens in the Rhodope Mountains, Bulgaria, revealed a new species of Soricinia. Soricinia genovi n. sp., is described and the syntype of Soricinia globosa (the only other Soricinia species known from Neomys) is redescribed. The new species differs from S. globosa in the number of proglottids, relative length of the cirrus-sac, number of eggs in gravid proglottids, absence of vaginal sphincter and other characters. Among Soricinia, parasitic in shrews of the genus Sorex, the new species is most similar to Soricinia quarta. Soricinia genovi can be distinguished from S. quarta by the length of the cirrus-sac, larger testes and ovary, position of vitellarium and armament of cirrus. Comparison of nuclear ribosomal 28S DNA sequences and mitochondrial nad1 sequences clearly distinguishes S. genovi sp. n. from S. quarta, Soricinia bargusinica and Soricinia infirma. The levels of interspecific sequence divergence among Soricinia species exceed those reported for some other hymenolepidids of mammals. Phylogenetic analysis places S. quarta and S. genovi sp. n. as the closest taxa which is in agreement with morphological evidence. Our data suggest that the specimens of Soricinia from the Altai Mountains that were morphologically closest to S. infirma represent a new species. Pairwise sequence comparisons and phylogenetic analysis also indicate that "S. infirma" group may constitute a genus separate from the remaining Soricinia.}, }
@article {pmid25341790, year = {2014}, author = {Schwarzländer, M and Wagner, S and Ermakova, YG and Belousov, VV and Radi, R and Beckman, JS and Buettner, GR and Demaurex, N and Duchen, MR and Forman, HJ and Fricker, MD and Gems, D and Halestrap, AP and Halliwell, B and Jakob, U and Johnston, IG and Jones, NS and Logan, DC and Morgan, B and Müller, FL and Nicholls, DG and Remington, SJ and Schumacker, PT and Winterbourn, CC and Sweetlove, LJ and Meyer, AJ and Dick, TP and Murphy, MP}, title = {The 'mitoflash' probe cpYFP does not respond to superoxide.}, journal = {Nature}, volume = {514}, number = {7523}, pages = {E12-4}, pmid = {25341790}, issn = {1476-4687}, support = {P30 ES005605/ES/NIEHS NIH HHS/United States ; R01 GM073929/GM/NIGMS NIH HHS/United States ; P30 CA086862/CA/NCI NIH HHS/United States ; R01 AG027349/AG/NIA NIH HHS/United States ; R01 CA169046/CA/NCI NIH HHS/United States ; MC_U105663142/MRC_/Medical Research Council/United Kingdom ; 098565//Wellcome Trust/United Kingdom ; R21 AG046799/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis elegans/*metabolism ; *Longevity ; Male ; Mitochondria/*metabolism ; Superoxides/*metabolism ; }, abstract = {Ageing and lifespan of organisms are determined by complicated interactions between their genetics and the environment, but the cellular mechanisms remain controversial. There have been a number of studies suggesting that cellular energy metabolism and free radical dynamics affect lifespan, implicating mitochondrial function. Recently, Shen et al. provided apparent mechanistic insight by reporting that mitochondrial oscillations of ‘free radical production’, called ‘mitoflashes’, in the pharynx of 3-day old Caenorhabditis elegans correlated inversely with lifespan. The interpretation of ‘mitoflashes’ as ‘bursts of superoxide’ radicals assumes that circularly permuted yellow fluorescent protein (cpYFP) is a reliable indicator of mitochondrial superoxide. This interpretation has been criticised because experiments and theoretical considerations both show that changes in cpYFP fluorescence are due to alterations in pH, not superoxide[-]. We now provide direct evidence that purified cpYFP is completely unresponsive to superoxide. Therefore ‘mitoflashes’ do not reflect superoxide generation and are not evidence for a link between mitochondrial free radical dynamics and lifespan.}, }
@article {pmid25340523, year = {2014}, author = {Smart, HC and Mast, FD and Chilije, MF and Tavassoli, M and Dacks, JB and Zaremberg, V}, title = {Phylogenetic analysis of glycerol 3-phosphate acyltransferases in opisthokonts reveals unexpected ancestral complexity and novel modern biosynthetic components.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e110684}, pmid = {25340523}, issn = {1932-6203}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Biocatalysis ; Endoplasmic Reticulum/enzymology ; Eukaryota/*enzymology ; Fungi/enzymology ; Gene Duplication ; Glycerol-3-Phosphate O-Acyltransferase/chemistry/*metabolism ; Glycolipids/*biosynthesis ; Humans ; Intracellular Space/metabolism ; Isoenzymes/metabolism ; Mitochondria/enzymology ; Models, Biological ; Molecular Sequence Data ; *Phylogeny ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {Glycerolipid synthesis represents a central metabolic process of all forms of life. In the last decade multiple genes coding for enzymes responsible for the first step of the pathway, catalyzed by glycerol 3-phosphate acyltransferase (GPAT), have been described, and characterized primarily in model organisms like Saccharomyces cerevisiae and mice. Notoriously, the fungal enzymes share low sequence identity with their known animal counterparts, and the nature of their homology is unclear. Furthermore, two mitochondrial GPAT isoforms have been described in animal cells, while no such enzymes have been identified in Fungi. In order to determine if the yeast and mammalian GPATs are representative of the set of enzymes present in their respective groups, and to test the hypothesis that metazoan orthologues are indeed absent from the fungal clade, a comparative genomic and phylogenetic analysis was performed including organisms spanning the breadth of the Opisthokonta supergroup. Surprisingly, our study unveiled the presence of 'fungal' orthologs in the basal taxa of the holozoa and 'animal' orthologues in the basal holomycetes. This includes a novel clade of fungal homologues, with putative peroxisomal targeting signals, of the mitochondrial/peroxisomal acyltransferases in Metazoa, thus potentially representing an undescribed metabolic capacity in the Fungi. The overall distribution of GPAT homologues is suggestive of high relative complexity in the ancestors of the opisthokont clade, followed by loss and sculpting of the complement in the descendent lineages. Divergence from a general versatile metabolic model, present in ancestrally deduced GPAT complements, points to distinctive contributions of each GPAT isoform to lipid metabolism and homeostasis in contemporary organisms like humans and their fungal pathogens.}, }
@article {pmid25333882, year = {2014}, author = {Song, H and Moulton, MJ and Whiting, MF}, title = {Rampant nuclear insertion of mtDNA across diverse lineages within Orthoptera (Insecta).}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e110508}, pmid = {25333882}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; DNA, Mitochondrial/chemistry/classification/*metabolism ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Molecular Sequence Data ; Orthoptera/*metabolism ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Nuclear mitochondrial pseudogenes (numts) are non-functional fragments of mtDNA inserted into the nuclear genome. Numts are prevalent across eukaryotes and a positive correlation is known to exist between the number of numts and the genome size. Most numt surveys have relied on model organisms with fully sequenced nuclear genomes, but such analyses have limited utilities for making a generalization about the patterns of numt accumulation for any given clade. Among insects, the order Orthoptera is known to have the largest nuclear genome and it is also reported to include several species with a large number of numts. In this study, we use Orthoptera as a case study to document the diversity and abundance of numts by generating numts of three mitochondrial loci across 28 orthopteran families, representing the phylogenetic diversity of the order. We discover that numts are rampant in all lineages, but there is no discernable and consistent pattern of numt accumulation among different lineages. Likewise, we do not find any evidence that a certain mitochondrial gene is more prone to nuclear insertion than others. We also find that numt insertion must have occurred continuously and frequently throughout the diversification of Orthoptera. Although most numts are the result of recent nuclear insertion, we find evidence of very ancient numt insertion shared by highly divergent families dating back to the Jurassic period. Finally, we discuss several factors contributing to the extreme prevalence of numts in Orthoptera and highlight the importance of exploring the utility of numts in evolutionary studies.}, }
@article {pmid25333787, year = {2014}, author = {Wang, Z and Wu, M}, title = {Phylogenomic reconstruction indicates mitochondrial ancestor was an energy parasite.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e110685}, pmid = {25333787}, issn = {1932-6203}, mesh = {Alphaproteobacteria/genetics/metabolism ; Biological Evolution ; Cell Respiration ; *Energy Metabolism ; Eukaryotic Cells/physiology ; *Evolution, Molecular ; Flagella/genetics/metabolism ; *Genome, Mitochondrial ; *Genomics ; Lipid Metabolism ; Metabolic Networks and Pathways ; Mitochondria/*genetics/*metabolism ; *Phylogeny ; }, abstract = {Reconstruction of mitochondrial ancestor has great impact on our understanding of the origin of mitochondria. Previous studies have largely focused on reconstructing the last common ancestor of all contemporary mitochondria (proto-mitochondria), but not on the more informative pre-mitochondria (the last common ancestor of mitochondria and their alphaproteobacterial sister clade). Using a phylogenomic approach and leveraging on the increased taxonomic sampling of alphaproteobacterial and eukaryotic genomes, we reconstructed the metabolisms of both proto-mitochondria and pre-mitochondria. Our reconstruction depicts a more streamlined proto-mitochondrion than these predicted by previous studies, and revealed several novel insights into the mitochondria-derived eukaryotic metabolisms including the lipid metabolism. Most strikingly, pre-mitochondrion was predicted to possess a plastid/parasite type of ATP/ADP translocase that imports ATP from the host, which posits pre-mitochondrion as an energy parasite that directly contrasts with the current role of mitochondria as the cell's energy producer. In addition, pre-mitochondrion was predicted to encode a large number of flagellar genes and several cytochrome oxidases functioning under low oxygen level, strongly supporting the previous finding that the mitochondrial ancestor was likely motile and capable of oxidative phosphorylation under microoxic condition.}, }
@article {pmid25329274, year = {2016}, author = {Joseph, S and Poriya, P and Kundu, R}, title = {Probing the phylogenetic relationships of a few newly recorded intertidal zoanthids of Gujarat coast (India) with mtDNA COI sequences.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {6}, pages = {3858-3864}, doi = {10.3109/19401736.2014.971239}, pmid = {25329274}, issn = {2470-1408}, mesh = {Animals ; Anthozoa/*genetics ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/genetics ; Genetic Variation/*genetics ; Geography ; India ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The present study reports the phylogenetic relationship of six zoanthid species belonging to three genera, Isaurus, Palythoa, and Zoanthus identified using systematic computational analysis of mtDNA gene sequences. All six species are first recorded from the coasts of Kathiawar Peninsula, India. Genus: Isaurus is represented by Isaurus tuberculatus, genus Zoanthus is represented by Zoanthus kuroshio and Zoanthus sansibaricus, while genus Palythoa is represented by Palythoa tuberculosa, P. sp. JVK-2006 and Palythoa heliodiscus. Results of the present study revealed that among the various species observed along the coastline, a minimum of 99% sequence divergence and a maximum of 96% sequence divergence were seen. An interspecific divergence of 1-4% and negligible intraspecific divergence was observed. These results not only highlighted the efficiency of the COI gene region in species identification but also demonstrated the genetic variability of zoanthids along the Saurashtra coastline of the west coast of India.}, }
@article {pmid25329272, year = {2016}, author = {Cai, S and Song, N and Zhang, L and Gao, T}, title = {The complete mitochondrial genome of Sillago aeolus (Perciformes: Sillaginidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1499-1500}, doi = {10.3109/19401736.2014.953110}, pmid = {25329272}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The long PCR and primer walking methods are used for determining the complete mitochondrial genome sequence of Sillago aeolus. The entire sequence is 16,499 bp in length including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 non-coding regions (L-strand replication origin and control region). Within the control region, we identified the termination-associated sequence domain (TAS), central conserved domains (CSB-F, CSB-E, CSB-D, CSB-C, CSB-B and CSB-A), and three conserved sequence blocks (CSB-1, CSB-2 and CSB-3).}, }
@article {pmid25317641, year = {2016}, author = {Soroka, M and Burzyński, A}, title = {Complete male mitochondrial genome of Anodonta anatina (Mollusca: Unionidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {3}, pages = {1679-1680}, doi = {10.3109/19401736.2014.958725}, pmid = {25317641}, issn = {2470-1408}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Haplotypes/genetics ; Male ; Unionidae/*genetics ; }, abstract = {Anodonta anatina is a freshwater mussel of the family Unionidae. These mussels have a unique mitochondria inheritance system named doubly uniparental inheritance (DUI). Under DUI males have two, potentially very divergent mitochondrial genomes: F-type inherited from mother and M-type inherited from father. F-type is present in soma whereas M-type is present in gonadal tissues and sperm. Here we report two M-type sequences of complete mitochondrial genomes from Anodonta anatina. They are 16,906 bp long and their sequences are similar (0.1% divergence). The genome organization is identical to the other Unionidean M-type genomes published to date. There are 38 genes, including the recently described M-type specific M ORF. The presence of tRNA-like repeat in one of the noncoding regions, suggests that the control region is located in this area. Nucleotide composition is quite extreme, with AT content (66.2%) higher than in any other of the six published Unionidean M genomes.}, }
@article {pmid25313038, year = {2014}, author = {Haag, KL and James, TY and Pombert, JF and Larsson, R and Schaer, TM and Refardt, D and Ebert, D}, title = {Evolution of a morphological novelty occurred before genome compaction in a lineage of extreme parasites.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {43}, pages = {15480-15485}, pmid = {25313038}, issn = {1091-6490}, mesh = {Animals ; *Evolution, Molecular ; Genome, Fungal/*genetics ; Genomics ; Microsporidia/*genetics/ultrastructure ; Molecular Sequence Annotation ; Molecular Sequence Data ; Parasites/*anatomy &amp; histology/*genetics/ultrastructure ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Intracellular parasitism results in extreme adaptations, whose evolutionary history is difficult to understand, because the parasites and their known free-living relatives are so divergent from one another. Microsporidia are intracellular parasites of humans and other animals, which evolved highly specialized morphological structures, but also extreme physiologic and genomic simplification. They are suggested to be an early-diverging branch on the fungal tree, but comparisons to other species are difficult because their rates of molecular evolution are exceptionally high. Mitochondria in microsporidia have degenerated into organelles called mitosomes, which have lost a genome and the ability to produce ATP. Here we describe a gut parasite of the crustacean Daphnia that despite having remarkable morphological similarity to the microsporidia, has retained genomic features of its fungal ancestors. This parasite, which we name Mitosporidium daphniae gen. et sp. nov., possesses a mitochondrial genome including genes for oxidative phosphorylation, yet a spore stage with a highly specialized infection apparatus--the polar tube--uniquely known only from microsporidia. Phylogenomics places M. daphniae at the root of the microsporidia. A comparative genomic analysis suggests that the reduction in energy metabolism, a prominent feature of microsporidian evolution, was preceded by a reduction in the machinery controlling cell cycle, DNA recombination, repair, and gene expression. These data show that the morphological features unique to M. daphniae and other microsporidia were already present before the lineage evolved the extreme host metabolic dependence and loss of mitochondrial respiration for which microsporidia are well known.}, }
@article {pmid25312050, year = {2015}, author = {Gonçalves, VF and Andreazza, AC and Kennedy, JL}, title = {Mitochondrial dysfunction in schizophrenia: an evolutionary perspective.}, journal = {Human genetics}, volume = {134}, number = {1}, pages = {13-21}, pmid = {25312050}, issn = {1432-1203}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Humans ; Mitochondria/*pathology ; Mitochondrial Diseases/*complications ; Schizophrenia/*etiology/*pathology ; }, abstract = {Schizophrenia (SCZ) is a severe psychiatric illness with a lifetime prevalence of 0.4 %. A disturbance of energy metabolism has been suggested as part of the etiopathogenesis of the disorder. Several lines of evidence have proposed a connection between etiopathogenesis of SCZ and human brain evolution, which was characterized by an increase in the energy requirement, demanding a co-evolution of the mitochondrial system. Mitochondria are key players in brain energy homeostasis and multiple lines of evidence suggest that the system is disrupted in SCZ. In this review, we will describe the current knowledge on pathways/system involved in the human brain evolution as well as the main theories regarding the evolutionary origin of SCZ. We will furthermore discuss the role of mitochondria in the context of brain energy metabolism and its role in the etiopathogenesis of SCZ. Understanding SCZ in the context of human brain evolution opens a new perspective to elucidate pathophysiological mechanisms involved in the origin and/or portions of the complex symptomatology of this severe mental disorder.}, }
@article {pmid25311909, year = {2015}, author = {Michel, CJ}, title = {An extended genetic scale of reading frame coding.}, journal = {Journal of theoretical biology}, volume = {365}, number = {}, pages = {164-174}, doi = {10.1016/j.jtbi.2014.09.040}, pmid = {25311909}, issn = {1095-8541}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Chloroplasts/genetics ; Codon/*genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; Mitochondria/genetics ; Reading Frames/*physiology ; }, abstract = {The reading frame coding (RFC) of codes (sets) of trinucleotides is a genetic concept which has been largely ignored during the last 50 years. An extended definition of the statistical parameter PrRFC (Michel, 2014) is proposed here for analysing the probability (efficiency) of reading frame coding of usage of any trinucleotide code. It is applied to the analysis of the RFC efficiency of usage of the C(3) self-complementary trinucleotide circular code X identified in prokaryotic and eukaryotic genes (Arquès and Michel, 1996). The usage of X is called usage XU. The highest RFC probabilities of usage XU are identified in bacterial plasmids and bacteria (about 49.0%). Then, by decreasing values, the RFC probabilities of usage XU are observed in archaea (47.5%), viruses (45.4%) and nuclear eukaryotes (42.8%). The lowest RFC probabilities of usage XU are found in mitochondria and chloroplasts (about 36.5%). Thus, genes contain information for reading frame coding. Such a genetic property which to our knowledge has never been identified, may bring new insights in the origin and evolution of the genetic code.}, }
@article {pmid25309834, year = {2014}, author = {Kim, C and Patel, P and Gouvin, LM and Brown, ML and Khalil, A and Henchey, EM and Heuck, AP and Yadava, N}, title = {Comparative Analysis of the Mitochondrial Physiology of Pancreatic β Cells.}, journal = {Bioenergetics : open access}, volume = {3}, number = {1}, pages = {110}, pmid = {25309834}, issn = {2167-7662}, support = {R21 NS057224/NS/NINDS NIH HHS/United States ; }, abstract = {The mitochondrial metabolism of β cells is thought to be highly specialized. Its direct comparison with other cells using isolated mitochondria is limited by the availability of islets/β cells in sufficient quantity. In this study, we have compared mitochondrial metabolism of INS1E/β cells with other cells in intact and permeabilized states. To selectively permeabilize the plasma membrane, we have evaluated the use of perfringolysin-O (PFO) in conjunction with microplate-based respirometry. PFO is a protein that binds membranes based on a threshold level of active cholesterol. Therefore, unless active cholesterol reaches a threshold level in mitochondria, they are expected to remain untouched by PFO. Cytochrome c sensitivity tests showed that in PFO-permeabilized cells, the mitochondrial integrity was completely preserved. Our data show that a time-dependent decline of the oligomycin-insensitive respiration observed in INS1E cells was due to a limitation in substrate supply to the respiratory chain. We predict that it is linked with the β cell-specific metabolism involving metabolites shuttling between the cytoplasm and mitochondria. In permeabilized β cells, the Complex l-dependent respiration was either transient or absent because of the inefficient TCA cycle. The TCA cycle insufficiency was confirmed by analysis of the CO2 evolution. This may be linked with lower levels of NAD[+], which is required as a co-factor for CO2 producing reactions of the TCA cycle. β cells showed comparable OxPhos and respiratory capacities that were not affected by the inorganic phosphate (Pi) levels in the respiration medium. They showed lower ADP-stimulation of the respiration on different substrates. We believe that this study will significantly enhance our understanding of the β cell mitochondrial metabolism.}, }
@article {pmid25307522, year = {2015}, author = {Camões, F and Islinger, M and Guimarães, SC and Kilaru, S and Schuster, M and Godinho, LF and Steinberg, G and Schrader, M}, title = {New insights into the peroxisomal protein inventory: Acyl-CoA oxidases and -dehydrogenases are an ancient feature of peroxisomes.}, journal = {Biochimica et biophysica acta}, volume = {1853}, number = {1}, pages = {111-125}, doi = {10.1016/j.bbamcr.2014.10.005}, pmid = {25307522}, issn = {0006-3002}, support = {BB/K006231/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Acyl-CoA Dehydrogenases/*metabolism ; Acyl-CoA Oxidase/*metabolism ; Fatty Acids/metabolism ; Fungi/metabolism ; Humans ; Oxidation-Reduction ; Peroxisomes/*metabolism ; Ustilago/metabolism ; }, abstract = {Peroxisomes are ubiquitous organelles which participate in a variety of essential biochemical pathways. An intimate interrelationship between peroxisomes and mitochondria is emerging in mammals, where both organelles cooperate in fatty acid β-oxidation and cellular lipid homeostasis. As mitochondrial fatty acid β-oxidation is lacking in yeast and plants, suitable genetically accessible model systems to study this interrelationship are scarce. Here, we propose the filamentous fungus Ustilago maydis as a suitable model for those studies. We combined molecular cell biology, bioinformatics and phylogenetic analyses and provide the first comprehensive inventory of U. maydis peroxisomal proteins and pathways. Studies with a peroxisome-deficient Δpex3 mutant revealed the existence of parallel and complex, cooperative β-oxidation pathways in peroxisomes and mitochondria, mimicking the situation in mammals. Furthermore, we provide evidence that acyl-CoA dehydrogenases (ACADs) are bona fide peroxisomal proteins in fungi and mammals and together with acyl-CoA oxidases (ACOX) belong to the basic enzymatic repertoire of peroxisomes. A genome comparison with baker's yeast and human gained new insights into the basic peroxisomal protein inventory shared by humans and fungi and revealed novel peroxisomal proteins and functions in U. maydis. The importance of our findings for the evolution and function of the complex interrelationship between peroxisomes and mitochondria in fatty acid β-oxidation is discussed.}, }
@article {pmid25306530, year = {2014}, author = {Zimorski, V and Ku, C and Martin, WF and Gould, SB}, title = {Endosymbiotic theory for organelle origins.}, journal = {Current opinion in microbiology}, volume = {22}, number = {}, pages = {38-48}, doi = {10.1016/j.mib.2014.09.008}, pmid = {25306530}, issn = {1879-0364}, support = {232975/ERC_/European Research Council/International ; }, mesh = {Adenosine Triphosphate/metabolism ; Cyanobacteria/physiology ; Eukaryotic Cells/physiology ; Mitochondria/metabolism ; Organelles/*metabolism ; Prokaryotic Cells/physiology ; Protein Transport ; Symbiosis/*physiology ; }, abstract = {Endosymbiotic theory goes back over 100 years. It explains the similarity of chloroplasts and mitochondria to free-living prokaryotes by suggesting that the organelles arose from prokaryotes through (endo)symbiosis. Gene trees provide important evidence in favour of symbiotic theory at a coarse-grained level, but the finer we get into the details of branches in trees containing dozens or hundreds of taxa, the more equivocal evidence for endosymbiotic events sometimes becomes. It seems that either the interpretation of some endosymbiotic events are wrong, or something is wrong with the interpretations of some gene trees having many leaves. There is a need for evidence that is independent of gene trees and that can help outline the course of symbiosis in eukaryote evolution. Protein import is the strongest evidence we have for the single origin of chloroplasts and mitochondria. It is probably also the strongest evidence we have to sort out the number and nature of secondary endosymbiotic events that have occurred in evolution involving the red plastid lineage. If we relax our interpretation of individual gene trees, endosymbiotic theory can tell us a lot.}, }
@article {pmid25302405, year = {2015}, author = {Greiner, S and Sobanski, J and Bock, R}, title = {Why are most organelle genomes transmitted maternally?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {37}, number = {1}, pages = {80-94}, pmid = {25302405}, issn = {1521-1878}, mesh = {Animals ; Female ; *Genome ; Humans ; Inheritance Patterns/*genetics ; Models, Genetic ; Organelles/*genetics ; Phylogeny ; Selection, Genetic ; }, abstract = {Why the DNA-containing organelles, chloroplasts, and mitochondria, are inherited maternally is a long standing and unsolved question. However, recent years have seen a paradigm shift, in that the absoluteness of uniparental inheritance is increasingly questioned. Here, we review the field and propose a unifying model for organelle inheritance. We argue that the predominance of the maternal mode is a result of higher mutational load in the paternal gamete. Uniparental inheritance evolved from relaxed organelle inheritance patterns because it avoids the spread of selfish cytoplasmic elements. However, on evolutionary timescales, uniparentally inherited organelles are susceptible to mutational meltdown (Muller's ratchet). To prevent this, fall-back to relaxed inheritance patterns occurs, allowing low levels of sexual organelle recombination. Since sexual organelle recombination is insufficient to mitigate the effects of selfish cytoplasmic elements, various mechanisms for uniparental inheritance then evolve again independently. Organelle inheritance must therefore be seen as an evolutionary unstable trait, with a strong general bias to the uniparental, maternal, mode.}, }
@article {pmid25288115, year = {2014}, author = {Labbé, K and Murley, A and Nunnari, J}, title = {Determinants and functions of mitochondrial behavior.}, journal = {Annual review of cell and developmental biology}, volume = {30}, number = {}, pages = {357-391}, doi = {10.1146/annurev-cellbio-101011-155756}, pmid = {25288115}, issn = {1530-8995}, support = {R01GM097432/GM/NIGMS NIH HHS/United States ; 5T32GM007377-34/GM/NIGMS NIH HHS/United States ; R01GM106019/GM/NIGMS NIH HHS/United States ; R01GM062942/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/metabolism ; Dynamins/physiology ; Endoplasmic Reticulum/physiology ; GTP Phosphohydrolases/physiology ; Homeostasis ; Humans ; Lipid Metabolism ; Microtubule-Associated Proteins/physiology ; Mitochondria/*physiology ; Mitochondrial Diseases/physiopathology ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/physiology ; Mitochondrial Turnover/*physiology ; Protein Conformation ; Signal Transduction/physiology ; }, abstract = {Mitochondria are ancient organelles evolved from bacteria. Over the course of evolution, the behavior of mitochondria inside eukaryotic cells has changed dramatically, and the corresponding machineries that control it are in most cases new inventions. The evolution of mitochondrial behavior reflects the necessity to create a dynamic compartment to integrate the myriad mitochondrial functions with the status of other endomembrane compartments, such as the endoplasmic reticulum, and with signaling pathways that monitor cellular homeostasis and respond to stress. Here we review what has been discovered about the molecular machineries that work together to control the collective behavior of mitochondria in cells, as well as their physiological roles in healthy and disease states.}, }
@article {pmid25278952, year = {2014}, author = {Moriyama, T and Sato, N}, title = {Enzymes involved in organellar DNA replication in photosynthetic eukaryotes.}, journal = {Frontiers in plant science}, volume = {5}, number = {}, pages = {480}, pmid = {25278952}, issn = {1664-462X}, abstract = {Plastids and mitochondria possess their own genomes. Although the replication mechanisms of these organellar genomes remain unclear in photosynthetic eukaryotes, several organelle-localized enzymes related to genome replication, including DNA polymerase, DNA primase, DNA helicase, DNA topoisomerase, single-stranded DNA maintenance protein, DNA ligase, primer removal enzyme, and several DNA recombination-related enzymes, have been identified. In the reference Eudicot plant Arabidopsis thaliana, the replication-related enzymes of plastids and mitochondria are similar because many of them are dual targeted to both organelles, whereas in the red alga Cyanidioschyzon merolae, plastids and mitochondria contain different replication machinery components. The enzymes involved in organellar genome replication in green plants and red algae were derived from different origins, including proteobacterial, cyanobacterial, and eukaryotic lineages. In the present review, we summarize the available data for enzymes related to organellar genome replication in green plants and red algae. In addition, based on the type and distribution of replication enzymes in photosynthetic eukaryotes, we discuss the transitional history of replication enzymes in the organelles of plants.}, }
@article {pmid25274566, year = {2014}, author = {Cavalcanti, JH and Esteves-Ferreira, AA and Quinhones, CG and Pereira-Lima, IA and Nunes-Nesi, A and Fernie, AR and Araújo, WL}, title = {Evolution and functional implications of the tricarboxylic acid cycle as revealed by phylogenetic analysis.}, journal = {Genome biology and evolution}, volume = {6}, number = {10}, pages = {2830-2848}, pmid = {25274566}, issn = {1759-6653}, mesh = {Biological Evolution ; Citric Acid Cycle/genetics/*physiology ; Mitochondria/metabolism ; Phylogeny ; Plant Proteins/genetics/metabolism ; }, abstract = {The tricarboxylic acid (TCA) cycle, a crucial component of respiratory metabolism, is composed of a set of eight enzymes present in the mitochondrial matrix. However, most of the TCA cycle enzymes are encoded in the nucleus in higher eukaryotes. In addition, evidence has accumulated demonstrating that nuclear genes were acquired from the mitochondrial genome during the course of evolution. For this reason, we here analyzed the evolutionary history of all TCA cycle enzymes in attempt to better understand the origin of these nuclear-encoded proteins. Our results indicate that prior to endosymbiotic events the TCA cycle seemed to operate only as isolated steps in both the host (eubacterial cell) and mitochondria (alphaproteobacteria). The origin of isoforms present in different cell compartments might be associated either with gene-transfer events which did not result in proper targeting of the protein to mitochondrion or with duplication events. Further in silico analyses allow us to suggest new insights into the possible roles of TCA cycle enzymes in different tissues. Finally, we performed coexpression analysis using mitochondrial TCA cycle genes revealing close connections among these genes most likely related to the higher efficiency of oxidative phosphorylation in this specialized organelle. Moreover, these analyses allowed us to identify further candidate genes which might be used for metabolic engineering purposes given the importance of the TCA cycle during development and/or stress situations.}, }
@article {pmid25272157, year = {2014}, author = {Sugita, C and Komura, Y and Tanaka, K and Kometani, K and Satoh, H and Sugita, M}, title = {Molecular characterization of three PRORP proteins in the moss Physcomitrella patens: nuclear PRORP protein is not essential for moss viability.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e108962}, pmid = {25272157}, issn = {1932-6203}, mesh = {Bryopsida/*chemistry/physiology ; Cell Nucleus/*chemistry ; Gene Knockdown Techniques ; Nuclear Proteins/*chemistry ; Phylogeny ; }, abstract = {RNase P is a ubiquitous endonuclease that removes the 5' leader sequence from pre-tRNAs in all organisms. In Arabidopsis thaliana, RNA-free proteinaceous RNase Ps (PRORPs) seem to be enzyme(s) for pre-tRNA 5'-end processing in organelles and the nucleus and are thought to have replaced the ribonucleoprotein RNase P variant. However, the evolution and function of plant PRORPs are not fully understood. Here, we identified and characterized three PRORP-like proteins, PpPPR_63, 67, and 104, in the basal land plant, the moss Physcomitrella patens. PpPPR_63 localizes to the nucleus, while PpPPR_67 and PpPPR_104 are found in both the mitochondria and chloroplasts. The three proteins displayed pre-tRNA 5'-end processing activity in vitro. Mutants with knockout (KO) of the PpPPR_63 gene displayed growth retardation of protonemal colonies, indicating that, unlike Arabidopsis nuclear RPORPs, the moss nuclear PpPPR_63 is not essential for viability. In the KO mutant, nuclear-encoded tRNAAsp (GUC) levels were slightly decreased, whereas most nuclear-encoded tRNA levels were not altered. This indicated that most of the cytosolic mature tRNAs were produced normally without proteinaceous RNase P-like PpPPR_63. Single PpPPR_67 or 104 gene KO mutants displayed different phenotypes of protonemal growth and chloroplast tRNA(Arg) (ACG) accumulation. However, the levels of all other tRNAs were not altered in the KO mutants. In addition, in vitro RNase P assays showed that PpPPR_67 and PpPPR_104 efficiently cleaved chloroplast pre-tRNA(Arg) (CCG) and pre-tRNA(Arg) (UCU) but they cleaved pre-tRNA(Arg) (ACG) with different efficiency. This suggests that the two proteins have overlapping function but their substrate specificity is not identical.}, }
@article {pmid25271376, year = {2014}, author = {Ju, YS and Alexandrov, LB and Gerstung, M and Martincorena, I and Nik-Zainal, S and Ramakrishna, M and Davies, HR and Papaemmanuil, E and Gundem, G and Shlien, A and Bolli, N and Behjati, S and Tarpey, PS and Nangalia, J and Massie, CE and Butler, AP and Teague, JW and Vassiliou, GS and Green, AR and Du, MQ and Unnikrishnan, A and Pimanda, JE and Teh, BT and Munshi, N and Greaves, M and Vyas, P and El-Naggar, AK and Santarius, T and Collins, VP and Grundy, R and Taylor, JA and Hayes, DN and Malkin, D and ,  and ,  and ,  and Foster, CS and Warren, AY and Whitaker, HC and Brewer, D and Eeles, R and Cooper, C and Neal, D and Visakorpi, T and Isaacs, WB and Bova, GS and Flanagan, AM and Futreal, PA and Lynch, AG and Chinnery, PF and McDermott, U and Stratton, MR and Campbell, PJ}, title = {Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer.}, journal = {eLife}, volume = {3}, number = {}, pages = {}, pmid = {25271376}, issn = {2050-084X}, support = {101876//Wellcome Trust/United Kingdom ; MR/K000608/1/MRC_/Medical Research Council/United Kingdom ; G0900871/MRC_/Medical Research Council/United Kingdom ; 088340//Wellcome Trust/United Kingdom ; P01 CA155258/CA/NCI NIH HHS/United States ; 096919//Wellcome Trust/United Kingdom ; 095663//Wellcome Trust/United Kingdom ; G1000729/MRC_/Medical Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Base Composition ; DNA/*genetics ; DNA Replication ; DNA, Mitochondrial/*genetics ; DNA, Neoplasm/*genetics ; Data Mining ; Evolution, Molecular ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Humans ; Mitochondria/genetics/pathology ; *Mutation ; Neoplasms/classification/*genetics/pathology ; Polymorphism, Single Nucleotide ; }, abstract = {Recent sequencing studies have extensively explored the somatic alterations present in the nuclear genomes of cancers. Although mitochondria control energy metabolism and apoptosis, the origins and impact of cancer-associated mutations in mtDNA are unclear. In this study, we analyzed somatic alterations in mtDNA from 1675 tumors. We identified 1907 somatic substitutions, which exhibited dramatic replicative strand bias, predominantly C > T and A > G on the mitochondrial heavy strand. This strand-asymmetric signature differs from those found in nuclear cancer genomes but matches the inferred germline process shaping primate mtDNA sequence content. A number of mtDNA mutations showed considerable heterogeneity across tumor types. Missense mutations were selectively neutral and often gradually drifted towards homoplasmy over time. In contrast, mutations resulting in protein truncation undergo negative selection and were almost exclusively heteroplasmic. Our findings indicate that the endogenous mutational mechanism has far greater impact than any other external mutagens in mitochondria and is fundamentally linked to mtDNA replication.}, }
@article {pmid25262830, year = {2014}, author = {Haynes, BT and Marcus, AD and Higgins, DP and Gongora, J and Gray, R and Šlapeta, J}, title = {Unexpected absence of genetic separation of a highly diverse population of hookworms from geographically isolated hosts.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {28}, number = {}, pages = {192-200}, doi = {10.1016/j.meegid.2014.09.022}, pmid = {25262830}, issn = {1567-7257}, mesh = {Ancylostomatoidea/classification/*enzymology/genetics ; Animal Migration ; Animals ; Australia ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Female ; Gene Flow ; Genetic Variation ; Haplotypes ; Hookworm Infections/parasitology/transmission/*veterinary ; Male ; Mitochondria/enzymology ; Mitochondrial Proteins/*genetics ; Phylogeny ; Sea Lions/genetics/*parasitology ; }, abstract = {The high natal site fidelity of endangered Australian sea lions (Neophoca cinerea) along the southern Australian coast suggests that their maternally transmitted parasitic species, such as hookworms, will have restricted potential for dispersal. If this is the case, we would expect to find a hookworm haplotype structure corresponding to that of the host mtDNA haplotype structure; that is, restricted among geographically separated colonies. In this study, we used a fragment of the cytochrome c oxidase I mitochondrial DNA (mtDNA) gene to investigate the diversity of hookworms (Uncinaria sanguinis) in N. cinerea to assess the importance of host distribution and ecology on the evolutionary history of the parasite. High haplotype (h=0.986) and nucleotide diversity (π=0.013) were seen, with 45 unique hookworm mtDNA haplotypes across N. cinerea colonies; with most of the variation (78%) arising from variability within hookworms from individual colonies. This is supported by the low genetic differentiation co-efficient (GST=0.007) and a high gene flow (Nm=35.25) indicating a high migration rate between the populations of hookworms. The haplotype network demonstrated no clear distribution and delineation of haplotypes according to geographical location. Our data rejects the vicariance hypothesis; that female host natal site fidelity and the transmammary route of infection restrict hookworm gene flow between N. cinerea populations and highlights the value of studies of parasite diversity and dispersal to challenge our understanding of parasite and host ecology.}, }
@article {pmid25260044, year = {2015}, author = {Kim, BM and Lee, JW and Seo, JS and Shin, KH and Rhee, JS and Lee, JS}, title = {Modulated expression and enzymatic activity of the monogonont rotifer Brachionus koreanus Cu/Zn- and Mn-superoxide dismutase (SOD) in response to environmental biocides.}, journal = {Chemosphere}, volume = {120}, number = {}, pages = {470-478}, doi = {10.1016/j.chemosphere.2014.08.042}, pmid = {25260044}, issn = {1879-1298}, mesh = {Animals ; Disinfectants/*toxicity ; Gene Expression Regulation, Enzymologic/drug effects ; Helminth Proteins/genetics/*metabolism ; Mitochondria/enzymology ; Oxidative Stress/genetics ; Phylogeny ; Rotifera/*drug effects/enzymology ; Superoxide Dismutase/genetics/*metabolism ; Water Pollutants, Chemical/*toxicity ; }, abstract = {Superoxide dismutases (SODs) are important antioxidant enzymes whose expression levels are often used as biomarkers for oxidative stress. To investigate the biomarker potential of the monogonont rotifer Brachionus koreanus SOD genes, the full-length Cu/Zn-SOD (Bk-Cu/Zn-SOD) and Mn-SOD (Bk-Mn-SOD) genes were cloned from genomic DNA and characterized. All amino acid residues involved in the formation of tertiary structure and metal binding in Bk-Cu/Zn-SOD and Bk-Mn-SOD were highly conserved across species. Phylogenetic analysis revealed that Bk-Mn-SOD, in particular, was closely clustered with mitochondrial Mn-SOD. Transcript analysis after exposure to six different biocides (alachlor, chlorpyrifos, dimethoate, endosulfan, lindane, and molinate) revealed that the transcriptional level of Bk-Cu/Zn-SOD was significantly increased in a dose-dependent manner. In contrast, the level of Bk-Mn-SOD transcript was significantly increased compared with control cells in response to chlorpyrifos, endosulfan, and molinate at their no observed effect concentrations (NOECs). However, exposure to alachlor, chlorpyrifos, and molinate significantly reduced the enzymatic activity of total SOD protein, while a decreased pattern was observed in all biocide treatments. Taken together, these results indicate that exposure to waterborne environmental biocides induces the transcription of Bk-Cu/Zn-SOD and Bk-Mn-SOD, but inhibits the enzymatic activity of Bk-SODs. These results contribute to our understanding of the modes of action of oxidative stress-mediating biocides on rotifer.}, }
@article {pmid25259854, year = {2014}, author = {Singh, K and Zouhar, M and Mazakova, J and Rysanek, P}, title = {Genome wide identification of the immunophilin gene family in Leptosphaeria maculans: a causal agent of Blackleg disease in Oilseed Rape (Brassica napus).}, journal = {Omics : a journal of integrative biology}, volume = {18}, number = {10}, pages = {645-657}, pmid = {25259854}, issn = {1557-8100}, mesh = {Amino Acid Sequence ; Ascomycota/*genetics ; Brassica napus/*microbiology ; Conserved Sequence ; Fungal Proteins/*genetics ; Gene Ontology ; Genome, Fungal ; Immunophilins/chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/microbiology ; Protein Structure, Tertiary ; Transcriptome ; }, abstract = {Abstract Phoma stem canker (blackleg) is a disease of world-wide importance on oilseed rape (Brassica napus) and can cause serious losses for crops globally. The disease is caused by dothideomycetous fungus, Leptosphaeria maculans, which is highly virulent/aggressive. Cyclophilins (CYPs) and FK506-binding proteins (FKBPs) are ubiquitous proteins belonging to the peptidyl-prolyl cis/trans isomerase (PPIase) family. They are collectively referred to as immunophilins (IMMs). In the present study, IMM genes, CYP and FKBP in haploid strain v23.1.3 of L. maculans genome, were identified and classified. Twelve CYPs and five FKBPs were determined in total. Domain architecture analysis revealed the presence of a conserved cyclophilin-like domain (CLD) in the case of CYPs and FKBP_C in the case of FKBPs. Interestingly, IMMs in L. maculans also subgrouped into single domain (SD) and multidomain (MD) proteins. They were primarily found to be localized in cytoplasm, nuclei, and mitochondria. Homologous and orthologous gene pairs were also determined by comparison with the model organism Saccharomyces cerevisiae. Remarkably, IMMs of L. maculans contain shorter introns in comparison to exons. Moreover, CYPs, in contrast with FKBPs, contain few exons. However, two CYPs were determined as being intronless. The expression profile of IMMs in both mycelium and infected primary leaves of B. napus demonstrated their potential role during infection. Secondary structure analysis revealed the presence of atypical eight β strands and two α helices fold architecture. Gene ontology analysis of IMMs predicted their significant role in protein folding and PPIase activity. Taken together, our findings for the first time present new prospects of this highly conserved gene family in phytopathogenic fungus.}, }
@article {pmid25259461, year = {2016}, author = {Ran, ML and Wang, MF and Yang, AQ and Li, Z and Chen, B}, title = {The complete mitochondrial genome of Congjiang miniature pig (Sus scrofa).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {3}, pages = {1787-1788}, doi = {10.3109/19401736.2014.963813}, pmid = {25259461}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Genome, Mitochondrial/*genetics ; Open Reading Frames/genetics ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Sus scrofa ; }, abstract = {Congjiang miniature pig is one of the most important local pig breeds in China. It is the first time that the complete mitochondrial genome sequence of Lantang pig is reported in this work, which is determined through the PCR-based method. The total length of the mitogenome is 16,772 bp, which contains 1 control region (D-loop region), 2 ribosomal RNA genes, 13 PCGs and 22 tRNA genes. The total base composition of Congjiang miniature pig mitochondrial genome is 34.78% for A, 26.21% for C, 25.78% for T and 13.22% for G and in the order A>C>T>G. The complete mitochondrial genome of Congjiang miniature pig provides an important data in genetic mechanism and the evolution genomes.}, }
@article {pmid25252967, year = {2014}, author = {Shin, SC and Ahn, DH and Kim, SJ and Pyo, CW and Lee, H and Kim, MK and Lee, J and Lee, JE and Detrich, HW and Postlethwait, JH and Edwards, D and Lee, SG and Lee, JH and Park, H}, title = {The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment.}, journal = {Genome biology}, volume = {15}, number = {9}, pages = {468}, pmid = {25252967}, issn = {1474-760X}, support = {R01 AG031922/AG/NIA NIH HHS/United States ; 5R01AG031922/AG/NIA NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Animals ; Evolution, Molecular ; Fish Proteins/genetics ; Gene Expression ; Genome ; Heat-Shock Response ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Organ Specificity ; Perciformes/*genetics/metabolism ; Phylogeny ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND: Antarctic fish have adapted to the freezing waters of the Southern Ocean. Representative adaptations to this harsh environment include a constitutive heat shock response and the evolution of an antifreeze protein in the blood. Despite their adaptations to the cold, genome-wide studies have not yet been performed on these fish due to the lack of a sequenced genome. Notothenia coriiceps, the Antarctic bullhead notothen, is an endemic teleost fish with a circumpolar distribution and makes a good model to understand the genomic adaptations to constant sub-zero temperatures.<br><br>RESULTS: We provide the draft genome sequence and annotation for N. coriiceps. Comparative genome-wide analysis with other fish genomes shows that mitochondrial proteins and hemoglobin evolved rapidly. Transcriptome analysis of thermal stress responses find alternative response mechanisms for evolution strategies in a cold environment. Loss of the phosphorylation-dependent sumoylation motif in heat shock factor 1 suggests that the heat shock response evolved into a simple and rapid phosphorylation-independent regulatory mechanism. Rapidly evolved hemoglobin and the induction of a heat shock response in the blood may support the efficient supply of oxygen to cold-adapted mitochondria.<br><br>CONCLUSIONS: Our data and analysis suggest that evolutionary strategies in efficient aerobic cellular respiration are controlled by hemoglobin and mitochondrial proteins, which may be important for the adaptation of Antarctic fish to their environment. The use of genome data from the Antarctic endemic fish provides an invaluable resource providing evidence of evolutionary adaptation and can be applied to other studies of Antarctic fish.}, }
@article {pmid25251766, year = {2014}, author = {Lozano-Jaramillo, M and Rico-Guevara, A and Cadena, CD}, title = {Genetic differentiation, niche divergence, and the origin and maintenance of the disjunct distribution in the Blossomcrown Anthocephala floriceps (Trochilidae).}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e108345}, pmid = {25251766}, issn = {1932-6203}, mesh = {Adaptation, Biological ; Animals ; Birds/*classification/*genetics ; Cell Nucleus/genetics ; Colombia ; DNA/*analysis ; *Genetic Variation ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {Studies of the origin and maintenance of disjunct distributions are of special interest in biogeography. Disjunct distributions can arise following extinction of intermediate populations of a formerly continuous range and later maintained by climatic specialization. We tested hypotheses about how the currently disjunct distribution of the Blossomcrown (Anthocephala floriceps), a hummingbird species endemic to Colombia, arose and how is it maintained. By combining molecular data and models of potential historical distributions we evaluated: (1) the timing of separation between the two populations of the species, (2) whether the disjunct distribution could have arisen as a result of fragmentation of a formerly widespread range due to climatic changes, and (3) if the disjunct distribution might be currently maintained by specialization of each population to different climatic conditions. We found that the two populations are reciprocally monophyletic for mitochondrial and nuclear loci, and that their divergence occurred ca. 1.4 million years before present (95% credibility interval 0.7-2.1 mybp). Distribution models based on environmental data show that climate has likely not been suitable for a fully continuous range over the past 130,000 years, but the potential distribution 6,000 ybp was considerably larger than at present. Tests of climatic divergence suggest that significant niche divergence between populations is a likely explanation for the maintenance of their disjunct ranges. However, based on climate the current range of A. floriceps could potentially be much larger than it currently is, suggesting other ecological or historical factors have influenced it. Our results showing that the distribution of A. floriceps has been discontinous for a long period of time and that populations exhibit different climatic niches have taxonomic and conservation implications.}, }
@article {pmid25251765, year = {2014}, author = {Rocha, AV and Rivera, LO and Martinez, J and Prestes, NP and Caparroz, R}, title = {Biogeography of speciation of two sister species of neotropical amazona (Aves, Psittaciformes) based on mitochondrial sequence data.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e108096}, pmid = {25251765}, issn = {1932-6203}, mesh = {Animals ; Argentina ; DNA, Mitochondrial/*genetics ; Genetic Speciation ; Genetic Variation ; Mitochondria/genetics ; Parrots/*genetics ; Phylogeny ; }, abstract = {Coalescent theory provides powerful models for population genetic inference and is now increasingly important in estimates of divergence times and speciation research. We use molecular data and methods based on coalescent theory to investigate whether genetic evidence supports the hypothesis of A. pretrei and A. tucumana as separate species and whether genetic data allow us to assess which allopatric model seems to better explain the diversification process in these taxa. We sampled 13 A. tucumana from two provinces in northern Argentina and 28 A. pretrei from nine localities of Rio Grande do Sul, Brazil. A 491 bp segment of the mitochondrial gene cytochrome c oxidase I was evaluated using the haplotype network and phylogenetic methods. The divergence time and other demographic quantities were estimated using the isolation and migration model based on coalescent theory. The network and phylogenetic reconstructions showed similar results, supporting reciprocal monophyly for these two taxa. The divergence time of lineage separation was estimated to be approximately 1.3 million years ago, which corresponds to the lower Pleistocene. Our results enforce the current taxonomic status for these two Amazon species. They also support that A. pretrei and A. tucumana diverged with little or no gene flow approximately 1.3 million years ago, most likely after the establishment of a small population in the Southern Yungas forest by dispersion of a few founders from the A. pretrei ancestral population. This process may have been favored by habitat corridors formed in hot and humid periods of the Quaternary. Considering that these two species are considered threatened, the results were evaluated for their implications for the conservation of these two species.}, }
@article {pmid25249225, year = {2015}, author = {Meriam, T and Wafa, T and Khawla, T and Tarek, H and Abdeljelil, G and Mhamed, E}, title = {Genetic diversity and population structure of Sepia officinalis from the Tunisian cost revealed by mitochondrial COI sequences.}, journal = {Molecular biology reports}, volume = {42}, number = {1}, pages = {77-86}, pmid = {25249225}, issn = {1573-4978}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Gene Flow ; *Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Mitochondria/*genetics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Sepia/*genetics ; Tunisia ; }, abstract = {Population substructure of Sepia officinalis sampled along the Tunisian coastline was studied. We have scored the genetic variation of the mitochondrial gene cytochrome oxidase 1. A total of 20 specimens from four sampling sites were analysed and revealed 12 different haplotypes. Haplotype diversity showed a decreasing north to south gradient which may be explained by the hydrogeography of the study area. The overall estimate of genetic divergence (FST) revealed significant genetic differentiation between the pair-wise population comparisons supported by the AMOVA analysis which reveals significant genetic divergence. Finally, populations showed an excess of rare haplotypes. The mismatch distribution and several population genetic statistics indicate that the excess of rare variants is due to a recent expansion for Djerba and Kelibia populations. For Rades and Bizerte populations a constant population size was detected. These findings are important for fisheries management to preserve this marine resource for long-term utilization.}, }
@article {pmid25245408, year = {2014}, author = {Gershoni, M and Levin, L and Ovadia, O and Toiw, Y and Shani, N and Dadon, S and Barzilai, N and Bergman, A and Atzmon, G and Wainstein, J and Tsur, A and Nijtmans, L and Glaser, B and Mishmar, D}, title = {Disrupting mitochondrial-nuclear coevolution affects OXPHOS complex I integrity and impacts human health.}, journal = {Genome biology and evolution}, volume = {6}, number = {10}, pages = {2665-2680}, pmid = {25245408}, issn = {1759-6653}, support = {R01 AG042188/AG/NIA NIH HHS/United States ; AG021654-01/AG/NIA NIH HHS/United States ; P01 AG021654/AG/NIA NIH HHS/United States ; R01 AG028872/AG/NIA NIH HHS/United States ; AG028872/AG/NIA NIH HHS/United States ; AG042188/AG/NIA NIH HHS/United States ; AG-18728-02A1/AG/NIA NIH HHS/United States ; R01 AG018728/AG/NIA NIH HHS/United States ; }, mesh = {DNA, Mitochondrial/*metabolism ; Electron Transport Complex I/*metabolism ; Evolution, Molecular ; Genotype ; Humans ; Mutagenesis, Site-Directed ; }, abstract = {The mutation rate of the mitochondrial DNA (mtDNA), which is higher by an order of magnitude as compared with the nuclear genome, enforces tight mitonuclear coevolution to maintain mitochondrial activities. Interruption of such coevolution plays a role in interpopulation hybrid breakdown, speciation events, and disease susceptibility. Previously, we found an elevated amino acid replacement rate and positive selection in the nuclear DNA-encoded oxidative phosphorylation (OXPHOS) complex I subunit NDUFC2, a phenomenon important for the direct interaction of NDUFC2 with the mtDNA-encoded complex I subunit ND4. This finding underlines the importance of mitonuclear coevolution to physical interactions between mtDNA and nuclear DNA-encoded factors. Nevertheless, it remains unclear whether this interaction is important for the stability and activity of complex I. Here, we show that siRNA silencing of NDUFC2 reduced growth of human D-407 retinal pigment epithelial cells, significantly diminished mitochondrial membrane potential, and interfered with complex I integrity. Moreover, site-directed mutagenesis of a positively selected amino acid in NDUFC2 significantly interfered with the interaction of NDUFC2 with its mtDNA-encoded partner ND4. Finally, we show that a genotype combination involving this amino acid (NDUFC2 residue 46) and the mtDNA haplogroup HV likely altered susceptibility to type 2 diabetes mellitus in Ashkenazi Jews. Therefore, mitonuclear coevolution is important for maintaining mitonuclear factor interactions, OXPHOS, and for human health.}, }
@article {pmid25242551, year = {2014}, author = {Suzuki, T and Tanaka, K and Wakabayashi, C and Saita, E and Yoshida, M}, title = {Chemomechanical coupling of human mitochondrial F1-ATPase motor.}, journal = {Nature chemical biology}, volume = {10}, number = {11}, pages = {930-936}, pmid = {25242551}, issn = {1552-4469}, mesh = {Adenosine Triphosphate/metabolism ; Azides/pharmacology ; Biocatalysis/drug effects ; Humans ; Hydrolysis/drug effects ; Mitochondria/*enzymology ; Models, Molecular ; Proton-Translocating ATPases/antagonists &amp; inhibitors/*chemistry/*metabolism ; Rotation ; }, abstract = {The rotary motor enzyme F1-ATPase (F1) is a catalytic subcomplex of FoF1-ATP synthase that produces most of the ATP in respiring cells. Chemomechanical coupling has been studied extensively for bacterial F1 but very little for mitochondrial F1. Here we report ATP-driven rotation of human mitochondrial F1. A rotor-shaft γ-subunit in the stator α3β3 ring rotates 120° per ATP with three catalytic steps: ATP binding to one β-subunit at 0°, inorganic phosphate (Pi) release from another β-subunit at 65° and ATP hydrolysis on the third β-subunit at 90°. Rotation is often interrupted at 90° by persistent ADP binding and is stalled at 65° by a specific inhibitor azide. A mitochondrial endogenous inhibitor for FoF1-ATP synthase, IF1, blocks rotation at 90°. These features differ from those of bacterial F1, in which both ATP hydrolysis and Pi release occur at around 80°, demonstrating that chemomechanical coupling angles of the γ-subunit are tuned during evolution.}, }
@article {pmid25241901, year = {2015}, author = {Schwarzer, A and Holtmann, H and Brugman, M and Meyer, J and Schauerte, C and Zuber, J and Steinemann, D and Schlegelberger, B and Li, Z and Baum, C}, title = {Hyperactivation of mTORC1 and mTORC2 by multiple oncogenic events causes addiction to eIF4E-dependent mRNA translation in T-cell leukemia.}, journal = {Oncogene}, volume = {34}, number = {27}, pages = {3593-3604}, pmid = {25241901}, issn = {1476-5594}, mesh = {Animals ; Cell Transformation, Neoplastic/genetics/metabolism ; Eukaryotic Initiation Factor-4E/*physiology ; Gene Expression Regulation, Leukemic ; Humans ; Leukemia, T-Cell/*genetics/*metabolism ; Mechanistic Target of Rapamycin Complex 1 ; Mechanistic Target of Rapamycin Complex 2 ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Multiprotein Complexes/*metabolism ; *Protein Biosynthesis/genetics ; Signal Transduction ; TOR Serine-Threonine Kinases/*metabolism ; Tumor Cells, Cultured ; }, abstract = {High activation of the PI3K-AKT-mTOR pathway is characteristic for T-cell acute lymphoblastic leukemia (T-ALL). The activity of the master regulator of this pathway, PTEN, is often impaired in T-ALL. However, experimental evidence suggests that input from receptor tyrosine kinases (RTKs) is required for sustained mTOR activation, even in the absence of PTEN. We previously reported the expression of Neurotrophin receptor tyrosine kinases (TRKs) and their respective ligands in primary human leukemia samples. In the present study we aimed to dissect the downstream signaling cascades of TRK-induced T-ALL in a murine model and show that T-ALLs induced by deregulated receptor tyrosine kinase signaling acquire activating mutations in Notch1 and lose PTEN during clonal evolution. Some clones additionally lost one allele of the homeodomain transcription factor Cux1. All events independently led to a gradual hyperactivation of both mTORC1 and mTORC2 signaling. We dissected the role of the individual mTOR complexes by shRNA knockdown and found that the separate depletion of mTORC1 or mTORC2 reduced the growth of T-ALL blasts, but was not sufficient to induce apoptosis. In contrast, knockdown of the mTOR downstream effector eIF4E caused a striking cytotoxic effect, demonstrating a critical addiction to cap-dependent mRNA-translation. Although high mTORC2-AKT activation is commonly associated with drug-resistance, we demonstrate that T-ALL displaying a strong mTORC2-AKT activation were specifically susceptible to 4EGI-1, an inhibitor of the eIF4E-eIF4G interaction. To decipher the mechanism of 4EGI-1, we performed a genome-wide analysis of mRNAs that are translationally regulated by 4EGI-1 in T-ALL. 4EGI-1 effectively reduced the ribosomal occupancy of mRNAs that were strongly upregulated in T-ALL blasts compared with normal thymocytes including transcripts important for translation, mitochondria and cell cycle progression, such as cyclins and ribosomal proteins. These data suggest that disrupting the eIF4E-eIF4G interaction constitutes a promising therapy strategy in mTOR-deregulated T-cell leukemia.}, }
@article {pmid25239514, year = {2014}, author = {Tripathi, V and Tripathi, P}, title = {Molecular phylogenetics and comparative modeling of MnSOD, an enzyme involved during environmental stress conditions in Oryza sativa.}, journal = {Interdisciplinary sciences, computational life sciences}, volume = {6}, number = {4}, pages = {251-258}, doi = {10.1007/s12539-011-0050-4}, pmid = {25239514}, issn = {1867-1462}, mesh = {Amino Acid Sequence ; Antioxidants/chemistry ; Catalysis ; Catalytic Domain/genetics ; Magnoliopsida ; Manganese/*chemistry ; Mitochondria/enzymology ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Oryza/*enzymology/*genetics ; Oxidative Stress/*genetics ; Peroxisomes/enzymology ; *Phylogeny ; Plant Proteins/chemistry/genetics ; Sequence Homology ; Structure-Activity Relationship ; Superoxide Dismutase/*chemistry/*genetics ; }, abstract = {Superoxide dismutases are a class of enzymes that catalyze the dismutation of superoxide into oxygen and hydrogen peroxide. As such, they are an important antioxidant defense in nearly all cells exposed to oxygen. Superoxide dismutase (SOD) acts as first line of defense against oxidative and genetic stress. Manganese superoxide dismutase (MnSOD), found in mitochondria or peroxisomes, contains Mn (III) at the active site. The three dimensional structure of MnSOD of Oryza sativa is not yet available in protein data bank so we have predicted the structure model of O. sativa MnSOD using homology modeling. The predicted model can further be explored for identification of ligand binding sites which may be useful for understanding specific role in functional site residues during catalysis. This study also demonstrated that the phylogenetic analysis of O. sativa MnSOD protein with distinct dicot and monocot plant species. The MnSOD protein of O. sativa has shown similarity with both monocot and as well as dicot plant species.}, }
@article {pmid25232993, year = {2014}, author = {Yue, Q and Wu, K and Qiu, D and Hu, J and Liu, D and Wei, X and Chen, J and Cook, CE}, title = {A formal re-description of the cockroach Hebardina concinna anchored on DNA Barcodes confirms wing polymorphism and identifies morphological characters for field identification.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e106789}, pmid = {25232993}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Cockroaches/*classification/*genetics ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genitalia, Male/*anatomy &amp; histology ; Male ; Mitochondria/genetics ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Wings, Animal/anatomy &amp; histology ; }, abstract = {BACKGROUND: Hebardina concinna is a domestic pest and potential vector of pathogens throughout East and Southeast Asia, yet identification of this species has been difficult due to a lack of diagnostic morphological characters, and to uncertainty in the relationship between macroptyrous (long-winged) and brachypterous (small-winged) morphotypes. In insects male genital structures are typically species-specific and are frequently used to identify species. However, male genital structures in H. concinna had not previously been described, in part due to difficulty in identifying conspecifics.<br><br>METHODS/PRINCIPAL FINDINGS: We collected 15 putative H. concinna individuals, from Chinese populations, of both wing morphotypes and both sexes and then generated mitochondrial COI (the standard barcode region) and COII sequences from five of these individuals. These confirmed that both morphotypes of both sexes are the same species. We then dissected male genitalia and compared genital structures from macropterous and brachypterous individuals, which we showed to be identical, and present here for the first time a detailed description of H. concinna male genital structures. We also present a complete re-description of the morphological characters of this species, including both wing morphs.<br><br>CONCLUSIONS/SIGNIFICANCE: This work describes a practical application of DNA barcoding to confirm that putatively polymorphic insects are conspecific and then to identify species-specific characters that can be used in the field to identify individuals and to obviate the delay and cost of returning samples to a laboratory for DNA sequencing.}, }
@article {pmid25232829, year = {2014}, author = {Greaves, LC and Nooteboom, M and Elson, JL and Tuppen, HA and Taylor, GA and Commane, DM and Arasaradnam, RP and Khrapko, K and Taylor, RW and Kirkwood, TB and Mathers, JC and Turnbull, DM}, title = {Clonal expansion of early to mid-life mitochondrial DNA point mutations drives mitochondrial dysfunction during human ageing.}, journal = {PLoS genetics}, volume = {10}, number = {9}, pages = {e1004620}, pmid = {25232829}, issn = {1553-7404}, support = {G0700718/MRC_/Medical Research Council/United Kingdom ; 096919Z/11/Z/WT_/Wellcome Trust/United Kingdom ; R01AG19787/AG/NIA NIH HHS/United States ; G0601943/MRC_/Medical Research Council/United Kingdom ; 096919/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; R01 AG019787/AG/NIA NIH HHS/United States ; BB/C008200/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adolescent ; Adult ; Age Factors ; Aged ; Aging/*genetics ; Cytochromes c/genetics/metabolism ; DNA Mutational Analysis ; DNA, Mitochondrial/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Intestinal Mucosa/metabolism ; Middle Aged ; Mitochondria/*genetics/*metabolism ; Mitochondrial Proteins/genetics/metabolism ; Mutation Rate ; *Point Mutation ; Sensitivity and Specificity ; Young Adult ; }, abstract = {Age-related decline in the integrity of mitochondria is an important contributor to the human ageing process. In a number of ageing stem cell populations, this decline in mitochondrial function is due to clonal expansion of individual mitochondrial DNA (mtDNA) point mutations within single cells. However the dynamics of this process and when these mtDNA mutations occur initially are poorly understood. Using human colorectal epithelium as an exemplar tissue with a well-defined stem cell population, we analysed samples from 207 healthy participants aged 17-78 years using a combination of techniques (Random Mutation Capture, Next Generation Sequencing and mitochondrial enzyme histochemistry), and show that: 1) non-pathogenic mtDNA mutations are present from early embryogenesis or may be transmitted through the germline, whereas pathogenic mtDNA mutations are detected in the somatic cells, providing evidence for purifying selection in humans, 2) pathogenic mtDNA mutations are present from early adulthood (<20 years of age), at both low levels and as clonal expansions, 3) low level mtDNA mutation frequency does not change significantly with age, suggesting that mtDNA mutation rate does not increase significantly with age, and 4) clonally expanded mtDNA mutations increase dramatically with age. These data confirm that clonal expansion of mtDNA mutations, some of which are generated very early in life, is the major driving force behind the mitochondrial dysfunction associated with ageing of the human colorectal epithelium.}, }
@article {pmid25231721, year = {2016}, author = {Xiao, J and Song, N and Gao, T and McKay, RJ}, title = {The complete mitochondrial genome of Sillago indica (Perciformes: Sillaginidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1445-1446}, doi = {10.3109/19401736.2014.953085}, pmid = {25231721}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {In this study, the complete mitochondrial genome (mitogenome) sequence of Sillago indica has been determined by long polymerase chain reaction and primer walking methods. The complete mitochondrial genome is a circular molecule of 16,647 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA)), and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS), the central conserved sequence block domains (CSB-F, CSB-E, CSB-D and CSB-C), and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3).}, }
@article {pmid25231712, year = {2016}, author = {Zhang, N and Song, N and Gao, T}, title = {The complete mitochondrial genome of Lota lota (Gadiformes: Gadidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1437-1438}, doi = {10.3109/19401736.2014.953081}, pmid = {25231712}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Gadiformes/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {In this study, the complete mitochondrial genome (mitogenome) sequence of Lota lota has been determined by long polymerase chain reaction and primer walking methods. The mitogenome is a circular molecule of 16,547 bp in length and contains 37 mitochondrial genes including 13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA) and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS), the central conserved sequence block domains (CSB-F and CSB-D), and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3).}, }
@article {pmid25224037, year = {2014}, author = {Oelkrug, R and Goetze, N and Meyer, CW and Jastroch, M}, title = {Antioxidant properties of UCP1 are evolutionarily conserved in mammals and buffer mitochondrial reactive oxygen species.}, journal = {Free radical biology &amp; medicine}, volume = {77}, number = {}, pages = {210-216}, doi = {10.1016/j.freeradbiomed.2014.09.004}, pmid = {25224037}, issn = {1873-4596}, mesh = {Acclimatization ; Adipose Tissue, Brown/metabolism ; Animals ; Biological Evolution ; Eulipotyphla/*metabolism ; Ion Channels/*physiology ; Membrane Potential, Mitochondrial ; Mitochondria/*metabolism ; Mitochondrial Proteins/*physiology ; Oxidative Stress ; Reactive Oxygen Species/*metabolism ; Uncoupling Protein 1 ; }, abstract = {Mitochondrial uncoupling reduces reactive oxygen species (ROS) production and appears to be important for cellular signaling/protection, making it a focus for the treatment of metabolic and age-related diseases. Whereas the physiological role of uncoupling protein 1 (UCP1) of brown adipose tissue is established for thermogenesis, the function of UCP1 in the reduction of ROS in cold-exposed animals is currently under debate. Here, we investigated the role of UCP1 in mitochondrial ROS handling in the Lesser hedgehog tenrec (Echinops telfairi), a unique protoendothermic Malagasy mammal with recently identified brown adipose tissue (BAT). We show that the reduction of ROS by UCP1 activity also occurs in BAT mitochondria of the tenrec, suggesting that the antioxidative role of UCP1 is an ancient mammalian trait. Our analysis shows that the quantity of UCP1 displays strong control over mitochondrial hydrogen peroxide release, whereas other factors, such as mild cold, nonshivering thermogenesis, oxidative capacity, and mitochondrial respiration, do not correlate. Furthermore, hydrogen peroxide release from recoupled BAT mitochondria was positively associated with mitochondrial membrane potential. These findings led to a model of UCP1 controlling mitochondrial ROS release and, presumably, being controlled by high membrane potential, as proposed in the canonical model of "mild uncoupling". Our study further promotes a conserved role for UCP1 in the prevention of oxidative stress, which was presumably established during evolution before UCP1 was physiologically integrated into nonshivering thermogenesis.}, }
@article {pmid25220172, year = {2014}, author = {Holt, IJ and Jacobs, HT}, title = {Unique features of DNA replication in mitochondria: a functional and evolutionary perspective.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {11}, pages = {1024-1031}, doi = {10.1002/bies.201400052}, pmid = {25220172}, issn = {1521-1878}, support = {MC_U105663140/MRC_/Medical Research Council/United Kingdom ; MC_UP_1202/14/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Biological Evolution ; DNA Breaks, Double-Stranded ; DNA Breaks, Single-Stranded ; DNA Replication/*genetics ; DNA, Mitochondrial/*biosynthesis/genetics ; Genomic Instability/*genetics ; Humans ; Mitochondria/*genetics ; }, abstract = {Last year, we reported a new mechanism of DNA replication in mammals. It occurs inside mitochondria and entails the use of processed transcripts, termed bootlaces, which hybridize with the displaced parental strand as the replication fork advances. Here we discuss possible reasons why such an unusual mechanism of DNA replication might have evolved. The bootlace mechanism can minimize the occurrence and impact of single-strand breaks that would otherwise threaten genome stability. Furthermore, by providing an implicit mismatch recognition system, it should limit the occurrence of replication-dependent deletions and insertions, and defend against invading elements. Such a mechanism may also limit attempts to manipulate the mammalian mitochondrial genome.}, }
@article {pmid25211091, year = {2016}, author = {Yan, J and Liao, H and Zhu, Z and Xie, K and Guo, Y and Cai, J}, title = {The complete mitochondria genome of Parasarcophaga similis (Diptera: Sarcophagidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {3}, pages = {1642-1643}, doi = {10.3109/19401736.2014.958708}, pmid = {25211091}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Genome, Mitochondrial/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sarcophagidae/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {The complete mitochondrial genome of Parasarcophaga similis collected from China was determined using PCR reactions. The mitogenome was 15,158 bp in length with a total A + T content of 76.4%, consisting of 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes and a control region. The gene contents of the mitogenome were identical to those observed in other insects. The overall base compositions of A, G, C and T were 39.54%, 9.43%, 14.20% and 36.83%, respectively. This paper aimed to improve and perfect dipteran mitochondrial genomes and provided the first complete mitochondrial genome of Parasarcophaga similis for entomologists as a potential tool for application of phylogenetic analysis and forensic entomology.}, }
@article {pmid25208173, year = {2016}, author = {Ran, ML and Yang, AQ and Li, Z and Chen, B}, title = {The complete sequence of the mitochondrial genome of Guanling pig (Sus scrofa).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {3}, pages = {1583-1584}, doi = {10.3109/19401736.2014.958679}, pmid = {25208173}, issn = {2470-1408}, mesh = {Animals ; Codon, Initiator ; Codon, Terminator ; DNA, Mitochondrial/chemistry/isolation &amp; purification/metabolism ; *Genome, Mitochondrial ; Inverted Repeat Sequences/genetics ; Open Reading Frames/genetics ; RNA, Ribosomal/chemistry/isolation &amp; purification/metabolism ; RNA, Transfer/chemistry/isolation &amp; purification/metabolism ; Sequence Analysis, DNA ; Sus scrofa/*genetics ; Swine ; }, abstract = {Guanling pig is one of the native breeds in Guizhou Province in China. The compete mitochondrial genome of Guanling pig was determined by polymerase chain reaction (PCR). The result shows that the compete mitochondrial genome of Guanling pig is 16,731 bp, and it contains a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. The mitochondrial DNA control region of the Guanling pig contains repeat motif TAC ACG TGC G, 5' nucleotide of the first repeat is at the position 814 bp, and the repeat number is 13. The mitochondrial genome of Guanling pig subsequently provides important information in genetic mechanism and the evolution genomes.}, }
@article {pmid25207599, year = {2014}, author = {Tan, DX and Zheng, X and Kong, J and Manchester, LC and Hardeland, R and Kim, SJ and Xu, X and Reiter, RJ}, title = {Fundamental issues related to the origin of melatonin and melatonin isomers during evolution: relation to their biological functions.}, journal = {International journal of molecular sciences}, volume = {15}, number = {9}, pages = {15858-15890}, pmid = {25207599}, issn = {1422-0067}, mesh = {Animals ; Archaea/classification/metabolism ; Arylalkylamine N-Acetyltransferase/chemistry/metabolism ; Biological Evolution ; Isomerism ; Melatonin/chemistry/*metabolism ; Mitochondria/metabolism ; Plants/classification/metabolism ; }, abstract = {Melatonin and melatonin isomers exist and/or coexist in living organisms including yeasts, bacteria and plants. The levels of melatonin isomers are significantly higher than that of melatonin in some plants and in several fermented products such as in wine and bread. Currently, there are no reports documenting the presence of melatonin isomers in vertebrates. From an evolutionary point of view, it is unlikely that melatonin isomers do not exist in vertebrates. On the other hand, large quantities of the microbial flora exist in the gut of the vertebrates. These microorganisms frequently exchange materials with the host. Melatonin isomers, which are produced by these organisms inevitably enter the host's system. The origins of melatonin and its isomers can be traced back to photosynthetic bacteria and other primitive unicellular organisms. Since some of these bacteria are believed to be the precursors of mitochondria and chloroplasts these cellular organelles may be the primary sites of melatonin production in animals or in plants, respectively. Phylogenic analysis based on its rate-limiting synthetic enzyme, serotonin N-acetyltransferase (SNAT), indicates its multiple origins during evolution. Therefore, it is likely that melatonin and its isomer are also present in the domain of archaea, which perhaps require these molecules to protect them against hostile environments including extremely high or low temperature. Evidence indicates that the initial and primary function of melatonin and its isomers was to serve as the first-line of defence against oxidative stress and all other functions were acquired during evolution either by the process of adoption or by the extension of its antioxidative capacity.}, }
@article {pmid25196503, year = {2014}, author = {Dobler, R and Rogell, B and Budar, F and Dowling, DK}, title = {A meta-analysis of the strength and nature of cytoplasmic genetic effects.}, journal = {Journal of evolutionary biology}, volume = {27}, number = {10}, pages = {2021-2034}, doi = {10.1111/jeb.12468}, pmid = {25196503}, issn = {1420-9101}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/genetics ; Cytoplasm/*genetics ; Female ; Genetic Variation ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Linear Models ; Male ; Models, Genetic ; *Phenotype ; Plants/genetics ; }, abstract = {Genetic variation in cytoplasmic genomes (i.e. the mitochondrial genome in animals, and the combined mitochondrial and chloroplast genomes in plants) was traditionally assumed to accumulate under a neutral equilibrium model. This view has, however, come under increasing challenge from studies that have experimentally linked cytoplasmic genetic effects to the expression of life history phenotypes. Such results suggest that genetic variance located within the cytoplasm might be of evolutionary importance and potentially involved in shaping population evolutionary trajectories. As a step towards assessing this assertion, here we conduct a formal meta-analytic review to quantitatively assess the extent to which cytoplasmic genetic effects contribute to phenotypic expression across animal and plant kingdoms. We report that cytoplasmic effect sizes are generally moderate in size and associated with variation across a range of factors. Specifically, cytoplasmic effects on morphological traits are generally larger than those on life history or metabolic traits. Cytoplasmic effect sizes estimated at the between-species scale (via interspecies mix-and-matching of cytoplasmic and nuclear genomes) are larger than those at the within-species scale. Furthermore, cytoplasmic effects tied to epistatic interactions with the nuclear genome tend to be stronger than additive cytoplasmic effects, at least when restricting the data set to gonochorous animal species. Our results thus confirm that cytoplasmic genetic variation is commonly tied to phenotypic expression across plants and animals, implicate the cytoplasmic-nuclear interaction as a key unit on which natural selection acts and generally suggest that the genetic variation that lies within the cytoplasm is likely to be entwined in adaptive evolutionary processes.}, }
@article {pmid25193669, year = {2014}, author = {Bharti, SK and Sommers, JA and Zhou, J and Kaplan, DL and Spelbrink, JN and Mergny, JL and Brosh, RM}, title = {DNA sequences proximal to human mitochondrial DNA deletion breakpoints prevalent in human disease form G-quadruplexes, a class of DNA structures inefficiently unwound by the mitochondrial replicative Twinkle helicase.}, journal = {The Journal of biological chemistry}, volume = {289}, number = {43}, pages = {29975-29993}, pmid = {25193669}, issn = {1083-351X}, support = {//Intramural NIH HHS/United States ; }, mesh = {Aging/genetics ; Animals ; Base Sequence ; Circular Dichroism ; Computational Biology ; Conserved Sequence/genetics ; DNA Damage ; DNA Helicases/*metabolism ; *DNA Replication ; DNA, Mitochondrial/*genetics ; Disease/*genetics ; Evolution, Molecular ; *G-Quadruplexes ; Genome, Mitochondrial/genetics ; Humans ; Mitochondria/*enzymology ; Mitochondrial Proteins/*metabolism ; Molecular Sequence Data ; Neoplasms/genetics ; Nucleic Acid Denaturation ; Nucleotide Motifs/genetics ; Recombinant Proteins/isolation &amp; purification/metabolism ; Sequence Deletion/*genetics ; Substrate Specificity ; Telomere/metabolism ; Ultraviolet Rays ; }, abstract = {Mitochondrial DNA deletions are prominent in human genetic disorders, cancer, and aging. It is thought that stalling of the mitochondrial replication machinery during DNA synthesis is a prominent source of mitochondrial genome instability; however, the precise molecular determinants of defective mitochondrial replication are not well understood. In this work, we performed a computational analysis of the human mitochondrial genome using the "Pattern Finder" G-quadruplex (G4) predictor algorithm to assess whether G4-forming sequences reside in close proximity (within 20 base pairs) to known mitochondrial DNA deletion breakpoints. We then used this information to map G4P sequences with deletions characteristic of representative mitochondrial genetic disorders and also those identified in various cancers and aging. Circular dichroism and UV spectral analysis demonstrated that mitochondrial G-rich sequences near deletion breakpoints prevalent in human disease form G-quadruplex DNA structures. A biochemical analysis of purified recombinant human Twinkle protein (gene product of c10orf2) showed that the mitochondrial replicative helicase inefficiently unwinds well characterized intermolecular and intramolecular G-quadruplex DNA substrates, as well as a unimolecular G4 substrate derived from a mitochondrial sequence that nests a deletion breakpoint described in human renal cell carcinoma. Although G4 has been implicated in the initiation of mitochondrial DNA replication, our current findings suggest that mitochondrial G-quadruplexes are also likely to be a source of instability for the mitochondrial genome by perturbing the normal progression of the mitochondrial replication machinery, including DNA unwinding by Twinkle helicase.}, }
@article {pmid25193309, year = {2014}, author = {Hough, J and Ågren, JA and Barrett, SC and Wright, SI}, title = {Chromosomal distribution of cytonuclear genes in a dioecious plant with sex chromosomes.}, journal = {Genome biology and evolution}, volume = {6}, number = {9}, pages = {2439-2443}, pmid = {25193309}, issn = {1759-6653}, mesh = {Cell Nucleus/genetics/metabolism ; Chloroplasts/genetics/metabolism ; Chromosomes, Plant/*genetics/metabolism ; Evolution, Molecular ; Germ Cells, Plant/cytology/*metabolism ; Mitochondria/genetics/metabolism ; Rumex/cytology/*genetics ; }, abstract = {The coordination between nuclear and organellar genes is essential to many aspects of eukaryotic life, including basic metabolism, energy production, and ultimately, organismal fitness. Although nuclear genes are biparentally inherited, mitochondrial and chloroplast genes are almost exclusively maternally inherited, and this asymmetry may lead to a bias in the chromosomal distribution of nuclear genes whose products act in the mitochondria or chloroplasts. In particular, because X-linked genes have a higher probability of cotransmission with organellar genes (2/3) compared with autosomal genes (1/2), selection for coadaptation has been predicted to lead to an overrepresentation of nuclear-mitochondrial and nuclear-chloroplast genes on the X chromosome relative to autosomes. In contrast, the occurrence of sexually antagonistic organellar mutations might lead to selection for movement of cytonuclear genes from the X chromosome to autosomes to reduce male mutation load. Recent broad-scale comparative studies of N-mt distributions in animals have found evidence for these hypotheses in some species, but not others. Here, we use transcriptome sequences to conduct the first study of the chromosomal distribution of cytonuclear interacting genes in a plant species with sex chromosomes (Rumex hastatulus; Polygonaceae). We found no evidence of under- or overrepresentation of either N-mt or N-cp genes on the X chromosome, and thus no support for either the coadaptation or the sexual-conflict hypothesis. We discuss how our results from a species with recently evolved sex chromosomes fit into an emerging picture of the evolutionary forces governing the chromosomal distribution of nuclear-mitochondrial and nuclear-chloroplast genes.}, }
@article {pmid25190806, year = {2014}, author = {Ulrich, T and Oberhettinger, P and Schütz, M and Holzer, K and Ramms, AS and Linke, D and Autenrieth, IB and Rapaport, D}, title = {Evolutionary conservation in biogenesis of β-barrel proteins allows mitochondria to assemble a functional bacterial trimeric autotransporter protein.}, journal = {The Journal of biological chemistry}, volume = {289}, number = {43}, pages = {29457-29470}, pmid = {25190806}, issn = {1083-351X}, mesh = {Adhesins, Bacterial/chemistry/*metabolism ; *Conserved Sequence ; *Evolution, Molecular ; HeLa Cells ; Humans ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/metabolism ; Molecular Chaperones/metabolism ; *Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport ; Proteolysis ; Saccharomyces cerevisiae/metabolism ; }, abstract = {Yersinia adhesin A (YadA) belongs to a class of bacterial adhesins that form trimeric structures. Their mature form contains a passenger domain and a C-terminal β-domain that anchors the protein in the outer membrane (OM). Little is known about how precursors of such proteins cross the periplasm and assemble into the OM. In the present study we took advantage of the evolutionary conservation in the biogenesis of β-barrel proteins between bacteria and mitochondria. We previously observed that upon expression in yeast cells, bacterial β-barrel proteins including the transmembrane domain of YadA assemble into the mitochondrial OM. In the current study we found that when expressed in yeast cells both the monomeric and trimeric forms of full-length YadA were detected in mitochondria but only the trimeric species was fully integrated into the OM. The oligomeric form was exposed on the surface of the organelle in its native conformation and maintained its capacity to adhere to host cells. The co-expression of YadA with a mitochondria-targeted form of the bacterial periplasmic chaperone Skp, but not with SurA or SecB, resulted in enhanced levels of both forms of YadA. Taken together, these results indicate that the proper assembly of trimeric autotransporter can occur also in a system lacking the lipoproteins of the BAM machinery and is specifically enhanced by the chaperone Skp.}, }
@article {pmid25188293, year = {2014}, author = {Koumandou, VL and Kossida, S}, title = {Evolution of the F0F1 ATP synthase complex in light of the patchy distribution of different bioenergetic pathways across prokaryotes.}, journal = {PLoS computational biology}, volume = {10}, number = {9}, pages = {e1003821}, pmid = {25188293}, issn = {1553-7358}, mesh = {Archaea/classification/*genetics ; Bacteria/classification/*genetics ; DNA, Archaeal/*analysis/chemistry ; DNA, Bacterial/*analysis/chemistry ; Energy Metabolism/genetics ; Phylogeny ; Proton-Translocating ATPases/*chemistry ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; }, abstract = {Bacteria and archaea are characterized by an amazing metabolic diversity, which allows them to persist in diverse and often extreme habitats. Apart from oxygenic photosynthesis and oxidative phosphorylation, well-studied processes from chloroplasts and mitochondria of plants and animals, prokaryotes utilize various chemo- or lithotrophic modes, such as anoxygenic photosynthesis, iron oxidation and reduction, sulfate reduction, and methanogenesis. Most bioenergetic pathways have a similar general structure, with an electron transport chain composed of protein complexes acting as electron donors and acceptors, as well as a central cytochrome complex, mobile electron carriers, and an ATP synthase. While each pathway has been studied in considerable detail in isolation, not much is known about their relative evolutionary relationships. Wanting to address how this metabolic diversity evolved, we mapped the distribution of nine bioenergetic modes on a phylogenetic tree based on 16S rRNA sequences from 272 species representing the full diversity of prokaryotic lineages. This highlights the patchy distribution of many pathways across different lineages, and suggests either up to 26 independent origins or 17 horizontal gene transfer events. Next, we used comparative genomics and phylogenetic analysis of all subunits of the F0F1 ATP synthase, common to most bacterial lineages regardless of their bioenergetic mode. Our results indicate an ancient origin of this protein complex, and no clustering based on bioenergetic mode, which suggests that no special modifications are needed for the ATP synthase to work with different electron transport chains. Moreover, examination of the ATP synthase genetic locus indicates various gene rearrangements in the different bacterial lineages, ancient duplications of atpI and of the beta subunit of the F0 subcomplex, as well as more recent stochastic lineage-specific and species-specific duplications of all subunits. We discuss the implications of the overall pattern of conservation and flexibility of the F0F1 ATP synthase genetic locus.}, }
@article {pmid25187425, year = {2016}, author = {Zhou, A and Chen, J and Xie, S and Chen, Y and Zou, J}, title = {The complete mitochondrial genome of Ophicephalus argus kimurai (Perciformes: Channidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1419-1420}, doi = {10.3109/19401736.2014.953073}, pmid = {25187425}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The complete sequence of the mitochondrial genome of Ophicephalus argus kimurai was determined in this study. The genome was 16,558 bp in length. As in other vertebrates, it consisted of 22 transfer RNA (tRNA) genes, 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 1 noncoding control region. The overall base composition was estimated to be A, 27.2%; T, 24.2%; C, 31.6% and G, 17% with AT bias of 51.4%. The genomic composition, organization, and gene order of O. argus kimurai was similar to that obtained in most vertebrates. These results may provide the basis for the study of genetic structure as well as resource conservation and protection of O. argus kimurai.}, }
@article {pmid25187350, year = {2016}, author = {Véliz, D and Vega-Retter, C and Quezada-Romegialli, C}, title = {Next generation sequencing yields the complete mitochondrial genome of the Endangered Chilean silverside Basilichthys microlepidotus (Jenyns, 1841) (Teleostei, Atherinopsidae), validated with RNA-seq.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1505-1506}, doi = {10.3109/19401736.2014.953113}, pmid = {25187350}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Endangered Species ; Fishes/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/*methods ; }, abstract = {The complete sequence of the mitochondrial genome for the Chilean silverside Basilichthys microlepidotus is reported for the first time. The entire mitochondrial genome was 16,544 bp in length (GenBank accession no. KM245937); gene composition and arrangement was conformed to that reported for most fishes and contained the typical structure of 2 rRNAs, 13 protein-coding genes, 22 tRNAs and a non-coding region. The assembled mitogenome was validated against sequences of COI and Control Region previously sequenced in our lab, functional genes from RNA-Seq data for the same species and the mitogenome of two other atherinopsid species available in Genbank.}, }
@article {pmid25186275, year = {2016}, author = {Bennett, KF and Bailey, AW and Brambert, DJ and Ferhati, EW and Karson, CA and Nafasat, U and Wadleigh, JK and Wright, AH}, title = {The F type mitochondrial genome of the scorched mussel: Brachidontes exustus, (Mytiloida, Mytilidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1501-1502}, doi = {10.3109/19401736.2014.953111}, pmid = {25186275}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Biological Evolution ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Mytilidae/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The nominal species Brachidontes exustus (Linnaeus, 1758) is a cryptic complex. Long polymerase chain reactions and direct sequencing by primer walking was used to determine the complete F type mitochondrial genome of the Gulf of Mexico clade. The genome is 16,600 bp long and contains a single large unassigned presumptive control region, 13 protein-coding genes, 23 tRNA genes, and 2 rRNA genes, all coded for on the heavy chain. As in many other bivalves, there is the addition of tRNA-Met(AUA). The gene order is different from all other mitogenomes known for the family. The B. exustus mitogenome will contribute to a better understanding of the evolutionary history and phylogenetic relationships of the Mytilidae.}, }
@article {pmid25186141, year = {2016}, author = {Wang, B and Wang, S and Hu, M and Wang, F}, title = {Complete mitochondrial genome of Rhodeus lighti (Cypriniformes: Cyprinidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1497-1498}, doi = {10.3109/19401736.2014.953109}, pmid = {25186141}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {In this study, the complete mitochondrial genome (mitogenome) sequence of Rhodeus lighti (Cypriniformes: Cyprinidae) was determined by long PCR and primer walking methods. The complete mitochondrial genome is 16,677 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes as well as a displacement loop (D-loop). The overall base composition of the genome is A (28.87%), T (27.22%), C (26.53%) and G (17.38%). The mitogenome of R. lighti displayed novel gene order arrangement compared with published Rhodeus sinensis to date. The mitogenome would contribute to resolving phylogenetic position and interrelationships of Acheilognathinae.}, }
@article {pmid25186060, year = {2016}, author = {Liu, F and Pang, S}, title = {Complete mitochondrial genome of the brown alga Scytosiphon lomentaria (Scytosiphonaceae, Phaeophyceae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1494-1496}, doi = {10.3109/19401736.2014.953108}, pmid = {25186060}, issn = {2470-1408}, mesh = {Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phaeophyceae/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {We determined the complete mitochondrial genome of Scytosiphon lomentaria (Lyngbye) Link, which is the first representative of the genus Scytosiphon C. Agardh. The circular mitogenome of S. lomentaria is 36,918 bp in length, with the overall A+T content of 65.86%. The genome contains 67 genes, including 3 ribosomal RNA genes (rRNA), 25 transfer RNA genes (tRNA), 35 protein-coding genes and 4 unidentified open reading frames (ORFs). The gene order of S. lomentaria mitogenome conforms to that of Ectocarpales mitogenomes (not including Pylaiella littoralis), i.e. Petalonia fascia, and Ectocarpus siliculosus, but differs from Laminariales, Desmarestiales, Fucales and Dictyotales with position variation of several genes. The S. lomentaria mitogenome has an overall nucleotide sequence identity of 80.4% with P. fascia, and 74.9% with E. siliculosus. The present data is of value to phylogenetic analyses of such a diverse Scytosiphonaceae family as well as to understanding of mitogenome evolution in brown algae.}, }
@article {pmid25186010, year = {2014}, author = {Philp, A and Rowland, T and Perez-Schindler, J and Schenk, S}, title = {Understanding the acetylome: translating targeted proteomics into meaningful physiology.}, journal = {American journal of physiology. Cell physiology}, volume = {307}, number = {9}, pages = {C763-73}, pmid = {25186010}, issn = {1522-1563}, support = {P30 AR-058878/AR/NIAMS NIH HHS/United States ; R24 HD-050837/HD/NICHD NIH HHS/United States ; R01 AG043120/AG/NIA NIH HHS/United States ; MR/K00414X/1/MRC_/Medical Research Council/United Kingdom ; R01 AG-043120/AG/NIA NIH HHS/United States ; }, mesh = {Acetylation ; Acetyltransferases/*metabolism ; Histone Acetyltransferases/metabolism ; Humans ; Lysine/metabolism ; Mitochondrial Proteins/metabolism ; Muscle, Skeletal/enzymology ; *Protein Processing, Post-Translational ; Proteomics ; }, abstract = {It is well established that exercise elicits a finely tuned adaptive response in skeletal muscle, with contraction frequency, duration, and recovery shaping skeletal muscle plasticity. Given the power of physical activity to regulate metabolic health, numerous research groups have focused on the molecular mechanisms that sense, interpret, and translate this contractile signal into postexercise adaptation. While our current understanding is that contraction-sensitive allosteric factors (e.g., Ca(2+), AMP, NAD(+), and acetyl-CoA) initiate signaling changes, how the muscle translates changes in these factors into the appropriate adaptive response remains poorly understood. During the past decade, systems biology approaches, utilizing "omics" screening techniques, have allowed researchers to define global processes of regulation with incredible sensitivity and specificity. As a result, physiologists are now able to study substrate flux with stable isotope tracers in combination with metabolomic approaches and to coordinate these functional changes with proteomic and transcriptomic analysis. In this review, we highlight lysine acetylation as an important posttranslational modification in skeletal muscle. We discuss the evolution of acetylation research and detail how large proteomic screens in diverse metabolic systems have led to the current hypothesis that acetylation may be a fundamental mechanism to fine-tune metabolic adaptation in skeletal muscle.}, }
@article {pmid25185954, year = {2016}, author = {Zhang, P and Fang, HY and Pan, WJ and Pan, HC}, title = {The complete mitochondrial genome of the writing spider Argiope amoena (Araneae: Araneidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1492-1493}, doi = {10.3109/19401736.2014.953107}, pmid = {25185954}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Codon ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Sequence Analysis, DNA/methods ; Spiders/*genetics ; }, abstract = {The complete mitochondrial genome of Argiope amoena is a circular molecule of 14,121 bp in length, contains 13 protein-coding genes, 2 ribosomal RNAs, 21 transfer RNAs genes and a control region. The A + T content of the overall base composition of H-strand is 72.1% (T: 38.2%; C: 10.6%; A: 33.9%; G: 17.3%). ND1, ND4, ND6 and ATP6 begin with ATA as start codon, ND4L begins with ATG, ATP8, Cyt b, ND2 and ND3 genes begin with ATT, and the other two protein-coding genes begin with TTG. ATP6, ATP8, COI, COII, COIII, Cyt b, ND1, ND2, ND3, ND4L and ND5 genes are terminated with TAA as stop codon, ND6 ends with TAG, and ND4 ends with T.}, }
@article {pmid25185794, year = {2016}, author = {Kim, EB and Lee, SG}, title = {The complete mitochondrial genome of the Mongolian gerbil, Meriones unguiculatus (Rodentia: Muridae: Gerbillinae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1457-1458}, doi = {10.3109/19401736.2014.953091}, pmid = {25185794}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Evolution, Molecular ; Genome Size ; *Genome, Mitochondrial ; Gerbillinae/*genetics ; Mitochondria/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The complete mitochondrial genome of the Mongolian gerbil, Meriones unguiculatus, was sequenced. The 16,360 bp long genome has 37 genes typical for rodent mitogenomes, including 22 tRNA genes, 2 rRNA genes, and 13 protein-coding genes. The total GC content of the mitochondrial genome is 36.96% with the base composition of 32.61% A, 23.71% C, 13.24% G, and 30.44% T. Translational terminators of three genes (cytb, cox3, and nad4) were generated by the addition of 3' A residues to the mRNA. This novel rodent mitochondrial genome will provide comparable information for understanding the rodent mitochondrial evolution.}, }
@article {pmid25185698, year = {2016}, author = {Deng, PJ and Wang, WM and Huang, XC and Wu, XP and Xie, GL and Ouyang, S}, title = {The complete mitochondrial genome of Chinese land snail Mastigeulota kiangsinensis (Gastropoda: Pulmonata: Bradybaenidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1441-1442}, doi = {10.3109/19401736.2014.953083}, pmid = {25185698}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Gene Rearrangement ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Snails/*genetics ; }, abstract = {Mastigeulota kiangsinensis is an endemic and widespread land snail in China. The complete mitochondrial genome of M. kiangsinensis was first determined using long PCR reactions and primer walking method (accession number KM083123). The genome has a length of 14,029 bp, containing 37 typical mitochondrial genes (13 protein-coding genes, 22 tRNA genes and 2 rRNA genes). The base composition of the whole heavy strand is A 29.48%, T 37.92%, C 14.38% and G 18.22%. Gene order of M. kiangsinensis is identical to Euhadra herklotsi, but gene rearrangements are found compared with other mitochondrial genomes described in Stylommatophora. tRNA(Thr) is located in COIII, which has not been found in other helicoids so far. This new complete mitochondrial genome can be the basic data for further studies on mitogenome comparison, molecular taxonomy and phylogenetic analysis in land snails and Molluscs at large.}, }
@article {pmid25185454, year = {2016}, author = {Wu, YP and Zhao, JL and Su, TJ and He, QS and Xie, JL and Zhu, CD}, title = {The complete mitochondrial genome of Carposina sasakii (Lepidoptera: Carposinidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1432-1434}, doi = {10.3109/19401736.2014.953079}, pmid = {25185454}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genome Size ; Genome, Insect ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Moths/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The peach fruit moth, Carposina sasakii belongs to Carposinidae in Lepidoptera. In this paper, we described the complete mitogenome of C. sasakii. It is 15,611 bp in length, including 13 PCGs, 2 rRNAs, 22 tRNAs and a major noncoding A + T-rich region, which revealed the typical gene content found in other metazoan mitogenomes. The overall base composition is 42.0% A, 39.5% T, 7.75% G and 10.75% C. The A + T-rich region is located between rrnS and trnM. There is a motif ATAGA in downstream of rrnS followed by a 19 bp Poly-T stretch. The Poly-A is not found in upstream of trnM, and the position of Poly-A is replaced by a stem-loop structure. There are eight mononucleotide repeat sequences (Tn/An) with the length of 7 bp-19bp, three dinucleotide repeat sequences (TA)n/(AT)n, and a longer repeat sequence (AATATATA)5 in A + T-rich region. The mononucleotide repeat sequences occur repeatedly in A + T-rich reigion of C. sasakii, which is special in insects sequenced of Lepidoptera.}, }
@article {pmid25184569, year = {2014}, author = {Harrison, E and Trexler, JC and Collins, TM and Vazquez-Domínguez, E and Razo-Mendivil, U and Matamoros, WA and Barrientos, C}, title = {Genetic evidence for multiple sources of the non-native fish Cichlasoma urophthalmus (Günther; Mayan Cichlids) in southern Florida.}, journal = {PloS one}, volume = {9}, number = {9}, pages = {e104173}, pmid = {25184569}, issn = {1932-6203}, mesh = {Animal Distribution ; Animals ; Cell Nucleus/genetics ; Cichlids/classification/*genetics ; Cytochromes b/genetics ; Ecosystem ; Female ; Florida ; *Genetic Speciation ; Genetic Variation ; Haplotypes ; *Hybridization, Genetic ; Male ; Microsatellite Repeats ; Mitochondria/genetics ; *Phylogeny ; Phylogeography ; South America ; }, abstract = {The number and diversity of source populations may influence the genetic diversity of newly introduced populations and affect the likelihood of their establishment and spread. We used the cytochrome b mitochondrial gene and nuclear microsatellite loci to identify the sources of a successful invader in southern Florida, USA, Cichlasoma urophthalmus (Mayan cichlid). Our cytochrome b data supported an introduction from Guatemala, while our microsatellite data suggested movement of Mayan Cichlids from the upper Yucatán Peninsula to Guatemala and introductions from Guatemala and Belize to Florida. The mismatch between mitochondrial and nuclear genomes suggests admixture of a female lineage from Guatemala, where all individuals were fixed for the mitochondrial haplotype found in the introduced population, and a more diverse but also relatively small number of individuals from Belize. The Florida cytochrome b haplotype appears to be absent from Belize (0 out of 136 fish screened from Belize had this haplotype). Genetic structure within the Florida population was minimal, indicating a panmictic population, while Mexican and Central American samples displayed more genetic subdivision. Individuals from the Upper Yucatán Peninsula and the Petén region of Guatemala were more genetically similar to each other than to fish from nearby sites and movement of Mayan Cichlids between these regions occurred thousands of generations ago, suggestive of pre-Columbian human transportation of Mayan Cichlids through this region. Mayan Cichlids present a rare example of cytonuclear disequilibrium and reduced genetic diversity in the introduced population that persists more than 30 years (at least 7-8 generations) after introduction. We suggest that hybridization occurred in ornamental fish farms in Florida and may contribute their establishment in the novel habitat. Hybridization prior to release may contribute to other successful invasions.}, }
@article {pmid25183231, year = {2014}, author = {Arockiaraj, J and Palanisamy, R and Bhatt, P and Kumaresan, V and Gnanam, AJ and Pasupuleti, M and Kasi, M}, title = {A novel murrel Channa striatus mitochondrial manganese superoxide dismutase: gene silencing, SOD activity, superoxide anion production and expression.}, journal = {Fish physiology and biochemistry}, volume = {40}, number = {6}, pages = {1937-1955}, pmid = {25183231}, issn = {1573-5168}, mesh = {Aeromonas hydrophila ; Amino Acid Sequence ; Animals ; Aphanomyces ; Base Sequence ; Cells, Cultured ; Computational Biology ; Fishes/*metabolism ; Gene Expression Regulation, Enzymologic/*physiology ; *Gene Silencing ; Gram-Negative Bacterial Infections/metabolism/veterinary ; Infections/metabolism/veterinary ; Mitochondria/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Species Specificity ; Superoxide Dismutase/genetics/*metabolism ; Superoxides/*metabolism ; }, abstract = {We have reported the molecular characterization including gene silencing, superoxide activity, superoxide anion production, gene expression and molecular characterization of a mitochondrial manganese superoxide dismutase (mMnSOD) from striped murrel Channa striatus (named as CsmMnSOD). The CsmMnSOD polypeptide contains 225 amino acids with a molecular weight of 25 kDa and a theoretical isoelectric point of 8.3. In the N-terminal region, CsmMnSOD carries a mitochondrial targeting sequence and a superoxide dismutases (SOD) Fe domain (28-109), and in C-terminal region, it carries another SOD Fe domain (114-220). The CsmMnSOD protein sequence shared significant similarity with its homolog of MnSOD from rock bream Oplegnathus fasciatus (96%). The phylogenetic analysis showed that the CsmMnSOD fell in the clade of fish mMnSOD group. The monomeric structure of CsmMnSOD possesses 9 α-helices (52.4%), 3 β-sheets (8.8%) and 38.8% random coils. The highest gene expression was noticed in liver, and its expression was inducted with fungal (Aphanomyces invadans) and bacterial (Aeromonas hydrophila) infections. The gene silencing results show that the fish that received dsRNA exhibited significant (P < 0.05) changes in expression when compared to their non-injected and fish physiological saline-injected controls. The SOD activity shows that the activity increases with the spread of infection and decreases once the molecule controls the pathogen. The capacity of superoxide anion production was determined by calculating the granular blood cell count during infection in murrel. It shows that the infection influenced the superoxide radical production which plays a major role in killing the pathogens. Overall, this study indicated the defense potentiality of CsmMnSOD; however, further research is necessary to explore its capability at protein level.}, }
@article {pmid25182379, year = {2015}, author = {Stone, JD and Storchova, H}, title = {The application of RNA-seq to the comprehensive analysis of plant mitochondrial transcriptomes.}, journal = {Molecular genetics and genomics : MGG}, volume = {290}, number = {1}, pages = {1-9}, pmid = {25182379}, issn = {1617-4623}, mesh = {Genome, Mitochondrial/genetics ; Mitochondria/*genetics ; Plants/*genetics ; RNA Editing/genetics ; Sequence Analysis, RNA/*methods ; Transcriptome/*genetics ; }, abstract = {We review current studies of plant mitochondrial transcriptomes performed by RNA-seq, highlighting methodological challenges unique to plant mitochondria. We propose ways to improve read mapping accuracy and sensitivity such as modifying a reference genome at RNA editing sites, using splicing- and ambiguity-competent aligners, and masking chloroplast- or nucleus-derived sequences. We also outline modified RNA-seq methods permitting more accurate detection and quantification of partially edited sites and the identification of transcription start sites on a genome-wide scale. The application of RNA-seq goes beyond genome-wide determination of transcript levels and RNA maturation events, and emerges as an elegant resource for the comprehensive identification of editing, splicing, and transcription start sites. Thus, improved RNA-seq methods customized for plant mitochondria hold tremendous potential for advancing our understanding of plant mitochondrial evolution and cyto-nuclear interactions in a broad array of plant species.}, }
@article {pmid25179144, year = {2014}, author = {Penny, D and Collins, LJ and Daly, TK and Cox, SJ}, title = {The relative ages of eukaryotes and akaryotes.}, journal = {Journal of molecular evolution}, volume = {79}, number = {5-6}, pages = {228-239}, pmid = {25179144}, issn = {1432-1432}, mesh = {Archaea/*chemistry/classification/cytology ; *Biological Evolution ; Cell Nucleus/genetics/metabolism ; Eukaryotic Cells/*chemistry/classification/metabolism ; Exons ; Introns ; Meiosis ; Mitochondria/chemistry/metabolism ; Mitosis ; *Origin of Life ; Phylogeny ; Prokaryotic Cells/*chemistry/classification/metabolism ; Spliceosomes/genetics ; Terminology as Topic ; Time Factors ; }, abstract = {The Last Eukaryote Common Ancestor (LECA) appears to have the genetics required for meiosis, mitosis, nucleus and nuclear substructures, an exon/intron gene structure, spliceosomes, many centres of DNA replication, etc. (and including mitochondria). Most of these features are not generally explained by models for the origin of the Eukaryotic cell based on the fusion of an Archeon and a Bacterium. We find that the term 'prokaryote' is ambiguous and the non-phylogenetic term akaryote should be used in its place because we do not yet know the direction of evolution between eukaryotes and akaryotes. We use the term 'protoeukaryote' for the hypothetical stem group ancestral eukaryote that took up a bacterium as an endosymbiont that formed the mitochondrion. It is easier to make detailed models with a eukaryote to an akaryote transition, rather than vice versa. So we really are at a phylogenetic impasse in not being confident about the direction of change between eukaryotes and akaryotes.}, }
@article {pmid25172904, year = {2014}, author = {Hehenberger, E and Imanian, B and Burki, F and Keeling, PJ}, title = {Evidence for the retention of two evolutionary distinct plastids in dinoflagellates with diatom endosymbionts.}, journal = {Genome biology and evolution}, volume = {6}, number = {9}, pages = {2321-2334}, pmid = {25172904}, issn = {1759-6653}, mesh = {*Biological Evolution ; Diatoms/classification/*genetics/physiology ; Dinoflagellida/classification/*genetics/physiology ; Molecular Sequence Data ; Phylogeny ; Plastids/*genetics/physiology ; *Symbiosis ; }, abstract = {Dinoflagellates harboring diatom endosymbionts (termed "dinotoms") have undergone a process often referred to as "tertiary endosymbiosis"--the uptake of algae containing secondary plastids and integration of those plastids into the new host. In contrast to other tertiary plastids, and most secondary plastids, the endosymbiont of dinotoms is distinctly less reduced, retaining a number of cellular features, such as their nucleus and mitochondria and others, in addition to their plastid. This has resulted in redundancy between host and endosymbiont, at least between some mitochondrial and cytosolic metabolism, where this has been investigated. The question of plastidial redundancy is particularly interesting as the fate of the host dinoflagellate plastid is unclear. The host cytosol possesses an eyespot that has been postulated to be a remnant of the ancestral peridinin plastid, but this has not been tested, nor has its possible retention of plastid functions. To investigate this possibility, we searched for plastid-associated pathways and functions in transcriptomic data sets from three dinotom species. We show that the dinoflagellate host has indeed retained genes for plastid-associated pathways and that these genes encode targeting peptides similar to those of other dinoflagellate plastid-targeted proteins. Moreover, we also identified one gene encoding an essential component of the dinoflagellate plastid protein import machinery, altogether suggesting the presence of a functioning plastid import system in the host, and by extension a relict plastid. The presence of the same plastid-associated pathways in the endosymbiont also extends the known functional redundancy in dinotoms, further confirming the unusual state of plastid integration in this group of dinoflagellates.}, }
@article {pmid25170648, year = {2014}, author = {Soltani, A and Ghavami, F and Mergoum, M and Hegstad, J and Noyszewski, A and Meinhardt, S and Kianian, SF}, title = {Analysis of ATP6 sequence diversity in the Triticum-Aegilops species group reveals the crucial role of rearrangement in mitochondrial genome evolution.}, journal = {Genome}, volume = {57}, number = {5}, pages = {279-288}, doi = {10.1139/gen-2014-0024}, pmid = {25170648}, issn = {1480-3321}, mesh = {Chromosomes, Plant ; Evolution, Molecular ; Gene Rearrangement ; *Genome, Mitochondrial ; Mitochondrial Proton-Translocating ATPases/*genetics ; Phylogeny ; Point Mutation ; Selection, Genetic ; Triticum/classification/*genetics ; }, abstract = {Mutation and chromosomal rearrangements are the two main forces of increasing genetic diversity for natural selection to act upon, and ultimately drive the evolutionary process. Although genome evolution is a function of both forces, simultaneously, the ratio of each can be varied among different genomes and genomic regions. It is believed that in plant mitochondrial genome, rearrangements play a more important role than point mutations, but relatively few studies have directly addressed this phenomenon. To address this issue, we isolated and sequenced the ATP6-1 and ATP6-2 genes from 46 different euplasmic and alloplasmic wheat lines. Four different ATP6-1 orthologs were detected, two of them reported for the first time. Expression analysis revealed that all four orthologs are transcriptionally active. Results also indicated that both point mutation and genomic rearrangement are involved in the evolution of ATP6. However, rearrangement is the predominant force that triggers drastic variation. Data also indicated that speciation of domesticated wheat cultivars were simultaneous with the duplication of this gene. These results directly support the notion that rearrangement plays a significant role in driving plant mitochondrial genome evolution.}, }
@article {pmid25168384, year = {2015}, author = {Pla-Martín, D and Calpena, E and Lupo, V and Márquez, C and Rivas, E and Sivera, R and Sevilla, T and Palau, F and Espinós, C}, title = {Junctophilin-1 is a modifier gene of GDAP1-related Charcot-Marie-Tooth disease.}, journal = {Human molecular genetics}, volume = {24}, number = {1}, pages = {213-229}, doi = {10.1093/hmg/ddu440}, pmid = {25168384}, issn = {1460-2083}, mesh = {Animals ; Calcium/metabolism ; Cell Line ; Charcot-Marie-Tooth Disease/*genetics/metabolism/*pathology ; Evolution, Molecular ; Genes, Modifier ; Genetic Predisposition to Disease ; Humans ; Membrane Proteins/*genetics/metabolism ; Mice ; Mitochondria/metabolism ; Mutation ; Neoplasm Proteins/metabolism ; Nerve Tissue Proteins/*genetics/*metabolism ; Phylogeny ; Stromal Interaction Molecule 1 ; }, abstract = {Mutations in the GDAP1 gene cause different forms of Charcot-Marie-Tooth (CMT) disease, and the primary clinical expression of this disease is markedly variable in the dominant inheritance form (CMT type 2K; CMT2K), in which carriers of the GDAP1 p.R120W mutation can display a wide range of clinical severity. We investigated the JPH1 gene as a genetic modifier of clinical expression variability because junctophilin-1 (JPH1) is a good positional and functional candidate. We demonstrated that the JPH1-GDAP1 cluster forms a paralogon and is conserved in vertebrates. Moreover, both proteins play a role in Ca(2+) homeostasis, and we demonstrated that JPH1 is able to restore the store-operated Ca(2+) entry (SOCE) activity in GDAP1-silenced cells. After the mutational screening of JPH1 in a series of 24 CMT2K subjects who harbour the GDAP1 p.R120W mutation, we characterized the JPH1 p.R213P mutation in one patient with a more severe clinical picture. JPH1(p.R213P) cannot rescue the SOCE response in GDAP1-silenced cells. We observed that JPH1 colocalizes with STIM1, which is the activator of SOCE, in endoplasmic reticulum-plasma membrane puncta structures during Ca(2+) release in a GDAP1-dependent manner. However, when GDAP1(p.R120W) is expressed, JPH1 seems to be retained in mitochondria. We also established that the combination of GDAP1(p.R120W) and JPH1(p.R213P) dramatically reduces SOCE activity, mimicking the effect observed in GDAP1 knock-down cells. In summary, we conclude that JPH1 and GDAP1 share a common pathway and depend on each other; therefore, JPH1 can contribute to the phenotypical consequences of GDAP1 mutations.}, }
@article {pmid25165143, year = {2014}, author = {Heublein, M and Burguillos, MA and Vögtle, FN and Teixeira, PF and Imhof, A and Meisinger, C and Ott, M}, title = {The novel component Kgd4 recruits the E3 subunit to the mitochondrial α-ketoglutarate dehydrogenase.}, journal = {Molecular biology of the cell}, volume = {25}, number = {21}, pages = {3342-3349}, pmid = {25165143}, issn = {1939-4586}, mesh = {Amino Acid Sequence ; Animals ; Cell Line ; Conserved Sequence ; Evolution, Molecular ; Gene Knockdown Techniques ; Ketoglutarate Dehydrogenase Complex/genetics/*metabolism ; Mice ; Microglia/cytology ; Mitochondria/metabolism ; Mitochondrial Proteins/genetics/isolation &amp; purification/*metabolism ; Molecular Sequence Data ; Protein Structure, Tertiary ; Protein Subunits/genetics/metabolism ; Ribosomal Proteins/genetics/isolation &amp; purification/*metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/isolation &amp; purification/*metabolism ; Sequence Homology, Amino Acid ; }, abstract = {The mitochondrial citric acid cycle is a central hub of cellular metabolism, providing intermediates for biosynthetic pathways and channeling electrons to the respiratory chain complexes. In this study, we elucidated the composition and organization of the multienzyme complex α-ketoglutarate dehydrogenase (α-KGDH). In addition to the three classical E1-E3 subunits, we identified a novel component, Kgd4 (Ymr31/MRPS36), which was previously assigned to be a subunit of the mitochondrial ribosome. Biochemical analyses demonstrate that this protein plays an evolutionarily conserved role in the organization of mitochondrial α-KGDH complexes of fungi and animals. By binding to both the E1-E2 core and the E3 subunit, Kgd4 acts as a molecular adaptor that is necessary to a form a stable α-KGDH enzyme complex. Our work thus reveals a novel subunit of a key citric acid-cycle enzyme and shows how this large complex is organized.}, }
@article {pmid25163032, year = {2016}, author = {Li, X and Wang, Y and Su, S and Yang, D}, title = {The complete mitochondrial genomes of Musca domestica and Scathophaga stercoraria (Diptera: Muscoidea: Muscidae and Scathophagidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1435-1436}, doi = {10.3109/19401736.2014.953080}, pmid = {25163032}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genome Size ; Genome, Insect ; *Genome, Mitochondrial ; Houseflies/*genetics ; Mitochondria/*genetics ; Muscidae/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The complete mitochondrial genomes of Musca domestica (Muscidae) and Scathophaga stercoraria (Scathophagidae) are circular molecules of 16,108 bp and 16,223 bp in length, respectively. The first complete mitochondrial genome of Scathophagidae is reported here. Both genomes contain all 37 genes, including 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a large control region, with conserved arrangement pattern reported in all cyclorrhaphan flies. All PCGs start with standard ATN codons except for the CO1 which starts with TCG in both species. All PCGs terminate with the common stop codons TAA or TAG, except for the CO2 and ND5 in both species and ND4 in S. stercoraria which end with a single T.}, }
@article {pmid25163015, year = {2016}, author = {Hu, XD and Gao, LZ}, title = {The complete mitochondrial genome of domestic sheep, Ovis aries.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1425-1427}, doi = {10.3109/19401736.2014.953076}, pmid = {25163015}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genetic Variation ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Sheep, Domestic/*genetics ; }, abstract = {In this study, we report a complete mitochondrial (mt) genome sequence of the Texel ewe, Ovis aries. The total genome is 16,615 bp in length and its overall base composition was estimated to be 33.68% for A, 27.36% for T, 25.86% for C, and 13.10% for G indicating an AT-rich (61.04%) feature in the O. aries mtgenome. It contains a total of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a control region (D-loop region). Comparisons with other publicly available sheep mitogenomes revealed a bunch of nucleotide diversity. This complete mitgenome sequence would enlarge useful genomic information for further studies on sheep evolution and domestication that will enhance germplasm conservation and breeding programs of O. aries.}, }
@article {pmid25162993, year = {2016}, author = {Tong, QL and Yao, YT and Lin, LH and Ji, X}, title = {The complete mitochondrial genome of Eremias vermiculata (Squamata: Lacertidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1447-1448}, doi = {10.3109/19401736.2014.953086}, pmid = {25162993}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genome Size ; *Genome, Mitochondrial ; Lizards/*genetics ; Mitochondria/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {In this paper, we report the complete mitochondrial genome of Eremias vermiculata (Squamata: Lacertidae), which is a circular molecule of 19,914 bp in size and consists of 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and 1 putative control region. The A + T content of overall base of the composition of H-strand is 59.8% (T: 28.9%, C: 27.2%, A: 30.9%, G: 13.0%). All of the results provide powerful data to further study of the molecular systematics, species identification and conservation genetics.}, }
@article {pmid25162966, year = {2016}, author = {Pan, WJ and Fang, HY and Zhang, P and Pan, HC}, title = {The complete mitochondrial genome of flat spider Selenops bursarius (Araneae: Selenopidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1488-1489}, doi = {10.3109/19401736.2014.953105}, pmid = {25162966}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Sequence Analysis, DNA/methods ; Spiders/*genetics ; }, abstract = {The complete mitochondrial genome of Selenops bursarius is a circular molecule of 14,272 bp in length, containing 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a control region. The A + T content of the overall base composition of H-strand is 74.4% (T: 41.8%; C: 8.7%; A: 32.6%; G: 16.9%). COI gene begins with TTA as start codon; COII gene begins with GTG as start codon; ATP6 and ATP8 genes begin with ATA as start codon; COIII and ND4 genes begin with TTG as start codon; ND1 and ND5 genes begin with ATC as start codon, while other five protein-coding genes start with ATT. ATP6, ATP8, COII, COIII, ND2, ND3, ND4 and ND5 genes are terminated with TAA as stop codon, ND1 ends with TAG, COI ends with TG, Cyt b, ND4L and ND6 end with T.}, }
@article {pmid25162799, year = {2016}, author = {Liu, F and Pang, S and Chen, W}, title = {Complete mitochondrial genome of the brown alga Sargassum hemiphyllum (Sargassaceae, Phaeophyceae): comparative analyses.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1468-1470}, doi = {10.3109/19401736.2014.953096}, pmid = {25162799}, issn = {2470-1408}, mesh = {Base Composition ; DNA, Intergenic ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sargassum/classification/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Sargassum hemiphyllum (Turner) C. Agardh is a common low intertidal brown alga in the northwestern Pacific, and two varieties (var. chinense and var. hemiphyllum) of this alga have been determined based on morphological and molecular data. In this study, we present the complete mitochondrial genome of S. hemiphyllum var. chinense. The circular-mapping S. hemiphyllum mitogenome of 34,686 bp has an overall A+T content of 63.43%, and contains 65 densely packed genes. The total intergenic spacer regions are 1597 bp, constituting 4.60% of the mitogenome. The gene content and genome organization of S. hemiphyllum are identical to that of other reported Sargassum species. The identity comparison of overall mitogenome sequences and phylogenomic analyses indicate that S. hemiphyllum has a closer evolutionary relationship with Sargassum muticum than other Sargassum species analyzed. The present mitogenomic data provide a powerful tool for definition of varieties and studies of population structure in S. hemiphyllum.}, }
@article {pmid25162765, year = {2016}, author = {Li, Y and Tang, M and Xue, Y and Chen, HJ and Ye, Q and Li, Y}, title = {Complete mitochondrial genome of the Chinese balitorine loach, Metahomaloptera omeiensis (Teleostei, Cypriniformes).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1449-1450}, doi = {10.3109/19401736.2014.953087}, pmid = {25162765}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Cypriniformes/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The Metahomaloptera omeiensis is the only one species within the genus, Metahomaloptera. The complete mitochondrial genome of M. omeiensis was sequenced, which was 16,558 bp in length, including 13 protein-coding genes, 7 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 1 control region. It has the typical circular molecule structure of vertebrate's mitochondrial genome. The whole base composition was estimated to be 29.44% A, 25.44% T, 28.28% C and 16.84% G with AT bias of 54.88%. The complete mitogenome of M. omeiensis provides the basis for genetic resources and phylogenetic analyses on this freshwater fish species.}, }
@article {pmid25162745, year = {2016}, author = {Chen, DS and Jin, PY and Hong, XY}, title = {The complete mitochondrial genome of Tetranychus truncatus Ehara (Acari: Tetranychidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1480-1481}, doi = {10.3109/19401736.2014.953101}, pmid = {25162745}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Tetranychidae/*genetics ; }, abstract = {The complete mitochondrial genome of Tetranychus truncatus Ehara (Acari: Tetranychidae) is a typical circular DNA with length of 13,089 bp (GenBank accession number: KM111296). The genome contains all 13 protein-coding genes (PCGs), an A + T-rich region, two rRNA genes and 22 tRNA genes. The A + T content of the mitochondrial genome is 84.5%. The AT-skew is positive (0.032) while the GC-skew is negative (-0.058). The gene arrangement is conserved in T. urticae, Panonychus citri and P. ulmi which are in the same family (Tetranychidae). The A + T-rich region is only 43 bp in length with high A + T content (97.7%). All the PCGs start with typical ATD codons. Eight PCGs have complete TAA stop codons, while five PCGs have an incomplete stop codon (T).}, }
@article {pmid25162732, year = {2016}, author = {Shi, Q and Zhang, W and Hao, J}, title = {The complete mitochondrial genome of Callerebia suroia (Lepidoptera: Nymphalidae: Satyrinae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1463-1465}, doi = {10.3109/19401736.2014.953094}, pmid = {25162732}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Butterflies/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The complete mitochondrial genome (mitogenome) of Callerebia suroia (Lepidoptera: Nymphalidae: Satyrinae) was determined and analyzed in this paper. The circular genome is 15,208 bp long, including 37 typical mitochondrial genes and one non-coding AT-rich region. All protein-coding genes (PCGs) started with ATN, except for COI gene with CGA(R), which is often found in other butterflies; nine PCGs harbor the typical stop codon TAA, whereas COI, COII, ND5 and ND4 end with a single T. All tRNA genes display typical secondary clover-leaf structures, except for tRNA(Ser)(AGN), whose dihydrouridine (DHU) arm is replaced by a simple loop. The lrRNA and srRNA genes are 1,347 bp and 753 bp in length, with their AT contents of 84.4% and 85.4%, respectively. The 417 bp AT-rich region contains non repetitive sequences, but harbor several features common to the lepidopterans, including the motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)8 element preceded by the ATTTA motif.}, }
@article {pmid25162626, year = {2016}, author = {Chen, J and Du, Y and Guo, X and Xie, L and Zhang, X and Ji, Y and Pang, B and Guo, S and Qi, D}, title = {The complete mitochondrial genome sequence of Platypharodon extremus (Cypriniformes: Cyprinidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1430-1431}, doi = {10.3109/19401736.2014.953078}, pmid = {25162626}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Endangered Species ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {Platypharodon extemus is a monotypic species of Schizothoracine fishes and it was listed as Endangered species in the "China Red Data Book (Pisces)", Vulnerable (V) by the National Environmental Protection Agency and Endangered Species Scientific Commission. So far, little mitochondrial genome information of this genus has been described. In this study, we obtained the complete mitochondrial DNA genome sequences of this species. The mitogenome was 16,668 bp in length, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 noncoding regions. The base composition of this mitochondrial genome was 28.6% A, 27.3% T, 18.2% G, 25.9% C, with a high A + T content (55.9%). The complete mitochondrial genome of P. extremus would be of great utility in the phylogenetic analysis of the schizothoracine fishes and also provide meritorious insights into the deeper problems of the phylogenic analysis.}, }
@article {pmid25162588, year = {2016}, author = {Hu, XD and Gao, LZ}, title = {The complete mitochondrial genome of eastern lowland gorilla, Gorilla beringei graueri, and comparative mitochondrial genomics of Gorilla species.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1484-1485}, doi = {10.3109/19401736.2014.953103}, pmid = {25162588}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Gene Order ; Genetic Variation ; Genome Size ; *Genome, Mitochondrial ; Gorilla gorilla/classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {In this study, we determined the complete mitochondrial (mt) genome of eastern lowland gorilla, Gorilla beringei graueri for the first time. The total genome was 16,416 bp in length. It contained a total of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region (D-loop region). The base composition was A (30.88%), G (13.10%), C (30.89%) and T (25.13%), indicating that the percentage of A+T (56.01%) was higher than G+C (43.99%). Comparisons with the other publicly available Gorilla mitogenome showed the conservation of gene order and base compositions but a bunch of nucleotide diversity. This complete mitochondrial genome sequence will provide valuable genetic information for further studies on conservation genetics of eastern lowland gorilla.}, }
@article {pmid25162495, year = {2016}, author = {Hengjiu, T and Jianwei, J and Shi, Y and Zhiming, Z and Laghari, MY and Narejo, NT and Lashari, P}, title = {Complete mitochondrial genome of Eagle Owl (Bubo bubo, Strigiformes; Strigidae) from China.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1455-1456}, doi = {10.3109/19401736.2014.953090}, pmid = {25162495}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Strigiformes/*genetics ; }, abstract = {In the present study, the complete mitochondrial genome sequence of Bubo bubo using PCR amplification, sequencing and assembling has been obtained for the first time. The total length of the mitochondrial genome was 16,250 bp, with the base composition of 29.88% A, 34.16% C, 14.35% G, and 21.58% T. It contained 37 genes (2 ribosomal RNA genes, 13 protein-coding genes and 22 transfer RNA genes) and a major non-coding control region (D-loop region). The complete mitochondrial genome sequence of Bubo bubo provides an important data set for further investigation on the phylogenetic relationships within Strigiformes.}, }
@article {pmid25162469, year = {2016}, author = {E, G and Na, RS and Zhao, YJ and Gao, HJ and An, TW and Huang, YF}, title = {Complete mitochondrial genome of the a rare subspecies of genus Bos, Tianzhu white yak from Tibetan area in China.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1443-1444}, doi = {10.3109/19401736.2014.953084}, pmid = {25162469}, issn = {2470-1408}, mesh = {Animals ; Animals, Domestic/classification/genetics ; Base Composition ; Cattle/classification/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Tibet ; }, abstract = {The population of domestic yak, Tianzhu white yak, from Tibetan area in China is considered as a rare Bos grunniens species. We first determined and annotated its complete mitochondrial genome. The mitogenome is 16,319 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a control region. As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. Its overall base composition is A: 33.7%, T: 27.2%, C: 25.8% and G: 13.2%. The complete mitogenome of the new subspecies of Bos grunniens could provide an important data to further explore the taxonomic status of the subspecies.}, }
@article {pmid25162454, year = {2016}, author = {Liang, R and Zhou, M and Gu, N}, title = {Complete mitochondrial genome of the yellow-banded sweetlips Plectorhinchus lineatus (Perciformes: Haemulidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1466-1467}, doi = {10.3109/19401736.2014.953095}, pmid = {25162454}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The complete mitochondrial genome of yellow-banded sweetlips Plectorhinchus lineatus was determined in this study. The genome was 16,548 bp in length and consisted of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and one non-coding control region. The overall base composition was estimated to be A, 28.2%; T, 24.8%; C, 30.7% and G, 16.2% with AT bias of 53.0%. All protein-coding genes used ATG as a start codon except for COI, which started with GTG. Six protein-coding genes ended with termination codon TAA, one ended with AGG, the remaining genes had incomplete stop codons TA or T. The genomic composition, organization, and gene order of P. lineatus was similar to most of vertebrates.}, }
@article {pmid25162381, year = {2016}, author = {Xue, Y and Chen, HJ and Li, Y and Tang, M and Chen, HJ and Ye, Q and Li, Y}, title = {Mitochondrial genome of the sucking disc gudgeon, Discogobio yunnanensis (Teleostei, Cypriniformes).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1451-1452}, doi = {10.3109/19401736.2014.953088}, pmid = {25162381}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Cypriniformes/*genetics ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The complete mitochondrial genome of Discogobio yunnanensis was determined using the polymerase chain reaction and directly sequenced with the primer walking method. The whole mitogenome was 16,602 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 1 control region. It had the typical circular molecule structure of vertebrate's mitogenome. The whole base composition was estimated to be 32.10% A, 26.79% T, 25.95% C, 15.16% G with AT bias of 58.89%. The complete mitogenome of D. yunnanensis provides the fundamental data for conservation genetics study on this freshwater fish species.}, }
@article {pmid25162312, year = {2016}, author = {Gao, J and Liang, A}, title = {The complete mitochondrial genome of Hemiodoecus leai (Hemiptera: Coleorrhyncha: Peloridiidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1421-1422}, doi = {10.3109/19401736.2014.953074}, pmid = {25162312}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; Genome, Insect ; *Genome, Mitochondrial ; Hemiptera/*genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {The mitochondrial genome of Hemiodoecus leai (Hemiptera: Coleorrhyncha: Peloridiidae) was determined and annotated. The entire genome was 15,949 bp in length, containing 37 genes of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and an A + T-rich region. The genome has a gene arrangement identical to the inferred ancestral insects. Twelve of the 13 PCGs initiate with the standard start codons ATN, whereas CO1 starts with CGA. The tRNAs have be folded into typical cloverleaf secondary structures, except that the stem of the DHU arm was absent in tRNA(Ser(GCT)). The non-coding AT-rich region is 1414 bp long and is located between the rrnS and tRNA(lle) genes. The complete mitogenome sequence of H. leai could provide fundamental data for the phylogenetic and biogeographic studies of the Peloriidae as well as the Coleorrhyncha and Hemiptera.}, }
@article {pmid25162155, year = {2016}, author = {Chen, Q and Wang, K and Tan, YL and Xing, LX}, title = {The complete mitochondrial genome of the subterranean termite, Reticulitermes chinensis Snyder (Isoptera: Rhinotermitidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1428-1429}, doi = {10.3109/19401736.2014.953077}, pmid = {25162155}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genome Size ; Genome, Insect ; *Genome, Mitochondrial ; Isoptera/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {We have determined the complete mitochondrial genome of Reticulitermes chinensis Snyder. The total length of the R. chinensis is 15,925 bp with 65.27% A + T content. It consists of 13 protein-coding, 22 tRNA, 2 rRNA genes and an A + T-rich control region. All the protein-coding genes used ATN as start codon. But the stop codons were TAA, TAG, and an incomplete termination codon (T) abutting an adjacent tRNA gene. The A + T-rich control region was 1125 bp in length with 67.02% A + T content.}, }
@article {pmid25162120, year = {2016}, author = {Pan, WJ and Fang, HY and Zhang, P and Pan, HC}, title = {The complete mitochondrial genome of pantropical jumping spider Plexippus paykulli (Araneae: Salticidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1490-1491}, doi = {10.3109/19401736.2014.953106}, pmid = {25162120}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Codon ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Sequence Analysis, DNA/methods ; Spiders/*genetics ; }, abstract = {The complete mitochondrial genome of Plexippus paykulli is a circular molecule of 14,316 bp in length, containing 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs and a control region. The A + T content of the overall base composition of H-strand is 73.5% (T: 40.6%; C: 9.0%; A: 32.9%; G: 17.5%). ATP6, Cyt b, ND2, ND5 and ND4 genes begin with ATA as start codon; ATP8, ND1, ND3 and ND4L genes begin with ATT as start codon; COII and COIII genes begin with TTG as start codon; COI gene begins with AGA as start codon, while ND6 gene start with a typical ATG initiation codon. ATP6, COI, COII, COIII and ND3 genes are terminated with TAA as stop codon, ND6 ends with TA, ATP8, ND1 and ND2 end with TAG, Cyt b, ND5, ND4 and ND4L end with T.}, }
@article {pmid25162119, year = {2016}, author = {Hu, XD and Li, K and Gao, LZ}, title = {The complete mitochondrial genome of Celebes wild boar, Sus celebensis (Cetartiodactyla: Suina: Suidae), and comparative mitochondrial genomics of the Sus species.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1476-1477}, doi = {10.3109/19401736.2014.953099}, pmid = {25162119}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Evolution, Molecular ; Genetic Variation ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Swine/classification/*genetics ; }, abstract = {In this study, the complete mitochondrial (mt) genome sequence of Sus celebensis was firstly determined. The total genome was 16,481 bp in length and its overall base composition was estimated to be 34.9% for A, 25.8% for T, 26.2% for C, 13.1% for G, respectively, indicating an A-T (60.7%)-rich feature in Celebes wild boar mitogenome. It harbored 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding control region (D-loop region). Comparisons with other publicly available pig mitogenomes revealed abundant nucleotide diversity. This complete mitgenome sequence would accelerate further studies on pig evolution and domestication that will enhance germplasm preservation and breeding programs of the pig gene pool.}, }
@article {pmid25160925, year = {2015}, author = {Azevedo-Martins, AC and Machado, AC and Klein, CC and Ciapina, L and Gonzaga, L and Vasconcelos, AT and Sagot, MF and DE Souza, W and Einicker-Lamas, M and Galina, A and Motta, MC}, title = {Mitochondrial respiration and genomic analysis provide insight into the influence of the symbiotic bacterium on host trypanosomatid oxygen consumption.}, journal = {Parasitology}, volume = {142}, number = {2}, pages = {352-362}, doi = {10.1017/S0031182014001139}, pmid = {25160925}, issn = {1469-8161}, mesh = {Bacteria/*classification/metabolism ; Biological Evolution ; Electron Transport/genetics/physiology ; Gene Expression Regulation ; Mitochondria/*metabolism ; Oxygen Consumption/*physiology ; Symbiosis/*physiology ; Trypanosomatina/genetics/*microbiology/*physiology ; }, abstract = {Certain trypanosomatids co-evolve with an endosymbiotic bacterium in a mutualistic relationship that is characterized by intense metabolic exchanges. Symbionts were able to respire for up to 4 h after isolation from Angomonas deanei. FCCP (carbonyl cyanide-4-(trifluoromethoxy)phenylhydrazone) similarly increased respiration in wild-type and aposymbiotic protozoa, though a higher maximal O2 consumption capacity was observed in the symbiont-containing cells. Rotenone, a complex I inhibitor, did not affect A. deanei respiration, whereas TTFA (thenoyltrifluoroacetone), a complex II activity inhibitor, completely blocked respiration in both strains. Antimycin A and cyanide, inhibitors of complexes III and IV, respectively, abolished O2 consumption, but the aposymbiotic protozoa were more sensitive to both compounds. Oligomycin did not affect cell respiration, whereas carboxyatractyloside (CAT), an inhibitor of the ADP-ATP translocator, slightly reduced O2 consumption. In the A. deanei genome, sequences encoding most proteins of the respiratory chain are present. The symbiont genome lost part of the electron transport system (ETS), but complex I, a cytochrome d oxidase, and FoF1-ATP synthase remain. In conclusion, this work suggests that the symbiont influences the mitochondrial respiration of the host protozoan.}, }
@article {pmid25152275, year = {2014}, author = {Cavalier-Smith, T and Chao, EE and Snell, EA and Berney, C and Fiore-Donno, AM and Lewis, R}, title = {Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa.}, journal = {Molecular phylogenetics and evolution}, volume = {81}, number = {}, pages = {71-85}, doi = {10.1016/j.ympev.2014.08.012}, pmid = {25152275}, issn = {1095-9513}, mesh = {Amoebozoa/classification/genetics ; Animals ; Bayes Theorem ; *Biological Evolution ; Eukaryota/*classification/genetics ; Fungi/classification/genetics ; Gene Library ; Invertebrates/classification/genetics ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Animals and fungi independently evolved from the protozoan phylum Choanozoa, these three groups constituting a major branch of the eukaryotic evolutionary tree known as opisthokonts. Opisthokonts and the protozoan phylum Amoebozoa (amoebae plus slime moulds) were previously argued to have evolved independently from the little-studied, largely flagellate, protozoan phylum, Sulcozoa. Sulcozoa are a likely evolutionary link between opisthokonts and the more primitive excavate flagellates that have ventral feeding grooves and the most primitive known mitochondria. To extend earlier sparse evidence for the ancestral (paraphyletic) nature of Sulcozoa, we sequenced transcriptomes from six gliding flagellates (two apusomonads; three planomonads; Mantamonas). Phylogenetic analyses of 173-192 genes and 73-122 eukaryote-wide taxa show Sulcozoa as deeply paraphyletic, confirming that opisthokonts and Amoebozoa independently evolved from sulcozoans by losing their ancestral ventral groove and dorsal pellicle: Apusozoa (apusomonads plus anaerobic breviate amoebae) are robustly sisters to opisthokonts and probably paraphyletic, breviates diverging before apusomonads; Varisulca (planomonads, Mantamonas, and non-gliding flagellate Collodictyon) are sisters to opisthokonts plus Apusozoa and Amoebozoa, and possibly holophyletic; Glissodiscea (planomonads, Mantamonas) may be holophyletic, but Mantamonas sometimes groups with Collodictyon instead. Taxon and gene sampling slightly affects tree topology; for the closest branches in Sulcozoa and opisthokonts, proportionally reducing missing data eliminates conflicts between homogeneous-model maximum-likelihood trees and evolutionarily more realistic site-heterogeneous trees. Sulcozoa, opisthokonts, and Amoebozoa constitute an often-pseudopodial 'podiate' clade, one of only three eukaryotic 'supergroups'. Our trees indicate that evolution of sulcozoan dorsal pellicle, ventral pseudopodia, and ciliary gliding (probably simultaneously) generated podiate eukaryotes from Malawimonas-like excavate flagellates.}, }
@article {pmid25151629, year = {2015}, author = {Chi, CS}, title = {Diagnostic approach in infants and children with mitochondrial diseases.}, journal = {Pediatrics and neonatology}, volume = {56}, number = {1}, pages = {7-18}, doi = {10.1016/j.pedneo.2014.03.009}, pmid = {25151629}, issn = {2212-1692}, mesh = {Algorithms ; Child ; DNA, Mitochondrial/genetics ; Humans ; Infant ; Mitochondria/genetics/metabolism ; Mitochondrial Diseases/*diagnosis/genetics ; }, abstract = {Mitochondrial diseases are a heterogeneous group of disorders affecting energy production in the human body. The diagnosis of mitochondrial diseases represents a challenge to clinicians, especially for pediatric cases, which show enormous variation in clinical presentations, as well as biochemical and genetic complexity. Different consensus diagnostic criteria for mitochondrial diseases in infants and children are available. The lack of standardized diagnostic criteria poses difficulties in evaluating diagnostic methodologies. Even though there are many diagnostic tools, none of them are sensitive enough to make a confirmative diagnosis without being used in combination with other tools. The current approach to diagnosing and classifying mitochondrial diseases incorporates clinical, biochemical, neuroradiological findings, and histological criteria, as well as DNA-based molecular diagnostic testing. The confirmation or exclusion of mitochondrial diseases remains a challenge in clinical practice, especially in cases with nonspecific clinical phenotypes. Therefore, follow-up evolution of clinical symptoms/signs and biochemical data is crucial. The purpose of this study is to review the molecular classification scheme and associated phenotypes in infants and children with mitochondrial diseases, in addition to providing an overview of the basic biochemical reactions and genetic characteristics in the mitochondrion, clinical manifestations, and diagnostic methods. A diagnostic algorithm for identifying mitochondrial disorders in pediatric neurology patients is proposed.}, }
@article {pmid25151510, year = {2015}, author = {Grimm, C and Böhl, L and Osiewacz, HD}, title = {Overexpression of Pa_1_10620 encoding a mitochondrial Podospora anserina protein with homology to superoxide dismutases and ribosomal proteins leads to lifespan extension.}, journal = {Current genetics}, volume = {61}, number = {1}, pages = {73-86}, pmid = {25151510}, issn = {1432-0983}, mesh = {Amino Acid Sequence ; Cloning, Molecular ; Gene Deletion ; *Gene Expression Regulation, Fungal ; Genes, Lethal ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Oxidative Stress ; Phylogeny ; Podospora/classification/*genetics/*metabolism ; Protein Transport ; Ribosomal Proteins/chemistry/*genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Superoxide Dismutase/chemistry/*genetics/metabolism ; Transcription, Genetic ; }, abstract = {In biological systems, reactive oxygen species (ROS) represent 'double edged swords': as signaling molecules they are essential for proper development, as reactive agents they cause molecular damage and adverse effects like degeneration and aging. A well-coordinated control of ROS is therefore of key importance. Superoxide dismutases (SODs) are enzymes active in the detoxification of superoxide. The number of isoforms of these proteins varies among species. Here we report the characterization of the putative protein encoded by Pa_1_10620 that has been previously annotated to code for a mitochondrial ribosomal protein but shares also sequence domains with SODs. We report that the gene is transcribed in P. anserina cultures of all ages and that the encoded protein localizes to mitochondria. In strains overexpressing Pa_1_10620 in a genetic background in which PaSod3, the mitochondrial MnSOD of P. anserina, is deleted, no SOD activity could be identified in isolated mitochondria. However, overexpression of the gene leads to lifespan extension suggesting a pro-survival function of the protein in P. anserina.}, }
@article {pmid25148700, year = {2014}, author = {Lozano, L and Lara-Lemus, R and Zenteno, E and Alvarado-Vásquez, N}, title = {The mitochondrial O-linked N-acetylglucosamine transferase (mOGT) in the diabetic patient could be the initial trigger to develop Alzheimer disease.}, journal = {Experimental gerontology}, volume = {58}, number = {}, pages = {198-202}, doi = {10.1016/j.exger.2014.08.008}, pmid = {25148700}, issn = {1873-6815}, mesh = {Alzheimer Disease/enzymology/*etiology/pathology ; Amyloid beta-Peptides/*metabolism ; Animals ; Blood Glucose/metabolism ; Diabetes Complications/blood/complications/*enzymology/pathology ; Glycosylation ; Hippocampus/*enzymology/pathology ; Humans ; Mitochondria/*enzymology/pathology ; N-Acetylglucosaminyltransferases/*metabolism ; Protein Processing, Post-Translational ; Risk Factors ; }, abstract = {Diabetes mellitus (DM) is considered a risk factor for the development of Alzheimer disease (AD); however, how DM favors evolution of AD is still insufficiently understood. Hyperglycemia in DM is associated to an increase in mitochondrial reactive oxygen species (ROS) generation, as well as damage of hippocampal cells, reflected by changes in morphological and mitochondrial functionality. Similar mitochondrial damage has been observed when amyloid beta (Aβ) accumulates in the brain of AD patients. In DM, the excess of glucose in the brain induces higher activity of the hexosamine biosynthesis pathway (HBP), it synthesizes UDP-N-acetylglucosamine (UDP-GlcNAc), which is used by O-linked N-acetylglucosamine transferase (OGT) to catalyze O-GlcNAcylation of numerous proteins. Although O-GlcNAcylation plays an important role in maintaining structure and cellular functionality, chronic activity of this pathway has been associated with insulin resistance and hyperglycemia-induced glucose toxicity. Three different forms of OGT are known: nucleocytoplasmic (ncOGT), short (sOGT), and mitochondrial (mOGT). Previous reports showed that overexpression of ncOGT is not toxic to the cell; in contrast, overexpression of mOGT is associated with cellular apoptosis. In this work, we suggest that hyperglycemia in the diabetic patient could induce greater expression and activity of mOGT, modifying the structure and functionality of mitochondria in hippocampal cells, accelerating neuronal damage, and favoring the start of AD. In consequence, mOGT activity could be a key point for AD development in patients with DM.}, }
@article {pmid25143035, year = {2014}, author = {Silva, G and Lima, FP and Martel, P and Castilho, R}, title = {Thermal adaptation and clinal mitochondrial DNA variation of European anchovy.}, journal = {Proceedings. Biological sciences}, volume = {281}, number = {1792}, pages = {}, pmid = {25143035}, issn = {1471-2954}, mesh = {*Adaptation, Biological ; Animals ; Atlantic Ocean ; Base Sequence ; DNA, Mitochondrial/*genetics ; *Environment ; Fishes/*classification/*genetics ; Genes, Mitochondrial ; Genetics, Population ; Mediterranean Sea ; Molecular Sequence Data ; Phylogeny ; *Temperature ; }, abstract = {Natural populations of widely distributed organisms often exhibit genetic clinal variation over their geographical ranges. The European anchovy, Engraulis encrasicolus, illustrates this by displaying a two-clade mitochondrial structure clinally arranged along the eastern Atlantic. One clade has low frequencies at higher latitudes, whereas the other has an anti-tropical distribution, with frequencies decreasing towards the tropics. The distribution pattern of these clades has been explained as a consequence of secondary contact after an ancient geographical isolation. However, it is not unlikely that selection acts on mitochondria whose genes are involved in relevant oxidative phosphorylation processes. In this study, we performed selection tests on a fragment of 1044 bp of the mitochondrial cytochrome b gene using 455 individuals from 18 locations. We also tested correlations of six environmental features: temperature, salinity, apparent oxygen utilization and nutrient concentrations of phosphate, nitrate and silicate, on a compilation of mitochondrial clade frequencies from 66 sampling sites comprising 2776 specimens from previously published studies. Positive selection in a single codon was detected predominantly (99%) in the anti-tropical clade and temperature was the most relevant environmental predictor, contributing with 59% of the variance in the geographical distribution of clade frequencies. These findings strongly suggest that temperature is shaping the contemporary distribution of mitochondrial DNA clade frequencies in the European anchovy.}, }
@article {pmid25142065, year = {2014}, author = {Oldenkott, B and Yamaguchi, K and Tsuji-Tsukinoki, S and Knie, N and Knoop, V}, title = {Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata.}, journal = {RNA (New York, N.Y.)}, volume = {20}, number = {10}, pages = {1499-1506}, pmid = {25142065}, issn = {1469-9001}, mesh = {Base Sequence ; Chloroplasts/*genetics ; Codon/*genetics ; Introns/*genetics ; Molecular Sequence Data ; RNA Editing/*genetics ; RNA, Chloroplast/*genetics ; Selaginellaceae/*genetics ; Transcriptome/*genetics ; }, abstract = {RNA editing in chloroplasts and mitochondria of land plants differs significantly in abundance. For example, some 200-500 sites of cytidine-to-uridine RNA editing exist in flowering plant mitochondria as opposed to only 30-50 such C-to-U editing events in their chloroplasts. In contrast, we predicted significantly more chloroplast RNA editing for the protein-coding genes in the available complete plastome sequences of two species of the spike moss genus Selaginella (Lycopodiophyta). To evaluate these predictions we investigated the Selaginella uncinata chloroplast transcriptome. Our exhaustive cDNA studies identified the extraordinary number of 3415 RNA-editing events, exclusively of the C-to-U type, in the 74 mRNAs encoding intact reading frames in the S. uncinata chloroplast. We find the overwhelming majority (61%) of the 428 silent editing events leaving codon meanings unaltered directly neighboring other editing events, possibly suggesting a sterically more flexible RNA-editing deaminase activity in Selaginella. No evidence of RNA editing was found for tRNAs or rRNAs but we identified a total of 74 editing sites in cDNA sequences of four group II introns (petBi6g2, petDi8g2, ycf3i124g2, and ycf3i354g2) retained in partially matured transcripts, which strongly contribute to improved base-pairing in the intron secondary structures as a likely prerequisite for their splicing.}, }
@article {pmid25141146, year = {2014}, author = {Evans, SR and Schielzeth, H and Forstmeier, W and Sheldon, BC and Husby, A}, title = {Nonautosomal genetic variation in carotenoid coloration.}, journal = {The American naturalist}, volume = {184}, number = {3}, pages = {374-383}, doi = {10.1086/677397}, pmid = {25141146}, issn = {1537-5323}, mesh = {Animals ; Beak ; Carotenoids/*genetics/metabolism ; Color ; Diet ; Feathers ; Female ; *Genetic Linkage ; Genetic Variation ; Male ; Passeriformes/*genetics/metabolism ; Phenotype ; Songbirds/*genetics/metabolism ; }, abstract = {Carotenoid-based coloration plays an important role in signaling, is often sexually dimorphic, and is potentially subject to directional and/or sex-specific selection. To understand the evolutionary dynamics of such color traits, it is essential to quantify patterns of inheritance, yet nonautosomal sources of genetic variation are easily overlooked by classical heritability analyses. Carotenoid metabolism has recently been linked to mitochondria, highlighting the potential for color variation to be explained by cytoplasmically inherited factors. In this study, we used quantitative genetic animal models to estimate the importance of mitochondrial and sex chromosome-linked sources of genetic variation in coloration in two songbird populations in which dietary carotenoids are either unmodified (great tit plumage) or metabolized into alternative color forms (zebra finch beak). We found no significant Z-linked genetic variance in great tit plumage coloration, while zebra finch beak coloration exhibited significant W linkage and cytoplasmic inheritance. Our results support cytoplasmic inheritance of color in the zebra finch, a trait based on endogenously metabolized carotenoids, and demonstrate the potential for nonautosomal sources to account for a considerable share of genetic variation in coloration. Although often overlooked, such nonautosomal genetic variation exhibits sex-dependent patterns of inheritance and potentially influences the evolution of sexual dichromatism.}, }
@article {pmid25133698, year = {2016}, author = {Tao, W and Zhao, H}, title = {The complete mitogenome of Gnathopogon polytaenia (Cypriniformes; Cyprinidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1307-1308}, doi = {10.3109/19401736.2014.945569}, pmid = {25133698}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitochondrial genome was sequenced from one of the endemic freshewater gudgeons (Gnathopogon polytaenia) in China. The mitochondrial genome sequence was 16,594 bp in size, and the gene order and contents were identical with the congeneric species G. strigatus and G. elongatus. Six genes (COII, ATP6, COIII, ND3, ND4, Cytb) had an incomplete stop codon. Base composition of the genome is A (29.1%), T (26.9%), C (25.9%) and G (18.1%) with an A + T rich feature (56%) as that of other vertebrate mitochondrial genomes.}, }
@article {pmid25133695, year = {2016}, author = {Wang, X and Zhang, Y and Zhang, H and Meng, T and Lin, Q}, title = {Complete mitochondrial genome sequence of the longsnout seahorse Hippocampus reidi (Ginsburg, 1933; Gasterosteiformes: Syngnathidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1401-1402}, doi = {10.3109/19401736.2014.947600}, pmid = {25133695}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Smegmamorpha/*genetics ; }, abstract = {The complete mitochondrial genome sequence of the longsnout seahorse Hippocampus reidi was fisrt determined in this article. The total length of H. reidi mitogenome is 16,529 bp and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region. The gene order and composition of H. reidi were similar to those of most other vertebrates. The overall base composition of H. reidi is 32.47% A, 29.41% T, 14.75% G and 23.37% C, with a slight A + T rich feature (61.88%).}, }
@article {pmid25132566, year = {2014}, author = {Zhao, YE and Cheng, J and Hu, L and Ma, JX}, title = {Molecular identification and phylogenetic study of Demodex caprae.}, journal = {Parasitology research}, volume = {113}, number = {10}, pages = {3601-3608}, pmid = {25132566}, issn = {1432-1955}, mesh = {Animals ; Base Sequence ; China ; Cyclooxygenase 1/*genetics ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry/genetics ; Dogs ; Female ; Mite Infestations/parasitology/*veterinary ; Mites/*classification/genetics ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Ovum ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The DNA barcode has been widely used in species identification and phylogenetic analysis since 2003, but there have been no reports in Demodex. In this study, to obtain an appropriate DNA barcode for Demodex, molecular identification of Demodex caprae based on mitochondrial cox1 was conducted. Firstly, individual adults and eggs of D. caprae were obtained for genomic DNA (gDNA) extraction; Secondly, mitochondrial cox1 fragment was amplified, cloned, and sequenced; Thirdly, cox1 fragments of D. caprae were aligned with those of other Demodex retrieved from GenBank; Finally, the intra- and inter-specific divergences were computed and the phylogenetic trees were reconstructed to analyze phylogenetic relationship in Demodex. Results obtained from seven 429-bp fragments of D. caprae showed that sequence identities were above 99.1% among three adults and four eggs. The intraspecific divergences in D. caprae, Demodex folliculorum, Demodex brevis, and Demodex canis were 0.0-0.9, 0.5-0.9, 0.0-0.2, and 0.0-0.5%, respectively, while the interspecific divergences between D. caprae and D. folliculorum, D. canis, and D. brevis were 20.3-20.9, 21.8-23.0, and 25.0-25.3, respectively. The interspecific divergences were 10 times higher than intraspecific ones, indicating considerable barcoding gap. Furthermore, the phylogenetic trees showed that four Demodex species gathered separately, representing independent species; and Demodex folliculorum gathered with canine Demodex, D. caprae, and D. brevis in sequence. In conclusion, the selected 429-bp mitochondrial cox1 gene is an appropriate DNA barcode for molecular classification, identification, and phylogenetic analysis of Demodex. D. caprae is an independent species and D. folliculorum is closer to D. canis than to D. caprae or D. brevis.}, }
@article {pmid25126842, year = {2014}, author = {García, G and Ríos, N and Gutiérrez, V and Varela, JG and Bouza Fernández, C and Pardo, BG and Portela, PM}, title = {Promiscuous speciation with gene flow in silverside fish genus Odontesthes (Atheriniformes, Atherinopsidae) from south western Atlantic Ocean basins.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e104659}, pmid = {25126842}, issn = {1932-6203}, mesh = {Animals ; Atlantic Ocean ; Base Sequence ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Fishes/*classification/genetics ; Gene Flow/*genetics ; Genetic Variation ; Genetics, Population ; Haplotypes/genetics ; Microsatellite Repeats/*genetics ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; }, abstract = {The present paper integrates phylogenetic and population genetics analyses based on mitochondrial and nuclear molecular markers in silversides, genus Odontesthes, from a non-sampled area in the SW Atlantic Ocean to address species discrimination and to define Managements Units for sustainable conservation. All phylogenetic analyses based on the COI mitochondrial gene were consistent to support the monophyly of the genus Odontesthes and to include O. argentinensis, O. perugiae-humensis and some O. bonariensis haplotypes in a basal polytomy conforming a major derivative clade. Microsatellites data revealed somewhat higher genetic variability values in the O. argentinensis-perugia populations than in O. bonariensis and O. perugia-humensis taxa. Contrasting population genetics structuring emerged from mitochondrial and microsatellites analyses in these taxa. Whereas mitochondrial data supported two major groups (O. argentinensis-perugia-humensis vs. O. bonariensis-perugiae-humensis populations), microsatellite data detected three major genetic entities represented by O. bonariensis, O. perugiae-humensis and an admixture of populations belonging to O. argentinensis-perugiae respectively. Therefore, the star COI polytomy in the tree topology involving these taxa could be interpreted by several hypothetic scenarios such as the existence of shared ancestral polymorphisms, incomplete lineage sorting in a radiating speciation process and/or reticulation events. Present findings support that promiscuous and recent contact between incipient species sharing asymmetric gene flow exchanges, blurs taxa boundaries yielding complicated taxonomy and Management Units delimitation in silverside genus Odontesthes from SW Atlantic Ocean basins.}, }
@article {pmid25122658, year = {2015}, author = {López Del Amo, V and Seco-Cervera, M and García-Giménez, JL and Whitworth, AJ and Pallardó, FV and Galindo, MI}, title = {Mitochondrial defects and neuromuscular degeneration caused by altered expression of Drosophila Gdap1: implications for the Charcot-Marie-Tooth neuropathy.}, journal = {Human molecular genetics}, volume = {24}, number = {1}, pages = {21-36}, doi = {10.1093/hmg/ddu416}, pmid = {25122658}, issn = {1460-2083}, mesh = {Animals ; Charcot-Marie-Tooth Disease ; Disease Models, Animal ; Drosophila Proteins/*genetics/*metabolism ; Drosophila melanogaster/*metabolism ; F-Box Proteins/*genetics/*metabolism ; Gene Expression Regulation ; Humans ; Mitochondria/*physiology ; Mitochondrial Size ; Nerve Tissue Proteins/metabolism ; Neuromuscular Diseases/*etiology/pathology ; Phylogeny ; Retina/metabolism ; }, abstract = {One of the genes involved in Charcot-Marie-Tooth (CMT) disease, an inherited peripheral neuropathy, is GDAP1. In this work, we show that there is a true ortholog of this gene in Drosophila, which we have named Gdap1. By up- and down-regulation of Gdap1 in a tissue-specific manner, we show that altering its levels of expression produces changes in mitochondrial size, morphology and distribution, and neuronal and muscular degeneration. Interestingly, muscular degeneration is tissue-autonomous and not dependent on innervation. Metabolic analyses of our experimental genotypes suggest that alterations in oxidative stress are not a primary cause of the neuromuscular degeneration but a long-term consequence of the underlying mitochondrial dysfunction. Our results contribute to a better understanding of the role of mitochondria in CMT disease and pave the way to generate clinically relevant disease models to study the relationship between mitochondrial dynamics and peripheral neurodegeneration.}, }
@article {pmid25121835, year = {2016}, author = {Del Río-Portilla, MA and Vargas-Peralta, CE and Farfán, C and Barriga-Sosa, Ide L and García-De-León, FJ}, title = {The complete mitochondrial DNA of the bay snook, Petenia splendida, a native Mexican cichlid.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1381-1382}, doi = {10.3109/19401736.2014.947590}, pmid = {25121835}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Cichlids/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {The mitogenome of the tenguayaca, Petenia splendida (GenBank accession number KJ914664) has a total length of 16,518 bp, and the arrangement consist of 15 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. Gene order was equal to the mitogenomes of other new world cichlids.}, }
@article {pmid25121834, year = {2016}, author = {Oh, JS and Ahn, do H and Lee, J and Choi, J and Chi, YM and Park, H}, title = {Complete mitochondrial genome of the Antarctic bullhead notothen, Notothenia coriiceps (Perciformes, Nototheniidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1407-1408}, doi = {10.3109/19401736.2014.947603}, pmid = {25121834}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The complete sequence of the mitochondrial genome of Notothenia coriiceps was obtained by genome assembly. The complete sequence was determined to be 18,347 base pairs in length and to contain 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 control regions. Of the thirteen protein-coding genes, two genes (cox1 and atp6) had GTG start codons, and six genes (nad2, cox2, cox3, nad3, nad4, and cytb) had incomplete stop codons that require the post-transcriptional addition of A bases. The base composition of the mitogenome was 26.3% A, 27.6% T, 17.5% G, and 28.5% C.}, }
@article {pmid25118050, year = {2014}, author = {Mentel, M and Röttger, M and Leys, S and Tielens, AG and Martin, WF}, title = {Of early animals, anaerobic mitochondria, and a modern sponge.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {10}, pages = {924-932}, doi = {10.1002/bies.201400060}, pmid = {25118050}, issn = {1521-1878}, support = {232975/ERC_/European Research Council/International ; }, mesh = {Anaerobiosis/genetics ; Animals ; Energy Metabolism/genetics ; Metabolic Networks and Pathways ; Mitochondria/genetics/*metabolism ; *Phylogeny ; Porifera/*metabolism ; }, abstract = {The origin and early evolution of animals marks an important event in life's history. This event is historically associated with an important variable in Earth history - oxygen. One view has it that an increase in oceanic oxygen levels at the end of the Neoproterozoic Era (roughly 600 million years ago) allowed animals to become large and leave fossils. How important was oxygen for the process of early animal evolution? New data show that some modern sponges can survive for several weeks at low oxygen levels. Many groups of animals have mechanisms to cope with low oxygen or anoxia, and very often, mitochondria - organelles usually associated with oxygen - are involved in anaerobic energy metabolism in animals. It is a good time to refresh our memory about the anaerobic capacities of mitochondria in modern animals and how that might relate to the ecology of early metazoans.}, }
@article {pmid25115678, year = {2016}, author = {Wang, Y and Song, N and Li, Y and Gao, T}, title = {The complete mitochondrial genome of Saurida umeyoshii (Aulopiformes: Synodontidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1399-1400}, doi = {10.3109/19401736.2014.947599}, pmid = {25115678}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Base Sequence ; Conserved Sequence ; Fishes/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {In this study, the complete mitochondrial genome (mitogenome) sequence of Saurida umeyoshii has been determined by long polymerase chain reaction and primer walking methods. The complete mitochondrial genome is 16,546 bp in length and contains 37 mitochondrial genes (13 protein-coding genes, 2 ribosomal RNA (rRNA), 22 transfer RNA (tRNA)), and a control region as other bony fishes. Within the control region, we identified the termination-associated sequence domain (TAS), the central conserved sequence block domains (CSB-F, CSB-E, CSB-D, CSB-C, CSB-B and CSB-A), and the conserved sequence block domains (CSB-1, CSB-2 and CSB-3).}, }
@article {pmid25115677, year = {2016}, author = {Peng, L and Lu, J and Sun, XW}, title = {Mitochondrial DNA sequence of Lampetra morri.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1391-1392}, doi = {10.3109/19401736.2014.947595}, pmid = {25115677}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; DNA, Mitochondrial/*genetics ; Gene Order ; Genome Size ; Lampreys/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {Lampetra morri belongs to the Petromyzontidae family. It is one of the most important freshwater aquaculture species in China. In this study, the complete sequence of mitochondrial genome of L. morri was 16,451 base pair, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 repeat regions. The percentage of G + C content was 39.33%. This is the first time of the mitochondrial genome of L. morri being sequenced, and it provides insights into the evolution of Cyclostomata mitochondrial genomes, particular in Lampetra family.}, }
@article {pmid25115033, year = {2014}, author = {Fabre, PH and Vilstrup, JT and Raghavan, M and Sarkissian, CD and Willerslev, E and Douzery, EJ and Orlando, L}, title = {Rodents of the Caribbean: origin and diversification of hutias unravelled by next-generation museomics.}, journal = {Biology letters}, volume = {10}, number = {7}, pages = {}, pmid = {25115033}, issn = {1744-957X}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Caribbean Region ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; Phylogeography ; RNA, Ribosomal/genetics ; Rodentia/*classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {The Capromyidae (hutias) are endemic rodents of the Caribbean and represent a model of dispersal for non-flying mammals in the Greater Antilles. This family has experienced severe extinctions during the Holocene and its phylogenetic affinities with respect to other caviomorph relatives are still debated as morphological and molecular data disagree. We used target enrichment and next-generation sequencing of mitochondrial and nuclear genes to infer the phylogenetic relationships of hutias, estimate their divergence ages, and understand their mode of dispersal in the Greater Antilles.We found that Capromyidae are nested within Echimyidae (spiny rats) and should be considered a subfamily thereof. We estimated that the split between hutias and Atlantic Forest spiny rats occurred 16.5 (14.8–18.2) million years ago (Ma), which is more recent than the GAARlandia land bridge hypothesis (34–35 Ma). This would suggest that during the Early Miocene, an echimyid-like ancestor colonized the Greater Antilles from an eastern South American source population via rafting. The basal divergence of the Hispaniolan Plagiodontia provides further support for a vicariant separation between Hispaniolan and western islands (Bahamas, Cuba, Jamaica) hutias. Recent divergences among these western hutias suggest Plio-Pleistocene dispersal waves associated with glacial cycles.}, }
@article {pmid25115012, year = {2014}, author = {Kao, WC and Hunte, C}, title = {The molecular evolution of the Qo motif.}, journal = {Genome biology and evolution}, volume = {6}, number = {7}, pages = {1894-1910}, pmid = {25115012}, issn = {1759-6653}, mesh = {Amino Acid Motifs ; *Evolution, Molecular ; *Models, Biological ; Oxidation-Reduction ; Phylogeny ; Ubiquinone/*analogs &amp; derivatives/chemistry ; }, abstract = {Quinol oxidation in the catalytic quinol oxidation site (Q(o) site) of cytochrome (cyt) bc(1) complexes is the key step of the Q cycle mechanism, which laid the ground for Mitchell's chemiosmotic theory of energy conversion. Bifurcated electron transfer upon quinol oxidation enables proton uptake and release on opposite membrane sides, thus generating a proton gradient that fuels ATP synthesis in cellular respiration and photosynthesis. The Q(o) site architecture formed by cyt b and Rieske iron-sulfur protein (ISP) impedes harmful bypass reactions. Catalytic importance is assigned to four residues of cyt b formerly described as PEWY motif in the context of mitochondrial complexes, which we now denominate Q(o) motif as comprehensive evolutionary sequence analysis of cyt b shows substantial natural variance of the motif with phylogenetically specific patterns. In particular, the Q(o) motif is identified as PEWY in mitochondria, α- and ε-Proteobacteria, Aquificae, Chlorobi, Cyanobacteria, and chloroplasts. PDWY is present in Gram-positive bacteria, Deinococcus-Thermus and haloarchaea, and PVWY in β- and γ-Proteobacteria. PPWF only exists in Archaea. Distinct patterns for acidophilic organisms indicate environment-specific adaptations. Importantly, the presence of PDWY and PEWY is correlated with the redox potential of Rieske ISP and quinone species. We propose that during evolution from low to high potential electron-transfer systems in the emerging oxygenic atmosphere, cyt bc(1) complexes with PEWY as Q(o) motif prevailed to efficiently use high potential ubiquinone as substrate, whereas cyt b with PDWY operate best with low potential Rieske ISP and menaquinone, with the latter being the likely composition of the ancestral cyt bc(1) complex.}, }
@article {pmid25114051, year = {2014}, author = {Salinas, T and El Farouk-Ameqrane, S and Ubrig, E and Sauter, C and Duchêne, AM and Maréchal-Drouard, L}, title = {Molecular basis for the differential interaction of plant mitochondrial VDAC proteins with tRNAs.}, journal = {Nucleic acids research}, volume = {42}, number = {15}, pages = {9937-9948}, pmid = {25114051}, issn = {1362-4962}, mesh = {DNA, Plant/metabolism ; Mitochondrial Proteins/*chemistry/metabolism ; Models, Molecular ; Plant Proteins/*chemistry/metabolism ; Protein Binding ; Protein Isoforms/metabolism ; RNA, Plant/metabolism ; RNA, Transfer/*metabolism ; Solanum tuberosum/genetics/metabolism ; Voltage-Dependent Anion Channels/*chemistry/metabolism ; }, abstract = {In plants, the voltage-dependent anion-selective channel (VDAC) is a major component of a pathway involved in transfer RNA (tRNA) translocation through the mitochondrial outer membrane. However, the way in which VDAC proteins interact with tRNAs is still unknown. Potato mitochondria contain two major mitochondrial VDAC proteins, VDAC34 and VDAC36. These two proteins, composed of a N-terminal α-helix and of 19 β-strands forming a β-barrel structure, share 75% sequence identity. Here, using both northwestern and gel shift experiments, we report that these two proteins interact differentially with nucleic acids. VDAC34 binds more efficiently with tRNAs or other nucleic acids than VDAC36. To further identify specific features and critical amino acids required for tRNA binding, 21 VDAC34 mutants were constructed and analyzed by northwestern. This allowed us to show that the β-barrel structure of VDAC34 and the first 50 amino acids that contain the α-helix are essential for RNA binding. Altogether the work shows that during evolution, plant mitochondrial VDAC proteins have diverged so as to interact differentially with nucleic acids, and this may reflect their involvement in various specialized biological functions.}, }
@article {pmid25112327, year = {2014}, author = {Thompson, FC and Skevington, JH}, title = {Afrotropical flower flies (Diptera: Syrphidae). A new genus and species from Kenya, with a review of the melanostomine group of genera.}, journal = {Zootaxa}, volume = {3847}, number = {1}, pages = {97-114}, doi = {10.11646/zootaxa.3847.1.5}, pmid = {25112327}, issn = {1175-5334}, mesh = {Animals ; Diptera/*anatomy &amp; histology/*classification/genetics ; Electron Transport Complex IV/genetics ; Female ; Kenya ; Male ; Mitochondria/enzymology/genetics ; Phylogeny ; Species Specificity ; Uganda ; }, abstract = {A new genus and species of flower flies (Diptera: Syrphidae: Syrphinae: Syrphini) are described from central Africa (Kenya &amp; Uganda), Afrostoma quadripunctatum. A key to the Afrotropical genera of the subfamily Syrphinae is given. A review of the melanostomine [Bacchini] genera and subgenera is provided along with a key to them. Phylogenetic placement of Afrostoma is included based on mitochondrial cytochrome c oxidase subunit I (COI) data.}, }
@article {pmid25111840, year = {2014}, author = {Herman, JS and McDevitt, AD and Kawałko, A and Jaarola, M and Wójcik, JM and Searle, JB}, title = {Land-bridge calibration of molecular clocks and the post-glacial Colonization of Scandinavia by the Eurasian field vole Microtus agrestis.}, journal = {PloS one}, volume = {9}, number = {8}, pages = {e103949}, pmid = {25111840}, issn = {1932-6203}, mesh = {Animals ; *Arvicolinae/genetics ; Calibration ; *Evolution, Molecular ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeography ; Scandinavian and Nordic Countries ; }, abstract = {Phylogeography interprets molecular genetic variation in a spatial and temporal context. Molecular clocks are frequently used to calibrate phylogeographic analyses, however there is mounting evidence that molecular rates decay over the relevant timescales. It is therefore essential that an appropriate rate is determined, consistent with the temporal scale of the specific analysis. This can be achieved by using temporally spaced data such as ancient DNA or by relating the divergence of lineages directly to contemporaneous external events of known time. Here we calibrate a Eurasian field vole (Microtus agrestis) mitochondrial genealogy from the well-established series of post-glacial geophysical changes that led to the formation of the Baltic Sea and the separation of the Scandinavian peninsula from the central European mainland. The field vole exhibits the common phylogeographic pattern of Scandinavian colonization from both the north and the south, however the southernmost of the two relevant lineages appears to have originated in situ on the Scandinavian peninsula, or possibly in the adjacent island of Zealand, around the close of the Younger Dryas. The mitochondrial substitution rate and the timescale for the genealogy are closely consistent with those obtained with a previous calibration, based on the separation of the British Isles from mainland Europe. However the result here is arguably more certain, given the level of confidence that can be placed in one of the central assumptions of the calibration, that field voles could not survive the last glaciation of the southern part of the Scandinavian peninsula. Furthermore, the similarity between the molecular clock rate estimated here and those obtained by sampling heterochronous (ancient) DNA (including that of a congeneric species) suggest that there is little disparity between the measured genetic divergence and the population divergence that is implicit in our land-bridge calibration.}, }
@article {pmid25110061, year = {2014}, author = {Zhou, T and Shen, X and Irwin, DM and Shen, Y and Zhang, Y}, title = {Mitogenomic analyses propose positive selection in mitochondrial genes for high-altitude adaptation in galliform birds.}, journal = {Mitochondrion}, volume = {18}, number = {}, pages = {70-75}, doi = {10.1016/j.mito.2014.07.012}, pmid = {25110061}, issn = {1872-8278}, mesh = {*Adaptation, Biological ; *Altitude ; Animals ; Biological Evolution ; DNA, Mitochondrial/genetics ; *Galliformes ; *Genes, Mitochondrial ; Genome, Mitochondrial ; Mitochondrial Proton-Translocating ATPases/genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; *Selection, Genetic ; Sequence Homology ; }, abstract = {Galliform birds inhabit very diverse habitats, including plateaus that are above 3000 m in altitude. At high altitude, lower temperature and hypoxia are two important factors influencing survival. Mitochondria, as the ultimate oxygen transductor, play an important role in aerobic respiration through oxidative phosphorylation (OXPHOS). We analyzed the mitochondrial genomes of six high-altitude phasianidae birds and sixteen low-altitude relatives in an attempt to determine the role of mitochondrial genes in high-altitude adaptation. We reconstructed the phylogenetic relationships of these phasianidae birds and relatives and found at least four lineages that independently occupied this high-altitude habitat. Selective analyses revealed significant evidence for positive selection in the genes ND2, ND4, and ATP6 in three of the high-altitude lineages. This result strongly suggests that adaptive evolution of mitochondrial genes played a critical role during the independent acclimatization to high altitude by galliform birds.}, }
@article {pmid25109630, year = {2016}, author = {Huo, TB and Peng, L and Lu, J and Jiang, ZF}, title = {Complete mitochondrial genome of the Lampetra japonica.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1293-1294}, doi = {10.3109/19401736.2014.945562}, pmid = {25109630}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Genome Size ; *Genome, Mitochondrial ; Lampreys/*genetics ; Mitochondria/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitochondrial genome of Lampetra japonica was 16,431 base pairs, it is circular molecule with a typical gene arrangement of vertebrate mitochondrial DNA, it contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 repeat regions. The study could be provided insights into the evolution of cyclostome mitochondrial geneomes, particularly in Lampetra family.}, }
@article {pmid25109629, year = {2016}, author = {Ran, ML and Liu, Z and Yang, AQ and Li, Z and Chen, B}, title = {The complete sequence of the mitochondrial genome of Lantang pig (Sus scrofa).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1376-1377}, doi = {10.3109/19401736.2014.947588}, pmid = {25109629}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Base Sequence ; *Genome, Mitochondrial ; Molecular Sequence Data ; Open Reading Frames ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sus scrofa/*genetics ; }, abstract = {Lantang pig is a native breed of Guangzhou Province in China. It is the first time that the complete mitochondrial genome sequence of Lantang pig is reported in this work, which is determined through the PCR-based method. The total length of the mitognome is 16,709 bp, which contains 2 ribosomal RNA genes, 22 tRNA genes, 13 PCGs and 1 conntrol region (D-loop region, Table 1). The total base composition of Lantang pig mitochondrial genome is 34.69% for A, 26.18% for C, 25.82% for T and 13.31% for G, in the order A>C>T>G. The complete mitochondrial genome of Lantang pig provides an important data in genetic mechanism and the evolution genomes.}, }
@article {pmid25103442, year = {2016}, author = {Gong, L and Si, LZ and Shi, W and Kong, XY}, title = {The complete mitochondrial genome of Zebrias crossolepis (Pleuronectiformes: Soleidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1235-1236}, doi = {10.3109/19401736.2014.945534}, pmid = {25103442}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence ; China ; DNA, Mitochondrial/*genetics ; Flatfishes/anatomy &amp; histology/*genetics ; Genome Size/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*veterinary ; Taiwan ; }, abstract = {Zebrias crossolepis belongs to the family Soleidae of Pleuronectiformes. This species and its congeners are characterized by eyes on right side and a compressed body with only anterior half of caudal fin margin connected with dorsal and anal fins. In this article, we determined and described the complete mitogenome of Z. crossolepis. The genome is 16,734 bp in length, and is typically consist of 37 genes, including 13 protein-coding, two ribosomal RNA, 22 transfer RNA genes, as well as a putative control region and an L-strand replication origin. The gene organization is identical to that of typical bony fishes. The overall base composition is 28.3, 26.4, 30.0, and 15.3% for A, T, C, and G, respectively, with a slight bias on AT content (54.7%). This result is expected to contribute to understanding the systematic evolution of the genus Zebrias and further phylogenetic studies of Soleidae and Pleuronectiformes.}, }
@article {pmid25103437, year = {2016}, author = {Su, YB and Kong, SC and Wang, LX and Chen, L and Fang, R}, title = {Complete mitochondrial genome of Philometra carassii (Nematoda: Philometridae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1397-1398}, doi = {10.3109/19401736.2014.947598}, pmid = {25103437}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; Genome, Helminth ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Nematoda/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The complete mitochondrial genome of Philometra carassii is 14,378 bp in size, containing 12 protein-coding genes (PCGs), 22 transfer RNA genes, 2 rRNA genes (12S and 16S), as well as one non-coding region (NCR, the control region), but lacks an atp8 gene. The genome organization, nucleotide composition and codon usage do not differ significantly from other nematodes. The complete mitogenome sequence information of P. carassii can provides useful data for further studies on phylogenetics, stock evaluation and conservation genetics.}, }
@article {pmid25103436, year = {2016}, author = {Huo, TB and Peng, L and Jiang, ZF and Lu, J}, title = {Complete mitochondrial genome of the Lampetra reissneri.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1395-1396}, doi = {10.3109/19401736.2014.947597}, pmid = {25103436}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Lampreys/*genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {The complete mitochondrial genome of Lampetra reissneri was 16,469 base pair, it contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 repeat regions. It is circular molecule with a typical gene arrangement of vertebrate mitochondrial DNA. The study could be provided insights into the evolution of cyclostome mitochondrial geneomes.}, }
@article {pmid25103435, year = {2016}, author = {Wang, H and Yang, X and Wang, X and Li, C and Gu, J and Yang, S and He, L and Lv, S and Huang, P}, title = {Sequence identification and description of the mitochondrial genome of Abbottina rivularis (Cypriniformes: Cyprinidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1393-1394}, doi = {10.3109/19401736.2014.947596}, pmid = {25103435}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Gene Order ; *Genes, Mitochondrial ; Genome Size ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {In this study, the complete mitochondrial genome of Abbottina rivularis was determined; the phylogenetic analysis with other individuals and closely related species of the gudgeons was carried out. The complete mitogenome of A. rivularis was 16,597 bp in length, which consists of 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes, and 2 non-coding regions: (D-loop and OL). The overall nucleotide composition of the A. rivularis mitogenome was A: 29.92%, T: 25.75%, G: 17.15% and C: 27.18%, respectively, with an A + T rich feature (57.1%). This study provides useful data to genetics, conservation and evolution study of the gudgeons.}, }
@article {pmid25103434, year = {2016}, author = {Liao, F and Zeng, G and Yuan, X and Li, S and Wang, C and Liang, Z}, title = {Complete mitochodrial genome of Elopichthys bambusa (Cypriniformes, Cyprinidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1387-1388}, doi = {10.3109/19401736.2014.947593}, pmid = {25103434}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/chemistry ; }, abstract = {The complete mitochondrial genome of Elopichthys bambusa was determined in this study. The gene composition, arrangement and transcriptional orientation in E. bambusa mitogenome were identical to most vertebrates. Two start codon patterns (ATG and GTG) and three stop codon patterns (TAG, TAA and T) were found in protein-coding genes. Only the tRNA-Ser2 could not fold into a typical clover-leaf secondary structure for lacking the dihydrouridine arm. Sequences alignment results suggest that the complete mitogenome of E. bambusa is an efficient tool to check species identification by comparing different gene sequences.}, }
@article {pmid25103433, year = {2016}, author = {Ren, Q and Qian, C and Yuan, J and Li, X and Yang, J and Wang, P and Jiang, L and Zhang, Q and Wang, Y and Kan, X}, title = {Complete mitochondrial genome of the Black-capped Bulbul, Pycnonotus melanicterus (Passeriformes: Pycnonotidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1378-1380}, doi = {10.3109/19401736.2014.947589}, pmid = {25103433}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Passeriformes/*genetics ; Phylogeny ; }, abstract = {The first complete maternally-inherited mitochondrial genome of Pycnonotus melanicterus has been sequenced and annotated in this study. The mitogenome is 17,011 bp in size with an A+T content of 55.15%, consisting of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (srRNA and lrRNA) genes, and 2 extensive heteroplasmic control regions. Genome organization and gene arrangements of P. melanicterus are similar to those of other bulbuls. All 13 PCGs initiated with ATG as the start codon, while terminated by seven types of stop codons. All tRNA genes sequences have the potential to fold into typical cloverleaf secondary structures. Gene overlapping was observed in the P. melanicterus mitogenome. Moreover, our results of phylogenetic analysis well support the monophyly of Pycnonotidae as previously studies.}, }
@article {pmid25102102, year = {2014}, author = {Kim, JY and Kim, EJ and Lopez-Maury, L and Bähler, J and Roe, JH}, title = {A metabolic strategy to enhance long-term survival by Phx1 through stationary phase-specific pyruvate decarboxylases in fission yeast.}, journal = {Aging}, volume = {6}, number = {7}, pages = {587-601}, pmid = {25102102}, issn = {1945-4589}, support = {/WT_/Wellcome Trust/United Kingdom ; 095598/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Fungal Proteins/genetics/*metabolism ; Gene Expression Regulation, Enzymologic/*physiology ; Gene Expression Regulation, Fungal/*physiology ; Mitochondria/metabolism ; Mutation ; Oxygen Consumption/physiology ; Phylogeny ; Pyruvate Decarboxylase/genetics/*metabolism ; Reactive Oxygen Species ; Schizosaccharomyces/genetics/*metabolism ; Stress, Physiological ; Thiamine ; Time Factors ; Transcription Factors/genetics/*metabolism ; Transcriptome ; }, abstract = {In the fission yeast Schizosaccharomyces pombe, the stationary phase-specific transcription factor Phx1 contributes to long-term survival, stress tolerance, and meiosis. We identified Phx1-dependent genes through transcriptome analysis, and further analyzed those related with carbohydrate and thiamine metabolism, whose expression decreased in ∆phx1. Consistent with mRNA changes, the level of thiamine pyrophosphate (TPP) and TPP-utilizing pyruvate decarboxylase activity that converts pyruvate to acetaldehyde were also reduced in the mutant. Therefore, Phx1 appears to shift metabolic flux by diverting pyruvate from the TCA cycle and respiration to ethanol fermentation. Among the four predicted genes for pyruvate decarboxylase, only the Phx1-dependent genes (pdc201+ and pdc202+) contributed to long-term survival as judged by mutation and overexpression studies. These findings indicate that the Phx1-mediated long-term survival is achieved primarily through increasing the synthesis and activity of pyruvate decarboxylase. Consistent with this hypothesis, we observed that Phx1 curtailed respiration when cells entered stationary phase. Introduction of Δphx1 mutation compromised the long-lived phenotypes of Δpka1 and Δsck2 mutants that are devoid of pro-aging kinases of nutrient-signalling pathways, and of the Δpyp1 mutant with constitutively activated stress-responsive kinase Sty1. Therefore, achievement of long-term viability through both nutrient limitation and anti-stress response appears to be dependent on Phx1.}, }
@article {pmid25096853, year = {2014}, author = {Zhang, C and Rannala, B and Yang, Z}, title = {Bayesian species delimitation can be robust to guide-tree inference errors.}, journal = {Systematic biology}, volume = {63}, number = {6}, pages = {993-1004}, pmid = {25096853}, issn = {1076-836X}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bayes Theorem ; Classification/*methods ; Genetic Speciation ; Mitochondria/genetics ; *Models, Genetic ; *Phylogeny ; Sample Size ; }, }
@article {pmid25090399, year = {2016}, author = {Zhang, Z and Sun, T and Kang, C and Liu, Y and Liu, S and Yue, B and Zeng, T}, title = {The complete mitochondrial genome of lesser long-tailed Hamster Cricetulus longicaudatus (Milne-Edwards, 1867) and phylogenetic implications.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1303-1304}, doi = {10.3109/19401736.2014.945567}, pmid = {25090399}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Bayes Theorem ; Cricetinae ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete mitochondrial genome sequence of Cricetulus longicaudatus (Rodentia Cricetidae: Cricetinae) was determined and was deposited in GenBank (GenBank accession no. KM067270). The mitochondrial genome of C. longicaudatus was 16,302 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region, with an identical order to that of other rodents' mitochondrial genomes. The phylogenetic analysis was performed with Bayesian inference based on the concatenated nucleotide sequence of 12 protein-coding genes on the heavy strand. The result showed that these species from Cricetidae and its two subfamilies (Cricetinae and Arvicolines) formed solid monophyletic group, respectively. The Cricetulus had close phylogenetic relationship with Tscherskia among three genera (Cricetulus, Cricetulus and Mesocricetus). Neodon irene and Myodes regulus were embedded in Microtus and Eothenomys, respectively. The unusual phylogenetic positions of Neodon irene and Myodes regulus remain further study in the future.}, }
@article {pmid25090381, year = {2016}, author = {Wang, LY and Xu, D and Ma, HM}, title = {The complete sequence of the mitochondrial genome of Rongchang pig (Sus Scrofa).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {1279-1280}, doi = {10.3109/19401736.2014.945555}, pmid = {25090381}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/genetics ; Sequence Analysis, DNA/*methods ; Sus scrofa/*genetics ; }, abstract = {Rongchang pig is one of the native breeds in Sichuan province in China. The total length of mitochondrial genome of Rongchang pig is 16,710 bp, including 34.67% A, 26.18% C, 25.82% T and 13.33% G, and in the order A > C > T > G. Mitochondrial genome contains a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. This is the first report of the complete mitochondrial genome sequence about Rongchang pig. The mitochondrial genome of Rongchang pig subsequently provides an important information in genetic mechanism and the evolution genomes.}, }
@article {pmid25089878, year = {2014}, author = {He, D and Zhang, H and Yang, P}, title = {The mitochondrion-located protein OsB12D1 enhances flooding tolerance during seed germination and early seedling growth in rice.}, journal = {International journal of molecular sciences}, volume = {15}, number = {8}, pages = {13461-13481}, pmid = {25089878}, issn = {1422-0067}, mesh = {Amino Acid Sequence ; Biological Evolution ; Floods ; Gene Expression Regulation, Plant ; Germination ; Mitochondria/*metabolism ; Molecular Sequence Data ; Oryza/classification/growth &amp; development/*metabolism ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Seeds/growth &amp; development/metabolism ; }, abstract = {B12D belongs to a function unknown subgroup of the Balem (Barley aleurone and embryo) proteins. In our previous work on rice seed germination, we identified a B12D-like protein encoded by LOC_Os7g41350 (named OsB12D1). OsB12D1 pertains to an ancient protein family with an amino acid sequence highly conserved from moss to angiosperms. Among the six OsB12Ds, OsB12D1 is one of the major transcripts and is primarily expressed in germinating seed and root. Bioinformatics analyses indicated that OsB12D1 is an anoxic or submergence resistance-related gene. RT-PCR results showed OsB12D1 is induced remarkably in the coleoptiles or roots by flooding during seed germination and early seedling growth. The OsB12D1-overexpressed rice seeds could protrude radicles in 8 cm deep water, further exhibiting significant flooding tolerance compared to the wild type. Moreover, this tolerance was not affected by the gibberellin biosynthesis inhibitor paclobutrazol. OsB12D1 was identified in the mitochondrion by subcellular localization analysis and possibly enhances electron transport through mediating Fe and oxygen availability under flooded conditions. This work indicated that OsB12D1 is a promising gene that can help to enhance rice seedling establishment in farming practices, especially for direct seeding.}, }
@article {pmid25089149, year = {2014}, author = {Nunn, AV and Guy, GW and Bell, JD}, title = {The intelligence paradox; will ET get the metabolic syndrome? Lessons from and for Earth.}, journal = {Nutrition &amp; metabolism}, volume = {11}, number = {}, pages = {34}, pmid = {25089149}, issn = {1743-7075}, support = {MC_U120061305/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Mankind is facing an unprecedented health challenge in the current pandemic of obesity and diabetes. We propose that this is the inevitable (and predictable) consequence of the evolution of intelligence, which itself could be an expression of life being an information system driven by entropy. Because of its ability to make life more adaptable and robust, intelligence evolved as an efficient adaptive response to the stresses arising from an ever-changing environment. These adaptive responses are encapsulated by the epiphenomena of "hormesis", a phenomenon we believe to be central to the evolution of intelligence and essential for the maintenance of optimal physiological function and health. Thus, as intelligence evolved, it would eventually reach a cognitive level with the ability to control its environment through technology and have the ability remove all stressors. In effect, it would act to remove the very hormetic factors that had driven its evolution. Mankind may have reached this point, creating an environmental utopia that has reduced the very stimuli necessary for optimal health and the evolution of intelligence - "the intelligence paradox". One of the hallmarks of this paradox is of course the rising incidence in obesity, diabetes and the metabolic syndrome. This leads to the conclusion that wherever life evolves, here on earth or in another part of the galaxy, the "intelligence paradox" would be the inevitable side-effect of the evolution of intelligence. ET may not need to just "phone home" but may also need to "phone the local gym". This suggests another possible reason to explain Fermi's paradox; Enrico Fermi, the famous physicist, suggested in the 1950s that if extra-terrestrial intelligence was so prevalent, which was a common belief at the time, then where was it? Our suggestion is that if advanced life has got going elsewhere in our galaxy, it can't afford to explore the galaxy because it has to pay its healthcare costs.}, }
@article {pmid25087963, year = {2014}, author = {Tawaraya, Y and Hyodo, M and Ara, MN and Yamada, Y and Harashima, H}, title = {RNA aptamers for targeting mitochondria using a mitochondria-based SELEX method.}, journal = {Biological &amp; pharmaceutical bulletin}, volume = {37}, number = {8}, pages = {1411-1415}, doi = {10.1248/bpb.b14-00112}, pmid = {25087963}, issn = {1347-5215}, mesh = {Animals ; Aptamers, Nucleotide/genetics/*metabolism ; Base Sequence ; Gene Library ; Ligands ; Male ; Mitochondria, Liver/*metabolism ; Rats, Wistar ; SELEX Aptamer Technique ; }, abstract = {The use of mitochondria-based systematic evolution of ligands by exponential enrichment (SELEX) was explored. Mitochondria were isolated from rat liver and confirmed intact by respiratory control index. Isolated mitochondria and a 2'-F RNA random library were mixed and the bound RNAs collected. The counter selection was applied with nucleus and unbound RNAs were collected. After 7 rounds of selection, two sequences (Mitomer1 and Mitomer2) were verified to bind to mitochondria and the truncated Mitomer2 (short Mitomer2) showed better binding to isolated mitochondria than Mitomer1.}, }
@article {pmid25078074, year = {2014}, author = {Jovanović, D&#x160; and Dorđević, M and Savković, U and Lazarević, J}, title = {The effect of mitochondrial complex I inhibitor on longevity of short-lived and long-lived seed beetles and its mitonuclear hybrids.}, journal = {Biogerontology}, volume = {15}, number = {5}, pages = {487-501}, doi = {10.1007/s10522-014-9520-5}, pmid = {25078074}, issn = {1573-6768}, mesh = {Aging/*metabolism ; Animals ; Cell Nucleus/drug effects/metabolism ; Coleoptera/*drug effects/genetics/*metabolism ; Electron Transport Complex I/*antagonists &amp; inhibitors/metabolism ; Female ; Longevity/*drug effects/physiology ; Male ; Mitochondria/drug effects/metabolism ; Pesticides/pharmacology ; Pyrazoles/pharmacology ; Reactive Oxygen Species/metabolism ; Species Specificity ; }, abstract = {Mitochondria are suggested to play a central role in ageing and evolution of longevity. Gradual decline in mitochondrial function during ageing and concomitant increase in production of reactive oxygen species (ROS) leads to oxidative damage of macromolecules and impairment of ATP synthesis. To assess relationship between ageing and oxidative stress resistance we exposed different longevity lines of the seed beetle (Acanthoscelides obtectus) to four concentrations of tebufenpyrad, mitochondrial complex I inhibitor. Complex I is one of main sites of ROS production during normal respiration and its inhibition elevates oxidative stress. Our results showed that 24 h of exposure to tebufenpyrad decreased survival and post-stress longevity due to increased baseline mortality. Higher resistance was recorded in beetles from lines selected for late reproduction and extended longevity (L) than in early reproducing beetles (E). Also, females were more resistant than males. Since complex I is under dual genetic control, our second aim was to disentangle relative contribution of nuclear and mitochondrial genes to the variation in longevity. We used crossed combinations of distinct mitochondrial and nuclear genotypes (E × L, L × E) and compared them to control hybrids where mitochondrial genome was "transplanted" onto the original background (E × E, L × L). Our study revealed significant effect of nucleus, i.e. higher survival and post-stress longevity in beetles harbouring L nucleus. Mitochondrion effect was significant only within L nuclear background where E mitochondrion gave advantage.}, }
@article {pmid25066801, year = {2014}, author = {Feillet-Coudray, C and Fouret, G and Ebabe Elle, R and Rieusset, J and Bonafos, B and Chabi, B and Crouzier, D and Zarkovic, K and Zarkovic, N and Ramos, J and Badia, E and Murphy, MP and Cristol, JP and Coudray, C}, title = {The mitochondrial-targeted antioxidant MitoQ ameliorates metabolic syndrome features in obesogenic diet-fed rats better than Apocynin or Allopurinol.}, journal = {Free radical research}, volume = {48}, number = {10}, pages = {1232-1246}, doi = {10.3109/10715762.2014.945079}, pmid = {25066801}, issn = {1029-2470}, support = {MC_U105663142/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Acetophenones/pharmacology ; Allopurinol/pharmacology ; Animals ; Antioxidants/*pharmacology ; Blotting, Western ; Diet, High-Fat ; Disease Models, Animal ; Male ; Metabolic Syndrome/*metabolism ; Mitochondria/*drug effects ; Obesity ; Organophosphorus Compounds/*pharmacology ; Oxidative Stress/*drug effects ; Rats ; Rats, Sprague-Dawley ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Ubiquinone/*analogs &amp; derivatives/pharmacology ; }, abstract = {The prevalence of metabolic syndrome (MetS) components including obesity, dyslipidemia, insulin resistance (IR), and hepatic steatosis is rapidly increasing in wealthy societies. It is accepted that inflammation/oxidative stress are involved in the initiation/evolution of the MetS features. The present work was designed to evaluate the effects of three major cellular ROS production systems on obesity, glucose tolerance, and hepatic steatosis development and on oxidative stress onset. To do so, 40 young male Sprague-Dawley rats were divided into 5 groups: 1-control group, 2-high fat (HF) group (60% energy from fat), 3-HF+ MitoQ (mitochondrial ROS scavenger), 4-HF+ Apocynin (NADPH oxidase inhibitor), 5-HF+ Allopurinol (xanthine oxidase inhibitor). After 8 weeks of these treatments, surrogate MetS, mitochondrial function, and oxidative stress markers were measured in blood and liver. As expected, rats that were fed the HF diet exhibited increased body weight, glucose intolerance, overt hepatic steatosis, and increased hepatic oxidative stress. The impacts of the studied ROS inhibitors on these aspects of the MetS were markedly different. MitoQ showed the most clinically relevant effects, attenuating body weight gain and glucose intolerance provoked by the HF diet. Both Apocynin and Allopurinol showed limited effects suggesting secondary roles of xanthine oxidase (XO) or NADPH oxidase-dependent ROS production in the onset of oxidative stress-dependent obesity, glucose intolerance, and hepatic steatosis process. Thus, MitoQ revealed the central role of mitochondrial oxidative stress in the development of MetS and suggested that mitochondria-targeted antioxidants may be worth considering as potentially helpful therapies for MetS features.}, }
@article {pmid25063856, year = {2014}, author = {Stier, A and Bize, P and Roussel, D and Schull, Q and Massemin, S and Criscuolo, F}, title = {Mitochondrial uncoupling as a regulator of life-history trajectories in birds: an experimental study in the zebra finch.}, journal = {The Journal of experimental biology}, volume = {217}, number = {Pt 19}, pages = {3579-3589}, doi = {10.1242/jeb.103945}, pmid = {25063856}, issn = {1477-9145}, mesh = {2,4-Dinitrophenol/pharmacology ; Aging/*physiology ; Animals ; Female ; Fertility ; Finches/growth &amp; development/metabolism/*physiology ; Immunity, Innate ; Inflammation ; Male ; Mitochondria/*metabolism ; Muscle, Skeletal/metabolism ; Oxidation-Reduction ; Oxidative Stress/*physiology ; Reactive Oxygen Species/*metabolism ; }, abstract = {Mitochondria have a fundamental role in the transduction of energy from food into ATP. The coupling between food oxidation and ATP production is never perfect, but may nevertheless be of evolutionary significance. The 'uncoupling to survive' hypothesis suggests that 'mild' mitochondrial uncoupling evolved as a protective mechanism against the excessive production of damaging reactive oxygen species (ROS). Because resource allocation and ROS production are thought to shape animal life histories, alternative life-history trajectories might be driven by individual variation in the degree of mitochondrial uncoupling. We tested this hypothesis in a small bird species, the zebra finch (Taeniopygia guttata), by treating adults with the artificial mitochondrial uncoupler 2,4-dinitrophenol (DNP) over a 32-month period. In agreement with our expectations, the uncoupling treatment increased metabolic rate. However, we found no evidence that treated birds enjoyed lower oxidative stress levels or greater survival rates, in contrast to previous results in other taxa. In vitro experiments revealed lower sensitivity of ROS production to DNP in mitochondria isolated from skeletal muscles of zebra finch than mouse. In addition, we found significant reductions in the number of eggs laid and in the inflammatory immune response in treated birds. Altogether, our data suggest that the 'uncoupling to survive' hypothesis may not be applicable for zebra finches, presumably because of lower effects of mitochondrial uncoupling on mitochondrial ROS production in birds than in mammals. Nevertheless, mitochondrial uncoupling appeared to be a potential life-history regulator of traits such as fecundity and immunity at adulthood, even with food supplied ad libitum.}, }
@article {pmid25063851, year = {2014}, author = {Kéver, L and Boyle, KS and Dragičević, B and Dulčić, J and Parmentier, E}, title = {A superfast muscle in the complex sonic apparatus of Ophidion rochei (Ophidiiformes): histological and physiological approaches.}, journal = {The Journal of experimental biology}, volume = {217}, number = {Pt 19}, pages = {3432-3440}, doi = {10.1242/jeb.105445}, pmid = {25063851}, issn = {1477-9145}, mesh = {Air Sacs/*physiology/ultrastructure ; Animals ; Electromyography ; Female ; Fishes/*anatomy &amp; histology/*physiology ; Male ; Muscle Contraction/physiology ; Muscle Fibers, Skeletal/physiology ; Muscle, Skeletal/*physiology/ultrastructure ; Myofibrils ; *Vocalization, Animal ; }, abstract = {In teleosts, superfast muscles are generally associated with the swimbladder wall, whose vibrations result in sound production. In Ophidion rochei, three pairs of muscles were named 'sonic' because their contractions affect swimbladder position: the dorsal sonic muscle (DSM), the intermediate sonic muscle (ISM), and the ventral sonic muscle (VSM). These muscles were investigated thanks to electron microscopy and electromyography in order to determine their function in sound production. Fibers of the VSM and DSM were much thinner than the fibers of the ISM and epaxial musculature. However, only VSM fibers had the typical ultrastructure of superfast muscles: low proportion of myofibrils, and high proportions of sarcoplasmic reticulum and mitochondria. In females, each sound onset was preceded by the onset of electrical activity in the VSM and the DSM (ISM was not tested). The electromyograms of the VSM were very similar to the waveforms of the sounds: means for the pulse period were 3.6±0.5 and 3.6±0.7 ms, respectively. This shows that the fast VSM (ca. 280 Hz) is responsible for the pulse period and fundamental frequency of female sounds. DSM electromyograms were generally characterized by one or two main peaks followed by periods of lower electrical activity, which suggests a sustained contraction over the course of the sound. The fiber morphology of the ISM and its antagonistic position relative to the DSM are not indicative of a muscle capable of superfast contractions. Overall, this study experimentally shows the complexity of the sound production mechanism in the nocturnal fish O. rochei.}, }
@article {pmid25063438, year = {2014}, author = {Kisslov, I and Naamati, A and Shakarchy, N and Pines, O}, title = {Dual-targeted proteins tend to be more evolutionarily conserved.}, journal = {Molecular biology and evolution}, volume = {31}, number = {10}, pages = {2770-2779}, doi = {10.1093/molbev/msu221}, pmid = {25063438}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Base Sequence ; Conserved Sequence ; *Evolution, Molecular ; Mitochondria/*metabolism ; Models, Genetic ; Phylogeny ; *Protein Transport ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; }, abstract = {In eukaryotic cells, identical proteins can be located in more than a single subcellular compartment, a phenomenon termed dual targeting. We hypothesized that dual-targeted proteins should be more evolutionary conserved than exclusive mitochondrial proteins, due to separate selective pressures administered by the different compartments to maintain the functions associated with the protein sequences. We employed codon usage bias, propensity for gene loss, phylogenetic relationships, conservation analysis at the DNA level, and gene expression, to test our hypothesis. Our findings indicate that, indeed, dual-targeted proteins are significantly more conserved than their exclusively targeted counterparts. We then used this trait of gene conservation, together with previously identified traits of dual-targeted proteins (such as protein net charge and mitochondrial targeting sequence strength) to 1) create, for the first time (due to addition of conservation parameters), a tool for the prediction of dual-targeted mitochondrial proteins based on protein and mRNA sequences, and 2) show that molecular mechanisms involving one versus two translation products are not correlated with specific dual-targeting parameters. Finally, we discuss what evolutionary pressure maintains protein dual targeting in eukaryotes and deduce, as we initially hypothesized, that it is the discrete functions of these proteins in the different subcellular compartments, regardless of their dual-targeting mechanism.}, }
@article {pmid25058696, year = {2014}, author = {Kim, MJ and Wang, AR and Park, JS and Kim, I}, title = {Complete mitochondrial genomes of five skippers (Lepidoptera: Hesperiidae) and phylogenetic reconstruction of Lepidoptera.}, journal = {Gene}, volume = {549}, number = {1}, pages = {97-112}, doi = {10.1016/j.gene.2014.07.052}, pmid = {25058696}, issn = {1879-0038}, mesh = {Animals ; Evolution, Molecular ; Gene Order ; Genome, Insect ; *Genome, Mitochondrial ; Insect Proteins/*genetics ; Lepidoptera/*classification/*genetics/metabolism ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA/genetics ; Sequence Analysis, DNA ; }, abstract = {We sequenced mitogenomes of five skippers (family Hesperiidae, Lepidoptera) to obtain further insight into the characteristics of butterfly mitogenomes and performed phylogenetic reconstruction using all available gene sequences (PCGs, rRNAs, and tRNAs) from 85 species (20 families in eight superfamilies). The general genomic features found in the butterflies also were found in the five skippers: a high A+T composition (79.3%-80.9%), dominant usage of TAA stop codon, similar skewness pattern in both strands, consistently length intergenic spacer sequence between tRNA(Gln) and ND2 (64-87 bp), conserved ATACTAA motif between tRNA(Ser (UCN)) and ND1, and characteristic features of the A+T-rich region (the ATAGA motif, varying length of poly-T stretch, and poly-A stretch). The start codon for COI was CGA in four skippers as typical, but Lobocla bifasciatus evidently possessed canonical ATG as start codon. All species had the ancestral arrangement tRNA(Asn)/tRNA(Ser (AGN)), instead of the rearrangement tRNA(Ser (AGN))/tRNA(Asn), found in another skipper species (Erynnis). Phylogenetic analyses using all available genes (PCGs, rRNAS, and tRNAs) yielded the consensus superfamilial relationships ((((((Bombycoidea+Noctuoidea+Geometroidea)+Pyraloidea)+Papilionoidea)+Tortricoidea)+Yponomeutoidea)+Hepialoidea), confirming the validity of Macroheterocera (Bombycoidea, Noctuoidea, and Geometroidea in this study) and its sister relationship to Pyraloidea. Within Rhopalocera (butterflies and skippers) the familial relationships (Papilionidae+(Hesperiidae+(Pieridae+((Lycaenidae+Riodinidae)+Nymphalidae)))) were strongly supported in all analyses (0.98-1 by BI and 96-100 by ML methods), rendering invalid the superfamily status for Hesperioidea. On the other hand, current mitogenome-based phylogeny did not find consistent superfamilial relationships among Noctuoidea, Geometroidea, and Bombycoidea and the familial relationships within Bombycoidea between analyses, requiring further taxon sampling in future studies.}, }
@article {pmid25057353, year = {2014}, author = {Gaude, E and Frezza, C}, title = {Defects in mitochondrial metabolism and cancer.}, journal = {Cancer &amp; metabolism}, volume = {2}, number = {}, pages = {10}, pmid = {25057353}, issn = {2049-3002}, support = {MC_UP_1101/3/MRC_/Medical Research Council/United Kingdom ; MC_UU_12022/6/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Cancer is a heterogeneous set of diseases characterized by different molecular and cellular features. Over the past decades, researchers have attempted to grasp the complexity of cancer by mapping the genetic aberrations associated with it. In these efforts, the contribution of mitochondria to the pathogenesis of cancer has tended to be neglected. However, more recently, a growing body of evidence suggests that mitochondria play a key role in cancer. In fact, dysfunctional mitochondria not only contribute to the metabolic reprogramming of cancer cells but they also modulate a plethora of cellular processes involved in tumorigenesis. In this review, we describe the link between mutations to mitochondrial enzymes and tumor formation. We also discuss the hypothesis that mutations to mitochondrial and nuclear DNA could cooperate to promote the survival of cancer cells in an evolving metabolic landscape.}, }
@article {pmid25050622, year = {2014}, author = {Sung, KH and Song, HK}, title = {Insights into the molecular evolution of HslU ATPase through biochemical and mutational analyses.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e103027}, pmid = {25050622}, issn = {1932-6203}, mesh = {Adenosine Triphosphatases/chemistry/genetics/*metabolism ; Amino Acid Sequence ; Bacteria/chemistry/*enzymology/genetics/metabolism ; Caseins/metabolism ; *Evolution, Molecular ; Models, Molecular ; Molecular Sequence Data ; Peptide Hydrolases/chemistry/genetics/*metabolism ; Point Mutation ; Sequence Alignment ; Trypanosomatina/chemistry/*enzymology/genetics/metabolism ; }, abstract = {The ATP-dependent HslVU complexes are found in all three biological kingdoms. A single HslV protease exists in each species of prokaryotes, archaea, and eukaryotes, but two HslUs (HslU1 and HslU2) are present in the mitochondria of eukaryotes. Previously, a tyrosine residue at the C-terminal tail of HslU2 has been identified as a key determinant of HslV activation in Trypanosoma brucei and a phenylalanine at the equivalent position to E. coli HslU is found in T. brucei HslU1. Unexpectedly, we found that an F441Y mutation in HslU enhanced the peptidase and caseinolytic activity of HslV in E. coli but it showed partially reduced ATPase and SulA degradation activity. Previously, only the C-terminal tail of HslU has been the focus of HslV activation studies. However, the Pro315 residue interacting with Phe441 in free HslU has also been found to be critical for HslV activation. Hence, our current biochemical analyses explore the importance of the loop region just before Pro315 for HslVU complex functionality. The proline and phenylalanine pair in prokaryotic HslU was replaced with the threonine and tyrosine pair from the functional eukaryotic HslU2. Sequence comparisons between multiple HslUs from three different biological kingdoms in combination with biochemical analysis of E. coli mutants have uncovered important new insights into the molecular evolutionary pathway of HslU.}, }
@article {pmid25049384, year = {2014}, author = {Nakayama, T and Kamikawa, R and Tanifuji, G and Kashiyama, Y and Ohkouchi, N and Archibald, JM and Inagaki, Y}, title = {Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {31}, pages = {11407-11412}, pmid = {25049384}, issn = {1091-6490}, mesh = {*Adaptation, Physiological ; Chromosomes, Bacterial/genetics ; Cyanobacteria/*genetics ; Diatoms/*microbiology ; Electron Transport ; Genome Size ; Genome, Bacterial/*genetics ; Intracellular Space/*microbiology ; Molecular Sequence Data ; Nitrogen Fixation/genetics ; Organelles/metabolism ; Photosynthesis/*genetics ; Symbiosis/genetics ; Thylakoids/metabolism ; }, abstract = {The evolution of mitochondria and plastids from bacterial endosymbionts were key events in the origin and diversification of eukaryotic cells. Although the ancient nature of these organelles makes it difficult to understand the earliest events that led to their establishment, the study of eukaryotic cells with recently evolved obligate endosymbiotic bacteria has the potential to provide important insight into the transformation of endosymbionts into organelles. Diatoms belonging to the family Rhopalodiaceae and their endosymbionts of cyanobacterial origin (i.e., "spheroid bodies") are emerging as a useful model system in this regard. The spheroid bodies, which appear to enable rhopalodiacean diatoms to use gaseous nitrogen, became established after the divergence of extant diatom families. Here we report what is, to our knowledge, the first complete genome sequence of a spheroid body, that of the rhopalodiacean diatom Epithemia turgida. The E. turgida spheroid body (EtSB) genome was found to possess a gene set for nitrogen fixation, as anticipated, but is reduced in size and gene repertoire compared with the genomes of their closest known free-living relatives. The presence of numerous pseudogenes in the EtSB genome suggests that genome reduction is ongoing. Most strikingly, our genomic data convincingly show that the EtSB has lost photosynthetic ability and is metabolically dependent on its host cell, unprecedented characteristics among cyanobacteria, and cyanobacterial symbionts. The diatom-spheroid body endosymbiosis is thus a unique system for investigating the processes underlying the integration of a bacterial endosymbiont into eukaryotic cells.}, }
@article {pmid25045044, year = {2014}, author = {Dolce, V and Cappello, AR and Capobianco, L}, title = {Mitochondrial tricarboxylate and dicarboxylate-tricarboxylate carriers: from animals to plants.}, journal = {IUBMB life}, volume = {66}, number = {7}, pages = {462-471}, doi = {10.1002/iub.1290}, pmid = {25045044}, issn = {1521-6551}, mesh = {Animals ; Base Sequence ; Carrier Proteins/*physiology ; Dicarboxylic Acid Transporters/*physiology ; Humans ; Mitochondria/metabolism ; Mitochondrial Proteins/physiology ; Molecular Sequence Data ; Organ Specificity ; Phylogeny ; Promoter Regions, Genetic ; }, abstract = {The citrate carrier (CiC), characteristic of animals, and the dicarboxylate-tricarboxylate carrier (DTC), characteristic of plants and protozoa, belong to the mitochondrial carrier protein family whose members are responsible for the exchange of metabolites, cofactors, and nucleotides between the cytoplasm and the mitochondrial matrix. Most of the functional data on these transporters are obtained from the studies performed with the protein purified from rat, eel yeast, and maize mitochondria or recombinant proteins from different sources incorporated into phospholipid vesicles (liposomes). The functional data indicate that CiC is responsible for the efflux of acetyl-CoA from the mitochondria to the cytosol in the form of citrate, the primer for fatty acid, cholesterol synthesis, and histone acetylation. Like the CiC, the citrate exported by DTC from the mitochondria to the cytosol in exchange for oxaloacetate can be cleaved by citrate lyase to acetyl-CoA and oxaloacetate and used for fatty acid elongation and isoprenoid synthesis. In addition to its role in fatty acid synthesis, CiC is involved in other processes such as gluconeogenesis, insulin secretion, inflammation, and cancer progression, whereas DTC is involved in the production of glycerate, nitrogen assimilation, ripening of fruits, ATP synthesis, and sustaining of respiratory flux in fruit cells. This review provides an assessment of the current understanding of CiC and DTC structural and biochemical characteristics, underlying the structure-function relationship of these carriers. Furthermore, a phylogenetic relationship between CiC and DTC is proposed.}, }
@article {pmid25042454, year = {2014}, author = {Norfatimah, MY and Teh, LK and Salleh, MZ and Mat Isa, MN and SitiAzizah, MN}, title = {Complete mitochondrial genome of Malaysian Mahseer (Tor tambroides).}, journal = {Gene}, volume = {548}, number = {2}, pages = {263-269}, doi = {10.1016/j.gene.2014.07.044}, pmid = {25042454}, issn = {1879-0038}, mesh = {Animals ; Cyprinidae/*genetics ; Cypriniformes/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {This is the first documentation of the complete mitochondrial genome sequence of the Malaysian Mahseer, Tor tambroides. The 16,690 bp mitogenome with GenBank accession number JX444718 contains 13 protein genes, 22 tRNAs, two rRNAs, and a noncoding control region (D-loop) as is typical of most vertebrates. The phylogenomic reconstruction of this newly generated data with 21 Cypriniformes GenBank accession ID concurs with the recognized status of T. tambroides within the subfamily Cyprininae. This is in agreement with previous hypotheses based on morphological and partial mitochondrial analyses.}, }
@article {pmid25040194, year = {2014}, author = {Watson, PM and Sorrell, SC and Brown, MW}, title = {Ptolemeba n. gen., a novel genus of hartmannellid amoebae (Tubulinea, Amoebozoa); with an emphasis on the taxonomy of Saccamoeba.}, journal = {The Journal of eukaryotic microbiology}, volume = {61}, number = {6}, pages = {611-619}, doi = {10.1111/jeu.12139}, pmid = {25040194}, issn = {1550-7408}, mesh = {DNA, Ribosomal/genetics ; Lobosea/*classification/genetics/ultrastructure ; Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Hartmannellid amoebae are an unnatural assemblage of amoeboid organisms that are morphologically difficult to discern from one another. In molecular phylogenetic trees of the nuclear-encoded small subunit rDNA, they occupy at least five lineages within Tubulinea, a well-supported clade in Amoebozoa. The polyphyletic nature of the hartmannellids has led to many taxonomic problems, in particular paraphyletic genera. Recent taxonomic revisions have alleviated some of the problems. However, the genus Saccamoeba is paraphyletic and is still in need of revision as it currently occupies two distinct lineages. Here, we report a new clade on the tree of Tubulinea, which we infer represents a novel genus that we name Ptolemeba n. gen. This genus subsumes a clade of hartmannellid amoebae that were previously considered in the genus Saccamoeba, but whose mitochondrial morphology is distinct from Saccamoeba. In accordance with previous research, we formalize the clade as distinct from Saccamoeba. Transmission electron microscopy of our isolates illustrate that both molecularly discrete species can be further differentiated by their unique mitochondrial cristal morphology.}, }
@article {pmid25038299, year = {2014}, author = {Jimenez, AG and Williams, JB}, title = {Cellular metabolic rates from primary dermal fibroblast cells isolated from birds of different body masses.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {176}, number = {}, pages = {41-48}, doi = {10.1016/j.cbpa.2014.07.009}, pmid = {25038299}, issn = {1531-4332}, mesh = {Animals ; Basal Metabolism/*physiology ; Birds/*physiology ; Body Size/physiology ; Body Weight/*physiology ; Cell Line ; Cell Respiration/physiology ; Fibroblasts/*physiology ; Mitochondria/physiology ; Oxygen Consumption/physiology ; Protons ; }, abstract = {The rate of metabolism is the speed at which organisms use energy, an integration of energy transformations within the body; it governs biological processes that influence rates of growth and reproduction. Progress at understanding functional linkages between whole organism metabolic rate and underlying mechanisms that influence its magnitude has been slow despite the central role this issue plays in evolutionary and physiological ecology. Previous studies that have attempted to relate how cellular processes translate into whole-organism physiology have done so over a range of body masses of subjects. However, the data still remains controversial when observing metabolic rates at the cellular level. To bridge the gap between these ideas, we examined cellular metabolic rate of primary dermal fibroblasts isolated from 49 species of birds representing a 32,000-fold range in body masses to test the hypothesis that metabolic rate of cultured cells scales with body size. We used a Seahorse XF-96 Extracellular flux analyzer to measure cellular respiration in fibroblasts. Additionally, we measured fibroblast size and mitochondrial content. We found no significant correlation between cellular metabolic rate, cell size, or mitochondrial content and body mass. Additionally, there was a significant relationship between cellular basal metabolic rate and proton leak in these cells. We conclude that metabolic rate of cells isolated in culture does not scale with body mass, but cellular metabolic rate is correlated to growth rate in birds.}, }
@article {pmid25038049, year = {2014}, author = {Poole, AM and Gribaldo, S}, title = {Eukaryotic origins: How and when was the mitochondrion acquired?.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {6}, number = {12}, pages = {a015990}, pmid = {25038049}, issn = {1943-0264}, mesh = {*Biological Evolution ; Eukaryota/*cytology ; Mitochondria/*physiology ; *Models, Biological ; Phagocytosis/*physiology ; *Phylogeny ; *Symbiosis ; }, abstract = {Comparative genomics has revealed that the last eukaryotic common ancestor possessed the hallmark cellular architecture of modern eukaryotes. However, the remarkable success of such analyses has created a dilemma. If key eukaryotic features are ancestral to this group, then establishing the relative timing of their origins becomes difficult. In discussions of eukaryote origins, special significance has been placed on the timing of mitochondrial acquisition. In one view, mitochondrial acquisition was the trigger for eukaryogenesis. Others argue that development of phagocytosis was a prerequisite to acquisition. Results from comparative genomics and molecular phylogeny are often invoked to support one or the other scenario. We show here that the associations between specific cell biological models of eukaryogenesis and evolutionary genomic data are not as strong as many suppose. Disentangling these eliminates many of the arguments that polarize current debate.}, }
@article {pmid25032851, year = {2014}, author = {Flores-Bellver, M and Bonet-Ponce, L and Barcia, JM and Garcia-Verdugo, JM and Martinez-Gil, N and Saez-Atienzar, S and Sancho-Pelluz, J and Jordan, J and Galindo, MF and Romero, FJ}, title = {Autophagy and mitochondrial alterations in human retinal pigment epithelial cells induced by ethanol: implications of 4-hydroxy-nonenal.}, journal = {Cell death &amp; disease}, volume = {5}, number = {7}, pages = {e1328}, pmid = {25032851}, issn = {2041-4889}, mesh = {Aldehydes/*adverse effects ; Apoptosis/drug effects ; Autophagy/*drug effects ; Cell Line ; Epithelial Cells/cytology/*drug effects/metabolism ; Ethanol/*adverse effects ; Humans ; Mitochondria/drug effects/*metabolism ; Oxidative Stress/drug effects ; Reactive Oxygen Species/metabolism ; Retinal Diseases/etiology/metabolism/*physiopathology ; Retinal Pigment Epithelium/*cytology/drug effects/metabolism ; }, abstract = {Retinal pigment epithelium has a crucial role in the physiology and pathophysiology of the retina due to its location and metabolism. Oxidative damage has been demonstrated as a pathogenic mechanism in several retinal diseases, and reactive oxygen species are certainly important by-products of ethanol (EtOH) metabolism. Autophagy has been shown to exert a protective effect in different cellular and animal models. Thus, in our model, EtOH treatment increases autophagy flux, in a concentration-dependent manner. Mitochondrial morphology seems to be clearly altered under EtOH exposure, leading to an apparent increase in mitochondrial fission. An increase in 2',7'-dichlorofluorescein fluorescence and accumulation of lipid peroxidation products, such as 4-hydroxy-nonenal (4-HNE), among others were confirmed. The characterization of these structures confirmed their nature as aggresomes. Hence, autophagy seems to have a cytoprotective role in ARPE-19 cells under EtOH damage, by degrading fragmented mitochondria and 4-HNE aggresomes. Herein, we describe the central implication of autophagy in human retinal pigment epithelial cells upon oxidative stress induced by EtOH, with possible implications for other conditions and diseases.}, }
@article {pmid25028670, year = {2014}, author = {Song, WH and Ballard, JW and Yi, YJ and Sutovsky, P}, title = {Regulation of mitochondrial genome inheritance by autophagy and ubiquitin-proteasome system: implications for health, fitness, and fertility.}, journal = {BioMed research international}, volume = {2014}, number = {}, pages = {981867}, pmid = {25028670}, issn = {2314-6141}, mesh = {Animals ; Autophagy/*physiology ; Female ; Fertility/*physiology ; Genome, Mitochondrial/*physiology ; Humans ; Male ; Mitophagy/physiology ; Oocytes/metabolism ; Proteasome Endopeptidase Complex/*physiology ; Proteolysis ; Sperm Maturation/physiology ; Spermatozoa/metabolism ; Ubiquitin/*metabolism ; }, abstract = {Mitochondria, the energy-generating organelles, play a role in numerous cellular functions including adenosine triphosphate (ATP) production, cellular homeostasis, and apoptosis. Maternal inheritance of mitochondria and mitochondrial DNA (mtDNA) is universally observed in humans and most animals. In general, high levels of mitochondrial heteroplasmy might contribute to a detrimental effect on fitness and disease resistance. Therefore, a disposal of the sperm-derived mitochondria inside fertilized oocytes assures normal preimplantation embryo development. Here we summarize the current research and knowledge concerning the role of autophagic pathway and ubiquitin-proteasome-dependent proteolysis in sperm mitophagy in mammals, including humans. Current data indicate that sperm mitophagy inside the fertilized oocyte could occur along multiple degradation routes converging on autophagic clearance of paternal mitochondria. The influence of assisted reproductive therapies (ART) such as intracytoplasmic sperm injection (ICSI), mitochondrial replacement (MR), and assisted fertilization of oocytes from patients of advanced reproductive age on mitochondrial function, inheritance, and fitness and for the development and health of ART babies will be of particular interest to clinical audiences. Altogether, the study of sperm mitophagy after fertilization has implications in the timing of evolution and developmental and reproductive biology and in human health, fitness, and management of mitochondrial disease.}, }
@article {pmid25028428, year = {2014}, author = {Erental, A and Kalderon, Z and Saada, A and Smith, Y and Engelberg-Kulka, H}, title = {Apoptosis-like death, an extreme SOS response in Escherichia coli.}, journal = {mBio}, volume = {5}, number = {4}, pages = {e01426-14}, pmid = {25028428}, issn = {2150-7511}, mesh = {Apoptosis/genetics/physiology ; DNA Damage/genetics ; Escherichia coli/*cytology/*genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; SOS Response, Genetics/genetics/*physiology ; }, abstract = {In bacteria, SOS is a global response to DNA damage, mediated by the recA-lexA genes, resulting in cell cycle arrest, DNA repair, and mutagenesis. Previously, we reported that Escherichia coli responds to DNA damage via another recA-lexA-mediated pathway resulting in programmed cell death (PCD). We called it apoptosis-like death (ALD) because it is characterized by membrane depolarization and DNA fragmentation, which are hallmarks of eukaryotic mitochondrial apoptosis. Here, we show that ALD is an extreme SOS response that occurs only under conditions of severe DNA damage. Furthermore, we found that ALD is characterized by additional hallmarks of eukaryotic mitochondrial apoptosis, including (i) rRNA degradation by the endoribonuclease YbeY, (ii) upregulation of a unique set of genes that we called extensive-damage-induced (Edin) genes, (iii) a decrease in the activities of complexes I and II of the electron transport chain, and (iv) the formation of high levels of OH˙ through the Fenton reaction, eventually resulting in cell death. Our genetic and molecular studies on ALD provide additional insight for the evolution of mitochondria and the apoptotic pathway in eukaryotes. Importance: The SOS response is the first described and the most studied bacterial response to DNA damage. It is mediated by a set of two genes, recA-lexA, and it results in DNA repair and thereby in the survival of the bacterial culture. We have shown that Escherichia coli responds to DNA damage by an additional recA-lexA-mediated pathway resulting in an apoptosis-like death (ALD). Apoptosis is a mode of cell death that has previously been reported only in eukaryotes. We found that E. coli ALD is characterized by several hallmarks of eukaryotic mitochondrial apoptosis. Altogether, our results revealed that recA-lexA is a DNA damage response coordinator that permits two opposite responses: life, mediated by the SOS, and death, mediated by the ALD. The choice seems to be a function of the degree of DNA damage in the cell.}, }
@article {pmid25026440, year = {2014}, author = {Gawryluk, RM and Chisholm, KA and Pinto, DM and Gray, MW}, title = {Compositional complexity of the mitochondrial proteome of a unicellular eukaryote (Acanthamoeba castellanii, supergroup Amoebozoa) rivals that of animals, fungi, and plants.}, journal = {Journal of proteomics}, volume = {109}, number = {}, pages = {400-416}, doi = {10.1016/j.jprot.2014.07.005}, pmid = {25026440}, issn = {1876-7737}, support = {MOP-4124//Canadian Institutes of Health Research/Canada ; }, mesh = {Acanthamoeba castellanii/genetics/*metabolism ; Animals ; Computational Biology ; Fungi ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/*metabolism ; Plants ; Proteome/*metabolism ; Proteomics ; Protozoan Proteins/*metabolism ; }, abstract = {UNLABELLED: We present a combined proteomic and bioinformatic investigation of mitochondrial proteins from the amoeboid protist Acanthamoeba castellanii, the first such comprehensive investigation in a free-living member of the supergroup Amoebozoa. This protist was chosen both for its phylogenetic position (as a sister to animals and fungi) and its ecological ubiquity and physiological flexibility. We report 1033 A. castellanii mitochondrial protein sequences, 709 supported by mass spectrometry data (676 nucleus-encoded and 33 mitochondrion-encoded), including two previously unannotated mtDNA-encoded proteins, which we identify as highly divergent mitochondrial ribosomal proteins. Other notable findings include duplicate proteins for all of the enzymes of the tricarboxylic acid (TCA) cycle-which, along with the identification of a mitochondrial malate synthase-isocitrate lyase fusion protein, suggests the interesting possibility that the glyoxylate cycle operates in A. castellanii mitochondria. Additionally, the A. castellanii genome encodes an unusually high number (at least 29) of mitochondrion-targeted pentatricopeptide repeat (PPR) proteins, organellar RNA metabolism factors in other organisms. We discuss several key mitochondrial pathways, including DNA replication, transcription and translation, protein degradation, protein import and Fe-S cluster biosynthesis, highlighting similarities and differences in these pathways in other eukaryotes. In compositional and functional complexity, the mitochondrial proteome of A. castellanii rivals that of multicellular eukaryotes.<br><br>BIOLOGICAL SIGNIFICANCE: Comprehensive proteomic surveys of mitochondria have been undertaken in a limited number of predominantly multicellular eukaryotes. This phylogenetically narrow perspective constrains and biases our insights into mitochondrial function and evolution, as it neglects protists, which account for most of the evolutionary and functional diversity within eukaryotes. We report here the first comprehensive investigation of the mitochondrial proteome in a member (A. castellanii) of the eukaryotic supergroup Amoebozoa. Through a combination of tandem mass spectrometry (MS/MS) and in silico data mining, we have retrieved 1033 candidate mitochondrial protein sequences, 709 having MS support. These data were used to reconstruct the metabolic pathways and protein complexes of A. castellanii mitochondria, and were integrated with data from other characterized mitochondrial proteomes to augment our understanding of mitochondrial proteome evolution. Our results demonstrate the power of combining direct proteomic and bioinformatic approaches in the discovery of novel mitochondrial proteins, both nucleus-encoded and mitochondrion-encoded, and highlight the compositional complexity of the A. castellanii mitochondrial proteome, which rivals that of animals, fungi and plants.}, }
@article {pmid25024271, year = {2014}, author = {Li, J and Coates, BS and Kim, KS and Bourguet, D and Ponsard, S and He, K and Wang, Z}, title = {The genetic structure of Asian corn borer, Ostrinia furnacalis, populations in China: haplotype variance in northern populations and potential impact on management of resistance to transgenic maize.}, journal = {The Journal of heredity}, volume = {105}, number = {5}, pages = {642-655}, doi = {10.1093/jhered/esu036}, pmid = {25024271}, issn = {1465-7333}, mesh = {Alleles ; Animals ; China ; Gene Flow ; Genetic Drift ; Genetic Loci ; Genetic Markers ; *Genetic Variation ; *Genetics, Population ; *Haplotypes ; Lepidoptera/*genetics ; Microsatellite Repeats ; Mitochondria/genetics ; Multigene Family ; Phylogeography ; Plants, Genetically Modified ; *Zea mays ; }, abstract = {Asian corn borer, Ostrinia furnacalis (Guenée), is a severe pest that infests cultivated maize in the major production regions of China. Populations show genotype-by-environment variation in voltinism, such that populations with a single generation (univoltine) are fixed in Northern China where growing seasons are short. Low genetic differentiation was found among samples from 33 collection sites across China and one site from North Korea (n=1673) using variation at 6 nuclear microsatellite loci (ENA corrected global FST=0.020; P value<0.05). Analysis of molecular variance indicated that geographic region, number of generations or voltinism accounted for <0.38% of the total genetic variation at nuclear loci and was corroborated by clustering of co-ancestries among genotypes using the program STRUCTURE. In contrast, a mitochondrial haplotype network identified 4 distinct clusters, where 70.5% of samples from univoltine populations were within a single group. Univoltine populations were also placed into a unique cluster using Population Graph and Principal component analyses, which showed significant differentiation with multivoltine populations (φST=0.400; P value<0.01). This study suggests that gene flow among O. furnacalis in China may be high among regions, with the exception of northeastern localities. Haplotype variation may be due to random genetic drift resulting from partial reproductive isolation between univoltine and multivoltine O. furnacalis populations. Such reproductive isolation might impact the potential spread of alleles that confer resistance to transgenic maize in China.}, }
@article {pmid25020128, year = {2014}, author = {Barbosa, AJ and Sampaio, I and Schneider, H and Santos, S}, title = {Molecular phylogeny of weakfish species of the Stellifer group (Sciaenidae, Perciformes) of the western South Atlantic based on mitochondrial and nuclear data.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e102250}, pmid = {25020128}, issn = {1932-6203}, mesh = {Animals ; Atlantic Ocean ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; Genetic Markers/genetics ; Mitochondria/*genetics ; Perciformes/*classification/*genetics ; *Phylogeny ; }, abstract = {The phylogenetic relationships within the Stellifer group of weakfishes (Stellifer, Odontoscion, Ophioscion, and Bairdiella) were evaluated using 2723 base pairs comprising sequences of nuclear (rhodopsin, TMO-4C4, RAG-1) and mitochondrial (16S rRNA and COI) markers obtained from specimens of nine species. Our results indicate a close relationship between Bairdiella and Odontoscion, and also that the genus Stellifer is not monophyletic, but rather that it consists of two distinct lineages, one clade containing S. microps/S. naso/S. brasiliensis and the other, S. rastrifer/S. stellifer/Stellifer sp. B, which is closer to Ophioscion than the former clade. The O. punctatissimus populations from the northern and southern Brazilian coast were also highly divergent in both nuclear (0.8% for rhodopsin and 0.9% for RAG-1) and mitochondrial sequences (2.2% for 16S rRNA and 7.3% for COI), which we conclude is consistent with the presence of two distinct species. The morphological similarities of the members of the Stellifer group is reinforced by the molecular data from both the present study and previous analyses, which have questioned the taxonomic status of the Stellifer group. If, on the one hand, the group is in fact composed of four genera (Stellifer, Ophioscion, Odontoscion, and Bairdiella), one of the two Stellifer clades should be reclassified as a new genus. However, if the close relationship and the reduced genetic divergence found within the group is confirmed in a more extensive study, including representatives of additional taxa, this, together with the morphological evidence, would support downgrading the whole group to a single genus. Obviously, these contradictory findings reinforce the need for a more systematic taxonomic revision of the Stellifer group as a whole.}, }
@article {pmid25015079, year = {2014}, author = {Klimeš, V and Gentekaki, E and Roger, AJ and Eliáš, M}, title = {A large number of nuclear genes in the human parasite blastocystis require mRNA polyadenylation to create functional termination codons.}, journal = {Genome biology and evolution}, volume = {6}, number = {8}, pages = {1956-1961}, pmid = {25015079}, issn = {1759-6653}, mesh = {Amino Acid Sequence ; Base Sequence ; Blastocystis/chemistry/*genetics ; Blastocystis Infections/*parasitology ; Codon, Terminator/chemistry/*genetics ; Humans ; Molecular Sequence Data ; *Polyadenylation ; Protozoan Proteins/chemistry/genetics ; RNA, Messenger/chemistry/*genetics ; }, abstract = {Termination codons in mRNA molecules are typically specified directly by the sequence of the corresponding gene. However, in mitochondria of a few eukaryotic groups, some mRNAs contain the termination codon UAA deriving one or both adenosines from transcript polyadenylation. Here, we show that a similar phenomenon occurs for a substantial number of nuclear genes in Blastocystis spp., divergent unicellular eukaryote gut parasites. Our analyses of published genomic data from Blastocystis sp. subtype 7 revealed that polyadenylation-mediated creation of termination codons occurs in approximately 15% of all nuclear genes. As this phenomenon has not been noticed before, the procedure previously employed to annotate the Blastocystis nuclear genome sequence failed to correctly define the structure of the 3'-ends of hundreds of genes. From sequence data we have obtained from the distantly related Blastocystis sp. subtype 1 strain, we show that this phenomenon is widespread within the Blastocystis genus. Polyadenylation in Blastocystis appears to be directed by a conserved GU-rich element located four nucleotides downstream of the polyadenylation site. Thus, the highly precise positioning of the polyadenylation in Blastocystis has allowed reduction of the 3'-untranslated regions to the point that, in many genes, only one or two nucleotides of the termination codon are left.}, }
@article {pmid25010076, year = {2016}, author = {Caragiulo, A and Dougherty, E and Soto, S and Rabinowitz, S and Amato, G}, title = {The complete mitochondrial genome structure of the jaguar (Panthera onca).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {914-915}, doi = {10.3109/19401736.2014.926483}, pmid = {25010076}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence ; Central America ; DNA, Mitochondrial/*genetics ; Genome Size ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Panthera/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*veterinary ; South America ; }, abstract = {The jaguar (Panthera onca) is the largest felid in the Western hemisphere, and the only member of the Panthera genus in the New World. The jaguar inhabits most countries within Central and South America, and is considered near threatened by the International Union for the Conservation of Nature. This study represents the first sequence of the entire jaguar mitogenome, which was the only Panthera mitogenome that had not been sequenced. The jaguar mitogenome is 17,049 bases and possesses the same molecular structure as other felid mitogenomes. Bayesian inference (BI) and maximum likelihood (ML) were used to determine the phylogenetic placement of the jaguar within the Panthera genus. Both BI and ML analyses revealed the jaguar to be sister to the tiger/leopard/snow leopard clade.}, }
@article {pmid25005920, year = {2014}, author = {Candat, A and Paszkiewicz, G and Neveu, M and Gautier, R and Logan, DC and Avelange-Macherel, MH and Macherel, D}, title = {The ubiquitous distribution of late embryogenesis abundant proteins across cell compartments in Arabidopsis offers tailored protection against abiotic stress.}, journal = {The Plant cell}, volume = {26}, number = {7}, pages = {3148-3166}, pmid = {25005920}, issn = {1532-298X}, mesh = {Amino Acid Motifs ; Arabidopsis/cytology/genetics/*physiology ; Arabidopsis Proteins/classification/genetics/metabolism ; Cell Membrane/metabolism ; Cold Temperature ; Computational Biology ; Desiccation ; Genes, Reporter ; Organelles/metabolism ; Phylogeny ; Plant Proteins/classification/genetics/*metabolism ; Plants, Genetically Modified ; Protein Transport ; Protoplasts ; Recombinant Fusion Proteins ; Seedlings/cytology/genetics/physiology ; Stress, Physiological ; }, abstract = {Late embryogenesis abundant (LEA) proteins are hydrophilic, mostly intrinsically disordered proteins, which play major roles in desiccation tolerance. In Arabidopsis thaliana, 51 genes encoding LEA proteins clustered into nine families have been inventoried. To increase our understanding of the yet enigmatic functions of these gene families, we report the subcellular location of each protein. Experimental data highlight the limits of in silico predictions for analysis of subcellular localization. Thirty-six LEA proteins localized to the cytosol, with most being able to diffuse into the nucleus. Three proteins were exclusively localized in plastids or mitochondria, while two others were found dually targeted to these organelles. Targeting cleavage sites could be determined for five of these proteins. Three proteins were found to be endoplasmic reticulum (ER) residents, two were vacuolar, and two were secreted. A single protein was identified in pexophagosomes. While most LEA protein families have a unique subcellular localization, members of the LEA_4 family are widely distributed (cytosol, mitochondria, plastid, ER, and pexophagosome) but share the presence of the class A α-helix motif. They are thus expected to establish interactions with various cellular membranes under stress conditions. The broad subcellular distribution of LEA proteins highlights the requirement for each cellular compartment to be provided with protective mechanisms to cope with desiccation or cold stress.}, }
@article {pmid25005355, year = {2014}, author = {Bertrand, C and Janzen, DH and Hallwachs, W and Burns, JM and Gibson, JF and Shokralla, S and Hajibabaei, M}, title = {Mitochondrial and nuclear phylogenetic analysis with Sanger and next-generation sequencing shows that, in Área de Conservación Guanacaste, northwestern Costa Rica, the skipper butterfly named Urbanus belli (family Hesperiidae) comprises three morphologically cryptic species.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {153}, pmid = {25005355}, issn = {1471-2148}, mesh = {Animals ; Butterflies/*classification/*genetics/microbiology ; Cell Nucleus/genetics ; Costa Rica ; DNA, Ribosomal Spacer/genetics ; High-Throughput Nucleotide Sequencing ; Mitochondria/genetics ; Phylogeny ; Wolbachia/genetics ; }, abstract = {BACKGROUND: Skipper butterflies (Hesperiidae) are a relatively well-studied family of Lepidoptera. However, a combination of DNA barcodes, morphology, and natural history data has revealed several cryptic species complexes within them. Here, we investigate three DNA barcode lineages of what has been identified as Urbanus belli (Hesperiidae, Eudaminae) in Área de Conservación Guanacaste (ACG), northwestern Costa Rica.<br><br>RESULTS: Although no morphological traits appear to distinguish among the three, congruent nuclear and mitochondrial lineage patterns show that "Urbanus belli" in ACG is a complex of three sympatric species. A single strain of Wolbachia present in two of the three cryptic species indicates that Urbanus segnestami Burns (formerly Urbanus belliDHJ01), Urbanus bernikerni Burns (formerly Urbanus belliDHJ02), and Urbanus ehakernae Burns (formerly Urbanus belliDHJ03) may be biologically separated by Wolbachia, as well as by their genetics. Use of parallel sequencing through 454-pyrosequencing improved the utility of ITS2 as a phylogenetic marker and permitted examination of the intra- and interlineage relationships of ITS2 variants within the species complex. Interlineage, intralineage and intragenomic compensatory base pair changes were discovered in the secondary structure of ITS2.<br><br>CONCLUSION: These findings corroborate the existence of three cryptic species. Our confirmation of a novel cryptic species complex, initially suggested by DNA barcode lineages, argues for using a multi-marker approach coupled with next-generation sequencing for exploration of other suspected species complexes.}, }
@article {pmid25005252, year = {2014}, author = {Abe, KT and Mariguela, TC and Avelino, GS and Foresti, F and Oliveira, C}, title = {Systematic and historical biogeography of the Bryconidae (Ostariophysi: Characiformes) suggesting a new rearrangement of its genera and an old origin of Mesoamerican ichthyofauna.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {152}, pmid = {25005252}, issn = {1471-2148}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; Central America ; Characiformes/*classification/*genetics ; Fossils ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; South America ; }, abstract = {BACKGROUND: Recent molecular hypotheses suggest that some traditional suprageneric taxa of Characiformes require revision, as they may not constitute monophyletic groups. This is the case for the Bryconidae. Various studies have proposed that this family (considered a subfamily by some authors) may be composed of different genera. However, until now, no phylogenetic study of all putative genera has been conducted.<br><br>RESULTS: In the present study, we analyzed 27 species (46 specimens) of all currently recognized genera of the Bryconidae (ingroup) and 208 species representing all other families and most genera of the Characiformes (outgroup). Five genes were sequenced: 16SrRNA, Cytochrome b, recombination activating gene 1 and 2 and myosin heavy chain 6 cardiac muscle. The final matrix contained 4699 bp and was analyzed by maximum likelihood, maximum parsimony and Bayesian analyses. The results show that the Bryconidae, composed of Brycon, Chilobrycon, Henochilus and Salminus, is monophyletic and is the sister group of Gasteropelecidae&#x2009;+&#x2009;Triportheidae. However, the genus Brycon is polyphyletic. Fossil studies suggest that the family originated approximately 47 million years ago (Ma) and that one of the two main lineages persisted only in trans-Andean rivers, including Central American rivers, suggesting a much older origin of Mesoamerican ichthyofauna than previously accepted.<br><br>CONCLUSION: Bryconidae is composed by five main clades, including the genera Brycon, Chilobrycon, Henochilus and Salminus, but a taxonomic review of these groups is needed. Our results point to a possible ancient invasion of Central America, dating about 20.3 &#xb1; 5.0 Ma (late Oligocene--early Miocene), to explain the occurrence of Brycon in Central America.}, }
@article {pmid25002117, year = {2014}, author = {Hess, KC and Liu, J and Manfredi, G and Mühlschlegel, FA and Buck, J and Levin, LR and Barrientos, A}, title = {A mitochondrial CO2-adenylyl cyclase-cAMP signalosome controls yeast normoxic cytochrome c oxidase activity.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {28}, number = {10}, pages = {4369-4380}, pmid = {25002117}, issn = {1530-6860}, support = {R01 GM105781/GM/NIGMS NIH HHS/United States ; R01 GM107442/GM/NIGMS NIH HHS/United States ; R01 GM062328/GM/NIGMS NIH HHS/United States ; GM-071775/GM/NIGMS NIH HHS/United States ; R01 HD059913/HD/NICHD NIH HHS/United States ; GM-088999A/GM/NIGMS NIH HHS/United States ; R01 GM071775/GM/NIGMS NIH HHS/United States ; R01 GM088999/GM/NIGMS NIH HHS/United States ; HD-059913/HD/NICHD NIH HHS/United States ; GM-062328/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Allosteric Regulation ; Carbon Dioxide/metabolism ; *Cell Hypoxia ; Cyclic AMP/*metabolism ; Cyclic AMP-Dependent Protein Kinases/metabolism ; Electron Transport Complex IV/genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Mutation ; Phosphorylation ; Saccharomyces cerevisiae/enzymology/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; }, abstract = {Mitochondria, the major source of cellular energy in the form of ATP, respond to changes in substrate availability and bioenergetic demands by employing rapid, short-term, metabolic adaptation mechanisms, such as phosphorylation-dependent protein regulation. In mammalian cells, an intramitochondrial CO2-adenylyl cyclase (AC)-cyclic AMP (cAMP)-protein kinase A (PKA) pathway regulates aerobic energy production. One target of this pathway involves phosphorylation of cytochrome c oxidase (COX) subunit 4-isoform 1 (COX4i1), which modulates COX allosteric regulation by ATP. However, the role of the CO2-sAC-cAMP-PKA signalosome in regulating COX activity and mitochondrial metabolism and its evolutionary conservation remain to be fully established. We show that in Saccharomyces cerevisiae, normoxic COX activity measured in the presence of ATP is 55% lower than in the presence of ADP. Moreover, the adenylyl cyclase Cyr1 activity is present in mitochondria, and it contributes to the ATP-mediated regulation of COX through the normoxic subunit Cox5a, homologue of human COX4i1, in a bicarbonate-sensitive manner. Furthermore, we have identified 2 phosphorylation targets in Cox5a (T65 and S43) that modulate its allosteric regulation by ATP. These residues are not conserved in the Cox5b-containing hypoxic enzyme, which is not regulated by ATP. We conclude that across evolution, a CO2-sAC-cAMP-PKA axis regulates normoxic COX activity.}, }
@article {pmid24999047, year = {2014}, author = {Zhang, T and Jiang, Y and Dong, W}, title = {A novel monopartite dsRNA virus isolated from the phytopathogenic fungus Ustilaginoidea virens and ancestrally related to a mitochondria-associated dsRNA in the green alga Bryopsis.}, journal = {Virology}, volume = {462-463}, number = {}, pages = {227-235}, doi = {10.1016/j.virol.2014.06.003}, pmid = {24999047}, issn = {1096-0341}, mesh = {China ; Chlorophyta/genetics ; Cluster Analysis ; Genome, Viral ; Hypocreales/*virology ; Mitochondria/genetics ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; RNA Viruses/*classification/genetics/*isolation &amp; purification ; RNA, Double-Stranded/*genetics ; RNA, Viral/*genetics ; Saccharomycetales/genetics ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {In this study, we describe a novel mycovirus isolated from Ustilaginoidea virens, which was designated Ustilaginoidea virens nonsegmented virus 1 (UvNV-1). The sequence analysis revealed that UvNV-1 has two open reading frames (ORFs). ORF1 encodes an unknown protein, which is similar to the hypothetical protein BN7_5177 of Wickerhamomyces ciferrii. ORF2 encodes a putative RNA-dependent RNA polymerase (RdRp), which is most closely related to Bryopsis mitochondria-associated dsRNA (BDRM) and is likely expressed by a +1 ribosomal frameshift within the sequence CCC_UUU_CGA. The phylogenetic analysis of the RdRp of UvNV-1 showed that UvNV-1 represents a new virus taxon of mycoviruses with a partitivirus-like lineage that is classified into the family of picorna-like viruses. Based on northern hybridization, UvNV-1 was found to be common to U. virens from different geographic locations in China. The biological comparison of virus-free and infected fungal strains revealed that UvNV-1 is likely to be cryptic to its host.}, }
@article {pmid24995987, year = {2014}, author = {Li, Y and Calvo, SE and Gutman, R and Liu, JS and Mootha, VK}, title = {Expansion of biological pathways based on evolutionary inference.}, journal = {Cell}, volume = {158}, number = {1}, pages = {213-225}, pmid = {24995987}, issn = {1097-4172}, support = {R01 GM077465/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; GM0077465/GM/NIGMS NIH HHS/United States ; }, mesh = {*Algorithms ; *Cluster Analysis ; Humans ; Mitochondria/metabolism ; *Phylogeny ; Plasmodium falciparum/genetics/metabolism ; Proteome/analysis ; Rhodophyta/genetics/metabolism ; Signal Transduction ; Yeasts/genetics/metabolism ; }, abstract = {The availability of diverse genomes makes it possible to predict gene function based on shared evolutionary history. This approach can be challenging, however, for pathways whose components do not exhibit a shared history but rather consist of distinct "evolutionary modules." We introduce a computational algorithm, clustering by inferred models of evolution (CLIME), which inputs a eukaryotic species tree, homology matrix, and pathway (gene set) of interest. CLIME partitions the gene set into disjoint evolutionary modules, simultaneously learning the number of modules and a tree-based evolutionary history that defines each module. CLIME then expands each module by scanning the genome for new components that likely arose under the inferred evolutionary model. Application of CLIME to ∼1,000 annotated human pathways and to the proteomes of yeast, red algae, and malaria reveals unanticipated evolutionary modularity and coevolving components. CLIME is freely available and should become increasingly powerful with the growing wealth of eukaryotic genomes.}, }
@article {pmid24985738, year = {2015}, author = {Chettoor, AM and Yi, G and Gomez, E and Hueros, G and Meeley, RB and Becraft, PW}, title = {A putative plant organelle RNA recognition protein gene is essential for maize kernel development.}, journal = {Journal of integrative plant biology}, volume = {57}, number = {3}, pages = {236-246}, doi = {10.1111/jipb.12234}, pmid = {24985738}, issn = {1744-7909}, mesh = {Alleles ; Biomarkers/metabolism ; Endosperm/cytology/*embryology/metabolism ; Gene Expression Regulation, Plant ; *Genes, Plant ; Mitochondria/metabolism ; Mutagenesis, Insertional/genetics ; Mutation/genetics ; Organelles/*genetics ; Phenotype ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Protein Transport ; RNA, Messenger/genetics/metabolism ; RNA, Plant/*genetics/metabolism ; Starch/deficiency/metabolism ; Nicotiana/genetics ; Zea mays/*embryology/*genetics ; }, abstract = {Basal endosperm transfer layer (BETL) cells are responsible for transferring apoplastic solutes from the maternal pedicel into the endosperm, supplying the grain with compounds required for embryo development and storage reserve accumulation. Here, we analyze the maize (Zea mays L.) empty pericarp6 (emp6) mutant, which causes early arrest in grain development. The Emp6+gene function is required independently in both the embryo and endosperm. The emp6 mutant causes a notable effect on the differentiation of BETL cells; the extensive cell wall ingrowths that distinguish BETL cells are diminished and BETL marker gene expression is compromised in mutant kernels. Transposon tagging identified the emp6 locus as encoding a putative plant organelle RNA recognition (PORR) protein, 1 of 15 PORR family members in maize. The emp6 transcript is widely detected in plant tissues with highest levels in embryos and developing kernels. EMP6-green fluorescent protein (GFP) fusion proteins transiently expressed in Nicotiana benthamiana leaves were targeted specifically to mitochondria. These results suggest that BETL cell differentiation might be particularly energy intensive, or alternatively, that mitochondria might confer a developmental function.}, }
@article {pmid24983244, year = {2014}, author = {Thaler, AD and Plouviez, S and Saleu, W and Alei, F and Jacobson, A and Boyle, EA and Schultz, TF and Carlsson, J and Van Dover, CL}, title = {Comparative population structure of two deep-sea hydrothermal-vent-associated decapods (Chorocaris sp. 2 and Munidopsis lauensis) from southwestern Pacific back-arc basins.}, journal = {PloS one}, volume = {9}, number = {7}, pages = {e101345}, pmid = {24983244}, issn = {1932-6203}, mesh = {Animals ; Anomura/*genetics ; Base Sequence ; Decapoda/*genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Genetics, Population ; *Hydrothermal Vents ; Microsatellite Repeats ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Snails/genetics ; }, abstract = {Studies of genetic connectivity and population structure in deep-sea chemosynthetic ecosystems often focus on endosymbiont-hosting species that are directly dependent on chemical energy extracted from vent effluent for survival. Relatively little attention has been paid to vent-associated species that are not exclusively dependent on chemosynthetic ecosystems. Here we assess connectivity and population structure of two vent-associated invertebrates--the shrimp Chorocaris sp. 2 and the squat lobster Munidopsis lauensis--that are common at deep-sea hydrothermal vents in the western Pacific. While Chorocaris sp. 2 has only been observed at hydrothermal vent sites, M. lauensis can be found throughout the deep sea but occurs in higher abundance around the periphery of active vents We sequenced mitochondrial COI genes and deployed nuclear microsatellite markers for both species at three sites in Manus Basin and either North Fiji Basin (Chorocaris sp. 2) or Lau Basin (Munidopsis lauensis). We assessed genetic differentiation across a range of spatial scales, from approximately 2.5 km to more than 3000 km. Population structure for Chorocaris sp. 2 was comparable to that of the vent-associated snail Ifremeria nautilei, with a single seemingly well-mixed population within Manus Basin that is genetically differentiated from conspecifics in North Fiji Basin. Population structure for Munidopsis lauensis was more complex, with two genetically differentiated populations in Manus Basin and a third well-differentiated population in Lau Basin. The unexpectedly high level of genetic differentiation between M. lauensis populations in Manus Basin deserves further study since it has implications for conservation and management of diversity in deep-sea hydrothermal vent ecosystems.}, }
@article {pmid24982758, year = {2014}, author = {Epstein, T and Xu, L and Gillies, RJ and Gatenby, RA}, title = {Separation of metabolic supply and demand: aerobic glycolysis as a normal physiological response to fluctuating energetic demands in the membrane.}, journal = {Cancer &amp; metabolism}, volume = {2}, number = {}, pages = {7}, pmid = {24982758}, issn = {2049-3002}, support = {P30 CA076292/CA/NCI NIH HHS/United States ; }, abstract = {BACKGROUND: Cancer cells, and a variety of normal cells, exhibit aerobic glycolysis, high rates of glucose fermentation in the presence of normal oxygen concentrations, also known as the Warburg effect. This metabolism is considered abnormal because it violates the standard model of cellular energy production that assumes glucose metabolism is predominantly governed by oxygen concentrations and, therefore, fermentative glycolysis is an emergency back-up for periods of hypoxia. Though several hypotheses have been proposed for the origin of aerobic glycolysis, its biological basis in cancer and normal cells is still not well understood.<br><br>RESULTS: We examined changes in glucose metabolism following perturbations in membrane activity in different normal and tumor cell lines and found that inhibition or activation of pumps on the cell membrane led to reduction or increase in glycolysis, respectively, while oxidative phosphorylation remained unchanged. Computational simulations demonstrated that these findings are consistent with a new model of normal physiological cellular metabolism in which efficient mitochondrial oxidative phosphorylation supplies chronic energy demand primarily for macromolecule synthesis and glycolysis is necessary to supply rapid energy demands primarily to support membrane pumps. A specific model prediction was that the spatial distribution of ATP-producing enzymes in the glycolytic pathway must be primarily localized adjacent to the cell membrane, while mitochondria should be predominantly peri-nuclear. The predictions were confirmed experimentally.<br><br>CONCLUSIONS: Our results show that glycolytic metabolism serves a critical physiological function under normoxic conditions by responding to rapid energetic demand, mainly from membrane transport activities, even in the presence of oxygen. This supports a new model for glucose metabolism in which glycolysis and oxidative phosphorylation supply different types of energy demand. Cells use efficient but slow-responding aerobic metabolism to meet baseline, steady energy demand and glycolytic metabolism, which is inefficient but can rapidly increase adenosine triphosphate (ATP) production, to meet short-timescale energy demands, mainly from membrane transport activities. In this model, the origin of the Warburg effect in cancer cells and aerobic glycolysis in general represents a normal physiological function due to enhanced energy demand for membrane transporters activity required for cell division, growth, and migration.}, }
@article {pmid24974962, year = {2014}, author = {Walther, EL and Valkiūnas, G and González, AD and Matta, NE and Ricklefs, RE and Cornel, A and Sehgal, RN}, title = {Description, molecular characterization, and patterns of distribution of a widespread New World avian malaria parasite (Haemosporida: Plasmodiidae), Plasmodium (Novyella) homopolare sp. nov.}, journal = {Parasitology research}, volume = {113}, number = {9}, pages = {3319-3332}, pmid = {24974962}, issn = {1432-1955}, mesh = {Americas/epidemiology ; Animals ; Cytochromes b/genetics ; Malaria, Avian/epidemiology/*parasitology ; Mitochondria/genetics ; Parasitemia/parasitology ; Passeriformes/*parasitology ; Phylogeny ; Plasmodium/classification/*genetics/*isolation &amp; purification ; }, abstract = {Plasmodium (Novyella) homopolare, a newly described Plasmodium species, was found in a wide range of Passeriformes species in California, USA, and Colombia. This parasite infected more than 20% of the sampled bird community (N = 399) in California and was found in 3.6% of birds sampled (N = 493) in Colombia. Thus far, it has been confirmed in North and South America where it is present in numerous species of migratory and resident birds from six families. Based on 100% matches, or near-100% matches (i.e., ≤2-nucleotide difference), to DNA sequences previously deposited in GenBank, this parasite is likely also distributed in the Eastern USA, Central America, and the Caribbean. Here, we describe the blood stages of P. homopolare and its mtDNA cytochrome b sequence. P. homopolare belongs to the subgenus Novyella and can be readily distinguished from the majority of other Novyella species, primarily, by the strictly polar or subpolar position of meronts and advanced trophozoites in infected erythrocytes. We explore possible reasons why this widespread parasite has not been described in earlier studies. Natural malarial parasitemias are usually light and co-infections predominate, making the parasites difficult to detect and identify to species when relying exclusively on microscopic examination of blood films. The combined application of sequence data and digital microscopy techniques, such as those used in this study, provides identifying markers that will facilitate the diagnosis of this parasite in natural avian populations. We also address the evolutionary relationship of this parasite to other species of Plasmodium using phylogenetic reconstruction.}, }
@article {pmid24963773, year = {2016}, author = {Dray, L and Neuhof, M and Diamant, A and Huchon, D}, title = {The complete mitochondrial genome of the gilthead seabream Sparus aurata L. (Sparidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {1}, pages = {781-782}, doi = {10.3109/19401736.2014.928861}, pmid = {24963773}, issn = {2470-1408}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; Open Reading Frames/genetics ; Phylogeny ; Sea Bream/*genetics ; }, abstract = {The complete mitochondrial genome of the gilthead seabream Sparus aurata Linnaeus 1758, one of the world's most important mariculture species, was sequenced using next generation sequencing technology. The genome sequence is comprised of 16,652 bp exhibiting the canonical vertebrate mitochondria gene order. Regions of gene overlap, tRNA length, as well as start and stop codon were similar to those observed in other Sparidae. Phylogenetic reconstructions based on mitochondrial protein coding genes corroborate the view that Sparidae is paraphyletic and includes Centracanthidae.}, }
@article {pmid24963769, year = {2016}, author = {Wang, L and Xu, J and Li, H and Song, L and Yu, Y and Zhang, W and Liu, G and Feng, C}, title = {The complete mitochondrial genome of Paecilomyces hepiali (Ascomycota, Eurotiomycetes).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {916-917}, doi = {10.3109/19401736.2014.926484}, pmid = {24963769}, issn = {2470-1408}, mesh = {Base Sequence ; China ; Codon, Initiator/genetics ; Codon, Terminator/genetics ; DNA, Mitochondrial/*genetics ; Genome, Mitochondrial/*genetics ; Medicine, Chinese Traditional ; Mitochondria/*genetics ; Paecilomyces/*genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {Paecilomyces hepiali, belonging to the Eurotiales order Ascomycota, is an endoparasitic fungus that commonly exists in the natural Cordyceps sinensis anamorph stage. Here, we report the complete mitochondrial DNA sequences of P. hepiali for the first time. The genome is 24,245 bp in length, encoding 15 protein-coding genes (PCGs), 2 rRNA genes, 25 tRNA genes and 3 homing endonucleases. The overall AT composition is 73.37% and the average AT content of PCG, rRNA, tRNA and non-coding region are 74.21%, 66.07%, 62.83% and 75.96%, respectively. Phylogenetic analysis with eight Ascomycota species and thirteen Basidiomycota species revealed that P. hepiali is was more closely related to Cordyceps bassiana, Cordycep smilitaris and Cordyceps brongniartii. It is confirmed that P. hepiali is a derivative of Cordyceps sinensis. This study provided valuable information on the gene contents of the mitochondrial genome and would facilitate the study of function and evolution of P. hepiali.}, }
@article {pmid24947012, year = {2014}, author = {Takahashi, S and Teranishi, M and Izumi, M and Takahashi, M and Takahashi, F and Hidema, J}, title = {Transport of rice cyclobutane pyrimidine dimer photolyase into mitochondria relies on a targeting sequence located in its C-terminal internal region.}, journal = {The Plant journal : for cell and molecular biology}, volume = {79}, number = {6}, pages = {951-963}, doi = {10.1111/tpj.12598}, pmid = {24947012}, issn = {1365-313X}, mesh = {Amino Acid Sequence ; Chloroplasts/ultrastructure ; DNA Damage ; Deoxyribodipyrimidine Photo-Lyase/chemistry/genetics/*metabolism ; Gene Expression ; *Gene Expression Regulation, Plant ; Genes, Reporter ; Mitochondria/ultrastructure ; Molecular Sequence Data ; Nuclear Localization Signals ; Oryza/*enzymology/genetics/radiation effects/ultrastructure ; Phylogeny ; Plants, Genetically Modified ; Protein Transport ; Pyrimidine Dimers/metabolism ; Recombinant Fusion Proteins ; Sequence Alignment ; Sequence Deletion ; Ultraviolet Rays ; }, abstract = {The cyclobutane pyrimidine dimer (CPD), which represents a major type of DNA damage induced by ultraviolet-B (UVB) radiation, is a principal cause of UVB-induced growth inhibition in plants. CPD photolyase is the primary enzyme for repairing CPDs and is crucial for determining the sensitivity of Oryza sativa (rice) to UVB radiation. CPD photolyase is widely distributed among species ranging from eubacteria to eukaryotes, and is classified into class I or II based on its primary structure. We previously demonstrated that rice CPD photolyase (OsPHR), which belongs to class II and is encoded by a single-copy gene, is a unique nuclear/mitochondrial/chloroplast triple-targeting protein; however, the location and nature of the organellar targeting information contained within OsPHR are unknown. Here, the nuclear and mitochondrial targeting signal sequences of OsPHR were identified by systematic deletion analysis. The nuclear and mitochondrial targeting sequences are harbored within residues 487-489 and 391-401 in the C-terminal region of OsPHR (506 amino acid residues), respectively. The mitochondrial targeting signal represents a distinct topogenic sequence that differs structurally and functionally from classical N-terminal pre-sequences, and this region, in addition to its role in localization to the mitochondria, is essential for the proper functioning of the CPD photolyase. Furthermore, the mitochondrial targeting sequence, which is characteristic of class-II CPD photolyases, was acquired before the divergence of class-II CPD photolyases in eukaryotes. These results indicate that rice plants have evolved a CPD photolyase that functions in mitochondria to protect cells from the harmful effects of UVB radiation.}, }
@article {pmid24946232, year = {2015}, author = {Abd El-Moneim, D and Contreras, R and Silva-Navas, J and Gallego, FJ and Figueiras, AM and Benito, C}, title = {On the consequences of aluminium stress in rye: repression of two mitochondrial malate dehydrogenase mRNAs.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {17}, number = {1}, pages = {123-133}, doi = {10.1111/plb.12219}, pmid = {24946232}, issn = {1438-8677}, mesh = {Aluminum/*metabolism ; Base Sequence ; Chromosome Mapping ; Lipid Peroxidation ; Malate Dehydrogenase/*genetics ; Malates/metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Plant Leaves/enzymology/genetics/physiology ; Plant Proteins/genetics ; Plant Roots/enzymology/genetics/physiology ; RNA, Messenger/genetics ; RNA, Plant/genetics ; Secale/enzymology/genetics/*physiology ; Seedlings/enzymology/genetics/physiology ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Plants have developed several external and internal aluminium (Al) tolerance mechanisms. The external mechanism best characterised is the exudation of organic acids induced by Al. Rye (Secale cereale L.), one of the most Al-tolerant cereal crops, secretes both citrate and malate from its roots in response to Al. However, the role of malate dehydrogenase (MDH) genes in Al-induced stress has not been studied in rye. We have isolated the ScMDH1 and ScMDH2 genes, encoding two different mitochondrial MDH isozymes, in three Al-tolerant rye cultivars (Ailés, Imperial and Petkus) and one sensitive inbred rye line (Riodeva). These genes, which have seven exons and six introns, were located on the 1R (ScMDH1) and 3RL (ScMDH2) chromosomes. Exon 1 of ScMDH1 and exon 7 of ScMDH2 were the most variable among the different ryes. The hypothetical proteins encoded by these genes were classified as putative mitochondrial MDH isoforms. The phylogenetic relationships obtained using both cDNA and protein sequences indicated that the ScMDH1 and ScMDH2 proteins are orthologous to mitochondrial MDH1 and MDH2 proteins of different Poaceae species. The expression studies of the ScMDH1 and ScMDH2 genes indicate that it is more intense in roots than in leaves. Moreover, the amount of their corresponding mRNAs in roots from plants treated and not treated with Al was higher in the tolerant cultivar Petkus than in the sensitive inbred line Riodeva. In addition, ScMDH1 and ScMDH2 mRNA levels decreased in response to Al stress (repressive behaviour) in the roots of both the tolerant Petkus and the sensitive line Riodeva.}, }
@article {pmid24941043, year = {2014}, author = {Low, VL and Adler, PH and Takaoka, H and Ya'cob, Z and Lim, PE and Tan, TK and Lim, YA and Chen, CD and Norma-Rashid, Y and Sofian-Azirun, M}, title = {Mitochondrial DNA markers reveal high genetic diversity but low genetic differentiation in the black fly Simulium tani Takaoka &amp; Davies along an elevational gradient in Malaysia.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e100512}, pmid = {24941043}, issn = {1932-6203}, mesh = {Altitude ; Amino Acid Sequence ; Animals ; DNA, Mitochondrial/*genetics ; Ecosystem ; Electron Transport Complex IV/*genetics ; Gene Flow ; Genetic Markers ; Genetic Variation ; Genetics, Population ; Haplotypes ; Malaysia ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; Protein Subunits/*genetics ; Simuliidae/classification/*genetics ; }, abstract = {The population genetic structure of Simulium tani was inferred from mitochondria-encoded sequences of cytochrome c oxidase subunits I (COI) and II (COII) along an elevational gradient in Cameron Highlands, Malaysia. A statistical parsimony network of 71 individuals revealed 71 haplotypes in the COI gene and 43 haplotypes in the COII gene; the concatenated sequences of the COI and COII genes revealed 71 haplotypes. High levels of genetic diversity but low levels of genetic differentiation were observed among populations of S. tani at five elevations. The degree of genetic diversity, however, was not in accordance with an altitudinal gradient, and a Mantel test indicated that elevation did not have a limiting effect on gene flow. No ancestral haplotype of S. tani was found among the populations. Pupae with unique structural characters at the highest elevation showed a tendency to form their own haplotype cluster, as revealed by the COII gene. Tajima's D, Fu's Fs, and mismatch distribution tests revealed population expansion of S. tani in Cameron Highlands. A strong correlation was found between nucleotide diversity and the levels of dissolved oxygen in the streams where S. tani was collected.}, }
@article {pmid24939707, year = {2014}, author = {Huu, NT and Yoshida, H and Umegawachi, T and Miyata, S and Yamaguchi, M}, title = {Structural characterization and subcellular localization of Drosophila organic solute carrier partner 1.}, journal = {BMC biochemistry}, volume = {15}, number = {}, pages = {11}, pmid = {24939707}, issn = {1471-2091}, mesh = {Animals ; Cell Membrane/*metabolism ; Dimerization ; Drosophila/genetics/*metabolism ; Drosophila Proteins/genetics/isolation &amp; purification/*metabolism ; Humans ; Larva ; Membrane Transport Proteins/genetics/isolation &amp; purification/*metabolism ; Molecular Structure ; Phylogeny ; Protein Transport ; Recombinant Proteins/genetics/*metabolism ; Sequence Alignment ; Transcriptome ; }, abstract = {BACKGROUND: Organic solute carrier partner 1 (OSCP1) is known to facilitate the transport of various organic solutes into cells and reported to play a role in cell growth and cell differentiation. Moreover, OSCP1 is known as a tumor suppressor gene that is frequently down-expressed in nasopharyngeal carcinomas and acute myeloid leukemia. However, the underlying mechanisms of action remain unclear and the subcellular localization of OSCP1 has yet to be determined in detail.<br><br>RESULTS: Drosophila contains a single orthologue of OSCP1 (dOSCP1) that shares 58% homology with its human counterpart. To study the expression pattern and subcellular localization of dOSCP1, we prepared a specific antibody. Subcellular localization analyses of dOSCP1 with these revealed localization in the plasma membrane, endoplasmic reticulum, Golgi apparatus and mitochondria, but no detection in cytosol. dOSCP1 signals were also detected in the nucleus, although at weaker intensity than in plasma membranes and subcellular organelles. In addition, native polyacrylamide gel electrophoresis analysis with and without &#x3b2;-mercaptoethanol treatment revealed that recombinant dOSCP1 forms dimers and trimers in solution. The dimer form of dOSCP1 could also be detected by Western immunoblot analyses in third instar larval extracts.<br><br>CONCLUSIONS: The data revealed that dOSCP1 localizes not only in the plasma membrane but also in the nucleus, ER, Golgi apparatus and mitochondria. It is therefore conceivable that this protein may interact with various partners or form multimeric complexes with other proteins to play multiple roles in cells, providing clues to understanding the functions of dOSCP1 during Drosophila development.}, }
@article {pmid24937575, year = {2016}, author = {Hassanin, A and Veron, G}, title = {The complete mitochondrial genome of the boky-boky, Mungotictis decemlineata, the first representative of the Malagasy carnivores (Mammalia, Carnivora, Eupleridae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {908-909}, doi = {10.3109/19401736.2014.926480}, pmid = {24937575}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence ; Codon, Initiator/genetics ; Codon, Terminator/genetics ; DNA, Mitochondrial/*genetics ; Eupleridae/*genetics ; Genome Size ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*veterinary ; }, abstract = {The complete mitochondrial genome of the boky-boky, Mungotictis decemlineata, was sequenced using overlapping PCRs. The genome is 16,910 base pairs in length and contains the 37 genes found in a typical mammalian genome: 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The overall base composition on the L-strand is A: 32.1%, C: 27.8%, G: 14.5%, T: 25.6%. The control region of M. decemlineata includes both RS2 and RS3 tandem repeats.}, }
@article {pmid24937573, year = {2016}, author = {Hassanin, A and Veron, G}, title = {The complete mitochondrial genome of the Spotted Linsang, Prionodon pardicolor, the first representative from the family Prionodontidae (Mammalia, Carnivora).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {912-913}, doi = {10.3109/19401736.2014.926482}, pmid = {24937573}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence ; DNA, Mitochondrial/*genetics ; Genome Size ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*veterinary ; Viverridae/*genetics ; }, abstract = {The complete mitochondrial genome of the Spotted Linsang, Prionodon pardicolor, was sequenced using overlapping PCR products. The genome is 16,718 base pairs in length and contains the 37 genes found in a typical mammalian genome: 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The overall base composition on the L-strand is A: 32.4%, C: 25.0%, G: 13.9%, T: 28.7%. The control region of P. pardicolor includes both RS2 and RS3 tandem repeats. Phylogenetic analyses support a sister relationship with the Felidae.}, }
@article {pmid24937571, year = {2016}, author = {Hassanin, A}, title = {The complete mitochondrial genome of the Servaline Genet, Genetta servalina, the first representative from the family Viverridae (Mammalia, Carnivora).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {906-907}, doi = {10.3109/19401736.2014.926479}, pmid = {24937571}, issn = {2470-1408}, mesh = {Africa ; Animals ; Base Composition/genetics ; Base Sequence ; DNA, Mitochondrial/*genetics ; Genome Size ; Genome, Mitochondrial/*genetics ; Male ; Mitochondria/*genetics ; Molecular Sequence Data ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*veterinary ; Tandem Repeat Sequences/genetics ; Viverridae/*genetics ; }, abstract = {Here I report the complete mitochondrial genome of the Servaline Genet, Genetta servalina, as sequenced from overlapping PCR products. The genome is 16,938 base pairs in length and contains the 37 genes found in a typical mammalian genome: 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The control region of G. servalina includes both RS2 and RS3 tandem repeats. The overall base composition on the L-strand is A: 32.8%, C: 25.5%, G: 13.5%, and T: 28.2%.}, }
@article {pmid24937569, year = {2016}, author = {Hassanin, A}, title = {The complete mitochondrial genome of the African palm civet, Nandinia binotata, the only representative of the family Nandiniidae (Mammalia, Carnivora).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {904-905}, doi = {10.3109/19401736.2014.926478}, pmid = {24937569}, issn = {2470-1408}, mesh = {Africa ; Animals ; Base Composition/genetics ; Base Sequence ; DNA, Mitochondrial/*genetics ; Genome Size ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Nandiniidae/*genetics ; Polymerase Chain Reaction/veterinary ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*veterinary ; Tandem Repeat Sequences/genetics ; }, abstract = {Here I report the complete mitochondrial genome of the African palm civet, (Nandinia binotata) as sequenced from overlapping PCR products. The genome is 17,103 bp in length and contains the 37 genes found in a typical mammalian genome: 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The control region of N. binotata includes both RS2 and RS3 tandem repeats. The overall base composition on the L-strand is A: 33.6%, C: 27.3%, G: 13.0%, and T: 26.1%.}, }
@article {pmid24931671, year = {2014}, author = {Siwar, BG and Myriam, G and Afif, BM and Emna, MR and Nozha, C and Afifa, S and Faiza, F and Leila, AK}, title = {Two novel mutations in COII and tRNA(His) mitochondrial genes in asthenozoospermic infertiles men.}, journal = {Biochemical and biophysical research communications}, volume = {450}, number = {1}, pages = {610-615}, doi = {10.1016/j.bbrc.2014.06.020}, pmid = {24931671}, issn = {1090-2104}, mesh = {Adult ; Asthenozoospermia/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Predisposition to Disease/*genetics ; Humans ; Male ; Middle Aged ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Mutation/*genetics ; Polymorphism, Single Nucleotide/genetics ; RNA, Transfer, His/*genetics ; Young Adult ; }, abstract = {In this study we performed a systematic sequence analysis of 7 mitochondrial genes (cytochrome oxidase I, cytochrome oxidase II, cytochrome oxidase III, adenosine triphosphate synthase6, ATP synthase8, cytochrome b and tRNA(His)) in 64 infertile men suffering from asthenospermia (n=31) in comparison to normospermic infertile men (n=33) from Tunisian population. A total of 92 nucleotide substitutions in sperm mitochondrial DNA were found; 88 of them were previously identified and reported in the human mitochondrial DNA database (www.mitomap.org) and 4 were novel. We also detected in 4 asthenospermic patients a double novels mutations, the first was found in COXII gene (m.8021 G/A) that was absent in normospermic infertile men. This mutation substituting the Isoleucine at position 146 to Valine in a conserved amino acid in the transmembrane functional domain of the protein. And the second was detected in the tRNA(His) gene (m.12187C>A) this mutation was found in homoplasmic state and was absent in normospermic patients. It was conserved throughout evolution and affects a wobble adenine in the T-loop region at the 54 codon of mitochondrial tRNA(His) .}, }
@article {pmid24927653, year = {2014}, author = {Polashock, J and Zelzion, E and Fajardo, D and Zalapa, J and Georgi, L and Bhattacharya, D and Vorsa, N}, title = {The American cranberry: first insights into the whole genome of a species adapted to bog habitat.}, journal = {BMC plant biology}, volume = {14}, number = {}, pages = {165}, pmid = {24927653}, issn = {1471-2229}, mesh = {Adaptation, Physiological/*genetics ; DNA Transposable Elements/genetics ; Disease Resistance/genetics ; Genetic Markers/genetics ; *Genome, Plant ; Inbreeding ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Phylogeny ; Plant Diseases/genetics ; Polymorphism, Single Nucleotide/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; Transcriptome/genetics ; Vaccinium macrocarpon/*genetics ; *Wetlands ; }, abstract = {BACKGROUND: The American cranberry (Vaccinium macrocarpon Ait.) is one of only three widely-cultivated fruit crops native to North America- the other two are blueberry (Vaccinium spp.) and native grape (Vitis spp.). In terms of taxonomy, cranberries are in the core Ericales, an order for which genome sequence data are currently lacking. In addition, cranberries produce a host of important polyphenolic secondary compounds, some of which are beneficial to human health. Whereas next-generation sequencing technology is allowing the advancement of whole-genome sequencing, one major obstacle to the successful assembly from short-read sequence data of complex diploid (and higher ploidy) organisms is heterozygosity. Cranberry has the advantage of being diploid (2n = 2x = 24) and self-fertile. To minimize the issue of heterozygosity, we sequenced the genome of a fifth-generation inbred genotype (F ≥ 0.97) derived from five generations of selfing originating from the cultivar Ben Lear.<br><br>RESULTS: The genome size of V. macrocarpon has been estimated to be about 470 Mb. Genomic sequences were assembled into 229,745 scaffolds representing 420 Mbp (N50&#x2009;=&#x2009;4,237 bp) with 20X average coverage. The number of predicted genes was 36,364 and represents 17.7% of the assembled genome. Of the predicted genes, 30,090 were assigned to candidate genes based on homology. Genes supported by transcriptome data totaled 13,170 (36%).<br><br>CONCLUSIONS: Shotgun sequencing of the cranberry genome, with an average sequencing coverage of 20X, allowed efficient assembly and gene calling. The candidate genes identified represent a useful collection to further study important biochemical pathways and cellular processes and to use for marker development for breeding and the study of horticultural characteristics, such as disease resistance.}, }
@article {pmid24924127, year = {2014}, author = {Hill, JM and De Stefani, D and Jones, AW and Ruiz, A and Rizzuto, R and Szabadkai, G}, title = {Measuring baseline Ca(2+) levels in subcellular compartments using genetically engineered fluorescent indicators.}, journal = {Methods in enzymology}, volume = {543}, number = {}, pages = {47-72}, doi = {10.1016/B978-0-12-801329-8.00003-9}, pmid = {24924127}, issn = {1557-7988}, mesh = {Calcium/*metabolism ; Cell Compartmentation ; Fluorescent Dyes/*metabolism ; Genetic Engineering ; Molecular Probes ; Subcellular Fractions/*metabolism ; }, abstract = {Intracellular Ca(2+) signaling is involved in a series of physiological and pathological processes. In particular, an intimate crosstalk between bioenergetic metabolism and Ca(2+) homeostasis has been shown to determine cell fate in resting conditions as well as in response to stress. The endoplasmic reticulum and mitochondria represent key hubs of cellular metabolism and Ca(2+) signaling. However, it has been challenging to specifically detect highly localized Ca(2+) fluxes such as those bridging these two organelles. To circumvent this issue, various recombinant Ca(2+) indicators that can be targeted to specific subcellular compartments have been developed over the past two decades. While the use of these probes for measuring agonist-induced Ca(2+) signals in various organelles has been extensively described, the assessment of basal Ca(2+) concentrations within specific organelles is often disregarded, in spite of the fact that this parameter is vital for several metabolic functions, including the enzymatic activity of mitochondrial dehydrogenases of the Krebs cycle and protein folding in the endoplasmic reticulum. Here, we provide an overview on genetically engineered, organelle-targeted fluorescent Ca(2+) probes and outline their evolution. Moreover, we describe recently developed protocols to quantify baseline Ca(2+) concentrations in specific subcellular compartments. Among several applications, this method is suitable for assessing how changes in basal Ca(2+) levels affect the metabolic profile of cancer cells.}, }
@article {pmid24923534, year = {2014}, author = {Li, XJ and Zhang, YF and Hou, M and Sun, F and Shen, Y and Xiu, ZH and Wang, X and Chen, ZL and Sun, SS and Small, I and Tan, BC}, title = {Small kernel 1 encodes a pentatricopeptide repeat protein required for mitochondrial nad7 transcript editing and seed development in maize (Zea mays) and rice (Oryza sativa).}, journal = {The Plant journal : for cell and molecular biology}, volume = {79}, number = {5}, pages = {797-809}, doi = {10.1111/tpj.12584}, pmid = {24923534}, issn = {1365-313X}, mesh = {Amino Acid Sequence ; Biological Evolution ; Cell Respiration ; DNA, Plant/chemistry/genetics ; Endosperm/genetics/growth &amp; development/ultrastructure ; *Gene Expression Regulation, Plant ; Mitochondria/genetics/ultrastructure ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; Mutagenesis, Insertional ; Oryza/*genetics/growth &amp; development/ultrastructure ; Phenotype ; Plant Proteins/*genetics/metabolism ; Plants, Genetically Modified ; *RNA Editing ; RNA, Plant/genetics ; Seedlings/genetics/growth &amp; development/ultrastructure ; Seeds/genetics/growth &amp; development/ultrastructure ; Sequence Alignment ; Sequence Analysis, DNA ; Zea mays/*genetics/growth &amp; development/ultrastructure ; }, abstract = {RNA editing modifies cytidines (C) to uridines (U) at specific sites in the transcripts of mitochondria and plastids, altering the amino acid specified by the DNA sequence. Here we report the identification of a critical editing factor of mitochondrial nad7 transcript via molecular characterization of a small kernel 1 (smk1) mutant in Zea mays (maize). Mutations in Smk1 arrest both the embryo and endosperm development. Cloning of Smk1 indicates that it encodes an E-subclass pentatricopeptide repeat (PPR) protein that is targeted to mitochondria. Loss of SMK1 function abolishes the C → U editing at the nad7-836 site, leading to the retention of a proline codon that is edited to encode leucine in the wild type. The smk1 mutant showed dramatically reduced complex-I assembly and NADH dehydrogenase activity, and abnormal biogenesis of the mitochondria. Analysis of the ortholog in Oryza sativa (rice) reveals that rice SMK1 has a conserved function in C → U editing of the mitochondrial nad7-836 site. T-DNA knock-out mutants showed abnormal embryo and endosperm development, resulting in embryo or seedling lethality. The leucine at NAD7-279 is highly conserved from bacteria to flowering plants, and analysis of genome sequences from many plants revealed a molecular coevolution between the requirement for C → U editing at this site and the existence of an SMK1 homolog. These results demonstrate that Smk1 encodes a PPR-E protein that is required for nad7-836 editing, and this editing is critical to NAD7 function in complex-I assembly in mitochondria, and hence to embryo and endosperm development in maize and rice.}, }
@article {pmid24918926, year = {2014}, author = {Yang, Y and Xu, S and Xu, J and Guo, Y and Yang, G}, title = {Adaptive evolution of mitochondrial energy metabolism genes associated with increased energy demand in flying insects.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e99120}, pmid = {24918926}, issn = {1932-6203}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; DNA, Mitochondrial/genetics ; *Energy Metabolism ; *Evolution, Molecular ; *Flight, Animal ; Insecta/*genetics/physiology ; Mitochondria/*metabolism ; }, abstract = {Insects are unique among invertebrates for their ability to fly, which raises intriguing questions about how energy metabolism in insects evolved and changed along with flight. Although physiological studies indicated that energy consumption differs between flying and non-flying insects, the evolution of molecular energy metabolism mechanisms in insects remains largely unexplored. Considering that about 95% of adenosine triphosphate (ATP) is supplied by mitochondria via oxidative phosphorylation, we examined 13 mitochondrial protein-encoding genes to test whether adaptive evolution of energy metabolism-related genes occurred in insects. The analyses demonstrated that mitochondrial DNA protein-encoding genes are subject to positive selection from the last common ancestor of Pterygota, which evolved primitive flight ability. Positive selection was also found in insects with flight ability, whereas no significant sign of selection was found in flightless insects where the wings had degenerated. In addition, significant positive selection was also identified in the last common ancestor of Neoptera, which changed its flight mode from direct to indirect. Interestingly, detection of more positively selected genes in indirect flight rather than direct flight insects suggested a stronger selective pressure in insects having higher energy consumption. In conclusion, mitochondrial protein-encoding genes involved in energy metabolism were targets of adaptive evolution in response to increased energy demands that arose during the evolution of flight ability in insects.}, }
@article {pmid24918426, year = {2014}, author = {Buj, I and Sanda, R and Marčić, Z and Caleta, M and Mrakovčić, M}, title = {Combining morphology and genetics in resolving taxonomy--a systematic revision of spined loaches (Genus Cobitis; Cypriniformes, Actinopterygii) in the Adriatic watershed.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e99833}, pmid = {24918426}, issn = {1932-6203}, mesh = {Animals ; Bosnia and Herzegovina ; Cypriniformes/*anatomy &amp; histology/*genetics ; DNA, Mitochondrial/genetics ; Fishes/*anatomy &amp; histology/*genetics ; Mitochondria/genetics ; Phylogeny ; Pigmentation/genetics ; Spine/anatomy &amp; histology ; }, abstract = {Taxonomic investigation of spined loaches from Dalmatia and Herzegovina was conducted on specimens from 14 localities. The results of the detailed morphological investigations were combined with genetic data (based on one mitochondrial and two nuclear genes) in order to resolve the taxonomic status of each Cobitis population. Among the investigated features of external morphology, the appearance of spots on the caudal fin base turned out to have the greatest diagnostic value. Furthermore, the number of branched fin rays enabled the discrimination of several species. No morphometric character alone could ensure determination of any Cobitis species. Nevertheless, groups of populations that are more similar in their body shapes correspond to mitochondrial phylogenetic lineages. Based on molecular genetic markers, Dalmatian and Herzegovinian spined loaches form independent lineages inside the Adriatic phylogenetic group. Mitochondrial DNA phylogenetic reconstruction revealed six monophyletic lineages, corresponding to six species distributed in the investigated area. The population distributed in Mostarsko blato karstic field in Bosnia and Herzegovina is described as a new species based on a unique combination of morphological characters: a single triangular Canestrini scale; usually 51/2 branched anal fin rays, 61/2 branched dorsal fin rays, 14 branched caudal fin rays; no spots in the surface pigmentation layer on the caudal fin base; scales on the body very small.}, }
@article {pmid24916662, year = {2014}, author = {Schrider, DR and Kern, AD}, title = {Discovering functional DNA elements using population genomic information: a proof of concept using human mtDNA.}, journal = {Genome biology and evolution}, volume = {6}, number = {7}, pages = {1542-1548}, pmid = {24916662}, issn = {1759-6653}, support = {F32 GM105231/GM/NIGMS NIH HHS/United States ; F32 GM105231-01/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Mitochondrial/*genetics ; *Genetics, Population ; Genome, Human/genetics ; Genome, Mitochondrial/*genetics ; Humans ; *Models, Genetic ; Mutation ; Phylogeny ; Polymorphism, Genetic ; }, abstract = {Identifying the complete set of functional elements within the human genome would be a windfall for multiple areas of biological research including medicine, molecular biology, and evolution. Complete knowledge of function would aid in the prioritization of loci when searching for the genetic bases of disease or adaptive phenotypes. Because mutations that disrupt function are disfavored by natural selection, purifying selection leaves a detectable signature within functional elements; accordingly, this signal has been exploited for over a decade through the use of genomic comparisons of distantly related species. While this is so, the functional complement of the genome changes extensively across time and between lineages; therefore, evidence of the current action of purifying selection in humans is essential. Because the removal of deleterious mutations by natural selection also reduces within-species genetic diversity within functional loci, dense population genetic data have the potential to reveal genomic elements that are currently functional. Here, we assess the potential of this approach by examining an ultradeep sample of human mitochondrial genomes (n = 16,411). We show that the high density of polymorphism in this data set precisely delineates regions experiencing purifying selection. Furthermore, we show that the number of segregating alleles at a site is strongly correlated with its divergence across species after accounting for known mutational biases in human mitochondrial DNA (ρ = 0.51; P < 2.2 × 10(-16)). These two measures track one another at a remarkably fine scale across many loci-a correlation that is purely the result of natural selection. Our results demonstrate that genetic variation has the potential to reveal with surprising precision which regions in the genome are currently performing important functions and likely to have deleterious fitness effects when mutated. As more complete human genomes are sequenced, similar power to reveal purifying selection may be achievable in the human nuclear genome.}, }
@article {pmid24914336, year = {2014}, author = {Grattagliano, I and Calamita, G and Cocco, T and Wang, DQ and Portincasa, P}, title = {Pathogenic role of oxidative and nitrosative stress in primary biliary cirrhosis.}, journal = {World journal of gastroenterology}, volume = {20}, number = {19}, pages = {5746-5759}, pmid = {24914336}, issn = {2219-2840}, mesh = {Animals ; Bile Acids and Salts/chemistry ; Glutathione/chemistry ; Humans ; Inflammation ; Liver/pathology ; Liver Cirrhosis, Biliary/*metabolism/*pathology ; Mitochondria/pathology ; Nitric Oxide/chemistry ; Nitrogen/*chemistry ; Oxidation-Reduction ; *Oxidative Stress ; Sulfhydryl Compounds/chemistry ; Thioredoxins/chemistry ; }, abstract = {Primary biliary cirrhosis is a multifactor autoimmune disease characterized by hepatic and systemic manifestations, with immune system dysregulation and abnormalities in the hepatic metabolism of bile salts, lipids, and nutrients, as well as destruction of membrane lipids and mitochondrial dysfunction. Both oxidative and nitrosative stress are associated with ongoing manifestations of the disease. In particular, abnormalities in nitric oxide metabolism and thiol oxidation already occur at early stages, thus leading to the hypothesis that these biochemical events play a pathogenic role in primary biliary cirrhosis. Moreover, the association of these metabolic abnormalities with the progression of the disease may indicate some biochemical parameters as early diagnostic markers of disease evolution, and may open up the potential for pharmacological intervention to inhibit intra- and extra-cellular stress events for resuming hepatocellular functions. The following paragraphs summarize the current knowledge by outlining molecular mechanisms of the disease related to these stress events.}, }
@article {pmid24911874, year = {2014}, author = {Kitazoe, Y and Tanaka, M}, title = {Evolution of mitochondrial power in vertebrate metazoans.}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e98188}, pmid = {24911874}, issn = {1932-6203}, mesh = {Animals ; *Computational Biology ; *Energy Metabolism ; *Evolution, Molecular ; Humans ; Hydrophobic and Hydrophilic Interactions ; Mitochondria/*metabolism ; Mitochondrial Proteins/chemistry/metabolism ; Protein Stability ; Protein Structure, Secondary ; *Vertebrates ; }, abstract = {BACKGROUND: Basal metabolic rate (BMR) has a very strong body-mass (M) dependence in an individual animal group, and BMR per unit mass (msBMR) converges on a markedly narrow range even across major taxonomic groups. However, it is here a basic question in metazoan biology how much BMR per unit mitochondrion (mtBMR) changes, and then whether mtBMR can be related to the original molecular mechanism of action of mt-encoded membrane proteins (MMPs) playing a central role in cellular energy production.<br><br>Analyzing variations of amino-acid compositions of MMPs across 13 metazoan animal groups, incorporating 2022 sequences, we found a strong inverse correlation between Ser/Thr composition (STC) and hydrophobicity (HYD). A majority of animal groups showed an evolutionary pathway of a gradual increase in HYD and decrease in STC, whereas only the deuterostome lineage revealed a rapid decrease in HYD and increase in STC. The strongest correlations appeared in 5 large subunits (ND4, ND5, ND2, CO1, and CO3) undergoing dynamic conformational changes for the proton-pumping function. The pathway of the majority groups is well understood as reflecting natural selection to reduce mtBMR, since simply raising HYD in MMPs (surrounded by the lipid bilayer) weakens their mobility and strengthens their stability. On the other hand, the marked decrease in HYD of the deuterostome elevates mtBMR, but is accompanied with their instability heightening a turnover rate of mitochondria and then cells. Interestingly, cooperative networks of interhelical hydrogen-bonds between motifs involving Ser and Thr residues can enhance MMP stability.<br><br>CONCLUSION/SIGNIFICANCE: This stability enhancement lowers turnover rates of mitochondria/cells and may prolong even longevity, and was indeed founded by strong positive correlations of STC with both mtBMR and longevity. The lowest HYD and highest STC in Aves and Mammals are congruent with their very high mtBMR and long longevity.}, }
@article {pmid24911382, year = {2014}, author = {Sahyoun, AH and Bernt, M and Stadler, PF and Tout, K}, title = {GC skew and mitochondrial origins of replication.}, journal = {Mitochondrion}, volume = {17}, number = {}, pages = {56-66}, doi = {10.1016/j.mito.2014.05.009}, pmid = {24911382}, issn = {1872-8278}, mesh = {Animals ; Base Composition ; Computational Biology/methods ; *DNA Replication ; DNA, Mitochondrial/*chemistry/*genetics ; Humans ; *Replication Origin ; Vertebrates ; }, abstract = {The comprehensive understanding of mitochondrial genome evolution requires a detailed mechanistic picture of mitogenomic replication. Despite many previous efforts it has remained a non-trivial problem to determine the origins of replication and trace their fate across rearrangements of the gene order even in the small genomes of animal mitochondria. We elaborate here on the observation that the GC skew is correlated with the distance from the replication origins. This effect has been explained as a consequence of the standard model of mitochondrial DNA replication, i.e. the strand displacement model. According to this model chemical damage accumulates proportional to the duration that DNA is exposed in single-stranded form during replication (Dssh) which depends on the relative position with respect to the replication origins. Based on this model we developed a computational method to infer the positions of both the heavy strand and the light strand origin from nucleotide skew data. In a comprehensive survey of deuterostome mitochondria we infer conserved replication origins for the vast majority of vertebrates and cephalochordates. Deviations from the consensus picture are presumably associated with genome rearrangements.}, }
@article {pmid24907441, year = {2014}, author = {Grewe, F and Edger, PP and Keren, I and Sultan, L and Pires, JC and Ostersetzer-Biran, O and Mower, JP}, title = {Comparative analysis of 11 Brassicales mitochondrial genomes and the mitochondrial transcriptome of Brassica oleracea.}, journal = {Mitochondrion}, volume = {19 Pt B}, number = {}, pages = {135-143}, doi = {10.1016/j.mito.2014.05.008}, pmid = {24907441}, issn = {1872-8278}, mesh = {Brassicaceae/*genetics ; DNA, Mitochondrial/chemistry/genetics ; Evolution, Molecular ; *Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; *Transcriptome ; }, abstract = {To elucidate the evolution of mitochondrial genomic diversity within a single order of angiosperms, we sequenced seven Brassicales genomes and the transcriptome of Brassica oleracea. In the common ancestor of Brassicaceae, several genes of known function were lost and the ccmFN gene was split into two independent genes, which also coincides with a trend of genome reduction towards the smallest sequenced angiosperm genomes of Brassica. For most ORFs of unknown function, the lack of conservation throughout Brassicales and the generally low expression and absence of RNA editing in B. oleracea argue against functionality. However, two chimeric ORFs were expressed and edited in B. oleracea, suggesting a potential role in cytoplasmic male sterility in certain nuclear backgrounds. These results demonstrate how frequent shifts in size, structure, and content of plant mitochondrial genomes can occur over short evolutionary time scales.}, }
@article {pmid24905695, year = {2014}, author = {Won, EJ and Ra, K and Kim, KT and Lee, JS and Lee, YM}, title = {Three novel superoxide dismutase genes identified in the marine polychaete Perinereis nuntia and their differential responses to single and combined metal exposures.}, journal = {Ecotoxicology and environmental safety}, volume = {107}, number = {}, pages = {36-45}, doi = {10.1016/j.ecoenv.2014.03.026}, pmid = {24905695}, issn = {1090-2414}, mesh = {Amino Acid Sequence ; Animals ; Antioxidants/metabolism ; Base Sequence ; Biomarkers/metabolism ; Ecosystem ; *Environmental Monitoring ; *Heavy Metal Poisoning ; Metals/metabolism ; Metals, Heavy/analysis/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; Poisoning/*metabolism ; Polychaeta/enzymology/*genetics ; RNA, Messenger/metabolism ; Superoxide Dismutase/*genetics/metabolism ; Water Pollution, Chemical/*analysis ; }, abstract = {To identify superoxide dismutase (SOD) genes and evaluate their usefulness as potential markers for monitoring metal toxicity in aquatic environment, we cloned, sequenced, and characterized 3 SOD genes (Cu/Zn-SOD1, Cu/Zn-SOD2, and Mn-SOD) from the marine polychaete Perinereis nuntia. The accumulated metal contents and expressions of 3 SOD genes were compared after exposure to single and combinations of heavy metals, As, Ni, and Pb. The deduced amino acid sequences of the 3 SODs had evolutionary conserved domains, such as metal binding sites, and signature sequences. The phylogenetic analysis revealed that Cu/Zn-SOD1, Cu/Zn-SOD2, and Mn-SOD were clustered with extracellular Cu/Zn-SOD, intracellular Cu/Zn-SOD and mitochondrial Mn-SOD, respectively, of other species. The accumulated contents of Ni and Pb increased significantly in a time - dependent manner after exposure to both single and combination of the metals. However, the concentration of As did not change significantly in the exposure test. The quantitative real-time polymerase chain reaction (PCR) array showed that the 3 SOD genes had differential expression patterns depending on the exposure condition. The expression of all SODs mRNAs was significantly elevated in response to Pb alone and in combination with As. The mRNA level of Cu/Zn-SOD1 was the highest after exposure to Pb alone, while that of Mn-SOD was remarkably enhanced after exposure to a combination of As and Pb. Exposure to Ni alone rapidly elevated the expression of Cu/Zn-SOD1 and Mn-SOD mRNA, which then gradually decreased. Exposure to As had no significant effect on the modulation of any of the SOD genes of P. nuntia. These results suggest that all SOD genes might play important roles in cellular protection as antioxidant enzymes against heavy metal toxicity via different modes of action in P. nuntia and might have the potential to act as indicators in an environment containing a mixture of metals.}, }
@article {pmid24904012, year = {2014}, author = {Christensen, AC}, title = {Genes and junk in plant mitochondria-repair mechanisms and selection.}, journal = {Genome biology and evolution}, volume = {6}, number = {6}, pages = {1448-1453}, pmid = {24904012}, issn = {1759-6653}, mesh = {*DNA Repair ; DNA, Plant/*genetics ; Fabaceae/*genetics ; *Genome, Mitochondrial ; Mutation Rate ; Phylogeny ; Selection, Genetic ; }, abstract = {Plant mitochondrial genomes have very low mutation rates. In contrast, they also rearrange and expand frequently. This is easily understood if DNA repair in genes is accomplished by accurate mechanisms, whereas less accurate mechanisms including nonhomologous end joining or break-induced replication are used in nongenes. An important question is how different mechanisms of repair predominate in coding and noncoding DNA, although one possible mechanism is transcription-coupled repair (TCR). This work tests the predictions of TCR and finds no support for it. Examination of the mutation spectra and rates in genes and junk reveals what DNA repair mechanisms are available to plant mitochondria, and what selective forces act on the repair products. A model is proposed that mismatches and other DNA damages are repaired by converting them into double-strand breaks (DSBs). These can then be repaired by any of the DSB repair mechanisms, both accurate and inaccurate. Natural selection will eliminate coding regions repaired by inaccurate mechanisms, accounting for the low mutation rates in genes, whereas mutations, rearrangements, and expansions generated by inaccurate repair in noncoding regions will persist. Support for this model includes the structure of the mitochondrial mutS homolog in plants, which is fused to a double-strand endonuclease. The model proposes that plant mitochondria do not distinguish a damaged or mismatched DNA strand from the undamaged strand, they simply cut both strands and perform homology-based DSB repair. This plant-specific strategy for protecting future generations from mitochondrial DNA damage has the side effect of genome expansions and rearrangements.}, }
@article {pmid24903145, year = {2014}, author = {Kutschera, VE and Bidon, T and Hailer, F and Rodi, JL and Fain, SR and Janke, A}, title = {Bears in a forest of gene trees: phylogenetic inference is complicated by incomplete lineage sorting and gene flow.}, journal = {Molecular biology and evolution}, volume = {31}, number = {8}, pages = {2004-2017}, pmid = {24903145}, issn = {1537-1719}, mesh = {Animals ; Cell Nucleus/genetics ; Evolution, Molecular ; *Gene Flow ; Genetic Speciation ; Introns ; Male ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA/*methods ; Ursidae/classification/*genetics ; Y Chromosome/*genetics ; }, abstract = {Ursine bears are a mammalian subfamily that comprises six morphologically and ecologically distinct extant species. Previous phylogenetic analyses of concatenated nuclear genes could not resolve all relationships among bears, and appeared to conflict with the mitochondrial phylogeny. Evolutionary processes such as incomplete lineage sorting and introgression can cause gene tree discordance and complicate phylogenetic inferences, but are not accounted for in phylogenetic analyses of concatenated data. We generated a high-resolution data set of autosomal introns from several individuals per species and of Y-chromosomal markers. Incorporating intraspecific variability in coalescence-based phylogenetic and gene flow estimation approaches, we traced the genealogical history of individual alleles. Considerable heterogeneity among nuclear loci and discordance between nuclear and mitochondrial phylogenies were found. A species tree with divergence time estimates indicated that ursine bears diversified within less than 2 My. Consistent with a complex branching order within a clade of Asian bear species, we identified unidirectional gene flow from Asian black into sloth bears. Moreover, gene flow detected from brown into American black bears can explain the conflicting placement of the American black bear in mitochondrial and nuclear phylogenies. These results highlight that both incomplete lineage sorting and introgression are prominent evolutionary forces even on time scales up to several million years. Complex evolutionary patterns are not adequately captured by strictly bifurcating models, and can only be fully understood when analyzing multiple independently inherited loci in a coalescence framework. Phylogenetic incongruence among gene trees hence needs to be recognized as a biologically meaningful signal.}, }
@article {pmid24898246, year = {2014}, author = {Lee, SC and Lin, CC and Wang, CH and Wu, PL and Huang, HW and Chang, CI and Wu, WG}, title = {Endocytotic routes of cobra cardiotoxins depend on spatial distribution of positively charged and hydrophobic domains to target distinct types of sulfated glycoconjugates on cell surface.}, journal = {The Journal of biological chemistry}, volume = {289}, number = {29}, pages = {20170-20181}, pmid = {24898246}, issn = {1083-351X}, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; CHO Cells ; Cell Line ; Cell Membrane/metabolism ; Cobra Cardiotoxin Proteins/*chemistry/genetics/*pharmacokinetics ; Cricetinae ; Cricetulus ; Crystallography, X-Ray ; Elapidae/genetics/metabolism ; Endocytosis ; Evolution, Molecular ; Glycoconjugates/chemistry/metabolism ; Heparitin Sulfate/chemistry/metabolism ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Protein Interaction Domains and Motifs ; Rats ; Static Electricity ; Structural Homology, Protein ; }, abstract = {Cobra cardiotoxins (CTX) are a family of three-fingered basic polypeptides known to interact with diverse targets such as heparan sulfates, sulfatides, and integrins on cell surfaces. After CTX bind to the membrane surface, they are internalized to intracellular space and exert their cytotoxicity via an unknown mechanism. By the combined in vitro kinetic binding, three-dimensional x-ray structure determination, and cell biology studies on the naturally abundant CTX homologues from the Taiwanese cobra, we showed that slight variations on the spatial distribution of positively charged or hydrophobic domains among CTX A2, A3, and A4 could lead to significant changes in their endocytotic pathways and action mechanisms via distinct sulfated glycoconjugate-mediated processes. The intracellular locations of these structurally similar CTX after internalization are shown to vary between the mitochondria and lysosomes via either dynamin2-dependent or -independent processes with distinct membrane cholesterol sensitivity. Evidence is presented to suggest that the shifting between the sulfated glycoconjugates as distinct targets of CTX A2, A3, and A4 might play roles in the co-evolutionary arms race between venomous snake toxins to cope with different membrane repair mechanisms at the cellular levels. The sensitivity of endocytotic routes to the spatial distribution of positively charged or hydrophobic domains may provide an explanation for the diverse endocytosis pathways of other cell-penetrating basic polypeptides.}, }
@article {pmid24893877, year = {2016}, author = {Zhang, D and Wang, L and Guo, H and Ma, Z and Jiang, S}, title = {The complete mitochondrial genome of snubnose pompano Trachinotus blochii (Teleostei, Carangidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {1}, pages = {431-432}, doi = {10.3109/19401736.2014.898291}, pmid = {24893877}, issn = {2470-1408}, mesh = {Animals ; Conserved Sequence/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Perciformes/*genetics ; Phylogeny ; *Sequence Analysis, DNA ; TATA Box/genetics ; }, abstract = {The complete mitochondrial genome of Trachinotus blochii was determined using the polymerase chain reaction. The complete mitochondrial DNA sequence is 16,558 bp in length. It consists of 13 protein-coding genes, 22 transfer RNA genes, two rRNA genes and two non-coding regions. Overall base composition of its mitochondrial genome is estimated to be 29.21% for A, 15.74% for G, 26.49% for T, 28.56% for C, respectively, with a high A + T content (55.70%). The control region contains three conserved sequence blocks, a termination-associated sequence and a TATA box. The complete mitochondrial genome sequence of T. blochii can provide a basic data for the studies on population structure, molecular systematic, stock evaluation and conservation genetics. It is also helpful to develop the rational management strategies for T. blochii resource.}, }
@article {pmid24892910, year = {2014}, author = {Maguire, F and Richards, TA}, title = {Organelle evolution: a mosaic of 'mitochondrial' functions.}, journal = {Current biology : CB}, volume = {24}, number = {11}, pages = {R518-20}, doi = {10.1016/j.cub.2014.03.075}, pmid = {24892910}, issn = {1879-0445}, mesh = {Eukaryota/*genetics/*metabolism ; Organelles/*metabolism ; *Proteome ; Sulfur/*metabolism ; }, abstract = {An ancient endosymbiosis of an α-proteobacterium produced a diverse range of organelles including mitochondria. Reconstruction of the Pygsuia biforma proteome adds to the mosaic of functional systems present in mitochondrial-related organelles and demonstrates the role of horizontal gene transfer.}, }
@article {pmid24892429, year = {2014}, author = {Rodrigues, AS and Silva, SE and Marabuto, E and Silva, DN and Wilson, MR and Thompson, V and Yurtsever, S and Halkka, A and Borges, PA and Quartau, JA and Paulo, OS and Seabra, SG}, title = {New mitochondrial and nuclear evidences support recent demographic expansion and an atypical phylogeographic pattern in the spittlebug Philaenus spumarius (Hemiptera, Aphrophoridae).}, journal = {PloS one}, volume = {9}, number = {6}, pages = {e98375}, pmid = {24892429}, issn = {1932-6203}, mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; Demography ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Genetic Variation ; Haplotypes/genetics ; Hemiptera/*genetics ; Humans ; Likelihood Functions ; Mitochondria/*genetics ; Phylogeny ; *Phylogeography ; Population Growth ; Time Factors ; }, abstract = {Philaenus spumarius is a widespread insect species in the Holarctic region. Here, by focusing on the mtDNA gene COI but also using the COII and Cyt b genes and the nuclear gene EF-1α, we tried to explain how and when its current biogeographic pattern evolved by providing time estimates of the main demographic and evolutionary events and investigating its colonization patterns in and out of Eurasia. Evidence of recent divergence and expansion events at less than 0.5 Ma ago indicate that climate fluctuations in the Mid-Late Pleistocene were important in shaping the current phylogeographic pattern of the species. Data support a first split and differentiation of P. spumarius into two main mitochondrial lineages: the "western", in the Mediterranean region and the "eastern", in Anatolia/Caucasus. It also supports a following differentiation of the "western" lineage into two sub-lineages: the "western-Mediterranean", in Iberia and the "eastern-Mediterranean" in the Balkans. The recent pattern seems to result from postglacial range expansion from Iberia and Caucasus/Anatolia, thus not following one of the four common paradigms. Unexpected patterns of recent gene-flow events between Mediterranean peninsulas, a close relationship between Iberia and North Africa, as well as high levels of genetic diversity being maintained in northern Europe were found. The mitochondrial pattern does not exactly match to the nuclear pattern suggesting that the current biogeographic pattern of P. spumarius may be the result of both secondary admixture and incomplete lineage sorting. The hypothesis of recent colonization of North America from both western and northern Europe is corroborated by our data and probably resulted from accidental human translocations. A probable British origin for the populations of the Azores and New Zealand was revealed, however, for the Azores the distribution of populations in high altitude native forests is somewhat puzzling and may imply a natural colonization of the archipelago.}, }
@article {pmid24891093, year = {2014}, author = {Shi, Y and Zhao, Z and Hong, X and Chen, K and Zhu, X}, title = {Characterization and functional analysis of voltage-dependent anion channel 1 (VDAC1) from orange-spotted grouper (Epinephelus coioides).}, journal = {Journal of biochemical and molecular toxicology}, volume = {28}, number = {7}, pages = {292-301}, doi = {10.1002/jbt.21565}, pmid = {24891093}, issn = {1099-0461}, mesh = {Amino Acid Sequence ; Animals ; Apoptosis ; Cell Line ; China ; Fishes/*metabolism ; Gene Expression Regulation ; Molecular Sequence Data ; Phylogeny ; Subcellular Fractions/metabolism ; Transfection ; Voltage-Dependent Anion Channel 1/chemistry/genetics/*metabolism ; }, abstract = {The voltage-dependent anion channel (VDAC) is a highly conserved integral protein of mitochondria in different eukaryotic species. It forms a selective channel in the mitochondrial outer membrane that serves as the controlled pathway for small metabolites and ions. In this study, a VDAC gene, EcVDAC1, was isolated from orange-spotted grouper (Epinephelus coioides). The EcVDAC1 exhibits ubiquitous expression in various tissues of orange-spotted grouper and is upregulated in liver, gill, and spleen after stimulation with lipopolysaccharides (LPS). Subcellular localization analysis shows that the EcVDAC1 protein colocalized with the mitochondria. A caspase-3 assay demonstrates that overexpression of the EcVDAC1 induced apoptotic cell death in fathead minnow cells. The data presented in this study provide new information regarding the relationship between LPS and the EcVDAC1 gene, suggesting that the fish VDAC1 gene may play an important role in antibacterial immune response.}, }
@article {pmid24890091, year = {2014}, author = {Lee, WJ and Simpson, AG}, title = {Morphological and molecular characterisation of Notosolenus urceolatus Larsen and Patterson 1990, a member of an understudied deep-branching euglenid group (petalomonads).}, journal = {The Journal of eukaryotic microbiology}, volume = {61}, number = {5}, pages = {463-479}, doi = {10.1111/jeu.12126}, pmid = {24890091}, issn = {1550-7408}, mesh = {DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Euglenida/*classification/genetics/*growth &amp; development/isolation &amp; purification ; Genes, rRNA ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Petalomonads are particularly important for understanding the early evolution of euglenids, but are arguably the least studied major group within this taxon. We have established a culture of the biflagellate petalomonad Notosolenus urceolatus, and conducted electron microscopy observations and molecular phylogenetic analysis. Notosolenus urceolatus has eight pellicular strips bordered by grooves and underlain by close-set microtubules. There are ventral and dorsal Golgi bodies. Mitochondria apparently contain fibrous inclusions, as in Petalomonas cantuscygni. A previously undocumented type of large, globular extrusome is present instead of the tubular extrusomes characteristic of Euglenozoa. The feeding apparatus lacks rods and vanes, and is partly supported by an "MTR". The flagella have complex transition zones that are extremely elongated but unswollen. Only the emergent portion of the anterior flagellum has an organised paraxonemal rod, and also has very fine mastigonemes. The basal bodies are offset and lack connecting fibres. 18S rRNA gene phylogenies show that N. urceolatus is closely related to Petalomonas sphagnophila and P. cantuscygni, not Notosolenus ostium, confirming that current generic assignments based on the number of emergent flagella are phylogenetically unreliable, and making it difficult to infer whether features shared by N. urceolatus and P. cantuscygni (for example) are general for petalomonads.}, }
@article {pmid24889638, year = {2014}, author = {Kovács-Bogdán, E and Sancak, Y and Kamer, KJ and Plovanich, M and Jambhekar, A and Huber, RJ and Myre, MA and Blower, MD and Mootha, VK}, title = {Reconstitution of the mitochondrial calcium uniporter in yeast.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {24}, pages = {8985-8990}, pmid = {24889638}, issn = {1091-6490}, support = {R24 DK080261/DK/NIDDK NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 DK080261/DK/NIDDK NIH HHS/United States ; }, mesh = {Calcium/*chemistry/metabolism ; Calcium Channels/*chemistry ; Cell Line ; Dictyostelium ; Genetic Techniques ; HEK293 Cells ; Humans ; Intracellular Membranes/metabolism ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/metabolism ; Saccharomyces cerevisiae/*metabolism ; }, abstract = {The mitochondrial calcium uniporter is a highly selective calcium channel distributed broadly across eukaryotes but absent in the yeast Saccharomyces cerevisiae. The molecular components of the human uniporter holocomplex (uniplex) have been identified recently. The uniplex consists of three membrane-spanning subunits--mitochondrial calcium uniporter (MCU), its paralog MCUb, and essential MCU regulator (EMRE)--and two soluble regulatory components--MICU1 and its paralog MICU2. The minimal components sufficient for in vivo uniporter activity are unknown. Here we consider Dictyostelium discoideum (Dd), a member of the Amoebazoa outgroup of Metazoa and Fungi, and show that it has a highly simplified uniporter machinery. We show that D. discoideum mitochondria exhibit membrane potential-dependent calcium uptake compatible with uniporter activity, and also that expression of DdMCU complements the mitochondrial calcium uptake defect in human cells lacking MCU or EMRE. Moreover, expression of DdMCU in yeast alone is sufficient to reconstitute mitochondrial calcium uniporter activity. Having established yeast as an in vivo reconstitution system, we then reconstituted the human uniporter. We show that coexpression of MCU and EMRE is sufficient for uniporter activity, whereas expression of MCU alone is insufficient. Our work establishes yeast as a powerful in vivo reconstitution system for the uniporter. Using this system, we confirm that MCU is the pore-forming subunit, define the minimal genetic elements sufficient for metazoan and nonmetazoan uniporter activity, and provide valuable insight into the evolution of the uniporter machinery.}, }
@article {pmid24889636, year = {2014}, author = {De Haes, W and Frooninckx, L and Van Assche, R and Smolders, A and Depuydt, G and Billen, J and Braeckman, BP and Schoofs, L and Temmerman, L}, title = {Metformin promotes lifespan through mitohormesis via the peroxiredoxin PRDX-2.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {24}, pages = {E2501-9}, pmid = {24889636}, issn = {1091-6490}, support = {P40 OD010440/OD/NIH HHS/United States ; }, mesh = {Acyl-CoA Dehydrogenase/metabolism ; Amino Acids, Branched-Chain/chemistry ; Animals ; Caenorhabditis elegans/*drug effects/metabolism ; Caenorhabditis elegans Proteins/*physiology ; Gene Expression Regulation ; Green Fluorescent Proteins/chemistry ; Hormesis/*drug effects ; Hot Temperature ; Hydrogen Peroxide/chemistry ; Hypoglycemic Agents/*pharmacology ; Longevity/*drug effects ; Metformin/*pharmacology ; Mitochondria/enzymology ; Models, Animal ; Oxidative Stress ; Oxygen Consumption ; Peroxiredoxins/*physiology ; Protein Unfolding ; Proteomics ; Reactive Oxygen Species ; Rotenone/chemistry ; Signal Transduction ; Time Factors ; }, abstract = {The antiglycemic drug metformin, widely prescribed as first-line treatment of type II diabetes mellitus, has lifespan-extending properties. Precisely how this is achieved remains unclear. Via a quantitative proteomics approach using the model organism Caenorhabditis elegans, we gained molecular understanding of the physiological changes elicited by metformin exposure, including changes in branched-chain amino acid catabolism and cuticle maintenance. We show that metformin extends lifespan through the process of mitohormesis and propose a signaling cascade in which metformin-induced production of reactive oxygen species increases overall life expectancy. We further address an important issue in aging research, wherein so far, the key molecular link that translates the reactive oxygen species signal into a prolongevity cue remained elusive. We show that this beneficial signal of the mitohormetic pathway is propagated by the peroxiredoxin PRDX-2. Because of its evolutionary conservation, peroxiredoxin signaling might underlie a general principle of prolongevity signaling.}, }
@article {pmid24883254, year = {2014}, author = {Pochon, X and Putnam, HM and Gates, RD}, title = {Multi-gene analysis of Symbiodinium dinoflagellates: a perspective on rarity, symbiosis, and evolution.}, journal = {PeerJ}, volume = {2}, number = {}, pages = {e394}, pmid = {24883254}, issn = {2167-8359}, abstract = {Symbiodinium, a large group of dinoflagellates, live in symbiosis with marine protists, invertebrate metazoans, and free-living in the environment. Symbiodinium are functionally variable and play critical energetic roles in symbiosis. Our knowledge of Symbiodinium has been historically constrained by the limited number of molecular markers available to study evolution in the genus. Here we compare six functional genes, representing three cellular compartments, in the nine known Symbiodinium lineages. Despite striking similarities among the single gene phylogenies from distinct organelles, none were evolutionarily identical. A fully concatenated reconstruction, however, yielded a well-resolved topology identical to the current benchmark nr28S gene. Evolutionary rates differed among cellular compartments and clades, a pattern largely driven by higher rates of evolution in the chloroplast genes of Symbiodinium clades D2 and I. The rapid rates of evolution observed amongst these relatively uncommon Symbiodinium lineages in the functionally critical chloroplast may translate into potential innovation for the symbiosis. The multi-gene analysis highlights the potential power of assessing genome-wide evolutionary patterns using recent advances in sequencing technology and emphasizes the importance of integrating ecological data with more comprehensive sampling of free-living and symbiotic Symbiodinium in assessing the evolutionary adaptation of this enigmatic dinoflagellate.}, }
@article {pmid24881086, year = {2014}, author = {Mungpakdee, S and Shinzato, C and Takeuchi, T and Kawashima, T and Koyanagi, R and Hisata, K and Tanaka, M and Goto, H and Fujie, M and Lin, S and Satoh, N and Shoguchi, E}, title = {Massive gene transfer and extensive RNA editing of a symbiotic dinoflagellate plastid genome.}, journal = {Genome biology and evolution}, volume = {6}, number = {6}, pages = {1408-1422}, pmid = {24881086}, issn = {1759-6653}, mesh = {Amino Acid Sequence ; Base Sequence ; Biological Evolution ; Dinoflagellida/chemistry/*cytology/*genetics ; Genes, Protozoan ; Genome, Plastid ; Models, Molecular ; Molecular Sequence Data ; Plastids/*genetics ; Protein Conformation ; Protozoan Proteins/chemistry/genetics ; *RNA Editing ; RNA, Protozoan/*genetics ; }, abstract = {Genome sequencing of Symbiodinium minutum revealed that 95 of 109 plastid-associated genes have been transferred to the nuclear genome and subsequently expanded by gene duplication. Only 14 genes remain in plastids and occur as DNA minicircles. Each minicircle (1.8-3.3 kb) contains one gene and a conserved noncoding region containing putative promoters and RNA-binding sites. Nine types of RNA editing, including a novel G/U type, were discovered in minicircle transcripts but not in genes transferred to the nucleus. In contrast to DNA editing sites in dinoflagellate mitochondria, which tend to be highly conserved across all taxa, editing sites employed in DNA minicircles are highly variable from species to species. Editing is crucial for core photosystem protein function. It restores evolutionarily conserved amino acids and increases peptidyl hydropathy. It also increases protein plasticity necessary to initiate photosystem complex assembly.}, }
@article {pmid24880237, year = {2014}, author = {Foitová, I and Civáňová, K and Baruš, V and Nurcahyo, W}, title = {Phylogenetic relationships between pinworms (Nematoda: Enterobiinae) parasitising the critically endangered orang-utan, according to the characterisation of molecular genomic and mitochondrial markers.}, journal = {Parasitology research}, volume = {113}, number = {7}, pages = {2455-2466}, pmid = {24880237}, issn = {1432-1955}, mesh = {Amino Acid Sequence ; Animals ; DNA, Intergenic/genetics ; Electron Transport Complex IV/genetics ; Enterobiasis/parasitology/*veterinary ; Enterobius/*classification/genetics ; Genetic Markers ; Genetic Speciation ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; Pongo abelii/*parasitology ; Pongo pygmaeus/*parasitology ; }, abstract = {Pinworms (Nematoda: Enterobiinae) include 52 species parasitising primates throughout the world. In the present study, we performed the first ever molecular analysis to investigate the phylogenetic position of recently described pinworms parasitising the Sumatran orang-utan. The phylogenetic analysis of mitochondrial CO1 and chromosomal 18S rDNA and ITS1 regions could support the independent status of several Nematoda species. Our molecular data clearly suggest that Enterobius (Colobenterobius) buckleyi and Lemuricola (Protenterobius) pongoi together with Pongobius hugoti form separate clades among other studied species, which significantly supports the hypothesis of recently described new species parasitising the orang-utan (Pongo abelii and Pongo pygmaeus). The phylogenetic tree based on cytochrome oxidase 1 (CO1) gene variability showed possible close relationships between L. (Protenterobius) pongoi and P. hugoti; thus, we can assume that these species could have initially diverged in sympatry from a common ancestor.}, }
@article {pmid24873932, year = {2014}, author = {Edwards, LM and Sigurdsson, MI and Robbins, PA and Weale, ME and Cavalleri, GL and Montgomery, HE and Thiele, I}, title = {Genome-scale methods converge on key mitochondrial genes for the survival of human cardiomyocytes in hypoxia.}, journal = {Circulation. Cardiovascular genetics}, volume = {7}, number = {4}, pages = {407-415}, doi = {10.1161/CIRCGENETICS.113.000269}, pmid = {24873932}, issn = {1942-3268}, support = {MR/J006742/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adenosine Triphosphate/metabolism ; Genome, Human ; Heme/metabolism ; Humans ; *Hypoxia ; Metabolic Networks and Pathways ; Mitochondria/*genetics/metabolism ; Models, Biological ; Myocytes, Cardiac/*metabolism ; Phospholipids/biosynthesis ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; Proteomics ; Transcriptome ; }, abstract = {BACKGROUND: Any reduction in myocardial oxygen delivery relative to its demands can impair cardiac contractile performance. Understanding the mitochondrial metabolic response to hypoxia is key to understanding ischemia tolerance in the myocardium. We used a novel combination of 2 genome-scale methods to study key processes underlying human myocardial hypoxia tolerance. In particular, we hypothesized that computational modeling and evolution would identify similar genes as critical to human myocardial hypoxia tolerance.<br><br>METHODS AND RESULTS: We analyzed a reconstruction of the cardiac mitochondrial metabolic network using constraint-based methods, under conditions of simulated hypoxia. We used flux balance analysis, random sampling, and principal component analysis to explore feasible steady-state solutions. Hypoxia blunted maximal ATP (-17%) and heme (-75%) synthesis and shrank the feasible solution space. Tricarboxylic acid and urea cycle fluxes were also reduced in hypoxia, but phospholipid synthesis was increased. Using mathematical optimization methods, we identified reactions that would be critical to hypoxia tolerance in the human heart. We used data regarding single-nucleotide polymorphism frequency and distribution in the genomes of Tibetans (whose ancestors have resided in persistent high-altitude hypoxia for several millennia). Six reactions were identified by both methods as being critical to mitochondrial ATP production in hypoxia: phosphofructokinase, phosphoglucokinase, complex II, complex IV, aconitase, and fumarase.<br><br>CONCLUSIONS: Mathematical optimization and evolution converged on similar genes as critical to human myocardial hypoxia tolerance. Our approach is unique and completely novel and demonstrates that genome-scale modeling and genomics can be used in tandem to provide new insights into cardiovascular genetics.}, }
@article {pmid24867259, year = {2014}, author = {Lee, SY and Choi, HC and Choe, YJ and Shin, SJ and Lee, SH and Kim, HS}, title = {Nutlin-3 induces BCL2A1 expression by activating ELK1 through the mitochondrial p53-ROS-ERK1/2 pathway.}, journal = {International journal of oncology}, volume = {45}, number = {2}, pages = {675-682}, doi = {10.3892/ijo.2014.2463}, pmid = {24867259}, issn = {1791-2423}, mesh = {Apoptosis/*physiology ; Cell Line, Tumor ; Enzyme Activation/drug effects ; Flow Cytometry ; Humans ; Imidazoles/*pharmacology ; Immunoblotting ; MAP Kinase Signaling System/physiology ; Minor Histocompatibility Antigens ; Mitochondria/drug effects/metabolism ; Osteosarcoma/metabolism ; Piperazines/*pharmacology ; Proto-Oncogene Proteins c-bcl-2/*biosynthesis ; RNA, Small Interfering ; Reactive Oxygen Species/metabolism ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Signal Transduction/drug effects/*physiology ; Transfection ; Tumor Suppressor Protein p53/metabolism ; ets-Domain Protein Elk-1/*metabolism ; }, abstract = {Nutlin-3 which occupies the p53 binding pocket in HDM2, has been reported to activate apoptosis through both the transcriptional activity-dependent and -independent programs of p53. Transcription-independent apoptosis by nutlin-3 is triggered by p53 which is translocated to mitochondria. However, we previously demonstrated that the nutlin-3-induced mitochondrial translocation of p53 stimulates ERK1/2 activation, an anti-apoptosis signal, via mitochondrial ROS generation. We report on how nutlin-3-stimulated ERK1/2 activity inhibits p53-induced apoptosis. Among the anti-apoptotic BCL2 family proteins, BCL2A1 expression was increased by nutlin-3 at both the mRNA and protein levels, and this increase was prevented by the inhibition of ERK1/2. TEMPO, a ROS scavenger, and PFT-μ , a blocker of the mitochondrial translocation of p53, also inhibited BCL2A1 expression as well as ERK1/2 phosphorylation. In addition, nutlin-3 stimulated phosphorylation of ELK1, which was prevented by all compounds that inhibited nutlin-3-induced ERK1/2 such as U0126, PFT-μ and TEMPO. Moreover, an increase in BCL2A1 expression was weakened by the knockdown of ELK1. Finally, nutlin-3-induced apoptosis was found to be potentiated by the knockdown of BCL2A1, as demonstrated by an increase of in hypo-diploidic cells and Annexin V-positive cells. Parallel to the increase in apoptotic cells, the knockdown of BCL2A1 augmented the cleavage of poly(ADP-ribose) polymerase-1. It is noteworthy that the augmented levels of apoptosis induced by the knockdown of BCL2A1 were comparable to those of apoptosis induced by U0126. Collectively, these results suggest that nutlin-3-activated ERK1/2 may stimulate the transcription of BCL2A1 via the activation of ELK1, and BCL2A1 expression may contribute to the inhibitory effect of ERK1/2 on nutlin-3-induced apoptosis, thereby constituting a negative feedback loop of p53-induced apoptosis.}, }
@article {pmid24865916, year = {2016}, author = {Que, YF and Xu, DM and Li, WT and Yang, Z and Tang, HY and Shao, K}, title = {The complete mitochondrial genome of Schizothorax chongi (Fang, 1936) (Teleostei, Cyprinidae, Schizothoracinae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {879-881}, doi = {10.3109/19401736.2014.919486}, pmid = {24865916}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence ; Cyprinidae/*genetics ; DNA, Mitochondrial/*genetics ; Genome Size ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*veterinary ; Tibet ; }, abstract = {Schizothorax chongi is an endemic and important polyploidy fish in the upper stream of the Yangtze River. S. chongi represents a typical model species to study historical adaptation and evolution in the Tibetan Plateau. In this study, the complete mitochondrial DNA genome sequence of S. chongi was first determined by DNA sequencing based on the PCR fragments. The complete mitochondrial DNA (mtDNA) genome sequence of S. chongi is a circular molecule of 16,584 bp in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region (D-loop). The gene nucleotide composition of S. chongi is 29.6% A, 27.1% C, 17.9% G, and 25.4% T, with a high AT content (55.0%). The results could provide useful data for further studies on phylogenetics, conservation genetics and rational resource management for S. chongi.}, }
@article {pmid24865908, year = {2016}, author = {Huo, JH and Wei, QP and Wan, MC and Liu, LX and Hu, LF and Zhou, QY and Xiong, LG and Yang, Q and Wu, YP}, title = {Population phylogenomic analysis and origin of mitochondrial DNA in Chinese domestic pig.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {2}, pages = {892-895}, doi = {10.3109/19401736.2014.919492}, pmid = {24865908}, issn = {2470-1408}, mesh = {Animals ; Animals, Domestic/genetics ; Base Sequence ; China ; DNA, Mitochondrial/*genetics ; Genetic Variation/genetics ; Genome Size ; Genome, Mitochondrial/*genetics ; Haplotypes/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA/*veterinary ; Sus scrofa/classification/*genetics ; }, abstract = {The genetic diversity of eight domestic pigs was analyzed using a hypervariable fragment in the mitochondrial (mt) DNA control region; a portion of the hypervariable control region (515 bp) was sequenced from 153 samples. Haplotype diversity and nucleotide diversity in Yushan black pig populations were significantly higher than other populations (p < 0.01). A neighbor-joining tree was constructed from domestic pig mtDNA and five wild pigs. The results indicate that there are only small differences among individual pigs from different regions. Networks of the domestic pigs were constructed to better visualize the relationships between sequences. Each core haplotype was surrounded by a star-like pattern, consistent with recent population expansion.}, }
@article {pmid24865350, year = {2014}, author = {Robins, JH and Tintinger, V and Aplin, KP and Hingston, M and Matisoo-Smith, E and Penny, D and Lavery, SD}, title = {Phylogenetic species identification in Rattus highlights rapid radiation and morphological similarity of New Guinean species.}, journal = {PloS one}, volume = {9}, number = {5}, pages = {e98002}, pmid = {24865350}, issn = {1932-6203}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Mitochondria/*genetics/radiation effects ; New Guinea ; *Phylogeny ; Polymerase Chain Reaction ; Radiation ; Rats/*anatomy &amp; histology/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {The genus Rattus is highly speciose, the taxonomy is complex, and individuals are often difficult to identify to the species level. Previous studies have demonstrated the usefulness of phylogenetic approaches to identification in Rattus but some species, especially among the endemics of the New Guinean region, showed poor resolution. Possible reasons for this are simple misidentification, incomplete gene lineage sorting, hybridization, and phylogenetically distinct lineages that are unrecognised taxonomically. To assess these explanations we analysed 217 samples, representing nominally 25 Rattus species, collected in New Guinea, Asia, Australia and the Pacific. To reduce misidentification problems we sequenced museum specimens from earlier morphological studies and recently collected tissues from samples with associated voucher specimens. We also reassessed vouchers from previously sequenced specimens. We inferred combined and separate phylogenies from two mitochondrial DNA regions comprising 550 base pair D-loop sequences and both long (655 base pair) and short (150 base pair) cytochrome oxidase I sequences. Our phylogenetic species identification for 17 species was consistent with morphological designations and current taxonomy thus reinforcing the usefulness of this approach. We reduced misidentifications and consequently the number of polyphyletic species in our phylogenies but the New Guinean Rattus clades still exhibited considerable complexity. Only three of our eight New Guinean species were monophyletic. We found good evidence for either incomplete mitochondrial lineage sorting or hybridization between species within two pairs, R. leucopus/R. cf. verecundus and R. steini/R. praetor. Additionally, our results showed that R. praetor, R. niobe and R. verecundus each likely encompass more than one species. Our study clearly points to the need for a revised taxonomy of the rats of New Guinea, based on broader sampling and informed by both morphology and phylogenetics. The remaining taxonomic complexity highlights the recent and rapid radiation of Rattus in the Australo-Papuan region.}, }
@article {pmid24864314, year = {2014}, author = {Speijer, D and Manjeri, GR and Szklarczyk, R}, title = {How to deal with oxygen radicals stemming from mitochondrial fatty acid oxidation.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {369}, number = {1646}, pages = {20130446}, pmid = {24864314}, issn = {1471-2970}, mesh = {Electron Transport/physiology ; Fatty Acids/*metabolism ; Humans ; Mitochondria/*metabolism ; Neurodegenerative Diseases/metabolism ; *Oxidation-Reduction ; Peroxisomes/*metabolism ; Reactive Oxygen Species/*metabolism ; }, abstract = {Oxygen radical formation in mitochondria is an incompletely understood attribute of eukaryotic cells. Recently, a kinetic model was proposed, in which the ratio between electrons entering the respiratory chain via FADH2 or NADH determines radical formation. During glucose breakdown, the ratio is low; during fatty acid breakdown, the ratio is high (the ratio increasing--asymptotically--with fatty acid length to 0.5, when compared with 0.2 for glucose). Thus, fatty acid oxidation would generate higher levels of radical formation. As a result, breakdown of fatty acids, performed without generation of extra FADH2 in mitochondria, could be beneficial for the cell, especially in the case of long and very long chained ones. This possibly has been a major factor in the evolution of peroxisomes. Increased radical formation, as proposed by the model, can also shed light on the lack of neuronal fatty acid oxidation and tells us about hurdles during early eukaryotic evolution. We specifically focus on extending and discussing the model in light of recent publications and findings.}, }
@article {pmid24864313, year = {2014}, author = {Wolff, JN and Ladoukakis, ED and Enríquez, JA and Dowling, DK}, title = {Mitonuclear interactions: evolutionary consequences over multiple biological scales.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {369}, number = {1646}, pages = {20130443}, pmid = {24864313}, issn = {1471-2970}, mesh = {*Biological Evolution ; DNA, Mitochondrial/*genetics/physiology ; Genetic Variation/*genetics/physiology ; Genotype ; Humans ; Mitochondria/*genetics/physiology ; Mitochondrial Diseases/genetics ; Phenotype ; Polymorphism, Genetic/*genetics/physiology ; }, abstract = {Fundamental biological processes hinge on coordinated interactions between genes spanning two obligate genomes--mitochondrial and nuclear. These interactions are key to complex life, and allelic variation that accumulates and persists at the loci embroiled in such intergenomic interactions should therefore be subjected to intense selection to maintain integrity of the mitochondrial electron transport system. Here, we compile evidence that suggests that mitochondrial-nuclear (mitonuclear) allelic interactions are evolutionarily significant modulators of the expression of key health-related and life-history phenotypes, across several biological scales--within species (intra- and interpopulational) and between species. We then introduce a new frontier for the study of mitonuclear interactions--those that occur within individuals, and are fuelled by the mtDNA heteroplasmy and the existence of nuclear-encoded mitochondrial gene duplicates and isoforms. Empirical evidence supports the idea of high-resolution tissue- and environment-specific modulation of intraindividual mitonuclear interactions. Predicting the penetrance, severity and expression patterns of mtDNA-induced mitochondrial diseases remains a conundrum. We contend that a deeper understanding of the dynamics and ramifications of mitonuclear interactions, across all biological levels, will provide key insights that tangibly advance our understanding, not only of core evolutionary processes, but also of the complex genetics underlying human mitochondrial disease.}, }
@article {pmid24864311, year = {2014}, author = {Beekman, M and Dowling, DK and Aanen, DK}, title = {The costs of being male: are there sex-specific effects of uniparental mitochondrial inheritance?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {369}, number = {1646}, pages = {20130440}, pmid = {24864311}, issn = {1471-2970}, mesh = {Alleles ; Animals ; *Biological Evolution ; DNA, Mitochondrial/genetics/*metabolism ; Female ; Gene Duplication/genetics/physiology ; Genetic Variation/genetics/*physiology ; Genome, Mitochondrial/genetics/*physiology ; Humans ; Male ; Mitochondria/genetics/*metabolism ; Oxidative Phosphorylation ; Selection, Genetic/genetics/*physiology ; }, abstract = {Eukaryotic cells typically contain numerous mitochondria, each with multiple copies of their own genome, the mtDNA. Uniparental transmission of mitochondria, usually via the mother, prevents the mixing of mtDNA from different individuals. While on the one hand, this should resolve the potential for selection for fast-replicating mtDNA variants that reduce organismal fitness, maternal inheritance will, in theory, come with another set of problems that are specifically relevant to males. Maternal inheritance implies that the mitochondrial genome is never transmitted through males, and thus selection can target only the mtDNA sequence when carried by females. A consequence is that mtDNA mutations that confer male-biased phenotypic expression will be prone to evade selection, and accumulate. Here, we review the evidence from the ecological, evolutionary and medical literature for male specificity of mtDNA mutations affecting fertility, health and ageing. While such effects have been discovered experimentally in the laboratory, their relevance to natural populations--including the human population--remains unclear. We suggest that the existence of male expression-biased mtDNA mutations is likely to be a broad phenomenon, but that these mutations remain cryptic owing to the presence of counter-adapted nuclear compensatory modifier mutations, which offset their deleterious effects.}, }
@article {pmid24864309, year = {2014}, author = {Aanen, DK and Spelbrink, JN and Beekman, M}, title = {What cost mitochondria? The maintenance of functional mitochondrial DNA within and across generations.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {369}, number = {1646}, pages = {20130438}, pmid = {24864309}, issn = {1471-2970}, mesh = {Animals ; *Biological Evolution ; DNA Replication/*genetics ; DNA, Mitochondrial/*genetics ; Humans ; Mitochondria/*genetics ; Mutation/*genetics ; *Selection, Genetic ; }, abstract = {The peculiar biology of mitochondrial DNA (mtDNA) potentially has detrimental consequences for organismal health and lifespan. Typically, eukaryotic cells contain multiple mitochondria, each with multiple mtDNA genomes. The high copy number of mtDNA implies that selection on mtDNA functionality is relaxed. Furthermore, because mtDNA replication is not strictly regulated, within-cell selection may favour mtDNA variants with a replication advantage, but a deleterious effect on cell fitness. The opportunities for selfish mtDNA mutations to spread are restricted by various organism-level adaptations, such as uniparental transmission, germline mtDNA bottlenecks, germline selection and, during somatic growth, regular alternation between fusion and fission of mitochondria. These mechanisms are all hypothesized to maintain functional mtDNA. However, the strength of selection for maintenance of functional mtDNA progressively declines with age, resulting in age-related diseases. Furthermore, organismal adaptations that most probably evolved to restrict the opportunities for selfish mtDNA create secondary problems. Owing to predominantly maternal mtDNA transmission, recombination among mtDNA from different individuals is highly restricted or absent, reducing the scope for repair. Moreover, maternal inheritance precludes selection against mtDNA variants with male-specific effects. We finish by discussing the consequences of life-history differences among taxa with respect to mtDNA evolution and make a case for the use of microorganisms to experimentally manipulate levels of selection.}, }
@article {pmid24864090, year = {2014}, author = {Saluk, J and Bijak, M and Ponczek, MB and Wachowicz, B}, title = {[The formation, metabolism and the evolution of blood platelets].}, journal = {Postepy higieny i medycyny doswiadczalnej (Online)}, volume = {68}, number = {}, pages = {384-391}, doi = {10.5604/17322693.1098145}, pmid = {24864090}, issn = {1732-2693}, mesh = {Animals ; Biological Evolution ; Blood Platelets/*cytology/*metabolism ; Cell Differentiation ; Cytoplasm/metabolism ; Hemostasis/physiology ; Humans ; Megakaryocytes ; Mitochondria/metabolism ; Organelles/metabolism ; Protein Biosynthesis ; }, abstract = {Platelets are the smallest, depleted of nucleus blood cells which contain a typical cellular organelles including the mitochondria, so that have active metabolism. Platelets possess the highly organized cytoskeleton, specific secretory granules and unique membrane receptors system responsible for their high reactivity. The key role of blood platelets is to maintain normal hemostasis, but they also play important roles in inflammation, immune processes and the cancer progression. The anucleated, small platelets occur in representatives of all clusters of mammals, so it seems to be an adaptation feature. In other vertebrates similar hemostatic functions are played by large nucleated platelets, which are much more weakly reactive. Small, reactive platelets, appearing in the evolution of mammals, allowed the formation of clots faster and slower blood loss in case of injury, but also increased the risk of thromboembolic and cardiovascular diseases. Daily the human body forms about 1x10[11] platelets, which are produced by a process of differentiation, maturation and fragmentation of the cytoplasm of mature megakaryocytes. The emergence of platelets is the final stage of megakaryocyte differentiation and is followed by formation of the direct precursors called proplatelets. The anucleated platelets are regarded as terminally differentiated cells, which are not capable of further cell division. However, despite the absence of a nucleus, in blood platelets the synthesis and transcription of mitochondrial DNA and protein synthesis occurring on the basis of mRNA from megakaryocytes has been confirmed. However, recent studies published in 2012 show that the platelets are capable not only of the process of protein synthesis, but also of generation of new cells, which are functionally and structurally similar to the parent platelets.}, }
@article {pmid24863547, year = {2015}, author = {Mouton, L and Gnankiné, O and Henri, H and Terraz, G and Ketoh, G and Martin, T and Fleury, F and Vavre, F}, title = {Detection of genetically isolated entities within the Mediterranean species of Bemisia tabaci: new insights into the systematics of this worldwide pest.}, journal = {Pest management science}, volume = {71}, number = {3}, pages = {452-458}, doi = {10.1002/ps.3834}, pmid = {24863547}, issn = {1526-4998}, mesh = {Africa, Western ; Animals ; Female ; Gene Flow ; Genotype ; Hemiptera/*classification/*genetics ; Insecticide Resistance/genetics ; Male ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; }, abstract = {BACKGROUND: The taxonomy of the species complex Bemisia tabaci, a serious agricultural pest worldwide, is not well resolved yet, even though species delimitation is critical for designing effective control strategies. Based on a threshold of 3.5% mitochondrial (mtCOI) sequence divergence, recent studies have identified 28 putative species. Among them, mitochondrial variability associated with particular symbiotic compositions (=cytotypes) can be observed, as in MED, which raises the question of whether it is a single or a complex of biological species.<br><br>RESULTS: Using microsatellites, an investigation was made of the genetic relatedness of Q1 and ASL cytotypes that belong to MED. Samples of the two cytotypes were collected in West Africa where they live in sympatry on the same hosts. Genotyping revealed a high level of differentiation, without evidence of gene flow. Moreover, they differed highly in frequencies of resistance alleles to insecticides, which were much higher in Q1 than in ASL.<br><br>CONCLUSION: Q1 and ASL are sufficiently reproductively isolated for the introgression of neutral alleles to be prevented, suggesting that they are actually different species. This indicates that nuclear genetic differentiation must be investigated within groups with less than 3.5% mtCOI divergence in order to elucidate the taxonomy of B. tabaci at a finer level. Overall, these data provide important information for pest management.}, }
@article {pmid24862258, year = {2014}, author = {Sciacovelli, M and Gaude, E and Hilvo, M and Frezza, C}, title = {The metabolic alterations of cancer cells.}, journal = {Methods in enzymology}, volume = {542}, number = {}, pages = {1-23}, doi = {10.1016/B978-0-12-416618-9.00001-7}, pmid = {24862258}, issn = {1557-7988}, support = {MC_UP_1101/3/MRC_/Medical Research Council/United Kingdom ; MC_UU_12022/6/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Cell Transformation, Neoplastic ; Diphosphoglyceric Acids/metabolism ; Fatty Acids/biosynthesis ; *Glycolysis ; Humans ; Isocitrate Dehydrogenase/genetics/metabolism ; Lipid Metabolism ; Mitochondria/*metabolism ; Mutation ; Neoplasms/genetics/*metabolism ; Oncogenes ; Phosphofructokinase-1/metabolism ; Phosphofructokinase-2/metabolism ; Phosphoglycerate Dehydrogenase/metabolism ; Phosphoglycerate Mutase/metabolism ; Pyruvate Kinase/metabolism ; }, abstract = {Cancer cells exhibit profound metabolic alterations, allowing them to fulfill the metabolic needs that come with increased proliferation and additional facets of malignancy. Such a metabolic transformation is orchestrated by the genetic changes that drive tumorigenesis, that is, the activation of oncogenes and/or the loss of oncosuppressor genes, and further shaped by environmental cues, such as oxygen concentration and nutrient availability. Understanding this metabolic rewiring is essential to elucidate the fundamental mechanisms of tumorigenesis as well as to find novel, therapeutically exploitable liabilities of malignant cells. Here, we describe key features of the metabolic transformation of cancer cells, which frequently include the switch to aerobic glycolysis, a profound mitochondrial reprogramming, and the deregulation of lipid metabolism, highlighting the notion that these pathways are not independent but rather cooperate to sustain proliferation. Finally, we hypothesize that only those genetic defects that effectively support anabolism are selected in the course of tumor progression, implying that cancer-associated mutations may undergo a metabolically convergent evolution.}, }
@article {pmid24859646, year = {2014}, author = {Yu, X and Wu, L and Xie, L and Yang, S and Charkraborty, T and Shi, H and Wang, D and Zhou, L}, title = {Characterization of two paralogous StAR genes in a teleost, Nile tilapia (Oreochromis niloticus).}, journal = {Molecular and cellular endocrinology}, volume = {392}, number = {1-2}, pages = {152-162}, doi = {10.1016/j.mce.2014.05.013}, pmid = {24859646}, issn = {1872-8057}, mesh = {Amino Acid Sequence ; Animals ; Chorionic Gonadotropin/administration &amp; dosage/pharmacology ; Cichlids/*genetics ; Female ; Gene Expression Profiling ; Humans ; Immunohistochemistry ; Injections ; Male ; Molecular Sequence Data ; Phosphoproteins/chemistry/*genetics/metabolism ; Phylogeny ; Real-Time Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; *Sequence Homology, Nucleic Acid ; Synteny/genetics ; }, abstract = {Steroidogenic acute regulatory protein (StAR) transports cholesterol, the substrate for steroid synthesis, to the inner membranes of mitochondria. It is well known that estrogen is essential for female sex determination/differentiation in fish. However, no reports showed that the conventional StAR, which was supposed to be essential for estrogen production, was expressed in female gonads during the critical timing of sex determination/differentiation. In this study, two different StAR isoforms, named as StAR1 and StAR2, were characterized from the gonads of Nile tilapia (Oreochromis niloticus). Phylogenetic and synteny analysis revealed that two StAR genes existed in teleosts, Xenopus and chicken indicating that the duplication event occurred before the divergence of teleosts and tetrapods. Real-time PCR revealed that StAR1 was dominantly expressed in the testis, head kidney and kidney; while StAR2 was expressed exclusively in the gonads. In situ hybridization and immunohistochemistry demonstrated that StAR1 was expressed in the interrenal cells of the head kidney and Leydig cells of the testis; while StAR2 was expressed in the Leydig cells of the testis and the interstitial cells of the ovary. Ontogenic analysis demonstrated that StAR2 was expressed abundantly from 5 days after hatching (dah) in the somatic cells in XX gonads, whereas in XY gonads, both StARs could be detected from 30 dah until adulthood. Intraperitoneal injection of human chorionic gonadotropin experiments showed that expression of StAR1 and 2 was significantly elevated at 8h and persisted until 24h after injection in the testis. Taken together, our data suggested that StAR1 is likely to be required for cortisol production in the head kidney, and StAR2 is probably involved in estrogen production during early sex differentiation in XX gonads. In contrast, both StARs might be required for androgen production in testes. For the first time, our data demonstrated that two fish StARs might be involved in steroidogenesis in a tissue and developmental stage dependent manner.}, }
@article {pmid24859248, year = {2014}, author = {Caspermeyer, J}, title = {New analysis of seven ant genomes reveals clues to longer life spans associated with sociality.}, journal = {Molecular biology and evolution}, volume = {31}, number = {7}, pages = {1937}, doi = {10.1093/molbev/msu158}, pmid = {24859248}, issn = {1537-1719}, mesh = {Animals ; Ants/*genetics ; Evolution, Molecular ; *Genes, Insect ; Mitochondria/genetics ; Phylogeny ; Selection, Genetic ; }, }
@article {pmid24858958, year = {2014}, author = {Ido, Y and Yoshitomi, T and Ohkura, K and Yamamoto, T and Shinohara, Y}, title = {Utility of syntenic relationships of VDAC1 pseudogenes for not only an understanding of the phylogenetic divergence history of rodents, but also ascertaining possible pseudogene candidates as genuine pseudogenes.}, journal = {Genomics}, volume = {104}, number = {2}, pages = {128-133}, doi = {10.1016/j.ygeno.2014.05.003}, pmid = {24858958}, issn = {1089-8646}, mesh = {Animals ; Evolution, Molecular ; Humans ; Mice ; *Phylogeny ; Pseudogenes/*genetics ; Rats ; Synteny/*genetics ; Voltage-Dependent Anion Channel 1/*genetics ; }, abstract = {Rodent and human genomes were screened to identify pseudogenes of the type 1 voltage-dependent anion channel (VDAC1) in mitochondria. In addition to the 16 pseudogenes of rat VDAC1 identified in our recent study, 15 and 13 sequences were identified as pseudogenes of VDAC1 in mouse and human genome, respectively; and 4, 2, and 1 sequences, showing lower similarities with the VDAC1 sequence, were identified as "possible pseudogene candidates" in rat, mouse, and human, respectively. No syntenic combination was observed between rodent and human pseudogenes, but 2 and 1 possible pseudogene candidates of VDAC1 of rat and mouse, respectively, were found to have syntenic counterparts in mouse and rat genome, respectively; and these syntenic counterparts were genuine VDAC1 pseudogenes. Therefore, syntenic combinations of pseudogenes of VDAC1 were useful not only for a better understanding of the phylogenetic divergence history of rodents but also for ascertaining possible pseudogene candidates as genuine pseudogenes.}, }
@article {pmid24858075, year = {2014}, author = {Wen, J and Chan, RH and Yau, SC and He, RL and Yau, SS}, title = {K-mer natural vector and its application to the phylogenetic analysis of genetic sequences.}, journal = {Gene}, volume = {546}, number = {1}, pages = {25-34}, pmid = {24858075}, issn = {1879-0038}, support = {SC3 GM098180/GM/NIGMS NIH HHS/United States ; 5 SC3 GM098180-04/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Animals ; DNA, Mitochondrial ; Evolution, Molecular ; *Genetic Vectors ; Genome ; *Genome, Human ; Humans ; Mammals/*genetics ; Mitochondria/genetics ; *Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Based on the well-known k-mer model, we propose a k-mer natural vector model for representing a genetic sequence based on the numbers and distributions of k-mers in the sequence. We show that there exists a one-to-one correspondence between a genetic sequence and its associated k-mer natural vector. The k-mer natural vector method can be easily and quickly used to perform phylogenetic analysis of genetic sequences without requiring evolutionary models or human intervention. Whole or partial genomes can be handled more effective with our proposed method. It is applied to the phylogenetic analysis of genetic sequences, and the obtaining results fully demonstrate that the k-mer natural vector method is a very powerful tool for analysing and annotating genetic sequences and determining evolutionary relationships both in terms of accuracy and efficiency.}, }
@article {pmid24856215, year = {2014}, author = {Stairs, CW and Eme, L and Brown, MW and Mutsaers, C and Susko, E and Dellaire, G and Soanes, DM and van der Giezen, M and Roger, AJ}, title = {A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia.}, journal = {Current biology : CB}, volume = {24}, number = {11}, pages = {1176-1186}, doi = {10.1016/j.cub.2014.04.033}, pmid = {24856215}, issn = {1879-0445}, support = {MOP-82809//Canadian Institutes of Health Research/Canada ; MOP-84260//Canadian Institutes of Health Research/Canada ; }, mesh = {Anaerobiosis ; Eukaryota/*genetics/*metabolism ; Molecular Sequence Data ; Organelles/*metabolism ; Phylogeny ; *Proteome ; Saccharomyces cerevisiae/metabolism ; Sequence Analysis, RNA ; Sulfur/*metabolism ; }, abstract = {BACKGROUND: Many microbial eukaryotes have evolved anaerobic alternatives to mitochondria known as mitochondrion-related organelles (MROs). Yet, only a few of these have been experimentally investigated. Here we report an RNA-seq-based reconstruction of the MRO proteome of Pygsuia biforma, an anaerobic representative of an unexplored deep-branching eukaryotic lineage.<br><br>RESULTS: Pygsuia's MRO has a completely novel suite of functions, defying existing "function-based" organelle classifications. Most notable is the replacement of the mitochondrial iron-sulfur cluster machinery by an archaeal sulfur mobilization (SUF) system acquired via lateral gene transfer (LGT). Using immunolocalization in Pygsuia and heterologous expression in yeast, we show that the SUF system does indeed localize to the MRO. The Pygsuia MRO also possesses a unique assemblage of features, including: cardiolipin, phosphonolipid, amino acid, and fatty acid metabolism; a partial Kreb's cycle; a reduced respiratory chain; and a laterally acquired rhodoquinone (RQ) biosynthesis enzyme. The latter observation suggests that RQ is an electron carrier of a fumarate reductase-type complex II in this MRO.<br><br>CONCLUSIONS: The unique functional profile of this MRO underscores the tremendous plasticity of mitochondrial function within eukaryotes and showcases the role of LGT in forging metabolic mosaics of ancestral and newly acquired organellar pathways.}, }
@article {pmid24850967, year = {2014}, author = {Zhong, X and Wang, N and Hu, D and Wang, J and Liu, T and Gu, X and Wang, S and Peng, X and Yang, G}, title = {Sequence analysis of cytb gene in Echinococcus granulosus from Western China.}, journal = {The Korean journal of parasitology}, volume = {52}, number = {2}, pages = {205-209}, pmid = {24850967}, issn = {1738-0006}, mesh = {Animals ; Animals, Domestic/parasitology ; Base Composition ; Base Sequence ; Cattle/*parasitology ; China ; Cytochromes b/*genetics ; DNA, Helminth/genetics ; Echinococcosis ; Echinococcus granulosus/classification/*genetics ; Genetic Variation ; Haplotypes/genetics ; Humans ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*veterinary ; Sequence Alignment ; Sequence Analysis, DNA ; Sheep/*parasitology ; Tibet ; }, abstract = {Echinococcus granulosus is the causative agent of cystic echinococcosis with medical and veterinary importance in China. Our main objective was to discuss the genotypes and genetic diversity of E. granulosus present in domestic animals and humans in western China. A total of 45 hydatid cyst samples were collected from sheep, humans, and a yak and subjected to an analysis of the sequences of mitochondrial cytochrome b (cytb) gene. The amplified PCR product for all samples was a 1,068 bp band. The phylogenetic analysis showed that all 45 samples were identified as E. granulosus (genotype G1). Ten haplotypes were detected among the samples, with the main haplotype being H1. The haplotype diversity was 0.626, while the nucleotide diversity was 0.001. These results suggested that genetic diversity was low among our samples collected from the west of China based on cytb gene analysis. These findings may provide more information on molecular characteristics of E. granulosus from this Chinese region.}, }
@article {pmid24850965, year = {2014}, author = {Song, SM and Yang, HW and Jung, MK and Heo, J and Cho, CM and Goo, YK and Hong, Y and Chung, DI}, title = {Two human cases of Diphyllobothrium nihonkaiense infection in Korea.}, journal = {The Korean journal of parasitology}, volume = {52}, number = {2}, pages = {197-199}, pmid = {24850965}, issn = {1738-0006}, mesh = {Adult ; Animals ; Anthelmintics/therapeutic use ; Base Sequence ; DNA, Helminth/*genetics ; Diphyllobothriasis/*diagnosis/drug therapy ; Diphyllobothrium/*genetics ; Electron Transport Complex IV/*genetics ; Humans ; Male ; Middle Aged ; Mitochondria/enzymology ; Phylogeny ; Praziquantel/therapeutic use ; Republic of Korea ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {Diphyllobothrium latum and Diphyllobothrium nihonkaiense are the 2 reported main causes of human diphyllobothriasis in the Republic of Korea. However, the differentiation of these 2 species based on morphologic features alone is difficult. The authors used nucleotide sequencing of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene to diagnose Diphyllobothrium spp. Two patients visited the emergency room at Kyungpook National University Hospital on 3 April and 12 April 2013, respectively, with fragments of parasites found while defecating. The parasites were identified as Diphyllobothrium spp. based on morphologic characteristics, and subsequent cox1 gene sequencing showed 99.9% similarity (1,478/1,480 bp) with D. nihonkaiense. Our findings support the hypothesis that D. nihonkaiense is a dominant species in Korea.}, }
@article {pmid24850960, year = {2014}, author = {Won, S and Park, BK and Kim, BJ and Kim, HW and Kang, JG and Park, TS and Seo, HY and Eun, Y and Kim, KG and Chae, JS}, title = {Molecular Identification of Haemadipsa rjukjuana (Hirudiniformes: Haemadipsidae) in Gageo Island, Korea.}, journal = {The Korean journal of parasitology}, volume = {52}, number = {2}, pages = {169-175}, pmid = {24850960}, issn = {1738-0006}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Genetic Markers/genetics ; Leeches/*classification/*genetics ; Mitochondria/enzymology/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/*genetics ; Republic of Korea ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {There are 60 species of blood-feeding land leeches, 50 species belonging to the family Haemadipsidae and 10 species belonging to the family Xerobdellidae. Despite recent papers on the land leeches, their taxonomic identification is not fully understood, especially at a species level. In Korea, there have been no historical records of the terrestrial leeches, but recently an unrecorded blood-feeding land leech was discovered at Gageo-do (Island), Korea. Molecular analysis was used to identify the species of 29 leeches collected from Mt. Dock-Sil in Gageo-do. Conventional PCR was conducted using nuclear 18S rRNA and mitochondrial cytochrome c oxidase subunit 1 (CO1) genetic marker. The 18S rRNA sequences revealed that the leeches share 99.9% identity with Haemadipsa rjukjuana (inhabiting Taiwan), and the CO1 sequences revealed that the leeches are very close to H. rjukjuana (inhabiting Taiwan). The CO1 sequences were separated into 2 categories, 1 with 94.6% and the other with 94.3% similarity to the H. rjukjuana L00115A (inhabiting Taiwan). This new finding of the land leech is the first record in Korea. In addition, the north range of the distribution of the blood-feeding leech (Hirudiniformes: Haemadipisidae) should be reconsidered including Korea.}, }
@article {pmid24848875, year = {2014}, author = {Speijer, D}, title = {How the mitochondrion was shaped by radical differences in substrates: what carnitine shuttles and uncoupling tell us about mitochondrial evolution in response to ROS.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {7}, pages = {634-643}, doi = {10.1002/bies.201400033}, pmid = {24848875}, issn = {1521-1878}, mesh = {Animals ; *Biological Evolution ; Biological Transport ; Carnitine/*metabolism ; Free Radicals/metabolism ; Humans ; Metabolic Networks and Pathways ; Mitochondria/*physiology ; Reactive Oxygen Species/*metabolism ; }, abstract = {As free-living organisms, alpha-proteobacteria produce reactive oxygen species (ROS) that diffuse into the surroundings; once constrained inside the archaeal ancestor of eukaryotes, however, ROS production presented evolutionary pressures - especially because the alpha-proteobacterial symbiont made more ROS, from a variety of substrates. I previously proposed that ratios of electrons coming from FADH2 and NADH (F/N ratios) correlate with ROS production levels during respiration, glucose breakdown having a much lower F/N ratio than longer fatty acid (FA) breakdown. Evidently, higher endogenous ROS formation did not hinder eukaryotic evolution, so how were its disadvantages mitigated? I propose that the resulting selection pressures favoured the evolution of a variety of eukaryotic 'innovations': peroxisomes for FA breakdown, carnitine shuttles, the linkage of beta-oxidation to antioxidant properties, uncoupling proteins (UCPs) and using mitochondrial uncoupling during beta-oxidation to reduce ROS. Recently observed relationships between peroxisomes and mitochondria further support the model.}, }
@article {pmid24845439, year = {2016}, author = {Li, Y and Huang, W and Yu, Q and Cheng, YT and Kong, QP}, title = {Lower mitochondrial DNA content relates to high-altitude adaptation in Tibetans.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {1}, pages = {753-757}, doi = {10.3109/19401736.2014.915526}, pmid = {24845439}, issn = {2470-1408}, mesh = {Adaptation, Physiological/*genetics ; Aging/genetics ; *Altitude ; Blood Glucose/metabolism ; Carbon Dioxide/metabolism ; Cholesterol/metabolism ; DNA, Mitochondrial/*genetics ; Female ; Gene Dosage ; Humans ; Male ; Tibet ; Triglycerides/metabolism ; }, abstract = {Mitochondrial DNA (mtDNA) is crucial to mitochondria in energy production and other physiological functions. When lowlanders arrive at high altitude, the mitochondrial content tends to decrease. However, the mtDNA content of native highlanders share the same feature as lowlanders remains unknown. It is also interesting to dissect the other changes in blood plasma that might accompany the change of mtDNA content. To address these issues, we recruited 241 Tibetan subjects in Tibet and 220 Han subjects in Shaanxi province. Relative mtDNA copy number and blood biochemical indexes were measured. Results show that relative mtDNA copy number in Tibetans is significantly lower as compared to Han subjects; sex, age, blood glucose, triglyceride and total cholesterol show no influence on mtDNA content, but carbon dioxide combining power is negatively correlated with mtDNA content. These results indicate that an increase in CO2 combining power along with lower mtDNA content may provide adaptive potential.}, }
@article {pmid24845122, year = {2014}, author = {Rey, B and Romestaing, C and Bodennec, J and Dumet, A and Fongy, A and Duchamp, C and Roussel, D}, title = {Thyroid status affects membranes susceptibility to free radicals and oxidative balance in skeletal muscle of Muscovy ducklings (Cairina moschata).}, journal = {Journal of experimental zoology. Part A, Ecological genetics and physiology}, volume = {321}, number = {8}, pages = {415-421}, doi = {10.1002/jez.1872}, pmid = {24845122}, issn = {1932-5231}, mesh = {Animals ; Antioxidants ; DNA/*metabolism ; DNA Damage ; Ducks/*metabolism ; Free Radicals/*metabolism ; Hyperthyroidism/*metabolism ; Hypothyroidism/*metabolism ; Lipid Peroxidation ; Mitochondria/metabolism ; Muscle, Skeletal/chemistry/*metabolism ; Oxidative Stress/*physiology ; Protein Carbonylation ; Proteins/metabolism ; Reactive Oxygen Species ; Thyroid Hormones/metabolism ; }, abstract = {Thyroid hormones (TH) are major contributor to oxidative stress in mammals because they (1) stimulate reactive oxygen species generation (ROS), (2) impair antioxidant defenses, and (3) increase the susceptibility to free radicals of most tissues. Unlike mammals, THs seem to diminish mitochondrial ROS while they have limited effect on the antioxidant machinery in birds. However, how THs modify the susceptibility to ROS has never been explored in an avian model, and very little is known about their effect on oxidative balance in birds. Therefore, the objective of our study was to examine the effect of chronic pharmacological hypo- and hyperthyroidism on (i) the susceptibility of mitochondrial membranes to ROS; and (ii) the level of oxidative stress assessed by measuring oxidative damage to lipids, nucleic acids and proteins in the gastrocnemius muscle of ducklings. We show that hypothyroidism had no effect on the susceptibility of mitochondrial membranes to free radicals. Hypothyroid ducklings had lower oxidized lipids (-31%) and DNA (-25%) but a similar level of protein carbonylation relative to controls. Conversely, mitochondrial membranes of hyperthyroid ducklings exhibited higher unsaturation (+12%) and peroxidation (+31%) indexes than in controls indicating a greater susceptibility to free radicals. However, hyperthyroid ducklings exhibited more oxidative damages on proteins (+67%) only, whereas lipid damages remained unchanged, and there was a slight reduction (-15%) in damages to DNA compared to euthyroid controls. Our results indicate that birds and mammals present fundamental differences in their oxidative stress response to thyroid status.}, }
@article {pmid24842572, year = {2014}, author = {Li, CL and Wang, M and Ma, XY and Zhang, W}, title = {NRGA1, a putative mitochondrial pyruvate carrier, mediates ABA regulation of guard cell ion channels and drought stress responses in Arabidopsis.}, journal = {Molecular plant}, volume = {7}, number = {10}, pages = {1508-1521}, doi = {10.1093/mp/ssu061}, pmid = {24842572}, issn = {1752-9867}, mesh = {Abscisic Acid/*pharmacology ; Adaptation, Physiological/drug effects ; Amino Acid Sequence ; Anion Transport Proteins/chemistry/genetics/*metabolism ; Arabidopsis/drug effects/genetics/*physiology ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Cell Movement/drug effects ; *Droughts ; Genetic Complementation Test ; Ion Channel Gating/drug effects ; Membrane Transport Proteins/*metabolism ; Mitochondria/drug effects/metabolism ; Mitochondrial Membrane Transport Proteins/chemistry/genetics/*metabolism ; Mitochondrial Proteins ; Models, Biological ; Molecular Sequence Data ; Monocarboxylic Acid Transporters ; Mutation/genetics ; Phylogeny ; Plant Stomata/*cytology ; Plants, Genetically Modified ; Potassium Channels/*metabolism ; Protein Transport/drug effects ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins ; Stress, Physiological/*drug effects ; Subcellular Fractions/drug effects/metabolism ; Transcription, Genetic/drug effects ; }, abstract = {Abscisic acid (ABA) regulates ion channel activity and stomatal movements in response to drought and other stresses. Here, we show that the Arabidopsis thaliana gene NRGA1 is a putative mitochondrial pyruvate carrier which negatively regulates ABA-induced guard cell signaling. NRGA1 transcript was abundant in the A. thaliana leaf and particularly in the guard cells, and its product was directed to the mitochondria. The heterologous co-expression of NRGA1 and AtMPC1 in yeast complemented a loss-of-function mitochondrial pyruvate carrier (MPC) mutant. The nrga1 loss-of-function mutant was very sensitive to the presence of ABA in the context of stomatal movements, and exhibited a heightened tolerance to drought stress. Disruption of NRGA1 gene resulted in increased ABA inhibition of inward K(+) currents and ABA activation of slow anion currents in guard cells. The nrga1/NRGA1 functional complementation lines restored the mutant's phenotypes. Furthermore, transgenic lines of constitutively overexpressing NRGA1 showed opposite stomatal responses, reduced drought tolerance, and ABA sensitivity of guard cell inward K(+) channel inhibition and anion channel activation. Our findings highlight a putative role for the mitochondrial pyruvate carrier in guard cell ABA signaling in response to drought.}, }
@article {pmid24841564, year = {2014}, author = {Hildenbeutel, M and Hegg, EL and Stephan, K and Gruschke, S and Meunier, B and Ott, M}, title = {Assembly factors monitor sequential hemylation of cytochrome b to regulate mitochondrial translation.}, journal = {The Journal of cell biology}, volume = {205}, number = {4}, pages = {511-524}, pmid = {24841564}, issn = {1540-8140}, support = {R01 GM101386/GM/NIGMS NIH HHS/United States ; GM101386/GM/NIGMS NIH HHS/United States ; }, mesh = {Cytochromes b/genetics/*metabolism ; Evolution, Molecular ; Feedback, Physiological/physiology ; Genes, Mitochondrial/genetics ; Heme/*metabolism ; Membrane Proteins/metabolism ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/metabolism ; Molecular Chaperones/metabolism ; Oxidation-Reduction ; Protein Biosynthesis/*physiology ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; }, abstract = {Mitochondrial respiratory chain complexes convert chemical energy into a membrane potential by connecting electron transport with charge separation. Electron transport relies on redox cofactors that occupy strategic positions in the complexes. How these redox cofactors are assembled into the complexes is not known. Cytochrome b, a central catalytic subunit of complex III, contains two heme bs. Here, we unravel the sequence of events in the mitochondrial inner membrane by which cytochrome b is hemylated. Heme incorporation occurs in a strict sequential process that involves interactions of the newly synthesized cytochrome b with assembly factors and structural complex III subunits. These interactions are functionally connected to cofactor acquisition that triggers the progression of cytochrome b through successive assembly intermediates. Failure to hemylate cytochrome b sequesters the Cbp3-Cbp6 complex in early assembly intermediates, thereby causing a reduction in cytochrome b synthesis via a feedback loop that senses hemylation of cytochrome b.}, }
@article {pmid24838097, year = {2014}, author = {Gabaldón, T}, title = {Evolutionary considerations on the origin of peroxisomes from the endoplasmic reticulum, and their relationships with mitochondria.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {71}, number = {13}, pages = {2379-2382}, pmid = {24838097}, issn = {1420-9071}, mesh = {Animals ; *Biological Evolution ; Endoplasmic Reticulum/*genetics ; Humans ; Organelles/*genetics ; Peroxisomes/*genetics ; }, }
@article {pmid24832905, year = {2014}, author = {Kawamura, K and Ueda, T and Arai, R and Smith, C}, title = {Phylogenetic relationships of bitterling fishes (Teleostei: Cypriniformes: Acheilognathinae), inferred from mitochondrial cytochrome B sequences.}, journal = {Zoological science}, volume = {31}, number = {5}, pages = {321-329}, doi = {10.2108/zs130233}, pmid = {24832905}, issn = {0289-0003}, mesh = {Animals ; Cypriniformes/*genetics ; Cytochromes b/genetics/*metabolism ; Gene Expression Regulation/*physiology ; Mitochondria/*enzymology ; *Phylogeny ; }, abstract = {Bitterling (Teleostei: Acheilognathinae) are small cyprinid fishes with a discrete distribution in East Asia and Europe. We used a complete mitochondrial cytochrome b sequence (1141 bp) from 49 species or subspecies in three genera (Tanakia, Rhodeus, and Acheilognathus), sampled across the major part of their distribution, to elucidate their phylogeny and biogeography, focusing particularly on their origin and dispersal. Based on high support value, the monophyletic Acheilognathinae separated into two major clades, Acheilognathus and Tanakia-Rhodeus. In the latter clade, the monophyly of Rhodeus was poorly supported, though it was topologically nested in Tanakia. On the basis of molecular-clock calibration, both clades diverged in the middle Miocene, with Tanakia-Rhodeus diverging slightly earlier than Acheilognathus. The Tanakia-Rhodeus clade expanded its distribution westward from the Far East, eventually reaching Europe, while Acheilognathus dispersed in the temperate regions of East Asia. A feature common to both clades is that most extant species, including Japanese endemics, appeared by the end of the Pliocene, corresponding with the present delineation of the Japanese archipelago. Autumn-spawning species with an embryonic diapause, unique to bitterling among cyprinid fishes, formed two distinct lineages (barbatulusrhombeus and longipinnis-typus) within Acheilognathus. The estimated time of divergence of the two lineages was approximately from the late Pliocene, a period characterized by glaciations. The timing of divergence suggests that the shift of spawning from spring to autumn, coupled with embryonic diapause, convergently emerged twice in the evolution of bitterling, possibly as an adaptation to the climate of the late Pliocene.}, }
@article {pmid24827527, year = {2014}, author = {Rottenberg, H}, title = {Exceptional longevity and exceptionally high metabolic rates in anthropoid primates are linked to a major modification of the ubiquinone reduction site of cytochrome b.}, journal = {Journal of bioenergetics and biomembranes}, volume = {46}, number = {5}, pages = {435-445}, pmid = {24827527}, issn = {1573-6881}, mesh = {Age Factors ; Animals ; Basal Metabolism ; Cytochromes b/*metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Longevity ; Mammals ; Mitochondria/*metabolism ; Models, Molecular ; Oxidation-Reduction ; Primates ; Reactive Oxygen Species/metabolism ; Ubiquinone/*metabolism ; }, abstract = {The maximal lifespan of Anthropoid primates (monkeys, apes and humans) exceed the lifespan of most other mammals of equal body mass. Unexpectedly, their exceptional longevity is associated with exceptionally high metabolic rates, in apparent contradiction to the Free Radical Theory of Aging. It was therefore suggested that in anthropoid primates (and several other taxa of mammals and birds) the mitochondrial electron transport complexes evolved to modify the relationship between basal electron transport and superoxide generation to allow for the evolution of exceptional longevity. Cytochrome b, the core protein of the bc1 complex is a major source of superoxide. The amino-acid sequence of cytochrome b evolved much faster in anthropoid than in prosimian primates, and most other mammals, resulting in a large change in the amino-acids composition of the protein. As a result of these changes cytochrome b in anthropoid primates is significantly less hydrophobic and contains more polar residues than other primates and most other mammals. Most of these changes are clustered around the reduction site of uboiquinone. In particular a key positively charged residue, arginine 313, that interacts with propionate D of heme bH, and thus raises its redox potential, is substituted in anthropoid primates with the neutral residue glutamine, most likely resulting in a lower redox potential of heme bH and faster reduction of ubiquinone at high proton motive force. It is suggested that these changes contribute to the observed increased rates of basal metabolism and reduce the rates of superoxide production, thus allowing for increased lifespan.}, }
@article {pmid24825743, year = {2014}, author = {Harrison, E and MacLean, RC and Koufopanou, V and Burt, A}, title = {Sex drives intracellular conflict in yeast.}, journal = {Journal of evolutionary biology}, volume = {27}, number = {8}, pages = {1757-1763}, doi = {10.1111/jeb.12408}, pmid = {24825743}, issn = {1420-9101}, mesh = {Analysis of Variance ; *Biological Evolution ; DNA Primers/genetics ; Meiosis/*physiology ; Mitochondria/genetics/*physiology ; Models, Genetic ; Plasmids/genetics/*physiology ; Polymerase Chain Reaction ; Reproduction/genetics ; Reproduction, Asexual/genetics ; Saccharomyces cerevisiae/*genetics ; Selection, Genetic ; *Sex ; }, abstract = {Theory predicts that sex can drive the evolution of conflict within the cell. During asexual reproduction, genetic material within the cell is inherited as a single unit, selecting for cooperation both within the genome as well as between the extra-genomic elements within the cell (e.g. plasmids and endosymbionts). Under sexual reproduction, this unity is broken down as parental genomes are distributed between meiotic progeny. Genetic elements able to transmit to more than 50% of meiotic progeny have a transmission advantage over the rest of the genome and are able to spread, even where they reduce the fitness of the individual as a whole. Sexual reproduction is therefore expected to drive the evolution of selfish genetic elements (SGEs). Here, we directly test this hypothesis by studying the evolution of two independent SGEs, the 2-μm plasmid and selfish mitochondria, in populations of Saccharomyces cerevisiae. Following 22 rounds of sexual reproduction, 2-μm copy number increased by approximately 13.2 (±5.6) copies per cell, whereas in asexual populations copy number decreased by approximately 5.1 (±1.5) copies per cell. Given that the burden imposed by this parasite increases with copy number, these results support the idea that sex drives the evolution of increased SGE virulence. Moreover, we found that mitochondria that are respiratory-deficient rapidly invaded sexual but not asexual populations, demonstrating that frequent outcrossed sex can drive the de novo evolution of genetic parasites. Our study highlights the genomic perils of sex and suggests that SGEs may play a key role in driving major evolutionary transitions, such as uniparental inheritance.}, }
@article {pmid24824642, year = {2014}, author = {Salavirta, H and Oksanen, I and Kuuskeri, J and Mäkelä, M and Laine, P and Paulin, L and Lundell, T}, title = {Mitochondrial genome of Phlebia radiata is the second largest (156 kbp) among fungi and features signs of genome flexibility and recent recombination events.}, journal = {PloS one}, volume = {9}, number = {5}, pages = {e97141}, pmid = {24824642}, issn = {1932-6203}, mesh = {Base Sequence ; Basidiomycota/*genetics ; Bayes Theorem ; Chromosome Mapping ; Computational Biology ; Genes, Mitochondrial/genetics ; Genome Size/*genetics ; Genome, Mitochondrial/*genetics ; Models, Genetic ; Molecular Sequence Annotation ; Molecular Sequence Data ; *Phylogeny ; Recombination, Genetic/*genetics ; Sequence Analysis, DNA ; }, abstract = {Mitochondria are eukaryotic organelles supporting individual life-style via generation of proton motive force and cellular energy, and indispensable metabolic pathways. As part of genome sequencing of the white rot Basidiomycota species Phlebia radiata, we first assembled its mitochondrial genome (mtDNA). So far, the 156 348 bp mtDNA is the second largest described for fungi, and of considerable size among eukaryotes. The P. radiata mtDNA assembled as single circular dsDNA molecule containing genes for the large and small ribosomal RNAs, 28 transfer RNAs, and over 100 open reading frames encoding the 14 fungal conserved protein subunits of the mitochondrial complexes I, III, IV, and V. Two genes (atp6 and tRNA-IleGAU) were duplicated within 6.1 kbp inverted region, which is a unique feature of the genome. The large mtDNA size, however, is explained by the dominance of intronic and intergenic regions (sum 80% of mtDNA sequence). The intergenic DNA stretches harness short (≤ 200 nt) repetitive, dispersed and overlapping sequence elements in abundance. Long self-splicing introns of types I and II interrupt eleven of the conserved genes (cox1,2,3; cob; nad1,2,4,4L,5; rnl; rns). The introns embrace a total of 57 homing endonucleases with LAGLIDADGD and GYI-YIG core motifs, which makes P. radiata mtDNA to one of the largest known reservoirs of intron-homing endonucleases. The inverted duplication, intergenic stretches, and intronic features are indications of dynamics and genetic flexibility of the mtDNA, not fully recognized to this extent in fungal mitochondrial genomes previously, thus giving new insights for the evolution of organelle genomes in eukaryotes.}, }
@article {pmid24822055, year = {2014}, author = {Watanabe, Y and Suematsu, T and Ohtsuki, T}, title = {Losing the stem-loop structure from metazoan mitochondrial tRNAs and co-evolution of interacting factors.}, journal = {Frontiers in genetics}, volume = {5}, number = {}, pages = {109}, pmid = {24822055}, issn = {1664-8021}, abstract = {Conventional tRNAs have highly conserved sequences, four-armed cloverleaf secondary structures, and L-shaped tertiary structures. However, metazoan mitochondrial tRNAs contain several exceptional structures. Almost all tRNAs(Ser) for AGY/N codons lack the D-arm. Furthermore, in some nematodes, no four-armed cloverleaf-type tRNAs are present: two tRNAs(Ser) without the D-arm and 20 tRNAs without the T-arm are found. Previously, we showed that in nematode mitochondria, an extra elongation factor Tu (EF-Tu) has evolved to support interaction with tRNAs lacking the T-arm, which interact with C-terminal domain 3 in conventional EF-Tu. Recent mitochondrial genome analyses have suggested that in metazoan lineages other than nematodes, tRNAs without the T-arm are present. Furthermore, even more simplified tRNAs are predicted in some lineages. In this review, we discuss mitochondrial tRNAs with divergent structures, as well as protein factors, including EF-Tu, that support the function of truncated metazoan mitochondrial tRNAs.}, }
@article {pmid24821793, year = {2014}, author = {Schnarwiler, F and Niemann, M and Doiron, N and Harsman, A and Käser, S and Mani, J and Chanfon, A and Dewar, CE and Oeljeklaus, S and Jackson, CB and Pusnik, M and Schmidt, O and Meisinger, C and Hiller, S and Warscheid, B and Schnaufer, AC and Ochsenreiter, T and Schneider, A}, title = {Trypanosomal TAC40 constitutes a novel subclass of mitochondrial β-barrel proteins specialized in mitochondrial genome inheritance.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {21}, pages = {7624-7629}, pmid = {24821793}, issn = {1091-6490}, support = {095831/WT_/Wellcome Trust/United Kingdom ; G0600129/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Base Sequence ; Cell Line ; Cluster Analysis ; Cytoskeleton/metabolism ; DNA, Mitochondrial/metabolism ; Fluorescent Antibody Technique ; Genes, Mitochondrial/*genetics ; Mass Spectrometry ; Microscopy, Electron, Transmission ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/*genetics ; *Models, Biological ; Molecular Sequence Data ; Organisms, Genetically Modified ; Phylogeny ; Porins/*genetics ; Protozoan Proteins/*genetics ; Sequence Analysis, DNA ; Sequence Homology ; Trypanosoma brucei brucei/*genetics ; }, abstract = {Mitochondria cannot form de novo but require mechanisms allowing their inheritance to daughter cells. In contrast to most other eukaryotes Trypanosoma brucei has a single mitochondrion whose single-unit genome is physically connected to the flagellum. Here we identify a β-barrel mitochondrial outer membrane protein, termed tripartite attachment complex 40 (TAC40), that localizes to this connection. TAC40 is essential for mitochondrial DNA inheritance and belongs to the mitochondrial porin protein family. However, it is not specifically related to any of the three subclasses of mitochondrial porins represented by the metabolite transporter voltage-dependent anion channel (VDAC), the protein translocator of the outer membrane 40 (TOM40), or the fungi-specific MDM10, a component of the endoplasmic reticulum-mitochondria encounter structure (ERMES). MDM10 and TAC40 mediate cellular architecture and participate in transmembrane complexes that are essential for mitochondrial DNA inheritance. In yeast MDM10, in the context of the ERMES, is postulated to connect the mitochondrial genomes to actin filaments, whereas in trypanosomes TAC40 mediates the linkage of the mitochondrial DNA to the basal body of the flagellum. However, TAC40 does not colocalize with trypanosomal orthologs of ERMES components and, unlike MDM10, it regulates neither mitochondrial morphology nor the assembly of the protein translocase. TAC40 therefore defines a novel subclass of mitochondrial porins that is distinct from VDAC, TOM40, and MDM10. However, whereas the architecture of the TAC40-containing complex in trypanosomes and the MDM10-containing ERMES in yeast is very different, both are organized around a β-barrel protein of the mitochondrial porin family that mediates a DNA-cytoskeleton linkage that is essential for mitochondrial DNA inheritance.}, }
@article {pmid24819950, year = {2014}, author = {Wang, W and Scheffler, K and Esbensen, Y and Strand, JM and Stewart, JB and Bjørås, M and Eide, L}, title = {Addressing RNA integrity to determine the impact of mitochondrial DNA mutations on brain mitochondrial function with age.}, journal = {PloS one}, volume = {9}, number = {5}, pages = {e96940}, pmid = {24819950}, issn = {1932-6203}, mesh = {Aging/*genetics ; Animals ; Brain/*cytology/metabolism ; DNA, Mitochondrial/*genetics ; Female ; Male ; Mice ; Mice, Inbred C57BL ; Mitochondria/*genetics/*metabolism ; Mutagenesis ; *Mutation ; Mutation Rate ; RNA/*genetics ; RNA, Mitochondrial ; Transcription, Genetic/genetics ; }, abstract = {Mitochondrial DNA (mtDNA) mutations can result in mitochondrial dysfunction, but emerging experimental data question the fundamental role of mtDNA mutagenesis in age-associated mitochondrial impairment. The multicopy nature of mtDNA renders the impact of a given mtDNA mutation unpredictable. In this study, we compared mtDNA stability and mtRNA integrity during normal aging. Seven distinct sites in mouse brain mtDNA and corresponding mtRNA were analyzed. Accumulation of mtDNA mutations during aging was highly site-specific. The variation in mutation frequencies overrode the age-mediated increase by more than 100-fold and aging generally did not influence mtDNA mutagenesis. Errors introduced by mtRNA polymerase were also site-dependent and up to two hundred-fold more frequent than mtDNA mutations, and independent of mtDNA mutation frequency. We therefore conclude that mitochondrial transcription fidelity limits the impact of mtDNA mutations.}, }
@article {pmid24816719, year = {2014}, author = {Dehghan Nayeri, F and Yarizade, K}, title = {Bioinformatics study of delta-12 fatty acid desaturase 2 (FAD2) gene in oilseeds.}, journal = {Molecular biology reports}, volume = {41}, number = {8}, pages = {5077-5087}, pmid = {24816719}, issn = {1573-4978}, mesh = {Amino Acid Sequence ; Computational Biology ; Fatty Acid Desaturases/*genetics/metabolism ; Fatty Acids, Unsaturated/biosynthesis ; Linoleic Acid/biosynthesis ; Molecular Sequence Data ; Oleic Acid/biosynthesis ; Phylogeny ; Plant Oils/analysis ; Plant Proteins/*genetics/metabolism ; Plants/classification/genetics ; Seeds/chemistry/*genetics ; }, abstract = {Fatty acid desaturases constitute a group of enzymes that introduce double bonds into the hydrocarbon chains of fatty acids to produce unsaturated fatty acids. In plants, seed-specific delta-12 fatty acid desaturase 2 (FAD2) is responsible for the high content of linoleic acid by inserting a double bond at the delta-12 (omega-6) position of oleic acid. In this study, sixteen FAD2 and FAD2-2 protein sequences from oilseeds were analyzed by computational tools including two databases of the NCBI and EXPASY and data management tools such as SignalP, TMHMM, Psort, ProtParam, TargetP, PLACE and PlantCARE. These services were used to predict the protein properties such as molecular mass, pI, signal peptide, transmembrane and conserved domains, secondary and spatial structures. The polypeptide sequences were aligned and a neighbour-joining tree was constructed using MEGA5.1 to elucidate phylogenetic relationships among FAD2 genes. Based on the phylogenetic analysis species with high similarity in FAD2 sequence grouped together. FAD2 proteins include highly conserved histidine-rich motifs (HECGHH, HRRHH and HV[A/C/T]HH) that are located by three to five transmembrane anchors. For further investigations Sesamum indicum FAD2 was selected and analyzed by bioinformatics tools. Analysis showed no N-terminal signal peptide for probable localization of FAD2 protein in cytoplasmic organelles such as chloroplast, mitochondria and Golgi. Instead the C-terminal signaling motif YNNKL, Y(K/N)NKF or YRNKI allows FAD2 protein to selectively bind to and embed in the endoplasmic reticulum. FAD2 promoter contains different cis-regulatory elements involve in the biotic and abiotic stresses response or control of gene expression specifically in seeds.}, }
@article {pmid24815909, year = {2014}, author = {Grand, RS and Martienssen, R and O'Sullivan, JM}, title = {Potential roles for interactions between the mitochondrial and nuclear DNA throughout the cell cycle of Schizosaccharomyces pombe.}, journal = {Mitochondrion}, volume = {17}, number = {}, pages = {141-149}, pmid = {24815909}, issn = {1872-8278}, support = {R01 GM076396/GM/NIGMS NIH HHS/United States ; }, mesh = {*Cell Cycle ; DNA, Fungal/chemistry/*genetics/*metabolism ; DNA, Mitochondrial/chemistry/*genetics/*metabolism ; Gene Expression Profiling ; Molecular Sequence Data ; Schizosaccharomyces/genetics/*physiology ; Sequence Analysis, DNA ; }, abstract = {Over the course of mitochondrial evolution, the majority of genes required for its function have been transferred and integrated into nuclear chromosomes. Ongoing transfer of mitochondrial DNA to the nucleus has been detected, but its functional significance has not been fully elucidated. Here by Genome Conformation Capture, we identify DNA-DNA interactions between the mitochondrial and nuclear chromosomes (mt-nDNA interactions) that vary in strength and number between the G1, G2 and M phases of the fission yeast cell cycle. Mt-nDNA interactions captured in mitotic anaphase were associated with nuclear genes required for the regulation of cell growth and energy availability. Furthermore, mt-nDNA interactions captured in the G1 phase involved high efficiency, early firing origins of DNA replication. Collectively, these results suggest functional roles for the ongoing transfer of regions of the mitochondrial genome to the nucleus.}, }
@article {pmid24815812, year = {2014}, author = {Pfenninger, M and Lerp, H and Tobler, M and Passow, C and Kelley, JL and Funke, E and Greshake, B and Erkoc, UK and Berberich, T and Plath, M}, title = {Parallel evolution of cox genes in H2S-tolerant fish as key adaptation to a toxic environment.}, journal = {Nature communications}, volume = {5}, number = {}, pages = {3873}, doi = {10.1038/ncomms4873}, pmid = {24815812}, issn = {2041-1723}, mesh = {Adaptation, Physiological/*genetics ; Amino Acid Substitution ; Animals ; Base Sequence ; Electron Transport Complex IV/*genetics ; Environment ; Evolution, Molecular ; Hydrogen Sulfide/*adverse effects ; Mitochondria/genetics ; Phylogeny ; Poecilia/*genetics ; Sequence Analysis, DNA ; }, abstract = {Populations that repeatedly adapt to the same environmental stressor offer a unique opportunity to study adaptation, especially if there are a priori predictions about the genetic basis underlying phenotypic evolution. Hydrogen sulphide (H2S) blocks the cytochrome-c oxidase complex (COX), predicting the evolution of decreased H2S susceptibility of the COX in three populations in the Poecilia mexicana complex that have colonized H2S-containing springs. Here, we demonstrate that decreased H2S susceptibility of COX evolved in parallel in two sulphide lineages, as evidenced by shared amino acid substitutions in cox1 and cox3 genes. One of the shared substitutions likely triggers conformational changes in COX1 blocking the access of H2S. In a third sulphide population, we detect no decreased H2S susceptibility of COX, suggesting that H2S resistance is achieved through another mechanism. Our study thus demonstrates that even closely related lineages follow both parallel and disparate molecular evolutionary paths to adaptation in response to the same selection pressure.}, }
@article {pmid24810173, year = {2014}, author = {Ataya, FS and Al-Jafari, AA and Daoud, MS and Al-Hazzani, AA and Shehata, AI and Saeed, HM and Fouad, D}, title = {Genomics, phylogeny and in silico analysis of mitochondrial glutathione S-transferase-kappa from the camel Camelus dromedarius.}, journal = {Research in veterinary science}, volume = {97}, number = {1}, pages = {46-54}, doi = {10.1016/j.rvsc.2014.04.004}, pmid = {24810173}, issn = {1532-2661}, mesh = {Amino Acid Sequence ; Animals ; Camelus/*genetics ; Cattle ; Cloning, Molecular ; Computer Simulation ; DNA, Complementary/genetics ; Dogs ; Genomics ; Glutathione Transferase/analysis/*chemistry/*genetics ; Haplorhini ; Horses ; Humans ; Male ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Rats ; Swine ; }, abstract = {The domesticated one-humped camel, Camelus dromedarius, is one of the most important animals in the Arabian Peninsula. For most of its life, this species is exposed to both intrinsic and extrinsic genotoxic factors that cause gross DNA alterations in many organisms. GST enzymes constitute an important supergene family involved in protection against the deleterious effects of oxidative stress and xenobiotics. Cloning the camel mitochondrial GST kappa (GSTK) gene and comparing its structural similarities with different species may aid in understanding its evolutionary relics. We cloned the camel GSTK using RT-PCR. This yielded an open reading frame of 678 nucleotides, encoding a protein of 226 amino acid residues. In a comparative analysis, the cloned GSTK was used to screen orthologues from different organisms. Phylogenetic analysis demonstrated that the camel GSTK apparently evolved from an ancestral GSTK gene that predated the appearance of vertebrates, and it grouped with pig, cattle, dog, horse, human and monkey GSTKs. The calculated molecular weight of the translated ORF was 25.52 kDa and the isoelectric point was 8.4. The deduced cGSTK sequence exhibited high identity with many mammals, such as Bactrian camel (99.55%), pig, cattle and human (>74%), and lower identity with other unrelated organisms, such as frog (Xenopus tropicalis, 61%), chicken (Gallus gallus, 57%), salmon (Salmo salar, 49%), sponge (Amphimedon queenslandica, 46%), tick (Amblyomma maculatum, 45%) and roundworm (Caenorhabditis elegans, 33%). A 3D structure was built based on the crystal structure of the human and rat enzymes. The levels of cGSTK expression in five camel tissues were examined via real-time PCR. The highest level of cGSTK transcripts was found in the camel liver, followed by the testis, spleen, kidney and lung.}, }
@article {pmid24807248, year = {2014}, author = {Moné, Y and Monnin, D and Kremer, N}, title = {The oxidative environment: a mediator of interspecies communication that drives symbiosis evolution.}, journal = {Proceedings. Biological sciences}, volume = {281}, number = {1785}, pages = {20133112}, pmid = {24807248}, issn = {1471-2954}, mesh = {*Biological Evolution ; Environment ; Models, Biological ; *Oxidation-Reduction ; Reactive Nitrogen Species/metabolism ; Reactive Oxygen Species/metabolism ; Signal Transduction ; *Symbiosis ; }, abstract = {Symbiotic interactions are ubiquitous in nature and play a major role in driving the evolution of life. Interactions between partners are often mediated by shared signalling pathways, which strongly influence both partners' biology and the evolution of the association in various environments. As an example of 'common language', the regulation of the oxidative environment plays an important role in driving the evolution of symbiotic associations. Such processes have been occurring for billions of years, including the increase in Earth's atmospheric oxygen and the subsequent evolution of mitochondria. The effect of reactive oxygen species and reactive nitrogen species (RONS) has been characterized functionally, but the molecular dialogue between partners has not been integrated within a broader evolutionary context yet. Given the pleiotropic role of RONS in cell-cell communication, development and immunity, but also their associated physiological costs, we discuss here how their regulation can influence the establishment, the maintenance and the breakdown of various symbiotic associations. By synthesizing recent developments in redox biology, we aim to provide an interdisciplinary understanding of the influence of such mediators of interspecies communication on the evolution and stability of symbioses, which in turn can shape ecosystems and play a role in health and disease.}, }
@article {pmid24804722, year = {2014}, author = {Degli Esposti, M and Chouaia, B and Comandatore, F and Crotti, E and Sassera, D and Lievens, PM and Daffonchio, D and Bandi, C}, title = {Evolution of mitochondria reconstructed from the energy metabolism of living bacteria.}, journal = {PloS one}, volume = {9}, number = {5}, pages = {e96566}, pmid = {24804722}, issn = {1932-6203}, mesh = {Bacteria/genetics/*metabolism ; Energy Metabolism/*physiology ; *Evolution, Molecular ; Mitochondria/genetics/*metabolism ; *Phylogeny ; }, abstract = {The ancestors of mitochondria, or proto-mitochondria, played a crucial role in the evolution of eukaryotic cells and derived from symbiotic α-proteobacteria which merged with other microorganisms - the basis of the widely accepted endosymbiotic theory. However, the identity and relatives of proto-mitochondria remain elusive. Here we show that methylotrophic α-proteobacteria could be the closest living models for mitochondrial ancestors. We reached this conclusion after reconstructing the possible evolutionary pathways of the bioenergy systems of proto-mitochondria with a genomic survey of extant α-proteobacteria. Results obtained with complementary molecular and genetic analyses of diverse bioenergetic proteins converge in indicating the pathway stemming from methylotrophic bacteria as the most probable route of mitochondrial evolution. Contrary to other α-proteobacteria, methylotrophs show transition forms for the bioenergetic systems analysed. Our approach of focusing on these bioenergetic systems overcomes the phylogenetic impasse that has previously complicated the search for mitochondrial ancestors. Moreover, our results provide a new perspective for experimentally re-evolving mitochondria from extant bacteria and in the future produce synthetic mitochondria.}, }
@article {pmid24803639, year = {2014}, author = {Gillett, CP and Crampton-Platt, A and Timmermans, MJ and Jordal, BH and Emerson, BC and Vogler, AP}, title = {Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea).}, journal = {Molecular biology and evolution}, volume = {31}, number = {8}, pages = {2223-2237}, pmid = {24803639}, issn = {1537-1719}, mesh = {Animals ; DNA/analysis ; Evolution, Molecular ; Genome, Insect ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/*methods ; Models, Genetic ; Phylogeny ; Sequence Analysis, DNA/*methods ; Weevils/*classification/genetics ; }, abstract = {Complete mitochondrial genomes have been shown to be reliable markers for phylogeny reconstruction among diverse animal groups. However, the relative difficulty and high cost associated with obtaining de novo full mitogenomes have frequently led to conspicuously low taxon sampling in ensuing studies. Here, we report the successful use of an economical and accessible method for assembling complete or near-complete mitogenomes through shot-gun next-generation sequencing of a single library made from pooled total DNA extracts of numerous target species. To avoid the use of separate indexed libraries for each specimen, and an associated increase in cost, we incorporate standard polymerase chain reaction-based "bait" sequences to identify the assembled mitogenomes. The method was applied to study the higher level phylogenetic relationships in the weevils (Coleoptera: Curculionoidea), producing 92 newly assembled mitogenomes obtained in a single Illumina MiSeq run. The analysis supported a separate origin of wood-boring behavior by the subfamilies Scolytinae, Platypodinae, and Cossoninae. This finding contradicts morphological hypotheses proposing a close relationship between the first two of these but is congruent with previous molecular studies, reinforcing the utility of mitogenomes in phylogeny reconstruction. Our methodology provides a technically simple procedure for generating densely sampled trees from whole mitogenomes and is widely applicable to groups of animals for which bait sequences are the only required prior genome knowledge.}, }
@article {pmid24803502, year = {2014}, author = {Sage, RF and Khoshravesh, R and Sage, TL}, title = {From proto-Kranz to C4 Kranz: building the bridge to C4 photosynthesis.}, journal = {Journal of experimental botany}, volume = {65}, number = {13}, pages = {3341-3356}, doi = {10.1093/jxb/eru180}, pmid = {24803502}, issn = {1460-2431}, mesh = {Biological Evolution ; Cell Respiration ; Glycine/metabolism ; Light ; Mitochondria/ultrastructure ; Models, Biological ; *Photosynthesis ; Phylogeny ; Plant Vascular Bundle/anatomy &amp; histology/genetics/radiation effects ; Plants/*anatomy &amp; histology/genetics/radiation effects ; Species Specificity ; }, abstract = {In this review, we examine how the specialized "Kranz" anatomy of C4 photosynthesis evolved from C3 ancestors. Kranz anatomy refers to the wreath-like structural traits that compartmentalize the biochemistry of C4 photosynthesis and enables the concentration of CO2 around Rubisco. A simplified version of Kranz anatomy is also present in the species that utilize C2 photosynthesis, where a photorespiratory glycine shuttle concentrates CO2 into an inner bundle-sheath-like compartment surrounding the vascular tissue. C2 Kranz is considered to be an intermediate stage in the evolutionary development of C4 Kranz, based on the intermediate branching position of C2 species in 14 evolutionary lineages of C4 photosynthesis. In the best-supported model of C4 evolution, Kranz anatomy in C2 species evolved from C3 ancestors with enlarged bundle sheath cells and high vein density. Four independent lineages have been identified where C3 sister species of C2 plants exhibit an increase in organelle numbers in the bundle sheath and enlarged bundle sheath cells. Notably, in all of these species, there is a pronounced shift of mitochondria to the inner bundle sheath wall, forming an incipient version of the C2 type of Kranz anatomy. This incipient version of C2 Kranz anatomy is termed proto-Kranz, and is proposed to scavenge photorespiratory CO2. By doing so, it may provide fitness benefits in hot environments, and thus represent a critical first stage of the evolution of both the C2 and C4 forms of Kranz anatomy.}, }
@article {pmid24800637, year = {2014}, author = {Martínez-Romero, &#xcd; and Herrero-Martín, MD and Llobet, L and Emperador, S and Martín-Navarro, A and Narberhaus, B and Ascaso, FJ and López-Gallardo, E and Montoya, J and Ruiz-Pesini, E}, title = {New MT-ND1 pathologic mutation for Leber hereditary optic neuropathy.}, journal = {Clinical &amp; experimental ophthalmology}, volume = {42}, number = {9}, pages = {856-864}, doi = {10.1111/ceo.12355}, pmid = {24800637}, issn = {1442-9071}, mesh = {Adult ; Base Sequence ; DNA Mutational Analysis ; DNA, Mitochondrial/*genetics ; Humans ; Male ; Mitochondria/*genetics ; Molecular Sequence Data ; NADH Dehydrogenase/*genetics ; Optic Atrophy, Hereditary, Leber/diagnosis/*genetics ; Phenotype ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; *Polymorphism, Single Nucleotide ; Protein Structure, Secondary ; Visual Field Tests ; Visual Fields ; }, abstract = {BACKGROUND: Mutations causing Leber hereditary optic neuropathy are usually homoplasmic, show incomplete penetrance, and many of the affected positions are not well conserved through evolution. A large percentage of patients harbouring these mutations have no family history of disease. Moreover, the transfer of the mutation in the cybrid model is frequently not accompanied by the transfer of the cellular, biochemical and molecular phenotype. All these features make difficult their classification as the etiologic factors for this disease. We report a patient who exhibits typical clinical features of Leber hereditary optic neuropathy but lacks all three of the most common mitochondrial DNA mutations.<br><br>METHODS: The diagnosis was made based on clinical studies. The mitochondrial DNA was completely sequenced, and the candidate mutation was analysed in more than 18&#x2009;000 individuals around the world, its conservation index was estimated in more than 3100 species from protists to mammals, its position was modelled in the crystal structure of a bacteria ortholog subunit, and its functional consequences were studied in a cybrid model.<br><br>RESULTS: Genetic analysis revealed an m.3472T>C transition in the MT-ND1 gene that changes a phenylalanine to leucine at position 56. Bioinformatics, molecular-genetic analysis and functional studies suggest that this transition is the etiological factor for the disorder.<br><br>CONCLUSIONS: This mutation expands the spectrum of deleterious changes in mitochondrial DNA-encoded complex I polypeptides associated with this pathology and highlights the difficulties in assigning pathogenicity to new homoplasmic mutations that show incomplete penetrance in sporadic Leber hereditary optic neuropathy patients.}, }
@article {pmid24799711, year = {2014}, author = {Kaushal, PS and Sharma, MR and Booth, TM and Haque, EM and Tung, CS and Sanbonmatsu, KY and Spremulli, LL and Agrawal, RK}, title = {Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {20}, pages = {7284-7289}, pmid = {24799711}, issn = {1091-6490}, support = {R01 GM061576/GM/NIGMS NIH HHS/United States ; R01 GM072686/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Binding Sites ; Cattle ; Cryoelectron Microscopy ; Cytoplasm/metabolism ; GTP-Binding Proteins/metabolism ; Image Processing, Computer-Assisted ; Liver/metabolism ; Mitochondria/*metabolism ; Protein Conformation ; RNA, Messenger/metabolism ; RNA, Ribosomal, 16S/metabolism ; RNA, Transfer/metabolism ; Ribosomal Proteins/metabolism ; Ribosomes/*metabolism/*ultrastructure ; }, abstract = {The mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing 13 membrane proteins that form essential components of the complexes involved in oxidative phosphorylation or ATP generation for the eukaryotic cell. The mammalian 55S mitoribosome contains significantly smaller rRNAs and a large mass of mitochondrial ribosomal proteins (MRPs), including large mito-specific amino acid extensions and insertions in MRPs that are homologous to bacterial ribosomal proteins and an additional 35 mito-specific MRPs. Here we present the cryo-EM structure analysis of the small (28S) subunit (SSU) of the 55S mitoribosome. We find that the mito-specific extensions in homologous MRPs generally are involved in inter-MRP contacts and in contacts with mito-specific MRPs, suggesting a stepwise evolution of the current architecture of the mitoribosome. Although most of the mito-specific MRPs and extensions of homologous MRPs are situated on the peripheral regions, they also contribute significantly to the formation of linings of the mRNA and tRNA paths, suggesting a tailor-made structural organization of the mito-SSU for the recruitment of mito-specific mRNAs, most of which do not possess a 5' leader sequence. In addition, docking of previously published coordinates of the large (39S) subunit (LSU) into the cryo-EM map of the 55S mitoribosome reveals that mito-specific MRPs of both the SSU and LSU are involved directly in the formation of six of the 15 intersubunit bridges.}, }
@article {pmid24799670, year = {2014}, author = {Donthamsetty, S and Brahmbhatt, M and Pannu, V and Rida, PC and Ramarathinam, S and Ogden, A and Cheng, A and Singh, KK and Aneja, R}, title = {Mitochondrial genome regulates mitotic fidelity by maintaining centrosomal homeostasis.}, journal = {Cell cycle (Georgetown, Tex.)}, volume = {13}, number = {13}, pages = {2056-2063}, pmid = {24799670}, issn = {1551-4005}, support = {I01 BX001716/BX/BLRD VA/United States ; R01CA121904/CA/NCI NIH HHS/United States ; R00 CA131489/CA/NCI NIH HHS/United States ; R01 CA169127/CA/NCI NIH HHS/United States ; R00CA131489/CA/NCI NIH HHS/United States ; R01 CA121904/CA/NCI NIH HHS/United States ; }, mesh = {Cell Line, Tumor ; Cell Proliferation ; Centrosome/*metabolism ; DNA Damage ; DNA, Mitochondrial/metabolism ; Down-Regulation ; Electron Transport Complex I/metabolism ; Genome, Mitochondrial/*physiology ; Homeostasis ; Humans ; Mitosis/*genetics ; Reactive Oxygen Species/metabolism ; Spindle Apparatus/metabolism ; Telomere/ultrastructure ; Tumor Suppressor Protein p53/metabolism ; }, abstract = {Centrosomes direct spindle morphogenesis to assemble a bipolar mitotic apparatus to enable error-free chromosome segregation and preclude chromosomal instability (CIN). Amplified centrosomes, a hallmark of cancer cells, set the stage for CIN, which underlies malignant transformation and evolution of aggressive phenotypes. Several studies report CIN and a tumorigenic and/or aggressive transformation in mitochondrial DNA (mtDNA)-depleted cells. Although several nuclear-encoded proteins are implicated in centrosome duplication and spindle organization, the involvement of mtDNA encoded proteins in centrosome amplification (CA) remains elusive. Here we show that disruption of mitochondrial function by depletion of mtDNA induces robust CA and mitotic aberrations in osteosarcoma cells. We found that overexpression of Aurora A, Polo-like kinase 4 (PLK4), and Cyclin E was associated with emergence of amplified centrosomes. Supernumerary centrosomes in rho0 (mtDNA-depleted) cells resulted in multipolar mitoses bearing "real" centrosomes with paired centrioles at the multiple poles. This abnormal phenotype was recapitulated by inhibition of respiratory complex I in parental cells, suggesting a role for electron transport chain (ETC) in maintaining numeral centrosomal homeostasis. Furthermore, rho0 cells displayed a decreased proliferative capacity owing to a G 2/M arrest. Downregulation of nuclear-encoded p53 in rho0 cells underscores the importance of mitochondrial and nuclear genome crosstalk and may perhaps underlie the observed mitotic aberrations. By contrast, repletion of wild-type mtDNA in rho0 cells (cybrid) demonstrated a much lesser extent of CA and spindle multipolarity, suggesting partial restoration of centrosomal homeostasis. Our study provides compelling evidence to implicate the role of mitochondria in regulation of centrosome duplication, spindle architecture, and spindle pole integrity.}, }
@article {pmid24798004, year = {2014}, author = {van der Goot, GF}, title = {Introduction: brief historical overview.}, journal = {Sub-cellular biochemistry}, volume = {80}, number = {}, pages = {3-6}, doi = {10.1007/978-94-017-8881-6_1}, pmid = {24798004}, issn = {0306-0225}, mesh = {Animals ; Bacteria/metabolism ; Bacterial Toxins/chemistry/*metabolism/pharmacology ; Cell Membrane/*physiology ; Humans ; Perforin/chemistry/pharmacology/physiology ; Pore Forming Cytotoxic Proteins/chemistry/pharmacology/*physiology ; }, abstract = {Membranes are essential in defining the border and ensuring function of all living cells. As such they are vulnerable and have been a preferred target of attack throughout evolution. The most powerful way of damaging a membrane is through the insertion of pore-forming proteins. Research over the last decades shows that such proteins are produced by bacteria to attack bacterial or eukaryotic cells, vertebrates to kill invading organisms or infected cells, and by eukaryotic cells to "kill" mitochondria and trigger apoptosis. The breadth of effect of these proteins is bringing together, in a very exciting way, research communities that used to be unaware of each other.}, }
@article {pmid24791751, year = {2014}, author = {Hill, GE}, title = {Cellular respiration: the nexus of stress, condition, and ornamentation.}, journal = {Integrative and comparative biology}, volume = {54}, number = {4}, pages = {645-657}, doi = {10.1093/icb/icu029}, pmid = {24791751}, issn = {1557-7023}, mesh = {Adenosine Triphosphate ; Animals ; Mitochondria/*physiology ; Oxidative Phosphorylation ; Oxygen Consumption/*physiology ; Sex Characteristics ; Stress, Physiological/*physiology ; }, abstract = {A fundamental hypothesis for the evolution and maintenance of ornamental traits is that ornaments convey information to choosing females about the quality of prospective mates. A diverse array of ornaments (e.g., colors, morphological features, and behaviors) has been associated with a wide range of measures of individual quality, but decades of study of such indicator traits have failed to produce general mechanisms of honest signaling. Here, I propose that efficiency of cellular respiration, as a product of mitochondrial function, underlies the associations between ornamentation and performance for a broad range of traits across taxa. A large biomedical literature documents the fundamental biochemical links between oxidative phosphorylation (OXPHOS) and the production of reactive oxygen species (ROS), the process of metabolism, the function of the immune system, the synthesis of proteins, and the development and function of the nervous system. The production of virtually all ornaments whose expressions have been demonstrated to be condition-dependent is directly affected by the efficiency of cellular respiration, suggesting that the signaling of respiratory efficiency may be the primary function of such traits. Furthermore, the production of ornaments links to stress-response systems, including particularly the neuroendocrine system, through mitochondrial function, thereby makes ornamental traits effective signals of the capacity to withstand environmental perturbations. The identification of a unifying mechanism of honest signaling holds the potential to connect many heretofore-disparate fields of study related to stress and ornamentation, including neuroendocrinology, respiratory physiology, metabolic physiology, and immunology.}, }
@article {pmid24789818, year = {2014}, author = {Lane, N}, title = {Bioenergetic constraints on the evolution of complex life.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {6}, number = {5}, pages = {a015982}, pmid = {24789818}, issn = {1943-0264}, mesh = {Animals ; *Biological Evolution ; Carbon Dioxide/metabolism ; *Energy Metabolism ; Gene Dosage ; Humans ; Mitochondria/metabolism ; Origin of Life ; Proteins/metabolism ; Symbiosis ; }, abstract = {All morphologically complex life on Earth, beyond the level of cyanobacteria, is eukaryotic. All eukaryotes share a common ancestor that was already a complex cell. Despite their biochemical virtuosity, prokaryotes show little tendency to evolve eukaryotic traits or large genomes. Here I argue that prokaryotes are constrained by their membrane bioenergetics, for fundamental reasons relating to the origin of life. Eukaryotes arose in a rare endosymbiosis between two prokaryotes, which broke the energetic constraints on prokaryotes and gave rise to mitochondria. Loss of almost all mitochondrial genes produced an extreme genomic asymmetry, in which tiny mitochondrial genomes support, energetically, a massive nuclear genome, giving eukaryotes three to five orders of magnitude more energy per gene than prokaryotes. The requirement for endosymbiosis radically altered selection on eukaryotes, potentially explaining the evolution of unique traits, including the nucleus, sex, two sexes, speciation, and aging.}, }
@article {pmid24788869, year = {2014}, author = {Kwan, JC and Tianero, MD and Donia, MS and Wyche, TP and Bugni, TS and Schmidt, EW}, title = {Host control of symbiont natural product chemistry in cryptic populations of the tunicate Lissoclinum patella.}, journal = {PloS one}, volume = {9}, number = {5}, pages = {e95850}, pmid = {24788869}, issn = {1932-6203}, support = {R01 GM092009/GM/NIGMS NIH HHS/United States ; GM092009/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*metabolism ; Base Sequence ; Biological Products/*chemistry/metabolism ; Electron Transport Complex IV/genetics ; *Host-Pathogen Interactions ; Mitochondria/enzymology ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; *Symbiosis ; Urochordata/*chemistry/genetics/metabolism/*microbiology ; }, abstract = {Natural products (secondary metabolites) found in marine invertebrates are often thought to be produced by resident symbiotic bacteria, and these products appear to play a major role in the symbiotic interaction of bacteria and their hosts. In these animals, there is extensive variation, both in chemistry and in the symbiotic bacteria that produce them. Here, we sought to answer the question of what factors underlie chemical variation in the ocean. As a model, we investigated the colonial tunicate Lissoclinum patella because of its rich and varied chemistry and its broad geographic range. We sequenced mitochondrial cytochrome c oxidase 1 (COXI) genes, and found that animals classified as L. patella fall into three phylogenetic groups that may encompass several cryptic species. The presence of individual natural products followed the phylogenetic relationship of the host animals, even though the compounds are produced by symbiotic bacteria that do not follow host phylogeny. In sum, we show that cryptic populations of animals underlie the observed chemical diversity, suggesting that the host controls selection for particular secondary metabolite pathways. These results imply novel approaches to obtain chemical diversity from the oceans, and also demonstrate that the diversity of marine natural products may be greatly impacted by cryptic local extinctions.}, }
@article {pmid24786592, year = {2014}, author = {Mueller, SJ and Reski, R}, title = {Evolution and communication of subcellular compartments: An integrated approach.}, journal = {Plant signaling &amp; behavior}, volume = {9}, number = {}, pages = {}, pmid = {24786592}, issn = {1559-2324}, abstract = {Compartmentation is a fundamental feature of eukaryotic cells and the basis for metabolic complexity. We recently reported on the protein compartmentation in the moss Physcomitrella patens. This study utilized a combination of quantitative proteomics, comparative genomics, and single protein tagging and provided data on the postendosymbiotic evolution of plastids and mitochondria, on organellar communication, as well as on inter- and intracellular heterogeneity of organelles. We highlight potential organelle interaction hubs with specific protein content such as plastid stromules, and report on the plasticity of protein targeting to organelles.}, }
@article {pmid24782883, year = {2014}, author = {Rigas, S and Daras, G and Tsitsekian, D and Alatzas, A and Hatzopoulos, P}, title = {Evolution and significance of the Lon gene family in Arabidopsis organelle biogenesis and energy metabolism.}, journal = {Frontiers in plant science}, volume = {5}, number = {}, pages = {145}, pmid = {24782883}, issn = {1664-462X}, abstract = {Lon is the first identified ATP-dependent protease highly conserved across all kingdoms. Model plant species Arabidopsis thaliana has a small Lon gene family of four members. Although these genes share common structural features, they have distinct properties in terms of gene expression profile, subcellular targeting and substrate recognition motifs. This supports the notion that their functions under different environmental conditions are not necessarily redundant. This article intends to unravel the biological role of Lon proteases in energy metabolism and plant growth through an evolutionary perspective. Given that plants are sessile organisms exposed to diverse environmental conditions and plant organelles are semi-autonomous, it is tempting to suggest that Lon genes in Arabidopsis are paralogs. Adaptive evolution through repetitive gene duplication events of a single archaic gene led to Lon genes with complementing sets of subfunctions providing to the organism rapid adaptability for canonical development under different environmental conditions. Lon1 function is adequately characterized being involved in mitochondrial biogenesis, modulating carbon metabolism, oxidative phosphorylation and energy supply, all prerequisites for seed germination and seedling establishment. Lon is not a stand-alone proteolytic machine in plant organelles. Lon in association with other nuclear-encoded ATP-dependent proteases builds up an elegant nevertheless, tight interconnected circuit. This circuitry channels properly and accurately, proteostasis and protein quality control among the distinct subcellular compartments namely mitochondria, chloroplasts, and peroxisomes.}, }
@article {pmid24781019, year = {2014}, author = {Mohanta, UK and Ichikawa-Seki, M and Shoriki, T and Katakura, K and Itagaki, T}, title = {Characteristics and molecular phylogeny of Fasciola flukes from Bangladesh, determined based on spermatogenesis and nuclear and mitochondrial DNA analyses.}, journal = {Parasitology research}, volume = {113}, number = {7}, pages = {2493-2501}, pmid = {24781019}, issn = {1432-1955}, mesh = {Animals ; Bangladesh ; Buffaloes/parasitology ; Cattle ; Cell Nucleus/chemistry ; DNA, Helminth/*genetics ; DNA, Intergenic/*genetics ; DNA, Mitochondrial/*genetics ; Fasciola hepatica/*classification/genetics ; Goats/parasitology ; Haplotypes ; Host Specificity ; Male ; Mitochondria/chemistry ; NADH Dehydrogenase/genetics ; *Phylogeny ; Phylogeography ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sheep/parasitology ; Spermatogenesis/*genetics ; }, abstract = {This study aimed to precisely discriminate Fasciola spp. based on DNA sequences of nuclear internal transcribed spacer 1 (ITS1) and mitochondrial nicotinamide adenine dinucleotide (NADH) dehydrogenase subunit 1 (nad1) gene. We collected 150 adult flukes from the bile ducts of cattle, buffaloes, sheep, and goats from six different regions of Bangladesh. Spermatogenic status was determined by analyzing stained seminal vesicles. The ITS1 types were analyzed using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The nad1 haplotypes were identified based on PCR and direct sequencing and analyzed phylogenetically by comparing with nad1 haplotypes of Fasciola spp. from other Asian countries. Of the 127 aspermic flukes, 98 were identified as Fg type in ITS1, whereas 29 were identified as Fh/Fg type, indicating a combination of ITS1 sequences of Fasciola hepatica and Fasciola gigantica. All the 127 aspermic flukes showed Fsp-NDI-Bd11 in nad1 haplotype with nucleotide sequences identical to aspermic Fasciola sp. from Asian countries. Further, 20 spermic flukes were identified as F. gigantica based on their spermatogenic status and Fg type in ITS1. F. gigantica population was thought to be introduced into Bangladesh considerably earlier than the aspermic Fasciola sp. because 11 haplotypes with high haplotype diversity were detected from the F. gigantica population. However, three flukes from Bangladesh could not be precisely identified, because their spermatogenic status, ITS1 types, and nad1 haplotypes were ambiguous. Therefore, developing a robust method to distinguish aspermic Fasciola sp. from other Fasciola species is necessary in the future.}, }
@article {pmid24780263, year = {2014}, author = {Hyodo, M and Sakurai, Y and Akita, H and Harashima, H}, title = {"Programmed packaging" for gene delivery.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {193}, number = {}, pages = {316-323}, doi = {10.1016/j.jconrel.2014.04.023}, pmid = {24780263}, issn = {1873-4995}, mesh = {Drug Carriers/chemistry ; Drug Delivery Systems/*methods ; *Gene Transfer Techniques ; Humans ; Intracellular Space/metabolism ; Lipids/chemistry ; Nanoparticles/chemistry ; Neoplasms/genetics/therapy ; RNA, Small Interfering/*administration &amp; dosage/genetics/pharmacokinetics ; Transfection ; }, abstract = {We report on the development of a multifunctional envelope-type nano device (MEND) based on our packaging concept "Programmed packaging" to control not only intracellular trafficking but also the biodistribution of encapsulated compounds such as nucleic acids/proteins/peptides. Our strategy for achieving this is based on molecular mechanisms of cell biology such as endocytosis, vesicular trafficking, etc. In this review, we summarize the concept of programmed packaging and discuss some of our recent successful examples of using MENDs. Systematic evolution of ligands by exponential enrichment (SELEX) was applied as a new methodology for identifying a new ligand toward cell or mitochondria. The delivery of siRNA to tumors and the tumor vasculature was achieved using pH sensitive lipid (YSK05), which was newly designed and optimized under in vivo conditions. The efficient delivery of pDNA to immune cells such as dendritic cells has also been developed using the KALA ligand, which can be a breakthrough technology for DNA vaccine. Finally, ss-cleavable and pH-activated lipid-like surfactant (ssPalm) which is a lipid like material with pH-activatable and SS-cleavable properties is also introduced as a proof of our concept.}, }
@article {pmid24779998, year = {2014}, author = {Zaspel, JM and Scott, CH and Hill, SR and Ignell, R and Kononenko, VS and Weller, SJ}, title = {Geographic distribution, phylogeny, and genetic diversity of the fruit- and blood-feeding moth Calyptra thalictri Borkhausen (Insecta: Lepidoptera: Erebidae).}, journal = {The Journal of parasitology}, volume = {100}, number = {5}, pages = {583-591}, doi = {10.1645/13-484.1}, pmid = {24779998}, issn = {1937-2345}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Biomarkers ; Climate ; DNA/chemistry/isolation &amp; purification ; *Genetic Variation ; Genetics, Population ; Geography ; Likelihood Functions ; Male ; Mitochondria/genetics ; Models, Biological ; Moths/classification/genetics/*physiology ; *Phylogeny ; Sequence Alignment ; }, abstract = {Facultative blood feeding on live animals or carrion is widespread within Lepidoptera. Male moths within the genus Calyptra are known to use their fruit-piercing mouthparts to occasionally feed on mammalian blood. The Palearctic species Calyptra thalictri is known to exhibit differential feeding behaviors that appear to be based on geographic location. This species is known to pierce fruit throughout its range but has recently been reported to also feed on human blood under experimental conditions in the Russian Far East. Here we document the distribution of this widespread species, reconstruct its evolutionary history, and calculate its genetic diversity for the first time. Recently collected samples are combined with museum specimens to model suitable environments for this taxon. Our findings suggest that while the blood-feeding populations are not monophyletic, there is geographical structure. Our analysis of macroclimate variables suggests that altitude and precipitation are the environmental variables most critical to habitat suitability in this lineage.}, }
@article {pmid24771619, year = {2014}, author = {Misonou, Y and Kikuchi, M and Sato, H and Inai, T and Kuroiwa, T and Tanaka, K and Miyakawa, I}, title = {Aldehyde dehydrogenase, Ald4p, is a major component of mitochondrial fluorescent inclusion bodies in the yeast Saccharomyces cerevisiae.}, journal = {Biology open}, volume = {3}, number = {5}, pages = {387-396}, pmid = {24771619}, issn = {2046-6390}, abstract = {When Saccharomyces cerevisiae strain 3626 was cultured to the stationary phase in a medium that contained glucose, needle-like structures that emitted autofluorescence were observed in almost all cells by fluorescence microscopy under UV excitation. The needle-like structures completely overlapped with the profile of straight elongated mitochondria. Therefore, these structures were designated as mitochondrial fluorescent inclusion bodies (MFIBs). The MFIB-enriched mitochondrial fractions were successfully isolated and 2D-gel electrophoresis revealed that a protein of 54 kDa was only highly concentrated in the fractions. Determination of the N-terminal amino acid sequence of the 54-kDa protein identified it as a mitochondrial aldehyde dehydrogenase, Ald4p. Immunofluorescence microscopy showed that anti-Ald4p antibody specifically stained MFIBs. Freeze-substitution electron microscopy demonstrated that cells that retained MFIBs had electron-dense filamentous structures with a diameter of 10 nm in straight elongated mitochondria. Immunoelectron microscopy showed that Ald4p was localized to the electron-dense filamentous structures in mitochondria. These results together showed that a major component of MFIBs is Ald4p. In addition, we demonstrate that MFIBs are common features that appear in mitochondria of many species of yeast.}, }
@article {pmid24769053, year = {2014}, author = {Touzet, P and Meyer, EH}, title = {Cytoplasmic male sterility and mitochondrial metabolism in plants.}, journal = {Mitochondrion}, volume = {19 Pt B}, number = {}, pages = {166-171}, doi = {10.1016/j.mito.2014.04.009}, pmid = {24769053}, issn = {1872-8278}, mesh = {Cell Respiration ; *Gametogenesis ; Mitochondria/*genetics/*metabolism ; *Plant Physiological Phenomena ; Pollen/*genetics/*physiology ; }, abstract = {Cytoplasmic male sterility (CMS) is a common feature encountered in plant species. It is the result of a genomic conflict between the mitochondrial and the nuclear genomes. CMS is caused by mitochondrial encoded factors which can be counteracted by nuclear encoded factors restoring male fertility. Despite extensive work, the molecular mechanism of male sterility still remains unknown. Several studies have suggested the involvement of respiration on the disruption of pollen production through an energy deficiency. By comparing recent works on CMS and respiratory mutants, we suggest that the "ATP hypothesis" might not be as obvious as previously suggested.}, }
@article {pmid24766822, year = {2014}, author = {Hornok, S and Kontschán, J and Kováts, D and Kovács, R and Angyal, D and Görföl, T and Polacsek, Z and Kalmár, Z and Mihalca, AD}, title = {Bat ticks revisited: Ixodes ariadnae sp. nov. and allopatric genotypes of I. vespertilionis in caves of Hungary.}, journal = {Parasites &amp; vectors}, volume = {7}, number = {}, pages = {202}, pmid = {24766822}, issn = {1756-3305}, mesh = {Animals ; Caves ; Chiroptera/*parasitology ; Electron Transport Complex IV/genetics/metabolism ; Female ; *Genotype ; Hungary/epidemiology ; Ixodes/*classification/*genetics ; Larva/classification/genetics ; Male ; Mitochondria/enzymology ; Nymph/classification/genetics ; Phylogeny ; Seasons ; Tick Infestations/epidemiology/parasitology/*veterinary ; }, abstract = {BACKGROUND: In Europe two ixodid bat tick species, Ixodes vespertilionis and I. simplex were hitherto known to occur.<br><br>METHODS: Bat ticks were collected from cave walls and bats in Hungary. Their morphology and genotypes were compared with microscopy and conventional PCR (followed by sequencing), respectively.<br><br>RESULTS: A year-round activity of I. vespertilionis was observed. Molecular analysis of the cytochrome oxidase subunit I (COI) gene of twenty ticks from different caves showed that the occurrence of the most common genotype was associated with the caves close to each other. A few specimens of a morphologically different tick variant were also found and their COI analysis revealed only 86-88% sequence homology with I. simplex and I. vespertilionis, respectively.<br><br>CONCLUSIONS: The microenvironment of caves (well separated from each other) appears to support the existence of allopatric I. vespertilionis COI genotypes, most likely related to the distance between caves and to bat migration over-bridging certain caves. The name I. ariadnae sp. nov. is given to the new tick species described here for the first time.}, }
@article {pmid24743154, year = {2014}, author = {Chien, CI and Chen, YW and Wu, YH and Chang, CY and Wang, TL and Wang, CC}, title = {Functional substitution of a eukaryotic glycyl-tRNA synthetase with an evolutionarily unrelated bacterial cognate enzyme.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e94659}, pmid = {24743154}, issn = {1932-6203}, mesh = {Aminoacylation ; Animals ; Bacteria/enzymology ; Base Sequence ; Cloning, Molecular ; Eukaryota/*enzymology ; *Evolution, Molecular ; Gene Knockout Techniques ; Glycine-tRNA Ligase/chemistry/deficiency/genetics/*metabolism ; Humans ; Mitochondria/genetics/metabolism ; Protein Multimerization ; Protein Structure, Quaternary ; Protein Transport ; }, abstract = {Two oligomeric types of glycyl-tRNA synthetase (GlyRS) are found in nature: a α2 type and a α2β2 type. The former has been identified in all three kingdoms of life and often pairs with tRNAGly that carries an A73 discriminator base, while the latter is found only in bacteria and chloroplasts and is almost always coupled with tRNAGly that contains U73. In the yeast Saccharomyces cerevisiae, a single GlyRS gene, GRS1, provides both the cytoplasmic and mitochondrial functions, and tRNAGly isoacceptors in both compartments possess A73. We showed herein that Homo sapiens and Arabidopsis thaliana cytoplasmic GlyRSs (both α2-type enzymes) can rescue both the cytoplasmic and mitochondrial defects of a yeast grs1- strain, while Escherichia coli GlyRS (a α2β2-type enzyme) and A. thaliana organellar GlyRS (a (αβ)2-type enzyme) failed to rescue either defect of the yeast mull allele. However, a head-to-tail αβ fusion of E. coli GlyRS effectively supported the mitochondrial function. Our study suggests that a α2-type eukaryotic GlyRS may be functionally substituted with a α2β2-type bacterial cognate enzyme despite their remote evolutionary relationships.}, }
@article {pmid24726960, year = {2014}, author = {Hu, L and Zhao, YE and Cheng, J and Ma, JX}, title = {Molecular identification of four phenotypes of human Demodex in China.}, journal = {Experimental parasitology}, volume = {142}, number = {}, pages = {38-42}, doi = {10.1016/j.exppara.2014.04.003}, pmid = {24726960}, issn = {1090-2449}, mesh = {Animals ; China ; Electron Transport Complex IV/genetics ; Humans ; Mites/anatomy &amp; histology/*classification/genetics ; Mitochondria/enzymology ; Phenotype ; Phylogeny ; }, abstract = {Traditional classification of Demodex mites by hosts and phenotypic characteristics is defective because of environmental influences. In this study, we proposed molecular identification of four phenotypes of two human Demodex species based on mitochondrial cox1 fragments for the first time. Mites collected from sufferers' facial skin were classified into four phenotypes: phenotype A-C with finger-like terminus, and phenotype D with cone-like terminus. The results of molecular data showed that cox1 sequences were all 429 bp. Divergences, genetic distances and transition/transversion ratios among the three phenotypes with finger-like terminus were 0.0-3.0%, 0.000-0.031, and 6/3-5/0, respectively, in line with intraspecific differences. However, those measures between the phenotype with cone-like terminus and phenotypes with finger-like terminus were 19.6-20.5%, 0.256-0.271, and 0.58 (31/53)-0.66 (35/53), respectively, reaching interspecific level. Phylogenetic trees also showed that the three phenotypes with finger-like terminus clustered as one clade, and the phenotype with cone-like terminus formed another one. Therefore, we conclude that mitochondrial cox1 sequence is a good marker for identification of two human Demodex species. Molecular data indicate no subspecies differentiation. Terminus is an effective character for species identification. Mites with finger-like terminus are Demodex folliculorum, and those with cone-like terminus are Demodex brevis.}, }
@article {pmid24718683, year = {2014}, author = {Zhao, Y and Cai, M and Zhang, X and Li, Y and Zhang, J and Zhao, H and Kong, F and Zheng, Y and Qiu, F}, title = {Genome-wide identification, evolution and expression analysis of mTERF gene family in maize.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e94126}, pmid = {24718683}, issn = {1932-6203}, mesh = {Adaptation, Physiological/genetics ; Amino Acid Motifs ; Amino Acid Sequence ; Basic-Leucine Zipper Transcription Factors/chemistry/classification/*genetics/physiology ; Chloroplast Proteins/chemistry/classification/genetics/physiology ; Chromosome Mapping ; Chromosomes, Plant/genetics ; Conserved Sequence ; Gene Duplication ; Gene Expression Regulation, Plant/drug effects/radiation effects ; *Genes, Plant ; Light ; Mitochondrial Proteins/chemistry/classification/*genetics/physiology ; Models, Molecular ; Molecular Sequence Data ; Organ Specificity ; Phylogeny ; Plant Growth Regulators/pharmacology ; Plant Leaves/metabolism ; Plant Proteins/chemistry/classification/*genetics/physiology ; Promoter Regions, Genetic/genetics ; Protein Conformation ; Salts/pharmacology ; Seedlings/drug effects/growth &amp; development/metabolism/radiation effects ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Zea mays/drug effects/*genetics/growth &amp; development/radiation effects ; }, abstract = {Plant mitochondrial transcription termination factor (mTERF) genes comprise a large family with important roles in regulating organelle gene expression. In this study, a comprehensive database search yielded 31 potential mTERF genes in maize (Zea mays L.) and most of them were targeted to mitochondria or chloroplasts. Maize mTERF were divided into nine main groups based on phylogenetic analysis, and group IX represented the mitochondria and species-specific clade that diverged from other groups. Tandem and segmental duplication both contributed to the expansion of the mTERF gene family in the maize genome. Comprehensive expression analysis of these genes, using microarray data and RNA-seq data, revealed that these genes exhibit a variety of expression patterns. Environmental stimulus experiments revealed differential up or down-regulation expression of maize mTERF genes in seedlings exposed to light/dark, salts and plant hormones, respectively, suggesting various important roles of maize mTERF genes in light acclimation and stress-related responses. These results will be useful for elucidating the roles of mTERF genes in the growth, development and stress response of maize.}, }
@article {pmid24718596, year = {2014}, author = {Fourrage, C and Swann, K and Gonzalez Garcia, JR and Campbell, AK and Houliston, E}, title = {An endogenous green fluorescent protein-photoprotein pair in Clytia hemisphaerica eggs shows co-targeting to mitochondria and efficient bioluminescence energy transfer.}, journal = {Open biology}, volume = {4}, number = {4}, pages = {130206}, pmid = {24718596}, issn = {2046-2441}, mesh = {Amino Acid Sequence ; Animals ; Fluorescence Resonance Energy Transfer ; Green Fluorescent Proteins/genetics/*metabolism ; Hydrozoa/growth &amp; development/*metabolism ; Life Cycle Stages ; Luminescent Proteins/classification/genetics/*metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Ovum/metabolism ; Recombinant Fusion Proteins/biosynthesis/genetics ; Sequence Alignment ; }, abstract = {Green fluorescent proteins (GFPs) and calcium-activated photoproteins of the aequorin/clytin family, now widely used as research tools, were originally isolated from the hydrozoan jellyfish Aequora victoria. It is known that bioluminescence resonance energy transfer (BRET) is possible between these proteins to generate flashes of green light, but the native function and significance of this phenomenon is unclear. Using the hydrozoan Clytia hemisphaerica, we characterized differential expression of three clytin and four GFP genes in distinct tissues at larva, medusa and polyp stages, corresponding to the major in vivo sites of bioluminescence (medusa tentacles and eggs) and fluorescence (these sites plus medusa manubrium, gonad and larval ectoderms). Potential physiological functions at these sites include UV protection of stem cells for fluorescence alone, and prey attraction and camouflaging counter-illumination for bioluminescence. Remarkably, the clytin2 and GFP2 proteins, co-expressed in eggs, show particularly efficient BRET and co-localize to mitochondria, owing to parallel acquisition by the two genes of mitochondrial targeting sequences during hydrozoan evolution. Overall, our results indicate that endogenous GFPs and photoproteins can play diverse roles even within one species and provide a striking and novel example of protein coevolution, which could have facilitated efficient or brighter BRET flashes through mitochondrial compartmentalization.}, }
@article {pmid24717771, year = {2014}, author = {Rak, M and Rustin, P}, title = {Supernumerary subunits NDUFA3, NDUFA5 and NDUFA12 are required for the formation of the extramembrane arm of human mitochondrial complex I.}, journal = {FEBS letters}, volume = {588}, number = {9}, pages = {1832-1838}, doi = {10.1016/j.febslet.2014.03.046}, pmid = {24717771}, issn = {1873-3468}, mesh = {Electron Transport Complex I/*metabolism ; Enzyme Stability ; Gene Knockdown Techniques ; HEK293 Cells ; Humans ; Mitochondria/enzymology ; Mitochondrial Membranes/enzymology ; NADH Dehydrogenase/*genetics/metabolism ; NADPH Dehydrogenase/*genetics/metabolism ; Protein Multimerization ; Protein Subunits/genetics/metabolism ; RNA Interference ; }, abstract = {Mammalian complex I is composed of fourteen highly conserved core subunits and additional thirty subunits acquired in the course of evolution. At present, the function of the majority of these supernumerary subunits is poorly understood. In this work, we have studied NDUFA3, NDUFA5 and NDUFA12 supernumerary subunits to gain insight into their role in CI activity and biogenesis. Using human cell lines in which the expression of these subunits was knocked down with miRNAs, we showed that they are necessary for the formation of a functional holoenzyme. Analysis of the assembly intermediates in mitochondria depleted for these subunits further suggested that they are required for assembly and/or stability of the electron transferring Q module in the peripheral arm of the CI.}, }
@article {pmid24711422, year = {2014}, author = {Lang, BF and Jakubkova, M and Hegedusova, E and Daoud, R and Forget, L and Brejova, B and Vinar, T and Kosa, P and Fricova, D and Nebohacova, M and Griac, P and Tomaska, L and Burger, G and Nosek, J}, title = {Massive programmed translational jumping in mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {16}, pages = {5926-5931}, pmid = {24711422}, issn = {1091-6490}, support = {MOP-79309//Canadian Institutes of Health Research/Canada ; }, mesh = {Carbon/pharmacology ; DNA, Mitochondrial/metabolism ; Fermentation/drug effects/genetics ; Genes, Fungal/genetics ; Genes, Mitochondrial/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Mutagenesis, Insertional/genetics ; Open Reading Frames/genetics ; Phylogeny ; Protein Biosynthesis/*genetics ; RNA Processing, Post-Transcriptional/drug effects/genetics ; RNA, Messenger/genetics/metabolism ; Yeasts/drug effects/*genetics/growth &amp; development ; }, abstract = {Programmed translational bypassing is a process whereby ribosomes "ignore" a substantial interval of mRNA sequence. Although discovered 25 y ago, the only experimentally confirmed example of this puzzling phenomenon is expression of the bacteriophage T4 gene 60. Bypassing requires translational blockage at a "takeoff codon" immediately upstream of a stop codon followed by a hairpin, which causes peptidyl-tRNA dissociation and reassociation with a matching "landing triplet" 50 nt downstream, where translation resumes. Here, we report 81 translational bypassing elements (byps) in mitochondria of the yeast Magnusiomyces capitatus and demonstrate in three cases, by transcript analysis and proteomics, that byps are retained in mitochondrial mRNAs but not translated. Although mitochondrial byps resemble the bypass sequence in the T4 gene 60, they utilize unused codons instead of stops for translational blockage and have relaxed matching rules for takeoff/landing sites. We detected byp-like sequences also in mtDNAs of several Saccharomycetales, indicating that byps are mobile genetic elements. These byp-like sequences lack bypassing activity and are tolerated when inserted in-frame in variable protein regions. We hypothesize that byp-like elements have the potential to contribute to evolutionary diversification of proteins by adding new domains that allow exploration of new structures and functions.}, }
@article {pmid24709562, year = {2014}, author = {Hirakawa, Y and Ishida, K}, title = {Polyploidy of endosymbiotically derived genomes in complex algae.}, journal = {Genome biology and evolution}, volume = {6}, number = {4}, pages = {974-980}, pmid = {24709562}, issn = {1759-6653}, mesh = {Cryptophyta/*genetics ; DNA, Plant/*genetics ; *Evolution, Molecular ; Genome, Plant/*physiology ; Symbiosis/*physiology ; *Tetraploidy ; }, abstract = {Chlorarachniophyte and cryptophyte algae have complex plastids that were acquired by the uptake of a green or red algal endosymbiont via secondary endosymbiosis. The plastid is surrounded by four membranes, and a relict nucleus, called the nucleomorph, remains in the periplastidal compartment that is the remnant cytoplasm of the endosymbiont. Thus, these two algae possess four different genomes in a cell: Nuclear, nucleomorph, plastid, and mitochondrial. Recently, sequencing of the nuclear genomes of the chlorarachniophyte Bigelowiella natans and the cryptophyte Guillardia theta has been completed, and all four genomes have been made available. However, the copy number of each genome has never been investigated. It is important to know the actual DNA content of each genome, especially the highly reduced nucleomorph genome, for studies on genome evolution. In this study, we calculated genomic copy numbers in B. natans and G. theta using a real-time quantitative polymerase chain reaction approach. The nuclear genomes were haploid in both species, whereas the nucleomorph genomes were estimated to be diploid and tetraploid, respectively. Mitochondria and plastids contained a large copy number of genomic DNA in each cell. In the secondary endosymbioses of chlorarachniophytes and cryptophytes, the endosymbiont nuclear genomes were highly reduced in size and in the number of coding genes, whereas the chromosomal copy number was increased, as in bacterial endosymbiont genomes. This suggests that polyploidization is a general characteristic of highly reduced genomes in broad prokaryotic and eukaryotic endosymbionts.}, }
@article {pmid24706597, year = {2014}, author = {Terraz, G and Gueguen, G and Arnó, J and Fleury, F and Mouton, L}, title = {Nuclear and cytoplasmic differentiation among Mediterranean populations of Bemisia tabaci: testing the biological relevance of cytotypes.}, journal = {Pest management science}, volume = {70}, number = {10}, pages = {1503-1513}, doi = {10.1002/ps.3792}, pmid = {24706597}, issn = {1526-4998}, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification ; Europe ; Hemiptera/*classification/*genetics/microbiology ; Insecticide Resistance/genetics ; Microsatellite Repeats/*genetics ; Mitochondria/*genetics ; *Phylogeography ; *Reproductive Isolation ; *Symbiosis ; }, abstract = {BACKGROUND: The taxonomy of the species complex Bemisia tabaci is still an unresolved issue. Recently, phylogenetic analysis based on mtCOI identified 31 cryptic species. However, mitochondrial diversity is observed within these species, associated with distinct symbiotic bacterial communities forming associations, which here are called cytotypes. The authors investigated the biological significance of two cytotypes (Q1 and Q2) belonging to the Mediterranean species, which have only been found in allopatry in the Western Mediterranean to date. Sampling was done over a few years in Western Europe, and sympatric situations were found that allowed their reproductive compatibility to be tested in the field with the use of microsatellites.<br><br>RESULTS: The field survey indicated that, in spite of its recent introduction, Q2 is well established in France and Spain, where it coexists with Q1. Microsatellite data showed that, in allopatry, Q1 and Q2 are highly differentiated, while there is little or no genetic differentiation when they coexist in sympatry, suggesting a high rate of hybridisation. Crossing experiments in the lab confirmed their interfertility.<br><br>CONCLUSION: Q1 and Q2 hybridise, which confirms that they belong to the same species, in spite of the high degree of genetic differentiation at both the cytoplasmic and nuclear levels, and also suggests that their symbiotic bacteria do not prevent hybridisation.}, }
@article {pmid24704805, year = {2014}, author = {Muftuoglu, M and Mori, MP and de Souza-Pinto, NC}, title = {Formation and repair of oxidative damage in the mitochondrial DNA.}, journal = {Mitochondrion}, volume = {17}, number = {}, pages = {164-181}, doi = {10.1016/j.mito.2014.03.007}, pmid = {24704805}, issn = {1872-8278}, mesh = {DNA Damage/*drug effects ; *DNA Repair ; DNA, Mitochondrial/*drug effects ; Humans ; Mitochondria/drug effects/*physiology ; Oxidants/*toxicity ; }, abstract = {The mitochondrial DNA (mtDNA) encodes for only 13 polypeptides, components of 4 of the 5 oxidative phosphorylation complexes. But despite this apparently small numeric contribution, all 13 subunits are essential for the proper functioning of the oxidative phosphorylation circuit. Thus, accumulation of lesions, mutations and deletions/insertions in the mtDNA could have severe functional consequences, including mitochondrial diseases, aging and age-related diseases. The DNA is a chemically unstable molecule, which can be easily oxidized, alkylated, deaminated and suffer other types of chemical modifications, throughout evolution the organisms that survived were those who developed efficient DNA repair processes. In the last two decades, it has become clear that mitochondria have DNA repair pathways, which operate, at least for some types of lesions, as efficiently as the nuclear DNA repair pathways. The mtDNA is localized in a particularly oxidizing environment, making it prone to accumulate oxidatively generated DNA modifications (ODMs). In this article, we: i) review the major types of ODMs formed in mtDNA and the known repair pathways that remove them; ii) discuss the possible involvement of other repair pathways, just recently characterized in mitochondria, in the repair of these modifications; and iii) address the role of DNA repair in mitochondrial function and a possible cross-talk with other pathways that may potentially participate in mitochondrial genomic stability, such as mitochondrial dynamics and nuclear-mitochondrial signaling. Oxidative stress and ODMs have been increasingly implicated in disease and aging, and thus we discuss how variations in DNA repair efficiency may contribute to the etiology of such conditions or even modulate their clinical outcomes.}, }
@article {pmid24702837, year = {2014}, author = {Du, J}, title = {Hypothesis of mitochondrial oncogenesis as the trigger of normal cells to cancer cells.}, journal = {Medical hypotheses}, volume = {82}, number = {6}, pages = {744-747}, doi = {10.1016/j.mehy.2014.02.032}, pmid = {24702837}, issn = {1532-2777}, mesh = {*Biological Evolution ; Carcinogenesis/*metabolism ; Cell Transformation, Neoplastic/*metabolism ; Energy Metabolism/*physiology ; Humans ; Mitochondria/*metabolism ; *Models, Biological ; }, abstract = {The Warburg Effect showed that energy metabolism of cancer cells was similar to prokaryotic cells, which were different from normal eucaryotic cells. The Endosymbiotic Theory offered a plausible explanation that the eucaryotic cells were evolved from prokaryotic cells, by which host cells (ancient prokaryotic cells) had ingested mitochondria (ancient aerobic bacteria), which depended on oxidative phosphorylation rather than glycolysis for generating energy. The alteration of energy metabolism might mean that the survival style of cancer cells were the re-evolution from eucaryotic cells to prokaryotic cells. But how this alteration happened was still unknown. This hypothesis tries to explain how mitochondria take part in the re-evolution from normal cell to cancer cell.}, }
@article {pmid24696399, year = {2014}, author = {Melo-Ferreira, J and Vilela, J and Fonseca, MM and da Fonseca, RR and Boursot, P and Alves, PC}, title = {The elusive nature of adaptive mitochondrial DNA evolution of an arctic lineage prone to frequent introgression.}, journal = {Genome biology and evolution}, volume = {6}, number = {4}, pages = {886-896}, pmid = {24696399}, issn = {1759-6653}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Base Sequence ; Codon/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Hares/*genetics ; Molecular Sequence Data ; Oxidative Phosphorylation ; }, abstract = {Mitochondria play a fundamental role in cellular metabolism, being responsible for most of the energy production of the cell in the oxidative phosphorylation (OXPHOS) pathway. Mitochondrial DNA (mtDNA) encodes for key components of this process, but its direct role in adaptation remains far from understood. Hares (Lepus spp.) are privileged models to study the impact of natural selection on mitogenomic evolution because 1) species are adapted to contrasting environments, including arctic, with different metabolic pressures, and 2) mtDNA introgression from arctic into temperate species is widespread. Here, we analyzed the sequences of 11 complete mitogenomes (ten newly obtained) of hares of temperate and arctic origins (including two of arctic origin introgressed into temperate species). The analysis of patterns of codon substitutions along the reconstructed phylogeny showed evidence for positive selection in several codons in genes of the OXPHOS complexes, most notably affecting the arctic lineage. However, using theoretical models, no predictable effect of these differences was found on the structure and physicochemical properties of the encoded proteins, suggesting that the focus of selection may lie on complex interactions with nuclear encoded peptides. Also, a cloverleaf structure was detected in the control region only from the arctic mtDNA lineage, which may influence mtDNA replication and transcription. These results suggest that adaptation impacted the evolution of hare mtDNA and may have influenced the occurrence and consequences of the many reported cases of massive mtDNA introgression. However, the origin of adaptation remains elusive.}, }
@article {pmid24691961, year = {2014}, author = {Koonin, EV and Yutin, N}, title = {The dispersed archaeal eukaryome and the complex archaeal ancestor of eukaryotes.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {6}, number = {4}, pages = {a016188}, pmid = {24691961}, issn = {1943-0264}, support = {//Intramural NIH HHS/United States ; }, mesh = {Archaea/*genetics ; Biological Evolution ; Cell Division ; Cytoskeleton/diagnostic imaging/physiology ; Eukaryota/genetics ; *Genes, Archaeal ; Genome ; *Phylogeny ; RNA Interference ; Signal Transduction ; Ubiquitin/metabolism/physiology ; Ultrasonography ; }, abstract = {The ancestral set of eukaryotic genes is a chimera composed of genes of archaeal and bacterial origins thanks to the endosymbiosis event that gave rise to the mitochondria and apparently antedated the last common ancestor of the extant eukaryotes. The proto-mitochondrial endosymbiont is confidently identified as an α-proteobacterium. In contrast, the archaeal ancestor of eukaryotes remains elusive, although evidence is accumulating that it could have belonged to a deep lineage within the TACK (Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota) superphylum of the Archaea. Recent surveys of archaeal genomes show that the apparent ancestors of several key functional systems of eukaryotes, the components of the archaeal "eukaryome," such as ubiquitin signaling, RNA interference, and actin-based and tubulin-based cytoskeleton structures, are identifiable in different archaeal groups. We suggest that the archaeal ancestor of eukaryotes was a complex form, rooted deeply within the TACK superphylum, that already possessed some quintessential eukaryotic features, in particular, a cytoskeleton, and perhaps was capable of a primitive form of phagocytosis that would facilitate the engulfment of potential symbionts. This putative group of Archaea could have existed for a relatively short time before going extinct or undergoing genome streamlining, resulting in the dispersion of the eukaryome. This scenario might explain the difficulty with the identification of the archaeal ancestor of eukaryotes despite the straightforward detection of apparent ancestors to many signature eukaryotic functional systems.}, }
@article {pmid24690754, year = {2014}, author = {Boratyński, Z and Melo-Ferreira, J and Alves, PC and Berto, S and Koskela, E and Pentikäinen, OT and Tarroso, P and Ylilauri, M and Mappes, T}, title = {Molecular and ecological signs of mitochondrial adaptation: consequences for introgression?.}, journal = {Heredity}, volume = {113}, number = {4}, pages = {277-286}, pmid = {24690754}, issn = {1365-2540}, mesh = {Adaptation, Physiological ; Animals ; Arvicolinae/classification/*genetics/physiology ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; *Ecosystem ; *Evolution, Molecular ; Genetic Variation ; Male ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Selection, Genetic ; }, abstract = {The evolution of the mitochondrial genome and its potential adaptive impact still generates vital debates. Even if mitochondria have a crucial functional role, as they are the main cellular energy suppliers, mitochondrial DNA (mtDNA) introgression is common in nature, introducing variation in populations upon which selection may act. Here we evaluated whether the evolution of mtDNA in a rodent species affected by mtDNA introgression is explained by neutral expectations alone. Variation in one mitochondrial and six nuclear markers in Myodes glareolus voles was examined, including populations that show mtDNA introgression from its close relative, Myodes rutilus. In addition, we modelled protein structures of the mtDNA marker (cytochrome b) and estimated the environmental envelopes of mitotypes. We found that massive mtDNA introgression occurred without any trace of introgression in the analysed nuclear genes. The results show that the native glareolus mtDNA evolved under past positive selection, suggesting that mtDNA in this system has selective relevance. The environmental models indicate that the rutilus mitotype inhabits colder and drier habitats than the glareolus one that can result from local adaptation or from the geographic context of introgression. Finally, homology models of the cytochrome b protein revealed a substitution in rutilus mtDNA in the vicinity of the catalytic fraction, suggesting that differences between mitotypes may result in functional changes. These results suggest that the evolution of mtDNA in Myodes may have functional, ecological and adaptive significance. This work opens perspective onto future experimental tests of the role of natural selection in mtDNA introgression in this system.}, }
@article {pmid24690192, year = {2014}, author = {Song, SD and Barker, SC and Shao, R}, title = {Variation in mitochondrial minichromosome composition between blood-sucking lice of the genus Haematopinus that infest horses and pigs.}, journal = {Parasites &amp; vectors}, volume = {7}, number = {}, pages = {144}, pmid = {24690192}, issn = {1756-3305}, mesh = {Animals ; Anoplura/classification/*genetics ; *Genome, Mitochondrial ; Horse Diseases/*parasitology ; Horses ; Lice Infestations/parasitology/*veterinary ; Mitochondria/*genetics ; Species Specificity ; Swine ; Swine Diseases/*parasitology ; }, abstract = {BACKGROUND: The genus Haematopinus contains 21 species of blood-sucking lice, parasitizing both even-toed ungulates (pigs, cattle, buffalo, antelopes, camels and deer) and odd-toed ungulates (horses, donkeys and zebras). The mitochondrial genomes of the domestic pig louse, Haematopinus suis, and the wild pig louse, Haematopinus apri, have been sequenced recently; both lice have fragmented mitochondrial genomes with 37 genes on nine minichromosomes. To understand whether the composition of mitochondrial minichromosomes and the gene content and gene arrangement of each minichromosome are stable within the genus, we sequenced the mitochondrial genome of the horse louse, Haematopinus asini.<br><br>METHODS: We used a PCR-based strategy to amplify four mitochondrial minichromosomes in near full-length, and then amplify the entire coding regions of all of the nine mitochondrial minichromosomes of the horse louse. These amplicons were sequenced with an Illumina Hiseq platform.<br><br>RESULTS: We identified all of the 37 mitochondrial genes typical of bilateral animals in the horse louse, Haematopinus asini; these genes are on nine circular minichromosomes. Each minichromosome is 3.5-5.0 kb in size and consists of a coding region and a non-coding region except R-nad4L-rrnS-C minichromosome, which contains two coding regions and two non-coding regions. Six of the nine minichromosomes of the horse louse have their counterparts in the pig lice with the same gene content and gene arrangement. However, the gene content and arrangement of the other three minichromosomes of the horse louse, including R-nad4L-rrnS-C, are different from that of the other three minichromosomes of the pig lice.<br><br>CONCLUSIONS: Comparison between the horse louse and the pig lice revealed variation in the composition of mitochondrial minichromosomes within the genus Haematopinus, which can be accounted for by gene translocation events between minichromosomes. The current study indicates that inter-minichromosome recombination plays a major role in generating the variation in the composition of mitochondrial minichromosomes and provides novel insights into the evolution of fragmented mitochondrial genomes in the blood-sucking lice.}, }
@article {pmid24684551, year = {2015}, author = {Paul, BD and Snyder, SH}, title = {Modes of physiologic H2S signaling in the brain and peripheral tissues.}, journal = {Antioxidants &amp; redox signaling}, volume = {22}, number = {5}, pages = {411-423}, pmid = {24684551}, issn = {1557-7716}, support = {DA 000266/DA/NIDA NIH HHS/United States ; MH18501/MH/NIMH NIH HHS/United States ; }, mesh = {Animals ; Brain/*metabolism ; Cardiovascular System/metabolism ; Gasotransmitters/*metabolism ; Gastrointestinal Tract/metabolism ; Homeostasis ; Humans ; Hydrogen Sulfide/*metabolism ; Inflammation/metabolism ; Mitochondria/metabolism ; Nitric Oxide/metabolism ; Oxidation-Reduction ; Parkinson Disease/metabolism ; Protein Processing, Post-Translational ; *Signal Transduction ; }, abstract = {SIGNIFICANCE: Hydrogen sulfide (H2S), once associated with rotten eggs and sewers, is now recognized as a gasotransmitter that is synthesized in vivo in a regulated fashion. This ancient gaseous molecule has been retained throughout evolution to perform various roles in different life forms. H2S modulates important signaling functions in diverse cellular processes ranging from regulation of blood pressure to redox homeostasis.<br><br>RECENT ADVANCES: One of the modes by which H2S signals is by post-translational modification of reactive cysteine residues in a process designated as sulfhydration, resulting in conversion of the -SH groups of target cysteine residues to -SSH. Using the modified biotin-switch assay and a fluorescent maleimide-based analysis, sulfhydration of several proteins has been detected in various cell types. Aberrant sulfhydration patterns occur in neurodegenerative conditions such as Parkinson's disease.<br><br>CRITICAL ISSUES: The exact concentration, source of H2S, and conditions under which various stores of H2S are utilized have not been fully elucidated. Currently, available inhibitors of the biosynthetic enzymes of H2S lack sufficient specificity to shed light on detailed mechanisms of H2S action. Probes with a higher sensitivity that can reliably detect cellular and tissue H2S levels are yet to be developed.<br><br>FUTURE DIRECTIONS: Availability of advanced probes and biosynthesis inhibitors would help in the measurement of real-time changes of endogenous H2S levels in an in vivo context. The study of the dynamics of sulfhydration and nitrosylation of critical cysteine residues of regulatory proteins involved in physiology and pathophysiology is an area of interest for the future.}, }
@article {pmid24683180, year = {2014}, author = {Pintó-Marijuan, M and Munné-Bosch, S}, title = {Photo-oxidative stress markers as a measure of abiotic stress-induced leaf senescence: advantages and limitations.}, journal = {Journal of experimental botany}, volume = {65}, number = {14}, pages = {3845-3857}, doi = {10.1093/jxb/eru086}, pmid = {24683180}, issn = {1460-2431}, mesh = {Adaptation, Physiological/radiation effects ; Biomarkers/*metabolism ; *Light ; Oxidative Stress/*radiation effects ; Plant Leaves/*growth &amp; development/metabolism/*radiation effects/ultrastructure ; Stress, Physiological/*radiation effects ; }, abstract = {Inside chloroplasts, several abiotic stresses (including drought, high light, salinity, or extreme temperatures) induce a reduction in CO2 assimilation rates with a consequent increase in reactive oxygen species (ROS) production, ultimately leading to leaf senescence and yield loss. Photo-oxidation processes should therefore be mitigated to prevent leaf senescence, and plants have evolved several mechanisms to either prevent the formation of ROS or eliminate them. Technology evolution during the past decade has brought faster and more precise methodologies to quantify ROS production effects and damage, and the capacities of plants to withstand oxidative stress. Nevertheless, it is very difficult to disentangle photo-oxidative processes that bring leaf defence and acclimation, from those leading to leaf senescence (and consequently death). It is important to avoid the mistake of discussing results on leaf extracts as being equivalent to chloroplast extracts without taking into account that other organelles, such as peroxisomes, mitochondria, or the apoplast also significantly contribute to the overall ROS production within the cell. Another important aspect is that studies on abiotic stress-induced leaf senescence in crops do not always include a time-course evolution of studied processes, which limits our knowledge about what photo-oxidative stress processes are required to irreversibly induce the senescence programme. This review will summarize the current technologies used to evaluate the extent of photo-oxidative stress in plants, and discuss their advantages and limitations in characterizing abiotic stress-induced leaf senescence in crops.}, }
@article {pmid24682152, year = {2014}, author = {Tsaousis, AD and Nyvltová, E and Sutak, R and Hrdy, I and Tachezy, J}, title = {A nonmitochondrial hydrogen production in Naegleria gruberi.}, journal = {Genome biology and evolution}, volume = {6}, number = {4}, pages = {792-799}, pmid = {24682152}, issn = {1759-6653}, mesh = {Cytosol/*enzymology ; Hydrogen/*metabolism ; Hydrogenase/genetics/*metabolism ; Mitochondria/genetics/metabolism ; Naegleria/*enzymology/genetics ; Protozoan Proteins/genetics/*metabolism ; }, abstract = {Naegleria gruberi is a free-living heterotrophic aerobic amoeba well known for its ability to transform from an amoeba to a flagellate form. The genome of N. gruberi has been recently published, and in silico predictions demonstrated that Naegleria has the capacity for both aerobic respiration and anaerobic biochemistry to produce molecular hydrogen in its mitochondria. This finding was considered to have fundamental implications on the evolution of mitochondrial metabolism and of the last eukaryotic common ancestor. However, no actual experimental data have been shown to support this hypothesis. For this reason, we have decided to investigate the anaerobic metabolism of the mitochondrion of N. gruberi. Using in vivo biochemical assays, we have demonstrated that N. gruberi has indeed a functional [FeFe]-hydrogenase, an enzyme that is attributed to anaerobic organisms. Surprisingly, in contrast to the published predictions, we have demonstrated that hydrogenase is localized exclusively in the cytosol, while no hydrogenase activity was associated with mitochondria of the organism. In addition, cytosolic localization displayed for HydE, a marker component of hydrogenase maturases. Naegleria gruberi, an obligate aerobic organism and one of the earliest eukaryotes, is producing hydrogen, a function that raises questions on the purpose of this pathway for the lifestyle of the organism and potentially on the evolution of eukaryotes.}, }
@article {pmid24682150, year = {2014}, author = {Dean, R and Zimmer, F and Mank, JE}, title = {The potential role of sexual conflict and sexual selection in shaping the genomic distribution of Mito-nuclear genes.}, journal = {Genome biology and evolution}, volume = {6}, number = {5}, pages = {1096-1104}, pmid = {24682150}, issn = {1759-6653}, support = {260233/ERC_/European Research Council/International ; }, mesh = {Adaptation, Physiological/genetics ; Animals ; Caenorhabditis elegans/genetics ; Cell Nucleus/genetics ; Drosophila melanogaster/genetics ; Female ; *Genes, Mitochondrial ; Genome ; Genome, Mitochondrial ; Inheritance Patterns ; Male ; Mammals/genetics ; *Phylogeny ; *Selection, Genetic ; *Sex Chromosomes ; X Chromosome ; }, abstract = {Mitochondrial interactions with the nuclear genome represent one of life's most important co-evolved mutualisms. In many organisms, mitochondria are maternally inherited, and in these cases, co-transmission between the mitochondrial and nuclear genes differs across different parts of the nuclear genome, with genes on the X chromosome having two-third probability of co-transmission, compared with one-half for genes on autosomes. These asymmetrical inheritance patterns of mitochondria and different parts of the nuclear genome have the potential to put certain gene combinations in inter-genomic co-adaptation or conflict. Previous work in mammals found strong evidence that the X chromosome has a dearth of genes that interact with the mitochondria (mito-nuclear genes), suggesting that inter-genomic conflict might drive genes off the X onto the autosomes for their male-beneficial effects. Here, we developed this idea to test coadaptation and conflict between mito-nuclear gene combinations across phylogenetically independent sex chromosomes on a far broader scale. We found that, in addition to therian mammals, only Caenorhabditis elegans showed an under-representation of mito-nuclear genes on the sex chromosomes. The remaining species studied showed no overall bias in their distribution of mito-nuclear genes. We discuss possible factors other than inter-genomic conflict that might drive the genomic distribution of mito-nuclear genes.}, }
@article {pmid24680917, year = {2014}, author = {Chong, J and Jackson, C and Kim, JI and Yoon, HS and Reyes-Prieto, A}, title = {Molecular markers from different genomic compartments reveal cryptic diversity within glaucophyte species.}, journal = {Molecular phylogenetics and evolution}, volume = {76}, number = {}, pages = {181-188}, doi = {10.1016/j.ympev.2014.03.019}, pmid = {24680917}, issn = {1095-9513}, mesh = {Cell Nucleus/genetics ; Chlorophyta/genetics ; Cyanophora/cytology/*genetics ; DNA Barcoding, Taxonomic ; Diatoms/genetics ; Genetic Markers/genetics ; Genetic Variation/*genetics ; Genome/*genetics ; Genomics ; Glaucophyta/cytology/*genetics ; Korea ; Mitochondria/genetics ; North America ; *Phylogeny ; Plastids/genetics ; Sequence Analysis, DNA ; }, abstract = {Glaucophytes are the least studied of the three major Archaeplastida (Plantae sensu lato) lineages. It has been largely recognized that comprehensive investigations of glaucophyte genetic and species diversity will shed light on the early evolution of photosynthetic eukaryotes. Here we used molecular phylogenetics and genetic distance estimations of diverse molecular markers to explore strain and species diversity within the glaucophyte genera Cyanophora and Glaucocystis. Single gene and concatenated maximum likelihood analyses of markers from three different genetic compartments consistently recovered similar intrageneric genetic groups. Distance analyses of plastid (psbA and rbcL) and mitochondrial (cob and cox1) genes, and the nuclear internal transcribed spacer (ITS) region, revealed substantial genetic divergence between some Cyanophora paradoxa and Glaucocystis nostochinearum strains. The genetic distances estimated between some glaucophyte strains currently considered the same species are similar or greater than divergence values calculated between different species in other unicellular algae, such as certain green algae and diatoms. The analyzed molecular markers are prospective candidates for future studies of species diversity in glaucophytes. Overall, our results unveil previously unrecognized cryptic diversity within Cyanophora and Glaucocystis species.}, }
@article {pmid24679453, year = {2014}, author = {Moraes, CT and Bacman, SR and Williams, SL}, title = {Manipulating mitochondrial genomes in the clinic: playing by different rules.}, journal = {Trends in cell biology}, volume = {24}, number = {4}, pages = {209-211}, pmid = {24679453}, issn = {1879-3088}, support = {R01 AG036871/AG/NIA NIH HHS/United States ; R01 EY010804/EY/NEI NIH HHS/United States ; R01 NS079965/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Humans ; Mitochondria/*genetics ; Patient Rights ; }, abstract = {Recently, several publications have surfaced describing methods to manipulate mitochondrial genomes in tissues and embryos. With them, a somewhat sensationalistic uproar about the generation of children with 'three parents' has dominated the discussion in the lay media. It is important that society understands the singularities of mitochondrial genetics to judge these procedures in a rational light, so that this ongoing discussion does not preclude the helping of patients and families harboring mutated mitochondrial genomes.}, }
@article {pmid24667833, year = {2014}, author = {Sazzini, M and Schiavo, G and De Fanti, S and Martelli, PL and Casadio, R and Luiselli, D}, title = {Searching for signatures of cold adaptations in modern and archaic humans: hints from the brown adipose tissue genes.}, journal = {Heredity}, volume = {113}, number = {3}, pages = {259-267}, pmid = {24667833}, issn = {1365-2540}, mesh = {*Adaptation, Physiological/genetics ; *Adipose Tissue, Brown/metabolism ; Alleles ; Biological Evolution ; Climate ; Cold Temperature ; Fossils ; *Genome/genetics ; *Thermogenesis/genetics ; Humans ; }, abstract = {Adaptation to low temperatures has been reasonably developed in the human species during the colonization of the Eurasian landmass subsequent to Out of Africa migrations of anatomically modern humans. In addition to morphological and cultural changes, also metabolic ones are supposed to have favored human isolation from cold and body heat production and this can be hypothesized also for most Neandertal and at least for some Denisovan populations, which lived in geographical areas that strongly experienced the last glacial period. Modulation of non-shivering thermogenesis, for which adipocytes belonging to the brown adipose tissue are the most specialized cells, might have driven these metabolic adaptations. To perform an exploratory analysis aimed at looking into this hypothesis, variation at 28 genes involved in such functional pathway was investigated in modern populations from different climate zones, as well as in Neandertal and Denisovan genomes. Patterns of variation at the LEPR gene, strongly related to increased heat dissipation by mitochondria, appeared to have been shaped by positive selection in modern East Asians, but not in Europeans. Moreover, a single potentially cold-adapted LEPR allele, different from the supposed adaptive one identified in Homo sapiens, was found also in Neandertal and Denisovan genomes. These findings suggest that independent mechanisms for cold adaptations might have been developed in different non-African human groups, as well as that the evolution of possible enhanced thermal efficiency in Neandertals and in some Denisovan populations has plausibly entailed significant changes also in other functional pathways than in the examined one.}, }
@article {pmid24667533, year = {2014}, author = {Quan, QM and Chen, LL and Wang, X and Li, S and Yang, XL and Zhu, YG and Wang, M and Cheng, Z}, title = {Genetic diversity and distribution patterns of host insects of Caterpillar Fungus Ophiocordyceps sinensis in the Qinghai-Tibet Plateau.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e92293}, pmid = {24667533}, issn = {1932-6203}, mesh = {Animals ; DNA, Fungal/analysis/chemistry/*genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; *Genetic Variation ; Genetics, Population ; Hypocreales/classification/*genetics ; Insecta/classification/*microbiology ; Mitochondria/enzymology ; Phylogeography ; }, abstract = {The caterpillar fungus Ophiocordyceps sinensis is one of the most valuable medicinal fungi in the world, and it requires host insects in family Hepialidae (Lepidoptera) to complete its life cycle. However, the genetic diversity and phylogeographic structures of the host insects remain to be explored. We analyzed the genetic diversity and temporal and spatial distribution patterns of genetic variation of the host insects throughout the O. sinensis distribution. Abundant haplotype and nucleotide diversity mainly existed in the areas of Nyingchi, ShangriLa, and around the edge of the Qinghai-Tibet Plateau, where are considered as the diversity center or micro-refuges of the host insects of O. sinensis. However, there was little genetic variation among host insects from 72.1% of all populations, indicating that the host species composition might be relatively simple in large-scale O. sinensis populations. All host insects are monophyletic except for those from four O. sinensis populations around Qinghai Lake. Significant phylogeographic structure (NST>GST, P<0.05) was revealed for the monophyletic host insects, and the three major phylogenetic groups corresponded with specific geographical areas. The divergence of most host insects was estimated to have occurred at ca. 3.7 Ma, shortly before the rapid uplift of the QTP. The geographical distribution and star-like network of the haplotypes implied that most host insects were derived from the relicts of a once-widespread host that subsequently became fragmented. Neutrality tests, mismatch distribution analysis, and expansion time estimation confirmed that most host insects presented recent demographic expansions that began ca. 0.118 Ma in the late Pleistocene. Therefore, the genetic diversity and distribution of the present-day insects should be attributed to effects of the Qinghai-Tibet Plateau uplift and glacial advance/retreat cycles during the Quaternary ice age. These results provide valuable information to guide the protection and sustainable use of these host insects as well as O. sinensis.}, }
@article {pmid24657631, year = {2014}, author = {Mariadassou, M and Pellay, FX}, title = {Identification of amino acids in mitochondrially encoded proteins that correlate with lifespan.}, journal = {Experimental gerontology}, volume = {56}, number = {}, pages = {53-58}, doi = {10.1016/j.exger.2014.03.009}, pmid = {24657631}, issn = {1873-6815}, mesh = {Age Factors ; Aging/genetics/*metabolism ; Amino Acid Sequence ; Animals ; Body Weight ; Computational Biology ; DNA, Mitochondrial/metabolism ; Databases, Genetic ; Humans ; Longevity ; Mitochondria/*metabolism ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Phylogeny ; Proteomics/methods ; Sequence Analysis, Protein ; }, abstract = {Animals show a huge diversity in their lifespan that can vary from a few weeks to over a hundred years in vertebrates. Size is a key element in this variation and the positive correlation between size and maximum lifespan can be observed in each class of vertebrate. Some groups and species clearly stand out in this size-lifespan relationship and the ones with exceptionally long lifespan have been studied to understand the biological causes of their low aging rate. Among the potential explanations of animals' lifespan variations, mitochondria and mitochondrially encoded genes have drawn attention because of their importance in the aging process. To understand both the extent of lifespan variations and their dependence to genes and amino acid variations in mitochondrial genes and DNA (mtDNA), we analyze in a systematic way all 13 proteins encoded by mitochondria in all vertebrates for which we had information on weight, maximum lifespan and mtDNA sequence. This comparison allows us to visualize positions, and even specific amino acids, in these sequences that correlate with lifespan. With this approach, we draw a map of 356 amino acid residues, at 296 positions within the sequence, that correlate with longer or shorter lifespan. We also compared this map with the human mitochondrial polymorphism to determine its potential as a predictive tool.}, }
@article {pmid24657595, year = {2014}, author = {Guzmán Mentesana, G and Báez, AL and Lo Presti, MS and Domínguez, R and Córdoba, R and Bazán, C and Strauss, M and Fretes, R and Rivarola, HW and Paglini-Oliva, P}, title = {Functional and structural alterations of cardiac and skeletal muscle mitochondria in heart failure patients.}, journal = {Archives of medical research}, volume = {45}, number = {3}, pages = {237-246}, doi = {10.1016/j.arcmed.2014.03.003}, pmid = {24657595}, issn = {1873-5487}, mesh = {Aged ; Case-Control Studies ; Female ; Heart Failure/*metabolism/*pathology ; Humans ; Male ; Middle Aged ; Mitochondria, Muscle/*metabolism/*pathology/ultrastructure ; Muscle, Skeletal/*metabolism/*pathology/ultrastructure ; Myocardium/*metabolism/*pathology/ultrastructure ; Reactive Oxygen Species/metabolism ; }, abstract = {BACKGROUND AND AIMS: The fundamental mechanisms involved in the genesis and progression of heart failure are not clearly understood. The present study was conducted to analyze the cardiac mitochondrial involvement in heart failure, the possible parallelism between cardiac and skeletal muscle and if there is a link between clinical symptoms and mitochondrial damage.<br><br>METHODS: Left ventricle and pectoral biopsies were obtained from patients with heart failure (n: 21) and patients with inter-auricular communication as the unique diagnosis for surgery (n: 6). Mitochondria were isolated from these tissues and studied through electron microscopy, spectrophotometry to measure the activity of respiratory complex III and immunohistochemistry to determine the presence of reactive oxygen species.<br><br>RESULTS: More than 90% of cardiac and skeletal muscle mitochondria presented structural and functional alterations in relation to an increment in the reactive oxygen species production, even in patients without the presence of any clinical Framingham criteria.<br><br>CONCLUSIONS: We demonstrated some parallelism between cardiac and skeletal muscle mitochondrial alterations in patients with heart failure and that these alterations begin before the major clinical Framingham criteria are installed, pointing to mitochondria as one of the possibly responsible factors for the evolution of cardiac disease.}, }
@article {pmid24650628, year = {2014}, author = {Grüber, G and Manimekalai, MS and Mayer, F and Müller, V}, title = {ATP synthases from archaea: the beauty of a molecular motor.}, journal = {Biochimica et biophysica acta}, volume = {1837}, number = {6}, pages = {940-952}, doi = {10.1016/j.bbabio.2014.03.004}, pmid = {24650628}, issn = {0006-3002}, mesh = {Archaea/*enzymology ; Archaeal Proteins/chemistry/*physiology ; Binding Sites ; Biocatalysis ; Catalytic Domain ; Mitochondrial Proton-Translocating ATPases/chemistry/*physiology ; Models, Molecular ; Molecular Motor Proteins/chemistry/*physiology ; }, abstract = {Archaea live under different environmental conditions, such as high salinity, extreme pHs and cold or hot temperatures. How energy is conserved under such harsh environmental conditions is a major question in cellular bioenergetics of archaea. The key enzymes in energy conservation are the archaeal A1AO ATP synthases, a class of ATP synthases distinct from the F1FO ATP synthase ATP synthase found in bacteria, mitochondria and chloroplasts and the V1VO ATPases of eukaryotes. A1AO ATP synthases have distinct structural features such as a collar-like structure, an extended central stalk, and two peripheral stalks possibly stabilizing the A1AO ATP synthase during rotation in ATP synthesis/hydrolysis at high temperatures as well as to provide the storage of transient elastic energy during ion-pumping and ATP synthesis/-hydrolysis. High resolution structures of individual subunits and subcomplexes have been obtained in recent years that shed new light on the function and mechanism of this unique class of ATP synthases. An outstanding feature of archaeal A1AO ATP synthases is their diversity in size of rotor subunits and the coupling ion used for ATP synthesis with H(+), Na(+) or even H(+) and Na(+) using enzymes. The evolution of the H(+) binding site to a Na(+) binding site and its implications for the energy metabolism and physiology of the cell are discussed.}, }
@article {pmid24642544, year = {2014}, author = {Calhoon, EA and Jimenez, AG and Harper, JM and Jurkowitz, MS and Williams, JB}, title = {Linkages between mitochondrial lipids and life history in temperate and tropical birds.}, journal = {Physiological and biochemical zoology : PBZ}, volume = {87}, number = {2}, pages = {265-275}, doi = {10.1086/674696}, pmid = {24642544}, issn = {1537-5293}, mesh = {Animals ; Birds/*physiology ; Clutch Size ; *Environment ; *Lipid Metabolism ; Mitochondrial Membranes/*metabolism ; Ohio ; Panama ; Tropical Climate ; }, abstract = {Temperate birds tend to have a fast pace of life and short life spans with high reproductive output, whereas tropical birds tend to have a slower pace of life, invest fewer resources in reproduction, and have higher adult survival rates. How these differences in life history at the organismal level are rooted in differences at the cellular level is a major focus of current research. Here, we cultured fibroblasts from phylogenetically paired tropical and temperate species, isolated mitochondria from each, and compared their mitochondrial membrane lipids. We also correlated the amounts of these lipids with an important life history parameter, clutch size. We found that tropical birds tended to have less mitochondrial lipid per cell, especially less cardiolipin per cell, suggesting that cells from tropical birds have fewer mitochondria or less inner mitochondrial membrane per cell. We also found that the mitochondria of tropical birds and the species with the smallest clutch sizes had higher amounts of plasmalogens, a lipid that could serve as an antioxidant. Overall, our findings are consistent with the idea that there are underlying molecular and cellular physiological traits that could account for the differences in whole-animal physiology between animals with different life histories.}, }
@article {pmid24634485, year = {2014}, author = {Sakamoto, W and Takami, T}, title = {Nucleases in higher plants and their possible involvement in DNA degradation during leaf senescence.}, journal = {Journal of experimental botany}, volume = {65}, number = {14}, pages = {3835-3843}, doi = {10.1093/jxb/eru091}, pmid = {24634485}, issn = {1460-2431}, mesh = {*DNA Fragmentation ; Deoxyribonucleases/*metabolism ; Phylogeny ; Plant Leaves/*metabolism ; Plants/*enzymology ; Subcellular Fractions/metabolism ; }, abstract = {During leaf senescence, macromolecules such as proteins and lipids are known to be degraded for redistribution into upper tissues. Similarly, nucleic acids appear to undergo fragmentation or degradation during senescence, but the physiological role of nucleic acid degradation, particularly of genomic DNA degradation, remains unclear. To date, more than a dozen of plant deoxyribonucleases have been reported, whereas it remains to be verified whether any of them degrade DNA during leaf senescence. This review summarizes current knowledge related to the plant nucleases that are induced developmentally or in a tissue-specific manner and are known to degrade DNA biochemically. Of these, several endonucleases (BFN1, CAN1, and CAN2) and an exonuclease (DPD1) in Arabidopsis seem to act in leaf senescence because they were shown to be inducible at the transcript level. This review specifically examines DPD1, which is dual-targeted to chloroplasts and mitochondria. Results show that, among the exonuclease family to which DPD1 belongs, DPD1 expression is extraordinary when estimated using a microarray database. DPD1 is the only example among the nucleases in which DNA degradation has been confirmed in vivo in pollen by mutant analysis. These data imply a significant role of organelle DNA degradation during leaf senescence and implicate DPD1 as a potential target for deciphering nucleotide salvage in plants.}, }
@article {pmid24631858, year = {2014}, author = {Scheel, BM and Hausdorf, B}, title = {Dynamic evolution of mitochondrial ribosomal proteins in Holozoa.}, journal = {Molecular phylogenetics and evolution}, volume = {76}, number = {}, pages = {67-74}, doi = {10.1016/j.ympev.2014.03.005}, pmid = {24631858}, issn = {1095-9513}, mesh = {Amoeba/genetics/metabolism ; Animals ; Bacterial Proteins/genetics/metabolism ; Ctenophora/genetics/metabolism ; DNA, Mitochondrial/genetics/metabolism ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome, Mitochondrial/genetics ; Genomics ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/*genetics/metabolism ; *Phylogeny ; RNA, Ribosomal/genetics/metabolism ; Ribosomal Proteins/*genetics/metabolism ; Ribosomes/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {We studied the highly dynamic evolution of mitochondrial ribosomal proteins (MRPs) in Holozoa. Most major clades within Holozoa are characterized by gains and/or losses of MRPs. The usefulness of gains of MRPs as rare genomic changes in phylogenetics is undermined by the high frequency of secondary losses. However, phylogenetic analyses of the MRP sequences provide evidence for the Acrosomata hypothesis, a sister group relationship between Ctenophora and Bilateria. An extensive restructuring of the mitochondrial genome and, as a consequence, of the mitochondrial ribosomes occurred in the ancestor of metazoans. The last MRP genes encoded in the mitochondrial genome were either moved to the nuclear genome or were lost. The strong decrease in size of the mitochondrial genome was probably caused by selection for rapid replication of mitochondrial DNA during oogenesis in the metazoan ancestor. A phylogenetic analysis of MRPL56 sequences provided evidence for a horizontal gene transfer of the corresponding MRP gene between metazoans and Dictyostelidae (Amoebozoa). The hypothesis that the requisition of additional MRPs compensated for a loss of rRNA segments in the mitochondrial ribosomes is corroborated by a significant negative correlation between the number of MRPs and length of the rRNA. Newly acquired MRPs evolved faster than bacterial MRPs and positions in eukaryote-specific MRPs were more strongly affected by coevolution than positions in prokaryotic MRPs in accordance with the necessity to fit these proteins into the pre-existing structure of the mitoribosome.}, }
@article {pmid24621225, year = {2016}, author = {Ba, H and Wu, L and Liu, Z and Li, C}, title = {An examination of the origin and evolution of additional tandem repeats in the mitochondrial DNA control region of Japanese sika deer (Cervus Nippon).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {1}, pages = {276-281}, doi = {10.3109/19401736.2014.892077}, pmid = {24621225}, issn = {2470-1408}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; Deer/*genetics ; Genetic Variation ; *Genome, Mitochondrial ; *Microsatellite Repeats ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA/veterinary ; }, abstract = {Tandem repeat units are only detected in the left domain of the mitochondrial DNA control region in sika deer. Previous studies showed that Japanese sika deer have more tandem repeat units than its cousins from the Asian continent and Taiwan, which often have only three repeat units. To determine the origin and evolution of these additional repeat units in Japanese sika deer, we obtained the sequence of repeat units from an expanded dataset of the control region from all sika deer lineages. The functional constraint is inferred to act on the first repeat unit because this repeat has the least sequence divergence in comparison to the other units. Based on slipped-strand mispairing mechanisms, the illegitimate elongation model could account for the addition or deletion of these additional repeat units in the Japanese sika deer population. We also report that these additional repeat units could be occurring in the internal positions of tandem repeat regions, possibly via coupling with a homogenization mechanism within and among these lineages. Moreover, the increased number of repeat units in the Japanese sika deer population could reflect a balance between mutation and selection, as well as genetic drift.}, }
@article {pmid24621222, year = {2016}, author = {Li, M and Chen, Z and Chen, T and Xiong, D and Fan, J and Liang, P}, title = {Whole mitogenome of the Japanese scad Decapterus maruadsi (Perciformes: Carangidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {1}, pages = {306-307}, doi = {10.3109/19401736.2014.892089}, pmid = {24621222}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Base Sequence ; DNA, Mitochondrial/*genetics ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA/veterinary ; }, abstract = {The Japanese scad (Decapterus maruadsi) is one of the most commercially important fish species that is popularly harvested in tropical and temperate seas in South East Asian countries. In the present study, we obtained the whole mitochondrial genome sequence of D. maruadsi by overlapped polymerase chain reactions. The entire sequence was 16,541 bp in length, with a gene content (13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 2 non-coding regions: the control region and the light strand replication origin) and organization similar to most of the other vertebrates. Overall base composition of the genome was 27.5% of A, 30.2% of C, 25.5% of T and 16.8% of G, showing an obvious anti G bias commonly observed in teleosts. The sequence data of D. maruadsi could provide useful information for the studies on conservation genetics and molecular phylogenetics.}, }
@article {pmid24619275, year = {2014}, author = {Kenny, NJ and Sin, YW and Shen, X and Zhe, Q and Wang, W and Chan, TF and Tobe, SS and Shimeld, SM and Chu, KH and Hui, JH}, title = {Genomic sequence and experimental tractability of a new decapod shrimp model, Neocaridina denticulata.}, journal = {Marine drugs}, volume = {12}, number = {3}, pages = {1419-1437}, pmid = {24619275}, issn = {1660-3397}, mesh = {Aminobenzoates/pharmacology ; Animal Husbandry ; Animals ; Chromosome Mapping ; DNA/chemistry/genetics ; DNA, Mitochondrial/genetics ; Daphnia ; Decapoda/*genetics/*metabolism ; Female ; Genes, Homeobox/genetics ; Genome ; Genomics ; Male ; Mitochondria/genetics ; Models, Genetic ; Phylogeny ; Sexual Maturation ; }, abstract = {The speciose Crustacea is the largest subphylum of arthropods on the planet after the Insecta. To date, however, the only publically available sequenced crustacean genome is that of the water flea, Daphnia pulex, a member of the Branchiopoda. While Daphnia is a well-established ecotoxicological model, previous study showed that one-third of genes contained in its genome are lineage-specific and could not be identified in any other metazoan genomes. To better understand the genomic evolution of crustaceans and arthropods, we have sequenced the genome of a novel shrimp model, Neocaridina denticulata, and tested its experimental malleability. A library of 170-bp nominal fragment size was constructed from DNA of a starved single adult and sequenced using the Illumina HiSeq2000 platform. Core eukaryotic genes, the mitochondrial genome, developmental patterning genes (such as Hox) and microRNA processing pathway genes are all present in this animal, suggesting it has not undergone massive genomic loss. Comparison with the published genome of Daphnia pulex has allowed us to reveal 3750 genes that are indeed specific to the lineage containing malacostracans and branchiopods, rather than Daphnia-specific (E-value: 10[-6]). We also show the experimental tractability of N. denticulata, which, together with the genomic resources presented here, make it an ideal model for a wide range of further aquacultural, developmental, ecotoxicological, food safety, genetic, hormonal, physiological and reproductive research, allowing better understanding of the evolution of crustaceans and other arthropods.}, }
@article {pmid24619178, year = {2014}, author = {Smietanka, B and Burzyński, A and Hummel, H and Wenne, R}, title = {Glacial history of the European marine mussels Mytilus, inferred from distribution of mitochondrial DNA lineages.}, journal = {Heredity}, volume = {113}, number = {3}, pages = {250-258}, pmid = {24619178}, issn = {1365-2540}, mesh = {Animals ; Bivalvia/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Gene Flow/genetics ; Genetic Variation/genetics ; Genetics, Population/methods ; Genome, Mitochondrial/genetics ; Haplotypes/genetics ; Mitochondria/genetics ; Mytilus/*genetics ; Oceans and Seas ; Phylogeny ; Species Specificity ; }, abstract = {Mussels of the genus Mytilus have been used to assess the circumglacial phylogeography of the intertidal zone. These mussels are representative components of the intertidal zone and have rapidly evolving mitochondrial DNA, suitable for high resolution phylogeographic analyses. In Europe, the three Mytilus species currently share mitochondrial haplotypes, owing to the cases of extensive genetic introgression. Genetic diversity of Mytilus edulis, Mytilus trossulus and Mytilus galloprovincialis was studied using a 900-bp long part of the most variable fragment of the control region from one of their two mitochondrial genomes. To this end, 985 specimens were sampled along the European coasts, at sites ranging from the Black Sea to the White Sea. The relevant DNA fragments were amplified, sequenced and analyzed. Contrary to the earlier findings, our coalescence and nested cladistics results show that only a single M. edulis glacial refugium existed in the Atlantic. Despite that, the species survived the glaciation retaining much of its diversity. Unsurprisingly, M. galloprovincialis survived in the Mediterranean Sea. In a relatively short time period, around the climatic optimum at 10 ky ago, the species underwent rapid expansion coupled with population differentiation. Following the expansion, further contemporary gene flow between populations was limited.}, }
@article {pmid24617491, year = {2016}, author = {Zhang, L and Jiang, J and Dong, Y and Qiu, J}, title = {Complete mitochondrial genome of a Pheretimoid earthworm Metaphire vulgaris (Oligochaeta: Megascolecidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {1}, pages = {297-298}, doi = {10.3109/19401736.2014.892085}, pmid = {24617491}, issn = {2470-1408}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; *Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; Oligochaeta/*genetics ; Open Reading Frames ; Phylogeny ; Sequence Analysis, DNA/veterinary ; }, abstract = {We have determined the mitochondrial genome of the first Pheretimoid earthworm, Metaphire vulgaris (Chen, 1930). This mitogenome is 15,061 bp in length containing 37 genes typical of other annelid. All genes are encoded by the same strand, ATP8 is not adjacent to ATP6, all 13 PCGs use ATG as a start codon. These features are consistent with first determined earthworm Lumbricus terrestris, but unusual among animal mtDNAs.}, }
@article {pmid24617472, year = {2016}, author = {Yu, Y and Yi, W and Ma, Z and Yang, R and Shen, J}, title = {The complete mitochondrial genome of Rhodeus fangi (Cypriniformes, Cyprinidae, Acheilognathinae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {1}, pages = {284-285}, doi = {10.3109/19401736.2014.892079}, pmid = {24617472}, issn = {2470-1408}, mesh = {Animals ; Base Composition/genetics ; Base Sequence ; Cyprinidae/*genetics ; Cypriniformes/*genetics ; DNA, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Species Specificity ; }, abstract = {The complete mitochondrial DNA (mtDNA) sequence of Rhodeus fangi is 16,733 bp in length. It consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosome RNA genes and 2 non-coding regions. Base composition of the genome is A (28.54%), G (17.67%), C (27.03%) and T (26.76%) with an A + T-rich hallmark as that of other vertebrate mitochondrial genomes. The complete mitogenome of the R. fangi can provide a basic data for phylogenetic relationship study and useful information for taxonomic identification of the R. smithii complex in genus Rhodeus.}, }
@article {pmid24617461, year = {2016}, author = {Wei, T and Wang, R and Shi, G and Xu, T}, title = {Complete mitochondrial genome of Lophius litulon (Lophiiforms, Lophiidae) and comparison of light strand replication origin in Lophiidae.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {1}, pages = {286-288}, doi = {10.3109/19401736.2014.892080}, pmid = {24617461}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Base Sequence ; DNA, Mitochondrial/*genetics ; Genes, Mitochondrial ; Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; Perciformes/*genetics ; Phylogeny ; Replication Origin ; Sequence Analysis, DNA/veterinary ; }, abstract = {In this study, the complete mitochondrial genome of yellow goosefish Lophius litulon (L. litulon) was determined. The genome was 16,431 bp in length, and comprised 13 protein-coding genes, 2 ribosomal RNA gene and 22 transfer RNA genes, with 2 main non-coding regions. Its gene order and composition was similar to most of the vertebrates. The overall base composition of L. litulon was 28.6% A; 29.1% C; 16.8% G; 25.5% T, with a slight AT bias of 54.1%. The origin of L-strand replication in L. litulon was located in a cluster of five tRNA genes (WANCY). Motif TCCGG was found in the origin of light strand replication (OL) of L. litulon, which was common in other mitogenome of Lophiidae. This mitogenome data would play key role in future studying phylogenetic analysis of the Lophiidae.}, }
@article {pmid24617458, year = {2016}, author = {Jeong, D and Lee, YH}, title = {Complete mitochondrial genome of the Yellownose skate: Zearaja chilensis (Rajiformes, Rajidae).}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {1}, pages = {293-294}, doi = {10.3109/19401736.2014.892083}, pmid = {24617458}, issn = {2470-1408}, mesh = {Animals ; Base Composition ; Base Sequence ; DNA, Mitochondrial/*genetics ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; Sequence Analysis, DNA/veterinary ; Skates, Fish/*genetics ; }, abstract = {The complete sequence of mitochondrial DNA of a Yellownose skate, Zearaja chilensis was determined for the first time. It is 16,909 bp in length covering 2 rRNA, 22 tRNA and 13 protein coding genes with the identical gene order and structure as those of other Rajidae species. The nucleotide of L-strand is composed of low G (14.3%), and slightly high A + T (58.9%) nucleotides. The strong codon usage bias against the use of G (6.0%) is found at the third codon positions. Twelve of the 13 protein coding genes use ATG as the start codon while COX1 starts with GTG. As for the stop codon, only ND4 shows an incomplete stop codon TA. This is the first report of the mitogenome for a species in the genus Zearaja, providing a valuable source of genetic information on the evolution of the family Rajidae and the genus Zearaja as well as for establishment of a sustainble fishery management plan of the species.}, }
@article {pmid24614072, year = {2014}, author = {Hill, JH and Chen, Z and Xu, H}, title = {Selective propagation of functional mitochondrial DNA during oogenesis restricts the transmission of a deleterious mitochondrial variant.}, journal = {Nature genetics}, volume = {46}, number = {4}, pages = {389-392}, pmid = {24614072}, issn = {1546-1718}, support = {ZIA HL006096-01//Intramural NIH HHS/United States ; ZIA HL006153-01//Intramural NIH HHS/United States ; ZIA HL006153-02//Intramural NIH HHS/United States ; }, mesh = {Animals ; Carbonyl Cyanide p-Trifluoromethoxyphenylhydrazone ; DNA Replication/*physiology ; DNA, Mitochondrial/*genetics/*physiology ; Drosophila melanogaster/genetics/*physiology ; *Evolution, Molecular ; Female ; Genes, Lethal/genetics ; Models, Genetic ; Oogenesis/genetics/*physiology ; Selection, Genetic/genetics/*physiology ; Temperature ; Time Factors ; }, abstract = {Although mitochondrial DNA (mtDNA) is prone to mutation and few mtDNA repair mechanisms exist, crippling mitochondrial mutations are exceedingly rare. Recent studies have demonstrated strong purifying selection in the mouse female germline. However, the mechanisms underlying positive selection of healthy mitochondria remain to be elucidated. We visualized mtDNA replication during Drosophila melanogaster oogenesis, finding that mtDNA replication commenced before oocyte determination during the late germarium stage and was dependent on mitochondrial fitness. We isolated a temperature-sensitive lethal mtDNA allele, mt:CoI(T300I), which resulted in reduced mtDNA replication in the germarium at the restrictive temperature. Additionally, the frequency of the mt:CoI(T300I) allele in heteroplasmic flies was decreased, both during oogenesis and over multiple generations, at the restrictive temperature. Furthermore, we determined that selection against mt:CoI(T300I) overlaps with the timing of selective replication of mtDNA in the germarium. These findings establish a previously uncharacterized developmental mechanism for the selective amplification of wild-type mtDNA, which may be evolutionarily conserved to limit the transmission of deleterious mutations.}, }
@article {pmid24603058, year = {2014}, author = {Martin, FN and Blair, JE and Coffey, MD}, title = {A combined mitochondrial and nuclear multilocus phylogeny of the genus Phytophthora.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {66}, number = {}, pages = {19-32}, doi = {10.1016/j.fgb.2014.02.006}, pmid = {24603058}, issn = {1096-0937}, mesh = {Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Mitochondria/*genetics ; Multilocus Sequence Typing ; Mycological Typing Techniques ; *Phylogeny ; Phytophthora/*classification/*genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {The most recent phylogenetic analysis of the genus Phytophthora was completed in 2008 (Blair et al., 2008) and utilized 8.1 kb of sequence data from seven nuclear loci. Given the large number of species that have recently been described, this study was undertaken to broaden the available information on the phylogeny of the genus. A total of 166 isolates representing 92 recognized species and 17 provisional species were analyzed, including many of the same isolates used in the nuclear multilocus study of Blair et al. (2008). Four mitochondrial genes (cox2, nad9, rps10 and secY) were sequenced with a total of 2373 bp used in the analysis; the species relationships recovered with mitochondrial data were largely consistent with those observed previously in the nuclear analysis. Combining the new mitochondrial data with the nuclear data from Blair et al. (2008) generated a dataset of 10,828 bp representing 11 loci, however resolution of basal clade relationships was still low. We therefore implemented a modified multispecies coalescent approach with a subset of the data, and recovered increased resolution and moderate to high support for clade relationships. A more detailed analysis of species from clades 2 and 8 identified an additional seven phylogenetic lineages that warrant further investigation to determine if they represent distinct species. As has been reported in other phylogenetic studies of the genus, there was no consistent correlation between phylogenetic relatedness and morphological features or ecology.}, }
@article {pmid24601779, year = {2014}, author = {Yamada, M and Ishibashi, R and Toyoda, K and Kawamura, K and Komaru, A}, title = {Phylogeography of the brackish water clam Corbicula japonica around the Japanese archipelago inferred from mitochondrial COII gene sequences.}, journal = {Zoological science}, volume = {31}, number = {3}, pages = {168-179}, doi = {10.2108/zsj.31.168}, pmid = {24601779}, issn = {0289-0003}, mesh = {Animals ; Bivalvia/*genetics/*physiology ; Demography ; Electron Transport Complex IV/genetics/*metabolism ; Gene Expression Regulation, Enzymologic ; Japan ; Mitochondria/*enzymology ; Pacific Ocean ; Phylogeny ; Phylogeography ; }, abstract = {We investigated the phylogeography of the Asian brackish water clam, Corbicula japonica, to clarify its demographic history using partial mitochondrial COII gene sequences (990 bp) from 283 individuals collected from around the Japanese archipelago and adjacent areas. Phylogenetic analyses revealed the presence of two major groups within our samples: monophyletic Group I comprising Lineages A-E of C. japonica and paraphyletic Group II consisting of Corbicula sp. Lineages A-C were distributed in Japan and Sakhalin Island, and Lineages D, E, and Corbicula sp. were distributed in the Korean Peninsula. Nested clade analysis (NCA) revealed that Lineage A-the dominant lineage in Japan-consisted of Pacific and Japan Sea lineages, the latter comprising southern and northern Japan Sea groups. Genetic diversity indices of the southern group were higher than those of the northern group, suggesting historical range expansion in the Sea of Japan from southwest to northeast. Geographical distribution of these genetic groups appears to have been influenced by major ocean currents around the Japanese archipelago. Dominant haplotypes in the star-shaped haplotype network of Lineage A were distributed throughout the entire distribution range of each genetic group, implying rapid range expansion of this species. The results of mismatch distribution analysis and molecular clock estimation suggest that expansion of lineage A occurred during the late Middle or Late Pleistocene. In contrast, restricted or past gene flow suggested by NCA and the many unique haplotypes (110/123; 89.4%) present in Lineage A suggest that gene flow among extant populations is rather limited.}, }
@article {pmid24594978, year = {2014}, author = {Reddy, PS and Kavi Kishor, PB and Seiler, C and Kuhlmann, M and Eschen-Lippold, L and Lee, J and Reddy, MK and Sreenivasulu, N}, title = {Unraveling regulation of the small heat shock proteins by the heat shock factor HvHsfB2c in barley: its implications in drought stress response and seed development.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e89125}, pmid = {24594978}, issn = {1932-6203}, mesh = {Computer Simulation ; DNA-Binding Proteins/metabolism ; *Droughts ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; *Gene Expression Regulation, Plant ; Gene Regulatory Networks/genetics ; Heat Shock Transcription Factors ; Heat-Shock Proteins, Small/*genetics/metabolism ; Heat-Shock Response/genetics ; Hordeum/*genetics/growth &amp; development/metabolism ; Hot Temperature ; Multigene Family ; Oryza/genetics/physiology ; Phylogeny ; Plant Development/genetics ; Plant Proteins/chemistry/genetics/*metabolism ; Promoter Regions, Genetic ; Protein Interaction Maps/genetics ; Seeds/*growth &amp; development/physiology ; *Stress, Physiological ; Structural Homology, Protein ; Transcription Factors/metabolism ; Transcription, Genetic ; }, abstract = {The rapid increase in heat shock proteins upon exposure to damaging stresses and during plant development related to desiccation events reveal their dual importance in plant development and stress tolerance. Genome-wide sequence survey identified 20 non-redundant small heat shock proteins (sHsp) and 22 heat shock factor (Hsf) genes in barley. While all three major classes (A, B, C) of Hsfs are localized in nucleus, the 20 sHsp gene family members are localized in different cell organelles like cytoplasm, mitochondria, plastid and peroxisomes. Hsf and sHsp members are differentially regulated during drought and at different seed developmental stages suggesting the importance of chaperone role under drought as well as seed development. In silico cis-regulatory motif analysis of Hsf promoters showed an enrichment with abscisic acid responsive cis-elements (ABRE), implying regulatory role of ABA in mediating transcriptional response of HvsHsf genes. Gene regulatory network analysis identified HvHsfB2c as potential central regulator of the seed-specific expression of several HvsHsps including 17.5CI sHsp. These results indicate that HvHsfB2c is co-expressed in the central hub of small Hsps and therefore it may be regulating the expression of several HvsHsp subclasses HvHsp16.88-CI, HvHsp17.5-CI and HvHsp17.7-CI. The in vivo relevance of binding specificity of HvHsfB2C transcription factor to HSE-element present in the promoter of HvSHP17.5-CI under heat stress exposure is confirmed by gel shift and LUC-reporter assays. Further, we isolated 477 bp cDNA from barley encoding a 17.5 sHsp polypeptide, which was predominantly upregulated under drought stress treatments and also preferentially expressed in developing seeds. Recombinant HvsHsp17.5-CI protein was expressed in E. coli and purified to homogeneity, which displayed in vitro chaperone activity. The predicted structural model of HvsHsp-17.5-CI protein suggests that the α-crystallin domain is evolutionarily highly conserved.}, }
@article {pmid24591518, year = {2014}, author = {Gray, MW}, title = {The pre-endosymbiont hypothesis: a new perspective on the origin and evolution of mitochondria.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {6}, number = {3}, pages = {}, pmid = {24591518}, issn = {1943-0264}, mesh = {Alphaproteobacteria/genetics ; *Biological Evolution ; DNA, Mitochondrial/chemistry ; Genome, Bacterial ; Genome, Mitochondrial ; Mitochondria/*genetics/physiology/ultrastructure ; Phylogeny ; Symbiosis ; }, abstract = {Mitochondrial DNA (mtDNA) is unquestionably the remnant of an α-proteobacterial genome, yet only ~10%-20% of mitochondrial proteins are demonstrably α-proteobacterial in origin (the "α-proteobacterial component," or APC). The evolutionary ancestry of the non-α-proteobacterial component (NPC) is obscure and not adequately accounted for in current models of mitochondrial origin. I propose that in the host cell that accommodated an α-proteobacterial endosymbiont, much of the NPC was already present, in the form of a membrane-bound metabolic organelle (the premitochondrion) that compartmentalized many of the non-energy-generating functions of the contemporary mitochondrion. I suggest that this organelle also possessed a protein import system and various ion and small-molecule transporters. In such a scenario, an α-proteobacterial endosymbiont could have been converted relatively directly and rapidly into an energy-generating organelle that incorporated the extant metabolic functions of the premitochondrion. This model (the "pre-endosymbiont hypothesis") effectively represents a synthesis of previous, contending mitochondrial origin hypotheses, with the bulk of the mitochondrial proteome (much of the NPC) having an endogenous origin and the minority component (the APC) having a xenogenous origin.}, }
@article {pmid24587288, year = {2014}, author = {Ruban, A and Fuchs, J and Marques, A and Schubert, V and Soloviev, A and Raskina, O and Badaeva, E and Houben, A}, title = {B chromosomes of Aegilops speltoides are enriched in organelle genome-derived sequences.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e90214}, pmid = {24587288}, issn = {1932-6203}, mesh = {Chromosomes, Plant/*genetics ; DNA, Plant/*genetics ; Genome, Plant/*genetics ; Organ Specificity ; Organelles/*genetics ; Poaceae/*genetics ; Polymorphism, Genetic ; Repetitive Sequences, Nucleic Acid/genetics ; *Sequence Analysis, DNA ; }, abstract = {B chromosomes (Bs) are dispensable components of the genome exhibiting non-Mendelian inheritance. Chromosome counts and flow cytometric analysis of the grass species Aegilops speltoides revealed a tissue-type specific distribution of the roughly 570 Mbp large B chromosomes. To address the question whether organelle-to-nucleus DNA transfer is a mechanism that drives the evolution of Bs, in situ hybridization was performed with labelled organellar DNA. The observed B-specific accumulation of chloroplast- and mitochondria-derived sequences suggests a reduced selection against the insertion of organellar DNA in supernumerary chromosomes. The distribution of B-localised organellar-derived sequences and other sequences differs between genotypes of different geographical origins.}, }
@article {pmid24586126, year = {2014}, author = {Amrine, KC and Swingley, WD and Ardell, DH}, title = {tRNA signatures reveal a polyphyletic origin of SAR11 strains among alphaproteobacteria.}, journal = {PLoS computational biology}, volume = {10}, number = {2}, pages = {e1003454}, pmid = {24586126}, issn = {1553-7358}, mesh = {Alphaproteobacteria/*classification/*genetics ; Bacterial Proteins/genetics ; Computational Biology ; Evolution, Molecular ; Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genome, Bacterial ; Models, Genetic ; Phylogeny ; RNA, Bacterial/*genetics ; RNA, Transfer/*genetics ; Rhodospirillales/classification/genetics ; }, abstract = {Molecular phylogenetics and phylogenomics are subject to noise from horizontal gene transfer (HGT) and bias from convergence in macromolecular compositions. Extensive variation in size, structure and base composition of alphaproteobacterial genomes has complicated their phylogenomics, sparking controversy over the origins and closest relatives of the SAR11 strains. SAR11 are highly abundant, cosmopolitan aquatic Alphaproteobacteria with streamlined, A+T-biased genomes. A dominant view holds that SAR11 are monophyletic and related to both Rickettsiales and the ancestor of mitochondria. Other studies dispute this, finding evidence of a polyphyletic origin of SAR11 with most strains distantly related to Rickettsiales. Although careful evolutionary modeling can reduce bias and noise in phylogenomic inference, entirely different approaches may be useful to extract robust phylogenetic signals from genomes. Here we develop simple phyloclassifiers from bioinformatically derived tRNA Class-Informative Features (CIFs), features predicted to target tRNAs for specific interactions within the tRNA interaction network. Our tRNA CIF-based model robustly and accurately classifies alphaproteobacterial genomes into one of seven undisputed monophyletic orders or families, despite great variability in tRNA gene complement sizes and base compositions. Our model robustly rejects monophyly of SAR11, classifying all but one strain as Rhizobiales with strong statistical support. Yet remarkably, conventional phylogenetic analysis of tRNAs classifies all SAR11 strains identically as Rickettsiales. We attribute this discrepancy to convergence of SAR11 and Rickettsiales tRNA base compositions. Thus, tRNA CIFs appear more robust to compositional convergence than tRNA sequences generally. Our results suggest that tRNA-CIF-based phyloclassification is robust to HGT of components of the tRNA interaction network, such as aminoacyl-tRNA synthetases. We explain why tRNAs are especially advantageous for prediction of traits governing macromolecular interactions from genomic data, and why such traits may be advantageous in the search for robust signals to address difficult problems in classification and phylogeny.}, }
@article {pmid24581801, year = {2014}, author = {Cristiano, MP and Cardoso, DC and Fernandes-Salomão, TM}, title = {Could pseudogenes be widespread in ants? Evidence of numts in the leafcutter ant Acromyrmex striatus (Roger, 1863) (Formicidae: Attini).}, journal = {Comptes rendus biologies}, volume = {337}, number = {2}, pages = {78-85}, doi = {10.1016/j.crvi.2013.11.007}, pmid = {24581801}, issn = {1768-3238}, mesh = {Animals ; Ants/*genetics ; Base Sequence ; Cytochromes b/genetics ; DNA/genetics ; DNA Primers ; DNA, Mitochondrial/chemistry/genetics ; Evolution, Molecular ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Polymerase Chain Reaction ; Pseudogenes/*genetics ; Sequence Analysis, DNA ; }, abstract = {The incorporation of fragments of mitochondrial DNA (mtDNA) in the nuclear genome, known as numts (nuclear mitochondrial pseudogenes), undermines general assumptions concerning the use of mtDNA in phylogenetic and phylogeographic studies. Accidental amplifications of these nuclear copies instead of the mitochondrial target can lead to crucial misinterpretations, thus the correct identification of numts and their differentiation from true mitochondrial sequences are important in preventing this kind of error. Our goal was to describe the existence of cytochrome b (cytb) numts in the leafcutter ant Acromyrmex striatus (Roger, 1863). PCR products were directly sequenced using a pair of universal primers designed to amplify the cytb gene of these insects. Other species of leafcutter ants were also sequenced. The sequences were analyzed and the numts were identified by the presence of double peaks, indels and premature stop codons. Only A. striatus clearly showed the presence of numts, while the other species displayed the expected amplification of the mtDNA cytb gene target using the same primer pair. We hope that our report will highlight the benefits and challenges of using mtDNA in the molecular phylogenetic reconstruction and phylogeographic studies of ants, while establishing the importance of numts reports for future studies.}, }
@article {pmid24563201, year = {2014}, author = {Li, F and Chung, T and Vierstra, RD}, title = {AUTOPHAGY-RELATED11 plays a critical role in general autophagy- and senescence-induced mitophagy in Arabidopsis.}, journal = {The Plant cell}, volume = {26}, number = {2}, pages = {788-807}, pmid = {24563201}, issn = {1532-298X}, mesh = {Amino Acid Sequence ; Arabidopsis/*cytology/genetics/*metabolism ; Arabidopsis Proteins/chemistry/*metabolism ; *Autophagy/genetics ; Autophagy-Related Proteins ; *Cellular Senescence/genetics ; Darkness ; Gene Expression Regulation, Plant ; Genes, Plant ; Genotype ; *Mitophagy/genetics ; Models, Biological ; Molecular Sequence Data ; Phenotype ; Phosphorylation ; Phylogeny ; Plant Leaves/cytology/growth &amp; development/metabolism ; Protein Binding ; Protein Subunits/metabolism ; Reverse Genetics ; Vacuoles/metabolism ; Vesicular Transport Proteins/chemistry/*metabolism ; }, abstract = {Autophagy-mediated turnover removes damaged organelles and unwanted cytoplasmic constituents and thus plays critical roles in cellular housekeeping and nutrient recycling. This "self eating" is tightly regulated by the AUTOPHAGY-RELATED1/13 (ATG1/13) kinase complex, which connects metabolic and environmental cues to the vacuolar delivery of autophagic vesicles. Here, we describe the Arabidopsis thaliana accessory proteins ATG11 and ATG101, which help link the ATG1/13 complex to autophagic membranes. ATG11 promotes vesicle delivery to the vacuole but is not essential for synthesizing the ATG12-ATG5 and ATG8-phosphatidylethanolamine adducts that are central to autophagic vesicle assembly. ATG11, ATG101, ATG1, and ATG13 colocalize with each other and with ATG8, with ATG1 tethered to ATG8 via a canonical ATG8-interacting motif. Also, the presence of ATG11 encourages starvation-induced phosphorylation of ATG1 and turnover of ATG1 and ATG13. Like other atg mutants, ATG11-deficient plants senesce prematurely and are hypersensitive to nitrogen and fixed-carbon limitations. Additionally, we discovered that the senescence-induced breakdown of mitochondria-resident proteins and mitochondrial vesicles occurs via an autophagic process requiring ATG11 and other ATG components. Together, our data indicate that ATG11 (and possibly ATG101) provides important scaffolds connecting the ATG1/13 complex to both general autophagy and selective mitophagy.}, }
@article {pmid24561573, year = {2014}, author = {Braun, HP and Binder, S and Brennicke, A and Eubel, H and Fernie, AR and Finkemeier, I and Klodmann, J and König, AC and Kühn, K and Meyer, E and Obata, T and Schwarzländer, M and Takenaka, M and Zehrmann, A}, title = {The life of plant mitochondrial complex I.}, journal = {Mitochondrion}, volume = {19 Pt B}, number = {}, pages = {295-313}, doi = {10.1016/j.mito.2014.02.006}, pmid = {24561573}, issn = {1872-8278}, mesh = {Electron Transport Complex I/genetics/*metabolism ; Mitochondria/*enzymology/genetics/metabolism ; Plants/*enzymology/genetics/metabolism ; *Protein Multimerization ; Protein Subunits/genetics/metabolism ; }, abstract = {The mitochondrial NADH dehydrogenase complex (complex I) of the respiratory chain has several remarkable features in plants: (i) particularly many of its subunits are encoded by the mitochondrial genome, (ii) its mitochondrial transcripts undergo extensive maturation processes (e.g. RNA editing, trans-splicing), (iii) its assembly follows unique routes, (iv) it includes an additional functional domain which contains carbonic anhydrases and (v) it is, indirectly, involved in photosynthesis. Comprising about 50 distinct protein subunits, complex I of plants is very large. However, an even larger number of proteins are required to synthesize these subunits and assemble the enzyme complex. This review aims to follow the complete "life cycle" of plant complex I from various molecular perspectives. We provide arguments that complex I represents an ideal model system for studying the interplay of respiration and photosynthesis, the cooperation of mitochondria and the nucleus during organelle biogenesis and the evolution of the mitochondrial oxidative phosphorylation system.}, }
@article {pmid24561571, year = {2014}, author = {Perez, E and Lapaille, M and Degand, H and Cilibrasi, L and Villavicencio-Queijeiro, A and Morsomme, P and González-Halphen, D and Field, MC and Remacle, C and Baurain, D and Cardol, P}, title = {The mitochondrial respiratory chain of the secondary green alga Euglena gracilis shares many additional subunits with parasitic Trypanosomatidae.}, journal = {Mitochondrion}, volume = {19 Pt B}, number = {}, pages = {338-349}, doi = {10.1016/j.mito.2014.02.001}, pmid = {24561571}, issn = {1872-8278}, mesh = {Computational Biology ; *Electron Transport ; Electrophoresis, Gel, Two-Dimensional ; Euglena gracilis/*enzymology/*genetics ; Mitochondria/*enzymology/*genetics ; Phylogeny ; Sequence Homology, Amino Acid ; Tandem Mass Spectrometry ; Trypanosomatina/*enzymology/*genetics ; }, abstract = {The mitochondrion is an essential organelle for the production of cellular ATP in most eukaryotic cells. It is extensively studied, including in parasitic organisms such as trypanosomes, as a potential therapeutic target. Recently, numerous additional subunits of the respiratory-chain complexes have been described in Trypanosoma brucei and Trypanosoma cruzi. Since these subunits had apparently no counterparts in other organisms, they were interpreted as potentially associated with the parasitic trypanosome lifestyle. Here we used two complementary approaches to characterise the subunit composition of respiratory complexes in Euglena gracilis, a non-parasitic secondary green alga related to trypanosomes. First, we developed a phylogenetic pipeline aimed at mining sequence databases for identifying homologues to known respiratory-complex subunits with high confidence. Second, we used MS/MS proteomics after two-dimensional separation of the respiratory complexes by Blue Native- and SDS-PAGE both to confirm in silico predictions and to identify further additional subunits. Altogether, we identified 41 subunits that are restricted to E. gracilis, T. brucei and T. cruzi, along with 48 classical subunits described in other eukaryotes (i.e. plants, mammals and fungi). This moreover demonstrates that at least half of the subunits recently reported in T. brucei and T. cruzi are actually not specific to Trypanosomatidae, but extend at least to other Euglenozoa, and that their origin and function are thus not specifically associated with the parasitic lifestyle. Furthermore, preliminary biochemical analyses suggest that some of these additional subunits underlie the peculiarities of the respiratory chain observed in Euglenozoa.}, }
@article {pmid24557444, year = {2014}, author = {Zhu, A and Guo, W and Jain, K and Mower, JP}, title = {Unprecedented heterogeneity in the synonymous substitution rate within a plant genome.}, journal = {Molecular biology and evolution}, volume = {31}, number = {5}, pages = {1228-1236}, doi = {10.1093/molbev/msu079}, pmid = {24557444}, issn = {1537-1719}, mesh = {Ajuga/*genetics ; Amino Acid Sequence ; Amino Acid Substitution ; Codon, Initiator/genetics ; *Evolution, Molecular ; Genome, Mitochondrial ; *Genome, Plant ; Genome, Plastid ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics ; Selection, Genetic ; Sequence Homology, Amino Acid ; }, abstract = {The synonymous substitution rate varies widely among species, but it is generally quite stable within a genome due to the absence of strong selective pressures. In plants, plastid genes tend to evolve faster than mitochondrial genes, rate variation among species generally correlates between the mitochondrial and plastid genomes, and few examples of intragenomic rate heterogeneity exist. To study the extent of substitution rate variation between and within plant organellar genomes, we sequenced the complete mitochondrial and plastid genomes from the bugleweed, Ajuga reptans, which was previously shown to exhibit rate heterogeneity for several mitochondrial genes. Substitution rates were accelerated specifically in the mitochondrial genome, which contrasts with correlated plastid and mitochondrial rate changes in most other angiosperms. Strikingly, we uncovered a 340-fold range of synonymous substitution rate variation among Ajuga mitochondrial genes. This is by far the largest amount of synonymous rate heterogeneity ever reported for a genome, but the evolutionary forces driving this phenomenon are unclear. Selective effects on synonymous sites in plant mitochondria are generally weak and thus unlikely to generate such unprecedented intragenomic rate heterogeneity. Quickly evolving genes are not clustered in the genome, arguing against localized hypermutation, although it is possible that they were clustered ancestrally given the high rate of genomic rearrangement in plant mitochondria. Mutagenic retroprocessing, involving error-prone reverse transcription and genomic integration of mature transcripts, is hypothesized as another potential explanation.}, }
@article {pmid24552149, year = {2014}, author = {Ericson, M and Janes, MA and Butter, F and Mann, M and Ullu, E and Tschudi, C}, title = {On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei.}, journal = {BMC biology}, volume = {12}, number = {}, pages = {14}, pmid = {24552149}, issn = {1741-7007}, support = {T32 AI007640/AI/NIAID NIH HHS/United States ; AI56333/AI/NIAID NIH HHS/United States ; AI28798/AI/NIAID NIH HHS/United States ; T32 AI007404/AI/NIAID NIH HHS/United States ; R01 AI043594/AI/NIAID NIH HHS/United States ; R37 AI028798/AI/NIAID NIH HHS/United States ; R01 AI056333/AI/NIAID NIH HHS/United States ; AI043594/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Cell Cycle ; Conserved Sequence ; Evolution, Molecular ; Humans ; Life Cycle Stages ; Mass Spectrometry ; Membrane Proteins/metabolism ; Mitochondrial Proteins/metabolism ; Molecular Sequence Data ; Open Reading Frames ; Parasites/growth &amp; development/*metabolism ; Protein Structure, Tertiary ; Proteome/*metabolism ; *Proteomics ; Protozoan Proteins/chemistry/genetics/*metabolism ; RNA Interference ; RNA, Messenger/genetics/metabolism ; Trypanosoma brucei brucei/growth &amp; development/*metabolism ; }, abstract = {BACKGROUND: Although technical advances in genomics and proteomics research have yielded a better understanding of the coding capacity of a genome, one major challenge remaining is the identification of all expressed proteins, especially those less than 100 amino acids in length. Such information can be particularly relevant to human pathogens, such as Trypanosoma brucei, the causative agent of African trypanosomiasis, since it will provide further insight into the parasite biology and life cycle.<br><br>RESULTS: Starting with 993&#x2009;T. brucei transcripts, previously shown by RNA-Sequencing not to coincide with annotated coding sequences (CDS), homology searches revealed that 173 predicted short open reading frames in these transcripts are conserved across kinetoplastids with 13 also conserved in representative eukaryotes. Mining mass spectrometry data sets revealed 42 transcripts encoding at least one matching peptide. RNAi-induced down-regulation of these 42 transcripts revealed seven to be essential in insect-form trypanosomes with two also required for the bloodstream life cycle stage. To validate the specificity of the RNAi results, each lethal phenotype was rescued by co-expressing an RNAi-resistant construct of each corresponding CDS. These previously non-annotated essential small proteins localized to a variety of cell compartments, including the cell surface, mitochondria, nucleus and cytoplasm, inferring the diverse biological roles they are likely to play in T. brucei. We also provide evidence that one of these small proteins is required for replicating the kinetoplast (mitochondrial) DNA.<br><br>CONCLUSIONS: Our studies highlight the presence and significance of small proteins in a protist and expose potential new targets to block the survival of trypanosomes in the insect vector and/or the mammalian host.}, }
@article {pmid24535861, year = {2014}, author = {Wang, YB and Guan, LL and Xu, YW and Shen, H and Wu, W}, title = {Cloning and sequence analysis of the safflower betaine aldehyde dehydrogenase gene.}, journal = {Genetics and molecular research : GMR}, volume = {13}, number = {1}, pages = {344-353}, doi = {10.4238/2014.January.21.2}, pmid = {24535861}, issn = {1676-5680}, mesh = {Amino Acid Sequence ; Base Sequence ; Betaine-Aldehyde Dehydrogenase/chemistry/*genetics/metabolism ; Carthamus tinctorius/chemistry/*enzymology/genetics ; Cloning, Molecular ; *Genes, Plant ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/*genetics/metabolism ; Protein Structure, Tertiary ; Protein Transport ; }, abstract = {In response to salinity or drought stress, many plants accumulate glycine betaine, which is a regulator of osmosis. In plants, the last step in betaine synthesis is catalyzed by betaine aldehyde dehydrogenase (BADH), a nuclear-encoded chloroplastic enzyme. Based on the conserved oligo amino acid residues of the published BADH genes from other higher plant species, a cDNA sequence, designated CtBADH, was isolated from safflower (Carthamus tinctorius L.) using a polymerase chain reaction approach. The clones were 1.7 kb on average, and contained an open reading frame predicting a polypeptide of 503 amino acids with 84.5% identity to that of Helianthus annuus. The deduced amino acid sequence showed a decapeptide, Val-Thr-Leu-Geu-Leu-Gly-Gly-Lys-Ser-Pro and Cys, which is essential for proper functioning of BADH. Phylogenetic analysis indicated that CtBADH grouped with other dicotyledonous plant BADH genes, and subgrouped in the composite family. Prediction of secondary structure and subcellular localization suggested that the protein encoded by CtBADH contains 33 coils, 15 alpha helixes, and 21 beta strands, and most likely targets the chloroplast or mitochondria.}, }
@article {pmid24532780, year = {2014}, author = {Tamuri, AU and Goldman, N and dos Reis, M}, title = {A penalized-likelihood method to estimate the distribution of selection coefficients from phylogenetic data.}, journal = {Genetics}, volume = {197}, number = {1}, pages = {257-271}, pmid = {24532780}, issn = {1943-2631}, mesh = {Animals ; Base Sequence ; *Computer Simulation ; *Evolution, Molecular ; Genetic Fitness ; Humans ; Likelihood Functions ; Mutation ; *Phylogeny ; Selection, Genetic ; }, abstract = {We develop a maximum penalized-likelihood (MPL) method to estimate the fitnesses of amino acids and the distribution of selection coefficients (S = 2Ns) in protein-coding genes from phylogenetic data. This improves on a previous maximum-likelihood method. Various penalty functions are used to penalize extreme estimates of the fitnesses, thus correcting overfitting by the previous method. Using a combination of computer simulation and real data analysis, we evaluate the effect of the various penalties on the estimation of the fitnesses and the distribution of S. We show the new method regularizes the estimates of the fitnesses for small, relatively uninformative data sets, but it can still recover the large proportion of deleterious mutations when present in simulated data. Computer simulations indicate that as the number of taxa in the phylogeny or the level of sequence divergence increases, the distribution of S can be more accurately estimated. Furthermore, the strength of the penalty can be varied to study how informative a particular data set is about the distribution of S. We analyze three protein-coding genes (the chloroplast rubisco protein, mammal mitochondrial proteins, and an influenza virus polymerase) and show the new method recovers a large proportion of deleterious mutations in these data, even under strong penalties, confirming the distribution of S is bimodal in these real data. We recommend the use of the new MPL approach for the estimation of the distribution of S in species phylogenies of protein-coding genes.}, }
@article {pmid24532674, year = {2014}, author = {Williams, TA and Embley, TM}, title = {Archaeal "dark matter" and the origin of eukaryotes.}, journal = {Genome biology and evolution}, volume = {6}, number = {3}, pages = {474-481}, pmid = {24532674}, issn = {1759-6653}, support = {268701/ERC_/European Research Council/International ; }, mesh = {Archaea/*genetics ; *Biological Evolution ; Eukaryota/*genetics ; Genome, Archaeal ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; Sequence Alignment ; }, abstract = {Current hypotheses about the history of cellular life are mainly based on analyses of cultivated organisms, but these represent only a small fraction of extant biodiversity. The sequencing of new environmental lineages therefore provides an opportunity to test, revise, or reject existing ideas about the tree of life and the origin of eukaryotes. According to the textbook three domains hypothesis, the eukaryotes emerge as the sister group to a monophyletic Archaea. However, recent analyses incorporating better phylogenetic models and an improved sampling of the archaeal domain have generally supported the competing eocyte hypothesis, in which core genes of eukaryotic cells originated from within the Archaea, with important implications for eukaryogenesis. Given this trend, it was surprising that a recent analysis incorporating new genomes from uncultivated Archaea recovered a strongly supported three domains tree. Here, we show that this result was due in part to the use of a poorly fitting phylogenetic model and also to the inclusion by an automated pipeline of genes of putative bacterial origin rather than nucleocytosolic versions for some of the eukaryotes analyzed. When these issues were resolved, analyses including the new archaeal lineages placed core eukaryotic genes within the Archaea. These results are consistent with a number of recent studies in which improved archaeal sampling and better phylogenetic models agree in supporting the eocyte tree over the three domains hypothesis.}, }
@article {pmid24532299, year = {2014}, author = {Kitahara, R and Ikeda, Y and Shimura, H and Masuta, C and Ezawa, T}, title = {A unique mitovirus from Glomeromycota, the phylum of arbuscular mycorrhizal fungi.}, journal = {Archives of virology}, volume = {159}, number = {8}, pages = {2157-2160}, doi = {10.1007/s00705-014-1999-1}, pmid = {24532299}, issn = {1432-8798}, mesh = {Amino Acid Sequence ; Base Sequence ; Genome, Viral ; Glomeromycota/*virology ; Molecular Sequence Data ; Mycorrhizae/*virology ; Open Reading Frames ; Phylogeny ; RNA Viruses/chemistry/*classification/genetics/*isolation &amp; purification ; Sequence Alignment ; Viral Proteins/chemistry/genetics ; }, abstract = {Arbuscular mycorrhizal (AM) fungi that belong to the phylum Glomeromycota associate with most land plants and supply mineral nutrients to the host plants. One of the four viral segments found by deep-sequencing of dsRNA in the AM fungus Rhizophagus clarus strain RF1 showed similarity to mitoviruses and is characterized in this report. The genome segment is 2,895 nucleotides in length, and the largest ORF was predicted by applying either the mold mitochondrial or the universal genetic code. The ORF encodes a polypeptide of 820 amino acids with a molecular mass of 91.2 kDa and conserves the domain of the mitovirus RdRp superfamily. Accordingly, the dsRNA was designated as R. clarus mitovirus 1 strain RF1 (RcMV1-RF1). Mitoviruses are localized exclusively in mitochondria and thus generally employ the mold mitochondrial genetic code. The distinct codon usage of RcMV1-RF1, however, suggests that the virus is potentially able to replicate not only in mitochondria but also in the cytoplasm. RcMV1-RF1 RdRp showed the highest similarity to the putative RdRp of a mitovirus-like ssRNA found in another AM fungus, followed by RdRp of a mitovirus in an ascomycotan ectomycorrhizal fungus. The three mitoviruses found in the three mycorrhizal fungi formed a deeply branching clade that is distinct from the two major clades in the genus Mitovirus.}, }
@article {pmid24531459, year = {2014}, author = {Fieulaine, S and Desmadril, M and Meinnel, T and Giglione, C}, title = {Understanding the highly efficient catalysis of prokaryotic peptide deformylases by shedding light on the determinants specifying the low activity of the human counterpart.}, journal = {Acta crystallographica. Section D, Biological crystallography}, volume = {70}, number = {Pt 2}, pages = {242-252}, doi = {10.1107/S1399004713026461}, pmid = {24531459}, issn = {1399-0047}, mesh = {Amidohydrolases/*chemistry/genetics ; Amino Acid Sequence ; Arabidopsis/*chemistry/enzymology ; Arabidopsis Proteins/*chemistry/genetics ; Bacterial Proteins/*chemistry/genetics ; Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; Escherichia coli/*chemistry/enzymology/genetics ; Gene Expression ; Humans ; Kinetics ; Leptospira interrogans/*chemistry/enzymology ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/genetics ; Sequence Alignment ; Static Electricity ; Structure-Activity Relationship ; Substrate Specificity ; }, abstract = {Peptide deformylases (PDFs), which are essential and ubiquitous enzymes involved in the removal of the N-formyl group from nascent chains, are classified into four subtypes based on the structural and sequence similarity of specific conserved domains. All PDFs share a similar three-dimensional structure, are functionally interchangeable in vivo and display similar properties in vitro, indicating that their molecular mechanism has been conserved during evolution. The human mitochondrial PDF is the only exception as despite its conserved fold it reveals a unique substrate-binding pocket together with an unusual kinetic behaviour. Unlike human PDF, the closely related mitochondrial PDF1As from plants have catalytic efficiencies and enzymatic parameters that are similar to those of other classes of PDFs. Here, the aim was to identify the structural basis underlying the properties of human PDF compared with all other PDFs by focusing on plant mitochondrial PDF1A. The construction of a chimaera composed of plant PDF1A with the nonrandom substitutions found in a conserved motif of its human homologue converted it into an enzyme with properties similar to the human enzyme, indicating the crucial role of these positions. The crystal structure of this human-like plant PDF revealed that substitution of two residues leads to a reduction in the volume of the ligand-binding site together with the introduction of negative charges, unravelling the origin of the weak affinity of human PDF for its substrate. In addition, the substitution of the two residues of human PDF modifies the transition state of the reaction through alteration of the network of interactions between the catalytic residues and the substrate, leading to an overall reduced reaction rate.}, }
@article {pmid24530798, year = {2014}, author = {Jimenez, AG and Cooper-Mullin, C and Anthony, NB and Williams, JB}, title = {Cellular metabolic rates in cultured primary dermal fibroblasts and myoblast cells from fast-growing and control Coturnix quail.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {171}, number = {}, pages = {23-30}, doi = {10.1016/j.cbpa.2014.02.006}, pmid = {24530798}, issn = {1531-4332}, mesh = {Acids/metabolism ; Animals ; *Basal Metabolism ; Cells, Cultured ; Coturnix/*growth &amp; development ; Dermis/*cytology ; Extracellular Space/metabolism ; Fibroblasts/*cytology/*metabolism ; Metabolome ; Mitochondria/metabolism ; Myoblasts/*cytology/*metabolism ; Oxygen Consumption ; Staining and Labeling ; }, abstract = {Fibroblast cells have been extensively used in research, including in medicine, physiology, physiological-ecology, and conservation biology. However, whether the physiology of fibroblasts reflects the physiology of other cell types in the same animal is unknown. Dermal fibroblasts are responsible for generating connective tissue and involved in wound healing, but generally, this cell type is thought to be metabolically inactive until it is required at the site of tissue damage. Thus, one might question whether fibroblasts are a representative model system to portray the metabolic profile of the whole organism, as compared with cells isolated from other tissues, like muscle, brain or kidneys. To explore whether fibroblasts have the same metabolic profile as do myoblast cells, we cultured cells from day-old chicks of quail (Coturnix coturnix japonica) selected for fast-growth or normal growth (our control group). Our results suggest that isolated primary fibroblasts and myoblast cells had higher rates of glycolysis, oxygen consumption and more mitochondria in the fast-growing line than in the control line. Our findings lend support for the idea that fibroblasts are a representative cell system to characterize the whole organism metabolic signature at the cellular-level. These data are striking, however, because fibroblasts had higher rates of metabolism for every parameter measured than myoblast cells isolated from the same individuals.}, }
@article {pmid24516391, year = {2014}, author = {Itsara, LS and Kennedy, SR and Fox, EJ and Yu, S and Hewitt, JJ and Sanchez-Contreras, M and Cardozo-Pelaez, F and Pallanck, LJ}, title = {Oxidative stress is not a major contributor to somatic mitochondrial DNA mutations.}, journal = {PLoS genetics}, volume = {10}, number = {2}, pages = {e1003974}, pmid = {24516391}, issn = {1553-7404}, support = {F31 NS071857/NS/NINDS NIH HHS/United States ; R01 GM104990/GM/NIGMS NIH HHS/United States ; P01 AG001751/AG/NIA NIH HHS/United States ; R01 GM086394/GM/NIGMS NIH HHS/United States ; T32 AG000057/AG/NIA NIH HHS/United States ; P30 AG013280/AG/NIA NIH HHS/United States ; }, mesh = {Aging/*genetics/pathology ; Animals ; DNA Glycosylases/genetics ; DNA Repair/genetics ; DNA, Mitochondrial/*genetics ; Drosophila Proteins/genetics ; Drosophila melanogaster ; Humans ; Mitochondria/genetics/pathology ; Models, Animal ; Mutation/*genetics ; Mutation Rate ; *Oxidative Stress ; Reactive Oxygen Species/metabolism ; Superoxide Dismutase/genetics ; }, abstract = {The accumulation of somatic mitochondrial DNA (mtDNA) mutations is implicated in aging and common diseases of the elderly, including cancer and neurodegenerative disease. However, the mechanisms that influence the frequency of somatic mtDNA mutations are poorly understood. To develop a simple invertebrate model system to address this matter, we used the Random Mutation Capture (RMC) assay to characterize the age-dependent frequency and distribution of mtDNA mutations in the fruit fly Drosophila melanogaster. Because oxidative stress is a major suspect in the age-dependent accumulation of somatic mtDNA mutations, we also used the RMC assay to explore the influence of oxidative stress on the somatic mtDNA mutation frequency. We found that many of the features associated with mtDNA mutations in vertebrates are conserved in Drosophila, including a comparable somatic mtDNA mutation frequency (∼10(-5)), an increased frequency of mtDNA mutations with age, and a prevalence of transition mutations. Only a small fraction of the mtDNA mutations detected in young or old animals were G∶C to T∶A transversions, a signature of oxidative damage, and loss-of-function mutations in the mitochondrial superoxide dismutase, Sod2, had no detectable influence on the somatic mtDNA mutation frequency. Moreover, a loss-of-function mutation in Ogg1, which encodes a DNA repair enzyme that removes oxidatively damaged deoxyguanosine residues (8-hydroxy-2'-deoxyguanosine), did not significantly influence the somatic mtDNA mutation frequency of Sod2 mutants. Together, these findings indicate that oxidative stress is not a major cause of somatic mtDNA mutations. Our data instead suggests that somatic mtDNA mutations arise primarily from errors that occur during mtDNA replication. Further studies using Drosophila should aid in the identification of factors that influence the frequency of somatic mtDNA mutations.}, }
@article {pmid24516191, year = {2014}, author = {Steiner, CC and Charter, SJ and Houck, ML and Ryder, OA}, title = {Molecular phylogeny and chromosomal evolution of Alcelaphini (Antilopinae).}, journal = {The Journal of heredity}, volume = {105}, number = {3}, pages = {324-333}, doi = {10.1093/jhered/esu004}, pmid = {24516191}, issn = {1465-7333}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Genetic Speciation ; *Genetic Variation ; Genetics, Population ; Genome, Mitochondrial ; Karyotype ; Mitochondria/genetics ; Phylogeny ; Ruminants/*classification/*genetics ; Translocation, Genetic ; }, abstract = {Robertsonian (Rb) translocations, in particular centric fusions, are thought to play a primary role in evolution and speciation of the Bovidae family. However, Rb fusions are often polymorphic within species, being suggested as phylogenetically uninformative characters. This work studies chromosome variation in 72 captive individuals of 6 species of Alcelaphini (Antilopinae): The hartebeest (genus Alcelaphus), hirola (Beatragus), black and blue wildebeests (Connochaetes), and the topi and bontebok (Damaliscus). We infer the phylogenic relationships among Alcelaphini species and determine patterns of chromosomal evolution using G-banded karyotypes and complete mitochondrial genome sequences. The molecular phylogeny showed an early divergence of Connochaetes, followed by the split of Alcelaphus plus Beatragus + Damaliscus as sister taxa. Mitochondrial and chromosomal phylogenies only differed in the position of the critically endangered Beatragus, likely due to homoplasic chromosome characters. Patterns of chromosome evolution, reconstructed using a probabilistic approach, suggest that chromosome changes leading to speciation in Alcelaphini do not exclusively involve consecutive reduction of diploid number through centric fusion but also the losses and reversions of Rb translocations in Beatragus and Damaliscus lineages. Our results provide evidence that complex scenarios of chromosomal rearrangements can be detected in relatively recent-diverged bovids, as in this group of antelopes.}, }
@article {pmid24515833, year = {2014}, author = {Mueller, SJ and Lang, D and Hoernstein, SN and Lang, EG and Schuessele, C and Schmidt, A and Fluck, M and Leisibach, D and Niegl, C and Zimmer, AD and Schlosser, A and Reski, R}, title = {Quantitative analysis of the mitochondrial and plastid proteomes of the moss Physcomitrella patens reveals protein macrocompartmentation and microcompartmentation.}, journal = {Plant physiology}, volume = {164}, number = {4}, pages = {2081-2095}, pmid = {24515833}, issn = {1532-2548}, mesh = {Biological Evolution ; Bryopsida/*metabolism ; *Cell Compartmentation ; Cluster Analysis ; Gene Knock-In Techniques ; Metabolic Networks and Pathways ; Mitochondria/metabolism ; Multivariate Analysis ; Plant Proteins/*metabolism ; Plastids/metabolism ; Proteome/*metabolism ; Proteomics/*methods ; Staining and Labeling ; Subcellular Fractions/metabolism ; Symbiosis ; }, abstract = {Extant eukaryotes are highly compartmentalized and have integrated endosymbionts as organelles, namely mitochondria and plastids in plants. During evolution, organellar proteomes are modified by gene gain and loss, by gene subfunctionalization and neofunctionalization, and by changes in protein targeting. To date, proteomics data for plastids and mitochondria are available for only a few plant model species, and evolutionary analyses of high-throughput data are scarce. We combined quantitative proteomics, cross-species comparative analysis of metabolic pathways, and localizations by fluorescent proteins in the model plant Physcomitrella patens in order to assess evolutionary changes in mitochondrial and plastid proteomes. This study implements data-mining methodology to classify and reliably reconstruct subcellular proteomes, to map metabolic pathways, and to study the effects of postendosymbiotic evolution on organellar pathway partitioning. Our results indicate that, although plant morphologies changed substantially during plant evolution, metabolic integration of organelles is largely conserved, with exceptions in amino acid and carbon metabolism. Retargeting or regulatory subfunctionalization are common in the studied nucleus-encoded gene families of organelle-targeted proteins. Moreover, complementing the proteomic analysis, fluorescent protein fusions revealed novel proteins at organelle interfaces such as plastid stromules (stroma-filled tubules) and highlight microcompartments as well as intercellular and intracellular heterogeneity of mitochondria and plastids. Thus, we establish a comprehensive data set for mitochondrial and plastid proteomes in moss, present a novel multilevel approach to organelle biology in plants, and place our findings into an evolutionary context.}, }
@article {pmid24515269, year = {2014}, author = {Wu, B and Hao, W}, title = {Horizontal transfer and gene conversion as an important driving force in shaping the landscape of mitochondrial introns.}, journal = {G3 (Bethesda, Md.)}, volume = {4}, number = {4}, pages = {605-612}, pmid = {24515269}, issn = {2160-1836}, mesh = {Deoxyribonucleases, Type II Site-Specific/genetics ; Exons ; Gene Conversion/*genetics ; Gene Transfer, Horizontal/*genetics ; *Genome, Mitochondrial ; Introns/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; Saccharomyces/classification/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Sequence Analysis, DNA ; }, abstract = {Group I introns are highly dynamic and mobile, featuring extensive presence-absence variation and widespread horizontal transfer. Group I introns can invade intron-lacking alleles via intron homing powered by their own encoded homing endonuclease gene (HEG) after horizontal transfer or via reverse splicing through an RNA intermediate. After successful invasion, the intron and HEG are subject to degeneration and sequential loss. It remains unclear whether these mechanisms can fully address the high dynamics and mobility of group I introns. Here, we found that HEGs undergo a fast gain-and-loss turnover comparable with introns in the yeast mitochondrial 21S-rRNA gene, which is unexpected, as the intron and HEG are generally believed to move together as a unit. We further observed extensively mosaic sequences in both the introns and HEGs, and evidence of gene conversion between HEG-containing and HEG-lacking introns. Our findings suggest horizontal transfer and gene conversion can accelerate HEG/intron degeneration and loss, or rescue and propagate HEG/introns, and ultimately result in high HEG/intron turnover rate. Given that up to 25% of the yeast mitochondrial genome is composed of introns and most mitochondrial introns are group I introns, horizontal transfer and gene conversion could have served as an important mechanism in introducing mitochondrial intron diversity, promoting intron mobility and consequently shaping mitochondrial genome architecture.}, }
@article {pmid24509797, year = {2014}, author = {Refulio-Rodriguez, NF and Olmstead, RG}, title = {Phylogeny of Lamiidae.}, journal = {American journal of botany}, volume = {101}, number = {2}, pages = {287-299}, doi = {10.3732/ajb.1300394}, pmid = {24509797}, issn = {1537-2197}, mesh = {Bayes Theorem ; DNA, Plant/*analysis ; *Evolution, Molecular ; Magnoliopsida/*genetics ; Mitochondria/*genetics ; *Phylogeny ; Plastids/*genetics ; Sequence Analysis, DNA ; }, abstract = {PREMISE OF THE STUDY: The Lamiidae, a clade composed of approximately 15% of all flowering plants, consists of five orders: Boraginales, Gentianales, Garryales, Lamiales, and Solanales; and four families unplaced in an order: Icacinaceae, Metteniusiaceae, Oncothecaceae, and Vahliaceae. Our understanding of the phylogenetic relationships of Lamiidae has improved significantly in recent years, however, relationships among the orders and unplaced families of the clade remain partly unresolved. Here, we present a phylogenetic analysis of the Lamiidae based on an expanded sampling, including all families together, for the first time, in a single phylogenetic analyses.<br><br>METHODS: Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood, and Bayesian approaches. Analyses included nine plastid regions (atpB, matK, ndhF, psbBTNH, rbcL, rps4, rps16, trnL-F, and trnV-atpE) and the mitochondrial rps3 region, and 129 samples representing all orders and unplaced families of Lamiidae.<br><br>KEY RESULTS: Maximum Likelihood (ML) and Bayesian trees provide good support for Boraginales sister to Lamiales, with successive outgroups (Solanales + Vahlia) and Gentianales, together comprising the core Lamiidae. Early branching patterns are less well supported, with Garryales only poorly supported as sister to the above 'core' and a weakly supported clade composed of Icacinaceae, Metteniusaceae, and Oncothecaceae sister to all other Lamiidae.<br><br>CONCLUSIONS: Our phylogeny of Lamiidae reveals increased resolution and support for internal relationships that have remained elusive. Within Lamiales, greater resolution also is obtained, but some family interrelationships remain a challenge.}, }
@article {pmid24508942, year = {2014}, author = {Jiang, L and Wang, G and Peng, R and Peng, Q and Zou, F}, title = {Phylogenetic and molecular dating analysis of Taiwan Blue Pheasant (Lophura swinhoii).}, journal = {Gene}, volume = {539}, number = {1}, pages = {21-29}, doi = {10.1016/j.gene.2014.01.067}, pmid = {24508942}, issn = {1879-0038}, mesh = {Animals ; DNA, Mitochondrial/analysis/genetics ; Evolution, Molecular ; Galliformes/*classification/genetics ; Genetic Variation ; Genome, Mitochondrial/genetics ; Geography ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Taiwan ; }, abstract = {The Swinhoe's Pheasant (Lophura swinhoii) is an endemic and most endangered species to Taiwan, China. It belongs to the genus Lophura, family Phasianidae. To further investigate the evolutionary history of L. swinhoii, we determined its complete mitochondrial genome and reconstructed a single, robust phylogenetic tree. Our results showed that L. swinhoii is clustered with Lophura nycthemera and forms a sister group of Lophura ignita. The genus Lophura is strongly supported as the sister taxon of the genus Crossoptilon. The molecular clock analysis showed that the genetic divergence of L. swinhoii occurred in 2.71 (1.31-4.22) Mya. The most common ancestor of L. swinhoii might have migrated from mainland of South East Asia to Taiwan Island by the land bridge at 2.71 Mya ago. Taiwan Island is separated from the mainland by the sea (Taiwan Strait) and formed a separate island at around 2.5 Mya because of the transgression and regression. Therefore, geographical isolation and climate change may accelerate the evolution of L. swinhoii. In this study, we propose a biogeographic hypothesis for speciation of the L. swinhoii based on known events of the geographic and geological history of South East Asia and southeast China, which would benefit the understanding of evolutionary history of L. swinhoii as well as other galliform birds.}, }
@article {pmid24508098, year = {2014}, author = {Guha, TK and Hausner, G}, title = {A homing endonuclease with a switch: characterization of a twintron encoded homing endonuclease.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {65}, number = {}, pages = {57-68}, doi = {10.1016/j.fgb.2014.01.004}, pmid = {24508098}, issn = {1096-0937}, mesh = {Chaetomium/*genetics/metabolism ; DNA, Fungal/genetics ; DNA, Mitochondrial/genetics ; Endonucleases/*genetics/metabolism ; Genes, Fungal ; Introns ; Open Reading Frames ; Phylogeny ; RNA Splicing ; Ribosome Subunits, Small/*genetics ; }, abstract = {The small ribosomal subunit gene residing in the mitochondrial DNA of the thermophilic fungus Chaetomium thermophilum var. thermophilum La Touche DSM 1495 is interrupted by a twintron at position mS1247. The mS1247 twintron represents the first mixed twintron found in fungal mtDNA, composed of an external group I intron encoding a LAGLIDADG open reading frame that is interrupted by an internal group II intron. Splicing of the internal group II intron reconstitutes the open reading frame and thus facilitates the expression of the encoded homing endonuclease. The cleavage assays suggest that the twintron encodes an active homing endonuclease that could potentially mobilize the twintron to rns genes that have not yet been invaded by this mobile composite element.}, }
@article {pmid24507247, year = {2014}, author = {Millot, S and Parmentier, E}, title = {Development of the ultrastructure of sonic muscles: a kind of neoteny?.}, journal = {BMC evolutionary biology}, volume = {14}, number = {}, pages = {24}, pmid = {24507247}, issn = {1471-2148}, mesh = {Animals ; Characiformes/*growth &amp; development/physiology ; Muscle Development ; Muscles/*physiology/*ultrastructure ; Sound ; }, abstract = {BACKGROUND: Drumming muscles of some sound-producing fish are 'champions' of contraction speed, their rate setting the fundamental frequency. In the piranha, contraction of these muscles at 150 Hz drives a sound at the same frequency. Drumming muscles of different not closely related species show evolutionary convergences. Interestingly, some characters of sonic muscles can also be found in the trunk muscles of newly hatched larvae that are able to maintain tail beat frequencies up to 100 Hz. The aim of this work was to study the development of sound production and sonic and epaxial muscles simultaneously in the red bellied piranhas (Pygocentrus nattereri) to seek for possible common characteristics.<br><br>RESULTS: Call, pulse and period durations increased significantly with the fish size, but the call dominant frequencies decreased, and the number of pulses and the call amplitude formed a bell curve. In epaxial muscles, the fibre diameters of younger fish are first positioned in the graphical slope corresponding to sonic muscles, before diverging. The fibre diameter of older fish trunk muscles was bigger, and the area of the myofibrils was larger than in sonic muscles. Moreover, in two of the biggest fish, the sonic muscles were invaded by fat cells and the sonic muscle ultrastructure was similar to the epaxial one. These two fish were also unable to produce any sound, meaning they lost their ability to contract quickly.<br><br>CONCLUSIONS: The volume occupied by myofibrils determines the force of contraction, the volume of sarcoplasmic reticulum sets the contraction frequency, and the volume of mitochondria sets the level of sustained performance. The functional outcomes in muscles are all attributable to shifts in the proportions of those structures. A single delay in the development restricts the quantity of myofibrils, maintains a high proportion of space in the sarcoplasm and develops sarcoplasmic reticulum. High-speed sonic muscles could thus be skeletal muscles with delayed development. This hypothesis has the advantage that it could easily explain why high-speed sonic muscles have evolved so many times in different lineages.}, }
@article {pmid24506331, year = {2014}, author = {Arnal, N and Quadrado, M and Simon, M and Mireau, H}, title = {A restorer-of-fertility like pentatricopeptide repeat gene directs ribonucleolytic processing within the coding sequence of rps3-rpl16 and orf240a mitochondrial transcripts in Arabidopsis thaliana.}, journal = {The Plant journal : for cell and molecular biology}, volume = {78}, number = {1}, pages = {134-145}, doi = {10.1111/tpj.12463}, pmid = {24506331}, issn = {1365-313X}, mesh = {Arabidopsis/*genetics ; Arabidopsis Proteins/genetics/*metabolism ; Chromosome Mapping ; Evolution, Molecular ; *Gene Expression Regulation, Plant ; Genes, Reporter ; Mitochondria/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Mutation ; Phylogeny ; Plant Infertility/genetics ; Plants, Genetically Modified ; RNA Cleavage ; RNA Processing, Post-Transcriptional ; RNA, Messenger/genetics/*metabolism ; RNA, Plant/genetics/metabolism ; Recombinant Fusion Proteins ; Ribosomal Proteins/genetics ; }, abstract = {The pentatricopeptide repeat (PPR) proteins represent a large family of RNA-binding proteins that have many roles in post-transcriptional RNA processes within plant organelles. Among the PPR proteins that target plant mitochondria, the restorer-of-fertility (Rf) proteins are characterized by their inhibitory action on mitochondrion-localized cytoplasmic male sterility (CMS) genes in various crop species. Close homologs to known Rfs from radish, petunia, and rice can be identified in most higher plant species and these proteins define the recognized subgroup of Rf-like (RFL) PPR proteins. In this paper we describe the function of the RFL9 gene from Arabidopsis thaliana, and show that it is associated with ribonucleolytic cleavages within the coding sequences of rps3-rpl16 and orf240a mitochondrial transcripts in the Col-0 accession. RFL9 therefore represents an Rf-like PPR gene that has the potential to compromise the function of an essential mitochondrial gene and whose function is also associated with a mitochondrial orf sharing significant homology with a proven CMS-causing orf. We observe that RFL9 is active in only a few Arabidopsis accessions genetically close to Col-0, which supports the idea that the genetic fixation of this gene represents a regional event in the recent evolution of Arabidopsis. Additionally, RFL9 counts among the RFL genes that are probably controlled by short regulatory RNAs, and our results provides a potential explanation for such control, which in the case of RFL9 might have evolved to limit its detrimental effect on rps3 expression.}, }
@article {pmid24505307, year = {2014}, author = {Vannini, C and Boscaro, V and Ferrantini, F and Benken, KA and Mironov, TI and Schweikert, M and Görtz, HD and Fokin, SI and Sabaneyeva, EV and Petroni, G}, title = {Flagellar movement in two bacteria of the family rickettsiaceae: a re-evaluation of motility in an evolutionary perspective.}, journal = {PloS one}, volume = {9}, number = {2}, pages = {e87718}, pmid = {24505307}, issn = {1932-6203}, mesh = {*Biodiversity ; *Biological Evolution ; Flagella/*physiology ; Humans ; Rickettsiaceae/*physiology ; Species Specificity ; }, abstract = {Bacteria of the family Rickettsiaceae have always been largely studied not only for their importance in the medical field, but also as model systems in evolutionary biology. In fact, they share a recent common ancestor with mitochondria. The most studied species, belonging to genera Rickettsia and Orientia, are hosted by terrestrial arthropods and include many human pathogens. Nevertheless, recent findings show that a large part of Rickettsiaceae biodiversity actually resides outside the group of well-known pathogenic bacteria. Collecting data on these recently described non-conventional members of the family is crucial in order to gain information on ancestral features of the whole group. Although bacteria of the family Rickettsiaceae, and of the whole order Rickettsiales, are formally described as non-flagellated prokaryotes, some recent findings renewed the debate about this feature. In this paper we report the first finding of members of the family displaying numerous flagella and active movement inside their host cells. These two new taxa are hosted in aquatic environments by protist ciliates and are described here by means of ultrastructural and molecular characterization. Data here reported suggest that the ancestor of Rickettsiales displayed flagellar movement and re-evaluate the hypothesis that motility played a key-role in the origin of mitochondria. Moreover, our study highlights that the aquatic environment represents a well exploited habitat for bacteria of the family Rickettsiaceae. Our results encourage a deep re-consideration of ecological and morphological traits of the family and of the whole order.}, }
@article {pmid24504088, year = {2014}, author = {Aguileta, G and de Vienne, DM and Ross, ON and Hood, ME and Giraud, T and Petit, E and Gabaldón, T}, title = {High variability of mitochondrial gene order among fungi.}, journal = {Genome biology and evolution}, volume = {6}, number = {2}, pages = {451-465}, pmid = {24504088}, issn = {1759-6653}, mesh = {DNA, Mitochondrial/*genetics ; Fungal Proteins/*genetics ; Fungi/classification/*genetics ; *Gene Order ; Gene Rearrangement ; *Genes, Mitochondrial ; *Genetic Variation ; Genome, Mitochondrial ; Introns ; Mitochondria/genetics ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; }, abstract = {From their origin as an early alpha proteobacterial endosymbiont to their current state as cellular organelles, large-scale genomic reorganization has taken place in the mitochondria of all main eukaryotic lineages. So far, most studies have focused on plant and animal mitochondrial (mt) genomes (mtDNA), but fungi provide new opportunities to study highly differentiated mtDNAs. Here, we analyzed 38 complete fungal mt genomes to investigate the evolution of mtDNA gene order among fungi. In particular, we looked for evidence of nonhomologous intrachromosomal recombination and investigated the dynamics of gene rearrangements. We investigated the effect that introns, intronic open reading frames (ORFs), and repeats may have on gene order. Additionally, we asked whether the distribution of transfer RNAs (tRNAs) evolves independently to that of mt protein-coding genes. We found that fungal mt genomes display remarkable variation between and within the major fungal phyla in terms of gene order, genome size, composition of intergenic regions, and presence of repeats, introns, and associated ORFs. Our results support previous evidence for the presence of mt recombination in all fungal phyla, a process conspicuously lacking in most Metazoa. Overall, the patterns of rearrangements may be explained by the combined influences of recombination (i.e., most likely nonhomologous and intrachromosomal), accumulated repeats, especially at intergenic regions, and to a lesser extent, mobile element dynamics.}, }
@article {pmid24496725, year = {2014}, author = {Huang, D and Ovcharenko, I}, title = {Genome-wide analysis of functional and evolutionary features of tele-enhancers.}, journal = {G3 (Bethesda, Md.)}, volume = {4}, number = {4}, pages = {579-593}, pmid = {24496725}, issn = {2160-1836}, support = {//Intramural NIH HHS/United States ; }, mesh = {Binding Sites ; Cell Line ; Chromatin Immunoprecipitation ; *Enhancer Elements, Genetic ; *Evolution, Molecular ; *Genome, Human ; Humans ; Mitochondria/metabolism ; Myocardium/metabolism ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Support Vector Machine ; Transcription Factors/chemistry/metabolism ; }, abstract = {We investigated sequence features of enhancers separated from their target gene by at least one intermediate gene/exon (named tele-enhancers in this study) and enhancers residing inside their target gene locus. In this study, we used whole genome enhancer maps and gene expression profiles to establish a large panel of tele-enhancers. By contrasting tele-enhancers to proximal enhancers targeting heart genes, we observed that heart tele-enhancers use unique regulatory mechanisms based on the cardiac transcription factors SRF, TEAD, and NKX-2.5, whereas proximal heart enhancers rely on GATA4 instead. A functional analysis showed that tele-enhancers preferentially regulate house-keeping genes and genes with a metabolic role during heart development. In addition, tele-enhancers are significantly more conserved than their proximal counterparts. Similar trends have been observed for non-heart tissues and cell types, suggesting that our findings represent general characteristics of tele-enhancers.}, }
@article {pmid24492708, year = {2014}, author = {Keeling, PJ}, title = {The impact of history on our perception of evolutionary events: endosymbiosis and the origin of eukaryotic complexity.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {6}, number = {2}, pages = {}, pmid = {24492708}, issn = {1943-0264}, mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; Mitochondria/genetics ; Plastids/genetics ; Symbiosis/*genetics ; }, abstract = {Evolutionary hypotheses are correctly interpreted as products of the data they set out to explain, but they are less often recognized as being heavily influenced by other factors. One of these is the history of preceding thought, and here I look back on historically important changes in our thinking about the role of endosymbiosis in the origin of eukaryotic cells. Specifically, the modern emphasis on endosymbiotic explanations for numerous eukaryotic features, including the cell itself (the so-called chimeric hypotheses), can be seen not only as resulting from the advent of molecular and genomic data, but also from the intellectual acceptance of the endosymbiotic origin of mitochondria and plastids. This transformative idea may have unduly affected how other aspects of the eukaryotic cell are explained, in effect priming us to accept endosymbiotic explanations for endogenous processes. Molecular and genomic data, which were originally harnessed to answer questions about cell evolution, now so dominate our thinking that they largely define the question, and the original questions about how eukaryotic cellular architecture evolved have been neglected. This is unfortunate because, as Roger Stanier pointed out, these cellular changes represent life's "greatest single evolutionary discontinuity," and on this basis I advocate a return to emphasizing evolutionary cell biology when thinking about the origin of eukaryotes, and suggest that endogenous explanations will prevail when we refocus on the evolution of the cell.}, }
@article {pmid24491108, year = {2016}, author = {Ding, Y and Huang, J}, title = {Is mitochondrial tRNA(Ser(UCN)) T7501C mutation associated with cardiovascular disease?.}, journal = {Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis}, volume = {27}, number = {1}, pages = {205-208}, doi = {10.3109/19401736.2014.880891}, pmid = {24491108}, issn = {2470-1408}, mesh = {Base Sequence ; Cardiovascular Diseases/*genetics ; Conserved Sequence/genetics ; Evolution, Molecular ; Haplotypes/genetics ; Humans ; Mitochondria/*genetics ; Molecular Sequence Data ; Mutation/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer, Ser/chemistry/*genetics ; }, abstract = {Mitochondrial DNA mutations are increasingly recognized as an important cause of cardiovascular diseases, point mutations in mitochondrial tRNA genes being the largest group among them. Most recently, mutation at position 7501 in mt-tRNA(Ser(UCN)) gene has been reported to be associated with human cardiovascular diseases including cardiomyopathy, sudden cardiac death (SCD) and Tetralogy of Fallot (TOF). However, its direct pathogenic role remained poorly understood. In this study, we performed an extensive web-based search for the published resources concerning this association. Through the application of bioinformatics tool, we observed that this mutation altered the mt-tRNA(Ser(UCN)) secondary structure, in addition, evolutionary conservation analysis of this mutation indicated that this mutation is highly conserved between different species. Notably, the T7501C mutation belonging to human mitochondrial haplogroup U8a1a1, a rare subgroup of U8, was present only in European population and was absent in Han Chinese population. Taken together, our result indicated that the T7501C mutation may occur infrequently and was probably pathogenic in cardiovascular disease development.}, }
@article {pmid24489775, year = {2014}, author = {Tzou, WS and Chu, Y and Lin, TY and Hu, CH and Pai, TW and Liu, HF and Lin, HJ and Cases, I and Rojas, A and Sanchez, M and You, ZY and Hsu, MW}, title = {Molecular evolution of multiple-level control of heme biosynthesis pathway in animal kingdom.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e86718}, pmid = {24489775}, issn = {1932-6203}, mesh = {5' Untranslated Regions/genetics ; Amino Acid Motifs ; Amino Acid Sequence ; Amino Acids/genetics ; Animals ; Base Sequence ; Biosynthetic Pathways/*genetics ; Conserved Sequence/genetics ; Deoxyribonucleases/metabolism ; *Evolution, Molecular ; Exons/genetics ; Genes ; Heme/*biosynthesis ; Introns/genetics ; Molecular Sequence Data ; Response Elements/genetics ; Selection, Genetic ; Sequence Alignment ; }, abstract = {Adaptation of enzymes in a metabolic pathway can occur not only through changes in amino acid sequences but also through variations in transcriptional activation, mRNA splicing and mRNA translation. The heme biosynthesis pathway, a linear pathway comprised of eight consecutive enzymes in animals, provides researchers with ample information for multiple types of evolutionary analyses performed with respect to the position of each enzyme in the pathway. Through bioinformatics analysis, we found that the protein-coding sequences of all enzymes in this pathway are under strong purifying selection, from cnidarians to mammals. However, loose evolutionary constraints are observed for enzymes in which self-catalysis occurs. Through comparative genomics, we found that in animals, the first intron of the enzyme-encoding genes has been co-opted for transcriptional activation of the genes in this pathway. Organisms sense the cellular content of iron, and through iron-responsive elements in the 5' untranslated regions of mRNAs and the intron-exon boundary regions of pathway genes, translational inhibition and exon choice in enzymes may be enabled, respectively. Pathway product (heme)-mediated negative feedback control can affect the transport of pathway enzymes into the mitochondria as well as the ubiquitin-mediated stability of enzymes. Remarkably, the positions of these controls on pathway activity are not ubiquitous but are biased towards the enzymes in the upstream portion of the pathway. We revealed that multiple-level controls on the activity of the heme biosynthesis pathway depend on the linear depth of the enzymes in the pathway, indicating a new strategy for discovering the molecular constraints that shape the evolution of a metabolic pathway.}, }
@article {pmid24487053, year = {2014}, author = {Xu, T and Tang, D and Cheng, Y and Wang, R}, title = {Mitogenomic perspectives into sciaenid fishes' phylogeny and evolution origin in the New World.}, journal = {Gene}, volume = {539}, number = {1}, pages = {91-98}, doi = {10.1016/j.gene.2014.01.048}, pmid = {24487053}, issn = {1879-0038}, mesh = {Animals ; Base Sequence ; Biological Evolution ; DNA, Mitochondrial/analysis/genetics ; Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Mitochondria/*genetics ; Perciformes/*classification/*genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*veterinary ; }, abstract = {Sciaenid fishes are widely distributed throughout the coastal waters and estuaries of the world. A total of 23 genera of this family are endemic to the Old World. However, evolutionary relationships among Old World sciaenid fishes and their origin have remained unresolved despite their diversity and importance. Besides, hypotheses that explain the origin and biogeographical distribution of sciaenid fishes are controversial. In this study, the complete mitochondrial genome sequences of seven representative sciaenid species were determined and a well-resolved tree was recovered. This new timescale demonstrated that the sciaenid originated during the late Jurassic to early Cretaceous Period. The estimated origin time of sciaenid fish is 208 Mya, and the origin of Old World sciaenid is estimated at 126 Mya. Reconstruction of ancestral distributions indicated a plesiomorphic distribution and center of origin in the New World, with at least one lineage subsequently dispersed to the Old World. Moreover, we conclude that the common ancestors of Old World sciaenid fishes were derived from species of New World.}, }
@article {pmid24476934, year = {2014}, author = {Rossig, C and Reinbothe, C and Gray, J and Valdes, O and von Wettstein, D and Reinbothe, S}, title = {New functions of the chloroplast Preprotein and Amino acid Transporter (PRAT) family members in protein import.}, journal = {Plant signaling &amp; behavior}, volume = {9}, number = {1}, pages = {e27693}, pmid = {24476934}, issn = {1559-2324}, mesh = {Chloroplasts/metabolism ; Gene Knockout Techniques ; Plant Cells/*metabolism ; Plant Proteins/genetics/*metabolism ; Quinone Reductases/metabolism ; RNA Interference ; }, abstract = {Plant cells contain distinct compartments such as the nucleus, the endomembrane system comprising the endoplasmic reticulum and Golgi apparatus, peroxisomes, vacuoles, as well as mitochondria and chloroplasts. All of these compartments are surrounded by 1 or 2 limiting membranes and need to import proteins from the cytosol. Previous work led to the conclusion that mitochondria and chloroplasts use structurally different protein import machineries in their outer and inner membranes for the uptake of cytosolic precursor proteins. Our most recent data show that there is some unexpected overlap. Three members of the family of preprotein and amino acid transporters, PRAT, were identified in chloroplasts that mediate the uptake of transit sequence-less proteins into the inner plastid envelope membrane. By analogy, mitochondria contain with TIM22 a related PRAT protein that is involved in the import of transit sequence-less proteins into the inner mitochondrial membrane. Both mitochondria and chloroplasts thus make use of similar import mechanisms to deliver some of their proteins to their final place. Because single homologs of HP20- and HP30-like proteins are present in algae such as Chlamydomonas, Ostreococcus, and Volvox, which diverged from land plants approximately 1 billion years ago, it is likely that the discovered PRAT-mediated mechanism of protein translocation evolved concomitantly with the secondary endosymbiotic event that gave rise to green plants.}, }
@article {pmid24470090, year = {2013}, author = {Brini, M and Ottolini, D and Calì, T and Carafoli, E}, title = {Calcium in health and disease.}, journal = {Metal ions in life sciences}, volume = {13}, number = {}, pages = {81-137}, doi = {10.1007/978-94-007-7500-8_4}, pmid = {24470090}, issn = {1559-0836}, mesh = {Animals ; Calcium/*metabolism ; Calcium Channels/*metabolism ; *Calcium Signaling ; Cardiomegaly/*metabolism/pathology ; Humans ; Mitochondria/metabolism ; Muscular Diseases/*metabolism/pathology ; Neurodegenerative Diseases/*metabolism/pathology ; }, abstract = {Evolution has exploited the chemical properties of Ca(2+), which facilitate its reversible binding to the sites of irregular geometry offered by biological macromolecules, to select it as a carrier of cellular signals. A number of proteins bind Ca(2+) to specific sites: those intrinsic to membranes play the most important role in the spatial and temporal regulation of the concentration and movements of Ca(2+) inside cells. Those which are soluble, or organized in non-membranous structures, also decode the Ca(2+) message to be then transmitted to the targets of its regulation. Since Ca(2+) controls the most important processes in the life of cells, it must be very carefully controlled within the cytoplasm, where most of the targets of its signaling function reside. Membrane channels (in the plasma membrane and in the organelles) mediate the entrance of Ca(2+) into the cytoplasm, ATPases, exchangers, and the mitochondrial Ca(2+) uptake system remove Ca(2+) from it. The concentration of Ca(2+) in the external spaces, which is controlled essentially by its dynamic exchanges in the bone system, is much higher than inside cells, and can, under conditions of pathology, generate a situation of dangerous internal Ca(2+) overload. When massive and persistent, the Ca(2+) overload culminates in the death of the cell. Subtle conditions of cellular Ca(2+) dyshomeostasis that affect individual systems that control Ca(2+), generate cell disease phenotypes that are particularly severe in tissues in which the signaling function of Ca(2+) has special importance, e.g., the nervous system.}, }
@article {pmid24470038, year = {2014}, author = {Colombo, S and Martegani, E}, title = {Methods to study the Ras2 protein activation state and the subcellular localization of Ras-GTP in Saccharomyces cerevisiae.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1120}, number = {}, pages = {391-405}, doi = {10.1007/978-1-62703-791-4_24}, pmid = {24470038}, issn = {1940-6029}, mesh = {Blotting, Western ; Cloning, Molecular ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/genetics ; Guanosine Triphosphate/*metabolism ; Intracellular Space/*metabolism ; Microscopy, Confocal ; Microscopy, Fluorescence ; Mitochondria/metabolism ; Protein Structure, Tertiary ; Protein Transport ; Proto-Oncogene Proteins c-raf/chemistry/metabolism ; Reactive Oxygen Species/metabolism ; Saccharomyces cerevisiae/*cytology/*enzymology/genetics ; Saccharomyces cerevisiae Proteins/*metabolism ; Signal Transduction ; Transformation, Genetic ; Vacuoles/metabolism ; ras Proteins/*metabolism ; }, abstract = {Ras proteins were highly conserved during evolution. They function as a point of convergence for different signalling pathways in eukaryotes and are involved in a wide range of cellular responses (shift from gluconeogenic to fermentative growth, breakdown of storage carbohydrates, stress resistance, growth control and determination of life span, morphogenesis and development, and others). These proteins are members of the small GTPase superfamily, which are active in the GTP-bound form and inactive in the GDP-bound form. Given the importance of studies on the Ras protein activation state to understand the detailed mechanism of Ras-mediated signal transduction, we provide here a simple, sensitive, and reliable method, based on the high affinity interaction of Ras-GTP with the Ras binding domain (RBD) of Raf1, to measure the level of Ras2-GTP on total Ras2 in Saccharomyces cerevisiae. Moreover, to study the localization of Ras-GTP in vivo in single S. cerevisiae cells, we expressed a probe consisting of a GFP fusion with a trimeric Ras Binding Domain of Raf1 (eGFP-RBD3), which was proven to be a useful live-cell biosensor for Ras-GTP in mammalian cells.}, }
@article {pmid24467909, year = {2014}, author = {Poirier, P and Meloni, D and Nourrisson, C and Wawrzyniak, I and Viscogliosi, E and Livrelli, V and Delbac, F}, title = {Molecular subtyping of Blastocystis spp. using a new rDNA marker from the mitochondria-like organelle genome.}, journal = {Parasitology}, volume = {141}, number = {5}, pages = {670-681}, doi = {10.1017/S0031182013001996}, pmid = {24467909}, issn = {1469-8161}, mesh = {Animals ; Base Sequence ; Blastocystis/*classification/genetics/isolation &amp; purification ; Blastocystis Infections/*parasitology ; Coinfection ; DNA Barcoding, Taxonomic ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genetic Markers/genetics ; Genome, Protozoan/*genetics ; Genotype ; Humans ; Mitochondria/genetics ; Molecular Sequence Data ; Molecular Typing ; Organelles/genetics ; Phylogeny ; *Polymorphism, Genetic ; RNA, Ribosomal, 18S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Blastocystis spp. are common anaerobic intestinal protozoa found in both human and animals. They are characterized by a high genetic diversity with at least 17 subtypes (STs) that have been described on the basis of a 600 bp 'barcoding region' from the 18S rDNA gene. However, analysis of the recently sequenced genome of a Blastocystis ST7 isolate (strain B) revealed the presence of multiple variable copies of the 18S rDNA gene, with 17 completely assembled copies. Comparison of the barcoding region from these 17 copies allowed us to classify the 18S rDNA sequences into 6 clusters, each cluster containing identical sequences. Surprisingly, 4 of these clusters had the highest homology with 18S rDNA sequences from 2 other Blastocystis ST7 isolates referred as QQ98-4 and H. These results suggest that the 18S rDNA gene is not the marker of choice to discriminate between strains within STs. In the present study, we identified a single-copy subtyping rDNA marker in the genome of the mitochondria-like organelles (MLOs). Using a partial sequence of the MLO rDNA, we successfully subtyped 66 isolates from both human and animals belonging to Blastocystis ST1 to ST10. Our results also indicate that this mitochondrial marker could be useful to detect co-infections by different isolates of a same ST.}, }
@article {pmid24465810, year = {2014}, author = {Shamblin, BM and Bolten, AB and Abreu-Grobois, FA and Bjorndal, KA and Cardona, L and Carreras, C and Clusa, M and Monzón-Argüello, C and Nairn, CJ and Nielsen, JT and Nel, R and Soares, LS and Stewart, KR and Vilaça, ST and Türkozan, O and Yilmaz, C and Dutton, PH}, title = {Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85956}, pmid = {24465810}, issn = {1932-6203}, mesh = {Animals ; Atlantic Ocean ; Conservation of Natural Resources ; DNA, Mitochondrial/*genetics ; Female ; *Genetic Variation ; Genetics, Population ; Haplotypes ; Indian Ocean ; Mediterranean Sea ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Turtles/*genetics ; }, abstract = {Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (∼800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting comprehensive international cooperative data management and research in marine ecology.}, }
@article {pmid24461455, year = {2014}, author = {Le, PT and Pontarotti, P and Raoult, D}, title = {Alphaproteobacteria species as a source and target of lateral sequence transfers.}, journal = {Trends in microbiology}, volume = {22}, number = {3}, pages = {147-156}, doi = {10.1016/j.tim.2013.12.006}, pmid = {24461455}, issn = {1878-4380}, mesh = {Alphaproteobacteria/*genetics ; Bacterial Secretion Systems ; Biological Evolution ; *Gene Transfer, Horizontal ; }, abstract = {Alphaproteobacterial genomes show a remarkable genome plasticity linked with different lifestyles (intracellular, facultative, and free-living). They represent the major source of the genome repertoire of mitochondria, and their genes (specifically those of Wolbachia) have been massively transferred into their modern eukaryotic hosts, such as arthropods and nematodes. Conversely, other organisms (bacteria, viruses, archaea, and eukaryotes) and selfish DNA have contributed to their genomes. This bidirectional lateral sequence transfer explains the mosaic nature of their genomes. In contrast to those living in allopatry, alphaproteobacteria living in sympatry (in protist cells such as in the environment) favor lateral sequence transfer. Evidence shows that intracellular transfer of the type IV secretion system might have played a critical role in the evolution of these alphaproteobacteria.}, }
@article {pmid24460856, year = {2014}, author = {Noyszewski, AK and Ghavami, F and Alnemer, LM and Soltani, A and Gu, YQ and Huo, N and Meinhardt, S and Kianian, PM and Kianian, SF}, title = {Accelerated evolution of the mitochondrial genome in an alloplasmic line of durum wheat.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {67}, pmid = {24460856}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; *Biological Evolution ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Mitochondrial Proteins/chemistry/genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Polymorphism, Single Nucleotide ; Sequence Alignment ; Sequence Analysis, DNA ; Triticum/*genetics/metabolism ; }, abstract = {BACKGROUND: Wheat is an excellent plant species for nuclear mitochondrial interaction studies due to availability of large collection of alloplasmic lines. These lines exhibit different vegetative and physiological properties than their parents. To investigate the level of sequence changes introduced into the mitochondrial genome under the alloplasmic condition, three mitochondrial genomes of the Triticum-Aegilops species were sequenced: 1) durum alloplasmic line with the Ae. longissima cytoplasm that carries the T. turgidum nucleus designated as (lo) durum, 2) the cytoplasmic donor line, and 3) the nuclear donor line.<br><br>RESULTS: The mitochondrial genome of the T. turgidum was 451,678 bp in length with high structural and nucleotide identity to the previously characterized T. aestivum genome. The assembled mitochondrial genome of the (lo) durum and the Ae. longissima were 431,959 bp and 399,005 bp in size, respectively. The high sequence coverage for all three genomes allowed analysis of heteroplasmy within each genome. The mitochondrial genome structure in the alloplasmic line was genetically distant from both maternal and paternal genomes. The alloplasmic durum and the Ae. longissima carry the same versions of atp6, nad6, rps19-p, cob and cox2 exon 2 which are different from the T. turgidum parent. Evidence of paternal leakage was also observed by analyzing nad9 and orf359 among all three lines. Nucleotide search identified a number of open reading frames, of which 27 were specific to the (lo) durum line.<br><br>CONCLUSIONS: Several heteroplasmic regions were observed within genes and intergenic regions of the mitochondrial genomes of all three lines. The number of rearrangements and nucleotide changes in the mitochondrial genome of the alloplasmic line that have occurred in less than half a century was significant considering the high sequence conservation between the T. turgidum and the T. aestivum that diverged from each other 10,000 years ago. We showed that the changes in genes were not limited to paternal leakage but were sufficiently significant to suggest that other mechanisms, such as recombination and mutation, were responsible. The newly formed ORFs, differences in gene sequences and copy numbers, heteroplasmy, and substoichiometric changes show the potential of the alloplasmic condition to accelerate evolution towards forming new mitochondrial genomes.}, }
@article {pmid24460170, year = {2015}, author = {Chen, X and Peng, Z and Cai, L and Xu, Y}, title = {Mitochondrial genome of the spot-tail shark Carcharhinus sorrah (Carcharhiniformes: Carcharhinidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {734-735}, doi = {10.3109/19401736.2013.845764}, pmid = {24460170}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Endangered Species ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Sharks/*genetics ; }, abstract = {In this article, we first presented the complete mitogenome of the spot-tail shark Carcharhinus sorrah, which is a medium-sized shark distributed in the tropical Indo-Pacific and is currently listed as "Near Threatened" on the International Union for Conservation of Nature (IUCN) Red List. The complete mitogenome of C. sorrah is 16,707 bp in length and contains typical 37 genes and one control region. The overall base composition is 31.4% A, 25.8% C, 13.2% G and 29.6% T. The control region is 1066 bp in length with the highest A + T content (66.8%) and lowest G content (13.2%).}, }
@article {pmid24460168, year = {2015}, author = {Chen, IS and Liao, CR and Shao, YT}, title = {The complete mitochondrial genome of Hainanese barbel steed Hemibarbus medius Yue (Teleostei: Cyprinidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {736-738}, doi = {10.3109/19401736.2013.845765}, pmid = {24460168}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {In this study, the complete mitogenome sequence of cyprinid fish, Hainanese barbel steed, Hemibarbus medius Yue (Teleostei: Cyprinidae) has been amplified and sequenced by employing long polymerase chain reaction method. The mitogenome, consisting of 16,614 base pairs (bp), had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a non-coding control region (CR). CR of 933 bp length is located between tRNA(Pro) and tRNA(Phe). The overall base composition of Hemibarbus medius is 29.8% for A, 27.2% for C, 25.9% for T and 17.1% for G, with a slight AT bias of 55.7%. The complete mitogenome may provide rather essential and important DNA molecular data for further phylogenetic analysis for not only congeneric species but also higher different taxa of Cyprinid fishes.}, }
@article {pmid24460167, year = {2015}, author = {Gong, L and Shi, W and Wang, SY and Kong, XY}, title = {The complete mitochondrial genome of Liachirus melanospilos (Pleuronectiformes: Soleidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {732-733}, doi = {10.3109/19401736.2013.845763}, pmid = {24460167}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Evolution, Molecular ; Flatfishes/*genetics/physiology ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Sequence Analysis, DNA ; }, abstract = {Liachirus melanospilos (Pleuronectiformes: Soleidae) is characterized by both eyes on the right side of the body and pale brown color with black dots, small irregular, brown spots and large vague ocelli. In this study, the complete mitogenome sequence of this carpet sole has been determined. The total length is 17,001 bp, including 13 protein-coding genes, 22 tRNA genes and 2 rRNA genes (12S and 16S), as well as one control region and one L-strand replication origin (OL). Gene contents, locations and arrangements are identical to those of typical bony fishes. The nucleotide composition of the genome is 30.9%, 27.8%, 15.9% and 25.5% for A, C, G and T, respectively, with a slight bias of A + T content (56.4%). The determination of L. melanospilos complete mitogenome sequence could contribute to a better understanding of the systematic evolution of Soleidae and Pleuronectiformes.}, }
@article {pmid24460163, year = {2015}, author = {Shao, L and Sun, Q and Hao, J}, title = {The complete mitochondrial genome of Parara guttata (Lepidoptera: Hesperiidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {724-725}, doi = {10.3109/19401736.2013.845759}, pmid = {24460163}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Base Sequence ; Conserved Sequence ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Lepidoptera/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {The mitochondrial genome (mitogenome) of Parara guttata (Hesperiidae: Hesperiinae) is a circular molecule of 15,441 bp in length, containing 37 typical animal mitochondrial genes: 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNAs and a non-coding AT-rich region. Its gene order and arrangement are identical to the common type found in most lepidopteran mitogenomes. All PCGs start with a typical ATN codon except for COI and ND1 which use CGA and GTG as their start codons, respectively. Some PCGs harbor TAG (ND1) or incomplete termination codon T (COI, COII, ND5, ND4), while others use standard TAA as their termination codons. The 411-bp long AT-rich region contains a conserved motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)5 element preceded by the ATTTA motif.}, }
@article {pmid24460159, year = {2015}, author = {Wu, X and Xie, Z and Yang, L and Yang, H and Yue, L and Hou, L and Zhang, Y and Shu, H}, title = {The complete mitochondrial genome of the duskytail grouper Epinephelus bleekeri (Serranidae: Epinephelinae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {722-723}, doi = {10.3109/19401736.2013.845758}, pmid = {24460159}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Bass/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The complete mitochondrial genome of Epinephelus bleekeri was first presented in this study. It is 17,227 bp in length, consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region. The overall base composition of the H-strand is 26.32% A, 28.65% T, 28.72% G and 16.31% C. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. In particular, gene duplication is found on the tRNA-Asp gene, and five tandem repeat of this gene in E. bleekeri is different from most other vertebrates. The control region is rich in A + T (67.12%) and poor in G (14.00%), and tandem repeat sequences are observed in this non-coding region, indicating a useful marker for population genetic studies.}, }
@article {pmid24460157, year = {2015}, author = {Chen, MY and Chaw, SM and Wang, JF and Villanueva, RJ and Nuñeza, OM and Lin, CP}, title = {Mitochondrial genome of a flashwing demoiselle, Vestalis melania from the Philippine Archipelago.}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {720-721}, doi = {10.3109/19401736.2013.845757}, pmid = {24460157}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Odonata/*genetics ; Philippines ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {This study determined the first complete mitochondrial genome of a demoiselle, Vestalis melania (Odonata, Zygoptera, Calopterygidae) using long-range PCR and a primer walking approach. This mitogenome is 16,685 bp long and contains the entire set of 37 genes and an A + T-rich control region typically found in insects. Presently, this mitogenome is the largest mitogenome of all available odonates, mainly because of its long A + T-rich region (2036 bp). The gene arrangement of the V. melania mitogenome is identical to that of other known odonates. The inter-genic spacer s5 shared by the Anisoptera is absent in V. melania, which supports the view that the absence of the s5 spacer is a synapomorphy of the Zygoptera.}, }
@article {pmid24459286, year = {2014}, author = {Moray, C and Lanfear, R and Bromham, L}, title = {Domestication and the mitochondrial genome: comparing patterns and rates of molecular evolution in domesticated mammals and birds and their wild relatives.}, journal = {Genome biology and evolution}, volume = {6}, number = {1}, pages = {161-169}, pmid = {24459286}, issn = {1759-6653}, mesh = {Animals ; Animals, Domestic/*genetics ; Cats ; Cattle ; Chickens ; Dogs ; *Evolution, Molecular ; *Genome, Mitochondrial ; Horses ; Pedigree ; *Selection, Genetic ; Sequence Alignment ; }, abstract = {Studies of domesticated animals have led to the suggestion that domestication could have significant effects on patterns of molecular evolution. In particular, analyses of mitochondrial genome sequences from domestic dogs and yaks have yielded higher ratios of non-synonymous to synonymous substitutions in the domesticated lineages than in their wild relatives. These results are important because they imply that changes to selection or population size operating over a short timescale can cause significant changes to the patterns of mitochondrial molecular evolution. In this study, our aim is to test whether the impact on mitochondrial genome evolution is a general feature of domestication or whether it is specific to particular examples. We test whether domesticated mammals and birds have consistently different patterns of molecular evolution than their wild relatives for 16 phylogenetically independent comparisons of mitochondrial genome sequences. We find no consistent difference in branch lengths or dN/dS between domesticated and wild lineages. We also find no evidence that our failure to detect a consistent pattern is due to the short timescales involved or low genetic distance between domesticated lineages and their wild relatives. However, removing comparisons where the wild relative may also have undergone a bottleneck does reveal a pattern consistent with reduced effective population size in domesticated lineages. Our results suggest that, although some domesticated lineages may have undergone changes to selective regime or effective population size that could have affected mitochondrial evolution, it is not possible to generalize these patterns over all domesticated mammals and birds.}, }
@article {pmid24458826, year = {2014}, author = {Shangguan, L and Wang, X and Leng, X and Liu, D and Ren, G and Tao, R and Zhang, C and Fang, J}, title = {Identification and bioinformatic analysis of signal responsive/calmodulin-binding transcription activators gene models in Vitis vinifera.}, journal = {Molecular biology reports}, volume = {41}, number = {5}, pages = {2937-2949}, pmid = {24458826}, issn = {1573-4978}, mesh = {Chromosome Mapping ; *Computational Biology/methods ; Databases, Nucleic Acid ; Gene Expression Profiling ; Intracellular Space/metabolism ; Models, Molecular ; Multigene Family ; Organ Specificity/genetics ; Phylogeny ; Plant Proteins/chemistry/*genetics/metabolism ; Protein Conformation ; Protein Transport ; Transcription Factors/chemistry/*genetics/metabolism ; Vitis/classification/*genetics/metabolism ; }, abstract = {In this study, 10 grapevine (Vitis vinifera) SR/CAMTA (Signal Responsive/Calmodulin-binding Transcription Activators) gene models were identified from three grapevine genome protein datasets. They belong to four gene groups: VvCAMTA1, VvCAMTA3, VvCAMTA4 and VvCAMTA5, which were located on chromosome 5, 7_random, 1 and 5, respectively. Alternative splicing could explain the multiple gene models in one gene group. Subcellular localization using the WoLF tool showed that most of the VvCAMTAs were located in the nucleus, except for VvCAMTA3.1, VvCAMTA3.2 and VvCAMTA5.2, which were located in the chloroplast, chloroplast and cytosol, respectively. Subcellular localization using TargetP showed that most of the VvCAMTAs were not located in the chloroplast, mitochondrion and secretory pathway in cells. VvCAMTA1.1 and VvCAMTA1.2 were located in the mitochondria. The digital gene expression profile showed that VvCAMTAs play important roles in Ca2+ signal transduction. The gene expression patterns of VvCAMTAs were different; for example, VvCAMTA1 was expressed mainly in the bud, while VvCAMTA3 was expressed mainly in fruit and inflorescence, with low expression in the bud. The results of this study make a substantial contribution to our knowledge concerning genes, genome annotation, and cell signal transduction in grapevine.}, }
@article {pmid24458431, year = {2014}, author = {Molina, J and Hazzouri, KM and Nickrent, D and Geisler, M and Meyer, RS and Pentony, MM and Flowers, JM and Pelser, P and Barcelona, J and Inovejas, SA and Uy, I and Yuan, W and Wilkins, O and Michel, CI and Locklear, S and Concepcion, GP and Purugganan, MD}, title = {Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae).}, journal = {Molecular biology and evolution}, volume = {31}, number = {4}, pages = {793-803}, pmid = {24458431}, issn = {1537-1719}, mesh = {Evolution, Molecular ; *Genome, Chloroplast ; Magnoliopsida/*genetics ; Mitochondria/genetics ; Photosynthesis/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Rafflesia is a genus of holoparasitic plants endemic to Southeast Asia that has lost the ability to undertake photosynthesis. With short-read sequencing technology, we assembled a draft sequence of the mitochondrial genome of Rafflesia lagascae Blanco, a species endemic to the Philippine island of Luzon, with ∼350× sequencing depth coverage. Using multiple approaches, however, we were only able to identify small fragments of plastid sequences at low coverage depth (<2×) and could not recover any substantial portion of a chloroplast genome. The gene fragments we identified included photosynthesis and energy production genes (atp, ndh, pet, psa, psb, rbcL), ribosomal RNA genes (rrn16, rrn23), ribosomal protein genes (rps7, rps11, rps16), transfer RNA genes, as well as matK, accD, ycf2, and multiple nongenic regions from the inverted repeats. None of the identified plastid gene sequences had intact reading frames. Phylogenetic analysis suggests that ∼33% of these remnant plastid genes may have been horizontally transferred from the host plant genus Tetrastigma with the rest having ambiguous phylogenetic positions (<50% bootstrap support), except for psaB that was strongly allied with the plastid homolog in Nicotiana. Our inability to identify substantial plastid genome sequences from R. lagascae using multiple approaches--despite success in identifying and developing a draft assembly of the much larger mitochondrial genome--suggests that the parasitic plant genus Rafflesia may be the first plant group for which there is no recognizable plastid genome, or if present is found in cryptic form at very low levels.}, }
@article {pmid24457623, year = {2014}, author = {Greggains, GD and Lister, LM and Tuppen, HA and Zhang, Q and Needham, LH and Prathalingam, N and Hyslop, LA and Craven, L and Polanski, Z and Murdoch, AP and Turnbull, DM and Herbert, M}, title = {Therapeutic potential of somatic cell nuclear transfer for degenerative disease caused by mitochondrial DNA mutations.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {3844}, pmid = {24457623}, issn = {2045-2322}, support = {MR/K000608/1/MRC_/Medical Research Council/United Kingdom ; 096919/Z/11/Z/WT_/Wellcome Trust/United Kingdom ; G0601157/MRC_/Medical Research Council/United Kingdom ; 096919/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amnion/cytology/metabolism ; Cell Differentiation ; Cell Nucleus/genetics ; Cells, Cultured ; *Cellular Reprogramming ; DNA, Mitochondrial/*genetics ; Embryonic Stem Cells/cytology/*metabolism ; Female ; Fibroblasts/cytology/metabolism ; Humans ; Mitochondria/*genetics ; Mutation/genetics ; Neurodegenerative Diseases/*therapy ; *Nuclear Transfer Techniques ; Oocytes/cytology/*metabolism ; Polymerase Chain Reaction ; Skin/cytology/metabolism ; }, abstract = {Induced pluripotent stem cells (iPSCs) hold much promise in the quest for personalised cell therapies. However, the persistence of founder cell mitochondrial DNA (mtDNA) mutations limits the potential of iPSCs in the development of treatments for mtDNA disease. This problem may be overcome by using oocytes containing healthy mtDNA, to induce somatic cell nuclear reprogramming. However, the extent to which somatic cell mtDNA persists following fusion with human oocytes is unknown. Here we show that human nuclear transfer (NT) embryos contain very low levels of somatic cell mtDNA. In light of a recent report that embryonic stem cells can be derived from human NT embryos, our results highlight the therapeutic potential of NT for mtDNA disease, and underscore the importance of using human oocytes to pursue this goal.}, }
@article {pmid24454907, year = {2014}, author = {Chen, H and Sun, S and Norenburg, JL and Sundberg, P}, title = {Mutation and selection cause codon usage and bias in mitochondrial genomes of ribbon worms (Nemertea).}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85631}, pmid = {24454907}, issn = {1932-6203}, mesh = {Animals ; Base Composition ; *Codon ; Evolution, Molecular ; Genome, Mitochondrial ; Invertebrates ; Mitochondria/*genetics ; Mutation ; RNA, Transfer/genetics ; Species Specificity ; }, abstract = {The phenomenon of codon usage bias is known to exist in many genomes and it is mainly determined by mutation and selection. To understand the patterns of codon usage in nemertean mitochondrial genomes, we use bioinformatic approaches to analyze the protein-coding sequences of eight nemertean species. Neutrality analysis did not find a significant correlation between GC12 and GC3. ENc-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENc values are below it. ENc-plot suggested that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally and we propose that codons containing A or U at third position are used preferentially in nemertean species, regardless of whether corresponding tRNAs are encoded in the mitochondrial DNA. Context-dependent analysis indicated that the nucleotide at the second codon position slightly affects synonymous codon choices. These results suggested that mutational and selection forces are probably acting to codon usage bias in nemertean mitochondrial genomes.}, }
@article {pmid24451261, year = {2014}, author = {Tetaud, E and Godard, F and Giraud, MF and Ackerman, SH and di Rago, JP}, title = {The depletion of F1 subunit ε in yeast leads to an uncoupled respiratory phenotype that is rescued by mutations in the proton-translocating subunits of F0.}, journal = {Molecular biology of the cell}, volume = {25}, number = {6}, pages = {791-799}, pmid = {24451261}, issn = {1939-4586}, mesh = {Cell Engineering ; Escherichia coli/genetics/metabolism ; Evolution, Molecular ; Gene Expression ; Genotype ; Mitochondria/genetics/*metabolism ; Mutation ; Oxidative Phosphorylation ; Phenotype ; Protein Subunits/chemistry/genetics/*metabolism ; Proteins/chemistry/genetics/*metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Thermodynamics ; ATPase Inhibitory Protein ; }, abstract = {The central stalk of the ATP synthase is an elongated hetero-oligomeric structure providing a physical connection between the catalytic sites in F1 and the proton translocation channel in F0 for energy transduction between the two subdomains. The shape of the central stalk and relevance to energy coupling are essentially the same in ATP synthases from all forms of life, yet the protein composition of this domain changed during evolution of the mitochondrial enzyme from a two- to a three-subunit structure (γ, δ, ε). Whereas the mitochondrial γ- and δ-subunits are homologues of the bacterial central stalk proteins, the deliberate addition of subunit ε is poorly understood. Here we report that down-regulation of the gene (ATP15) encoding the ε-subunit rapidly leads to lethal F0-mediated proton leaks through the membrane because of the loss of stability of the ATP synthase. The ε-subunit is thus essential for oxidative phosphorylation. Moreover, mutations in F0 subunits a and c, which slow the proton translocation rate, are identified that prevent ε-deficient ATP synthases from dissipating the electrochemical potential. Cumulatively our data lead us to propose that the ε-subunit evolved to permit operation of the central stalk under the torque imposed at the normal speed of proton movement through mitochondrial F0.}, }
@article {pmid24448982, year = {2014}, author = {Kamikawa, R and Kolisko, M and Nishimura, Y and Yabuki, A and Brown, MW and Ishikawa, SA and Ishida, K and Roger, AJ and Hashimoto, T and Inagaki, Y}, title = {Gene content evolution in Discobid mitochondria deduced from the phylogenetic position and complete mitochondrial genome of Tsukubamonas globosa.}, journal = {Genome biology and evolution}, volume = {6}, number = {2}, pages = {306-315}, pmid = {24448982}, issn = {1759-6653}, mesh = {DNA, Mitochondrial/genetics ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; *Genome, Mitochondrial ; *Phylogeny ; }, abstract = {The unicellular eukaryotic assemblage Discoba (Excavata) comprises four lineages: the Heterolobosea, Euglenozoa, Jakobida, and Tsukubamonadida. Discoba has been considered as a key assemblage for understanding the early evolution of mitochondrial (mt) genomes, as jakobids retain the most gene-rich (i.e., primitive) genomes compared with any other eukaryotes determined to date. However, to date, mt genome sequences have been completed for only a few groups within Discoba, including jakobids, two closely related heteroloboseans, and kinetoplastid euglenozoans. The Tsukubamonadida is the least studied lineage, as the order was only recently established with the description of a sole representative species, Tsukubamonas globosa. The evolutionary relationship between T. globosa and other discobids has yet to be resolved, and no mt genome data are available for this particular organism. Here, we use a "phylogenomic" approach to resolve the relationship between T. globosa, heteroloboseans, euglenozoans, and jakobids. In addition, we have characterized the mt genome of T. globosa (48,463 bp in length), which encodes 52 putative protein-coding and 29 RNA genes. By mapping the gene repertoires of discobid mt genomes onto the well-resolved Discoba tree, we model gene loss events during the evolution of discobid mt genomes.}, }
@article {pmid24447698, year = {2014}, author = {Yuasa, T and Takahashi, O}, title = {Ultrastructural morphology of the reproductive swarmers of Sphaerozoum punctatum (Huxley) from the East China Sea.}, journal = {European journal of protistology}, volume = {50}, number = {2}, pages = {194-204}, doi = {10.1016/j.ejop.2013.12.001}, pmid = {24447698}, issn = {1618-0429}, mesh = {China ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Inclusion Bodies/chemistry ; Microscopy, Electron, Scanning ; Molecular Sequence Data ; Oceans and Seas ; Phylogeny ; Rhizaria/chemistry/classification/genetics/*ultrastructure ; Seawater/parasitology ; Spectrometry, X-Ray Emission ; }, abstract = {Reproductive swarmers of the polycystine radiolarian Sphaerozoum punctatum (Huxley) collected from the East China Sea were examined using light, scanning and transmission electron microscopy. The swarmer cells were about 8-10 μm in length with a pear-like shape and a conical end with two flagella. A nucleus, mitochondria, Golgi body, lipid droplets and, characteristically, a single, large, vacuole-bound SrSO4 crystal were present in the cytoplasm. Centering on the crystal inclusion, swarmers swam in a rapid rotational movement both clockwise and anticlockwise. Small subunit (SSU) rDNA sequences obtained for the reproductive swarmer cells from S. punctatum show a monophyletic group together with colonial spumellarians and grouped with S. punctatum from Bermuda in the clade. The morphological features and molecular phylogeny of the reproductive swarmers of S. punctatum show evidence of ancestral traits of radiolarians; acantharians and polycystines have a common ancestry. In addition, SrSO4 inclusion of the swarmer cell may be a form of ballast deposited by the swarmer to allow proper positioning in the water column. We hypothesize that radiolarian-affiliated sequences from SSU rDNA clone libraries of marine picoeukaryotes may be derived from the picoplanktonic cells of radiolarians; i.e., small flagellated life stages such as reproductive swarmers or gametes.}, }
@article {pmid24446543, year = {2013}, author = {Leisinger, AK and Janzen, DH and Hallwachs, W and Igloi, GL}, title = {Amino acid discrimination by the nuclear encoded mitochondrial arginyl-tRNA synthetase of the larva of a bruchid beetle (Caryedes brasiliensis) from northwestern Costa Rica.}, journal = {Insect biochemistry and molecular biology}, volume = {43}, number = {12}, pages = {1172-1180}, pmid = {24446543}, issn = {1879-0240}, mesh = {Amino Acids/genetics ; Animals ; Arginine-tRNA Ligase/chemistry/genetics/*metabolism ; Canavanine/chemistry/*toxicity ; Cell Nucleus/genetics/*metabolism ; Coleoptera/drug effects/enzymology/metabolism ; Costa Rica ; Dioclea/chemistry ; Kinetics ; Larva/drug effects/growth &amp; development ; Mitochondria/genetics/*metabolism ; }, abstract = {L-canavanine, the toxic guanidinooxy analogue of L-arginine, is the product of plant secondary metabolism. The need for a detoxifying mechanism for the producer plant is self-evident but the larvae of the bruchid beetle Caryedes brasiliensis, that is itself a non-producer, have specialized in feeding on the Lcanavanine-containing seeds of Dioclea megacarpa. The evolution of a seed predator that can imitate the enzymatic abilities of the host permits us to address the question of whether the same problem of amino acid recognition in two different kingdoms has been solved by the same mechanism. A discriminating arginyl-tRNA synthetase, detected in a crude C. brasiliensis larval extract, was proposed to be responsible for insect's ability to survive the diet of L-canavanine (Rosenthal, G. A., Dahlman, D. L., and Janzen, D. H. (1976) A novel means for dealing with L-canavanine, a toxic metabolite. Science 192, 256e258). Since the arginyl-tRNA synthetase of at least three genetic compartments (insect cytoplasmic, insect mitochondrial and insect gut microflora) may participate in conferring L-canavanine resistance, we investigated whether the nuclear-encoded C. brasiliensis mitochondrial arginyl-tRNA synthetase plays a role in this discrimination. Steady state kinetics of the cloned, recombinant enzyme have revealed and quantified an amino acid discriminating potential of the mitochondrial enzyme that is sufficient to account for the overall L-canavanine misincorporation rate observed in vivo. As in the cytoplasmic enzyme of the L-canavanine producer plant, the mitochondrial arginyl-tRNA synthetases from a specialist seed predator relies on a kinetic discrimination that prevents L-canavanine misincorporation into proteins.}, }
@article {pmid24443224, year = {2014}, author = {Abu-Bakar, SB and Razali, NM and Naggs, F and Wade, C and Mohd-Nor, SA and Aileen-Tan, SH}, title = {The mitochondrial 16 s rRNA reveals high anthropogenic influence on land snail diversity in a preliminary island survey.}, journal = {Molecular biology reports}, volume = {41}, number = {3}, pages = {1799-1805}, pmid = {24443224}, issn = {1573-4978}, mesh = {Animals ; Base Sequence ; *Genetic Variation ; Malaysia ; Mitochondria ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; Snails/*genetics ; }, abstract = {A total of 30 specimens belonging to five species, namely; Cryptozona siamensis, Sarika resplendens and Sarika sp. from the family Ariophantidae as well as Quantula striata and Quantula sp. from the family Dyakiidae were collected from the Langkawi Island in Northern Peninsular Malaysia. All specimens were identified through comparisons of shell morphology and amplification of a 500 bp segment of the 16S rRNA mtDNA gene. To assess phylogenetic insights, the sequences were aligned using ClustalW and phylogenetic trees were constructed. The analyses showed two major lineages in both Maximum Parsimony and Neighbour Joining phylogenetic trees. Each putative taxonomic group formed a monophyletic cluster. Our study revealed low species and intraspecies genetic diversities based on the 16S rRNA gene sequences. Thus, this study has provided an insight of land snail diversity in populations of an island highly influenced by anthropogenic activities through complementary use of shell morphological and molecular data.}, }
@article {pmid24438310, year = {2015}, author = {Feng, P and Zhao, H and Lu, X}, title = {Evolution of mitochondrial DNA and its relation to basal metabolic rate.}, journal = {Mitochondrial DNA}, volume = {26}, number = {4}, pages = {566-571}, doi = {10.3109/19401736.2013.873895}, pmid = {24438310}, issn = {1940-1744}, mesh = {Animals ; Basal Metabolism/*genetics ; DNA, Mitochondrial/*chemistry ; *Evolution, Molecular ; Likelihood Functions ; Locomotion/genetics ; Mammals/*genetics ; Phylogeny ; Selection, Genetic ; }, abstract = {Energy metabolism is essential for the survival of animals, which can be characterized by maximum metabolic rate (MMR) and basal metabolic rate (BMR). Because of the crucial roles of mitochondria in energy metabolism, mitochondrial DNA (mtDNA) has been subjected to stronger purifying selection in strongly locomotive than weakly locomotive birds and mammals. Although maximum locomotive speed (an indicator of MMR) showed a negative correlation with the evolutionary rate of mtDNA, it is unclear whether BMR has driven the evolution of mtDNA. Here, we take advantage of the large amount of mtDNA and BMR data in 106 mammals to test whether BMR has influenced the mtDNA evolution. Our results showed that, in addition to the locomotive speed, mammals with higher BMR have subjected to stronger purifying selection on mtDNA than did those with lower BMR. The evolution of mammalian mtDNA has been modified by two levels of energy metabolism, including MMR and BMR. Our study provides a more comprehensive view of mtDNA evolution in relation to energy metabolism.}, }
@article {pmid24438034, year = {2014}, author = {Dong, WG and Song, S and Jin, DC and Guo, XG and Shao, R}, title = {Fragmented mitochondrial genomes of the rat lice, Polyplax asiatica and Polyplax spinulosa: intra-genus variation in fragmentation pattern and a possible link between the extent of fragmentation and the length of life cycle.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {44}, pmid = {24438034}, issn = {1471-2164}, mesh = {Animals ; Anoplura/*genetics/*growth &amp; development ; Base Sequence ; DNA Fragmentation ; Evolution, Molecular ; *Genome, Mitochondrial ; Life Cycle Stages/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/chemistry/metabolism ; Rats ; Sequence Alignment ; Untranslated Regions ; }, abstract = {BACKGROUND: Blood-sucking lice (suborder Anoplura) parasitize eutherian mammals with 67% of the 540 described species found on rodents. The five species of blood-sucking lice that infest humans and pigs have fragmented mitochondrial genomes and differ substantially in the extent of fragmentation. To understand whether, or not, any life-history factors are linked to such variation, we sequenced the mt genomes of Polyplax asiatica and Polyplax spinulosa, collected from the greater bandicoot rat, Bandicota indica, and the Asian house rat, Rattus tanezumi, respectively.<br><br>RESULTS: We identified all of the 37 mitochondrial genes common to animals in Polyplax asiatica and Polyplax spinulosa. The mitochondrial genes of these two rat lice are on 11 circular minichromosomes; each minichromosome is 2-4 kb long and has 2-7 genes. The two rat lice share the same pattern for the distribution of the protein-coding genes and ribosomal RNA genes over the minichromosomes, but differ in the pattern for the distribution of 8 of the 22 transfer RNA genes. The mitochondrial genomes of the Polyplax rat lice have 3.4 genes, on average, on each minichromosome and, thus, are less fragmented than those of the human lice (2.1 and 2.4 genes per minichromosome), but are more fragmented than those of the pig lice (4.1 genes per minichromosome).<br><br>CONCLUSIONS: Our results revealed distinct patterns of mitochondrial genome fragmentation within the genus Polyplax and, furthermore, indicated a possible inverse link between the extent of mitochondrial genome fragmentation and the length of life cycle of the blood-sucking lice.}, }
@article {pmid24434588, year = {2014}, author = {Zhang, Y and Pan, YH and Yin, Q and Yang, T and Dong, D and Liao, CC and Zhang, S}, title = {Critical roles of mitochondria in brain activities of torpid Myotis ricketti bats revealed by a proteomic approach.}, journal = {Journal of proteomics}, volume = {105}, number = {}, pages = {266-284}, doi = {10.1016/j.jprot.2014.01.006}, pmid = {24434588}, issn = {1876-7737}, mesh = {Animals ; Brain/*metabolism ; Chiroptera/*metabolism ; Gene Expression Regulation/*physiology ; Mitochondria/*metabolism ; Mitochondrial Proteins/*biosynthesis ; Protein Processing, Post-Translational/*physiology ; Proteomics/methods ; Synaptic Transmission/physiology ; }, abstract = {UNLABELLED: Bats are the only mammals that fly and hibernate. Little is known about their overall metabolism in the brain during hibernation. In this study, brain proteins of torpid and active Myotis ricketti bats were fractionated and compared using a proteomic approach. Results showed that 21% (23 proteins) of identified proteins with significant expression changes were associated with amino acid metabolism and proteostasis. The expression levels of proteins involved in energy metabolism (15 proteins), cytoskeletal structure (18 proteins), and stress response (13 proteins) were also significantly altered in torpid bats. Over 30% (34 proteins) of differentially expressed proteins were associated with mitochondrial functions. Various post-translational modifications (PTMs) on PDHB, DLD, and ARG1 were detected, suggesting that bats use PTMs to regulate protein functions during torpor. Antioxidation and stress responses in torpid bats were similar to those of hibernated squirrels, suggesting a common strategy adopted by small hibernators against brain dysfunction. Since many amino acids that metabolize in mitochondria modulate neuronal transmissions, results of this study reveal pivotal roles of mitochondria in neural communication, metabolic regulation, and brain cell survival during bat hibernation. This article is part of a Special Issue entitled: Proteomics of non-model organisms.<br><br>BIOLOGICAL SIGNIFICANCE: This study reveals the mechanisms used by bats to regulate brain activities during torpor. These mechanisms include post-translational modifications and differential expression of proteins involved in mitochondrial electron transport, anaerobic glycolysis, TCA cycle efflux, cytoskeletal plasticity, amino acid metabolism, vesicle structure, antioxidation defense, stress response, and proteostasis. Our study provides insights in metabolic regulation of flying mammals during torpor and common strategies used by small hibernators in response to hibernation. This article is part of a Special Issue entitled: Proteomics of non-model organisms.}, }
@article {pmid24430572, year = {2014}, author = {Ji, Y and Liang, M and Zhang, J and Zhang, M and Zhu, J and Meng, X and Zhang, S and Gao, M and Zhao, F and Wei, QP and Jiang, P and Tong, Y and Liu, X and Qin Mo, J and Guan, MX}, title = {Mitochondrial haplotypes may modulate the phenotypic manifestation of the LHON-associated ND1 G3460A mutation in Chinese families.}, journal = {Journal of human genetics}, volume = {59}, number = {3}, pages = {134-140}, pmid = {24430572}, issn = {1435-232X}, mesh = {Amino Acid Substitution/genetics ; Asian People/genetics ; China ; Cohort Studies ; DNA Mutational Analysis ; DNA, Mitochondrial/genetics ; Diagnostic Techniques, Ophthalmological ; Family ; Female ; *Genetic Predisposition to Disease ; Genome, Mitochondrial/genetics ; Haplotypes/*genetics ; Humans ; Male ; Mitochondria/*genetics ; Mutation/*genetics ; Mutation, Missense/genetics ; NADH Dehydrogenase/*genetics ; Optic Atrophy, Hereditary, Leber/*enzymology/*genetics ; Phenotype ; Phylogeny ; RNA, Ribosomal/genetics ; }, abstract = {To investigate the pathophysiology of Leber's hereditary optic neuropathy (LHON), a cohort of 1164 Han Chinese subjects with LHON were screened for ND1 G3460A mutation. A total of 295 subjects from 16 Han Chinese families carrying the G3460A mutation underwent a clinical and genetic evaluation and molecular analysis of mitochondrial (mt)DNA. The incidence of G3460A mutation was 1.4% in this cohort of Chinese subjects with LHON. Twenty-seven (20 males/7 females) of 109 matrilineal relatives among 10 Chinese pedigrees carrying this mutation exhibited a wide range of severity and age-at-onset in visual impairment. Penetrances of optic neuropathy ranged from 7.1% to 50%, with the average of 24.5%. The age-at-onset of 27 affected matrilineal relatives varied from 10 to 40 years, with the average of 22 years. Molecular analysis identified the homoplasmic G3460A mutation and distinct sets of variants belonging to eight haplogroups. Haplogroup M with G3460A mutation was of higher frequency than those in controls. The penetrances of visual loss in families carrying mitochondrial DNA haplogroups A, B and M were higher than those in other families. Furthermore, haplogroup-specific variants tRNA(Ser(AGY)) A12223G, tRNA(Thr) G15927A and tRNA(Glu) A14693G may enhance the penetrance of visual loss in these families. The G3460A mutation occurred through recurrent origins and founder events in Chinese population. Mitochondrial modifiers may modulate the penetrance and expressivity of optic neuropathy among Chinese pedigrees carrying the G3460A mutation. Thus, our findings may provide new insights into the understanding of pathophysiology and valuable information on the management of LHON.}, }
@article {pmid24429632, year = {2014}, author = {Friedman, JR and Nunnari, J}, title = {Mitochondrial form and function.}, journal = {Nature}, volume = {505}, number = {7483}, pages = {335-343}, pmid = {24429632}, issn = {1476-4687}, support = {R01 GM097432/GM/NIGMS NIH HHS/United States ; R01 GM062942/GM/NIGMS NIH HHS/United States ; R01GM097432/GM/NIGMS NIH HHS/United States ; R01GM106019/GM/NIGMS NIH HHS/United States ; R01 GM106019/GM/NIGMS NIH HHS/United States ; R01GM062942/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Chromosome Segregation ; Chromosomes/genetics/metabolism ; DNA, Mitochondrial/genetics/metabolism ; Dynamins/metabolism ; Endoplasmic Reticulum/metabolism ; Eukaryotic Cells/cytology/metabolism ; Genome, Mitochondrial ; Humans ; Mitochondria/*genetics/*physiology ; Organelle Shape ; Stress, Physiological ; }, abstract = {Mitochondria are one of the major ancient endomembrane systems in eukaryotic cells. Owing to their ability to produce ATP through respiration, they became a driving force in evolution. As an essential step in the process of eukaryotic evolution, the size of the mitochondrial chromosome was drastically reduced, and the behaviour of mitochondria within eukaryotic cells radically changed. Recent advances have revealed how the organelle's behaviour has evolved to allow the accurate transmission of its genome and to become responsive to the needs of the cell and its own dysfunction.}, }
@article {pmid24429285, year = {2014}, author = {Hartmann, A and Hellmund, M and Lucius, R and Voelker, DR and Gupta, N}, title = {Phosphatidylethanolamine synthesis in the parasite mitochondrion is required for efficient growth but dispensable for survival of Toxoplasma gondii.}, journal = {The Journal of biological chemistry}, volume = {289}, number = {10}, pages = {6809-6824}, pmid = {24429285}, issn = {1083-351X}, mesh = {Amino Acid Sequence ; Animals ; Carboxy-Lyases/classification/genetics/*metabolism ; Cell Survival ; Cytidine Diphosphate/analogs &amp; derivatives/metabolism ; Diglycerides/metabolism ; Ethanolamines/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phosphatidylethanolamines/*biosynthesis ; Phylogeny ; Protozoan Proteins/classification/genetics/*metabolism ; Toxoplasma/genetics/*growth &amp; development/metabolism ; }, abstract = {Toxoplasma gondii is a highly prevalent obligate intracellular parasite of the phylum Apicomplexa, which also includes other parasites of clinical and/or veterinary importance, such as Plasmodium, Cryptosporidium, and Eimeria. Acute infection by Toxoplasma is hallmarked by rapid proliferation in its host cells and requires a significant synthesis of parasite membranes. Phosphatidylethanolamine (PtdEtn) is the second major phospholipid class in T. gondii. Here, we reveal that PtdEtn is produced in the parasite mitochondrion and parasitophorous vacuole by decarboxylation of phosphatidylserine (PtdSer) and in the endoplasmic reticulum by fusion of CDP-ethanolamine and diacylglycerol. PtdEtn in the mitochondrion is synthesized by a phosphatidylserine decarboxylase (TgPSD1mt) of the type I class. TgPSD1mt harbors a targeting peptide at its N terminus that is required for the mitochondrial localization but not for the catalytic activity. Ablation of TgPSD1mt expression caused up to 45% growth impairment in the parasite mutant. The PtdEtn content of the mutant was unaffected, however, suggesting the presence of compensatory mechanisms. Indeed, metabolic labeling revealed an increased usage of ethanolamine for PtdEtn synthesis by the mutant. Likewise, depletion of nutrients exacerbated the growth defect (∼56%), which was partially restored by ethanolamine. Besides, the survival and residual growth of the TgPSD1mt mutant in the nutrient-depleted medium also indicated additional routes of PtdEtn biogenesis, such as acquisition of host-derived lipid. Collectively, the work demonstrates a metabolic cooperativity between the parasite organelles, which ensures a sustained lipid synthesis, survival and growth of T. gondii in varying nutritional milieus.}, }
@article {pmid24416271, year = {2014}, author = {Thomas, RC and Willette, DA and Carpenter, KE and Santos, MD}, title = {Hidden diversity in sardines: genetic and morphological evidence for cryptic species in the goldstripe sardinella, Sardinella gibbosa (Bleeker, 1849).}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e84719}, pmid = {24416271}, issn = {1932-6203}, mesh = {Animals ; Cell Nucleus/genetics ; Fishes/*anatomy &amp; histology/*genetics ; Genetic Markers/genetics ; *Genetic Variation ; Genotyping Techniques ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; }, abstract = {Cryptic species continue to be uncovered in many fish taxa, posing challenges for fisheries conservation and management. In Sardinella gibbosa, previous investigations revealed subtle intra-species variations, resulting in numerous synonyms and a controversial taxonomy for this sardine. Here, we tested for cryptic diversity within S. gibbosa using genetic data from two mitochondrial and one nuclear gene regions of 248 individuals of S. gibbosa, collected from eight locations across the Philippine archipelago. Deep genetic divergence and subsequent clustering was consistent across both mitochondrial and nuclear markers. Clade distribution is geographically limited: Clade 1 is widely distributed in the central Philippines, while Clade 2 is limited to the northernmost sampling site. In addition, morphometric analyses revealed a unique head shape that characterized each genetic clade. Hence, both genetic and morphological evidence strongly suggests a hidden diversity within this common and commercially-important sardine.}, }
@article {pmid24415954, year = {2014}, author = {Trier, CN and Hermansen, JS and Sætre, GP and Bailey, RI}, title = {Evidence for mito-nuclear and sex-linked reproductive barriers between the hybrid Italian sparrow and its parent species.}, journal = {PLoS genetics}, volume = {10}, number = {1}, pages = {e1004075}, pmid = {24415954}, issn = {1553-7404}, mesh = {Animals ; Cell Nucleus/genetics ; Chimera/*genetics ; Genome, Mitochondrial ; Genotype ; *Hybridization, Genetic ; Polymorphism, Single Nucleotide ; *Reproductive Isolation ; Sequence Analysis, DNA ; Sparrows/*genetics ; Species Specificity ; }, abstract = {Studies of reproductive isolation between homoploid hybrid species and their parent species have rarely been carried out. Here we investigate reproductive barriers between a recently recognized hybrid bird species, the Italian sparrow Passer italiae and its parent species, the house sparrow P. domesticus and Spanish sparrow P. hispaniolensis. Reproductive barriers can be difficult to study in hybrid species due to lack of geographical contact between taxa. However, the Italian sparrow lives parapatrically with the house sparrow and both sympatrically and parapatrically with the Spanish sparrow. Through whole-transcriptome sequencing of six individuals of each of the two parent species we identified a set of putatively parent species-diagnostic single nucleotide polymorphism (SNP) markers. After filtering for coverage, genotyping success (>97%) and multiple SNPs per gene, we retained 86 species-informative, genic, nuclear and mitochondrial SNP markers from 84 genes for analysis of 612 male individuals. We show that a disproportionately large number of sex-linked genes, as well as the mitochondria and nuclear genes with mitochondrial function, exhibit sharp clines at the boundaries between the hybrid and the parent species, suggesting a role for mito-nuclear and sex-linked incompatibilities in forming reproductive barriers. We suggest that genomic conflict via interactions between mitochondria and sex-linked genes with mitochondrial function ("mother's curse") at one boundary and centromeric drive at the other may best explain our findings. Hybrid speciation in the Italian sparrow may therefore be influenced by mechanisms similar to those involved in non-hybrid speciation, but with the formation of two geographically separated species boundaries instead of one. Spanish sparrow alleles at some loci have spread north to form reproductive barriers with house sparrows, while house sparrow alleles at different loci, including some on the same chromosome, have spread in the opposite direction to form barriers against Spanish sparrows.}, }
@article {pmid24410953, year = {2014}, author = {Kaur, C and Mustafiz, A and Sarkar, AK and Ariyadasa, TU and Singla-Pareek, SL and Sopory, SK}, title = {Expression of abiotic stress inducible ETHE1-like protein from rice is higher in roots and is regulated by calcium.}, journal = {Physiologia plantarum}, volume = {152}, number = {1}, pages = {1-16}, doi = {10.1111/ppl.12147}, pmid = {24410953}, issn = {1399-3054}, mesh = {Amino Acid Sequence ; Calcium/*metabolism ; Dioxygenases/*genetics/metabolism ; *Gene Expression Regulation, Plant ; Genes, Reporter ; Light ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; Mutation ; Onions/cytology/genetics/physiology ; Organ Specificity ; Oryza/drug effects/genetics/*physiology/radiation effects ; Phylogeny ; Plant Epidermis/drug effects/genetics/physiology/radiation effects ; Plant Growth Regulators/pharmacology ; Plant Proteins/genetics/metabolism ; Plant Roots/drug effects/genetics/physiology/radiation effects ; Plants, Genetically Modified ; Promoter Regions, Genetic/genetics ; Recombinant Fusion Proteins ; Sequence Alignment ; *Stress, Physiological ; }, abstract = {ETHYLMALONIC ENCEPHALOPATHY PROTEIN 1 (ETHE1) encodes sulfur dioxygenase (SDO) activity regulating sulfide levels in living organisms. It is an essential gene and mutations in ETHE1 leads to ethylmalonic encephalopathy (EE) in humans and embryo lethality in Arabidopsis. At present, very little is known regarding the role of ETHE1 beyond the context of EE and almost nothing is known about factors affecting its regulation in plant systems. In this study, we have identified, cloned and characterized OsETHE1, a gene encoding ETHE1-like protein from Oryza sativa. ETHE1 proteins in general are most similar to glyoxalase II (GLYII) and hence OsETHE1 has been earlier annotated as OsGLYII1, a putative GLYII gene. Here we show that OsETHE1 lacks GLYII activity and is instead an ETHE1 homolog being localized in mitochondria like its human and Arabidopsis counterparts. We have isolated and analyzed 1618 bp OsETHE1 promoter (pOsETHE1) to examine the factors affecting OsETHE1 expression. For this, transcriptional promoter pOsETHE1: 5-bromo-5-chloro-3-indolyl-β-D-glucuronide (GUS) fusion construct was made and stably transformed into rice. GUS expression pattern of transgenic pOsETHE1:GUS plants reveal a high root-specific expression of OsETHE1. The pOsETHE1 activity was stimulated by Ca(II) and required light for induction. Moreover, pOsETHE1 activity was induced under various abiotic stresses such as heat, salinity and oxidative stress, suggesting a potential role of OsETHE1 in stress response.}, }
@article {pmid24850385, year = {2014}, author = {Hardie, DG}, title = {AMP-activated protein kinase: maintaining energy homeostasis at the cellular and whole-body levels.}, journal = {Annual review of nutrition}, volume = {34}, number = {}, pages = {31-55}, pmid = {24850385}, issn = {1545-4312}, support = {//Wellcome Trust/United Kingdom ; 097726//Wellcome Trust/United Kingdom ; /CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {AMP-Activated Protein Kinases/*metabolism ; Animals ; *Energy Intake ; *Energy Metabolism ; *Homeostasis ; Humans ; *Models, Biological ; *Signal Transduction ; }, abstract = {The adenosine monophosphate (AMP)-activated protein kinase (AMPK) signaling pathway arose early during evolution of eukaryotic cells, when it appears to have been involved in the response to glucose starvation and perhaps also in monitoring the output of the newly acquired mitochondria. Due to the advent of hormonal regulation of glucose homeostasis, glucose starvation is a less frequent event for mammalian cells than for single-celled eukaryotes. Nevertheless, the AMPK system has been preserved in mammals where, by monitoring cellular AMP:adenosine triphosphate (ATP) and adenosine diphosphate (ADP):ATP ratios and balancing the rates of catabolism and ATP consumption, it maintains energy homeostasis at a cell-autonomous level. In addition, hormones involved in maintaining energy balance at the whole-body level interact with AMPK in the hypothalamus. AMPK is activated by two widely used clinical drugs, metformin and aspirin, and also by many natural products of plants that are either derived from traditional medicines or are promoted as "nutraceuticals."}, }
@article {pmid24970134, year = {2012}, author = {El-Shehawi, AM and Fahmi, AI and Sayed, SM and Elseehy, MM}, title = {Genetic Fingerprinting of Wheat and Its Progenitors by Mitochondrial Gene orf256.}, journal = {Biomolecules}, volume = {2}, number = {2}, pages = {228-239}, pmid = {24970134}, issn = {2218-273X}, abstract = {orf256 is a wheat mitochondrial gene associated with cytoplasmic male sterility (CMS) that has different organization in various species. This study exploited the orf256 gene as a mitochondrial DNA marker to study the genetic fingerprint of Triticum and Aegilops species. PCR followed by sequencing of common parts of the orf256 gene were employed to determine the fingerprint and molecular evolution of Triticum and Aegilops species. Although many primer pairs were used, two pairs of orf256 specific primers (5:-94/C: 482, 5:253/C: 482), amplified DNA fragments of 576 bp and 230 bp respectively in all species were tested. A common 500 bp of nine species of Triticum and Aegilops were aligned and showed consistent results with that obtained from other similar chloroplast or nuclear genes. Base alignment showed that there were various numbers of base substitutions in all species compared to S. cereal (Sc) (the outgroup species). Phylogenetic relationship revealed similar locations and proximity on phylogenetic trees established using plastid and nuclear genes. The results of this study open a good route to use unknown function genes of mitochondria in studying the molecular relationships and evolution of wheat and complex plant genomes.}, }
@article {pmid25792771, year = {2007}, author = {Futai, M}, title = {Our research on proton pumping ATPases over three decades: their biochemistry, molecular biology and cell biology.}, journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences}, volume = {82}, number = {10}, pages = {416-438}, pmid = {25792771}, issn = {0386-2208}, abstract = {ATP is synthesized by F-type proton-translocating ATPases (F-ATPases) coupled with an electrochemical proton gradient established by an electron transfer chain. This mechanism is ubiquitously found in mitochondria, chloroplasts and bacteria. Vacuolar-type ATPases (V-ATPases) are found in endomembrane organelles, including lysosomes, endosomes, synaptic vesicles, etc., of animal and plant cells. These two physiologically different proton pumps exhibit similarities in subunit assembly, catalysis and the coupling mechanism from chemistry to proton transport through subunit rotation. We mostly discuss our own studies on the two proton pumps over the last three decades, including ones on purification, kinetic analysis, rotational catalysis and the diverse roles of acidic luminal organelles. The diversity of organellar proton pumps and their stochastic fluctuation are the important concepts derived recently from our studies.}, }
@article {pmid24414012, year = {1978}, author = {Iino, M and Hashimoto, T and Heber, U}, title = {Inhibition of photosynthesis and respiration by batatasins.}, journal = {Planta}, volume = {138}, number = {2}, pages = {167-172}, pmid = {24414012}, issn = {0032-0935}, abstract = {Effects of batatasins I, III and V, phenolic growth inhibitors occuring in dormant bulbils of Dioscorea batatas Decne., on photosynthetic reactions of chloroplasts from spinach (Spinacia oleracea L.) and on respiration of mitochondria from potatoes (Solanum tuberosum L.) were investigated. In chloroplasts, the batatasins effectively inhibited CO2-dependent oxygen evolution and electron flow from water to acceptors such as dichlorophenolindophenol, ferricyanide and methylviologen. Photosystem-I dependent electron transport from ascorbate to oxygen was stimulated. The proton conductivity of thylakoid membranes was increased and phosphorylation was uncoupled from electron transport. Inhibition of electron transport with water as electron donor appeared to precede uncoupling. In mitochondrial, batatasin I did not much inhibit succinate-dependent O2 uptake in the absence of ADP, but caused strong inhibition in the presence of ADP. Batatasins III and V inhibited oxygen uptake irrespective of the presence or absence of ADP. Inhibition of chloroplast and mitochondrial reactions by batatasins was shown to be reversible.}, }
@article {pmid24425216, year = {1977}, author = {Rathnam, CK and Edwards, GE}, title = {C4-Dicarboxylic acid metabolism in bundle-sheath chloroplasts, mitochondria and strands of Eriochloa borumensis Hack., a phosphoenolpyruvate-carboxykinase type C4 species.}, journal = {Planta}, volume = {133}, number = {2}, pages = {135-144}, pmid = {24425216}, issn = {0032-0935}, abstract = {C4-acid metabolism by isolated bundlesheath chloroplasts, mitochondria and strands of Eriochloa borumensis Hack., a phosphoennolpyruvate-carboxykinase (PEP-CK) species, was investigated. Aspartate, oxaloacetate (OAA) and malate were decarboxylated by strands with several-fold stimulation upon illumination. There was strictly light-dependent decarboxylation of OAA and malate by the chloroplasts, but the chloroplasts did not decarboxylate aspartate in light or dark. PEP was a primary product of OAA or malate decarboxylation by the chloroplasts and its formation was inhibited by 3-(3,4-dichlorophenyl)-1, 1-dimethylurea or NH4Cl. There was very little conversion of PEP to pyruvate by bundle-sheath chloroplasts, mitochondria or strands. Decarboxylation of the three C4-acids by mitochondria was light-independent. Pyruvate was the only product of mitochondrial metabolism of C4-acids, and was apparently transaminated in the cytoplasm since PEP and alanine were primarily exported out of the bundle-sheath strands. Light-dependent C4-acid decarboxylation by the chloroplasts is suggested to be through the PEP-CK, while the mitochondrial C4-acid decarboxylation may proceed through the NAD-malic enzyme (NAD-ME) system. In vivo both aspartate and malate are considered as transport metobolites from mesophyll to bundle-sheath cells in PEP-CK species. Aspartate would be metabolized by the mitochondria to OAA. Part of the OAA may be converted to malate and decarboxylated through NAD-ME, and part may be transported to the chloroplasts for decarboxylation through PEP-CK localized in the chloroplasts. Malate transported from mesophyll cells may serve as carboxyl donor to chloroplasts through the chloroplastic NAD-malate dehydrogenase and PEP-CK. Bundle-sheath strands and chloroplasts fixed (14)CO2 at high rates and exhibited C4-acid-dependent O2 evolution in the light. Studies with 3-mercaptopicolinic acid, a specific inhibitor of PEP-CK, have indicated that most (about 70%) of the OAA formed from aspartate is decarboxylated through the chloroplastic PEP-CK and the remaining (about 30%) OAA through the mitochondrial NAD-ME. Pyruvate stimulation of aspartate decarboxylation is discussed; a pyruvate-alanine shuttle and an aspartate-alanine shuttle are proposed between the mesophyll and bundle-sheath cells during aspartate decarboxylation through the PEP-CK and NAD-ME system respectively.}, }
@article {pmid24407855, year = {2014}, author = {Moriyama, T and Tajima, N and Sekine, K and Sato, N}, title = {Localization and phylogenetic analysis of enzymes related to organellar genome replication in the unicellular rhodophyte Cyanidioschyzon merolae.}, journal = {Genome biology and evolution}, volume = {6}, number = {1}, pages = {228-237}, pmid = {24407855}, issn = {1759-6653}, mesh = {DNA Helicases/genetics/metabolism ; *DNA Replication ; DNA-Directed DNA Polymerase/genetics/metabolism ; Evolution, Molecular ; *Genome, Chloroplast ; *Genome, Mitochondrial ; *Genome, Plant ; *Phylogeny ; Plant Proteins/genetics/metabolism ; Protein Transport ; Rhodophyta/enzymology/*genetics/metabolism ; }, abstract = {Plants and algae possess plastids and mitochondria harboring their own genomes, which are replicated by the apparatus consisting of DNA polymerase, DNA primase, DNA helicase, DNA topoisomerase, single-stranded DNA maintenance protein, DNA ligase, and primer removal enzyme. In the higher plant Arabidopsis thaliana, organellar replication-related enzymes (OREs) are similar in plastids and mitochondria because many of them are dually targeted to plastids and mitochondria. In the red algae, there is a report about a DNA replicase, plant/protist organellar DNA polymerase, which is localized to both plastids and mitochondria. However, other OREs remain unclear in algae. Here, we identified OREs possibly localized to organelles in the unicellular rhodophyte Cyanidioschyzon merolae. We then examined intracellular localization of green fluorescent protein-fusion proteins of these enzymes in C. merolae, whose cell has a single plastid and a single mitochondrion and is suitable for localization analysis, demonstrating that the plastid and the mitochondrion contain markedly different components of replication machinery. Phylogenetic analyses revealed that the organelle replication apparatus was composed of enzymes of various different origins, such as proteobacterial, cyanobacterial, and eukaryotic, in both red algae and green plants. Especially in the red alga, many enzymes of cyanobacterial origin remained. Finally, on the basis of the results of localization and phylogenetic analyses, we propose a model on the succession of OREs in eukaryotes.}, }
@article {pmid24401337, year = {2014}, author = {Stocks, PA and Barton, V and Antoine, T and Biagini, GA and Ward, SA and O'Neill, PM}, title = {Novel inhibitors of the Plasmodium falciparum electron transport chain.}, journal = {Parasitology}, volume = {141}, number = {1}, pages = {50-65}, doi = {10.1017/S0031182013001571}, pmid = {24401337}, issn = {1469-8161}, support = {G1002586/MRC_/Medical Research Council/United Kingdom ; MC_PC_12017/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Antimalarials/chemistry/*pharmacology ; Dihydroorotate Dehydrogenase ; Electron Transport/*drug effects ; Electron Transport Complex III/antagonists &amp; inhibitors/chemistry/metabolism ; Enzyme Inhibitors/chemistry/*pharmacology ; Humans ; Malaria, Falciparum/drug therapy/parasitology ; Mitochondria/drug effects/enzymology ; Molecular Docking Simulation ; NADH, NADPH Oxidoreductases/antagonists &amp; inhibitors/chemistry/metabolism ; Oxidoreductases Acting on CH-CH Group Donors/antagonists &amp; inhibitors/chemistry/metabolism ; Plasmodium falciparum/*drug effects/enzymology ; Protozoan Proteins/*antagonists &amp; inhibitors/chemistry/metabolism ; Structure-Activity Relationship ; }, abstract = {Due to an increased need for new antimalarial chemotherapies that show potency against Plasmodium falciparum, researchers are targeting new processes within the parasite in an effort to circumvent or delay the onset of drug resistance. One such promising area for antimalarial drug development has been the parasite mitochondrial electron transport chain (ETC). Efforts have been focused on targeting key processes along the parasite ETC specifically the dihydroorotate dehydrogenase (DHOD) enzyme, the cytochrome bc 1 enzyme and the NADH type II oxidoreductase (PfNDH2) pathway. This review summarizes the most recent efforts in antimalarial drug development reported in the literature and describes the evolution of these compounds.}, }
@article {pmid24400487, year = {2013}, author = {Gao, FL and Shen, JG and Shi, FY and Chang, F and Xie, LH and Zhan, JS}, title = {[Sequence variation and protein structure of pipo gene in Potato virus Y].}, journal = {Yi chuan = Hereditas}, volume = {35}, number = {9}, pages = {1125-1134}, doi = {10.3724/sp.j.1005.2013.01125}, pmid = {24400487}, issn = {0253-9772}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Base Sequence ; *Genetic Variation ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/virology ; Potyvirus/classification/*genetics/*isolation &amp; purification/metabolism ; Protein Transport ; Sequence Alignment ; Solanum tuberosum/*virology ; Viral Proteins/*chemistry/*genetics/metabolism ; }, abstract = {The objectives of this study were to understand the sequence variation and the putative protein structure of pipo gene in the Potato virus Y (PVY) collected from Solanum tuberosum. The pipo gene in PVY was cloned using a pair of degenerate primers designed from its conserved region and its sequences were used to re-construct phylogenetic tree in Potyvirus genera by a Bayesian inference method. An expected fragment of 235 bp was amplified in all 20 samples by RT-PCR and the pipo genes in the 20 samples assayed shared more than 92% nucleotide sequence similarity with the published sequences of PVY strains. Among the 20 pipo gene sequences, 13 polymorphic sites were detected, including 4 parsimony informative sites and 9 singleton variable sites. These results indicate that PVY pipo gene is highly conserved but some sequence variations exist. Further analyses suggest that the pipo gene encodes a hydrophilic protein without signal peptide and transmembrane region. The protein has theoretical isoelectric points (pI) ranging from 11.26 to 11.62 and contains three highly conserved regions, especially between aa 10 and 59. The protein is likely located in the mitochondria and has a-helix secondary structure. Bayesian inference of phylogenetic trees reveals that PVY isolates are clustered in the same branch with high posterior probability, while Sunflower chlorotic mottle virus (SoCMoV) and Pepper severe mosaic virus (PepSMV) are closely related, consisting with the classification of Potyvirus genera using other approaches. Our analyses suggest that the pipo gene can be a new marker for phylogenetic analysis of the genera. The results reported in this paper provide useful insights in the genetic variation and the evolution of PVY and can stimulate further research on structure and function of the PIPO protein.}, }
@article {pmid24398998, year = {2013}, author = {Mirancea, N and Moroşanu, AM and Mirancea, GV and Juravle, FD and Mănoiu, VS}, title = {Infrastructure of the telocytes from tumor stroma in the skin basal and squamous cell carcinomas.}, journal = {Romanian journal of morphology and embryology = Revue roumaine de morphologie et embryologie}, volume = {54}, number = {4}, pages = {1025-1037}, pmid = {24398998}, issn = {2066-8279}, mesh = {Carcinoma, Basal Cell/*pathology/*ultrastructure ; Carcinoma, Squamous Cell/*pathology/*ultrastructure ; Dermis/abnormalities/pathology/ultrastructure ; Desmosomes/ultrastructure ; Humans ; Mitochondria/ultrastructure ; Phenotype ; Skin Neoplasms/*pathology/*ultrastructure ; Stromal Cells/pathology/ultrastructure ; }, abstract = {In this paper, we focus our interest on the ultrastructure of telocytes (TCs) present inside of tumor-stroma in basal cell carcinoma (BCC) and squamous cell carcinoma (SCC). Tumor-stroma cooperation is necessary for tumor growth, invasive behavior and ectopic development of microtumors. There is a plethora of reports about the role of different stromal cell types in tumor evolution in the human body. In this line, almost nothing is known about the recently identified interstitial cell type called telocyte (TC). To our best knowledge, this is the first study to publish TCs in malignant tumors, namely BCC and SCC. Here, we described the infrastructural aspects of TCs as well as their relationships with other tumor stroma components. TC from the tumor stroma has cell body where the nucleus is located and exhibits two (rarely more) very long cell extensions of tens (over 60-100 μm) termed telopodes. A telopode appears as an alternation of very thin segments called podomers and dilated segments called podomes, which accommodate mitochondria, rough endoplasmic reticulum, cytoskeleton, caveolae, as well as coated vesicles. TCs establish homocellular junctions leading to a 3-D network inside of peritumoral stroma. TCs may play an important role in intercellular signaling via stromal synapses and shed microvesicle transfer. Comparative evaluation with normal dermal skin showed that telocytes from tumor stroma have a very restraint number of heterocellular junctions. The limitation of TCs heterocellular junctions suggests a possible involvement in induction of cell-cell communication alterations into the peritumoral stroma and, consequently, into the whole tumor mass.}, }
@article {pmid24398322, year = {2014}, author = {Sloan, DB and Nakabachi, A and Richards, S and Qu, J and Murali, SC and Gibbs, RA and Moran, NA}, title = {Parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects.}, journal = {Molecular biology and evolution}, volume = {31}, number = {4}, pages = {857-871}, pmid = {24398322}, issn = {1537-1719}, support = {S10 RR029676/RR/NCRR NIH HHS/United States ; RR19895/RR/NCRR NIH HHS/United States ; F32 GM099334/GM/NIGMS NIH HHS/United States ; U54 HG003273/HG/NHGRI NIH HHS/United States ; S10 RR019895/RR/NCRR NIH HHS/United States ; 1F32GM099334/GM/NIGMS NIH HHS/United States ; RR029676-01/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Gammaproteobacteria/*genetics ; Gene Expression ; *Gene Transfer, Horizontal ; Genes, Insect ; Genome, Bacterial ; Hemiptera/*genetics ; Metabolic Networks and Pathways/genetics ; Phylogeny ; RNA, Messenger/genetics ; Sequence Analysis, RNA ; Symbiosis/*genetics ; }, abstract = {Bacteria confined to intracellular environments experience extensive genome reduction. In extreme cases, insect endosymbionts have evolved genomes that are so gene-poor that they blur the distinction between bacteria and endosymbiotically derived organelles such as mitochondria and plastids. To understand the host's role in this extreme gene loss, we analyzed gene content and expression in the nuclear genome of the psyllid Pachypsylla venusta, a sap-feeding insect that harbors an ancient endosymbiont (Carsonella) with one of the most reduced bacterial genomes ever identified. Carsonella retains many genes required for synthesis of essential amino acids that are scarce in plant sap, but most of these biosynthetic pathways have been disrupted by gene loss. Host genes that are upregulated in psyllid cells housing Carsonella appear to compensate for endosymbiont gene losses, resulting in highly integrated metabolic pathways that mirror those observed in other sap-feeding insects. The host contribution to these pathways is mediated by a combination of native eukaryotic genes and bacterial genes that were horizontally transferred from multiple donor lineages early in the evolution of psyllids, including one gene that appears to have been directly acquired from Carsonella. By comparing the psyllid genome to a recent analysis of mealybugs, we found that a remarkably similar set of functional pathways have been shaped by independent transfers of bacterial genes to the two hosts. These results show that horizontal gene transfer is an important and recurring mechanism driving coevolution between insects and their bacterial endosymbionts and highlight interesting similarities and contrasts with the evolutionary history of mitochondria and plastids.}, }
@article {pmid24398320, year = {2014}, author = {Rochette, NC and Brochier-Armanet, C and Gouy, M}, title = {Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes.}, journal = {Molecular biology and evolution}, volume = {31}, number = {4}, pages = {832-845}, pmid = {24398320}, issn = {1537-1719}, mesh = {Archaea/genetics ; Bacteria/genetics ; Biological Evolution ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Speciation ; Genome, Human ; Humans ; *Models, Genetic ; Phylogeny ; Symbiosis/genetics ; Yeasts/genetics ; }, abstract = {The evolutionary origin of eukaryotes is a question of great interest for which many different hypotheses have been proposed. These hypotheses predict distinct patterns of evolutionary relationships for individual genes of the ancestral eukaryotic genome. The availability of numerous completely sequenced genomes covering the three domains of life makes it possible to contrast these predictions with empirical data. We performed a systematic analysis of the phylogenetic relationships of ancestral eukaryotic genes with archaeal and bacterial genes. In contrast with previous studies, we emphasize the critical importance of methods accounting for statistical support, horizontal gene transfer, and gene loss, and we disentangle the processes underlying the phylogenomic pattern we observe. We first recover a clear signal indicating that a fraction of the bacteria-like eukaryotic genes are of alphaproteobacterial origin. Then, we show that the majority of bacteria-related eukaryotic genes actually do not point to a relationship with a specific bacterial taxonomic group. We also provide evidence that eukaryotes branch close to the last archaeal common ancestor. Our results demonstrate that there is no phylogenetic support for hypotheses involving a fusion with a bacterium other than the ancestor of mitochondria. Overall, they leave only two possible interpretations, respectively, based on the early-mitochondria hypotheses, which suppose an early endosymbiosis of an alphaproteobacterium in an archaeal host and on the slow-drip autogenous hypothesis, in which early eukaryotic ancestors were particularly prone to horizontal gene transfers.}, }
@article {pmid24397768, year = {2015}, author = {Marín, A and Alfaro, R and Fujimoto, T and Arai, K}, title = {Mitochondrial genome of the Peruvian scallop Argopecten purpuratus (Bivalvia: Pectinidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {726-727}, doi = {10.3109/19401736.2013.845760}, pmid = {24397768}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Codon, Initiator ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Pectinidae/*genetics ; Peru ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The mitochondrial genome of the Peruvian scallop Argopecten purpuratus was determined. The length of the mitochondrial coding region is 15,608 bp. A typical bivalve mitochondrial composition was detected with 12 protein-coding genes, 2 ribosomal RNA genes and 21 transfer RNA genes, with the absence of the atp8 gene. Fifty percent of the protein-coding genes use typical ATG start codon, whereas five genes utilize ATA as their start codon. Only one gene was found to utilize TTG as its start codon. The A. purpuratus mitogenome shows a significant similarity to that of A. irradians irradians, in length as well as in gene composition.}, }
@article {pmid24397757, year = {2015}, author = {Wang, JF and Chen, MY and Chaw, SM and Morii, Y and Yoshimura, M and Sota, T and Lin, CP}, title = {Complete mitochondrial genome of an enigmatic dragonfly, Epiophlebia superstes (Odonata, Epiophlebiidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {718-719}, doi = {10.3109/19401736.2013.845756}, pmid = {24397757}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Odonata/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {This study reported the 15,435 bp-long complete mitochondrial genome of the relict Epiophlebia superstes (Odonata, Epiophlebiidae), an enigmatic dragonfly of the paraphyletic 'Anisozygoptera' possessing characteristics similar to members of both extant odonate suborders, the Zygoptera and the Anisoptera. This mitogenome comprises the common set of 37 genes and an A + T-rich control region, and has a gene arrangement identical to those of all available odonates. The genome contains three non-coding inter-genic spacers (s1-s3), which occurs in all of other known odonates, but it lacks the inter-genic spacer s5 typically found in the Anisoptera. This result suggests that E. superstes possesses a mitogenmic organization more closely related to that of the Zygoptera than that of the Anizoptera.}, }
@article {pmid24396269, year = {2013}, author = {Prochiantz, A}, title = {Signaling with homeoprotein transcription factors in development and throughout adulthood.}, journal = {Current genomics}, volume = {14}, number = {6}, pages = {361-370}, pmid = {24396269}, issn = {1389-2029}, abstract = {The concept of homeoprotein transduction as a novel signaling pathway has dramatically evolved since it was first proposed in 1991. It is now well established in several biological systems from plants to mammals. In this review, the different steps that have led to this unexpected observation are recalled and the developmental and physiological models that have allowed us (and a few others) to consolidate the original hypothesis are described. Because homeoprotein signaling is active in plants and animals it is proposed that it has predated the separation between animals and plants and is thus very ancient. This may explain why the basic phenomenon of homeoprotein transduction is so minimalist, requiring no specific receptors or transduction pathways beside those offered by mitochondria, organelles present in all eukaryotic cells. Indeed complexity has been added in the course of evolution and the conservation of homeoprotein transduction is discussed in the context of its synergy with bona fide signaling mechanism that may have added robustness to this primitive cell communication device. The same synergy possibly explains why homeoprotein signaling is important both in embryonic development and in adult functions fulfilled by signaling entities (e.g. growth factors) themselves active throughout development and in the adult. The cell biological mechanism of homeoprotein transfer is also discussed. Although it is clear that many questions are still in want of precise answers, it appears that the sequences responsible both for secretion and internalization are in the DNA-binding domain and very highly conserved among most homeoproteins. On this basis, it is proposed that this signaling pathway is likely to imply as many as 200 proteins that participate in a myriad of developmental and physiological pathways.}, }
@article {pmid24395295, year = {2014}, author = {Cho, WK and Jo, Y and Chu, H and Park, SH and Kim, KH}, title = {Integration of latex protein sequence data provides comprehensive functional overview of latex proteins.}, journal = {Molecular biology reports}, volume = {41}, number = {3}, pages = {1469-1481}, pmid = {24395295}, issn = {1573-4978}, mesh = {Amino Acid Sequence ; Computer Simulation ; Latex/*metabolism ; Plant Proteins/biosynthesis/*metabolism ; *Proteome ; }, abstract = {The laticiferous system is one of the most important conduit systems in higher plants, which produces a milky-like sap known as latex. Latex contains diverse secondary metabolites with various ecological functions. To obtain a comprehensive overview of the latex proteome, we integrated available latex proteins sequences and constructed a comprehensive dataset composed of 1,208 non-redundant latex proteins from 20 various latex-bearing plants. The results of functional analyses revealed that latex proteins are involved in various biological processes, including transcription, translation, protein degradation and the plant response to environmental stimuli. The results of the comparative analysis showed that the functions of the latex proteins are similar to those of phloem, suggesting the functional conservation of plant vascular proteins. The presence of latex proteins in mitochondria and plastids suggests the production of diverse secondary metabolites. Furthermore, using a BLAST search, we identified 854 homologous latex proteins in eight plant species, including three latex-bearing plants, such as papaya, caster bean and cassava, suggesting that latex proteins were newly evolved in vascular plants. Taken together, this study is the largest and most comprehensive in silico analysis of the latex proteome. The results obtained here provide useful resources and information for characterizing the evolution of the latex proteome.}, }
@article {pmid24392831, year = {2014}, author = {Osada, E and Akematsu, T and Asano, T and Endoh, H}, title = {A novel mitochondrial nuclease-associated protein: a major executor of the programmed nuclear death in Tetrahymena thermophila.}, journal = {Biology of the cell}, volume = {106}, number = {3}, pages = {97-109}, doi = {10.1111/boc.201300037}, pmid = {24392831}, issn = {1768-322X}, mesh = {Macronucleus/*pathology ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Tetrahymena thermophila/*cytology/*enzymology/metabolism ; }, abstract = {BACKGROUND INFORMATION: Programmed nuclear death (PND) in the ciliate Tetrahymena is an apoptosis-like phenomenon that occurs in a restricted space of cytoplasm during conjugation. In the process, only the parental macronucleus is selectively eliminated from the progeny cytoplasm, in conjunction with differentiation of new macronuclei for the next generation. For the last decade, mitochondria have been elucidated to be a crucial executioner like apoptosis: apoptosis-inducing factor and yet-unidentified nucleases localised in mitochondria are major factors for PND.<br><br>RESULTS: To identify such nucleases, we performed a DNase assay in a PAGE (SDS-DNA-PAGE) using total mitochondrial proteins. Some proteins showed DNase activity, but particularly a 17 kDa protein exhibited the highest and predominant activity. Mass spectrometric analysis revealed a novel mitochondrial nuclease, named TMN1, whose homologue has been discovered only in the ciliate Paramecium tetraurelia, but not in other eukaryotes. Gene disruption of TMN1 led to a drastic reduction of mitochondrial nuclease activity and blocked nuclear degradation during conjugation, but did not affect accumulation of autophagic and lysosomal machinery around the parental macronucleus.<br><br>CONCLUSIONS: These observations strongly suggest that the mitochondrial nuclease-associated protein plays a key role in PND as a major executor. Taking the novel protein specific to ciliates in consideration, Tetrahymena would have diverted a different protein from common apoptotic factors shared in eukaryotes to PND in the course of ciliate evolution.}, }
@article {pmid24389926, year = {2014}, author = {Liu, H and Xin, Y and Xun, L}, title = {Distribution, diversity, and activities of sulfur dioxygenases in heterotrophic bacteria.}, journal = {Applied and environmental microbiology}, volume = {80}, number = {5}, pages = {1799-1806}, pmid = {24389926}, issn = {1098-5336}, mesh = {Cloning, Molecular ; Cluster Analysis ; Cyanobacteria/*enzymology/*genetics/metabolism ; Dioxygenases/*genetics/*metabolism ; Escherichia coli/genetics ; Gene Expression ; *Genetic Variation ; Heterotrophic Processes ; Iron/metabolism ; Oxidation-Reduction ; Phylogeny ; Proteobacteria/*enzymology/*genetics/metabolism ; Recombinant Proteins/genetics/isolation &amp; purification/metabolism ; Sequence Analysis, DNA ; Sulfur/metabolism ; }, abstract = {Sulfur oxidation by chemolithotrophic bacteria is well known; however, sulfur oxidation by heterotrophic bacteria is often ignored. Sulfur dioxygenases (SDOs) (EC 1.13.11.18) were originally found in the cell extracts of some chemolithotrophic bacteria as glutathione (GSH)-dependent sulfur dioxygenases. GSH spontaneously reacts with elemental sulfur to generate glutathione persulfide (GSSH), and SDOs oxidize GSSH to sulfite and GSH. However, SDOs have not been characterized for bacteria, including chemolithotrophs. The gene coding for human SDO (human ETHE1 [hETHE1]) in mitochondria was discovered because its mutations lead to a hereditary human disease, ethylmalonic encephalopathy. Using sequence analysis and activity assays, we discovered three subgroups of bacterial SDOs in the proteobacteria and cyanobacteria. Ten selected SDO genes were cloned and expressed in Escherichia coli, and the recombinant proteins were purified. The SDOs used Fe(2+) for catalysis and displayed considerable variations in specific activities. The wide distribution of SDO genes reveals the likely source of the hETHE1 gene and highlights the potential of sulfur oxidation by heterotrophic bacteria.}, }
@article {pmid24379079, year = {2014}, author = {Yin, Y and Qu, F and Yang, Z and Zhang, X and Yue, B}, title = {Structural characteristics and phylogenetic analysis of the mitochondrial genome of the rice leafroller, Cnaphalocrocis medinalis (Lepidoptera: Crambidae).}, journal = {Molecular biology reports}, volume = {41}, number = {2}, pages = {1109-1116}, pmid = {24379079}, issn = {1573-4978}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; Lepidoptera/*genetics/ultrastructure ; Oryza/genetics ; Pest Control ; *Phylogeny ; }, abstract = {The rice leafroller, Cnaphalocrocis medinalis, is one of the most important pests on rice and possesses striking flight ability. We have determined the nucleotide sequence of the 15,377 bp of a C. medinalis mitochondrial genome (mtDNA). The mtDNA encodes 37 genes and shows a unique lepidopteran CR-M-I-Q arrangement. Three possible substructures were detected in C. medinalis and some other lepidopteran insects' control region. The findings might be relevant to the regulation of mtDNA replication and transcription. Phylogenetic relationships were reconstructed among 19 families in Lepidoptera so far. Cnaphalocrocis medinalis forms a reciprocal monophyletic group with Ostrinia in clade Crambidae instead of Pyralidae. The topology between Papilionoidea and other superfamilies showed an apparent contradiction with traditional Lepidopteran classification. As a well-known migratory insect, the molecular information contained in C. medinalis mtDNA may provide a further insight into the evolution of mitochondria genes and insect species, and may help to better understanding the energy metabolism of invertebrates.}, }
@article {pmid24376692, year = {2013}, author = {Maccari, M and Amat, F and Gómez, A}, title = {Origin and genetic diversity of diploid parthenogenetic Artemia in Eurasia.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e83348}, pmid = {24376692}, issn = {1932-6203}, mesh = {Animals ; Artemia/*classification/genetics ; Asia ; *Biological Evolution ; Cell Nucleus/genetics ; DNA, Intergenic/classification/genetics ; *Diploidy ; Europe ; Female ; Genes, Mitochondrial ; *Genetic Variation ; Male ; Mitochondria/genetics ; Parthenogenesis/*genetics ; *Phylogeny ; Phylogeography ; Sodium-Potassium-Exchanging ATPase/classification/genetics ; }, abstract = {There is wide interest in understanding how genetic diversity is generated and maintained in parthenogenetic lineages, as it will help clarify the debate of the evolution and maintenance of sexual reproduction. There are three mechanisms that can be responsible for the generation of genetic diversity of parthenogenetic lineages: contagious parthenogenesis, repeated hybridization and microorganism infections (e.g. Wolbachia). Brine shrimps of the genus Artemia (Crustacea, Branchiopoda, Anostraca) are a good model system to investigate evolutionary transitions between reproductive systems as they include sexual species and lineages of obligate parthenogenetic populations of different ploidy level, which often co-occur. Diploid parthenogenetic lineages produce occasional fully functional rare males, interspecific hybridization is known to occur, but the mechanisms of origin of asexual lineages are not completely understood. Here we sequenced and analysed fragments of one mitochondrial and two nuclear genes from an extensive set of populations of diploid parthenogenetic Artemia and sexual species from Central and East Asia to investigate the evolutionary origin of diploid parthenogenetic Artemia, and geographic origin of the parental taxa. Our results indicate that there are at least two, possibly three independent and recent maternal origins of parthenogenetic lineages, related to A. urmiana and Artemia sp. from Kazakhstan, but that the nuclear genes are very closely related in all the sexual species and parthenogegetic lineages except for A. sinica, who presumable took no part on the origin of diploid parthenogenetic strains. Our data cannot rule out either hybridization between any of the very closely related Asiatic sexual species or rare events of contagious parthenogenesis via rare males as the contributing mechanisms to the generation of genetic diversity in diploid parthenogenetic Artemia lineages.}, }
@article {pmid24376088, year = {2014}, author = {Sharma, V and O'Halloran, DM}, title = {Recent structural and functional insights into the family of sodium calcium exchangers.}, journal = {Genesis (New York, N.Y. : 2000)}, volume = {52}, number = {2}, pages = {93-109}, doi = {10.1002/dvg.22735}, pmid = {24376088}, issn = {1526-968X}, mesh = {Animals ; Caenorhabditis elegans/chemistry/metabolism ; Calcium/*metabolism ; Calcium Signaling ; Gene Expression Regulation ; Humans ; Mitochondria/metabolism ; Models, Molecular ; *Multigene Family ; Phylogeny ; Sodium-Calcium Exchanger/*chemistry/genetics/*metabolism ; }, abstract = {Maintenance of calcium homeostasis is necessary for the development and survival of all animals. Calcium ions modulate excitability and bind effectors capable of initiating many processes such as muscular contraction and neurotransmission. However, excessive amounts of calcium in the cytosol or within intracellular calcium stores can trigger apoptotic pathways in cells that have been implicated in cardiac and neuronal pathologies. Accordingly, it is critical for cells to rapidly and effectively regulate calcium levels. The Na(+) /Ca(2+) exchangers (NCX), Na(+) /Ca(2+) /K(+) exchangers (NCKX), and Ca(2+) /Cation exchangers (CCX) are the three classes of sodium calcium antiporters found in animals. These exchanger proteins utilize an electrochemical gradient to extrude calcium. Although they have been studied for decades, much is still unknown about these proteins. In this review, we examine current knowledge about the structure, function, and physiology and also discuss their implication in various developmental disorders. Finally, we highlight recent data characterizing the family of sodium calcium exchangers in the model system, Caenorhabditis elegans, and propose that C. elegans may be an ideal model to complement other systems and help fill gaps in our knowledge of sodium calcium exchange biology.}, }
@article {pmid24365595, year = {2014}, author = {Hu, G and Zou, G and Liu, X and Liang, H and Li, Z and Hu, S}, title = {The carp-goldfish nucleocytoplasmic hybrid has mitochondria from the carp as the nuclear donor species.}, journal = {Gene}, volume = {536}, number = {2}, pages = {265-271}, doi = {10.1016/j.gene.2013.12.024}, pmid = {24365595}, issn = {1879-0038}, mesh = {Active Transport, Cell Nucleus/*genetics ; Animals ; Carps/*genetics ; Cell Nucleus/*genetics ; Cytoplasm/*genetics ; DNA, Mitochondrial/*genetics ; Female ; Goldfish/*genetics ; Male ; Mitochondria/*genetics ; Oocytes ; Phylogeny ; }, abstract = {It is widely accepted that mitochondria and its DNA (mtDNA) exhibit strict maternal inheritance, with sperm contributing no or non-detectable mitochondria to the next generation. In fish, nuclear transfer (NT) through the combination of a donor nucleus and an enucleated oocyte can produce fertile nucleocytoplasmic hybrids (NCHs) even between different genera and subfamilies. One of the best studied fish NCHs is CyCa produced by transplanting the nuclei plus cytoplasm from the common carp (Cyprinus carpio var. wuyuanensis) into the oocytes of the wild goldfish (Carassius auratus), which has been propagated by self-mating for three generations. These NCH fish thus provide a unique model to study the origin of mitochondria. Here we report the complete mtDNA sequence of the CyCa hybrid and its parental species carp and goldfish as nuclear donor and cytoplasm host, respectively. Interestingly, the mtDNA of NCH fish CyCa is 99.69% identical to the nuclear donor species carp, and 89.25% identical to the oocyte host species goldfish. Furthermore, an amino acid sequence comparison of 13 mitochondrial proteins reveals that CyCa is 99.68% identical to the carp and 87.68% identical to the goldfish. On an mtDNA-based phylogenetic tree, CyCa is clustered with the carp but separated from the goldfish. A real-time PCR analysis revealed the presence of carp mtDNA but the absence of goldfish mtDNA. These results demonstrate--for the first time to our knowledge--that the mtDNA of a NCH such as CyCa fish may originate from its nuclear donor rather than its oocyte host.}, }
@article {pmid24362565, year = {2014}, author = {Greber, BJ and Boehringer, D and Leitner, A and Bieri, P and Voigts-Hoffmann, F and Erzberger, JP and Leibundgut, M and Aebersold, R and Ban, N}, title = {Architecture of the large subunit of the mammalian mitochondrial ribosome.}, journal = {Nature}, volume = {505}, number = {7484}, pages = {515-519}, pmid = {24362565}, issn = {1476-4687}, mesh = {Animals ; Cattle ; Cryoelectron Microscopy ; Hydrophobic and Hydrophilic Interactions ; Mass Spectrometry ; Mitochondria/*chemistry/ultrastructure ; Mitochondrial Proteins/chemistry/ultrastructure ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; RNA, Ribosomal, 16S/chemistry/ultrastructure ; Ribosomal Proteins/chemistry/ultrastructure ; Ribosome Subunits/*chemistry/ultrastructure ; Swine ; }, abstract = {Mitochondrial ribosomes synthesize a number of highly hydrophobic proteins encoded on the genome of mitochondria, the organelles in eukaryotic cells that are responsible for energy conversion by oxidative phosphorylation. The ribosomes in mammalian mitochondria have undergone massive structural changes throughout their evolution, including ribosomal RNA shortening and acquisition of mitochondria-specific ribosomal proteins. Here we present the three-dimensional structure of the 39S large subunit of the porcine mitochondrial ribosome determined by cryo-electron microscopy at 4.9 Å resolution. The structure, combined with data from chemical crosslinking and mass spectrometry experiments, reveals the unique features of the 39S subunit at near-atomic resolution and provides detailed insight into the architecture of the polypeptide exit site. This region of the mitochondrial ribosome has been considerably remodelled compared to its bacterial counterpart, providing a specialized platform for the synthesis and membrane insertion of the highly hydrophobic protein components of the respiratory chain.}, }
@article {pmid24360837, year = {2014}, author = {Hoepfner, D and Helliwell, SB and Sadlish, H and Schuierer, S and Filipuzzi, I and Brachat, S and Bhullar, B and Plikat, U and Abraham, Y and Altorfer, M and Aust, T and Baeriswyl, L and Cerino, R and Chang, L and Estoppey, D and Eichenberger, J and Frederiksen, M and Hartmann, N and Hohendahl, A and Knapp, B and Krastel, P and Melin, N and Nigsch, F and Oakeley, EJ and Petitjean, V and Petersen, F and Riedl, R and Schmitt, EK and Staedtler, F and Studer, C and Tallarico, JA and Wetzel, S and Fishman, MC and Porter, JA and Movva, NR}, title = {High-resolution chemical dissection of a model eukaryote reveals targets, pathways and gene functions.}, journal = {Microbiological research}, volume = {169}, number = {2-3}, pages = {107-120}, doi = {10.1016/j.micres.2013.11.004}, pmid = {24360837}, issn = {1618-0623}, mesh = {Antifungal Agents/pharmacology ; Biosynthetic Pathways ; Drug Resistance, Fungal ; Gene Expression Regulation, Fungal ; High-Throughput Screening Assays ; Molecular Sequence Data ; Phylogeny ; Saccharomyces cerevisiae/*chemistry/classification/drug effects/*genetics ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; }, abstract = {Due to evolutionary conservation of biology, experimental knowledge captured from genetic studies in eukaryotic model organisms provides insight into human cellular pathways and ultimately physiology. Yeast chemogenomic profiling is a powerful approach for annotating cellular responses to small molecules. Using an optimized platform, we provide the relative sensitivities of the heterozygous and homozygous deletion collections for nearly 1800 biologically active compounds. The data quality enables unique insights into pathways that are sensitive and resistant to a given perturbation, as demonstrated with both known and novel compounds. We present examples of novel compounds that inhibit the therapeutically relevant fatty acid synthase and desaturase (Fas1p and Ole1p), and demonstrate how the individual profiles facilitate hypothesis-driven experiments to delineate compound mechanism of action. Importantly, the scale and diversity of tested compounds yields a dataset where the number of modulated pathways approaches saturation. This resource can be used to map novel biological connections, and also identify functions for unannotated genes. We validated hypotheses generated by global two-way hierarchical clustering of profiles for (i) novel compounds with a similar mechanism of action acting upon microtubules or vacuolar ATPases, and (ii) an un-annotated ORF, YIL060w, that plays a role in respiration in the mitochondria. Finally, we identify and characterize background mutations in the widely used yeast deletion collection which should improve the interpretation of past and future screens throughout the community. This comprehensive resource of cellular responses enables the expansion of our understanding of eukaryotic pathway biology.}, }
@article {pmid24357311, year = {2013}, author = {Rice, DW and Alverson, AJ and Richardson, AO and Young, GJ and Sanchez-Puerta, MV and Munzinger, J and Barry, K and Boore, JL and Zhang, Y and dePamphilis, CW and Knox, EB and Palmer, JD}, title = {Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella.}, journal = {Science (New York, N.Y.)}, volume = {342}, number = {6165}, pages = {1468-1473}, doi = {10.1126/science.1246275}, pmid = {24357311}, issn = {1095-9203}, support = {R01-GM-76012/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Bryophyta/classification/genetics ; Chlorophyta/classification/genetics ; DNA, Mitochondrial/*genetics ; *Gene Transfer, Horizontal ; *Genome, Plant ; Membrane Fusion ; *Mitochondrial Dynamics ; Molecular Sequence Data ; Phylogeny ; Tracheophyta/classification/*genetics ; }, abstract = {We report the complete mitochondrial genome sequence of the flowering plant Amborella trichopoda. This enormous, 3.9-megabase genome contains six genome equivalents of foreign mitochondrial DNA, acquired from green algae, mosses, and other angiosperms. Many of these horizontal transfers were large, including acquisition of entire mitochondrial genomes from three green algae and one moss. We propose a fusion-compatibility model to explain these findings, with Amborella capturing whole mitochondria from diverse eukaryotes, followed by mitochondrial fusion (limited mechanistically to green plant mitochondria) and then genome recombination. Amborella's epiphyte load, propensity to produce suckers from wounds, and low rate of mitochondrial DNA loss probably all contribute to the high level of foreign DNA in its mitochondrial genome.}, }
@article {pmid24353213, year = {2014}, author = {Jovaisaite, V and Mouchiroud, L and Auwerx, J}, title = {The mitochondrial unfolded protein response, a conserved stress response pathway with implications in health and disease.}, journal = {The Journal of experimental biology}, volume = {217}, number = {Pt 1}, pages = {137-143}, pmid = {24353213}, issn = {1477-9145}, support = {R01 AG043930/AG/NIA NIH HHS/United States ; R01 HL106511/HL/NHLBI NIH HHS/United States ; 1R01HL10651/HL/NHLBI NIH HHS/United States ; R01AG043930/AG/NIA NIH HHS/United States ; }, mesh = {Aging ; Animals ; Caenorhabditis elegans/metabolism/*physiology ; Endoplasmic Reticulum/*physiology ; Heat-Shock Proteins/metabolism ; Heat-Shock Response/*physiology ; Mitochondria ; Protein Folding ; Signal Transduction ; Stress, Physiological/physiology ; Unfolded Protein Response/*physiology ; }, abstract = {The ability to respond to various intracellular and/or extracellular stresses allows the organism to adapt to changing environmental conditions and drives evolution. It is now well accepted that a progressive decline of the efficiency of stress response pathways occurs with aging. In this context, a correct proteostasis is essential for the functionality of the cell, and its dysfunction has been associated with protein aggregation and age-related degenerative diseases. Complex response mechanisms have evolved to deal with unfolded protein stress in different subcellular compartments and their moderate activation translates into positive effects on health. In this review, we focus on the mitochondrial unfolded protein response (UPR(mt)), a response to proteotoxic stress specifically in mitochondria, an organelle with a wide array of fundamental functions, most notably the harvesting of energy from food and the control of cell death. We compare UPR(mt) with the extensively characterized cytosolic heat shock response (HSR) and the unfolded protein response in endoplasmic reticulum (UPR(ER)), and discuss the current knowledge about UPR(mt) signaling pathways as well as their potential involvement in physiology.}, }
@article {pmid24349502, year = {2013}, author = {Ferla, MP and Thrash, JC and Giovannoni, SJ and Patrick, WM}, title = {New rRNA gene-based phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e83383}, pmid = {24349502}, issn = {1932-6203}, mesh = {Alphaproteobacteria/*genetics ; Genes, Bacterial/*genetics ; Genes, rRNA/*physiology ; Mitochondria/*genetics ; *Phylogeny ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {Bacteria in the class Alphaproteobacteria have a wide variety of lifestyles and physiologies. They include pathogens of humans and livestock, agriculturally valuable strains, and several highly abundant marine groups. The ancestor of mitochondria also originated in this clade. Despite significant effort to investigate the phylogeny of the Alphaproteobacteria with a variety of methods, there remains considerable disparity in the placement of several groups. Recent emphasis on phylogenies derived from multiple protein-coding genes remains contentious due to disagreement over appropriate gene selection and the potential influences of systematic error. We revisited previous investigations in this area using concatenated alignments of the small and large subunit (SSU and LSU) rRNA genes, as we show here that these loci have much lower GC bias than whole genomes. This approach has allowed us to update the canonical 16S rRNA gene tree of the Alphaproteobacteria with additional important taxa that were not previously included, and with added resolution provided by concatenating the SSU and LSU genes. We investigated the topological stability of the Alphaproteobacteria by varying alignment methods, rate models, taxon selection and RY-recoding to circumvent GC content bias. We also introduce RYMK-recoding and show that it avoids some of the information loss in RY-recoding. We demonstrate that the topology of the Alphaproteobacteria is sensitive to inclusion of several groups of taxa, but it is less affected by the choice of alignment and rate methods. The majority of topologies and comparative results from Approximately Unbiased tests provide support for positioning the Rickettsiales and the mitochondrial branch within a clade. This composite clade is a sister group to the abundant marine SAR11 clade (Pelagibacterales). Furthermore, we add support for taxonomic assignment of several recently sequenced taxa. Accordingly, we propose three subclasses within the Alphaproteobacteria: the Caulobacteridae, the Rickettsidae, and the Magnetococcidae.}, }
@article {pmid24349158, year = {2013}, author = {Demirci, S and Koban Baştanlar, E and Dağtaş, ND and Pişkin, E and Engin, A and Ozer, F and Yüncü, E and Doğan, SA and Togan, I}, title = {Mitochondrial DNA diversity of modern, ancient and wild sheep(Ovis gmelinii anatolica) from Turkey: new insights on the evolutionary history of sheep.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e81952}, pmid = {24349158}, issn = {1932-6203}, mesh = {Animals ; *Biological Evolution ; Cytochromes b/*classification/genetics ; DNA, Mitochondrial/*classification/genetics ; Female ; Haplotypes ; Humans ; Male ; Mitochondria/genetics ; Multigene Family ; *Phylogeny ; Phylogeography ; Polymorphism, Genetic ; Sheep/*classification/genetics ; Sheep, Domestic/*classification/genetics ; Turkey ; }, abstract = {In the present study, to contribute to the understanding of the evolutionary history of sheep, the mitochondrial (mt) DNA polymorphisms occurring in modern Turkish native domestic (n = 628), modern wild (Ovis gmelinii anatolica) (n = 30) and ancient domestic sheep from Oylum Höyük in Kilis (n = 33) were examined comparatively with the accumulated data in the literature. The lengths (75 bp/76 bp) of the second and subsequent repeat units of the mtDNA control region (CR) sequences differentiated the five haplogroups (HPGs) observed in the domestic sheep into two genetic clusters as was already implied by other mtDNA markers: the first cluster being composed of HPGs A, B, D and the second cluster harboring HPGs C, E. To manifest genetic relatedness between wild Ovis gmelinii and domestic sheep haplogroups, their partial cytochrome B sequences were examined together on a median-joining network. The two parallel but wider aforementioned clusters were observed also on the network of Ovis gmelenii individuals, within which domestic haplogroups were embedded. The Ovis gmelinii wilds of the present day appeared to be distributed on two partially overlapping geographic areas parallel to the genetic clusters that they belong to (the first cluster being in the western part of the overall distribution). Thus, the analyses suggested that the domestic sheep may be the products of two maternally distinct ancestral Ovis gmelinii populations. Furthermore, Ovis gmelinii anatolica individuals exhibited a haplotype of HPG A (n = 22) and another haplotype (n = 8) from the second cluster which was not observed among the modern domestic sheep. HPG E, with the newly observed members (n = 11), showed signs of expansion. Studies of ancient and modern mtDNA suggest that HPG C frequency increased in the Southeast Anatolia from 6% to 22% some time after the beginning of the Hellenistic period, 500 years Before Common Era (BCE).}, }
@article {pmid24346499, year = {2014}, author = {Hill, GE}, title = {Sex linkage of nuclear-encoded mitochondrial genes.}, journal = {Heredity}, volume = {112}, number = {5}, pages = {469-470}, pmid = {24346499}, issn = {1365-2540}, mesh = {Animals ; *Epistasis, Genetic ; *Evolution, Molecular ; Female ; Male ; Mammals/*genetics ; Mitochondria/*genetics ; X Chromosome/*genetics ; }, }
@article {pmid24342661, year = {2014}, author = {Guerra, D and Ghiselli, F and Passamonti, M}, title = {The largest unassigned regions of the male- and female-transmitted mitochondrial DNAs in Musculista senhousia (Bivalvia Mytilidae).}, journal = {Gene}, volume = {536}, number = {2}, pages = {316-325}, doi = {10.1016/j.gene.2013.12.005}, pmid = {24342661}, issn = {1879-0038}, mesh = {Animals ; Base Sequence ; Bivalvia/*genetics ; Codon, Nonsense/*genetics ; DNA, Mitochondrial/*genetics ; Female ; Genome, Mitochondrial/*genetics ; Male ; Mitochondria/*genetics ; Molecular Sequence Data ; }, abstract = {Musculista senhousia is a marine mussel with doubly uniparental inheritance (DUI) of mitochondria. In this study we analyzed the largest unassigned region (LUR) of its female- and male-transmitted mitochondrial genomes, described their fine characteristics and searched for shared features. Our results suggest that both LURs contain the control region of their respective mitochondrial genomes. The female-transmitted control region is duplicated in tandem, with the two copies evolving in concert. This makes the F-mtDNA of M. senhousia the first Bivalve mitochondrial genome with this feature. We also compared M. senhousia control regions to that of other Mytilidae, and demonstrated that signals for basic mtDNA functions are retained over evolutionary times even among the fast-evolving mitochondrial genomes of DUI species. Finally, we discussed how similarities between female and male LURs may be explained in the context of DUI evolution and if the duplicated female control region might have influenced the DUI system in this species.}, }
@article {pmid24342657, year = {2014}, author = {Fajardo, D and Schlautman, B and Steffan, S and Polashock, J and Vorsa, N and Zalapa, J}, title = {The American cranberry mitochondrial genome reveals the presence of selenocysteine (tRNA-Sec and SECIS) insertion machinery in land plants.}, journal = {Gene}, volume = {536}, number = {2}, pages = {336-343}, doi = {10.1016/j.gene.2013.11.104}, pmid = {24342657}, issn = {1879-0038}, mesh = {DNA Transposable Elements/*genetics ; DNA, Mitochondrial/genetics ; Embryophyta/*genetics ; Genome, Mitochondrial/*genetics ; Genome, Plant/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/*genetics ; Selenocysteine/*genetics ; Vaccinium macrocarpon/*genetics ; }, abstract = {This is the first de novo assembly and annotation of a complete mitochondrial genome in the Ericales order from the American cranberry (Vaccinium macrocarpon Ait.). Moreover, only four complete Asterid mitochondrial genomes have been made publicly available. The cranberry mitochondrial genome was assembled and reconstructed from whole genome 454 Roche GS-FLX and Illumina shotgun sequences. Compared with other Asterids, the reconstruction of the genome revealed an average size mitochondrion (459,678 nt) with relatively little repetitive sequences and DNA of plastid origin. The complete mitochondrial genome of cranberry was annotated obtaining a total of 34 genes classified based on their putative function, plus three ribosomal RNAs, and 17 transfer RNAs. Maternal organellar cranberry inheritance was inferred by analyzing gene variation in the cranberry mitochondria and plastid genomes. The annotation of cranberry mitochondrial genome revealed the presence of two copies of tRNA-Sec and a selenocysteine insertion sequence (SECIS) element which were lost in plants during evolution. This is the first report of a land plant possessing selenocysteine insertion machinery at the sequence level.}, }
@article {pmid24341464, year = {2013}, author = {Hollingsworth, PR and Simons, AM and Fordyce, JA and Hulsey, CD}, title = {Explosive diversification following a benthic to pelagic shift in freshwater fishes.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {272}, pmid = {24341464}, issn = {1471-2148}, mesh = {Animals ; Biodiversity ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Ecosystem ; Fishes/*classification/*genetics ; Fresh Water ; *Genetic Speciation ; Mitochondria/genetics ; Molecular Sequence Data ; North America ; Phylogeny ; }, abstract = {BACKGROUND: Interspecific divergence along a benthic to pelagic habitat axis is ubiquitous in freshwater fishes inhabiting lentic environments. In this study, we examined the influence of this habitat axis on the macroevolution of a diverse, lotic radiation using mtDNA and nDNA phylogenies for eastern North America's most species-rich freshwater fish clade, the open posterior myodome (OPM) cyprinids. We used ancestral state reconstruction to identify the earliest benthic to pelagic transition in this group and generated fossil-calibrated estimates of when this shift occurred. This transition could have represented evolution into a novel adaptive zone, and therefore, we tested for a period of accelerated lineage accumulation after this historical habitat shift.<br><br>RESULTS: Ancestral state reconstructions inferred a similar and concordant region of our mtDNA and nDNA based gene trees as representing the shift from benthic to pelagic habitats in the OPM clade. Two independent tests conducted on each gene tree suggested an increased diversification rate after this inferred habitat transition. Furthermore, lineage through time analyses indicated rapid early cladogenesis in the clade arising after the benthic to pelagic shift.<br><br>CONCLUSIONS: A burst of diversification followed the earliest benthic to pelagic transition during the radiation of OPM cyprinids in eastern North America. As such, the benthic/pelagic habitat axis has likely influenced the generation of biodiversity across disparate freshwater ecosystems.}, }
@article {pmid24336923, year = {2014}, author = {Sloan, DB and Triant, DA and Wu, M and Taylor, DR}, title = {Cytonuclear interactions and relaxed selection accelerate sequence evolution in organelle ribosomes.}, journal = {Molecular biology and evolution}, volume = {31}, number = {3}, pages = {673-682}, doi = {10.1093/molbev/mst259}, pmid = {24336923}, issn = {1537-1719}, mesh = {Animals ; Arabidopsis/genetics ; Base Sequence ; Cell Nucleus/*genetics ; Cytosol/*metabolism ; *Evolution, Molecular ; Genome, Plant/genetics ; Mitochondria/genetics ; Mutation Rate ; Polymorphism, Genetic ; RNA, Ribosomal/genetics ; Ribosomal Proteins/genetics ; Ribosome Subunits, Large/genetics ; Ribosomes/*genetics ; *Selection, Genetic ; Silene/genetics ; Species Specificity ; }, abstract = {Many mitochondrial and plastid protein complexes contain subunits that are encoded in different genomes. In animals, nuclear-encoded mitochondrial proteins often exhibit rapid sequence evolution, which has been hypothesized to result from selection for mutations that compensate for changes in interacting subunits encoded in mutation-prone animal mitochondrial DNA. To test this hypothesis, we analyzed nuclear genes encoding cytosolic and organelle ribosomal proteins in flowering plants. The model angiosperm genus Arabidopsis exhibits low organelle mutation rates, typical of most plants. Nevertheless, we found that (nuclear-encoded) subunits of organelle ribosomes in Arabidopsis have higher amino acid sequence polymorphism and divergence than their counterparts in cytosolic ribosomes, suggesting that organelle ribosomes experience relaxed functional constraint. However, the observed difference between organelle and cytosolic ribosomes was smaller than in animals and could be partially attributed to rapid evolution in N-terminal organelle-targeting peptides that are not involved in ribosome function. To test the role of organelle mutation more directly, we used transcriptomic data from an angiosperm genus (Silene) with highly variable rates of organelle genome evolution. We found that Silene species with unusually fast-evolving mitochondrial and plastid DNA exhibited increased amino acid sequence divergence in ribosomal proteins targeted to the organelles but not in those that function in cytosolic ribosomes. Overall, these findings support the hypothesis that rapid organelle genome evolution has selected for compensatory mutations in nuclear-encoded proteins. We conclude that coevolution between interacting subunits encoded in different genomic compartments within the eukaryotic cell is an important determinant of variation in rates of protein sequence evolution.}, }
@article {pmid24336283, year = {2013}, author = {Williams, TA and Foster, PG and Cox, CJ and Embley, TM}, title = {An archaeal origin of eukaryotes supports only two primary domains of life.}, journal = {Nature}, volume = {504}, number = {7479}, pages = {231-236}, pmid = {24336283}, issn = {1476-4687}, support = {BB/C006143/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/C508777/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaea/*classification/cytology/genetics ; Bacteria/classification/genetics ; Cell Membrane/metabolism ; Eukaryota/*classification/cytology/genetics ; Mitochondria/genetics ; *Models, Biological ; *Phylogeny ; RNA, Ribosomal/genetics ; Symbiosis ; }, abstract = {The discovery of the Archaea and the proposal of the three-domains 'universal' tree, based on ribosomal RNA and core genes mainly involved in protein translation, catalysed new ideas for cellular evolution and eukaryotic origins. However, accumulating evidence suggests that the three-domains tree may be incorrect: evolutionary trees made using newer methods place eukaryotic core genes within the Archaea, supporting hypotheses in which an archaeon participated in eukaryotic origins by founding the host lineage for the mitochondrial endosymbiont. These results provide support for only two primary domains of life--Archaea and Bacteria--because eukaryotes arose through partnership between them.}, }
@article {pmid24334395, year = {2013}, author = {Angione, C and Carapezza, G and Costanza, J and Lió, P and Nicosia, G}, title = {Pareto optimality in organelle energy metabolism analysis.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {10}, number = {4}, pages = {1032-1044}, doi = {10.1109/TCBB.2013.95}, pmid = {24334395}, issn = {1557-9964}, mesh = {Adenosine Triphosphate/metabolism ; Algorithms ; Anaerobiosis ; Computational Biology ; Energy Metabolism/*physiology ; *Models, Biological ; Organelles/*metabolism ; Trichomonas vaginalis ; }, abstract = {In low and high eukaryotes, energy is collected or transformed in compartments, the organelles. The rich variety of size, characteristics, and density of the organelles makes it difficult to build a general picture. In this paper, we make use of the Pareto-front analysis to investigate the optimization of energy metabolism in mitochondria and chloroplasts. Using the Pareto optimality principle, we compare models of organelle metabolism on the basis of single- and multiobjective optimization, approximation techniques (the Bayesian Automatic Relevance Determination), robustness, and pathway sensitivity analysis. Finally, we report the first analysis of the metabolic model for the hydrogenosome of Trichomonas vaginalis, which is found in several protozoan parasites. Our analysis has shown the importance of the Pareto optimality for such comparison and for insights into the evolution of the metabolism from cytoplasmic to organelle bound, involving a model order reduction. We report that Pareto fronts represent an asymptotic analysis useful to describe the metabolism of an organism aimed at maximizing concurrently two or more metabolite concentrations.}, }
@article {pmid24330701, year = {2013}, author = {Bazzocchi, C and Mariconti, M and Sassera, D and Rinaldi, L and Martin, E and Cringoli, G and Urbanelli, S and Genchi, C and Bandi, C and Epis, S}, title = {Molecular and serological evidence for the circulation of the tick symbiont Midichloria (Rickettsiales: Midichloriaceae) in different mammalian species.}, journal = {Parasites &amp; vectors}, volume = {6}, number = {}, pages = {350}, pmid = {24330701}, issn = {1756-3305}, mesh = {Alphaproteobacteria/*genetics/*isolation &amp; purification ; Animals ; Gene Expression Regulation, Bacterial/*physiology ; Italy ; Ixodidae/*microbiology ; Mammals/blood/*microbiology ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Symbiosis ; }, abstract = {BACKGROUND: The Midichloriaceae is a novel family of the order Rickettsiales, that encompasses intracellular bacteria associated with hard ticks (Ixodidae) and other arthropods. The most intensively investigated member of this family is Midichloria mitochondrii, a symbiotic bacterium of the sheep tick Ixodes ricinus, characterized by the capacity of multiplying inside the mitochondria. A recent study suggested that these bacteria might be inoculated into the human host during the tick bite. The purpose of this study was to determine the potential infectivity of Midichloria bacteria for non-human animals exposed to the risk of tick bite.<br><br>METHODS: Blood from horses, cattle, sheep and dogs exposed to the risk of tick bite was included in this study. DNAs were extracted, and amplified using 16S ribosomal RNA primers conserved in the Midichloria genus. Furthermore, sera from dogs exposed to the risk of tick bite were analyzed in order to evaluate the presence of antibodies against the recombinant flagellar protein (rFliD) from M. mitochondrii using an ELISA test.<br><br>RESULTS: Here we present two lines of evidence that support the possibility that bacteria from the genus Midichloria are inoculated into vertebrate hosts during a tick bite: (i) a direct evidence, i.e. the detection of circulating DNA from bacteria related with M. mitochondrii, in the blood of vertebrates exposed to tick parasitism; (ii) a further indirect evidence, i.e. the presence of antibodies against an antigen from M. mitochondrii in dogs exposed to the risk of tick bite. It is interesting to note that variability was detected in the Midichloria gene sequences recovered from positive animals, and that some of these sequences were identical to those generated from tick-associated Midichloria.<br><br>CONCLUSIONS: Based on the results, and on the overall information so far published on the genus Midichloria, we suggest that these bacteria are likely to represent a novel group of vector-borne agents, with the potential of infecting mammalian hosts. Whether inoculation of Midichloria bacteria could cause a true infection and pathological alteration in mammalian hosts is still to be determined. Surely, results emphasize the relevance of Midichloria bacteria in investigations on tick immunology and tick-bite markers.}, }
@article {pmid24328820, year = {2015}, author = {Tian, SQ and Cui, P and Fang, SF and Liu, GH and Wang, CR and Zhu, XQ}, title = {The complete mitochondrial genome sequence of Eimeria magna (Apicomplexa: Coccidia).}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {714-715}, doi = {10.3109/19401736.2013.843088}, pmid = {24328820}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Chickens/parasitology ; Coccidiosis/*parasitology/veterinary ; Eimeria/*genetics/isolation &amp; purification ; Genes, Protozoan ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Rabbits ; Sequence Analysis, DNA ; }, abstract = {In the present study, we determined the complete mitochondrial DNA (mtDNA) sequence of Eimeria magna from rabbits for the first time, and compared its gene contents and genome organizations with that of seven Eimeria spp. from domestic chickens. The size of the complete mt genome sequence of E. magna is 6249 bp, which consists of 3 protein-coding genes (cytb, cox1 and cox3), 12 gene fragments for the large subunit (LSU) rRNA, and 7 gene fragments for the small subunit (SSU) rRNA, without transfer RNA genes, in accordance with that of Eimeria spp. from chickens. The putative direction of translation for three genes (cytb, cox1 and cox3) was the same as those of Eimeria species from domestic chickens. The content of A + T is 65.16% for E. magna mt genome (29.73% A, 35.43% T, 17.09 G and 17.75% C). The E. magna mt genome sequence provides novel mtDNA markers for studying the molecular epidemiology and population genetics of Eimeria spp. and has implications for the molecular diagnosis and control of rabbit coccidiosis.}, }
@article {pmid24325672, year = {2015}, author = {Mu, XD and Yang, YX and Liu, Y and Song, HM and Luo, JR and Hu, YC}, title = {Complete mitochondrial genome of northern spotted barramundi, Scleropages jardinii.}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {698-699}, doi = {10.3109/19401736.2013.843080}, pmid = {24325672}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Fishes/*genetics ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {We sequenced the complete mitogenome of northern spotted barramundi Scleropages jardinii, an ancestral bonytongue with economic and conservation value. The mitogenome is 16,670 bp in length with an A + T content of 52.9%, and contains 13 protein-coding genes, 2rRNAs, 22 tRNAs and a control region. The gene order and arrangement is similar to that of other Osteoglossidae species, as is base composition and codon usage. These data will provide useful molecular information for phylogenetic relationships within the family Osteoglossidae species.}, }
@article {pmid24325670, year = {2015}, author = {Geng, L and Jiang, H and Yang, J and Xu, M and Xu, W}, title = {The complete mitochondrial genome of Alburnus chalcoides aralensis.}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {702-703}, doi = {10.3109/19401736.2013.843082}, pmid = {24325670}, issn = {1940-1744}, mesh = {Animals ; Cyprinidae/*genetics ; DNA, Mitochondrial/chemistry ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Sequence Analysis, DNA ; }, abstract = {The complete mitochondrial genome of Alburnus chalcoides aralensis is 16,604 bp in length and includes 13 protein-coding genes, 2 ribosomal genes, 22 transfer RNA genes and 2 non-coding sequences. The major non-coding sequence (D-loop control region) contains five conserved sequence blocks (CSB-1, CSB-2, CSB-3, CSB-D and CSB-F) and one termination associated sequence. The other non-coding sequence is the origin of light-strand replication, which has the potential to fold into a stable stem-loop secondary structure. The mitochondrial genomic sequence will help us study the conservation genetics and evolution of Cyprinidae.}, }
@article {pmid24324834, year = {2013}, author = {Zehendner, CM and Librizzi, L and Hedrich, J and Bauer, NM and Angamo, EA and de Curtis, M and Luhmann, HJ}, title = {Moderate hypoxia followed by reoxygenation results in blood-brain barrier breakdown via oxidative stress-dependent tight-junction protein disruption.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e82823}, pmid = {24324834}, issn = {1932-6203}, mesh = {Animals ; Blood-Brain Barrier/*metabolism/pathology ; Cell Membrane/metabolism ; Claudin-5/metabolism ; Endothelial Cells/metabolism ; Guinea Pigs ; Hypoxia/*metabolism ; Microvessels/metabolism/pathology ; Mitochondria/metabolism ; *Oxidative Stress ; Permeability ; Reactive Oxygen Species/metabolism ; Reperfusion Injury/metabolism ; Tight Junction Proteins/*metabolism ; Tight Junctions/*metabolism ; Tyrosine/analogs &amp; derivatives/metabolism ; Zonula Occludens-1 Protein/metabolism ; }, abstract = {Re-canalization of cerebral vessels in ischemic stroke is pivotal to rescue dysfunctional brain areas that are exposed to moderate hypoxia within the penumbra from irreversible cell death. Goal of the present study was to evaluate the effect of moderate hypoxia followed by reoxygenation (MHR) on the evolution of reactive oxygen species (ROS) and blood-brain barrier (BBB) integrity in brain endothelial cells (BEC). BBB integrity was assessed in BEC in vitro and in microvessels of the guinea pig whole brain in situ preparation. Probes were exposed to MHR (2 hours 67-70 mmHg O2, 3 hours reoxygenation, BEC) or towards occlusion of the arteria cerebri media (MCAO) with or without subsequent reperfusion in the whole brain preparation. In vitro BBB integrity was evaluated using trans-endothelial electrical resistance (TEER) and transwell permeability assays. ROS in BEC were evaluated using 2',7'-dichlorodihydrofluorescein diacetate (DCF), MitoSox and immunostaining for nitrotyrosine. Tight-junction protein (TJ) integrity in BEC, stainings for nitrotyrosine and FITC-albumin extravasation in the guinea pig brain preparation were assessed by confocal microscopy. Diphenyleneiodonium (DPI) was used to investigate NADPH oxidase dependent ROS evolution and its effect on BBB parameters in BEC. MHR impaired TJ proteins zonula occludens 1 (ZO-1) and claudin 5 (Cl5), decreased TEER, and significantly increased cytosolic ROS in BEC. These events were blocked by the NADPH oxidase inhibitor DPI. MCAO with or without subsequent reoxygenation resulted in extravasation of FITC-albumin and ROS generation in the penumbra region of the guinea pig brain preparation and confirmed BBB damage. BEC integrity may be impaired through ROS in MHR on the level of TJ and the BBB is also functionally impaired in moderate hypoxic conditions followed by reperfusion in a complex guinea pig brain preparation. These findings suggest that the BBB is susceptible towards MHR and that ROS play a key role in this process.}, }
@article {pmid24324722, year = {2013}, author = {Hagino, K and Onuma, R and Kawachi, M and Horiguchi, T}, title = {Discovery of an endosymbiotic nitrogen-fixing cyanobacterium UCYN-A in Braarudosphaera bigelowii (Prymnesiophyceae).}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e81749}, pmid = {24324722}, issn = {1932-6203}, mesh = {Base Sequence ; Cyanobacteria/*physiology ; DNA, Ribosomal/genetics ; Haptophyta/genetics/*microbiology/ultrastructure ; Likelihood Functions ; Molecular Sequence Data ; *Nitrogen Fixation/genetics ; Phylogeny ; Spores/ultrastructure ; *Symbiosis/genetics ; }, abstract = {Braarudosphaera bigelowii (Prymnesiophyceae) is a coastal coccolithophore with a long fossil record, extending back to the late Cretaceous (ca. 100 Ma). A recent study revealed close phylogenetic relationships between B. bigelowii, Chrysochromulina parkeae (Prymnesiophyceae), and a prymnesiophyte that forms a symbiotic association with the nitrogen-fixing cyanobacterium UCYN-A. In order to further examine these relationships, we conducted transmission electron microscopic and molecular phylogenetic studies of B. bigelowii. TEM studies showed that, in addition to organelles, such as the nucleus, chloroplasts and mitochondria, B. bigelowii contains one or two spheroid bodies with internal lamellae. In the 18S rDNA tree of the Prymnesiophyceae, C. parkeae fell within the B. bigelowii clade, and was close to B. bigelowii Genotype III (99.89% similarity). Plastid 16S rDNA sequences obtained from B. bigelowii were close to the unidentified sequences from the oligotrophic SE Pacific Ocean (e.g. HM133411) (99.86% similarity). Bacterial16S rDNA sequences obtained from B. bigelowii were identical to the UCYN-A sequence AY621693 from Arabian Sea, and fell in the UCYN-A clade. From these results, we suggest that; 1) C. parkeae is the alternate life cycle stage of B. bigelowii sensu stricto or that of a sibling species of B. bigelowii, and 2) the spheroid body of B. bigelowii originated from endosymbiosis of the nitrogen-fixing cyanobacterium UCYN-A.}, }
@article {pmid24316280, year = {2014}, author = {Makiuchi, T and Nozaki, T}, title = {Highly divergent mitochondrion-related organelles in anaerobic parasitic protozoa.}, journal = {Biochimie}, volume = {100}, number = {}, pages = {3-17}, doi = {10.1016/j.biochi.2013.11.018}, pmid = {24316280}, issn = {1638-6183}, mesh = {Alveolata/physiology/ultrastructure ; Amoebozoa/physiology/ultrastructure ; Anaerobiosis ; Biodiversity ; *Biological Evolution ; Cryptophyta/physiology/ultrastructure ; Diplomonadida/physiology/ultrastructure ; Gene Expression Regulation ; Genome, Mitochondrial ; Humans ; Mitochondria/*genetics/*metabolism/ultrastructure ; Mitochondrial Proteins/genetics/*metabolism ; Neocallimastix/physiology/ultrastructure ; Phylogeny ; Protein Transport ; }, abstract = {The mitochondria have arisen as a consequence of endosymbiosis of an ancestral α-proteobacterium with a methane-producing archae. The main function of the canonical aerobic mitochondria include ATP generation via oxidative phosphorylation, heme and phospholipid synthesis, calcium homeostasis, programmed cell death, and the formation of iron-sulfur clusters. Under oxygen-restricted conditions, the mitochondrion has often undergone remarkable reductive alterations of its content and function, leading to the generation of mitochondrion-related organelles (MROs), such as mitosomes, hydrogenosomes, and mithochondrion-like organelles, which are found in a wide range of anaerobic/microaerophilic eukaryotes that include several medically important parasitic protists such as Entamoeba histolytica, Giardia intestinalis, Trichomonas vaginalis, Cryptosporidium parvum, Blastocystis hominis, and Encephalitozoon cuniculi, as well as free-living protists such as Sawyeria marylandensis, Neocallimastix patriciarum, and Mastigamoeba balamuthi. The transformation from canonical aerobic mitochondria to MROs apparently have occurred in independent lineages, and resulted in the diversity of their components and functions. Due to medical and veterinary importance of the MRO-possessing human- and animal-pathogenic protozoa, their genomic, transcriptomic, proteomic, and biochemical evidence has been accumulated. Detailed analyses of the constituents and functions of the MROs in such anaerobic pathogenic protozoa, which reside oxygen-deprived or oxygen-poor environments such as the mammalian intestine and the genital organs, should illuminate the current evolutionary status of the MROs in these organisms, and give insight to environmental constraints that drive the evolution of eukaryotes and their organelles. In this review, we summarize and discuss the diverse metabolic functions and protein transport systems of the MROs from anaerobic parasitic protozoa.}, }
@article {pmid24314104, year = {2013}, author = {Alburaki, M and Bertrand, B and Legout, H and Moulin, S and Alburaki, A and Sheppard, WS and Garnery, L}, title = {A fifth major genetic group among honeybees revealed in Syria.}, journal = {BMC genetics}, volume = {14}, number = {}, pages = {117}, pmid = {24314104}, issn = {1471-2156}, mesh = {Animals ; Bees/classification/*genetics ; Cluster Analysis ; DNA, Mitochondrial/chemistry/metabolism ; Genetic Loci ; Genetic Variation ; Genetics, Population ; *Genome ; Haplotypes ; Heterozygote ; Microsatellite Repeats ; Mitochondria/genetics ; Principal Component Analysis ; Syria ; }, abstract = {BACKGROUND: Apiculture has been practiced in North Africa and the Middle-East from antiquity. Several thousand years of selective breeding have left a mosaic of Apis mellifera subspecies in the Middle-East, many uniquely adapted and survived to local environmental conditions. In this study we explore the genetic diversity of A. mellifera from Syria (n = 1258), Lebanon (n = 169) and Iraq (n = 35) based on 14 short tandem repeat (STR) loci in the context of reference populations from throughout the Old World (n = 732).<br><br>RESULTS: Our data suggest that the Syrian honeybee Apis mellifera syriaca occurs in both Syrian and Lebanese territories, with no significant genetic variability between respective populations from Syria and Lebanon. All studied populations clustered within a new fifth independent nuclear cluster, congruent with an mtDNA Z haplotype identified in a previous study. Syrian honeybee populations are not associated with Oriental lineage O, except for sporadic introgression into some populations close to the Turkish and Iraqi borders. Southern Syrian and Lebanese populations demonstrated high levels of genetic diversity compared to the northern populations.<br><br>CONCLUSION: This study revealed the effects of foreign queen importations on Syrian bee populations, especially for the region of Tartus, where extensive introgression of A. m. anatolica and/or A. m. caucasica alleles were identified. The policy of creating genetic conservation centers for the Syrian subspecies should take into consideration the influence of the oriental lineage O from the northern Syrian border and the large population of genetically divergent indigenous honeybees located in southern Syria.}, }
@article {pmid24312599, year = {2013}, author = {Zhang, L and Liu, X and Liu, J and Zhang, Z}, title = {Characteristics and function of sulfur dioxygenase in Echiuran worm Urechis unicinctus.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e81885}, pmid = {24312599}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biocatalysis ; Cloning, Molecular ; DNA, Complementary/genetics ; Dioxygenases/*chemistry/genetics/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Phylogeny ; Polychaeta/*enzymology ; Protein Refolding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; }, abstract = {BACKGROUND: Sulfide is a common toxin to animals and is abundant in coastal and aquatic sediments. Sulfur dioxygenase (SDO) is thought to be the key enzyme involved in sulfide oxidation in some organisms. The echiuran worm, Urechis unicinctus, inhabits coastal sediment and tolerates high concentrations of sulfide. The SDO is presumably important for sulfide tolerance in U. unicinctus.<br><br>RESULTS: The full-length cDNA of SDO from the echiuran worm U. unicinctus, proven to be located in the mitochondria, was cloned and the analysis of its sequence suggests that it belongs to the metallo-&#x3b2;-lactamase superfamily. The enzyme was produced using an E. coli expression system and the measured activity is approximately 0.80 U mg protein(-1). Furthermore, the expression of four sub-segments of the U. unicinctus SDO was accomplished leading to preliminary identification of functional domains of the enzyme. The identification of the conserved metal I (H113, H115, H169 and D188), metal II (D117, H118, H169 and H229) as well as the potential glutathione (GSH) (R197, Y231, M279 and I283) binding sites was determined by enzyme activity and GSH affinity measurements. The key residues responsible for SDO activity were identified by analysis of simultaneous mutations of residues D117 and H118 located close to the metal II binding site.<br><br>CONCLUSION: The recombinant SDO from U. unicinctus was produced, purified and characterized. The metal binding sites in the SDO were identified and Y231 recognized as the mostly important amino acid residue for GSH binding. Our results show that SDO is located in the mitochondria where it plays an important role in sulfide detoxification of U. unicinctus.}, }
@article {pmid24312576, year = {2013}, author = {Coia, V and Capocasa, M and Anagnostou, P and Pascali, V and Scarnicci, F and Boschi, I and Battaggia, C and Crivellaro, F and Ferri, G and Alù, M and Brisighelli, F and Busby, GB and Capelli, C and Maixner, F and Cipollini, G and Viazzo, PP and Zink, A and Destro Bisol, G}, title = {Demographic histories, isolation and social factors as determinants of the genetic structure of Alpine linguistic groups.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e81704}, pmid = {24312576}, issn = {1932-6203}, mesh = {Chromosomes, Human, Y/*genetics ; Demography/*history ; Ethnicity/genetics/history ; Evolution, Molecular ; Female ; *Gene Flow ; *Genetic Variation ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Humans ; *Linguistics ; Male ; Mitochondria/genetics ; Polymorphism, Single Nucleotide ; White People/ethnology/*genetics/*history ; }, abstract = {Great European mountain ranges have acted as barriers to gene flow for resident populations since prehistory and have offered a place for the settlement of small, and sometimes culturally diverse, communities. Therefore, the human groups that have settled in these areas are worth exploring as an important potential source of diversity in the genetic structure of European populations. In this study, we present new high resolution data concerning Y chromosomal variation in three distinct Alpine ethno-linguistic groups, Italian, Ladin and German. Combining unpublished and literature data on Y chromosome and mitochondrial variation, we were able to detect different genetic patterns. In fact, within and among population diversity values observed vary across linguistic groups, with German and Italian speakers at the two extremes, and seem to reflect their different demographic histories. Using simulations we inferred that the joint effect of continued genetic isolation and reduced founding group size may explain the apportionment of genetic diversity observed in all groups. Extending the analysis to other continental populations, we observed that the genetic differentiation of Ladins and German speakers from Europeans is comparable or even greater to that observed for well known outliers like Sardinian and Basques. Finally, we found that in south Tyroleans, the social practice of Geschlossener Hof, a hereditary norm which might have favored male dispersal, coincides with a significant intra-group diversity for mtDNA but not for Y chromosome, a genetic pattern which is opposite to those expected among patrilocal populations. Together with previous evidence regarding the possible effects of "local ethnicity" on the genetic structure of German speakers that have settled in the eastern Italian Alps, this finding suggests that taking socio-cultural factors into account together with geographical variables and linguistic diversity may help unveil some yet to be understood aspects of the genetic structure of European populations.}, }
@article {pmid24312557, year = {2013}, author = {Plouviez, S and Faure, B and Le Guen, D and Lallier, FH and Bierne, N and Jollivet, D}, title = {A new barrier to dispersal trapped old genetic clines that escaped the Easter Microplate tension zone of the Pacific vent mussels.}, journal = {PloS one}, volume = {8}, number = {12}, pages = {e81555}, pmid = {24312557}, issn = {1932-6203}, mesh = {Adenosylhomocysteinase/genetics ; *Animal Distribution ; Animals ; Base Sequence ; Bivalvia/cytology/enzymology/*genetics/*physiology ; Cell Nucleus/genetics ; Evolution, Molecular ; Haplotypes ; *Hydrothermal Vents ; Isoenzymes/genetics ; Mitochondria/genetics ; Pacific Ocean ; Polymorphism, Genetic ; *Selection, Genetic ; }, abstract = {Comparative phylogeography of deep-sea hydrothermal vent species has uncovered several genetic breaks between populations inhabiting northern and southern latitudes of the East Pacific Rise. However, the geographic width and position of genetic clines are variable among species. In this report, we further characterize the position and strength of barriers to gene flow between populations of the deep-sea vent mussel Bathymodiolus thermophilus. Eight allozyme loci and DNA sequences of four nuclear genes were added to previously published sequences of the cytochrome c oxidase subunit I gene. Our data confirm the presence of two barriers to gene flow, one located at the Easter Microplate (between 21°33'S and 31°S) recently described as a hybrid zone, and the second positioned between 7°25'S and 14°S with each affecting different loci. Coalescence analysis indicates a single vicariant event at the origin of divergence between clades for all nuclear loci, although the clines are now spatially discordant. We thus hypothesize that the Easter Microplate barrier has recently been relaxed after a long period of isolation and that some genetic clines have escaped the barrier and moved northward where they have subsequently been trapped by a reinforcing barrier to gene flow between 7°25'S and 14°S.}, }
@article {pmid24303002, year = {2013}, author = {Wilson, NG and Maschek, JA and Baker, BJ}, title = {A species flock driven by predation? Secondary metabolites support diversification of slugs in antarctica.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e80277}, pmid = {24303002}, issn = {1932-6203}, mesh = {Animals ; Antarctic Regions ; *Biodiversity ; DNA, Mitochondrial/genetics ; Gastropoda/classification/genetics/*metabolism ; *Metabolome ; *Metabolomics/methods ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; *Predatory Behavior ; Selection, Genetic ; }, abstract = {Antarctica's rich marine animal biodiversity has been substantially influenced by a complex glacial history, but it is unclear why some taxa responded with diversification while others did not. Despite being considered a single endemic sea slug species in the Southern Ocean, mitochondrial DNA sequencing of Doris kerguelenensis (Bergh, 1884) revealed a multitude of highly divergent lineages. But because of the uniparental inheritance of mitochondria, it was unclear whether those lineages represented a radiation of cryptic species or simply stochastic sorting patterns of populations that rarely reach equilibrium. Here we demonstrate that the mitochondrial groups in D. kerguelenensis also correlate with nuclear DNA. Additionally, by extracting secondary metabolites from the same individuals we sequenced, we were also able to directly link the secondary metabolome to a mitochondrial lineage. These metabolites are not derived from the diet, but instead are synthesized de novo and implicated in an anti-predatory role. The strong linkage between these metabolites and the mitochondrial lineages strongly suggests that these lineages represent cryptic species in an adaptive radiation. Over millions of years, episodic glacial cycles reduced the distribution of a formerly widespread slug into a series of small vicariant refuges, vulnerable to genetic drift and predation pressure. The recognition of this marine invertebrate species flock implicates a strongly synergistic role for selection and allopatry driving speciation in this system.}, }
@article {pmid24297697, year = {2014}, author = {Wexler-Cohen, Y and Stevens, GC and Barnoy, E and van der Bliek, AM and Johnson, PJ}, title = {A dynamin-related protein contributes to Trichomonas vaginalis hydrogenosomal fission.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {28}, number = {3}, pages = {1113-1121}, pmid = {24297697}, issn = {1530-6860}, support = {R01 GM051866/GM/NIGMS NIH HHS/United States ; GM051866/GM/NIGMS NIH HHS/United States ; R01 AI027857/AI/NIAID NIH HHS/United States ; AI27857/AI/NIAID NIH HHS/United States ; R37 AI027857/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Dynamins/chemistry/*physiology ; Humans ; Microscopy, Electron ; Molecular Sequence Data ; Organelles/*physiology ; Protozoan Proteins/chemistry/*physiology ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/*cytology/ultrastructure ; }, abstract = {Trichomonas vaginalis is a highly divergent, unicellular eukaryote of the phylum Metamonada, class Parabasalia, and the source of a common sexually transmitted infection. This parasite lacks mitochondria, but harbors an evolutionarily related organelle, the hydrogenosome. We explored the role of dynamin-related proteins (DRPs) in the division of the hydrogenosome. Eight DRP homologues [T. vaginalis DRPs (TvDRPs)], which can be grouped into 3 subclasses, are present in T. vaginalis. We examined 5 TvDRPs that are representative of each subclass, by introducing dominant negative mutations analogous to those known to interfere with mitochondrial division in yeast, worms, and mammals. Microscopic and cell fractionation analyses of parasites expressing one of the mutated TvDRPs (TVAG_350040) demonstrated that this protein localizes to hydrogenosomes. Moreover, these organelles were found to be increased in size and reduced in number in cells expressing this dominant negative protein, relative to parasites expressing the corresponding wild-type TvDRP, the other 4 mutant TvDRPs, or an empty vector control. Our data indicate a role for a TvDRP in the fission of T. vaginalis hydrogenosomes, similar to that described for peroxisomes and mitochondria. These findings reveal a conservation of core components involved in the division of diverse eukaryotic organelles across broad phylogenetic distances.}, }
@article {pmid24297327, year = {2014}, author = {Van Belleghem, SM and Hendrickx, F}, title = {A tight association in two genetically unlinked dispersal related traits in sympatric and allopatric salt marsh beetle populations.}, journal = {Genetica}, volume = {142}, number = {1}, pages = {1-9}, pmid = {24297327}, issn = {1573-6857}, mesh = {Animals ; Coleoptera/classification/*genetics/physiology ; Europe ; Evolution, Molecular ; Gene Flow ; Genes, Insect ; Genes, Mitochondrial ; Genetic Association Studies ; Genetic Fitness ; Genetic Speciation ; Isocitrate Dehydrogenase/*genetics/metabolism ; Mitochondria/*metabolism ; Phylogeography ; Salt Tolerance ; Sympatry ; Wetlands ; Wings, Animal/*growth &amp; development ; }, abstract = {Local adaptation likely involves selection on multiple, genetically unlinked traits to increase fitness in divergent habitats. Conversely, recombination is expected to counteract local adaptation under gene flow by breaking down adaptive gene combinations. Western European populations of the salt marsh beetle Pogonus chalceus are characterized by large interpopulation variation at various geographical ranges in two traits related to dispersal ability, i.e. wing size and different allozymes of the mitochondrial NADP(+)-dependent isocitrate dehydrogenase (mtIdh) gene. In this study, we tested whether variation in wing length was as strongly genetically determined in locally adapted populations in a sympatric mosaic compared to allopatric populations, and if variation in mtIDH and wing size was genetically unlinked. We demonstrate that the genetic determination of wing size is very high (h (2) = 0.90) in sympatry and of comparable magnitude as geographically separated populations. Second, we show that, although frequencies of mtIDH allozymes are tightly associated with mean population wing size across Western European populations, the correlation is strongly reduced within some of the populations. These findings demonstrate that the divergence involves at least two traits under independent genetic control and that the genetically distinct ecotypes are retained at geographical distances with ample opportunity for gene flow.}, }
@article {pmid24291103, year = {2014}, author = {Verkhratsky, A and Parpura, V}, title = {Calcium signalling and calcium channels: evolution and general principles.}, journal = {European journal of pharmacology}, volume = {739}, number = {}, pages = {1-3}, pmid = {24291103}, issn = {1879-0712}, support = {R21 HD078678/HD/NICHD NIH HHS/United States ; HS078678/HS/AHRQ HHS/United States ; }, mesh = {Animals ; Calcium/metabolism ; *Calcium Channels/metabolism ; *Calcium Signaling ; Evolution, Molecular ; Homeostasis ; }, abstract = {Calcium as a divalent cation was selected early in evolution as a signaling molecule to be used by both prokaryotes and eukaryotes. Its low cytosolic concentration likely reflects the initial concentration of this ion in the primordial soup/ocean as unicellular organisms were formed. As the concentration of calcium in the ocean subsequently increased, so did the diversity of homeostatic molecules handling calcium. This includes the plasma membrane channels that allowed the calcium entry, as well as extrusion mechanisms, i.e., exchangers and pumps. Further diversification occurred with the evolution of intracellular organelles, in particular the endoplasmic reticulum and mitochondria, which also contain channels, exchanger(s) and pumps to handle the homeostasis of calcium ions. Calcium signalling system, based around coordinated interactions of the above molecular entities, can be activated by the opening of voltage-gated channels, neurotransmitters, second messengers and/or mechanical stimulation, and as such is all-pervading pathway in physiology and pathophysiology of organisms.}, }
@article {pmid24289148, year = {2015}, author = {Zheng, XH and Cao, DC and Lv, WH and Wu, J and Sun, XW}, title = {The complete mitochondrial genome sequence of Chinese lizard gudgeon (Saurogobio dabryi).}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {708-709}, doi = {10.3109/19401736.2013.843085}, pmid = {24289148}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Genome Size ; *Genome, Mitochondrial ; Lizards/*genetics ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The complete mitochondrial genome of Saurogobio dabryi is 16,604 bp in length with 55.88% AT content, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. The termination-associated sequence and six conserved sequence blocks were also identified. Compared all protein-coding genes and whole genome sequence with four species, Saurogobio dabryi has higher similarity with Gobio gobio than others. The mitogenome sequence of Saurogobio dabryi would play an important role in population structure and conservation genetic studies.}, }
@article {pmid24274788, year = {2014}, author = {Zimorski, V and Martin, WF}, title = {Subcellular targeting of proteins and pathways during evolution.}, journal = {The New phytologist}, volume = {201}, number = {1}, pages = {1-2}, doi = {10.1111/nph.12566}, pmid = {24274788}, issn = {1469-8137}, mesh = {Arabidopsis/*genetics ; Arabidopsis Proteins/*genetics ; Chloroplast Proteins/*genetics ; Chloroplasts/*genetics ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Nuclear Proteins/*genetics ; }, }
@article {pmid24274753, year = {2013}, author = {Takenaka, M and Zehrmann, A and Verbitskiy, D and Härtel, B and Brennicke, A}, title = {RNA editing in plants and its evolution.}, journal = {Annual review of genetics}, volume = {47}, number = {}, pages = {335-352}, doi = {10.1146/annurev-genet-111212-133519}, pmid = {24274753}, issn = {1545-2948}, mesh = {Arabidopsis Proteins/genetics ; Codon/genetics ; Evolution, Molecular ; Mitochondria/genetics ; Plant Proteins/genetics/physiology ; Plants/*genetics ; Plastids/genetics ; *RNA Editing ; RNA, Messenger/genetics ; RNA, Plant/*genetics ; }, abstract = {RNA editing alters the identity of nucleotides in RNA molecules such that the information for a protein in the mRNA differs from the prediction of the genomic DNA. In chloroplasts and mitochondria of flowering plants, RNA editing changes C nucleotides to U nucleotides; in ferns and mosses, it also changes U to C. The approximately 500 editing sites in mitochondria and 40 editing sites in plastids of flowering plants are individually addressed by specific proteins, genes for which are amplified in plant species with organellar RNA editing. These proteins contain repeat elements that bind to cognate RNA sequence motifs just 5' to the edited nucleotide. In flowering plants, the site-specific proteins interact selectively with individual members of a different, smaller family of proteins. These latter proteins may be connectors between the site-specific proteins and the as yet unknown deaminating enzymatic activity.}, }
@article {pmid24272752, year = {2014}, author = {Suematsu, T and Watanabe, O and Kita, K and Yokobori, S and Watanabe, Y}, title = {Arabidopsis thaliana mitochondrial EF-G1 functions in two different translation steps.}, journal = {Journal of biochemistry}, volume = {155}, number = {2}, pages = {107-114}, doi = {10.1093/jb/mvt105}, pmid = {24272752}, issn = {1756-2651}, mesh = {Arabidopsis/classification/genetics/*metabolism ; Evolution, Molecular ; Fusidic Acid/pharmacology ; GTP Phosphohydrolases/drug effects ; Humans ; Mitochondria/*metabolism ; Peptide Elongation Factor G/*physiology ; Phylogeny ; *Protein Biosynthesis ; Protein Synthesis Inhibitors/pharmacology ; }, abstract = {Translation elongation factor G (EF-G) in bacteria catalyses the translocation of transfer RNA on ribosomes in the elongation step as well as dissociation of post-termination state ribosomes into two subunits in the recycling step. In contrast, the dual functions of EF-G are exclusively divided into two different paralogues in human mitochondria, named EF-G1mt for translocation and EF-G2mt for ribosomal dissociation. Many of the two eukaryotic EF-G paralogues are phylogenetically associated with EF-G1mt and EF-G2mt groups. However, plant paralogues are associated with EF-G1mt and plastid EF-G, not with EF-G2mt. In this study, we phylogenetically and biochemically characterized Arabidopsis thaliana EF-G1mt (AtEF-G1mt) to clarify the factor responsible for the dissociation of ribosomes in plant mitochondria. We showed that eukaryotic EF-G1mts form one monophyletic group separated from bacterial EF-G and are classified into five sister groups. AtEF-G1mt is classified into a different group from its human counterpart. We also demonstrated that AtEF-G1mt catalyses both translocation and ribosomal dissociation, unlike in humans. Meanwhile, AtEF-G1mt is resistant to fusidic acid, an inhibitor of bacterial EF-G. Here, we propose that the functional division is not necessarily conserved among mitochondriate eukaryotes and also that EF-G1mt in organisms lacking EF-G2mt functions in two steps, similar to conventional bacterial EF-G.}, }
@article {pmid24270388, year = {2013}, author = {Aphasizheva, I and Maslov, DA and Aphasizhev, R}, title = {Kinetoplast DNA-encoded ribosomal protein S12: a possible functional link between mitochondrial RNA editing and translation in Trypanosoma brucei.}, journal = {RNA biology}, volume = {10}, number = {11}, pages = {1679-1688}, pmid = {24270388}, issn = {1555-8584}, support = {R01 AI091914/AI/NIAID NIH HHS/United States ; AI091914/AI/NIAID NIH HHS/United States ; R21 AI088292/AI/NIAID NIH HHS/United States ; AI088292/AI/NIAID NIH HHS/United States ; R01 AI101057/AI/NIAID NIH HHS/United States ; }, mesh = {DNA, Kinetoplast/*metabolism ; Evolution, Molecular ; Gene Expression Regulation ; Gene Knockdown Techniques ; Genome, Protozoan ; Mitochondria/*genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Protozoan Proteins/genetics/metabolism ; *RNA Editing ; RNA, Messenger/genetics/metabolism ; RNA, Protozoan/genetics/metabolism ; RNA, Ribosomal/*metabolism ; Ribosomal Proteins/genetics/metabolism ; Trypanosoma brucei brucei/cytology/genetics/*metabolism ; }, abstract = {Mitochondrial ribosomes of Trypanosoma brucei are composed of 9S and 12S rRNAs, which are encoded by the kinetoplast genome, and more than 150 proteins encoded in the nucleus and imported from the cytoplasm. However, a single ribosomal protein RPS12 is encoded by the kinetoplast DNA (kDNA) in all trypanosomatid species examined. As typical for these organisms, the gene itself is cryptic and its transcript undergoes an extensive U-insertion/deletion editing. An evolutionary trend to reduce or eliminate RNA editing could be traced with other cryptogenes, but the invariably pan-edited RPS12 cryptogene is apparently spared. Here we inquired whether editing of RPS12 mRNA is essential for mitochondrial translation. By RNAi-mediated knockdowns of RNA editing complexes and inducible knock-in of a key editing enzyme in procyclic parasites, we could reversibly downregulate production of edited RPS12 mRNA and, by inference, synthesis of this protein. While inhibition of editing decreased edited mRNA levels, the translation of edited (Cyb) and unedited (COI) mRNAs was blocked. Furthermore, the population of SSU-related 45S complexes declined upon inactivation of editing and so did the amount of mRNA-bound ribosomes. In bloodstream parasites, which lack active electron transport chain but still require translation of ATP synthase subunit 6 mRNA (A6), both edited RPS12 and A6 mRNAs were detected in translation complexes. Collectively, our results indicate that a single ribosomal protein gene retained by the kinetoplast mitochondrion serves as a possible functional link between editing and translation processes and provide the rationale for the evolutionary conservation of RPS12 pan-editing.}, }
@article {pmid24269344, year = {2014}, author = {Jia, H and Sun, R and Shi, W and Yan, Y and Li, H and Guo, X and Xu, B}, title = {Characterization of a mitochondrial manganese superoxide dismutase gene from Apis cerana cerana and its role in oxidative stress.}, journal = {Journal of insect physiology}, volume = {60}, number = {}, pages = {68-79}, doi = {10.1016/j.jinsphys.2013.11.004}, pmid = {24269344}, issn = {1879-1611}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Bees/enzymology/*genetics/radiation effects ; Gene Components ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; *Stress, Physiological ; Superoxide Dismutase/*genetics/isolation &amp; purification/metabolism ; Transcription Factors/metabolism ; }, abstract = {Mitochondrial manganese superoxide dismutase (mMnSOD) plays a vital role in the defense against reactive oxygen species (ROS) in eukaryotic mitochondria. In this study, we isolated and identified a mMnSOD gene from Apis cerana cerana, which we named AccSOD2. Several putative transcription factor-binding sites were identified within the 5'-flanking region of AccSOD2, which suggests that AccSOD2 may be involved in organismal development and/or environmental stress responses. Quantitative real-time PCR analysis showed that AccSOD2 is highly expressed in larva and pupae during different developmental stages. In addition, the expression of AccSOD2 could be induced by cold (4 °C), heat (42 °C), H2O2, ultraviolet light (UV), HgCl2, and pesticide treatment. Using a disc diffusion assay, we provide evidence that recombinant AccSOD2 protein can play a functional role in protecting cells from oxidative stress. Finally, the in vivo activities of AccSOD2 were measured under a variety of stressful conditions. Taken together, our results indicate that AccSOD2 plays an important role in cellular stress responses and anti-oxidative processes and that it may be of critical importance to honeybee survival.}, }
@article {pmid24265196, year = {2013}, author = {Bonini, MG and Gantner, BN}, title = {The multifaceted activities of AMPK in tumor progression--why the "one size fits all" definition does not fit at all?.}, journal = {IUBMB life}, volume = {65}, number = {11}, pages = {889-896}, doi = {10.1002/iub.1213}, pmid = {24265196}, issn = {1521-6551}, support = {1S10RR027848-01A1/RR/NCRR NIH HHS/United States ; 5T32HL072742-09/HL/NHLBI NIH HHS/United States ; }, mesh = {AMP-Activated Protein Kinases/*metabolism ; Apoptosis/drug effects ; Apoptosis Regulatory Proteins/physiology ; Cell Line, Tumor ; Cell Transformation, Neoplastic ; Disease Progression ; Enzyme Activation ; Epithelial-Mesenchymal Transition/physiology ; Glycolysis ; Humans ; Metformin/pharmacology ; Mitochondria/drug effects ; Neoplasms/*physiopathology ; Neoplastic Stem Cells/drug effects/physiology ; Proto-Oncogene Proteins c-akt/metabolism ; Tumor Suppressor Proteins/physiology ; }, abstract = {AMP-activated kinase (AMPK) is a central cellular energetic biosensor and regulator of a broad array of cellular metabolic routes activated by nutrient deprivation, mitochondrial dysfunction, oxidative stress, and cytokines. The activation of AMPK maintains ATP levels in response to hypoxia, mitochondrial dysfunction, and shortage of essential metabolic fuels. Activated AMPK turns on energy sparing pathways and promotes antiapoptotic functions thereby permitting cells to survive extremely hostile conditions for prolonged periods of time. Cancer cells in solid tumors are generally subjected to such harsh conditions; however, they manage to efficiently survive and proliferate. This is likely due, in great part, to a peculiar form of metabolism that is heavily reliant on glycolysis and which promotes cancer cell adaptation and tumor progression. AMPK controls the influx and utilization of glucose by cancer cells and therefore has emerged as an attractive target to treat cancer. Investigations exploring this possibility demonstrated that activators or inhibitors of AMPK impact cancer cell viability and possibly cancer progression. For example, the AMPK activator metformin induces apoptosis in a variety of cancer cell lines and models. A major problem with many of the studies on metformin is that little effort has been invested in unraveling how metformin activates AMPK in the many contexts it has been tested. This is significant because many AMPK-independent effects of metformin have been documented. The notion that AMPK acts solely as a tumor suppressor also conflicts with findings that it confers resistance to nutrient deprivation, sustains NADPH levels in cancer cells, facilitates stress-induced gene transcription, promotes cell survival via antiapoptotic function upregulation, intermediates epithelial-to-mesenchymal transition, and increases malignant transformation. These are all recognized steps necessary for the successful evolution of tumors. This review highlights some of these findings and proposes that the role of AMPK in cancer should be reconsidered in light of the complex roles of AMPK under different metabolic conditions.}, }
@article {pmid24259313, year = {2013}, author = {Wisecaver, JH and Brosnahan, ML and Hackett, JD}, title = {Horizontal gene transfer is a significant driver of gene innovation in dinoflagellates.}, journal = {Genome biology and evolution}, volume = {5}, number = {12}, pages = {2368-2381}, pmid = {24259313}, issn = {1759-6653}, mesh = {Cells, Cultured ; Databases, Nucleic Acid ; Dinoflagellida/*genetics/metabolism ; Evolution, Molecular ; Gene Deletion ; *Gene Transfer, Horizontal ; Genetic Variation ; Genome, Protozoan/genetics ; Isocitrate Dehydrogenase/genetics ; Ketone Oxidoreductases/genetics ; Mitochondria/*genetics/metabolism ; Molecular Sequence Data ; NADH Dehydrogenase/genetics ; Oxidative Phosphorylation ; Pentose Phosphate Pathway/genetics ; Phylogeny ; Sequence Analysis, DNA ; Transcriptome/genetics ; }, abstract = {The dinoflagellates are an evolutionarily and ecologically important group of microbial eukaryotes. Previous work suggests that horizontal gene transfer (HGT) is an important source of gene innovation in these organisms. However, dinoflagellate genomes are notoriously large and complex, making genomic investigation of this phenomenon impractical with currently available sequencing technology. Fortunately, de novo transcriptome sequencing and assembly provides an alternative approach for investigating HGT. We sequenced the transcriptome of the dinoflagellate Alexandrium tamarense Group IV to investigate how HGT has contributed to gene innovation in this group. Our comprehensive A. tamarense Group IV gene set was compared with those of 16 other eukaryotic genomes. Ancestral gene content reconstruction of ortholog groups shows that A. tamarense Group IV has the largest number of gene families gained (314-1,563 depending on inference method) relative to all other organisms in the analysis (0-782). Phylogenomic analysis indicates that genes horizontally acquired from bacteria are a significant proportion of this gene influx, as are genes transferred from other eukaryotes either through HGT or endosymbiosis. The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation. Some of these missing genes have been functionally replaced by bacterial and eukaryotic xenologs. The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT.}, }
@article {pmid24259312, year = {2013}, author = {Maier, UG and Zauner, S and Woehle, C and Bolte, K and Hempel, F and Allen, JF and Martin, WF}, title = {Massively convergent evolution for ribosomal protein gene content in plastid and mitochondrial genomes.}, journal = {Genome biology and evolution}, volume = {5}, number = {12}, pages = {2318-2329}, pmid = {24259312}, issn = {1759-6653}, mesh = {Biological Evolution ; Cell Membrane/genetics ; Chlorophyta/genetics ; Chloroplasts/genetics ; Cyanobacteria/*genetics ; Electron Transport Chain Complex Proteins/genetics ; Energy Metabolism/genetics ; Eukaryotic Cells/cytology ; Evolution, Molecular ; *Genome, Mitochondrial ; Membrane Proteins/genetics ; Mitochondria/*genetics ; Photosynthesis/genetics ; Plastids/*genetics ; Respiration/genetics ; Ribosomal Proteins/*genetics ; Ribosomes/*genetics ; }, abstract = {Plastid and mitochondrial genomes have undergone parallel evolution to encode the same functional set of genes. These encode conserved protein components of the electron transport chain in their respective bioenergetic membranes and genes for the ribosomes that express them. This highly convergent aspect of organelle genome evolution is partly explained by the redox regulation hypothesis, which predicts a separate plastid or mitochondrial location for genes encoding bioenergetic membrane proteins of either photosynthesis or respiration. Here we show that convergence in organelle genome evolution is far stronger than previously recognized, because the same set of genes for ribosomal proteins is independently retained by both plastid and mitochondrial genomes. A hitherto unrecognized selective pressure retains genes for the same ribosomal proteins in both organelles. On the Escherichia coli ribosome assembly map, the retained proteins are implicated in 30S and 50S ribosomal subunit assembly and initial rRNA binding. We suggest that ribosomal assembly imposes functional constraints that govern the retention of ribosomal protein coding genes in organelles. These constraints are subordinate to redox regulation for electron transport chain components, which anchor the ribosome to the organelle genome in the first place. As organelle genomes undergo reduction, the rRNAs also become smaller. Below size thresholds of approximately 1,300 nucleotides (16S rRNA) and 2,100 nucleotides (26S rRNA), all ribosomal protein coding genes are lost from organelles, while electron transport chain components remain organelle encoded as long as the organelles use redox chemistry to generate a proton motive force.}, }
@article {pmid24233690, year = {2013}, author = {Yoshizawa, K and Johnson, KP}, title = {Changes in base composition bias of nuclear and mitochondrial genes in lice (Insecta: Psocodea).}, journal = {Genetica}, volume = {141}, number = {10-12}, pages = {491-499}, pmid = {24233690}, issn = {1573-6857}, mesh = {Animals ; *Base Composition ; Cell Nucleolus/*genetics ; Evolution, Molecular ; *Genes, Insect ; *Genes, Mitochondrial ; Insecta/*classification/*genetics ; Mitochondria/*genetics ; Phthiraptera/genetics ; Phylogeny ; RNA, Ribosomal ; Selection, Genetic ; }, abstract = {While it is well known that changes in the general processes of molecular evolution have occurred on a variety of timescales, the mechanisms underlying these changes are less well understood. Parasitic lice ("Phthiraptera") and their close relatives (infraorder Nanopsocetae of the insect order Psocodea) are a group of insects well known for their unusual features of molecular evolution. We examined changes in base composition across parasitic lice and bark lice. We identified substantial differences in percent GC content between the clade comprising parasitic lice plus closely related bark lice (=Nanopsocetae) versus all other bark lice. These changes occurred for both nuclear and mitochondrial protein coding and ribosomal RNA genes, often in the same direction. To evaluate whether correlations in base composition change also occurred within lineages, we used phylogenetically controlled comparisons, and in this case few significant correlations were identified. Examining more constrained sites (first/second codon positions and rRNA) revealed that, in comparison to the other bark lice, the GC content of parasitic lice and close relatives tended towards 50 % either up from less than 50 % GC or down from greater than 50 % GC. In contrast, less constrained sites (third codon positions) in both nuclear and mitochondrial genes showed less of a consistent change of base composition in parasitic lice and very close relatives. We conclude that relaxed selection on this group of insects is a potential explanation of the change in base composition for both mitochondrial and nuclear genes, which could lead to nucleotide frequencies closer to random expectation (i.e., 50 % GC) in the absence of any mutation bias. Evidence suggests this relaxed selection arose once in the non-parasitic common ancestor of Phthiraptera + Nanopsocetae and is not directly related to the evolution of the parasitism in lice.}, }
@article {pmid24231807, year = {2013}, author = {Sancak, Y and Markhard, AL and Kitami, T and Kovács-Bogdán, E and Kamer, KJ and Udeshi, ND and Carr, SA and Chaudhuri, D and Clapham, DE and Li, AA and Calvo, SE and Goldberger, O and Mootha, VK}, title = {EMRE is an essential component of the mitochondrial calcium uniporter complex.}, journal = {Science (New York, N.Y.)}, volume = {342}, number = {6164}, pages = {1379-1382}, pmid = {24231807}, issn = {1095-9203}, support = {F32HL107021/HL/NHLBI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R24 DK080261/DK/NIDDK NIH HHS/United States ; P30 HD018655/HD/NICHD NIH HHS/United States ; F32 HL107021/HL/NHLBI NIH HHS/United States ; DK080261/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Calcium Channels/chemistry/genetics/*metabolism ; Calcium-Binding Proteins/genetics/*metabolism ; Cation Transport Proteins/genetics/*metabolism ; Cell Membrane/*metabolism ; EF Hand Motifs ; Gene Knockdown Techniques ; HEK293 Cells ; Humans ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Proteomics ; }, abstract = {The mitochondrial uniporter is a highly selective calcium channel in the organelle's inner membrane. Its molecular components include the EF-hand-containing calcium-binding proteins mitochondrial calcium uptake 1 (MICU1) and MICU2 and the pore-forming subunit mitochondrial calcium uniporter (MCU). We sought to achieve a full molecular characterization of the uniporter holocomplex (uniplex). Quantitative mass spectrometry of affinity-purified uniplex recovered MICU1 and MICU2, MCU and its paralog MCUb, and essential MCU regulator (EMRE), a previously uncharacterized protein. EMRE is a 10-kilodalton, metazoan-specific protein with a single transmembrane domain. In its absence, uniporter channel activity was lost despite intact MCU expression and oligomerization. EMRE was required for the interaction of MCU with MICU1 and MICU2. Hence, EMRE is essential for in vivo uniporter current and additionally bridges the calcium-sensing role of MICU1 and MICU2 with the calcium-conducting role of MCU.}, }
@article {pmid24230915, year = {2014}, author = {Gjerde, B}, title = {Sarcocystis species in red deer revisited: with a re-description of two known species as Sarcocystis elongata n. sp. and Sarcocystis truncata n. sp. based on mitochondrial cox1 sequences.}, journal = {Parasitology}, volume = {141}, number = {3}, pages = {441-452}, doi = {10.1017/S0031182013001819}, pmid = {24230915}, issn = {1469-8161}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry/genetics ; DNA, Protozoan/chemistry/genetics ; Deer/*parasitology ; Electron Transport Complex IV/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/genetics ; Reindeer ; Sarcocystis/*classification/genetics/isolation &amp; purification ; Sarcocystosis/parasitology/*veterinary ; Sequence Analysis, DNA/veterinary ; Species Specificity ; }, abstract = {In a previous investigation, five Sarcocystis species were described from Norwegian red deer and believed to be conspecific with species occurring in either reindeer or moose based on sarcocyst morphology and nucleotide sequences of the nuclear ribosomal DNA unit. The aim of the present study was to characterize numerous isolates of these sarcocyst types at the mitochondrial cytochrome c oxidase subunit I gene (cox1) in order to corroborate or refute previous species designations of Sarcocystis in red deer. The Sarcocystis tarandi- and Sarcocystis rangiferi-like taxa in red deer and reindeer, respectively, were thoroughly compared by sequencing 14-27 isolates of each type. Sequence comparisons revealed four distinct sequence types, which by phylogenetic analyses were placed in four monophyletic groups according to host origin, and they were therefore considered to represent four separate species. The two taxa of this type in red deer were named Sarcocystis elongata and Sarcocystis truncata, respectively. Sequencing of many isolates of Sarcocystis hjorti and Sarcocystis ovalis from red deer and moose confirmed that these species occur in both hosts. A revised description of the two new species is given and the current knowledge concerning all six Sarcocystis species in red deer is reviewed.}, }
@article {pmid24221027, year = {2014}, author = {Zhang, L and An, B and Backström, N and Liu, N}, title = {Phylogeography-based delimitation of subspecies boundaries in the common pheasant (Phasianus colchicus).}, journal = {Biochemical genetics}, volume = {52}, number = {1-2}, pages = {38-51}, doi = {10.1007/s10528-013-9626-5}, pmid = {24221027}, issn = {1573-4927}, mesh = {Animals ; China ; Galliformes/blood/*genetics ; Genetic Variation ; Mitochondria/genetics ; Mutation Rate ; Phylogeography ; Species Specificity ; }, abstract = {To test the validity of subspecies status within the common pheasant (Phasianus colchicus), we used genetic data to assess differences among five subspecies distributed across the Loess Plateau in central China. Samples were collected from 191 individuals representing subspecies P. c. strauchi, P. c. satscheuensis, P. c. kiangsuensis, P. c. suehschanensis, and P. c. edzinensis. Analysis of mitochondrial genetic variation suggested that there were no phylogenetically distinct subspecies clades, and we could not exclude that hybridization has occurred among subspecies. A potential explanation of the observed pattern is that an increase in common pheasant rearing farms may have led to enforcement of hybridization between different subspecies. Consistent with phenotypic data, our analysis suggests that a previously identified common pheasant subspecies (P. c. strauchi) represents an intermediate form between the subspecies P. c. satscheuensis and P. c. suehschanensis.}, }
@article {pmid24216442, year = {2013}, author = {Zhang, YK and Ding, XL and Zhang, KJ and Hong, XY}, title = {Wolbachia play an important role in affecting mtDNA variation of Tetranychus truncatus (Trombidiformes: Tetranychidae).}, journal = {Environmental entomology}, volume = {42}, number = {6}, pages = {1240-1245}, doi = {10.1603/EN13085}, pmid = {24216442}, issn = {1938-2936}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Female ; Genetic Variation ; Haplotypes ; Phylogeny ; Tetranychidae/genetics/*microbiology ; Wolbachia/*genetics/physiology ; }, abstract = {The prevalence of the endosymbiont Wolbachia and its effects on mitochondria variation were analyzed in seven natural populations of Tetranychus truncatus Ehara (Trombidiformes: Tetranychidae) in current study. Five Wolbachia strains (wtru1, wtru5, wtru7, wtru8, and wtru12) were detected based on the surface protein of Wolbachia (wsp) sequence data and the multiple locus sequences typing data, suggesting that multiple separate invasions have occurred. Part of mitochondrial cytochrome oxidase subunit I gene was sequenced from infected individuals revealing 10 different haplotypes. As predicted, the haplotype and nucleotide diversity were lower in infected individuals than that in uninfected individuals. Furthermore, phylogenetic and analysis of molecular variance analyses revealed that the distribution of mtDNA haplotypes is not associated with geography. Rather, it is strongly concordant with infection status. These data support the hypothesis that Wolbachia infection can affect the genetic structure and diversity of the host mites.}, }
@article {pmid24216019, year = {2014}, author = {Smith, DR and Arrigo, KR and Alderkamp, AC and Allen, AE}, title = {Massive difference in synonymous substitution rates among mitochondrial, plastid, and nuclear genes of Phaeocystis algae.}, journal = {Molecular phylogenetics and evolution}, volume = {71}, number = {}, pages = {36-40}, doi = {10.1016/j.ympev.2013.10.018}, pmid = {24216019}, issn = {1095-9513}, mesh = {Cell Nucleus/*genetics ; Genome ; Haptophyta/classification/*genetics ; Mitochondria/*genetics ; Mutation Rate ; *Phylogeny ; Plastids/*genetics ; Sequence Analysis, DNA ; }, abstract = {We are just beginning to understand how mutation rates differ among mitochondrial, plastid, and nuclear genomes. In most seed plants the mitochondrial mutation rate is estimated to be lower than those of the plastid and nucleus, whereas in the red alga Porphyra the opposite is true, and in certain green algae all three genomes appear to have similar rates of mutation. Relative rate statistics of organelle vs nuclear genes, however, are lacking for lineages that acquired their plastids through secondary endosymbiosis, but recent organelle DNA analyses suggest that they may differ drastically from what is observed in lineages with primary plastids, such as green plants and red algae. Here, by measuring synonymous nucleotide substitutions, we approximate the relative mutation rates within the haptophyte genus Phaeocystis, which has a red-algal-derived, secondary plastid. Synonymous-site divergence data indicate that for Phaeocystis antarctica and P. globosa the mitochondrial mutation rate is 10 and 3 times that of the plastid and nucleus, respectively. This differs drastically from relative rate estimates for primary-plastid-bearing lineages and presents a much more dynamic view of organelle vs nuclear mutation rates across the eukaryotic domain.}, }
@article {pmid24214533, year = {2014}, author = {Fristedt, R and Scharff, LB and Clarke, CA and Wang, Q and Lin, C and Merchant, SS and Bock, R}, title = {RBF1, a plant homolog of the bacterial ribosome-binding factor RbfA, acts in processing of the chloroplast 16S ribosomal RNA.}, journal = {Plant physiology}, volume = {164}, number = {1}, pages = {201-215}, pmid = {24214533}, issn = {1532-2548}, support = {R01 GM056265/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Chlamydomonas reinhardtii/genetics ; Chloroplasts/*genetics/metabolism/ultrastructure ; Escherichia coli Proteins ; Genetic Complementation Test ; Molecular Sequence Data ; Mutation ; Photosynthesis/genetics ; Plants, Genetically Modified ; Plastids/metabolism ; RNA, Ribosomal, 16S/*metabolism ; Ribosomal Proteins ; Sequence Homology, Amino Acid ; Thylakoids/genetics/metabolism ; }, abstract = {Plastids (chloroplasts) possess 70S ribosomes that are very similar in structure and function to the ribosomes of their bacterial ancestors. While most components of the bacterial ribosome (ribosomal RNAs [rRNAs] and ribosomal proteins) are well conserved in the plastid ribosome, little is known about the factors mediating the biogenesis of plastid ribosomes. Here, we have investigated a putative homolog of the bacterial RbfA (for ribosome-binding factor A) protein that was identified as a cold-shock protein and an auxiliary factor acting in the 5' maturation of the 16S rRNA. The unicellular green alga Chlamydomonas reinhardtii and the vascular plant Arabidopsis (Arabidopsis thaliana) both encode a single RbfA-like protein in their nuclear genomes. By generating specific antibodies against this protein, we show that the plant RbfA-like protein functions exclusively in the plastid, where it is associated with thylakoid membranes. Analysis of mutants for the corresponding gene (termed RBF1) reveals that the gene function is essential for photoautotrophic growth. Weak mutant alleles display reduced levels of plastid ribosomes, a specific depletion in 30S ribosomal subunits, and reduced activity of plastid protein biosynthesis. Our data suggest that, while the function in ribosome maturation and 16S rRNA 5' end processing is conserved, the RBF1 protein has assumed an additional role in 3' end processing. Together with the apparent absence of a homologous protein from plant mitochondria, our findings illustrate that the assembly process of the 70S ribosome is not strictly conserved and has undergone some modifications during organelle evolution.}, }
@article {pmid24205167, year = {2013}, author = {Moreno-Letelier, A and Ortíz-Medrano, A and Piñero, D}, title = {Niche divergence versus neutral processes: combined environmental and genetic analyses identify contrasting patterns of differentiation in recently diverged pine species.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e78228}, pmid = {24205167}, issn = {1932-6203}, mesh = {Chloroplasts/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Ecology ; Ecosystem ; Environment ; Evolution, Molecular ; Gene Flow/genetics ; Genetic Testing/methods ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Models, Genetic ; Phylogeny ; Pinus/*genetics ; Polymorphism, Genetic/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND AND AIMS: Solving relationships of recently diverged taxa, poses a challenge due to shared polymorphism and weak reproductive barriers. Multiple lines of evidence are needed to identify independently evolving lineages. This is especially true of long-lived species with large effective population sizes, and slow rates of lineage sorting. North American pines are an interesting group to test this multiple approach. Our aim is to combine cytoplasmic genetic markers with environmental information to clarify species boundaries and relationships of the species complex of Pinus flexilis, Pinus ayacahuite, and Pinus strobiformis.<br><br>METHODS: Mitochondrial and chloroplast sequences were combined with previously obtained microsatellite data and contrasted with environmental information to reconstruct phylogenetic relationships of the species complex. Ecological niche models were compared to test if ecological divergence is significant among species.<br><br>KEY RESULTS AND CONCLUSION: Separately, both genetic and ecological evidence support a clear differentiation of all three species but with different topology, but also reveal an ancestral contact zone between P. strobiformis and P. ayacahuite. The marked ecological differentiation of P. flexilis suggests that ecological speciation has occurred in this lineage, but this is not reflected in neutral markers. The inclusion of environmental traits in phylogenetic reconstruction improved the resolution of internal branches. We suggest that combining environmental and genetic information would be useful for species delimitation and phylogenetic studies in other recently diverged species complexes.}, }
@article {pmid24203231, year = {2014}, author = {Couturier, J and Wu, HC and Dhalleine, T and Pégeot, H and Sudre, D and Gualberto, JM and Jacquot, JP and Gaymard, F and Vignols, F and Rouhier, N}, title = {Monothiol glutaredoxin-BolA interactions: redox control of Arabidopsis thaliana BolA2 and SufE1.}, journal = {Molecular plant}, volume = {7}, number = {1}, pages = {187-205}, doi = {10.1093/mp/sst156}, pmid = {24203231}, issn = {1752-9867}, mesh = {Arabidopsis/cytology/enzymology/*metabolism ; Arabidopsis Proteins/chemistry/*metabolism ; Catalytic Domain ; Conserved Sequence ; DNA-Binding Proteins/chemistry/*metabolism ; Enzyme Activation ; Glutaredoxins/*metabolism ; Intracellular Space/metabolism ; Oxidation-Reduction ; Photosynthesis ; Phylogeny ; Protein Binding ; Protein Transport ; Sulfurtransferases/*metabolism ; }, abstract = {A functional relationship between monothiol glutaredoxins and BolAs has been unraveled by genomic analyses and in several high-throughput studies. Phylogenetic analyses coupled to transient expression of green fluorescent protein (GFP) fusions indicated that, in addition to the sulfurtransferase SufE1, which contains a C-terminal BolA domain, three BolA isoforms exist in Arabidopsis thaliana, BolA1 being plastidial, BolA2 nucleo-cytoplasmic, and BolA4 dual-targeted to mitochondria and plastids. Binary yeast two-hybrid experiments demonstrated that all BolAs and SufE1, via its BolA domain, can interact with all monothiol glutaredoxins. Most interactions between protein couples of the same subcellular compartment have been confirmed by bimolecular fluorescence complementation. In vitro experiments indicated that monothiol glutaredoxins could regulate the redox state of BolA2 and SufE1, both proteins possessing a single conserved reactive cysteine. Indeed, a glutathionylated form of SufE1 lost its capacity to activate the cysteine desulfurase, Nfs2, but it is reactivated by plastidial glutaredoxins. Besides, a monomeric glutathionylated form and a dimeric disulfide-bridged form of BolA2 can be preferentially reduced by the nucleo-cytoplasmic GrxS17. These results indicate that the glutaredoxin-BolA interaction occurs in several subcellular compartments and suggest that a redox regulation mechanism, disconnected from their capacity to form iron-sulfur cluster-bridged heterodimers, may be physiologically relevant for BolA2 and SufE1.}, }
@article {pmid24195633, year = {2014}, author = {Tao, M and You, CP and Zhao, RR and Liu, SJ and Zhang, ZH and Zhang, C and Liu, Y}, title = {Animal mitochondria: evolution, function, and disease.}, journal = {Current molecular medicine}, volume = {14}, number = {1}, pages = {115-124}, doi = {10.2174/15665240113136660081}, pmid = {24195633}, issn = {1875-5666}, mesh = {Aging/genetics/metabolism ; Animals ; Biological Evolution ; DNA, Mitochondrial/genetics/metabolism ; Energy Metabolism ; Humans ; Mitochondria/*physiology ; Mitochondrial Diseases/genetics/metabolism ; Neoplasms/genetics/metabolism ; Signal Transduction ; }, abstract = {Mitochondria are sub-cellular organelles responsible for producing the majority of cellular energy through the process of oxidative phosphorylation (OXPHOS), and are found in nearly all eukaryotic cells. Mitochondria have a unique genetic system, mitochondrial DNA (mtDNA), which is a small, self-replicating and diverse genome. In the past 30 years, mtDNA has made significant contribution to molecular ecology and phylogeography. Mitochondria also represent a unique system of mitochondrial-nuclear genomic cooperation. Additionally, mitochondrial dysfunction can be fatal. In this paper, we review several aspects of mitochondria, including evolution and the origin of mitochondria, energy supply and the central role of mitochondria in apoptosis, and mitochondrial dysfunction. It is shown that mitochondria play a critical role in many aspects of life.}, }
@article {pmid24194927, year = {2013}, author = {Chen, X and Ghazanfar, B and Khan, AR and Hayat, S and Cheng, Z}, title = {Comparative analysis of putative orthologues of mitochondrial import motor subunit: Pam18 and Pam16 in plants.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e78400}, pmid = {24194927}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Arabidopsis Proteins/*genetics ; Cluster Analysis ; Computational Biology/methods ; Conserved Sequence/genetics ; Data Mining ; Microarray Analysis ; Mitochondrial Membrane Transport Proteins/*genetics ; Mitochondrial Precursor Protein Import Complex Proteins ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Plants/*genetics ; Sequence Alignment ; Sequence Homology ; Species Specificity ; }, abstract = {Pam18/Tim14 and Pam16/Tim16, highly conserved proteins among eukaryotes, are two essential subunits of protein import motors localized in the inner mitochondrial membrane. The heterodimer formed by Pam18 and Pam16 via their J-type domains serves a regulatory function in protein translocation. Here, we report that thirty-one Pam18 and twenty-six Pam16 putative orthologues in twelve plant species were identified and analyzed through bioinformatics strategy. Results data revealed that Pam18 and Pam16 were also highly conserved among plants including their J-type domains within the hydrophilic region. Key amino acid residues and an HPD motif of Pam18 were identical among the orthologues except OsPam18L5. N-myristoylation sites of Pam18 and casein kinase II phosphorylation sites of Pam 16 were more abundant, which might be important functional sites. Some Pam18 and Pam16 proteins contained a transmembrane region at the N-terminal region. Sub-cellular prediction results indicated that many orthologues localized at mitochondria. Gene expression analyses revealed that Pam18 and Pam16 in Arabidopsis might play roles in senescence and abiotic stress responses. Our detailed study provides a better understanding of Pam18 and Pam16 in plant kingdom.}, }
@article {pmid24189582, year = {2014}, author = {Kamyingkird, K and Cao, S and Masatani, T and Moumouni, PF and Vudriko, P and Mousa, AA and Terkawi, MA and Nishikawa, Y and Igarashi, I and Xuan, X}, title = {Babesia bovis dihydroorotate dehydrogenase (BboDHODH) is a novel molecular target of drug for bovine babesiosis.}, journal = {The Journal of veterinary medical science}, volume = {76}, number = {3}, pages = {323-330}, pmid = {24189582}, issn = {1347-7439}, mesh = {Amino Acid Sequence ; Animals ; Babesia bovis/*enzymology ; Babesiosis/*drug therapy/metabolism ; Blotting, Western ; Cattle ; Cattle Diseases/*drug therapy/*parasitology ; Cloning, Molecular ; Computational Biology ; DNA Primers/genetics ; Dihydroorotate Dehydrogenase ; Drug Delivery Systems ; Drug Discovery ; Enzyme Inhibitors/*metabolism ; Escherichia coli ; Microscopy, Confocal ; Molecular Sequence Data ; Oxidoreductases Acting on CH-CH Group Donors/genetics/*metabolism ; Phylogeny ; Recombinant Fusion Proteins/genetics/metabolism ; }, abstract = {The emergence of drug resistance and adverse side effects of current bovine babesiosis treatment suggest that the search of new drug targets and development of safer and effective compounds are required. This study focuses on dihydroorotate dehydrogenase (DHODH), the fourth enzyme of pyrimidine biosynthesis pathway as a potential drug target for bovine babesiosis. Recombinant Babesia bovis DHODH protein (rBboDHODH) was produced in Escherichia coli and used for characterization and measurement of enzymatic activity. Furthermore, the effects of DHODH inhibitors were evaluated in vitro. The recombinant B. bovis DHODH histidine fusion protein (rBboDHODH) had 42.4-kDa molecular weight and exhibited a specific activity of 475.7 ± 245 Unit/mg, a Km = 276.2 µM for L-dihydroorotate and a Km= 94.41 µM for decylubiquinone. A 44-kDa band of native BboDHODH was detected by Western blot analysis and found in parasites mitochondria using a confocal microscope. Among DHODH inhibitors, atovaquone (ATV) and leflunomide (LFN) significantly inhibited the activity of rBboDHODH as well as the growth of B. bovis in vitro. The half maximal inhibitory concentration (IC50) of ATV and LFN was 2.38 ± 0.53 nM and 52.41 ± 11.47 µM, respectively. These results suggest that BboDHODH might be a novel target for development of new drug for treatment of B. bovis infection.}, }
@article {pmid24186265, year = {2014}, author = {Gribbins, KM and Matchett, CL and DelBello, KA and Rheubert, J and Villagrán-SantaCruz, M and Granados-González, G and Hernández-Gallegos, O}, title = {The ultrastructure of spermatid development during spermiogenesis within the rosebelly lizard, Sceloporus variabilis (Reptilia, Squamata, Phrynosomatidae).}, journal = {Journal of morphology}, volume = {275}, number = {3}, pages = {258-268}, doi = {10.1002/jmor.20212}, pmid = {24186265}, issn = {1097-4687}, mesh = {Acrosome/ultrastructure ; Animals ; Cell Nucleus/ultrastructure ; Chromatin/ultrastructure ; Golgi Apparatus/ultrastructure ; Lizards/*anatomy &amp; histology/physiology ; Male ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Phylogeny ; Spermatids/*growth &amp; development/*ultrastructure ; *Spermatogenesis ; }, abstract = {Several recent studies have mapped out the characters of spermiogenesis within several species of squamates. Many of these data have shown both conserved and possibly apomorphic morphological traits that could be important in future phylogenetic analysis within Reptilia. There, however, has not been a recent study that compares spermiogenesis and its similarities or differences between two species of reptile that reside in the same genus. Thus, the present analysis details the changes to spermiogenesis in Sceloporus variabilis and then compares spermatid morphologies to that of Sceloporus bicanthalis. Many of the morphological changes that the spermatids undergo in these two species are similar or conserved, which is similar to what has been reported in other squamates. There are six main character differences that can be observed during the development of the spermatids between these two sceloporid lizards. They include the presence (S. variabilis) or absence (S. bicanthalis) of a mitochondrial/endoplasmic reticulum complex near the Golgi apparatus during acrosome development, a shallow (S. variabilis) or deep (S. bicanthalis) nuclear indentation that accommodates the acrosomal vesicle, filamentous (S. variabilis) or granular (S. bicanthalis) chromatin condensation, no spiraling (S. variabilis) or spiraling (S. bicanthalis) of chromatin during condensation, absence (S. variabilis) or presence (S. bicanthalis) of the longitudinal manchette microtubules, and the lack of (S. variabilis) or presence (S. bicanthalis) of nuclear lacunae. This is the first study that compares spermiogenic ultrastructural characters between species within the same genus. The significance of the six character differences between two distantly related species within Sceloporus is still unknown, but these data do suggest that spermiogenesis might be a good model to study the hypothesis that spermatid ontogeny is species specific.}, }
@article {pmid24186072, year = {2013}, author = {Wallace, DC and Chalkia, D}, title = {Mitochondrial DNA genetics and the heteroplasmy conundrum in evolution and disease.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {5}, number = {11}, pages = {a021220}, pmid = {24186072}, issn = {1943-0264}, support = {NS21328/NS/NINDS NIH HHS/United States ; NS070298/NS/NINDS NIH HHS/United States ; R01 NS070298/NS/NINDS NIH HHS/United States ; DK73691/DK/NIDDK NIH HHS/United States ; AG24373/AG/NIA NIH HHS/United States ; R01 AG024373/AG/NIA NIH HHS/United States ; R01 DK073691/DK/NIDDK NIH HHS/United States ; R01 NS021328/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Cattle ; DNA, Mitochondrial/*genetics ; Female ; Genetics, Population ; Genome, Mitochondrial ; Humans ; Inheritance Patterns ; Macaca ; Male ; Mice ; Mitochondria/*genetics ; Mitochondrial Diseases/*genetics ; Models, Genetic ; *Mutation ; Oxidative Phosphorylation ; Phenotype ; Phylogeny ; Polymorphism, Genetic ; }, abstract = {The unorthodox genetics of the mtDNA is providing new perspectives on the etiology of the common "complex" diseases. The maternally inherited mtDNA codes for essential energy genes, is present in thousands of copies per cell, and has a very high mutation rate. New mtDNA mutations arise among thousands of other mtDNAs. The mechanisms by which these "heteroplasmic" mtDNA mutations come to predominate in the female germline and somatic tissues is poorly understood, but essential for understanding the clinical variability of a range of diseases. Maternal inheritance and heteroplasmy also pose major challengers for the diagnosis and prevention of mtDNA disease.}, }
@article {pmid24184823, year = {2014}, author = {Deceglie, S and Lionetti, C and Stewart, JB and Habermann, B and Roberti, M and Cantatore, P and Loguercio Polosa, P}, title = {Characterization of the sea urchin mitochondrial transcription factor A reveals unusual features.}, journal = {Mitochondrion}, volume = {14}, number = {1}, pages = {34-41}, doi = {10.1016/j.mito.2013.10.003}, pmid = {24184823}, issn = {1872-8278}, support = {GGP06233/TI_/Telethon/Italy ; }, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; DNA Footprinting ; DNA, Mitochondrial/*metabolism ; DNA-Binding Proteins/chemistry/*genetics/*metabolism ; Genetic Variation ; Mitochondrial Proteins/chemistry/*genetics/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Sea Urchins/*genetics ; Transcription Factors/chemistry/*genetics/*metabolism ; }, abstract = {Sea urchin mtDNA is transcribed via a different mechanism compared to vertebrates. To gain information on the apparatus of sea urchin mitochondrial transcription we have characterized the DNA binding properties of the mitochondrial transcription factor A (TFAM). The protein contains two HMG box domains but, differently from vertebrates, displays a very short C-terminal tail. Phylogenetic analysis showed that the distribution of tail length is mixed in the different lineages, indicating that it is a trait that undergoes rapid changes during evolution. Homology modeling suggests that the protein adopts the same configuration of the human counterpart and possibly a similar mode of binding to DNA. DNase I footprinting showed that TFAM specifically contacts mtDNA at a fixed distance from three AT-rich consensus sequences that were supposed to act as transcriptional initiation sites. Bound sequences are homologous and contain an inverted repeat motif, which resembles that involved in the intercalation of human TFAM in LSP DNA. The here reported data indicate that sea urchin TFAM specifically binds mtDNA. The protein could intercalate residues at the DNA inverted motif and, despite its short tail, might have a role in mitochondrial transcription.}, }
@article {pmid24184470, year = {2013}, author = {Dietlmeier, J and Ghita, O and Duessmann, H and Prehn, JH and Whelan, PF}, title = {Unsupervised mitochondria segmentation using recursive spectral clustering and adaptive similarity models.}, journal = {Journal of structural biology}, volume = {184}, number = {3}, pages = {401-408}, doi = {10.1016/j.jsb.2013.10.013}, pmid = {24184470}, issn = {1095-8657}, mesh = {Algorithms ; Animals ; Cluster Analysis ; Image Interpretation, Computer-Assisted/*methods ; Microscopy, Electron ; *Mitochondria ; Molecular Imaging/*methods ; Pattern Recognition, Automated/methods ; Sciuridae ; }, abstract = {The unsupervised segmentation method proposed in the current study follows the evolutional ability of human vision to extrapolate significant structures in an image. In this work we adopt the perceptual grouping strategy by selecting the spectral clustering framework, which is known to capture perceptual organization features, as well as by developing similarity models according to Gestaltic laws of visual segregation. Our proposed framework applies but is not limited to the detection of cells and organelles in microscopic images and attempts to provide an effective alternative to presently dominating manual segmentation and tissue classification practice. The main theoretical contribution of our work resides in the formulation of robust similarity models which automatically adapt to the statistical structure of the biological domain and return optimal performance in pixel classification tasks under the wide variety of distributional assumptions.}, }
@article {pmid24183947, year = {2013}, author = {Pohl, H and Dallai, R and Gottardo, M and Beutel, RG}, title = {The spermatozoon of Mengenilla moldrzyki (Strepsiptera, Mengenillidae): ultrastructure and phylogenetic considerations.}, journal = {Tissue &amp; cell}, volume = {45}, number = {6}, pages = {446-451}, doi = {10.1016/j.tice.2013.10.002}, pmid = {24183947}, issn = {1532-3072}, mesh = {Acrosome/ultrastructure ; Animals ; Cell Nucleus/ultrastructure ; Centrioles/ultrastructure ; Flagella/ultrastructure ; Insecta/*ultrastructure ; Male ; Mitochondria/ultrastructure ; *Phylogeny ; *Species Specificity ; Spermatozoa/*ultrastructure ; }, abstract = {Even though the spermatozoa of several strepsipteran species were described earlier, no data were available for the basal family Mengenillidae. Well-fixed material of the recently described Tunisian species Mengenilla moldrzyki was used for a detailed examination of the sperm ultrastructure. The total length is c. 30 μm. The head region contains a conical acrosome vesicle (0.3-0.35 μm) and an elongated nucleus (7.3 μm) with dense chromatin. Some granular material along with a uniformely dense centriole adjunct and two mitochondrial derivatives are visible at the posterior end of the nucleus. The material of the centriole adjunct does not extend along the flagellum and accessory bodies are absent. The mitochondrial derivatives are elongated structures crossed by a longitudinal crista but lacking parallel transverse cristae and paracrystalline material in the dense matrix. The mitochondrial derivatives gradually reduce their size and end at the most posterior tail region. The flagellar axoneme has a 9 + 9 + 2 pattern and originates beneath the nucleus. In the terminal tail region the axoneme gradually disintegrates. Despite the extreme specialization of the endoparasitc group, strepsipteran spermatozoa are mostly characterized by plesiomorphies. The pattern within the order is largely uniform, but Mengenilla displays several apomorphic features compared to the presumptive strepsipteran groundplan (e.g., absence of crystallizations and cristae in the mitochondrial derivatives). The subdivision of the intertubular material into two compartments with a dense beak-like structure adhering to the tubular wall supports a clade Coleopterida (= Strepsiptera + Coleoptera) + Neuropterida.}, }
@article {pmid24163630, year = {2013}, author = {Wang, Z and Zhang, H and Yang, J and Chen, Y and Xu, X and Mao, X and Li, C}, title = {Phylogenetic, expression, and bioinformatic analysis of the ABC1 gene family in Populus trichocarpa.}, journal = {TheScientificWorldJournal}, volume = {2013}, number = {}, pages = {785070}, pmid = {24163630}, issn = {1537-744X}, mesh = {Computational Biology/*methods ; Gene Expression Regulation, Plant ; Phylogeny ; Plant Proteins/classification/*genetics ; Populus/*chemistry ; }, abstract = {We studied 17 ABC1 genes in Populus trichocarpa, all of which contained an ABC1 domain consisting of about 120 amino acid residues. Most of the ABC1 gene products were located in the mitochondria or chloroplasts. All had a conserved VAVK-like motif and a DFG motif. Phylogenetic analysis grouped the genes into three subgroups. In addition, the chromosomal locations of the genes on the 19 Populus chromosomes were determined. Gene structure was studied through exon/intron organization and the MEME motif finder, while heatmap was used to study the expression diversity using EST libraries. According to the heatmap, PtrABC1P14 was highlighted because of the high expression in tension wood which related to secondary cell wall formation and cellulose synthesis, thus making a contribution to follow-up experiment in wood formation. Promoter cis-element analysis indicated that almost all of the ABC1 genes contained one or two cis-elements related to ABA signal transduction pathway and drought stress. Quantitative real-time PCR was carried out to evaluate the expression of all of the genes under abiotic stress conditions (ABA, CdCl2, high temperature, high salinity, and drought); the results showed that some of the genes were affected by these stresses and confirmed the results of promoter cis-element analysis.}, }
@article {pmid24153405, year = {2013}, author = {Huang, Y and Chen, X and Liu, Y and Roth, C and Copeland, C and McFarlane, HE and Huang, S and Lipka, V and Wiermer, M and Li, X}, title = {Mitochondrial AtPAM16 is required for plant survival and the negative regulation of plant immunity.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {2558}, doi = {10.1038/ncomms3558}, pmid = {24153405}, issn = {2041-1723}, mesh = {Arabidopsis/genetics/*immunology/microbiology ; Arabidopsis Proteins/genetics/*immunology ; Gene Expression Regulation, Plant/*immunology ; Green Fluorescent Proteins ; High-Throughput Screening Assays ; Mitochondria/genetics/*immunology ; Mitochondrial Membrane Transport Proteins/classification/genetics/*immunology ; Mitochondrial Precursor Protein Import Complex Proteins ; Mutation ; Oomycetes/immunology ; Phylogeny ; Plant Diseases/genetics/immunology/microbiology ; Plant Immunity/*genetics ; Reactive Oxygen Species/metabolism ; Recombinant Fusion Proteins/genetics/immunology ; Saccharomyces cerevisiae Proteins/genetics/immunology ; Sequence Homology, Amino Acid ; Signal Transduction ; }, abstract = {Proteins containing nucleotide-binding and leucine-rich repeat domains (NB-LRRs) serve as immune receptors in plants and animals. Negative regulation of immunity mediated by NB-LRR proteins is crucial, as their overactivation often leads to autoimmunity. Here we describe a new mutant, snc1-enhancing (muse) forward genetic screen, targeting unknown negative regulators of NB-LRR-mediated resistance in Arabidopsis. From the screen, we identify MUSE5, which is renamed as AtPAM16 because it encodes the ortholog of yeast PAM16, part of the mitochondrial inner membrane protein import motor. Consistently, AtPAM16-GFP localizes to the mitochondrial inner membrane. AtPAM16L is a paralog of AtPAM16. Double mutant Atpam16-1 Atpam16l is lethal, indicating that AtPAM16 function is essential. Single mutant Atpam16 plants exhibit a smaller size and enhanced resistance against virulent pathogens. They also display elevated reactive oxygen species (ROS) accumulation. Therefore, AtPAM16 seems to be involved in importing a negative regulator of plant immunity into mitochondria, thus protecting plants from over-accumulation of ROS and preventing autoimmunity.}, }
@article {pmid24150037, year = {2013}, author = {Caspermeyer, J}, title = {Examining the source behind Sherpa mountain fitness.}, journal = {Molecular biology and evolution}, volume = {30}, number = {12}, pages = {2735}, doi = {10.1093/molbev/mst161}, pmid = {24150037}, issn = {1537-1719}, mesh = {*Adaptation, Physiological ; *Altitude ; DNA, Mitochondrial/*genetics ; Ethnicity/*genetics ; *Evolution, Molecular ; Humans ; Mitochondria/*genetics ; NADH Dehydrogenase/*genetics ; }, }
@article {pmid24149657, year = {2014}, author = {Melo-Ferreira, J and Farelo, L and Freitas, H and Suchentrunk, F and Boursot, P and Alves, PC}, title = {Home-loving boreal hare mitochondria survived several invasions in Iberia: the relative roles of recurrent hybridisation and allele surfing.}, journal = {Heredity}, volume = {112}, number = {3}, pages = {265-273}, pmid = {24149657}, issn = {1365-2540}, mesh = {Animals ; *DNA, Mitochondrial ; Female ; Gene Flow ; Genetics, Population ; Haplotypes ; Hares/*genetics ; *Hybridization, Genetic ; Male ; Microsatellite Repeats ; Phylogeography ; Spain ; X Chromosome ; Y Chromosome ; }, abstract = {Genetic introgression from a resident species into an invading close relative can result from repeated hybridisation along the invasion front and/or allele surfing on the expansion wave. Cases where the phenomenon is massive and systematic, such as for hares (genus Lepus) in Iberia, would be best explained by recurrent hybridisation but this is difficult to prove because the donor populations are generally extinct. In the Pyrenean foothills, Lepus europaeus presumably replaced Lepus granatensis recently and the present species border is parallel to the direction of invasion, so that populations of L. granatensis in the contact zone represent proxies of existing variation before the invasion. Among three pairs of populations sampled across this border, we find less differentiation of mitochondrial DNA (mtDNA) across than along it, as predicted under recurrent hybridisation at the invasion front. Using autosomal microsatellite loci and X- and Y-linked diagnostic loci, we show that admixture across the border is quasi-absent, making it unlikely that lack of interspecific mtDNA differentiation results from ongoing gene flow. Furthermore, we find that the local species ranges are climatically contrasted, making it also unlikely that ongoing ecology-driven movement of the contact account for mtDNA introgression. The lack of mtDNA differentiation across the boundary is mostly due to sharing of mtDNA from a boreal species currently extinct in Iberia (Lepus timidus) whose mitochondria have thus remained in place since the last deglaciation despite successive invasions by two other species. Home-loving mitochondria thus witness past species distribution rather than ongoing exchanges across stabilised contact zones.}, }
@article {pmid24147765, year = {2013}, author = {Narsai, R and Devenish, J and Castleden, I and Narsai, K and Xu, L and Shou, H and Whelan, J}, title = {Rice DB: an Oryza Information Portal linking annotation, subcellular location, function, expression, regulation, and evolutionary information for rice and Arabidopsis.}, journal = {The Plant journal : for cell and molecular biology}, volume = {76}, number = {6}, pages = {1057-1073}, pmid = {24147765}, issn = {1365-313X}, mesh = {Arabidopsis/genetics/metabolism ; Base Sequence ; Biological Evolution ; *Databases, Genetic ; Genome, Plant/*genetics ; *Genomics ; Internet ; Mitochondria/genetics ; Molecular Sequence Annotation ; Oryza/*genetics/metabolism ; Plant Proteins/genetics/metabolism ; Proteome ; RNA, Messenger/genetics ; RNA, Plant/genetics ; Software ; Transcriptome ; *User-Computer Interface ; }, abstract = {Omics research in Oryza sativa (rice) relies on the use of multiple databases to obtain different types of information to define gene function. We present Rice DB, an Oryza information portal that is a functional genomics database, linking gene loci to comprehensive annotations, expression data and the subcellular location of encoded proteins. Rice DB has been designed to integrate the direct comparison of rice with Arabidopsis (Arabidopsis thaliana), based on orthology or 'expressology', thus using and combining available information from two pre-eminent plant models. To establish Rice DB, gene identifiers (more than 40 types) and annotations from a variety of sources were compiled, functional information based on large-scale and individual studies was manually collated, hundreds of microarrays were analysed to generate expression annotations, and the occurrences of potential functional regulatory motifs in promoter regions were calculated. A range of computational subcellular localization predictions were also run for all putative proteins encoded in the rice genome, and experimentally confirmed protein localizations have been collated, curated and linked to functional studies in rice. A single search box allows anything from gene identifiers (for rice and/or Arabidopsis), motif sequences, subcellular location, to keyword searches to be entered, with the capability of Boolean searches (such as AND/OR). To demonstrate the utility of Rice DB, several examples are presented including a rice mitochondrial proteome, which draws on a variety of sources for subcellular location data within Rice DB. Comparisons of subcellular location, functional annotations, as well as transcript expression in parallel with Arabidopsis reveals examples of conservation between rice and Arabidopsis, using Rice DB (http://ricedb.plantenergy.uwa.edu.au).}, }
@article {pmid24147756, year = {2013}, author = {Kay, CJ and Lawler, K and Kerr, ID}, title = {Analysis of the Sam50 translocase of excavate organisms supports evolution of divergent organelles from a common endosymbiotic event.}, journal = {Bioscience reports}, volume = {33}, number = {6}, pages = {}, pmid = {24147756}, issn = {1573-4935}, support = {BB/F016956/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Evolution, Molecular ; Mitochondria/*genetics/metabolism ; Mitochondrial Membrane Transport Proteins/*genetics/metabolism ; Phylogeny ; Protein Multimerization ; Protein Transport ; Protozoan Proteins/*genetics/metabolism ; Symbiosis/genetics ; Trichomonas vaginalis/*genetics/metabolism ; }, abstract = {As free-living organisms the ancestors of mitochondria and plastids encoded complete genomes, proteomes and metabolomes. As these symbionts became organelles all these aspects were reduced - genomes have degenerated with the host nucleus now encoding the most of the remaining endosymbiont proteome, while the metabolic processes of the symbiont have been streamlined to the functions of the emerging organelle. By contrast, the topology of the endosymbiont membrane has been preserved, necessitating the development of complex pathways for membrane insertion and translocation. In this study, we examine the characteristics of the endosymbiont-derived β-barrel insertase Sam501 in the excavate super-group. A candidate is further characterized in Trichomonas vaginalis, an unusual eukaryote possessing degenerate hydrogen-producing mitochondria called hydrogenosomes. This information supports a mitochondriate eukaryotic common ancestor with a similarly evolved β-barrel insertase, which has continued to be conserved in degenerate mitochondria.}, }
@article {pmid24141138, year = {2014}, author = {Tan, AS and Baty, JW and Berridge, MV}, title = {The role of mitochondrial electron transport in tumorigenesis and metastasis.}, journal = {Biochimica et biophysica acta}, volume = {1840}, number = {4}, pages = {1454-1463}, doi = {10.1016/j.bbagen.2013.10.016}, pmid = {24141138}, issn = {0006-3002}, mesh = {Animals ; Carcinogenesis/*genetics ; Electron Transport/*genetics ; Humans ; Mitochondria/*genetics ; Mutation ; Neoplasm Metastasis/*genetics ; Tumor Microenvironment ; }, abstract = {BACKGROUND: Tumor formation and spread via the circulatory and lymphatic drainage systems is associated with metabolic reprogramming that often includes increased glycolytic metabolism relative to mitochondrial energy production. However, cells within a tumor are not identical due to genetic change, clonal evolution and layers of epigenetic reprogramming. In addition, cell hierarchy impinges on metabolic status while tumor cell phenotype and metabolic status will be influenced by the local microenvironment including stromal cells, developing blood and lymphatic vessels and innate and adaptive immune cells. Mitochondrial mutations and changes in mitochondrial electron transport contribute to metabolic remodeling in cancer in ways that are poorly understood.<br><br>SCOPE OF REVIEW: This review concerns the role of mitochondria, mitochondrial mutations and mitochondrial electron transport function in tumorigenesis and metastasis.<br><br>MAJOR CONCLUSIONS: It is concluded that mitochondrial electron transport is required for tumor initiation, growth and metastasis. Nevertheless, defects in mitochondrial electron transport that compromise mitochondrial energy metabolism can contribute to tumor formation and spread. These apparently contradictory phenomena can be reconciled by cells in individual tumors in a particular environment adapting dynamically to optimally balance mitochondrial genome changes and bioenergetic status.<br><br>GENERAL SIGNIFICANCE: Tumors are complex evolving biological systems characterized by genetic and adaptive epigenetic changes. Understanding the complexity of these changes in terms of bioenergetics and metabolic changes will permit the development of better combination anticancer therapies. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research.}, }
@article {pmid24135058, year = {2013}, author = {Flinner, N and Ellenrieder, L and Stiller, SB and Becker, T and Schleiff, E and Mirus, O}, title = {Mdm10 is an ancient eukaryotic porin co-occurring with the ERMES complex.}, journal = {Biochimica et biophysica acta}, volume = {1833}, number = {12}, pages = {3314-3325}, doi = {10.1016/j.bbamcr.2013.10.006}, pmid = {24135058}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Consensus Sequence ; Cytosol/metabolism ; *Evolution, Molecular ; Membrane Proteins/chemistry/*metabolism ; Mitochondria/metabolism ; Mitochondrial Membranes/metabolism ; Models, Molecular ; Molecular Sequence Data ; Multiprotein Complexes/*metabolism ; Phylogeny ; Porins/chemistry/*metabolism ; Protein Structure, Secondary ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; Sequence Alignment ; Sequence Deletion ; Structural Homology, Protein ; Voltage-Dependent Anion Channels/chemistry/metabolism ; }, abstract = {Mitochondrial β-barrel proteins fulfill central functions in the outer membrane like metabolite exchange catalyzed by the voltage-dependent anion channel (VDAC) and protein biogenesis by the central components of the preprotein translocase of the outer membrane (Tom40) or of the sorting and assembly machinery (Sam50). The mitochondrial division and morphology protein Mdm10 is another essential outer membrane protein with proposed β-barrel fold, which has so far only been found in Fungi. Mdm10 is part of the endoplasmic reticulum mitochondria encounter structure (ERMES), which tethers the ER to mitochondria and associates with the SAM complex. In here, we provide evidence that Mdm10 phylogenetically belongs to the VDAC/Tom40 superfamily. Contrary to Tom40 and VDAC, Mdm10 exposes long loops towards both sides of the membrane. Analyses of single loop deletion mutants of Mdm10 in the yeast Saccharomyces cerevisiae reveal that the loops are dispensable for Mdm10 function. Sequences similar to fungal Mdm10 can be found in species from Excavates to Fungi, but neither in Metazoa nor in plants. Strikingly, the presence of Mdm10 coincides with the appearance of the other ERMES components. Mdm10's presence in both unikonts and bikonts indicates an introduction at an early time point in eukaryotic evolution.}, }
@article {pmid24133452, year = {2013}, author = {Mohanty, A and McBride, HM}, title = {Emerging roles of mitochondria in the evolution, biogenesis, and function of peroxisomes.}, journal = {Frontiers in physiology}, volume = {4}, number = {}, pages = {268}, pmid = {24133452}, issn = {1664-042X}, abstract = {In the last century peroxisomes were thought to have an endosymbiotic origin. Along with mitochondria and chloroplasts, peroxisomes primarily regulate their numbers through the growth and division of pre-existing organelles, and they house specific machinery for protein import. These features were considered unique to endosymbiotic organelles, prompting the idea that peroxisomes were key cellular elements that helped facilitate the evolution of multicellular organisms. The functional similarities to mitochondria within mammalian systems expanded these ideas, as both organelles scavenge peroxide and reactive oxygen species, both organelles oxidize fatty acids, and at least in higher eukaryotes, the biogenesis of both organelles is controlled by common nuclear transcription factors of the PPAR family. Over the last decade it has been demonstrated that the fission machinery of both organelles is also shared, and that both organelles act as critical signaling platforms for innate immunity and other pathways. Taken together it is clear that the mitochondria and peroxisomes are functionally coupled, regulating cellular metabolism and signaling through a number of common mechanisms. However, recent work has focused primarily on the role of the ER in the biogenesis of peroxisomes, potentially overshadowing the critical importance of the mitochondria as a functional partner. In this review, we explore the mechanisms of functional coupling of the peroxisomes to the mitochondria/ER networks, providing some new perspectives on the potential contribution of the mitochondria to peroxisomal biogenesis.}, }
@article {pmid24125831, year = {2014}, author = {Taillebois, L and Castelin, M and Lord, C and Chabarria, R and Dettaï, A and Keith, P}, title = {New Sicydiinae phylogeny (Teleostei: Gobioidei) inferred from mitochondrial and nuclear genes: insights on systematics and ancestral areas.}, journal = {Molecular phylogenetics and evolution}, volume = {70}, number = {}, pages = {260-271}, doi = {10.1016/j.ympev.2013.09.026}, pmid = {24125831}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; *Cell Nucleus/metabolism ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Female ; *Mitochondria/metabolism ; Perciformes/classification/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The Sicydiinae subfamily (Teleostei: Gobioidei) is the biggest contributor to the diversity of fish communities in river systems of tropical islands. These species are found in the Indo-Pacific area, the Caribbean region and West Africa. They spawn in freshwater, their planktotrophic larvae drift downstream to the sea where they develop, before returning to the rivers to grow and reproduce. Hence, they are called amphidromous. Their phylogeny has been explored using a total of 3545 sites from 5 molecular markers (mitochondrial DNA: 16S rDNA, cytochrome oxidase I, cytochrome b; nuclear DNA: rhodopsin gene and a nuclear marker specially developed for this study, the interferon regulatory factor 2 binding protein 1-IRF2PB1). Sequences were obtained for 59 Sicydiinae specimens of 9 known genera. The Bayesian and maximum likelihood analyses support the monophyly of the subfamily as well as the monophylyof all genera except Sicydium, which is paraphyletic. Five major clades were identified within this subfamily. One clade contained the genus Stiphodon. Another clade contained Sicyopterus, Sicydium and Parasicydium with Sicyopterus as sister genus of Sicydium. The non-monophyly of Sicydium subclade, because it includes the monotypic genus Parasicydium, challenged the validity of Parasicydium genus. Ancestral area reconstruction showed that the subfamily emerged in the Central West Pacific region implying that previous hypotheses proposing a dispersal route for Sicydiinae into the Atlantic Ocean are unsupported by the present analysis. Our results suggest that the hypotheses for the dispersal route of the genus Sicydium should be reconsidered.}, }
@article {pmid24124589, year = {2013}, author = {Fan, J and Papadopoulos, V}, title = {Evolutionary origin of the mitochondrial cholesterol transport machinery reveals a universal mechanism of steroid hormone biosynthesis in animals.}, journal = {PloS one}, volume = {8}, number = {10}, pages = {e76701}, pmid = {24124589}, issn = {1932-6203}, support = {MOP-102647//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; *Biological Evolution ; Biological Transport ; Carrier Proteins/chemistry/genetics/metabolism ; Cholesterol/*metabolism ; Cholesterol Side-Chain Cleavage Enzyme/genetics/metabolism ; Computational Biology/methods ; Cyclic AMP-Dependent Protein Kinase RIalpha Subunit/genetics/metabolism ; Evolution, Molecular ; Gene Duplication ; Gonadal Steroid Hormones/*biosynthesis ; Humans ; Membrane Transport Proteins/chemistry/genetics/*metabolism ; Mitochondria/genetics/*metabolism ; Mitogen-Activated Protein Kinase 3/genetics/metabolism ; Models, Molecular ; Multigene Family ; Phylogeny ; Protein Binding ; Protein Conformation ; Protein Interaction Domains and Motifs ; Signal Transduction ; Steroids/biosynthesis/metabolism ; Vertebrates ; Voltage-Dependent Anion Channels/genetics/metabolism ; }, abstract = {Steroidogenesis begins with the transport of cholesterol from intracellular stores into mitochondria via a series of protein-protein interactions involving cytosolic and mitochondrial proteins located at both the outer and inner mitochondrial membranes. In adrenal glands and gonads, this process is accelerated by hormones, leading to the production of high levels of steroids that control tissue development and function. A hormone-induced multiprotein complex, the transduceosome, was recently identified, and is composed of cytosolic and outer mitochondrial membrane proteins that control the rate of cholesterol entry into the outer mitochondrial membrane. More recent studies unveiled the steroidogenic metabolon, a bioactive, multimeric protein complex that spans the outer-inner mitochondrial membranes and is responsible for hormone-induced import, segregation, targeting, and metabolism of cholesterol by cytochrome P450 family 11 subfamily A polypeptide 1 (CYP11A1) in the inner mitochondrial membrane. The availability of genome information allowed us to systematically explore the evolutionary origin of the proteins involved in the mitochondrial cholesterol transport machinery (transduceosome, steroidogenic metabolon, and signaling proteins), trace the original archetype, and predict their biological functions by molecular phylogenetic and functional divergence analyses, protein homology modeling and molecular docking. Although most members of these complexes have a history of gene duplication and functional divergence during evolution, phylogenomic analysis revealed that all vertebrates have the same functional complex members, suggesting a common mechanism in the first step of steroidogenesis. An archetype of the complex was found in invertebrates. The data presented herein suggest that the cholesterol transport machinery is responsible for steroidogenesis among all vertebrates and is evolutionarily conserved throughout the entire animal kingdom.}, }
@article {pmid24123495, year = {2014}, author = {Castillo-Páez, A and Sosa-Nishizaki, O and Sandoval-Castillo, J and Galván-Magaña, F and Blanco-Parra, MD and Rocha-Olivares, A}, title = {Strong population structure and shallow mitochondrial phylogeny in the banded guitarfish, Zapteryx exasperata (Jordan y Gilbert, 1880), from the Northern Mexican Pacific.}, journal = {The Journal of heredity}, volume = {105}, number = {1}, pages = {91-100}, doi = {10.1093/jhered/est067}, pmid = {24123495}, issn = {1465-7333}, mesh = {Animals ; DNA, Mitochondrial/genetics/*isolation &amp; purification ; Gene Flow ; Genetic Variation ; Haplotypes ; Mexico ; Mitochondria/genetics ; *Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; Skates, Fish/*classification/*genetics ; }, abstract = {The northern Mexican Pacific (NMP), the Gulf of California (GC), and Baja California have been recognized as an ecological and evolutionarily dynamic region having experienced significant tectonic and climatic changes leading to the diversification of terrestrial and marine biotas. Zapteryx exasperata is a predominant ray caught in the artisanal fisheries of the NMP. Morphometric and reproductive differences between rays from the GC and the Pacific coast of Baja California (PCBC) regions suggest the presence of distinct populations. We investigate whether this distinction correlates with differences in genetic diversity and differentiation using sequences of the mitochondrial nicotinamide adenine dinucleotide dehydrogenase subunit 2 (ND2) gene and the noncoding control region (CR) in 63 specimens. Contrary to our expectations, ND2 bore significantly more diversity (h = 0.76) than CR (h = 0.39). Geographic patterns of diversity of CR were opposite to those of ND2, with GC being significantly less (ND2) and more (CR) diverse than PCBC. The diversity of concatenated haplotypes was high (h = 0.84). Low nucleotide diversity suggests the recent coancestry of haplotypes. Marked genetic structure (Φst = 0.23, P < 0.0001) revealed the existence of reproductive isolation and limited matrilineal gene flow between GC and PCBC, which correlates with their phenotypic distinction. These results suggest the influence of factors such as female reproductive philopatry, and ecological or historical vicariant barriers to gene flow. Our results point to the existence of a distinct management unit of banded guitarfish in each region, and add to the increasing evidence attesting to the diversifying nature of this evolutionarily dynamic region.}, }
@article {pmid24122038, year = {2013}, author = {Kiyonaka, S and Kajimoto, T and Sakaguchi, R and Shinmi, D and Omatsu-Kanbe, M and Matsuura, H and Imamura, H and Yoshizaki, T and Hamachi, I and Morii, T and Mori, Y}, title = {Genetically encoded fluorescent thermosensors visualize subcellular thermoregulation in living cells.}, journal = {Nature methods}, volume = {10}, number = {12}, pages = {1232-1238}, pmid = {24122038}, issn = {1548-7105}, mesh = {Adenoviridae/genetics ; Adipocytes, Brown/cytology ; Bacterial Proteins/chemistry ; DNA, Complementary/metabolism ; Escherichia coli/metabolism ; Green Fluorescent Proteins/*chemistry ; HeLa Cells ; Hot Temperature ; Humans ; Luminescent Proteins/metabolism ; Microscopy, Fluorescence/methods ; Mitochondria/metabolism ; Muscle Fibers, Skeletal/metabolism ; Muscle, Skeletal/metabolism ; Protein Conformation ; Salmonella enterica/*metabolism ; *Temperature ; }, abstract = {In mammals and birds, thermoregulation to conserve body temperature is vital to life. Multiple mechanisms of thermogeneration have been proposed, localized in different subcellular organelles. However, visualizing thermogenesis directly in intact organelles has been challenging. Here we have developed genetically encoded, GFP-based thermosensors (tsGFPs) that enable visualization of thermogenesis in discrete organelles in living cells. In tsGFPs, a tandem formation of coiled-coil structures of the Salmonella thermosensing protein TlpA transmits conformational changes to GFP to convert temperature changes into visible and quantifiable fluorescence changes. Specific targeting of tsGFPs enables visualization of thermogenesis in the mitochondria of brown adipocytes and the endoplasmic reticulum of myotubes. In HeLa cells, tsGFP targeted to mitochondria reveals heterogeneity in thermogenesis that correlates with the electrochemical gradient. Thus, tsGFPs are powerful tools to noninvasively assess thermogenesis in living cells.}, }
@article {pmid24120687, year = {2014}, author = {Schwenzer, H and Scheper, GC and Zorn, N and Moulinier, L and Gaudry, A and Leize, E and Martin, F and Florentz, C and Poch, O and Sissler, M}, title = {Released selective pressure on a structural domain gives new insights on the functional relaxation of mitochondrial aspartyl-tRNA synthetase.}, journal = {Biochimie}, volume = {100}, number = {}, pages = {18-26}, doi = {10.1016/j.biochi.2013.09.027}, pmid = {24120687}, issn = {1638-6183}, mesh = {Alternative Splicing ; Alveolata/enzymology/genetics ; Amino Acid Sequence ; Amoebozoa/enzymology/genetics ; Animals ; Archaea/enzymology/genetics ; Aspartate-tRNA Ligase/*chemistry/genetics/metabolism ; Base Sequence ; Evolution, Molecular ; Fungi/enzymology/genetics ; Gene Expression ; Humans ; Mitochondria/enzymology/*genetics ; Mitochondrial Proteins/*chemistry/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Insertional ; *Protein Biosynthesis ; Protein Structure, Tertiary ; RNA, Messenger/*chemistry/genetics/metabolism ; Selection, Genetic ; Sequence Alignment ; Viridiplantae/enzymology/genetics ; }, abstract = {Mammalian mitochondrial aminoacyl-tRNA synthetases are nuclear-encoded enzymes that are essential for mitochondrial protein synthesis. Due to an endosymbiotic origin of the mitochondria, many of them share structural domains with homologous bacterial enzymes of same specificity. This is also the case for human mitochondrial aspartyl-tRNA synthetase (AspRS) that shares the so-called bacterial insertion domain with bacterial homologs. The function of this domain in the mitochondrial proteins is unclear. Here, we show by bioinformatic analyses that the sequences coding for the bacterial insertion domain are less conserved in opisthokont and protist than in bacteria and viridiplantae. The divergence suggests a loss of evolutionary pressure on this domain for non-plant mitochondrial AspRSs. This discovery is further connected with the herein described occurrence of alternatively spliced transcripts of the mRNAs coding for some mammalian mitochondrial AspRSs. Interestingly, the spliced transcripts alternately lack one of the four exons that code for the bacterial insertion domain. Although we showed that the human alternative transcript is present in all tested tissues; co-exists with the full-length form, possesses 5'- and 3'-UTRs, a poly-A tail and is bound to polysomes, we were unable to detect the corresponding protein. The relaxed selective pressure combined with the occurrence of alternative splicing, involving a single structural sub-domain, favors the hypothesis of the loss of function of this domain for AspRSs of mitochondrial location. This evolutionary divergence is in line with other characteristics, established for the human mt-AspRS, that indicate a functional relaxation of non-viridiplantae mt-AspRSs when compared to bacterial and plant ones, despite their common ancestry.}, }
@article {pmid24120448, year = {2014}, author = {Reijnen, BT and McFadden, CS and Hermanlimianto, YT and van Ofwegen, LP}, title = {A molecular and morphological exploration of the generic boundaries in the family Melithaeidae (Coelenterata: Octocorallia) and its taxonomic consequences.}, journal = {Molecular phylogenetics and evolution}, volume = {70}, number = {}, pages = {383-401}, doi = {10.1016/j.ympev.2013.09.028}, pmid = {24120448}, issn = {1095-9513}, mesh = {Animals ; Anthozoa/anatomy &amp; histology/classification/*genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Evolution, Molecular ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The validity of the currently recognized melithaeid genera (Acabaria, Clathraria, Melithaea, Mopsella, Wrightella) with the exception of the recently added genus Asperaxis, has puzzled scientists for almost a century. Diagnostic morphological characters are often missing or are obscured by the variation in sclerite forms. Consequently, species are difficult to assign to genera. In this study the current genera and their taxonomic positions are reviewed and reassessed based on material collected from the Indo-Pacific, Red Sea and Indian Ocean as far south as South Africa. Molecular data were obtained for four different loci, both mitochondrial (COI, mtMutS, ND6) and nuclear (28S rDNA). Combining the molecular and morphological data revealed that all former genera, except for the monotypic genus Asperaxis and the genus Wrightella are paraphyletic. Molecular data for the two subfamilies (Asperaxinae and Melithaeinae) within the Melithaeidae, in comparison with the outgroup, indicated that the family is also paraphyletic. Furthermore we observed that species did not cluster according to their present morphological classification but instead clustered according to a biogeographical pattern. Species from the Red Sea, Indian Ocean and Central Pacific, respectively, grouped into well supported clades. Consequently, we did not find morphological- or phylogenetic support to maintain the generic names Acabaria, Clathraria, Mopsella and Wrightella. Therefore these names are synonymised with the oldest available generic name, Melithaea. As a result, five secondary homonyms originated; these junior homonyms are herein renamed, viz. Melithaea hendersoni nom. nov, Melithaea mcqueeni nom. nov., Melithaea shanni nom. nov., Melithaea thorpeae nom. nov., and Melithaea wrighti nom. nov. Additionally, neotypes are selected for Melithaea ochracea to stabilize the genus Melithaea, and for Acabaria rubra.}, }
@article {pmid24117191, year = {2015}, author = {Li, D and Song, S and Chen, T and Zhang, C and Chang, C}, title = {Complete mitochondrial genome of the desert toad-headed agama, Phrynocephalus przewalskii (Reptilia, Squamata, Agamidae), a novel gene organization in vertebrate mtDNA.}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {696-697}, doi = {10.3109/19401736.2013.843079}, pmid = {24117191}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; DNA, Mitochondrial/analysis ; Gene Order ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Reptiles/*genetics ; Sequence Analysis, DNA ; }, abstract = {The mitogenome of the desert toad-headed agama, Phrynocephalus przewalskii, was amplified using polymerase chain reaction (PCR), long-and-accurate PCR and directly sequenced by primer walking. The complete mitogenome was 16,892 bp in size and contained 13 protein-coding, 23 tRNA, and 2 rRNA genes, and 1 control region. The mitogenome of the P. przewalskii was similar to those of other Phrynocephalus sand lizards in gene arrangement and composition, except that tRNA-Phe and tRNA-Pro were exchanged and tRNA-Phe had two copies. The control region comprised three parts, one between tRNA-Thr and tRNA-Phe, a second between the two tRNA-Phe copies, and a third between tRNA-Pro and 12S RNA. The overall nucleotide composition of the H-strand was 36.3% A, 26.7% T, 12.5% G, 24.6% C. The complete mitogenome of P. przewalskii will contribute to understanding the evolution of the genus Phrynocephalus and the family Agamidae.}, }
@article {pmid24117105, year = {2014}, author = {Roy, MJ and Vom, A and Czabotar, PE and Lessene, G}, title = {Cell death and the mitochondria: therapeutic targeting of the BCL-2 family-driven pathway.}, journal = {British journal of pharmacology}, volume = {171}, number = {8}, pages = {1973-1987}, pmid = {24117105}, issn = {1476-5381}, mesh = {Cell Death/*drug effects/*physiology ; Drug Discovery/methods ; Humans ; Models, Biological ; Molecular Targeted Therapy/*methods ; Peptides/*pharmacology ; Protein Structure, Tertiary ; Proto-Oncogene Proteins c-bcl-2/antagonists &amp; inhibitors/*drug effects/*physiology ; Signal Transduction/drug effects ; Sulfonamides/pharmacology ; }, abstract = {The principal biological role of mitochondria is to supply energy to cells; although intriguingly, evolution has bestowed another essential function upon these cellular organelles: under physiological stress, mitochondria become the cornerstone of apoptotic cell death. Specifically, mitochondrial outer membrane permeabilization (MOMP) allows cell death factors such as cytochrome c to be released into the cytoplasm, thus inducing caspase activation and the eventual destruction of essential cellular components. Proteins of the B-cell lymphoma 2 (BCL-2) family control the tightly regulated pathway that causes MOMP. The equilibrium between pro-survival and pro-apoptotic members of the BCL-2 family dictates the fate of cells, the homeostasis of organs and, by extension, the health of whole organisms. Dysregulation of this equilibrium is involved in a large number of diseases such as cancer, autoimmunity and neurodegenerative conditions. Modulating the activity of the BCL-2 family of proteins with small molecules or peptides is an attractive but challenging therapeutic goal. This review highlights the latest developments in this field and provides evidence that this strategy is likely to have a positive effect on the treatment of still poorly addressed medical conditions.}, }
@article {pmid24114701, year = {2013}, author = {Wilson, DF}, title = {Regulation of cellular metabolism: programming and maintaining metabolic homeostasis.}, journal = {Journal of applied physiology (Bethesda, Md. : 1985)}, volume = {115}, number = {11}, pages = {1583-1588}, doi = {10.1152/japplphysiol.00894.2013}, pmid = {24114701}, issn = {1522-1601}, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Cells/*metabolism ; *Energy Metabolism ; Homeostasis ; Humans ; Metabolic Networks and Pathways ; Mitochondria/metabolism ; *Oxidative Phosphorylation ; }, abstract = {Mitochondrial oxidative phosphorylation is programmed to set and maintain metabolic homeostasis. This is accomplished through an intrinsic program that determines the metabolic [ATP]/[ADP]/[Pi], where [Pi] is the concentration of inorganic phosphate (energy state) and maintains it through a bidirectional sensory/signaling control network that reaches every aspect of cellular metabolism. The program sets the energy state with high precision (to better than one part in 10(9)) and can respond to transient changes in energy demand (ATP use) to more than 100 times the resting rate. Epigenetic and environmental factors are able to "fine tune" the programmed set point over a narrow range to meet the special needs associated with cell differentiation and chronic changes in metabolic requirements. The result is robust, across platform control of metabolism, essential to cellular differentiation and the evolution of complex organisms.}, }
@article {pmid24109983, year = {2013}, author = {Zhang, S and Han, J and Zhong, D and Wang, T}, title = {Analysis of selective constraints on mitochondrial DNA, flight ability and physiological index on avian.}, journal = {Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference}, volume = {2013}, number = {}, pages = {1498-1501}, doi = {10.1109/EMBC.2013.6609796}, pmid = {24109983}, issn = {2694-0604}, mesh = {Animal Migration ; Animals ; Birds/*genetics/*physiology ; DNA, Mitochondrial/*genetics ; Flight, Animal/*physiology ; Imaging, Three-Dimensional ; Locomotion ; Open Reading Frames/genetics ; Phylogeny ; Wings, Animal/physiology ; }, abstract = {For most of the birds in the word, they can be divided into two main groups, i.e. resident birds and migratory ones. Most of the energy required for long-distance migration is supplied by mitochondria via oxidative phosphorylation. Therefore, the evolutionary constraints acted on the mitochondria DNA (mtDNA) are considered to vary with the locomotive abilities and flight speed. The flight speed is assumed to increase with mass and wing loading according to the fundamental aerodynamic theories, which is common between aves and aircrafts. We compared 148 avian mitochondrial genomes and main physiological parameters. More nonsynonymous nucleotide substitutions than synonymous ones are accumulated in low-speed and flightless birds rather than high-speed flying birds. No matter how the speed is obtained, directly measured or estimated through physiological index. Our results demonstrated that, besides artificial and environmental factors, selective constraints relevant to flight ability play an essential role in the evolution of mtDNA, even it might cause the extinction of avian species.}, }
@article {pmid24108366, year = {2013}, author = {Mikami, E and Fuku, N and Kong, QP and Takahashi, H and Ohiwa, N and Murakami, H and Miyachi, M and Higuchi, M and Tanaka, M and Pitsiladis, YP and Kawahara, T}, title = {Comprehensive analysis of common and rare mitochondrial DNA variants in elite Japanese athletes: a case-control study.}, journal = {Journal of human genetics}, volume = {58}, number = {12}, pages = {780-787}, doi = {10.1038/jhg.2013.102}, pmid = {24108366}, issn = {1435-232X}, mesh = {Asian People/*genetics ; Athletes ; Athletic Performance/*physiology ; Case-Control Studies ; DNA, Mitochondrial/*genetics ; Female ; Genetic Variation/*genetics ; Haplotypes/genetics ; Humans ; Male ; Mitochondria/*genetics ; Polymorphism, Genetic ; }, abstract = {The purpose of the present study was to identify mitochondrial DNA (mtDNA) polymorphisms and rare variants that associate with elite Japanese athletic status. Subjects comprised 185 elite Japanese athletes who had represented Japan at international competitions (that is, 100 endurance/middle-power athletes: EMA; 85 sprint/power athletes: SPA) and 672 Japanese controls (CON). The entire mtDNA sequences (16 569 bp) were analyzed by direct sequencing. Nucleotide variants were detected at 1488 sites in the 857 entire mtDNA sequences. A total of 311 variants were polymorphisms (minor allele frequency 1% in CON), and the frequencies of these polymorphisms were compared among the three groups. The EMA displayed excess of seven polymorphisms, including subhaplogroup D4e2- and D4g-specific polymorphisms, compared with CON (P<0.05), whereas SPA displayed excess of three polymorphisms and dearth of nine polymorphisms, including haplogroup G- and subhaplogroup G2a-specific polymorphisms, compared with CON (P<0.05). The frequencies of 10 polymorphisms, including haplogroup G- and subhaplogroup G2a-specific polymorphisms, were different between EMA and SPA (P<0.05): although none of these polymorphisms differed significantly between groups after correcting for multiple comparison (false discovery rate q-value 0.05). The number of rare variants in the 12S ribosomal RNA and NADH dehydrogenase subunit I genes were also higher in SPA than in CON (P<0.05). Analysis of the entire mtDNA of elite Japanese athletes revealed several haplogroup- and subhaplogroup-specific polymorphisms to be potentially associated with elite Japanese athletic status.}, }
@article {pmid24108212, year = {2013}, author = {Uhrig, RG and Kerk, D and Moorhead, GB}, title = {Evolution of bacterial-like phosphoprotein phosphatases in photosynthetic eukaryotes features ancestral mitochondrial or archaeal origin and possible lateral gene transfer.}, journal = {Plant physiology}, volume = {163}, number = {4}, pages = {1829-1843}, pmid = {24108212}, issn = {1532-2548}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Archaea/*metabolism ; Bacteria/*enzymology ; Eukaryota/*enzymology ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phosphoprotein Phosphatases/chemistry/*genetics ; Photosynthesis ; *Phylogeny ; Protein Transport ; Subcellular Fractions/enzymology ; }, abstract = {Protein phosphorylation is a reversible regulatory process catalyzed by the opposing reactions of protein kinases and phosphatases, which are central to the proper functioning of the cell. Dysfunction of members in either the protein kinase or phosphatase family can have wide-ranging deleterious effects in both metazoans and plants alike. Previously, three bacterial-like phosphoprotein phosphatase classes were uncovered in eukaryotes and named according to the bacterial sequences with which they have the greatest similarity: Shewanella-like (SLP), Rhizobiales-like (RLPH), and ApaH-like (ALPH) phosphatases. Utilizing the wealth of data resulting from recently sequenced complete eukaryotic genomes, we conducted database searching by hidden Markov models, multiple sequence alignment, and phylogenetic tree inference with Bayesian and maximum likelihood methods to elucidate the pattern of evolution of eukaryotic bacterial-like phosphoprotein phosphatase sequences, which are predominantly distributed in photosynthetic eukaryotes. We uncovered a pattern of ancestral mitochondrial (SLP and RLPH) or archaeal (ALPH) gene entry into eukaryotes, supplemented by possible instances of lateral gene transfer between bacteria and eukaryotes. In addition to the previously known green algal and plant SLP1 and SLP2 protein forms, a more ancestral third form (SLP3) was found in green algae. Data from in silico subcellular localization predictions revealed class-specific differences in plants likely to result in distinct functions, and for SLP sequences, distinctive and possibly functionally significant differences between plants and nonphotosynthetic eukaryotes. Conserved carboxyl-terminal sequence motifs with class-specific patterns of residue substitutions, most prominent in photosynthetic organisms, raise the possibility of complex interactions with regulatory proteins.}, }
@article {pmid24105984, year = {2013}, author = {Nomura, S and Umeda, T and Tomiyama, T and Mori, H}, title = {The E693Δ (Osaka) mutation in amyloid precursor protein potentiates cholesterol-mediated intracellular amyloid β toxicity via its impaired cholesterol efflux.}, journal = {Journal of neuroscience research}, volume = {91}, number = {12}, pages = {1541-1550}, doi = {10.1002/jnr.23278}, pmid = {24105984}, issn = {1097-4547}, mesh = {Alzheimer Disease/genetics/metabolism ; Amyloid beta-Peptides/*metabolism ; Amyloid beta-Protein Precursor/*genetics ; Cholesterol/*metabolism ; HEK293 Cells ; Humans ; Immunohistochemistry ; Intracellular Space/metabolism ; *Mutation ; Protein Transport/*genetics ; Transfection ; }, abstract = {It has been shown that amyloid β (Aβ) secretion regulates cholesterol efflux from cells and that the E693Δ (Osaka) mutation in amyloid precursor protein (APP) promotes intracellular accumulation of Aβ and thus reduces its secretion. These findings led us to speculate that APP with the Osaka mutation (APPOSK) might have a defect in cholesterol efflux and thus cause cellular malfunction. We therefore examined the effects of this mutation on intracellular cholesterol transport and efflux in cultured cells. Upon cholesterol loading, APPOSK -expressing cells exhibited higher levels of cellular cholesterol than wild-type APP-expressing cells, suggesting impaired cholesterol efflux. It is known that, after its internalization, cholesterol is transported from the endosomes to the endoplasmic reticulum (ER) and Golgi apparatus and then to the plasma membrane. In APPOSK -expressing cells, cholesterol accumulated with Aβ in the ER and Golgi apparatus and alone in endosomes/lysosomes. These results imply that the mutation-induced disturbance of Aβ trafficking from the ER to the plasma membrane affects cholesterol transport to cause cholesterol accumulation in the ER and Golgi apparatus and, consequently, in endosomes. Furthermore, we detected an enhanced mitochondrial accumulation of Aβ and cholesterol in APPOSK -expressing cells, and this was accompanied by an increase in the generation of reactive oxygen species (ROS). The present findings suggest that Aβ trafficking is important for intracellular cholesterol transport and efflux and that the Osaka mutation potentiates cholesterol-dependent exacerbation of intracellular Aβ toxicity, i.e. Aβ-induced ROS generation, by disturbing Aβ-mediated cholesterol efflux from the cell.}, }
@article {pmid24103336, year = {2013}, author = {Latrofa, MS and Dantas-Torres, F and Annoscia, G and Cantacessi, C and Otranto, D}, title = {Comparative analyses of mitochondrial and nuclear genetic markers for the molecular identification of Rhipicephalus spp.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {20}, number = {}, pages = {422-427}, doi = {10.1016/j.meegid.2013.09.027}, pmid = {24103336}, issn = {1567-7257}, mesh = {Animals ; Arthropod Vectors/classification/genetics ; Base Sequence ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Markers ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Rhipicephalus/*classification/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The genus Rhipicephalus (Acari: Ixodidae) comprises a large number of vectors of pathogens of substantial medical and veterinary concern; however, species identification based solely on morphological features is often challenging. In the present study, genetic distance within selected Rhipicephalus species (i.e., Rhipicephalus bursa, Rhipicephalus guilhoni, Rhipicephalus muhsamae, Rhipicephalus sanguineus sensu lato and Rhipicephalus turanicus), were investigated based on molecular and phylogenetic analyses of fragments of the mitochondrial 16S, 12S and cytochrome c oxidase subunit 1 (cox1) genes, as well as of the whole sequences of the ribosomal internal transcribed spacer-2 (ITS-2) region. Mean values of inter-specific genetic distance (e.g., up to 12.6%, 11.1% and 15.2%), as well as of intra-specific genetic distance (e.g., 0.9%, 0.9% and 1%), calculated using the Kimura-2 parameter substitution model with uniform rates among sites for 16S, 12S and cox1 genes, respectively, confirmed the differentiation of the rhipicephaline species herein examined. The molecular identification was also supported by the distinct separation of species-specific clades inferred from the phylogenetic analyses of all mitochondrial sequences. Conversely, little interspecific divergence was detected amongst ribosomal ITS-2 sequences (i.e., up to 2.8%) for species belonging to the R. sanguineus complex, which resulted in the ambiguous placement of selected R. sanguineus s.l. and R. turanicus sequences in the corresponding phylogenetic tree. Results from this study confirm the suitability of mtDNA markers for the reliable identification of ticks within the Rhipicephalus genus and provide a framework for future studies of taxonomy, speciation history and evolution of this group of ticks.}, }
@article {pmid24102609, year = {2015}, author = {Mohindra, V and Singh, RK and Kumar, R and Sah, RS and Lal, KK}, title = {Complete mitochondrial genome sequences of two endangered Indian catfish species, Clarias batrachus and Pangasius pangasius.}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {678-679}, doi = {10.3109/19401736.2013.840604}, pmid = {24102609}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Catfishes/*classification/*genetics ; Endangered Species ; Gene Order ; *Genome, Mitochondrial ; India ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Complete mitogenome sequences for Clarias batrachus (magur) and Pangasius pangasius (family Claridae and Pangasiidae, respectively) were generated, which were 16,511 and 16,476 bp, respectively. Both the mitogenomes contained 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs and 1 non-coding (control) region. The order of the genes was identical to that observed in most other vertebrates. The genome resource of complete mitogenome sequence of Indian catfish species generated during this study would be useful in phylogenetic studies.}, }
@article {pmid24102605, year = {2015}, author = {Chiang, TY and Chen, IS and Lin, HD and Hsiao, ST and Ju, YM}, title = {Complete mitochondrial genome of the amphidromous, red-tailed goby Sicyopterus lagocephalus (Pallas) (Teleostei, Gobiidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {670-671}, doi = {10.3109/19401736.2013.840600}, pmid = {24102605}, issn = {1940-1744}, mesh = {Animals ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {In this article, the complete mitogenome of the amphidromous, red-tailed goby, Sicyopterus lagocephalus has been amplified and sequenced by long polymerase chain reaction. This mitochondrial genome consists of 16,500 bp, with 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a non-coding control region (CR), and its gene arrangement is identical to those of most vertebrates. The CR (841 bp) is located between tRNA(Pro) and tRNA(Phe). The overall base composition of the heavy strand is A, 28.9%; G, 16.4%; C, 28.3%; and T, 26.4%, with a slight AT bias of 55.3%. The complete mitogenomic data may provide more informative for phylogenetic approach for gobioid phylogeny especially for Sicydiine gobies.}, }
@article {pmid24102604, year = {2015}, author = {Shin, HW and Jang, KH and Ryu, SH and Choi, EH and Hwang, UW}, title = {Complete mitochondrial genome of the Korean reeves's turtle Mauremys reevesii (Reptilia, Testudines, Geoemydidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {676-677}, doi = {10.3109/19401736.2013.840603}, pmid = {24102604}, issn = {1940-1744}, mesh = {Animals ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Sequence Analysis, DNA ; Turtles/*genetics ; }, abstract = {The mitochondrial genome of Korean reeves's turtle Mauremys reevesii (Reptilia, Testudines, Geoemydidae) was studied. The complete mitochondrial genome sequence of M. reevesii was 16,784 bp in length and its gene arrangement pattern, gene content and gene organization is identical to those of geoemydids. The control region (CR) was located between the tRNA(Pro) and tRNA(Phe) genes and is 1253 bp in length. The typical conserved domains such as TAS and CSB-F, and CSB1, CSB2 and CSB3 were identified in the CR of geoemydids.}, }
@article {pmid24102603, year = {2015}, author = {Li, H and Gao, J and Cai, W}, title = {Complete mitochondrial genome of the assassin bug Oncocephalus breviscutum (Hemiptera: Reduviidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {674-675}, doi = {10.3109/19401736.2013.840602}, pmid = {24102603}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; Reduviidae/*genetics ; }, abstract = {The mitochondrial genome of an assassin bug, Oncocephalus breviscutum Reuter, is a typical circular DNA molecule of 15,984 bp with 37 genes and a large control region. The gene order is identical to that of the putative ancestral arrangement of insects. Twelve protein-coding genes start with ATN codon and ND4L uses GTG. All of the 22 tRNAs, ranging from 61 to 70 bp, have the clover-leaf structure except for the dihydrouridine (DHU) arm of trnS2 forms a simple loop. The control region is 1345 bp in length and includes six tandem repeats of three 31-nt and three 145-nt units.}, }
@article {pmid24102602, year = {2015}, author = {Wang, K and Hao, J and Zhao, H}, title = {Characterization of complete mitochondrial genome of the skipper butterfly, Celaenorrhinus maculosus (Lepidoptera: Hesperiidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {690-691}, doi = {10.3109/19401736.2013.840610}, pmid = {24102602}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Butterflies/*genetics ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {The skipper butterfly, Celaenorrhinus maculosus (Lepidoptera: Hesperiidae), is a small butterfly species that is widely distributed in Taiwan and mainland China. In this work, we sequenced and characterized the complete mitochondrial genome of the butterfly. The circular genome of 15,282 bp in length contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a non-coding AT-rich region. Overall base composition of the complete mt genome was 33.97% A, 39.90% T, 12.38% C and 7.75% G, with an AT bias of 79.87%. All protein-coding genes start with an ATN codon, and terminate with the typical stop codon TAA or a single T. The non-coding AT-rich region is 331 bp in length, including a 18 bp poly-T stretch and a microsatellite-like (TA)7 element. The genome sequence is useful for future studies of phylogenetics, molecular evolution, conservation genetics and agricultural control.}, }
@article {pmid24102595, year = {2015}, author = {Sun, Y and Wei, T and Jin, X}, title = {Unusual features of control region and a novel NADH 6 genes in mitochondrial genome of the finespot goby, Chaeturichthys stigmatias (Perciformes, Gobiidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {5}, pages = {665-667}, doi = {10.3109/19401736.2013.840598}, pmid = {24102595}, issn = {1940-1744}, mesh = {Animals ; Fish Proteins/genetics ; Gene Order ; Genome, Mitochondrial ; Mitochondria/*enzymology/genetics ; NADH Dehydrogenase/*genetics ; Perciformes/*genetics ; }, abstract = {In this article, we determined the complete mitogenome of finespot goby Chaeturichthys stigmatias with emphasis on the arranged gene order and gene feature with published Gobiidae species. The C. stigmatias mtDNA was 18,562 bp in length (56.94% AT), and comprised 37 genes (13 protein genes, 2 rRNAs and 22 tRNAs) that was typical for mitochondrial genome of Gobiidae species. Unusually, the NADH 6 gene was very large in length compared with other Gobiidae species. Mitogenome of C. stigmatias had a long putative control region with high AT content (71.28%). Within this sequence, we determined repeat regions, the termination-associated sequence and the conserved sequence block for this region. The origin of L-strand replication in C. stigmatias was located in a cluster of five tRNA genes (WANCY). The conserved motif (5'-GCCGG-3') was also determined at the base of the stem in the tRNA-Cys gene. This study will provide a better understanding of Gobiidae mitogenomes and offer useful information for future studies concerning Gobiidae mitogenome evolution.}, }
@article {pmid24102562, year = {2014}, author = {Toews, DP and Mandic, M and Richards, JG and Irwin, DE}, title = {Migration, mitochondria, and the yellow-rumped warbler.}, journal = {Evolution; international journal of organic evolution}, volume = {68}, number = {1}, pages = {241-255}, doi = {10.1111/evo.12260}, pmid = {24102562}, issn = {1558-5646}, mesh = {*Animal Migration ; Animals ; Cell Respiration ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genetic Speciation ; *Genetic Variation ; Mitochondria/*genetics/metabolism ; Songbirds/*genetics ; }, abstract = {Discordance between mitochondrial and nuclear DNA has been noted in many systems. Asymmetric introgression of mitochondria is a common cause of such discordances, although in most cases the drivers of introgression are unknown. In the yellow-rumped warbler, evidence suggests that mtDNA from the eastern, myrtle warbler, has introgressed across much of the range of the western form, the Audubon's warbler. Within the southwestern United States myrtle mtDNA comes into contact with another clade that occurs in the Mexican black-fronted warbler. Both northern forms exhibit seasonal migration, whereas black-fronted warblers are nonmigratory. We investigated the link between mitochondrial introgression, mitochondrial function, and migration using novel genetic, isotopic, biochemical, and phenotypic data obtained from populations in the transition zone. Isotopes suggest the zone is coincident with a shift in migration, with individuals in the south being resident and populations further north becoming increasingly more migratory. Mitochondrial respiration in flight muscles demonstrates that myrtle-type individuals have a significantly greater acceptor control ratio of mitochondria, suggesting it may be more metabolically efficient. To our knowledge this is the first time this type of intraspecific variation in mitochondrial respiration has been measured in wild birds and we discuss how such mitochondrial adaptations may have facilitated introgression.}, }
@article {pmid24101722, year = {2013}, author = {André, J and Harrison, S and Towers, K and Qi, X and Vaughan, S and McKean, PG and Ginger, ML}, title = {The tubulin cofactor C family member TBCCD1 orchestrates cytoskeletal filament formation.}, journal = {Journal of cell science}, volume = {126}, number = {Pt 23}, pages = {5350-5356}, doi = {10.1242/jcs.136515}, pmid = {24101722}, issn = {1477-9137}, support = {BBG0210581/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/G021058/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/1000402/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBF0109311/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F010931/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Centrioles/metabolism/ultrastructure ; Chlamydomonas reinhardtii/genetics/metabolism ; *Cytoskeleton/metabolism/ultrastructure ; Evolution, Molecular ; Golgi Apparatus/metabolism/ultrastructure ; Humans ; Mitochondria/metabolism/ultrastructure ; Molecular Chaperones/genetics/*metabolism ; Protozoan Proteins/genetics/*metabolism ; Trypanosoma brucei brucei/genetics/*metabolism/ultrastructure ; }, abstract = {TBCCD1 is an enigmatic member of the tubulin-binding cofactor C (TBCC) family of proteins required for mother-daughter centriole linkage in the green alga Chlamydomonas reinhardtii and nucleus-centrosome-Golgi linkage in mammalian cells. Loss of these linkages has severe morphogenetic consequences, but the mechanism(s) through which TBCCD1 contributes to cell organisation is unknown. In the African sleeping sickness parasite Trypanosoma brucei a microtubule-dominant cytoskeleton dictates cell shape, influencing strongly the positioning and inheritance patterns of key intracellular organelles. Here, we show the trypanosome orthologue of TBCCD1 is found at multiple locations: centrioles, the centriole-associated Golgi 'bi-lobe', and the anterior end of the cell body. Loss of Trypanosoma brucei TBCCD1 results in disorganisation of the structurally complex bi-lobe architecture and loss of centriole linkage to the single unit-copy mitochondrial genome (or kinetoplast) of the parasite. We therefore identify TBCCD1 as an essential protein associated with at least two filament-based structures in the trypanosome cytoskeleton. The last common ancestor of trypanosomes, animals and green algae was arguably the last common ancestor of all eukaryotes. On the basis of our observations, and interpretation of published data, we argue for an unexpected co-option of the TBCC domain for an essential non-tubulin-related function at an early point during evolution of the eukaryotic cytoskeleton.}, }
@article {pmid24098763, year = {2013}, author = {Hou, CC and Yang, WX}, title = {Acroframosome-dependent KIFC1 facilitates acrosome formation during spermatogenesis in the caridean shrimp Exopalaemon modestus.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e76065}, pmid = {24098763}, issn = {1932-6203}, mesh = {Acrosome/*physiology ; Animals ; Base Sequence ; Blotting, Western ; Cell Movement/physiology ; China ; Cloning, Molecular ; Cluster Analysis ; Computational Biology ; DNA Primers/genetics ; DNA, Complementary/genetics ; Fluorescent Antibody Technique ; In Situ Hybridization ; Kinesins/genetics/*metabolism ; Male ; Microscopy, Electron, Transmission ; Microtubules/metabolism/*physiology ; Molecular Sequence Data ; Palaemonidae/genetics/*physiology ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Spermatogenesis/*physiology ; }, abstract = {BACKGROUND: Acrosome formation and nuclear shaping are the main events in spermatogenesis. During spermiogenesis in Exopalaemon modestus, a unique microtubular structure called the acroframosome (AFS) forms in spermatids. The AFS links to a temporary organelle called the lamellar complex (LCx) leading to the formation of an everted umbrella-shaped acrosome and a dish-shaped nucleus in the mature sperm. These morphological changes require complex cell motility in which the C-terminal kinesin motor protein called KIFC1 is involved. In this study, we demonstrate that KIFC1 moves along the AFS and plays an important role in acrosome formation and nuclear shaping during spermatogenesis in E. modestus.<br><br>We cloned a 3125 bp complete cDNA of kifc1 from the testis of E. modestus by PCR. The predicted secondary and tertiary structures of E. modestus KIFC1 contain three domains: a) the C-terminus, b) the stalk region, and the c) N-terminusl. Semi-quantitative RT-PCR detected the expression of kifc1 mRNA in different tissues of E. modestus. In situ hybridization demonstrated the temporal and spatial expression profile of kifc1 during spermiogenesis. Western blot identified the expression of KIFC1 in different tissues of E. modestus, including the testis. Immunofluorescence localized KIFC1, tubulin, GM130, and mitochondria in order to elucidate their role during spermiogenesis in E. modestus.<br><br>CONCLUSION/SIGNIFICANCE: Our results indicate that KIFC1 transports the Golgi complex, mitochondria, and other cellular components that results in acrosome formation and nuclear shaping in E. modestus. The KIFC1 transport function depends upon the microtubular structure called the acroframosome (AFS). This study describes some of the molecular mechanisms involved in the acrosome formation and nuclear shaping in E. modestus. In addition, this study may provide a model for studying the molecular mechanisms involved in spermatogenesis in other crustacean species and lead to a better understanding of the fertilization process in crustaceans.}, }
@article {pmid24096889, year = {2013}, author = {Ubaidillah, M and Kim, KA and Kim, YH and Lee, IJ and Yun, BW and Kim, DH and Loake, GJ and Kim, KM}, title = {Identification of a drought-induced rice gene, OsSAP, that suppresses Bax-induced cell death in yeast.}, journal = {Molecular biology reports}, volume = {40}, number = {11}, pages = {6113-6121}, pmid = {24096889}, issn = {1573-4978}, support = {BB/H000984/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Apoptosis/genetics ; Base Sequence ; Biomass ; Cellular Senescence/genetics ; *Droughts ; Gene Expression ; Gene Expression Profiling ; *Genes, Plant ; Molecular Sequence Data ; Oryza/chemistry/*genetics ; Phylogeny ; Stress, Physiological/*genetics ; Water/chemistry ; Yeasts/*genetics/metabolism ; bcl-2-Associated X Protein/*genetics/metabolism ; }, abstract = {We identified rice genes that might be involved in drought stress tolerance by virtue of their anti-apoptotic activity. Potential anti-apoptosis related genes were identified by screening an Oryza sativa cDNA library derived from drought stressed tissues in a yeast functional assay. About 28 O. sativa cDNAs promoted yeast survival following engagement of Bax-induced apoptosis. An O. sativa cDNA encoding R12H780 was a highly conserved putative senescence-associated-protein (OsSAP). OsSAP was both highly and rapidly expressed in response to drought stress. Additionally, OsSAP was found to be localized to the mitochondria. Overall, OsSAP represents a new type of Bax suppressor related gene and endows multiple stress tolerance in yeast.}, }
@article {pmid24096056, year = {2014}, author = {Schönhuth, S and Perdices, A and Lozano-Vilano, L and García-de-León, FJ and Espinosa, H and Mayden, RL}, title = {Phylogenetic relationships of North American western chubs of the genus Gila (Cyprinidae, Teleostei), with emphasis on southern species.}, journal = {Molecular phylogenetics and evolution}, volume = {70}, number = {}, pages = {210-230}, doi = {10.1016/j.ympev.2013.09.021}, pmid = {24096056}, issn = {1095-9513}, mesh = {Animals ; Cyprinidae/classification/*genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Hybridization, Genetic ; Mexico ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Southwestern United States ; }, abstract = {Species of Gila comprise a heterogeneous and widespread group of freshwater fishes inhabiting drainage systems of western North America. The classification of species of Gila and relatives has been complicated and sometimes compromised by differences in body shapes, sizes, habitats, variable taxonomic placement by early taxonomists, and instances of hypothesized hybridization. While most attention on Gila has focused on hybridization in USA, little is actually know about their intra and intergeneric relationships. We present a molecular phylogeny using 173 specimens for all 19 recognized species of Gila, covering their entire distributions in 31 major drainages. Using one mitochondrial and three nuclear genes, specimens of Gila were analyzed with 10 other North American genera that comprise the Revised Western Clade. All analyses identified most species of Gila in a lineage that always included the monotypic genera Moapa and Acrocheilus, and we recommend the synonymy of both genera with Gila. The composition of this Gila lineage varied depending on the genes analyzed. Within the Gila lineage, similar morphotypes (forms adapted to fast currents vs. general forms) were not resolved as closest relatives. Analyses of mitochondrial DNA resolved all species of Gila from Mexico in reciprocally monophyletic clades except G. modesta. Most species of Gila in the USA were nested in 3 major clades, potentially indicating some level of historic or contemporary interspecific hybridization. Herein, we redefine the ranges for all species of Gila in Mexico. Relevant taxonomic and conservation implications stemming from the results are discussed.}, }
@article {pmid24086244, year = {2013}, author = {Leger, MM and Gawryluk, RM and Gray, MW and Roger, AJ}, title = {Evidence for a hydrogenosomal-type anaerobic ATP generation pathway in Acanthamoeba castellanii.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e69532}, pmid = {24086244}, issn = {1932-6203}, support = {U54 HG002051/HG/NHGRI NIH HHS/United States ; MOP-62809/CAPMC/CIHR/Canada ; MOP-4124/CAPMC/CIHR/Canada ; U01 HG02051/HG/NHGRI NIH HHS/United States ; }, mesh = {Acanthamoeba castellanii/enzymology/genetics/*metabolism ; Adenosine Triphosphate/*biosynthesis ; Amino Acid Sequence ; Anaerobiosis ; Electron Transport ; Enzymes/chemistry/metabolism ; Expressed Sequence Tags ; Genome, Protozoan ; Hydrogen/*metabolism ; Molecular Sequence Data ; Phylogeny ; Tandem Mass Spectrometry ; }, abstract = {Diverse, distantly-related eukaryotic lineages have adapted to low-oxygen environments, and possess mitochondrion-related organelles that have lost the capacity to generate adenosine triphosphate (ATP) through oxidative phosphorylation. A subset of these organelles, hydrogenosomes, has acquired a set of characteristic ATP generation enzymes commonly found in anaerobic bacteria. The recipient of these enzymes could not have survived prior to their acquisition had it not still possessed the electron transport chain present in the ancestral mitochondrion. In the divergence of modern hydrogenosomes from mitochondria, a transitional organelle must therefore have existed that possessed both an electron transport chain and an anaerobic ATP generation pathway. Here, we report a modern analog of this organelle in the habitually aerobic opportunistic pathogen, Acanthamoeba castellanii. This organism possesses a complete set of enzymes comprising a hydrogenosome-like ATP generation pathway, each of which is predicted to be targeted to mitochondria. We have experimentally confirmed the mitochondrial localizations of key components of this pathway using tandem mass spectrometry. This evidence is the first supported by localization and proteome data of a mitochondrion possessing both an electron transport chain and hydrogenosome-like energy metabolism enzymes. Our work provides insight into the first steps that might have occurred in the course of the emergence of modern hydrogenosomes.}, }
@article {pmid24084698, year = {2013}, author = {Morelli, AM and Ravera, S and Calzia, D and Panfoli, I}, title = {Hypothesis of lipid-phase-continuity proton transfer for aerobic ATP synthesis.}, journal = {Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism}, volume = {33}, number = {12}, pages = {1838-1842}, pmid = {24084698}, issn = {1559-7016}, mesh = {Adenosine Triphosphate/*metabolism ; Animals ; Cardiolipins/metabolism ; Humans ; Membrane Lipids/*metabolism ; Oxidative Phosphorylation ; Proton-Translocating ATPases/*metabolism ; Protons ; }, abstract = {The basic processes harvesting chemical energy for life are driven by proton (H(+)) movements. These are accomplished by the mitochondrial redox complex V, integral membrane supramolecular aggregates, whose structure has recently been described by advanced studies. These did not identify classical aqueous pores. It was proposed that H(+) transfer for oxidative phosphorylation (OXPHOS) does not occur between aqueous sources and sinks, where an energy barrier would be insurmountable. This suggests a novel hypothesis for the proton transfer. A lipid-phase-continuity H(+) transfer is proposed in which H(+) are always bound to phospholipid heads and cardiolipin, according to Mitchell's hypothesis of asymmetric vectorial H(+) diffusion. A phase separation is proposed among the proton flow, following an intramembrane pathway, and the ATP synthesis, occurring in the aqueous phase. This view reminiscent of Grotthus mechanism would better account for the distance among the Fo and F1 moieties of FoF1-ATP synthase, for its mechanical coupling, as well as the necessity of a lipid membrane. A unique active role for lipids in the evolution of life can be envisaged. Interestingly, this view would also be consistent with the evidence of an OXPHOS outside mitochondria also found in non-vesicular membranes, housing the redox complexes.}, }
@article {pmid24080405, year = {2014}, author = {Murcha, MW and Wang, Y and Narsai, R and Whelan, J}, title = {The plant mitochondrial protein import apparatus - the differences make it interesting.}, journal = {Biochimica et biophysica acta}, volume = {1840}, number = {4}, pages = {1233-1245}, doi = {10.1016/j.bbagen.2013.09.026}, pmid = {24080405}, issn = {0006-3002}, mesh = {Membrane Transport Proteins/*physiology ; Mitochondria/genetics/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Plant Proteins/genetics/*metabolism ; Plants/*metabolism/ultrastructure ; Protein Transport/physiology ; Saccharomyces cerevisiae/*metabolism/ultrastructure ; Saccharomyces cerevisiae Proteins/*metabolism ; }, abstract = {BACKGROUND: Mitochondria play essential roles in the life and death of almost all eukaryotic cells, ranging from single-celled to multi-cellular organisms that display tissue and developmental differentiation. As mitochondria only arose once in evolution, much can be learned from studying single celled model systems such as yeast and applying this knowledge to other organisms. However, two billion years of evolution have also resulted in substantial divergence in mitochondrial function between eukaryotic organisms.<br><br>SCOPE OF REVIEW: Here we review our current understanding of the mechanisms of mitochondrial protein import between plants and yeast (Saccharomyces cerevisiae) and identify a high level of conservation for the essential subunits of plant mitochondrial import apparatus. Furthermore, we investigate examples whereby divergence and acquisition of functions have arisen and highlight the emerging examples of interactions between the import apparatus and components of the respiratory chain.<br><br>MAJOR CONCLUSIONS: After more than three decades of research into the components and mechanisms of mitochondrial protein import of plants and yeast, the differences between these systems are examined. Specifically, expansions of the small gene families that encode the mitochondrial protein import apparatus in plants are detailed, and their essential role in seed viability is revealed.<br><br>GENERAL SIGNIFICANCE: These findings point to the essential role of the inner mitochondrial protein translocases in Arabidopsis, establishing their necessity for seed viability and the crucial role of mitochondrial biogenesis during germination. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research.}, }
@article {pmid24080200, year = {2013}, author = {Jafari, M and Sadeghi, M and Mirzaie, M and Marashi, SA and Rezaei-Tavirani, M}, title = {Evolutionarily conserved motifs and modules in mitochondrial protein-protein interaction networks.}, journal = {Mitochondrion}, volume = {13}, number = {6}, pages = {668-675}, doi = {10.1016/j.mito.2013.09.006}, pmid = {24080200}, issn = {1872-8278}, mesh = {Algorithms ; *Biological Evolution ; *Conserved Sequence ; Mitochondrial Proteins/*metabolism ; Protein Binding ; Proteins/*metabolism ; }, abstract = {Advances in organelle interactomics have led to new insights into organelle functions. In this study, we considered the common mitochondrial PIN of four evolutionarily distant eukaryotic species, namely Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans. By comparative interactomics analysis of mitochondrial PINs in these organisms, five conserved modules were identified. Modules comprise the main mitochondrial tasks, including proteins involved in translation process, mitochondrial import inner membrane proteins, TCA cycle enzymes, mitochondrial electron transport chain, and metabolic enzymes. Furthermore, we reemphasize that subgraphs of network, i.e., motifs and themes, may represent evolutionarily conserved topological units which are biologically significant.}, }
@article {pmid24078157, year = {2013}, author = {Wu, Y and Wu, Y and Wu, Y and Tang, H and Wu, H and Zhang, G and Wang, W}, title = {Screening of candidate proteins interacting with IE-2 of Bombyx mori nucleopolyhedrovirus.}, journal = {Molecular biology reports}, volume = {40}, number = {10}, pages = {5797-5804}, pmid = {24078157}, issn = {1573-4978}, mesh = {Amino Acid Sequence ; Animals ; Bombyx/*virology ; Cell Line ; Computational Biology ; Electrophoresis, Polyacrylamide Gel ; Genes, Viral/genetics ; Mass Spectrometry ; Mitochondria/metabolism ; Molecular Sequence Data ; Multiprotein Complexes/isolation &amp; purification/metabolism ; Nucleopolyhedroviruses/*metabolism ; Phylogeny ; Protein Binding ; Protein Transport ; Viral Proteins/chemistry/*metabolism ; }, abstract = {IE-2 of Bombyx mori nucleopolyhedrovirus (BmNPV) has been shown to play important roles in baculovirus infection, which are involved in gene expression and viral replication. However, the mechanism remains unknown. In this paper, by TargetP software, four genes, i.e.-2, odv-e26, odv-e56 and BmNPV-gp101 (Ac-orf116) of BmNPV and Autographa californica multiple NPV (AcMNPV) were predicted to be located in mitochondria. By BLAST tool using BmNPV IE-2 protein sequence, 14 NPVs were found to have IE-2 homologues in GenBank, and most of them were predicted to be located in mitochondria, except for that of Antheraea pernyi NPV (AnpeNPV) and Anticarsia gemmatalis NPV (AngeNPV). To observe the subcellular localization of BmNPV IE-2, a recombinant virus overexpressed the IE-2 and eGFP fusion protein was constructed. In infected BmN cells, the fluorescence specifically enriched in the cellular mitochondria. This evidence was accordant with the prediction. Further, Pull-down assay was used to select protein candidates interacting with IE-2 in B. mori cells infected with BmNPV. Of several isolated protein components, sixteen candidates were identified by MALDI-TOF mass-spectrometry, eight baculoviral proteins (ALK-EXO, F protein, IAP-1, LEF-3, LEF-9, ODV-NC42, TLP, and VP39), and eight proteins from B. mori (Actin, ADP/ATP translocase, ATP synthase subunit beta, Beta-tubulin, DNA topoisomerase 2, Histone H4, Soluble guanylyl cyclae alpha-1 subunit, Transketolase). From the functional point of view, most of these proteins were generally divided into two groups, mitochondrial interaction proteins and viral DNA replication proteins. These results implied that the IE-2 had multiple functions involved in regulating viral gene expression, viral replication and also as a component of mitochondrial factors to regulate the cellular energy supply and apoptosis.}, }
@article {pmid24075923, year = {2013}, author = {Dunham-Snary, KJ and Ballinger, SW}, title = {Mitochondrial genetics and obesity: evolutionary adaptation and contemporary disease susceptibility.}, journal = {Free radical biology &amp; medicine}, volume = {65}, number = {}, pages = {1229-1237}, pmid = {24075923}, issn = {1873-4596}, support = {HL103859/HL/NHLBI NIH HHS/United States ; R01HL94518/HL/NHLBI NIH HHS/United States ; P30 DK079626/DK/NIDDK NIH HHS/United States ; R01 HL103859/HL/NHLBI NIH HHS/United States ; R01 HL094518/HL/NHLBI NIH HHS/United States ; }, mesh = {Adaptation, Physiological/genetics ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Genetic Predisposition to Disease ; Humans ; Inflammation/*genetics ; Mitochondria/*genetics ; Obesity/epidemiology/*genetics ; Oxidative Stress/*genetics ; }, abstract = {Obesity is a leading risk factor for a variety of metabolic diseases including cardiovascular disease, diabetes, and cancer. Although in its simplest terms, obesity may be thought of as a consequence of excessive caloric intake and sedentary lifestyle, it is also evident that individual propensity for weight gain can vary. The etiology of individual susceptibility to obesity seems to be complex-involving a combination of environmental-genetic interactions. Herein, we suggest that the mitochondrion plays a major role in influencing individual susceptibility to this disease via mitochondrial-nuclear interaction processes and that environmentally influenced selection events for mitochondrial function that conveyed increased reproductive and survival success during the global establishment of human populations during prehistoric times can influence individual susceptibility to weight gain and obesity.}, }
@article {pmid24075874, year = {2014}, author = {Gualberto, JM and Mileshina, D and Wallet, C and Niazi, AK and Weber-Lotfi, F and Dietrich, A}, title = {The plant mitochondrial genome: dynamics and maintenance.}, journal = {Biochimie}, volume = {100}, number = {}, pages = {107-120}, doi = {10.1016/j.biochi.2013.09.016}, pmid = {24075874}, issn = {1638-6183}, mesh = {DNA Repair ; DNA Replication ; DNA, Mitochondrial/chemistry/*genetics/metabolism ; Gene Expression Regulation ; Genome Size ; *Genome, Mitochondrial ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Plant Proteins/chemistry/*genetics/metabolism ; Plants/*genetics/metabolism ; Plasmids/chemistry/metabolism ; Protein Biosynthesis ; RNA, Transfer/chemistry/metabolism ; Recombination, Genetic ; }, abstract = {Plant mitochondria have a complex and peculiar genetic system. They have the largest genomes, as compared to organelles from other eukaryotic organisms. These can expand tremendously in some species, reaching the megabase range. Nevertheless, whichever the size, the gene content remains modest and restricted to a few polypeptides required for the biogenesis of the oxidative phosphorylation chain complexes, ribosomal proteins, transfer RNAs and ribosomal RNAs. The presence of autonomous plasmids of essentially unknown function further enhances the level of complexity. The physical organization of the plant mitochondrial DNA includes a set of sub-genomic forms resulting from homologous recombination between repeats, with a mixture of linear, circular and branched structures. This material is compacted into membrane-bound nucleoids, which are the inheritance units but also the centers of genome maintenance and expression. Recombination appears to be an essential characteristic of plant mitochondrial genetic processes, both in shaping and maintaining the genome. Under nuclear surveillance, recombination is also the basis for the generation of new mitotypes and is involved in the evolution of the mitochondrial DNA. In line with, or as a consequence of its complex physical organization, replication of the plant mitochondrial DNA is likely to occur through multiple mechanisms, potentially involving recombination processes. We give here a synthetic view of these aspects.}, }
@article {pmid24071901, year = {2014}, author = {Hegedusova, E and Brejova, B and Tomaska, L and Sipiczki, M and Nosek, J}, title = {Mitochondrial genome of the basidiomycetous yeast Jaminaea angkorensis.}, journal = {Current genetics}, volume = {60}, number = {1}, pages = {49-59}, pmid = {24071901}, issn = {1432-0983}, mesh = {Basidiomycota/*genetics ; Codon ; Gene Order ; *Genes, Fungal ; Genes, rRNA ; *Genome, Mitochondrial ; Molecular Sequence Annotation ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Jaminaea angkorensis is an anamorphic basidiomycetous yeast species originally isolated from decaying leaves in Cambodia. Taxonomically, J. angkorensis is affiliated with Microstromatales (Exobasidiomycetes, Ustilaginomycotina, Basidiomycota) and represents a basal phylogenetic lineage of this fungal order. To perform a comparative analysis of J. angkorensis with other basidiomycetes, we determined and analyzed its complete mitochondrial DNA sequence. The mitochondrial genome is represented by 29,999 base pairs long, circular DNA containing 32 % guanine and cytosine residues. Its genetic organization is relatively compact and comprises typical genes for 15 conserved proteins involved in oxidative phosphorylation (atp6, 8, and 9; cob; cox1, 2, and 3; and nad1, 2, 3, 4, 4L, 5, and 6) and translation (rps3), two ribosomal RNAs (rnl and rns) and twenty-two transfer RNAs (trnA-Y). Although the gene content is similar to other basidiomycetes, the gene orders in the examined species exhibit only a limited synteny, reflecting their phylogenetic distances and extensive genome rearrangements. In addition, a comparative analysis of basidiomycete mitochondrial genomes indicates that stop-to-tryptophan reassignment of the UGA codon was accompanied by structural alterations of tRNA-Trp(CCA). These results provide an insight into the evolution of the genetic code in fungal mitochondria.}, }
@article {pmid24068653, year = {2013}, author = {de Paula, WB and Agip, AN and Missirlis, F and Ashworth, R and Vizcay-Barrena, G and Lucas, CH and Allen, JF}, title = {Female and male gamete mitochondria are distinct and complementary in transcription, structure, and genome function.}, journal = {Genome biology and evolution}, volume = {5}, number = {10}, pages = {1969-1977}, pmid = {24068653}, issn = {1759-6653}, mesh = {Adenosine Triphosphate/biosynthesis ; Aging/genetics ; Animals ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; Electron Transport/genetics ; Female ; Free Radicals/metabolism ; Germ Cells/metabolism ; Male ; Mitochondria/genetics/metabolism ; Oocytes/*metabolism ; Oxygen/metabolism ; Spermatozoa/*metabolism ; *Transcription, Genetic ; Zebrafish/metabolism ; }, abstract = {Respiratory electron transport in mitochondria is coupled to ATP synthesis while generating mutagenic oxygen free radicals. Mitochondrial DNA mutation then accumulates with age, and may set a limit to the lifespan of individual, multicellular organisms. Why is this mutation not inherited? Here we demonstrate that female gametes-oocytes-have unusually small and simple mitochondria that are suppressed for DNA transcription, electron transport, and free radical production. By contrast, male gametes-sperm-and somatic cells of both sexes transcribe mitochondrial genes for respiratory electron carriers and produce oxygen free radicals. This germ-line division between mitochondria of sperm and egg is observed in both the vinegar fruitfly and the zebrafish-species spanning a major evolutionary divide within the animal kingdom. We interpret these findings as an evidence that oocyte mitochondria serve primarily as genetic templates, giving rise, irreversibly and in each new generation, to the familiar energy-transducing mitochondria of somatic cells and male gametes. Suppressed mitochondrial metabolism in the female germ line may therefore constitute a mechanism for increasing the fidelity of mitochondrial DNA inheritance.}, }
@article {pmid24065666, year = {2013}, author = {Zhang, WQ and Zhang, MH}, title = {Complete mitochondrial genomes reveal phylogeny relationship and evolutionary history of the family Felidae.}, journal = {Genetics and molecular research : GMR}, volume = {12}, number = {3}, pages = {3256-3262}, doi = {10.4238/2013.September.3.1}, pmid = {24065666}, issn = {1676-5680}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Dogs ; Evolution, Molecular ; Felidae/*genetics ; *Genome, Mitochondrial ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Many mitochondrial DNA sequences are used to estimate phylogenetic relationships among animal taxa and perform molecular phylogenetic evolution analysis. With the continuous development of sequencing technology, numerous mitochondrial sequences have been released in public databases, especially complete mitochondrial DNA sequences. Using multiple sequences is better than using single sequences for phylogenetic analysis of animals because multiple sequences have sufficient information for evolutionary process reconstruction. Therefore, we performed phylogenetic analyses of 14 species of Felidae based on complete mitochondrial genome sequences, with Canis familiaris as an outgroup, using neighbor joining, maximum likelihood, maximum parsimony, and Bayesian inference methods. The consensus phylogenetic trees supported the monophyly of Felidae, and the family could be divided into 2 subfamilies, Felinae and Pantherinae. The genus Panthera and species tigris were also studied in detail. Meanwhile, the divergence of this family was estimated by phylogenetic analysis using the Bayesian method with a relaxed molecular clock, and the results shown were consistent with previous studies. In summary, the evolution of Felidae was reconstructed by phylogenetic analysis based on mitochondrial genome sequences. The described method may be broadly applicable for phylogenetic analyses of anima taxa.}, }
@article {pmid24064930, year = {2013}, author = {Sage, TL and Busch, FA and Johnson, DC and Friesen, PC and Stinson, CR and Stata, M and Sultmanis, S and Rahman, BA and Rawsthorne, S and Sage, RF}, title = {Initial events during the evolution of C4 photosynthesis in C3 species of Flaveria.}, journal = {Plant physiology}, volume = {163}, number = {3}, pages = {1266-1276}, pmid = {24064930}, issn = {1532-2548}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Carbon Cycle/genetics/physiology ; Carbon Dioxide/metabolism ; Chloroplasts/metabolism/ultrastructure ; Evolution, Molecular ; Flaveria/classification/genetics/*metabolism ; Glycine Dehydrogenase (Decarboxylating)/metabolism ; Helianthus/genetics/metabolism ; Microscopy, Electron, Transmission ; Mitochondria/metabolism/ultrastructure ; Photosynthesis/genetics/*physiology ; Phylogeny ; Plant Leaves/genetics/*metabolism/ultrastructure ; Plant Vascular Bundle/genetics/*metabolism/ultrastructure ; Ribulose-Bisphosphate Carboxylase/metabolism ; Species Specificity ; }, abstract = {The evolution of C4 photosynthesis in many taxa involves the establishment of a two-celled photorespiratory CO2 pump, termed C2 photosynthesis. How C3 species evolved C2 metabolism is critical to understanding the initial phases of C4 plant evolution. To evaluate early events in C4 evolution, we compared leaf anatomy, ultrastructure, and gas-exchange responses of closely related C3 and C2 species of Flaveria, a model genus for C4 evolution. We hypothesized that Flaveria pringlei and Flaveria robusta, two C3 species that are most closely related to the C2 Flaveria species, would show rudimentary characteristics of C2 physiology. Compared with less-related C3 species, bundle sheath (BS) cells of F. pringlei and F. robusta had more mitochondria and chloroplasts, larger mitochondria, and proportionally more of these organelles located along the inner cell periphery. These patterns were similar, although generally less in magnitude, than those observed in the C2 species Flaveria angustifolia and Flaveria sonorensis. In F. pringlei and F. robusta, the CO2 compensation point of photosynthesis was slightly lower than in the less-related C3 species, indicating an increase in photosynthetic efficiency. This could occur because of enhanced refixation of photorespired CO2 by the centripetally positioned organelles in the BS cells. If the phylogenetic positions of F. pringlei and F. robusta reflect ancestral states, these results support a hypothesis that increased numbers of centripetally located organelles initiated a metabolic scavenging of photorespired CO2 within the BS. This could have facilitated the formation of a glycine shuttle between mesophyll and BS cells that characterizes C2 photosynthesis.}, }
@article {pmid24063717, year = {2013}, author = {Langford S, SM and Kraitsek, S and Baskerville, B and Ho, SY and Gongora, J}, title = {Australian and Pacific contributions to the genetic diversity of Norfolk Island feral chickens.}, journal = {BMC genetics}, volume = {14}, number = {}, pages = {91}, pmid = {24063717}, issn = {1471-2156}, mesh = {Animals ; Australia ; Chickens/classification/*genetics ; DNA, Mitochondrial/*chemistry/metabolism ; *Genetic Variation ; Genome ; Haplotypes ; Melanesia ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Norfolk Island has a population of feral chickens which could be the result of domestic stock introduced onto the island by British settlers in 1788. However, there is ongoing debate about their origins because multiple human arrivals to the island may have brought chickens with them. Here we investigate the genetic origins of these feral chickens by sequencing their mitochondrial control region. We infer their phylogenetic relationships using a large dataset of novel sequences from Australian mainland domestic chickens and published sequences from around the world.<br><br>RESULTS: Eleven control region haplotypes were found among the Norfolk Island feral and Australian mainland domestic chickens. Six of the Norfolk Island haplotypes fall within haplogroup E, but given the worldwide distribution of this haplogroup, the putative European origin of these chickens requires further investigation. One haplotype common among Norfolk Island and Australian samples belonged to a subgroup of haplogroup D, which appears to be restricted to chickens from Indonesia, Vanuatu and Guam.<br><br>CONCLUSIONS: Our data show that at least two mitochondrial DNA haplogroups (D and E) have contributed to the genetic make-up of Norfolk Island feral chickens. In addition, we have provided insights into the discrete geographical distribution and diversity of the chicken haplogroup D. In view of the worldwide interest in the characterisation of poultry resources, further assessment of chicken populations of Island Southeast Asia and the Pacific region is warranted.}, }
@article {pmid24059529, year = {2013}, author = {Angerer, H}, title = {The superfamily of mitochondrial Complex1_LYR motif-containing (LYRM) proteins.}, journal = {Biochemical Society transactions}, volume = {41}, number = {5}, pages = {1335-1341}, doi = {10.1042/BST20130116}, pmid = {24059529}, issn = {1470-8752}, mesh = {Apoptosis Regulatory Proteins/chemistry/*genetics ; Bacteria/genetics ; Electron Transport Complex I/*genetics ; Eukaryota/genetics ; Humans ; Insulin Resistance/*genetics ; Mitochondria/*genetics/physiology ; Oxidative Phosphorylation ; Phylogeny ; Protein Interaction Maps ; }, abstract = {Mitochondrial LYRM (leucine/tyrosine/arginine motif) proteins are members of the Complex1_LYR-like superfamily. Individual LYRM proteins have been identified as accessory subunits or assembly factors of mitochondrial OXPHOS (oxidative phosphorylation) complexes I, II, III and V respectively, and they play particular roles in the essential Fe-S cluster biogenesis and in acetate metabolism. LYRM proteins have been implicated in mitochondrial dysfunction, e.g. in the context of insulin resistance. However, the functional significance of the common LYRM is still unknown. Analysis of protein-protein interaction screens suggests that LYRM proteins form protein complexes with phylogenetically ancient proteins of bacterial origin. Interestingly, the mitochondrial FAS (fatty acid synthesis) type II acyl-carrier protein ACPM associates with some of the LYRM protein-containing complexes. Eukaryotic LYRM proteins interfere with mitochondrial homoeostasis and might function as adaptor-like 'accessory factors'.}, }
@article {pmid24058926, year = {2013}, author = {Losos, JB and Leal, M}, title = {The evolution of species recognition signals.}, journal = {Molecular ecology}, volume = {22}, number = {15}, pages = {3879-3881}, doi = {10.1111/mec.12377}, pmid = {24058926}, issn = {1365-294X}, mesh = {Animals ; Gene Flow/*genetics ; *Genetic Variation ; Lizards/*genetics ; Mitochondria/*genetics ; *Reproductive Isolation ; }, }
@article {pmid24058559, year = {2013}, author = {Tanveer, A and Allen, SM and Jackson, KE and Charan, M and Ralph, SA and Habib, S}, title = {An FtsH protease is recruited to the mitochondrion of Plasmodium falciparum.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e74408}, pmid = {24058559}, issn = {1932-6203}, mesh = {Adenosine Triphosphate/pharmacology ; Animals ; Cytokinesis/drug effects ; Escherichia coli/metabolism ; Fluorescent Antibody Technique ; Membrane Proteins/metabolism ; Mitochondria/drug effects/*enzymology ; Parasites/cytology/drug effects/enzymology ; Peptide Hydrolases/chemistry/*metabolism ; Phylogeny ; Plasmodium falciparum/cytology/drug effects/*enzymology ; Protein Processing, Post-Translational/drug effects ; Protein Structure, Quaternary ; Protein Transport/drug effects ; Protozoan Proteins/chemistry/*metabolism ; Recombinant Proteins/metabolism ; Sequence Homology, Amino Acid ; Zinc/pharmacology ; }, abstract = {The two organelles, apicoplast and mitochondrion, of the malaria parasite Plasmodium falciparum have unique morphology in liver and blood stages; they undergo complex branching and looping prior to division and segregation into daughter merozoites. Little is known about the molecular processes and proteins involved in organelle biogenesis in the parasite. We report the identification of an AAA+/FtsH protease homolog (PfFtsH1) that exhibits ATP- and Zn(2+)-dependent protease activity. PfFtsH1 undergoes processing, forms oligomeric assemblies, and is associated with the membrane fraction of the parasite cell. Generation of a transfectant parasite line with hemagglutinin-tagged PfFtsH1, and immunofluorescence assay with anti-PfFtsH1 Ab demonstrated that the protein localises to P. falciparum mitochondria. Phylogenetic analysis and the single transmembrane region identifiable in PfFtsH1 suggest that it is an i-AAA like inner mitochondrial membrane protein. Expression of PfFtsH1 in Escherichia coli converted a fraction of bacterial cells into division-defective filamentous forms implying a sequestering effect of the Plasmodium factor on the bacterial homolog, indicative of functional conservation with EcFtsH. These results identify a membrane-associated mitochondrial AAA+/FtsH protease as a candidate regulatory protein for organelle biogenesis in P. falciparum.}, }
@article {pmid24056090, year = {2013}, author = {Dalby, SJ and Bonen, L}, title = {Impact of low temperature on splicing of atypical group II introns in wheat mitochondria.}, journal = {Mitochondrion}, volume = {13}, number = {6}, pages = {647-655}, doi = {10.1016/j.mito.2013.09.001}, pmid = {24056090}, issn = {1872-8278}, mesh = {Base Sequence ; DNA Primers ; *Introns ; Mitochondria/*genetics ; *RNA Splicing ; Reverse Transcriptase Polymerase Chain Reaction ; Seeds ; Triticum/*genetics ; }, abstract = {To investigate the impact of cold on group II intron splicing, we compared the physical forms of excised mitochondrial introns from wheat embryos germinated at room temperature and 4°C. For introns which deviate from the conventional branchpoint structure, we observed predominantly heterogeneous circularized introns in the cold rather than linear polyadenylated forms arising from a hydrolytic pathway as seen at room temperature. In addition, intron-containing precursors are elevated relative to mature mRNAs upon cold treatment. Our findings indicate that low temperature growth not only reduces splicing efficiency, but also shifts the splicing biochemistry of atypical group II introns to novel, yet productive, pathways.}, }
@article {pmid24055494, year = {2014}, author = {Steele, SL and Prykhozhij, SV and Berman, JN}, title = {Zebrafish as a model system for mitochondrial biology and diseases.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {163}, number = {2}, pages = {79-98}, doi = {10.1016/j.trsl.2013.08.008}, pmid = {24055494}, issn = {1878-1810}, support = {287512//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Mitochondria/*physiology ; Mitochondrial Diseases/*physiopathology ; *Models, Animal ; Zebrafish/*physiology ; }, abstract = {Animal models for studying human disease are essential to the continuing evolution of medicine. Rodent models are attractive for the obvious similarities in development and genetic makeup compared with humans, but have cost and technical limitations. The zebrafish (Danio rerio) represents an ideal alternative vertebrate model of human disease because of its high conservation of genetic information and physiological processes, inexpensive maintenance, and optical clarity facilitating direct observation. This review highlights recent advances in understanding genetic disease states associated with the dynamic organelle, the mitochondrion, using the zebrafish. Mitochondrial diseases that have been replicated in the zebrafish include those affecting the nervous and cardiovascular systems, as well as red blood cell function. Gene silencing techniques, including morpholino knockdown and transcription activator-like (TAL)-effector endonucleases, have been exploited to demonstrate how loss of function can induce human disease-like states in zebrafish. Moreover, modeling mitochondrial diseases has been facilitated greatly by the creation of transgenic fish with fluorescently labeled mitochondria for in vivo visualization of these structures. In addition, behavioral assays have been developed to examine changes in motor activity and sensory responses, particularly in larval stages. Zebrafish are poised to advance our understanding of the pathogenesis of human mitochondrial diseases beyond the current state of knowledge and provide a key tool in the development of novel therapeutic approaches to treat these conditions.}, }
@article {pmid24055401, year = {2014}, author = {Kowald, A and Dawson, M and Kirkwood, TB}, title = {Mitochondrial mutations and ageing: can mitochondrial deletion mutants accumulate via a size based replication advantage?.}, journal = {Journal of theoretical biology}, volume = {340}, number = {}, pages = {111-118}, doi = {10.1016/j.jtbi.2013.09.009}, pmid = {24055401}, issn = {1095-8541}, support = {MR/K006312/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Aging ; Animals ; Computer Simulation ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Genetic Drift ; Humans ; Longevity ; Mice ; Mitochondria/genetics ; Models, Biological ; Mutation Rate ; Rats ; *Sequence Deletion ; Stochastic Processes ; Time Factors ; }, abstract = {The mitochondrial theory of ageing is one of the main contenders to explain the biochemical basis of the ageing process. An important line of support comes from the observation that mtDNA deletions accumulate over the life course in post-mitotic cells of many species. A single mutant expands clonally and finally replaces the wild-type population of a whole cell. One proposal to explain the driving force behind this accumulation states that the reduced size leads to a shorter replication time, which provides a selection advantage. However, this idea has been questioned on the grounds that the mitochondrial half-life is much longer than the replication time, so that the latter cannot be a rate limiting step. To clarify this question, we modelled this process mathematically and performed extensive deterministic and stochastic computer simulations to study the effects of replication time, mitochondrial half-life and deletion size. Our study shows that the shorter size does in principle provide a selection advantage, which can lead to an accumulation of the deletion mutant. However, this selection advantage diminishes the shorter is the replication time of wt mtDNA in relation to its half-life. Using generally accepted literature values, the resulting time frame for the accumulation of mutant mtDNAs is only compatible with the ageing process in very long lived species like humans, but could not reasonably explain ageing in short lived species like mice and rats.}, }
@article {pmid24052294, year = {2013}, author = {Reinhardt, K and Dowling, DK and Morrow, EH}, title = {Medicine. Mitochondrial replacement, evolution, and the clinic.}, journal = {Science (New York, N.Y.)}, volume = {341}, number = {6152}, pages = {1345-1346}, doi = {10.1126/science.1237146}, pmid = {24052294}, issn = {1095-9203}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Female ; Fertilization in Vitro ; Genetic Therapy/*methods ; Germ Cells/ultrastructure ; Humans ; Macaca ; Male ; Mice ; Mitochondria/*genetics ; Mitochondrial Diseases/genetics/prevention &amp; control/*therapy ; Mutation ; Oocytes/ultrastructure ; Risk ; }, }
@article {pmid24050258, year = {2013}, author = {Ghanta, S and Grossmann, RE and Brenner, C}, title = {Mitochondrial protein acetylation as a cell-intrinsic, evolutionary driver of fat storage: chemical and metabolic logic of acetyl-lysine modifications.}, journal = {Critical reviews in biochemistry and molecular biology}, volume = {48}, number = {6}, pages = {561-574}, pmid = {24050258}, issn = {1549-7798}, support = {K01 GM109309/GM/NIGMS NIH HHS/United States ; T32 DK007734/DK/NIDDK NIH HHS/United States ; K01GM109309/GM/NIGMS NIH HHS/United States ; }, mesh = {Acetylation ; Animals ; Caloric Restriction ; *Energy Metabolism ; Humans ; *Lipid Metabolism ; Lipids ; *Lipogenesis ; Lysine/chemistry/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Niacinamide/analogs &amp; derivatives/metabolism ; Oxaloacetic Acid/chemistry ; Oxidation-Reduction ; Pyridinium Compounds ; Sirtuin 3/metabolism ; }, abstract = {Hormone systems evolved over 500 million years of animal natural history to motivate feeding behavior and convert excess calories to fat. These systems produced vertebrates, including humans, who are famine-resistant but sensitive to obesity in environments of persistent overnutrition. We looked for cell-intrinsic metabolic features, which might have been subject to an evolutionary drive favoring lipogenesis. Mitochondrial protein acetylation appears to be such a system. Because mitochondrial acetyl-coA is the central mediator of fuel oxidation and is saturable, this metabolite is postulated to be the fundamental indicator of energy excess, which imprints a memory of nutritional imbalances by covalent modification. Fungal and invertebrate mitochondria have highly acetylated mitochondrial proteomes without an apparent mitochondrially targeted protein lysine acetyltransferase. Thus, mitochondrial acetylation is hypothesized to have evolved as a nonenzymatic phenomenon. Because the pKa of a nonperturbed Lys is 10.4 and linkage of a carbonyl carbon to an ε amino group cannot be formed with a protonated Lys, we hypothesize that acetylation occurs on residues with depressed pKa values, accounting for the propensity of acetylation to hit active sites and suggesting that regulatory Lys residues may have been under selective pressure to avoid or attract acetylation throughout animal evolution. In addition, a shortage of mitochondrial oxaloacetate under ketotic conditions can explain why macronutrient insufficiency also produces mitochondrial hyperacetylation. Reduced mitochondrial activity during times of overnutrition and undernutrition would improve fitness by virtue of resource conservation. Micronutrient insufficiency is predicted to exacerbate mitochondrial hyperacetylation. Nicotinamide riboside and Sirt3 activity are predicted to relieve mitochondrial inhibition.}, }
@article {pmid24049072, year = {2014}, author = {Ling, J and Daoud, R and Lajoie, MJ and Church, GM and Söll, D and Lang, BF}, title = {Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria.}, journal = {Nucleic acids research}, volume = {42}, number = {1}, pages = {499-508}, pmid = {24049072}, issn = {1362-4962}, support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; GM022854/GM/NIGMS NIH HHS/United States ; }, mesh = {Alanine/metabolism ; Alanine-tRNA Ligase/metabolism ; Amino Acid Sequence ; Base Sequence ; *Codon ; Eremothecium/enzymology/*genetics ; Leucine/metabolism ; Mitochondria/enzymology/*genetics ; Mitochondrial Proteins/chemistry/genetics ; Molecular Sequence Data ; RNA, Transfer/chemistry/metabolism ; RNA, Transfer, Ala/chemistry/*metabolism ; }, abstract = {The discovery of diverse codon reassignment events has demonstrated that the canonical genetic code is not universal. Studying coding reassignment at the molecular level is critical for understanding genetic code evolution, and provides clues to genetic code manipulation in synthetic biology. Here we report a novel reassignment event in the mitochondria of Ashbya (Eremothecium) gossypii, a filamentous-growing plant pathogen related to yeast (Saccharomycetaceae). Bioinformatics studies of conserved positions in mitochondrial DNA-encoded proteins suggest that CUU and CUA codons correspond to alanine in A. gossypii, instead of leucine in the standard code or threonine in yeast mitochondria. Reassignment of CUA to Ala was confirmed at the protein level by mass spectrometry. We further demonstrate that a predicted tRNA(Ala)UAG is transcribed and accurately processed in vivo, and is responsible for Ala reassignment. Enzymatic studies reveal that tRNA(Ala)UAG is efficiently recognized by A. gossypii mitochondrial alanyl-tRNA synthetase (AgAlaRS). AlaRS typically recognizes the G3:U70 base pair of tRNA(Ala); a G3A change in Ashbya tRNA(Ala)UAG abolishes its recognition by AgAlaRS. Conversely, an A3G mutation in Saccharomyces cerevisiae tRNA(Thr)UAG confers tRNA recognition by AgAlaRS. Our work highlights the dynamic feature of natural genetic codes in mitochondria, and the relative simplicity by which tRNA identity may be switched.}, }
@article {pmid24047186, year = {2015}, author = {Wares, JP}, title = {Mitochondrial evolution across lineages of the vampire barnacle Notochthamalus scabrosus.}, journal = {Mitochondrial DNA}, volume = {26}, number = {1}, pages = {7-10}, doi = {10.3109/19401736.2013.825791}, pmid = {24047186}, issn = {1940-1744}, mesh = {Animals ; Chile ; Computational Biology ; *Evolution, Molecular ; Gene Order ; Genes, Mitochondrial ; Genome, Mitochondrial ; Genomics ; High-Throughput Nucleotide Sequencing ; Mitochondria/*genetics ; Open Reading Frames ; Polymorphism, Genetic ; Thoracica/classification/*genetics ; }, abstract = {Eight whole mitochondrial genomes from the barnacle Notochthamalus scabrosus, with one from the northern lineage and seven from the divergent southern lineage, are presented. The annotated and aligned data were analyzed for signals of non-neutral evolution. Overall, these data are consistent with purifying selection operating on the protein-coding regions of the mitochondrion. However, a notable region of nonsynonymous substitution at the 3' end of the ND2 gene region, along with unusual site frequency spectra in two other gene regions, was identified.}, }
@article {pmid24045017, year = {2013}, author = {Ng, S and Ivanova, A and Duncan, O and Law, SR and Van Aken, O and De Clercq, I and Wang, Y and Carrie, C and Xu, L and Kmiec, B and Walker, H and Van Breusegem, F and Whelan, J and Giraud, E}, title = {A membrane-bound NAC transcription factor, ANAC017, mediates mitochondrial retrograde signaling in Arabidopsis.}, journal = {The Plant cell}, volume = {25}, number = {9}, pages = {3450-3471}, pmid = {24045017}, issn = {1532-298X}, mesh = {Arabidopsis/cytology/*genetics/growth &amp; development/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Binding Sites ; Cell Nucleus/metabolism ; Endoplasmic Reticulum/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Genes, Reporter ; Hydrogen Peroxide/pharmacology ; Mitochondria/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Mutation ; Oligonucleotide Array Sequence Analysis ; Oxidoreductases/genetics/metabolism ; Phenotype ; Phylogeny ; Plant Proteins/genetics/metabolism ; Protein Structure, Tertiary ; Recombinant Fusion Proteins ; Seedlings/cytology/genetics/growth &amp; development/metabolism ; *Signal Transduction ; Stress, Physiological ; Transcription Factors/genetics/metabolism ; Transcriptome ; }, abstract = {Plants require daily coordinated regulation of energy metabolism for optimal growth and survival and therefore need to integrate cellular responses with both mitochondrial and plastid retrograde signaling. Using a forward genetic screen to characterize regulators of alternative oxidase1a (rao) mutants, we identified RAO2/Arabidopsis NAC domain-containing protein17 (ANAC017) as a direct positive regulator of AOX1a. RAO2/ANAC017 is targeted to connections and junctions in the endoplasmic reticulum (ER) and F-actin via a C-terminal transmembrane (TM) domain. A consensus rhomboid protease cleavage site is present in ANAC017 just prior to the predicted TM domain. Furthermore, addition of the rhomboid protease inhibitor N-p-Tosyl-l-Phe chloromethyl abolishes the induction of AOX1a upon antimycin A treatment. Simultaneous fluorescent tagging of ANAC017 with N-terminal red fluorescent protein (RFP) and C-terminal green fluorescent protein (GFP) revealed that the N-terminal RFP domain migrated into the nucleus, while the C-terminal GFP tag remained in the ER. Genome-wide analysis of the transcriptional network regulated by RAO2/ANAC017 under stress treatment revealed that RAO2/ANAC017 function was necessary for >85% of the changes observed as a primary response to cytosolic hydrogen peroxide (H2O2), but only ~33% of transcriptional changes observed in response to antimycin A treatment. Plants with mutated rao2/anac017 were more stress sensitive, whereas a gain-of-function mutation resulted in plants that had lower cellular levels of H2O2 under untreated conditions.}, }
@article {pmid24043313, year = {2013}, author = {Aich, A and Shaha, C}, title = {Novel role of calmodulin in regulating protein transport to mitochondria in a unicellular eukaryote.}, journal = {Molecular and cellular biology}, volume = {33}, number = {22}, pages = {4579-4593}, pmid = {24043313}, issn = {1098-5549}, mesh = {Amino Acid Sequence ; Binding Sites ; Calmodulin/*metabolism ; Humans ; Leishmania donovani/chemistry/genetics/*metabolism ; Leishmaniasis, Visceral/parasitology ; Mitochondria/*metabolism ; Molecular Sequence Data ; Mutation ; Peroxidases/analysis/genetics/*metabolism ; Protein Sorting Signals ; Protein Transport ; Protozoan Proteins/analysis/genetics/*metabolism ; }, abstract = {Lower eukaryotes like the kinetoplastid parasites are good models to study evolution of cellular pathways during steps to eukaryogenesis. In this study, a kinetoplastid parasite, Leishmania donovani, was used to understand the process of mitochondrial translocation of a nucleus-encoded mitochondrial protein, the mitochondrial tryparedoxin peroxidase (mTXNPx). We report the presence of an N-terminal cleavable mitochondrial targeting signal (MTS) validated through deletion and grafting experiments. We also establish a novel finding of calmodulin (CaM) binding to the MTS of mTXNPx through specific residues. Mutation of CaM binding residues, keeping intact the residues involved in mitochondrial targeting and biochemical inhibition of CaM activity both in vitro and in vivo, prevented mitochondrial translocation. Through reconstituted import assays, we demonstrate obstruction of mitochondrial translocation either in the absence of CaM or Ca(2+) or in the presence of CaM inhibitors. We also demonstrate the prevention of temperature-driven mTXNPx aggregation in the presence of CaM. These findings establish the idea that CaM is required for the transport of the protein to mitochondria through maintenance of translocation competence posttranslation.}, }
@article {pmid24042202, year = {2014}, author = {Fulcher, N and Derboven, E and Valuchova, S and Riha, K}, title = {If the cap fits, wear it: an overview of telomeric structures over evolution.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {71}, number = {5}, pages = {847-865}, pmid = {24042202}, issn = {1420-9071}, support = {Y 418/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Chromosomes/*genetics ; DNA/*chemistry ; *Evolution, Molecular ; *Models, Molecular ; Nuclear Proteins/metabolism ; *Nucleic Acid Conformation ; Telomerase/*metabolism ; Telomere/*genetics ; Telomere Homeostasis/*physiology ; }, abstract = {Genome organization into linear chromosomes likely represents an important evolutionary innovation that has permitted the development of the sexual life cycle; this process has consequently advanced nuclear expansion and increased complexity of eukaryotic genomes. Chromosome linearity, however, poses a major challenge to the internal cellular machinery. The need to efficiently recognize and repair DNA double-strand breaks that occur as a consequence of DNA damage presents a constant threat to native chromosome ends known as telomeres. In this review, we present a comparative survey of various solutions to the end protection problem, maintaining an emphasis on DNA structure. This begins with telomeric structures derived from a subset of prokaryotes, mitochondria, and viruses, and will progress into the typical telomere structure exhibited by higher organisms containing TTAGG-like tandem sequences. We next examine non-canonical telomeres from Drosophila melanogaster, which comprise arrays of retrotransposons. Finally, we discuss telomeric structures in evolution and possible switches between canonical and non-canonical solutions to chromosome end protection.}, }
@article {pmid24042146, year = {2013}, author = {Jerlström-Hultqvist, J and Einarsson, E and Xu, F and Hjort, K and Ek, B and Steinhauf, D and Hultenby, K and Bergquist, J and Andersson, JO and Svärd, SG}, title = {Hydrogenosomes in the diplomonad Spironucleus salmonicida.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {2493}, pmid = {24042146}, issn = {2041-1723}, mesh = {Diplomonadida/genetics/*metabolism ; Hydrogen/*metabolism ; Hydrogenase/metabolism ; Mitochondria/metabolism ; Models, Biological ; Organelles/*metabolism ; Phylogeny ; Proteomics ; Pyruvates/metabolism ; }, abstract = {Acquisition of the mitochondrion is a key event in the evolution of the eukaryotic cell, but diversification of the organelle has occurred during eukaryotic evolution. One example of such mitochondria-related organelles (MROs) are hydrogenosomes, which produce ATP by substrate-level phosphorylation with hydrogen as a byproduct. The diplomonad parasite Giardia intestinalis harbours mitosomes, another type of MRO. Here we identify MROs in the salmon parasite Spironucleus salmonicida with similar protein import and Fe-S cluster assembly machineries as in Giardia mitosomes. We find that hydrogen production is prevalent in the diplomonad genus Spironucleus, and that S. salmonicida MROs contain enzymes characteristic of hydrogenosomes. Evolutionary analyses of known hydrogenosomal components indicate their presence in the diplomonad ancestor, and subsequent loss in Giardia. Our results suggest that hydrogenosomes are metabolic adaptations predating the split between parabasalids and diplomonads, which is deeper than the split between animals and fungi in the eukaryotic tree.}, }
@article {pmid24039288, year = {2013}, author = {Yang, D and Ren, Y and Fu, Y and Xie, Y and Nie, H and Nong, X and Gu, X and Wang, S and Peng, X and Yang, G}, title = {Genetic variation of Taenia pisiformis collected from Sichuan, China, based on the mitochondrial cytochrome B gene.}, journal = {The Korean journal of parasitology}, volume = {51}, number = {4}, pages = {449-452}, pmid = {24039288}, issn = {1738-0006}, mesh = {Animals ; China ; Cytochromes b/*genetics ; *Genetic Variation ; Helminth Proteins/*genetics ; Humans ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Rabbits ; Taenia/classification/genetics/*isolation &amp; purification ; Taeniasis/*parasitology ; }, abstract = {Taenia pisiformis is one of the most important parasites of canines and rabbits. T. pisiformis cysticercus (the larval stage) causes severe damage to rabbit breeding, which results in huge economic losses. In this study, the genetic variation of T. pisiformis was determined in Sichuan Province, China. Fragments of the mitochondrial cytochrome b (cytb) (922 bp) gene were amplified in 53 isolates from 8 regions of T. pisiformis. Overall, 12 haplotypes were found in these 53 cytb sequences. Molecular genetic variations showed 98.4% genetic variation derived from intra-region. FST and Nm values suggested that 53 isolates were not genetically differentiated and had low levels of genetic diversity. Neutrality indices of the cytb sequences showed the evolution of T. pisiformis followed a neutral mode. Phylogenetic analysis revealed no correlation between phylogeny and geographic distribution. These findings indicate that 53 isolates of T. pisiformis keep a low genetic variation, which provide useful knowledge for monitoring changes in parasite populations for future control strategies.}, }
@article {pmid24037739, year = {2013}, author = {Huang, J}, title = {Horizontal gene transfer in eukaryotes: the weak-link model.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {10}, pages = {868-875}, pmid = {24037739}, issn = {1521-1878}, mesh = {Animals ; Eukaryota/*genetics ; Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Mitochondria/genetics ; *Models, Genetic ; Phylogeny ; Plastids/genetics ; Symbiosis/genetics ; }, abstract = {The significance of horizontal gene transfer (HGT) in eukaryotic evolution remains controversial. Although many eukaryotic genes are of bacterial origin, they are often interpreted as being derived from mitochondria or plastids. Because of their fixed gene pool and gene loss, however, mitochondria and plastids alone cannot adequately explain the presence of all, or even the majority, of bacterial genes in eukaryotes. Available data indicate that no insurmountable barrier to HGT exists, even in complex multicellular eukaryotes. In addition, the discovery of both recent and ancient HGT events in all major eukaryotic groups suggests that HGT has been a regular occurrence throughout the history of eukaryotic evolution. A model of HGT is proposed that suggests both unicellular and early developmental stages as likely entry points for foreign genes into multicellular eukaryotes.}, }
@article {pmid24034565, year = {2013}, author = {Khanshour, AM and Cothran, EG}, title = {Maternal phylogenetic relationships and genetic variation among Arabian horse populations using whole mitochondrial DNA D-loop sequencing.}, journal = {BMC genetics}, volume = {14}, number = {}, pages = {83}, pmid = {24034565}, issn = {1471-2156}, mesh = {Animals ; Base Sequence ; Cluster Analysis ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; Genetics, Population ; Haplotypes ; Horses/*classification/*genetics ; Middle East ; Mitochondria/*genetics ; *Phylogeny ; Principal Component Analysis ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Maternal inheritance is an essential point in Arabian horse population genetics and strains classification. The mitochondrial DNA (mtDNA) sequencing is a highly informative tool to investigate maternal lineages. We sequenced the whole mtDNA D-loop of 251 Arabian horses to study the genetic diversity and phylogenetic relationships of Arabian populations and to examine the traditional strain classification system that depends on maternal family lines using native Arabian horses from the Middle East.<br><br>RESULTS: The variability in the upstream region of the D-loop revealed additional differences among the haplotypes that had identical sequences in the hypervariable region 1 (HVR1). While the American-Arabians showed relatively low diversity, the Syrian population was the most variable and contained a very rare and old haplogroup. The Middle Eastern horses had major genetic contributions to the Western horses and there was no clear pattern of differentiation among all tested populations. Our results also showed that several individuals from different strains shared a single haplotype, and individuals from a single strain were represented in clearly separated haplogroups.<br><br>CONCLUSIONS: The whole mtDNA D-loop sequence was more powerful for analysis of the maternal genetic diversity in the Arabian horses than using just the HVR1. Native populations from the Middle East, such as Syrians, could be suggested as a hot spot of genetic diversity and may help in understanding the evolution history of the Arabian horse breed. Most importantly, there was no evidence that the Arabian horse breed has clear subdivisions depending on the traditional maternal based strain classification system.}, }
@article {pmid24029811, year = {2013}, author = {Straub, SC and Cronn, RC and Edwards, C and Fishbein, M and Liston, A}, title = {Horizontal transfer of DNA from the mitochondrial to the plastid genome and its subsequent evolution in milkweeds (apocynaceae).}, journal = {Genome biology and evolution}, volume = {5}, number = {10}, pages = {1872-1885}, pmid = {24029811}, issn = {1759-6653}, mesh = {Apocynaceae/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Gene Conversion ; *Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Genome, Plastid ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Pseudogenes/genetics ; }, abstract = {Horizontal gene transfer (HGT) of DNA from the plastid to the nuclear and mitochondrial genomes of higher plants is a common phenomenon; however, plastid genomes (plastomes) are highly conserved and have generally been regarded as impervious to HGT. We sequenced the 158 kb plastome and the 690 kb mitochondrial genome of common milkweed (Asclepias syriaca [Apocynaceae]) and found evidence of intracellular HGT for a 2.4-kb segment of mitochondrial DNA to the rps2-rpoC2 intergenic spacer of the plastome. The transferred region contains an rpl2 pseudogene and is flanked by plastid sequence in the mitochondrial genome, including an rpoC2 pseudogene, which likely provided the mechanism for HGT back to the plastome through double-strand break repair involving homologous recombination. The plastome insertion is restricted to tribe Asclepiadeae of subfamily Asclepiadoideae, whereas the mitochondrial rpoC2 pseudogene is present throughout the subfamily, which confirms that the plastid to mitochondrial HGT event preceded the HGT to the plastome. Although the plastome insertion has been maintained in all lineages of Asclepiadoideae, it shows minimal evidence of transcription in A. syriaca and is likely nonfunctional. Furthermore, we found recent gene conversion of the mitochondrial rpoC2 pseudogene in Asclepias by the plastid gene, which reflects continued interaction of these genomes.}, }
@article {pmid24026678, year = {2014}, author = {Bicker, A and Dietrich, D and Gleixner, E and Kristiansen, G and Gorr, TA and Hankeln, T}, title = {Extensive transcriptional complexity during hypoxia-regulated expression of the myoglobin gene in cancer.}, journal = {Human molecular genetics}, volume = {23}, number = {2}, pages = {479-490}, doi = {10.1093/hmg/ddt438}, pmid = {24026678}, issn = {1460-2083}, mesh = {Adenocarcinoma/genetics ; Alternative Splicing ; Animals ; Breast Neoplasms/*genetics/*metabolism ; *Cell Hypoxia ; Cell Line, Tumor ; Colorectal Neoplasms/genetics/metabolism ; Exons ; Female ; Gene Expression Regulation, Neoplastic ; Humans ; Mice ; Mitochondria/metabolism ; Myoglobin/*genetics/metabolism ; Phylogeny ; Promoter Regions, Genetic ; Transcriptome ; }, abstract = {Recently, the ectopic expression of myoglobin (MB) was reported in human epithelial cancer cell lines and breast tumor tissues, where MB expression increased with hypoxia. The better prognosis of MB-positive breast cancer patients suggested that the globin exerts a tumor-suppressive role, possibly by impairing mitochondrial activity in hypoxic breast carcinoma cells. To better understand MB gene regulation in cancer, we systematically investigated the architecture of the human MB gene, its transcripts and promoters. In silico analysis of transcriptome data from normal human tissues and cancer cell lines, followed by RACE-PCR verification, revealed seven novel exons in the MB gene region, most of which are untranslated exons located 5'-upstream of the coding DNA sequence (CDS). Sixteen novel alternatively spliced MB transcripts were detected, most of which predominantly occur in tumor tissue or cell lines. Quantitative RT-PCR analyses of MB expression in surgical breast cancer specimen confirmed the preferential usage of a hitherto unknown, tumor-associated MB promoter, which was functionally validated by luciferase reporter gene assays. In line with clinical observations of MB up-regulation in avascular breast tumors, the novel cancer-associated MB splice variants exhibited increased expression in tumor cells subjected to experimental hypoxia. The novel gene regulatory mechanisms unveiled in this study support the idea of a non-canonical role of MB during carcinogenesis.}, }
@article {pmid24026503, year = {2014}, author = {Richter, U and Richter, B and Weihe, A and Börner, T}, title = {A third mitochondrial RNA polymerase in the moss Physcomitrella patens.}, journal = {Current genetics}, volume = {60}, number = {1}, pages = {25-34}, pmid = {24026503}, issn = {1432-0983}, mesh = {Amino Acid Sequence ; Biological Transport ; Bryopsida/classification/*enzymology/*genetics ; DNA-Directed RNA Polymerases/chemistry/*genetics/*metabolism ; Genes, Mitochondrial ; Mitochondria/*enzymology/*genetics ; Molecular Sequence Data ; Phylogeny ; Plastids/chemistry/genetics ; RNA/chemistry ; RNA, Mitochondrial ; Sequence Alignment ; }, abstract = {In most organisms, the mitochondrial genes are transcribed by RNA polymerases related to the single-subunit RNA polymerases of bacteriophages like T3 and T7. In flowering plants, duplication(s) of the RpoTm gene coding for the mitochondrial RNA polymerase (RPOTm) led to the evolution of additional RNA polymerases transcribing genes in plastids (RPOTp) or in both mitochondria and plastids (RPOTmp). Two putative RPOTmp enzymes were previously described to be encoded by the nuclear genes RpoTmp1 and RpoTmp2 in the moss Physcomitrella patens. Here, we report on a third Physcomitrella RpoT gene. We determined the sequence of the cDNA. Comparison of the deduced amino acid sequence with sequences of plant organellar RNA polymerases suggests that this gene encodes a functional phage-type RNA polymerase. The 78 N-terminal amino acids of the putative RNA polymerase were fused to GFP and found to target the fusion protein exclusively to mitochondria in Arabidopsis protoplasts. P. patens is the only known organism to possess three mitochondrial RNA polymerases.}, }
@article {pmid24026098, year = {2013}, author = {Hoekstra, LA and Siddiq, MA and Montooth, KL}, title = {Pleiotropic effects of a mitochondrial-nuclear incompatibility depend upon the accelerating effect of temperature in Drosophila.}, journal = {Genetics}, volume = {195}, number = {3}, pages = {1129-1139}, pmid = {24026098}, issn = {1943-2631}, mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics/metabolism ; DNA, Mitochondrial/genetics ; Drosophila/*genetics/growth &amp; development/*physiology ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/*genetics/growth &amp; development/*physiology ; Epistasis, Genetic ; Evolution, Molecular ; Female ; Fertility/genetics/physiology ; Genes, Insect ; Genetic Fitness ; Hot Temperature ; Larva/genetics/growth &amp; development/metabolism ; Male ; Mitochondria/genetics/metabolism ; Mutation ; RNA, Transfer, Tyr/chemistry/genetics/metabolism ; Selection, Genetic ; Species Specificity ; Tyrosine-tRNA Ligase/genetics/metabolism ; }, abstract = {Interactions between mitochondrial and nuclear gene products that underlie eukaryotic energy metabolism can cause the fitness effects of mutations in one genome to be conditional on variation in the other genome. In ectotherms, the effects of these interactions are likely to depend upon the thermal environment, because increasing temperature accelerates molecular rates. We find that temperature strongly modifies the pleiotropic phenotypic effects of an incompatible interaction between a Drosophila melanogaster polymorphism in the nuclear-encoded, mitochondrial tyrosyl-transfer (t)RNA synthetase and a D. simulans polymorphism in the mitochondrially encoded tRNA(Tyr). The incompatible mitochondrial-nuclear genotype extends development time, decreases larval survivorship, and reduces pupation height, indicative of decreased energetic performance. These deleterious effects are ameliorated when larvae develop at 16° and exacerbated at warmer temperatures, leading to complete sterility in both sexes at 28°. The incompatible genotype has a normal metabolic rate at 16° but a significantly elevated rate at 25°, consistent with the hypothesis that inefficient energy metabolism extends development in this genotype at warmer temperatures. Furthermore, the incompatibility decreases metabolic plasticity of larvae developed at 16°, indicating that cooler development temperatures do not completely mitigate the deleterious effects of this genetic interaction. Our results suggest that the epistatic fitness effects of metabolic mutations may generally be conditional on the thermal environment. The expression of epistatic interactions in some environments, but not others, weakens the efficacy of selection in removing deleterious epistatic variants from populations and may promote the accumulation of incompatibilities whose fitness effects will depend upon the environment in which hybrids occur.}, }
@article {pmid24023783, year = {2013}, author = {Van der Eecken, V and Clippe, A and Dekoninck, S and Goemaere, J and Walbrecq, G and Van Veldhoven, PP and Knoops, B}, title = {Abolition of peroxiredoxin-5 mitochondrial targeting during canid evolution.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e72844}, pmid = {24023783}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Cell Line ; Dogs ; Humans ; Molecular Sequence Data ; Oxidative Stress/genetics/physiology ; Peroxiredoxins/*chemistry/genetics/*metabolism ; }, abstract = {In human, the subcellular targeting of peroxiredoxin-5 (PRDX5), a thioredoxin peroxidase, is dependent on the use of multiple alternative transcription start sites and two alternative in-frame translation initiation sites, which determine whether or not the region encoding a mitochondrial targeting sequence (MTS) is translated. In the present study, the abolition of PRDX5 mitochondrial targeting in dog is highlighted and the molecular mechanism underlying the loss of mitochondrial PRDX5 during evolution is examined. Here, we show that the absence of mitochondrial PRDX5 is generalized among the extant canids and that the first events leading to PRDX5 MTS abolition in canids involve a mutation in the more 5' translation initiation codon as well as the appearance of a STOP codon. Furthermore, we found that PRDX5 MTS functionality is maintained in giant panda and northern elephant seal, which are phylogenetically closely related to canids. Also, the functional consequences of the restoration of mitochondrial PRDX5 in dog Madin-Darby canine kidney (MDCK) cells were investigated. The restoration of PRDX5 mitochondrial targeting in MDCK cells, instead of protecting, provokes deleterious effects following peroxide exposure independently of its peroxidase activity, indicating that mitochondrial PRDX5 gains cytotoxic properties under acute oxidative stress in MDCK cells. Altogether our results show that, although mitochondrial PRDX5 cytoprotective function against oxidative stress has been clearly demonstrated in human and rodents, PRDX5 targeting to mitochondria has been evolutionary lost in canids. Moreover, restoration of mitochondrial PRDX5 in dog MDCK cells, instead of conferring protection against peroxide exposure, makes them more vulnerable.}, }
@article {pmid24021005, year = {2015}, author = {He, K and Jiang, XL}, title = {Mitochondrial phylogeny reveals cryptic genetic diversity in the genus Niviventer (Rodentia, Muroidea).}, journal = {Mitochondrial DNA}, volume = {26}, number = {1}, pages = {48-55}, doi = {10.3109/19401736.2013.823167}, pmid = {24021005}, issn = {1940-1744}, mesh = {Animals ; Cytochromes b/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; *Genetic Variation ; Geography ; Mitochondria/*genetics ; *Phylogeny ; Phylogeography ; Rodentia/*classification/*genetics ; }, abstract = {Niviventer is a muroid genus with 17 species widely distributed in East and Southeast Asia. These animals are important components of both extant and fossil small mammal communities, and they are among the most common infectious agents in humans. In this study, we employed partitioned Bayesian and relaxed clock divergence dating analyses and included the Niviventer mitochondrial cytochrome b genes of from GenBank (n = 223). Although the intra-generic relationships were not fully resolved, we recognized four major clades/subclades that could support further division of the genus. Paraphyletic and polyphyletic species were discovered, and 21 putative species were recognized through species delimitation analysis, which indicated an imperfect taxonomy and the existent of cryptic species. Molecular dating supported Niviventer origination in the late Miocene, and relatively higher diversification rates were observed in the late Pliocene and the Pleistocene, which might correlate with climate fluctuations.}, }
@article {pmid24019145, year = {2013}, author = {Martínez-Fábregas, J and Díaz-Moreno, I and González-Arzola, K and Janocha, S and Navarro, JA and Hervás, M and Bernhardt, R and Díaz-Quintana, A and De la Rosa, M&#xc1;}, title = {New Arabidopsis thaliana cytochrome c partners: a look into the elusive role of cytochrome c in programmed cell death in plants.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {12}, number = {12}, pages = {3666-3676}, pmid = {24019145}, issn = {1535-9484}, mesh = {Apoptosis/*genetics ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Chromatography, Affinity ; Cytochromes c/genetics/*metabolism ; Cytosol/chemistry/metabolism ; Energy Metabolism ; Evolution, Molecular ; *Gene Expression Regulation, Plant ; HEK293 Cells ; Humans ; Mass Spectrometry ; Mitochondria/chemistry/metabolism ; Molecular Sequence Annotation ; Oxidative Stress ; Protein Binding ; Protein Interaction Mapping ; Protein Transport ; Protoplasts/chemistry/metabolism ; RNA, Messenger/genetics/metabolism ; Signal Transduction ; Surface Plasmon Resonance ; }, abstract = {Programmed cell death is an event displayed by many different organisms along the evolutionary scale. In plants, programmed cell death is necessary for development and the hypersensitive response to stress or pathogenic infection. A common feature in programmed cell death across organisms is the translocation of cytochrome c from mitochondria to the cytosol. To better understand the role of cytochrome c in the onset of programmed cell death in plants, a proteomic approach was developed based on affinity chromatography and using Arabidopsis thaliana cytochrome c as bait. Using this approach, ten putative new cytochrome c partners were identified. Of these putative partners and as indicated by bimolecular fluorescence complementation, nine of them bind the heme protein in plant protoplasts and human cells as a heterologous system. The in vitro interaction between cytochrome c and such soluble cytochrome c-targets was further corroborated using surface plasmon resonance. Taken together, the results obtained in the study indicate that Arabidopsis thaliana cytochrome c interacts with several distinct proteins involved in protein folding, translational regulation, cell death, oxidative stress, DNA damage, energetic metabolism, and mRNA metabolism. Interestingly, some of these novel Arabidopsis thaliana cytochrome c-targets are closely related to those for Homo sapiens cytochrome c (Martínez-Fábregas et al., unpublished). These results indicate that the evolutionarily well-conserved cytosolic cytochrome c, appearing in organisms from plants to mammals, interacts with a wide range of targets on programmed cell death. The data have been deposited to the ProteomeXchange with identifier PXD000280.}, }
@article {pmid24018281, year = {2013}, author = {Navarrete, ML and Cerdeño, MC and Serra, MC and Conejero, R}, title = {[Mitochondrial and microcirculatory distress syndrome in the critical patient. Therapeutic implications].}, journal = {Medicina intensiva}, volume = {37}, number = {7}, pages = {476-484}, doi = {10.1016/j.medin.2013.03.001}, pmid = {24018281}, issn = {1578-6749}, mesh = {Animals ; Antioxidants/therapeutic use ; Cell Hypoxia ; Disease Progression ; Electron Transport/drug effects ; Energy Metabolism/drug effects ; Free Radical Scavengers/therapeutic use ; Hemodynamics ; Hibernation ; Humans ; Hypothermia, Induced ; Microcirculation/*physiology ; Mitochondria/drug effects/physiology ; Mitochondrial Diseases/diagnosis/*etiology/physiopathology ; Models, Animal ; Multiple Organ Failure/etiology/physiopathology/prevention &amp; control ; Nitric Oxide/physiology/therapeutic use ; Oxidative Phosphorylation/drug effects ; Reactive Oxygen Species ; Syndrome ; Systemic Inflammatory Response Syndrome/*complications/physiopathology ; }, abstract = {Mitochondrial and microcirculatory distress syndrome (MMDS) can occur during systemic inflammatory response syndrome (SIRS), and is characterized by cytopathic tissue hypoxia uncorrected by oxygen transport optimization, and associated with an acquired defect in the use of oxygen and energy production in mitochondria, leading to multiple organ dysfunction (MOD). We examine the pathogenesis of MMDS, new diagnostic methods, and recent therapeutic approaches adapted to each of the three phases in the evolution of the syndrome. In the initial phase, the aim is prevention and early reversal of mitochondrial dysfunction. Once the latter is established, the aim is to restore flow of the electron chain, mitochondrial respiration, and to avoid cellular energy collapse. Finally, in the third (resolution) stage, treatment should focus on stimulating mitochondrial biogenesis and the repair or replacement of damaged mitochondria.}, }
@article {pmid24009203, year = {2013}, author = {Zhao, YE and Ma, JX and Hu, L and Wu, LP and De Rojas, M}, title = {Discrimination between Demodex folliculorum (Acari: Demodicidae) isolates from China and Spain based on mitochondrial cox1 sequences.}, journal = {Journal of Zhejiang University. Science. B}, volume = {14}, number = {9}, pages = {829-836}, pmid = {24009203}, issn = {1862-1783}, mesh = {Animals ; Base Sequence ; China ; Cloning, Molecular ; Cyclooxygenase 1/*genetics ; DNA, Mitochondrial/genetics ; Humans ; Mite Infestations/parasitology ; Mites/classification/*enzymology/*genetics ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Nucleic Acid ; Spain ; Species Specificity ; }, abstract = {For a long time, classification of Demodex mites has been based mainly on their hosts and phenotypic characteristics. A new subspecies of Demodex folliculorum has been proposed, but not confirmed. Here, cox1 partial sequences of nine isolates of three Demodex species from two geographical sources (China and Spain) were studied to conduct molecular identification of D. folliculorum. Sequencing showed that the mitochondrial cox1 fragments of five D. folliculorum isolates from the facial skin of Chinese individuals were 429 bp long and that their sequence identity was 97.4%. The average sequence divergence was 1.24% among the five Chinese isolates, 0.94% between the two geographical isolate groups (China (5) and Spain (1)), and 2.15% between the two facial tissue sources (facial skin (6) and eyelids (1)). The genetic distance and rate of third-position nucleotide transition/transversion were 0.0125, 2.7 (3/1) among the five Chinese isolates, 0.0094, 3.1 (3/1) between the two geographical isolate groups, and 0.0217, 4.4 (3/1) between the two facial tissue sources. Phylogenetic trees showed that D. folliculorum from the two geographical isolate groups did not form sister clades, while those from different facial tissue sources did. According to the molecular characteristics, it appears that subspecies differentiation might not have occurred and that D. folliculorum isolates from the two geographical sources are of the same population. However, population differentiation might be occurring between isolates from facial skin and eyelids.}, }
@article {pmid24009133, year = {2013}, author = {Bar-Yaacov, D and Bouskila, A and Mishmar, D}, title = {The first Chameleon transcriptome: comparative genomic analysis of the OXPHOS system reveals loss of COX8 in Iguanian lizards.}, journal = {Genome biology and evolution}, volume = {5}, number = {10}, pages = {1792-1799}, pmid = {24009133}, issn = {1759-6653}, mesh = {Adenosine Triphosphate/genetics/metabolism ; Animals ; Electron Transport Complex IV/*genetics ; *Evolution, Molecular ; *Gene Expression Profiling ; Genome ; High-Throughput Nucleotide Sequencing ; Humans ; Lizards/*genetics ; Mitochondria/genetics ; Molecular Sequence Annotation ; Oxidative Phosphorylation ; }, abstract = {Recently, we found dramatic mitochondrial DNA divergence of Israeli Chamaeleo chamaeleon populations into two geographically distinct groups. We aimed to examine whether the same pattern of divergence could be found in nuclear genes. However, no genomic resource is available for any chameleon species. Here we present the first chameleon transcriptome, obtained using deep sequencing (SOLiD). Our analysis identified 164,000 sequence contigs of which 19,000 yielded unique BlastX hits. To test the efficacy of our sequencing effort, we examined whether the chameleon and other available reptilian transcriptomes harbored complete sets of genes comprising known biochemical pathways, focusing on the nDNA-encoded oxidative phosphorylation (OXPHOS) genes as a model. As a reference for the screen, we used the human 86 (including isoforms) known structural nDNA-encoded OXPHOS subunits. Analysis of 34 publicly available vertebrate transcriptomes revealed orthologs for most human OXPHOS genes. However, OXPHOS subunit COX8 (Cytochrome C oxidase subunit 8), including all its known isoforms, was consistently absent in transcriptomes of iguanian lizards, implying loss of this subunit during the radiation of this suborder. The lack of COX8 in the suborder Iguania is intriguing, since it is important for cellular respiration and ATP production. Our sequencing effort added a new resource for comparative genomic studies, and shed new light on the evolutionary dynamics of the OXPHOS system.}, }
@article {pmid24008156, year = {2013}, author = {Duarte, FV and Gomes, AP and Teodoro, JS and Varela, AT and Moreno, AJ and Rolo, AP and Palmeira, CM}, title = {Dibenzofuran-induced mitochondrial dysfunction: Interaction with ANT carrier.}, journal = {Toxicology in vitro : an international journal published in association with BIBRA}, volume = {27}, number = {8}, pages = {2160-2168}, doi = {10.1016/j.tiv.2013.08.009}, pmid = {24008156}, issn = {1879-3177}, mesh = {Adenosine Triphosphatases/metabolism ; Animals ; Benzofurans/*toxicity ; Peptidyl-Prolyl Isomerase F ; Cyclophilins/metabolism ; Environmental Pollutants/*toxicity ; Male ; Membrane Potential, Mitochondrial/drug effects ; Mitochondria, Liver/*drug effects/physiology ; Mitochondrial ADP, ATP Translocases/*metabolism ; Oxygen/metabolism ; Rats ; Rats, Wistar ; }, abstract = {Exposure to environmental pollutants such as dibenzofurans and furans is linked to the pathophysiology of several diseases. Dibenzofuran (DBF) is listed as a pollutant of concern due to its persistence in the environment, bioaccumulation and toxicity to humans, being associated with the development of lung diseases and cancers, due to its extremely toxic properties such as carcinogenic and teratogenic. Mitochondria play a key role in cellular homeostasis and keeping a proper energy supply for eukaryotic cells is essential in the fulfillment of the tissues energy-demand. Therefore, interference with mitochondrial function leads to cell death and organ failure. In this work, the effects of DBF on isolated rat liver mitochondria were analyzed. DBF exposure caused a markedly increase in the lag phase that follows depolarization induced by ADP, indicating an effect in the phosphorylative system. This was associated with a dose-dependent decrease in ATPase activity. Moreover, DBF also increased the threshold to the induction of the mitochondrial permeability transition (MPT) by calcium. Pretreatment of mitochondria with DBF also increased the concentration of carboxyatractyloside (CAT) necessary to abolish ADP phosphorylation and to induce the MPT, suggesting that DBF may interfere with mitochondria through an effect on the adenine nucleotide translocase (ANT). By co-immunoprecipitating ANT and Cyclophilin D (CypD) following MPT induction, we observed that in the presence of DBF, the ratio CypD/ANT was decreased. This demonstrates that DBF interferes with the ANT and so prevents CypD binding to the ANT, causing decreased phosphorylative capacity and inhibiting the MPT, which is also reflected by an increase in calcium retention capacity. Clarifying the role of pollutants in some mechanisms of toxicity, such as unbalance of bioenergetics status and mitochondrial function, may help to explain the progressive and chronic evolution of diseases derived from exposure to environmental pollutants.}, }
@article {pmid24006922, year = {2013}, author = {Dumas, E and Atyame, CM and Milesi, P and Fonseca, DM and Shaikevich, EV and Unal, S and Makoundou, P and Weill, M and Duron, O}, title = {Population structure of Wolbachia and cytoplasmic introgression in a complex of mosquito species.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {181}, pmid = {24006922}, issn = {1471-2148}, mesh = {Animals ; Biological Evolution ; Culex/classification/*microbiology ; DNA, Mitochondrial/genetics ; Genetic Variation ; Haplotypes ; Polymerase Chain Reaction ; Wolbachia/classification/genetics/*isolation &amp; purification ; }, abstract = {BACKGROUND: The maternally inherited bacterium Wolbachia often acts as a subtle parasite that manipulates insect reproduction, resulting potentially in reproductive isolation between host populations. Whilst distinct Wolbachia strains are documented in a group of evolutionarily closely related mosquitoes known as the Culex pipiens complex, their impact on mosquito population genetics remains unclear. To this aim, we developed a PCR-RFLP test that discriminates the five known Wolbachia groups found in this host complex. We further examined the Wolbachia genetic diversity, the variability in the coinherited host mitochondria and their partitioning among members of the Cx. pipiens complex, in order to assess the impact of Wolbachia on host population structure.<br><br>RESULTS: There was a strong association between Wolbachia and mitochondrial haplotypes indicating a stable co-transmission in mosquito populations. Despite evidence that members of the Cx. pipiens complex are genetically distinct on the basis of nuclear DNA, the association of Wolbachia and mtDNA with members of the Cx. pipiens complex were limited. The Wolbachia wPip-I group, by far the most common, was associated with divergent Cx. pipiens members, including Cx. quinquefasciatus, Cx. pipiens pipiens form pipiens and Cx. pipiens pipiens form molestus. Four other wPip groups were also found in mosquito populations and all were shared between diverse Cx. pipiens members.<br><br>CONCLUSION: This data overall supports the hypothesis that wPip infections, and their allied mitochondria, are associated with regular transfers between Cx. pipiens members rather than specific host associations. Overall, this is suggestive of a recent and likely ongoing cytoplasmic introgression through hybridization events across the Cx. pipiens complex.}, }
@article {pmid24006867, year = {2015}, author = {Wang, W and Guo, B and Li, J and Wang, H and Qi, P and Lv, Z and Wu, C}, title = {Complete mitochondrial genome of the spineless cuttlefish Sepiella inermis (Sepioidea, Sepiidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {1}, pages = {151-152}, doi = {10.3109/19401736.2013.819498}, pmid = {24006867}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Decapodiformes/*genetics ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {In this study, we determined the complete mitochondrial genome of the spineless cuttlefish Sepiella inermis. The genome was 16,191 bp in length and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 2 main non-coding regions [both are control regions (CR)]. The composition and order of genes, for the mitogenome found in S. inermis were similar to most other invertebrates. The overall base composition of S. inermis is T 35.6%, C 16.4%, A 40.0% and G 8.0%, with a highly A + T bias of 75.6%. Two control regions contain both termination-associated sequences and conserved sequence blocks. Thus, mitogenome sequence data would play an important role in the investigation of phylogenetic relationship, taxonomic resolution and phylogeography of the Sepiidae.}, }
@article {pmid24004908, year = {2013}, author = {Liu, S and Melonek, J and Boykin, LM and Small, I and Howell, KA}, title = {PPR-SMRs: ancient proteins with enigmatic functions.}, journal = {RNA biology}, volume = {10}, number = {9}, pages = {1501-1510}, pmid = {24004908}, issn = {1555-8584}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics ; Arabidopsis Proteins/genetics/metabolism ; Chloroplasts/genetics ; Molecular Sequence Data ; Mutation ; *Phylogeny ; Plant Proteins/*genetics/metabolism ; Protein Structure, Tertiary ; RNA-Binding Proteins/*genetics/metabolism ; Zea mays/genetics ; }, abstract = {A small subset of the large pentatricopeptide repeat (PPR) protein family in higher plants contain a C-terminal small MutS-related (SMR) domain. Although few in number, they figure prominently in the chloroplast biogenesis and retrograde signaling literature due to their striking mutant phenotypes. In this review, we summarize current knowledge of PPR-SMR proteins focusing on Arabidopsis and maize proteomic and mutant studies. We also examine their occurrence in other organisms and have determined by phylogenetic analysis that, while they are limited to species that contain chloroplasts, their presence in algae and early branching land plant lineages indicates that the coupling of PPR motifs and an SMR domain into a single protein occurred early in the evolution of the Viridiplantae clade. In addition, we discuss their possible function and have examined conservation between SMR domains from Arabidopsis PPR proteins with those from other species that have been shown to possess endonucleolytic activity.}, }
@article {pmid24004309, year = {2015}, author = {Bai, XH and Guo, XW and Zhang, XJ and Song, W and Li, YH and Luo, W and Cao, XJ and Wang, WM}, title = {Species identification and evolutionary inference of the genera Megalobrama and Parabramis (Cyprinidae: Cultrinae) in China.}, journal = {Mitochondrial DNA}, volume = {26}, number = {3}, pages = {357-366}, doi = {10.3109/19401736.2013.823166}, pmid = {24004309}, issn = {1940-1744}, mesh = {Animals ; Base Sequence ; China ; Cyprinidae/*classification/genetics ; DNA/analysis/isolation &amp; purification/metabolism ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Genetic Linkage ; Haplotypes ; Mitochondria/metabolism ; Molecular Sequence Data ; NADH Dehydrogenase/genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; }, abstract = {The species boundaries and evolutionary relationships of two closely related genera, Megalobrama and Parabramis, were inferred from the partial mitochondrial cytochrome oxidase subunit I (COI) gene, NADH dehydrogenase subunit 2 (ND2) gene and their concatenated segment. Phylogenetic reconstructions showed that among the three breams, Megalobrama amblycephala and Megalobrama skolkovii are more closely related to each other than either is to Megalobrama terminalis. The taxonomy of M. pellegrini should be reconsidered. The divergence time estimation based on the assumption of a global molecular clock indicated that speciation and dispersal of the two genera might have occurred at approximately Pliocene to Late Pleistocene, due to major paleo-environmental events associated with monsoon evolution and the formation of the Three Gorges of the Yangtze River.}, }
@article {pmid24002810, year = {2013}, author = {Kang, L and Zheng, HX and Chen, F and Yan, S and Liu, K and Qin, Z and Liu, L and Zhao, Z and Li, L and Wang, X and He, Y and Jin, L}, title = {mtDNA lineage expansions in Sherpa population suggest adaptive evolution in Tibetan highlands.}, journal = {Molecular biology and evolution}, volume = {30}, number = {12}, pages = {2579-2587}, doi = {10.1093/molbev/mst147}, pmid = {24002810}, issn = {1537-1719}, mesh = {*Adaptation, Physiological ; *Altitude ; Bayes Theorem ; DNA, Mitochondrial/*genetics/metabolism ; Ethnicity/*genetics ; *Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Genome, Mitochondrial ; Haplotypes ; Humans ; Mitochondria/*genetics/metabolism ; Mutation ; NADH Dehydrogenase/*genetics ; Optic Atrophy, Hereditary, Leber/genetics ; Oxidative Phosphorylation ; Phylogeny ; Tibet ; }, abstract = {Sherpa population is an ethnic group living in south mountainside of Himalayas for hundreds of years. They are famous as extraordinary mountaineers and guides, considered as a good example for successful adaptation to low oxygen environment in Tibetan highlands. Mitochondrial DNA (mtDNA) variations might be important in the highland adaption given its role in coding core subunits of oxidative phosphorylation in mitochondria. In this study, we sequenced the complete mtDNA genomes of 76 unrelated Sherpa individuals. Generally, Sherpa mtDNA haplogroup constitution was close to Tibetan populations. However, we found three lineage expansions in Sherpas, two of which (C4a3b1 and A4e3a) were Sherpa-specific. Both lineage expansions might begin within the past hundreds of years. Especially, nine individuals carry identical Haplogroup C4a3b1. According to the history of Sherpas and Bayesian skyline plot, we constructed various demographic models and found out that it is unlikely for these lineage expansions to occur in neutral models especially for C4a3b1. Nonsynonymous mutations harbored in C4a3b1 (G3745A) and A4e3a (T4216C) are both ND1 mutants (A147T and Y304H, respectively). Secondary structure predictions showed that G3745A were structurally closing to other pathogenic mutants, whereas T4216C itself was reported as the primary mutation for Leber's hereditary optic neuropathy. Thus, we propose that these mutations had certain effect on Complex I function and might be important in the high altitude adaptation for Sherpa people.}, }
@article {pmid23995460, year = {2013}, author = {Zhang, F and Broughton, RE}, title = {Mitochondrial-nuclear interactions: compensatory evolution or variable functional constraint among vertebrate oxidative phosphorylation genes?.}, journal = {Genome biology and evolution}, volume = {5}, number = {10}, pages = {1781-1791}, pmid = {23995460}, issn = {1759-6653}, mesh = {Animals ; Catalytic Domain/genetics ; Cell Nucleus/*genetics ; Energy Metabolism/*genetics ; Evolution, Molecular ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics/metabolism ; *Oxidative Phosphorylation ; Vertebrates/genetics ; }, abstract = {Oxidative phosphorylation (OXPHOS), the major energy-producing pathway in aerobic organisms, includes protein subunits encoded by both mitochondrial (mt) and nuclear (nu) genomes. How these independent genomes have coevolved is a long-standing question in evolutionary biology. Although mt genes evolve faster than most nu genes, maintenance of OXPHOS structural stability and functional efficiency may involve correlated evolution of mt and nu OXPHOS genes. The nu OXPHOS genes might be predicted to exhibit accelerated evolutionary rates to accommodate the elevated substitution rates of mt OXPHOS subunits with which they interact. Evolutionary rates of nu OXPHOS genes should, therefore, be higher than that of nu genes that are not involved in OXPHOS (nu non-OXPHOS). We tested the compensatory evolution hypothesis by comparing the evolutionary rates (synonymous substitution rate dS and nonsynonymous substitution rate dN) among 13 mt OXPHOS genes, 60 nu OXPHOS genes, and 77 nu non-OXPHOS genes in vertebrates (7 fish and 40 mammal species). The results from a combined analysis of all OXPHOS subunits fit the predictions of the hypothesis. However, results from two OXPHOS complexes did not fit this pattern when analyzed separately. We found that the d(N) of nu OXPHOS genes for "core" subunits (those involved in the major catalytic activity) was lower than that of "noncore" subunits, whereas there was no significant difference in d(N) between genes for nu non-OXPHOS and core subunits. This latter finding suggests that compensatory changes play a minor role in the evolution of OXPHOS genes and that the observed accelerated nu substitution rates are due largely to reduced functional constraint on noncore subunits.}, }
@article {pmid23994494, year = {2014}, author = {Hewitt, VL and Gabriel, K and Traven, A}, title = {The ins and outs of the intermembrane space: diverse mechanisms and evolutionary rewiring of mitochondrial protein import routes.}, journal = {Biochimica et biophysica acta}, volume = {1840}, number = {4}, pages = {1246-1253}, doi = {10.1016/j.bbagen.2013.08.013}, pmid = {23994494}, issn = {0006-3002}, mesh = {Animals ; *Biological Evolution ; Candida albicans/genetics/metabolism ; Humans ; Mitochondria/genetics/*metabolism ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Protein Transport/physiology ; Saccharomyces cerevisiae/enzymology/genetics/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; }, abstract = {BACKGROUND: Mitochondrial biogenesis is an essential process in all eukaryotes. Import of proteins from the cytosol into mitochondria is a key step in organelle biogenesis. Recent evidence suggests that a given mitochondrial protein does not take the same import route in all organisms, suggesting that pathways of mitochondrial protein import can be rewired through evolution. Examples of this process so far involve proteins destined to the mitochondrial intermembrane space (IMS).<br><br>SCOPE OF REVIEW: Here we review the components, substrates and energy sources of the known mechanisms of protein import into the IMS. We discuss evolutionary rewiring of the IMS import routes, focusing on the example of the lactate utilisation enzyme cytochrome b2 (Cyb2) in the model yeast Saccharomyces cerevisiae and the human fungal pathogen Candida albicans.<br><br>MAJOR CONCLUSIONS: There are multiple import pathways used for protein entry into the IMS and they form a network capable of importing a diverse range of substrates. These pathways have been rewired, possibly in response to environmental pressures, such as those found in the niches in the human body inhabited by C. albicans.<br><br>GENERAL SIGNIFICANCE: We propose that evolutionary rewiring of mitochondrial import pathways can adjust the metabolic fitness of a given species to their environmental niche. This article is part of a Special Issue entitled Frontiers of Mitochondrial.}, }
@article {pmid23994165, year = {2014}, author = {Halas, D and Simons, AM}, title = {Cryptic speciation reversal in the Etheostoma zonale (Teleostei: Percidae) species group, with an examination of the effect of recombination and introgression on species tree inference.}, journal = {Molecular phylogenetics and evolution}, volume = {70}, number = {}, pages = {13-28}, doi = {10.1016/j.ympev.2013.08.014}, pmid = {23994165}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; North America ; Perches/classification/*genetics ; *Phylogeny ; Phylogeography ; *Recombination, Genetic ; }, abstract = {Mitochondrial and nuclear introgression among closely related taxa can greatly complicate the process of determining their phylogenetic relationships. In the Central Highlands of North America, many fish taxa have undergone introgression; in this study, we demonstrate the existence of an unusual introgression event in the Etheostoma zonale species group. We used one mitochondrial and seven nuclear loci to determine the relationships of the taxa within the E. zonale group, and their degree of differentiation. We found evidence of multiple divergent populations within each species; much of the divergence within species has taken place during the Pleistocene. We also found evidence of a previously unknown cryptic species in the Upper Tennessee River which diverged from the remainder of the group during the Pliocene, and has undergone mitochondrial and nuclear introgression with E. zonale, in an apparent process of speciation reversal. We examined the effects that using varying types of recombination tests to eliminate the signal of recombination from nuclear loci would have on the phylogenetic placement of this introgressed lineage in our species tree analyses.}, }
@article {pmid23993419, year = {2013}, author = {Bakhoum, AJ and Kacem, H and Neifar, L and Miquel, J}, title = {Ultrastructure of the spermatozoon of Centroderma spinosissima (Stossich, 1886) (Digenea: Mesometridae) and its phylogenetic potential.}, journal = {Tissue &amp; cell}, volume = {45}, number = {6}, pages = {428-433}, doi = {10.1016/j.tice.2013.07.006}, pmid = {23993419}, issn = {1532-3072}, mesh = {Animals ; Axoneme/*ultrastructure ; Cell Membrane/ultrastructure ; Cell Nucleus ; Male ; *Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; *Phylogeny ; Spermatozoa/*ultrastructure ; Trematoda/ultrastructure ; }, abstract = {The Mesometridae includes only five genera and eight species. The available data on the ultrastructure of sperm cells of mesometrid species referred to two species only, Elstia stossichianum and Wardula capitellata. The present study revealed the ultrastructure of the spermatozoon of a third genus and third species of Mesometridae, Centroderma spinosissima. The mature spermatozoon of C. spinosissima presents two axonemes with different lengths of the Ehlers' 9 + '1' trepaxonematan pattern, a nucleus, two mitochondria, two bundles of parallel cortical microtubules, external ornamentation of the plasma membrane, a lateral expansion, spine-like bodies, cytoplasmic ornamented buttons and granules of glycogen. The spermatozoon of C. spinosissima is similar to those of the previously studied mesometrids. However, some peculiarities such as the presence of two mitochondria, the disposition of the external ornamentation of the plasma membrane and the morphology of the posterior spermatozoon extremity, characterize the male gamete of C. spinosissima. Moreover, the presence of cytoplasmic ornamented buttons is a characteristic found only in the mature spermatozoon of mesometrids and it probably represents an autapomorphy for this family.}, }
@article {pmid23990946, year = {2013}, author = {Qiu, D and Huang, L and Liu, S and Zhang, H and Lin, S}, title = {Apical groove type and molecular phylogeny suggests reclassification of Cochlodinium geminatum as Polykrikos geminatum.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e71346}, pmid = {23990946}, issn = {1932-6203}, mesh = {Cell Nucleus/genetics ; Cell Separation ; China ; Classification ; Dinoflagellida/*classification/cytology/genetics ; Estuaries ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; }, abstract = {Traditionally Cocholodinium and Gymnodinium sensu lato clade are distinguished based on the cingulum turn number, which has been increasingly recognized to be inadequate for Gymnodiniales genus classification. This has been improved by the combination of the apical groove characteristics and molecular phylogeny, which has led to the erection of several new genera (Takayama, Akashiwo, Karenia, and Karlodinium). Taking the apical groove characteristics and molecular phylogeny combined approach, we reexamined the historically taxonomically uncertain species Cochlodinium geminatum that formed massive blooms in Pearl River Estuary, China, in recent years. Samples were collected from a bloom in 2011 for morphological, characteristic pigment, and molecular analyses. We found that the cingulum in this species wraps around the cell body about 1.2 turns on average but can appear under the light microscopy to be >1.5 turns after the cells have been preserved. The shape of its apical groove, however, was stably an open-ended anticlockwise loop of kidney bean shape, similar to that of Polykrikos. Furthermore, the molecular phylogenetic analysis using 18S rRNA-ITS-28S rRNA gene cistron we obtained in this study also consistently placed this species closest to Polykrikos within the Gymnodinium sensu stricto clade and set it far separated from the clade of Cochlodinium. These results suggest that this species should be transferred to Polykrikos as Polykrikos geminatum. Our results reiterate the need to use the combination of apical groove morphology and molecular phylogeny for the classification of species within the genus of Cochlodinium and other Gymnodiniales lineages.}, }
@article {pmid23986113, year = {2013}, author = {Hadjivasiliou, Z and Lane, N and Seymour, RM and Pomiankowski, A}, title = {Dynamics of mitochondrial inheritance in the evolution of binary mating types and two sexes.}, journal = {Proceedings. Biological sciences}, volume = {280}, number = {1769}, pages = {20131920}, pmid = {23986113}, issn = {1471-2954}, mesh = {Biological Evolution ; Cell Nucleus/*genetics ; Eukaryota/*genetics ; *Genes, Mitochondrial ; Genetic Fitness ; *Heredity ; Models, Genetic ; *Mutation ; Reproduction ; Selection, Genetic ; }, abstract = {The uniparental inheritance (UPI) of mitochondria is thought to explain the evolution of two mating types or even true sexes with anisogametes. However, the exact role of UPI is not clearly understood. Here, we develop a new model, which considers the spread of UPI mutants within a biparental inheritance (BPI) population. Our model explicitly considers mitochondrial mutation and selection in parallel with the spread of UPI mutants and self-incompatible mating types. In line with earlier work, we find that UPI improves fitness under mitochondrial mutation accumulation, selfish conflict and mitonuclear coadaptation. However, we find that as UPI increases in the population its relative fitness advantage diminishes in a frequency-dependent manner. The fitness benefits of UPI 'leak' into the biparentally reproducing part of the population through successive matings, limiting the spread of UPI. Critically, while this process favours some degree of UPI, it neither leads to the establishment of linked mating types nor the collapse of multiple mating types to two. Only when two mating types exist beforehand can associated UPI mutants spread to fixation under the pressure of high mitochondrial mutation rate, large mitochondrial population size and selfish mutants. Variation in these parameters could account for the range of UPI actually observed in nature, from strict UPI in some Chlamydomonas species to BPI in yeast. We conclude that UPI of mitochondria alone is unlikely to have driven the evolution of two mating types in unicellular eukaryotes.}, }
@article {pmid23986111, year = {2013}, author = {Brown, MW and Sharpe, SC and Silberman, JD and Heiss, AA and Lang, BF and Simpson, AG and Roger, AJ}, title = {Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads.}, journal = {Proceedings. Biological sciences}, volume = {280}, number = {1769}, pages = {20131755}, pmid = {23986111}, issn = {1471-2954}, support = {MOP-62809//Canadian Institutes of Health Research/Canada ; }, mesh = {Ecosystem ; Estuaries ; Eukaryota/*classification/*genetics/ultrastructure ; Evolution, Molecular ; Genes, rRNA ; Geologic Sediments ; Molecular Sequence Data ; *Phylogeny ; RNA, Protozoan/genetics/metabolism ; Sequence Analysis, RNA ; }, abstract = {Most eukaryotic lineages belong to one of a few major groups. However, several protistan lineages have not yet been robustly placed in any of these groups. Both the breviates and apusomonads are two such lineages that appear to be related to the Amoebozoa and Opisthokonta (i.e. the 'unikonts' or Amorphea); however, their precise phylogenetic positions remain unclear. Here, we describe a novel microaerophilic breviate, Pygsuia biforma gen. nov. sp. nov., isolated from a hypoxic estuarine sediment. Ultrastructurally, this species resembles the breviate genera Breviata and Subulatomonas but has two cell morphologies, adherent and swimming. Phylogenetic analyses of the small sub-unit rRNA gene show that Pygsuia is the sister to the other breviates. We constructed a 159-protein supermatrix, including orthologues identified in RNA-seq data from Pygsuia. Phylogenomic analyses of this dataset show that breviates, apusomonads and Opisthokonta form a strongly supported major eukaryotic grouping we name the Obazoa. Although some phylogenetic methods disagree, the balance of evidence suggests that the breviate lineage forms the deepest branch within Obazoa. We also found transcripts encoding a nearly complete integrin adhesome from Pygsuia, indicating that this protein complex involved in metazoan multicellularity may have evolved earlier in eukaryote evolution than previously thought.}, }
@article {pmid23979261, year = {2013}, author = {Guo, W and Mower, JP}, title = {Evolution of plant mitochondrial intron-encoded maturases: frequent lineage-specific loss and recurrent intracellular transfer to the nucleus.}, journal = {Journal of molecular evolution}, volume = {77}, number = {1-2}, pages = {43-54}, pmid = {23979261}, issn = {1432-1432}, mesh = {*Evolution, Molecular ; Genes, Mitochondrial ; Intracellular Space/metabolism ; *Introns ; Mitochondria/*enzymology/*genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Plants/classification/*genetics/*metabolism ; Protein Transport ; }, abstract = {Among land plants, mitochondrial and plastid group II introns occasionally encode proteins called maturases that are important for splicing. Angiosperm nuclear genomes also encode maturases that are targeted to the organelles, but it is not known whether nucleus-encoded maturases exist in other land plant lineages. To examine the evolutionary diversity and history of this essential gene family, we searched for maturase homologs in recently sequenced nuclear and mitochondrial genomes from diverse land plants. We found that maturase content in mitochondrial genomes is highly lineage specific, such that orthologous maturases are rarely shared among major land plant groups. The presence of numerous mitochondrial pseudogenes in the mitochondrial genomes of several species implies that the sporadic maturase distribution is due to frequent inactivation and eventual loss over time. We also identified multiple maturase paralogs in the nuclear genomes of the lycophyte Selaginella moellendorffii, the moss Physcomitrella patens, and the representative angiosperm Vitis vinifera. Phylogenetic analyses of organelle- and nucleus-encoded maturases revealed that the nuclear maturase genes in angiosperms, lycophytes, and mosses arose by multiple shared and independent transfers of mitochondrial paralogs to the nuclear genome during land plant evolution. These findings indicate that plant mitochondrial maturases have experienced a surprisingly dynamic history due to a complex interaction of multiple evolutionary forces that affect the rates of maturase gain, retention, and loss.}, }
@article {pmid23969110, year = {2014}, author = {Paparoditis, P and Västermark, A and Le, AJ and Fuerst, JA and Saier, MH}, title = {Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica.}, journal = {Biochimica et biophysica acta}, volume = {1838}, number = {1 Pt B}, pages = {193-215}, pmid = {23969110}, issn = {0006-3002}, support = {R01 GM077402/GM/NIGMS NIH HHS/United States ; GM077402/GM/NIGMS NIH HHS/United States ; }, mesh = {Aquatic Organisms ; Bacterial Proteins/genetics/*metabolism ; Biological Evolution ; *Computational Biology ; Databases, Genetic ; Electron Transport ; *Genome, Bacterial ; Membrane Proteins/genetics/*metabolism ; Membrane Transport Proteins/genetics/*metabolism ; Phylogeny ; Planctomycetales/classification/genetics/*metabolism ; }, abstract = {Rhodopirellula baltica (R. baltica) is a Planctomycete, known to have intracellular membranes. Because of its unusual cell structure and ecological significance, we have conducted comprehensive analyses of its transmembrane transport proteins. The complete proteome of R. baltica was screened against the Transporter Classification Database (TCDB) to identify recognizable integral membrane transport proteins. 342 proteins were identified with a high degree of confidence, and these fell into several different classes. R. baltica encodes in its genome channels (12%), secondary carriers (33%), and primary active transport proteins (41%) in addition to classes represented in smaller numbers. Relative to most non-marine bacteria, R. baltica possesses a larger number of sodium-dependent symporters but fewer proton-dependent symporters, and it has dimethylsulfoxide (DMSO) and trimethyl-amine-oxide (TMAO) reductases, consistent with its Na(+)-rich marine environment. R. baltica also possesses a Na(+)-translocating NADH:quinone dehydrogenase (Na(+)-NDH), a Na(+) efflux decarboxylase, two Na(+)-exporting ABC pumps, two Na(+)-translocating F-type ATPases, two Na(+):H(+) antiporters and two K(+):H(+) antiporters. Flagellar motility probably depends on the sodium electrochemical gradient. Surprisingly, R. baltica also has a complete set of H(+)-translocating electron transport complexes similar to those present in α-proteobacteria and eukaryotic mitochondria. The transport proteins identified proved to be typical of the bacterial domain with little or no indication of the presence of eukaryotic-type transporters. However, novel functionally uncharacterized multispanning membrane proteins were identified, some of which are found only in Rhodopirellula species, but others of which are widely distributed in bacteria. The analyses lead to predictions regarding the physiology, ecology and evolution of R. baltica.}, }
@article {pmid23968920, year = {2013}, author = {van der Giezen, M}, title = {Evolution: one thread to unite them all.}, journal = {Current biology : CB}, volume = {23}, number = {16}, pages = {R679-81}, doi = {10.1016/j.cub.2013.06.048}, pmid = {23968920}, issn = {1879-0445}, mesh = {Animals ; Chytridiomycota/*genetics ; DNA, Fungal/*genetics ; DNA, Protozoan/*genetics ; *Genome, Fungal ; *Genome, Protozoan ; Microsporidia/*genetics ; *Phylogeny ; Rhizaria/*genetics ; }, abstract = {Mitochondria play import roles in the overall metabolism of eukaryotes. Traditionally, they have played a secondary role to the nucleus in the origin of eukaryotes. However, their relative positions in this crucial event for eukaryotic evolution might be reversed.}, }
@article {pmid23958563, year = {2014}, author = {Rackham, O and Filipovska, A}, title = {Supernumerary proteins of mitochondrial ribosomes.}, journal = {Biochimica et biophysica acta}, volume = {1840}, number = {4}, pages = {1227-1232}, doi = {10.1016/j.bbagen.2013.08.010}, pmid = {23958563}, issn = {0006-3002}, mesh = {Animals ; Disease/etiology ; Gene Expression Regulation ; Humans ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/*physiology ; Ribosomal Proteins/*physiology ; Ribosomes/genetics/*metabolism ; }, abstract = {BACKGROUND: Messenger RNAs encoded by mitochondrial genomes are translated on mitochondrial ribosomes that have unique structure and protein composition compared to prokaryotic and cytoplasmic ribosomes. Mitochondrial ribosomes are a patchwork of core proteins that share homology with prokaryotic ribosomal proteins and new, supernumerary proteins that can be unique to different organisms. In mammals, there are specific supernumerary ribosomal proteins that are not present in other eukaryotes.<br><br>SCOPE OF REVIEW: Here we discuss the roles of supernumerary proteins in the regulation of mitochondrial gene expression and compare them among different eukaryotic systems. Furthermore, we consider if differences in the structure and organization of mitochondrial genomes may have contributed to the acquisition of mitochondrial ribosomal proteins with new functions.<br><br>MAJOR CONCLUSIONS: The distinct and diverse compositions of mitochondrial ribosomes illustrate the high evolutionary divergence found between mitochondrial genetic systems.<br><br>GENERAL SIGNIFICANCE: Elucidating the role of the organism-specific supernumerary proteins may provide a window into the regulation of mitochondrial gene expression through evolution in response to distinct evolutionary paths taken by mitochondria in different organisms. This article is part of a Special Issue entitled Frontiers of Mitochondrial Research.}, }
@article {pmid23958440, year = {2014}, author = {Wende, S and Platzer, EG and Jühling, F and Pütz, J and Florentz, C and Stadler, PF and Mörl, M}, title = {Biological evidence for the world's smallest tRNAs.}, journal = {Biochimie}, volume = {100}, number = {}, pages = {151-158}, doi = {10.1016/j.biochi.2013.07.034}, pmid = {23958440}, issn = {1638-6183}, mesh = {Animals ; Base Sequence ; Genome, Mitochondrial ; Mermithoidea/*genetics/metabolism ; Mitochondria/*genetics/metabolism ; Molecular Sequence Annotation ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Biosynthesis ; RNA, Transfer/*chemistry/genetics/metabolism ; Transcription, Genetic ; }, abstract = {Due to their function as adapters in translation, tRNA molecules share a common structural organization in all kingdoms and organelles with ribosomal protein biosynthesis. A typical tRNA has a cloverleaf-like secondary structure, consisting of acceptor stem, D-arm, anticodon arm, a variable region, and T-arm, with an average length of 73 nucleotides. In several mitochondrial genomes, however, tRNA genes encode transcripts that show a considerable deviation of this standard, having reduced D- or T-arms or even completely lack one of these elements, resulting in tRNAs as small as 66 nts. An extreme case of such truncations is found in the mitochondria of Enoplea. Here, several tRNA genes are annotated that lack both the D- and the T-arm, suggesting even shorter transcripts with a length of only 42 nts. However, direct evidence for these exceptional tRNAs, which were predicted by purely computational means, has been lacking so far. Here, we demonstrate that several of these miniaturized armless tRNAs consisting only of acceptor- and anticodon-arms are indeed transcribed and correctly processed by non-encoded CCA addition in the mermithid Romanomermis culicivorax. This is the first direct evidence for the existence and functionality of the smallest tRNAs ever identified so far. It opens new possibilities towards exploration/assessment of minimal structural motifs defining a functional tRNA and their evolution.}, }
@article {pmid23954798, year = {2014}, author = {Kuzmenko, A and Atkinson, GC and Levitskii, S and Zenkin, N and Tenson, T and Hauryliuk, V and Kamenski, P}, title = {Mitochondrial translation initiation machinery: conservation and diversification.}, journal = {Biochimie}, volume = {100}, number = {100}, pages = {132-140}, pmid = {23954798}, issn = {1638-6183}, support = {202994/ERC_/European Research Council/International ; BB/J006378/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Biological Evolution ; Electron Transport/genetics ; Humans ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/*genetics/metabolism ; Molecular Sequence Data ; *Peptide Chain Initiation, Translational ; Prokaryotic Initiation Factor-2/genetics/metabolism ; Prokaryotic Initiation Factor-3/genetics/metabolism ; Pseudomonas/genetics/metabolism ; RNA, Messenger/*genetics/metabolism ; Ribosomes/genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {The highly streamlined mitochondrial genome encodes almost exclusively a handful of transmembrane components of the respiratory chain complex. In order to ensure the correct assembly of the respiratory chain, the products of these genes must be produced in the correct stoichiometry and inserted into the membrane, posing a unique challenge to the mitochondrial translational system. In this review we describe the proteins orchestrating mitochondrial translation initiation: bacterial-like general initiation factors mIF2 and mIF3, as well as mitochondria-specific components - mRNA-specific translational activators and mRNA-nonspecific accessory initiation factors. We consider how the fast rate of evolution in these organelles has not only created a system that is divergent from that of its bacterial ancestors, but has led to a huge diversity in lineage specific mechanistic features of mitochondrial translation initiation among eukaryotes.}, }
@article {pmid23954756, year = {2013}, author = {Talavera, G and Lukhtanov, VA and Rieppel, L and Pierce, NE and Vila, R}, title = {In the shadow of phylogenetic uncertainty: the recent diversification of Lysandra butterflies through chromosomal change.}, journal = {Molecular phylogenetics and evolution}, volume = {69}, number = {3}, pages = {469-478}, doi = {10.1016/j.ympev.2013.08.004}, pmid = {23954756}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Butterflies/*classification/genetics ; *Chromosomal Instability ; Chromosomes ; *Evolution, Molecular ; Genetic Markers ; Hybridization, Genetic ; Karyotype ; Male ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The phylogeny of the butterfly genus Lysandra (Lycaenidae, Polyommatinae) has been intractable using both molecular and morphological characters, which could be a result of speciation due to karyotype instability. Here we reconstruct the phylogeny of the group using multi-locus coalescent-based methods on seven independent genetic markers. While the genus is ca. 4.9 Mya old, the diversification of the extant lineages was extremely recent (ca. 1.5 Mya) and involved multiple chromosomal rearrangements. We find that relationships are uncertain due to both incomplete lineage sorting and hybridization. Minimizing the impact of reticulation in inferring the species tree by testing for mitochondrial introgression events yields a partially resolved tree with three main supported clades: L. punctifera+L. bellargus, the corydonius taxa, and L. coridon+the Iberian taxa, plus three independent lineages without apparently close relatives (L. ossmar, L. syriaca and L. dezina). Based on these results and new karyotypic data, we propose a rearrangement recognizing ten species within the genus. Finally, we hypothesize that chromosomal instability may have played a crucial role in the Lysandra recent diversification. New chromosome rearrangements might be fixed in populations after severe bottlenecks, which at the same time might promote rapid sorting of neutral molecular markers. We argue that population bottlenecks might be a prerequisite for chromosomal speciation in this group.}, }
@article {pmid23954723, year = {2013}, author = {Gao, D and Xu, Z and Zhang, X and Zhu, C and Wang, Y and Min, W}, title = {Cadmium triggers kidney cell apoptosis of purse red common carp (Cyprinus carpio) without caspase-8 activation.}, journal = {Developmental and comparative immunology}, volume = {41}, number = {4}, pages = {728-737}, doi = {10.1016/j.dci.2013.08.004}, pmid = {23954723}, issn = {1879-0089}, mesh = {Amino Acid Sequence ; Animals ; Apoptosis/*drug effects ; Cadmium Compounds/*pharmacology ; Carps/anatomy &amp; histology/metabolism/*physiology ; Caspase 8/genetics/*metabolism ; China ; Cytoplasm/genetics/metabolism ; DNA, Complementary/genetics ; Enzyme Activation ; Epithelial Cells/cytology/drug effects/metabolism ; Kidney Tubules/cytology/*drug effects/metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sulfates/*pharmacology ; Zebrafish ; }, abstract = {Caspase-8, the essential initiator caspase, is believed to play a pivotal role in death receptor-mediated apoptotic pathway. It also participates in mitochondria-mediated apoptosis via cleavage of proapoptotic Bid in mammals. However, its role in fish remains elusive in Cadmium-induced apoptotic pathway. In this study, we isolated the caspase-8 gene from common carp, one of the most important industrial aquatic animals in China using rapid amplification of cDNA ends (RACE). The deduced amino acid sequence of caspase-8 comprised 475 amino acids, which showed approximately 64.1% identity and 79.8% similarity to zebrafish (Danio rerio) caspase-8, possessed two conserved death effector domains, a large subunit and a small subunit. Phylogenetic analysis demonstrated that caspase-8 formed a clade with zebrafish caspase-8. In kidney, cadmium (Cd) exposure triggered apoptosis and increased caspase-3 and -9 activities, whereas it did not affect caspase-8 activity. Real-time quantitative PCR analysis revealed that caspase-8 transcriptional level was not significantly increased in kidney after exposure to Cd. Using Western blot analysis, no caspase-8 cleaved fragment was detected and no significant alteration of procaspase-8 level was found with the same Cd-treated condition. Moreover, the immunopositive staining was predominantly limited to the cytoplasm of renal tubular epithelial cells and no remarkable changes of immunoreactivities were observed using immunohistochemical detection after Cd treatment. The results reveal that Cd can trigger apoptosis, while it cannot activate caspase-8 in purse red common carp.}, }
@article {pmid23954411, year = {2014}, author = {Urban, Z and Davis, EC}, title = {Cutis laxa: intersection of elastic fiber biogenesis, TGFβ signaling, the secretory pathway and metabolism.}, journal = {Matrix biology : journal of the International Society for Matrix Biology}, volume = {33}, number = {}, pages = {16-22}, pmid = {23954411}, issn = {1569-1802}, support = {R01 HL090648/HL/NHLBI NIH HHS/United States ; HL090648/HL/NHLBI NIH HHS/United States ; }, mesh = {Cutis Laxa/*metabolism ; Elastic Tissue/*metabolism ; Humans ; Protein Transport ; Protein-Lysine 6-Oxidase ; Reactive Oxygen Species/metabolism ; *Secretory Pathway ; Signal Transduction ; Transforming Growth Factor beta/*physiology ; Transport Vesicles/metabolism ; }, abstract = {Cutis laxa (CL), a disease characterized by redundant and inelastic skin, displays extensive locus heterogeneity. Together with geroderma osteodysplasticum and arterial tortuosity syndrome, which show phenotypic overlap with CL, eleven CL-related genes have been identified to date, which encode proteins within 3 groups. Elastin, fibulin-4, fibulin-5 and latent transforming growth factor-β-binding protein 4 are secreted proteins which form elastic fibers and are involved in the sequestration and subsequent activation of transforming growth factor-β (TGFβ). Proteins within the second group, localized to the secretory pathway, perform transport and membrane trafficking functions necessary for the modification and secretion of elastic fiber components. Key proteins include a subunit of the vacuolar-type proton pump, which ensures the efficient secretion of tropoelastin, the precursor or elastin. A copper transporter is required for the activity of lysyl oxidases, which crosslink collagen and elastin. A Rab6-interacting goglin recruits kinesin motors to Golgi-vesicles facilitating the transport from the Golgi to the plasma membrane. The Rab and Ras interactor 2 regulates the activity of Rab5, a small guanosine triphosphatase essential for the endocytosis of various cell surface receptors, including integrins. Proteins of the third group related to CL perform metabolic functions within the mitochondria, inhibiting the accumulation of reactive oxygen species. Two of these proteins catalyze subsequent steps in the conversion of glutamate to proline. The third transports dehydroascorbate into mitochondria. Recent studies on CL-related proteins highlight the intricate connections among membrane trafficking, metabolism, extracellular matrix assembly, and TGFβ signaling.}, }
@article {pmid23946486, year = {2013}, author = {Majewska, J and Ciesielski, SJ and Schilke, B and Kominek, J and Blenska, A and Delewski, W and Song, JY and Marszalek, J and Craig, EA and Dutkiewicz, R}, title = {Binding of the chaperone Jac1 protein and cysteine desulfurase Nfs1 to the iron-sulfur cluster scaffold Isu protein is mutually exclusive.}, journal = {The Journal of biological chemistry}, volume = {288}, number = {40}, pages = {29134-29142}, pmid = {23946486}, issn = {1083-351X}, support = {R01 GM027870/GM/NIGMS NIH HHS/United States ; GM27870/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Amino Acids/metabolism ; Binding, Competitive ; Carbon-Sulfur Lyases/chemistry/*metabolism ; Conserved Sequence ; Evolution, Molecular ; Iron-Sulfur Proteins/chemistry/*metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; Models, Biological ; Models, Molecular ; Molecular Chaperones/chemistry/*metabolism ; Molecular Sequence Data ; Protein Binding ; Saccharomyces cerevisiae/cytology/growth &amp; development/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; Structure-Activity Relationship ; Sulfurtransferases/chemistry/*metabolism ; }, abstract = {Biogenesis of mitochondrial iron-sulfur (Fe/S) cluster proteins requires the interaction of multiple proteins with the highly conserved 14-kDa scaffold protein Isu, on which clusters are built prior to their transfer to recipient proteins. For example, the assembly process requires the cysteine desulfurase Nfs1, which serves as the sulfur donor for cluster assembly. The transfer process requires Jac1, a J-protein Hsp70 cochaperone. We recently identified three residues on the surface of Jac1 that form a hydrophobic patch critical for interaction with Isu. The results of molecular modeling of the Isu1-Jac1 interaction, which was guided by these experimental data and structural/biophysical information available for bacterial homologs, predicted the importance of three hydrophobic residues forming a patch on the surface of Isu1 for interaction with Jac1. Using Isu variants having alterations in residues that form the hydrophobic patch on the surface of Isu, this prediction was experimentally validated by in vitro binding assays. In addition, Nfs1 was found to require the same hydrophobic residues of Isu for binding, as does Jac1, suggesting that Jac1 and Nfs1 binding is mutually exclusive. In support of this conclusion, Jac1 and Nfs1 compete for binding to Isu. Evolutionary analysis revealed that residues involved in these interactions are conserved and that they are critical residues for the biogenesis of Fe/S cluster protein in vivo. We propose that competition between Jac1 and Nfs1 for Isu binding plays an important role in transitioning the Fe/S cluster biogenesis machinery from the cluster assembly step to the Hsp70-mediated transfer of the Fe/S cluster to recipient proteins.}, }
@article {pmid23943303, year = {2013}, author = {Mitra, K}, title = {Mitochondrial fission-fusion as an emerging key regulator of cell proliferation and differentiation.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {11}, pages = {955-964}, doi = {10.1002/bies.201300011}, pmid = {23943303}, issn = {1521-1878}, mesh = {Animals ; Cell Cycle ; *Cell Differentiation ; *Cell Proliferation ; Cyclin E/genetics/metabolism ; Evolution, Molecular ; Mitochondria/physiology ; Mitochondrial Dynamics/*physiology ; Models, Molecular ; Signal Transduction ; Stem Cells ; Yeasts/genetics/metabolism ; }, abstract = {Mitochondrial shape change, brought about by molecules that promote either fission or fusion between individual mitochondria, has been documented in several model systems. However, the deeper significance of mitochondrial shape change has only recently begun to emerge: among others, it appears to play a role in the regulation of cell proliferation. Here, I review the emerging interplay between mitochondrial fission-fusion components with cell cycle regulatory machineries and how that may impact cell differentiation. Regulation of mitochondrial shape may modulate mitochondrial metabolism and/or energetics to promote crosstalk between signaling components and the cell cycle machinery. Focused research in this area will reveal the exact role of mitochondria in development and disease, specifically in stem cell regulation and tumorigenesis. Such research may also reveal whether and how the endosymbiotic event that gave rise to the mitochondrion was crucial for the evolution of cell cycle regulatory mechanisms in eukaryotes that are absent in prokaryotes.}, }
@article {pmid23942320, year = {2013}, author = {Suga, H and Chen, Z and de Mendoza, A and Sebé-Pedrós, A and Brown, MW and Kramer, E and Carr, M and Kerner, P and Vervoort, M and Sánchez-Pons, N and Torruella, G and Derelle, R and Manning, G and Lang, BF and Russ, C and Haas, BJ and Roger, AJ and Nusbaum, C and Ruiz-Trillo, I}, title = {The Capsaspora genome reveals a complex unicellular prehistory of animals.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {2325}, pmid = {23942320}, issn = {2041-1723}, support = {HG003067-05/HG/NHGRI NIH HHS/United States ; U54 HG003067/HG/NHGRI NIH HHS/United States ; HG003067-09/HG/NHGRI NIH HHS/United States ; 206883/ERC_/European Research Council/International ; HG003067-07/HG/NHGRI NIH HHS/United States ; HG003067-06/HG/NHGRI NIH HHS/United States ; HG003067-10/HG/NHGRI NIH HHS/United States ; HG003067-08/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Apoptosis/genetics ; Base Sequence ; Biological Evolution ; Cell Adhesion/genetics ; Choanoflagellata/*genetics/metabolism ; Evolution, Molecular ; Genome ; Intercellular Signaling Peptides and Proteins/*genetics/metabolism ; Mesomycetozoea/*genetics ; Mitochondria/genetics ; Phylogeny ; Protein Structure, Tertiary/genetics ; Sequence Analysis, DNA ; Signal Transduction/genetics ; Transcription, Genetic/genetics ; }, abstract = {To reconstruct the evolutionary origin of multicellular animals from their unicellular ancestors, the genome sequences of diverse unicellular relatives are essential. However, only the genome of the choanoflagellate Monosiga brevicollis has been reported to date. Here we completely sequence the genome of the filasterean Capsaspora owczarzaki, the closest known unicellular relative of metazoans besides choanoflagellates. Analyses of this genome alter our understanding of the molecular complexity of metazoans' unicellular ancestors showing that they had a richer repertoire of proteins involved in cell adhesion and transcriptional regulation than previously inferred only with the choanoflagellate genome. Some of these proteins were secondarily lost in choanoflagellates. In contrast, most intercellular signalling systems controlling development evolved later concomitant with the emergence of the first metazoans. We propose that the acquisition of these metazoan-specific developmental systems and the co-option of pre-existing genes drove the evolutionary transition from unicellular protists to metazoans.}, }
@article {pmid23942268, year = {2013}, author = {Venâncio, C and Antunes, L and Félix, L and Rodrigues, P and Summavielle, T and Peixoto, F}, title = {Chronic ketamine administration impairs mitochondrial complex I in the rat liver.}, journal = {Life sciences}, volume = {93}, number = {12-14}, pages = {464-470}, doi = {10.1016/j.lfs.2013.08.001}, pmid = {23942268}, issn = {1879-0631}, mesh = {Analgesics/*toxicity ; Animals ; Electron Transport Complex I/*metabolism ; Glycogen/metabolism ; Ketamine/*toxicity ; Liver/drug effects/*enzymology ; Male ; Mitochondria, Liver/drug effects/*enzymology ; Oxidative Stress ; Oxygen Consumption ; Rats ; Rats, Wistar ; Weight Gain/drug effects ; }, abstract = {AIM: Ketamine can induce hepatotoxicity which has been suggested to be dependent on mitochondrial impairment. This study investigated the long-term effects of chronic low-dose ketamine on liver mitochondrial function, oxidative stress parameters, liver histology and glycogen content.<br><br>MAIN METHODS: Adult rats were administered with saline or ketamine (5 or 10mg/kg) twice a day for a fourteen-day period in order to mimic chronic treatments. Effects between groups were compared ten days after the treatment had ended. Liver mitochondrial function was monitored in isolated mitochondrial extracts through evaluation of respiration parameters and activity of respiratory complexes, as well as oxidative stress, through lipid peroxidation, protein oxidation and superoxide dismutase activity. The hepatic histology and liver glycogen content were also evaluated.<br><br>KEY FINDINGS: Ketamine groups showed a decreased evolution in body weight gains during the treatment period. Ketamine had no effect either on serum liver enzymes or on the oxidative stress parameters of liver mitochondria. Ketamine decreased the hepatic glycogen content, inhibited mitochondrial complex I and oxygen consumption when glutamate-malate substrate was used.<br><br>SIGNIFICANCE: These findings reflect a long-term mitochondrial bioenergetic deterioration induced by ketamine, which may explain the increased susceptibility of some patients to its prolonged or repeated use.}, }
@article {pmid23942147, year = {2013}, author = {Day, M}, title = {Yeast petites and small colony variants: for everything there is a season.}, journal = {Advances in applied microbiology}, volume = {85}, number = {}, pages = {1-41}, doi = {10.1016/B978-0-12-407672-3.00001-0}, pmid = {23942147}, issn = {0065-2164}, mesh = {Mutation ; Phenotype ; Saccharomyces ; *Saccharomyces cerevisiae ; Seasons ; Staphylococcal Infections ; *Staphylococcus aureus ; Yeast, Dried ; }, abstract = {The yeast petite mutant was first found in the yeast Saccharomyces cerevisiae. The colony is small because of a block in the aerobic respiratory chain pathway, which generates ATP. The petite yeasts are thus unable to grow on nonfermentable carbon sources (such as glycerol or ethanol), and form small anaerobic-sized colonies when grown in the presence of fermentable carbon sources (such as glucose). The petite phenotype results from mutations in the mitochondrial genome, loss of mitochondria, or mutations in the host cell genome. The latter mutations affect nuclear-encoded genes involved in oxidative phosphorylation and these mutants are termed neutral petites. They all produce wild-type progeny when crossed with a wild-type strain. The staphylococcal small colony variant (SCV) is a slow-growing mutant that typically exhibits the loss of many phenotypic characteristics and pathogenic traits. SCVs are mostly small, nonpigmented, and nonhaemolytic. Their small size is often due to an inability to synthesize electron transport chain components and so cannot generate ATP by oxidative phosphorylation. Evidence suggests that they are responsible for persistent and/or recurrent infections. This chapter compares the physiological and genetic basis of the petite mutants and SCVs. The review focuses principally on two representatives, the eukaryote S. cerevisiae and the prokaryote Staphylococcus aureus. There is, clearly, commonality in the physiological response. Interestingly, the similarity, based on their physiological states, has not been commented on previously. The finding of an overlapping physiological response that occurs across a taxonomic divide is novel.}, }
@article {pmid23940792, year = {2013}, author = {Hagen, CM and Aidt, FH and Hedley, PL and Jensen, MK and Havndrup, O and Kanters, JK and Moolman-Smook, JC and Larsen, SO and Bundgaard, H and Christiansen, M}, title = {Mitochondrial haplogroups modify the risk of developing hypertrophic cardiomyopathy in a Danish population.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e71904}, pmid = {23940792}, issn = {1932-6203}, mesh = {Adult ; Aged ; Cardiomyopathy, Hypertrophic/*epidemiology/*genetics ; DNA, Mitochondrial/*genetics ; Denmark/epidemiology ; Female ; Genetic Predisposition to Disease ; Genetics, Population ; *Haplotypes ; Humans ; Male ; Middle Aged ; Mitochondria/genetics ; Phylogeny ; Risk Factors ; }, abstract = {Hypertrophic cardiomyopathy (HCM) is a genetic disorder caused by mutations in genes coding for proteins involved in sarcomere function. The disease is associated with mitochondrial dysfunction. Evolutionarily developed variation in mitochondrial DNA (mtDNA), defining mtDNA haplogroups and haplogroup clusters, is associated with functional differences in mitochondrial function and susceptibility to various diseases, including ischemic cardiomyopathy. We hypothesized that mtDNA haplogroups, in particular H, J and K, might modify disease susceptibility to HCM. Mitochondrial DNA, isolated from blood, was sequenced and haplogroups identified in 91 probands with HCM. The association with HCM was ascertained using two Danish control populations. Haplogroup H was more prevalent in HCM patients, 60% versus 46% (p = 0.006) and 41% (p = 0.003), in the two control populations. Haplogroup J was less prevalent, 3% vs. 12.4% (p = 0.017) and 9.1%, (p = 0.06). Likewise, the UK haplogroup cluster was less prevalent in HCM, 11% vs. 22.1% (p = 0.02) and 22.8% (p = 0.04). These results indicate that haplogroup H constitutes a susceptibility factor and that haplogroup J and haplogroup cluster UK are protective factors in the development of HCM. Thus, constitutive differences in mitochondrial function may influence the occurrence and clinical presentation of HCM. This could explain some of the phenotypic variability in HCM. The fact that haplogroup H and J are also modifying factors in ischemic cardiomyopathy suggests that mtDNA haplotypes may be of significance in determining whether a physiological hypertrophy develops into myopathy. mtDNA haplotypes may have the potential of becoming significant biomarkers in cardiomyopathy.}, }
@article {pmid23940520, year = {2013}, author = {Liu, G and Cao, D and Li, S and Su, A and Geng, J and Grover, CE and Hu, S and Hua, J}, title = {The complete mitochondrial genome of Gossypium hirsutum and evolutionary analysis of higher plant mitochondrial genomes.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e69476}, pmid = {23940520}, issn = {1932-6203}, mesh = {*Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Genome, Plant/*genetics ; Gossypium/*genetics ; }, abstract = {BACKGROUND: Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (Gossypium hirsutum L.) is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt) genome could be helpful for the evolution research of plant mt genomes.<br><br>We utilized 454 technology for sequencing and combined with Fosmid library of the Gossypium hirsutum mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on Cycas taitungensis and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of G. hirsutum was obtained. The completed G.hirsutum mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes.<br><br>CONCLUSION: The G. hirsutum mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species.}, }
@article {pmid23940100, year = {2013}, author = {Smith, DR and Hua, J and Archibald, JM and Lee, RW}, title = {Palindromic genes in the linear mitochondrial genome of the nonphotosynthetic green alga Polytomella magna.}, journal = {Genome biology and evolution}, volume = {5}, number = {9}, pages = {1661-1667}, pmid = {23940100}, issn = {1759-6653}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Chlorophyta/*genetics/physiology ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; Genome, Plastid ; Inverted Repeat Sequences/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Open Reading Frames/*genetics ; Photosynthesis ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Organelle DNA is no stranger to palindromic repeats. But never has a mitochondrial or plastid genome been described in which every coding region is part of a distinct palindromic unit. While sequencing the mitochondrial DNA of the nonphotosynthetic green alga Polytomella magna, we uncovered precisely this type of genic arrangement. The P. magna mitochondrial genome is linear and made up entirely of palindromes, each containing 1-7 unique coding regions. Consequently, every gene in the genome is duplicated and in an inverted orientation relative to its partner. And when these palindromic genes are folded into putative stem-loops, their predicted translational start sites are often positioned in the apex of the loop. Gel electrophoresis results support the linear, 28-kb monomeric conformation of the P. magna mitochondrial genome. Analyses of other Polytomella taxa suggest that palindromic mitochondrial genes were present in the ancestor of the Polytomella lineage and lost or retained to various degrees in extant species. The possible origins and consequences of this bizarre genomic architecture are discussed.}, }
@article {pmid23933583, year = {2013}, author = {Al-Furoukh, N and Goffart, S and Szibor, M and Wanrooij, S and Braun, T}, title = {Binding to G-quadruplex RNA activates the mitochondrial GTPase NOA1.}, journal = {Biochimica et biophysica acta}, volume = {1833}, number = {12}, pages = {2933-2942}, doi = {10.1016/j.bbamcr.2013.07.022}, pmid = {23933583}, issn = {0006-3002}, mesh = {Animals ; Arginine/metabolism ; Base Sequence ; Enzyme Activation ; *G-Quadruplexes ; GTP Phosphohydrolases/isolation &amp; purification/*metabolism ; Hydrolysis ; Lysine/metabolism ; Mice ; Mitochondria/*enzymology ; Mutant Proteins/isolation &amp; purification/metabolism ; Protein Binding ; RNA/*chemistry/*metabolism ; RNA, Ribosomal/metabolism ; Recombinant Proteins/metabolism ; SELEX Aptamer Technique ; Substrate Specificity ; }, abstract = {NOA1 is an evolutionary conserved, nuclear encoded GTPase essential for mitochondrial function and cellular survival. The function of NOA1 for assembly of mitochondrial ribosomes and regulation of OXPHOS activity depends on its GTPase activity, but so far no ligands have been identified that regulate the GTPase activity of NOA1. To identify nucleic acids that bind to the RNA-binding domain of NOA1 we employed SELEX (Systemic Evolution of Ligands by EXponential Enrichment) using recombinant mouse wildtype NOA1 and the GTPase mutant NOA1-K353R. We found that NOA1 binds specifically to oligonucleotides that fold into guanine tetrads (G-quadruplexes). Binding of G-quadruplex oligonucleotides stimulated the GTPase activity of NOA1 suggesting a regulatory link between G-quadruplex containing RNAs, NOA1 function and assembly of mitochondrial ribosomes.}, }
@article {pmid23932204, year = {2013}, author = {Small, ID and Rackham, O and Filipovska, A}, title = {Organelle transcriptomes: products of a deconstructed genome.}, journal = {Current opinion in microbiology}, volume = {16}, number = {5}, pages = {652-658}, doi = {10.1016/j.mib.2013.07.011}, pmid = {23932204}, issn = {1879-0364}, mesh = {Animals ; Chloroplasts/*genetics/physiology ; Mitochondria/*genetics/physiology ; Plant Cells/*physiology ; Plants/genetics ; *Transcriptome ; }, abstract = {Genetic drift and mutational pressure have shaped the evolution of mitochondrial and chloroplast genomes, giving rise to mechanisms that regulate their gene expression, which often differ from those in their prokaryotic ancestors. Advances in next generation sequencing technologies have enabled highly detailed characterization of organelle transcriptomes and the discovery of new transcripts and mechanisms for controlling gene expression. Here we discuss the common features of organelle transcriptomes that stem from their prokaryotic origin and some of the new innovations that are unique to organelles of multicellular organisms.}, }
@article {pmid23932202, year = {2013}, author = {Klinger, CM and Nisbet, RE and Ouologuem, DT and Roos, DS and Dacks, JB}, title = {Cryptic organelle homology in apicomplexan parasites: insights from evolutionary cell biology.}, journal = {Current opinion in microbiology}, volume = {16}, number = {4}, pages = {424-431}, pmid = {23932202}, issn = {1879-0364}, support = {R37 AI028724/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Apicomplexa/*genetics/physiology ; *Evolution, Molecular ; Organelles/*genetics/physiology ; }, abstract = {The economic and clinical significance of apicomplexan parasites drives interest in their many evolutionary novelties. Distinctive intracellular organelles play key roles in parasite motility, invasion, metabolism, and replication, and understanding their relationship with the organelles of better-studied eukaryotic systems suggests potential targets for therapeutic intervention. Recent work has demonstrated divergent aspects of canonical eukaryotic components in the Apicomplexa, including Golgi bodies and mitochondria. The apicoplast is a relict plastid of secondary endosymbiotic origin, harboring metabolic pathways distinct from those of host species. The inner membrane complex (IMC) is derived from the cortical alveoli defining the superphylum Alveolata, but in apicomplexans functions in parasite motility and replication. Micronemes and rhoptries are associated with establishment of the intracellular niche, and define the apical complex for which the phylum is named. Morphological, cell biological and molecular evidence strongly suggest that these organelles are derived from the endocytic pathway.}, }
@article {pmid23928301, year = {2013}, author = {Zhang, X and Zhao, Q and Huang, Y}, title = {Partitioning of the nuclear and mitochondrial tRNA 3'-end processing activities between two different proteins in Schizosaccharomyces pombe.}, journal = {The Journal of biological chemistry}, volume = {288}, number = {38}, pages = {27415-27422}, pmid = {23928301}, issn = {1083-351X}, mesh = {Cell Nucleus/genetics/*metabolism ; Endoribonucleases/genetics/*metabolism ; Evolution, Molecular ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Nuclear Proteins/genetics/*metabolism ; RNA Processing, Post-Transcriptional/*physiology ; RNA, Fungal/genetics/*metabolism ; RNA, Transfer/genetics/*metabolism ; Schizosaccharomyces/genetics/*metabolism ; Schizosaccharomyces pombe Proteins/genetics/*metabolism ; }, abstract = {tRNase Z is an essential endonuclease responsible for tRNA 3'-end maturation. tRNase Z exists in a short form (tRNase Z(S)) and a long form (tRNase Z(L)). Prokaryotes have only tRNase Z(S), whereas eukaryotes can have both forms of tRNase Z. Most eukaryotes characterized thus far, including Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and humans, contain only one tRNase Z(L) gene encoding both nuclear and mitochondrial forms of tRNase Z(L). In contrast, Schizosaccharomyces pombe contains two essential tRNase Z(L) genes (trz1 and trz2) encoding two tRNase Z(L) proteins, which are targeted to the nucleus and mitochondria, respectively. Trz1 protein levels are notably higher than Trz2 protein levels. Here, using temperature-sensitive mutants of trz1 and trz2, we provide in vivo evidence that trz1 and trz2 are involved in nuclear and mitochondrial tRNA 3'-end processing, respectively. In addition, trz2 is also involved in generation of the 5'-ends of other mitochondrial RNAs, whose 5'-ends coincide with the 3'-end of tRNA. Thus, our results provide a rare example showing partitioning of the nuclear and mitochondrial tRNase Z(L) activities between two different proteins in S. pombe. The evolution of two tRNase Z(L) genes and their differential expression in fission yeast may avoid toxic off-target effects.}, }
@article {pmid23927894, year = {2013}, author = {Sheiner, L and Vaidya, AB and McFadden, GI}, title = {The metabolic roles of the endosymbiotic organelles of Toxoplasma and Plasmodium spp.}, journal = {Current opinion in microbiology}, volume = {16}, number = {4}, pages = {452-458}, pmid = {23927894}, issn = {1879-0364}, support = {K99 AI103032/AI/NIAID NIH HHS/United States ; R01 AI028398/AI/NIAID NIH HHS/United States ; R56-AI100569/AI/NIAID NIH HHS/United States ; R56 AI100569/AI/NIAID NIH HHS/United States ; K99-AI103032/AI/NIAID NIH HHS/United States ; R01-AI098413/AI/NIAID NIH HHS/United States ; R01-AI028398/AI/NIAID NIH HHS/United States ; R01 AI098413/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Apicoplasts/*metabolism ; Citric Acid Cycle ; Electron Transport ; Humans ; Lipid Metabolism ; Mammals ; Mitochondria/*metabolism ; Models, Biological ; Plasmodium/*metabolism ; Toxoplasma/*metabolism ; }, abstract = {The apicoplast and the mitochondrion of Apicomplexa cooperate in providing essential metabolites. Their co-evolution during the ancestral acquisition of a plastid and subsequent loss of photosynthesis resulted in divergent metabolic pathways compared with mammals and plants. This is most evident in their chimerical haem synthesis pathway. Toxoplasma and Plasmodium mitochondria operate canonical tricarboxylic acid (TCA) cycles and electron transport chains, although the roles differ between Toxoplasma tachyzoites and Plasmodium erythrocytic stages. Glutamine catabolism provides TCA intermediates in both parasites. Isoprenoid precursor synthesis is the only essential role of the apicoplast in Plasmodium erythrocytic stages. An apicoplast-located fatty acid synthesis is dispensable in these stages, which instead predominantly salvage fatty acids, while in Plasmodium liver stages and in Toxoplasma tachyzoites fatty acid synthesis is an essential role of the plastid.}, }
@article {pmid23925311, year = {2013}, author = {Pinker, F and Bonnard, G and Gobert, A and Gutmann, B and Hammani, K and Sauter, C and Gegenheimer, PA and Giegé, P}, title = {PPR proteins shed a new light on RNase P biology.}, journal = {RNA biology}, volume = {10}, number = {9}, pages = {1457-1468}, pmid = {23925311}, issn = {1555-8584}, mesh = {Arabidopsis Proteins/genetics/metabolism ; Cell Nucleus/genetics/metabolism ; Chloroplasts/genetics/metabolism ; Eukaryotic Cells/metabolism ; Humans ; Mitochondria/genetics/metabolism ; Plant Proteins/genetics/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; RNA Precursors/genetics/metabolism ; RNA, Transfer/metabolism ; RNA-Binding Proteins/chemistry/genetics/*metabolism ; Ribonuclease P/genetics/*metabolism ; Trypanosoma brucei brucei/genetics/metabolism ; }, abstract = {A fast growing number of studies identify pentatricopeptide repeat (PPR) proteins as major players in gene expression processes. Among them, a subset of PPR proteins called PRORP possesses RNase P activity in several eukaryotes, both in nuclei and organelles. RNase P is the endonucleolytic activity that removes 5' leader sequences from tRNA precursors and is thus essential for translation. Before the characterization of PRORP, RNase P enzymes were thought to occur universally as ribonucleoproteins, although some evidence implied that some eukaryotes or cellular compartments did not use RNA for RNase P activity. The characterization of PRORP reveals a two-domain enzyme, with an N-terminal domain containing multiple PPR motifs and assumed to achieve target specificity and a C-terminal domain holding catalytic activity. The nature of PRORP interactions with tRNAs suggests that ribonucleoprotein and protein-only RNase P enzymes share a similar substrate binding process.}, }
@article {pmid23923009, year = {2013}, author = {Manna, S and Le, P and Barth, C}, title = {A unique mitochondrial transcription factor B protein in Dictyostelium discoideum.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e70614}, pmid = {23923009}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; DNA-Binding Proteins/analysis/*metabolism ; Dictyostelium/chemistry/genetics/*metabolism ; Humans ; Methylation ; Mitochondria/metabolism ; Mitochondrial Proteins/analysis/*metabolism ; Molecular Sequence Data ; Protozoan Proteins/analysis/*metabolism ; RNA, Ribosomal/metabolism ; Sequence Alignment ; Transcription Factors/analysis/*metabolism ; Transcriptional Activation ; }, abstract = {Unlike their bacteriophage homologs, mitochondrial RNA polymerases require the assistance of transcription factors in order to transcribe mitochondrial DNA efficiently. The transcription factor A family has been shown to be important for transcription of the human mitochondrial DNA, with some of its regulatory activity located in its extended C-terminal tail. The mitochondrial transcription factor B family often has functions not only in transcription, but also in mitochondrial rRNA modification, a hallmark of its α-proteobacterial origin. We have identified and characterised a mitochondrial transcription factor B homolog in the soil dwelling cellular slime mould Dictyostelium discoideum, an organism widely established as a model for studying eukaryotic cell biology. Using in bacterio functional assays, we demonstrate that the mitochondrial transcription factor B homolog not only functions as a mitochondrial transcription factor, but that it also has a role in rRNA methylation. Additionally, we show that the transcriptional activation properties of the D. discoideum protein are located in its extended C-terminal tail, a feature not seen before in the mitochondrial transcription factor B family, but reminiscent of the human mitochondrial transcription factor A. This report contributes to our current understanding of the complexities of mitochondrial transcription, and its evolution in eukaryotes.}, }
@article {pmid23918809, year = {2013}, author = {Chong, RA and Mueller, RL}, title = {Evolution along the mutation gradient in the dynamic mitochondrial genome of salamanders.}, journal = {Genome biology and evolution}, volume = {5}, number = {9}, pages = {1652-1660}, pmid = {23918809}, issn = {1759-6653}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Gene Rearrangement ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics ; Mutation ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Urodela/*genetics ; }, abstract = {Mitochondria are intracellular organelles where oxidative phosphorylation is carried out to complete ATP synthesis. Mitochondria have their own genome; in metazoans, this is a small, circular molecule encoding 13 electron transport proteins, 22 tRNAs, and 2 rRNAs. In invertebrates, mitochondrial gene rearrangement is common, and it is correlated with increased substitution rates. In vertebrates, mitochondrial gene rearrangement is rare, and its relationship to substitution rate remains unexplored. Mitochondrial genes can also show spatial variation in substitution rates around the genome due to the mechanism of mtDNA replication, which produces a mutation gradient. To date, however, the strength of the mutation gradient and whether movement along the gradient in rearranged (or otherwise modified) genomes impacts genic substitution rates remain unexplored in the majority of vertebrates. Salamanders include both normal mitochondrial genomes and independently derived rearrangements and expansions, providing a rare opportunity to test the effects of large-scale changes to genome architecture on vertebrate mitochondrial gene sequence evolution. We show that: 1) rearranged/expanded genomes have higher substitution rates; 2) most genes in rearranged/expanded genomes maintain their position along the mutation gradient, substitution rates of the genes that do move are unaffected by their new position, and the gradient in salamanders is weak; and 3) genomic rearrangements/expansions occur independent of levels of selective constraint on genes. Together, our results demonstrate that large-scale changes to genome architecture impact mitochondrial gene evolution in predictable ways; however, despite these impacts, the same functional constraints act on mitochondrial protein-coding genes in both modified and normal genomes.}, }
@article {pmid23916093, year = {2013}, author = {Papah, MB and Kisia, SM and Ojoo, RO and Makanya, AN and Wood, CM and Kavembe, GD and Maina, JN and Johannsson, OE and Bergman, HL and Laurent, P and Chevalier, C and Bianchini, A and Bianchini, LF and Onyango, DW}, title = {Morphological evaluation of spermatogenesis in Lake Magadi tilapia (Alcolapia grahami): a fish living on the edge.}, journal = {Tissue &amp; cell}, volume = {45}, number = {6}, pages = {371-382}, doi = {10.1016/j.tice.2013.06.004}, pmid = {23916093}, issn = {1532-3072}, mesh = {Animals ; Humans ; Lakes ; Male ; *Meiosis ; Phylogeny ; Spermatids/ultrastructure ; *Spermatogenesis ; Spermatozoa/*ultrastructure ; Testis/growth &amp; development ; *Tilapia ; }, abstract = {Spermatogenesis in Lake Magadi tilapia (Alcolapia grahami), a cichlid fish endemic to the highly alkaline and saline Lake Magadi in Kenya, was evaluated using light and transmission electron microscopy. Spermatogenesis, typified by its three major phases (spermatocytogenesis, meiosis and spermiogenesis), was demonstrated by the presence of maturational spermatogenic cells namely spermatogonia, spermatocytes, spermatids and spermatozoa. Primary spermatogonia, the largest of all the germ cells, underwent a series of mitotic divisions producing primary spermatocytes, which then entered two consecutive meiotic divisions to produce secondary spermatocytes and spermatids. Spermatids, in turn, passed through three structurally distinct developmental stages typical of type-I spermiogenesis to yield typical primitive anacrosomal spermatozoa of the externally fertilizing type (aquasperm). The spermatozoon of this fish exhibited a spheroidal head with the nucleus containing highly electron-dense chromatin globules, a midpiece containing ten ovoid mitochondria arranged in two rows and a flagellum formed by the typical 9 + 2 microtubule axoneme. In addition, the midpiece, with no cytoplasmic sheath, appeared to end blindly distally in a lobe-like pattern around the flagellum; a feature that was unique and considered adaptive for the spermatozoon of this species to the harsh external environment. These observations show that the testis of A. grahami often undergoes active spermatogenesis despite the harsh environmental conditions to which it is exposed on a daily basis within the lake. Further, the spermiogenic features and spermatozoal ultrastructure appear to be characteristic of Cichlidae and, therefore, may be of phylogenetic significance.}, }
@article {pmid23915300, year = {2013}, author = {Fuss, J and Liegmann, O and Krause, K and Rensing, SA}, title = {Green targeting predictor and ambiguous targeting predictor 2: the pitfalls of plant protein targeting prediction and of transient protein expression in heterologous systems.}, journal = {The New phytologist}, volume = {200}, number = {4}, pages = {1022-1033}, doi = {10.1111/nph.12433}, pmid = {23915300}, issn = {1469-8137}, mesh = {Arabidopsis/metabolism ; Bryopsida/*metabolism ; Computer Simulation ; Databases, Protein ; *Gene Expression ; Plant Proteins/*metabolism ; Plants/*metabolism ; *Protein Sorting Signals ; Protein Transport ; Reproducibility of Results ; *Software ; Species Specificity ; Nicotiana/metabolism ; }, abstract = {The challenges of plant protein targeting prediction are the existence of dual subcellular targets and the bias of experimentally confirmed data towards few and mostly nonplant model species. To assess whether training with proteins from evolutionarily distant species has a negative impact on prediction accuracy, we developed the Green Targeting Predictor tool, which was trained with a species-specific data set for Physcomitrella patens. Its performance was compared with that of the same tool trained with a mixed data set. In addition, we updated the Ambiguous Targeting Predictor. We found that predictions deviated from in vivo observations predominantly for proteins diverging within the green lineage, as well as for dual targeted proteins. To evaluate the usefulness of heterologous expression systems, selected proteins were subjected to localization studies in P. patens, Arabidopsis thaliana and Nicotiana tabacum. Four out of six proteins that show dual targeting in the original plant system were located only in a single compartment in one or both heterologous systems. We conclude that targeting signals of divergent plant species exhibit differences, calling for custom in silico and in vivo approaches when aiming to unravel the actual distribution patterns of proteins within a plant cell.}, }
@article {pmid23913925, year = {2013}, author = {Bar-Yaacov, D and Avital, G and Levin, L and Richards, AL and Hachen, N and Rebolledo Jaramillo, B and Nekrutenko, A and Zarivach, R and Mishmar, D}, title = {RNA-DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA.}, journal = {Genome research}, volume = {23}, number = {11}, pages = {1789-1796}, pmid = {23913925}, issn = {1549-5469}, mesh = {Alleles ; Cell Line ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Female ; Genome, Human ; High-Throughput Nucleotide Sequencing ; Humans ; Mitochondria/*genetics ; Models, Molecular ; Phylogeny ; RNA/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Alignment ; Thymine/metabolism ; }, abstract = {RNA transcripts are generally identical to the underlying DNA sequences. Nevertheless, RNA-DNA differences (RDDs) were found in the nuclear human genome and in plants and animals but not in human mitochondria. Here, by deep sequencing of human mitochondrial DNA (mtDNA) and RNA, we identified three RDD sites at mtDNA positions 295 (C-to-U), 13710 (A-to-U, A-to-G), and 2617 (A-to-U, A-to-G). Position 2617, within the 16S rRNA, harbored the most prevalent RDDs (>30% A-to-U and ∼15% A-to-G of the reads in all tested samples). The 2617 RDDs appeared already at the precursor polycistrone mitochondrial transcript. By using traditional Sanger sequencing, we identified the A-to-U RDD in six different cell lines and representative primates (Gorilla gorilla, Pongo pigmaeus, and Macaca mulatta), suggesting conservation of the mechanism generating such RDD. Phylogenetic analysis of more than 1700 vertebrate mtDNA sequences supported a thymine as the primate ancestral allele at position 2617, suggesting that the 2617 RDD recapitulates the ancestral 16S rRNA. Modeling U or G (the RDDs) at position 2617 stabilized the large ribosomal subunit structure in contrast to destabilization by an A (the pre-RDDs). Hence, these mitochondrial RDDs are likely functional.}, }
@article {pmid23913384, year = {2013}, author = {Yin, L and Ji, T}, title = {Genetic diversity of the honeybee Apis cerana in Yunnan, China, based on mitochondrial DNA.}, journal = {Genetics and molecular research : GMR}, volume = {12}, number = {2}, pages = {2002-2009}, doi = {10.4238/2013.June.20.1}, pmid = {23913384}, issn = {1676-5680}, mesh = {Animals ; Bees/*genetics ; China ; *DNA, Mitochondrial ; Evolution, Molecular ; Genetic Variation ; Genome, Mitochondrial ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer, Leu/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {DNA sequence diversity in the tRNA(leu)-COII portion of the mitochondrial genome was investigated in samples of Apis cerana from Yunnan, China. A fragment of about 480 bp in tRNA(leu)-COII, including a noncoding area and part of COII, was sequenced. The noncoding area was 97-98 bp; 8 haplotypes were found, among which 5 had been reported previously, while 3 were new. The mean diversity of haplotypes was 0.752 ± 0.030 (0.378-0.698), and nucleotide diversity was 0.01073 ± 0.00087 (0.00412-0.01123). A neighbor-joining tree was constructed based on 73 sequences of noncoding intergenic regions in the mtDNA of A. cerana from China and other Asian countries; all haplotypes found in China fell into the mainland Asian group. This result does not support the hypothesis that A. cerana indica occurs in southern Yunnan, which was concluded in a recent report based on morphological variation.}, }
@article {pmid23906599, year = {2013}, author = {Nietlisbach, P and Wandeler, P and Parker, PG and Grant, PR and Grant, BR and Keller, LF and Hoeck, PE}, title = {Hybrid ancestry of an island subspecies of Galápagos mockingbird explains discordant gene trees.}, journal = {Molecular phylogenetics and evolution}, volume = {69}, number = {3}, pages = {581-592}, doi = {10.1016/j.ympev.2013.07.020}, pmid = {23906599}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Ecuador ; *Evolution, Molecular ; *Genetics, Population ; Haplotypes ; Hybridization, Genetic ; Microsatellite Repeats ; Passeriformes/anatomy &amp; histology/*classification/genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Introgression of genes through hybridization has been proposed to be an important driver of speciation, but in animals this has been shown only in relatively few cases until recently. Additionally, introgressive hybridization among non-sister species leads to a change in the gene tree topology of the concerned loci and thus complicates phylogenetic reconstruction. However, such cases of ancient introgression have been very difficult to demonstrate in birds. Here, we present such an example in an island bird subspecies, the Genovesa mockingbird (Mimus parvulus bauri). We assessed phylogenetic relationships and population structure among mockingbirds of the Galápagos archipelago using mitochondrial and nuclear DNA sequences, autosomal microsatellites, and morphological measurements. Mitochondrial haplotypes of Genovesa mockingbirds clustered closely with the haplotypes from two different species, San Cristóbal (M. melanotis) and Española (M. macdonaldi) mockingbirds. The same pattern was found for some haplotypes of two nuclear gene introns, while the majority of nuclear haplotypes of Genovesa mockingbirds were shared with other populations of the same species (M. parvulus). At 26 autosomal microsatellites, Genovesa mockingbirds grouped with other M. parvulus populations. This pattern shows that Genovesa mockingbirds contain mitochondria and some autosomal alleles that have most likely introgressed from M. melanotis into a largely M. parvulus background, making Genovesa mockingbirds a lineage of mixed ancestry, possibly undergoing speciation. Consistent with this hypothesis, mockingbirds on Genovesa are more clearly differentiated morphologically from other M. parvulus populations than M. melanotis is from M. parvulus.}, }
@article {pmid23901921, year = {2015}, author = {Huang, SP and Shen, CN and Chen, IS}, title = {The complete mitochondrial genome of the Java fat-nose goby Pseudogobius javanicus (Teleostei, Gobiidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {1}, pages = {159-161}, doi = {10.3109/19401736.2013.819502}, pmid = {23901921}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {In this study, the complete mitochondrial genome of the fat-nose goby Pseudogobius javanicus has been amplified. P. javanicus is widely contributed species in Southeast to East Asia. The complete mitochondrial genome is 16,493 base pairs (bp) in total length, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, 1 control region (CR) and 1 light-strand replication origin (OL). The overall base composition of P. javanicus is 27.1% for A, 27.3% for T, 28.6% for C, 17.0% for G, with higher AT content of 54.4%. This study will contribute for understanding the phylogenetic approach in genus Pseudogobius.}, }
@article {pmid23901920, year = {2015}, author = {Wei, SJ and Wu, QL and Liu, W}, title = {Sequencing and characterization of the Monocellicampa pruni (Hymenoptera: Tenthredinidae) mitochondrial genome.}, journal = {Mitochondrial DNA}, volume = {26}, number = {1}, pages = {157-158}, doi = {10.3109/19401736.2013.819501}, pmid = {23901920}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Codon, Terminator ; Gene Order ; *Genome, Mitochondrial ; Hymenoptera/*genetics ; Insect Proteins/genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/chemistry/genetics ; Sequence Analysis, DNA ; }, abstract = {The mitochondrial genome of the Monocellicampa pruni (Hymenoptera: Tenthredinidae) (GenBank accession No. JX566509) has been reported in this study. This is the first sequenced mitochondrial genome from the family Tenthredinidae of the order Hymenoptera. The sequenced region of this mitochondrial genome is 15,169 bp with an A + T content of 77.21%, including 13 protein-coding, 2 rRNA and 19 tRNA genes, and a partial region of the A + T-rich region. Three tRNA genes, i.e. trnI. trnQ and trnM, between the A + T-rich region and the nad2 gene were failed to sequence because of the present of PolyAT structure. The gene arrangement of the sequenced region was similar to the pupative ancestral arrangement of insects. There are two large non-coding regions located between trnC and trnY. trnF and nad5 with a length of 107 and 177 bp, respectively. All protein-coding genes start with ATN start codon. Eleven protein-coding genes stop with termination codon TAA, whereas one protein-coding gene uses incomplete stop codon TA and one uses T. All of the 22 tRNA genes have a typical cloverleaf structure except for the trnS1, in which, the D-stem pairings in the DHU arm are absent.}, }
@article {pmid23901918, year = {2015}, author = {Huang, SP and Shen, CN and Chen, IS}, title = {The complete mitochondrial genome of the Abe's mangrove goby Mugilogobius abei (Teleostei, Gobiidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {1}, pages = {143-144}, doi = {10.3109/19401736.2013.819494}, pmid = {23901918}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Perciformes/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {In this study, the complete mitochondrial genome of the Abe's mangrove goby Mugilogobius abei has been amplified. Mugilogobius abei is widely contributed species in Northeast to East Asia. The complete mitogenome is 16,483 base pairs (bp) in total length, had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 2 rRNAs, 22 tRNAs, and 1 control region (CR). The overall base composition of M. abei is 27.7% for A, 27.0% for T, 28.6% for C, 16.7% for G, with higher AT content of 54.7%. This study will contribute for understanding the phylogenetic approach in genus Mugilogobius and related gobiid genera.}, }
@article {pmid23901917, year = {2015}, author = {Chen, IS and Han, M and Wang, CL and Shen, CN}, title = {The complete mitochondrial genome of rainbow barbel Acrossocheilus barbodon (Nichols and Pope) (Teleostei, Cyprinidae, Barbinae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {1}, pages = {145-146}, doi = {10.3109/19401736.2013.819495}, pmid = {23901917}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {In this study, the complete mitogenome sequence of rainbow barbel Acrossocheilus barbodon has been amplified and sequenced by employing long polymerase chain reaction method. The mitogenome, consisting of 16,596 base pairs (bp), had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a noncoding control region (CR). CR of 934 bp length is located between tRNAPro and tRNAPhe. The overall base composition of A. hemispinus is 31.5% for A, 28.2% for C, 24.4% for T and 15.9 % for G, with a higher AC content of 55.9%. The complete mitogenome may provide very essential and important DNA molecular data for further phylogenetic analysis for not only congeneric species but also higher different taxa of Cyprinid fishes.}, }
@article {pmid23901915, year = {2015}, author = {Shedko, SV and Miroshnichenko, IL and Nemkova, GA}, title = {Complete mitochondrial genome of the poorly known Amur sculpin Mesocottus haitej (Cottoidei: Cottidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {1}, pages = {147-148}, doi = {10.3109/19401736.2013.819496}, pmid = {23901915}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Data ; Perciformes/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {The complete mitochondrial genome sequence of Mesocottus haitej has been obtained by the next generation sequencing, which contained 22 tRNA genes, 13 protein-coding genes, 2 rRNA genes and non-coding control region with the total length of 16,527 bp. The gene content, arrangement, codon usage and base composition of M. haitej mitogenome have no unusual features that distinguish it from most other teleost fishes. According to the result of a pilot phylogenetic analysis, the freshwater Mesocottus is a sister lineage to the Cottus clade. The new mitogenomic data could provide useful information for the further studies on molecular systematics and conservation genetics of cottids.}, }
@article {pmid23901913, year = {2015}, author = {Han, M and Wang, CL and Shen, CN and Chen, IS}, title = {The complete mitochondrial genome of half-spined barbel Acrossocheilus hemispinus (Nichols) (Teleostei, Cyprinidae, Barbinae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {1}, pages = {133-134}, doi = {10.3109/19401736.2013.815172}, pmid = {23901913}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Cyprinidae/*genetics ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {In this study, the complete mitogenome sequence of half-spined barbel Acrossocheilus hemispinus has been amplified and sequenced by employing long polymerase chain reaction method. The mitogenome, consisting of 16,590 base pairs (bp), had the typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes and a noncoding control region (CR). CR of 940 bp length is located between tRNA(Pro) and tRNA(Phe). The overall base composition of A. hemispinus is 31.2% for A, 28.2% for C, 24.4% for T and 15.9 % for G, with a slight AT bias of 55.6%. The complete mitogenome may provide rather essential and important DNA molecular data for further phylogenetic analysis for not only congeneric species but also higher different taxa of Cyprinid fishes.}, }
@article {pmid23899506, year = {2013}, author = {Schallenberg-Rüdinger, M and Lenz, H and Polsakiewicz, M and Gott, JM and Knoop, V}, title = {A survey of PPR proteins identifies DYW domains like those of land plant RNA editing factors in diverse eukaryotes.}, journal = {RNA biology}, volume = {10}, number = {9}, pages = {1549-1556}, pmid = {23899506}, issn = {1555-8584}, mesh = {Acanthamoeba castellanii/genetics/metabolism ; Embryophyta/*genetics/metabolism ; *Eukaryota ; Naegleria/genetics ; Nitella/genetics/metabolism ; Organelles/genetics/metabolism ; Phylogeny ; Physarum polycephalum/genetics/metabolism ; Plant Proteins/genetics/*metabolism ; Prokaryotic Cells/metabolism ; Protein Structure, Tertiary ; *RNA Editing ; RNA-Binding Proteins/genetics/*metabolism ; }, abstract = {The pentatricopeptide repeat modules of PPR proteins are key to their sequence-specific binding to RNAs. Gene families encoding PPR proteins are greatly expanded in land plants where hundreds of them participate in RNA maturation, mainly in mitochondria and chloroplasts. Many plant PPR proteins contain additional carboxyterminal domains and have been identified as essential factors for specific events of C-to-U RNA editing, which is abundant in the two endosymbiotic plant organelles. Among those carboxyterminal domain additions to plant PPR proteins, the so-called DYW domain is particularly interesting given its similarity to cytidine deaminases. The frequency of organelle C-to-U RNA editing and the diversity of DYW-type PPR proteins correlate well in plants and both were recently identified outside of land plants, in the protist Naegleria gruberi. Here we present a systematic survey of PPR protein genes and report on the identification of additional DYW-type PPR proteins in the protists Acanthamoeba castellanii, Malawimonas jakobiformis, and Physarum polycephalum. Moreover, DYW domains were also found in basal branches of multi-cellular lineages outside of land plants, including the alga Nitella flexilis and the rotifers Adineta ricciae and Philodina roseola. Intriguingly, the well-characterized and curious patterns of mitochondrial RNA editing in the slime mold Physarum also include examples of C-to-U changes. Finally, we identify candidate sites for mitochondrial RNA editing in Malawimonas, further supporting a link between DYW-type PPR proteins and C-to-U editing, which may have remained hitherto unnoticed in additional eukaryote lineages.}, }
@article {pmid23899268, year = {2014}, author = {Shi, SF and Li, M and Yan, S and Wang, M and Yang, CP and Lun, ZR and Brown, CL and Yang, TB}, title = {Phylogeography and demographic history of Gotocotyla sawara (Monogenea: Gotocotylidae) on Japanese Spanish mackerel (Scomberomorus niphonius) along the Coast of China.}, journal = {The Journal of parasitology}, volume = {100}, number = {1}, pages = {85-92}, doi = {10.1645/13-235.1}, pmid = {23899268}, issn = {1937-2345}, mesh = {Animals ; China/epidemiology ; DNA, Helminth/chemistry/isolation &amp; purification ; DNA, Ribosomal Spacer/genetics ; Demography ; Electron Transport Complex IV/genetics ; Fish Diseases/epidemiology/*parasitology ; Genetic Variation ; Genetics, Population ; Gills/parasitology ; Haplotypes ; Ice Cover ; Mitochondria/enzymology ; Perciformes/*parasitology ; Phylogeny ; Phylogeography ; Platyhelminths/genetics/*isolation &amp; purification/physiology ; Polymerase Chain Reaction/veterinary ; Seawater ; Sequence Alignment/veterinary ; Sequence Analysis, DNA/veterinary ; Trematode Infections/epidemiology/parasitology/*veterinary ; }, abstract = {Recent studies indicate that the northwestern Pacific Ocean is an ideal system in which to study and understand the roles of the Pleistocene sea-level fluctuations and ocean currents in shaping phylogeographic patterns of species, but most of these investigations have been concerned with vertebrates, and only a few have focused on invertebrates. In the present study, we examined the genetic population structure and historic demography of a platyhelminth species, Gotocotyla sawara (Monogenea, Gotocotylidae), a gill parasite of Japanese Spanish mackerel, Scomberomorus niphonius , along the coast of China. A fragment of the mitochondrial cytochrome oxidase I (COI) gene for 169 individuals and the internal transcribed spacers for 24 individuals were sequenced from specimens representing 8 populations of this parasite along the coast of China. High levels of COI haplotype diversity (0.9994) and nucleotide diversity (0.015805) were detected for G. sawara. Phylogenetic analysis revealed no phylogeographical pattern for G. sawara in the sample area. Analysis of molecular variance (AMOVA) revealed no significant differences at all hierarchical levels, and pairwise FST analysis demonstrated a high rate of gene flow of this parasite among different populations in coastal Chinese waters. Moreover, the exact test of differentiation supported the null hypothesis that G. sawara along the coast of China constitutes a panmictic population. Both neutrality tests and mismatch distribution revealed that G. sawara underwent population expansion in the late Pleistocene era. Recent range expansion after the last glacial maximum and insufficient time to attain migration-drift equilibrium may account in part for the lack of genetic structure in the geographic areas considered in this study. Dispersal of parasite eggs and larvae along ocean currents, coupled with the long-distance migrations of host fishes, could also be responsible for genetic homogeneity of this parasite. It is also possible that other hosts of this monogean, such as the ridged-eye flounder, Pleruonichthys cornutus, may contribute to the genetic mixing of Gotocotyla sawara populations.}, }
@article {pmid23891721, year = {2013}, author = {Shi, Z and Wang, ZJ and Xu, HL and Tian, Y and Li, X and Bao, JK and Sun, SR and Yue, BS}, title = {Modeling, docking and dynamics simulations of a non-specific lipid transfer protein from Peganum harmala L.}, journal = {Computational biology and chemistry}, volume = {47}, number = {}, pages = {56-65}, doi = {10.1016/j.compbiolchem.2013.07.001}, pmid = {23891721}, issn = {1476-928X}, mesh = {Antigens, Plant/*chemistry/*metabolism ; Carrier Proteins/*chemistry/*metabolism ; *Molecular Docking Simulation ; *Molecular Dynamics Simulation ; Peganum/*chemistry ; Phylogeny ; Plant Proteins/*chemistry/*metabolism ; }, abstract = {Non-specific lipid transfer proteins (ns-LTPs), ubiquitously found in various types of plants, have been well-known to transfer amphiphilic lipids and promote the lipid exchange between mitochondria and microbody. In this study, an in silico analysis was proposed to study ns-LTP in Peganum harmala L., which may belong to ns-LTP1 family, aiming at constructing its three-dimensional structure. Moreover, we adopted MEGA to analyze ns-LTPs and other species phylogenetically, which brought out an initial sequence alignment of ns-LTPs. In addition, we used molecular docking and molecular dynamics simulations to further investigate the affinities and stabilities of ns-LTP with several ligands complexes. Taken together, our results about ns-LTPs and their ligand-binding activities can provide a better understanding of the lipid-protein interactions, indicating some future applications of ns-LTP-mediated transport.}, }
@article {pmid23891116, year = {2013}, author = {Burki, F and Corradi, N and Sierra, R and Pawlowski, J and Meyer, GR and Abbott, CL and Keeling, PJ}, title = {Phylogenomics of the intracellular parasite Mikrocytos mackini reveals evidence for a mitosome in rhizaria.}, journal = {Current biology : CB}, volume = {23}, number = {16}, pages = {1541-1547}, doi = {10.1016/j.cub.2013.06.033}, pmid = {23891116}, issn = {1879-0445}, support = {MOP-42517//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; DNA, Complementary/genetics/metabolism ; DNA, Protozoan/*genetics/metabolism ; Evolution, Molecular ; Gene Expression Profiling ; *Genome, Protozoan ; Molecular Sequence Data ; Ostreidae/parasitology ; *Phylogeny ; Rhizaria/classification/*genetics/metabolism/physiology ; Sequence Analysis, DNA ; }, abstract = {Mikrocytos mackini is an intracellular protistan parasite of oysters whose position in the phylogenetic tree of eukaryotes has been a mystery for many years [1,2]. M. mackini is difficult to isolate, has not been cultured, and has no defining morphological feature. Furthermore, its only phylogenetic marker that has been successfully sequenced to date (the small subunit ribosomal RNA) is highly divergent and has failed to resolve its evolutionary position [2]. M. mackini is also one of the few eukaryotes that lacks mitochondria [1], making both its phylogenetic position and comparative analysis of mitochondrial function particularly important. Here, we have obtained transcriptomic data for M. mackini from enriched isolates and constructed a 119-gene phylogenomic data set. M. mackini proved to be among the fastest-evolving eukaryote lineages known to date, but, nevertheless, our analysis robustly placed it within Rhizaria. Searching the transcriptome for genetic evidence of a mitochondrion-related organelle (MRO) revealed only four mitochondrion-derived genes: IscS, IscU, mtHsp70, and FdxR. Interestingly, all four genes are involved in iron-sulfur cluster formation, a biochemical pathway common to other highly reduced "mitosomes" in unrelated MRO-containing lineages [7]. This is the first evidence of MRO in Rhizaria, and it suggests the parallel evolution of mitochondria to mitosomes in this supergroup.}, }
@article {pmid23888858, year = {2013}, author = {Pease, JB and Hahn, MW}, title = {More accurate phylogenies inferred from low-recombination regions in the presence of incomplete lineage sorting.}, journal = {Evolution; international journal of organic evolution}, volume = {67}, number = {8}, pages = {2376-2384}, pmid = {23888858}, issn = {1558-5646}, support = {T32 GM007757/GM/NIGMS NIH HHS/United States ; T32-GM007757/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/genetics ; Drosophila/*classification/*genetics ; Humans ; *Phylogeny ; Primates/*classification/*genetics ; X Chromosome ; }, abstract = {When speciation events occur in rapid succession, incomplete lineage sorting (ILS) can cause disagreement among individual gene trees. The probability that ILS affects a given locus is directly related to its effective population size (Ne), which in turn is proportional to the recombination rate if there is strong selection across the genome. Based on these expectations, we hypothesized that low-recombination regions of the genome, as well as sex chromosomes and nonrecombining chromosomes, should exhibit lower levels of ILS. We tested this hypothesis in phylogenomic datasets from primates, the Drosophila melanogaster clade, and the Drosophila simulans clade. In all three cases, regions of the genome with low or no recombination showed significantly stronger support for the putative species tree, although results from the X chromosome differed among clades. Our results suggest that recurrent selection is acting in these low-recombination regions, such that current levels of diversity also reflect past decreases in the effective population size at these same loci. The results also demonstrate how considering the genomic context of a gene tree can assist in more accurate determination of the true species phylogeny, especially in cases where a whole-genome phylogeny appears to be an unresolvable polytomy.}, }
@article {pmid23885060, year = {2013}, author = {Blackstone, NW}, title = {Evolution and cell physiology. 2. The evolution of cell signaling: from mitochondria to Metazoa.}, journal = {American journal of physiology. Cell physiology}, volume = {305}, number = {9}, pages = {C909-15}, doi = {10.1152/ajpcell.00216.2013}, pmid = {23885060}, issn = {1522-1563}, mesh = {Animals ; *Biological Evolution ; Cell Physiological Phenomena/*physiology ; Humans ; Mitochondria/*physiology ; Signal Transduction/*physiology ; }, abstract = {The history of life is a history of levels-of-selection transitions. Each transition requires mechanisms that mediate conflict among the lower-level units. In the origins of multicellular eukaryotes, cell signaling is one such mechanism. The roots of cell signaling, however, may extend to the previous major transition, the origin of eukaryotes. Energy-converting protomitochondria within a larger cell allowed eukaryotes to transcend the surface-to-volume constraints inherent in the design of prokaryotes. At the same time, however, protomitochondria can selfishly allocate energy to their own replication. Metabolic signaling may have mediated this principal conflict in several ways. Variation of the protomitochondria was constrained by stoichiometry and strong metabolic demand (state 3) exerted by the protoeukaryote. Variation among protoeukaryotes was increased by the sexual stage of the life cycle, triggered by weak metabolic demand (state 4), resulting in stochastic allocation of protomitochondria to daughter cells. Coupled with selection, many selfish protomitochondria could thus be removed from the population. Hence, regulation of states 3 and 4, as, for instance, provided by the CO2/soluble adenylyl cyclase/cAMP pathway in mitochondria, was critical for conflict mediation. Subsequently, as multicellular eukaryotes evolved, metabolic signaling pathways employed by eukaryotes to mediate conflict within cells could now be co-opted into conflict mediation between cells. For example, in some fungi, the CO2/soluble adenylyl cyclase/cAMP pathway regulates the transition from yeast to forms with hyphae. In animals, this pathway regulates the maturation of sperm. While the particular features (sperm and hyphae) are distinct, both may involve between-cell conflicts that required mediation.}, }
@article {pmid23883182, year = {2015}, author = {Jeong, D and Lee, YH}, title = {The complete mitochondrial genome of the Longnose skate: Raja rhina (Rajiformes, Rajidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {1}, pages = {123-124}, doi = {10.3109/19401736.2013.814113}, pmid = {23883182}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Codon, Initiator ; Codon, Terminator ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Skates, Fish/*genetics ; }, abstract = {The complete sequence of mitochondrial DNA of a longnose skate, Raja rhina was determined for the first time. It is 16,910 bp in length containing 2 rRNA, 22 tRNA and 13 protein coding genes with the same gene order and structure as those of other Rajidae species. The nucleotide of L-strand is composed of 30.1% A, 27.2% C, 28.5% T and 14.2% G, showing a slight A + T bias. The G is the least used base and markedly lower at the third codon position (5.4%). Twelve of the 13 protein coding genes use ATG as their start codon while the COX1 starts with GTG. As for stop codon, only ND4 shows incomplete stop codon TA. This mitogenome is the first report for a species of the genus Raja, and providing a valuable resource of genetic information for understanding the phylogenetic relationship and the evolution of the genus Raja as well as the family, Rajidae.}, }
@article {pmid23882128, year = {2013}, author = {Ghiselli, F and Milani, L and Guerra, D and Chang, PL and Breton, S and Nuzhdin, SV and Passamonti, M}, title = {Structure, transcription, and variability of metazoan mitochondrial genome: perspectives from an unusual mitochondrial inheritance system.}, journal = {Genome biology and evolution}, volume = {5}, number = {8}, pages = {1535-1554}, pmid = {23882128}, issn = {1759-6653}, support = {R01 GM098741/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Female ; *Genetic Variation ; *Genome, Mitochondrial ; Genomic Structural Variation ; Gonads ; Male ; Molecular Sequence Data ; *Polymorphism, Single Nucleotide ; *Transcription, Genetic ; }, abstract = {Despite its functional conservation, the mitochondrial genome (mtDNA) presents strikingly different features among eukaryotes, such as size, rearrangements, and amount of intergenic regions. Nonadaptive processes such as random genetic drift and mutation rate play a fundamental role in shaping mtDNA: the mitochondrial bottleneck and the number of germ line replications are critical factors, and different patterns of germ line differentiation could be responsible for the mtDNA diversity observed in eukaryotes. Among metazoan, bivalve mollusc mtDNAs show unusual features, like hypervariable gene arrangements, high mutation rates, large amount of intergenic regions, and, in some species, an unique inheritance system, the doubly uniparental inheritance (DUI). The DUI system offers the possibility to study the evolutionary dynamics of mtDNAs that, despite being in the same organism, experience different genetic drift and selective pressures. We used the DUI species Ruditapes philippinarum to study intergenic mtDNA functions, mitochondrial transcription, and polymorphism in gonads. We observed: 1) the presence of conserved functional elements and novel open reading frames (ORFs) that could explain the evolutionary persistence of intergenic regions and may be involved in DUI-specific features; 2) that mtDNA transcription is lineage-specific and independent from the nuclear background; and 3) that male-transmitted and female-transmitted mtDNAs have a similar amount of polymorphism but of different kinds, due to different population size and selection efficiency. Our results are consistent with the hypotheses that mtDNA evolution is strongly dependent on the dynamics of germ line formation, and that the establishment of a male-transmitted mtDNA lineage can increase male fitness through selection on sperm function.}, }
@article {pmid23881394, year = {2013}, author = {Voznesenskaya, EV and Koteyeva, NK and Akhani, H and Roalson, EH and Edwards, GE}, title = {Structural and physiological analyses in Salsoleae (Chenopodiaceae) indicate multiple transitions among C3, intermediate, and C4 photosynthesis.}, journal = {Journal of experimental botany}, volume = {64}, number = {12}, pages = {3583-3604}, pmid = {23881394}, issn = {1460-2431}, mesh = {Blotting, Western ; Carbon Cycle ; Carbon Isotopes/metabolism ; Chenopodiaceae/classification/*physiology/*ultrastructure ; DNA, Ribosomal Spacer/genetics/metabolism ; *Evolution, Molecular ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; *Photosynthesis ; Phylogeny ; Plant Proteins/genetics/metabolism ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {In subfamily Salsoloideae (family Chenopodiaceae) most species are C4 plants having terete leaves with Salsoloid Kranz anatomy characterized by a continuous dual chlorenchyma layer of Kranz cells (KCs) and mesophyll (M) cells, surrounding water storage and vascular tissue. From section Coccosalsola sensu Botschantzev, leaf structural and photosynthetic features were analysed on selected species of Salsola which are not performing C4 based on leaf carbon isotope composition. The results infer the following progression in distinct functional and structural forms from C3 to intermediate to C4 photosynthesis with increased leaf succulence without changes in vein density: From species performing C3 photosynthesis with Sympegmoid anatomy with two equivalent layers of elongated M cells, with few organelles in a discontinuous layer of bundle sheath (BS) cells (S. genistoides, S. masenderanica, S. webbii) > development of proto-Kranz BS cells having mitochondria in a centripetal position and increased chloroplast number (S. montana) > functional C3-C4 intermediates having intermediate CO2 compensation points with refixation of photorespired CO2, development of Kranz-like anatomy with reduction in the outer M cell layer to hypodermal-like cells, and increased specialization (but not size) of a Kranz-like inner layer of cells with increased cell wall thickness, organelle number, and selective expression of mitochondrial glycine decarboxylase (Kranz-like Sympegmoid, S. arbusculiformis; and Kranz-like Salsoloid, S. divaricata) > selective expression of enzymes between the two cell types for performing C4 with Salsoloid-type anatomy. Phylogenetic analysis of tribe Salsoleae shows the occurrence of C3 and intermediates in several clades, and lineages of interest for studying different forms of anatomy.}, }
@article {pmid23876871, year = {2013}, author = {Ali, V and Nozaki, T}, title = {Iron-sulphur clusters, their biosynthesis, and biological functions in protozoan parasites.}, journal = {Advances in parasitology}, volume = {83}, number = {}, pages = {1-92}, doi = {10.1016/B978-0-12-407705-8.00001-X}, pmid = {23876871}, issn = {2163-6079}, mesh = {Blastocystis/*physiology ; Cell Physiological Phenomena ; Entamoeba/*physiology ; Gene Expression Regulation ; Giardia/*physiology ; Iron/metabolism ; Metalloproteins/*metabolism ; Microsporidia/*physiology ; Protozoan Proteins/*metabolism ; Sulfur/metabolism ; Trichomonas/*physiology ; }, abstract = {Fe-S clusters are ensembles of sulphide-linked di-, tri-, and tetra-iron centres of a variety of metalloproteins that play important roles in reduction and oxidation of mitochondrial electron transport, energy metabolism, regulation of gene expression, cell survival, nitrogen fixation, and numerous other metabolic pathways. The Fe-S clusters are assembled by one of four distinct systems: NIF, SUF, ISC, and CIA machineries. The ISC machinery is a house-keeping system conserved widely from prokaryotes to higher eukaryotes, while the other systems are present in a limited range of organisms and play supplementary roles under certain conditions such as stress. Fe-S cluster-containing proteins and the components required for Fe-S cluster biosynthesis are modulated under stress conditions, drug resistance, and developmental stages. It is also known that a defect in Fe-S proteins and Fe-S cluster biogenesis leads to many genetic disorders in humans, which indicates the importance of the systems. In this review, we describe the biological and physiological significance of Fe-S cluster-containing proteins and their biosynthesis in parasitic protozoa including Plasmodium, Trypanosoma, Leishmania, Giardia, Trichomonas, Entamoeba, Cryptosporidium, Blastocystis, and microsporidia. We also discuss the roles of Fe-S cluster biosynthesis in proliferation, differentiation, and stress response in protozoan parasites. The heterogeneity of the systems and the compartmentalization of Fe-S cluster biogenesis in the protozoan parasites likely reflect divergent evolution under highly diverse environmental niches, and influence their parasitic lifestyle and pathogenesis. Finally, both Fe-S cluster-containing proteins and their biosynthetic machinery in protozoan parasites are remarkably different from those in their mammalian hosts. Thus, they represent a rational target for the development of novel chemotherapeutic and prophylactic agents against protozoan infections.}, }
@article {pmid23876191, year = {2015}, author = {Kim, SJ and Pak, SJ and Ju, SJ}, title = {Mitochondrial genome of the hydrothermal vent shrimp Nautilocaris saintlaurentae (Crustacea: Caridea: Alvinocarididae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {1}, pages = {127-128}, doi = {10.3109/19401736.2013.815169}, pmid = {23876191}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Codon, Initiator ; Codon, Terminator ; Decapoda/*genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {We determined the mitochondrial genome (mitogenome) of Nautilocaris saintlaurentae, sampled at vent fields of the Tofua Arc in the southwestern Pacific. The genome was 15,928 bp in length and had the typical mitogenome structure of the infraorder Caridea. Its protein-coding genes were very similar to other alvinocaridid species in respect to length, AT content, and start and stop codons. However, N. saintlaurentae showed a 17.4--19.2% divergence in the nucleotide sequence from other alvinocaridid species. This information will be helpful in understanding the genetic relationship among members of the alvinocaridid shrimps.}, }
@article {pmid23873918, year = {2013}, author = {Blanc-Mathieu, R and Sanchez-Ferandin, S and Eyre-Walker, A and Piganeau, G}, title = {Organellar inheritance in the green lineage: insights from Ostreococcus tauri.}, journal = {Genome biology and evolution}, volume = {5}, number = {8}, pages = {1503-1511}, pmid = {23873918}, issn = {1759-6653}, mesh = {Chlorophyta/*genetics ; Evolution, Molecular ; Genetic Variation ; *Genome, Chloroplast ; *Genome, Mitochondrial ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Recombination, Genetic ; Sequence Analysis, DNA ; Streptophyta/*genetics ; }, abstract = {Along the green lineage (Chlorophyta and Streptophyta), mitochondria and chloroplast are mainly uniparentally transmitted and their evolution is thus clonal. The mode of organellar inheritance in their ancestor is less certain. The inability to make clear phylogenetic inference is partly due to a lack of information for deep branching organisms in this lineage. Here, we investigate organellar evolution in the early branching green alga Ostreococcus tauri using population genomics data from the complete mitochondrial and chloroplast genomes. The haplotype structure is consistent with clonal evolution in mitochondria, while we find evidence for recombination in the chloroplast genome. The number of recombination events in the genealogy of the chloroplast suggests that recombination, and thus biparental inheritance, is not rare. Consistent with the evidence of recombination, we find that the ratio of the number of nonsynonymous to the synonymous polymorphisms per site is lower in chloroplast than in the mitochondria genome. We also find evidence for the segregation of two selfish genetic elements in the chloroplast. These results shed light on the role of recombination and the evolutionary history of organellar inheritance in the green lineage.}, }
@article {pmid23872480, year = {2013}, author = {Dahan, J and Mireau, H}, title = {The Rf and Rf-like PPR in higher plants, a fast-evolving subclass of PPR genes.}, journal = {RNA biology}, volume = {10}, number = {9}, pages = {1469-1476}, pmid = {23872480}, issn = {1555-8584}, mesh = {Arabidopsis Proteins/genetics/metabolism ; Cytoplasm/genetics ; Evolution, Molecular ; Gene Expression Regulation, Plant ; *Genes, Plant ; Genome, Plant ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Oryza/genetics ; Plant Infertility/*genetics ; Plant Proteins/genetics/*metabolism ; RNA Processing, Post-Transcriptional ; RNA, Messenger/metabolism ; RNA-Binding Proteins/genetics/*metabolism ; }, abstract = {In the last years, a number of nuclear genes restoring cytoplasmic male sterility (CMS) have been cloned in various crop species. The majority of these genes have been shown to encode pentatricopeptide repeat proteins (PPR) that act by specifically suppressing the expression of sterility-causing mitochondrial transcripts. Functional analysis of these proteins has indicated that the inhibitory effects of restoring PPR (Rf-PPR) proteins involve various mechanisms, including RNA cleavage, RNA destabilization, or translation inhibition. Cross-species sequence comparison of PPR protein complements revealed that most plant genomes encode 10-30 Rf-like (RFL) proteins sharing high-sequence similarity with the identified Rf-PPRs from crops. Evolutionary analyses further showed that they constitute a monophyletic group apart in the PPR family, with peculiar evolution dynamic and constraints. Here we review recent data on RF-PPRs and present the latest discoveries on the RFL family, with prospects on the functionality and evolution of this peculiar subclass of PPR.}, }
@article {pmid23871937, year = {2013}, author = {Dibrova, DV and Cherepanov, DA and Galperin, MY and Skulachev, VP and Mulkidjanian, AY}, title = {Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates.}, journal = {Biochimica et biophysica acta}, volume = {1827}, number = {11-12}, pages = {1407-1427}, pmid = {23871937}, issn = {0006-3002}, support = {Z99 MH999999/ImNIH/Intramural NIH HHS/United States ; ZIA LM000073/ImNIH/Intramural NIH HHS/United States ; Z99 LM999999/ImNIH/Intramural NIH HHS/United States ; ZIA LM000073-14/ImNIH/Intramural NIH HHS/United States ; Z99 CL999999/ImNIH/Intramural NIH HHS/United States ; Z99 HL999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Animals ; Apoptosis/genetics ; Bacterial Proteins/chemistry/*genetics/metabolism ; Cytochrome b6f Complex/chemistry/*genetics/metabolism ; Electron Transport Complex III/chemistry/*genetics/metabolism ; *Evolution, Molecular ; Humans ; Membrane Proteins/chemistry/genetics/metabolism ; Models, Molecular ; Oxidoreductases/chemistry/genetics/metabolism ; Protein Conformation ; Vertebrates/genetics ; }, abstract = {This review traces the evolution of the cytochrome bc complexes from their early spread among prokaryotic lineages and up to the mitochondrial cytochrome bc1 complex (complex III) and its role in apoptosis. The results of phylogenomic analysis suggest that the bacterial cytochrome b6f-type complexes with short cytochromes b were the ancient form that preceded in evolution the cytochrome bc1-type complexes with long cytochromes b. The common ancestor of the b6f-type and the bc1-type complexes probably resembled the b6f-type complexes found in Heliobacteriaceae and in some Planctomycetes. Lateral transfers of cytochrome bc operons could account for the several instances of acquisition of different types of bacterial cytochrome bc complexes by archaea. The gradual oxygenation of the atmosphere could be the key evolutionary factor that has driven further divergence and spread of the cytochrome bc complexes. On the one hand, oxygen could be used as a very efficient terminal electron acceptor. On the other hand, auto-oxidation of the components of the bc complex results in the generation of reactive oxygen species (ROS), which necessitated diverse adaptations of the b6f-type and bc1-type complexes, as well as other, functionally coupled proteins. A detailed scenario of the gradual involvement of the cardiolipin-containing mitochondrial cytochrome bc1 complex into the intrinsic apoptotic pathway is proposed, where the functioning of the complex as an apoptotic trigger is viewed as a way to accelerate the elimination of the cells with irreparably damaged, ROS-producing mitochondria. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.}, }
@article {pmid23870133, year = {2013}, author = {Soini, HK and Moilanen, JS and Vilmi-Kerälä, T and Finnilä, S and Majamaa, K}, title = {Mitochondrial DNA variant m.15218A &gt; G in Finnish epilepsy patients who have maternal relatives with epilepsy, sensorineural hearing impairment or diabetes mellitus.}, journal = {BMC medical genetics}, volume = {14}, number = {}, pages = {73}, pmid = {23870133}, issn = {1471-2350}, mesh = {Base Sequence ; DNA, Mitochondrial/*genetics ; Diabetes Mellitus/*genetics ; Epilepsy/*genetics ; Female ; Finland ; Genetic Variation ; Hearing Loss, Sensorineural/*genetics ; Humans ; Male ; Mitochondria/*genetics ; Mitochondrial Diseases/genetics ; Pedigree ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Mitochondrial diseases caused by mutations in mitochondrial DNA (mtDNA) affect tissues with high energy demand. Epilepsy is one of the manifestations of mitochondrial dysfunction when the brain is affected. We have studied here 79 Finnish patients with epilepsy and who have maternal first- or second-degree relatives with epilepsy, sensorineural hearing impairment or diabetes mellitus.<br><br>METHODS: The entire mtDNA was studied by using conformation sensitive gel electrophoresis and PCR fragments that differed in mobility were directly sequenced.<br><br>RESULTS: We found a common nonsynonymous variant m.15218A&#x2009;>&#x2009;G (p.T158A, MTCYB) that occurs in haplogroup U5a1 to be more frequent in patients with epilepsy. The m.15218A&#x2009;>&#x2009;G variant was present in five patients with epilepsy and in four out of 403 population controls (p&#x2009;=&#x2009;0.0077). This variant was present in two branches in the phylogenetic network constructed on the basis of mtDNA variation among the patients. Three algorithms predicted that m.15218A&#x2009;>&#x2009;G is damaging in effect.<br><br>CONCLUSIONS: We suggest that the m.15218A&#x2009;>&#x2009;G variant is mildly deleterious and that mtDNA involvement should be considered in patients with epilepsy and who have a maternal history of epilepsy, sensorineural hearing impairment or diabetes mellitus.}, }
@article {pmid23867147, year = {2013}, author = {Millet, CO and Williams, CF and Hayes, AJ and Hann, AC and Cable, J and Lloyd, D}, title = {Mitochondria-derived organelles in the diplomonad fish parasite Spironucleus vortens.}, journal = {Experimental parasitology}, volume = {135}, number = {2}, pages = {262-273}, doi = {10.1016/j.exppara.2013.07.003}, pmid = {23867147}, issn = {1090-2449}, mesh = {Animals ; Diplomonadida/immunology/metabolism/*ultrastructure ; Fish Diseases/parasitology ; Fisheries ; Fishes ; Fluorescent Antibody Technique ; Fluorescent Dyes ; Hydrogen/metabolism ; Iron-Binding Proteins/analysis/immunology ; Membrane Potentials ; Microscopy, Confocal ; Microscopy, Electron, Transmission ; Mitochondrial Proteins/analysis/immunology ; Optical Imaging ; Organelles/immunology/metabolism/*ultrastructure ; Spectrophotometry ; Frataxin ; }, abstract = {In some eukaryotes, mitochondria have become modified during evolution to yield derived organelles (MDOs) of a similar size (hydrogenosomes), or extremely reduced to produce tiny cellular vesicles (mitosomes). The current study provides evidence for the presence of MDOs in the highly infectious fish pathogen Spironucleus vortens, an organism that produces H2 and is shown here to have no detectable cytochromes. Transmission electron microscopy (TEM) reveals that S. vortens trophozoites contain electron-dense, membranous structures sometimes with an electron-dense core (200 nm-1 μm), resembling the hydrogenosomes previously described in other protists from habitats deficient in O2. Confocal microscopy establishes that these organelles exhibit autofluorescence emission spectra similar to flavoprotein constituents previously described for mitochondria and also present in hydrogenosomes. These organelles possess a membrane potential and are labelled by a fluorescently labeled antibody against Fe-hydrogenase from Blastocystis hominis. Heterologous antibodies raised to mitochondrial proteins frataxin and Isu1, also exhibit a discrete punctate pattern of localization in S. vortens; however these labelled structures are distinctly smaller (90-150 nm) than hydrogenosomes as observed previously in other organisms. TEM confirms the presence of double-membrane bounded organelles of this smaller size. In addition, strong background immunostaining occurs in the cytosol for frataxin and Isu1, and labelling by anti-ferredoxin antibody is generally distributed and not specifically localized except for at the anterior polar region. This suggests that some of the functions traditionally attributed to such MDOs may also occur elsewhere. The specialized parasitic life-style of S. vortens may necessitate more complex intracellular compartmentation of redox reactions than previously recognized. Control of infection requires biochemical characterization of redox-related organelles.}, }
@article {pmid23864529, year = {2013}, author = {Pett, W and Lavrov, DV}, title = {The twin-arginine subunit C in Oscarella: origin, evolution, and potential functional significance.}, journal = {Integrative and comparative biology}, volume = {53}, number = {3}, pages = {495-502}, doi = {10.1093/icb/ict079}, pmid = {23864529}, issn = {1557-7023}, mesh = {Amino Acid Sequence ; Animals ; Bayes Theorem ; Computational Biology/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex III/genetics/metabolism ; *Evolution, Molecular ; Membrane Transport Proteins/*genetics/metabolism ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Porifera/*genetics ; Sequence Alignment ; Sequence Homology ; }, abstract = {The twin-arginine translocation (Tat) pathway is a protein transport system that moves completely folded proteins across lipid membranes. Genes encoding components of the pathway have been found in the genomes of many Bacteria, Archaea, and eukaryotic organelles including chloroplasts, plant mitochondria, and the mitochondria of many protists. However, with a single exception, Tat genes are absent from the mitochondrial genomes of all animals. The only exception comes from the homoscleromorph sponges in the family Oscarellidae, whose mitochondrial genomes encode a gene for tatC, the largest subunit of the complex. Here, we explore the origin and evolution of the mitochondrial tatC gene in Oscarellidae, and use bioinformatic approaches to evaluate its functional significance. We conclude that tatC in Homoscleromorpha sponges was likely inherited from the ancestral proto-mitochondrial genome, implying multiple independent losses of the mitochondrial Tat pathway during the evolution of opisthokonts. In addition, bioinformatic evidence suggests that tatC comprises the entire Tat pathway in Oscarellidae, and that the Rieske Fe/S protein of mitochondrial complex III is its likely substrate.}, }
@article {pmid23864032, year = {2014}, author = {Tillander, V and Arvidsson Nordström, E and Reilly, J and Strozyk, M and Van Veldhoven, PP and Hunt, MC and Alexson, SE}, title = {Acyl-CoA thioesterase 9 (ACOT9) in mouse may provide a novel link between fatty acid and amino acid metabolism in mitochondria.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {71}, number = {5}, pages = {933-948}, pmid = {23864032}, issn = {1420-9071}, mesh = {Amino Acids/*metabolism ; Animals ; Base Sequence ; Blotting, Western ; Chromatography, High Pressure Liquid ; Chromosome Mapping ; Cloning, Molecular ; Cluster Analysis ; Computational Biology ; DNA Primers/genetics ; Fatty Acids/*metabolism ; Mice ; Mice, Inbred C57BL ; Mitochondria/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Spectrophotometry ; Thiolester Hydrolases/*genetics/*metabolism ; }, abstract = {Acyl-CoA thioesterase (ACOT) activities are found in prokaryotes and in several compartments of eukaryotes where they hydrolyze a wide range of acyl-CoA substrates and thereby regulate intracellular acyl-CoA/CoA/fatty acid levels. ACOT9 is a mitochondrial ACOT with homologous genes found from bacteria to humans and in this study we have carried out an in-depth kinetic characterization of ACOT9 to determine its possible physiological function. ACOT9 showed unusual kinetic properties with activity peaks for short-, medium-, and saturated long-chain acyl-CoAs with highest V max with propionyl-CoA and (iso) butyryl-CoA while K cat/K m was highest with saturated long-chain acyl-CoAs. Further characterization of the short-chain acyl-CoA activity revealed that ACOT9 also hydrolyzes a number of short-chain acyl-CoAs and short-chain methyl-branched CoA esters that suggest a role for ACOT9 in regulation also of amino acid metabolism. In spite of markedly different K ms, ACOT9 can hydrolyze both short- and long-chain acyl-CoAs simultaneously, indicating that ACOT9 may provide a novel regulatory link between fatty acid and amino acid metabolism in mitochondria. Based on similar acyl-CoA chain-length specificities of recombinant ACOT9 and ACOT activity in mouse brown adipose tissue and kidney mitochondria, we conclude that ACOT9 is the major mitochondrial ACOT hydrolyzing saturated C2-C20-CoA in these tissues. Finally, ACOT9 activity is strongly regulated by NADH and CoA, suggesting that mitochondrial metabolic state regulates the function of ACOT9.}, }
@article {pmid23860571, year = {2013}, author = {Oelkrug, R and Goetze, N and Exner, C and Lee, Y and Ganjam, GK and Kutschke, M and Müller, S and Stöhr, S and Tschöp, MH and Crichton, PG and Heldmaier, G and Jastroch, M and Meyer, CW}, title = {Brown fat in a protoendothermic mammal fuels eutherian evolution.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {2140}, pmid = {23860571}, issn = {2041-1723}, mesh = {Adaptation, Physiological ; Adipose Tissue, Brown/*physiology ; Animals ; Biological Evolution ; Body Temperature/physiology ; Eulipotyphla/*physiology ; Female ; Gene Expression ; HEK293 Cells ; Humans ; Ion Channels/genetics/*metabolism ; Male ; Mice ; Mitochondria/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Phylogeny ; Reproduction/*physiology ; Thermogenesis/*physiology ; Uncoupling Protein 1 ; }, abstract = {Endothermy has facilitated mammalian species radiation, but the sequence of events leading to sustained thermogenesis is debated in multiple evolutionary models. Here we study the Lesser hedgehog tenrec (Echinops telfairi), a phylogenetically ancient, 'protoendothermic' eutherian mammal, in which constantly high body temperatures are reported only during reproduction. Evidence for nonshivering thermogenesis is found in vivo during periodic ectothermic-endothermic transitions. Anatomical studies reveal large brown fat-like structures in the proximity of the reproductive organs, suggesting physiological significance for parental care. Biochemical analysis demonstrates high mitochondrial proton leak catalysed by an uncoupling protein 1 ortholog. Strikingly, bioenergetic profiling of tenrec uncoupling protein 1 reveals similar thermogenic potency as modern mouse uncoupling protein 1, despite the large phylogenetic distance. The discovery of functional brown adipose tissue in this 'protoendothermic' mammal links nonshivering thermogenesis directly to the roots of eutherian evolution, suggesting physiological importance prior to sustained body temperatures and migration to the cold.}, }
@article {pmid23859054, year = {2015}, author = {Li, Q and Wei, SJ and Shi, M and Chen, XX}, title = {Complete mitochondrial genome of Neochauliodes bowringi (MacLachlan) (Megaloptera: Corydalidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {1}, pages = {112-113}, doi = {10.3109/19401736.2013.803542}, pmid = {23859054}, issn = {1940-1744}, mesh = {Animals ; Codon, Initiator ; Codon, Terminator ; Gene Order ; Genes, Insect ; *Genome, Mitochondrial ; Insecta/*genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {We describe and analyze the complete mitochondrial genome of Neochauliodes bowringi (MacLachlan) (Megaloptera: Corydalidae). The length of the genome is 16,064 bp (GenBank accession No. JQ351950), the longest mitochondrial genome in the order Megaloptera already got, which includes 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNAs and an A + T-rich region. The gene arrangement is similar to that of Drosophila yakuba, the presumed ancestral insect mitochondrial gene arrangement. All protein-coding genes start with ATN start codon except for the gene ND4, which uses GTG as start codon. Eight protein-coding genes use TAA as stop codon and others use incomplete stop codons "T" or "TA". The A + T-rich region is located between rrnS and trnI with a length of 1328 bp.}, }
@article {pmid23853512, year = {2013}, author = {Naito, K and Kaga, A and Tomooka, N and Kawase, M}, title = {De novo assembly of the complete organelle genome sequences of azuki bean (Vigna angularis) using next-generation sequencers.}, journal = {Breeding science}, volume = {63}, number = {2}, pages = {176-182}, pmid = {23853512}, issn = {1344-7610}, abstract = {Since chloroplasts and mitochondria are maternally inherited and have unique features in evolution, DNA sequences of those organelle genomes have been broadly used in phylogenetic studies. Thanks to recent progress in next-generation sequencer (NGS) technology, whole-genome sequencing can be easily performed. Here, using NGS data generated by Roche GS Titanium and Illumina Hiseq 2000, we performed a hybrid assembly of organelle genome sequences of Vigna angularis (azuki bean). Both the mitochondrial genome (mtDNA) and the chloroplast genome (cpDNA) of V. angularis have very similar size and gene content to those of V. radiata (mungbean). However, in structure, mtDNA sequences have undergone many recombination events after divergence from the common ancestor of V. angularis and V. radiata, whereas cpDNAs are almost identical between the two. The stability of cpDNAs and the variability of mtDNAs was further confirmed by comparative analysis of Vigna organelles with model plants Lotus japonicus and Arabidopsis thaliana.}, }
@article {pmid23853355, year = {2013}, author = {Dong, WG and Guo, XG and Jin, DC and Xue, SP and Qin, F and Simon, S and Stephen, CB and Renfu, S}, title = {[Understanding mitochondrial genome fragmentation in parasitic lice (Insecta: Phthiraptera)].}, journal = {Yi chuan = Hereditas}, volume = {35}, number = {7}, pages = {847-855}, doi = {10.3724/sp.j.1005.2013.00847}, pmid = {23853355}, issn = {0253-9772}, mesh = {Animals ; Chromosome Mapping ; *Genome, Insect ; *Genome, Mitochondrial ; Phthiraptera/classification/*genetics ; Phylogeny ; }, abstract = {Lice are obligate ectoparasites of mammals and birds. Extensive fragmentation of mitochondrial genomes has been found in some louse species in the families Pediculidae, Pthiridae, Philopteridae and Trichodectidae. For example, the mt genomes of human body louse (Pediculus humanus), head louse (Pediculus capitis), and public louse (Pthirus pubis) have 20, 20 and 14 mini-chromosomes, respectively. These mini-chromosomes might be the results of deletion and recombination of mt genes. The factors and mechanisms of mitochondrial genome fragmentation are currently unknown. The fragmentation might be the results of evolutionary selection or random genetic drift or it is probably related to the lack of mtSSB (mitochondrial single-strand DNA binding protein). Understanding the fragmentation of mitochondrial genomes is of significance for understanding the origin and evolution of mitochondria. This paper reviews the recent advances in the studies of mito-chondrial genome fragmentation in lice, including the phenomena of mitochondrial genome fragmentation, characteristics of fragmented mitochondrial genomes, and some factors and mechanisms possibly leading to the mitochondrial genome fragmentation of lice. Perspectives for future studies on fragmented mt genomes are also discussed.}, }
@article {pmid23850633, year = {2013}, author = {Lunetti, P and Cappello, AR and Marsano, RM and Pierri, CL and Carrisi, C and Martello, E and Caggese, C and Dolce, V and Capobianco, L}, title = {Mitochondrial glutamate carriers from Drosophila melanogaster: biochemical, evolutionary and modeling studies.}, journal = {Biochimica et biophysica acta}, volume = {1827}, number = {10}, pages = {1245-1255}, doi = {10.1016/j.bbabio.2013.07.002}, pmid = {23850633}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Amino Acid Transport System X-AG/chemistry ; Animals ; Binding Sites ; DNA Primers/chemistry/genetics ; Drosophila Proteins/genetics/isolation &amp; purification/*metabolism ; Drosophila melanogaster/genetics/growth &amp; development/*metabolism ; *Evolution, Molecular ; Exons/genetics ; Glutamic Acid/*metabolism ; Humans ; Hydrogen-Ion Concentration ; Introns/genetics ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/chemistry/genetics/isolation &amp; purification/*metabolism ; Mitochondrial Proteins/chemistry ; Models, Molecular ; Molecular Sequence Data ; Real-Time Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; }, abstract = {The mitochondrial carriers are members of a family of transport proteins that mediate solute transport across the inner mitochondrial membrane. Two isoforms of the glutamate carriers, GC1 and GC2 (encoded by the SLC25A22 and SLC25A18 genes, respectively), have been identified in humans. Two independent mutations in SLC25A22 are associated with severe epileptic encephalopathy. In the present study we show that two genes (CG18347 and CG12201) phylogenetically related to the human GC encoding genes are present in the D. melanogaster genome. We have functionally characterized the proteins encoded by CG18347 and CG12201, designated as DmGC1p and DmGC2p respectively, by overexpression in Escherichia coli and reconstitution into liposomes. Their transport properties demonstrate that DmGC1p and DmGC2p both catalyze the transport of glutamate across the inner mitochondrial membrane. Computational approaches have been used in order to highlight residues of DmGC1p and DmGC2p involved in substrate binding. Furthermore, gene expression analysis during development and in various adult tissues reveals that CG18347 is ubiquitously expressed in all examined D. melanogaster tissues, while the expression of CG12201 is strongly testis-biased. Finally, we identified mitochondrial glutamate carrier orthologs in 49 eukaryotic species in order to attempt the reconstruction of the evolutionary history of the glutamate carrier function. Comparison of the exon/intron structure and other key features of the analyzed orthologs suggests that eukaryotic glutamate carrier genes descend from an intron-rich ancestral gene already present in the common ancestor of lineages that diverged as early as bilateria and radiata.}, }
@article {pmid23850535, year = {2013}, author = {Marijuán, PC and del Moral, R and Navarro, J}, title = {On eukaryotic intelligence: signaling system's guidance in the evolution of multicellular organization.}, journal = {Bio Systems}, volume = {114}, number = {1}, pages = {8-24}, doi = {10.1016/j.biosystems.2013.06.005}, pmid = {23850535}, issn = {1872-8324}, mesh = {*Biological Evolution ; Cell Communication/*physiology ; Cell Cycle/*physiology ; Cytoskeleton/*physiology ; Eukaryotic Cells/*cytology/*physiology ; *Models, Biological ; Signal Transduction/*physiology ; }, abstract = {Communication with the environment is an essential characteristic of the living cell, even more when considering the origins and evolution of multicellularity. A number of changes and tinkering inventions were necessary in the evolutionary transition between prokaryotic and eukaryotic cells, which finally made possible the appearance of genuine multicellular organisms. In the study of this process, however, the transformations experimented by signaling systems themselves have been rarely object of analysis, obscured by other more conspicuous biological traits: incorporation of mitochondria, segregated nucleus, introns/exons, flagellum, membrane systems, etc. Herein a discussion of the main avenues of change from prokaryotic to eukaryotic signaling systems and a review of the signaling resources and strategies underlying multicellularity will be attempted. In the expansion of prokaryotic signaling systems, four main systemic resources were incorporated: molecular tools for detection of solutes, molecular tools for detection of solvent (Donnan effect), the apparatuses of cell-cycle control, and the combined system endocytosis/cytoskeleton. The multiple kinds of enlarged, mixed pathways that emerged made possible the eukaryotic revolution in morphological and physiological complexity. The massive incorporation of processing resources of electro-molecular nature, derived from the osmotic tools counteracting the Donnan effect, made also possible the organization of a computational tissue with huge information processing capabilities: the nervous system. In the central nervous systems of vertebrates, and particularly in humans, neurons have achieved both the highest level of molecular-signaling complexity and the highest degree of information-processing adaptability. Theoretically, it can be argued that there has been an accelerated pace of evolutionary change in eukaryotic signaling systems, beyond the other general novelties introduced by eukaryotic cells in their handling of DNA processes. Under signaling system's guidance, the whole processes of transcription, alternative splicing, mobile elements, and other elements of domain recombination have become closely intertwined and have propelled the differentiation capabilities of multicellular tissues and morphologies. An amazing variety of signaling and self-construction strategies have emerged out from the basic eukaryotic design of multicellular complexity, in millions and millions of new species evolved. This design can also be seen abstractly as a new kind of quasi-universal problem-solving 'engine' implemented at the biomolecular scale-providing the fundamentals of eukaryotic 'intelligence'. Analyzing in depth the problem-solving intelligence of eukaryotic cells would help to establish an integrative panorama of their information processing organization, and of their capability to handle the morphological and physiological complexity associated. Whether an informational updating of the venerable "cell theory" is feasible or not, becomes, at the time being - right in the middle of the massive data deluge/revolution from omic disciplines - a matter to careful consider.}, }
@article {pmid23844272, year = {2013}, author = {Rodríguez, MJ and Martínez-Moreno, M and Ortega, FJ and Mahy, N}, title = {Targeting microglial K(ATP) channels to treat neurodegenerative diseases: a mitochondrial issue.}, journal = {Oxidative medicine and cellular longevity}, volume = {2013}, number = {}, pages = {194546}, pmid = {23844272}, issn = {1942-0994}, mesh = {Animals ; Humans ; Microglia/*metabolism ; Mitochondria/*metabolism ; Neurodegenerative Diseases/*metabolism ; Potassium Channels/*metabolism ; }, abstract = {Neurodegeneration is a complex process involving different cell types and neurotransmitters. A common characteristic of neurodegenerative disorders is the occurrence of a neuroinflammatory reaction in which cellular processes involving glial cells, mainly microglia and astrocytes, are activated in response to neuronal death. Microglia do not constitute a unique cell population but rather present a range of phenotypes closely related to the evolution of neurodegeneration. In a dynamic equilibrium with the lesion microenvironment, microglia phenotypes cover from a proinflammatory activation state to a neurotrophic one directly involved in cell repair and extracellular matrix remodeling. At each moment, the microglial phenotype is likely to depend on the diversity of signals from the environment and of its response capacity. As a consequence, microglia present a high energy demand, for which the mitochondria activity determines the microglia participation in the neurodegenerative process. As such, modulation of microglia activity by controlling microglia mitochondrial activity constitutes an innovative approach to interfere in the neurodegenerative process. In this review, we discuss the mitochondrial KATP channel as a new target to control microglia activity, avoid its toxic phenotype, and facilitate a positive disease outcome.}, }
@article {pmid23841539, year = {2013}, author = {Xu, L and Law, SR and Murcha, MW and Whelan, J and Carrie, C}, title = {The dual targeting ability of type II NAD(P)H dehydrogenases arose early in land plant evolution.}, journal = {BMC plant biology}, volume = {13}, number = {}, pages = {100}, pmid = {23841539}, issn = {1471-2229}, mesh = {Amino Acid Sequence ; Embryophyta/classification/*enzymology/genetics ; *Evolution, Molecular ; Molecular Sequence Data ; NAD/metabolism ; NADP/metabolism ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Protein Transport ; }, abstract = {BACKGROUND: Type II NAD(PH) dehydrogenases are located on the inner mitochondrial membrane of plants, fungi, protists and some primitive animals. However, recent observations have been made which identify several Arabidopsis type II dehydrogenases as dual targeted proteins. Targeting either mitochondria and peroxisomes or mitochondria and chloroplasts.<br><br>RESULTS: Members of the ND protein family were identified in various plant species. Phylogenetic analyses and subcellular targeting predictions were carried out for all proteins. All ND proteins from three model plant species Arabidopsis, rice and Physcomitrella were cloned as N- and C-terminal GFP fusions and subcellular localisations were determined. Dual targeting of plant type II dehydrogenases was observed to have evolved early in plant evolution and to be widespread throughout different plant species. In all three species tested dual targeting to both mitochondria and peroxisomes was found for at least one NDA and NDB type protein. In addition two NDB type proteins from Physcomitrella were also found to target chloroplasts. The dual targeting of NDC type proteins was found to have evolved later in plant evolution.<br><br>CONCLUSIONS: The functions of type II dehydrogenases within plant cells will have to be re-evaluated in light of this newly identified subcellular targeting information.}, }
@article {pmid23840400, year = {2013}, author = {Srivastava, S and Ratha, BK}, title = {Unique hepatic cytosolic arginase evolved independently in ureogenic freshwater air-breathing teleost, Heteropneustes fossilis.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e66057}, pmid = {23840400}, issn = {1932-6203}, mesh = {Animals ; Antibodies/chemistry ; Arginase/chemistry/*genetics/immunology/metabolism ; Blotting, Western ; Catfishes/*genetics ; Cytoplasm/enzymology ; Evolution, Molecular ; Fish Proteins/chemistry/*genetics/immunology/metabolism ; Hydrogen-Ion Concentration ; Isoelectric Focusing ; Kinetics ; Liver/*enzymology ; Male ; Manganese/chemistry ; Mitochondrial Membranes/enzymology ; Molecular Weight ; Ornithine/chemistry ; Phylogeny ; Rabbits ; }, abstract = {Hepatic cytosolic arginase (ARG I), an enzyme of the urea cycle operating in the liver of ureotelic animals, is reported to be present in an ammoniotelic freshwater air-breathing teleost, Heteropneustes fossilis which has ureogenic potential. Antibodies available against mammalian ARG I showed no cross reactivity with the H. fossilis ARG I. We purified unique ARG I from H. fossilis liver. Purified ARG I is a homotrimer with molecular mass 75 kDa and subunit molecular mass of 24 kDa. The pI value of the enzyme was 8.5. It showed maximum activity at pH 10.5 and 55°C. The Km of purified enzyme for L-arginine was 2.65±0.39 mM. L-ornithine and N(ω)-hydroxy-L-arginine showed inhibition of the ARG I activity, with Ki values 0.52±0.02mM and 0.08±0.006mM, respectively. Antibody raised against the purified fish liver ARG I showed exclusive specificity, and has no cross reactivity against fish liver ARG II and mammalian liver ARG I and ARG II. We found another isoform of arginase bound to the outer membrane of the mitochondria which was released by 150-200 mM KCl in the extraction medium. This isoform was immunologically different from the soluble cytosolic and mitochondrial arginase. The results of present study support that hepatic cytosolic arginase evolved in this ureogenic freshwater teleost, H. fossilis. Phylogenetic analysis confirms an independent evolution event that occurred much after the evolution of the cytosolic arginase of ureotelic vertebrates.}, }
@article {pmid23840368, year = {2013}, author = {Grindon, AJ and Davison, A}, title = {Irish Cepaea nemoralis Land Snails Have a Cryptic Franco-Iberian Origin That Is Most Easily Explained by the Movements of Mesolithic Humans.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e65792}, pmid = {23840368}, issn = {1932-6203}, mesh = {Animals ; DNA, Mitochondrial/*analysis ; Fossils ; France ; Human Migration ; Humans ; Ireland ; Mitochondria/*genetics ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA/*methods ; Snails/*classification/genetics ; Spain ; }, abstract = {The origins of flora and fauna that are only found in Ireland and Iberia, but which are absent from intervening countries, is one of the enduring questions of biogeography. As Southern French, Iberian and Irish populations of the land snail Cepaea nemoralis sometimes have a similar shell character, we used mitochondrial phylogenies to begin to understand if there is a shared "Lusitanian" history. Although much of Europe contains snails with A and D lineages, by far the majority of Irish individuals have a lineage, C, that in mainland Europe was only found in a restricted region of the Eastern Pyrenees. A past extinction of lineage C in the rest of Europe cannot be ruled out, but as there is a more than 8000 year continuous record of Cepaea fossils in Ireland, the species has long been a food source in the Pyrenees, and the Garonne river that flanks the Pyrenees is an ancient human route to the Atlantic, then we suggest that the unusual distribution of the C lineage is most easily explained by the movements of Mesolithic humans. If other Irish species have a similarly cryptic Lusitanian element, then this raises the possibility of a more widespread and significant pattern.}, }
@article {pmid23840326, year = {2013}, author = {Teng, CY and Dang, Y and Danne, JC and Waller, RF and Green, BR}, title = {Mitochondrial Genes of Dinoflagellates Are Transcribed by a Nuclear-Encoded Single-Subunit RNA Polymerase.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e65387}, pmid = {23840326}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Bacteriophage T7/enzymology/genetics ; Cell Nucleus/genetics/metabolism ; Conserved Sequence ; DNA-Directed RNA Polymerases/*physiology ; Dinoflagellida/*genetics/ultrastructure ; *Genes, Mitochondrial ; Genome, Mitochondrial ; Phylogeny ; Protein Subunits ; RNA, Nuclear/*physiology ; *Transcription, Genetic ; }, abstract = {Dinoflagellates are a large group of algae that contribute significantly to marine productivity and are essential photosynthetic symbionts of corals. Although these algae have fully-functioning mitochondria and chloroplasts, both their organelle genomes have been highly reduced and the genes fragmented and rearranged, with many aberrant transcripts. However, nothing is known about their RNA polymerases. We cloned and sequenced the gene for the nuclear-encoded mitochondrial polymerase (RpoTm) of the dinoflagellate Heterocapsa triquetra and showed that the protein presequence targeted a GFP construct into yeast mitochondria. The gene belongs to a small gene family, which includes a variety of 3'-truncated copies that may have originated by retroposition. The catalytic C-terminal domain of the protein shares nine conserved sequence blocks with other single-subunit polymerases and is predicted to have the same fold as the human enzyme. However, the N-terminal (promoter binding/transcription initiation) domain is not well-conserved. In conjunction with the degenerate nature of the mitochondrial genome, this suggests a requirement for novel accessory factors to ensure the accurate production of functional mRNAs.}, }
@article {pmid23839086, year = {2013}, author = {Evangelou, VI and Bouga, M and Emmanouel, NG and Perdikis, DCh and Papadoulis, GT}, title = {Discrimination of two natural biocontrol agents in the Mediterranean region based on mitochondrial DNA sequencing data.}, journal = {Biochemical genetics}, volume = {51}, number = {11-12}, pages = {825-840}, doi = {10.1007/s10528-013-9610-0}, pmid = {23839086}, issn = {1573-4927}, mesh = {Animals ; Asteraceae ; *Biological Control Agents ; Crosses, Genetic ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Female ; Genes, Mitochondrial ; Greece ; Haplotypes ; Heteroptera/*classification/genetics ; Male ; Mitochondria/genetics ; Phylogeny ; *Sequence Analysis, DNA ; Solanum ; Spain ; }, abstract = {Macrolophus pygmaeus and M. melanotoma (Hemiptera: Miridae) are biological control agents used in greenhouse crops, the former preferring plants of the Solanaceae family and the latter the aster Dittrichia viscosa. The discrimination of these species is of high significance for effective biological pest control, but identification based on morphological characters of the host plant is not always reliable. In this study, sequencing analysis of mitochondrial gene segments 12S rDNA and COI has been combined with crossing experiments and morphological observations to develop new markers for Macrolophus spp. discrimination and to provide new data on their genetic variability. This is the first comprehensive research in Greece on M. pygmaeus and M. melanotoma genetic variability based on sequencing data from 12S rDNA and COI gene segments. The relationship of this variability to host plant preference must be investigated in an agricultural ecosystem.}, }
@article {pmid23838143, year = {2013}, author = {Seo, MY and Mekuchi, M and Teranishi, K and Kaneko, T}, title = {Expression of ion transporters in gill mitochondrion-rich cells in Japanese eel acclimated to a wide range of environmental salinity.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {166}, number = {2}, pages = {323-332}, doi = {10.1016/j.cbpa.2013.07.004}, pmid = {23838143}, issn = {1531-4332}, mesh = {*Acclimatization ; Anguilla/*metabolism ; Animals ; Cloning, Molecular ; Fish Proteins/genetics/*metabolism ; Gene Expression ; Gene Expression Regulation ; Gills/*metabolism/ultrastructure ; Ion Transport ; Mitochondria/metabolism/ultrastructure ; Organ Specificity ; Osmoregulation ; Phylogeny ; Protein Subunits/metabolism ; RNA, Messenger/genetics/metabolism ; Salinity ; Salt Tolerance ; Sodium-Hydrogen Exchangers/genetics/metabolism ; Solute Carrier Family 12, Member 2/genetics/metabolism ; Vacuolar Proton-Translocating ATPases/genetics/metabolism ; }, abstract = {We examined morphological changes and molecular mechanisms of ion regulation in mitochondrion-rich (MR) cells of Japanese eel acclimated to different environmental salinities. Electron microscopic observations revealed that the apical membrane of MR cells appeared as a flat or slightly projecting disk with a mesh-like structure on its surface in eel acclimated to freshwater (FW). In seawater (SW)-acclimated eel, in contrast, the apical membrane of MR cells showed a slightly concave surface without a mesh-like structure. The mRNA expression of Na(+)/H(+) exchanger-3 (NHE3) in deionized FW and normal SW was higher than that in normal FW and 30%-diluted SW. Expression of Na(+)/K(+)/2Cl(-) cotransporter-1a (NKCC1a) became higher with increasing environmental salinity. Immunofluorescence staining showed that the apical NHE3 immunoreaction was stronger in deionized FW and normal SW than in the other groups. Basolateral NKCC1 immunoreaction was most intense in normal SW. These results indicate that apical NHE3 is involved in ion uptake in fish acclimated to hypotonic environments, and that basolateral NKCC1 is important for acclimation to hypertonic environments. The relatively high expression of NHE3 in SW further indicates a possible role of NHE3 in acid-base regulation in the gills in SW-acclimated fish.}, }
@article {pmid23831752, year = {2013}, author = {Jimenez-Gutierrez, LR and Hernandez-Lopez, J and Islas-Osuna, MA and Muhlia-Almazan, A}, title = {Three nucleus-encoded subunits of mitochondrial cytochrome c oxidase of the whiteleg shrimp Litopenaeus vannamei: cDNA characterization, phylogeny and mRNA expression during hypoxia and reoxygenation.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {166}, number = {1}, pages = {30-39}, doi = {10.1016/j.cbpb.2013.06.008}, pmid = {23831752}, issn = {1879-1107}, mesh = {Adenosine Triphosphate/biosynthesis ; Amino Acid Sequence ; Animals ; Cell Nucleus/enzymology ; DNA, Complementary/*genetics ; Electron Transport Complex IV/*genetics/metabolism ; Gene Expression ; Hypoxia/genetics/metabolism ; Mitochondria/*enzymology/genetics ; Oxygen/metabolism ; Penaeidae ; Phylogeny ; Protein Subunits/*genetics ; }, abstract = {The mitochondrial cytochrome c oxidase (COX) catalyzes the reduction of oxygen to water playing a key role in the respiratory chain and ATP synthesis. The nucleus-encoded COX subunits do not participate in catalysis, but some are known to play a role in the expression, assembly and activity of the enzyme. Since hypoxia continuously affects the shrimp environment, it is important to study COX to understand their ability to deal with low oxygen levels. The goal of this research was to characterize the complementary DNA (cDNA) sequences of three nucleus-encoded subunits -coxIV, coxVa, and coxVb- and to evaluate the shrimp COX response to hypoxia by measuring their gene expression. The cDNA sequence of coxIV consisted of 532bp, which encodes a 17.47kDa protein, while coxVa cDNA consisted of 460bp and coded a protein of 17.11kDa, and the coxVb coding sequence consisted of 364bp encoding a 13.74kDa protein. Shrimp subunits do not have isoforms, and they are not differentially expressed during hypoxia, as observed in mammals. Coordinated changes were detected in the mRNA amounts of nuclear and mitochondrial subnits; these changes, at the transcriptional level, are suggested to be controlled through transcriptional factors Sp1 and NRF2.}, }
@article {pmid23829495, year = {2013}, author = {Rondeau, EB and Messmer, AM and Sanderson, DS and Jantzen, SG and von Schalburg, KR and Minkley, DR and Leong, JS and Macdonald, GM and Davidsen, AE and Parker, WA and Mazzola, RS and Campbell, B and Koop, BF}, title = {Genomics of sablefish (Anoplopoma fimbria): expressed genes, mitochondrial phylogeny, linkage map and identification of a putative sex gene.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {452}, pmid = {23829495}, issn = {1471-2164}, mesh = {Animals ; *Chromosome Mapping ; Female ; Fishes/*genetics/physiology ; Genetic Markers/genetics ; Genome, Mitochondrial/genetics ; *Genomics ; Genotyping Techniques ; Male ; Mitochondria/*genetics ; Phenotype ; *Phylogeny ; *Sex Characteristics ; Sex Determination Processes/*genetics ; Smegmamorpha/genetics ; Synteny/genetics ; }, abstract = {BACKGROUND: The sablefish (order: Scorpaeniformes) is an economically important species in commercial fisheries of the North Pacific and an emerging species in aquaculture. Aside from a handful of sequences in NCBI and a few published microsatellite markers, little is known about the genetics of this species. The development of genetic tools, including polymorphic markers and a linkage map will allow for the successful development of future broodstock and mapping of phenotypes of interest. The significant sexual dimorphism between females and males makes a genetic test for early identification of sex desirable.<br><br>RESULTS: A full mitochondrial genome is presented and the resulting phylogenetic analysis verifies the placement of the sablefish within the Scorpaeniformes. Nearly 35,000 assembled transcript sequences are used to identify genes and obtain polymorphic SNP and microsatellite markers. 360 transcribed polymorphic loci from two sablefish families produce a map of 24 linkage groups. The sex phenotype maps to sablefish LG14 of the male map. We show significant conserved synteny and conservation of gene-order between the threespine stickleback Gasterosteus aculeatus and sablefish. An additional 1843 polymorphic SNP markers are identified through next-generation sequencing techniques. Sex-specific markers and sequence insertions are identified immediately upstream of the gene gonadal-soma derived factor (gsdf), the master sex determinant locus in the medaka species Oryzias luzonensis.<br><br>CONCLUSIONS: The first genomic resources for sablefish provide a foundation for further studies. Over 35,000 transcripts are presented, and the genetic map represents, as far as we can determine, the first linkage map for a member of the Scorpaeniformes. The observed level of conserved synteny and comparative mapping will allow the use of the stickleback genome in future genetic studies on sablefish and other related fish, particularly as a guide to whole-genome assembly. The identification of sex-specific insertions immediately upstream of a known master sex determinant implicates gsdf as an excellent candidate for the master sex determinant for sablefish.}, }
@article {pmid23826813, year = {2013}, author = {Wei, Q and Wang, S and Yao, J and Lu, Y and Chen, Z and Xing, G and Cao, X}, title = {Genetic mutations of GJB2 and mitochondrial 12S rRNA in nonsyndromic hearing loss in Jiangsu Province of China.}, journal = {Journal of translational medicine}, volume = {11}, number = {}, pages = {163}, pmid = {23826813}, issn = {1479-5876}, mesh = {Adolescent ; Adult ; Case-Control Studies ; Child ; Child, Preschool ; China ; Connexin 26 ; Connexins/*genetics ; DNA, Mitochondrial/genetics ; Deafness/genetics ; Female ; Heterozygote ; Humans ; Male ; Middle Aged ; Mitochondria/*genetics ; *Mutation ; Nucleic Acid Conformation ; Phylogeny ; RNA, Messenger/genetics ; RNA, Ribosomal/*genetics ; Sequence Analysis, DNA ; Young Adult ; }, abstract = {BACKGROUND: Hearing loss is caused by several environmental and genetic factors and the proportion attributed to inherited causes is assumed at 50 ~ 60% . Mutations in GJB2 and mitochondrial DNA (mtDNA) 12S rRNA are the most common molecular etiology for nonsyndromic sensorineural hearing loss (NSHL). The mutation spectra of these genes vary among different ethnic groups.<br><br>METHODS: To add the molecular etiologic information of hearing loss in the Chinese population, a total of 658 unrelated patients with NSHL from Jiangsu Province of China were selected for mutational screening including GJB2 and mtDNA 12S rRNA genes using PCR and DNA sequencing technology. As for controls, 462 normal-hearing individuals were collected.<br><br>RESULTS: A total of 9 pathogenic mutations in the GJB2 and 7 pathogenic mutations in the 12S rRNA gene were identified. Of all patients, 70 had monoallelic GJB2 coding region mutation in the heterozygous state, 94 carried two confirmed pathogenic mutations including 79 homozygotes and 15 compound heterozygotes. The 235delC appears to be the most common deafness-causing GJB2 mutation (102/658, 15.50%). No mutations or variants in the GJB2 exon1 and basal promoter region were found. In these patients, 4 subjects carried the m.1494C&#x2009;>&#x2009;T mutation (0.61%) and 39 subjects harbored the m.1555A&#x2009;>&#x2009;G mutation (5.93%) in mtDNA 12S rRNA gene. A novel sequence variant at m.1222A&#x2009;>&#x2009;G in the 12S rRNA gene was identified, which could alter the secondary structure of the 12S rRNA.<br><br>CONCLUSION: The mutation spectrum and prevalence of GJB2 and mtDNA 12S rRNA genes in Jiangsu population are similar to other areas of China. There are in total 31.46% of the patients with NSHL carry deafness-causing mutation in GJB2 or mtDNA 12S rRNA genes. Mutation in GJB2 gene is the most common factor, mtDNA 12S rRNA also plays an important part in the pathogenesis of hearing loss in Jiangsu Province areas. The m.1222A&#x2009;>&#x2009;G was found to be a new candidate mutation associated with hearing loss. Our results indicated the necessity of genetic screening for mutations of these genes in Jiangsu patients with NSHL.}, }
@article {pmid23825690, year = {2013}, author = {Doyle, SR and Kasinadhuni, NR and Chan, CK and Grant, WN}, title = {Evidence of evolutionary constraints that influences the sequence composition and diversity of mitochondrial matrix targeting signals.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e67938}, pmid = {23825690}, issn = {1932-6203}, mesh = {Adaptation, Physiological ; Animals ; Arabidopsis/cytology/metabolism/physiology ; *Computational Biology ; *Evolution, Molecular ; Humans ; Mice ; Mitochondria/*metabolism ; Multivariate Analysis ; Oryza/cytology/metabolism/physiology ; *Protein Sorting Signals ; Protein Transport ; Saccharomyces cerevisiae/cytology/metabolism/physiology ; Species Specificity ; }, abstract = {Mitochondrial targeting signals (MTSs) are responsible for trafficking nuclear encoded proteins to their final destination within mitochondria. These sequences are diverse, sharing little amino acid homology and vary significantly in length, and although the formation of a positively-charged amphiphilic alpha helix within the MTS is considered to be necessary and sufficient to mediate import, such a feature does not explain their diversity, nor how such diversity influences target sequence function, nor how such dissimilar signals interact with a single, evolutionarily conserved import mechanism. An in silico analysis of 296 N-terminal, matrix destined MTSs from Homo sapiens, Mus musculus, Saccharomyces cerevisiae, Arabidopsis thaliana, and Oryza sativa was undertaken to investigate relationships between MTSs, and/or, relationships between an individual targeting signal sequence and the protein that it imports. We present evidence that suggests MTS diversity is influenced in part by physiochemical and N-terminal characteristics of their mature sequences, and that some of these correlated characteristics are evolutionarily maintained across a number of taxa. Importantly, some of these associations begin to explain the variation in MTS length and composition.}, }
@article {pmid23824218, year = {2013}, author = {Milani, L and Ghiselli, F and Guerra, D and Breton, S and Passamonti, M}, title = {A comparative analysis of mitochondrial ORFans: new clues on their origin and role in species with doubly uniparental inheritance of mitochondria.}, journal = {Genome biology and evolution}, volume = {5}, number = {7}, pages = {1408-1434}, pmid = {23824218}, issn = {1759-6653}, mesh = {Animals ; Bivalvia/*genetics ; DNA, Mitochondrial/*genetics/metabolism ; Evolution, Molecular ; Female ; Inheritance Patterns ; Male ; Mitochondria/*genetics ; Mytilidae/*genetics ; *Open Reading Frames/genetics/physiology ; }, abstract = {Despite numerous comparative mitochondrial genomics studies revealing that animal mitochondrial genomes are highly conserved in terms of gene content, supplementary genes are sometimes found, often arising from gene duplication. Mitochondrial ORFans (ORFs having no detectable homology and unknown function) were found in bivalve molluscs with Doubly Uniparental Inheritance (DUI) of mitochondria. In DUI animals, two mitochondrial lineages are present: one transmitted through females (F-type) and the other through males (M-type), each showing a specific and conserved ORF. The analysis of 34 mitochondrial major Unassigned Regions of Musculista senhousia F- and M-mtDNA allowed us to verify the presence of novel mitochondrial ORFs in this species and to compare them with ORFs from other species with ascertained DUI, with other bivalves and with animals showing new mitochondrial elements. Overall, 17 ORFans from nine species were analyzed for structure and function. Many clues suggest that the analyzed ORFans arose from endogenization of viral genes. The co-option of such novel genes by viral hosts may have determined some evolutionary aspects of host life cycle, possibly involving mitochondria. The structure similarity of DUI ORFans within evolutionary lineages may also indicate that they originated from independent events. If these novel ORFs are in some way linked to DUI establishment, a multiple origin of DUI has to be considered. These putative proteins may have a role in the maintenance of sperm mitochondria during embryo development, possibly masking them from the degradation processes that normally affect sperm mitochondria in species with strictly maternal inheritance.}, }
@article {pmid23815665, year = {2013}, author = {Gibson, JD and Niehuis, O and Peirson, BR and Cash, EI and Gadau, J}, title = {Genetic and developmental basis of F2 hybrid breakdown in Nasonia parasitoid wasps.}, journal = {Evolution; international journal of organic evolution}, volume = {67}, number = {7}, pages = {2124-2132}, doi = {10.1111/evo.12080}, pmid = {23815665}, issn = {1558-5646}, mesh = {Animals ; Chromosomes, Insect ; Female ; Gene Flow ; Genetic Speciation ; Male ; Sympatry ; Wasps/anatomy &amp; histology/classification/*genetics/*growth &amp; development ; }, abstract = {Speciation is responsible for the vast diversity of life, and hybrid inviability, by reducing gene flow between populations, is a major contributor to this process. In the parasitoid wasp genus Nasonia, F2 hybrid males of Nasonia vitripennis and Nasonia giraulti experience an increased larval mortality rate relative to the parental species. Previous studies indicated that this increase of mortality is a consequence of incompatibilities between multiple nuclear loci and cytoplasmic factors of the parental species, but could only explain ∼40% of the mortality rate in hybrids with N. giraulti cytoplasm. Here we report a locus on chromosome 5 that can explain the remaining mortality in this cross. We show that hybrid larvae that carry the incompatible allele on chromosome 5 halt growth early in their development and that ∼98% die before they reach adulthood. On the basis of these new findings, we identified a nuclear-encoded OXPHOS gene as a strong candidate for being causally involved in the observed hybrid breakdown, suggesting that the incompatible mitochondrial locus is one of the six mitochondrial-encoded NADH genes. By identifying both genetic and physiological mechanisms that reduce gene flow between species, our results provide valuable and novel insights into the evolutionary dynamics of speciation.}, }
@article {pmid23815330, year = {2015}, author = {Ma, Z and Huang, Z and Zhang, S and Xie, L and Yang, X and Zhang, X and Yang, R}, title = {The complete mitochondrial genome of Micropercops swinhonis (Perciformes: Gobioidei: Odontobutidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {1}, pages = {116-117}, doi = {10.3109/19401736.2013.809446}, pmid = {23815330}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Data ; Perciformes/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {For understanding the phylogenetic position of Micropercops swinhonis within the family Odontobutidae, the complete nucleotide sequence of M. swinhonis mitochondrial genome was firstly determined. The genome is 16,493 bp in length, and consists of 37 genes (13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes) and 2 main noncoding regions (the control region and the origin of the light strand replication). The gene composition and order of which were similar to most other vertebrates. Within the control region, typical conserved domains, such as the termination-associated sequence, central and conserved sequence blocks domains were identified.}, }
@article {pmid23813918, year = {2013}, author = {Wideman, JG and Gawryluk, RM and Gray, MW and Dacks, JB}, title = {The ancient and widespread nature of the ER-mitochondria encounter structure.}, journal = {Molecular biology and evolution}, volume = {30}, number = {9}, pages = {2044-2049}, doi = {10.1093/molbev/mst120}, pmid = {23813918}, issn = {1537-1719}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Acanthamoeba castellanii/genetics/metabolism/*ultrastructure ; Animals ; *Biological Evolution ; Computational Biology ; Endoplasmic Reticulum/genetics/metabolism/ultrastructure ; Intracellular Membranes/chemistry/*classification/metabolism ; Membrane Proteins/genetics/metabolism ; Mitochondria/genetics/metabolism/ultrastructure ; Mitochondrial Proteins/genetics/metabolism ; *Phylogeny ; Saccharomyces cerevisiae/genetics/metabolism/*ultrastructure ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {Mitochondria are the result of a billion years of integrative evolution, converting a once free-living bacterium to an organelle deeply linked to diverse cellular processes. One way in which mitochondria are integrated with nonendosymbiotically derived organelles is via endoplasmic reticulum (ER)-mitochondria contact sites. The ER membrane is physically tethered to the mitochondrial outer membrane by the ER-mitochondria encounter structure (ERMES). However, to date, ERMES has only ever been found in the fungal lineage. Here, we bioinformatically demonstrate that ERMES is present in lineages outside Fungi and validate this inference by mass spectrometric identification of ERMES components in Acanthamoeba castellanii mitochondria. We further demonstrate that ERMES is retained in hydrogenosome-bearing but not mitosome-bearing organisms, yielding insight into the process of reductive mitochondrial evolution. Finally, we find that the taxonomic distribution of ERMES is most consistent with rooting the eukaryotic tree between Amorphea (Animals + Fungi + Amoebozoa) + Excavata and all other eukaryotes (Diaphoratickes).}, }
@article {pmid23805212, year = {2013}, author = {He, XL and Ding, CQ and Han, JL}, title = {Lack of Structural Variation but Extensive Length Polymorphisms and Heteroplasmic Length Variations in the Mitochondrial DNA Control Region of Highly Inbred Crested Ibis, Nipponia nippon.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e66324}, pmid = {23805212}, issn = {1932-6203}, mesh = {Animals ; Birds/*genetics ; DNA, Mitochondrial/chemistry/*genetics/metabolism ; *Endangered Species ; Genotype ; Inbreeding ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Pedigree ; *Polymorphism, Genetic ; Sequence Analysis, DNA ; }, abstract = {The animal mitochondrial DNA (mtDNA) length polymorphism and heteroplasmy are accepted to be universal. Here we report the lack of structural variation but the presence of length polymorphism as well as heteroplasmy in mtDNA control region of an endangered avian species - the Crested Ibis (Nipponia nippon). The complete control region was directly sequenced while the distribution pattern and inheritance of the length variations were examined using both direct sequencing and genotyping of the PCR fragments from captive birds with pedigrees, wild birds and a historical specimen. Our results demonstrated that there was no structural variation in the control region, however, different numbers of short tandem repeats with an identical motif of CA3CA2CA3 at the 3'-end of the control region determined the length polymorphisms among and heteroplasmy within individual birds. There were one to three predominant fragments in every bird; nevertheless multiple minor fragments coexist in all birds. These extremely high polymorphisms were suggested to have derived from the 'replication slippage' of a perfect microsatellite evolution following the step-wise mutational model. The patterns of heteroplasmy were found to be shifted between generations and among siblings but rather stable between blood and feather samples. This study provides the first evidence of a very extensive mtDNA length polymorphism and heteroplasmy in the highly inbred Crested Ibis which carries an mtDNA genome lack of structural genetic diversity. The analysis of pedigreed samples also sheds light on the transmission of mtDNA length heteroplasmy in birds following the genetic bottleneck theory. Further research focusing on the generation and transmission of particular mtDNA heteroplasmy patterns in single germ line of Crested Ibis is encouraged by this study.}, }
@article {pmid23804750, year = {2013}, author = {Giacomotto, J and Brouilly, N and Walter, L and Mariol, MC and Berger, J and Ségalat, L and Becker, TS and Currie, PD and Gieseler, K}, title = {Chemical genetics unveils a key role of mitochondrial dynamics, cytochrome c release and IP3R activity in muscular dystrophy.}, journal = {Human molecular genetics}, volume = {22}, number = {22}, pages = {4562-4578}, doi = {10.1093/hmg/ddt302}, pmid = {23804750}, issn = {1460-2083}, mesh = {Animals ; Animals, Genetically Modified ; Binding Sites ; Caenorhabditis elegans/genetics/metabolism ; Caenorhabditis elegans Proteins/genetics/metabolism ; Cell Death ; Cyclophilins/antagonists &amp; inhibitors/*metabolism ; Cyclosporine/*pharmacology ; Cytochromes c/genetics/*metabolism ; Gene Knockdown Techniques ; Humans ; Inositol 1,4,5-Trisphosphate Receptors/genetics/*metabolism ; Methazolamide/pharmacology ; *Mitochondrial Dynamics/drug effects/genetics ; Mitochondrial Proteins/genetics/metabolism ; Muscular Dystrophy, Animal/*drug therapy/pathology ; Muscular Dystrophy, Duchenne/genetics/*metabolism/pathology ; Phylogeny ; Sequence Homology ; Zebrafish/embryology/genetics ; }, abstract = {Duchenne muscular dystrophy (DMD) is a neuromuscular disease caused by mutations in the dystrophin gene. The subcellular mechanisms of DMD remain poorly understood and there is currently no curative treatment available. Using a Caenorhabditis elegans model for DMD as a pharmacologic and genetic tool, we found that cyclosporine A (CsA) reduces muscle degeneration at low dose and acts, at least in part, through a mitochondrial cyclophilin D, CYN-1. We thus hypothesized that CsA acts on mitochondrial permeability modulation through cyclophilin D inhibition. Mitochondrial patterns and dynamics were analyzed, which revealed dramatic mitochondrial fragmentation not only in dystrophic nematodes, but also in a zebrafish model for DMD. This abnormal mitochondrial fragmentation occurs before any obvious sign of degeneration can be detected. Moreover, we demonstrate that blocking/delaying mitochondrial fragmentation by knocking down the fission-promoting gene drp-1 reduces muscle degeneration and improves locomotion abilities of dystrophic nematodes. Further experiments revealed that cytochrome c is involved in muscle degeneration in C. elegans and seems to act, at least in part, through an interaction with the inositol trisphosphate receptor calcium channel, ITR-1. Altogether, our findings reveal that mitochondria play a key role in the early process of muscle degeneration and may be a target of choice for the design of novel therapeutics for DMD. In addition, our results provide the first indication in the nematode that (i) mitochondrial permeability transition can occur and (ii) cytochrome c can act in cell death.}, }
@article {pmid23804672, year = {2013}, author = {Chung-Davidson, YW and Priess, MC and Yeh, CY and Brant, CO and Johnson, NS and Li, K and Nanlohy, KG and Bryan, MB and Brown, CT and Choi, J and Li, W}, title = {A thermogenic secondary sexual character in male sea lamprey.}, journal = {The Journal of experimental biology}, volume = {216}, number = {Pt 14}, pages = {2702-2712}, pmid = {23804672}, issn = {1477-9145}, support = {R24 GM083982/GM/NIGMS NIH HHS/United States ; 5R24GM83982/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/metabolism ; Adipose Tissue/*physiology/ultrastructure ; Animals ; Electron Transport Complex IV/metabolism ; Fatty Acids/metabolism ; Gas Chromatography-Mass Spectrometry ; Gene Expression Regulation/*physiology ; Immunohistochemistry ; Male ; Microscopy, Electron, Transmission ; Petromyzon/*physiology ; Phylogeny ; Real-Time Polymerase Chain Reaction ; *Sex Characteristics ; Sexual Behavior, Animal/*physiology ; Thermogenesis/*physiology ; Transcriptome ; }, abstract = {Secondary sexual characters in animals are exaggerated ornaments or weapons for intrasexual competition. Unexpectedly, we found that a male secondary sexual character in sea lamprey (Petromyzon marinus) is a thermogenic adipose tissue that instantly increases its heat production during sexual encounters. This secondary sexual character, developed in front of the anterior dorsal fin of mature males, is a swollen dorsal ridge known as the 'rope' tissue. It contains nerve bundles, multivacuolar adipocytes and interstitial cells packed with small lipid droplets and mitochondria with dense and highly organized cristae. The fatty acid composition of the rope tissue is rich in unsaturated fatty acids. The cytochrome c oxidase activity is high but the ATP concentration is very low in the mitochondria of the rope tissue compared with those of the gill and muscle tissues. The rope tissue temperature immediately rose up to 0.3°C when the male encountered a conspecific. Mature males generated more heat in the rope and muscle tissues when presented with a mature female than when presented with a male (paired t-test, P<0.05). On average, the rope generated 0.027±0.013 W cm(-3) more heat than the muscle in 10 min. Transcriptome analyses revealed that genes involved in fat cell differentiation are upregulated whereas those involved in oxidative-phosphorylation-coupled ATP synthesis are downregulated in the rope tissue compared with the gill and muscle tissues. Sexually mature male sea lamprey possess the only known thermogenic secondary sexual character that shows differential heat generation toward individual conspecifics.}, }
@article {pmid23800987, year = {2014}, author = {Pierri, CL and Palmieri, F and De Grassi, A}, title = {Single-nucleotide evolution quantifies the importance of each site along the structure of mitochondrial carriers.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {71}, number = {2}, pages = {349-364}, pmid = {23800987}, issn = {1420-9071}, mesh = {Amino Acid Motifs ; Animals ; *Biological Evolution ; Databases, Genetic ; Genome ; Humans ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins/chemistry/*genetics/metabolism ; Protein Binding ; Protein Structure, Secondary ; Substrate Specificity ; }, abstract = {Mitochondrial carriers are membrane-embedded proteins consisting of a tripartite structure, a three-fold pseudo-symmetry, related sequences, and similar folding whose main function is to catalyze the transport of various metabolites, nucleotides, and coenzymes across the inner mitochondrial membrane. In this study, the evolutionary rate in vertebrates was screened at each of the approximately 50,000 nucleotides corresponding to the amino acids of the 53 human mitochondrial carriers. Using this information as a starting point, a scoring system was developed to quantify the evolutionary pressure acting on each site of the common mitochondrial carrier structure and estimate its functional or structural relevance. The degree of evolutionary selection varied greatly among all sites, but it was highly similar among the three symmetric positions in the tripartite structure, known as symmetry-related sites or triplets, suggesting that each triplet constitutes an evolutionary unit. Based on evolutionary selection, 111 structural sites (37 triplets) were found to be important. These sites play a key role in structure/function of mitochondrial carriers and are involved in either conformational changes (sites of the gates, proline-glycine levels, and aromatic belts) or in binding and specificity of the transported substrates (sites of the substrate-binding area in between the two gates). Furthermore, the evolutionary pressure analysis revealed that the matrix short helix sites underwent different degrees of selection with high inter-paralog variability. Evidence is presented that these sites form a new sequence motif in a subset of mitochondrial carriers, including the ADP/ATP translocator, and play a regulatory function by interacting with ligands and/or proteins of the mitochondrial matrix.}, }
@article {pmid23799924, year = {2013}, author = {Zhang, KJ and Zhu, WC and Rong, X and Zhang, YK and Ding, XL and Liu, J and Chen, DS and Du, Y and Hong, XY}, title = {The complete mitochondrial genomes of two rice planthoppers, Nilaparvata lugens and Laodelphax striatellus: conserved genome rearrangement in Delphacidae and discovery of new characteristics of atp8 and tRNA genes.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {417}, pmid = {23799924}, issn = {1471-2164}, mesh = {Animals ; Base Composition ; Conserved Sequence/*genetics ; DNA, Mitochondrial/chemistry/genetics ; Gene Order/genetics ; Gene Rearrangement/*genetics ; Genes, Mitochondrial/genetics ; Genome, Mitochondrial/*genetics ; *Genomics ; Hemiptera/enzymology/*genetics ; Mitochondrial Proton-Translocating ATPases/*genetics ; Molecular Sequence Data ; RNA, Transfer/*genetics ; Regulatory Sequences, Nucleic Acid/genetics ; Species Specificity ; }, abstract = {BACKGROUND: Nilaparvata lugens (the brown planthopper, BPH) and Laodelphax striatellus (the small brown planthopper, SBPH) are two of the most important pests of rice. Up to now, there was only one mitochondrial genome of rice planthopper has been sequenced and very few dependable information of mitochondria could be used for research on population genetics, phylogeographics and phylogenetic evolution of these pests. To get more valuable information from the mitochondria, we sequenced the complete mitochondrial genomes of BPH and SBPH. These two planthoppers were infected with two different functional Wolbachia (intracellular endosymbiont) strains (wLug and wStri). Since both mitochondria and Wolbachia are transmitted by cytoplasmic inheritance and it was difficult to separate them when purified the Wolbachia particles, concomitantly sequencing the genome of Wolbachia using next generation sequencing method, we also got nearly complete mitochondrial genome sequences of these two rice planthoppers. After gap closing, we present high quality and reliable complete mitochondrial genomes of these two planthoppers.<br><br>RESULTS: The mitogenomes of N. lugens (BPH) and L. striatellus (SBPH) are 17, 619 bp and 16, 431 bp long with A + T contents of 76.95% and 77.17%, respectively. Both species have typical circular mitochondrial genomes that encode the complete set of 37 genes which are usually found in metazoans. However, the BPH mitogenome also possesses two additional copies of the trnC gene. In both mitochondrial genomes, the lengths of the atp8 gene were conspicuously shorter than that of all other known insect mitochondrial genomes (99 bp for BPH, 102 bp for SBPH). That two rearrangement regions (trnC-trnW and nad6-trnP-trnT) of mitochondrial genomes differing from other known insect were found in these two distantly related planthoppers revealed that the gene order of mitochondria might be conservative in Delphacidae. The large non-coding fragment (the A+T-rich region) putatively corresponding responsible for the control of replication and transcription of mitochondria contained a variable number of tandem repeats (VNTRs) block in different natural individuals of these two planthoppers. Comparison with a previously sequenced individual of SBPH revealed that the mitochondrial genetic variation within a species exists not only in the sequence and secondary structure of genes, but also in the gene order (the different location of trnH gene).<br><br>CONCLUSION: The mitochondrial genome arrangement pattern found in planthoppers was involved in rearrangements of both tRNA genes and protein-coding genes (PCGs). Different species from different genera of Delphacidae possessing the same mitochondrial gene rearrangement suggests that gene rearrangements of mitochondrial genome probably occurred before the differentiation of this family. After comparatively analyzing the gene order of different species of Hemiptera, we propose that except for some specific taxonomical group (e.g. the whiteflies) the gene order might have diversified in family level of this order. The VNTRs detected in the control region might provide additional genetic markers for studying population genetics, individual difference and phylogeographics of planthoppers.}, }
@article {pmid23792080, year = {2013}, author = {Flipphi, M and Fekete, E and Ag, N and Scazzocchio, C and Karaffa, L}, title = {Spliceosome twin introns in fungal nuclear transcripts.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {57}, number = {}, pages = {48-57}, doi = {10.1016/j.fgb.2013.06.003}, pmid = {23792080}, issn = {1096-0937}, mesh = {Alternative Splicing/genetics ; Chloroplasts/chemistry/genetics ; Conserved Sequence ; Introns ; *Nucleic Acid Conformation ; Phylogeny ; RNA/chemistry/*genetics ; RNA Splicing/*genetics ; RNA, Messenger/genetics ; Spliceosomes/*genetics ; }, abstract = {The spliceosome is an RNA/protein complex, responsible for intron excision from eukaryotic nuclear transcripts. In bacteria, mitochondria and plastids, intron excision does not involve the spliceosome, but occurs through mechanisms dependent on intron RNA secondary and tertiary structure. For group II/III chloroplast introns, "twintrons" (introns within introns) have been described. The excision of the external intron, and thus proper RNA maturation, necessitates prior removal of the internal intron, which interrupts crucial sequences of the former. We have here predicted analogous instances of spliceosomal twintrons ("stwintrons") in filamentous fungi. In two specific cases, where the internal intron interrupts the donor of the external intron after the first or after the second nucleotide, respectively, we show that intermediates with the sequence predicted by the "stwintron" hypothesis, are produced in the splicing process. This implies that two successive rounds of RNA scanning by the spliceosome are necessary to produce the mature mRNA. The phylogenetic distributions of the stwintrons we have identified suggest that they derive from "late" events, subsequent to the appearance of the host intron. They may well not be limited to fungal nuclear transcripts, and their generation and eventual disappearance in the evolutionary process are relevant to hypotheses of intron origin and alternative splicing.}, }
@article {pmid23789774, year = {2015}, author = {Wang, SY and Shi, W and Wang, ZM and Gong, L and Kong, XY}, title = {The complete mitochondrial genome sequence of Aesopia cornuta (Pleuronectiformes: Soleidae).}, journal = {Mitochondrial DNA}, volume = {26}, number = {1}, pages = {114-115}, doi = {10.3109/19401736.2013.803544}, pmid = {23789774}, issn = {1940-1744}, mesh = {Animals ; Base Composition ; Flatfishes/*genetics ; *Genome, Mitochondrial ; Mitochondria/*genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Replication Origin ; Sequence Analysis, DNA/methods ; }, abstract = {Aesopia cornuta belongs to the family Soleidae of Pleuronectiformes, and the morphological characters are much similar to those of Zebrias. In this article, we sequenced, characterized, and compared the complete mitogenome of A. cornuta for the first time. The genome is 16,737 base pairs in length, and is typically consist of 37 genes, including 13 protein-coding genes, two ribosomal RNA, 22 transfer RNA, as well as a putative L-strand replication origin and a putative control region. The gene organization is identical to that of typical bony fishes. The overall base composition is 29.1, 28.3, 26.8 and 15.8% for C, A, T and G, respectively, with a slight AT bias of 55.1%. This result is expected to contribute to understanding the systematic evolution of the genus Aesopia and further taxonomic and phylogenetic studies of Soleidae and Pleuronectiformes.}, }
@article {pmid23786355, year = {2013}, author = {Camargo, A and Werneck, FP and Morando, M and Sites, JW and Avila, LJ}, title = {Quaternary range and demographic expansion of Liolaemus darwinii (Squamata: Liolaemidae) in the Monte Desert of Central Argentina using Bayesian phylogeography and ecological niche modelling.}, journal = {Molecular ecology}, volume = {22}, number = {15}, pages = {4038-4054}, doi = {10.1111/mec.12369}, pmid = {23786355}, issn = {1365-294X}, mesh = {Animals ; Argentina ; Bayes Theorem ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Demography ; Desert Climate ; Ecosystem ; *Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Iguanas/*genetics ; Mitochondria/genetics ; Phylogeography ; Sequence Analysis, DNA ; }, abstract = {Until recently, most phylogeographic approaches have been unable to distinguish between demographic and range expansion processes, making it difficult to test for the possibility of range expansion without population growth and vice versa. In this study, we applied a Bayesian phylogeographic approach to reconstruct both demographic and range expansion in the lizard Liolaemus darwinii of the Monte Desert in Central Argentina, during the Late Quaternary. Based on analysis of 14 anonymous nuclear loci and the cytochrome b mitochondrial DNA gene, we detected signals of demographic expansion starting at ~55 ka based on Bayesian Skyline and Skyride Plots. In contrast, Bayesian relaxed models of spatial diffusion suggested that range expansion occurred only between ~95 and 55 ka, and more recently, diffusion rates were very low during demographic expansion. The possibility of population growth without substantial range expansion could account for the shared patterns of demographic expansion during the Last Glacial Maxima (OIS 2 and 4) in fish, small mammals and other lizards of the Monte Desert. We found substantial variation in diffusion rates over time, and very high rates during the range expansion phase, consistent with a rapidly advancing expansion front towards the southeast shown by palaeo-distribution models. Furthermore, the estimated diffusion rates are congruent with observed dispersal rates of lizards in field conditions and therefore provide additional confidence to the temporal scale of inferred phylogeographic patterns. Our study highlights how the integration of phylogeography with palaeo-distribution models can shed light on both demographic and range expansion processes and their potential causes.}, }
@article {pmid23783412, year = {2013}, author = {Wu, TM and Lin, WR and Kao, YT and Hsu, YT and Yeh, CH and Hong, CY and Kao, CH}, title = {Identification and characterization of a novel chloroplast/mitochondria co-localized glutathione reductase 3 involved in salt stress response in rice.}, journal = {Plant molecular biology}, volume = {83}, number = {4-5}, pages = {379-390}, pmid = {23783412}, issn = {1573-5028}, mesh = {Amino Acid Sequence ; Chloroplasts/*enzymology ; Conserved Sequence ; Escherichia coli/genetics/metabolism ; Gene Expression ; Gene Expression Regulation, Plant/*drug effects ; Glutathione Reductase/drug effects/*genetics/metabolism ; Isoenzymes ; Mitochondria/*enzymology ; Molecular Sequence Data ; Oryza/drug effects/*enzymology/genetics/ultrastructure ; Phylogeny ; Plant Growth Regulators/pharmacology ; Plant Proteins/drug effects/genetics/metabolism ; Plant Roots/drug effects/enzymology/genetics/ultrastructure ; Plant Shoots/drug effects/enzymology/genetics/ultrastructure ; Plants, Genetically Modified ; Recombinant Fusion Proteins ; Salicylic Acid/pharmacology ; Salinity ; Seedlings/drug effects/enzymology/genetics/ultrastructure ; Sequence Alignment ; Sodium Chloride/pharmacology ; Stress, Physiological/*drug effects ; }, abstract = {Glutathione reductases (GRs) are important components of the antioxidant machinery that plants use to respond against abiotic stresses. In rice, one cytosolic and two chloroplastic GR isoforms have been identified. In this work, we describe the cloning and characterization of the full-length cDNA encoding OsGR3, a chloroplast-localized GR that up to now was considered as a non-functional enzyme because of assumed lack of N-terminal conserved domains. The expression of OsGR3 in E. coli validated that it can be translated as a protein with GR activity. OsGR3 shows 76 and 53 % identity with OsGR1 (chloroplastic) and OsGR2 (cytosolic), respectively. Phylogenetic analysis revealed 2 chloroplastic GRs in Poaceae species, including rice, sorghum and brachypodium, but only one chloroplastic GR in dicots. A plastid transit peptide is located at the N terminus of OsGR3, and genetic transformation of rice with a GR3-GFP fusion construct further confirmed its localization in chloroplasts. Furthermore, OsGR1 and OsGR3 are also targeted to mitochondria, which suggest a combined antioxidant mechanism in both chloroplasts and mitochondria. However, both isoforms showed a distinct response to salinity: the expression of OsGR3 but not OsGR1 was induced by salt stress. In addition, the transcript level of OsGR3 was greatly increased with salicylic acid treatment but was not significantly affected by methyl jasmonate, dehydration or heat shock stress. Our results provide new clues about the possible roles of functional OsGR3 in salt stress and biotic stress tolerance.}, }
@article {pmid23782838, year = {2013}, author = {Chauvigné, F and Boj, M and Vilella, S and Finn, RN and Cerdà, J}, title = {Subcellular localization of selectively permeable aquaporins in the male germ line of a marine teleost reveals spatial redistribution in activated spermatozoa.}, journal = {Biology of reproduction}, volume = {89}, number = {2}, pages = {37}, doi = {10.1095/biolreprod.113.110783}, pmid = {23782838}, issn = {1529-7268}, mesh = {Animals ; Aquaporins/genetics/*metabolism ; Germ Cells/*metabolism ; Male ; Phylogeny ; Sea Bream ; Sperm Motility/genetics ; Spermatogenesis/genetics ; Spermatozoa/*metabolism ; }, abstract = {In oviparous vertebrates such as the marine teleost gilthead seabream, water and fluid homeostasis associated with testicular physiology and the external activation of spermatozoa is potentially mediated by multiple aquaporins. To test this hypothesis, we isolated five novel members of the aquaporin superfamily from gilthead seabream and developed paralog-specific antibodies to localize the cellular sites of protein expression in the male reproductive tract. Together with phylogenetic classification, functional characterization of four of the newly isolated paralogs, Aqp0a, -7, -8b, and -9b, demonstrated that they were water permeable, while Aqp8b was also permeable to urea, and Aqp7 and -9b were permeable to glycerol and urea. Immunolocalization experiments indicated that up to seven paralogous aquaporins are differentially expressed in the seabream testis: Aqp0a and -9b in Sertoli and Leydig cells, respectively; Aqp1ab, -7, and -10b from spermatogonia to spermatozoa; and Aqp1aa and -8b in spermatids and sperm. In the efferent duct, only Aqp10b was found in the luminal epithelium. Ejaculated spermatozoa showed a segregated spatial distribution of five aquaporins: Aqp1aa and -7 in the entire flagellum or the head, respectively, and Aqp1ab, -8b, and -10b both in the head and the anterior tail. The combination of immunofluorescence microscopy and biochemical fractionation of spermatozoa indicated that Aqp10b and phosphorylated Aqp1ab are rapidly translocated to the head plasma membrane upon activation, whereas Aqp8b accumulates in the mitochondrion of the spermatozoa. In contrast, Aqp1aa and -7 remained unchanged. These data reveal that aquaporin expression in the teleost testis shares conserved features of the mammalian system, and they suggest that the piscine channels may play different roles in water and solute transport during spermatogenesis, sperm maturation and nutrition, and the initiation and maintenance of sperm motility.}, }
@article {pmid23782532, year = {2013}, author = {Du, Y and Zhang, H and Hong, L and Wang, J and Zheng, X and Zhang, Z}, title = {Acetolactate synthases MoIlv2 and MoIlv6 are required for infection-related morphogenesis in Magnaporthe oryzae.}, journal = {Molecular plant pathology}, volume = {14}, number = {9}, pages = {870-884}, pmid = {23782532}, issn = {1364-3703}, mesh = {Acetolactate Synthase/chemistry/*metabolism ; Amino Acids/biosynthesis/pharmacology ; Biosynthetic Pathways/drug effects ; Fungal Proteins/chemistry/*metabolism ; Hyphae/drug effects/growth &amp; development ; Magnaporthe/drug effects/*enzymology/*growth &amp; development/pathogenicity ; Molecular Sequence Data ; *Morphogenesis/drug effects ; Mutation/genetics ; Phylogeny ; Pigmentation/drug effects ; Plant Diseases/*microbiology ; Protein Binding/drug effects ; Protein Structure, Tertiary ; Spores, Fungal/drug effects/growth &amp; development ; Structure-Activity Relationship ; }, abstract = {Amino acids are important components in the metabolism of a variety of pathogens, plants and animals. Acetolactate synthase (ALS) catalyses the first common step in leucine, isoleucine and valine biosynthesis, and is the target of several classes of inhibitors. Here, MoIlv2, an orthologue of the Saccharomyces cerevisiae ALS catalytic subunit Ilv2, and MoIlv6, an orthologue of the S. cerevisiae ALS regulatory subunit Ilv6, were identified. To characterize MoILV2 and MoILV6 functions, we generated the deletion mutants ΔMoilv2 and ΔMoilv6. Phenotypic analysis showed that both mutants were auxotrophic for leucine, isoleucine and valine, and were defective in conidial morphogenesis, appressorial penetration and pathogenicity. Further studies suggested that MoIlv2 and MoIlv6 play a critical role in maintaining the balance of intracellular amino acid levels. MoIlv2 and MoIlv6 are both localized to the mitochondria and the signal peptide of MoIlv6 is critical for its localization. In summary, our evidence indicates that MoIlv2 plays a crucial role in isoleucine and valine biosynthesis, whereas MoIlv6 contributes to isoleucine and leucine biosynthesis; both genes are required for fungal pathogenicity. This study indicates the potential of targeting branched-chain amino acid biosynthesis for anti-rice blast management.}, }
@article {pmid23781066, year = {2013}, author = {Maddocks, OD and Scanlon, KM and Donnenberg, MS}, title = {An Escherichia coli effector protein promotes host mutation via depletion of DNA mismatch repair proteins.}, journal = {mBio}, volume = {4}, number = {3}, pages = {e00152-13}, pmid = {23781066}, issn = {2150-7511}, support = {R01 AI032074/AI/NIAID NIH HHS/United States ; R21 CA141038/CA/NCI NIH HHS/United States ; R01 AI32074/AI/NIAID NIH HHS/United States ; }, mesh = {Carrier Proteins/*metabolism ; *DNA Mismatch Repair ; DNA Repair Enzymes/*metabolism ; Enteropathogenic Escherichia coli/*genetics/*metabolism ; Escherichia coli Proteins/*metabolism ; *Host-Pathogen Interactions ; Humans ; Intracellular Signaling Peptides and Proteins ; Mitochondria/metabolism ; *Mutation ; Mutation Rate ; Protein Transport ; Virulence Factors/metabolism ; }, abstract = {Enteropathogenic Escherichia coli (EPEC) is an attaching and effacing (A/E) human pathogen that causes diarrhea during acute infection, and it can also sustain asymptomatic colonization. A/E E. coli depletes host cell DNA mismatch repair (MMR) proteins in colonic cell lines and has been detected in colorectal cancer (CRC) patients. However, until now, a direct link between infection and host mutagenesis has not been fully demonstrated. Here we show that the EPEC-secreted effector protein EspF is critical for complete EPEC-induced depletion of MMR proteins. The mechanism of EspF activity on MMR protein was posttranscriptional and dependent on EspF mitochondrial targeting. EPEC infection also induced EspF-independent elevation of host reactive oxygen species levels. Moreover, EPEC infection significantly increased spontaneous mutation frequency in host cells, and this effect was dependent on mitochondrially targeted EspF. Taken together, these results support the hypothesis that A/E E. coli can promote colorectal carcinogenesis in humans.}, }
@article {pmid23777277, year = {2013}, author = {Behura, SK and Severson, DW}, title = {Overlapping genes of Aedes aegypti: evolutionary implications from comparison with orthologs of Anopheles gambiae and other insects.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {124}, pmid = {23777277}, issn = {1471-2148}, support = {AI059342/AI/NIAID NIH HHS/United States ; AI079125/AI/NIAID NIH HHS/United States ; }, mesh = {Aedes/*genetics ; Animals ; Anopheles/*genetics ; *Evolution, Molecular ; Genes, Overlapping ; Genome, Insect ; Insect Proteins/*genetics ; Insecta/classification/*genetics ; Introns ; Phylogeny ; }, abstract = {BACKGROUND: Although gene overlapping is a common feature of prokaryote and mitochondria genomes, such genes have also been identified in many eukaryotes. The overlapping genes in eukaryotes are extensively rearranged even between closely related species. In this study, we investigated retention and rearrangement of positionally overlapping genes between the mosquitoes Aedes aegypti (dengue virus vector) and Anopheles gambiae (malaria vector). The overlapping gene pairs of A. aegypti were further compared with orthologs of other selected insects to conduct several hypothesis driven investigations relating to the evolution and rearrangement of overlapping genes.<br><br>RESULTS: The results show that as much as ~10% of the predicted genes of A. aegypti and A. gambiae are localized in positional overlapping manner. Furthermore, the study shows that differential abundance of introns and simple sequence repeats have significant association with positional rearrangement of overlapping genes between the two species. Gene expression analysis further suggests that antisense transcripts generated from the oppositely oriented overlapping genes are differentially regulated and may have important regulatory functions in these mosquitoes. Our data further shows that synonymous and non-synonymous mutations have differential but non-significant effect on overlapping localization of orthologous genes in other insect genomes.<br><br>CONCLUSION: Gene overlapping in insects may be a species-specific evolutionary process as evident from non-dependency of gene overlapping with species phylogeny. Based on the results, our study suggests that overlapping genes may have played an important role in genome evolution of insects.}, }
@article {pmid23776247, year = {2013}, author = {Shih, PM and Matzke, NJ}, title = {Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {30}, pages = {12355-12360}, pmid = {23776247}, issn = {1091-6490}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Adenosine Triphosphatases/classification/*metabolism ; Calibration ; *Phylogeny ; *Symbiosis ; }, abstract = {Chloroplasts and mitochondria descended from bacterial ancestors, but the dating of these primary endosymbiosis events remains very uncertain, despite their importance for our understanding of the evolution of both bacteria and eukaryotes. All phylogenetic dating in the Proterozoic and before is difficult: Significant debates surround potential fossil calibration points based on the interpretation of the Precambrian microbial fossil record, and strict molecular clock methods cannot be expected to yield accurate dates over such vast timescales because of strong heterogeneity in rates. Even with more sophisticated relaxed-clock analyses, nodes that are distant from fossil calibrations will have a very high uncertainty in dating. However, endosymbiosis events and gene duplications provide some additional information that has never been exploited in dating; namely, that certain nodes on a gene tree must represent the same events, and thus must have the same or very similar dates, even if the exact date is uncertain. We devised techniques to exploit this information: cross-calibration, in which node date calibrations are reused across a phylogeny, and cross-bracing, in which node date calibrations are formally linked in a hierarchical Bayesian model. We apply these methods to proteins with ancient duplications that have remained associated and originated from plastid and mitochondrial endosymbionts: the α and β subunits of ATP synthase and its relatives, and the elongation factor thermo unstable. The methods yield reductions in dating uncertainty of 14-26% while only using date calibrations derived from phylogenetically unambiguous Phanerozoic fossils of multicellular plants and animals. Our results suggest that primary plastid endosymbiosis occurred ∼900 Mya and mitochondrial endosymbiosis occurred ∼1,200 Mya.}, }
@article {pmid23773966, year = {2013}, author = {Marotta, DH and Nantel, A and Sukala, L and Teubl, JR and Rauceo, JM}, title = {Genome-wide transcriptional profiling and enrichment mapping reveal divergent and conserved roles of Sko1 in the Candida albicans osmotic stress response.}, journal = {Genomics}, volume = {102}, number = {4}, pages = {363-371}, pmid = {23773966}, issn = {1089-8646}, support = {SC2 GM089556/GM/NIGMS NIH HHS/United States ; SC2 GM089556-01/GM/NIGMS NIH HHS/United States ; /CAPMC/CIHR/Canada ; }, mesh = {Basic-Leucine Zipper Transcription Factors/genetics/metabolism ; Candida albicans/*genetics/metabolism ; Computer Simulation ; Evolution, Molecular ; Fungal Proteins/*genetics/metabolism ; *Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Genome, Fungal ; Mitochondria/metabolism ; Mitogen-Activated Protein Kinases/*genetics/metabolism ; Osmoregulation/*genetics ; Phylogeny ; Promoter Regions, Genetic ; Repressor Proteins/*genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {Candida albicans maintains both commensal and pathogenic states in humans. Here, we have defined the genomic response to osmotic stress mediated by transcription factor Sko1. We performed microarray analysis of a sko1Δ/Δ mutant strain subjected to osmotic stress, and we utilized gene sequence enrichment analysis and enrichment mapping to identify Sko1-dependent osmotic stress-response genes. We found that Sko1 regulates distinct gene classes with functions in ribosomal synthesis, mitochondrial function, and vacuolar transport. Our in silico analysis suggests that Sko1 may recognize two unique DNA binding motifs. Our C. albicans genomic analyses and complementation studies in Saccharomyces cerevisiae showed that Sko1 is conserved as a regulator of carbohydrate metabolism, redox metabolism, and glycerol synthesis. Further, our real time-qPCR results showed that osmotic stress-response genes that are dependent on the kinase Hog1 also require Sko1 for full expression. Our findings reveal divergent and conserved aspects of Sko1-dependent osmotic stress signaling.}, }
@article {pmid23773332, year = {2013}, author = {Kaiser, WJ and Upton, JW and Mocarski, ES}, title = {Viral modulation of programmed necrosis.}, journal = {Current opinion in virology}, volume = {3}, number = {3}, pages = {296-306}, pmid = {23773332}, issn = {1879-6265}, support = {DP5 OD012198/OD/NIH HHS/United States ; R01 AI030363/AI/NIAID NIH HHS/United States ; R21 AI030363/AI/NIAID NIH HHS/United States ; R56 AI030363/AI/NIAID NIH HHS/United States ; OD012198/OD/NIH HHS/United States ; AI030363/AI/NIAID NIH HHS/United States ; R01 AI020211/AI/NIAID NIH HHS/United States ; AI020211/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Apoptosis ; DNA Viruses/*immunology/*pathogenicity ; Humans ; *Necrosis ; }, abstract = {Apoptosis and programmed necrosis balance each other as alternate first line host defense pathways against which viruses have evolved countermeasures. Intrinsic apoptosis, the critical programmed cell death pathway that removes excess cells during embryonic development and tissue homeostasis, follows a caspase cascade triggered at mitochondria and modulated by virus-encoded anti-apoptotic B cell leukemia (BCL)2-like suppressors. Extrinsic apoptosis controlled by caspase 8 arose during evolution to trigger executioner caspases directly, circumventing viral suppressors of intrinsic (mitochondrial) apoptosis and providing the selective pressure for viruses to acquire caspase 8 suppressors. Programmed necrosis likely evolved most recently as a 'trap door' adaptation to extrinsic apoptosis. Receptor interacting protein (RIP)3 kinase (also called RIPK3) becomes active when either caspase 8 activity or polyubiquitylation of RIP1 is compromised. This evolutionary dialog implicates caspase 8 as a 'supersensor' alternatively activating and suppressing cell death pathways.}, }
@article {pmid23762459, year = {2013}, author = {Remón, N and Galán, P and Vila, M and Arribas, O and Naveira, H}, title = {Causes and evolutionary consequences of population subdivision of an Iberian mountain lizard, Iberolacerta monticola.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e66034}, pmid = {23762459}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA, Mitochondrial/genetics ; *Ecosystem ; Genetic Loci ; Genetic Variation ; Geography ; Haplotypes/genetics ; Humans ; Lizards/*genetics/*growth &amp; development ; Microsatellite Repeats ; Mitochondria ; Molecular Sequence Data ; Phylogeny ; Population Density ; Population Dynamics ; Spain ; }, abstract = {AIM: The study of the factors that influence population connectivity and spatial distribution of genetic variation is crucial for understanding speciation and for predicting the effects of landscape modification and habitat fragmentation, which are considered severe threats to global biodiversity. This dual perspective is obtained from analyses of subalpine mountain species, whose present distribution may have been shaped both by cyclical climate changes over ice ages and anthropogenic perturbations of their habitats. Here, we examine the phylogeography, population structure and genetic diversity of the lacertid lizard Iberolacerta monticola, an endemism considered to be facing a high risk of extinction in several populations.<br><br>LOCATION: Northwestern quadrant of the Iberian Peninsula.<br><br>METHODS: We analyzed the mtDNA variation at the control region (454 bp) and the cytochrome b (598 bp) loci, as well as at 10 nuclear microsatellite loci from 17 populations throughout the distribution range of the species.<br><br>RESULTS: According to nuclear markers, most sampling sites are defined as distinct, genetically differentiated populations, and many of them show traces of recent bottlenecks. Mitochondrial data identify a relatively old, geographically restricted lineage, and four to six younger geographically vicariant sister clades, whose origin may be traced back to the mid-Pleistocene revolution, with several subclades possibly associated to the mid-Bruhnes transition. Geographic range fragmentation of one of these clades, which includes lowland sites, is very recent, and most likely due to the accelerated loss of Atlantic forests by human intervention.<br><br>MAIN CONCLUSIONS: Altogether, the data fit a "refugia within refugia" model, some lack of pattern uniformity notwithstanding, and suggest that these mountains might be the cradles of new species of Iberolacerta. However, the changes operated during the Holocene severely compromise the long-term survival of those genetic lineages more exposed to the anthropogenic perturbations of their habitats.}, }
@article {pmid23761034, year = {2014}, author = {Engel, PC}, title = {Glutamate dehydrogenases: the why and how of coenzyme specificity.}, journal = {Neurochemical research}, volume = {39}, number = {3}, pages = {426-432}, pmid = {23761034}, issn = {1573-6903}, mesh = {Animals ; Coenzymes/*metabolism ; Glutamate Dehydrogenase/*metabolism ; Humans ; Mitochondria/*metabolism ; NAD/*metabolism ; NADP/*metabolism ; Substrate Specificity/physiology ; }, abstract = {NAD(+) and NADP(+), chemically similar and with almost identical standard oxidation-reduction potentials, nevertheless have distinct roles, NAD(+) serving catabolism and ATP generation whereas NADPH is the biosynthetic reductant. Separating these roles requires strict specificity for one or the other coenzyme for most dehydrogenases. In many organisms this holds also for glutamate dehydrogenases (GDH), NAD(+)-dependent for glutamate oxidation, NADP(+)-dependent for fixing ammonia. In higher animals, however, GDH has dual specificity. It has been suggested that GDH in mitochondria reacts only with NADP(H), the NAD(+) reaction being an in vitro artefact. However, contrary evidence suggests mitochondrial GDH not only reacts with NAD(+) but maintains equilibrium using the same pool as accessed by β-hydroxybutyrate dehydrogenase. Another complication is the presence of an energy-linked dehydrogenase driving NADP(+) reduction by NADH, maintaining the coenzyme pools at different oxidation-reduction potentials. Its coexistence with GDH makes possible a futile cycle, control of which is not yet properly explained. Structural studies show NAD(+)-dependent, NADP(+)-dependent and dual-specificity GDHs are closely related and a few site-directed mutations can reverse specificity. Specificity for NAD(+) or for NADP(+) has probably emerged repeatedly during evolution, using different structural solutions on different occasions. In various GDHs the P7 position in the coenzyme-binding domain plays a key role. However, whereas in other dehydrogenases an acidic P7 residue usually hydrogen bonds to the 2'- and 3'-hydroxyls, dictating NAD(+) specificity, among GDHs, depending on detailed conformation of surrounding residues, an acidic P7 may permit binding of NAD(+) only, NADP(+) only, or in higher animals both.}, }
@article {pmid23758841, year = {2013}, author = {Stier, A and Bize, P and Schull, Q and Zoll, J and Singh, F and Geny, B and Gros, F and Royer, C and Massemin, S and Criscuolo, F}, title = {Avian erythrocytes have functional mitochondria, opening novel perspectives for birds as animal models in the study of ageing.}, journal = {Frontiers in zoology}, volume = {10}, number = {1}, pages = {33}, pmid = {23758841}, issn = {1742-9994}, abstract = {BACKGROUND: In contrast to mammalian erythrocytes, which have lost their nucleus and mitochondria during maturation, the erythrocytes of almost all other vertebrate species are nucleated throughout their lifespan. Little research has been done however to test for the presence and functionality of mitochondria in these cells, especially for birds. Here, we investigated those two points in erythrocytes of one common avian model: the zebra finch (Taeniopygia guttata).<br><br>RESULTS: Transmission electron microscopy showed the presence of mitochondria in erythrocytes of this small passerine bird, especially after removal of haemoglobin interferences. High-resolution respirometry revealed increased or decreased rates of oxygen consumption by erythrocytes in response to the addition of respiratory chain substrates or inhibitors, respectively. Fluorometric assays confirmed the production of mitochondrial superoxide by avian erythrocytes. Interestingly, measurements of plasmatic oxidative markers indicated lower oxidative stress in blood of the zebra finch compared to a size-matched mammalian model, the mouse.<br><br>CONCLUSIONS: Altogether, those findings demonstrate that avian erythrocytes possess functional mitochondria in terms of respiratory activities and reactive oxygen species (ROS) production. Interestingly, since blood oxidative stress was lower for our avian model compared to a size-matched mammalian, our results also challenge the idea that mitochondrial ROS production could have been one actor leading to this loss during the course of evolution. Opportunities to assess mitochondrial functioning in avian erythrocytes open new perspectives in the use of birds as models for longitudinal studies of ageing via lifelong blood sampling of the same subjects.}, }
@article {pmid23756438, year = {2014}, author = {Delfin, F and Min-Shan Ko, A and Li, M and Gunnarsdóttir, ED and Tabbada, KA and Salvador, JM and Calacal, GC and Sagum, MS and Datar, FA and Padilla, SG and De Ungria, MC and Stoneking, M}, title = {Complete mtDNA genomes of Filipino ethnolinguistic groups: a melting pot of recent and ancient lineages in the Asia-Pacific region.}, journal = {European journal of human genetics : EJHG}, volume = {22}, number = {2}, pages = {228-237}, pmid = {23756438}, issn = {1476-5438}, mesh = {Asian People/genetics ; Bayes Theorem ; Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Gene Frequency ; Genetics, Population ; Genome, Human ; Haplotypes ; History, Ancient ; Human Migration/*history ; Humans ; Language ; Mitochondria/genetics ; Models, Genetic ; Native Hawaiian or Other Pacific Islander/genetics ; Philippines ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The Philippines is a strategic point in the Asia-Pacific region for the study of human diversity, history and origins, as it is a cross-road for human migrations and consequently exhibits enormous ethnolinguistic diversity. Following on a previous in-depth study of Y-chromosome variation, here we provide new insights into the maternal genetic history of Filipino ethnolinguistic groups by surveying complete mitochondrial DNA (mtDNA) genomes from a total of 14 groups (11 groups in this study and 3 groups previously published) including previously published mtDNA hypervariable segment (HVS) data from Filipino regional center groups. Comparison of HVS data indicate genetic differences between ethnolinguistic and regional center groups. The complete mtDNA genomes of 14 ethnolinguistic groups reveal genetic aspects consistent with the Y-chromosome, namely: diversity and heterogeneity of groups, no support for a simple dichotomy between Negrito and non-Negrito groups, and different genetic affinities with Asia-Pacific groups that are both ancient and recent. Although some mtDNA haplogroups can be associated with the Austronesian expansion, there are others that associate with South Asia, Near Oceania and Australia that are consistent with a southern migration route for ethnolinguistic group ancestors into the Asia-Pacific, with a timeline that overlaps with the initial colonization of the Asia-Pacific region, the initial colonization of the Philippines and a possible separate post-colonization migration into the Philippine archipelago.}, }
@article {pmid23754818, year = {2013}, author = {Wallace, DC}, title = {Bioenergetics in human evolution and disease: implications for the origins of biological complexity and the missing genetic variation of common diseases.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {368}, number = {1622}, pages = {20120267}, pmid = {23754818}, issn = {1471-2970}, support = {NS21328/NS/NINDS NIH HHS/United States ; NS070298/NS/NINDS NIH HHS/United States ; R01 NS070298/NS/NINDS NIH HHS/United States ; DK73691/DK/NIDDK NIH HHS/United States ; AG24373/AG/NIA NIH HHS/United States ; R01 AG024373/AG/NIA NIH HHS/United States ; R01 DK073691/DK/NIDDK NIH HHS/United States ; R01 NS021328/NS/NINDS NIH HHS/United States ; }, mesh = {*Biological Evolution ; Energy Metabolism/*genetics ; Gene Expression Regulation ; *Genetic Predisposition to Disease ; *Genetic Variation ; Humans ; }, abstract = {Two major inconsistencies exist in the current neo-Darwinian evolutionary theory that random chromosomal mutations acted on by natural selection generate new species. First, natural selection does not require the evolution of ever increasing complexity, yet this is the hallmark of biology. Second, human chromosomal DNA sequence variation is predominantly either neutral or deleterious and is insufficient to provide the variation required for speciation or for predilection to common diseases. Complexity is explained by the continuous flow of energy through the biosphere that drives the accumulation of nucleic acids and information. Information then encodes complex forms. In animals, energy flow is primarily mediated by mitochondria whose maternally inherited mitochondrial DNA (mtDNA) codes for key genes for energy metabolism. In mammals, the mtDNA has a very high mutation rate, but the deleterious mutations are removed by an ovarian selection system. Hence, new mutations that subtly alter energy metabolism are continuously introduced into the species, permitting adaptation to regional differences in energy environments. Therefore, the most phenotypically significant gene variants arise in the mtDNA, are regional, and permit animals to occupy peripheral energy environments where rarer nuclear DNA (nDNA) variants can accumulate, leading to speciation. The neutralist-selectionist debate is then a consequence of mammals having two different evolutionary strategies: a fast mtDNA strategy for intra-specific radiation and a slow nDNA strategy for speciation. Furthermore, the missing genetic variation for common human diseases is primarily mtDNA variation plus regional nDNA variants, both of which have been missed by large, inter-population association studies.}, }
@article {pmid23754817, year = {2013}, author = {Blackstone, NW}, title = {Why did eukaryotes evolve only once? Genetic and energetic aspects of conflict and conflict mediation.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {368}, number = {1622}, pages = {20120266}, pmid = {23754817}, issn = {1471-2970}, mesh = {*Biological Evolution ; *Energy Metabolism ; Eukaryota/*genetics/*physiology ; Genetic Variation ; Genome ; Mitochondria ; }, abstract = {According to multi-level theory, evolutionary transitions require mediating conflicts between lower-level units in favour of the higher-level unit. By this view, the origin of eukaryotes and the origin of multicellularity would seem largely equivalent. Yet, eukaryotes evolved only once in the history of life, whereas multicellular eukaryotes have evolved many times. Examining conflicts between evolutionary units and mechanisms that mediate these conflicts can illuminate these differences. Energy-converting endosymbionts that allow eukaryotes to transcend surface-to-volume constraints also can allocate energy into their own selfish replication. This principal conflict in the origin of eukaryotes can be mediated by genetic or energetic mechanisms. Genome transfer diminishes the heritable variation of the symbiont, but requires the de novo evolution of the protein-import apparatus and was opposed by selection for selfish symbionts. By contrast, metabolic signalling is a shared primitive feature of all cells. Redox state of the cytosol is an emergent feature that cannot be subverted by an individual symbiont. Hypothetical scenarios illustrate how metabolic regulation may have mediated the conflicts inherent at different stages in the origin of eukaryotes. Aspects of metabolic regulation may have subsequently been coopted from within-cell to between-cell pathways, allowing multicellularity to emerge repeatedly.}, }
@article {pmid23754807, year = {2013}, author = {Lane, N and Martin, WF and Raven, JA and Allen, JF}, title = {Energy, genes and evolution: introduction to an evolutionary synthesis.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {368}, number = {1622}, pages = {20120253}, pmid = {23754807}, issn = {1471-2970}, mesh = {Animals ; *Biological Evolution ; Energy Metabolism/*genetics/*physiology ; Gene Expression Regulation/*physiology ; Genome ; }, abstract = {Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. No energy, no evolution. The 'modern synthesis' of the past century explained evolution in terms of genes, but this is only part of the story. While the mechanisms of natural selection are correct, and increasingly well understood, they do little to explain the actual trajectories taken by life on Earth. From a cosmic perspective-what is the probability of life elsewhere in the Universe, and what are its probable traits?-a gene-based view of evolution says almost nothing. Irresistible geological and environmental changes affected eukaryotes and prokaryotes in very different ways, ones that do not relate to specific genes or niches. Questions such as the early emergence of life, the morphological and genomic constraints on prokaryotes, the singular origin of eukaryotes, and the unique and perplexing traits shared by all eukaryotes but not found in any prokaryote, are instead illuminated by bioenergetics. If nothing in biology makes sense except in the light of evolution, nothing in evolution makes sense except in the light of energetics. This Special Issue of Philosophical Transactions examines the interplay between energy transduction and genome function in the major transitions of evolution, with implications ranging from planetary habitability to human health. We hope that these papers will contribute to a new evolutionary synthesis of energetics and genetics.}, }
@article {pmid23751376, year = {2013}, author = {Bogart, JP and Bi, K}, title = {Genetic and genomic interactions of animals with different ploidy levels.}, journal = {Cytogenetic and genome research}, volume = {140}, number = {2-4}, pages = {117-136}, doi = {10.1159/000351593}, pmid = {23751376}, issn = {1424-859X}, mesh = {Ambystoma/classification/genetics ; Animals ; Chromosomes/*genetics ; Diploidy ; Evolution, Molecular ; Meiosis ; Microsatellite Repeats ; Mitochondria/genetics ; Parthenogenesis ; Phylogeny ; *Ploidies ; *Recombination, Genetic ; Translocation, Genetic ; Xenopus/classification/genetics ; }, abstract = {Polyploid animals have independently evolved from diploids in diverse taxa across the tree of life. We review a few polyploid animal species or biotypes where recently developed molecular and cytogenetic methods have significantly improved our understanding of their genetics, reproduction and evolution. Mitochondrial sequences that target the maternal ancestor of a polyploid show that polyploids may have single (e.g. unisexual salamanders in the genus Ambystoma) or multiple (e.g. parthenogenetic polyploid lizards in the genus Aspidoscelis) origins. Microsatellites are nuclear markers that can be used to analyze genetic recombinations, reproductive modes (e.g. Ambystoma) and recombination events (e.g. polyploid frogs such as Pelophylax esculentus). Hom(e)ologous chromosomes and rare intergenomic exchanges in allopolyploids have been distinguished by applying genome-specific fluorescent probes to chromosome spreads. Polyploids arise, and are maintained, through perturbations of the 'normal' meiotic program that would include pre-meiotic chromosome replication and genomic integrity of homologs. When possible, asexual, unisexual and bisexual polyploid species or biotypes interact with diploid relatives, and genes are passed from diploid to polyploid gene pools, which increase genetic diversity and ultimately evolutionary flexibility in the polyploid. When diploid relatives do not exist, polyploids can interact with another polyploid (e.g. species of African Clawed Frogs in the genus Xenopus). Some polyploid fish (e.g. salmonids) and frogs (Xenopus) represent independent lineages whose ancestors experienced whole genome duplication events. Some tetraploid frogs (P. esculentus) and fish (Squaliusalburnoides) may be in the process of becoming independent species, but diploid and triploid forms of these 'species' continue to genetically interact with the comparatively few tetraploid populations. Genetic and genomic interaction between polyploids and diploids is a complex and dynamic process that likely plays a crucial role for the evolution and persistence of polyploid animals. See also other articles in this themed issue.}, }
@article {pmid23747399, year = {2013}, author = {Pang, K and Li, Y and Liu, M and Meng, Z and Yu, Y}, title = {Inventory and general analysis of the ATP-binding cassette (ABC) gene superfamily in maize (Zea mays L.).}, journal = {Gene}, volume = {526}, number = {2}, pages = {411-428}, doi = {10.1016/j.gene.2013.05.051}, pmid = {23747399}, issn = {1879-0038}, mesh = {ATP-Binding Cassette Transporters/classification/*genetics ; Cluster Analysis ; Computational Biology ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Multigene Family ; Phylogeny ; Zea mays/*genetics ; }, abstract = {The metabolic functions of ATP-binding cassette (or ABC) proteins, one of the largest families of proteins presented in all organisms, have been investigated in many protozoan, animal and plant species. To facilitate more systematic and complicated studies on maize ABC proteins in the future, we present the first complete inventory of these proteins, including 130 open reading frames (ORFs), and provide general descriptions of their classifications, basic structures, typical functions, evolution track analysis and expression profiles. The 130 ORFs were assigned to eight subfamilies based on their structures and homological features. Five of these subfamilies consist of 109 proteins, containing transmembrane domains (TM) performing as transporters. The rest three subfamilies contain 21 soluble proteins involved in various functions other than molecular transport. A comparison of ABC proteins among nine selected species revealed either convergence or divergence in each of the ABC subfamilies. Generally, plant genomes contain far more ABC genes than animal genomes. The expression profiles and evolution track of each maize ABC gene were further investigated, the results of which could provide clues for analyzing their functions. Quantitative real-time polymerase chain reaction experiments (PCR) were conducted to detect induced expression in select ABC genes under several common stresses. This investigation provides valuable information for future research on stress tolerance in plants and potential strategies for enhancing maize production under stressful conditions.}, }
@article {pmid23742009, year = {2013}, author = {Kowald, A and Kirkwood, TB}, title = {Mitochondrial mutations and aging: random drift is insufficient to explain the accumulation of mitochondrial deletion mutants in short-lived animals.}, journal = {Aging cell}, volume = {12}, number = {4}, pages = {728-731}, doi = {10.1111/acel.12098}, pmid = {23742009}, issn = {1474-9726}, support = {MR/K006312/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Aging ; Animals ; Computer Simulation ; DNA, Mitochondrial/genetics/*metabolism ; *Genetic Drift ; Longevity ; Mitochondria/genetics/metabolism ; Models, Biological ; Mutation Rate ; *Sequence Deletion ; Species Specificity ; Time Factors ; }, abstract = {Mitochondrial DNA deletions accumulate over the life course in post-mitotic cells of many species and may contribute to aging. Often a single mutant expands clonally and finally replaces the wild-type population of a whole cell. One proposal to explain the driving force behind this accumulation states that random drift alone, without any selection advantage, is sufficient to explain the clonal accumulation of a single mutant. Existing mathematical models show that such a process might indeed work for humans. However, to be a general explanation for the clonal accumulation of mtDNA mutants, it is important to know whether random drift could also explain the accumulation process in short-lived species like rodents. To clarify this issue, we modelled this process mathematically and performed extensive computer simulations to study how different mutation rates affect accumulation time and the resulting degree of heteroplasmy. We show that random drift works for lifespans of around 100 years, but for short-lived animals, the resulting degree of heteroplasmy is incompatible with experimental observations.}, }
@article {pmid23741315, year = {2013}, author = {Wang, N and Kimball, RT and Braun, EL and Liang, B and Zhang, Z}, title = {Assessing phylogenetic relationships among galliformes: a multigene phylogeny with expanded taxon sampling in Phasianidae.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e64312}, pmid = {23741315}, issn = {1932-6203}, mesh = {Animals ; Anseriformes/*classification/genetics ; Cell Nucleus/chemistry ; DNA, Mitochondrial/*classification/genetics ; Evolution, Molecular ; Galliformes/*classification/genetics ; *Genetic Speciation ; Introns/*genetics ; Mitochondria/chemistry ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Galliform birds (relatives of the chicken and turkey) have attracted substantial attention due to their importance to society and value as model systems. This makes understanding the evolutionary history of Galliformes, especially the species-rich family Phasianidae, particularly interesting and important for comparative studies in this group. Previous studies have differed in their conclusions regarding galliform phylogeny. Some of these studies have suggested that specific clades within this order underwent rapid radiations, potentially leading to the observed difficulty in resolving their phylogenetic relationships. Here we presented analyses of six nuclear intron sequences and two mitochondrial regions, an amount of sequence data larger than many previous studies, and expanded taxon sampling by collecting data from 88 galliform species and four anseriform outgroups. Our results corroborated recent studies describing relationships among the major families, and provided further evidence that the traditional division of the largest family, the Phasianidae into two major groups ("pheasants" and "partridges") is not valid. Within the Phasianidae, relationships among many genera have varied among studies and there has been little consensus for the placement of many taxa. Using this large dataset, with substantial sampling within the Phasianidae, we obtained strong bootstrap support to confirm some previously hypothesized relationships and we were able to exclude others. In addition, we added the first nuclear sequence data for the partridge and quail genera Ammoperdix, Caloperdix, Excalfactoria, and Margaroperdix, placing these taxa in the galliform tree of life with confidence. Despite the novel insights obtained by combining increased sampling of taxa and loci, our results suggest that additional data collection will be necessary to solve the remaining uncertainties.}, }
@article {pmid23737959, year = {2013}, author = {Gazave, E and Lavrov, DV and Cabrol, J and Renard, E and Rocher, C and Vacelet, J and Adamska, M and Borchiellini, C and Ereskovsky, AV}, title = {Systematics and molecular phylogeny of the family oscarellidae (homoscleromorpha) with description of two new oscarella species.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e63976}, pmid = {23737959}, issn = {1932-6203}, mesh = {Animals ; Databases, Factual ; Evolution, Molecular ; Geography ; Mitochondria/genetics ; *Phylogeny ; Porifera/*classification/cytology/genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, RNA ; Uncertainty ; }, abstract = {The family Oscarellidae is one of the two families in the class Homoscleromorpha (phylum Porifera) and is characterized by the absence of a skeleton and the presence of a specific mitochondrial gene, tatC. This family currently encompasses sponges in two genera: Oscarella with 17 described species and Pseudocorticium with one described species. Although sponges in this group are relatively well-studied, phylogenetic relationships among members of Oscarellidae and the validity of genus Pseudocorticium remain open questions. Here we present a phylogenetic analysis of Oscarellidae using four markers (18S rDNA, 28S rDNA, atp6, tatC), and argue that it should become a mono-generic family, with Pseudocorticium being synonymized with Oscarella, and with the transfer of Pseudocorticium jarrei to Oscarella jarrei. We show that the genus Oscarella can be subdivided into four clades, each of which is supported by either a small number of morphological characters or by molecular synapomorphies. In addition, we describe two new species of Oscarella from Norwegian fjords: O. bergenensis sp. nov. and O. nicolae sp. nov., and we compare their morphology, anatomy, and cytology with other species in this genus. Internal anatomical characters are similar in both species, but details of external morphology and particularly of cytological characters provide diagnostic features. Our study also confirms that O. lobularis and O. tuberculata are two distinct polychromic sibling species. This study highlights the difficulties of species identification in skeleton-less sponges and, more generally, in groups where morphological characters are scarce. Adopting a multi-marker approach is thus highly suitable for these groups.}, }
@article {pmid23733656, year = {2013}, author = {Maklakov, AA and Lummaa, V}, title = {Evolution of sex differences in lifespan and aging: causes and constraints.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {8}, pages = {717-724}, doi = {10.1002/bies.201300021}, pmid = {23733656}, issn = {1521-1878}, mesh = {*Aging ; Animals ; Biological Evolution ; Female ; Genetic Variation ; Humans ; *Longevity ; Male ; Mitochondria ; Reproduction/genetics ; Selection, Genetic ; *Sex Factors ; }, abstract = {Why do the two sexes have different lifespans and rates of aging? Two hypotheses based on asymmetric inheritance of sex chromosomes ("unguarded X") or mitochondrial genomes ("mother's curse") explain sex differences in lifespan as sex-specific maladaptation leading to increased mortality in the shorter-lived sex. While asymmetric inheritance hypotheses equate long life with high fitness, considerable empirical evidence suggests that sexes resolve the fundamental tradeoff between reproduction and survival differently resulting in sex-specific optima for lifespan. However, selection for sex-specific values in life-history traits is constrained by intersexual genetic correlations resulting in intra-locus sexual conflict over optimal lifespan. The available data suggest that the evolution of sexual dimorphism only partially resolves these conflicts. Sexual conflict over optimal trait values, which has been demonstrated in model organisms and in humans, is likely to play a key role in shaping the evolution of lifespan, as well as in maintaining genetic variation for sex-specific diseases.}, }
@article {pmid23732471, year = {2013}, author = {van der Bliek, AM and Shen, Q and Kawajiri, S}, title = {Mechanisms of mitochondrial fission and fusion.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {5}, number = {6}, pages = {}, pmid = {23732471}, issn = {1943-0264}, mesh = {Apoptosis/*physiology ; *Biological Evolution ; Cytoskeleton/*physiology ; Dynamins/*metabolism ; Mitochondrial Dynamics/*physiology ; *Models, Biological ; Phosphorylation ; Ubiquitination ; }, abstract = {Mitochondria continually change shape through the combined actions of fission, fusion, and movement along cytoskeletal tracks. The lengths of mitochondria and the degree to which they form closed networks are determined by the balance between fission and fusion rates. These rates are influenced by metabolic and pathogenic conditions inside mitochondria and by their cellular environment. Fission and fusion are important for growth, for mitochondrial redistribution, and for maintenance of a healthy mitochondrial network. In addition, mitochondrial fission and fusion play prominent roles in disease-related processes such as apoptosis and mitophagy. Three members of the Dynamin family are key components of the fission and fusion machineries. Their functions are controlled by different sets of adaptor proteins on the surface of mitochondria and by a range of regulatory processes. Here, we review what is known about these proteins and the processes that regulate their actions.}, }
@article {pmid23732234, year = {2013}, author = {Schmitz, J and Tierbach, A and Lenz, H and Meschenmoser, K and Knoop, V}, title = {Membrane protein interactions between different Arabidopsis thaliana MRS2-type magnesium transporters are highly permissive.}, journal = {Biochimica et biophysica acta}, volume = {1828}, number = {9}, pages = {2032-2040}, doi = {10.1016/j.bbamem.2013.05.019}, pmid = {23732234}, issn = {0006-3002}, mesh = {Arabidopsis/*chemistry/metabolism ; Arabidopsis Proteins/*chemistry/genetics/metabolism ; Binding Sites ; Cation Transport Proteins/*chemistry/genetics/metabolism ; Escherichia coli Proteins/chemistry/metabolism ; Magnesium/*chemistry/metabolism ; Mitochondria/*chemistry/metabolism ; Mitochondrial Proteins/*chemistry/genetics/metabolism ; Models, Molecular ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Isoforms/chemistry/genetics/metabolism ; Protein Structure, Secondary ; Recombinant Proteins/chemistry/genetics/metabolism ; Structural Homology, Protein ; Two-Hybrid System Techniques ; }, abstract = {Membrane proteins of the Arabidopsis thaliana MRS2 (MGT) family have been characterised as magnesium transporters. Like their bacterial CorA homologues, the plant MRS2 proteins are characterised by an invariable GMN tripeptide motif terminating the first of two closely spaced transmembrane domains at the carboxy-termini. The functional Mg(2+) transport channel is assembled as a pentamer in the case of CorA. However, in contrast to the single CorA genes of bacteria, plant genomes encode up to 10 highly divergent MRS2 proteins. To elucidate structure-function relationships and the possibility of plant MRS2 hetero-pentamer formation, we performed protein-protein interaction studies in the yeast mating-based split-ubiquitin system (mbSUS) and concomitant protein modelling using I-TASSER. Despite very restricted sequence similarities and variable polypeptide insertions all AtMRS2 proteins feature the key structural elements determined for the CorA crystal structure. The mbSUS setup conclusively demonstrates protein-protein interactions of any given AtMRS2 protein not only with itself but also highly permissive interactions to varying degrees among all AtMRS2 proteins. AtMRS2-3 seems particularly prone to non-selective, strong interactions with the other homologues. Deletion constructs show that six amino acids may be deleted from the carboxy-terminus and 27 (but not 41) from the amino-terminus of AtMRS2-7 without impairment of homologous or heterologous protein interactions. Despite significant diversification, the plant MRS2 proteins have obviously retained an ancient CorA/MRS2 core structure and the capacity for protein-protein interactions. Plant magnesium homeostasis may be influenced by hetero-oligomer channel formation where different plant MRS2 proteins meet in the same membrane naturally or in transgenic approaches.}, }
@article {pmid23720544, year = {2013}, author = {Stiebens, VA and Merino, SE and Roder, C and Chain, FJ and Lee, PL and Eizaguirre, C}, title = {Living on the edge: how philopatry maintains adaptive potential.}, journal = {Proceedings. Biological sciences}, volume = {280}, number = {1763}, pages = {20130305}, pmid = {23720544}, issn = {1471-2954}, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Female ; Gene Flow ; *Genetic Variation ; *Genetics, Population ; *Homing Behavior ; Male ; Microsatellite Repeats ; Mitochondria/genetics ; *Sexual Behavior, Animal ; *Turtles/genetics/physiology ; }, abstract = {Without genetic variation, species cannot cope with changing environments, and evolution does not proceed. In endangered species, adaptive potential may be eroded by decreased population sizes and processes that further reduce gene flow such as philopatry and local adaptations. Here, we focused on the philopatric and endangered loggerhead sea turtle (Caretta caretta) nesting in Cape Verde as a model system to investigate the link between adaptive potential and philopatry. We produced a dataset of three complementary genomic regions to investigate female philopatric behaviour (mitochondrial DNA), male-mediated gene flow (microsatellites) and adaptive potential (major histocompatibility complex, MHC). Results revealed genetically distinct nesting colonies, indicating remarkably small-scale philopatric behaviour of females. Furthermore, these colonies also harboured local pools of MHC alleles, especially at the margins of the population's distribution, which are therefore important reserves of additional diversity for the population. Meanwhile, directional male-mediated gene flow from the margins of distribution sustains the adaptive potential for the entire rookery. We therefore present the first evidence for a positive association between philopatry and locally adapted genomic regions. Contrary to expectation, we propose that philopatry conserves a high adaptive potential at the margins of a distribution, while asymmetric gene flow maintains genetic connectivity with the rest of the population.}, }
@article {pmid23707480, year = {2013}, author = {Pichaud, N and Messmer, M and Correa, CC and Ballard, JW}, title = {Diet influences the intake target and mitochondrial functions of Drosophila melanogaster males.}, journal = {Mitochondrion}, volume = {13}, number = {6}, pages = {817-822}, doi = {10.1016/j.mito.2013.05.008}, pmid = {23707480}, issn = {1872-8278}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Diet ; Drosophila melanogaster/genetics/*physiology ; Haplotypes ; Male ; Mitochondria/*physiology ; }, abstract = {In this study, we examine the dietary protein to carbohydrate ratio (P:C) on the mitochondrial functions of two Drosophila melanogaster mtDNA haplotypes. We investigated multiple physiological parameters on flies fed with either 1:12 P:C or 1:3 P:C diets. Our results provide experimental evidence that a specific haplotype has a reduction of complex I activity when the flies are fed with the 1:12 P:C diet. This study is of particular importance to understand the influence of diet on mitochondrial evolution in invasive and broadly distributed species including humans.}, }
@article {pmid23706390, year = {2013}, author = {Ling, Q and Jarvis, P}, title = {Dynamic regulation of endosymbiotic organelles by ubiquitination.}, journal = {Trends in cell biology}, volume = {23}, number = {8}, pages = {399-408}, doi = {10.1016/j.tcb.2013.04.008}, pmid = {23706390}, issn = {1879-3088}, support = {BB/D016541/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/H008039/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Mitochondria/metabolism ; Organelles/*metabolism ; Plastids/metabolism ; Proteasome Endopeptidase Complex/metabolism ; *Symbiosis ; *Ubiquitination ; }, abstract = {Recent work has revealed that mitochondria and chloroplasts are subject to direct control by the ubiquitin-proteasome system (UPS). Ubiquitin E3 ligases are present at the outer membrane of both organelles where they mediate ubiquitination and turnover of other organellar proteins. Both organelles exhibit remarkable structural dynamism and UPS control is particularly concerned with these properties. In mitochondria, the UPS targets factors involved in organellar fission and fusion, with significant impacts upon organellar morphology, mitophagy, and apoptosis. In chloroplasts (and other plastids), the UPS targets components of the protein import machinery, facilitating reorganization of the organellar proteome to determine organellar development and functions. Acquisition of such regulatory control during evolution is perhaps linked to the dynamic characteristics of the two organelles, which are not paralleled in their prokaryotic relatives. Here we discuss our current understanding of the role of the UPS in the regulation of endosymbiotic organelles.}, }
@article {pmid23705496, year = {2013}, author = {Grechko, VV}, title = {[The problems of molecular phylogenetics on the example of squamata reptiles. Mitochondrial DNA markers].}, journal = {Molekuliarnaia biologiia}, volume = {47}, number = {1}, pages = {61-82}, doi = {10.7868/s0026898413010059}, pmid = {23705496}, issn = {0026-8984}, mesh = {Animals ; Biomarkers ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genetic Drift ; Lizards/genetics ; Mitochondria/*genetics/physiology ; *Phylogeny ; Snakes/genetics ; }, abstract = {The review is devoted to the recent problems of molecular phylogenetics based on the mitochondrial and chromosomal DNA sequences. The main subjects of the paper are the most widely used mtDNA markers though their application is not well enough (of critically considered) supported from the point of physiology and biochemistry of these organelles. Besides some well known aspects embarrassing the mt-markers phylogeny interpretations (hybridization and introgression events, ancestral polymorphism and nuclear paralogs of mtDNA) the attention is concentrated on non-neutrality and disproportional mutability of mt-genes and their fragments, on uniparental inheritance violations, recombinational events and heteroplasmy. These factors may influence the congruence of phylogenetic inferences and trees based on different mt-markers and when they compared with nuclear markers. Many authors suppose that the sequence comparisons of mt-genes and their fragments alone are not adequate to the studies of evolution. The notion is put forward that the influence of external conditions on metabolism and physiology of mitochondria could not be fully taken into account and modelled to be applied for phylogenetic tasks. The values of mt-markers could be revealed by the comparison of the whole mtDNA sequences of different taxa and searching the informative syn- and apomorphic properties and nuclear paralogs.}, }
@article {pmid23700350, year = {2013}, author = {Watanabe, S and Hanaoka, M and Ohba, Y and Ono, T and Ohnuma, M and Yoshikawa, H and Taketani, S and Tanaka, K}, title = {Mitochondrial localization of ferrochelatase in a red alga Cyanidioschyzon merolae.}, journal = {Plant &amp; cell physiology}, volume = {54}, number = {8}, pages = {1289-1295}, doi = {10.1093/pcp/pct077}, pmid = {23700350}, issn = {1471-9053}, mesh = {Algal Proteins/genetics/*metabolism ; Animals ; Ferrochelatase/genetics/*metabolism ; Immune Sera ; Mice ; Microscopy, Fluorescence ; Mitochondria/*enzymology ; Recombinant Fusion Proteins ; Rhodophyta/cytology/genetics/*metabolism ; Tetrapyrroles/metabolism ; }, abstract = {Ferrochelatase (FECH) is an essential enzyme for the final step of heme biosynthesis. In green plants, its activity has been reported in both plastids and mitochondria. However, the precise subcellular localization of FECH remains uncertain. In this study, we analyzed the localization of FECH in the unicellular red alga, Cyanidioschyzon merolae. Immunoblot and enzyme activity analyses of subcellular fractions localized little FECH in the plastid. In addition, immunofluorescence microscopy identified that both intrinsic and hemagglutinin (HA)-tagged FECH are localized in the mitochondrion. We therefore conclude that FECH is localized in the mitochondrion in C. merolae.}, }
@article {pmid23698443, year = {2013}, author = {Houtkooper, RH and Mouchiroud, L and Ryu, D and Moullan, N and Katsyuba, E and Knott, G and Williams, RW and Auwerx, J}, title = {Mitonuclear protein imbalance as a conserved longevity mechanism.}, journal = {Nature}, volume = {497}, number = {7450}, pages = {451-457}, pmid = {23698443}, issn = {1476-4687}, support = {P20-DA 21131/DA/NIDA NIH HHS/United States ; UO1AA13499/AA/NIAAA NIH HHS/United States ; R01 AG043930/AG/NIA NIH HHS/United States ; P20 DA021131/DA/NIDA NIH HHS/United States ; 231138/ERC_/European Research Council/International ; U01 AA013499/AA/NIAAA NIH HHS/United States ; U01AA14425/AA/NIAAA NIH HHS/United States ; U01 AA014425/AA/NIAAA NIH HHS/United States ; R01AG043930/AG/NIA NIH HHS/United States ; }, mesh = {Aging/genetics/metabolism ; Animals ; Anti-Bacterial Agents/pharmacology ; Caenorhabditis elegans/drug effects/genetics/*physiology ; Caenorhabditis elegans Proteins/genetics/metabolism ; Doxycycline/pharmacology ; Evolution, Molecular ; Female ; Longevity/drug effects/genetics/*physiology ; Male ; Mice ; Mice, Inbred Strains ; Mitochondria/drug effects/genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Quantitative Trait Loci ; RNA Interference ; Reproducibility of Results ; Ribosomal Proteins/genetics/*metabolism ; Sirolimus/pharmacology ; Unfolded Protein Response/genetics/physiology ; }, abstract = {Longevity is regulated by a network of closely linked metabolic systems. We used a combination of mouse population genetics and RNA interference in Caenorhabditis elegans to identify mitochondrial ribosomal protein S5 (Mrps5) and other mitochondrial ribosomal proteins as metabolic and longevity regulators. MRP knockdown triggers mitonuclear protein imbalance, reducing mitochondrial respiration and activating the mitochondrial unfolded protein response. Specific antibiotics targeting mitochondrial translation and ethidium bromide (which impairs mitochondrial DNA transcription) pharmacologically mimic mrp knockdown and extend worm lifespan by inducing mitonuclear protein imbalance, a stoichiometric imbalance between nuclear and mitochondrially encoded proteins. This mechanism was also conserved in mammalian cells. In addition, resveratrol and rapamycin, longevity compounds acting on different molecular targets, similarly induced mitonuclear protein imbalance, the mitochondrial unfolded protein response and lifespan extension in C. elegans. Collectively these data demonstrate that MRPs represent an evolutionarily conserved protein family that ties the mitochondrial ribosome and mitonuclear protein imbalance to the mitochondrial unfolded protein response, an overarching longevity pathway across many species.}, }
@article {pmid23696374, year = {2013}, author = {Vianello, D and Sevini, F and Castellani, G and Lomartire, L and Capri, M and Franceschi, C}, title = {HAPLOFIND: a new method for high-throughput mtDNA haplogroup assignment.}, journal = {Human mutation}, volume = {34}, number = {9}, pages = {1189-1194}, doi = {10.1002/humu.22356}, pmid = {23696374}, issn = {1098-1004}, mesh = {Algorithms ; DNA, Mitochondrial/*classification/*genetics ; *Databases, Nucleic Acid ; Genetic Variation ; *Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Molecular Sequence Annotation ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {Deep sequencing technologies are completely revolutionizing the approach to DNA analysis. Mitochondrial DNA (mtDNA) studies entered in the "postgenomic era": the burst in sequenced samples observed in nuclear genomics is expected also in mitochondria, a trend that can already be detected checking complete mtDNA sequences database submission rate. Tools for the analysis of these data are available, but they fail in throughput or in easiness of use. We present here a new pipeline based on previous algorithms, inherited from the "nuclear genomic toolbox," combined with a newly developed algorithm capable of efficiently and easily classify new mtDNA sequences according to PhyloTree nomenclature. Detected mutations are also annotated using data collected from publicly available databases. Thanks to the analysis of all freely available sequences with known haplogroup obtained from GenBank, we were able to produce a PhyloTree-based weighted tree, taking into account each haplogroup pattern conservation. The combination of a highly efficient aligner, coupled with our algorithm and massive usage of asynchronous parallel processing, allowed us to build a high-throughput pipeline for the analysis of mtDNA sequences that can be quickly updated to follow the ever-changing nomenclature. HaploFind is freely accessible at the following Web address: https://haplofind.unibo.it.}, }
@article {pmid23685010, year = {2013}, author = {Zhao, C and Feng, B and Cao, Y and Xie, P and Xu, J and Pang, Y and Liu, X and Li, Q}, title = {Identification and characterisation of ROS modulator 1 in Lampetra japonica.}, journal = {Fish &amp; shellfish immunology}, volume = {35}, number = {2}, pages = {278-283}, doi = {10.1016/j.fsi.2013.04.039}, pmid = {23685010}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Exocrine Glands/metabolism ; Fish Proteins/chemistry/*genetics/metabolism ; *Gene Expression Regulation ; Lampreys/*genetics/*immunology/metabolism ; Lipopolysaccharides/physiology ; Membrane Proteins/chemistry/*genetics/metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Organ Specificity ; Phylogeny ; Reactive Oxygen Species/*metabolism ; Real-Time Polymerase Chain Reaction/veterinary ; Sequence Alignment ; }, abstract = {Reactive oxygen species (ROS) are a heterogeneous group of highly reactive molecules that oxidise targets in biological systems. ROS are also considered important immune regulators. In this study, we identified a homologue of reactive oxygen species modulator 1 (Romo1) in the Japanese lamprey (Lampetra japonica). The L japonica Romo1 (Lj-Romo1) gene shares high sequence homology with the Romo1 genes of jawed vertebrates. Real-time quantitative PCR demonstrated the wide distribution of Lj-Romo1 in lamprey tissues. Furthermore, after the lampreys were stimulated with lipopolysaccharide (LPS), the level of Lj-Romo1 mRNA was markedly up-regulated in the liver, gill, kidney, and intestine tissues. Lj-Romo1 was localised to the mitochondria and has the capacity to increase the ROS level in cells. The results obtained in the present study will help us to understand the roles of Romo1 in ROS production and innate immune responses in jawless vertebrates.}, }
@article {pmid23680032, year = {2013}, author = {Dixon, BJ and Tang, J and Zhang, JH}, title = {The evolution of molecular hydrogen: a noteworthy potential therapy with clinical significance.}, journal = {Medical gas research}, volume = {3}, number = {1}, pages = {10}, pmid = {23680032}, issn = {2045-9912}, support = {P20 MD006988/MD/NIMHD NIH HHS/United States ; R25 GM060507/GM/NIGMS NIH HHS/United States ; }, abstract = {Studies on molecular hydrogen have evolved tremendously from its humble beginnings and have continued to change throughout the years. Hydrogen is extremely unique since it has the capability to act at the cellular level. Hydrogen is qualified to cross the blood brain barrier, to enter the mitochondria, and even has the ability to translocate to the nucleus under certain conditions. Once in these ideal locations of the cell, previous studies have shown that hydrogen exerts antioxidant, anti-apoptotic, anti-inflammatory, and cytoprotective properties that are beneficial to the cell. Hydrogen is most commonly applied as a gas, water, saline, and can be applied in a variety of other mediums. There are also few side effects involving hydrogen, thus making hydrogen a perfect medical gas candidate for the convention of novel therapeutic strategies against cardiovascular, cerebrovascular, cancer, metabolic, and respiratory diseases and disorders. Although hydrogen appears to be faultless at times, there still are several deficiencies or snares that need to be investigated by future studies. This review article seeks to delve and comprehensively analyze the research and experiments that alludes to molecular hydrogen being a novel therapeutic treatment that medicine desperately needs.}, }
@article {pmid23673559, year = {2013}, author = {Voelter-Mahlknecht, S and Mahlknecht, U}, title = {Cloning, chromosomal characterization and FISH mapping of the NAD(+)-dependent histone deacetylase gene sirtuin 5 in the mouse.}, journal = {International journal of oncology}, volume = {43}, number = {1}, pages = {237-245}, doi = {10.3892/ijo.2013.1939}, pmid = {23673559}, issn = {1791-2423}, mesh = {Amino Acid Sequence ; Animals ; Chromosome Mapping ; *Cloning, Molecular ; Group III Histone Deacetylases/*genetics ; In Situ Hybridization, Fluorescence ; Mice ; NAD/genetics/*metabolism ; Phylogeny ; Sequence Alignment ; Sirtuins/*genetics/metabolism ; }, abstract = {Sirtuin 5 (SIRT5) is a nicotinamide adenine dinucleotide (NAD+)-dependent deacetylase, belonging to the silent information regulator 2 (Sir2) family of sirtuin histone deacetylases (sirtuins). The yeast Sir2 protein and its mammalian derivatives are important in epigenetic gene silencing, DNA repair and recombination, cell cycle, microtubule organization and in the regulation of aging. In mammals, 7 sirtuin isoforms have been identified to date of which three (SIRT3, SIRT4 and SIRT5) are localized in the mitochondria, which serve as the center of energy management and the initiation of cellular apoptosis. In the study presented herein, we report the genomic organization and chromosomal localization of the murine sirt5 gene. We have isolated and characterized the murine sirt5 genomic sequence, which spans a region of 24,449 bp and which has one single genomic locus. The murine sirt5 gene consists of 8 exons and encodes a 310-aa protein with a predictive mo-lecular weight of 34.1 kDa and an isoelectric point of 8.90. For the murine sirt5 gene only one single genomic locus has been identified. The gene has been localized to mouse chromosome 13A4 and is flanked by STS-marker 164522 (synonymous WI MRC-RH: 506859).}, }
@article {pmid23670558, year = {2013}, author = {Zhu, P and Zhai, B and Lin, X and Idnurm, A}, title = {Congenic strains for genetic analysis of virulence traits in Cryptococcus gattii.}, journal = {Infection and immunity}, volume = {81}, number = {7}, pages = {2616-2625}, pmid = {23670558}, issn = {1098-5522}, support = {R01 AI097599/AI/NIAID NIH HHS/United States ; R21 AI094364/AI/NIAID NIH HHS/United States ; AI094364/AI/NIAID NIH HHS/United States ; AI097599/AI/NIAID NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Chromosomes, Fungal/genetics/metabolism ; Coculture Techniques ; Coinfection ; Cryptococcosis/*microbiology ; Cryptococcus gattii/*genetics/metabolism/pathogenicity ; Cryptococcus neoformans/genetics/metabolism/pathogenicity ; Female ; Fungal Proteins/genetics/metabolism ; *Genes, Fungal ; Genetic Complementation Test ; Genetic Loci ; Genetic Markers ; Genetic Variation ; Humans ; Inheritance Patterns ; Mice ; Mice, Inbred A ; Mitochondria/genetics/metabolism ; Recombination, Genetic ; Transcription Factors/genetics/metabolism ; Transcription, Genetic ; Virulence ; }, abstract = {Cryptococcus gattii is responsible for a large outbreak of potentially fatal disease that started in the late 1990s on Vancouver Island, Canada. How this fungus and the outbreak isolates in particular cause disease in immunocompetent people is unknown, with differing hypotheses. To explore genetic contributions, a pair of congenic a and α mating type strains was generated by a series of 11 backcrosses to introgress the MAT locus from a nonoutbreak strain into the background of strain R265, isolated from a Vancouver Island patient. The congenic pair was used to investigate three traits: mitochondrial inheritance, the effect of the MAT alleles on virulence, and the impact of a predicted virulence factor on pathogenicity. The two congenic strains show the same virulence in different models of cryptococcosis and equivalent levels of competition in coinfection assays. These results rule out a role of the MAT locus and mitochondrial genotype as major virulence factors in the outbreak strains. Disruption of Bwc2, a light-dependent transcription factor, resulted in reduced virulence, consistent with a similar function in the related species Cryptococcus neoformans. The C. gattii congenic strains represent a new resource for exploring the evolution of virulence in the C. neoformans-C. gattii clade.}, }
@article {pmid23665874, year = {2013}, author = {White, DJ and Bryant, D and Gemmell, NJ}, title = {How good are indirect tests at detecting recombination in human mtDNA?.}, journal = {G3 (Bethesda, Md.)}, volume = {3}, number = {7}, pages = {1095-1104}, pmid = {23665874}, issn = {2160-1836}, mesh = {DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Humans ; Linkage Disequilibrium ; Mitochondria/*genetics ; *Recombination, Genetic ; }, abstract = {Empirical proof of human mitochondrial DNA (mtDNA) recombination in somatic tissues was obtained in 2004; however, a lack of irrefutable evidence exists for recombination in human mtDNA at the population level. Our inability to demonstrate convincingly a signal of recombination in population data sets of human mtDNA sequence may be due, in part, to the ineffectiveness of current indirect tests. Previously, we tested some well-established indirect tests of recombination (linkage disequilibrium vs. distance using D' and r(2), Homoplasy Test, Pairwise Homoplasy Index, Neighborhood Similarity Score, and Max χ(2)) on sequence data derived from the only empirically confirmed case of human mtDNA recombination thus far and demonstrated that some methods were unable to detect recombination. Here, we assess the performance of these six well-established tests and explore what characteristics specific to human mtDNA sequence may affect their efficacy by simulating sequence under various parameters with levels of recombination (ρ) that vary around an empirically derived estimate for human mtDNA (population parameter ρ = 5.492). No test performed infallibly under any of our scenarios, and error rates varied across tests, whereas detection rates increased substantially with ρ values > 5.492. Under a model of evolution that incorporates parameters specific to human mtDNA, including rate heterogeneity, population expansion, and ρ = 5.492, successful detection rates are limited to a range of 7-70% across tests with an acceptable level of false-positive results: the neighborhood similarity score incompatibility test performed best overall under these parameters. Population growth seems to have the greatest impact on recombination detection probabilities across all models tested, likely due to its impact on sequence diversity. The implications of our findings on our current understanding of mtDNA recombination in humans are discussed.}, }
@article {pmid23665487, year = {2013}, author = {Zhang, J and Zhao, F and Fu, Q and Liang, M and Tong, Y and Liu, X and Lin, B and Mi, H and Zhang, M and Wei, QP and Xue, L and Jiang, P and Zhou, X and Mo, JQ and Huang, T and Qu, J and Guan, MX}, title = {Mitochondrial haplotypes may modulate the phenotypic manifestation of the LHON-associated m.14484T&gt;C (MT-ND6) mutation in Chinese families.}, journal = {Mitochondrion}, volume = {13}, number = {6}, pages = {772-781}, doi = {10.1016/j.mito.2013.05.002}, pmid = {23665487}, issn = {1872-8278}, mesh = {China ; Female ; Genome, Mitochondrial ; *Haplotypes ; Humans ; Male ; Mitochondria/*genetics ; *Mutation ; Optic Atrophy, Hereditary, Leber ; Pedigree ; Phenotype ; Phylogeny ; }, abstract = {Mitochondrial m.14484T>C (MT-ND6) mutation has been associated with Leber's hereditary optic neuropathy. Previous investigations revealed that the m.14484T>C mutation is a primary factor underlying the development of optic neuropathy but is not sufficient to produce a clinical phenotype. However, mitochondrial haplogroups have been proposed to modulate the phenotypic manifestation of the m.14484T>C mutation. Here, we performed the clinical, genetic evaluation and complete mitochondrial genome sequence analysis of 41 Han Chinese pedigrees carrying the m.14484T>C mutation. These families exhibited a wide range of penetrances and expressivities of optic neuropathy. The average ratio between affected male/female matrilineal relatives from 41 families was 2:1. The penetrance of optic neuropathy in these Chinese pedigrees ranged from 5.6% to 100%, with the average of 23.8%. Furthermore, the age-of-onset for optic neuropathy varied from 4 to 44 years, with the average of 19.3 years. Sequence analysis of their mitochondrial genomes identified distinct sets of polymorphisms belonging to ten Eastern Asian haplogroups, indicating that the m.14484T>C mutation occurred through recurrent origins and founder events. We showed that mitochondrial haplogroups M9, M10 and N9 increased the penetrance of optic neuropathy in these Chinese families. In particular, these mitochondrial haplogroup specific variants: m.3394T>C (MT-ND1), m.14502T>C (MT-ND4) and m.14693A>G (MT-TE) enhanced the penetrance of visual loss in these Chinese families. These data provided the direct evidence that mitochondrial modifiers modulate the variable penetrance and expressivity of optic neuropathy among Chinese pedigrees carrying the m.14484T>C mutation.}, }
@article {pmid23664893, year = {2013}, author = {Neimanis, K and Staples, JF and Hüner, NP and McDonald, AE}, title = {Identification, expression, and taxonomic distribution of alternative oxidases in non-angiosperm plants.}, journal = {Gene}, volume = {526}, number = {2}, pages = {275-286}, doi = {10.1016/j.gene.2013.04.072}, pmid = {23664893}, issn = {1879-0038}, mesh = {Amino Acid Sequence ; Base Sequence ; Binding Sites ; Computational Biology ; Databases, Genetic ; Evolution, Molecular ; Iron/metabolism ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Oxidoreductases/chemistry/*genetics/metabolism ; Plant Proteins/chemistry/*genetics/metabolism ; Plants/*classification/enzymology/*genetics ; Protein Binding ; Sequence Alignment ; Viridiplantae/classification/enzymology/genetics ; }, abstract = {Alternative oxidase (AOX) is a terminal ubiquinol oxidase present in the respiratory chain of all angiosperms investigated to date, but AOX distribution in other members of the Viridiplantae is less clear. We assessed the taxonomic distribution of AOX using bioinformatics. Multiple sequence alignments compared AOX proteins and examined amino acid residues involved in AOX catalytic function and post-translational regulation. Novel AOX sequences were found in both Chlorophytes and Streptophytes and we conclude that AOX is widespread in the Viridiplantae. AOX multigene families are common in non-angiosperm plants and the appearance of AOX1 and AOX2 subtypes pre-dates the divergence of the Coniferophyta and Magnoliophyta. Residues involved in AOX catalytic function are highly conserved between Chlorophytes and Streptophytes, while AOX post-translational regulation likely differs in these two lineages. We demonstrate experimentally that an AOX gene is present in the moss Physcomitrella patens and that the gene is transcribed. Our findings suggest that AOX will likely exert an influence on plant respiration and carbon metabolism in non-angiosperms such as green algae, bryophytes, liverworts, lycopods, ferns, gnetophytes, and gymnosperms and that further research in these systems is required.}, }
@article {pmid23663090, year = {2013}, author = {Jezkova, T and Leal, M and Rodríguez-Robles, JA}, title = {Genetic drift or natural selection? Hybridization and asymmetric mitochondrial introgression in two Caribbean lizards (Anolis pulchellus and Anolis krugi).}, journal = {Journal of evolutionary biology}, volume = {26}, number = {7}, pages = {1458-1471}, doi = {10.1111/jeb.12149}, pmid = {23663090}, issn = {1420-9101}, mesh = {Animals ; Caribbean Region ; DNA, Mitochondrial ; *Genetic Drift ; *Genetics, Population ; *Hybridization, Genetic ; Likelihood Functions ; Lizards/*genetics ; Mitochondria/genetics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Puerto Rico ; }, abstract = {Hybridization and gene introgression can occur frequently between closely related taxa, but appear to be rare phenomena among members of the species-rich West Indian radiation of Anolis lizards. We investigated the pattern and possible mechanism of introgression between two sister species from Puerto Rico, Anolis pulchellus and Anolis krugi, using mitochondrial (ND2) and nuclear (DNAH3, NKTR) DNA sequences. Our findings demonstrated extensive introgression of A. krugi mtDNA (k-mtDNA) into the genome of A. pulchellus in western Puerto Rico, to the extent that k-mtDNA has mostly or completely replaced the native mtDNA of A. pulchellus on this part of the island. We proposed two not mutually exclusive scenarios to account for the interspecific matings between A. pulchellus and A. krugi. We inferred that hybridization events occurred independently in several populations, and determined that k-mtDNA haplotypes harboured in individuals of A. pulchellus can be assigned to four of the five major mtDNA clades of A. krugi. Further, the spatial distribution of k-mtDNA clades in the two species is largely congruent. Based on this evidence, we concluded that natural selection was the probable driving mechanism for the extensive k-mtDNA introgression into A. pulchellus. Our two nuclear data sets yielded different results. DNAH3 showed reciprocal monophyly of A. pulchellus and A. krugi, indicating no effect of hybridization on this marker. In contrast, the two species shared nine NKTR alleles, probably due to incomplete lineage sorting. Our study system will provide an excellent opportunity to experimentally assess the behavioural and ecological mechanisms that can lead to hybridization in closely related taxa.}, }
@article {pmid23658748, year = {2013}, author = {Sauer, J and Oldeland, J and Hausdorf, B}, title = {Continuing fragmentation of a widespread species by geographical barriers as initial step in a land snail radiation on crete.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e62569}, pmid = {23658748}, issn = {1932-6203}, mesh = {Amplified Fragment Length Polymorphism Analysis ; *Animal Distribution ; Animals ; Electron Transport Complex IV/genetics ; Gene Flow ; Genetic Markers ; Greece ; Haplotypes ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; Multigene Family ; Phylogeny ; Phylogeography ; Selection, Genetic ; Snails/*genetics ; }, abstract = {The phylogeographic structure of the land snail Xerocrassa mesostena on Crete inferred from AFLP markers and mitochondrial cox1 sequences can be explained by three mechanisms: gene flow restriction, population expansion and leptokurtic dispersal. Gene flow restriction by geographic barriers caused subdivision of the gene pool into distinct clusters. Population expansion was probably facilitated by deforestation of Crete in the postglacial. Newly available areas were colonized by leptokurtic dispersal, i.e. slow active expansion resulting in isolation by distance within the clusters and occasional long distance dispersal events that resulted in departures from the isolation by distance model. Less than one percent of the AFLP markers show correlations with environmental variables. Random phylogeographic breaks in the distribution of the mitochondrial haplotype groups indicate that single locus markers, especially mitochondrial DNA, might result in a misleading picture of the phylogeographic structure of a species. Restriction of gene flow between metapopulations caused by geographical barriers can interact with sexual selection resulting in the differentiation of these metapopulations into separate species without noticeable ecological differentiation. Evidence for gene flow between parapatrically distributed evolutionary units representing different stages of the speciation process suggests that the ongoing process of fragmentation of the X. mesostena complex might be an example for parapatric speciation. The lack of ecological differentiation between these units confirms theoretical predictions that divergent selection for local adaptation is not required for rapid speciation.}, }
@article {pmid23658632, year = {2013}, author = {Gobron, N and Waszczak, C and Simon, M and Hiard, S and Boivin, S and Charif, D and Ducamp, A and Wenes, E and Budar, F}, title = {A cryptic cytoplasmic male sterility unveils a possible gynodioecious past for Arabidopsis thaliana.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e62450}, pmid = {23658632}, issn = {1932-6203}, mesh = {Arabidopsis/classification/*genetics ; Biological Evolution ; Cell Nucleus/genetics ; Chromosomes, Plant ; Crosses, Genetic ; Cytoplasm/genetics ; *Genetic Loci ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Open Reading Frames ; Phylogeny ; Plant Infertility/*genetics ; }, abstract = {Gynodioecy, the coexistence of hermaphrodites and females (i.e. male-sterile plants) in natural plant populations, most often results from polymorphism at genetic loci involved in a particular interaction between the nuclear and cytoplasmic genetic compartments (cytonuclear epistasis): cytoplasmic male sterility (CMS). Although CMS clearly contributes to the coevolution of involved nuclear loci and cytoplasmic genomes in gynodioecious species, the occurrence of CMS genetic factors in the absence of sexual polymorphism (cryptic CMS) is not easily detected and rarely taken in consideration. We found cryptic CMS in the model plant Arabidopsis thaliana after crossing distantly related accessions, Sha and Mr-0. Male sterility resulted from an interaction between the Sha cytoplasm and two Mr-0 genomic regions located on chromosome 1 and chromosome 3. Additional accessions with either nuclear sterility maintainers or sterilizing cytoplasms were identified from crosses with either Sha or Mr-0. By comparing two very closely related cytoplasms with different male-sterility inducing abilities, we identified a novel mitochondrial ORF, named orf117Sha, that is most likely the sterilizing factor of the Sha cytoplasm. The presence of orf117Sha was investigated in worldwide natural accessions. It was found mainly associated with a single chlorotype in accessions belonging to a clade predominantly originating from Central Asia. More than one-third of accessions from this clade carried orf117Sha, indicating that the sterilizing-inducing cytoplasm had spread in this lineage. We also report the coexistence of the sterilizing cytoplasm with a non-sterilizing cytoplasm at a small, local scale in a natural population; in addition a correlation between cytotype and nuclear haplotype was detected in this population. Our results suggest that this CMS system induced sexual polymorphism in A. thaliana populations, at the time when the species was mainly outcrossing.}, }
@article {pmid23650209, year = {2013}, author = {Lin, Z and Wang, TY and Tsai, BS and Wu, FT and Yu, FJ and Tseng, YJ and Sung, HM and Li, WH}, title = {Identifying cis-regulatory changes involved in the evolution of aerobic fermentation in yeasts.}, journal = {Genome biology and evolution}, volume = {5}, number = {6}, pages = {1065-1078}, pmid = {23650209}, issn = {1759-6653}, mesh = {Aerobiosis ; Base Sequence ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics/metabolism ; Binding Sites ; Biological Evolution ; Evolution, Molecular ; *Fermentation ; *Gene Expression Regulation, Fungal ; Genes, Fungal ; Mitochondria/genetics/metabolism ; Promoter Regions, Genetic ; Protein Binding ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Yeasts/*genetics/*metabolism ; }, abstract = {Gene regulation change has long been recognized as an important mechanism for phenotypic evolution. We used the evolution of yeast aerobic fermentation as a model to explore how gene regulation has evolved and how this process has contributed to phenotypic evolution and adaptation. Most eukaryotes fully oxidize glucose to CO2 and H2O in mitochondria to maximize energy yield, whereas some yeasts, such as Saccharomyces cerevisiae and its relatives, predominantly ferment glucose into ethanol even in the presence of oxygen, a phenomenon known as aerobic fermentation. We examined the genome-wide gene expression levels among 12 different yeasts and found that a group of genes involved in the mitochondrial respiration process showed the largest reduction in gene expression level during the evolution of aerobic fermentation. Our analysis revealed that the downregulation of these genes was significantly associated with massive loss of binding motifs of Cbf1p in the fermentative yeasts. Our experimental assays confirmed the binding of Cbf1p to the predicted motif and the activator role of Cbf1p. In summary, our study laid a foundation to unravel the long-time mystery about the genetic basis of evolution of aerobic fermentation, providing new insights into understanding the role of cis-regulatory changes in phenotypic evolution.}, }
@article {pmid23648483, year = {2013}, author = {Pereira, B and Videira, A and Duarte, M}, title = {Novel insights into the role of Neurospora crassa NDUFAF2, an evolutionarily conserved mitochondrial complex I assembly factor.}, journal = {Molecular and cellular biology}, volume = {33}, number = {13}, pages = {2623-2634}, pmid = {23648483}, issn = {1098-5549}, mesh = {Amino Acid Sequence ; Conserved Sequence ; Electron Transport Complex I/genetics/metabolism ; Evolution, Molecular ; Fungal Proteins/genetics/*metabolism ; Intracellular Membranes/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Mutation ; Neurospora crassa/genetics/*metabolism ; Protein Subunits ; }, abstract = {Complex I deficiency is commonly associated with mitochondrial oxidative phosphorylation diseases. Mutations in nuclear genes encoding structural subunits or assembly factors of complex I have been increasingly identified as the cause of the diseases. One such factor, NDUFAF2, is a paralog of the NDUFA12 structural subunit of the enzyme, but the mechanism by which it exerts its function remains unknown. Herein, we demonstrate that the Neurospora crassa NDUFAF2 homologue, the 13.4 L protein, is a late assembly factor that associates with complex I assembly intermediates containing the membrane arm and the connecting part but lacking the N module of the enzyme. Furthermore, we provide evidence that dissociation of the assembly factor is dependent on the incorporation of the putative regulatory module composed of the subunits of 13.4 (NDUFA12), 18.4 (NDUFS6), and 21 (NDUFS4) kDa. Our results demonstrate that the 13.4 L protein is a complex I assembly factor functionally conserved from fungi to mammals.}, }
@article {pmid23640425, year = {2013}, author = {Valencak, TG and Ruf, T}, title = {Phospholipid composition and longevity: lessons from Ames dwarf mice.}, journal = {Age (Dordrecht, Netherlands)}, volume = {35}, number = {6}, pages = {2303-2313}, pmid = {23640425}, issn = {1574-4647}, support = {P 22323/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Brain/growth &amp; development/metabolism/pathology ; Cell Membrane/metabolism ; Cells, Cultured ; Disease Models, Animal ; Dwarfism/*metabolism ; Fatty Acids/*metabolism ; Female ; Lipid Peroxidation ; Longevity/*physiology ; Male ; Mice ; Mitochondria, Liver/metabolism/pathology ; *Oxidative Stress ; Phospholipids/*metabolism ; }, abstract = {Membrane fatty acid (FA) composition is correlated with longevity in mammals. The "membrane pacemaker hypothesis of ageing" proposes that animals which cellular membranes contain high amounts of polyunsaturated FAs (PUFAs) have shorter life spans because their membranes are more susceptible to peroxidation and further oxidative damage. It remains to be shown, however, that long-lived phenotypes such as the Ames dwarf mouse have membranes containing fewer PUFAs and thus being less prone to peroxidation, as would be predicted from the membrane pacemaker hypothesis of ageing. Here, we show that across four different tissues, i.e., muscle, heart, liver and brain as well as in liver mitochondria, Ames dwarf mice possess membrane phospholipids containing between 30 and 60 % PUFAs (depending on the tissue), which is similar to PUFA contents of their normal-sized, short-lived siblings. However, we found that that Ames dwarf mice membrane phospholipids were significantly poorer in n-3 PUFAs. While lack of a difference in PUFA contents is contradicting the membrane pacemaker hypothesis, the lower n-3 PUFAs content in the long-lived mice provides some support for the membrane pacemaker hypothesis of ageing, as n-3 PUFAs comprise those FAs being blamed most for causing oxidative damage. By comparing tissue composition between 1-, 2- and 6-month-old mice in both phenotypes, we found that membranes differed both in quantity of PUFAs and in the prevalence of certain PUFAs. In sum, membrane composition in the Ames dwarf mouse supports the concept that tissue FA composition is related to longevity.}, }
@article {pmid23638969, year = {2013}, author = {Hendricks, SA and Flannery, ME and Spicer, GS}, title = {Cophylogeny of quill mites from the genus Syringophilopsis (Acari: Syringophilidae) and their North American passerine hosts.}, journal = {The Journal of parasitology}, volume = {99}, number = {5}, pages = {827-834}, doi = {10.1645/GE-2400.1}, pmid = {23638969}, issn = {1937-2345}, mesh = {Animals ; Bayes Theorem ; Biological Evolution ; Bird Diseases/*parasitology ; DNA, Mitochondrial/chemistry ; DNA, Ribosomal/chemistry ; Electron Transport Complex IV/genetics ; Feathers/*parasitology ; Genetic Speciation ; Host-Parasite Interactions ; Mite Infestations/parasitology/*veterinary ; Mites/anatomy &amp; histology/*classification/genetics ; Mitochondria/enzymology ; North America ; Passeriformes/classification/genetics/*parasitology ; Phylogeny ; RNA, Ribosomal, 28S/genetics ; Sequence Alignment ; }, abstract = {Species of Syringophilopsis quill mites are found in the flight feathers of passerine birds. A phylogeny of species from this genus infecting North American passerines was inferred from the mitochondrial cytochrome oxidase I gene and the nuclear 28S ribosomal RNA gene. Based on the large genetic distance among lineages, the genus appears to be composed of several cryptic species. A reconciliation analysis of these mites and their avian hosts indicates a limited, but significant, degree of cophylogeny. However, strict cospeciation is not found to be occurring in this system.}, }
@article {pmid23636354, year = {2013}, author = {VanBuren, R and Ming, R}, title = {Organelle DNA accumulation in the recently evolved papaya sex chromosomes.}, journal = {Molecular genetics and genomics : MGG}, volume = {288}, number = {5-6}, pages = {277-284}, pmid = {23636354}, issn = {1617-4623}, mesh = {Carica/*genetics ; Chloroplasts/genetics ; Chromosomes, Artificial, Bacterial ; *Chromosomes, Plant ; DNA, Plant/*metabolism ; *Evolution, Molecular ; Mitochondria/genetics ; Retroelements ; Ribosomal Proteins/genetics ; Sex Chromosomes ; }, abstract = {Sex chromosomes are a pair of specialized chromosomes containing a sex determination region that is suppressed for recombination. Without recombination, Y chromosomes are thought to accumulate repetitive DNA sequences which contribute to their degeneration. A pair of primitive sex chromosomes controls sex type in papaya with male and hermaphrodite determined by the slightly different male-specific region of the Y (MSY) and hermaphrodite-specific region of Y(h) (HSY) chromosomes, respectively. Here, we show that the papaya HSY and MSY in the absence of recombination have accumulated nearly 12 times the amount of chloroplast-derived DNA than the corresponding region of the X chromosome and 4 times the papaya genome-wide average. Furthermore, a chloroplast genome fragment containing the rsp15 gene has been amplified 23 times in the HSY, evidence of retrotransposon-mediated duplication. Surprisingly, mitochondria-derived sequences are less abundant in the X and HSY compared to the whole genome. Shared organelle integrations are sparse between X and HSY, with only 11 % of chloroplast and 12 % of mitochondria fragments conserved, respectively, suggesting that the accelerated accumulation of organelle DNA occurred after the HSY was suppressed for recombination. Most of the organelle-derived sequences have divergence times of <7 MYA, reinforcing this notion. The accumulated chloroplast DNA is evidence of the slow degeneration of the HSY.}, }
@article {pmid23626734, year = {2013}, author = {Zhao, Z and Su, TJ and Chesters, D and Wang, SD and Ho, SY and Zhu, CD and Chen, XL and Zhang, CT}, title = {The mitochondrial genome of Elodia flavipalpis Aldrich (Diptera: Tachinidae) and the evolutionary timescale of Tachinid flies.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e61814}, pmid = {23626734}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Biological Evolution ; Chromosome Mapping ; Diptera/classification/*genetics ; Fossils ; *Genes, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; Moths/parasitology ; Nucleic Acid Conformation ; Pest Control, Biological ; Phylogeny ; RNA, Transfer/chemistry/classification/*genetics ; Time Factors ; }, abstract = {Tachinid flies are natural enemies of many lepidopteran and coleopteran pests of forests, crops, and fruit trees. In order to address the lack of genetic data in this economically important group, we sequenced the complete mitochondrial genome of the Palaearctic tachinid fly Elodia flavipalpis Aldrich, 1933. Usually found in Northern China and Japan, this species is one of the primary natural enemies of the leaf-roller moths (Tortricidae), which are major pests of various fruit trees. The 14,932-bp mitochondrial genome was typical of Diptera, with 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. However, its control region is only 105 bp in length, which is the shortest found so far in flies. In order to estimate dipteran evolutionary relationships, we conducted a phylogenetic analysis of 58 mitochondrial genomes from 23 families. Maximum-likelihood and Bayesian methods supported the monophyly of both Tachinidae and superfamily Oestroidea. Within the subsection Calyptratae, Muscidae was inferred as the sister group to Oestroidea. Within Oestroidea, Calliphoridae and Sarcophagidae formed a sister clade to Oestridae and Tachinidae. Using a Bayesian relaxed clock calibrated with fossil data, we estimated that Tachinidae originated in the middle Eocene.}, }
@article {pmid23620797, year = {2013}, author = {Parmakelis, A and Kotsakiozi, P and Rand, D}, title = {Animal mitochondria, positive selection and cyto-nuclear coevolution: insights from pulmonates.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e61970}, pmid = {23620797}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Cell Nucleus/*genetics ; Cytochromes c/genetics ; DNA, Mitochondrial ; *Evolution, Molecular ; Genetic Variation ; Likelihood Functions ; Mitochondria/*genetics ; Mutation/genetics ; *Selection, Genetic ; Snails/*genetics ; Species Specificity ; }, abstract = {Pulmonate snails have remarkably high levels of mtDNA polymorphism within species and divergence between species, making them an interesting group for the study of mutation and selection on mitochondrial genomes. The availability of sequence data from most major lineages - collected largely for studies of phylogeography - provides an opportunity to perform several tests of selection that may provide general insights into the evolutionary forces that have produced this unusual pattern. Several protein coding mtDNA datasets of pulmonates were analyzed towards this direction. Two different methods for the detection of positive selection were used, one based on phylogeny, and the other on the McDonald-Kreitman test. The cyto-nuclear coevolution hypothesis, often implicated to account for the high levels of mtDNA divergence of some organisms, was also addressed by assessing the divergence pattern exhibited by a nuclear gene. The McDonald-Kreitman test indicated multiple signs of positive selection in the mtDNA genes, but was significantly biased when sequence divergence was high. The phylogenetic method identified five mtDNA datasets as affected by positive selection. In the nuclear gene, the McDonald-Kreitman test provided no significant results, whereas the phylogenetic method identified positive selection as likely present. Overall, our findings indicate that: 1) slim support for the cyto-nuclear coevolution hypothesis is present, 2) the elevated rates of mtDNA polymorphims and divergence in pulmonates do not appear to be due to pervasive positive selection, 3) more stringent tests show that spurious positive selection is uncovered when distant taxa are compared and 4) there are significant examples of positive selection acting in some cases, so it appears that mtDNA evolution in pulmonates can escape from strict deleterious evolution suggested by the Muller's ratchet effect.}, }
@article {pmid23619407, year = {2013}, author = {Pichaud, N and Garratt, M and Ballard, JW and Brooks, RC}, title = {Physiological adaptations to reproduction. II. Mitochondrial adjustments in livers of lactating mice.}, journal = {The Journal of experimental biology}, volume = {216}, number = {Pt 15}, pages = {2889-2895}, doi = {10.1242/jeb.082685}, pmid = {23619407}, issn = {1477-9145}, mesh = {*Adaptation, Physiological ; Analysis of Variance ; Animals ; Cell Respiration ; Citrate (si)-Synthase/metabolism ; Electron Transport Complex IV/metabolism ; Female ; Lactation/*physiology ; Mice ; Mitochondria, Liver/*metabolism ; Oxygen/metabolism ; Oxygen Consumption/physiology ; Permeability ; Reproduction/*physiology ; }, abstract = {Reproduction imposes significant costs and is characterized by an increased energy demand. As a consequence, individuals adjust their cellular structure and function in response to this physiological constraint. Because mitochondria are central to energy production, changes in their functional properties are likely to occur during reproduction. Such changes could cause adjustments in reactive oxygen species (ROS) production and consequently in oxidative stress levels. In this study, we investigated several mechanisms involved in energy production, including mitochondrial respiration at different steps of the electron transport system (ETS) and related the results to citrate synthase activity in the liver of non-reproductive and reproductive (two and eight pups) female house mice at peak lactation. Whereas we did not find differences between females having different litter sizes, liver mitochondria of reproductive females showed lower ETS activity and an increase in mitochondrial density when compared with the non-reproductive females. Although it is possible that these changes were due to combined processes involved in reproduction and not to the relative investment in lactation, we propose that the mitochondrial adjustment in liver might help to spare substrates and therefore energy for milk production in the mammary gland. Moreover, our results suggest that these changes lead to an increase in ROS production that subsequently upregulates antioxidant defence activity and decreases oxidative stress.}, }
@article {pmid23619144, year = {2013}, author = {Hirata, D and Mano, T and Abramov, AV and Baryshnikov, GF and Kosintsev, PA and Vorobiev, AA and Raichev, EG and Tsunoda, H and Kaneko, Y and Murata, K and Fukui, D and Masuda, R}, title = {Molecular phylogeography of the brown bear (Ursus arctos) in Northeastern Asia based on analyses of complete mitochondrial DNA sequences.}, journal = {Molecular biology and evolution}, volume = {30}, number = {7}, pages = {1644-1652}, doi = {10.1093/molbev/mst077}, pmid = {23619144}, issn = {1537-1719}, mesh = {Animals ; Asia ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Haplotypes ; Mitochondria/*genetics ; *Phylogeography ; Sequence Analysis, DNA ; Ursidae/*genetics ; }, abstract = {To further elucidate the migration history of the brown bears (Ursus arctos) on Hokkaido Island, Japan, we analyzed the complete mitochondrial DNA (mtDNA) sequences of 35 brown bears from Hokkaido, the southern Kuril Islands (Etorofu and Kunashiri), Sakhalin Island, and the Eurasian Continent (continental Russia, Bulgaria, and Tibet), and those of four polar bears. Based on these sequences, we reconstructed the maternal phylogeny of the brown bear and estimated divergence times to investigate the timing of brown bear migrations, especially in northeastern Eurasia. Our gene tree showed the mtDNA haplotypes of all 73 brown and polar bears to be divided into eight divergent lineages. The brown bear on Hokkaido was divided into three lineages (central, eastern, and southern). The Sakhalin brown bear grouped with eastern European and western Alaskan brown bears. Etorofu and Kunashiri brown bears were closely related to eastern Hokkaido brown bears and could have diverged from the eastern Hokkaido lineage after formation of the channel between Hokkaido and the southern Kuril Islands. Tibetan brown bears diverged early in the eastern lineage. Southern Hokkaido brown bears were closely related to North American brown bears.}, }
@article {pmid23615204, year = {2013}, author = {Seufferheld, MJ and Caetano-Anollés, G}, title = {Phylogenomics supports a cellularly structured urancestor.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {23}, number = {1-2}, pages = {178-191}, doi = {10.1159/000346552}, pmid = {23615204}, issn = {1660-2412}, support = {AI079478-02/AI/NIAID NIH HHS/United States ; }, mesh = {Archaea/cytology/genetics/metabolism ; Bacteria/cytology/genetics/metabolism ; *Biological Evolution ; *Cell Compartmentation ; Cell Membrane ; *Energy Metabolism ; Eukaryota/cytology/genetics/metabolism ; *Evolution, Molecular ; Genomics ; Organelles/metabolism/ultrastructure ; *Origin of Life ; Phylogeny ; }, abstract = {Cells and viruses are structured and harbor complex organization. This manifests in intra- and extracellular compartments such as reticuli and periplasmic spaces, storage and energy-harvesting organelles such as acidocalcisomes and mitochondria, and specialized structures that hold genomic repositories such as nuclei and capsids. Structural phylogenomic reconstruction of the protein repertoire of the common ancestor of life, the urancestor, suggests these entities that existed 2.9 billion years ago were not only complex from a structural and functional point of view, but were also cellularly structured. We also provide support to the existence of urancestral storage organelles that were analogous to acidocalcisomes. These cellular structures probably accumulated compounds that stored energy in their phosphoanhydride bonds, such as polyphosphates. These energy-rich compounds necessary for thioester and pyrophosphate intermediates would have channeled the abundant redox energy of early Earth to the early metabolic needs of the primordial cells. Our findings are compatible with a relatively complex urancestral cell and with abundant microfossil evidence supporting the existence of primordial microbial communities as far back as 3.4 billion years ago. Results highlight the centrality of the cellular compartment and bioenergetics in the early evolutionary stages of life.}, }
@article {pmid23615192, year = {2013}, author = {Arechaga, I}, title = {Membrane invaginations in bacteria and mitochondria: common features and evolutionary scenarios.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {23}, number = {1-2}, pages = {13-23}, doi = {10.1159/000346515}, pmid = {23615192}, issn = {1660-2412}, mesh = {Biological Evolution ; Cardiolipins/metabolism ; Cell Membrane/*physiology/*ultrastructure ; Cellular Structures/metabolism ; Escherichia coli/*ultrastructure ; Escherichia coli Proteins/metabolism ; Membrane Proteins/metabolism ; Mitochondria/metabolism/*ultrastructure ; Mitochondrial Membranes/*physiology/*ultrastructure ; }, abstract = {Nonphotosynthetic bacteria generally lack intracellular membranes (ICMs). However, large scale overproduction of membrane proteins in Escherichia coli can be accompanied by a massive proliferation of new ICMs in the cytoplasm. In some cases, like in the overexpression of the ATP synthase b subunit in E. coli, the morphology of these internal invaginations resembles that of the inner mitochondrial cristae. Moreover, the new ICMs have a higher content in cardiolipin than the bacterial inner and outer membranes. This review covers the features that seem to apply to membrane proliferation in bacteria and highlights the similarities with those behind the formation of the mitochondrial inner cristae.}, }
@article {pmid23612305, year = {2013}, author = {Brotherton, P and Haak, W and Templeton, J and Brandt, G and Soubrier, J and Jane Adler, C and Richards, SM and Der Sarkissian, C and Ganslmeier, R and Friederich, S and Dresely, V and van Oven, M and Kenyon, R and Van der Hoek, MB and Korlach, J and Luong, K and Ho, SYW and Quintana-Murci, L and Behar, DM and Meller, H and Alt, KW and Cooper, A and , }, title = {Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {1764}, pmid = {23612305}, issn = {2041-1723}, support = {079643/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Base Sequence ; Demography ; Evolution, Molecular ; Genetics, Population ; Genome, Human/*genetics ; Genome, Mitochondrial/*genetics ; Haplotypes/*genetics ; Humans ; Molecular Sequence Data ; *Phylogeny ; Principal Component Analysis ; Sequence Analysis, DNA ; Time Factors ; White People/*genetics ; }, abstract = {Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this 'real-time' genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.}, }
@article {pmid23610429, year = {2013}, author = {Wu, B and Novelli, J and Jiang, D and Dailey, HA and Landmann, F and Ford, L and Taylor, MJ and Carlow, CK and Kumar, S and Foster, JM and Slatko, BE}, title = {Interdomain lateral gene transfer of an essential ferrochelatase gene in human parasitic nematodes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {19}, pages = {7748-7753}, pmid = {23610429}, issn = {1091-6490}, support = {L30 DK096501/DK/NIDDK NIH HHS/United States ; R01 DK096051/DK/NIDDK NIH HHS/United States ; DK96501/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Animals, Genetically Modified ; Bayes Theorem ; Brugia malayi/*enzymology/genetics ; Caenorhabditis elegans/genetics ; Cloning, Molecular ; Escherichia coli/metabolism ; Exons ; Female ; Ferrochelatase/*genetics ; *Gene Transfer, Horizontal ; Genetic Complementation Test ; Genome ; Green Fluorescent Proteins/metabolism ; In Situ Hybridization ; Male ; Microscopy, Confocal ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA Interference ; }, abstract = {Lateral gene transfer events between bacteria and animals highlight an avenue for evolutionary genomic loss/gain of function. Herein, we report functional lateral gene transfer in animal parasitic nematodes. Members of the Nematoda are heme auxotrophs, lacking the ability to synthesize heme; however, the human filarial parasite Brugia malayi has acquired a bacterial gene encoding ferrochelatase (BmFeCH), the terminal step in heme biosynthesis. BmFeCH, encoded by a 9-exon gene, is a mitochondrial-targeted, functional ferrochelatase based on enzyme assays, complementation, and inhibitor studies. Homologs have been identified in several filariae and a nonfilarial nematode. RNAi and ex vivo inhibitor experiments indicate that BmFeCH is essential for viability, validating it as a potential target for filariasis control.}, }
@article {pmid23600852, year = {2013}, author = {Suraniti, E and Vajrala, VS and Goudeau, B and Bottari, SP and Rigoulet, M and Devin, A and Sojic, N and Arbault, S}, title = {Monitoring metabolic responses of single mitochondria within poly(dimethylsiloxane) wells: study of their endogenous reduced nicotinamide adenine dinucleotide evolution.}, journal = {Analytical chemistry}, volume = {85}, number = {10}, pages = {5146-5152}, doi = {10.1021/ac400494e}, pmid = {23600852}, issn = {1520-6882}, mesh = {Dimethylpolysiloxanes/*chemistry ; Microarray Analysis/*methods ; Mitochondria/*metabolism ; NAD/*metabolism ; Saccharomyces cerevisiae/cytology ; Spectrometry, Fluorescence ; }, abstract = {It is now demonstrated that mitochondria individually function differently because of specific energetic needs in cell compartments but also because of the genetic heterogeneity within the mitochondrial pool-network of a cell. Consequently, understanding mitochondrial functioning at the single organelle level is of high interest for biomedical research, therefore being a target for analyticians. In this context, we developed easy-to-build platforms of milli- to microwells for fluorescence microscopy of single isolated mitochondria. Poly(dimethylsiloxane) (PDMS) was determined to be an excellent material for mitochondrial deposition and observation of their NADH content. Because of NADH autofluorescence, the metabolic status of each mitochondrion was analyzed following addition of a respiratory substrate (stage 2), ethanol herein, and a respiratory inhibitor (stage 3), Antimycin A. Mean levels of mitochondrial NADH were increased by 32% and 62% under stages 2 and 3, respectively. Statistical studies of NADH value distributions evidenced different types of responses, at least three, to ethanol and Antimycin A within the mitochondrial population. In addition, we showed that mitochondrial ability to generate high levels of NADH, that is its metabolic performance, is not correlated either to the initial energetic state or to the respective size of each mitochondrion.}, }
@article {pmid23597031, year = {2013}, author = {Taylor-Brown, E and Hurd, H}, title = {The first suicides: a legacy inherited by parasitic protozoans from prokaryote ancestors.}, journal = {Parasites &amp; vectors}, volume = {6}, number = {}, pages = {108}, pmid = {23597031}, issn = {1756-3305}, mesh = {*Apoptosis ; Bacteria/genetics ; Biological Evolution ; Leishmania/genetics/*physiology ; Mitochondria/metabolism ; Phenotype ; Plasmodium/genetics/*physiology ; Trypanosoma/genetics/*physiology ; }, abstract = {It is more than 25 years since the first report that a protozoan parasite could die by a process resulting in a morphological phenotype akin to apoptosis. Since then these phenotypes have been observed in many unicellular parasites, including trypanosomatids and apicomplexans, and experimental evidence concerning the molecular pathways that are involved is growing. These observations support the view that this form of programmed cell death is an ancient one that predates the evolution of multicellularity. Here we review various hypotheses that attempt to explain the origin of apoptosis, and look for support for these hypotheses amongst the parasitic protists as, with the exception of yeast, most of the work on death mechanisms in unicellular organisms has focussed on them. We examine the role that addiction modules may have played in the original eukaryote cell and the part played by mitochondria in the execution of present day cells, looking for examples from Leishmania spp. Trypanosoma spp. and Plasmodium spp. In addition, the expanding knowledge of proteases, nucleases and other molecules acting in protist execution pathways has enabled comparisons to be made with extant Archaea and bacteria and with biochemical pathways that evolved in metazoans. These comparisons lend support to the original sin hypothesis but also suggest that present-day death pathways may have had multifaceted beginnings.}, }
@article {pmid23595059, year = {2013}, author = {Howard, MJ and Liu, X and Lim, WH and Klemm, BP and Fierke, CA and Koutmos, M and Engelke, DR}, title = {RNase P enzymes: divergent scaffolds for a conserved biological reaction.}, journal = {RNA biology}, volume = {10}, number = {6}, pages = {909-914}, pmid = {23595059}, issn = {1555-8584}, support = {R01 GM055387/GM/NIGMS NIH HHS/United States ; }, mesh = {Arabidopsis/enzymology/genetics/metabolism ; Arabidopsis Proteins/*chemistry/genetics/*metabolism ; Catalytic Domain ; Chloroplasts/*enzymology/genetics/metabolism ; Evolution, Molecular ; Mitochondria/*enzymology/genetics/metabolism ; RNA Precursors/chemistry/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Catalytic/genetics/metabolism ; RNA, Transfer/genetics/*metabolism ; Ribonuclease P/*chemistry/genetics/*metabolism ; }, abstract = {Ribonuclease P (RNase P) catalyzes the maturation of the 5' end of precursor-tRNAs (pre-tRNA) and is conserved in all domains of life. However, the composition of RNase P varies from bacteria to archaea and eukarya, making RNase P one of the most diverse enzymes characterized. Most known RNase P enzymes contain a large catalytic RNA subunit that associates with one to 10 proteins. Recently, a protein-only form of RNase P was discovered in mitochondria and chloroplasts of many higher eukaryotes. This proteinaceous RNase P (PRORP) represents a new class of metallonucleases. Here we discuss our recent crystal structure of PRORP1 from Arabidopsis thaliana and speculate on the reasons for the replacement of catalytic RNA by a protein catalyst. We conclude, based on an analysis of the catalytic efficiencies of ribonucleoprotein (RNP) and PRORP enzymes, that the need for greater catalytic efficiency is most likely not the driving force behind the replacement of the RNA with a protein catalyst. The emergence of a protein-based RNase P more likely reflects the increasing complexity of the biological system, including difficulties in importation into organelles and vulnerability of organellar RNAs to cleavage.}, }
@article {pmid23584995, year = {2013}, author = {Mavrianos, J and Berkow, EL and Desai, C and Pandey, A and Batish, M and Rabadi, MJ and Barker, KS and Pain, D and Rogers, PD and Eugenin, EA and Chauhan, N}, title = {Mitochondrial two-component signaling systems in Candida albicans.}, journal = {Eukaryotic cell}, volume = {12}, number = {6}, pages = {913-922}, pmid = {23584995}, issn = {1535-9786}, support = {R01AI058145/AI/NIAID NIH HHS/United States ; R01 MH096625/MH/NIMH NIH HHS/United States ; AG030504/AG/NIA NIH HHS/United States ; MH076679/MH/NIMH NIH HHS/United States ; K01 MH076679/MH/NIMH NIH HHS/United States ; R01 AG030504/AG/NIA NIH HHS/United States ; R01 AI058145/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Apoptosis ; Bacterial Proteins/*genetics/metabolism ; Biological Evolution ; Candida albicans/*genetics/metabolism/ultrastructure ; Fungal Proteins/*genetics/metabolism ; Gene Deletion ; Gene Expression Regulation, Fungal ; Heat-Shock Proteins/deficiency/*genetics ; Histidine Kinase ; Mitochondria/*metabolism/ultrastructure ; Molecular Sequence Data ; Phylogeny ; Protein Kinases/deficiency/*genetics ; Protein Transport ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; *Signal Transduction ; }, abstract = {Two-component signal transduction pathways are one of the primary means by which microorganisms respond to environmental signals. These signaling cascades originated in prokaryotes and were inherited by eukaryotes via endosymbiotic lateral gene transfer from ancestral cyanobacteria. We report here that the nuclear genome of the pathogenic fungus Candida albicans contains elements of a two-component signaling pathway that seem to be targeted to the mitochondria. The C. albicans two-component response regulator protein Srr1 (stress response regulator 1) contains a mitochondrial targeting sequence at the N terminus, and fluorescence microscopy reveals mitochondrial localization of green fluorescent protein-tagged Srr1. Moreover, phylogenetic analysis indicates that C. albicans Srr1 is more closely related to histidine kinases and response regulators found in marine bacteria than are other two-component proteins present in the fungi. These data suggest conservation of this protein during the evolutionary transition from endosymbiont to a subcellular organelle. We used microarray analysis to determine whether the phenotypes observed with a srr1Δ/Δ mutant could be correlated with gene transcriptional changes. The expression of mitochondrial genes was altered in the srr1Δ/Δ null mutant in comparison to their expression in the wild type. Furthermore, apoptosis increased significantly in the srr1Δ/Δ mutant strain compared to the level of apoptosis in the wild type, suggesting the activation of a mitochondrion-dependent apoptotic cell death pathway in the srr1Δ/Δ mutant. Collectively, this study shows for the first time that a lower eukaryote like C. albicans possesses a two-component response regulator protein that has survived in mitochondria and regulates a subset of genes whose functions are associated with the oxidative stress response and programmed cell death (apoptosis).}, }
@article {pmid23580434, year = {2013}, author = {Sehrawat, A and Gupta, R and Deswal, R}, title = {Nitric oxide-cold stress signalling cross-talk, evolution of a novel regulatory mechanism.}, journal = {Proteomics}, volume = {13}, number = {12-13}, pages = {1816-1835}, doi = {10.1002/pmic.201200445}, pmid = {23580434}, issn = {1615-9861}, mesh = {*Cold Shock Proteins and Peptides ; *Cold-Shock Response ; *Nitric Oxide ; Plant Proteins ; Proteomics ; *Signal Transduction ; }, abstract = {Plants enhance their cold stress tolerance by cold acclimation, a process which results in vast reprogramming of transcriptome, proteome and metabolome. Evidence suggests nitric oxide (NO) production during cold stress which regulates genes (especially the C-repeat binding factor (CBF) cold stress signalling pathway), diverse proteins including transcription factors (TFs) and phosphosphingolipids. About 59% (redox), 50% (defence/stress) and 30% (signalling) cold responsive proteins are modulated by NO-based post translational modifications (PTMs) namely S-nitrosylation, tyrosine nitration and S-glutathionylation, suggesting a cross-talk between NO and cold. Analysis of cold stress responsive deep proteome in apoplast, mitochondria, chloroplast and nucleus suggested continuation of this cross-talk in sub-cellular systems. Modulation of cold responsive proteins by these PTMs right from cytoskeletal elements in plasma membrane to TFs in nucleus suggests a novel regulation of cold stress signalling. NO-mediated altered protein transport in nucleus seems an important stress regulatory mechanism. This review addresses the NO and cold stress signalling cross-talk to present the overview of this novel regulatory mechanism.}, }
@article {pmid23575541, year = {2013}, author = {Zhang, CQ and Chen, BB and Chen, YY and Liu, XJ and Zheng, J and Gao, JJ and Huang, SY and Nan, BY and Zhang, YY and Yu, X and Guan, MX}, title = {[Prevalence of common genetic mutations and clinical characteristics analysis in patients at different ages with nonsyndromic hearing impairment].}, journal = {Yi chuan = Hereditas}, volume = {35}, number = {3}, pages = {352-358}, doi = {10.3724/sp.j.1005.2013.00352}, pmid = {23575541}, issn = {0253-9772}, mesh = {Adolescent ; Adult ; Age Factors ; Child ; Child, Preschool ; Connexin 26 ; Connexins/genetics ; DNA, Mitochondrial/genetics ; Female ; Genetic Testing ; Hearing Loss, Sensorineural/*diagnosis/*genetics ; Humans ; Infant ; Male ; Middle Aged ; *Mutation ; Mutation Rate ; Young Adult ; }, abstract = {To evaluate the correlation between genetic mutations and the age in nonsyndromic hearing impairment (NSHI) and the clinical characteristics of NSHI, 215 patients with NSHI were enrolled between April 2006 and April 2012. All patients were divided into four groups according to ages of hearing loss onset and clinic presentation (0-3, 3-6, 6-18 and 18+ years). The mutations of GJB2 and mitochondria DNA (mtDNA) 1555G/C1494T were screened from peripheral blood samples in each age group. The prevalence of mutations and the age ratio were obtained. The study showed that 18.14% of all patients were found to have GJB2 mutations and 11.16% were found to have mtDNA A1555G/C1494T mutations. The prevalence of GJB2 mutation in adult group (5.26%) was lower than juvenile group who sought medical attention at 0-18 years of age (22.36%), while the prevalence of mtDNA A1555G/C1494T in adult group (31.48%) was higher than juvenile group (4.97%). Significant differences in the prevalence of GJB2 (χ2=7.108, P=0.008) and mtDNA A1555G/C1494T (χ2=20.852, P=0.000) were observed in both of two groups. The prevalence of GJB2 mutations between adult and juvenile groups according to ages of hearing loss onset was statistically significant different (0%, 20.10%, respectively, and P=0.023), while the prevalence of mtDNA A1555G/C1494T mutations was not different (14.29%, 11.34%, respectively, and P=0.698). The onset age of 66.67% of patients with GJB2 mutations was less than 1 year old, while the onset of patients with mtDNA A1555G/C1494T mutations could be found at any age group. Different standardizations of hearing loss could also show different results. These data strongly suggest that most of GJB2 mutations are found in congenital deafness and mtDNA A1555G/C1494T mutations mainly represent acquired deafness, which can be induced or aggravated by aminoglycoside antibiotics in all age groups and should be tested mainly ranging from 4 kHz to 8 kHz. Both newborn hearing screening and genetic testing are important to find early deafness.}, }
@article {pmid23575228, year = {2013}, author = {van Bon, BW and Oortveld, MA and Nijtmans, LG and Fenckova, M and Nijhof, B and Besseling, J and Vos, M and Kramer, JM and de Leeuw, N and Castells-Nobau, A and Asztalos, L and Viragh, E and Ruiter, M and Hofmann, F and Eshuis, L and Collavin, L and Huynen, MA and Asztalos, Z and Verstreken, P and Rodenburg, RJ and Smeitink, JA and de Vries, BB and Schenck, A}, title = {CEP89 is required for mitochondrial metabolism and neuronal function in man and fly.}, journal = {Human molecular genetics}, volume = {22}, number = {15}, pages = {3138-3151}, doi = {10.1093/hmg/ddt170}, pmid = {23575228}, issn = {1460-2083}, mesh = {Animals ; Cell Cycle Proteins/genetics/*metabolism ; Child ; Chromosomes, Human, Pair 19 ; Cytochrome-c Oxidase Deficiency/genetics/metabolism ; Cytosol ; Disease Models, Animal ; Drosophila/genetics/*metabolism ; Drosophila Proteins/genetics/*metabolism ; Female ; Gene Deletion ; Gene Expression ; Gene Knockdown Techniques ; Homozygote ; Humans ; Learning ; Microtubule-Associated Proteins ; Mitochondria/genetics/*metabolism ; Mutation ; Neurons/*metabolism ; Organ Specificity/genetics ; Polymorphism, Single Nucleotide ; Protein Transport ; Synapses/genetics/metabolism ; }, abstract = {It is estimated that the human mitochondrial proteome consists of 1000-1500 distinct proteins. The majority of these support the various biochemical pathways that are active in these organelles. Individuals with an oxidative phosphorylation disorder of unknown cause provide a unique opportunity to identify novel genes implicated in mitochondrial biology. We identified a homozygous deletion of CEP89 in a patient with isolated complex IV deficiency, intellectual disability and multisystemic problems. CEP89 is a ubiquitously expressed and highly conserved gene of unknown function. Immunocytochemistry and cellular fractionation experiments showed that CEP89 is present both in the cytosol and in the mitochondrial intermembrane space. Furthermore, we ascertained in vitro that downregulation of CEP89 resulted in a severe decrease in complex IV in-gel activity and altered mobility, suggesting that the complex is aberrantly formed. Two-dimensional BN-SDS gel analysis revealed that CEP89 associates with a high-molecular weight complex. Together, these data confirm a role for CEP89 in mitochondrial metabolism. In addition, we modeled CEP89 loss of function in Drosophila. Ubiquitous knockdown of fly Cep89 decreased complex IV activity and resulted in complete lethality. Furthermore, Cep89 is required for mitochondrial integrity, membrane depolarization and synaptic transmission of photoreceptor neurons, and for (sub)synaptic organization of the larval neuromuscular junction. Finally, we tested neuronal Cep89 knockdown flies in the light-off jump reflex habituation assay, which revealed its role in learning. We conclude that CEP89 proteins play an important role in mitochondrial metabolism, especially complex IV activity, and are required for neuronal and cognitive function across evolution.}, }
@article {pmid23572355, year = {2013}, author = {Xu, L and Fan, Y and Jiang, XL and Yao, YG}, title = {[Molecular evidence on the phylogenetic position of tree shrews].}, journal = {Dong wu xue yan jiu = Zoological research}, volume = {34}, number = {2}, pages = {70-76}, doi = {10.3724/SP.J.1141.2013.02070}, pmid = {23572355}, issn = {0254-5853}, mesh = {Animals ; Humans ; *Phylogeny ; Primates/classification/genetics/growth &amp; development/physiology ; Tupaiidae/*classification/*genetics/growth &amp; development/physiology ; }, abstract = {The tree shrew is currently located in the Order Scandentia and is widely distributed in Southeast Asia, South Asia, and South China. Due to its unique characteristics, such as small body size, high brain-to-body mass ratio, short reproductive cycle and life span, and low-cost of maintenance, the tree shrew has been proposed as an alternative experimental animal to primates in biomedical research. However, there is unresolved debate regarding the phylogenetic affinity of tree shrews to primates and their phylogenetic position in Euarchontoglires. To help settle this debate, we summarized the available molecular evidence on the phylogenetic position of the tree shrew. Most nuclear DNA data, including recent genome data, suggested that the tree shrew belongs to the Euarchonta clade harboring primates and flying lemurs (colugos). However, analyses of mitochondrial DNA (mtDNA) data suggested a close relationship to lagomorphs and rodents. These different clustering patterns could be explained by nuclear gene data and mtDNA data discrepancies, as well as the different phylogenetic approaches used in previous studies. Taking all available conclusions together, the robust data from whole genome of this species supports tree shrews being genetically closely related to primates.}, }
@article {pmid23563972, year = {2013}, author = {Mach, J and Poliak, P and Matusková, A and Zárský, V and Janata, J and Lukes, J and Tachezy, J}, title = {An Advanced System of the Mitochondrial Processing Peptidase and Core Protein Family in Trypanosoma brucei and Multiple Origins of the Core I Subunit in Eukaryotes.}, journal = {Genome biology and evolution}, volume = {5}, number = {5}, pages = {860-875}, pmid = {23563972}, issn = {1759-6653}, mesh = {Amino Acid Sequence ; Base Sequence ; Eukaryota/*genetics ; Evolution, Molecular ; Metalloendopeptidases/*genetics ; Mitochondria/genetics ; Mitochondrial Proteins/*genetics/metabolism ; Phylogeny ; Trypanosoma brucei brucei/*genetics ; Mitochondrial Processing Peptidase ; }, abstract = {Mitochondrial processing peptidase (MPP) consists of α and β subunits that catalyze the cleavage of N-terminal mitochondrial-targeting sequences (N-MTSs) and deliver preproteins to the mitochondria. In plants, both MPP subunits are associated with the respiratory complex bc1, which has been proposed to represent an ancestral form. Subsequent duplication of MPP subunits resulted in separate sets of genes encoding soluble MPP in the matrix and core proteins (cp1 and cp2) of the membrane-embedded bc1 complex. As only α-MPP was duplicated in Neurospora, its single β-MPP functions in both MPP and bc1 complexes. Herein, we investigated the MPP/core protein family and N-MTSs in the kinetoplastid Trypanosoma brucei, which is often considered one of the most ancient eukaryotes. Analysis of N-MTSs predicted in 336 mitochondrial proteins showed that trypanosomal N-MTSs were comparable with N-MTSs from other organisms. N-MTS cleavage is mediated by a standard heterodimeric MPP, which is present in the matrix of procyclic and bloodstream trypanosomes, and its expression is essential for the parasite. Distinct Genes encode cp1 and cp2, and in the bloodstream forms the expression of cp1 is downregulated along with the bc1 complex. Phylogenetic analysis revealed that all eukaryotic lineages include members with a Neurospora-type MPP/core protein family, whereas cp1 evolved independently in metazoans, some fungi and kinetoplastids. Evolution of cp1 allowed the independent regulation of respiration and protein import, which is essential for the procyclic and bloodstream forms of T. brucei. These results indicate that T. brucei possesses a highly derived MPP/core protein family that likely evolved in response to its complex life cycle and does not appear to have an ancient character proposed earlier for this eukaryote.}, }
@article {pmid23563965, year = {2013}, author = {Levin, L and Zhidkov, I and Gurman, Y and Hawlena, H and Mishmar, D}, title = {Functional recurrent mutations in the human mitochondrial phylogeny: dual roles in evolution and disease.}, journal = {Genome biology and evolution}, volume = {5}, number = {5}, pages = {876-890}, pmid = {23563965}, issn = {1759-6653}, mesh = {Codon/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Humans ; Mitochondria/*genetics ; Mutation/*genetics ; Phylogeny ; RNA/genetics ; Selection, Genetic ; }, abstract = {Mutations frequently reoccur in the human mitochondrial DNA (mtDNA). However, it is unclear whether recurrent mtDNA nodal mutations (RNMs), that is, recurrent mutations in stems of unrelated phylogenetic nodes, are functional and hence selectively constrained. To answer this question, we performed comprehensive parsimony and maximum likelihood analyses of 9,868 publicly available whole human mtDNAs revealing 1,606 single nodal mutations (SNMs) and 679 RNMs. We then evaluated the potential functionality of synonymous, nonsynonymous and RNA SNMs and RNMs. For synonymous mutations, we have implemented the Codon Adaptation Index. For nonsynonymous mutations, we assessed evolutionary conservation, and employed previously described pathogenicity score assessment tools. For RNA genes' mutations, we designed a bioinformatic tool which compiled evolutionary conservation and potential effect on RNA structure. While comparing the functionality scores of nonsynonymous and RNA SNMs and RNMs with those of disease-causing mtDNA mutations, we found significant difference (P < 0.001). However, 24 RNMs and 67 SNMs had comparable values with disease-causing mutations reflecting their potential function thus being the best candidates to participate in adaptive events of unrelated lineages. Strikingly, some functional RNMs occurred in unrelated mtDNA lineages that independently altered susceptibility to the same diseases, thus suggesting common functionality. To our knowledge, this is the most comprehensive analysis of selective signatures in the mtDNA not only within proteins but also within RNA genes. For the first time, we discover virtually all positively selected RNMs in our phylogeny while emphasizing their dual role in past evolutionary events and in disease today.}, }
@article {pmid23557683, year = {2013}, author = {Palinauskas, V and Iezhova, TA and Križanauskienė, A and Markovets, MY and Bensch, S and Valkiūnas, G}, title = {Molecular characterization and distribution of Haemoproteus minutus (Haemosporida, Haemoproteidae): a pathogenic avian parasite.}, journal = {Parasitology international}, volume = {62}, number = {4}, pages = {358-363}, doi = {10.1016/j.parint.2013.03.006}, pmid = {23557683}, issn = {1873-0329}, mesh = {Animals ; Bird Diseases/epidemiology/*parasitology ; Birds/blood/*parasitology ; Cytochromes b/genetics ; DNA, Protozoan/genetics ; Haemosporida/classification/*genetics ; Mitochondria/genetics ; Phylogeny ; *Protozoan Infections, Animal ; }, abstract = {Recently, the lineage hTURDUS2 of Haemoproteus minutus (Haemosporida, Haemoproteidae) was reported to cause mortality in captive parrots. This parasite lineage is widespread and prevalent in the blackbird Turdus merula throughout its entire distribution range. Species identity of other closely related lineages recently reported in dead parrots remains unclear, but will be important to determine for a better understanding of the epidemiology of haemoproteosis. Using polymerase chain reaction (PCR)-based and microscopic methods, we analyzed 265 blood samples collected from 52 species of wild birds in Eurasia (23 samples from Kamchatka Peninsula, 73 from Sakhalin Island, 150 from Ekaterinburg and 19 from Irkutsk regions of Russia). Single infections of the lineages hTURDUS2 (hosts are redwing Turdus iliacus and fieldfare Turdus pilaris), hTUPHI1 (song thrush Turdus philomelos) and hTUCHR01 (fieldfare, redwing, song thrush and brown-headed thrush Turdus chysolaus) were detected. We identified species of these haemoproteids based on morphology of their blood stages and conclude that these lineages belong to H. minutus, a widespread parasite of different species of thrushes (genus Turdus), which serve as reservoir hosts of this haemoproteid infection. Phylogenetic analysis shows that the lineages hTURDUS2, hTUCHR01 and hTUPHI1 of H. minutus are closely related to Haemoproteus pallidus (lineages hPFC1 and hCOLL2), Haemoproteus pallidulus (hSYAT03), and Haemoproteus sp. (hMEUND3); genetic distance among their mitochondrial cytochrome b (cyt b) lineages is small (<1% or<4 nucleotides). All these blood parasites are different in many morphological characters, but are similar due to one feature, which is the pale staining of their macrogametocytes' cytoplasm with Giemsa. Because of the recent publications about mortality caused by the lineages hTUPHI1 and hTURDUS2 of H. minutus in captive parrots in Europe, H. minutus and the closely related H. pallidus and H. pallidulus are worth more attention as these are possible agents of haemoproteosis in exotic birds. The present study provides barcodes for molecular detection of different lineages of H. minutus, and extends information about the distribution of this blood parasite.}, }
@article {pmid23555709, year = {2013}, author = {Seenivasan, R and Sausen, N and Medlin, LK and Melkonian, M}, title = {Picomonas judraskeda gen. et sp. nov.: the first identified member of the Picozoa phylum nov., a widespread group of picoeukaryotes, formerly known as 'picobiliphytes'.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e59565}, pmid = {23555709}, issn = {1932-6203}, mesh = {Cell Movement ; Eukaryota/cytology/genetics/*isolation &amp; purification/ultrastructure ; Flow Cytometry ; Microscopy, Electron ; Mitochondria/metabolism ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; }, abstract = {In 2007, a novel, putatively photosynthetic picoeukaryotic lineage, the 'picobiliphytes', with no known close eukaryotic relatives, was reported from 18S environmental clone library sequences and fluorescence in situ hybridization. Although single cell genomics later showed these organisms to be heterotrophic rather than photosynthetic, until now this apparently widespread group of pico-(or nano-)eukaryotes has remained uncultured and the organisms could not be formally recognized. Here, we describe Picomonas judraskeda gen. et sp. nov., from marine coastal surface waters, which has a 'picobiliphyte' 18S rDNA signature. Using vital mitochondrial staining and cell sorting by flow cytometry, a single cell-derived culture was established. The cells are biflagellate, 2.5-3.8×2-2.5 µm in size, lack plastids and display a novel stereotypic cycle of cell motility (described as the "jump, drag, and skedaddle"-cycle). They consist of two hemispherical parts separated by a deep cleft, an anterior part that contains all major cell organelles including the flagellar apparatus, and a posterior part housing vacuoles/vesicles and the feeding apparatus, both parts separated by a large vacuolar cisterna. From serial section analyses of cells, fixed at putative stages of the feeding cycle, it is concluded that cells are not bacterivorous, but feed on small marine colloids of less than 150 nm diameter by fluid-phase, bulk flow endocytosis. Based on the novel features of cell motility, ultrastructure and feeding, and their isolated phylogenetic position, we establish a new phylum, Picozoa, for Picomonas judraskeda, representing an apparently widespread and ecologically important group of heterotrophic picoeukaryotes, formerly known as 'picobiliphytes'.}, }
@article {pmid23551461, year = {2013}, author = {Lambert, SM and Geneva, AJ and Luke Mahler, D and Glor, RE}, title = {Using genomic data to revisit an early example of reproductive character displacement in Haitian Anolis lizards.}, journal = {Molecular ecology}, volume = {22}, number = {15}, pages = {3981-3995}, doi = {10.1111/mec.12292}, pmid = {23551461}, issn = {1365-294X}, mesh = {Adaptation, Biological/genetics ; Amplified Fragment Length Polymorphism Analysis ; Animals ; DNA, Mitochondrial/analysis ; Gene Flow/*genetics ; Genetic Speciation ; *Genetic Variation ; Haiti ; Lizards/*genetics ; Mitochondria/*genetics ; NADH Dehydrogenase/genetics ; *Reproductive Isolation ; Selection, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The pattern of reproductive character displacement (RCD)-in which traits associated with reproductive isolation are more different where two species occur together than where they occur in isolation-is frequently attributed to reinforcement, a process during which natural selection acting against maladaptive mating events leads to enhanced prezygotic isolation between species or incipient species. One of the first studies of RCD to include molecular genetic data was described 40 years ago in a complex of Haitian trunk anole lizards using a small number of allozyme loci. In this example, Anolis caudalis appears to experience divergence in the color and pattern of an extensible throat fan, or dewlap, in areas of contact with closely related species at the northern and southern limits of its range. However, this case study has been largely overlooked for decades; meanwhile, explanations for geographic variation in dewlap color and pattern have focused primarily on adaptation to local signalling environments. We reinvestigate this example using amplified fragment length polymorphism (AFLP) genome scans, mtDNA sequence data, information on dewlap phenotypes and GIS data on environmental variation to test the hypothesis of RCD generated by reinforcement in Haitian trunk anoles. Together, our phenotypic and genetic results are consistent with RCD at the southern and northern limits of the range of A. caudalis. We evaluate the evidence for reinforcement as the explanation for RCD in Haitian trunk anoles, consider alternative explanations and provide suggestions for future work on the relationship between dewlap variation and speciation in Haitian trunk anoles.}, }
@article {pmid23550759, year = {2013}, author = {Marden, JH and Fescemyer, HW and Schilder, RJ and Doerfler, WR and Vera, JC and Wheat, CW}, title = {Genetic variation in HIF signaling underlies quantitative variation in physiological and life-history traits within lowland butterfly populations.}, journal = {Evolution; international journal of organic evolution}, volume = {67}, number = {4}, pages = {1105-1115}, doi = {10.1111/evo.12004}, pmid = {23550759}, issn = {1558-5646}, mesh = {Aging ; Alleles ; Altitude ; Animals ; Butterflies/*genetics/metabolism ; Ecosystem ; Flight, Animal ; Genes, Insect ; *Genetic Variation ; Hypoxia-Inducible Factor 1/*genetics/metabolism ; Insect Proteins/genetics/metabolism ; Mitochondria, Muscle/metabolism ; Muscle, Skeletal/metabolism/physiology ; Population/genetics ; Signal Transduction/*genetics ; Succinate Dehydrogenase/genetics/metabolism ; Succinic Acid/metabolism ; Trachea/physiology ; Transcription, Genetic ; }, abstract = {Oxygen conductance to the tissues determines aerobic metabolic performance in most eukaryotes but has cost/benefit tradeoffs. Here we examine in lowland populations of a butterfly a genetic polymorphism affecting oxygen conductance via the hypoxia-inducible factor (HIF) pathway, which senses intracellular oxygen and controls the development of oxygen delivery networks. Genetically distinct clades of Glanville fritillary (Melitaea cinxia) across a continental scale maintain, at intermediate frequencies, alleles in a metabolic enzyme (succinate dehydrogenase, SDH) that regulates HIF-1α. One Sdhd allele was associated with reduced SDH activity rate, twofold greater cross-sectional area of tracheoles in flight muscle, and better flight performance. Butterflies with less tracheal development had greater post-flight hypoxia signaling, swollen &amp; disrupted mitochondria, and accelerated aging of flight metabolic performance. Allelic associations with metabolic and aging phenotypes were replicated in samples from different clades. Experimentally elevated succinate in pupae increased the abundance of HIF-1α and expression of genes responsive to HIF activation, including tracheal morphogenesis genes. These results indicate that the hypoxia inducible pathway, even in lowland populations, can be an important axis for genetic variation underlying intraspecific differences in oxygen delivery, physiological performance, and life history.}, }
@article {pmid23545131, year = {2013}, author = {Conceição, PA and Crainey, JL and Almeida, TP and Shelley, AJ and Luz, SL}, title = {New molecular identifiers for Simulium limbatum and Simulium incrustatum s.l. and the detection of genetic substructure with potential implications for onchocerciasis epidemiology in the Amazonia focus of Brazil.}, journal = {Acta tropica}, volume = {127}, number = {2}, pages = {118-125}, doi = {10.1016/j.actatropica.2013.03.012}, pmid = {23545131}, issn = {1873-6254}, mesh = {Animals ; Brazil/epidemiology ; Cytochromes/genetics ; Female ; Gene Expression Regulation ; Genetic Markers ; Humans ; Insect Vectors/genetics/parasitology ; Mitochondria/genetics ; Onchocerciasis/*epidemiology ; Phylogeny ; Simuliidae/*genetics ; Species Specificity ; }, abstract = {The Amazonia onchocerciasis focus of southern Venezuela and northern Brazil is the larger of the two remaining Latin American onchocerciasis foci where disease transmission still occurs and is often regarded as the most challenging of all the Latin American foci to eliminate onchocerciasis. The site is home to a population of over 20,000 semi-nomadic, hunter-gatherer Yanomami people and is made-up of a mosaic of rainforest and savannah ecologies, which are influenced by the area's undulating terrain and rich geological diversity. At least six blackfly vectors have been implicated in onchocerciasis transmission in this focus; however, because of the difficulty in their routine identification the relative importance of each has been obscured. Simulium limbatum and Simulium incrustatum s.l. have both been recorded as vectors in the Amazonia focus, but they are difficult to discriminate morphologically and thus the ecological range of these species, and indeed the presence of S. limbatum in the Amazonia focus at all, have remained controversial. In the work described here, we report 15 S. incrustatum s.l. CO1 sequences and 27 S. limbatum sequences obtained from field-caught adult female blackflies collected from forest and savannah localities, inside and just outside the Amazonia focus. Phylogenetic analysis with the sequences generated in this study, showed that both the S. limbatum and the S. incrustatum s.l. CO1 sequences obtained (even from specimens living in sympatry) all fell into discrete species-specific bootstrap-supported monophyletic groups and thus confirmed the utility of the CO1 gene for identifying both these species inside the Amazonia focus. As the S. limbatum-exclusive cluster included CO1 sequences obtained from forest-caught and morphologically identified specimens these results provide the clearest evidence yet of the presence of S. limbatum inside the Amazonia focus. The question, however, of whether S. limbatum is actually a vector in the focus still remains unanswered as the data presented here also suggest that S. limbatum found in the savannahs adjacent to, but outside the Amazonia focus (and which represent the only S. limbatum population to be unambiguously incriminated as a host of Onchocerca volvulus), are genetically distinct from those living inside the focus. These findings highlight the need for a clearer picture of the vector taxonomy inside the Amazonia onchocerciasis focus.}, }
@article {pmid23542002, year = {2013}, author = {Dunz, AR and Schliewen, UK}, title = {Molecular phylogeny and revised classification of the haplotilapiine cichlid fishes formerly referred to as "Tilapia".}, journal = {Molecular phylogenetics and evolution}, volume = {68}, number = {1}, pages = {64-80}, doi = {10.1016/j.ympev.2013.03.015}, pmid = {23542002}, issn = {1095-9513}, mesh = {Africa, Eastern ; Africa, Western ; Animals ; Cell Nucleus/chemistry/genetics ; DNA, Mitochondrial/*classification/genetics ; Genetic Speciation ; Mitochondria/chemistry/genetics ; NADH Dehydrogenase/*classification/genetics ; Nuclear Proteins/*classification/genetics ; Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S/*classification/genetics ; Tilapia/*classification/genetics ; }, abstract = {African cichlids formerly referred to as "Tilapia" represent a paraphyletic species assemblage belonging to the so called haplotilapiine lineage which gave rise to the spectacular East African cichlid radiations (EARs) as well as to globally important aquaculture species. We present a comprehensive molecular phylogeny of representative haplotilapiine cichlids, combining in one data set four mitochondrial and five nuclear loci for 76 species, and compare it with phylogenetic information of a second data set of 378 mitochondrial ND2 haplotypes representing almost all important "Tilapia" or Tilapia-related lineages as well as most EAR lineages. The monophyly of haplotilapiines is supported, as is the nested sister group relationship of Etia and mouthbrooding tilapiines with the remaining haplotilapiines. The latter are consistently placed in eight monophyletic clades over all datasets and analyses, but several dichotomous phylogenetic relationships appear compromised by cytonuclear discordant phylogenetic signal. Based on these results as well as on extensive morphological evidence we propose a novel generic and suprageneric classification including a (re-)diagnosis of 20 haplotilapiine cichlid genera and nine tribes. New tribes are provided for the former subgenera Coptodon Gervais, 1853, HeterotilapiaRegan, 1920 and PelmatolapiaThys van den Audenaerde, 1969, in addition for "Tilapia" joka, Tilapia sensu stricto and Chilochromis, Etia, Steatocranus sensu stricto, the mouthbrooding tilapiines and for a clade of West African tilapiines.}, }
@article {pmid23541838, year = {2013}, author = {Mariguela, TC and Ortí, G and Avelino, GS and Abe, KT and Oliveira, C}, title = {Composition and interrelationships of a large Neotropical freshwater fish group, the subfamily Cheirodontinae (Characiformes: Characidae): a case study based on mitochondrial and nuclear DNA sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {68}, number = {1}, pages = {23-34}, doi = {10.1016/j.ympev.2013.03.011}, pmid = {23541838}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/chemistry/*genetics ; Characidae/*classification/genetics ; Cytochromes b/classification/genetics ; DNA, Mitochondrial/*classification/genetics ; DNA-Binding Proteins/classification/genetics ; Fresh Water ; Genetic Speciation ; Homeodomain Proteins/classification/genetics ; Mitochondria/chemistry/*genetics ; Myosin Heavy Chains/classification/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*classification/genetics ; }, abstract = {Characidae is the most species-rich family of freshwater fishes in the order Characiformes, with more than 1000 valid species that correspond to approximately 55% of the order. Few hypotheses about the composition and internal relationships within this family are available and most fail to reach an agreement. Among Characidae, Cheirodontinae is an emblematic group that includes 18 genera (1 fossil) and approximately 60 described species distributed throughout the Neotropical region. The taxonomic and systematic history of Cheirodontinae is complex, and only two hypotheses about the internal relationships in this subfamily have been reported to date. In the present study, we test the composition and relationships of fishes assigned to Cheirodontinae based on a broad taxonomic sample that also includes some characid incertae sedis taxa that were previously considered to be part of Cheirodontinae. We present phylogenetic analyses of a large molecular dataset of mitochondrial and nuclear DNA sequences. Our results reject the monophyly of Cheirodontinae as previously conceived, as well as the tribes Cheirodontini and Compsurini, and the genera Cheirodon, Compsura, Leptagoniates, Macropsobrycon, Odontostilbe, and Serrapinnus. On the basis of these results we propose: (1) the exclusion of Amazonspinther and Spintherobolus from the subfamily Cheirodontinae since they are the sister-group of all remaining Characidae; (2) the removal of Macropsobrycon xinguensis of the genus Macropsobrycon; (3) the removal of Leptagoniates pi of the genus Leptagoniates; (4) the inclusion of Leptagoniates pi in the subfamily Cheirodontinae; (5) the removal of Cheirodon stenodon of the genus Cheirodon and its inclusion in the subfamily Cheirodontinae under a new genus name; (6) the need to revise the polyphyletic genera Compsura, Odontostilbe, and Serrapinnus; and (7) the division of Cheirodontinae in three newly defined monophyletic tribes: Cheirodontini, Compsurini, and Pseudocheirodontini. Our results suggest that our knowledge about the largest Neotropical fish family, Characidae, still is incipient.}, }
@article {pmid23541082, year = {2013}, author = {Khalifa, ME and Pearson, MN}, title = {Molecular characterization of three mitoviruses co-infecting a hypovirulent isolate of Sclerotinia sclerotiorum fungus.}, journal = {Virology}, volume = {441}, number = {1}, pages = {22-30}, doi = {10.1016/j.virol.2013.03.002}, pmid = {23541082}, issn = {1096-0341}, mesh = {Ascomycota/isolation &amp; purification/*virology ; Cluster Analysis ; Mitochondria/ultrastructure/virology ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames ; Phylogeny ; RNA Viruses/*classification/genetics/*isolation &amp; purification ; RNA, Double-Stranded/genetics ; RNA, Viral/*genetics ; RNA-Dependent RNA Polymerase/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Viral Proteins/genetics ; }, abstract = {Three double-stranded RNAs (dsRNAs) of 2438 nts (A), 2588 nts (B), and 2744 nts (C), from a single isolate of Sclerotinia sclerotiorum were sequenced. All three sequences showed similarity to known mitoviruses, consisting of a single open reading frame (ORF) with the characteristic conserved motifs of RNA-dependent RNA polymerase (RdRp). Mitochondrial malformations and reduced virulence and growth were associated with the presence of the dsRNAs. The terminal sequences of the (+) strand of the three dsRNAs could be folded into stem-loop structures and the inverted terminal complimentary sequences of dsRNA-A potentially form a panhandle structure. Sequence A showed 91.6% aa similarity to the previously described Sclerotinia sclerotiorum mitovirus 2 and was tentatively assigned the acronym SsMV2/NZ1. Sequences B and C showed only 16.4% similarity to each other and 15-48% aa similarity to the previously described mitoviruses and consequently appear to be new mitoviruses.}, }
@article {pmid23539619, year = {2013}, author = {Gherasim, C and Lofgren, M and Banerjee, R}, title = {Navigating the B(12) road: assimilation, delivery, and disorders of cobalamin.}, journal = {The Journal of biological chemistry}, volume = {288}, number = {19}, pages = {13186-13193}, pmid = {23539619}, issn = {1083-351X}, support = {R01 DK045776/DK/NIDDK NIH HHS/United States ; DK45776/DK/NIDDK NIH HHS/United States ; }, mesh = {5-Methyltetrahydrofolate-Homocysteine S-Methyltransferase/biosynthesis/chemistry ; Animals ; Biological Transport ; Cobalt/chemistry/metabolism ; Coenzymes/chemistry/metabolism ; GTP-Binding Proteins/metabolism ; Humans ; Intestinal Absorption ; Lysosomes/metabolism ; Methylmalonyl-CoA Mutase/biosynthesis/chemistry ; Mitochondria/metabolism ; Molecular Conformation ; Vitamin B 12/chemistry/*metabolism ; }, abstract = {The reactivity of the cobalt-carbon bond in cobalamins is the key to their chemical versatility, supporting both methyl transfer and isomerization reactions. During evolution of higher eukaryotes that utilize vitamin B12, the high reactivity of the cofactor coupled with its low abundance pressured development of an efficient system for uptake, assimilation, and delivery of the cofactor to client B12-dependent enzymes. Although most proteins suspected to be involved in B12 trafficking were discovered by 2009, the recent identification of a new protein reveals that the quest for elucidating the intracellular B12 highway is still far from complete. Herein, we review the biochemistry of cobalamin trafficking.}, }
@article {pmid23538482, year = {2013}, author = {Elrod, JW and Molkentin, JD}, title = {Physiologic functions of cyclophilin D and the mitochondrial permeability transition pore.}, journal = {Circulation journal : official journal of the Japanese Circulation Society}, volume = {77}, number = {5}, pages = {1111-1122}, pmid = {23538482}, issn = {1347-4820}, support = {/HHMI_/Howard Hughes Medical Institute/United States ; F32 HL092737/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Apoptosis ; Peptidyl-Prolyl Isomerase F ; Cyclophilins/genetics/*metabolism ; Energy Metabolism ; Humans ; Mitochondria, Heart/*metabolism/pathology ; Mitochondrial Membrane Transport Proteins/*metabolism ; Mitochondrial Membranes/*metabolism/pathology ; Mitochondrial Permeability Transition Pore ; Myocardial Reperfusion Injury/metabolism/mortality ; Myocytes, Cardiac/*metabolism/pathology ; Necrosis ; Phylogeny ; Protein Processing, Post-Translational ; }, abstract = {This review focuses on the role of cyclophilin D (CypD) as a prominent mediator of the mitochondrial permeability transition pore (MPTP) and subsequent effects on cardiovascular physiology and pathology. Although a great number of reviews have been written on the MPTP and its effects on cell death, we focus on the biology surrounding CypD itself and the non-cell death physiologic functions of the MPTP. A greater understanding of the physiologic functions of the MPTP and its regulation by CypD will likely suggest novel therapeutic approaches for cardiovascular disease, both dependent and independent of programmed necrotic cell death mechanisms.}, }
@article {pmid23535017, year = {2013}, author = {Kou, Q and Li, X and Chan, TY and Chu, KH and Huang, H and Gan, Z}, title = {Phylogenetic relationships among genera of the Periclimenes complex (Crustacea: Decapoda: Pontoniinae) based on mitochondrial and nuclear DNA.}, journal = {Molecular phylogenetics and evolution}, volume = {68}, number = {1}, pages = {14-22}, doi = {10.1016/j.ympev.2013.03.010}, pmid = {23535017}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/chemistry/*genetics ; DNA, Mitochondrial/*classification/genetics ; Decapoda/*classification/genetics ; Genetic Speciation ; Mitochondria/chemistry/*genetics ; Phosphoenolpyruvate Carboxykinase (ATP)/classification/genetics ; Phosphopyruvate Hydratase/classification/genetics ; *Phylogeny ; Protein Serine-Threonine Kinases/classification/genetics ; RNA, Ribosomal, 16S/*classification/genetics ; Sequence Analysis, DNA ; }, abstract = {The genus Periclimenes Costa, 1844 is the most species-rich genus in the subfamily Pontoniinae. Recent studies have suggested that it might be a polyphyletic taxon and could be further subdivided. In this study, three protein-coding nuclear genes and one mitochondrial ribosomal gene were used to analyze the phylogenetic relationships among the genera of the Periclimenes complex, includes the genus Periclimenes and 15 related genera, viz. Ancylomenes, Brucecaris, Crinotonia, Cuapetes, Harpiliopsis, Harpilius, Laomenes, Leptomenaeus, Manipontonia, Palaemonella, Periclimenella, Philarius, Phycomenes, Unguicaris and Vir. Based on both independent and combined data analyses, the results support that the genus Periclimenes is a polyphyletic group. Furthermore, the studied Periclimenes species could be divided into several independent groups, and the taxonomic status of P. commensalis, P. brevicarpalis and P. digitalis may need to be reconsidered. Besides, the majority of the related genera of Periclimenes are suggested to be monophyletic. Our analyses also reveal that these genera approximately form two main clades, despite some deep relationships are still obscure.}, }
@article {pmid23533597, year = {2013}, author = {Soares, P and Abrantes, D and Rito, T and Thomson, N and Radivojac, P and Li, B and Macaulay, V and Samuels, DC and Pereira, L}, title = {Evaluating purifying selection in the mitochondrial DNA of various mammalian species.}, journal = {PloS one}, volume = {8}, number = {3}, pages = {e58993}, pmid = {23533597}, issn = {1932-6203}, mesh = {Animals ; Cattle ; DNA, Mitochondrial/*genetics ; Dogs ; Mammals ; Mice ; Phylogeny ; Sus scrofa ; Whale, Killer ; }, abstract = {Mitochondrial DNA (mtDNA), the circular DNA molecule inside the mitochondria of all eukaryotic cells, has been shown to be under the effect of purifying selection in several species. Traditional testing of purifying selection has been based simply on ratios of nonsynonymous to synonymous mutations, without considering the relative age of each mutation, which can be determined by phylogenetic analysis of this non-recombining molecule. The incorporation of a mutation time-ordering from phylogeny and of predicted pathogenicity scores for nonsynonymous mutations allow a quantitative evaluation of the effects of purifying selection in human mtDNA. Here, by using this additional information, we show that purifying selection undoubtedly acts upon the mtDNA of other mammalian species/genera, namely Bos sp., Canis lupus, Mus musculus, Orcinus orca, Pan sp. and Sus scrofa. The effects of purifying selection were comparable in all species, leading to a significant major proportion of nonsynonymous variants with higher pathogenicity scores in the younger branches of the tree. We also derive recalibrated mutation rates for age estimates of ancestors of these various species and proposed a correction curve in order to take into account the effects of selection. Understanding this selection is fundamental to evolutionary studies and to the identification of deleterious mutations.}, }
@article {pmid23522384, year = {2013}, author = {Chang, S and Chen, J and Wang, Y and Gu, B and He, J and Chu, P and Guan, R}, title = {The mitochondrial genome of Raphanus sativus and gene evolution of cruciferous mitochondrial types.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {40}, number = {3}, pages = {117-126}, doi = {10.1016/j.jgg.2013.01.003}, pmid = {23522384}, issn = {1673-8527}, mesh = {Base Sequence ; *Evolution, Molecular ; *Genes, Mitochondrial ; *Genes, Plant ; *Genome, Mitochondrial ; Mitochondria/genetics ; Open Reading Frames ; Phylogeny ; Polymorphism, Single Nucleotide ; RNA, Plant/genetics/*metabolism ; RNA, Transfer/genetics/metabolism ; Raphanus/classification/*genetics ; Repetitive Sequences, Nucleic Acid ; Species Specificity ; }, abstract = {To explore the mitochondrial genes of the Cruciferae family, the mitochondrial genome of Raphanus sativus (sat) was sequenced and annotated. The circular mitochondrial genome of sat is 239,723 bp and includes 33 protein-coding genes, three rRNA genes and 17 tRNA genes. The mitochondrial genome also contains a pair of large repeat sequences 5.9 kb in length, which may mediate genome reorganization into two sub-genomic circles, with predicted sizes of 124.8 kb and 115.0 kb, respectively. Furthermore, gene evolution of mitochondrial genomes within the Cruciferae family was analyzed using sat mitochondrial type (mitotype), together with six other reported mitotypes. The cruciferous mitochondrial genomes have maintained almost the same set of functional genes. Compared with Cycas taitungensis (a representative gymnosperm), the mitochondrial genomes of the Cruciferae have lost nine protein-coding genes and seven mitochondrial-like tRNA genes, but acquired six chloroplast-like tRNAs. Among the Cruciferae, to maintain the same set of genes that are necessary for mitochondrial function, the exons of the genes have changed at the lowest rates, as indicated by the numbers of single nucleotide polymorphisms. The open reading frames (ORFs) of unknown function in the cruciferous genomes are not conserved. Evolutionary events, such as mutations, genome reorganizations and sequence insertions or deletions (indels), have resulted in the non-conserved ORFs in the cruciferous mitochondrial genomes, which is becoming significantly different among mitotypes. This work represents the first phylogenic explanation of the evolution of genes of known function in the Cruciferae family. It revealed significant variation in ORFs and the causes of such variation.}, }
@article {pmid23520284, year = {2013}, author = {Perry, CG and Kane, DA and Lanza, IR and Neufer, PD}, title = {Methods for assessing mitochondrial function in diabetes.}, journal = {Diabetes}, volume = {62}, number = {4}, pages = {1041-1053}, pmid = {23520284}, issn = {1939-327X}, support = {R01-DK074825/DK/NIDDK NIH HHS/United States ; R01 DK074825/DK/NIDDK NIH HHS/United States ; R01 DK096907/DK/NIDDK NIH HHS/United States ; KL2 TR000136/TR/NCATS NIH HHS/United States ; R01-DK096907/DK/NIDDK NIH HHS/United States ; }, mesh = {Diabetes Mellitus/etiology/*metabolism ; Energy Metabolism ; Humans ; Mitochondria/*metabolism ; Oxygen Consumption ; }, abstract = {A growing body of research is investigating the potential contribution of mitochondrial function to the etiology of type 2 diabetes. Numerous in vitro, in situ, and in vivo methodologies are available to examine various aspects of mitochondrial function, each requiring an understanding of their principles, advantages, and limitations. This review provides investigators with a critical overview of the strengths, limitations and critical experimental parameters to consider when selecting and conducting studies on mitochondrial function. In vitro (isolated mitochondria) and in situ (permeabilized cells/tissue) approaches provide direct access to the mitochondria, allowing for study of mitochondrial bioenergetics and redox function under defined substrate conditions. Several experimental parameters must be tightly controlled, including assay media, temperature, oxygen concentration, and in the case of permeabilized skeletal muscle, the contractile state of the fibers. Recently developed technology now offers the opportunity to measure oxygen consumption in intact cultured cells. Magnetic resonance spectroscopy provides the most direct way of assessing mitochondrial function in vivo with interpretations based on specific modeling approaches. The continuing rapid evolution of these technologies offers new and exciting opportunities for deciphering the potential role of mitochondrial function in the etiology and treatment of diabetes.}, }
@article {pmid23519071, year = {2013}, author = {Davila, AF and Zamorano, P}, title = {Mitochondria and the evolutionary roots of cancer.}, journal = {Physical biology}, volume = {10}, number = {2}, pages = {026008}, doi = {10.1088/1478-3975/10/2/026008}, pmid = {23519071}, issn = {1478-3975}, mesh = {Alphaproteobacteria/physiology ; Animals ; Apoptosis ; Archaea/physiology ; *Biological Evolution ; Cell Hypoxia ; Glycolysis ; Humans ; Mitochondria/genetics/*metabolism/pathology ; Neoplasms/genetics/*metabolism/pathology ; Oxidative Stress ; Phenotype ; Symbiosis ; }, abstract = {Cancer disease is inherent to, and widespread among, metazoans. Yet, some of the hallmarks of cancer such as uncontrolled cell proliferation, lack of apoptosis, hypoxia, fermentative metabolism and free cell motility (metastasis) are akin to a prokaryotic lifestyle, suggesting a link between cancer disease and evolution. In this hypothesis paper, we propose that cancer cells represent a phenotypic reversion to the earliest stage of eukaryotic evolution. This reversion is triggered by the dysregulation of the mitochondria due to cumulative oxidative damage to mitochondrial and nuclear DNA. As a result, the phenotype of normal, differentiated cells gradually reverts to the phenotype of a facultative anaerobic, heterotrophic cell optimized for survival and proliferation in hypoxic environments. This phenotype matches the phenotype of the last eukaryotic common ancestor (LECA) that resulted from the endosymbiosis between an α-proteobacteria (which later became the mitochondria) and an archaebacteria. As such, the evolution of cancer within one individual can be viewed as a recapitulation of the evolution of the eukaryotic cell from fully differentiated cells to LECA. This evolutionary model of cancer is compatible with the current understanding of the disease, and explains the evolutionary basis for most of the hallmarks of cancer, as well as the link between the disease and aging. It could also open new avenues for treatment directed at reestablishing the synergy between the mitochondria and the cancerous cell.}, }
@article {pmid23517666, year = {2013}, author = {Yubuki, N and Simpson, AG and Leander, BS}, title = {Comprehensive ultrastructure of Kipferlia bialata provides evidence for character evolution within the Fornicata (Excavata).}, journal = {Protist}, volume = {164}, number = {3}, pages = {423-439}, doi = {10.1016/j.protis.2013.02.002}, pmid = {23517666}, issn = {1618-0941}, mesh = {Animals ; *Biological Evolution ; Cytoskeleton/genetics/metabolism/ultrastructure ; Eukaryota/genetics/metabolism/*ultrastructure ; *Evolution, Molecular ; Flagella/genetics/metabolism/ultrastructure ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Microtubules/genetics/metabolism/ultrastructure ; Mitochondria/genetics/metabolism/ultrastructure ; Phylogeny ; }, abstract = {Carpediemonas-like organisms (CLOs) are important for understanding the evolutionary history of anaerobic excavates (e.g. diplomonads and parabasalids), especially their cytoskeletal traits and the functions of their modified mitochondria (e.g., hydrogenosomes and mitosomes). Kipferlia bialata is probably the most commonly encountered CLO and has an intriguing molecular phylogenetic position within the Fornicata; however, this species has yet to be described at the ultrastructural level. This study provides a comprehensive account of the ultrastructure of this excavate using light microscopy, SEM, and serial TEM sectioning. The pattern of flagellar transformation observed with SEM confirms that the posterior basal body is the 'eldest', enabling us to emend the numbering system and associated terminology of the flagellar apparatus in excavates. This revised terminology is fundamental for comparing the cytoskeletons of the Excavata supergroup with other eukaryotes. Moreover, K. bialata had several unusal features, such as a hood, a distinct gutter within the ventral groove, and hairs along a single flagellar vane. The ultrastractural data reported here significantly improve our understanding of fornicate morphology, and when placed within a molecular phylogenetic context, these data shed light onto patterns of character evolution within the Excavata.}, }
@article {pmid23516901, year = {2012}, author = {Torgunakova, OA and Egorova, TA and Semenova, SK}, title = {[Comparative analysis of variability of three mitochondrial genes of cytochrome oxidase complex (cox1, cox2, and cox3) in wild and domestic carp (Cyprinus carpio L.)].}, journal = {Genetika}, volume = {48}, number = {12}, pages = {1401-1409}, pmid = {23516901}, issn = {0016-6758}, mesh = {Animals ; Animals, Domestic/genetics ; Animals, Wild/genetics ; Carps/classification/*genetics ; Electron Transport Complex IV/classification/*genetics ; Genes, Mitochondrial ; Haplotypes ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {For the first time, we studied the polymorphism of three mitochondrial genes of the cytochrome oxidase complex (cox1, cox2, and cox3) in natural populations of wild carp living in the Volga, Amur, and Don River Basins, as well as in European Hungarian carp and two pedigree lines of Ropsha carp of domestic breeding. The highest level of nucleotide and haplotype diversity in the studied samples was detected for the cox1 gene (pi = 0.61, h = 100%). Two lines of the Ropsha carp (pi = 0.61, h = 100%) and the Far East population of Amur wild carp from Shershikh strait (Am: pi = 0.20, h = 70%) were the most polymorphic for three genes. The second sample of Amur wild carp from the Amur River (Ac), as well as the samples of Volga and Don wild carp and Hungarian carp had lower values of variability. The presence of two main genealogical lines of the wild carp and carp was demonstrated based on the total sequence of three genes, as well as the corresponding amino acid sequences in the studied area. One of these lines (line I) is typical of the sample of Amur wild carp (Am) and three members of the Ropsha carp. Line II is developed by sequences of Volga, Don, and Amur wild carp (Ac), as well as European Hungarian carp and seven other members of the Ropsha carp. Three to four sublines, which differ in nucleotide and amino acid substitutions, were found within the lines. Possible reasons for the origin of genomic variability in wild carp, as well as in European and Russian breeds of carp, are discussed.}, }
@article {pmid23515736, year = {2012}, author = {Carbone Junior, C and Roselino, JE and Mello, VR and Evora, PR and Sader, AA}, title = {Sanguineous normothermic, intermittent cardioplegia, effects on hypertrophic myocardium. Morphometric, metabolic and ultrastructural studies in rabbits hearts.}, journal = {Revista brasileira de cirurgia cardiovascular : orgao oficial da Sociedade Brasileira de Cirurgia Cardiovascular}, volume = {27}, number = {4}, pages = {621-630}, doi = {10.5935/1678-9741.20120105}, pmid = {23515736}, mesh = {Animals ; Body Weight/*physiology ; Cardiomyopathy, Hypertrophic/metabolism/*pathology ; Disease Models, Animal ; Glycogen/*metabolism ; Heart/anatomy &amp; histology ; Heart Arrest, Induced/*methods ; Mitochondria, Heart/*metabolism ; Myocardial Reperfusion Injury/*prevention &amp; control ; Myocardium/metabolism/*ultrastructure ; Organ Size/physiology ; Oxygen Consumption/physiology ; Rabbits ; Random Allocation ; Statistics, Nonparametric ; }, abstract = {OBJECTIVES: The present investigation aimed to study the protective effect of intermittent normothermic cardioplegia in rabbit's hypertrophic hearts.<br><br>METHODS: The parameters chosen were 1) the ratio heart weight / body weight, 2) the myocardial glycogen levels, 3) ultrastructural changes of light and electron microscopy, and 4) mitochondrial respiration.<br><br>RESULTS: 1) The experimental model, coarctation of the aorta induced left ventricular hypertrophy; 2) the temporal evolution of the glycogen levels in hypertrophic myocardium demonstrates that there is a significant decrease; 3) It was observed a time-dependent trend of higher oxygen consumption values in the hypertrophic group; 4) there was a significant time-dependent decrease in the respiratory coefficient rate in the hypertrophic group; 5) the stoichiometries values of the ADP: O2 revealed the downward trend of the values of the hypertrophic group; 6) It was possible to observe damaged mitochondria from hypertrophic myocardium emphasizing the large heterogeneity of data.<br><br>CONCLUSION: The acquisition of biochemical data, especially the increase in speed of glycogen breakdown, when anatomical changes are not detected, represents an important result even when considering all the difficulties inherent in the process of translating experimental results into clinical practice. With regard to the adopted methods, it is clear that morphometric methods are less specific. Otherwise, the biochemical data allow detecting alterations of glycogen concentrations and mitochondria respiration before the morphometric alterations should be detected.}, }
@article {pmid23512741, year = {2013}, author = {Ka, S and Markljung, E and Ring, H and Albert, FW and Harun-Or-Rashid, M and Wahlberg, P and Garcia-Roves, PM and Zierath, JR and Denbow, DM and Pääbo, S and Siegel, PB and Andersson, L and Hallböök, F}, title = {Expression of carnitine palmitoyl-CoA transferase-1B is influenced by a cis-acting eQTL in two chicken lines selected for high and low body weight.}, journal = {Physiological genomics}, volume = {45}, number = {9}, pages = {367-376}, doi = {10.1152/physiolgenomics.00078.2012}, pmid = {23512741}, issn = {1531-2267}, mesh = {Animals ; Base Sequence ; Body Weight/*genetics ; Carnitine O-Palmitoyltransferase/*genetics/metabolism ; Chickens/*genetics ; Chromosome Mapping ; Chromosomes/genetics ; Crosses, Genetic ; Evolution, Molecular ; Female ; *Gene Expression Regulation, Enzymologic ; Genotype ; Humans ; Hypothalamus/enzymology ; Male ; Mitochondrial Proteins/metabolism ; Multigene Family/genetics ; Muscles/enzymology ; Organ Specificity/genetics ; Phylogeny ; Polymorphism, Genetic ; Quantitative Trait Loci/*genetics ; RNA, Messenger/genetics/metabolism ; Synteny/genetics ; }, abstract = {Carnitine palmitoyl-CoA transferase-1B is a mitochondrial enzyme in the fatty acid oxidation pathway. In a previous study, CPT1B was identified as differentially expressed in the hypothalamus of two lines of chickens established by long-term selection for high (HWS) or low (LWS) body weight. Mammals have three paralogs (CPT1a, b and c) while nonmammalian vertebrates only have two (CPT1A, B). CPT1A is expressed in liver and CPT1B in muscle. CPT1c is expressed in hypothalamus, where it regulates feeding and energy expenditure. We identified an intronic length polymorphism, fixed for different alleles in the two populations, and mapped the hitherto missing CPT1B locus in the chicken genome assembly, to the distal tip of chromosome 1p. Based on molecular phylogeny and gene synteny we suggest that chicken CPT1B is pro-orthologous of the mammalian CPT1c. Chicken CPT1B was differentially expressed in both muscle and hypothalamus but in opposite directions: higher levels in hypothalamus but lower levels in muscle in the HWS than in the LWS line. Using an advanced intercross population of the lines, we found CPT1B expression to be influenced by a cis-acting expression quantitative trait locus in muscle. The increased expression in hypothalamus and reduced expression in muscle is consistent with an increased food intake in the HWS line and at the same time reduced fatty acid oxidation in muscle yielding a net accumulation of energy intake and storage. The altered expression of CPT1B in hypothalamus and peripheral tissue is likely to be a mechanism contributing to the remarkable difference between lines.}, }
@article {pmid23506162, year = {2013}, author = {Paul, P and Simm, S and Blaumeiser, A and Scharf, KD and Fragkostefanakis, S and Mirus, O and Schleiff, E}, title = {The protein translocation systems in plants - composition and variability on the example of Solanum lycopersicum.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {189}, pmid = {23506162}, issn = {1471-2164}, mesh = {Arabidopsis/genetics ; Computational Biology ; Conserved Sequence/genetics ; *Evolution, Molecular ; Gene Expression Regulation, Plant ; Genome, Plant ; Solanum lycopersicum/*genetics/physiology ; Metabolic Networks and Pathways/genetics ; *Phylogeny ; Protein Transport/*genetics ; Species Specificity ; }, abstract = {BACKGROUND: Protein translocation across membranes is a central process in all cells. In the past decades the molecular composition of the translocation systems in the membranes of the endoplasmic reticulum, peroxisomes, mitochondria and chloroplasts have been established based on the analysis of model organisms. Today, these results have to be transferred to other plant species. We bioinformatically determined the inventory of putative translocation factors in tomato (Solanum lycopersicum) by orthologue search and domain architecture analyses. In addition, we investigated the diversity of such systems by comparing our findings to the model organisms Saccharomyces cerevisiae, Arabidopsis thaliana and 12 other plant species.<br><br>RESULTS: The literature search end up in a total of 130 translocation components in yeast and A. thaliana, which are either experimentally confirmed or homologous to experimentally confirmed factors. From our bioinformatic analysis (PGAP and OrthoMCL), we identified (co-)orthologues in plants, which in combination yielded 148 and 143 orthologues in A. thaliana and S. lycopersicum, respectively. Interestingly, we traced 82% overlap in findings from both approaches though we did not find any orthologues for 27% of the factors by either procedure. In turn, 29% of the factors displayed the presence of more than one (co-)orthologue in tomato. Moreover, our analysis revealed that the genomic composition of the translocation machineries in the bryophyte Physcomitrella patens resemble more to higher plants than to single celled green algae. The monocots (Z. mays and O. sativa) follow more or less a similar conservation pattern for encoding the translocon components. In contrast, a diverse pattern was observed in different eudicots.<br><br>CONCLUSIONS: The orthologue search shows in most cases a clear conservation of components of the translocation pathways/machineries. Only the Get-dependent integration of tail-anchored proteins seems to be distinct. Further, the complexity of the translocation pathway in terms of existing orthologues seems to vary among plant species. This might be the consequence of palaeoploidisation during evolution in plants; lineage specific whole genome duplications in Arabidopsis thaliana and triplications in Solanum lycopersicum.}, }
@article {pmid23498859, year = {2013}, author = {Rzigui, T and De Paepe, R and Cornic, G and Streb, P}, title = {In the mitochondrial CMSII mutant of Nicotiana sylvestris photosynthetic activity remains higher than in the WT under persisting mild water stress.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {205-206}, number = {}, pages = {20-28}, doi = {10.1016/j.plantsci.2013.01.010}, pmid = {23498859}, issn = {1873-2259}, mesh = {Acclimatization ; Carbon/metabolism ; Carbon Dioxide/*metabolism ; Chlorophyll/metabolism ; Chloroplasts/metabolism ; Dehydration ; Genotype ; Light ; Mitochondria/metabolism ; Mutation ; Oxygen/metabolism ; Photosynthesis/*physiology ; Photosystem II Protein Complex/*physiology ; Plant Leaves/genetics/physiology ; Plant Stomata ; Plant Transpiration ; Nicotiana/genetics/*physiology/radiation effects ; Water/*physiology ; }, abstract = {Photosynthetic responses to persisting mild water stress were compared between the wild type (WT) and the respiratory complex I mutant CMSII of Nicotiana sylvestris. In both genotypes, plants kept at 80% leaf-RWC (WT80 and CMSII80) had lower photosynthetic activity and stomatal/mesophyll conductances compared to well-watered controls. While the stomatal conductance and the chloroplastic CO2 molar ratio were similar in WT80 and CMSII80 leaves, net photosynthesis was higher in CMSII80. Carboxylation efficiency was lowest in WT80 leaves both, on the basis of the same internal and chloroplastic CO2 molar ratio. Photosynthetic and fluorescence parameters indicate that WT80 leaves were only affected in the presence of oxygen. Photorespiration, as estimated by electron flux to oxygen, increased slightly in CMSII80 and WT80 leaves in accordance with increased glycerate contents but maximum photorespiration at low chloroplastic CO2 was markedly lowest in WT80 leaves. This suggests that carbon assimilation of WT80 leaves is impaired by limited photorespiratory activity. The results are discussed with respect to a possible pre-acclimation of complex I deficient leaves in CMSII to drive photosynthesis and photorespiration at low CO2 partial pressure.}, }
@article {pmid23497158, year = {2013}, author = {Zhu, F and Moural, TW and Shah, K and Palli, SR}, title = {Integrated analysis of cytochrome P450 gene superfamily in the red flour beetle, Tribolium castaneum.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {174}, pmid = {23497158}, issn = {1471-2164}, mesh = {Animals ; Catalytic Domain ; Cytochrome P-450 Enzyme System/chemistry/*genetics/metabolism ; Evolution, Molecular ; Exons/genetics ; Gene Expression Profiling ; Genomics ; Introns/genetics ; Mitochondria/genetics ; Models, Molecular ; Molecular Sequence Annotation ; Multigene Family/genetics ; Phylogeny ; Tribolium/cytology/*embryology/*genetics ; }, abstract = {BACKGROUND: The functional and evolutionary diversification of insect cytochrome P450s (CYPs) shaped the success of insects. CYPs constitute one of the largest and oldest gene superfamilies that are found in virtually all aerobic organisms. Because of the availability of whole genome sequence and well functioning RNA interference (RNAi), the red flour beetle, Tribolium castaneum serves as an ideal insect model for conducting functional genomics studies. Although several T. castaneum CYPs had been functionally investigated in our previous studies, the roles of the majority of CYPs remain largely unknown. Here, we comprehensively analyzed the phylogenetic relationship of all T. castaneum CYPs with genes in other insect species, investigated the CYP6BQ gene cluster organization, function and evolution, as well as examined the mitochondrial CYPs gene expression patterns and intron-exon organization.<br><br>RESULTS: A total 143 CYPs were identified and classified into 26 families and 59 subfamilies. The phylogenetic trees of CYPs among insects across taxa provided evolutionary insight for the genetic distance and function. The percentage of singleton (33.3%) in T. castaneum CYPs is much less than those in Drosophila melanogaster (52.5%) and Bombyx mori (51.2%). Most members in the largest CYP6BQ gene cluster may make contribution to deltamethrin resistance in QTC279 strain. T. castaneum genome encodes nine mitochondrial CYPs, among them CYP12H1 is only expressed in the final instar larval stage. The intron-exon organizations of these mitochondrial CYPs are highly diverse.<br><br>CONCLUSION: Our studies provide a platform to understand the evolution and functions of T. castaneum CYP gene superfamily which will help reveal the strategies employed by insects to cope with their environment.}, }
@article {pmid23496286, year = {2014}, author = {Constenla, M and Padrós, F and Palenzuela, O}, title = {Endolimax piscium sp. nov. (Amoebozoa), causative agent of systemic granulomatous disease of cultured sole, Solea senegalensis Kaup.}, journal = {Journal of fish diseases}, volume = {37}, number = {3}, pages = {229-240}, doi = {10.1111/jfd.12097}, pmid = {23496286}, issn = {1365-2761}, mesh = {Amebiasis/immunology/parasitology/*veterinary ; Animals ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Endolimax/*classification/*physiology/ultrastructure ; Fish Diseases/immunology/*parasitology ; Fisheries ; *Flatfishes ; Microscopy, Electron, Transmission/veterinary ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Spain ; Species Specificity ; }, abstract = {A new amoeba species pathogenic for Senegalese sole is described based on ultrastructural analysis and SSU rDNA phylogenetic inference. The parasite presents round to ovoid trophozoites (<5 μm) with a high degree of intracellular simplification. No mitochondria were observed, but mitosome-like organelles were present. No cysts could be detected. Phylogenetic analysis confirmed the Senegalese sole parasite as an amitochondriate Archamoeba related to Endolimax nana and Iodamoeba spp., and we tentatively describe it as a new species in the genus Endolimax, Endolimax piscium. However, the genetic distance with E. nana is quite large, with only 60% pairwise identity between both SSU rDNA genotypes. Although the overall topology of the Archamoebae cladograms containing E. piscium was consistent, the support for the branching of Endolimax spp. relative to its closest neighbours was variable, being higher with distance or parsimony-based inference methods than with ML or Bayesian trees. The use of stringent alignment sampling masks also caused instability and reduced support for some branches, including the monophyly of Endolimax spp. in the most conservative data sets. The characterization of other Archamoebae parasitizing fish could help to clarify the status of E. piscium and to interpret the large genetic distance observed between Endolimax species.}, }
@article {pmid23480379, year = {2013}, author = {Zhang, HL and Zhao, L and Zheng, ZM and Huang, Y}, title = {Complete mitochondrial genome of Gomphocerus sibiricus (Orthoptera: Acrididae) and comparative analysis in four Gomphocerinae mitogenomes.}, journal = {Zoological science}, volume = {30}, number = {3}, pages = {192-204}, doi = {10.2108/zsj.30.192}, pmid = {23480379}, issn = {0289-0003}, mesh = {Animals ; Base Sequence ; Gene Expression Regulation ; Genome, Insect/*genetics ; Insect Proteins/genetics/metabolism ; Mitochondria/*genetics ; Orthoptera/*genetics ; Phylogeny ; RNA/chemistry/genetics ; Species Specificity ; }, abstract = {The complete mitochondrial genome (mitogenome) of Gomphocerus sibiricus, consisting of 15,590 bp, was determined and analyzed. It displays typical genome organization found in other Caelifera mitogenomes: 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one A+T rich region. In this paper, we focused on the comparative analyses of mitogenomes from four Gomphocerinae taxa to find characteristics of nucleotide composition and overlapping and non-coding regions. In addition, we compared variable sites in the structure of 22 tRNAs and two rRNAs, and differences in some common conserved elements of A+T rich regions. Furthermore, we analyzed phylogenetic relationships of 12 Caelifera species using maximum likelihood (ML) and Bayesian inference (BI) based on two different datasets from mitogenomes. Our results reveal that G. sibiricus has a close relationship with Gomphocerus licenti of the four Gomphocerinae taxa examined in these analyses.}, }
@article {pmid23480375, year = {2013}, author = {Aoki, G and Matsui, M and Nishikawa, K}, title = {Mitochondrial cytochrome B phylogeny and historical biogeography of the Tohoku salamander, Hynobius lichenatus (Amphibia, Caudata).}, journal = {Zoological science}, volume = {30}, number = {3}, pages = {167-173}, doi = {10.2108/zsj.30.167}, pmid = {23480375}, issn = {0289-0003}, mesh = {Animals ; Cytochromes b/genetics/*metabolism ; DNA, Mitochondrial ; Demography ; Gene Expression Regulation, Enzymologic ; Japan ; Larva/genetics/physiology ; Mitochondria/*enzymology ; Phylogeny ; Phylogeography ; Urodela/*genetics/*physiology ; }, abstract = {The Tohoku salamander, Hynobius lichenatus Boulenger, 1883, is a lentic breeding species widespread throughout montane regions of northeastern Japan. To explore intraspecific genetic variation and infer evolutionary history of H. lichenatus, we performed mitochondrial DNA analysis (complete 1141 bp sequences of the mitochondrial cytochrome b gene) using 215 adult and larval individuals collected from 75 localities, encompassing known distributional range of the species. Hynobius lichenatus proved to be monophyletic, including three well-supported and geographically structured clades (Clade I from northern Kanto, Clade II from southern Tohoku, and Clade III from northern Tohoku). These clades, respectively, comprise several subclades, and show genetic distances as large as those seen between different species of Hynobius. Results of population statistic analyses indicate that all clades and most subclades have maintained high genetic diversity and demographic stability over long periods. Molecular dating indicates divergence in H. lichenatus concords with topographic evolution of northeastern Japan from late Miocene to early Pleistocene, suggesting that paleogeographic events in this region, such as orogenesis, sea level change, and volcanic activity, have been crucial for shaping genetic patterns and diversity in this species. Hynobius lichenatus greatly differs from many other animal species from northeastern Japan in its much older periods and the pattern of genetic differentiation, and is suggested as an old faunal element in this region.}, }
@article {pmid23467004, year = {2013}, author = {Hind, KR and Saunders, GW}, title = {Molecular markers from three organellar genomes unravel complex taxonomic relationships within the coralline algal genus Chiharaea (Corallinales, Rhodophyta).}, journal = {Molecular phylogenetics and evolution}, volume = {67}, number = {2}, pages = {529-540}, doi = {10.1016/j.ympev.2013.02.022}, pmid = {23467004}, issn = {1095-9513}, mesh = {Cell Nucleus/genetics ; Evolution, Molecular ; Genome ; Mitochondria/genetics ; Organelles/*genetics ; *Phylogeny ; Plastids/genetics ; *Rhodophyta/classification/genetics ; }, abstract = {The use of molecular markers in taxonomic studies has become a standard practice in biology. However, consensus on which markers to use at the species level is lacking because evolutionary lineages show differences in divergence rates between organellar genomes. Ideally, researchers use multiple lines of evidence when first describing a species, such as the incorporation of several molecular markers from varied genomes (mitochondrion, plastid and nucleus). This study examined species boundaries in the red algal genus Chiharaea. We used five molecular markers, with at least one marker from each genome, coupled with thorough morphological analyses. We recognized three species in Chiharaea (C.americana, C. rhododactyla sp. nov., C. silvae) and two forms (C. americana f. americana and C. americana f. bodegensis (H.W. Johansen) stat. nov.). For C. americana f. americana and C. americana f. bodegensis differentiation based on morphological data was reflected in the plastid-encoded large subunit of RuBisCO (rbcL), but was not concordant with either the mitochondrial cytochrome c oxidase subunit 1 (COI-5P) or nuclear internal transcribed spacer (ITS) sequence data. We suggest that this discordance is indicative of ongoing hybridization and introgression between populations of C. americana f. americana and C. americana f. bodegensis. In addition, we used a PCR assay with ITS specific primers to amplify multiple ITS variants for collections assignable to C. americana indicating that there is genetic variability within ITS copies most likely due to introgression, crossing over and/or the retention of ancestral variants.}, }
@article {pmid23466751, year = {2013}, author = {Hikosaka, K and Kita, K and Tanabe, K}, title = {Diversity of mitochondrial genome structure in the phylum Apicomplexa.}, journal = {Molecular and biochemical parasitology}, volume = {188}, number = {1}, pages = {26-33}, doi = {10.1016/j.molbiopara.2013.02.006}, pmid = {23466751}, issn = {1872-9428}, mesh = {Apicomplexa/*genetics ; Evolution, Molecular ; *Genetic Variation ; *Genome, Mitochondrial ; }, abstract = {Mitochondria are ubiquitous organelles in all eukaryotes that are essential for a range of cellular processes and cellular signaling. Nearly all mitochondria have their own DNA or mitochondrial (mt) genome, which varies considerably in size, structure and organization. The phylum Apicomplexa includes a variety of unicellular eukaryotes, some of which are parasites of clinical or economic importance. Recent studies have demonstrated that apicomplexan mt genomes, which include the smallest 6 kb genome of the malaria parasites, exhibit remarkably diverse structures. Apicomplexan parasites are interesting model organisms in order to understand the evolution of mt genomes. This review summarizes the structure of apicomplexan mt genomes and highlights the unique features and the evolution of the mt genome.}, }
@article {pmid23463776, year = {2013}, author = {Liu, YJ and Xiu, ZH and Meeley, R and Tan, BC}, title = {Empty pericarp5 encodes a pentatricopeptide repeat protein that is required for mitochondrial RNA editing and seed development in maize.}, journal = {The Plant cell}, volume = {25}, number = {3}, pages = {868-883}, pmid = {23463776}, issn = {1532-298X}, mesh = {Alleles ; Amino Acid Sequence ; Cloning, Molecular ; Electron Transport Complex IV/genetics/metabolism ; Genes, Plant ; Heterozygote ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Molecular Sequence Data ; NADH Dehydrogenase/genetics/metabolism ; Oryza/genetics/growth &amp; development/metabolism ; Phylogeny ; Plants, Genetically Modified/genetics/metabolism ; Protein Structure, Tertiary ; RNA/genetics/*metabolism ; *RNA Editing ; RNA, Mitochondrial ; RNA, Plant/genetics/metabolism ; Seeds/genetics/*growth &amp; development/metabolism ; Zea mays/genetics/growth &amp; development/*metabolism ; }, abstract = {In flowering plants, RNA editing is a posttranscriptional mechanism that converts specific cytidines to uridines in both mitochondrial and plastidial transcripts, altering the information encoded by these genes. Here, we report the molecular characterization of the empty pericarp5 (emp5) mutants in maize (Zea mays). Null mutation of Emp5 results in abortion of embryo and endosperm development at early stages. Emp5 encodes a mitochondrion-targeted DYW subgroup pentatricopeptide repeat (PPR) protein. Analysis of the mitochondrial transcripts revealed that loss of the EMP5 function abolishes the C-to-U editing of ribosomal protein L16 at the rpl16-458 site (100% edited in the wild type), decreases the editing at nine sites in NADH dehydrogenase9 (nad9), cytochrome c oxidase3 (cox3), and ribosomal protein S12 (rps12), and surprisingly increases the editing at five sites of ATP synthase F0 subunit a (atp6), apocytochrome b (cob), nad1, and rpl16. Mutant EMP5-4 lacking the E+ and DYW domains still retains the substrate specificity and editing function, only at reduced efficiency. This suggests that the E+ and DYW domains of EMP5 are not essential to the EMP5 editing function but are necessary for efficiency. Analysis of the ortholog in rice (Oryza sativa) indicates that rice EMP5 has a conserved function in C-to-U editing of the rice mitochondrial rpl16-458 site. EMP5 knockdown expression in transgenics resulted in slow growth and defective seeds. These results demonstrate that Emp5 encodes a PPR-DYW protein that is required for the editing of multiple transcripts in mitochondria, and the editing events, particularly the C-to-U editing at the rpl16-458 site, are critical to the mitochondrial functions and, hence, to seed development in maize.}, }
@article {pmid23463613, year = {2013}, author = {Tang, S and Wang, J and Zhang, VW and Li, FY and Landsverk, M and Cui, H and Truong, CK and Wang, G and Chen, LC and Graham, B and Scaglia, F and Schmitt, ES and Craigen, WJ and Wong, LJ}, title = {Transition to next generation analysis of the whole mitochondrial genome: a summary of molecular defects.}, journal = {Human mutation}, volume = {34}, number = {6}, pages = {882-893}, doi = {10.1002/humu.22307}, pmid = {23463613}, issn = {1098-1004}, mesh = {Adolescent ; Adult ; Aged ; Child ; Child, Preschool ; Female ; Follow-Up Studies ; Gene Deletion ; *Genome, Mitochondrial ; Genomics ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Male ; Middle Aged ; Mitochondria/genetics/metabolism ; Mitochondrial Diseases/*diagnosis/*genetics ; Mutation ; Mutation Rate ; Young Adult ; }, abstract = {The diagnosis of mitochondrial disorders is challenging because of the clinical variability and genetic heterogeneity. Conventional analysis of the mitochondrial genome often starts with a screening panel for common mitochondrial DNA (mtDNA) point mutations and large deletions (mtScreen). If negative, it has been traditionally followed by Sanger sequencing of the entire mitochondrial genome (mtWGS). The recently developed "Next-Generation Sequencing" (NGS) technology offers a robust high-throughput platform for comprehensive mtDNA analysis. Here, we summarize the results of the past 6 years of clinical practice using the mtScreen and mtWGS tests on 9,261 and 2,851 unrelated patients, respectively. A total of 344 patients (3.7%) had mutations identified by mtScreen and 99 (3.5%) had mtDNA mutations identified by mtWGS. The combinatorial analyses of mtDNA and POLG revealed a diagnostic yield of 6.7% in patients with suspected mitochondrial disorders but no recognizable syndromes. From the initial mtWGS-NGS cohort of 391 patients, 21 mutation-positive cases (5.4%) have been identified. The mtWGS-NGS provides a one-step approach to detect common and uncommon point mutations, as well as deletions. Additionally, NGS provides accurate, sensitive heteroplasmy measurement, and the ability to map deletion breakpoints. A new era of more efficient molecular diagnosis of mtDNA mutations has arrived.}, }
@article {pmid23462316, year = {2013}, author = {Burak, E and Yogev, O and Sheffer, S and Schueler-Furman, O and Pines, O}, title = {Evolving dual targeting of a prokaryotic protein in yeast.}, journal = {Molecular biology and evolution}, volume = {30}, number = {7}, pages = {1563-1573}, doi = {10.1093/molbev/mst039}, pmid = {23462316}, issn = {1537-1719}, mesh = {Citric Acid Cycle/genetics ; Cytosol/enzymology ; Escherichia coli/enzymology/*genetics ; Fumarate Hydratase/*genetics ; Mitochondria ; Prokaryotic Cells/enzymology ; Protein Folding ; Saccharomyces cerevisiae/enzymology/*genetics ; *Sequence Homology, Amino Acid ; }, abstract = {Dual targeting is an important and abundant phenomenon. Indeed, we estimate that more than a third of the yeast mitochondrial proteome is dual localized. The enzyme fumarase is a highly conserved protein in all organisms with respect to its sequence, structure, and enzymatic activity. In eukaryotes, it is dual localized to the cytosol and mitochondria. In Saccharomyces cerevisiae, the dual localization of fumarase is achieved by the reverse translocation mechanism; all fumarase molecules harbor a mitochondrial targeting sequence (MTS), are targeted to mitochondria, begin their translocation, and are processed by mitochondrial processing peptidase in the matrix. A subset of these processed fumarase molecules in transit is then fully imported into the matrix, whereas the majority moves back into the cytosol by reverse translocation. The proposed driving force for fumarase distribution is protein folding during import. Here, we asked how reverse translocation could have evolved on a prokaryotic protein that had already acquired expression from the nuclear genome and a targeting sequence. To address this question, we used, as a model, the Escherichia coli FumC Class II fumarase, which is homologous to eukaryotic fumarases (∼58% identity and ∼74% similarity to the yeast Fum1). Starting with an exclusively mitochondrial targeted FumC (attached to a strong MTS), we show that two randomly acquired mutations within the prokaryotic FumC sequence are sufficient to cause substantial dual targeting by reverse translocation. In fact, the unmutated MTS-FumC also has some ability to be dual targeted but only at low temperatures. Our results suggest that in this case, evolution of dual targeting by reverse translocation is based on naturally occurring and fortuitously conserved features of fumarase folding.}, }
@article {pmid23461338, year = {2013}, author = {Chong, RA and Mueller, RL}, title = {Low metabolic rates in salamanders are correlated with weak selective constraints on mitochondrial genes.}, journal = {Evolution; international journal of organic evolution}, volume = {67}, number = {3}, pages = {894-899}, doi = {10.1111/j.1558-5646.2012.01830.x}, pmid = {23461338}, issn = {1558-5646}, mesh = {Animals ; Anura/*genetics/metabolism ; *Basal Metabolism ; Evolution, Molecular ; *Genes, Mitochondrial ; Oxidative Phosphorylation ; *Selection, Genetic ; Urodela/*genetics/metabolism ; }, abstract = {Mitochondria are the site for the citric acid cycle and oxidative phosphorylation (OXPHOS), the final steps of ATP synthesis via cellular respiration. Each mitochondrion contains its own genome; in vertebrates, this is a small, circular DNA molecule that encodes 13 subunits of the multiprotein OXPHOS electron transport complexes. Vertebrate lineages vary dramatically in metabolic rates; thus, functional constraints on mitochondrial-encoded proteins likely differ, potentially impacting mitochondrial genome evolution. Here, we examine mitochondrial genome evolution in salamanders, which have the lowest metabolic requirements among tetrapods. We show that salamanders experience weaker purifying selection on protein-coding sequences than do frogs, a comparable amphibian clade with higher metabolic rates. In contrast, we find no evidence for weaker selection against mitochondrial genome expansion in salamanders. Together, these results suggest that different aspects of mitochondrial genome evolution (i.e., nucleotide substitution, accumulation of noncoding sequences) are differently affected by metabolic variation across tetrapod lineages.}, }
@article {pmid23460830, year = {2013}, author = {Simonato, M and Battisti, A and Kerdelhué, C and Burban, C and Lopez-Vaamonde, C and Pivotto, I and Salvato, P and Negrisolo, E}, title = {Host and phenology shifts in the evolution of the social moth genus Thaumetopoea.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e57192}, pmid = {23460830}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA, Intergenic/genetics ; DNA, Mitochondrial/genetics ; Genes, Insect/genetics ; Host Specificity/*genetics ; Mitochondria ; Molecular Sequence Data ; Moths/*genetics/*physiology ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer/chemistry/genetics ; *Social Behavior ; }, abstract = {The genus Thaumetopoea contains the processionary moths, a group of lepidopteran associated with forest trees, well known for the social behaviour of the larvae and for carrying urticating setae. The taxonomy of the genus is partly unresolved and a phylogenetic approach is lacking. The goal of this work is to produce a phylogeny for Thaumetopoea and to identify the main traits driving the evolution of this group. Eighteen mitochondrial and three nuclear genes were fully/partly sequenced. Markers were aligned and analysed singularly or in various combinations. Phylogenetic analyses were performed according to maximum likelihood and Bayesian inference methods. Trees obtained from largest data sets provided identical topologies that received strong statistical support. Three main clades were identified within Thaumetopoea and were further supported by several signatures located in the mitochondrial tRNAs and intergenic spacers. The reference topology was used to investigate the evolution of life history traits related to biogeography, host plant, ecology, and morphology. A multigenic approach allowed to produce a robust phylogenetic analysis of the genus Thaumetopoea, with the identification of three major clades linked to different ecological and life history traits. The first clade is associated with Angiosperm host plants and has a fast spring development of larvae on young foliage. The other clades have originated by one event of host plant shift to Gymnosperm Pinaceae, which implied a longer larval developmental time due to the lower nutritional quality of leaves. These clades showed different adaptations to such a constraint, the first with a switch of larval feeding to cold season (winter pine processionary moths), and the second with a retraction to high altitude and latitude and a development cycle extended over two years (summer pine processionary moths). Recent global warming is affecting all species and seems able to further shape the evolution of the group.}, }
@article {pmid23459037, year = {2013}, author = {Xi, Z and Wang, Y and Bradley, RK and Sugumaran, M and Marx, CJ and Rest, JS and Davis, CC}, title = {Massive mitochondrial gene transfer in a parasitic flowering plant clade.}, journal = {PLoS genetics}, volume = {9}, number = {2}, pages = {e1003265}, pmid = {23459037}, issn = {1553-7404}, mesh = {DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Flowers/genetics ; Gene Transfer, Horizontal/*genetics ; Genome, Mitochondrial ; Genome, Plant ; Host-Parasite Interactions/*genetics ; Phylogeny ; Plants/*genetics/parasitology ; RNA, Ribosomal/genetics ; Symbiosis ; }, abstract = {Recent studies have suggested that plant genomes have undergone potentially rampant horizontal gene transfer (HGT), especially in the mitochondrial genome. Parasitic plants have provided the strongest evidence of HGT, which appears to be facilitated by the intimate physical association between the parasites and their hosts. A recent phylogenomic study demonstrated that in the holoparasite Rafflesia cantleyi (Rafflesiaceae), whose close relatives possess the world's largest flowers, about 2.1% of nuclear gene transcripts were likely acquired from its obligate host. Here, we used next-generation sequencing to obtain the 38 protein-coding and ribosomal RNA genes common to the mitochondrial genomes of angiosperms from R. cantleyi and five additional species, including two of its closest relatives and two host species. Strikingly, our phylogenetic analyses conservatively indicate that 24%-41% of these gene sequences show evidence of HGT in Rafflesiaceae, depending on the species. Most of these transgenic sequences possess intact reading frames and are actively transcribed, indicating that they are potentially functional. Additionally, some of these transgenes maintain synteny with their donor and recipient lineages, suggesting that native genes have likely been displaced via homologous recombination. Our study is the first to comprehensively assess the magnitude of HGT in plants involving a genome (i.e., mitochondria) and a species interaction (i.e., parasitism) where it has been hypothesized to be potentially rampant. Our results establish for the first time that, although the magnitude of HGT involving nuclear genes is appreciable in these parasitic plants, HGT involving mitochondrial genes is substantially higher. This may represent a more general pattern for other parasitic plant clades and perhaps more broadly for angiosperms.}, }
@article {pmid23451266, year = {2013}, author = {Phillips, MJ and Haouchar, D and Pratt, RC and Gibb, GC and Bunce, M}, title = {Inferring kangaroo phylogeny from incongruent nuclear and mitochondrial genes.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e57745}, pmid = {23451266}, issn = {1932-6203}, mesh = {Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; *Genes, Mitochondrial ; Macropodidae/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The marsupial genus Macropus includes three subgenera, the familiar large grazing kangaroos and wallaroos of M. (Macropus) and M. (Osphranter), as well as the smaller mixed grazing/browsing wallabies of M. (Notamacropus). A recent study of five concatenated nuclear genes recommended subsuming the predominantly browsing Wallabia bicolor (swamp wallaby) into Macropus. To further examine this proposal we sequenced partial mitochondrial genomes for kangaroos and wallabies. These sequences strongly favour the morphological placement of W. bicolor as sister to Macropus, although place M. irma (black-gloved wallaby) within M. (Osphranter) rather than as expected, with M. (Notamacropus). Species tree estimation from separately analysed mitochondrial and nuclear genes favours retaining Macropus and Wallabia as separate genera. A simulation study finds that incomplete lineage sorting among nuclear genes is a plausible explanation for incongruence with the mitochondrial placement of W. bicolor, while mitochondrial introgression from a wallaroo into M. irma is the deepest such event identified in marsupials. Similar such coalescent simulations for interpreting gene tree conflicts will increase in both relevance and statistical power as species-level phylogenetics enters the genomic age. Ecological considerations in turn, hint at a role for selection in accelerating the fixation of introgressed or incompletely sorted loci. More generally the inclusion of the mitochondrial sequences substantially enhanced phylogenetic resolution. However, we caution that the evolutionary dynamics that enhance mitochondria as speciation indicators in the presence of incomplete lineage sorting may also render them especially susceptible to introgression.}, }
@article {pmid23448890, year = {2013}, author = {Okie, JG}, title = {General models for the spectra of surface area scaling strategies of cells and organisms: fractality, geometric dissimilitude, and internalization.}, journal = {The American naturalist}, volume = {181}, number = {3}, pages = {421-439}, doi = {10.1086/669150}, pmid = {23448890}, issn = {1537-5323}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {*Biological Evolution ; *Body Surface Area ; *Cell Size ; Cells/*cytology ; Fractals ; Linear Models ; *Models, Biological ; }, abstract = {Surface areas and volumes of biological systems-from molecules to organelles, cells, and organisms-affect their biological rates and kinetics. Therefore, surface area-to-volume ratios and the scaling of surface area with volume profoundly influence ecology, physiology, and evolution. The zeroth-order geometric expectation is that surface area scales with body mass or volume as a power law with an exponent of two-thirds, with consequences for surface area-to-volume (SA : V) ratios and constraints on size; however, organisms have adaptations for altering the surface area scaling and SA : V ratios of their bodies and structures. The strategies fall into three groups: (1) fractal-like surface convolutions and crinkles; (2) classic geometric dissimilitude through elongating, flattening, fattening, and hollowing; and (3) internalization of surfaces. Here I develop general quantitative theory to model the spectra of effects of these strategies on SA : V ratios and surface area scaling, from exponents of less than two-thirds to superlinear scaling and mixed-power laws. Applying the theory to cells helps quantitatively evaluate the effects of membrane fractality, shape-shifting, vacuoles, vesicles, and mitochondria on surface area scaling, informing understanding of cell allometry, morphology, and evolution. Analysis of compiled data indicates that through hollowness and surface internalization, eukaryotic phytoplankton increase their effective surface area scaling, attaining near-linear scaling in larger cells. This unifying theory highlights the fundamental role of biological surfaces in metabolism and morphological evolution.}, }
@article {pmid23437234, year = {2013}, author = {Jackson, CJ and Waller, RF}, title = {A widespread and unusual RNA trans-splicing type in dinoflagellate mitochondria.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e56777}, pmid = {23437234}, issn = {1932-6203}, mesh = {Dinoflagellida/enzymology/*genetics ; Electron Transport Complex IV/*genetics ; Exons ; Genome, Mitochondrial ; Mitochondria/enzymology/*genetics ; Phylogeny ; RNA, Messenger/*genetics ; RNA, Spliced Leader/genetics ; Trans-Splicing/*genetics ; }, abstract = {Cytochrome oxidase subunit 3 (Cox3) is a mitochondrion-encoded core membrane protein of complex IV of the mitochondrial respiratory chain, and consists of seven trans-membrane helices. Here we show that in diverse later-branching dinoflagellates, cox3 is consistently split into two exons in the mitochondrial genome between helices six and seven. Gene exons are transcribed as two discrete oligoadenylated precursor RNAs, and these are subsequently trans-spliced to form a complete coding mRNA. This trans-splicing is highly unusual in that some of the oligoadenylated tail is incorporated at the splice site, such that a short string of adenosines links the two coding exons. This feature is consistently represented in diverse dinoflagellates, however the number of adenosines added varies according to the size of the coding gap between the two exons. Thus we observed between zero (Amphidinium carterae) and 10 (Symbiodinium sp.) adenosines added in different taxa, but the final coding sequence length is identical with the reading frame maintained. Northern analyses show that precursor cox3 transcripts are approximately equally abundant as mature cox3 mRNAs, suggesting a slow or regulated maturation process. These data indicate that the splicing mechanism in dinoflagellate mitochondria is tolerant of variations in the length of the precursor coding sequence, and implicates the use of a splicing template, or guide molecule, during splicing that controls mature mRNA length.}, }
@article {pmid23437098, year = {2013}, author = {Letcher, PM and Lopez, S and Schmieder, R and Lee, PA and Behnke, C and Powell, MJ and McBride, RC}, title = {Characterization of Amoeboaphelidium protococcarum, an algal parasite new to the cryptomycota isolated from an outdoor algal pond used for the production of biofuel.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e56232}, pmid = {23437098}, issn = {1932-6203}, mesh = {Animals ; *Biofuels ; Eukaryota/classification/growth &amp; development/*isolation &amp; purification/ultrastructure ; Life Cycle Stages ; Parasites/cytology/growth &amp; development/*isolation &amp; purification/ultrastructure ; Phylogeny ; Ponds/*parasitology ; Scenedesmus/growth &amp; development/*parasitology ; Sequence Analysis, DNA ; }, abstract = {Mass culture of algae for the production of biofuels is a developing technology designed to offset the depletion of fossil fuel reserves. However, large scale culture of algae in open ponds can be challenging because of incidences of infestation with algal parasites. Without knowledge of the identity of the specific parasite and how to control these pests, algal-based biofuel production will be limited. We have characterized a eukaryotic parasite of Scenedesmus dimorphus growing in outdoor ponds used for biofuel production. We demonstrated that as the genomic DNA of parasite FD01 increases, the concentration of S. dimorphus cells decreases; consequently, this is a highly destructive pathogen. Techniques for culture of the parasite and host were developed, and the endoparasite was identified as the Aphelidea, Amoeboaphelidium protococcarum. Phylogenetic analysis of ribosomal sequences revealed that parasite FD01 placed within the recently described Cryptomycota, a poorly known phylum based on two species of Rozella and environmental samples. Transmission electron microscopy demonstrated that aplanospores of the parasite produced filose pseudopodia, which contained fine fibers the diameter of actin microfilaments. Multiple lipid globules clustered and were associated with microbodies, mitochondria and a membrane cisternae, an arrangement characteristic of the microbody-lipid globule complex of chytrid zoospores. After encystment and attachment to the host cells, the parasite injected its protoplast into the host between the host cell wall and plasma membrane. At maturity the unwalled parasite occupied the entire host cell. After cleavage of the protoplast into aplanospores, a vacuole and lipids remained in the host cell. Amoeboaphelidium protococcarum isolate FD01 is characteristic of the original description of this species and is different from strain X-5 recently characterized. Our results help put a face on the Cryptomycota, revealing that the phylum is more diverse than previously understood and include some of the Aphelidea as well as Rozella species and potentially Microsporidia.}, }
@article {pmid23433225, year = {2013}, author = {Krenek, S and Schlegel, M and Berendonk, TU}, title = {Convergent evolution of heat-inducibility during subfunctionalization of the Hsp70 gene family.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {49}, pmid = {23433225}, issn = {1471-2148}, mesh = {Biological Evolution ; *Evolution, Molecular ; HSP70 Heat-Shock Proteins ; Heat-Shock Proteins/*genetics ; Paramecium/classification/*genetics/physiology ; Paramecium caudatum/genetics ; *Phylogeny ; Protozoan Proteins/*genetics ; Tetrahymena/genetics ; }, abstract = {BACKGROUND: Heat-shock proteins of the 70 kDa family (Hsp70s) are essential chaperones required for key cellular functions. In eukaryotes, four subfamilies can be distinguished according to their function and localisation in different cellular compartments: cytosol, endoplasmic reticulum, mitochondria and chloroplasts. Generally, multiple cytosol-type Hsp70s can be found in metazoans that show either constitutive expression and/or stress-inducibility, arguing for the evolution of different tasks and functions. Information about the hsp70 copy number and diversity in microbial eukaryotes is, however, scarce, and detailed knowledge about the differential gene expression in most protists is lacking. Therefore, we have characterised the Hsp70 gene family of Paramecium caudatum to gain insight into the evolution and differential heat stress response of the distinct family members in protists and to investigate the diversification of eukaryotic hsp70s focusing on the evolution of heat-inducibility.<br><br>RESULTS: Eleven putative hsp70 genes could be detected in P. caudatum comprising homologs of three major Hsp70-subfamilies. Phylogenetic analyses revealed five evolutionarily distinct Hsp70-groups, each with a closer relationship to orthologous sequences of Paramecium tetraurelia than to another P. caudatum Hsp70-group. These highly diverse, paralogous groups resulted from duplications preceding Paramecium speciation, underwent divergent evolution and were subject to purifying selection. Heat-shock treatments were performed to test for differential expression patterns among the five Hsp70-groups as well as for a functional conservation within Paramecium. These treatments induced exceptionally high mRNA up-regulations in one cytosolic group with a low basal expression, indicative for the major heat inducible hsp70s. All other groups showed comparatively high basal expression levels and moderate heat-inducibility, signifying constitutively expressed genes. Comparative EST analyses for P. tetraurelia hsp70s unveiled a corresponding expression pattern, which supports a functionally conserved evolution of the Hsp70 gene family in Paramecium.<br><br>CONCLUSIONS: Our analyses suggest an independent evolution of the heat-inducible cytosol-type hsp70s in Paramecium and in its close relative Tetrahymena, as well as within higher eukaryotes. This result indicates convergent evolution during hsp70 subfunctionalization and implies that heat-inducibility evolved several times during the course of eukaryotic evolution.}, }
@article {pmid23426914, year = {2013}, author = {Kasumovic, MM and Seebacher, F}, title = {The active metabolic rate predicts a male spider's proximity to females and expected fitness.}, journal = {Biology letters}, volume = {9}, number = {2}, pages = {20121164}, pmid = {23426914}, issn = {1744-957X}, mesh = {Animals ; Australia ; Basal Metabolism ; Behavior, Animal/*physiology ; Biological Evolution ; Body Size ; Citrate (si)-Synthase/*metabolism ; Energy Metabolism/*physiology ; Enzyme Activation ; Female ; *Genetic Fitness ; L-Lactate Dehydrogenase/metabolism ; Male ; Mitochondria/enzymology/physiology ; Oxygen Consumption ; Species Specificity ; Spiders/*metabolism/physiology ; }, abstract = {Conspicuous traits, such as weaponry and body size, are often correlated with fitness. By contrast, we understand less about how inconspicuous physiological traits affect fitness. Not only is linking physiology directly to fitness a challenge, but in addition, behavioural studies most often focus on resting or basal metabolic rates, resulting in a poor understanding of how active metabolic rates affect fitness. Here we use the golden orb-web spider (Nephila plumipes), a species for which proximity to a female on the web predicts a male's paternity share, to examine the role of resting and active metabolic rates in fitness. Using a semi-natural experimental set-up, we show that males closer to a female have higher active metabolic rates than males further from females. This higher metabolic activity is paralleled by increased citrate synthase activity, suggesting greater mitochondrial densities. Our results link both higher active metabolic rates and increased citrate synthase activity with fitness. Coupled with the behaviour and life history of N. plumipes, these results provide insight into the evolution of physiological systems.}, }
@article {pmid23424644, year = {2013}, author = {Yu, G and Zhang, M and Rao, D and Yang, J}, title = {Effect of Pleistocene climatic oscillations on the phylogeography and demography of red knobby newt (Tylototriton shanjing) from southwestern China.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e56066}, pmid = {23424644}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; China ; *Climate Change ; Evolution, Molecular ; Genetic Variation ; *Geological Phenomena ; Humans ; Mitochondria/genetics ; Phylogeography ; Salamandridae/classification/*genetics ; Sequence Analysis ; }, abstract = {Factors that determine the genetic structure of species in southwestern China remain largely unknown. In this study, phylogeography and demography of Tylototriton shanjing was investigated from a mitochondrial perspective to address the role of the Quaternary ice ages in shaping phylogeographic history and genetic diversity of Yunnan. A total of 146 individuals from 19 populations across the entire range of the species were collected. We detected four maternal phylogenetic lineages corresponding to four population groups, and found that major glaciation events during the Pleistocene have triggered the intra-specific divergence. Coalescent simulations indicated that the populations retreated to different refugia located in southern Yunnan, northwestern Yunnan, the border region of western Yunnan with Myanmar, and middle-western Yunnan, respectively, during previous glacial periods in the Pleistocene, and these four refugia were not retained during the Last Glacial Maximum. Population expansions occurred during the last inter-glaciation, during which ice core and pollen data indicated that the temperature and precipitation gradually increased, and declines of population sizes started after the beginning of the Last Glacial Maximum when the climate became cooler and dryer. The paleo-drainage system had no contribution to the current genetic structure and the rivers were not dispersal barriers for this salamander.}, }
@article {pmid23419240, year = {2013}, author = {Hudson, NJ and Lyons, RE and Reverter, A and Greenwood, PL and Dalrymple, BP}, title = {Inferring the in vivo cellular program of developing bovine skeletal muscle from expression data.}, journal = {Gene expression patterns : GEP}, volume = {13}, number = {3-4}, pages = {109-125}, doi = {10.1016/j.gep.2013.02.001}, pmid = {23419240}, issn = {1872-7298}, mesh = {Animals ; Basic Helix-Loop-Helix Transcription Factors/genetics ; Cattle ; Cell Differentiation/genetics ; *Evolution, Molecular ; *Gene Expression Regulation, Developmental ; Humans ; Mice ; *Mitochondria, Muscle/genetics/metabolism ; Muscle Development/*genetics ; Muscle, Skeletal/*growth &amp; development/metabolism ; Myogenic Regulatory Factor 5/genetics ; Myogenin/genetics ; PAX7 Transcription Factor/genetics ; Repressor Proteins/genetics ; Transcription Factors/genetics/metabolism ; }, abstract = {We outline an in vivo cellular program of bovine longissimus muscle development inferred from expression data from 60 days post conception to 3months postnatal. Analytic challenges included changes in cellular composition, ambiguous 'diagnostic' markers of cell type and contrasts between cattle human and mouse myogenesis. Nevertheless, the expression profiles of the myosin isoforms support slow and fast muscle fibres emanating from primary and secondary myogenesis respectively, while expression of the prenatal myosin subunits is down regulated prior to birth. Of the canonical pro-myogenic transcription factors (TF), MYF6 and MYF5 are negatively co-expressed, with MYF6 displaying higher expression in the post-natal samples and MYF5, MYOG, HES6 and PAX7 displaying higher expression in early development. A set of TFs (SIX1, EYA2 and DACH2) considered important in undifferentiated murine cells were equally abundant in differentiated bovine cells. An examination of mammalian regulators of fibre composition, muscle mass and muscle metabolism, underscored the roles of PPARGC1A, TGFβ signalling and the NHR4 Nuclear Hormone Receptors on bovine muscle development. Enriched among the most variably expressed genes from the entire data set were molecules regulating mitochondrial metabolism of carbohydrate (PDK4), fat (UCP3), protein (AGXT2L1) and high energy phosphate (CKMT2). The dramatic increase in the expression of these transcripts, which may enable the peri-natal transition to metabolic independence critical for new-born herbivores, provides surprising evidence for substantial developmental remodelling of muscle mitochondria and reflects changes in nutrient availability. Overall, despite differences in size, metabolism and physiology, the muscle structural subunit expression program appears very similar in ruminants, rodents and humans.}, }
@article {pmid23418572, year = {2013}, author = {Hayward, DC and Dosztányi, Z and Clark-Walker, GD}, title = {The N-terminal intrinsically disordered domain of Mgm101p is localized to the mitochondrial nucleoid.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e56465}, pmid = {23418572}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Anthozoa/genetics ; Binding Sites/genetics ; DNA, Mitochondrial/genetics/metabolism ; GTP-Binding Proteins/chemistry/genetics/*metabolism ; Genetic Complementation Test ; Green Fluorescent Proteins/genetics/metabolism ; Microscopy, Fluorescence ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Mutation ; Saccharomyces cerevisiae/genetics/growth &amp; development/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Sequence Homology, Amino Acid ; }, abstract = {The mitochondrial genome maintenance gene, MGM101, is essential for yeasts that depend on mitochondrial DNA replication. Previously, in Saccharomyces cerevisiae, it has been found that the carboxy-terminal two-thirds of Mgm101p has a functional core. Furthermore, there is a high level of amino acid sequence conservation in this region from widely diverse species. By contrast, the amino-terminal region, that is also essential for function, does not have recognizable conservation. Using a bioinformatic approach we find that the functional core from yeast and a corresponding region of Mgm101p from the coral Acropora millepora have an ordered structure, while the N-terminal domains of sequences from yeast and coral are predicted to be disordered. To examine whether ordered and disordered domains of Mgm101p have specific or general functions we made chimeric proteins from yeast and coral by swapping the two regions. We find, by an in vivo assay in S.cerevisiae, that the ordered domain of A.millepora can functionally replace the yeast core region but the disordered domain of the coral protein cannot substitute for its yeast counterpart. Mgm101p is found in the mitochondrial nucleoid along with enzymes and proteins involved in mtDNA replication. By attaching green fluorescent protein to the N-terminal disordered domain of yeast Mgm101p we find that GFP is still directed to the mitochondrial nucleoid where full-length Mgm101p-GFP is targeted.}, }
@article {pmid23411694, year = {2013}, author = {Xu, J and Yang, J and Wu, Z and Liu, H and Huang, F and Wu, Y and Carrie, C and Narsai, R and Murcha, M and Whelan, J and Wu, P}, title = {Identification of a dual-targeted protein belonging to the mitochondrial carrier family that is required for early leaf development in rice.}, journal = {Plant physiology}, volume = {161}, number = {4}, pages = {2036-2048}, pmid = {23411694}, issn = {1532-2548}, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Arabidopsis/genetics/metabolism ; Chloroplasts/metabolism/ultrastructure ; Cloning, Molecular ; Escherichia coli/metabolism ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Genetic Complementation Test ; Kinetics ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Mutation/genetics ; Oryza/genetics/*growth &amp; development/*metabolism ; Phenotype ; Phylogeny ; Plant Leaves/*growth &amp; development/*metabolism ; Plant Proteins/*metabolism ; Protein Transport ; RNA Interference ; Subcellular Fractions/metabolism ; Time Factors ; }, abstract = {A dual-targeted protein belonging to the mitochondrial carrier family was characterized in rice (Oryza sativa) and designated 3'-Phosphoadenosine 5'-Phosphosulfate Transporter1 (PAPST1). The papst1 mutant plants showed a defect in thylakoid development, resulting in leaf chlorosis at an early leaf developmental stage, while normal leaf development was restored 4 to 6 d after leaf emergence. OsPAPST1 is highly expressed in young leaves and roots, while the expression is reduced in mature leaves, in line with the recovery of chloroplast development seen in the older leaves of papst1 mutant plants. OsPAPST1 is located on the outer mitochondrial membrane and chloroplast envelope. Whole-genome transcriptomic analysis reveals reduced expression of genes encoding photosynthetic components (light reactions) in papst1 mutant plants. In addition, sulfur metabolism is also perturbed in papst1 plants, and it was seen that PAPST1 can act as a nucleotide transporter when expressed in Escherichia coli that can be inhibited significantly by 3'-phosphoadenosine 5'-phosphosulfate. Given these findings, together with the altered phenotype seen only when leaves are first exposed to light, it is proposed that PAPST1 may act as a 3'-phosphoadenosine 5'-phosphosulfate carrier that has been shown to act as a retrograde signal between chloroplasts and the nucleus.}, }
@article {pmid23411276, year = {2013}, author = {Papi, A and Farabegoli, F and Iori, R and Orlandi, M and De Nicola, GR and Bagatta, M and Angelino, D and Gennari, L and Ninfali, P}, title = {Vitexin-2-O-xyloside, raphasatin and (-)-epigallocatechin-3-gallate synergistically affect cell growth and apoptosis of colon cancer cells.}, journal = {Food chemistry}, volume = {138}, number = {2-3}, pages = {1521-1530}, doi = {10.1016/j.foodchem.2012.11.112}, pmid = {23411276}, issn = {1873-7072}, mesh = {Apigenin/*pharmacology ; Apoptosis/*drug effects ; Caspase 3/metabolism ; Catechin/*analogs &amp; derivatives/pharmacology ; Cell Line, Tumor ; Cell Proliferation/*drug effects ; Colonic Neoplasms/drug therapy/*physiopathology ; Drug Synergism ; Humans ; Isothiocyanates/*pharmacology ; Mitochondria/drug effects/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {Cytotoxic effects of the combination of the food components vitexin-2-O-xyloside (X), raphasatin (4-methylsulphanyl-3-butenyl isothiocyanates; G) and (-)-epigallocatechin-3-gallate (E) were investigated in colon (LoVo and CaCo-2) and breast (MDA-MB-231 and MCF-7) cancer cells. Breast cancer cells were more resistant than colon cells to X, G and E inhibition. On the contrary, marked synergistic effects among X, G and E on cell growth were found in both colon cancer cells. Further analysis revealed a G0/G1 arrest of the phase cell progression and apoptosis, linked to modulation of Bax, Bcl2, caspase-9 and poly(ADP-ribose) polymerase as well as Reactive Oxygen Species (ROS) generation in both colon cancer cells, whereas apoptosis and ROS were not significantly detected in normal human lymphocytes. We conclude that the X, G and E mixture might act by mitochondrial pathway activation of apoptosis, possibly elicited by ROS and the mixture may be effective in the chemoprevention of colon cancer.}, }
@article {pmid23409181, year = {2013}, author = {Tahara, EB and Cunha, FM and Basso, TO and Della Bianca, BE and Gombert, AK and Kowaltowski, AJ}, title = {Calorie restriction hysteretically primes aging Saccharomyces cerevisiae toward more effective oxidative metabolism.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e56388}, pmid = {23409181}, issn = {1932-6203}, mesh = {Biomass ; Caloric Restriction ; Cell Respiration ; Cell Survival ; Culture Media/chemistry ; Energy Metabolism ; Glucose/metabolism ; Hydrogen-Ion Concentration ; Mitochondria/metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; Saccharomyces cerevisiae/cytology/*metabolism ; Time Factors ; }, abstract = {Calorie restriction (CR) is an intervention known to extend the lifespan of a wide variety of organisms. In S. cerevisiae, chronological lifespan is prolonged by decreasing glucose availability in the culture media, a model for CR. The mechanism has been proposed to involve an increase in the oxidative (versus fermentative) metabolism of glucose. Here, we measured wild-type and respiratory incompetent (ρ(0)) S. cerevisiae biomass formation, pH, oxygen and glucose consumption, and the evolution of ethanol, glycerol, acetate, pyruvate and succinate levels during the course of 28 days of chronological aging, aiming to identify metabolic changes responsible for the effects of CR. The concomitant and quantitative measurements allowed for calculations of conversion factors between different pairs of substrates and products, maximum specific substrate consumption and product formation rates and maximum specific growth rates. Interestingly, we found that the limitation of glucose availability in CR S. cerevisiae cultures hysteretically increases oxygen consumption rates many hours after the complete exhaustion of glucose from the media. Surprisingly, glucose-to-ethanol conversion and cellular growth supported by glucose were not quantitatively altered by CR. Instead, we found that CR primed the cells for earlier, faster and more efficient metabolism of respiratory substrates, especially ethanol. Since lifespan-enhancing effects of CR are absent in respiratory incompetent ρ(0) cells, we propose that the hysteretic effect of glucose limitation on oxidative metabolism is central toward chronological lifespan extension by CR in this yeast.}, }
@article {pmid23394930, year = {2013}, author = {Ambrosio, AB and do Nascimento, LC and Oliveira, BV and Teixeira, PJ and Tiburcio, RA and Toledo Thomazella, DP and Leme, AF and Carazzolle, MF and Vidal, RO and Mieczkowski, P and Meinhardt, LW and Pereira, GA and Cabrera, OG}, title = {Global analyses of Ceratocystis cacaofunesta mitochondria: from genome to proteome.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {91}, pmid = {23394930}, issn = {1471-2164}, mesh = {Ascomycota/classification/*genetics/pathogenicity ; Cacao/genetics/microbiology ; Computational Biology ; DNA, Mitochondrial/*genetics ; Gene Expression Regulation, Fungal ; *Genome, Mitochondrial ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/*genetics ; Phylogeny ; Plant Diseases/genetics/microbiology ; Proteome/analysis/genetics ; }, abstract = {BACKGROUND: The ascomycete fungus Ceratocystis cacaofunesta is the causal agent of wilt disease in cacao, which results in significant economic losses in the affected producing areas. Despite the economic importance of the Ceratocystis complex of species, no genomic data are available for any of its members. Given that mitochondria play important roles in fungal virulence and the susceptibility/resistance of fungi to fungicides, we performed the first functional analysis of this organelle in Ceratocystis using integrated "omics" approaches.<br><br>RESULTS: The C. cacaofunesta mitochondrial genome (mtDNA) consists of a single, 103,147-bp circular molecule, making this the second largest mtDNA among the Sordariomycetes. Bioinformatics analysis revealed the presence of 15 conserved genes and 37 intronic open reading frames in C. cacaofunesta mtDNA. Here, we predicted the mitochondrial proteome (mtProt) of C. cacaofunesta, which is comprised of 1,124 polypeptides - 52 proteins that are mitochondrially encoded and 1,072 that are nuclearly encoded. Transcriptome analysis revealed 33 probable novel genes. Comparisons among the Gene Ontology results of the predicted mtProt of C. cacaofunesta, Neurospora crassa and Saccharomyces cerevisiae revealed no significant differences. Moreover, C. cacaofunesta mitochondria were isolated, and the mtProt was subjected to mass spectrometric analysis. The experimental proteome validated 27% of the predicted mtProt. Our results confirmed the existence of 110 hypothetical proteins and 7 novel proteins of which 83 and 1, respectively, had putative mitochondrial localization.<br><br>CONCLUSIONS: The present study provides the first partial genomic analysis of a species of the Ceratocystis genus and the first predicted mitochondrial protein inventory of a phytopathogenic fungus. In addition to the known mitochondrial role in pathogenicity, our results demonstrated that the global function analysis of this organelle is similar in pathogenic and non-pathogenic fungi, suggesting that its relevance in the lifestyle of these organisms should be based on a small number of specific proteins and/or with respect to differential gene regulation. In this regard, particular interest should be directed towards mitochondrial proteins with unknown function and the novel protein that might be specific to this species. Further functional characterization of these proteins could enhance our understanding of the role of mitochondria in phytopathogenicity.}, }
@article {pmid23393310, year = {2013}, author = {Edvardson, S and Porcelli, V and Jalas, C and Soiferman, D and Kellner, Y and Shaag, A and Korman, SH and Pierri, CL and Scarcia, P and Fraenkel, ND and Segel, R and Schechter, A and Frumkin, A and Pines, O and Saada, A and Palmieri, L and Elpeleg, O}, title = {Agenesis of corpus callosum and optic nerve hypoplasia due to mutations in SLC25A1 encoding the mitochondrial citrate transporter.}, journal = {Journal of medical genetics}, volume = {50}, number = {4}, pages = {240-245}, doi = {10.1136/jmedgenet-2012-101485}, pmid = {23393310}, issn = {1468-6244}, mesh = {Adolescent ; Agenesis of Corpus Callosum/*genetics/pathology ; Anion Transport Proteins/*genetics/metabolism ; Carrier Proteins/genetics/metabolism ; Female ; Humans ; Mitochondria/*genetics ; Mitochondrial Diseases ; Mitochondrial Proteins/*genetics/metabolism ; Mutation ; Optic Nerve/metabolism/*pathology ; Organic Anion Transporters ; }, abstract = {BACKGROUND: Agenesis of corpus callosum has been associated with several defects of the mitochondrial respiratory chain and the citric acid cycle. We now report the results of the biochemical and molecular studies of a patient with severe neurodevelopmental disease manifesting by agenesis of corpus callosum and optic nerve hypoplasia.<br><br>METHODS AND RESULTS: A mitochondrial disease was suspected in this patient based on the prominent excretion of 2-hydroxyglutaric acid and Krebs cycle intermediates in urine and the finding of increased reactive oxygen species content and decreased mitochondrial membrane potential in her fibroblasts. Whole exome sequencing disclosed compound heterozygosity for two pathogenic variants in the SLC25A1 gene, encoding the mitochondrial citrate transporter. These variants, G130D and R282H, segregated in the family and were extremely rare in controls. The mutated residues were highly conserved throughout evolution and in silico modeling investigations indicated that the mutations would have a deleterious effect on protein function, affecting either substrate binding to the transporter or its translocation mechanism. These predictions were validated by the observation that a yeast strain harbouring the mutations at equivalent positions in the orthologous protein exhibited a growth defect under stress conditions and by the loss of activity of citrate transport by the mutated proteins reconstituted into liposomes.<br><br>CONCLUSIONS: We report for the first time a patient with a mitochondrial citrate carrier deficiency. Our data support a role for citric acid cycle defects in agenesis of corpus callosum as already reported in patients with aconitase or fumarate hydratase deficiency.}, }
@article {pmid23390424, year = {2013}, author = {Simm, S and Papasotiriou, DG and Ibrahim, M and Leisegang, MS and Müller, B and Schorge, T and Karas, M and Mirus, O and Sommer, MS and Schleiff, E}, title = {Defining the core proteome of the chloroplast envelope membranes.}, journal = {Frontiers in plant science}, volume = {4}, number = {}, pages = {11}, pmid = {23390424}, issn = {1664-462X}, abstract = {High-throughput protein localization studies require multiple strategies. Mass spectrometric analysis of defined cellular fractions is one of the complementary approaches to a diverse array of cell biological methods. In recent years, the protein content of different cellular (sub-)compartments was approached. Despite of all the efforts made, the analysis of membrane fractions remains difficult, in that the dissection of the proteomes of the envelope membranes of chloroplasts or mitochondria is often not reliable because sample purity is not always warranted. Moreover, proteomic studies are often restricted to single (model) species, and therefore limited in respect to differential individual evolution. In this study we analyzed the chloroplast envelope proteomes of different plant species, namely, the individual proteomes of inner and outer envelope (OE) membrane of Pisum sativum and the mixed envelope proteomes of Arabidopsis thaliana and Medicago sativa. The analysis of all three species yielded 341 identified proteins in total, 247 of them being unique. 39 proteins were genuine envelope proteins found in at least two species. Based on this and previous envelope studies we defined the core envelope proteome of chloroplasts. Comparing the general overlap of the available six independent studies (including ours) revealed only a number of 27 envelope proteins. Depending on the stringency of applied selection criteria we found 231 envelope proteins, while less stringent criteria increases this number to 649 putative envelope proteins. Based on the latter we provide a map of the outer and inner envelope core proteome, which includes many yet uncharacterized proteins predicted to be involved in transport, signaling, and response. Furthermore, a foundation for the functional characterization of yet unidentified functions of the inner and OE for further analyses is provided.}, }
@article {pmid23389667, year = {2013}, author = {Hardouin, EA and Tautz, D}, title = {Increased mitochondrial mutation frequency after an island colonization: positive selection or accumulation of slightly deleterious mutations?.}, journal = {Biology letters}, volume = {9}, number = {2}, pages = {20121123}, pmid = {23389667}, issn = {1744-957X}, mesh = {Animals ; Evolution, Molecular ; Founder Effect ; Genes, rRNA ; Genetic Drift ; Genome, Mitochondrial ; Haplotypes ; Islands ; Mice/*genetics ; Mice, Inbred Strains/genetics ; Mitochondria/*genetics ; Mutation ; *Mutation Rate ; NADH Dehydrogenase/genetics ; *Selection, Genetic ; Time Factors ; }, abstract = {Island colonizations are excellent models for studying early processes of evolution. We found in a previous study on mice that had colonized the sub-Antarctic Kerguelen Archipelago about 200 years ago that they were derived from a single founder lineage and that this showed an unexpectedly large number of new mutations in the mitochondrial D-loop. To assess whether positive selection has played a role in the emergence of these variants, we have obtained 16 full mitochondrial genome sequences from these mice. For comparison, we have compiled 57 mitochondrial genome sequences from laboratory inbred lines that became established about 100 years ago, also starting from a single founder lineage. We find that the island mice and the laboratory lines show very similar mutation frequencies and patterns. None of the patterns in the Kerguelen mice provides evidence for positive selection. We conclude that nearly neutral evolutionary processes that assume the presence of slightly deleterious variants can fully explain the patterns. This supports the notion of time-dependency of molecular evolution and provides a new calibration point. Based on the observed mutation frequency, we calculate an average evolutionary rate of 0.23 substitutions per site per Myr for the earliest time frame of divergence, which is about six times higher than the long-term rate of 0.037 substitutions per site per Myr.}, }
@article {pmid23382693, year = {2013}, author = {Meiklejohn, CD and Holmbeck, MA and Siddiq, MA and Abt, DN and Rand, DM and Montooth, KL}, title = {An Incompatibility between a mitochondrial tRNA and its nuclear-encoded tRNA synthetase compromises development and fitness in Drosophila.}, journal = {PLoS genetics}, volume = {9}, number = {1}, pages = {e1003238}, pmid = {23382693}, issn = {1553-7404}, support = {F32 GM076812/GM/NIGMS NIH HHS/United States ; NIH R01GM067862/GM/NIGMS NIH HHS/United States ; R01AG027849/AG/NIA NIH HHS/United States ; F31 AG040925/AG/NIA NIH HHS/United States ; R01 GM067862/GM/NIGMS NIH HHS/United States ; NIH NRSA GM076812/GM/NIGMS NIH HHS/United States ; NIH F31AG040925/AG/NIA NIH HHS/United States ; NIH NRSA GM072399/GM/NIGMS NIH HHS/United States ; F32 GM072399/GM/NIGMS NIH HHS/United States ; R01 AG027849/AG/NIA NIH HHS/United States ; }, mesh = {Amino Acids ; *Amino Acyl-tRNA Synthetases/genetics/metabolism ; Animals ; Cell Nucleus/genetics/metabolism ; *Drosophila/genetics/growth &amp; development/physiology ; Epistasis, Genetic ; Evolution, Molecular ; Genetic Fitness ; Humans ; Mitochondria/genetics/metabolism ; Mitochondrial Diseases ; Molecular Sequence Data ; *Oxidative Phosphorylation ; Polymorphism, Genetic ; *RNA, Transfer/genetics ; Tyrosine-tRNA Ligase/metabolism ; }, abstract = {Mitochondrial transcription, translation, and respiration require interactions between genes encoded in two distinct genomes, generating the potential for mutations in nuclear and mitochondrial genomes to interact epistatically and cause incompatibilities that decrease fitness. Mitochondrial-nuclear epistasis for fitness has been documented within and between populations and species of diverse taxa, but rarely has the genetic or mechanistic basis of these mitochondrial-nuclear interactions been elucidated, limiting our understanding of which genes harbor variants causing mitochondrial-nuclear disruption and of the pathways and processes that are impacted by mitochondrial-nuclear coevolution. Here we identify an amino acid polymorphism in the Drosophila melanogaster nuclear-encoded mitochondrial tyrosyl-tRNA synthetase that interacts epistatically with a polymorphism in the D. simulans mitochondrial-encoded tRNA(Tyr) to significantly delay development, compromise bristle formation, and decrease fecundity. The incompatible genotype specifically decreases the activities of oxidative phosphorylation complexes I, III, and IV that contain mitochondrial-encoded subunits. Combined with the identity of the interacting alleles, this pattern indicates that mitochondrial protein translation is affected by this interaction. Our findings suggest that interactions between mitochondrial tRNAs and their nuclear-encoded tRNA synthetases may be targets of compensatory molecular evolution. Human mitochondrial diseases are often genetically complex and variable in penetrance, and the mitochondrial-nuclear interaction we document provides a plausible mechanism to explain this complexity.}, }
@article {pmid23365671, year = {2013}, author = {Jacobson, AL and Booth, W and Vargo, EL and Kennedy, GG}, title = {Thrips tabaci population genetic structure and polyploidy in relation to competency as a vector of tomato spotted wilt virus.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e54484}, pmid = {23365671}, issn = {1932-6203}, mesh = {Animals ; Electron Transport Complex IV/classification/*genetics ; *Genetics, Population ; Host-Pathogen Interactions ; Insect Vectors/*genetics/virology ; Microsatellite Repeats ; Mitochondria/enzymology/genetics ; North Carolina ; Phylogeny ; Plant Diseases/prevention &amp; control/virology ; Polyploidy ; Protein Subunits/classification/*genetics ; Reproduction/*genetics ; Sequence Analysis, DNA ; Thysanoptera/*genetics/virology ; Tospovirus/*physiology ; }, abstract = {Knowledge of population-level genetic differences can help explain variation among populations of insect vectors in their role in the epidemiology of specific viruses. Variation in competency to transmit Tomato spotted wilt virus (TSWV) that exists among populations of Thrips tabaci has been associated with the presence of cryptic species that exhibit different modes of reproduction and host ranges. However, recent findings suggest that vector competency of T. tabaci at any given location depends on the thrips and virus populations that are present. This study characterizes the population genetic structure of T. tabaci collected from four locations in North Carolina and examines the relationship between population genetic structure and variation in TSWV transmission by T. tabaci. Mitochondrial COI sequence analysis revealed the presence of two genetically distinct groups with one characterized by thelytokous, parthenogenetic reproduction and the other by arrhenotokous, sexual reproduction. Using a set of 11 microsatellite markers that we developed to investigate T. tabaci population genetic structure, we identified 17 clonal groups and found significant genetic structuring among the four NC populations that corresponded to the geographic locations where the populations were collected. Application of microsatellite markers also led to the discovery of polyploidy in this species. All four populations contained tetraploid individuals, and three contained both diploid and tetraploid individuals. Analysis of variation in transmission ofTSWV among isofemale lines initiated with individuals used in this study revealed that 'clone assignment,' 'virus isolate' and their interaction significantly influenced vector competency. These results highlight the importance of interactions between specific T. tabaci clonal types and specific TSWV isolates underlying transmission of TSWV by T. tabaci.}, }
@article {pmid23362369, year = {2013}, author = {Lenz, H and Knoop, V}, title = {PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation.}, journal = {Bioinformatics and biology insights}, volume = {7}, number = {}, pages = {1-19}, pmid = {23362369}, issn = {1177-9322}, abstract = {RNA editing is vast in some genetic systems, with up to thousands of targeted C-to-U and U-to-C substitutions in mitochondria and chloroplasts of certain plants. Efficient prognoses of RNA editing in organelle genomes will help to reveal overlooked cases of editing. We present PREPACT 2.0 (http://www.prepact.de) with numerous enhancements of our previously developed Plant RNA Editing Prediction &amp; Analysis Computer Tool. Reference organelle transcriptomes for editing prediction have been extended and reorganized to include 19 curated mitochondrial and 13 chloroplast genomes, now allowing to distinguish RNA editing sites from "pre-edited" sites. Queries may be run against multiple references and a new "commons" function identifies and highlights orthologous candidate editing sites congruently predicted by multiple references. Enhancements to the BLASTX mode in PREPACT 2.0 allow querying of complete novel organelle genomes within a few minutes, identifying protein genes and candidate RNA editing sites simultaneously without prior user analyses.}, }
@article {pmid23361615, year = {2013}, author = {Greiner, S and Bock, R}, title = {Tuning a ménage à trois: co-evolution and co-adaptation of nuclear and organellar genomes in plants.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {35}, number = {4}, pages = {354-365}, doi = {10.1002/bies.201200137}, pmid = {23361615}, issn = {1521-1878}, mesh = {Adaptation, Biological/*genetics ; Biological Evolution ; Cell Nucleus/genetics/physiology ; Chloroplasts/genetics/physiology ; Cytoplasm/genetics ; DNA, Plant/genetics ; Evolution, Molecular ; *Genome, Chloroplast ; *Genome, Mitochondrial ; *Genome, Plant ; Mitochondria/genetics/physiology ; Plant Physiological Phenomena ; Plants/*genetics ; }, abstract = {Plastids and mitochondria arose through endosymbiotic acquisition of formerly free-living bacteria. During more than a billion years of subsequent concerted evolution, the three genomes of plant cells have undergone dramatic structural changes to optimize the expression of the compartmentalized genetic material and to fine-tune the communication between the nucleus and the organelles. The chimeric composition of many multiprotein complexes in plastids and mitochondria (one part of the subunits being nuclear encoded and another one being encoded in the organellar genome) provides a paradigm for co-evolution at the cellular level. In this paper, we discuss the co-evolution of nuclear and organellar genomes in the context of environmental adaptation in species and populations. We highlight emerging genetic model systems and new experimental approaches that are particularly suitable to elucidate the molecular basis of co-adaptation processes and describe how nuclear-cytoplasmic co-evolution can cause genetic incompatibilities that contribute to the establishment of hybridization barriers, ultimately leading to the formation of new species.}, }
@article {pmid23360288, year = {2013}, author = {Loureiro, R and Mesquita, KA and Oliveira, PJ and Vega-Naredo, I}, title = {Mitochondria in cancer stem cells: a target for therapy.}, journal = {Recent patents on endocrine, metabolic &amp; immune drug discovery}, volume = {7}, number = {2}, pages = {102-114}, doi = {10.2174/18722148113079990006}, pmid = {23360288}, issn = {2212-3334}, mesh = {Animals ; Antineoplastic Agents/*pharmacology ; Drug Design ; Energy Metabolism/drug effects ; Humans ; Mitochondria/*drug effects/metabolism/pathology ; Mitochondrial Membrane Transport Proteins/drug effects/metabolism ; Mitochondrial Permeability Transition Pore ; Neoplasms/*drug therapy/metabolism/pathology ; Neoplastic Stem Cells/*drug effects/metabolism/pathology ; Oxidation-Reduction ; Patents as Topic ; }, abstract = {Complete knowledge about the evolution of the carcinogenic process has to include cancer stem cells (CSCs), which are essential to understand tumor occurrence, recurrence, and also its reduction rate after radio- and/or chemotherapeutic treatments. Understanding CSCs physiology and metabolism may be crucial for the development of novel effective therapies. Therefore, being mitochondria an undeniable target for cancer therapy and a central hub in metabolism and cell and death decisions, it is essential to take this organelle into account and explore its actions and involvements in the context of CSCs physiology. In this review, we focus on recent patents and discoveries about mitochondrial bioenergetics and physiology of CSCs. A full understanding of the role of mitochondrial activity in CSCs and the creation of new strategies, methods and discoveries to support actual treatments with novel ones are of pivotal importance in order to ultimately eradicate cancer.}, }
@article {pmid23358826, year = {2013}, author = {Szczesny, RJ and Hejnowicz, MS and Steczkiewicz, K and Muszewska, A and Borowski, LS and Ginalski, K and Dziembowski, A}, title = {Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels.}, journal = {Nucleic acids research}, volume = {41}, number = {5}, pages = {3144-3161}, pmid = {23358826}, issn = {1362-4962}, mesh = {Amino Acid Substitution ; Catalytic Domain ; DNA Cleavage ; DNA, Mitochondrial/*metabolism ; DNA, Single-Stranded/chemistry ; Exodeoxyribonucleases/chemistry/*genetics/metabolism ; Gene Expression ; Gene Knockdown Techniques ; HeLa Cells ; Humans ; Hydrogen-Ion Concentration ; Mitochondria/*enzymology/genetics ; Models, Molecular ; Molecular Sequence Annotation ; Mutagenesis, Site-Directed ; Phylogeny ; Protein Structure, Secondary ; Protein Transport ; RNA, Small Interfering/genetics ; Sequence Analysis, DNA ; }, abstract = {Although the human mitochondrial genome has been investigated for several decades, the proteins responsible for its replication and expression, especially nucleolytic enzymes, are poorly described. Here, we characterized a novel putative PD-(D/E)XK nuclease encoded by the human C20orf72 gene named Ddk1 for its predicted catalytic residues. We show that Ddk1 is a mitochondrially localized metal-dependent DNase lacking detectable ribonuclease activity. Ddk1 degrades DNA mainly in a 3'-5' direction with a strong preference for single-stranded DNA. Interestingly, Ddk1 requires free ends for its activity and does not degrade circular substrates. In addition, when a chimeric RNA-DNA substrate is provided, Ddk1 can slide over the RNA fragment and digest DNA endonucleolytically. Although the levels of the mitochondrial DNA are unchanged on RNAi-mediated depletion of Ddk1, the mitochondrial single-stranded DNA molecule (7S DNA) accumulates. On the other hand, overexperssion of Ddk1 decreases the levels of 7S DNA, suggesting an important role of the protein in 7S DNA regulation. We propose a structural model of Ddk1 and discuss its similarity to other PD-(D/E)XK superfamily members.}, }
@article {pmid23356268, year = {2013}, author = {Ballinger, SW}, title = {Beyond retrograde and anterograde signalling: mitochondrial-nuclear interactions as a means for evolutionary adaptation and contemporary disease susceptibility.}, journal = {Biochemical Society transactions}, volume = {41}, number = {1}, pages = {111-117}, pmid = {23356268}, issn = {1470-8752}, support = {R01HL94518/HL/NHLBI NIH HHS/United States ; P30 DK079626/DK/NIDDK NIH HHS/United States ; R01 HL103859/HL/NHLBI NIH HHS/United States ; R01 HL094518/HL/NHLBI NIH HHS/United States ; R01HL103859/HL/NHLBI NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Cell Nucleus/*metabolism ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; *Genetic Predisposition to Disease ; Humans ; Mitochondria/*metabolism ; Mutation ; *Signal Transduction ; }, abstract = {Although there is general agreement that most forms of common disease develop as a consequence of a combination of factors, including genetic, environmental and behavioural contributors, the actual mechanistic basis of how these factors initiate or promote diabetes, cancer, neurodegenerative and cardiovascular diseases in some individuals but not in others with seemingly identical risk factor profiles, is not clearly understood. In this respect, consideration of the potential role for mitochondrial genetics, damage and function in influencing common disease susceptibility seems merited, given that the prehistoric challenges were the original factors that moulded cellular function, and these were based upon the mitochondrial-nuclear relationships that were established during evolutionary history. These interactions were probably refined during prehistoric environmental selection events that, at present, are largely absent. Contemporary risk factors such as diet, sedentary lifestyle and increased longevity, which influence our susceptibility to a variety of chronic diseases were not part of the dynamics that defined the processes of mitochondrial-nuclear interaction, and thus cell function. Consequently, the prehistoric challenges that contributed to cell functionality and evolution should be considered when interpreting and designing experimental data and strategies. Although several molecular epidemiological studies have generally supported this notion, studies that probe beyond these associations are required. Such investigation will mark the initial steps for mechanistically addressing the provocative concept that contemporary human disease susceptibility is the result of prehistoric selection events for mitochondrial-nuclear function, which increased the probability for survival and reproductive success during evolution.}, }
@article {pmid23350036, year = {2013}, author = {Makiuchi, T and Mi-ichi, F and Nakada-Tsukui, K and Nozaki, T}, title = {Novel TPR-containing subunit of TOM complex functions as cytosolic receptor for Entamoeba mitosomal transport.}, journal = {Scientific reports}, volume = {3}, number = {}, pages = {1129}, pmid = {23350036}, issn = {2045-2322}, mesh = {Biological Transport ; Carrier Proteins/chemistry/genetics/*metabolism ; Entamoeba/*metabolism ; Gene Silencing ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Phenotype ; Protein Subunits/genetics/metabolism ; Protozoan Proteins/chemistry/genetics/*metabolism ; }, abstract = {Under anaerobic environments, the mitochondria have undergone remarkable reduction and transformation into highly reduced structures, referred as mitochondrion-related organelles (MROs), which include mitosomes and hydrogenosomes. In agreement with the concept of reductive evolution, mitosomes of Entamoeba histolytica lack most of the components of the TOM (translocase of the outer mitochondrial membrane) complex, which is required for the targeting and membrane translocation of preproteins into the canonical aerobic mitochondria. Here we showed, in E. histolytica mitosomes, the presence of a 600-kDa TOM complex composed of Tom40, a conserved pore-forming subunit, and Tom60, a novel lineage-specific receptor protein. Tom60, containing multiple tetratricopeptide repeats, is localized to the mitosomal outer membrane and the cytosol, and serves as a receptor of both mitosomal matrix and membrane preproteins. Our data indicate that Entamoeba has invented a novel lineage-specific shuttle receptor of the TOM complex as a consequence of adaptation to an anaerobic environment.}, }
@article {pmid23349865, year = {2013}, author = {Ilinsky, Y}, title = {Coevolution of Drosophila melanogaster mtDNA and Wolbachia genotypes.}, journal = {PloS one}, volume = {8}, number = {1}, pages = {e54373}, pmid = {23349865}, issn = {1932-6203}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Drosophila melanogaster/*genetics ; Evolution, Molecular ; Female ; Genetic Variation ; Genotype ; Haplotypes ; Host-Parasite Interactions/*genetics ; Mitochondria/genetics ; Phylogeny ; Wolbachia/*genetics ; }, abstract = {Maternally inherited microorganisms can influence the mtDNA pattern of variation in hosts. This influence is driven by selection among symbionts and can cause the frequency of mitochondrial variants in the population to eventually increase or decrease. Wolbachia infection is common and widespread in Drosophila melanogaster populations. We compared genetic variability of D. melanogaster mitotypes with Wolbachia genotypes among isofemale lines associated with different geographic locations and time intervals to study coevolution of the mtDNA and Wolbachia. Phylogenetic analysis of D. melanogaster mtDNA revealed two clades diverged in Africa, each associated with one of the two Wolbachia genotype groups. No evidence of horizontal transmission of Wolbachia between maternal lineages has been found. All the mtDNA variants that occur in infected isofemale lines are found in uninfected isofemale lines and vice versa, which is indicative of a recent loss of infection from some maternal fly lineages and confirms a significant role of Wolbachia in the D. melanogaster mtDNA pattern of variation. Finally, we present a comparative analysis of biogeographic distribution of D. melanogaster mitotypes all over the world.}, }
@article {pmid23345534, year = {2013}, author = {Klaus, S and Mendoza, JC and Liew, JH and Plath, M and Meier, R and Yeo, DC}, title = {Rapid evolution of troglomorphic characters suggests selection rather than neutral mutation as a driver of eye reduction in cave crabs.}, journal = {Biology letters}, volume = {9}, number = {2}, pages = {20121098}, pmid = {23345534}, issn = {1744-957X}, mesh = {Adaptation, Biological ; Animals ; Bayes Theorem ; Brachyura/classification/*genetics/growth &amp; development ; Caves ; Darkness ; *Evolution, Molecular ; Eye/*cytology/growth &amp; development ; Genetic Drift ; Genetic Variation ; Islands ; Mitochondria/genetics ; *Mutation ; Organ Size ; Philippines ; Phylogeny ; *Selection, Genetic ; Sensilla/growth &amp; development ; Time Factors ; }, abstract = {This study asked whether reductive traits in cave organisms evolve at a slower pace (suggesting neutral evolution under relaxed selection) than constructive changes, which are likely to evolve under directional selection. We investigated 11 subterranean and seven surface populations of Sundathelphusa freshwater crabs on Bohol Island, Philippines, and examined constructive traits associated with improved food finding in darkness (increased leg and setae length) and reductive traits (reduced cornea size and eyestalk length). All changes occurred rapidly, given that the age of the most recent common ancestor was estimated to be 722-271 ka based on three mitochondrial markers. In order to quantify the speed of character change, we correlated the degree of morphological change with genetic distances between surface and subterranean individuals. The temporal pattern of character change following the transition to subterranean life was indistinguishable for constructive and reductive traits, characterized by an immediate onset and rapid evolutionary change. We propose that the evolution of these reductive traits-just like constructive traits-is most likely driven by strong directional selection.}, }
@article {pmid23344321, year = {2013}, author = {Tumonggor, MK and Karafet, TM and Hallmark, B and Lansing, JS and Sudoyo, H and Hammer, MF and Cox, MP}, title = {The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific.}, journal = {Journal of human genetics}, volume = {58}, number = {3}, pages = {165-173}, doi = {10.1038/jhg.2012.154}, pmid = {23344321}, issn = {1435-232X}, mesh = {Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/*genetics ; Emigration and Immigration ; Ethnicity/genetics ; Female ; *Genetic Variation ; Genetics, Population/*methods ; Haplotypes ; Humans ; Indonesia ; Male ; Mitochondria/genetics ; Pacific Islands ; Phylogeny ; Population Dynamics ; Sequence Analysis, DNA ; }, abstract = {Indonesia, an island nation linking mainland Asia with the Pacific world, hosts a wide range of linguistic, ethnic and genetic diversity. Despite the complexity of this cultural environment, genetic studies in Indonesia remain surprisingly sparse. Here, we report mitochondrial DNA (mtDNA) and associated Y-chromosome diversity for the largest cohort of Indonesians examined to date-2740 individuals from 70 communities spanning 12 islands across the breadth of the Indonesian archipelago. We reconstruct 50 000 years of population movements, from mitochondrial lineages reflecting the very earliest settlers in island southeast Asia, to Neolithic population dispersals. Historic contacts from Chinese, Indians, Arabs and Europeans comprise a noticeable fraction of Y-chromosome variation, but are not reflected in the maternally inherited mtDNA. While this historic immigration favored men, patterns of genetic diversity show that women moved more widely in earlier times. However, measures of population differentiation signal that Indonesian communities are trending away from the matri- or ambilocality of early Austronesian societies toward the more common practice of patrilocal residence today. Such sex-specific dispersal patterns remain even after correcting for the different mutation rates of mtDNA and the Y chromosome. This detailed palimpsest of Indonesian genetic diversity is a direct outcome of the region's complex history of immigration, transitory migrants and populations that have endured in situ since the region's first settlement.}, }
@article {pmid23340427, year = {2013}, author = {Davydov, II and Wohlgemuth, I and Artamonova, II and Urlaub, H and Tonevitsky, AG and Rodnina, MV}, title = {Evolution of the protein stoichiometry in the L12 stalk of bacterial and organellar ribosomes.}, journal = {Nature communications}, volume = {4}, number = {}, pages = {1387}, pmid = {23340427}, issn = {2041-1723}, mesh = {Amino Acid Sequence ; Bacteria/genetics/*metabolism ; Bacterial Proteins/chemistry/*genetics/metabolism ; Chloroplasts/metabolism ; *Evolution, Molecular ; Gene Dosage ; Humans ; Mass Spectrometry ; Mitochondria/metabolism ; Mitochondrial Proteins/chemistry/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Binding ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Ribosomal, 16S/genetics ; Ribosomal Protein L10 ; Ribosomal Proteins/chemistry/*genetics/metabolism ; Ribosomes/*metabolism ; Synechococcus/metabolism ; Thermotoga maritima/genetics/metabolism ; }, abstract = {The emergence of ribosomes and translation factors is central for understanding the origin of life. Recruitment of translation factors to bacterial ribosomes is mediated by the L12 stalk composed of protein L10 and several copies of protein L12, the only multi-copy protein of the ribosome. Here we predict stoichiometries of L12 stalk for >1,200 bacteria, mitochondria and chloroplasts by a computational analysis, and validate the predictions by quantitative mass spectrometry. The majority of bacteria have L12 stalks allowing for binding of four or six copies of L12, largely independent of the taxonomic group or living conditions of the bacteria, whereas some cyanobacteria have eight copies. Mitochondrial and chloroplast ribosomes can accommodate six copies of L12. The last universal common ancestor probably had six molecules of L12 molecules bound to L10. Changes of the stalk composition provide a unique possibility to trace the evolution of protein components of the ribosome.}, }
@article {pmid23331624, year = {2014}, author = {Bezzaouia, A and Gallo, A and Silvestre, F and Tekaya, S and Tosti, E}, title = {Distribution pattern and activity of mitochondria during oocyte growth and maturation in the ascidian Styela plicata.}, journal = {Zygote (Cambridge, England)}, volume = {22}, number = {4}, pages = {462-469}, doi = {10.1017/S0967199412000640}, pmid = {23331624}, issn = {1469-8730}, mesh = {Animals ; Cytoplasm/metabolism ; Female ; Microscopy, Electron, Transmission ; Mitochondria/*metabolism ; Oocytes/cytology/growth &amp; development/*physiology ; Urochordata ; }, abstract = {The process of oocyte maturation is underlined by a redistribution of cellular organelles, among which mitochondria play a functional role for the acquisition of fertilization and developmental competence. In this paper, we applied electron and confocal microscopy by using DIOC6 and JC-1 stain to evaluate mitochondria distribution pattern and activity during different stages of oocyte growth in the ascidian Styela plicata. Three categories of oocytes at the germinal vesicle stage underlying the vitellogenic process were characterized on the basis of size, pigmentation and accessory cells. Mitochondria were spread throughout the cytoplasm at the smallest oocyte stage and gradually migrated to the periphery of the subcortical cytoplasm at the intermediate stage. At the fully grown oocyte stage, mitochondria were aggregated in the subcortical cytoplasm. This pattern of polarized mitochondria distribution correlates significantly with an increase in mitochondria potential and activity. In this paper we discuss the relationship of mitochondria to the acquisition of oocyte developmental competence.}, }
@article {pmid23329686, year = {2013}, author = {Sahi, C and Kominek, J and Ziegelhoffer, T and Yu, HY and Baranowski, M and Marszalek, J and Craig, EA}, title = {Sequential duplications of an ancient member of the DnaJ-family expanded the functional chaperone network in the eukaryotic cytosol.}, journal = {Molecular biology and evolution}, volume = {30}, number = {5}, pages = {985-998}, pmid = {23329686}, issn = {1537-1719}, support = {R01 GM031107/GM/NIGMS NIH HHS/United States ; R37 GM031107/GM/NIGMS NIH HHS/United States ; GM31107/GM/NIGMS NIH HHS/United States ; }, mesh = {Cytosol/*metabolism ; Evolution, Molecular ; Gene Duplication/*genetics ; HSP40 Heat-Shock Proteins/*genetics/metabolism ; HSP70 Heat-Shock Proteins/genetics/metabolism ; Heat-Shock Proteins/genetics/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {Across eukaryotes, Hsp70-based chaperone machineries display an underlying unity in their sequence, structure, and biochemical mechanism of action, while working in a myriad of cellular processes. In good part, this extraordinary functional versatility is derived from the ability of a single Hsp70 to interact with an array of J-protein cochaperones to form a functional chaperone network. Among J-proteins, the DnaJ-type is the most prevalent, being present in all three kingdoms and in several different compartments of eukaryotic cells. However, because these ancient DnaJ-type proteins diverged at the base of the eukaryotic phylogeny, little is understood about the evolutionary basis of their diversification and thus the functional expansion of the chaperone network. Here, we report results of evolutionary and experimental analyses of two more recent members of the cytosolic DnaJ family of Saccharomyces cerevisiae, Xdj1 and Apj1, which emerged by sequential duplications of the ancient YDJ1 in Ascomycota. Sequence comparison and molecular modeling revealed that both Xdj1 and Apj1 maintained a domain organization similar to that of multifunctional Ydj1. However, despite these similarities, both Xdj1 and Apj1 evolved highly specialized functions. Xdj1 plays a unique role in the translocation of proteins from the cytosol into mitochondria. Apj1's specialized role is related to degradation of sumolyated proteins. Together these data provide the first clear example of cochaperone duplicates that evolved specialized functions, allowing expansion of the chaperone functional network, while maintaining the overall structural organization of their parental gene.}, }
@article {pmid23327366, year = {2013}, author = {Chen, HN and Høeg, JT and Chan, BK}, title = {Morphometric and molecular identification of individual barnacle cyprids from wild plankton: an approach to detecting fouling and invasive barnacle species.}, journal = {Biofouling}, volume = {29}, number = {2}, pages = {133-145}, doi = {10.1080/08927014.2012.753061}, pmid = {23327366}, issn = {1029-2454}, mesh = {Animals ; *Biofouling ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/analysis/genetics ; Ecosystem ; Electron Transport Complex IV/genetics ; Genetic Variation ; Introduced Species ; Larva/classification/genetics/ultrastructure ; Microscopy, Electron, Scanning ; Mitochondria/genetics ; Multivariate Analysis ; Phylogeny ; Species Specificity ; Taiwan ; Thoracica/anatomy &amp; histology/*classification/genetics ; }, abstract = {The present study used DNA barcodes to identify individual cyprids to species. This enables accurate quantification of larvae of potential fouling species in the plankton. In addition, it explains the settlement patterns of barnacles and serves as an early warning system of unwanted immigrant species. Sequences from a total of 540 individual cypris larvae from Taiwanese waters formed 36 monophyletic clades (species) in a phylogenetic tree. Of these clades, 26 were identified to species, but 10 unknown monophyletic clades represented non-native species. Cyprids of the invasive barnacle, Megabalanus cocopoma, were identified. Multivariate analysis of antennular morphometric characters revealed three significant clusters in a nMDS plot, viz. a bell-shaped attachment organ (most species), a shoe-shaped attachment organ (some species), and a spear-shaped attachment organ (coral barnacles only). These differences in attachment organ structure indicate that antennular structures interact directly with the diverse substrata involved in cirripede settlement.}, }
@article {pmid23316809, year = {2013}, author = {Stöck, M and Savary, R and Betto-Colliard, C and Biollay, S and Jourdan-Pineau, H and Perrin, N}, title = {Low rates of X-Y recombination, not turnovers, account for homomorphic sex chromosomes in several diploid species of Palearctic green toads (Bufo viridis subgroup).}, journal = {Journal of evolutionary biology}, volume = {26}, number = {3}, pages = {674-682}, doi = {10.1111/jeb.12086}, pmid = {23316809}, issn = {1420-9101}, mesh = {Alleles ; Animals ; Bufonidae/classification/*genetics/metabolism ; DNA, Mitochondrial/analysis/genetics ; *Diploidy ; Evolution, Molecular ; Female ; Genetic Linkage ; Genotyping Techniques ; Inbreeding ; Male ; Mitochondria/genetics ; Phylogeny ; *Recombination, Genetic ; Sequence Analysis, DNA ; Time Factors ; X Chromosome/genetics/*metabolism ; Y Chromosome/genetics/*metabolism ; }, abstract = {Contrasting with birds and mammals, most ectothermic vertebrates present homomorphic sex chromosomes, which might be due either to a high turnover rate or to occasional X-Y recombination. We tested these two hypotheses in a group of Palearctic green toads that diverged some 3.3 million years ago. Using sibship analyses of sex-linked markers, we show that all four species investigated share the same pair of sex chromosomes and a pattern of male heterogamety with drastically reduced X-Y recombination in males. Phylogenetic analyses of sex-linked sequences show that X and Y alleles cluster by species, not by gametolog. We conclude that X-Y homomorphy and fine-scale sequence similarity in these species do not stem from recent sex-chromosome turnovers, but from occasional X-Y recombination.}, }
@article {pmid23313296, year = {2013}, author = {Marshall, HD and Baker, AJ and Grant, AR}, title = {Complete mitochondrial genomes from four subspecies of common chaffinch (Fringilla coelebs): new inferences about mitochondrial rate heterogeneity, neutral theory, and phylogenetic relationships within the order Passeriformes.}, journal = {Gene}, volume = {517}, number = {1}, pages = {37-45}, doi = {10.1016/j.gene.2012.12.093}, pmid = {23313296}, issn = {1879-0038}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Finches/classification/*genetics ; *Genetic Variation ; Genome, Mitochondrial/*genetics ; Humans ; Mitochondria/genetics ; *Phylogeny ; }, abstract = {We describe whole mitochondrial genome sequences from four subspecies of the common chaffinch (Fringilla coelebs), and compare them to 31 publicly available mitochondrial genome sequences from other Passeriformes. Rates and patterns of mitochondrial gene evolution are analyzed at different taxonomic levels within this avian order, and evidence is adduced for and against the nearly neutral theory of molecular evolution and the role of positive selection in shaping genetic variation of this small but critical genome. We find evidence of mitochondrial rate heterogeneity in birds as in other vertebrates, likely due to differences in mutational pressure across the genome. Unlike in gadine fish and some of the human mitochondrial work we do not observe strong support for the nearly neutral theory of molecular evolution; instead evidence from molecular clocks, distribution of dN/dS ratios at different levels of the taxonomic hierarchy and in different lineages, McDonald-Kreitman tests within Fringillidae, and site-specific tests of selection within Passeriformes, all point to a role for positive selection, especially for the complex I NADH dehydrogenase genes. The protein-coding mitogenome phylogeny of the order Passeriformes is broadly consistent with previously-reported molecular findings, but provides support for a sister relationship between the superfamilies Muscicapoidea and Passeroidea on a short basal internode of the Passerida where relationships have been difficult to resolve. An unexpected placement of the Paridae (represented by Hume's groundpecker) within the Muscicapoidea was observed. Consistent with other molecular studies the mtDNA phylogeny reveals paraphyly within the Muscicapoidea and a sister relationship of Fringilla with Carduelis rather than Emberiza.}, }
@article {pmid23311980, year = {2013}, author = {Watt, WB and Hudson, RR and Wang, B and Wang, E}, title = {A genetic polymorphism evolving in parallel in two cell compartments and in two clades.}, journal = {BMC evolutionary biology}, volume = {13}, number = {}, pages = {9}, pmid = {23311980}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Butterflies/enzymology/*genetics ; Citric Acid Cycle ; Cytosol/enzymology ; *Evolution, Molecular ; Genes, Insect ; Glycolysis ; Likelihood Functions ; Mitochondria/enzymology ; Models, Genetic ; Molecular Sequence Data ; Phosphoenolpyruvate Carboxykinase (ATP)/*genetics ; *Polymorphism, Genetic ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: The enzyme phosphoenolpyruvate carboxykinase, PEPCK, occurs in its guanosine-nucleotide-using form in animals and a few prokaryotes. We study its natural genetic variation in Colias (Lepidoptera, Pieridae). PEPCK offers a route, alternative to pyruvate kinase, for carbon skeletons to move between cytosolic glycolysis and mitochondrial Krebs cycle reactions.<br><br>RESULTS: PEPCK is expressed in both cytosol and mitochondrion, but differently in diverse animal clades. In vertebrates and independently in Drosophila, compartment-specific paralogous genes occur. In a contrasting expression strategy, compartment-specific PEPCKs of Colias and of the silkmoth, Bombyx, differ only in their first, 5', exons; these are alternatively spliced onto a common series of following exons. In two Colias species from distinct clades, PEPCK sequence is highly variable at nonsynonymous and synonymous sites, mainly in its common exons. Three major amino acid polymorphisms, Gly 335 &#x2194; Ser, Asp 503 &#x2194; Glu, and Ile 629 &#x2194; Val occur in both species, and in the first two cases are similar in frequency between species. Homology-based structural modelling shows that the variants can alter hydrogen bonding, salt bridging, or van der Waals interactions of amino acid side chains, locally or at one another's sites which are distant in PEPCK's structure, and thus may affect its enzyme function. We ask, using coalescent simulations, if these polymorphisms' cross-species similarities are compatible with neutral evolution by genetic drift, but find the probability of this null hypothesis is 0.001&#x2009;&#x2264;&#x2009;P&#x2009;&#x2264;&#x2009;0.006 under differing scenarios.<br><br>CONCLUSION: Our results make the null hypothesis of neutrality of these PEPCK polymorphisms quite unlikely, but support an alternative hypothesis that they are maintained by natural selection in parallel in the two species. This alternative can now be justifiably tested further via studies of PEPCK genotypes' effects on function, organismal performance, and fitness. This case emphasizes the importance, for evolutionary insight, of studying gene-specific mechanisms affected by natural genetic variation as an essential complement to surveys of such variation.}, }
@article {pmid23305819, year = {2013}, author = {Matsunaga, M and Takahashi, Y and Yui-Kurino, R and Mikami, T and Kubo, T}, title = {Evolutionary aspects of a unique internal mitochondrial targeting signal in nuclear-migrated rps19 of sugar beet (Beta vulgaris L.).}, journal = {Gene}, volume = {517}, number = {1}, pages = {19-26}, doi = {10.1016/j.gene.2012.12.099}, pmid = {23305819}, issn = {1879-0038}, mesh = {Amino Acid Sequence ; Beta vulgaris/*metabolism ; *Biological Evolution ; Cell Nucleus/*genetics ; Cloning, Molecular ; DNA, Mitochondrial/genetics ; Genome, Plant ; Mitochondria/genetics/*metabolism ; Mitochondrial Membranes/metabolism ; Molecular Sequence Data ; Phylogeny ; Ribosomal Proteins/genetics/*metabolism ; Sequence Homology, Amino Acid ; Nicotiana/*metabolism ; }, abstract = {The endosymbiotic theory postulates that many genes migrated from endosymbionts to the nuclear genomes of their hosts. Some migrated genes lack presequences directing proteins to mitochondria, and their mitochondrial targeting signals appear to be inscribed in the core coding regions as internal targeting signals (ITSs). ITSs may have evolved after sequence transfer to nuclei or ITSs may have pre-existed before sequence transfer. Here, we report the molecular cloning of a sugar beet gene for ribosomal protein S19 (Rps19; the first letter is capitalized when the gene is a nuclear gene). We show that sugar beet Rps19 (BvRps19) is an ITS-type gene. Based on amino-acid sequence comparison, dicotyledonous rps19s (the first letter is lower-cased when the gene is a mitochondrial gene), such as tobacco rps19 (Ntrps19), resemble an ancestral form of BvRps19. We investigated whether differences in amino-acid sequences between BvRps19 and Ntrps19 were involved in ITS evolution. Analyses of the intracellular localization of chimaeric GFP-fusion proteins that were transiently expressed in Welsh onion cells showed that Ntrps19-gfp was not localized in mitochondria. When several BvRps19-type amino acid substitutions, none of which was seen in any other angiosperm rps19, were introduced into Ntrps19-gfp, the modified Ntrps19-gfp became localized in mitochondria, supporting the notion that an ITS in BvRps19 evolved following sequence transfer to nuclei. Not all of these substitutions were seen in other ITS-type Rps19s, suggesting that the ITSs of Rps19 are diverse.}, }
@article {pmid23305496, year = {2013}, author = {Horne, JB and van Herwerden, L}, title = {Long-term panmixia in a cosmopolitan Indo-Pacific coral reef fish and a nebulous genetic boundary with its broadly sympatric sister species.}, journal = {Journal of evolutionary biology}, volume = {26}, number = {4}, pages = {783-799}, doi = {10.1111/jeb.12092}, pmid = {23305496}, issn = {1420-9101}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/*analysis/genetics ; *Evolution, Molecular ; Gene Flow ; Genetic Loci ; Genetic Markers ; *Genetic Variation ; Genetics, Population ; Introns ; Mitochondria/genetics ; Perciformes/*genetics ; Phylogeography ; Population Density ; Reproductive Isolation ; *Sympatry ; }, abstract = {Phylogeographical studies have shown that some shallow-water marine organisms, such as certain coral reef fishes, lack spatial population structure at oceanic scales, despite vast distances of pelagic habitat between reefs and other dispersal barriers. However, whether these dispersive widespread taxa constitute long-term panmictic populations across their species ranges remains unknown. Conventional phylogeographical inferences frequently fail to distinguish between long-term panmixia and metapopulations connected by gene flow. Moreover, marine organisms have notoriously large effective population sizes that confound population structure detection. Therefore, at what spatial scale marine populations experience independent evolutionary trajectories and ultimately species divergence is still unclear. Here, we present a phylogeographical study of a cosmopolitan Indo-Pacific coral reef fish Naso hexacanthus and its sister species Naso caesius, using two mtDNA and two nDNA markers. The purpose of this study was two-fold: first, to test for broad-scale panmixia in N. hexacanthus by fitting the data to various phylogeographical models within a Bayesian statistical framework, and second, to explore patterns of genetic divergence between the two broadly sympatric species. We report that N. hexacanthus shows little population structure across the Indo-Pacific and a range-wide, long-term panmictic population model best fit the data. Hence, this species presently comprises a single evolutionary unit across much of the tropical Indian and Pacific Oceans. Naso hexacanthus and N. caesius were not reciprocally monophyletic in the mtDNA markers but showed varying degrees of population level divergence in the two nuclear introns. Overall, patterns are consistent with secondary introgression following a period of isolation, which may be attributed to oceanographic conditions of the mid to late Pleistocene, when these two species appear to have diverged.}, }
@article {pmid23304069, year = {2012}, author = {Bi, R and Zhang, AM and Jia, X and Zhang, Q and Yao, YG}, title = {Complete mitochondrial DNA genome sequence variation of Chinese families with mutation m.3635G&gt;A and Leber hereditary optic neuropathy.}, journal = {Molecular vision}, volume = {18}, number = {}, pages = {3087-3094}, pmid = {23304069}, issn = {1090-0535}, mesh = {Adolescent ; Adult ; *Asian People ; DNA, Mitochondrial/*genetics ; Female ; *Genetic Variation ; Genome, Mitochondrial ; Haplotypes ; Humans ; Male ; Mitochondria/*genetics ; Optic Atrophy, Hereditary, Leber/*genetics ; Pedigree ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {PURPOSE: The majority of Leber hereditary optic neuropathy (LHON) cases are caused by one of three mitochondrial DNA (mtDNA) primary mutations (m.3460G>A, m.11778G>A, and m.14484T>C). In recent studies, we and others have shown that mutation m.3635G>A is a primary LHON mutation, particularly in Chinese. The purpose of this study was to perform a thorough analysis for the complete mtDNA genome sequence variation in Chinese patients with m.3635G>A and to identify potentially functional variants cosegregated with m.3635G>A.<br><br>METHODS: The complete mtDNA genomes of five Chinese patients with LHON carrying m.3635G>A were determined. A phylogenetic tree was constructed to distinguish the private and ancestral mtDNA variants in each lineage. Previously unreported variants in each mtDNA were defined with a web-based and database search. mtDNA variants that changed the structure of the membrane-spanning region of the protein were also evaluated, together with evolutionary conservation analysis, to predict their potential pathogenicity.<br><br>RESULTS: The five patients with LHON sequenced in this study belonged to haplogroups M7b4 (Le131), F1a (Le329 and Le337), B5b (Le569), and M7b6 (Le834), which suggested multiple origins of m.3635G>A. Private variants m.12811T>C, m.14063T>C, m.15237T>C, and m.9071C>T in these patients were predicted to change the structure of the membrane-spanning region of the respective proteins.<br><br>CONCLUSIONS: Mutation m.3635G>A had multiple origins in Chinese patients with LHON. We also identified several potentially functional variants cosegregated with m.3635G>A.}, }
@article {pmid23300257, year = {2013}, author = {Xu, H and Zhang, F and Liu, B and Huhman, DV and Sumner, LW and Dixon, RA and Wang, G}, title = {Characterization of the formation of branched short-chain fatty acid:CoAs for bitter acid biosynthesis in hop glandular trichomes.}, journal = {Molecular plant}, volume = {6}, number = {4}, pages = {1301-1317}, doi = {10.1093/mp/sst004}, pmid = {23300257}, issn = {1752-9867}, mesh = {Cloning, Molecular ; Coenzyme A/*metabolism ; Fatty Acids/*biosynthesis/*chemistry/metabolism ; Gene Expression Regulation, Plant ; Humulus/cytology/genetics/growth &amp; development/*metabolism ; Intracellular Space/metabolism ; Ligases/genetics/metabolism ; Organ Specificity ; Phylogeny ; Sequence Analysis ; Sequence Homology, Nucleic Acid ; Trichomes/*metabolism ; }, abstract = {Bitter acids, known for their use as beer flavoring and for their diverse biological activities, are predominantly formed in hop (Humulus lupulus) glandular trichomes. Branched short-chain acyl-CoAs (e.g. isobutyryl-CoA, isovaleryl-CoA and 2-methylbutyryl-CoA), derived from the degradation of branched-chain amino acids (BCAAs), are essential building blocks for the biosynthesis of bitter acids in hops. However, little is known regarding what components are needed to produce and maintain the pool of branched short-chain acyl-CoAs in hop trichomes. Here, we present several lines of evidence that both CoA ligases and thioesterases are likely involved in bitter acid biosynthesis. Recombinant HlCCL2 (carboxyl CoA ligase) protein had high specific activity for isovaleric acid as a substrate (K cat /K m = 4100 s(-1) M(-1)), whereas recombinant HlCCL4 specifically utilized isobutyric acid (Kcat/K m = 1800 s(-1) M(-1)) and 2-methylbutyric acid (Kcat/K m = 6900 s(-1) M(-1)) as substrates. Both HlCCLs, like hop valerophenone synthase (HlVPS), were expressed strongly in glandular trichomes and localized to the cytoplasm. Co-expression of HlCCL2 and HlCCL4 with HlVPS in yeast led to significant production of acylphloroglucinols (the direct precursors for bitter acid biosynthesis), which further confirmed the biochemical function of these two HlCCLs in vivo. Functional identification of a thioesterase that catalyzed the reverse reaction of CCLs in mitochondria, together with the comprehensive analysis of genes involved BCAA catabolism, supported the idea that cytosolic CoA ligases are required for linking BCAA degradation and bitter acid biosynthesis in glandular trichomes. The evolution and other possible physiological roles of branched short-chain fatty acid:CoA ligases in planta are also discussed.}, }
@article {pmid23300255, year = {2013}, author = {Smith, DR and Hamaji, T and Olson, BJ and Durand, PM and Ferris, P and Michod, RE and Featherston, J and Nozaki, H and Keeling, PJ}, title = {Organelle genome complexity scales positively with organism size in volvocine green algae.}, journal = {Molecular biology and evolution}, volume = {30}, number = {4}, pages = {793-797}, doi = {10.1093/molbev/mst002}, pmid = {23300255}, issn = {1537-1719}, mesh = {Chlamydomonas reinhardtii/cytology/*genetics ; Evolution, Molecular ; Genetic Drift ; Genetic Variation ; *Genome, Mitochondrial ; Genome, Plant ; *Genome, Plastid ; Mitochondria/*genetics ; Models, Genetic ; Plastids/*genetics ; Volvocida/cytology/genetics ; }, abstract = {It has been argued that for certain lineages, noncoding DNA expansion is a consequence of the increased random genetic drift associated with long-term escalations in organism size. But a lack of data has prevented the investigation of this hypothesis in most plastid-bearing protists. Here, using newly sequenced mitochondrial and plastid genomes, we explore the relationship between organelle DNA noncoding content and organism size within volvocine green algae. By looking at unicellular, colonial, and differentiated multicellular algae, we show that organelle DNA complexity scales positively with species size and cell number across the volvocine lineage. Moreover, silent-site genetic diversity data suggest that the volvocine species with the largest cell numbers and most bloated organelle genomes have the smallest effective population sizes. Together, these findings support the view that nonadaptive processes, like random genetic drift, promote the expansion of noncoding regions in organelle genomes.}, }
@article {pmid23297357, year = {2013}, author = {Nelson, DR and Goldstone, JV and Stegeman, JJ}, title = {The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {368}, number = {1612}, pages = {20120474}, pmid = {23297357}, issn = {1471-2970}, support = {P42 ES007381/ES/NIEHS NIH HHS/United States ; U41 HG003345/HG/NHGRI NIH HHS/United States ; F32-ES012794/ES/NIEHS NIH HHS/United States ; 5R01-ES015912/ES/NIEHS NIH HHS/United States ; F32 ES012794/ES/NIEHS NIH HHS/United States ; 2P42ES07381/ES/NIEHS NIH HHS/United States ; R01 ES015912/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Chromosome Mapping ; Chromosomes/genetics/metabolism ; Cnidaria/classification/enzymology/*genetics ; Cytochrome P-450 Enzyme System/classification/*genetics/metabolism ; *Evolution, Molecular ; Gene Duplication ; Genes, Homeobox ; Genetic Linkage ; *Genetic Loci ; Humans ; Mitochondria/enzymology/genetics ; Multigene Family ; Phylogeny ; Placozoa/classification/enzymology/*genetics ; Retinoids/metabolism ; Synteny ; }, abstract = {The neighbourhoods of cytochrome P450 (CYP) genes in deuterostome genomes, as well as those of the cnidarians Nematostella vectensis and Acropora digitifera and the placozoan Trichoplax adhaerens were examined to find clues concerning the evolution of CYP genes in animals. CYP genes created by the 2R whole genome duplications in chordates have been identified. Both microsynteny and macrosynteny were used to identify genes that coexisted near CYP genes in the animal ancestor. We show that all 11 CYP clans began in a common gene environment. The evidence implies the existence of a single locus, which we term the 'cytochrome P450 genesis locus', where one progenitor CYP gene duplicated to create a tandem set of genes that were precursors of the 11 animal CYP clans: CYP Clans 2, 3, 4, 7, 19, 20, 26, 46, 51, 74 and mitochondrial. These early CYP genes existed side by side before the origin of cnidarians, possibly with a few additional genes interspersed. The Hox gene cluster, WNT genes, an NK gene cluster and at least one ARF gene were close neighbours to this original CYP locus. According to this evolutionary scenario, the CYP74 clan originated from animals and not from land plants nor from a common ancestor of plants and animals. The CYP7 and CYP19 families that are chordate-specific belong to CYP clans that seem to have originated in the CYP genesis locus as well, even though this requires many gene losses to explain their current distribution. The approach to uncovering the CYP genesis locus overcomes confounding effects because of gene conversion, sequence divergence, gene birth and death, and opens the way to understanding the biodiversity of CYP genes, families and subfamilies, which in animals has been obscured by more than 600 Myr of evolution.}, }
@article {pmid23296446, year = {2013}, author = {Boscaro, V and Petroni, G and Ristori, A and Verni, F and Vannini, C}, title = {"Candidatus Defluviella procrastinata" and "Candidatus Cyrtobacter zanobii", two novel ciliate endosymbionts belonging to the "Midichloria clade".}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {302-310}, pmid = {23296446}, issn = {1432-184X}, mesh = {Alphaproteobacteria/*classification/genetics/isolation &amp; purification ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Euplotes/*microbiology ; In Situ Hybridization, Fluorescence ; Paramecium/*microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {The "Midichloria clade" is a recently discovered but well-established evolutionary lineage clustering inside the order Rickettsiales (Alphaproteobacteria). Not much is known about the biology of these organisms. The best characterized ones are endocellular symbionts of very different eukaryotic hosts, ranging from arthropods to protists. "Candidatus Midichloria mitochondrii", the most studied organism of the group, is an interesting object of study because of its unique capability to infect metazoans' mitochondria and the presence of flagellar genes in its genome. With this work, we aim at increasing the knowledge on the biodiversity and phylogeny of the "Midichloria group". We characterized according to the "full cycle rRNA approach" two novel endosymbionts of ciliated protozoa, i.e. Paramecium nephridiatum and Euplotes aediculatus. According to the nomenclatural rules for uncultivated prokaryotes, we established the novel taxa "Candidatus Defluviella procrastinata" and "Candidatus Cyrtobacter zanobii" for the two bacterial symbionts. Our phylogenetic analysis based on 16S rRNA gene sequences confirms that the evolutionary histories of "Midichloria clade" representatives and of their hosts are very different. This suggests that the symbiotic processes arose many times independently, perhaps through ways of transmission still not described in Rickettsiales.}, }
@article {pmid23291162, year = {2013}, author = {Duncan, O and van der Merwe, MJ and Daley, DO and Whelan, J}, title = {The outer mitochondrial membrane in higher plants.}, journal = {Trends in plant science}, volume = {18}, number = {4}, pages = {207-217}, doi = {10.1016/j.tplants.2012.12.004}, pmid = {23291162}, issn = {1878-4372}, mesh = {Arabidopsis/genetics/*metabolism/physiology ; Arabidopsis Proteins/genetics/metabolism ; Biological Evolution ; Lipids ; Membrane Proteins/genetics/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/genetics/metabolism ; Phylogeny ; Protein Transport ; Proteome ; Signal Transduction ; Stress, Physiological ; }, abstract = {The acquisition and integration of intracellular organelles, such as mitochondria and plastids, were important steps in the emergence of complex multicellular life. Although the outer membranes of these organelles have lost many of the functions of their free-living bacterial ancestor, others were acquired during organellogenesis. To date, the biological roles of these proteins have not been systematically characterized. In this review, we discuss the evolutionary origins and functions of outer membrane mitochondrial (OMM) proteins in Arabidopsis thaliana. Our analysis, using phylogenetic inference, indicates that several OMM proteins either acquired novel functional roles or were recruited from other subcellular localizations during evolution in Arabidopsis. These observations suggest the existence of novel communication routes and functions between organelles within plant cells.}, }
@article {pmid23287894, year = {2013}, author = {Shellman, ER and Burant, CF and Schnell, S}, title = {Network motifs provide signatures that characterize metabolism.}, journal = {Molecular bioSystems}, volume = {9}, number = {3}, pages = {352-360}, pmid = {23287894}, issn = {1742-2051}, support = {P30 DK089503/DK/NIDDK NIH HHS/United States ; T32 GM008322/GM/NIGMS NIH HHS/United States ; U24 DK097153/DK/NIDDK NIH HHS/United States ; P30 DK020572/DK/NIDDK NIH HHS/United States ; R01 DK079084/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Archaeal Proteins/classification/genetics ; Enzymes/classification/genetics ; Escherichia coli/enzymology ; Escherichia coli Proteins/classification/genetics ; Evolution, Molecular ; Humans ; *Metabolic Networks and Pathways ; Methanosarcina barkeri/enzymology ; Mitochondria/enzymology ; Models, Biological ; Plant Proteins/classification/genetics ; Plants/enzymology ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae Proteins/classification/genetics ; }, abstract = {Motifs are repeating patterns that determine the local properties of networks. In this work, we characterized all 3-node motifs using enzyme commission numbers of the International Union of Biochemistry and Molecular Biology to show that motif abundance is related to biochemical function. Further, we present a comparative analysis of motif distributions in the metabolic networks of 21 species across six kingdoms of life. We found the distribution of motif abundances to be similar between species, but unique across cellular organelles. Finally, we show that motifs are able to capture inter-species differences in metabolic networks and that molecular differences between some biological species are reflected by the distribution of motif abundances in metabolic networks.}, }
@article {pmid23286296, year = {2013}, author = {Lagisz, M and Poulin, R and Nakagawa, S}, title = {You are where you live: parasitic nematode mitochondrial genome size is associated with the thermal environment generated by hosts.}, journal = {Journal of evolutionary biology}, volume = {26}, number = {3}, pages = {683-690}, doi = {10.1111/jeb.12068}, pmid = {23286296}, issn = {1420-9101}, mesh = {Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Base Sequence ; Body Size ; DNA Replication ; DNA, Helminth/*analysis/genetics ; DNA, Mitochondrial/*analysis/genetics ; Ecosystem ; Evolution, Molecular ; Female ; Gene Order ; Genetic Variation ; *Genome Size ; *Genome, Mitochondrial ; Longevity ; Male ; Mitochondria/genetics ; Nematoda/classification/*genetics ; Phylogeny ; Selection, Genetic ; Species Specificity ; Temperature ; }, abstract = {There exists remarkable interspecific variation in mitochondrial sequence evolution rates and in mitochondrial genome sizes. A number of hypotheses based on the forces of mutation and selection have been proposed to explain this variation. Among such hypotheses, we test three: 1) the 'longevity-dependent selection', 2) the 'functional constraints' and 3) the 'race for replication' hypotheses, using published mtDNA genomic sequences of 47 Nematoda species. We did not find any relationship between body size (used as a proxy for longevity) and genome size or the substitution rate of protein sequences, providing little evidence for the first hypothesis. Parasitic species from different thermal habitats, as determined by their definitive host type (ectothermal vs. endothermal), did not differ in their rates of protein evolution. Therefore, little support was obtained for the second hypothesis. However, we revealed that mitogenomes of parasites of endotherms were significantly smaller than those of parasites of ectotherms, supporting the race for replication hypothesis. As mitochondrial genomes of endothermal animals are usually more compact than those of ectothermal animals, intriguingly, nematode parasites of endotherms and ectotherms exhibit similar patterns of mtDNA length variation to their hosts.}, }
@article {pmid23282997, year = {2013}, author = {Rowe, M and Laskemoen, T and Johnsen, A and Lifjeld, JT}, title = {Evolution of sperm structure and energetics in passerine birds.}, journal = {Proceedings. Biological sciences}, volume = {280}, number = {1753}, pages = {20122616}, pmid = {23282997}, issn = {1471-2954}, mesh = {Adenosine Triphosphate/*metabolism ; Animals ; Bayes Theorem ; *Biological Evolution ; Luminescent Measurements ; Male ; Mitochondria/*metabolism ; Models, Biological ; Norway ; Songbirds/genetics/*physiology ; Species Specificity ; Sperm Motility ; Spermatozoa/*cytology/*physiology ; }, abstract = {Spermatozoa exhibit considerable interspecific variability in size and shape. Our understanding of the adaptive significance of this diversity, however, remains limited. Determining how variation in sperm structure translates into variation in sperm performance will contribute to our understanding of the evolutionary diversification of sperm form. Here, using data from passerine birds, we test the hypothesis that longer sperm swim faster because they have more available energy. We found that sperm with longer midpieces have higher levels of intracellular adenosine triphosphate (ATP), but that greater energy reserves do not translate into faster-swimming sperm. Additionally, we found that interspecific variation in sperm ATP concentration is not associated with the level of sperm competition faced by males. Finally, using Bayesian methods, we compared the evolutionary trajectories of sperm morphology and ATP content, and show that both traits have undergone directional evolutionary change. However, in contrast to recent suggestions in other taxa, we show that changes in ATP are unlikely to have preceded changes in morphology in passerine sperm. These results suggest that variable selective pressures are likely to have driven the evolution of sperm traits in different taxa, and highlight fundamental biological differences between taxa with internal and external fertilization, as well as those with and without sperm storage.}, }
@article {pmid23279810, year = {2013}, author = {Bartelli, TF and Ferreira, RC and Colombo, AL and Briones, MR}, title = {Intraspecific comparative genomics of Candida albicans mitochondria reveals non-coding regions under neutral evolution.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {14}, number = {}, pages = {302-312}, doi = {10.1016/j.meegid.2012.12.012}, pmid = {23279810}, issn = {1567-7257}, mesh = {Base Sequence ; Candida albicans/classification/*genetics ; Candidiasis ; DNA, Intergenic ; *DNA, Mitochondrial ; *Genetic Drift ; Genetic Variation ; Genome, Mitochondrial ; *Genomics ; Haplotypes ; Humans ; Molecular Sequence Data ; Mutation ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Alignment ; }, abstract = {The opportunistic fungal pathogen Candida albicans causes serious hematogenic hospital acquired candidiasis with worldwide impact on public health. Because of its importance as a nosocomial etiologic agent, C. albicans genome has been largely studied to identify intraspecific variation and several typing methods have been developed to distinguish closely related strains. Mitochondrial DNA can be useful for this purpose because, as compared to nuclear DNA, its higher mutational load and evolutionary rate readily reveals microvariants. Accordingly, we sequenced and assembled, with 8-fold coverage, the mitochondrial genomes of two C. albicans clinical isolates (L296 and L757) and compared these sequences with the genome sequence of reference strain SC5314. The genome alignment of 33,928 positions revealed 372 polymorphic sites being 230 in coding and 142 in non-coding regions. Three intergenic regions located between genes tRNAGly/COX1, NAD3/COB and ssurRNA/NAD4L, named IG1, IG2 and IG3, respectively, which showed high number of neutral substitutions, were amplified and sequenced from 18 clinical isolates from different locations in Latin America and 2 ATCC standard C. albicans strains. High variability of sequence and size were observed, ranging up to 56bp size difference and phylogenies based on IG1, IG2 and IG3 revealed three groups. Insertions of up to 49bp were observed exclusively in Argentinean strains relative to the other sequences which could suggest clustering by geographical polymorphism. Because of neutral evolution, high variability, easy isolation by PCR and full length sequencing these mitochondrial intergenic regions can contribute with a novel perspective in molecular studies of C. albicans isolates, complementing well established multilocus sequence typing methods.}, }
@article {pmid23279335, year = {2013}, author = {Limenitakis, J and Oppenheim, RD and Creek, DJ and Foth, BJ and Barrett, MP and Soldati-Favre, D}, title = {The 2-methylcitrate cycle is implicated in the detoxification of propionate in Toxoplasma gondii.}, journal = {Molecular microbiology}, volume = {87}, number = {4}, pages = {894-908}, pmid = {23279335}, issn = {1365-2958}, support = {/WT_/Wellcome Trust/United Kingdom ; 085349/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Acyl Coenzyme A/metabolism/toxicity ; Animals ; Carbon-Carbon Lyases/genetics/metabolism ; Citrates/*metabolism ; Humans ; Mice ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Propionates/*metabolism/toxicity ; Protozoan Proteins/genetics/metabolism ; Toxoplasma/classification/enzymology/genetics/*metabolism ; Toxoplasmosis/*parasitology ; }, abstract = {Toxoplasma gondii belongs to the coccidian subgroup of the Apicomplexa phylum. The Coccidia are obligate intracellular pathogens that establish infection in their mammalian host via the enteric route. These parasites lack a mitochondrial pyruvate dehydrogenase complex but have preserved the degradation of branched-chain amino acids (BCAA) as a possible pathway to generate acetyl-CoA. Importantly, degradation of leucine, isoleucine and valine could lead to concomitant accumulation of propionyl-CoA, a toxic metabolite that inhibits cell growth. Like fungi and bacteria, the Coccidia possess the complete set of enzymes necessary to metabolize and detoxify propionate by oxidation to pyruvate via the 2-methylcitrate cycle (2-MCC). Phylogenetic analysis provides evidence that the 2-MCC was acquired via horizontal gene transfer. In T. gondii tachyzoites, this pathway is split between the cytosol and the mitochondrion. Although the rate-limiting enzyme 2-methylisocitrate lyase is dispensable for parasite survival, its substrates accumulate in parasites deficient in the enzyme and its absence confers increased sensitivity to propionic acid. BCAA is also dispensable in tachyzoites, leaving unresolved the source of mitochondrial acetyl-CoA.}, }
@article {pmid23278298, year = {2013}, author = {Kornfeld, A and Heskel, M and Atkin, OK and Gough, L and Griffin, KL and Horton, TW and Turnbull, MH}, title = {Respiratory flexibility and efficiency are affected by simulated global change in Arctic plants.}, journal = {The New phytologist}, volume = {197}, number = {4}, pages = {1161-1172}, doi = {10.1111/nph.12083}, pmid = {23278298}, issn = {1469-8137}, mesh = {*Acclimatization ; Arctic Regions ; Betula/metabolism/*physiology/ultrastructure ; Carbon Dioxide/*metabolism ; Climate Change ; Cyperaceae/metabolism/*physiology/ultrastructure ; Cytochromes/metabolism ; Electron Transport Complex IV/metabolism ; Mitochondria/metabolism/ultrastructure ; Mitochondrial Proteins/metabolism ; Oxidoreductases/metabolism ; Plant Leaves/metabolism/ultrastructure ; Plant Proteins/metabolism ; Rosaceae/metabolism/*physiology/ultrastructure ; Temperature ; }, abstract = {Laboratory studies indicate that, in response to environmental conditions, plants modulate respiratory electron partitioning between the 'energy-wasteful' alternative pathway (AP) and the 'energy-conserving' cytochrome pathway (CP). Field data, however, are scarce. Here we investigate how 20-yr field manipulations simulating global change affected electron partitioning in Alaskan Arctic tundra species. We sampled leaves from three dominant tundra species - Betula nana, Eriophorum vaginatum and Rubus chamaemorus - that had been strongly affected by manipulations of soil nutrients, light availability, and warming. We measured foliar dark respiration, in-vivo electron partitioning and alternative oxidase/cytochrome c oxidase concentrations in addition to leaf traits and mitochondrial ultrastructure. Changes in leaf traits and ultrastructure were similar across species. Respiration at 20°C (R(20)) was reduced 15% in all three species grown at elevated temperature, suggesting thermal acclimation of respiration. In Betula, the species with the largest growth response to added nutrients, CP activity increased from 9.4 ± 0.8 to 16.6 ± 1.6 nmol O(2) g(-1) DM s(-1) whereas AP activity was unchanged. The ability of Betula to selectively increase CP activity in response to the environment may contribute to its overall ecological success by increasing respiratory energy efficiency, and thus retaining more carbon for growth.}, }
@article {pmid23272130, year = {2012}, author = {Jin, L and Zhang, M and Ma, J and Zhang, J and Zhou, C and Liu, Y and Wang, T and Jiang, AA and Chen, L and Wang, J and Jiang, Z and Zhu, L and Shuai, S and Li, R and Li, M and Li, X}, title = {Mitochondrial DNA evidence indicates the local origin of domestic pigs in the upstream region of the Yangtze River.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e51649}, pmid = {23272130}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; Breeding ; China ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Geography ; Haplotypes ; Mitochondria/genetics ; Models, Genetic ; Models, Statistical ; Phylogeny ; Rivers ; Sequence Analysis, DNA ; Sus scrofa/genetics ; }, abstract = {Previous studies have indicated two main domestic pig dispersal routes in East Asia: one is from the Mekong region, through the upstream region of the Yangtze River (URYZ) to the middle and upstream regions of the Yellow River, the other is from the middle and downstream regions of the Yangtze River to the downstream region of the Yellow River, and then to northeast China. The URYZ was regarded as a passageway of the former dispersal route; however, this assumption remains to be further investigated. We therefore analyzed the hypervariable segements of mitochondrial DNA from 513 individual pigs mainly from Sichuan and the Tibet highlands and 1,394 publicly available sequences from domestic pigs and wild boars across Asia. From the phylogenetic tree, most of the samples fell into a mixed group that was difficult to distinguish by breed or geography. The total network analysis showed that the URYZ pigs possessed a dominant position in haplogroup A and domestic pigs shared the same core haplotype with the local wild boars, suggesting that pigs in group A were most likely derived from the URYZ pool. In addition, a region-wise network analysis determined that URYZ contains 42 haplotypes of which 22 are unique indicating the high diversity in this region. In conclusion, our findings confirmed that pigs from the URYZ were domesticated in situ.}, }
@article {pmid23269854, year = {2013}, author = {Payo, DA and Leliaert, F and Verbruggen, H and D'hondt, S and Calumpong, HP and De Clerck, O}, title = {Extensive cryptic species diversity and fine-scale endemism in the marine red alga Portieria in the Philippines.}, journal = {Proceedings. Biological sciences}, volume = {280}, number = {1753}, pages = {20122660}, pmid = {23269854}, issn = {1471-2954}, mesh = {Algal Proteins/genetics/metabolism ; *Biodiversity ; Cell Nucleus/genetics ; Conservation of Natural Resources ; Mitochondria/genetics ; Molecular Sequence Data ; Philippines ; Phylogeny ; Plastids/genetics ; Polymerase Chain Reaction ; Rhodophyta/*classification/cytology/*genetics/metabolism ; Sequence Analysis, DNA ; Sequence Homology ; }, abstract = {We investigated species diversity and distribution patterns of the marine red alga Portieria in the Philippine archipelago. Species boundaries were tested based on mitochondrial, plastid and nuclear encoded loci, using a general mixed Yule-coalescent (GMYC) model-based approach and a bayesian multilocus species delimitation method. The outcome of the GMYC analysis of the mitochondrial encoded cox2-3 dataset was highly congruent with the multilocus analysis. In stark contrast with the current morphology-based assumption that the genus includes a single, widely distributed species in the Indo-West Pacific (Portieria hornemannii), DNA-based species delimitation resulted in the recognition of 21 species within the Philippines. Species distributions were found to be highly structured with most species restricted to island groups within the archipelago. These extremely narrow species ranges and high levels of intra-archipelagic endemism contrast with the wide-held belief that marine organisms generally have large geographical ranges and that endemism is at most restricted to the archipelagic level. Our results indicate that speciation in the marine environment may occur at spatial scales smaller than 100 km, comparable with some terrestrial systems. Our finding of fine-scale endemism has important consequences for marine conservation and management.}, }
@article {pmid23269202, year = {2013}, author = {Silveira, P and Belo, NO and Lacorte, GA and Kolesnikovas, CK and Vanstreels, RE and Steindel, M and Catão-Dias, JL and Valkiūnas, G and Braga, EM}, title = {Parasitological and new molecular-phylogenetic characterization of the malaria parasite Plasmodium tejerai in South American penguins.}, journal = {Parasitology international}, volume = {62}, number = {2}, pages = {165-171}, doi = {10.1016/j.parint.2012.12.004}, pmid = {23269202}, issn = {1873-0329}, mesh = {Animals ; Base Sequence ; Brazil ; Cytochromes b/genetics ; DNA, Protozoan/chemistry/genetics ; Endothelial Cells/parasitology ; Fatal Outcome ; Macrophages/parasitology ; Malaria, Avian/blood/*parasitology/pathology ; Mitochondria/metabolism ; Molecular Sequence Data ; Myocardium/pathology ; Parasitemia ; Phylogeny ; Plasmodium/classification/cytology/genetics/*isolation &amp; purification ; Protozoan Proteins/genetics ; Sequence Analysis, DNA ; Species Specificity ; Spheniscidae/*parasitology ; }, abstract = {This study is the first report on mortality of Spheniscus magellanicus, penguin of South America, caused by Plasmodium tejerai, which was identified using morphological and molecular analyses. Blood stages (trophozoites, meronts and gametocytes) were reported and illustrated. The necropsy revealed marked splenomegaly and pulmonary edema, as well as moderate hepatomegaly and hydropericardium. The histopathology revealed the presence of tissue meronts in the macrophages and endothelial cells of multiple organs. The molecular analyses showed 5.6% of genetic divergence in cytochrome b gene between P. tejerai and Plasmodium relictum. Morphology of blood and tissue stages of P. tejerai is similar to P. relictum; the distinction between these two species requires experience in the identification of avian Plasmodium species. Molecular studies associated with reliably identified morphological species are useful for barcoding and comparisons with previous studies of wildlife malaria infections as well as for posterior phylogenetic and phylogeographic studies. S. magellanicus is a new host record of P. tejerai, which is the virulent parasite and worth more attention in avian conservation and veterinary medicine projects in South America.}, }
@article {pmid23266989, year = {2013}, author = {McStay, GP and Su, CH and Tzagoloff, A}, title = {Modular assembly of yeast cytochrome oxidase.}, journal = {Molecular biology of the cell}, volume = {24}, number = {4}, pages = {440-452}, pmid = {23266989}, issn = {1939-4586}, support = {R01 GM050187/GM/NIGMS NIH HHS/United States ; R01 GM111864/GM/NIGMS NIH HHS/United States ; GM50187/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Evolution ; Electron Transport Complex IV/*genetics/metabolism ; *Gene Expression Regulation, Fungal ; Holoenzymes/genetics/metabolism ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/*genetics/metabolism ; Mutation ; Protein Biosynthesis ; Protein Subunits/*genetics/metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; }, abstract = {Previous studies of yeast cytochrome oxidase (COX) biogenesis identified Cox1p, one of the three mitochondrially encoded core subunits, in two high-molecular weight complexes combined with regulatory/assembly factors essential for expression of this subunit. In the present study we use pulse-chase labeling experiments in conjunction with isolated mitochondria to identify new Cox1p intermediates and place them in an ordered pathway. Our results indicate that before its assimilation into COX, Cox1p transitions through five intermediates that are differentiated by their compositions of accessory factors and of two of the eight imported subunits. We propose a model of COX biogenesis in which Cox1p and the two other mitochondrial gene products, Cox2p and Cox3p, constitute independent assembly modules, each with its own complement of subunits. Unlike their bacterial counterparts, which are composed only of the individual core subunits, the final sequence in which the mitochondrial modules associate to form the holoenzyme may have been conserved during evolution.}, }
@article {pmid23266975, year = {2012}, author = {Chen, X and Shen, YY and Zhang, YP}, title = {[Review of mtDNA in molecular evolution studies].}, journal = {Dong wu xue yan jiu = Zoological research}, volume = {33}, number = {6}, pages = {566-573}, doi = {10.3724/SP.J.1141.2012.06566}, pmid = {23266975}, issn = {0254-5853}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; DNA, Mitochondrial/*genetics/metabolism ; *Evolution, Molecular ; Genome, Mitochondrial ; Humans ; Mitochondria/*genetics/metabolism ; }, abstract = {Mitochondria are old organelles found in most eukaryotic cells. Due to its rapid mutation ratio, mitochondrial DNA (mtDNA) has been widely used as a DNA marker in molecular studies and has long been suggested to undergo neutral evolution or purifying selection. Mitochondria produces 95% of the adenosine triphosphate (ATP) needed for locomotion, and heat for thermoregulation. Recent studies had found that mitochondria play critical roles in energy metabolism, and proved that functional constraints acting on mitochondria, due to energy metabolism and/or thermoregulation, influence the evolution of mtDNA. This review summarizes mitochondrial genome composition, evolution, and its applications in molecular evolution studies (reconstruction of species phylogenesis, the relationship between biological energy metabolism and mtDNA evolution, and the mtDNA codon reassignment influences the adaptation in different creatures).}, }
@article {pmid23266212, year = {2013}, author = {Daugbjerg, N and Jensen, MH and Hansen, PJ}, title = {Using nuclear-encoded LSU and SSU rDNA sequences to identify the eukaryotic endosymbiont in Amphisolenia bidentata (Dinophyceae).}, journal = {Protist}, volume = {164}, number = {3}, pages = {411-422}, doi = {10.1016/j.protis.2012.10.001}, pmid = {23266212}, issn = {1618-0941}, mesh = {Alveolata/classification/*genetics ; Animals ; Chloroplasts/genetics ; DNA, Ribosomal/*analysis ; Eukaryota/*classification/*genetics ; Indian Ocean ; Microscopy, Fluorescence ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Symbiosis ; }, abstract = {The marine dinoflagellate Amphisolenia bidentata possesses complete intracellular symbionts of prokaryotic and eukaryotic origin. This was confirmed ultrastructurally little over 20 years ago when it was showed that the eukaryotic endosymbiont had a nucleus, a chloroplast and mitochondria. We collected Amphisolenia bidentata cells in the Indian Ocean and the identity of the eukaryotic endosymbionts was investigated using both microscopical and molecular methods. Individual specimens of Amphisolenia bidentata were identified by light microscopy and selected for single-cell PCR. Host and endosymbiont nuclear-encoded LSU and SSU rDNA sequences were determined by PCR cloning. Blast searches showed the endosymbiont LSU sequence to have affinity to Pelagophyceae, an algal class within Chromalveolata that also includes dinoflagellates. Since more SSU rDNA sequences from pelagophytes are available we performed a SSU based phylogeny of chromalveolates. The eukaryotic endosymbiont clustered within a clade comprising flagellated and coccoid pelagophytes whereas Amphisolenia bidentata formed a sister taxon to other dinophysioids. Molecular data therefore resolved the endosymbiont in A. bidentata being a pelagophyte and thus identified the ninth novel chloroplast type in dinoflagellates and a new species association. Based on sequence divergence estimates and phylogenetic inference the endosymbiont in A. bidentata likely represents an undescribed genus of pelagophytes.}, }
@article {pmid23264646, year = {2013}, author = {Basu, S and Leonard, JC and Desai, N and Mavridou, DA and Tang, KH and Goddard, AD and Ginger, ML and Lukeš, J and Allen, JW}, title = {Divergence of Erv1-associated mitochondrial import and export pathways in trypanosomes and anaerobic protists.}, journal = {Eukaryotic cell}, volume = {12}, number = {2}, pages = {343-355}, pmid = {23264646}, issn = {1535-9786}, support = {BB/D019753/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Substitution ; Cytochromes c/chemistry ; Evolution, Molecular ; Gene Knockdown Techniques ; Kinetics ; Mitochondria/enzymology/ultrastructure ; Mitochondrial Proteins/*chemistry/genetics ; Mitochondrial Swelling ; Mutagenesis, Site-Directed ; Oxidants ; Oxidation-Reduction ; Oxidoreductases/*chemistry/genetics ; Oxygen/chemistry ; Phylogeny ; Protein Folding ; Protein Transport ; Protozoan Proteins/*chemistry/genetics ; RNA Interference ; Trypanosoma brucei brucei/cytology/*enzymology ; }, abstract = {In yeast (Saccharomyces cerevisiae) and animals, the sulfhydryl oxidase Erv1 functions with Mia40 in the import and oxidative folding of numerous cysteine-rich proteins in the mitochondrial intermembrane space (IMS). Erv1 is also required for Fe-S cluster assembly in the cytosol, which uses at least one mitochondrially derived precursor. Here, we characterize an essential Erv1 orthologue from the protist Trypanosoma brucei (TbERV1), which naturally lacks a Mia40 homolog. We report kinetic parameters for physiologically relevant oxidants cytochrome c and O(2), unexpectedly find O(2) and cytochrome c are reduced simultaneously, and demonstrate that efficient reduction of O(2) by TbERV1 is not dependent upon a simple O(2) channel defined by conserved histidine and tyrosine residues. Massive mitochondrial swelling following TbERV1 RNA interference (RNAi) provides evidence that trypanosome Erv1 functions in IMS protein import despite the natural absence of the key player in the yeast and animal import pathways, Mia40. This suggests significant evolutionary divergence from a recently established paradigm in mitochondrial cell biology. Phylogenomic profiling of genes also points to a conserved role for TbERV1 in cytosolic Fe-S cluster assembly. Conversely, loss of genes implicated in precursor delivery for cytosolic Fe-S assembly in Entamoeba, Trichomonas, and Giardia suggests fundamental differences in intracellular trafficking pathways for activated iron or sulfur species in anaerobic versus aerobic eukaryotes.}, }
@article {pmid23257241, year = {2013}, author = {Xu, L and Carrie, C and Law, SR and Murcha, MW and Whelan, J}, title = {Acquisition, conservation, and loss of dual-targeted proteins in land plants.}, journal = {Plant physiology}, volume = {161}, number = {2}, pages = {644-662}, pmid = {23257241}, issn = {1532-2548}, mesh = {Arabidopsis/genetics/*metabolism ; Ascorbate Peroxidases/classification/genetics/metabolism ; Bryopsida/genetics/*metabolism ; Evolution, Molecular ; Hexokinase/classification/genetics/metabolism ; Luminescent Proteins/genetics/metabolism ; Microscopy, Fluorescence ; Mitochondria/metabolism ; NADH, NADPH Oxidoreductases/classification/genetics/metabolism ; Organelles/*metabolism ; Oryza/genetics/*metabolism ; Peroxisomes/metabolism ; Phylogeny ; Plant Proteins/classification/genetics/*metabolism ; Plants, Genetically Modified ; Plastids/metabolism ; Protein Transport/genetics ; }, abstract = {The dual-targeting ability of a variety of proteins from Physcomitrella patens, rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) was tested to determine when dual targeting arose and to what extent it was conserved in land plants. Overall, the targeting ability of over 80 different proteins from rice and P. patens, representing 42 dual-targeted proteins in Arabidopsis, was tested. We found that dual targeting arose early in land plant evolution, as it was evident in many cases with P. patens proteins that were conserved in rice and Arabidopsis. Furthermore, we found that the acquisition of dual-targeting ability is still occurring, evident in P. patens as well as rice and Arabidopsis. The loss of dual-targeting ability appears to be rare, but does occur. Ascorbate peroxidase represents such an example. After gene duplication in rice, individual genes encode proteins that are targeted to a single organelle. Although we found that dual targeting was generally conserved, the ability to detect dual-targeted proteins differed depending on the cell types used. Furthermore, it appears that small changes in the targeting signal can result in a loss (or gain) of dual-targeting ability. Overall, examination of the targeting signals within this study did not reveal any clear patterns that would predict dual-targeting ability. The acquisition of dual-targeting ability also appears to be coordinated between proteins. Mitochondrial intermembrane space import and assembly protein40, a protein involved in oxidative folding in mitochondria and peroxisomes, provides an example where acquisition of dual targeting is accompanied by the dual targeting of substrate proteins.}, }
@article {pmid23251637, year = {2012}, author = {Alex, A and Vasconcelos, V and Tamagnini, P and Santos, A and Antunes, A}, title = {Unusual symbiotic cyanobacteria association in the genetically diverse intertidal marine sponge Hymeniacidon perlevis (Demospongiae, Halichondrida).}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e51834}, pmid = {23251637}, issn = {1932-6203}, mesh = {Animals ; Atlantic Ocean ; Cyanobacteria/classification/*genetics ; Ecosystem ; Genetic Variation ; Microscopy, Electron, Transmission/methods ; Mitochondria/genetics ; Phylogeny ; Porifera/*genetics/*microbiology ; Portugal ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Cyanobacteria represent one of the most common members of the sponge-associated bacterial community and are abundant symbionts of coral reef ecosystems. In this study we used Transmission Electron Microscopy (TEM) and molecular techniques (16S rRNA gene marker) to characterize the spatial distribution of cyanobionts in the widely dispersed marine intertidal sponge Hymeniacidon perlevis along the coast of Portugal (Atlantic Ocean). We described new sponge associated cyanobacterial morphotypes (Xenococcus-like) and we further observed Acaryochloris sp. as a sponge symbiont, previously only reported in association with ascidians. Besides these two unique cyanobacteria, H. perlevis predominantly harbored Synechococcus sp. and uncultured marine cyanobacteria. Our study supports the hypothesis that the community of sponge cyanobionts varies irrespective of the geographical location and is likely influenced by seasonal fluctuations. The observed multiple cyanobacterial association among sponges of the same host species over a large distance may be attributed to horizontal transfer of symbionts. This may explain the absence of a co-evolutionary pattern between the sponge host and its symbionts. Finally, in spite of the short geographic sampling distance covered, we observed an unexpected high intra-specific genetic diversity in H. perlevis using the mitochondrial genes ATP6 (π = 0.00177), COI (π = 0.00241) and intergenic spacer SP1 (π = 0.00277) relative to the levels of genetic variation of marine sponges elsewhere. Our study suggests that genotypic variation among the sponge host H. perlevis and the associated symbiotic cyanobacteria diversity may be larger than previously recognized.}, }
@article {pmid23250235, year = {2013}, author = {Soll, J}, title = {Special issue on evolution and biogenesis of chloroplasts and mitochondria.}, journal = {Planta}, volume = {237}, number = {2}, pages = {379}, doi = {10.1007/s00425-012-1830-8}, pmid = {23250235}, issn = {1432-2048}, mesh = {Biological Evolution ; Cell Nucleus/genetics/metabolism ; Chloroplasts/genetics/*physiology ; Eukaryotic Cells/cytology/physiology ; Genome, Chloroplast ; Genome, Mitochondrial ; Mitochondria/genetics/*physiology ; *Mitochondrial Turnover ; Symbiosis ; }, }
@article {pmid23233680, year = {2013}, author = {Eckers, E and Petrungaro, C and Gross, D and Riemer, J and Hell, K and Deponte, M}, title = {Divergent molecular evolution of the mitochondrial sulfhydryl:cytochrome C oxidoreductase Erv in opisthokonts and parasitic protists.}, journal = {The Journal of biological chemistry}, volume = {288}, number = {4}, pages = {2676-2688}, pmid = {23233680}, issn = {1083-351X}, mesh = {Amino Acid Sequence ; Animals ; Cell Lineage ; Computational Biology/methods ; Cytochrome Reductases/*chemistry ; Cytochromes c/*chemistry ; Electrons ; Genetic Complementation Test ; Kinetics ; Kinetoplastida/metabolism ; Leishmania ; Mitochondria/metabolism ; Mitochondrial Proteins/genetics/*physiology ; Molecular Conformation ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Oxidoreductases/*chemistry ; Oxidoreductases Acting on Sulfur Group Donors/genetics/*physiology ; Plasmodium/metabolism ; Protein Transport ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics/*physiology ; Sequence Homology, Amino Acid ; }, abstract = {Mia40 and the sulfhydryl:cytochrome c oxidoreductase Erv1/ALR are essential for oxidative protein import into the mitochondrial intermembrane space in yeast and mammals. Although mitochondrial protein import is functionally conserved in the course of evolution, many organisms seem to lack Mia40. Moreover, except for in organello import studies and in silico analyses, nothing is known about the function and properties of protist Erv homologues. Here we compared Erv homologues from yeast, the kinetoplastid parasite Leishmania tarentolae, and the non-related malaria parasite Plasmodium falciparum. Both parasite proteins have altered cysteine motifs, formed intermolecular disulfide bonds in vitro and in vivo, and could not replace Erv1 from yeast despite successful mitochondrial protein import in vivo. To analyze its enzymatic activity, we established the expression and purification of recombinant full-length L. tarentolae Erv and compared the mechanism with related and non-related flavoproteins. Enzyme assays indeed confirmed an electron transferase activity with equine and yeast cytochrome c, suggesting a conservation of the enzymatic activity in different eukaryotic lineages. However, although Erv and non-related flavoproteins are intriguing examples of convergent molecular evolution resulting in similar enzyme properties, the mechanisms of Erv homologues from parasitic protists and opisthokonts differ significantly. In summary, the Erv-mediated reduction of cytochrome c might be highly conserved throughout evolution despite the apparent absence of Mia40 in many eukaryotes. Nevertheless, the knowledge on mitochondrial protein import in yeast and mammals cannot be generally transferred to all other eukaryotes, and the corresponding pathways, components, and mechanisms remain to be analyzed.}, }
@article {pmid23230444, year = {2012}, author = {Hüner, NP and Bode, R and Dahal, K and Hollis, L and Rosso, D and Krol, M and Ivanov, AG}, title = {Chloroplast redox imbalance governs phenotypic plasticity: the "grand design of photosynthesis" revisited.}, journal = {Frontiers in plant science}, volume = {3}, number = {}, pages = {255}, pmid = {23230444}, issn = {1664-462X}, abstract = {Sunlight, the ultimate energy source for life on our planet, enters the biosphere as a direct consequence of the evolution of photoautotrophy. Photoautotrophs must balance the light energy absorbed and trapped through extremely fast, temperature-insensitive photochemistry with energy consumed through much slower, temperature-dependent biochemistry and metabolism. The attainment of such a balance in cellular energy flow between chloroplasts, mitochondria and the cytosol is called photostasis. Photoautotrophs sense cellular energy imbalances through modulation of excitation pressure which is a measure of the relative redox state of Q(A), the first stable quinone electron acceptor of photosystem II reaction centers. High excitation pressure constitutes a potential stress condition that can be caused either by exposure to an irradiance that exceeds the capacity of C, N, and S assimilation to utilize the electrons generated from the absorbed energy or by low temperature or any stress that decreases the capacity of the metabolic pathways downstream of photochemistry to utilize photosynthetically generated reductants. The similarities and differences in the phenotypic responses between cyanobacteria, green algae, crop plants, and variegation mutants of Arabidopsis thaliana as a function of cold acclimation and photoacclimation are reconciled in terms of differential responses to excitation pressure and the predisposition of photoautotrophs to maintain photostasis. The various acclimation strategies associated with green algae and cyanobacteria versus winter cereals and A. thaliana are discussed in terms of retrograde regulation and the "grand design of photosynthesis" originally proposed by Arnon (1982).}, }
@article {pmid23228551, year = {2013}, author = {Saigo, M and Alvarez, CE and Andreo, CS and Drincovich, MF}, title = {Plastidial NADP-malic enzymes from grasses: unraveling the way to the C4 specific isoforms.}, journal = {Plant physiology and biochemistry : PPB}, volume = {63}, number = {}, pages = {39-48}, doi = {10.1016/j.plaphy.2012.11.009}, pmid = {23228551}, issn = {1873-2690}, mesh = {Amino Acid Sequence ; Malate Dehydrogenase/chemistry/*metabolism ; Molecular Sequence Data ; Oryza/*enzymology ; Photosynthesis/genetics/physiology ; Plastids/*enzymology ; Polymerase Chain Reaction ; Sorghum/*enzymology ; Structure-Activity Relationship ; Zea mays/*enzymology ; }, abstract = {Malic enzyme is present in many plant cell compartments such as plastids, cytosol and mitochondria. Particularly relevant is the plastidial isoform that participates in the C(4) cycle providing CO(2) to RuBisCO in C(4) species. This type of photosynthesis is more frequent among grasses where anatomical preconditioning would have facilitated the evolution of the C(4) syndrome. In maize (C(4) grass), the photosynthetic NADP dependent Malic enzyme (ZmC(4)-NADP-ME, l-malate:NADP oxidoreductase, E.C. 1.1.1.40) and the closest related non-photosynthetic isoform (ZmnonC(4)-NADP-ME, l-malate:NADP oxidoreductase, E.C. 1.1.1.40) are both plastidial but differ in expression pattern, kinetics and structure. Features like high catalytic efficiency, inhibition by high malate concentration at pH 7.0, redox modulation and tetramerization are characteristic of the photosynthetic NADP-ME. In this work, the proteins encoded by sorghum (C(4) grass) and rice (C(3) grass) NADP-ME genes, orthologues of the plastidial NADP-MEs from maize, were recombinantly expressed, purified and characterized. In a global comparison, we could identify a small group of residues which may explain the special features of C(4) enzymes. Overall, the present work presents biochemical and molecular data that helps to elucidate the changes that took place in the evolution of C(4) NADP-ME in grasses.}, }
@article {pmid23227215, year = {2012}, author = {Schmidt-Roach, S and Miller, KJ and Woolsey, E and Gerlach, G and Baird, AH}, title = {Broadcast spawning by Pocillopora species on the Great Barrier Reef.}, journal = {PloS one}, volume = {7}, number = {12}, pages = {e50847}, pmid = {23227215}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*physiology ; Australia ; *Coral Reefs ; Female ; Islands ; Male ; Mitochondria/genetics ; Open Reading Frames/genetics ; Phylogeny ; Reproduction/physiology ; Species Specificity ; }, abstract = {The coral genus Pocillopora is one of the few to include some species that broadcast spawn gametes and some species that brood larvae, although reports of reproductive mode and timing vary within and among species across their range. Notably, the ubiquitous Pocillopora damicornis has been described as both a brooder and spawner, although evidence of broadcast spawning is rare. Here, we report observations of broadcast-spawning in four species of Pocillopora on the Great Barrier Reef (GBR), including P. damicornis. All species spawned predictably during the early morning, two days following the full moon, and spawning was observed in multiple months over the summer period (November to February). Eggs and sperm were free-spawned concurrently. Eggs were negatively buoyant and contained Symbiodinium. This newfound knowledge on the mode, timing and regularity of broadcast spawning in Pocillopora spp. on the GBR brings us one step closer to elucidating the complex reproductive ecology of these species.}, }
@article {pmid23221899, year = {2013}, author = {Niemann, M and Wiese, S and Mani, J and Chanfon, A and Jackson, C and Meisinger, C and Warscheid, B and Schneider, A}, title = {Mitochondrial outer membrane proteome of Trypanosoma brucei reveals novel factors required to maintain mitochondrial morphology.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {12}, number = {2}, pages = {515-528}, pmid = {23221899}, issn = {1535-9484}, mesh = {Animals ; Gene Expression Profiling ; Gene Expression Regulation ; Humans ; Life Cycle Stages/genetics ; Mitochondria/genetics/*metabolism/*ultrastructure ; Mitochondrial Membranes/chemistry/*metabolism ; Mitochondrial Proteins/antagonists &amp; inhibitors/*genetics/metabolism ; Organelle Shape/genetics ; Proteome/antagonists &amp; inhibitors/*genetics/metabolism ; Protozoan Proteins/antagonists &amp; inhibitors/*genetics/metabolism ; RNA, Small Interfering/genetics ; Saccharomyces cerevisiae/genetics/metabolism ; Tandem Mass Spectrometry ; Trypanosoma brucei brucei/chemistry/*genetics/metabolism ; }, abstract = {Trypanosoma brucei is a unicellular parasite that causes devastating diseases in humans and animals. It diverged from most other eukaryotes very early in evolution and, as a consequence, has an unusual mitochondrial biology. Moreover, mitochondrial functions and morphology are highly regulated throughout the life cycle of the parasite. The outer mitochondrial membrane defines the boundary of the organelle. Its properties are therefore key for understanding how the cytosol and mitochondria communicate and how the organelle is integrated into the metabolism of the whole cell. We have purified the mitochondrial outer membrane of T. brucei and characterized its proteome using label-free quantitative mass spectrometry for protein abundance profiling in combination with statistical analysis. Our results show that the trypanosomal outer membrane proteome consists of 82 proteins, two-thirds of which have never been associated with mitochondria before. 40 proteins share homology with proteins of known functions. The function of 42 proteins, 33 of which are specific to trypanosomatids, remains unknown. 11 proteins are essential for the disease-causing bloodstream form of T. brucei and therefore may be exploited as novel drug targets. A comparison with the outer membrane proteome of yeast defines a set of 17 common proteins that are likely present in the mitochondrial outer membrane of all eukaryotes. Known factors involved in the regulation of mitochondrial morphology are virtually absent in T. brucei. Interestingly, RNAi-mediated ablation of three outer membrane proteins of unknown function resulted in a collapse of the network-like mitochondrion of procyclic cells and for the first time identified factors that control mitochondrial shape in T. brucei.}, }
@article {pmid23220190, year = {2013}, author = {Yao, P and Lu, W and Meng, F and Wang, X and Xu, B and Guo, X}, title = {Molecular cloning, expression and oxidative stress response of a mitochondrial thioredoxin peroxidase gene (AccTpx-3) from Apis cerana cerana.}, journal = {Journal of insect physiology}, volume = {59}, number = {3}, pages = {273-282}, doi = {10.1016/j.jinsphys.2012.11.005}, pmid = {23220190}, issn = {1879-1611}, mesh = {Amino Acid Sequence ; Animals ; Bees/classification/*enzymology/genetics/*metabolism ; *Cloning, Molecular ; Insect Proteins/chemistry/*genetics/metabolism ; Mitochondria/chemistry/*enzymology/metabolism ; Molecular Sequence Data ; Oxidative Stress ; Peroxiredoxins/chemistry/*genetics/metabolism ; Phylogeny ; Sequence Alignment ; }, abstract = {Thioredoxin peroxidase (Tpxs) plays an important role in maintaining redox homeostasis and in protecting organisms from the accumulation of toxic reactive oxygen species (ROS). Here, we isolated a mitochondrial thioredoxin peroxidase gene from Apis cerana cerana, AccTpx-3. The open reading frame (ORF) of AccTpx-3 is 729 bp in length and encodes a predicted protein of 242 amino acids, 27.084 kDa and an isoelectric point of 8.70. Furthermore, the 980 bp 5' flanking region was cloned, and the transcription factor binding sites were predicted. A quantitative RT-PCR (Q-PCR) analysis indicated that AccTpx-3 was expressed higher in muscle than other tissues, with its highest expression occurring on the fourth day of the larval stage, followed by the fifteenth day of the adult stage. Moreover, the expression of the AccTpx-3 transcript was upregulated by such abiotic stresses as 4°C, 42°C, H(2)O(2), cyhalothrin, acaricide and phoxime treatments. In contrast, AccTpx-3 transcription was downregulated by other abiotic stresses, including 16°C, 25°C, ultraviolet light and HgCl(2). Recombinant AccTpx-3 protein acted as a potent antioxidant that resisted paraquat-induced oxidative stress and protected DNA from oxidative damage. Taken together, these results suggest that the AccTpx-3 protein is an antioxidant enzyme that may protect organisms from oxidative stress.}, }
@article {pmid23217164, year = {2012}, author = {Liu, J and Zhan, X and Li, M and Li, G and Zhang, P and Xiao, Z and Shao, M and Peng, F and Hu, R and Chen, Z}, title = {Mitochondrial proteomics of nasopharyngeal carcinoma metastasis.}, journal = {BMC medical genomics}, volume = {5}, number = {}, pages = {62}, pmid = {23217164}, issn = {1755-8794}, mesh = {Blotting, Western ; Carcinoma ; Cell Count ; Cell Line, Tumor ; Cell Migration Assays ; Cell Movement ; Humans ; Mass Spectrometry ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Nasopharyngeal Carcinoma ; Nasopharyngeal Neoplasms/*metabolism/*pathology ; Neoplasm Metastasis ; Peptide Mapping ; Peroxiredoxin III/metabolism ; Protein Interaction Maps ; *Proteomics ; RNA, Small Interfering/metabolism ; Reproducibility of Results ; Transfection ; Two-Dimensional Difference Gel Electrophoresis ; Up-Regulation ; }, abstract = {BACKGROUND: Mitochondrial proteomic alterations of nasopharyngeal carcinoma metastasis remain unknown. Our purpose is to screen mitochondrial proteins for the elucidation of the molecular mechanisms of nasopharyngeal carcinoma metastasis and the discovery of metastasis-related biomarkers.<br><br>METHODS: Mitochondria were isolated from nasopharyngeal carcinoma metastatic (5-8F) and nonmetastatic (6-10B) cell lines, respectively. After characterization of isolated mitochondria, mitochondrial differentially expressed proteins (DEPs) were quantified by two-dimensional difference in-gel electrophoresis (2D-DIGE), and identified by peptide mass fingerprint (PMF) and tandem mass spectrometry (MS/MS). A functional enrichment analysis and a protein-protein interaction sub-network analysis for DEPs were carried out with bioinformatics. Furthermore, siRNAs transient transfections were used to suppress expressions of some up-regulated DEPs in metastatic cells (5-8F), followed by Transwell Migration assay.<br><br>RESULTS: Sixteen mitochondrial DEPs including PRDX3 and SOD2 were identified. Those 5-8F cells with suppression of PRDX3 showed an increased mobility potential. The functional enrichment analyses of DEPs discovered five significant biological processes including cellular response to reactive oxygen species, hydrogen peroxide metabolic process, regulation of mitochondrial membrane potential, cell redox homeostasis and oxidation reduction, and five significant molecular functions including oxidoreductase activity, caspase inhibitor activity, peroxiredoxin activity, porin activity and antioxidant activity. A protein-protein interaction sub-network of DEPs was generated with literature data. Ten mitochondrial DEPs including PRDX3, PRDX6, SOD2, ECH1, SERPINB5, COX5A, PDIA5, EIF5A, IDH3B, and PSMC4 were rationalized in the tumor-stroma co-evolution model that mitochondrial oxidative stress directly contributes to tumor metastasis.<br><br>CONCLUSIONS: Sixteen mitochondrial DEPs were identified with mass spectrometry and ten of them were rationalized in the tumor-stroma co-evolution model. Those 5-8F cells with suppression of PRDX3 showed an increased mobility potential. These data suggest that those mitochondrial DEPs are potential biomarkers for NPC metastasis, and their dysregulation would play important roles in mitochondria oxidative stress-mediated NPC metastatic process.}, }
@article {pmid23212402, year = {2012}, author = {Hao, XL and Yao, HF and Cheng, YZ and Wang, RX}, title = {Homology cloning, sequence characterization, and expression analysis of cDNA encoding electron transfer flavoprotein beta polypeptide in mud crab (Scylla paramamosain).}, journal = {Genetics and molecular research : GMR}, volume = {11}, number = {4}, pages = {4316-4322}, doi = {10.4238/2012.November.12.11}, pmid = {23212402}, issn = {1676-5680}, mesh = {Amino Acid Sequence ; Animals ; Arthropod Proteins/chemistry/*genetics/metabolism ; Base Sequence ; Brachyura/*genetics/metabolism ; Cloning, Molecular ; Conserved Sequence ; DNA, Complementary/genetics ; Electron-Transferring Flavoproteins/chemistry/*genetics/metabolism ; Gene Expression ; Molecular Sequence Data ; Organ Specificity ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Electron transfer flavoproteins (ETFs) are αβ-heterodimers found in eukaryotic mitochondria and bacteria. Herein we report a full-length complementary DNA of a mud crab (Scylla paramamosain) ETF β subunit (Scpa-ETFB) isolated with a homology cloning strategy. The complete complementary DNA of the Scpa-ETFB contains a 17-nt 5'-untranslated region, a 765-nt open reading frame encoding 254 amino acids, and a 248-nt 3'-untranslated region. The high identity of Scpa-ETFB with ETFB in other organisms indicated that Scpa-ETFB is a new member of the ETFB family. Although the conserved motif associated with flavin adenine dinucleotide binding is absent in Scpa-ETFB, the signature sequences of the ETF superfamily were identified. Using reverse transcriptase polymerase chain reaction, we detected the messenger RNA transcript of Scpa-ETFB in high levels in the tissues of the hepatopancreas, ovary, heart, and muscle. Phylogenetic analysis showed that Scpa-ETFB is most closely related to the ETFB genes of Caligus rogercresseyi and Lepeophtheirus salmonis. These results provided basic information for elucidating the molecular mechanism of energy production in the mud crab.}, }
@article {pmid23212326, year = {2012}, author = {Meng, ZN and Yang, S and Fan, B and Wang, L and Lin, HR}, title = {Genetic variation and balancing selection at MHC class II exon 2 in cultured stocks and wild populations of orange-spotted grouper (Epinephelus coioides).}, journal = {Genetics and molecular research : GMR}, volume = {11}, number = {4}, pages = {3869-3881}, doi = {10.4238/2012.November.12.4}, pmid = {23212326}, issn = {1676-5680}, mesh = {Animals ; Animals, Wild/*genetics/growth &amp; development ; Asia, Southeastern ; Bass/*genetics/*growth &amp; development ; China ; Cytochromes b/genetics ; Exons/*genetics ; Genes, MHC Class II/*genetics ; *Genetic Variation ; Genetics, Population ; Geography ; Histocompatibility Antigens Class II/genetics ; Likelihood Functions ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Pigmentation/genetics ; *Selection, Genetic ; }, abstract = {Major histocompatibility complex (MHC) molecules play vital roles in triggering adaptive immune responses and are considered the most variable molecules in vertebrates. Recently, many studies have focused on the polymorphism and evolution mode of MHC in both model and non-model organisms. Here, we analyzed the MHC class II exon 2-encoding β chain in comparison with the mitochondrial Cytb gene and our previously published microsatellite data set in three cultured stocks and four wild populations of the orange-spotted grouper (Epinephelus coioides) in order to investigate its genetic variation and mechanism of evolution. We detected one to four alleles in one individual, suggesting that at least two loci exist in the orange-spotted grouper, as well as a particularly high level of allelic diversity at the MHC loci. Furthermore, the cultured stocks exhibited reduced allelic diversity compared to the wild counterparts. We found evidence of balancing selection at MHC class II exon 2, and codon sites under positive selection were largely correspondent to the protein-binding region. In addition, MHC class II exon 2 revealed significant differences between population differentiation patterns from the neutral mitochondrial Cytb and microsatellites, which may indicate local adaptation at MHC loci in orange-spotted grouper originating from the South China Sea and Southeast Asia.}, }
@article {pmid23210891, year = {2013}, author = {Zimorski, V and Major, P and Hoffmann, K and Brás, XP and Martin, WF and Gould, SB}, title = {The N-terminal sequences of four major hydrogenosomal proteins are not essential for import into hydrogenosomes of Trichomonas vaginalis.}, journal = {The Journal of eukaryotic microbiology}, volume = {60}, number = {1}, pages = {89-97}, doi = {10.1111/jeu.12012}, pmid = {23210891}, issn = {1550-7408}, mesh = {Organelles/chemistry/*enzymology/genetics ; Protein Isoforms/chemistry/genetics/metabolism ; Protein Sorting Signals ; Protein Transport ; Protozoan Proteins/*chemistry/genetics/metabolism ; Trichomonas vaginalis/chemistry/*enzymology/genetics ; }, abstract = {The human pathogen Trichomonas vaginalis harbors hydrogenosomes, organelles of mitochondrial origin that generate ATP through hydrogen-producing fermentations. They contain neither genome nor translation machinery, but approximately 500 proteins that are imported from the cytosol. In contrast to well-studied organelles like Saccharomyces mitochondria, very little is known about how proteins are transported across the two membranes enclosing the hydrogenosomal matrix. Recent studies indicate that-in addition to N-terminal transit peptides-internal targeting signals might be more common in hydrogenosomes than in mitochondria. To further characterize the extent to which N-terminal and internal motifs mediate hydrogenosomal protein targeting, we transfected Trichomonas with 24 hemagglutinin (HA) tag fusion constructs, encompassing 13 different hydrogenosomal and cytosolic proteins of the parasite. Hydrogenosomal targeting of these proteins was analyzed by subcellular fractionation and independently by immunofluorescent localization. The investigated proteins include some of the most abundant hydrogenosomal proteins, such as pyruvate ferredoxin oxidoreductase (PFO), which possesses an amino-terminal targeting signal that is processed on import into hydrogenosomes, but is shown here not to be required for import into hydrogenosomes. Our results demonstrate that the deletion of N-terminal signals of hydrogenosomal precursors generally has little, if any, influence upon import into hydrogenosomes. Although the necessary and sufficient signals for hydrogenosomal import recognition appear complex, targeting to the organelle is still highly specific, as demonstrated by the finding that six HA-tagged glycolytic enzymes, highly expressed under the same promoter as other constructs studied here, localized exclusively to the cytosol and did not associate with hydrogenosomes.}, }
@article {pmid23209679, year = {2012}, author = {Addamo, AM and Reimer, JD and Taviani, M and Freiwald, A and Machordom, A}, title = {Desmophyllum dianthus (Esper, 1794) in the scleractinian phylogeny and its intraspecific diversity.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e50215}, pmid = {23209679}, issn = {1932-6203}, mesh = {Animals ; Anthozoa ; Base Sequence ; Cell Nucleus/metabolism ; DNA/genetics ; DNA, Intergenic/metabolism ; DNA, Mitochondrial/genetics ; Dianthus/*physiology ; Ecosystem ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Haplotypes ; Mediterranean Region ; Mitochondria/metabolism ; Phylogeny ; Polymerase Chain Reaction/methods ; Polymorphism, Genetic ; Sequence Analysis, DNA ; }, abstract = {The cosmopolitan solitary deep-water scleractinian coral Desmophyllum dianthus (Esper, 1794) was selected as a representative model species of the polyphyletic Caryophylliidae family to (1) examine phylogenetic relationships with respect to the principal Scleractinia taxa, (2) check population structure, (3) test the widespread connectivity hypothesis and (4) assess the utility of different nuclear and mitochondrial markers currently in use. To carry out these goals, DNA sequence data from nuclear (ITS and 28S) and mitochondrial (16S and COI) markers were analyzed for several coral species and for Mediterranean populations of D. dianthus. Three phylogenetic methodologies (ML, MP and BI), based on data from the four molecular markers, all supported D. dianthus as clearly belonging to the "robust" clade, in which the species Lophelia pertusa and D. dianthus not only grouped together, but also shared haplotypes for some DNA markers. Molecular results also showed shared haplotypes among D. dianthus populations distributed in regions separated by several thousands of kilometers and by clear geographic barriers. These results could reflect limited molecular and morphological taxonomic resolution rather than real widespread connectivity. Additional studies are needed in order to find molecular markers and morphological features able to disentangle the complex phylogenetic relationship in the Order Scleractinia and to differentiate isolated populations, thus avoiding the homoplasy found in some morphological characters that are still considered in the literature.}, }
@article {pmid23209127, year = {2013}, author = {Chauton, MS and Winge, P and Brembu, T and Vadstein, O and Bones, AM}, title = {Gene regulation of carbon fixation, storage, and utilization in the diatom Phaeodactylum tricornutum acclimated to light/dark cycles.}, journal = {Plant physiology}, volume = {161}, number = {2}, pages = {1034-1048}, pmid = {23209127}, issn = {1532-2548}, mesh = {Acclimatization/genetics/radiation effects ; Carbohydrate Metabolism/genetics/radiation effects ; Carbon/*metabolism ; Carbon Cycle/*genetics ; Diatoms/genetics/metabolism/*radiation effects ; Gene Expression Profiling ; Gene Expression Regulation/*radiation effects ; Gluconeogenesis/genetics/radiation effects ; Glycolysis/genetics/radiation effects ; Lipid Metabolism/genetics/radiation effects ; Membrane Transport Proteins/classification/genetics ; Mitochondria/genetics/metabolism/radiation effects ; Mitosis/genetics/radiation effects ; Monocarboxylic Acid Transporters ; Oligonucleotide Array Sequence Analysis ; *Photoperiod ; Phylogeny ; Plastids/genetics/metabolism/radiation effects ; Pyruvate Dehydrogenase Complex/classification/genetics ; }, abstract = {The regulation of carbon metabolism in the diatom Phaeodactylum tricornutum at the cell, metabolite, and gene expression levels in exponential fed-batch cultures is reported. Transcriptional profiles and cell chemistry sampled simultaneously at all time points provide a comprehensive data set on carbon incorporation, fate, and regulation. An increase in Nile Red fluorescence (a proxy for cellular neutral lipids) was observed throughout the light period, and water-soluble glucans increased rapidly in the light period. A near-linear decline in both glucans and lipids was observed during the dark period, and transcription profile data indicated that this decline was associated with the onset of mitosis. More than 4,500 transcripts that were differentially regulated during the light/dark cycle are identified, many of which were associated with carbohydrate and lipid metabolism. Genes not previously described in algae and their regulation in response to light were integrated in this analysis together with proposed roles in metabolic processes. Some very fast light-responding genes in, for example, fatty acid biosynthesis were identified and allocated to biosynthetic processes. Transcripts and cell chemistry data reflect the link between light energy availability and light energy-consuming metabolic processes. Our data confirm the spatial localization of processes in carbon metabolism to either plastids or mitochondria or to glycolysis/gluconeogenesis, which are localized to the cytosol, chloroplast, and mitochondria. Localization and diel expression pattern may be of help to determine the roles of different isoenzymes and the mining of genes involved in light responses and circadian rhythms.}, }
@article {pmid23199637, year = {2012}, author = {Durand, JD and Chen, WJ and Shen, KN and Fu, C and Borsa, P}, title = {Genus-level taxonomic changes implied by the mitochondrial phylogeny of grey mullets (Teleostei: Mugilidae).}, journal = {Comptes rendus biologies}, volume = {335}, number = {10-11}, pages = {687-697}, doi = {10.1016/j.crvi.2012.09.005}, pmid = {23199637}, issn = {1768-3238}, mesh = {Animals ; Classification ; DNA, Mitochondrial/genetics ; Mitochondria/*genetics/*physiology ; Molecular Biology ; Phylogeny ; Sequence Analysis, DNA ; Smegmamorpha/*classification/*genetics ; Species Specificity ; }, abstract = {A comprehensive mitochondrial phylogeny of the family Mugilidae (Durand et al., Mol. Phylogenet. Evol. 64 (2012) 73-92) demonstrated the polyphyly or paraphyly of a proportion of the 20 genera in the family. Based on these results, here we propose a revised classification with 25 genera, including 15 genera currently recognized as valid (Agonostomus, Aldrichetta, Cestraeus, Chaenomugil, Chelon, Crenimugil, Ellochelon, Joturus, Mugil, Myxus, Neomyxus, Oedalechilus, Rhinomugil, Sicamugil and Trachystoma), 7 resurrected genera [Dajaus (for Agonostomus monticola), Gracilimugil (for Liza argentea), Minimugil (for Sicamugil cascasia), Osteomugil (for several species currently under Moolgarda and Valamugil, including M. cunnesius, M. engeli, M. perusii, and V. robustus), Planiliza (for Indo-Pacific Chelon spp., Indo-Pacific Liza spp., and Paramugil parmatus), Plicomugil (for Oedalechilus labiosus), and Squalomugil (for Rhinomugil nasutus)] and 3 new genera: Neochelon gen. nov. (for Liza falcipinnis), Parachelon gen. nov. (for L. grandisquamis) and Pseudomyxus gen. nov. (for Myxus capensis). Genus Chelon was shown to include exclusively Chelon spp. and Liza spp. from the Atlantic and the Mediterranean, and Liza spp. species endemic to eastern southern Africa. Genus Crenimugil should now include C. crenilabis, Moolgarda seheli and V. buchanani. Genus names Liza, Moolgarda, Paramugil, Valamugil and Xenomugil should be abandoned because they are no longer valid. Further genetic evidence is required to confirm or infirm the validity of the genus Paracrenimugil Senou 1988. The mitochondrial phylogeny of the 25 genera from the present revision is the following: [(Sicamugil, (Minimugil, Rhinomugil)); Trachystoma; ((Myxus, Neomyxus), (Cestraeus, Chaenomugil, (Agonostomus, Dajaus, Joturus), Mugil)); (Aldrichetta, Gracilimugil); Neochelon gen. nov.; (Pseudomyxus gen. nov., (Chelon, Oedalechilus, Planiliza, Parachelon gen. nov.)); ((Squalomugil, (Ellochelon, Plicomugil)), (Crenimugil, Osteomugil))]. Agonostomus monticola and several species with large distribution ranges (including Moolgarda seheli, Mugil cephalus and M. curema) consist of separate lineages whose geographic distribution suggests they are cryptic species, thus warranting further taxonomic work in the Mugilidae at the infra-generic level.}, }
@article {pmid23199631, year = {2012}, author = {Kacem, H and Bakhoum, AJ and Eira, C and Neifar, L and Miquel, J}, title = {Ultrastructural characters of the spermatozoon of the digenean Hypocreadium caputvadum Kacem et al., 2011 (Lepocreadioidea: Lepocreadiidae), an intestinal parasite of Balistes capriscus in Tunisia.}, journal = {Comptes rendus biologies}, volume = {335}, number = {10-11}, pages = {637-644}, doi = {10.1016/j.crvi.2012.10.002}, pmid = {23199631}, issn = {1768-3238}, mesh = {Animals ; Axoneme/ultrastructure ; Cell Membrane/ultrastructure ; Glycogen/metabolism ; Indicators and Reagents ; Intestines/*parasitology ; Male ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Parasites ; Phylogeny ; Spermatozoa/*ultrastructure ; Tetraodontiformes/*parasitology ; Trematoda/*physiology ; Tunisia ; }, abstract = {The ultrastructural organization of the spermatozoon of the digenean Hypocreadium caputvadum (Lepocreadioidea: Lepocreadiidae) is described. Live digeneans were collected from Balistes capriscus (Teleostei: Balistidae) from the Gulf of Gabès, Tunisia (Eastern Mediterranean Sea). The mature spermatozoon of H. caputvadum shows several ultrastructural characters such as two axonemes of different lengths exhibiting the classical 9+"1" trepaxonematan pattern, a nucleus, two mitochondria, granules of glycogen, external ornamentation of the plasma membrane and two bundles of parallel cortical microtubules. Moreover, in the anterior extremity, the second axoneme is partly surrounded by a discontinuous and submembranous layer of electron-dense material. Our study provides new data on the spermatozoon of H. caputvadum in order to improve the understanding of phylogenetic relationships in the Digenea, particularly in the superfamily Lepocreadioidea. In this context, the electron-dense material surrounding one of the axonemes in the anterior spermatozoon extremity constitutes the unique distinguishing ultrastructural character of lepocreadioideans, and it is present in spermatozoa of lepocreadiids, aephnidiogenids and gyliauchenids.}, }
@article {pmid23199630, year = {2012}, author = {Fadhlaoui-Zid, K and Knittweis, L and Aurelle, D and Nafkha, C and Ezzeddine, S and Fiorentino, F and Ghmati, H and Ceriola, L and Jarboui, O and Maltagliati, F}, title = {Genetic structure of Octopus vulgaris (Cephalopoda, Octopodidae) in the central Mediterranean Sea inferred from the mitochondrial COIII gene.}, journal = {Comptes rendus biologies}, volume = {335}, number = {10-11}, pages = {625-636}, doi = {10.1016/j.crvi.2012.10.004}, pmid = {23199630}, issn = {1768-3238}, mesh = {Algorithms ; Analysis of Variance ; Animals ; DNA/biosynthesis/genetics ; DNA, Mitochondrial/genetics ; Demography ; Electron Transport Complex IV/*genetics ; Gene Flow ; Genetic Variation ; Mediterranean Sea ; Mitochondria/*enzymology/*genetics ; Molecular Biology ; Octopodiformes/*enzymology/*genetics ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {The polymorphism of the mitochondrial gene cytochrome oxidase III was studied in the Mediterranean octopus, Octopus vulgaris Cuvier, 1797. A total of 202 specimens from seven sampling sites were analysed with the aim of elucidating patterns of genetic structure in the central Mediterranean Sea and to give an insight into the phylogeny of the Octopus genus. Phylogenetic analyses showed that individuals from the central Mediterranean belong to the O. vulgaris species whose limits should nevertheless be clarified. Concerning genetic structure, two high-frequency haplotypes were present in all locations. The overall genetic divergence (Φ(ST)=0.05, P<0.05) indicated a significant genetic structuring in the study area and an AMOVA highlighted a significant break between western and eastern Mediterranean basins (Φ(CT)=0.094, P<0.05). Possible explanations for the observed patterns of genetic structuring are discussed with reference to their relevance for fisheries management.}, }
@article {pmid23199478, year = {2013}, author = {Bertucci, A and Moya, A and Tambutté, S and Allemand, D and Supuran, CT and Zoccola, D}, title = {Carbonic anhydrases in anthozoan corals-A review.}, journal = {Bioorganic &amp; medicinal chemistry}, volume = {21}, number = {6}, pages = {1437-1450}, doi = {10.1016/j.bmc.2012.10.024}, pmid = {23199478}, issn = {1464-3391}, mesh = {Animals ; Anthozoa/*enzymology ; Calcium Carbonate/chemistry/metabolism ; Carbonic Anhydrase Inhibitors/chemistry/metabolism ; Carbonic Anhydrases/chemistry/classification/*metabolism ; Humans ; Isoenzymes/chemistry/metabolism ; Mitochondria/enzymology ; Photosynthesis ; Phylogeny ; Symbiosis ; }, abstract = {Coral reefs are among the most biologically diverse and economically important ecosystems on the planet. The deposition of massive calcium carbonate skeletons (biomineralization or calcification) by scleractinian corals forms the coral reef framework/architecture that serves as habitat for a large diversity of organisms. This process would not be possible without the intimate symbiosis between corals and photosynthetic dinoflagellates, commonly called zooxanthellae. Carbonic anhydrases play major roles in those two essential processes of coral's physiology: they are involved in the carbon supply for calcium carbonate precipitation as well as in carbon-concentrating mechanisms for symbiont photosynthesis. Here, we review the current understanding of diversity and function of carbonic anhydrases in corals and discuss the perspective of theses enzymes as a key to understanding impacts of environmental changes on coral reefs.}, }
@article {pmid23198851, year = {2013}, author = {Funes, S and Westerburg, H and Jaimes-Miranda, F and Woellhaf, MW and Aguilar-Lopez, JL and Janßen, L and Bonnefoy, N and Kauff, F and Herrmann, JM}, title = {Partial suppression of Oxa1 mutants by mitochondria-targeted signal recognition particle provides insights into the evolution of the cotranslational insertion systems.}, journal = {The FEBS journal}, volume = {280}, number = {3}, pages = {904-915}, doi = {10.1111/febs.12082}, pmid = {23198851}, issn = {1742-4658}, mesh = {Bacterial Proteins/genetics/metabolism ; Blotting, Western ; Electron Transport Complex IV/genetics/*metabolism ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli Proteins/genetics/metabolism ; Membrane Proteins/genetics/metabolism ; Mitochondria/genetics/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Models, Genetic ; Mutation ; Nuclear Proteins/genetics/*metabolism ; Protein Binding ; Protein Biosynthesis/genetics ; Protein Transport ; Receptors, Cytoplasmic and Nuclear/genetics/metabolism ; Ribosomes/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Signal Recognition Particle/genetics/*metabolism ; }, abstract = {The biogenesis of hydrophobic membrane proteins involves their cotranslational membrane integration in order to prevent their unproductive aggregation. In the cytosol of bacteria and eukaryotes, membrane targeting of ribosomes that synthesize membrane proteins is achieved by signal recognition particles (SRPs) and their cognate membrane-bound receptors. As is evident from the genomes of fully sequenced eukaryotes, mitochondria generally lack an SRP system. Instead, mitochondrial ribosomes are physically associated with the protein insertion machinery in the inner membrane. Accordingly, deletion of ribosome-binding sites on the Oxa1 insertase and the Mba1 ribosome receptor in yeast leads to severe defects in cotranslational protein insertion and results in respiration-deficient mutants. In this study, we expressed mitochondria-targeted versions of the bacterial SRP protein Ffh and its receptor FtsY in these yeast mutants. Interestingly, Ffh was found to bind to the large subunit of mitochondrial ribosomes, and could relieve, to some degree, the defect of these insertion mutants. Although FtsY could also bind to mitochondrial membranes, it did not improve membrane protein biogenesis in this strain, presumably because of its inability to interact with Ffh. Hence, mitochondrial ribosomes are still able to interact physically and functionally with the bacterial SRP system. Our observations are consistent with a model according to which the protein insertion system in mitochondria evolved in three steps. The loss of genes for hydrophilic polypeptides (step 1) allowed the development of ribosome-binding sites on membrane proteins (step 2), which finally made the existence of an SRP-mediated system dispensable (step 3).}, }
@article {pmid23196969, year = {2013}, author = {Coppe, A and Agostini, C and Marino, IA and Zane, L and Bargelloni, L and Bortoluzzi, S and Patarnello, T}, title = {Genome evolution in the cold: Antarctic icefish muscle transcriptome reveals selective duplications increasing mitochondrial function.}, journal = {Genome biology and evolution}, volume = {5}, number = {1}, pages = {45-60}, pmid = {23196969}, issn = {1759-6653}, mesh = {Adaptation, Physiological/genetics ; Animals ; Antarctic Regions ; *Cold Temperature ; Computational Biology ; *Evolution, Molecular ; *Gene Duplication ; Genome, Mitochondrial ; Mitochondria, Muscle/*genetics/metabolism ; Muscle, Skeletal/*metabolism ; Oxygen Consumption/genetics ; Perciformes/*genetics ; Selection, Genetic ; *Transcriptome ; }, abstract = {Antarctic notothenioids radiated over millions of years in subzero waters, evolving peculiar features, such as antifreeze glycoproteins and absence of heat shock response. Icefish, family Channichthyidae, also lack oxygen-binding proteins and display extreme modifications, including high mitochondrial densities in aerobic tissues. A genomic expansion accompanying the evolution of these fish was reported, but paucity of genomic information limits the understanding of notothenioid cold adaptation. We reconstructed and annotated the first skeletal muscle transcriptome of the icefish Chionodraco hamatus providing a new resource for icefish genomics (http://compgen.bio.unipd.it/chamatusbase/, last accessed December 12, 2012). We exploited deep sequencing of this energy-dependent tissue to test the hypothesis of selective duplication of genes involved in mitochondrial function. We developed a bioinformatic approach to univocally assign C. hamatus transcripts to orthology groups extracted from phylogenetic trees of five model species. Chionodraco hamatus duplicates were recorded for each orthology group allowing the identification of duplicated genes specific to the icefish lineage. Significantly more duplicates were found in the icefish when transcriptome data were compared with whole-genome data of model species. Indeed, duplicated genes were significantly enriched in proteins with mitochondrial localization, involved in mitochondrial function and biogenesis. In cold conditions and without oxygen-carrying proteins, energy production is challenging. The combination of high mitochondrial densities and the maintenance of duplicated genes involved in mitochondrial biogenesis and aerobic respiration might confer a selective advantage by improving oxygen diffusion and energy supply to aerobic tissues. Our results provide new insights into the genomic basis of icefish cold adaptation.}, }
@article {pmid23196804, year = {2013}, author = {Olson, KR}, title = {Hydrogen sulfide as an oxygen sensor.}, journal = {Clinical chemistry and laboratory medicine}, volume = {51}, number = {3}, pages = {623-632}, doi = {10.1515/cclm-2012-0551}, pmid = {23196804}, issn = {1437-4331}, mesh = {Animals ; Humans ; Hydrogen Sulfide/*metabolism ; Hypoxia ; Mitochondria/metabolism ; Muscle, Smooth, Vascular/metabolism ; Oxygen/blood/*metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {The ability to monitor oxygen (O2) availability and delivery is crucial to an animal's survival. Vertebrates have a number of O2 'sensing' cells that monitor environmental oxygen and ensure adequate delivery to the tissues. While there is little doubt that these cells perform important homeostatic functions, there is little consensus on how a change in O2 concentration, or partial pressure (pO2), is transduced into a physiological response. We recently proposed that the metabolism of hydrogen sulfide (H2S) functions as the O2 sensor in a variety of tissues. In this mechanism, the concentration of biologically active H2S is regulated by the simple balance between constitutive H2S production and its oxidation by mitochondria. This hypothesis is supported by a number of experimental observations in a wide range of O2 sensing tissues: 1) exogenous H2S produces the same physiological response as hypoxia; 2) cellular H2S production is inversely related to pO2 at physiologically relevant pO2s; 3) agonists and antagonists of H2S biosynthesis augment and inhibit hypoxic responses, respectively; and 4) H2S and hypoxia appear to act via common effector pathways. The reciprocal relationship between H2S and O2 also has a long evolutionary history suggesting these gases have been inexorably intertwined throughout evolution. The intent of this review is to elaborate on the mechanism of H2S-mediated O2 sensing.}, }
@article {pmid23179441, year = {2013}, author = {Benz, M and Soll, J and Ankele, E}, title = {Arabidopsis thaliana Oxa proteins locate to mitochondria and fulfill essential roles during embryo development.}, journal = {Planta}, volume = {237}, number = {2}, pages = {573-588}, pmid = {23179441}, issn = {1432-2048}, mesh = {Arabidopsis/*embryology/genetics/metabolism ; Cloning, Molecular ; DNA, Complementary/genetics/metabolism ; Electron Transport Complex IV/genetics/*metabolism ; Evolution, Molecular ; *Gene Expression Regulation, Plant ; Genes, Plant ; Germination ; Heterozygote ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Multigene Family ; Nuclear Proteins/genetics/*metabolism ; Pisum sativum/genetics/metabolism ; Phenotype ; Protein Isoforms/metabolism ; Protein Transport ; RNA, Messenger/genetics/metabolism ; Seeds/genetics/*growth &amp; development/metabolism ; Transcription, Genetic ; }, abstract = {Members of the Alb3/Oxa1/YidC protein family function as insertases in chloroplasts, mitochondria, and bacteria. Due to independent gene duplications, all organisms possess two isoforms, Oxa1 and Oxa2 except gram-negative bacteria, which encode only for one YidC-like protein. The genome of Arabidopsis thaliana however, encodes for eight different isoforms. The localization of three of these isoforms has been identified earlier: Alb3 and Alb4 located in thylakoid membranes of chloroplasts while AtOxa1 was found in the inner membrane of mitochondria. Here, we show that the second Oxa1 protein, Oxa1b as well as two Oxa2 proteins are also localized in mitochondria. The last two isoforms most likely encode truncated versions of Oxa-like proteins, which might be inoperable pseudogenes. Homozygous mutant lines were only obtained for Oxa1b, which did not reveal any significant phenotypes, while T-DNA insertion lines of Oxa1a, Oxa2a and Oxa2b resulted only in heterozygous plants indicating that these genes are indispensable for plant development. Phenotyping heterozygous lines showed that embryos are either retarded in growth, display an albino phenotype or embryo formation was entirely abolished suggesting that Oxa1a and both Oxa2 proteins function in embryo formation although at different developmental stages as indicated by the various phenotypes observed.}, }
@article {pmid23178692, year = {2013}, author = {Shi, Y and Zhao, Z and Zhu, X and Chen, K and Zhang, Q}, title = {Expression and functional characterization of a gene associated with retinoid-interferon-induced mortality 19 (GRIM-19) from orange-spotted grouper (Epinephelus coioides).}, journal = {Fish &amp; shellfish immunology}, volume = {34}, number = {1}, pages = {273-279}, doi = {10.1016/j.fsi.2012.11.017}, pmid = {23178692}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Apoptosis ; Bass/*genetics/*metabolism ; Caspases/metabolism ; Cloning, Molecular ; DNA, Complementary/genetics ; Fish Proteins/*genetics/*metabolism ; HeLa Cells ; Humans ; Interferon-beta/metabolism ; Lipopolysaccharides/pharmacology ; Molecular Sequence Data ; Organ Specificity ; Phylogeny ; RNA/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Alignment ; Transfection ; Tretinoin/metabolism ; }, abstract = {GRIM-19 is a nuclear encoded subunit of complex I that has been implicated in apoptosis. The protein participates in multiple functions including the innate immune response. GRIM-19 has been studied in humans and other mammals; however, fish GRIM-19 has not been well characterized. In this study, a new GRIM-19 gene, EcGRIM-19, was isolated from the orange-spotted grouper (Epinephelus coioides) cDNA library, which was constructed following LPS treatment. EcGRIM-19 is a 582-bp gene that encodes a 144-amino acid protein. The gene is a true ortholog of mammalian GRIM-19. EcGRIM-19 exhibits ubiquitous and constitutive expression in the different tissues of the orange-spotted grouper. The expression levels of EcGRIM-19 are altered in the gill, spleen, kidney and liver after induction with LPS. The subcellular localization analysis demonstrated that the EcGRIM-19 protein is localized predominantly in the mitochondria. In addition, amino acids 30-50 of the protein are responsible for the mitochondrial localization of EcGRIM-19. The caspase assay demonstrated that the overexpression of GRIM-19 enhanced the cellular sensitivity to interferon(IFN)-β- and retinoic acid (RA)-induced death in HeLa cells. The data presented in this study are important for further understanding the EcGRIM-19 gene function in fish.}, }
@article {pmid23176215, year = {2013}, author = {Sunggip, C and Kitajima, N and Nishida, M}, title = {Redox control of cardiovascular homeostasis by angiotensin II.}, journal = {Current pharmaceutical design}, volume = {19}, number = {17}, pages = {3022-3032}, doi = {10.2174/1381612811319170008}, pmid = {23176215}, issn = {1873-4286}, mesh = {Angiotensin II/*physiology ; Cardiovascular System/*metabolism ; Cellular Senescence ; Genes, ras ; *Homeostasis ; Humans ; Mitochondria/physiology ; NADPH Oxidases/physiology ; Nitric Oxide Synthase Type III/physiology ; Oxidation-Reduction ; Reactive Oxygen Species/metabolism ; Receptor, Angiotensin, Type 1/physiology ; Renin-Angiotensin System/physiology ; Signal Transduction ; }, abstract = {Covalent modification of sulfur-containing amino acids in proteins by reactive oxygen species (ROS) has been attracting attention as a major post-translational modification regulating intracellular signal transduction pathways. Angiotensin II Ang II, a major physiologically active substrate in renin-angiotensin (RAS) system, plays a central role in the pathophysiology of cardiovascular systems. Many evidences show that Ang II activates several signaling pathways via an oxidative modification of proteins by Ang II-induced ROS. Ang II induced ROS production is predominantly regulated by three enzymes: NADPH oxidase, mitochondrial respiratory complex, and nitric oxide synthase (NOS), and each enzyme-generating ROS are found to activate appropriate signaling pathways via selective oxidation of specific proteins. These reactions are negatively regulated by ROS-scavenging enzymes or disulfide bridge reducing enzymes, and functional disorders of these enzymes are found to cause cardiovascular dysfunctions. Thus, the spatial and temporal regulation of oxidative modification of signaling proteins by ROS is essential to maintain cardiovascular homeostasis by Ang II. This review brings in the new aspect in understanding ROS-mediated regulation of cardiovascular homeostasis by Ang II, and provides the possible mechanisms underlying metamorphosis of cardiovascular homeostasis by ROS.}, }
@article {pmid23175285, year = {2013}, author = {Gilloteaux, J and Ott, DW and Oldham-Ott, CK}, title = {The gallbladder of the electric ray Torpedo marmorata Risso displays excrescent cholecystocytes with merocrine and apocrine-like secretions.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {296}, number = {1}, pages = {79-95}, doi = {10.1002/ar.22621}, pmid = {23175285}, issn = {1932-8494}, mesh = {Animals ; Cholecystitis/pathology ; Cholelithiasis/pathology ; Cytoplasmic Vesicles/ultrastructure ; Desmosomes/ultrastructure ; Epithelium/metabolism/pathology/ultrastructure ; Female ; Gallbladder/*metabolism/*pathology/ultrastructure ; Male ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Microvilli/ultrastructure ; Mitochondria/ultrastructure ; Mucins/*metabolism ; Torpedo/*anatomy &amp; histology/*metabolism ; }, abstract = {The gallbladder of Torpedo marmorata exhibits a mucosal surface layer of simple columnar epithelium with very tall cholecystocytes. The apical domain of each cell has few microvilli, but many mucous vesicles that are secreted by exocytosis at the cell apices. The apical regions may also elongate and undergo self-excision while shedding mucus and cell debris into the gallbladder lumen in a manner similar to that described in mammals as a result of sex steroid treatment to induce gallstones and to that found in the cholecystitis associated with cholelithiasis. Numerous small mitochondria, spherical to elongated, are distributed throughout the cells, while the nuclei are often located in the lower third of each cell. In the lower part of the cholecystocytes, large and very densely contrasted lysosomes can be found. All cells are tightly joined by junctional complexes, including long, highly contrasted desmosomes. The fibromuscular layer is made of a loose stroma with a limited muscular component and a poor blood supply. Large diameter blood vessels can only be found in the subserosal layer. It is hypothesized that the obligatorily carnivorous diet of this ureotelic fish has resulted in the evolution of a gallbladder ultrastructure resembling that found in cholecystitis but without the associated cholelithiasis.}, }
@article {pmid23175281, year = {2012}, author = {Galluzzi, L and Kepp, O and Kroemer, G}, title = {Mitochondria: master regulators of danger signalling.}, journal = {Nature reviews. Molecular cell biology}, volume = {13}, number = {12}, pages = {780-788}, pmid = {23175281}, issn = {1471-0080}, mesh = {Animals ; *Apoptosis ; Humans ; Mice ; Mitochondria/*physiology ; Signal Transduction ; }, abstract = {Throughout more than 1.5 billion years of obligate endosymbiotic co-evolution, mitochondria have developed not only the capacity to control distinct molecular cascades leading to cell death but also the ability to sense (and react to) multiple situations of cellular stress, including viral infection. In addition, mitochondria can emit danger signals that alert the cell or the whole organism of perturbations in homeostasis, hence promoting the induction of cell-intrinsic or systemic adaptive responses, respectively. As such, mitochondria can be considered as master regulators of danger signalling.}, }
@article {pmid23172144, year = {2012}, author = {Hughes, AL and Gottschling, DE}, title = {An early age increase in vacuolar pH limits mitochondrial function and lifespan in yeast.}, journal = {Nature}, volume = {492}, number = {7428}, pages = {261-265}, pmid = {23172144}, issn = {1476-4687}, support = {P30 CA015704/CA/NCI NIH HHS/United States ; R01 AG023779/AG/NIA NIH HHS/United States ; R01 AG037512/AG/NIA NIH HHS/United States ; P01 AG001751/AG/NIA NIH HHS/United States ; AG023779/AG/NIA NIH HHS/United States ; AG037512/AG/NIA NIH HHS/United States ; T32 AG000057/AG/NIA NIH HHS/United States ; R37 AG023779/AG/NIA NIH HHS/United States ; }, mesh = {Amino Acids/metabolism ; Gene Expression ; Homeostasis/physiology ; Hydrogen-Ion Concentration ; Lysosomes/chemistry/physiology ; *Microbial Viability ; Mitochondria/*metabolism ; Proton-Translocating ATPases/genetics/metabolism ; Saccharomyces cerevisiae/chemistry/metabolism/*physiology ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Vacuoles/*chemistry/physiology ; }, abstract = {Mitochondria have a central role in ageing. They are considered to be both a target of the ageing process and a contributor to it. Alterations in mitochondrial structure and function are evident during ageing in most eukaryotes, but how this occurs is poorly understood. Here we identify a functional link between the lysosome-like vacuole and mitochondria in Saccharomyces cerevisiae, and show that mitochondrial dysfunction in replicatively aged yeast arises from altered vacuolar pH. We found that vacuolar acidity declines during the early asymmetric divisions of a mother cell, and that preventing this decline suppresses mitochondrial dysfunction and extends lifespan. Surprisingly, changes in vacuolar pH do not limit mitochondrial function by disrupting vacuolar protein degradation, but rather by reducing pH-dependent amino acid storage in the vacuolar lumen. We also found that calorie restriction promotes lifespan extension at least in part by increasing vacuolar acidity via conserved nutrient-sensing pathways. Interestingly, although vacuolar acidity is reduced in aged mother cells, acidic vacuoles are regenerated in newborn daughters, coinciding with daughter cells having a renewed lifespan potential. Overall, our results identify vacuolar pH as a critical regulator of ageing and mitochondrial function, and outline a potentially conserved mechanism by which calorie restriction delays the ageing process. Because the functions of the vacuole are highly conserved throughout evolution, we propose that lysosomal pH may modulate mitochondrial function and lifespan in other eukaryotic cells.}, }
@article {pmid23171165, year = {2012}, author = {Wylezich, C and Karpov, SA and Mylnikov, AP and Anderson, R and Jürgens, K}, title = {Ecologically relevant choanoflagellates collected from hypoxic water masses of the Baltic Sea have untypical mitochondrial cristae.}, journal = {BMC microbiology}, volume = {12}, number = {}, pages = {271}, pmid = {23171165}, issn = {1471-2180}, mesh = {Anaerobiosis ; Choanoflagellata/*classification/isolation &amp; purification/physiology/*ultrastructure ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Microscopy ; Mitochondria/*ultrastructure ; Molecular Sequence Data ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Seawater/*parasitology ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Protist communities inhabiting oxygen depleted waters have so far been characterized through both microscopical observations and sequence based techniques. However, the lack of cultures for abundant taxa severely hampers our knowledge on the morphology, ecology and energy metabolism of hypoxic protists. Cultivation of such protists has been unsuccessful in most cases, and has never yet succeeded for choanoflagellates, even though these small bacterivorous flagellates are known to be ecologically relevant components of aquatic protist communities.<br><br>RESULTS: Quantitative data for choanoflagellates and the vertical distribution of Codosiga spp. at Gotland and Landsort Deep (Baltic Sea) indicate its preference for oxygen-depleted zones. Strains isolated and cultivated from these habitats revealed ultrastructural peculiarities such as mitochondria showing tubular cristae never seen before for choanoflagellates, and the first observation of intracellular prokaryotes in choanoflagellates. Analysis of their partial 28S rRNA gene sequence complements the description of two new species, Codosiga minima n. sp. and C. balthica n. sp. These are closely related with but well separated from C. gracilis (C. balthica and C. minima p-distance to C. gracilis 4.8% and 11.6%, respectively). In phylogenetic analyses the 18S rRNA gene sequences branch off together with environmental sequences from hypoxic habitats resulting in a wide cluster of hypoxic Codosiga relatives so far only known from environmental sequencing approaches.<br><br>CONCLUSIONS: Here, we establish the morphological and ultrastructural identity of an environmental choanoflagellate lineage. Data from microscopical observations, supplemented by findings from previous culture-independent methods, indicate that C. balthica is likely an ecologically relevant player of Baltic Sea hypoxic waters. The possession of derived mitochondria could be an adaptation to life in hypoxic environments periodically influenced by small-scale mixing events and changing oxygen content allowing the reduction of oxygen consuming components. In view of the intricacy of isolating and cultivating choanoflagellates, the two new cultured species represent an important advance to the understanding of the ecology of this group, and mechanisms of adaptations to hypoxia in protists in general.}, }
@article {pmid23161662, year = {2013}, author = {Zhang, G and Morin, C and Zhu, X and Bao Huynh, M and Ouidir Ouidja, M and Sepulveda-Diaz, JE and Raisman-Vozari, R and Li, P and Papy-Garcia, D}, title = {Self-evolving oxidative stress with identifiable pre- and postmitochondrial phases in PC12 cells.}, journal = {Journal of neuroscience research}, volume = {91}, number = {2}, pages = {273-284}, doi = {10.1002/jnr.23146}, pmid = {23161662}, issn = {1097-4547}, mesh = {Aconitate Hydratase/metabolism ; Animals ; Apoptosis/drug effects ; Caspase 3/metabolism ; Caspase 9/metabolism ; Cathepsin D/metabolism ; Cathepsin E/metabolism ; Cell Survival/drug effects ; Enzyme Inhibitors/pharmacology ; Hydrogen Peroxide/pharmacology ; Lipid Peroxidation/drug effects ; Lysosomes/drug effects/metabolism ; Malondialdehyde/metabolism ; Mitochondria/drug effects/*metabolism ; Oxidation-Reduction/drug effects ; Oxidative Stress/drug effects/*physiology ; PC12 Cells/drug effects/enzymology ; Rats ; Reactive Oxygen Species/*metabolism ; Superoxide Dismutase/metabolism ; Time Factors ; }, abstract = {During the neurodegenerative process in several brain diseases, oxidative stress is known to play important roles in disease severity and evolution. Although early events of stress, such as increased lipid peroxidation and decreased superoxide dismutase, are known to characterize early onsets of these diseases, little is known about the events that participate in maintaining the chronic evolving phase influencing the disease progression in neurons. Here, we used differentiated PC12 cells to identify premitochondrial and postmitochondrial events occurring during the oxidative stress cascade leading to apoptosis. Our data indicate that an acute and strong oxidative impulse (500 μM H(2)O(2), 30 min) can induce, in this model, a 24-hr self-evolving stress, which advances from a premitochondrial phase characterized by lysosomes and cathepsin B and D translocations to cytosol and early mitochondrial membrane hyperpolarization. This phase lasts for about 5 hr and is followed by a postmitochondrial phase distinguished by mitochondrial membrane depolarization, reactive oxygen species increase, caspase-9 and caspase-3 activations, and apoptosis. Inhibition of cathepsins B and D suggests that cells can be protected at the premitochondrial phase of stress evolution and that new cathepsins regulators, such as glycosaminoglycans mimetics, can be considered as new therapeutic prototypes for neurodegeneration. Insofar as early oxidative stress markers have been related to the early onset of neurodegeneration, strategies protecting cells at the premitochondrial phase of oxidative stress may have important therapeutic applications.}, }
@article {pmid23156681, year = {2012}, author = {Cheng, YZ and Xu, TJ and Jin, XX and Tang, D and Wei, T and Sun, YY and Meng, FQ and Shi, G and Wang, RX}, title = {Universal primers for amplification of the complete mitochondrial control region in marine fish species.}, journal = {Molekuliarnaia biologiia}, volume = {46}, number = {5}, pages = {810-813}, pmid = {23156681}, issn = {0026-8984}, mesh = {Animals ; Aquatic Organisms ; Base Sequence ; Conserved Sequence ; DNA Primers/*chemistry/genetics ; DNA, Mitochondrial/*genetics ; Fishes/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Transfer, Phe/*genetics ; RNA, Transfer, Thr/*genetics ; }, abstract = {Through multiple alignment analysis of mitochondrial tRNA-Thr and tRNA-Phe sequences from 161 fishes, new universal primers specially targeting the entire mitochondrial control region were designed. This new primer set successfully amplified the expected PCR products from various kinds of marine fish species, belonging to various families, and the amplified segments were confirmed to be the control region by sequencing. These primers provide a useful tool to study the control region diversity in economically important fish species, the possible mechanism of control region evolution, and the functions of the conserved motifs in the control region.}, }
@article {pmid23155377, year = {2012}, author = {Nicolas, V and Herbreteau, V and Couloux, A and Keovichit, K and Douangboupha, B and Hugot, JP}, title = {A remarkable case of micro-endemism in Laonastes aenigmamus (Diatomyidae, Rodentia) revealed by nuclear and mitochondrial DNA sequence data.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e48145}, pmid = {23155377}, issn = {1932-6203}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Genetic Variation ; Genetics, Population ; Mitochondria/genetics ; Rodentia/*genetics ; Sequence Analysis, DNA ; }, abstract = {L. aenigmamus is endemic to the limestone formations of the Khammuan Province (Lao PDR), and is strongly specialized ecologically. From the survey of 137 individuals collected from 38 localities, we studied the phylogeography of this species using one mitochondrial (Cyt b) and two nuclear genes (BFIBR and GHR). Cyt b analyses reveal a strong mtDNA phylogeographical structure: 8 major geographical clades differing by 5-14% sequence divergence were identified, most of them corresponding to distinct karst areas. Nuclear markers display congruent results but with a less genetic structuring. Together, the data strongly suggest an inland insular model for Laonastes population structure. With 8 to 16 evolutionary significant units in a small area (about 200×50 km) this represents an exceptional example of micro-endemism. Our results suggest that L. aenigmamus may represent a complex of species and/or sub-species. The common ancestor of all Laonastes may have been widely distributed within the limestone formations of the Khammuan Province at the end of Miocene/beginning of the Pliocene. Parallel events of karst fragmentation and population isolation would have occurred during the Pleistocene or/and the end of the Pliocene. The limited gene flow detected between populations from different karst blocks restrains the likelihood of survival of Laonastes. This work increases the necessity for a strict protection of this rare animal and its habitat and provides exclusive information, essential to the organization of its protection.}, }
@article {pmid23153022, year = {2012}, author = {Irisarri, I and San Mauro, D and Abascal, F and Ohler, A and Vences, M and Zardoya, R}, title = {The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {626}, pmid = {23153022}, issn = {1471-2164}, mesh = {Acceleration ; Animals ; Anura/*genetics ; Cell Nucleus/*genetics ; *Evolution, Molecular ; Gene Rearrangement/genetics ; Genome, Mitochondrial/genetics ; Mitochondria/*genetics ; Phylogeny ; Selection, Genetic ; Sequence Analysis ; Species Specificity ; }, abstract = {BACKGROUND: Understanding the causes underlying heterogeneity of molecular evolutionary rates among lineages is a long-standing and central question in evolutionary biology. Although several earlier studies showed that modern frogs (Neobatrachia) experienced an acceleration of mitochondrial gene substitution rates compared to non-neobatrachian relatives, no further characterization of this phenomenon was attempted. To gain new insights on this topic, we sequenced the complete mitochondrial genomes and nine nuclear loci of one pelobatoid (Pelodytes punctatus) and five neobatrachians, Heleophryne regis (Heleophrynidae), Lechriodus melanopyga (Limnodynastidae), Calyptocephalella gayi (Calyptocephalellidae), Telmatobius bolivianus (Ceratophryidae), and Sooglossus thomasseti (Sooglossidae). These represent major clades not included in previous mitogenomic analyses, and most of them are remarkably species-poor compared to other neobatrachians.<br><br>RESULTS: We reconstructed a fully resolved and robust phylogeny of extant frogs based on the new mitochondrial and nuclear sequence data, and dated major cladogenetic events. The reconstructed tree recovered Heleophryne as sister group to all other neobatrachians, the Australasian Lechriodus and the South American Calyptocephalella formed a clade that was the sister group to Nobleobatrachia, and the Seychellois Sooglossus was recovered as the sister group of Ranoides. We used relative-rate tests and direct comparison of branch lengths from mitochondrial and nuclear-based trees to demonstrate that both mitochondrial and nuclear evolutionary rates are significantly higher in all neobatrachians compared to their non-neobatrachian relatives, and that such rate acceleration started at the origin of Neobatrachia.<br><br>CONCLUSIONS: Through the analysis of the selection coefficient (&#x3c9;) in different branches of the tree, we found compelling evidence of relaxation of purifying selection in neobatrachians, which could (at least in part) explain the observed higher mitochondrial and nuclear substitution rates in this clade. Our analyses allowed us to discard that changes in substitution rates could be correlated with increased mitochondrial genome rearrangement or diversification rates observed in different lineages of neobatrachians.}, }
@article {pmid23151580, year = {2012}, author = {Vafai, SB and Mootha, VK}, title = {Mitochondrial disorders as windows into an ancient organelle.}, journal = {Nature}, volume = {491}, number = {7424}, pages = {374-383}, pmid = {23151580}, issn = {1476-4687}, mesh = {Biological Evolution ; Electron Transport/physiology ; Humans ; Mitochondria/*genetics/*metabolism/pathology ; Mitochondrial Diseases/*genetics/*pathology ; }, abstract = {Much of our current knowledge about mitochondria has come from studying patients who have respiratory chain disorders. These disorders comprise a large collection of individually rare syndromes, each presenting in a unique and often devastating way. In recent years, there has been great progress in defining their genetic basis, but we still know little about the cascade of events that gives rise to such diverse pathology. Here, we review these disorders and explore them in the context of a contemporary understanding of mitochondrial evolution, biochemistry and genetics. Fully deciphering their pathogenesis is a challenging next step that will inspire the development of drug treatments for rare and common diseases.}, }
@article {pmid23151513, year = {2012}, author = {Hewitt, VL and Heinz, E and Shingu-Vazquez, M and Qu, Y and Jelicic, B and Lo, TL and Beilharz, TH and Dumsday, G and Gabriel, K and Traven, A and Lithgow, T}, title = {A model system for mitochondrial biogenesis reveals evolutionary rewiring of protein import and membrane assembly pathways.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {49}, pages = {E3358-66}, pmid = {23151513}, issn = {1091-6490}, mesh = {*Biological Evolution ; Candida albicans/*physiology ; Carrier Proteins/*metabolism ; Cluster Analysis ; Computational Biology ; Electron Transport Chain Complex Proteins/*metabolism ; Electrophoresis, Polyacrylamide Gel ; Markov Chains ; Mitochondria/*physiology ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/*metabolism ; *Models, Biological ; Oxygen Consumption/physiology ; Phylogeny ; Protein Transport/physiology ; Saccharomyces cerevisiae ; Species Specificity ; }, abstract = {The controlled biogenesis of mitochondria is a key cellular system coordinated with the cell division cycle, and major efforts in systems biology currently are directed toward understanding of the control points at which this coordination is achieved. Here we present insights into the function, evolution, and regulation of mitochondrial biogenesis through the study of the protein import machinery in the human fungal pathogen, Candida albicans. Features that distinguish C. albicans from baker's yeast (Saccharomyces cerevisiae) include the stringency of metabolic control at the level of oxygen consumption, the potential for ATP exchange through the porin in the outer membrane, and components and domains in the sorting and assembling machinery complex, a molecular machine that drives the assembly of proteins in the outer mitochondrial membrane. Analysis of targeting sequences and assays of mitochondrial protein import show that components of the electron transport chain are imported by distinct pathways in C. albicans and S. cerevisiae, representing an evolutionary rewiring of mitochondrial import pathways. We suggest that studies using this pathogen as a model system for mitochondrial biogenesis will greatly enhance our knowledge of how mitochondria are made and controlled through the course of the cell-division cycle.}, }
@article {pmid23145081, year = {2012}, author = {Yin, LF and Hu, MJ and Wang, F and Kuang, H and Zhang, Y and Schnabel, G and Li, GQ and Luo, CX}, title = {Frequent gain and loss of introns in fungal cytochrome b genes.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e49096}, pmid = {23145081}, issn = {1932-6203}, mesh = {Ascomycota/genetics ; Cytochromes b/*genetics ; DNA Transposable Elements/genetics ; *Evolution, Molecular ; Fungi/*genetics ; Introns/*genetics ; Phylogeny ; Species Specificity ; }, abstract = {In this study, all available cytochrome b (Cyt b) genes from the GOBASE database were compiled and the evolutionary dynamics of the Cyt b gene introns was assessed. Cyt b gene introns were frequently present in the fungal kingdom and some lower plants, but generally absent or rare in Chromista, Protozoa, and Animalia. Fungal Cyt b introns were found at 35 positions in Cyt b genes and the number of introns varied at individual positions from a single representative to 32 different introns at position 131, showing a wide and patchy distribution. Many homologous introns were present at the same position in distantly related species but absent in closely related species, suggesting that introns of the Cyt b genes were frequently lost. On the other hand, highly similar intron sequences were observed in some distantly related species rather than in closely related species, suggesting that these introns were gained independently, likely through lateral transfers. The intron loss-and-gain events could be mediated by transpositions that might have occurred between nuclear and mitochondria. Southern hybridization analysis confirmed that some introns contained repetitive sequences and might be transposable elements. An intron gain in Botryotinia fuckeliana prevented the development of QoI fungicide resistance, suggesting that intron loss-and-gain events were not necessarily beneficial to their host organisms.}, }
@article {pmid23143325, year = {2013}, author = {Kabashima, Y and Sone, N and Kusumoto, T and Sakamoto, J}, title = {Purification and characterization of malate:quinone oxidoreductase from thermophilic Bacillus sp. PS3.}, journal = {Journal of bioenergetics and biomembranes}, volume = {45}, number = {1-2}, pages = {131-136}, pmid = {23143325}, issn = {1573-6881}, mesh = {Bacillus/*enzymology/genetics ; Bacterial Proteins/*chemistry/genetics/*isolation &amp; purification/metabolism ; Geobacillus/enzymology/genetics ; Kinetics ; Membrane Proteins/*chemistry/genetics/*isolation &amp; purification/metabolism ; Oxidation-Reduction ; Oxidoreductases/*chemistry/genetics/*isolation &amp; purification/metabolism ; Phylogeny ; Vitamin K 2/chemistry ; }, abstract = {Several bacteria possess membrane-bound dehydrogenases other than cytosolic dehydrogenases in their respiratory chains. In many cases, the membrane-bound malate:quinone oxidoreductases (MQOs) are essential for growth. However, these MQOs are absent in mammalian mitochondria, and therefore may be a potential drug target for pathogenic bacteria. To characterize the kinetic properties of MQOs, we purified MQO from Bacillus sp. PS3, which is a gram-positive and thermophilic bacterium, and cloned the gene encoding MQO based on the obtained partial N-terminus sequence. Purified MQOs showed a molecular mass of ~90 kDa, which was estimated using gel filtration, and it consists of two subunits with a molecular mass of ~50 kDa. Phylogenetic analysis showed a high similarity to the MQO of the Geobacillus group rather than the Bacillus group. Additionally, the purified enzyme was thermostable and it retained menaquinol reduction activity at high temperatures. Although it is difficult to conduct experiments using menaquinol because of its instability, we were able to measure the oxidase activity of cytochrome bd-type quinol oxidase by using menaquinol-1 by coupling this molecule with the menaquinol reduction reaction using purified MQOs.}, }
@article {pmid23142697, year = {2013}, author = {Bernt, M and Braband, A and Schierwater, B and Stadler, PF}, title = {Genetic aspects of mitochondrial genome evolution.}, journal = {Molecular phylogenetics and evolution}, volume = {69}, number = {2}, pages = {328-338}, doi = {10.1016/j.ympev.2012.10.020}, pmid = {23142697}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/genetics ; DNA Repair ; *DNA Replication ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Gene Rearrangement ; Genetic Code ; *Genome, Mitochondrial ; Mitochondria/genetics ; Models, Genetic ; Phylogeny ; Sequence Analysis, DNA ; Transcriptome ; }, abstract = {Many years of extensive studies of metazoan mitochondrial genomes have established differences in gene arrangements and genetic codes as valuable phylogenetic markers. Understanding the underlying mechanisms of replication, transcription and the role of the control regions which cause e.g. different gene orders is important to assess the phylogenetic signal of such events. This review summarises and discusses, for the Metazoa, the general aspects of mitochondrial transcription and replication with respect to control regions as well as several proposed models of gene rearrangements. As whole genome sequencing projects accumulate, more and more observations about mitochondrial gene transfer to the nucleus are reported. Thus occurrence and phylogenetic aspects concerning nuclear mitochondrial-like sequences (NUMTS) is another aspect of this review.}, }
@article {pmid23139076, year = {2013}, author = {Boyle, KS and Dewan, AK and Tricas, TC}, title = {Fast drum strokes: novel and convergent features of sonic muscle ultrastructure, innervation, and motor neuron organization in the Pyramid Butterflyfish (Hemitaurichthys polylepis).}, journal = {Journal of morphology}, volume = {274}, number = {4}, pages = {377-394}, doi = {10.1002/jmor.20096}, pmid = {23139076}, issn = {1097-4687}, mesh = {Air Sacs/innervation/ultrastructure ; Animals ; Coral Reefs ; Efferent Pathways/ultrastructure ; Motor Neurons/*ultrastructure ; Muscle Fibers, Skeletal/ultrastructure ; Muscle, Skeletal/*innervation/*ultrastructure ; Perciformes/anatomy &amp; histology/*physiology ; Sarcomeres/ultrastructure ; Spinal Nerves/ultrastructure ; *Vocalization, Animal ; }, abstract = {Sound production that is mediated by intrinsic or extrinsic swim bladder musculature has evolved multiple times in teleost fishes. Sonic muscles must contract rapidly and synchronously to compress the gas-filled bladder with sufficient velocity to produce sound. Muscle modifications that may promote rapid contraction include small fiber diameter, elaborate sarcoplasmic reticulum (SR), triads at the A-I boundary, and cores of sarcoplasm. The diversity of innervation patterns indicate that sonic muscles have independently evolved from different trunk muscle precursors. The analysis of sonic motor pathways in distantly related fishes is required to determine the relationships between sonic muscle evolution and function in acoustic signaling. We examined the ultrastructure of sonic and adjacent hypaxial muscle fibers and the distribution of sonic motor neurons in the coral reef Pyramid Butterflyfish (Chaetodontidae: Hemitaurichthys polylepis) that produces sound by contraction of extrinsic sonic muscles near the anterior swim bladder. Relative to adjacent hypaxial fibers, sonic muscle fibers were sparsely arranged among the endomysium, smaller in cross-section, had longer sarcomeres, a more elaborate SR, wider t-tubules, and more radially arranged myofibrils. Both sonic and non-sonic muscle fibers possessed triads at the Z-line, lacked sarcoplasmic cores, and had mitochondria among the myofibrils and concentrated within the peripheral sarcoplasm. Sonic muscles of this derived eutelost possess features convergent with other distant vocal taxa (other euteleosts and non-euteleosts): small fiber diameter, a well-developed SR, and radial myofibrils. In contrast with some sonic fishes, however, Pyramid Butterflyfish sonic muscles lack sarcoplasmic cores and A-I triads. Retrograde nerve label experiments show that sonic muscle is innervated by central and ventrolateral motor neurons associated with spinal nerves 1-3. This restricted distribution of sonic motor neurons in the spinal cord differs from many euteleosts and likely reflects the embryological origin of sonic muscles from hypaxial trunk precursors rather than occipital somites.}, }
@article {pmid23137057, year = {2013}, author = {Tan, DX and Manchester, LC and Liu, X and Rosales-Corral, SA and Acuna-Castroviejo, D and Reiter, RJ}, title = {Mitochondria and chloroplasts as the original sites of melatonin synthesis: a hypothesis related to melatonin's primary function and evolution in eukaryotes.}, journal = {Journal of pineal research}, volume = {54}, number = {2}, pages = {127-138}, doi = {10.1111/jpi.12026}, pmid = {23137057}, issn = {1600-079X}, mesh = {Animals ; Antioxidants/metabolism ; Chloroplasts/*metabolism ; Cyanobacteria/metabolism ; Free Radicals/metabolism ; Humans ; Melatonin/*metabolism ; Mitochondria/*metabolism ; }, abstract = {Mitochondria and chloroplasts are major sources of free radical generation in living organisms. Because of this, these organelles require strong protection from free radicals and associated oxidative stress. Melatonin is a potent free radical scavenger and antioxidant. It meets the criteria as a mitochondrial and chloroplast antioxidant. Evidence has emerged to show that both mitochondria and chloroplasts may have the capacity to synthesize and metabolize melatonin. The activity of arylalkylamine N-acetyltransferase (AANAT), the reported rate-limiting enzyme in melatonin synthesis, has been identified in mitochondria, and high levels of melatonin have also been found in this organelle. From an evolutionary point of view, the precursor of mitochondria probably is the purple nonsulfur bacterium, particularly, Rhodospirillum rubrum, and chloroplasts are probably the descendents of cyanobacteria. These bacterial species were endosymbionts of host proto-eukaryotes and gradually transformed into cellular organelles, that is, mitochondria and chloroplasts, respectively, thereby giving rise to eukaryotic cells. Of special importance, both purple nonsulfur bacteria (R. rubrum) and cyanobacteria synthesize melatonin. The enzyme activities required for melatonin synthesis have also been detected in these primitive species. It is our hypothesis that mitochondria and chloroplasts are the original sites of melatonin synthesis in the early stage of endosymbiotic organisms; this synthetic capacity was carried into host eukaryotes by the above-mentioned bacteria. Moreover, their melatonin biosynthetic capacities have been preserved during evolution. In most, if not in all cells, mitochondria and chloroplasts may continue to be the primary sites of melatonin generation. Melatonin production in other cellular compartments may have derived from mitochondria and chloroplasts. On the basis of this hypothesis, it is also possible to explain why plants typically have higher melatonin levels than do animals. In plants, both chloroplasts and mitochondria likely synthesize melatonin, while animal cells contain only mitochondria. The high levels of melatonin produced by mitochondria and chloroplasts are used to protect these important cellular organelles against oxidative stress and preserve their physiological functions. The superior beneficial effects of melatonin in both mitochondria and chloroplasts have been frequently reported.}, }
@article {pmid23135986, year = {2013}, author = {Oner, Y and Calvo, JH and Elmaci, C}, title = {Investigation of the genetic diversity among native Turkish sheep breeds using mtDNA polymorphisms.}, journal = {Tropical animal health and production}, volume = {45}, number = {4}, pages = {947-951}, pmid = {23135986}, issn = {1573-7438}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry/genetics ; Female ; Genetic Variation ; Haplotypes/genetics ; Male ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Polymorphism, Single Nucleotide ; Sequence Alignment ; Sequence Analysis, DNA ; Sheep/*genetics ; Turkey ; }, abstract = {A total of 135 unrelated sheep from nine Turkish native sheep breeds (Daglıc, Kivircik, Imroz, Chios, Morkaraman, Ivesi, Hemsin, Karayaka and Akkaraman) were investigated to determinate the maternal genetic diversity using a sequence of a 531-bp segment of the mtDNA control region. Analysis of the mtDNA control region sequence revealed 63 haplotypes and 53 polymorphic sites. Haplotype diversity, nucleotide diversity and the average number of nucleotide differences were estimated to be 0.9496 ± 0.011, 0.01407 ± 0.00060 and 7.456, respectively. The sequence analysis also revealed high level of genetic diversity among the native Turkish breeds. These breeds were grouped into three major maternal haplogroups: A, B and C, with one animal belonging from the Akkaraman breed to the rare haplogroup E. Irregular shape of mismatch distribution of haplogroup C could be an indicator that haplogroup C may represent different haplogroups. Contrarily to previous studies carried out on Turkish native breeds, majority of animals grouped in haplogroup A in the present study. This result and the irregular shape of mismatch curve of haplogroup C indicate that genetic structure of Turkish native sheep breeds could be more complicated than it is thought.}, }
@article {pmid23133520, year = {2012}, author = {Micheletti, S and Parra, E and Routman, EJ}, title = {Adaptive color polymorphism and unusually high local genetic diversity in the side-blotched lizard, Uta stansburiana.}, journal = {PloS one}, volume = {7}, number = {10}, pages = {e47694}, pmid = {23133520}, issn = {1932-6203}, mesh = {Alleles ; Animals ; Base Sequence ; Color ; Cytochromes b/genetics ; DNA, Mitochondrial/metabolism ; Genetic Markers/genetics ; *Genetic Variation ; Genetics, Population ; Lizards/*genetics ; Mitochondria/metabolism ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Polymorphism, Genetic ; Receptor, Melanocortin, Type 1/genetics ; Sequence Analysis, DNA ; }, abstract = {Recently, studies of adaptive color variation have become popular as models for examining the genetics of natural selection. We examined color pattern polymorphism and genetic variation in a population of side-blotched lizards (Uta stansburiana) that is found in habitats with both dark (lava) and light colored (granite) substrates. We conducted a limited experiment for adult phenotypic plasticity in laboratory conditions. We recorded both substrate and lizard color patterns in the field to determine whether lizards tended to match their substrate. Finally we examined genetic variation in a gene (melanocortin 1 receptor) that has been shown to affect lizard color in other species and in a presumably neutral gene (mitochondrial cytochrome b). Populations were sampled in the immediate area of the lava flows as well as from a more distant site to examine the role of population structure. Our captive Uta did not change color to match their background. We show that side-blotched lizards tend to match the substrate on which it was caught in the field and that variation in the melanocortin 1 receptor gene does not correlate well with color pattern in this population. Perhaps the most remarkable result is that this population of side-blotched lizards shows extremely high levels of variation at both genetic markers, in the sense of allele numbers, with relatively low levels of between-allele sequence variation. Genetic variation across this small region was as great or greater than that seen in samples of pelagic fish species collected worldwide. Statistical analysis of genetic variation suggests rapid population expansion may be responsible for the high levels of variation.}, }
@article {pmid23133373, year = {2012}, author = {Heinz, E and Williams, TA and Nakjang, S and Noël, CJ and Swan, DC and Goldberg, AV and Harris, SR and Weinmaier, T and Markert, S and Becher, D and Bernhardt, J and Dagan, T and Hacker, C and Lucocq, JM and Schweder, T and Rattei, T and Hall, N and Hirt, RP and Embley, TM}, title = {The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution.}, journal = {PLoS pathogens}, volume = {8}, number = {10}, pages = {e1002979}, pmid = {23133373}, issn = {1553-7374}, support = {/WT_/Wellcome Trust/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Acquired Immunodeficiency Syndrome/microbiology ; Biological Evolution ; Energy Metabolism/*genetics ; Evolution, Molecular ; *Genome, Fungal ; Humans ; Microsporidia/*genetics/isolation &amp; purification ; Mitochondria ; Phylogeny ; Proteome/*genetics ; Proteomics ; RNA Interference ; RNA, Small Interfering ; Sequence Analysis, DNA ; }, abstract = {The dynamics of reductive genome evolution for eukaryotes living inside other eukaryotic cells are poorly understood compared to well-studied model systems involving obligate intracellular bacteria. Here we present 8.5 Mb of sequence from the genome of the microsporidian Trachipleistophora hominis, isolated from an HIV/AIDS patient, which is an outgroup to the smaller compacted-genome species that primarily inform ideas of evolutionary mode for these enormously successful obligate intracellular parasites. Our data provide detailed information on the gene content, genome architecture and intergenic regions of a larger microsporidian genome, while comparative analyses allowed us to infer genomic features and metabolism of the common ancestor of the species investigated. Gene length reduction and massive loss of metabolic capacity in the common ancestor was accompanied by the evolution of novel microsporidian-specific protein families, whose conservation among microsporidians, against a background of reductive evolution, suggests they may have important functions in their parasitic lifestyle. The ancestor had already lost many metabolic pathways but retained glycolysis and the pentose phosphate pathway to provide cytosolic ATP and reduced coenzymes, and it had a minimal mitochondrion (mitosome) making Fe-S clusters but not ATP. It possessed bacterial-like nucleotide transport proteins as a key innovation for stealing host-generated ATP, the machinery for RNAi, key elements of the early secretory pathway, canonical eukaryotic as well as microsporidian-specific regulatory elements, a diversity of repetitive and transposable elements, and relatively low average gene density. Microsporidian genome evolution thus appears to have proceeded in at least two major steps: an ancestral remodelling of the proteome upon transition to intracellular parasitism that involved reduction but also selective expansion, followed by a secondary compaction of genome architecture in some, but not all, lineages.}, }
@article {pmid23129619, year = {2012}, author = {Sung, W and Tucker, AE and Doak, TG and Choi, E and Thomas, WK and Lynch, M}, title = {Extraordinary genome stability in the ciliate Paramecium tetraurelia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {47}, pages = {19339-19344}, pmid = {23129619}, issn = {1091-6490}, support = {R01 GM036827/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Substitution/genetics ; DNA-Directed DNA Polymerase/metabolism ; Genome, Protozoan/*genetics ; Genomic Instability/*genetics ; Mitochondria/genetics ; Mutation Rate ; Paramecium tetraurelia/enzymology/*genetics ; Reproduction/genetics ; }, abstract = {Mutation plays a central role in all evolutionary processes and is also the basis of genetic disorders. Established base-substitution mutation rates in eukaryotes range between ∼5 × 10(-10) and 5 × 10(-8) per site per generation, but here we report a genome-wide estimate for Paramecium tetraurelia that is more than an order of magnitude lower than any previous eukaryotic estimate. Nevertheless, when the mutation rate per cell division is extrapolated to the length of the sexual cycle for this protist, the measure obtained is comparable to that for multicellular species with similar genome sizes. Because Paramecium has a transcriptionally silent germ-line nucleus, these results are consistent with the hypothesis that natural selection operates on the cumulative germ-line replication fidelity per episode of somatic gene expression, with the germ-line mutation rate per cell division evolving downward to the lower barrier imposed by random genetic drift. We observe ciliate-specific modifications of widely conserved amino acid sites in DNA polymerases as one potential explanation for unusually high levels of replication fidelity.}, }
@article {pmid23109865, year = {2012}, author = {Mipam, TD and Wen, Y and Fu, C and Li, S and Zhao, H and Ai, Y and Li, L and Zhang, L and Zou, D}, title = {Maternal phylogeny of a newly-found yak population in china.}, journal = {International journal of molecular sciences}, volume = {13}, number = {9}, pages = {11455-11470}, pmid = {23109865}, issn = {1422-0067}, mesh = {Animals ; Base Sequence ; Cattle/anatomy &amp; histology/*genetics ; China ; DNA, Mitochondrial/*genetics ; Female ; Haplotypes/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length/*genetics ; Sequence Analysis, DNA/*veterinary ; }, abstract = {The Jinchuan yak is a new yak population identified in Sichuan, China. This population has a special anatomical characteristic: an additional pair of ribs compared with other yak breeds. The genetic structure of this population is unknown. In the present study, we investigated the maternal phylogeny of this special yak population using the mitochondrial DNA variation. A total of 23 Jinchuan yaks were sequenced for a 823-bp fragment of D-loop control region and three individuals were sequenced for the whole mtDNA genome with a length of 16,371-bp. To compare with the data from other yaks, we extracted sequence data from Genebank, including D-loop of 398 yaks (from 12 breeds) and 55 wild yaks, and whole mitochondrial genomes of 53 yaks (from 12 breeds) and 21 wild yaks. A total of 127 haplotypes were defined, based on the D-loop data. Thirteen haplotypes were defined from 23 mtDNA D-loop sequences of Jinchuan yaks, six of which were shared only by Jinchuan, and one was shared by Jinchuan and wild yaks. The Jinquan yaks were found to carry clades A and B from lineage I and clade C of lineage II, respectively. It was also suggested that the Jinchuan population has no distinct different phylogenetic relationship in maternal inheritance with other breeds of yak. The highly haplotype diversity of the Pali breed, Jinchuan population, Maiwa breed and Jiulong breed suggested that the yak was first domesticated from wild yaks in the middle Himalayan region and the northern Hengduan Mountains. The special anatomic characteristic that we found in the Jinchuan population needs further studies based on nuclear data.}, }
@article {pmid23109542, year = {2012}, author = {Zerbes, RM and van der Klei, IJ and Veenhuis, M and Pfanner, N and van der Laan, M and Bohnert, M}, title = {Mitofilin complexes: conserved organizers of mitochondrial membrane architecture.}, journal = {Biological chemistry}, volume = {393}, number = {11}, pages = {1247-1261}, doi = {10.1515/hsz-2012-0239}, pmid = {23109542}, issn = {1437-4315}, mesh = {Animals ; *Conserved Sequence ; Humans ; Mitochondrial Membranes/chemistry/*metabolism ; Mitochondrial Proteins/*chemistry/*metabolism ; Models, Biological ; Muscle Proteins/chemistry/metabolism ; }, abstract = {Mitofilin proteins are crucial organizers of mitochondrial architecture. They are located in the inner mitochondrial membrane and interact with several protein complexes of the outer membrane, thereby generating contact sites between the two membrane systems of mitochondria. Within the inner membrane, mitofilins are part of hetero-oligomeric protein complexes that have been termed the mitochondrial inner membrane organizing system (MINOS). MINOS integrity is required for the maintenance of the characteristic morphology of the inner mitochondrial membrane, with an inner boundary region closely apposed to the outer membrane and cristae membranes, which form large tubular invaginations that protrude into the mitochondrial matrix and harbor the enzyme complexes of the oxidative phosphorylation machinery. MINOS deficiency comes along with a loss of crista junction structures and the detachment of cristae from the inner boundary membrane. MINOS has been conserved in evolution from unicellular eukaryotes to humans, where alterations of MINOS subunits are associated with multiple pathological conditions.}, }
@article {pmid23106560, year = {2012}, author = {Yu, JN and Han, SH and Kim, BH and Kryukov, AP and Kim, S and Lee, BY and Kwak, M}, title = {Insights into Korean red fox (Vulpes vulpes) based on mitochondrial cytochrome b sequence variation in East Asia.}, journal = {Zoological science}, volume = {29}, number = {11}, pages = {753-760}, doi = {10.2108/zsj.29.753}, pmid = {23106560}, issn = {0289-0003}, mesh = {Animals ; Base Sequence ; Cytochromes b/genetics/*metabolism ; Demography ; Asia, Eastern ; Foxes/*genetics/physiology ; Gene Expression Regulation, Enzymologic ; Genetic Variation ; Mitochondria/*enzymology ; Phylogeny ; Republic of Korea ; }, abstract = {The red fox (Vulpes vulpes) is the most widely distributed terrestrial carnivore in the world, occurring throughout most of North America, Europe, Asia, and North Africa. In South Korea, however, this species has been drastically reduced due to habitat loss and poaching. Consequently, it is classified as an endangered species in Korea. As a first step of a planned red fox restoration project, preserved red fox museum specimens were used to determine the genetic status of red foxes that had previously inhabited South Korea against red foxes from neighboring countries. Total eighty three mtDNA cytochrome b sequences, including 22 newly obtained East Asian red fox sequences and worldwide red fox sequences from NCBI, were clustered into three clades (i.e., I, II, and III) based on haplotype network and neighbor-joining trees. The mean genetic distance between clades was 2.0%. Clade III contained South Korean and other East Asian samples in addition to Eurasian and North Pacific individuals. In clade III, South Korean individuals were separated into two lineages of Eurasian and North Pacific groups, showing unclear phylogeographic structuring and admixture. This suggests that South Korean red fox populations may have been composed of individuals from these two different genetic lineages.}, }
@article {pmid23102266, year = {2012}, author = {Sena, LA and Chandel, NS}, title = {Physiological roles of mitochondrial reactive oxygen species.}, journal = {Molecular cell}, volume = {48}, number = {2}, pages = {158-167}, pmid = {23102266}, issn = {1097-4164}, support = {F30 ES019815/ES/NIEHS NIH HHS/United States ; P01 HL071643/HL/NHLBI NIH HHS/United States ; R01 CA123067/CA/NCI NIH HHS/United States ; T32-HL76139/HL/NHLBI NIH HHS/United States ; R01CA123067/CA/NCI NIH HHS/United States ; T32 HL076139/HL/NHLBI NIH HHS/United States ; F30ES019815/ES/NIEHS NIH HHS/United States ; 5P01HL071643/HL/NHLBI NIH HHS/United States ; }, mesh = {Aging/metabolism/physiology ; Antioxidants/*metabolism ; Autophagy/physiology ; Cell Differentiation/physiology ; Humans ; Immunity/physiology ; Mitochondria/*metabolism/physiology ; Oxidative Stress/*physiology ; Reactive Oxygen Species/*metabolism ; }, abstract = {Historically, mitochondrial reactive oxygen species (mROS) were thought to exclusively cause cellular damage and lack a physiological function. Accumulation of ROS and oxidative damage have been linked to multiple pathologies, including neurodegenerative diseases, diabetes, cancer, and premature aging. Thus, mROS were originally envisioned as a necessary evil of oxidative metabolism, a product of an imperfect system. Yet few biological systems possess such flagrant imperfections, thanks to the persistent optimization of evolution, and it appears that oxidative metabolism is no different. More and more evidence suggests that mROS are critical for healthy cell function. In this Review, we discuss this evidence following some background on the generation and regulation of mROS.}, }
@article {pmid23097428, year = {2012}, author = {Chujo, T and Suzuki, T}, title = {Trmt61B is a methyltransferase responsible for 1-methyladenosine at position 58 of human mitochondrial tRNAs.}, journal = {RNA (New York, N.Y.)}, volume = {18}, number = {12}, pages = {2269-2276}, pmid = {23097428}, issn = {1469-9001}, mesh = {Adenosine/*analogs &amp; derivatives/metabolism ; Amino Acid Sequence ; Bacterial Proteins/genetics ; HeLa Cells ; Humans ; Mitochondria/metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Protein Structure, Quaternary ; RNA/chemistry/genetics/*metabolism ; RNA, Mitochondrial ; RNA, Transfer/chemistry/genetics/*metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Homology, Amino Acid ; tRNA Methyltransferases/chemistry/genetics/*metabolism ; }, abstract = {In human mitochondria, 1-methyladenosine (m[1]A) occurs at position 58 of tRNA(Leu(UUR)). In addition, partial m[1]A58 modifications have been found in human mitochondrial tRNA(Lys) and tRNA(Ser(UCN)). We identified human Trmt61B, which encodes a mitochondria-specific tRNA methyltransferase responsible for m[1]A58 in these three tRNAs. Trmt61B is dominantly localized to the mitochondria. m[1]A58 formation in human mitochondrial tRNA(Leu(UUR)) could be reconstituted in vitro using recombinant Trmt61B in the presence of Ado-Met as a methyl donor. Unlike the cytoplasmic tRNA m[1]A58 methyltransferase that consists of an α2β2 heterotetramer formed by Trmt61A and Trmt6, Trmt61B formed a homo-oligomer (presumably a homotetramer) that resembled the bacterial homotetrameric m[1]A58 methyltransferase. The bacterial origin of Trmt61B is supported by the results of the phylogenetic analysis.}, }
@article {pmid23096487, year = {2013}, author = {Regalado, A and Pierri, CL and Bitetto, M and Laera, VL and Pimentel, C and Francisco, R and Passarinho, J and Chaves, MM and Agrimi, G}, title = {Characterization of mitochondrial dicarboxylate/tricarboxylate transporters from grape berries.}, journal = {Planta}, volume = {237}, number = {3}, pages = {693-703}, pmid = {23096487}, issn = {1432-2048}, mesh = {Amino Acid Sequence ; Carrier Proteins/chemistry/*metabolism ; Cloning, Molecular ; Dicarboxylic Acid Transporters/chemistry/*metabolism ; Escherichia coli/metabolism ; Fruit/enzymology/genetics/growth &amp; development/*metabolism ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Kinetics ; Malates/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Recombinant Proteins/metabolism ; Sequence Alignment ; Substrate Specificity ; Vitis/enzymology/genetics/growth &amp; development/*metabolism ; }, abstract = {Grape berries (Vitis vinifera L fruit) exhibit a double-sigmoid pattern of development that results from two successive periods of vacuolar swelling during which the nature of accumulated solutes changes significantly. Throughout the first period, called green or herbaceous stage, berries accumulate high levels of organic acids, mainly malate and tartrate. At the cellular level fruit acidity comprises both metabolism and vacuolar storage. Malic acid compartmentation is critical for optimal functioning of cytosolic enzymes. Therefore, the identification and characterization of the carriers involved in malate transport across sub-cellular compartments is of great importance. The decrease in acid content during grape berry ripening has been mainly associated to mitochondrial malate oxidation. However, no Vitis vinifera mitochondrial carrier involved in malate transport has been reported to date. Here we describe the identification of three V. vinifera mitochondrial dicarboxylate/tricarboxylate carriers (VvDTC1-3) putatively involved in mitochondrial malate, citrate and other di/tricarboxylates transport. The three VvDTCs are very similar, sharing a percentage of identical residues of at least 83 %. Expression analysis of the encoding VvDTC genes in grape berries shows that they are differentially regulated exhibiting a developmental pattern of expression. The simultaneous high expression of both VvDTC2 and VvDTC3 in grape berry mesocarp close to the onset of ripening suggests that these carriers might be involved in the transport of malate into mitochondria.}, }
@article {pmid23093202, year = {2012}, author = {Jia, M and Meng, F and Smerin, SE and Xing, G and Zhang, L and Su, DM and Benedek, D and Ursano, R and Su, YA and Li, H}, title = {Biomarkers in an animal model for revealing neural, hematologic, and behavioral correlates of PTSD.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {68}, pages = {}, pmid = {23093202}, issn = {1940-087X}, mesh = {Animals ; Behavior, Animal ; Biomarkers/blood/metabolism ; Brain/metabolism/*physiopathology/surgery ; *Disease Models, Animal ; Dissection ; Enzyme-Linked Immunosorbent Assay ; Gene Expression Profiling ; Male ; Mitochondria/genetics ; Rats ; Rats, Sprague-Dawley ; Reflex, Startle ; Stress Disorders, Post-Traumatic/genetics/metabolism/pathology/*physiopathology ; }, abstract = {Identification of biomarkers representing the evolution of the pathophysiology of Post Traumatic Stress Disorder (PTSD) is vitally important, not only for objective diagnosis but also for the evaluation of therapeutic efficacy and resilience to trauma. Ongoing research is directed at identifying molecular biomarkers for PTSD, including traumatic stress induced proteins, transcriptomes, genomic variances and genetic modulators, using biologic samples from subjects' blood, saliva, urine, and postmortem brain tissues. However, the correlation of these biomarker molecules in peripheral or postmortem samples to altered brain functions associated with psychiatric symptoms in PTSD remains unresolved. Here, we present an animal model of PTSD in which both peripheral blood and central brain biomarkers, as well as behavioral phenotype, can be collected and measured, thus providing the needed correlation of the central biomarkers of PTSD, which are mechanistic and pathognomonic but cannot be collected from people, with the peripheral biomarkers and behavioral phenotypes, which can. Our animal model of PTSD employs restraint and tail shocks repeated for three continuous days - the inescapable tail-shock model (ITS) in rats. This ITS model mimics the pathophysiology of PTSD (17, 7, 4, 10). We and others have verified that the ITS model induces behavioral and neurobiological alterations similar to those found in PTSD subjects (17, 7, 10, 9). Specifically, these stressed rats exhibit (1) a delayed and exaggerated startle response appearing several days after stressor cessation, which given the compressed time scale of the rat's life compared to a humans, corresponds to the one to three months delay of symptoms in PTSD patients (DSM-IV-TR PTSD Criterian D/E (13)), (2) enhanced plasma corticosterone (CORT) for several days, indicating compromise of the hypothalamopituitary axis (HPA), and (3) retarded body weight gain after stressor cessation, indicating dysfunction of metabolic regulation. The experimental paradigms employed for this model are: (1) a learned helplessness paradigm in the rat assayed by measurement of acoustic startle response (ASR) and a charting of body mass; (2) microdissection of the rat brain into regions and nuclei; (3) enzyme-linked immunosorbent assay (ELISA) for blood levels of CORT; (4) a gene expression microarray plus related bioinformatics tools (18). This microarray, dubbed rMNChip, focuses on mitochondrial and mitochondria-related nuclear genes in the rat so as to specifically address the neuronal bioenergetics hypothesized to be involved in PTSD.}, }
@article {pmid23091644, year = {2012}, author = {Biacchesi, S and Mérour, E and Lamoureux, A and Bernard, J and Brémont, M}, title = {Both STING and MAVS fish orthologs contribute to the induction of interferon mediated by RIG-I.}, journal = {PloS one}, volume = {7}, number = {10}, pages = {e47737}, pmid = {23091644}, issn = {1932-6203}, mesh = {Adaptor Proteins, Signal Transducing/chemistry/genetics/*metabolism ; Amino Acid Sequence ; Animals ; Cell Line ; DEAD-box RNA Helicases/*metabolism ; DNA Viruses/immunology ; Endoplasmic Reticulum/metabolism ; Fish Diseases/genetics/immunology/virology ; Fishes/genetics/immunology/*metabolism ; Gene Expression ; Gene Expression Regulation ; Interferons/*biosynthesis ; Membrane Proteins/chemistry/genetics/*metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Mutation ; Phylogeny ; Protein Binding ; Protein Transport ; RNA Viruses/immunology ; Sequence Alignment ; Virus Diseases/genetics/immunology/virology ; }, abstract = {Viral infections are detected in most cases by the host innate immune system through pattern-recognition receptors (PRR), the sensors for pathogen-associated molecular patterns (PAMPs), which induce the production of cytokines, such as type I interferons (IFN). Recent identification in mammalian and teleost fish of cytoplasmic viral RNA sensors, RIG-I-like receptors (RLRs), and their mitochondrial adaptor: the mitochondrial antiviral signaling (MAVS) protein, also called IPS-1, highlight their important role in the induction of IFN at the early stage of a virus infection. More recently, an endoplasmic reticulum (ER) adaptor: the stimulator of interferon genes (STING) protein, also called MITA, ERIS and MPYS, has been shown to play a pivotal role in response to both non-self-cytosolic RNA and dsDNA. In this study, we cloned STING cDNAs from zebrafish and showed that it was an ortholog to mammalian STING. We demonstrated that overexpression of this ER protein in fish cells led to a constitutive induction of IFN and interferon-stimulated genes (ISGs). STING-overexpressing cells were almost fully protected against RNA virus infection with a strong inhibition of both DNA and RNA virus replication. In addition, we found that together with MAVS, STING was an important player in the RIG-I IFN-inducing pathway. This report provides the demonstration that teleost fish possess a functional RLR pathway in which MAVS and STING are downstream signaling molecules of RIG-I. The Sequences presented in this article have been submitted to GenBank under accession numbers: Zebrafish STING (HE856619); EPC STING (HE856620); EPC IRF3 (HE856621); EPC IFN promoter (HE856618).}, }
@article {pmid23091033, year = {2012}, author = {Beinart, RA and Sanders, JG and Faure, B and Sylva, SP and Lee, RW and Becker, EL and Gartman, A and Luther, GW and Seewald, JS and Fisher, CR and Girguis, PR}, title = {Evidence for the role of endosymbionts in regional-scale habitat partitioning by hydrothermal vent symbioses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {47}, pages = {E3241-50}, pmid = {23091033}, issn = {1091-6490}, mesh = {Animals ; Bayes Theorem ; Carbon Isotopes ; *Ecosystem ; Electrochemical Techniques ; Electron Transport Complex IV/genetics ; Epsilonproteobacteria/*genetics ; Gammaproteobacteria/*genetics ; Gastropoda/*genetics/*microbiology ; Geography ; Haplotypes/genetics ; Hydrothermal Vents/*microbiology ; Isotope Labeling ; Mitochondria/genetics ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; Protein Subunits/genetics ; RNA, Ribosomal, 16S/genetics ; Symbiosis/*genetics ; Temperature ; }, abstract = {Deep-sea hydrothermal vents are populated by dense communities of animals that form symbiotic associations with chemolithoautotrophic bacteria. To date, our understanding of which factors govern the distribution of host/symbiont associations (or holobionts) in nature is limited, although host physiology often is invoked. In general, the role that symbionts play in habitat utilization by vent holobionts has not been thoroughly addressed. Here we present evidence for symbiont-influenced, regional-scale niche partitioning among symbiotic gastropods (genus Alviniconcha) in the Lau Basin. We extensively surveyed Alviniconcha holobionts from four vent fields using quantitative molecular approaches, coupled to characterization of high-temperature and diffuse vent-fluid composition using gastight samplers and in situ electrochemical analyses, respectively. Phylogenetic analyses exposed cryptic host and symbiont diversity, revealing three distinct host types and three different symbiont phylotypes (one ε-proteobacteria and two γ-proteobacteria) that formed specific associations with one another. Strikingly, we observed that holobionts with ε-proteobacterial symbionts were dominant at the northern fields, whereas holobionts with γ-proteobacterial symbionts were dominant in the southern fields. This pattern of distribution corresponds to differences in the vent geochemistry that result from deep subsurface geological and geothermal processes. We posit that the symbionts, likely through differences in chemolithoautotrophic metabolism, influence niche utilization among these holobionts. The data presented here represent evidence linking symbiont type to habitat partitioning among the chemosynthetic symbioses at hydrothermal vents and illustrate the coupling between subsurface geothermal processes and niche availability.}, }
@article {pmid23090476, year = {2012}, author = {Wanrooij, S and Miralles Fusté, J and Stewart, JB and Wanrooij, PH and Samuelsson, T and Larsson, NG and Gustafsson, CM and Falkenberg, M}, title = {In vivo mutagenesis reveals that OriL is essential for mitochondrial DNA replication.}, journal = {EMBO reports}, volume = {13}, number = {12}, pages = {1130-1137}, pmid = {23090476}, issn = {1469-3178}, mesh = {Animals ; Conserved Sequence ; DNA/genetics ; DNA Helicases/genetics/metabolism ; DNA Replication/*genetics ; *DNA, Mitochondrial/biosynthesis/genetics ; Humans ; Mice ; Mitochondria/genetics ; Mitochondrial Proteins/genetics/metabolism ; Models, Genetic ; *Mutagenesis ; Phylogeny ; Replication Origin/*genetics ; Sequence Analysis, DNA ; }, abstract = {The mechanisms of mitochondrial DNA replication have been hotly debated for a decade. The strand-displacement model states that lagging-strand DNA synthesis is initiated from the origin of light-strand DNA replication (OriL), whereas the strand-coupled model implies that OriL is dispensable. Mammalian mitochondria cannot be transfected and the requirements of OriL in vivo have therefore not been addressed. We here use in vivo saturation mutagenesis to demonstrate that OriL is essential for mtDNA maintenance in the mouse. Biochemical and bioinformatic analyses show that OriL is functionally conserved in vertebrates. Our findings strongly support the strand-displacement model for mtDNA replication.}, }
@article {pmid23088322, year = {2013}, author = {Kehrein, K and Bonnefoy, N and Ott, M}, title = {Mitochondrial protein synthesis: efficiency and accuracy.}, journal = {Antioxidants &amp; redox signaling}, volume = {19}, number = {16}, pages = {1928-1939}, doi = {10.1089/ars.2012.4896}, pmid = {23088322}, issn = {1557-7716}, mesh = {Animals ; Humans ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/*biosynthesis ; Oxidative Phosphorylation ; }, abstract = {SIGNIFICANCE: The mitochondrial genetic system is responsible for the production of a few core-subunits of the respiratory chain and ATP synthase, the membrane protein complexes driving oxidative phosphorylation (OXPHOS). Efficiency and accuracy of mitochondrial protein synthesis determines how efficiently new OXPHOS complexes can be made.<br><br>RECENT ADVANCES: The system responsible for expression of the mitochondrial-encoded subunits developed from that of the bacterial ancestor of mitochondria. Importantly, many aspects of genome organization, transcription, and translation have diverged during evolution. Recent research has provided new insights into the architecture, regulation, and organelle-specific features of mitochondrial translation. Mitochondrial ribosomes contain a number of proteins absent from prokaryotic ribosomes, implying that in mitochondria, ribosomes were tailored to fit the requirements of the organelle. In addition, mitochondrial gene expression is regulated post-transcriptionally by a number of mRNA-specific translational activators. At least in yeast, these factors can regulate translation in respect to OXPHOS complex assembly to adjust the level of newly synthesized proteins to amounts that can be successfully assembled into respiratory chain complexes.<br><br>CRITICAL ISSUES: Mitochondrial gene expression is determining aging in eukaryotes, and a number of recent reports indicate that efficiency of translation directly influences this process.<br><br>FUTURE DIRECTIONS: Here we will summarize recent advances in our understanding of mitochondrial protein synthesis by comparing the knowledge acquired in the systems most commonly used to study mitochondrial biogenesis. However, many steps have not been understood mechanistically. Innovative biochemical and genetic approaches have to be elaborated to shed light on these important processes.}, }
@article {pmid23087700, year = {2012}, author = {Kleine, T}, title = {Arabidopsis thaliana mTERF proteins: evolution and functional classification.}, journal = {Frontiers in plant science}, volume = {3}, number = {}, pages = {233}, pmid = {23087700}, issn = {1664-462X}, abstract = {Organellar gene expression (OGE) is crucial for plant development, photosynthesis, and respiration, but our understanding of the mechanisms that control it is still relatively poor. Thus, OGE requires various nucleus-encoded proteins that promote transcription, splicing, trimming, and editing of organellar RNAs, and regulate translation. In metazoans, proteins of the mitochondrial Transcription tERmination Factor (mTERF) family interact with the mitochondrial chromosome and regulate transcriptional initiation and termination. Sequencing of the Arabidopsis thaliana genome led to the identification of a diversified MTERF gene family but, in contrast to mammalian mTERFs, knowledge about the function of these proteins in photosynthetic organisms is scarce. In this hypothesis article, I show that tandem duplications and one block duplication contributed to the large number of MTERF genes in A. thaliana, and propose that the expansion of the family is related to the evolution of land plants. The MTERF genes-especially the duplicated genes-display a number of distinct mRNA accumulation patterns, suggesting functional diversification of mTERF proteins to increase adaptability to environmental changes. Indeed, hypothetical functions for the different mTERF proteins can be predicted using co-expression analysis and gene ontology (GO) annotations. On this basis, mTERF proteins can be sorted into five groups. Members of the "chloroplast" and "chloroplast-associated" clusters are principally involved in chloroplast gene expression, embryogenesis, and protein catabolism, while representatives of the "mitochondrial" cluster seem to participate in DNA and RNA metabolism in that organelle. Moreover, members of the "mitochondrion-associated" cluster and the "low expression" group may act in the nucleus and/or the cytosol. As proteins involved in OGE and presumably nuclear gene expression (NGE), mTERFs are ideal candidates for the coordination of the expression of organelle and nuclear genomes.}, }
@article {pmid23085481, year = {2013}, author = {Butterfield, ER and Howe, CJ and Nisbet, RE}, title = {An analysis of dinoflagellate metabolism using EST data.}, journal = {Protist}, volume = {164}, number = {2}, pages = {218-236}, doi = {10.1016/j.protis.2012.09.001}, pmid = {23085481}, issn = {1618-0941}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Dinoflagellida/*genetics/*metabolism ; Evolution, Molecular ; *Expressed Sequence Tags ; Metabolic Networks and Pathways/*genetics ; Models, Biological ; }, abstract = {The dinoflagellates are an important group of eukaryotic, single celled algae. They are the sister group of the Apicomplexa, a group of intracellular parasites and photosynthetic algae including the malaria parasite Plasmodium. Many apicomplexan mitochondria have a number of unusual features, including the lack of a pyruvate dehydrogenase and the existence of a branched TCA cycle. Here, we analyse dinoflagellate EST (expressed sequence tag) data to determine whether these features are apicomplexan-specific, or if they are more widespread. We show that dinoflagellates have replaced a key subunit (E1) of pyruvate dehydrogenase with a subunit of bacterial origin and that transcripts encoding many of the proteins that are essential in a conventional ATP synthase/Complex V are absent, as is the case in Apicomplexa. There is a pathway for synthesis of starch or glycogen as a storage carbohydrate. Transcripts encoding isocitrate lyase and malate synthase are present, consistent with ultrastructural reports of a glyoxysome. Finally, evidence for a conventional haem biosynthesis pathway is found, in contrast to the Apicomplexa, Chromera and early branching dinoflagellates (Perkinsus, Oxyrrhis).}, }
@article {pmid23072391, year = {2012}, author = {Hsu, CY and Huang, PL and Chen, CM and Mao, CT and Chaw, SM}, title = {Tangy scent in Toona sinensis (Meliaceae) leaflets: isolation, functional characterization, and regulation of TsTPS1 and TsTPS2, two key terpene synthase genes in the biosynthesis of the scent compound.}, journal = {Current pharmaceutical biotechnology}, volume = {13}, number = {15}, pages = {2721-2732}, doi = {10.2174/138920112804724864}, pmid = {23072391}, issn = {1873-4316}, mesh = {Alkyl and Aryl Transferases/*genetics ; Amino Acid Sequence ; Genes, Plant/*genetics ; Meliaceae/*genetics/metabolism ; Molecular Sequence Data ; Odorants ; Phylogeny ; Plant Leaves/metabolism ; Plant Roots/metabolism ; Terpenes/isolation &amp; purification ; }, abstract = {Toona sinensis (Chinese Mahogany; Meliaceae), a subtropical deciduous tree, has a tangy scent resembling a mix of shallots and garlic. T. sinensis has long been known for its medicinal efficacy for treating enteritis, dysentery, itch and some cancers. However, its volatile components and their biosynthesis remain unexamined. In this study, we identified the spectrum of volatile compounds, isolated and functionally characterized two terpene synthase genes, Tstps1 and Tstps2, responsible for terpenoid synthesis in T. sinensis leaflets. TsTPS1 and TsTPS2 afford multiple products upon incubation with geranyl and farnesyl diphosphate respectively and mainly regulate the biosynthesis of (+) limonene and β- elemene in vitro, respectively. Headspace analyses show that 98% of leaflet volatiles were sesquiterpenoids and the developing leaflets released a greater diversity and quantity of volatiles than the mature leaflets did, and that β-elemene was the dominant component in both of them. These data suggested that tangy scent of T. sinensis consists of a combination of terpenoids and that Tstps2 was the major gene involved in the terpenoid biosynthesis in T. sinensis. In situ hybridization revealed that glandular cells of the leaf rachises accumulated abundant Tstps1 mRNA transcripts. Our GFP-based assay further unprecedentedly demonstrated that the transit-peptide of TsTPS1 targets specifically to the mitochondria.}, }
@article {pmid23071102, year = {2013}, author = {Nabholz, B and Ellegren, H and Wolf, JB}, title = {High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes.}, journal = {Molecular biology and evolution}, volume = {30}, number = {2}, pages = {272-284}, doi = {10.1093/molbev/mss238}, pmid = {23071102}, issn = {1537-1719}, mesh = {Animals ; Biological Evolution ; Birds ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; *Gene Expression ; Insecta ; Mammals ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/*genetics/metabolism ; Oxidative Phosphorylation ; Selection, Genetic ; }, abstract = {The nearly neutral theory of molecular evolution has been widely accepted as the guiding principle for understanding how selection affects gene sequence evolution. One of its central predictions is that the rate at which proteins evolve should negatively scale with effective population size (N(e)). In contrast to the expectation of reduced selective constraint in the mitochondrial genome following from its lower N(e), we observe what can be interpreted as the opposite: for a taxonomically diverse set of organisms (birds, mammals, insects, and nematodes), mitochondrially encoded protein-coding genes from the oxidative phosphorylation pathway (mtOXPHOS; n = 12-13) show markedly stronger signatures of purifying selection (illustrated by low d(N)/d(S)) than their nuclear counterparts interacting in the same pathway (nuOXPHOS; n: ∼75). To understand these unexpected evolutionary dynamics, we consider a number of structural and functional parameters including gene expression, hydrophobicity, transmembrane position, gene ontology, GC content, substitution rate, proportion of amino acids in transmembrane helices, and protein-protein interaction. Across all taxa, unexpectedly large differences in gene expression levels (RNA-seq) between nuclear and mitochondrially encoded genes, and to a lower extent hydrophobicity, explained most of the variation in d(N)/d(S). Similarly, differences in d(N)/d(S) between functional OXPHOS protein complexes could largely be explained by gene expression differences. Overall, by including gene expression and other functional parameters, the unexpected mitochondrial evolutionary dynamics can be understood. Our results not only reaffirm the link between gene expression and protein evolution but also open new questions about the functional role of expression level variation between mitochondrial genes.}, }
@article {pmid23069387, year = {2013}, author = {Jeelani, G and Husain, A and Sato, D and Soga, T and Suematsu, M and Nozaki, T}, title = {Biochemical and functional characterization of novel NADH kinase in the enteric protozoan parasite Entamoeba histolytica.}, journal = {Biochimie}, volume = {95}, number = {2}, pages = {309-319}, doi = {10.1016/j.biochi.2012.09.034}, pmid = {23069387}, issn = {1638-6183}, mesh = {Adenosine Triphosphate/chemistry ; Amino Acid Sequence ; Cations, Divalent ; Conserved Sequence ; Entamoeba histolytica/drug effects/*enzymology/genetics ; Gene Expression/drug effects ; Hydrogen Peroxide/pharmacology ; Kinetics ; Magnesium/chemistry ; Molecular Sequence Data ; NAD/*metabolism ; NADP/*metabolism ; Phosphorylation ; Phosphotransferases (Alcohol Group Acceptor)/genetics/*metabolism ; Phylogeny ; Polyphosphates/chemistry ; Protozoan Proteins/genetics/*metabolism ; Reactive Oxygen Species ; Sequence Alignment ; Substrate Specificity ; }, abstract = {NAD(H) kinase catalyzes the phosphorylation of NAD(H) to form NADP(H) using ATP or inorganic polyphosphate as a phosphoryl donor. While the enzyme is conserved throughout prokaryotes and eukaryotes, remarkable differences in kinetic parameters including substrate preference, cation dependence, and physiological roles exist among the organisms. In the present study, we biochemically characterized NAD(H) kinase from the anaerobic/microaerophilic fermentative protozoan parasite Entamoeba histolytica, which lacks the conventional mitochondria capable of oxidative phosphorylation, leading to ATP. The kinetic properties of E. histolytica NAD(H) kinase recombinantly produced in Escherichia coli showed remarkable differences from those in bacteria and higher eukaryotes. Entamoeba NAD(H) kinase preferred NADH to NAD+ as the phosphoryl acceptor, utilized nucleoside triphosphates including ATP, GTP and deoxyATP, but not nucleoside di-, mono-phosphates, or inorganic polyphosphates, as the phosphoryl donor. To further understand the physiological roles in E. histolytica, we generated a stable transformant overexpressing NAD(H) kinase. Overexpression of NAD(H) kinase resulted in a 1.6-2 fold increase in the NADPH and NADP+ concentrations, a 40% reduction of the intracellular concentration of reactive oxygen species, and also led to increased tolerance toward hydrogen peroxide. These data, together with the essentially of NAD(H) kinase gene, underscore its significance as an NADP(H)-producing enzyme in this organism, and should help in designing of drugs targeting this enzyme.}, }
@article {pmid23064754, year = {2012}, author = {Krnáčová, K and Vesteg, M and Hampl, V and Vlček, &#x10c; and Horváth, A}, title = {Euglena gracilis and Trypanosomatids possess common patterns in predicted mitochondrial targeting presequences.}, journal = {Journal of molecular evolution}, volume = {75}, number = {3-4}, pages = {119-129}, pmid = {23064754}, issn = {1432-1432}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Computational Biology ; Euglena gracilis/chemistry/*genetics ; Evolution, Molecular ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/*chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/*chemistry/genetics ; Trypanosomatina/chemistry/*genetics ; }, abstract = {Euglena gracilis possessing chloroplasts of secondary green algal origin and parasitic trypanosomatids Trypanosoma brucei, Trypanosoma cruzi and Leishmania major belong to the protist phylum Euglenozoa. Euglenozoa might be among the earliest eukaryotic branches bearing ancestral traits reminiscent of the last eukaryotic common ancestor (LECA) or missing features present in other eukaryotes. LECA most likely possessed mitochondria of endosymbiotic α-proteobacterial origin. In this study, we searched for the presence of homologs of mitochondria-targeted proteins from other organisms in the currently available EST dataset of E. gracilis. The common motifs in predicted N-terminal presequences and corresponding homologs from T. brucei, T. cruzi and L. major (if found) were analyzed. Other trypanosomatid mitochondrial protein precursor (e.g., those involved in RNA editing) were also included in the analysis. Mitochondrial presequences of E. gracilis and these trypanosomatids seem to be highly variable in sequence length (5-118 aa), but apparently share statistically significant similarities. In most cases, the common (M/L)RR motif is present at the N-terminus and it is probably responsible for recognition via import apparatus of mitochondrial outer membrane. Interestingly, this motif is present inside the predicted presequence region in some cases. In most presequences, this motif is followed by a hydrophobic region rich in alanine, leucine, and valine. In conclusion, either RR motif or arginine-rich region within hydrophobic aa-s present at the N-terminus of a preprotein can be sufficient signals for mitochondrial import irrespective of presequence length in Euglenozoa.}, }
@article {pmid23064401, year = {2013}, author = {Villanueva-Noriega, MJ and Baker, CS and Medrano-González, L}, title = {Evolution of the MHC-DQB exon 2 in marine and terrestrial mammals.}, journal = {Immunogenetics}, volume = {65}, number = {1}, pages = {47-61}, pmid = {23064401}, issn = {1432-1211}, mesh = {Animals ; Artiodactyla/*genetics/immunology ; Base Sequence ; CD4-Positive T-Lymphocytes/immunology ; Cetacea/*genetics/immunology ; Cytochromes b/genetics ; *Evolution, Molecular ; Exons ; *Genes, MHC Class II ; Genetic Variation ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Primates/*genetics/immunology ; }, abstract = {On the basis of a general low polymorphism, several studies suggest that balancing selection in the class II major histocompatibility complex (MHC) is weaker in marine mammals as compared with terrestrial mammals. We investigated such differential selection among Cetacea, Artiodactyla, and Primates at exon 2 of MHC-DQB gene by contrasting indicators of molecular evolution such as occurrence of transpecific polymorphisms, patterns of phylogenetic branch lengths by codon position, rates of nonsynonymous and synonymous substitutions as well as accumulation of variable sites on the sampling of alleles. These indicators were compared between the DQB and the mitochondrial cytochrome b gene (cytb) as a reference of neutral expectations and differences between molecular clocks resulting from life history and historical demography. All indicators showed that the influence of balancing selection on the DQB is more variable and overall weaker for cetaceans. In our sampling, ziphiids, the sperm whale, monodontids and the finless porpoise formed a group with lower DQB polymorphism, while mysticetes exhibited a higher DQB variation similar to that of terrestrial mammals as well as higher occurrence of transpecific polymorphisms. Different dolphins appeared in the two groups. Larger variation of selection on the cetacean DQB could be related to greater stochasticity in their historical demography and thus, to a greater complexity of the general ecology and disease processes of these animals.}, }
@article {pmid23063117, year = {2012}, author = {Lane, N}, title = {The problem with mixing mitochondria.}, journal = {Cell}, volume = {151}, number = {2}, pages = {246-248}, doi = {10.1016/j.cell.2012.09.028}, pmid = {23063117}, issn = {1097-4172}, abstract = {Mixing of mitochondrial DNAs (heteroplasmy) is unfavorable for reasons unknown. Sharpley et al. show that heteroplasmy has surprising genetic and behavioral effects in mice, even when each haplotype alone produces a normal phenotype. This interference is bioenergetic and may have contributed to the evolution of sexes.}, }
@article {pmid23046553, year = {2012}, author = {Zhang, Y and Lin, J and Gao, Y}, title = {In silico identification of a multi-functional regulatory protein involved in Holliday junction resolution in bacteria.}, journal = {BMC systems biology}, volume = {6 Suppl 1}, number = {Suppl 1}, pages = {S20}, pmid = {23046553}, issn = {1752-0509}, mesh = {Amino Acid Sequence ; Bacteria/classification/*genetics/*metabolism ; Bacterial Proteins/chemistry/*metabolism ; DNA, Bacterial/genetics/*metabolism ; DNA, Cruciform/genetics/*metabolism ; Genomics/*methods ; Homologous Recombination ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; }, abstract = {BACKGROUND: Homologous recombination is a fundamental cellular process that is most widely used by cells to rearrange genes and accurately repair DNA double-strand breaks. It may result in the formation of a critical intermediate named Holliday junction, which is a four-way DNA junction and needs to be resolved to allow chromosome segregation. Different Holliday junction resolution systems and enzymes have been characterized from all three domains of life. In bacteria, the RuvABC complex is the most important resolution system.<br><br>RESULTS: In this study, we conducted comparative genomics studies to identify a novel DNA-binding protein, YebC, which may serve as a key transcriptional regulator that mainly regulates the gene expression of RuvABC resolvasome in bacteria. On the other hand, the presence of YebC orthologs in some organisms lacking RuvC implied that it might participate in other biological processes. Further phylogenetic analysis of YebC protein sequences revealed two functionally different subtypes: YebC_I and YebC_II. Distribution of YebC_I is much wider than YebC_II. Only YebC_I proteins may play an important role in regulating RuvABC gene expression in bacteria. Investigation of YebC-like proteins in eukaryotes suggested that they may have originated from YebC_II proteins and evolved a new function as a specific translational activator in mitochondria. Finally, additional phylum-specific genes associated with Holliday junction resolution were predicted.<br><br>CONCLUSIONS: Overall, our data provide new insights into the basic mechanism of Holliday junction resolution and homologous recombination in bacteria.}, }
@article {pmid23046955, year = {2012}, author = {Magalon, A and Arias-Cartin, R and Walburger, A}, title = {Supramolecular organization in prokaryotic respiratory systems.}, journal = {Advances in microbial physiology}, volume = {61}, number = {}, pages = {217-266}, doi = {10.1016/B978-0-12-394423-8.00006-8}, pmid = {23046955}, issn = {2162-5468}, mesh = {Bacteria/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Biological Evolution ; Biological Transport ; *Lipid Metabolism ; Macromolecular Substances/*metabolism ; Mitochondria/genetics/metabolism ; Oxygen/*metabolism ; }, abstract = {Prokaryotes are characterized by an extreme flexibility of their respiratory systems allowing them to cope with various extreme environments. To date, supramolecular organization of respiratory systems appears as a conserved evolutionary feature as supercomplexes have been isolated in bacteria, archaea, and eukaryotes. Most of the yet identified supercomplexes in prokaryotes are involved in aerobic respiration and share similarities with those reported in mitochondria. Supercomplexes likely reflect a snapshot of the cellular respiration in a given cell population. While the exact nature of the determinants for supramolecular organization in prokaryotes is not understood, lipids, proteins, and subcellular localization can be seen as key players. Owing to the well-reported supramolecular organization of the mitochondrial respiratory chain in eukaryotes, several hypotheses have been formulated to explain the consequences of such arrangement and can be tested in the context of prokaryotes. Considering the inherent metabolic flexibility of a number of prokaryotes, cellular distribution and composition of the supramolecular assemblies should be studied in regards to environmental signals. This would pave the way to new concepts in cellular respiration.}, }
@article {pmid23041381, year = {2012}, author = {Su, HJ and Hu, JM}, title = {Rate heterogeneity in six protein-coding genes from the holoparasite Balanophora (Balanophoraceae) and other taxa of Santalales.}, journal = {Annals of botany}, volume = {110}, number = {6}, pages = {1137-1147}, pmid = {23041381}, issn = {1095-8290}, mesh = {Balanophoraceae/*genetics/ultrastructure ; DNA, Mitochondrial/chemistry/genetics ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Evolution, Molecular ; Flowers/*genetics/ultrastructure ; Inflorescence/genetics/ultrastructure ; Microscopy, Electron, Scanning ; Mitochondria/genetics ; Nuclear Proteins/genetics ; *Phylogeny ; Plant Epidermis/genetics/ultrastructure ; Plant Proteins/*genetics ; RNA, Ribosomal, 18S/genetics ; Santalaceae/*genetics/ultrastructure ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND AND AIMS: The holoparasitic flowering plant Balanophora displays extreme floral reduction and was previously found to have enormous rate acceleration in the nuclear 18S rDNA region. So far, it remains unclear whether non-ribosomal, protein-coding genes of Balanophora also evolve in an accelerated fashion and whether the genes with high substitution rates retain their functionality. To tackle these issues, six different genes were sequenced from two Balanophora species and their rate variation and expression patterns were examined.<br><br>METHODS: Sequences including nuclear PI, euAP3, TM6, LFY and RPB2 and mitochondrial matR were determined from two Balanophora spp. and compared with selected hemiparasitic species of Santalales and autotrophic core eudicots. Gene expression was detected for the six protein-coding genes and the expression patterns of the three B-class genes (PI, AP3 and TM6) were further examined across different organs of B. laxiflora using RT-PCR.<br><br>KEY RESULTS: Balanophora mitochondrial matR is highly accelerated in both nonsynonymous (d(N)) and synonymous (d(S)) substitution rates, whereas the rate variation of nuclear genes LFY, PI, euAP3, TM6 and RPB2 are less dramatic. Significant d(S) increases were detected in Balanophora PI, TM6, RPB2 and d(N) accelerations in euAP3. All of the protein-coding genes are expressed in inflorescences, indicative of their functionality. PI is restrictively expressed in tepals, synandria and floral bracts, whereas AP3 and TM6 are widely expressed in both male and female inflorescences.<br><br>CONCLUSIONS: Despite the observation that rates of sequence evolution are generally higher in Balanophora than in hemiparasitic species of Santalales and autotrophic core eudicots, the five nuclear protein-coding genes are functional and are evolving at a much slower rate than 18S rDNA. The mechanism or mechanisms responsible for rapid sequence evolution and concomitant rate acceleration for 18S rDNA and matR are currently not well understood and require further study in Balanophora and other holoparasites.}, }
@article {pmid23028451, year = {2012}, author = {Mezil, L and Berruyer-Pouyet, C and Cabaud, O and Josselin, E and Combes, S and Brunel, JM and Viens, P and Collette, Y and Birnbaum, D and Lopez, M}, title = {Tumor selective cytotoxic action of a thiomorpholin hydroxamate inhibitor (TMI-1) in breast cancer.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e43409}, pmid = {23028451}, issn = {1932-6203}, mesh = {Animals ; Antineoplastic Agents/*pharmacology/toxicity ; Apoptosis/drug effects ; Breast Neoplasms/drug therapy/*metabolism ; Caspases/metabolism ; Cell Cycle Checkpoints/drug effects ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Cell Survival/drug effects ; Dose-Response Relationship, Drug ; Female ; Humans ; Metalloproteases/antagonists &amp; inhibitors ; Mice ; Mice, Transgenic ; Mitochondria/drug effects/metabolism ; Morpholines/*pharmacology/toxicity ; Neoplastic Stem Cells/drug effects/metabolism ; Receptor, ErbB-2/metabolism ; Signal Transduction/drug effects ; Spheroids, Cellular/drug effects ; Tumor Cells, Cultured ; }, abstract = {BACKGROUND: Targeted therapies, associated with standard chemotherapies, have improved breast cancer care. However, primary and acquired resistances are frequently observed and the development of new concepts is needed. High-throughput approaches to identify new active and safe molecules with or without an "a priori" are currently developed. Also, repositioning already-approved drugs in cancer therapy is of growing interest. The thiomorpholine hydroxamate compound TMI-1 has been previously designed to inhibit metalloproteinase activity for the treatment of rheumatoid arthritis. We present here the repositioning of TMI-1 drug in breast cancer.<br><br>We tested the effect of TMI-1 on luminal, basal and ERBB2-overexpressing breast tumor cell lines and on MMTV-ERBB2/neu tumor evolution. We measured the effects on i) cell survival, ii) cell cycle, iii) extrinsic and intrinsic apoptotic pathways, iv) association with doxorubicin, docetaxel and lapatinib, v) cancer stem cells compartment. In contrast with conventional cytotoxic drugs, TMI-1 was highly selective for tumor cells and cancer stem cells at submicromolar range. All non-malignant cells tested were resistant even at high concentration. TMI-1 was active on triple negative (TN) and ERBB2-overexpressing breast tumor cell lines, and was also highly efficient on human and murine "primary" ERBB2-overexpressing cells. Treatment of transgenic MMTV-ERBB2/neu mice with 100 mg/kg/day TMI-1 alone induced tumor apoptosis, inhibiting mammary gland tumor occurrence and development. No adverse effects were noticed during the treatment. This compound had a strong synergistic effect in association with docetaxel, doxorubicin and lapatinib. We showed that TMI-1 mediates its selective effects by caspase-dependent apoptosis. TMI-1 was efficient in 34/40 tumor cell lines of various origins (ED50: 0.6 &#xb5;M to 12.5 &#xb5;M).<br><br>CONCLUSIONS/SIGNIFICANCE: This is the first demonstration of the tumor selective cytotoxic action of a thiomorpholin hydroxamate compound. TMI-1 is a novel repositionable drug not only for the treatment of adverse prognosis breast cancers but also for other neoplasms.}, }
@article {pmid23028354, year = {2012}, author = {Salinas, T and Duby, F and Larosa, V and Coosemans, N and Bonnefoy, N and Motte, P and Maréchal-Drouard, L and Remacle, C}, title = {Co-evolution of mitochondrial tRNA import and codon usage determines translational efficiency in the green alga Chlamydomonas.}, journal = {PLoS genetics}, volume = {8}, number = {9}, pages = {e1002946}, pmid = {23028354}, issn = {1553-7404}, mesh = {Biological Transport ; Cell Respiration/genetics ; Chlamydomonas/*genetics ; Codon/genetics ; Evolution, Molecular ; Genome, Mitochondrial ; Membrane Potential, Mitochondrial ; Mitochondria/*genetics/metabolism ; Point Mutation ; *Protein Biosynthesis ; RNA, Transfer/*genetics/metabolism ; }, abstract = {Mitochondria from diverse phyla, including protozoa, fungi, higher plants, and humans, import tRNAs from the cytosol in order to ensure proper mitochondrial translation. Despite the broad occurrence of this process, our understanding of tRNA import mechanisms is fragmentary, and crucial questions about their regulation remain unanswered. In the unicellular green alga Chlamydomonas, a precise correlation was found between the mitochondrial codon usage and the nature and amount of imported tRNAs. This led to the hypothesis that tRNA import might be a dynamic process able to adapt to the mitochondrial genome content. By manipulating the Chlamydomonas mitochondrial genome, we introduced point mutations in order to modify its codon usage. We find that the codon usage modification results in reduced levels of mitochondrial translation as well as in subsequent decreased levels and activities of respiratory complexes. These effects are linked to the consequential limitations of the pool of tRNAs in mitochondria. This indicates that tRNA mitochondrial import cannot be rapidly regulated in response to a novel genetic context and thus does not appear to be a dynamic process. It rather suggests that the steady-state levels of imported tRNAs in mitochondria result from a co-evolutive adaptation between the tRNA import mechanism and the requirements of the mitochondrial translation machinery.}, }
@article {pmid23028295, year = {2012}, author = {Selivanov, VA and Cascante, M and Friedman, M and Schumaker, MF and Trucco, M and Votyakova, TV}, title = {Multistationary and oscillatory modes of free radicals generation by the mitochondrial respiratory chain revealed by a bifurcation analysis.}, journal = {PLoS computational biology}, volume = {8}, number = {9}, pages = {e1002700}, pmid = {23028295}, issn = {1553-7358}, mesh = {Binding Sites ; Biological Clocks ; Computer Simulation ; Electron Transport ; Electron Transport Chain Complex Proteins/*chemistry ; Free Radicals ; Mitochondria/*metabolism ; Mitochondrial Proteins/*chemistry ; *Models, Chemical ; *Models, Molecular ; Oscillometry/methods ; Protein Binding ; Reactive Oxygen Species/*chemistry ; }, abstract = {The mitochondrial electron transport chain transforms energy satisfying cellular demand and generates reactive oxygen species (ROS) that act as metabolic signals or destructive factors. Therefore, knowledge of the possible modes and bifurcations of electron transport that affect ROS signaling provides insight into the interrelationship of mitochondrial respiration with cellular metabolism. Here, a bifurcation analysis of a sequence of the electron transport chain models of increasing complexity was used to analyze the contribution of individual components to the modes of respiratory chain behavior. Our algorithm constructed models as large systems of ordinary differential equations describing the time evolution of the distribution of redox states of the respiratory complexes. The most complete model of the respiratory chain and linked metabolic reactions predicted that condensed mitochondria produce more ROS at low succinate concentration and less ROS at high succinate levels than swelled mitochondria. This prediction was validated by measuring ROS production under various swelling conditions. A numerical bifurcation analysis revealed qualitatively different types of multistationary behavior and sustained oscillations in the parameter space near a region that was previously found to describe the behavior of isolated mitochondria. The oscillations in transmembrane potential and ROS generation, observed in living cells were reproduced in the model that includes interaction of respiratory complexes with the reactions of TCA cycle. Whereas multistationarity is an internal characteristic of the respiratory chain, the functional link of respiration with central metabolism creates oscillations, which can be understood as a means of auto-regulation of cell metabolism.}, }
@article {pmid23025608, year = {2012}, author = {Pichaud, N and Ballard, JW and Tanguay, RM and Blier, PU}, title = {Naturally occurring mitochondrial DNA haplotypes exhibit metabolic differences: insight into functional properties of mitochondria.}, journal = {Evolution; international journal of organic evolution}, volume = {66}, number = {10}, pages = {3189-3197}, doi = {10.1111/j.1558-5646.2012.01683.x}, pmid = {23025608}, issn = {1558-5646}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Analysis of Variance ; Animals ; DNA, Mitochondrial/*genetics ; Drosophila/genetics/*metabolism ; Female ; Haplotypes ; Male ; Mitochondria/*metabolism ; }, abstract = {Linking the mitochondrial genotype and the organismal phenotype is of paramount importance in evolution of mitochondria. In this study, we determined the differences in catalytic properties of mitochondria dictated by divergences in the siII and siIII haplogroups of Drosophila simulans using introgressions of siII mtDNA type into the siIII nuclear background. We used a novel in situ method (permeabilized fibers) that allowed us to accurately measure the consumption of oxygen by mitochondria in constructed siII-introgressed flies and in siIII-control flies. Our results showed that the catalytic capacity of the electron transport system is not impaired by introgressions, suggesting that the functional properties of mitochondria are tightly related to the mtDNA haplogroup and not to the nuclear DNA or to the mito-nuclear interactions. This is the first study, to our knowledge, that demonstrates a naturally occurring haplogroup can confer specific functional differences in aspects of mitochondrial metabolism. This study illustrates the importance of mtDNA changes on organelle evolution and highlights the potential bioenergetic and metabolic impacts that divergent mitochondrial haplogroups may have upon a wide variety of species including humans.}, }
@article {pmid23024290, year = {2012}, author = {Yamaguchi, M and Mori, Y and Kozuka, Y and Okada, H and Uematsu, K and Tame, A and Furukawa, H and Maruyama, T and Worman, CO and Yokoyama, K}, title = {Prokaryote or eukaryote? A unique microorganism from the deep sea.}, journal = {Journal of electron microscopy}, volume = {61}, number = {6}, pages = {423-431}, doi = {10.1093/jmicro/dfs062}, pmid = {23024290}, issn = {1477-9986}, mesh = {*Aquatic Organisms ; *Biological Evolution ; *Eukaryotic Cells ; *Phylogeny ; *Prokaryotic Cells ; }, abstract = {There are only two kinds of organisms on the Earth: prokaryotes and eukaryotes. Although eukaryotes are considered to have evolved from prokaryotes, there were no previously known intermediate forms between them. The differences in their cellular structures are so vast that the problem of how eukaryotes could have evolved from prokaryotes is one of the greatest enigmas in biology. Here, we report a unique organism with cellular structures appearing to have intermediate features between prokaryotes and eukaryotes, which was discovered in the deep sea off the coast of Japan using electron microscopy and structome analysis. The organism was 10 µm long and 3 µm in diameter, having >100 times the volume of Escherichia coli. It had a large 'nucleoid', consisting of naked DNA fibers, with a single nucleoid membrane and endosymbionts that resemble bacteria, but no mitochondria. Because this organism appears to be a life form distinct from both prokaryotes and eukaryotes but similar to eukaryotes, we named this unique microorganism the 'Myojin parakaryote' with the scientific name of Parakaryon myojinensis ('next to (eu)karyote from Myojin') after the discovery location and its intermediate morphology. The existence of this organism is an indication of a potential evolutionary path between prokaryotes and eukaryotes.}, }
@article {pmid23023207, year = {2013}, author = {Bernt, M and Braband, A and Middendorf, M and Misof, B and Rota-Stabelli, O and Stadler, PF}, title = {Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {69}, number = {2}, pages = {320-327}, doi = {10.1016/j.ympev.2012.09.019}, pmid = {23023207}, issn = {1095-9513}, mesh = {Animals ; Computational Biology/*methods ; Databases, Genetic ; Evolution, Molecular ; Gene Order ; Gene Rearrangement ; *Genome, Mitochondrial ; Models, Genetic ; Molecular Sequence Annotation ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {In this review we provide an overview of various bioinformatics methods and tools for the analysis of metazoan mitochondrial genomes. We compare available dedicated databases and present current tools for accurate genome annotation, identification of protein coding genes, and determination of tRNA and rRNA models.We also evaluate various tools and models for phylogenetic tree inference using gene order or sequence based data. As for gene order based methods, we compare rearrangement based and gene cluster based methods for gene order rearrangement analysis. As for sequence based methods, we give special emphasis to substitution models or data treatment that reduces certain systematic biases that are typical for metazoan mitogenomes such as within genome and/or among lineage compositional heterogeneity.}, }
@article {pmid23020104, year = {2012}, author = {Lee-Yaw, JA and Irwin, DE}, title = {Large geographic range size reflects a patchwork of divergent lineages in the long-toed salamander (Ambystoma macrodactylum).}, journal = {Journal of evolutionary biology}, volume = {25}, number = {11}, pages = {2276-2287}, doi = {10.1111/j.1420-9101.2012.02604.x}, pmid = {23020104}, issn = {1420-9101}, mesh = {Ambystoma/genetics/*physiology ; Amplified Fragment Length Polymorphism Analysis ; Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genetic Loci ; *Genetic Variation ; Geography ; Haplotypes ; Mitochondria/genetics ; Phylogeography/*methods ; Population Density ; Population Dynamics ; Species Specificity ; }, abstract = {For northern taxa, persistence in multiple vs. single Pleistocene refugia may have been an important determinant of contemporary range size, with larger ranges achieved by species that colonized the north from several glacial refugia. Under this hypothesis, widespread species are expected to demonstrate marked phylogeographic structure in previously glaciated regions. We use a genome-wide survey to characterize genetic structure and evaluate this hypothesis in the most widely distributed salamander in the Pacific Northwest, the long-toed salamander (Ambystoma macrodactylum). Patterns of variation based on 751 amplified fragment length polymorphism (AFLP) loci and mitochondrial sequence data were concordant and support the recognition of at least four distinct lineages of long-toed salamander. The distributions of these lineages indicate that multiple refugia contributed to the species' large contemporary range. At the same time, with up to 133 AFLP bands differing between lineages and levels of sequence divergence ranging from 2.5 to 5.8%, these lineages would be considered separate species by some definitions. Such splitting would partition the large geographic range of the long-toed salamander into several relatively restricted ranges. Our results thus also underscore the potential for estimates of geographic range size to vary considerably depending on the taxonomic treatment of cryptic lineages.}, }
@article {pmid23017992, year = {2012}, author = {Frank, SA}, title = {Evolution: mitochondrial burden on male health.}, journal = {Current biology : CB}, volume = {22}, number = {18}, pages = {R797-9}, doi = {10.1016/j.cub.2012.07.066}, pmid = {23017992}, issn = {1879-0445}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Drosophila melanogaster/*genetics ; Female ; *Genome, Mitochondrial ; Longevity/*genetics ; Male ; Mitochondria/*genetics ; }, abstract = {In many animal species, males suffer more from age-related disease than females. Is there a common cause for this burden on male health? Recent work supports the theory that the female transmission of mitochondria disproportionately increases the mutation load in males.}, }
@article {pmid23017987, year = {2012}, author = {Martin, RD}, title = {Primates.}, journal = {Current biology : CB}, volume = {22}, number = {18}, pages = {R785-90}, doi = {10.1016/j.cub.2012.07.015}, pmid = {23017987}, issn = {1879-0445}, mesh = {Animals ; *Biological Evolution ; Dental Physiological Phenomena ; Fossils ; Geography ; Mitochondria/genetics ; *Primates/anatomy &amp; histology/classification/genetics/physiology ; Social Environment ; Tooth ; }, }
@article {pmid22998186, year = {2012}, author = {Itahana, Y and Itahana, K}, title = {Emerging roles of mitochondrial p53 and ARF.}, journal = {Current drug targets}, volume = {13}, number = {13}, pages = {1633-1640}, doi = {10.2174/138945012803529992}, pmid = {22998186}, issn = {1873-5592}, mesh = {Alternative Splicing/genetics ; Animals ; Apoptosis/genetics/*physiology ; Cyclin-Dependent Kinase Inhibitor p16/genetics/*physiology ; Humans ; Mice ; Mitochondrial Proteins/genetics/metabolism/*physiology ; Proto-Oncogene Proteins c-mdm2/antagonists &amp; inhibitors/genetics/*physiology ; Tumor Suppressor Protein p53/genetics/*physiology ; }, abstract = {After mitochondria colonized eukaryotic cells more than a billion years ago, they acquired numerous functions over the course of evolution, such as those involved in controlling apoptosis, autophagy, and cellular metabolism together with host cells. The major tumor suppressors, p53 and ARF in the nucleus also participate in such crosstalk between host cells and mitochondria by activating p53 target genes involved in varied mitochondrial functions. However, recent evidence suggests that p53 and ARF can also directly localize to mitochondria and contribute to this cross talk to maintain tissue homeostasis for the prevention of various diseases. Here, we discuss the functions of mitochondrial p53 and ARF via interactions with mitochondrial proteins as well as the mechanism of the localization of p53 and ARF to mitochondria. Because mitochondrial dysregulation is involved in the development of several disease types, such as cancer, neurodegenerative diseases, and age-related diseases, understanding the roles of p53 and ARF in mitochondria may facilitate the development of novel mitochondrial-specific drug targets against such diseases.}, }
@article {pmid22994357, year = {2012}, author = {Wall, JD and Slatkin, M}, title = {Paleopopulation genetics.}, journal = {Annual review of genetics}, volume = {46}, number = {}, pages = {635-649}, pmid = {22994357}, issn = {1545-2948}, support = {R01 GM040282/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Fossils ; Gene Frequency ; Genetic Variation ; Genetics, Population/*methods ; *Genome, Human ; Humans ; Mitochondria/genetics ; Neanderthals/classification/*genetics ; Phylogeny ; Population Density ; Sequence Analysis, DNA ; }, abstract = {Paleopopulation genetics is a new field that focuses on the population genetics of extinct groups and ancestral populations (i.e., populations ancestral to extant groups). With recent advances in DNA sequencing technologies, we now have unprecedented ability to directly assay genetic variation from fossils. This allows us to address issues, such as past population structure, changes in population size, and evolutionary relationships between taxa, at a much greater resolution than can traditional population genetics studies. In this review, we discuss recent developments in this emerging field as well as prospects for the future.}, }
@article {pmid22991464, year = {2012}, author = {Howard, MJ and Lim, WH and Fierke, CA and Koutmos, M}, title = {Mitochondrial ribonuclease P structure provides insight into the evolution of catalytic strategies for precursor-tRNA 5' processing.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {40}, pages = {16149-16154}, pmid = {22991464}, issn = {1091-6490}, support = {R01 GM055387/GM/NIGMS NIH HHS/United States ; GM55387/GM/NIGMS NIH HHS/United States ; }, mesh = {Arabidopsis/*enzymology ; Crystallography, X-Ray ; Evolution, Molecular ; Humans ; Mitochondria/*enzymology/physiology ; *Models, Molecular ; Protein Structure, Tertiary ; RNA Precursors/*metabolism ; RNA Processing, Post-Transcriptional/*physiology ; Ribonuclease P/*chemistry/*metabolism ; }, abstract = {Ribonuclease P (RNase P) catalyzes the maturation of the 5' end of tRNA precursors. Typically these enzymes are ribonucleoproteins with a conserved RNA component responsible for catalysis. However, protein-only RNase P (PRORP) enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana. PRORP enzymes are nuclear encoded and conserved among many eukaryotes, having evolved recently as yeast mitochondrial genomes encode an RNase P RNA. Here we report the crystal structure of PRORP1 from A. thaliana at 1.75 Å resolution, revealing a prototypical metallonuclease domain tethered to a pentatricopeptide repeat (PPR) domain by a structural zinc-binding domain. The metallonuclease domain is a unique high-resolution structure of a Nedd4-BP1, YacP Nucleases (NYN) domain that is a member of the PIN domain-like fold superfamily, including the FLAP nuclease family. The structural similarity between PRORP1 and the FLAP nuclease family suggests that they evolved from a common ancestor. Biochemical data reveal that conserved aspartate residues in PRORP1 are important for catalytic activity and metal binding and that the PPR domain also enhances activity, likely through an interaction with pre-tRNA. These results provide a foundation for understanding tRNA maturation in organelles. Furthermore, these studies allow for a molecular-level comparison of the catalytic strategies used by the only known naturally evolved protein and RNA-based catalysts that perform the same biological function, pre-tRNA maturation, thereby providing insight into the differences between the prebiotic RNA world and the present protein-dominated world.}, }
@article {pmid22988821, year = {2013}, author = {Schwartz, TS and Bronikowski, AM}, title = {Dissecting molecular stress networks: identifying nodes of divergence between life-history phenotypes.}, journal = {Molecular ecology}, volume = {22}, number = {3}, pages = {739-756}, doi = {10.1111/j.1365-294X.2012.05750.x}, pmid = {22988821}, issn = {1365-294X}, mesh = {Animals ; Colubridae/genetics/*physiology ; Corticosterone/blood ; DNA Damage ; *Ecotype ; Female ; Gene Expression Profiling ; Heat-Shock Response ; Hot Temperature ; Liver/metabolism ; Male ; Microsatellite Repeats ; Mitochondria, Liver/metabolism ; Molecular Sequence Data ; Oxidative Stress/*genetics ; Reactive Oxygen Species/blood/metabolism ; }, abstract = {The complex molecular network that underlies physiological stress response is comprised of nodes (proteins, metabolites, mRNAs, etc.) whose connections span cells, tissues and organs. Variable nodes are points in the network upon which natural selection may act. Thus, identifying variable nodes will reveal how this molecular stress network may evolve among populations in different habitats and how it might impact life-history evolution. Here, we use physiological and genetic assays to test whether laboratory-born juveniles from natural populations of garter snakes (Thamnophis elegans), which have diverged in their life-history phenotypes, vary concomitantly at candidate nodes of the stress response network, (i) under unstressed conditions and (ii) in response to an induced stress. We found that two common measures of stress (plasma corticosterone and liver gene expression of heat shock proteins) increased under stress in both life-history phenotypes. In contrast, the phenotypes diverged at four nodes both under unstressed conditions and in response to stress: circulating levels of reactive oxygen species (superoxide, H(2)O(2)); liver gene expression of GPX1 and erythrocyte DNA damage. Additionally, allele frequencies for SOD2 diverge from neutral markers, suggesting diversifying selection on SOD2 alleles. This study supports the hypothesis that these life-history phenotypes have diverged at the molecular level in how they respond to stress, particularly in nodes regulating oxidative stress. Furthermore, the differences between the life-history phenotypes were more pronounced in females. We discuss the responses to stress in the context of the associated life-history phenotype and the evolutionary pressures thought to be responsible for divergence between the phenotypes.}, }
@article {pmid22984095, year = {2012}, author = {Heskel, MA and Anderson, OR and Atkin, OK and Turnbull, MH and Griffin, KL}, title = {Leaf- and cell-level carbon cycling responses to a nitrogen and phosphorus gradient in two Arctic tundra species.}, journal = {American journal of botany}, volume = {99}, number = {10}, pages = {1702-1714}, doi = {10.3732/ajb.1200251}, pmid = {22984095}, issn = {1537-2197}, mesh = {Analysis of Variance ; Arctic Regions ; Betula/cytology/growth &amp; development/*metabolism/ultrastructure ; Biomass ; *Carbon Cycle/radiation effects ; Carbon Dioxide/metabolism ; Cell Respiration/radiation effects ; Chloroplasts/metabolism/radiation effects/ultrastructure ; Cyperaceae/cytology/growth &amp; development/*metabolism/ultrastructure ; Fertilization/radiation effects ; Light ; Mesophyll Cells/cytology/radiation effects/ultrastructure ; Mitochondria/metabolism/radiation effects/ultrastructure ; Nitrogen/*metabolism ; Oxygen Consumption/radiation effects ; Phosphorus/*metabolism ; Photosynthesis/radiation effects ; Plant Leaves/anatomy &amp; histology/*cytology/*metabolism/radiation effects ; Seasons ; Temperature ; }, abstract = {PREMISE OF THE STUDY: Consequences of global climate change are detectable in the historically nitrogen- and phosphorus-limited Arctic tundra landscape and have implications for the terrestrial carbon cycle. Warmer temperatures and elevated soil nutrient availability associated with increased microbial activity may influence rates of photosynthesis and respiration. •<br><br>METHODS: This study examined leaf-level gas exchange, cellular ultrastructure, and related leaf traits in two dominant tundra species, Betula nana, a woody shrub, and Eriophorum vaginatum, a tussock sedge, under a 3-yr-old treatment gradient of nitrogen (N) and phosphorus (P) fertilization in the North Slope of Alaska. &#x2022;<br><br>KEY RESULTS: Respiration increased with N and P addition-the highest rates corresponding to the highest concentrations of leaf N in both species. The inhibition of respiration by light ("Kok effect") significantly reduced respiration rates in both species (P < 0.001), ranged from 12-63% (mean 34%), and generally decreased with fertilization for both species. However, in both species, observed rates of photosynthesis did not increase, and photosynthetic nitrogen use efficiency generally decreased under increasing fertilization. Chloroplast and mitochondrial size and density were highly sensitive to N and P fertilization (P < 0.001), though species interactions indicated divergent cellular organizational strategies. &#x2022;<br><br>CONCLUSIONS: Results from this study demonstrate a species-specific decoupling of respiration and photosynthesis under N and P fertilization, implying an alteration of the carbon balance of the tundra ecosystem under future conditions.}, }
@article {pmid22983951, year = {2013}, author = {Popadin, KY and Nikolaev, SI and Junier, T and Baranova, M and Antonarakis, SE}, title = {Purifying selection in mammalian mitochondrial protein-coding genes is highly effective and congruent with evolution of nuclear genes.}, journal = {Molecular biology and evolution}, volume = {30}, number = {2}, pages = {347-355}, doi = {10.1093/molbev/mss219}, pmid = {22983951}, issn = {1537-1719}, mesh = {Amino Acid Substitution ; Animals ; Cell Nucleus/genetics ; *Evolution, Molecular ; Female ; *Genome ; *Genome, Mitochondrial ; Humans ; Male ; Mammals/genetics ; Mitochondrial Proteins/*genetics ; Mutation ; *Selection, Genetic ; }, abstract = {The mammalian mitochondrial genomes differ from the nuclear genomes by maternal inheritance, absence of recombination, and higher mutation rate. All these differences decrease the effective population size of mitochondrial genome and make it more susceptible to accumulation of slightly deleterious mutations. It was hypothesized that mitochondrial genes, especially in species with low effective population size, irreversibly degrade leading to decrease of organismal fitness and even to extinction of species through the mutational meltdown. To interrogate this hypothesis, we compared the purifying selections acting on the representative set of mitochondrial (potentially degrading) and nuclear (potentially not degrading) protein-coding genes in species with different effective population size. For 21 mammalian species, we calculated the ratios of accumulation of slightly deleterious mutations approximated by Kn/Ks separately for mitochondrial and nuclear genomes. The 75% of variation in Kn/Ks is explained by two independent variables: type of a genome (mitochondrial or nuclear) and effective population size of species approximated by generation time. First, we observed that purifying selection is more effective in mitochondria than in the nucleus that implies strong evolutionary constraints of mitochondrial genome. Mitochondrial de novo nonsynonymous mutations have at least 5-fold more harmful effect when compared with nuclear. Second, Kn/Ks of mitochondrial and nuclear genomes is positively correlated with generation time of species, indicating relaxation of purifying selection with decrease of species-specific effective population size. Most importantly, the linear regression lines of mitochondrial and nuclear Kn/Ks's from generation times of species are parallel, indicating congruent relaxation of purifying selection in both genomes. Thus, our results reveal that the distribution of selection coefficients of de novo nonsynonymous mitochondrial mutations has a similar shape with the distribution of de novo nonsynonymous nuclear mutations, but its mean is five times smaller. The harmful effect of mitochondrial de novo nonsynonymous mutations triggers highly effective purifying selection, which maintains the fitness of the mammalian mitochondrial genome.}, }
@article {pmid22983685, year = {2012}, author = {Ruan, L and Wang, Y and Hu, J and Ouyang, Y}, title = {Polyphyletic origin of the genus Amaurornis inferred from molecular phylogenetic analysis of rails.}, journal = {Biochemical genetics}, volume = {50}, number = {11-12}, pages = {959-966}, doi = {10.1007/s10528-012-9535-z}, pmid = {22983685}, issn = {1573-4927}, mesh = {Animals ; Base Sequence ; Birds/classification/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Genetic Variation ; Genotype ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, }
@article {pmid22982435, year = {2013}, author = {Bernt, M and Donath, A and Jühling, F and Externbrink, F and Florentz, C and Fritzsch, G and Pütz, J and Middendorf, M and Stadler, PF}, title = {MITOS: improved de novo metazoan mitochondrial genome annotation.}, journal = {Molecular phylogenetics and evolution}, volume = {69}, number = {2}, pages = {313-319}, doi = {10.1016/j.ympev.2012.08.023}, pmid = {22982435}, issn = {1095-9513}, mesh = {Animals ; *Computational Biology ; Evolution, Molecular ; *Genome, Mitochondrial ; Internet ; *Molecular Sequence Annotation ; Phylogeny ; Sequence Analysis, DNA ; *Software ; }, abstract = {About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de.}, }
@article {pmid22982315, year = {2012}, author = {Ma, HZ and Liu, GQ and Li, CW and Kang, GZ and Guo, TC}, title = {Identification of the TaBTF3 gene in wheat (Triticum aestivum L.) and the effect of its silencing on wheat chloroplast, mitochondria and mesophyll cell development.}, journal = {Biochemical and biophysical research communications}, volume = {426}, number = {4}, pages = {608-614}, doi = {10.1016/j.bbrc.2012.08.137}, pmid = {22982315}, issn = {1090-2104}, mesh = {Amino Acid Sequence ; Chloroplasts/genetics/*physiology ; Gene Expression Regulation, Plant ; Gene Silencing ; Genes, Mitochondrial ; Mesophyll Cells/metabolism/*physiology/ultrastructure ; Mitochondria/genetics/*physiology ; Molecular Sequence Data ; Nuclear Proteins/classification/genetics/*physiology ; Phylogeny ; Transcription Factors/classification/genetics/*physiology ; Transcription, Genetic ; Triticum/genetics/*growth &amp; development/ultrastructure ; }, abstract = {The full-length cDNA (882bp) and DNA (1742bp) sequences encoding a basic transcription factor 3, designated as TaBTF3, were first isolated from common wheat (Triticum aestivum L.). Subcellular localization studies revealed that the TaBTF3 protein was mainly located in the cytoplasm and nucleus. In TaBTF3-silenced transgenic wheat seedlings obtained using the Virus-induced gene silencing (VIGS) method, the chlorophyll pigment content was markedly reduced. However, the malonaldehyde (MDA) and H(2)O(2) contents were enhanced, and the structure of the wheat mesophyll cell was seriously damaged. Furthermore, transcripts of the chloroplast- and mitochondrial-encoded genes were significantly reduced in TaBTF3-silenced transgenic wheat plants. These results suggest that the TaBTF3 gene might function in the development of the wheat chloroplast, mitochondria and mesophyll cell. This paper is the first report to describe the involvement of TaBTF3 in maintaining the normal plant mesophyll cell structure.}, }
@article {pmid22978553, year = {2013}, author = {Radak, Z and Zhao, Z and Koltai, E and Ohno, H and Atalay, M}, title = {Oxygen consumption and usage during physical exercise: the balance between oxidative stress and ROS-dependent adaptive signaling.}, journal = {Antioxidants &amp; redox signaling}, volume = {18}, number = {10}, pages = {1208-1246}, pmid = {22978553}, issn = {1557-7716}, mesh = {Animals ; Exercise/*physiology ; Humans ; Oxidative Stress/physiology ; Oxygen Consumption/*physiology ; Reactive Oxygen Species/*metabolism ; Signal Transduction/physiology ; }, abstract = {The complexity of human DNA has been affected by aerobic metabolism, including endurance exercise and oxygen toxicity. Aerobic endurance exercise could play an important role in the evolution of Homo sapiens, and oxygen was not important just for survival, but it was crucial to redox-mediated adaptation. The metabolic challenge during physical exercise results in an elevated generation of reactive oxygen species (ROS) that are important modulators of muscle contraction, antioxidant protection, and oxidative damage repair, which at moderate levels generate physiological responses. Several factors of mitochondrial biogenesis, such as peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α), mitogen-activated protein kinase, and SIRT1, are modulated by exercise-associated changes in the redox milieu. PGC-1α activation could result in decreased oxidative challenge, either by upregulation of antioxidant enzymes and/or by an increased number of mitochondria that allows lower levels of respiratory activity for the same degree of ATP generation. Endogenous thiol antioxidants glutathione and thioredoxin are modulated with high oxygen consumption and ROS generation during physical exercise, controlling cellular function through redox-sensitive signaling and protein-protein interactions. Endurance exercise-related angiogenesis, up to a significant degree, is regulated by ROS-mediated activation of hypoxia-inducible factor 1α. Moreover, the exercise-associated ROS production could be important to DNA methylation and post-translation modifications of histone residues, which create heritable adaptive conditions based on epigenetic features of chromosomes. Accumulating data indicate that exercise with moderate intensity has systemic and complex health-promoting effects, which undoubtedly involve regulation of redox homeostasis and signaling.}, }
@article {pmid22975005, year = {2012}, author = {Niccoli, T and Partridge, L}, title = {Ageing as a risk factor for disease.}, journal = {Current biology : CB}, volume = {22}, number = {17}, pages = {R741-52}, doi = {10.1016/j.cub.2012.07.024}, pmid = {22975005}, issn = {1879-0445}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {*Aging ; Autophagy ; Cardiovascular Diseases/epidemiology/pathology ; DNA Damage ; Humans ; Life Expectancy ; Mitochondria/physiology ; Neoplasms/epidemiology/pathology ; Neurodegenerative Diseases/epidemiology/pathology ; Risk Factors ; Signal Transduction ; Time Factors ; }, abstract = {Age is the main risk factor for the prevalent diseases of developed countries: cancer, cardiovascular disease and neurodegeneration. The ageing process is deleterious for fitness, but can nonetheless evolve as a consequence of the declining force of natural selection at later ages, attributable to extrinsic hazards to survival: ageing can then occur as a side-effect of accumulation of mutations that lower fitness at later ages, or of natural selection in favour of mutations that increase fitness of the young but at the cost of a higher subsequent rate of ageing. Once thought of as an inexorable, complex and lineage-specific process of accumulation of damage, ageing has turned out to be influenced by mechanisms that show strong evolutionary conservation. Lowered activity of the nutrient-sensing insulin/insulin-like growth factor/Target of Rapamycin signalling network can extend healthy lifespan in yeast, multicellular invertebrates, mice and, possibly, humans. Mitochondrial activity can also promote ageing, while genome maintenance and autophagy can protect against it. We discuss the relationship between evolutionarily conserved mechanisms of ageing and disease, and the associated scientific challenges and opportunities.}, }
@article {pmid22973548, year = {2012}, author = {Jung, PP and Friedrich, A and Reisser, C and Hou, J and Schacherer, J}, title = {Mitochondrial genome evolution in a single protoploid yeast species.}, journal = {G3 (Bethesda, Md.)}, volume = {2}, number = {9}, pages = {1103-1111}, pmid = {22973548}, issn = {2160-1836}, mesh = {DNA, Mitochondrial ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Mitochondrial ; Introns ; Open Reading Frames ; Phylogeny ; Polymorphism, Single Nucleotide ; Saccharomyces/classification/*genetics ; }, abstract = {Mitochondria are organelles, which play a key role in some essential functions, including respiration, metabolite biosynthesis, ion homeostasis, and apoptosis. The vast numbers of mitochondrial DNA (mtDNA) sequences of various yeast species, which have recently been published, have also helped to elucidate the structural diversity of these genomes. Although a large corpus of data are now available on the diversity of yeast species, little is known so far about the mtDNA diversity in single yeast species. To study the genetic variations occurring in the mtDNA of wild yeast isolates, we performed a genome-wide polymorphism survey on the mtDNA of 18 Lachancea kluyveri (formerly Saccharomyces kluyveri) strains. We determined the complete mt genome sequences of strains isolated from various geographical locations (in North America, Asia, and Europe) and ecological niches (Drosophila, tree exudates, soil). The mt genome of the NCYC 543 reference strain is 51,525 bp long. It contains the same core of genes as Lachancea thermotolerans, the nearest relative to L. kluyveri. To explore the mt genome variations in a single yeast species, we compared the mtDNAs of the 18 isolates. The phylogeny and population structure of L. kluyveri provide clear-cut evidence for the existence of well-defined geographically isolated lineages. Although these genomes are completely syntenic, their size and the intron content were found to vary among the isolates studied. These genomes are highly polymorphic, showing an average diversity of 28.5 SNPs/kb and 6.6 indels/kb. Analysis of the SNP and indel patterns showed the existence of a particularly high overall level of polymorphism in the intergenic regions. The dN/dS ratios obtained are consistent with purifying selection in all these genes, with the noteworthy exception of the VAR1 gene, which gave a very high ratio. These data suggest that the intergenic regions have evolved very fast in yeast mitochondrial genomes.}, }
@article {pmid22970728, year = {2012}, author = {Yruela, I and Contreras-Moreira, B}, title = {Protein disorder in plants: a view from the chloroplast.}, journal = {BMC plant biology}, volume = {12}, number = {}, pages = {165}, pmid = {22970728}, issn = {1471-2229}, mesh = {Amino Acid Sequence ; Cell Nucleus/genetics/*metabolism ; Chloroplast Proteins/genetics/*metabolism ; Chloroplasts/genetics/*metabolism ; Computational Biology ; Evolution, Molecular ; *Genome, Plant ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Nuclear Proteins/genetics/metabolism ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plants/genetics/*metabolism ; Protein Transport ; Ribosomal Proteins/genetics/metabolism ; }, abstract = {BACKGROUND: The intrinsically unstructured state of some proteins, observed in all living organisms, is essential for basic cellular functions. In this field the available information from plants is limited but it has been reached a point where these proteins can be comprehensively classified on the basis of disorder, function and evolution.<br><br>RESULTS: Our analysis of plant genomes confirms that nuclear-encoded proteins follow the same trend than other multi-cellular eukaryotes; however, chloroplast- and mitochondria- encoded proteins conserve the patterns of Archaea and Bacteria, in agreement with their phylogenetic origin. Based on current knowledge about gene transference from the chloroplast to the nucleus, we report a strong correlation between the rate of disorder of transferred and nuclear-encoded proteins, even for polypeptides that play functional roles back in the chloroplast. We further investigate this trend by reviewing the set of chloroplast ribosomal proteins, one of the most representative transferred gene clusters, finding that the ribosomal large subunit, assembled from a majority of nuclear-encoded proteins, is clearly more unstructured than the small one, which integrates mostly plastid-encoded proteins.<br><br>CONCLUSIONS: Our observations suggest that the evolutionary dynamics of the plant nucleus adds disordered segments to genes alike, regardless of their origin, with the notable exception of proteins currently encoded in both genomes, probably due to functional constraints.}, }
@article {pmid22970129, year = {2012}, author = {de Saint Pierre, M and Bravi, CM and Motti, JM and Fuku, N and Tanaka, M and Llop, E and Bonatto, SL and Moraga, M}, title = {An alternative model for the early peopling of southern South America revealed by analyses of three mitochondrial DNA haplogroups.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e43486}, pmid = {22970129}, issn = {1932-6203}, mesh = {Base Sequence ; Bayes Theorem ; DNA, Mitochondrial/*genetics ; *Emigration and Immigration ; Ethnicity/genetics ; Genetic Variation ; *Genetics, Population ; Haplotypes/*genetics ; Humans ; Mitochondria/genetics ; *Models, Biological ; Molecular Sequence Data ; Mutation Rate ; Nucleic Acid Conformation ; Phylogeny ; South America ; Time Factors ; }, abstract = {After several years of research, there is now a consensus that America was populated from Asia through Beringia, probably at the end of the Pleistocene. But many details such as the timing, route(s), and origin of the first settlers remain uncertain. In the last decade genetic evidence has taken on a major role in elucidating the peopling of the Americas. To study the early peopling of South America, we sequenced the control region of mitochondrial DNA from 300 individuals belonging to indigenous populations of Chile and Argentina, and also obtained seven complete mitochondrial DNA sequences. We identified two novel mtDNA monophyletic clades, preliminarily designated B2l and C1b13, which together with the recently described D1g sub-haplogroup have locally high frequencies and are basically restricted to populations from the extreme south of South America. The estimated ages of D1g and B2l, about ~15,000 years BP, together with their similar population dynamics and the high haplotype diversity shown by the networks, suggests that they probably appeared soon after the arrival of the first settlers and agrees with the dating of the earliest archaeological sites in South America (Monte Verde, Chile, 14,500 BP). One further sub-haplogroup, D4h3a5, appears to be restricted to Fuegian-Patagonian populations and reinforces our hypothesis of the continuity of the current Patagonian populations with the initial founders. Our results indicate that the extant native populations inhabiting South Chile and Argentina are a group which had a common origin, and suggest a population break between the extreme south of South America and the more northern part of the continent. Thus the early colonization process was not just an expansion from north to south, but also included movements across the Andes.}, }
@article {pmid22968790, year = {2012}, author = {Zilberg, D and Jones, JB and Burger, MA and Nicholls, PK and Nolan, D and Crockford, M and Stephens, F}, title = {New pathological condition in cultured mulloway Argyrosomus japonicus: histopathological, ultrastructural and molecular studies.}, journal = {Diseases of aquatic organisms}, volume = {100}, number = {3}, pages = {219-230}, doi = {10.3354/dao02495}, pmid = {22968790}, issn = {0177-5103}, mesh = {Animals ; Aquaculture ; Fish Diseases/*pathology ; Kidney/pathology ; Kidney Diseases/pathology/*veterinary ; Myxozoa/classification/genetics/isolation &amp; purification ; Parasitic Diseases, Animal/*parasitology/pathology ; *Perciformes ; Phylogeny ; }, abstract = {Mulloway Argyrosomus japonicus is a native fish species in Western Australia, for which aquaculture production has recently been developed. A single cohort was stocked in a cage offshore at Geraldton, Western Australia, at a water depth of 6 m. Fish appeared healthy before stocking. Routine histological analysis was carried out from 10 mo post stocking and until completion of harvest (about 2.5 yr post stocking). No gross pathology was evident. Microscopically, however, granulomatous lesions were present in the kidneys of almost 100% of the fish examined. Enclosed in the granuloma was an aggregate of organisms, 4.2 to 5.4 µm in diameter. Kidney granulomas appeared as multi-focal aggregates. Granulomas at different stages of formation and finally fibrosing granulomas were observed. Granulomas also appeared infrequently in other organs: a few granulomas were found in the liver and spleen and a single granuloma in the heart of one fish. Transmission electron microscopy (TEM) revealed that the organism was composed of 2 cells, an outer cell enclosing an inner cell. The inner cell was surrounded by a double membrane and the outer cell by a single membrane. Cellular material, presumably of parasitic nature, surrounded the outer cell. The organism contained primitive mitochondria and abundant free ribosomes. Small subunit ribosomal DNA (SSU rDNA) sequence obtained by PCR revealed an 84% sequence identity with the myxosporean Latyspora scomberomori. Based on TEM and preliminary molecular results, we suggest that the organism is the extrasporogonic developmental stage of a myxozoan parasite, which failed to form spores in the mulloway host.}, }
@article {pmid22963522, year = {2012}, author = {Daimon, T and Yago, M and Hsu, YF and Fujii, T and Nakajima, Y and Kokusho, R and Abe, H and Katsuma, S and Shimada, T}, title = {Molecular phylogeny, laboratory rearing, and karyotype of the bombycid moth, Trilocha varians.}, journal = {Journal of insect science (Online)}, volume = {12}, number = {}, pages = {49}, pmid = {22963522}, issn = {1536-2442}, mesh = {Animals ; Cell Nucleus/genetics ; Female ; Japan ; Karyotype ; Male ; Mitochondria/genetics ; Moths/*genetics/*growth &amp; development ; Phylogeny ; Sex Chromosomes/genetics ; Taiwan ; }, abstract = {This study describes the molecular phylogeny, laboratory rearing, and karyotype of a bombycid moth, Trilocha varians (F. Walker) (Lepidoptera: Bombycidae), which feeds on leaves of Ficus spp. (Rosales: Moraceae). The larvae of this species were collected in Taipei city, Taiwan, and the Ryukyu Archipelago (Ishigaki and Okinawa Islands, Japan). Molecular phylogenetic analyses revealed that T. varians belongs to the subfamily Bombycinae, thus showing a close relationship to the domesticated silkworm Bombyx mori (L.), a lepidopteran model insect. A laboratory method was developed for rearing T. varians and the time required for development from the embryo to adult was determined. From oviposition to adult emergence, the developmental zero was 10.47 °C and total effective temperature was 531.2 day-degrees, i.e., approximately 30 days for one generation when reared at 28 °C. The haploid of T. varians consisted of n = 26 chromosomes. In highly polyploid somatic nuclei, females showed a large heterochromatin body, indicating that the sex chromosome system in T. varians is WZ/ZZ (female/male). The results of the present study should facilitate the utilization of T. varians as a reference species for B. mori, thereby leading to a greater understanding of the ecology and evolution of bombycid moths.}, }
@article {pmid22962606, year = {2012}, author = {Wang, Z and Zheng, J and Zhang, X and Peng, J and Liu, J and Huang, Y}, title = {Identification and sequence analysis of metazoan tRNA 3'-end processing enzymes tRNase Zs.}, journal = {PloS one}, volume = {7}, number = {9}, pages = {e44264}, pmid = {22962606}, issn = {1932-6203}, mesh = {Alternative Splicing ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cell Nucleus/*enzymology/genetics ; Endoribonucleases/*chemistry/genetics/metabolism ; Humans ; Isoenzymes/chemistry/genetics/metabolism ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; *RNA 3' End Processing ; RNA Precursors/metabolism ; RNA, Transfer/*metabolism ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {tRNase Z is the endonuclease responsible for removing the 3'-trailer sequences from precursor tRNAs, a prerequisite for the addition of the CCA sequence. It occurs in the short (tRNase Z(S)) and long (tRNase Z(L)) forms. Here we report the identification and sequence analysis of candidate tRNase Zs from 81 metazoan species. We found that the vast majority of deuterostomes, lophotrochozoans and lower metazoans have one tRNase Z(S) and one tRNase Z(L) genes, whereas ecdysozoans possess only a single tRNase Z(L) gene. Sequence analysis revealed that in metazoans, a single nuclear tRNase Z(L) gene is likely to encode both the nuclear and mitochondrial forms of tRNA 3'-end processing enzyme through mechanisms that include alternative translation initiation from two in-frame start codons and alternative splicing. Sequence conservation analysis revealed a variant PxKxRN motif, PxPxRG, which is located in the N-terminal region of tRNase Z(S)s. We also identified a previously unappreciated motif, AxDx, present in the C-terminal region of both tRNase Z(S)s and tRNase Z(L)s. The AxDx motif consisting mainly of a very short loop is potentially close enough to form hydrogen bonds with the loop containing the PxKxRN or PxPxRG motif. Through complementation analysis, we demonstrated the likely functional importance of the AxDx motif. In conclusion, our analysis supports the notion that in metazoans a single tRNase Z(L) has evolved to participate in both nuclear and mitochondrial tRNA 3'-end processing, whereas tRNase Z(S) may have evolved new functions. Our analysis also unveils new evolutionarily conserved motifs in tRNase Zs, including the C-terminal AxDx motif, which may have functional significance.}, }
@article {pmid22959613, year = {2012}, author = {Webb, CT and Heinz, E and Lithgow, T}, title = {Evolution of the β-barrel assembly machinery.}, journal = {Trends in microbiology}, volume = {20}, number = {12}, pages = {612-620}, doi = {10.1016/j.tim.2012.08.006}, pmid = {22959613}, issn = {1878-4380}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/chemistry/metabolism ; Bacterial Outer Membrane Proteins/*metabolism ; Cell Membrane/chemistry/metabolism ; Evolution, Molecular ; Humans ; Models, Biological ; Models, Molecular ; Organelles/chemistry/metabolism ; Plants ; *Protein Multimerization ; }, abstract = {Proteins from the Omp85 family have roles in membrane biogenesis, and the archetypal protein of this family is the bacterial outer membrane protein BamA. Through evolution, BamA has acquired membrane protein partner subunits, but distinct partner subunits are evident in the various bacterial lineages. As a result, experimental work on several species of bacteria has revealed varietal forms of the β-barrel assembly machinery (BAM complex). This scenario extends even into mitochondria and plastids, organelles of eukaryotic cells that evolved from intracellular bacterial ancestors. In addition to the BAM complex, other molecular machines, namely the two-partner secretion system (TPS) and the translocation and assembly module (the TAM), probably evolved from gene duplication events involving BamA. We discuss what is known about the diverse composition of the BAM complex in various bacterial lineages, and how this diversity impacts on our understanding of the mechanism underlying the assembly of bacterial outer membranes.}, }
@article {pmid22954310, year = {2013}, author = {Terencio, ML and Schneider, CH and Gross, MC and Feldberg, E and Porto, JI}, title = {Structure and organization of the mitochondrial DNA control region with tandemly repeated sequence in the Amazon ornamental fish.}, journal = {Mitochondrial DNA}, volume = {24}, number = {1}, pages = {74-82}, doi = {10.3109/19401736.2012.717934}, pmid = {22954310}, issn = {1940-1744}, mesh = {Animals ; Base Sequence ; Brazil ; Characiformes/*genetics ; DNA, Mitochondrial/chemistry/*genetics ; Evolution, Molecular ; Minisatellite Repeats/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Tandem Repeat Sequences/genetics ; }, abstract = {Tandemly repeated sequences are a common feature of vertebrate mitochondrial DNA control regions. However, questions still remain about their mode of evolution and function. To better understand patterns of variation in length and to explore the existence of previously described domain, we have characterized the control region structure of the Amazonian ornamental fish Nannostomus eques and Nannostomus unifasciatus. The control region ranged from 1121 to 1142 bp in length and could be separated into three domains: the domain associated with the extended terminal associated sequences, the central conserved domain, and the conserved sequence blocks domain. In the first domain, we encountered a sequence repeated 10 times in tandem (variable number tandem repeat (VNTR)) that could adopt an "inverted repetitions" type structural conformation. The results suggest that the VNTR pattern encountered in both N. eques and N. unifasciatus is consistent with the prerequisites of the illegitimate elongation model in which the unequal pairing of the chains near the 5'-end of the control region favors the formation of repetitions.}, }
@article {pmid22952398, year = {2012}, author = {Gray, MW}, title = {Mitochondrial evolution.}, journal = {Cold Spring Harbor perspectives in biology}, volume = {4}, number = {9}, pages = {a011403}, pmid = {22952398}, issn = {1943-0264}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {*Biological Evolution ; Evolution, Molecular ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Models, Biological ; Phylogeny ; Proteome ; Symbiosis ; }, abstract = {Viewed through the lens of the genome it contains, the mitochondrion is of unquestioned bacterial ancestry, originating from within the bacterial phylum α-Proteobacteria (Alphaproteobacteria). Accordingly, the endosymbiont hypothesis--the idea that the mitochondrion evolved from a bacterial progenitor via symbiosis within an essentially eukaryotic host cell--has assumed the status of a theory. Yet mitochondrial genome evolution has taken radically different pathways in diverse eukaryotic lineages, and the organelle itself is increasingly viewed as a genetic and functional mosaic, with the bulk of the mitochondrial proteome having an evolutionary origin outside Alphaproteobacteria. New data continue to reshape our views regarding mitochondrial evolution, particularly raising the question of whether the mitochondrion originated after the eukaryotic cell arose, as assumed in the classical endosymbiont hypothesis, or whether this organelle had its beginning at the same time as the cell containing it.}, }
@article {pmid22952250, year = {2012}, author = {Azzabi, G and Pinnola, A and Betterle, N and Bassi, R and Alboresi, A}, title = {Enhancement of non-photochemical quenching in the Bryophyte Physcomitrella patens during acclimation to salt and osmotic stress.}, journal = {Plant &amp; cell physiology}, volume = {53}, number = {10}, pages = {1815-1825}, doi = {10.1093/pcp/pcs124}, pmid = {22952250}, issn = {1471-9053}, mesh = {*Acclimatization ; Bryopsida/drug effects/*physiology ; Chloroplasts/drug effects/metabolism ; Droughts ; Light ; Osmotic Pressure ; Oxidative Stress ; Plant Proteins/metabolism ; Salt Tolerance ; Sodium Chloride/pharmacology ; Sorbitol/pharmacology ; Thylakoid Membrane Proteins/metabolism ; Thylakoids/metabolism ; Xanthophylls/metabolism ; Zeaxanthins ; }, abstract = {Drought and salt stress are major abiotic constraints affecting plant growth worldwide. Under these conditions, the production of reactive oxygen species (ROS) is a common phenomenon taking place mainly in chloroplasts, peroxisomes, mitochondria and apoplasts, especially when associated with high light stress. ROS are harmful because of their high reactivity to cell components, thereby leading to cytotoxicity and cell death. During the Ordovician and early Devonian period, photosynthetic organisms colonized terrestrial habitats, and the acquisition of desiccation tolerance has been a major component of their evolution. We have studied the capacity for acclimation to drought and salt stress of the moss Physcomitrella patens, a representative of the early land colonization stage. Exposure to high concentrations of NaCl and sorbitol strongly affects chloroplast development, the Chl content and the thylakoid protein composition in this moss. Under sublethal conditions (0.2 M NaCl and 0.4 M sorbitol), the photosynthetic apparatus of P. patens responds to oxidative stress by increasing non-photochemical quenching (NPQ). Surprisingly, the accumulation of PSBS and LHCSR, the two polypeptides essential for NPQ in P. patens, was not up-regulated in these conditions. Rather, an increased NPQ amplitude correlated with the overaccumulation of zeaxanthin and the presence of the enzyme violaxanthin de-epoxidase. These results suggest that the regulation of excess energy dissipation through control of PSBS and LHCSR is mainly driven by light conditions, while osmotic and salt stress act through acclimative regulation of the xanthophyll cycle. We conclude that regulation of the xanthophyll cycle is an important anticipatory strategy against photoinhibition by high light.}, }
@article {pmid22949873, year = {2012}, author = {Zhang, R and Huang, X and Jiang, L and Lei, F and Qiao, G}, title = {Species differentiation of Chinese mollitrichosiphum (Aphididae: greenideinae) driven by geographical isolation and host plant acquirement.}, journal = {International journal of molecular sciences}, volume = {13}, number = {8}, pages = {10441-10460}, pmid = {22949873}, issn = {1422-0067}, mesh = {Animals ; Aphids/*classification/*genetics ; Cell Nucleus/metabolism ; Cytochromes b/*genetics ; DNA/genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Fagaceae/*genetics ; Genetic Variation/genetics ; Geography ; Haplotypes/genetics ; Mitochondria/metabolism ; Peptide Elongation Factor 1/*genetics ; Species Specificity ; }, abstract = {The impact of both the uplift of the Qinghai-Tibetan Plateau (QTP) and the separation of the Taiwan and Hainan Islands on the evolution of the fauna and flora in adjacent regions has been a topic of considerable interest. Mollitrichosiphum is a polyphagous insect group with a wide range of host plants (14 families) and distributions restricted to Southeast Asia. Based on the mitochondrial Cytochrome C Oxidase Subunit I (COI) and Cytochrome b (Cytb) genes, the nuclear elongation factor-1α (EF-1α) gene, and the detailed distribution and host plant data, we investigated the species differentiation modes of the Chinese Mollitrichosiphum species. Phylogenetic analyses supported the monophyly of Mollitrichosiphum. The divergence time of Mollitrichosiphum tenuicorpus (c. 11.0 mya (million years ago)), Mollitrichosiphum nandii and Mollitrichosiphum montanum (c. 10.6 mya) was within the time frame of the uplift of the QTP. Additionally, basal species mainly fed on Fagaceae, while species that fed on multiple plants diverged considerably later. Ancestral state reconstruction suggests that Fagaceae may be the first acquired host, and the acquisition of new hosts and the expansion of host range may have promoted species differentiation within this genus. Overall, it can be concluded that geographical isolation and the expansion of the host plant range may be the main factors driving species differentiation of Mollitrichosiphum.}, }
@article {pmid22943112, year = {2012}, author = {Selva Kumar, C and Nair, RR and Sivaramakrishnan, KG and Ganesh, D and Janarthanan, S and Arunachalam, M and Sivaruban, T}, title = {Influence of certain forces on evolution of synonymous codon usage bias in certain species of three basal orders of aquatic insects.}, journal = {Mitochondrial DNA}, volume = {23}, number = {6}, pages = {447-460}, doi = {10.3109/19401736.2012.710203}, pmid = {22943112}, issn = {1940-1744}, mesh = {Animals ; Aquatic Organisms/genetics ; Base Sequence ; Codon/*genetics ; Ecosystem ; Genes, Mitochondrial ; Genetic Code/genetics/physiology ; *Genetic Speciation ; Insecta/classification/*genetics ; Odonata/classification/genetics ; Open Reading Frames/genetics ; Phylogeny ; Selection, Genetic/physiology ; }, abstract = {Forces that influence the evolution of synonymous codon usage bias are analyzed in six species of three basal orders of aquatic insects. The rationale behind choosing six species of aquatic insects (three from Ephemeroptera, one from Plecoptera, and two from Odonata) for the present analysis is based on phylogenetic position at the basal clades of the Order Insecta facilitating the understanding of the evolution of codon bias and of factors shaping codon usage patterns in primitive clades of insect lineages and their subtle differences in some of their ecological and environmental requirements in terms of habitat-microhabitat requirements, altitudinal preferences, temperature tolerance ranges, and consequent responses to climate change impacts. The present analysis focuses on open reading frames of the 13 protein-coding genes in the mitochondrial genome of six carefully chosen insect species to get a comprehensive picture of the evolutionary intricacies of codon bias. In all the six species, A and T contents are observed to be significantly higher than G and C, and are used roughly equally. Since transcription hypothesis on codon usage demands A richness and T poorness, it is quite likely that mutation pressure may be the key factor associated with synonymous codon usage (SCU) variations in these species because the mutation hypothesis predicts AT richness and GC poorness in the mitochondrial DNA. Thus, AT-biased mutation pressure seems to be an important factor in framing the SCU variation in all the selected species of aquatic insects, which in turn explains the predominance of A and T ending codons in these species. This study does not find any association between microhabitats and codon usage variations in the mitochondria of selected aquatic insects. However, this study has identified major forces, such as compositional constraints and mutation pressure, which shape patterns of codon usage in mitochondrial genes in the primitive clades of insect lineages.}, }
@article {pmid22942688, year = {2012}, author = {Jiang, JH and Tong, J and Tan, KS and Gabriel, K}, title = {From evolution to pathogenesis: the link between β-barrel assembly machineries in the outer membrane of mitochondria and gram-negative bacteria.}, journal = {International journal of molecular sciences}, volume = {13}, number = {7}, pages = {8038-8050}, pmid = {22942688}, issn = {1422-0067}, mesh = {Animals ; Bacterial Outer Membrane Proteins/chemistry/*metabolism ; Evolution, Molecular ; Gram-Negative Bacteria/*metabolism ; Humans ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; Protein Folding ; Protein Structure, Secondary ; Protein Transport ; }, abstract = {β-barrel proteins are the highly abundant in the outer membranes of Gram-negative bacteria and the mitochondria in eukaryotes. The assembly of β-barrels is mediated by two evolutionary conserved machineries; the β-barrel Assembly Machinery (BAM) in Gram-negative bacteria; and the Sorting and Assembly Machinery (SAM) in mitochondria. Although the BAM and SAM have functionally conserved roles in the membrane integration and folding of β-barrel proteins, apart from the central BamA and Sam50 proteins, the remaining components of each of the complexes have diverged remarkably. For example all of the accessory components of the BAM complex characterized to date are located in the bacterial periplasm, on the same side as the N-terminal domain of BamA. This is the same side of the membrane as the substrates that are delivered to the BAM. On the other hand, all of the accessory components of the SAM complex are located on the cytosolic side of the membrane, the opposite side of the membrane to the N-terminus of Sam50 and the substrate receiving side of the membrane. Despite the accessory subunits being located on opposite sides of the membrane in each system, it is clear that each system is functionally equivalent with bacterial proteins having the ability to use the eukaryotic SAM and vice versa. In this review, we summarize the similarities and differences between the BAM and SAM complexes, highlighting the possible selecting pressures on bacteria and eukaryotes during evolution. It is also now emerging that bacterial pathogens utilize the SAM to target toxins and effector proteins to host mitochondria and this will also be discussed from an evolutionary perspective.}, }
@article {pmid22933312, year = {2012}, author = {Venton, D}, title = {Highlight: "keeping the boys in the conversation: male fitness shapes the location of genes that interact with mitochondria".}, journal = {Genome biology and evolution}, volume = {4}, number = {8}, pages = {769-770}, pmid = {22933312}, issn = {1759-6653}, mesh = {Animals ; *Epistasis, Genetic ; *Evolution, Molecular ; Female ; Male ; Mammals/*genetics ; Mitochondria/*genetics ; X Chromosome/*genetics ; }, }
@article {pmid22928879, year = {2012}, author = {Ginger, ML and Sam, KA and Allen, JW}, title = {Probing why trypanosomes assemble atypical cytochrome c with an AxxCH haem-binding motif instead of CxxCH.}, journal = {The Biochemical journal}, volume = {448}, number = {2}, pages = {253-260}, doi = {10.1042/BJ20120757}, pmid = {22928879}, issn = {1470-8728}, support = {BB/D019753/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Motifs ; Base Sequence ; Binding Sites ; Crithidia fasciculata/genetics/*metabolism ; Cytochromes c/*chemistry/genetics/*metabolism ; DNA Primers/genetics ; Electron Transport ; Evolution, Molecular ; Heme/chemistry ; Protozoan Proteins/*chemistry/genetics/*metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Spectrometry, Mass, Electrospray Ionization ; Trypanosoma brucei brucei/genetics/*metabolism ; }, abstract = {Mitochondrial cytochromes c and c1 are core components of the respiratory chain of all oxygen-respiring eukaryotes. These proteins contain haem, covalently bound to the polypeptide in a catalysed post-translational modification. In all eukaryotes, except members of the protist phylum Euglenozoa, haem attachment is to the cysteine residues of a CxxCH haem-binding motif. In the Euglenozoa, which include medically relevant trypanosomatid parasites, haem attachment is to a single cysteine residue in an AxxCH haem-binding motif. Moreover, genes encoding known c-type cytochrome biogenesis machineries are all absent from trypanosomatid genomes, indicating the presence of a novel biosynthetic apparatus. In the present study, we investigate expression and maturation of cytochrome c with a typical CxxCH haem-binding motif in the trypanosomatids Crithidia fasciculata and Trypanosoma brucei. Haem became attached to both cysteine residues of the haem-binding motif, indicating that, in contrast with previous hypotheses, nothing prevents formation of a CxxCH cytochrome c in euglenozoan mitochondria. The cytochrome variant was also able to replace the function of wild-type cytochrome c in T. brucei. However, the haem attachment to protein was not via the stereospecifically conserved linkage universally observed in natural c-type cytochromes, suggesting that the trypanosome cytochrome c biogenesis machinery recognized and processed only the wild-type single-cysteine haem-binding motif. Moreover, the presence of the CxxCH cytochrome c resulted in a fitness cost in respiration. The level of cytochrome c biogenesis in trypanosomatids was also found to be limited, with the cells operating at close to maximum capacity.}, }
@article {pmid22925885, year = {2012}, author = {Nagaraj, R and Gururaja-Rao, S and Jones, KT and Slattery, M and Negre, N and Braas, D and Christofk, H and White, KP and Mann, R and Banerjee, U}, title = {Control of mitochondrial structure and function by the Yorkie/YAP oncogenic pathway.}, journal = {Genes &amp; development}, volume = {26}, number = {18}, pages = {2027-2037}, pmid = {22925885}, issn = {1549-5477}, support = {R01 EY008152/EY/NEI NIH HHS/United States ; R01EY008152/EY/NEI NIH HHS/United States ; }, mesh = {Animals ; Cell Proliferation ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster/cytology/genetics/metabolism ; Gene Expression Profiling ; Humans ; Mitochondria/*metabolism/ultrastructure ; Nuclear Proteins/genetics/*metabolism ; Phenotype ; Trans-Activators/genetics/*metabolism ; YAP-Signaling Proteins ; }, abstract = {Mitochondrial structure and function are highly dynamic, but the potential roles for cell signaling pathways in influencing these properties are not fully understood. Reduced mitochondrial function has been shown to cause cell cycle arrest, and a direct role of signaling pathways in controlling mitochondrial function during development and disease is an active area of investigation. Here, we show that the conserved Yorkie/YAP signaling pathway implicated in the control of organ size also functions in the regulation of mitochondria in Drosophila as well as human cells. In Drosophila, activation of Yorkie causes direct transcriptional up-regulation of genes that regulate mitochondrial fusion, such as opa1-like (opa1) and mitochondria assembly regulatory factor (Marf), and results in fused mitochondria with dramatic reduction in reactive oxygen species (ROS) levels. When mitochondrial fusion is genetically attenuated, the Yorkie-induced cell proliferation and tissue overgrowth are significantly suppressed. The function of Yorkie is conserved across evolution, as activation of YAP2 in human cell lines causes increased mitochondrial fusion. Thus, mitochondrial fusion is an essential and direct target of the Yorkie/YAP pathway in the regulation of organ size control during development and could play a similar role in the genesis of cancer.}, }
@article {pmid22923466, year = {2013}, author = {Danne, JC and Gornik, SG and Macrae, JI and McConville, MJ and Waller, RF}, title = {Alveolate mitochondrial metabolic evolution: dinoflagellates force reassessment of the role of parasitism as a driver of change in apicomplexans.}, journal = {Molecular biology and evolution}, volume = {30}, number = {1}, pages = {123-139}, doi = {10.1093/molbev/mss205}, pmid = {22923466}, issn = {1537-1719}, mesh = {Adenosine Triphosphate/biosynthesis/genetics ; Amino Acids/metabolism ; Apicomplexa/classification/*genetics/*parasitology ; DNA, Complementary ; Dinoflagellida/classification/*genetics ; Electron Transport Chain Complex Proteins/genetics/metabolism ; Evolution, Molecular ; Genes, Mitochondrial ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/metabolism ; Sequence Analysis, RNA ; Tetrapyrroles/biosynthesis ; Transcriptome ; Tricarboxylic Acids/metabolism ; }, abstract = {Mitochondrial metabolism is central to the supply of ATP and numerous essential metabolites in most eukaryotic cells. Across eukaryotic diversity, however, there is evidence of much adaptation of the function of this organelle according to specific metabolic requirements and/or demands imposed by different environmental niches. This includes substantial loss or retailoring of mitochondrial function in many parasitic groups that occupy potentially nutrient-rich environments in their metazoan hosts. Infrakingdom Alveolata comprises a well-supported alliance of three disparate eukaryotic phyla-dinoflagellates, apicomplexans, and ciliates. These major taxa represent diverse lifestyles of free-living phototrophs, parasites, and predators and offer fertile territory for exploring character evolution in mitochondria. The mitochondria of apicomplexan parasites provide much evidence of loss or change of function from analysis of mitochondrial protein genes. Much less, however, is known of mitochondrial function in their closest relatives, the dinoflagellate algae. In this study, we have developed new models of mitochondrial metabolism in dinoflagellates based on gene predictions and stable isotope labeling experiments. These data show that many changes in mitochondrial gene content previously only known from apicomplexans are found in dinoflagellates also. For example, loss of the pyruvate dehydrogenase complex and changes in tricarboxylic acid (TCA) cycle enzyme complement are shared by both groups and, therefore, represent ancestral character states. Significantly, we show that these changes do not result in loss of typical TCA cycle activity fueled by pyruvate. Thus, dinoflagellate data show that many changes in alveolate mitochondrial metabolism are independent of the major lifestyle changes seen in these lineages and provide a revised view of mitochondria character evolution during evolution of parasitism in apicomplexans.}, }
@article {pmid22923044, year = {2012}, author = {Anderson, MZ and Baller, JA and Dulmage, K and Wigen, L and Berman, J}, title = {The three clades of the telomere-associated TLO gene family of Candida albicans have different splicing, localization, and expression features.}, journal = {Eukaryotic cell}, volume = {11}, number = {10}, pages = {1268-1275}, pmid = {22923044}, issn = {1535-9786}, support = {R01 AI075096/AI/NIAID NIH HHS/United States ; AI075096-03S1/AI/NIAID NIH HHS/United States ; }, mesh = {Candida albicans/*genetics/metabolism ; Cell Nucleus/metabolism ; Fungal Proteins/*genetics/metabolism ; Introns ; Mediator Complex/genetics/metabolism ; Mitochondria/metabolism ; *Multigene Family ; Phylogeny ; Protein Subunits/genetics/metabolism ; RNA Splicing ; Telomere-Binding Proteins/*genetics/metabolism ; Transcription, Genetic ; }, abstract = {Candida albicans grows within a wide range of host niches, and this adaptability enhances its success as a commensal and as a pathogen. The telomere-associated TLO gene family underwent a recent expansion from one or two copies in other CUG clade members to 14 expressed copies in C. albicans. This correlates with increased virulence and clinical prevalence relative to those of other Candida clade species. The 14 expressed TLO gene family members have a conserved Med2 domain at the N terminus, suggesting a role in general transcription. The C-terminal half is more divergent, distinguishing three clades: clade α and clade β have no introns and encode proteins that localize primarily to the nucleus; clade γ sometimes undergoes splicing, and the gene products localize within the mitochondria as well as the nuclei. Additionally, TLOα genes are generally expressed at much higher levels than are TLOγ genes. We propose that expansion of the TLO gene family and the predicted role of Tlo proteins in transcription regulation provide C. albicans with the ability to adapt rapidly to the broad range of different environmental niches within the human host.}, }
@article {pmid22920973, year = {2012}, author = {Hooks, KB and Turner, JE and Graham, IA and Runions, J and Hooks, MA}, title = {GFP-tagging of Arabidopsis acyl-activating enzymes raises the issue of peroxisome-chloroplast import competition versus dual localization.}, journal = {Journal of plant physiology}, volume = {169}, number = {16}, pages = {1631-1638}, doi = {10.1016/j.jplph.2012.05.026}, pmid = {22920973}, issn = {1618-1328}, support = {P19408//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Arabidopsis/*enzymology/genetics/radiation effects/ultrastructure ; Arabidopsis Proteins/metabolism ; Chloroplasts/enzymology/*metabolism ; Coenzyme A Ligases/*metabolism ; Cytosol/enzymology/metabolism ; Green Fluorescent Proteins ; Light ; Luminescent Agents ; Microscopy, Confocal ; Mitochondria/enzymology/*metabolism ; Molecular Sequence Data ; Mutation ; Peroxisomes/enzymology/*metabolism ; Phenotype ; Phylogeny ; Plants, Genetically Modified ; Protein Transport ; Recombinant Fusion Proteins/genetics/metabolism ; Seedlings/enzymology/genetics/radiation effects/ultrastructure ; Sequence Alignment ; }, abstract = {Protein sequence analysis of a subfamily of 18 Arabidopsis acyl-activating enzymes (AAE) for organelle targeting signals revealed that eight of them possessed putative peroxisomal targeting signals (PTS1), five of which belonged to Clade VI of the AAE superfamily. Peroxisomal localization was confirmed by confocal microscopy of green fluorescent protein (GFP)-AAE fusion proteins co-localizing with peroxisomal RFP. The sequence analysis also revealed that all enzymes of Clade VI possess N-terminal regions indicative of chloroplast transit peptides (cTP). Among the five Clade VI peroxisomal enzymes tested, masking the PTS1 signal with GFP redirected three to plastids. In addition, three other peroxisomal AAEs appeared to be redirected to plastids in AAE-GFP fusion constructs. Due to the lack of evidence supporting plastid localization, we propose that competition dictates the exclusive localization to peroxisomes. AAE2 of Clade VI was the only enzyme with a putative mitochondrial targeting sequence, and it appeared to be targeted to mitochondria. The remainder of the AAEs appeared to be localized to plastids or cytosol. The AAE9-GFP fusion protein appeared to be located within discreet structures within plastids that may be plastoglobules. AAE15-GFP, but not AAE16-GFP appeared to be located in the chloroplast envelope. The number of examples is increasing whereby proteins located within other compartments contribute to plastid function. We provide an example of this through the light-sensitive phenotype of mutants of AAE2.}, }
@article {pmid22917911, year = {2012}, author = {Cao, LF and Niu, DF and He, SY and Kuang, HO and Hu, FL}, title = {[Phylogenetic relationships of honey bees (Hymenoptera: Apinae) inferred from mitochondrial and nuclear DNA sequences].}, journal = {Yi chuan = Hereditas}, volume = {34}, number = {8}, pages = {1057-1063}, doi = {10.3724/sp.j.1005.2012.01057}, pmid = {22917911}, issn = {0253-9772}, mesh = {Animals ; *Base Sequence ; Bees/*genetics ; DNA, Mitochondrial/*genetics ; *Genes, Insect ; Insect Proteins/*genetics ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Phylogeny ; Species Specificity ; }, abstract = {The sequences of mitochondrial ND2, CO2, and 16S rRNA genes and nuclear ITPR gene were obtained from 22 samples of 5 Apis species from China. The characteristics of the sequences and the pairwise distances among species were analyzed. Phylogenetic trees were reconstructed for Apis species using maximum parsimony, neighbor-joining and maximum likelihood methods together with the sequences of the other 4 Apis species downloaded from GenBank. Results supported that Apis species were divided into three major clusters: dwarf bees (A. florea and A. andreniformis), giant bees (A. dorsata and A. laboriosa), and cavity-nesting bees (A. mellifera, A. cerana, A. koschevnikovi, A. nigrocinta, and A. nuluensis). The dwarf honey bees were confirmed as basal lineage. Our study also revealed a high level of genetic divergence between A. dorsata from Hainan Island and China mainland.}, }
@article {pmid22916040, year = {2012}, author = {Barkan, A and Rojas, M and Fujii, S and Yap, A and Chong, YS and Bond, CS and Small, I}, title = {A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins.}, journal = {PLoS genetics}, volume = {8}, number = {8}, pages = {e1002910}, pmid = {22916040}, issn = {1553-7404}, mesh = {Amino Acid Sequence ; Base Sequence ; Binding Sites ; Chloroplasts/genetics/*metabolism ; Electrophoretic Mobility Shift Assay ; Evolution, Molecular ; Mitochondria/genetics/*metabolism ; Molecular Sequence Data ; Plant Proteins/*chemistry/genetics/metabolism ; Plants/genetics/metabolism ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Plant/*chemistry/metabolism ; RNA-Binding Proteins/*chemistry/genetics/metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Repetitive Sequences, Amino Acid/*genetics ; Sequence Alignment ; }, abstract = {The pentatricopeptide repeat (PPR) is a helical repeat motif found in an exceptionally large family of RNA-binding proteins that functions in mitochondrial and chloroplast gene expression. PPR proteins harbor between 2 and 30 repeats and typically bind single-stranded RNA in a sequence-specific fashion. However, the basis for sequence-specific RNA recognition by PPR tracts has been unknown. We used computational methods to infer a code for nucleotide recognition involving two amino acids in each repeat, and we validated this model by recoding a PPR protein to bind novel RNA sequences in vitro. Our results show that PPR tracts bind RNA via a modular recognition mechanism that differs from previously described RNA-protein recognition modes and that underpins a natural library of specific protein/RNA partners of unprecedented size and diversity. These findings provide a significant step toward the prediction of native binding sites of the enormous number of PPR proteins found in nature. Furthermore, the extraordinary evolutionary plasticity of the PPR family suggests that the PPR scaffold will be particularly amenable to redesign for new sequence specificities and functions.}, }
@article {pmid22916027, year = {2012}, author = {Bietenhader, M and Martos, A and Tetaud, E and Aiyar, RS and Sellem, CH and Kucharczyk, R and Clauder-Münster, S and Giraud, MF and Godard, F and Salin, B and Sagot, I and Gagneur, J and Déquard-Chablat, M and Contamine, V and Hermann-Le Denmat, S and Sainsard-Chanet, A and Steinmetz, LM and di Rago, JP}, title = {Experimental relocation of the mitochondrial ATP9 gene to the nucleus reveals forces underlying mitochondrial genome evolution.}, journal = {PLoS genetics}, volume = {8}, number = {8}, pages = {e1002876}, pmid = {22916027}, issn = {1553-7404}, mesh = {Biological Evolution ; Cell Nucleus/enzymology/*genetics ; Fungal Proteins/*genetics/metabolism ; Gene Deletion ; Genes, Mitochondrial ; Genome, Mitochondrial ; Mitochondria/enzymology/*genetics ; Mitochondrial Proton-Translocating ATPases/*genetics/metabolism ; Oxidative Phosphorylation ; Podospora/enzymology/*genetics ; Protein Subunits/genetics/metabolism ; Saccharomyces cerevisiae/enzymology/*genetics ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; Transgenes ; }, abstract = {Only a few genes remain in the mitochondrial genome retained by every eukaryotic organism that carry out essential functions and are implicated in severe diseases. Experimentally relocating these few genes to the nucleus therefore has both therapeutic and evolutionary implications. Numerous unproductive attempts have been made to do so, with a total of only 5 successes across all organisms. We have taken a novel approach to relocating mitochondrial genes that utilizes naturally nuclear versions from other organisms. We demonstrate this approach on subunit 9/c of ATP synthase, successfully relocating this gene for the first time in any organism by expressing the ATP9 genes from Podospora anserina in Saccharomyces cerevisiae. This study substantiates the role of protein structure in mitochondrial gene transfer: expression of chimeric constructs reveals that the P. anserina proteins can be correctly imported into mitochondria due to reduced hydrophobicity of the first transmembrane segment. Nuclear expression of ATP9, while permitting almost fully functional oxidative phosphorylation, perturbs many cellular properties, including cellular morphology, and activates the heat shock response. Altogether, our study establishes a novel strategy for allotopic expression of mitochondrial genes, demonstrates the complex adaptations required to relocate ATP9, and indicates a reason that this gene was only transferred to the nucleus during the evolution of multicellular organisms.}, }
@article {pmid22908957, year = {2012}, author = {Ito, M and Tohsato, Y and Sugisawa, H and Kohara, S and Fukuchi, S and Nishikawa, I and Nishikawa, K}, title = {Intrinsically disordered proteins in human mitochondria.}, journal = {Genes to cells : devoted to molecular &amp; cellular mechanisms}, volume = {17}, number = {10}, pages = {817-825}, doi = {10.1111/gtc.12000}, pmid = {22908957}, issn = {1365-2443}, mesh = {Computational Biology/methods ; Databases, Protein ; Enzymes/chemistry/metabolism ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/chemistry/classification/*metabolism ; Protein Sorting Signals ; Protein Transport ; }, abstract = {Intrinsically disordered (ID) proteins (IDPs) are abundant in eukaryotes but are scarce in prokaryotes. Mitochondria, cellular organelles that descended from Rickettsia-like α-proteobacteria, are at the intersection between prokaryotes and eukaryotes. Although IDPs are reportedly as rare in mitochondria as in bacteria, these details remained to be clarified. Human mitochondrial proteins (n = 706) were obtained from the UniProt database, and information on ID regions of all human proteins was extracted from the DICHOT database. A BLAST search carried out against all α-proteobacterial proteins identified two types of mitochondrial proteins: those with (B) and without (E) bacterial homologues. The B-type proteins (n = 387) descended from a bacterial ancestor, whereas the E-type proteins (n = 319) were more recently added to the mitochondria via the host cell during the early evolution of eukaryotes. The average ID ratios of B-type/E-type proteins are 10.3% and 21.4%, respectively. The 706 proteins were further classified into four groups based on the mitochondrial subcompartment, namely, the matrix, intermembrane space, inner membrane, or outer membrane. The ID ratios in these different locations suggest that the frequency of IDPs in mitochondria might be due to the evolutionary origin (B-type/E-type) of the protein, rather than differences in its functional environment.}, }
@article {pmid22903087, year = {2013}, author = {Pichrtová, M and Remias, D and Lewis, LA and Holzinger, A}, title = {Changes in phenolic compounds and cellular ultrastructure of arctic and antarctic strains of Zygnema (Zygnematophyceae, Streptophyta) after exposure to experimentally enhanced UV to PAR ratio.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {68-83}, pmid = {22903087}, issn = {1432-184X}, support = {P 24242/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Antarctic Regions ; Arctic Regions ; Chlorophyll/analysis ; Chlorophyll A ; Chromatography, High Pressure Liquid ; DNA, Plant/genetics ; Microscopy, Electron, Transmission ; Phenols/*analysis ; Photosynthesis/radiation effects ; Photosystem II Protein Complex/radiation effects ; Phylogeny ; Streptophyta/chemistry/*radiation effects/*ultrastructure ; *Ultraviolet Rays ; Xanthophylls/analysis ; }, abstract = {Ultraviolet (UV) radiation has become an important stress factor in polar regions due to anthropogenically induced ozone depletion. Although extensive research has been conducted on adaptations of polar organisms to this stress factor, few studies have focused on semi-terrestrial algae so far, in spite of their apparent vulnerability. This study investigates the effect of UV on two semi-terrestrial arctic strains (B, G) and one Antarctic strain (E) of the green alga Zygnema, isolated from Arctic and Antarctic habitats. Isolates of Zygnema were exposed to experimentally enhanced UV A and B (predominant UV A) to photosynthetic active radiation (PAR) ratio. The pigment content, photosynthetic performance and ultrastructure were studied by means of high-performance liquid chromatography (HPLC), chlorophyll a fluorescence and transmission electron microscopy (TEM). In addition, phylogenetic relationships of the investigated strains were characterised using rbcL sequences, which determined that the Antarctic isolate (E) and one of the Arctic isolates (B) were closely related, while G is a distinct lineage. The production of protective phenolic compounds was confirmed in all of the tested strains by HPLC analysis for both controls and UV-exposed samples. Moreover, in strain E, the content of phenolics increased significantly (p = 0.001) after UV treatment. Simultaneously, the maximum quantum yield of photosystem II photochemistry significantly decreased in UV-exposed strains E and G (p < 0.001), showing a clear stress response. The phenolics were most probably stored at the cell periphery in vacuoles and cytoplasmic bodies that appear as electron-dense particles when observed by TEM after high-pressure freeze fixation. While two strains reacted moderately on UV exposure in their ultrastructure, in strain G, damage was found in chloroplasts and mitochondria. Plastidal pigments and xanthophyll cycle pigments were investigated by HPLC analysis; UV A- and UV B-exposed samples had a higher deepoxidation state as controls, particularly evident in strain B. The results indicate that phenolics are involved in UV protection of Zygnema and also revealed different responses to UV stress across the three strains, suggesting that other protection mechanisms may be involved in these organisms.}, }
@article {pmid22902511, year = {2013}, author = {Huynen, MA and Duarte, I and Szklarczyk, R}, title = {Loss, replacement and gain of proteins at the origin of the mitochondria.}, journal = {Biochimica et biophysica acta}, volume = {1827}, number = {2}, pages = {224-231}, doi = {10.1016/j.bbabio.2012.08.001}, pmid = {22902511}, issn = {0006-3002}, mesh = {Mitochondria/*metabolism ; Oxidative Phosphorylation ; Proteins/*metabolism ; }, abstract = {We review what has been inferred about the changes at the level of the proteome that accompanied the evolution of the mitochondrion from an alphaproteobacterium. We regard these changes from an alphaproteobacterial perspective: which proteins were lost during mitochondrial evolution? And, of the proteins that were lost, which ones have been replaced by other, non-orthologous proteins with a similar function? Combining literature-supported replacements with quantitative analyses of mitochondrial proteomics data we infer that most of the loss and replacements that separate current day mitochondria in mammals from alphaproteobacteria took place before the radiation of the eukaryotes. Recent analyses show that also the acquisition of new proteins to the large protein complexes of the oxidative phosphorylation and the mitochondrial ribosome occurred mainly before the divergence of the eukaryotes. These results indicate a significant number of pivotal evolutionary events between the acquisition of the endosymbiont and the radiation of the eukaryotes and therewith support an early acquisition of mitochondria in eukaryotic evolution. Technically, advancements in the reconstruction of the evolutionary trajectories of loss, replacement and gain of mitochondrial proteins depend on using profile-based homology detection methods for sequence analysis. We highlight the mitochondrial Holliday junction resolvase endonuclease, for which such methods have detected new "family members" and in which function differentiation is accompanied by the loss of catalytic residues for the original enzymatic function and the gain of a protein domain for the new function. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.}, }
@article {pmid22900140, year = {2012}, author = {Valmalette, JC and Dombrovsky, A and Brat, P and Mertz, C and Capovilla, M and Robichon, A}, title = {Light- induced electron transfer and ATP synthesis in a carotene synthesizing insect.}, journal = {Scientific reports}, volume = {2}, number = {}, pages = {579}, pmid = {22900140}, issn = {2045-2322}, mesh = {Adenosine Triphosphate/*biosynthesis ; Animals ; Aphids/genetics/*metabolism ; Carotenoids/*biosynthesis ; *Electron Transport ; Eye/metabolism ; Genes, Insect ; *Light ; Mitochondria/metabolism ; NAD/metabolism ; Phenotype ; Photosynthesis ; Spectrum Analysis, Raman ; }, abstract = {A singular adaptive phenotype of a parthenogenetic insect species (Acyrthosiphon pisum) was selected in cold conditions and is characterized by a remarkable apparition of a greenish colour. The aphid pigments involve carotenoid genes well defined in chloroplasts and cyanobacteria and amazingly present in the aphid genome, likely by lateral transfer during evolution. The abundant carotenoid synthesis in aphids suggests strongly that a major and unknown physiological role is related to these compounds beyond their canonical anti-oxidant properties. We report here that the capture of light energy in living aphids results in the photo induced electron transfer from excited chromophores to acceptor molecules. The redox potentials of molecules involved in this process would be compatible with the reduction of the NAD+ coenzyme. This appears as an archaic photosynthetic system consisting of photo-emitted electrons that are in fine funnelled into the mitochondrial reducing power in order to synthesize ATP molecules.}, }
@article {pmid22889167, year = {2012}, author = {Chaudhari, R and Narayan, A and Patankar, S}, title = {A novel trafficking pathway in Plasmodium falciparum for the organellar localization of glutathione peroxidase-like thioredoxin peroxidase.}, journal = {The FEBS journal}, volume = {279}, number = {20}, pages = {3872-3888}, doi = {10.1111/j.1742-4658.2012.08746.x}, pmid = {22889167}, issn = {1742-4658}, mesh = {Blotting, Western ; Brefeldin A/pharmacology ; Cold Temperature ; Cytosol/metabolism ; Endoplasmic Reticulum/metabolism ; Erythrocytes/parasitology ; Gene Expression ; Glutathione Peroxidase/genetics/*metabolism ; Golgi Apparatus/metabolism ; Humans ; Microscopy, Fluorescence ; Mitochondria/metabolism ; Organelles/*metabolism ; Peroxiredoxins/genetics/*metabolism ; Plasmodium falciparum/genetics/growth &amp; development/*metabolism ; Protein Synthesis Inhibitors/pharmacology ; Protein Transport/drug effects ; Protozoan Proteins/genetics/*metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Although common in plants, very few proteins are currently known to be localized to both the plastid and the mitochondrion in Plasmodium falciparum. One such protein is P. falciparum glutathione peroxidase-like thioredoxin peroxidase (PfTPx(Gl)) which we show, by immunofluorescence imaging and bioinformatics predictions, is localized to the apicoplast, the mitochondrion and the cytosol. The distribution of PfTPx(Gl) was random in the population, with the protein localizing to any one organelle in some parasites and to both in others. It has been proposed that targeting to each organelle occurs via independent pathways that do not proceed via the Golgi. However, for PfTPx(Gl), both incubation at low temperature (15 °C) and Brefeldin A treatment reversibly blocked targeting to these organelles, suggesting the involvement of a novel trafficking route, most probably via the endoplasmic reticulum and Golgi. This idea is further supported by the lack of cleavage of the putative N-terminal signal sequence of PfTPx(Gl), and this N-terminal extension did not compromise PfTPx(Gl) enzyme activity. In the context of evolution, a common pathway for the dual localization of a single gene product, such as the primitive endoplasmic reticulum-Golgi route, may have been retained as opposed to optimization for individual organellar import pathways.}, }
@article {pmid22888835, year = {2012}, author = {Park, JS and De Jonckheere, JF and Simpson, AG}, title = {Characterization of Selenaion koniopes n. gen., n. sp., an amoeba that represents a new major lineage within heterolobosea, isolated from the Wieliczka salt mine.}, journal = {The Journal of eukaryotic microbiology}, volume = {59}, number = {6}, pages = {601-613}, doi = {10.1111/j.1550-7408.2012.00641.x}, pmid = {22888835}, issn = {1550-7408}, mesh = {Amoeba/*classification/cytology/genetics/*isolation &amp; purification ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Microscopy ; Molecular Sequence Data ; Organelles/ultrastructure ; Phylogeny ; Poland ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Saline Solution, Hypertonic ; Sequence Analysis, DNA ; Water/*parasitology ; }, abstract = {A new heterolobosean amoeba, Selenaion koniopes n. gen., n. sp., was isolated from 73‰ saline water in the Wieliczka salt mine, Poland. The amoeba had eruptive pseudopodia, a prominent uroid, and a nucleus without central nucleolus. Cysts had multiple crater-like pore plugs. No flagellates were observed. Transmission electron microscopy revealed several typical heterolobosean features: flattened mitochondrial cristae, mitochondria associated with endoplasmic reticulum, and an absence of obvious Golgi dictyosomes. Two types of larger and smaller granules were sometimes abundant in the cytoplasm--these may be involved in cyst formation. Mature cysts had a fibrous endocyst that could be thick, plus an ectocyst that was covered with small granules. Pore plugs had a flattened dome shape, were bipartite, and penetrated only the endocyst. Phylogenies based on the 18S rRNA gene and the presence of 18S rRNA helix 17_1 strongly confirmed assignment to Heterolobosea. The organism was not closely related to any described genus, and instead formed the deepest branch within the Heterolobosea clade after Pharyngomonas, with support for this deep-branching position being moderate (i.e. maximum likelihood bootstrap support--67%; posterior probability--0.98). Cells grew at 15-150‰ salinity. Thus, S. koniopes is a halotolerant, probably moderately halophilic heterolobosean, with a potentially pivotal evolutionary position within this large eukaryote group.}, }
@article {pmid22884976, year = {2012}, author = {Liesa, M and Qiu, W and Shirihai, OS}, title = {Mitochondrial ABC transporters function: the role of ABCB10 (ABC-me) as a novel player in cellular handling of reactive oxygen species.}, journal = {Biochimica et biophysica acta}, volume = {1823}, number = {10}, pages = {1945-1957}, pmid = {22884976}, issn = {0006-3002}, support = {R01 DK074778/DK/NIDDK NIH HHS/United States ; R01 HL071629/HL/NHLBI NIH HHS/United States ; R01HL071629-03/HL/NHLBI NIH HHS/United States ; R01DK074778/DK/NIDDK NIH HHS/United States ; }, mesh = {ATP-Binding Cassette Transporters/chemistry/genetics/*metabolism ; Amino Acid Sequence ; Animals ; Humans ; Mitochondria/*metabolism ; Molecular Sequence Data ; Oxidative Stress ; Phylogeny ; Reactive Oxygen Species/*metabolism ; Structure-Activity Relationship ; }, abstract = {Mitochondria are one of the major sources of reactive oxygen species (ROS) in the cell. When exceeding the capacity of antioxidant mechanisms, ROS production may lead to different pathologies, such as ischemia-reperfusion injury, neurodegeneration, anemia and ageing. As a consequence of the endosymbiotic origin of mitochondria, eukaryotic cells have developed different transport mechanisms that coordinate mitochondrial function with other cellular compartments. Four mitochondrial ATP-binding cassette (ABC) transporters have been described to date in mammals: ABCB6, ABCB8, ABCB7 and ABCB10. ABCB10 is located in the inner mitochondrial membrane forming homodimers, with the ATP binding domain facing the mitochondrial matrix. ABCB10 expression is highly induced during erythroid differentiation and its overexpression increases hemoglobin synthesis in erythroid cells. However, ABCB10 is also expressed in nonerythroid tissues, suggesting a role not directly related to hemoglobin synthesis. Recent evidence points toward ABCB10 as an important player in the protection from oxidative stress in mammals. In this regard, ABCB10 is required for normal erythropoiesis and cardiac recovery after ischemia-reperfusion, processes intimately related to mitochondrial ROS generation. Here, we review the current knowledge on mitochondrial ABC transporters and ABCB10 and discuss the potential mechanisms by which ABCB10 and its transport activity may regulate oxidative stress. We discuss ABCB10 as a potential therapeutic target for diseases in which increased mitochondrial ROS production and oxidative stress play a major role.}, }
@article {pmid22876320, year = {2012}, author = {Prole, DL and Taylor, CW}, title = {Identification and analysis of cation channel homologues in human pathogenic fungi.}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e42404}, pmid = {22876320}, issn = {1932-6203}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Calcium Channels/chemistry/genetics/metabolism ; Cations/metabolism ; Fungi/*genetics/metabolism ; Humans ; Ion Channels/chemistry/*genetics/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Potassium Channels/chemistry/genetics/metabolism ; Sequence Alignment ; Transient Receptor Potential Channels/chemistry/genetics/metabolism ; }, abstract = {Fungi are major causes of human, animal and plant disease. Human fungal infections can be fatal, but there are limited options for therapy, and resistance to commonly used anti-fungal drugs is widespread. The genomes of many fungi have recently been sequenced, allowing identification of proteins that may become targets for novel therapies. We examined the genomes of human fungal pathogens for genes encoding homologues of cation channels, which are prominent drug targets. Many of the fungal genomes examined contain genes encoding homologues of potassium (K(+)), calcium (Ca(2+)) and transient receptor potential (Trp) channels, but not sodium (Na(+)) channels or ligand-gated channels. Some fungal genomes contain multiple genes encoding homologues of K(+) and Trp channel subunits, and genes encoding novel homologues of voltage-gated K(v) channel subunits are found in Cryptococcus spp. Only a single gene encoding a homologue of a plasma membrane Ca(2+) channel was identified in the genome of each pathogenic fungus examined. These homologues are similar to the Cch1 Ca(2+) channel of Saccharomyces cerevisiae. The genomes of Aspergillus spp. and Cryptococcus spp., but not those of S. cerevisiae or the other pathogenic fungi examined, also encode homologues of the mitochondrial Ca(2+) uniporter (MCU). In contrast to humans, which express many K(+), Ca(2+) and Trp channels, the genomes of pathogenic fungi encode only very small numbers of K(+), Ca(2+) and Trp channel homologues. Furthermore, the sequences of fungal K(+), Ca(2+), Trp and MCU channels differ from those of human channels in regions that suggest differences in regulation and susceptibility to drugs.}, }
@article {pmid22870907, year = {2013}, author = {Gems, D and de la Guardia, Y}, title = {Alternative Perspectives on Aging in Caenorhabditis elegans: Reactive Oxygen Species or Hyperfunction?.}, journal = {Antioxidants &amp; redox signaling}, volume = {19}, number = {3}, pages = {321-329}, pmid = {22870907}, issn = {1557-7716}, support = {098565/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Aging ; Animals ; Biological Evolution ; Caenorhabditis elegans/*metabolism ; Oxidation-Reduction ; Oxidative Stress ; Reactive Oxygen Species/*metabolism ; Signal Transduction ; }, abstract = {SIGNIFICANCE: The biological mechanisms at the heart of the aging process are a long-standing mystery. An influential theory has it that aging is the result of an accumulation of molecular damage, caused in particular by reactive oxygen species produced by mitochondria. This theory also predicts that processes that protect against oxidative damage (involving detoxification, repair, and turnover) protect against aging and increase lifespan.<br><br>RECENT ADVANCES: However, recent tests of the oxidative damage theory, many using the short-lived nematode worm Caenorhabditis elegans, have often failed to support the theory. This motivates consideration of alternative models. One new theory, conceived by M.V. Blagosklonny, proposes that aging is caused by hyperfunction, that is, overactivity during adulthood of processes (particularly biosynthetic) that contribute to development and reproduction. Such hyperfunction can lead to hypertrophy-associated pathologies, which cause the age increase in death.<br><br>CRITICAL ISSUES: Here we assess whether the hyperfunction theory is at all consistent with what is known about C. elegans aging, and conclude that it is. In particular, during adulthood, C. elegans shows a number of changes that may reflect pathology and/or hyperfunction. Such changes seem to contribute to death, at least in some cases (e.g., yolk accumulation).<br><br>FUTURE DIRECTIONS: Our assessment suggests that the hyperfunction theory is a plausible alternative to the molecular damage theory to explain aging in C. elegans.}, }
@article {pmid22870259, year = {2012}, author = {Idei, M and Osada, K and Sato, S and Toyoda, K and Nagumo, T and Mann, DG}, title = {Gametogenesis and auxospore development in Actinocyclus (Bacillariophyta).}, journal = {PloS one}, volume = {7}, number = {8}, pages = {e41890}, pmid = {22870259}, issn = {1932-6203}, mesh = {Diatoms/*physiology/ultrastructure ; Endoplasmic Reticulum/*metabolism/ultrastructure ; Gametogenesis/*physiology ; Golgi Apparatus/*metabolism/ultrastructure ; Mitochondria/*metabolism/ultrastructure ; Vacuoles/*metabolism/ultrastructure ; }, abstract = {cGametogenesis and auxospore development have been studied in detail in surprisingly few centric diatoms. We studied the development of sperm, eggs and auxospores in Actinocyclus sp., a radially symmetrical freshwater diatom collected from Japan, using LM and electron microscopy of living cultures and thin sections. Actinocyclus represents a deep branch of the 'radial centric' diatoms and should therefore contribute useful insights into the evolution of sexual reproduction in diatoms. Spermatogenesis was examined by LM and SEM and involved the formation of two spermatogonia (sperm mother-cells) in each spermatogonangium through an equal mitotic division. The spermatogonia produced a reduced 'lid' valve, resembling a large flat scale with irregular radial thickenings. Sperm formation was merogenous, producing four sperm per spermatogonium, which were released by dehiscence of the 'lid' valve. The sperm were spindle-shaped with numerous surface globules and, as usual for diatoms, the single anterior flagellum bore mastigonemes. One egg cell was produced per oogonium. Immature eggs produced a thin layer of circular silica scales before fertilization, while the eggs were still contained within the oogonium. Sperm were attracted in large numbers to each egg and were apparently able to contact the egg surface via a gap formed between the long hypotheca and shorter epitheca of the oogonium and a small underlying hole in the scale-case. Auxospores expanded isodiametrically and many new scales were added to its envelope during expansion. Finally, new slightly-domed initial valves were produced at right angles to the oogonium axis, after a strong contraction of the cell away from the auxospore wall. At different stages, Golgi bodies were associated with chloroplasts or mitochondria, contrasting with the constancy of Golgi-ER-mitochondrion (G-ER-M) units in some other centric diatoms, which has been suggested to have phylogenetic significance. Electron-dense bodies in the vacuole of Actinocyclus are probably acidocalcisomes containing polyphosphate.}, }
@article {pmid22863313, year = {2012}, author = {Camus, MF and Clancy, DJ and Dowling, DK}, title = {Mitochondria, maternal inheritance, and male aging.}, journal = {Current biology : CB}, volume = {22}, number = {18}, pages = {1717-1721}, doi = {10.1016/j.cub.2012.07.018}, pmid = {22863313}, issn = {1879-0445}, mesh = {Aging/genetics ; Animals ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Drosophila melanogaster/*genetics ; Evolution, Molecular ; Female ; *Genome, Mitochondrial ; Inheritance Patterns ; Longevity/*genetics ; Male ; Mitochondria/*genetics ; Molecular Sequence Data ; Mutation ; Sex Characteristics ; Sex Factors ; }, abstract = {The maternal transmission of mitochondrial genomes invokes a sex-specific selective sieve, whereby mutations in mitochondrial DNA can only respond to selection acting directly on females. In theory, this enables male-harming mutations to accumulate in mitochondrial genomes when these same mutations are neutral, beneficial, or only slightly deleterious in their effects on females. Ultimately, this evolutionary process could result in the evolution of male-specific mitochondrial mutation loads; an idea previously termed Mother's Curse. Here, we present evidence that the effects of this process are broader than hitherto realized, and that it has resulted in mutation loads affecting patterns of aging in male, but not female Drosophila melanogaster. Furthermore, our results indicate that the mitochondrial mutation loads affecting male aging generally comprise numerous mutations over multiple sites. Our findings thus suggest that males are subject to dramatic consequences that result from the maternal transmission of mitochondrial genomes. They implicate the diminutive mitochondrial genome as a hotspot for mutations that affect sex-specific patterns of aging, thus promoting the idea that a sex-specific selective sieve in mitochondrial genome evolution is a contributing factor to sexual dimorphism in aging, commonly observed across species.}, }
@article {pmid22847499, year = {2013}, author = {Rey, B and Roussel, D and Rouanet, JL and Duchamp, C}, title = {Differential effects of thyroid status on regional H2O2 production in slow- and fast-twitch muscle of ducklings.}, journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology}, volume = {183}, number = {1}, pages = {135-143}, pmid = {22847499}, issn = {1432-136X}, mesh = {Acclimatization ; Animals ; Animals, Inbred Strains ; Cell Membrane Permeability/drug effects ; Cold Temperature/adverse effects ; Ducks/blood/*metabolism ; France ; Glycolysis/drug effects ; Hormone Replacement Therapy/veterinary ; Hydrogen Peroxide/*metabolism ; Hypothyroidism/drug therapy/physiopathology/*veterinary ; Male ; Membrane Potential, Mitochondrial/drug effects ; Mitochondria, Muscle/drug effects/metabolism ; Muscle Fibers, Fast-Twitch/drug effects/*metabolism ; Muscle Fibers, Slow-Twitch/drug effects/*metabolism ; Oxidative Phosphorylation/drug effects ; Oxidative Stress/drug effects ; Poultry Diseases/drug therapy/*physiopathology ; Random Allocation ; Reactive Oxygen Species/metabolism ; Thyroid Gland/drug effects/metabolism/*physiopathology ; Triiodothyronine/blood/metabolism/therapeutic use ; }, abstract = {Birds seem to employ powerful physiological strategies to curb the harmful effects of reactive oxygen species (ROS) because they generally live longer than predicted by the free radical theory of aging. However, little is known about the physiological mechanisms that confer protection to birds against excessive ROS generation. Hence, we investigated the ability of birds to control mitochondrial ROS generation during physiologically stressful periods. In our study, we analyzed the relationship between the thyroid status and the function of intermyofibrillar and subsarcolemmal mitochondria located in glycolytic and oxidative muscles of ducklings. We found that the intermyofibrillar mitochondria of both glycolytic and oxidative muscles down regulate ROS production when plasma T3 levels rise. The intermyofibrillar mitochondria of the gastrocnemius muscle (an oxidative muscle) produced less ROS and were more sensitive than the pectoralis muscle (a glycolytic muscle) to changes in plasma T3. Such differences in the ROS production by glycolytic and oxidative muscles were associated with differences in the membrane proton permeability and in the rate of free radical leakage within the respiratory chain. This is the first evidence which shows that in birds, the amount of ROS that the mitochondria release is dependent on: (1) their location within the muscle; (2) the type of muscle (glycolytic or oxidative) and (3) on the thyroid status. Reducing muscle mitochondrial ROS generation might be an important mechanism in birds to limit oxidative damage during periods of physiological stress.}, }
@article {pmid22827366, year = {2012}, author = {Mukai, C and Travis, AJ}, title = {What sperm can teach us about energy production.}, journal = {Reproduction in domestic animals = Zuchthygiene}, volume = {47 Suppl 4}, number = {0 4}, pages = {164-169}, pmid = {22827366}, issn = {1439-0531}, support = {DP1 EB016541/EB/NIBIB NIH HHS/United States ; DP1 OD006431/OD/NIH HHS/United States ; 5DP1-OD-006431/OD/NIH HHS/United States ; }, mesh = {Animals ; Energy Metabolism/*physiology ; Male ; Mammals/*physiology ; Species Specificity ; Sperm Motility ; Spermatozoa/*physiology ; }, abstract = {Mammalian sperm have evolved under strict selection pressures that have resulted in a highly polarized and efficient design. A critical component of that design is the compartmentalization of specific metabolic pathways to specific regions of the cell. Although the restricted localization of mitochondria to the midpiece is the best known example of this design, the organization of the enzymes of glycolysis along the fibrous sheath is the primary focus of this review. Evolution of variants of these metabolic enzymes has allowed them to function when tethered, enabling localized energy production that is essential for sperm motility. We close by exploring how this design might be mimicked to provide an energy-producing platform technology for applications in nanobiotechnology.}, }
@article {pmid22842546, year = {2012}, author = {Oftedal, L and Myhren, L and Jokela, J and Gausdal, G and Sivonen, K and Døskeland, SO and Herfindal, L}, title = {The lipopeptide toxins anabaenolysin A and B target biological membranes in a cholesterol-dependent manner.}, journal = {Biochimica et biophysica acta}, volume = {1818}, number = {12}, pages = {3000-3009}, doi = {10.1016/j.bbamem.2012.07.015}, pmid = {22842546}, issn = {0006-3002}, mesh = {Anabaena ; Animals ; Apoptosis ; Bacterial Toxins/chemistry/*metabolism/toxicity ; Cell Line, Tumor ; Cell Membrane/*metabolism/ultrastructure ; Cholesterol/*metabolism ; Cytochromes c ; Digitonin/chemistry/metabolism/toxicity ; Hemolysin Proteins/chemistry/*metabolism ; Lipopeptides/chemistry/*metabolism/toxicity ; Liposomes/chemistry/metabolism ; Liver/metabolism ; Membrane Potential, Mitochondrial ; Mitochondria/metabolism/ultrastructure ; Mitochondria, Liver/metabolism ; Models, Molecular ; Peptides, Cyclic/chemistry/metabolism/toxicity ; Propidium ; Rats ; }, abstract = {The two novel cyanobacterial cyclic lipopeptides, anabaenolysin (Abl) A and B permeabilised mammalian cells, leading to necrotic death. Abl A was a more potent haemolysin than other known biodetergents, including digitonin, and induced discocyte-echinocyte transformation in erythrocytes. The mitochondria of the dead cells appeared intact with regard to both ultrastructure and membrane potential. Also isolated rat liver mitochondria were resistant to Abl, judged by their ultrastructure and lack of cytochrome c release. The sparing of the mitochondria could be related to the low cholesterol content of their outer membrane. In fact, a supplement of cholesterol in liposomes sensitised them to Abl. In contrast, the prokaryote-directed cyclic lipopeptide surfactin lysed preferentially non-cholesterol-containing membranes. In silico comparison of the positions of relevant functional chemical structures revealed that Abl A matched poorly with surfactin in spite of the common cyclic lipopeptide structure. Abl A and the plant-derived glycolipid digitonin had, however, predicted overlaps of functional groups, particularly in the cholesterol-binding tail of digitonin. This may suggest independent evolution of Abl and digitonin to target eukaryotic cholesterol-containing membranes. Sub-lytic concentrations of Abl A or B allowed influx of propidium iodide into cells without interfering with their long-term cell viability. The transient permeability increase allowed the influx of enough of the cyanobacterial cyclic peptide toxin nodularin to induce apoptosis. The anabaenolysins might therefore not only act solely as lysins, but also as cofactors for the internalisation of other toxins. They represent a potent alternative to digitonin to selectively disrupt cholesterol-containing biological membranes.}, }
@article {pmid22841711, year = {2012}, author = {Kluth, J and Schmidt, A and März, M and Krupinska, K and Lorbiecke, R}, title = {Arabidopsis Zinc Ribbon 3 is the ortholog of yeast mitochondrial HSP70 escort protein HEP1 and belongs to an ancient protein family in mitochondria and plastids.}, journal = {FEBS letters}, volume = {586}, number = {19}, pages = {3071-3076}, doi = {10.1016/j.febslet.2012.07.052}, pmid = {22841711}, issn = {1873-3468}, mesh = {Amino Acid Sequence ; Animals ; Arabidopsis Proteins/*genetics/metabolism ; Chloroplast Proteins/genetics/metabolism ; Genetic Complementation Test ; HSP70 Heat-Shock Proteins/genetics/metabolism ; Humans ; Mitochondrial Proteins/genetics/metabolism ; Molecular Chaperones/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Recombinant Proteins/genetics/metabolism ; Saccharomyces cerevisiae Proteins/*genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {ZR proteins belong to a phylogenetically conserved family of small zinc-ribbon proteins in plastids and mitochondria of higher plants. The function of these proteins is so far unclear. The mitochondrial proteins share sequence similarities with mitochondrial Hsp70 escort proteins (HEP) from Saccharomyces cerevisiae (HEP1) and human. Expression of the mitochondrial ZR protein from Arabidopsis, ZR3, rescued a hep1 knockout mutant from yeast. Accordingly, ZR3 was found to physically interact with mitochondrial Hsp70 from Arabidopsis. Our findings support the idea that mitochondrial and plastidic ZR proteins from higher plants are orthologs of HEP proteins.}, }
@article {pmid22840995, year = {2012}, author = {Asensio, AC and Gil-Monreal, M and Pires, L and Gogorcena, Y and Aparicio-Tejo, PM and Moran, JF}, title = {Two Fe-superoxide dismutase families respond differently to stress and senescence in legumes.}, journal = {Journal of plant physiology}, volume = {169}, number = {13}, pages = {1253-1260}, doi = {10.1016/j.jplph.2012.04.019}, pmid = {22840995}, issn = {1618-1328}, mesh = {Antibodies/analysis ; Cytosol/*enzymology ; Fabaceae/*enzymology/growth &amp; development ; Isoenzymes ; Phylogeny ; Plant Leaves/enzymology ; Plant Roots/enzymology ; Plastids/*enzymology ; Glycine max/enzymology/growth &amp; development ; Stress, Physiological/*physiology ; Superoxide Dismutase/classification/immunology/*metabolism ; Time ; }, abstract = {Three main families of SODs in plants may be distinguished according to the metal in the active center: CuZnSODs, MnSOD, and FeSOD. CuZnSODs have two sub-families localized either in plant cell cytosol or in plastids, the MnSOD family is essentially restricted to mitochondria, and the FeSOD enzyme family has been typically localized into the plastid. Here, we describe, based on a phylogenetic tree and experimental data, the existence of two FeSOD sub-families: a plastidial localized sub-family that is universal to plants, and a cytosolic localized FeSOD sub-family observed in determinate-forming nodule legumes. Anti-cytosolic FeSOD (cyt_FeSOD) antibodies were employed, together with a novel antibody raised against plastidial FeSOD (p_FeSOD). Stress conditions, such as nitrate excess or drought, markedly increased cyt_FeSOD contents in soybean tissues. Also, cyt_FeSOD content and activity increased with age in both soybean and cowpea plants, while the cyt_CuZnSOD isozyme was predominant during early stages. p_FeSOD in leaves decreased with most of the stresses applied, but this isozyme markedly increased with abscisic acid in roots. The great differences observed for p_FeSOD and cyt_FeSOD contents in response to stress and aging in plant tissues reveal distinct functionality and confirm the existence of two immunologically differentiated FeSOD sub-families. The in-gel FeSOD activity patterns showed a good correlation to cyt_FeSOD contents but not to those of p_FeSOD. This indicates that cyt_FeSOD is the main active FeSOD in soybean and cowpea tissues. The diversity of functions associated with the complexity of FeSOD isoenzymes depending of the location is discussed.}, }
@article {pmid22835786, year = {2012}, author = {Wernegreen, JJ}, title = {Endosymbiosis.}, journal = {Current biology : CB}, volume = {22}, number = {14}, pages = {R555-61}, doi = {10.1016/j.cub.2012.06.010}, pmid = {22835786}, issn = {1879-0445}, mesh = {Archaea/genetics/physiology ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; Biodiversity ; *Biological Evolution ; Eukaryota/genetics/*physiology ; Nitrogen Fixation ; Nutritional Physiological Phenomena ; Photosynthesis ; *Symbiosis ; }, abstract = {The phenomenon of endosymbiosis, or one organism living within another, has deeply impacted the evolution of life and continues to shape the ecology of countless species. Traditionally, biologists have viewed evolution as a largely bifurcating pattern, reflecting mutations and other changes in existing genetic information and the occasional speciation and divergence of lineages. While lineage bifurcation has clearly been important in evolution, the merging of two lineages through endosymbiosis has also made profound contributions to evolutionary novelty. Mitochondria and chloroplasts are relicts of ancient bacterial endosymbionts that ultimately extended the range of acceptable habitats for life by allowing hosts to thrive in the presence of oxygen and to convert light into energy. Today, the sheer abundance of endosymbiotic relationships across diverse host lineages and habitats testifies to their continued significance.}, }
@article {pmid22830417, year = {2012}, author = {Evans, ML and Bernatchez, L}, title = {Oxidative phosphorylation gene transcription in whitefish species pairs reveals patterns of parallel and nonparallel physiological divergence.}, journal = {Journal of evolutionary biology}, volume = {25}, number = {9}, pages = {1823-1834}, doi = {10.1111/j.1420-9101.2012.02570.x}, pmid = {22830417}, issn = {1420-9101}, mesh = {Adaptation, Biological ; Adenosine Triphosphate/genetics/metabolism ; Animals ; Base Sequence ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Ecosystem ; Gene Expression Profiling/methods ; Gene Expression Regulation ; Genes, Mitochondrial ; Genetic Speciation ; Genetics, Population/methods ; Lakes ; Maine ; Mitochondria/genetics ; *Oxidative Phosphorylation ; Salmonidae/*genetics/metabolism/*physiology ; Species Specificity ; Statistics, Nonparametric ; Sympatry ; *Transcription, Genetic ; Up-Regulation ; }, abstract = {Across multiple lakes in North America, lake whitefish (Coregonus clupeaformis) have independently evolved 'dwarf' and 'normal' sympatric species pairs that exhibit pronounced phenotypic and genetic divergence. In particular, traits associated with metabolism have been shown to be highly differentiated between whitefish species. Here, we examine the transcription of genes associated with the five mitochondrial and nuclear genome-encoded oxidative phosphorylation (OXPHOS) complexes, the primary physiological mechanism responsible for the production of ATP, in whitefish species pairs from Cliff Lake and Webster Lake in Maine, USA. We observed OXPHOS gene transcription divergence between dwarf and normal whitefish in each of the two lakes, with the former exhibiting transcription upregulation for genes associated with each of the OXPHOS complexes. We also observed a significant influence of lake on transcription levels for some of the genes, indicating that inter-lake ecological or genetic differences are contributing to variation in OXPHOS gene transcription levels. Together, our results support the hypothesis that metabolic divergence is a critical adaptation involved in whitefish speciation and implicate OXPHOS gene upregulation as a factor involved in meeting the enhanced energetic demands of dwarf whitefish. Further studies are now needed to evaluate the contribution of genetically vs. plasticity driven variation in transcription associated with this critical physiological pathway.}, }
@article {pmid22829778, year = {2012}, author = {Häuser, R and Pech, M and Kijek, J and Yamamoto, H and Titz, B and Naeve, F and Tovchigrechko, A and Yamamoto, K and Szaflarski, W and Takeuchi, N and Stellberger, T and Diefenbacher, ME and Nierhaus, KH and Uetz, P}, title = {RsfA (YbeB) proteins are conserved ribosomal silencing factors.}, journal = {PLoS genetics}, volume = {8}, number = {7}, pages = {e1002815}, pmid = {22829778}, issn = {1553-7404}, support = {R01 GM079710/GM/NIGMS NIH HHS/United States ; R01GM79710/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteria/genetics/growth &amp; development/metabolism ; Bacterial Proteins/genetics/metabolism ; Binding Sites ; Conserved Sequence ; *Eukaryota/genetics/growth &amp; development/metabolism ; HeLa Cells ; Humans ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Binding ; Protein Biosynthesis/genetics ; Ribosomal Proteins/*chemistry/metabolism ; Ribosome Subunits, Large/*chemistry/metabolism ; Sequence Homology, Amino Acid ; Transcription Factors/genetics/metabolism ; }, abstract = {The YbeB (DUF143) family of uncharacterized proteins is encoded by almost all bacterial and eukaryotic genomes but not archaea. While they have been shown to be associated with ribosomes, their molecular function remains unclear. Here we show that YbeB is a ribosomal silencing factor (RsfA) in the stationary growth phase and during the transition from rich to poor media. A knock-out of the rsfA gene shows two strong phenotypes: (i) the viability of the mutant cells are sharply impaired during stationary phase (as shown by viability competition assays), and (ii) during transition from rich to poor media the mutant cells adapt slowly and show a growth block of more than 10 hours (as shown by growth competition assays). RsfA silences translation by binding to the L14 protein of the large ribosomal subunit and, as a consequence, impairs subunit joining (as shown by molecular modeling, reporter gene analysis, in vitro translation assays, and sucrose gradient analysis). This particular interaction is conserved in all species tested, including Escherichia coli, Treponema pallidum, Streptococcus pneumoniae, Synechocystis PCC 6803, as well as human mitochondria and maize chloroplasts (as demonstrated by yeast two-hybrid tests, pull-downs, and mutagenesis). RsfA is unrelated to the eukaryotic ribosomal anti-association/60S-assembly factor eIF6, which also binds to L14, and is the first such factor in bacteria and organelles. RsfA helps cells to adapt to slow-growth/stationary phase conditions by down-regulating protein synthesis, one of the most energy-consuming processes in both bacterial and eukaryotic cells.}, }
@article {pmid22824141, year = {2012}, author = {Yoshida, Y and Miyagishima, SY and Kuroiwa, H and Kuroiwa, T}, title = {The plastid-dividing machinery: formation, constriction and fission.}, journal = {Current opinion in plant biology}, volume = {15}, number = {6}, pages = {714-721}, doi = {10.1016/j.pbi.2012.07.002}, pmid = {22824141}, issn = {1879-0356}, mesh = {Arabidopsis/genetics/metabolism/physiology ; Arabidopsis Proteins/genetics/metabolism ; Biological Evolution ; Chloroplast Proteins/genetics/*metabolism ; Cytosol/metabolism ; Dynamins/metabolism ; Glucans/metabolism ; Intracellular Membranes/*metabolism/physiology ; Membrane Proteins/genetics/metabolism ; Mitochondria/metabolism/physiology ; Mitochondrial Dynamics ; Plastids/metabolism/*physiology ; Protein Transport ; }, abstract = {Plastids divide by constriction of the plastid-dividing (PD) machinery, which encircles the division site. The PD machinery consists of the stromal inner machinery which includes the inner PD and filamenting temperature-sensitive mutant Z (FtsZ) rings and the cytosolic outer machinery which includes the outer PD and dynamin rings. The major constituent of the PD machinery is the outer PD ring, which consists of a bundle of polyglucan filaments. In addition, recent proteomic studies suggest that the PD machinery contains additional proteins that have not been characterized. The PD machinery forms from the inside to the outside of the plastid. The constriction seems to occur by sliding of the polyglucan filaments of the outer PD ring, aided by dynamin. The final fission of the plastid is probably promoted by the 'pinchase' activity of dynamin.}, }
@article {pmid22823504, year = {2012}, author = {Johnston, AR and Anthony, NM}, title = {A multi-locus species phylogeny of African forest duikers in the subfamily Cephalophinae: evidence for a recent radiation in the Pleistocene.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {120}, pmid = {22823504}, issn = {1471-2148}, mesh = {Animals ; Biological Evolution ; Cell Nucleus/genetics ; Climate ; Introns ; Mitochondria/genetics ; Multilocus Sequence Typing ; Phylogeny ; Ruminants/*classification/*genetics ; }, abstract = {BACKGROUND: Duikers in the subfamily Cephalophinae are a group of tropical forest mammals believed to have first originated during the late Miocene. However, knowledge of phylogenetic relationships, pattern and timing of their subsequent radiation is poorly understood. Here we present the first multi-locus phylogeny of this threatened group of tropical artiodactyls and use a Bayesian uncorrelated molecular clock to estimate divergence times.<br><br>RESULTS: A total of 4152 bp of sequence data was obtained from two mitochondrial genes and four nuclear introns. Phylogenies were estimated using maximum parsimony, maximum likelihood, and Bayesian analysis of concatenated mitochondrial, nuclear and combined datasets. A relaxed molecular clock with two fossil calibration points was used to estimate divergence times. The first was based on the age of the split between the two oldest subfamilies within the Bovidae whereas the second was based on the earliest known fossil appearance of the Cephalophinae and molecular divergence time estimates for the oldest lineages within this group. Findings indicate strong support for four major lineages within the subfamily, all of which date to the late Miocene/early Pliocene. The first of these to diverge was the dwarf duiker genus Philantomba, followed by the giant, eastern and western red duiker lineages, all within the genus Cephalophus. While these results uphold the recognition of Philantomba, they do not support the monotypic savanna-specialist genus Sylvicapra, which as sister to the giant duikers leaves Cephalophus paraphyletic. BEAST analyses indicate that most sister species pairs originated during the Pleistocene, suggesting that repeated glacial cycling may have played an important role in the recent diversification of this group. Furthermore, several red duiker sister species pairs appear to be either paraphyletic (C.callipygus/C. ogilbyi and C. harveyi/C. natalensis) or exhibit evidence of mitochondrial admixture (C. nigrifrons and C. rufilatus), consistent with their recent divergence and/or possible hybridization with each other.<br><br>CONCLUSIONS: Molecular phylogenetic analyses suggest that Pleistocene-era climatic oscillations have played an important role in the speciation of this largely forest-dwelling group. Our results also reveal the most well supported species phylogeny for the subfamily to date, but also highlight several areas of inconsistency between our current understanding of duiker taxonomy and the evolutionary relationships depicted here. These findings may therefore prove particularly relevant to future conservation efforts, given that many species are presently regulated under the Convention for Trade in Endangered Species.}, }
@article {pmid22820118, year = {2012}, author = {Peng, Q and Tang, L and Tan, S and Li, Z and Wang, J and Zou, F}, title = {Mitogenomic analysis of the genus Pseudois: evidence of adaptive evolution of morphological variation in the ATP synthase genes.}, journal = {Mitochondrion}, volume = {12}, number = {5}, pages = {500-505}, doi = {10.1016/j.mito.2012.07.107}, pmid = {22820118}, issn = {1872-8278}, mesh = {Amino Acid Substitution ; Animals ; Asia, Central ; Cluster Analysis ; *Evolution, Molecular ; Mitochondrial Proton-Translocating ATPases/*genetics ; Molecular Sequence Data ; Mutation Rate ; Phylogeography ; Ruminants/*genetics ; Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {The genus Pseudois includes two variable taxa, blue sheep (Pseudois nayaur) and dwarf blue sheep (Pseudois schaeferi), that exhibit notable geographic variation in morphology and ecological niche, suggesting the potential for significant adaptive differentiation between these two goats. Blue sheep are broadly distributed in the Tibetan Plateau and peripheral mountains through Central Asia, while dwarf blue sheep are only found in the gorges of the upper Yangtze River (Jinsha River) near Batang county, Sichuan province and adjacent mountains. Although they are all adapted to high altitude environments, endangered dwarf blue sheep show unique morphological variation and niche shifts compared to blue sheep. Mitochondria play important roles in oxygen usage and energy metabolism. The energetically demanding lifestyles of these high altitude species may have altered the selective regimes on mitochondrial genes encoding proteins related to cellular respiration. Here, we compared the sequences of 13 protein-coding genes in the mitochondrial genome of dwarf blue sheep with those of blue sheep to understand the genetic basis of morphological variation. Using neighbor-joining, maximum-likelihood and Bayesian approaches, we estimated rates of synonymous (d(S)) and nonsynonymous (d(N)) substitutions. Independent analyses showed that no ω ratio was larger than 1, suggesting that all mitochondrial 13 genes were under the purifying selection. Surprisingly, we found that the ω ratio (d(N)/d(S)) of the ATP synthase complex (ATP6 and ATP8) in blue sheep is sixteen times that of dwarf blue sheep (0.340 compared to 0.021). This result was confirmed by a separate analysis of ATP synthase genes from two additional P. schaeferi individuals and two P. nayaur individuals. We hypothesize that the large body size and diverse feeding styles are factors influencing the nonsynonymous substitutions in the ATP synthase complex of blue sheep.}, }
@article {pmid22817532, year = {2012}, author = {Skulachev, VP}, title = {What is "phenoptosis" and how to fight it?.}, journal = {Biochemistry. Biokhimiia}, volume = {77}, number = {7}, pages = {689-706}, doi = {10.1134/S0006297912070012}, pmid = {22817532}, issn = {1608-3040}, mesh = {Aging/*genetics ; Animals ; Apoptosis/*genetics ; Biological Evolution ; Caloric Restriction ; *Death ; Genome/genetics ; Humans ; Mitochondria/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {Phenoptosis is the death of an organism programmed by its genome. Numerous examples of phenoptosis are described in prokaryotes, unicellular eukaryotes, and all kingdoms of multicellular eukaryotes (animals, plants, and fungi). There are very demonstrative cases of acute phenoptosis when actuation of a specific biochemical or behavioral program results in immediate death. Rapid (taking days) senescence of semelparous plants is described as phenoptosis controlled by already known genes and mediated by toxic phytohormones like abscisic acid. In soya, the death signal is transmitted from beans to leaves via xylem, inducing leaf fall and death of the plant. Mutations in two genes of Arabidopsis thaliana, required for the flowering and subsequent formation of seeds, prevent senescence, strongly prolonging the lifespan of this small semelparous grass that becomes a big bush with woody stem, and initiate substitution of vegetative for sexual reproduction. The death of pacific salmon immediately after spawning is surely programmed. In this case, numerous typical traits of aging, including amyloid plaques in the brain, appear on the time scale of days. There are some indications that slow aging of higher animals and humans is also programmed, being the final step of ontogenesis. It is assumed that stepwise decline of many physiological functions during such aging increases pressure of natural selection on organisms stimulating in this way biological evolution. As a working hypothesis, the biochemical mechanism of slow aging is proposed. It is assumed that mitochondria-generated reactive oxygen species (ROS) is a tool to stimulate apoptosis, an effect decreasing with age the cell number (cellularity) of organs and tissues. A group of SkQ-type substances composed of plastoquinone and a penetrating cation were synthesized to target an antioxidant into mitochondria and to prevent the age-linked rise of the mitochondrial ROS level. Such targeting is due to the fact that mitochondria are the only cellular organelles that are negatively charged compared to the cytosol. SkQs are shown to strongly decrease concentration of ROS in mitochondria, prolong lifespan of fungi, invertebrates, fish, and mammals, and retard appearance of numerous traits of aging. Clinical trials of SkQ1 (plastoquinonyl decyltriphenylphosphonium) have been successfully completed so that the Ministry of Health of the Russian Federation recommends drops of very dilute (0.25 µM) solution of this antioxidant as a medicine to treat the syndrome of dry eye, which was previously considered an incurable disease developing with age. These drops are already available in drugstores. Thus, SkQ1 is the first mitochondria-targeted drug employed in medical practice.}, }
@article {pmid22815925, year = {2012}, author = {Gonçalves, RL and Oliveira, JH and Oliveira, GA and Andersen, JF and Oliveira, MF and Oliveira, PL and Barillas-Mury, C}, title = {Mitochondrial reactive oxygen species modulate mosquito susceptibility to Plasmodium infection.}, journal = {PloS one}, volume = {7}, number = {7}, pages = {e41083}, pmid = {22815925}, issn = {1932-6203}, support = {//Intramural NIH HHS/United States ; }, mesh = {Aedes/metabolism/*parasitology ; Animals ; Anopheles/metabolism/*parasitology ; Anti-Bacterial Agents/chemistry ; Cloning, Molecular ; Gene Silencing ; Hydrogen Peroxide/chemistry ; Malaria/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/genetics/*metabolism ; Models, Biological ; Molecular Conformation ; Oxidation-Reduction ; Oxidative Phosphorylation ; Oxygen Consumption ; Phylogeny ; Plasmodium berghei/*metabolism ; Protons ; Protozoan Proteins/genetics/*metabolism ; RNA, Double-Stranded/metabolism ; *Reactive Oxygen Species ; }, abstract = {BACKGROUND: Mitochondria perform multiple roles in cell biology, acting as the site of aerobic energy-transducing pathways and as an important source of reactive oxygen species (ROS) that modulate redox metabolism.<br><br>We demonstrate that a novel member of the mitochondrial transporter protein family, Anopheles gambiae mitochondrial carrier 1 (AgMC1), is required to maintain mitochondrial membrane potential in mosquito midgut cells and modulates epithelial responses to Plasmodium infection. AgMC1 silencing reduces mitochondrial membrane potential, resulting in increased proton-leak and uncoupling of oxidative phosphorylation. These metabolic changes reduce midgut ROS generation and increase A. gambiae susceptibility to Plasmodium infection.<br><br>CONCLUSION: We provide direct experimental evidence indicating that ROS derived from mitochondria can modulate mosquito epithelial responses to Plasmodium infection.}, }
@article {pmid22813893, year = {2012}, author = {Hutchison, EA and Bueche, JA and Glass, NL}, title = {Diversification of a protein kinase cascade: IME-2 is involved in nonself recognition and programmed cell death in Neurospora crassa.}, journal = {Genetics}, volume = {192}, number = {2}, pages = {467-482}, pmid = {22813893}, issn = {1943-2631}, support = {P01 GM068087/GM/NIGMS NIH HHS/United States ; R01 GM060468/GM/NIGMS NIH HHS/United States ; GM60468/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics ; Cell Death/*genetics/physiology ; Evolution, Molecular ; Intracellular Signaling Peptides and Proteins/genetics/metabolism ; Meiosis/genetics ; Mutation ; *Neurospora crassa/genetics/metabolism/physiology ; Phosphorylation ; Protein Serine-Threonine Kinases/*genetics/metabolism/physiology ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; *Sequence Homology, Amino Acid ; Signal Transduction ; }, abstract = {Kinase cascades and the modification of proteins by phosphorylation are major mechanisms for cell signaling and communication, and evolution of these signaling pathways can contribute to new developmental or environmental response pathways. The Saccharomyces cerevisiae kinase Ime2 has been well characterized for its role in meiosis. However, recent studies have revealed alternative functions for Ime2 in both S. cerevisiae and other fungi. In the filamentous fungus Neurospora crassa, the IME2 homolog (ime-2) is not required for meiosis. Here we determine that ime-2 interacts genetically with a transcription factor vib-1 during nonself recognition and programmed cell death (PCD). Mutations in vib-1 (Δvib-1) suppress PCD due to nonself recognition events; however, a Δvib-1 Δime-2 mutant restored wild-type levels of cell death. A role for ime-2 in the post-translational processing and localization of a mitochondrial matrix protein was identified, which may implicate mitochondria in N. crassa nonself recognition and PCD. Further, Δvib-1 strains do not produce extracellular proteases, but protease secretion reverted to near wild-type levels in a Δvib-1 Δime-2 strain. Mass spectrometry analysis revealed that the VIB-1 protein is phosphorylated at several sites, including a site that matches the IME-2 consensus. The genetic and biochemical data for ime-2 and vib-1 indicate that IME-2 is a negative regulator of VIB-1 and suggest parallel negative regulation by IME-2 of a cell death pathway in N. crassa that functions in concert with the VIB-1 cell death pathway. Thus, IME2 kinase function has evolved following the divergence of S. cerevisiae and N. crassa and provides insight into the evolution of kinases and their regulatory targets.}, }
@article {pmid22813777, year = {2012}, author = {Drown, DM and Preuss, KM and Wade, MJ}, title = {Evidence of a paucity of genes that interact with the mitochondrion on the X in mammals.}, journal = {Genome biology and evolution}, volume = {4}, number = {8}, pages = {763-768}, pmid = {22813777}, issn = {1759-6653}, support = {R01 GM065414/GM/NIGMS NIH HHS/United States ; R01 GM084238/GM/NIGMS NIH HHS/United States ; R01GM084238/GM/NIGMS NIH HHS/United States ; R01GM065414/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Nucleus/genetics ; *Epistasis, Genetic ; *Evolution, Molecular ; Female ; Male ; Mammals/*genetics ; Mitochondria/*genetics ; X Chromosome/*genetics ; }, abstract = {Mitochondria are essential organelles whose replication, development, and physiology are dependent upon coordinated gene interactions with both the mitochondrial and the nuclear genomes. The evolution of coadapted (CA) nuclear-mitochondrial gene combinations would be facilitated if such nuclear genes were located on the X-chromosome instead of on the autosomes because of the increased probability of cotransmission. Here, we test the prediction of the CA hypothesis by investigating the chromosomal distribution of nuclear genes that interact with mitochondria. Using the online genome database BIOMART, we compared the density of genes that have a mitochondrion cellular component annotation across chromosomes in 16 vertebrates. We find a strong and highly significant genomic pattern against the CA hypothesis: nuclear genes interacting with the mitochondrion are significantly underrepresented on the X-chromosome in mammals but not in birds. We interpret our findings in terms of sexual conflict as a mechanism that may generate the observed pattern. Our finding extends single-gene theory for the evolution of sexually antagonistic genes to nuclear-mitochondrial gene combinations.}, }
@article {pmid22806564, year = {2013}, author = {Zhao, J and Lendahl, U and Nistér, M}, title = {Regulation of mitochondrial dynamics: convergences and divergences between yeast and vertebrates.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {70}, number = {6}, pages = {951-976}, pmid = {22806564}, issn = {1420-9071}, mesh = {Animals ; *Biological Evolution ; Cell Line ; Dynamins ; GTP Phosphohydrolases/physiology ; Humans ; Microtubule-Associated Proteins/*metabolism/physiology ; Mitochondrial Dynamics/*physiology ; Mitochondrial Proteins/physiology ; *Models, Biological ; Saccharomyces cerevisiae/*physiology ; Species Specificity ; Vertebrates/*physiology ; }, abstract = {In eukaryotic cells, the shape of mitochondria can be tuned to various physiological conditions by a balance of fusion and fission processes termed mitochondrial dynamics. Mitochondrial dynamics controls not only the morphology but also the function of mitochondria, and therefore is crucial in many aspects of a cell's life. Consequently, dysfunction of mitochondrial dynamics has been implicated in a variety of human diseases including cancer. Several proteins important for mitochondrial fusion and fission have been discovered over the past decade. However, there is emerging evidence that there are as yet unidentified proteins important for these processes and that the fusion/fission machinery is not completely conserved between yeast and vertebrates. The recent characterization of several mammalian proteins important for the process that were not conserved in yeast, may indicate that the molecular mechanisms regulating and controlling the morphology and function of mitochondria are more elaborate and complex in vertebrates. This difference could possibly be a consequence of different needs in the different cell types of multicellular organisms. Here, we review recent advances in the field of mitochondrial dynamics. We highlight and discuss the mechanisms regulating recruitment of cytosolic Drp1 to the mitochondrial outer membrane by Fis1, Mff, and MIEF1 in mammals and the divergences in regulation of mitochondrial dynamics between yeast and vertebrates.}, }
@article {pmid22804568, year = {2013}, author = {Winslow, RM}, title = {Oxygen: the poison is in the dose.}, journal = {Transfusion}, volume = {53}, number = {2}, pages = {424-437}, doi = {10.1111/j.1537-2995.2012.03774.x}, pmid = {22804568}, issn = {1537-2995}, mesh = {Animals ; Biological Evolution ; Cell Respiration/physiology ; Dose-Response Relationship, Drug ; Energy Metabolism/physiology ; Hemoglobins/adverse effects ; Humans ; Microcirculation/physiology ; Mitochondria/metabolism/physiology ; Oxygen/administration &amp; dosage/metabolism/*poisoning/therapeutic use ; Oxygen Consumption/physiology ; }, abstract = {Cell-free hemoglobin (Hb) has been blamed for a spectrum of problems, including vasoconstriction pancreatitis, myocardial infarction, and pulmonary hypertension in hemolytic anemia, malaria, and sickle cell anemia, and from Hb-based oxygen carriers (HBOCs). Toxicities have been attributed to scavenging of nitric oxide (NO). However, while NO scavenging may explain many in vitro effects, and some effects in animal models and clinical trials with HBOCs, key inconsistencies in the theory require alternative explanations. This review considers the hypothesis that cell-free Hb oversupplies oxygen to tissues, leading to oxygen-related toxicity, possibly through formation of reactive oxygen species and local destruction of NO. Evidence for this hypothesis comes from various sources, establishing that tissue oxygen levels are maintained over very narrow (and low) levels, even at high oxygen consumption. Tissue is normally protected from excessive oxygen by its extremely low solubility in plasma, but introduction of cell-free Hb, even at low concentration, greatly augments oxygen supply, engaging protective mechanisms that include vasoconstriction and ischemia. The requirement to limit oxygen supply by cell-free Hb suggests novel ways to modify it to overcome vasoconstriction, independent of the intrinsic reaction of Hb with NO. This control is essential to the design of a safe and effective cell-free HBOC.}, }
@article {pmid22803798, year = {2012}, author = {Katz, LA}, title = {Origin and diversification of eukaryotes.}, journal = {Annual review of microbiology}, volume = {66}, number = {}, pages = {411-427}, doi = {10.1146/annurev-micro-090110-102808}, pmid = {22803798}, issn = {1545-3251}, support = {1R15GM081865-01/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biodiversity ; *Biological Evolution ; Eukaryota/*classification/*genetics ; }, abstract = {The bulk of the diversity of eukaryotic life is microbial. Although the larger eukaryotes-namely plants, animals, and fungi-dominate our visual landscapes, microbial lineages compose the greater part of both genetic diversity and biomass, and contain many evolutionary innovations. Our understanding of the origin and diversification of eukaryotes has improved substantially with analyses of molecular data from diverse lineages. These data have provided insight into the nature of the genome of the last eukaryotic common ancestor (LECA). Yet, the origin of key eukaryotic features, namely the nucleus and cytoskeleton, remains poorly understood. In contrast, the past decades have seen considerable refinement in hypotheses on the major branching events in the evolution of eukaryotic diversity. New insights have also emerged, including evidence for the acquisition of mitochondria at the time of the origin of eukaryotes and data supporting the dynamic nature of genomes in LECA.}, }
@article {pmid22797472, year = {2012}, author = {Melonek, J and Matros, A and Trösch, M and Mock, HP and Krupinska, K}, title = {The core of chloroplast nucleoids contains architectural SWIB domain proteins.}, journal = {The Plant cell}, volume = {24}, number = {7}, pages = {3060-3073}, pmid = {22797472}, issn = {1532-298X}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/metabolism ; Cell Nucleus/genetics/metabolism ; Chloroplasts/*genetics/metabolism ; Chromosomes, Plant/genetics/metabolism ; DNA-Binding Proteins/genetics/isolation &amp; purification/metabolism ; Electrophoresis, Gel, Two-Dimensional ; Escherichia coli/cytology/genetics/metabolism ; Green Fluorescent Proteins ; Luminescent Proteins ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Mutation ; Phylogeny ; Plant Leaves/genetics/metabolism ; Plant Proteins/*genetics/isolation &amp; purification/metabolism ; Protein Structure, Tertiary ; Proteomics ; Recombinant Fusion Proteins ; Sequence Alignment ; Spinacia oleracea/cytology/*genetics/metabolism ; Nicotiana/cytology/genetics/metabolism ; Red Fluorescent Protein ; }, abstract = {A highly enriched fraction of the transcriptionally active chromosome from chloroplasts of spinach (Spinacia oleracea) was analyzed by two-dimensional gel electrophoresis and mass spectrometry to identify proteins involved in structuring of the nucleoid core. Among such plastid nucleoid-associated candidate proteins a 12-kD SWIB (SWI/SNF complex B) domain-containing protein was identified. It belongs to a subgroup of low molecular mass SWIB domain proteins, which in Arabidopsis thaliana has six members (SWIB-1 to SWIB-6) with predictions for localization in the two DNA-containing organelles. Green/red fluorescent protein fusions of four of them were shown to be targeted to chloroplasts, where they colocalize with each other as well as with the plastid envelope DNA binding protein in structures corresponding to plastid nucleoids. For SWIB-6 and SWIB-4, a second localization in mitochondria and nucleus, respectively, could be observed. SWIB-4 has a histone H1 motif next to the SWIB domain and was shown to bind to DNA. Moreover, the recombinant SWIB-4 protein was shown to induce compaction and condensation of nucleoids and to functionally complement a mutant of Escherichia coli lacking the histone-like nucleoid structuring protein H-NS.}, }
@article {pmid22791239, year = {2012}, author = {Lynch, MD and Bartram, AK and Neufeld, JD}, title = {Targeted recovery of novel phylogenetic diversity from next-generation sequence data.}, journal = {The ISME journal}, volume = {6}, number = {11}, pages = {2067-2077}, pmid = {22791239}, issn = {1751-7370}, mesh = {Arctic Regions ; Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Genes, rRNA ; High-Throughput Nucleotide Sequencing ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Soil Microbiology ; }, abstract = {Next-generation sequencing technologies have led to recognition of a so-called 'rare biosphere'. These microbial operational taxonomic units (OTUs) are defined by low relative abundance and may be specifically adapted to maintaining low population sizes. We hypothesized that mining of low-abundance next-generation 16S ribosomal RNA (rRNA) gene data would lead to the discovery of novel phylogenetic diversity, reflecting microorganisms not yet discovered by previous sampling efforts. Here, we test this hypothesis by combining molecular and bioinformatic approaches for targeted retrieval of phylogenetic novelty within rare biosphere OTUs. We combined BLASTN network analysis, phylogenetics and targeted primer design to amplify 16S rRNA gene sequences from unique potential bacterial lineages, comprising part of the rare biosphere from a multi-million sequence data set from an Arctic tundra soil sample. Demonstrating the feasibility of the protocol developed here, three of seven recovered phylogenetic lineages represented extremely divergent taxonomic entities. These divergent target sequences correspond to (a) a previously unknown lineage within the BRC1 candidate phylum, (b) a sister group to the early diverging and currently recognized monospecific Cyanobacteria Gloeobacter, a genus containing multiple plesiomorphic traits and (c) a highly divergent lineage phylogenetically resolved within mitochondria. A comparison to twelve next-generation data sets from additional soils suggested persistent low-abundance distributions of these novel 16S rRNA genes. The results demonstrate this sequence analysis and retrieval pipeline as applicable for exploring underrepresented phylogenetic novelty and recovering taxa that may represent significant steps in bacterial evolution.}, }
@article {pmid22784095, year = {2012}, author = {Balakirev, ES and Krupnova, TN and Ayala, FJ}, title = {DNA variation in the phenotypically-diverse brown alga Saccharina japonica.}, journal = {BMC plant biology}, volume = {12}, number = {}, pages = {108}, pmid = {22784095}, issn = {1471-2229}, mesh = {Base Sequence ; Cell Nucleus/genetics ; DNA, Algal/*genetics ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Electron Transport Complex IV/genetics ; Genetic Markers ; Mitochondria/genetics ; Molecular Sequence Data ; Phaeophyceae/*genetics ; *Phenotype ; Phylogeny ; Plastids/genetics ; *Polymorphism, Genetic ; Recombination, Genetic ; Ribulose-Bisphosphate Carboxylase/genetics ; }, abstract = {BACKGROUND: Saccharina japonica (Areschoug) Lane, Mayes, Druehl et Saunders is an economically important and highly morphologically variable brown alga inhabiting the northwest Pacific marine waters. On the basis of nuclear (ITS), plastid (rbcLS) and mitochondrial (COI) DNA sequence data, we have analyzed the genetic composition of typical Saccharina japonica (TYP) and its two common morphological varieties, known as the "longipes" (LON) and "shallow-water" (SHA) forms seeking to clarify their taxonomical status and to evaluate the possibility of cryptic species within S. japonica.<br><br>RESULTS: The data show that the TYP and LON forms are very similar genetically in spite of drastic differences in morphology, life history traits, and ecological preferences. Both, however, are genetically quite different from the SHA form. The two Saccharina lineages are distinguished by 109 fixed single nucleotide differences as well as by seven fixed length polymorphisms (based on a 4,286 bp concatenated dataset that includes three gene regions). The GenBank database reveals a close affinity of the TYP and LON forms to S. japonica and the SHA form to S. cichorioides. The three gene markers used in the present work have different sensitivity for the algal species identification. COI gene was the most discriminant gene marker. However, we have detected instances of interspecific COI recombination reflecting putative historical hybridization events between distantly related algal lineages. The recombinant sequences show highly contrasted level of divergence in the 5'- and 3'- regions of the gene, leading to significantly different tree topologies depending on the gene segment (5'- or 3'-) used for tree reconstruction. Consequently, the 5'-COI "barcoding" region (~ 650 bp) can be misleading for identification purposes, at least in the case of algal species that might have experienced historical hybridization events.<br><br>CONCLUSION: Taking into account the potential roles of phenotypic plasticity in evolution, we conclude that the TYP and LON forms represent examples of algae phenotypic diversification that enables successful adaptation to contrasting shallow- and deep-water marine environments, while the SHA form is very similar to S. cichorioides and should be considered a different species. Practical applications for algal management and conservation are briefly considered.}, }
@article {pmid22778261, year = {2012}, author = {Harsman, A and Niemann, M and Pusnik, M and Schmidt, O and Burmann, BM and Hiller, S and Meisinger, C and Schneider, A and Wagner, R}, title = {Bacterial origin of a mitochondrial outer membrane protein translocase: new perspectives from comparative single channel electrophysiology.}, journal = {The Journal of biological chemistry}, volume = {287}, number = {37}, pages = {31437-31445}, pmid = {22778261}, issn = {1083-351X}, mesh = {Bacteria/*genetics/metabolism ; Bacterial Outer Membrane Proteins/*genetics/metabolism ; *Evolution, Molecular ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/*genetics/metabolism ; *Protein Folding ; Protozoan Proteins/*genetics/metabolism ; Trypanosoma brucei brucei/*genetics/metabolism ; }, abstract = {Mitochondria are of bacterial ancestry and have to import most of their proteins from the cytosol. This process is mediated by Tom40, an essential protein that forms the protein-translocating pore in the outer mitochondrial membrane. Tom40 is conserved in virtually all eukaryotes, but its evolutionary origin is unclear because bacterial orthologues have not been identified so far. Recently, it was shown that the parasitic protozoon Trypanosoma brucei lacks a conventional Tom40 and instead employs the archaic translocase of the outer mitochondrial membrane (ATOM), a protein that shows similarities to both eukaryotic Tom40 and bacterial protein translocases of the Omp85 family. Here we present electrophysiological single channel data showing that ATOM forms a hydrophilic pore of large conductance and high open probability. Moreover, ATOM channels exhibit a preference for the passage of cationic molecules consistent with the idea that it may translocate unfolded proteins targeted by positively charged N-terminal presequences. This is further supported by the fact that the addition of a presequence peptide induces transient pore closure. An in-depth comparison of these single channel properties with those of other protein translocases reveals that ATOM closely resembles bacterial-type protein export channels rather than eukaryotic Tom40. Our results support the idea that ATOM represents an evolutionary intermediate between a bacterial Omp85-like protein export machinery and the conventional Tom40 that is found in mitochondria of other eukaryotes.}, }
@article {pmid22776908, year = {2013}, author = {Hillman, SS and Hancock, TV and Hedrick, MS}, title = {A comparative meta-analysis of maximal aerobic metabolism of vertebrates: implications for respiratory and cardiovascular limits to gas exchange.}, journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology}, volume = {183}, number = {2}, pages = {167-179}, pmid = {22776908}, issn = {1432-136X}, mesh = {Animals ; *Biological Evolution ; Carbon Dioxide/*metabolism ; Energy Metabolism/*physiology ; *Models, Biological ; Oxygen/*metabolism ; Pulmonary Gas Exchange/*physiology ; Species Specificity ; Vertebrates/*metabolism ; }, abstract = {Maximal aerobic metabolic rates (MMR) in vertebrates are supported by increased conductive and diffusive fluxes of O(2) from the environment to the mitochondria necessitating concomitant increases in CO(2) efflux. A question that has received much attention has been which step, respiratory or cardiovascular, provides the principal rate limitation to gas flux at MMR? Limitation analyses have principally focused on O(2) fluxes, though the excess capacity of the lung for O(2) ventilation and diffusion remains unexplained except as a safety factor. Analyses of MMR normally rely upon allometry and temperature to define these factors, but cannot account for much of the variation and often have narrow phylogenetic breadth. The unique aspect of our comparative approach was to use an interclass meta-analysis to examine cardio-respiratory variables during the increase from resting metabolic rate to MMR among vertebrates from fish to mammals, independent of allometry and phylogeny. Common patterns at MMR indicate universal principles governing O(2) and CO(2) transport in vertebrate cardiovascular and respiratory systems, despite the varied modes of activities (swimming, running, flying), different cardio-respiratory architecture, and vastly different rates of metabolism (endothermy vs. ectothermy). Our meta-analysis supports previous studies indicating a cardiovascular limit to maximal O(2) transport and also implicates a respiratory system limit to maximal CO(2) efflux, especially in ectotherms. Thus, natural selection would operate on the respiratory system to enhance maximal CO(2) excretion and the cardiovascular system to enhance maximal O(2) uptake. This provides a possible evolutionary explanation for the conundrum of why the respiratory system appears functionally over-designed from an O(2) perspective, a unique insight from previous work focused solely on O(2) fluxes. The results suggest a common gas transport blueprint, or Bauplan, in the vertebrate clade.}, }
@article {pmid22773745, year = {2012}, author = {Manavski, N and Guyon, V and Meurer, J and Wienand, U and Brettschneider, R}, title = {An essential pentatricopeptide repeat protein facilitates 5' maturation and translation initiation of rps3 mRNA in maize mitochondria.}, journal = {The Plant cell}, volume = {24}, number = {7}, pages = {3087-3105}, pmid = {22773745}, issn = {1532-298X}, mesh = {5' Untranslated Regions/*genetics ; Amino Acid Sequence ; Base Sequence ; Endosperm/metabolism ; Gene Expression Regulation, Plant ; Genetic Complementation Test ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; Mutagenesis, Insertional ; Organ Specificity ; Phenotype ; Phylogeny ; Plant Leaves/cytology/embryology/genetics/metabolism ; Plant Proteins/genetics/isolation &amp; purification/*metabolism ; Plants, Genetically Modified ; RNA, Messenger/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Recombinant Fusion Proteins ; Ribosomal Proteins/*genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Zea mays/cytology/embryology/genetics/*metabolism ; }, abstract = {Pentatricopeptide repeat (PPR) proteins are members of one of the largest nucleus-encoded protein families in plants. Here, we describe the previously uncharacterized maize (Zea mays) PPR gene, MPPR6, which was isolated from a Mutator-induced collection of maize kernel mutants by a cDNA-based forward genetic approach. Identification of a second mutant allele and cosegregation analysis confirmed correlation with the mutant phenotype. Histological investigations revealed that the mutation coincides with abnormities in the transfer cell layer, retardation of embryo development, and a considerable reduction of starch level. The function of MPPR6 is conserved across a wide phylogenetic distance as revealed by heterologous complementation of the Arabidopsis thaliana mutant in the orthologous APPR6 gene. MPPR6 appeared to be exclusively present in mitochondria. RNA coimmunoprecipitation and in vitro binding studies revealed a specific physical interaction of MPPR6 with the 5' untranslated region of ribosomal protein S3 (rps3) mRNA. Mapping of transcript termini showed specifically extended rps3 5' ends in the mppr6 mutant. Considerable reduction of mitochondrial translation was observed, indicating loss of RPS3 function. This is consistent with the appearance of truncated RPS3 protein lacking the N terminus in mppr6. Our results suggest that MPPR6 is directly involved in 5' maturation and translation initiation of rps3 mRNA.}, }
@article {pmid22771899, year = {2012}, author = {Weiss, M and Zahavi, A}, title = {The information provided by the adrenal cortical steroids: a hypothesis.}, journal = {Journal of theoretical biology}, volume = {311}, number = {}, pages = {66-68}, doi = {10.1016/j.jtbi.2012.06.040}, pmid = {22771899}, issn = {1095-8541}, mesh = {Adenosine Triphosphate/metabolism ; Adrenal Cortex/*physiology ; Animals ; Blood Glucose/*metabolism ; Glucocorticoids/*metabolism ; Humans ; Mitochondria/metabolism ; *Models, Biological ; Sodium/*metabolism ; }, abstract = {We present the hypothesis that in vertebrates their closed blood circulation facilitated the evolution of the adrenal cortex as a central processing unit that provides the rest of the body with information on the effect of changes in the blood glucose and sodium levels on the functioning of the mitochondria, and of sodium transporters in the adrenal cortex. When cells in the glomerulosa can no longer increase the synthesis of aldosterone, the message to the body is that a higher level of sodium in the blood may damage the cells. When the fasiculata cells cannot increase the synthesis of glucorticoids, the message to the body is that their mitochondria cannot produce more ATP, and that higher levels of glucose in the blood may harm the organism.}, }
@article {pmid22771735, year = {2012}, author = {Vianello, A and Casolo, V and Petrussa, E and Peresson, C and Patui, S and Bertolini, A and Passamonti, S and Braidot, E and Zancani, M}, title = {The mitochondrial permeability transition pore (PTP) - an example of multiple molecular exaptation?.}, journal = {Biochimica et biophysica acta}, volume = {1817}, number = {11}, pages = {2072-2086}, doi = {10.1016/j.bbabio.2012.06.620}, pmid = {22771735}, issn = {0006-3002}, mesh = {Animals ; Calcium/metabolism ; Evolution, Molecular ; Humans ; Mitochondrial Membrane Transport Proteins/genetics/*physiology ; Mitochondrial Permeability Transition Pore ; Phylogeny ; Potassium Channels/physiology ; Reactive Oxygen Species/metabolism ; }, abstract = {The mitochondrial permeability transition (PT) is a well-recognized phenomenon that allows mitochondria to undergo a sudden increase of permeability to solutes with molecular mass ≤ 1500Da, leading to organelle swelling and structural modifications. The relevance of PT relies on its master role in the manifestation of programmed cell death (PCD). This function is performed by a mega-channel (in some cases inhibited by cyclosporin A) named permeability transition pore (PTP), whose function could derive from the assembly of different mitochondrial proteins. In this paper we examine the distribution and characteristics of PTP in mitochondria of eukaryotic organisms so far investigated in order to draw a hypothesis on the mechanism of its evolution. As a result, we suggest that PTP may have arisen as a new function linked to a multiple molecular exaptation of different mitochondrial proteins, even though they could nevertheless still play their original role. Furthermore, we suggest that the early appearance of PTP could have had a crucial role in the establishment of endosymbiosis in eukaryotic cells, by the coordinated balancing of ATP production by glycolysis (performed by the primary phagocyte) and oxidative phosphorylation (accomplished by the endosymbiont). Indeed, we argue on the possibility that this new energetic equilibrium could have opened the way to the subsequent evolution toward metazoans.}, }
@article {pmid22768139, year = {2012}, author = {Konrad, C and Kiss, G and Torocsik, B and Adam-Vizi, V and Chinopoulos, C}, title = {Absence of Ca2+-induced mitochondrial permeability transition but presence of bongkrekate-sensitive nucleotide exchange in C. crangon and P. serratus.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e39839}, pmid = {22768139}, issn = {1932-6203}, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Bongkrekic Acid/*pharmacology ; Calcium/*pharmacology ; Crangonidae/drug effects/*metabolism ; Ligands ; Membrane Potential, Mitochondrial/drug effects ; Mice ; Mitochondria/drug effects/metabolism/ultrastructure ; Mitochondrial ADP, ATP Translocases/chemistry/genetics/metabolism ; Mitochondrial Membrane Transport Proteins/metabolism ; Mitochondrial Permeability Transition Pore ; Molecular Sequence Data ; Nucleotides/*metabolism ; Palaemonidae/drug effects/*metabolism ; Permeability/drug effects ; Phylogeny ; Sequence Alignment ; }, abstract = {Mitochondria from the embryos of brine shrimp (Artemia franciscana) do not undergo Ca(2+)-induced permeability transition in the presence of a profound Ca(2+) uptake capacity. Furthermore, this crustacean is the only organism known to exhibit bongkrekate-insensitive mitochondrial adenine nucleotide exchange, prompting the conjecture that refractoriness to bongkrekate and absence of Ca(2+)-induced permeability transition are somehow related phenomena. Here we report that mitochondria isolated from two other crustaceans, brown shrimp (Crangon crangon) and common prawn (Palaemon serratus) exhibited bongkrekate-sensitive mitochondrial adenine nucleotide transport, but lacked a Ca(2+)-induced permeability transition. Ca(2+) uptake capacity was robust in the absence of adenine nucleotides in both crustaceans, unaffected by either bongkrekate or cyclosporin A. Transmission electron microscopy images of Ca(2+)-loaded mitochondria showed needle-like formations of electron-dense material strikingly similar to those observed in mitochondria from the hepatopancreas of blue crab (Callinectes sapidus) and the embryos of Artemia franciscana. Alignment analysis of the partial coding sequences of the adenine nucleotide translocase (ANT) expressed in Crangon crangon and Palaemon serratus versus the complete sequence expressed in Artemia franciscana reappraised the possibility of the 208-214 amino acid region for conferring sensitivity to bongkrekate. However, our findings suggest that the ability to undergo Ca(2+)-induced mitochondrial permeability transition and the sensitivity of adenine nucleotide translocase to bongkrekate are not necessarily related phenomena.}, }
@article {pmid22767487, year = {2012}, author = {Flight, PA and Rand, DM}, title = {Genetic variation in the acorn barnacle from allozymes to population genomics.}, journal = {Integrative and comparative biology}, volume = {52}, number = {3}, pages = {418-429}, pmid = {22767487}, issn = {1557-7023}, support = {GM067862/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Gene Flow ; Gene Frequency ; Gene Library ; Genetic Loci ; *Genetic Variation ; Genetics, Population/methods ; Genomics/methods ; Isoenzymes/*genetics ; Microsatellite Repeats ; Mitochondria/genetics ; *Selection, Genetic ; Species Specificity ; Thoracica/*genetics ; }, abstract = {Understanding the patterns of genetic variation within and among populations is a central problem in population and evolutionary genetics. We examine this question in the acorn barnacle, Semibalanus balanoides, in which the allozyme loci Mpi and Gpi have been implicated in balancing selection due to varying selective pressures at different spatial scales. We review the patterns of genetic variation at the Mpi locus, compare this to levels of population differentiation at mtDNA and microsatellites, and place these data in the context of genome-wide variation from high-throughput sequencing of population samples spanning the North Atlantic. Despite considerable geographic variation in the patterns of selection at the Mpi allozyme, this locus shows rather low levels of population differentiation at ecological and trans-oceanic scales (F(ST) ~ 5%). Pooled population sequencing was performed on samples from Rhode Island (RI), Maine (ME), and Southwold, England (UK). Analysis of more than 650 million reads identified approximately 335,000 high-quality SNPs in 19 million base pairs of the S. balanoides genome. Much variation is shared across the Atlantic, but there are significant examples of strong population differentiation among samples from RI, ME, and UK. An F(ST) outlier screen of more than 22,000 contigs provided a genome-wide context for interpretation of earlier studies on allozymes, mtDNA, and microsatellites. F(ST) values for allozymes, mtDNA and microsatellites are close to the genome-wide average for random SNPs, with the exception of the trans-Atlantic F(ST) for mtDNA. The majority of F(ST) outliers were unique between individual pairs of populations, but some genes show shared patterns of excess differentiation. These data indicate that gene flow is high, that selection is strong on a subset of genes, and that a variety of genes are experiencing diversifying selection at large spatial scales. This survey of polymorphism in S. balanoides provides a number of genomic tools that promise to make this a powerful model for ecological genomics of the rocky intertidal.}, }
@article {pmid22759300, year = {2012}, author = {Stelbrink, B and Albrecht, C and Hall, R and von Rintelen, T}, title = {The biogeography of Sulawesi revisited: is there evidence for a vicariant origin of taxa on Wallace's "anomalous island"?.}, journal = {Evolution; international journal of organic evolution}, volume = {66}, number = {7}, pages = {2252-2271}, doi = {10.1111/j.1558-5646.2012.01588.x}, pmid = {22759300}, issn = {1558-5646}, mesh = {Animals ; Bayes Theorem ; Biodiversity ; Cell Nucleus/genetics ; Ecosystem ; *Evolution, Molecular ; *Genetic Speciation ; Geography ; Geological Phenomena ; Indonesia ; Invertebrates/classification/*genetics ; Mitochondria/genetics ; Phylogeny ; Vertebrates/classification/*genetics ; }, abstract = {Sulawesi, the largest island in the Indonesian biodiversity hotspot region Wallacea, hosts a diverse endemic fauna whose origin has been debated for more than 150 years. We use a comparative approach based on dated phylogenies and geological constraints to test the role of vicariance versus dispersal in the origin of Sulawesi taxa. Most divergence time estimates for the split of Sulawesi lineages from their sister groups postdate relevant tectonic vicariant events, suggesting that the island was predominantly colonized by dispersal. Vicariance cannot be refuted for 20% of the analyzed taxa, though. Although vicariance across Wallace's Line was only supported for one arthropod taxon, divergence time estimates were consistent with a "tectonic dispersal" vicariance hypothesis from the East in three (invertebrate and vertebrate) taxa. Speciation on Sulawesi did not occur before the Miocene, which is consistent with geological evidence for more extensive land on the island from that time. The Pliocene onset of periodic sea-level changes may have played a role in increasing the potential for dispersal to Sulawesi. A more extensive taxon sampling in Wallacea will be crucial for refining our understanding of the region's biogeography and for testing hypotheses on the origin of taxa on its most important island.}, }
@article {pmid22750312, year = {2013}, author = {Celedon, JM and Cline, K}, title = {Intra-plastid protein trafficking: how plant cells adapted prokaryotic mechanisms to the eukaryotic condition.}, journal = {Biochimica et biophysica acta}, volume = {1833}, number = {2}, pages = {341-351}, pmid = {22750312}, issn = {0006-3002}, support = {R01 GM046951/GM/NIGMS NIH HHS/United States ; R01 GM46951/GM/NIGMS NIH HHS/United States ; }, mesh = {Chloroplast Proteins/*metabolism ; Chloroplasts/*metabolism ; Eukaryotic Cells/metabolism ; Plant Cells/*metabolism ; Plastids/*metabolism ; Prokaryotic Cells/metabolism ; Protein Transport ; }, abstract = {Protein trafficking and localization in plastids involve a complex interplay between ancient (prokaryotic) and novel (eukaryotic) translocases and targeting machineries. During evolution, ancient systems acquired new functions and novel translocation machineries were developed to facilitate the correct localization of nuclear encoded proteins targeted to the chloroplast. Because of its post-translational nature, targeting and integration of membrane proteins posed the biggest challenge to the organelle to avoid aggregation in the aqueous compartments. Soluble proteins faced a different kind of problem since some had to be transported across three membranes to reach their destination. Early studies suggested that chloroplasts addressed these issues by adapting ancient-prokaryotic machineries and integrating them with novel-eukaryotic systems, a process called 'conservative sorting'. In the last decade, detailed biochemical, genetic, and structural studies have unraveled the mechanisms of protein targeting and localization in chloroplasts, suggesting a highly integrated scheme where ancient and novel systems collaborate at different stages of the process. In this review we focus on the differences and similarities between chloroplast ancestral translocases and their prokaryotic relatives to highlight known modifications that adapted them to the eukaryotic situation. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.}, }
@article {pmid22749883, year = {2013}, author = {Barajas-López, Jde D and Blanco, NE and Strand, &#xc5;}, title = {Plastid-to-nucleus communication, signals controlling the running of the plant cell.}, journal = {Biochimica et biophysica acta}, volume = {1833}, number = {2}, pages = {425-437}, doi = {10.1016/j.bbamcr.2012.06.020}, pmid = {22749883}, issn = {0006-3002}, mesh = {Cell Communication/*physiology ; Cell Nucleus/genetics/*metabolism ; Plant Cells/*metabolism ; Plant Proteins/genetics/*metabolism ; Plastids/genetics/*metabolism ; Protein Transport ; Signal Transduction ; }, abstract = {The presence of genes encoding organellar proteins in both the nucleus and the organelle necessitates tight coordination of expression by the different genomes, and this has led to the evolution of sophisticated intracellular signaling networks. Organelle-to-nucleus signaling, or retrograde control, coordinates the expression of nuclear genes encoding organellar proteins with the metabolic and developmental state of the organelle. Complex networks of retrograde signals orchestrate major changes in nuclear gene expression and coordinate cellular activities and assist the cell during plant development and stress responses. It has become clear that, even though the chloroplast depends on the nucleus for its function, plastid signals play important roles in an array of different cellular processes vital to the plant. Hence, the chloroplast exerts significant control over the running of the cell. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.}, }
@article {pmid22747896, year = {2012}, author = {Ruegg, K and Anderson, EC and Slabbekoorn, H}, title = {Differences in timing of migration and response to sexual signalling drive asymmetric hybridization across a migratory divide.}, journal = {Journal of evolutionary biology}, volume = {25}, number = {9}, pages = {1741-1750}, doi = {10.1111/j.1420-9101.2012.02554.x}, pmid = {22747896}, issn = {1420-9101}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Animal Migration/*physiology ; Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Ecotype ; Female ; Gene Flow ; *Genetic Speciation ; Genetics, Population ; Hybridization, Genetic/genetics/*physiology ; Male ; Mating Preference, Animal/physiology ; Mitochondria/genetics ; Reproductive Isolation ; Seasons ; Singing/*physiology ; Songbirds/genetics/*physiology ; Sympatry ; Time Factors ; }, abstract = {Ecological traits and sexual signals may both contribute to the process of ecological speciation. Here we investigate the roles of an ecological trait, seasonal migratory behaviour and a sexual trait, song, in restricting or directing gene flow across a migratory divide in the Swainson's thrush (Catharus ustulatus). We show that short-distance migratory ecotypes wintering in Central America arrive earlier at the breeding grounds than long-distance migratory ecotypes wintering primarily in South America, providing the potential for some premating isolation. Playback experiments suggest that early- and late-arriving forms recognize each other as competitors, but that the early-arriving form responds more aggressively to a broader spectrum of stimuli. Genetic analysis suggests that hybridization occurs more often between males of the early-arriving ecotype and females of the late-arriving ecotype. Together our results suggest that differences in arrival times may reduce the temporal coincidence of mate choice, but asymmetry in response to heterotypic song may hinder complete divergence. These data provide further insight into the roles of ecological traits and sexual signals during the incipient stages of speciation.}, }
@article {pmid22746216, year = {2012}, author = {Liang, R and Zhuo, X and Yang, G and Luo, D and Zhong, S and Zou, J}, title = {Molecular phylogenetic relationships of family Haemulidae (Perciformes: Percoidei) and the related species based on mitochondrial and nuclear genes.}, journal = {Mitochondrial DNA}, volume = {23}, number = {4}, pages = {264-277}, doi = {10.3109/19401736.2012.690746}, pmid = {22746216}, issn = {1940-1744}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genes, Mitochondrial/*genetics ; Mitochondria/genetics ; Perciformes/*classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Haemulidae species are morphologically diversified fishes with wondrous and changeable coloration. These species are prevalent in global tropical, subtropical, and temperate inshore reef areas. Previous morphological classification within Haemulidae and some related families was problematic, and no comprehensive molecular evaluation was conducted on these groups. In this study, we revealed the first molecular phylogenetic analysis involving representative species within Haemulidae and the relevant families (Nemipteridae and Teraponidae). The analysis was performed using both mitochondrial DNA (16S rRNA) and nuclear DNA (TMO-4c4) genes to construct maximum parsimony, maximum likelihood, and Bayesian analysis tree topologies. The molecular phylogeny recovered well-resolved relationships within Haemulidae species and the problematic taxa. In the trees, the Haemulidae species (except for genus Hapalogenys) were divided into two distinct sister lineages, including grunts (Haemulinae) and sweetlips (Plectorhynchinae). Hapalogenys was positioned outside the major Haemulidae tribe and formed an independent group, which challenged the traditional taxonomy that Hapalogenys was classified into Haemulidae. The results did agree with most current studies that Hapalogenys was only distantly related to Haemulidae and could potentially be removed from this family. Additionally, the genus Diagramma was observed to be tightly grouped inside the clade Plectorhinchus, indicating its highly close affinity within Plectorhinchus. Regarding interfamily relationships, the phylogenetic constructions suggested distant relationships within two pairs: between Scolopsis and Haemulidae and between Teraponidae and Haemulidae. Scolopsis was revealed to be highly close with Nemipteridae, and Teraponidae was clustered in an independent group, which was in accordance with most current taxonomic studies.}, }
@article {pmid22739827, year = {2012}, author = {Yi, H and Juergens, M and Jez, JM}, title = {Structure of soybean β-cyanoalanine synthase and the molecular basis for cyanide detoxification in plants.}, journal = {The Plant cell}, volume = {24}, number = {6}, pages = {2696-2706}, pmid = {22739827}, issn = {1532-298X}, mesh = {Catalytic Domain ; Crystallography, X-Ray ; Cyanides/*pharmacokinetics ; Cysteine Synthase/chemistry/metabolism ; Inactivation, Metabolic ; Lyases/*chemistry/genetics/*metabolism ; Models, Molecular ; Mutation ; Protein Conformation ; Glycine max/drug effects/enzymology/*metabolism ; Substrate Specificity ; }, abstract = {Plants produce cyanide (CN-) during ethylene biosynthesis in the mitochondria and require β-cyanoalanine synthase (CAS) for CN- detoxification. Recent studies show that CAS is a member of the β-substituted alanine synthase (BSAS) family, which also includes the Cys biosynthesis enzyme O-acetylserine sulfhydrylase (OASS), but how the BSAS evolved distinct metabolic functions is not understood. Here we show that soybean (Glycine max) CAS and OASS form α-aminoacrylate reaction intermediates from Cys and O-acetylserine, respectively. To understand the molecular evolution of CAS and OASS in the BSAS enzyme family, the crystal structures of Gm-CAS and the Gm-CAS K95A mutant with a linked pyridoxal phosphate (PLP)-Cys molecule in the active site were determined. These structures establish a common fold for the plant BSAS family and reveal a substrate-induced conformational change that encloses the active site for catalysis. Comparison of CAS and OASS identified residues that covary in the PLP binding site. The Gm-OASS T81M, S181M, and T185S mutants altered the ratio of OASS:CAS activity but did not convert substrate preference to that of a CAS. Generation of a triple mutant Gm-OASS successfully switched reaction chemistry to that of a CAS. This study provides new molecular insight into the evolution of diverse enzyme functions across the BSAS family in plants.}, }
@article {pmid22736308, year = {2012}, author = {Ip, YK and Loong, AM and Chng, YR and Hiong, KC and Chew, SF}, title = {Hepatic carbamoyl phosphate synthetase (CPS) I and urea contents in the hylid tree frog, Litoria caerulea: transition from CPS III to CPS I.}, journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology}, volume = {182}, number = {8}, pages = {1081-1094}, pmid = {22736308}, issn = {1432-136X}, mesh = {*Adaptation, Physiological ; Amino Acid Sequence ; Amphibian Proteins/chemistry/*metabolism ; Animals ; Anura/*physiology ; Carbamoyl-Phosphate Synthase (Ammonia)/chemistry/*metabolism ; Carbon-Nitrogen Ligases/chemistry/*metabolism ; Cytosol/enzymology/metabolism ; Droughts ; Enzyme Activation ; Isoenzymes/chemistry/metabolism ; Liver/enzymology/*metabolism ; Mitochondria, Liver/enzymology/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Transport ; Sequence Alignment ; Sequence Homology, Amino Acid ; Urea/blood/*metabolism ; Water-Electrolyte Balance ; }, abstract = {The complete cDNA sequence of CPS I obtained from the liver of the hylid tree frog, Litoria caerulea, consisted of 4,485 bp which coded for 1,495 amino acids with an estimated molecular mass of 163.7 kDa. The deduced CPS I consisted of a mitochondrial targeting sequence of 33 amino acid residues, a glutaminase amidotransferase component spanning from tyrosine 95 to leucine 425, and a methylglyoxal synthetase-like component spanning from valine 441 to lysine 1566. It also comprised two cysteine residues (cysteine 1360 and cysteine 1370) that are characteristic of N-acetyl-L-glutamate dependency. Similar to the CPS I of Rana catesbeiana and Cps III of lungfishes and teleosts, it contained the Cys-His-Glu catalytic triad (cysteine 304, histidine 388 and glutamate 390). All Cps III contain methionine 305 and glutamine 308, which are essential for the Cys-His-Glu triad to react with glutamine, but the CPS I of R. catesbeiana contains lysine 305 and glutamate 308, and therefore cannot effectively utilize glutamine as a substrate. However, the CPS I of L. caerulea, unlike that of R. catesbeiana, contained besides glutamate 308, methionine 305 instead of lysine 305, and thus represented a transitional form between Cps III and CPS I. Indeed, CPS I of L. caerulea could utilize glutamine or NH4[+] as a substrate in vitro, but the activity obtained with glutamine + NH4[+] reflected that obtained with NH4[+] alone. Furthermore, only <5 % of the glutamine synthetase activity was present in the hepatic mitochondria, indicating that CPS I of L. caerulea did not have an effective supply of glutamine in vivo. Hence, our results confirmed that the evolution of CPS I from Cps III occurred in amphibians. Since L. caerulea contained high levels of urea in its muscle and liver, which increased significantly in response to desiccation, its CPS I had the dual functions of detoxifying ammonia to urea and producing urea to reduce evaporative water loss.}, }
@article {pmid22729862, year = {2012}, author = {Ramzan, R and Weber, P and Kadenbach, B and Vogt, S}, title = {Individual biochemical behaviour versus biological robustness: spotlight on the regulation of cytochrome c oxidase.}, journal = {Advances in experimental medicine and biology}, volume = {748}, number = {}, pages = {265-281}, doi = {10.1007/978-1-4614-3573-0_11}, pmid = {22729862}, issn = {0065-2598}, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Allosteric Regulation ; Amino Acid Sequence ; Animals ; Electron Transport Complex IV/*physiology ; Humans ; Membrane Potential, Mitochondrial ; Molecular Sequence Data ; Phosphorylation ; }, abstract = {During evolution from prokaryotes to eukaryotes, the main function of cytochrome c oxidase (COX), i.e., the coupling of oxygen reduction to proton translocation without the production of ROS (reactive oxygen species) remained unchanged demonstrating its robustness. A new regulation of respiration by the ATP/ADP ratio was introduced in eukaryotes based on nucleotide interaction with the added COX subunit IV. This allosteric ATP-inhibition was proposed to keep the mitochondrial membrane potential (ΔΨ(m)) at low healthy values and thus prevents the formation of ROS at complexes I and III. ROS have been implicated in various degenerative diseases. The allosteric ATP-inhibition of COX is reversibly switched on and off by phosphorylation of COX at a serine or threonine. In more than 100 individual preparations of rat heart and liver mitochondria, prepared under identical conditions, the extent of allosteric ATP-inhibition varied. This variability correlates with the variable inhibition of uncoupled respiration in intact isolated mitochondria by ATP. It is concluded that in higher organisms the allosteric ATP-inhibition is continually switched on and off by neuronal signalling in order to change oxidative phosphorylation from optimal efficiency with lower rate of ATP synthesis under resting conditions (low ΔΨ(m) and ROS production) to maximal rate of ATP synthesis under active (working, stress) conditions (elevated ΔΨ(m) and ROS production).}, }
@article {pmid22729859, year = {2012}, author = {Pierron, D and Wildman, DE and Hüttemann, M and Letellier, T and Grossman, LI}, title = {Evolution of the couple cytochrome c and cytochrome c oxidase in primates.}, journal = {Advances in experimental medicine and biology}, volume = {748}, number = {}, pages = {185-213}, pmid = {22729859}, issn = {0065-2598}, support = {R01 GM089900/GM/NIGMS NIH HHS/United States ; R24 GM065580/GM/NIGMS NIH HHS/United States ; GM089900/GM/NIGMS NIH HHS/United States ; GM65580/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Brain/metabolism ; Cytochromes c/*physiology ; Electron Transport Complex IV/*physiology ; *Evolution, Molecular ; Humans ; Mutation ; Primates/*metabolism ; Protein Subunits ; Selection, Genetic ; }, abstract = {Mitochondrial energy metabolism has been affected by a broad set of ancient and recent evolutionary events. The oldest example is the endosymbiosis theory that led to mitochondria and a recently proposed example is adaptation to cold climate by anatomically modern human lineages. Mitochondrial energy metabolism has also been associated with an important area in anthropology and evolutionary biology, brain enlargement in human evolution. Indeed, several studies have pointed to the need for a major metabolic rearrangement to supply a sufficient amount of energy for brain development in primates.The genes encoding for the coupled cytochrome c (Cyt c) and cytochrome c oxidase (COX, complex IV, EC 1.9.3.1) seem to have an exceptional pattern of evolution in the anthropoid lineage. It has been proposed that this evolution was linked to the rearrangement of energy metabolism needed for brain enlargement. This hypothesis is reinforced by the fact that the COX enzyme was proposed to have a large role in control of the respiratory chain and thereby global energy production.After summarizing major events that occurred during the evolution of COX and cytochrome c on the primate lineage, we review the different evolutionary forces that could have influenced primate COX evolution and discuss the probable causes and consequences of this evolution. Finally, we discuss and review the co-occurring primate phenotypic evolution.}, }
@article {pmid22729852, year = {2012}, author = {Kadenbach, B}, title = {Introduction to mitochondrial oxidative phosphorylation.}, journal = {Advances in experimental medicine and biology}, volume = {748}, number = {}, pages = {1-11}, doi = {10.1007/978-1-4614-3573-0_1}, pmid = {22729852}, issn = {0065-2598}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Humans ; Mitochondria/*metabolism ; *Oxidative Phosphorylation ; Proton-Translocating ATPases/chemistry ; Reactive Oxygen Species/metabolism ; }, abstract = {The basic mechanism of ATP synthesis in the mitochondria by oxidative phosphorylation (OxPhos) was revealed in the second half of the twentieth century. The OxPhos complexes I-V have been analyzed concerning their subunit composition, genes, and X-ray structures. This book presents new developments regarding the morphology, biogenesis, gene evolution, heat, and reactive oxygen species (ROS) generation in mitochondria, as well as the structure and supercomplex formation of OxPhos complexes. In addition, multiple mitochondrial diseases based on mutations of nuclear-encoded genes have been identified. Little is known, however, of the regulation of OxPhos according to the variable cellular demands of ATP. In particular, the functions of the supernumerary (nuclear-encoded) subunits of mitochondrial OxPhos complexes, which are mostly absent in bacteria, remain largely unknown, although the corresponding and conserved core subunits exhibit the same catalytic activity. Identification of regulatory pathways modulating OxPhos activity, by subunit isoform expression, by allosteric interaction with ATP/ADP, by reversible phosphorylation of protein subunits, or by supercomplex formation, will help to understand the role of mitochondria in the many degenerative diseases, mostly based on ROS formation in mitochondria and/or insufficient energy production.}, }
@article {pmid22723492, year = {2012}, author = {Lease, HM and Klok, CJ and Kaiser, A and Harrison, JF}, title = {Body size is not critical for critical PO2 in scarabaeid and tenebrionid beetles.}, journal = {The Journal of experimental biology}, volume = {215}, number = {Pt 14}, pages = {2524-2533}, doi = {10.1242/jeb.057141}, pmid = {22723492}, issn = {1477-9145}, mesh = {Anaerobiosis ; Animals ; *Body Size ; Body Weight ; Carbon Dioxide/metabolism ; Coleoptera/*anatomy &amp; histology/genetics/*metabolism ; Flight, Animal/physiology ; Oxygen/*metabolism ; Partial Pressure ; Phylogeny ; Sample Size ; Species Specificity ; Tenebrio/*anatomy &amp; histology/genetics/*metabolism ; }, abstract = {Constraints on oxygen delivery potentially limit animal body size. Because diffusion rates are highly distance dependent, and because tracheal length increases with size, gas exchange was traditionally thought to be more difficult for larger insects. As yet the effect of body size on critical oxygen partial pressure (P(crit)) has not been measured for any clade of insect species for which there are interspecific data on tracheal scaling. We addressed this deficiency by measuring P(crit) over a 4150-fold mass range (ratio of largest to smallest species mean) of two families of Coleoptera (Tenebrionidae and Scarabaeidae). We exposed adult beetles to progressively lower oxygen levels and measured their ability to maintain CO(2) release rates. Absolute metabolic rates increased hypometrically with beetle body mass (M) at both normoxic (M(0.748)) and hypoxic (M(0.846)) conditions. P(crit), however, was independent of body size. Maximum overall conductances for oxygen from air to mitochondria (G(O(2),max)) matched metabolic rates as insects became larger, likely enabling the similar P(crit) values observed in large and small beetles. These data suggest that current atmospheric oxygen levels do not limit body size of insects because of limitations on gas exchange. However, increasing relative investment in the tracheal system in larger insects may produce trade-offs or meet spatial limits that constrain insect size.}, }
@article {pmid22709906, year = {2012}, author = {Gawryluk, RM and Chisholm, KA and Pinto, DM and Gray, MW}, title = {Composition of the mitochondrial electron transport chain in acanthamoeba castellanii: structural and evolutionary insights.}, journal = {Biochimica et biophysica acta}, volume = {1817}, number = {11}, pages = {2027-2037}, doi = {10.1016/j.bbabio.2012.06.005}, pmid = {22709906}, issn = {0006-3002}, mesh = {Acanthamoeba castellanii/genetics/*metabolism ; Amino Acid Sequence ; Computational Biology ; Electron Transport ; Electron Transport Chain Complex Proteins/*analysis/*chemistry/physiology ; Electron Transport Complex I/analysis/chemistry/physiology ; Electron Transport Complex II/analysis/physiology ; Electron Transport Complex III/analysis/physiology ; Electron Transport Complex IV/analysis/physiology ; Evolution, Molecular ; Mitochondria/*metabolism ; Molecular Sequence Data ; Proteome ; }, abstract = {The mitochondrion, derived in evolution from an α-proteobacterial progenitor, plays a key metabolic role in eukaryotes. Mitochondria house the electron transport chain (ETC) that couples oxidation of organic substrates and electron transfer to proton pumping and synthesis of ATP. The ETC comprises several multiprotein enzyme complexes, all of which have counterparts in bacteria. However, mitochondrial ETC assemblies from animals, plants and fungi are generally more complex than their bacterial counterparts, with a number of 'supernumerary' subunits appearing early in eukaryotic evolution. Little is known, however, about the ETC of unicellular eukaryotes (protists), which are key to understanding the evolution of mitochondria and the ETC. We present an analysis of the ETC proteome from Acanthamoeba castellanii, an ecologically, medically and evolutionarily important member of Amoebozoa (sister to Opisthokonta). Data obtained from tandem mass spectrometric (MS/MS) analyses of purified mitochondria as well as ETC complexes isolated via blue native polyacrylamide gel electrophoresis are combined with the results of bioinformatic queries of sequence databases. Our bioinformatic analyses have identified most of the ETC subunits found in other eukaryotes, confirming and extending previous observations. The assignment of proteins as ETC subunits by MS/MS provides important insights into the primary structures of ETC proteins and makes possible, through the use of sensitive profile-based similarity searches, the identification of novel constituents of the ETC along with the annotation of highly divergent but phylogenetically conserved ETC subunits.}, }
@article {pmid22708864, year = {2012}, author = {Li, X and Wu, X and Yu, Z}, title = {Complete mitochondrial genome of the Asian green mussel Perna viridis (Bivalvia, Mytilidae).}, journal = {Mitochondrial DNA}, volume = {23}, number = {5}, pages = {358-360}, doi = {10.3109/19401736.2012.690756}, pmid = {22708864}, issn = {1940-1744}, mesh = {Animals ; DNA, Mitochondrial/chemistry/genetics ; *Genome, Mitochondrial ; Perna/classification/*genetics ; }, abstract = {The complete mitochondrial (mt) genome of the Asian green mussel Perna viridis (16,627 bp), an economically important bivalve, was newly sequenced and annotated. P. viridis is the shortest and has a comparatively highest overall A+T content (68%) among six available genomes of marine mussels to date. The atp8 gene's length (49 a.a.) of the green mussel is unexpectedly greatly shorter than that of other marine mussels (87 a.a.). Comparison of the gene order demonstrated that the six marine mussels share no identical gene blocks although they belong to the same family, which indicates that this group should be a good model to study mtDNA evolution and mitochondria inheritance.}, }
@article {pmid22706794, year = {2012}, author = {Poole, AM and Kobayashi, T and Ganley, AR}, title = {A positive role for yeast extrachromosomal rDNA circles? Extrachromosomal ribosomal DNA circle accumulation during the retrograde response may suppress mitochondrial cheats in yeast through the action of TAR1.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {34}, number = {9}, pages = {725-729}, pmid = {22706794}, issn = {1521-1878}, mesh = {Chromosomes, Fungal/*genetics ; DNA, Circular/genetics/metabolism ; DNA, Fungal/*genetics/metabolism ; DNA, Ribosomal/*genetics/metabolism ; Evolution, Molecular ; Gene Dosage ; Gene Expression Regulation, Fungal ; Genotype ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Models, Genetic ; Protein Transport ; Replication Origin ; Ribosomes/genetics/metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Stress, Physiological ; }, }
@article {pmid22701687, year = {2012}, author = {van de Sande, WW}, title = {Phylogenetic analysis of the complete mitochondrial genome of Madurella mycetomatis confirms its taxonomic position within the order Sordariales.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e38654}, pmid = {22701687}, issn = {1932-6203}, mesh = {Base Sequence ; DNA Primers/genetics ; DNA, Ribosomal Spacer/genetics ; Genome, Mitochondrial/*genetics ; Humans ; Likelihood Functions ; Madurella/*classification/*genetics ; Models, Genetic ; Molecular Sequence Annotation ; Molecular Sequence Data ; Mycetoma/*microbiology ; *Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Sudan ; }, abstract = {BACKGROUND: Madurella mycetomatis is the most common cause of human eumycetoma. The genus Madurella has been characterized by overall sterility on mycological media. Due to this sterility and the absence of other reliable morphological and ultrastructural characters, the taxonomic classification of Madurella has long been a challenge. Mitochondria are of monophyletic origin and mitochondrial genomes have been proven to be useful in phylogenetic analyses.<br><br>RESULTS: The first complete mitochondrial DNA genome of a mycetoma-causative agent was sequenced using 454 sequencing. The mitochondrial genome of M. mycetomatis is a circular DNA molecule with a size of 45,590 bp, encoding for the small and the large subunit rRNAs, 27 tRNAs, 11 genes encoding subunits of respiratory chain complexes, 2 ATP synthase subunits, 5 hypothetical proteins, 6 intronic proteins including the ribosomal protein rps3. In phylogenetic analyses using amino acid sequences of the proteins involved in respiratory chain complexes and the 2 ATP synthases it appeared that M. mycetomatis clustered together with members of the order Sordariales and that it was most closely related to Chaetomium thermophilum. Analyses of the gene order showed that within the order Sordariales a similar gene order is found. Furthermore also the tRNA order seemed mostly conserved.<br><br>CONCLUSION: Phylogenetic analyses of fungal mitochondrial genomes confirmed that M. mycetomatis belongs to the order of Sordariales and that it was most closely related to Chaetomium thermophilum, with which it also shared a comparable gene and tRNA order.}, }
@article {pmid22697611, year = {2012}, author = {Rizzi, E and Lari, M and Gigli, E and De Bellis, G and Caramelli, D}, title = {Ancient DNA studies: new perspectives on old samples.}, journal = {Genetics, selection, evolution : GSE}, volume = {44}, number = {1}, pages = {21}, pmid = {22697611}, issn = {1297-9686}, mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; DNA Damage ; DNA, Mitochondrial/analysis/*genetics ; *Evolution, Molecular ; Extinction, Biological ; Genome, Human ; Humans ; Mitochondria/genetics ; Polymerase Chain Reaction/methods/standards ; Sequence Analysis, DNA/*methods ; Time Factors ; }, abstract = {In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field.}, }
@article {pmid22694836, year = {2012}, author = {Lundquist, PK and Davis, JI and van Wijk, KJ}, title = {ABC1K atypical kinases in plants: filling the organellar kinase void.}, journal = {Trends in plant science}, volume = {17}, number = {9}, pages = {546-555}, pmid = {22694836}, issn = {1878-4372}, support = {T32 GM008500/GM/NIGMS NIH HHS/United States ; 5T32GM008500/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Motifs ; Benzoquinones/metabolism ; Evolution, Molecular ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant/genetics ; Magnoliopsida/*enzymology/genetics/ultrastructure ; Mitochondria/*enzymology ; Multigene Family ; Phylogeny ; Plant Proteins/genetics/metabolism ; Plastids/*enzymology ; Protein Kinases/*genetics/metabolism ; Protein Structure, Tertiary ; Yeasts/enzymology/genetics ; }, abstract = {Surprisingly few protein kinases have been demonstrated in chloroplasts or mitochondria. Here, we discuss the activity of bc(1) complex kinase (ABC1K) protein family, which we suggest locate in mitochondria and plastids, thus filling the kinase void. The ABC1Ks are atypical protein kinases and their ancestral function is the regulation of quinone synthesis. ABC1Ks have proliferated from one or two members in non-photosynthetic organisms to more than 16 members in algae and higher plants. In this review, we reconstruct the evolutionary history of the ABC1K family, provide a functional domain analysis for angiosperms and a nomenclature for ABC1Ks in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and maize (Zea mays). Finally, we hypothesize that targets of ABC1Ks include enzymes of prenyl-lipid metabolism as well as components of the organellar gene expression machineries.}, }
@article {pmid22688947, year = {2012}, author = {Duarte, I and Nabuurs, SB and Magno, R and Huynen, M}, title = {Evolution and diversification of the organellar release factor family.}, journal = {Molecular biology and evolution}, volume = {29}, number = {11}, pages = {3497-3512}, pmid = {22688947}, issn = {1537-1719}, mesh = {Amino Acid Motifs ; Bayes Theorem ; Eukaryota/genetics ; *Evolution, Molecular ; Genetic Code/genetics ; *Genetic Variation ; Models, Molecular ; *Multigene Family ; Organelles/*metabolism ; Peptide Termination Factors/chemistry/classification/*genetics/metabolism ; Phylogeny ; Plastids/genetics ; Protein Transport ; Ribosomes/metabolism ; Subcellular Fractions/metabolism ; }, abstract = {Translation termination is accomplished by proteins of the Class I release factor family (RF) that recognize stop codons and catalyze the ribosomal release of the newly synthesized peptide. Bacteria have two canonical RFs: RF1 recognizes UAA and UAG, RF2 recognizes UAA and UGA. Despite that these two release factor proteins are sufficient for de facto translation termination, the eukaryotic organellar RF protein family, which has evolved from bacterial release factors, has expanded considerably, comprising multiple subfamilies, most of which have not been functionally characterized or formally classified. Here, we integrate multiple sources of information to analyze the remarkable differentiation of the RF family among organelles. We document the origin, phylogenetic distribution and sequence structure features of the mitochondrial and plastidial release factors: mtRF1a, mtRF1, mtRF2a, mtRF2b, mtRF2c, ICT1, C12orf65, pRF1, and pRF2, and review published relevant experimental data. The canonical release factors (mtRF1a, mtRF2a, pRF1, and pRF2) and ICT1 are derived from bacterial ancestors, whereas the others have resulted from gene duplications of another release factor. These new RF family members have all lost one or more specific motifs relevant for bona fide release factor function but are mostly targeted to the same organelle as their ancestor. We also characterize the subset of canonical release factor proteins that bear nonclassical PxT/SPF tripeptide motifs and provide a molecular-model-based rationale for their retained ability to recognize stop codons. Finally, we analyze the coevolution of canonical RFs with the organellar genetic code. Although the RF presence in an organelle and its stop codon usage tend to coevolve, we find three taxa that encode an RF2 without using UGA stop codons, and one reverse scenario, where mamiellales green algae use UGA stop codons in their mitochondria without having a mitochondrial type RF2. For the latter, we put forward a "stop-codon reinvention" hypothesis that involves the retargeting of the plastid release factor to the mitochondrion.}, }
@article {pmid22688819, year = {2012}, author = {Müller, M and Mentel, M and van Hellemond, JJ and Henze, K and Woehle, C and Gould, SB and Yu, RY and van der Giezen, M and Tielens, AG and Martin, WF}, title = {Biochemistry and evolution of anaerobic energy metabolism in eukaryotes.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {76}, number = {2}, pages = {444-495}, pmid = {22688819}, issn = {1098-5557}, support = {232975/ERC_/European Research Council/International ; R01 AI011942/AI/NIAID NIH HHS/United States ; AI 11942/AI/NIAID NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/metabolism ; Anaerobiosis/physiology ; *Energy Metabolism ; Eukaryota/*metabolism ; *Evolution, Molecular ; Mitochondria/metabolism ; }, abstract = {Major insights into the phylogenetic distribution, biochemistry, and evolutionary significance of organelles involved in ATP synthesis (energy metabolism) in eukaryotes that thrive in anaerobic environments for all or part of their life cycles have accrued in recent years. All known eukaryotic groups possess an organelle of mitochondrial origin, mapping the origin of mitochondria to the eukaryotic common ancestor, and genome sequence data are rapidly accumulating for eukaryotes that possess anaerobic mitochondria, hydrogenosomes, or mitosomes. Here we review the available biochemical data on the enzymes and pathways that eukaryotes use in anaerobic energy metabolism and summarize the metabolic end products that they generate in their anaerobic habitats, focusing on the biochemical roles that their mitochondria play in anaerobic ATP synthesis. We present metabolic maps of compartmentalized energy metabolism for 16 well-studied species. There are currently no enzymes of core anaerobic energy metabolism that are specific to any of the six eukaryotic supergroup lineages; genes present in one supergroup are also found in at least one other supergroup. The gene distribution across lineages thus reflects the presence of anaerobic energy metabolism in the eukaryote common ancestor and differential loss during the specialization of some lineages to oxic niches, just as oxphos capabilities have been differentially lost in specialization to anoxic niches and the parasitic life-style. Some facultative anaerobes have retained both aerobic and anaerobic pathways. Diversified eukaryotic lineages have retained the same enzymes of anaerobic ATP synthesis, in line with geochemical data indicating low environmental oxygen levels while eukaryotes arose and diversified.}, }
@article {pmid22688299, year = {2012}, author = {Kontro, H and Hulmi, JJ and Rahkila, P and Kainulainen, H}, title = {Cellular and tissue expression of DAPIT, a phylogenetically conserved peptide.}, journal = {European journal of histochemistry : EJH}, volume = {56}, number = {2}, pages = {e18}, pmid = {22688299}, issn = {2038-8306}, mesh = {Animals ; Antibodies ; Gene Expression Regulation/*physiology ; HEK293 Cells ; Human Umbilical Vein Endothelial Cells ; Humans ; Lysosomes/*metabolism ; Membrane Proteins/*biosynthesis ; Mitochondria/*metabolism ; Mitochondrial Proteins/*biosynthesis ; Organ Specificity ; Phylogeny ; Proton Pumps/metabolism ; Rats ; }, abstract = {DAPIT (Diabetes Associated Protein in Insulin-sensitive Tissues) is a small, phylogenetically conserved, 58 amino acid peptide that was previously shown to be down-regulated at mRNA level in insulin-sensitive tissues of type 1 diabetes rats. In this study we characterize a custom made antibody against DAPIT and confirm the mitochondrial presence of DAPIT on cellular level. We also show that DAPIT is localized in lysosomes of HUVEC and HEK 293T cells. In addition, we describe the histological expression of DAPIT in several tissues of rat and man and show that it is highly expressed especially in cells with high aerobic metabolism and epithelial cells related to active transport of nutrients and ions. We propose that DAPIT, in addition to indicated subunit of mitochondrial F-ATPase, is also a subunit of lysosomal V-ATPase suggesting that it is a common component in different proton pumps.}, }
@article {pmid22683762, year = {2013}, author = {Carrie, C and Small, I}, title = {A reevaluation of dual-targeting of proteins to mitochondria and chloroplasts.}, journal = {Biochimica et biophysica acta}, volume = {1833}, number = {2}, pages = {253-259}, doi = {10.1016/j.bbamcr.2012.05.029}, pmid = {22683762}, issn = {0006-3002}, mesh = {Chloroplasts/genetics/*metabolism ; Mitochondria/genetics/*metabolism ; Plant Proteins/*metabolism ; Plastids/genetics/*metabolism ; Protein Transport ; }, abstract = {Over 100 proteins are found in both mitochondria and chloroplasts, via a variety of processes known generally as 'dual-targeting'. Dual-targeting has attracted interest from many different research groups because of its profound implications concerning the mechanisms of protein import into these organelles and the evolution of both the protein import machinery and the targeting sequences within the imported proteins. Beyond these aspects, dual-targeting is also interesting for its implications concerning shared functions between mitochondria and chloroplasts, and especially the control of the activities of these two very different energy organelles. We discuss each of these points in the light of the latest relevant research findings and make some suggestions for where research might be most illuminating in the near future. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.}, }
@article {pmid22683761, year = {2013}, author = {Sheiner, L and Striepen, B}, title = {Protein sorting in complex plastids.}, journal = {Biochimica et biophysica acta}, volume = {1833}, number = {2}, pages = {352-359}, pmid = {22683761}, issn = {0006-3002}, support = {AI64671/AI/NIAID NIH HHS/United States ; R56 AI084415/AI/NIAID NIH HHS/United States ; AI804415/AI/NIAID NIH HHS/United States ; R01 AI084415/AI/NIAID NIH HHS/United States ; R01 AI064671/AI/NIAID NIH HHS/United States ; }, mesh = {Plastids/genetics/*metabolism ; *Protein Transport ; Proteins/genetics/*metabolism ; }, abstract = {Taming a cyanobacterium in a pivitol event of endosymbiosis brought photosynthesis to eukaryotes, and gave rise to the plastids found in glaucophytes, red and green algae, and the descendants of the latter, the plants. Ultrastructural as well as molecular research over the last two decades has demonstrated that plastids have enjoyed surprising lateral mobility across the tree of life. Numerous independent secondary and tertiary endosymbiosis have led to a spread of plastids into a variety of, up to that point, non-photosynthetic lineages. Happily eating and subsequently domesticating one another protists conquered a wide variety of ecological niches. The elaborate evolution of secondary, or complex, plastids is reflected in the numerous membranes that bound them (three or four compared to the two membranes of the primary plastids). Gene transfer to the host nucleus is a hallmark of endosymbiosis and provides centralized cellular control. Here we review how these proteins find their way back into the stroma of the organelle and describe the advances in the understanding of the molecular mechanisms that allow protein translocation across four membranes. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.}, }
@article {pmid22682566, year = {2012}, author = {Vázquez-Limón, C and Hoogewijs, D and Vinogradov, SN and Arredondo-Peter, R}, title = {The evolution of land plant hemoglobins.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {191-192}, number = {}, pages = {71-81}, doi = {10.1016/j.plantsci.2012.04.013}, pmid = {22682566}, issn = {1873-2259}, mesh = {Embryophyta/*metabolism ; *Evolution, Molecular ; Hemoglobins/chemistry/*metabolism ; Phylogeny ; Symbiosis ; Time Factors ; }, abstract = {This review discusses the evolution of land plant hemoglobins within the broader context of eukaryote hemoglobins and the three families of bacterial globins. Most eukaryote hemoglobins, including metazoan globins and the symbiotic and non-symbiotic plant hemoglobins, are homologous to the bacterial 3/3-fold flavohemoglobins. The remaining plant hemoglobins are homologous to the bacterial 2/2-fold group 2 hemoglobins. We have proposed that all eukaryote globins were acquired via horizontal gene transfer concomitant with the endosymbiotic events responsible for the origin of mitochondria and chloroplasts. Although the 3/3 hemoglobins originated in the ancestor of green algae and plants prior to the emergence of embryophytes at about 450 mya, the 2/2 hemoglobins appear to have originated via horizontal gene transfer from a bacterium ancestral to present day Chloroflexi. Unlike the 2/2 hemoglobins, the evolution of the 3/3 hemoglobins was accompanied by duplication, diversification, and functional adaptations. Duplication of the ancestral plant nshb gene into the nshb-1 and nshb-2 lineages occurred prior to the monocot-dicot divergence at ca. 140 mya. It was followed by the emergence of symbiotic hemoglobins from a non-symbiotic hemoglobin precursor and further specialization, leading to leghemoglobins in N2-fixing legume nodules concomitant with the origin of nodulation at ca. 60 mya. The transition of non-symbiotic to symbiotic hemoglobins (including to leghemoglobins) was accompanied by the alteration of heme-Fe coordination from hexa- to penta-coordination. Additional genomic information about Charophyte algae, the sister group to land plants, is required for the further clarification of plant globin phylogeny.}, }
@article {pmid22679783, year = {2012}, author = {Radchenko, OA and Chereshnev, IA and Petrovskaia, AV}, title = {[Position of the genera Lycenchelys gill and Lycodapus gilbert in the family Zoarcidae (Perciformes: Zoarcoidei) inferred from molecular genetic analysis].}, journal = {Genetika}, volume = {48}, number = {3}, pages = {361-371}, pmid = {22679783}, issn = {0016-6758}, mesh = {Animals ; Cytochromes b/genetics ; Evolution, Molecular ; Genetic Variation ; Mitochondria/genetics ; Perciformes/*classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Sequence variation ofthe mitochondrial COI, cytochrome b, and 16S RNA genes, as well as nuclear RNF213 gene was examined in the genera Lycenchelys and Lycodapus with the purpose of determination of their positions in the system of the family Zoarcidae. It was demonstrated that the genus Lycodapus was considerably closer to the generic group of Lycogramminae (Lycogrammoides, Bothrocara, Allolepis, Bothrocarhichthys) than the genus Lycenchelys. However, on the phylogenetic trees both of these genera were located in the clade of the subfamily Lycodinae. Genetic heterogeneity of the genus Lycenchelys, represented by two species groups differing in distribution patterns (northeastern Pacific and Antarctic) and showing more profound differences than the genera of subfamily Lycodinae, was demonstrated.}, }
@article {pmid22679782, year = {2012}, author = {Chertilina, OV and Simonov, EP and Lopatina, NW and Litvinov, IuN}, title = {[Genetic diversity of flat-headed vole (Alticola strelzowi (Kastschenko, 1899)) inferred from cytochrome b variation].}, journal = {Genetika}, volume = {48}, number = {3}, pages = {352-360}, pmid = {22679782}, issn = {0016-6758}, mesh = {Animals ; Arvicolinae/*genetics ; Cytochromes b/*genetics ; Evolution, Molecular ; Genetic Speciation ; *Genetic Variation ; Haplotypes ; Mitochondria/genetics ; *Phylogeography ; }, abstract = {Variation of the cytochrome b gene fragment was examined in 27 flat-headed voles Alticola strelzowi from different parts of the species range. A total of 15 haplotypes were described, while the species as a whole was characterized by low levels of genetic differentiation and polymorphism. The haplotypes fell into three haplogroups, one of which corresponded to the subspecies A. s. strelzowi, and the other two, to A. s. desertorum. Based on different index values, the level of genetic polymorphism in the later subspecies was considered to be higher than in the first one. Phylogeographic analysis suggested post-glacial dispersal of flat-headed voles from a single refugium located in Western Altai. Using different techniques, relatively recent colonization of the Central Altai territory was demonstrated (subspecies A. s. strelzowi), which determined low level of genetic variation in this territory.}, }
@article {pmid22678792, year = {2012}, author = {Chen, H and Guan, MX}, title = {[Mitochondrial genetics and human essential hypertension].}, journal = {Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics}, volume = {29}, number = {3}, pages = {293-295}, doi = {10.3760/cma.j.issn.1003-9406.2012.03.010}, pmid = {22678792}, issn = {1003-9406}, mesh = {DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Humans ; Hypertension/*genetics ; Mitochondria/*genetics ; *Mutation ; }, abstract = {Mitochondrial DNA (mtDNA) exhibits matrilineal inherence. Familial mitochondrial diseases caused by mtDNA mutations are generally involved in organs featuring high energy consumption, which include heart, brain and skeletal muscle. Recently, it has been found that some essential hypertension patients featured classical maternal inheritance, which has confirmed and enriched mtDNA mutations as one of the molecular mechanisms underlying maternally inherited hypertension. Nevertheless, more general as well as radical questions are still to be answered. This article reviews recent advance in mitochondrial genome evolution, mtDNA genetics and the role of mtDNA mutations in maternally inherited hypertension.}, }
@article {pmid22678102, year = {2012}, author = {Williams-Newkirk, AJ and Rowe, LA and Mixson-Hayden, TR and Dasch, GA}, title = {Presence, genetic variability, and potential significance of "Candidatus Midichloria mitochondrii" in the lone star tick Amblyomma americanum.}, journal = {Experimental &amp; applied acarology}, volume = {58}, number = {3}, pages = {291-300}, pmid = {22678102}, issn = {1572-9702}, support = {CC999999//Intramural CDC HHS/United States ; }, mesh = {Alphaproteobacteria/*genetics/ultrastructure ; Animals ; Base Sequence ; DNA, Bacterial/chemistry/isolation &amp; purification ; *Genetic Variation ; Ixodidae/*microbiology ; Mitochondria/*genetics/ultrastructure ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {We used next generation sequencing to detect the bacterium "Candidatus Midichloria mitochondrii" for the first time in lone star ticks (Amblyomma americanum) from the eastern United States. 177 individuals and 11 tick pools from seven sites in four states were tested by pyrosequencing with barcoded 16S rRNA gene eubacterial primers targeting variable regions 5-3. Average infection prevalence was 0.15 across all surveyed populations (range 0-0.29) and only the site with the smallest sample size (n = 5) was negative. Three genotypes differing by 2.6-4.1 % in a 271 bp region of 16S rRNA gene were identified. Two variants co-occurred in sites in North Carolina and New York, but were not observed in the same tick at those sites. The third genotype was found only in Georgia. Phylogenetic analysis of this fragment indicated that the three variants are more closely related to "Candidatus Midichloria mitochondrii" genotypes from other tick species than to each other. This variation suggests that multiple independent introductions occurred in A. americanum which may provide insight into bacterial spread within its ecosystem and parasitism on this tick. Whether the presence of this bacterium affects acquisition or maintenance of other pathogens and symbionts in A. americanum or the survival, biology and evolution of the tick itself is unknown.}, }
@article {pmid22677398, year = {2012}, author = {Yamauchi, A and Telschow, A}, title = {Bistability of endosymbiont evolution of genome size and host sex control.}, journal = {Journal of theoretical biology}, volume = {309}, number = {}, pages = {58-66}, doi = {10.1016/j.jtbi.2012.05.014}, pmid = {22677398}, issn = {1095-8541}, mesh = {Animals ; Computer Simulation ; *Evolution, Molecular ; Female ; Genome Size/*genetics ; Male ; Models, Biological ; *Sex Ratio ; Symbiosis/*genetics ; }, abstract = {Eukaryotic organisms often harbor several genetic factors in their cytoplasm. These cytoplasmic genetic elements (CGEs) include both eukaryotic organelles (mitochondria, chloroplasts) and bacterial endosymbionts, which have evolved from free-living bacteria. A common feature of CGEs is their cytoplasmic inheritance from mother to offspring. A striking difference is that some CGEs have evolved a short genome size (e.g., animal mitochondria), while others cause a sex ratio distortion (SRD) in their hosts (e.g., Wolbachia). In this study, we sought to resolve the evolution of these endosymbiont properties using a population genetics approach. Our model divides the endosymbiont genome into a functional part and a part that can cause SRD, and our results indicate that the cytoplasmic inheritance system at the initiation of symbiosis plays a key role in determining the evolutionary trajectory of CGEs. We show that in endosymbiotic evolution, two states can be bistable, depending on the parameters. The evolution of the cytoplasmic inheritance system from biparental to uniparental can result in hysteresis in the evolution of cytoplasmic symbionts.}, }
@article {pmid22676139, year = {2013}, author = {Těšitel, J and Tesařová, M}, title = {Ultrastructure of hydathode trichomes of hemiparasitic Rhinanthus alectorolophus and Odontites vernus: how important is their role in physiology and evolution of parasitism in Orobanchaceae?.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {15}, number = {1}, pages = {119-125}, doi = {10.1111/j.1438-8677.2012.00610.x}, pmid = {22676139}, issn = {1438-8677}, mesh = {Biological Evolution ; Cell Respiration ; Cell Wall/ultrastructure ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; Orobanchaceae/genetics/physiology/*ultrastructure ; Plant Epidermis/genetics/physiology/ultrastructure ; Plant Leaves/genetics/physiology/*ultrastructure ; Plant Transpiration ; Plasmodesmata/ultrastructure ; Water/metabolism ; Xylem/genetics/physiology/ultrastructure ; }, abstract = {The Rhinanthoid clade of the family Orobanchaceae comprises plants displaying a hemiparasitic or holoparasitic strategy of resource acquisition. Some of its species (mainly Rhinanthus spp.) are often used as models for studies of hemiparasite physiology. Although there is a well-developed concept covering their physiological processes, most recent studies have neglected the existence of hydathode trichomes present on leaves of these hemiparasitic plants. As a first step for the proposed integration of these structures in the theory of physiological processes of the hemiparasites, we described the outer micromorphology and ultrastructure of the hydathode trichomes on leaves of hemiparasitic Rhinanthus alectorolophus and Odontites vernus with scanning and transmission electron microscopy (SEM and TEM, respectively). The TEM inspections of both types of trichome revealed typical ultrastructural features: labyrinthine cell wall, high content of cytoplasm in cells with numerous mitochondria and presence of plasmodesmata. All these features indicate high metabolic activity complying with their function as glandular trichomes actively secreting water. The active secretion of water by the hydathode trichomes (evidence for which is summarised here) also presents a possible mechanism explaining results of previous gas exchange measurements detecting high dark respiration and transpiration rates and a tight inter-correlation between them in hemiparasitic Orobanchaceae. In addition, this process is hypothesised to have allowed multiple evolutionary transitions from facultative to obligate hemiparasitism and unique xylem-feeding holoparasitism of Lathraea with a long-lived underground stage featuring a rhizome covered by scales of leaf origin.}, }
@article {pmid22671555, year = {2012}, author = {Xiao, JH and Wang, NX and Murphy, RW and Cook, J and Jia, LY and Huang, DW}, title = {Wolbachia infection and dramatic intraspecific mitochondrial DNA divergence in a fig wasp.}, journal = {Evolution; international journal of organic evolution}, volume = {66}, number = {6}, pages = {1907-1916}, doi = {10.1111/j.1558-5646.2011.01561.x}, pmid = {22671555}, issn = {1558-5646}, mesh = {Animals ; Base Sequence ; DNA Primers ; DNA, Mitochondrial/genetics ; Gene Transfer, Horizontal ; Gram-Negative Bacterial Infections/*genetics/microbiology ; Haplotypes ; Polymerase Chain Reaction ; Wasps/*genetics ; Wolbachia/*isolation &amp; purification ; }, abstract = {Mitochondria and Wolbachia are maternally inherited genomes that exhibit strong linkage disequilibrium in many organisms. We surveyed Wolbachia infections in 187 specimens of the fig wasp species, Ceratosolen solmsi, and found an infection prevalence of 89.3%. DNA sequencing of 20 individuals each from Wolbachia-infected and -uninfected subpopulations revealed extreme mtDNA divergence (up to 9.2% and 15.3% in CO1 and cytochrome b, respectively) between infected and uninfected wasps. Further, mtDNA diversity was significantly reduced within the infected group. Our sequencing of a large part of the mitochondrial genome from both Wolbachia-infected and -uninfected individuals revealed that high sequence divergence is common throughout the mitochondrial genome. These patterns suggest a partial selective sweep of mitochondria subsequent to the introduction of Wolbachia into C. solsmi, by hybrid introgression from a related species.}, }
@article {pmid22663076, year = {2012}, author = {Neupert, W}, title = {A mitochondrial odyssey.}, journal = {Annual review of biochemistry}, volume = {81}, number = {}, pages = {1-33}, doi = {10.1146/annurev-biochem-083109-171531}, pmid = {22663076}, issn = {1545-4509}, mesh = {Animals ; Cell Biology/*history ; Germany ; History, 20th Century ; Mitochondria/chemistry/genetics/*metabolism ; Mitochondrial Proteins/metabolism ; Protein Folding ; Protein Transport ; Proteins/metabolism ; }, abstract = {Good fortune let me be an innocent child during World War II, a hopeful adolescent with encouraging parents during the years of German recovery, and a self-determined adult in a period of peace, freedom, and wealth. My luck continued as a scientist who could entirely follow his fancy. My mind was always set on understanding how things are made. At a certain point, I found myself confronted with the question of how mitochondria and organelles, which cannot be formed de novo, are put together. Intracellular transport of proteins, their translocation across the mitochondrial membranes, and their folding and assembly were the processes that fascinated me. Now, after some 30 years, we have wonderful insights, unimagined views of a complex and at the same time simple machinery and its workings. We have glimpses of how orderly processes are established in the cell to assemble from single molecules our beautiful mitochondria that every day make some 50 kg of ATP for each of us. At the same time, we have learned amazing lessons from the tinkering of evolution that developed mitochondria from bacteria.}, }
@article {pmid22661327, year = {2012}, author = {Goyal, S and Balick, DJ and Jerison, ER and Neher, RA and Shraiman, BI and Desai, MM}, title = {Dynamic mutation-selection balance as an evolutionary attractor.}, journal = {Genetics}, volume = {191}, number = {4}, pages = {1309-1319}, pmid = {22661327}, issn = {1943-2631}, support = {260686/ERC_/European Research Council/International ; R01 GM086793/GM/NIGMS NIH HHS/United States ; GM086793/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Computer Simulation ; Genetic Fitness ; Genetics, Population ; *Models, Genetic ; *Mutation ; Mutation Rate ; Population Density ; Reproduction, Asexual/genetics ; *Selection, Genetic ; }, abstract = {The vast majority of mutations are deleterious and are eliminated by purifying selection. Yet in finite asexual populations, purifying selection cannot completely prevent the accumulation of deleterious mutations due to Muller's ratchet: once lost by stochastic drift, the most-fit class of genotypes is lost forever. If deleterious mutations are weakly selected, Muller's ratchet can lead to a rapid degradation of population fitness. Evidently, the long-term stability of an asexual population requires an influx of beneficial mutations that continuously compensate for the accumulation of the weakly deleterious ones. Hence any stable evolutionary state of a population in a static environment must involve a dynamic mutation-selection balance, where accumulation of deleterious mutations is on average offset by the influx of beneficial mutations. We argue that such a state can exist for any population size N and mutation rate U and calculate the fraction of beneficial mutations, ε, that maintains the balanced state. We find that a surprisingly low ε suffices to achieve stability, even in small populations in the face of high mutation rates and weak selection, maintaining a well-adapted population in spite of Muller's ratchet. This may explain the maintenance of mitochondria and other asexual genomes.}, }
@article {pmid22659202, year = {2012}, author = {Vendetti, JE and Trowbridge, CD and Krug, PJ}, title = {Poecilogony and population genetic structure in Elysia pusilla (Heterobranchia: Sacoglossa), and reproductive data for five sacoglossans that express dimorphisms in larval development.}, journal = {Integrative and comparative biology}, volume = {52}, number = {1}, pages = {138-150}, doi = {10.1093/icb/ics077}, pmid = {22659202}, issn = {1557-7023}, mesh = {Animals ; DNA, Mitochondrial/analysis/genetics ; Ecosystem ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Gastropoda/classification/genetics/*growth &amp; development/physiology ; Genetic Variation ; *Genetics, Population ; Larva/growth &amp; development/physiology ; Mitochondria/genetics ; Organ Size ; Ovum/growth &amp; development/*physiology ; Phylogeny ; Phylogeography ; Reproduction/genetics/*physiology ; Species Specificity ; }, abstract = {Credible cases of poecilogony, the production of two distinct larval morphs within a species, are extremely rare in marine invertebrates, yet peculiarly common in a clade of herbivorous sea slugs, the Sacoglossa. Only five animal species have been reported to express dimorphic egg sizes that result in planktotrophic and lecithotrophic larvae: the spionid polychaete Streblospio benedicti and four sacoglossans distributed in temperate estuaries or the Caribbean. Here, we present developmental and genetic evidence for a fifth case of poecilogony via egg-size dimorphism in the Sacoglossa and the first example from the tropical Indo-Pacific. The sea slug Elysia pusilla produced both planktotrophic and lecithotrophic larvae in Guam and Japan. Levels of genetic divergence within populations were markedly low and rule out cryptic species. However, divergence among populations was exceptionally high (10-12% at the mitochondrial cytochrome c oxidase I locus), illustrating that extensive phylogeographic structure can persist in spite of the dispersal potential of planktotrophic larvae. We review reproductive, developmental, and ecological data for the five known cases of poecilogony in the Sacoglossa, including new data for Costasiella ocellifera from the Caribbean. We hypothesize that sacoglossans achieve lecithotrophy at smaller egg sizes than do related clades of marine heterobranchs, which may facilitate developmental plasticity that is otherwise vanishingly rare among animals. Insight into the environmental drivers and evolutionary results of shifts in larval type will continue to be gleaned from population-level studies of poecilogonous taxa like E. pusilla, and should inform life-history theory about the causes and consequences of alternative development modes in marine animals.}, }
@article {pmid22659201, year = {2012}, author = {Sheehy, CM and Solórzano, A and Pfaller, JB and Lillywhite, HB}, title = {Preliminary insights into the phylogeography of the yellow-bellied sea snake, Pelamis platurus.}, journal = {Integrative and comparative biology}, volume = {52}, number = {2}, pages = {321-330}, doi = {10.1093/icb/ics088}, pmid = {22659201}, issn = {1557-7023}, mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Elapidae/classification/*genetics/physiology ; Gene Flow ; Genes, RAG-1 ; Genetic Variation ; Genetics, Population ; Haplotypes ; Mitochondria/genetics ; Pacific Ocean ; Phylogeny ; *Phylogeography ; Population Growth ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The yellow-bellied sea snake, Pelamis platurus (Elapidae, Hydrophiinae), has the largest distribution of any snake species, and patterns related to its distribution and regional color variation suggest there is population structuring in this species. Here, we use mitochondrial (ND4, Cyt-b) and nuclear (RAG-1) DNA to (1) test whether genetic variation is associated with local variation in color pattern, and (2) assess whether large-scale patterns of genetic variation are correlated with geographic distribution across the Pacific Ocean. We found low levels of genetic variation and shallow population structure that are correlated with local variation in color pattern and with geographic distribution. The low levels of genetic divergence indicate a relatively high rate of gene flow throughout the Pacific region and/or a recent expansion of range, both of which could be attributable to the passive drifting of these snakes on oceanic surface currents. The mtDNA data conform closely to a model of past exponential population growth, and this may have been associated with the species' large eastward and westward expansion of range. The pattern of low nucleotide and high haplotype diversity suggests that this population growth occurred in the relatively recent past. Data from drifting buoys can potentially act as informative models for predicting patterns of drifting in Pelamis and for generating additional testable hypotheses relating to its population structure and biogeography. Future studies should employ nuclear microsatellite markers to investigate population structure in this species at a finer scale. The exploitation of oceanic currents as a novel and highly efficient dispersal mechanism has likely facilitated gene flow throughout the Pacific Ocean in this uniquely pelagic species of sea snake, resulting in a distribution spanning over half of the earth's circumference.}, }
@article {pmid22655034, year = {2012}, author = {Fang, Y and Wu, H and Zhang, T and Yang, M and Yin, Y and Pan, L and Yu, X and Zhang, X and Hu, S and Al-Mssallem, IS and Yu, J}, title = {A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e37164}, pmid = {22655034}, issn = {1932-6203}, mesh = {Arecaceae/*genetics ; DNA, Mitochondrial/genetics ; *Gene Expression Profiling ; *Genome, Mitochondrial ; Genome, Plant ; Phylogeny ; Plant Proteins/genetics ; Polymorphism, Single Nucleotide ; RNA Editing ; RNA, Plant/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {Based on next-generation sequencing data, we assembled the mitochondrial (mt) genome of date palm (Phoenix dactylifera L.) into a circular molecule of 715,001 bp in length. The mt genome of P. dactylifera encodes 38 proteins, 30 tRNAs, and 3 ribosomal RNAs, which constitute a gene content of 6.5% (46,770 bp) over the full length. The rest, 93.5% of the genome sequence, is comprised of cp (chloroplast)-derived (10.3% with respect to the whole genome length) and non-coding sequences. In the non-coding regions, there are 0.33% tandem and 2.3% long repeats. Our transcriptomic data from eight tissues (root, seed, bud, fruit, green leaf, yellow leaf, female flower, and male flower) showed higher gene expression levels in male flower, root, bud, and female flower, as compared to four other tissues. We identified 120 potential SNPs among three date palm cultivars (Khalas, Fahal, and Sukry), and successfully found seven SNPs in the coding sequences. A phylogenetic analysis, based on 22 conserved genes of 15 representative plant mitochondria, showed that P. dactylifera positions at the root of all sequenced monocot mt genomes. In addition, consistent with previous discoveries, there are three co-transcribed gene clusters-18S-5S rRNA, rps3-rpl16 and nad3-rps12-in P. dactylifera, which are highly conserved among all known mitochondrial genomes of angiosperms.}, }
@article {pmid22651232, year = {2012}, author = {Marín, MA and López, A and Uribe, SI}, title = {Interspecific variation in mitochondrial serine transfer RNA (UCN) in Euptychiina butterflies (Lepidoptera: Satyrinae): structure and alignment.}, journal = {Mitochondrial DNA}, volume = {23}, number = {3}, pages = {208-215}, doi = {10.3109/19401736.2012.668895}, pmid = {22651232}, issn = {1940-1744}, mesh = {Animals ; Base Sequence ; Butterflies/classification/*genetics ; *Genetic Variation ; Mitochondria/*genetics ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer, Ser/chemistry/*genetics ; *Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {The nucleotide variation and structural patterns of mitochondrial RNA molecule have been proposed as useful tools in molecular systematics; however, their usefulness is always subject to a proper assessment of homology in the sequence alignment. The present study describes the secondary structure of mitochondrial tRNA for the amino acid serine (UCN) on 13 Euptychiina species and the evaluation of its potential use for evolutionary studies in this group of butterflies. The secondary structure of tRNAs showed variation among the included species except between Hermeuptychia sp1 and sp2. Variation was concentrated in the ribotimidina-pseudouridine-cystosine (TψC), dihydrouridine (DHU) and variable loops and in the DHU and TψC arms. These results suggest this region as a potential marker useful for taxonomic differentiation of species in this group and also confirm the importance of including information from the secondary structure of tRNA to optimize the alignments.}, }
@article {pmid22641820, year = {2012}, author = {Ord, TJ and Garcia-Porta, J}, title = {Is sociality required for the evolution of communicative complexity? Evidence weighed against alternative hypotheses in diverse taxonomic groups.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {367}, number = {1597}, pages = {1811-1828}, pmid = {22641820}, issn = {1471-2970}, mesh = {Adaptation, Physiological ; *Animal Communication ; Animals ; Ants/classification/genetics/physiology ; Anura/genetics/physiology ; *Biological Evolution ; Birds/genetics/physiology ; Body Size/physiology ; DNA, Mitochondrial/genetics ; Ecosystem ; Female ; Lizards/genetics/physiology ; Male ; Mitochondria/genetics ; Models, Biological ; Pheromones/classification/genetics ; Phylogeny ; *Social Dominance ; Time Factors ; }, abstract = {Complex social communication is expected to evolve whenever animals engage in many and varied social interactions; that is, sociality should promote communicative complexity. Yet, informal comparisons among phylogenetically independent taxonomic groups seem to cast doubt on the putative role of social factors in the evolution of complex communication. Here, we provide a formal test of the sociality hypothesis alongside alternative explanations for the evolution of communicative complexity. We compiled data documenting variations in signal complexity among closely related species for several case study groups--ants, frogs, lizards and birds--and used new phylogenetic methods to investigate the factors underlying communication evolution. Social factors were only implicated in the evolution of complex visual signals in lizards. Ecology, and to some degree allometry, were most likely explanations for complexity in the vocal signals of frogs (ecology) and birds (ecology and allometry). There was some evidence for adaptive evolution in the pheromone complexity of ants, although no compelling selection pressure was identified. For most taxa, phylogenetic null models were consistently ranked above adaptive models and, for some taxa, signal complexity seems to have accumulated in species via incremental or random changes over long periods of evolutionary time. Becoming social presumably leads to the origin of social communication in animals, but its subsequent influence on the trajectory of signal evolution has been neither clear-cut nor general among taxonomic groups.}, }
@article {pmid22639632, year = {2012}, author = {Haferkamp, I and Schmitz-Esser, S}, title = {The plant mitochondrial carrier family: functional and evolutionary aspects.}, journal = {Frontiers in plant science}, volume = {3}, number = {}, pages = {2}, pmid = {22639632}, issn = {1664-462X}, abstract = {Mitochondria play a key role in respiration and energy production and are involved in multiple eukaryotic but also in several plant specific metabolic pathways. Solute carriers in the inner mitochondrial membrane connect the internal metabolism with that of the surrounding cell. Because of their common basic structure, these transport proteins affiliate to the mitochondrial carrier family (MCF). Generally, MCF proteins consist of six membrane spanning helices, exhibit typical conserved domains and appear as homodimers in the native membrane. Although structurally related, MCF proteins catalyze the specific transport of various substrates, such as nucleotides, amino acids, dicarboxylates, cofactors, phosphate or H(+). Recent investigations identified MCF proteins also in several other cellular compartments and therefore their localization and physiological function is not only restricted to mitochondria. MCF proteins are a characteristic feature of eukaryotes and bacterial genomes lack corresponding sequences. Therefore, the evolutionary origin of MCF proteins is most likely associated with the establishment of mitochondria. It is not clear whether the host cell, the symbiont, or the chimerical organism invented the ancient MCF sequence. Here, we try to explain the establishment of different MCF proteins and focus on the characteristics of members from plants, in particular from Arabidopsis thaliana.}, }
@article {pmid22639063, year = {2012}, author = {Özdil, F and Ilhan, F}, title = {Diversity of Apis mellifera subspecies from Turkey revealed by sequence analysis of mitochondrial 16s rDNA region.}, journal = {Biochemical genetics}, volume = {50}, number = {9-10}, pages = {748-760}, doi = {10.1007/s10528-012-9517-1}, pmid = {22639063}, issn = {1573-4927}, mesh = {Animals ; Bees/classification/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Genetic Variation ; Genetics, Population/methods ; *Genome, Insect ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Turkey ; }, abstract = {Mitochondrial DNA sequence variation can be used to infer honeybee evolutionary relationships. In this study, DNA sequence diversity of the mitochondrial 16s rDNA region was investigated in 112 honeybees from 15 populations in Turkey, which is mainly populated with Apis mellifera anatoliaca, A. m. caucasica, and A. m. meda. The study revealed 11 haplotypes for this segment, with 13 variable sites and nine parsimony informative sites. The haplotypes were not discriminated according to their geographical locations in a neighbor-joining dendrogram based on 16s rDNA sequences available in Genbank, but all the haplotypes obtained in this study are clustered with published haplotypes such as A. mellifera TAS (AF214666) and A. m. ligustica (EF116868) and with some unpublished Genbank records (HQ318928, HQ318934, and HQ318938). This study expands the knowledge of the mitochondrial 16s rDNA region, and it presents the first comprehensive sequence analysis of this region in Turkish honeybees.}, }
@article {pmid22635304, year = {2012}, author = {Iwao, Y}, title = {Egg activation in physiological polyspermy.}, journal = {Reproduction (Cambridge, England)}, volume = {144}, number = {1}, pages = {11-22}, doi = {10.1530/REP-12-0104}, pmid = {22635304}, issn = {1741-7899}, mesh = {Animals ; Calcium/analysis/physiology ; Cell Nucleus ; Citrate (si)-Synthase/pharmacology/physiology ; Fertilization/*physiology ; Mitochondria/enzymology ; Ovum/chemistry/*physiology ; Salamandridae/physiology ; Zygote/ultrastructure ; }, abstract = {Fertilization is indispensable not only for restoring diploid genomes but also for the initiation of early embryonic cell cycles in sexual reproduction. While most animals exhibit monospermy, which is ensured by polyspermy blocks to prevent the entry of extra sperm into the egg at fertilization, several animals exhibit physiological polyspermy, in which the entry of several sperm is permitted but only one sperm nucleus participates in the formation of a zygote nucleus. Polyspermy requires that the sperm transmit the egg activation signal more slowly, thus allowing the egg to accept several sperm. An increase in intracellular Ca(2+) concentration induced by the fertilizing sperm is both necessary and sufficient for egg activation in polyspermy. Multiple small Ca(2+) waves induced by several fertilizing sperm result in a long-lasting Ca(2+) rise, which is a characteristic of polyspermic amphibian eggs. We introduced a novel soluble sperm factor for egg activation, sperm-specific citrate synthase, into polyspermic newt eggs to cause Ca(2+) waves. Citrate synthase may perform dual functions: as an enzyme in mitochondria and as a Ca(2+)-inducing factor in egg cytoplasm. We also discuss the close relationship between the mode of fertilization and the Ca(2+) rise at egg activation and consider changes in this process through evolution in vertebrates.}, }
@article {pmid22634358, year = {2012}, author = {Sanders, KL and Rasmussen, AR and Elmberg, J}, title = {Independent innovation in the evolution of paddle-shaped tails in viviparous sea snakes (Elapidae: Hydrophiinae).}, journal = {Integrative and comparative biology}, volume = {52}, number = {2}, pages = {311-320}, doi = {10.1093/icb/ics066}, pmid = {22634358}, issn = {1557-7023}, mesh = {Adaptation, Biological ; Animals ; Bayes Theorem ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; Elapidae/*anatomy &amp; histology/classification/genetics/physiology ; Male ; Mitochondria/genetics ; Models, Biological ; Phylogeny ; Species Specificity ; Spine/anatomy &amp; histology/physiology ; Tail/*anatomy &amp; histology/physiology ; Time Factors ; }, abstract = {The viviparous sea snakes (Hydrophiinae) comprise ~90% of living marine reptiles and display many physical and behavioral adaptations for breathing, diving, and achieving osmotic balance in marine habitats. Among the most important innovations found in marine snakes are their paddle-shaped (dorsoventrally expanded) tails, which provide propulsive thrust in the dense aquatic medium. Here, we reconstruct the evolution of caudal paddles in viviparous sea snakes using a dated molecular phylogeny for all major lineages and computed tomography of internal osteological structures. Bayesian ancestral state reconstructions show that extremely large caudal paddles supported by elongated vertebral processes are unlikely to have been present in the most recent common ancestor of extant sea snakes. Instead, these characters appear to have been acquired independently in two highly marine lineages of relatively recent origin. Both the Aipysurus and Hydrophis lineages have elongated neural spines that support the dorsal edge of their large paddles. However, whereas in the Aipysurus lineage the ventral edge of the paddle is supported by elongated haemapophyses, this support is provided by elongated and ventrally directed pleurapophyses in the Hydrophis lineage. Three semi-marine lineages (Hydrelaps, Ephalophis, and Parahydrophis) form the sister group to the Hydrophis clade and have small paddles with poorly developed dorsal and ventral supports, consistent with their amphibious lifestyle. Overall, our results suggest that not only are the viviparous hydrophiines the only lineage of marine snakes to have acquired extremely large, skeletally supported caudal paddles but also that this innovation has occurred twice in the group in the past ~2-6 million years.}, }
@article {pmid22629338, year = {2012}, author = {Papura, D and Burban, C and van Helden, M and Giresse, X and Nusillard, B and Guillemaud, T and Kerdelhué, C}, title = {Microsatellite and mitochondrial data provide evidence for a single major introduction for the Neartic leafhopper Scaphoideus titanus in Europe.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e36882}, pmid = {22629338}, issn = {1932-6203}, mesh = {Animals ; Europe ; Genetic Loci ; Genetic Variation ; Genetics, Population ; Haplotypes ; Hemiptera/*genetics ; *Microsatellite Repeats ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Scaphoideus titanus, a leafhopper native to North America and invasive in Europe, is the vector of the Flavescence dorée phytoplasma, the causal agent of the most important form of grapevine yellows in European vineyards. We studied 10 polymorphic microsatellite loci and a 623 bp fragment of the mitochondrial cytochrome oxidase II gene in native S. titanus from north-eastern America and introduced European populations, to elucidate the colonization scenario. Consistent with their recent history, invasive European populations were less genetically diverse than American populations for both types of markers, suggesting a recent bottleneck. Significant isolation by distance was detected between American populations but not between European populations. None of the European mitochondrial haplotypes was found in the American vineyards, from which they are assumed to have originated. The precise source of the invasive S. titanus populations therefore remains unclear. Nevertheless, the high heterozygosity of North-East American populations (which contained 92% of the observed alleles) suggests that this region is part of the native range of S. titanus. Clustering population genetics analyses with microsatellite and mitochondrial data suggested that European populations originated from a single introduction event. Most of the introduced populations clustered with populations from Long Island, the Atlantic Coast winegrowing region in which Vitis aestivalis occurs.}, }
@article {pmid22629248, year = {2012}, author = {Jazwinski, SM and Kriete, A}, title = {The yeast retrograde response as a model of intracellular signaling of mitochondrial dysfunction.}, journal = {Frontiers in physiology}, volume = {3}, number = {}, pages = {139}, pmid = {22629248}, issn = {1664-042X}, support = {R37 AG006168/AG/NIA NIH HHS/United States ; }, abstract = {Mitochondrial dysfunction activates intracellular signaling pathways that impact yeast longevity, and the best known of these pathways is the retrograde response. More recently, similar responses have been discerned in other systems, from invertebrates to human cells. However, the identity of the signal transducers is either unknown or apparently diverse, contrasting with the well-established signaling module of the yeast retrograde response. On the other hand, it has become equally clear that several other pathways and processes interact with the retrograde response, embedding it in a network responsive to a variety of cellular states. An examination of this network supports the notion that the master regulator NFκB aggregated a variety of mitochondria-related cellular responses at some point in evolution and has become the retrograde transcription factor. This has significant consequences for how we view some of the deficits associated with aging, such as inflammation. The support for NFκB as the retrograde response transcription factor is not only based on functional analyses. It is bolstered by the fact that NFκB can regulate Myc-Max, which is activated in human cells with dysfunctional mitochondria and impacts cellular metabolism. Myc-Max is homologous to the yeast retrograde response transcription factor Rtg1-Rtg3. Further research will be needed to disentangle the pro-aging from the anti-aging effects of NFκB. Interestingly, this is also a challenge for the complete understanding of the yeast retrograde response.}, }
@article {pmid22628468, year = {2012}, author = {Sharma, PP and Giribet, G}, title = {Out of the Neotropics: Late Cretaceous colonization of Australasia by American arthropods.}, journal = {Proceedings. Biological sciences}, volume = {279}, number = {1742}, pages = {3501-3509}, pmid = {22628468}, issn = {1471-2954}, mesh = {Americas ; Animals ; Arachnida/*genetics ; Asia, Southeastern ; Australasia ; Bayes Theorem ; Cell Nucleus/*genetics ; *Evolution, Molecular ; Likelihood Functions ; Male ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeography ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The origins of tropical southwest Pacific diversity are traditionally attributed to southeast Asia or Australia. Oceanic and fragment islands are typically colonized by lineages from adjacent continental margins, resulting in attrition of diversity with distance from the mainland. Here, we show that an exceptional tropical family of harvestmen with a trans-Pacific disjunct distribution has its origin in the Neotropics. We found in a multi-locus phylogenetic analysis that the opilionid family Zalmoxidae, which is distributed in tropical forests on both sides of the Pacific, is a monophyletic entity with basal lineages endemic to Amazonia and Mesoamerica. Indo-Pacific Zalmoxidae constitute a nested clade, indicating a single colonization event. Lineages endemic to putative source regions, including Australia and New Guinea, constitute derived groups. Divergence time estimates and probabilistic ancestral area reconstructions support a Neotropical origin of the group, and a Late Cretaceous (ca 82 Ma) colonization of Australasia out of the Fiji Islands and/or Borneo, which are consistent with a transoceanic dispersal event. Our results suggest that the endemic diversity within traditionally defined zoogeographic boundaries might have more complex evolutionary origins than previously envisioned.}, }
@article {pmid22628314, year = {2012}, author = {Eckers, E and Cyrklaff, M and Simpson, L and Deponte, M}, title = {Mitochondrial protein import pathways are functionally conserved among eukaryotes despite compositional diversity of the import machineries.}, journal = {Biological chemistry}, volume = {393}, number = {6}, pages = {513-524}, doi = {10.1515/hsz-2011-0255}, pmid = {22628314}, issn = {1437-4315}, mesh = {*Computational Biology ; Leishmania/*cytology/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/*metabolism ; Protein Transport ; Protozoan Proteins/*metabolism ; Sequence Analysis ; }, abstract = {Mitochondrial protein import (MPI) is essential for the biogenesis of mitochondria in all eukaryotes. Current models of MPI are predominantly based on experiments with one group of eukaryotes, the opisthokonts. Although fascinating genome database-driven hypotheses on the evolution of the MPI machineries have been published, previous experimental research on non-opisthokonts usually focused on the analysis of single pathways or components in, for example, plants and parasites. In this study, we have established the kinetoplastid parasite Leishmania tarentolae as a model organism for the comprehensive analysis of non-opisthokont MPI into all four mitochondrial compartments. We found that opisthokont marker proteins are efficiently imported into isolated L. tarentolae mitochondria. Vice versa, L. tarentolae marker proteins of all compartments are also imported into mitochondria from yeast. The results are remarkable because only a few of the more than 25 classical components of the opisthokont MPI machineries are found in parasite genome databases. Our results demonstrate that different MPI pathways are functionally conserved among eukaryotes despite significant compositional differences of the MPI machineries. Moreover, our model system could lead to the identification of significantly altered or even novel MPI components in non-opisthokonts. Such differences might serve as starting points for drug development against parasitic protists.}, }
@article {pmid22628160, year = {2012}, author = {Ball, ER and Matsuda, MM and Dye, L and Hoffmann, V and Zerfas, PM and Szarek, E and Rich, A and Chitnis, AB and Stratakis, CA}, title = {Ultra-structural identification of interstitial cells of Cajal in the zebrafish Danio rerio.}, journal = {Cell and tissue research}, volume = {349}, number = {2}, pages = {483-491}, pmid = {22628160}, issn = {1432-0878}, support = {R15 DK071588/DK/NIDDK NIH HHS/United States ; ZIA HD008920-01//Intramural NIH HHS/United States ; }, mesh = {Animals ; Interstitial Cells of Cajal/*ultrastructure ; Intestines/cytology/*ultrastructure ; Microscopy, Electron ; Proto-Oncogene Proteins c-kit/analysis ; Zebrafish/*anatomy &amp; histology ; }, abstract = {The interstitial cells of Cajal (ICCs) are important mediators of gastrointestinal (GI) motility because of their role as pacemakers in the GI tract. In addition to their function, ICCs are also structurally distinct cells most easily identified by their ultra-structural features and expression of the tyrosine kinase receptor c-KIT. ICCs have been described in mammals, rodents, birds, reptiles, and amphibians, but there are no reports at the ultra-structural level of ICCs within the GI tract of an organism from the teleost lineage. We describe the presence of cells in the muscularis of the zebrafish intestine; these cells have similar features to ICCs in other vertebrates. The ICC-like cells are associated with the muscularis, are more electron-dense than surrounding smooth muscle cells, possess long cytoplasmic processes and mitochondria, and are situated opposing enteric nervous structures. In addition, immunofluorescent and immunoelectron-microscopic studies with antibodies targeting the zebrafish ortholog of a putative ICC marker, c-KIT (kita), showed c-kit immunoreactivity in zebrafish ICCs. Taken together, these data represent the first ultra-structural characterization of cells in the muscularis of the zebrafish Danio rerio and suggest that ICC differentiation in vertebrate evolution dates back to the teleost lineage.}, }
@article {pmid22621371, year = {2012}, author = {Grant, JR and Arantes, AS and Stothard, P}, title = {Comparing thousands of circular genomes using the CGView Comparison Tool.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {202}, pmid = {22621371}, issn = {1471-2164}, mesh = {Chloroplasts/genetics ; Genome, Bacterial/*genetics ; Mitochondria/genetics ; Plasmids/genetics ; Sequence Analysis, DNA/*methods ; *Software ; }, abstract = {BACKGROUND: Continued sequencing efforts coupled with advances in sequencing technology will lead to the completion of a vast number of small genomes. Whole-genome comparisons represent an important part of the analysis of any new genome sequence, as they can provide a better understanding of the biology and evolution of the source organism. Visualization of the results is important, as it allows information from a variety of sources to be integrated and interpreted. However, existing graphical comparison tools lack features needed for efficiently comparing a new genome to hundreds or thousands of existing sequences. Moreover, existing tools are limited in terms of the types of comparisons that can be performed, the extent to which the output can be customized, and the ease with which the entire process can be automated.<br><br>RESULTS: The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences of interest to existing genomes or sequence collections. The comparisons are conducted using BLAST, and the BLAST results are presented in the form of graphical maps that can also show sequence features, gene and protein names, COG (Clusters of Orthologous Groups of proteins) category assignments, and sequence composition characteristics. CCT can generate maps in a variety of sizes, including 400 Megapixel maps suitable for posters. Comparisons can be conducted within a particular species or genus, or all available genomes can be used. The entire map creation process, from downloading sequences to redrawing zoomed maps, can be completed easily using scripts included with the CCT. User-defined features or analysis results can be included on maps, and maps can be extensively customized. To simplify program setup, a CCT virtual machine that includes all dependencies preinstalled is available. Detailed tutorials illustrating the use of CCT are included with the CCT documentation.<br><br>CONCLUSION: CCT can be used to visually compare a reference sequence to thousands of existing genomes or sequence collections (next-generation sequencing reads for example) on a standard desktop computer. It provides analysis and visualization functionality not available in any existing circular genome visualization tool. By visually presenting sequence conservation information along with functional classifications and sequence composition characteristics, CCT can be a useful tool for identifying rapidly evolving or novel sequences, horizontally transferred sequences, or unusual functional properties in newly sequenced genomes. CCT is freely available for download at http://stothard.afns.ualberta.ca/downloads/CCT/.}, }
@article {pmid22615898, year = {2012}, author = {Shi, W and Kerdelhué, C and Ye, H}, title = {Genetic structure and inferences on potential source areas for Bactrocera dorsalis (Hendel) based on mitochondrial and microsatellite markers.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e37083}, pmid = {22615898}, issn = {1932-6203}, mesh = {Animal Migration ; Animal Population Groups/genetics ; Animals ; Asia, Southeastern ; Gene Flow ; Genetic Structures ; Genetic Variation ; Geography ; *Microsatellite Repeats ; Mitochondria/*genetics ; Phylogeny ; Pilot Projects ; Tephritidae/*genetics ; }, abstract = {Bactrocera dorsalis (Diptera: Tephritidae) is mainly distributed in tropical and subtropical Asia and in the Pacific region. Despite its economic importance, very few studies have addressed the question of the wide genetic structure and potential source area of this species. This pilot study attempts to infer the native region of this pest and its colonization pathways in Asia. Combining mitochondrial and microsatellite markers, we evaluated the level of genetic diversity, genetic structure, and the gene flow among fly populations collected across Southeast Asia and China. A complex and significant genetic structure corresponding to the geographic pattern was found with both types of molecular markers. However, the genetic structure found was rather weak in both cases, and no pattern of isolation by distance was identified. Multiple long-distance dispersal events and miscellaneous host selection by this species may explain the results. These complex patterns may have been influenced by human-mediated transportation of the pest from one area to another and the complex topography of the study region. For both mitochondrial and microsatellite data, no signs of bottleneck or founder events could be identified. Nonetheless, maximal genetic diversity was observed in Myanmar, Vietnam and Guangdong (China) and asymmetric migration patterns were found. These results provide indirect evidence that the tropical regions of Southeast Asia and southern coast of China may be considered as the native range of the species and the population expansion is northward. Yunnan (China) is a contact zone that has been colonized from different sources. Regions along the southern coast of Vietnam and China probably served to colonize mainly the southern region of China. Southern coastal regions of China may also have colonized central parts of China and of central Yunnan.}, }
@article {pmid22614282, year = {2012}, author = {Özdil, F and İlhan, F}, title = {Phylogenetic relationship of Turkish Apis mellifera subspecies based on sequencing of mitochondrial cytochrome C oxidase I region.}, journal = {Genetics and molecular research : GMR}, volume = {11}, number = {2}, pages = {1130-1141}, doi = {10.4238/2012.April.27.12}, pmid = {22614282}, issn = {1676-5680}, mesh = {Animals ; Bees/classification/*genetics ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; Turkey ; }, abstract = {Mitochondrial DNA sequence variation can be used to infer honey bee evolutionary relationships. We examined DNA sequence diversity in the cytochrome C oxidase I (COI or Cox1) gene segment of the mitochondrial genome in 112 samples of Apis mellifera from 15 different populations in Turkey. Six novel haplotypes were found for the COI gene segment. There were eight variable sites in the COI gene, although only three were parsimony-informative sites. The mean pairwise genetic distance was 0.3% for the COI gene segment. Neighbor-joining (NJ) trees of the COI gene segment were constructed with the published sequences of A. mellifera haplotypes that are available in GenBank; the genetic variation was compared among the different honeybee haplotypes. The NJ dendogram based on the COI sequences available in GenBank showed that Eastern European races were clustered together, whereas the Mellifera and Iberian haplotypes were clustered far apart. The haplotypes found in this study were clustered together with A. mellifera ligustica and some of the Greek honey bees (accession Nos. GU056169 and GU056170) found in NCBI GenBank database. This study expands the knowledge about the mitochondrial COI region and presents the first comprehensive sequence analysis of this region in Turkish honeybees.}, }
@article {pmid22606358, year = {2012}, author = {Nishimura, Y and Kamikawa, R and Hashimoto, T and Inagaki, Y}, title = {Separate origins of group I introns in two mitochondrial genes of the katablepharid Leucocryptos marina.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e37307}, pmid = {22606358}, issn = {1932-6203}, mesh = {Base Sequence ; Cytochromes b/genetics ; Electron Transport Complex IV/genetics ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Mitochondrial ; Genome, Mitochondrial ; Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA/chemistry/genetics ; }, abstract = {Mitochondria are descendants of the endosymbiotic α-proteobacterium most likely engulfed by the ancestral eukaryotic cells, and the proto-mitochondrial genome should have been severely streamlined in terms of both genome size and gene repertoire. In addition, mitochondrial (mt) sequence data indicated that frequent intron gain/loss events contributed to shaping the modern mt genome organizations, resulting in the homologous introns being shared between two distantly related mt genomes. Unfortunately, the bulk of mt sequence data currently available are of phylogenetically restricted lineages, i.e., metazoans, fungi, and land plants, and are insufficient to elucidate the entire picture of intron evolution in mt genomes. In this work, we sequenced a 12 kbp-fragment of the mt genome of the katablepharid Leucocryptos marina. Among nine protein-coding genes included in the mt genome fragment, the genes encoding cytochrome b and cytochrome c oxidase subunit I (cob and cox1) were interrupted by group I introns. We further identified that the cob and cox1 introns host open reading frames for homing endonucleases (HEs) belonging to distantly related superfamilies. Phylogenetic analyses recovered an affinity between the HE in the Leucocryptos cob intron and two green algal HEs, and that between the HE in the Leucocryptos cox1 intron and a fungal HE, suggesting that the Leucocryptos cob and cox1 introns possess distinct evolutionary origins. Although the current intron (and intronic HE) data are insufficient to infer how the homologous introns were distributed to distantly related mt genomes, the results presented here successfully expanded the evolutionary dynamism of group I introns in mt genomes.}, }
@article {pmid22606053, year = {2012}, author = {Rout, PK and Thangraj, K and Mandal, A and Roy, R}, title = {Genetic variation and population structure in Jamunapari goats using microsatellites, mitochondrial DNA, and milk protein genes.}, journal = {TheScientificWorldJournal}, volume = {2012}, number = {}, pages = {618909}, pmid = {22606053}, issn = {1537-744X}, mesh = {Alleles ; Animals ; Breeding ; DNA, Mitochondrial/*genetics ; Genetic Carrier Screening/methods ; Genetic Drift ; Genetic Loci ; *Genetic Variation ; Genetics, Population/*methods ; Goats/*genetics ; Heterozygote ; India ; Linkage Disequilibrium ; Male ; *Microsatellite Repeats ; Milk Proteins/*genetics ; Mitochondria/genetics ; Population Density ; Selection, Genetic ; Y Chromosome/genetics ; }, abstract = {Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation decision and management of the breed.}, }
@article {pmid22606033, year = {2012}, author = {Liu, CC and Liu, BG and Yang, ZW and Li, CM and Wang, BC and Yang, CP}, title = {Genome-wide identification and in silico analysis of poplar peptide deformylases.}, journal = {International journal of molecular sciences}, volume = {13}, number = {4}, pages = {5112-5124}, pmid = {22606033}, issn = {1422-0067}, mesh = {Amidohydrolases/*genetics/metabolism ; Amino Acid Sequence ; Arabidopsis/enzymology/genetics ; Arabidopsis Proteins/metabolism ; Base Sequence ; Genome, Plant ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Populus/*enzymology/*genetics ; Sequence Alignment ; }, abstract = {Peptide deformylases (PDF) behave as monomeric metal cation hydrolases for the removal of the N-formyl group (Fo). This is an essential step in the N-terminal Met excision (NME) that occurs in these proteins from eukaryotic mitochondria or chloroplasts. Although PDFs have been identified and their structure and function have been characterized in several herbaceous species, it remains as yet unexplored in poplar. Here, we report on the first identification of two genes (PtrPDF1A and PtrPDF1B) respectively encoding two putative PDF polypeptides in Populus trichocarpa by genome-wide investigation. One of them (XP_002300047.1) encoded by PtrPDF1B (XM_002300011.1) was truncated, and then revised into a complete sequence based on its ESTs support with high confidence. We document that the two PDF1s of Populus are evolutionarily divergent, likely as a result of independent duplicated events. Furthermore, in silico simulations demonstrated that PtrPDF1A and PtrPDF1B should act as similar PDF catalytic activities to their corresponding PDF orthologs in Arabidopsis. This result would be value of for further assessment of their biological activities in poplar, and further experiments are now required to confirm them.}, }
@article {pmid22605770, year = {2012}, author = {Bick, AG and Calvo, SE and Mootha, VK}, title = {Evolutionary diversity of the mitochondrial calcium uniporter.}, journal = {Science (New York, N.Y.)}, volume = {336}, number = {6083}, pages = {886}, pmid = {22605770}, issn = {1095-9203}, support = {R01 GM097136/GM/NIGMS NIH HHS/United States ; T32GM007753-33/GM/NIGMS NIH HHS/United States ; R01GM077465/GM/NIGMS NIH HHS/United States ; R01 GM077465/GM/NIGMS NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; R01GM097136/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*chemistry/genetics/metabolism ; Bacterial Proteins/chemistry/genetics ; Calcium Channels/*chemistry/genetics ; Calcium-Binding Proteins/chemistry/genetics ; Cation Transport Proteins/chemistry/genetics ; Eukaryota/*chemistry/genetics/metabolism ; *Evolution, Molecular ; Genome ; Humans ; Mitochondria/*chemistry ; Mitochondrial Membrane Transport Proteins/*chemistry/genetics ; Phylogeny ; Protein Structure, Tertiary ; Proteome ; }, abstract = {Calcium uptake into mitochondria occurs via a recently identified ion channel called the uniporter. Here, we characterize the phylogenomic distribution of the uniporter's membrane-spanning pore subunit (MCU) and regulatory partner (MICU1). Homologs of both components tend to co-occur in all major branches of eukaryotic life, but both have been lost along certain protozoan and fungal lineages. Several bacterial genomes also contain putative MCU homologs that may represent prokaryotic calcium channels. The analyses indicate that the uniporter may have been an early feature of mitochondria.}, }
@article {pmid22605678, year = {2012}, author = {Hernandez-Cid, A and Aguirre-Sampieri, S and Diaz-Vilchis, A and Torres-Larios, A}, title = {Ribonucleases P/MRP and the expanding ribonucleoprotein world.}, journal = {IUBMB life}, volume = {64}, number = {6}, pages = {521-528}, doi = {10.1002/iub.1052}, pmid = {22605678}, issn = {1521-6551}, mesh = {Animals ; Catalytic Domain ; Endoribonucleases/chemistry/*physiology ; Evolution, Molecular ; Humans ; Nucleic Acid Conformation ; RNA/chemistry/genetics ; Ribonuclease P/chemistry/*physiology ; Ribonucleoproteins/chemistry/*physiology ; }, abstract = {One of the hallmarks of life is the widespread use of certain essential ribozymes. The ubiquitous ribonuclease P (RNase P) and eukaryotic RNase MRP are essential complexes where a structured, noncoding RNA acts in catalysis. Recent discoveries have elucidated the three-dimensional structure of the ancestral ribonucleoprotein complex, suggested the possibility of a protein-only composition in organelles, and even noted the absence of RNase P in a non-free-living organism. With respect to these last two findings, import mechanisms for RNases P/MRP into mitochondria have been demonstrated, and RNase P is present in organisms with some of the smallest known genomes. Together, these results have led to an ongoing debate regarding the precise definition of how "essential" these ribozymes truly are.}, }
@article {pmid22595823, year = {2012}, author = {Warner, AH and Chakrabortee, S and Tunnacliffe, A and Clegg, JS}, title = {Complexity of the heat-soluble LEA proteome in Artemia species.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {7}, number = {3}, pages = {260-267}, doi = {10.1016/j.cbd.2012.04.002}, pmid = {22595823}, issn = {1878-0407}, mesh = {Animals ; Artemia/*embryology/genetics/*metabolism ; Blotting, Western ; Desiccation ; Electrophoresis, Polyacrylamide Gel ; Embryo, Nonmammalian/metabolism ; *Embryonic Development/genetics ; Female ; Gene Expression Regulation, Developmental ; Geography ; *Hot Temperature ; Organelles/metabolism ; Proteome/genetics/*metabolism ; Solubility ; Species Specificity ; Subcellular Fractions/metabolism ; }, abstract = {The brine shrimp Artemia is a well known stress tolerant invertebrate found on most continents. Under certain conditions females produce cysts (encysted gastrulae) that enter diapause, a state of obligate dormancy. During developmental formation of diapause embryos several different types of stress proteins accumulate in large amounts, including the late embryogenesis abundant (LEA) proteins. In this study we used a combination of heterologous group 3 LEA antibodies to demonstrate that the heat-soluble proteome of the cysts contains up to 12 distinct putative group 3 LEA proteins that complement the group 1 LEA proteins found previously. Most antibody-positive, heat-soluble proteins were larger than 50 kDa although antibody positive proteins of 20-38 kDa were also detected. Both nuclei and mitochondria had distinct complements of the putative group 3 LEA proteins. A few small group 3 LEA proteins were induced by cycles of hydration-dehydration along with one protein of about 62 kDa. The expression of group 3 LEA proteins, unlike members of group 1, was not restricted to encysted diapause embryos. Three to five putative group 3 LEA proteins were expressed in gravid females and in larvae. Cysts of different species from various geographic locations had distinct complements of group 3 LEA proteins suggesting rapid evolution of the LEA proteins or differences in the type of group 3 Lea genes expressed. Our results demonstrate the potential importance of group 3 LEA proteins in embryos and other life cycle stages of this animal extremophile.}, }
@article {pmid22591206, year = {2012}, author = {Ho, SY and Lanfear, R}, title = {Mito-communications.}, journal = {Mitochondrial DNA}, volume = {23}, number = {4}, pages = {321-322}, doi = {10.3109/19401736.2012.683187}, pmid = {22591206}, issn = {1940-1744}, mesh = {Animals ; Arthropods/genetics ; Coleoptera/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genome, Insect/genetics ; Genome, Mitochondrial/*genetics ; Genome, Plant/genetics ; Invertebrates/*genetics ; Marine Biology ; Mitochondria/*genetics ; Plants/*genetics ; }, }
@article {pmid22590575, year = {2012}, author = {Fonseca, MM and Rocha, S and Posada, D}, title = {Base-pairing versatility determines wobble sites in tRNA anticodons of vertebrate mitogenomes.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e36605}, pmid = {22590575}, issn = {1932-6203}, mesh = {Animals ; Anticodon/*genetics ; Base Pairing/genetics ; Genome, Mitochondrial/*genetics ; Humans ; RNA/*genetics ; RNA, Mitochondrial ; }, abstract = {BACKGROUND: Vertebrate mitochondrial genomes typically have one transfer RNA (tRNA) for each synonymous codon family. This limited anticodon repertoire implies that each tRNA anticodon needs to wobble (establish a non-Watson-Crick base pairing between two nucleotides in RNA molecules) to recognize one or more synonymous codons. Different hypotheses have been proposed to explain the factors that determine the nucleotide composition of wobble sites in vertebrate mitochondrial tRNA anticodons. Until now, the two major postulates--the "codon-anticodon adaptation hypothesis" and the "wobble versatility hypothesis"--have not been formally tested in vertebrate mitochondria because both make the same predictions regarding the composition of anticodon wobble sites. The same is true for the more recent "wobble cost hypothesis".<br><br>PRINCIPAL FINDINGS: In this study we have analyzed the occurrence of synonymous codons and tRNA anticodon wobble sites in 1553 complete vertebrate mitochondrial genomes, focusing on three fish species with mtDNA codon usage bias reversal (L-strand is GT-rich). These mitogenomes constitute an excellent opportunity to study the evolution of the wobble nucleotide composition of tRNA anticodons because due to the reversal the predictions for the anticodon wobble sites differ between the existing hypotheses. We observed that none of the wobble sites of tRNA anticodons in these unusual mitochondrial genomes coevolved to match the new overall codon usage bias, suggesting that nucleotides at the wobble sites of tRNA anticodons in vertebrate mitochondrial genomes are determined by wobble versatility.<br><br>CONCLUSIONS/SIGNIFICANCE: Our results suggest that, at wobble sites of tRNA anticodons in vertebrate mitogenomes, selection favors the most versatile nucleotide in terms of wobble base-pairing stability and that wobble site composition is not influenced by codon usage. These results are in agreement with the "wobble versatility hypothesis".}, }
@article {pmid22585970, year = {2012}, author = {Lopes, CM and de Freitas, TR}, title = {Human impact in naturally patched small populations: genetic structure and conservation of the burrowing rodent, tuco-tuco (Ctenomys lami).}, journal = {The Journal of heredity}, volume = {103}, number = {5}, pages = {672-681}, doi = {10.1093/jhered/ess027}, pmid = {22585970}, issn = {1465-7333}, mesh = {Animals ; Biological Evolution ; Brazil ; *Conservation of Natural Resources ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Female ; Gene Flow ; Genetic Loci ; Genetic Variation ; Haplotypes ; Karyotyping ; Linkage Disequilibrium ; Male ; Microsatellite Repeats ; Mitochondria/genetics ; Multigene Family ; Pedigree ; Phylogeography ; Rodentia/classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {Isolated or semi-isolated small populations are commonly found among species, due to a naturally patchy occupancy of suitable habitats or also as a result of habitat alterations. These populations are subject to an increased risk of local extinction because they are more vulnerable to demographic, genetic, and environmental stochasticity. Considering that natural areas have been becoming progressively more fragmented and smaller, understanding the genetic structure and evolutionary dynamics of small populations is critical. Ctenomys lami has 26 karyotypes distributed in a small area (936 km(2)) continually modified by human actions. We assessed the genetic geographical structure of this species, examining 178 specimens sampled on a fine scale, using information from chromosomal variability, mitochondrial DNA control region and cytochrome c oxidase subunit I sequences, and 14 microsatellite loci. The observed isolation-by-distance pattern and a clinal genetic variation suggest a stepping-stone population model. The results did not indicate genetic structuring associated with distinct karyotypes. However, mitochondrial and nuclear molecular markers demonstrated the existence of 2 demes, which are not completely isolated but are probably reinforced by a geographical barrier. The vulnerability of C. lami is greater than previously supposed, and our data support the designation of one Evolutionary Significant Unit and one Management Unit, and also the inclusion of this species' conservation status as vulnerable.}, }
@article {pmid22578654, year = {2012}, author = {Shi, H and Liu, R and Sha, Z and Ma, J}, title = {Complete mitochondrial DNA sequence of Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) and a novel tRNA gene cluster.}, journal = {Marine genomics}, volume = {6}, number = {}, pages = {7-15}, doi = {10.1016/j.margen.2011.11.002}, pmid = {22578654}, issn = {1876-7478}, mesh = {Animals ; Base Composition ; Base Sequence ; Codon ; DNA, Mitochondrial/*chemistry/genetics ; Decapoda/classification/*genetics ; Gene Order ; Molecular Sequence Data ; Phylogeny ; Proteins/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/chemistry/*genetics ; Species Specificity ; Translocation, Genetic ; }, abstract = {As a phylogenetically valuable decapoda, a complete mitochondrial genome from Stenopodidea has not been reported to date. Here, we determined the complete mitochondrial DNA sequence of Stenopus hispidus (Olivier, 1811). The 15,528 bp genome is a circular molecule and consists of 13 protein-coding genes (PCGs) and two ribosomal RNA (rRNA) genes plus the putative control region (CR). This finding is similar to other metazoan animals but with the exception of 23 transfer RNA (tRNA) genes, which contain an additional tRNA-Gln compared with other crustaceans. With respect to the pancrustacean ground pattern mitochondria gene order, 5 tRNAs appear to be rearranged (tRNAs-Leu (CUN), Arg, Glu, Gln, and Met), one of which has also undergone inversion (tRNA-Leu (CUN)). Phylogenetic analyses reveal Stenopodidea and Reptantia form a clade sister to Caridea, which agrees with Abele and Felgenhauer's (1986) hypothesis. This topology contrasts with previous results based on morphological and some molecular data.}, }
@article {pmid22574125, year = {2012}, author = {Mallet, S and Weiss, S and Jacques, N and Leh-Louis, V and Sacerdot, C and Casaregola, S}, title = {Insights into the life cycle of yeasts from the CTG clade revealed by the analysis of the Millerozyma (Pichia) farinosa species complex.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e35842}, pmid = {22574125}, issn = {1932-6203}, mesh = {Aneuploidy ; Animals ; Cattle ; Chimera ; Chromosomes, Fungal/genetics ; DNA, Fungal/genetics ; DNA, Mitochondrial/genetics ; Genome, Fungal/genetics ; Haploidy ; Humans ; Life Cycle Stages ; *Phylogeny ; Reproducibility of Results ; Reproduction/genetics ; Saccharomycetales/*classification/genetics/*growth &amp; development ; Spores, Fungal/growth &amp; development ; }, abstract = {Among ascomycetous yeasts, the CTG clade is so-called because its constituent species translate CTG as serine instead of leucine. Though the biology of certain pathogenic species such as Candida albicans has been much studied, little is known about the life cycles of non-pathogen species of the CTG clade. Taking advantage of the recently obtained sequence of the biotechnological Millerozyma (Pichiasorbitophila) farinosa strain CBS 7064, we used MLST to better define phylogenic relationships between most of the Millerozyma farinosa strains available in public collections. This led to the constitution of four phylogenetic clades diverging from 8% to 15% at the DNA level and possibly constituting a species complex (M. farinosa) and to the proposal of two new species:Millerozyma miso sp. nov. CBS 2004(T) (= CLIB 1230(T)) and Candida pseudofarinosa sp. nov.NCYC 386(T)(= CLIB 1231(T)). Further analysis showed that M. farinosa isolates exist as haploid and inter-clade hybrids. Despite the sequence divergence between the clades, secondary contacts after reproductive isolation were evidenced, as revealed by both introgression and mitochondria transfer between clades. We also showed that the inter-clade hybrids do sporulate to generate mainly viable vegetative diploid spores that are not the result of meiosis, and very rarely aneuploid spores possibly through the loss of heterozygosity during sporulation. Taken together, these results show that in this part of the CTG clade, non-Mendelian genetic exchanges occur at high rates through hybridization between divergent strains from distinct clades and subsequent massive loss of heterozygosity. This combination of mechanisms could constitute an alternative sexuality leading to an unsuspected biodiversity.}, }
@article {pmid22570495, year = {2012}, author = {Sinturel, F and Bréchemier-Baey, D and Kiledjian, M and Condon, C and Bénard, L}, title = {Activation of 5'-3' exoribonuclease Xrn1 by cofactor Dcs1 is essential for mitochondrial function in yeast.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {21}, pages = {8264-8269}, pmid = {22570495}, issn = {1091-6490}, support = {R01 GM067005/GM/NIGMS NIH HHS/United States ; GM67005/GM/NIGMS NIH HHS/United States ; }, mesh = {Catalysis ; Enzyme Activation/physiology ; Exoribonucleases/genetics/*metabolism ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Fungal ; Glycerol/metabolism ; Mitochondria/*enzymology ; N-Glycosyl Hydrolases/genetics/*metabolism ; RNA Processing, Post-Transcriptional/physiology ; RNA Stability/physiology ; RNA, Messenger/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics/growth &amp; development ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Signal Transduction/physiology ; Substrate Specificity ; }, abstract = {The scavenger decapping enzyme Dcs1 has been shown to facilitate the activity of the cytoplasmic 5'-3' exoribonuclease Xrn1 in eukaryotes. Dcs1 has also been shown to be required for growth in glycerol medium. We therefore wondered whether the capacity to activate RNA degradation could account for its requirement for growth on this carbon source. Indeed, a catalytic mutant of Xrn1 is also unable to grow in glycerol medium, and removal of the nuclear localization signal of Rat1, the nuclear homolog of Xrn1, restores glycerol growth. A cytoplasmic 5'-3' exoribonuclease activity is therefore essential for yeast growth on glycerol, suggesting that Xrn1 activation by Dcs1 is physiologically important. In fact, Xrn1 is essentially inactive in the absence of Dcs1 in vivo. We analyzed the role of Dcs1 in the control of exoribonuclease activity in vitro and propose that Dcs1 is a specific cofactor of Xrn1. Dcs1 does not stimulate the activity of other 5'-3' exoribonucleases, such as Rat1, in vitro. We demonstrate that Dcs1 improves the apparent affinity of Xrn1 for RNA and that Xrn1 and Dcs1 can form a complex in vitro. We examined the biological significance of this regulation by performing 2D protein gel analysis. We observed that a set of proteins showing decreased levels in a DCS deletion strain, some essential for respiration, are also systematically decreased in an XRN1 deletion mutant. Therefore, we propose that the activation of Xrn1 by Dcs1 is important for respiration.}, }
@article {pmid22569362, year = {2012}, author = {López-Doménech, G and Serrat, R and Mirra, S and D'Aniello, S and Somorjai, I and Abad, A and Vitureira, N and García-Arumí, E and Alonso, MT and Rodriguez-Prados, M and Burgaya, F and Andreu, AL and García-Sancho, J and Trullas, R and Garcia-Fernàndez, J and Soriano, E}, title = {The Eutherian Armcx genes regulate mitochondrial trafficking in neurons and interact with Miro and Trak2.}, journal = {Nature communications}, volume = {3}, number = {}, pages = {814}, pmid = {22569362}, issn = {2041-1723}, mesh = {Animals ; Armadillo Domain Proteins/genetics/*metabolism ; Carrier Proteins/genetics/*metabolism ; Cell Line ; *Evolution, Molecular ; Humans ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Multigene Family ; Nerve Tissue Proteins/genetics/*metabolism ; Neurons/*metabolism ; Protein Binding ; Protein Transport ; rho GTP-Binding Proteins/genetics/*metabolism ; }, abstract = {Brain function requires neuronal activity-dependent energy consumption. Neuronal energy supply is controlled by molecular mechanisms that regulate mitochondrial dynamics, including Kinesin motors and Mitofusins, Miro1-2 and Trak2 proteins. Here we show a new protein family that localizes to the mitochondria and controls mitochondrial dynamics. This family of proteins is encoded by an array of armadillo (Arm) repeat-containing genes located on the X chromosome. The Armcx cluster is unique to Eutherian mammals and evolved from a single ancestor gene (Armc10). We show that these genes are highly expressed in the developing and adult nervous system. Furthermore, we demonstrate that Armcx3 expression levels regulate mitochondrial dynamics and trafficking in neurons, and that Alex3 interacts with the Kinesin/Miro/Trak2 complex in a Ca(2+)-dependent manner. Our data provide evidence of a new Eutherian-specific family of mitochondrial proteins that controls mitochondrial dynamics and indicate that this key process is differentially regulated in the brain of higher vertebrates.}, }
@article {pmid22569235, year = {2012}, author = {Huynen, MA and Duarte, I and Chrzanowska-Lightowlers, ZM and Nabuurs, SB}, title = {Structure based hypothesis of a mitochondrial ribosome rescue mechanism.}, journal = {Biology direct}, volume = {7}, number = {}, pages = {14}, pmid = {22569235}, issn = {1745-6150}, support = {096919/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Carboxylic Ester Hydrolases/metabolism ; Codon, Terminator ; Conserved Sequence ; Humans ; Mitochondria/genetics ; Mitochondrial Proteins/*genetics ; *Models, Biological ; Peptide Chain Termination, Translational ; Peptide Termination Factors/*genetics ; Phylogeny ; *Protein Biosynthesis ; RNA, Bacterial/genetics ; RNA, Transfer, Amino Acyl/metabolism ; Ribosomes/*metabolism ; Sequence Alignment ; Sequence Analysis, Protein ; Thermus thermophilus/genetics ; Vertebrates/*genetics ; }, abstract = {BACKGROUND: mtRF1 is a vertebrate mitochondrial protein with an unknown function that arose from a duplication of the mitochondrial release factor mtRF1a. To elucidate the function of mtRF1, we determined the positions that are conserved among mtRF1 sequences but that are different in their mtRF1a paralogs. We subsequently modeled the 3D structure of mtRF1a and mtRF1 bound to the ribosome, highlighting the structural implications of these differences to derive a hypothesis for the function of mtRF1.<br><br>RESULTS: Our model predicts, in agreement with the experimental data, that the 3D structure of mtRF1a allows it to recognize the stop codons UAA and UAG in the A-site of the ribosome. In contrast, we show that mtRF1 likely can only bind the ribosome when the A-site is devoid of mRNA. Furthermore, while mtRF1a will adopt its catalytic conformation, in which it functions as a peptidyl-tRNA hydrolase in the ribosome, only upon binding of a stop codon in the A-site, mtRF1 appears specifically adapted to assume this extended, peptidyl-tRNA hydrolyzing conformation in the absence of mRNA in the A-site.<br><br>CONCLUSIONS: We predict that mtRF1 specifically recognizes ribosomes with an empty A-site and is able to function as a peptidyl-tRNA hydrolase in those situations. Stalled ribosomes with empty A-sites that still contain a tRNA bound to a peptide chain can result from the translation of truncated, stop-codon less mRNAs. We hypothesize that mtRF1 recycles such stalled ribosomes, performing a function that is analogous to that of tmRNA in bacteria.}, }
@article {pmid22567860, year = {2012}, author = {Torgunakova, OA and Khrisanfov, VE and Prizenko, VK and Bogeruk, AK and Egorova, TA and Semenova, SK}, title = {[Polymorphism of the cytochrome oxidase b gene (cyt b) in Russian populations of common carp and wild common carp (Cyprinus carpio L.)].}, journal = {Genetika}, volume = {48}, number = {1}, pages = {104-111}, pmid = {22567860}, issn = {0016-6758}, mesh = {Animals ; Carps/*genetics ; Cytochromes b/*genetics ; Haplotypes/*genetics ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Population/genetics ; Russia ; Sequence Analysis, DNA ; }, abstract = {Polymorphism of the mitochondrial cyt b gene was examined in 35 individuals of common carp and wild common carp (Cyprinus carpio L.). The fish examined represented two natural populations from Khabarovsk krai (Ac and Am), Volga wild common carp, Don wild common carp, and two common carp breeds, Ropsha (strains BB and MM) common carp and Hungarian common carp. The highest level of nucleotide (pi) and haplotype (h) diversity was detected in two strains of Ropsha common carp (MM, pi = 0.67%, h = 0.7; and BB, pi = 0.21%, h = 0.9) and in one population (Am) of Amur wild common carp (pi = 0.26%; h = 0.6). The second population of Amur wild common carp (Ac) and Hungarian common carp were characterized by lower variation estimates (pi = 0.035%, h = 0.4; and pi = 0.09%, h = 0.7, respectively). Genetic homogeneity was demonstrated for the populations of Volga and Don wild common carp (pi = 0, h = 0). In the sample of the cyt b sequences examined, three lineages were identified. Lineages I and II united all haplotypes of the Am Amur wild common carp along with two haplotypes of Ropsha common carp, strain MM. The third lineage (III) was formed by the haplotypes of three individuals of Ropsha common carp strain MM, all representatives of Ropsha common carp strain BB, Hungarian common carp, Ac Amur wild common carp, and Don and Volga wild common carps. Statistically significant amino acid differences were observed only for the sequences, corresponding to haplotypes of lineage III, and the sum of sequences of lineages I and II. Effectiveness of different types of markers to differentiate the two subspecies of European and Amur wild common carp (C. c. carpio and C. c. haematopterus) is discussed, as well as the issues of the origin and dispersal of Russian common carp and wild common carp breeds.}, }
@article {pmid22567162, year = {2012}, author = {Smith, MA and Bertrand, C and Crosby, K and Eveleigh, ES and Fernandez-Triana, J and Fisher, BL and Gibbs, J and Hajibabaei, M and Hallwachs, W and Hind, K and Hrcek, J and Huang, DW and Janda, M and Janzen, DH and Li, Y and Miller, SE and Packer, L and Quicke, D and Ratnasingham, S and Rodriguez, J and Rougerie, R and Shaw, MR and Sheffield, C and Stahlhut, JK and Steinke, D and Whitfield, J and Wood, M and Zhou, X}, title = {Wolbachia and DNA barcoding insects: patterns, potential, and problems.}, journal = {PloS one}, volume = {7}, number = {5}, pages = {e36514}, pmid = {22567162}, issn = {1932-6203}, mesh = {Animals ; DNA Barcoding, Taxonomic/*methods ; DNA, Mitochondrial/genetics ; Insecta/classification/*genetics/*microbiology ; Phylogeny ; Wolbachia/*genetics ; }, abstract = {Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein--wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor--which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region.}, }
@article {pmid22560092, year = {2012}, author = {Pala, M and Olivieri, A and Achilli, A and Accetturo, M and Metspalu, E and Reidla, M and Tamm, E and Karmin, M and Reisberg, T and Hooshiar Kashani, B and Perego, UA and Carossa, V and Gandini, F and Pereira, JB and Soares, P and Angerhofer, N and Rychkov, S and Al-Zahery, N and Carelli, V and Sanati, MH and Houshmand, M and Hatina, J and Macaulay, V and Pereira, L and Woodward, SR and Davies, W and Gamble, C and Baird, D and Semino, O and Villems, R and Torroni, A and Richards, MB}, title = {Mitochondrial DNA signals of late glacial recolonization of Europe from near eastern refugia.}, journal = {American journal of human genetics}, volume = {90}, number = {5}, pages = {915-924}, pmid = {22560092}, issn = {1537-6605}, mesh = {DNA, Mitochondrial/*genetics/*metabolism ; Europe ; Europe, Eastern/epidemiology ; Genetic Variation ; Genetics, Population ; Humans ; Middle East ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; White People/*genetics ; }, abstract = {Human populations, along with those of many other species, are thought to have contracted into a number of refuge areas at the height of the last Ice Age. European populations are believed to be, to a large extent, the descendants of the inhabitants of these refugia, and some extant mtDNA lineages can be traced to refugia in Franco-Cantabria (haplogroups H1, H3, V, and U5b1), the Italian Peninsula (U5b3), and the East European Plain (U4 and U5a). Parts of the Near East, such as the Levant, were also continuously inhabited throughout the Last Glacial Maximum, but unlike western and eastern Europe, no archaeological or genetic evidence for Late Glacial expansions into Europe from the Near East has hitherto been discovered. Here we report, on the basis of an enlarged whole-genome mitochondrial database, that a substantial, perhaps predominant, signal from mitochondrial haplogroups J and T, previously thought to have spread primarily from the Near East into Europe with the Neolithic population, may in fact reflect dispersals during the Late Glacial period, ∼19-12 thousand years (ka) ago.}, }
@article {pmid22558439, year = {2012}, author = {Lin, LH and Qu, YF and Li, H and Zhou, KY and Ji, X}, title = {Genetic structure and demographic history should inform conservation: Chinese cobras currently treated as homogenous show population divergence.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e36334}, pmid = {22558439}, issn = {1932-6203}, mesh = {Animals ; Cell Nucleus/genetics ; Conservation of Natural Resources/*methods ; Elapidae/classification/*genetics ; Genetic Markers/genetics ; Genetic Variation ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Population Dynamics ; }, abstract = {An understanding of population structure and genetic diversity is crucial for wildlife conservation and for determining the integrity of wildlife populations. The vulnerable Chinese cobra (Naja atra) has a distribution from the mouth of the Yangtze River down to northern Vietnam and Laos, within which several large mountain ranges and water bodies may influence population structure. We combined 12 microsatellite loci and 1117 bp of the mitochondrial cytochrome b gene to explore genetic structure and demographic history in this species, using 269 individuals from various localities in Mainland China and Vietnam. High levels of genetic variation were identified for both mtDNA and microsatellites. mtDNA data revealed two main (Vietnam + southern China + southwestern China; eastern + southeastern China) and one minor (comprising only two individuals from the westernmost site) clades. Microsatellite data divided the eastern + southeastern China clade further into two genetic clusters, which include individuals from the eastern and southeastern regions, respectively. The Luoxiao and Nanling Mountains may be important barriers affecting the diversification of lineages. In the haplotype network of cytchrome b, many haplotypes were represented within a "star" cluster and this and other tests suggest recent expansion. However, microsatellite analyses did not yield strong evidence for a recent bottleneck for any population or genetic cluster. The three main clusters identified here should be considered as independent management units for conservation purposes. The release of Chinese cobras into the wild should cease unless their origin can be determined, and this will avoid problems arising from unnatural homogenization.}, }
@article {pmid22548482, year = {2012}, author = {Reding, DM and Bronikowski, AM and Johnson, WE and Clark, WR}, title = {Pleistocene and ecological effects on continental-scale genetic differentiation in the bobcat (Lynx rufus).}, journal = {Molecular ecology}, volume = {21}, number = {12}, pages = {3078-3093}, doi = {10.1111/j.1365-294X.2012.05595.x}, pmid = {22548482}, issn = {1365-294X}, support = {//Intramural NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/*analysis ; Ecosystem ; Evolution, Molecular ; Gene Flow ; Genetic Drift ; *Genetic Variation ; Geography ; Lynx/*genetics ; *Microsatellite Repeats ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeography ; United States ; }, abstract = {The potential for widespread, mobile species to exhibit genetic structure without clear geographic barriers is a topic of growing interest. Yet the patterns and mechanisms of structure--particularly over broad spatial scales--remain largely unexplored for these species. Bobcats occur across North America and possess many characteristics expected to promote gene flow. To test whether historical, topographic or ecological factors have influenced genetic differentiation in this species, we analysed 1 kb mtDNA sequence and 15 microsatellite loci from over 1700 samples collected across its range. The primary signature in both marker types involved a longitudinal cline with a sharp transition, or suture zone, occurring along the Great Plains. Thus, the data distinguished bobcats in the eastern USA from those in the western half, with no obvious physical barrier to gene flow. Demographic analyses supported a scenario of expansion from separate Pleistocene refugia, with the Great Plains representing a zone of secondary contact. Substructure within the two main lineages likely reflected founder effects, ecological factors, anthropogenic/topographic effects or a combination of these forces. Two prominent topographic features, the Mississippi River and Rocky Mountains, were not supported as significant genetic barriers. Ecological regions and environmental correlates explained a small but significant proportion of genetic variation. Overall, results implicate historical processes as the primary cause of broad-scale genetic differentiation, but contemporary forces seem to also play a role in promoting and maintaining structure. Despite the bobcat's mobility and broad niche, large-scale landscape changes have contributed to significant and complex patterns of genetic structure.}, }
@article {pmid22536961, year = {2012}, author = {Calabrese, FM and Simone, D and Attimonelli, M}, title = {Primates and mouse NumtS in the UCSC Genome Browser.}, journal = {BMC bioinformatics}, volume = {13 Suppl 4}, number = {Suppl 4}, pages = {S15}, pmid = {22536961}, issn = {1471-2105}, mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; *Genes, Mitochondrial ; Genome ; Humans ; Macaca mulatta/*genetics ; Mice/*genetics ; Mitochondria/genetics ; Pan troglodytes/*genetics ; *Software ; }, abstract = {BACKGROUND: NumtS (Nuclear MiTochondrial Sequences) are mitochondrial DNA sequences that, after stress events involving the mitochondrion, colonized the nuclear genome. Accurate mapping of NumtS avoids contamination during mtDNA PCR amplification, thus supplying reliable bases for detecting false heteroplasmies. In addition, since they commonly populate mammalian genomes (especially primates) and are polymorphic, in terms of presence/absence and content of SNPs, they may be used as evolutionary markers in intra- and inter-species population analyses.<br><br>RESULTS: The need for an exhaustive NumtS annotation led us to produce the Reference Human NumtS compilation, followed, as reported in this paper, by those for chimpanzee, rhesus macaque and mouse ones. Identification of NumtS inside the UCSC Genome Browser and their inter-species comparison required the design and the implementation of NumtS tracks, starting from the compilation data. NumtS retrieval through the UCSC Genome Browser, in the species examined, is now feasible at a glance.<br><br>CONCLUSIONS: Analyses involving NumtS tracks, together with other genome element tracks publicly available at the UCSC Genome Browser, can provide deep insight into genome evolution and comparative genomics, thus improving studies dealing with the mechanisms that drove the generation of NumtS. In addition, the NumtS tracks constitute a useful tool in the design of mitochondrial DNA primers.}, }
@article {pmid24298354, year = {2012}, author = {Trosko, JE and Kang, KS}, title = {Evolution of energy metabolism, stem cells and cancer stem cells: how the warburg and barker hypotheses might be linked.}, journal = {International journal of stem cells}, volume = {5}, number = {1}, pages = {39-56}, pmid = {24298354}, issn = {2005-3606}, abstract = {The evolutionary transition from single cells to the metazoan forced the appearance of adult stem cells and a hypoxic niche, when oxygenation of the environment forced the appearance of oxidative phosphorylation from that of glycolysis. The prevailing paradigm in the cancer field is that cancers start from the "immortalization" or "re-programming" of a normal, differentiated cell with many mitochondria, that metabolize via oxidative phosphorylation. This paradigm has been challenged with one that assumes that the target cell for carcinogenesis is the normal, immortal adult stem cell, with few mitochondria. This adult organ-specific stem cell is blocked from "mortalizing" or from "programming" to be terminally differentiated. Two hypotheses have been offered to explain cancers, namely, the "stem cell theory" and the "de-differentiation" or "re-programming" theory. This Commentary postulates that the paleochemistry of the oceans, which, initially, provided conditions for life' s energy to arise via glycolysis, changed to oxidative phosphorylation for life' s processes. In doing so, stem cells evolved, within hypoxic niches, to protect the species germinal and somatic genomes. This Commentary provides support for the "stem cell theory", in that cancer cells, which, unlike differentiated cells, have few mitochondria and metabolize via glycolysis. The major argument against the "de-differentiation theory" is that, if re-programming of a differentiated cell to an "induced pluri-potent stem cell" happened in an adult, teratomas, rather than carcinomas, should be the result.}, }
@article {pmid22544773, year = {2012}, author = {Crawford, MA and Broadhurst, CL}, title = {The role of docosahexaenoic and the marine food web as determinants of evolution and hominid brain development: the challenge for human sustainability.}, journal = {Nutrition and health}, volume = {21}, number = {1}, pages = {17-39}, doi = {10.1177/0260106012437550}, pmid = {22544773}, issn = {0260-1060}, mesh = {Animals ; Aquaculture ; *Biological Evolution ; Brain/growth &amp; development/*physiology ; Brain Diseases/physiopathology ; Cell Membrane/chemistry ; Docosahexaenoic Acids/genetics/metabolism/*physiology ; Hominidae/*physiology ; Humans ; *Marine Biology ; *Nutritional Physiological Phenomena ; Seafood ; }, abstract = {Life originated on this planet about 3 billion years ago. For the first 2.5 billion years of life there was ample opportunity for DNA modification. Yet there is no evidence of significant change in life forms during that time. It was not until about 600 million years ago, when the oxygen tension rose to a point where air-breathing life forms became thermodynamically possible, that a major change can be abruptly seen in the fossil record. The sudden appearance of the 32 phyla in the Cambrian fossil record was also associated with the appearance of intracellular detail not seen in previous life forms. That detail was provided by cell membranes made with lipids (membrane fats) as structural essentials. Lipids thus played a major, as yet unrecognised, role as determinants in evolution. The compartmentalisation of intracellular, specialist functions as in the nucleus, mitochondria, reticulo-endothelial system and plasma membrane led to cellular specialisation and then speciation. Thus, not only oxygen but also the marine lipids were drivers in the Cambrian explosion. Docosahexaenoic acid (DHA) (all-cis-docosa-4,7,10,13,16,19-hexaenoic acid, C22:6ω3 or C22:6, n-3, DHA) is a major feature of marine lipids. It requires six oxygen atoms to insert its six double bonds, so it would not have been abundant before oxidative metabolism became plentiful. DHA provided the membrane backbone for the emergence of new photoreceptors that converted photons into electricity, laying the foundation for the evolution of other signalling systems, the nervous system and the brain. Hence, the ω3 DHA from the marine food web must have played a critical role in human evolution. There is also clear evidence from molecular biology that DHA is a determinant of neuronal migration, neurogenesis and the expression of several genes involved in brain growth and function. That same process was essential to the ultimate cerebral expansion in human evolution. There is now incontrovertible support of this hypothesis from fossil evidence of human evolution taking advantage of the marine food web. Lipids are still modifying the present evolutionary phase of our species; their signature is evident in the changing panorama of non-communicable diseases. The most worrying change in disease pattern is the sharp rise in brain disorders, which, in the European Union, has overtaken the cost of all other burdens of ill health at €386 billion for the 25 member states at 2004 prices. In 2007, the UK cost was estimated at £77 billion and confirmed in 2010 at £105 billion - greater than heart disease and cancer combined. The rise in mental ill health is now being globalised. The solution to the rising vascular disorders in the last century and now brain disorders in this century lies in a radical reappraisal of the food system, which last century was focussed on protein and calories, with little attention paid to the requirements of the brain - the very organ that was the determinant of human evolution. With the marine fish catch having plateaued 20 years ago and its sustainability now under threat, a critical aspect of this revision is the development of marine agriculture from estuarine, coastal and oceanic resources. Such action is likely to play a key role in future health and intelligence.}, }
@article {pmid22543690, year = {2012}, author = {Birke, H and Müller, SJ and Rother, M and Zimmer, AD and Hoernstein, SN and Wesenberg, D and Wirtz, M and Krauss, GJ and Reski, R and Hell, R}, title = {The relevance of compartmentation for cysteine synthesis in phototrophic organisms.}, journal = {Protoplasma}, volume = {249 Suppl 2}, number = {}, pages = {S147-55}, pmid = {22543690}, issn = {1615-6102}, mesh = {*Cell Compartmentation ; Cysteine/*biosynthesis ; *Phototrophic Processes ; Plant Proteins/metabolism ; Subcellular Fractions/metabolism ; Sulfur/metabolism ; }, abstract = {In the vascular plant Arabidopsis thaliana, synthesis of cysteine and its precursors O-acetylserine and sulfide is distributed between the cytosol, chloroplasts, and mitochondria. This compartmentation contributes to regulation of cysteine synthesis. In contrast to Arabidopsis, cysteine synthesis is exclusively restricted to chloroplasts in the unicellular green alga Chlamydomonas reinhardtii. Thus, the question arises, whether specification of compartmentation was driven by multicellularity and specified organs and tissues. The moss Physcomitrella patens colonizes land but is still characterized by a simple morphology compared to vascular plants. It was therefore used as model organism to study evolution of compartmented cysteine synthesis. The presence of O-acetylserine(thiol)lyase (OAS-TL) proteins, which catalyze the final step of cysteine synthesis, in different compartments was applied as criterion. Purification and characterization of native OAS-TL proteins demonstrated the presence of five OAS-TL protein species encoded by two genes in Physcomitrella. At least one of the gene products is dual targeted to plastids and cytosol, as shown by combination of GFP fusion localization studies, purification of chloroplasts, and identification of N termini from native proteins. The bulk of OAS-TL protein is targeted to plastids, whereas there is no evidence for a mitochondrial OAS-TL isoform and only a minor part of OAS-TL protein is localized in the cytosol. This demonstrates that subcellular diversification of cysteine synthesis is already initialized in Physcomitrella but appears to gain relevance later during evolution of vascular plants.}, }
@article {pmid22535382, year = {2012}, author = {Goda, N and Kanai, M}, title = {Hypoxia-inducible factors and their roles in energy metabolism.}, journal = {International journal of hematology}, volume = {95}, number = {5}, pages = {457-463}, pmid = {22535382}, issn = {1865-3774}, mesh = {Animals ; Carbohydrate Metabolism ; *Energy Metabolism ; Humans ; Hypoxia/metabolism ; Hypoxia-Inducible Factor 1/*metabolism ; Lactic Acid/metabolism ; Lipid Metabolism ; Oxygen Consumption ; Pyruvic Acid/metabolism ; }, abstract = {Over the course of evolution, aerobic organisms have developed sophisticated systems for responding to alterations in oxygen concentration, as oxygen acts as a final electron acceptor in oxidative phosphorylation for energy production. Hypoxia-inducible factor (HIF) plays a central role in the adaptive regulation of energy metabolism, by triggering a switch from mitochondrial oxidative phosphorylation to anaerobic glycolysis in hypoxic conditions. HIF also reduces oxygen consumption in mitochondria by inhibiting conversion of pyruvate to acetyl CoA, suppressing mitochondrial biogenesis and activating autophagy of mitochondria concomitantly with reduction in reactive oxygen species production. In addition, metabolic reprogramming in response to hypoxia through HIF activation is not limited to the regulation of carbohydrate metabolism; it occurs in lipid metabolism as well. Recent studies using in vivo gene-targeting technique have revealed unexpected, but novel functions of HIF in energy metabolism in a context- and cell type-specific manner, and shed light on the possibility of pharmaceutical targeting HIF as a new therapy against many diseases, including cancer, diabetes, and fatty liver.}, }
@article {pmid22530989, year = {2012}, author = {McNulty, SN and Mullin, AS and Vaughan, JA and Tkach, VV and Weil, GJ and Fischer, PU}, title = {Comparing the mitochondrial genomes of Wolbachia-dependent and independent filarial nematode species.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {145}, pmid = {22530989}, issn = {1471-2164}, support = {R03 AI092306/AI/NIAID NIH HHS/United States ; T32-AI007172/AI/NIAID NIH HHS/United States ; R03-AI092306/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Filarioidea/classification/*genetics ; *Genome, Mitochondrial ; Loa/classification/genetics ; Mitochondrial Proteins/genetics/metabolism ; Nucleic Acid Conformation ; Onchocerca/classification/genetics ; Phylogeny ; RNA, Ribosomal/chemistry/metabolism ; RNA, Transfer/chemistry/metabolism ; Wuchereria bancrofti/classification/*genetics ; }, abstract = {BACKGROUND: Many species of filarial nematodes depend on Wolbachia endobacteria to carry out their life cycle. Other species are naturally Wolbachia-free. The biological mechanisms underpinning Wolbachia-dependence and independence in filarial nematodes are not known. Previous studies have indicated that Wolbachia have an impact on mitochondrial gene expression, which may suggest a role in energy metabolism. If Wolbachia can supplement host energy metabolism, reduced mitochondrial function in infected filarial species may account for Wolbachia-dependence. Wolbachia also have a strong influence on mitochondrial evolution due to vertical co-transmission. This could drive alterations in mitochondrial genome sequence in infected species. Comparisons between the mitochondrial genome sequences of Wolbachia-dependent and independent filarial worms may reveal differences indicative of altered mitochondrial function.<br><br>RESULTS: The mitochondrial genomes of 5 species of filarial nematodes, Acanthocheilonema viteae, Chandlerella quiscali, Loa loa, Onchocerca flexuosa, and Wuchereria bancrofti, were sequenced, annotated and compared with available mitochondrial genome sequences from Brugia malayi, Dirofilaria immitis, Onchocerca volvulus and Setaria digitata. B. malayi, D. immitis, O. volvulus and W. bancrofti are Wolbachia-dependent while A. viteae, C. quiscali, L. loa, O. flexuosa and S. digitata are Wolbachia-free. The 9 mitochondrial genomes were similar in size and AT content and encoded the same 12 protein-coding genes, 22 tRNAs and 2 rRNAs. Synteny was perfectly preserved in all species except C. quiscali, which had a different order for 5 tRNA genes. Protein-coding genes were expressed at the RNA level in all examined species. In phylogenetic trees based on mitochondrial protein-coding sequences, species did not cluster according to Wolbachia dependence.<br><br>CONCLUSIONS: Thus far, no discernable differences were detected between the mitochondrial genome sequences of Wolbachia-dependent and independent species. Additional research will be needed to determine whether mitochondria from Wolbachia-dependent filarial species show reduced function in comparison to the mitochondria of Wolbachia-independent species despite their sequence-level similarities.}, }
@article {pmid22523127, year = {2012}, author = {Tsang, LM and Wu, TH and Shih, HT and Williams, GA and Chu, KH and Chan, BK}, title = {Genetic and morphological differentiation of the Indo-West Pacific intertidal barnacle Chthamalus malayensis.}, journal = {Integrative and comparative biology}, volume = {52}, number = {3}, pages = {388-409}, pmid = {22523127}, issn = {1557-7023}, mesh = {Animals ; DNA, Mitochondrial/analysis/*genetics ; Ecosystem ; Electron Transport Complex IV/genetics ; Gene Flow ; Genetics, Population/methods ; Indian Ocean ; Mitochondria/genetics ; Oceans and Seas ; Pacific Ocean ; Phylogeny ; Phylogeography ; Population Density ; Reproductive Isolation ; Species Specificity ; Temperature ; Thoracica/*anatomy &amp; histology/classification/*genetics/growth &amp; development ; }, abstract = {Chthamalus malayensis is a common intertidal acorn barnacle widely distributed in the Indo-West Pacific. Analysis of sequences of mitochondrial cytochrome c oxidase subunit I reveals four genetically differentiated clades with almost allopatric distribution in this region. The four clades exhibit morphological differences in arthropodal characters, including the number of conical spines and number of setules of the basal guard setae on the cirri. These characters are, however, highly variable within each clade; such that the absolute range of the number of conical spines and setules overlaps between clades, and therefore, these are not diagnostic characters for taxonomic identification. The geographic distribution of the four clades displays a strong relationship between surface temperatures of the sea and ocean-current realms. The Indo-Malay (IM) clade is widespread in the tropical, equatorial region, including the Indian Ocean, Malay Peninsula, and North Borneo. The South China (SC) and Taiwan (TW) clades are found in tropical to subtropical regions, with the former distributed along the coasts of southern China, Vietnam, Thailand, and the western Philippines under the influence of the South China Warm Current. The TW clade is endemic to Taiwan, while the Christmas Island (CI) clade is confined to CI. There was weak or no population subdivision observed within these clades, suggesting high gene flow within the range of the clades. The clades demonstrate clear signatures of recent demographic expansion that predated the Last Glacial Maximum (LGM), but they have maintained a relatively stable effective population in the past 100,000 years. The persistence of intertidal fauna through the LGM may, therefore, be a common biogeographic pattern. The lack of genetic subdivision in the IM clade across the Indian and Pacific Oceans may be attributed to recent expansion of ranges and the fact that a mutation-drift equilibrium has not been reached, or the relaxed habitat requirements of C. malayensis that facilitates high concurrent gene flow. Further studies are needed to determine between these alternative hypotheses.}, }
@article {pmid22523123, year = {2012}, author = {Ewers, C and Wares, JP}, title = {Examining an outlier: molecular diversity in the cirripedia.}, journal = {Integrative and comparative biology}, volume = {52}, number = {3}, pages = {410-417}, doi = {10.1093/icb/ics047}, pmid = {22523123}, issn = {1557-7023}, mesh = {Alleles ; Animals ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Gene Frequency ; *Genes, Mitochondrial ; *Genetic Variation ; Genetics, Population/methods ; Mitochondria/genetics ; Phylogeny ; Population Density ; Selection, Genetic ; Sequence Analysis, DNA/*methods ; Species Specificity ; Thoracica/classification/*genetics/physiology ; }, abstract = {Despite the typical assumption in studies of mitochondrial diversity that such data are useful for approximating population size and demography, studies of sequence diversity in mitochondrial DNA across the Metazoa have shown a surprising excess of rare alleles, a pattern associated either with strong selection or population growth. Previous work has shown that this bias toward an excess of rare alleles is typical across the Crustacea, and in particular, in the Cirripedia (barnacles). Here, we directly evaluate sequence data from studies of barnacle populations to ensure that inclusion of cryptic species is not the cause of this pattern. The results shown here reinforce previous studies that suggest caution in interpreting such patterns of allele frequencies, as they are likely to be influenced both by demographic changes and selection.}, }
@article {pmid22519660, year = {2012}, author = {Davis, AM and Unmack, PJ and Pusey, BJ and Johnson, JB and Pearson, RG}, title = {Marine-freshwater transitions are associated with the evolution of dietary diversification in terapontid grunters (Teleostei: Terapontidae).}, journal = {Journal of evolutionary biology}, volume = {25}, number = {6}, pages = {1163-1179}, doi = {10.1111/j.1420-9101.2012.02504.x}, pmid = {22519660}, issn = {1420-9101}, mesh = {Animals ; Australasia ; Base Sequence ; Carnivory ; Cell Nucleus/genetics ; *Diet ; *Ecosystem ; *Evolution, Molecular ; Fishes/classification/genetics/*physiology ; *Fresh Water ; Genes, Mitochondrial ; Genetic Speciation ; Genetic Variation ; Marine Biology ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Species Specificity ; }, abstract = {The ecological opportunities associated with transitions across the marine-freshwater interface are regarded as an important catalyst of diversification in a range of aquatic taxa. Here, we examined the role of these major habitat transitions and trophic diversification in a radiation of Australasian fishes using a new molecular phylogeny incorporating 37 Terapontidae species. A combined mitochondrial and nuclear gene analysis yielded a well-supported tree with most nodes resolved. Ancestral terapontids appear to have been euryhaline in habitat affiliation, with a single transition to freshwater environments producing all Australasian freshwater species. Mapping of terapontid feeding modes onto the molecular phylogeny-predicted carnivorous dietary habits was displayed by ancestral terapontids, which subsequently diversified into a range of additional carnivorous, omnivorous, herbivorous and detritivorous dietary modes upon transition to freshwater habitats. Comparative analyses suggested that following the freshwater invasion, the single freshwater clade has exhibited an increased rate of diversification at almost three times the background rate evident across the rest of the family. The marine-freshwater transition within Terapontidae appears to have resulted in substantial dietary radiation in freshwater environments, as well as increased lineage diversification rates relative to euryhaline-marine habitats.}, }
@article {pmid22518007, year = {2012}, author = {Kanesaki, Y and Imamura, S and Minoda, A and Tanaka, K}, title = {External light conditions and internal cell cycle phases coordinate accumulation of chloroplast and mitochondrial transcripts in the red alga Cyanidioschyzon merolae.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {19}, number = {3}, pages = {289-303}, pmid = {22518007}, issn = {1756-1663}, mesh = {Cell Cycle/*genetics ; Cell Nucleus/genetics/metabolism ; Chlamydomonas reinhardtii/genetics/metabolism ; Chloroplasts/*genetics/metabolism ; Cluster Analysis ; Gene Expression Profiling/methods ; *Gene Expression Regulation, Plant ; Light ; Mitochondria/*genetics/metabolism ; Rhodophyta/cytology/*genetics/physiology ; Transcriptome ; }, abstract = {The mitochondria and chloroplasts in plant cells are originated from bacterial endosymbioses, and they still replicate their own genome and divide in a similar manner as their ancestors did. It is thus likely that the organelle transcription is coordinated with its proliferation cycle. However, this possibility has not extensively been explored to date, because in most plant cells there are many mitochondria and chloroplasts that proliferate asynchronously. It is generally believed that the gene transfer from the organellar to nuclear genome has enabled nuclear control of the organelle functions during the evolution of eukaryotic plant cells. Nevertheless, no significant relationship has been reported between the organelle transcriptome and the host cell cycle even in Chlamydomonas reinhardtii. While the organelle proliferation cycle is not coordinated with the cell cycle in vascular plants, in the unicellular red alga Cyanidioschyzon merolae that contains only one mitochondrion, one chloroplast, and one nucleus per cell, each of the organelles is known to proliferate at a specific phase of the cell cycle. Here, we show that the expression of most of the organelle genes is highly coordinated with the cell cycle phases as well as with light regimes in clustering analyses. In addition, a strong correlation was observed between the gene expression profiles in the mitochondrion and chloroplast, resulting in the identification of a network of functionally related genes that are co-expressed during organelle proliferation.}, }
@article {pmid22516813, year = {2012}, author = {Wang, D and Lloyd, AH and Timmis, JN}, title = {Nuclear genome diversity in somatic cells is accelerated by environmental stress.}, journal = {Plant signaling &amp; behavior}, volume = {7}, number = {5}, pages = {595-597}, pmid = {22516813}, issn = {1559-2324}, mesh = {Biological Transport ; Cell Nucleus/*genetics ; Chloroplasts/*genetics ; DNA, Chloroplast/*metabolism ; DNA, Mitochondrial/*metabolism ; Genes, Reporter ; *Genome, Plant ; Heat-Shock Response/*genetics ; Plants, Genetically Modified ; Nicotiana/*genetics ; }, abstract = {DNA transfer to the nucleus from prokaryotic ancestors of the cytoplasmic organelles (mitochondria and plastids) has occurred during endosymbiotic evolution in eukaryotes. In most eukaryotes, organelle DNA transfer to nucleus is a continuing process. The frequency of DNA transposition from plastid (chloroplast) to nucleus has been measured in tobacco plants (Nicotiana tabacum) experimentally. We have monitored the effects of environmental stress on the rate of DNA transfer from plastid to nucleus by exploiting nucleus-specific reporter genes in two transplastomic tobacco lines. DNA migration from plastids to the nucleus is markedly increased by mild heat stress. In addition, insertions of mitochondrial DNA into induced double-strand breaks are observed after heat treatment. These results show that movement of organelle DNA to the nucleus is remarkably increased by heat stress.}, }
@article {pmid22513280, year = {2012}, author = {Gómez-Díaz, E and Morris-Pocock, JA and González-Solís, J and McCoy, KD}, title = {Trans-oceanic host dispersal explains high seabird tick diversity on Cape Verde islands.}, journal = {Biology letters}, volume = {8}, number = {4}, pages = {616-619}, pmid = {22513280}, issn = {1744-957X}, mesh = {Animals ; Bird Diseases/epidemiology/parasitology ; Birds/*parasitology ; Cabo Verde/epidemiology ; *Genes, Mitochondrial ; Genes, rRNA ; *Genetic Variation ; Genetics, Population/methods ; Haplotypes ; Mitochondria/genetics ; Ornithodoros/classification/*genetics/growth &amp; development ; Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S/analysis/genetics ; Tick Infestations/epidemiology/parasitology/veterinary ; }, abstract = {Parasites represent ideal models for unravelling biogeographic patterns and mechanisms of diversification on islands. Both host-mediated dispersal and within-island adaptation can shape parasite island assemblages. In this study, we examined patterns of genetic diversity and structure of Ornithodoros seabird ticks within the Cape Verde Archipelago in relation to their global phylogeography. Contrary to expectations, ticks from multiple, geographically distant clades mixed within the archipelago. Trans-oceanic colonization via host movements probably explains high local tick diversity, contrasting with previous research that suggests little large-scale dispersal in these birds. Although host specificity was not obvious at a global scale, host-associated genetic structure was found within Cape Verde colonies, indicating that post-colonization adaptation to specific hosts probably occurs. These results highlight the role of host metapopulation dynamics in the evolutionary ecology and epidemiology of avian parasites and pathogens.}, }
@article {pmid22512685, year = {2012}, author = {Kakizaki, Y and Moore, AL and Ito, K}, title = {Different molecular bases underlie the mitochondrial respiratory activity in the homoeothermic spadices of Symplocarpus renifolius and the transiently thermogenic appendices of Arum maculatum.}, journal = {The Biochemical journal}, volume = {445}, number = {2}, pages = {237-246}, pmid = {22512685}, issn = {1470-8728}, support = {BB/E015328/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Araceae/genetics/*metabolism ; Arum/genetics/*metabolism ; Blotting, Western ; Electron Transport ; Electrophoresis, Gel, Two-Dimensional ; Flowers ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Molecular Sequence Data ; NADPH Dehydrogenase/genetics/metabolism ; Oxidoreductases/genetics/*metabolism ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Sequence Homology, Amino Acid ; Tandem Mass Spectrometry ; *Thermogenesis ; }, abstract = {Symplocarpus renifolius and Arum maculatum are known to produce significant heat during the course of their floral development, but they use different regulatory mechanisms, i.e. homoeothermic compared with transient thermogenesis. To further clarify the molecular basis of species-specific thermogenesis in plants, in the present study we have analysed the native structures and expression patterns of the mitochondrial respiratory components in S. renifolius and A. maculatum. Our comparative analysis using Blue native PAGE combined with nano LC (liquid chromatography)-MS/MS (tandem MS) has revealed that the constituents of the respiratory complexes in both plants were basically similar, but that several mitochondrial components appeared to be differently expressed in their thermogenic organs. Namely, complex II in S. renifolius was detected as a 340 kDa product, suggesting an oligomeric or supramolecular structure in vivo. Moreover, the expression of an external NAD(P)H dehydrogenase was found to be higher in A. maculatum than in S. renifolius, whereas an internal NAD(P)H dehydrogenase was expressed at a similar level in both species. Alternative oxidase was detected as smear-like signals that were elongated on the first dimension with a peak at around 200 kDa in both species. The significance and implication of these data are discussed in terms of thermoregulation in plants.}, }
@article {pmid22510273, year = {2012}, author = {Boudina, S and Sena, S and Sloan, C and Tebbi, A and Han, YH and O'Neill, BT and Cooksey, RC and Jones, D and Holland, WL and McClain, DA and Abel, ED}, title = {Early mitochondrial adaptations in skeletal muscle to diet-induced obesity are strain dependent and determine oxidative stress and energy expenditure but not insulin sensitivity.}, journal = {Endocrinology}, volume = {153}, number = {6}, pages = {2677-2688}, pmid = {22510273}, issn = {1945-7170}, support = {R01 HL73167/HL/NHLBI NIH HHS/United States ; R01 HL073167/HL/NHLBI NIH HHS/United States ; R01 DK081842/DK/NIDDK NIH HHS/United States ; P30 HL101310/HL/NHLBI NIH HHS/United States ; U01 HL087947/HL/NHLBI NIH HHS/United States ; }, mesh = {Adaptation, Physiological ; Adenosine Triphosphate/metabolism ; Animals ; Blood Glucose/metabolism ; Blotting, Western ; Diet, High-Fat/adverse effects ; Diglycerides/metabolism ; Energy Metabolism/*physiology ; Female ; Insulin/blood ; Ion Channels/genetics/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Mitochondria, Muscle/genetics/metabolism/*physiology ; Mitochondrial Proteins/genetics/metabolism ; Muscle, Skeletal/metabolism ; Obesity/etiology/metabolism/*physiopathology ; Oxidative Stress/*physiology ; Reactive Oxygen Species/metabolism ; Superoxide Dismutase/metabolism ; Time Factors ; Triglycerides/metabolism ; Uncoupling Protein 3 ; }, abstract = {This study sought to elucidate the relationship between skeletal muscle mitochondrial dysfunction, oxidative stress, and insulin resistance in two mouse models with differential susceptibility to diet-induced obesity. We examined the time course of mitochondrial dysfunction and insulin resistance in obesity-prone C57B and obesity-resistant FVB mouse strains in response to high-fat feeding. After 5 wk, impaired insulin-mediated glucose uptake in skeletal muscle developed in both strains in the absence of any impairment in proximal insulin signaling. Impaired mitochondrial oxidative capacity preceded the development of insulin resistant glucose uptake in C57B mice in concert with increased oxidative stress in skeletal muscle. By contrast, mitochondrial uncoupling in FVB mice, which prevented oxidative stress and increased energy expenditure, did not prevent insulin resistant glucose uptake in skeletal muscle. Preventing oxidative stress in C57B mice treated systemically with an antioxidant normalized skeletal muscle mitochondrial function but failed to normalize glucose tolerance and insulin sensitivity. Furthermore, high fat-fed uncoupling protein 3 knockout mice developed increased oxidative stress that did not worsen glucose tolerance. In the evolution of diet-induced obesity and insulin resistance, initial but divergent strain-dependent mitochondrial adaptations modulate oxidative stress and energy expenditure without influencing the onset of impaired insulin-mediated glucose uptake.}, }
@article {pmid22509906, year = {2012}, author = {Scholl, K and Allen, JM and Leendertz, FH and Chapman, CA and Reed, DL}, title = {Variable microsatellite loci for population genetic analysis of Old World monkey lice (Pedicinus sp.).}, journal = {The Journal of parasitology}, volume = {98}, number = {5}, pages = {930-937}, doi = {10.1645/GE-3060.1}, pmid = {22509906}, issn = {1937-2345}, mesh = {Alleles ; Animals ; Anoplura/classification/*genetics ; Colobus/*parasitology ; Cote d'Ivoire ; DNA/chemistry/isolation &amp; purification ; Electron Transport Complex IV/genetics ; Genetics, Population ; Genome, Insect ; Heterozygote ; Humans ; Lice Infestations/parasitology/*veterinary ; Likelihood Functions ; Linkage Disequilibrium ; Microsatellite Repeats/*genetics ; Mitochondria/enzymology ; Monkey Diseases/*parasitology ; Phylogeny ; Sequence Analysis, DNA ; Uganda ; }, abstract = {Parasitic lice have been valuable informants of their host's evolutionary history because they complete their entire life cycle on the host and move between hosts primarily through direct host-to-host contact. Therefore, lice are confined to their hosts both in ecological and evolutionary time. Lice on great apes have been studied to examine details of their host's evolutionary history; however, species of Pedicinus, which parasitize the Old World monkeys, are less well known. We sampled lice from 2 groups of red colobus (Procolobus spp.) in Kibale National Park in Uganda and from red colobus and black and white colobus (Procolobus polycomos) in Taï National Park in Côte d'Ivoire. We used next-generation sequencing data analysis and the human body louse (Pediculus humanus humanus) genome to search for microsatellites for population genetic studies of Pedicinus lice. The 96 primer sets for microsatellite loci designed from the human body louse genome failed to amplify microsatellites in Pedicinus sp., perhaps due to the fast rate of evolution in parasitic lice. Of 63 microsatellites identified by next-generation sequencing data analysis of Pedicinus sp., 12 were variable among populations and 9 were variable within a single population. Our results suggest that these loci will be useful across the genus Pedicinus. We found that the lice in Uganda are not structured according to their hosts' social group; rather, 2 non-interbreeding populations of lice were found on both groups of red colobus. Because direct host-to-host contact is usually required for lice to move among hosts, these lice could be useful for identification and study of behavioral interactions between primate species.}, }
@article {pmid22509325, year = {2012}, author = {Yang, XM and Sun, JT and Xue, XF and Li, JB and Hong, XY}, title = {Invasion genetics of the Western flower thrips in China: evidence for genetic bottleneck, hybridization and bridgehead effect.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e34567}, pmid = {22509325}, issn = {1932-6203}, mesh = {Animals ; China ; Evolution, Molecular ; Female ; Genes, Insect/genetics ; Hybridization, Genetic/*genetics ; *Introduced Species ; Male ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic/genetics ; Population Dynamics ; Thysanoptera/*genetics ; }, abstract = {The western flower thrips, Frankliniella occidentalis (Pergande), is an invasive species and the most economically important pest within the insect order Thysanoptera. F. occidentalis, which is endemic to North America, was initially detected in Kunming in southwestern China in 2000 and since then it has rapidly invaded several other localities in China where it has greatly damaged greenhouse vegetables and ornamental crops. Controlling this invasive pest in China requires an understanding of its genetic makeup and migration patterns. Using the mitochondrial COI gene and 10 microsatellites, eight of which were newly isolated and are highly polymorphic, we investigated the genetic structure and the routes of range expansion of 14 F. occidentalis populations in China. Both the mitochondrial and microsatellite data revealed that the genetic diversity of F. occidentalis of the Chinese populations is lower than that in its native range. Two previously reported cryptic species (or ecotypes) were found in the study. The divergence in the mitochondrial COI of two Chinese cryptic species (or ecotypes) was about 3.3% but they cannot be distinguished by nuclear markers. Hybridization might produce such substantial mitochondrial-nuclear discordance. Furthermore, we found low genetic differentiation (global F(ST) = 0.043, P<0.001) among all the populations and strong evidence for gene flow, especially from the three southwestern populations (Baoshan, Dali and Kunming) to the other Chinese populations. The directional gene flow was further supported by the higher genetic diversity of these three southwestern populations. Thus, quarantine and management of F. occidentalis should focus on preventing it from spreading from the putative source populations to other parts of China.}, }
@article {pmid22506081, year = {2012}, author = {Messenger, LA and Llewellyn, MS and Bhattacharyya, T and Franzén, O and Lewis, MD and Ramírez, JD and Carrasco, HJ and Andersson, B and Miles, MA}, title = {Multiple mitochondrial introgression events and heteroplasmy in trypanosoma cruzi revealed by maxicircle MLST and next generation sequencing.}, journal = {PLoS neglected tropical diseases}, volume = {6}, number = {4}, pages = {e1584}, pmid = {22506081}, issn = {1935-2735}, support = {/WT_/Wellcome Trust/United Kingdom ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Cluster Analysis ; DNA, Circular/chemistry/genetics ; DNA, Mitochondrial/chemistry/*genetics ; *Genetic Variation ; Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; Mitochondria/*genetics ; Molecular Sequence Data ; Multilocus Sequence Typing ; Phylogeny ; Recombination, Genetic ; Trypanosoma cruzi/*genetics ; }, abstract = {BACKGROUND: Mitochondrial DNA is a valuable taxonomic marker due to its relatively fast rate of evolution. In Trypanosoma cruzi, the causative agent of Chagas disease, the mitochondrial genome has a unique structural organization consisting of 20-50 maxicircles (∼20 kb) and thousands of minicircles (0.5-10 kb). T. cruzi is an early diverging protist displaying remarkable genetic heterogeneity and is recognized as a complex of six discrete typing units (DTUs). The majority of infected humans are asymptomatic for life while 30-35% develop potentially fatal cardiac and/or digestive syndromes. However, the relationship between specific clinical outcomes and T. cruzi genotype remains elusive. The availability of whole genome sequences has driven advances in high resolution genotyping techniques and re-invigorated interest in exploring the diversity present within the various DTUs.<br><br>To describe intra-DTU diversity, we developed a highly resolutive maxicircle multilocus sequence typing (mtMLST) scheme based on ten gene fragments. A panel of 32 TcI isolates was genotyped using the mtMLST scheme, GPI, mini-exon and 25 microsatellite loci. Comparison of nuclear and mitochondrial data revealed clearly incongruent phylogenetic histories among different geographical populations as well as major DTUs. In parallel, we exploited read depth data, generated by Illumina sequencing of the maxicircle genome from the TcI reference strain Sylvio X10/1, to provide the first evidence of mitochondrial heteroplasmy (heterogeneous mitochondrial genomes in an individual cell) in T. cruzi.<br><br>CONCLUSIONS/SIGNIFICANCE: mtMLST provides a powerful approach to genotyping at the sub-DTU level. This strategy will facilitate attempts to resolve phenotypic variation in T. cruzi and to address epidemiologically important hypotheses in conjunction with intensive spatio-temporal sampling. The observations of both general and specific incidences of nuclear-mitochondrial phylogenetic incongruence indicate that genetic recombination is geographically widespread and continues to influence the natural population structure of TcI, a conclusion which challenges the traditional paradigm of clonality in T. cruzi.}, }
@article {pmid22506002, year = {2012}, author = {Johnson, RF and Gosliner, TM}, title = {Traditional taxonomic groupings mask evolutionary history: a molecular phylogeny and new classification of the chromodorid nudibranchs.}, journal = {PloS one}, volume = {7}, number = {4}, pages = {e33479}, pmid = {22506002}, issn = {1932-6203}, mesh = {Animals ; Atlantic Ocean ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Gastropoda/*classification/*genetics ; Mitochondria/genetics ; Oceans and Seas ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Chromodorid nudibranchs (16 genera, 300+ species) are beautiful, brightly colored sea slugs found primarily in tropical coral reef habitats and subtropical coastal waters. The chromodorids are the most speciose family of opisthobranchs and one of the most diverse heterobranch clades. Chromodorids have the potential to be a model group with which to study diversification, color pattern evolution, are important source organisms in natural products chemistry and represent a stunning and widely compelling example of marine biodiversity. Here, we present the most complete molecular phylogeny of the chromodorid nudibranchs to date, with a broad sample of 244 specimens (142 new), representing 157 (106 new) chromodorid species, four actinocylcid species and four additional dorid species utilizing two mitochondrial markers (16s and COI). We confirmed the monophyly of the Chromodorididae and its sister group relationship with the Actinocyclidae. We were also able to, for the first time, test generic monophyly by including more than one member of all 14 of the non-monotypic chromodorid genera. Every one of these 14 traditional chromodorid genera are either non-monophyletic, or render another genus paraphyletic. Additionally, both the monotypic genera Verconia and Diversidoris are nested within clades. Based on data shown here, there are three individual species and five clades limited to the eastern Pacific and Atlantic Oceans (or just one of these ocean regions), while the majority of chromodorid clades and species are strictly Indo-Pacific in distribution. We present a new classification of the chromodorid nudibranchs. We use molecular data to untangle evolutionary relationships and retain a historical connection to traditional systematics by using generic names attached to type species as clade names.}, }
@article {pmid22504659, year = {2012}, author = {Palese, LL and Bossis, F}, title = {The human extended mitochondrial metabolic network: new hubs from lipids.}, journal = {Bio Systems}, volume = {109}, number = {2}, pages = {151-158}, doi = {10.1016/j.biosystems.2012.04.001}, pmid = {22504659}, issn = {1872-8324}, mesh = {Humans ; *Lipid Metabolism ; Mitochondria/*metabolism ; }, abstract = {Even if systems thinking is not new in biology, rationalizing the explosively growing amount of knowledge has been the compelling reason for the sudden rise and spreading of systems biology. Based on 'omics' data, several genome-scale metabolic networks have been reconstructed and validated. One of the most striking aspects of complex metabolic networks is the pervasive power-law appearance of metabolite connectivity. However, the combinatorial diversity of some classes of compounds, such as lipids, has been scarcely considered so far. In this work, a lipid-extended human mitochondrial metabolic network has been built and analyzed. It is shown that, considering combinatorial diversity of lipids and multipurpose enzymes, an intimate connection between membrane lipids and oxidative phosphorilation appears. This finding leads to some biomedical considerations on diseases involving mitochondrial enzymes. Moreover, the lipid-extended network still shows power-law features. Power-law distributions are intrinsic to metabolic network organization and evolution. Hubs in the lipid-extended mitochondrial network strongly suggest that the "RNA world" and the "lipid world" hypothesis are both correct.}, }
@article {pmid22503399, year = {2012}, author = {Zhang, B and Dai, W}, title = {Ultrastructure of the spermatozoa of Cicadella viridis (Linnaeus) and its bearing on the phylogeny of Auchenorrhyncha.}, journal = {Micron (Oxford, England : 1993)}, volume = {43}, number = {9}, pages = {978-984}, doi = {10.1016/j.micron.2012.03.022}, pmid = {22503399}, issn = {1878-4291}, mesh = {Acrosome/ultrastructure ; Animals ; Cell Nucleus/ultrastructure ; Centrioles/ultrastructure ; Flagella/ultrastructure ; Hemiptera/*genetics/*ultrastructure ; Male ; Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; *Phylogeny ; Species Specificity ; Spermatozoa/*ultrastructure ; }, abstract = {The ultrastructure of mature spermatozoa of the leafhopper Cicadella viridis (Linnaeus) was investigated using light and transmission electron microscopy. The spermatozoon is composed of a head containing an acrosome and an elongated nucleus, and a long tail, which consists of a flagellum. The acrosome is conical and invaginated to form a subacrosomal space, and the acrosomal contents are filled with electron-dense tubular substructures. The nucleus is linear and filled with homogeneously condensed chromatin. The centriolar adjunct is parallel to the nucleus and connects the nucleus with the mid-piece/flagellum. The flagellum is formed by a 9+9+2 axoneme, two mitochondrial derivatives and two accessory bodies. The mitochondrial derivatives with an orderly array of peripheral cristae are symmetrical. The accessory bodies are small and slightly elliptical. The end of the axoneme shows progressive loss of microtubules. Comparison of sperm ultrastructure of C. viridis with those of other Auchenorrhyncha families supports the major relationships within Cicadomorpha as (Membracoidea (Cicadoidea, Cercopoidea)).}, }
@article {pmid22497212, year = {2012}, author = {Koban, E and Denizci, M and Aslan, O and Aktoprakligil, D and Aksu, S and Bower, M and Balcioglu, BK and Ozdemir Bahadir, A and Bilgin, R and Erdag, B and Bagis, H and Arat, S}, title = {High microsatellite and mitochondrial diversity in Anatolian native horse breeds shows Anatolia as a genetic conduit between Europe and Asia.}, journal = {Animal genetics}, volume = {43}, number = {4}, pages = {401-409}, doi = {10.1111/j.1365-2052.2011.02285.x}, pmid = {22497212}, issn = {1365-2052}, mesh = {Animals ; Asia ; Breeding ; DNA, Mitochondrial/*genetics/metabolism ; Europe ; *Genetic Variation ; Genotype ; Horses/*genetics ; *Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; Statistics as Topic ; }, abstract = {The horse has been a food source, but more importantly, it has been a means for transport. Its domestication was one of the crucial steps in the history of human civilization. Despite the archaeological and molecular studies carried out on the history of horse domestication, which would contribute to conservation of the breeds, the details of the domestication of horses still remain to be resolved. We employed 21 microsatellite loci and mitochondrial control region partial sequences to analyse genetic variability within and among four Anatolian native horse breeds, Ayvacık Pony, Malakan Horse, Hınıs Horse and Canik Horse, as well as samples from indigenous horses of unknown breed ancestry. The aims of the study were twofold: first, to produce data from the prehistorically and historically important land bridge, Anatolia, in order to assess its role in horse domestication and second, to analyse the data from a conservation perspective to help the ministry improve conservation and management strategies regarding native horse breeds. Even though the microsatellite data revealed a high allelic diversity, 98% of the genetic variation partitioned within groups. Genetic structure did not correlate with a breed or geographic origin. High diversity was also detected in mtDNA control region sequence analysis. Frequencies of two haplogroups (HC and HF) revealed a cline between Asia and Europe, suggesting Anatolia as a probable connection route between the two continents. This first detailed genetic study on Anatolian horse breeds revealed high diversity among horse mtDNA haplogroups in Anatolia and suggested Anatolia's role as a conduit between the two continents. The study also provides an important basis for conservation practices in Turkey.}, }
@article {pmid22491760, year = {2012}, author = {Koblmüller, S and Wayne, RK and Leonard, JA}, title = {Impact of Quaternary climatic changes and interspecific competition on the demographic history of a highly mobile generalist carnivore, the coyote.}, journal = {Biology letters}, volume = {8}, number = {4}, pages = {644-647}, pmid = {22491760}, issn = {1744-957X}, mesh = {Animals ; Bayes Theorem ; Canada ; Carnivory/*physiology ; *Climate Change ; Competitive Behavior/*physiology ; Coyotes/classification/genetics/*physiology ; Ecosystem ; Genetics, Population/methods ; Geography ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Population Dynamics ; United States ; }, abstract = {Recurrent cycles of climatic change during the Quaternary period have dramatically affected the population genetic structure of many species. We reconstruct the recent demographic history of the coyote (Canis latrans) through the use of Bayesian techniques to examine the effects of Late Quaternary climatic perturbations on the genetic structure of a highly mobile generalist species. Our analysis reveals a lack of phylogeographic structure throughout the range but past population size changes correlated with climatic changes. We conclude that even generalist carnivorous species are very susceptible to environmental changes associated with climatic perturbations. This effect may be enhanced in coyotes by interspecific competition with larger carnivores.}, }
@article {pmid22487608, year = {2012}, author = {Quicke, DL and Smith, MA and Janzen, DH and Hallwachs, W and Fernandez-Triana, J and Laurenne, NM and Zaldívar-Riverón, A and Shaw, MR and Broad, GR and Klopfstein, S and Shaw, SR and Hrcek, J and Hebert, PD and Miller, SE and Rodriguez, JJ and Whitfield, JB and Sharkey, MJ and Sharanowski, BJ and Jussila, R and Gauld, ID and Chesters, D and Vogler, AP}, title = {Utility of the DNA barcoding gene fragment for parasitic wasp phylogeny (Hymenoptera: Ichneumonoidea): data release and new measure of taxonomic congruence.}, journal = {Molecular ecology resources}, volume = {12}, number = {4}, pages = {676-685}, doi = {10.1111/j.1755-0998.2012.03143.x}, pmid = {22487608}, issn = {1755-0998}, mesh = {Animals ; *DNA Barcoding, Taxonomic ; DNA Primers ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Mitochondria ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Wasps/*classification/*genetics ; }, abstract = {The enormous cytochrome oxidase subunit I (COI) sequence database being assembled from the various DNA barcoding projects as well as from independent phylogenetic studies constitutes an almost unprecedented amount of data for molecular systematics, in addition to its role in species identification and discovery. As part of a study of the potential of this gene fragment to improve the accuracy of phylogenetic reconstructions, and in particular, exploring the effects of dense taxon sampling, we have assembled a data set for the hyperdiverse, cosmopolitan parasitic wasp superfamily Ichneumonoidea, including the release of 1793 unpublished sequences. Of approximately 84 currently recognized Ichneumonoidea subfamilies, 2500 genera and 41,000 described species, barcoding 5'-COI data were assembled for 4168 putative species-level terminals (many undescribed), representing 671 genera and all but ten of the currently recognized subfamilies. After the removal of identical and near-identical sequences, the 4174 initial sequences were reduced to 3278. We show that when subjected to phylogenetic analysis using both maximum likelihood and parsimony, there is a broad correlation between taxonomic congruence and number of included sequences. We additionally present a new measure of taxonomic congruence based upon the Simpson diversity index, the Simpson dominance index, which gives greater weight to morphologically recognized taxonomic groups (subfamilies) recovered with most representatives in one or a few contiguous groups or subclusters.}, }
@article {pmid22486892, year = {2012}, author = {Lin, L and Pan, G and Li, T and Dang, X and Deng, Y and Ma, C and Chen, J and Luo, J and Zhou, Z}, title = {The protein import pore Tom40 in the microsporidian Nosema bombycis.}, journal = {The Journal of eukaryotic microbiology}, volume = {59}, number = {3}, pages = {251-257}, doi = {10.1111/j.1550-7408.2012.00618.x}, pmid = {22486892}, issn = {1550-7408}, mesh = {Computational Biology ; Fungal Proteins/genetics/*metabolism ; Microsporidia/classification/metabolism ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/genetics/*metabolism ; Mitochondrial Membranes/metabolism ; Nosema/classification/*metabolism ; Phylogeny ; Saccharomyces cerevisiae/genetics/metabolism ; }, abstract = {Microsporidia, an unusual group of unicellular parasites related to fungi, possess a highly reduced mitochondrion known as the mitosome. Since mitosomes lack an organellar genome, their proteins must be translated in the cytosol before being imported into the mitosome via translocases. We have identified a Tom40 gene (NbTom40), the main component of the translocase of the outer mitochondrial membrane, in the genome of the microsporidian Nosema bombycis. NbTom40 is reduced in size, but it is predicted to form a β-barrel structure composed of 19 β-strands. Phylogenetic analysis confirms that NbTom40 forms a clade with Tom40 sequences from other species, distinct from a related clade of voltage-dependent anion channels (VDACs). The NbTom40 contains a β-signal motif that the polar residue is substituted by glycine. Furthermore, we show that expression of NbTom40, as a GFP fusion protein within yeast cells, directs GFP to mitochondria of yeast. These findings suggest that NbTom40 may serve as an import channel of the microsporidian mitosome and facilitate protein translocation into this organelle.}, }
@article {pmid22484699, year = {2012}, author = {Cuenca, A and Petersen, G and Seberg, O and Jahren, AH}, title = {Genes and processed paralogs co-exist in plant mitochondria.}, journal = {Journal of molecular evolution}, volume = {74}, number = {3-4}, pages = {158-169}, pmid = {22484699}, issn = {1432-1432}, mesh = {Alismatales/genetics ; Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal ; *Genes, Mitochondrial ; *Genes, Plant ; Genome, Plant ; Mitochondria/genetics ; Phylogeny ; *RNA Editing ; }, abstract = {RNA-mediated gene duplication has been proposed to create processed paralogs in the plant mitochondrial genome. A processed paralog may retain signatures left by the maturation process of its RNA precursor, such as intron removal and no need of RNA editing. Whereas it is well documented that an RNA intermediary is involved in the transfer of mitochondrial genes to the nucleus, no direct evidence exists for insertion of processed paralogs in the mitochondria (i.e., processed and un-processed genes have never been found simultaneously in the mitochondrial genome). In this study, we sequenced a region of the mitochondrial gene nad1, and identified a number of taxa were two different copies of the region co-occur in the mitochondria. The two nad1 paralogs differed in their (a) presence or absence of a group II intron, and (b) number of edited sites. Thus, this work provides the first evidence of co-existence of processed paralogs and their precursors within the plant mitochondrial genome. In addition, mapping the presence/absence of the paralogs provides indirect evidence of RNA-mediated gene duplication as an essential process shaping the mitochondrial genome in plants.}, }
@article {pmid22484221, year = {2012}, author = {Hederstedt, L}, title = {Heme A biosynthesis.}, journal = {Biochimica et biophysica acta}, volume = {1817}, number = {6}, pages = {920-927}, doi = {10.1016/j.bbabio.2012.03.025}, pmid = {22484221}, issn = {0006-3002}, mesh = {Animals ; Bacteria/metabolism ; Bacterial Proteins/genetics/metabolism/physiology ; Chlorophyll/biosynthesis ; Electron Transport ; Evolution, Molecular ; Ferrochelatase/genetics/metabolism/*physiology ; Heme/*analogs &amp; derivatives/biosynthesis/chemistry/physiology ; Humans ; Mitochondria/enzymology/metabolism ; Mutation, Missense ; Protein Conformation ; }, abstract = {Respiration in plants, most animals and many aerobic microbes is dependent on heme A. This is a highly specialized type of heme found as prosthetic group in cytochrome a-containing respiratory oxidases. Heme A differs structurally from heme B (protoheme IX) by the presence of a hydroxyethylfarnesyl group instead of a vinyl side group at the C2 position and a formyl group instead of a methyl side group at position C8 of the porphyrin macrocycle. Heme A synthase catalyzes the formation of the formyl side group and is a poorly understood heme-containing membrane bound atypical monooxygenase. This review presents our current understanding of heme A synthesis at the molecular level in mitochondria and aerobic bacteria. This article is part of a Special Issue entitled: Biogenesis/Assembly of Respiratory Enzyme Complexes.}, }
@article {pmid22479690, year = {2011}, author = {Lloyd, AH and Timmis, JN}, title = {Endosybiotic evolution in action: Real-time observations of chloroplast to nucleus gene transfer.}, journal = {Mobile genetic elements}, volume = {1}, number = {3}, pages = {216-220}, pmid = {22479690}, issn = {2159-2543}, abstract = {The origin of new genes has long been considered a fundamental question in evolutionary biology. In eukaryotes, a major pathway for the 'birth' of new nuclear genes has been transfer of genes from the cytoplasmic organelles (mitochondria and plastids) to the nucleus. While the vast majority of gene transfer occurred shortly after endosymbiosis, the process continues today and is still driving the evolution of nuclear genomes. In tobacco (Nicotiana tabacum) a number of studies have indicated that DNA can transfer from the chloroplast to the nucleus at relatively high frequency. Less has been known, however, about how a newly transferred organelle gene can become activated in this new genetic environment. In a recent report we observed, in real-time, the activation of a plastid reporter gene newly transferred to the nucleus. A key observation from this study was that non-homologous repair is an important generator of novel sequence combinations which, in rare instances, can result in the nuclear activation of plastid genes. In addition, the activation of relocated genes can be aided by the fortuitous presence of plastid sequences able to promote nuclear expression.}, }
@article {pmid22471645, year = {2012}, author = {Ding, Y and Leng, J}, title = {Is mitochondrial tRNA Leu(UUR) 3291T&gt;C mutation pathogenic?.}, journal = {Mitochondrial DNA}, volume = {23}, number = {4}, pages = {323-326}, doi = {10.3109/19401736.2012.674119}, pmid = {22471645}, issn = {1940-1744}, mesh = {Aged ; Asian People/genetics ; Base Sequence ; DNA, Mitochondrial/*genetics ; Family ; Female ; *Genetic Predisposition to Disease ; Humans ; Male ; Mitochondria/*genetics ; Mitochondrial Diseases/*genetics/pathology ; Mitochondrial Myopathies/genetics ; Molecular Sequence Data ; *Mutation ; Phylogeny ; RNA, Transfer, Leu/chemistry/*genetics/metabolism ; Sequence Alignment ; Thermodynamics ; }, abstract = {According to a recent report by Sunami et al., a maternally inherited Japanese family with variable phenotypes including mitochondrial myopathy, recurrent headache, and myoclonus and epilepsy had been described to be associated with mitochondrial tRNA(Leu(UUR)) 3291T>C mutation. In order to verify this association, we reanalyzed the clinical and molecular datasets obtained from Sunami's work; in addition, a phylogenetic approach was employed to evaluate the conservation index of this mutation among different species. We further utilized RNA Fold Web Server to predict the minimum free energy (MFE) of tRNA(Leu(UUR)) gene with and without this mutation. Most strikingly, a low level of conservation was found regarding 3291T>C mutation and a slight change in MFE had been observed between the wild type and the mutant. Our negative results gave no support for an active role for this mutation on the clinical expression of mitochondrial disorders.}, }
@article {pmid22470557, year = {2012}, author = {Baruffini, E and Serafini, F and Ferrero, I and Lodi, T}, title = {Overexpression of DNA polymerase zeta reduces the mitochondrial mutability caused by pathological mutations in DNA polymerase gamma in yeast.}, journal = {PloS one}, volume = {7}, number = {3}, pages = {e34322}, pmid = {22470557}, issn = {1932-6203}, support = {GGP07019/TI_/Telethon/Italy ; }, mesh = {DNA Polymerase I/genetics/*metabolism ; DNA Polymerase gamma ; DNA, Mitochondrial/metabolism ; DNA-Directed DNA Polymerase/*genetics/metabolism ; *Gene Expression ; Mitochondria/*enzymology ; *Mutation ; *Saccharomyces cerevisiae/enzymology/genetics ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; }, abstract = {In yeast, DNA polymerase zeta (Rev3 and Rev7) and Rev1, involved in the error-prone translesion synthesis during replication of nuclear DNA, localize also in mitochondria. We show that overexpression of Rev3 reduced the mtDNA extended mutability caused by a subclass of pathological mutations in Mip1, the yeast mitochondrial DNA polymerase orthologous to human Pol gamma. This beneficial effect was synergistic with the effect achieved by increasing the dNTPs pools. Since overexpression of Rev3 is detrimental for nuclear DNA mutability, we constructed a mutant Rev3 isoform unable to migrate into the nucleus: its overexpression reduced mtDNA mutability without increasing the nuclear one.}, }
@article {pmid22461064, year = {2012}, author = {Venkateshappa, C and Harish, G and Mahadevan, A and Srinivas Bharath, MM and Shankar, SK}, title = {Elevated oxidative stress and decreased antioxidant function in the human hippocampus and frontal cortex with increasing age: implications for neurodegeneration in Alzheimer's disease.}, journal = {Neurochemical research}, volume = {37}, number = {8}, pages = {1601-1614}, pmid = {22461064}, issn = {1573-6903}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Aging/physiology ; Alzheimer Disease/*physiopathology ; Antioxidants/*metabolism ; Cerebellum/metabolism ; Child ; Child, Preschool ; Electron Transport Complex I/metabolism ; Female ; Frontal Lobe/*metabolism ; Glial Fibrillary Acidic Protein/metabolism ; Glutathione/metabolism ; Glutathione Transferase ; Hippocampus/*metabolism ; Humans ; Infant ; Male ; Middle Aged ; Mitochondria/metabolism ; Neurodegenerative Diseases/metabolism ; *Oxidative Stress ; }, abstract = {Oxidative stress and mitochondrial damage are implicated in the evolution of neurodegenerative diseases. Increased oxidative damage in specific brain regions during aging might render the brain susceptible to degeneration. Previously, we demonstrated increased oxidative damage and lowered antioxidant function in substantia nigra during aging making it vulnerable to degeneration associated with Parkinson's disease. To understand whether aging contributes to the vulnerability of brain regions in Alzheimer's disease, we assessed the oxidant and antioxidant markers, glutathione (GSH) metabolic enzymes, glial fibrillary acidic protein (GFAP) expression and mitochondrial complex I (CI) activity in hippocampus (HC) and frontal cortex (FC) compared with cerebellum (CB) in human brains with increasing age (0.01-80 years). We observed significant increase in protein oxidation (HC: p = 0.01; FC: p = 0.0002) and protein nitration (HC: p = 0.001; FC: p = 0.02) and increased GFAP expression (HC: p = 0.03; FC: p = 0.001) with a decreasing trend in CI activity in HC and FC compared to CB with increasing age. These changes were associated with a decrease in antioxidant enzyme activities, such as superoxide dismutase (HC: p = 0.005), catalase (HC: p = 0.02), thioredoxin reductase (FC: p = 0.04), GSH reductase (GR) (HC: p = 0.005), glutathione-s-transferase (HC: p = 0.0001; FC: p = 0.03) and GSH (HC: p = 0.01) with age. However, these parameters were relatively unaltered in CB. We suggest that the regions HC and FC are subjected to widespread oxidative stress, loss of antioxidant function and enhanced GFAP expression during aging which might make them more susceptible to deranged physiology and selective neuronal degeneration.}, }
@article {pmid22457064, year = {2012}, author = {Atkinson, GC and Kuzmenko, A and Kamenski, P and Vysokikh, MY and Lakunina, V and Tankov, S and Smirnova, E and Soosaar, A and Tenson, T and Hauryliuk, V}, title = {Evolutionary and genetic analyses of mitochondrial translation initiation factors identify the missing mitochondrial IF3 in S. cerevisiae.}, journal = {Nucleic acids research}, volume = {40}, number = {13}, pages = {6122-6134}, pmid = {22457064}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Conserved Sequence ; Eukaryotic Initiation Factor-2/chemistry/classification/genetics ; Eukaryotic Initiation Factor-3/chemistry/classification/*genetics ; Genetic Complementation Test ; Mitochondrial Proteins/chemistry/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/chemistry/classification/*genetics ; Sequence Alignment ; }, abstract = {Mitochondrial translation is essentially bacteria-like, reflecting the bacterial endosymbiotic ancestry of the eukaryotic organelle. However, unlike the translation system of its bacterial ancestors, mitochondrial translation is limited to just a few mRNAs, mainly coding for components of the respiratory complex. The classical bacterial initiation factors (IFs) IF1, IF2 and IF3 are universal in bacteria, but only IF2 is universal in mitochondria (mIF2). We analyse the distribution of mitochondrial translation initiation factors and their sequence features, given two well-propagated claims: first, a sequence insertion in mitochondrial IF2 (mIF2) compensates for the universal lack of IF1 in mitochondria, and secondly, no homologue of mitochondrial IF3 (mIF3) is identifiable in Saccharomyces cerevisiae. Our comparative sequence analysis shows that, in fact, the mIF2 insertion is highly variable and restricted in length and primary sequence conservation to vertebrates, while phylogenetic and in vivo complementation analyses reveal that an uncharacterized S. cerevisiae mitochondrial protein currently named Aim23p is a bona fide evolutionary and functional orthologue of mIF3. Our results highlight the lineage-specific nature of mitochondrial translation and emphasise that comparative analyses among diverse taxa are essential for understanding whether generalizations from model organisms can be made across eukaryotes.}, }
@article {pmid22450032, year = {2013}, author = {Herrmann, JM and Woellhaf, MW and Bonnefoy, N}, title = {Control of protein synthesis in yeast mitochondria: the concept of translational activators.}, journal = {Biochimica et biophysica acta}, volume = {1833}, number = {2}, pages = {286-294}, doi = {10.1016/j.bbamcr.2012.03.007}, pmid = {22450032}, issn = {0006-3002}, mesh = {Fungal Proteins/*biosynthesis/genetics ; Mitochondria/*metabolism ; Mitochondrial Proteins/*biosynthesis/genetics ; *Protein Biosynthesis ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/biosynthesis/genetics ; Yeasts/genetics/*metabolism ; }, abstract = {Mitochondria contain their own genome which codes for a small number of proteins. Most mitochondrial translation products are part of the membrane-embedded reaction centers of the respiratory chain complexes. In the yeast Saccharomyces cerevisiae, the expression of these proteins is regulated by translational activators that bind mitochondrial mRNAs, in most cases to their 5'-untranslated regions, and each mitochondrial mRNA appears to have its own translational activator(s). Recent studies showed that these translational activators can be part of feedback control loops which only permit translation if the downstream assembly of nascent translation products can occur. In several cases, the accumulation of a non-assembled protein prevents further synthesis of this protein but not translation in general. These control loops prevent the synthesis of potentially harmful assembly intermediates of the reaction centers of mitochondrial enzymes. Since such regulatory feedback loops only work if translation occurs in the compartment in which the complexes of the respiratory chain are assembled, these control mechanisms require the presence of a translation machinery in mitochondria. This might explain why eukaryotic cells maintained DNA in mitochondria during the last two billion years of evolution. This review gives an overview of the mitochondrial translation system and summarizes the current knowledge on translational activators and their role in the regulation of mitochondrial protein synthesis. This article is part of a Special Issue entitled: Protein import and quality control in mitochondria and plastids.}, }
@article {pmid22444141, year = {2012}, author = {Lynn, DH and Doerder, FP}, title = {The life and times of Tetrahymena.}, journal = {Methods in cell biology}, volume = {109}, number = {}, pages = {9-27}, doi = {10.1016/B978-0-12-385967-9.00002-5}, pmid = {22444141}, issn = {0091-679X}, mesh = {Cell Nucleus/genetics/metabolism ; Cyclooxygenase 1/genetics/metabolism ; Evolution, Molecular ; *Genes, Mitochondrial ; *Genes, Protozoan ; Genes, rRNA ; Genetic Variation ; Mitochondria/genetics/metabolism ; Phylogeny ; Reproduction ; Ribosome Subunits, Small, Eukaryotic/genetics/metabolism ; Tetrahymena/classification/*genetics/growth &amp; development ; }, abstract = {The genus Tetrahymena is defined on the basis of a four-part oral structure composed of an undulating membrane and three membranelles. It is a monophyletic genus with 41 named species and numerous unnamed species, many of which are morphologically indistinguishable. Nuclear small subunit rRNA and mitochondrial cytochrome c oxidase subunit 1 sequences indicate two major clades, a "borealis" clade of less closely related species and an "australis" clade of more closely related species that correlate to differences in mating-type determination and frequency of amicronucleates. Members of both clades show convergence for histophagy (primarily facultative), macrostome transformation, and (rare) cyst formation. Life cycle parameters of species are presented and problematic species discussed.}, }
@article {pmid22440923, year = {2011}, author = {Wang, LF and Walker, PJ and Poon, LL}, title = {Mass extinctions, biodiversity and mitochondrial function: are bats 'special' as reservoirs for emerging viruses?.}, journal = {Current opinion in virology}, volume = {1}, number = {6}, pages = {649-657}, pmid = {22440923}, issn = {1879-6265}, mesh = {Animals ; Biological Evolution ; Chiroptera/genetics/*virology ; Communicable Diseases, Emerging/genetics/transmission/*virology ; DNA, Mitochondrial/genetics ; Disease Reservoirs/*veterinary/virology ; *Extinction, Biological ; Genetic Variation ; Humans ; Mitochondria/*physiology ; Viruses/*genetics ; Zoonoses/transmission/*virology ; }, abstract = {For the past 10-15 years, bats have attracted growing attention as reservoirs of emerging zoonotic viruses. This has been due to a combination of factors including the emergence of highly virulent zoonotic pathogens, such as Hendra, Nipah, SARS and Ebola viruses, and the high rate of detection of a large number of previously unknown viral sequences in bat specimens. As bats have ancient evolutionary origins and are the only flying mammals, it has been hypothesized that some of their unique biological features may have made them especially suitable hosts for different viruses. So the question 'Are bats different, special or exceptional?' has become a focal point in the field of virology, bat biology and virus-host co-evolution. In this brief review, we examine the topic in a relatively unconventional way, that is, our discussion will be based on both scientific discoveries and theoretical predictions. This approach was chosen partially because the data in this field are so limited that it is impossible to conduct a useful review based on published results only and also because we believe it is important to provoke original, speculative or even controversial ideas or theories in this important field of research.}, }
@article {pmid22439925, year = {2012}, author = {Ward, PS and Thompson, CB}, title = {Metabolic reprogramming: a cancer hallmark even warburg did not anticipate.}, journal = {Cancer cell}, volume = {21}, number = {3}, pages = {297-308}, pmid = {22439925}, issn = {1878-3686}, support = {P01 CA104838/CA/NCI NIH HHS/United States ; P01 CA104838-05/CA/NCI NIH HHS/United States ; R01 CA105463/CA/NCI NIH HHS/United States ; R01 CA105463-09/CA/NCI NIH HHS/United States ; }, mesh = {Alternative Splicing ; Biomarkers, Tumor/*metabolism ; Cell Differentiation ; Cell Proliferation ; Epigenesis, Genetic ; Evolution, Molecular ; Humans ; Isoenzymes/metabolism/physiology ; Mitochondria/physiology ; Models, Biological ; Neoplasms/genetics/*metabolism/pathology ; Proto-Oncogene Proteins c-myc/metabolism ; Signal Transduction ; }, abstract = {Cancer metabolism has long been equated with aerobic glycolysis, seen by early biochemists as primitive and inefficient. Despite these early beliefs, the metabolic signatures of cancer cells are not passive responses to damaged mitochondria but result from oncogene-directed metabolic reprogramming required to support anabolic growth. Recent evidence suggests that metabolites themselves can be oncogenic by altering cell signaling and blocking cellular differentiation. No longer can cancer-associated alterations in metabolism be viewed as an indirect response to cell proliferation and survival signals. We contend that altered metabolism has attained the status of a core hallmark of cancer.}, }
@article {pmid22439812, year = {2012}, author = {Ladner, JT and Palumbi, SR}, title = {Extensive sympatry, cryptic diversity and introgression throughout the geographic distribution of two coral species complexes.}, journal = {Molecular ecology}, volume = {21}, number = {9}, pages = {2224-2238}, doi = {10.1111/j.1365-294X.2012.05528.x}, pmid = {22439812}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/*classification/*genetics ; DNA, Mitochondrial/genetics ; *Genetic Speciation ; *Genetic Variation ; Geography ; Hybridization, Genetic ; Mitochondria/genetics ; Multilocus Sequence Typing ; Phylogeny ; Sequence Analysis, DNA ; *Sympatry ; }, abstract = {The identification of species is one of the most basic, and yet critically important, issues in biology with far-reaching potential implications for fields such as biodiversity conservation, population ecology and epidemiology. Morphology has long been the primary tool biologists have used to categorize life. However, we now know that a significant portion of natural diversity is morphologically hidden, and therefore, we must integrate nonmorphological tools into the description of biodiversity. Here, we demonstrate the utility of multilocus population genetic data for identifying and characterizing cryptic species complexes, even when species share large amounts of genetic variability. Specifically, we have used DNA sequence data from 12 genomic regions to characterize two widespread species complexes in the coral genus Acropora: A. cytherea and A. hyacinthus. These two morphospecies have each been sampled from 5 to 7 locations throughout their Indo-Pacific distributions, and with the use of structure and hierarchical clustering, we demonstrate the presence of at least six widespread cryptic species within these two morphospecies complexes. After identifying cryptic lineages, we then utilize the genetic data to examine the history of introgressive hybridization within and between these morphospecies complexes. Our data indicate that these two complexes form a global syngameon with consistent patterns of introgression between species across large geographic distributions.}, }
@article {pmid22438588, year = {2012}, author = {Jiang, H and Guo, X and Xu, L and Gu, Z}, title = {Rewiring of posttranscriptional RNA regulons: Puf4p in fungi as an example.}, journal = {Molecular biology and evolution}, volume = {29}, number = {9}, pages = {2169-2176}, pmid = {22438588}, issn = {1537-1719}, support = {R01 AI085286/AI/NIAID NIH HHS/United States ; 1R01AI085286/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Cluster Analysis ; Fungi/*genetics ; *Gene Expression Regulation, Fungal ; *Gene Regulatory Networks ; Genes, Mitochondrial ; Molecular Sequence Data ; Phylogeny ; *RNA Processing, Post-Transcriptional ; *RNA, Fungal ; RNA-Binding Proteins/chemistry/genetics ; Sequence Alignment ; }, abstract = {It has been increasingly clear that changes in gene regulation play important roles in physiological and phenotypic evolution. Rewiring gene-regulatory networks, i.e., alteration of the gene-regulation system for different biological functions, has been demonstrated in various species. Posttranscriptional regulons have prominent roles in coordinating gene expression in a variety of eukaryotes. In this study, using Puf4p in fungi as an example, we demonstrate that posttranscriptional regulatory networks can also be rewired during evolution. Although Puf4p is highly conserved in fungi, targets of the posttranscriptional regulon are functionally diverse among known fungal species. In the Saccharomycotina subdivision, target genes of Puf4p mostly conduct function in the nucleolus; however, in the Pezizomycotina subdivision, they are enriched in the mitochondria. Furthermore, we demonstrate different regulation efficiencies of mitochondrial function by PUF proteins in different fungal clades. Our results indicate that rewiring of posttranscription regulatory networks may be an important way of generating genetic novelties in gene regulation during evolution.}, }
@article {pmid22437208, year = {2012}, author = {Wang, HW and Li, YC and Sun, F and Zhao, M and Mitra, B and Chaudhuri, TK and Regmi, P and Wu, SF and Kong, QP and Zhang, YP}, title = {Revisiting the role of the Himalayas in peopling Nepal: insights from mitochondrial genomes.}, journal = {Journal of human genetics}, volume = {57}, number = {4}, pages = {228-234}, doi = {10.1038/jhg.2012.8}, pmid = {22437208}, issn = {1435-232X}, mesh = {Asian People/genetics ; Chromosomes, Human, Y/genetics ; DNA, Mitochondrial/classification/*genetics ; Gene Flow ; *Genetics, Population ; *Genome, Human ; *Genome, Mitochondrial ; Haplotypes ; Humans ; India ; Mitochondria/*genetics ; Nepal ; Phylogeny ; Principal Component Analysis ; Sequence Analysis, DNA ; Tibet ; Time Factors ; }, abstract = {Himalayas was believed to be a formidably geographical barrier between South and East Asia. The observed high frequency of the East Eurasian paternal lineages in Nepal led some researchers to suggest that these lineages were introduced into Nepal from Tibet directly; however, it is also possible that the East Eurasian genetic components might trace their origins to northeast India where abundant East Eurasian maternal lineages have been detected. To trace the origin of the Nepalese maternal genetic components, especially those of East Eurasian ancestry, and then to better understand the role of the Himalayas in peopling Nepal, we have studied the matenal genetic composition extensively, especially the East Eurasian lineages, in Nepalese and its surrounding populations. Our results revealed the closer affinity between the Nepalese and the Tibetans, specifically, the Nepalese lineages of the East Eurasian ancestry generally are phylogenetically closer with the ones from Tibet, albeit a few mitochondrial DNA haplotypes, likely resulted from recent gene flow, were shared between the Nepalese and northeast Indians. It seems that Tibet was most likely to be the homeland for most of the East Eurasian in the Nepalese. Taking into account the previous observation on Y chromosome, now it is convincing that bearer of the East Eurasian genetic components had entered Nepal across the Himalayas around 6 kilo years ago (kya), a scenario in good agreement with the previous results from linguistics and archeology.}, }
@article {pmid22430869, year = {2012}, author = {Olson, KR}, title = {Mitochondrial adaptations to utilize hydrogen sulfide for energy and signaling.}, journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology}, volume = {182}, number = {7}, pages = {881-897}, pmid = {22430869}, issn = {1432-136X}, mesh = {Adaptation, Biological/*physiology ; Adenosine Triphosphate/biosynthesis ; Energy Metabolism/*physiology ; Hydrogen Sulfide/*metabolism/toxicity ; Mitochondria/metabolism/*physiology ; Molecular Structure ; *Organelle Biogenesis ; Oxidation-Reduction ; Oxygen/*metabolism ; Signal Transduction/*physiology ; }, abstract = {Sulfur is a versatile molecule with oxidation states ranging from -2 to +6. From the beginning, sulfur has been inexorably entwined with the evolution of organisms. Reduced sulfur, prevalent in the prebiotic Earth and supplied from interstellar sources, was an integral component of early life as it could provide energy through oxidization, even in a weakly oxidizing environment, and it spontaneously reacted with iron to form iron-sulfur clusters that became the earliest biological catalysts and structural components of cells. The ability to cycle sulfur between reduced and oxidized states may have been key in the great endosymbiotic event that incorporated a sulfide-oxidizing α-protobacteria into a host sulfide-reducing Archea, resulting in the eukaryotic cell. As eukaryotes slowly adapted from a sulfidic and anoxic (euxinic) world to one that was highly oxidizing, numerous mechanisms developed to deal with increasing oxidants; namely, oxygen, and decreasing sulfide. Because there is rarely any reduced sulfur in the present-day environment, sulfur was historically ignored by biologists, except for an occasional report of sulfide toxicity. Twenty-five years ago, it became evident that the organisms in sulfide-rich environments could synthesize ATP from sulfide, 10 years later came the realization that animals might use sulfide as a signaling molecule, and only within the last 4 years did it become apparent that even mammals could derive energy from sulfide generated in the gastrointestinal tract. It has also become evident that, even in the present-day oxic environment, cells can exploit the redox chemistry of sulfide, most notably as a physiological transducer of oxygen availability. This review will examine how the legacy of sulfide metabolism has shaped natural selection and how some of these ancient biochemical pathways are still employed by modern-day eukaryotes.}, }
@article {pmid22429457, year = {2012}, author = {Boyd, BM and Reed, DL}, title = {Taxonomy of lice and their endosymbiotic bacteria in the post-genomic era.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {18}, number = {4}, pages = {324-331}, doi = {10.1111/j.1469-0691.2012.03782.x}, pmid = {22429457}, issn = {1469-0691}, mesh = {Animals ; Ecology ; Evolution, Molecular ; Gammaproteobacteria/*classification/genetics/growth &amp; development ; Genes, Mitochondrial ; Genetic Markers ; Genetics, Population ; *Genome, Bacterial ; *Genome, Insect ; Mitochondria/genetics ; Phthiraptera/*classification/genetics/*microbiology ; Phylogeny ; Species Specificity ; *Symbiosis ; }, abstract = {Recent studies of molecular and genomic data from the parasitic lice of birds and mammals, as well as their mutualistic endosymbiotic bacteria, are changing the phylogenetic relationships and taxonomy of these organisms. Phylogenetic studies of lice suggest that vertebrate parasitism arose multiple times from free-living book and bark lice. Molecular clocks show that the major families of lice arose in the late Mesozoic and radiated in the early Cenozoic, following the radiation of mammals and birds. The recent release of the human louse genome has provided new opportunities for research. The genome is being used to find new genetic markers for phylogenetics and population genetics, to understand the complex evolutionary relationships of mitochondrial genes, and to study genome evolution. Genomes are informing us not only about lice, but also about their obligate endosymbiotic bacteria. In contrast to lice and their hosts, lice and their endosymbionts do not share common evolutionary histories, suggesting that endosymbionts are either replaced over time or that there are multiple independent origins of symbiosis in lice. Molecular phylogenetics and whole genome sequencing have recently provided the first insights into the phylogenetic placement and metabolic characteristics of these distantly related bacteria. Comparative genomics between distantly related louse symbionts can provide insights into conserved metabolic functions and can help to explain how distantly related species are fulfilling their role as mutualistic symbionts. In lice and their endosymbionts, molecular data and genome sequencing are driving our understanding of evolutionary relationships and classification, and will for the foreseeable future.}, }
@article {pmid22429403, year = {2012}, author = {Zhang, LT and Zhang, ZS and Gao, HY and Meng, XL and Yang, C and Liu, JG and Meng, QW}, title = {The mitochondrial alternative oxidase pathway protects the photosynthetic apparatus against photodamage in Rumex K-1 leaves.}, journal = {BMC plant biology}, volume = {12}, number = {}, pages = {40}, pmid = {22429403}, issn = {1471-2229}, mesh = {Chlorophyll/metabolism ; Chloroplasts/drug effects/metabolism ; Electron Transport ; Enzyme Activation ; Hydrogen Peroxide/metabolism ; Hydrogen-Ion Concentration ; Light ; Malate Dehydrogenase (NADP+)/metabolism ; Mitochondria/*enzymology ; Mitochondrial Proteins/antagonists &amp; inhibitors/*metabolism ; NADP/metabolism ; Oxidation-Reduction ; Oxidoreductases/antagonists &amp; inhibitors/*metabolism ; Oxygen/metabolism ; *Photosynthesis ; Photosystem I Protein Complex/metabolism ; Photosystem II Protein Complex/metabolism ; Plant Leaves/drug effects/enzymology/*radiation effects ; Plant Proteins/antagonists &amp; inhibitors/*metabolism ; Rumex/drug effects/*enzymology/radiation effects ; Salicylamides/pharmacology ; Sodium Bicarbonate/pharmacology ; }, abstract = {BACKGROUND: It is known that excess reducing equivalents in the form of NADPH in chloroplasts can be transported via shuttle machineries, such as the malate-oxaloacetate (OAA) shuttle, into the mitochondria, where they are efficiently oxidised by the mitochondrial alternative oxidase (AOX) respiratory pathway. Therefore, it has been speculated that the AOX pathway may protect plants from photoinhibition, but the mechanism by which this protection occurs remains to be elucidated.<br><br>RESULTS: The observation that the malate-OAA shuttle activity and the AOX pathway capacity increased markedly after intense light treatment in Rumex K-1 leaves indicates that excess NADPH was transported from the chloroplasts and oxidised by the AOX pathway. The inhibition of the AOX pathway by salicylhydroxamic acid (SHAM) caused the over-reduction of the photosystem I (PSI) acceptor side, as indicated by the increases in the extent of reduction of P700+. Furthermore, the photosynthetic linear electron flow was restricted, which was indicated by the decreases in the PSII electron transport rate (ETR) and the photosynthetic O&#x2082; evolution rate. The restriction of the photosynthetic linear electron flow, which generates the thylakoid &#x394;pH, inevitably decreased the de-epoxidation of the xanthophyll cycle (&#x394;PRI). Therefore, the induction of non-photochemical quenching (NPQ) was suppressed when the AOX pathway was inhibited. The effect of the inhibition of the AOX pathway on NPQ induction was less at 20 mM NaHCO&#x2083; than at 1 mM NaHCO&#x2083;. The suppression of NPQ induction by the inhibition of the AOX pathway was also observed during the induction phase of photosynthesis. In addition, the inhibition of the AOX pathway increased the accumulation of hydrogen peroxide (H&#x2082;O&#x2082;), suggesting that the AOX pathway functions as an antioxidant mechanism.<br><br>CONCLUSIONS: The inhibition of the AOX pathway resulted in the rapid accumulation of NADPH in the chloroplasts, which caused the over-reduction of the PSI acceptor side. Furthermore, the restriction of the photosynthetic linear electron flow due to the inhibition of the AOX pathway limited the generation of the thylakoid &#x394;pH and suppressed the induction of NPQ. Therefore, the mitochondrial AOX pathway protected the photosynthetic apparatus against photodamage by alleviating the over-reduction of the PSI acceptor side and accelerating the induction of NPQ in Rumex K-1 leaves.}, }
@article {pmid22426856, year = {2012}, author = {Frelin, O and Agrimi, G and Laera, VL and Castegna, A and Richardson, LG and Mullen, RT and Lerma-Ortiz, C and Palmieri, F and Hanson, AD}, title = {Identification of mitochondrial thiamin diphosphate carriers from Arabidopsis and maize.}, journal = {Functional &amp; integrative genomics}, volume = {12}, number = {2}, pages = {317-326}, pmid = {22426856}, issn = {1438-7948}, mesh = {Acetolactate Synthase/metabolism ; Arabidopsis/*genetics ; Cell Line ; Genetic Complementation Test ; Mitochondria/enzymology/metabolism ; Mitochondrial Membrane Transport Proteins/biosynthesis/*genetics ; Phylogeny ; Plant Proteins/biosynthesis/*genetics ; Protein Transport ; Saccharomyces cerevisiae/genetics ; Thiamine Monophosphate/metabolism ; Thiamine Pyrophosphate/*metabolism ; Zea mays/*genetics ; }, abstract = {It is currently held that thiamin is made in chloroplasts and converted in the cytosol to the active cofactor thiamin diphosphate (ThDP), and that mitochondria and plastids import ThDP. The organellar transporters that mediate ThDP import in plants have not been identified. Comparative genomic analysis indicated that two members of the mitochondrial carrier family (MCF) in Arabidopsis (At5g48970 and At3g21390) and two in maize (GRMZM2G118515 and GRMZM2G124911) are related to the ThDP carriers of animals and Saccharomyces cerevisiae. Expression of each of these plant proteins in a S. cerevisiae ThDP carrier (TPC1) null mutant complemented the growth defect on fermentable carbon sources and restored the level of mitochondrial ThDP and the activity of the mitochondrial ThDP-dependent enzyme acetolactate synthase. The plant proteins were targeted to mitochondria as judged by dual import assays with purified pea mitochondria and chloroplasts, and by microscopic analysis of the subcellular localization of green fluorescent protein fusions in transiently transformed tobacco suspension cells. Both maize genes were shown to be expressed throughout the plant, which is consistent with the known ubiquity of mitochondrial ThDP-dependent enzymes. Collectively, these data establish that plants have mitochondrially located MCF carriers for ThDP, and indicate that these carriers are highly evolutionarily conserved. Our data provide a firm basis to propagate the functional annotation of mitochondrial ThDP carriers to other angiosperm genomes.}, }
@article {pmid22417115, year = {2012}, author = {Potter, S and Eldridge, MD and Taggart, DA and Cooper, SJ}, title = {Multiple biogeographical barriers identified across the monsoon tropics of northern Australia: phylogeographic analysis of the brachyotis group of rock-wallabies.}, journal = {Molecular ecology}, volume = {21}, number = {9}, pages = {2254-2269}, doi = {10.1111/j.1365-294X.2012.05523.x}, pmid = {22417115}, issn = {1365-294X}, mesh = {Animal Migration ; Animals ; Bayes Theorem ; *Biodiversity ; Biological Evolution ; DNA, Mitochondrial/*genetics ; *Ecosystem ; Genetic Loci ; Genetic Speciation ; Genetic Variation ; Geography ; Macropodidae/classification/*genetics/physiology ; Mitochondria/genetics ; Northern Territory ; Phylogeny ; Phylogeography/*methods ; Sequence Analysis, DNA ; Tropical Climate ; Western Australia ; }, abstract = {The monsoon tropics of northern Australia are a globally significant biodiversity hotspot, but its phylogeography is poorly known. A major challenge for this region is to understand the biogeographical processes that have shaped the distribution and diversity of taxa, without detailed knowledge of past climatic and environmental fluctuations. Although molecular data have great potential to address these questions, only a few species have been examined phylogeographically. Here, we use the widely distributed and abundant short-eared rock-wallaby (Petrogale brachyotis; n = 101), together with the sympatric monjon (P. burbidgei; n = 11) and nabarlek (P. concinna; n = 1), to assess historical evolutionary and biogeographical processes in northern Australia. We sequenced ∼1000 bp of mitochondrial DNA (control region, ND2) and ∼3000 bp of nDNA (BRCA1, ω-globin and two anonymous loci) to investigate phylogeographic structuring and delineate the time-scale of diversification within the region. Our results indicate multiple barriers between the Top End (Northern Territory) and Kimberley (Western Australia), which have caused divergence throughout the Plio-Pleistocene. Eight geographically discrete and genetically distinct lineages within the brachyotis group were identified, five of which are separated by major river valleys (Ord, Victoria, Daly), arid lowlands and discontinuous sandstone ranges. It is likely that these barriers have similarly influenced genetic structure in other monsoonal biota.}, }
@article {pmid22415515, year = {2012}, author = {Miller-Messmer, M and Kühn, K and Bichara, M and Le Ret, M and Imbault, P and Gualberto, JM}, title = {RecA-dependent DNA repair results in increased heteroplasmy of the Arabidopsis mitochondrial genome.}, journal = {Plant physiology}, volume = {159}, number = {1}, pages = {211-226}, pmid = {22415515}, issn = {1532-2548}, mesh = {Arabidopsis/drug effects/enzymology/*genetics ; Bleomycin/pharmacology ; Crossing Over, Genetic ; DNA Breaks ; DNA, Mitochondrial/genetics/metabolism ; DNA, Plant/genetics/metabolism ; Enzyme Activation ; Escherichia coli/genetics/metabolism ; Evolution, Molecular ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Genetic Complementation Test ; *Genome, Mitochondrial ; Mitochondria/drug effects/enzymology/*genetics ; Phenotype ; Polymorphism, Genetic ; Rec A Recombinases/genetics/*metabolism ; *Recombinational DNA Repair ; Seedlings/genetics/metabolism ; Stress, Physiological ; }, abstract = {Plant mitochondria have very active DNA recombination activities that are responsible for its plastic structures and that should be involved in the repair of double-strand breaks in the mitochondrial genome. Little is still known on plant mitochondrial DNA repair, but repair by recombination is believed to be a major determinant in the rapid evolution of plant mitochondrial genomes. In flowering plants, mitochondria possess at least two eubacteria-type RecA proteins that should be core components of the mitochondrial repair mechanisms. We have performed functional analyses of the two Arabidopsis (Arabidopsis thaliana) mitochondrial RecAs (RECA2 and RECA3) to assess their potential roles in recombination-dependent repair. Heterologous expression in Escherichia coli revealed that RECA2 and RECA3 have overlapping as well as specific activities that allow them to partially complement bacterial repair pathways. RECA2 and RECA3 have similar patterns of expression, and mutants of either display the same molecular phenotypes of increased recombination between intermediate-size repeats, thus suggesting that they act in the same recombination pathways. However, RECA2 is essential past the seedling stage and should have additional important functions. Treatment of plants with several DNA-damaging drugs further showed that RECA3 is required for different recombination-dependent repair pathways that significantly contribute to plant fitness under stress. Replication repair of double-strand breaks results in the accumulation of crossovers that increase the heteroplasmic state of the mitochondrial DNA. It was shown that these are transmitted to the plant progeny, enhancing the potential for mitochondrial genome evolution.}, }
@article {pmid22415349, year = {2012}, author = {Zeyland, J and Wolko, L and Lipiński, D and Woźniak, A and Nowak, A and Szalata, M and Bocianowski, J and Słomski, R}, title = {Tracking of wisent-bison-yak mitochondrial evolution.}, journal = {Journal of applied genetics}, volume = {53}, number = {3}, pages = {317-322}, pmid = {22415349}, issn = {2190-3883}, mesh = {Animals ; Bison/*genetics ; Cattle/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Mitochondria/*genetics ; Models, Genetic ; Phylogeny ; }, abstract = {One of the most informative sources which allow the drawing of far-reaching conclusions about the origins and phylogenetics of many species, including domestic animals and humans, is mitochondrial DNA (mtDNA). One of the important research targets should include the identification of similarities between wild and domestic species. The analysis involved the nucleotide sequences of mtDNA of wisent, auroch, bison, yak, bovine reference sequence (BRS) T3, T3a, T3b, T1, T1a, T1'2'3, T2, T3, T4, T5, Q, Q1, P, R, I1, and I2 bovine haplotypes. The non-coding D-loop regions were excluded from the evolutionary analysis and 15,419-bp coding sequences were used in the final dataset. Trees constructed on the basis of whole mitochondrial genomes or on total mtDNA coding sequences alignment were generally in agreement with previous studies on the Bovini tribe. American bison shows stronger maternal relationships to yak than to wisent. It seems that the isolation and divergence of wisent took place early, almost 2 to 1.6 million years ago. This appears to be compatible with the paleontological date, indicating Late Pleistocene speciation of Bison bonasus. The yak/bison mitochondrial transfer model is in agreement with our mutation analysis and phylogenetic tree. The bison/yak mutations were collected in the bison mitochondrial genome before the transfer. After the transfer, the parallel accumulation of unique mutations took place. According to our assessment, the transfer took place at about 700 ky. The characteristic feature of the wisent and bison evolution is the maintenance of mtDNA variability, despite the fact that both species underwent population bottlenecks. Our studies did not reveal any impact of these phenomena populations in the analyzed mitochondrial genomes.}, }
@article {pmid22411852, year = {2012}, author = {Nadimi, M and Beaudet, D and Forget, L and Hijri, M and Lang, BF}, title = {Group I intron-mediated trans-splicing in mitochondria of Gigaspora rosea and a robust phylogenetic affiliation of arbuscular mycorrhizal fungi with Mortierellales.}, journal = {Molecular biology and evolution}, volume = {29}, number = {9}, pages = {2199-2210}, doi = {10.1093/molbev/mss088}, pmid = {22411852}, issn = {1537-1719}, mesh = {Codon ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Exons ; Fungi/classification/genetics ; Gene Order ; *Genome, Mitochondrial ; Glomeromycota/classification/*genetics ; *Introns ; Nucleic Acid Conformation ; *Phylogeny ; Plasmids/genetics ; RNA, Ribosomal/chemistry/genetics ; *Trans-Splicing ; }, abstract = {Gigaspora rosea is a member of the arbuscular mycorrhizal fungi (AMF; Glomeromycota) and a distant relative of Glomus species that are beneficial to plant growth. To allow for a better understanding of Glomeromycota, we have sequenced the mitochondrial DNA of G. rosea. A comparison with Glomus mitochondrial genomes reveals that Glomeromycota undergo insertion and loss of mitochondrial plasmid-related sequences and exhibit considerable variation in introns. The gene order between the two species is almost completely reshuffled. Furthermore, Gigaspora has fragmented cox1 and rns genes, and an unorthodox initiator tRNA that is tailored to decoding frequent UUG initiation codons. For the fragmented cox1 gene, we provide evidence that its RNA is joined via group I-mediated trans-splicing, whereas rns RNA remains in pieces. According to our model, the two cox1 precursor RNA pieces are brought together by flanking cox1 exon sequences that form a group I intron structure, potentially in conjunction with the nad5 intron 3 sequence. Finally, we present analyses that address the controversial phylogenetic association of Glomeromycota within fungi. According to our results, Glomeromycota are not a separate group of paraphyletic zygomycetes but branch together with Mortierellales, potentially also Harpellales.}, }
@article {pmid22409430, year = {2012}, author = {Tian, HF and Feng, JM and Wen, JF}, title = {The evolution of cardiolipin biosynthesis and maturation pathways and its implications for the evolution of eukaryotes.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {32}, pmid = {22409430}, issn = {1471-2148}, mesh = {Base Sequence ; Bayes Theorem ; Biosynthetic Pathways/*physiology ; Cardiolipins/*biosynthesis/*metabolism ; Eukaryota/*enzymology/genetics/metabolism ; *Evolution, Molecular ; Likelihood Functions ; Membrane Proteins/metabolism/*physiology ; Models, Genetic ; Molecular Sequence Data ; Phospholipases A2, Calcium-Independent/genetics/metabolism ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Transferases (Other Substituted Phosphate Groups)/metabolism/*physiology ; }, abstract = {BACKGROUND: Cardiolipin (CL) is an important component in mitochondrial inner and bacterial membranes. Its appearance in these two biomembranes has been considered as evidence of the endosymbiotic origin of mitochondria. But CL was reported to be synthesized through two distinct enzymes--CLS_cap and CLS_pld in eukaryotes and bacteria. Therefore, how the CL biosynthesis pathway evolved is an interesting question.<br><br>RESULTS: Phylogenetic distribution investigation of CL synthase (CLS) showed: most bacteria have CLS_pld pathway, but in partial bacteria including proteobacteria and actinobacteria CLS_cap pathway has already appeared; in eukaryotes, Supergroup Opisthokonta and Archaeplastida, and Subgroup Stramenopiles, which all contain multicellular organisms, possess CLS_cap pathway, while Supergroup Amoebozoa and Excavata and Subgroup Alveolata, which all consist exclusively of unicellular eukaryotes, bear CLS_pld pathway; amitochondriate protists in any supergroups have neither. Phylogenetic analysis indicated the CLS_cap in eukaryotes have the closest relationship with those of alpha proteobacteria, while the CLS_pld in eukaryotes share a common ancestor but have no close correlation with those of any particular bacteria.<br><br>CONCLUSIONS: The first eukaryote common ancestor (FECA) inherited the CLS_pld from its bacterial ancestor (e. g. the bacterial partner according to any of the hypotheses about eukaryote evolution); later, when the FECA evolved into the last eukaryote common ancestor (LECA), the endosymbiotic mitochondria (alpha proteobacteria) brought in CLS_cap, and then in some LECA individuals the CLS_cap substituted the CLS_pld, and these LECAs would evolve into the protist lineages from which multicellular eukaryotes could arise, while in the other LECAs the CLS_pld was retained and the CLS_cap was lost, and these LECAs would evolve into the protist lineages possessing CLS_pld. Besides, our work indicated CL maturation pathway arose after the emergence of eukaryotes probably through mechanisms such as duplication of other genes, and gene duplication and loss occurred frequently at different lineage levels, increasing the pathway diversity probably to fit the complicated cellular process in various cells. Our work also implies the classification putting Stramenopiles and Alveolata together to form Chromalveolata may be unreasonable; the absence of CL synthesis and maturation pathways in amitochondriate protists is most probably due to secondary loss.}, }
@article {pmid22409411, year = {2012}, author = {Ovchinnikov, S and Masta, SE}, title = {Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {31}, pmid = {22409411}, issn = {1471-2148}, mesh = {Animals ; Arachnida/*genetics ; Base Composition ; DNA, Mitochondrial/chemistry/genetics ; Gene Order ; *Gene Rearrangement ; Genes, rRNA/genetics ; Genome/*genetics ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA/*genetics ; RNA, Transfer/chemistry/genetics ; }, abstract = {BACKGROUND: Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes.<br><br>RESULTS: We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do not encode cloverleaf-shaped tRNA structures. Indeed, in one genome, all 22 tRNA genes lack sequence to encode canonical cloverleaf structures. We also find that the large ribosomal RNA genes are substantially shorter than those of most arthropods. We inferred secondary structures of the LSU rRNAs from both pseudoscorpions, and find that they have lost multiple helices. Based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with tRNA T-arms or D-arms as they pass through the ribosome during protein synthesis.The mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. One genome is rearranged with respect to the location of protein-coding genes, the small rRNA gene, and at least 8 tRNA genes. The other genome contains 6 tRNA genes in novel locations. Most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the CA nucleotide bias typical for arthropods on their major coding strand, and instead possess a GT bias. Yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a CA bias on the major coding strand. Phylogenetic analyses of all 13 mitochondrial protein-coding gene sequences consistently yield trees that place pseudoscorpions as sister to acariform mites.<br><br>CONCLUSION: The well-supported phylogenetic placement of pseudoscorpions as sister to Acariformes differs from some previous analyses based on morphology. However, these two lineages share multiple molecular evolutionary traits, including substantial mitochondrial genome rearrangements, extensive nucleotide substitution, and loss of helices in their inferred tRNA and rRNA structures.}, }
@article {pmid22409213, year = {2012}, author = {McDonald, DE and Daniels, SR}, title = {Phylogeography of the Cape velvet worm (Onychophora: Peripatopsis capensis) reveals the impact of Pliocene/Pleistocene climatic oscillations on Afromontane forest in the Western Cape, South Africa.}, journal = {Journal of evolutionary biology}, volume = {25}, number = {5}, pages = {824-835}, doi = {10.1111/j.1420-9101.2012.02482.x}, pmid = {22409213}, issn = {1420-9101}, mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; *Climate Change ; DNA, Mitochondrial/genetics ; Ecosystem ; Genetic Variation ; Genetics, Population ; Invertebrates/classification/*genetics/physiology ; Mitochondria/genetics ; Phylogeny ; *Phylogeography ; Population Dynamics ; Rain ; Sequence Analysis, DNA ; South Africa ; Species Specificity ; Time Factors ; Trees ; }, abstract = {Habitat specialists such as soft-bodied invertebrates characterized by low dispersal capability and sensitivity to dehydration can be employed to examine biome histories. In this study, the Cape velvet worm (Peripatopsis capensis) was used to examine the impacts of climatic oscillations on historical Afromontane forest in the Western Cape, South Africa. Divergence time estimates suggest that the P. capensis species complex diverged during the Pliocene epoch. This period was characterized by dramatic climatic and topographical change. Subsequently, forest expansion and contraction cycles led to diversification within P. capensis. Increased levels of genetic differentiation were observed along a west-to-south-easterly trajectory because the south-eastern parts of the Cape Fold Mountain chain harbour larger, more stable fragments of forest patches, have more pronounced habitat heterogeneity and have historically received higher levels of rainfall. These results suggest the presence of three putative species within P. capensis, which are geographically discreet and genetically distinct.}, }
@article {pmid22406071, year = {2013}, author = {Duncan, O and Murcha, MW and Whelan, J}, title = {Unique components of the plant mitochondrial protein import apparatus.}, journal = {Biochimica et biophysica acta}, volume = {1833}, number = {2}, pages = {304-313}, doi = {10.1016/j.bbamcr.2012.02.015}, pmid = {22406071}, issn = {0006-3002}, mesh = {Animals ; Arabidopsis/metabolism ; Membrane Transport Proteins/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/*metabolism ; Plant Proteins/*metabolism ; Plants/*metabolism ; Protein Transport ; }, abstract = {The basic mitochondrial protein import apparatus was established in the earliest eukaryotes. Over the subsequent course of evolution and the divergence of the plant, animal and fungal lineages, this basic import apparatus has been modified and expanded in order to meet the specific needs of protein import in each kingdom. In the plant kingdom, the arrival of the plastid complicated the process of protein trafficking and is thought to have given rise to the evolution of a number of unique components that allow specific and efficient targeting of mitochondrial proteins from their site of synthesis in the cytosol, to their final location in the organelle. This includes the evolution of two unique outer membrane import receptors, plant Translocase of outer membrane 20 kDa subunit (TOM20) and Outer membrane protein of 64 kDa (OM64), the loss of a receptor domain from an ancestral import component, Translocase of outer membrane 22 kDa subunit (TOM22), evolution of unique features in the disulfide relay system of the inter membrane space, and the addition of an extra membrane spanning domain to another ancestral component of the inner membrane, Translocase of inner membrane 17 kDa subunit (TIM17). Notably, many of these components are encoded by multi-gene families and exhibit differential sub-cellular localisation and functional specialisation. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.}, }
@article {pmid22404699, year = {2012}, author = {Brace, S and Barnes, I and Powell, A and Pearson, R and Woolaver, LG and Thomas, MG and Turvey, ST}, title = {Population history of the Hispaniolan hutia Plagiodontia aedium (Rodentia: Capromyidae): testing the model of ancient differentiation on a geotectonically complex Caribbean island.}, journal = {Molecular ecology}, volume = {21}, number = {9}, pages = {2239-2253}, doi = {10.1111/j.1365-294X.2012.05514.x}, pmid = {22404699}, issn = {1365-294X}, mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Dominican Republic ; Gene Flow ; *Genetic Speciation ; Genetic Variation ; Geography ; Haiti ; Haplotypes ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Population Density ; Rodentia/*genetics ; Sequence Analysis, DNA ; }, abstract = {Hispaniola is a geotectonically complex island consisting of two palaeo-islands that docked c. 10 Ma, with a further geological boundary subdividing the southern palaeo-island into eastern and western regions. All three regions have been isolated by marine barriers during the late Cenozoic and possess biogeographically distinct terrestrial biotas. However, there is currently little evidence to indicate whether Hispaniolan mammals show distributional patterns reflecting this geotectonic history, as the island's endemic land mammal fauna is now almost entirely extinct. We obtained samples of Hispaniolan hutia (Plagiodontia aedium), one of the two surviving Hispaniolan land mammal species, through fieldwork and historical museum collections from seven localities distributed across all three of the island's biogeographic regions. Phylogenetic analysis using mitochondrial DNA (cytochrome b) reveals a pattern of historical allopatric lineage divergence in this species, with the spatial distribution of three distinct hutia lineages biogeographically consistent with the island's geotectonic history. Coalescent modelling, approximate Bayesian computation and approximate Bayes factor analyses support our phylogenetic inferences, indicating near-complete genetic isolation of these biogeographically separate populations and differing estimates of their effective population sizes. Spatial congruence of hutia lineage divergence is not however matched by temporal congruence with divergences in other Hispaniolan taxa or major events in Hispaniola's geotectonic history; divergence between northern and southern hutia lineages dates to c. 0.6 Ma, significantly later than the unification of the palaeo-islands. The three allopatric Plagiodontia populations should all be treated as distinct management units for conservation, with particular attention required for the northern population (low haplotype diversity) and the south-western population (high haplotype diversity but highly threatened).}, }
@article {pmid22404472, year = {2012}, author = {Sage, RF and Sage, TL and Kocacinar, F}, title = {Photorespiration and the evolution of C4 photosynthesis.}, journal = {Annual review of plant biology}, volume = {63}, number = {}, pages = {19-47}, doi = {10.1146/annurev-arplant-042811-105511}, pmid = {22404472}, issn = {1545-2123}, mesh = {Biological Evolution ; Carbon/*metabolism ; Carbon Dioxide/metabolism ; Carbon Isotopes/analysis ; Cell Respiration/*physiology ; Chenopodiaceae/classification ; *Climate Change ; Ecosystem ; Fossils ; Magnoliopsida/classification ; Oxygen/metabolism ; Photosynthesis/*physiology ; Phylogeny ; Plants/*classification/*metabolism ; Poaceae/classification ; Ribulose-Bisphosphate Carboxylase/metabolism ; Species Specificity ; }, abstract = {C(4) photosynthesis is one of the most convergent evolutionary phenomena in the biological world, with at least 66 independent origins. Evidence from these lineages consistently indicates that the C(4) pathway is the end result of a series of evolutionary modifications to recover photorespired CO(2) in environments where RuBisCO oxygenation is high. Phylogenetically informed research indicates that the repositioning of mitochondria in the bundle sheath is one of the earliest steps in C(4) evolution, as it may establish a single-celled mechanism to scavenge photorespired CO(2) produced in the bundle sheath cells. Elaboration of this mechanism leads to the two-celled photorespiratory concentration mechanism known as C(2) photosynthesis (commonly observed in C(3)-C(4) intermediate species) and then to C(4) photosynthesis following the upregulation of a C(4) metabolic cycle.}, }
@article {pmid22399435, year = {2012}, author = {Grzybowski, T and Rogalla, U}, title = {Mitochondria in anthropology and forensic medicine.}, journal = {Advances in experimental medicine and biology}, volume = {942}, number = {}, pages = {441-453}, doi = {10.1007/978-94-007-2869-1_20}, pmid = {22399435}, issn = {0065-2598}, mesh = {*Anthropology ; DNA, Mitochondrial/genetics ; *Forensic Medicine ; Humans ; Mitochondria/*physiology ; Phylogeny ; }, abstract = {Mitochondria's role in crucial metabolic pathways is probably the first answer which comes to our minds for the question: what do these tiny organelles serve for? However, specific features of their DNA made them extremely useful also in the field of anthropology and forensics. MtDNA analyses became a milestone in the complex task of unraveling earliest human migrations. Evidence provided by these experiments left no doubts on modern humans origins pointing to Africa being our cradle. It also contributed to interpretation of putative ways of our dispersal around Asia and Americas thousands years ago. On the other hand, analysis of mtDNA is well established and valuable tool in forensic genetics. When other definitely more popular markers give no answer on identity, it is the time to employ information carried by mitochondria. This chapter summarizes not only current reports on the role of mitochondria in forensics and reconstruction of modern humans phylogeny, but also calls one's attention to a broad range of difficulties and constraints associated with mtDNA analyses.}, }
@article {pmid22399377, year = {2012}, author = {Muñoz-Pinedo, C}, title = {Signaling pathways that regulate life and cell death: evolution of apoptosis in the context of self-defense.}, journal = {Advances in experimental medicine and biology}, volume = {738}, number = {}, pages = {124-143}, doi = {10.1007/978-1-4614-1680-7_8}, pmid = {22399377}, issn = {0065-2598}, support = {08-0621/AICR_/Worldwide Cancer Research/United Kingdom ; }, mesh = {Animals ; Apoptosis/*immunology ; *Biological Evolution ; Granzymes/immunology ; Humans ; Inhibitor of Apoptosis Proteins/immunology ; Mitochondria/immunology ; Receptors, Death Domain/immunology ; Signal Transduction/*immunology ; Stress, Physiological/*immunology ; }, abstract = {Programmed Cell Death is essential for the life cycle of many organisms. Cell death in multicellular organisms can occur as a consequence of massive damage (necrosis) or in a controlled form, through engagement of diverse biochemical programs. The best well known form of programmed cell death is apoptosis. Apoptosis occurs in animals as a consequence of a variety of stimuli including stress and social signals and it plays essential roles in morphogenesis and immune defense. The machinery of apoptosis is well conserved among animals and it is composed of caspases (the proteases which execute cell death), adapter proteins (caspase activators), Bcl-2 family proteins and Inhibitor of Apoptosis Proteins (IAPs). We will describe in this chapter the main apoptotic pathways in animals: the extrinsic (death receptor-mediated), the intrinsic/mitochondrial and the Granzyme B pathway. Other forms of non-apoptotic Programmed Cell Death which occur in animals will also be discussed. We will summarize the current knowledge about apoptotic-like and other forms of cell death in other organisms such as plants and protists.Additionally, we will discuss the hypothesis that apoptosis originated as part of a host defense mechanism. We will explore the similarities between the protein complexes which mediate apoptosis (apoptosomes) and complexes involved in immunity: inflammasomes. Additional functions of apoptotic proteins related to immune function will be summarized, in an effort to explore the evolutionary origins of cell death.}, }
@article {pmid22397376, year = {2012}, author = {Abascal, F and Posada, D and Zardoya, R}, title = {The evolution of the mitochondrial genetic code in arthropods revisited.}, journal = {Mitochondrial DNA}, volume = {23}, number = {2}, pages = {84-91}, doi = {10.3109/19401736.2011.653801}, pmid = {22397376}, issn = {1940-1744}, mesh = {Animals ; Arthropods/classification/*genetics ; Bayes Theorem ; Codon/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genetic Code/*genetics ; Genome, Mitochondrial/genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer, Lys/genetics ; RNA, Transfer, Ser/genetics ; }, abstract = {A variant of the invertebrate mitochondrial genetic code was previously identified in arthropods (Abascal et al. 2006a, PLoS Biol 4:e127) in which, instead of translating the AGG codon as serine, as in other invertebrates, some arthropods translate AGG as lysine. Here, we revisit the evolution of the genetic code in arthropods taking into account that (1) the number of arthropod mitochondrial genomes sequenced has triplicated since the original findings were published; (2) the phylogeny of arthropods has been recently resolved with confidence for many groups; and (3) sophisticated probabilistic methods can be applied to analyze the evolution of the genetic code in arthropod mitochondria. According to our analyses, evolutionary shifts in the genetic code have been more common than previously inferred, with many taxonomic groups displaying two alternative codes. Ancestral character-state reconstruction using probabilistic methods confirmed that the arthropod ancestor most likely translated AGG as lysine. Point mutations at tRNA-Lys and tRNA-Ser correlated with the meaning of the AGG codon. In addition, we identified three variables (GC content, number of AGG codons, and taxonomic information) that best explain the use of each of the two alternative genetic codes.}, }
@article {pmid22397374, year = {2012}, author = {He, W and Lu, WH and Li, XG and Lu, NN and Sun, DF and Li, YZ}, title = {Taxonomic status of Chinese bahaba (Bahaba taipingensis) and its phylogenetic relationship with other species in the family Sciaenidae.}, journal = {Mitochondrial DNA}, volume = {23}, number = {2}, pages = {53-61}, doi = {10.3109/19401736.2011.653797}, pmid = {22397374}, issn = {1940-1744}, mesh = {Animals ; Bayes Theorem ; China ; Cytochromes b/genetics ; Genes, rRNA ; Mitochondria/enzymology ; Perciformes/*classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Sciaenidae is one of the largest fish families, but the phylogeny and taxonomy of these fishes are still being disputed. Furthermore, the taxonomic status of the Chinese bahaba (Bahaba taipingensis), which is an endemic species to China, had never been studied through molecular method. In this study, phylogenetic relationships among sciaenid species were reconstructed using DNA sequence data from the mitochondrial cytochrome b (cyt b) gene and the 16S ribosomal RNA (16S rRNA) gene through Bayesian inference (BI) analyses. The phylogenetic trees indicated that the Chinese bahaba closely related to Collichthys and Pseudosciaena. Previous studies (Meng et al. 2004. Prog Nat Sci 14(5):514-521, [in Chinese]) showed that the subfamily Pseudosciaeninae represented the latest evolutionary sort, which was more suitable with the current environment. Based on our 16S rRNA, the Chinese bahaba showed close relationship with Pseudosciaena, thus the divergence of the Chinese bahaba maybe also very late within the family Sciaenidae. It was probably that the oceanographic or ecological discontinuities of these species vary considerably causing particularly strong breaks. Furthermore, combined with previous studies, we suggested that there was only one genus, Otolithes, within the subfamily Otolithinae. Nevertheless, the taxonomic status of the Chinese bahaba and the phylogeny of the whole family were not completely solved. Additional samples of more species are required to develop a clearer picture of the evolutionary history of Sciaenidae.}, }
@article {pmid22395773, year = {2012}, author = {Houtkooper, RH and Pirinen, E and Auwerx, J}, title = {Sirtuins as regulators of metabolism and healthspan.}, journal = {Nature reviews. Molecular cell biology}, volume = {13}, number = {4}, pages = {225-238}, pmid = {22395773}, issn = {1471-0080}, support = {231138/ERC_/European Research Council/International ; }, mesh = {Aging/genetics/*metabolism ; Animals ; Energy Metabolism ; Glucose/metabolism ; Histones/genetics/metabolism ; Homeostasis ; Humans ; Insulin/metabolism ; Insulin Secretion ; Lipid Metabolism ; Longevity/genetics ; Multigene Family ; NAD/metabolism ; Phylogeny ; Protein Processing, Post-Translational ; Resveratrol ; Sirtuins/*physiology ; Stilbenes/pharmacology ; }, abstract = {Since the beginning of the century, the mammalian sirtuin protein family (comprising SIRT1-SIRT7) has received much attention for its regulatory role, mainly in metabolism and ageing. Sirtuins act in different cellular compartments: they deacetylate histones and several transcriptional regulators in the nucleus, but also specific proteins in other cellular compartments, such as in the cytoplasm and in mitochondria. As a consequence, sirtuins regulate fat and glucose metabolism in response to physiological changes in energy levels, thereby acting as crucial regulators of the network that controls energy homeostasis and as such determines healthspan.}, }
@article {pmid22387373, year = {2012}, author = {Nevitt, T and Ohrvik, H and Thiele, DJ}, title = {Charting the travels of copper in eukaryotes from yeast to mammals.}, journal = {Biochimica et biophysica acta}, volume = {1823}, number = {9}, pages = {1580-1593}, pmid = {22387373}, issn = {0006-3002}, support = {R01 DK074192-11/DK/NIDDK NIH HHS/United States ; GM41840/GM/NIGMS NIH HHS/United States ; DK07492/DK/NIDDK NIH HHS/United States ; R01 GM041840-24/GM/NIGMS NIH HHS/United States ; R01 GM041840/GM/NIGMS NIH HHS/United States ; R01 DK074192/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Biological Transport ; Cation Transport Proteins/*metabolism ; Copper/chemistry/*metabolism ; Homeostasis/physiology ; Humans ; Iron/metabolism ; Mammals/*metabolism ; Mitochondria/metabolism ; Molecular Chaperones/metabolism ; Oxidation-Reduction ; Oxidative Stress ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Superoxide Dismutase/metabolism ; Superoxide Dismutase-1 ; }, abstract = {Throughout evolution, all organisms have harnessed the redox properties of copper (Cu) and iron (Fe) as a cofactor or structural determinant of proteins that perform critical functions in biology. At its most sobering stance to Earth's biome, Cu biochemistry allows photosynthetic organisms to harness solar energy and convert it into the organic energy that sustains the existence of all nonphotosynthetic life forms. The conversion of organic energy, in the form of nutrients that include carbohydrates, amino acids and fatty acids, is subsequently released during cellular respiration, itself a Cu-dependent process, and stored as ATP that is used to drive a myriad of critical biological processes such as enzyme-catalyzed biosynthetic processes, transport of cargo around cells and across membranes, and protein degradation. The life-supporting properties of Cu incur a significant challenge to cells that must not only exquisitely balance intracellular Cu concentrations, but also chaperone this redox-active metal from its point of cellular entry to its ultimate destination so as to avert the potential for inappropriate biochemical interactions or generation of damaging reactive oxidative species (ROS). In this review we chart the travels of Cu from the extracellular milieu of fungal and mammalian cells, its path within the cytosol as inferred by the proteins and ligands that escort and deliver Cu to intracellular organelles and protein targets, and its journey throughout the body of mammals. This article is part of a Special Issue entitled: Cell Biology of Metals.}, }
@article {pmid22384087, year = {2012}, author = {Hoogewijs, D and Dewilde, S and Vierstraete, A and Moens, L and Vinogradov, SN}, title = {A phylogenetic analysis of the globins in fungi.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e31856}, pmid = {22384087}, issn = {1932-6203}, mesh = {Bacteria/genetics ; Bayes Theorem ; Candida/genetics ; Computational Biology/methods ; Evolution, Molecular ; Fungi/genetics/*metabolism ; *Gene Expression Regulation, Fungal ; Genome ; Genome, Fungal ; Globins/*chemistry ; Neurospora/genetics ; Phylogeny ; Protein Structure, Tertiary ; Saccharomyces cerevisiae/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: All globins belong to one of three families: the F (flavohemoglobin) and S (sensor) families that exhibit the canonical 3/3 α-helical fold, and the T (truncated 3/3 fold) globins characterized by a shortened 2/2 α-helical fold. All eukaryote 3/3 hemoglobins are related to the bacterial single domain F globins. It is known that Fungi contain flavohemoglobins and single domain S globins. Our aims are to provide a census of fungal globins and to examine their relationships to bacterial globins.<br><br>RESULTS: Examination of 165 genomes revealed that globins are present in >90% of Ascomycota and ~60% of Basidiomycota genomes. The S globins occur in Blastocladiomycota and Chytridiomycota in addition to the phyla that have FHbs. Unexpectedly, group 1 T globins were found in one Blastocladiomycota and one Chytridiomycota genome. Phylogenetic analyses were carried out on the fungal globins, alone and aligned with representative bacterial globins. The Saccharomycetes and Sordariomycetes with two FHbs form two widely divergent clusters separated by the remaining fungal sequences. One of the Saccharomycete groups represents a new subfamily of FHbs, comprising a previously unknown N-terminal and a FHb missing the C-terminal moiety of its reductase domain. The two Saccharomycete groups also form two clusters in the presence of bacterial FHbs; the surrounding bacterial sequences are dominated by Proteobacteria and Bacilli (Firmicutes). The remaining fungal FHbs cluster with Proteobacteria and Actinobacteria. The Sgbs cluster separately from their bacterial counterparts, except for the intercalation of two Planctomycetes and a Proteobacterium between the Fungi incertae sedis and the Blastocladiomycota and Chytridiomycota.<br><br>CONCLUSION: Our results are compatible with a model of globin evolution put forward earlier, which proposed that eukaryote F, S and T globins originated via horizontal gene transfer of their bacterial counterparts to the eukaryote ancestor, resulting from the endosymbiotic events responsible for the origin of mitochondria and chloroplasts.}, }
@article {pmid22383961, year = {2012}, author = {Storchova, H and Müller, K and Lau, S and Olson, MS}, title = {Mosaic origins of a complex chimeric mitochondrial gene in Silene vulgaris.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e30401}, pmid = {22383961}, issn = {1932-6203}, mesh = {Alleles ; Arabidopsis Proteins/genetics ; Blotting, Southern ; Codon ; Crosses, Genetic ; DNA Primers/genetics ; Evolution, Molecular ; Gene Expression Regulation ; *Genes, Mitochondrial ; Genes, Plant ; Genetic Variation ; Genome, Plant ; Likelihood Functions ; Models, Genetic ; Mosaicism ; Phylogeny ; Polymerase Chain Reaction ; Proton-Translocating ATPases/genetics ; RNA, Messenger/metabolism ; Recombination, Genetic ; Silene/*genetics ; Species Specificity ; Transcription, Genetic ; }, abstract = {Chimeric genes are significant sources of evolutionary innovation that are normally created when portions of two or more protein coding regions fuse to form a new open reading frame. In plant mitochondria astonishingly high numbers of different novel chimeric genes have been reported, where they are generated through processes of rearrangement and recombination. Nonetheless, because most studies do not find or report nucleotide variation within the same chimeric gene, evolution after the origination of these chimeric genes remains unstudied. Here we identify two alleles of a complex chimera in Silene vulgaris that are divergent in nucleotide sequence, genomic position relative to other mitochondrial genes, and expression patterns. Structural patterns suggest a history partially influenced by gene conversion between the chimeric gene and functional copies of subunit 1 of the mitochondrial ATP synthase gene (atp1). We identified small repeat structures within the chimeras that are likely recombination sites allowing generation of the chimera. These results establish the potential for chimeric gene divergence in different plant mitochondrial lineages within the same species. This result contrasts with the absence of diversity within mitochondrial chimeras found in crop species.}, }
@article {pmid22373076, year = {2012}, author = {Pereira-da-Conceicoa, LL and Price, BW and Barber-James, HM and Barker, NP and de Moor, FC and Villet, MH}, title = {Cryptic variation in an ecological indicator organism: mitochondrial and nuclear DNA sequence data confirm distinct lineages of Baetis harrisoni Barnard (Ephemeroptera: Baetidae) in southern Africa.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {26}, pmid = {22373076}, issn = {1471-2148}, mesh = {Animals ; Cell Nucleus/genetics ; *Genetic Variation ; Insecta/*classification/cytology/*genetics ; Mitochondria/genetics ; Phylogeny ; South Africa ; }, abstract = {BACKGROUND: Baetis harrisoni Barnard is a mayfly frequently encountered in river studies across Africa, but the external morphological features used for identifying nymphs have been observed to vary subtly between different geographic locations. It has been associated with a wide range of ecological conditions, including pH extremes of pH 2.9-10.0 in polluted waters. We present a molecular study of the genetic variation within B. harrisoni across 21 rivers in its distribution range in southern Africa.<br><br>RESULTS: Four gene regions were examined, two mitochondrial (cytochrome c oxidase subunit I [COI] and small subunit ribosomal 16S rDNA [16S]) and two nuclear (elongation factor 1 alpha [EF1&#x3b1;] and phosphoenolpyruvate carboxykinase [PEPCK]). Bayesian and parsimony approaches to phylogeny reconstruction resulted in five well-supported major lineages, which were confirmed using a general mixed Yule-coalescent (GMYC) model. Results from the EF1&#x3b1; gene were significantly incongruent with both mitochondrial and nuclear (PEPCK) results, possibly due to incomplete lineage sorting of the EF1&#x3b1; gene. Mean between-clade distance estimated using the COI and PEPCK data was found to be an order of magnitude greater than the within-clade distance and comparable to that previously reported for other recognised Baetis species. Analysis of the Isolation by Distance (IBD) between all samples showed a small but significant effect of IBD. Within each lineage the contribution of IBD was minimal. Tentative dating analyses using an uncorrelated log-normal relaxed clock and two published estimates of COI mutation rates suggest that diversification within the group occurred throughout the Pliocene and mid-Miocene (~2.4-11.5 mya).<br><br>CONCLUSIONS: The distinct lineages of B. harrisoni correspond to categorical environmental variation, with two lineages comprising samples from streams that flow through acidic Table Mountain Sandstone and three lineages with samples from neutral-to-alkaline streams found within eastern South Africa, Malawi and Zambia. The results of this study suggest that B. harrisoni as it is currently recognised is not a single species with a wide geographic range and pH-tolerance, but may comprise up to five species under the phylogenetic species concept, each with limited pH-tolerances, and that the B. harrisoni species group is thus in need of taxonomic review.}, }
@article {pmid22372851, year = {2012}, author = {Zhou, MJ and Xiao, JH and Bian, SN and Li, YW and Niu, LM and Hu, HY and Wu, WS and Murphy, RW and Huang, DW}, title = {Molecular approaches identify known species, reveal cryptic species and verify host specificity of Chinese Philotrypesis (Hymenoptera: Pteromalidae).}, journal = {Molecular ecology resources}, volume = {12}, number = {4}, pages = {598-606}, doi = {10.1111/j.1755-0998.2012.03127.x}, pmid = {22372851}, issn = {1755-0998}, mesh = {Animals ; Base Sequence ; DNA, Intergenic/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Female ; Genetic Variation ; Host Specificity/*genetics ; Male ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; *Sex Characteristics ; Sex Determination Processes/*genetics ; Wasps/*classification/*genetics ; }, abstract = {Philotrypesis, a major component of the fig wasp community (Hymenoptera: Pteromalidae), is a model taxon for studying male fighting and mating behaviour. Its extreme sexual dimorphism and male polymorphism render species identification uncertain and in-depth research on its ecology, behaviour and other evolutionary topics challenging. The fig wasps' enclosed habitat within the syconia makes their mating behaviour inaccessible, to the extent of matching conspecific females and males. In this study, we combine morphological and molecular analyses to identify species of Philotrypesis sampled from south China and to associate their extraordinarily dimorphic genders and labile male morphologies. Morphological evaluations of females identify 22 species and 28 male morphs. The mitochondrial cytochrome c oxidase I and nuclear internal transcribed spacer 2 data detect 21 species using females, and 15 species among the males. Most of the males match the species as delimited by females. Both markers reveal cryptic species in P. quadrisetosa on Ficus vasculosa. Most species of wasps live on one species of fig but three species co-occur in two hosts (F. microcarpa and F. benjamina), which indicates host switching.}, }
@article {pmid22371600, year = {2012}, author = {Nowack, EC and Grossman, AR}, title = {Trafficking of protein into the recently established photosynthetic organelles of Paulinella chromatophora.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {14}, pages = {5340-5345}, pmid = {22371600}, issn = {1091-6490}, mesh = {Amoeba/*metabolism ; Animals ; Electrophoresis, Polyacrylamide Gel ; Microscopy, Immunoelectron ; Organelles/*metabolism ; *Photosynthesis ; Protein Transport ; }, abstract = {Endosymbiotic acquisition of bacteria by a protist, with subsequent evolution of the bacteria into mitochondria and plastids, had a transformative impact on eukaryotic biology. Reconstructing events that created a stable association between endosymbiont and host during the process of organellogenesis--including establishment of regulated protein import into nascent organelles--is difficult because they date back more than 1 billion years. The amoeba Paulinella chromatophora contains nascent photosynthetic organelles of more recent evolutionary origin (∼60 Mya) termed chromatophores (CRs). After the initial endosymbiotic event, the CR genome was reduced to approximately 30% of its presumed original size and more than 30 expressed genes were transferred from the CR to the amoebal nuclear genome. Three transferred genes--psaE, psaK1, and psaK2--encode subunits of photosystem I. Here we report biochemical evidence that PsaE, PsaK1, and PsaK2 are synthesized in the amoeba cytoplasm and traffic into CRs, where they assemble with CR-encoded subunits into photosystem I complexes. Additionally, our data suggest that proteins routed to CRs pass through the Golgi apparatus. Whereas genome reduction and transfer of genes from bacterial to host genome have been reported to occur in other obligate bacterial endosymbioses, this report outlines the import of proteins encoded by such transferred genes into the compartment derived from the bacterial endosymbiont. Our study showcases P. chromatophora as an exceptional model in which to study early events in organellogenesis, and suggests that protein import into bacterial endosymbionts might be a phenomenon much more widespread than currently assumed.}, }
@article {pmid22371076, year = {2012}, author = {Kumar, P and Vasupalli, N and Srinivasan, R and Bhat, SR}, title = {An evolutionarily conserved mitochondrial orf108 is associated with cytoplasmic male sterility in different alloplasmic lines of Brassica juncea and induces male sterility in transgenic Arabidopsis thaliana.}, journal = {Journal of experimental botany}, volume = {63}, number = {8}, pages = {2921-2932}, doi = {10.1093/jxb/err459}, pmid = {22371076}, issn = {1460-2431}, mesh = {Arabidopsis/*genetics ; Base Sequence ; Conserved Sequence/*genetics ; DNA, Complementary/genetics ; *Evolution, Molecular ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Genome, Mitochondrial/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Mustard Plant/*genetics ; Open Reading Frames/*genetics ; Plant Infertility/*genetics ; Plants, Genetically Modified ; Polymerase Chain Reaction ; RNA, Messenger/genetics/metabolism ; Sequence Alignment ; Species Specificity ; }, abstract = {Nuclear-mitochondrial gene interactions governing cytoplasmic male sterility (CMS) in angiosperms have been found to be unique to each system. Fertility restoration of three diverse alloplasmic CMS lines of Brassica juncea by a line carrying the fertility-restorer gene introgressed from Moricandia arvensis prompted this investigation to examine the molecular basis of CMS in these lines. Since previous studies had found altered atpA transcription associated with CMS in these lines, the atpA genes and transcripts of CMS, fertility-restored, and euplasmic lines were cloned and compared. atpA coding and downstream sequences were conserved among CMS and euplasmic lines but major differences were found in the 5' flanking sequences of atpA. A unique open reading frame (ORF), orf108, co-transcribed with atpA, was found in male sterile flowers of CMS lines carrying mitochondrial genomes of Diplotaxis berthautii, D. catholica, or D. erucoides. In presence of the restorer gene, the bicistronic orf108-atpA transcript was cleaved within orf108 to yield a monocistronic atpA transcript. Transgenic expression of orf108 with anther-specific Atprx18 promoter in Arabidopsis thaliana gave 50% pollen sterility, indicating that Orf108 is lethal at the gametophytic stage. Further, lack of transmission of orf108 to the progeny showed for the first time that mitochondrial ORFs could also cause female sterility. orf108 was found to be widely distributed among wild relatives of Brassica, indicating its ancient origin. This is the first report that shows that CMS lines of different origin and morphology could share common molecular basis. The gametic lethality of Orf108 offers a novel opportunity for transgene containment.}, }
@article {pmid22368181, year = {2012}, author = {Kabran, P and Rossignol, T and Gaillardin, C and Nicaud, JM and Neuvéglise, C}, title = {Alternative splicing regulates targeting of malate dehydrogenase in Yarrowia lipolytica.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {19}, number = {3}, pages = {231-244}, pmid = {22368181}, issn = {1756-1663}, mesh = {Alternative Splicing/*genetics ; Citric Acid Cycle/genetics ; Cytosol/enzymology ; Fungal Proteins/*genetics/metabolism ; *Gene Expression Regulation, Enzymologic ; *Gene Expression Regulation, Fungal ; Genes, Fungal ; Introns/genetics ; Malate Dehydrogenase/classification/*genetics/metabolism ; Mitochondria/enzymology ; Peroxisomes/enzymology ; Phylogeny ; RNA Precursors/genetics/metabolism ; Saccharomyces cerevisiae/enzymology/genetics ; Yarrowia/enzymology/*genetics ; }, abstract = {Alternative pre-mRNA splicing is a major mechanism contributing to the proteome complexity of most eukaryotes, especially mammals. In less complex organisms, such as yeasts, the numbers of genes that contain introns are low and cases of alternative splicing (AS) with functional implications are rare. We report the first case of AS with functional consequences in the yeast Yarrowia lipolytica. The splicing pattern was found to govern the cellular localization of malate dehydrogenase, an enzyme of the central carbon metabolism. This ubiquitous enzyme is involved in the tricarboxylic acid cycle in mitochondria and in the glyoxylate cycle, which takes place in peroxisomes and the cytosol. In Saccharomyces cerevisiae, three genes encode three compartment-specific enzymes. In contrast, only two genes exist in Y. lipolytica. One gene (YlMDH1, YALI0D16753g) encodes a predicted mitochondrial protein, whereas the second gene (YlMDH2, YALI0E14190g) generates the cytosolic and peroxisomal forms through the alternative use of two 3'-splice sites in the second intron. Both splicing variants were detected in cDNA libraries obtained from cells grown under different conditions. Mutants expressing the individual YlMdh2p isoforms tagged with fluorescent proteins confirmed that they localized to either the cytosolic or the peroxisomal compartment.}, }
@article {pmid22366764, year = {2012}, author = {Morita, M and Imanaka, T}, title = {Peroxisomal ABC transporters: structure, function and role in disease.}, journal = {Biochimica et biophysica acta}, volume = {1822}, number = {9}, pages = {1387-1396}, doi = {10.1016/j.bbadis.2012.02.009}, pmid = {22366764}, issn = {0006-3002}, mesh = {ATP-Binding Cassette Transporters/genetics/metabolism/*physiology ; Acyl Coenzyme A/metabolism ; Adrenoleukodystrophy/metabolism/pathology ; Animals ; Biological Transport, Active ; Humans ; Lipid Metabolism ; Neurons/metabolism ; Peroxisomes/*metabolism ; Phylogeny ; Protein Conformation ; Protein Transport ; }, abstract = {ATP-binding cassette (ABC) transporters belong to one of the largest families of membrane proteins, and are present in almost all living organisms from eubacteria to mammals. They exist on plasma membranes and intracellular compartments such as the mitochondria, peroxisomes, endoplasmic reticulum, Golgi apparatus and lysosomes, and mediate the active transport of a wide variety of substrates in a variety of different cellular processes. These include the transport of amino acids, polysaccharides, peptides, lipids and xenobiotics, including drugs and toxins. Three ABC transporters belonging to subfamily D have been identified in mammalian peroxisomes. The ABC transporters are half-size and assemble mostly as a homodimer after posttranslational transport to peroxisomal membranes. ABCD1/ALDP and ABCD2/ALDRP are suggested to be involved in the transport of very long chain acyl-CoA with differences in substrate specificity, and ABCD3/PMP70 is involved in the transport of long and branched chain acyl-CoA. ABCD1 is known to be responsible for X-linked adrenoleukodystrophy (X-ALD), an inborn error of peroxisomal β-oxidation of very long chain fatty acids. Here, we summarize recent advances and important points in our advancing understanding of how these ABC transporters target and assemble to peroxisomal membranes and perform their functions in physiological and pathological processes, including the neurodegenerative disease, X-ALD.}, }
@article {pmid22366452, year = {2012}, author = {Elias, M and Brighouse, A and Gabernet-Castello, C and Field, MC and Dacks, JB}, title = {Sculpting the endomembrane system in deep time: high resolution phylogenetics of Rab GTPases.}, journal = {Journal of cell science}, volume = {125}, number = {Pt 10}, pages = {2500-2508}, pmid = {22366452}, issn = {1477-9137}, support = {/WT_/Wellcome Trust/United Kingdom ; 082813/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Classification/*methods ; Eukaryotic Cells/*classification/*enzymology ; Evolution, Molecular ; Humans ; Intracellular Membranes/*enzymology ; Molecular Sequence Data ; Phylogeny ; rab GTP-Binding Proteins/*genetics/metabolism ; }, abstract = {The presence of a nucleus and other membrane-bounded intracellular compartments is the defining feature of eukaryotic cells. Endosymbiosis accounts for the origins of mitochondria and plastids, but the evolutionary ancestry of the remaining cellular compartments is incompletely documented. Resolving the evolutionary history of organelle-identity encoding proteins within the endomembrane system is a necessity for unravelling the origins and diversification of the endogenously derived organelles. Comparative genomics reveals events after the last eukaryotic common ancestor (LECA), but resolution of events prior to LECA, and a full account of the intracellular compartments present in LECA, has proved elusive. We have devised and exploited a new phylogenetic strategy to reconstruct the history of the Rab GTPases, a key family of endomembrane-specificity proteins. Strikingly, we infer a remarkably sophisticated organellar composition for LECA, which we predict possessed as many as 23 Rab GTPases. This repertoire is significantly greater than that present in many modern organisms and unexpectedly indicates a major role for secondary loss in the evolutionary diversification of the endomembrane system. We have identified two Rab paralogues of unknown function but wide distribution, and thus presumably ancient nature; RabTitan and RTW. Furthermore, we show that many Rab paralogues emerged relatively suddenly during early metazoan evolution, which is in stark contrast to the lack of significant Rab family expansions at the onset of most other major eukaryotic groups. Finally, we reconstruct higher-order ancestral clades of Rabs primarily linked with endocytic and exocytic process, suggesting the presence of primordial Rabs associated with the establishment of those pathways and giving the deepest glimpse to date into pre-LECA history of the endomembrane system.}, }
@article {pmid22366436, year = {2013}, author = {Heinz, E and Lithgow, T}, title = {Back to basics: a revealing secondary reduction of the mitochondrial protein import pathway in diverse intracellular parasites.}, journal = {Biochimica et biophysica acta}, volume = {1833}, number = {2}, pages = {295-303}, doi = {10.1016/j.bbamcr.2012.02.006}, pmid = {22366436}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Cryptosporidiidae/genetics/*metabolism ; Fungal Proteins/genetics/*metabolism ; Microsporidia/genetics/*metabolism ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Molecular Sequence Data ; Protein Transport ; Signal Transduction ; }, abstract = {Mitochondria are present in all eukaryotes, but remodeling of their metabolic contribution has in some cases left them almost unrecognizable and they are referred to as mitochondria-like organelles, hydrogenosomes or, in the case where evolution has led to a great deal of simplification, as mitosomes. Mitochondria rely on the import of proteins encoded in the nucleus and the protein import machinery has been investigated in detail in yeast: several sophisticated molecular machines act in concert to import substrate proteins across the outer mitochondrial membrane and deliver them to a precise sub-mitochondrial compartment. Because these machines are so sophisticated, it has been a major challenge to conceptualize the first phase of their evolution. Here we review recent studies on the protein import pathway in parasitic species that have mitosomes: in the course of their evolution for highly specialized niches these parasites, particularly Cryptosporidia and Microsporidia, have secondarily lost numerous protein functions, in accordance with the evolution of their genomes towards a minimal size. Microsporidia are related to fungi, Cryptosporidia are apicomplexans and kin to the malaria parasite Plasmodium; and this great phylogenetic distance makes it remarkable that Microsporidia and Cryptosporidia have independently evolved skeletal protein import pathways that are almost identical. We suggest that the skeletal pathway reflects the protein import machinery of the first eukaryotes, and defines the essential roles of the core elements of the mitochondrial protein import machinery. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.}, }
@article {pmid22364773, year = {2012}, author = {Takishita, K and Kolisko, M and Komatsuzaki, H and Yabuki, A and Inagaki, Y and Cepicka, I and Smejkalová, P and Silberman, JD and Hashimoto, T and Roger, AJ and Simpson, AG}, title = {Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of 'amitochondriate' diplomonads and retortamonads.}, journal = {Protist}, volume = {163}, number = {3}, pages = {344-355}, doi = {10.1016/j.protis.2011.12.007}, pmid = {22364773}, issn = {1618-0941}, mesh = {Animals ; Anura/*parasitology ; Diplomonadida/*classification/genetics/isolation &amp; purification ; Evolution, Molecular ; Molecular Sequence Data ; *Phylogeny ; Protozoan Proteins/*genetics ; Retortamonadidae/*classification/genetics/isolation &amp; purification ; }, abstract = {Diplomonads, retortamonads, and "Carpediemonas-like" organisms (CLOs) are a monophyletic group of protists that are microaerophilic/anaerobic and lack typical mitochondria. Most diplomonads and retortamonads are parasites, and the pathogen Giardia intestinalis is known to possess reduced mitochondrion-related organelles (mitosomes) that do not synthesize ATP. By contrast, free-living CLOs have larger organelles that superficially resemble some hydrogenosomes, organelles that in other protists are known to synthesize ATP anaerobically. This group represents an excellent system for studying the evolution of parasitism and anaerobic, mitochondrion-related organelles. Understanding these evolutionary transitions requires a well-resolved phylogeny of diplomonads, retortamonads and CLOs. Unfortunately, until now the deep relationships amongst these taxa were unresolved due to limited data for almost all of the CLO lineages. To address this, we assembled a dataset of up to six protein-coding genes that includes representatives from all six CLO lineages, and complements existing rRNA datasets. Multigene phylogenetic analyses place CLOs as well as the retortamonad Chilomastix as a paraphyletic basal assemblage to the lineage comprising diplomonads and the retortamonad Retortamonas. In particular, the CLO Dysnectes was shown to be the closest relative of the diplomonads + Retortamonas clade, with strong support. This phylogeny is consistent with a drastic degeneration of mitochondrion-related organelles during the evolution from a free-living organism resembling extant CLOs to a probable parasite/commensal common ancestor of diplomonads and Retortamonas.}, }
@article {pmid22364126, year = {2012}, author = {Fan, J and Lindemann, P and Feuilloley, MG and Papadopoulos, V}, title = {Structural and functional evolution of the translocator protein (18 kDa).}, journal = {Current molecular medicine}, volume = {12}, number = {4}, pages = {369-386}, doi = {10.2174/1566524011207040369}, pmid = {22364126}, issn = {1875-5666}, support = {MOP 102647//Canadian Institutes of Health Research/Canada ; R01 ES07747/ES/NIEHS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Archaeal Proteins/chemistry/genetics/metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Conserved Sequence ; Evolution, Molecular ; Fungal Proteins/chemistry/genetics/metabolism ; Humans ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/genetics/metabolism ; Protein Structure, Tertiary ; Receptors, Cytoplasmic and Nuclear/chemistry/*genetics/metabolism ; Receptors, GABA/chemistry/*genetics/metabolism ; }, abstract = {Translocator proteins (TSPO) are the products of a family of genes that is evolutionarily conserved from bacteria to humans and expressed in most mammalian tissues and cells. Human TSPO (18 kDa) is expressed at high levels in steroid synthesizing endocrine tissues where it localizes to mitochondria and functions in the first step of steroid formation, the transport of cholesterol into the mitochondria. TSPO expression is elevated in cancerous tissues and during tissue injury, which has lead to the hypothesis that TSPO has roles in apoptosis and the maintenance of mitochondrial integrity. We recently identified a new paralog of Tspo in both the human and mouse. This paralog arose from an ancient gene duplication event before the divergence of the classes aves and mammals, and appears to have specialized tissue-, cell-, and organelle-specific functions. Evidence from the study of TSPO homologs in mammals, bacteria, and plants supports the conclusion that the TSPO family of proteins regulates specialized functions related to oxygen-mediated metabolism. In this review, we provide a comprehensive overview of the divergent function and evolutionary origin of Tspo genes in Bacteria, Archaea, and Eukarya domains.}, }
@article {pmid22363756, year = {2012}, author = {Mark, FC and Lucassen, M and Strobel, A and Barrera-Oro, E and Koschnick, N and Zane, L and Patarnello, T and Pörtner, HO and Papetti, C}, title = {Mitochondrial function in Antarctic nototheniids with ND6 translocation.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e31860}, pmid = {22363756}, issn = {1932-6203}, mesh = {Amino Acids/metabolism ; Animals ; Antarctic Regions ; Cell Respiration ; Electron Transport ; Enzyme Activation ; Enzyme Stability ; Fishes/*genetics ; Membrane Potential, Mitochondrial ; Mitochondria/*enzymology/*genetics ; NADH Dehydrogenase/*genetics ; Oxygen Consumption ; Species Specificity ; *Translocation, Genetic ; }, abstract = {Fish of the suborder Notothenioidei have successfully radiated into the Southern Ocean and today comprise the dominant fish sub-order in Antarctic waters in terms of biomass and species abundance. During evolution in the cold and stable Antarctic climate, the Antarctic lineage of notothenioids developed several unique physiological adaptations, which make them extremely vulnerable to the rapid warming of Antarctic waters currently observed. Only recently, a further phenomenon exclusive to notothenioid fish was reported: the translocation of the mitochondrial gene encoding the NADH Dehydrogenase subunit 6 (ND6), an indispensable part of complex I in the mitochondrial electron transport system.This study investigated the potential physiological consequences of ND6 translocation for the function and thermal sensitivity of the electron transport system in isolated liver mitochondria of the two nototheniid species Notothenia coriiceps and Notothenia rossii, with special attention to the contributions of complex I (NADH DH) and complex II (Succinate DH) to oxidative phosphorylation. Furthermore, enzymatic activities of NADH:Cytochrome c Oxidoreductase and Cytochrome C Oxidase were measured in membrane-enriched tissue extracts.During acute thermal challenge (0-15°C), capacities of mitochondrial respiration and enzymatic function in the liver could only be increased until 9°C. Mitochondrial complex I (NADH Dehydrogenase) was fully functional but displayed a higher thermal sensitivity than the other complexes of the electron transport system, which may specifically result from its unique amino acid composition, revealing a lower degree of stability in notothenioids in general. We interpret the translocation of ND6 as functionally neutral but the change in amino acid sequence as adaptive and supportive of cold stenothermy in Antarctic nototheniids. From these findings, an enhanced sensitivity to ocean warming can be deduced for Antarctic notothenioid fish.}, }
@article {pmid22363720, year = {2012}, author = {Kawafune, K and Hongoh, Y and Hamaji, T and Nozaki, H}, title = {Molecular identification of rickettsial endosymbionts in the non-phagotrophic volvocalean green algae.}, journal = {PloS one}, volume = {7}, number = {2}, pages = {e31749}, pmid = {22363720}, issn = {1932-6203}, mesh = {Base Sequence ; Cell Size ; Chlorophyta/cytology/growth &amp; development/*microbiology ; Host-Pathogen Interactions ; Humans ; In Situ Hybridization, Fluorescence ; Indoles/metabolism ; Molecular Sequence Data ; Nucleotides/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rickettsiaceae/*genetics ; Species Specificity ; Staining and Labeling ; Symbiosis/*genetics ; }, abstract = {BACKGROUND: The order Rickettsiales comprises gram-negative obligate intracellular bacteria (also called rickettsias) that are mainly associated with arthropod hosts. This group is medically important because it contains human-pathogenic species that cause dangerous diseases. Until now, there has been no report of non-phagotrophic photosynthetic eukaryotes, such as green plants, harboring rickettsias.<br><br>We examined the bacterial endosymbionts of two freshwater volvocalean green algae: unicellular Carteria cerasiformis and colonial Pleodorina japonica. Epifluorescence microscopy using 4'-6-deamidino-2-phenylindole staining revealed the presence of endosymbionts in all C. cerasiformis NIES-425 cells, and demonstrated a positive correlation between host cell size and the number of endosymbionts. Strains both containing and lacking endosymbionts of C. cerasiformis (NIES-425 and NIES-424) showed a >10-fold increase in cell number and typical sigmoid growth curves over 192 h. A phylogenetic analysis of 16 S ribosomal (r)RNA gene sequences from the endosymbionts of C. cerasiformis and P. japonica demonstrated that they formed a robust clade (hydra group) with endosymbionts of various non-arthropod hosts within the family Rickettsiaceae. There were significantly fewer differences in the 16 S rRNA sequences of the rickettsiacean endosymbionts between C. cerasiformis and P. japonica than in the chloroplast 16 S rRNA or 18 S rRNA of the host volvocalean cells. Fluorescence in situ hybridization demonstrated the existence of the rickettsiacean endosymbionts in the cytoplasm of two volvocalean species.<br><br>CONCLUSIONS/SIGNIFICANCE: The rickettsiacean endosymbionts are likely not harmful to their volvocalean hosts and may have been recently transmitted from other non-arthropod organisms. Because rickettsias are the closest relatives of mitochondria, incipient stages of mitochondrial endosymbiosis may be deduced using both strains with and without C. cerasiformis endosymbionts.}, }
@article {pmid22362155, year = {2012}, author = {Morén, C and Noguera-Julian, A and Garrabou, G and Catalán, M and Rovira, N and Tobías, E and Cardellach, F and Miró, &#xd2; and Fortuny, C}, title = {Mitochondrial evolution in HIV-infected children receiving first- or second-generation nucleoside analogues.}, journal = {Journal of acquired immune deficiency syndromes (1999)}, volume = {60}, number = {2}, pages = {111-116}, doi = {10.1097/QAI.0b013e318250455e}, pmid = {22362155}, issn = {1944-7884}, mesh = {Anti-HIV Agents/*administration &amp; dosage/*adverse effects ; CD4 Lymphocyte Count ; Child ; DNA, Mitochondrial/analysis ; Female ; HIV Infections/*drug therapy ; Humans ; Lactates/analysis ; Leukocytes, Mononuclear/chemistry ; Longitudinal Studies ; Male ; Mitochondria/*drug effects ; Mitochondrial Proteins/analysis ; Nucleosides/administration &amp; dosage/adverse effects ; Oxidative Stress ; Treatment Outcome ; Viral Load ; }, abstract = {BACKGROUND: Highly active antiretroviral therapy (HAART) and HIV-related mitochondrial toxicity lead to several adverse effects and have become a major issue, especially in children. The main goal in the treatment of HIV-infected children is to maximize cost-effectiveness while minimizing toxicity. We aimed to study the evolution of mitochondrial parameters over time in children receiving different types antiretroviral regimens.<br><br>METHODS: We followed-up 28 HIV-infected children receiving HAART including either first-generation nucleoside reverse transcriptase inhibitors (1gNRTIs; didanosine, zidovudine, or stavudine; n = 15) or second-generation NRTIs (2gNRTIs; the remaining drugs; n = 13) for a period of 2 years for their immunovirological and mitochondrial status, and compared these subjects with a group of untreated HIV-infected patients (n = 10) and uninfected controls (n = 27). We measured T-lymphocyte CD4+ content (flow cytometry), viral load (real-time polymerase chain reaction), and lactate levels (spectrophotometry); we assessed mtDNA content (real-time polymerase chain reaction), mitochondrial protein levels (Western blot), oxidative stress, mitochondrial mass, and electron transport chain function (spectrophotometry) in peripheral blood mononuclear cells.<br><br>RESULTS: At the second time point, lactate levels were significantly higher in children on 1gNRTIs compared with those receiving 2gNRTIs (1.28 &#xb1; 0.08 vs. 1.00 &#xb1; 0.07 mmol/L, respectively; P = 0.022). MtDNA content was similar among all HIV-infected groups and significantly lower than in healthy controls at baseline. Oxidative stress tended to increase over time in all the groups, with no differences among them. However, a significant decrease in cytochrome c oxidase activity was found over time in HIV-infected patients; this decline was greater in the 1gNRTIs group.<br><br>CONCLUSIONS: HIV infection and the use of 1gNRTIs caused greater mitochondrial damage than 2gNRTIs over time. The higher lactate levels and the significant decrease observed in cytochrome c oxidase activity argue against the use of 1gNRTIs in HIV-infected children when an alternative is available, in accordance with international recommendations.}, }
@article {pmid22361213, year = {2012}, author = {Päckert, M and Martens, J and Wink, M and Feigl, A and Tietze, DT}, title = {Molecular phylogeny of Old World swifts (Aves: Apodiformes, Apodidae, Apus and Tachymarptis) based on mitochondrial and nuclear markers.}, journal = {Molecular phylogenetics and evolution}, volume = {63}, number = {3}, pages = {606-616}, doi = {10.1016/j.ympev.2012.02.002}, pmid = {22361213}, issn = {1095-9513}, mesh = {Animals ; Avian Proteins/genetics ; Bayes Theorem ; Birds/classification/*genetics ; Cell Nucleus/*genetics ; Cytochromes b/genetics ; Genetic Markers ; Likelihood Functions ; Mitochondria/*genetics ; Models, Genetic ; Multilocus Sequence Typing ; *Phylogeny ; RNA, Ribosomal/genetics ; }, abstract = {We provide a molecular phylogeny for Old World swifts of genera Apus and Tachymarptis (tribe Apodini) based on a taxon-complete sampling at the species level. Phylogenetic reconstructions were based on two mitochondrial (cytochrome b, 12S rRNA) and three nuclear markers (introns of fibrinogen and glyceraldehyde 3-phosphate dehydrogenase plus anonymous marker 12884) while the myoglobin intron 2 did not show any intergeneric variation or phylogenetic signal among the target taxa at all. In contrast to previous hypotheses, the two genera Apus and Tachymarptis were shown as reciprocally monophyletic in all reconstructions. Apus was consistently divided into three major clades: (1) East Asian clade of A. pacificus and A. acuticauda, (2) African-Asian clade of A. caffer, A. batesi, A. horus, A. affinis and A. nipalensis, (3) African-Palearctic clade of eight currently accepted species among which sequences of A. apus and A. pallidus clustered in a terminal crown clade. Phylogenetic signal of all four nuclear markers was extremely shallow within and among species of tribe Apodini and even among genera, such that intra- and intergeneric relationships of Apus, Tachymarptis and Cypsiurus were poorly resolved by nuclear data alone. Four species, A. pacificus, A. barbatus, A. affinis and A. caffer were consistently found to be paraphyletic with respect to their closest relatives and possible taxonomic consequences are discussed without giving particular recommendations due to limitations of sampling. Incomplete mitochondrial lineage sorting with cytochrome-b haplotypes shared among species and across large geographic distances was observed in two species pairs: A. affinis/A. nipalensis and A. apus/A. pallidus. Mitochondrial introgression caused by extant or past gene flow was ruled out as an explanation for the low interspecific differentiation in these two cases because all nuclear markers appeared to be highly unsorted among Apus species, too. Apparently, the two extant species pairs originated from very recent dispersal and/or speciation events. The currently accepted superspecies classification within Apus was not supported by our results.}, }
@article {pmid22355532, year = {2011}, author = {Thrash, JC and Boyd, A and Huggett, MJ and Grote, J and Carini, P and Yoder, RJ and Robbertse, B and Spatafora, JW and Rappé, MS and Giovannoni, SJ}, title = {Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade.}, journal = {Scientific reports}, volume = {1}, number = {}, pages = {13}, pmid = {22355532}, issn = {2045-2322}, mesh = {Alphaproteobacteria/*genetics ; Base Sequence ; *Biological Evolution ; *Chromosome Mapping ; Coxiellaceae/*genetics ; Genome/*genetics ; Genome, Mitochondrial/*genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Mitochondria share a common ancestor with the Alphaproteobacteria, but determining their precise origins is challenging due to inherent difficulties in phylogenetically reconstructing ancient evolutionary events. Nonetheless, phylogenetic accuracy improves with more refined tools and expanded taxon sampling. We investigated mitochondrial origins with the benefit of new, deeply branching genome sequences from the ancient and prolific SAR11 clade of Alphaproteobacteria and publicly available alphaproteobacterial and mitochondrial genome sequences. Using the automated phylogenomic pipeline Hal, we systematically studied the effect of taxon sampling and missing data to accommodate small mitochondrial genomes. The evidence supports a common origin of mitochondria and SAR11 as a sister group to the Rickettsiales. The simplest explanation of these data is that mitochondria evolved from a planktonic marine alphaproteobacterial lineage that participated in multiple inter-specific cell colonization events, in some cases yielding parasitic relationships, but in at least one case producing a symbiosis that characterizes modern eukaryotic life.}, }
@article {pmid22355196, year = {2012}, author = {Thiergart, T and Landan, G and Schenk, M and Dagan, T and Martin, WF}, title = {An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin.}, journal = {Genome biology and evolution}, volume = {4}, number = {4}, pages = {466-485}, pmid = {22355196}, issn = {1759-6653}, support = {232975/ERC_/European Research Council/International ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; *Genome ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {To test the predictions of competing and mutually exclusive hypotheses for the origin of eukaryotes, we identified from a sample of 27 sequenced eukaryotic and 994 sequenced prokaryotic genomes 571 genes that were present in the eukaryote common ancestor and that have homologues among eubacterial and archaebacterial genomes. Maximum-likelihood trees identified the prokaryotic genomes that most frequently contained genes branching as the sister to the eukaryotic nuclear homologues. Among the archaebacteria, euryarchaeote genomes most frequently harbored the sister to the eukaryotic nuclear gene, whereas among eubacteria, the α-proteobacteria were most frequently represented within the sister group. Only 3 genes out of 571 gave a 3-domain tree. Homologues from α-proteobacterial genomes that branched as the sister to nuclear genes were found more frequently in genomes of facultatively anaerobic members of the rhiozobiales and rhodospirilliales than in obligate intracellular ricketttsial parasites. Following α-proteobacteria, the most frequent eubacterial sister lineages were γ-proteobacteria, δ-proteobacteria, and firmicutes, which were also the prokaryote genomes least frequently found as monophyletic groups in our trees. Although all 22 higher prokaryotic taxa sampled (crenarchaeotes, γ-proteobacteria, spirochaetes, chlamydias, etc.) harbor genes that branch as the sister to homologues present in the eukaryotic common ancestor, that is not evidence of 22 different prokaryotic cells participating at eukaryote origins because prokaryotic "lineages" have laterally acquired genes for more than 1.5 billion years since eukaryote origins. The data underscore the archaebacterial (host) nature of the eukaryotic informational genes and the eubacterial (mitochondrial) nature of eukaryotic energy metabolism. The network linking genes of the eukaryote ancestor to contemporary homologues distributed across prokaryotic genomes elucidates eukaryote gene origins in a dialect cognizant of gene transfer in nature.}, }
@article {pmid22345667, year = {2012}, author = {Xiong, R and Nie, L and Xiang, LX and Shao, JZ}, title = {Characterization of a PIAS4 homologue from zebrafish: insights into its conserved negative regulatory mechanism in the TRIF, MAVS, and IFN signaling pathways during vertebrate evolution.}, journal = {Journal of immunology (Baltimore, Md. : 1950)}, volume = {188}, number = {6}, pages = {2653-2668}, doi = {10.4049/jimmunol.1100959}, pmid = {22345667}, issn = {1550-6606}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Blotting, Western ; Cell Line ; Conserved Sequence ; Female ; Humans ; Interferons/immunology/metabolism ; Male ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Inhibitors of Activated STAT/*genetics/immunology/metabolism ; Protein Structure, Tertiary ; Signal Transduction/*physiology ; Transfection ; Vertebrates/genetics ; Zebrafish/*genetics/immunology/metabolism ; }, abstract = {Members of the protein inhibitor of activated STAT (PIAS) family are key regulators of various human and mammalian signaling pathways, but data on their occurrence and functions in ancient vertebrates are limited. This study characterizes for the first time to our knowledge a PIAS4 homologue (PIAS4a) from zebrafish. Structurally, this zebrafish PIAS4a (zfPIAS4a) shares a number of conserved functional domains with mammalian PIAS4 proteins, including the scaffold attachment factor A/B/acinus/PIAS box, PINIT, and RING-finger-like zinc-binding domains and a highly acidic domain in the C-terminal region. Subcellular localization analysis shows that zfPIAS4a is a nuclear-localized protein and that the C terminus of the molecule harbors strict nuclear localization signals. Functionally, zfPIAS4a expression can be dramatically induced by the stimulation of polyinosinic-polycytidylic acid and zebrafish IFN1. It acts as a critical negative regulator of the TIR domain-containing adapter inducing IFN-β, mitochondrial antiviral signaling (MAVS), and IFN signaling pathways, and it is the first PIAS protein that plays a role in the MAVS-mediated pathway to be identified. The structure and functionality of PIAS4 seem highly conserved from zebrafish to mammals, making zebrafish an attractive model for screens designed to uncover genes involved in IFN- and inflammatory cytokine-induced signaling pathways. This study provides preliminary evidence that the PIAS regulatory mechanism already existed in fish during vertebrate evolution. It presents valuable clues for improving the understanding of not only the negative regulation of cytokine signaling in fish but also the evolutionary history of the PIAS family from fish to mammals as a whole.}, }
@article {pmid22345519, year = {2012}, author = {Fan, W and Lin, CS and Potluri, P and Procaccio, V and Wallace, DC}, title = {mtDNA lineage analysis of mouse L-cell lines reveals the accumulation of multiple mtDNA mutants and intermolecular recombination.}, journal = {Genes &amp; development}, volume = {26}, number = {4}, pages = {384-394}, pmid = {22345519}, issn = {1549-5477}, support = {R01 NS041850/NS/NINDS NIH HHS/United States ; AG16573/AG/NIA NIH HHS/United States ; DK73691/DK/NIDDK NIH HHS/United States ; AG24373/AG/NIA NIH HHS/United States ; R01 AG024373/AG/NIA NIH HHS/United States ; NS41850/NS/NINDS NIH HHS/United States ; R01 NS211328/NS/NINDS NIH HHS/United States ; P50 AG016573/AG/NIA NIH HHS/United States ; R01 DK073691/DK/NIDDK NIH HHS/United States ; R01 NS021328/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Cell Lineage ; Cell Proliferation ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genotype ; L Cells ; Mice ; Mitochondria/*genetics ; *Mutation ; Reactive Oxygen Species ; *Recombination, Genetic ; }, abstract = {The role of mitochondrial DNA (mtDNA) mutations and mtDNA recombination in cancer cell proliferation and developmental biology remains controversial. While analyzing the mtDNAs of several mouse L cell lines, we discovered that every cell line harbored multiple mtDNA mutants. These included four missense mutations, two frameshift mutations, and one tRNA homopolymer expansion. The LA9 cell lines lacked wild-type mtDNAs but harbored a heteroplasmic mixture of mtDNAs, each with a different combination of these variants. We isolated each of the mtDNAs in a separate cybrid cell line. This permitted determination of the linkage phase of each mtDNA and its physiological characteristics. All of the polypeptide mutations inhibited their oxidative phosphorylation (OXPHOS) complexes. However, they also increased mitochondrial reactive oxygen species (ROS) production, and the level of ROS production was proportional to the cellular proliferation rate. By comparing the mtDNA haplotypes of the different cell lines, we were able to reconstruct the mtDNA mutational history of the L-L929 cell line. This revealed that every heteroplasmic L-cell line harbored a mtDNA that had been generated by intracellular mtDNA homologous recombination. Therefore, deleterious mtDNA mutations that increase ROS production can provide a proliferative advantage to cancer or stem cells, and optimal combinations of mutant loci can be generated through recombination.}, }
@article {pmid22343532, year = {2012}, author = {Ling, J and Peterson, KM and Simonović, I and Cho, C and Söll, D and Simonović, M}, title = {Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {9}, pages = {3281-3286}, pmid = {22343532}, issn = {1091-6490}, support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R01 GM097042/GM/NIGMS NIH HHS/United States ; R37 GM022854/GM/NIGMS NIH HHS/United States ; GM022854/GM/NIGMS NIH HHS/United States ; }, mesh = {Aeropyrum/enzymology ; Amino Acid Sequence ; Anticodon/genetics ; Catalytic Domain ; Codon/genetics ; Crystallography, X-Ray ; Escherichia coli/enzymology ; Evolution, Molecular ; Leucine ; Mitochondria/enzymology ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Tertiary ; RNA Editing ; RNA, Transfer, Amino Acyl/genetics/*metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Sequence Alignment ; Species Specificity ; Staphylococcus aureus/enzymology ; Substrate Specificity ; Threonine ; Threonine-tRNA Ligase/chemistry/genetics/*metabolism ; }, abstract = {Aminoacyl-tRNA synthetases (aaRSs) ensure faithful translation of mRNA into protein by coupling an amino acid to a set of tRNAs with conserved anticodon sequences. Here, we show that in mitochondria of Saccharomyces cerevisiae, a single aaRS (MST1) recognizes and aminoacylates two natural tRNAs that contain anticodon loops of different size and sequence. Besides a regular tRNA(2Thr) with a threonine (Thr) anticodon, MST1 also recognizes an unusual tRNA(1Thr), which contains an enlarged anticodon loop and an anticodon triplet that reassigns the CUN codons from leucine to threonine. Our data show that MST1 recognizes the anticodon loop in both tRNAs, but employs distinct recognition mechanisms. The size but not the sequence of the anticodon loop is critical for tRNA(1Thr) recognition, whereas the anticodon sequence is essential for aminoacylation of tRNA(2Thr). The crystal structure of MST1 reveals that, while lacking the N-terminal editing domain, the enzyme closely resembles the bacterial threonyl-tRNA synthetase (ThrRS). A detailed structural comparison with Escherichia coli ThrRS, which is unable to aminoacylate tRNA(1Thr), reveals differences in the anticodon-binding domain that probably allow recognition of the distinct anticodon loops. Finally, our mutational and modeling analyses identify the structural elements in MST1 (e.g., helix α11) that define tRNA selectivity. Thus, MTS1 exemplifies that a single aaRS can recognize completely divergent anticodon loops of natural isoacceptor tRNAs and that in doing so it facilitates the reassignment of the genetic code in yeast mitochondria.}, }
@article {pmid22342934, year = {2012}, author = {Espíndola, A and Buerki, S and Alvarez, N}, title = {Ecological and historical drivers of diversification in the fly genus Chiastocheta Pokorny.}, journal = {Molecular phylogenetics and evolution}, volume = {63}, number = {2}, pages = {466-474}, doi = {10.1016/j.ympev.2012.01.018}, pmid = {22342934}, issn = {1095-9513}, mesh = {Animals ; Biodiversity ; Climate ; DNA, Mitochondrial/genetics ; Diptera/*classification/*genetics ; Evolution, Molecular ; Genetic Speciation ; Genetic Variation ; Geography ; Mitochondria/genetics ; *Phylogeny ; Plants ; Sequence Analysis, DNA ; }, abstract = {Coevolution is among the main forces shaping the biodiversity on Earth. In Eurasia, one of the best-known plant-insect interactions showing highly coevolved features involves the fly genus Chiastocheta and its host-plant Trollius. Although this system has been widely studied from an ecological point of view, the phylogenetic relationships and biogeographic history of the flies have remained little investigated. In this integrative study, we aim to test the monophyly of the five Chiastocheta eco-morphological groups, defined by Pellmyr in 1992, by inferring a mitochondrial phylogeny. We further apply a new approach to assess the effect of (i) different molecular substitution rates and (ii) phylogenetic uncertainty on the inference of the spatio-temporal evolution of the group. From a taxonomic point of view, we demonstrate that only two of Pellmyr's groups (rotundiventris and dentifera) are phylogenetically supported, the other species appearing para- or polyphyletic. We also identify the position of C. lophota, which was not included in previous surveys. From a spatio-temporal perspective, we show that the genus arose during the Pliocene in Europe. Our results also indicate that at least four large-scale dispersal events are required to explain the current distribution of Chiastocheta. Moreover, each dispersal to or from Asia is associated with a host-shift and seems to correspond to an increase in speciation rates. Finally, we highlight the correlation between diversification and climatic fluctuations, which indicate that the cycles of global cooling over the last million years had an influence on the radiation of the group.}, }
@article {pmid22342870, year = {2012}, author = {Tarcz, S and Potekhin, A and Rautian, M and Przyboś, E}, title = {Variation in ribosomal and mitochondrial DNA sequences demonstrates the existence of intraspecific groups in Paramecium multimicronucleatum (Ciliophora, Oligohymenophorea).}, journal = {Molecular phylogenetics and evolution}, volume = {63}, number = {2}, pages = {500-509}, doi = {10.1016/j.ympev.2012.01.024}, pmid = {22342870}, issn = {1095-9513}, mesh = {DNA, Intergenic/genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; Genetic Variation ; Mitochondria/genetics ; Paramecium/*classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 5.8S/*genetics ; }, abstract = {This is the first phylogenetic study of the intraspecific variability within Paramecium multimicronucleatum with the application of two-loci analysis (ITS1-5.8S-ITS2-5'LSU rDNA and COI mtDNA) carried out on numerous strains originated from different continents. The species has been shown to have a complex structure of several sibling species within taxonomic species. Our analysis revealed the existence of 10 haplotypes for the rDNA fragment and 15 haplotypes for the COI fragment in the studied material. The mean distance for all of the studied P. multimicronucleatum sequence pairs was p=0.025/0.082 (rDNA/COI). Despite the greater variation of the COI fragment, the COI-derived tree topology is similar to the tree topology constructed on the basis of the rDNA fragment. P. multimicronucleatum strains are divided into three main clades. The tree based on COI fragment analysis presents a greater resolution of the studied P. multimicronucleatum strains. Our results indicate that the strains of P. multimicronucleatum that appear in different clades on the trees could belong to different syngens.}, }
@article {pmid22342071, year = {2012}, author = {Scalais, E and Francois, B and Schlesser, P and Stevens, R and Nuttin, C and Martin, JJ and Van Coster, R and Seneca, S and Roels, F and Van Goethem, G and Löfgren, A and De Meirleir, L}, title = {Polymerase gamma deficiency (POLG): clinical course in a child with a two stage evolution from infantile myocerebrohepatopathy spectrum to an Alpers syndrome and neuropathological findings of Leigh's encephalopathy.}, journal = {European journal of paediatric neurology : EJPN : official journal of the European Paediatric Neurology Society}, volume = {16}, number = {5}, pages = {542-548}, doi = {10.1016/j.ejpn.2012.01.013}, pmid = {22342071}, issn = {1532-2130}, mesh = {Brain/*pathology ; Child, Preschool ; DNA Polymerase gamma ; DNA, Mitochondrial/genetics ; DNA-Directed DNA Polymerase/*deficiency ; Diffuse Cerebral Sclerosis of Schilder/*genetics/pathology ; Disease Progression ; Fatal Outcome ; Female ; Hepatic Encephalopathy/genetics/pathology ; Humans ; Infant ; Leigh Disease/*genetics/pathology ; Liver Failure/*genetics/pathology ; Mutation ; }, abstract = {AIMS: Description of the clinical course in a child compound heterozygous for POLG1 mutations, neuropathology findings and results of dietary treatment based on fasting avoidance and long chain triglycerides (LCT) restriction.<br><br>RESULTS: At 3(1/2) months of age the patient presented with severe hypoglycemia, hyperlactatemia, moderate ketosis and hepatic failure. Fasting hypoglycemia occurred 8&#xa0;h after meals. The hypoglycemia did not respond to glucagon. She was supplemented with IV glucose and/or frequent feedings, but developed liver insufficiency which was reversed by long-chain triglyceride (LCT) restriction. Alpha-foeto-protein (AFP) levels were elevated and returned to low values after dietary treatment. Liver biopsy displayed cirrhosis, bile ductular proliferation, steatosis, isolated complex IV defect in part of the liver mitochondria, and mitochondrial DNA depletion (27% of control values). Two heterozygous mutations (p. [Ala467Thr]&#xa0;+&#xa0;p. [Gly848Ser]) were found in the POLG1 gene. At 3 years of age she progressively developed refractory mixed type seizures including a focal component and psychomotor regression which fulfilled the criteria of Alpers syndrome (AS) although the initial presentation was compatible with infantile myocerebrohepatopathy spectrum (MCHS). She died at 5 years of age of respiratory insufficiency. Neuropathologic investigation revealed lesions in the right striatal area and the inferior colliculi typical for Leigh's encephalopathy.<br><br>CONCLUSION: The present patient showed an evolution from infantile MCHS to AS, and dietary treatment seemed to slow the progression of liver failure. In spite of the late clinical features of AS, it extends the neuropathological spectrum of AS and polymerase gamma deficiency (POLG) to Leigh syndrome lesions.}, }
@article {pmid22337505, year = {2012}, author = {Egan, SP and Hood, GR and Feder, JL and Ott, JR}, title = {Divergent host-plant use promotes reproductive isolation among cynipid gall wasp populations.}, journal = {Biology letters}, volume = {8}, number = {4}, pages = {605-608}, pmid = {22337505}, issn = {1744-957X}, mesh = {Adaptation, Biological ; Animals ; Body Size ; Copulation ; DNA, Mitochondrial/analysis/genetics ; Ecosystem ; Electron Transport Complex IV/genetics ; Female ; *Genetic Speciation ; Genetics, Population/methods ; Host-Parasite Interactions ; Male ; Mitochondria/genetics ; Plant Tumors/parasitology ; Quercus/*parasitology ; Reproduction ; *Reproductive Isolation ; Wasps/anatomy &amp; histology/genetics/*pathogenicity ; }, abstract = {Ecological speciation occurs when reproductive isolation evolves as a consequence of divergent natural selection among environments. A direct prediction of this process is that ecologically divergent pairs of populations will exhibit greater reproductive isolation than ecologically similar pairs of populations. By comparing allopatric populations of the cynipid gall wasp Belonocnema treatae infesting Quercus virginiana and Quercus geminata, we tested the role that divergent host use plays in generating ecological divergence and sexual isolation. We found differences in body size and gall structure associated with divergent host use, but no difference in neutral genetic divergence between populations on the same or different host plant. We observed significant assortative mating between populations from alternative host plants but not between allopatric populations on the same host plant. Thus, we provide evidence that divergent host use promotes speciation among gall wasp populations.}, }
@article {pmid22331485, year = {2012}, author = {Dubey, B and Meganathan, PR and Haque, I}, title = {Complete mitochondrial genome sequence from an endangered Indian snake, Python molurus molurus (Serpentes, Pythonidae).}, journal = {Molecular biology reports}, volume = {39}, number = {7}, pages = {7403-7412}, pmid = {22331485}, issn = {1573-4978}, mesh = {Adenosine Triphosphate/genetics ; Animals ; Base Sequence ; Boidae/*genetics ; Chromosome Mapping ; DNA, Mitochondrial/genetics ; Electron Transport Complex I/genetics ; Endangered Species ; Gene Order ; *Genome, Mitochondrial ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {This paper reports the complete mitochondrial genome sequence of an endangered Indian snake, Python molurus molurus (Indian Rock Python). A typical snake mitochondrial (mt) genome of 17258 bp length comprising of 37 genes including the 13 protein coding genes, 22 tRNA genes, and 2 ribosomal RNA genes along with duplicate control regions is described herein. The P. molurus molurus mt. genome is relatively similar to other snake mt. genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases. The nucleotide composition of the genome shows that there are more A-C % than T-G% on the positive strand as revealed by positive AT and CG skews. Comparison of individual protein coding genes, with other snake genomes suggests that ATP8 and NADH3 genes have high divergence rates. Codon usage analysis reveals a preference of NNC codons over NNG codons in the mt. genome of P. molurus. Also, the synonymous and non-synonymous substitution rates (ka/ks) suggest that most of the protein coding genes are under purifying selection pressure. The phylogenetic analyses involving the concatenated 13 protein coding genes of P. molurus molurus conformed to the previously established snake phylogeny.}, }
@article {pmid22327014, year = {2012}, author = {Chen, LY and Chen, JM and Gituru, RW and Temam, TD and Wang, QF}, title = {Generic phylogeny and historical biogeography of Alismataceae, inferred from multiple DNA sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {63}, number = {2}, pages = {407-416}, doi = {10.1016/j.ympev.2012.01.016}, pmid = {22327014}, issn = {1095-9513}, mesh = {Alismataceae/*classification/*genetics ; DNA, Chloroplast/genetics ; DNA, Intergenic/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Evolution, Molecular ; Geography ; Molecular Sequence Data ; *Phylogeny ; *Phylogeography ; }, abstract = {Alismataceae is an aquatic or semi-aquatic herb family with a subcosmopolitan distribution. The family is one of the oldest lineages within monocots and plays an important role in the systematics, biogeography and evolutionary processes of flowering plants. However, the generic relationships of the family are still a subject of debate, and its historical biogeography is less studied. In the present study, we carried out a comprehensive phylogenetic analysis based on multiple DNA sequences (nuclear: ITS; chloroplast: psbA, rbcL, matK, rpoB, rpoC1, trnK 5' intron and trnK 3' intron; mitochondria: cob and atp1). The result supports merging Limnocharitaceae into Alismataceae as one family. Two well-supported clades were obtained based on the combined ITS, psbA, rbcL and matK dataset. Clade B consists of Luronium, Damasonium, Baldellia and Alisma; and clade A consists of the remaining genera of Alismataceae as well as Limnocharitaceae. Biogeographic analysis and bayesian molecular dating suggested that Alismataceae originated in West Palearctic or Afrotropical area during the Late Cretaceous, and subsequently split into two clades. Clade A and clade B diversified in Afrotropical area and West Palearctic area, respectively. The intercontinental distribution of this family mainly resulted from dispersals involving migration across land bridges and long-distance dispersal.}, }
@article {pmid22327013, year = {2012}, author = {Upham, NS and Patterson, BD}, title = {Diversification and biogeography of the Neotropical caviomorph lineage Octodontoidea (Rodentia: Hystricognathi).}, journal = {Molecular phylogenetics and evolution}, volume = {63}, number = {2}, pages = {417-429}, doi = {10.1016/j.ympev.2012.01.020}, pmid = {22327013}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Evolution, Molecular ; Genetic Variation ; Membrane Proteins/genetics ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/genetics ; Rats ; Receptors, Somatotropin/genetics ; Rodentia/*classification/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; von Willebrand Factor/genetics ; }, abstract = {The rodent superfamily Octodontoidea comprises 6 families, 38 genera, and 193 living species of spiny rats, tuco-tucos, degus, hutias, and their relatives. All are endemic to the Neotropical Region where they represent roughly three-quarters of extant caviomorphs. Although caviomorph monophyly is well established and phylogenetic hypotheses exist for several families, understanding of octodontoid relationships is clouded by sparse taxon sampling and single-gene analyses. We examined sequence variation in one mitochondrial (12S rRNA) and three nuclear genes (vWF, GHR, and RAG1) across all caviomorph families (including 47 octodontoid species), all phiomorph families, and the sole remaining hystricognath family, using the gundi (Ctenodactylus) and springhaas (Pedetes) as outgroups. Our analyses support the monophyly of Phiomorpha, Caviomorpha, and the caviomorph superfamilies Cavioidea (Dasyproctidae, Cuniculidae, and Caviidae, the latter including Hydrochoerus), Erethizontoidea, Chinchilloidea (including Dinomyidae), and Octodontoidea. Cavioids and erethizontoids are strongly supported as sisters, whereas chinchilloids appear to be sister to octodontoids. Among octodontoids, Abrocomidae is consistently recovered as the basal element, sister to a pair of strongly supported clades; one includes Octodontidae and Ctenomyidae as reciprocally monophyletic lineages, whereas the other includes taxa currently allocated to Echimyidae, Capromyidae and Myocastoridae. Capromys appears near the base of this clade, in keeping with current classification, but Myocastor is nested securely inside a clade of Echimyidae that also contains eumysopines, echimyines and dactylomyines. Another, more weakly supported clade of Echimyidae contains fossorial and scansorial taxa from the Chaco-Cerrado-Caatinga and the Atlantic Forest. Biogeographic analyses robustly recover the Patagonia-Southern Andes complex as ancestral for the Octodontoidea, with three component lineages emerging by the Oligocene-Miocene boundary (∼23Ma): (1) stem abrocomids in the Central and Southern Andes; (2) a lineage leading to octodontids plus ctenomyids in Patagonia, later dispersing into the Chaco-Cerrado-Caatinga; and (3) a lineage leading to echimyids, capromyids, and myocastorids that subsequently radiated in more mesic biomes, including Amazonia, Atlantic Forest, and the Antilles. This reconstruction refutes earlier ideas that the diverse, generalized, mainly lowland family Echimyidae, which appears early in the fossil record, gave rise to the Andean lineages of octodontoids-instead, the reverse derivation appears to be true. We recommend formal synonymy of Myocastoridae with Echimyidae but defer a similar treatment of Capromyidae until additional hutia taxa and sequences can be analyzed.}, }
@article {pmid22326838, year = {2012}, author = {Doucet-Beaupré, H and Blier, PU and Chapman, EG and Piontkivska, H and Dufresne, F and Sietman, BE and Mulcrone, RS and Hoeh, WR}, title = {Pyganodon (Bivalvia: Unionoida: Unionidae) phylogenetics: a male- and female-transmitted mitochondrial DNA perspective.}, journal = {Molecular phylogenetics and evolution}, volume = {63}, number = {2}, pages = {430-444}, doi = {10.1016/j.ympev.2012.01.017}, pmid = {22326838}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Cyclooxygenase 1/genetics ; Cyclooxygenase 2/genetics ; DNA, Mitochondrial/*genetics ; Female ; Genes, Mitochondrial/genetics ; Genetic Speciation ; Genetic Variation ; Male ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sex Determination Processes/genetics ; Unionidae/*classification/*genetics ; }, abstract = {Species boundaries, evolutionary relationships and geographic distributions of many unionoid bivalve species, like those in the genus Pyganodon, remain unresolved in Eastern North America. Because unionoid bivalves are one of the most imperiled groups of animals in the world, understanding the genetic variation within and among populations as well as among species is crucial for effective conservation planning. Conservation of unionoid species is indispensable from a freshwater habitat perspective but also because they possess a unique mitochondrial inheritance system where distinct gender-associated mitochondrial DNA lineages coexist: a female-transmitted (F) mt genome and a male-transmitted (M) mt genome that are involved in the maintenance of separate sexes (=dioecy). In this study, 42 populations of Pyganodon sp. were sampled across a large geographical range and fragments of two mitochondrial genes (cox1 and cox2) were sequenced from both the M- and F-transmitted mtDNA genomes. Our results support the recency of the divergence between P. cataracta and P. fragilis. We also found two relatively divergent F and M lineages within P. grandis. Surprisingly, the relationships among the P. grandis specimens in the F and M sequence trees are not congruent. We found that a single haplotype in P. lacustris has recently swept throughout the M genotype space leading to an unexpectedly low diversity in the M lineage in that species. Our survey put forward some challenging results that force us to rethink hybridization and species boundaries in the genus Pyganodon. As the M and F genomes do not always display the same phylogeographic story in each species, we also discuss the importance of being careful in the interpretation of molecular data based solely on maternal transmitted mtDNA genomes. The involvement of F and M genomes in unionoid bivalve sex determination likely played a role in the genesis of the unorthodox phylogeographic patterns reported herein.}, }
@article {pmid22326460, year = {2012}, author = {Robinson, AJ and Kunji, ER and Gross, A}, title = {Mitochondrial carrier homolog 2 (MTCH2): the recruitment and evolution of a mitochondrial carrier protein to a critical player in apoptosis.}, journal = {Experimental cell research}, volume = {318}, number = {11}, pages = {1316-1323}, doi = {10.1016/j.yexcr.2012.01.026}, pmid = {22326460}, issn = {1090-2422}, support = {MC_U105663139/MRC_/Medical Research Council/United Kingdom ; MC_U105674181/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Apoptosis ; Choanoflagellata ; Evolution, Molecular ; Humans ; Mitochondrial Membrane Transport Proteins/genetics/metabolism/*physiology ; Mitochondrial Proteins/metabolism/physiology ; Protein Transport ; }, abstract = {Recent studies report mitochondrial carrier homolog 2 (MTCH2) as a novel and uncharacterized protein that acts as a receptor-like protein for the truncated BH3-interacting domain death agonist (tBID) protein in the outer membrane of mitochondria. These studies, using mouse embryonic stem cells and fibroblasts as well as mice with a conditional knockout of MTCH2 in the liver, showed that deletion of MTCH2 hindered recruitment of tBID to the mitochondria with subsequent reductions in the activation of pro-apoptotic proteins, mitochondrial outer membrane permeabilization and apoptosis. Sequence analysis shows that MTCH2 is present in all examined multicellular Metazoa as well as unicellular Choanoflagellata, and is a highly derived member of the mitochondrial carrier family. Mitochondrial carriers are monomeric transport proteins that are usually found in the inner mitochondrial membrane, where they exchange small substrates between the mitochondrial matrix and intermembrane space. There are extensive differences between the protein sequences of MTCH2 and other mitochondrial carriers that may explain the ability of MTCH2 to associate with tBID and thus its role in apoptosis. We review the experimental evidence for the role of MTCH2 in apoptosis and suggest that the original transport function of the ancestral MTCH2 mitochondrial carrier has been co-opted by the apoptotic machinery to provide a receptor and signaling mechanism.}, }
@article {pmid22321689, year = {2012}, author = {Newman, CE and Feinberg, JA and Rissler, LJ and Burger, J and Shaffer, HB}, title = {A new species of leopard frog (Anura: Ranidae) from the urban northeastern US.}, journal = {Molecular phylogenetics and evolution}, volume = {63}, number = {2}, pages = {445-455}, pmid = {22321689}, issn = {1095-9513}, support = {P30 ES005022/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Bayes Theorem ; DNA, Mitochondrial ; Genetics, Population ; Likelihood Functions ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Rana pipiens/*classification/*genetics ; Sequence Analysis, DNA ; United States ; }, abstract = {Past confusion about leopard frog (genus Rana) species composition in the Tri-State area of the US that includes New York (NY), New Jersey (NJ), and Connecticut (CT) has hindered conservation and management efforts, especially where populations are declining or imperiled. We use nuclear and mitochondrial genetic data to clarify the identification and distribution of leopard frog species in this region. We focus on four problematic frog populations of uncertain species affiliation in northern NJ, southeastern mainland NY, and Staten Island to test the following hypotheses: (1) they are conspecific with Rana sphenocephala or R. pipiens, (2) they are hybrids between R. sphenocephala and R. pipiens, or (3) they represent one or more previously undescribed cryptic taxa. Bayesian phylogenetic and cluster analyses revealed that the four unknown populations collectively form a novel genetic lineage, which represents a previously undescribed cryptic leopard frog species, Rana sp. nov. Statistical support for R. sp. nov. was strong in both the Bayesian (pp=1.0) and maximum-likelihood (bootstrap=99) phylogenetic analyses as well as the Structure cluster analyses. While our data support recognition of R. sp. nov. as a novel species, we recommend further study including fine-scaled sampling and ecological, behavioral, call, and morphological analyses before it is formally described.}, }
@article {pmid22319153, year = {2012}, author = {Liu, Y and Xu, H and Yuan, X and Rossiter, SJ and Zhang, S}, title = {Multiple adaptive losses of alanine-glyoxylate aminotransferase mitochondrial targeting in fruit-eating bats.}, journal = {Molecular biology and evolution}, volume = {29}, number = {6}, pages = {1507-1511}, doi = {10.1093/molbev/mss013}, pmid = {22319153}, issn = {1537-1719}, mesh = {Adaptation, Biological/*genetics ; Animals ; Base Sequence ; Chiroptera ; Conserved Sequence ; Evolution, Molecular ; Herbivory/genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Peptide Chain Initiation, Translational ; Phylogeny ; Protein Sorting Signals/*genetics ; Selection, Genetic ; Sequence Analysis, DNA ; Sequence Deletion ; Transaminases/*genetics ; }, abstract = {The enzyme alanine-glyoxylate aminotransferase 1 (AGT) functions to detoxify glyoxylate before it is converted into harmful oxalate. In mammals, mitochondrial targeting of AGT in carnivorous species versus peroxisomal targeting in herbivores is controlled by two signal peptides that correspond to these respective organelles. Differential expression of the mitochondrial targeting sequence (MTS) is considered an adaptation to diet-specific subcellular localization of glyoxylate precursors. Bats are an excellent group in which to study adaptive changes in dietary enzymes; they show unparalleled mammalian dietary diversification as well as independent origins of carnivory, frugivory, and nectarivory. We studied the AGT gene in bats and other mammals with diverse diets and found that the MTS has been lost in unrelated lineages of frugivorous bats. Conversely, species exhibiting piscivory, carnivory, insectivory, and sanguinivory possessed intact MTSs. Detected positive selection in the AGT of ancestral fruit bats further supports adaptations related to evolutionary changes in diet.}, }
@article {pmid22318359, year = {2012}, author = {Li, S and Rousseau, D}, title = {ATAD3, a vital membrane bound mitochondrial ATPase involved in tumor progression.}, journal = {Journal of bioenergetics and biomembranes}, volume = {44}, number = {1}, pages = {189-197}, pmid = {22318359}, issn = {1573-6881}, mesh = {ATPases Associated with Diverse Cellular Activities ; Adenosine Triphosphatases/*genetics/*metabolism ; Amino Acid Sequence ; Base Sequence ; Cell Line, Tumor ; Cell Transformation, Neoplastic/*genetics ; Enzyme-Linked Immunosorbent Assay ; Fluorescent Antibody Technique ; Gene Components ; Humans ; Membrane Proteins/*genetics/*metabolism ; Mitochondrial Proteins/*genetics/*metabolism ; Models, Molecular ; Molecular Sequence Data ; *Phylogeny ; Sequence Homology ; Species Specificity ; }, abstract = {ATAD3 (ATPase family AAA Domain-containing protein 3) is a mitochondrial membrane bound ATPase whose function has not yet been discovered but its role is essential for embryonic development. The ATAD3 gene has existed since the pluri-cellular organisms with specialized tissues and has remained unique until vertebrates. In primates and human, two other genes have appeared (called ATAD3B and ATAD3C versus ATAD3A the ancestral gene). ATAD3 knock-down in different non-transformed cell lines is associated with drastic changes in the mitochondrial network, inhibition of proliferation and modification of the functional interactions between mitochondria and endoplasmic reticulum. However, the analysis of the cellular properties of ATAD3A and ATAD3B in different human cancer cell lines shows on the contrary that they can present anti-proliferative and chemoresistant properties. ATAD3 may therefore be implicated in an unknown but essential and growth-linked mitochondrial function existing since pluri-cellular organization and involved in tumorigenesis.}, }
@article {pmid22317974, year = {2012}, author = {Chen, H and Zheng, J and Xue, L and Meng, Y and Wang, Y and Zheng, B and Fang, F and Shi, S and Qiu, Q and Jiang, P and Lu, Z and Mo, JQ and Lu, J and Guan, MX}, title = {The 12S rRNA A1555G mutation in the mitochondrial haplogroup D5a is responsible for maternally inherited hypertension and hearing loss in two Chinese pedigrees.}, journal = {European journal of human genetics : EJHG}, volume = {20}, number = {6}, pages = {607-612}, pmid = {22317974}, issn = {1476-5438}, support = {R01 DC007696/DC/NIDCD NIH HHS/United States ; R01DC07696/DC/NIDCD NIH HHS/United States ; }, mesh = {Adult ; Aged ; Asian People/genetics ; Base Sequence ; DNA, Mitochondrial/chemistry ; Female ; Hearing Loss/*ethnology/*genetics ; Humans ; Hypertension/*ethnology/*genetics ; Male ; Middle Aged ; Mitochondria/*metabolism ; Molecular Sequence Data ; *Mutation ; Pedigree ; Phenotype ; Phylogeny ; RNA, Ribosomal/*genetics/metabolism ; }, abstract = {We reported here clinical, genetic evaluations and molecular analysis of mitochondrial DNA (mtDNA) in two Han Chinese families carrying the known mitochondrial 12S rRNA A1555G mutation. In contrast with the previous data that hearing loss as a sole phenotype was present in the maternal lineage of other families carrying the A1555G mutation, matrilineal relatives among these two Chinese families exhibited both hearing loss and hypertension. Of 21 matrilineal relatives, 9 subjects exhibited both hearing loss and hypertension, 2 individuals suffered from only hypertension and 1 member had only hearing loss. The average age at onset of hypertension in the affected matrilineal relatives of these families was 60 and 46 years, respectively, whereas those of hearing loss in these two families were 33 and 55 years, respectively. Molecular analysis of their mtDNA identified distinct sets of variants belonging to the Eastern Asian haplogroup D5a. In contrast, the A1555G mutation occurred among other mtDNA haplogroups D, B, R, F, G, Y, M and N, respectively. Our data further support that the A1555G mutation is necessary but by itself insufficient to produce the clinical phenotype. The other modifiers are responsible for the phenotypic variability of matrilineal relatives within and among these families carrying the A1555G mutation. Our investigation provides the first evidence that the 12S rRNA A1555G mutation leads to both of hearing loss and hypertension. Thus, our findings may provide the new insights into the understanding of pathophysiology and valuable information for management and treatment of maternally inherited hearing loss and hypertension.}, }
@article {pmid22315334, year = {2012}, author = {Takeuchi, T and Kawashima, T and Koyanagi, R and Gyoja, F and Tanaka, M and Ikuta, T and Shoguchi, E and Fujiwara, M and Shinzato, C and Hisata, K and Fujie, M and Usami, T and Nagai, K and Maeyama, K and Okamoto, K and Aoki, H and Ishikawa, T and Masaoka, T and Fujiwara, A and Endo, K and Endo, H and Nagasawa, H and Kinoshita, S and Asakawa, S and Watabe, S and Satoh, N}, title = {Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {19}, number = {2}, pages = {117-130}, pmid = {22315334}, issn = {1756-1663}, mesh = {Alleles ; Animals ; Chromosome Mapping ; Chromosomes/genetics ; DNA, Complementary/genetics/*isolation &amp; purification ; Expressed Sequence Tags ; *Genome ; Mitochondria/genetics ; Multigene Family ; Phylogeny ; Pinctada/classification/*genetics ; Sequence Analysis, DNA ; Tandem Repeat Sequences ; Transcription Factors/genetics ; Transcriptome ; }, abstract = {The study of the pearl oyster Pinctada fucata is key to increasing our understanding of the molecular mechanisms involved in pearl biosynthesis and biology of bivalve molluscs. We sequenced ~1150-Mb genome at ~40-fold coverage using the Roche 454 GS-FLX and Illumina GAIIx sequencers. The sequences were assembled into contigs with N50 = 1.6 kb (total contig assembly reached to 1024 Mb) and scaffolds with N50 = 14.5 kb. The pearl oyster genome is AT-rich, with a GC content of 34%. DNA transposons, retrotransposons, and tandem repeat elements occupied 0.4, 1.5, and 7.9% of the genome, respectively (a total of 9.8%). Version 1.0 of the P. fucata draft genome contains 23 257 complete gene models, 70% of which are supported by the corresponding expressed sequence tags. The genes include those reported to have an association with bio-mineralization. Genes encoding transcription factors and signal transduction molecules are present in numbers comparable with genomes of other metazoans. Genome-wide molecular phylogeny suggests that the lophotrochozoan represents a distinct clade from ecdysozoans. Our draft genome of the pearl oyster thus provides a platform for the identification of selection markers and genes for calcification, knowledge of which will be important in the pearl industry.}, }
@article {pmid22312314, year = {2012}, author = {Ikenaka, K and Katsuno, M and Kawai, K and Ishigaki, S and Tanaka, F and Sobue, G}, title = {Disruption of axonal transport in motor neuron diseases.}, journal = {International journal of molecular sciences}, volume = {13}, number = {1}, pages = {1225-1238}, pmid = {22312314}, issn = {1422-0067}, mesh = {Animals ; Axonal Transport/*physiology ; Axons/metabolism ; Dynactin Complex ; Dyneins/chemistry/metabolism ; Humans ; Intermediate Filaments/metabolism ; Kinesins/chemistry/metabolism ; Microtubule-Associated Proteins/chemistry/metabolism ; Mitochondria/metabolism ; Motor Neuron Disease/*metabolism/pathology ; }, abstract = {Motor neurons typically have very long axons, and fine-tuning axonal transport is crucial for their survival. The obstruction of axonal transport is gaining attention as a cause of neuronal dysfunction in a variety of neurodegenerative motor neuron diseases. Depletions in dynein and dynactin-1, motor molecules regulating axonal trafficking, disrupt axonal transport in flies, and mutations in their genes cause motor neuron degeneration in humans and rodents. Axonal transport defects are among the early molecular events leading to neurodegeneration in mouse models of amyotrophic lateral sclerosis (ALS). Gene expression profiles indicate that dynactin-1 mRNA is downregulated in degenerating spinal motor neurons of autopsied patients with sporadic ALS. Dynactin-1 mRNA is also reduced in the affected neurons of a mouse model of spinal and bulbar muscular atrophy, a motor neuron disease caused by triplet CAG repeat expansion in the gene encoding the androgen receptor. Pathogenic androgen receptor proteins also inhibit kinesin-1 microtubule-binding activity and disrupt anterograde axonal transport by activating c-Jun N-terminal kinase. Disruption of axonal transport also underlies the pathogenesis of spinal muscular atrophy and hereditary spastic paraplegias. These observations suggest that the impairment of axonal transport is a key event in the pathological processes of motor neuron degeneration and an important target of therapy development for motor neuron diseases.}, }
@article {pmid22311013, year = {2012}, author = {Zhang, M and Nie, X and Cao, T and Wang, J and Li, T and Zhang, X and Guo, Y and Ma, E and Zhong, Y}, title = {The complete mitochondrial genome of the butterfly Apatura metis (Lepidoptera: Nymphalidae).}, journal = {Molecular biology reports}, volume = {39}, number = {6}, pages = {6529-6536}, pmid = {22311013}, issn = {1573-4978}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Butterflies/*genetics ; Gene Order ; Genes, Insect ; *Genes, Mitochondrial ; *Genome, Mitochondrial ; Likelihood Functions ; Locus Control Region ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {As an important pest in the Slender Leaved Willow (Salix alba), Apatura metis is called Freyer's purple emperor, and its mitochondrial genome is 15,236 bp long. The encoded genes for 22 tRNA genes, two ribosomal RNA (rrnL and rrnS) genes, and 13 protein-coding genes (PCGs), and a control region in the A. metis mitochondria are highly homologous to other lepidopteran species. The mitochondrial genome of A. metis is biased toward a high A + T content (A + T = 80.5%). All protein-coding genes, except for COI begins with the CGA codon as observed in other lepidopterans, start with a typical ATN initiation codon. All tRNAs show the classic clover-leaf structure, except that the dihydrouridine (DHU) arm of tRNA(Ser(AGN)) forms a simple loop. The A. metis A + T-rich region contains some conserved structures including a structure combining the motif 'ATAGA' and 19 bp poly (T) stretch, which is similar to those found in other lepidopteran mitogenomes. The phylogenetic analyses of lepidopterans based on mitogenomes sequences demonstrate that each of the six superfamilies is monophyletic, and the relationship among them is (((Noctuoidea + (Geometroidea + Bombycoidea)) + Pyraloidea) + Papilionoidea) + Tortricoidea. In Papilionoidea group, our conclusion argues that ((Lycaenidae + Pieridae) + Nymphalidae) + Papilionidae.}, }
@article {pmid22310498, year = {2012}, author = {Back, P and Matthijssens, F and Vanfleteren, JR and Braeckman, BP}, title = {A simplified hydroethidine method for fast and accurate detection of superoxide production in isolated mitochondria.}, journal = {Analytical biochemistry}, volume = {423}, number = {1}, pages = {147-151}, doi = {10.1016/j.ab.2012.01.008}, pmid = {22310498}, issn = {1096-0309}, mesh = {Acetone/chemistry ; Animals ; Antimycin A/pharmacology ; Caenorhabditis elegans ; Carbonyl Cyanide p-Trifluoromethoxyphenylhydrazone/pharmacology ; Chemistry Techniques, Analytical/*methods ; Ethidium/analogs &amp; derivatives/analysis ; *Fluorometry ; Mitochondria/drug effects/*metabolism ; Oxidation-Reduction ; Phenanthridines/*chemistry ; Superoxides/*analysis ; }, abstract = {Because superoxide is involved in various physiological processes, many efforts have been made to improve its accurate quantification. We optimized and validated a superoxide-specific and -sensitive detection method. The protocol is based on fluorescence detection of the superoxide-specific hydroethidine (HE) oxidation product, 2-hydroxyethidium. We established a method for the quantification of superoxide production in isolated mitochondria without the need for acetone extraction and purification chromatography as described in previous studies.}, }
@article {pmid22309213, year = {2012}, author = {Scott, I and Webster, BR and Li, JH and Sack, MN}, title = {Identification of a molecular component of the mitochondrial acetyltransferase programme: a novel role for GCN5L1.}, journal = {The Biochemical journal}, volume = {443}, number = {3}, pages = {655-661}, pmid = {22309213}, issn = {1470-8728}, support = {ZIA HL006047/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Acetylation ; Acetyltransferases/*metabolism ; Animals ; Gene Knockdown Techniques ; Humans ; Immunoprecipitation ; Mice ; Mitochondria/*enzymology ; Nerve Tissue Proteins/genetics/metabolism/*physiology ; Oxidative Stress ; Phylogeny ; Sirtuin 3/physiology ; }, abstract = {SIRT3 (sirtuin 3) modulates respiration via the deacetylation of lysine residues in electron transport chain proteins. Whether mitochondrial protein acetylation is controlled by a counter-regulatory program has remained elusive. In the present study we identify an essential component of this previously undefined mitochondrial acetyltransferase system. We show that GCN5L1 [GCN5 (general control of amino acid synthesis 5)-like 1; also known as Bloc1s1] counters the acetylation and respiratory effects of SIRT3. GCN5L1 is mitochondrial-enriched and displays significant homology with a prokaryotic acetyltransferase. Genetic knockdown of GCN5L1 blunts mitochondrial protein acetylation, and its reconstitution in intact mitochondria restores protein acetylation. GCN5L1 interacts with and promotes acetylation of SIRT3 respiratory chain targets and reverses global SIRT3 effects on mitochondrial protein acetylation, respiration and bioenergetics. The results of the present study identify GCN5L1 as a critical prokaryote-derived component of the mitochondrial acetyltransferase programme.}, }
@article {pmid22306468, year = {2012}, author = {Ciesielski, SJ and Schilke, BA and Osipiuk, J and Bigelow, L and Mulligan, R and Majewska, J and Joachimiak, A and Marszalek, J and Craig, EA and Dutkiewicz, R}, title = {Interaction of J-protein co-chaperone Jac1 with Fe-S scaffold Isu is indispensable in vivo and conserved in evolution.}, journal = {Journal of molecular biology}, volume = {417}, number = {1-2}, pages = {1-12}, pmid = {22306468}, issn = {1089-8638}, support = {GM074942/GM/NIGMS NIH HHS/United States ; GM27870/GM/NIGMS NIH HHS/United States ; R01 GM027870/GM/NIGMS NIH HHS/United States ; R01 GM027870-31/GM/NIGMS NIH HHS/United States ; U54 GM074942/GM/NIGMS NIH HHS/United States ; }, mesh = {*Evolution, Molecular ; HSP70 Heat-Shock Proteins/genetics/metabolism ; Iron-Sulfur Proteins/chemistry/genetics/metabolism ; Mitochondria/metabolism ; *Mitochondrial Proteins/genetics/metabolism ; Models, Molecular ; Molecular Chaperones/genetics/metabolism ; Protein Binding ; *Saccharomyces cerevisiae ; *Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {The ubiquitous mitochondrial J-protein Jac1, called HscB in Escherichia coli, and its partner Hsp70 play a critical role in the transfer of Fe-S clusters from the scaffold protein Isu to recipient proteins. Biochemical results from eukaryotic and prokaryotic systems indicate that formation of the Jac1-Isu complex is important for both targeting of the Isu for Hsp70 binding and stimulation of Hsp70's ATPase activity. However, in apparent contradiction, we previously reported that an 8-fold decrease in Jac1's affinity for Isu1 is well tolerated in vivo, raising the question as to whether the Jac1:Isu interaction actually plays an important biological role. Here, we report the determination of the structure of Jac1 from Saccharomyces cerevisiae. Taking advantage of this information and recently published data from the homologous bacterial system, we determined that a total of eight surface-exposed residues play a role in Isu binding, as assessed by a set of biochemical assays. A variant having alanines substituted for these eight residues was unable to support growth of a jac1-Δ strain. However, replacement of three residues caused partial loss of function, resulting in a significant decrease in the Jac1:Isu1 interaction, a slow growth phenotype, and a reduction in the activity of Fe-S cluster-containing enzymes. Thus, we conclude that the Jac1:Isu1 interaction plays an indispensable role in the essential process of mitochondrial Fe-S cluster biogenesis.}, }
@article {pmid22306043, year = {2012}, author = {Gaya, E and Högnabba, F and Holguin, A and Molnar, K and Fernández-Brime, S and Stenroos, S and Arup, U and Søchting, U and Van den Boom, P and Lücking, R and Sipman, HJ and Lutzoni, F}, title = {Implementing a cumulative supermatrix approach for a comprehensive phylogenetic study of the Teloschistales (Pezizomycotina, Ascomycota).}, journal = {Molecular phylogenetics and evolution}, volume = {63}, number = {2}, pages = {374-387}, doi = {10.1016/j.ympev.2012.01.012}, pmid = {22306043}, issn = {1095-9513}, mesh = {Ascomycota/*classification/*genetics ; Base Sequence ; Genetic Variation ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; RNA/genetics ; RNA Polymerase II/genetics ; RNA, Fungal/genetics ; RNA, Mitochondrial ; RNA, Ribosomal/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The resolution of the phylogenetic relationships within the order Teloschistales (Ascomycota, lichen-forming-fungi), with nearly 2000 known species and outstanding phenotypic diversity, has been hindered by the limitation in the resolving power that single-locus or two-locus phylogenetic studies have provided to date. In this context, an extensive taxon sampling within the Teloschistales with more loci (especially nuclear protein-coding genes) was needed to confront the current taxonomic delimitations and to understand evolutionary trends within this order. Comprehensive maximum likelihood and bayesian analyses were performed based on seven loci using a cumulative supermatrix approach, including protein-coding genes RPB1 and RPB2 in addition to nuclear and mitochondrial ribosomal RNA-coding genes. We included 167 taxa representing 12 of the 15 genera recognized within the currently accepted Teloschistineae, 22 of the 43 genera within the Physciineae, 49 genera of the closely related orders Lecanorales, Lecideales, and Peltigerales, and the dubiously placed family Brigantiaeaceae and genus Sipmaniella. Although the progressive addition of taxa (cumulative supermatrix approach) with increasing amounts of missing data did not dramatically affect the loss of support and resolution, the monophyly of the Teloschistales in the current sense was inconsistent, depending on the loci-taxa combination analyzed. Therefore, we propose a new, but provisional, classification for the re-circumscribed orders Caliciales and Teloschistales (previously referred to as Physciineae and Teloschistineae, respectively). We report here that the family Brigantiaeaceae, previously regarded as incertae sedis within the subclass Lecanoromycetidae, and Sipmaniella, are members of the Teloschistales in a strict sense. Within this order, one lineage led to the diversification of the mostly epiphytic crustose Brigantiaeaceae and Letrouitiaceae, with a circumpacific center of diversity and found mostly in the tropics. The other main lineage led to another epiphytic crustose family, mostly tropical, and with an Australasian center of diversity--the Megalosporaceae--which is sister to the mainly rock-inhabiting, cosmopolitan, and species rich Teloschistaceae, with a diversity of growth habits ranging from crustose to fruticose. Our results confirm the use of a cumulative supermatrix approach as a viable method to generate comprehensive phylogenies summarizing relationships of taxa with multi-locus to single locus data.}, }
@article {pmid22303278, year = {2011}, author = {Hell, R and Wirtz, M}, title = {Molecular Biology, Biochemistry and Cellular Physiology of Cysteine Metabolism in Arabidopsis thaliana.}, journal = {The arabidopsis book}, volume = {9}, number = {}, pages = {e0154}, pmid = {22303278}, issn = {1543-8120}, abstract = {Cysteine is one of the most versatile molecules in biology, taking over such different functions as catalysis, structure, regulation and electron transport during evolution. Research on Arabidopsis has contributed decisively to the understanding of cysteine synthesis and its role in the assimilatory pathways of S, N and C in plants. The multimeric cysteine synthase complex is present in the cytosol, plastids and mitochondria and forms the centre of a unique metabolic sensing and signaling system. Its association is reversible, rendering the first enzyme of cysteine synthesis active and the second one inactive, and vice-versa. Complex formation is triggered by the reaction intermediates of cysteine synthesis in response to supply and demand and gives rise to regulation of genes of sulfur metabolism to adjust cellular sulfur homeostasis. Combinations of biochemistry, forward and reverse genetics, structural- and cell-biology approaches using Arabidopsis have revealed new enzyme functions and the unique pattern of spatial distribution of cysteine metabolism in plant cells. These findings place the synthesis of cysteine in the centre of the network of primary metabolism.}, }
@article {pmid22302222, year = {2012}, author = {Rüdinger, M and Volkmar, U and Lenz, H and Groth-Malonek, M and Knoop, V}, title = {Nuclear DYW-type PPR gene families diversify with increasing RNA editing frequencies in liverwort and moss mitochondria.}, journal = {Journal of molecular evolution}, volume = {74}, number = {1-2}, pages = {37-51}, pmid = {22302222}, issn = {1432-1432}, mesh = {Bryophyta/*genetics ; Computational Biology ; DNA, Complementary/genetics ; *Genetic Variation ; Hepatophyta/*genetics ; Likelihood Functions ; Mitochondria/*genetics ; Models, Genetic ; Multigene Family/*genetics ; Phylogeny ; Plant Proteins/*genetics ; Protein Structure, Tertiary ; RNA Editing/*genetics/physiology ; Species Specificity ; }, abstract = {RNA editing in mitochondria and chloroplasts of land plants alters transcript sequences by site-specific conversions of cytidines into uridines. RNA editing frequencies vary extremely between land plant clades, ranging from zero in some liverworts to more than 2,000 sites in lycophytes. Unique pentatricopeptide repeat (PPR) proteins with variable domain extension (E/E+/DYW) have recently been identified as specific editing site recognition factors in model plants. The distinctive functions of these PPR protein domain additions have remained unclear, although deaminase function has been proposed for the DYW domain. To shed light on diversity of RNA editing and DYW proteins at the origin of land plant evolution, we investigated editing patterns of the mitochondrial nad5, nad4, and nad2 genes in a wide sampling of more than 100 liverworts and mosses using the recently developed PREPACT program (www.prepact.de) and exemplarily confirmed predicted RNA editing sites in selected taxa. Extreme variability in RNA editing frequency is seen both in liverworts and mosses. Only few editings exist in the liverwort Lejeunea cavifolia or the moss Pogonatum urnigerum whereas up to 20% of cytidines are edited in the liverwort Haplomitrium mnioides or the moss Takakia lepidozioides. Interestingly, the latter are taxa that branch very early within their respective clades. Amplicons targeting the E/E+/DYW domains and subsequent random clone sequencing show DYW domains among bryophytes to be highly conserved in comparison with their angiosperm counterparts and to correlate well with RNA editing frequencies regarding their diversities. We propose that DYW proteins are the key players of RNA editing at the origin of land plants.}, }
@article {pmid22301089, year = {2012}, author = {Yamane, K and Suzuki, Y and Tachi, E and Li, T and Chen, X and Nakao, M and Nkouawa, A and Yanagida, T and Sako, Y and Ito, A and Sato, H and Okamoto, M}, title = {Recent hybridization between Taenia asiatica and Taenia saginata.}, journal = {Parasitology international}, volume = {61}, number = {2}, pages = {351-355}, doi = {10.1016/j.parint.2012.01.005}, pmid = {22301089}, issn = {1873-0329}, mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; DNA, Helminth/chemistry/genetics ; DNA, Mitochondrial/chemistry/genetics ; Genotype ; Heterozygote ; Humans ; Hybridization, Genetic/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Multiplex Polymerase Chain Reaction ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Taenia/*classification/genetics/isolation &amp; purification ; Taenia saginata/*classification/genetics/isolation &amp; purification ; Taeniasis/*parasitology ; Tibet ; }, abstract = {Five Taenia tapeworms collected from humans in Tibetan Plateau, Sichuan, China, where three species of human Taenia are sympatrically endemic, were examined for the mitochondrial cox1 gene and two nuclear genes, ef1 and elp. Phylogenetic analyses of these genes revealed that two adult worms showed nuclear-mitochondrial discordance, suggesting that they originated from hybridization between Taenia saginata and Taenia asiatica. One of two worms had T. asiatica-type mtDNA, whereas another worm had T. saginata-type mtDNA, indicating that reciprocal hybridization between T. saginata and T. asiatica could occur. The worm having T. asiatica-type mtDNA was heterozygous at both nuclear loci with T. saginata-type alleles and T. asiatica-type alleles. In another worm, the ef1 locus was heterozygous with a T. saginata-type alleles and T. asiatica-type alleles, while the elp locus was homozygous with T. saginata-type alleles. Self-fertilization is the main reproductive method of the genus Taenia. Since self-fertilization represents a type of inbreeding, each locus in the offspring would become homozygous over generations with genetic drift. The fact that some nuclear loci are still heterozygous means that hybridization might have occurred recently. Hybridization between T. asiatica and T. saginata is probably an ongoing event in many areas in which they are sympatrically endemic.}, }
@article {pmid22299033, year = {2012}, author = {Hughes, S and Fernández, H and Cucchi, T and Duffraisse, M and Casabianca, F and Istria, D and Pompanon, F and Vigne, JD and Hänni, C and Taberlet, P}, title = {A dig into the past mitochondrial diversity of Corsican goats reveals the influence of secular herding practices.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e30272}, pmid = {22299033}, issn = {1932-6203}, mesh = {Agriculture ; Animal Husbandry/*history ; Animals ; Animals, Domestic ; *Archaeology/methods ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Female ; France ; *Genetic Variation/physiology ; Goats/*genetics/physiology ; History, 21st Century ; History, Ancient ; Male ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The goat (Capra hircus) is one of the earliest domesticated species ca. 10,500 years ago in the Middle-East where its wild ancestor, the bezoar (Capra aegagrus), still occurs. During the Neolithic dispersal, the domestic goat was then introduced in Europe, including the main Mediterranean islands. Islands are interesting models as they maintain traces of ancient colonization, historical exchanges or of peculiar systems of husbandry. Here, we compare the mitochondrial genetic diversity of both medieval and extant goats in the Island of Corsica that presents an original and ancient model of breeding with free-ranging animals. We amplified a fragment of the Control Region for 21 medieval and 28 current goats. Most of them belonged to the A haplogroup, the most worldwide spread and frequent today, but the C haplogroup is also detected at low frequency in the current population. Present Corsican goats appeared more similar to medieval goats than to other European goat populations. Moreover, 16 out of the 26 haplotypes observed were endemic to Corsica and the inferred demographic history suggests that the population has remained constant since the Middle Ages. Implications of these results on management and conservation of endangered Corsican goats currently decimated by a disease are addressed.}, }
@article {pmid22293987, year = {2012}, author = {Vazquez, AL and Fukuda, M and Kim, SG}, title = {Evolution of the dynamic changes in functional cerebral oxidative metabolism from tissue mitochondria to blood oxygen.}, journal = {Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism}, volume = {32}, number = {4}, pages = {745-758}, pmid = {22293987}, issn = {1559-7016}, support = {R21-EB006571/EB/NIBIB NIH HHS/United States ; R01 NS044589/NS/NINDS NIH HHS/United States ; F32 NS056682/NS/NINDS NIH HHS/United States ; F32-NS056682/NS/NINDS NIH HHS/United States ; R01-NS044589/NS/NINDS NIH HHS/United States ; R21 EB006571/EB/NIBIB NIH HHS/United States ; R01 EB003375/EB/NIBIB NIH HHS/United States ; K01 NS066131/NS/NINDS NIH HHS/United States ; R01-EB003375/EB/NIBIB NIH HHS/United States ; K01-NS066131/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Cerebral Cortex/*blood supply/diagnostic imaging/*metabolism ; Cerebrovascular Circulation/*physiology ; Magnetic Resonance Imaging/methods ; Male ; Mitochondria/*metabolism ; Oxygen/*blood ; Oxygen Consumption/*physiology ; Radiography ; Rats ; Rats, Sprague-Dawley ; }, abstract = {The dynamic properties of the cerebral metabolic rate of oxygen consumption (CMR(O2)) during changes in brain activity remain unclear. Therefore, the spatial and temporal evolution of functional increases in CMR(O2) was investigated in the rat somato-sensory cortex during forelimb stimulation under a suppressed blood flow response condition. Temporally, stimulation elicited a fast increase in tissue mitochondria CMR(O2) described by a time constant of ~1 second measured using flavoprotein autofluorescence imaging. CMR(O2)-driven changes in the tissue oxygen tension measured using an oxygen electrode and blood oxygenation measured using optical imaging of intrinsic signal followed; however, these changes were slow with time constants of ~5 and ~10 seconds, respectively. This slow change in CMR(O2)-driven blood oxygenation partly explains the commonly observed post-stimulus blood oxygen level-dependent (BOLD) undershoot. Spatially, the changes in mitochondria CMR(O2) were similar to the changes in blood oxygenation. Finally, the increases in CMR(O2) were well correlated with the evoked multi-unit spiking activity. These findings show that dynamic CMR(O2) calculations made using only blood oxygenation data (e.g., BOLD functional magnetic resonance imaging (fMRI)) do not directly reflect the temporal changes in the tissue's mitochondria metabolic rate; however, the findings presented can bridge the gap between the changes in cellular oxidative rate and blood oxygenation.}, }
@article {pmid22293155, year = {2012}, author = {Nakajima, Y and Nishikawa, A and Iguchi, A and Sakai, K}, title = {The population genetic approach delineates the species boundary of reproductively isolated corymbose acroporid corals.}, journal = {Molecular phylogenetics and evolution}, volume = {63}, number = {2}, pages = {527-531}, doi = {10.1016/j.ympev.2012.01.006}, pmid = {22293155}, issn = {1095-9513}, mesh = {Animals ; Anthozoa/*classification/*genetics ; Genetic Variation ; Genetics, Population ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; *Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; }, abstract = {In this study, we used a population genetic approach with microsatellite markers to attempt to clarify the species boundary of Acropora corals. Species in this taxon are usually difficult to distinguish with the usual molecular phylogenetic approach. We used Acropora sp. 1 and Acropora digitifera as the target species to shed light on the species boundary of Acropora at the population level. These species are morphologically and ecologically similar but are reproductively isolated by differences of a few months in their spawning seasons. We could not distinguish these species using a phylogenetic analysis of the mitochondrial control region, as previously reported in other Acropora species. In contrast, a population genetic approach clearly distinguished these species both sympatrically and allopatrically. Our results suggest that recent speciation and shared ancestral polymorphisms could partly explain the para- and polyphyly of several Acropora species.}, }
@article {pmid22293154, year = {2012}, author = {Lo, EY and Donoghue, MJ}, title = {Expanded phylogenetic and dating analyses of the apples and their relatives (Pyreae, Rosaceae).}, journal = {Molecular phylogenetics and evolution}, volume = {63}, number = {2}, pages = {230-243}, doi = {10.1016/j.ympev.2011.10.005}, pmid = {22293154}, issn = {1095-9513}, mesh = {Bayes Theorem ; Chloroplasts/genetics ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Evolution, Molecular ; Genetic Speciation ; Likelihood Functions ; Malus/*classification/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {Despite previous efforts to elucidate relationships within the Pyreae (Rosaceae), relationships among the major sub-lineages, generic limits, and divergence times have remained uncertain. The present study greatly expands phylogenetic analyses of the Pyreae by using a combination of 11 chloroplast regions plus nuclear ribosomal ITS sequences from 486 individuals representing 331 species and 27 genera. Maximum likelihood and bayesian analyses generally support existing generic boundary, although Sorbus, as previously circumscribed, is clearly non-monophyletic. Two significant conflicts were detected between the chloroplast and ITS phylogenies, suggesting that hybridization played a role in the origins of Micromeles and Pseudocydonia. In addition, we provide estimates of the divergence times of the major lineages. Our findings support the view that the major Pyreae lineages were established during the Eocene-Oligocene period, but that most of the modern diversity did not originate until the Miocene. At least five major, early Old World-New World disjunctions were detected and these vicariance events are generally most consistent with movement through the Beringia.}, }
@article {pmid22291975, year = {2012}, author = {Rodríguez-Ezpeleta, N and Embley, TM}, title = {The SAR11 group of alpha-proteobacteria is not related to the origin of mitochondria.}, journal = {PloS one}, volume = {7}, number = {1}, pages = {e30520}, pmid = {22291975}, issn = {1932-6203}, mesh = {Alphaproteobacteria/*classification/*genetics/physiology ; Amino Acid Sequence ; Base Sequence ; *Biological Evolution ; Classification/methods ; DNA, Mitochondrial/analysis/genetics ; Genome, Mitochondrial ; Humans ; Mitochondria/*genetics/*physiology ; Mitochondrial Proteins/genetics/metabolism ; Phylogeny ; }, abstract = {Although free living, members of the successful SAR11 group of marine alpha-proteobacteria contain a very small and A+T rich genome, two features that are typical of mitochondria and related obligate intracellular parasites such as the Rickettsiales. Previous phylogenetic analyses have suggested that Candidatus Pelagibacter ubique, the first cultured member of this group, is related to the Rickettsiales+mitochondria clade whereas others disagree with this conclusion. In order to determine the evolutionary position of the SAR11 group and its relationship to the origin of mitochondria, we have performed phylogenetic analyses on the concatenation of 24 proteins from 5 mitochondria and 71 proteobacteria. Our results support that SAR11 group is not the sistergroup of the Rickettsiales+mitochondria clade and confirm that the position of this group in the alpha-proteobacterial tree is strongly affected by tree reconstruction artefacts due to compositional bias. As a consequence, genome reduction and bias toward a high A+T content may have evolved independently in the SAR11 species, which points to a different direction in the quest for the closest relatives to mitochondria and Rickettsiales. In addition, our analyses raise doubts about the monophyly of the newly proposed Pelagibacteraceae family.}, }
@article {pmid22291168, year = {2012}, author = {Steele, PR and Hertweck, KL and Mayfield, D and McKain, MR and Leebens-Mack, J and Pires, JC}, title = {Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae.}, journal = {American journal of botany}, volume = {99}, number = {2}, pages = {330-348}, doi = {10.3732/ajb.1100491}, pmid = {22291168}, issn = {1537-2197}, mesh = {Cell Nucleus/genetics ; Computational Biology/methods ; DNA, Plant/genetics ; DNA, Ribosomal/genetics ; Databases, Genetic ; Evolution, Molecular ; Genome Size ; *Genome, Chloroplast ; Genome, Mitochondrial ; Liliaceae/classification/*genetics ; Mitochondria/genetics ; Molecular Sequence Annotation ; Phylogeny ; Plastids/genetics ; Poaceae/classification/*genetics ; Reference Standards ; Sensitivity and Specificity ; Sequence Analysis, DNA/methods ; }, abstract = {PREMISE OF THE STUDY: Genome survey sequences (GSS) from massively parallel sequencing have potential to provide large, cost-effective data sets for phylogenetic inference, replace single gene or spacer regions as DNA barcodes, and provide a plethora of data for other comparative molecular evolution studies. Here we report on the application of this method to estimating the molecular phylogeny of core Asparagales, investigating plastid gene losses, assembling complete plastid genomes, and determining the type and quality of assembled genomic data attainable from Illumina 80-120-bp reads.<br><br>METHODS: We sequenced total genomic DNA from samples in two lineages of monocotyledonous plants, Poaceae and Asparagales, on the Illumina platform in a multiplex arrangement. We compared reference-based assemblies to de novo contigs, evaluated consistency of assemblies resulting from use of various references sequences, and assessed our methods to obtain sequence assemblies in nonmodel taxa.<br><br>KEY RESULTS: Our method returned reliable, robust organellar and nrDNA sequences in a variety of plant lineages. High quality assemblies are not dependent on genome size, amount of plastid present in the total genomic DNA template, or relatedness of available reference sequences for assembly. Phylogenetic results revealed familial and subfamilial relationships within Asparagales with high bootstrap support, although placement of the monotypic genus Aphyllanthes was placed with moderate confidence.<br><br>CONCLUSIONS: The well-supported molecular phylogeny provides evidence for delineation of subfamilies within core Asparagales. With advances in technology and bioinformatics tools, the use of massively parallel sequencing will continue to become easier and more affordable for phylogenomic and molecular evolutionary biology investigations.}, }
@article {pmid22288602, year = {2012}, author = {Van Der Giezen, M and Lenton, TM}, title = {The rise of oxygen and complex life.}, journal = {The Journal of eukaryotic microbiology}, volume = {59}, number = {2}, pages = {111-113}, doi = {10.1111/j.1550-7408.2011.00605.x}, pmid = {22288602}, issn = {1550-7408}, mesh = {Biological Evolution ; Ecosystem ; Environment ; Eukaryota/*genetics/metabolism ; Mitochondria/metabolism ; Oxygen/analysis/*metabolism ; }, abstract = {Mitochondria have been put forward as the saviours of anaerobes when their environment became oxygenated. However, despite oxygenic photosynthesis evolving around 2.7 billion years ago (Ga), followed by the "Great Oxidation" of the atmosphere ~ 2.4 Ga, the deep oceans remained largely anoxic and either iron-enriched or sulphidic until 580 million years ago, when the eukaryotic radiation was well underway. Atmospheric oxygen probably remained at an intermediate concentration (1-10% of the present level) from ~ 2.4 until ~ 0.8 Ga when a "lesser oxidation" began. This drastically changes the textbook view of the ecological conditions under which the mitochondrial endosymbiont established itself. It could explain the widespread distribution of anaerobic biochemistry in every eukaryotic supergroup: anaerobic biochemistry is hard-wired into the eukaryotes.}, }
@article {pmid22288487, year = {2012}, author = {Zehtindjiev, P and Križanauskienė, A and Bensch, S and Palinauskas, V and Asghar, M and Dimitrov, D and Scebba, S and Valkiūnas, G}, title = {A new morphologically distinct avian malaria parasite that fails detection by established polymerase chain reaction-based protocols for amplification of the cytochrome B gene.}, journal = {The Journal of parasitology}, volume = {98}, number = {3}, pages = {657-665}, doi = {10.1645/GE-3006.1}, pmid = {22288487}, issn = {1937-2345}, mesh = {Animal Migration ; Animals ; Cytochromes b/*genetics ; DNA, Protozoan/chemistry/isolation &amp; purification ; Diagnosis, Differential ; Erythroblasts/parasitology ; Erythroid Precursor Cells/parasitology ; Female ; Italy/epidemiology ; Malaria, Avian/blood/diagnosis/epidemiology/*parasitology ; Male ; Mitochondria/enzymology/genetics ; Parasitemia/diagnosis/parasitology/veterinary ; Plasmodium/*classification/genetics/isolation &amp; purification/ultrastructure ; Prevalence ; Real-Time Polymerase Chain Reaction/veterinary ; Songbirds/*parasitology ; }, abstract = {Plasmodium polymorphum n. sp. (Haemosporida, Plasmodiidae) was found in the skylark, Alauda arvensis (Passeriformes: Alaudidae), during autumnal migration in southern Italy. This organism is illustrated and described based on the morphology of its blood stages. The most distinctive feature of this malaria parasite is the clear preference of its blood stages (trophozoites, meronts, and gametocytes) for immature red blood cells, including erythroblasts. Based on preference of erythrocytic meronts for immature red blood cells, P. polymorphum is most similar to species of the subgenus Huffia . This parasite can be readily distinguished from all other bird malaria parasites, including Plasmodium (Huffia) spp., due to preferential development and maturation of its gametocytes in immature red blood cells, a unique character for avian Plasmodium spp. In addition, the margins of nuclei in blood stages of P. polymorphum are markedly smooth and distinct; this is also a distinct diagnostic feature of this parasite. Plasmodium polymorphum has been recorded only in the skylark; it is probably a rare parasite, whose host range and geographical distribution remain unclear. Microscopic examination detected a light infection of Plasmodium relictum (lineage GRW11, parasitemia of <0.01%) in the same sample with P. polymorphum ; the latter parasite clearly predominated (3.5% parasitemia). However, experienced researchers were unable to detect sequences of mitochondrial cytochrome b gene (cyt b) of P. polymorphum from the microscopically positive sample by using published and newly designed primers for DNA amplification of avian Plasmodium spp. The light parasitemia of P. relictum was easily detectable using several polymerase chain reaction (PCR)-based assays, but P. polymorphum was undetectable in all applied assays. Quantitative PCR also showed the presence of light parasitemia (0.06%) of the lineage GRW11 in this sample. This supports the conclusion that the morphologically distinct parasite observed along with P. relictum and predominant in the sample is genetically dissimilar from the lineage GRW11 based on cyt b sequence. In samples with co-infections, general PCR protocols tend to favor the amplification of the parasite with the higher parasitemia or the amplification with the best matching sequence to the primers. Because the parasitemia of P. polymorphum was >50-fold higher than that of P. relictum and several different primers were tested, we suggest that the failure to amplify P. polymorphum is a more complex problem than why co-infections are commonly overlooked in PCR-based studies. We suggest possible explanations of these results and call for additional research on evolution of mitochondrial genome of hemosporidian parasites.}, }
@article {pmid22284828, year = {2012}, author = {Fernandes, V and Alshamali, F and Alves, M and Costa, MD and Pereira, JB and Silva, NM and Cherni, L and Harich, N and Cerny, V and Soares, P and Richards, MB and Pereira, L}, title = {The Arabian cradle: mitochondrial relicts of the first steps along the southern route out of Africa.}, journal = {American journal of human genetics}, volume = {90}, number = {2}, pages = {347-355}, pmid = {22284828}, issn = {1537-6605}, mesh = {Africa ; Arabia ; Asian People/genetics ; Black People/*genetics ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Emigration and Immigration ; Ethnicity/*genetics ; Evolution, Molecular ; Genetic Variation/genetics ; Genetics, Population/methods ; Geography ; Haplotypes/*genetics ; Humans ; Middle East ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; White People/genetics ; }, abstract = {A major unanswered question regarding the dispersal of modern humans around the world concerns the geographical site of the first human steps outside of Africa. The "southern coastal route" model predicts that the early stages of the dispersal took place when people crossed the Red Sea to southern Arabia, but genetic evidence has hitherto been tenuous. We have addressed this question by analyzing the three minor west-Eurasian haplogroups, N1, N2, and X. These lineages branch directly from the first non-African founder node, the root of haplogroup N, and coalesce to the time of the first successful movement of modern humans out of Africa, ∼60 thousand years (ka) ago. We sequenced complete mtDNA genomes from 85 Southwest Asian samples carrying these haplogroups and compared them with a database of 300 European examples. The results show that these minor haplogroups have a relict distribution that suggests an ancient ancestry within the Arabian Peninsula, and they most likely spread from the Gulf Oasis region toward the Near East and Europe during the pluvial period 55-24 ka ago. This pattern suggests that Arabia was indeed the first staging post in the spread of modern humans around the world.}, }
@article {pmid22275765, year = {2012}, author = {Liu, Y and Moskwa, NL and Goffinet, B}, title = {Development of eight mitochondrial markers for Funariaceae (Musci) and their amplification success in other mosses.}, journal = {American journal of botany}, volume = {99}, number = {2}, pages = {e62-5}, doi = {10.3732/ajb.1100402}, pmid = {22275765}, issn = {1537-2197}, mesh = {Base Sequence ; Bryophyta/classification/*genetics ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/genetics ; Databases, Genetic ; Genetic Loci ; Genetic Markers ; INDEL Mutation ; Mitochondria/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {PREMISE OF THE STUDY: In comparison to the wide use of chloroplast markers, few mitochondrial markers are available for phylogenetic studies in bryophytes. We investigated the phylogenetic suitability of several mtDNA markers within the Funariaceae and across mosses.<br><br>METHODS AND RESULTS: By comparing mitochondrial genomes of two mosses, eight regions with higher substitution rates were identified and sequenced for three species in the Funariaceae and one outgroup taxon. Variations in the substitution rate of these new loci were compared to previously used markers. Thirty-four samples representing all major moss lineages were targeted to assess the universality of the newly designed primers.<br><br>CONCLUSIONS: The new markers provided similar or more sequence variations in Funariaceae compared to previously developed mtDNA markers. Five out of eight loci were amplified in 70% of other taxa, indicating that these markers may be suitable for phylogenetic studies in other moss lineages.}, }
@article {pmid22272183, year = {2012}, author = {Sloan, DB and Alverson, AJ and Chuckalovcak, JP and Wu, M and McCauley, DE and Palmer, JD and Taylor, DR}, title = {Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates.}, journal = {PLoS biology}, volume = {10}, number = {1}, pages = {e1001241}, pmid = {22272183}, issn = {1545-7885}, support = {F32 GM080079/GM/NIGMS NIH HHS/United States ; R01 GM070612/GM/NIGMS NIH HHS/United States ; R01-GM-70612/GM/NIGMS NIH HHS/United States ; 1F32GM080079/GM/NIGMS NIH HHS/United States ; }, mesh = {Chromosomes, Plant/*genetics ; *Evolution, Molecular ; Flowers/genetics/*physiology ; Genes, Plant/genetics ; Genome Size/genetics ; Genome, Mitochondrial/*genetics ; Genome, Plant/*genetics ; INDEL Mutation/genetics ; Inheritance Patterns/genetics ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; *Mutation Rate ; Nucleotides/genetics ; Phylogeny ; Plant Proteins/genetics ; Polymorphism, Genetic ; RNA, Plant/genetics ; Recombination, Genetic/genetics ; Silene/*genetics ; Species Specificity ; }, abstract = {Genome size and complexity vary tremendously among eukaryotic species and their organelles. Comparisons across deeply divergent eukaryotic lineages have suggested that variation in mutation rates may explain this diversity, with increased mutational burdens favoring reduced genome size and complexity. The discovery that mitochondrial mutation rates can differ by orders of magnitude among closely related angiosperm species presents a unique opportunity to test this hypothesis. We sequenced the mitochondrial genomes from two species in the angiosperm genus Silene with recent and dramatic accelerations in their mitochondrial mutation rates. Contrary to theoretical predictions, these genomes have experienced a massive proliferation of noncoding content. At 6.7 and 11.3 Mb, they are by far the largest known mitochondrial genomes, larger than most bacterial genomes and even some nuclear genomes. In contrast, two slowly evolving Silene mitochondrial genomes are smaller than average for angiosperms. Consequently, this genus captures approximately 98% of known variation in organelle genome size. The expanded genomes reveal several architectural changes, including the evolution of complex multichromosomal structures (with 59 and 128 circular-mapping chromosomes, ranging in size from 44 to 192 kb). They also exhibit a substantial reduction in recombination and gene conversion activity as measured by the relative frequency of alternative genome conformations and the level of sequence divergence between repeat copies. The evolution of mutation rate, genome size, and chromosome structure can therefore be extremely rapid and interrelated in ways not predicted by current evolutionary theories. Our results raise the hypothesis that changes in recombinational processes, including gene conversion, may be a central force driving the evolution of both mutation rate and genome structure.}, }
@article {pmid22266481, year = {2012}, author = {Pokorny, L and Ho, BC and Frahm, JP and Quandt, D and Shaw, AJ}, title = {Phylogenetic analyses of morphological evolution in the gametophyte and sporophyte generations of the moss order Hookeriales (Bryopsida).}, journal = {Molecular phylogenetics and evolution}, volume = {63}, number = {2}, pages = {351-364}, doi = {10.1016/j.ympev.2012.01.005}, pmid = {22266481}, issn = {1095-9513}, mesh = {Base Sequence ; Biological Evolution ; Bryopsida/anatomy &amp; histology/*classification/*genetics ; DNA, Plant/genetics ; DNA, Ribosomal Spacer/genetics ; Evolution, Molecular ; Germ Cells, Plant/classification/*physiology ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Morphological characters from the gametophyte and sporophyte generations have been used in land plants to infer relationships and construct classifications, but sporophytes provide the vast majority of data for the systematics of vascular plants. In bryophytes both generations are well developed and characters from both are commonly used to classify these organisms. However, because morphological traits of gametophytes and sporophytes can have different genetic bases and experience different selective pressures, taxonomic emphasis on one generation or the other may yield incongruent classifications. The moss order Hookeriales has a controversial taxonomic history because previous classifications have focused almost exclusively on either gametophytes or sporophytes. The Hookeriales provide a model for comparing morphological evolution in gametophytes and sporophytes, and its impact on alternative classification systems. In this study we reconstruct relationships among mosses that are or have been included in the Hookeriales based on sequences from five gene regions, and reconstruct morphological evolution of six sporophyte and gametophyte traits that have been used to differentiate families and genera. We found that the Hookeriales, as currently circumscribed, are monophyletic and that both sporophyte and gametophyte characters are labile. We documented parallel changes and reversals in traits from both generations. This study addresses the general issue of morphological reversals to ancestral states, and resolves novel relationships in the Hookeriales.}, }
@article {pmid22266240, year = {2012}, author = {Dunams-Morel, DB and Reichard, MV and Torretti, L and Zarlenga, DS and Rosenthal, BM}, title = {Discernible but limited introgression has occurred where Trichinella nativa and the T6 genotype occur in sympatry.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {12}, number = {3}, pages = {530-538}, doi = {10.1016/j.meegid.2012.01.004}, pmid = {22266240}, issn = {1567-7257}, mesh = {Animals ; Bayes Theorem ; DNA, Helminth/*genetics/metabolism ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics/metabolism ; Evolution, Molecular ; Genetic Markers ; Genetic Speciation ; *Genotype ; Genotyping Techniques ; Inheritance Patterns ; Larva/genetics/metabolism ; Microsatellite Repeats ; Mitochondria/genetics ; Mustelidae/parasitology ; Phylogeny ; *Sympatry ; Trichinella/classification/*genetics/isolation &amp; purification/metabolism ; }, abstract = {The genetic diversity within and among parasite populations provides clues to their evolutionary history. Here, we sought to determine whether mitochondrial and microsatellite DNA variation could be used to evaluate the extent of differentiation, gene flow and historical reproductive isolation among the freeze resistant parasites Trichinella nativa and the Trichinella T6 genotype infecting wolverines (Gulo gulo) in Nunavut, Canada. To this end, we genotyped Trichinella isolates derived from the diaphragms of 39 wolverines from this locale to reference strains of T. nativa and the Trichinella T6 genotype. Results showed that among a subset of 13 isolates examined, individuals resembled T. nativa in their mitochondrial DNA, but resembled the Trichinella T6 genotype when assayed at expansion segment V and the internal transcribed spacer of the nuclear rDNA. To adjudicate among these conflicting diagnoses, we further characterized each isolate at several nuclear microsatellite loci and again compared these to data from reference strains. Statistical assignment established that the nuclear genomes of most Nunavut isolates corresponded to those of the Trichinella T6 genotype; however, two isolates corresponded to T. nativa, and one isolate exhibited equal similarity to both reference strains. Taken as a whole, the evidence suggests that these isolates derive from the T. nativa matrilineage, but that their nuclear genomes resemble individuals previously designated as Trichinella T6. Assuming distinct lineages, this argues for cross-hybridization among these genotypes. Although introgression has occurred, recognizable genetic distinctions persist. One possibility is that selection disfavors the survival of hybrid offspring in most instances. Alternatively, the recent disappearance of glacial barriers might have increased contact, and therefore introgression. Broader geographic sampling will be required to determine the extent to which hybridization occurs beyond this particular geographic focus.}, }
@article {pmid22266183, year = {2012}, author = {Burns, M and Hedin, M and Shultz, JW}, title = {Molecular phylogeny of the leiobunine harvestmen of eastern North America (Opiliones: Sclerosomatidae: Leiobuninae).}, journal = {Molecular phylogenetics and evolution}, volume = {63}, number = {2}, pages = {291-298}, doi = {10.1016/j.ympev.2011.12.025}, pmid = {22266183}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Evolution, Molecular ; Genetic Variation ; Genitalia, Male/anatomy &amp; histology ; Male ; Mitochondria/genetics ; NAD/genetics ; North America ; Peptide Elongation Factor 1/genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; Spiders/anatomy &amp; histology/*classification/*genetics ; }, abstract = {Phylogenetic relationships among the leiobunine harvestmen or "daddy-longlegs" of eastern North America (Leiobunum, Hadrobunus, Eumesosoma) are poorly known, and systematic knowledge of the group has been limited largely to species descriptions and proposed species groups. Here we obtained mitochondrial (NADH1, 16S and 12S rDNA) and nuclear (28S rDNA, EF-1α introns and exons) DNA sequences from representatives of each genus, virtually all Leiobunum species from the USA and Canada, four western North American outgroup species and the distantly related Phalangium opilio. We applied bayesian, maximum-likelihood and parsimony methods under various data-partition treatments to reconstruct phylogeny and to test taxonomy-based phylogenetic hypotheses. Results were largely congruent among methods and treatments and well supported by bootstrap and posterior probability values. We recovered Leiobunum as paraphyletic with respect to Eumesosoma and Hadrobunus. Most species were encompassed by five well-supported clades that broadly correspond to groups based on male reproductive morphology (Hadrobunus group, an early-season Leiobunum group, L. vittatum group, L. politum group and L. calcar group). Relationships within species groups were often ambiguous or inconsistent with morphology, suggesting the presence of gene introgression or deep coalescence and/or the need for taxonomic revision.}, }
@article {pmid22248533, year = {2012}, author = {Umasuthan, N and Revathy, KS and Lee, Y and Whang, I and Lee, J}, title = {Mitochondrial thioredoxin-2 from Manila clam (Ruditapes philippinarum) is a potent antioxidant enzyme involved in antibacterial response.}, journal = {Fish &amp; shellfish immunology}, volume = {32}, number = {4}, pages = {513-523}, doi = {10.1016/j.fsi.2011.12.010}, pmid = {22248533}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Antioxidants ; Base Sequence ; Bivalvia/*enzymology/*immunology/microbiology ; Escherichia coli/genetics/metabolism ; Gene Expression Regulation, Enzymologic/*immunology ; Mitochondria/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; RNA, Messenger/metabolism ; Thioredoxins/genetics/*metabolism ; Transcription, Genetic/immunology ; }, abstract = {Thioredoxin (TRx) is a ubiquitous protein involved in the regulation of multiple biological processes. The TRx-2 isoform is exclusively expressed in mitochondria, where it contributes to mitochondrial redox state maintenance. In the present study, a novel thioredoxin-2 gene was identified in the Manila clam, Ruditapes philippinarum. The full-length sequence of RpTRx-2 (1561 bp) consists of a 498 bp coding region encoding a 166 amino acid protein. The N-terminal region of RpTRx-2 harbors a mitochondrial localization signal (56 amino acids), while the C-terminal portion contains the characteristic (89)WCGPC(93) catalytic active site. Phylogenetic analysis revealed that RpTRx-2 is closest to its ortholog from abalone. The broad distribution pattern of RpTRx-2 mRNA in healthy animal tissues implicates a generally significant function in normal clam physiology. The transcription level of RpTRx-2, however, is highest in hemocytes. Lipopolysaccharide and Vibrio tapetis bacterium caused up-regulation of the RpTrx-2 transcript levels in gill and hemocytes. Interestingly, clam manganese superoxide dismutase (MnSOD) mRNA levels in hemocytes elicited a corresponding response to these immune challenges. RpTRx-2 was recombinantly expressed in Escherichia coli BL21 (DE3) and used in insulin disulfide reduction assay as well as metal-catalyzed oxidation assay to elucidate its antioxidant property by reducing substrate and protecting super-coiled DNA from oxidative damage through free radical scavenging, respectively. Collectively, our data indicated that RpTRx-2, a mitochondrial TRx-2 family member, is an antioxidant enzyme that may be involved in antibacterial defense of clams.}, }
@article {pmid22247039, year = {2012}, author = {Blouin, NA and Lane, CE}, title = {Red algal parasites: models for a life history evolution that leaves photosynthesis behind again and again.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {34}, number = {3}, pages = {226-235}, doi = {10.1002/bies.201100139}, pmid = {22247039}, issn = {1521-1878}, mesh = {*Evolution, Molecular ; Genome, Mitochondrial ; Host-Parasite Interactions ; Mitochondria/genetics/physiology ; Models, Biological ; *Photosynthesis ; Phylogeny ; Plant Proteins/genetics/physiology ; Plastids/physiology ; Rhodophyta/anatomy &amp; histology/classification/genetics/*physiology ; Species Specificity ; }, abstract = {Many of the most virulent and problematic eukaryotic pathogens have evolved from photosynthetic ancestors, such as apicomplexans, which are responsible for a wide range of diseases including malaria and toxoplasmosis. The primary barrier to understanding the early stages of evolution of these parasites has been the difficulty in finding parasites with closely related free-living lineages with which to make comparisons. Parasites found throughout the florideophyte red algal lineage, however, provide a unique and powerful model to investigate the genetic origins of a parasitic lifestyle. This is because they share a recent common ancestor with an extant free-living red algal species and parasitism has independently arisen over 100 times within this group. Here, we synthesize the relevant hypotheses with respect to how these parasites have proliferated. We also place red algal research in the context of recent developments in understanding the genome evolution of other eukaryotic photosynthesizers turned parasites.}, }
@article {pmid22245358, year = {2012}, author = {Timmermans, MJ and Vogler, AP}, title = {Phylogenetically informative rearrangements in mitochondrial genomes of Coleoptera, and monophyly of aquatic elateriform beetles (Dryopoidea).}, journal = {Molecular phylogenetics and evolution}, volume = {63}, number = {2}, pages = {299-304}, doi = {10.1016/j.ympev.2011.12.021}, pmid = {22245358}, issn = {1095-9513}, mesh = {Animals ; Aquatic Organisms/classification/genetics ; Coleoptera/*classification/*genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Gene Rearrangement ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Sequence Deletion ; }, abstract = {Mitochondrial gene order in Coleoptera has been thought to be conservative but a survey of 60 complete or nearly complete genomes revealed a total of seven different gene rearrangements (deletions, gene order reversals), mainly affecting tRNA genes. All of these were found to be limited to a single taxon or a subclade of Coleoptera. The phylogenetic distribution of a translocation of tRNA(Pro) in three species of elateriform beetles was investigated further by sequencing three nearly complete mitochondrial genomes (Dascillidae, Byrrhidae, Limnichidae) and ten additional individuals for a ∼1370 bp diagnostic fragment spanning the relevant region. Phylogenetic analysis consistently recovered the monophyly of families previously grouped in the contentious superfamily Dryopoidea, a group of approximately 10 beetle families with mainly aquatic lifestyles. The Byrrhidae (moss beetles) were not part of this lineage, although they may be its sister group, to recover the widely accepted Byrrhoidea. The tRNA(Pro) translocation was present in all members of Dryopoidea, but not in any other Elateriformia, providing independent support for this lineage and for a single origin of aquatic habits.}, }
@article {pmid22244915, year = {2012}, author = {Seligmann, H}, title = {An overlapping genetic code for frameshifted overlapping genes in Drosophila mitochondria: antisense antitermination tRNAs UAR insert serine.}, journal = {Journal of theoretical biology}, volume = {298}, number = {}, pages = {51-76}, doi = {10.1016/j.jtbi.2011.12.026}, pmid = {22244915}, issn = {1095-8541}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Codon/genetics ; Drosophila/classification/*genetics ; Genes, Mitochondrial ; Genes, Overlapping/*genetics ; *Genetic Code ; Mitochondria/*genetics ; Molecular Sequence Data ; RNA, Antisense/genetics ; RNA, Transfer/genetics ; Sequence Alignment ; Serine/genetics ; Species Specificity ; }, abstract = {Mitochondrial Drosophila genomes possess at least one antisense antiterminator (suppressor) tRNA matching stop codons UAR: antitermination might enable translation after ribosomal frameshift. Proteins translated from samestrand frameshifted and antisense sequences match 26 Genbank proteins (16 are samestrand). Natural frameshifted sequences match more Genbank proteins than after randomizing synonymous codons, suggesting optimization for overlap coding, but some genes avoid overlap coding. Alignments reassign serine to UAR: translational activity by antitermination tRNAs defines a new, presumably stopless overlapping genetic code. Cloverleaf formation by antisense suppressor tRNAs UAA and UAG coevolve with overlapping samestrand and antisense genes, respectively. Coevolution between suppressor tRNAs and sense as well as antisense overlapping genes increases with relative abundances of corresponding sense and antisense (m)RNAs, strong functional evidence for this parallel coding system. Antisense tRNA abundances converge with computed adaptations of antisense tRNAs for translation. Some short frameshifted coding regions are apparently programmed frameshifts putatively producing altered forms of the known main frame protein; most overlapping genes apparently code for unknown proteins. Overlap coding increases gene density without increasing genome size, but decreases with genome size. Parallel genetic systems coded by an additional mitochondrial genetic code in Drosophila confirm similar phenomena in primate mitochondria.}, }
@article {pmid22238375, year = {2012}, author = {Wanschers, BF and Szklarczyk, R and Pajak, A and van den Brand, MA and Gloerich, J and Rodenburg, RJ and Lightowlers, RN and Nijtmans, LG and Huynen, MA}, title = {C7orf30 specifically associates with the large subunit of the mitochondrial ribosome and is involved in translation.}, journal = {Nucleic acids research}, volume = {40}, number = {9}, pages = {4040-4051}, pmid = {22238375}, issn = {1362-4962}, support = {096919/WT_/Wellcome Trust/United Kingdom ; BB/F011520/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Cell Line, Tumor ; Gene Knockdown Techniques ; Genes, Bacterial ; HEK293 Cells ; Humans ; Mitochondria/genetics ; Mitochondrial Proteins/chemistry/genetics/*physiology ; Molecular Sequence Data ; Nucleotides/metabolism ; Operon ; Phylogeny ; *Protein Biosynthesis ; Protein Structure, Tertiary ; Ribosomal Proteins/chemistry/genetics/*physiology ; Ribosome Subunits, Large, Eukaryotic/*chemistry ; Sequence Analysis, DNA ; }, abstract = {In a comparative genomics study for mitochondrial ribosome-associated proteins, we identified C7orf30, the human homolog of the plant protein iojap. Gene order conservation among bacteria and the observation that iojap orthologs cannot be transferred between bacterial species predict this protein to be associated with the mitochondrial ribosome. Here, we show colocalization of C7orf30 with the large subunit of the mitochondrial ribosome using isokinetic sucrose gradient and 2D Blue Native polyacrylamide gel electrophoresis (BN-PAGE) analysis. We co-purified C7orf30 with proteins of the large subunit, and not with proteins of the small subunit, supporting interaction that is specific to the large mitoribosomal complex. Consistent with this physical association, a mitochondrial translation assay reveals negative effects of C7orf30 siRNA knock-down on mitochondrial gene expression. Based on our data we propose that C7orf30 is involved in ribosomal large subunit function. Sequencing the gene in 35 patients with impaired mitochondrial translation did not reveal disease-causing mutations in C7orf30.}, }
@article {pmid22237536, year = {2012}, author = {Horn, S}, title = {Case study: enrichment of ancient mitochondrial DNA by hybridization capture.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {189-195}, doi = {10.1007/978-1-61779-516-9_22}, pmid = {22237536}, issn = {1940-6029}, mesh = {Animals ; DNA, Mitochondrial/*genetics/*isolation &amp; purification ; *Fossils ; *Gene Library ; High-Throughput Nucleotide Sequencing/*methods ; Mitochondria/genetics ; Phylogeny ; Polymerase Chain Reaction/methods ; Rodentia/*genetics ; Sequence Analysis, DNA/methods ; }, abstract = {In ancient DNA studies focusing on estimating population histories, genetic markers are sequenced from a large number of samples belonging to the same species. Targeting loci of interest using traditional PCR can be time-consuming, in particular when samples are not well preserved and multiple overlapping fragments are required. Here, I describe the process of generating DNA libraries from ancient DNA (aDNA) extracts for high-throughput sequencing. I use a serial in-solution DNA hybridization approach with subsequent bead capture to enrich libraries for the target locus, in this case the mitochondrial control region of ancient beavers (Castor fiber). The resulting sequencing reads are run through quality control filters to obtain reliable consensus sequences. Using these sequences, I construct a phylogenetic tree, which agrees with previously published data regarding phylogeographic relationships among beavers.}, }
@article {pmid22237528, year = {2012}, author = {Mohandesan, E and Prost, S and Hofreiter, M}, title = {Case study: using a nondestructive DNA extraction method to generate mtDNA sequences from historical chimpanzee specimens.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {840}, number = {}, pages = {101-110}, doi = {10.1007/978-1-61779-516-9_14}, pmid = {22237528}, issn = {1940-6029}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/genetics/*isolation &amp; purification ; Mitochondria/genetics ; Museums ; Paleontology/methods ; Pan troglodytes/*genetics ; Phylogeny ; Phylogeography ; Polymerase Chain Reaction/methods ; }, abstract = {A major challenge for ancient DNA (aDNA) studies using museum specimens is that sampling procedures usually involve at least the partial destruction of each specimen used, such as the removal of skin, pieces of bone, or a tooth. Recently, a nondestructive DNA extraction method was developed for the extraction of amplifiable DNA fragments from museum specimens without appreciable damage to the specimen. Here, we examine the utility of this method by attempting DNA extractions from historic (older than 70 years) chimpanzee specimens. Using this method, we PCR-amplified part of the mitochondrial HVR-I region from 65% (56/86) of the specimens from which we attempted DNA extraction. However, we found a high incidence of multiple sequences in individual samples, suggesting substantial cross-contamination among samples, most likely originating from storage and handling in the museums. Consequently, reproducible sequences could be reconstructed from only 79% (44/56) of the successfully extracted samples, even after multiple extractions and amplifications. This resulted in an overall success rate of just over half (44/86 of samples, or 51% success), from which 39 distinct HVR-I haplotypes were recovered. We found a high incidence of C to T changes, arguing for both low concentrations of and substantial damage to the endogenous DNA. This chapter highlights both the potential and the limitations of nondestructive DNA extraction from museum specimens.}, }
@article {pmid22236206, year = {2012}, author = {Luévano-Martínez, LA and Barba-Ostria, C and Araiza-Olivera, D and Chiquete-Félix, N and Guerrero-Castillo, S and Rial, E and Georgellis, D and Uribe-Carvajal, S}, title = {A critical tyrosine residue determines the uncoupling protein-like activity of the yeast mitochondrial oxaloacetate carrier.}, journal = {The Biochemical journal}, volume = {443}, number = {1}, pages = {317-325}, doi = {10.1042/BJ20110992}, pmid = {22236206}, issn = {1470-8728}, mesh = {Amino Acid Motifs ; Anion Transport Proteins/chemistry/genetics/*metabolism ; Hydrogen-Ion Concentration ; Linoleic Acid/pharmacology/physiology ; Membrane Potential, Mitochondrial ; Mitochondria/metabolism ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Oxaloacetic Acid/metabolism ; Phylogeny ; Point Mutation ; Protons ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Sequence Alignment ; Sulfates/metabolism ; Yarrowia/*genetics ; }, abstract = {The mitochondrial Oac (oxaloacetate carrier) found in some fungi and plants catalyses the uptake of oxaloacetate, malonate and sulfate. Despite their sequence similarity, transport specificity varies considerably between Oacs. Indeed, whereas ScOac (Saccharomyces cerevisiae Oac) is a specific anion-proton symporter, the YlOac (Yarrowia lipolytica Oac) has the added ability to transport protons, behaving as a UCP (uncoupling protein). Significantly, we identified two amino acid changes at the matrix gate of YlOac and ScOac, tyrosine to phenylalanine and methionine to leucine. We studied the role of these amino acids by expressing both wild-type and specifically mutated Oacs in an Oac-null S. cerevisiae strain. No phenotype could be associated with the methionine to leucine substitution, whereas UCP-like activity was dependent on the presence of the tyrosine residue normally expressed in the YlOac, i.e. Tyr-ScOac mediated proton transport, whereas Phe-YlOac lost its protonophoric activity. These findings indicate that the UCP-like activity of YlOac is determined by the tyrosine residue at position 146.}, }
@article {pmid22236077, year = {2012}, author = {Smith, DR and Keeling, PJ}, title = {Twenty-fold difference in evolutionary rates between the mitochondrial and plastid genomes of species with secondary red plastids.}, journal = {The Journal of eukaryotic microbiology}, volume = {59}, number = {2}, pages = {181-184}, doi = {10.1111/j.1550-7408.2011.00601.x}, pmid = {22236077}, issn = {1550-7408}, mesh = {Babesia/genetics ; Biological Evolution ; Eukaryota/cytology/*genetics ; *Evolution, Molecular ; *Genome, Mitochondrial ; *Genome, Plastid ; Haptophyta/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Mutation Rate ; Plastids/*genetics ; Rhodophyta/*genetics ; }, abstract = {Within plastid-bearing species, the relative rates of evolution between mitochondrial and plastid genomes are poorly studied, but for the few lineages in which they have been explored, including land plants and green algae, the mitochondrial DNA mutation rate is nearly always estimated to be lower than or equal to that of the plastid DNA. Here, we show that in protists from three distinct lineages with secondary, red algal-derived plastids, the opposite is true: their mitochondrial genomes are evolving 5-30 times faster than their plastid genomes, even when the plastid is nonphotosynthetic. These findings have implications for understanding the origins and evolution of organelle genome architecture and the genes they encode.}, }
@article {pmid22230029, year = {2012}, author = {Highton, R and Hastings, AP and Palmer, C and Watts, R and Hass, CA and Culver, M and Arnold, SJ}, title = {Concurrent speciation in the eastern woodland salamanders (Genus Plethodon): DNA sequences of the complete albumin nuclear and partial mitochondrial 12s genes.}, journal = {Molecular phylogenetics and evolution}, volume = {63}, number = {2}, pages = {278-290}, doi = {10.1016/j.ympev.2011.12.018}, pmid = {22230029}, issn = {1095-9513}, mesh = {Albumins/genetics ; Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Genetic Speciation ; Mitochondria/genetics ; North America ; *Phylogeny ; Salamandridae/*classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {Salamanders of the North American plethodontid genus Plethodon are important model organisms in a variety of studies that depend on a phylogenetic framework (e.g., chemical communication, ecological competition, life histories, hybridization, and speciation), and consequently their systematics has been intensively investigated over several decades. Nevertheless, we lack a synthesis of relationships among the species. In the analyses reported here we use new DNA sequence data from the complete nuclear albumin gene (1818 bp) and the 12s mitochondrial gene (355 bp), as well as published data for four other genes (Wiens et al., 2006), up to a total of 6989 bp, to infer relationships. We relate these results to past systematic work based on morphology, allozymes, and DNA sequences. Although basal relationships show a strong consensus across studies, many terminal relationships remain in flux despite substantial sequencing and other molecular and morphological studies. This systematic instability appears to be a consequence of contemporaneous bursts of speciation in the late Miocene and Pliocene, yielding many closely related extant species in each of the four eastern species groups. Therefore we conclude that many relationships are likely to remain poorly resolved in the face of additional sequencing efforts. On the other hand, the current classification of the 45 eastern species into four species groups is supported. The Plethodon cinereus group (10 species) is the sister group to the clade comprising the other three groups, but these latter groups (Plethodon glutinosus [28 species], Plethodon welleri [5 species], and Plethodon wehrlei [2 species]) probably diverged from each other at approximately the same time.}, }
@article {pmid22227114, year = {2012}, author = {Otranto, D and Latrofa, MS and Brianti, E and Annoscia, G and Parisi, A and Dantas-Torres, F and Bain, O and Gasser, RB}, title = {An assessment of genetic variability in the mitochondrial cytochrome c oxidase subunit 1 gene of Cercopithifilaria sp. (Spirurida, Onchocercidae) from dog and Rhipicephalus sanguineus populations.}, journal = {Molecular and cellular probes}, volume = {26}, number = {2}, pages = {81-89}, doi = {10.1016/j.mcp.2011.12.002}, pmid = {22227114}, issn = {1096-1194}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Dog Diseases/*parasitology ; Dogs ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Greece ; Haplotypes ; Italy ; Mediterranean Region ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Onchocerca/enzymology/*genetics ; Onchocerciasis/parasitology/*veterinary ; Phylogeny ; Phylogeography ; Protein Subunits/*genetics ; Rhipicephalus sanguineus/*parasitology ; Sequence Analysis, DNA ; Skin/parasitology ; Spain ; }, abstract = {This study investigates sequence variation in mitochondrial cytochrome c oxidase subunit 1 gene within Cercopithifilaria sp. recorded recently in Italy. Fourteen sequence types (haplotypes) were characterized for 163 (7.7%) amplicons from 2111 Genomic DNA samples prepared from skin samples from dogs and from Rhipicephalus sanguineus (ticks) from different geographical areas of the Mediterranean basin (i.e., Italy, Spain and Greece). The most prevalent sequence types represented haplotypes I (70.5%) and X (16.0%), followed by haplotype VIII (4.9%) and other 11 haplotypes (8.6%). Three haplotypes (II, V and VI) were found exclusively in ticks. The overall intraspecific nucleotide variation among pcox1 haplotypes ranged from 0.4 to 3.5% (mean = 1.6%), whereas a mean interspecific difference of 9.5% was detected as compared with other onchocercids. Phylogenetic analysis of the nucleotide sequence data showed a clustering of Cercopithifilaria sp. with the other Cercopithifilaria species (with strong statistical support) to the exclusion of other onchocercids. The number of haplotypes identified here might be explained by complex ecology and transmission patterns as well as the high mutation rate of mitochondrial DNA and/or inbreeding associated with hosts and their vectors.}, }
@article {pmid22226162, year = {2012}, author = {Hassanin, A and Delsuc, F and Ropiquet, A and Hammer, C and Jansen van Vuuren, B and Matthee, C and Ruiz-Garcia, M and Catzeflis, F and Areskoug, V and Nguyen, TT and Couloux, A}, title = {Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes.}, journal = {Comptes rendus biologies}, volume = {335}, number = {1}, pages = {32-50}, doi = {10.1016/j.crvi.2011.11.002}, pmid = {22226162}, issn = {1768-3238}, mesh = {Animals ; *Biological Evolution ; Buffaloes ; Camelus ; Cetacea/classification/*genetics/physiology ; Classification ; DNA, Mitochondrial/*genetics ; Databases, Factual ; Fossils ; Genome/*genetics ; Mammals/classification/*genetics/physiology ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Species Specificity ; }, abstract = {The order Cetartiodactyla includes cetaceans (whales, dolphins and porpoises) that are found in all oceans and seas, as well as in some rivers, and artiodactyls (ruminants, pigs, peccaries, hippos, camels and llamas) that are present on all continents, except Antarctica and until recent invasions, Australia. There are currently 332 recognized cetartiodactyl species, which are classified into 132 genera and 22 families. Most phylogenetic studies have focused on deep relationships, and no comprehensive time-calibrated tree for the group has been published yet. In this study, 128 new complete mitochondrial genomes of Cetartiodactyla were sequenced and aligned with those extracted from nucleotide databases. Our alignment includes 14,902 unambiguously aligned nucleotide characters for 210 taxa, representing 183 species, 107 genera, and all cetartiodactyl families. Our mtDNA data produced a statistically robust tree, which is largely consistent with previous classifications. However, a few taxa were found to be para- or polyphyletic, including the family Balaenopteridae, as well as several genera and species. Accordingly, we propose several taxonomic changes in order to render the classification compatible with our molecular phylogeny. In some cases, the results can be interpreted as possible taxonomic misidentification or evidence for mtDNA introgression. The existence of three new cryptic species of Ruminantia should therefore be confirmed by further analyses using nuclear data. We estimate divergence times using Bayesian relaxed molecular clock models. The deepest nodes appeared very sensitive to prior assumptions leading to unreliable estimates, primarily because of the misleading effects of rate heterogeneity, saturation and divergent outgroups. In addition, we detected that Whippomorpha contains slow-evolving taxa, such as large whales and hippos, as well as fast-evolving taxa, such as river dolphins. Our results nevertheless indicate that the evolutionary history of cetartiodactyls was punctuated by four main phases of rapid radiation during the Cenozoic era: the sudden occurrence of the three extant lineages within Cetartiodactyla (Cetruminantia, Suina and Tylopoda); the basal diversification of Cetacea during the Early Oligocene; and two radiations that involve Cetacea and Pecora, one at the Oligocene/Miocene boundary and the other in the Middle Miocene. In addition, we show that the high species diversity now observed in the families Bovidae and Cervidae accumulated mainly during the Late Miocene and Plio-Pleistocene.}, }
@article {pmid22222877, year = {2012}, author = {Peris, D and Belloch, C and Lopandić, K and Álvarez-Pérez, JM and Querol, A and Barrio, E}, title = {The molecular characterization of new types of Saccharomyces cerevisiae×S. kudriavzevii hybrid yeasts unveils a high genetic diversity.}, journal = {Yeast (Chichester, England)}, volume = {29}, number = {2}, pages = {81-91}, doi = {10.1002/yea.2891}, pmid = {22222877}, issn = {1097-0061}, mesh = {Base Sequence ; Chimera ; DNA, Fungal/genetics ; Electron Transport Complex IV/genetics ; Fungal Proteins/genetics ; *Genetic Variation ; Genome, Fungal/*genetics ; Haplotypes ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Saccharomyces/*genetics ; Saccharomyces cerevisiae/classification/*genetics ; Sequence Analysis, DNA ; Wine/microbiology ; }, abstract = {New double- and triple-hybrid Saccharomyces yeasts were characterized using PCR-restriction fragment length polymorphism of 35 nuclear genes, located on different chromosome arms, and the sequencing of one nuclear and one mitochondrial gene. Most of these new hybrids were originally isolated from fermentations; however, two of them correspond to clinical and dietary supplement isolates. This is the first time that the presence of double-hybrid S. cerevisiae×S. kudriavzevii in non-fermentative substrates has been reported and investigated. Phylogenetic analysis of the MET6 nuclear gene confirmed the double or triple parental origin of the new hybrids. Restriction analysis of gene regions in these hybrids revealed a high diversity of genome types. From these molecular characterizations, a reduction of the S. kudriavzevii fraction of the hybrid genomes is observed in most hybrids. Mitochondrial inheritance in hybrids was deduced from the analysis of mitochondrial COX2 gene sequences, which showed that most hybrids received the mitochondrial genome from the S. kudriavzevii parent. However, two strains inherited a S. cerevisiae COX2, being the first report of S. cerevisiae×S. kudriavzevii hybrids with S. cerevisiae mitochondrial genomes. These two strains are those showing a higher S. kudriavzevii nuclear genome reduction, especially in the wine hybrid AMH. This may be due to the release of selective pressures acting on the other hybrids to maintain kudriavzevii mitochondria-interacting genes.}, }
@article {pmid22219516, year = {2012}, author = {Csiszar, A and Podlutsky, A and Podlutskaya, N and Sonntag, WE and Merlin, SZ and Philipp, EE and Doyle, K and Davila, A and Recchia, FA and Ballabh, P and Pinto, JT and Ungvari, Z}, title = {Testing the oxidative stress hypothesis of aging in primate fibroblasts: is there a correlation between species longevity and cellular ROS production?.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {67}, number = {8}, pages = {841-852}, pmid = {22219516}, issn = {1758-535X}, support = {AT006526/AT/NCCIH NIH HHS/United States ; AG022873/AG/NIA NIH HHS/United States ; AG025063/AG/NIA NIH HHS/United States ; P01 AG011370/AG/NIA NIH HHS/United States ; R01 HL108213/HL/NHLBI NIH HHS/United States ; R01 AT006526/AT/NCCIH NIH HHS/United States ; AG031085/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Cell Line ; Cellular Senescence/*physiology ; Fibroblasts/*physiology ; Haplorhini/physiology ; Hominidae/physiology ; Humans ; Longevity/*physiology ; Mitochondria/metabolism ; Oxidative Stress/*physiology ; Oxygen/metabolism ; Primates/*physiology ; Reactive Oxygen Species/*metabolism ; Species Specificity ; }, abstract = {The present study was conducted to test predictions of the oxidative stress theory of aging assessing reactive oxygen species production and oxidative stress resistance in cultured fibroblasts from 13 primate species ranging in body size from 0.25 to 120 kg and in longevity from 20 to 90 years. We assessed both basal and stress-induced reactive oxygen species production in fibroblasts from five great apes (human, chimpanzee, bonobo, gorilla, and orangutan), four Old World monkeys (baboon, rhesus and crested black macaques, and patas monkey), three New World monkeys (common marmoset, red-bellied tamarin, and woolly monkey), and one lemur (ring-tailed lemur). Measurements of cellular MitoSox fluorescence, an indicator of mitochondrial superoxide (O2(·-)) generation, showed an inverse correlation between longevity and steady state or metabolic stress-induced mitochondrial O2(·-) production, but this correlation was lost when the effects of body mass were removed, and the data were analyzed using phylogenetically independent contrasts. Fibroblasts from longer-lived primate species also exhibited superior resistance to H(2)O(2)-induced apoptotic cell death than cells from shorter-living primates. After correction for body mass and lack of phylogenetic independence, this correlation, although still discernible, fell short of significance by regression analysis. Thus, increased longevity in this sample of primates is not causally associated with low cellular reactive oxygen species generation, but further studies are warranted to test the association between increased cellular resistance to oxidative stressor and primate longevity.}, }
@article {pmid22214610, year = {2012}, author = {Kalifa, L and Quintana, DF and Schiraldi, LK and Phadnis, N and Coles, GL and Sia, RA and Sia, EA}, title = {Mitochondrial genome maintenance: roles for nuclear nonhomologous end-joining proteins in Saccharomyces cerevisiae.}, journal = {Genetics}, volume = {190}, number = {3}, pages = {951-964}, pmid = {22214610}, issn = {1943-2631}, support = {F31 GM078700/GM/NIGMS NIH HHS/United States ; }, mesh = {Antigens, Nuclear/genetics/metabolism ; Cell Nucleus/genetics/metabolism ; DNA Breaks, Double-Stranded ; DNA End-Joining Repair/*physiology ; DNA Repair ; DNA, Mitochondrial/*metabolism ; DNA-Binding Proteins/genetics/*metabolism ; Deoxyribonucleases, Type II Site-Specific/metabolism ; Endodeoxyribonucleases/genetics/metabolism ; Exodeoxyribonucleases/genetics/metabolism ; Gene Order ; Genome, Mitochondrial ; Ku Autoantigen ; Mitochondria/genetics/metabolism ; Models, Genetic ; Mutation Rate ; Nuclear Proteins/*metabolism ; Phenotype ; Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; Saccharomyces cerevisiae/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Sequence Deletion ; Signal Transduction ; }, abstract = {Mitochondrial DNA (mtDNA) deletions are associated with sporadic and inherited diseases and age-associated neurodegenerative disorders. Approximately 85% of mtDNA deletions identified in humans are flanked by short directly repeated sequences; however, mechanisms by which these deletions arise are unknown. A limitation in deciphering these mechanisms is the essential nature of the mitochondrial genome in most living cells. One exception is budding yeast, which are facultative anaerobes and one of the few organisms for which directed mtDNA manipulation is possible. Using this model system, we have developed a system to simultaneously monitor spontaneous direct-repeat-mediated deletions (DRMDs) in the nuclear and mitochondrial genomes. In addition, the mitochondrial DRMD reporter contains a unique KpnI restriction endonuclease recognition site that is not present in otherwise wild-type (WT) mtDNA. We have expressed KpnI fused to a mitochondrial localization signal to induce a specific mitochondrial double-strand break (mtDSB). Here we report that loss of the MRX (Mre11p, Rad50p, Xrs2p) and Ku70/80 (Ku70p, Ku80p) complexes significantly impacts the rate of spontaneous deletion events in mtDNA, and these proteins contribute to the repair of induced mtDSBs. Furthermore, our data support homologous recombination (HR) as the predominant pathway by which mtDNA deletions arise in yeast, and suggest that the MRX and Ku70/80 complexes are partially redundant in mitochondria.}, }
@article {pmid22209780, year = {2012}, author = {Halsne, R and Esbensen, Y and Wang, W and Scheffler, K and Suganthan, R and Bjørås, M and Eide, L}, title = {Lack of the DNA glycosylases MYH and OGG1 in the cancer prone double mutant mouse does not increase mitochondrial DNA mutagenesis.}, journal = {DNA repair}, volume = {11}, number = {3}, pages = {278-285}, doi = {10.1016/j.dnarep.2011.12.001}, pmid = {22209780}, issn = {1568-7856}, mesh = {Animals ; Cell Respiration/genetics ; DNA Damage/genetics ; DNA Glycosylases/*deficiency/metabolism ; DNA, Mitochondrial/*genetics ; Mice ; Mice, Inbred C57BL ; Mice, Mutant Strains ; Mutagenesis/*genetics ; Mutation/*genetics ; Mutation Rate ; Neoplasms/*enzymology/*genetics ; Organ Specificity/genetics ; }, abstract = {Reactive oxygen species (ROS) are formed as natural byproducts during aerobic metabolism and readily induce premutagenic base lesions in the DNA. The 8-oxoguanine DNA glycosylase (OGG1) and MutY homolog 1 (MYH) synergistically prevent mutagenesis and cancer formation in mice. Their localization in the mitochondria as well as in the nucleus suggests that mutations in mitochondrial DNA (mtDNA) contribute to the carcinogenesis in the myh[-]/[-]/ogg1[-]/[-] double knockout mouse. In order to test this hypothesis, we analyzed mtDNA mutagenesis and mitochondrial function in young (1month) and adult (6months) wt and myh[-]/[-]/ogg1[-]/[-] mice. To our surprise, the absence of OGG1 and MYH had no impact on mtDNA mutation rates in these mice, even at the onset of cancer. This indicates that mtDNA mutagenesis is not responsible for the carcinogenesis of myh[-]/[-]/ogg1[-]/[-] mice. In line with these results, mitochondrial function was unaffected in the cancerous tissues liver and lung, whereas a significant reduction in respiration capacity was observed in brain mitochondria from the adult myh[-]/[-]/ogg1[-]/[-] mouse. The reduced respiration capacity correlated with a specific reduction (-25%) in complex I biochemical activity in brain mitochondria. Our results demonstrate that mtDNA mutations are not associated with cancer development in myh[-]/[-]/ogg1[-]/[-] mice, and that impairment of mitochondrial function in brain could be linked to nuclear DNA mutations in this strain. OGG1 and MYH appear to be dispensable for antimutator function in mitochondria.}, }
@article {pmid22203571, year = {2011}, author = {Choi, YJ and Thines, M and Han, JG and Shin, HD}, title = {Mitochondrial phylogeny reveals intraspecific variation in Peronospora effusa, the spinach downy mildew pathogen.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {49}, number = {6}, pages = {1039-1043}, pmid = {22203571}, issn = {1976-3794}, mesh = {*Genetic Variation ; Mitochondria/*genetics ; Molecular Sequence Data ; Peronospora/*classification/genetics/*isolation &amp; purification ; *Phylogeny ; Plant Diseases/*parasitology ; Spinacia oleracea/*parasitology ; }, abstract = {Since about two hundred years, downy mildew caused by Peronospora effusa is probably the most economically important disease of spinach (Spinacia oleracea). However, there is no information on the global phylogeographic structure of the pathogen and thus it is unclear whether a single genotype occurs worldwide or whether some local genetic variation exists. To investigate the genetic variability of this pathogen, a sequence analysis of two partial mitochondrial DNA genes, cox2 and nad1, was carried out. Thirty-three specimens of Peronospora effusa from four continents were analyzed, including samples from Australia, China, Japan, Korea, Mexico, Russia, Sweden, and the USA. Despite the potential anthropogenic admixture of genotypes, a phylogeographic pattern was observed, which corresponds to two major groups, an Asian/Oceanian clade and another group, which includes American/European specimens. Notably, two of six Japanese specimens investigated did not belong to the Asian/Oceanian clade, but were identical to three of the specimens from the USA, suggestive of a recent introduction from the USA to Japan. As similar introduction events may be occurring as a result of the globalised trade with plant and seed material, a better knowledge of the phylogeographic distribution of pathogens is highly warranted for food security purposes.}, }
@article {pmid22202891, year = {2011}, author = {Samach, A and Melamed-Bessudo, C and Avivi-Ragolski, N and Pietrokovski, S and Levy, AA}, title = {Identification of plant RAD52 homologs and characterization of the Arabidopsis thaliana RAD52-like genes.}, journal = {The Plant cell}, volume = {23}, number = {12}, pages = {4266-4279}, pmid = {22202891}, issn = {1532-298X}, mesh = {Amino Acid Sequence ; Arabidopsis/classification/drug effects/*genetics/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Cell Nucleus/genetics/metabolism ; Chloroplasts/genetics/metabolism ; Computational Biology ; Evolution, Molecular ; Gene Duplication ; Gene Expression Regulation, Plant ; Genes, Plant ; Genetic Complementation Test ; Homologous Recombination ; Mitochondria/genetics/metabolism ; Mitomycin/pharmacology ; Open Reading Frames ; Phylogeny ; Protein Isoforms/genetics/metabolism ; RNA Interference ; RNA Splicing ; Rad51 Recombinase/*genetics/metabolism ; Rad52 DNA Repair and Recombination Protein/*genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Sequence Alignment ; }, abstract = {RADiation sensitive52 (RAD52) mediates RAD51 loading onto single-stranded DNA ends, thereby initiating homologous recombination and catalyzing DNA annealing. RAD52 is highly conserved among eukaryotes, including animals and fungi. This article reports that RAD52 homologs are present in all plants whose genomes have undergone extensive sequencing. Computational analyses suggest a very early RAD52 gene duplication, followed by later lineage-specific duplications, during the evolution of higher plants. Plant RAD52 proteins have high sequence similarity to the oligomerization and DNA binding N-terminal domain of RAD52 proteins. Remarkably, the two identified Arabidopsis thaliana RAD52 genes encode four open reading frames (ORFs) through differential splicing, each of which specifically localized to the nucleus, mitochondria, or chloroplast. The A. thaliana RAD52-1A ORF provided partial complementation to the yeast rad52 mutant. A. thaliana mutants and RNA interference lines defective in the expression of RAD52-1 or RAD52-2 showed reduced fertility, sensitivity to mitomycin C, and decreased levels of intrachromosomal recombination compared with the wild type. In summary, computational and experimental analyses provide clear evidence for the presence of functional RAD52 DNA-repair homologs in plants.}, }
@article {pmid22200666, year = {2012}, author = {Stael, S and Wurzinger, B and Mair, A and Mehlmer, N and Vothknecht, UC and Teige, M}, title = {Plant organellar calcium signalling: an emerging field.}, journal = {Journal of experimental botany}, volume = {63}, number = {4}, pages = {1525-1542}, pmid = {22200666}, issn = {1460-2431}, support = {P 19825/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Calcium/*metabolism ; Calcium Signaling/*physiology ; Organelles/*metabolism ; Plants/*metabolism ; }, abstract = {This review provides a comprehensive overview of the established and emerging roles that organelles play in calcium signalling. The function of calcium as a secondary messenger in signal transduction networks is well documented in all eukaryotic organisms, but so far existing reviews have hardly addressed the role of organelles in calcium signalling, except for the nucleus. Therefore, a brief overview on the main calcium stores in plants-the vacuole, the endoplasmic reticulum, and the apoplast-is provided and knowledge on the regulation of calcium concentrations in different cellular compartments is summarized. The main focus of the review will be the calcium handling properties of chloroplasts, mitochondria, and peroxisomes. Recently, it became clear that these organelles not only undergo calcium regulation themselves, but are able to influence the Ca(2+) signalling pathways of the cytoplasm and the entire cell. Furthermore, the relevance of recent discoveries in the animal field for the regulation of organellar calcium signals will be discussed and conclusions will be drawn regarding potential homologous mechanisms in plant cells. Finally, a short overview on bacterial calcium signalling is included to provide some ideas on the question where this typically eukaryotic signalling mechanism could have originated from during evolution.}, }
@article {pmid22197826, year = {2012}, author = {Rupp, A and Morrison, I and Barrie, JA and Halstead, SK and Townson, KH and Greenshields, KN and Willison, HJ}, title = {Motor nerve terminal destruction and regeneration following anti-ganglioside antibody and complement-mediated injury: an in and ex vivo imaging study in the mouse.}, journal = {Experimental neurology}, volume = {233}, number = {2}, pages = {836-848}, doi = {10.1016/j.expneurol.2011.12.010}, pmid = {22197826}, issn = {1090-2430}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Antibodies, Monoclonal/*administration &amp; dosage/toxicity ; Autoantibodies/*administration &amp; dosage/toxicity ; Complement System Proteins/*toxicity ; Gangliosides/*immunology ; Humans ; Mice ; Mice, Transgenic ; Motor Neurons/immunology/*pathology ; Neck Muscles/immunology/pathology ; Neuromuscular Junction/immunology/*injuries/pathology ; Presynaptic Terminals/*immunology ; Regeneration/immunology/*physiology ; }, abstract = {Both the neural and glial components of the neuromuscular junction (NMJ) have been identified as potential sites for anti-ganglioside antibody (Ab) binding and complement-mediated injury in murine models for the human peripheral nerve disorder Guillain-Barré syndrome (GBS). Some patients suffering from the acute motor axonal neuropathy (AMAN) forms of GBS recover very rapidly from paralysis; it has been proposed that in these cases the injury was restricted to the distal motor axons and nerve terminals (NTs) which are able to regenerate over a very short time-frame. To test this hypothesis, the ventral neck muscles of mice (n=45) expressing cytosolic fluorescent proteins in their axons (CFP) and Schwann cells (GFP) were subjected to a single topical application of anti-ganglioside Ab followed by a source of complement. Group A (n=15) received Ab that selectively bound to the NTs, group B (n=15) received Abs that bound both to the NTs and the perisynaptic Schwann cells (pSCs) and group C (control animals; n=15) only received complement. Evolution of the injury was documented by in vivo imaging, and following euthanasia the muscles were reimaged ex vivo both quantitatively and qualitatively, either immediately, or after 1, 2, 3 or 5 days of regeneration (each n=3 per group). Within 15 minutes of complement application, a rapid loss of CFP overlying the NMJ could be seen; in group A, the GFP signal remained unchanged, whereas in group B the GFP signal was also lost. In group C no changes to either CFP or GFP were observed. At 24 h, 6% of the superficial NMJs in group A and 12% of the NMJs in group B exhibited CFP. In both groups, CFP returned within the next five days (group A: 93.5%, group B: 94%; p=0.739), with the recovery of CFP being preceded by a return of GFP-positive cells overlying the NMJ in group B. Auxiliary investigations revealed that the loss of CFP at the NMJ correlated with a loss of NT neurofilament immuno-reactivity and a return of CFP at the NMJ was accompanied by a return of neurofilament. In ultrastructural investigations, injured NTs were electron lucent and exhibited damaged mitochondria, a loss of filaments and a loss of synaptic vesicles. The examination of muscles after five days of regeneration revealed physiological NT-profiles. The results described above indicate that following a single anti-ganglioside Ab-mediated and complement-mediated attack, independent of whether there are healthy and mature perisynaptic Schwann cells overlying the NMJ, the murine NT is capable of recovering both its architectural and axolemmal integrity very rapidly. This data supports the notion that an equivalent mechanism may account for the rapid recovery seen in some clinical cases of AMAN.}, }
@article {pmid22194213, year = {2011}, author = {Yu, DB and Chen, R and Kaleri, HA and Jiang, BC and Xu, HX and Du, WX}, title = {Testing the utility of mitochondrial cytochrome oxidase subunit 1 sequences for phylogenetic estimates of relationships between crane (Grus) species.}, journal = {Genetics and molecular research : GMR}, volume = {10}, number = {4}, pages = {4048-4062}, doi = {10.4238/2011.December.21.7}, pmid = {22194213}, issn = {1676-5680}, mesh = {Animals ; Birds/*genetics/metabolism ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry ; Electron Transport Complex IV/*genetics/metabolism ; Evolution, Molecular ; Genes, Mitochondrial ; Genetic Variation ; Mitochondria/*enzymology/metabolism ; *Phylogeny ; Protein Subunits/genetics ; }, abstract = {Morphology and biogeography are widely used in animal taxonomy. Recent study has suggested that a DNA-based identification system, using a 648-bp portion of the mitochondrial gene cytochrome oxidase subunit 1 (CO1), also known as the barcoding gene, can aid in the resolution of inferences concerning phylogenetic relationships and for identification of species. However, the effectiveness of DNA barcoding for identifying crane species is unknown. We amplified and sequenced 894-bp DNA fragments of CO1 from Grus japonensis (Japanese crane), G. grus (Eurasian crane), G. monacha (hooded crane), G. canadensis (sandhill crane), G. leucogeranus (Siberian crane), and Balearica pavonina (crowned crane), along with those of 15 species obtained from GenBank and DNA barcoding, to construct four algorithms using Tringa stagnatilis, Scolopax rusticola, and T. erythropus as outgroups. The four phylum profiles showed good resolution of the major taxonomic groups. We concluded that reconstruction of the molecular phylogenetic tree can be helpful for classification and that CO1 sequences are suitable for studying the molecular evolution of cranes. Although support for several deeper branches was limited, CO1 data gave remarkably good separations, especially considering that our analysis was based on just a fragment of the gene and that CO1 has generally been viewed as useful only for resolving shallow divergences.}, }
@article {pmid22192748, year = {2011}, author = {Li, S and Rousseau, D}, title = {[ATAD3, a vital membrane-bound mitochondrial ATPase involved in tumor progression].}, journal = {Medecine sciences : M/S}, volume = {27}, number = {12}, pages = {1089-1095}, doi = {10.1051/medsci/20112712015}, pmid = {22192748}, issn = {0767-0974}, mesh = {ATPases Associated with Diverse Cellular Activities ; Adenosine Triphosphatases/genetics/metabolism/*physiology ; Animals ; Disease Progression ; Humans ; Membrane Proteins/genetics/metabolism/*physiology ; Mitochondrial Membranes/enzymology/metabolism/physiology ; Mitochondrial Proteins/genetics/metabolism/*physiology ; Models, Biological ; Neoplasms/*genetics/metabolism/*pathology ; Phylogeny ; Primates ; }, abstract = {ATAD3 (ATPase family AAA domain-containing protein 3) is a mitochondrial membrane bound ATPase whose function has not yet been discovered but its role is essential for the embryonic development. The ATAD3 gene exists since the pluri-cellular organisms with specialized tissues and remains unique until vertebrates. In primates and humans, two other genes have appeared (called ATAD3B and ATAD3C versus ATAD3A the ancestral gene). ATAD3 knock down in different non-transformed cell lines is associated with drastic changes in the mitochondrial network, inhibition of proliferation and modification of the functional interactions between mitochondria and endoplasmic reticulum. However, the analysis of the functions of ATAD3A and ATAD3B in different human cancer cell lines shows on the contrary that they can have anti-proliferative effects and induce chemoresistant properties. ATAD3 may therefore be implicated in an unknown but essential and growth-linked mitochondrial function existing since pluri-cellular -organization and involved in tumorigenesis.}, }
@article {pmid22187346, year = {2012}, author = {Mao, HT and Wang, DH and Lan, Z and Zhou, H and Yang, WX}, title = {Gene expression profiles of prohibitin in testes of Octopus tankahkeei (ot-phb) revealing its possible role during spermiogenesis.}, journal = {Molecular biology reports}, volume = {39}, number = {5}, pages = {5519-5528}, pmid = {22187346}, issn = {1573-4978}, mesh = {Animals ; *Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Male ; Models, Molecular ; Molecular Sequence Data ; Octopodiformes/*genetics/growth &amp; development ; Phylogeny ; Prohibitins ; Protein Structure, Tertiary ; RNA, Messenger/genetics/metabolism ; Repressor Proteins/chemistry/*genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Spermatogenesis/*genetics ; Testis/*metabolism ; Time Factors ; Xenopus Proteins ; }, abstract = {Prohibitin is essential for intracellular homeostasis and stabilization of mitochondrial respiratory chain complexes. To explore its functions during spermiogenesis of Octopus tankahkeei (O. tankahkeei), we have cloned and sequenced the cDNA of this mammalian PHB homologue (termed ot-PHB) from the testes of O. tankahkeei. The 1165 bp ot-phb cDNA contains a 100 bp 5' UTR, a 882 bp open reading frame and a 183 bp 3' UTR. The putative ot-PHB protein owns a transmembrane domain from 6 to 31 amino acid (aa) and a putative PHB domain from 26 to 178 aa. Protein alignment demonstrated that ot-PHB had 73.3, 73.6, 74.0, 75.1, and 45.4% identity with its homologues in Homo sapiens, Mus muculus, Danio rerio, Xenopus tropicalis and Trypanosoma brucei, respectively. Tissue distribution profile analysis revealed its presence in all the tissues examined. In situ hybridization in spermiogenic cells demonstrated that ot-phb was expressed moderately at the beginning of the spermiogenesis. The abundance of transcripts increased in intermediate spermatids and in drastically remodeling final spermatids. In mature spermatozoa, the residuary transcripts concentrated around the chondriosomal mantle where mitochondria assemble around. In summary, the expression of ot-phb during spermiogenesis implicates a potential function of this protein during mitochondrial ubiquitination. It is the first time to implicate the role of prohibitin in cephalopod spermiogenesis.}, }
@article {pmid22178219, year = {2012}, author = {Skonieczna, K and Malyarchuk, BA and Grzybowski, T}, title = {The landscape of mitochondrial DNA variation in human colorectal cancer on the background of phylogenetic knowledge.}, journal = {Biochimica et biophysica acta}, volume = {1825}, number = {2}, pages = {153-159}, doi = {10.1016/j.bbcan.2011.11.004}, pmid = {22178219}, issn = {0006-3002}, mesh = {Colorectal Neoplasms/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Neoplasm/*genetics ; Genetic Variation ; Genome, Mitochondrial ; Humans ; Mitochondria/*genetics/pathology ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Recently, an increasing number of studies indicate that mutations in mitochondrial genome may contribute to cancer development or metastasis. Hence, it is important to determine whether the mitochondrial DNA might be a good, clinically applicable marker of cancer. This review describes hereditary as well as somatic mutations reported in mitochondrial DNA of colorectal cancer cells. We showed here that the entire mitochondrial genome mutational spectra are different in colorectal cancer and non-tumor cells. We also placed the described mutations on the phylogenetic context, which highlighted the recurrent problem of data quality. Therefore, the most important rules for adequately assessing the quality of mitochondrial DNA sequence analysis in cancer have been summarized. As follows from this review, neither the reliable spectrum of mtDNA somatic mutations nor the association between hereditary mutations and colorectal cancer risk have been resolved. This indicates that only high resolution studies on mtDNA variability, followed by a proper data interpretation employing phylogenetic knowledge may finally verify the utility of mtDNA sequence (if any) in clinical practice.}, }
@article {pmid22174833, year = {2011}, author = {Sokolowski, B and Orchard, S and Harvey, M and Sridhar, S and Sakai, Y}, title = {Conserved BK channel-protein interactions reveal signals relevant to cell death and survival.}, journal = {PloS one}, volume = {6}, number = {12}, pages = {e28532}, pmid = {22174833}, issn = {1932-6203}, support = {R01 DC004295/DC/NIDCD NIH HHS/United States ; FP7-HEALTH-2007-223411/FP/OFP OASH HHS/United States ; R01DC004295/DC/NIDCD NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Cell Death ; Cell Survival ; Chickens ; Cochlea/*cytology ; Conserved Sequence ; Electrophoresis, Gel, Two-Dimensional ; Humans ; Immunoprecipitation ; Large-Conductance Calcium-Activated Potassium Channels/chemistry/*metabolism ; Mice ; Molecular Sequence Data ; Phylogeny ; Prohibitins ; Protein Binding ; Protein Interaction Maps ; Protein Transport ; RNA, Small Interfering/metabolism ; *Signal Transduction ; Species Specificity ; Subcellular Fractions/metabolism ; }, abstract = {The large-conductance Ca(2+)-activated K(+) (BK) channel and its β-subunit underlie tuning in non-mammalian sensory or hair cells, whereas in mammals its function is less clear. To gain insights into species differences and to reveal putative BK functions, we undertook a systems analysis of BK and BK-Associated Proteins (BKAPS) in the chicken cochlea and compared these results to other species. We identified 110 putative partners from cytoplasmic and membrane/cytoskeletal fractions, using a combination of coimmunoprecipitation, 2-D gel, and LC-MS/MS. Partners included 14-3-3γ, valosin-containing protein (VCP), stathmin (STMN), cortactin (CTTN), and prohibitin (PHB), of which 16 partners were verified by reciprocal coimmunoprecipitation. Bioinformatics revealed binary partners, the resultant interactome, subcellular localization, and cellular processes. The interactome contained 193 proteins involved in 190 binary interactions in subcellular compartments such as the ER, mitochondria, and nucleus. Comparisons with mice showed shared hub proteins that included N-methyl-D-aspartate receptor (NMDAR) and ATP-synthase. Ortholog analyses across six species revealed conserved interactions involving apoptosis, Ca(2+) binding, and trafficking, in chicks, mice, and humans. Functional studies using recombinant BK and RNAi in a heterologous expression system revealed that proteins important to cell death/survival, such as annexinA5, γ-actin, lamin, superoxide dismutase, and VCP, caused a decrease in BK expression. This revelation led to an examination of specific kinases and their effectors relevant to cell viability. Sequence analyses of the BK C-terminus across 10 species showed putative binding sites for 14-3-3, RAC-α serine/threonine-protein kinase 1 (Akt), glycogen synthase kinase-3β (GSK3β) and phosphoinositide-dependent kinase-1 (PDK1). Knockdown of 14-3-3 and Akt caused an increase in BK expression, whereas silencing of GSK3β and PDK1 had the opposite effect. This comparative systems approach suggests conservation in BK function across different species in addition to novel functions that may include the initiation of signals relevant to cell death/survival.}, }
@article {pmid22174774, year = {2011}, author = {Hirst, MB and Kita, KN and Dawson, SC}, title = {Uncultivated microbial eukaryotic diversity: a method to link ssu rRNA gene sequences with morphology.}, journal = {PloS one}, volume = {6}, number = {12}, pages = {e28158}, pmid = {22174774}, issn = {1932-6203}, support = {R01 AI077571/AI/NIAID NIH HHS/United States ; T32 GM007377/GM/NIGMS NIH HHS/United States ; 3R01AI077571-01A1S1/AI/NIAID NIH HHS/United States ; }, mesh = {Actin Cytoskeleton/metabolism ; Bacteria/*genetics ; Base Sequence ; *Biodiversity ; Cilia/metabolism ; Eukaryota/*cytology/*genetics ; Genes, rRNA/*genetics ; Hydrogen/metabolism ; In Situ Hybridization, Fluorescence ; Microtubules/metabolism ; Mitochondria/metabolism ; Phylogeny ; RNA, Ribosomal/*genetics ; Ribosome Subunits, Small/*genetics ; Staining and Labeling ; }, abstract = {Protists have traditionally been identified by cultivation and classified taxonomically based on their cellular morphologies and behavior. In the past decade, however, many novel protist taxa have been identified using cultivation independent ssu rRNA sequence surveys. New rRNA "phylotypes" from uncultivated eukaryotes have no connection to the wealth of prior morphological descriptions of protists. To link phylogenetically informative sequences with taxonomically informative morphological descriptions, we demonstrate several methods for combining whole cell rRNA-targeted fluorescent in situ hybridization (FISH) with cytoskeletal or organellar immunostaining. Either eukaryote or ciliate-specific ssu rRNA probes were combined with an anti-α-tubulin antibody or phalloidin, a common actin stain, to define cytoskeletal features of uncultivated protists in several environmental samples. The eukaryote ssu rRNA probe was also combined with Mitotracker® or a hydrogenosomal-specific anti-Hsp70 antibody to localize mitochondria and hydrogenosomes, respectively, in uncultivated protists from different environments. Using rRNA probes in combination with immunostaining, we linked ssu rRNA phylotypes with microtubule structure to describe flagellate and ciliate morphology in three diverse environments, and linked Naegleria spp. to their amoeboid morphology using actin staining in hay infusion samples. We also linked uncultivated ciliates to morphologically similar Colpoda-like ciliates using tubulin immunostaining with a ciliate-specific rRNA probe. Combining rRNA-targeted FISH with cytoskeletal immunostaining or stains targeting specific organelles provides a fast, efficient, high throughput method for linking genetic sequences with morphological features in uncultivated protists. When linked to phylotype, morphological descriptions of protists can both complement and vet the increasing number of sequences from uncultivated protists, including those of novel lineages, identified in diverse environments.}, }
@article {pmid22173057, year = {2012}, author = {M Santos, J and Graindorge, A and Soldati-Favre, D}, title = {New insights into parasite rhomboid proteases.}, journal = {Molecular and biochemical parasitology}, volume = {182}, number = {1-2}, pages = {27-36}, doi = {10.1016/j.molbiopara.2011.11.010}, pmid = {22173057}, issn = {1872-9428}, mesh = {Animals ; Apicomplexa/chemistry/classification/*enzymology ; Catalytic Domain ; Cell Membrane/chemistry/enzymology ; Enzyme Activation ; Membrane Proteins/chemistry ; Mitochondria/chemistry ; Mitochondrial Proteins/chemistry ; Peptide Hydrolases/*chemistry ; Phylogeny ; Protozoan Proteins/*chemistry/classification ; *Signal Transduction ; Substrate Specificity ; }, abstract = {The rhomboid-like proteins constitute a large family of intramembrane serine proteases that are present in all branches of life. First studied in Drosophila, these enzymes catalyse the release of the active forms of proteins from the membrane and hence trigger signalling events. In protozoan parasites, a limited number of rhomboid-like proteases have been investigated and some of them are associated to pathogenesis. In Apicomplexans, rhomboid-like protease activity is involved in shedding adhesins from the surface of the zoites during motility and host cell entry. Recently, a Toxoplasma gondii rhomboid was also implicated in an intracellular signalling mechanism leading to parasite proliferation. In Entamoeba histolytica, the capacity to adhere to host cells and to phagocytose cells is potentiated by a rhomboid-like protease. Survey of a small number of protozoan parasite genomes has uncovered species-specific rhomboid-like protease genes, many of which are predicted to encode inactive enzymes. Functional investigation of the rhomboid-like proteases in other protozoan parasites will likely uncover novel and unexpected implications for this family of proteases.}, }
@article {pmid22165826, year = {2011}, author = {Xu, J and Fonseca, DM}, title = {One-way sequencing of multiple amplicons from tandem repetitive mitochondrial DNA control region.}, journal = {Mitochondrial DNA}, volume = {22}, number = {5-6}, pages = {155-158}, doi = {10.3109/19401736.2011.636434}, pmid = {22165826}, issn = {1940-1744}, mesh = {Aedes/genetics ; Animals ; Base Sequence ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; Mitochondria/chemistry ; Polymerase Chain Reaction/methods ; *Repetitive Sequences, Nucleic Acid ; Sequence Analysis/*methods ; }, abstract = {Repetitive DNA sequences not only exist abundantly in eukaryotic nuclear genomes, but also occur as tandem repeats in many animal mitochondrial DNA (mtDNA) control regions. Due to concerted evolution, these repetitive sequences are highly similar or even identical within a genome. When long repetitive regions are the targets of amplification for the purpose of sequencing, multiple amplicons may result if one primer has to be located inside the repeats. Here, we show that, without separating these amplicons by gel purification or cloning, directly sequencing the mitochondrial repeats with the primer outside repetitive region is feasible and efficient. We exemplify it by sequencing the mtDNA control region of the mosquito Aedes albopictus, which harbors typical large tandem DNA repeats. This one-way sequencing strategy is optimal for population surveys.}, }
@article {pmid22162179, year = {2012}, author = {Castandet, B and Araya, A}, title = {The nucleocytoplasmic conflict, a driving force for the emergence of plant organellar RNA editing.}, journal = {IUBMB life}, volume = {64}, number = {2}, pages = {120-125}, doi = {10.1002/iub.581}, pmid = {22162179}, issn = {1521-6551}, mesh = {Biological Evolution ; Cell Nucleus/genetics ; Chloroplasts/*genetics/metabolism ; Cytoplasm/genetics ; Humans ; Mitochondria/*genetics/metabolism ; Plant Infertility ; Plant Proteins/metabolism ; Plants/*genetics/metabolism ; *RNA Editing ; RNA, Plant/metabolism ; Reproduction ; }, abstract = {RNA editing challenges the central dogma of molecular biology by changing the genetic information at the transcript level. In plant organelles, RNAs are modified by deamination of some specific cytosine residues, but the origin of this process remains puzzling. Different from the generally accepted neutral model to explain the emergence of RNA editing in plant organelles, we propose a new hypothesis based on the nucleocytoplasmic conflict theory. We assume that mutations in organellar genomes arose first and spread into the population provided they increased the transmission of their own maternally inherited genome. RNA editing appeared subsequently as a nuclear-encoded correction mechanism to restore the transmission of the nuclear genome. In plants, a well-known consequence of the nucleocytoplasmic conflict is cytoplasmic male sterility (CMS) which is counteracted by the emergence of fertility restorer genes (Rf) belonging to the pentatricopeptide repeat (PPR) protein family. Interestingly, RNA-editing deficiency can lead to CMS, and it now clearly appears that PPR proteins are major players in RNA editing. This striking similarity between the mechanisms of fertility restoration and RNA editing can be explained if both reactions are the consequence of the same driving force, the nucleocytoplasmic conflict. Similarly, the prevalence of RNA editing in eukaryotic organellar genomes could also be a consequence of the genetic antagonism between organellar and nuclear genomes.}, }
@article {pmid22158961, year = {2012}, author = {Hadjivasiliou, Z and Pomiankowski, A and Seymour, RM and Lane, N}, title = {Selection for mitonuclear co-adaptation could favour the evolution of two sexes.}, journal = {Proceedings. Biological sciences}, volume = {279}, number = {1734}, pages = {1865-1872}, pmid = {22158961}, issn = {1471-2954}, mesh = {*Biological Evolution ; Cell Nucleus/*genetics ; DNA, Mitochondrial/genetics ; Extrachromosomal Inheritance ; Genes, Mitochondrial/*genetics ; Genome, Mitochondrial ; Mitochondria/*genetics ; *Models, Genetic ; *Mutation Rate ; Ploidies ; }, abstract = {Mitochondria are descended from free-living bacteria that were engulfed by another cell between one and a half to two billion years ago. A redistribution of DNA led to most genetic information being lost or transferred to a large central genome in the nucleus, leaving a residual genome in each mitochondrion. Oxidative phosphorylation, the most critical function of mitochondria, depends on the functional compatibility of proteins encoded by both the nucleus and mitochondria. We investigate whether selection for adaptation between the nuclear and mitochondrial genomes (mitonuclear co-adaptation) could, in principle, have promoted uniparental inheritance of mitochondria and thereby the evolution of two mating types or sexes. Using a mathematical model, we explore the importance of the radical differences in ploidy levels, sexual and asexual modes of inheritance, and mutation rates of the nucleus and mitochondria. We show that the major features of mitochondrial inheritance, notably uniparental inheritance and bottlenecking, enhance the co-adaptation of mitochondrial and nuclear genes and therefore improve fitness. We conclude that, under a wide range of conditions, selection for mitonuclear co-adaptation favours the evolution of two distinct mating types or sexes in sexual species.}, }
@article {pmid22157015, year = {2012}, author = {Herrmann, JM and Riemer, J}, title = {Mitochondrial disulfide relay: redox-regulated protein import into the intermembrane space.}, journal = {The Journal of biological chemistry}, volume = {287}, number = {7}, pages = {4426-4433}, pmid = {22157015}, issn = {1083-351X}, mesh = {Animals ; Bacteria/*metabolism ; Bacterial Proteins/*metabolism ; Cytochrome Reductases/*metabolism ; Disulfides/*metabolism ; Electron Transport/physiology ; Evolution, Molecular ; Humans ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/*metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Oxidation-Reduction ; Oxidoreductases Acting on Sulfur Group Donors ; Periplasm/*metabolism ; Protein Transport/physiology ; }, abstract = {99% of all mitochondrial proteins are synthesized in the cytosol, from where they are imported into mitochondria. In contrast to matrix proteins, many proteins of the intermembrane space (IMS) lack presequences and are imported in an oxidation-driven reaction by the mitochondrial disulfide relay. Incoming polypeptides are recognized and oxidized by the IMS-located receptor Mia40. Reoxidation of Mia40 is facilitated by the sulfhydryl oxidase Erv1 and the respiratory chain. Although structurally unrelated, the mitochondrial disulfide relay functionally resembles the Dsb (disufide bond) system of the bacterial periplasm, the compartment from which the IMS was derived 2 billion years ago.}, }
@article {pmid22155732, year = {2012}, author = {Wojtkowska, M and Jąkalski, M and Pieńkowska, JR and Stobienia, O and Karachitos, A and Przytycka, TM and Weiner, J and Kmita, H and Makałowski, W}, title = {Phylogenetic analysis of mitochondrial outer membrane β-barrel channels.}, journal = {Genome biology and evolution}, volume = {4}, number = {2}, pages = {110-125}, pmid = {22155732}, issn = {1759-6653}, support = {//Intramural NIH HHS/United States ; }, mesh = {Acanthamoeba/genetics/*metabolism ; Amino Acid Sequence ; Dictyostelium/metabolism ; Evolution, Molecular ; Genetic Markers ; Likelihood Functions ; Membrane Proteins/*genetics ; Mitochondrial Membranes/*metabolism ; Molecular Sequence Data ; *Phylogeny ; Protozoan Proteins/*genetics ; Voltage-Dependent Anion Channels/*genetics ; }, abstract = {Transport of molecules across mitochondrial outer membrane is pivotal for a proper function of mitochondria. The transport pathways across the membrane are formed by ion channels that participate in metabolite exchange between mitochondria and cytoplasm (voltage-dependent anion-selective channel, VDAC) as well as in import of proteins encoded by nuclear genes (Tom40 and Sam50/Tob55). VDAC, Tom40, and Sam50/Tob55 are present in all eukaryotic organisms, encoded in the nuclear genome, and have β-barrel topology. We have compiled data sets of these protein sequences and studied their phylogenetic relationships with a special focus on the position of Amoebozoa. Additionally, we identified these protein-coding genes in Acanthamoeba castellanii and Dictyostelium discoideum to complement our data set and verify the phylogenetic position of these model organisms. Our analysis show that mitochondrial β-barrel channels from Archaeplastida (plants) and Opisthokonta (animals and fungi) experienced many duplication events that resulted in multiple paralogous isoforms and form well-defined monophyletic clades that match the current model of eukaryotic evolution. However, in representatives of Amoebozoa, Chromalveolata, and Excavata (former Protista), they do not form clearly distinguishable clades, although they locate basally to the plant and algae branches. In most cases, they do not posses paralogs and their sequences appear to have evolved quickly or degenerated. Consequently, the obtained phylogenies of mitochondrial outer membrane β-channels do not entirely reflect the recent eukaryotic classification system involving the six supergroups: Chromalveolata, Excavata, Archaeplastida, Rhizaria, Amoebozoa, and Opisthokonta.}, }
@article {pmid22154145, year = {2012}, author = {Al Kaddissi, S and Legeay, A and Elia, AC and Gonzalez, P and Camilleri, V and Gilbin, R and Simon, O}, title = {Effects of uranium on crayfish Procambarus clarkii mitochondria and antioxidants responses after chronic exposure: what have we learned?.}, journal = {Ecotoxicology and environmental safety}, volume = {78}, number = {}, pages = {218-224}, doi = {10.1016/j.ecoenv.2011.11.026}, pmid = {22154145}, issn = {1090-2414}, mesh = {Animals ; Astacoidea/metabolism/*radiation effects ; Catalase/metabolism ; Gene Expression/radiation effects ; Genes, Mitochondrial ; Gills/metabolism/radiation effects ; Glutathione Peroxidase/metabolism ; Glutathione Transferase/metabolism ; Hepatopancreas/metabolism ; Male ; Mitochondria/*radiation effects ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; Superoxide Dismutase/metabolism ; Toxicity Tests, Chronic ; Uranium/*toxicity ; Water Pollutants, Radioactive/*toxicity ; }, abstract = {We examined the impacts of Uranium (U) on mitochondria and on the response of antioxidants in the gills and the hepatopancreas of crayfish Procambarus clarkii after long-term exposure (30 and 60 days) to an environmentally relevant concentration (30 μg U/L). The expression of mitochondrial genes (12s, atp6, and cox1), as well as the genes involved in oxidative stress responses (sod(Mn) and mt) were evaluated. The activities of antioxidant enzymes (SOD, CAT, GPX and GST) were also studied. U accumulation in organs induced changes in genes' expression. The evolution of these transcriptional responses and differences between gene expression levels at high and low doses of exposure were also discussed. This study demonstrated that, after long-term exposure, U caused a decrease in antioxidant activities and induced oxidative stress. A possible ROS-mediated U cytotoxic mechanism is proposed. Expression levels of the investigated genes can possibly be used as a tool to evaluate U toxicity and seem to be more sensitive than the enzymatic activities. However a multiple biomarker approach is recommended as the perturbed pathways and the mode of action of this pollutant are not completely understood.}, }
@article {pmid22153838, year = {2012}, author = {Yabuki, A and Chao, EE and Ishida, K and Cavalier-Smith, T}, title = {Microheliella maris (Microhelida ord. n.), an ultrastructurally highly distinctive new axopodial protist species and genus, and the unity of phylum Heliozoa.}, journal = {Protist}, volume = {163}, number = {3}, pages = {356-388}, doi = {10.1016/j.protis.2011.10.001}, pmid = {22153838}, issn = {1618-0941}, mesh = {Eukaryota/*classification/genetics/*ultrastructure ; Evolution, Molecular ; Heat-Shock Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; }, abstract = {A new heliozoan, Microheliella maris, has sufficiently distinctive ultrastructure to merit a new order, Microhelida. Its 18S and 28S rRNA genes were sequenced earlier under the informal name 'marine microheliozoan'; we here sequenced its Hsp90 gene. A three-gene tree suggests that it is distantly related to centrohelids and others in chromist subkingdom Hacrobia; but it is too divergent to be placed accurately by few genes. Unlike centrohelids, its central spherical centrosome has two concentric granular shells and a dense core devoid of a trilaminar central disc. Microtubules radiate from the centrosomal shells. Unlike centrohelids, axopodia have only three microtubules, fixed basally by dense plasma membrane anchors, and bear terminal and lateral haptosome-like extrusomes. As in the heliomonad Heliomorpha, the centrosome is embedded in a nuclear cavity, and centrosomal microtubules traverse the nucleus inside cytoplasmic channels. A novel filogranular network interconnects mitochondria, ER, and plasma membrane. The microbody is attached to the nucleus and mitochondrion, which has vermicular tubular cristae. We group Microhelida and Heliomonadida, purged of dissimilar flagellates, as a new tubulicristate class Endohelea within phylum Heliozoa. Previously misassigned GenBank 18S rDNA sequences reveal Microhelida as diverse and ancient. We discuss principles underlying the biogenesis and diversity of axopodial patterns.}, }
@article {pmid22143034, year = {2012}, author = {Kang, GZ and Peng, HF and Han, QX and Wang, YH and Guo, TC}, title = {Identification and expression pattern of ribosomal L5 gene in common wheat (Triticum aestivum L.).}, journal = {Gene}, volume = {493}, number = {1}, pages = {62-68}, doi = {10.1016/j.gene.2011.11.023}, pmid = {22143034}, issn = {1879-0038}, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Genes, Plant ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Ribosomal Proteins/*genetics/metabolism ; Stress, Psychological ; Triticum/*genetics ; }, abstract = {The full-length cDNA sequence (1158 bp) encoding a ribosomal L5 protein, designated as TaL5, was firstly isolated from common wheat (Triticum aestivum L.) using the rapid amplification of cDNA ends method (RACE). The open reading frame (ORF) of TaL5 gene was 906 bp, and its deduced amino acid sequence (301 residues) shared high similarity to those of other higher plant L5 proteins. TaL5 protein contained a putative 5S binding region (74 amino acids). TaL5 DNA sequence was further cloned, and sequence analysis showed that it contained 7 introns and 8 exons. Predicated using TargetP software, TaL5 protein was putatively located in mitochondria and contains a transit peptide of 12 amino acids. During grain filling period, temporal expression pattern of TaL5 gene was approximately consistent with the rates of starch accumulation in grains. Additionally, TaL5 gene was dramatically induced by salt, drought and freezing stresses, exogenous abscisic acid (ABA) and salicylic acid (SA) in wheat seedlings. These implied that TaL5 gene could function in growth, development and abiotic stresses in wheat plants.}, }
@article {pmid22140228, year = {2012}, author = {Burstein, D and Gould, SB and Zimorski, V and Kloesges, T and Kiosse, F and Major, P and Martin, WF and Pupko, T and Dagan, T}, title = {A machine learning approach to identify hydrogenosomal proteins in Trichomonas vaginalis.}, journal = {Eukaryotic cell}, volume = {11}, number = {2}, pages = {217-228}, pmid = {22140228}, issn = {1535-9786}, mesh = {Amino Acid Sequence ; *Artificial Intelligence ; Genes, Protozoan ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Protozoan Proteins/*chemistry/genetics/metabolism ; Sequence Alignment ; Trichomonas vaginalis/*metabolism ; }, abstract = {The protozoan parasite Trichomonas vaginalis is the causative agent of trichomoniasis, the most widespread nonviral sexually transmitted disease in humans. It possesses hydrogenosomes-anaerobic mitochondria that generate H(2), CO(2), and acetate from pyruvate while converting ADP to ATP via substrate-level phosphorylation. T. vaginalis hydrogenosomes lack a genome and translation machinery; hence, they import all their proteins from the cytosol. To date, however, only 30 imported proteins have been shown to localize to the organelle. A total of 226 nuclear-encoded proteins inferred from the genome sequence harbor a characteristic short N-terminal presequence, reminiscent of mitochondrial targeting peptides, which is thought to mediate hydrogenosomal targeting. Recent studies suggest, however, that the presequences might be less important than previously thought. We sought to identify new hydrogenosomal proteins within the 59,672 annotated open reading frames (ORFs) of T. vaginalis, independent of the N-terminal targeting signal, using a machine learning approach. Our training set included 57 gene and protein features determined for all 30 known hydrogenosomal proteins and 576 nonhydrogenosomal proteins. Several classifiers were trained on this set to yield an import score for all proteins encoded by T. vaginalis ORFs, predicting the likelihood of hydrogenosomal localization. The machine learning results were tested through immunofluorescence assay and immunodetection in isolated cell fractions of 14 protein predictions using hemagglutinin constructs expressed under the homologous SCSα promoter in transiently transformed T. vaginalis cells. Localization of 6 of the 10 top predicted hydrogenosome-localized proteins was confirmed, and two of these were found to lack an obvious N-terminal targeting signal.}, }
@article {pmid22139921, year = {2012}, author = {Jühling, F and Pütz, J and Bernt, M and Donath, A and Middendorf, M and Florentz, C and Stadler, PF}, title = {Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements.}, journal = {Nucleic acids research}, volume = {40}, number = {7}, pages = {2833-2845}, pmid = {22139921}, issn = {1362-4962}, mesh = {Animals ; *Evolution, Molecular ; Gene Order ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Molecular Sequence Annotation/*methods ; Pseudogenes ; RNA/*chemistry/*genetics ; RNA, Mitochondrial ; RNA, Transfer/*chemistry/*genetics ; }, abstract = {Transfer RNAs (tRNAs) are present in all types of cells as well as in organelles. tRNAs of animal mitochondria show a low level of primary sequence conservation and exhibit 'bizarre' secondary structures, lacking complete domains of the common cloverleaf. Such sequences are hard to detect and hence frequently missed in computational analyses and mitochondrial genome annotation. Here, we introduce an automatic annotation procedure for mitochondrial tRNA genes in Metazoa based on sequence and structural information in manually curated covariance models. The method, applied to re-annotate 1876 available metazoan mitochondrial RefSeq genomes, allows to distinguish between remaining functional genes and degrading 'pseudogenes', even at early stages of divergence. The subsequent analysis of a comprehensive set of mitochondrial tRNA genes gives new insights into the evolution of structures of mitochondrial tRNA sequences as well as into the mechanisms of genome rearrangements. We find frequent losses of tRNA genes concentrated in basal Metazoa, frequent independent losses of individual parts of tRNA genes, particularly in Arthropoda, and wide-spread conserved overlaps of tRNAs in opposite reading direction. Direct evidence for several recent Tandem Duplication-Random Loss events is gained, demonstrating that this mechanism has an impact on the appearance of new mitochondrial gene orders.}, }
@article {pmid22128139, year = {2012}, author = {Hu, C and Lin, SY and Chi, WT and Charng, YY}, title = {Recent gene duplication and subfunctionalization produced a mitochondrial GrpE, the nucleotide exchange factor of the Hsp70 complex, specialized in thermotolerance to chronic heat stress in Arabidopsis.}, journal = {Plant physiology}, volume = {158}, number = {2}, pages = {747-758}, pmid = {22128139}, issn = {1532-2548}, mesh = {*Adaptation, Physiological ; Arabidopsis/genetics/metabolism/*physiology ; Arabidopsis Proteins/*metabolism ; *Gene Duplication ; Genome, Plant ; HSP70 Heat-Shock Proteins/*metabolism ; *Hot Temperature ; Mitochondria/*metabolism ; Phylogeny ; *Stress, Physiological ; }, abstract = {The duplication and divergence of heat stress (HS) response genes might help plants adapt to varied HS conditions, but little is known on the topic. Here, we examined the evolution and function of Arabidopsis (Arabidopsis thaliana) mitochondrial GrpE (Mge) proteins. GrpE acts as a nucleotide-exchange factor in the Hsp70/DnaK chaperone machinery. Genomic data show that AtMge1 and AtMge2 arose from a recent whole-genome duplication event. Phylogenetic analysis indicated that duplication and preservation of Mges occurred independently in many plant species, which suggests a common tendency in the evolution of the genes. Intron retention contributed to the divergence of the protein structure of Mge paralogs in higher plants. In both Arabidopsis and tomato (Solanum lycopersicum), Mge1 is induced by ultraviolet B light and Mge2 is induced by heat, which suggests regulatory divergence of the genes. Consistently, AtMge2 but not AtMge1 is under the control of HsfA1, the master regulator of the HS response. Heterologous expression of AtMge2 but not AtMge1 in the temperature-sensitive Escherichia coli grpE mutant restored its growth at 43°C. Arabidopsis T-DNA knockout lines under different HS regimes revealed that Mge2 is specifically required for tolerating prolonged exposure to moderately high temperature, as compared with the need of the heat shock protein 101 and the HS-associated 32-kD protein for short-term extreme heat. Therefore, with duplication and subfunctionalization, one copy of the Arabidopsis Mge genes became specialized in a distinct type of HS. We provide direct evidence supporting the connection between gene duplication and adaptation to environmental stress.}, }
@article {pmid22127869, year = {2012}, author = {Kobayashi, K and Kawabata, M and Hisano, K and Kazama, T and Matsuoka, K and Sugita, M and Nakamura, T}, title = {Identification and characterization of the RNA binding surface of the pentatricopeptide repeat protein.}, journal = {Nucleic acids research}, volume = {40}, number = {6}, pages = {2712-2723}, pmid = {22127869}, issn = {1362-4962}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Amino Acids/chemistry ; Arabidopsis Proteins/*chemistry/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Position-Specific Scoring Matrices ; Protein Binding ; RNA/*chemistry/metabolism ; RNA-Binding Proteins/*chemistry/genetics/metabolism ; }, abstract = {The expressions of chloroplast and mitochondria genes are tightly controlled by numerous nuclear-encoded proteins, mainly at the post-transcriptional level. Recent analyses have identified a large, plant-specific family of pentatricopeptide repeat (PPR) motif-containing proteins that are exclusively involved in RNA metabolism of organelle genes via sequence-specific RNA binding. A tandem array of PPR motifs within the protein is believed to facilitate the RNA interaction, although little is known of the mechanism. Here, we describe the RNA interacting framework of a PPR protein, Arabidopsis HCF152. First, we demonstrated that a Pfam model could be relevant to the PPR motif function. A series of proteins with two PPR motifs showed significant differences in their RNA binding affinities, indicating functional differences among PPR motifs. Mutagenesis and informatics analysis putatively identified five amino acids organizing its RNA binding surface [the 1st, 4th, 8th, 12th and 'ii'(-2nd) amino acids] and their complex connections. SELEX (Systematic evolution of ligands by exponential enrichment) and nucleobase preference assays determined the nucleobases with high affinity for HCF152 and suggested several characteristic amino acids that may be involved in determining specificity and/or affinity of the PPR/RNA interaction.}, }
@article {pmid22126655, year = {2011}, author = {Zhang, T and Zhang, X and Hu, S and Yu, J}, title = {An efficient procedure for plant organellar genome assembly, based on whole genome data from the 454 GS FLX sequencing platform.}, journal = {Plant methods}, volume = {7}, number = {}, pages = {38}, pmid = {22126655}, issn = {1746-4811}, abstract = {MOTIVATION: Complete organellar genome sequences (chloroplasts and mitochondria) provide valuable resources and information for studying plant molecular ecology and evolution. As high-throughput sequencing technology advances, it becomes the norm that a shotgun approach is used to obtain complete genome sequences. Therefore, to assemble organellar sequences from the whole genome, shotgun reads are inevitable. However, associated techniques are often cumbersome, time-consuming, and difficult, because true organellar DNA is difficult to separate efficiently from nuclear copies, which have been transferred to the nucleus through the course of evolution.<br><br>RESULTS: We report a new, rapid procedure for plant chloroplast and mitochondrial genome sequencing and assembly using the Roche/454 GS FLX platform. Plant cells can contain multiple copies of the organellar genomes, and there is a significant correlation between the depth of sequence reads in contigs and the number of copies of the genome. Without isolating organellar DNA from the mixture of nuclear and organellar DNA for sequencing, we retrospectively extracted assembled contigs of either chloroplast or mitochondrial sequences from the whole genome shotgun data. Moreover, the contig connection graph property of Newbler (a platform-specific sequence assembler) ensures an efficient final assembly. Using this procedure, we assembled both chloroplast and mitochondrial genomes of a resurrection plant, Boea hygrometrica, with high fidelity. We also present information and a minimal sequence dataset as a reference for the assembly of other plant organellar genomes.}, }
@article {pmid22124893, year = {2012}, author = {Rupwate, SD and Rajasekharan, R}, title = {C2 domain is responsible for targeting rice phosphoinositide specific phospholipase C.}, journal = {Plant molecular biology}, volume = {78}, number = {3}, pages = {247-258}, pmid = {22124893}, issn = {1573-5028}, mesh = {Amino Acid Sequence ; Base Sequence ; Calcium Signaling ; Catalytic Domain/genetics ; Conserved Sequence ; DNA, Plant/genetics ; Genes, Plant ; Models, Molecular ; Molecular Sequence Data ; Oryza/*enzymology/genetics ; Phosphoinositide Phospholipase C/*chemistry/genetics/*metabolism ; Phylogeny ; Plant Proteins/*chemistry/genetics/*metabolism ; Protein Structure, Tertiary ; Structural Homology, Protein ; }, abstract = {Phosphoinositide-specific phospholipase C (PLC) is involved in Ca[2+] mediated signalling events that lead to altered cellular status. Using various sequence-analysis methods, we identified two conserved motifs in known PLC sequences. The identified motifs are located in the C2 domain of plant PLCs and are not found in any other protein. These motifs are specifically found in the Ca[2+] binding loops and form adjoining beta strands. Further, we identified certain conserved residues that are highly distinct from corresponding residues of animal PLCs. The motifs reported here could be used to annotate plant-specific phospholipase C sequences. Furthermore, we demonstrated that the C2 domain alone is capable of targeting PLC to the membrane in response to a Ca[2+] signal. We also showed that the binding event results from a change in the hydrophobicity of the C2 domain upon Ca[2+] binding. Bioinformatic analyses revealed that all PLCs from Arabidopsis and rice lack a transmembrane domain, myristoylation and GPI-anchor protein modifications. Our bioinformatic study indicates that plant PLCs are located in the cytoplasm, the nucleus and the mitochondria. Our results suggest that there are no distinct isoforms of plant PLCs, as have been proposed to exist in the soluble and membrane associated fractions. The same isoform could potentially be present in both subcellular fractions, depending on the calcium level of the cytosol. Overall, these data suggest that the C2 domain of PLC plays a vital role in calcium signalling.}, }
@article {pmid22117417, year = {2011}, author = {ZvychaĬnaia, EIu and Danilkin, AA and Kholodova, MV and Sipko, TP and Berber, AP}, title = {[Analysis of the variability of the control region and cytochrome b gene of mtDNA of Capreolus pygargus Pall].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {5}, pages = {511-517}, pmid = {22117417}, issn = {1026-3470}, mesh = {Animals ; Cytochromes b/*genetics ; DNA, Mitochondrial/*genetics ; Deer/*genetics ; *Genetic Variation ; Haplotypes/genetics ; Kazakhstan ; Mitochondria/genetics ; Phylogeny ; *Polymorphism, Genetic ; Russia ; }, abstract = {Analysis the of cytochrome b gene (1140 b.p.) polymorphism and polymorphism of 79 specimens of the control region (934 b.p.) of mtDNA of the Siberian roe deer Capreolus pygargus from 23 regions of Russia and Kazakhstan has been carried out. The combined alignment of two fragments ofmitochondrial DNA revealed 36 haplotypes, which are distributed in three haplogroups. The net distance was 0.8, 1.3, and 1.3%. The specific pattern of haplogroups was described for roe deer of each region (Ural, trans-Ural, Eastern Siberia, Far East, Northeastern China). Unrelated haplogroups were found in populations of the Urals and Siberia. The variation pattern and spatial distribution of mitochondrial lines allowed us to suggest that a haplogroup that initially belongs to C. p. tianschanicus occurs secondarily in C. p. pygargus.}, }
@article {pmid22117087, year = {2012}, author = {Williams, LE and Wernegreen, JJ}, title = {Purifying selection, sequence composition, and context-specific indel mutations shape intraspecific variation in a bacterial endosymbiont.}, journal = {Genome biology and evolution}, volume = {4}, number = {1}, pages = {44-51}, pmid = {22117087}, issn = {1759-6653}, support = {R01 GM062626/GM/NIGMS NIH HHS/United States ; R01GM062626/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ants/genetics/microbiology ; Bacteria/*genetics ; DNA Replication/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; *Genome, Bacterial ; Genotype ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; *Mutation ; Polymorphism, Genetic ; Recombination, Genetic ; Replication Origin/genetics ; Symbiosis/*genetics ; }, abstract = {Comparative genomics of closely related bacterial strains can clarify mutational processes and selective forces that impact genetic variation. Among primary bacterial endosymbionts of insects, such analyses have revealed ongoing genome reduction, raising questions about the ultimate evolutionary fate of these partnerships. Here, we explored genomic variation within Blochmannia vafer, an obligate mutualist of the ant Camponotus vafer. Polymorphism analysis of the Illumina data set used previously for de novo assembly revealed a second Bl. vafer genotype. To determine why a single ant colony contained two symbiont genotypes, we examined polymorphisms in 12 C. vafer mitochondrial sequences assembled from the Illumina data; the spectrum of variants suggests that the colony contained two maternal lineages, each harboring a distinct Bl. vafer genotype. Comparing the two Bl. vafer genotypes revealed that purifying selection purged most indels and nonsynonymous differences from protein-coding genes. We also discovered that indels occur frequently in multimeric simple sequence repeats, which are relatively abundant in Bl. vafer and may play a more substantial role in generating variation in this ant mutualist than in the aphid endosymbiont Buchnera. Finally, we explored how an apparent relocation of the origin of replication in Bl. vafer and the resulting shift in strand-associated mutational pressures may have caused accelerated gene loss and an elevated rate of indel polymorphisms in the region spanning the origin relocation. Combined, these results point to significant impacts of purifying selection on genomic polymorphisms as well as distinct patterns of indels associated with unusual genomic features of Blochmannia.}, }
@article {pmid22117085, year = {2012}, author = {Smith, DR and Kayal, E and Yanagihara, AA and Collins, AG and Pirro, S and Keeling, PJ}, title = {First complete mitochondrial genome sequence from a box jellyfish reveals a highly fragmented linear architecture and insights into telomere evolution.}, journal = {Genome biology and evolution}, volume = {4}, number = {1}, pages = {52-58}, pmid = {22117085}, issn = {1759-6653}, support = {U54 MD007584/MD/NIMHD NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Cubozoa/*genetics ; DNA Fragmentation ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Gene Conversion ; *Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; Recombination, Genetic ; Telomere/*genetics ; }, abstract = {Animal mitochondrial DNAs (mtDNAs) are typically single circular chromosomes, with the exception of those from medusozoan cnidarians (jellyfish and hydroids), which are linear and sometimes fragmented. Most medusozoans have linear monomeric or linear bipartite mitochondrial genomes, but preliminary data have suggested that box jellyfish (cubozoans) have mtDNAs that consist of many linear chromosomes. Here, we present the complete mtDNA sequence from the winged box jellyfish Alatina moseri (the first from a cubozoan). This genome contains unprecedented levels of fragmentation: 18 unique genes distributed over eight 2.9- to 4.6-kb linear chromosomes. The telomeres are identical within and between chromosomes, and recombination between subtelomeric sequences has led to many genes initiating or terminating with sequences from other genes (the most extreme case being 150 nt of a ribosomal RNA containing the 5' end of nad2), providing evidence for a gene conversion-based model of telomere evolution. The silent-site nucleotide variation within the A. moseri mtDNA is among the highest observed from a eukaryotic genome and may be associated with elevated rates of recombination.}, }
@article {pmid22116655, year = {2012}, author = {Chigri, F and Flosdorff, S and Pilz, S and Kölle, E and Dolze, E and Gietl, C and Vothknecht, UC}, title = {The Arabidopsis calmodulin-like proteins AtCML30 and AtCML3 are targeted to mitochondria and peroxisomes, respectively.}, journal = {Plant molecular biology}, volume = {78}, number = {3}, pages = {211-222}, pmid = {22116655}, issn = {1573-5028}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/*metabolism/ultrastructure ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Bacterial Proteins/genetics/metabolism ; Biological Transport, Active ; Calmodulin/chemistry/genetics/*metabolism ; Intracellular Calcium-Sensing Proteins/chemistry/genetics/*metabolism ; Luminescent Proteins/genetics/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Peroxisomes/metabolism ; Phylogeny ; Plants, Genetically Modified ; Protein Conformation ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Signal Transduction ; Nicotiana/genetics/metabolism/ultrastructure ; }, abstract = {Calmodulin (CaM) is a ubiquitous sensor/transducer of calcium signals in eukaryotic organisms. While CaM mediated calcium regulation of cytosolic processes is well established, there is growing evidence for the inclusion of organelles such as chloroplasts, mitochondria and peroxisomes into the calcium/calmodulin regulation network. A number of CaM-binding proteins have been identified in these organelles and processes such as protein import into chloroplasts and mitochondria have been shown to be governed by CaM regulation. What have been missing to date are the mediators of this regulation since no CaM or calmodulin-like protein (CML) has been identified in any of these organelles. Here we show that two Arabidopsis CMLs, AtCML3 and AtCML30, are localized in peroxisomes and mitochondria, respectively. AtCML3 is targeted via an unusual C-terminal PTS1-like tripeptide while AtCML30 utilizes an N-terminal, non-cleavable transit peptide. Both proteins possess the typical structure of CaMs, with two pairs of EF-hand motifs separated by a short linker domain. They furthermore display common characteristics, such as calcium-dependent alteration of gel mobility and calcium-dependent exposure of a hydrophobic surface. This indicates that they can function in a similar manner as canonical CaMs. The presence of close homologues to AtCML3 and AtCML30 in other plants further indicates that organellar targeting of these CMLs is not a specific feature of Arabidopsis. The identification of peroxisomal and mitochondrial CMLs is an important step in the understanding how these organelles are integrated into the cellular calcium/calmodulin signaling pathways.}, }
@article {pmid22115958, year = {2012}, author = {Yeung, BH and Law, AY and Wong, CK}, title = {Evolution and roles of stanniocalcin.}, journal = {Molecular and cellular endocrinology}, volume = {349}, number = {2}, pages = {272-280}, doi = {10.1016/j.mce.2011.11.007}, pmid = {22115958}, issn = {1872-8057}, mesh = {Animals ; Apoptosis ; Autocrine Communication/physiology ; Biological Evolution ; Calcium/blood ; Cell Transformation, Neoplastic/genetics/metabolism ; Endocrine System/physiology ; Endoplasmic Reticulum/physiology ; Gene Expression Regulation ; Glycoproteins/blood/*genetics ; Homeostasis ; Humans ; Ion Transport/physiology ; Mitochondria/physiology ; Neoplasms/genetics/metabolism/pathology ; Paracrine Communication/physiology ; Phosphates/blood ; Protein Isoforms/blood/genetics ; }, abstract = {In fish, stanniocalcin-1 (STC1) is a key endocrine factor that acts on gill, intestine and kidney to regulate serum calcium and phosphate homeostasis. The recent identification and study of mammalian STCs (STC1 and STC2) revealed that the hormones are made in virtually all tissues and they act primarily as paracrine/autocrine factors to regulate various biological functions. Based on their ubiquitous expression patterns and generally undetectable levels in blood serum, it is unlikely that the mammalian STCs play important roles in serum Ca(2+)/P(i) homeostasis. However current evidences still support the local action of STCs in Ca(2+) and P(i) transport, probably via their action on Ca(2+)-channels and Na(+)/P(i) co-transporter. At present, information about the sequence, expression and distribution of the STC receptor(s) is lacking. However, recent emerging evidence hints the involvement of STC1 and STC2 in the sub-cellular functions of mitochondria and endoplasmic reticulum respectively, particularly responding to oxidative stress and unfolded protein response. With increasing evidence that demonstrates the local actions of STCs, the focus of the research has been moved to cellular inflammation and carcinogenesis. This review integrates the information available on STCs in fish and mammals, focusing mainly on their embryonic origin, tissue distribution, their potential regulatory mechanisms and the modes of action, and their physiological and pathophysiological functions, particularly in cancer biology.}, }
@article {pmid22114710, year = {2011}, author = {Foury, F and Szczepanowska, K}, title = {Antimutator alleles of yeast DNA polymerase gamma modulate the balance between DNA synthesis and excision.}, journal = {PloS one}, volume = {6}, number = {11}, pages = {e27847}, pmid = {22114710}, issn = {1932-6203}, mesh = {Alleles ; DNA Polymerase I/genetics/metabolism ; DNA Polymerase gamma ; *DNA Replication ; DNA, Mitochondrial/*genetics/*metabolism ; DNA-Directed DNA Polymerase/chemistry/*genetics/metabolism ; Electrophoretic Mobility Shift Assay ; Exonucleases/metabolism ; Humans ; Mutation/*genetics ; Mutation Rate ; Phenotype ; Protein Conformation ; Saccharomyces cerevisiae/*enzymology/*genetics ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {Mutations in mitochondrial DNA (mtDNA) are an important cause of disease and perhaps aging in human. DNA polymerase gamma (pol γ), the unique replicase inside mitochondria, plays a key role in the fidelity of mtDNA replication through selection of the correct nucleotide and 3'-5' exonuclease proofreading. For the first time, we have isolated and characterized antimutator alleles in the yeast pol γ (Mip1). These mip1 mutations, localised in the 3'-5' exonuclease and polymerase domains, elicit a 2-15 fold decrease in the frequency of mtDNA point mutations in an msh1-1 strain which is partially deficient in mtDNA mismatch-repair. In vitro experiments show that in all mutants the balance between DNA synthesis and exonucleolysis is shifted towards excision when compared to wild-type, suggesting that in vivo more opportunity is given to the editing function for removing the replicative errors. This results in partial compensation for the mismatch-repair defects and a decrease in mtDNA point mutation rate. However, in all mutants but one the antimutator trait is lost in the wild-type MSH1 background. Accordingly, the polymerases of selected mutants show reduced oligonucleotide primed M13 ssDNA synthesis and to a lesser extent DNA binding affinity, suggesting that in mismatch-repair proficient cells efficient DNA synthesis is required to reach optimal accuracy. In contrast, the Mip1-A256T polymerase, which displays wild-type like DNA synthesis activity, increases mtDNA replication fidelity in both MSH1 and msh1-1 backgrounds. Altogether, our data show that accuracy of wild-type Mip1 is probably not optimal and can be improved by specific (often conservative) amino acid substitutions that define a pol γ area including a loop of the palm subdomain, two residues near the ExoII motif and an exonuclease helix-coil-helix module in close vicinity to the polymerase domain. These elements modulate in a subtle manner the balance between DNA polymerization and excision.}, }
@article {pmid22113796, year = {2012}, author = {Kayal, E and Bentlage, B and Collins, AG and Kayal, M and Pirro, S and Lavrov, DV}, title = {Evolution of linear mitochondrial genomes in medusozoan cnidarians.}, journal = {Genome biology and evolution}, volume = {4}, number = {1}, pages = {1-12}, pmid = {22113796}, issn = {1759-6653}, mesh = {Animals ; Base Sequence ; Cell Lineage/genetics ; Cnidaria/*genetics ; Cubozoa/genetics ; DNA Fragmentation ; DNA Replication/genetics ; DNA, Mitochondrial/*genetics ; DNA-Directed DNA Polymerase/genetics ; *Evolution, Molecular ; Gene Order/genetics ; Genome, Mitochondrial/*genetics ; Hydrozoa/genetics ; Mitochondria/genetics ; Molecular Sequence Annotation/methods ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames/genetics ; Phylogeny ; Recombination, Genetic/genetics ; Scyphozoa/genetics ; Transcription, Genetic/genetics ; }, abstract = {In nearly all animals, mitochondrial DNA (mtDNA) consists of a single circular molecule that encodes several subunits of the protein complexes involved in oxidative phosphorylation as well as part of the machinery for their expression. By contrast, mtDNA in species belonging to Medusozoa (one of the two major lineages in the phylum Cnidaria) comprises one to several linear molecules. Many questions remain on the ubiquity of linear mtDNA in medusozoans and the mechanisms responsible for its evolution, replication, and transcription. To address some of these questions, we determined the sequences of nearly complete linear mtDNA from 24 species representing all four medusozoan classes: Cubozoa, Hydrozoa, Scyphozoa, and Staurozoa. All newly determined medusozoan mitochondrial genomes harbor the 17 genes typical for cnidarians and map as linear molecules with a high degree of gene order conservation relative to the anthozoans. In addition, two open reading frames (ORFs), polB and ORF314, are identified in cubozoan, schyphozoan, staurozoan, and trachyline hydrozoan mtDNA. polB belongs to the B-type DNA polymerase gene family, while the product of ORF314 may act as a terminal protein that binds telomeres. We posit that these two ORFs are remnants of a linear plasmid that invaded the mitochondrial genomes of the last common ancestor of Medusozoa and are responsible for its linearity. Hydroidolinan hydrozoans have lost the two ORFs and instead have duplicated cox1 at each end of their mitochondrial chromosome(s). Fragmentation of mtDNA occurred independently in Cubozoa and Hydridae (Hydrozoa, Hydroidolina). Our broad sampling allows us to reconstruct the evolutionary history of linear mtDNA in medusozoans.}, }
@article {pmid22113794, year = {2012}, author = {Jackson, CJ and Gornik, SG and Waller, RF}, title = {The mitochondrial genome and transcriptome of the basal dinoflagellate Hematodinium sp.: character evolution within the highly derived mitochondrial genomes of dinoflagellates.}, journal = {Genome biology and evolution}, volume = {4}, number = {1}, pages = {59-72}, pmid = {22113794}, issn = {1759-6653}, mesh = {Amino Acid Sequence ; Base Sequence ; Cell Culture Techniques ; Codon, Terminator/genetics ; DNA, Mitochondrial/genetics ; Dinoflagellida/*genetics ; *Evolution, Molecular ; Gene Amplification/genetics ; Genes, rRNA/genetics ; *Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; RNA Editing/genetics ; RNA, Messenger/genetics ; Recombination, Genetic/*genetics ; Transcription, Genetic/genetics ; *Transcriptome ; }, abstract = {The sister phyla dinoflagellates and apicomplexans inherited a drastically reduced mitochondrial genome (mitochondrial DNA, mtDNA) containing only three protein-coding (cob, cox1, and cox3) genes and two ribosomal RNA (rRNA) genes. In apicomplexans, single copies of these genes are encoded on the smallest known mtDNA chromosome (6 kb). In dinoflagellates, however, the genome has undergone further substantial modifications, including massive genome amplification and recombination resulting in multiple copies of each gene and gene fragments linked in numerous combinations. Furthermore, protein-encoding genes have lost standard stop codons, trans-splicing of messenger RNAs (mRNAs) is required to generate complete cox3 transcripts, and extensive RNA editing recodes most genes. From taxa investigated to date, it is unclear when many of these unusual dinoflagellate mtDNA characters evolved. To address this question, we investigated the mitochondrial genome and transcriptome character states of the deep branching dinoflagellate Hematodinium sp. Genomic data show that like later-branching dinoflagellates Hematodinium sp. also contains an inflated, heavily recombined genome of multicopy genes and gene fragments. Although stop codons are also lacking for cox1 and cob, cox3 still encodes a conventional stop codon. Extensive editing of mRNAs also occurs in Hematodinium sp. The mtDNA of basal dinoflagellate Hematodinium sp. indicates that much of the mtDNA modification in dinoflagellates occurred early in this lineage, including genome amplification and recombination, and decreased use of standard stop codons. Trans-splicing, on the other hand, occurred after Hematodinium sp. diverged. Only RNA editing presents a nonlinear pattern of evolution in dinoflagellates as this process occurs in Hematodinium sp. but is absent in some later-branching taxa indicating that this process was either lost in some lineages or developed more than once during the evolution of the highly unusual dinoflagellate mtDNA.}, }
@article {pmid22110477, year = {2012}, author = {Ma, ZA and Zhao, Z and Turk, J}, title = {Mitochondrial dysfunction and β-cell failure in type 2 diabetes mellitus.}, journal = {Experimental diabetes research}, volume = {2012}, number = {}, pages = {703538}, pmid = {22110477}, issn = {1687-5303}, support = {R01 NS063962/NS/NINDS NIH HHS/United States ; R37 DK034388/DK/NIDDK NIH HHS/United States ; P30 DK056341/DK/NIDDK NIH HHS/United States ; R37-DK34388/DK/NIDDK NIH HHS/United States ; P60 DK020579/DK/NIDDK NIH HHS/United States ; P30 DK020579/DK/NIDDK NIH HHS/United States ; P41 RR000954/RR/NCRR NIH HHS/United States ; P30 DK056341-11/DK/NIDDK NIH HHS/United States ; R01-NS063962/NS/NINDS NIH HHS/United States ; P60-DK20579/DK/NIDDK NIH HHS/United States ; P41-RR00954/RR/NCRR NIH HHS/United States ; P30-DK56341/DK/NIDDK NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/biosynthesis ; Apoptosis ; Diabetes Mellitus, Type 2/*physiopathology ; Fatty Acids, Unsaturated/chemistry ; Group IV Phospholipases A2/deficiency/physiology ; Humans ; Insulin Resistance ; Insulin-Secreting Cells/*physiology ; Ion Channels/physiology ; Lipid Peroxidation ; Mitochondria/*physiology ; Mitochondrial Membranes/physiology ; Mitochondrial Proteins/physiology ; Oxidation-Reduction ; Phospholipids/chemistry ; Reactive Oxygen Species/metabolism ; Uncoupling Protein 2 ; }, abstract = {Type 2 diabetes mellitus (T2DM) is the most common human endocrine disease and is characterized by peripheral insulin resistance and pancreatic islet β-cell failure. Accumulating evidence indicates that mitochondrial dysfunction is a central contributor to β-cell failure in the evolution of T2DM. As reviewed elsewhere, reactive oxygen species (ROS) produced by β-cell mitochondria as a result of metabolic stress activate several stress-response pathways. This paper focuses on mechanisms whereby ROS affect mitochondrial structure and function and lead to β-cell failure. ROS activate UCP2, which results in proton leak across the mitochondrial inner membrane, and this leads to reduced β-cell ATP synthesis and content, which is a critical parameter in regulating glucose-stimulated insulin secretion. In addition, ROS oxidize polyunsaturated fatty acids in mitochondrial cardiolipin and other phospholipids, and this impairs membrane integrity and leads to cytochrome c release into cytosol and apoptosis. Group VIA phospholipase A2 (iPLA2β) appears to be a component of a mechanism for repairing mitochondrial phospholipids that contain oxidized fatty acid substituents, and genetic or acquired iPLA2β-deficiency increases β-cell mitochondrial susceptibility to injury from ROS and predisposes to developing T2DM. Interventions that attenuate ROS effects on β-cell mitochondrial phospholipids might prevent or retard development of T2DM.}, }
@article {pmid22102053, year = {2012}, author = {Fan, GL and Li, QZ}, title = {Predicting protein submitochondria locations by combining different descriptors into the general form of Chou's pseudo amino acid composition.}, journal = {Amino acids}, volume = {43}, number = {2}, pages = {545-555}, doi = {10.1007/s00726-011-1143-4}, pmid = {22102053}, issn = {1438-2199}, mesh = {Algorithms ; Amino Acid Sequence ; *Computer Simulation ; Evolution, Molecular ; Mitochondrial Proteins/*chemistry/genetics ; *Models, Molecular ; Protein Sorting Signals ; Protein Transport ; Software ; Support Vector Machine ; }, abstract = {Knowledge of the submitochondria location of protein is integral to understanding its function and a necessity in the proteomics era. In this work, a new submitochondria data set is constructed, and an approach for predicting protein submitochondria locations is proposed by combining the amino acid composition, dipeptide composition, reduced physicochemical properties, gene ontology, evolutionary information, and pseudo-average chemical shift. The overall prediction accuracy is 93.57% for the submitochondria location and 97.79% for the three membrane protein types in the mitochondria inner membrane using the algorithm of the increment of diversity combined with the support vector machine. The performance of the pseudo-average chemical shift is excellent. For contrast, the method is also used to predict submitochondria locations in the data set constructed by Du and Li; an accuracy of 94.95% is obtained by our method, which is better than that of other existing methods.}, }
@article {pmid22099629, year = {2011}, author = {Liu, Z and Li, X and Zhao, P and Gui, J and Zheng, W and Zhang, Y}, title = {Tracing the evolution of the mitochondrial protein import machinery.}, journal = {Computational biology and chemistry}, volume = {35}, number = {6}, pages = {336-340}, doi = {10.1016/j.compbiolchem.2011.10.005}, pmid = {22099629}, issn = {1476-928X}, mesh = {Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Organelles/metabolism ; Protein Subunits/metabolism ; Protein Transport ; Saccharomyces cerevisiae/cytology/*metabolism ; }, abstract = {Mitochondria are eukaryotic organelles originated from a single bacterial endosymbiosis about 2 billion years ago. One of the earliest events in the evolution of mitochondria was the acquisition of a mechanism that facilitated the import of proteins from cytosol. The mitochondrial protein import machinery consists of dozens of subunits, and they are of modular design. However, to date, it is not clear when certain component was added to the machinery. Using extensive homology searches, the evolutionary history of the mitochondrial protein import machinery was reconstructed. The results indicated that 6 of the 35 subunits have homologs in prokaryote, suggesting that they were prokaryotic origin; the major subunit gains were occurred in the earliest stage of eukaryotic evolution; subsequent to the gain of these conserved set of subunits, the mitochondrial protein import machinery components diversified along the eukaryotic lineages and a number of lineage-specific subunits can be observed. Furthermore, protein import systems of mitochondria-like organelles (hydrogenosomes and mitosomes) have dramatically reduced their subunit contents, however, they share most of the prokaryotic origin components with mitochondrion.}, }
@article {pmid22082251, year = {2011}, author = {Lippold, S and Matzke, NJ and Reissmann, M and Hofreiter, M}, title = {Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {328}, pmid = {22082251}, issn = {1471-2148}, support = {R01 GM069801/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Animals, Wild/*genetics ; Bayes Theorem ; Biological Evolution ; DNA, Mitochondrial/genetics ; Female ; *Genome, Mitochondrial ; Horses/*genetics ; Mitochondria/genetics ; Phylogeny ; }, abstract = {BACKGROUND: DNA target enrichment by micro-array capture combined with high throughput sequencing technologies provides the possibility to obtain large amounts of sequence data (e.g. whole mitochondrial DNA genomes) from multiple individuals at relatively low costs. Previously, whole mitochondrial genome data for domestic horses (Equus caballus) were limited to only a few specimens and only short parts of the mtDNA genome (especially the hypervariable region) were investigated for larger sample sets.<br><br>RESULTS: In this study we investigated whole mitochondrial genomes of 59 domestic horses from 44 breeds and a single Przewalski horse (Equus przewalski) using a recently described multiplex micro-array capture approach. We found 473 variable positions within the domestic horses, 292 of which are parsimony-informative, providing a well resolved phylogenetic tree. Our divergence time estimate suggests that the mitochondrial genomes of modern horse breeds shared a common ancestor around 93,000 years ago and no later than 38,000 years ago. A Bayesian skyline plot (BSP) reveals a significant population expansion beginning 6,000-8,000 years ago with an ongoing exponential growth until the present, similar to other domestic animal species. Our data further suggest that a large sample of wild horse diversity was incorporated into the domestic population; specifically, at least 46 of the mtDNA lineages observed in domestic horses (73%) already existed before the beginning of domestication about 5,000 years ago.<br><br>CONCLUSIONS: Our study provides a window into the maternal origins of extant domestic horses and confirms that modern domestic breeds present a wide sample of the mtDNA diversity found in ancestral, now extinct, wild horse populations. The data obtained allow us to detect a population expansion event coinciding with the beginning of domestication and to estimate both the minimum number of female horses incorporated into the domestic gene pool and the time depth of the domestic horse mtDNA gene pool.}, }
@article {pmid22081211, year = {2011}, author = {Gonçalves, RL and Barreto, RF and Polycarpo, CR and Gadelha, FR and Castro, SL and Oliveira, MF}, title = {A comparative assessment of mitochondrial function in epimastigotes and bloodstream trypomastigotes of Trypanosoma cruzi.}, journal = {Journal of bioenergetics and biomembranes}, volume = {43}, number = {6}, pages = {651-661}, pmid = {22081211}, issn = {1573-6881}, mesh = {Adaptation, Physiological/physiology ; Animals ; Chagas Disease/immunology/metabolism/parasitology ; Electron Transport Complex II/immunology/*metabolism ; Electron Transport Complex III/immunology/*metabolism ; Humans ; Hydrogen Peroxide/immunology/metabolism ; Life Cycle Stages/*physiology ; Mitochondria/immunology/*metabolism ; Protozoan Proteins/immunology/*metabolism ; Trypanosoma cruzi/growth &amp; development/immunology/*metabolism ; }, abstract = {Trypanosoma cruzi is a hemoflagellate protozoan that causes Chagas' disease. The life cycle of T. cruzi is complex and involves different evolutive forms that have to encounter different environmental conditions provided by the host. Herein, we performed a functional assessment of mitochondrial metabolism in the following two distinct evolutive forms of T. cruzi: the insect stage epimastigote and the freshly isolated bloodstream trypomastigote. We observed that in comparison to epimastigotes, bloodstream trypomastigotes facilitate the entry of electrons into the electron transport chain by increasing complex II-III activity. Interestingly, cytochrome c oxidase (CCO) activity and the expression of CCO subunit IV were reduced in bloodstream forms, creating an "electron bottleneck" that favored an increase in electron leakage and H(2)O(2) formation. We propose that the oxidative preconditioning provided by this mechanism confers protection to bloodstream trypomastigotes against the host immune system. In this scenario, mitochondrial remodeling during the T. cruzi life cycle may represent a key metabolic adaptation for parasite survival in different hosts.}, }
@article {pmid22079833, year = {2011}, author = {Schneider, RE and Brown, MT and Shiflett, AM and Dyall, SD and Hayes, RD and Xie, Y and Loo, JA and Johnson, PJ}, title = {The Trichomonas vaginalis hydrogenosome proteome is highly reduced relative to mitochondria, yet complex compared with mitosomes.}, journal = {International journal for parasitology}, volume = {41}, number = {13-14}, pages = {1421-1434}, pmid = {22079833}, issn = {1879-0135}, support = {T32 AI007323/AI/NIAID NIH HHS/United States ; 2-T32-AI-007323/AI/NIAID NIH HHS/United States ; F32 AI080084/AI/NIAID NIH HHS/United States ; R37 AI027857/AI/NIAID NIH HHS/United States ; R37 AI027587/AI/NIAID NIH HHS/United States ; F32-AI080084/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Mass Spectrometry ; Mitochondria/chemistry/genetics/*metabolism ; Organelles/chemistry/genetics/*metabolism ; Phylogeny ; Proteome/chemistry/genetics/*metabolism ; Proteomics ; Protozoan Proteins/chemistry/genetics/*metabolism ; Trichomonas vaginalis/chemistry/classification/genetics/*metabolism ; }, abstract = {The human pathogen Trichomonas vaginalis lacks conventional mitochondria and instead contains divergent mitochondrial-related organelles. These double-membrane bound organelles, called hydrogenosomes, produce molecular hydrogen. Phylogenetic and biochemical analyses of hydrogenosomes indicate a common origin with mitochondria; however identification of hydrogenosomal proteins and studies on its metabolism have been limited. Here we provide a detailed proteomic analysis of the T. vaginalis hydrogenosome. The proteome of purified hydrogenosomes consists of 569 proteins, a number substantially lower than the 1,000-1,500 proteins reported for fungal and animal mitochondrial proteomes, yet considerably higher than proteins assigned to mitosomes. Pathways common to and distinct from both mitochondria and mitosomes were revealed by the hydrogenosome proteome. Proteins known to function in amino acid and energy metabolism, Fe-S cluster assembly, flavin-mediated catalysis, oxygen stress response, membrane translocation, chaperonin functions, proteolytic processing and ATP hydrolysis account for ∼30% of the hydrogenosome proteome. Of the 569 proteins in the hydrogenosome proteome, many appear to be associated with the external surface of hydrogenosomes, including large numbers of GTPases and ribosomal proteins. Glycolytic proteins were also found to be associated with the hydrogenosome proteome, similar to that previously observed for mitochondrial proteomes. Approximately 18% of the hydrogenosomal proteome is composed of hypothetical proteins of unknown function, predictive of multiple activities and properties yet to be uncovered for these highly adapted organelles.}, }
@article {pmid22079552, year = {2012}, author = {Murray, SW and Campbell, P and Kingston, T and Zubaid, A and Francis, CM and Kunz, TH}, title = {Molecular phylogeny of hipposiderid bats from Southeast Asia and evidence of cryptic diversity.}, journal = {Molecular phylogenetics and evolution}, volume = {62}, number = {2}, pages = {597-611}, doi = {10.1016/j.ympev.2011.10.021}, pmid = {22079552}, issn = {1095-9513}, mesh = {Animals ; Asia, Southeastern ; Bayes Theorem ; *Biological Evolution ; Cell Nucleus/*genetics ; Chiroptera/anatomy &amp; histology/classification/*genetics ; *Computational Biology ; DNA, Mitochondrial/classification/*genetics/isolation &amp; purification ; Echolocation/physiology ; Female ; Genetic Speciation ; Genetic Variation ; Male ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Old World leaf-nosed bats (Hipposideridae) are among the most widespread and ecologically diverse groups of insectivorous bats in the Old World tropics. However, phylogenetic relationships in Hipposideridae are poorly resolved at both the generic and species levels, and deep genetic divergence within several Southeast Asian species suggests that current taxonomy underestimates hipposiderid diversity in this region. We used mitochondrial and nuclear sequence data to conduct the first extensive molecular phylogenetic analysis of Southeast Asian hipposiderid bats. Inclusion of multiple samples per taxon allowed testing for evidence of evolutionarily distinct lineages within taxa currently defined as single species. In contrast to earlier phylogenies based on morphometrics, molecular data support monophyly of Hipposideros, but are ambiguous regarding the monophyly of Hipposideridae. With a few exceptions, molecular data also support currently recognized species groups classified by qualitative morphological characters. Widespread paraphyly and polyphyly within many currently recognized species of Hipposideros indicates that evolutionary diversity in the genus is underrepresented by current nomenclature. Comparison of available morphological and echolocation data suggest that both geographic isolation and ecological selection have contributed to the diversification of Southeast Asian hipposiderid bats.}, }
@article {pmid22078888, year = {2011}, author = {Pearlman, SM and Serber, Z and Ferrell, JE}, title = {A mechanism for the evolution of phosphorylation sites.}, journal = {Cell}, volume = {147}, number = {4}, pages = {934-946}, pmid = {22078888}, issn = {1097-4172}, support = {T32 CA009302/CA/NCI NIH HHS/United States ; T15 LM007033-23/LM/NLM NIH HHS/United States ; R01 GM046383-23/GM/NIGMS NIH HHS/United States ; R01 GM046383/GM/NIGMS NIH HHS/United States ; T15 LM007033/LM/NLM NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics/metabolism ; Eukaryota/genetics/metabolism ; *Evolution, Molecular ; Humans ; Mitochondria/genetics/metabolism ; Models, Molecular ; *Phosphorylation ; Phylogeny ; Proteins/chemistry/*metabolism ; }, abstract = {Protein phosphorylation provides a mechanism for the rapid, reversible control of protein function. Phosphorylation adds negative charge to amino acid side chains, and negatively charged amino acids (Asp/Glu) can sometimes mimic the phosphorylated state of a protein. Using a comparative genomics approach, we show that nature also employs this trick in reverse by evolving serine, threonine, and tyrosine phosphorylation sites from Asp/Glu residues. Structures of three proteins where phosphosites evolved from acidic residues (DNA topoisomerase II, enolase, and C-Raf) show that the relevant acidic residues are present in salt bridges with conserved basic residues, and that phosphorylation has the potential to conditionally restore the salt bridges. The evolution of phosphorylation sites from glutamate and aspartate provides a rationale for why phosphorylation sometimes activates proteins, and helps explain the origins of this important and complex process.}, }
@article {pmid22072896, year = {2011}, author = {Güçlü, O and Ulger, C and Türkozan, O}, title = {Genetic variation of the Nile soft-shelled turtle (Trionyx triunguis).}, journal = {International journal of molecular sciences}, volume = {12}, number = {10}, pages = {6418-6431}, pmid = {22072896}, issn = {1422-0067}, mesh = {Alleles ; Animals ; Biological Evolution ; DNA, Mitochondrial/analysis ; *Genetic Variation ; Haplotypes ; Mediterranean Region ; Microsatellite Repeats ; Mitochondria/genetics ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Turtles/classification/*genetics ; }, abstract = {We studied the genetic structure of Trionyx triunguis populations from the Mediterranean and African continent based on mtDNA D-loop (776 bp) and nine microsatellite loci. A total of 102 polymorphic sites and 13 mtDNA haplotypes were described. Nucleotide diversity and haplotypes diversity were 0.047 and 0.974 respectively. Both mtDNA and nDNA supported the existence of two main management units as the Mediterranean and Africa. Based on the mtDNA results, the Mediterranean can be divided into two subunits; western Turkey and the eastern Mediterranean.}, }
@article {pmid22071672, year = {2011}, author = {Zhong, ZR and Li, N and Qian, D and Jin, JH and Chen, T}, title = {Maternal inheritance of plastids and mitochondria in Cycas L. (Cycadaceae).}, journal = {Molecular genetics and genomics : MGG}, volume = {286}, number = {5-6}, pages = {411-416}, pmid = {22071672}, issn = {1617-4623}, mesh = {Biological Evolution ; *Crosses, Genetic ; Cycas/*genetics/ultrastructure ; DNA, Mitochondrial ; DNA, Plant ; *Inheritance Patterns ; Microscopy, Electron ; Mitochondria/*genetics ; Organelles ; Plastids/*genetics ; }, abstract = {Cycas is often considered a living fossil, thereby providing a unique model for revealing the evolution of spermatophytes. To date, the genetic inheritance of these archaic plants is not fully understood. The present study seeks to document the process of organelle inheritance in an interspecific cross of Cycas species. Extranuclear organelle DNA from chloroplasts and mitochondria was analyzed using both polymerase chain reaction-restriction fragment length polymorphism analysis and microscopy. Here, we show that the chloroplasts and mitochondria in the progeny of interspecific crosses between Cycas taitungensis and Cycas ferruginea were exclusively inherited from the female parent. Epifluorescence microscopic analyses of the pollen cells from Cycas elongata indicated that there was a significant degradation of organelle DNA in male reproductive cells following maturation; the DNA fluorescent signals were only seen after pollen mitosis two, but not detectable at mature stage. Lack of organelle DNA fluorescent signal in prothallial cells was confirmed by the absence of plastids and mitochondria in electronic microscopic images. In conclusion, these data suggest that the maternal plastid and mitochondrial inheritance in Cycas, native to the old world, are the same as seen in seed plants.}, }
@article {pmid22069449, year = {2011}, author = {Jimenez-Morales, D and Liang, J}, title = {Pattern of amino acid substitutions in transmembrane domains of β-barrel membrane proteins for detecting remote homologs in bacteria and mitochondria.}, journal = {PloS one}, volume = {6}, number = {11}, pages = {e26400}, pmid = {22069449}, issn = {1932-6203}, support = {R01 GM081682/GM/NIGMS NIH HHS/United States ; P50 GM086145/GM/NIGMS NIH HHS/United States ; GM079804/GM/NIGMS NIH HHS/United States ; GM081682/GM/NIGMS NIH HHS/United States ; R01 GM079804/GM/NIGMS NIH HHS/United States ; GM086145/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Substitution ; Bacteria/*metabolism ; Bacterial Proteins/*chemistry/*metabolism ; Bayes Theorem ; Genome, Bacterial ; Membrane Proteins/*chemistry/*metabolism ; Mitochondria/*metabolism ; Phylogeny ; Protein Structure, Secondary ; }, abstract = {β-barrel membrane proteins play an important role in controlling the exchange and transport of ions and organic molecules across bacterial and mitochondrial outer membranes. They are also major regulators of apoptosis and are important determinants of bacterial virulence. In contrast to β-helical membrane proteins, their evolutionary pattern of residue substitutions has not been quantified, and there are no scoring matrices appropriate for their detection through sequence alignment. Using a Bayesian Monte Carlo estimator, we have calculated the instantaneous substitution rates of transmembrane domains of bacterial β-barrel membrane proteins. The scoring matrices constructed from the estimated rates, called bbTM for β-barrel Transmembrane Matrices, improve significantly the sensitivity in detecting homologs of β-barrel membrane proteins, while avoiding erroneous selection of both soluble proteins and other membrane proteins of similar composition. The estimated evolutionary patterns are general and can detect β-barrel membrane proteins very remote from those used for substitution rate estimation. Furthermore, despite the separation of 2-3 billion years since the proto-mitochondrion entered the proto-eukaryotic cell, mitochondria outer membrane proteins in eukaryotes can also be detected accurately using these scoring matrices derived from bacteria. This is consistent with the suggestion that there is no eukaryote-specific signals for translocation. With these matrices, remote homologs of β-barrel membrane proteins with known structures can be reliably detected at genome scale, allowing construction of high quality structural models of their transmembrane domains, at the rate of 131 structures per template protein. The scoring matrices will be useful for identification, classification, and functional inference of membrane proteins from genome and metagenome sequencing projects. The estimated substitution pattern will also help to identify key elements important for the structural and functional integrity of β-barrel membrane proteins, and will aid in the design of mutagenesis studies.}, }
@article {pmid22066674, year = {2012}, author = {Martin, FN and Coffey, MD}, title = {Mitochondrial haplotype analysis for differentiation of isolates of Phytophthora cinnamomi.}, journal = {Phytopathology}, volume = {102}, number = {2}, pages = {229-239}, doi = {10.1094/PHYTO-04-11-0115}, pmid = {22066674}, issn = {0031-949X}, mesh = {Base Sequence ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial/genetics ; Genetic Loci/*genetics ; Genome, Mitochondrial/*genetics ; Geography ; Haplotypes/*genetics ; Mitochondria/*classification/genetics ; Molecular Sequence Data ; Mutation ; Phylogeny ; Phytophthora/*classification/genetics/isolation &amp; purification ; Polymorphism, Genetic/*genetics ; Sequence Analysis, DNA ; }, abstract = {Although Phytophthora cinnamomi is heterothallic, there are few instances of successful crossing in laboratory experiments, and analysis of field populations indicates a clonally reproducing population. In the absence of sexual recombination, the ability to monitor mitochondrial haplotypes may provide an additional tool for identification of clonal isolates and analysis of population structure. To determine mitochondrial haplotypes for this species, seven mitochondrial loci spanning a total of 6,961 bp were sequenced for 62 isolates representing a geographically diverse collection of isolates with A1 and A2 mating type. Three of the regions were primarily intergenic regions between trnG and rns, rns and nad3, and nad6 and cox1, while the remaining loci spanned cox2, nad9, rps10, and secY coding regions and some of the flanking spacer regions. In total, 45 mitochondrial haplotypes were identified (75% of the total isolates examined) with differences due to single-nucleotide polymorphisms (SNPs, totaling 152 bp) and length mutations (17 indels >2 bp representing a total of 910 bp in length). SNPs were the predominate mutation in the four coding regions and their flanking intergenic regions, while both SNPs and length mutations were observed in the three primarily intergenic regions. Some of the length mutations in these regions were due to addition or loss of unique sequences while others were due to variable numbers of subrepeats (in the trnG-rns region, there were 3 to 12 copies of a 24-bp subrepeat sequence that differentiated 17 haplotypes). Network analysis of the haplotypes identified eight primary clades, with the most divergent clade representing primarily A1 isolates collected from Papua New Guinea. The isolate grouping in the network corresponded to mating type and previously published isozyme classifications, with three exceptions: a haplotype representing an A1 mating type (H29) was placed well within the A2 mating type haplotype grouping, one haplotype (H26) had isolates with two isozyme classifications, and one isozyme group was represented on separate network clades, suggesting that recombination has occurred in the past. Among the 62 isolates examined, several examples were identified of isolates recovered from different geographic regions having the same mitochondrial haplotype, suggesting movement of isolates via plant material. Analysis of the data set to determine whether fewer loci could be sequenced to classify haplotypes indicated that the trnG-rns and rns-nad6 loci would classify 87% of the haplotypes identified in this study, while additional sequencing of the nad9 or secY loci would further differentiate the remaining six haplotypes. Based on conservation of gene order in Phytophthora spp., the trnG-rns locus should be useful for mitochondrial haplotype classification in other species, as should the cox2, nad9, rps10, and secY loci. However, the rns-nad3 and nad6-cox1 loci span regions that can have a different gene order in some Phytophthora spp.}, }
@article {pmid22066495, year = {2011}, author = {San Francisco, B and Bretsnyder, EC and Rodgers, KR and Kranz, RG}, title = {Heme ligand identification and redox properties of the cytochrome c synthetase, CcmF.}, journal = {Biochemistry}, volume = {50}, number = {50}, pages = {10974-10985}, pmid = {22066495}, issn = {1520-4995}, support = {R15 AI072719/AI/NIAID NIH HHS/United States ; R01 GM047909-17/GM/NIGMS NIH HHS/United States ; AI072719/AI/NIAID NIH HHS/United States ; R01 GM047909/GM/NIGMS NIH HHS/United States ; GM47909/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Substitution ; Binding Sites ; Biocatalysis ; Enzyme Activation/drug effects ; Escherichia coli Proteins/chemistry/genetics/isolation &amp; purification/*metabolism ; Heme/chemistry/*metabolism ; Histidine/chemistry ; Holoenzymes/chemistry/genetics/isolation &amp; purification/metabolism ; Imidazoles/pharmacology ; Indicators and Reagents/pharmacology ; Ligands ; Lyases/chemistry/genetics/isolation &amp; purification/*metabolism ; Models, Molecular ; Mutant Proteins/chemistry/isolation &amp; purification/metabolism ; Oxidation-Reduction ; Phylogeny ; Protein Conformation ; Protein Subunits/chemistry/genetics/isolation &amp; purification/metabolism ; Recombinant Proteins/chemistry/isolation &amp; purification/metabolism ; Spectrum Analysis, Raman ; }, abstract = {Cytochrome c maturation in many bacteria, archaea, and plant mitochondria involves the integral membrane protein CcmF, which is thought to function as a cytochrome c synthetase by facilitating the final covalent attachment of heme to the apocytochrome c. We previously reported that the E. coli CcmF protein contains a b-type heme that is stably and stoichiometrically associated with the protein and is not the heme attached to apocytochrome c. Here, we show that mutation of either of two conserved transmembrane histidines (His261 or His491) impairs stoichiometric b-heme binding in CcmF and results in spectral perturbations in the remaining heme. Exogeneous imidazole is able to correct cytochrome c maturation for His261 and His491 substitutions with small side chains (Ala or Gly), suggesting that a "cavity" is formed in these CcmF mutants in which imidazole binds and acts as a functional ligand to the b-heme. The results of resonance Raman spectroscopy on wild-type CcmF are consistent with a hexacoordinate low-spin b-heme with at least one endogeneous axial His ligand. Analysis of purified recombinant CcmF proteins from diverse prokaryotes reveals that the b-heme in CcmF is widely conserved. We have also determined the reduction potential of the CcmF b-heme (E(m,7) = -147 mV). We discuss these results in the context of CcmF structure and functions as a heme reductase and cytochrome c synthetase.}, }
@article {pmid22064560, year = {2011}, author = {McCutcheon, JP and Moran, NA}, title = {Extreme genome reduction in symbiotic bacteria.}, journal = {Nature reviews. Microbiology}, volume = {10}, number = {1}, pages = {13-26}, pmid = {22064560}, issn = {1740-1534}, mesh = {*Bacterial Physiological Phenomena ; Evolution, Molecular ; *Genome Size ; *Genome, Bacterial ; Models, Biological ; *Sequence Deletion ; *Symbiosis ; }, abstract = {Since 2006, numerous cases of bacterial symbionts with extraordinarily small genomes have been reported. These organisms represent independent lineages from diverse bacterial groups. They have diminutive gene sets that rival some mitochondria and chloroplasts in terms of gene numbers and lack genes that are considered to be essential in other bacteria. These symbionts have numerous features in common, such as extraordinarily fast protein evolution and a high abundance of chaperones. Together, these features point to highly degenerate genomes that retain only the most essential functions, often including a considerable fraction of genes that serve the hosts. These discoveries have implications for the concept of minimal genomes, the origins of cellular organelles, and studies of symbiosis and host-associated microbiota.}, }
@article {pmid22062157, year = {2011}, author = {Stael, S and Rocha, AG and Robinson, AJ and Kmiecik, P and Vothknecht, UC and Teige, M}, title = {Arabidopsis calcium-binding mitochondrial carrier proteins as potential facilitators of mitochondrial ATP-import and plastid SAM-import.}, journal = {FEBS letters}, volume = {585}, number = {24}, pages = {3935-3940}, doi = {10.1016/j.febslet.2011.10.039}, pmid = {22062157}, issn = {1873-3468}, support = {MC_U105674181/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adenosine Triphosphate/*metabolism ; Amino Acid Sequence ; Arabidopsis/*cytology/genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/metabolism ; Calcium/metabolism ; Calcium Signaling ; Calcium-Binding Proteins/chemistry/genetics/*metabolism ; EF Hand Motifs ; Genome, Plant/genetics ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Plastids/*metabolism ; Protein Transport ; S-Adenosylmethionine/*metabolism ; Substrate Specificity ; }, abstract = {Chloroplasts and mitochondria are central to crucial cellular processes in plants and contribute to a whole range of metabolic pathways. The use of calcium ions as a secondary messenger in and around organelles is increasingly appreciated as an important mediator of plant cell signaling, enabling plants to develop or to acclimatize to changing environmental conditions. Here, we have studied the four calcium-dependent mitochondrial carriers that are encoded in the Arabidopsis genome. An unknown substrate carrier, which was previously found to localize to chloroplasts, is proposed to present a calcium-dependent S-adenosyl methionine carrier. For three predicted ATP/phosphate carriers, we present experimental evidence that they can function as mitochondrial ATP-importers.}, }
@article {pmid22045327, year = {2011}, author = {Herrero, MT and Pagonabarraga, J and Linazasoro, G}, title = {Neuroprotective role of dopamine agonists: evidence from animal models and clinical studies.}, journal = {The neurologist}, volume = {17}, number = {6 Suppl 1}, pages = {S54-66}, doi = {10.1097/NRL.0b013e31823968fc}, pmid = {22045327}, issn = {2331-2637}, mesh = {Animals ; Antiparkinson Agents/*therapeutic use ; Clinical Trials as Topic ; Disease Models, Animal ; Disease Progression ; Dopamine Agonists/*therapeutic use ; Humans ; Levodopa/*therapeutic use ; Neuroprotective Agents/*therapeutic use ; Parkinson Disease/*drug therapy/physiopathology ; }, abstract = {Parkinson disease is a progressive neurodegenerative disease that affects, among other neurotransmitter systems, the nigrostriatal dopaminergic projection. Palliative treatment with levodopa and/or dopamine agonists improves motor symptoms even though patients continue to get clinically worse by the neurodegenerative process that continues to act as the major factor of physiological aging. Studies (in vitro and in vivo) with experimental models have shown that dopamine agonists have neuroprotective effects, directly or indirectly mediated by their ability to stabilize mitochondria, antioxidant effects, synthesis of growth factors, stabilization of the ubiquitin-proteasome system, activation of autophagy, antiapoptotic induction of Bcl2 family, or enhancement of neurogenesis (proliferation and migration) in the subventricular zone. Clinical studies have not completely confirmed these effects. Analysis in better characterized groups of patients with similar clinical symptoms, identical treatments, and the same evolution time are required. Technological advances which enable the learning of the etiology and the pathogenesis (genetic and environmental) of the disease, together with clinical assessment methods, bring hope to the development of new molecules in the symptomatic treatment of Parkinson disease. These molecules must display neuroprotective potential (prophylactic and/or therapeutic) which must be able to maintain the brain's physiological function and to modify or slow the natural course of the disease.}, }
@article {pmid22057391, year = {2012}, author = {Nickens, KP and Han, Y and Shandilya, H and Larrimore, A and Gerard, GF and Kaldjian, E and Patierno, SR and Ceryak, S}, title = {Acquisition of mitochondrial dysregulation and resistance to mitochondrial-mediated apoptosis after genotoxic insult in normal human fibroblasts: a possible model for early stage carcinogenesis.}, journal = {Biochimica et biophysica acta}, volume = {1823}, number = {2}, pages = {264-272}, pmid = {22057391}, issn = {0006-3002}, support = {R01 ES009961/ES/NIEHS NIH HHS/United States ; R01ES05304/ES/NIEHS NIH HHS/United States ; R01 CA107972-05/CA/NCI NIH HHS/United States ; R21 ES017334-01A1/ES/NIEHS NIH HHS/United States ; R01 ES005304-17/ES/NIEHS NIH HHS/United States ; R21 ES017334/ES/NIEHS NIH HHS/United States ; R01 ES009961-04/ES/NIEHS NIH HHS/United States ; R01 CA107972-05S1/CA/NCI NIH HHS/United States ; R01ES09961/ES/NIEHS NIH HHS/United States ; R01 CA107972/CA/NCI NIH HHS/United States ; R01 ES005304/ES/NIEHS NIH HHS/United States ; R01CA107972/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Apoptosis/*drug effects ; Apoptosis Regulatory Proteins ; Caspase 3/metabolism ; Cells, Cultured ; Chromium/*toxicity ; DNA Damage/drug effects ; Fibroblasts/cytology/*drug effects/*physiology ; Humans ; Intracellular Signaling Peptides and Proteins/metabolism ; Mitochondria/*drug effects/genetics/*metabolism/ultrastructure ; Mitochondrial Proteins/metabolism ; Mutagens/*toxicity ; }, abstract = {Acquisition of death-resistance is critical in the evolution of neoplasia. Our aim was to model the early stages of carcinogenesis by examining intracellular alterations in cells that have acquired apoptosis-resistance after exposure to a complex genotoxin. We previously generated sub-populations of BJ-hTERT human diploid fibroblasts, which have acquired death-resistance following exposure to hexavalent chromium [Cr(VI)], a broad-spectrum genotoxicant. Long-term exposure to certain forms of Cr(VI) is associated with respiratory carcinogenesis. Here, we report on the death-sensitivity of subclonal populations derived from clonogenic survivors of BJ-hTERT cells treated with 5 μM Cr(VI) (DR1, DR2), or selected by dilution-based cloning without treatment (CC1). Following Cr(VI) treatment, CC1 cells downregulated expression of the anti-apoptotic protein Bcl-2 and exhibited extensive expression of cleaved caspase 3. In contrast, the DR cells exhibited no cleaved caspase 3 expression and maintained expression of Bcl-2 following recovery from 24 h Cr(VI) exposure. The DR cells also exhibited attenuated mitochondrial-membrane depolarization and mitochondrial retention of cytochrome c and SMAC/DIABLO following Cr(VI) exposure. The DR cells exhibited less basal mtDNA damage, as compared to CC1 cells, which correlates with intrinsic (non-induced) death-resistance. Notably, there was no difference in p53 protein expression before or after treatment among all cell lines. Taken together, our data suggest the presence of more resilient mitochondria in death-resistant cells, and that death-resistance can be acquired in normal human cells early after genotoxin exposure. We postulate that resistance to mitochondrial-mediated cell death and mitochondrial dysregulation may be an initial phenotypic alteration observed in early stage carcinogenesis.}, }
@article {pmid22046482, year = {2011}, author = {Kowald, A and Kirkwood, TB}, title = {The evolution and role of mitochondrial fusion and fission in aging and disease.}, journal = {Communicative &amp; integrative biology}, volume = {4}, number = {5}, pages = {627-629}, pmid = {22046482}, issn = {1942-0889}, abstract = {Mitochondria contain their own genetic material and evolved from prokaryotic ancestors some two billion years ago. They are the main source of the cell's energy supply and are involved in such important processes as apoptosis, mitochondrial diseases and aging. Mitochondria display a complex dynamical behavior involving cycles of fusion and fission, the function of which is as yet unknown. We recently proposed a concise theory that explains: (1) why fusion and fission have evolved, (2) how these processes relate to the accumulation of mitochondrial mutants during aging and (3) why mtDNA is located close to the respiration complexes where most radicals are generated. We also believe that this 'organelle control' theory may explain why mutations in mitochondrial tRNA genes are the most prevalent kind of defect associated with inherited human mitochondrial diseases, despite the fact that mt-tRNA genes account for only 5% of the mtDNA coding sequence.}, }
@article {pmid22044752, year = {2011}, author = {Chen, H and Deng, L and Jiang, Y and Lu, P and Yu, J}, title = {RNA editing sites exist in protein-coding genes in the chloroplast genome of Cycas taitungensis.}, journal = {Journal of integrative plant biology}, volume = {53}, number = {12}, pages = {961-970}, doi = {10.1111/j.1744-7909.2011.01082.x}, pmid = {22044752}, issn = {1744-7909}, mesh = {Amino Acids/metabolism ; Base Sequence ; Cycas/*genetics ; Genes, Chloroplast/*genetics ; Genes, Plant/*genetics ; Genome, Chloroplast/*genetics ; Hydrophobic and Hydrophilic Interactions ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Open Reading Frames/*genetics ; RNA Editing/*genetics ; Species Specificity ; }, abstract = {RNA editing is a post-transcriptional process that results in modifications of ribonucleotides at specific locations. In land plants editing can occur in both mitochondria and chloroplasts and most commonly involves C-to-U changes, especially in seed plants. Using prediction and experimental determination, we investigated RNA editing in 40 protein-coding genes from the chloroplast genome of Cycas taitungensis. A total of 85 editing sites were identified in 25 transcripts. Comparison analysis of the published editotypes of these 25 transcripts in eight species showed that RNA editing events gradually disappear during plant evolution. The editing in the first and third codon position disappeared quicker than that in the second codon position. ndh genes have the highest editing frequency while serine and proline codons were more frequently edited than the codons of other amino acids. These results imply that retained RNA editing sites have imbalanced distribution in genes and most of them may function by changing protein structure or interaction. Mitochondrion protein-coding genes have three times the editing sites compared with chloroplast genes of Cycas, most likely due to slower evolution speed.}, }
@article {pmid22044624, year = {2012}, author = {Bar-Yaacov, D and Blumberg, A and Mishmar, D}, title = {Mitochondrial-nuclear co-evolution and its effects on OXPHOS activity and regulation.}, journal = {Biochimica et biophysica acta}, volume = {1819}, number = {9-10}, pages = {1107-1111}, doi = {10.1016/j.bbagrm.2011.10.008}, pmid = {22044624}, issn = {0006-3002}, mesh = {*Biological Evolution ; DNA Replication/genetics ; DNA, Mitochondrial/*genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Eukaryota ; Mitochondria/*genetics/metabolism ; *Nuclear Proteins/genetics/metabolism ; Oxidative Phosphorylation ; RNA, Messenger/genetics/metabolism ; RNA, Mitochondrial ; RNA-Binding Proteins/genetics/metabolism ; Transcription, Genetic ; }, abstract = {Factors required for mitochondrial function are encoded both by the nuclear and mitochondrial genomes. The order of magnitude higher mutation rate of animal mitochondrial DNA (mtDNA) enforces tight co-evolution of mtDNA and nuclear DNA encoded factors. In this essay we argue that such co evolution exists at the population and inter-specific levels and affect disease susceptibility. We also argue for the existence of three modes of co-evolution in the mitochondrial genetic system, which include the interaction of mtDNA and nuclear DNA encoded proteins, nuclear protein - mtDNA-encoded RNA interaction within the mitochondrial translation machinery and nuclear DNA encoded proteins-mtDNA binging sites interaction in the frame of the mtDNA replication and transcription machineries. These modes of co evolution require co-regulation of the interacting factors encoded by the two genomes. Thus co evolution plays an important role in modulating mitochondrial activity. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.}, }
@article {pmid22041769, year = {2011}, author = {Fong, MY and Lau, YL and Chin, LC and Al-Mekhlafi, AM}, title = {Sequence analysis on the mitochondrial COXI gene of recent clinical isolates of Plasmodium knowlesi in Klang Valley, peninsular Malaysia.}, journal = {Tropical biomedicine}, volume = {28}, number = {2}, pages = {457-463}, pmid = {22041769}, issn = {2521-9855}, mesh = {Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; Electron Transport Complex IV/*genetics ; Humans ; Malaria/parasitology ; Malaysia ; Mitochondria/*enzymology/*genetics ; Molecular Sequence Data ; Phylogeny ; Plasmodium knowlesi/*enzymology/*genetics/isolation &amp; purification ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The cytochrome oxidase subunit I (COXI) gene sequences of three recent (2007-2008) clinical Plasmodium knowlesi isolates from Klang Valley, peninsular Malaysia, were determined and compared with those of older (1960's) peninsular Malaysia, recent isolates from Sarawak (on Borneo Island), and an isolate from Thailand. Multiple alignment of the sequences showed that the three clinical isolates were more similar to the older peninsular Malaysia isolates than to those from Sarawak and Thailand. Phylogenetic tree based on the COXI sequences revealed three distinct clusters of P. knowlesi. The first cluster consisted of isolates from peninsular Malaysia, the second consisted of Sarawak isolates and the third composed of the Thailand isolate. The findings of this study highlight the usefulness of mitochondrial COXI gene as a suitable marker for phylogeographic studies of P. knowlesi.}, }
@article {pmid22041657, year = {2011}, author = {Simsek, D and Jasin, M}, title = {DNA ligase III: a spotty presence in eukaryotes, but an essential function where tested.}, journal = {Cell cycle (Georgetown, Tex.)}, volume = {10}, number = {21}, pages = {3636-3644}, pmid = {22041657}, issn = {1551-4005}, support = {R01 GM054668/GM/NIGMS NIH HHS/United States ; GM54668/GM/NIGMS NIH HHS/United States ; }, mesh = {Conserved Sequence ; DNA Ligase ATP ; DNA Ligases/chemistry/*physiology ; Eukaryota/*enzymology ; Evolution, Molecular ; Mitochondria/enzymology ; Phylogeny ; Poly-ADP-Ribose Binding Proteins ; Xenopus Proteins ; }, abstract = {DNA ligases are crucial for most DNA transactions, including DNA replication, repair, and recombination. Recently, DNA ligase III (Lig3) has been demonstrated to be crucial for cell survival due to its catalytic function in mitochondria. This review summarizes these recent results and reports on a hitherto unappreciated widespread phylogenetic presence of Lig3 in eukaryotes, including in some organisms before the divergence of metazoa. Analysis of these putative Lig3 homologs suggests that many of them are likely to be found in mitochondria and to be critical for mitochondrial function.}, }
@article {pmid22036291, year = {2011}, author = {Hafez, M and Hausner, G}, title = {The highly variable mitochondrial small-subunit ribosomal RNA gene of Ophiostoma minus.}, journal = {Fungal biology}, volume = {115}, number = {11}, pages = {1122-1137}, doi = {10.1016/j.funbio.2011.07.007}, pmid = {22036291}, issn = {1878-6146}, mesh = {Base Sequence ; *Genetic Variation ; Introns ; Mitochondria/chemistry/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames ; Ophiostoma/chemistry/classification/*genetics ; Phylogeny ; RNA, Fungal/chemistry/genetics ; RNA, Ribosomal/chemistry/*genetics ; Ribosome Subunits, Small/chemistry/*genetics ; }, abstract = {Mitochondrial genomes in the true fungi are highly variable both in size and organization. Most of this size variation is due to the presence of introns and intron-encoded open reading frames (ORFs). The objectives for this work were to examine the mitochondrial small-subunit ribosomal RNA (rns) gene of strains of Ophiostoma minus for the presence of introns and to characterize such introns and their encoded ORFs. DNA sequence analysis showed that among different strains of O. minus various rns gene exon/intron configurations can be observed. Based on comparative sequence analysis and RNA secondary structure modeling group I introns with LAGLIDADG ORFs were uncovered at positions mS569 and mS1224 and group II introns were present at positions mS379 and mS952. The mS379 group II intron encoded a fragmented reverse transcriptase (RT)-like ORF and the mS952 group II intron encoded a LAGLIDADG-type ORF. Examples of intron ORF degeneration due to frameshift mutations were observed. The mS379 group II intron is the first mitochondrial group II intron to have an ORF inserted within domain II, typically RT-like ORFs are inserted in domain IV. The evolutionary dynamics of the intron-encoded ORFs have also been examined.}, }
@article {pmid22035660, year = {2011}, author = {Urban, S and Dickey, SW}, title = {The rhomboid protease family: a decade of progress on function and mechanism.}, journal = {Genome biology}, volume = {12}, number = {10}, pages = {231}, pmid = {22035660}, issn = {1474-760X}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Cell Membrane/chemistry/enzymology ; DNA-Binding Proteins/*chemistry/classification/genetics ; Drosophila/chemistry/*enzymology/genetics ; Drosophila Proteins/chemistry/genetics ; Endopeptidases/*chemistry/classification/genetics ; Enzyme Activation ; Epidermal Growth Factor/chemistry/genetics ; Escherichia coli/chemistry/*enzymology/genetics ; Escherichia coli Proteins/*chemistry/classification/genetics ; Homeostasis ; Humans ; Membrane Proteins/*chemistry/classification/genetics ; Mitochondria/chemistry/genetics ; Phylogeny ; Proteolysis ; Quorum Sensing ; Signal Transduction ; Structure-Activity Relationship ; }, abstract = {Rhomboid proteases are the largest family of enzymes that hydrolyze peptide bonds within the cell membrane. Although discovered to be serine proteases only a decade ago, rhomboid proteases are already considered to be the best understood intramembrane proteases. The presence of rhomboid proteins in all domains of life emphasizes their importance but makes their evolutionary history difficult to chart with confidence. Phylogenetics nevertheless offers three guiding principles for interpreting rhomboid function. The near ubiquity of rhomboid proteases across evolution suggests broad, organizational roles that are not directly essential for cell survival. Functions have been deciphered in only about a dozen organisms and fall into four general categories: initiating cell signaling in animals, facilitating bacterial quorum sensing, regulating mitochondrial homeostasis, and dismantling adhesion complexes of parasitic protozoa. Although in no organism has the full complement of rhomboid function yet been elucidated, links to devastating human disease are emerging rapidly, including to Parkinson's disease, type II diabetes, cancer, and bacterial and malaria infection. Rhomboid proteases are unlike most proteolytic enzymes, because they are membrane-immersed; understanding how the membrane immersion affects their function remains a key challenge.}, }
@article {pmid22033901, year = {2011}, author = {Arif, IA and Khan, HA and Shobrak, M and Williams, J}, title = {Cytochrome c oxidase subunit I barcoding of the green bee-eater (Merops orientalis).}, journal = {Genetics and molecular research : GMR}, volume = {10}, number = {4}, pages = {3992-3998}, doi = {10.4238/2011.October.21.2}, pmid = {22033901}, issn = {1676-5680}, mesh = {Animals ; Base Sequence ; Birds/*genetics ; *DNA Barcoding, Taxonomic ; DNA, Mitochondrial/chemistry ; Electron Transport Complex IV/*genetics/metabolism ; Evolution, Molecular ; Genetic Variation ; Mitochondria/enzymology/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Subunits/genetics/metabolism ; Saudi Arabia ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {DNA barcoding using mitochondrial cytochrome c oxidase subunit I (COI) is regarded as a standard method for species identification. Recent reports have also shown extended applications of COI gene analysis in phylogeny and molecular diversity studies. The bee-eaters are a group of near passerine birds in the family Meropidae. There are 26 species worldwide; five of them are found in Saudi Arabia. Until now, GenBank included a COI barcode for only one species of bee-eater, the European bee-eater (Merops apiaster). We sequenced the 694-bp segment of the COI gene of the green bee-eater M. orientalis and compared the sequences with those of M. apiaster. Pairwise sequence comparison showed 66 variable sites across all the eight sequences from both species, with an interspecific genetic distance of 0.0362. Two and one within-species variable sites were found, with genetic distances of 0.0005 and 0.0003 for M. apiaster and M. orientalis, respectively. This is the first study reporting barcodes for M. orientalis.}, }
@article {pmid22032638, year = {2011}, author = {Jiang, JH and Davies, JK and Lithgow, T and Strugnell, RA and Gabriel, K}, title = {Targeting of Neisserial PorB to the mitochondrial outer membrane: an insight on the evolution of β-barrel protein assembly machines.}, journal = {Molecular microbiology}, volume = {82}, number = {4}, pages = {976-987}, doi = {10.1111/j.1365-2958.2011.07880.x}, pmid = {22032638}, issn = {1365-2958}, mesh = {Electrophoretic Mobility Shift Assay ; *Host-Pathogen Interactions ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/metabolism ; Models, Biological ; Models, Molecular ; Molecular Chaperones/metabolism ; Neisseria gonorrhoeae/metabolism/pathogenicity ; Porins/*metabolism ; *Protein Multimerization ; Protein Transport ; }, abstract = {Mitochondria originated from Gram-negative bacteria through endosymbiosis. In modern day mitochondria, the Sorting and Assembly Machinery (SAM) is responsible for eukaryotic β-barrel protein assembly in the mitochondrial outer membrane. The SAM is the functional equivalent of the β-barrel assembly machinery found in the outer membrane of Gram-negative bacteria. In this study we examined the import pathway of a pathogenic bacterial protein, PorB, which is targeted from pathogenic Neisseria to the host mitochondria. We have developed a new method for measurement of PorB assembly into mitochondria that relies on the mobility shift exhibited by bacterial β-barrel proteins once folded and separated under semi-native electrophoretic conditions. We show that PorB is targeted to the outer mitochondrial membrane with a dependence on the intermembrane space shuttling chaperones and the core component of the SAM, Sam50, which is a functional homologue of BamA that is required for PorB assembly in bacteria. The peripheral subunits of the SAM, Sam35 and Sam37, which are essential for eukaryotic β-barrel protein assembly but do not have distinguishable functional homologues in bacteria, are not required for PorB assembly in eukaryotes. This shows that PorB uses an evolutionary conserved 'bacterial like' mechanism to infiltrate the host mitochondrial outer membrane.}, }
@article {pmid22030339, year = {2012}, author = {Aanen, DK and Maas, MF}, title = {Recruitment of healthy mitochondria fuels transmissible cancers.}, journal = {Trends in genetics : TIG}, volume = {28}, number = {1}, pages = {1-6}, doi = {10.1016/j.tig.2011.10.001}, pmid = {22030339}, issn = {0168-9525}, mesh = {Animals ; Cell Lineage ; DNA, Mitochondrial/*genetics ; Genome, Mitochondrial ; Humans ; Mitochondria/*genetics ; Mutation ; Neoplasms/*genetics/*pathology ; }, abstract = {The replication of mitochondrial DNA (mtDNA) is not under strict control of the nucleus. Therefore, within-cell selection can favour mtDNA variants with a replication or survival advantage even if deleterious for the cell. Here, we consider how the balance between selection within and among cells is shifted in cancer cell lineages, and how this affects the somatic evolution of mitochondria. Cancer cell lineages are known to be prone to mitochondrial genetic erosion. Nevertheless, some cancer lineages are long lived and a few exceptional lineages even can survive their host because of horizontal transmission to other individuals. Recent work now shows that such transmissible cancer cell lineages occasionally secondarily recruit the mitochondrial genome of their host, which we propose as a means to replace genetically eroded mitochondrial genomes. Studying the dynamics of the horizontal exchange of mtDNA between somatic cells may provide important insight into the evolution of mitochondria during somatic growth and in mitochondrial diseases.}, }
@article {pmid22025381, year = {2012}, author = {Sever, DM and Freeborn, LR}, title = {Observations on the anterior testicular ducts in snakes with emphasis on sea snakes and ultrastructure in the yellow-bellied sea snake, Pelamis platurus.}, journal = {Journal of morphology}, volume = {273}, number = {3}, pages = {324-336}, doi = {10.1002/jmor.11025}, pmid = {22025381}, issn = {1097-4687}, mesh = {Animals ; Biological Evolution ; Cilia/ultrastructure ; Cytoplasm/ultrastructure ; Elapidae/*anatomy &amp; histology ; Epididymis/cytology/ultrastructure ; Epithelial Cells/cytology/ultrastructure ; Epithelium/ultrastructure ; Male ; Mitochondria/ultrastructure ; Phylogeny ; Rete Testis/cytology/ultrastructure ; Seminiferous Tubules/cytology/ultrastructure ; Snakes ; Spermatozoa/cytology/ultrastructure ; Testis/cytology/*ultrastructure ; Vas Deferens/cytology/ultrastructure ; }, abstract = {The anterior testicular ducts of squamates transport sperm from the seminiferous tubules to the ductus deferens. These ducts consist of the rete testis, ductuli efferentes, and ductus epididymis. Many histological and a few ultrastructural studies of the squamate reproductive tract exist, but none concern the Hydrophiidae, the sea snakes and sea kraits. In this study, we describe the anterior testicular ducts of six species of hydrophiid snakes as well as representatives from the Elapidae, Homolapsidae, Leptotyphlopidae, and Uropeltidae. In addition, we examine the ultrastructure of these ducts in the yellow-bellied Sea Snake, Pelamis platurus, only the third such study on snakes. The anterior testicular ducts are similar in histology in all species examined. The rete testis is simple squamous or cuboidal epithelium and transports sperm from the seminiferous tubules to the ductuli efferentes in the extratesticular epididymal sheath. The ductuli efferentes are branched, convoluted tubules composed of simple cuboidal, ciliated epithelium, and many species possess periodic acid-Schiff+ granules in the cytoplasm. The ductus epididymis at the light microscopy level appears composed of pseudostratified columnar epithelium. At the ultrastructural level, the rete testis and ductuli efferentes of P. platurus possess numerous small coated vesicles and lack secretory vacuoles. Apocrine blebs in the ductuli efferentes, however, indicate secretory activity, possibly by a constitutive pathway. Ultrastructure reveals three types of cells in the ductus epididymis of P. platurus: columnar principal cells, squamous basal cells, and mitochondria-rich apical cells. This is the first report of apical cells in a snake. In addition, occasional principal cells possess a single cilium, which has not been reported in reptiles previously but is known in some birds. Finally, the ductus epididymis of P. platurus differs from other snakes that have been studied in possession of apical, biphasic secretory vacuoles. All of the proximal ducts are characterized by widening of adjacent plasma membranes into wide intercellular spaces, especially between the principal cells of the ductus epididymis. Our results contribute to a larger, collaborative study of the evolution of the squamate reproductive tract and to the potential for utilizing cellular characters in future phylogenetic inferences.}, }
@article {pmid22024028, year = {2011}, author = {Faure, E and Delaye, L and Tribolo, S and Levasseur, A and Seligmann, H and Barthélémy, RM}, title = {Probable presence of an ubiquitous cryptic mitochondrial gene on the antisense strand of the cytochrome oxidase I gene.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {56}, pmid = {22024028}, issn = {1745-6150}, mesh = {Alphaproteobacteria/genetics/metabolism ; Amino Acid Sequence ; Animals ; Codon/genetics/metabolism ; Codon, Nonsense/genetics/metabolism ; Computer Simulation ; DNA, Antisense/*genetics/metabolism ; DNA, Mitochondrial/*genetics/metabolism ; Electron Transport Complex IV/*genetics/metabolism ; Evolution, Molecular ; Expressed Sequence Tags ; *Genes, Mitochondrial ; Humans ; Mammals ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/*genetics/metabolism ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Probability ; RNA, Transfer/genetics/metabolism ; Sequence Alignment ; }, abstract = {BACKGROUND: Mitochondria mediate most of the energy production that occurs in the majority of eukaryotic organisms. These subcellular organelles contain a genome that differs from the nuclear genome and is referred to as mitochondrial DNA (mtDNA). Despite a disparity in gene content, all mtDNAs encode at least two components of the mitochondrial electron transport chain, including cytochrome c oxidase I (Cox1).<br><br>A positionally conserved ORF has been found on the complementary strand of the cox1 genes of both eukaryotic mitochondria (protist, plant, fungal and animal) and alpha-proteobacteria. This putative gene has been named gau for gene antisense ubiquitous in mtDNAs. The length of the deduced protein is approximately 100 amino acids. In vertebrates, several stop codons have been found in the mt gau region, and potentially functional gau regions have been found in nuclear genomes. However, a recent bioinformatics study showed that several hypothetical overlapping mt genes could be predicted, including gau; this involves the possible import of the cytosolic AGR tRNA into the mitochondria and/or the expression of mt antisense tRNAs with anticodons recognizing AGR codons according to an alternative genetic code that is induced by the presence of suppressor tRNAs. Despite an evolutionary distance of at least 1.5 to 2.0 billion years, the deduced Gau proteins share some conserved amino acid signatures and structure, which suggests a possible conserved function. Moreover, BLAST analysis identified rare, sense-oriented ESTs with poly(A) tails that include the entire gau region. Immunohistochemical analyses using an anti-Gau monoclonal antibody revealed strict co-localization of Gau proteins and a mitochondrial marker.<br><br>TESTING THE HYPOTHESIS: This hypothesis could be tested by purifying the gau gene product and determining its sequence. Cell biological experiments are needed to determine the physiological role of this protein.<br><br>Studies of the gau ORF will shed light on the origin of novel genes and their functions in organelles and could also have medical implications for human diseases that are caused by mitochondrial dysfunction. Moreover, this strengthens evidence for mitochondrial genes coded according to an overlapping genetic code.}, }
@article {pmid22023825, year = {2012}, author = {Zuccon, D and Prŷs-Jones, R and Rasmussen, PC and Ericson, PG}, title = {The phylogenetic relationships and generic limits of finches (Fringillidae).}, journal = {Molecular phylogenetics and evolution}, volume = {62}, number = {2}, pages = {581-596}, doi = {10.1016/j.ympev.2011.10.002}, pmid = {22023825}, issn = {1095-9513}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/*genetics ; *Computational Biology ; DNA, Mitochondrial/classification/*genetics/isolation &amp; purification ; Female ; Finches/classification/*genetics ; Male ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Phylogenetic relationships among the true finches (Fringillidae) have been confounded by the recurrence of similar plumage patterns and use of similar feeding niches. Using a dense taxon sampling and a combination of nuclear and mitochondrial sequences we reconstructed a well resolved and strongly supported phylogenetic hypothesis for this family. We identified three well supported, subfamily level clades: the Holoarctic genus Fringilla (subfamly Fringillinae), the Neotropical Euphonia and Chlorophonia (subfamily Euphoniinae), and the more widespread subfamily Carduelinae for the remaining taxa. Although usually separated in a different family-group taxon (Drepanidinae), the Hawaiian honeycreepers are deeply nested within the Carduelinae and sister to a group of Asian Carpodacus. Other new relationships recovered by this analysis include the placement of the extinct Chaunoproctus ferreorostris as sister to some Asian Carpodacus, a clade combining greenfinches (Carduelis chloris and allies), Rhodospiza and Rhynchostruthus, and a well-supported clade with the aberrant Callacanthis and Pyrrhoplectes together with Carpodacus rubescens. Although part of the large Carduelis-Serinus complex, the poorly known Serinus estherae forms a distinct lineage without close relatives. The traditionally delimited genera Carduelis, Serinus, Carpodacus, Pinicola and Euphonia are polyphyletic or paraphyletic. Based on our results we propose a revised generic classification of finches and describe a new monotypic genus for Carpodacus rubescens.}, }
@article {pmid22023720, year = {2012}, author = {Rigas, S and Daras, G and Tsitsekian, D and Hatzopoulos, P}, title = {The multifaceted role of Lon proteolysis in seedling establishment and maintenance of plant organelle function: living from protein destruction.}, journal = {Physiologia plantarum}, volume = {145}, number = {1}, pages = {215-223}, doi = {10.1111/j.1399-3054.2011.01537.x}, pmid = {22023720}, issn = {1399-3054}, mesh = {Arabidopsis/enzymology/genetics/physiology ; Arabidopsis Proteins/genetics/metabolism ; Chloroplasts/metabolism ; Evolution, Molecular ; Germination ; Mitochondria/metabolism/*physiology ; Oxidation-Reduction ; Peroxisomes/metabolism ; Plant Physiological Phenomena ; Protease La/genetics/*metabolism ; Protein Transport ; *Proteolysis ; Seedlings/metabolism/*physiology ; Seeds/metabolism/physiology ; Serine Endopeptidases/genetics/metabolism ; }, abstract = {Intracellular selective proteolysis is an important post-translational regulatory mechanism maintaining protein quality control by removing defective, damaged or even deleterious protein aggregates. The ATP-dependent Lon protease is a key component of protein quality control that is highly conserved across the kingdoms of living organisms. Major advancements have been made in bacteria and in non-plant organisms to understand the role of Lon in protection against protein oxidation, ageing and neurodegenerative diseases. This review presents the progress currently made in plants. The Lon gene family in Arabidopsis consists of four members that produce distinct protein isoforms localized in several organelles. Lon1 and Lon4 that potentially originate from a recent gene duplication event are dual-targeted to mitochondria and chloroplasts through distinct mechanisms revealing divergent evolution. Arabidopsis mutant analysis showed that mitochondria and peroxisomes biogenesis or maintenance of function is modulated by Lon1 and Lon2, respectively. Consequently, the lack of Lon selective proteolysis leading to growth retardation and impaired seedling establishment can be attributed to defects in the oil reserve mobilization pathway. The current progress in Arabidopsis research uncovers the role of Lon in the proteome homeostasis of plant organelles and stimulates biotechnology scenarios of plant tolerance against harsh abiotic conditions because of climate instability.}, }
@article {pmid22022812, year = {2012}, author = {Llinás, GA and Gardenal, CN}, title = {Phylogeography of Aedes aegypti in Argentina: long-distance colonization and rapid restoration of fragmented relicts after a continental control campaign.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {12}, number = {3}, pages = {254-261}, doi = {10.1089/vbz.2011.0696}, pmid = {22022812}, issn = {1557-7759}, mesh = {Aedes/genetics/*physiology/virology ; Animals ; Argentina/epidemiology ; Base Sequence ; Biological Evolution ; Bolivia/epidemiology ; DNA, Mitochondrial/chemistry/genetics ; Dengue/epidemiology/transmission/virology ; Genetic Variation/*genetics ; Haplotypes ; Humans ; Insect Control ; Insect Vectors/genetics/*physiology/virology ; Larva ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeography ; Population Dynamics ; Sequence Analysis, DNA ; Uruguay/epidemiology ; }, abstract = {Aedes (Stegomyia) aegypti, the main vector of Dengue and Yellow Fever viruses, is present in all the northern and central provinces of Argentina. During 2009, a Dengue outbreak spread broadly throughout the country, causing 27,752 infections in 13 provinces. In Argentina, little is known about the demographic history of this vector, which suffered a drastic decrease in abundance and distribution during a major control campaign performed in the Americas between 1950 and 1960. With the aim of uncovering the past and present events that determined the present distribution of the genetic variability in Ae. aegypti populations, we analyzed the distribution and abundance of mitochondrial haplotypes obtained by sequencing a 450-bp fragment of the ND5 gene. We detected 14 haplotypes among the sequences of 197 individuals from 22 populations that cover most of the distribution of the species in Argentina; one population from Bolivia and one from Paraguay were also included. A high heterogeneity in the geographical distribution of the genetic polymorphism was observed, with a pattern of isolation by distance in the north-west of Argentina. Haplotypes nested in three haplogroups, representing different colonization events and evolutionary histories in distant geographical areas. North-western and north-eastern populations correspond to independent introduced stocks for which a past fragmentation and rapid restoration from highly polymorphic relicts were inferred. By contrast, a unique genetic variant was detected in the east, probably as the result of a recent re-colonization event after the major control campaign; in this area, the mosquito would have been practically eradicated as a consequence of the continental control campaign.}, }
@article {pmid22022283, year = {2011}, author = {Bratic, A and Wredenberg, A and Grönke, S and Stewart, JB and Mourier, A and Ruzzenente, B and Kukat, C and Wibom, R and Habermann, B and Partridge, L and Larsson, NG}, title = {The bicoid stability factor controls polyadenylation and expression of specific mitochondrial mRNAs in Drosophila melanogaster.}, journal = {PLoS genetics}, volume = {7}, number = {10}, pages = {e1002324}, pmid = {22022283}, issn = {1553-7404}, mesh = {Animals ; Body Weight/genetics ; Drosophila Proteins/*genetics/metabolism ; Drosophila melanogaster/*genetics/*growth &amp; development/physiology ; Fertility/genetics ; Gene Expression Regulation, Developmental ; Gene Knockdown Techniques ; Mitochondria/*genetics/physiology ; Mitochondrial Proteins/genetics/metabolism ; Oxidative Phosphorylation ; Phylogeny ; Polyadenylation/*genetics ; Protein Biosynthesis ; RNA Interference ; RNA, Messenger/*genetics ; RNA-Binding Proteins/*genetics/metabolism ; }, abstract = {The bicoid stability factor (BSF) of Drosophila melanogaster has been reported to be present in the cytoplasm, where it stabilizes the maternally contributed bicoid mRNA and binds mRNAs expressed from early zygotic genes. BSF may also have other roles, as it is ubiquitously expressed and essential for survival of adult flies. We have performed immunofluorescence and cell fractionation analyses and show here that BSF is mainly a mitochondrial protein. We studied two independent RNAi knockdown fly lines and report that reduced BSF protein levels lead to a severe respiratory deficiency and delayed development at the late larvae stage. Ubiquitous knockdown of BSF results in a severe reduction of the polyadenylation tail lengths of specific mitochondrial mRNAs, accompanied by an enrichment of unprocessed polycistronic RNA intermediates. Furthermore, we observed a significant reduction in mRNA steady state levels, despite increased de novo transcription. Surprisingly, mitochondrial de novo translation is increased and abnormal mitochondrial translation products are present in knockdown flies, suggesting that BSF also has a role in coordinating the mitochondrial translation in addition to its role in mRNA maturation and stability. We thus report a novel function of BSF in flies and demonstrate that it has an important intra-mitochondrial role, which is essential for maintaining mtDNA gene expression and oxidative phosphorylation.}, }
@article {pmid22017975, year = {2011}, author = {Miyagishima, SY and Nakanishi, H and Kabeya, Y}, title = {Structure, regulation, and evolution of the plastid division machinery.}, journal = {International review of cell and molecular biology}, volume = {291}, number = {}, pages = {115-153}, doi = {10.1016/B978-0-12-386035-4.00004-5}, pmid = {22017975}, issn = {1937-6448}, mesh = {Archaeal Proteins/classification/genetics/metabolism ; Bacterial Proteins/classification/genetics/metabolism ; *Biological Evolution ; Cell Division/physiology ; Cytoskeletal Proteins/classification/genetics/metabolism ; Dynamins/classification/genetics/metabolism ; Genome ; Mitochondria/physiology/ultrastructure ; Phylogeny ; Plastids/*physiology/ultrastructure ; Symbiosis ; }, abstract = {Plastids have evolved from a cyanobacterial endosymbiont, and their continuity is maintained by the plastid division and segregation which is regulated by the eukaryotic host cell. Plastids divide by constriction of the inner- and outer-envelope membranes. Recent studies revealed that this constriction is performed by a large protein and glucan complex at the division site that spans the two envelope membranes. The division complex has retained certain components of the cyanobacterial division complex along with components developed by the host cell. Based on the information on the division complex at the molecular level, we are beginning to understand how the division complex has evolved and how it is assembled, constricted, and regulated in the host cell. This chapter reviews the current understanding of the plastid division machinery and some of the questions that will be addressed in the near future.}, }
@article {pmid22017974, year = {2011}, author = {Leister, D and Kleine, T}, title = {Role of intercompartmental DNA transfer in producing genetic diversity.}, journal = {International review of cell and molecular biology}, volume = {291}, number = {}, pages = {73-114}, doi = {10.1016/B978-0-12-386035-4.00003-3}, pmid = {22017974}, issn = {1937-6448}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Cell Nucleus/*genetics/metabolism ; DNA/genetics/*metabolism ; *Gene Transfer, Horizontal ; *Genetic Variation ; Genome ; Humans ; Mitochondria/*genetics/metabolism ; Plastids/*genetics/metabolism ; RNA, Transfer/genetics/metabolism ; Symbiosis/genetics ; Nicotiana/genetics ; }, abstract = {In eukaryotic cells, genes are found in three compartments-the nucleus, mitochondria, and plastids-and extensive gene transfer has occurred between them. Most organellar genes in the nucleus migrated there long ago, but transfer is ongoing and ubiquitous. It now generates mostly noncoding nuclear DNA, can also disrupt gene functions, and reshape genes by adding novel exons. Plastid or nuclear sequences have also contributed to the formation of mitochondrial tRNA genes. It is now clear that organelle-to-nucleus DNA transfer involves the escape of DNA molecules from the organelles at times of stress or at certain developmental stages, and their subsequent incorporation at sites of double-stranded breaks in nuclear DNA by nonhomologous recombination. Intercompartmental DNA transfer thus appears to be an inescapable phenomenon that has had a broad impact on eukaryotic evolution, affecting DNA repair, gene and genome evolution, and redirecting proteins to different target compartments.}, }
@article {pmid22017868, year = {2011}, author = {Wagener, N and Ackermann, M and Funes, S and Neupert, W}, title = {A pathway of protein translocation in mitochondria mediated by the AAA-ATPase Bcs1.}, journal = {Molecular cell}, volume = {44}, number = {2}, pages = {191-202}, doi = {10.1016/j.molcel.2011.07.036}, pmid = {22017868}, issn = {1097-4164}, mesh = {ATPases Associated with Diverse Cellular Activities ; Gene Products, tat/genetics/metabolism ; Membrane Proteins/genetics/*metabolism ; Mitochondria/*enzymology/metabolism ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Models, Biological ; Molecular Chaperones/genetics/*metabolism ; Nuclear Pore Complex Proteins/genetics/metabolism ; Protein Folding ; Protein Transport ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; }, abstract = {The AAA+ family in eukaryotes has many members in various cellular compartments with a role in protein unfolding and degradation. We show that the mitochondrial AAA-ATPase Bcs1 has an unusual function in protein translocation. Bcs1 mediates topogenesis of the Rieske protein, Rip1, a component of respiratory chains in bacteria, mitochondria, and chloroplasts. The oligomeric AAA-ATPase Bcs1 is involved in export of the folded Fe-S domain of Rip1 across the inner membrane and insertion of its transmembrane segment into an assembly intermediate of the cytochrome bc(1) complex, thus revealing an unexpected mechanistical concept of protein translocation across membranes. Furthermore, we describe structural elements of Rip1 required for recognition and export by as well as ATP-dependent lateral release from the AAA-ATPase. In bacteria and chloroplasts Rip1 uses the Tat machinery for topogenesis; however, mitochondria have lost this machinery during evolution and a member of the AAA-ATPase family has taken over its function.}, }
@article {pmid22016847, year = {2011}, author = {Hampl, V and Stairs, CW and Roger, AJ}, title = {The tangled past of eukaryotic enzymes involved in anaerobic metabolism.}, journal = {Mobile genetic elements}, volume = {1}, number = {1}, pages = {71-74}, pmid = {22016847}, issn = {2159-2543}, abstract = {There is little doubt that genes can spread across unrelated prokaryotes, eukaryotes and even between these domains. It is expected that organisms inhabiting a common niche may exchange their genes even more often due to their physical proximity and similar demands. One such niche is anaerobic or microaerophilic environments in some sediments and intestines of animals. Indeed, enzymes advantageous for metabolism in these environments often exhibit an evolutionary history incoherent with the history of their hosts indicating potential transfers. The evolutionary paths of some very basic enzymes for energy metabolism of anaerobic eukaryotes (pyruvate formate lyase, pyruvate:ferredoxin oxidoreductase, [FeFe]hydrogenase and arginine deiminase) seems to be particularly intriguing and although their histories are not identical they share several unexpected features in common. Every enzyme mentioned above is present in groups of eukaryotes that are unrelated to each other. Although the enzyme phylogenies are not always robustly supported, they always suggest that the eukaryotic homologues form one or two clades, in which the relationships are not congruent with the eukaryotic phylogeny. Finally, these eukaryotic enzymes are never specifically related to homologues from α-proteobacteria, ancestors of mitochondria. The most plausible explanation for evolution of this pattern expects one or two interdomain transfers to one or two eukaryotes from prokaryotes, who were not the mitochondrial endosymbiont. Once the genes were introduced into the eukaryotic domain they have spread to other eukaryotic groups exclusively via eukaryote-to-eukaryote transfers. Currently, eukaryote-to-eukaryote gene transfers have been regarded as less common than prokaryote-to-eukaryote transfers. The fact that eukaryotes accepted genes for these enzymes solely from other eukaryotes and not prokaryotes present in the same environment is surprising.}, }
@article {pmid22014084, year = {2011}, author = {Georgiades, K and Raoult, D}, title = {The rhizome of Reclinomonas americana, Homo sapiens, Pediculus humanus and Saccharomyces cerevisiae mitochondria.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {55}, pmid = {22014084}, issn = {1745-6150}, mesh = {Alphaproteobacteria/genetics/metabolism ; Animals ; *Evolution, Molecular ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genes, Fungal ; *Genes, Mitochondrial ; Genome, Human ; Humans ; Mitochondria/*genetics/metabolism ; Pediculus/*genetics/metabolism ; Phylogeny ; Ribosomal Proteins/genetics/metabolism ; Ribosomes/genetics/metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; }, abstract = {BACKGROUND: Mitochondria are thought to have evolved from eubacteria-like endosymbionts; however, the origin of the mitochondrion remains a subject of debate. In this study, we investigated the phenomenon of chimerism in mitochondria to shed light on the origin of these organelles by determining which species played a role in their formation. We used the mitochondria of four distinct organisms, Reclinomonas americana, Homo sapiens, Saccharomyces cerevisiae and multichromosome Pediculus humanus, and attempted to identify the origin of each mitochondrial gene.<br><br>RESULTS: Our results suggest that the origin of mitochondrial genes is not limited to the Rickettsiales and that the creation of these genes did not occur in a single event, but through multiple successive events. Some of these events are very old and were followed by events that are more recent and occurred through the addition of elements originating from current species. The points in time that the elements were added and the parental species of each gene in the mitochondrial genome are different to the individual species. These data constitute strong evidence that mitochondria do not have a single common ancestor but likely have numerous ancestors, including proto-Rickettsiales, proto-Rhizobiales and proto-Alphaproteobacteria, as well as current alphaproteobacterial species. The analysis of the multichromosome P. humanus mitochondrion supports this mechanism.<br><br>CONCLUSIONS: The most plausible scenario of the origin of the mitochondrion is that ancestors of Rickettsiales and Rhizobiales merged in a proto-eukaryotic cell approximately one billion years ago. The fusion of the Rickettsiales and Rhizobiales cells was followed by gene loss, genomic rearrangements and the addition of alphaproteobacterial elements through ancient and more recent recombination events. Each gene of each of the four studied mitochondria has a different origin, while in some cases, multichromosomes may allow for enhanced gene exchange. Therefore, the tree of life is not sufficient to explain the chimeric structure of current genomes, and the theory of a single common ancestor and a top-down tree does not reflect our current state of knowledge. Mitochondrial evolution constitutes a rhizome, and it should be represented as such.}, }
@article {pmid22013386, year = {2011}, author = {Franzini-Armstrong, C and Boncompagni, S}, title = {The evolution of the mitochondria-to-calcium release units relationship in vertebrate skeletal muscles.}, journal = {Journal of biomedicine &amp; biotechnology}, volume = {2011}, number = {}, pages = {830573}, pmid = {22013386}, issn = {1110-7251}, support = {R01 H 48093//PHS HHS/United States ; }, mesh = {Amphibians ; Animals ; Biological Evolution ; Birds ; Calcium/metabolism ; Calcium Channels/metabolism/*ultrastructure ; Cell Membrane/*ultrastructure ; Fishes ; Humans ; Mammals ; Mitochondria/metabolism/*ultrastructure ; Muscle, Skeletal/*ultrastructure ; Reptiles ; Ryanodine Receptor Calcium Release Channel/metabolism/*ultrastructure ; Sarcoplasmic Reticulum/ultrastructure ; }, abstract = {The spatial relationship between mitochondria and the membrane systems, more specifically the calcium release units (CRUs) of skeletal muscle, is of profound functional significance. CRUs are the sites at which Ca(2+) is released from the sarcoplasmic reticulum during muscle activation. Close mitochondrion-CRU proximity allows the organelles to take up Ca(2+) and thus stimulate aerobic metabolism. Skeletal muscles of most mammals display an extensive, developmentally regulated, close mitochondrion-CRU association, fostered by tethering links between the organelles. A comparative look at the vertebrate subphylum however shows that this specific association is only present in the higher vertebrates (mammals). Muscles in all other vertebrates, even if capable of fast activity, rely on a less precise and more limited mitochondrion-CRU proximity, despite some tethering connections. This is most evident in fish muscles. Clustering of free subsarcolemmal mitochondria in proximity of capillaries is also more frequently achieved in mammalian than in other vertebrates.}, }
@article {pmid22013080, year = {2012}, author = {Costa-Urrutia, P and Abud, C and Secchi, ER and Lessa, EP}, title = {Population genetic structure and social kin associations of franciscana dolphin, Pontoporia blainvillei.}, journal = {The Journal of heredity}, volume = {103}, number = {1}, pages = {92-102}, doi = {10.1093/jhered/esr103}, pmid = {22013080}, issn = {1465-7333}, mesh = {Animals ; Atlantic Ocean ; Bayes Theorem ; Brazil ; Dolphins/*genetics ; Endangered Species ; Female ; Genetic Structures ; *Genetic Variation ; Haplotypes ; Male ; Markov Chains ; Microsatellite Repeats ; Mitochondria/genetics ; Monte Carlo Method ; Multilocus Sequence Typing ; Phylogeny ; Phylogeography ; Sexual Behavior, Animal ; Social Behavior ; Uruguay ; }, abstract = {We investigated population and social structure of the franciscana dolphin, Pontoporia blainvillei, an endemic and the most endangered cetacean of the southwestern Atlantic Ocean. We analyzed samples from the Rio de la Plata estuary obtained in Uruguayan waters and from the Atlantic Ocean obtained in both Uruguayan and Brazilian waters. Mitochondrial and microsatellite DNA markers were used to study differentiation between the estuary and the ocean and the association between kinship and social group structure. Although multilocus analyses suggested that franciscanas are structured into 2 subpopulations (K = 2, divergence among clusters: F(ST) = 0.06, P = 0.002; R(ST) = 0.3, P = 0.001), mitochondrial markers did not support such divergence (F(ST) = 0.02, P = 0.12; Ф(ST) = 0.06, P =0.06). However, these units are not entirely segregated geographically. Regarding social structure, some groups are composed by first-order related individuals (R ≥ 0.5, P < 0.5). Overall, the data suggest that matrilines could be the social unit in this species. We argue that the divergence found could be associated to local adaptation and social structure, resulting from either feature leading to a recent divergence or reflecting equilibrium between local differentiation and gene flow. This evidence supports considering franciscanas from the Rio de la Plata estuary a discrete management unit.}, }
@article {pmid22012225, year = {2011}, author = {Bourke, BP and Nagaki, SS and Bergo, ES and Cardoso, Jda C and Sallum, MA}, title = {Molecular phylogeny of the Myzorhynchella Section of Anopheles (Nyssorhynchus) (Diptera: Culicidae): genetic support for recently described and resurrected species.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {106}, number = {6}, pages = {705-715}, doi = {10.1590/s0074-02762011000600010}, pmid = {22012225}, issn = {1678-8060}, mesh = {Animals ; Anopheles/classification/*genetics ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex IV/*genetics ; Female ; Genes, Insect/*genetics ; Mitochondria/enzymology ; Phylogeny ; Species Specificity ; }, abstract = {Phylogenetic relationships among species of the Myzorhynchella Section of Anopheles (Nyssorhynchus) were investigated using the nuclear ribosomal DNA second internal transcribed spacer (ITS2), the nuclear whitegene and mitochondrial cytochrome oxidase subunit I (COI) regions. The recently described Anopheles pristinus and resurrected Anopheles guarani were also included in the study. Bayesian phylogenetic analyses found Anopheles parvus to be the most distantly related species within the Section, a finding that is consistent with morphology. An. pristinus and An. guarani were clearly resolved from Anopheles antunesi and Anopheles lutzii, respectively. An. lutzii collected in the same mountain range as the type locality were found within a strongly supported clade, whereas individuals from the southern state of Rio Grande do Sul, tentatively identified as An. lutzii based on adult female external morphology, were distinct from An. lutzii, An. antunesi and from each other, and may therefore represent two new sympatric species. A more detailed examination of An. lutzii sensu latoalong its known geographic range is recommended to resolve these anomalous relationships.}, }
@article {pmid22008946, year = {2011}, author = {Vesteg, M and Krajčovič, J}, title = {The falsifiability of the models for the origin of eukaryotes.}, journal = {Current genetics}, volume = {57}, number = {6}, pages = {367-390}, pmid = {22008946}, issn = {1432-0983}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; *Eukaryotic Cells ; Models, Biological ; Phylogeny ; Symbiosis ; }, abstract = {One group of hypotheses suggests archaeal and/or bacterial ancestry of eukaryotes, while the second group suggests that the ancestor of eukaryotes was different. Especially, the followers of the first group of hypotheses should ask the following: is the replacement of archaeal lipids by bacterial (or vice versa) possible? Do the phylogenies support the origin of one domain from another (or the others)? Can we consider the nutritional mode to resolve the problems of cell origin(s)? Is there any evidence that the ancestor of eukaryotes was intron-free? Would the symbiosis of α-proteobacterial ancestors of mitochondria be successful in an asexual host? Is there evidence that the last universal common ancestor (LUCA) or the last eukaryotic common ancestor was bounded by one membrane only? With respect to the current knowledge about cells and their molecular components, the answer to most of these questions is: No! A model for the origins of domains is briefly presented which cannot be assigned as false through the current scientific data, and is rather consistent with the assumption that eukaryotes are direct descendants of neither archaea nor bacteria. It is proposed that the domain Bacteria arose the first, and that the last common ancestor of Archaea and Eukarya was a pre-cell or a progenote similar to LUCA. The pre-karyote (the host entity for α-proteobacterial ancestors of mitochondria) was probably bounded by two membranes, possessed spliceosomal introns and spliceosomes, was sexual, and α-proteobacterial ancestors of mitochondria were most likely parasites of the pre-karyote periplasm (intermembrane space).}, }
@article {pmid22008467, year = {2012}, author = {Johnson, JL}, title = {Evolution and function of diverse Hsp90 homologs and cochaperone proteins.}, journal = {Biochimica et biophysica acta}, volume = {1823}, number = {3}, pages = {607-613}, doi = {10.1016/j.bbamcr.2011.09.020}, pmid = {22008467}, issn = {0006-3002}, mesh = {Adenosine Triphosphatases/genetics/metabolism ; Animals ; Evolution, Molecular ; HSP70 Heat-Shock Proteins/genetics/metabolism ; HSP90 Heat-Shock Proteins/*genetics/*metabolism ; Humans ; Molecular Chaperones/*genetics/*metabolism ; Multiprotein Complexes/genetics/metabolism ; Protein Folding ; }, abstract = {Members of the Hsp90 molecular chaperone family are found in the cytosol, ER, mitochondria and chloroplasts of eukaryotic cells, as well as in bacteria. These diverse family members cooperate with other proteins, such as the molecular chaperone Hsp70, to mediate protein folding, activation and assembly into multiprotein complexes. All examined Hsp90 homologs exhibit similar ATPase rates and undergo similar conformational changes. One of the key differences is that cytosolic Hsp90 interacts with a large number of cochaperones that regulate the ATPase activity of Hsp90 or have other functions, such as targeting clients to Hsp90. Diverse Hsp90 homologs appear to chaperone different types of client proteins. This difference may reflect either the pool of clients requiring Hsp90 function or the requirement for cochaperones to target clients to Hsp90. This review discusses known functions, similarities and differences between Hsp90 family members and how cochaperones are known to affect these functions. This article is part of a Special Issue entitled: Heat Shock Protein 90 (HSP90).}, }
@article {pmid22008223, year = {2011}, author = {Boissin, E and Stöhr, S and Chenuil, A}, title = {Did vicariance and adaptation drive cryptic speciation and evolution of brooding in Ophioderma longicauda (Echinodermata: Ophiuroidea), a common Atlanto-Mediterranean ophiuroid?.}, journal = {Molecular ecology}, volume = {20}, number = {22}, pages = {4737-4755}, doi = {10.1111/j.1365-294X.2011.05309.x}, pmid = {22008223}, issn = {1365-294X}, mesh = {Adaptation, Biological/*genetics ; Alleles ; Animals ; Atlantic Ocean ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer ; Echinodermata/*genetics ; Gene Flow ; *Genetic Speciation ; Genetic Variation ; Geography ; Mediterranean Sea ; Mitochondria/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Over the last decade, cryptic speciation has been discovered in an increasing number of taxa. Species complexes are useful models for the understanding of speciation processes. Motivated by the discovery of brooding specimens in the common Atlanto-Mediterranean broadcast spawning brittle star, Ophioderma longicauda, a recent study revealed the occurrence of divergent mitochondrial lineages. We analysed 218 specimens from 23 locations spread over the geographic range of the species with partial Cytochrome c Oxidase subunit I (COI) sequences. A subset of this sample was also surveyed with the internal transcribed spacer of the ribosomal DNA cluster (nuclear ITS-1). Our study revealed six highly divergent mitochondrial lineages, and the ITS-1 data confirmed that they most likely represent a species complex. Geographic ranges, abundances and genetic structures are contrasted among the putative cryptic species. Lineages in which brooding specimens have been found form a monophyletic group and are restricted to the Eastern Mediterranean basin, an oligotrophic zone. A phylogeny-trait association analysis revealed a phylogenetic signal for low 'chlorophyll a' values (our proxy for oligotrophy). An ecological shift related to the hyper oligotrophy of the Eastern Mediterranean region is therefore likely to have played a role in the evolution of brooding. This study revealed that a complex mixture of vicariance, population expansion, adaptive divergence and possibly high local diversification rates resulting from brooding has shaped the evolution of this species complex. The dating analysis showed that these events probably occurred in the Pleistocene epoch.}, }
@article {pmid22008015, year = {2012}, author = {Schuhmann, H and Adamska, I}, title = {Deg proteases and their role in protein quality control and processing in different subcellular compartments of the plant cell.}, journal = {Physiologia plantarum}, volume = {145}, number = {1}, pages = {224-234}, doi = {10.1111/j.1399-3054.2011.01533.x}, pmid = {22008015}, issn = {1399-3054}, mesh = {Arabidopsis/enzymology ; Arabidopsis Proteins/*metabolism ; Cell Nucleus/enzymology ; Chloroplast Proteins/metabolism ; Chloroplasts/*enzymology ; Mitochondria/enzymology ; Oxidation-Reduction ; Peroxisomes/*enzymology/physiology ; Photosynthesis ; Phylogeny ; Plant Cells/*enzymology/physiology ; Proteolysis ; Serine Endopeptidases/*metabolism ; }, abstract = {Degradation of periplasmic proteins (Deg)/high temperature requirement A (HtrA) proteases are ATP-independent serine endopeptidases found in almost every organism. Database searches revealed that 16 Deg paralogues are encoded by the genome of Arabidopsis thaliana, six of which were experimentally shown to be located in chloroplasts, one in peroxisomes, one in mitochondria and one in the nucleus. Two more Deg proteases are predicted to reside in chloroplasts, five in mitochondria (one of them with a dual chloroplastidial/mitochondrial localization) and the subcellular location of one protein is uncertain. This review summarizes the current knowledge on the role of Deg proteases in maintaining protein homeostasis and protein processing in various subcompartments of the plant cell. The chloroplast Deg proteases are the best examined so far, especially with respect to their role in the degradation of photodamaged photosynthetic proteins and in biogenesis of photosystem II (PSII). A combined action of thylakoid lumen and stroma Deg proteases in the primary cleavage of photodamaged D1 protein from PSII reaction centre is discussed on the basis of a recently resolved crystal structure of plant Deg1. The peroxisomal Deg protease is a processing enzyme responsible for the cleavage of N-terminal peroxisomal targeting signals (PTSs). A. thaliana mutants lacking this enzyme show reduced peroxisomal β-oxidation, indicating for the first time the impact of protein processing on peroxisomal functions in plants. Much less data is available for mitochondrial and nuclear Deg proteases. Based on the available expression data we hypothesize a role in general protein quality control and during acquired heat resistance.}, }
@article {pmid22007289, year = {2011}, author = {Watanabe, K and Yokobori, S}, title = {tRNA Modification and Genetic Code Variations in Animal Mitochondria.}, journal = {Journal of nucleic acids}, volume = {2011}, number = {}, pages = {623095}, pmid = {22007289}, issn = {2090-021X}, abstract = {In animal mitochondria, six codons have been known as nonuniversal genetic codes, which vary in the course of animal evolution. They are UGA (termination codon in the universal genetic code changes to Trp codon in all animal mitochondria), AUA (Ile to Met in most metazoan mitochondria), AAA (Lys to Asn in echinoderm and some platyhelminth mitochondria), AGA/AGG (Arg to Ser in most invertebrate, Arg to Gly in tunicate, and Arg to termination in vertebrate mitochondria), and UAA (termination to Tyr in a planaria and a nematode mitochondria, but conclusive evidence is lacking in this case). We have elucidated that the anticodons of tRNAs deciphering these nonuniversal codons (tRNA(Trp) for UGA, tRNA(Met) for AUA, tRNA(Asn) for AAA, and tRNA(Ser) and tRNA(Gly) for AGA/AGG) are all modified; tRNA(Trp) has 5-carboxymethylaminomethyluridine or 5-taurinomethyluridine, tRNA(Met) has 5-formylcytidine or 5-taurinomethyluridine, tRNA(Ser) has 7-methylguanosine and tRNA(Gly) has 5-taurinomethyluridine in their anticodon wobble position, and tRNA(Asn) has pseudouridine in the anticodon second position. This review aims to clarify the structural relationship between these nonuniversal codons and the corresponding tRNA anticodons including modified nucleosides and to speculate on the possible mechanisms for explaining the evolutional changes of these nonuniversal codons in the course of animal evolution.}, }
@article {pmid22004680, year = {2011}, author = {Coyne, RS and Hannick, L and Shanmugam, D and Hostetler, JB and Brami, D and Joardar, VS and Johnson, J and Radune, D and Singh, I and Badger, JH and Kumar, U and Saier, M and Wang, Y and Cai, H and Gu, J and Mather, MW and Vaidya, AB and Wilkes, DE and Rajagopalan, V and Asai, DJ and Pearson, CG and Findly, RC and Dickerson, HW and Wu, M and Martens, C and Van de Peer, Y and Roos, DS and Cassidy-Hanley, DM and Clark, TG}, title = {Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control.}, journal = {Genome biology}, volume = {12}, number = {10}, pages = {R100}, pmid = {22004680}, issn = {1474-760X}, support = {/HHMI/Howard Hughes Medical Institute/United States ; R01 GM099820/GM/NIGMS NIH HHS/United States ; R01 GM077402/GM/NIGMS NIH HHS/United States ; SC1 AI080579/AI/NIAID NIH HHS/United States ; R01 AI028398/AI/NIAID NIH HHS/United States ; SC1 GM081068/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Antigens, Protozoan/genetics ; Base Composition ; Chromosome Mapping ; Ciliophora Infections/*prevention &amp; control ; DNA, Mitochondrial/genetics ; DNA, Protozoan/genetics ; Databases, Genetic ; Genes, Protozoan ; Genome Size ; Genomics/*methods ; Host-Parasite Interactions ; Hymenostomatida/classification/*genetics/growth &amp; development/pathogenicity ; Ictaluridae/parasitology ; *Life Cycle Stages ; Macronucleus/genetics ; Membrane Transport Proteins/genetics ; Metabolic Networks and Pathways ; Mitochondria/enzymology/genetics ; Mitochondrial Proton-Translocating ATPases/genetics ; Molecular Sequence Annotation ; Phylogeny ; Protein Kinases/classification/genetics ; Protozoan Proteins/genetics ; RNA, Protozoan/genetics ; Zebrafish/genetics/*parasitology ; }, abstract = {BACKGROUND: Ichthyophthirius multifiliis, commonly known as Ich, is a highly pathogenic ciliate responsible for 'white spot', a disease causing significant economic losses to the global aquaculture industry. Options for disease control are extremely limited, and Ich's obligate parasitic lifestyle makes experimental studies challenging. Unlike most well-studied protozoan parasites, Ich belongs to a phylum composed primarily of free-living members. Indeed, it is closely related to the model organism Tetrahymena thermophila. Genomic studies represent a promising strategy to reduce the impact of this disease and to understand the evolutionary transition to parasitism.<br><br>RESULTS: We report the sequencing, assembly and annotation of the Ich macronuclear genome. Compared with its free-living relative T. thermophila, the Ich genome is reduced approximately two-fold in length and gene density and three-fold in gene content. We analyzed in detail several gene classes with diverse functions in behavior, cellular function and host immunogenicity, including protein kinases, membrane transporters, proteases, surface antigens and cytoskeletal components and regulators. We also mapped by orthology Ich's metabolic pathways in comparison with other ciliates and a potential host organism, the zebrafish Danio rerio.<br><br>CONCLUSIONS: Knowledge of the complete protein-coding and metabolic potential of Ich opens avenues for rational testing of therapeutic drugs that target functions essential to this parasite but not to its fish hosts. Also, a catalog of surface protein-encoding genes will facilitate development of more effective vaccines. The potential to use T. thermophila as a surrogate model offers promise toward controlling 'white spot' disease and understanding the adaptation to a parasitic lifestyle.}, }
@article {pmid22001261, year = {2012}, author = {Yang, EC and Boo, GH and Kim, HJ and Cho, SM and Boo, SM and Andersen, RA and Yoon, HS}, title = {Supermatrix data highlight the phylogenetic relationships of photosynthetic stramenopiles.}, journal = {Protist}, volume = {163}, number = {2}, pages = {217-231}, doi = {10.1016/j.protis.2011.08.001}, pmid = {22001261}, issn = {1618-0941}, mesh = {Cell Nucleus/genetics ; *Genes, Chloroplast ; Genes, Mitochondrial ; Mitochondria/genetics ; Photosynthesis ; *Phylogeny ; Plastids/genetics ; RNA, Ribosomal/genetics ; Ribosomes/genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; Stramenopiles/*classification/genetics ; }, abstract = {Molecular data had consistently recovered monophyletic classes for the heterokont algae, however, the relationships among the classes had remained only partially resolved. Furthermore, earlier studies did not include representatives from all taxonomic classes. We used a five-gene (nuclear encoded SSU rRNA; plastid encoded rbcL, psaA, psbA, psbC) analysis with a subset of 89 taxa representing all 16 heterokont classes to infer a phylogenetic tree. There were three major clades. The Aurearenophyceae, Chrysomerophyceae, Phaeophyceae, Phaeothamniophyceae, Raphidophyceae, Schizocladiophyceae and Xanthophyceae formed the SI clade. The Chrysophyceae, Eustigmatophyceae, Pinguiophyceae, Synchromophyceae and Synurophyceae formed the SII clade. The Bacillariophyceae, Bolidophyceae, Dictyochophyceae and Pelagophyceae formed the SIII clade. These three clades were also found in a ten-gene analysis. The approximately unbiased test rejected alternative hypotheses that forced each class into either of the other two clades. Morphological and biochemical data were not available for all 89 taxa, however, existing data were consistent with the molecular phylogenetic tree, especially for the SIII clade.}, }
@article {pmid22000100, year = {2011}, author = {Pusnik, M and Schmidt, O and Perry, AJ and Oeljeklaus, S and Niemann, M and Warscheid, B and Lithgow, T and Meisinger, C and Schneider, A}, title = {Mitochondrial preprotein translocase of trypanosomatids has a bacterial origin.}, journal = {Current biology : CB}, volume = {21}, number = {20}, pages = {1738-1743}, doi = {10.1016/j.cub.2011.08.060}, pmid = {22000100}, issn = {1879-0445}, mesh = {Bacterial Outer Membrane Proteins ; Bacterial Proteins/genetics/metabolism ; Escherichia coli Proteins ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Methotrexate/pharmacology ; Mitochondrial Membrane Transport Proteins/chemistry/genetics/*metabolism ; Mitochondrial Membranes/*metabolism ; Protein Conformation ; Protein Transport ; Recombinant Fusion Proteins/genetics/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Tetrahydrofolate Dehydrogenase/genetics/metabolism ; Trypanosoma brucei brucei/drug effects/genetics/*metabolism ; Voltage-Dependent Anion Channels/genetics/metabolism ; }, abstract = {Mitochondria are found in all eukaryotic cells and derive from a bacterial endosymbiont [1, 2]. The evolution of a protein import system was a prerequisite for the conversion of the endosymbiont into a true organelle. Tom40, the essential component of the protein translocase of the outer membrane, is conserved in mitochondria of almost all eukaryotes but lacks bacterial orthologs [3-6]. It serves as the gateway through which all mitochondrial proteins are imported. The parasitic protozoa Trypanosoma brucei and its relatives do not have a Tom40-like protein, which raises the question of how proteins are imported by their mitochondria [7, 8]. Using a combination of bioinformatics and in vivo and in vitro studies, we have discovered that T. brucei likely employs a different import channel, termed ATOM (archaic translocase of the outer mitochondrial membrane). ATOM mediates the import of nuclear-encoded proteins into mitochondria and is essential for viability of trypanosomes. It is not related to Tom40 but is instead an ortholog of a subgroup of the Omp85 protein superfamily that is involved in membrane translocation and insertion of bacterial outer membrane proteins [9]. This suggests that the protein import channel in trypanosomes is a relic of an archaic protein transport system that was operational in the ancestor of all eukaryotes.}, }
@article {pmid21998669, year = {2011}, author = {De Barro, P and Ahmed, MZ}, title = {Genetic networking of the Bemisia tabaci cryptic species complex reveals pattern of biological invasions.}, journal = {PloS one}, volume = {6}, number = {10}, pages = {e25579}, pmid = {21998669}, issn = {1932-6203}, mesh = {Animals ; Electron Transport Complex IV/genetics ; Genes, Insect/*genetics ; Genetic Variation/genetics ; Haplotypes/genetics ; Hemiptera/*classification/*genetics ; *Introduced Species ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {BACKGROUND: A challenge within the context of cryptic species is the delimitation of individual species within the complex. Statistical parsimony network analytics offers the opportunity to explore limits in situations where there are insufficient species-specific morphological characters to separate taxa. The results also enable us to explore the spread in taxa that have invaded globally.<br><br>Using a 657 bp portion of mitochondrial cytochrome oxidase 1 from 352 unique haplotypes belonging to the Bemisia tabaci cryptic species complex, the analysis revealed 28 networks plus 7 unconnected individual haplotypes. Of the networks, 24 corresponded to the putative species identified using the rule set devised by Dinsdale et al. (2010). Only two species proposed in Dinsdale et al. (2010) departed substantially from the structure suggested by the analysis. The analysis of the two invasive members of the complex, Mediterranean (MED) and Middle East - Asia Minor 1 (MEAM1), showed that in both cases only a small number of haplotypes represent the majority that have spread beyond the home range; one MEAM1 and three MED haplotypes account for >80% of the GenBank records. Israel is a possible source of the globally invasive MEAM1 whereas MED has two possible sources. The first is the eastern Mediterranean which has invaded only the USA, primarily Florida and to a lesser extent California. The second are western Mediterranean haplotypes that have spread to the USA, Asia and South America. The structure for MED supports two home range distributions, a Sub-Saharan range and a Mediterranean range. The MEAM1 network supports the Middle East - Asia Minor region.<br><br>CONCLUSION/SIGNIFICANCE: The network analyses show a high level of congruence with the species identified in a previous phylogenetic analysis. The analysis of the two globally invasive members of the complex support the view that global invasion often involve very small portions of the available genetic diversity.}, }
@article {pmid21998376, year = {2011}, author = {Lane, N}, title = {Evolution. The costs of breathing.}, journal = {Science (New York, N.Y.)}, volume = {334}, number = {6053}, pages = {184-185}, doi = {10.1126/science.1214012}, pmid = {21998376}, issn = {1095-9203}, mesh = {Adaptation, Physiological ; Adenosine Triphosphate/metabolism ; Aging ; Animals ; Apoptosis ; *Biological Evolution ; Cell Nucleus/*genetics/metabolism ; *Cell Respiration ; Cytochromes c/metabolism ; Electron Transport ; Embryonic Development ; Fertility ; *Genes, Mitochondrial ; Genetic Fitness ; Longevity ; Mitochondria/*metabolism ; Models, Biological ; Mutation ; Reactive Oxygen Species/*metabolism ; *Selection, Genetic ; Species Specificity ; }, }
@article {pmid21998274, year = {2012}, author = {Xu, S and Schaack, S and Seyfert, A and Choi, E and Lynch, M and Cristescu, ME}, title = {High mutation rates in the mitochondrial genomes of Daphnia pulex.}, journal = {Molecular biology and evolution}, volume = {29}, number = {2}, pages = {763-769}, pmid = {21998274}, issn = {1537-1719}, support = {R01 GM036827/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Daphnia/*genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; Mitochondria/genetics ; Mutation ; *Mutation Rate ; Phylogeny ; Recombination, Genetic ; }, abstract = {Despite the great utility of mitochondrial DNA (mtDNA) sequence data in population genetics and phylogenetics, key parameters describing the process of mitochondrial mutation (e.g., the rate and spectrum of mutational change) are based on few direct estimates. Furthermore, the variation in the mtDNA mutation process within species or between lineages with contrasting reproductive strategies remains poorly understood. In this study, we directly estimate the mtDNA mutation rate and spectrum using Daphnia pulex mutation-accumulation (MA) lines derived from sexual (cyclically parthenogenetic) and asexual (obligately parthenogenetic) lineages. The nearly complete mitochondrial genome sequences of 82 sexual and 47 asexual MA lines reveal high mtDNA mutation rate of 1.37 × 10(-7) and 1.73 × 10(-7) per nucleotide per generation, respectively. The Daphnia mtDNA mutation rate is among the highest in eukaryotes, and its spectrum is dominated by insertions and deletions (70%), largely due to the presence of mutational hotspots at homopolymeric nucleotide stretches. Maximum likelihood estimates of the Daphnia mitochondrial effective population size reveal that between five and ten copies of mitochondrial genomes are transmitted per female per generation. Comparison between sexual and asexual lineages reveals no statistically different mutation rates and highly similar mutation spectra.}, }
@article {pmid21967349, year = {2011}, author = {Bindoff, LA}, title = {Mitochondrial function and pathology in status epilepticus.}, journal = {Epilepsia}, volume = {52 Suppl 8}, number = {}, pages = {6-7}, doi = {10.1111/j.1528-1167.2011.03223.x}, pmid = {21967349}, issn = {1528-1167}, mesh = {DNA Polymerase gamma ; DNA, Mitochondrial/genetics ; DNA-Directed DNA Polymerase/genetics ; Humans ; Mitochondria/genetics/*pathology ; Mitochondrial Diseases/*complications ; Mutation/genetics ; Status Epilepticus/*etiology/genetics/*pathology ; }, abstract = {The mitochondrial respiratory chain is the final common pathway for energy production. Defects affecting this pathway can give rise to disease that presents at any age and affects any tissue. However, irrespective of genetic defect, epilepsy is common and there is a significant risk of status epilepticus. We have studied two types of mitochondrial disease: one arising from a defect in mitochondrial DNA (mtDNA) (MELAS) and one due to a nuclear gene mutation (POLG). These two disorders show similarities in their clinicopathologic evolution and in findings in postmortem samples. Our findings based on antemortem magnetic resonance imaging (MRI) and postmortem studies suggest that the status epilepticus that is seen in both appears to be the result of cortical damage resulting from a common mechanism, namely energy failure.}, }
@article {pmid21988877, year = {2011}, author = {Ito, K and Ogata, T and Kakizaki, Y and Elliott, C and Albury, MS and Moore, AL}, title = {Identification of a gene for pyruvate-insensitive mitochondrial alternative oxidase expressed in the thermogenic appendices in Arum maculatum.}, journal = {Plant physiology}, volume = {157}, number = {4}, pages = {1721-1732}, pmid = {21988877}, issn = {1532-2548}, support = {BB/E015328/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Arum/drug effects/*enzymology/genetics ; Base Sequence ; Cell Respiration ; Chromatography, Liquid ; DNA, Complementary/genetics ; DNA, Plant/chemistry/genetics ; Flowers/*enzymology/genetics ; Hot Temperature ; Mitochondrial Proteins/drug effects/genetics/*metabolism ; Molecular Sequence Data ; Organ Specificity ; Oxidoreductases/drug effects/genetics/*metabolism ; Phylogeny ; Plant Proteins/drug effects/genetics/*metabolism ; Pyruvic Acid/*pharmacology ; Schizosaccharomyces/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Tandem Mass Spectrometry ; }, abstract = {Heat production in thermogenic plants has been attributed to a large increase in the expression of the alternative oxidase (AOX). AOX acts as an alternative terminal oxidase in the mitochondrial respiratory chain, where it reduces molecular oxygen to water. In contrast to the mitochondrial terminal oxidase, cytochrome c oxidase, AOX is nonprotonmotive and thus allows the dramatic drop in free energy between ubiquinol and oxygen to be dissipated as heat. Using reverse transcription-polymerase chain reaction-based cloning, we reveal that, although at least seven cDNAs for AOX exist (AmAOX1a, -1b, -1c, -1d, -1e, -1f, and -1g) in Arum maculatum, the organ and developmental regulation for each is distinct. In particular, the expression of AmAOX1e transcripts appears to predominate in thermogenic appendices among the seven AmAOXs. Interestingly, the amino acid sequence of AmAOX1e indicates that the ENV element found in almost all other AOX sequences, including AmAOX1a, -1b, -1c, -1d, and -1f, is substituted by QNT. The existence of a QNT motif in AmAOX1e was confirmed by nano-liquid chromatography-tandem mass spectrometry analysis of mitochondrial proteins from thermogenic appendices. Further functional analyses with mitochondria prepared using a yeast heterologous expression system demonstrated that AmAOX1e is insensitive to stimulation by pyruvate. These data suggest that a QNT type of pyruvate-insensitive AOX, AmAOX1e, plays a crucial role in stage- and organ-specific heat production in the appendices of A. maculatum.}, }
@article {pmid21986531, year = {2011}, author = {Nozawa, A and Fujimoto, R and Matsuoka, H and Tsuboi, T and Tozawa, Y}, title = {Cell-free synthesis, reconstitution, and characterization of a mitochondrial dicarboxylate-tricarboxylate carrier of Plasmodium falciparum.}, journal = {Biochemical and biophysical research communications}, volume = {414}, number = {3}, pages = {612-617}, doi = {10.1016/j.bbrc.2011.09.130}, pmid = {21986531}, issn = {1090-2104}, mesh = {Carrier Proteins/biosynthesis/*chemistry/classification/genetics ; Cell-Free System/chemistry ; Dicarboxylic Acid Transporters/biosynthesis/*chemistry/classification/genetics ; Mitochondria/*metabolism ; Phylogeny ; Plasmodium falciparum/genetics/*metabolism ; Protozoan Proteins/biosynthesis/*chemistry/classification/genetics ; Tricarboxylic Acids/*metabolism ; }, abstract = {The malaria parasite, Plasmodium falciparum, was recently shown to operate a branched pathway of tricarboxylic acid (TCA) metabolism. To identify and characterize membrane transporters required for such TCA metabolism in the parasite, we isolated a cDNA for a dicarboxylate-tricarboxylate carrier homolog (PfDTC), synthesized the encoded protein with the use of a cell-free translation system, and determined the substrate specificity of its transport activity with a proteoliposome reconstitution system. PfDTC was found to mediate efficient oxoglutarate-malate, oxoglutarate-oxaloacetate, or oxoglutarate-oxoglutarate exchange across the liposome membrane. Our results suggest that PfDTC may mediate the oxoglutarate-malate exchange across the inner mitochondrial membrane required for the branched pathway of TCA metabolism in the malaria parasite.}, }
@article {pmid21985407, year = {2011}, author = {Pett, W and Ryan, JF and Pang, K and Mullikin, JC and Martindale, MQ and Baxevanis, AD and Lavrov, DV}, title = {Extreme mitochondrial evolution in the ctenophore Mnemiopsis leidyi: Insight from mtDNA and the nuclear genome.}, journal = {Mitochondrial DNA}, volume = {22}, number = {4}, pages = {130-142}, pmid = {21985407}, issn = {1940-1744}, support = {ZIA HG000140-13/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Cell Nucleus/*genetics ; Ctenophora/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; *Genome ; *Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {Recent advances in sequencing technology have led to a rapid accumulation of mitochondrial DNA (mtDNA) sequences, which now represent the wide spectrum of animal diversity. However, one animal phylum--Ctenophora--has, to date, remained completely unsampled. Ctenophores, a small group of marine animals, are of interest due to their unusual biology, controversial phylogenetic position, and devastating impact as invasive species. Using data from the Mnemiopsis leidyi genome sequencing project, we Polymerase Chain Reaction (PCR) amplified and analyzed its complete mitochondrial (mt-) genome. At just over 10 kb, the mt-genome of M. leidyi is the smallest animal mtDNA ever reported and is among the most derived. It has lost at least 25 genes, including atp6 and all tRNA genes. We show that atp6 has been relocated to the nuclear genome and has acquired introns and a mitochondrial targeting presequence, while tRNA genes have been genuinely lost, along with nuclear-encoded mt-aminoacyl tRNA synthetases. The mt-genome of M. leidyi also displays extremely high rates of sequence evolution, which likely led to the degeneration of both protein and rRNA genes. In particular, encoded rRNA molecules possess little similarity with their homologs in other organisms and have highly reduced secondary structures. At the same time, nuclear encoded mt-ribosomal proteins have undergone expansions, likely to compensate for the reductions in mt-rRNA. The unusual features identified in M. leidyi mtDNA make this organism an interesting system for the study of various aspects of mitochondrial biology, particularly protein and tRNA import and mt-ribosome structures, and add to its value as an emerging model species. Furthermore, the fast-evolving M. leidyi mtDNA should be a convenient molecular marker for species- and population-level studies.}, }
@article {pmid21984653, year = {2012}, author = {Waller, JC and Ellens, KW and Alvarez, S and Loizeau, K and Ravanel, S and Hanson, AD}, title = {Mitochondrial and plastidial COG0354 proteins have folate-dependent functions in iron-sulphur cluster metabolism.}, journal = {Journal of experimental botany}, volume = {63}, number = {1}, pages = {403-411}, pmid = {21984653}, issn = {1460-2431}, support = {UL1 TR000064/TR/NCATS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Arabidopsis Proteins/chemistry/*metabolism ; Iron/*metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Plastids/*metabolism ; Sequence Homology, Amino Acid ; Sulfur/*metabolism ; }, abstract = {COG0354 proteins have been implicated in synthesis or repair of iron/sulfur (Fe/S) clusters in all domains of life, and those of bacteria, animals, and protists have been shown to require a tetrahydrofolate to function. Two COG0354 proteins were identified in Arabidopsis and many other plants, one (At4g12130) related to those of α-proteobacteria and predicted to be mitochondrial, the other (At1g60990) related to those of cyanobacteria and predicted to be plastidial. Grasses and poplar appear to lack the latter. The predicted subcellular locations of the Arabidopsis proteins were validated by in vitro import assays with purified pea organelles and by targeting assays in Arabidopsis and tobacco protoplasts using green fluorescent protein fusions. The At4g12130 protein was shown to be expressed mainly in flowers, siliques, and seeds, whereas the At1g60990 protein was expressed mainly in young leaves. The folate dependence of both Arabidopsis proteins was established by functional complementation of an Escherichia coli COG0354 (ygfZ) deletant; both plant genes restored in vivo activity of the Fe/S enzyme MiaB but restoration was abrogated when folates were eliminated by deleting folP. Insertional inactivation of At4g12130 was embryo lethal; this phenotype was reversed by genetic complementation of the mutant. These data establish that COG0354 proteins have a folate-dependent function in mitochondria and plastids, and that the mitochondrial protein is essential. That plants retain mitochondrial and plastidial COG0354 proteins with distinct phylogenetic origins emphasizes how deeply the extant Fe/S cluster assembly machinery still reflects the ancient endosymbioses that gave rise to plants.}, }
@article {pmid21984067, year = {2012}, author = {Alcock, F and Webb, CT and Dolezal, P and Hewitt, V and Shingu-Vasquez, M and Likić, VA and Traven, A and Lithgow, T}, title = {A small Tim homohexamer in the relict mitochondrion of Cryptosporidium.}, journal = {Molecular biology and evolution}, volume = {29}, number = {1}, pages = {113-122}, doi = {10.1093/molbev/msr165}, pmid = {21984067}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Carrier Proteins/*chemistry/genetics/metabolism ; Cryptosporidium/chemistry/*genetics ; Evolution, Molecular ; Mitochondria/chemistry/*genetics ; Molecular Chaperones/*chemistry/genetics/metabolism ; Molecular Sequence Data ; Protein Conformation ; Protein Multimerization ; Protein Subunits ; Sequence Alignment ; }, abstract = {The apicomplexan parasite Cryptosporidium parvum possesses a mitosome, a relict mitochondrion with a greatly reduced metabolic capability. This mitosome houses a mitochondrial-type protein import apparatus, but elements of the protein import pathway have been reduced, and even lost, through evolution. The small Tim protein family is a case in point. The genomes of C. parvum and related species of Cryptosporidium each encode just one small Tim protein, CpTimS. This observation challenged the tenet that small Tim proteins are always found in pairs as α3β3 hexamers. We show that the atypical CpTimS exists as a relatively unstable homohexamer, shedding light both on the early evolution of the small Tim protein family and on small Tim hexamer formation in contemporary eukaryotes.}, }
@article {pmid21982590, year = {2011}, author = {Wone, B and Donovan, ER and Hayes, JP}, title = {Metabolomics of aerobic metabolism in mice selected for increased maximal metabolic rate.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {6}, number = {4}, pages = {399-405}, pmid = {21982590}, issn = {1878-0407}, support = {P20 RR016464/RR/NCRR NIH HHS/United States ; P20 RR-016464/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; *Basal Metabolism ; Fatty Acids/*metabolism ; Gas Chromatography-Mass Spectrometry ; Liver/metabolism ; Male ; *Metabolome ; Metabolomics ; Mice/*metabolism ; Muscle, Skeletal/metabolism ; }, abstract = {Maximal aerobic metabolic rate (MMR) is an important physiological and ecological variable that sets an upper limit to sustained, vigorous activity. How the oxygen cascade from the external environment to the mitochondria may affect MMR has been the subject of much interest, but little is known about the metabolic profiles that underpin variation in MMR. We tested how seven generations of artificial selection for high mass-independent MMR affected metabolite profiles of two skeletal muscles (gastrocnemius and plantaris) and the liver. MMR was 12.3% higher in mass selected for high MMR than in controls. Basal metabolic rate was 3.5% higher in selected mice than in controls. Artificial selection did not lead to detectable changes in the metabolic profiles from plantaris muscle, but in the liver amino acids and tricarboxylic acid cycle (TCA cycle) metabolites were lower in high-MMR mice than in controls. In gastrocnemius, amino acids and TCA cycle metabolites were higher in high-MMR mice than in controls, indicating elevated amino acid and energy metabolism. Moreover, in gastrocnemius free fatty acids and triacylglycerol fatty acids were lower in high-MMR mice than in controls. Because selection for high MMR was associated with changes in the resting metabolic profile of both liver and gastrocnemius, the result suggests a possible mechanistic link between resting metabolism and MMR. In addition, it is well established that diet and exercise affect the composition of fatty acids in muscle. The differences that we found between control lines and lines selected for high MMR demonstrate that the composition of fatty acids in muscle is also affected by genetic factors.}, }
@article {pmid21974833, year = {2012}, author = {Naidu, A and Fitak, RR and Munguia-Vega, A and Culver, M}, title = {Novel primers for complete mitochondrial cytochrome b gene sequencing in mammals.}, journal = {Molecular ecology resources}, volume = {12}, number = {2}, pages = {191-196}, doi = {10.1111/j.1755-0998.2011.03078.x}, pmid = {21974833}, issn = {1755-0998}, mesh = {Animals ; Cytochromes b/*genetics ; DNA Primers/*genetics ; Mammals/classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Sequence-based species identification relies on the extent and integrity of sequence data available in online databases such as GenBank. When identifying species from a sample of unknown origin, partial DNA sequences obtained from the sample are aligned against existing sequences in databases. When the sequence from the matching species is not present in the database, high-scoring alignments with closely related sequences might produce unreliable results on species identity. For species identification in mammals, the cytochrome b (cyt b) gene has been identified to be highly informative; thus, large amounts of reference sequence data from the cyt b gene are much needed. To enhance availability of cyt b gene sequence data on a large number of mammalian species in GenBank and other such publicly accessible online databases, we identified a primer pair for complete cyt b gene sequencing in mammals. Using this primer pair, we successfully PCR amplified and sequenced the complete cyt b gene from 40 of 44 mammalian species representing 10 orders of mammals. We submitted 40 complete, correctly annotated, cyt b protein coding sequences to GenBank. To our knowledge, this is the first single primer pair to amplify the complete cyt b gene in a broad range of mammalian species. This primer pair can be used for the addition of new cyt b gene sequences and to enhance data available on species represented in GenBank. The availability of novel and complete gene sequences as high-quality reference data can improve the reliability of sequence-based species identification.}, }
@article {pmid21973214, year = {2012}, author = {Volkmar, U and Groth-Malonek, M and Heinrichs, J and Muhle, H and Polsakiewicz, M and Knoop, V}, title = {Exclusive conservation of mitochondrial group II intron nad4i548 among liverworts and its use for phylogenetic studies in this ancient plant clade.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {14}, number = {2}, pages = {382-391}, doi = {10.1111/j.1438-8677.2011.00499.x}, pmid = {21973214}, issn = {1438-8677}, mesh = {Base Sequence ; Conserved Sequence ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Evolution, Molecular ; Hepatophyta/*classification/*genetics ; Introns/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Liverworts occupy a pivotal position in land plant (embryophyte) phylogeny as the presumed earliest-branching major clade, sister to all other land plants, including the mosses, hornworts, lycophytes, monilophytes and seed plants. Molecular support for this earliest dichotomy in land plant phylogeny comes from strikingly different occurrences of introns in mitochondrial genes distinguishing liverworts from all other embryophytes. Exceptionally, however, the nad5 gene--the mitochondrial locus hitherto used most widely to elucidate early land plant phylogeny--carries a group I type intron that is shared between liverworts and mosses. We here explored whether a group II intron, the other major type of organellar intron, would similarly be conserved in position across the entire diversity of extant liverworts and could be of use for phylogenetic analyses in this supposedly most ancient embryophyte clade. To this end, we investigated the nad4 gene as a candidate locus possibly featuring different introns in liverworts as opposed to the non-liverwort embryophyte (NLE) lineage. We indeed found group II intron nad4i548 universally conserved in a wide phylogenetic sampling of 55 liverwort taxa, confirming clade specificity and surprising evolutionary stability of plant mitochondrial introns. As expected, intron nad4i548g2 carries phylogenetic information in its variable sequences, which confirms and extends previous cladistic insights on liverwort evolution. We integrate the new nad4 data with those of the previously established mitochondrial nad5 and the chloroplast rbcL and rps4 genes and present a phylogeny based on the fused datasets. Notably, the phylogenetic analyses suggest a reconsideration of previous phylogenetic and taxonomic assignments for the genera Calycularia and Mylia and resolve a sister group relationship of Ptilidiales and Porellales.}, }
@article {pmid21969854, year = {2011}, author = {Garvin, MR and Bielawski, JP and Gharrett, AJ}, title = {Positive Darwinian selection in the piston that powers proton pumps in complex I of the mitochondria of Pacific salmon.}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e24127}, pmid = {21969854}, issn = {1932-6203}, mesh = {Adenosine Triphosphate/chemistry ; Amino Acid Sequence ; Animals ; Bayes Theorem ; Biological Evolution ; Evolution, Molecular ; Genomics ; Mitochondria/*metabolism ; Molecular Conformation ; Molecular Sequence Data ; Oxygen/chemistry ; Phosphorylation ; Phylogeny ; Proton Pumps/*physiology ; Salmon ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {The mechanism of oxidative phosphorylation is well understood, but evolution of the proteins involved is not. We combined phylogenetic, genomic, and structural biology analyses to examine the evolution of twelve mitochondrial encoded proteins of closely related, yet phenotypically diverse, Pacific salmon. Two separate analyses identified the same seven positively selected sites in ND5. A strong signal was also detected at three sites of ND2. An energetic coupling analysis revealed several structures in the ND5 protein that may have co-evolved with the selected sites. These data implicate Complex I, specifically the piston arm of ND5 where it connects the proton pumps, as important in the evolution of Pacific salmon. Lastly, the lineage to Chinook experienced rapid evolution at the piston arm.}, }
@article {pmid21967640, year = {2012}, author = {Antico Arciuch, VG and Elguero, ME and Poderoso, JJ and Carreras, MC}, title = {Mitochondrial regulation of cell cycle and proliferation.}, journal = {Antioxidants &amp; redox signaling}, volume = {16}, number = {10}, pages = {1150-1180}, pmid = {21967640}, issn = {1557-7716}, mesh = {Animals ; *Cell Cycle ; Cell Death ; Cell Proliferation ; Humans ; Mitochondria/*physiology ; Oxidation-Reduction ; Phosphotransferases/metabolism ; Reactive Oxygen Species/metabolism ; Signal Transduction ; }, abstract = {Eukaryotic mitochondria resulted from symbiotic incorporation of α-proteobacteria into ancient archaea species. During evolution, mitochondria lost most of the prokaryotic bacterial genes and only conserved a small fraction including those encoding 13 proteins of the respiratory chain. In this process, many functions were transferred to the host cells, but mitochondria gained a central role in the regulation of cell proliferation and apoptosis, and in the modulation of metabolism; accordingly, defective organelles contribute to cell transformation and cancer, diabetes, and neurodegenerative diseases. Most cell and transcriptional effects of mitochondria depend on the modulation of respiratory rate and on the production of hydrogen peroxide released into the cytosol. The mitochondrial oxidative rate has to remain depressed for cell proliferation; even in the presence of O2, energy is preferentially obtained from increased glycolysis (Warburg effect). In response to stress signals, traffic of pro- and antiapoptotic mitochondrial proteins in the intermembrane space (B-cell lymphoma-extra large, Bcl-2-associated death promoter, Bcl-2 associated X-protein and cytochrome c) is modulated by the redox condition determined by mitochondrial O2 utilization and mitochondrial nitric oxide metabolism. In this article, we highlight the traffic of the different canonical signaling pathways to mitochondria and the contributions of organelles to redox regulation of kinases. Finally, we analyze the dynamics of the mitochondrial population in cell cycle and apoptosis.}, }
@article {pmid21966954, year = {2011}, author = {Štefka, J and Hoeck, PE and Keller, LF and Smith, VS}, title = {A hitchhikers guide to the Galápagos: co-phylogeography of Galápagos mockingbirds and their parasites.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {284}, pmid = {21966954}, issn = {1471-2148}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/genetics ; Ecuador ; Genetic Variation ; *Host-Parasite Interactions ; Microsatellite Repeats ; Mites/genetics/*physiology ; Mitochondria/genetics ; Passeriformes/*genetics/*parasitology ; Phthiraptera/genetics/*physiology ; *Phylogeny ; Phylogeography ; }, abstract = {BACKGROUND: Parasites are evolutionary hitchhikers whose phylogenies often track the evolutionary history of their hosts. Incongruence in the evolutionary history of closely associated lineages can be explained through a variety of possible events including host switching and host independent speciation. However, in recently diverged lineages stochastic population processes, such as retention of ancestral polymorphism or secondary contact, can also explain discordant genealogies, even in fully co-speciating taxa. The relatively simple biogeographic arrangement of the Galápagos archipelago, compared with mainland biomes, provides a framework to identify stochastic and evolutionary informative components of genealogic data in these recently diverged organisms.<br><br>RESULTS: Mitochondrial DNA sequences were obtained for four species of Gal&#xe1;pagos mockingbirds and three sympatric species of ectoparasites--two louse and one mite species. These data were complemented with nuclear EF1&#x3b1; sequences in selected samples of parasites and with information from microsatellite loci in the mockingbirds. Mitochondrial sequence data revealed differences in population genetic diversity between all taxa and varying degrees of topological congruence between host and parasite lineages. A very low level of genetic variability and lack of congruence was found in one of the louse parasites, which was excluded from subsequent joint analysis of mitochondrial data. The reconciled multi-species tree obtained from the analysis is congruent with both the nuclear data and the geological history of the islands.<br><br>CONCLUSIONS: The gene genealogies of Gal&#xe1;pagos mockingbirds and two of their ectoparasites show strong phylogeographic correlations, with instances of incongruence mostly explained by ancestral genetic polymorphism. A third parasite genealogy shows low levels of genetic diversity and little evidence of co-phylogeny with their hosts. These differences can mostly be explained by variation in life-history characteristics, primarily host specificity and dispersal capabilities. We show that pooling genetic data from organisms living in close ecological association reveals a more accurate phylogeographic history for these taxa. Our results have implications for the conservation and taxonomy of Gal&#xe1;pagos mockingbirds and their parasites.}, }
@article {pmid21966477, year = {2011}, author = {Verma, S and Mehta, A and Shaha, C}, title = {CYP5122A1, a novel cytochrome P450 is essential for survival of Leishmania donovani.}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e25273}, pmid = {21966477}, issn = {1932-6203}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Blotting, Western ; Cricetinae ; Cytochrome P-450 Enzyme System/classification/genetics/*metabolism ; Electrophoresis, Polyacrylamide Gel ; Ergosterol/metabolism ; Genome, Protozoan/genetics ; Immunohistochemistry ; Leishmania donovani/genetics/*metabolism/*pathogenicity ; Leishmaniasis, Visceral/parasitology ; Mesocricetus ; Mitochondria/drug effects/metabolism ; Phylogeny ; Protozoan Proteins/classification/genetics/*metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {BACKGROUND: Cytochrome P450s (CYP450s) are hemoproteins catalysing diverse biochemical reactions important for metabolism of xenobiotics and synthesis of physiologically important compounds such as sterols. Therefore, they are functionally important for survival of invading pathogens. One such opportunistic pathogen Leishmania donovani causes visceral leishmaniasis worldwide, which is an important public health problem due to significant disease burden. The parasite genome database, Gene DB, annotates 3 CYP450s in Leishmania, however, the functional role of cytochrome P450 enzymes in Leishmania spp. remains elusive.<br><br>A CYP450-like gene cloned from Leishmania donovani was identified as a novel CYP450, the CYP5122A1. Upon co-localization with organelle specific markers, CYP5122A1 distribution was shown to be localized in the promastigote ER, mitochondria and the glycosomes. Replacement of one allele of CYP5122A1 with either neomycin or hygromycin gene by homologous recombination in Leishmania promastigotes induced substantial reduction of CYP5122A1 expression. These parasites showed impaired growth, lower mitochondrial Ca(2+) and membrane potential resulting in low ATP generation. Also, these parasites were less infective in vitro and in vivo than their wild-type counterparts as assessed by incubation of Leishmania promastigotes with macrophages in vitro as well as through administration of parasites into hamsters. The HKOs were more susceptible to drugs like miltefosine and antimony, but showed reduced sensitivity to amphotericin B. Removal of two alleles of CYP5122A1 did not allow the parasites to survive. The mutant parasites showed 3.5 times lower ergosterol level as compared to the wild-type parasites when estimated by Gas chromatography/mass spectrometry. Complementation of CYP5122A1 through episomal expression of protein by using pXG-GFP+2 vector partially rescued CYP5122A1 expression and restored ergosterol levels by 1.8 times. Phenotype reversal included restored growth pattern and lesser drug susceptibility.<br><br>CONCLUSIONS/SIGNIFICANCE: In summary, this study establishes CYP5122A1 as an important molecule linked to processes like cell growth, infection and ergosterol biosynthesis in Leishmania donovani.}, }
@article {pmid21957961, year = {2012}, author = {Alloni, D and Campa, A and Friedland, W and Mariotti, L and Ottolenghi, A}, title = {Track structure, radiation quality and initial radiobiological events: considerations based on the PARTRAC code experience.}, journal = {International journal of radiation biology}, volume = {88}, number = {1-2}, pages = {77-86}, doi = {10.3109/09553002.2011.627976}, pmid = {21957961}, issn = {1362-3095}, mesh = {Alpha Particles/adverse effects ; DNA Breaks, Double-Stranded/radiation effects ; DNA Breaks, Single-Stranded/radiation effects ; Electrons/adverse effects ; Humans ; *Monte Carlo Method ; Photons/adverse effects ; Radiobiology/*methods ; }, abstract = {PURPOSE: The role of track structures for understanding the biological effects of radiation has been the subject of research activities for decades. The physics that describes such processes is the core Monte Carlo codes, such as the biophysical PARTRAC (PARticle TRACks) code described in this review, which follow the mechanisms of radiation-matter interaction from the early stage. In this paper a review of the track structure theory (and of its possible extension concerning non-DNA targets) is presented.<br><br>MATERIALS AND METHODS: The role of radiation quality and track structure is analyzed starting from the heavy ions results obtained with the biophysical Monte Carlo code PARTRAC (PARticles TRACks). PARTRAC calculates DNA damage in human cells based on the superposition of simulated track structures in liquid water to an 'atom-by-atom' model of human DNA.<br><br>RESULTS: Calculations for DNA fragmentation compared with experimental data for different radiation qualities are illustrated. As an example, the strong dependence of the complexity of DNA damage on radiation track structure, and the very large production of very small DNA fragments (lower than 1 kbp (kilo base pairs) usually not detected experimentally) after high LET (high-Linear Energy Transfer) irradiation is shown. Furthermore the possible importance of non-nuclear/non-DNA targets is discussed in the particular case of cellular membrane and mitochondria.<br><br>CONCLUSIONS: The importance of the track structure is underlined, in particular the dependence of a given late cellular effect on the spatial distribution of DNA double-strand breaks (DSB) along the radiation track. These results show that the relative biological effectiveness (RBE) for DSB production can be significantly larger than 1. Moreover the cluster properties of high LET radiation may determine specific initial targets and damage evolution.}, }
@article {pmid21957463, year = {2011}, author = {Georgiades, K and Madoui, MA and Le, P and Robert, C and Raoult, D}, title = {Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion.}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e24857}, pmid = {21957463}, issn = {1932-6203}, mesh = {Alphaproteobacteria/*genetics ; DNA, Bacterial/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; *Genomics ; Mitochondria/*genetics ; *Phylogeny ; }, abstract = {BACKGROUND: The evolution of the Alphaproteobacteria and origin of the mitochondria are topics of considerable debate. Most studies have placed the mitochondria ancestor within the Rickettsiales order. Ten years ago, the bacterium Odyssella thessalonicensis was isolated from Acanthamoeba spp., and the 16S rDNA phylogeny placed it within the Rickettsiales. Recently, the whole genome of O. thessalonicensis has been sequenced, and 16S rDNA phylogeny and more robust and accurate phylogenomic analyses have been performed with 65 highly conserved proteins.<br><br>The results suggested that the O. thessalonicensis emerged between the Rickettsiales and other Alphaproteobacteria. The mitochondrial proteins of the Reclinomonas americana have been used to locate the phylogenetic position of the mitochondrion ancestor within the Alphaproteobacteria tree. Using the K tree score method, nine mitochondrion-encoded proteins, whose phylogenies were congruent with the Alphaproteobacteria phylogenomic tree, have been selected and concatenated for Bayesian and Maximum Likelihood phylogenies. The Reclinomonas americana mitochondrion is a sister taxon to the free-living bacteria Candidatus Pelagibacter ubique, and together, they form a clade that is deeply rooted in the Rickettsiales clade.<br><br>CONCLUSIONS/SIGNIFICANCE: The Reclinomonas americana mitochondrion phylogenomic study confirmed that mitochondria emerged deeply in the Rickettsiales clade and that they are closely related to Candidatus Pelagibacter ubique.}, }
@article {pmid21955145, year = {2011}, author = {Soria-Carrasco, V and Castresana, J}, title = {Patterns of mammalian diversification in recent evolutionary times: global tendencies and methodological issues.}, journal = {Journal of evolutionary biology}, volume = {24}, number = {12}, pages = {2611-2623}, doi = {10.1111/j.1420-9101.2011.02384.x}, pmid = {21955145}, issn = {1420-9101}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; *Biological Evolution ; Cytochromes b/genetics ; *Genetic Variation ; Mammals/*genetics ; Mitochondria/*genetics ; Models, Genetic ; Phylogeny ; Sequence Alignment ; Sequence Analysis/methods ; }, abstract = {Changes in diversification patterns estimated from phylogenetic trees are an important source of information about the dynamics of evolution. To study the diversification of mammals, we reconstructed phylogenetic trees of 29 families and fitted both constant-rate and variable-rate models of diversification. In addition, we investigated the effect of clock models and phylogenetic reconstruction problems on diversification analyses. We observed, first, that none of the families increased its diversification rate during the last few million years, including the Pleistocene. Furthermore, we detected a decrease in diversification that, after application of different tests, was significant only for a minority of families. However, when diversification variation was analysed in a combined tree of all families, a global decline in diversification became significant. Therefore, although distorted by some methodological artefacts, we found an underlying signal of gradually decreasing diversification that suggests that ecological factors may have shaped the recent diversification of mammals.}, }
@article {pmid21950843, year = {2012}, author = {Ducluzeau, AL and Wamboldt, Y and Elowsky, CG and Mackenzie, SA and Schuurink, RC and Basset, GJ}, title = {Gene network reconstruction identifies the authentic trans-prenyl diphosphate synthase that makes the solanesyl moiety of ubiquinone-9 in Arabidopsis.}, journal = {The Plant journal : for cell and molecular biology}, volume = {69}, number = {2}, pages = {366-375}, doi = {10.1111/j.1365-313X.2011.04796.x}, pmid = {21950843}, issn = {1365-313X}, mesh = {Alkyl and Aryl Transferases/genetics/*metabolism ; Arabidopsis/*enzymology/genetics/metabolism/ultrastructure ; Chloroplasts/enzymology ; Cloning, Molecular ; Gene Knockout Techniques ; Gene Regulatory Networks/*genetics ; Genetic Complementation Test ; Green Fluorescent Proteins ; Mitochondria/enzymology ; Mutation ; Phylogeny ; Plants, Genetically Modified ; Plastoquinone/metabolism ; RNA Interference ; Saccharomyces cerevisiae/genetics/metabolism ; Terpenes/chemistry/metabolism ; Ubiquinone/chemistry/*metabolism ; }, abstract = {Ubiquinone (coenzyme Q) is the generic name of a class of lipid-soluble electron carriers formed of a redox active benzoquinone ring attached to a prenyl side chain. The length of the latter varies among species, and depends upon the product specificity of a trans-long-chain prenyl diphosphate synthase that elongates an allylic diphosphate precursor. In Arabidopsis, this enzyme is assumed to correspond to an endoplasmic reticulum-located solanesyl diphosphate synthase, although direct genetic evidence was lacking. In this study, the reconstruction of the functional network of Arabidopsis genes linked to ubiquinone biosynthesis singled out an unsuspected solanesyl diphosphate synthase candidate--product of gene At2g34630--that, extraordinarily, had been shown previously to be targeted to plastids and to contribute to the biosynthesis of gibberellins. Green fluorescent protein (GFP) fusion experiments in tobacco and Arabidopsis, and complementation of a yeast coq1 knockout lacking mitochondrial hexaprenyl diphosphate synthase demonstrated that At2g34630 is also targeted to mitochondria. At2g34630 is the main--if not sole--contributor to solanesyl diphosphate synthase activity required for the biosynthesis of ubiquinone, as demonstrated by the dramatic (75-80%) reduction of the ubiquinone pool size in corresponding RNAi lines. Overexpression of At2g34630 gave up to a 40% increase in ubiquinone content compared to wild-type plants. None of the silenced or overexpressing lines, in contrast, displayed altered levels of plastoquinone. Phylogenetic analyses revealed that At2g34630 is the only Arabidopsis trans-long-chain prenyl diphosphate synthase that clusters with the Coq1 orthologs involved in the biosynthesis of ubiquinone in other eukaryotes.}, }
@article {pmid21948753, year = {2011}, author = {Lopes, IF and Tomasulo-Seccomandi, AM and Bryan, AL and Brisbin, IL and Glenn, TC and Del Lama, SN}, title = {Genetic status of the wood stork (Mycteria americana) from the southeastern United States and the Brazilian Pantanal as revealed by mitochondrial DNA analysis.}, journal = {Genetics and molecular research : GMR}, volume = {10}, number = {3}, pages = {1910-1922}, doi = {10.4238/vol10-3gmr1217}, pmid = {21948753}, issn = {1676-5680}, mesh = {Animals ; Base Sequence ; Birds/*genetics ; Brazil ; DNA, Mitochondrial/*analysis/*genetics ; Endangered Species ; Evolution, Molecular ; Genetic Variation ; Genotype ; Haplotypes ; Mitochondria/*genetics ; Sequence Analysis, DNA ; United States ; }, abstract = {The wood stork (Mycteria americana) is a colonial wading bird that inhabits the Neotropical region from the southeastern United States (US) to northern Argentina. The species is considered to be endangered in the US due to degradation of its foraging and breeding habitat. In other parts of its range, such as in the Brazilian Pantanal region, breeding populations of this species appear to be stable. We compared the levels of genetic variability and population structuring of the US and the Pantanal breeding populations using mitochondrial DNA (mtDNA) control region sequences. Twenty-seven haplotypes were identified among 88 wood stork samples collected from eight breeding colonies in the US and eight in the Pantanal. Patterns indicative of heteroplasmy were observed in 35.3% of the mtDNA sequences that were examined. Significantly higher levels of haplotype diversity were observed in the Pantanal samples compared to those from the US, suggesting that during the last century, demographic declines or a recent evolutionary bottleneck reduced the levels of mtDNA variability of the US population. Analyses of genetic structuring revealed non-significant genetic differentiation between these regions, indicating that either the populations were only recently separated or that gene flow continues to occur at low levels. Haplotype network analysis indicated low current levels of gene flow between populations that were closely related in the past.}, }
@article {pmid21947849, year = {2012}, author = {Zifa, E and Daniil, Z and Skoumi, E and Stavrou, M and Papadimitriou, K and Terzenidou, M and Kostikas, K and Bagiatis, V and Gourgoulianis, KI and Mamuris, Z}, title = {Mitochondrial genetic background plays a role in increasing risk to asthma.}, journal = {Molecular biology reports}, volume = {39}, number = {4}, pages = {4697-4708}, pmid = {21947849}, issn = {1573-4978}, mesh = {Adult ; Asthma/*genetics ; Base Sequence ; Case-Control Studies ; DNA Mutational Analysis ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex I/chemistry ; Female ; Genes, Mitochondrial/genetics ; *Genetic Predisposition to Disease ; Haplotypes/genetics ; Humans ; Male ; Mitochondria/*genetics ; Molecular Sequence Data ; Mutation/genetics ; Nucleic Acid Conformation ; Phylogeny ; Polymerase Chain Reaction ; Protein Structure, Tertiary ; RNA, Ribosomal/chemistry/genetics ; RNA, Transfer/genetics ; Risk Factors ; }, abstract = {A number of studies suggest that mitochondrial dysfunction plays a role in the pathogenesis of asthma. To shed light for the first time on the role of the mitochondrial genome in the etiology of asthma we analyzed the mitochondrial tRNA genes and part of their flanking regions in patients with asthma compared with a set of healthy controls. We found a total of 10 mutations in 56 out of 76 asthmatic patients. Four of these mutations were not found in the control group, five were observed at a significantly lower frequency in controls, but none of the combinations of mutations detected in asthma patients was observed in the controls. Furthermore, we observed that 27.6% of the asthma patients (vs. 4% of the controls) belonged to the haplogroup U (Fisher test P = 0.00) and a positive significant correlation was found between the occurrence of the haplogroup U and the severity of the disease (Fisher test P = 0.02). Whereas further studies in larger cohorts are needed to confirm these observations we suggest that the mitochondrial genetic background plays a key role in asthma development.}, }
@article {pmid21947009, year = {2011}, author = {Ringel, R and Sologub, M and Morozov, YI and Litonin, D and Cramer, P and Temiakov, D}, title = {Structure of human mitochondrial RNA polymerase.}, journal = {Nature}, volume = {478}, number = {7368}, pages = {269-273}, pmid = {21947009}, issn = {1476-4687}, mesh = {AT Rich Sequence/genetics ; Amino Acid Sequence ; Bacteriophage T7/enzymology ; Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; DNA/chemistry/genetics/metabolism ; DNA-Directed RNA Polymerases/*chemistry/metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Mitochondria/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Denaturation ; Promoter Regions, Genetic/genetics ; Protein Structure, Tertiary ; Sequence Alignment ; Templates, Genetic ; Viral Proteins/chemistry ; }, abstract = {Transcription of the mitochondrial genome is performed by a single-subunit RNA polymerase (mtRNAP) that is distantly related to the RNAP of bacteriophage T7, the pol I family of DNA polymerases, and single-subunit RNAPs from chloroplasts. Whereas T7 RNAP can initiate transcription by itself, mtRNAP requires the factors TFAM and TFB2M for binding and melting promoter DNA. TFAM is an abundant protein that binds and bends promoter DNA 15-40 base pairs upstream of the transcription start site, and stimulates the recruitment of mtRNAP and TFB2M to the promoter. TFB2M assists mtRNAP in promoter melting and reaches the active site of mtRNAP to interact with the first base pair of the RNA-DNA hybrid. Here we report the X-ray structure of human mtRNAP at 2.5 Å resolution, which reveals a T7-like catalytic carboxy-terminal domain, an amino-terminal domain that remotely resembles the T7 promoter-binding domain, a novel pentatricopeptide repeat domain, and a flexible N-terminal extension. The pentatricopeptide repeat domain sequesters an AT-rich recognition loop, which binds promoter DNA in T7 RNAP, probably explaining the need for TFAM during promoter binding. Consistent with this, substitution of a conserved arginine residue in the AT-rich recognition loop, or release of this loop by deletion of the N-terminal part of mtRNAP, had no effect on transcription. The fingers domain and the intercalating hairpin, which melts DNA in phage RNAPs, are repositioned, explaining the need for TFB2M during promoter melting. Our results provide a new venue for the mechanistic analysis of mitochondrial transcription. They also indicate how an early phage-like mtRNAP lost functions in promoter binding and melting, which were provided by initiation factors in trans during evolution, to enable mitochondrial gene regulation and the adaptation of mitochondrial function to changes in the environment.}, }
@article {pmid21945877, year = {2011}, author = {Feng, J and Zhang, J and Liu, M and Wan, G and Qi, K and Zheng, C and Lv, Z and Hu, C and Zeng, Y and Gregory, SG and Yang, Z}, title = {Association of mtDNA haplogroup F with healthy longevity in the female Chuang population, China.}, journal = {Experimental gerontology}, volume = {46}, number = {12}, pages = {987-993}, doi = {10.1016/j.exger.2011.09.001}, pmid = {21945877}, issn = {1873-6815}, mesh = {Aged ; Aged, 80 and over ; Aging/*genetics/physiology ; Asian People/*genetics ; China/epidemiology ; DNA, Mitochondrial/*genetics ; Female ; Gene Frequency ; Genotype ; Haplotypes/*genetics ; Humans ; Longevity/*genetics/physiology ; Middle Aged ; Phenotype ; Phylogeny ; }, abstract = {Human longevity is a complex heritable genetic trait. Based on substantial evidence from model organisms, it is clear that mitochondria play a pivotal role in aging and lifespan. However, the effects that mitochondrial genome variations have upon longevity and longevity-related phenotypes in Chuang people in China have yet to be established. By genotyping 15 variants for 10 haplogroups in 738 Chuang subjects, including 367 long-lived individuals and 371 controls, we found that haplogroup F was significantly associated with longevity in females of Zhuang population of China (p=0.003, OR: 2.01, 95%CI: 1.263-3.197). Additionally, haplogroup F was related to higher HDL levels (p<0.05) in long-lived individuals. Further analysis suggests that the non-synonymous variant m.13928G>C in haplogroup F was also associated with longevity in female Zhuang Chinese which might account for the beneficial effect of F.}, }
@article {pmid21945528, year = {2011}, author = {Ewen, KM and Hannemann, F and Iametti, S and Morleo, A and Bernhardt, R}, title = {Functional characterization of Fdx1: evidence for an evolutionary relationship between P450-type and ISC-type ferredoxins.}, journal = {Journal of molecular biology}, volume = {413}, number = {5}, pages = {940-951}, doi = {10.1016/j.jmb.2011.09.010}, pmid = {21945528}, issn = {1089-8638}, mesh = {Aconitate Hydratase/metabolism ; Amino Acid Sequence ; Animals ; Bacterial Proteins/*chemistry/isolation &amp; purification/*metabolism ; Cattle ; Cholesterol Side-Chain Cleavage Enzyme/*chemistry/metabolism ; Circular Dichroism ; Cloning, Molecular ; Computational Biology ; *Evolution, Molecular ; Ferredoxins/*chemistry/isolation &amp; purification/*metabolism ; Iron/analysis ; Iron-Sulfur Proteins/*chemistry/metabolism ; Mitochondria/*enzymology ; Molecular Sequence Data ; Myxococcales/genetics/metabolism ; NADP ; Oxidation-Reduction ; Phylogeny ; Sequence Homology, Amino Acid ; Sulfite Reductase (Ferredoxin)/metabolism ; }, abstract = {Ferredoxins are ubiquitous proteins with electron transfer activity involved in a variety of biological processes. In this work, we investigated the characteristics and function of Fdx1 from Sorangium cellulosum So ce56 by using a combination of bioinformatics and of biochemical/biophysical approaches. We were able to experimentally confirm a role of Fdx1 in the iron-sulfur cluster biosynthesis by in vitro reduction studies with cluster-loaded So ce56 IscU and by transfer studies of the cluster from the latter protein to apo-aconitase A. Moreover, we found that Fdx1 can replace mammalian adrenodoxin in supporting the activity of bovine CYP11A1. This makes S. cellulosum Fdx1 the first prokaryotic ferredoxin reported to functionally interact with this mammalian enzyme. Although the interaction with CYP11A1 is non-physiological, this is-to the best of our knowledge-the first study to experimentally prove the activity of a postulated ISC-type ferredoxin in both the ISC assembly and a cytochrome P450 system. This proves that a single ferredoxin can be structurally able to provide electrons to both cytochromes P450 and IscU and thus support different biochemical processes. Combining this finding with phylogenetic and evolutionary trace analyses led us to propose the evolution of eukaryotic mitochondrial P450-type ferredoxins and ISC-type ferredoxins from a common prokaryotic ISC-type ancestor.}, }
@article {pmid21945051, year = {2012}, author = {Müller, MJ and von Mühlen, C and Valiati, VH and da Silva Valente, VL}, title = {Wolbachia pipientis is associated with different mitochondrial haplotypes in natural populations of Drosophila willistoni.}, journal = {Journal of invertebrate pathology}, volume = {109}, number = {1}, pages = {152-155}, doi = {10.1016/j.jip.2011.08.011}, pmid = {21945051}, issn = {1096-0805}, mesh = {Animals ; Brazil ; DNA, Mitochondrial/genetics ; Drosophila/genetics/*microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Gram-Negative Bacterial Infections/microbiology/*veterinary ; Haplotypes ; Host-Pathogen Interactions ; Mitochondria/*genetics/microbiology ; Pest Control, Biological ; Symbiosis ; Wolbachia/*pathogenicity/physiology ; }, abstract = {The prevalence of the endosymbiont Wolbachia pipientis and its effects on mitochondrial genetic diversity were analyzed in natural populations of Drosophila willistoni, a neotropical species recently infected. Total infection rate was 55% and no evidence was found that the Wolbachia infection decreased the diversity of mtDNA. Wolbachia was seen to be associated with different mitochondria, suggesting multiple horizontal transmission events and/or transmission paternal leakage of mitochondrial and/or Wolbachia. These hypotheses are evaluated in the context of the present study and other research.}, }
@article {pmid21942368, year = {2011}, author = {Ni, M and Feretzaki, M and Sun, S and Wang, X and Heitman, J}, title = {Sex in fungi.}, journal = {Annual review of genetics}, volume = {45}, number = {}, pages = {405-430}, pmid = {21942368}, issn = {1545-2948}, support = {R37 AI039115/AI/NIAID NIH HHS/United States ; AI50113/AI/NIAID NIH HHS/United States ; T32-AI52080/AI/NIAID NIH HHS/United States ; AI085331/AI/NIAID NIH HHS/United States ; R37 AI039115-15/AI/NIAID NIH HHS/United States ; AI39115/AI/NIAID NIH HHS/United States ; T32 AI052080/AI/NIAID NIH HHS/United States ; R01 AI050113/AI/NIAID NIH HHS/United States ; R01 AI039115/AI/NIAID NIH HHS/United States ; R21 AI085331/AI/NIAID NIH HHS/United States ; }, mesh = {Aneuploidy ; Chromosomes, Fungal/genetics/metabolism ; *Evolution, Molecular ; Fungi/genetics/metabolism/*physiology ; Genes, Mating Type, Fungal ; Genetic Loci ; Germ Cells/cytology/metabolism ; Inheritance Patterns ; Mitochondria/physiology ; Mycelium/physiology ; Recombination, Genetic ; Reproduction/genetics/physiology ; Sex Chromosomes/genetics/metabolism ; Signal Transduction ; Spores, Fungal/genetics/metabolism/physiology ; }, abstract = {Sexual reproduction enables genetic exchange in eukaryotic organisms as diverse as fungi, animals, plants, and ciliates. Given its ubiquity, sex is thought to have evolved once, possibly concomitant with or shortly after the origin of eukaryotic organisms themselves. The basic principles of sex are conserved, including ploidy changes, the formation of gametes via meiosis, mate recognition, and cell-cell fusion leading to the production of a zygote. Although the basic tenants are shared, sex determination and sexual reproduction occur in myriad forms throughout nature, including outbreeding systems with more than two mating types or sexes, unisexual selfing, and even examples in which organisms switch mating type. As robust and diverse genetic models, fungi provide insights into the molecular nature of sex, sexual specification, and evolution to advance our understanding of sexual reproduction and its impact throughout the eukaryotic tree of life.}, }
@article {pmid21940640, year = {2012}, author = {Wang, N and Braun, EL and Kimball, RT}, title = {Testing hypotheses about the sister group of the passeriformes using an independent 30-locus data set.}, journal = {Molecular biology and evolution}, volume = {29}, number = {2}, pages = {737-750}, doi = {10.1093/molbev/msr230}, pmid = {21940640}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Mitochondria/genetics ; Models, Genetic ; Passeriformes/classification/*genetics ; *Phylogeny ; Psittaciformes/classification/*genetics ; Sequence Alignment ; }, abstract = {Although many phylogenetic studies have focused on developing hypotheses about relationships, advances in data collection and computation have increased the feasibility of collecting large independent data sets to rigorously test controversial hypotheses or carefully assess artifacts that may be misleading. One such relationship in need of independent evaluation is the position of Passeriformes (perching birds) in avian phylogeny. This order comprises more than half of all extant birds, and it includes one of the most important avian model systems (the zebra finch). Recent large-scale studies using morphology, mitochondrial, and nuclear sequence data have generated very different hypotheses about the sister group of Passeriformes, and all conflict with an older hypothesis generated using DNA-DNA hybridization. We used novel data from 30 nuclear loci, primarily introns, for 28 taxa to evaluate five major a priori hypotheses regarding the phylogenetic position of Passeriformes. Although previous studies have suggested that nuclear introns are ideal for the resolution of ancient avian relationships, introns have also been criticized because of the potential for alignment ambiguities and the loss of signal due to saturation. To examine these issues, we generated multiple alignments using several alignment programs, varying alignment parameters, and using guide trees that reflected the different a priori hypotheses. Although different alignments and analyses yielded slightly different results, our analyses excluded all but one of the five a priori hypotheses. In many cases, the passerines were sister to the Psittaciformes (parrots), and taxa were members of a larger clade that includes Falconidae (falcons) and Cariamidae (seriemas). However, the position of Coliiformes (mousebirds) was highly unstable in our analyses of 30 loci, and this represented the primary source of incongruence among analyses. Mousebirds were united with passerines or parrots in some analyses, suggesting an additional hypothesis that needs to be considered in future studies. There was no clear evidence that base-compositional convergence, saturation, or long-branch attraction affected our conclusions. These results provide independent evidence excluding four major hypotheses about the position of passerines, allowing the extensive studies on this group to be placed in a more rigorous evolutionary framework.}, }
@article {pmid21937710, year = {2011}, author = {Hardie, DG}, title = {AMP-activated protein kinase: an energy sensor that regulates all aspects of cell function.}, journal = {Genes &amp; development}, volume = {25}, number = {18}, pages = {1895-1908}, pmid = {21937710}, issn = {1549-5477}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {AMP-Activated Protein Kinases/*metabolism ; Animals ; Cell Polarity ; Cell Proliferation ; Cells/cytology/*enzymology ; *Energy Metabolism ; Gene Expression Regulation, Enzymologic ; Humans ; Mitochondria/enzymology ; Neoplasms/enzymology ; Virus Diseases/enzymology ; }, abstract = {AMP-activated protein kinase (AMPK) is a sensor of energy status that maintains cellular energy homeostasis. It arose very early during eukaryotic evolution, and its ancestral role may have been in the response to starvation. Recent work shows that the kinase is activated by increases not only in AMP, but also in ADP. Although best known for its effects on metabolism, AMPK has many other functions, including regulation of mitochondrial biogenesis and disposal, autophagy, cell polarity, and cell growth and proliferation. Both tumor cells and viruses establish mechanisms to down-regulate AMPK, allowing them to escape its restraining influences on growth.}, }
@article {pmid21935411, year = {2011}, author = {Brindefalk, B and Ettema, TJ and Viklund, J and Thollesson, M and Andersson, SG}, title = {A phylometagenomic exploration of oceanic alphaproteobacteria reveals mitochondrial relatives unrelated to the SAR11 clade.}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e24457}, pmid = {21935411}, issn = {1932-6203}, mesh = {Alphaproteobacteria/classification/*genetics ; Bacterial Proteins/*genetics ; Genome, Bacterial/genetics ; *Metagenomics ; *Phylogeny ; }, abstract = {BACKGROUND: According to the endosymbiont hypothesis, the mitochondrial system for aerobic respiration was derived from an ancestral Alphaproteobacterium. Phylogenetic studies indicate that the mitochondrial ancestor is most closely related to the Rickettsiales. Recently, it was suggested that Candidatus Pelagibacter ubique, a member of the SAR11 clade that is highly abundant in the oceans, is a sister taxon to the mitochondrial-Rickettsiales clade. The availability of ocean metagenome data substantially increases the sampling of Alphaproteobacteria inhabiting the oxygen-containing waters of the oceans that likely resemble the originating environment of mitochondria.<br><br>We present a phylogenetic study of the origin of mitochondria that incorporates metagenome data from the Global Ocean Sampling (GOS) expedition. We identify mitochondrially related sequences in the GOS dataset that represent a rare group of Alphaproteobacteria, designated OMAC (Oceanic Mitochondria Affiliated Clade) as the closest free-living relatives to mitochondria in the oceans. In addition, our analyses reject the hypothesis that the mitochondrial system for aerobic respiration is affiliated with that of the SAR11 clade.<br><br>CONCLUSIONS/SIGNIFICANCE: Our results allude to the existence of an alphaproteobacterial clade in the oxygen-rich surface waters of the oceans that represents the closest free-living relative to mitochondria identified thus far. In addition, our findings underscore the importance of expanding the taxonomic diversity in phylogenetic analyses beyond that represented by cultivated bacteria to study the origin of mitochondria.}, }
@article {pmid21933443, year = {2011}, author = {Slade, KM and Freggiaro, S and Cottrell, KA and Smith, JJ and Wiley, EA}, title = {Sirtuin-mediated nuclear differentiation and programmed degradation in Tetrahymena.}, journal = {BMC cell biology}, volume = {12}, number = {}, pages = {40}, pmid = {21933443}, issn = {1471-2121}, mesh = {Active Transport, Cell Nucleus/drug effects ; Amino Acid Sequence ; Apoptosis/drug effects ; Cell Nucleus/*metabolism ; Cells, Cultured ; Chromatin Assembly and Disassembly/drug effects ; Conjugation, Genetic/drug effects ; DNA Fragmentation ; Meiosis/drug effects ; Mitochondria/*metabolism ; Molecular Sequence Data ; Niacinamide/pharmacology ; Phylogeny ; Protein Multimerization/drug effects ; Protein Transport ; Protozoan Proteins/antagonists &amp; inhibitors/genetics/*metabolism ; Sirtuins/antagonists &amp; inhibitors/genetics/*metabolism ; Tetrahymena/*physiology ; }, abstract = {BACKGROUND: The NAD(+)-dependent histone deacetylases, known as "sirtuins", participate in a variety of processes critical for single- and multi-cellular life. Recent studies have elucidated the importance of sirtuin activity in development, aging, and disease; yet, underlying mechanistic pathways are not well understood. Specific sirtuins influence chromatin structure and gene expression, but differences in their pathways as they relate to distinct chromatin functions are just beginning to emerge. To further define the range of global chromatin changes dependent on sirtuins, unique biological features of the ciliated protozoan Tetrahymena thermophila can be exploited. This system offers clear spatial and temporal separation of multiple whole genome restructuring events critical for the life cycle.<br><br>RESULTS: Inhibition with nicotinamide revealed that sirtuin deacetylase activity in Tetrahymena cells promotes chromatin condensation during meiotic prophase, differentiation of heterochromatin from euchromatin during development, and chromatin condensation/degradation during programmed nuclear death. We identified a class I sirtuin, called Thd14, that resides in mitochondria and nucleoli during vegetative growth, and forms a large sub-nuclear aggregate in response to prolonged cell starvation that may be peripherally associated with nucleoli. During sexual conjugation and development Thd14 selectively concentrates in the parental nucleus prior to its apoptotic-like degradation.<br><br>CONCLUSIONS: Sirtuin activity is important for several functionally distinct events requiring global chromatin condensation. Our findings suggest a novel role for sirtuins in promoting programmed pycnosis by acting on chromatin destined for degradation. The sirtuin Thd14, which displays physiological-dependent differential localization within the nucleus, is a candidate for a chromatin condensation enzyme that is coupled to nuclear degradation.}, }
@article {pmid21930219, year = {2011}, author = {Mardulyn, P and Othmezouri, N and Mikhailov, YE and Pasteels, JM}, title = {Conflicting mitochondrial and nuclear phylogeographic signals and evolution of host-plant shifts in the boreo-montane leaf beetle Chrysomela lapponica.}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {3}, pages = {686-696}, doi = {10.1016/j.ympev.2011.09.001}, pmid = {21930219}, issn = {1095-9513}, mesh = {Alleles ; Animals ; Betula/parasitology ; Cell Nucleus/*genetics ; Coleoptera/*genetics ; Ecosystem ; Europe ; *Evolution, Molecular ; Genes, Insect/genetics ; Genetic Loci/genetics ; Genetic Variation ; Host-Parasite Interactions/*genetics ; Likelihood Functions ; Mitochondria/*genetics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; *Phylogeography ; Plant Leaves/parasitology ; Plants/*parasitology ; Salix/parasitology ; }, abstract = {We conducted a phylogeographic study on the cold-adapted leaf beetle Chrysomela lapponica, that feeds on willow or birch, by sampling several populations throughout most of the geographic distribution of the species, and by sequencing for each individual one mitochondrial and two nuclear DNA fragments. Patterns of DNA sequence variation from the mitochondrial and nuclear loci, as displayed in the median-joining networks, appear to display contradicting historical signal: a deep genealogical divergence is observed with the mitochondrial genome between the Alpine population and all other populations found in the Euro-Siberian distribution of the species, that is completely absent with both nuclear loci. We use coalescence simulations of DNA sequence evolution to test the hypothesis that this apparent conflict is compatible with a neutral model of sequence evolution (i.e., to check whether the stochastic nature of the coalescence process can explain these patterns). Because the simulations show that this is highly unlikely, we consider two alternative hypotheses: (1) introgression of the mitochondrial genome of another species and (2) the effect of natural selection. Although introgression is the most plausible explanation, we fail to identify the source species of the introgressed mitochondrial genome among all known species closely related to C. lapponica. We therefore suggest that the putative introgression event is ancient and the source species is either extinct or currently outside the geographic range of C. lapponica explored in this study. The observed DNA sequence variation also suggests that a host-plant shift from willow to birch has occurred recently and independently in each of the three birch-feeding populations. This emphasizes further the relative ease with which these beetles can escape their ancestral host-plant specialization on willow, but shows at the same time that host-plant shifts are highly constrained, as they only occur between willow and birch.}, }
@article {pmid21927814, year = {2012}, author = {Sun, P and Shi, ZH and Yin, F and Peng, SM}, title = {Genetic variation analysis of Mugil cephalus in China sea based on mitochondrial COI gene sequences.}, journal = {Biochemical genetics}, volume = {50}, number = {3-4}, pages = {180-191}, doi = {10.1007/s10528-011-9460-6}, pmid = {21927814}, issn = {1573-4927}, mesh = {Animals ; China ; Cluster Analysis ; Conservation of Natural Resources ; Electron Transport Complex IV/*genetics ; Fish Proteins/*genetics ; *Genetic Variation ; Haplotypes ; Likelihood Functions ; Mitochondria/*enzymology/genetics ; Oceans and Seas ; Phylogeny ; Phylogeography ; Protein Subunits/genetics ; Sequence Analysis, DNA ; Smegmamorpha/*genetics ; }, abstract = {In this study, genetic diversity and population genetic structure of flathead grey mullet, Mugil cephalus, among four China Sea populations were investigated by COI sequences. All the populations studied had high values of haplotype and nucleotide diversity, except for the Yellow Sea population. In the phylogenetic tree, these haplotypes clustered in two groups, one for the populations from the Bohai and East China seas, and the other from the Yellow and South China seas. Analysis of molecular variance indicated that the northern populations (Bohai and East China) had lower genetic divergence (0.0725, P > 0.05) than that of the southern population (South China) (0.4530-0.6827, P < 0.001), suggesting that two distinct genetic groups exist in Chinese waters. Tests of neutral evolution and mismatch distribution indicated that no historical demographic expansion occurred in these populations. The results provide new information for genetic assessment, fishery management, and conservation of this species.}, }
@article {pmid21926070, year = {2012}, author = {Dornburg, A and Brandley, MC and McGowen, MR and Near, TJ}, title = {Relaxed clocks and inferences of heterogeneous patterns of nucleotide substitution and divergence time estimates across whales and dolphins (Mammalia: Cetacea).}, journal = {Molecular biology and evolution}, volume = {29}, number = {2}, pages = {721-736}, doi = {10.1093/molbev/msr228}, pmid = {21926070}, issn = {1537-1719}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/genetics ; Dolphins/*genetics ; *Evolution, Molecular ; *Genetic Variation ; Genome ; Genome, Mitochondrial ; Mitochondria/genetics ; Mutation ; Nucleotides ; Phylogeny ; Time Factors ; Whales/*genetics ; }, abstract = {Various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, thereby relaxing the assumptions of the strict molecular clock. Recently developed "uncorrelated relaxed clock" and "random local clock" (RLC) models allow decoupling of nucleotide substitution rates between descendant lineages and are thus predicted to perform better in the presence of lineage-specific rate heterogeneity. However, it is uncertain how these models perform in the presence of punctuated shifts in substitution rate, especially between closely related clades. Using cetaceans (whales and dolphins) as a case study, we test the performance of these two substitution models in estimating both molecular rates and divergence times in the presence of substantial lineage-specific rate heterogeneity. Our RLC analyses of whole mitochondrial genome alignments find evidence for up to ten clade-specific nucleotide substitution rate shifts in cetaceans. We provide evidence that in the uncorrelated relaxed clock framework, a punctuated shift in the rate of molecular evolution within a subclade results in posterior rate estimates that are either misled or intermediate between the disparate rate classes present in baleen and toothed whales. Using simulations, we demonstrate abrupt changes in rate isolated to one or a few lineages in the phylogeny can mislead rate and age estimation, even when the node of interest is calibrated. We further demonstrate how increasing prior age uncertainty can bias rate and age estimates, even while the 95% highest posterior density around age estimates decreases; in other words, increased precision for an inaccurate estimate. We interpret the use of external calibrations in divergence time studies in light of these results, suggesting that rate shifts at deep time scales may mislead inferences of absolute molecular rates and ages.}, }
@article {pmid21926069, year = {2012}, author = {Crandall, ED and Sbrocco, EJ and Deboer, TS and Barber, PH and Carpenter, KE}, title = {Expansion dating: calibrating molecular clocks in marine species from expansions onto the Sunda Shelf Following the Last Glacial Maximum.}, journal = {Molecular biology and evolution}, volume = {29}, number = {2}, pages = {707-719}, doi = {10.1093/molbev/msr227}, pmid = {21926069}, issn = {1537-1719}, mesh = {Animals ; Aquatic Organisms/*genetics ; Arthropods/genetics ; *Biological Evolution ; Bivalvia/genetics ; DNA/genetics ; Echinodermata/genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genetic Variation ; Ice Cover ; Mitochondria/genetics ; Models, Genetic ; Mutation Rate ; Phylogeny ; Phylogeography/*methods ; Time Factors ; }, abstract = {The rate of change in DNA is an important parameter for understanding molecular evolution and hence for inferences drawn from studies of phylogeography and phylogenetics. Most rate calibrations for mitochondrial coding regions in marine species have been made from divergence dating for fossils and vicariant events older than 1-2 My and are typically 0.5-2% per lineage per million years. Recently, calibrations made with ancient DNA (aDNA) from younger dates have yielded faster rates, suggesting that estimates of the molecular rate of change depend on the time of calibration, decaying from the instantaneous mutation rate to the phylogenetic substitution rate. aDNA methods for recent calibrations are not available for most marine taxa so instead we use radiometric dates for sea-level rise onto the Sunda Shelf following the Last Glacial Maximum (starting ∼18,000 years ago), which led to massive population expansions for marine species. Instead of divergence dating, we use a two-epoch coalescent model of logistic population growth preceded by a constant population size to infer a time in mutational units for the beginning of these expansion events. This model compares favorably to simpler coalescent models of constant population size, and exponential or logistic growth, and is far more precise than estimates from the mismatch distribution. Mean rates estimated with this method for mitochondrial coding genes in three invertebrate species are elevated in comparison to older calibration points (2.3-6.6% per lineage per million years), lending additional support to the hypothesis of calibration time dependency for molecular rates.}, }
@article {pmid21922504, year = {2011}, author = {Lane, N}, title = {Mitonuclear match: optimizing fitness and fertility over generations drives ageing within generations.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {33}, number = {11}, pages = {860-869}, doi = {10.1002/bies.201100051}, pmid = {21922504}, issn = {1521-1878}, mesh = {Adenosine Triphosphate/metabolism ; Aging/genetics/metabolism/*physiology ; Animals ; Apoptosis ; Cell Nucleus/genetics/metabolism/*physiology ; Cell Respiration ; DNA, Mitochondrial/genetics/metabolism ; Electron Transport ; Female ; *Fertility ; Free Radicals/metabolism ; *Genetic Fitness ; Genetic Speciation ; Humans ; Male ; Mammals ; Membrane Potential, Mitochondrial ; Mitochondria/genetics/metabolism/*physiology ; Selection, Genetic ; Signal Transduction ; }, abstract = {Many conserved eukaryotic traits, including apoptosis, two sexes, speciation and ageing, can be causally linked to a bioenergetic requirement for mitochondrial genes. Mitochondrial genes encode proteins involved in cell respiration, which interact closely with proteins encoded by nuclear genes. Functional respiration requires the coadaptation of mitochondrial and nuclear genes, despite divergent tempi and modes of evolution. Free-radical signals emerge directly from the biophysics of mosaic respiratory chains encoded by two genomes prone to mismatch, with apoptosis being the default penalty for compromised respiration. Selection for genomic matching is facilitated by two sexes, and optimizes fitness, adaptability and fertility in youth. Mismatches cause infertility, low fitness, hybrid breakdown, and potentially speciation. The dynamics of selection for mitonuclear function optimize fitness over generations, but the same selective processes also operate within generations, driving ageing and age-related diseases. This coherent view of eukaryotic energetics offers striking insights into infertility and age-related diseases.}, }
@article {pmid21921696, year = {2011}, author = {Bashir, K and Ishimaru, Y and Nishizawa, NK}, title = {Identification and characterization of the major mitochondrial Fe transporter in rice.}, journal = {Plant signaling &amp; behavior}, volume = {6}, number = {10}, pages = {1591-1593}, pmid = {21921696}, issn = {1559-2324}, mesh = {Gene Expression Regulation, Plant ; Glucuronidase/metabolism ; Iron/*metabolism ; Membrane Transport Proteins/genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Oryza/cytology/genetics/growth &amp; development/*metabolism ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Promoter Regions, Genetic/genetics ; }, abstract = {The uptake, translocation, and compartmentalization of Fe are essential for plant cell function and life cycle. Despite rapid progress in our understanding of Fe homeostasis in plants, Fe transport from the cytoplasm to mitochondria was, until recently, poorly understood. The screening of 3,993 mutant lines for symptoms of Fe deficiency resulted in the identification and characterization of a major mitochondrial Fe transporter (MIT) in rice. MIT was found to localize to mitochondria and to complement the growth of a yeast strain defective in mitochondrial Fe transport. The knock-out of MIT resulted in a lethal phenotype, and in knock-down plants, several agronomic characteristics were compromised, such as plant height, average number of tillers, days to flower, fertility, and yield. Changes in the expression of genes involved in Fe transport suggested a disturbance of cellular Fe transport. Furthermore, the mitochondrial Fe concentration and the activity of the mitochondrial Fe-S enzyme aconitase were significantly reduced compared with wild-type plants. The identification of MIT is a significant advance in the field of plant Fe nutrition and should facilitate the cloning of paralogs from other plant species.}, }
@article {pmid21914666, year = {2011}, author = {Guastella, AM and Zuccaro, A and Criscione, A and Marletta, D and Bordonaro, S}, title = {Genetic analysis of Sicilian autochthonous horse breeds using nuclear and mitochondrial DNA markers.}, journal = {The Journal of heredity}, volume = {102}, number = {6}, pages = {753-758}, doi = {10.1093/jhered/esr091}, pmid = {21914666}, issn = {1465-7333}, mesh = {Animals ; Breeding ; Cluster Analysis ; DNA Fingerprinting/*methods ; DNA, Mitochondrial/*genetics ; Endangered Species ; Female ; Genetic Markers ; Genetic Variation ; Haplotypes ; Horses/*genetics ; Male ; *Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Sicily ; }, abstract = {Genetic diversity and relationship among 3 Sicilian horse breeds were investigated using 16 microsatellite markers and a 397-bp length mitochondrial D-loop sequence. The analysis of autosomal DNA was performed on 191 horses (80 Siciliano [SIC], 61 Sanfratellano [SAN], and 50 Sicilian Oriental Purebred [SOP]). SIC and SAN breeds were notably higher in genetic variability than the SOP. Genetic distances and cluster analysis showed a close relationship between SIC and SAN breeds, as expected according to the breeds' history. Sequencing of hypervariable mitochondrial DNA region was performed on a subset of 60 mares (20 for each breed). Overall, 20 haplotypes with 31 polymorphic sites were identified: A higher haplotype diversity was detected in SIC and SAN breeds, with 13 and 11 haplotypes respectively, whereas only one haplotype was found in SOP. These were compared with 118 sequences from GenBank. BLAST showed that 17 of the 20 haplotypes had been reported previously in other breeds. One haplotype, found in SIC, traces back to a Bronze Age archaeological site (Inner Mongolia). The 3 Sicilian breeds are now rare, and 2 of them are officially endangered. Our results represent a valuable tool for management strategies as well as for conservation purposes.}, }
@article {pmid21910249, year = {2011}, author = {Ben-Menachem, R and Tal, M and Shadur, T and Pines, O}, title = {A third of the yeast mitochondrial proteome is dual localized: a question of evolution.}, journal = {Proteomics}, volume = {11}, number = {23}, pages = {4468-4476}, doi = {10.1002/pmic.201100199}, pmid = {21910249}, issn = {1615-9861}, mesh = {Evolution, Molecular ; Mitochondria/*chemistry/genetics ; Mitochondrial Proteins/*analysis/genetics ; Proteome/analysis/genetics ; RNA, Messenger/genetics ; Saccharomyces cerevisiae/*cytology/genetics ; Saccharomyces cerevisiae Proteins/*analysis/genetics ; }, abstract = {There are a growing number of examples of identical or almost identical proteins, which are localized to two (or more) separate compartments, a phenomenon that is termed protein dual localization, dual distribution or dual targeting. We previously divided a reference set of known yeast mitochondrial proteins into two groups, suggested to be dual localized or exclusive mitochondrial proteins. Here we examined this evaluation by screening 320 mitochondrial gene products for dual targeting, using the α-complementation assay. The analysis of the results of this experimentally independent screen supports our previous evaluation that dual localized mitochondrial proteins constitute a subgroup of mitochondrial proteins with distinctive properties. These proteins are characterized by a lower probability of mitochondrial localization (MitoProtII score), a lower net charge and are enriched for proteins with a weaker mitochondrial targeting sequence. Conversely, mRNAs of exclusive mitochondrial proteins are enriched in polysomes associated with mitochondria. Based on the discovery of more than 60 new gene products that are now assumed to be dual targeted, we have updated an annotation list of dual-targeted proteins. We currently estimate that more than a third of the mitochondrial proteome is dual targeted, and suggest that this abundant dual targeting presents an evolutionary advantage.}, }
@article {pmid21909460, year = {2011}, author = {Sreekumar, PG and Hinton, DR and Kannan, R}, title = {Methionine sulfoxide reductase A: Structure, function and role in ocular pathology.}, journal = {World journal of biological chemistry}, volume = {2}, number = {8}, pages = {184-192}, pmid = {21909460}, issn = {1949-8454}, support = {P30 EY003040/EY/NEI NIH HHS/United States ; R01 EY001545/EY/NEI NIH HHS/United States ; }, abstract = {Methionine is a highly susceptible amino acid that can be oxidized to S and R diastereomeric forms of methionine sulfoxide by many of the reactive oxygen species generated in biological systems. Methionine sulfoxide reductases (Msrs) are thioredoxin-linked enzymes involved in the enzymatic conversion of methionine sulfoxide to methionine. Although MsrA and MsrB have the same function of methionine reduction, they differ in substrate specificity, active site composition, subcellular localization, and evolution. MsrA has been localized in different ocular regions and is abundantly expressed in the retina and in retinal pigment epithelial (RPE) cells. MsrA protects cells from oxidative stress. Overexpression of MsrA increases resistance to cell death, while silencing or knocking down MsrA decreases cell survival; events that are mediated by mitochondria. MsrA participates in protein-protein interaction with several other cellular proteins. The interaction of MsrA with α-crystallins is of utmost importance given the known functions of the latter in protein folding, neuroprotection, and cell survival. Oxidation of methionine residues in α-crystallins results in loss of chaperone function and possibly its antiapoptotic properties. Recent work from our laboratory has shown that MsrA is co-localized with αA and αB crystallins in the retinal samples of patients with age-related macular degeneration. We have also found that chemically induced hypoxia regulates the expression of MsrA and MsrB2 in human RPE cells. Thus, MsrA is a critical enzyme that participates in cell and tissue protection, and its interaction with other proteins/growth factors may provide a target for therapeutic strategies to prevent degenerative diseases.}, }
@article {pmid21907205, year = {2011}, author = {Mazet, M and Harijan, RK and Kiema, TR and Haapalainen, AM and Morand, P and Morales, J and Bringaud, F and Wierenga, RK and Michels, PA}, title = {The characterization and evolutionary relationships of a trypanosomal thiolase.}, journal = {International journal for parasitology}, volume = {41}, number = {12}, pages = {1273-1283}, doi = {10.1016/j.ijpara.2011.07.009}, pmid = {21907205}, issn = {1879-0135}, mesh = {Acetyl-CoA C-Acyltransferase/*genetics/*metabolism ; Cloning, Molecular ; Cluster Analysis ; Computational Biology/methods ; Escherichia coli/genetics ; Gene Expression ; Gene Expression Profiling ; Humans ; Isoenzymes/genetics ; Leishmania/enzymology ; Mitochondria/enzymology ; Phylogeny ; Protein Sorting Signals ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Trypanosoma/*enzymology ; }, abstract = {Thiolases are enzymes that remove an acetyl-coenzyme A group from acyl-CoA in the catabolic β-oxidation of fatty acids, or catalyse the reverse condensation reaction for anabolic processes such as the biosynthesis of sterols and ketone bodies. In humans, six homologous isoforms of thiolase have been described, differing from each other in sequence, oligomeric state, substrate specificity and subcellular localization. A bioinformatics analysis of parasite genomes, being (i) different species of African trypanosomes, (ii) Trypanosoma cruzi and (iii) Leishmania spp., using the six human sequences as queries, showed that the distribution of thiolases in human and each of the studied Trypanosomatidae is completely different. Only one of these isoforms, called SCP2-thiolase, was found in each of the Trypanosomatidae, whereas the TFE-thiolase was also found in T. cruzi and Leishmania spp., and the AB-thiolase only in T. cruzi. Each of the trypanosomatid thiolases clusters with its orthologues from other organisms in a phylogenetic analysis and shares with them the isoform-specific sequence fingerprints. The single T. brucei SCP2-thiolase has been expressed in Escherichia coli and characterized. It shows activity in both the degradative and synthetic directions. Transcripts of this thiolase were detected in both bloodstream- and procyclic-form trypanosomes, but the protein was found only in the procyclic form. The encoded protein has both a predicted N-terminal mitochondrial signal peptide and a C-terminal candidate type 1 peroxisomal-targeting signal for sorting it into glycosomes. However experimentally, only a mitochondrial localization was found for both procyclic trypanosomes grown with glucose and cells cultured with amino acids as an energy source. When the thiolase expression in procyclic cells was knocked down by RNA interference, no important change in growth rate occurred, irrespective of whether the cells were grown with or without glucose, indicating that the metabolic pathway(s) involving this enzyme is/are not essential for the parasite under either of these growth conditions.}, }
@article {pmid21904059, year = {2011}, author = {Ferrell, M and Abendroth, J and Zhang, Y and Sankaran, B and Edwards, TE and Staker, BL and Van Voorhis, WC and Stewart, LJ and Myler, PJ}, title = {Structure of aldose reductase from Giardia lamblia.}, journal = {Acta crystallographica. Section F, Structural biology and crystallization communications}, volume = {67}, number = {Pt 9}, pages = {1113-1117}, pmid = {21904059}, issn = {1744-3091}, support = {HHSN272200700057C/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Aldehyde Reductase/*chemistry ; Amino Acid Sequence ; Crystallography, X-Ray ; Giardia lamblia/*enzymology ; Humans ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {Giardia lamblia is an anaerobic aerotolerant eukaryotic parasite of the intestines. It is believed to have diverged early from eukarya during evolution and is thus lacking in many of the typical eukaryotic organelles and biochemical pathways. Most conspicuously, mitochondria and the associated machinery of oxidative phosphorylation are absent; instead, energy is derived from substrate-level phosphorylation. Here, the 1.75 Å resolution crystal structure of G. lamblia aldose reductase heterologously expressed in Escherichia coli is reported. As in other oxidoreductases, G. lamblia aldose reductase adopts a TIM-barrel conformation with the NADP(+)-binding site located within the eight β-strands of the interior.}, }
@article {pmid21896183, year = {2011}, author = {Passamonti, M and Ricci, A and Milani, L and Ghiselli, F}, title = {Mitochondrial genomes and Doubly Uniparental Inheritance: new insights from Musculista senhousia sex-linked mitochondrial DNAs (Bivalvia Mytilidae).}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {442}, pmid = {21896183}, issn = {1471-2164}, mesh = {Animals ; Base Sequence ; Cyclooxygenase 2/genetics ; DNA, Mitochondrial/*genetics ; Female ; *Genome, Mitochondrial ; *Inheritance Patterns ; Male ; Molecular Sequence Data ; Mytilidae/*genetics ; Nucleic Acid Conformation ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Doubly Uniparental Inheritance (DUI) is a fascinating exception to matrilinear inheritance of mitochondrial DNA (mtDNA). Species with DUI are characterized by two distinct mtDNAs that are inherited either through females (F-mtDNA) or through males (M-mtDNA). DUI sex-linked mitochondrial genomes share several unusual features, such as additional protein coding genes and unusual gene duplications/structures, which have been related to the functionality of DUI. Recently, new evidence for DUI was found in the mytilid bivalve Musculista senhousia. This paper describes the complete sex-linked mitochondrial genomes of this species.<br><br>RESULTS: Our analysis highlights that both M and F mtDNAs share roughly the same gene content and order, but with some remarkable differences. The Musculista sex-linked mtDNAs have differently organized putative control regions (CR), which include repeats and palindromic motifs, thought to provide sites for DNA-binding proteins involved in the transcriptional machinery. Moreover, in male mtDNA, two cox2 genes were found, one (M-cox2b) 123bp longer.<br><br>CONCLUSIONS: The complete mtDNA genome characterization of DUI bivalves is the first step to unravel the complex genetic signals allowing Doubly Uniparental Inheritance, and the evolutionary implications of such an unusual transmission route in mitochondrial genome evolution in Bivalvia. The observed redundancy of the palindromic motifs in Musculista M-mtDNA may have a role on the process by which sperm mtDNA becomes dominant or exclusive of the male germline of DUI species. Moreover, the duplicated M-COX2b gene may have a different, still unknown, function related to DUI, in accordance to what has been already proposed for other DUI species in which a similar cox2 extension has been hypothesized to be a tag for male mitochondria.}, }
@article {pmid21890067, year = {2011}, author = {Krakowetz, CN and Lindsay, LR and Chilton, NB}, title = {Genetic diversity in Ixodes scapularis (Acari: Ixodidae) from six established populations in Canada.}, journal = {Ticks and tick-borne diseases}, volume = {2}, number = {3}, pages = {143-150}, doi = {10.1016/j.ttbdis.2011.05.003}, pmid = {21890067}, issn = {1877-9603}, mesh = {Animals ; *Arachnid Vectors/classification/genetics ; Borrelia burgdorferi/pathogenicity ; Canada ; Endemic Diseases/*prevention &amp; control ; Genetics, Population/*methods ; Haplotypes ; Humans ; *Ixodes/classification/genetics ; Lyme Disease/epidemiology/microbiology/transmission ; Mitochondria/*chemistry/genetics ; Molecular Typing ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Single-Stranded Conformational ; Public Health ; RNA, Ribosomal, 16S/analysis ; Rodentia ; Sequence Analysis, DNA ; }, abstract = {Although Ixodes scapularis is the most important vector of Borrelia burgdorferi sensu stricto, the causative agent of Lyme disease in North America, little is known of the genetic diversity in this tick species within the recently established populations in Canada. In the present study, 153 I. scapularis adults collected from southern Canada were compared genetically using single-strand conformation polymorphism (SSCP) analyses in combination with DNA sequencing of the mitochondrial 16S rRNA gene. Nineteen haplotypes were detected, 8 of which have not been reported in the U.S.A. One 'new' haplotype was only detected at Lunenburg, Nova Scotia, and comprised 38% of the ticks examined for that population. The population in the southeast corner of Manitoba contained 3 'new' haplotypes. Although the most common haplotype (Is-1) was present in all 6 populations of I. scapularis in Canada, there were significant differences in the genetic structure among population. This suggests different geographical origins for the tick populations in Canada, which may be related to the transportation of larval and nymphal ticks by migratory passerines using different flyways. Determination of the origins of the endemic populations of I. scapularis in Canada, as well as those predicted to establish in the near future, has important implications with respect to understanding the risk of exposure to pathogenic bacteria infecting these ticks.}, }
@article {pmid21888892, year = {2011}, author = {Gessmann, D and Flinner, N and Pfannstiel, J and Schlösinger, A and Schleiff, E and Nussberger, S and Mirus, O}, title = {Structural elements of the mitochondrial preprotein-conducting channel Tom40 dissolved by bioinformatics and mass spectrometry.}, journal = {Biochimica et biophysica acta}, volume = {1807}, number = {12}, pages = {1647-1657}, doi = {10.1016/j.bbabio.2011.08.006}, pmid = {21888892}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Animals ; Computational Biology/*methods ; Fungal Proteins/*chemistry/classification/genetics/metabolism ; Mass Spectrometry/*methods ; Mice ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/*chemistry/classification/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Neurospora crassa/chemistry/cytology ; Phylogeny ; *Protein Structure, Secondary ; *Protein Structure, Tertiary ; Voltage-Dependent Anion Channel 1/chemistry/genetics ; }, abstract = {Most mitochondrial proteins are imported into mitochondria from the cytosolic compartment. Proteins destined for the outer or inner membrane, the inter-membrane space, or the matrix are recognized and translocated by the TOM machinery containing the specialized protein import channel Tom40. The latter is a protein with β-barrel shape, which is suggested to have evolved from a porin-type protein. To obtain structural insights in the absence of a crystal structure the membrane topology of Tom40 from Neurospora crassa was determined by limited proteolysis combined with mass spectrometry. The results were interpreted on the basis of a structural model that has been generated for NcTom40 by using the structure of mouse VDAC-1 as a template and amino acid sequence information of approximately 270 different Tom40 and approximately 480 VDAC amino acid sequences for refinement. The model largely explains the observed accessible cleavage sites and serves as a structural basis for the investigation of physicochemical properties of the ensemble of our Tom40 sequence data set. By this means we discovered two conserved polar slides in the pore interior. One is possibly involved in the positioning of a pore-inserted helix; the other one might be important for mitochondrial pre-sequence peptide binding as it is only present in Tom40 but not in VDAC proteins. The outer surface of the Tom40 barrel reveals two conserved amino acid clusters. They may be involved in binding other components of the TOM complex or bridging components of the TIM machinery of the mitochondrial inner membrane.}, }
@article {pmid21876672, year = {2011}, author = {Fookes, M and Schroeder, GN and Langridge, GC and Blondel, CJ and Mammina, C and Connor, TR and Seth-Smith, H and Vernikos, GS and Robinson, KS and Sanders, M and Petty, NK and Kingsley, RA and Bäumler, AJ and Nuccio, SP and Contreras, I and Santiviago, CA and Maskell, D and Barrow, P and Humphrey, T and Nastasi, A and Roberts, M and Frankel, G and Parkhill, J and Dougan, G and Thomson, NR}, title = {Salmonella bongori provides insights into the evolution of the Salmonellae.}, journal = {PLoS pathogens}, volume = {7}, number = {8}, pages = {e1002191}, pmid = {21876672}, issn = {1553-7374}, support = {//Wellcome Trust/United Kingdom ; 076964/WT_/Wellcome Trust/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Biological Evolution ; Enteropathogenic Escherichia coli/genetics ; Genes, Bacterial ; Genomic Islands/genetics ; Humans ; Phylogeny ; Salmonella/*genetics ; Salmonella enterica/genetics ; Sequence Analysis, DNA ; Translocation, Genetic ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {The genus Salmonella contains two species, S. bongori and S. enterica. Compared to the well-studied S. enterica there is a marked lack of information regarding the genetic makeup and diversity of S. bongori. S. bongori has been found predominantly associated with cold-blooded animals, but it can infect humans. To define the phylogeny of this species, and compare it to S. enterica, we have sequenced 28 isolates representing most of the known diversity of S. bongori. This cross-species analysis allowed us to confidently differentiate ancestral functions from those acquired following speciation, which include both metabolic and virulence-associated capacities. We show that, although S. bongori inherited a basic set of Salmonella common virulence functions, it has subsequently elaborated on this in a different direction to S. enterica. It is an established feature of S. enterica evolution that the acquisition of the type III secretion systems (T3SS-1 and T3SS-2) has been followed by the sequential acquisition of genes encoding secreted targets, termed effectors proteins. We show that this is also true of S. bongori, which has acquired an array of novel effector proteins (sboA-L). All but two of these effectors have no significant S. enterica homologues and instead are highly similar to those found in enteropathogenic Escherichia coli (EPEC). Remarkably, SboH is found to be a chimeric effector protein, encoded by a fusion of the T3SS-1 effector gene sopA and a gene highly similar to the EPEC effector nleH from enteropathogenic E. coli. We demonstrate that representatives of these new effectors are translocated and that SboH, similarly to NleH, blocks intrinsic apoptotic pathways while being targeted to the mitochondria by the SopA part of the fusion. This work suggests that S. bongori has inherited the ancestral Salmonella virulence gene set, but has adapted by incorporating virulence determinants that resemble those employed by EPEC.}, }
@article {pmid21872668, year = {2011}, author = {Salicini, I and Ibáñez, C and Juste, J}, title = {Multilocus phylogeny and species delimitation within the Natterer's bat species complex in the Western Palearctic.}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {3}, pages = {888-898}, doi = {10.1016/j.ympev.2011.08.010}, pmid = {21872668}, issn = {1095-9513}, mesh = {Alleles ; Animals ; Arctic Regions ; Bayes Theorem ; Cell Nucleus/genetics ; Chiroptera/*genetics ; Cluster Analysis ; Genetic Loci/*genetics ; Genetic Markers ; Geography ; Introns/genetics ; Mediterranean Region ; Mitochondria/genetics ; *Phylogeny ; Population Dynamics ; Sequence Analysis, DNA ; Software ; Species Specificity ; }, abstract = {Delimiting species is a crucial issue for many biological disciplines and is of primary importance for designing effective conservation plans. Traditional taxonomy based on morphological characters can be misled by the presence of phenotypic plesiomorphism or adaptative convergence. The use of multiple locus genetic data appears thus as a powerful tool for recognizing species boundaries. In this study, we used six nuclear introns and two mitochondrial markers to conduct a phylogenetic study of the Myotis nattereri species complex in the Western Palearctic. We combined tree-based and non-tree-based analyses, and also used concatenated phylogenetic methods of the separated nuclear and mitochondrial dataset as well as a recent coalescence-based multilocus approach. The strong concordance between the results of the analyses conducted confirms that M. nattereri is a paraphyletic group that is composed of four well-differentiated lineages in the study area. In the framework of the unified species concept, these four clades can be confidently considered as four valid species. This recognition of new cryptic species in the Western Mediterranean region shows that the biodiversity of this well-studied area is still not fully understood.}, }
@article {pmid21867770, year = {2011}, author = {Ichikawa, M and Bawn, S and Maw, NN and Htun, LL and Thein, M and Gyi, A and Sunn, K and Katakura, K and Itagaki, T}, title = {Characterization of Fasciola spp. in Myanmar on the basis of spermatogenesis status and nuclear and mitochondrial DNA markers.}, journal = {Parasitology international}, volume = {60}, number = {4}, pages = {474-479}, doi = {10.1016/j.parint.2011.08.007}, pmid = {21867770}, issn = {1873-0329}, mesh = {Animals ; Biomarkers/analysis ; Cattle ; Cattle Diseases/epidemiology/*parasitology/transmission ; DNA, Helminth/analysis/genetics ; DNA, Mitochondrial/analysis/genetics ; DNA, Ribosomal Spacer/analysis/genetics ; Fasciola/classification/*genetics/isolation &amp; purification ; Fascioliasis/epidemiology/*parasitology/transmission/*veterinary ; Haplotypes ; Male ; Mitochondria/chemistry/genetics ; Myanmar ; NADH Dehydrogenase/analysis/genetics ; Phylogeny ; Phylogeography ; Polymorphism, Restriction Fragment Length ; Protein Subunits/analysis/genetics ; Sequence Analysis, DNA ; Spermatogenesis/*genetics ; }, abstract = {Fasciola spp. in Myanmar were characterized on the basis of spermatogenesis status and DNA markers of nuclear internal transcribed spacer 1 (ITS1) and mitochondrial NADH dehydrogenase subunit 1 (nad1). We collected 88 adult flukes from Yangon, Lashio, and Myitkyina. Spermatogenesis status was analyzed by the presence of sperm in the seminal vesicles, and 8 aspermic and 80 spermic flukes were detected. The flukes were identified on the basis of spermatogenesis status and ITS1 types which were analyzed by a PCR-RFLP method, and 80 spermic flukes were identified as F. gigantica. A very low detection rate of aspermic Fasciola sp. indicated that they are not established in Myanmar. In phylogenetic analyses, the 7 aspermic Fasciola sp. from Myitkyina displayed a haplotype in nad1 sequence, which was identical to that of aspermic Fasciola sp. from other Asian countries including China. Therefore, they were probably introduced from China through an infected domestic ruminant. On the other hand, 17 nad1 haplotypes detected in F. gigantica belonged to 2 clades unique to Myanmar, each with a distinct founder haplotype in a network analysis. This indicated a unique history of F. gigantica introduction into Myanmar involving ancient artificial movements of domestic ruminants.}, }
@article {pmid21864691, year = {2011}, author = {Derkarabetian, S and Ledford, J and Hedin, M}, title = {Genetic diversification without obvious genitalic morphological divergence in harvestmen (Opiliones, Laniatores, Sclerobunus robustus) from montane sky islands of western North America.}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {3}, pages = {844-853}, doi = {10.1016/j.ympev.2011.08.004}, pmid = {21864691}, issn = {1095-9513}, mesh = {Animals ; Arachnida/*anatomy &amp; histology/*genetics ; Bayes Theorem ; *Ecosystem ; Electron Transport Complex IV/genetics ; *Genetic Variation ; *Geography ; Introns/genetics ; Male ; Mitochondria/genetics ; North America ; Penis/*anatomy &amp; histology/ultrastructure ; Peptide Elongation Factor 1/genetics ; Phylogeny ; Population Dynamics ; Software ; }, abstract = {The southern Rocky Mountains and adjacent Intermontane Plateau Highlands region of western North America is a geographically diverse area with an active geologic history. Given the topological complexity and extensive geologic activity, organisms inhabiting this region are expected to show some degree of morphological and genetic divergence, especially populations found on the southern montane 'sky islands' of this region. Here we examine the phylogeographic history and diversification of a montane forest inhabiting harvestmen, Sclerobunus robustus, using a combination of genetic and morphological data. Divergence time estimates indicate that much of the diversification within and between major groups S. robustus predate the Pleistocene glacial cycles. The most widespread subspecies, Sclerobunus robustus robustus, is recovered as six genetically distinct, geographically cohesive mitochondrial phylogroups. Gene tree data for a single nuclear gene reveals congruent, albeit slightly more conservative, patterns of genetic divergence. Despite high levels of genetic divergence throughout their distribution, phylogroups show extreme conservation in somatic and reproductive morphology. This uncoupling of morphological and genetic differentiation may be due to morphological conservatism associated with a conserved microhabitat preference. Based on these data, it is obvious that S. robustus has undergone some level of cryptic diversification.}, }
@article {pmid21858844, year = {2011}, author = {McInerney, JO and Martin, WF and Koonin, EV and Allen, JF and Galperin, MY and Lane, N and Archibald, JM and Embley, TM}, title = {Planctomycetes and eukaryotes: a case of analogy not homology.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {33}, number = {11}, pages = {810-817}, pmid = {21858844}, issn = {1521-1878}, support = {Z99 MH999999/ImNIH/Intramural NIH HHS/United States ; Z99 LM999999/ImNIH/Intramural NIH HHS/United States ; Z01 LM000073-13/ImNIH/Intramural NIH HHS/United States ; Z99 CL999999/ImNIH/Intramural NIH HHS/United States ; Z99 HL999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Bacterial Proteins/genetics/physiology ; Biological Evolution ; Cell Nucleus/physiology ; Chlamydia/classification/*cytology/genetics/physiology ; Endoplasmic Reticulum/physiology ; Eukaryota/classification/*cytology/genetics/physiology ; Gene Transfer, Horizontal ; Mitochondria/genetics/physiology ; Nuclear Envelope/physiology ; Phylogeny ; Planctomycetales/classification/*cytology/genetics/physiology ; Verrucomicrobia/classification/*cytology/genetics/physiology ; }, abstract = {Planctomycetes, Verrucomicrobia and Chlamydia are prokaryotic phyla, sometimes grouped together as the PVC superphylum of eubacteria. Some PVC species possess interesting attributes, in particular, internal membranes that superficially resemble eukaryotic endomembranes. Some biologists now claim that PVC bacteria are nucleus-bearing prokaryotes and are considered evolutionary intermediates in the transition from prokaryote to eukaryote. PVC prokaryotes do not possess a nucleus and are not intermediates in the prokaryote-to-eukaryote transition. Here we summarise the evidence that shows why all of the PVC traits that are currently cited as evidence for aspiring eukaryoticity are either analogous (the result of convergent evolution), not homologous, to eukaryotic traits; or else they are the result of horizontal gene transfers.}, }
@article {pmid21841184, year = {2011}, author = {Schulte, PM and Healy, TM and Fangue, NA}, title = {Thermal performance curves, phenotypic plasticity, and the time scales of temperature exposure.}, journal = {Integrative and comparative biology}, volume = {51}, number = {5}, pages = {691-702}, doi = {10.1093/icb/icr097}, pmid = {21841184}, issn = {1557-7023}, mesh = {*Acclimatization ; Animals ; Biological Evolution ; Cell Respiration ; Climate Change ; Environment ; Fundulidae/metabolism/*physiology ; Mitochondria/metabolism/physiology ; *Oxygen Consumption ; Phenotype ; *Temperature ; Thermodynamics ; Time Factors ; }, abstract = {Thermal performance curves (TPCs) describe the effects of temperature on biological rate processes. Here, we use examples from our work on common killifish (Fundulus heteroclitus) to illustrate some important conceptual issues relating to TPCs in the context of using these curves to predict the responses of organisms to climate change. Phenotypic plasticity has the capacity to alter the shape and position of the TPCs for acute exposures, but these changes can be obscured when rate processes are measured only following chronic exposures. For example, the acute TPC for mitochondrial respiration in killifish is exponential in shape, but this shape changes with acclimation. If respiration rate is measured only at the acclimation temperature, the TPC is linear, concealing the underlying mechanistic complexity at an acute time scale. These issues are particularly problematic when attempting to use TPCs to predict the responses of organisms to temperature change in natural environments. Many TPCs are generated using laboratory exposures to constant temperatures, but temperature fluctuates in the natural environment, and the mechanisms influencing performance at acute and chronic time scales, and the responses of the performance traits at these time scales may be quite different. Unfortunately, our current understanding of the mechanisms underlying the responses of organisms to temperature change is incomplete, particularly with respect to integrating from processes occurring at the level of single proteins up to whole-organism functions across different time scales, which is a challenge for the development of strongly grounded mechanistic models of responses to global climate change.}, }
@article {pmid21835450, year = {2011}, author = {Silva, RC and Báo, SN and Jivago, JL and Lucci, CM}, title = {Ultrastructural characterization of porcine oocytes and adjacent follicular cells during follicle development: lipid component evolution.}, journal = {Theriogenology}, volume = {76}, number = {9}, pages = {1647-1657}, doi = {10.1016/j.theriogenology.2011.06.029}, pmid = {21835450}, issn = {1879-3231}, mesh = {Animals ; Female ; Lipid Metabolism ; Microscopy, Electron, Transmission ; Oocytes/growth &amp; development/metabolism/*ultrastructure ; Ovarian Follicle/growth &amp; development/metabolism/*ultrastructure ; Swine/*growth &amp; development ; }, abstract = {The objective of this study was to characterize the morphometry and ultrastructure of porcine preantral and antral follicles, especially the lipid component evolution. Ovarian tissue was processed for light microscopy. Ovarian tissue and dissected antral follicles (< 2, 2-4, and 4-6 mm) were also processed for transmission electron microscopy using routine methods and using an osmium-imidazole method for lipid detection. Primordial follicles (34 ± 5 μm in diameter, mean ± SD) had one layer of flattened-cuboidal granulosa cells around the oocyte, primary follicles (40 ± 7 μm) had a single layer of cuboidal granulosa cells around the oocyte, and secondary follicles (102 ± 58 μm) had two or more layers of cuboidal granulosa cells around the oocyte. Preantral follicle oocytes had many round mitochondria and both rough and smooth endoplasmic reticulum. In oocytes of primordial and primary follicles, lipid droplets were abundant and were mostly located at the cell poles. In secondary and antral follicles, the zona pellucida completely surrounded the oocyte, whereas some microvilli and granulosa cells projected through it. Numerous electron-lucent vesicles and vacuoles were present in the oolemma of secondary and antral follicles. Based on osmium-imidazole staining, most of these structures were shown to be lipid droplets. As the follicle developed, the appearance of the lipid droplets changed from small and black to large and gray, dark or dark with light streaks, suggesting that their nature may change over time. In summary, although porcine follicles and oocytes had many similarities to those of other mammalian species, they were rich in lipids, with lipid droplets with varying morphological patterns as the follicle developed.}, }
@article {pmid21830829, year = {2011}, author = {García-Cañaveras, JC and Donato, MT and Castell, JV and Lahoz, A}, title = {A comprehensive untargeted metabonomic analysis of human steatotic liver tissue by RP and HILIC chromatography coupled to mass spectrometry reveals important metabolic alterations.}, journal = {Journal of proteome research}, volume = {10}, number = {10}, pages = {4825-4834}, doi = {10.1021/pr200629p}, pmid = {21830829}, issn = {1535-3907}, mesh = {Adult ; Aged ; Antioxidants/metabolism ; Bile Acids and Salts/chemistry ; Biomarkers/metabolism ; Chromatography, Liquid/methods ; Fatty Liver/*metabolism ; Female ; *Gene Expression Profiling ; Gene Expression Regulation ; Humans ; Lipid Metabolism ; Liver/metabolism ; Male ; Mass Spectrometry/methods ; Metabolomics/*methods ; Middle Aged ; Mitochondria/metabolism ; Phospholipids/chemistry ; Solvents ; }, abstract = {Steatosis, or excessive accumulation of lipids in the liver, is a generally accepted previous step to the development of more severe conditions like nonalcoholic steatohepatitis, fibrosis, and cirrhosis. We aimed to characterize the metabolic profile that defines simple steatosis in human tissue and to identify potential disturbances in the hepatic metabolism that could favor the switch to progressive liver damage. A total of 46 samples, 23 from steatotic and 23 from nonsteatotic human livers, were analyzed following a holistic LC-MS-based metabonomic analysis that combines RP and HILIC chromatographic separations. Multivariate statistical data analysis satisfactorily classified samples and revealed steatosis-associated biomarkers. Increased levels of bile acids and phospholipid degradation products, and decreased levels of antioxidant species, were found in steatotic livers, indicating disturbances in lipid and bile acid homeostasis and mitochondrial dysfunction. Changes in hypoxanthine, creatinine, glutamate, glutamine, or γ-glutamyl-dipeptides concentrations, suggestive of alterations in energy metabolism and amino acid metabolism and transport, were also found. The results show that the proposed analytical strategy is suitable to achieve a comprehensive metabolic profile of steatotic human liver tissue and provide new insights into the metabolic alterations occurring in fatty liver that could contribute to its predisposition to damage evolution.}, }
@article {pmid21829391, year = {2011}, author = {Wenger, JW and Piotrowski, J and Nagarajan, S and Chiotti, K and Sherlock, G and Rosenzweig, F}, title = {Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency.}, journal = {PLoS genetics}, volume = {7}, number = {8}, pages = {e1002202}, pmid = {21829391}, issn = {1553-7404}, support = {GM007790/GM/NIGMS NIH HHS/United States ; T32 GM007790/GM/NIGMS NIH HHS/United States ; P20 RR017670/RR/NCRR NIH HHS/United States ; P20RR017670/RR/NCRR NIH HHS/United States ; R01 HG003328/HG/NHGRI NIH HHS/United States ; }, mesh = {Adaptation, Biological/*physiology ; Biological Evolution ; Carbon/*metabolism ; Cluster Analysis ; Environment ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Genetic Fitness ; Genome, Fungal/genetics ; Glucose/metabolism ; Mitochondria/metabolism ; Mutation/genetics ; Signal Transduction/genetics ; Yeasts/genetics/*metabolism ; }, abstract = {As organisms adaptively evolve to a new environment, selection results in the improvement of certain traits, bringing about an increase in fitness. Trade-offs may result from this process if function in other traits is reduced in alternative environments either by the adaptive mutations themselves or by the accumulation of neutral mutations elsewhere in the genome. Though the cost of adaptation has long been a fundamental premise in evolutionary biology, the existence of and molecular basis for trade-offs in alternative environments are not well-established. Here, we show that yeast evolved under aerobic glucose limitation show surprisingly few trade-offs when cultured in other carbon-limited environments, under either aerobic or anaerobic conditions. However, while adaptive clones consistently outperform their common ancestor under carbon limiting conditions, in some cases they perform less well than their ancestor in aerobic, carbon-rich environments, indicating that trade-offs can appear when resources are non-limiting. To more deeply understand how adaptation to one condition affects performance in others, we determined steady-state transcript abundance of adaptive clones grown under diverse conditions and performed whole-genome sequencing to identify mutations that distinguish them from one another and from their common ancestor. We identified mutations in genes involved in glucose sensing, signaling, and transport, which, when considered in the context of the expression data, help explain their adaptation to carbon poor environments. However, different sets of mutations in each independently evolved clone indicate that multiple mutational paths lead to the adaptive phenotype. We conclude that yeasts that evolve high fitness under one resource-limiting condition also become more fit under other resource-limiting conditions, but may pay a fitness cost when those same resources are abundant.}, }
@article {pmid21825284, year = {2011}, author = {Ueno, O}, title = {Structural and biochemical characterization of the C3-C4 intermediate Brassica gravinae and relatives, with particular reference to cellular distribution of Rubisco.}, journal = {Journal of experimental botany}, volume = {62}, number = {15}, pages = {5347-5355}, pmid = {21825284}, issn = {1460-2431}, mesh = {Brassica/*anatomy &amp; histology/*metabolism ; Cell Respiration/physiology ; Chloroplasts/metabolism ; Glycine Dehydrogenase (Decarboxylating)/metabolism ; Photosynthesis/physiology ; Plant Leaves/*anatomy &amp; histology/*metabolism ; Ribulose-Bisphosphate Carboxylase/*metabolism ; }, abstract = {On the basis of its CO(2) compensation concentration, Brassica gravinae Ten. has been reported to be a C(3)-C(4) intermediate. This study investigated the structural and biochemical features of photosynthetic metabolism in B. gravinae. The cellular distribution of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) was also examined in B. gravinae, B. napus L. (C(3)), Raphanus sativus L. (C(3)), and Diplotaxis tenuifolia (L.) DC. (C(3)-C(4)) by immunogold electron microscopy to elucidate Rubisco expression during the evolution from C(3) to C(3)-C(4) intermediate plants. The bundle sheath (BS) cells of B. gravinae contained centrifugally located chloroplasts as well as centripetally located chloroplasts and mitochondria. Glycine decarboxylase P-protein was localized in the BS mitochondria. Brassica gravinae had low C(4) enzyme activities and high activities of Rubisco and photorespiratory enzymes, suggesting that it reduces photorespiratory CO(2) loss by the glycine shuttle. In B. gravinae, the labelling density of Rubisco was higher in the mesophyll chloroplasts than in the BS chloroplasts. A similar cellular pattern was found in other Brassicaceae species. These data demonstrate that, during the evolution from C(3) to C(3)-C(4) intermediate plants, the intercellular pattern of Rubisco expression did not change greatly, although the amount of chloroplasts in the BS cells increased. It also appears that intracellular variation in Rubisco distribution may occur within the BS cells of B. gravinae.}, }
@article {pmid21825140, year = {2011}, author = {Sommer, MS and Daum, B and Gross, LE and Weis, BL and Mirus, O and Abram, L and Maier, UG and Kühlbrandt, W and Schleiff, E}, title = {Chloroplast Omp85 proteins change orientation during evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {33}, pages = {13841-13846}, pmid = {21825140}, issn = {1091-6490}, mesh = {Arabidopsis/chemistry/*metabolism ; Arabidopsis Proteins/*chemistry/*metabolism ; Chloroplasts/*chemistry ; Cytoplasm ; *Evolution, Molecular ; Intracellular Membranes/chemistry ; Membrane Proteins/*chemistry/*metabolism ; Protein Precursors/*chemistry ; Protein Structure, Tertiary ; Protein Transport ; }, abstract = {The majority of outer membrane proteins (OMPs) from gram-negative bacteria and many of mitochondria and chloroplasts are β-barrels. Insertion and assembly of these proteins are catalyzed by the Omp85 protein family in a seemingly conserved process. All members of this family exhibit a characteristic N-terminal polypeptide-transport-associated (POTRA) and a C-terminal 16-stranded β-barrel domain. In plants, two phylogenetically distinct and essential Omp85's exist in the chloroplast outer membrane, namely Toc75-III and Toc75-V. Whereas Toc75-V, similar to the mitochondrial Sam50, is thought to possess the original bacterial function, its homolog, Toc75-III, evolved to the pore-forming unit of the TOC translocon for preprotein import. In all current models of OMP biogenesis and preprotein translocation, a topology of Omp85 with the POTRA domain in the periplasm or intermembrane space is assumed. Using self-assembly GFP-based in vivo experiments and in situ topology studies by electron cryotomography, we show that the POTRA domains of both Toc75-III and Toc75-V are exposed to the cytoplasm. This unexpected finding explains many experimental observations and requires a reevaluation of current models of OMP biogenesis and TOC complex function.}, }
@article {pmid21824868, year = {2011}, author = {Kitazoe, Y and Kishino, H and Hasegawa, M and Matsui, A and Lane, N and Tanaka, M}, title = {Stability of mitochondrial membrane proteins in terrestrial vertebrates predicts aerobic capacity and longevity.}, journal = {Genome biology and evolution}, volume = {3}, number = {}, pages = {1233-1244}, pmid = {21824868}, issn = {1759-6653}, mesh = {Animals ; Cell Respiration ; Humans ; Hydrogen Bonding ; Longevity ; Membrane Proteins/*metabolism ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/*metabolism ; Serine/genetics ; Threonine/genetics ; Vertebrates ; }, abstract = {The cellular energy produced by mitochondria is a fundamental currency of life. However, the extent to which mitochondrial (mt) performance (power and endurance) is adapted to habitats and life strategies of vertebrates is not well understood. A global analysis of mt genomes revealed that hydrophobicity (HYD) of mt membrane proteins (MMPs) is much lower in terrestrial vertebrates than in fishes and shows a strong negative correlation with serine/threonine composition (STC). Here, we present evidence that this systematic feature of MMPs was crucial for the evolution of large terrestrial vertebrates with high aerobic capacity. An Arrhenius-type equation gave positive correlations between STC and maximum life span (MLS) in terrestrial vertebrates (with a few exceptions relating to the lifestyle of small animals with a high resting metabolic rate [RMR]) and negative correlations in secondary marine vertebrates, such as cetaceans and alligators (which returned from land to water, utilizing buoyancy with increased body size). In particular, marked STC increases in primates (especially hominoids) among placentals were associated with very high MLS values. We connected these STC increases in MMPs with greater stability of respiratory complexes by estimating the degradation of the Arrhenius plot given by accelerating mtRMR up to mt maximum metabolic rate. Both mtRMR and HYD in terrestrial vertebrates decreased with increasing body mass. Decreases in mtRMR raise MMP stability when high mobility is not required, whereas decreased HYD may weaken this stability under the hydrophobic environment of lipid bilayer. High maximal metabolic rates (5-10 RMR), which we postulate require high MMP mobility, presumably render MMPs more unstable. A marked rise in STC may therefore be essential to stabilize MMPs, perhaps as dynamic supercomplexes, via hydrogen bonds associated with serine/threonine motifs.}, }
@article {pmid21819941, year = {2011}, author = {Santos, MA and Gomes, AC and Santos, MC and Carreto, LC and Moura, GR}, title = {The genetic code of the fungal CTG clade.}, journal = {Comptes rendus biologies}, volume = {334}, number = {8-9}, pages = {607-611}, doi = {10.1016/j.crvi.2011.05.008}, pmid = {21819941}, issn = {1768-3238}, mesh = {Amino Acids/genetics ; Codon/genetics ; Cytoplasm/metabolism ; Fungi/*genetics ; Genetic Code/*genetics ; Proteomics ; }, abstract = {Genetic code alterations discovered over the last 40 years in bacteria and eukaryotes invalidate the hypothesis that the code is universal and frozen. Mitochondria of various yeast species translate the UGA stop codon as tryptophan (Trp) and leucine (Leu) CUN codons (N = any nucleotide) as threonine (Thr) and fungal CTG clade species reassigned Leu CUG codons to serine and translate them ambiguously in their cytoplasms. This unique sense-to-sense genetic code alteration is mediated by a Ser-tRNA containing a Leu 5'-CAG-3'anticodon (ser-tRNA(CAG)), which is recognized and charged with Ser (~97%) by the seryl-tRNA synthetase (SerRS) and with Leu (~3%) by the leucyl-tRNA synthetase (LeuRS). This unusual tRNA appeared 272 ± 25 million years ago and had a profound impact on the evolution of the CTG clade species. Here, we review the most recent results and concepts arising from the study of this codon reassignment and we highlight how its study is changing our views of the evolution of the genetic code.}, }
@article {pmid21818295, year = {2011}, author = {Frieden, BR and Gatenby, RA}, title = {Information dynamics in living systems: prokaryotes, eukaryotes, and cancer.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e22085}, pmid = {21818295}, issn = {1932-6203}, support = {U54 CA143970/CA/NCI NIH HHS/United States ; 1U54CA143970-01/CA/NCI NIH HHS/United States ; }, mesh = {Cell Proliferation ; Entropy ; Eukaryotic Cells/*metabolism ; Glycolysis ; Humans ; *Information Theory ; Neoplasms/*metabolism/pathology ; Prokaryotic Cells/*metabolism ; }, abstract = {BACKGROUND: Living systems use information and energy to maintain stable entropy while far from thermodynamic equilibrium. The underlying first principles have not been established.<br><br>FINDINGS: We propose that stable entropy in living systems, in the absence of thermodynamic equilibrium, requires an information extremum (maximum or minimum), which is invariant to first order perturbations. Proliferation and death represent key feedback mechanisms that promote stability even in a non-equilibrium state. A system moves to low or high information depending on its energy status, as the benefit of information in maintaining and increasing order is balanced against its energy cost. Prokaryotes, which lack specialized energy-producing organelles (mitochondria), are energy-limited and constrained to an information minimum. Acquisition of mitochondria is viewed as a critical evolutionary step that, by allowing eukaryotes to achieve a sufficiently high energy state, permitted a phase transition to an information maximum. This state, in contrast to the prokaryote minima, allowed evolution of complex, multicellular organisms. A special case is a malignant cell, which is modeled as a phase transition from a maximum to minimum information state. The minimum leads to a predicted power-law governing the in situ growth that is confirmed by studies measuring growth of small breast cancers.<br><br>CONCLUSIONS: We find living systems achieve a stable entropic state by maintaining an extreme level of information. The evolutionary divergence of prokaryotes and eukaryotes resulted from acquisition of specialized energy organelles that allowed transition from information minima to maxima, respectively. Carcinogenesis represents a reverse transition: of an information maximum to minimum. The progressive information loss is evident in accumulating mutations, disordered morphology, and functional decline characteristics of human cancers. The findings suggest energy restriction is a critical first step that triggers the genetic mutations that drive somatic evolution of the malignant phenotype.}, }
@article {pmid21814545, year = {2011}, author = {Clare, EL}, title = {Cryptic species? Patterns of maternal and paternal gene flow in eight neotropical bats.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e21460}, pmid = {21814545}, issn = {1932-6203}, mesh = {Animals ; Chiroptera/classification/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Fathers ; Female ; *Gene Flow ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes/genetics ; Male ; Mitochondria/genetics ; Mothers ; Phylogeny ; Reproductive Isolation ; Species Specificity ; }, abstract = {Levels of sequence divergence at mitochondrial loci are frequently used in phylogeographic analysis and species delimitation though single marker systems cannot assess bi-parental gene flow. In this investigation I compare the phylogeographic patterns revealed through the maternally inherited mitochondrial COI region and the paternally inherited 7(th) intron region of the Dby gene on the Y-chromosome in eight common Neotropical bat species. These species are diverse and include members of two families from the feeding guilds of sanguivores, nectarivores, frugivores, carnivores and insectivores. In each case, the currently recognized taxon is comprised of distinct, substantially divergent intraspecific mitochondrial lineages suggesting cryptic species complexes. In Chrotopterus auritus, and Saccopteryx bilineata I observed congruent patterns of divergence in both genetic regions suggesting a cessation of gene flow between intraspecific groups. This evidence supports the existence of cryptic species complexes which meet the criteria of the genetic species concept. In Glossophaga soricina two intraspecific groups with largely sympatric South American ranges show evidence for incomplete lineage sorting or frequent hybridization while a third group with a Central American distribution appears to diverge congruently at both loci suggesting speciation. Within Desmodus rotundus and Trachops cirrhosus the paternally inherited region was monomorphic and thus does not support or refute the potential for cryptic speciation. In Uroderma bilobatum, Micronycteris megalotis and Platyrrhinus helleri the gene regions show conflicting patterns of divergence and I cannot exclude ongoing gene flow between intraspecific groups. This analysis provides a comprehensive comparison across taxa and employs both maternally and paternally inherited gene regions to validate patterns of gene flow. I present evidence for previously unrecognized species meeting the criteria of the genetic species concept but demonstrate that estimates of mitochondrial diversity alone do not accurately represent gene flow in these species and that contact/hybrid zones must be explored to evaluate reproductive isolation.}, }
@article {pmid21813655, year = {2011}, author = {Falara, V and Akhtar, TA and Nguyen, TT and Spyropoulou, EA and Bleeker, PM and Schauvinhold, I and Matsuba, Y and Bonini, ME and Schilmiller, AL and Last, RL and Schuurink, RC and Pichersky, E}, title = {The tomato terpene synthase gene family.}, journal = {Plant physiology}, volume = {157}, number = {2}, pages = {770-789}, pmid = {21813655}, issn = {1532-2548}, mesh = {Alkyl and Aryl Transferases/*genetics/metabolism ; Cyclopentanes/pharmacology ; Cytosol/enzymology ; Diterpenes, Kaurane/metabolism ; Evolution, Molecular ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Genome, Plant ; Solanum lycopersicum/drug effects/enzymology/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Monoterpenes/metabolism ; Multigene Family ; Oxylipins/pharmacology ; Plant Proteins/*genetics/metabolism ; }, abstract = {Compounds of the terpenoid class play numerous roles in the interactions of plants with their environment, such as attracting pollinators and defending the plant against pests. We show here that the genome of cultivated tomato (Solanum lycopersicum) contains 44 terpene synthase (TPS) genes, including 29 that are functional or potentially functional. Of these 29 TPS genes, 26 were expressed in at least some organs or tissues of the plant. The enzymatic functions of eight of the TPS proteins were previously reported, and here we report the specific in vitro catalytic activity of 10 additional tomato terpene synthases. Many of the tomato TPS genes are found in clusters, notably on chromosomes 1, 2, 6, 8, and 10. All TPS family clades previously identified in angiosperms are also present in tomato. The largest clade of functional TPS genes found in tomato, with 12 members, is the TPS-a clade, and it appears to encode only sesquiterpene synthases, one of which is localized to the mitochondria, while the rest are likely cytosolic. A few additional sesquiterpene synthases are encoded by TPS-b clade genes. Some of the tomato sesquiterpene synthases use z,z-farnesyl diphosphate in vitro as well, or more efficiently than, the e,e-farnesyl diphosphate substrate. Genes encoding monoterpene synthases are also prevalent, and they fall into three clades: TPS-b, TPS-g, and TPS-e/f. With the exception of two enzymes involved in the synthesis of ent-kaurene, the precursor of gibberellins, no other tomato TPS genes could be demonstrated to encode diterpene synthases so far.}, }
@article {pmid21811791, year = {2012}, author = {Karsten, U and Holzinger, A}, title = {Light, temperature, and desiccation effects on photosynthetic activity, and drought-induced ultrastructural changes in the green alga Klebsormidium dissectum (Streptophyta) from a high alpine soil crust.}, journal = {Microbial ecology}, volume = {63}, number = {1}, pages = {51-63}, pmid = {21811791}, issn = {1432-184X}, mesh = {*Adaptation, Physiological ; Dehydration ; Droughts ; Light ; *Photosynthesis ; Soil ; Streptophyta/*metabolism/*ultrastructure ; Temperature ; }, abstract = {Members of the cosmopolitan green algal genus Klebsormidium (Klebsormidiales, Streptophyta) are typical components of terrestrial microbiotic communities such as biological soil crusts, which have many important ecological functions. In the present study, Klebsormidium dissectum (Gay) Ettl &amp; Gärtner was isolated from a high alpine soil crust in the Tyrolean Alps, Austria. Physiological performance in terms of growth and photosynthesis was investigated under different controlled abiotic conditions and compared with ultrastructural changes under the treatments applied. K. dissectum showed very low light requirements as reflected in growth patterns and photosynthetic efficiency. Increasing temperatures from 5°C to 40°C led to different effects on respiratory oxygen consumption and photosynthetic oxygen evolution. While at low temperatures (5-10°C), respiration was not detectable or on a very low level, photosynthesis was relatively high, Reversely, at the highest temperature, respiration was unaffected, and photosynthesis strongly inhibited pointing to strong differences in temperature sensitivity between both physiological processes. Although photosynthetic performance of K. dissectum was strongly affected under short-term desiccation and recovered only partly after rehydration, this species was capable to survive even 3 weeks at 5% relative air humidity. K. dissectum cells have a cell width of 5.6 ± 0.3 μm and a cell length of 8.4 ± 2.0 μm. Desiccated cells showed a strongly reduced cell width (46% of control) and cell length (65% of control). In addition, in desiccated cells, fewer mitochondria were stained by DIOC(6), and damaged plasma membranes were detected by FM 1-43 staining. High-pressure freeze fixation as well as chemical fixation allowed visualizing ultrastructural changes caused by desiccation. In such cells, the nucleus and chloroplast were still visibly intact, but the extremely thin cell walls (75-180 nm) were substantially deformed. The cytoplasm appeared electron dense and mitochondria were altered. Although K. dissectum can be characterized as euryoecious species, all ecophysiological and ultrastructural data indicate susceptibility to desiccation. However, the steadily occurring fragmentation of filaments into smaller units leads to improved self protection and thus may represent a life strategy to better survive longer periods of drought in exposed alpine soil crusts.}, }
@article {pmid21803970, year = {2011}, author = {Deen, PM and Robben, JH}, title = {Succinate receptors in the kidney.}, journal = {Journal of the American Society of Nephrology : JASN}, volume = {22}, number = {8}, pages = {1416-1422}, doi = {10.1681/ASN.2010050481}, pmid = {21803970}, issn = {1533-3450}, mesh = {Adipose Tissue/metabolism ; Animals ; Apoptosis ; Citric Acid Cycle ; Humans ; Kidney/metabolism ; Kidney Diseases/metabolism ; Lipolysis ; Mice ; Mitochondria/metabolism ; Models, Biological ; Phylogeny ; Receptors, G-Protein-Coupled/metabolism ; Receptors, Purinergic P2Y/metabolism ; Retinal Diseases/pathology ; Succinates/chemistry/*metabolism ; Tissue Distribution ; }, abstract = {The G protein-coupled succinate and α-ketoglutarate receptors are closely related to the family of P2Y purinoreceptors. Although the α-ketoglutarate receptor is almost exclusively expressed in the kidney, its function is unknown. In contrast, the succinate receptor, SUCRN1, is expressed in a variety of tissues, including blood cells, adipose tissue, liver, retina, and the kidney. Recent evidence suggests SUCRN1 and its succinate ligand are novel detectors of local stress, including ischemia, hypoxia, toxicity, and hyperglycemia. Local levels of succinate in the kidney also activate the renin-angiotensin system and together with SUCRN1 may play a key role in the development of hypertension and the complications of diabetes mellitus, metabolic disease, and liver damage. This makes the succinate receptor a promising drug target to counteract an expanding number of interrelated disorders.}, }
@article {pmid21803764, year = {2011}, author = {Smith, DR}, title = {Extending the limited transfer window hypothesis to inter-organelle DNA migration.}, journal = {Genome biology and evolution}, volume = {3}, number = {}, pages = {743-748}, pmid = {21803764}, issn = {1759-6653}, mesh = {Biological Transport ; Cell Nucleus/*genetics ; DNA/genetics/*metabolism ; Eukaryota/*genetics ; *Evolution, Molecular ; Genome, Mitochondrial ; Genome, Plastid ; Mitochondria/*genetics ; Models, Genetic ; Plastids/*genetics ; }, abstract = {Mitochondrial genomes often contain large amounts of plastid DNA (ptDNA)-derived sequences (MTPTs). It has been suggested that the intercompartmental transfer of ptDNA is greatly reduced in species with only a single plastid per cell (monoplastidic) as compared with those with many plastids per cell (polyplastidic). This hypothesis has not been applied to the movement of DNA from plastids to mitochondria. By analyzing the organelle genomes from diverse mono- and polyplastidic taxa, I show that MTPTs are restricted to the mitochondrial genomes of species with many plastids per cell and are absent from those with one plastid per cell or with monoplastidic meristematic systems. Moreover, the most bloated mitochondrial genomes that were explored had the largest MTPT contents. These data, like previous results on ptDNA-derived sequences in nuclear genomes, support the hypothesis that plastid number and the forces governing the expansion and contraction of noncoding mitochondrial DNA (mtDNA) influence MTPT abundance. I also show that plastid genomes are depauperate in mtDNA-derived sequences (PTMTs), irrespective of the number of mitochondria per cell and plastid genome size, which may reflect the lack of a DNA uptake system in plastids.}, }
@article {pmid21801381, year = {2011}, author = {Bilewitch, JP and Degnan, SM}, title = {A unique horizontal gene transfer event has provided the octocoral mitochondrial genome with an active mismatch repair gene that has potential for an unusual self-contained function.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {228}, pmid = {21801381}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Animals ; Anthozoa/*genetics ; Computational Biology ; DNA Repair/genetics/*physiology ; *Evolution, Molecular ; Gene Expression Profiling ; Gene Transfer, Horizontal/*genetics ; Genome, Mitochondrial/*genetics ; *Models, Molecular ; Molecular Sequence Data ; MutS DNA Mismatch-Binding Protein/chemistry/*genetics ; Mutation/genetics ; Sequence Alignment ; Species Specificity ; }, abstract = {BACKGROUND: The mitochondrial genome of the Octocorallia has several characteristics atypical for metazoans, including a novel gene suggested to function in DNA repair. This mtMutS gene is favored for octocoral molecular systematics, due to its high information content. Several hypotheses concerning the origins of mtMutS have been proposed, and remain equivocal, although current weight of support is for a horizontal gene transfer from either an epsilonproteobacterium or a large DNA virus. Here we present new and compelling evidence on the evolutionary origin of mtMutS, and provide the very first data on its activity, functional capacity and stability within the octocoral mitochondrial genome.<br><br>RESULTS: The mtMutS gene has the expected conserved amino acids, protein domains and predicted tertiary protein structure. Phylogenetic analysis indicates that mtMutS is not a member of the MSH family and therefore not of eukaryotic origin. MtMutS clusters closely with representatives of the MutS7 lineage; further support for this relationship derives from the sharing of a C-terminal endonuclease domain that confers a self-contained mismatch repair function. Gene expression analyses confirm that mtMutS is actively transcribed in octocorals. Rates of mitochondrial gene evolution in mtMutS-containing octocorals are lower than in their hexacoral sister-group, which lacks the gene, although paradoxically the mtMutS gene itself has higher rates of mutation than other octocoral mitochondrial genes.<br><br>CONCLUSIONS: The octocoral mtMutS gene is active and codes for a protein with all the necessary components for DNA mismatch repair. A lower rate of mitochondrial evolution, and the presence of a nicking endonuclease domain, both indirectly support a theory of self-sufficient DNA mismatch repair within the octocoral mitochondrion. The ancestral affinity of mtMutS to non-eukaryotic MutS7 provides compelling support for an origin by horizontal gene transfer. The immediate vector of transmission into octocorals can be attributed to either an epsilonproteobacterium in an endosymbiotic association or to a viral infection, although DNA viruses are not currently known to infect both bacteria and eukaryotes, nor mitochondria in particular. In consolidating the first known case of HGT into an animal mitochondrial genome, these findings suggest the need for reconsideration of the means by which metazoan mitochondrial genomes evolve.}, }
@article {pmid21799887, year = {2011}, author = {Karunakaran, K and Mehlitz, A and Rudel, T}, title = {Evolutionary conservation of infection-induced cell death inhibition among Chlamydiales.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e22528}, pmid = {21799887}, issn = {1932-6203}, mesh = {Animals ; Baculoviral IAP Repeat-Containing 3 Protein ; Caspase Inhibitors ; *Cell Death ; Chlamydiales/*genetics/*physiology ; Cytochromes c/metabolism ; *Evolution, Molecular ; HeLa Cells ; Humans ; Inhibitor of Apoptosis Proteins/genetics/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; Ubiquitin-Protein Ligases ; Up-Regulation ; bcl-2 Homologous Antagonist-Killer Protein/metabolism ; bcl-2-Associated X Protein/metabolism ; }, abstract = {Control of host cell death is of paramount importance for the survival and replication of obligate intracellular bacteria. Among these, human pathogenic Chlamydia induces the inhibition of apoptosis in a variety of different host cells by directly interfering with cell death signaling. However, the evolutionary conservation of cell death regulation has not been investigated in the order Chlamydiales, which also includes Chlamydia-like organisms with a broader host spectrum. Here, we investigated the apoptotic response of human cells infected with the Chlamydia-like organism Simkania negevensis (Sn). Simkania infected cells exhibited strong resistance to apoptosis induced by intrinsic stress or by the activation of cell death receptors. Apoptotic signaling was blocked upstream of mitochondria since Bax translocation, Bax and Bak oligomerisation and cytochrome c release were absent in these cells. Infected cells turned on pro-survival pathways like cellular Inhibitor of Apoptosis Protein 2 (cIAP-2) and the Akt/PI3K pathway. Blocking any of these inhibitory pathways sensitized infected host cell towards apoptosis induction, demonstrating their role in infection-induced apoptosis resistance. Our data support the hypothesis of evolutionary conserved signaling pathways to apoptosis resistance as common denominators in the order Chlamydiales.}, }
@article {pmid21793251, year = {2011}, author = {Pereverzeva, VV and Zasypkin, MY and Solovenchuk, LL and Primak, AA and Dubinin, EA}, title = {[Variability of mitochondrial DNA cytochrome b gene in the red vole Clethrionomys rutilus pallas, 1779, population in the flood-plain middle stream of the Kolyma River].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {3}, pages = {283-288}, pmid = {21793251}, issn = {1026-3470}, mesh = {Amino Acid Sequence ; Animals ; Arvicolinae/*genetics ; Base Sequence ; Biomarkers ; Cytochromes b/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Mitochondria/genetics ; Phylogeny ; *Polymorphism, Genetic ; Russia ; Species Specificity ; }, abstract = {The intrapopulation variability of a cytochrome b gene fragment and the corresponding amino acid sequence was studied in the red vole Clethrionomys rutilus Pallas, 1779 from the flood-plain of the Kolyma River. Wide polymorphic variability of these properties was observed. Differences in the cytochrome b gene sequence were determined between the red voles of the studied population and the species collected in neighborhoods of Novosibirsk and Omsk. The revealed results point to the urgency of the cytochrome b gene nucleotide sequence and the variants of the respective amino acid sequence as genetic markers of originality of different red vole populations.}, }
@article {pmid21790065, year = {2011}, author = {Tang, KF and Pantoja, CR and Redman, RM and Navarro, SA and Lightner, DV}, title = {Ultrastructural and sequence characterization of Penaeus vannamei nodavirus (PvNV) from Belize.}, journal = {Diseases of aquatic organisms}, volume = {94}, number = {3}, pages = {179-187}, doi = {10.3354/dao02335}, pmid = {21790065}, issn = {0177-5103}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Belize ; Genome, Viral ; Molecular Sequence Data ; Nodaviridae/*genetics/*ultrastructure ; Penaeidae/*virology ; Phylogeny ; RNA, Viral/*genetics ; Viral Proteins/genetics/metabolism ; }, abstract = {The Penaeus vannamei nodavirus (PvNV), which causes muscle necrosis in Penaeus vannamei from Belize, was identified in 2005. Infected shrimp show clinical signs of white, opaque lesions in the tail muscle. Under transmission electron microscopy, the infected cells exhibit increases in various organelles, including mitochondria, Golgi stacks, and rough endoplasmic reticulum. Cytoplasmic inclusions containing para-crystalline arrays of virions were visualized. The viral particle is spherical in shape and 19 to 27 nm in diameter. A cDNA library was constructed from total RNA extracted from infected shrimp. Through nucleotide sequencing from the cDNA clones and northern blot hybridization, the PvNV genome was shown to consist of 2 segments: RNA1 (3111 bp) and RNA2 (1183 bp). RNA1 contains 2 overlapped open reading frames (ORF A and B), which may encode a RNA-dependent RNA polymerase (RdRp) and a B2 protein, respectively. RNA2 contains a single ORF that may encode the viral capsid protein. Sequence analyses showed the presence of 4 RdRp characteristic motifs and 2 conserved domains (RNA-binding B2 protein and viral coat protein) in the PvNV genome. Phylogenetic analysis based on the translated amino acid sequence of the RdRp reveals that PvNV is a member of the genus Alphanodavirus and closely related to Macrobrachium rosenbergii nodavirus (MrNV). In a study investigating potential PvNV vectors, we monitored the presence of PvNV by RT-PCR in seabird feces and various aquatic organisms collected around a shrimp farm in Belize. PvNV was detected in mosquitofish, seabird feces, barnacles, and zooplankton, suggesting that PvNV can be spread via these carriers.}, }
@article {pmid21787343, year = {2011}, author = {Kopec, KO and Alva, V and Lupas, AN}, title = {Bioinformatics of the TULIP domain superfamily.}, journal = {Biochemical Society transactions}, volume = {39}, number = {4}, pages = {1033-1038}, doi = {10.1042/BST0391033}, pmid = {21787343}, issn = {1470-8752}, mesh = {Animals ; Carrier Proteins/*genetics ; Cluster Analysis ; Computational Biology ; Evolution, Molecular ; Humans ; Lipids/chemistry ; Protein Structure, Tertiary/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {Proteins of the BPI (bactericidal/permeability-increasing protein)-like family contain either one or two tandem copies of a fold that usually provides a tubular cavity for the binding of lipids. Bioinformatic analyses show that, in addition to its known members, which include BPI, LBP [LPS (lipopolysaccharide)-binding protein)], CETP (cholesteryl ester-transfer protein), PLTP (phospholipid-transfer protein) and PLUNC (palate, lung and nasal epithelium clone) protein, this family also includes other, more divergent groups containing hypothetical proteins from fungi, nematodes and deep-branching unicellular eukaryotes. More distantly, BPI-like proteins are related to a family of arthropod proteins that includes hormone-binding proteins (Takeout-like; previously described to adopt a BPI-like fold), allergens and several groups of uncharacterized proteins. At even greater evolutionary distance, BPI-like proteins are homologous with the SMP (synaptotagmin-like, mitochondrial and lipid-binding protein) domains, which are found in proteins associated with eukaryotic membrane processes. In particular, SMP domain-containing proteins of yeast form the ERMES [ER (endoplasmic reticulum)-mitochondria encounter structure], required for efficient phospholipid exchange between these organelles. This suggests that SMP domains themselves bind lipids and mediate their exchange between heterologous membranes. The most distant group of homologues we detected consists of uncharacterized animal proteins annotated as TM (transmembrane) 24. We propose to group these families together into one superfamily that we term as the TULIP (tubular lipid-binding) domain superfamily.}, }
@article {pmid21783224, year = {2011}, author = {Rizwan-ul-Haq, M and Gong, L and Hu, M and Luo, J}, title = {Apolipophorin III and transmission electron microscopy as toxicity indicators for harmaline and tea saponin in Spodoptera exigua (Noctuidae: Lepidoptera).}, journal = {Chemosphere}, volume = {85}, number = {6}, pages = {995-1001}, doi = {10.1016/j.chemosphere.2011.06.089}, pmid = {21783224}, issn = {1879-1298}, mesh = {Amino Acid Sequence ; Animals ; Apolipoproteins/chemistry/*genetics ; Base Sequence ; Gene Expression Regulation/drug effects ; Harmaline/*toxicity ; Intestinal Mucosa/drug effects/ultrastructure ; *Microscopy, Electron, Transmission ; Molecular Sequence Data ; Phylogeny ; Saponins/*toxicity ; Sequence Analysis, DNA ; Spodoptera/*drug effects/genetics/ultrastructure ; Tea/*chemistry ; Toxicity Tests/*methods ; }, abstract = {Apolipophorin III, traditionally known for lipid transport in insects is fairly established as toxicity indicator against harmaline and tea saponin during this study. Apolipophorin III expressed in the hemolymph and midgut tissues of 3rd, 4th, 5th larval instars and pupae of Spodoptera exigua. Apolipophorin III presence was further confirmed by achieving its partial cDNA (Genbank accession no. FJ606822) of 448bp. qRT PCR revealed that tea saponin resulted in significant reduction of gene expression in 3rd and 4th larval instars but increased in 5th instar as compared to control. Harmaline caused gradual increase of gene expression in 3rd, 4th and 5th instars after feeding on the treated diet. Fifth instar larvae synonymously resulted in the highest gene expressions against both the biochemicals. After the injection of harmaline and tea saponin abrupt increase in gene expression of 4th, 5th larval instar and pupae was observed as compared to control treatment. Transmission electron microscopy of midgut epithelium after being fed with harmaline and tea saponin depicted certain cytological changes. Harmaline treatment lead to cytoplasm vacuolization, mitochondrial disruption, spherocrystals with concentric layers, irregular nucleus and floating nuclei in cytoplasm. Tea saponin treatment resulted in denser cytoplasm, higher intracellular osmotic concentration and reduced complement of apical microvilli. Cells were found to have only a few mitochondria and glycogen deposits in comparison to control treatment.}, }
@article {pmid21776000, year = {2011}, author = {Schlebusch, CM and de Jongh, M and Soodyall, H}, title = {Different contributions of ancient mitochondrial and Y-chromosomal lineages in 'Karretjie people' of the Great Karoo in South Africa.}, journal = {Journal of human genetics}, volume = {56}, number = {9}, pages = {623-630}, doi = {10.1038/jhg.2011.71}, pmid = {21776000}, issn = {1435-232X}, mesh = {Black People/*genetics ; Chromosomes, Human, Y/*genetics ; DNA, Mitochondrial/*genetics ; Female ; Genetic Variation ; Haplotypes ; Humans ; Male ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; South Africa/ethnology ; }, abstract = {The Karretjie people of the South African Great Karoo are itinerants who subsist by sheep shearing. Although officially classified 'Coloured', they are aware of their Khoe and San roots. To investigate the maternal and paternal ancestries of the Karretjie people we analyzed their mitochondrial and Y-chromosome DNA variation. Their genetic ancestry was compared with a neighboring group of 'Coloured' individuals. We found that the mitochondrial DNA (mtDNA) haplogroup L0d was present in all the Karretjie people examined, suggesting a maternal contribution, exclusively from the Khoe and San, whereas the paternal ancestry in males was more heterogeneous. The Coloured sample, on the other hand, were found to have a lower frequency of L0d (64.5%), but did harbor other African (27.6%) and non-African (7.9%) mtDNA haplogroups. Similar to the Karretjie people, the Y-chromosome lineages identified in the Coloured group had heterogeneous origins. This study also enabled an assessment of mtDNA variation within L0d sub-haplogroups. All seven of the L0d sub-clades were identified in the combined sample and were used to construct an L0d network.}, }
@article {pmid21771715, year = {2012}, author = {Delfin, F and Myles, S and Choi, Y and Hughes, D and Illek, R and van Oven, M and Pakendorf, B and Kayser, M and Stoneking, M}, title = {Bridging near and remote Oceania: mtDNA and NRY variation in the Solomon Islands.}, journal = {Molecular biology and evolution}, volume = {29}, number = {2}, pages = {545-564}, doi = {10.1093/molbev/msr186}, pmid = {21771715}, issn = {1537-1719}, mesh = {Chromosomes, Human, Y/*genetics ; DNA, Mitochondrial/*genetics ; Ethnicity/genetics ; Evolution, Molecular ; Female ; Gene Frequency ; Genetic Variation ; Genetics, Population ; Haplotypes ; Humans ; Male ; Melanesia ; Mitochondria/*genetics ; Molecular Sequence Data ; Native Hawaiian or Other Pacific Islander/genetics ; *Phylogeny ; }, abstract = {Although genetic studies have contributed greatly to our understanding of the colonization of Near and Remote Oceania, important gaps still exist. One such gap is the Solomon Islands, which extend between Bougainville and Vanuatu, thereby bridging Near and Remote Oceania, and include both Austronesian-speaking and Papuan-speaking groups. Here, we describe patterns of mitochondrial DNA (mtDNA) and nonrecombining Y chromosome (NRY) variation in over 700 individuals from 18 populations in the Solomons, including 11 Austronesian-speaking groups, 3 Papuan-speaking groups, and 4 Polynesian Outliers (descended via back migration from Polynesia). We find evidence for ancient (pre-Lapita) colonization of the Solomons in old NRY paragroups as well as from M2-M353, which probably arose in the Solomons ∼9,200 years ago and is the most frequent NRY haplogroup there. There are no consistent genetic differences between Austronesian-speaking and Papuan-speaking groups, suggesting extensive genetic contact between them. Santa Cruz, which is located in Remote Oceania, shows unusually low frequencies of mtDNA and NRY haplogroups of recent Asian ancestry. This is in apparent contradiction with expectations based on archaeological and linguistic evidence for an early (∼3,200 years ago), direct colonization of Santa Cruz by Lapita people from the Bismarck Archipelago, via a migration that "leapfrogged" over the rest of the Solomons. Polynesian Outliers show dramatic island-specific founder events involving various NRY haplogroups. We also find that NRY, but not mtDNA, genetic distance is correlated with the geographic distance between Solomons groups and that historically attested spheres of cultural interaction are associated with the recent genetic structure of Solomons groups, as revealed by mtDNA HV1 sequence and Y-STR haplotype diversity. Our results fill an important lacuna in human genetic studies of Oceania and aid in understanding the colonization and genetic history of this region.}, }
@article {pmid21768775, year = {2011}, author = {Martinez-Outschoorn, UE and Lin, Z and Ko, YH and Goldberg, AF and Flomenberg, N and Wang, C and Pavlides, S and Pestell, RG and Howell, A and Sotgia, F and Lisanti, MP}, title = {Understanding the metabolic basis of drug resistance: therapeutic induction of the Warburg effect kills cancer cells.}, journal = {Cell cycle (Georgetown, Tex.)}, volume = {10}, number = {15}, pages = {2521-2528}, pmid = {21768775}, issn = {1551-4005}, support = {R01 CA075503/CA/NCI NIH HHS/United States ; R01 CA098779/CA/NCI NIH HHS/United States ; R01-CA-120876/CA/NCI NIH HHS/United States ; R01 CA120876/CA/NCI NIH HHS/United States ; R01-CA-70896/CA/NCI NIH HHS/United States ; R01-CA-098779/CA/NCI NIH HHS/United States ; R01-CA-86072/CA/NCI NIH HHS/United States ; R01-AR-055660/AR/NIAMS NIH HHS/United States ; R01-CA-080250/CA/NCI NIH HHS/United States ; R01 CA070896/CA/NCI NIH HHS/United States ; R01 CA107382/CA/NCI NIH HHS/United States ; P30 CA056036/CA/NCI NIH HHS/United States ; P30-CA-56036/CA/NCI NIH HHS/United States ; R01-CA-107382/CA/NCI NIH HHS/United States ; R01 AR055660/AR/NIAMS NIH HHS/United States ; R01-CA-75503/CA/NCI NIH HHS/United States ; R01 CA080250/CA/NCI NIH HHS/United States ; R01 CA086072/CA/NCI NIH HHS/United States ; }, mesh = {Antineoplastic Agents, Hormonal/pharmacology/therapeutic use ; Apoptosis ; Breast Neoplasms/drug therapy/*metabolism/pathology ; Cell Line ; Coculture Techniques ; Dasatinib ; *Drug Resistance, Neoplasm ; Female ; Fibroblasts/metabolism ; Glycolysis ; Humans ; Pyrimidines/pharmacology/therapeutic use ; Tamoxifen/pharmacology/therapeutic use ; Telomerase/metabolism ; Thiazoles/pharmacology/therapeutic use ; }, abstract = {Previously, we identified a form of epithelial-stromal metabolic coupling, in which cancer cells induce aerobic glycolysis in adjacent stromal fibroblasts, via oxidative stress, driving autophagy and mitophagy. In turn, these cancer-associated fibroblasts provide recycled nutrients to epithelial cancer cells, "fueling" oxidative mitochondrial metabolism and anabolic growth. An additional consequence is that these glycolytic fibroblasts protect cancer cells against apoptosis, by providing a steady nutrient stream of to mitochondria in cancer cells. Here, we investigated whether these interactions might be the basis of tamoxifen-resistance in ER(+) breast cancer cells. We show that MCF7 cells alone are Tamoxifen-sensitive, but become resistant when co-cultured with hTERT-immortalized human fibroblasts. Next, we searched for a drug combination (Tamoxifen + Dasatinib) that could over-come fibroblast-induced Tamoxifen-resistance. Importantly, we show that this drug combination acutely induces the Warburg effect (aerobic glycolysis) in MCF7 cancer cells, abruptly cutting off their ability to use their fuel supply, effectively killing these cancer cells. Thus, we believe that the Warburg effect in tumor cells is not the "root cause" of cancer, but rather it may provide the necessary clues to preventing chemo-resistance in cancer cells. Finally, we observed that this drug combination (Tamoxifen + Dasatinib) also had a generalized anti-oxidant effect, on both co-cultured fibroblasts and cancer cells alike, potentially reducing tumor-stroma co-evolution. Our results are consistent with the idea that chemo-resistance may be both a metabolic and stromal phenomenon that can be overcome by targeting mitochondrial function in epithelial cancer cells. Thus, simultaneously targeting both (1) the tumor stroma and (2) the epithelial cancer cells, with combination therapies, may be the most successful approach to anti-cancer therapy. This general strategy of combination therapy for overcoming drug resistance could be applicable to many different types of cancer.}, }
@article {pmid21764378, year = {2011}, author = {Kissinger, JC and DeBarry, J}, title = {Genome cartography: charting the apicomplexan genome.}, journal = {Trends in parasitology}, volume = {27}, number = {8}, pages = {345-354}, pmid = {21764378}, issn = {1471-5007}, support = {R01 AI068908/AI/NIAID NIH HHS/United States ; R01 AI068908-04/AI/NIAID NIH HHS/United States ; }, mesh = {Apicomplexa/*genetics ; Centromere/genetics ; Chromatin/*genetics ; Chromosome Mapping ; Evolution, Molecular ; Gene Expression Regulation ; Gene Transfer, Horizontal ; *Genes, Protozoan ; *Genome ; Mitochondria/genetics ; Synteny ; Telomere ; }, abstract = {Genes reside in particular genomic contexts that can be mapped at many levels. Historically, 'genetic maps' were used primarily to locate genes. Recent technological advances in the determination of genome sequences have made the analysis and comparison of whole genomes possible and increasingly tractable. What do we see if we shift our focus from gene content (the 'inventory' of genes contained within a genome) to the composition and organization of a genome? This review examines what has been learned about the evolution of the apicomplexan genome as well as the significance and impact of genomic location on our understanding of the eukaryotic genome and parasite biology.}, }
@article {pmid21763786, year = {2011}, author = {Van der Eecken, V and Clippe, A and Van Veldhoven, PP and Knoops, B}, title = {Mitochondrial targeting of peroxiredoxin 5 is preserved from annelids to mammals but is absent in pig Sus scrofa domesticus.}, journal = {Mitochondrion}, volume = {11}, number = {6}, pages = {973-981}, doi = {10.1016/j.mito.2011.06.013}, pmid = {21763786}, issn = {1872-8278}, mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; Humans ; Mammals ; Mitochondria/*metabolism ; Molecular Sequence Data ; Peroxiredoxins/*metabolism ; Polychaeta ; Protein Sorting Signals ; Protein Transport ; Sequence Alignment ; }, abstract = {Peroxiredoxin 5 (PRDX5) is a thioredoxin peroxidase able to reduce hydrogen peroxide, alkyl hydroperoxides and peroxynitrite. In human, PRDX5 was reported to be localized in the cytosol, the mitochondria, the peroxisomes and the nucleus. Mitochondrial localization results from the presence of an N-terminal mitochondrial targeting sequence (MTS). Here, we examined the conservation of mitochondrial localization of PRDX5 in animal species. We found that PRDX5 MTS is present and functional in the annelid lugworm Arenicola marina. Surprisingly, although mitochondrial targeting is well conserved among animals, PRDX5 is missing in mitochondria of domestic pig. Thus, it appears that mitochondrial targeting of PRDX5 may have been lost throughout evolution in animal species, including pig, with unknown functional consequences.}, }
@article {pmid21762422, year = {2011}, author = {Smith, DR and Lee, RW}, title = {Nucleotide diversity of the colorless green alga Polytomella parva (Chlorophyceae, Chlorophyta): high for the mitochondrial telomeres, surprisingly low everywhere else.}, journal = {The Journal of eukaryotic microbiology}, volume = {58}, number = {5}, pages = {471-473}, doi = {10.1111/j.1550-7408.2011.00569.x}, pmid = {21762422}, issn = {1550-7408}, mesh = {Chlorophyta/*genetics ; Evolution, Molecular ; *Genetic Variation ; Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Data ; Telomere/*genetics ; }, abstract = {Silent-site nucleotide diversity data (π(silent)) can provide insights into the forces driving genome evolution. Here we present π(silent) statistics for the mitochondrial and nuclear DNAs of Polytomella parva, a nonphotosynthetic green alga with a highly reduced, linear fragmented mitochondrial genome. We show that this species harbors very little genetic diversity, with the exception of the mitochondrial telomeres, which have an excess of polymorphic sites. These data are compared with previously published π(silent) values from the mitochondrial and nuclear genomes of the model species Chlamydomonas reinhardtii and Volvox carteri, which are close relatives of P. parva, and are used to understand the modes and tempos of genome evolution within green algae.}, }
@article {pmid21761280, year = {2011}, author = {Zhang, J and Jia, J and Breen, J and Kong, X}, title = {Recent insertion of a 52-kb mitochondrial DNA segment in the wheat lineage.}, journal = {Functional &amp; integrative genomics}, volume = {11}, number = {4}, pages = {599-609}, pmid = {21761280}, issn = {1438-7948}, mesh = {Chromosomes, Artificial, Bacterial/genetics ; Chromosomes, Plant/genetics ; DNA, Mitochondrial/*genetics ; Gene Expression ; Gene Order ; Genes, Mitochondrial ; Genetic Variation ; *Genome, Plant ; Haplotypes ; Molecular Sequence Annotation ; *Mutagenesis, Insertional ; Sequence Analysis, DNA ; Triticum/*genetics ; }, abstract = {The assembly of a 1.3-Mb size region of the wheat genome has provided the opportunity to study a recent nuclear mitochondrial DNA insertion (NUMT). In the present study, we have studied two bacterial artificial chromosomes (BACs) and characterized a 52-kb NUMT segment from the tetraploid and hexaploid wheat BAC libraries. The conserved orthologous NUMT regions from tetraploid and hexaploid wheat Langdon and Chinese Spring shared identical gene haplotypes even though mutations (insertions, deletions, and substitutions) had occurred. The 52-kb NUMT was present in hexaploid variety Chinese Spring, but absent in variety Hope, by sequence comparison of their corresponding region. Amplifying the NUMT junctions using a set of the wheat materials including diploid, tetraploid, and hexaploid lines showed that none of the diploid wheat carried the region and only some tetraploid and hexaploid wheat were positive for the NUMT. Age estimation of the NUMT displayed the mean ages of Langdon NUMT and Chinese Spring NUMT to be 378,000 and 416,000 years ago, respectively. Reverse transcription PCR and sequencing of the nad7 gene showed 28 C → U RNA editing sites and four partial editing sites, as expected for mitochondrial DNA expression. Specific SNPs discriminated between cDNA from the nucleus and the mitochondria and suggested that the nuclear copy was not expressed. The mitochondrial DNA studied was inserted into the genome quite recently within the wheat lineage and gave rise to the non-coding nuclear nad7 gene. The NUMT segment could be lost and acquired frequently during the wheat evolution.}, }
@article {pmid21760940, year = {2011}, author = {Schlüter, A and Ruiz-Trillo, I and Pujol, A}, title = {Phylogenomic evidence for a myxococcal contribution to the mitochondrial fatty acid beta-oxidation.}, journal = {PloS one}, volume = {6}, number = {7}, pages = {e21989}, pmid = {21760940}, issn = {1932-6203}, mesh = {Acyl Coenzyme A/metabolism ; Eukaryota/metabolism ; Fatty Acids/*metabolism ; *Genomics ; Metabolic Networks and Pathways ; Mitochondria/*genetics ; Models, Biological ; Myxococcales/*genetics ; Oxidation-Reduction ; *Phylogeny ; Proteins/genetics ; }, abstract = {BACKGROUND: The origin of eukaryotes remains a fundamental question in evolutionary biology. Although it is clear that eukaryotic genomes are a chimeric combination of genes of eubacterial and archaebacterial ancestry, the specific ancestry of most eubacterial genes is still unknown. The growing availability of microbial genomes offers the possibility of analyzing the ancestry of eukaryotic genomes and testing previous hypotheses on their origins.<br><br>Here, we have applied a phylogenomic analysis to investigate a possible contribution of the Myxococcales to the first eukaryotes. We conducted a conservative pipeline with homologous sequence searches against a genomic sampling of 40 eukaryotic and 357 prokaryotic genomes. The phylogenetic reconstruction showed that several eukaryotic proteins traced to Myxococcales. Most of these proteins were associated with mitochondrial lipid intermediate pathways, particularly enzymes generating reducing equivalents with pivotal roles in fatty acid &#x3b2;-oxidation metabolism. Our data suggest that myxococcal species with the ability to oxidize fatty acids transferred several genes to eubacteria that eventually gave rise to the mitochondrial ancestor. Later, the eukaryotic nucleocytoplasmic lineage acquired those metabolic genes through endosymbiotic gene transfer.<br><br>CONCLUSIONS/SIGNIFICANCE: Our results support a prokaryotic origin, different from &#x3b1;-proteobacteria, for several mitochondrial genes. Our data reinforce a fluid prokaryotic chromosome model in which the mitochondrion appears to be an important entry point for myxococcal genes to enter eukaryotes.}, }
@article {pmid21757490, year = {2011}, author = {Andrade, IDS and Vianez-Júnior, JL and Goulart, CL and Homblé, F and Ruysschaert, JM and Almeida von Krüger, WM and Bisch, PM and de Souza, W and Mohana-Borges, R and Motta, MCM}, title = {Characterization of a porin channel in the endosymbiont of the trypanosomatid protozoan Crithidia deanei.}, journal = {Microbiology (Reading, England)}, volume = {157}, number = {Pt 10}, pages = {2818-2830}, doi = {10.1099/mic.0.049247-0}, pmid = {21757490}, issn = {1465-2080}, mesh = {Amino Acid Sequence ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Bacterial Physiological Phenomena ; Bacterial Proteins/*chemistry/genetics/metabolism ; Crithidia/*microbiology/physiology ; Molecular Sequence Data ; Phylogeny ; Porins/*chemistry/genetics/metabolism ; Sequence Alignment ; *Symbiosis ; }, abstract = {Crithidia deanei is a trypanosomatid protozoan that harbours a symbiotic bacterium. The partners maintain a mutualistic relationship, thus constituting an excellent model for studying metabolic exchanges between the host and the symbiont, the origin of organelles and cellular evolution. According to molecular analysis, symbionts of different trypanosomatid species share high identity and descend from a common ancestor, a β-proteobacterium of the genus Bordetella. The endosymbiont is surrounded by two membranes, like Gram-negative bacteria, but its envelope presents special features, since phosphatidylcholine is a major membrane component and the peptidoglycan layer is highly reduced, as described in other obligate intracellular bacteria. Like the process that generated mitochondria and plastids, the endosymbiosis in trypanosomatids depends on pathways that facilitate the intensive metabolic exchanges between the bacterium and the host protozoan. A search of the annotated symbiont genome database identified one sequence with identity to porin-encoding genes of the genus Bordetella. Considering that the symbiont outer membrane has a great accessibility to cytoplasm host factors, it was important to characterize this single porin-like protein using biochemical, molecular, computational and ultrastructural approaches. Antiserum against the recombinant porin-like molecule revealed that it is mainly located in the symbiont envelope. Secondary structure analysis and comparative modelling predicted the protein 3D structure as an 18-domain β-barrel, which is consistent with porin channels. Electrophysiological measurements showed that the porin displays a slight preference for cations over anions. Taken together, the data presented herein suggest that the C. deanei endosymbiont porin is phylogenetically and structurally similar to those described in Gram-negative bacteria, representing a diffusion channel that might contribute to the exchange of nutrients and metabolic precursors between the symbiont and its host cell.}, }
@article {pmid21755337, year = {2011}, author = {Pamplona, R and Barja, G}, title = {An evolutionary comparative scan for longevity-related oxidative stress resistance mechanisms in homeotherms.}, journal = {Biogerontology}, volume = {12}, number = {5}, pages = {409-435}, doi = {10.1007/s10522-011-9348-1}, pmid = {21755337}, issn = {1573-6768}, mesh = {Animals ; *Biological Evolution ; *Longevity ; Mitochondria/metabolism ; *Oxidative Stress ; Reactive Oxygen Species/metabolism ; }, abstract = {Key mechanisms relating oxidative stress to longevity from an interespecies comparative approach are reviewed. Long-lived animal species show low rates of reactive oxygen species (ROS) generation and oxidative damage at their mitochondria. Comparative physiology also shows that the specific compositional pattern of tissue macromolecules (proteins, lipids and nucleic acids) in long-lived animal species gives them an intrinsically high resistance to modification that likely contributes to their superior longevity. This is obtained in the case of lipids by decreasing the degree of fatty acid unsaturation, and in the case of proteins by lowering their methionine content. These findings are also substantiated from a phylogenomic approach. Nutritional or/and pharmacological interventions focused to modify some of these molecular traits were translated with modifications in animal longevity. It is proposed that natural selection tends to decrease the mitochondrial ROS generation and to increase the molecular resistance to the oxidative damage in long-lived species.}, }
@article {pmid21749854, year = {2011}, author = {Cardol, P}, title = {Mitochondrial NADH:ubiquinone oxidoreductase (complex I) in eukaryotes: a highly conserved subunit composition highlighted by mining of protein databases.}, journal = {Biochimica et biophysica acta}, volume = {1807}, number = {11}, pages = {1390-1397}, doi = {10.1016/j.bbabio.2011.06.015}, pmid = {21749854}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Animals ; Data Mining ; *Databases, Protein ; Electron Transport Complex I/chemistry/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Protein Subunits/chemistry/*genetics ; Sequence Alignment ; }, abstract = {Complex I (NADH:ubiquinone oxidoreductase) is the largest enzyme of the mitochondrial respiratory chain. Compared to its bacterial counterpart which encompasses 14-17 subunits, mitochondrial complex I has almost tripled its subunit composition during evolution of eukaryotes, by recruitment of so-called accessory subunits, part of them being specific to distinct evolutionary lineages. The increasing availability of numerous broadly sampled eukaryotic genomes now enables the reconstruction of the evolutionary history of this large protein complex. Here, a combination of profile-based sequence comparisons and basic structural properties analyses at the protein level enabled to pinpoint homology relationships between complex I subunits from fungi, mammals or green plants, previously identified as "lineage-specific" subunits. In addition, homologs of at least 40 mammalian complex I subunits are present in representatives of all major eukaryote assemblages, half of them having not been investigated so far (Excavates, Chromalveolates, Amoebozoa). This analysis revealed that complex I was subject to a phenomenal increase in size that predated the diversification of extant eukaryotes, followed by very few lineage-specific additions/losses of subunits. The implications of this subunit conservation for studies of complex I are discussed.}, }
@article {pmid21749736, year = {2012}, author = {Castalanelli, MA and Baker, AM and Munyard, KA and Grimm, M and Groth, DM}, title = {Molecular phylogeny supports the paraphyletic nature of the genus Trogoderma (Coleoptera: Dermestidae) collected in the Australasian ecozone.}, journal = {Bulletin of entomological research}, volume = {102}, number = {1}, pages = {17-28}, doi = {10.1017/S0007485311000319}, pmid = {21749736}, issn = {1475-2670}, mesh = {Animals ; Australia ; Bayes Theorem ; Cell Nucleus/genetics ; Coleoptera/*classification/*genetics ; Conserved Sequence ; Cytochromes b/genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Mitochondria/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 18S/genetics ; Seasons ; Sequence Analysis, DNA ; }, abstract = {To date, a molecular phylogenetic approach has not been used to investigate the evolutionary structure of Trogoderma and closely related genera. Using two mitochondrial genes, Cytochrome Oxidase I and Cytochrome B, and the nuclear gene, 18S, the reported polyphyletic positioning of Trogoderma was examined. Paraphyly in Trogoderma was observed, with one Australian Trogoderma species reconciled as sister to all Dermestidae and the Anthrenocerus genus deeply nested within the Australian Trogoderma clade. In addition, time to most recent common ancestor for a number of Dermestidae was calculated. Based on these estimations, the Dermestidae origin exceeded 175 million years, placing the origins of this family in Pangaea.}, }
@article {pmid21748354, year = {2012}, author = {Najm, NA and Silaghi, C and Bell-Sakyi, L and Pfister, K and Passos, LM}, title = {Detection of bacteria related to Candidatus Midichloria mitochondrii in tick cell lines.}, journal = {Parasitology research}, volume = {110}, number = {1}, pages = {437-442}, pmid = {21748354}, issn = {1432-1955}, mesh = {Alphaproteobacteria/classification/genetics/*isolation &amp; purification ; Animals ; Cell Line ; Cluster Analysis ; DNA Primers/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics/isolation &amp; purification ; Female ; Ixodes/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Rhipicephalus/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Many ticks have been shown to be infected with intracellular bacteria. One of these bacteria is Candidatus Midichloria mitochondrii which is the only characterized bacterium that has the ability to invade the mitochondria within ovarian cells and consume them without any effect on the female tick's reproduction. In the present study, eight cell lines derived from the ticks Ixodes ricinus, Ixodes scapularis, Rhipicephalus (Boophilus) microplus, and Rhipicephalus (Boophilus) decoloratus were examined for the presence of the bacterium Ca. Midichloria mitochondrii. PCR assays for this bacterium were carried out using two sets of primers targeting the eubacterial 16SrRNA gene and a set of primers specific for the gyrB gene of Ca. Midichloria mitochondrii. With the 16S rRNA primers, DNA was amplified from two cell lines (R. (B.) decoloratus line BDE/CTVM14 and I. ricinus line IRE/CTVM19) on one out of three occasions each. Sequencing of the PCR products showed that the two cell lines gave sequences with 100% similarity to Ca. Midichloria mitochondrii. However, all cell lines, including the two positive cell lines, were negative with the specific primers. Phylogenetic analysis shows that our sequences belong to the subclass α-proteobacteria. They were identical to the sequences amplified from the tick I. ricinus. The results suggest that two cell lines, IRE/CTVM19 and BDE/CTVM14, may contain bacteria closely related to Ca. Midichloria mitochondrii and identical with it in a 350-bp part of the 16S rRNA gene sequence. To our knowledge, this constitutes the first report of the presence of DNA similar to the DNA of Ca. Midichloria mitochondrii in tick cell lines.}, }
@article {pmid21743250, year = {2011}, author = {Robinson, JL and Hall, JR and Charman, M and Ewart, KV and Driedzic, WR}, title = {Molecular analysis, tissue profiles, and seasonal patterns of cytosolic and mitochondrial GPDH in freeze-resistant rainbow smelt (Osmerus mordax).}, journal = {Physiological and biochemical zoology : PBZ}, volume = {84}, number = {4}, pages = {363-376}, doi = {10.1086/660162}, pmid = {21743250}, issn = {1537-5293}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Acclimatization ; Amino Acid Sequence ; Animals ; Cytosol/metabolism ; DNA, Complementary/genetics ; Electrophoresis ; Freezing ; Gene Dosage ; Gene Expression Profiling ; *Gene Expression Regulation, Enzymologic ; Glycerol/blood/metabolism ; Glycerolphosphate Dehydrogenase/*genetics/*metabolism ; Liver/enzymology/metabolism ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Newfoundland and Labrador ; Osmeriformes/*genetics/*metabolism ; Phylogeny ; Polymerase Chain Reaction ; Protein Isoforms/genetics/metabolism ; RNA, Messenger/metabolism ; Salmon/metabolism ; Seasons ; Species Specificity ; }, abstract = {Rainbow smelt (Osmerus mordax) is an anadromous teleost that, beginning in late fall, accumulates plasma glycerol in excess of 200 mM, which subsequently decreases in the spring. The activity of cytosolic glycerol-3-phosphate dehydrogenase (cGPDH) is higher (i) in liver of smelt than in that of Atlantic salmon and capelin (nonglycerol accumulators), (ii) in liver of smelt maintained at 1°C than in that of smelt held at 8°-10°C, and (iii) in smelt liver than in smelt muscle, heart, brain, or kidney. In addition, transcript levels of cGPDH in liver peak in December during the onset of glycerol production and then decline over the remainder of the season. There are four cGPDH protein isoforms in smelt liver that are present regardless of glycerol production status. A minimum of four cGPDH gene copies identified by Southern blotting provide adequate genetic potential to yield multiple protein isoforms. A full-length cDNA for smelt mitochondrial glycerol-3-phosphate dehydrogenase (mGPDH) was cloned and characterized. The 2,790-bp cDNA contains a 109-bp 5'UTR, a 2,193-bp open reading frame, and a 488-bp 3'UTR; transcripts are ubiquitously expressed in both warm- and cold-acclimated smelt tissues. Smelt mGPDH encodes a 730-aa protein that clusters with that of zebrafish and frog and contains several common structural motifs. mGPDH transcript levels generally increase late in the seasonal glycerol cycle, and mGPDH enzyme activity increases significantly during the glycerol decrease phase. Taken together, these findings suggest that liver cGPDH and mGPDH play a key role in the glycerol accumulation and decrease phases, respectively.}, }
@article {pmid21723951, year = {2011}, author = {Tomasco, IH and Lessa, EP}, title = {The evolution of mitochondrial genomes in subterranean caviomorph rodents: adaptation against a background of purifying selection.}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {1}, pages = {64-70}, doi = {10.1016/j.ympev.2011.06.014}, pmid = {21723951}, issn = {1095-9513}, mesh = {*Adaptation, Physiological ; Anaerobiosis ; Animals ; Biological Evolution ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genetic Variation ; *Genome, Mitochondrial ; Mitochondria/genetics ; Phylogeny ; Proteins/*genetics ; Rodentia/*classification/*genetics/physiology ; *Selection, Genetic ; }, abstract = {South American tuco-tucos (Ctenomys) and the related coruro (Spalacopus) are two rodent lineages that have independently colonised the subterranean niche. The energetically demanding lifestyles of these species, coupled with the hypoxic atmospheres characteristic of subterranean environments, may have altered the selective regimes on genes encoding proteins related to cellular respiration. Here, we examined the molecular evolution of 13 protein-coding genes in the mitochondrial genome of seven caviomorph rodents, including these two subterranean genera and their above-ground relatives. Using maximum-likelihood and Bayesian approaches, we estimated rates of synonymous (dS) and nonsynonymous (dN) substitutions. We found a significantly higher ω ratio (dN/dS) in subterranean groups as compared to their non-subterranean counterparts in 11 of 13 genes, although no ω ratio was larger than 1. Additionally, we applied a method based on quantitative physicochemical properties to test for positive selection. Amino acid changes implicated in radical structural or functional shifts in the protein property were found to be ubiquitous across the phylogeny, but concentrated in the subterranean lineages. Convergent changes were also found between the subterranean genera used in this study and other mammals adapted to hypoxia. The results of this study suggest a link between niche shifts and weak directional (or episodic) selection at the molecular level against a background of purifying selection.}, }
@article {pmid21714942, year = {2011}, author = {Martin, WF}, title = {Early evolution without a tree of life.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {36}, pmid = {21714942}, issn = {1745-6150}, mesh = {Adenosine Triphosphate/metabolism ; *Biological Evolution ; *Energy Metabolism ; Environment ; Eukaryotic Cells/chemistry/cytology ; Genes ; Hydrogen/chemistry ; Mitochondria/chemistry/genetics ; Origin of Life ; Oxygen/chemistry ; Phagocytosis ; Phylogeny ; Prokaryotic Cells/chemistry/cytology ; Symbiosis ; }, abstract = {Life is a chemical reaction. Three major transitions in early evolution are considered without recourse to a tree of life. The origin of prokaryotes required a steady supply of energy and electrons, probably in the form of molecular hydrogen stemming from serpentinization. Microbial genome evolution is not a treelike process because of lateral gene transfer and the endosymbiotic origins of organelles. The lack of true intermediates in the prokaryote-to-eukaryote transition has a bioenergetic cause.}, }
@article {pmid21714941, year = {2011}, author = {Lane, N}, title = {Energetics and genetics across the prokaryote-eukaryote divide.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {35}, pmid = {21714941}, issn = {1745-6150}, mesh = {Adenosine Triphosphate/metabolism ; *Biological Evolution ; Cell Cycle ; Cell Membrane/physiology ; Cell Nucleus/genetics ; Cytoplasm/genetics/physiology ; *Energy Metabolism ; Eukaryotic Cells/*cytology/physiology ; Gene Transfer, Horizontal ; Genes, Mitochondrial ; Introns ; Mitochondria/genetics/physiology ; Mutation ; Oxidative Phosphorylation ; Phylogeny ; Prokaryotic Cells/*cytology/physiology ; Selection, Genetic ; *Symbiosis ; }, abstract = {BACKGROUND: All complex life on Earth is eukaryotic. All eukaryotic cells share a common ancestor that arose just once in four billion years of evolution. Prokaryotes show no tendency to evolve greater morphological complexity, despite their metabolic virtuosity. Here I argue that the eukaryotic cell originated in a unique prokaryotic endosymbiosis, a singular event that transformed the selection pressures acting on both host and endosymbiont.<br><br>RESULTS: The reductive evolution and specialisation of endosymbionts to mitochondria resulted in an extreme genomic asymmetry, in which the residual mitochondrial genomes enabled the expansion of bioenergetic membranes over several orders of magnitude, overcoming the energetic constraints on prokaryotic genome size, and permitting the host cell genome to expand (in principle) over 200,000-fold. This energetic transformation was permissive, not prescriptive; I suggest that the actual increase in early eukaryotic genome size was driven by a heavy early bombardment of genes and introns from the endosymbiont to the host cell, producing a high mutation rate. Unlike prokaryotes, with lower mutation rates and heavy selection pressure to lose genes, early eukaryotes without genome-size limitations could mask mutations by cell fusion and genome duplication, as in allopolyploidy, giving rise to a proto-sexual cell cycle. The side effect was that a large number of shared eukaryotic basal traits accumulated in the same population, a sexual eukaryotic common ancestor, radically different to any known prokaryote.<br><br>CONCLUSIONS: The combination of massive bioenergetic expansion, release from genome-size constraints, and high mutation rate favoured a protosexual cell cycle and the accumulation of eukaryotic traits. These factors explain the unique origin of eukaryotes, the absence of true evolutionary intermediates, and the evolution of sex in eukaryotes but not prokaryotes.<br><br>REVIEWERS: This article was reviewed by: Eugene Koonin, William Martin, Ford Doolittle and Mark van der Giezen. For complete reports see the Reviewers' Comments section.}, }
@article {pmid21708274, year = {2011}, author = {Zhan, A and Fu, J}, title = {Past and present: Phylogeography of the Bufo gargarizans species complex inferred from multi-loci allele sequence and frequency data.}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {1}, pages = {136-148}, doi = {10.1016/j.ympev.2011.06.009}, pmid = {21708274}, issn = {1095-9513}, mesh = {Animal Migration ; Animals ; Base Sequence ; Bayes Theorem ; Bufonidae/*classification/*genetics/physiology ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Gene Frequency ; Genetic Variation ; Genotype ; Geography ; Mitochondria/genetics ; Molecular Sequence Data ; Multilocus Sequence Typing ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; }, abstract = {Using multi-locus DNA sequence and frequency data, we examined the phylogeographic patterns of the Asian toad Bufo gargarizans species complex. A total of 166 individuals from 56 sites were genotyped for one mitochondrial locus (516 base pairs, ND2 gene) and five nuclear intron loci (Sox9-2, Rho-3, CCNB2-3, UCH-2, DBI-2; 250-350 base pairs each). We conducted a phylogenetic analysis of the allele sequence data to construct gene trees for each individual locus using Bayesian inference, a multi-locus phylogeny based on all five nuclear loci using POFAD, and a phylogenetic network using the NeighborNet algorithm. Furthermore, we used population-genetic analysis of the allele frequency data to reveal ongoing processes, including an analysis of molecular variance (AMOVA), a Bayesian assignment analysis, and a non-equilibrium Bayesian method for estimating recent migration rate. Our phylogenetic analyses showed that the observed divergence in the B. gargarizans species complex likely dated back to 7-8 million years ago. Repeated range expansions during the inter-glacial periods of Pleistocene likely established the current distribution of genetic diversity, although historical vicariant events were still evidenced. Both the west and the southeast regions may have served as refugia during the glaciation, and the range expansion was in general from west to northeast. Additionally, we detected strong ongoing migration both from west to the other regions and from south to north, which likely represents a meta-population dynamic that has emerged over the past ∼10,000 years. The morphologically identified species Bufo tibetanus is not genetically diagnosable, and therefore should be considered a junior synonym of B. gargarizans.}, }
@article {pmid21704175, year = {2011}, author = {Yeung, CK and Lin, RC and Lei, F and Robson, C and Hung, le M and Liang, W and Zhou, F and Han, L and Li, SH and Yang, X}, title = {Beyond a morphological paradox: complicated phylogenetic relationships of the parrotbills (Paradoxornithidae, Aves).}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {1}, pages = {192-202}, doi = {10.1016/j.ympev.2011.06.004}, pmid = {21704175}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Birds/*classification/*genetics ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genetic Variation ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The parrotbills (Paradoxornithidae, meaning "birds of paradox," Aves) are a group of Old World passerines with perplexing taxonomic histories due to substantial morphological and ecological variation at various levels. In this study, phylogenetic relationships of the parrotbills were reconstructed based on sequences of two mitochondrial segments and three nuclear coding regions. Three major clades with characteristic body size and plumage coloration were found in both mtDNA and nuclear gene trees. However, mtDNA phylogeny suggested that the Paradoxornithidae is paraphyletic and relationships among three major parrotbill clades were poorly resolved. On the contrary, apparent and well-supported monophyletic relationships among the three major clades of Paradoxornithidae were revealed by concatenated nuclear dataset. Since paraphyly based on mtDNA data has commonly been found within avian taxa, the conflicting phylogenetic signal between mtDNA and nuclear loci revealed in this study indicates that results obtained from mtDNA dataset alone need to be evaluated with caution. Taxonomic implications of our phylogenetic findings are discussed. These phylogenies also point out areas for future investigation regarding the rapid diversification, morphological evolution and environmental adaptation of various parrotbill species or species complexes.}, }
@article {pmid21701047, year = {2011}, author = {Hirschey, MD and Shimazu, T and Capra, JA and Pollard, KS and Verdin, E}, title = {SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2.}, journal = {Aging}, volume = {3}, number = {6}, pages = {635-642}, pmid = {21701047}, issn = {1945-4589}, support = {C06 RR018928/RR/NCRR NIH HHS/United States ; R01 GM082901/GM/NIGMS NIH HHS/United States ; GM82901/GM/NIGMS NIH HHS/United States ; RR18928-01/RR/NCRR NIH HHS/United States ; }, mesh = {Acetate-CoA Ligase/classification/genetics/*metabolism ; Acetylation ; Animals ; *Evolution, Molecular ; Humans ; Hydroxymethylglutaryl-CoA Synthase/classification/genetics/*metabolism ; Isoenzymes/classification/genetics/*metabolism ; Phylogeny ; Sirtuin 1/classification/genetics/*metabolism ; Sirtuin 3/classification/genetics/*metabolism ; }, abstract = {SIRT1 and SIRT3 are NAD+-dependent protein deacetylases that are evolutionarily conserved across mammals. These proteins are located in the cytoplasm/nucleus and mitochondria, respectively. Previous reports demonstrated that human SIRT1 deacetylates Acetyl-CoA Synthase 1 (AceCS1) in the cytoplasm, whereas SIRT3 deacetylates the homologous Acetyl-CoA Synthase 2 (AceCS2) in the mitochondria. We recently showed that 3-hydroxy-3-methylglutaryl CoA synthase 2 (HMGCS2) is deacetylated by SIRT3 in mitochondria, and we demonstrate here that SIRT1 deacetylates the homologous 3-hydroxy-3-methylglutaryl CoA synthase 1 (HMGCS1) in the cytoplasm. This novel pattern of substrate homology between cytoplasmic SIRT1 and mitochondrial SIRT3 suggests that considering evolutionary relationships between the sirtuins and their substrates may help to identify and understand the functions and interactions of this gene family. In this perspective, we take a first step by characterizing the evolutionary history of the sirtuins and these substrate families.}, }
@article {pmid21699590, year = {2011}, author = {Kitazaki, K and Kubo, T and Kagami, H and Matsumoto, T and Fujita, A and Matsuhira, H and Matsunaga, M and Mikami, T}, title = {A horizontally transferred tRNA(Cys) gene in the sugar beet mitochondrial genome: evidence that the gene is present in diverse angiosperms and its transcript is aminoacylated.}, journal = {The Plant journal : for cell and molecular biology}, volume = {68}, number = {2}, pages = {262-272}, doi = {10.1111/j.1365-313X.2011.04684.x}, pmid = {21699590}, issn = {1365-313X}, mesh = {Amino Acyl-tRNA Synthetases/*genetics/metabolism ; Aminoacylation/*genetics ; Beta vulgaris/enzymology/*genetics/metabolism ; Biological Evolution ; DNA, Complementary/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Databases, Nucleic Acid ; Gene Dosage ; Gene Transfer, Horizontal ; Genome, Mitochondrial/*genetics ; Magnoliopsida/enzymology/*genetics/metabolism ; Mitochondria/genetics/metabolism ; Nucleic Acid Conformation ; Plant Proteins/genetics/metabolism ; RNA, Plant/genetics ; RNA, Transfer, Cys/genetics/*metabolism ; Sequence Analysis, DNA ; }, abstract = {Of the two tRNA(Cys) (GCA) genes, trnC1-GCA and trnC2-GCA, previously identified in mitochondrial genome of sugar beet, the former is a native gene and probably a pseudo-copy, whereas the latter, of unknown origin, is transcribed into a tRNA [tRNA(Cys2) (GCA)]. In this study, the trnC2-GCA sequence was mined from various public databases. To evaluate whether or not the trnC2-GCA sequence is located in the mitochondrial genome, the relative copy number of its sequence to nuclear gene was assessed in a number of angiosperm species, using a quantitative real-time PCR assay. The trnC2-GCA sequence was found to exist sporadically in the mitochondrial genomes of a wide range of angiosperms. The mitochondrial tRNA(Cys2) (GCA) species from sugar beet (Beta vulgaris), spinach (Spinacea oleracea) and cucumber (Cucumis sativus) were found to be aminoacylated, indicating that they may participate in translation. We also identified a sugar beet nuclear gene that encodes cysteinyl-tRNA synthetase, which is dual-targeted to mitochondria and plastids, and may aminoacylate tRNA(Cys2) (GCA). What is of particular interest is that trnC1-GCA and trnC2-GCA co-exist in the mitochondrial genomes of eight diverse angiosperms, including spinach, and that the spinach tRNA(Cys1) (GCA) is also aminoacylated. Taken together, our observations lead us to surmise that trnC2-GCA may have been horizontally transferred to a common ancestor of eudicots, followed by co-existence and dual expression of trnC1-GCA and trnC2-GCA in mitochondria with occasional loss or inactivation of either trnC-GCA gene during evolution.}, }
@article {pmid21695207, year = {2011}, author = {Johnson, RA and McFadden, GI and Goodman, CD}, title = {Characterization of two malaria parasite organelle translation elongation factor G proteins: the likely targets of the anti-malarial fusidic acid.}, journal = {PloS one}, volume = {6}, number = {6}, pages = {e20633}, pmid = {21695207}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Cell Nucleus/drug effects/metabolism ; Computational Biology ; Fusidic Acid/*pharmacology ; Life Cycle Stages/drug effects ; Malaria/*parasitology ; Mitochondrial Proteins/metabolism ; Molecular Sequence Data ; Organelles/drug effects/*metabolism ; Parasites/drug effects/growth &amp; development/*metabolism ; Peptide Elongation Factor G/chemistry/*metabolism ; Phylogeny ; Plasmodium falciparum/drug effects/growth &amp; development ; Protein Biosynthesis/*drug effects ; Protozoan Proteins/chemistry/*metabolism ; Sequence Alignment ; }, abstract = {Malaria parasites harbour two organelles with bacteria-like metabolic processes that are the targets of many anti-bacterial drugs. One such drug is fusidic acid, which inhibits the translation component elongation factor G. The response of P. falciparum to fusidic acid was characterised using extended SYBR-Green based drug trials. This revealed that fusidic acid kills in vitro cultured P. falciparum parasites by immediately blocking parasite development. Two bacterial-type protein translation elongation factor G genes are identified as likely targets of fusidic acid. Sequence analysis suggests that these proteins function in the mitochondria and apicoplast and both should be sensitive to fusidic acid. Microscopic examination of protein-reporter fusions confirm the prediction that one elongation factor G is a component of parasite mitochondria whereas the second is a component of the relict plastid or apicoplast. The presence of two putative targets for a single inhibitory compound emphasizes the potential of elongation factor G as a drug target in malaria.}, }
@article {pmid21693193, year = {2011}, author = {Francisco, SM and Congiu, L and von der Heyden, S and Almada, VC}, title = {Multilocus phylogenetic analysis of the genus Atherina (Pisces: Atherinidae).}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {1}, pages = {71-78}, doi = {10.1016/j.ympev.2011.06.002}, pmid = {21693193}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Fresh Water ; Genetic Speciation ; Geography ; Mitochondria/genetics ; Multilocus Sequence Typing ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Rhodopsin/*genetics ; Seawater ; Sequence Analysis, DNA ; Smegmamorpha/*classification/*genetics/physiology ; }, abstract = {Sand-smelts are small fishes inhabiting inshore, brackish and freshwater environments and with a distribution in the eastern Atlantic and Mediterranean Sea, extending south into the Indian Ocean. Here, we present a broad phylogenetic analysis of the genus Atherina using three mitochondrial (control region, 12S and 16S) and two nuclear markers (rhodopsin and 2nd intron of S7). Phylogenetic analyses fully support the monophyly of the genus. Two anti-tropical clades were identified, separating the South African Atherina breviceps from the north-eastern Atlantic and Mediterranean Atherina' species. In European waters, two groups were found. The first clade formed by a well supported species-pair: Atherina presbyter (eastern Atlantic) and Atherina hepsetus (Mediterranean), both living in marine waters; a second clade included Atherina boyeri (brackish and freshwater environments) and two independent lineages of marine punctated and non-punctated fishes, recently proposed as separate species. Sequence divergence values strongly suggest multiple species within the A. boyeri complex.}, }
@article {pmid21693192, year = {2011}, author = {Clemente-Carvalho, RB and Klaczko, J and Ivan Perez, S and Alves, AC and Haddad, CF and dos Reis, SF}, title = {Molecular phylogenetic relationships and phenotypic diversity in miniaturized toadlets, genus Brachycephalus (Amphibia: Anura: Brachycephalidae).}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {1}, pages = {79-89}, doi = {10.1016/j.ympev.2011.05.017}, pmid = {21693192}, issn = {1095-9513}, mesh = {Animals ; *Anura/anatomy &amp; histology/classification/genetics ; Base Sequence ; Bayes Theorem ; *Biological Evolution ; Brazil ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Evolution, Molecular ; Mitochondria/genetics ; Molecular Sequence Data ; Multilocus Sequence Typing ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Skull/anatomy &amp; histology ; Species Specificity ; }, abstract = {Toadlets of the genus Brachycephalus are endemic to the Atlantic rainforests of southeastern and southern Brazil. The 14 species currently described have snout-vent lengths less than 18 mm and are thought to have evolved through miniaturization: an evolutionary process leading to an extremely small adult body size. Here, we present the first comprehensive phylogenetic analysis for Brachycephalus, using a multilocus approach based on two nuclear (Rag-1 and Tyr) and three mitochondrial (Cyt b, 12S, and 16S rRNA) gene regions. Phylogenetic relationships were inferred using a partitioned Bayesian analysis of concatenated sequences and the hierarchical Bayesian method (BEST) that estimates species trees based on the multispecies coalescent model. Individual gene trees showed conflict and also varied in resolution. With the exception of the mitochondrial gene tree, no gene tree was completely resolved. The concatenated gene tree was completely resolved and is identical in topology and degree of statistical support to the individual mtDNA gene tree. On the other hand, the BEST species tree showed reduced significant node support relative to the concatenate tree and recovered a basal trichotomy, although some bipartitions were significantly supported at the tips of the species tree. Comparison of the log likelihoods for the concatenated and BEST trees suggests that the method implemented in BEST explains the multilocus data for Brachycephalus better than the Bayesian analysis of concatenated data. Landmark-based geometric morphometrics revealed marked variation in cranial shape between the species of Brachycephalus. In addition, a statistically significant association was demonstrated between variation in cranial shape and genetic distances estimated from the mtDNA and nuclear loci. Notably, B. ephippium and B. garbeana that are predicted to be sister-species in the individual and concatenated gene trees and the BEST species tree share an evolutionary novelty, the hyperossified dorsal plate.}, }
@article {pmid21690562, year = {2011}, author = {Sassera, D and Lo, N and Epis, S and D'Auria, G and Montagna, M and Comandatore, F and Horner, D and Peretó, J and Luciano, AM and Franciosi, F and Ferri, E and Crotti, E and Bazzocchi, C and Daffonchio, D and Sacchi, L and Moya, A and Latorre, A and Bandi, C}, title = {Phylogenomic evidence for the presence of a flagellum and cbb(3) oxidase in the free-living mitochondrial ancestor.}, journal = {Molecular biology and evolution}, volume = {28}, number = {12}, pages = {3285-3296}, doi = {10.1093/molbev/msr159}, pmid = {21690562}, issn = {1537-1719}, mesh = {Base Sequence ; *Biological Evolution ; Electron Transport Complex IV/*genetics ; Eukaryotic Cells ; Evolution, Molecular ; Flagella/*genetics ; Genome, Bacterial ; Mitochondria/*genetics/*physiology/*ultrastructure ; Oxidative Phosphorylation ; Phylogeny ; Rickettsieae/*genetics ; Sequence Analysis, DNA ; *Symbiosis/genetics ; }, abstract = {The initiation of the intracellular symbiosis that would give rise to mitochondria and eukaryotes was a major event in the history of life on earth. Hypotheses to explain eukaryogenesis fall into two broad and competing categories: those proposing that the host was a phagocytotic proto-eukaryote that preyed upon the free-living mitochondrial ancestor (hereafter FMA), and those proposing that the host was an archaebacterium that engaged in syntrophy with the FMA. Of key importance to these hypotheses are whether the FMA was motile or nonmotile, and the atmospheric conditions under which the FMA thrived. Reconstructions of the FMA based on genome content of Rickettsiales representatives-generally considered to be the closest living relatives of mitochondria-indicate that it was nonmotile and aerobic. We have sequenced the genome of Candidatus Midichloria mitochondrii, a novel and phylogenetically divergent member of the Rickettsiales. We found that it possesses unique gene sets found in no other Rickettsiales, including 26 genes associated with flagellar assembly, and a cbb(3)-type cytochrome oxidase. Phylogenomic analyses show that these genes were inherited in a vertical fashion from an ancestral α-proteobacterium, and indicate that the FMA possessed a flagellum, and could undergo oxidative phosphorylation under both aerobic and microoxic conditions. These results indicate that the FMA played a more active and potentially parasitic role in eukaryogenesis than currently appreciated and provide an explanation for how the symbiosis could have evolved under low levels of oxygen.}, }
@article {pmid21687738, year = {2011}, author = {García-Giménez, JL and Gimeno, A and Gonzalez-Cabo, P and Dasí, F and Bolinches-Amorós, A and Mollá, B and Palau, F and Pallardó, FV}, title = {Differential expression of PGC-1α and metabolic sensors suggest age-dependent induction of mitochondrial biogenesis in Friedreich ataxia fibroblasts.}, journal = {PloS one}, volume = {6}, number = {6}, pages = {e20666}, pmid = {21687738}, issn = {1932-6203}, mesh = {AMP-Activated Protein Kinases/metabolism ; Adenosine Triphosphate/metabolism ; Adolescent ; Adult ; Aging/*genetics/*metabolism ; Alleles ; Antioxidants/pharmacology ; Catalase/metabolism ; Child ; DNA-Binding Proteins/metabolism ; Disease Progression ; Energy Metabolism/drug effects ; Female ; Fibroblasts/drug effects/enzymology/*pathology ; Friedreich Ataxia/genetics/metabolism/*pathology ; *Gene Expression Regulation/drug effects ; Glutathione Peroxidase/metabolism ; Heat-Shock Proteins/*genetics ; Humans ; Male ; Middle Aged ; Mitochondria/drug effects/enzymology/*metabolism/pathology ; Mitochondrial Proteins/metabolism ; Oxidative Stress/drug effects ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha ; Reactive Oxygen Species/metabolism ; Signal Transduction/drug effects ; Superoxide Dismutase/metabolism ; Transcription Factors/*genetics/metabolism ; Trinucleotide Repeats/genetics ; Ubiquinone/analogs &amp; derivatives/pharmacology ; p38 Mitogen-Activated Protein Kinases/metabolism ; }, abstract = {BACKGROUND: Friedreich's ataxia (FRDA) is a mitochondrial rare disease, which molecular origin is associated with defect in the expression of frataxin. The pathological consequences are degeneration of nervous system structures and cardiomyopathy with necrosis and fibrosis, among others.<br><br>PRINCIPAL FINDINGS: Using FRDA fibroblasts we have characterized the oxidative stress status and mitochondrial biogenesis. We observed deficiency of MnSOD, increased ROS levels and low levels of ATP. Expression of PGC-1&#x3b1; and mtTFA was increased and the active form of the upstream signals p38 MAPK and AMPK in fibroblasts from two patients. Interestingly, the expression of energetic factors correlated with the natural history of disease of the patients, the age when skin biopsy was performed and the size of the GAA expanded alleles. Furthermore, idebenone inhibit mitochondriogenic responses in FRDA cells.<br><br>CONCLUSIONS: The induction of mitochondrial biogenesis in FRDA may be a consequence of the mitochondrial impairment associated with disease evolution. The increase of ROS and the involvement of the oxidative phosphorylation may be an early event in the cell pathophysiology of frataxin deficiency, whereas increase of mitochondriogenic response might be a later phenomenon associated to the individual age and natural history of the disease, being more evident as the patient age increases and disease evolves. This is a possible explanation of heart disease in FRDA.}, }
@article {pmid21685886, year = {2011}, author = {Baughman, JM and Perocchi, F and Girgis, HS and Plovanich, M and Belcher-Timme, CA and Sancak, Y and Bao, XR and Strittmatter, L and Goldberger, O and Bogorad, RL and Koteliansky, V and Mootha, VK}, title = {Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter.}, journal = {Nature}, volume = {476}, number = {7360}, pages = {341-345}, pmid = {21685886}, issn = {1476-4687}, support = {GM0077465/GM/NIGMS NIH HHS/United States ; R24 DK080261/DK/NIDDK NIH HHS/United States ; R01 GM077465-01A1/GM/NIGMS NIH HHS/United States ; DK080261/DK/NIDDK NIH HHS/United States ; R01 GM077465/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Calcium/metabolism ; Calcium Channels/*chemistry/genetics/*metabolism ; *Genomics ; HEK293 Cells ; HeLa Cells ; Humans ; Ion Transport ; Mice ; Mitochondria, Liver/metabolism ; Mitochondrial Membranes/chemistry/metabolism ; Molecular Sequence Data ; Mutant Proteins/genetics/metabolism ; Phylogeny ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; }, abstract = {Mitochondria from diverse organisms are capable of transporting large amounts of Ca(2+) via a ruthenium-red-sensitive, membrane-potential-dependent mechanism called the uniporter. Although the uniporter's biophysical properties have been studied extensively, its molecular composition remains elusive. We recently used comparative proteomics to identify MICU1 (also known as CBARA1), an EF-hand-containing protein that serves as a putative regulator of the uniporter. Here, we use whole-genome phylogenetic profiling, genome-wide RNA co-expression analysis and organelle-wide protein coexpression analysis to predict proteins functionally related to MICU1. All three methods converge on a novel predicted transmembrane protein, CCDC109A, that we now call 'mitochondrial calcium uniporter' (MCU). MCU forms oligomers in the mitochondrial inner membrane, physically interacts with MICU1, and resides within a large molecular weight complex. Silencing MCU in cultured cells or in vivo in mouse liver severely abrogates mitochondrial Ca(2+) uptake, whereas mitochondrial respiration and membrane potential remain fully intact. MCU has two predicted transmembrane helices, which are separated by a highly conserved linker facing the intermembrane space. Acidic residues in this linker are required for its full activity. However, an S259A point mutation retains function but confers resistance to Ru360, the most potent inhibitor of the uniporter. Our genomic, physiological, biochemical and pharmacological data firmly establish MCU as an essential component of the mitochondrial Ca(2+) uniporter.}, }
@article {pmid21684869, year = {2011}, author = {Li, L and Liang, HW and Li, Z and Luo, XZ and Hu, GF and Zhang, ZW and Zhu, YY and Zou, GW}, title = {[Sequence and phylogeny analysis of the complete mitochondrial genome of Pelteobagrus vachelli].}, journal = {Yi chuan = Hereditas}, volume = {33}, number = {6}, pages = {627-635}, doi = {10.3724/sp.j.1005.2011.00627}, pmid = {21684869}, issn = {0253-9772}, mesh = {Animals ; Catfishes/*classification/*genetics ; Genome, Mitochondrial/*genetics ; Genomics ; Open Reading Frames/genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {Morphological classification of Bagridae fishes is relatively difficult due to various kinds and similar shape, and the phyletic evolution is not very clear in some species. To provide basic data to the classification of Bagridae and Siluriformes fishes, the complete mitochondrial genome of Pelteobagrus vachelli was obtained by PCR based on 16 primers, which were designed on the basis of related species mtDNA sequences. The complete mitochondrial genome is 16 527 bp in length, including 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes, and a non-coding control region. The organization and location of genes in the mitochondrial genome of Pelteobagrus vachelli were consistent with Siluriformes fishes published in GenBank. It has high homology with other families, such as Pseudobagrus Bleeker (91%) within Siluriformes. The phylogenetic analysis of Bagridae fishes was made from the level of mitochondria genome based on 9 species of 6 genera, which belong to 4 families of the Siluriformes, combining with 3 outgroups' complete mitochondrial genomes sequences. The result indicated that Pelteobagrus vachelli, Pelteobagrus fulvidraco, Pelteobagrus nitidus and Pseudobagrus tokiensis of the Bagridae formed a monophyletic group; the Pseudobagrus Bleeker and Pelteobagrus Bleeker formed a sister group. Moreover, Pelteobagrus vachelli was more relative to Pelteobagrus nitidus than Pelteobagrus fulvidraco in Pelteobagrus Bleeker.}, }
@article {pmid21684341, year = {2011}, author = {Novo, M and Almodóvar, A and Fernández, R and Giribet, G and Díaz Cosín, DJ}, title = {Understanding the biogeography of a group of earthworms in the Mediterranean basin--the phylogenetic puzzle of Hormogastridae (Clitellata: Oligochaeta).}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {1}, pages = {125-135}, doi = {10.1016/j.ympev.2011.05.018}, pmid = {21684341}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Biomarkers ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Genetic Speciation ; Genetic Variation ; Geography ; Histones/genetics ; Mediterranean Sea ; Mitochondria/genetics ; Molecular Sequence Data ; Oligochaeta/*classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; RNA, Transfer, Ala/genetics ; RNA, Transfer, Leu/genetics ; RNA, Transfer, Ser/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Traditional earthworm taxonomy is hindered due to their anatomical simplicity and the plasticity of the characteristics often used for diagnosing species. Making phylogenetic inferences based on these characters is more than difficult. In this study we use molecular tools to unravel the phylogeny of the clitellate family Hormogastridae. The family includes species of large to mid-sized earthworms distributed almost exclusively in the western Mediterranean region where they play an important ecological role. We analyzed individuals from 46 locations spanning the Iberian Peninsula to Corsica and Sardinia, representing the four described genera in the family and 20 species. Molecular markers include mitochondrial regions of the cytochrome c oxidase subunit I gene (COI), 16S rRNA and tRNAs for Leu, Ala, and Ser, two nuclear ribosomal genes (nearly complete 18S rRNA and a fragment of 28S rRNA) and two nuclear protein-encoding genes (histones H3 and H4). Analyses of the data using different approaches corroborates monophyly of Hormogastridae, but the genus Hormogaster is paraphyletic and Hormogaster pretiosa appears polyphyletic, stressing the need for taxonomic revisionary work in the family. The genus Vignysa could represent an early offshoot in the family, although the relationships with other genera are uncertain. The genus Hemigastrodrilus is related to the Hormogaster elisae complex and both are found in the Atlantic drainage of the Iberian Peninsula and France. From a biogeographic perspective Corsica and Sardinia include members of two separate hormogastrid lineages. The species located in Corsica and Northern Sardinia are related to Vignysa, whereas Hormogaster pretiosa pretiosa, from Southern Sardinia, is closely related to the Hormogaster species from the NE Iberian Peninsula. A molecular dating of the tree using the separation of the Sardinian microplate as a calibration point (at 33 MY) and assuming a model of vicariance indicates that the diversification of Hormogastridae may be ancient, ranging from 97 to 67 Ma.}, }
@article {pmid21681429, year = {2012}, author = {Prosdocimi, F and de Carvalho, DC and de Almeida, RN and Beheregaray, LB}, title = {The complete mitochondrial genome of two recently derived species of the fish genus Nannoperca (Perciformes, Percichthyidae).}, journal = {Molecular biology reports}, volume = {39}, number = {3}, pages = {2767-2772}, pmid = {21681429}, issn = {1573-4978}, mesh = {Animals ; Base Sequence ; *Evolution, Molecular ; Genome Components ; Genome, Mitochondrial/*genetics ; Molecular Sequence Annotation ; Molecular Sequence Data ; Perciformes/*genetics ; Polymorphism, Single Nucleotide/*genetics ; Sequence Analysis, DNA ; South Australia ; Species Specificity ; }, abstract = {Here we report the complete sequence of mitochondrial genomes for two sister taxa of freshwater teleosts, the recently derived Yarra pigmy perch Nannoperca obscura and the southern pigmy perch Nannoperca australis. These represent the first complete mitochondrial genomes for Percichthyidae (Perciformes), a family mostly distributed in Australia. The de novo genome assembly of 316,430 pyrosequencing reads from 454 libraries has produced the entire mitochondria for N. obscura and a nearly complete version for N. australis. The mtDNA genome from the latter was completed through the design of one primer set and standard Sanger sequencing for genome finishing, followed by the hybrid assembly of reads with MIRA software using N. obscura sequence as reference genome. The complete mitogenomes of N. obscura and N. australis are 16,496 and 16,494 bp in size, respectively. Both genomes contain 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a control region. Several characteristics of mitochondria typically found in teleost fishes were detected, such as: (i) most genes found in the heavy strand, with the exception of ND6 and eight tRNA genes; (ii) avoidance of G as the third base of codons; (iii) presence of gene overlapping; (iv) percentage of bases usage. We found only eight indels and 197 nucleotide substitutions between these Nannoperca mitogenomes, consistent with a previous hypothesis of recent speciation. The data reported here provide a resource for comparative analysis of recent evolution of mitochondrial genomes.}, }
@article {pmid21674231, year = {2011}, author = {Bengtsson, J and Eriksson, KM and Hartmann, M and Wang, Z and Shenoy, BD and Grelet, GA and Abarenkov, K and Petri, A and Rosenblad, MA and Nilsson, RH}, title = {Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets.}, journal = {Antonie van Leeuwenhoek}, volume = {100}, number = {3}, pages = {471-475}, doi = {10.1007/s10482-011-9598-6}, pmid = {21674231}, issn = {1572-9699}, mesh = {Archaea/*genetics/isolation &amp; purification ; Bacteria/*genetics/isolation &amp; purification ; Chloroplasts/*genetics ; Databases, Nucleic Acid ; Eukaryota/*genetics/isolation &amp; purification ; Metagenome ; Metagenomics/instrumentation/*methods ; Mitochondria/*genetics ; Phylogeny ; Ribosome Subunits, Small/*genetics ; Sequence Alignment ; *Software ; }, abstract = {The ribosomal small subunit (SSU) rRNA gene has emerged as an important genetic marker for taxonomic identification in environmental sequencing datasets. In addition to being present in the nucleus of eukaryotes and the core genome of prokaryotes, the gene is also found in the mitochondria of eukaryotes and in the chloroplasts of photosynthetic eukaryotes. These three sets of genes are conceptually paralogous and should in most situations not be aligned and analyzed jointly. To identify the origin of SSU sequences in complex sequence datasets has hitherto been a time-consuming and largely manual undertaking. However, the present study introduces Metaxa (http://microbiology.se/software/metaxa/), an automated software tool to extract full-length and partial SSU sequences from larger sequence datasets and assign them to an archaeal, bacterial, nuclear eukaryote, mitochondrial, or chloroplast origin. Using data from reference databases and from full-length organelle and organism genomes, we show that Metaxa detects and scores SSU sequences for origin with very low proportions of false positives and negatives. We believe that this tool will be useful in microbial and evolutionary ecology as well as in metagenomics.}, }
@article {pmid21673740, year = {2011}, author = {McDevitt, AD and Vega, R and Rambau, RV and Yannic, G and Herman, JS and Hayden, TJ and Searle, JB}, title = {Colonization of Ireland: revisiting 'the pygmy shrew syndrome' using mitochondrial, Y chromosomal and microsatellite markers.}, journal = {Heredity}, volume = {107}, number = {6}, pages = {548-557}, pmid = {21673740}, issn = {1365-2540}, mesh = {Animals ; Cytochromes b/genetics ; Genetic Variation ; Human Activities ; Humans ; Ireland ; *Microsatellite Repeats ; Mitochondria/*genetics ; Phylogeny ; Shrews/classification/*genetics/*growth &amp; development ; Y Chromosome/*genetics ; }, abstract = {There is great uncertainty about how Ireland attained its current fauna and flora. Long-distance human-mediated colonization from southwestern Europe has been seen as a possible way that Ireland obtained many of its species; however, Britain has (surprisingly) been neglected as a source area for Ireland. The pygmy shrew has long been considered an illustrative model species, such that the uncertainty of the Irish colonization process has been dubbed 'the pygmy shrew syndrome'. Here, we used new genetic data consisting of 218 cytochrome (cyt) b sequences, 153 control region sequences, 17 Y-intron sequences and 335 microsatellite multilocus genotypes to distinguish between four possible hypotheses for the colonization of the British Isles, formulated in the context of previously published data. Cyt b sequences from western Europe were basal to those found in Ireland, but also to those found in the periphery of Britain and several offshore islands. Although the central cyt b haplotype in Ireland was found in northern Spain, we argue that it most likely occurred in Britain also, from where the pygmy shrew colonized Ireland as a human introduction during the Holocene. Y-intron and microsatellite data are consistent with this hypothesis, and the biological traits and distributional data of pygmy shrews argue against long-distance colonization from Spain. The compact starburst of the Irish cyt b expansion and the low genetic diversity across all markers strongly suggests a recent colonization. This detailed molecular study of the pygmy shrew provides a new perspective on an old colonization question.}, }
@article {pmid21670310, year = {2011}, author = {Bochman, ML and Judge, CP and Zakian, VA}, title = {The Pif1 family in prokaryotes: what are our helicases doing in your bacteria?.}, journal = {Molecular biology of the cell}, volume = {22}, number = {12}, pages = {1955-1959}, pmid = {21670310}, issn = {1939-4586}, support = {R01 GM026938/GM/NIGMS NIH HHS/United States ; R37 GM026938/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*enzymology/genetics ; Base Sequence ; DNA Helicases/genetics/*metabolism ; DNA Repair ; DNA Replication ; Mitochondria/genetics/metabolism ; Phylogeny ; Recombination, Genetic ; }, abstract = {Pif1 family helicases, which are found in nearly all eukaryotes, have important roles in both nuclear and mitochondrial genome maintenance. Recently, the increasing availability of genome sequences has revealed that Pif1 helicases are also widely found in diverse prokaryotes, but it is currently unknown what physiological function(s) prokaryotic Pif1 helicases might perform. This Perspective aims to briefly introduce the reader to the well-studied eukaryotic Pif1 family helicases and speculate on what roles such enzymes may play in bacteria. On the basis of our hypotheses, we predict that Pif1 family helicases are important for resolving common issues that arise during DNA replication, recombination, and repair rather than functioning in a eukaryotic-specific manner.}, }
@article {pmid21669295, year = {2011}, author = {Ugelvig, LV and Vila, R and Pierce, NE and Nash, DR}, title = {A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade.}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {1}, pages = {237-243}, doi = {10.1016/j.ympev.2011.05.016}, pmid = {21669295}, issn = {1095-9513}, mesh = {Animals ; Biological Evolution ; Butterflies/*classification/*genetics/physiology ; Cell Nucleus/genetics ; DNA, Mitochondrial/classification/genetics ; Evolution, Molecular ; Life Cycle Stages ; Mitochondria/genetics ; Pedigree ; Phylogeny ; }, abstract = {Despite much research on the socially parasitic large blue butterflies (genus Maculinea) in the past 40 years, their relationship to their closest relatives, Phengaris, is controversial and the relationships among the remaining genera in the Glaucopsyche section are largely unresolved. The evolutionary history of this butterfly section is particularly important to understand the evolution of life history diversity connected to food-plant and host-ant associations in the larval stage. In the present study, we use a combination of four nuclear and two mitochondrial genes to reconstruct the phylogeny of the Glaucopsyche section, and in particular, to study the relationships among and within the Phengaris-Maculinea species. We find a clear pattern between the clades recovered in the Glaucopsyche section phylogeny and their food-plant associations, with only the Phengaris-Maculinea clade utilising more than one plant family. Maculinea is, for the first time, recovered with strong support as a monophyletic group nested within Phengaris, with the closest relative being the rare genus Caerulea. The genus Glaucopsyche is polyphyletic, including the genera Sinia and Iolana. Interestingly, we find evidence for additional potential cryptic species within the highly endangered Maculinea, which has long been suspected from morphological, ecological and molecular studies.}, }
@article {pmid21669293, year = {2011}, author = {Hollingsworth, PR and Darrin Hulsey, C}, title = {Reconciling gene trees of eastern North American minnows.}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {1}, pages = {149-156}, doi = {10.1016/j.ympev.2011.05.020}, pmid = {21669293}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; Cell Nucleus/*genetics ; Cyprinidae/*classification/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genetic Speciation ; Genetic Variation ; Mitochondria/*genetics ; Models, Genetic ; Molecular Sequence Data ; North America ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Most eastern North American cyprinid fishes belong to a clade known as the "open posterior myodome" (OPM) minnows, but phylogenetic relationships within this clade have been difficult to ascertain. Previous attempts to resolve relationships among the generally benthic "chubs" and the more pelagic "shiners", that constitute the majority of OPM minnows, have led to highly discordant phylogenetic hypotheses. To further examine relationships among the OPM minnows, we utilized both a concatenated Bayesian approach and a coalescent-based species tree method to analyze data from six protein coding nuclear loci (Enc1, Ptr, Ryr3, Sh3px3, Tbr1, and Zic1), as well as the mitochondrial locus (Cytb). We focused our analyses on the chub-like genus Phenacobius, a group that has drifted topologically between other benthic chubs and the more pelagic shiners, and also included exemplar taxa from 11 other OPM lineages. Individual gene trees were highly discordant regarding relationships within Phenacobius and across the OPM clade. The concatenated Bayesian analysis and coalescent-based species tree reconstruction recovered slightly different phylogenetic topologies. Additionally, the posterior support values for clades using the coalescent-based approach were consistently lower than the concatenated analysis. However, Phenacobius was resolved as monophyletic and as the sister lineage to Erimystax regardless of the combined data approach taken. Furthermore, Phenacobius+Erimystax was recovered as more closely related to the shiners we examined than to other chubs. Relationships within Phenacobius varied depending on the combined phylogenetic method utilized. Our results highlight the importance of multi-locus, coalescent-based approaches for resolving the phylogeny of diverse clades like the eastern North American OPM minnows.}, }
@article {pmid21669250, year = {2011}, author = {Seligmann, H}, title = {Two genetic codes, one genome: frameshifted primate mitochondrial genes code for additional proteins in presence of antisense antitermination tRNAs.}, journal = {Bio Systems}, volume = {105}, number = {3}, pages = {271-285}, doi = {10.1016/j.biosystems.2011.05.010}, pmid = {21669250}, issn = {1872-8324}, mesh = {Animals ; Base Sequence ; Biological Evolution ; *Frameshift Mutation ; *Genes, Mitochondrial ; Genetic Code ; Humans ; Mitochondrial Proteins/classification/genetics ; Phylogeny ; Primates/classification/*genetics ; RNA, Transfer/*genetics ; *Transcription, Genetic ; }, abstract = {Genomic amino acid usages coevolve with cloverleaf formation capacities of corresponding primate mitochondrial tRNAs, also for antisense tRNAs, suggesting translational function for sense and antisense tRNAs. Some antisense tRNAs are antitermination tRNAs (anticodons match stops (UAR: UAA, UAG; AGR: AGA, AGG)). Genomes possessing antitermination tRNAs avoid corresponding stops in frames 0 and +1, preventing translational antitermination. In frame +2, AGR stop frequencies and corresponding antisense antitermination tRNAs coevolve positively. This suggests expression of frameshifted overlapping genes, potentially shortening genomes, increasing metabolic efficiency. Blast analyses of hypothetical proteins translated from one and seven +1, respectively, +2 frameshifted human mitochondrial protein coding genes align with eleven GenBank sequences (31% of the mitochondrial coding regions). These putative overlap genes contain few UARs, AGRs align with arginine. Overlap gene numbers increase in presence of, and with time since evolution of antitermination tRNA AGR in 57 primate mitochondrial genomes. Numbers of putative proteins translated from antisense protein coding sequences and detected by blast also coevolve positively with antitermination tRNAs; expression of two of these 'antisense' mRNAs increases under low resource availability. Although more direct evidence is still lacking for the existence of proteins translated from overlapping mitochondrial genes and for antisense tRNAs activity, coevolutions between predicted overlap genes and the antitermination tRNAs required to translate them suggest expression of overlapping genes by an overlapping genetic code. Functions of overlapping genes remain unknown, perhaps originating from dual lifestyles of ancestral free living-parasitic mitochondria. Their amino acid composition suggests expression under anaerobic conditions.}, }
@article {pmid21668973, year = {2011}, author = {Wang, J and Wang, Y and Wang, Z and Liu, L and Zhu, XG and Ma, X}, title = {Synchronization of cytoplasmic and transferred mitochondrial ribosomal protein gene expression in land plants is linked to Telo-box motif enrichment.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {161}, pmid = {21668973}, issn = {1471-2148}, support = {HG001696/HG/NHGRI NIH HHS/United States ; }, mesh = {Base Sequence ; Biological Evolution ; Chloroplasts/*genetics ; Chromosomes, Plant ; Cytosol/metabolism ; *Gene Expression Regulation, Plant ; Genome, Plant ; Mitochondrial Proteins/*genetics ; Plant Proteins/*genetics ; Plants/*genetics ; Promoter Regions, Genetic ; Ribosomal Proteins/*genetics ; Transcription Factors/genetics ; }, abstract = {BACKGROUND: Chloroplasts and mitochondria evolved from the endosymbionts of once free-living eubacteria, and they transferred most of their genes to the host nuclear genome during evolution. The mechanisms used by plants to coordinate the expression of such transferred genes, as well as other genes in the host nuclear genome, are still poorly understood.<br><br>RESULTS: In this paper, we use nuclear-encoded chloroplast (cpRPGs), as well as mitochondrial (mtRPGs) and cytoplasmic (euRPGs) ribosomal protein genes to study the coordination of gene expression between organelles and the host. Results show that the mtRPGs, but not the cpRPGs, exhibit strongly synchronized expression with euRPGs in all investigated land plants and that this phenomenon is linked to the presence of a telo-box DNA motif in the promoter regions of mtRPGs and euRPGs. This motif is also enriched in the promoter regions of genes involved in DNA replication. Sequence analysis further indicates that mtRPGs, in contrast to cpRPGs, acquired telo-box from the host nuclear genome.<br><br>CONCLUSIONS: Based on our results, we propose a model of plant nuclear genome evolution where coordination of activities in mitochondria and chloroplast and other cellular functions, including cell cycle, might have served as a strong selection pressure for the differential acquisition of telo-box between mtRPGs and cpRPGs. This research also highlights the significance of physiological needs in shaping transcriptional regulatory evolution.}, }
@article {pmid21658458, year = {2011}, author = {Matsui, M and Hamidy, A and Belabut, DM and Ahmad, N and Panha, S and Sudin, A and Khonsue, W and Oh, HS and Yong, HS and Jiang, JP and Nishikawa, K}, title = {Systematic relationships of Oriental tiny frogs of the family Microhylidae (Amphibia, Anura) as revealed by mtDNA genealogy.}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {1}, pages = {167-176}, doi = {10.1016/j.ympev.2011.05.015}, pmid = {21658458}, issn = {1095-9513}, mesh = {Animals ; Anura/*classification/*genetics ; Base Sequence ; Bayes Theorem ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Mitochondria/genetics ; Pedigree ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {We estimated the genealogical relationships and assessed systematic relationships among 45 out of 89 named species and four unnamed taxa from 11 of 14 genera of the Oriental microhylids from 1767 bp sequences of the mitochondrial DNA genes 12S rRNA and 16S rRNA using maximum parsimony, maximum likelihood, and Bayesian inference methods. Monophyly was rejected for the subfamily Microhylinae, and our data reveal four well-supported clades whose relationships to each other are unresolved: (A) Microhyla, Calluella, and Glyphoglossus, (B) Chaperina, (C) Kaloula, Phrynella, and Metaphrynella, and (D) Micryletta. They were genetically as divergent from each other as from another Oriental subfamily Kalophryninae, and could be recognized as distinct subfamilies. Within Clade A, our data reveal three well-supported subclades whose relationships to each other are unresolved: (AI) Microhyla-I, (AII) Calluella and Glyphoglossus, and (AIII) Microhyla-II. Of the two enigmatic Malaysian genera, whose subfamilial placement has been undetermined, Phrynella was found to be the sister species of Metaphrynella in Clade C, whereas Gastrophrynoides was grouped in the Papua-Australian subfamily Asterophryinae. Currently recognized subgenera and species groups within Microhyla based on morphology were not supported phylogenetically, and require thorough reassessments.}, }
@article {pmid21647378, year = {2011}, author = {Gottlieb, A and Frenkel-Morgenstern, M and Safro, M and Horn, D}, title = {Common peptides study of aminoacyl-tRNA synthetases.}, journal = {PloS one}, volume = {6}, number = {5}, pages = {e20361}, pmid = {21647378}, issn = {1932-6203}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/*chemistry/genetics/*metabolism ; Carbon-Nitrogen Ligases/chemistry/metabolism ; Computational Biology/*methods ; Evolution, Molecular ; Mitochondria/enzymology ; Molecular Sequence Data ; Peptide Fragments/*chemistry/metabolism ; Sequence Alignment ; }, abstract = {BACKGROUND: Aminoacyl tRNA synthetases (aaRSs) constitute an essential enzyme super-family, providing fidelity of the translation process of mRNA to proteins in living cells. They are common to all kingdoms and are of utmost importance to all organisms. It is thus of great interest to understand the evolutionary relationships among them and underline signature motifs defining their common domains.<br><br>RESULTS: We utilized the Common Peptides (CPs) framework, based on extracted deterministic motifs from all aaRSs, to study family-specific properties. We identified novel aaRS-class related signatures that may supplement the current classification methods and provide a basis for identifying functional regions specific to each aaRS class. We exploited the space spanned by the CPs in order to identify similarities between aaRS families that are not observed using sequence alignment methods, identifying different inter-aaRS associations across different kingdom of life. We explored the evolutionary history of the aaRS families and evolutionary origins of the mitochondrial aaRSs. Lastly, we showed that prevalent CPs significantly overlap known catalytic and binding sites, suggesting that they have meaningful functional roles, as well as identifying a motif shared between aaRSs and a the Biotin-[acetyl-CoA carboxylase] synthetase (birA) enzyme overlapping binding sites in both families.<br><br>CONCLUSIONS: The study presents the multitude of ways to exploit the CP framework in order to extract meaningful patterns from the aaRS super-family. Specific CPs, discovered in this study, may play important roles in the functionality of these enzymes. We explored the evolutionary patterns in each aaRS family and tracked remote evolutionary links between these families.}, }
@article {pmid21647091, year = {2011}, author = {Krzywanski, DM and Moellering, DR and Fetterman, JL and Dunham-Snary, KJ and Sammy, MJ and Ballinger, SW}, title = {The mitochondrial paradigm for cardiovascular disease susceptibility and cellular function: a complementary concept to Mendelian genetics.}, journal = {Laboratory investigation; a journal of technical methods and pathology}, volume = {91}, number = {8}, pages = {1122-1135}, pmid = {21647091}, issn = {1530-0307}, support = {R01 HL077419/HL/NHLBI NIH HHS/United States ; P30 DK079626/DK/NIDDK NIH HHS/United States ; T32 HL007457/HL/NHLBI NIH HHS/United States ; T32 HL007918/HL/NHLBI NIH HHS/United States ; 56005705/HHMI/Howard Hughes Medical Institute/United States ; P60 DK079626/DK/NIDDK NIH HHS/United States ; HL94518/HL/NHLBI NIH HHS/United States ; R01 HL094518/HL/NHLBI NIH HHS/United States ; P60 DK79626/DK/NIDDK NIH HHS/United States ; HL77419/HL/NHLBI NIH HHS/United States ; }, mesh = {Biological Evolution ; Cardiovascular Diseases/*etiology ; DNA, Mitochondrial/*genetics ; Diet/adverse effects ; Disease Susceptibility ; Humans ; Mitochondria/*physiology ; Oxidation-Reduction ; Selection, Genetic ; }, abstract = {While there is general agreement that cardiovascular disease (CVD) development is influenced by a combination of genetic, environmental, and behavioral contributors, the actual mechanistic basis of how these factors initiate or promote CVD development in some individuals while others with identical risk profiles do not, is not clearly understood. This review considers the potential role for mitochondrial genetics and function in determining CVD susceptibility from the standpoint that the original features that molded cellular function were based upon mitochondrial-nuclear relationships established millions of years ago and were likely refined during prehistoric environmental selection events that today, are largely absent. Consequently, contemporary risk factors that influence our susceptibility to a variety of age-related diseases, including CVD were probably not part of the dynamics that defined the processes of mitochondrial-nuclear interaction, and thus, cell function. In this regard, the selective conditions that contributed to cellular functionality and evolution should be given more consideration when interpreting and designing experimental data and strategies. Finally, future studies that probe beyond epidemiologic associations are required. These studies will serve as the initial steps for addressing the provocative concept that contemporary human disease susceptibility is the result of selection events for mitochondrial function that increased chances for prehistoric human survival and reproductive success.}, }
@article {pmid21646529, year = {2011}, author = {Kowald, A and Kirkwood, TB}, title = {Evolution of the mitochondrial fusion-fission cycle and its role in aging.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {25}, pages = {10237-10242}, pmid = {21646529}, issn = {1091-6490}, mesh = {Aging/*physiology ; Animals ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Genotype ; Mitochondria/*physiology/ultrastructure ; Models, Biological ; Mutation ; Oxidative Phosphorylation ; Phenotype ; Plant Cells ; Reactive Oxygen Species/metabolism ; }, abstract = {Mitochondria are organelles of eukaryotic cells that contain their own genetic material and evolved from prokaryotic ancestors some 2 billion years ago. They are the main source of the cell's energy supply and are involved in such important processes as apoptosis, mitochondrial diseases, and aging. During recent years it also became apparent that mitochondria display a complex dynamical behavior of fission and fusion, the function of which is as yet unknown. In this paper we develop a concise theory that explains why fusion and fission have evolved, how these processes are related to the accumulation of mitochondrial mutants during aging, why the mitochondrial DNA has to be located close to the respiration complexes where most radicals are generated, and what selection pressures shaped the slightly different structure of animal and plant mitochondria. We believe that this "organelle control" theory will help in understanding key processes involved in the evolution of the mitochondrial genome and the aging process.}, }
@article {pmid21645626, year = {2011}, author = {Snoj, A and Marić, S and Bajec, SS and Berrebi, P and Janjani, S and Schöffmann, J}, title = {Phylogeographic structure and demographic patterns of brown trout in North-West Africa.}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {1}, pages = {203-211}, doi = {10.1016/j.ympev.2011.05.011}, pmid = {21645626}, issn = {1095-9513}, mesh = {Africa, Northern ; Africa, Western ; Animals ; Base Sequence ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genetic Variation ; L-Lactate Dehydrogenase/genetics ; Microsatellite Repeats ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeography ; Sequence Alignment ; Sequence Analysis, DNA ; Trout/*classification/*genetics ; }, abstract = {The objectives of the study were to determine the phylogeographic structure of brown trout (Salmo trutta) in Morocco, elucidate their colonization patterns in North-West Africa and identify the mtDNA lineages involved in this process. We also aimed to resolve whether certain brown trout entities are also genetically distinct. Sixty-two brown trout from eleven locations across the Mediterranean and the Atlantic drainages in Morocco were surveyed using sequence analysis of the mtDNA control region and nuclear gene LDH, and by genotyping twelve microsatellite loci. Our study confirms that in Morocco both the Atlantic and Mediterranean basins are populated by Atlantic mtDNA lineage brown trout only, demonstrating that the Atlantic lineage (especially its southern clade) invaded initially not only the western part of the Mediterranean basin in Morocco but also expanded deep into the central area. Atlantic haplotypes identified here sort into three distinct groups suggesting Morocco was colonized in at least three successive waves (1.2, 0.4 and 0.2-0.1 MY ago). This notion becomes more pronounced with the finding of a distinct haplotype in the Dades river system, whose origin appears to coalesce with the nascent stage of the basal mtDNA evolutionary lineages of brown trout. According to our results, Salmo akairos, Salmo pellegrini and "green trout" from Lake Isli do not exhibited any character states that distinctively separate them from the other brown trout populations studied. Therefore, their status as distinct species was not confirmed.}, }
@article {pmid21633985, year = {2011}, author = {Varshavsky, A}, title = {The N-end rule pathway and regulation by proteolysis.}, journal = {Protein science : a publication of the Protein Society}, volume = {20}, number = {8}, pages = {1298-1345}, pmid = {21633985}, issn = {1469-896X}, support = {R01 DK039520/DK/NIDDK NIH HHS/United States ; R01 GM031530/GM/NIGMS NIH HHS/United States ; }, mesh = {Acetylation ; Amino Acid Sequence ; Animals ; Evolution, Molecular ; Humans ; *Metabolic Networks and Pathways ; Molecular Sequence Data ; *Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Proteins/*metabolism ; *Proteolysis ; Ubiquitination ; }, abstract = {The N-end rule relates the regulation of the in vivo half-life of a protein to the identity of its N-terminal residue. Degradation signals (degrons) that are targeted by the N-end rule pathway include a set called N-degrons. The main determinant of an N-degron is a destabilizing N-terminal residue of a protein. In eukaryotes, the N-end rule pathway is a part of the ubiquitin system and consists of two branches, the Ac/N-end rule and the Arg/N-end rule pathways. The Ac/N-end rule pathway targets proteins containing N(α) -terminally acetylated (Nt-acetylated) residues. The Arg/N-end rule pathway recognizes unacetylated N-terminal residues and involves N-terminal arginylation. Together, these branches target for degradation a majority of cellular proteins. For example, more than 80% of human proteins are cotranslationally Nt-acetylated. Thus most proteins harbor a specific degradation signal, termed (Ac)N-degron, from the moment of their birth. Specific N-end rule pathways are also present in prokaryotes and in mitochondria. Enzymes that produce N-degrons include methionine-aminopeptidases, caspases, calpains, Nt-acetylases, Nt-amidases, arginyl-transferases and leucyl-transferases. Regulated degradation of specific proteins by the N-end rule pathway mediates a legion of physiological functions, including the sensing of heme, oxygen, and nitric oxide; selective elimination of misfolded proteins; the regulation of DNA repair, segregation and condensation; the signaling by G proteins; the regulation of peptide import, fat metabolism, viral and bacterial infections, apoptosis, meiosis, spermatogenesis, neurogenesis, and cardiovascular development; and the functioning of adult organs, including the pancreas and the brain. Discovered 25 years ago, this pathway continues to be a fount of biological insights.}, }
@article {pmid21632624, year = {2012}, author = {Polymeropoulos, ET and Heldmaier, G and Frappell, PB and McAllan, BM and Withers, KW and Klingenspor, M and White, CR and Jastroch, M}, title = {Phylogenetic differences of mammalian basal metabolic rate are not explained by mitochondrial basal proton leak.}, journal = {Proceedings. Biological sciences}, volume = {279}, number = {1726}, pages = {185-193}, pmid = {21632624}, issn = {1471-2954}, mesh = {Animals ; *Basal Metabolism ; Body Weight ; Cell Respiration ; Cricetinae ; Electrodes ; Liver/metabolism ; Marsupialia/*metabolism ; Mesocricetus/*metabolism ; Mitochondria, Liver/*metabolism ; Mitochondria, Muscle/*metabolism ; Muscle, Skeletal/metabolism ; Onium Compounds/chemistry ; Oxygen/chemistry ; Phylogeny ; *Protons ; Queensland ; Regression Analysis ; Species Specificity ; Trityl Compounds/chemistry ; }, abstract = {Metabolic rates of mammals presumably increased during the evolution of endothermy, but molecular and cellular mechanisms underlying basal metabolic rate (BMR) are still not understood. It has been established that mitochondrial basal proton leak contributes significantly to BMR. Comparative studies among a diversity of eutherian mammals showed that BMR correlates with body mass and proton leak. Here, we studied BMR and mitochondrial basal proton leak in liver of various marsupial species. Surprisingly, we found that the mitochondrial proton leak was greater in marsupials than in eutherians, although marsupials have lower BMRs. To verify our finding, we kept similar-sized individuals of a marsupial opossum (Monodelphis domestica) and a eutherian rodent (Mesocricetus auratus) species under identical conditions, and directly compared BMR and basal proton leak. We confirmed an approximately 40 per cent lower mass specific BMR in the opossum although its proton leak was significantly higher (approx. 60%). We demonstrate that the increase in BMR during eutherian evolution is not based on a general increase in the mitochondrial proton leak, although there is a similar allometric relationship of proton leak and BMR within mammalian groups. The difference in proton leak between endothermic groups may assist in elucidating distinct metabolic and habitat requirements that have evolved during mammalian divergence.}, }
@article {pmid21632289, year = {2011}, author = {Matus-Ortega, MG and Salmerón-Santiago, KG and Flores-Herrera, O and Guerra-Sánchez, G and Martínez, F and Rendón, JL and Pardo, JP}, title = {The alternative NADH dehydrogenase is present in mitochondria of some animal taxa.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {6}, number = {3}, pages = {256-263}, doi = {10.1016/j.cbd.2011.05.002}, pmid = {21632289}, issn = {1878-0407}, mesh = {Amino Acid Sequence ; Animals ; Archaea/enzymology ; Bacteria/enzymology ; Computational Biology ; Evolution, Molecular ; Isoenzymes/classification/genetics/*metabolism ; Mitochondria/*enzymology ; Mitochondrial Proteins/classification/genetics/metabolism ; Molecular Sequence Data ; NADH Dehydrogenase/classification/genetics/*metabolism ; Oxidoreductases/classification/genetics/metabolism ; Phylogeny ; Plant Proteins/classification/genetics/metabolism ; Sequence Alignment ; }, abstract = {The distribution of the alternative NADH dehydrogenase (NDH-2) in the living world was explored. The enzyme, although present in representatives of all living kingdoms, does not have a universal distribution. With the exception of ε-proteobacteria, the enzyme was found in all eubacterial groups. In contrast with the known presence of the NDH-2 in Archaea, the alternative oxidase (AOX) is absent in this group. With regard to the Eukarya domain, the NDH-2 was found in representatives of Protista, Fungi, Plantae, and Animalia. In the latter, however, the presence of the enzyme was restricted to some primitive Metazoa (Placozoa and Cnidaria), and two members of the Deuterostomate lineage of the Bilateria (Echinodermata and Urochordata). No evidence for the presence of the NDH-2 was found in any representative of the Protostomate branch of the Bilateria, contrasting with the existence of the AOX in this same group. It is worth mentioning that those animal species containing the NDH-2 also have an AOX. The actual distribution of the NDH-2 in the various living kingdoms is discussed within the framework of the endosymbiotic theory; in addition, a hypothesis is proposed to explain the disappearance of the alternative NDH-2 and AOX from the majority of the animals.}, }
@article {pmid21631534, year = {2011}, author = {Muhaidat, R and Sage, TL and Frohlich, MW and Dengler, NG and Sage, RF}, title = {Characterization of C3--C4 intermediate species in the genus Heliotropium L. (Boraginaceae): anatomy, ultrastructure and enzyme activity.}, journal = {Plant, cell &amp; environment}, volume = {34}, number = {10}, pages = {1723-1736}, doi = {10.1111/j.1365-3040.2011.02367.x}, pmid = {21631534}, issn = {1365-3040}, mesh = {Biological Evolution ; Carbon Isotopes/analysis ; Flaveria/*anatomy &amp; histology/*enzymology/metabolism ; Glycine Dehydrogenase (Decarboxylating)/metabolism ; Heliotropium/*anatomy &amp; histology/*enzymology/metabolism ; Malate Dehydrogenase/metabolism ; Phosphoenolpyruvate Carboxylase/metabolism ; Photosynthesis ; Plant Leaves/anatomy &amp; histology/*enzymology/metabolism ; Plant Proteins/*metabolism ; Ribulose-Bisphosphate Carboxylase/metabolism ; }, abstract = {Photosynthetic pathway characteristics were studied in nine species of Heliotropium (sensu lato, including Euploca), using assessments of leaf anatomy and ultrastructure, activities of PEP carboxylase and C4 acid decarboxylases, and immunolocalization of ribulose 1·5-bisphosphate carboxylase/oxygenase (Rubisco) and the P-subunit of glycine decarboxylase (GDC). Heliotropium europaeum, Heliotropium calcicola and Heliotropium tenellum are C3 plants, while Heliotropium texanum and Heliotropium polyphyllum are C4 species. Heliotropium procumbens and Heliotropium karwinskyi are functionally C3, but exhibit 'proto-Kranz' anatomy where bundle sheath (BS) cells are enlarged and mitochondria primarily occur along the centripetal (inner) wall of the BS cells; GDC is present throughout the leaf. Heliotropium convolvulaceum and Heliotropium greggii are C3--C4 intermediates, with Kranz-like enlargement of the BS cells, localization of mitochondria along the inner BS wall and a loss of GDC in the mesophyll (M) tissue. These C3--C4 species of Heliotropium probably shuttle photorespiratory glycine from the M to the BS tissue for decarboxylation. Heliotropium represents an important new model for studying C4 evolution. Where existing models such as Flaveria emphasize diversification of C3--C4 intermediates, Heliotropium has numerous C3 species expressing proto-Kranz traits that could represent a critical initial phase in the evolutionary origin of C4 photosynthesis.}, }
@article {pmid21622264, year = {2011}, author = {Otasevic, V and Korac, A and Buzadzic, B and Stancic, A and Jankovic, A and Korac, B}, title = {Nitric oxide and thermogenesis--challenge in molecular cell physiology.}, journal = {Frontiers in bioscience (Scholar edition)}, volume = {3}, number = {3}, pages = {1180-1195}, doi = {10.2741/219}, pmid = {21622264}, issn = {1945-0524}, mesh = {Adenosine Triphosphate/biosynthesis ; Adipose Tissue, Brown/cytology/*physiology ; Gene Expression Regulation/*physiology ; Humans ; Ion Channels/metabolism ; Mitochondria/*physiology ; Mitochondrial Proteins/metabolism ; Nitric Oxide Synthase/genetics/*metabolism ; Oxidation-Reduction ; Oxidative Phosphorylation ; Reactive Oxygen Species/*metabolism ; Signal Transduction/*physiology ; Thermogenesis/*physiology ; Uncoupling Protein 1 ; }, abstract = {Only recently we can link thermogenesis, mitochondria, nitric oxide, and redox regulation in biochemical terms. Currently, we are discussing these processes from the aspect of fundamental principles of molecular physiology. Thus, the present article highlights both cell physiology and the principles of the maintenance of energy homeostasis in organisms. Energy homeostasis means much more than simple combustion; adipose tissues at this point of evolution development are related to a broad spectrum of metabolic disturbances and all aspects of cellular remodeling (i.e. structural, metabolic and endocrine changes). Therefore, this paper addresses not only thermogenesis but also energy homeostasis, oxidative phosphorylation and ATP production, proliferation and differentiation of brown adipocytes, their life and death, mitochondriogenesis and angiogenesis. These processes will be united by molecular players of oxidation/reduction reactions, thus creating the principles based on the redox regulation.}, }
@article {pmid21622019, year = {2011}, author = {Haferkamp, I and Fernie, AR and Neuhaus, HE}, title = {Adenine nucleotide transport in plants: much more than a mitochondrial issue.}, journal = {Trends in plant science}, volume = {16}, number = {9}, pages = {507-515}, doi = {10.1016/j.tplants.2011.04.001}, pmid = {21622019}, issn = {1878-4372}, mesh = {Adenine Nucleotides/*metabolism ; Adenosine Triphosphate/metabolism ; Arabidopsis/metabolism ; Biological Transport ; Chloroplasts/metabolism ; Diatoms/metabolism ; Endoplasmic Reticulum/metabolism ; Golgi Apparatus/metabolism ; Intracellular Membranes/*metabolism ; Membrane Potential, Mitochondrial ; Mitochondria/*metabolism ; Nucleotide Transport Proteins/*metabolism ; Peroxisomes/metabolism ; Plant Proteins/metabolism ; Plants/*metabolism ; Substrate Specificity ; }, abstract = {Adenine nucleotides play a vital role in plant metabolism and physiology, essentially representing the major energy currency of the cell. Heterotrophic cells regenerate most of the ATP in mitochondria, whereas autotrophic cells also possess chloroplasts, representing a second powerhouse for ATP regeneration. Even though the synthesis of these nucleotides is restricted to a few locations, their use is nearly ubiquitous across the cell and thereby highly efficient systems are required to transport these molecules into and out of different compartments. Here, we discuss the location, biochemical characterization and evolution of corresponding transport systems in plants. We include recent scientific findings concerning organellar transporters from plants and algae and also focus on the physiological importance of adenine nucleotide exchange in these cells.}, }
@article {pmid21621741, year = {2011}, author = {Yang, M and Ge, Y and Wu, J and Xiao, J and Yu, J}, title = {Coevolution study of mitochondria respiratory chain proteins: toward the understanding of protein--protein interaction.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {38}, number = {5}, pages = {201-207}, doi = {10.1016/j.jgg.2011.04.003}, pmid = {21621741}, issn = {1673-8527}, mesh = {Artificial Intelligence ; Electron Transport ; Electron Transport Chain Complex Proteins/chemistry/*genetics/*metabolism ; *Evolution, Molecular ; Humans ; Mitochondria/*metabolism ; Models, Biological ; Models, Molecular ; Protein Binding ; Protein Structure, Tertiary ; }, abstract = {Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein--protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using "Mirror tree" method on the respiratory chain (RC) proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein--protein interaction in intra-complex and the binary protein--protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions (Wilcoxon test, p-value = 4.4 × 10(-6)). Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein--protein interaction. Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study.}, }
@article {pmid21619630, year = {2011}, author = {Pigneur, LM and Marescaux, J and Roland, K and Etoundi, E and Descy, JP and Van Doninck, K}, title = {Phylogeny and androgenesis in the invasive Corbicula clams (Bivalvia, Corbiculidae) in Western Europe.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {147}, pmid = {21619630}, issn = {1471-2148}, mesh = {Americas ; Animals ; Asia ; Corbicula/anatomy &amp; histology/enzymology/*genetics ; Cytochrome b Group/genetics ; Europe ; Haplotypes ; Male ; Microsatellite Repeats ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; Spermatozoa/cytology ; }, abstract = {BACKGROUND: The genus Corbicula is one of the most invasive groups of molluscs. It includes both sexual and androgenetic lineages. The present study re-assessed the different morphotypes and haplotypes of West European Corbicula in order to clarify their taxonomic identification and phylogenetic relationships with American and Asian Corbicula clams. We studied several populations from West European river basins (Meuse, Seine, Rhine and Rhône) through an "integrative taxonomy" approach. We combined morphology, partial mitochondrial COI and cyt b sequences and eleven microsatellite loci. Furthermore, we looked for discrepancies between mtDNA and nrDNA/morphology, indicative of androgenesis between lineages.<br><br>RESULTS: There are three Corbicula morphotypes in Western Europe associated to three mitochondrial lineages and three genotypes. Form R shares the same COI haplotype as the American form A and the Japanese C. leana. Form S and the American form C have the same haplotype, although their morphologies seem divergent. The European form Rlc belongs to the same mitochondrial lineage as both the American form B and the Asian C. fluminea.Interestingly, within each haplotype/genotype or lineage, no genetic diversity was found although their invasive success is high. Moreover, we detected rare mismatches between mtDNA and nrDNA/morphology, indicative of androgenesis and mitochondrial capture between form R and form S and therefore challenging the phylogenetic relatedness and the species status within this genus. The global phylogenetic analysis revealed that the sexual Corbicula lineages seem restricted to the native areas while their androgenetic relatives are widespread and highly invasive.<br><br>CONCLUSIONS: We clarified the discrepancies and incongruent results found in the literature about the European morphotypes of Corbicula and associated mitochondrial lineages. The three West European morphotypes belong to three distinct nuclear and mitochondrial lineages. However mitochondrial capture occurs in sympatric populations of forms R and S. The species status of the morphotypes therefore remains doubtful. Moreover the androgenetic lineages seem widely distributed compared to their sexual relatives, suggesting that androgenesis and invasive success may be linked in the genus Corbicula.}, }
@article {pmid21618648, year = {2011}, author = {Goizet, C and Depienne, C and Benard, G and Boukhris, A and Mundwiller, E and Solé, G and Coupry, I and Pilliod, J and Martin-Négrier, ML and Fedirko, E and Forlani, S and Cazeneuve, C and Hannequin, D and Charles, P and Feki, I and Pinel, JF and Ouvrard-Hernandez, AM and Lyonnet, S and Ollagnon-Roman, E and Yaouanq, J and Toutain, A and Dussert, C and Fontaine, B and Leguern, E and Lacombe, D and Durr, A and Rossignol, R and Brice, A and Stevanin, G}, title = {REEP1 mutations in SPG31: frequency, mutational spectrum, and potential association with mitochondrial morpho-functional dysfunction.}, journal = {Human mutation}, volume = {32}, number = {10}, pages = {1118-1127}, doi = {10.1002/humu.21542}, pmid = {21618648}, issn = {1098-1004}, mesh = {Adolescent ; Adult ; Aged ; Base Sequence ; Child ; Child, Preschool ; Energy Metabolism ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Membrane Transport Proteins/*genetics ; Middle Aged ; Mitochondria/*metabolism ; Muscle, Skeletal/metabolism/pathology ; *Mutation ; Mutation Rate ; Pedigree ; Phenotype ; Sequence Deletion ; Spastic Paraplegia, Hereditary/*genetics/metabolism ; Young Adult ; }, abstract = {Hereditary spastic paraplegias (HSP) constitute a heterogeneous group of neurodegenerative disorders characterized at least by slowly progressive spasticity of the lower limbs. Mutations in REEP1 were recently associated with a pure dominant HSP, SPG31. We sequenced all exons of REEP1 and searched for rearrangements by multiplex ligation-dependent probe amplification (MLPA) in a large panel of 175 unrelated HSP index patients from kindreds with dominant inheritance (AD-HSP), with either pure (n = 102) or complicated (n = 73) forms of the disease, after exclusion of other known HSP genes. We identified 12 different heterozygous mutations, including two exon deletions, associated with either a pure or a complex phenotype. The overall mutation rate in our clinically heterogeneous sample was 4.5% in French families with AD-HSP. The phenotype was restricted to pyramidal signs in the lower limbs in most patients but nine had a complex phenotype associating axonal peripheral neuropathy (= 5/11 patients) including a Silver-like syndrome in one patient, and less frequently cerebellar ataxia, tremor, dementia. Interestingly, we evidenced abnormal mitochondrial network organization in fibroblasts of one patient in addition to defective mitochondrial energy production in both fibroblasts and muscle, but whether these anomalies are directly or indirectly related to the mutations remains uncertain.}, }
@article {pmid21617372, year = {2011}, author = {Pan, R and Hu, J}, title = {The conserved fission complex on peroxisomes and mitochondria.}, journal = {Plant signaling &amp; behavior}, volume = {6}, number = {6}, pages = {870-872}, pmid = {21617372}, issn = {1559-2324}, mesh = {Arabidopsis/metabolism ; Arabidopsis Proteins/metabolism ; *Conserved Sequence ; *Evolution, Molecular ; Mitochondria/*metabolism ; Peroxisomes/*metabolism ; }, abstract = {Peroxisomes are eukaryotic organelles highly versatile and dynamic in content and abundance. Plant peroxisomes mediate various metabolic pathways, a number of which are completed sequentially in peroxisomes and other subcellular organelles, including mitochondria and chloroplasts. To understand how peroxisomal dynamics contribute to changes in plant physiology and adaptation, the multiplication pathways of peroxisomes are being dissected. Research in Arabidopsis thaliana has identified several evolutionarily conserved families of proteins in peroxisome division. These include five PEROXIN11 proteins (PEX11a to -e) that induce peroxisome elongation, and the fission machinery, which is composed of three dynamin-related proteins (DRP3A, -3B, and -5B) and DRP's membrane receptor, FISSION1 (FIS1A and -1B). While the function of PEX11 is restricted to peroxisomes, the fission factors are more promiscuous. DRP3 and FIS1 proteins are shared between peroxisomes and mitochondria, and DRP5B plays a dual role in the division of chloroplasts and peroxisomes. Analysis of the Arabidopsis genome suggests that higher plants may also contain functional homologs of the yeast Mdv1/Caf4 proteins, adaptor proteins that link DRPs to FIS1 on the membrane of both peroxisomes and mitochondria. Sharing a conserved fission machine between these metabolically linked subcellular compartments throughout evolution may have some biological significance.}, }
@article {pmid21613169, year = {2011}, author = {Soltis, DE and Smith, SA and Cellinese, N and Wurdack, KJ and Tank, DC and Brockington, SF and Refulio-Rodriguez, NF and Walker, JB and Moore, MJ and Carlsward, BS and Bell, CD and Latvis, M and Crawley, S and Black, C and Diouf, D and Xi, Z and Rushworth, CA and Gitzendanner, MA and Sytsma, KJ and Qiu, YL and Hilu, KW and Davis, CC and Sanderson, MJ and Beaman, RS and Olmstead, RG and Judd, WS and Donoghue, MJ and Soltis, PS}, title = {Angiosperm phylogeny: 17 genes, 640 taxa.}, journal = {American journal of botany}, volume = {98}, number = {4}, pages = {704-730}, doi = {10.3732/ajb.1000404}, pmid = {21613169}, issn = {1537-2197}, mesh = {Cell Nucleus/genetics ; Chloroplasts/genetics ; DNA, Plant/*analysis ; *Evolution, Molecular ; *Genes, Plant ; *Genome, Plant ; Magnoliopsida/classification/*genetics ; Mitochondria/genetics ; Nucleotides/*analysis ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {PREMISE OF THE STUDY: Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses.<br><br>METHODS: We conducted two primary analyses based on 640 species representing 330 families. The first included 25260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19846 aligned bp from 13 genes (representing only the nucleus and plastid).<br><br>KEY RESULTS: Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms (Mesangiospermae), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae]. Eudicotyledoneae contains a basal grade subtending Gunneridae. Within Gunneridae, Gunnerales are sister to the remainder (Pentapetalae), which comprises (1) Superrosidae, consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae, comprising Berberidopsidales, Santalales, Caryophyllales, Asteridae, and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae, most deep-level relationships are resolved with strong support.<br><br>CONCLUSIONS: Our analyses confirm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.}, }
@article {pmid21611166, year = {2011}, author = {Delage, L and Leblanc, C and Nyvall Collén, P and Gschloessl, B and Oudot, MP and Sterck, L and Poulain, J and Aury, JM and Cock, JM}, title = {In silico survey of the mitochondrial protein uptake and maturation systems in the brown alga Ectocarpus siliculosus.}, journal = {PloS one}, volume = {6}, number = {5}, pages = {e19540}, pmid = {21611166}, issn = {1932-6203}, mesh = {Animals ; Computational Biology/*methods ; Humans ; Likelihood Functions ; Mitochondria/enzymology ; Mitochondrial Membranes/metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; Multiprotein Complexes/metabolism ; Peptide Hydrolases/metabolism ; Phaeophyceae/*metabolism ; Protein Structure, Secondary ; Protein Transport ; Sequence Alignment ; Substrate Specificity ; }, abstract = {The acquisition of mitochondria was a key event in eukaryote evolution. The aim of this study was to identify homologues of the components of the mitochondrial protein import machinery in the brown alga Ectocarpus and to use this information to investigate the evolutionary history of this fundamental cellular process. Detailed searches were carried out both for components of the protein import system and for related peptidases. Comparative and phylogenetic analyses were used to investigate the evolution of mitochondrial proteins during eukaryote diversification. Key observations include phylogenetic evidence for very ancient origins for many protein import components (Tim21, Tim50, for example) and indications of differences between the outer membrane receptors that recognize the mitochondrial targeting signals, suggesting replacement, rearrangement and/or emergence of new components across the major eukaryotic lineages. Overall, the mitochondrial protein import components analysed in this study confirmed a high level of conservation during evolution, indicating that most are derived from very ancient, ancestral proteins. Several of the protein import components identified in Ectocarpus, such as Tim21, Tim50 and metaxin, have also been found in other stramenopiles and this study suggests an early origin during the evolution of the eukaryotes.}, }
@article {pmid21610726, year = {2011}, author = {Gontijo, AM and Miguela, V and Whiting, MF and Woodruff, RC and Dominguez, M}, title = {Intron retention in the Drosophila melanogaster Rieske Iron Sulphur Protein gene generated a new protein.}, journal = {Nature communications}, volume = {2}, number = {}, pages = {}, pmid = {21610726}, issn = {2041-1723}, mesh = {Alternative Splicing ; Amino Acid Sequence ; Animals ; Base Sequence ; Drosophila Proteins/*genetics/metabolism ; Drosophila melanogaster/chemistry/classification/*genetics/metabolism ; Electron Transport Complex III/*genetics/metabolism ; Evolution, Molecular ; *Introns ; Molecular Sequence Data ; Phylogeny ; RNA Splice Sites ; Sequence Alignment ; }, abstract = {Genomes can encode a variety of proteins with unrelated architectures and activities. It is known that protein-coding genes of de novo origin have significantly contributed to this diversity. However, the molecular mechanisms and evolutionary processes behind these originations are still poorly understood. Here we show that the last 102 codons of a novel gene, Noble, assembled directly from non-coding DNA following an intronic deletion that induced alternative intron retention at the Drosophila melanogaster Rieske Iron Sulphur Protein (RFeSP) locus. A systematic analysis of the evolutionary processes behind the origin of Noble showed that its emergence was strongly biased by natural selection on and around the RFeSP locus. Noble mRNA is shown to encode a bona fide protein that lacks an iron sulphur domain and localizes to mitochondria. Together, these results demonstrate the generation of a novel protein at a naturally selected site.}, }
@article {pmid21607544, year = {2012}, author = {Salgado, MC and Metón, I and Anemaet, IG and González, JD and Fernández, F and Baanante, IV}, title = {Hepatocyte nuclear factor 4α transactivates the mitochondrial alanine aminotransferase gene in the kidney of Sparus aurata.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {14}, number = {1}, pages = {46-62}, pmid = {21607544}, issn = {1436-2236}, mesh = {Alanine Transaminase/genetics/*metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Cell Line ; Cloning, Molecular ; DNA, Complementary/genetics ; Gene Expression Regulation, Enzymologic ; Hepatocyte Nuclear Factor 4/genetics/*metabolism ; Intracellular Signaling Peptides and Proteins ; Kidney/*metabolism ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Promoter Regions, Genetic ; Real-Time Polymerase Chain Reaction ; Response Elements ; Sea Bream/*metabolism ; }, abstract = {Alanine aminotransferase (ALT) plays an important role in amino acid metabolism and gluconeogenesis. The preference of carnivorous fish for protein amino acids instead of carbohydrates as a source of energy lead us to study the transcriptional regulation of the mitochondrial ALT (mALT) gene and to characterize the enzyme kinetics and modulation of mALT expression in the kidney of gilthead sea bream (Sparus aurata) under different nutritional and hormonal conditions. 5'-Deletion analysis of mALT promoter in transiently transfected HEK293 cells, site-directed mutagenesis and electrophoretic mobility shift assays allowed us to identify HNF4α as a new factor involved in the transcriptional regulation of mALT expression. Quantitative RT-PCR assays showed that starvation and the administration of streptozotocin (STZ) decreased HNF4α levels in the kidney of S. aurata, leading to the downregulation of mALT transcription. Analysis of the tissue distribution showed that kidney, liver, and intestine were the tissues with higher mALT and HNF4α expression. Kinetic analysis indicates that mALT enzyme is more efficient in catalyzing the conversion of L: -alanine to pyruvate than the reverse reaction. From these results, we conclude that HNF4α transactivates the mALT promoter and that the low levels of mALT expression found in the kidney of starved and STZ-treated fish result from a decreased expression of HNF4α. Our findings suggest that the mALT isoenzyme plays a major role in oxidazing dietary amino acids, and points to ALT as a target for a biotechnological action to spare protein and optimize the use of dietary nutrients for fish culture.}, }
@article {pmid21605691, year = {2011}, author = {Rivas Plata, E and Lumbsch, HT}, title = {Parallel evolution and phenotypic divergence in lichenized fungi: a case study in the lichen-forming fungal family Graphidaceae (Ascomycota: Lecanoromycetes: Ostropales).}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {1}, pages = {45-63}, doi = {10.1016/j.ympev.2011.04.025}, pmid = {21605691}, issn = {1095-9513}, mesh = {Ascomycota/*classification/*genetics ; *Biological Evolution ; DNA, Fungal/chemistry/genetics ; DNA, Mitochondrial/classification/*genetics ; DNA, Ribosomal/classification/*genetics ; Evolution, Molecular ; Lichens/classification/genetics ; Mitochondria/genetics ; Phenotype ; Phylogeny ; Ribosome Subunits, Small/classification/*genetics ; Sequence Alignment ; Spores, Fungal/genetics ; }, abstract = {A molecular phylogeny of combined mtSSU, nuLSU, and RPB2 data revealed previously unrecognized levels of parallel evolution and phenotypic divergence in the lichen family Graphidaceae. Five clades were supported within the family: the Fissurina, Ocellularia, Graphis, Topeliopsis, and Thelotrema clades, containing 33 of the 42 currently accepted genera within the family. The results for the first time provide a fully resolved phylogeny of this family and confirm the synonymy of Graphidaceae and Thelotremataceae. Ancestral character state reconstruction using likelihood, Bayesian, and parsimony approaches indicate that lirellate ascomata evolved independently in each of the five clades. Carbonized ascomata evolved independently in at least four of the five clades. An unexpected result was the independent evolution of columella structures in the Fissurina and Ocellularia clades. Besides these more general findings, we document several cases in which evolution of several traits in parallel resulted in striking look-alikes within unrelated lineages, such as Topeliopsismuscigena and Chapsameridensis in the Topeliopsis and Thelotrema clades, Leptotremawightii, Myriotremalaeviusculum, and Leucodectonphaeosporum in the Ocellularia and Thelotrema clades, Ocellulariastylothecia and Melanotremameiosporum in the Fissurina and Ocellularia clades, and Myriotremapycnoporellum, Myriotremaclandestinum and Wirthiotremaglaucopallens in the Fissurina, Ocellularia, and Topeliopsis clades. Pagel's test of independent character evolution suggested that at least for some of the traits involved in these cases, ecological constraints may have caused their evolution in parallel. The most intriguing find is the correlation between gall-forming thalli and vertical columns of calcium oxalate crystals, suggesting that these crystals do not function as light distributors, as previously assumed, but instead stabilize the thalli which are usually hollow beneath, similar to a dome-shaped structure. Ancestral character state reconstruction together with an approach to visualize the phenotype of putative ancestral lineages suggested the alpha-Graphidaceae to resemble some of the extant species currently classified in Myriotrema s.lat., with pore-like ascomata, and non-amyloid ascospores with lens-shaped lumina.}, }
@article {pmid21596145, year = {2011}, author = {Benz, BW and Robbins, MB}, title = {Molecular phylogenetics, vocalizations, and species limits in Celeus woodpeckers (Aves: Picidae).}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {1}, pages = {29-44}, doi = {10.1016/j.ympev.2011.05.001}, pmid = {21596145}, issn = {1095-9513}, mesh = {Animals ; Base Sequence ; *Birds/anatomy &amp; histology/classification/genetics/physiology ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; *Vocalization, Animal ; }, abstract = {Species limits and the evolutionary mechanisms that have shaped diversification of woodpeckers and allies (Picidae) remain obscure, as inter and intraspecific phylogenetic relationships have yet to be comprehensively resolved for most genera. Herein, we analyzed 5020 base pairs of nucleotide sequence data from the mitochondrial and nuclear genomes to reconstruct the evolutionary history of Celeus woodpeckers. Broad geographic sampling was employed to assess species limits in phenotypically variable lineages and provide a first look at the evolution of song and plumage traits in this poorly known Neotropical genus. Our results strongly support the monophyly of Celeus and reveal several novel relationships across a shallow phylogenetic topology. We confirm the close sister relationship between Celeus spectabilis and the enigmatic Celeus obrieni, both of which form a clade with Celeus flavus. The Mesoamerican Celeus castaneus was placed as sister to a Celeus undatus-grammicus lineage, with the species status of the latter drawn into question given the lack of substantial genetic, morphological, and vocal variation in these taxa. We recovered paraphyly in Celeus elegans; however, this result appears to be the consequence of mitochondrial introgression from Celeus lugubris considering the monophyly of elegans at the ß-FIBI7 locus. A second instance of paraphyly was observed in Celeus flavescens with deep genetic splits and substantial phenotypic variation indicating the presence of two distinct species in this broadly distributed lineage. As such, we advocate elevation of Celeus flavescens ochraceus to species status. Our analysis of Celeus vocalizations and plumage characters demonstrates a pattern of lability consistent with a relatively recent origin of the genus and potentially rapid speciation history.}, }
@article {pmid21595926, year = {2011}, author = {Blanco, R and Mayordomo, E and Montoya, J and Ruiz-Pesini, E}, title = {Rebooting the human mitochondrial phylogeny: an automated and scalable methodology with expert knowledge.}, journal = {BMC bioinformatics}, volume = {12}, number = {}, pages = {174}, pmid = {21595926}, issn = {1471-2105}, mesh = {*Algorithms ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Humans ; Mitochondria/*genetics ; *Phylogeny ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: Mitochondrial DNA is an ideal source of information to conduct evolutionary and phylogenetic studies due to its extraordinary properties and abundance. Many insights can be gained from these, including but not limited to screening genetic variation to identify potentially deleterious mutations. However, such advances require efficient solutions to very difficult computational problems, a need that is hampered by the very plenty of data that confers strength to the analysis.<br><br>RESULTS: We develop a systematic, automated methodology to overcome these difficulties, building from readily available, public sequence databases to high-quality alignments and phylogenetic trees. Within each stage in an autonomous workflow, outputs are carefully evaluated and outlier detection rules defined to integrate expert knowledge and automated curation, hence avoiding the manual bottleneck found in past approaches to the problem. Using these techniques, we have performed exhaustive updates to the human mitochondrial phylogeny, illustrating the power and computational scalability of our approach, and we have conducted some initial analyses on the resulting phylogenies.<br><br>CONCLUSIONS: The problem at hand demands careful definition of inputs and adequate algorithmic treatment for its solutions to be realistic and useful. It is possible to define formal rules to address the former requirement by refining inputs directly and through their combination as outputs, and the latter are also of help to ascertain the performance of chosen algorithms. Rules can exploit known or inferred properties of datasets to simplify inputs through partitioning, therefore cutting computational costs and affording work on rapidly growing, otherwise intractable datasets. Although expert guidance may be necessary to assist the learning process, low-risk results can be fully automated and have proved themselves convenient and valuable.}, }
@article {pmid21595768, year = {2011}, author = {Dyer, KA and Burke, C and Jaenike, J}, title = {Wolbachia-mediated persistence of mtDNA from a potentially extinct species.}, journal = {Molecular ecology}, volume = {20}, number = {13}, pages = {2805-2817}, doi = {10.1111/j.1365-294X.2011.05128.x}, pmid = {21595768}, issn = {1365-294X}, mesh = {Animals ; Base Sequence ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Drosophila/*genetics/microbiology ; Female ; Gene Transfer, Horizontal ; Haplotypes ; Maine ; Models, Genetic ; Molecular Sequence Data ; Multilocus Sequence Typing ; New York ; Pennsylvania ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Symbiosis ; Time Factors ; Wolbachia/*genetics ; }, abstract = {Drosophila quinaria is polymorphic for infection with Wolbachia, a maternally transmitted endosymbiont. Wolbachia-infected individuals carry mtDNA that is only distantly related to the mtDNA of uninfected individuals, and the clade encompassing all mtDNA haplotypes within D. quinaria also includes the mtDNA of several other species of Drosophila. Nuclear gene variation reveals no difference between the Wolbachia-infected and uninfected individuals of D. quinaria, indicating that they all belong to the same interbreeding biological species. We suggest that the Wolbachia and the mtDNA with which it is associated were derived via interspecific hybridization and introgression. The sequences in the Wolbachia and the associated mtDNA are ≥6% divergent from those of any known Drosophila species. Thus, in spite of nearly complete species sampling, the sequences from which these mitochondria were derived remain unknown, raising the possibility that the donor species is extinct. The association between Wolbachia infection and mtDNA type within D. quinaria suggests that Wolbachia may be required for the continued persistence of the mtDNA from an otherwise extinct Drosophila species. We hypothesize that pathogen-protective effects conferred by Wolbachia operate in a negative frequency-dependent manner, thus bringing about a stable polymorphism for Wolbachia infection.}, }
@article {pmid21590781, year = {2012}, author = {Giari, L and Dezfuli, BS and Astolfi, L and Martini, A}, title = {Ultrastructural effects of cisplatin on the inner ear and lateral line system of zebrafish (Danio rerio) larvae.}, journal = {Journal of applied toxicology : JAT}, volume = {32}, number = {4}, pages = {293-299}, doi = {10.1002/jat.1691}, pmid = {21590781}, issn = {1099-1263}, mesh = {Animals ; Cisplatin/*pharmacology ; Dose-Response Relationship, Drug ; Ear, Inner/*drug effects/*ultrastructure ; Hair Cells, Auditory/drug effects/ultrastructure ; Larva/ultrastructure ; Lateral Line System/*drug effects/*ultrastructure ; Mechanoreceptors ; Microscopy, Electron, Scanning ; Zebrafish/*growth &amp; development ; }, abstract = {Zebrafish, Danio rerio, has been a prominent model vertebrate for the study of chemical toxicity and human disease. Zebrafish hair cells (HCs) show significant structural, functional and molecular similarities to the mammalian inner ear HCs. We examined the effects of cisplatin, an anti-cancer drug, on HCs of the inner ear and on HCs and support cells (SCs) of neuromasts in zebrafish using transmission and scanning electron microscopy. Forty-five zebrafish larvae, 12 days post-fertilization, were assessed: 15 unexposed controls, 15 exposed to 10 µM cisplatin solution, and 15 exposed to 50 µM cisplatin solution. Hair cells in the cristae and maculae of the inner ear and of neuromasts were extremely sensitive to cisplatin. The drug was associated with vacuolization and the presence of myelinoid bodies in HC cytoplasm and with a condensation of the nuclear chromatin. The predominant pattern of injury was widespread degeneration of mitochondria, which appeared swollen and less electron-dense with disorganized or reduced cristae. Severity of damage seemed to be concentration-dependent, and the inner ear suffered more damage than the lateral line. Alterations similar to those in HCs were also observed in SCs of the neuromasts. Scanning electron microscopy showed loss of kinocilia in neuromasts of fish exposed to the higher concentration of cisplatin.}, }
@article {pmid21566257, year = {2011}, author = {Valerio, A and D'Antona, G and Nisoli, E}, title = {Branched-chain amino acids, mitochondrial biogenesis, and healthspan: an evolutionary perspective.}, journal = {Aging}, volume = {3}, number = {5}, pages = {464-478}, pmid = {21566257}, issn = {1945-4589}, mesh = {Amino Acids, Branched-Chain/*metabolism ; Animals ; *Biological Evolution ; Caloric Restriction ; Diet ; Dietary Supplements ; Energy Metabolism ; Humans ; Longevity/*physiology ; Mitochondria/*metabolism ; Nutritional Status ; }, abstract = {Malnutrition is common among older persons, with important consequences increasing frailty and morbidity and reducing health expectancy. On the contrary, calorie restriction (CR, a low-calorie dietary regimen with adequate nutrition) slows the progression of age-related diseases and extends the lifespan of many species. Identification of strategies mimicking key CR mechanisms - increased mitochondrial respiration and reduced production of oxygen radicals - is a hot topic in gerontology. Dietary supplementation with essential and/or branched chain amino acids (BCAAs) exerts a variety of beneficial effects in experimental animals and humans and has been recently demonstrated to support cardiac and skeletal muscle mitochondrial biogenesis, prevent oxidative damage, and enhance physical endurance in middle-aged mice, resulting in prolonged survival. Here we review recent studies addressing the possible role of BCAAs in energy metabolism and in the longevity of species ranging from unicellular organisms to mammals. We also summarize observations from human studies supporting the exciting hypothesis that dietary BCAA enriched mixture supplementation might be a health-promoting strategy in aged patients at risk.}, }
@article {pmid21566193, year = {2011}, author = {Innocenti, P and Morrow, EH and Dowling, DK}, title = {Experimental evidence supports a sex-specific selective sieve in mitochondrial genome evolution.}, journal = {Science (New York, N.Y.)}, volume = {332}, number = {6031}, pages = {845-848}, doi = {10.1126/science.1201157}, pmid = {21566193}, issn = {1095-9203}, mesh = {Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Drosophila melanogaster/*genetics/physiology ; *Evolution, Molecular ; Female ; Fertility ; *Gene Expression ; Gene Expression Profiling ; Genes, Insect ; Genetic Fitness ; *Genome, Insect ; *Genome, Mitochondrial ; Male ; *Mutation ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Genetic ; Selection, Genetic ; Sex Characteristics ; Transcription, Genetic ; }, abstract = {Mitochondria are maternally transmitted; hence, their genome can only make a direct and adaptive response to selection through females, whereas males represent an evolutionary dead end. In theory, this creates a sex-specific selective sieve, enabling deleterious mutations to accumulate in mitochondrial genomes if they exert male-specific effects. We tested this hypothesis, expressing five mitochondrial variants alongside a standard nuclear genome in Drosophila melanogaster, and found striking sexual asymmetry in patterns of nuclear gene expression. Mitochondrial polymorphism had few effects on nuclear gene expression in females but major effects in males, modifying nearly 10% of transcripts. These were mostly male-biased in expression, with enrichment hotspots in the testes and accessory glands. Our results suggest an evolutionary mechanism that results in mitochondrial genomes harboring male-specific mutation loads.}, }
@article {pmid21562960, year = {2011}, author = {Artamonova, VS and Kucheryavyy, AV and Pavlov, DS}, title = {Nucleotide sequences of the mitochondrial cytochrome oxidase subunit I (COI) gene of lamprey classified with Lethenteron camtschaticum and the Lethenteron reissneri complex show no species-level differences.}, journal = {Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections}, volume = {437}, number = {}, pages = {113-118}, pmid = {21562960}, issn = {0012-4966}, mesh = {Animals ; Base Sequence ; Electron Transport Complex IV/*classification/*genetics ; Evolution, Molecular ; Genetic Variation ; Haplotypes/genetics ; Lampreys/*classification/*genetics ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Phylogeography ; }, }
@article {pmid21562953, year = {2011}, author = {Kiryukhina, NA and Kholodova, MV}, title = {Mitochondrial DNA control region analysis in aboriginal and invasive populations of Black Sea pipefish Syngnathus nigrolineatus Eichwald 1831.}, journal = {Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections}, volume = {437}, number = {}, pages = {88-90}, pmid = {21562953}, issn = {0012-4966}, mesh = {Animal Migration ; Animals ; Black Sea ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Smegmamorpha/*classification/*genetics ; }, }
@article {pmid21558255, year = {2010}, author = {O'Brien, KM and Mueller, IA}, title = {The unique mitochondrial form and function of Antarctic channichthyid icefishes.}, journal = {Integrative and comparative biology}, volume = {50}, number = {6}, pages = {993-1008}, doi = {10.1093/icb/icq038}, pmid = {21558255}, issn = {1557-7023}, mesh = {*Adaptation, Physiological ; Animals ; Antarctic Regions ; Cold Temperature ; Hemoglobins/genetics/metabolism ; Mitochondria/enzymology/genetics/*metabolism/ultrastructure ; Muscle Fibers, Skeletal/cytology/metabolism ; Myocytes, Cardiac/cytology/metabolism ; Myoglobin/genetics/metabolism ; Nitric Oxide/metabolism ; Perciformes/classification/*genetics/*metabolism ; Phylogeny ; }, abstract = {Antarctic icefishes of the family Channichthyidae are the only vertebrate animals that as adults do not express the circulating oxygen-binding protein hemoglobin (Hb). Six of the 16 family members also lack the intracellular oxygen-binding protein myoglobin (Mb) in the ventricle of their hearts and all lack Mb in oxidative skeletal muscle. The loss of Hb has led to substantial remodeling in the cardiovascular system of icefishes to facilitate adequate oxygenation of tissues. One of the more curious adaptations to the loss of Hb and Mb is an increase in mitochondrial density in cardiac myocytes and oxidative skeletal muscle fibers. The proliferation of mitochondria in the aerobic musculature of icefishes does not arise through a canonical pathway of mitochondrial biogenesis. Rather, the biosynthesis of mitochondrial phospholipids is up-regulated independently of the synthesis of proteins and mitochondrial DNA, and newly-synthesized phospholipids are targeted primarily to the outer-mitochondrial membrane. Consequently, icefish mitochondria have a higher lipid-to-protein ratio compared to those from red-blooded species. Elevated levels of nitric oxide in the blood plasma of icefishes, compared to red-blooded notothenioids, may mediate alterations in mitochondrial density and architecture. Modifications in mitochondrial structure minimally impact state III respiration rates but may significantly enhance intracellular diffusion of oxygen. The rate of oxygen diffusion is greater within the hydrocarbon core of membrane lipids compared to the aqueous cytosol and impeded only by proteins within the lipid bilayer. Thus, the proliferation of icefish's mitochondrial membranes provides an optimal conduit for the intracellular diffusion of oxygen and compensates for the loss of Hb and Mb. Currently little is known about how mitochondrial phospholipid synthesis is regulated and integrated into mitochondrial biogenesis. The unique architecture of the oxidative muscle cells of icefishes highlights the need for further studies in this area.}, }
@article {pmid21549606, year = {2011}, author = {Selosse, MA}, title = {Morts d'amour: mitochondria are bacteria that sometimes become extinct through symbiosis.}, journal = {Trends in microbiology}, volume = {19}, number = {6}, pages = {255-256}, doi = {10.1016/j.tim.2011.04.001}, pmid = {21549606}, issn = {1878-4380}, mesh = {Bacteria/*genetics ; *Biological Evolution ; Mitochondria/*genetics/physiology ; *Symbiosis ; }, }
@article {pmid21549602, year = {2011}, author = {Noguchi, T and Koizumi, M and Hayashi, S}, title = {Sustained elongation of sperm tail promoted by local remodeling of giant mitochondria in Drosophila.}, journal = {Current biology : CB}, volume = {21}, number = {10}, pages = {805-814}, doi = {10.1016/j.cub.2011.04.016}, pmid = {21549602}, issn = {1879-0445}, mesh = {Animals ; Biological Evolution ; *Cell Size ; Drosophila Proteins/metabolism ; Drosophila melanogaster/*physiology ; Male ; Microtubules/*physiology ; Mitochondria/*physiology ; Morphogenesis/*physiology ; Nerve Tissue Proteins/metabolism ; Nocodazole ; Sperm Tail/*physiology/ultrastructure ; Spermatozoa/cytology/*growth &amp; development ; Time-Lapse Imaging ; }, abstract = {BACKGROUND: Sperm length in Drosophilidae varies from a few hundred microns to 6 cm as a result of evolutionary selection. In postcopulatory competition, longer sperm have an advantage in positioning their head closer to the egg. Sperm cell elongation can proceed in the absence of an axoneme, suggesting that a mechanism besides intraflagellar transport emerged to sustain it.<br><br>RESULTS: Here we report that sperm elongation in Drosophila melanogaster is driven by the interdependent extension of giant mitochondria and microtubule array that is formed around the mitochondrial surface. In primary cultures of elongating spermatids, we demonstrated that the mitochondrial integrity and local dynamics of microtubules at the tail tip region are essential for uniaxial elongation of the sperm tail. Mitochondria-microtubule linker protein Milton accumulated on mitochondria near the tail tip and is required for the sliding movement of microtubules. Disruption of Milton and its associated protein dMiro, and of potential microtubule crosslinkers Nebbish and Fascetto, caused strong elongation defects, indicating that mitochondria-microtubule association and microtubule crosslinking are required for spermatid tail elongation.<br><br>CONCLUSIONS: Mitochondria play unexpected roles in sperm tail elongation in Drosophila by providing a structural platform for microtubule reorganization to support the robust elongation taking place at the tip of the very long sperm tail. The identification of mitochondria as an organizer of cytoskeletal dynamics extends our understanding of mechanisms of cell morphogenesis.}, }
@article {pmid21546354, year = {2011}, author = {Lipinski, KA and Puchta, O and Surendranath, V and Kudla, M and Golik, P}, title = {Revisiting the yeast PPR proteins--application of an Iterative Hidden Markov Model algorithm reveals new members of the rapidly evolving family.}, journal = {Molecular biology and evolution}, volume = {28}, number = {10}, pages = {2935-2948}, doi = {10.1093/molbev/msr120}, pmid = {21546354}, issn = {1537-1719}, mesh = {*Algorithms ; Amino Acid Sequence ; Cluster Analysis ; *Evolution, Molecular ; Genome, Mitochondrial ; Genomics/*methods ; *Markov Chains ; Molecular Sequence Data ; Phylogeny ; RNA-Binding Proteins/*genetics ; Saccharomyces cerevisiae Proteins/*genetics ; Sequence Alignment ; }, abstract = {Pentatricopeptide repeat (PPR) proteins are the largest known RNA-binding protein family, and are found in all eukaryotes, being particularly abundant in higher plants. PPR proteins localize mostly to mitochondria and chloroplasts, and many were shown to modulate organellar genome expression on the posttranscriptional level. Although the genomes of land plants encode hundreds of PPR proteins, only a few have been identified in Fungi and Metazoa. As the current PPR motif profiles are built mainly on the basis of the predominant plant sequences, they are unlikely to be optimal for detecting fungal and animal members of the family, and many putative PPR proteins in these genomes may remain undetected. In order to verify this hypothesis, we designed a hidden Markov model-based bioinformatic tool called Supervised Clustering-based Iterative Phylogenetic Hidden Markov Model algorithm for the Evaluation of tandem Repeat motif families (SCIPHER) using sequence data from orthologous clusters from available yeast genomes. This approach allowed us to assign 12 new proteins in Saccharomyces cerevisiae to the PPR family. Similarly, in other yeast species, we obtained a 5-fold increase in the detection of PPR motifs, compared with the previous tools. All the newly identified S. cerevisiae PPR proteins localize in the mitochondrion and are a part of the RNA processing interaction network. Furthermore, the yeast PPR proteins seem to undergo an accelerated divergent evolution. Analysis of single and double amino acid substitutions in the Dmr1 protein of S. cerevisiae suggests that cooperative interactions between motifs and pseudoreversion could be the force driving this rapid evolution.}, }
@article {pmid21543229, year = {2011}, author = {Rheubert, JL and Siegel, DS and Venable, KJ and Sever, DM and Gribbins, KM}, title = {Ultrastructural description of spermiogenesis within the Mediterranean Gecko, Hemidactylus turcicus (Squamata: Gekkonidae).}, journal = {Micron (Oxford, England : 1993)}, volume = {42}, number = {7}, pages = {680-690}, doi = {10.1016/j.micron.2011.03.006}, pmid = {21543229}, issn = {1878-4291}, mesh = {Acrosome/*ultrastructure ; Animals ; Cytoplasm/metabolism ; DNA/metabolism ; Lizards/*anatomy &amp; histology ; Male ; Microscopy, Electron, Transmission ; Microtubules/metabolism ; Mitochondria ; Sertoli Cells/metabolism ; Spermatids/*ultrastructure ; *Spermatogenesis ; Spermatozoa/*ultrastructure ; }, abstract = {We studied spermiogenesis in the Mediterranean Gecko, Hemidactylus turcicus, at the electron microscope level and compared to what is known within other Lepidosaurs. In H. turcicus germ cells are connected via cytoplasmic bridges where organelle and cytoplasm sharing is observed. The acrosome develops from merging transport vesicles that arise from the Golgi and subsequently partition into an acrosomal cap containing an acrosomal cortex, acrosomal medulla, perforatorium, and subacrosomal cone. Condensation of DNA occurs in a spiral fashion and elongation is aided by microtubules of the manchette. A nuclear rostrum extends into the subacrosomal cone and is capped by an epinuclear lucent zone. Mitochondria and rough endoplasmic reticulum migrate to the posterior portion of the developing germ cell during the cytoplasmic shift and the flagellum elongates. Mitochondria surround the midpiece as the anlage of the annulus forms. The fibrous sheath begins at mitochondrial tier 3 and continues into the principal piece. Peripheral fibers associated with microtubule doublets 3 and 8 are grossly enlarged. During the final stages of germ cell development spermatids are wrapped with a series of Sertoli cell processes, which exhibit ectoplasmic specializations and differing cytoplasmic consistencies. The results observed here corroborate previous studies, which show the conservative nature of sperm morphology. However, ultrastructural character combinations specific to sperm and spermiogenesis seem to differ among taxa. Further studies into sperm morphology are needed in order to judge the relevance of the ontogenic changes recorded here and to determine their role in future studies on amniote evolution.}, }
@article {pmid21535276, year = {2011}, author = {Agudo, R and Alcaide, M and Rico, C and Lemus, JA and Blanco, G and Hiraldo, F and Donázar, JA}, title = {Major histocompatibility complex variation in insular populations of the Egyptian vulture: inferences about the roles of genetic drift and selection.}, journal = {Molecular ecology}, volume = {20}, number = {11}, pages = {2329-2340}, doi = {10.1111/j.1365-294X.2011.05107.x}, pmid = {21535276}, issn = {1365-294X}, mesh = {Alleles ; Amino Acid Sequence ; Amino Acid Substitution/genetics ; Animals ; Birds/*genetics ; Crosses, Genetic ; Egypt ; Female ; Gene Frequency/genetics ; *Genetic Drift ; Genetic Loci/genetics ; *Genetic Variation ; Genotype ; *Geography ; Major Histocompatibility Complex/*genetics ; Male ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Polymorphism, Genetic ; Population Dynamics ; *Selection, Genetic ; Sequence Alignment ; }, abstract = {Insular populations have attracted the attention of evolutionary biologists because of their morphological and ecological peculiarities with respect to their mainland counterparts. Founder effects and genetic drift are known to distribute neutral genetic variability in these demes. However, elucidating whether these evolutionary forces have also shaped adaptive variation is crucial to evaluate the real impact of reduced genetic variation in small populations. Genes of the major histocompatibility complex (MHC) are classical examples of evolutionarily relevant loci because of their well-known role in pathogen confrontation and clearance. In this study, we aim to disentangle the partial roles of genetic drift and natural selection in the spatial distribution of MHC variation in insular populations. To this end, we integrate the study of neutral (22 microsatellites and one mtDNA locus) and MHC class II variation in one mainland (Iberia) and two insular populations (Fuerteventura and Menorca) of the endangered Egyptian vulture (Neophron percnopterus). Overall, the distribution of the frequencies of individual MHC alleles (n=17 alleles from two class II B loci) does not significantly depart from neutral expectations, which indicates a prominent role for genetic drift over selection. However, our results point towards an interesting co-evolution of gene duplicates that maintains different pairs of divergent alleles in strong linkage disequilibrium on islands. We hypothesize that the co-evolution of genes may counteract the loss of genetic diversity in insular demes, maximize antigen recognition capabilities when gene diversity is reduced, and promote the co-segregation of the most efficient allele combinations to cope with local pathogen communities.}, }
@article {pmid21533994, year = {2011}, author = {Perina, D and Bosnar, MH and Mikoč, A and Müller, WE and Cetković, H}, title = {Characterization of Nme6-like gene/protein from marine sponge Suberites domuncula.}, journal = {Naunyn-Schmiedeberg's archives of pharmacology}, volume = {384}, number = {4-5}, pages = {451-460}, pmid = {21533994}, issn = {1432-1912}, mesh = {Animals ; Base Sequence ; Escherichia coli/genetics ; *Evolution, Molecular ; HeLa Cells ; Humans ; Introns/genetics ; Microscopy, Confocal ; Molecular Sequence Data ; NM23 Nucleoside Diphosphate Kinases/*chemistry/genetics/metabolism ; Protein Structure, Secondary ; Subcellular Fractions ; Suberites/*enzymology/*genetics/ultrastructure ; Transfection ; }, abstract = {Nucleoside diphosphate kinases (NDPKs) are evolutionarily conserved enzymes involved in many biological processes such as metastasis, proliferation, development, differentiation, ciliary functions, vesicle transport and apoptosis in vertebrates. Biochemical mechanisms of these processes are still largely unknown. Sponges (Porifera) are simple metazoans without tissues, closest to the common ancestor of all animals. They changed little during evolution and probably provide the best insight into the metazoan ancestors' genomic features. The purpose of this study was to address structural and functional properties of group II Nme6 gene/protein ortholog from the marine sponge Suberites domuncula, Nme6, in order to elucidate its evolutionary history. Sponge Nme6 gene and promoter were sequenced and analysed with various bioinformatical tools. Nme6 and Nme6Δ31 proteins were produced in E. coli strain BL21 and NDPK activity was measured using a coupled pyruvate kinase-lactate dehydrogenase assay. Subcellular localization in human tumour cells was examined by confocal scanning microscopy. Our results show that the sponge Nme6 compared to human Nme6 does not possess NDPK activity, does not localize in mitochondria at least in human cells although it has a putative mitochondrial signal sequence, lacks two recent introns that comprise miRNAs and have different transcriptional binding sites in the promoter region. Therefore, we conclude that the structure of Nme6 gene has changed during metazoan evolution possibly in correlation with the function of the protein.}, }
@article {pmid21533097, year = {2011}, author = {Agapakis, CM and Niederholtmeyer, H and Noche, RR and Lieberman, TD and Megason, SG and Way, JC and Silver, PA}, title = {Towards a synthetic chloroplast.}, journal = {PloS one}, volume = {6}, number = {4}, pages = {e18877}, pmid = {21533097}, issn = {1932-6203}, support = {T32 GM080177/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/genetics ; Base Sequence ; *Chloroplasts ; DNA/genetics ; DNA Primers ; Evolution, Molecular ; Genetic Engineering ; Macrophages/microbiology ; Photosynthesis ; Plasmids ; Synechococcus/genetics/growth &amp; development/*physiology ; Zebrafish/embryology ; }, abstract = {BACKGROUND: The evolution of eukaryotic cells is widely agreed to have proceeded through a series of endosymbiotic events between larger cells and proteobacteria or cyanobacteria, leading to the formation of mitochondria or chloroplasts, respectively. Engineered endosymbiotic relationships between different species of cells are a valuable tool for synthetic biology, where engineered pathways based on two species could take advantage of the unique abilities of each mutualistic partner.<br><br>RESULTS: We explored the possibility of using the photosynthetic bacterium Synechococcus elongatus PCC 7942 as a platform for studying evolutionary dynamics and for designing two-species synthetic biological systems. We observed that the cyanobacteria were relatively harmless to eukaryotic host cells compared to Escherichia coli when injected into the embryos of zebrafish, Danio rerio, or taken up by mammalian macrophages. In addition, when engineered with invasin from Yersinia pestis and listeriolysin O from Listeria monocytogenes, S. elongatus was able to invade cultured mammalian cells and divide inside macrophages.<br><br>CONCLUSION: Our results show that it is possible to engineer photosynthetic bacteria to invade the cytoplasm of mammalian cells for further engineering and applications in synthetic biology. Engineered invasive but non-pathogenic or immunogenic photosynthetic bacteria have great potential as synthetic biological devices.}, }
@article {pmid21533077, year = {2011}, author = {Moreno-Loshuertos, R and Ferrín, G and Acín-Pérez, R and Gallardo, ME and Viscomi, C and Pérez-Martos, A and Zeviani, M and Fernández-Silva, P and Enríquez, JA}, title = {Evolution meets disease: penetrance and functional epistasis of mitochondrial tRNA mutations.}, journal = {PLoS genetics}, volume = {7}, number = {4}, pages = {e1001379}, pmid = {21533077}, issn = {1553-7404}, mesh = {Alleles ; Animals ; Cell Line ; Cloning, Molecular ; *Epistasis, Genetic ; *Evolution, Molecular ; Humans ; Mice ; Mice, Inbred BALB C ; Mitochondria/*genetics/metabolism ; Mutation ; Oxidative Phosphorylation ; Protein Folding ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Transfer, Ile/*genetics/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {About half of the mitochondrial DNA (mtDNA) mutations causing diseases in humans occur in tRNA genes. Particularly intriguing are those pathogenic tRNA mutations than can reach homoplasmy and yet show very different penetrance among patients. These mutations are scarce and, in addition to their obvious interest for understanding human pathology, they can be excellent experimental examples to model evolution and fixation of mitochondrial tRNA mutations. To date, the only source of this type of mutations is human patients. We report here the generation and characterization of the first mitochondrial tRNA pathological mutation in mouse cells, an m.3739G>A transition in the mitochondrial mt-Ti gene. This mutation recapitulates the molecular hallmarks of a disease-causing mutation described in humans, an m.4290T>C transition affecting also the human mt-Ti gene. We could determine that the pathogenic molecular mechanism, induced by both the mouse and the human mutations, is a high frequency of abnormal folding of the tRNA(Ile) that cannot be charged with isoleucine. We demonstrate that the cells harboring the mouse or human mutant tRNA have exacerbated mitochondrial biogenesis triggered by an increase in mitochondrial ROS production as a compensatory response. We propose that both the nature of the pathogenic mechanism combined with the existence of a compensatory mechanism can explain the penetrance pattern of this mutation. This particular behavior can allow a scenario for the evolution of mitochondrial tRNAs in which the fixation of two alleles that are individually deleterious can proceed in two steps and not require the simultaneous mutation of both.}, }
@article {pmid21527419, year = {2011}, author = {Chauveau, O and Eggers, L and Raquin, C and Silvério, A and Brown, S and Couloux, A and Cruaud, C and Kaltchuk-Santos, E and Yockteng, R and Souza-Chies, TT and Nadot, S}, title = {Evolution of oil-producing trichomes in Sisyrinchium (Iridaceae): insights from the first comprehensive phylogenetic analysis of the genus.}, journal = {Annals of botany}, volume = {107}, number = {8}, pages = {1287-1312}, pmid = {21527419}, issn = {1095-8290}, mesh = {Animals ; Bayes Theorem ; Bees/*physiology ; *Biological Evolution ; DNA, Plant/chemistry/genetics ; Flowers/*metabolism ; Genes, Plant/genetics ; Geography ; Iridaceae/*classification/*genetics/metabolism ; Likelihood Functions ; Mitochondria/genetics ; North America ; Phylogeny ; Plant Oils/*metabolism ; Plastids/genetics ; Pollination ; Sequence Alignment ; South America ; }, abstract = {BACKGROUND AND AIMS: Sisyrinchium (Iridaceae: Iridoideae: Sisyrinchieae) is one of the largest, most widespread and most taxonomically complex genera in Iridaceae, with all species except one native to the American continent. Phylogenetic relationships within the genus were investigated and the evolution of oil-producing structures related to specialized oil-bee pollination examined.<br><br>METHODS: Phylogenetic analyses based on eight molecular markers obtained from 101 Sisyrinchium accessions representing 85 species were conducted in the first extensive phylogenetic analysis of the genus. Total evidence analyses confirmed the monophyly of the genus and retrieved nine major clades weakly connected to the subdivisions previously recognized. The resulting phylogenetic hypothesis was used to reconstruct biogeographical patterns, and to trace the evolutionary origin of glandular trichomes present in the flowers of several species.<br><br>KEY RESULTS AND CONCLUSIONS: Glandular trichomes evolved three times independently in the genus. In two cases, these glandular trichomes are oil-secreting, suggesting that the corresponding flowers might be pollinated by oil-bees. Biogeographical patterns indicate expansions from Central America and the northern Andes to the subandean ranges between Chile and Argentina and to the extended area of the Paran&#xe1; river basin. The distribution of oil-flower species across the phylogenetic trees suggests that oil-producing trichomes may have played a key role in the diversification of the genus, a hypothesis that requires future testing.}, }
@article {pmid21526402, year = {2012}, author = {Sýkorová, Z and Börstler, B and Zvolenská, S and Fehrer, J and Gryndler, M and Vosátka, M and Redecker, D}, title = {Long-term tracing of Rhizophagus irregularis isolate BEG140 inoculated on Phalaris arundinacea in a coal mine spoil bank, using mitochondrial large subunit rDNA markers.}, journal = {Mycorrhiza}, volume = {22}, number = {1}, pages = {69-80}, pmid = {21526402}, issn = {1432-1890}, mesh = {Base Sequence ; Coal Mining ; Czech Republic ; DNA, Fungal/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/*genetics ; Genetic Markers ; Glomeromycota/*genetics/isolation &amp; purification/physiology ; Haplotypes ; Mitochondria/*genetics ; Molecular Sequence Data ; Mycorrhizae/genetics/*isolation &amp; purification/physiology ; Phalaris/*microbiology/physiology ; Phylogeny ; Plant Roots/microbiology ; Polymerase Chain Reaction/methods ; Sequence Alignment ; Sequence Analysis, DNA ; Soil Microbiology ; Symbiosis ; }, abstract = {During the last decade, the application of arbuscular mycorrhizal fungi (AMF) as bioenhancers has increased significantly. However, until now, it has been difficult to verify the inoculation success in terms of fungal symbiont establishment in roots of inoculated plants because specific fungal strains could not be detected within colonized roots. Using mitochondrial large subunit ribosomal DNA, we show that Rhizophagus irregularis (formerly known as Glomus intraradices) isolate BEG140 consists of two different haplotypes. We developed nested PCR assays to specifically trace each of the two haplotypes in the roots of Phalaris arundinacea from a field experiment in a spoil bank of a former coal mine, where BEG140 was used as inoculant. We revealed that despite the relatively high diversity of native R. irregularis strains, R. irregularis BEG140 survived and proliferated successfully in the field experiment and was found significantly more often in the inoculated than control plots. This work is the first one to show tracing of an inoculated AMF isolate in the roots of target plants and to verify its survival and propagation in the field. These results will have implications for basic research on the ecology of AMF at the intraspecific level as well as for commercial users of mycorrhizal inoculation.}, }
@article {pmid21524706, year = {2011}, author = {Chiesa, S and Scalici, M and Negrini, R and Gibertini, G and Nonnis Marzano, F}, title = {Fine-scale genetic structure, phylogeny and systematics of threatened crayfish species complex.}, journal = {Molecular phylogenetics and evolution}, volume = {61}, number = {1}, pages = {1-11}, doi = {10.1016/j.ympev.2011.03.031}, pmid = {21524706}, issn = {1095-9513}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Animals ; Astacoidea/anatomy &amp; histology/*classification/*genetics ; Base Sequence ; DNA Fingerprinting ; DNA, Mitochondrial/*genetics ; *Endangered Species ; Evolution, Molecular ; Genetic Variation ; Genome ; Haplotypes ; Italy ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Shellfish/classification ; }, abstract = {Systematic uncertainties in the crayfish Austropotamobius pallipes are well grounded by the number of species and subspecies described using different approaches, causing scientists to define this taxon as "complex". However, a key task that conservation programmes are facing regarding the recent and drastic decline of European populations, is the coherent systematic classification of this threatened species. Here we present results obtained by coupling mtDNA and genome analysis suggestive of a novel evolutionary framework to explain the relationships among phylogenetic lineages of A. pallipes. The direct sequencing of mtDNA COI gene fragment revealed a strong geographic structure with four distinct haplogroups separated by a range of 5-25 mutations. However, mitochondrial data were not supported by genomic fingerprinting based on 535 AFLP polymorphisms. Nuclear markers showed an unexpected moderate level of genetic differentiation and the absence of any geographic structure. Consequently, this study proposes that the taxonomic hypothesis of a single species of A. pallipes settling the Italian continental waters, is affected by complex evolutionary events. To solve the paradox, we hypothesized an evolutive scenario in which the separation of ancient mtDNA lineages likely occurred before the latest glacial periods. However, the speciation process remained incomplete due to secondary intensive postglacial contacts that forced the mingling of the genomes, and confounds the phylogeographic signature still detectable within mtDNA. Postglacial dispersion and the following demographic events, such as founder effects, drift and bottlenecks, abruptly depleted the local mtDNA variation, and shaped the current genetic population structure of white-clawed crayfish.}, }
@article {pmid21524275, year = {2011}, author = {O'Leary, B and Park, J and Plaxton, WC}, title = {The remarkable diversity of plant PEPC (phosphoenolpyruvate carboxylase): recent insights into the physiological functions and post-translational controls of non-photosynthetic PEPCs.}, journal = {The Biochemical journal}, volume = {436}, number = {1}, pages = {15-34}, doi = {10.1042/BJ20110078}, pmid = {21524275}, issn = {1470-8728}, mesh = {Amino Acid Sequence ; Arabidopsis/enzymology/metabolism ; Bacterial Proteins/chemistry/metabolism ; Genetic Variation ; Mitochondria/enzymology/metabolism ; Models, Biological ; Molecular Sequence Data ; Phosphoenolpyruvate Carboxylase/*chemistry/genetics/*metabolism ; Phylogeny ; Plant Proteins/*chemistry/genetics/*metabolism ; Plants/*enzymology ; Protein Processing, Post-Translational ; }, abstract = {PEPC [PEP (phosphoenolpyruvate) carboxylase] is a tightly controlled enzyme located at the core of plant C-metabolism that catalyses the irreversible β-carboxylation of PEP to form oxaloacetate and Pi. The critical role of PEPC in assimilating atmospheric CO(2) during C(4) and Crassulacean acid metabolism photosynthesis has been studied extensively. PEPC also fulfils a broad spectrum of non-photosynthetic functions, particularly the anaplerotic replenishment of tricarboxylic acid cycle intermediates consumed during biosynthesis and nitrogen assimilation. An impressive array of strategies has evolved to co-ordinate in vivo PEPC activity with cellular demands for C(4)-C(6) carboxylic acids. To achieve its diverse roles and complex regulation, PEPC belongs to a small multigene family encoding several closely related PTPCs (plant-type PEPCs), along with a distantly related BTPC (bacterial-type PEPC). PTPC genes encode ~110-kDa polypeptides containing conserved serine-phosphorylation and lysine-mono-ubiquitination sites, and typically exist as homotetrameric Class-1 PEPCs. In contrast, BTPC genes encode larger ~117-kDa polypeptides owing to a unique intrinsically disordered domain that mediates BTPC's tight interaction with co-expressed PTPC subunits. This association results in the formation of unusual ~900-kDa Class-2 PEPC hetero-octameric complexes that are desensitized to allosteric effectors. BTPC is a catalytic and regulatory subunit of Class-2 PEPC that is subject to multi-site regulatory phosphorylation in vivo. The interaction between divergent PEPC polypeptides within Class-2 PEPCs adds another layer of complexity to the evolution, physiological functions and metabolic control of this essential CO(2)-fixing plant enzyme. The present review summarizes exciting developments concerning the functions, post-translational controls and subcellular location of plant PTPC and BTPC isoenzymes.}, }
@article {pmid21518062, year = {2011}, author = {Horne, JB and Momigliano, P and Welch, DJ and Newman, SJ and Van Herwerden, L}, title = {Limited ecological population connectivity suggests low demands on self-recruitment in a tropical inshore marine fish (Eleutheronema tetradactylum: Polynemidae).}, journal = {Molecular ecology}, volume = {20}, number = {11}, pages = {2291-2306}, doi = {10.1111/j.1365-294X.2011.05097.x}, pmid = {21518062}, issn = {1365-294X}, mesh = {Animals ; Australia ; Base Pairing/genetics ; Discriminant Analysis ; *Ecological and Environmental Phenomena ; Electron Transport Complex IV/genetics ; Gene Frequency/genetics ; Genetic Variation ; Microsatellite Repeats/genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Perciformes/*genetics ; Population Dynamics ; Principal Component Analysis ; Sample Size ; *Seawater ; *Tropical Climate ; }, abstract = {The diversity of geographic scales at which marine organisms display genetic variation mirrors the biophysical and ecological complexity of dispersal by pelagic larvae. Yet little is known about the effect of larval ecology on genetic population patterns, partly because detailed data of larval ecology do not yet exist for most taxa. One species for which this data is available is Eleutheronema tetradactylum, a tropical Indo-West Pacific shorefish. Here, we use a partial sequence mitochondrial cytochrome oxidase subunit 1 (COI) marker and five microsatellite loci to survey the genetic structure of E. tetradactylum across northern Australia. Structure was found throughout the range and isolation by distance was strong, explaining approximately 87 and 64% of the genetic variation in microsatellites and mtDNA, respectively. Populations separated by as little as 15 km also showed significant genetic structure, implying that local populations are mainly insular and self-seeding on an ecological time frame. Because the larvae of E. tetradactylum have lower swimming performance and poor orientation compared with other tropical fishes, even modest larval abilities may permit self-recruitment rather than passive dispersal.}, }
@article {pmid21515811, year = {2011}, author = {Atyame, CM and Delsuc, F and Pasteur, N and Weill, M and Duron, O}, title = {Diversification of Wolbachia endosymbiont in the Culex pipiens mosquito.}, journal = {Molecular biology and evolution}, volume = {28}, number = {10}, pages = {2761-2772}, doi = {10.1093/molbev/msr083}, pmid = {21515811}, issn = {1537-1719}, mesh = {Animals ; Cluster Analysis ; Culex/genetics/*microbiology ; DNA, Mitochondrial/genetics ; Gene Rearrangement ; Genetic Markers ; Phylogeny ; Phylogeography ; Symbiosis ; Wolbachia/*genetics ; }, abstract = {The α-proteobacteria Wolbachia are among the most common intracellular bacteria and have recently emerged as important drivers of arthropod biology. Wolbachia commonly act as reproductive parasites in arthropods by inducing cytoplasmic incompatibility (CI), a type of conditional sterility between hosts harboring incompatible infections. In this study, we examined the evolutionary histories of Wolbachia infections, known as wPip, in the common house mosquito Culex pipiens, which exhibits the greatest variation in CI crossing patterns observed in any insect. We first investigated a panel of 20 wPip strains for their genetic diversity through a multilocus scheme combining 13 Wolbachia genes. Because Wolbachia depend primarily on maternal transmission for spreading within arthropod populations, we also studied the variability in the coinherited Cx. pipiens mitochondria. In total, we identified 14 wPip haplotypes, which all share a monophyletic origin and clearly cluster into five distinct wPip groups. The diversity of Cx. pipiens mitochondria was extremely reduced, which is likely a consequence of cytoplasmic hitchhiking driven by a unique and recent Wolbachia invasion. Phylogenetic evidence indicates that wPip infections and mitochondrial DNA have codiverged through stable cotransmission within the cytoplasm and shows that a rapid diversification of wPip has occurred. The observed pattern demonstrates that a considerable degree of Wolbachia diversity can evolve within a single host species over short evolutionary periods. In addition, multiple signatures of recombination were found in most wPip genomic regions, leading us to conclude that the mosaic nature of wPip genomes may play a key role in their evolution.}, }
@article {pmid21513896, year = {2011}, author = {Heras, S and Roldán, MI}, title = {Phylogenetic inference in Odontesthes and Atherina (Teleostei: Atheriniformes) with insights into ecological adaptation.}, journal = {Comptes rendus biologies}, volume = {334}, number = {4}, pages = {273-281}, doi = {10.1016/j.crvi.2011.03.004}, pmid = {21513896}, issn = {1768-3238}, mesh = {Adaptation, Biological/*physiology ; Animals ; Classification ; Cytochromes b/genetics ; DNA/genetics ; *Environment ; Fishes/classification/*physiology ; Fresh Water ; Genetic Variation ; Haplotypes ; Mitochondria/metabolism ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Seawater ; Smegmamorpha ; Species Specificity ; }, abstract = {This contribution provides an insight into Atheriniformes systematics based on four mitochondrial regions: 12S rRNA, cytb, COI and control region (2794bp in total). In the Atherinopsoidei (New World silversides), comparisons among five species of Odontesthes, O. argentinensis, O. bonariensis, O. smitti, O. hatcheri and O. incisa revealed a putative marine-freshwater pairing pattern of Odontesthes species, possibly driven by sea level fluctuations of South American waters. This study represents the first data on molecular phylogeny of Odontesthes species that can be of usefulness to biodiversity conservation policies. In the Atherinoidei (Old World silversides), Atherina boyeri was corroborated as a species complex constituted by a marine form, a marine with dark spots form and a brackish form. Concretely, Odontesthes and Atherina may represent geographically replicated models to study genetic adaptation and speciation of marine species to brackish and freshwater habitats. In addition, phylogenetic analyses supported Odontesthes and Atherina as monophyletic taxa and their separation into two differentiated suborders Atherinopsoidei and Atherinoidei, respectively.}, }
@article {pmid21513775, year = {2012}, author = {Bayram-Weston, Z and Jones, L and Dunnett, SB and Brooks, SP}, title = {Light and electron microscopic characterization of the evolution of cellular pathology in HdhQ92 Huntington's disease knock-in mice.}, journal = {Brain research bulletin}, volume = {88}, number = {2-3}, pages = {171-181}, doi = {10.1016/j.brainresbull.2011.03.013}, pmid = {21513775}, issn = {1873-2747}, support = {G1001257/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Brain/metabolism/*pathology ; Disease Models, Animal ; Female ; Gene Knock-In Techniques ; Glial Fibrillary Acidic Protein/genetics/metabolism ; Huntingtin Protein ; Huntington Disease/genetics/metabolism/*pathology ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Microscopy, Electron ; Nerve Tissue Proteins/genetics/*metabolism ; Neurons/metabolism/*ultrastructure ; Nuclear Proteins/genetics/*metabolism ; }, abstract = {Huntington's disease (HD) is a fatally progressive neurodegenerative disease that is characterized anatomically by the abnormal accumulation of fragments of mutant huntingtin protein, within the glia and neurons of the brain. Several genetic (transgenic and knock-in) animal models have been established to mimic human HD. None of these models represent all of the elements of the human disease, but they provide an opportunity to understand the processes of the disease and aid in the development of therapeutic strategies. In this study, the Hdh(Q92) mouse model of Huntington's disease was analysed at different time points across the lifespan of the animal. At 4 months of age, Hdh(Q92/Q92) mice showed dense nuclear staining and nuclear inclusions in the olfactory tubercle and striatum with the mutant N-terminal antibody S830. Widespread formation of mutant huntingtin aggregates in the neuronal nuclei and cytosol increased in number with age and disease progression. Electron microscopy revealed that at 14 and at 21 months of age neurons showed the features of both necrotic and apoptotic cell death, such as irregular nuclear and cytoplasmic membranes, dark condensed nuclei, vacuolated cytoplasm, and swollen mitochondria. The spatial spread of NIIs progressed along the anterior-posterior and ventral-dorsal planes. Our detailed analyses of the Hdh(Q92) mouse line demonstrated a progressive and marked early focal striatal pathology with later widespread neuronal changes, including cellular degeneration, mutant protein aggregation and inclusion formation. We have demonstrated that the distribution of intra- and extra nuclear inclusions in this animal model expresses many features similar to the human pathology.}, }
@article {pmid21511013, year = {2012}, author = {Bayram-Weston, Z and Torres, EM and Jones, L and Dunnett, SB and Brooks, SP}, title = {Light and electron microscopic characterization of the evolution of cellular pathology in the Hdh(CAG)150 Huntington's disease knock-in mouse.}, journal = {Brain research bulletin}, volume = {88}, number = {2-3}, pages = {189-198}, doi = {10.1016/j.brainresbull.2011.03.014}, pmid = {21511013}, issn = {1873-2747}, support = {G1001257/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Cerebral Cortex/metabolism/pathology/ultrastructure ; Corpus Striatum/metabolism/pathology/ultrastructure ; Disease Models, Animal ; Female ; Gene Knock-In Techniques ; Glial Fibrillary Acidic Protein/genetics/metabolism ; Huntingtin Protein ; Huntington Disease/genetics/metabolism/*pathology ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Microscopy, Electron ; Nerve Tissue Proteins/genetics/*metabolism ; Neurons/metabolism/*ultrastructure ; Nuclear Proteins/genetics/*metabolism ; }, abstract = {Huntington's disease is an autosomal dominant, progressive neurodegenerative disease in which a single mutation in the gene responsible for the protein huntingtin leads to a primarily striatal and cortical neuronal loss, resulting progressive motor, cognitive and psychiatric disability and ultimately death. The mutation induces an abnormal protein accumulation within cells, although the precise role of this accumulation in the disease process is unknown. Several animal models have been created to model the disease. In the present study, the pathology of the Hdh(CAG(150)) mouse model was analyzed longitudinally over 24 months. At 5 months of age, the mutant N-terminal antibody S830 found dense nuclear staining and nuclear inclusions in the olfactory tubercle and striatum of the Hdh(Q150/Q150) mice. Nuclear inclusions increased in number and size with age and disease progression, and spread in ventral to dorsal, and anterior to posterior pattern. Electron microscopy observations at 14 months of age revealed that the neurons showed a normal nucleus having a circular shape and regular membranes in a densely packed cytoplasm, whereas by 21 months the cytoplasm was vacuolated and contained swollen mitochondria with many degenerated cytoplasmic organelles. Immunogold labelling of the S830 antibody was found to be specifically localised to the inner area of the neuronal intra-nuclear inclusions. Our data demonstrate a marked and progressive cellular phenotype that begins at 5 months of age and progresses with time. The pathology the Hdh(Q150/Q150) line was focused on the striatum and cortex until the late stage of the disease, consistent with the human condition.}, }
@article {pmid21505865, year = {2011}, author = {Barrero-Sicilia, C and Hernando-Amado, S and González-Melendi, P and Carbonero, P}, title = {Structure, expression profile and subcellular localisation of four different sucrose synthase genes from barley.}, journal = {Planta}, volume = {234}, number = {2}, pages = {391-403}, pmid = {21505865}, issn = {1432-2048}, mesh = {Anaerobiosis ; Cell Membrane/metabolism ; Cold Temperature ; Cytoplasm/metabolism ; DNA, Complementary/chemistry/genetics ; Droughts ; Gene Expression Regulation, Plant/genetics ; Germination ; Glucosyltransferases/chemistry/genetics/*metabolism ; Hordeum/*genetics/*metabolism/ultrastructure ; Isoenzymes/chemistry/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Plant Leaves/genetics/metabolism ; Plant Proteins/chemistry/genetics/metabolism ; RNA, Plant/genetics/isolation &amp; purification ; Recombinant Fusion Proteins ; Seeds/genetics/metabolism ; Sodium Chloride/pharmacology ; Stress, Physiological ; Sucrose/metabolism ; Water/metabolism ; }, abstract = {Genes encoding two new isoforms of sucrose synthase from barley, HvSs3 and HvSs4, have been characterised and their expression patterns compared with those previously described for HvSs1 and HvSs2, in different organs and during seed maturation and germination. Their response to several abiotic stimuli has also been investigated in leaves: HvSs1 is up-regulated by anoxia and HvSs3 by water deprivation while no response is observed to 150 mM NaCl treatment; HvSs1 and HvSs3 are also induced by cold temperatures. Using translational fusions and transient expression analyses, the four isozymes have been localised not only to the cytoplasm but also along several cytoplasmic tracks and at the inner side of the cell membrane; besides, HvSS1 is also associated with mitochondria, a localisation that has been predicted in silico with the TargetP and Predotar programmes. These data suggest distinct although partially overlapping roles, for the four barley sucrose synthase isoforms, in the channelling of carbon towards different metabolic pathways within the cell.}, }
@article {pmid21504868, year = {2011}, author = {Smathers, RL and Petersen, DR}, title = {The human fatty acid-binding protein family: evolutionary divergences and functions.}, journal = {Human genomics}, volume = {5}, number = {3}, pages = {170-191}, pmid = {21504868}, issn = {1479-7364}, support = {F31 AA018898/AA/NIAAA NIH HHS/United States ; R37AA09300/AA/NIAAA NIH HHS/United States ; 5 F31 AA018898-02/AA/NIAAA NIH HHS/United States ; R01 DK074487-01/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Caenorhabditis elegans/genetics/metabolism ; Drosophila melanogaster/genetics/metabolism ; *Evolution, Molecular ; Fatty Acid-Binding Proteins/*genetics/*metabolism ; Genome, Human ; Humans ; Mice ; Molecular Sequence Data ; *Multigene Family ; Protein Structure, Tertiary ; Species Specificity ; }, abstract = {Fatty acid-binding proteins (FABPs) are members of the intracellular lipid-binding protein (iLBP) family and are involved in reversibly binding intracellular hydrophobic ligands and trafficking them throughout cellular compartments, including the peroxisomes, mitochondria, endoplasmic reticulum and nucleus. FABPs are small, structurally conserved cytosolic proteins consisting of a water-filled, interior-binding pocket surrounded by ten anti-parallel beta sheets, forming a beta barrel. At the superior surface, two alpha-helices cap the pocket and are thought to regulate binding. FABPs have broad specificity, including the ability to bind long-chain (C16-C20) fatty acids, eicosanoids, bile salts and peroxisome proliferators. FABPs demonstrate strong evolutionary conservation and are present in a spectrum of species including Drosophila melanogaster, Caenorhabditis elegans, mouse and human. The human genome consists of nine putatively functional protein-coding FABP genes. The most recently identified family member, FABP12, has been less studied.}, }
@article {pmid21498600, year = {2011}, author = {Sun, S and Evans, BJ and Golding, GB}, title = {"Patchy-tachy" leads to false positives for recombination.}, journal = {Molecular biology and evolution}, volume = {28}, number = {9}, pages = {2549-2559}, doi = {10.1093/molbev/msr076}, pmid = {21498600}, issn = {1537-1719}, mesh = {Animals ; Computer Simulation ; DNA, Mitochondrial/*genetics ; Linkage Disequilibrium ; Mitochondria/genetics ; Models, Genetic ; *Mutation Rate ; *Recombination, Genetic ; }, abstract = {Indirect tests have detected recombination in mitochondrial DNA (mtDNA) from many animal lineages, including mammals. However, it is possible that features of the molecular evolutionary process without recombination could be incorrectly inferred by indirect tests as being due to recombination. We have identified one such example, which we call "patchy-tachy" (PT), where different partitions of sequences evolve at different rates, that leads to an excess of false positives for recombination inferred by indirect tests. To explore this phenomena, we characterized the false positive rates of six widely used indirect tests for recombination using simulations of general models for mtDNA evolution with PT but without recombination. All tests produced 30-99% false positives for recombination, although the conditions that produced the maximal level of false positives differed between the tests. To evaluate the degree to which conditions that exacerbate false positives are found in published sequence data, we turned to 20 animal mtDNA data sets in which recombination is suggested by indirect tests. Using a model where different regions of the sequences were free to evolve at different rates in different lineages, we demonstrated that PT is prevalent in many data sets in which recombination was previously inferred using indirect tests. Taken together, our results argue that PT without recombination is a viable alternative explanation for detection of widespread recombination in animal mtDNA using indirect tests.}, }
@article {pmid21497133, year = {2011}, author = {Yamaguchi, H and Nakayama, T and Kai, A and Inouye, I}, title = {Taxonomy and phylogeny of a new kleptoplastidal dinoflagellate, Gymnodinium myriopyrenoides sp. nov. (Gymnodiniales, Dinophyceae), and its cryptophyte symbiont.}, journal = {Protist}, volume = {162}, number = {4}, pages = {650-667}, doi = {10.1016/j.protis.2011.01.002}, pmid = {21497133}, issn = {1618-0941}, mesh = {Cluster Analysis ; Cryptophyta/*classification/genetics/isolation &amp; purification/physiology ; DNA, Ribosomal/chemistry/genetics ; Dinoflagellida/*classification/cytology/genetics/*parasitology ; Microscopy ; Organelles ; Phylogeny ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {A new kleptoplastidal dinoflagellate, Gymnodinium myriopyrenoides sp. nov., was described using light microscopy, electron microscopy and phylogengetic analysis based on partial LSU rDNA sequences. Cells were dorsiventrally flattened, elongate-elliptical in ventral view. There was no displacement of the cingulum encircling the anterior part of the cell. The cingulum was curved posteriorly at the terminal junction with the sulcus. The sulcus was generally narrow but expanded in the posterior end. The epicone possessed an apical groove made of one and one-half counterclockwise revolutions. Phylogenetic analysis based on LSU rDNA showed that the sequence of G. myriopyrenoides was included in the Gymnodiniales sensu stricto clade and had special affinities with the species Amphidinium poecilochroum and Gymnodinium acidotum, which also harbor kleptochloroplasts. Phylogenetic analysis based on plastid-encoded SSU rDNA and ultrastructural observations suggested that the symbionts of G. myriopyrenoides were cryptophytes of the genus Chroomonas or Hemiselmis. Organelles including the nucleus, the nucleomorph, mitochondria, Golgi bodies and large chloroplasts remained in the cytoplasm of the symbionts, but not the periplast, ejectosomes or flagellar apparatus. The symbiotic level of G. myriopyrenoides was estimated to be a relatively early stage in the unarmored kleptoplastidal dinoflagellates.}, }
@article {pmid21497132, year = {2012}, author = {Ota, S and Vaulot, D}, title = {Lotharella reticulosa sp. nov.: a highly reticulated network forming chlorarachniophyte from the Mediterranean Sea.}, journal = {Protist}, volume = {163}, number = {1}, pages = {91-104}, doi = {10.1016/j.protis.2011.02.004}, pmid = {21497132}, issn = {1618-0941}, mesh = {Cercozoa/classification/genetics/*growth &amp; development/*isolation &amp; purification ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Mediterranean Sea ; Molecular Sequence Data ; Phylogeny ; Seawater/*parasitology ; }, abstract = {A new chlorarachniophyte Lotharella reticulosa sp. nov. is described from a culture isolated from the Mediterranean Sea. This strain is maintained as strain RCC375 at the Roscoff Culture Collection, France. This species presents a multiphasic life cycle: vegetative cells of this species were observed to be coccoid, but amoeboid cells with filopodia and globular suspended cells were also present in the life cycle, both of which were not dominant phases. Flagellate cells were also observed but remained very rare in culture. The vegetative cells were 9-16 μm in diameter and highly vacuolated, containing several green chloroplasts with a projecting pyrenoid, mitochondria, and a nucleus. The chloroplast was surrounded by four membranes possessing a nucleomorph in the periplastidial compartment near the pyrenoid base. According to ultrastructural observations of the pyrenoid and nucleomorph, the present species belongs to the genus Lotharella in the phylum Chlorarachniophyta. This taxonomic placement is consistent with the molecular phylogenetic trees of the 18S rRNA gene and ITS sequences. This species showed a unique colonization pattern. Clusters of cells extended cytoplasmic strands radially. Then, amoeboid cells being born proximately moved distally along the cytoplasmic strand like on a "railway track". Subsequently the amoeboid cell became coccoid near the strand. In this way, daughter cells were dispersed evenly on the substratum. We also observed that the present species regularly formed a structure of filopodial nodes in mid-stage and later-stage cultures, which is a novel phenotype in chlorarachniophytes. The unique colonization pattern and other unique features demonstrate that RCC375 is a new chlorarachniophyte belonging to genus Lotharella, which we describe as Lotharella reticulosa sp. nov.}, }
@article {pmid21494602, year = {2011}, author = {Sørmo, CG and Brembu, T and Winge, P and Bones, AM}, title = {Arabidopsis thaliana MIRO1 and MIRO2 GTPases are unequally redundant in pollen tube growth and fusion of polar nuclei during female gametogenesis.}, journal = {PloS one}, volume = {6}, number = {4}, pages = {e18530}, pmid = {21494602}, issn = {1932-6203}, mesh = {Alleles ; Arabidopsis/embryology/*enzymology/genetics/growth &amp; development ; Arabidopsis Proteins/genetics/*metabolism ; Cell Nucleus/*enzymology ; Chromosome Segregation/genetics ; DNA, Bacterial/genetics ; Evolution, Molecular ; GTP Phosphohydrolases/genetics/*metabolism ; *Gametogenesis ; Gene Expression Profiling ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Microfilament Proteins/genetics/*metabolism ; Mutation/genetics ; Organ Size ; Phylogeny ; Pollen Tube/*enzymology/*growth &amp; development ; Seeds/anatomy &amp; histology/embryology ; Tissue Survival ; }, abstract = {MIRO GTPases have evolved to regulate mitochondrial trafficking and morphology in eukaryotic organisms. A previous study showed that T-DNA insertion in the Arabidopsis MIRO1 gene is lethal during embryogenesis and affects pollen tube growth and mitochondrial morphology in pollen, whereas T-DNA insertion in MIRO2 does not affect plant development visibly. Phylogenetic analysis of MIRO from plants revealed that MIRO 1 and 2 orthologs in dicots cluster in two separate groups due to a gene/genome duplication event, suggesting that functional redundancy may exists between the two MIRO genes. To investigate this possibility, we generated miro1(+/-)/miro2-2(-/-) plants. Compared to miro1(+/-) plants, the miro1(+/-)/miro2-2(-/-) plants showed increased segregation distortion. miro1(+/-)/miro2-2(-/-) siliques contained less aborted seeds, but more than 3 times the number of undeveloped ovules. In addition, reciprocal crosses showed that co-transmission through the male gametes was nearly absent, whereas co-transmission through the female gametes was severely reduced in miro1(+/-)/miro2-2(-/-) plants. Further investigations revealed that loss of MIRO2 (miro2(-/-)) function in the miro1(+/-) background enhanced pollen tube growth defects. In developing miro1(+/-)/miro2(-/-) embryo sacs, fusion of polar nuclei was further delayed or impaired compared to miro1 plants. This phenotype has not been reported previously for miro1 plants and coincides with studies showing that defects in some mitochondria-targeted genes results in the same phenotype. Our observations show that loss of function in MIRO2 in a miro1(+/-) background enhances the miro1(+/-) phenotype significantly, even though miro2(-/-) plants alone does not display any phenotypes. Based on these findings, we conclude that MIRO1 and MIRO2 are unequally redundant and that a proportion of the miro1(+/-)/miro2(-/-) plants haploid gametes displays the complete null phenotype of MIRO GTPase function at key developmental stages.}, }
@article {pmid21491374, year = {2011}, author = {Ang, KC and Leow, JW and Yeap, WK and Hood, S and Mahani, MC and Md-Zain, BM}, title = {Phylogenetic relationships of the Orang Asli and Iban of Malaysia based on maternal markers.}, journal = {Genetics and molecular research : GMR}, volume = {10}, number = {2}, pages = {640-649}, doi = {10.4238/vol10-2gmr1011}, pmid = {21491374}, issn = {1676-5680}, mesh = {Base Sequence ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Female ; Genetic Markers ; Humans ; Malaysia/ethnology ; Male ; Mitochondria/genetics ; *Phylogeny ; Phylogeography ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Malaysia remains as a crossroad of different cultures and peoples, and it has long been recognized that studying its population history can provide crucial insight into the prehistory of Southeast Asia as a whole. The earliest inhabitants were the Orang Asli in Peninsular Malaysia and the indigenous groups in Sabah and Sarawak. Although they were the earliest migrants in this region, these tribes are divided geographically by the South China Sea. We analyzed DNA sequences of 18 Orang Asli using mitochondrial DNA extracted from blood samples, each representing one sub-tribe, and from five Sarawakian Iban. Mitochondrial DNA was extracted from hair samples in order to examine relationships with the main ethnic groups in Malaysia. The D-loop region and cytochrome b genes were used as the candidate loci. Phylogenetic relationships were investigated using maximum parsimony and neighbor joining algorithms, and each tree was subjected to bootstrap analysis with 1000 replicates. Analyses of the HVS I region showed that the Iban are not a distinct group from the Orang Asli; they form a sub-clade within the Orang Asli. Based on the cytochrome b gene, the Iban clustered with the Orang Asli in the same clade. We found evidence for considerable gene flow between Orang Asli and Iban. We concluded that the Orang Asli, Iban and the main ethnic groups of Malaysia are probably derived from a common ancestor. This is in agreement with a single-route migration theory, but it does not dismiss a two-route migration theory.}, }
@article {pmid21485362, year = {2011}, author = {Demari-Silva, B and Vesgueiro, FT and Sallum, MA and Marrelli, MT}, title = {Taxonomic and phylogenetic relationships between species of the genus Culex (Diptera: culicidae) from Brazil inferred from the cytochrome c oxidase I mitochondrial gene.}, journal = {Journal of medical entomology}, volume = {48}, number = {2}, pages = {272-279}, doi = {10.1603/me09293}, pmid = {21485362}, issn = {0022-2585}, mesh = {Animals ; Brazil ; Culex/*enzymology/*genetics ; Electron Transport Complex IV/genetics/*metabolism ; Gene Expression Regulation, Enzymologic/physiology ; Insect Proteins/genetics/*metabolism ; Larva/enzymology/genetics ; Male ; Mitochondria/*genetics ; Phylogeny ; Protein Subunits ; Pupa/enzymology/genetics ; }, abstract = {Species of the genus Culex Linnaeus have been incriminated as the main vectors of lymphatic filariases and are important vectors of arboviruses, including West Nile virus. Sequences corresponding to a fragment of 478 bp of the cytochrome c oxidase subunit I gene, which includes part of the barcode region, of 37 individuals of 17 species of genus Culex were generated to establish relationships among five subgenera, Culex, Phenacomyia, Melanoconion, Microculex, and Carrollia, and one species of the genus Lutzia that occurs in Brazil. Bayesian methods were employed for the phylogenetic analyses. Results of sequence comparisons showed that individuals identified as Culex dolosus, Culex mollis, and Culex imitator possess high intraspecific divergence (3.1, 2.3, and 3.5%, respectively) when using the Kimura two parameters model. These differences were associated either with distinct morphological characteristics of the male genitalia or larval and pupal stages, suggesting that these may represent species complexes. The Bayesian topology suggested that the genus and subgenus Culex are paraphyletic relative to Lutzia and Phenacomyia, respectively. The cytochrome c oxidase subunit I sequences may be a useful tool to both estimate phylogenetic relationships and identify morphologically similar species of the genus Culex.}, }
@article {pmid21483757, year = {2011}, author = {Fraser, HB and Babak, T and Tsang, J and Zhou, Y and Zhang, B and Mehrabian, M and Schadt, EE}, title = {Systematic detection of polygenic cis-regulatory evolution.}, journal = {PLoS genetics}, volume = {7}, number = {3}, pages = {e1002023}, pmid = {21483757}, issn = {1553-7404}, mesh = {Adaptation, Biological/*genetics ; Animals ; Databases, Genetic ; *Evolution, Molecular ; Gene Expression Profiling ; *Gene Expression Regulation ; Growth and Development/genetics ; Locomotion/genetics ; Memory ; Mice ; Mice, Inbred C57BL ; Mitochondria/genetics ; Multifactorial Inheritance/*genetics ; Phenotype ; Quantitative Trait Loci/*genetics ; Selection, Genetic ; }, abstract = {The idea that most morphological adaptations can be attributed to changes in the cis-regulation of gene expression levels has been gaining increasing acceptance, despite the fact that only a handful of such cases have so far been demonstrated. Moreover, because each of these cases involves only one gene, we lack any understanding of how natural selection may act on cis-regulation across entire pathways or networks. Here we apply a genome-wide test for selection on cis-regulation to two subspecies of the mouse Mus musculus. We find evidence for lineage-specific selection at over 100 genes involved in diverse processes such as growth, locomotion, and memory. These gene sets implicate candidate genes that are supported by both quantitative trait loci and a validated causality-testing framework, and they predict a number of phenotypic differences, which we confirm in all four cases tested. Our results suggest that gene expression adaptation is widespread and that these adaptations can be highly polygenic, involving cis-regulatory changes at numerous functionally related genes. These coordinated adaptations may contribute to divergence in a wide range of morphological, physiological, and behavioral phenotypes.}, }
@article {pmid21479820, year = {2011}, author = {Mullineux, ST and Willows, K and Hausner, G}, title = {Evolutionary dynamics of the mS952 intron: a novel mitochondrial group II intron encoding a LAGLIDADG homing endonuclease gene.}, journal = {Journal of molecular evolution}, volume = {72}, number = {5-6}, pages = {433-449}, pmid = {21479820}, issn = {1432-1432}, mesh = {Ascomycota/classification/*genetics ; Biological Evolution ; Endonucleases/*genetics ; *Genes, Fungal ; Introns/*genetics ; Mitochondria/*genetics ; Models, Genetic ; Phylogeny ; }, abstract = {Examination of the mitochondrial small subunit ribosomal RNA (rns) gene of five species of the fungal genus Leptographium revealed that the gene has been invaded at least once at position 952 by a group II intron encoding a LAGLIDADG homing endonuclease gene. Phylogenetic analyses of the intron and homing endonuclease sequences indicated that each element in Leptographium species forms a single clade and is closely related to the group II intron/homing endonuclease gene composite element previously reported at position 952 of the mitochondrial rns gene of Cordyceps species and of Cryphonectria parasitica. The results of an intron survey of the mt rns gene of Leptographium species superimposed onto the phylogenetic analysis of the host organisms suggest that the composite element was transmitted vertically in Leptographium lundbergii. However, its stochastic distribution among strains of L. wingfieldii, L. terebrantis, and L. truncatum suggests that it has been horizontally transmitted by lateral gene transfer among these species, although the random presence of the intron may reflect multiple random loss events. A model is proposed describing the initial invasion of the group II intron in the rns gene of L. lundbergii by a LAGLIDADG homing endonuclease gene and subsequent evolution of this gene to recognize a novel DNA target site, which may now promote the mobility of the intron and homing endonuclease gene as a composite element.}, }
@article {pmid21474435, year = {2011}, author = {Pouvreau, B and Baud, S and Vernoud, V and Morin, V and Py, C and Gendrot, G and Pichon, JP and Rouster, J and Paul, W and Rogowsky, PM}, title = {Duplicate maize Wrinkled1 transcription factors activate target genes involved in seed oil biosynthesis.}, journal = {Plant physiology}, volume = {156}, number = {2}, pages = {674-686}, pmid = {21474435}, issn = {1532-2548}, mesh = {Arabidopsis/genetics ; Base Sequence ; Fatty Acids/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Genes, Duplicate/*genetics ; Genes, Plant/*genetics ; Genetic Complementation Test ; Glycolysis/genetics ; Models, Biological ; Molecular Sequence Data ; Mutation/genetics ; Phylogeny ; Plant Oils/*metabolism ; Plant Proteins/*genetics/metabolism ; Seeds/*genetics ; Transcription Factors/metabolism ; Triglycerides/biosynthesis ; Zea mays/*genetics ; }, abstract = {WRINKLED1 (WRI1), a key regulator of seed oil biosynthesis in Arabidopsis (Arabidopsis thaliana), was duplicated during the genome amplification of the cereal ancestor genome 90 million years ago. Both maize (Zea mays) coorthologs ZmWri1a and ZmWri1b show a strong transcriptional induction during the early filling stage of the embryo and complement the reduced fatty acid content of Arabidopsis wri1-4 seeds, suggesting conservation of molecular function. Overexpression of ZmWri1a not only increases the fatty acid content of the mature maize grain but also the content of certain amino acids, of several compounds involved in amino acid biosynthesis, and of two intermediates of the tricarboxylic acid cycle. Transcriptomic experiments identified 18 putative target genes of this transcription factor, 12 of which contain in their upstream regions an AW box, the cis-element bound by AtWRI1. In addition to functions related to late glycolysis and fatty acid biosynthesis in plastids, the target genes also have functions related to coenzyme A biosynthesis in mitochondria and the production of glycerol backbones for triacylglycerol biosynthesis in the cytoplasm. Interestingly, the higher seed oil content in ZmWri1a overexpression lines is not accompanied by a reduction in starch, thus opening possibilities for the use of the transgenic maize lines in breeding programs.}, }
@article {pmid22688916, year = {2011}, author = {Valenzuela, CY}, title = {Heterogeneous periodicity of drosophila mtDNA: new refutations of neutral and nearly neutral evolution.}, journal = {Biological research}, volume = {44}, number = {3}, pages = {283-293}, pmid = {22688916}, issn = {0717-6287}, mesh = {Amino Acid Sequence ; Animals ; *Base Sequence ; DNA, Mitochondrial/*genetics ; Drosophila/*genetics ; *Genetic Drift ; *Mutation Rate ; }, abstract = {We found a consistent 3-site periodicity of the X[2]9 values for the heterogeneity of the distribution of the second base in relation to the first base of dinucleotides separated by 0 (contiguous), 1, 2, 3 ... 17 (K) nucleotide sites in Drosophila mtDNA. Triplets of X[2]9 values were found where the first was over 300 and the second and third ranged between 37 and 114 (previous studies). In this study, the periodicity was significant until separation of 2011K, and a structure of deviations from randomness among dinucleotides was found. The most deviant dinucleotides were G-G, G-C and C-G for the first, second and third element of the triplet, respectively. In these three cases there were more dinucleotides observed than expected. This inter-bases correlation and periodicity may be related to the tertiary structure of circular DNA, like that of prokaryotes and mitochondria, to protect and preserve it. The mtDNA with 19.517 bp was divided into four equal segments of 4.879 bp. The fourth sub-segment presented a very low proportion of G and C, the internucleotide interaction was weaker in this sub-segment and no periodicity was found. The maintenance of this mtDNA structure and organization for millions of generations, in spite of a high recurrent mutation rate, does not support the notion of neutralism or near neutralism. The high level of internucleotide interaction and periodicity indicate that every nucleotide is co-adapted with the residual genome.}, }
@article {pmid23908782, year = {2010}, author = {Mishmar, D}, title = {The impact of darwinian evolution on medicine: the maternal side of the story.}, journal = {Rambam Maimonides medical journal}, volume = {1}, number = {1}, pages = {e0010}, pmid = {23908782}, issn = {2076-9172}, abstract = {Complex disorders are common in the human population and are caused by interplay between genetic and environmental factors. Therefore the quest for the genetic basis of such disorders has much similarity to deciphering the genetic basis of macro-evolutionary processes, such as speciation. Here I discuss conceptual connections between the principles underlying and processes occurring in disease and evolution. Special focus is given to the tremendous mitochondrial genetic variability in the population and within individuals and the impact of both types of variability on evolutionary processes and diseases.}, }
@article {pmid21669854, year = {2009}, author = {Crockford, SJ}, title = {Evolutionary roots of iodine and thyroid hormones in cell-cell signaling.}, journal = {Integrative and comparative biology}, volume = {49}, number = {2}, pages = {155-166}, doi = {10.1093/icb/icp053}, pmid = {21669854}, issn = {1557-7023}, abstract = {In vertebrates, thyroid hormones (THs, thyroxine, and triiodothyronine) are critical cell signaling molecules. THs regulate and coordinate physiology within and between cells, tissues, and whole organisms, in addition to controlling embryonic growth and development, via dose-dependent regulatory effects on essential genes. While invertebrates and plants do not have thyroid glands, many utilize THs for development, while others store iodine as TH derivatives or TH precursor molecules (iodotyrosines)-or produce similar hormones that act in analogous ways. Such common developmental roles for iodotyrosines across kingdoms suggest that a common endocrine signaling mechanism may account for coordinated evolutionary change in all multi-cellular organisms. Here, I expand my earlier hypothesis for the role of THs in vertebrate evolution by proposing a critical evolutionary role for iodine, the essential ingredient in all iodotyrosines and THs. Iodine is known to be crucial for life in many unicellular organisms (including evolutionarily ancient cyanobacteria), in part, because it acts as a powerful antioxidant. I propose that during the last 3-4 billion years, the ease with which various iodine species become volatile, react with simple organic compounds, and catalyze biochemical reactions explains why iodine became an essential constituent of life and the Earth's atmosphere-and a potential marker for the origins of life. From an initial role as membrane antioxidant and biochemical catalyst, spontaneous coupling of iodine with tyrosine appears to have created a versatile, highly reactive and mobile molecule, which over time became integrated into the machinery of energy production, gene function, and DNA replication in mitochondria. Iodotyrosines later coupled together to form THs, the ubiquitous cell-signaling molecules used by all vertebrates. Thus, due to their evolutionary history, THs, and their derivative and precursors molecules not only became essential for communicating within and between cells, tissues and organs, and for coordinating development and whole-body physiology in vertebrates, but they can also be shared between organisms from different kingdoms.}, }
@article {pmid21676810, year = {2005}, author = {David, CN and Schmidt, N and Schade, M and Pauly, B and Alexandrova, O and Böttger, A}, title = {Hydra and the evolution of apoptosis.}, journal = {Integrative and comparative biology}, volume = {45}, number = {4}, pages = {631-638}, doi = {10.1093/icb/45.4.631}, pmid = {21676810}, issn = {1540-7063}, abstract = {Programmed cell death occurs in most, if not all life forms. It is used to sculpt tissue during embryogenesis, to remove damaged cells, to protect against pathogen infection and to regulate cell numbers and tissue homeostasis. In animals cell death often occurs by a morphologically and biochemically conserved process called apoptosis. A novel group of cysteine proteases, referred to as caspases, constitute the central component of this process. Caspases are activated following the induction of apoptosis and cleave a variety of cellular substrates, thus giving rise to the characteristic morphological events of apoptosis. Apoptosis is rapid and cell corpses are removed by phagocytosis. Recent work has shown that apoptosis also occurs in Cnidaria and Porifera, thus extending the origin of this evolutionary innovation down to the first metazoan animal phyla. Here, we review several examples of the role of apoptosis in cnidarians and then summarize new results on the subcellular localization of caspases and the control of apoptosis in Hydra. We show by immuncytochemistry that caspases in Hydra are localized in mitochondria. Following induction of apoptosis caspases are released from mitochondria as proenzymes and then activated by proteolytic cleavage in the cytoplasm. We also present evidence that apoptosis in Hydra is dramatically stimulated by inhibitors of PI3-kinase. Since PI3-kinase is a central component of growth factor signaling cascades in higher metazoans, this result suggests that control of apoptosis by growth factors is also evolutionarily conserved. We speculate on the role of growth factors in the evolution of apoptosis.}, }
@article {pmid21653428, year = {2004}, author = {Chat, J and Jáuregui, B and Petit, RJ and Nadot, S}, title = {Reticulate evolution in kiwifruit (Actinidia, Actinidiaceae) identified by comparing their maternal and paternal phylogenies.}, journal = {American journal of botany}, volume = {91}, number = {5}, pages = {736-747}, doi = {10.3732/ajb.91.5.736}, pmid = {21653428}, issn = {0002-9122}, abstract = {Evolutionary relationships within Actinidia, a genus known for the contrasting mode of inheritance of its plastids and mitochondria, were studied. The phylogenetic analysis is based on chloroplast (cp) and mitochondrial (mt) restriction site and sequence data (matK, psbC-trnS, rbcL, and trnL-trnF for cpDNA; nad1-2/3 and nad4-1/2 for mtDNA). The analysis of cp sequence data confirms the hypothesis that the four currently recognized sections are not monophyletic. The detection of incongruences among phylogenies (mtDNA vs. cpDNA tree) coupled with the detection of intraspecific polymorphisms confirms some of the reticulations previously emphasized, diagnoses new hybridization/introgression events, and provides evidence for multiple origin of at least two polyploid taxa. A number of hybridization/introgression events at the diploid, tetraploid, and possibly hexaploid levels are documented. The extensive reticulate evolution undergone by Actinidia could account for the lack of clear morphological discontinuities at the species level.}, }
@article {pmid21708562, year = {1997}, author = {Dinnetz, P}, title = {Male sterility, protogyny, and pollen-pistil interference in Plantago maritima (Plantaginaceae), a wind-pollinated, self-incompatible perennial.}, journal = {American journal of botany}, volume = {84}, number = {11}, pages = {1588}, pmid = {21708562}, issn = {0002-9122}, abstract = {Evolution and maintenance of male sterility in seed plants can be explained by the maternal inheritance of mitochondria, which encode the trait, and by adaptive functions that enhance female fecundity in male-sterile compared to hermaphrodite individuals. Protogyny and male sterility can independently decrease the negative effect of pollen-pistil interference in self-incompatible species. In Plantago maritima, which possesses both traits, protogyny increases seed set in hermaphrodite individuals. This is shown both by a significantly positive association between seed set and retarded dehiscence of the anthers and by a more than 50% reduction in seed set following self-pollination. Male sterility does not seem to increase seed set further, as female and hermaphrodite plants do not differ significantly in mean seed set per capsule. Bagging experiments demonstrate strong self-incompatibility in the study populations. Hence, in P. maritima male sterility seems neither to prevent selfing nor to reduce the effect of pollen-pistil interference. Females had significantly larger stigmas than hermaphrodites, but seed set varied negatively with stigma length among females, indicating that the evolution of unisexuality in P. maritima is not due to prefertilization sex allocation. I therefore conclude that the genetical system of nucleocytoplasmic determination of gender is the main cause for maintenance of male sterility in P. maritima.}, }
@article {pmid23604306, year = {1997}, author = {Droy-Lefaix, MT}, title = {Effect of the antioxidant action of Ginkgo biloba extract (EGb 761) on aging and oxidative stress.}, journal = {Age}, volume = {20}, number = {3}, pages = {141-149}, pmid = {23604306}, abstract = {Aging is responsible for oxidative damage to DNA, protein, lipid, and other macromolecules linked to tissue alterations. The resultant damage contributes significantly to degenerative diseases, to include those of the brain, sensorial tissues, and cardiovascular system. To protect cellular components from oxyradical attack, especially lipoperoxidation, a substantial interest in the use of antioxidants has evolved. A free radical scavenger, Ginkgo biloba extract (EGb 761) may be effective in fighting the oxidative stress related to aging. Many data support the efficacy of EGb 761 in biological model systems. In aging processes, EGb 761 may ameliorate the mitochondria respiratory chain function by quenching the superoxide anion, and the hydroxyl and peroxyl radicals. It protects the brain by facilitating the uptake of neurotransmitters and by reducing ischemia-reperfusion episodes and level of apoptosis. Moreover, in sensorial tissues, EGb 761 reduces apoptosis in the olfactive bulb and in the retinal pigmented epithelium of the eye, and protects against the lipoperoxidation alteration of the retina that results in a decrease of the electroretinogram response. In the cardiovascular system, by a direct effect on oxidative low density lipoproteins, EGb 761 may decrease atherosclerosis evolution, and is shown to accelerate cardiac mechanical recovery after ischemia-reperfusion. In conclusion, the antioxidant effects of EGb 761 noted in many experimental data, may explain the therapeutic efficacy observed in clinical trials of the elderly. These beneficial properties seem in part to come from the activity of EGb 761 constituents, such as flavonoids and terpens.}, }
@article {pmid23195535, year = {1993}, author = {Sitte, P}, title = {Symbiogenetic evolution of complex cells and complex plastids.}, journal = {European journal of protistology}, volume = {29}, number = {2}, pages = {131-143}, doi = {10.1016/S0932-4739(11)80266-X}, pmid = {23195535}, issn = {0932-4739}, abstract = {It is generally accepted today that mitochondria and plastids of eukaryotic cells ("eucytes") have their phylogenetic origins in prokaryotic cells ("protocytes") that had been taken up into urkaryotic host cells as intracellular symbionts. This concept, strongly supported (among other evidence) by comparisons of rRNA and protein sequence data, has many important consequences for understanding both cellular evolution and cellular compartmentation. According to the Serial Endosymbiont Theory (SET), the eucyte came about by the formation of stable intracellular symbioses of quite different cells. The formation of such symbioses is referred to here as intertaxonic combination (ITC). In addition to mutation and genetic recombination, ITC emerges as a third progressive power in evolution. The situation can be complicated by repeated ITC. This is discussed in detail by taking the evolution of complex plastids as an example. Plastids of this kind, possessing 3 or 4 enveloping membranes instead of 2, are widespread in algae. They appear to be remnants of eukaryotic, and phototrophic, endocytobionts in phagotrophic host cells. The phylogeny of complex plastids could recently be fully reconstructed in the case of cryptomonads, and partly also in the case of Chlorarachnion.}, }
@article {pmid24248956, year = {1993}, author = {Hejl, AA and Einhellig, FA and Rasmussen, JA}, title = {Effects of juglone on growth, photosynthesis, and respiration.}, journal = {Journal of chemical ecology}, volume = {19}, number = {3}, pages = {559-568}, pmid = {24248956}, issn = {0098-0331}, abstract = {The impacts of juglone on plant growth and several other physiological functions were evaluated in this study. Juglone inhibitedLemna minor growth, chlorophyll content, and net photosynthesis at treatments between 10 and 40μM. Soybean leaf disks vacuum infiltrated with as little as 10μM juglone had reduced photosynthesis. Oxygen evolution by chloroplasts isolated fromPisum sativum was inhibited by juglone with an I50 of 2μM. Micromolar treatments of juglone stimulated oxygen uptake in mitochondria isolated fromGlycine max. These data suggest perturbations of chloroplast and mitochondrial functions may contribute to plant growth reductions observed in juglone-mediated allelopathy.}, }
@article {pmid24408574, year = {1992}, author = {Gogarten, JP and Taiz, L}, title = {Evolution of proton pumping ATPases: Rooting the tree of life.}, journal = {Photosynthesis research}, volume = {33}, number = {2}, pages = {137-146}, pmid = {24408574}, issn = {0166-8595}, abstract = {Proton pumping ATPases are found in all groups of present day organisms. The F-ATPases of eubacteria, mitochondria and chloroplasts also function as ATP synthases, i.e., they catalyze the final step that transforms the energy available from reduction/oxidation reactions (e.g., in photosynthesis) into ATP, the usual energy currency of modern cells. The primary structure of these ATPases/ATP synthases was found to be much more conserved between different groups of bacteria than other parts of the photosynthetic machinery, e.g., reaction center proteins and redox carrier complexes.These F-ATPases and the vacuolar type ATPase, which is found on many of the endomembranes of eukaryotic cells, were shown to be homologous to each other; i.e., these two groups of ATPases evolved from the same enzyme present in the common ancestor. (The term eubacteria is used here to denote the phylogenetic group containing all bacteria except the archaebacteria.) Sequences obtained for the plasmamembrane ATPase of various archaebacteria revealed that this ATPase is much more similar to the eukaryotic than to the eubacterial counterpart. The eukaryotic cell of higher organisms evolved from a symbiosis between eubacteria (that evolved into mitochondria and chloroplasts) and a host organism. Using the vacuolar type ATPase as a molecular marker for the cytoplasmic component of the eukaryotic cell reveals that this host organism was a close relative of the archaebacteria.A unique feature of the evolution of the ATPases is the presence of a non-catalytic subunit that is paralogous to the catalytic subunit, i.e., the two types of subunits evolved from a common ancestral gene. Since the gene duplication that gave rise to these two types of subunits had already occurred in the last common ancestor of all living organisms, this non-catalytic subunit can be used to root the tree of life by means of an outgroup; that is, the location of the last common ancestor of the major domains of living organisms (archaebacteria, eubacteria and eukaryotes) can be located in the tree of life without assuming constant or equal rates of change in the different branches.A correlation between structure and function of ATPases has been established for present day organisms. Implications resulting from this correlation for biochemical pathways, especially photosynthesis, that were operative in the last common ancestor and preceding life forms are discussed.}, }
@article {pmid24213342, year = {1991}, author = {Giorini, S and Galili, G}, title = {Characterization of HSP-70 cognate proteins from wheat.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {82}, number = {5}, pages = {615-620}, pmid = {24213342}, issn = {0040-5752}, abstract = {Animal and plant cells contain a family of constitutively expressed HSP-70 cognate proteins that are localized in different subcellular locations and are presumed to play a role in protein folding and transport. Utilizing antibodies raised against the yeast endoplasmicreticulum-localized HSP-70 cognate termed BiP/GRP-78, as well as antibodies raised against the Escherichia coli HSP-70 protein DnaK, we have identified and characterized a large family of closely related proteins in wheat. One protein band of 78 kDa that is apparently closely related to yeast BiP was localized in the endoplasmic reticulum. This band cross-reacted with the yeast BiP but not with the DnaK-specific antibodies. The yeast BiP antibodies also recognized a cytoplasmic protein of 70 kDa that is probably related to the HSC-70 cognate proteins. These two proteins were further confirmed as HSP-70 cognates by their ability to bind to an ATP-agarose column. Probing of proteins from purified wheat mitochondrial preparations with the yeast BiP and DnaK-specific antibodies showed that this organelle contained a family of HSP-70-related proteins. The yeast BiP antibodies recognized two mitochondrial proteins of 60 and 58 kDa, but failed to detect any protein in the size rang of 70 to 80 kDa. However, the presence of immunologically distinct proteins of 90 and 78 kDa, as well as of lower molecular weight from this family in the mitochondria, was shown by probing with the DnaK-specific antibodies. A new protein of 30 kDa, cross-reacting with anti-yeast BiP antibodies, was detected only in developing seeds, close to their maturity. The evolution of HSP-70 cognate proteins in wheat as shown in this study is discussed.}, }
@article {pmid23196279, year = {1991}, author = {Fenchel, T and Finlay, BJ}, title = {The biology of free-living anaerobic ciliates.}, journal = {European journal of protistology}, volume = {26}, number = {3-4}, pages = {201-215}, doi = {10.1016/S0932-4739(11)80143-4}, pmid = {23196279}, issn = {0932-4739}, abstract = {Anaerobic ciliates are incapable of using oxidative phosphorylation in their energy metabolism and they are more or less sensitive to oxygen. All anaerobic ciliates possess mitochondria-like organelles (with a double outer membrane and often a few cristae) but these do not contain typical mitochondrial enzymes (e.g., cytochromes, cytochrome oxidase). In some species these organelles are capable of fermenting pyruvate into acetate and H2 and they are then referred to as hydrogenosomes. At least six orders of ciliates include anaerobic species. It is concluded that the evolution of anaerobic forms has taken place independently within different taxonomic groups and that hydrogenosomes are modified mitochondria. Many anaerobic ciliates harbour ecto- or endosymbiotic bacteria. Several ciliate species which produce hydrogen as a metabolic waste product harbour endosymbiotic methanogenic bacteria; in some cases this symbiosis represents a mutualistic relationship in which the host controls the life cycle of the symbionts and gains from their presence in terms of growth rate and growth efficiency. Many marine anaerobic ciliates harbour ectosymbiotic bacteria, but the nature of these bacteria and the significance of the association is not yet understood. The present paper reviews what is known about the biology of anaerobic ciliates with special emphasis on free-living forms, including a discussion of their habitats and their role in the microbial communities of anoxic environments.}, }
@article {pmid24258368, year = {1984}, author = {Holaday, AS and Lee, KW and Chollet, R}, title = {C3-C 4 Intermediate species in the genus Flaveria: leaf anatomy, ultrastructure, and the effect of O2 on the CO 2 compensation concentration.}, journal = {Planta}, volume = {160}, number = {1}, pages = {25-32}, pmid = {24258368}, issn = {0032-0935}, abstract = {Leaf anatomical, ultrastructural, and CO2-exchange analyses of three closely related species of Flaveria indicate that they are C3-C4 intermediate plants. The leaf mesophyll of F. floridana J.R. Johnston, F. linearis Lag., and F. chloraefolia A. Gray is typical of that in dicotyledonous C3 plants, but the bundle sheath cells contain granal, starch-containing chloroplasts. In F. floridana and F. chloraefolia, the chloroplasts and numerous associated mitochondria are arranged largely centripetally, as in the closely related C4 species, F. brownii A.M. Powell. In F. linearis, fewer mitochondria are present and the chloroplasts are more evenly distributed throughout the bundle sheath cytosol. There is no correlation between the bundle sheath ultrastructure and CO2 compensation concentration. (Γ) values of these C3-C4 intermediate Flaveria species. At 21% O2 and 25°C, Γ for F. chloraefolia, F. linearis, and F. floridana is 23-26, 14-19, and 8-10 μl CO2 l(-1), respectively. The O2 dependence of Γ is the greatest for F. chloraefolia and F. linearis (similar to that for C3-C4 intermediate Panicum and Moricandia species) and the least for F. floridana, whose O2 response is identical to that for F. brownii from 1.5 to 21% O2, but greater at higher pO2. The variation in leaf anatomy, bundle sheath ultrastructure, and O2 dependence of Γ among these Flaveria species may indicate an active evolution in the pathway of photosynthetic carbon metabolism within this genus.}, }
@article {pmid24301846, year = {1981}, author = {Medina, FJ and Risueño, MC and Rodriguez-Garsia, MI}, title = {Evolution of the cytoplasmic organelles during female meiosis in Pisum sativum L.}, journal = {Planta}, volume = {151}, number = {3}, pages = {215-225}, pmid = {24301846}, issn = {0032-0935}, abstract = {In this paper we have traced the evolution of the cytoplasmic organelles in the female germinal cell of Pisum sativum L., from the beginning of meiosis to the early stages of the maturing megaspore, in order to correlate the morphological changes with the physiological aspects of megasporogenesis.A process of intense cytoplasmic vacuolation takes place in the megaspore mother cell (MMC) during prophase I, probably proceeding from the smooth endoplasmic reticulum and dictyosomes; it results in the formation of big vacuoles, which play a role in MMC polarization. By means of this polarization most plastids and mitochondria are incorporated into the functional megaspore at the end of meiosis.There are plastid and mitochondria cycles which consist of dedifferentiation followed by redifferentiation, During these cycles a transient morphology appears, called a cup-shaped form, which we interpret as an expression of low organelle activity.The wall of the MMC thickens throughout megasporogenesis and loses its plasmodesmata during middle prophase I. The ribosome population is reduced during prophase I and then restored during the early stages of the megaspore maturing process, as shown by the quantitative study that we have carried out. The nucleolar cytoplasmic bodies play a part in this restoring process. These bodies have a special morphology and appear to be originated from the activity of the nucleolar organizing region (NOR) during nucleolar disorganization in prophase I.We think that this cytoplasmic evolution is a response to nuclear genic recombination, in order to provide the most adequate expression of the zygote genome.}, }
@article {pmid24301725, year = {1981}, author = {Briand, J and Calvayrac, R and Laval-Martin, D and Farineau, J}, title = {Evolution of carboxylating enzymes involved in paramylon synthesis (phosphoenolpyruvate carboxylase and carboxykinase) in heterotrophically grown Euglena gracilis.}, journal = {Planta}, volume = {151}, number = {2}, pages = {168-175}, pmid = {24301725}, issn = {0032-0935}, abstract = {Heterotrophically grown Euglena synthesize grains of paramylon, its reserve carbohydrate, in a vesicular complex of mitochondrial origin. A CO2 fixation activity in dark grown Euglena was demonstrated in the mitochondria via paramylon. At the beginning of the exponential phase of growth, the activity of phosphoenolpyruvate carboxykinase increases before the augmentation of paramylon.At the end of the exponential phase, the activity of this enzyme decreases, and low residual levels persist in the transition and stationary phases of growth. The activity of phosphoenolpyruvate carboxylase evolves inversely during the heterotrophic growth of the algae in succinate- or a lactate-containing medium. A compartmentalized scheme of carbon metabolism in mitochondria is presented.}, }
@article {pmid24301664, year = {1981}, author = {Bouvier-Durand, M and Dereuddre, J and Côme, D}, title = {Ultrastructural changes in the endoplasmic reticulum during dormancy release of apple embryos (Pyrus malus L.).}, journal = {Planta}, volume = {151}, number = {1}, pages = {6-14}, pmid = {24301664}, issn = {0032-0935}, abstract = {Apple embryos were treated by cold (0°C) within the fruits, to break their dormancy; the controls were treated at 12°C or at 20°C. Ultrastructural features of meristematic cells in the embryonic axis were compared for each treatment. The organization of the cells of dormant embryos was described: Endoplasmic reticulum consisted in some short rough cisternae; lipid droplets regularly arranged near the plasmalemma constituted a kind of shell; mitochondria had a few cristae; and dictyosomes were rarely observed. All these features are typical of dry seeds. After cold treatments, the only evolution observed was in the endoplasmic reticulum, where highly organized stacks appeared progressively as a function of time at 0°C. An intermediate temperature (12°C) induced similar formations in the reticulum but they were rarely observed and their degree of organization was lower than that obtained at 0°C. At 20°C, endoplasmic reticulum resembled that of the dormant embryo cells. The relation between the appearance of these structures in the reticulum and the disappearance of dormancy induced by cold is discussed.}, }
@article {pmid24317560, year = {1979}, author = {Rathnam, CK}, title = {Metabolic regulation of carbon flux during C4 photosynthesis : II. In situ evidence for reffixation of photorespiratory CO2 by C 4 phosphoenolpyruvate carboxylase.}, journal = {Planta}, volume = {145}, number = {1}, pages = {13-23}, pmid = {24317560}, issn = {0032-0935}, abstract = {The potential for glycolate and glycine metabolism and the mechanism of refixation of photorespiratory CO2 in leaves of C4 plants were studied by parallel inhibitor experiments with thin leaf slices, different leaf cell types and isolated mitochondria of C3 and C4 Panicum species. CO2 evolution by leaf slices of P. bisulcatum, a C3 species, fed glycolate or glycine was light-independent and O2-sensitive. The C4 P. maximum and P. miliaceum leaf slices fed glycolate or glycine evolved CO2 in the dark but not in the light. In C4 species, dark CO2 evolution was abolished by the addition of phosphoenolpyruvate (PEP)(4). The addition of maleate, a PEP carboxylase inhibitor, resulted in photorespiratory CO2 efflux by C4 leaf slices in the light also. However, PEP and maleate had no effect on either glycolate-dependent O2 uptake by the C4 leaf slices or on glycolate and glycine metabolism in C3 leaf slices. The rate of photorespiratory CO2 evolution in the C3 Panicum species was 3 times higher than that observed with the C4 species. The ratio of glycolate-dependent CO2 evolution to O2 uptake in both groups was 1:2. Isolated C4 mesophyll protoplasts or their mitochondria did not metabolize glycolate or glycine. However, both C3 mesophyll protoplasts and C4 bundle sheath strands readily metabolized glycolate and glycine in a light-independent, O2-sensitive manner, and the addition of PEP or maleate had no effect. C4 bundle sheath- and C3-mitochondria were capable of oxidizing glycine. This oxidation was linked to the mitochondrial electron transport chain, was coupled to three phosphorylation sites and was sensitive to electron transport inhibitors. C4 bundle sheath- and C3-mitochondrial glycine decarboxylation was stimulated by oxaloacetate and NAD had no effect. In marked contrast, mitochondria isolated from C4 mesophyll cells were incapable of oxidizing or decarboxylating added glycine. The results suggest that in leaves of C4 plants bundle sheath cells are the primary site of O2-sensitive photorespiratory CO2 evolution and the PEP carboxylase present in the mesophyll cells has the Potential for efficiently refixing CO2 before it escapes out of the leaf. The relative role of the PEP carboxylase mediated CO2 pump and reassimilation of photorespiratory CO2 are discussed in relation to the apparent lack of photorespiration in leaves of C4 species.}, }
@article {pmid21470914, year = {2011}, author = {Seligmann, H}, title = {Error compensation of tRNA misacylation by codon-anticodon mismatch prevents translational amino acid misinsertion.}, journal = {Computational biology and chemistry}, volume = {35}, number = {2}, pages = {81-95}, doi = {10.1016/j.compbiolchem.2011.03.001}, pmid = {21470914}, issn = {1476-928X}, mesh = {Acylation ; Animals ; Anticodon/*genetics ; *Base Pair Mismatch ; Codon/*genetics ; Escherichia coli/genetics/growth &amp; development/metabolism ; Humans ; Polymorphism, Genetic ; *RNA Processing, Post-Transcriptional ; RNA, Transfer/*metabolism ; }, abstract = {Codon-anticodon mismatches and tRNA misloadings cause translational amino acid misinsertions, producing dysfunctional proteins. Here I explore the original hypothesis whether mismatches tend to compensate misacylation, so as to insert the amino acid coded by the codon. This error compensation is promoted by the fact that codon-anticodon mismatch stabilities increase with tRNA misacylation potentials (predicted by 'tfam') by non-cognate amino acids coded by the mismatched codons for most tRNAs examined. Error compensation is independent of preferential misacylation by non-cognate amino acids physico-chemically similar to cognate amino acids, a phenomenon that decreases misinsertion impacts. Error compensation correlates negatively with (a) codon/anticodon abundance (in human mitochondria and Escherichia coli); (b) developmental instability (estimated by fluctuating asymmetry in bilateral counts of subdigital lamellae, in each of two lizard genera, Anolis and Sceloporus); and (c) pathogenicity of human mitochondrial tRNA polymorphisms. Patterns described here suggest that tRNA misacylation is sometimes compensated by codon-anticodon mismatches. Hence translation inserts the amino acid coded by the mismatched codon, despite mismatch and misloading. Results suggest that this phenomenon is sufficiently important to affect whole organism phenotypes, as shown by correlations with pathologies and morphological estimates of developmental stability.}, }
@article {pmid21463708, year = {2011}, author = {Waleckx, E and Salas, R and Huamán, N and Buitrago, R and Bosseno, MF and Aliaga, C and Barnabé, C and Rodriguez, R and Zoveda, F and Monje, M and Baune, M and Quisberth, S and Villena, E and Kengne, P and Noireau, F and Brenière, SF}, title = {New insights on the Chagas disease main vector Triatoma infestans (Reduviidae, Triatominae) brought by the genetic analysis of Bolivian sylvatic populations.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {11}, number = {5}, pages = {1045-1057}, doi = {10.1016/j.meegid.2011.03.020}, pmid = {21463708}, issn = {1567-7257}, mesh = {Animals ; Base Sequence ; Bolivia/epidemiology ; Chagas Disease/epidemiology/*transmission ; Cytochromes b ; DNA/genetics ; DNA, Intergenic ; Demography ; Genetic Variation ; Humans ; Mitochondria ; Molecular Sequence Data ; Phylogeny ; Triatoma/*genetics/physiology ; }, abstract = {Triatoma infestans is the main and most widespread vector of Chagas disease in South America. For the first time, a large sample of sylvatic populations of T. infestans was analyzed by ITS-2 and mtCytB sequencing. ITS-2 showed a low level of polymorphism but revealed a dichotomy between the Andean and non-Andean sylvatic populations. On the contrary, mtCytB sequences showed a high polymorphism (19 haplotypes determined by 35 variable sites) revealing a strong structuring between most of the sylvatic populations and possible ancient isolation and bottleneck in the Northern Andes. The dichotomy Andean vs. non-Andean populations was not observed with this marker. Moreover, mtCytB haplotype genealogies showed that the non-Andean haplotypes would have derived from the Andean ones, supporting somewhat an Andean origin of the species. Nevertheless, a non-Andean origin could not be discarded because a remarkable genetic diversity was found in the non-Andean sample. The comparison of the sylvatic haplotypes with the domestic ones from GenBank suggested multiple events of T. infestans domestication in Andean and non-Andean areas, instead of a major and unique domestication event in the Bolivian Andes, as previously proposed.}, }
@article {pmid21459769, year = {2011}, author = {Maier, A and Zell, MB and Maurino, VG}, title = {Malate decarboxylases: evolution and roles of NAD(P)-ME isoforms in species performing C(4) and C(3) photosynthesis.}, journal = {Journal of experimental botany}, volume = {62}, number = {9}, pages = {3061-3069}, doi = {10.1093/jxb/err024}, pmid = {21459769}, issn = {1460-2431}, mesh = {Arabidopsis/enzymology/genetics/metabolism ; Biological Evolution ; Carbon Cycle ; Chloroplasts/enzymology/genetics/metabolism ; Kinetics ; Malate Dehydrogenase/genetics/*metabolism ; Malates/metabolism ; Mitochondria/enzymology/genetics/metabolism ; Photosynthesis/*physiology ; Phylogeny ; Plants/*enzymology/genetics/metabolism ; Protein Isoforms/genetics/*metabolism ; }, abstract = {In the C(4) pathway of photosynthesis two types of malate decarboxylases release CO(2) in bundle sheath cells, NADP- and NAD-dependent malic enzyme (NADP-ME and NAD-ME), located in the chloroplasts and the mitochondria of these cells, respectively. The C(4) decarboxylases involved in C(4) photosynthesis did not evolve de novo; they were recruited from existing housekeeping isoforms. NADP-ME housekeeping isoforms would function in the control of malate levels during hypoxia, pathogen defence responses, and microspore separation, while NAD-ME participates in the respiration of malate in the tricarboxylic acid cycle. Recently, the existence of three enzymatic NAD-ME entities in Arabidopsis, occurring by alternative association of two subunits, was described as a novel mechanism to regulate NAD-ME activity under changing metabolic environments. The C(4) NADP-ME is thought to have evolved from a C(3) chloroplastic ancestor, which in turn would have evolved from an ancient cytosolic enzyme. In this way, the C(4) NADP-ME would have emerged through gene duplication, acquisition of a new promoter, and neo-functionalization. In contrast, there would exist a unique NAD-ME in C(4) plants, which would have been adapted to perform a dual function through changes in the kinetic and regulatory properties of the C(3) ancestors. In addition to this, for the evolution of C(4) NAD-ME, insertion of promoters or enhancers into the single-copy genes of the C(3) ancestors would have changed the expression without gene duplication.}, }
@article {pmid21459765, year = {2011}, author = {Sage, TL and Sage, RF and Vogan, PJ and Rahman, B and Johnson, DC and Oakley, JC and Heckel, MA}, title = {The occurrence of C(2) photosynthesis in Euphorbia subgenus Chamaesyce (Euphorbiaceae).}, journal = {Journal of experimental botany}, volume = {62}, number = {9}, pages = {3183-3195}, doi = {10.1093/jxb/err059}, pmid = {21459765}, issn = {1460-2431}, mesh = {Biological Evolution ; Carbon Dioxide/analysis/metabolism ; Carbon Isotopes/analysis ; Caribbean Region ; Cell Respiration/physiology ; Chloroplasts/ultrastructure ; Euphorbia/enzymology/*physiology/ultrastructure ; Malate Dehydrogenase/metabolism ; Mexico ; Mitochondria/ultrastructure ; Phosphoenolpyruvate Carboxylase/metabolism ; Photosynthesis/*physiology ; Phylogeny ; Plant Leaves/enzymology/physiology/ultrastructure ; Plant Transpiration/physiology ; Ribulose-Bisphosphate Carboxylase/metabolism ; Temperature ; Texas ; }, abstract = {This study investigated whether Euphorbia subgenus Chamaesyce subsection Acutae contains C(3)-C(4) intermediate species utilizing C(2) photosynthesis, the process where photorespired CO(2) is concentrated into bundle sheath cells. Euphorbia species in subgenus Chamaesyce are generally C(4), but three species in subsection Acutae (E. acuta, E. angusta, and E. johnstonii) have C(3) isotopic ratios. Phylogenetically, subsection Acutae branches between basal C(3) clades within Euphorbia and the C(4) clade in subgenus Chamaesyce. Euphorbia angusta is C(3), as indicated by a photosynthetic CO(2) compensation point (Г) of 69 μmol mol(-1) at 30 °C, a lack of Kranz anatomy, and the occurrence of glycine decarboxylase in mesophyll tissues. Euphorbia acuta utilizes C(2) photosynthesis, as indicated by a Г of 33 μmol mol(-1) at 30 °C, Kranz-like anatomy with mitochondria restricted to the centripetal (inner) wall of the bundle sheath cells, and localization of glycine decarboxlyase to bundle sheath mitochondria. Low activities of PEP carboxylase, NADP malic enzyme, and NAD malic enzyme demonstrated no C(4) cycle activity occurs in E. acuta thereby classifying it as a Type I C(3)-C(4) intermediate. Kranz-like anatomy in E. johnstonii indicates it also utilizes C(2) photosynthesis. Given the phylogenetically intermediate position of E. acuta and E. johnstonii, these results support the hypothesis that C(2) photosynthesis is an evolutionary intermediate condition between C(3) and C(4) photosynthesis.}, }
@article {pmid21457795, year = {2011}, author = {Quisberth, S and Waleckx, E and Monje, M and Chang, B and Noireau, F and Brenière, SF}, title = {"Andean" and "non-Andean" ITS-2 and mtCytB haplotypes of Triatoma infestans are observed in the Gran Chaco (Bolivia): population genetics and the origin of reinfestation.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {11}, number = {5}, pages = {1006-1014}, doi = {10.1016/j.meegid.2011.03.014}, pmid = {21457795}, issn = {1567-7257}, mesh = {Animals ; Bolivia ; Cytochromes b/*genetics ; DNA/genetics ; DNA, Intergenic/*genetics ; Demography ; Genetic Variation ; Haplotypes/*genetics ; Mitochondria ; Phylogeny ; Triatoma/*genetics ; }, abstract = {In Bolivia, the Gran Chaco ecoregion suffers from serious problems of house reinfestation with Triatoma infestans despite vector control by insecticides spraying. In order to identify the origin of the triatomines collected after spraying, the genetic structure of T. infestans populations collected in four neighboring villages, before and after spraying, was analyzed using ITS-2 and mtCytB sequencing. Before spraying, only the mtCytB marker detected genetic differentiation among the 4 populations. After spraying, the mtCytB analysis of the populations from two of the studied villages supported the hypothesis in favor of a local origin for the triatomines in each village. Surprisingly, ITS-2 and mtCytB haplotypes previously found only in Andean areas were also present with high frequencies in the studied populations; these domestic populations of the Gran Chaco seem to be the result of a mixture of "Andean" and "non-Andean" triatomines probably generated by the human passive transport of triatomines from the Andes to the Gran Chaco.}, }
@article {pmid21453719, year = {2011}, author = {Schindeldecker, M and Stark, M and Behl, C and Moosmann, B}, title = {Differential cysteine depletion in respiratory chain complexes enables the distinction of longevity from aerobicity.}, journal = {Mechanisms of ageing and development}, volume = {132}, number = {4}, pages = {171-179}, doi = {10.1016/j.mad.2011.03.002}, pmid = {21453719}, issn = {1872-6216}, mesh = {Aerobiosis ; Aging ; Animals ; Cell Nucleus/metabolism ; Cysteine/*metabolism ; *Electron Transport ; Humans ; Membrane Proteins/chemistry ; Mitochondria/metabolism ; Oxidative Stress ; Oxygen Consumption ; Phylogeny ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sulfhydryl Compounds/chemistry ; Time Factors ; }, abstract = {Mitochondrially encoded proteins in long-lived animals exhibit a characteristic anomaly on the amino acid usage level: they abstain from the use of cysteine in a lifespan-dependent fashion. Here, we have further investigated this phenomenon by analyzing respiratory chain complex subunits individually. We find that complex I cysteine depletion is the almost exclusive carrier of the cysteine-lifespan correlation, whereas complex IV cysteine depletion is uniform in all aerobic animals, unrelated to longevity, but even more pronounced than complex I cysteine depletion in the longest-lived species. In nuclear encoded subunits of the respiratory chain, we find lifespan-independent cysteine depletion ranging from moderate in complex I to severe in complex V. However, a separate analysis of the transmembrane domains of these proteins unmasks an intramembrane pattern of cysteine usage that significantly correlates with longevity. Hence, cysteine usage in the respiratory chain seems to be governed by two independent molecular mechanisms acting on the protein level: a global trend of cysteine avoidance in all proteins, and a specific effect on transmembrane domain cysteines that reflects longevity. To account for these characteristic patterns, a thiyl radical-based molecular mechanism of intramembrane hydrophobic cross-linking is discussed.}, }
@article {pmid21443807, year = {2011}, author = {Liu, H and Cui, P and Zhan, K and Lin, Q and Zhuo, G and Guo, X and Ding, F and Yang, W and Liu, D and Hu, S and Yu, J and Zhang, A}, title = {Comparative analysis of mitochondrial genomes between a wheat K-type cytoplasmic male sterility (CMS) line and its maintainer line.}, journal = {BMC genomics}, volume = {12}, number = {}, pages = {163}, pmid = {21443807}, issn = {1471-2164}, mesh = {Comparative Genomic Hybridization ; DNA Transposable Elements ; DNA, Plant/genetics ; Gene Expression Regulation, Plant ; *Genome, Mitochondrial ; *Genome, Plant ; Genomic Library ; Open Reading Frames ; Physical Chromosome Mapping ; Plant Infertility/*genetics ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Triticum/*genetics ; }, abstract = {BACKGROUND: Plant mitochondria, semiautonomous organelles that function as manufacturers of cellular ATP, have their own genome that has a slow rate of evolution and rapid rearrangement. Cytoplasmic male sterility (CMS), a common phenotype in higher plants, is closely associated with rearrangements in mitochondrial DNA (mtDNA), and is widely used to produce F1 hybrid seeds in a variety of valuable crop species. Novel chimeric genes deduced from mtDNA rearrangements causing CMS have been identified in several plants, such as rice, sunflower, pepper, and rapeseed, but there are very few reports about mtDNA rearrangements in wheat. In the present work, we describe the mitochondrial genome of a wheat K-type CMS line and compare it with its maintainer line.<br><br>RESULTS: The complete mtDNA sequence of a wheat K-type (with cytoplasm of Aegilops kotschyi) CMS line, Ks3, was assembled into a master circle (MC) molecule of 647,559 bp and found to harbor 34 known protein-coding genes, three rRNAs (18 S, 26 S, and 5 S rRNAs), and 16 different tRNAs. Compared to our previously published sequence of a K-type maintainer line, Km3, we detected Ks3-specific mtDNA (> 100 bp, 11.38%) and repeats (> 100 bp, 29 units) as well as genes that are unique to each line: rpl5 was missing in Ks3 and trnH was absent from Km3. We also defined 32 single nucleotide polymorphisms (SNPs) in 13 protein-coding, albeit functionally irrelevant, genes, and predicted 22 unique ORFs in Ks3, representing potential candidates for K-type CMS. All these sequence variations are candidates for involvement in CMS. A comparative analysis of the mtDNA of several angiosperms, including those from Ks3, Km3, rice, maize, Arabidopsis thaliana, and rapeseed, showed that non-coding sequences of higher plants had mostly divergent multiple reorganizations during the mtDNA evolution of higher plants.<br><br>CONCLUSION: The complete mitochondrial genome of the wheat K-type CMS line Ks3 is very different from that of its maintainer line Km3, especially in non-coding sequences. Sequence rearrangement has produced novel chimeric ORFs, which may be candidate genes for CMS. Comparative analysis of several angiosperm mtDNAs indicated that non-coding sequences are the most frequently reorganized during mtDNA evolution in higher plants.}, }
@article {pmid21443625, year = {2011}, author = {Michaud, M and Cognat, V and Duchêne, AM and Maréchal-Drouard, L}, title = {A global picture of tRNA genes in plant genomes.}, journal = {The Plant journal : for cell and molecular biology}, volume = {66}, number = {1}, pages = {80-93}, doi = {10.1111/j.1365-313X.2011.04490.x}, pmid = {21443625}, issn = {1365-313X}, mesh = {Active Transport, Cell Nucleus ; Base Sequence ; Chlorophyta/genetics ; Evolution, Molecular ; Genes, Plant ; *Genome, Plant ; Introns ; Magnoliopsida/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Pseudogenes ; RNA, Plant/genetics ; RNA, Transfer/*genetics ; Sequence Analysis, DNA ; *Short Interspersed Nucleotide Elements ; TATA Box ; }, abstract = {Although transfer RNA (tRNA) has a fundamental role in cell life, little is known about tRNA gene organization and expression on a genome-wide scale in eukaryotes, particularly plants. Here, we analyse the content and distribution of tRNA genes in five flowering plants and one green alga. The tRNA gene content is homogenous in plants, and is mostly correlated with genome size. The number of tRNA pseudogenes and organellar-like tRNA genes present in nuclear genomes varies greatly from one plant species to another. These pseudogenes or organellar-like genes appear to be generated or inserted randomly during evolution. Interestingly, we identified a new family of tRNA-related short interspersed nuclear elements (SINEs) in the Populus trichocarpa nuclear genome. In higher plants, intron-containing tRNA genes are rare, and correspond to genes coding for tRNA(Tyr) and tRNA(Mete) . By contrast, in green algae, more than half of the tRNA genes contain an intron. This suggests divergent means of intron acquisition and the splicing process between green algae and land plants. Numerous tRNAs are co-transcribed in Chlamydomonas, but they are mostly transcribed as a single unit in flowering plants. The only exceptions are tRNA(Gly) -snoRNA and tRNA(Mete) -snoRNA cotranscripts in dicots and monocots, respectively. The internal or external motifs required for efficient transcription of tRNA genes by RNA polymerase III are well conserved among angiosperms. A brief analysis of the mitochondrial and plastidial tRNA gene populations is also provided.}, }
@article {pmid21436122, year = {2011}, author = {Hecht, J and Grewe, F and Knoop, V}, title = {Extreme RNA editing in coding islands and abundant microsatellites in repeat sequences of Selaginella moellendorffii mitochondria: the root of frequent plant mtDNA recombination in early tracheophytes.}, journal = {Genome biology and evolution}, volume = {3}, number = {}, pages = {344-358}, pmid = {21436122}, issn = {1759-6653}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Mitochondrial/*genetics ; *Genome, Mitochondrial ; Introns ; *Microsatellite Repeats ; Mitochondria/*genetics ; Molecular Sequence Data ; Plant Proteins/genetics ; *RNA Editing ; *Recombination, Genetic ; Selaginellaceae/*genetics ; }, abstract = {Using an independent fosmid cloning approach and comprehensive transcriptome analysis to complement data from the Selaginella moellendorffii genome project, we determined the complete mitochondrial genome structure of this spikemoss. Numerous recombination events mediated mainly via long sequence repeats extending up to 7 kbp result in a complex mtDNA network structure. Peculiar features associated with the repeat sequences are more than 80 different microsatellite sites (predominantly trinucleotide motifs). The S. moellendorffii mtDNA encodes a plant-typical core set of a twin-arginine translocase (tatC), 17 respiratory chain subunits, and 2 rRNAs but lacks atp4 and any tRNA genes. As a further novelty among plant chondromes, the nad4L gene is encoded within an intron of the nad1 gene. A total of 37 introns occupying the 20 mitochondrial genes (four of which are disrupted into trans-splicing arrangements including two novel instances of trans-splicing introns) make the S. moellendorffii chondrome the intron-richest and gene-poorest plant mtDNA known. Our parallel transcriptome analyses demonstrates functional splicing of all 37 introns and reveals a new record amount of plant organelle RNA editing with a total of 2,139 sites in mRNAs and 13 sites in the two rRNAs, all of which are exclusively of the C-to-U type.}, }
@article {pmid21436119, year = {2011}, author = {Kiethega, GN and Turcotte, M and Burger, G}, title = {Evolutionarily conserved cox1 trans-splicing without cis-motifs.}, journal = {Molecular biology and evolution}, volume = {28}, number = {9}, pages = {2425-2428}, doi = {10.1093/molbev/msr075}, pmid = {21436119}, issn = {1537-1719}, support = {MOP-79309//Canadian Institutes of Health Research/Canada ; }, mesh = {Base Sequence ; Cyclooxygenase 1/*genetics ; *Evolution, Molecular ; Genome, Mitochondrial ; Introns ; Meiotic Prophase I/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA Editing/genetics ; Trans-Splicing/*genetics ; }, abstract = {In the protist Diplonema papillatum (Diplonemea, Euglenozoa), mitochondrial genes are systematically fragmented with each nonoverlapping piece (module) encoded individually on a distinct circular chromosome. Gene modules are transcribed separately, and precursor transcripts are assembled to mature mRNA by a trans-splicing process of yet unknown mechanism. Expression of the cox1 gene that consists of nine modules, also involves RNA editing by which six uridines are added between Modules 4 and 5. Here, we investigate whether the unusual features of cox1 are shared by all Diplonemea and what the mechanism of trans-splicing might be. We examine three additional species representing both Diplonemea genera, namely D. papillatum described before, and D. ambulator, Diplonema sp.2, and Rhynchopus euleeides and discover that in all Diplonemea, the cox1 gene is discontinuous and split up into nine modules that each reside on a distinct chromosome. Positions of gene breakpoints vary by up to two nucleotides. Further, all taxa have six nonencoded uridines inserted in cox1 mRNA at exactly the same position as D. papillatum. In silico searches do not detect signatures of introns known to engage in trans-splicing, in particular Group I, Group II, spliceosomal, and transfer RNA introns. Nor did we find statistically significant reverse-complementary motifs between adjacent modules and their flanking regions, or residues conserved within or across species. This provides compelling evidence that trans-splicing in Diplonemea mitochondria does not rely on sequence elements in cis but rather proceeds by a mechanism employing matchmaking trans factors, such as RNAs or proteins.}, }
@article {pmid21434420, year = {2010}, author = {Maĭkova, OO and Itskovich, VB and Semiturkina, NA and Kaliuzhnaia, OV and Belikov, SI}, title = {[Phylogenetic position of sponges from Chagytaĭ and Tore-Khol' lakes].}, journal = {Genetika}, volume = {46}, number = {12}, pages = {1670-1677}, pmid = {21434420}, issn = {0016-6758}, mesh = {Animals ; Base Sequence ; Fresh Water ; Genetic Markers ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Porifera/*genetics ; RNA, Transfer, Met/genetics ; RNA, Transfer, Tyr/genetics ; Siberia ; Untranslated Regions ; }, abstract = {Morphological and molecular genetic data for freshwater sponges from the lakes of Tuva Depression, Baikalospongia dzhegatajensis (Rezvo, 1936), forms Dzh05 and Dzh06, from Chagatai Lake, as well as forms TKhl and TKh2, from the Lake Tore-Khol, were obtained and examined. In the sponges examined, which on phylogenetic tree clustered together with the Ephydatia fluviatilis (Linneaus, 1758) sponge from the family Spongillidae, the ITS rDNA regions were sequenced. Comparison of highly variable interal spacer regions of the mitochondrial genome was performed using corresponding sequences of three sponges from the family Spongillidae (E. fluviatilis, E. muelleri and Spongilla lacustris), sponges from the Chagatai and Tore-Khol lakes (Dzh06 and TKh2) with an unknown status, and sponges from the Baikalian family Lubomirskiidae. Minimum genetic differences were observed between E. fluviatilis, Dzh06, and TKh2 (from 0.003 to 0.01% of nucleotide substitutions), while maximum differences were found between the species of Lubomirskiidae and Spongillidae (from 0.928 to 2.06%). The data obtained indicated that sponges from Chagatai and Tore-Khol lakes were most close to E. fluviatilis.}, }
@article {pmid21428694, year = {2011}, author = {Morel, F and Aninat, C}, title = {The glutathione transferase kappa family.}, journal = {Drug metabolism reviews}, volume = {43}, number = {2}, pages = {281-291}, doi = {10.3109/03602532.2011.556122}, pmid = {21428694}, issn = {1097-9883}, mesh = {Amino Acid Sequence ; Animals ; Glutathione Transferase/chemistry/genetics/*physiology ; Humans ; Isoenzymes ; Mitochondria/enzymology ; Molecular Sequence Data ; Organ Specificity ; Peroxisomes/enzymology ; Phylogeny ; Sequence Alignment ; Species Specificity ; Substrate Specificity ; }, abstract = {Glutathione transferase (GST) kappa, also named mitochondrial GST, is a very ancient protein family with orthologs in bacteria and eukaryotes. Both the structure and the subcellular localization of GSTK1-1, in mitochondria and peroxisomes, make this enzyme distinct from cytosolic GSTs. Rodent and human GSTK1 exhibit activity towards a number of model GST substrates and, in Caenorhabditis elegans, this enzyme may be involved in energy and lipid metabolism, two functions related to mitochondria and peroxisomes. Interestingly, GST kappa is also a key regulator of adiponectin biosynthesis and multimerization suggesting that it might function as a chaperone to facilitate correct folding and assembly of proteins. Since adiponectin expression has been correlated with insulin resistance, obesity and diabetes, GSTK1 expression level which is negatively correlated with obesity in mice and human adipose tissues may be an important factor in these metabolic disorders. Furthermore, a polymorphism in the hGSTK1 promoter has been associated with insulin secretion and fat deposition.}, }
@article {pmid21424613, year = {2012}, author = {Beakes, GW and Glockling, SL and Sekimoto, S}, title = {The evolutionary phylogeny of the oomycete "fungi".}, journal = {Protoplasma}, volume = {249}, number = {1}, pages = {3-19}, pmid = {21424613}, issn = {1615-6102}, mesh = {Adaptation, Biological ; Animals ; Aquatic Organisms/classification/cytology/pathogenicity/physiology ; *Evolution, Molecular ; Flagella/physiology ; Host-Pathogen Interactions ; Microscopy, Electron ; Mitochondria/physiology ; Nematoda/microbiology ; Oomycetes/*classification/cytology/genetics/pathogenicity/physiology ; *Phylogeny ; Species Specificity ; Spores, Fungal/ultrastructure ; }, abstract = {Molecular sequencing has helped resolve the phylogenetic relationships amongst the diverse groups of algal, fungal-like and protist organisms that constitute the Chromalveolate "superkingdom" clade. It is thought that the whole clade evolved from a photosynthetic ancestor and that there have been at least three independent plastid losses during their evolutionary history. The fungal-like oomycetes and hyphochytrids, together with the marine flagellates Pirsonia and Developayella, form part of the clade defined by Cavalier-Smith and Chao (2006) as the phylum "Pseudofungi", which is a sister to the photosynthetic chromistan algae (phylum Ochrophyta). Within the oomycetes, a number of predominantly marine holocarpic genera appear to diverge before the main "saprolegnian" and "peronosporalean" lines, into which all oomycetes had been traditionally placed. It is now clear that oomycetes have their evolutionary roots in the sea. The earliest diverging oomycete genera so far documented, Eurychasma and Haptoglossa, are both obligate parasites that show a high degree of complexity and sophistication in their host parasite interactions and infection structures. Key morphological and cytological features of the oomycetes will be reviewed in the context of our revised understanding of their likely phylogeny. Recent genomic studies have revealed a number of intriguing similarities in host-pathogen interactions between the oomycetes with their distant apicocomplexan cousins. Therefore, the earlier view that oomycetes evolved from the largely saprotrophic "saprolegnian line" is not supported and current evidence shows these organisms evolved from simple holocarpic marine parasites. Both the hyphal-like pattern of growth and the acquisition of oogamous sexual reproduction probably developed largely after the migration of these organisms from the sea to land.}, }
@article {pmid21423759, year = {2011}, author = {Darling, JA}, title = {Interspecific hybridization and mitochondrial introgression in invasive carcinus shore crabs.}, journal = {PloS one}, volume = {6}, number = {3}, pages = {e17828}, pmid = {21423759}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; Brachyura/*genetics ; Cluster Analysis ; Factor Analysis, Statistical ; Gene Pool ; Genetic Variation ; Genetics, Population ; Geography ; *Hybridization, Genetic ; *Introduced Species ; Japan ; Linkage Disequilibrium/genetics ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Phylogeny ; Species Specificity ; }, abstract = {Interspecific hybridization plays an important role in facilitating adaptive evolutionary change. More specifically, recent studies have demonstrated that hybridization may dramatically influence the establishment, spread, and impact of invasive populations. In Japan, previous genetic evidence for the presence of two non-native congeners, the European green crab Carcinus maenas and the Mediterranean green crab C. aestuarii, has raised questions regarding the possibility of hybridization between these sister species. Here I present analysis based on both nuclear microsatellites and the mitochondrial cytochrome C oxidase subunit I (COI) gene which unambiguously argues for a hybrid origin of Japanese Carcinus. Despite the presence of mitochondrial lineages derived from both C. maenas and C. aestuarii, the Japanese population is panmictic at nuclear loci and has achieved cytonuclear equilibrium throughout the sampled range in Japan. Furthermore, analysis of admixture at nuclear loci indicates dramatic introgression of the C. maenas mitochondrial genome into a predominantly C. aestuarii nuclear background. These patterns, along with inferences drawn from the observational record, argue for a hybridization event pre-dating the arrival of Carcinus in Japan. The clarification of both invasion history and evolutionary history afforded by genetic analysis provides information that may be critically important to future studies aimed at assessing risks posed by invasive Carcinus populations to Japan and the surrounding region.}, }
@article {pmid21423700, year = {2011}, author = {Chen, J and Guan, R and Chang, S and Du, T and Zhang, H and Xing, H}, title = {Substoichiometrically different mitotypes coexist in mitochondrial genomes of Brassica napus L.}, journal = {PloS one}, volume = {6}, number = {3}, pages = {e17662}, pmid = {21423700}, issn = {1932-6203}, mesh = {Base Sequence ; Brassica napus/*genetics ; Evolution, Molecular ; Gene Dosage/genetics ; Genome, Mitochondrial/*genetics ; Genome, Plant/*genetics ; Mitochondria/*genetics ; Open Reading Frames/genetics ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Alignment ; Synteny/genetics ; }, abstract = {Cytoplasmic male sterility (CMS) has been identified in numerous plant species. Brassica napus CMS plants, such as Polima (pol), MI, and Shaan 2A, have been identified independently by different researchers with different materials in conventional breeding processes. How this kind of CMS emerges is unclear. Here, we report the mitochondrial genome sequence of the prevalent mitotype in the most widely used pol-CMS line, which has a length of 223,412 bp and encodes 34 proteins, 3 ribosomal RNAs, and 18 tRNAs, including two near identical copies of trnH. Of these 55 genes, 48 were found to be identical to their equivalents in the "nap" cytoplasm. The nap mitotype carries only one copy of trnH, and the sequences of five of the six remaining genes are highly similar to their equivalents in the pol mitotype. Forty-four open reading frames (ORFs) with unknown function were detected, including two unique to the pol mitotype (orf122 and orf132). At least five rearrangement events are required to account for the structural differences between the pol and nap sequences. The CMS-related orf224 neighboring region (∼5 kb) rearranged twice. PCR profiling based on mitotype-specific primer pairs showed that both mitotypes are present in B. napus cultivars. Quantitative PCR showed that the pol cytoplasm consists mainly of the pol mitotype, and the nap mitotype is the main genome of nap cytoplasm. Large variation in the copy number ratio of mitotypes was found, even among cultivars sharing the same cytoplasm. The coexistence of mitochondrial mitotypes and substoichiometric shifting can explain the emergence of CMS in B. napus.}, }
@article {pmid21422103, year = {2011}, author = {Klimov, PB and Knowles, LL}, title = {Repeated parallel evolution of minimal rRNAs revealed from detailed comparative analysis.}, journal = {The Journal of heredity}, volume = {102}, number = {3}, pages = {283-293}, doi = {10.1093/jhered/esr005}, pmid = {21422103}, issn = {1465-7333}, mesh = {Animals ; Base Sequence ; *Evolution, Molecular ; Mites/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Ribosomal/chemistry/*genetics ; Sequence Alignment ; }, abstract = {The concept of a minimal ribosomal RNA-containing ribosome, a structure with a minimal set of elements capable of providing protein biosynthesis, is essential for understanding this fundamental cellular process. Nematodes and trypanosomes have minimal mitochondrial rRNAs and detailed reconstructions of their secondary structures indicate that certain conserved helices have been lost in these taxa. In contrast, several recent studies on acariform mites have argued that minimal rRNAs may evolve via shortening of secondary structure elements but not the loss of these elements as shown for trypanosomes and nematodes. Based on extensive structural analysis of chelicerate arthropods, we demonstrate that extremely short rRNAs of acariform mites share certain structural modifications with nematodes and trypanosomes: loss of helices of the GTPase region and divergence in the evolutionarily conserved connecting loop between helices H1648 and H1764 of the large subunit rRNA. These highly concerted parallel modifications indicate that minimal rRNAs were generated under the strong selection that favored or tolerated reductions of helices in particular locations while maintaining the functionality of the rRNA molecules throughout evolution. We also discuss potential evolution of minimal rRNAs and atypical transfer RNAs.}, }
@article {pmid21421812, year = {2011}, author = {Watkins, KP and Rojas, M and Friso, G and van Wijk, KJ and Meurer, J and Barkan, A}, title = {APO1 promotes the splicing of chloroplast group II introns and harbors a plant-specific zinc-dependent RNA binding domain.}, journal = {The Plant cell}, volume = {23}, number = {3}, pages = {1082-1092}, pmid = {21421812}, issn = {1532-298X}, mesh = {Arabidopsis/genetics ; Arabidopsis Proteins/chemistry/*genetics ; Carrier Proteins/*genetics ; Chloroplasts/*genetics/metabolism ; Introns/*genetics ; Phylogeny ; *RNA Splicing ; RNA, Messenger/analysis ; RNA-Binding Proteins/*genetics/metabolism ; Zea mays/genetics ; }, abstract = {Arabidopsis thaliana APO1 is required for the accumulation of the chloroplast photosystem I and NADH dehydrogenase complexes and had been proposed to facilitate the incorporation of [4Fe-4S] clusters into these complexes. The identification of maize (Zea mays) APO1 in coimmunoprecipitates with a protein involved in chloroplast RNA splicing prompted us to investigate a role for APO1 in splicing. We show here that APO1 promotes the splicing of several chloroplast group II introns: in Arabidopsis apo1 mutants, ycf3-intron 2 remains completely unspliced, petD intron splicing is strongly reduced, and the splicing of several other introns is compromised. These splicing defects can account for the loss of photosynthetic complexes in apo1 mutants. Recombinant APO1 from both maize and Arabidopsis binds RNA with high affinity in vitro, demonstrating that DUF794, the domain of unknown function that makes up almost the entirety of APO1, is an RNA binding domain. We provide evidence that DUF794 harbors two motifs that resemble zinc fingers, that these bind zinc, and that they are essential for APO1 function. DUF794 is found in a plant-specific protein family whose members are all predicted to localize to mitochondria or chloroplasts. Thus, DUF794 adds a new example to the repertoire of plant-specific RNA binding domains that emerged as a product of nuclear-organellar coevolution.}, }
@article {pmid21420357, year = {2011}, author = {Heiss, AA and Walker, G and Simpson, AG}, title = {The ultrastructure of Ancyromonas, a eukaryote without supergroup affinities.}, journal = {Protist}, volume = {162}, number = {3}, pages = {373-393}, doi = {10.1016/j.protis.2010.08.004}, pmid = {21420357}, issn = {1618-0941}, mesh = {Biological Evolution ; Cell Division ; Eukaryota/*classification/cytology/physiology/*ultrastructure ; Flagella/*ultrastructure ; Heterotrophic Processes ; Imaging, Three-Dimensional ; Microscopy, Electron, Transmission ; Microscopy, Phase-Contrast ; Microtubules/*ultrastructure ; Models, Biological ; Organelles/*ultrastructure ; }, abstract = {The small heterotrophic flagellate Ancyromonas (=Planomonas) lacks close relatives in most molecular phylogenies, and it is suspected that it does not belong to any of the recognized eukaryote 'supergroups', making it an organism of great evolutionary interest. Proposed relatives include apusomonads and excavates, but limited understanding of the ancyromonad cytoskeleton has precluded identification of candidate structural homologies. We present a detailed analysis of the ultrastructure of Ancyromonas through computer-based reconstruction of serial sections. We confirm or extend previous observations of its major organelles (mitochondria, Golgi body, extrusomes, etc.) and pellicle, and distinguish a system of stacked endomembranes that may be developmentally connected to the glycocalyx. Ancyromonas has two basal bodies, each with its own flagellar pocket. The anterior basal body associates with two microtubular elements: a doublet root that runs from between the basal bodies to support the cell's rostrum, and a short singlet root. The posterior basal body is associated with two multi-microtubular structures and a singlet root. One multi-microtubular structure, L1, is a conventional microtubular root. The other structure appears as a curved ribbon of ∼8 microtubules near the basal body, but then flares out into two multi-microtubular elements, L2 and L3, plus two single microtubules. The posterior singlet root originates independently near this second complex. L1, the singlet, L2, and L3 all support the posterior flagellar pocket and channel. We also identified several groups of peripheral microtubules. Possible homologies with the flagellar apparatus of both apusomonads and excavates include a splitting root on the right side of the posterior basal body and a singlet root, both supporting a longitudinal channel or groove associated with the posterior flagellum. The anterior flagellar apparatus in each includes a root supporting structures to the left of the anterior flagellum. Given the probable deep divergences of Ancyromonas, apusomonads and excavates within eukaryotes, it is possible that the eukaryotic cenancestor also possessed these features.}, }
@article {pmid21414588, year = {2011}, author = {Sieber, F and Duchêne, AM and Maréchal-Drouard, L}, title = {Mitochondrial RNA import: from diversity of natural mechanisms to potential applications.}, journal = {International review of cell and molecular biology}, volume = {287}, number = {}, pages = {145-190}, doi = {10.1016/B978-0-12-386043-9.00004-9}, pmid = {21414588}, issn = {1937-6448}, mesh = {Animals ; Base Sequence ; Biological Evolution ; DNA/metabolism ; Humans ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA/*metabolism ; RNA, Fungal/genetics/*metabolism ; RNA, Mitochondrial ; RNA, Plant/genetics/*metabolism ; RNA, Protozoan/genetics/*metabolism ; RNA, Ribosomal/genetics/metabolism ; RNA, Transfer/chemistry/genetics/*metabolism ; Ribonuclease P/genetics/metabolism ; }, abstract = {Mitochondria, owing to their bacterial origin, still contain their own DNA. However, the majority of bacterial genes were lost or transferred to the nuclear genome and the biogenesis of the "present-day" mitochondria mainly depends on the expression of the nuclear genome. Thus, most mitochondrial proteins and a small number of mitochondrial RNAs (mostly tRNAs) expressed from nuclear genes need to be imported into the organelle. During evolution, macromolecule import systems were universally established. The processes of protein mitochondrial import are very well described in the literature. By contrast, deciphering the mitochondrial RNA import phenomenon is still a real challenge. The purpose of this review is to present a general survey of our present knowledge in this field in different model organisms, protozoa, plants, yeast, and mammals. Questions still under debate and major challenges are discussed. Mitochondria are involved in numerous human diseases. The targeting of macromolecule to mitochondria represents a promising way to fight mitochondrial disorders and recent developments in this area of research are presented.}, }
@article {pmid21390322, year = {2011}, author = {Jedelský, PL and Doležal, P and Rada, P and Pyrih, J and Smíd, O and Hrdý, I and Sedinová, M and Marcinčiková, M and Voleman, L and Perry, AJ and Beltrán, NC and Lithgow, T and Tachezy, J}, title = {The minimal proteome in the reduced mitochondrion of the parasitic protist Giardia intestinalis.}, journal = {PloS one}, volume = {6}, number = {2}, pages = {e17285}, pmid = {21390322}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Cluster Analysis ; Evolution, Molecular ; Giardia lamblia/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/analysis/chemistry/metabolism ; Mitochondrial Size/*physiology ; Molecular Sequence Data ; Parasites/metabolism ; Protein Folding ; Protein Multimerization ; Proteome/*analysis/metabolism ; Tandem Mass Spectrometry ; }, abstract = {The mitosomes of Giardia intestinalis are thought to be mitochondria highly-reduced in response to the oxygen-poor niche. We performed a quantitative proteomic assessment of Giardia mitosomes to increase understanding of the function and evolutionary origin of these enigmatic organelles. Mitosome-enriched fractions were obtained from cell homogenate using Optiprep gradient centrifugation. To distinguish mitosomal proteins from contamination, we used a quantitative shot-gun strategy based on isobaric tagging of peptides with iTRAQ and tandem mass spectrometry. Altogether, 638 proteins were identified in mitosome-enriched fractions. Of these, 139 proteins had iTRAQ ratio similar to that of the six known mitosomal markers. Proteins were selected for expression in Giardia to verify their cellular localizations and the mitosomal localization of 20 proteins was confirmed. These proteins include nine components of the FeS cluster assembly machinery, a novel diflavo-protein with NADPH reductase activity, a novel VAMP-associated protein, and a key component of the outer membrane protein translocase. None of the novel mitosomal proteins was predicted by previous genome analyses. The small proteome of the Giardia mitosome reflects the reduction in mitochondrial metabolism, which is limited to the FeS cluster assembly pathway, and a simplicity in the protein import pathway required for organelle biogenesis.}, }
@article {pmid21388704, year = {2011}, author = {Fernández-Ocaña, A and Chaki, M and Luque, F and Gómez-Rodríguez, MV and Carreras, A and Valderrama, R and Begara-Morales, JC and Hernández, LE and Corpas, FJ and Barroso, JB}, title = {Functional analysis of superoxide dismutases (SODs) in sunflower under biotic and abiotic stress conditions. Identification of two new genes of mitochondrial Mn-SOD.}, journal = {Journal of plant physiology}, volume = {168}, number = {11}, pages = {1303-1308}, doi = {10.1016/j.jplph.2011.01.020}, pmid = {21388704}, issn = {1618-1328}, mesh = {Chloroplasts/genetics/metabolism ; Cloning, Molecular ; Computational Biology ; Gene Expression Regulation, Plant ; *Genes, Mitochondrial ; Genes, Plant ; Helianthus/enzymology/*genetics/microbiology ; Mitochondria/genetics/metabolism ; Oomycetes/pathogenicity ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plant Roots/genetics/metabolism ; Seedlings/enzymology/microbiology ; Sequence Analysis, Protein ; *Stress, Physiological ; Superoxide Dismutase/genetics/*metabolism ; Superoxides/analysis ; Temperature ; }, abstract = {Superoxide dismutases (SODs) are a family of metalloenzymes that catalyse the disproportionation of superoxide radicals into hydrogen peroxide and oxygen. In sunflower (Helianthus annuus L.) seedlings, two new Mn-SOD isozymes, designated as I and II, were identified. However, no evidence for a Fe-SOD was found. Both Mn-SOD I and Mn-SOD II have a cleaved sequence of 14 residues that target the mitochondrion with a probability of 81% and 95%, respectively. The gene expression of these new mitochondrial Mn-SODs as well as the previously reported cytosolic and chloroplastic CuZnSODs was analyzed by real-time quantitative reverse transcription-PCR. This was done in the main organs (roots, hypocotyls, and cotyledons) of sunflower seedlings and also under biotic (infection by the pathogen Plasmopara halstedii) and abiotic stress conditions, including high and low temperature and mechanical wounding. Both CuZn-SODs had a gene expression of 1000-fold higher than that of mitochondrial Mn-SODs. And the expression of the Mn-SOD I was approximately 12-fold higher than that of Mn-SOD II. The Mn-SOD I showed a significant modulation in response to the assayed biotic and abiotic stresses even when it had no apparent oxidative stress, such as low temperature. Thus, it is proposed that the mitochondrial Mn-SOD I gene could act as an early sensor of adverse conditions to prevent potential oxidative damage.}, }
@article {pmid21385626, year = {2011}, author = {Uribe-Carvajal, S and Luévano-Martínez, LA and Guerrero-Castillo, S and Cabrera-Orefice, A and Corona-de-la-Peña, NA and Gutiérrez-Aguilar, M}, title = {Mitochondrial Unselective Channels throughout the eukaryotic domain.}, journal = {Mitochondrion}, volume = {11}, number = {3}, pages = {382-390}, doi = {10.1016/j.mito.2011.02.004}, pmid = {21385626}, issn = {1872-8278}, mesh = {Biological Transport ; Eukaryota ; Mitochondria/*metabolism ; Mitochondrial Membranes/*metabolism ; Models, Biological ; Permeability ; }, abstract = {Mitochondria from diverse species can undergo a massive permeability increase known as the permeability transition, a process first thought to be an artifact. It is currently accepted that in the inner mitochondrial membrane there is a Mitochondrial Unselective Channel (MUC), also known as the permeability transition pore. Regardless of the species, MUC opening leads to uncoupling of oxidative phosphorylation. In each species, MUC regulation appears to be different, probably as a result of the adaptation of each organism to its specific environment. To date, the components and the putative physiological role of MUCs are still a matter of debate. Current hypothesis suggests that proteins normally participating in diverse metabolic functions constitute MUCs. Among these proteins, the Adenine Nucleotide Translocase and the phosphate carrier have been proposed as putative MUC components in mammalian and yeast mitochondria. In this review, the characteristics of MUCs from different species and strains are discussed. The data from the literature reinforce the current notion that these channels are preserved through evolution albeit with different control factors. We emphasize the knowledge available of Mitochondrial Unselective Channels from different yeast species.}, }
@article {pmid21383132, year = {2011}, author = {Tocchini-Valentini, GD and Fruscoloni, P and Tocchini-Valentini, GP}, title = {Evolution of introns in the archaeal world.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {12}, pages = {4782-4787}, pmid = {21383132}, issn = {1091-6490}, mesh = {Archaea/*physiology ; Archaeal Proteins/genetics/metabolism ; Endonucleases/genetics/metabolism ; *Evolution, Molecular ; Introns/*physiology ; *RNA Precursors/genetics/metabolism ; RNA Splicing/*physiology ; *RNA, Archaeal/genetics/metabolism ; *RNA, Ribosomal, 23S/genetics/metabolism ; }, abstract = {The self-splicing group I introns are removed by an autocatalytic mechanism that involves a series of transesterification reactions. They require RNA binding proteins to act as chaperones to correctly fold the RNA into an active intermediate structure in vivo. Pre-tRNA introns in Bacteria and in higher eukaryote plastids are typical examples of self-splicing group I introns. By contrast, two striking features characterize RNA splicing in the archaeal world. First, self-splicing group I introns cannot be found, to this date, in that kingdom. Second, the RNA splicing scenario in Archaea is uniform: All introns, whether in pre-tRNA or elsewhere, are removed by tRNA splicing endonucleases. We suggest that in Archaea, the protein recruited for splicing is the preexisting tRNA splicing endonuclease and that this enzyme, together with the ligase, takes over the task of intron removal in a more efficient fashion than the ribozyme. The extinction of group I introns in Archaea would then be a consequence of recruitment of the tRNA splicing endonuclease. We deal here with comparative genome analysis, focusing specifically on the integration of introns into genes coding for 23S rRNA molecules, and how this newly acquired intron has to be removed to regenerate a functional RNA molecule. We show that all known oligomeric structures of the endonuclease can recognize and cleave a ribosomal intron, even when the endonuclease derives from a strain lacking rRNA introns. The persistence of group I introns in mitochondria and chloroplasts would be explained by the inaccessibility of these introns to the endonuclease.}, }
@article {pmid21378103, year = {2011}, author = {de Graaf, RM and Ricard, G and van Alen, TA and Duarte, I and Dutilh, BE and Burgtorf, C and Kuiper, JW and van der Staay, GW and Tielens, AG and Huynen, MA and Hackstein, JH}, title = {The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of Nyctotherus ovalis.}, journal = {Molecular biology and evolution}, volume = {28}, number = {8}, pages = {2379-2391}, pmid = {21378103}, issn = {1537-1719}, mesh = {Biological Evolution ; Cell Nucleus/genetics/metabolism ; Ciliophora/classification/*genetics/*metabolism ; Gene Transfer, Horizontal ; Genes, Protozoan/genetics ; Genome, Mitochondrial/*genetics ; Hydrogen/*metabolism ; Mitochondria/*genetics/*metabolism ; Organelles/genetics/metabolism ; Phylogeny ; Protozoan Proteins/genetics/metabolism ; }, abstract = {It is generally accepted that hydrogenosomes (hydrogen-producing organelles) evolved from a mitochondrial ancestor. However, until recently, only indirect evidence for this hypothesis was available. Here, we present the almost complete genome of the hydrogen-producing mitochondrion of the anaerobic ciliate Nyctotherus ovalis and show that, except for the notable absence of genes encoding electron transport chain components of Complexes III, IV, and V, it has a gene content similar to the mitochondrial genomes of aerobic ciliates. Analysis of the genome of the hydrogen-producing mitochondrion, in combination with that of more than 9,000 genomic DNA and cDNA sequences, allows a preliminary reconstruction of the organellar metabolism. The sequence data indicate that N. ovalis possesses hydrogen-producing mitochondria that have a truncated, two step (Complex I and II) electron transport chain that uses fumarate as electron acceptor. In addition, components of an extensive protein network for the metabolism of amino acids, defense against oxidative stress, mitochondrial protein synthesis, mitochondrial protein import and processing, and transport of metabolites across the mitochondrial membrane were identified. Genes for MPV17 and ACN9, two hypothetical proteins linked to mitochondrial disease in humans, were also found. The inferred metabolism is remarkably similar to the organellar metabolism of the phylogenetically distant anaerobic Stramenopile Blastocystis. Notably, the Blastocystis organelle and that of the related flagellate Proteromonas lacertae also lack genes encoding components of Complexes III, IV, and V. Thus, our data show that the hydrogenosomes of N. ovalis are highly specialized hydrogen-producing mitochondria.}, }
@article {pmid21377961, year = {2011}, author = {Wei, JP and Pan, XF and Li, HQ and Duan, F}, title = {[Distribution and evolution of simple repeats in the mtDNA D-loop in mammalian].}, journal = {Yi chuan = Hereditas}, volume = {33}, number = {1}, pages = {67-74}, doi = {10.3724/sp.j.1005.2011.00067}, pmid = {21377961}, issn = {0253-9772}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*chemistry ; Evolution, Molecular ; Humans ; Mammals/*genetics ; Molecular Sequence Data ; *Repetitive Sequences, Nucleic Acid ; }, abstract = {Simple sequence repeats (SSR) distribute extensively in genomes of all organisms, but the molecular mechanism underlined is poorly understood. In this study, we characterized distribution and biological significance of the simple repetitive DNA sequences in the D-loop region in mitochondria DNA of 256 mammal species, and classified the mammal carriers into three groups including 53 species with hexanucleotide repeats, 104 species with other types of simple repeats (>6 bp) and 99 species without any repeat sequences, respectively. Furthermore, we found that the hexanucleotide repeats dispersed significantly in the interval space between CSB1 and CSB2, while other repeats dispersed mainly in the termination region, central conserved region and the conserve sequence block (CSB) regions. In addition, comparison on the base composition and the DNA contexts of the central conserved region, CSB1, CSB2, and CSB3 revealed a lack of significant differences in similarity among different species with or without repeat sequences. Moreover, a phylogenetic analysis with 256 mammal species using N-J method suggested loss of the repeat sequences in mammals in evolution.}, }
@article {pmid21376606, year = {2011}, author = {Araújo, VA and Lino-Neto, J and de Sousa Ramalho, F and Zanuncio, JC and Serrão, JE}, title = {Ultrastructure and heteromorphism of spermatozoa in five species of bugs (Pentatomidae: Heteroptera).}, journal = {Micron (Oxford, England : 1993)}, volume = {42}, number = {6}, pages = {560-567}, doi = {10.1016/j.micron.2011.02.001}, pmid = {21376606}, issn = {1878-4291}, mesh = {Acrosome/ultrastructure ; Animals ; Axoneme ; Cell Nucleus/ultrastructure ; Centrioles/ultrastructure ; Flagella/ultrastructure ; Heteroptera/genetics/*ultrastructure ; Male ; Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; Phylogeny ; Spermatozoa/metabolism/*ultrastructure ; }, abstract = {Pentatomidae is one of the largest Heteroptera families, comprising about 10% of the species estimated for the suborder. In spite of existing studies, doubts remain regarding the systematics of Pentatomomorpha. In this study, five species of Pentatomidae spermatozoa were examined to achieve characteristics that enable inferences in the phylogeny of the group and in behavioral issues associated with the presence of polymorphisms. Spermatozoa polymorphisms, characterized by two classes of sizes, are found in Podisus nigrispinus, Podisus distinctus, and Brontocoris tabidus, whereas Thynacanta marginata (Dallas) and Supputius cincticeps have single-size spermatozoa. The head region consists of an acrosome, a nucleus, and part of the centriolar adjunct. In the more anterior region, the nucleus is parallel to the centriolar adjunct. In the nucleus-flagellum transition region, the nucleus overlaps the anterior region of the mitochondrial derivatives, just above the axoneme. The mitochondrial derivatives and the axoneme run the entire extent of the flagellum. In species in which the spermatozoa are polymorphic, the larger spermatozoa have derivatives mitochondrial approximately 3-fold larger than the smaller spermatozoa. Characteristics derived from the morphology of spermatozoa indicate synapomorphies and are promising for systematic studies.}, }
@article {pmid21376056, year = {2011}, author = {Danne, JC and Waller, RF}, title = {Analysis of dinoflagellate mitochondrial protein sorting signals indicates a highly stable protein targeting system across eukaryotic diversity.}, journal = {Journal of molecular biology}, volume = {408}, number = {4}, pages = {643-653}, doi = {10.1016/j.jmb.2011.02.057}, pmid = {21376056}, issn = {1089-8638}, mesh = {Amino Acid Sequence ; Base Sequence ; Biodiversity ; Dinoflagellida/genetics/*metabolism ; Mitochondrial Proteins/*chemistry/genetics ; Molecular Sequence Data ; *Protein Sorting Signals ; Protein Transport ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {Protein targeting into mitochondria from the cytoplasm is fundamental to the cell biology of all eukaryotes. Our understanding of this process is heavily biased towards "model" organisms, such as animals and fungi, and it is less clear how conserved this process is throughout diverse eukaryotes. In this study, we have surveyed mitochondrial protein sorting signals from a representative of the dinoflagellate algae. Dinoflagellates are a phylum belonging to the group Alveolata, which also includes apicomplexan parasites and ciliates. We generated 46 mitochondrial gene sequences from the dinoflagellate Karlodinium micrum and analysed these for mitochondrial sorting signals. Most of the sequences contain predicted N-terminal peptide extensions that conform to mitochondrial targeting peptides from animals and fungi in terms of length, amino acid composition, and propensity to form amphipathic α-helices. The remainder lack predicted mitochondrial targeting peptides and represent carrier proteins of the inner mitochondrial membrane that have internal targeting signals in model eukaryotes. We tested for functional conservation of the dinoflagellate mitochondrial sorting signals by expressing K. micrum mitochondrial proteins in the fungus Saccharomyces cerevisiae. Both the N-terminal and internal targeting signals were sufficiently conserved to operate in this distantly related system. This study indicates that the character of mitochondrial sorting signals was well established prior to the radiation of major eukaryotic lineages and has shown remarkable conservation during long periods of evolution.}, }
@article {pmid21365259, year = {2011}, author = {Tachibana, M and Allen, AE and Kikutani, S and Endo, Y and Bowler, C and Matsuda, Y}, title = {Localization of putative carbonic anhydrases in two marine diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana.}, journal = {Photosynthesis research}, volume = {109}, number = {1-3}, pages = {205-221}, pmid = {21365259}, issn = {1573-5079}, mesh = {Amino Acid Sequence ; Carbon Dioxide/*metabolism ; Carbonic Anhydrases/genetics/*metabolism ; Cell Membrane/enzymology/metabolism/ultrastructure ; Chloroplasts/enzymology/metabolism/ultrastructure ; Cloning, Molecular ; Diatoms/*enzymology/genetics/metabolism/ultrastructure ; Gene Expression Regulation, Enzymologic ; Green Fluorescent Proteins ; Mitochondria/enzymology/metabolism/ultrastructure ; Phylogeny ; RNA, Messenger/genetics ; Recombinant Fusion Proteins ; Seawater ; Sequence Alignment ; Transformation, Genetic ; }, abstract = {It is believed that intracellular carbonic anhydrases (CAs) are essential components of carbon concentrating mechanisms in microalgae. In this study, putative CA-encoding genes were identified in the genome sequences of the marine diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. Subsequently, the subcellular localizations of the encoded proteins were determined. Nine and thirteen CA sequences were found in the genomes of P. tricornutum and T. pseudonana, respectively. Two of the β-CA genes in P. tricornutum corresponded to ptca1 and ptca2 identified previously. Immunostaining transmission electron microscopy of a PtCA1:YFP fusion expressed in the cells of P. tricornutum clearly showed the localization of PtCA1 within the central part of the pyrenoid structure in the chloroplast. Besides these two β-CA genes, P. tricornutum likely contains five α- and two γ-CA genes, whereas T. pseudonana has three α-, five γ-, four δ-, and one ζ-CA genes. Semi-quantitative reverse transcription PCR performed on mRNA from the two diatoms grown in changing light and CO(2) conditions revealed that levels of six putative α- and γ-CA mRNAs in P. tricornutum did not change between cells grown in air-level CO(2) and 5% CO(2). However, mRNA levels of one putative α-CA gene, CA-VII in P. tricornutum, were reduced in the dark compared to that in the light. In T. pseudonana, mRNA accumulation levels of putative α-CA (CA-1), ζ-CA (CA-3) and δ-CA (CA-7) were analyzed and all levels found to be significantly reduced when cells were grown in 0.16% CO(2). Intercellular localizations of eight putative CAs were analyzed by expressing GFP fusion in P. tricornutum and T. pseudonana. In P. tricornutum, CA-I and II localized in the periplastidial compartment, CA-III, VI, VII were found in the chloroplast endoplasmic reticulum, and CA-VIII was localized in the mitochondria. On the other hand, T. pseudonana CA-1 localized in the stroma and CA-3 was found in the periplasm. These results suggest that CAs are constitutively present in the four chloroplastic membrane systems in P. tricornutum and that CO(2) responsive CAs occur in the pyrenoid of P. tricornutum, and in the stroma and periplasm of T. pseudonana.}, }
@article {pmid21360638, year = {2011}, author = {Devlin, C and Greco, S and Martelli, F and Ivan, M}, title = {miR-210: More than a silent player in hypoxia.}, journal = {IUBMB life}, volume = {63}, number = {2}, pages = {94-100}, pmid = {21360638}, issn = {1521-6551}, support = {R01 CA155332/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Apoptosis ; Biomarkers/*analysis ; Cardiovascular Diseases/genetics/metabolism ; Cell Hypoxia/genetics ; Cell Line, Tumor ; Cell Survival ; DNA Repair ; Gene Expression Profiling ; Gene Expression Regulation ; Humans ; Hypoxia/genetics/*metabolism ; Hypoxia-Inducible Factor 1/genetics/*metabolism ; Mice ; Mice, Inbred Strains ; *MicroRNAs/biosynthesis/genetics ; Mitochondria/metabolism ; Molecular Targeted Therapy ; Neoplasms/genetics/metabolism ; Neovascularization, Pathologic/genetics/metabolism ; Oxidative Stress ; Prognosis ; }, abstract = {Multiple studies have consistently established that miR (microRNA)-210 induction is a feature of the hypoxic response in both normal and transformed cells. Here, we discuss the emerging biochemical functions of this miRNA and anticipate potential clinical applications. miR-210 is a robust target of hypoxia-inducible factor, and its overexpression has been detected in a variety of cardiovascular diseases and solid tumors. High levels of miR-210 have been linked to an in vivo hypoxic signature and associated with adverse prognosis in cancer patients. A wide spectrum of miR-210 targets have been identified, with roles in mitochondrial metabolism, angiogenesis, DNA repair, and cell survival. Such targets may broadly affect the evolution of tumors and other pathological settings, such as ischemic disorders. Harnessing the knowledge of miR-210's actions may lead to novel diagnostic and therapeutic approaches.}, }
@article {pmid21352954, year = {2011}, author = {Piccinali, RV and Marcet, PL and Ceballos, LA and Kitron, U and Gürtler, RE and Dotson, EM}, title = {Genetic variability, phylogenetic relationships and gene flow in Triatoma infestans dark morphs from the Argentinean Chaco.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {11}, number = {5}, pages = {895-903}, pmid = {21352954}, issn = {1567-7257}, support = {R01 TW005836/TW/FIC NIH HHS/United States ; R01 TW005836-01/TW/FIC NIH HHS/United States ; #R01TW05836/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Argentina ; Base Sequence ; DNA, Intergenic ; Electron Transport Complex IV ; Gene Expression Regulation ; *Gene Flow ; *Genetic Variation ; Haplotypes ; Mitochondria/enzymology ; Phylogeny ; Pigments, Biological ; Triatoma/*genetics ; }, abstract = {The recent discovery of sylvatic populations of Triatoma infestans outside the Andean Valleys of Bolivia prompted an evolutionary question about the putative ancestral area of origin and dispersal of the species, and an epidemiological question regarding the possible role of these sylvatic populations in the recolonization process of insecticide-treated houses. The finding of a population of sylvatic melanic T. infestans (dark morphs) in the Argentinean dry Chaco at 7 km from a peridomestic bug population of typical coloration gave us the opportunity to test both questions simultaneously by employing phylogenetic and population genetic approaches. For this purpose we analyzed sylvatic and peridomestic bugs using sequence-based mitochondrial and nuclear markers (mtCOI and ITS-1) and microsatellites. Sylvatic bugs were confirmed to be T. infestans and not hybrids, and showed high levels of genetic variability and departures from neutral expectations for mtCOI variation. New ITS-1 and mtCOI haplotypes were recorded, as well as haplotypes shared with peridomestic and/or domestic bugs from previous records. The peridomestic population was invariant for ITS-1 and mtCOI, but showed variability for microsatellites and signatures of a population bottleneck, probably due to a limited number of founders. Phylogenetic analyses were consistent with the presence of ancestral haplotypes in sylvatic bugs. According to F-statistics and assignment methods there was a significant differentiation between sylvatic and peridomestic bugs and gene flow was low and asymmetric, with more bugs moving from the peridomicile to the sylvatic environment. These results support the hypothesis of the Chaco region as the area of origin of T. infestans, and a limited role of sylvatic melanic T. infestans in peridomestic infestation in the Argentinean Chaco.}, }
@article {pmid21352234, year = {2011}, author = {Lazzarotto, F and Teixeira, FK and Rosa, SB and Dunand, C and Fernandes, CL and de Vasconcelos Fontenele, A and Silveira, JAG and Verli, H and Margis, R and Margis-Pinheiro, M}, title = {Ascorbate peroxidase-related (APx-R) is a new heme-containing protein functionally associated with ascorbate peroxidase but evolutionarily divergent.}, journal = {The New phytologist}, volume = {191}, number = {1}, pages = {234-250}, doi = {10.1111/j.1469-8137.2011.03659.x}, pmid = {21352234}, issn = {1469-8137}, mesh = {Amino Acid Sequence ; Antioxidants/metabolism ; Arabidopsis/genetics ; Ascorbate Peroxidases ; Catalytic Domain ; Chloroplasts/enzymology ; Conserved Sequence ; Dimerization ; *Evolution, Molecular ; Mitochondria/enzymology ; Molecular Sequence Data ; Oryza/*enzymology/genetics/growth &amp; development ; Peroxidases/chemistry/genetics/*physiology ; Phylogeny ; Plant Proteins/chemistry/genetics/*physiology ; Populus/genetics ; RNA, Messenger/metabolism ; Sequence Alignment ; Stress, Physiological ; }, abstract = {• Peroxidases are involved in several important processes, such as development and responses to environmental cues. In higher plants, most peroxidases are encoded by large, multigenic families that mainly originated from gene and chromosomal duplications. • Using phylogenetic, genomic and functional analyses, we have identified and characterized a new class of putative heme peroxidases, called ascorbate peroxidase-related (APx-R), which arose specifically in the lineage of plants. • The APx-R protein is structurally related to the ascorbate peroxidases, although the active site contains many conserved substitutions. Unlike all other plant peroxidases, which are encoded by gene families, APx-R is encoded by a single-copy gene in virtually all the species analyzed. APx-R proteins are targeted to the chloroplast and can physically interact with chloroplastic APx proteins. APx-R-knockdown rice (Oryza sativa) plants presented delayed development and a disturbed steady state of the antioxidant system compared with wild type. Moreover, the accumulation of APx-R transcripts was modulated by drought, UV irradiation, cold, and aluminum exposure in rice, suggesting the involvement of APx-R in the environmental stress response. • Our results reveal the existence of a new class of heme peroxidase which seems to play a role in the antioxidant system in plants, probably by modulating the activity of chloroplastic APx proteins.}, }
@article {pmid21338551, year = {2011}, author = {Dijcker, JC and Plantinga, EA and van Baal, J and Hendriks, WH}, title = {Influence of nutrition on feline calcium oxalate urolithiasis with emphasis on endogenous oxalate synthesis.}, journal = {Nutrition research reviews}, volume = {24}, number = {1}, pages = {96-110}, doi = {10.1017/S0954422410000351}, pmid = {21338551}, issn = {1475-2700}, mesh = {Amino Acid Transport Systems/metabolism ; *Animal Nutritional Physiological Phenomena ; Animals ; Calcium Oxalate/*metabolism ; Calcium, Dietary/*metabolism ; Carnivory ; Cat Diseases/*etiology/metabolism ; Cats ; *Diet ; Urinary Calculi/*metabolism ; }, abstract = {The prevalence of calcium oxalate (CaOx) uroliths detected in cats with lower urinary tract disease has shown a sharp increase over the last decades with a concomitant reciprocal decrease in the occurrence of struvite (magnesium ammonium phosphate) uroliths. CaOx stone-preventative diets are available nowadays, but seem to be marginally effective, as CaOx urolith recurrence occurs in patients fed these diets. In order to improve the preventative measures against CaOx urolithiasis, it is important to understand its aetiopathogenesis. The main research focus in CaOx formation in cats has been on the role of Ca, whereas little research effort has been directed towards the role and origin of urinary oxalates. As in man, the exogenous origin of urinary oxalates in cats is thought to be of minor importance, although the precise contribution of dietary oxalates remains unclear. The generally accepted dietary risk factors for CaOx urolithiasis in cats are discussed and a model for the biosynthetic pathways of oxalate in feline liver is provided. Alanine:glyoxylate aminotransferase 1 (AGT1) in endogenous oxalate metabolism is a liver-specific enzyme targeted in the mitochondria in cats, and allows for efficient conversion of glyoxylate to glycine when fed a carnivorous diet. The low peroxisomal activity of AGT1 in cat liver is compatible with the view that felids utilised a low-carbohydrate diet throughout evolution. Future research should focus on understanding de novo biosynthesis of oxalate in cats and their adaptation(s) in oxalate metabolism, and on dietary oxalate intake and absorption by cats.}, }
@article {pmid21336668, year = {2011}, author = {Rumpler, Y and Hauwy, M and Fausser, JL and Roos, C and Zaramody, A and Andriaholinirina, N and Zinner, D}, title = {Comparing chromosomal and mitochondrial phylogenies of the Indriidae (Primates, Lemuriformes).}, journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology}, volume = {19}, number = {2}, pages = {209-224}, pmid = {21336668}, issn = {1573-6849}, mesh = {Animals ; Biological Evolution ; Chromosomes/*genetics ; Genetic Speciation ; Mitochondria/*genetics ; *Phylogeny ; Strepsirhini/*genetics ; }, abstract = {The Malagasy primate family Indriidae comprises three genera with up to 19 species. Cytogenetic and molecular phylogenies of the Indriidae have been performed with special attention to the genus Propithecus. Comparative R-banding and FISH with human paints were applied to karyotypes of representatives of all three genera and confirmed most of the earlier R-banding results. However, additional chromosomal rearrangements were detected. A reticulated and a cladistic phylogeny, the latter including hemiplasies, have been performed. Cladistic analysis of cytogenetic data resulted in a phylogenetic tree revealing (1) monophyly of the family Indriidae, (2) monophyly of the genus Avahi, (3) sister-group relationships between Propithecus diadema and Propithecus edwardsi, and (4) the grouping of the latter with Indri indri, Propithecus verreauxi, and Propithecus tattersalli, and thus suggesting paraphyly of the genus Propithecus. A molecular phylogeny based on complete mitochondrial cytochrome b sequences of 16 species indicated some identical relationships, such as the monophyly of Avahi and the sister-group relationships of the eastern (P. diadema and P. edwardsi) to the western Propithecus species (P. verreauxi, Propithecus coquereli, and P. tattersalli). However, the main difference between the molecular and cytogenetic phylogenies consists in an early divergence of Indri in the molecular phylogeny while in the chromosomal phylogeny it is nested within Propithecus. The similarities and differences between molecular and cytogenetic phylogenies in relation to data on the species' geographic distributions and mating systems allow us to propose a scenario of the evolution of Indriidae. Chromosomal and molecular processes alone or in combination created a reproductive barrier that was then followed by further speciation processes.}, }
@article {pmid21335340, year = {2011}, author = {Chan, YW and Mohr, R and Millard, AD and Holmes, AB and Larkum, AW and Whitworth, AL and Mann, NH and Scanlan, DJ and Hess, WR and Clokie, MR}, title = {Discovery of cyanophage genomes which contain mitochondrial DNA polymerase.}, journal = {Molecular biology and evolution}, volume = {28}, number = {8}, pages = {2269-2274}, doi = {10.1093/molbev/msr041}, pmid = {21335340}, issn = {1537-1719}, mesh = {Bacteriophages/classification/*enzymology/*genetics ; Cyanobacteria/virology ; DNA, Mitochondrial/*genetics ; DNA-Directed DNA Polymerase/*genetics/metabolism ; Evolution, Molecular ; Gene Expression Regulation, Viral ; Genome, Viral ; Phylogeny ; }, abstract = {DNA polymerase γ is a family A DNA polymerase responsible for the replication of mitochondrial DNA in eukaryotes. The origins of DNA polymerase γ have remained elusive because it is not present in any known bacterium, though it has been hypothesized that mitochondria may have inherited the enzyme by phage-mediated nonorthologous displacement. Here, we present an analysis of two full-length homologues of this gene, which were found in the genomes of two bacteriophages, which infect the chlorophyll-d containing cyanobacterium Acaryochloris marina. Phylogenetic analyses of these phage DNA polymerase γ proteins show that they branch deeply within the DNA polymerase γ clade and therefore share a common origin with their eukaryotic homologues. We also found homologues of these phage polymerases in the environmental Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA) database, which fell in the same clade. An analysis of the CAMERA assemblies containing the environmental homologues together with the filter fraction metadata indicated some of these assemblies may be of bacterial origin. We also show that the phage-encoded DNA polymerase γ is highly transcribed as the phage genomes are replicated. These findings provide data that may assist in reconstructing the evolution of mitochondria.}, }
@article {pmid21334091, year = {2011}, author = {Dunning Hotopp, JC}, title = {Horizontal gene transfer between bacteria and animals.}, journal = {Trends in genetics : TIG}, volume = {27}, number = {4}, pages = {157-163}, pmid = {21334091}, issn = {0168-9525}, support = {DP2 OD007372/OD/NIH HHS/United States ; DP2 OD007372-01/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*genetics ; Biological Evolution ; *Gene Transfer, Horizontal ; Genome ; Humans ; }, abstract = {Horizontal gene transfer is increasingly described between bacteria and animals. Such transfers that are vertically inherited have the potential to influence the evolution of animals. One classic example is the transfer of DNA from mitochondria and chloroplasts to the nucleus after the acquisition of these organelles by eukaryotes. Even today, many of the described instances of bacteria-to-animal transfer occur as part of intimate relationships such as those of endosymbionts and their invertebrate hosts, particularly insects and nematodes, while numerous transfers are also found in asexual animals. Both of these observations are consistent with modern evolutionary theory, in particular the serial endosymbiotic theory and Muller's ratchet. Although it is tempting to suggest that these particular lifestyles promote horizontal gene transfer, it is difficult to ascertain given the nonrandom sampling of animal genome sequencing projects and the lack of a systematic analysis of animal genomes for such transfers.}, }
@article {pmid21333758, year = {2011}, author = {de la Rua, N and Stevens, L and Dorn, PL}, title = {High genetic diversity in a single population of Triatoma sanguisuga (LeConte, 1855) inferred from two mitochondrial markers: Cytochrome b and 16S ribosomal DNA.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {11}, number = {3}, pages = {671-677}, doi = {10.1016/j.meegid.2011.02.009}, pmid = {21333758}, issn = {1567-7257}, mesh = {Animals ; Base Sequence ; Cytochromes b/*genetics ; Disease Vectors ; Female ; Genetic Markers ; Genetic Variation ; Haplotypes ; Host-Parasite Interactions ; Male ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; RNA, Ribosomal, 16S/*genetics ; Triatoma/classification/*genetics/parasitology ; Trypanosoma cruzi/physiology ; }, abstract = {Chagas disease remains endemic across much of Latin America, but is largely enzootic--restricted to wild mammals and triatomine vectors in the United States. Within the United States, there are ten recognized species of triatomines and 18 mammals reported naturally infected with Trypanosoma cruzi, the causative agent of Chagas disease. However, only six cases of autochthonous vector-borne transmission of T. cruzi to humans have been reported in the United States. As a follow-up to the sixth reported case, triatomine insects were collected from the index case site, in a rural area of New Orleans, LA, USA. During the summer months of 2006 and 2007, 344 Triatoma sanguisuga were collected and showed a T. cruzi infection prevalence of 56%. A subset of these insects was analyzed to infer intraspecific genetic variation from a 606 bp fragment of cytochrome b (n=54) and a 340 bp fragment of 16S ribosomal DNA (n=17). From the 54 samples, 37 cytb haplotypes (H(d)=0.978) were observed and 14.7% of positions were polymorphic. Phylogenetic analysis divides the population into two distinct groups with an average pairwise genetic distance of ~5%. The 16S rDNA sequences revealed 6 haplotypes among 17 specimens (H(d)=0.713) with 1.2% of the positions exhibiting polymorphisms. 16S polymorphism data support the concept of two groups within this single population. The genetic distance of Group 1 from Group 2 suggests that Group 1 could represent a sub-species as this level of divergence is similar to that observed among other triatomine subspecies.}, }
@article {pmid21333023, year = {2011}, author = {Gross, J and Bhattacharya, D}, title = {Endosymbiont or host: who drove mitochondrial and plastid evolution?.}, journal = {Biology direct}, volume = {6}, number = {}, pages = {12}, pmid = {21333023}, issn = {1745-6150}, mesh = {*Biological Evolution ; Genome/genetics ; Mitochondria/*genetics ; Models, Biological ; Plastids/*genetics ; Prokaryotic Cells/metabolism ; *Symbiosis ; }, abstract = {The recognition that mitochondria and plastids are derived from alphaproteobacterial and cyanobacterial endosymbionts, respectively, was one of the greatest advances in modern evolutionary biology. Researchers have yet however to provide detailed cell biological descriptions of how these once free-living prokaryotes were transformed into intracellular organelles. A key area of study in this realm is elucidating the evolution of the molecular machines that control organelle protein topogenesis. Alcock et al. (Science 2010, 327 [5966]:649-650) suggest that evolutionary innovations that established the mitochondrial protein sorting system were driven by the alphaproteobacterial endosymbiont (an "insiders' perspective"). In contrast, here we argue that evolution of mitochondrial and plastid topogenesis may better be understood as an outcome of selective pressures acting on host cell chromosomes (the "outsiders' view").}, }
@article {pmid21325020, year = {2011}, author = {Kim, YK and Hong, YJ and Min, MS and Kim, KS and Kim, YJ and Voloshina, I and Myslenkov, A and Smith, GJ and Cuong, ND and Tho, HH and Han, SH and Yang, DH and Kim, CB and Lee, H}, title = {Genetic status of Asiatic black bear (Ursus thibetanus) reintroduced into South Korea based on mitochondrial DNA and microsatellite loci analysis.}, journal = {The Journal of heredity}, volume = {102}, number = {2}, pages = {165-174}, doi = {10.1093/jhered/esq121}, pmid = {21325020}, issn = {1465-7333}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; Genetics, Population ; Genotype ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Republic of Korea ; Ursidae/*genetics ; }, abstract = {The Asiatic black bear is one of the most endangered mammals in South Korea owing to population declines resulting from human exploitation and habitat fragmentation. To restore the black bear population in South Korea, 27 bear cubs from North Korea and Russian Far East (Primorsky Krai) were imported and released into Jirisan National Park, a reservoir of the largest wild population in South Korea, in 2004. To monitor the success of this reintroduction, the genetic diversity and population structure of the reintroduced black bears were measured using both mitochondrial and nuclear DNA markers. Mitochondrial D-loop region DNA sequences (615 bp) of 43 Japanese black bears from previous study and 14 Southeast Asian black bears in this study were employed to obtain phylogenetic inference of the reintroduced black bears. The mitochondrial phylogeny indicated Asiatic black bear populations from Russian Far East and North Korea form a single evolutionary unit distinct from populations from Japan and Southeast Asia. Mean expected heterozygosity (H(E)) across 16 microsatellite loci was 0.648 for Russian and 0.676 for North Korean populations. There was a moderate but significant level of microsatellite differentiation (F(ST) = 0.063) between black bears from the 2 source areas. In addition, genetic evidences revealed that 2 populations are represented as diverging groups, with lingering genetic admixture among individuals of 2 source populations. Relatedness analysis based on genetic markers indicated several discrepancies with the pedigree records. Implication of the phylogenetic and genetic evidences on long-term management of Asiatic black bears in South Korea is discussed.}, }
@article {pmid21324380, year = {2011}, author = {Dsouli, N and Delsuc, F and Michaux, J and De Stordeur, E and Couloux, A and Veuille, M and Duvallet, G}, title = {Phylogenetic analyses of mitochondrial and nuclear data in haematophagous flies support the paraphyly of the genus Stomoxys (Diptera: Muscidae).}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {11}, number = {3}, pages = {663-670}, doi = {10.1016/j.meegid.2011.02.004}, pmid = {21324380}, issn = {1567-7257}, mesh = {Animals ; Bayes Theorem ; Cytochromes b/genetics ; DNA, Concatenated ; DNA, Ribosomal Spacer ; Electron Transport Complex IV/genetics ; *Genetic Speciation ; Markov Chains ; Mitochondria/*genetics ; Models, Genetic ; Monte Carlo Method ; Muscidae/classification/*genetics ; *Phylogeny ; Phylogeography ; Sequence Analysis, DNA ; }, abstract = {The genus Stomoxys Geoffroy (Diptera; Muscidae) contains species of parasitic flies that are of medical and economic importance. We conducted a phylogenetic analysis including 10 representative species of the genus including multiple exemplars, together with the closely related genera Prostomoxys Zumpt, Haematobosca Bezzi, and Haematobia Lepeletier &amp; Serville. Phylogenetic relationships were inferred using maximum likelihood and Bayesian methods from DNA fragments from the cytochrome c oxidase subunit I (COI, 753bp) and cytochrome b (CytB, 587bp) mitochondrial genes, and the nuclear ribosomal internal transcribed spacer 2 (ITS2, 426bp). The combination of mitochondrial and nuclear data strongly supports the paraphyly of the genus Stomoxys because of the inclusion of Prostomoxys saegerae Zumpt. This unexpected result suggests that Prostomoxys should be renamed into Stomoxys. Also, the deep molecular divergence observed between the subspecies Stomoxys niger niger Macquart and S. niger bilineatus Grünbreg led us to propose that they should rather be considered as distinct species, in agreement with ecological data. Bayesian phylogenetic analyses support three distinct lineages within the genus Stomoxys with a strong biogeographical component. The first lineage consists solely of the divergent Asian species S. indicus Picard which appears as the sister-group to all remaining Stomoxys species. The second clade groups the strictly African species Stomoxys inornatus Grünbreg, Stomoxys transvittatus Villeneuve, Stomoxys omega Newstead, and Stomoxys pallidus Roubaud. Finally, the third clade includes both African occurring and more widespread species such as the livestock pest Stomoxys calcitrans Linnaeus. Divergence time estimates indicate that the genus Stomoxys originated in the late Oligocene around 30 million years ago, with the major lineages diversifying in the Early Miocene between 20 and 15 million years ago at a time when temperate forests developed in the Northern Hemisphere.}, }
@article {pmid21321019, year = {2011}, author = {Su, D and Lieberman, A and Lang, BF and Simonovic, M and Söll, D and Ling, J}, title = {An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine.}, journal = {Nucleic acids research}, volume = {39}, number = {11}, pages = {4866-4874}, pmid = {21321019}, issn = {1362-4962}, support = {GM022854/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Codon ; Evolution, Molecular ; Histidine-tRNA Ligase/metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; RNA/*chemistry/genetics/metabolism ; RNA, Mitochondrial ; RNA, Transfer/chemistry/genetics/metabolism ; RNA, Transfer, His/*chemistry/genetics/metabolism ; RNA, Transfer, Thr/*chemistry/genetics/metabolism ; Saccharomyces cerevisiae/enzymology/*genetics ; Sequence Alignment ; Threonine/*metabolism ; Threonine-tRNA Ligase/metabolism ; }, abstract = {The standard genetic code is used by most living organisms, yet deviations have been observed in many genomes, suggesting that the genetic code has been evolving. In certain yeast mitochondria, CUN codons are reassigned from leucine to threonine, which requires an unusual tRNA(Thr) with an enlarged 8-nt anticodon loop (). To trace its evolutionary origin we performed a comprehensive phylogenetic analysis which revealed that evolved from yeast mitochondrial tRNA(His). To understand this tRNA identity change, we performed mutational and biochemical experiments. We show that Saccharomyces cerevisiae mitochondrial threonyl-tRNA synthetase (MST1) could attach threonine to both and the regular , but not to the wild-type tRNA(His). A loss of the first nucleotide (G(-1)) in tRNA(His) converts it to a substrate for MST1 with a K(m) value (0.7 μM) comparable to that of (0.3 μM), and addition of G(-1) to allows efficient histidylation by histidyl-tRNA synthetase. We also show that MST1 from Candida albicans, a yeast in which CUN codons remain assigned to leucine, could not threonylate , suggesting that MST1 has coevolved with . Our work provides the first clear example of a recent recoding event caused by alloacceptor tRNA gene recruitment.}, }
@article {pmid21317544, year = {2010}, author = {Roy, S and Ueda, M and Kadowaki, K and Tsutsumi, N}, title = {Different status of the gene for ribosomal protein S16 in the chloroplast genome during evolution of the genus Arabidopsis and closely related species.}, journal = {Genes &amp; genetic systems}, volume = {85}, number = {5}, pages = {319-326}, doi = {10.1266/ggs.85.319}, pmid = {21317544}, issn = {1880-5779}, mesh = {Arabidopsis/*genetics ; Base Sequence ; *Biological Evolution ; Genes, Plant/genetics ; *Genome, Chloroplast ; Molecular Sequence Data ; Phylogeny ; RNA Splicing ; Ribosomal Proteins/*genetics ; Sequence Alignment ; }, abstract = {The ribosomal protein S16 (RPS16), the product of the rps16, is generally encoded in the chloroplast genomes of flowering plants. However, it has been reported that chloroplast-encoded RPS16 in mono- and dicotyledonous plants has been substituted by the product of nuclear-encoded rps16, which was transferred from the mitochondria to the nucleus before the early divergence of angiosperms. Current databases show that the chloroplast-encoded rps16 has become a pseudogene in four species of the Brassicaceae (Aethionema grandiflorum, Arabis hirsuta, Draba nemorosa, and Lobularia maritima). Further analysis of Arabidopsis thaliana and its close relatives has shown that pseudogenization has also occurred via the loss of its splicing capacity (Arabidopsis thaliana and Olimarabidopsis pumila). In contrast, the spliced product of chloroplast-encoded rps16 is observed in close relatives of Arabidopsis thaliana (Arabidopsis arenosa, Arabidopsis lyrata, and Crucihimalaya lasiocarpa). In this study, we identified the different functional status of rps16 in several chloroplast genomes in the genus Arabidopsis and its close relatives. Our results strongly suggest that nuclear- and chloroplast-encoded rps16 genes coexisted for at least 126 million years. We raise the possibility of the widespread pseudogenization of rps16 in the angiosperm chloroplast genomes via the loss of its splicing capacity, even when the rps16 encoded in the chloroplast genome is transcriptionally active.}, }
@article {pmid21315164, year = {2011}, author = {Carvalho-Costa, LF and Piorski, NM and Willis, SC and Galetti, PM and Ortí, G}, title = {Molecular systematics of the neotropical shovelnose catfish genus Pseudoplatystoma Bleeker 1862 based on nuclear and mtDNA markers.}, journal = {Molecular phylogenetics and evolution}, volume = {59}, number = {1}, pages = {177-194}, doi = {10.1016/j.ympev.2011.02.005}, pmid = {21315164}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Catfishes/classification/*genetics ; Cytochromes b/genetics ; Genes, RAG-1 ; Genetic Markers ; Haplotypes ; Introns ; Likelihood Functions ; Mitochondria/*genetics ; Multilocus Sequence Typing ; *Phylogeny ; Rivers ; South America ; Tropical Climate ; }, abstract = {Pseudoplatystoma is a commercially important genus of Neotropical migratory catfishes widely distributed in all major river basins of South America. Historically, only three species were recognized, but a recent revision proposed eight putative morphospecies for the genus. A molecular study based on mitochondria DNA (mtDNA) provided support for recognition of only some of the species and raised questions about species boundaries in this group. We present a more encompassing analysis based on mtDNA (cytochrome b, 818bp) and nuclear DNA-based phylogenies (Rag1 intron 1, 664bp and S7 intron 1, 635bp) for a more extensive sampling (279 individuals from 42 localities) of all putative species in all major river basins. Patterns generated by individual gene genealogies and a multispecies coalescent analysis provided evidence to suggest recognition of only four distinct species in this genus: Pseudoplatystoma magdaleniatum, Pseudoplatystoma corruscans, Pseudoplatystoma tigrimun (sensu lato) and Pseudoplatystoma fasciatum (sensu lato). The species phylogeny places P. magdaleniatum as the sister group to all the other species in the genus, but the relationships among P. fasciatum s.l, P. tigrimum s.l., and P. corruscans could not be resolved with confidence.}, }
@article {pmid21307286, year = {2011}, author = {Araújo, WL and Nunes-Nesi, A and Osorio, S and Usadel, B and Fuentes, D and Nagy, R and Balbo, I and Lehmann, M and Studart-Witkowski, C and Tohge, T and Martinoia, E and Jordana, X and Damatta, FM and Fernie, AR}, title = {Antisense inhibition of the iron-sulphur subunit of succinate dehydrogenase enhances photosynthesis and growth in tomato via an organic acid-mediated effect on stomatal aperture.}, journal = {The Plant cell}, volume = {23}, number = {2}, pages = {600-627}, pmid = {21307286}, issn = {1532-298X}, mesh = {Biomass ; Carbon Dioxide/metabolism ; *Citric Acid Cycle ; Cloning, Molecular ; Iron-Sulfur Proteins/metabolism ; Solanum lycopersicum/genetics/*growth &amp; development ; Mitochondria/metabolism ; Oxygen Consumption ; *Photosynthesis ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plant Stomata/*drug effects ; Plant Transpiration ; Plants, Genetically Modified/genetics/growth &amp; development ; RNA, Antisense/genetics ; RNA, Plant/genetics ; Succinate Dehydrogenase/genetics/*metabolism ; }, abstract = {Transgenic tomato (Solanum lycopersicum) plants expressing a fragment of the Sl SDH2-2 gene encoding the iron sulfur subunit of the succinate dehydrogenase protein complex in the antisense orientation under the control of the 35S promoter exhibit an enhanced rate of photosynthesis. The rate of the tricarboxylic acid (TCA) cycle was reduced in these transformants, and there were changes in the levels of metabolites associated with the TCA cycle. Furthermore, in comparison to wild-type plants, carbon dioxide assimilation was enhanced by up to 25% in the transgenic plants under ambient conditions, and mature plants were characterized by an increased biomass. Analysis of additional photosynthetic parameters revealed that the rate of transpiration and stomatal conductance were markedly elevated in the transgenic plants. The transformants displayed a strongly enhanced assimilation rate under both ambient and suboptimal environmental conditions, as well as an elevated maximal stomatal aperture. By contrast, when the Sl SDH2-2 gene was repressed by antisense RNA in a guard cell-specific manner, changes in neither stomatal aperture nor photosynthesis were observed. The data obtained are discussed in the context of the role of TCA cycle intermediates both generally with respect to photosynthetic metabolism and specifically with respect to their role in the regulation of stomatal aperture.}, }
@article {pmid21300273, year = {2011}, author = {Richards, TA and Archibald, JM}, title = {Cell evolution: gene transfer agents and the origin of mitochondria.}, journal = {Current biology : CB}, volume = {21}, number = {3}, pages = {R112-4}, doi = {10.1016/j.cub.2010.12.036}, pmid = {21300273}, issn = {1879-0445}, mesh = {Alphaproteobacteria/*genetics ; Biological Evolution ; DNA Transposable Elements ; *Gene Transfer, Horizontal ; Mitochondria/*genetics ; *Models, Genetic ; Oceans and Seas ; Phylogeny ; Seawater/microbiology ; }, abstract = {Recently, α-proteobacteria have been shown to possess virus-like gene transfer agents that facilitate high frequency gene transfer in natural environments between distantly related lineages. This system could have driven the genomic integration of the mitochondrial progenitor and its proto-eukaryote host and contributed to the evolutionary mosaic of genes seen in modern-day prokaryotic and eukaryotic genomes.}, }
@article {pmid21294799, year = {2011}, author = {Vergilino, R and Markova, S and Ventura, M and Manca, M and Dufresne, F}, title = {Reticulate evolution of the Daphnia pulex complex as revealed by nuclear markers.}, journal = {Molecular ecology}, volume = {20}, number = {6}, pages = {1191-1207}, doi = {10.1111/j.1365-294X.2011.05004.x}, pmid = {21294799}, issn = {1365-294X}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Daphnia/classification/*genetics ; Hybridization, Genetic/genetics ; Microsatellite Repeats/genetics ; Phylogeny ; Polyploidy ; rab4 GTP-Binding Proteins/genetics ; }, abstract = {The study of species complexes is of particular interest to understand how evolutionary young species maintain genomic integrity. The Daphnia pulex complex has been intensively studied as it includes species that dominate freshwater environments in the Northern hemisphere and as it is the sole North American complex that shows transitions to obligate parthenogenesis. Past studies using mitochondrial markers have revealed the presence of 10 distinct lineages in the complex. This study is the first to examine genetic relationships among seven species of the complex at nuclear markers (nine microsatellite loci and one protein-coding gene). Clones belonging to the seven species of the Daphnia pulex complex were characterized at the mitochondrial NADH dehydrogenase (ND5) gene and at the Lactate dehydrogenase (LDH) locus. K-means, principal coordinate analyses and phylogenetic network analyses on the microsatellite data all separated European D. pulicaria, D. tenebrosa, North American D. pulex, D. pulicaria and their hybrids into distinct clusters. The hybrid cluster was composed of diploid and polyploid hybrids with D. pulex mitochondria and some clones with D. pulicaria mitochondria. By contrast, the phylogeny of the D. pulex complex using Rab4 was not well resolved but still showed clusters consisting mostly of D. pulex alleles and others of D. pulicaria alleles. Incomplete lineage sorting and hybridization may obscure genetic relationships at this locus. This study shows that hybridization and introgression have played an important role in the evolution of this complex.}, }
@article {pmid21293046, year = {2011}, author = {Stairs, CW and Roger, AJ and Hampl, V}, title = {Eukaryotic pyruvate formate lyase and its activating enzyme were acquired laterally from a Firmicute.}, journal = {Molecular biology and evolution}, volume = {28}, number = {7}, pages = {2087-2099}, doi = {10.1093/molbev/msr032}, pmid = {21293046}, issn = {1537-1719}, support = {MOP 62809//Canadian Institutes of Health Research/Canada ; }, mesh = {Acetyltransferases/*genetics ; Archamoebae/enzymology/genetics ; Bacterial Proteins/genetics ; Bayes Theorem ; Computer Simulation ; Enzymes/*genetics ; Eukaryota/enzymology/*genetics ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Gram-Positive Bacteria/enzymology/*genetics ; Phylogeny ; }, abstract = {Most of the major groups of eukaryotes have microbial representatives that thrive in low oxygen conditions. Those that have been studied in detail generate ATP via pathways involving anaerobically functioning enzymes of pyruvate catabolism that are typically absent in aerobic eukaryotes and whose origins remain controversial. These enzymes include pyruvate:ferredoxin oxidoreductase, pyruvate:NADP(+) oxidoreductase, and pyruvate formate lyase (Pfl). Pfl catalyzes the nonoxidative generation of formate and acetyl-Coenzyme A (CoA) from pyruvate and CoA and is activated by Pfl activating enzyme (Pfla). Within eukaryotes, this extremely oxygen-sensitive pathway was first described in the hydrogenosomes of anaerobic chytrid fungi and has more recently been characterized in the mitochondria and chloroplasts of the chlorophyte alga Chlamydomonas reinhardtii. To clarify the origins of this pathway, we have comprehensively searched for homologs of Pfl and Pfla in publicly available large-scale eukaryotic genomic and cDNA sequencing data, including our own from the anaerobic amoebozoan Mastigamoeba balamuthi. Surprisingly, we find that these enzymes are widely distributed and are present in diverse facultative or obligate anaerobic eukaryotic representatives of the archaeplastidan, metazoan, amoebozoan, and haptophyte lineages. Using maximum likelihood and Bayesian phylogenetic methods, we show that the eukaryotic Pfl and Pfla sequences each form monophyletic groups that are most closely related to homologs in firmicute gram-positive bacteria. Topology tests exclude both α-proteobacterial and cyanobacterial affinities for these genes suggesting that neither originated from the endosymbiotic ancestors of mitochondria or chloroplasts. Furthermore, the topologies of the eukaryote portion of the Pfl and Pfla trees significantly differ from well-accepted eukaryote relationships. Collectively, these results indicate that the Pfl pathway was first acquired by lateral gene transfer into a eukaryotic lineage most probably from a firmicute bacterial lineage and that it has since been spread across diverse eukaryotic groups by more recent eukaryote-to-eukaryote transfer events.}, }
@article {pmid21292038, year = {2011}, author = {Yu, L and Wang, X and Ting, N and Zhang, Y}, title = {Mitogenomic analysis of Chinese snub-nosed monkeys: Evidence of positive selection in NADH dehydrogenase genes in high-altitude adaptation.}, journal = {Mitochondrion}, volume = {11}, number = {3}, pages = {497-503}, doi = {10.1016/j.mito.2011.01.004}, pmid = {21292038}, issn = {1872-8278}, mesh = {*Adaptation, Biological ; Altitude ; Animals ; China ; Cold Temperature ; Colobinae/genetics/*physiology ; DNA, Mitochondrial/chemistry/genetics ; Energy Metabolism ; *Genome, Mitochondrial ; Hypoxia ; Mitochondria/genetics/*physiology ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Oxidative Phosphorylation ; Sequence Analysis, DNA ; }, abstract = {Chinese snub-nosed monkeys belong to the genus Rhinopithecus and are limited in distribution to six isolated mountainous areas in the temperate regions of Central and Southwest China. Compared to the other members of the subfamily Colobinae (or leaf-eating monkeys), these endangered primates are unique in being adapted to a high altitude environment and display a remarkable ability to tolerate low temperatures and hypoxia. They thus offer an interesting organismal model of adaptation to extreme environmental stress. Mitochondria generate energy by oxidative phosphorylation (OXPHOS) and play important roles in oxygen usage and energy metabolism. We analyzed the mitochondrial genomes of two Chinese snub-nosed monkey species and eight other colobines in the first attempt to understand the genetic basis of high altitude adaptation in non-human primates. We found significant evidence of positive selection in one Chinese snub-nosed monkey, Rhinopithecus roxellana, which is suggestive of adaptive change related to high altitude and cold weather stress. In addition, our study identified two potentially important adaptive amino acid residues (533 and 3307) in the NADH2 and NADH6 genes, respectively. Surprisingly, no evidence for positive selection was found in Rhinopithecus bieti (the other Chinese snub-nosed monkey analyzed). This finding is intriguing, especially considering that R. bieti inhabits a higher altitudinal distribution than R. roxellana. We hypothesize that a different adaptive genetic basis to high altitude survival exists in R. bieti from those seen in other mammals, and that positive selection and functionally associated mutations in this species may be detected in nuclear genes related to energy and oxygen metabolism. More information on the structure, function, and evolution of mitochondrial and nuclear genomes in Chinese snub-nosed monkeys is required to reveal the molecular mechanisms that underlie adaptations to high altitude survival in non-human primates.}, }
@article {pmid21289219, year = {2011}, author = {Roth, J and Szulc, AL and Danoff, A}, title = {Energy, evolution, and human diseases: an overview.}, journal = {The American journal of clinical nutrition}, volume = {93}, number = {4}, pages = {875S-83}, doi = {10.3945/ajcn.110.001909}, pmid = {21289219}, issn = {1938-3207}, mesh = {Adipose Tissue/physiology ; *Biological Evolution ; *Energy Metabolism ; Humans ; *Immunity ; *Infections ; Life Expectancy ; *Obesity ; Reproduction/physiology ; }, abstract = {In the symposium entitled "Transcriptional controls of energy sensing," the authors presented recent advances on 1) AMP kinase, an intracellular energy sensor; 2) PGC-1α (peroxisome proliferator-activated receptor γ co-activator 1α), a transcriptional co-activator that has powerful effects on mitochondria; 3) methylation and demethylation in response to metabolic fluctuations; and 4) FGF21 (fibroblast growth factor 21) as an emerging hormone-like intercellular metabolic coordinator. This introduction places these advances within a broad overview of energy sensing and energy balance, with a focus on human evolution and disease. Four key elements of human biology are analyzed: 1) elevated body temperature; 2) complex prolonged reproductive pathways; 3) emergence of 4 large, well-defined fat depots, each with its own functional role; and 4) an immune system that is often up-regulated by nutrition-related signals, independent of the actual presence of a pathogen. We propose that an overactive immune system, including the "metabolic syndrome," was adopted evolutionarily in the distant past to help hold out against unconquerable infections such as tuberculosis, malaria, and trypanosomiasis. This immune activation is advantageous in the absence of other disease management methods, especially under conditions in which life expectancy is short. The inflammation has become a major agent of pathology in wealthy populations in whom the pathogens are a minor threat and life expectancy is long. The "Conclusions" section sketches cautiously how understanding the molecules involved in energy sensing and energy balance may lead to specific therapies for obesity and diabetes and for their complications.}, }
@article {pmid21279320, year = {2011}, author = {Werner, M and Simmons, LW}, title = {Ultrastructure of spermatozoa of Onthophagus taurus (Coleoptera, Scarabaeidae) exhibits heritable variation.}, journal = {Die Naturwissenschaften}, volume = {98}, number = {3}, pages = {213-223}, pmid = {21279320}, issn = {1432-1904}, mesh = {Animals ; Coleoptera/*cytology/*genetics/ultrastructure ; Flagella/ultrastructure ; *Genetic Variation ; Male ; Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; Phenotype ; Spermatozoa/cytology/ultrastructure ; }, abstract = {Sperm competition is thought to be an important selective pressure shaping sperm form and function. However, few studies have moved beyond gross examinations of sperm morphology. Sperm length is subject to sexual selection via sperm competition in the scarab beetle Onthophagus taurus. Here, the structure and ultrastructure of spermatozoa in this species were investigated using light and electron microscopy. Spermatozoa were found to be filiform, measuring about 1,200 mm in length. The sperm head consists of a three-layered acrosome and a nuclear region bearing the anterior extension of the centriole adjunct. Acrosome and nuclear regions are bilaterally symmetric, with their axes of symmetry being orthogonal to each other. Head and flagellar structures are connected by a well-developed centriole adjunct. The sperm heads are asymmetrically surrounded by accessory material and embedded into the cytoplasm of the spermatocyst cell. The accessory material is produced inside the spermatids and then transferred to the outside due to a new membrane formed around the sperm's organelles. The old spermatid membrane separates the accessory material from the cyst cell. The flagellum contains a 9+9+2 axoneme, two accessory bodies, and two mitochondrial derivatives of unequal size. The major mitochondrial derivative is significantly larger than the minor one. The axoneme is arranged in a sinusoidal manner parallel along the major mitochondrial derivative. The spermatozoa show no progressive motility when released in buffer solution which is likely to be the result of the flagellar arrangement and the structure of the major mitochondrial derivative. The cross-sectional area of the minor and the major mitochondrial derivatives show different patterns of genetic variation. The data provide the first estimates of genetic variation in sperm ultrastructure for any species, and give evidence for the persistence of genetic variation in ultrastructure required for the rapid and divergent evolution that characterizes spermatozoa generally.}, }
@article {pmid21273215, year = {2011}, author = {Grobler, JP and Jones, JW and Johnson, NA and Neves, RJ and Hallerman, EM}, title = {Homogeneity at nuclear microsatellite loci masks mitochondrial haplotype diversity in the endangered fanshell pearlymussel (Cyprogenia stegaria).}, journal = {The Journal of heredity}, volume = {102}, number = {2}, pages = {196-206}, doi = {10.1093/jhered/esq120}, pmid = {21273215}, issn = {1465-7333}, mesh = {Alleles ; Animals ; Bivalvia/*genetics ; Cell Nucleus/*genetics ; DNA, Mitochondrial ; Gene Frequency ; *Genetic Variation ; Genetics, Population ; Geography ; *Haplotypes ; *Microsatellite Repeats ; Mitochondria/*genetics ; Molecular Sequence Data ; Ohio ; Phylogeny ; Tennessee ; }, abstract = {We report on multiple patterns of differentiation and connectivity in the fanshell pearlymussel (Cyprogenia stegaria), based on different markers. Knowledge of genetic variation and genetic connectivity among remaining populations of this federally endangered species is needed to initiate implementation of the species recovery plan. We collected tissue samples from 96 specimens from the Green, Rolling Fork, and Licking Rivers, tributaries to the Ohio River, and the Clinch River, a tributary to the Tennessee River, providing broad coverage of the current distributional range of the species. Results from 7 nuclear DNA microsatellite markers suggested minimal population-level differentiation, whereas a mitochondrial DNA (mtDNA) marker (ND1) exhibited significant differentiation between C. stegaria in the Clinch River and the Ohio River populations. The ND1 data also confirm the existence of 2 distinct mtDNA lineages in the genus that transcends species boundaries. Further analyses suggest that the disproportionally strong signal from 2 very divergent ND1 lineages possibly masks finer-grained structure in the Ohio River population, based on one of the mtDNA lineages only. We recommend further sampling to confirm the absence of one lineage from the upper Clinch River drainage and suggest that provisional management guidelines should limit reciprocal exchanges among C. stegaria populations from the Clinch River and those in the Ohio River system.}, }
@article {pmid21267457, year = {2011}, author = {Colón, M and Hernández, F and López, K and Quezada, H and González, J and López, G and Aranda, C and González, A}, title = {Saccharomyces cerevisiae Bat1 and Bat2 aminotransferases have functionally diverged from the ancestral-like Kluyveromyces lactis orthologous enzyme.}, journal = {PloS one}, volume = {6}, number = {1}, pages = {e16099}, pmid = {21267457}, issn = {1932-6203}, mesh = {Amino Acids, Branched-Chain/metabolism ; *Evolution, Molecular ; Gene Duplication ; Kluyveromyces/*enzymology/genetics ; Mitochondrial Proteins/*genetics ; Saccharomyces cerevisiae/*enzymology/genetics ; Saccharomyces cerevisiae Proteins/*genetics ; Transaminases/*genetics ; }, abstract = {BACKGROUND: Gene duplication is a key evolutionary mechanism providing material for the generation of genes with new or modified functions. The fate of duplicated gene copies has been amply discussed and several models have been put forward to account for duplicate conservation. The specialization model considers that duplication of a bifunctional ancestral gene could result in the preservation of both copies through subfunctionalization, resulting in the distribution of the two ancestral functions between the gene duplicates. Here we investigate whether the presumed bifunctional character displayed by the single branched chain amino acid aminotransferase present in K. lactis has been distributed in the two paralogous genes present in S. cerevisiae, and whether this conservation has impacted S. cerevisiae metabolism.<br><br>PRINCIPAL FINDINGS: Our results show that the KlBat1 orthologous BCAT is a bifunctional enzyme, which participates in the biosynthesis and catabolism of branched chain aminoacids (BCAAs). This dual role has been distributed in S. cerevisiae Bat1 and Bat2 paralogous proteins, supporting the specialization model posed to explain the evolution of gene duplications. BAT1 is highly expressed under biosynthetic conditions, while BAT2 expression is highest under catabolic conditions. Bat1 and Bat2 differential relocalization has favored their physiological function, since biosynthetic precursors are generated in the mitochondria (Bat1), while catabolic substrates are accumulated in the cytosol (Bat2). Under respiratory conditions, in the presence of ammonium and BCAAs the bat1&#x394; bat2&#x394; double mutant shows impaired growth, indicating that Bat1 and Bat2 could play redundant roles. In K. lactis wild type growth is independent of BCAA degradation, since a Klbat1&#x394; mutant grows under this condition.<br><br>CONCLUSIONS: Our study shows that BAT1 and BAT2 differential expression and subcellular relocalization has resulted in the distribution of the biosynthetic and catabolic roles of the ancestral BCAT in two isozymes improving BCAAs metabolism and constituting an adaptation to facultative metabolism.}, }
@article {pmid21266473, year = {2011}, author = {Valach, M and Farkas, Z and Fricova, D and Kovac, J and Brejova, B and Vinar, T and Pfeiffer, I and Kucsera, J and Tomaska, L and Lang, BF and Nosek, J}, title = {Evolution of linear chromosomes and multipartite genomes in yeast mitochondria.}, journal = {Nucleic acids research}, volume = {39}, number = {10}, pages = {4202-4219}, pmid = {21266473}, issn = {1362-4962}, support = {2-R03-TW005654-04A1/TW/FIC NIH HHS/United States ; HHMI 55005622//Howard Hughes Medical Institute/United States ; }, mesh = {Base Sequence ; Candida/classification/*genetics ; Chromosome Mapping ; *Chromosomes, Fungal ; DNA, Mitochondrial/*chemistry ; Electrophoresis, Gel, Pulsed-Field ; *Evolution, Molecular ; Gene Order ; *Genome, Fungal ; *Genome, Mitochondrial ; Inverted Repeat Sequences ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Mitochondrial genome diversity in closely related species provides an excellent platform for investigation of chromosome architecture and its evolution by means of comparative genomics. In this study, we determined the complete mitochondrial DNA sequences of eight Candida species and analyzed their molecular architectures. Our survey revealed a puzzling variability of genome architecture, including circular- and linear-mapping and multipartite linear forms. We propose that the arrangement of large inverted repeats identified in these genomes plays a crucial role in alterations of their molecular architectures. In specific arrangements, the inverted repeats appear to function as resolution elements, allowing genome conversion among different topologies, eventually leading to genome fragmentation into multiple linear DNA molecules. We suggest that molecular transactions generating linear mitochondrial DNA molecules with defined telomeric structures may parallel the evolutionary emergence of linear chromosomes and multipartite genomes in general and may provide clues for the origin of telomeres and pathways implicated in their maintenance.}, }
@article {pmid21263042, year = {2011}, author = {Hayes, ML and Mulligan, RM}, title = {Pentatricopeptide repeat proteins constrain genome evolution in chloroplasts.}, journal = {Molecular biology and evolution}, volume = {28}, number = {7}, pages = {2029-2039}, doi = {10.1093/molbev/msr023}, pmid = {21263042}, issn = {1537-1719}, mesh = {Base Sequence ; Chloroplasts/*genetics ; *Evolution, Molecular ; *Genome, Plant ; Magnoliopsida/genetics ; Membrane Proteins ; Mitochondrial Proteins ; Molecular Sequence Data ; Mutation ; Phylogeny ; Plant Proteins/*genetics ; Repetitive Sequences, Nucleic Acid ; Sequence Alignment ; Transcription Factors/*genetics ; }, abstract = {Higher plants encode hundreds of pentatricopeptide repeat proteins (PPRs) that are involved in several types of RNA processing reactions. Most PPR genes are predicted to be targeted to chloroplasts or mitochondria, and many are known to affect organellar gene expression. In some cases, RNA binding has been directly demonstrated, and the sequences of the cis-elements are known. In this work, we demonstrate that RNA cis-elements recognized by PPRs are constrained in chloroplast genome evolution. Cis-elements for two PPR genes and several RNA editing sites were analyzed for sequence changes by pairwise nucleotide substitution frequency, pairwise indel frequency, and maximum likelihood (ML) phylogenetic distances. All three of these analyses demonstrated that sequences within the cis-element are highly conserved compared with surrounding sequences. In addition, we have compared sequences around chloroplast editing sites and homologous sequences in species that lack an editing site due to the presence of a genomic T. Cis-elements for RNA editing sites are highly conserved in angiosperms; by contrast, comparable sequences around a genomically encoded T exhibit higher rates of nucleotide substitution, higher frequencies of indels, and greater ML distances. The loss in requirement for editing to create the ndhD start codon has resulted in the conversion of the PPR gene responsible for editing that site to a pseudogene. We show that organellar dependence on nuclear-encoded PPR proteins for gene expression has constrained the evolution of cis-elements that are required at the level of RNA processing. Thus, the expansion of the PPR gene family in plants has had a dramatic effect on the evolution of plant organelle genomes.}, }
@article {pmid21252340, year = {2011}, author = {Rebbeck, CA and Leroi, AM and Burt, A}, title = {Mitochondrial capture by a transmissible cancer.}, journal = {Science (New York, N.Y.)}, volume = {331}, number = {6015}, pages = {303}, doi = {10.1126/science.1197696}, pmid = {21252340}, issn = {1095-9203}, mesh = {Animals ; Coyotes/genetics ; Dog Diseases/*genetics/metabolism/pathology ; Dogs/genetics ; Gene Transfer, Horizontal ; *Genome, Mitochondrial ; *Mitochondria/genetics/metabolism ; Phylogeny ; Polymorphism, Genetic ; Selection, Genetic ; Sequence Analysis, DNA ; Venereal Tumors, Veterinary/*genetics/*metabolism/pathology ; Wolves/genetics ; }, abstract = {Canine transmissible venereal tumor (CTVT) is an infectious cell line circulating in many feral dog populations. It originated once, about 10,000 years ago. Phylogenetic analyses of mitochondrial sequences from dogs, wolves, and a geographically diverse collection of CTVT samples indicate that the cancer has periodically acquired mitochondria from its host. We suggest that this may be because the cancer's own mitochondria have a tendency to degenerate, due to high mutation rates and relaxed selection, resulting in host mitochondria being more fit.}, }
@article {pmid21252282, year = {2011}, author = {Lloyd, AH and Timmis, JN}, title = {The origin and characterization of new nuclear genes originating from a cytoplasmic organellar genome.}, journal = {Molecular biology and evolution}, volume = {28}, number = {7}, pages = {2019-2028}, doi = {10.1093/molbev/msr021}, pmid = {21252282}, issn = {1537-1719}, mesh = {Base Sequence ; Cell Nucleus/*genetics ; Chloroplasts/*genetics ; *Evolution, Molecular ; Gene Rearrangement ; *Genes, Plant ; *Genome, Plastid ; Models, Genetic ; Molecular Sequence Data ; Mutation ; Plant Proteins/genetics ; Nicotiana/genetics ; Transcriptional Activation ; Transformation, Genetic ; }, abstract = {Endosymbiotic transfer of DNA and functional genes from the cytoplasmic organelles (mitochondria and chloroplasts) to the nucleus has been a major factor driving the origin of new nuclear genes, a process central to eukaryote evolution. Although organelle DNA transfers very frequently to the nucleus, most is quickly deleted, decays, or is alternatively scrapped. However, a very small proportion of it gives rise, immediately or eventually, to functional genes. To simulate the process of functional transfer, we screened for nuclear activation of a chloroplast reporter gene aadA, which had been transferred from the chloroplast to independent nuclear loci in 16 different plant lines. Cryptic nuclear activity of the chloroplast promoter was revealed, which became conspicuous when present in multiple nuclear copies. We screened ∼50 million cells of each line and retrieved three plants in which aadA showed strong nuclear activation. Activation occurred by acquisition of the CaMV 35S nuclear promoter or by nuclear activation of the native chloroplast promoter. Two fortuitous sites within the 3' UTR of aadA mRNA both promoted polyadenylation without any sequence change. Complete characterization of one nuclear sequence before and after gene transfer demonstrated integration by nonhomologous end joining involving simultaneous insertion of multiple chloroplast DNA fragments. The real-time observation of three different means by which a chloroplast gene can become expressed in the nucleus suggests that the process, though rare, may be more readily achieved than previously envisaged.}, }
@article {pmid21250982, year = {2011}, author = {Mastrodonato, M and Calamita, G and Rossi, R and Mentino, D and Bonfrate, L and Portincasa, P and Ferri, D and Liquori, GE}, title = {Altered distribution of caveolin-1 in early liver steatosis.}, journal = {European journal of clinical investigation}, volume = {41}, number = {6}, pages = {642-651}, doi = {10.1111/j.1365-2362.2010.02459.x}, pmid = {21250982}, issn = {1365-2362}, mesh = {Animals ; Caveolin 1/*metabolism ; Choline/metabolism ; Diet ; Fatty Liver/*metabolism/pathology ; Immunoblotting ; Male ; Rats ; Rats, Wistar ; Statistics as Topic ; }, abstract = {BACKGROUND: Caveolin-1, the main structural protein of caveolae, is involved in cholesterol homoeostasis, transcytosis, endocytosis and signal transduction and thought to play an important role in lipidogenesis. Little is known about the pathophysiological role of caveolin-1 in nonalcoholic fatty liver disease (NAFLD), a condition frequently associated with the metabolic syndrome and characterized by abnormal accumulation of intrahepatic triglycerides with a potentially harmful risk of evolution to liver fibrosis, cirrhosis and hepatocellular carcinoma.<br><br>MATERIALS AND METHODS: Liver steatosis (micro/macrovesicular) was induced in adult rats fed a choline-deficient diet for 14days and compared with a control normal diet. The expression and subcellular distribution of caveolin-1 was assessed using light and electron microscopy by immunohistochemical and immunocytochemical techniques and by Western blotting.<br><br>RESULTS: Caveolin-1 was mainly associated with the hepatocyte basolateral plasma membrane. Fatty hepatocytes were characterized by a significant increase in the expression of caveolin-1 around and within the lipid droplets as well as in the inner membrane of mitochondria.<br><br>CONCLUSIONS: Our data suggest the involvement of caveolin-1 in the case of abnormal lipogenesis and mitochondrial function typical of steatotic hepatocytes in NAFLD. Addressing the role played by caveolin-1 in liver membranes in NAFLD may help future therapeutic choices in a frequent metabolic liver disease.}, }
@article {pmid21245414, year = {2011}, author = {Hayashi, M and Schilke, B and Marszalek, J and Williams, B and Craig, EA}, title = {Ancient gene duplication provided a key molecular step for anaerobic growth of Baker's yeast.}, journal = {Molecular biology and evolution}, volume = {28}, number = {7}, pages = {2005-2017}, pmid = {21245414}, issn = {1537-1719}, support = {R01 GM027870/GM/NIGMS NIH HHS/United States ; GM278709/GM/NIGMS NIH HHS/United States ; }, mesh = {Aerobiosis ; Amino Acid Sequence ; Anaerobiosis/genetics ; Blotting, Western ; Electrophoresis, Polyacrylamide Gel ; *Evolution, Molecular ; *Gene Duplication ; Membrane Proteins/genetics/metabolism ; Membrane Transport Proteins/genetics/metabolism ; Mitochondria ; Mitochondrial Precursor Protein Import Complex Proteins ; Molecular Sequence Data ; Phylogeny ; Protein Transport ; Saccharomyces cerevisiae/*genetics/*growth &amp; development/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Sequence Alignment ; }, abstract = {Mitochondria are essential organelles required for a number of key cellular processes. As most mitochondrial proteins are nuclear encoded, their efficient translocation into the organelle is critical. Transport of proteins across the inner membrane is driven by a multicomponent, matrix-localized "import motor," which is based on the activity of the molecular chaperone Hsp70 and a J-protein cochaperone. In Saccharomyces cerevisiae, two paralogous J-proteins, Pam18 and Mdj2, can form the import motor. Both contain transmembrane and matrix domains, with Pam18 having an additional intermembrane space (IMS) domain. Evolutionary analyses revealed that the origin of the IMS domain of S. cerevisiae Pam18 coincides with a gene duplication event that generated the PAM18/MDJ2 gene pair. The duplication event and origin of the Pam18 IMS domain occurred at the relatively ancient divergence of the fungal subphylum Saccharomycotina. The timing of the duplication event also corresponds with a number of additional functional changes related to mitochondrial function and respiration. Physiological and genetic studies revealed that the IMS domain of Pam18 is required for efficient growth under anaerobic conditions, even though it is dispensable when oxygen is present. Thus, the gene duplication was beneficial for growth capacity under particular environmental conditions as well as diversification of the import motor components.}, }
@article {pmid21244359, year = {2011}, author = {Acuña Castroviejo, D and López, LC and Escames, G and López, A and García, JA and Reiter, RJ}, title = {Melatonin-mitochondria interplay in health and disease.}, journal = {Current topics in medicinal chemistry}, volume = {11}, number = {2}, pages = {221-240}, doi = {10.2174/156802611794863517}, pmid = {21244359}, issn = {1873-4294}, mesh = {Aging ; Animals ; Antioxidants/*metabolism ; Apoptosis ; Biological Evolution ; DNA, Mitochondrial/metabolism ; Energy Metabolism/physiology ; Humans ; Hydrogen/metabolism ; Melatonin/metabolism/*pharmacology/therapeutic use ; Mice ; Mitochondria/*metabolism ; Mitochondrial Diseases/physiopathology/prevention &amp; control/therapy ; Oxidation-Reduction ; Oxidative Stress ; Oxygen/metabolism ; Rats ; Reactive Nitrogen Species/*metabolism ; Reactive Oxygen Species/*metabolism ; Symbiosis ; }, abstract = {Although two main hypotheses of mitochondrial origin have been proposed, i.e., the autogenous and the endosymbiotic, only the second is being seriously considered currently. The 'hydrogen hypothesis' invokes metabolic symbiosis as the driving force for a symbiotic association between an anaerobic, strictly hydrogen-dependent (the host) and an eubacterium (the symbiont) that was able to respire, but which generated molecular hydrogen as an end product of anaerobic metabolism. The resulting proto-eukaryotic cell would have acquired the essentials of eukaryotic energy metabolism, evolving not only aerobic respiration, but also the physiological cost of the oxygen consumption, i.e., generation of reactive oxygen species (ROS) and the associated oxidative damage. This is not the only price to pay for respiring oxygen: mitochondria possess nitric oxide (NO·) for regulatory purposes but, in some instances it may react with superoxide anion radical to produce the toxic reactive nitrogen species (RNS), i.e. peroxynitrite anion, and the subsequent nitrosative damage. New mitochondria contain their own genome with a modified genetic code that is highly conserved among mammals. The transcription of certain mitochondrial genes may depend on the redox potential of the mitochondrial membrane. Mitochondria are related to the life and death of cells. They are involved in energy production and conservation, having an uncoupling mechanism to produce heat instead of ATP, but they are also involved in programmed cell death. Increasing evidence suggest the participation of mitochondria in neurodegenerative and neuromuscular diseases involving alterations in both nuclear (nDNA) and mitochondrial (mtDNA) DNA. Melatonin is a known powerful antioxidant and anti-inflammatory and increasing experimental and clinical evidence shows its beneficial effects against oxidative/nitrosative stress status, including that involving mitochondrial dysfunction. This review summarizes the data and mechanisms of action of melatonin in relation to mitochondrial pathologies.}, }
@article {pmid21232104, year = {2011}, author = {Tourmente, M and Gomendio, M and Roldan, ER}, title = {Sperm competition and the evolution of sperm design in mammals.}, journal = {BMC evolutionary biology}, volume = {11}, number = {}, pages = {12}, pmid = {21232104}, issn = {1471-2148}, mesh = {Animals ; *Biological Evolution ; Cell Size ; Humans ; Male ; Mammals/classification/genetics/*physiology ; Phylogeny ; Sperm Motility ; Spermatozoa/classification/*cytology ; }, abstract = {BACKGROUND: The influence of sperm competition upon sperm size has been a controversial issue during the last 20 years which remains unresolved for mammals. The hypothesis that, when ejaculates compete with rival males, an increase in sperm size would make sperm more competitive because it would increase sperm swimming speed, has generated contradictory results from both theoretical and empirical studies. In addition, the debate has extended to which sperm components should increase in size: the midpiece to accommodate more mitochondria and produce more energy to fuel motility, or the principal piece to generate greater propulsion forces.<br><br>RESULTS: In this study we examined the influence of sperm competition upon sperm design in mammals using a much larger data set (226 species) than in previous analyses, and we corrected for phylogenetic effects by using a more complete and resolved phylogeny, and more robust phylogenetic control methods. Our results show that, as sperm competition increases, all sperm components increase in an integrated manner and sperm heads become more elongated. The increase in sperm length was found to be associated with enhanced swimming velocity, an adaptive trait under sperm competition.<br><br>CONCLUSIONS: We conclude that sperm competition has played an important role in the evolution of sperm design in mammals, and discuss why previous studies have failed to detect it.}, }
@article {pmid21222161, year = {2011}, author = {Kern, R and Bauwe, H and Hagemann, M}, title = {Evolution of enzymes involved in the photorespiratory 2-phosphoglycolate cycle from cyanobacteria via algae toward plants.}, journal = {Photosynthesis research}, volume = {109}, number = {1-3}, pages = {103-114}, pmid = {21222161}, issn = {1573-5079}, mesh = {Alcohol Oxidoreductases/genetics ; Arabidopsis/enzymology/genetics ; Bacterial Proteins/genetics ; *Biological Evolution ; Cell Respiration ; Chloroplasts/genetics ; Cyanobacteria/enzymology/*genetics ; Glycine Dehydrogenase (Decarboxylating)/genetics ; Glycine Hydroxymethyltransferase/genetics ; Glycolates/*metabolism ; Hydroxypyruvate Reductase/genetics ; Mitochondria/genetics ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; Photosynthesis ; Phylogeny ; Plant Proteins/genetics ; Plants/enzymology/*genetics ; Proteobacteria/enzymology/*genetics ; }, abstract = {The photorespiratory pathway was shown to be essential for organisms performing oxygenic photosynthesis, cyanobacteria, algae, and plants, in the present day O(2)-containing atmosphere. The identification of a plant-like 2-phosphoglycolate cycle in cyanobacteria indicated that not only genes of oxygenic photosynthesis but also genes encoding photorespiratory enzymes were endosymbiotically conveyed from ancient cyanobacteria to eukaryotic oxygenic phototrophs. Here, we investigated the origin of the photorespiratory pathway in photosynthetic eukaryotes by phylogenetic analysis. We found that a mixture of photorespiratory enzymes of either cyanobacterial or α-proteobacterial origin is present in algae and higher plants. Three enzymes in eukaryotic phototrophs clustered closely with cyanobacterial homologs: glycolate oxidase, glycerate kinase, and hydroxypyruvate reductase. On the other hand, the mitochondrial enzymes of the photorespiratory cycle in algae and plants, glycine decarboxylase subunits and serine hydroxymethyltransferase, evolved from proteobacteria. Other than most genes for proteins of the photosynthetic machinery, nearly all enzymes involved in the 2-phosphogylcolate metabolism coexist in the genomes of cyanobacteria and heterotrophic bacteria.}, }
@article {pmid21220331, year = {2011}, author = {Fujii, S and Bond, CS and Small, ID}, title = {Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {108}, number = {4}, pages = {1723-1728}, pmid = {21220331}, issn = {1091-6490}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Cell Nucleus/genetics ; Cytoplasm/genetics ; Evolution, Molecular ; Fertility/genetics ; Genes, Plant/genetics ; Genome, Mitochondrial/*genetics ; Genome, Plant/*genetics ; Magnoliopsida/classification/*genetics ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Plant Infertility/genetics ; Plant Proteins/chemistry/classification/genetics ; Protein Structure, Secondary ; Repetitive Sequences, Amino Acid ; *Selection, Genetic ; }, abstract = {Eukaryotic cells have harbored mitochondria for at least 1.5 billion years in an apparently mutually beneficial symbiosis. Studies on the agronomically important crop trait cytoplasmic male sterility (CMS) have suggested the semblance of a host-parasite relationship between the nuclear and mitochondrial genomes, but molecular evidence for this is lacking. Key players in CMS systems are the fertility restorer (Rf) genes required for the development of a functional male gametophyte in plants carrying a mitochondrial CMS gene. In the majority of cases, Rf genes encode pentatricopeptide repeat (PPR) proteins. We show that most angiosperms for which extensive genomic sequence data exist contain multiple PPR genes related to Rf genes. These Rf-like genes show a number of characteristic features compared with other PPR genes, including chromosomal clustering and unique patterns of evolution, notably high rates of nonsynonymous to synonymous substitutions, suggesting diversifying selection. The highest probabilities of diversifying selection were seen for amino acid residues 1, 3, and 6 within the PPR motif. PPR proteins are involved in RNA processing, and mapping the selection data to a predicted consensus structure of an array of PPR motifs suggests that these residues are likely to form base-specific contacts to the RNA ligand. We suggest that the selection patterns on Rf-like genes reveal a molecular "arms-race" between the nuclear and mitochondrial genomes that has persisted throughout most of the evolutionary history of angiosperms.}, }
@article {pmid21217797, year = {2011}, author = {Abhishek, A and Bavishi, A and Bavishi, A and Choudhary, M}, title = {Bacterial genome chimaerism and the origin of mitochondria.}, journal = {Canadian journal of microbiology}, volume = {57}, number = {1}, pages = {49-61}, doi = {10.1139/w10-099}, pmid = {21217797}, issn = {1480-3275}, mesh = {Alphaproteobacteria/*classification/*genetics ; *Biological Evolution ; Eukaryota/classification/genetics ; Genome, Bacterial/*genetics ; Mitochondria/genetics/*physiology ; Mitochondrial Proteins/*genetics ; *Phylogeny ; Saccharomyces cerevisiae/classification/genetics ; }, abstract = {Many studies have sought to determine the origin and evolution of mitochondria. Although the Alphaproteobacteria are thought to be the closest relatives of the mitochondrial progenitor, there is dispute as to what its particular sister group is. Some have argued that mitochondria originated from ancestors of the order Rickettsiales, or more specifically of the Rickettsiaceae family, while others believe that ancestors of the family Rhodospirillaceae are also equally likely the progenitors. To resolve some of these disputes, sequence similarity searches and phylogenetic analyses were performed against mitochondria-related proteins in Saccharomyces cerevisiae. The 86 common matches of 5 Alphaproteobacteria (Rickettsia prowazekii, Rhodospirillum rubrum, Rhodopseudomonas palustris, Rhodobacter sphaeroides, and Ochrobactrum anthropi) to yeast mitochondrial proteins were distributed fairly evenly among the 5 species when sorted by highest identity or score. Moreover, exploratory phylogenetic analyses revealed that among these common matches, 44.19% (38) had branched most closely with O. anthropi, while only 34.88% (30) corresponded with Rickettsia prowazekii. More detailed phylogenetic analyses with additional Alphaproteobacteria and including genes from the mitochondria of Reclinomonas americana found matches of mitochondrial genes to those of members of the Rickettsiaceae, Anaplasmataceae, and Rhodospirillaceae families. The results support the idea that notable bacterial genome chimaerism has occurred en route to the formation of mitochondria.}, }
@article {pmid21216618, year = {2011}, author = {Oldham, S}, title = {Obesity and nutrient sensing TOR pathway in flies and vertebrates: Functional conservation of genetic mechanisms.}, journal = {Trends in endocrinology and metabolism: TEM}, volume = {22}, number = {2}, pages = {45-52}, pmid = {21216618}, issn = {1879-3061}, support = {R01 HL084949-04/HL/NHLBI NIH HHS/United States ; R01 HL084949/HL/NHLBI NIH HHS/United States ; R01 HL084949-03/HL/NHLBI NIH HHS/United States ; R01 HL084949-01/HL/NHLBI NIH HHS/United States ; R01 HL084949-02/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Diabetes Mellitus, Type 2/etiology ; Dietary Fats/*administration &amp; dosage ; *Drosophila ; Heart Diseases/etiology ; Humans ; Insulin/physiology ; Lipid Metabolism/genetics ; Longevity ; Mitochondria/genetics/physiology ; Models, Biological ; Obesity/complications/*genetics ; Signal Transduction ; TOR Serine-Threonine Kinases/genetics/*physiology ; }, abstract = {The global prevalence of obesity has grown to epidemic proportions, and 400 million people are now considered to be obese. Excessive accumulation of dietary lipids (obesity) is a known risk factor for the development of deleterious metabolic conditions and has been strongly linked to the progression of heart disease and type 2 diabetes. Investigating the origin and effects of high-fat diet (HFD)-induced obesity and its genetic mediators is an important step in understanding the mechanisms that contribute to obesity. However, the mechanisms that underlie HFD pathophysiology have yet to be elucidated fully. Here we describe recent work in a Drosophila model to investigate the origin and genetic mechanisms that could underlie HFD-induced obesity, type 2 diabetes and cardiac dysfunction.}, }
@article {pmid21216297, year = {2011}, author = {Jesse, R and Grudinski, M and Klaus, S and Streit, B and Pfenninger, M}, title = {Evolution of freshwater crab diversity in the Aegean region (Crustacea: Brachyura: Potamidae).}, journal = {Molecular phylogenetics and evolution}, volume = {59}, number = {1}, pages = {23-33}, doi = {10.1016/j.ympev.2010.12.011}, pmid = {21216297}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Brachyura/classification/*genetics ; Bulgaria ; Electron Transport Complex IV/genetics ; *Fresh Water ; *Genetic Variation ; Greece ; Italy ; Mediterranean Sea ; Mitochondria/genetics ; Morocco ; NADH Dehydrogenase/genetics ; Phylogeny ; Phylogeography ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 28S/genetics ; RNA, Transfer, Leu/genetics ; Turkey ; }, abstract = {The aim of this study was to estimate the influence of the palaeogeographic and climatic history of the Aegean region on the diversity of freshwater crabs of the genus Potamon and to test whether this area served as source or reservoir in species diversity. Necessary species delimitation was accomplished by phylogenetic analyses of the mitochondrial markers COX1 and ND1, partial 16S rRNA gene and the tRNALeu gene. We found 14 genetic lineages of which nine could be assigned to previously recognised species. Temporal estimates of the splitting pattern in the phylogeny of Potamon indicated that a combination of geological and climatic events influenced their diversification. Within Potamon, the lineages separated into a western group and an eastern group. This first split in the genus occurred approximately 8.3-5.5 Mya, thus possibly correlated with the Messinian salinity crisis. A likelihood approach to geographic range evolution suggested for most species, occurring in the Aegean area, an origin in the Middle East. Moreover, there were no insular endemics in the central Aegean archipelago, therefore low sea-levels during the Pleistocene glacial periods possibly enabled dispersal to these islands, but subsequent rise in sea-level did not cause speciation. Nevertheless, the diversification of most lineages occurred during the Pleistocene epoch thus coinciding with Quaternary fluctuations of the climate.}, }
@article {pmid21214654, year = {2011}, author = {Greiner, S and Rauwolf, U and Meurer, J and Herrmann, RG}, title = {The role of plastids in plant speciation.}, journal = {Molecular ecology}, volume = {20}, number = {4}, pages = {671-691}, doi = {10.1111/j.1365-294X.2010.04984.x}, pmid = {21214654}, issn = {1365-294X}, mesh = {Evolution, Molecular ; *Genetic Speciation ; Genome, Plant ; Genome, Plastid ; Hybridization, Genetic ; Phenotype ; Plants/genetics ; Plastids/*genetics ; }, abstract = {Understanding the molecular basis of how new species arise is a central question and prime challenge in evolutionary biology and includes understanding how genomes diversify. Eukaryotic cells possess an integrated compartmentalized genetic system of endosymbiotic ancestry. The cellular subgenomes in nucleus, mitochondria and plastids communicate in a complex way and co-evolve. The application of hybrid and cybrid technologies, most notably those involving interspecific exchanges of plastid and nuclear genomes, has uncovered a multitude of species-specific nucleo-organelle interactions. Such interactions can result in plastome-genome incompatibilities, which can phenotypically often be recognized as hybrid bleaching, hybrid variegation or disturbance of the sexual phase. The plastid genome, because of its relatively low number of genes, can serve as a valuable tool to investigate the origin of these incompatibilities. In this article, we review progress on understanding how plastome-genome co-evolution contributes to speciation. We genetically classify incompatible phenotypes into four categories. We also summarize genetic, physiological and environmental influence and other possible selection forces acting on plastid-nuclear co-evolution and compare taxa providing molecular access to the underlying loci. It appears that plastome-genome incompatibility can establish hybridization barriers, comparable to the Dobzhansky-Muller model of speciation processes. Evidence suggests that the plastid-mediated hybridization barriers associated with hybrid bleaching primarily arise through modification of components in regulatory networks, rather than of complex, multisubunit structures themselves that are frequent targets.}, }
@article {pmid21209838, year = {2010}, author = {Ramirez, O and Illera, JC and Rando, JC and Gonzalez-Solis, J and Alcover, JA and Lalueza-Fox, C}, title = {Ancient DNA of the extinct lava shearwater (Puffinus olsoni) from the Canary Islands reveals incipient differentiation within the P. puffinus complex.}, journal = {PloS one}, volume = {5}, number = {12}, pages = {e16072}, pmid = {21209838}, issn = {1932-6203}, mesh = {Animals ; Biological Evolution ; Birds/*genetics/*physiology ; Bone and Bones/pathology ; DNA/*genetics ; DNA, Mitochondrial/*genetics ; Ecosystem ; *Extinction, Biological ; Genetic Variation ; Geography ; Haplotypes ; History, Ancient ; Mitochondria/metabolism ; Models, Genetic ; Phylogeny ; Predatory Behavior ; Spain ; }, abstract = {BACKGROUND: The loss of species during the Holocene was, dramatically more important on islands than on continents. Seabirds from islands are very vulnerable to human-induced alterations such as habitat destruction, hunting and exotic predators. For example, in the genus Puffinus (family Procellariidae) the extinction of at least five species has been recorded during the Holocene, two of them coming from the Canary Islands.<br><br>We used bones of the two extinct Canary shearwaters (P. olsoni and P. holeae) to obtain genetic data, for use in providing insights into the differentiation process within the genus Puffinus. Although mitochondrial DNA (mtDNA) cytochrome b sequences were successfully retrieved from four Holocene specimens of the extinct Lava shearwater (P. olsoni) from Fuerteventura (Canary Islands), the P. holeae specimens yielded no DNA. Only one haplotype was detected in P. olsoni, suggesting a low genetic diversity within this species.<br><br>CONCLUSIONS: The phylogenetic analyses based on the DNA data reveal that: (i) the "Puffinus puffinus complex", an assemblage of species defined using osteological characteristics (P. puffinus, P. olsoni, P. mauretanicus, P. yelkouan and probably P. holeae), shows unresolved phylogenetic relationships; (ii) despite the differences in body size and proportions, P. olsoni and the extant P. puffinus are sister species. Several hypotheses can be considered to explain the incipient differentiation between P. olsoni and P. puffinus.}, }
@article {pmid21207102, year = {2011}, author = {Traba, J and Satrústegui, J and del Arco, A}, title = {Adenine nucleotide transporters in organelles: novel genes and functions.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {68}, number = {7}, pages = {1183-1206}, pmid = {21207102}, issn = {1420-9071}, mesh = {Adenine Nucleotides/*metabolism ; Animals ; Eukaryota/cytology/metabolism ; Humans ; Mitochondrial ADP, ATP Translocases/chemistry/classification/*genetics/*metabolism ; Organelles/*metabolism ; Phylogeny ; Protein Conformation ; Protein Isoforms/chemistry/genetics/metabolism ; }, abstract = {In eukaryotes, cellular energy in the form of ATP is produced in the cytosol via glycolysis or in the mitochondria via oxidative phosphorylation and, in photosynthetic organisms, in the chloroplast via photophosphorylation. Transport of adenine nucleotides among cell compartments is essential and is performed mainly by members of the mitochondrial carrier family, among which the ADP/ATP carriers are the best known. This work reviews the carriers that transport adenine nucleotides into the organelles of eukaryotic cells together with their possible functions. We focus on novel mechanisms of adenine nucleotide transport, including mitochondrial carriers found in organelles such as peroxisomes, plastids, or endoplasmic reticulum and also mitochondrial carriers found in the mitochondrial remnants of many eukaryotic parasites of interest. The extensive repertoire of adenine nucleotide carriers highlights an amazing variety of new possible functions of adenine nucleotide transport across eukaryotic organelles.}, }
@article {pmid21203427, year = {2010}, author = {Hendrich, L and Pons, J and Ribera, I and Balke, M}, title = {Mitochondrial cox1 sequence data reliably uncover patterns of insect diversity but suffer from high lineage-idiosyncratic error rates.}, journal = {PloS one}, volume = {5}, number = {12}, pages = {e14448}, pmid = {21203427}, issn = {1932-6203}, mesh = {Animals ; Australia ; Classification ; Coleoptera ; Computational Biology/methods ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Electronic Data Processing ; Genetic Variation ; Insecta ; Likelihood Functions ; Mitochondria/*metabolism ; Phylogeny ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The demand for scientific biodiversity data is increasing, but taxonomic expertise is often limited or not available. DNA sequencing is a potential remedy to overcome this taxonomic impediment. Mitochondrial DNA is most commonly used, e.g., for species identification ("DNA barcoding"). Here, we present the first study in arthropods based on a near-complete species sampling of a family-level taxon from the entire Australian region. We aimed to assess how reliably mtDNA data can capture species diversity when many sister species pairs are included. Then, we contrasted phylogenetic subsampling with the hitherto more commonly applied geographical subsampling, where sister species are not necessarily captured.<br><br>We sequenced 800 bp cox1 for 1,439 individuals including 260 Australian species (78% species coverage). We used clustering with thresholds of 1 to 10% and general mixed Yule Coalescent (GMYC) analysis for the estimation of species richness. The performance metrics used were taxonomic accuracy and agreement between the morphological and molecular species richness estimation. Clustering (at the 3% level) and GMYC reliably estimated species diversity for single or multiple geographic regions, with an error for larger clades of lower than 10%, thus outperforming parataxonomy. However, the rates of error were higher for some individual genera, with values of up to 45% when very recent species formed nonmonophyletic clusters. Taxonomic accuracy was always lower, with error rates above 20% and a larger variation at the genus level (0 to 70%). S&#xf8;rensen similarity indices calculated for morphospecies, 3% clusters and GMYC entities for different pairs of localities was consistent among methods and showed expected decrease over distance.<br><br>CONCLUSION/SIGNIFICANCE: Cox1 sequence data are a powerful tool for large-scale species richness estimation, with a great potential for use in ecology and &#x3b2;-diversity studies and for setting conservation priorities. However, error rates can be high in individual lineages.}, }
@article {pmid21199027, year = {2011}, author = {Humphries, EM and Winker, K}, title = {Discord reigns among nuclear, mitochondrial and phenotypic estimates of divergence in nine lineages of trans-Beringian birds.}, journal = {Molecular ecology}, volume = {20}, number = {3}, pages = {573-583}, doi = {10.1111/j.1365-294X.2010.04965.x}, pmid = {21199027}, issn = {1365-294X}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Animals ; Anseriformes/classification/genetics ; Birds/classification/*genetics ; Cell Nucleus/genetics ; Charadriiformes/classification/genetics ; DNA/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; *Genetic Speciation ; Genetic Variation ; Genetics, Population ; Genome ; Mitochondria, Muscle/genetics ; Passeriformes/classification/genetics ; Phenotype ; Sequence Analysis, DNA ; }, abstract = {Proposals for genetic thresholds for species delimitation assume that simple genetic data sets (e.g. mitochondrial sequence data) are correlated with speciation; i.e. such data sets accurately reflect organismal lineage divergence. We used taxonomically stratified phenotypic levels of differentiation (populations, subspecies and species) among nine avian lineages using paired, trans-Beringian samples from three lineages each in three orders (Anseriformes, Charadriiformes, and Passeriformes) to test this assumption. Using mitochondrial DNA sequence data and nuclear genomic data (amplified fragment length polymorphisms), we found a lack of concordance between these two genomes in their respective estimates of divergence and little or no relationship between phenotype (taxonomic relatedness) and genetic differentiation between taxon pairs. There are several possible reasons for the discord observed (e.g. selection on one of the genomes or perhaps lineage sorting), but the implications are that genetic estimates of lineage divergence may not be correlated with estimates from other parts of the genome, are not well correlated with the speciation process and are thus not reliable indicators of species limits.}, }
@article {pmid21196381, year = {2011}, author = {Silva, JE}, title = {Physiological importance and control of non-shivering facultative thermogenesis.}, journal = {Frontiers in bioscience (Scholar edition)}, volume = {3}, number = {1}, pages = {352-371}, doi = {10.2741/s156}, pmid = {21196381}, issn = {1945-0524}, support = {//CIHR/Canada ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Adaptation, Biological/*physiology ; Adipose Tissue, Brown/*metabolism ; Animals ; Basal Metabolism/physiology ; *Biological Evolution ; Ion Channels/*metabolism ; Mice ; Mitochondrial Proteins/*metabolism ; Shivering/physiology ; Sympathetic Nervous System/*physiology ; Thermogenesis/*physiology ; Thyroid Hormones/*metabolism ; Uncoupling Protein 1 ; }, abstract = {This review examines general and evolutionary aspects of temperature homeostasis, focusing on mammalian facultative or adaptive thermogenesis and its control by the sympathetic nervous system and hormones. Thyroid hormone acquired a new role with the advent of homeothermy enhancing facultative thermogenesis by interacting synergistically with the sympathetic nervous system, and directly increasing basal metabolic rate (obligatory thermogenesis). Facultative thermogenesis is triggered by cold. The major site of facultative thermogenesis in mammals is brown adipose tissue, endowed with abundant mitochondria rich in a protein called uncoupling protein-1. This protein can uncouple phosphorylation in a controlled manner, releasing the energy of the proton-motive force as heat. Its synthesis and function are regulated synergistically by the sympathetic nervous system and thyroid hormone and modulated by other hormones directly, or indirectly, modulating sympathetic activity as well as thyroid hormone secretion and activation in brown adipose tissue. Alternate, evolutionary older forms of facultative thermogenesis activated in transgenic mice with disabled brown adipose tissue thermogenesis reveal this latter as the culmination of energy-efficient facultative thermogenesis.}, }
@article {pmid21195140, year = {2011}, author = {Wang, X and Lavrov, DV}, title = {Gene recruitment--a common mechanism in the evolution of transfer RNA gene families.}, journal = {Gene}, volume = {475}, number = {1}, pages = {22-29}, doi = {10.1016/j.gene.2010.12.009}, pmid = {21195140}, issn = {1879-0038}, mesh = {Animals ; Cell Nucleus/genetics ; *Evolution, Molecular ; *Gene Expression Regulation ; Genome ; Humans ; Mitochondria/genetics ; Phylogeny ; RNA, Transfer/*classification/*genetics ; RNA, Transfer, Amino Acyl/classification/genetics ; }, abstract = {The evolution of alloacceptor transfer RNAs (tRNAs) has been traditionally thought to occur vertically and reflect the evolution of the genetic code. Yet there have been several indications that a tRNA gene could evolve horizontally, from a copy of an alloacceptor tRNA gene in the same genome. Earlier, we provided the first unambiguous evidence for the occurrence of such "tRNA gene recruitment" in nature--in the mitochondrial (mt) genome of the demosponge Axinella corrugata. Yet the extent and the pattern of this process in the evolution of tRNA gene families remained unclear. Here we analyzed tRNA genes from 21 mt genomes of demosponges as well as nuclear genomes of rhesus macaque, chimpanzee and human. We found four new cases of alloacceptor tRNA gene recruitment in mt genomes and eleven cases in the nuclear genomes. In most of these cases we observed a single nucleotide substitution at the middle position of the anticodon, which resulted in the change of not only the tRNA's amino-acid identity but also the class of the amino-acyl tRNA synthetases (aaRSs) involved in amino-acylation. We hypothesize that the switch to a different class of aaRSs may have prevented the conflict between anticodon and amino-acid identities of recruited tRNAs. Overall our results suggest that gene recruitment is a common phenomenon in tRNA multigene family evolution and should be taken into consideration when tRNA evolutionary history is reconstructed.}, }
@article {pmid21194367, year = {2011}, author = {Funes, S and Kauff, F and van der Sluis, EO and Ott, M and Herrmann, JM}, title = {Evolution of YidC/Oxa1/Alb3 insertases: three independent gene duplications followed by functional specialization in bacteria, mitochondria and chloroplasts.}, journal = {Biological chemistry}, volume = {392}, number = {1-2}, pages = {13-19}, doi = {10.1515/BC.2011.013}, pmid = {21194367}, issn = {1437-4315}, mesh = {*Bacteria/enzymology/genetics ; *Chloroplasts/enzymology/genetics ; Electron Transport Complex IV/genetics/metabolism ; *Evolution, Molecular ; *Gene Duplication ; Membrane Transport Proteins/*genetics/*metabolism ; *Mitochondria/enzymology/genetics ; Mitochondrial Proteins/genetics/metabolism ; Nuclear Proteins/genetics/metabolism ; Phylogeny ; Protein Folding ; }, abstract = {Members of the YidC/Oxa1/Alb3 protein family facilitate the insertion, folding and assembly of proteins of the inner membranes of bacteria and mitochondria and the thylakoid membrane of plastids. All homologs share a conserved hydrophobic core region comprising five transmembrane domains. On the basis of phylogenetic analyses, six subgroups of the family can be distinguished which presumably arose from three independent gene duplications followed by functional specialization. During evolution of bacteria, mitochondria and chloroplasts, subgroup-specific regions were added to the core domain to facilitate the association with ribosomes or other components contributing to the substrate spectrum of YidC/Oxa1/Alb3 proteins.}, }
@article {pmid21190582, year = {2010}, author = {Jimenez-Lopez, JC and Gachomo, EW and Seufferheld, MJ and Kotchoni, SO}, title = {The maize ALDH protein superfamily: linking structural features to functional specificities.}, journal = {BMC structural biology}, volume = {10}, number = {}, pages = {43}, pmid = {21190582}, issn = {1472-6807}, mesh = {Aldehyde Dehydrogenase/*chemistry/genetics/*metabolism ; Amino Acid Sequence ; Base Sequence ; Binding Sites ; Chemical Phenomena ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/*chemistry/genetics/isolation &amp; purification/*metabolism ; Models, Molecular ; Molecular Sequence Annotation ; Multigene Family ; Phylogeny ; Protein Binding ; Protein Structure, Quaternary ; Sequence Alignment ; Static Electricity ; Zea mays/*enzymology/*genetics/metabolism ; }, abstract = {BACKGROUND: The completion of maize genome sequencing has resulted in the identification of a large number of uncharacterized genes. Gene annotation and functional characterization of gene products are important to uncover novel protein functionality.<br><br>RESULTS: In this paper, we identify, and annotate members of all the maize aldehyde dehydrogenase (ALDH) gene superfamily according to the revised nomenclature criteria developed by ALDH Gene Nomenclature Committee (AGNC). The maize genome contains 24 unique ALDH sequences encoding members of ten ALDH protein families including the previously identified male fertility restoration RF2A gene, which encodes a member of mitochondrial class 2 ALDHs. Using computational modeling analysis we report here the identification, the physico-chemical properties, and the amino acid residue analysis of a novel tunnel like cavity exclusively found in the maize sterility restorer protein, RF2A/ALDH2B2 by which this protein is suggested to bind variably long chain molecular ligands and/or potentially harmful molecules.<br><br>CONCLUSIONS: Our finding indicates that maize ALDH superfamily is the most expanded of plant ALDHs ever characterized, and the mitochondrial maize RF2A/ALDH2B2 is the only plant ALDH that harbors a newly defined pocket/cavity with suggested functional specificity.}, }
@article {pmid21182560, year = {2011}, author = {Anderson, OR and Wang, W and Faucher, SP and Bi, K and Shuman, HA}, title = {A new heterolobosean amoeba Solumitrus palustris n. g., n. sp. isolated from freshwater marsh soil.}, journal = {The Journal of eukaryotic microbiology}, volume = {58}, number = {1}, pages = {60-67}, doi = {10.1111/j.1550-7408.2010.00520.x}, pmid = {21182560}, issn = {1550-7408}, support = {R01 AI023549/AI/NIAID NIH HHS/United States ; 5R01AI23549/AI/NIAID NIH HHS/United States ; 5R01AI064481/AI/NIAID NIH HHS/United States ; }, mesh = {Amoeba/*classification/genetics/growth &amp; development/*isolation &amp; purification ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Fresh Water/*parasitology ; Molecular Sequence Data ; Phylogeny ; Soil/*parasitology ; Wetlands ; }, abstract = {During the course of research on the bacterial feeding behavior and resistance of amoebae to virulent pathogens, we isolated a new strain of amoeba from organic rich soil at the margin of freshwater swamp in the northeastern United States. Light microscopic morphology is characteristically heterolobosean, resembling vahlkampfiids, including a broadened, limax shape, and eruptive locomotion, but occasionally becoming more contracted and less elongated with lateral or anterior bulges and somewhat branching sparse, uroidal filaments. Electron microscopic evidence, including mitochondria with flattened cristae surrounded by rough endoplasmic reticulum, further indicates a heterolobosean affinity. The solitary nucleus contains a centrally located nucleolus. Cysts are rounded with occasionally an eccentrically located nucleus. The cyst walls are relatively thin, becoming crenated, and loosely enclosing the cyst when mature. Molecular genetic evidence places this isolate among the Heterolobosea, branching most closely in a clade including Allovahlkampfia spelaea and previously isolated, un-named strains of soil amoebae. Based on differentiated features, including morphology of the uroid, cyst wall structure, and molecular genetic evidence that distinguish it from A. spelaea, a new genus and species, Solumitrus palustris, is proposed for this new heterolobosean.}, }
@article {pmid21177940, year = {2011}, author = {Richards, JG}, title = {Physiological, behavioral and biochemical adaptations of intertidal fishes to hypoxia.}, journal = {The Journal of experimental biology}, volume = {214}, number = {Pt 2}, pages = {191-199}, doi = {10.1242/jeb.047951}, pmid = {21177940}, issn = {1477-9145}, mesh = {*Acclimatization ; Animals ; Behavior, Animal ; Fishes/metabolism/*physiology ; Oxygen/*metabolism ; Phylogeny ; }, abstract = {Hypoxia survival in fish requires a well-coordinated response to either secure more O(2) from the hypoxic environment or to limit the metabolic consequences of an O(2) restriction at the mitochondria. Although there is a considerable amount of information available on the physiological, behavioral, biochemical and molecular responses of fish to hypoxia, very little research has attempted to determine the adaptive value of these responses. This article will review current attempts to use the phylogenetically corrected comparative method to define physiological and behavioral adaptations to hypoxia in intertidal fish and further identify putatively adaptive biochemical traits that should be investigated in the future. In a group of marine fishes known as sculpins, from the family Cottidae, variation in hypoxia tolerance, measured as a critical O(2) tension (P(crit)), is primarily explained by variation in mass-specific gill surface area, red blood cell hemoglobin-O(2) binding affinity, and to a lesser extent variation in routine O(2) consumption rate (M(O(2))). The most hypoxia-tolerant sculpins consistently show aquatic surface respiration (ASR) and aerial emergence behavior during hypoxia exposure, but no phylogenetically independent relationship has been found between the thresholds for initiating these behaviors and P(crit). At O(2) levels below P(crit), hypoxia survival requires a rapid reorganization of cellular metabolism to suppress ATP consumption to match the limited capacity for O(2)-independent ATP production. Thus, it is reasonable to speculate that the degree of metabolic rate suppression and the quantity of stored fermentable fuel is strongly selected for in hypoxia-tolerant fishes; however, these assertions have not been tested in a phylogenetic comparative model.}, }
@article {pmid21177938, year = {2011}, author = {Suarez, RK and Herrera M, LG and Welch, KC}, title = {The sugar oxidation cascade: aerial refueling in hummingbirds and nectar bats.}, journal = {The Journal of experimental biology}, volume = {214}, number = {Pt 2}, pages = {172-178}, doi = {10.1242/jeb.047936}, pmid = {21177938}, issn = {1477-9145}, mesh = {Animals ; Biological Evolution ; Birds/*metabolism ; Body Temperature Regulation ; *Carbohydrate Metabolism ; Chiroptera/*metabolism ; Energy Metabolism ; Feeding Behavior ; Oxidation-Reduction ; }, abstract = {Most hummingbirds and some species of nectar bats hover while feeding on floral nectar. While doing so, they achieve some of the highest mass-specific V(O(2)) values among vertebrates. This is made possible by enhanced functional capacities of various elements of the 'O(2) transport cascade', the pathway of O(2) from the external environment to muscle mitochondria. Fasted hummingbirds and nectar bats fly with respiratory quotients (RQs; V(CO(2))/V(O(2))) of ~0.7, indicating that fat fuels flight in the fasted state. During repeated hover-feeding on dietary sugar, RQ values progressively climb to ~1.0, indicating a shift from fat to carbohydrate oxidation. Stable carbon isotope experiments reveal that recently ingested sugar directly fuels ~80 and 95% of energy metabolism in hover-feeding nectar bats and hummingbirds, respectively. We name the pathway of carbon flux from flowers, through digestive and cardiovascular systems, muscle membranes and into mitochondria the 'sugar oxidation cascade'. O(2) and sugar oxidation cascades operate in parallel and converge in muscle mitochondria. Foraging behavior that favours the oxidation of dietary sugar avoids the inefficiency of synthesizing fat from sugar and breaking down fat to fuel foraging. Sugar oxidation yields a higher P/O ratio (ATP made per O atom consumed) than fat oxidation, thus requiring lower hovering V(O(2)) per unit mass. We propose that dietary sugar is a premium fuel for flight in nectarivorous, flying animals.}, }
@article {pmid21172831, year = {2011}, author = {Breton, S and Stewart, DT and Shepardson, S and Trdan, RJ and Bogan, AE and Chapman, EG and Ruminas, AJ and Piontkivska, H and Hoeh, WR}, title = {Novel protein genes in animal mtDNA: a new sex determination system in freshwater mussels (Bivalvia: Unionoida)?.}, journal = {Molecular biology and evolution}, volume = {28}, number = {5}, pages = {1645-1659}, pmid = {21172831}, issn = {1537-1719}, support = {R15 GM086782/GM/NIGMS NIH HHS/United States ; R15 GM086782-01A1/GM/NIGMS NIH HHS/United States ; GM86782-01A1/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Chromosome Mapping ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics/metabolism ; Female ; Fresh Water ; Likelihood Functions ; Male ; Mitochondrial Proteins/*genetics/metabolism ; Molecular Sequence Data ; Open Reading Frames ; Ovum/metabolism ; Phylogeny ; Protein Structure, Secondary ; Sequence Analysis, DNA ; Sex Characteristics ; Sex Determination Analysis/*methods ; Transcription, Genetic ; Unionidae/classification/*genetics/metabolism ; }, abstract = {Mitochondrial (mt) function depends critically on optimal interactions between components encoded by mt and nuclear DNAs. mitochondrial DNA (mtDNA) inheritance (SMI) is thought to have evolved in animal species to maintain mito-nuclear complementarity by preventing the spread of selfish mt elements thus typically rendering mtDNA heteroplasmy evolutionarily ephemeral. Here, we show that mtDNA intraorganismal heteroplasmy can have deterministic underpinnings and persist for hundreds of millions of years. We demonstrate that the only exception to SMI in the animal kingdom, that is, the doubly uniparental mtDNA inheritance system in bivalves, with its three-way interactions among egg mt-, sperm mt- and nucleus-encoded gene products, is tightly associated with the maintenance of separate male and female sexes (dioecy) in freshwater mussels. Specifically, this mother-through-daughter and father-through-son mtDNA inheritance system, containing highly differentiated mt genomes, is found in all dioecious freshwater mussel species. Conversely, all hermaphroditic species lack the paternally transmitted mtDNA (=possess SMI) and have heterogeneous macromutations in the recently discovered, novel protein-coding gene (F-orf) in their maternally transmitted mt genomes. Using immunoelectron microscopy, we have localized the F-open reading frame (ORF) protein, likely involved in specifying separate sexes, in mitochondria and in the nucleus. Our results support the hypothesis that proteins coded by the highly divergent maternally and paternally transmitted mt genomes could be directly involved in sex determination in freshwater mussels. Concomitantly, our study demonstrates novel features for animal mt genomes: the existence of additional, lineage-specific, mtDNA-encoded proteins with functional significance and the involvement of mtDNA-encoded proteins in extra-mt functions. Our results open new avenues for the identification, characterization, and functional analyses of ORFs in the intergenic regions, previously defined as "noncoding," found in a large proportion of animal mt genomes.}, }
@article {pmid21164222, year = {2010}, author = {Artal-Sanz, M and Tavernarakis, N}, title = {Opposing function of mitochondrial prohibitin in aging.}, journal = {Aging}, volume = {2}, number = {12}, pages = {1004-1011}, pmid = {21164222}, issn = {1945-4589}, mesh = {Aging/*metabolism ; Animals ; Cellular Senescence ; Energy Metabolism ; Evolution, Molecular ; Humans ; Longevity ; Mitochondria/*metabolism ; Oxidative Stress ; Prohibitins ; Repressor Proteins/*metabolism ; *Signal Transduction ; }, abstract = {While specific signalling cascades involved in aging, such as the insulin/IGF-1 pathway, are well-described, the actual metabolic changes they elicit to prolong lifespan remain obscure. Nevertheless, the tuning of cellular metabolism towards maximal survival is the molecular basis of longevity. The eukaryotic mitochondrial prohibitin complex is a macromolecular structure at the inner mitochondrial membrane, implicated in several important cellular processes such as mitochondrial biogenesis and function, molecular signalling, replicative senescence, and cell death. Recent studies inC. elegans have revealed that prohibitin differentially influences aging by moderating fat metabolism and energy production, in response to both intrinsic signalling events and extrinsic cues. These findings indicate that prohibitin is a context-dependent modulator of longevity. The tight evolutionary conservation and ubiquitous expression of prohibitin proteins suggest a similar role for the mitochondrial prohibitin complex during aging in other organisms.}, }
@article {pmid21148473, year = {2011}, author = {Ishibashi, K and Kondo, S and Hara, S and Morishita, Y}, title = {The evolutionary aspects of aquaporin family.}, journal = {American journal of physiology. Regulatory, integrative and comparative physiology}, volume = {300}, number = {3}, pages = {R566-76}, doi = {10.1152/ajpregu.90464.2008}, pmid = {21148473}, issn = {1522-1490}, mesh = {Amino Acid Sequence ; Animals ; Aquaporins/chemistry/classification/*metabolism ; Conserved Sequence ; *Evolution, Molecular ; Humans ; Molecular Sequence Data ; Protein Conformation ; Structure-Activity Relationship ; Water/*metabolism ; *Water-Electrolyte Balance ; }, abstract = {Aquaporins (AQPs) were originally identified as channels facilitating water transport across the plasma membrane. They have a pair of highly conserved signature sequences, asparagine-proline-alanine (NPA) boxes, to form a pore. However, some have little conserved amino acid sequences around the NPA boxes unclassifiable to two previous AQP subfamilies, classical AQPs and aquaglyceroporins. These will be called unorthodox AQPs in this review. Interestingly, these unorthodox AQPs have a highly conserved cysteine residue downstream of the second NPA box. AQPs also have a diversity of functions: some related to water transport such as fluid secretion, fluid absorption, and cell volume regulation, and the others not directly related to water transport such as cell adhesion, cell migration, cell proliferation, and cell differentiation. Some AQPs even permeate nonionic small molecules, ions, metals, and possibly gasses. AQP gene disruption studies have revealed their physiological roles: water transport in the kidney and exocrine glands, glycerol transport in fat metabolism and in skin moisture, and nutrient uptakes in plants. Furthermore, AQPs are also present at intracellular organelles, including tonoplasts, mitochondria, and the endoplasmic reticulum. This review focuses on the evolutionary aspects of AQPs from bacteria to humans in view of the structural and functional diversities of AQPs.}, }
@article {pmid21148414, year = {2011}, author = {Voss, B and Meinecke, L and Kurz, T and Al-Babili, S and Beck, CF and Hess, WR}, title = {Hemin and magnesium-protoporphyrin IX induce global changes in gene expression in Chlamydomonas reinhardtii.}, journal = {Plant physiology}, volume = {155}, number = {2}, pages = {892-905}, pmid = {21148414}, issn = {1532-2548}, mesh = {Chlamydomonas reinhardtii/drug effects/*genetics ; Cluster Analysis ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Genes, Plant ; Heat-Shock Proteins/genetics/metabolism ; Hemin/*pharmacology ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Plant Proteins/genetics/metabolism ; Protoporphyrins/*pharmacology ; RNA, Plant/genetics ; }, abstract = {Retrograde signaling is a pathway of communication from mitochondria and plastids to the nucleus in the context of cell differentiation, development, and stress response. In Chlamydomonas reinhardtii, the tetrapyrroles magnesium-protoporphyrin IX and heme are only synthesized within the chloroplast, and they have been implicated in the retrograde control of nuclear gene expression in this unicellular green alga. Feeding the two tetrapyrroles to Chlamydomonas cultures was previously shown to transiently induce five nuclear genes, three of which encode the heat shock proteins HSP70A, HSP70B, and HSP70E. In contrast, controversial results exist on the possible role of magnesium-protoporphyrin IX in the repression of genes for light-harvesting proteins in higher plants, raising the question of how important this mode of regulation is. Here, we used genome-wide transcriptional profiling to measure the global impact of these tetrapyrroles on gene regulation and the scope of the response. We identified almost 1,000 genes whose expression level changed transiently but significantly. Among them were only a few genes for photosynthetic proteins but several encoding enzymes of the tricarboxylic acid cycle, heme-binding proteins, stress-response proteins, as well as proteins involved in protein folding and degradation. More than 50% of the latter class of genes was also regulated by heat shock. The observed drastic fold changes at the RNA level did not correlate with similar changes in protein concentrations under the tested experimental conditions. Phylogenetic profiling revealed that genes of putative endosymbiontic origin are not overrepresented among the responding genes. This and the transient nature of changes in gene expression suggest a signaling role of both tetrapyrroles as secondary messengers for adaptive responses affecting the entire cell and not only organellar proteins.}, }
@article {pmid21146880, year = {2011}, author = {Sun, LL and Jiang, BG and Li, WT and Zou, JJ and Shi, YQ and Liu, ZM}, title = {MicroRNA-15a positively regulates insulin synthesis by inhibiting uncoupling protein-2 expression.}, journal = {Diabetes research and clinical practice}, volume = {91}, number = {1}, pages = {94-100}, doi = {10.1016/j.diabres.2010.11.006}, pmid = {21146880}, issn = {1872-8227}, mesh = {3' Untranslated Regions ; Adenosine Triphosphate/metabolism ; Animals ; Cell Line ; *Gene Expression Regulation ; Genes, Reporter ; HEK293 Cells ; Humans ; Hyperglycemia/metabolism ; Insulin/*biosynthesis/genetics ; Ion Channels/genetics/*metabolism ; Islets of Langerhans/*metabolism ; Mice ; Mice, Inbred C57BL ; MicroRNAs/antagonists &amp; inhibitors/genetics/*metabolism ; Mitochondria/drug effects/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Organ Culture Techniques ; Oxygen/metabolism ; RNA, Messenger/metabolism ; Time Factors ; Uncoupling Agents/pharmacology ; Uncoupling Protein 2 ; }, abstract = {MicroRNAs are small noncoding RNAs that have been highly conserved during evolution and have been implicated to play an important role in many diseases, including diabetes. Several reports indicated the function of miRNAs in insulin production. However, the mechanisms by which miRNAs regulate this process remain poorly understood. Here we found that the expression of miR-15a was up-regulated in the presence of high glucose for 1h, whereas prolonged periods of high glucose exposure resulted in depressed expression of miR-15a, and the change in expression levels of miR-15a coincided with insulin biosynthesis. Moreover, ectopic expression of miR-15a promoted insulin biosynthesis in MIN6 cells, whereas its repression was sufficient to inhibit insulin biosynthesis. Further, we verified that miR-15a directly targeted and inhibited uncoupling protein-2 (UCP-2) gene expression. miR-15a mimics inhibited UCP-2 3'UTR luciferase reporter activity. Western blot analysis showed that miR-15a inhibited endogenous UCP-2 protein levels, and resulted in the increase in oxygen consumption and reduced ATP generation. This study suggests miR-15a is a mediator of β cell function and insulin biosynthesis, thus offering a new target for the development of preventive or therapeutic agents against diabetes.}, }
@article {pmid21143683, year = {2010}, author = {Soto, G and Fox, R and Ayub, N and Alleva, K and Guaimas, F and Erijman, EJ and Mazzella, A and Amodeo, G and Muschietti, J}, title = {TIP5;1 is an aquaporin specifically targeted to pollen mitochondria and is probably involved in nitrogen remobilization in Arabidopsis thaliana.}, journal = {The Plant journal : for cell and molecular biology}, volume = {64}, number = {6}, pages = {1038-1047}, doi = {10.1111/j.1365-313X.2010.04395.x}, pmid = {21143683}, issn = {1365-313X}, mesh = {Aquaporins/genetics/*metabolism ; Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Hydrogen-Ion Concentration ; Mitochondria/*genetics ; Mutagenesis, Insertional ; Nitrogen/*metabolism ; Phylogeny ; Pollen Tube/*genetics ; RNA, Plant/genetics ; Water/metabolism ; }, abstract = {In plant sexual reproduction, water and solute movement are tightly regulated, suggesting the involvement of aquaporins. We previously identified TIP5;1 and TIP1;3 as the only Arabidopsis aquaporin genes that are selectively and highly expressed in mature pollen, and showed that they can transport both water and urea when expressed in Xenopus oocytes. Here, we show that TIP5;1 has unusual characteristics, as its water transport activity is regulated by pH. Analysis of the water transport activity of a mutant version of TIP5;1 (TIP5;1-H131A) and amino acid alignment with other plant aquaporins regulated by pH suggested that a conserved motif is involved in pH sensing. GFP-TIP5;1 is located in the mitochondria of pollen tubes. The single mutants tip1;3 and tip5;1, as well as the tip1;3 tip5;1 double mutant, are fertile, but all mutants had shorter than normal pollen tubes when germinated in vitro in the absence of exogenous nitrogen. Thus, we propose that TIP5;1 and TIP1;3 are involved in nitrogen recycling in pollen tubes of Arabidopsis thaliana.}, }
@article {pmid21143489, year = {2011}, author = {Dana, N and Megens, HJ and Crooijmans, RP and Hanotte, O and Mwacharo, J and Groenen, MA and van Arendonk, JA}, title = {East Asian contributions to Dutch traditional and western commercial chickens inferred from mtDNA analysis.}, journal = {Animal genetics}, volume = {42}, number = {2}, pages = {125-133}, doi = {10.1111/j.1365-2052.2010.02134.x}, pmid = {21143489}, issn = {1365-2052}, mesh = {Animals ; Asia, Southeastern ; Base Sequence ; Breeding ; Chickens/*genetics ; DNA, Mitochondrial/chemistry/*genetics ; Europe ; Female ; *Genetic Variation ; Haplotypes ; Male ; Mitochondria/genetics ; Molecular Sequence Data ; Netherlands ; Phylogeny ; Sequence Analysis, DNA/veterinary ; Species Specificity ; }, abstract = {Understanding the complex origin of domesticated populations is of vital importance for understanding, preserving and exploiting breed genetic diversity. Here, we aim to assess Asian contributions to European traditional breeds and western commercial chickens for mitochondrial genetic diversity. To this end, a 365-bp fragment of the chicken mtDNA D-loop region of 16 Dutch fancy breeds (113 individuals) was surveyed, comprising almost the entire breed diversity of The Netherlands. We also sequenced the same fragment for 160 commercial birds representing all important commercial types from multiple commercial companies that together represent more than 50% of the worldwide commercial value. We identified 20 different haplotypes. The haplotypes clustered into five clades. The commonest clade (E-clade) supposedly originates from the Indian subcontinent. In addition, both in commercial chicken and Dutch fancy breeds, many haplotypes were found with a clear East Asian origin. However, the erratic occurrence of many different East Asian mitochondrial clades indicates that there were many independent instances where breeders used imported exotic chickens for enhancing local breeds. Nucleotide diversity and haplotype diversity analyses showed the influence of the introgression of East Asian chicken on genetic diversity. All populations that had haplotypes of multiple origin displayed high inferred diversity, as opposed to most populations that had only a single mitochondrial haplotype signature. Most fancy breeds were found to have a much lower within-population diversity compared to broilers and layers, although this is not the case for mitochondrial estimates in fancy breeds that have multiple origin haplotypes.}, }
@article {pmid21137096, year = {2011}, author = {Speijer, D}, title = {Oxygen radicals shaping evolution: why fatty acid catabolism leads to peroxisomes while neurons do without it: FADH2/NADH flux ratios determining mitochondrial radical formation were crucial for the eukaryotic invention of peroxisomes and catabolic tissue differentiation.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {33}, number = {2}, pages = {88-94}, doi = {10.1002/bies.201000097}, pmid = {21137096}, issn = {1521-1878}, mesh = {*Biological Evolution ; Cell Differentiation ; Electron Transport/physiology ; Eukaryota/physiology ; Fatty Acids/metabolism ; Flavin-Adenine Dinucleotide/*analogs &amp; derivatives/metabolism ; Glucose/metabolism ; Kinetics ; Mitochondria/metabolism ; Models, Biological ; NAD/*metabolism ; Neurons/metabolism ; Oxidation-Reduction ; Peroxisomes/metabolism ; Reactive Oxygen Species/*metabolism ; }, abstract = {Oxygen radical formation in mitochondria is a highly important, but incompletely understood, attribute of eukaryotic cells. I propose a kinetic model in which the ratio between electrons entering the respiratory chain via FADH2 or NADH is a major determinant in radical formation. During the breakdown of glucose, this ratio is low; during fatty acid breakdown, this ratio is much higher. The longer the fatty acid, the higher the ratio and the higher the level of radical formation. This means that very long chain fatty acids should be broken down without generation of FADH2 for mitochondria. This is accomplished in peroxisomes, thus explaining their role and evolution. The model explains many recent observations regarding radical formation by the respiratory chain. It also sheds light on the reasons for the lack of neuronal fatty acid (beta-) oxidation and for beneficial aspects of unsaturated fatty acids. Last but not least, it has very important implications for all models describing eukaryotic origins.}, }
@article {pmid21134269, year = {2010}, author = {Yin, C and Richter, U and Börner, T and Weihe, A}, title = {Evolution of plant phage-type RNA polymerases: the genome of the basal angiosperm Nuphar advena encodes two mitochondrial and one plastid phage-type RNA polymerases.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {379}, pmid = {21134269}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Cloning, Molecular ; DNA, Complementary/genetics ; DNA-Directed RNA Polymerases/*genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genes, Plant ; *Genome, Plant ; Mitochondria/genetics ; Molecular Sequence Data ; Nuphar/*genetics ; Phylogeny ; Plastids/genetics ; Protein Biosynthesis ; RNA, Messenger/genetics ; RNA, Plant/genetics ; }, abstract = {BACKGROUND: In mono- and eudicotyledonous plants, a small nuclear gene family (RpoT, RNA polymerase of the T3/T7 type) encodes mitochondrial as well as chloroplast RNA polymerases homologous to the T-odd bacteriophage enzymes. RpoT genes from angiosperms are well characterized, whereas data from deeper branching plant species are limited to the moss Physcomitrella and the spikemoss Selaginella. To further elucidate the molecular evolution of the RpoT polymerases in the plant kingdom and to get more insight into the potential importance of having more than one phage-type RNA polymerase (RNAP) available, we searched for the respective genes in the basal angiosperm Nuphar advena.<br><br>RESULTS: By screening a set of BAC library filters, three RpoT genes were identified. Both genomic gene sequences and full-length cDNAs were determined. The NaRpoT mRNAs specify putative polypeptides of 996, 990 and 985 amino acids, respectively. All three genes comprise 19 exons and 18 introns, conserved in their positions with those known from RpoT genes of other land plants. The encoded proteins show a high degree of conservation at the amino acid sequence level, including all functional crucial regions and residues known from the phage T7 RNAP. The N-terminal transit peptides of two of the encoded polymerases, NaRpoTm1 and NaRpoTm2, conferred targeting of green fluorescent protein (GFP) exclusively to mitochondria, whereas the third polymerase, NaRpoTp, was targeted to chloroplasts. Remarkably, translation of NaRpoTp mRNA has to be initiated at a CUG codon to generate a functional plastid transit peptide. Thus, besides AGAMOUS in Arabidopsis and the Nicotiana RpoTp gene, N. advena RpoTp provides another example for a plant mRNA that is exclusively translated from a non-AUG codon. In contrast to the RpoT of the lycophyte Selaginella and those of the moss Physcomitrella, which are according to phylogenetic analyses in sister positions to all other phage-type polymerases of angiosperms, the Nuphar RpoTs clustered with the well separated clades of mitochondrial (NaRpoTm1 and NaRpoTm2) and plastid (NaRpoTp) polymerases.<br><br>CONCLUSIONS: Nuphar advena encodes two mitochondrial and one plastid phage-type RNAP. Identification of a plastid-localized phage-type RNAP in this basal angiosperm, orthologous to all other RpoTp enzymes of flowering plants, suggests that the duplication event giving rise to a nuclear gene-encoded plastid RNA polymerase, not present in lycopods, took place after the split of lycopods from all other tracheophytes. A dual-targeted mitochondrial and plastididal RNA polymerase (RpoTmp), as present in eudicots but not monocots, was not detected in Nuphar suggesting that its occurrence is an evolutionary novelty of eudicotyledonous plants like Arabidopsis.}, }
@article {pmid21131095, year = {2011}, author = {Vlahou, G and Eliáš, M and von Kleist-Retzow, JC and Wiesner, RJ and Rivero, F}, title = {The Ras related GTPase Miro is not required for mitochondrial transport in Dictyostelium discoideum.}, journal = {European journal of cell biology}, volume = {90}, number = {4}, pages = {342-355}, doi = {10.1016/j.ejcb.2010.10.012}, pmid = {21131095}, issn = {1618-1298}, mesh = {Amino Acid Sequence ; Biological Evolution ; Biological Transport/genetics ; Calcium/metabolism ; Dictyostelium/*enzymology/genetics ; Glucose/metabolism ; Kinesins/genetics/metabolism ; Microtubules/genetics/metabolism ; Mitochondria/*enzymology ; Mitochondrial Membrane Transport Proteins/metabolism ; Molecular Sequence Data ; Oxygen Consumption ; Phylogeny ; rho GTP-Binding Proteins/classification/genetics/*metabolism ; }, abstract = {Ras-related GTPases of the Miro family have been implicated in mitochondrial homeostasis and microtubule-dependent transport. They consist of two GTP-binding domains separated by calcium-binding motifs and of a C-terminal transmembrane domain that targets the protein to the outer mitochondrial membrane. We disrupted the single Miro-encoding gene in Dictyostelium discoideum and observed a substantial growth defect that we attribute to a decreased mitochondrial mass and cellular ATP content. However, mutant cells even showed an increased rate of oxygen consumption, while glucose consumption, mitochondrial transmembrane potential and production of reactive oxygen species were unaltered. Processes characteristic of the multicellular stage of the D. discoideum life cycle were also unaltered. Although mitochondria occasionally use microtubules for transport in D. discoideum, their size and distribution were not visibly affected. We found Miro in all branches of the eukaryotic tree with the exception of a few protist lineages (mainly those lacking typical mitochondria). Trypanosomatids and ciliates possess structurally unique homologs lacking the N-terminal or the C-terminal GTPase domain, respectively. We propose that in D. discoideum, as in yeasts and plants, Miro plays roles in mitochondrial homeostasis, but the ability to build a complex that regulates its association to kinesin for microtubule-dependent transport probably arose in metazoans.}, }
@article {pmid21130768, year = {2011}, author = {Qi, Y and Wang, H and Zou, Y and Liu, C and Liu, Y and Wang, Y and Zhang, W}, title = {Over-expression of mitochondrial heat shock protein 70 suppresses programmed cell death in rice.}, journal = {FEBS letters}, volume = {585}, number = {1}, pages = {231-239}, doi = {10.1016/j.febslet.2010.11.051}, pmid = {21130768}, issn = {1873-3468}, mesh = {*Apoptosis ; Blotting, Western ; Cell Survival ; Chromatin/metabolism ; DNA Fragmentation ; Gene Expression Regulation, Plant ; HSP70 Heat-Shock Proteins/classification/genetics/*metabolism ; Hot Temperature ; Hydrogen Peroxide/pharmacology ; In Situ Nick-End Labeling ; Membrane Potential, Mitochondrial ; Microscopy, Fluorescence ; Oryza/cytology/genetics/*metabolism ; Oxidants/pharmacology ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plants, Genetically Modified ; Protoplasts/cytology/drug effects/metabolism ; Reactive Oxygen Species/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {In this study, we identified and functionally characterized the mitochondrial heat shock protein 70 (mtHsp70). Over-expression of mtHsp70 suppressed heat- and H(2)O(2)-induced programmed cell death (PCD) in rice protoplasts, as reflected by higher cell viability, decreased DNA laddering and chromatin condensation. Mitochondrial membrane potential (Δψ(m)) after heat shock was destroyed gradually in protoplasts, but mtHsp70 over-expression showed higher Δψ(m) relative to the vector control cells, and partially inhibited cytochrome c release from mitochondria to cytosol. Heat treatment also significantly increased reactive oxygen species (ROS) generation, a phenomenon not observed in protoplasts over-expressing mtHsp70. Together, these results suggest that mtHsp70 may suppress PCD in rice protoplasts by maintaining mitochondrial Δψ(m) and inhibiting the amplification of ROS.}, }
@article {pmid21123072, year = {2011}, author = {Pallen, MJ}, title = {Time to recognise that mitochondria are bacteria?.}, journal = {Trends in microbiology}, volume = {19}, number = {2}, pages = {58-64}, doi = {10.1016/j.tim.2010.11.001}, pmid = {21123072}, issn = {1878-4380}, mesh = {Bacteria/genetics ; Biological Evolution ; Eukaryotic Cells/*cytology/physiology ; Mitochondria/*classification/genetics/physiology ; Symbiosis ; }, abstract = {The scientific community is comfortable with recognising mitochondria as organelles that happen to be descendants of bacteria. Here, I playfully explore the arguments for and against a phylogenetic fundamentalism that states that mitochondria are bacteria and should be given their own taxonomic family, the Mitochondriaceae. I also explore the consequences of recognizing mitochondria as bacteria for our understanding of the systemic response to trauma and for the prospects of creating transgenic mitochondria.}, }
@article {pmid21115831, year = {2010}, author = {Hao, W and Richardson, AO and Zheng, Y and Palmer, JD}, title = {Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {50}, pages = {21576-21581}, pmid = {21115831}, issn = {1091-6490}, support = {R01 GM070612/GM/NIGMS NIH HHS/United States ; R01-GM-70612/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Base Sequence ; *Biological Evolution ; *Gene Conversion ; *Gene Transfer, Horizontal ; *Genes, Mitochondrial ; Genes, Plant ; Genetic Speciation ; Genome, Bacterial ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {The best known outcome of horizontal gene transfer (HGT) is the introduction of novel genes, but other outcomes have been described. When a transferred gene has a homolog in the recipient genome, the native gene may be functionally replaced (and subsequently lost) or partially overwritten by gene conversion with transiently present foreign DNA. Here we report the discovery, in two lineages of plant mitochondrial genes, of novel gene combinations that arose by conversion between coresident native and foreign homologs. These lineages have undergone intricate conversion between native and foreign copies, with conversion occurring repeatedly and differentially over the course of speciation, leading to radiations of mosaic genes involved in respiration and intron splicing. Based on these findings, we develop a model--the duplicative HGT and differential gene conversion model--that integrates HGT and ongoing gene conversion in the context of speciation. Finally, we show that one of these HGT-driven gene-conversional radiations followed two additional types of conversional chimerism, namely, intramitochondrial retroprocessing and interorganellar gene conversion across the 2 billion year divide between mitochondria and chloroplasts. These findings expand our appreciation of HGT and gene conversion as creative evolutionary forces, establish plant mitochondria as a premiere system for studying the evolutionary dynamics of HGT and its genetic reverberations, and recommend careful examination of bacterial and other genomes for similar, likely overlooked phenomena.}, }
@article {pmid21115482, year = {2011}, author = {Yip, CY and Harbour, ME and Jayawardena, K and Fearnley, IM and Sazanov, LA}, title = {Evolution of respiratory complex I: "supernumerary" subunits are present in the alpha-proteobacterial enzyme.}, journal = {The Journal of biological chemistry}, volume = {286}, number = {7}, pages = {5023-5033}, pmid = {21115482}, issn = {1083-351X}, support = {MC_U105674180/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Bacterial Proteins/*genetics/metabolism ; Catalytic Domain/genetics ; Cattle ; Electron Transport Complex I/*genetics/metabolism ; *Evolution, Molecular ; Mitochondrial Proteins/*genetics/metabolism ; Paracoccus denitrificans/enzymology/*genetics ; }, abstract = {Modern α-proteobacteria are thought to be closely related to the ancient symbiont of eukaryotes, an ancestor of mitochondria. Respiratory complex I from α-proteobacteria and mitochondria is well conserved at the level of the 14 "core" subunits, consistent with that notion. Mitochondrial complex I contains the core subunits, present in all species, and up to 31 "supernumerary" subunits, generally thought to have originated only within eukaryotic lineages. However, the full protein composition of an α-proteobacterial complex I has not been established previously. Here, we report the first purification and characterization of complex I from the α-proteobacterium Paracoccus denitrificans. Single particle electron microscopy shows that the complex has a well defined L-shape. Unexpectedly, in addition to the 14 core subunits, the enzyme also contains homologues of three supernumerary mitochondrial subunits as follows: B17.2, AQDQ/18, and 13 kDa (bovine nomenclature). This finding suggests that evolution of complex I via addition of supernumerary or "accessory" subunits started before the original endosymbiotic event that led to the creation of the eukaryotic cell. It also provides further confirmation that α-proteobacteria are the closest extant relatives of mitochondria.}, }
@article {pmid21103375, year = {2010}, author = {Fourrage, C and Chevalier, S and Houliston, E}, title = {A highly conserved Poc1 protein characterized in embryos of the hydrozoan Clytia hemisphaerica: localization and functional studies.}, journal = {PloS one}, volume = {5}, number = {11}, pages = {e13994}, pmid = {21103375}, issn = {1932-6203}, mesh = {Animals ; Blotting, Western ; Cell Cycle Proteins/classification/genetics/*metabolism ; Centrioles/*metabolism ; DNA, Complementary/chemistry/genetics ; Embryo, Nonmammalian/embryology/*metabolism ; Female ; Fluorescent Antibody Technique ; Gene Expression Regulation, Developmental ; Gene Library ; Hydrozoa/embryology/genetics/*metabolism ; In Situ Hybridization ; Microscopy, Confocal ; Molecular Sequence Data ; Oocytes/metabolism ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Poc1 (Protein of Centriole 1) proteins are highly conserved WD40 domain-containing centriole components, well characterized in the alga Chlamydomonas, the ciliated protazoan Tetrahymena, the insect Drosophila and in vertebrate cells including Xenopus and zebrafish embryos. Functions and localizations related to the centriole and ciliary axoneme have been demonstrated for Poc1 in a range of species. The vertebrate Poc1 protein has also been reported to show an additional association with mitochondria, including enrichment in the specialized "germ plasm" region of Xenopus oocytes. We have identified and characterized a highly conserved Poc1 protein in the cnidarian Clytia hemisphaerica. Clytia Poc1 mRNA was found to be strongly expressed in eggs and early embryos, showing a punctate perinuclear localization in young oocytes. Fluorescence-tagged Poc1 proteins expressed in developing embryos showed strong localization to centrioles, including basal bodies. Anti-human Poc1 antibodies decorated mitochondria in Clytia, as reported in human cells, but failed to recognise endogenous or fluorescent-tagged Clytia Poc1. Injection of specific morpholino oligonucleotides into Clytia eggs prior to fertilization to repress Poc1 mRNA translation interfered with cell division from the blastula stage, likely corresponding to when neosynthesis normally takes over from maternally supplied protein. Cell cycle lengthening and arrest were observed, phenotypes consistent with an impaired centriolar biogenesis or function. The specificity of the defects could be demonstrated by injection of synthetic Poc1 mRNA, which restored normal development. We conclude that in Clytia embryos, Poc1 has an essentially centriolar localization and function.}, }
@article {pmid21097998, year = {2011}, author = {Atkinson, GC and Baldauf, SL}, title = {Evolution of elongation factor G and the origins of mitochondrial and chloroplast forms.}, journal = {Molecular biology and evolution}, volume = {28}, number = {3}, pages = {1281-1292}, doi = {10.1093/molbev/msq316}, pmid = {21097998}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; Chloroplasts/genetics/metabolism ; Conserved Sequence/genetics ; Deltaproteobacteria/genetics/metabolism ; Eukaryota/genetics/metabolism ; Humans ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Peptide Elongation Factor G/*genetics/metabolism ; Phylogeny ; Ribosomal Proteins/*genetics/metabolism ; Ribosomes/genetics/metabolism ; Sequence Homology, Amino Acid ; Spirochaetales/genetics/metabolism ; }, abstract = {Protein synthesis elongation factor G (EF-G) is an essential protein with central roles in both the elongation and ribosome recycling phases of protein synthesis. Although EF-G evolution is predicted to be conservative, recent reports suggest otherwise. We have characterized EF-G in terms of its molecular phylogeny, genomic context, and patterns of amino acid substitution. We find that most bacteria carry a single "canonical" EF-G, which is phylogenetically conservative and encoded in an str operon. However, we also find a number of EF-G paralogs. These include a pair of EF-Gs that are mostly found together and in an eclectic subset of bacteria, specifically δ-proteobacteria, spirochaetes, and planctomycetes (the "spd" bacteria). These spdEFGs have also given rise to the mitochondrial factors mtEFG1 and mtEFG2, which probably arrived in eukaryotes before the eukaryotic last common ancestor. Meanwhile, chloroplasts apparently use an α-proteobacterial-derived EF-G rather than the expected cyanobacterial form. The long-term comaintenance of the spd/mtEFGs may be related to their subfunctionalization for translocation and ribosome recycling. Consistent with this, patterns of sequence conservation and site-specific evolutionary rate shifts suggest that the faster evolving spd/mtEFG2 has lost translocation function, but surprisingly, the protein also shows little conservation of sites related to recycling activity. On the other hand, spd/mtEFG1, although more slowly evolving, shows signs of substantial remodeling. This is particularly extensive in the GTPase domain, including a highly conserved three amino acid insertion in switch I. We suggest that subfunctionalization of the spd/mtEFGs is not a simple case of specialization for subsets of original activities. Rather, the duplication allows the release of one paralog from the selective constraints imposed by dual functionality, thus allowing it to become more highly specialized. Thus, the potential for fine tuning afforded by subfunctionalization may explain the maintenance of EF-G paralogs.}, }
@article {pmid21093612, year = {2011}, author = {Dsouli-Aymes, N and Michaux, J and De Stordeur, E and Couloux, A and Veuille, M and Duvallet, G}, title = {Global population structure of the stable fly (Stomoxys calcitrans) inferred by mitochondrial and nuclear sequence data.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {11}, number = {2}, pages = {334-342}, doi = {10.1016/j.meegid.2010.11.001}, pmid = {21093612}, issn = {1567-7257}, mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal Spacer/*genetics ; Demography ; Genes, Insect ; Genes, rRNA ; Genetic Markers ; Genetic Variation ; Haplotypes ; Humans ; Mitochondria/genetics ; Molecular Sequence Data ; Muscidae/*genetics ; Phylogeography ; Sequence Analysis, DNA ; }, abstract = {Stomoxys calcitrans (Diptera: Muscidae: Stomoxyini), a synanthropic fly with a worldwide distribution, is recognized to have an important medical and veterinary impact. We conducted a phylogeographic analysis based on several populations from five major zoogeographic regions of the world in order to analyse population genetic structure of S. calcitrans and to trace its global dispersion. Results from mitochondrial (COI, Cyt-b and ND1-16S) and nuclear (ITS2) DNA show a substantial differentiation of Oriental populations (first lineage) from the Afrotropical, Palearctic, Nearctic, Neotropical and Oceanian populations (second lineage). The divergence time analyses suggest the separation between the two lineages approximately in mid-Pleistocene. Oriental populations are isolated and would not have participated in the colonization of other regions, unlike the Afrotropical one which seems to be the source of S. calcitrans dispersion towards other regions. Demographic analyses indicate that Oriental, Afrotropical and Palearctic regions have undergone a population expansion during late Pleistocene-early Holocene. The expansion time of this cosmopolitan species could have been influenced by continental human expansions and by animal domestication.}, }
@article {pmid21088908, year = {2011}, author = {Li, Q and Liu, X and He, Q and Hu, L and Ling, Y and Wu, Y and Yang, X and Yu, L}, title = {Systematic analysis of gene expression level with tissue-specificity, function and protein subcellular localization in human transcriptome.}, journal = {Molecular biology reports}, volume = {38}, number = {4}, pages = {2597-2602}, pmid = {21088908}, issn = {1573-4978}, mesh = {Cell Membrane/metabolism ; Cytoplasm/metabolism ; *Evolution, Molecular ; Extracellular Matrix/metabolism ; *Gene Expression ; Gene Expression Profiling/*methods ; Genes/genetics ; Humans ; Organ Specificity/*genetics ; Organelles/metabolism ; Proteins/genetics/*metabolism ; }, abstract = {Recent studies have shown that, in mammals, the highly expressed genes have shorter gene length and their protein products have relatively lower evolutionary rates. However, the global relationship between genes' expression level and their features such as tissue-specificity, function and protein subcellular localization has not been investigated extensively, especially in mammalian. In order to solve it, we analysed 8,570 genes across 46 human tissues. Our results suggest that widely expressed genes have higher mean expression levels than tissue-specific ones and genes encoding zinc-finger proteins have low expression levels similar to that of DNA-binding proteins. In the analysis of protein subcellular localization, it is shown that nuclear and Golgi apparatus proteins have lower mean expression levels than those of mitochondria, endoplasmic reticulum and membrane proteins, while genes encoding cytoplasm and extracellular components display the highest expression levels. When comparing the gene expression levels and the number of expressed genes in different tissues, we found that some tissues have less active genes while single gene encodes relatively more transcripts. Taken together, gene expression levels are clearly correlated with their tissue-specificity, function and protein subcellular localization, and are highly conserved during evolution.}, }
@article {pmid21087461, year = {2010}, author = {Martínez-Fernández, M and Bernatchez, L and Rolán-Alvarez, E and Quesada, H}, title = {Insights into the role of differential gene expression on the ecological adaptation of the snail Littorina saxatilis.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {356}, pmid = {21087461}, issn = {1471-2148}, mesh = {Adaptation, Physiological/*genetics ; Amplified Fragment Length Polymorphism Analysis ; Animals ; DNA, Complementary/genetics ; DNA, Mitochondrial/genetics ; Ecology ; Electron Transport Complex IV/genetics ; Female ; *Gene Expression Profiling ; Gene Flow ; *Genetic Speciation ; Male ; Sequence Analysis, DNA ; Snails/*genetics ; }, abstract = {BACKGROUND: In the past 40 years, there has been increasing acceptance that variation in levels of gene expression represents a major source of evolutionary novelty. Gene expression divergence is therefore likely to be involved in the emergence of incipient species, namely, in a context of adaptive radiation. In this study, a genome-wide expression profiling approach (cDNA-AFLP), validated by quantitative real-time polymerase chain reaction (qPCR) were used to get insights into the role of differential gene expression on the ecological adaptation of the marine snail Littorina saxatilis. This gastropod displays two sympatric ecotypes (RB and SU) which are becoming one of the best studied systems for ecological speciation.<br><br>RESULTS: Among the 99 transcripts shared between ecotypes, 12.12% showed significant differential expression. At least 4% of these transcripts still displayed significant differences after correction for multiple tests, highlighting that gene expression can differ considerably between subpopulations adapted to alternative habitats in the face of gene flow. One of the transcripts identified was Cytochrome c Oxidase subunit I (COI). In addition, 6 possible reference genes were validated to normalize and confirm this result using qPCR. &#x3b1;-Tubulin and histone H3.3 showed the more stable expression levels, being therefore chosen as the best option for normalization. The qPCR analysis confirmed a higher COI expression in SU individuals.<br><br>CONCLUSIONS: At least 4% of the transcriptome studied is being differentially expressed between ecotypes living in alternative habitats, even when gene flow is still substantial between ecotypes. We could identify a candidate transcript of such ecotype differentiation: Cytochrome c Oxidase Subunit I (COI), a mitochondrial gene involved in energy metabolism. Quantitative PCR was used to confirm the differences found in COI and its over-expression in the SU ecotype. Interestingly, COI is involved in the oxidative phosphorylation, suggesting an enhanced mitochondrial gene expression (or increased number of mitochondria) to improve energy supply in the ecotype subjected to the strongest wave action.}, }
@article {pmid21081480, year = {2011}, author = {Tong, J and Dolezal, P and Selkrig, J and Crawford, S and Simpson, AG and Noinaj, N and Buchanan, SK and Gabriel, K and Lithgow, T}, title = {Ancestral and derived protein import pathways in the mitochondrion of Reclinomonas americana.}, journal = {Molecular biology and evolution}, volume = {28}, number = {5}, pages = {1581-1591}, pmid = {21081480}, issn = {1537-1719}, mesh = {Active Transport, Cell Nucleus ; Amino Acid Sequence ; Cell Nucleus/metabolism ; Cyclooxygenase 2/genetics/metabolism ; Eukaryota/*genetics/ultrastructure ; Evolution, Molecular ; Gene Transfer, Horizontal ; Hydrophobic and Hydrophilic Interactions ; Mitochondria/ultrastructure ; Mitochondrial Membrane Transport Proteins/*genetics/metabolism ; Models, Genetic ; Molecular Sequence Data ; Protein Sorting Signals/genetics ; Protein Transport/*genetics ; Recombinant Proteins/genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The evolution of mitochondria from ancestral bacteria required that new protein transport machinery be established. Recent controversy over the evolution of these new molecular machines hinges on the degree to which ancestral bacterial transporters contributed during the establishment of the new protein import pathway. Reclinomonas americana is a unicellular eukaryote with the most gene-rich mitochondrial genome known, and the large collection of membrane proteins encoded on the mitochondrial genome of R. americana includes a bacterial-type SecY protein transporter. Analysis of expressed sequence tags shows R. americana also has components of a mitochondrial protein translocase or "translocase in the inner mitochondrial membrane complex." Along with several other membrane proteins encoded on the mitochondrial genome Cox11, an assembly factor for cytochrome c oxidase retains sequence features suggesting that it is assembled by the SecY complex in R. americana. Despite this, protein import studies show that the RaCox11 protein is suited for import into mitochondria and functional complementation if the gene is transferred into the nucleus of yeast. Reclinomonas americana provides direct evidence that bacterial protein transport pathways were retained, alongside the evolving mitochondrial protein import machinery, shedding new light on the process of mitochondrial evolution.}, }
@article {pmid21080492, year = {2010}, author = {Szklarczyk, R and Huynen, MA}, title = {Mosaic origin of the mitochondrial proteome.}, journal = {Proteomics}, volume = {10}, number = {22}, pages = {4012-4024}, doi = {10.1002/pmic.201000329}, pmid = {21080492}, issn = {1615-9861}, mesh = {Animals ; Biological Evolution ; Humans ; Mice ; Mitochondria/*genetics/metabolism ; *Proteome ; Symbiosis ; }, abstract = {Although the origin of mitochondria from the endosymbiosis of an α-proteobacterium is well established, the nature of the host cell, the metabolic complexity of the endosymbiont and the subsequent evolution of the proto-mitochondrion into all its current appearances are still the subject of discovery and sometimes debate. Here we review what has been inferred about the original composition and subsequent evolution of the mitochondrial proteome and essential mitochondrial systems. The evolutionary mosaic that currently constitutes mitochondrial proteomes contains (i) endosymbiotic proteins (15-45%), (ii) proteins without detectable orthologs outside the eukaryotic lineage (40%), and (iii) proteins that are derived from non-proteobacterial Bacteria, Bacteriophages and Archaea (15%, specifically multiple tRNA-modification proteins). Protein complexes are of endosymbiotic origin, but have greatly expanded with novel eukaryotic proteins; in contrast to mitochondrial enzymes that are both of proteobacterial and non-proteobacterial origin. This disparity is consistent with the complexity hypothesis, which argues that proteins that are a part of large, multi-subunit complexes are unlikely to undergo horizontal gene transfer. We observe that they neither change their subcellular compartments in the course of evolution, even when their genes do.}, }
@article {pmid21078193, year = {2010}, author = {Carrie, C and Murcha, MW and Whelan, J}, title = {An in silico analysis of the mitochondrial protein import apparatus of plants.}, journal = {BMC plant biology}, volume = {10}, number = {}, pages = {249}, pmid = {21078193}, issn = {1471-2229}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/metabolism ; Chlamydomonas reinhardtii/genetics/metabolism ; Chlorella/genetics/metabolism ; Genetic Variation ; Membrane Transport Proteins/classification/*genetics/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/classification/*genetics/metabolism ; Molecular Sequence Data ; Oryza/genetics/metabolism ; Phaeophyceae/genetics/metabolism ; Phylogeny ; Picea/genetics/metabolism ; Plant Proteins/*genetics/metabolism ; Protein Transport ; Rhodophyta/genetics/metabolism ; Sequence Alignment/methods ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {BACKGROUND: An in silico analysis of the mitochondrial protein import apparatus from a variety of species; including Chlamydomonas reinhardtii, Chlorella variabilis, Ectocarpus siliculosus, Cyanidioschyzon merolae, Physcomitrella patens, Selaginella moellendorffii, Picea glauca, Oryza sativa and Arabidopsis thaliana was undertaken to determine if components differed within and between plant and non-plant species.<br><br>RESULTS: The channel forming subunits of the outer membrane components Tom40 and Sam50 are conserved between plant groups and other eukaryotes. In contrast, the receptor component(s) in green plants, particularly Tom20, (C. reinhardtii, C. variabilis, P. patens, S. moellendorffii, P. glauca, O. sativa and A. thaliana) are specific to this lineage. Red algae contain a Tom22 receptor that is orthologous to yeast Tom22. Furthermore, plant mitochondrial receptors display differences between various plant lineages. These are evidenced by distinctive motifs in all plant Metaxins, which are absent in red algae, and the presence of the outer membrane receptor OM64 in Angiosperms (rice and Arabidopsis), but not in lycophytes (S. moellendorffii) and gymnosperms (P. glauca). Furthermore, although the intermembrane space receptor Mia40 is conserved across a wide phylogenetic range, its function differs between lineages. In all plant lineages, Tim17 contains a C-terminal extension, which may act as a receptor component for the import of nucleic acids into plant mitochondria.<br><br>CONCLUSIONS: It is proposed that the observed functional divergences are due to the selective pressure to sort proteins between mitochondria and chloroplasts, resulting in differences in protein receptor components between plant groups and other organisms. Additionally, diversity of receptor components is observed within the plant kingdom. Even when receptor components are orthologous across plant and non-plant species, it appears that the functions of these have expanded or diverged in a lineage specific manner.}, }
@article {pmid21075209, year = {2012}, author = {Glor, RE and Laport, RG}, title = {Are subspecies of Anolis lizards that differ in dewlap color and pattern also genetically distinct? A mitochondrial analysis.}, journal = {Molecular phylogenetics and evolution}, volume = {64}, number = {2}, pages = {255-260}, doi = {10.1016/j.ympev.2010.11.004}, pmid = {21075209}, issn = {1095-9513}, mesh = {Animals ; Bahamas ; DNA, Mitochondrial/*genetics ; Dominican Republic ; Female ; Genetic Drift ; Genetic Variation ; Haplotypes ; Lizards/*classification/*genetics ; Male ; Mitochondria/genetics ; Phylogeny ; Phylogeography ; *Pigmentation ; RNA, Transfer/genetics/metabolism ; Skin ; Species Specificity ; }, abstract = {Subspecies of Anolis lizards are often defined on the basis of geographic variation in the color and pattern of the dewlap, an extensible throat fan considered central to species recognition and sexual selection. Among the most impressive examples of this phenomenon are two species of trunk anoles found across Hispaniola and the Bahamas: Anolis distichus is divided into 16 subspecies with dewlap colors ranging from deep wine red to pale yellow while Anolis brevirostris is divided into three subspecies with dewlaps ranging from pale yellow to orange. Limited sampling of allozyme data indicates some genetic divergence among subspecies and suggests that they may deserve recognition at the species-level. Our goal here is to use more comprehensive geographic sampling of mtDNA haplotypes to test whether the five subspecies of A. distichus and three subspecies of A. brevirostris that occur in the Dominican Republic correspond with genetically distinct populations that may warrant recognition under the general lineage concept. We obtain an aligned dataset of 1462bp comprised of the genes encoding ND2 and adjacent tRNAs from 76 individuals of A. distichus from 28 localities and 12 individuals of A. brevirostris from five localities. We find that haplotypes sampled from each Dominican subspecies of A. distichus form well-supported and deeply divergent clades (>10% uncorrected sequence divergence). Strong concordance between mtDNA haplotype structure and previously diagnosed phenotypic variation in traits central to interspecific communication (i.e., the dewlap) leads us to hypothesize that each of the presently recognized Dominican subspecies of A. distichus and A. brevirostris deserves elevation to full species status under the general lineage concept.}, }
@article {pmid21074581, year = {2011}, author = {Morada, M and Smid, O and Hampl, V and Sutak, R and Lam, B and Rappelli, P and Dessì, D and Fiori, PL and Tachezy, J and Yarlett, N}, title = {Hydrogenosome-localization of arginine deiminase in Trichomonas vaginalis.}, journal = {Molecular and biochemical parasitology}, volume = {176}, number = {1}, pages = {51-54}, pmid = {21074581}, issn = {1872-9428}, support = {R01 AI049785-01A1/AI/NIAID NIH HHS/United States ; }, mesh = {Gene Expression Regulation, Enzymologic ; Hydrolases/genetics/*metabolism ; Organelles/enzymology ; Phylogeny ; Protein Transport ; Recombinant Fusion Proteins/genetics/metabolism ; Trichomonas vaginalis/*enzymology/*genetics ; }, abstract = {The arginine dihydrolase (ADH) pathway has an analogous function to the urea cycle in mitochondria-containing cells, by removing nitrogen from amino acids and generating ATP. Subcellular localization of the ADH pathway enzymes in Trichomonas vaginalis revealed that arginine deiminase (ADI) localizes to the hydrogenosome, a mitochondrion-like organelle of anaerobic protists. However the other enzymes of the ADH pathway, ornithine carbamyltransferase and carbamate kinase localize to the cytosol. Three gene sequences of T. vaginalis ADI (ADI 1-3) were identified in the T. vaginalis genome, all having putative mitochondrial targeting sequences. The ADI sequences were cloned and used to probe T. vaginalis using a carboxyterminal di-hemogglutinin epitope tag which demonstrated co-localization with malic enzyme confirming the hydrogenosome localization of this enzyme.}, }
@article {pmid21072538, year = {2011}, author = {Yang, B and Cai, J and Cheng, X}, title = {Identification of astigmatid mites using ITS2 and COI regions.}, journal = {Parasitology research}, volume = {108}, number = {2}, pages = {497-503}, pmid = {21072538}, issn = {1432-1955}, mesh = {Animals ; DNA Barcoding, Taxonomic ; DNA, Mitochondrial ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex IV/*genetics ; Mites/classification/*genetics ; Mitochondria/enzymology ; Phylogeny ; Species Specificity ; }, abstract = {Identification of astigmatid mites based on their morphological characteristics is difficult because of the similarity of their organs, especially in immature mites. The ribosomal second internal transcribed spacer (ITS2) and the mitochondrial cytochrome oxidase subunit I (COI) regions are highly conserved in the eukaryotes and are usually used as barcodes. The ITS2 and COI regions of six species of astigmatid mites (Aleuroglyphus ovatus, Blomia tropicalis, Dermatophagoides farinae, Dermatophagoides pteronyssinus, Euroglyphus maynei, Tyrophagus putrescentiae) were obtained by polymerase chain reaction and sequenced. The lengths of the ITS2 sequences varied from 316 to 488 bp, while the COI regions were 377 or 378 bp long. Considering the ITS2 genes, the intraspecific genetic distance was in the range of 0.00-0.077844, whereas the interspecific genetic distance was 0.202426-0.912959. The values were 0.000-0.029748 and 0.138403-0.279304 for intra- and interspecific genetic distances when COI genes were used. The phylogenetic trees inferred from the ITS2 and the COI regions, by using maximum parsimony and neighbor-joining methods, were identical to those based on their morphological classification. Thus, the ITS2 and COI regions can be applied as barcodes to identify different species of astigmatid mites.}, }
@article {pmid21071654, year = {2010}, author = {Gray, MW and Lukes, J and Archibald, JM and Keeling, PJ and Doolittle, WF}, title = {Cell biology. Irremediable complexity?.}, journal = {Science (New York, N.Y.)}, volume = {330}, number = {6006}, pages = {920-921}, doi = {10.1126/science.1198594}, pmid = {21071654}, issn = {1095-9203}, mesh = {Animals ; *Biological Evolution ; *Cell Physiological Phenomena ; Genome, Mitochondrial ; Introns ; Mitochondria/genetics/physiology ; Models, Biological ; Mutation ; RNA Editing ; RNA Splicing ; Ribosomes/physiology ; Selection, Genetic ; Spliceosomes/genetics/physiology ; }, }
@article {pmid21070620, year = {2010}, author = {Cuenca, A and Petersen, G and Seberg, O and Davis, JI and Stevenson, DW}, title = {Are substitution rates and RNA editing correlated?.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {349}, pmid = {21070620}, issn = {1471-2148}, mesh = {Alismatales/*genetics ; Mitochondrial Proteins/classification/genetics ; Phylogeny ; RNA Editing/*genetics ; RNA, Plant/*genetics ; }, abstract = {BACKGROUND: RNA editing is a post-transcriptional process that, in seed plants, involves a cytosine to uracil change in messenger RNA, causing the translated protein to differ from that predicted by the DNA sequence. RNA editing occurs extensively in plant mitochondria, but large differences in editing frequencies are found in some groups. The underlying processes responsible for the distribution of edited sites are largely unknown, but gene function, substitution rate, and gene conversion have been proposed to influence editing frequencies.<br><br>RESULTS: We studied five mitochondrial genes in the monocot order Alismatales, all showing marked differences in editing frequencies among taxa. A general tendency to lose edited sites was observed in all taxa, but this tendency was particularly strong in two clades, with most of the edited sites lost in parallel in two different areas of the phylogeny. This pattern is observed in at least four of the five genes analyzed. Except in the groups that show an unusually low editing frequency, the rate of C-to-T changes in edited sites was not significantly higher that in non-edited 3rd codon positions. This may indicate that selection is not actively removing edited sites in nine of the 12 families of the core Alismatales. In all genes but ccmB, a significant correlation was found between frequency of change in edited sites and synonymous substitution rate. In general, taxa with higher substitution rates tend to have fewer edited sites, as indicated by the phylogenetically independent correlation analyses. The elimination of edited sites in groups that lack or have reduced levels of editing could be a result of gene conversion involving a cDNA copy (retroprocessing). If so, this phenomenon could be relatively common in the Alismatales, and may have affected some groups recurrently. Indirect evidence of retroprocessing without a necessary correlation with substitution rate was found mostly in families Alismataceae and Hydrocharitaceae (e.g., groups that suffered a rapid elimination of all their edited sites, without a change in substitution rate).<br><br>CONCLUSIONS: The effects of substitution rate, selection, and/or gene conversion on the dynamics of edited sites in plant mitochondria remain poorly understood. Although we found an inverse correlation between substitution rate and editing frequency, this correlation is partially obscured by gene retroprocessing in lineages that have lost most of their edited sites. The presence of processed paralogs in plant mitochondria deserves further study, since most evidence of their occurrence is circumstantial.}, }
@article {pmid21064038, year = {2011}, author = {Shi, LZ and Nascimento, J and Botvinick, E and Durrant, B and Berns, MW}, title = {An interdisciplinary systems approach to study sperm physiology and evolution.}, journal = {Wiley interdisciplinary reviews. Systems biology and medicine}, volume = {3}, number = {1}, pages = {36-47}, doi = {10.1002/wsbm.106}, pmid = {21064038}, issn = {1939-005X}, mesh = {Algorithms ; Biological Evolution ; Glycolysis/physiology ; Humans ; Male ; Oxidative Phosphorylation ; Sperm Motility ; Spermatozoa/*physiology ; }, abstract = {Optical trapping is a noninvasive biophotonic tool that has been developed to study the physiological and biomechanical properties of cells. The custom-designed optical system is built to direct near-infrared laser light into an inverted microscope to create a single-point three-dimensional gradient laser trap at the microscope focal point. A real-time automated tracking and trapping system (RATTS) is described that provides a remote user-friendly robotic interface. The combination of laser tweezers, fluorescent imaging, and RATTS can measure sperm swimming speed and swimming force simultaneously with mitochondrial membrane potential (MMP). The roles of two sources of adenosine triphosphate in sperm motility/energetics are studied: oxidative phosphorylation, which occurs in the mitochondria located in the sperm midpiece, and glycolysis, which occurs along the length of the sperm tail (flagellum). The effects of glucose, oxidative phosphorylation inhibitors, and glycolytic inhibitors on human sperm motility are studied. This combination of photonic physical and engineering tools has been used to examine the evolutionary effect of sperm competition in primates. The results demonstrate a correlation between mating type and sperm motility: sperm from polygamous (multi-partner) primate species swim faster and with greater force than sperm from polygynous (single partner) primate species. In summary, engineering and biological systems are combined to provide a powerful interdisciplinary approach to study the complex biological systems that drive the sperm toward the egg.}, }
@article {pmid21061630, year = {2010}, author = {Lukhtanov, VA and Kuznetsova, VG}, title = {[What gene and chromosomes say about the origin and evolution of insects and other arthropods].}, journal = {Genetika}, volume = {46}, number = {9}, pages = {1258-1265}, pmid = {21061630}, issn = {0016-6758}, mesh = {Animals ; Arthropods/*genetics ; *Biological Evolution ; Chromosomes/*genetics/ultrastructure ; Chromosomes, Insect/genetics/ultrastructure ; Insecta/genetics ; Mitochondria/genetics/ultrastructure ; Phylogeny ; Tandem Repeat Sequences ; Telomere/genetics ; }, abstract = {At the turn of the 21st century, the use of molecular and molecular cytogenetic methods led to revolutionary advances in systematics of insects and other arthropods. Analysis of nuclear and mitochondrial genes, as well as investigation of structural rearrangements in the mitochondrial chromosome convincingly supported the Pancrustacea hypothesis, according to which insects originated directly from crustaceans, whereas myriapods are not closely related to them. The presence of the specific telomeric motif TTAGG confirmed the monophyletic origin of arthropods (Arthropoda) and the assignment of tongue worms (Pentastomida) to this type. Several different types of telomeric sequences have been found within the class of insects. Investigation of the molecular organization of these sequences may shed light on the relationships between the orders Diptera, Siphonaptera, and Mecoptera and on the origin of such enigmatic groups as the orders Strepsiptera, Zoraptera and suborder Coleorrhyncha.}, }
@article {pmid21029305, year = {2010}, author = {Lei, X and Zhang, S and Emani, B and Barbour, SE and Ramanadham, S}, title = {A link between endoplasmic reticulum stress-induced β-cell apoptosis and the group VIA Ca2+-independent phospholipase A2 (iPLA2β).}, journal = {Diabetes, obesity &amp; metabolism}, volume = {12 Suppl 2}, number = {0 2}, pages = {93-98}, pmid = {21029305}, issn = {1463-1326}, support = {R37 DK034388/DK/NIDDK NIH HHS/United States ; P60-DK20579/DK/NIDDK NIH HHS/United States ; R01 DK069455/DK/NIDDK NIH HHS/United States ; P30 DK056341/DK/NIDDK NIH HHS/United States ; R01-DK69455/DK/NIDDK NIH HHS/United States ; R37-DK34388/DK/NIDDK NIH HHS/United States ; P60 DK020579/DK/NIDDK NIH HHS/United States ; P41 RR000954/RR/NCRR NIH HHS/United States ; P41-RR00954/RR/NCRR NIH HHS/United States ; P30-DK56341/DK/NIDDK NIH HHS/United States ; }, mesh = {Apoptosis/*physiology ; Calcium/metabolism ; Ceramides/metabolism ; Diabetes Mellitus, Type 2/genetics/*physiopathology ; Endoplasmic Reticulum/genetics/*physiology ; Group VI Phospholipases A2/metabolism/*physiology ; Humans ; Insulin-Secreting Cells/*metabolism ; Mitochondria/physiology ; Stress, Physiological ; }, abstract = {Endoplasmic reticulum (ER) stress is becoming recognized as an important contributing factor in various diseases, including diabetes mellitus. Prolonged ER stress can cause β-cell apoptosis; however, the underlying mechanism(s) that contribute to this process are not well understood. Early reports suggested that arachidonic acid metabolites and a Ca(2+)-independent phospholipase A(2) (iPLA(2)) activity play a role in β-cell apoptosis. The PLA(2) family of enzymes catalyse the hydrolysis of the sn-2 substituent (i.e. arachidonic acid) of membrane phospholipids. In light of our findings that the pancreatic islet β-cells are enriched in arachidonate-containing phospholipids and express the group VIA iPLA(2)β, we considered the possibility that iPLA(2)β participates in ER stress-induced β-cell apoptosis. Our work revealed a novel mechanism, involving ceramide generation and triggering of mitochondrial abnormalities, by which iPLA(2)β participates in the β-cell apoptosis process. Here, we review our evidence linking ER stress, β-cell apoptosis and iPLA(2)β. Continued studies in this area will increase our understanding of the contribution of iPLA(2)β to the evolution of diabetes mellitus and will further our knowledge of factors that influence β-cell health in diabetes mellitus and identify potential targets for future therapeutic interventions to prevent β-cell death.}, }
@article {pmid21045377, year = {2010}, author = {Shankar, SK}, title = {Biology of aging brain.}, journal = {Indian journal of pathology &amp; microbiology}, volume = {53}, number = {4}, pages = {595-604}, doi = {10.4103/0377-4929.71995}, pmid = {21045377}, issn = {0974-5130}, mesh = {Aging/*physiology ; Animals ; Brain/*physiology ; Calcium/metabolism ; Cognition/physiology ; Humans ; Mitochondria/metabolism/physiology ; Neurons/physiology ; Reactive Oxygen Species/metabolism ; Synapses/physiology ; }, abstract = {Normal aging of the nervous system is associated with some degree of decline in a number of cognitive functions. With the present day attempts to increase the life span, understanding the metabolic interactions and various mechanisms involved in normal neuronal aging continues to be a challenge. Loss of neurons is now recognized to be more modest than the initial estimates suggested and the loss only affected some of the specific neuroanatomical areas like hippocampus and prefrontal cortex. Individual neurons in addition show reduced size of dendritic and axonal arborization. Neurons have significant homeostatic control of the essential physiological functions like synaptic excitability, gene expression and metabolic regulation. Deviation in these normal events can have severe consequences as observed in aging and neurodegeneration. Based on experimental evidence, the evolution of aging is probably the result of altered metabolic triad: the mitochondria, reactive oxygen species and intracellular calcium homeostasis. Perturbations in the metabolic and functional state of this triad lead to a state of decreased homeostatic reserve, where the aged neurons still could maintain adequate function during normal activity. However, these neurons become vulnerable to the stress of excessive metabolic loads associated with spells of ischemia, trauma progressing to neuronal degeneration. Age-related neuronal dysfunction probably involves a host of subtle changes involving the synapses, receptors, neurotransmitters, cytological alterations, electrical transmission, leading to cognitive dysfunction. An exaggeration of it could be the clinical manifestation of dementia, with intraneuronal accumulation of protein aggregates deranging the metabolic state. This review deals with some of the structural, functional and metabolic features of aging nervous system and discusses briefly the functional consequences.}, }
@article {pmid21038434, year = {2011}, author = {Agrawal, GK and Bourguignon, J and Rolland, N and Ephritikhine, G and Ferro, M and Jaquinod, M and Alexiou, KG and Chardot, T and Chakraborty, N and Jolivet, P and Doonan, JH and Rakwal, R}, title = {Plant organelle proteomics: collaborating for optimal cell function.}, journal = {Mass spectrometry reviews}, volume = {30}, number = {5}, pages = {772-853}, doi = {10.1002/mas.20301}, pmid = {21038434}, issn = {1098-2787}, support = {BBS/E/J/00000129/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Arabidopsis/chemistry/genetics/ultrastructure ; Biomarkers/metabolism ; Cell Fractionation ; *Gene Expression Regulation, Plant ; Mass Spectrometry/instrumentation/methods ; Organelles/*chemistry/ultrastructure ; Oryza/chemistry/genetics/ultrastructure ; Plant Cells/*chemistry/ultrastructure ; Plant Proteins/*analysis ; Proteomics/instrumentation/*methods ; Staining and Labeling ; Zea mays/chemistry/genetics/ultrastructure ; }, abstract = {Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.}, }
@article {pmid21037180, year = {2010}, author = {Barberà, MJ and Ruiz-Trillo, I and Tufts, JY and Bery, A and Silberman, JD and Roger, AJ}, title = {Sawyeria marylandensis (Heterolobosea) has a hydrogenosome with novel metabolic properties.}, journal = {Eukaryotic cell}, volume = {9}, number = {12}, pages = {1913-1924}, pmid = {21037180}, issn = {1535-9786}, mesh = {Amino Acid Sequence ; Eukaryota/classification/*enzymology/metabolism/ultrastructure ; Hydrogenase/chemistry/genetics/*metabolism ; Mitochondria/chemistry/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Pyruvate Synthase/chemistry/genetics/*metabolism ; Sequence Alignment ; }, abstract = {Protists that live under low-oxygen conditions often lack conventional mitochondria and instead possess mitochondrion-related organelles (MROs) with distinct biochemical functions. Studies of mostly parasitic organisms have suggested that these organelles could be classified into two general types: hydrogenosomes and mitosomes. Hydrogenosomes, found in parabasalids, anaerobic chytrid fungi, and ciliates, metabolize pyruvate anaerobically to generate ATP, acetate, CO(2), and hydrogen gas, employing enzymes not typically associated with mitochondria. Mitosomes that have been studied have no apparent role in energy metabolism. Recent investigations of free-living anaerobic protists have revealed a diversity of MROs with a wider array of metabolic properties that defy a simple functional classification. Here we describe an expressed sequence tag (EST) survey and ultrastructural investigation of the anaerobic heteroloboseid amoeba Sawyeria marylandensis aimed at understanding the properties of its MROs. This organism expresses typical anaerobic energy metabolic enzymes, such as pyruvate:ferredoxin oxidoreductase, [FeFe]-hydrogenase, and associated hydrogenase maturases with apparent organelle-targeting peptides, indicating that its MRO likely functions as a hydrogenosome. We also identified 38 genes encoding canonical mitochondrial proteins in S. marylandensis, many of which possess putative targeting peptides and are phylogenetically related to putative mitochondrial proteins of its heteroloboseid relative Naegleria gruberi. Several of these proteins, such as a branched-chain alpha keto acid dehydrogenase, likely function in pathways that have not been previously associated with the well-studied hydrogenosomes of parabasalids. Finally, morphological reconstructions based on transmission electron microscopy indicate that the S. marylandensis MROs form novel cup-like structures within the cells. Overall, these data suggest that Sawyeria marylandensis possesses a hydrogenosome of mitochondrial origin with a novel combination of biochemical and structural properties.}, }
@article {pmid21035093, year = {2010}, author = {Han, L and Qin, G and Kang, D and Chen, Z and Gu, H and Qu, LJ}, title = {A nuclear-encoded mitochondrial gene AtCIB22 is essential for plant development in Arabidopsis.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {37}, number = {10}, pages = {667-683}, doi = {10.1016/S1673-8527(09)60085-0}, pmid = {21035093}, issn = {1673-8527}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/*growth &amp; development/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Cell Nucleus/genetics ; Ethanol/pharmacology ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Germination/drug effects ; Green Fluorescent Proteins/genetics/metabolism ; Microscopy, Confocal ; Mitochondria/metabolism ; Mitochondrial Proteins/classification/*genetics/metabolism ; Molecular Sequence Data ; Mutation ; Oxidoreductases/genetics/metabolism ; Phylogeny ; Plant Proteins ; Plants, Genetically Modified ; RNA Interference ; Recombinant Fusion Proteins/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Seeds/genetics/growth &amp; development/metabolism ; Sequence Homology, Amino Acid ; Sucrose/pharmacology ; }, abstract = {Complex I (the NADH:ubiquinone oxidoreductase) of the mitochondrial respiratory chain is a complicated, multi-subunit, membrane-bound assembly and contains more than 40 different proteins in higher plants. In this paper, we characterize the Arabidopsis homologue (designated as AtCIB22) of the B22 subunit of eukaryotic mitochondrial Complex I. AtCIB22 is a single-copy gene and is highly conserved throughout eukaryotes. AtCIB22 protein is located in mitochondria and the AtCIB22 gene is widely expressed in different tissues. Mutant Arabidopsis plants with a disrupted AtCIB22 gene display pleiotropic phenotypes including shorter roots, smaller plants and delayed flowering. Stress analysis indicates that the AtCIB22 mutants' seed germination and early seedling growth are severely inhibited by sucrose deprivation stress but more tolerant to ethanol stress. Molecular analysis reveals that in moderate knockdown AtCIB22 mutants, genes including cell redox proteins and stress related proteins are significantly up-regulated, and that in severe knockdown AtCIB22 mutants, the alternative respiratory pathways including NDA1, NDB2, AOX1a and AtPUMP1 are remarkably elevated. These data demonstrate that AtCIB22 is essential for plant development and mitochondrial electron transport chains in Arabidopsis. Our findings also enhance our understanding about the physiological role of Complex I in plants.}, }
@article {pmid21034815, year = {2011}, author = {Desmond, E and Brochier-Armanet, C and Forterre, P and Gribaldo, S}, title = {On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes.}, journal = {Research in microbiology}, volume = {162}, number = {1}, pages = {53-70}, doi = {10.1016/j.resmic.2010.10.004}, pmid = {21034815}, issn = {1769-7123}, mesh = {Eukaryota/*genetics ; *Evolution, Molecular ; Mitochondria/*genetics ; *Phylogeny ; Ribosomes/*genetics ; }, abstract = {Understanding early evolution is a major challenge for the post-genomic era. A promising way to tackle this issue is to analyze the evolutionary history of key cellular systems through phylogenomic approaches. The current availability of genomic data from representatives of diverse lineages (especially eukaryotes), together with the ever growing number of proteomic characterizations now provides ample material to apply this type of analyses to trace back the origin and evolution of the three domains of life. Here, we have reconstructed the composition of the ancestral mitochondrial ribosome in the Last Eukaryotic Common Ancestor (LECA) and investigated its subsequent evolution in six major eukaryotic supergroups. We infer that LECA possessed a mitochondrial ribosome that was already much larger than its bacterial ancestor, with 19 additional specific proteins, indicating that a certain amount of time occurred between initial endosymbiosis at the origin of the mitochondrion and the diversification of present-day eukaryotic supergroups. Subsequently, mitochondrial ribosomes appear to have undergone a very dynamic evolutionary history in the different eukaryotic lineages, involving the loss of different sets of ribosomal protein-coding genes, their transfer to the host genome, as well as the acquisition of many novel components. This chaotic history for a such fundamental cellular machinery is puzzling, especially when compared to cytosolic, bacterial or chloroplastic ribosomes, which are much more stable. Intriguingly, archaeal ribosomes also show a very dynamic nature, with multiple independent losses among lineages.}, }
@article {pmid21034814, year = {2011}, author = {Poole, AM and Neumann, N}, title = {Reconciling an archaeal origin of eukaryotes with engulfment: a biologically plausible update of the Eocyte hypothesis.}, journal = {Research in microbiology}, volume = {162}, number = {1}, pages = {71-76}, doi = {10.1016/j.resmic.2010.10.002}, pmid = {21034814}, issn = {1769-7123}, mesh = {Archaea/*genetics/physiology ; Bacteria/genetics ; *Biological Evolution ; Eukaryota/*genetics ; Mitochondria/genetics ; Phagocytosis ; }, abstract = {An archaeal origin of eukaryotes is often equated with the engulfment of the bacterial ancestor of mitochondria by an archaeon. Such an event is problematic in that it is not supported by archaeal cell biology. We show that placing phylogenetic results within a stem-and-crown framework eliminates such incompatibilities, and that an archaeal origin for eukaryotes (as suggested from recent phylogenies) can be uncontroversially reconciled with phagocytosis as the mechanism for engulfment of the mitochondrial ancestor. This is significant because it eliminates a perceived problem with eukaryote origins: that an archaeal origin of eukaryotes (as under the Eocyte hypothesis) cannot be reconciled with existing cell biological mechanisms through which bacteria may take up residence inside eukaryote cells.}, }
@article {pmid20978534, year = {2011}, author = {Zaragoza, MV and Brandon, MC and Diegoli, M and Arbustini, E and Wallace, DC}, title = {Mitochondrial cardiomyopathies: how to identify candidate pathogenic mutations by mitochondrial DNA sequencing, MITOMASTER and phylogeny.}, journal = {European journal of human genetics : EJHG}, volume = {19}, number = {2}, pages = {200-207}, pmid = {20978534}, issn = {1476-5438}, support = {NS21328/NS/NINDS NIH HHS/United States ; AG16573/AG/NIA NIH HHS/United States ; DK73691/DK/NIDDK NIH HHS/United States ; P50 AG016573/AG/NIA NIH HHS/United States ; K08 HL081222/HL/NHLBI NIH HHS/United States ; AG24373/AG/NIA NIH HHS/United States ; R01 AG024373/AG/NIA NIH HHS/United States ; R01 DK073691/DK/NIDDK NIH HHS/United States ; R01 NS021328/NS/NINDS NIH HHS/United States ; R01 AG013154/AG/NIA NIH HHS/United States ; AG13154/AG/NIA NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Cardiomyopathies/*genetics/pathology ; Child ; DNA, Mitochondrial/*genetics ; *Databases, Genetic ; Echocardiography ; Female ; Genes, Mitochondrial ; *Genetic Variation ; Humans ; Infant ; Italy ; Male ; Middle Aged ; Mitochondria/genetics ; Mitochondrial Diseases/*genetics/pathology ; Mutation ; Pedigree ; *Phylogeny ; Sequence Analysis, DNA/*methods ; }, abstract = {Pathogenic mitochondrial DNA (mtDNA) mutations leading to mitochondrial dysfunction can cause cardiomyopathy and heart failure. Owing to a high mutation rate, mtDNA defects may occur at any nucleotide in its 16 569 bp sequence. Complete mtDNA sequencing may detect pathogenic mutations, which can be difficult to interpret because of normal ethnic/geographic-associated haplogroup variation. Our goal is to show how to identify candidate mtDNA mutations by sorting out polymorphisms using readily available online tools. The purpose of this approach is to help investigators in prioritizing mtDNA variants for functional analysis to establish pathogenicity. We analyzed complete mtDNA sequences from 29 Italian patients with mitochondrial cardiomyopathy or suspected disease. Using MITOMASTER and PhyloTree, we characterized 593 substitution variants by haplogroup and allele frequencies to identify all novel, non-haplogroup-associated variants. MITOMASTER permitted determination of each variant's location, amino acid change and evolutionary conservation. We found that 98% of variants were common or rare, haplogroup-associated variants, and thus unlikely to be primary cause in 80% of cases. Six variants were novel, non-haplogroup variants and thus possible contributors to disease etiology. Two with the greatest pathogenic potential were heteroplasmic, nonsynonymous variants: m.15132T>C in MT-CYB for a patient with hypertrophic dilated cardiomyopathy and m.6570G>T in MT-CO1 for a patient with myopathy. In summary, we have used our automated information system, MITOMASTER, to make a preliminary distinction between normal mtDNA variation and pathogenic mutations in patient samples; this fast and easy approach allowed us to select the variants for traditional analysis to establish pathogenicity.}, }
@article {pmid20977882, year = {2010}, author = {Gralle, M and Schäfer, I and Seibel, P and Pääbo, S}, title = {A functional test of Neandertal and modern human mitochondrial targeting sequences.}, journal = {Biochemical and biophysical research communications}, volume = {402}, number = {4}, pages = {747-749}, doi = {10.1016/j.bbrc.2010.10.099}, pmid = {20977882}, issn = {1090-2104}, mesh = {Amino Acid Substitution/*genetics ; Base Sequence ; Cell Line ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; *Genetic Speciation ; Genetic Testing ; Genome, Human/*genetics ; Humans ; Phylogeny ; }, abstract = {Targeting of nuclear-encoded proteins to different organelles, such as mitochondria, is a process that can result in the redeployment of proteins to new intracellular destinations during evolution. With the sequencing of the Neandertal genome, it has become possible to identify amino acid substitutions that occurred on the modern human lineage since its separation from the Neandertal lineage. Here we analyze the function of two substitutions in mitochondrial targeting sequences that occurred and rose to high frequency recently during recent human evolution. The ancestral and modern versions of the two targeting sequences do not differ in the efficiency with which they direct a protein to the mitochondria, an observation compatible with the neutral theory of molecular evolution.}, }
@article {pmid20977744, year = {2010}, author = {Hardouin, EA and Chapuis, JL and Stevens, MI and van Vuuren, JB and Quillfeldt, P and Scavetta, RJ and Teschke, M and Tautz, D}, title = {House mouse colonization patterns on the sub-Antarctic Kerguelen Archipelago suggest singular primary invasions and resilience against re-invasion.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {325}, pmid = {20977744}, issn = {1471-2148}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Europe ; Genetics, Population ; *Geography ; Haplotypes/genetics ; Mice ; Microsatellite Repeats/genetics ; Phylogeny ; Y Chromosome/genetics ; }, abstract = {BACKGROUND: Starting from Western Europe, the house mouse (Mus musculus domesticus) has spread across the globe in historic times. However, most oceanic islands were colonized by mice only within the past 300 years. This makes them an excellent model for studying the evolutionary processes during early stages of new colonization. We have focused here on the Kerguelen Archipelago, located within the sub-Antarctic area and compare the patterns with samples from other Southern Ocean islands.<br><br>RESULTS: We have typed 18 autosomal and six Y-chromosomal microsatellite loci and obtained mitochondrial D-loop sequences for a total of 534 samples, mainly from the Kerguelen Archipelago, but also from the Falkland Islands, Marion Island, Amsterdam Island, Antipodes Island, Macquarie Island, Auckland Islands and one sample from South Georgia. We find that most of the mice on the Kerguelen Archipelago have the same mitochondrial haplotype and all share the same major Y-chromosomal haplotype. Two small islands (Cochons Island and Cimeti&#xe8;re Island) within the archipelago show a different mitochondrial haplotype, are genetically distinct for autosomal loci, but share the major Y-chromosomal haplotype. In the mitochondrial D-loop sequences, we find several single step mutational derivatives of one of the major mitochondrial haplotypes, suggesting an unusually high mutation rate, or the occurrence of selective sweeps in mitochondria.<br><br>CONCLUSIONS: Although there was heavy ship traffic for over a hundred years to the Kerguelen Archipelago, it appears that the mice that have arrived first have colonized the main island (Grande Terre) and most of the associated small islands. The second invasion that we see in our data has occurred on islands that are detached from Grande Terre and were likely to have had no resident mice prior to their arrival. The genetic data suggest that the mice of both primary invasions originated from related source populations. Our data suggest that an area colonized by mice is refractory to further introgression, possibly due to fast adaptations of the resident mice to local conditions.}, }
@article {pmid20969904, year = {2011}, author = {Brune, W}, title = {Inhibition of programmed cell death by cytomegaloviruses.}, journal = {Virus research}, volume = {157}, number = {2}, pages = {144-150}, doi = {10.1016/j.virusres.2010.10.012}, pmid = {20969904}, issn = {1872-7492}, mesh = {Animals ; *Apoptosis ; Caspases/metabolism ; Cytomegalovirus/genetics/metabolism/*pathogenicity ; Cytomegalovirus Infections/*pathology ; Herpesviridae Infections/pathology ; Humans ; Inhibitor of Apoptosis Proteins/metabolism ; Mice ; Mitochondria/metabolism/virology ; Muromegalovirus/genetics/metabolism/pathogenicity ; Necrosis ; Receptors, Death Domain/metabolism ; }, abstract = {The elimination of infected cells by programmed cell death (PCD) is one of the most ancestral defense mechanisms against infectious agents. This mechanism should be most effective against intracellular parasites, such as viruses, which depend on the host cell for their replication. However, even large and slowly replicating viruses like the cytomegaloviruses (CMVs) can prevail and persist in face of cellular suicide programs and other innate defense mechanisms. During evolution, these viruses have developed an impressive set of countermeasures against premature demise of the host cell. In the last decade, several genes encoding suppressors of apoptosis and necrosis have been identified in the genomes of human and murine CMV (HCMV and MCMV). Curiously, most of the gene products are not homologous to cellular antiapoptotic proteins, suggesting that the CMVs did not capture the genes from the host cell genome. This review summarizes our current understanding of how the CMVs suppress PCD and which signaling pathways they target.}, }
@article {pmid20967780, year = {2010}, author = {Gruschke, S and Ott, M}, title = {The polypeptide tunnel exit of the mitochondrial ribosome is tailored to meet the specific requirements of the organelle.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {32}, number = {12}, pages = {1050-1057}, doi = {10.1002/bies.201000081}, pmid = {20967780}, issn = {1521-1878}, mesh = {Bacteria/genetics/metabolism ; Electron Transport ; Evolution, Molecular ; Membrane Proteins/metabolism ; Mitochondria/*genetics/*metabolism ; Mitochondrial Proteins/biosynthesis/chemistry/genetics/*metabolism ; Oxidative Phosphorylation ; Protein Biosynthesis ; Ribosomal Proteins/chemistry/genetics/*metabolism ; Ribosomes/chemistry/genetics/*metabolism ; }, abstract = {The ribosomal polypeptide tunnel exit is the site where a variety of factors interact with newly synthesized proteins to guide them through the early steps of their biogenesis. In mitochondrial ribosomes, this site has been considerably modified in the course of evolution. In contrast to all other translation systems, mitochondrial ribosomes are responsible for the synthesis of only a few hydrophobic membrane proteins that are essential subunits of the mitochondrial respiratory chain. Membrane insertion of these proteins occurs co-translationally and is connected to a sophisticated assembly process that not only includes the assembly of the different subunits but also the acquisition of redox co-factors. Here, we describe how mitochondrial translation is organized in the context of respiratory chain assembly and speculate how alteration of the ribosomal tunnel exit might allow the establishment of a subset of specialized ribosomes that individually organize the early steps in the biogenesis of distinct mitochondrially-encoded proteins.}, }
@article {pmid20962839, year = {2010}, author = {Lane, N and Martin, W}, title = {The energetics of genome complexity.}, journal = {Nature}, volume = {467}, number = {7318}, pages = {929-934}, pmid = {20962839}, issn = {1476-4687}, mesh = {Aerobiosis ; Anaerobiosis ; Animals ; Cell Nucleus/genetics ; Cell Size ; *Energy Metabolism ; Eukaryotic Cells/*cytology/*metabolism/ultrastructure ; Gene Expression ; Genes, Mitochondrial/genetics ; Genome/*genetics ; Humans ; Mitochondria/metabolism ; *Models, Biological ; Prokaryotic Cells/*cytology/*metabolism/ultrastructure ; Symbiosis/genetics/physiology ; }, abstract = {All complex life is composed of eukaryotic (nucleated) cells. The eukaryotic cell arose from prokaryotes just once in four billion years, and otherwise prokaryotes show no tendency to evolve greater complexity. Why not? Prokaryotic genome size is constrained by bioenergetics. The endosymbiosis that gave rise to mitochondria restructured the distribution of DNA in relation to bioenergetic membranes, permitting a remarkable 200,000-fold expansion in the number of genes expressed. This vast leap in genomic capacity was strictly dependent on mitochondrial power, and prerequisite to eukaryote complexity: the key innovation en route to multicellular life.}, }
@article {pmid20958223, year = {2010}, author = {Oh, DJ and Oh, BS and Jung, MM and Jung, YH}, title = {Complete mitochondrial genome of three Branchiostegus (Perciformes, Malacanthidae) species: genome description and phylogenetic considerations.}, journal = {Mitochondrial DNA}, volume = {21}, number = {5}, pages = {151-159}, doi = {10.3109/19401736.2010.503241}, pmid = {20958223}, issn = {1940-1744}, mesh = {Animals ; Cloning, Molecular ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial/genetics ; *Genome, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; Perciformes/*classification/*genetics ; *Phylogeny ; Proteins/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {We cloned and sequenced the complete mitochondrial DNA (mtDNA) of three tilefishes (Branchiostegus albus, Branchiostegus argentatus, and Branchiostegus japonicus) to characterize and compare their mitochondrial genomes (mitogenomes). The mitogenomes of B. albus, B. argentatus, and B. japonicus were 16,532, 16,550, and 16,541 bp long, respectively, and all consisted of 37 genes (13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNA (tRNAs)), which are typical for vertebrate mtDNA. As in other bony fishes, most genes were encoded on the H-strand, except for the nad6 and eight tRNA genes that were encoded on the L-strand. Among the 13 protein-coding genes of all three tilefishes, 2 reading-frame overlaps were found on the same strand: atp8 and atp6 overlapped by 10 nucleotides, and nad4L and nad4 overlapped by 7 nucleotides. The identity of the nad4 gene between B. albus and B. argentatus was the lowest at 87%. Conversely, the identity of the nad6 gene between B. albus and B. japonicus was the highest at 99%. Most tRNA genes were similar in length among the three species, while the tRNA-Ser((AGY)) of B. japonicus was 9 bp longer than those of B. albus and B. argentatus. The control region of the mitogenome spanned 853, 862, and 856 bp in B. albus, B. argentatus, and B. japonicus, respectively. A maximum likelihood tree constructed using 11,035 sites contained five independent groups with bootstrap values of 100% in support of their divergence. All three tilefishes examined were clustered with the Pomacanthidae species in Group II.}, }
@article {pmid20943133, year = {2010}, author = {Giachini, AJ and Hosaka, K and Nouhra, E and Spatafora, J and Trappe, JM}, title = {Phylogenetic relationships of the Gomphales based on nuc-25S-rDNA, mit-12S-rDNA, and mit-atp6-DNA combined sequences.}, journal = {Fungal biology}, volume = {114}, number = {2-3}, pages = {224-234}, doi = {10.1016/j.funbio.2010.01.002}, pmid = {20943133}, issn = {1878-6146}, mesh = {Basidiomycota/*classification/*genetics ; DNA, Fungal/analysis/genetics/isolation &amp; purification ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/classification/*genetics ; Mitochondria/genetics ; Mitochondrial Proton-Translocating ATPases/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Phylogenetic relationships among Geastrales, Gomphales, Hysterangiales, and Phallales were estimated via combined sequences: nuclear large subunit ribosomal DNA (nuc-25S-rDNA), mitochondrial small subunit ribosomal DNA (mit-12S-rDNA), and mitochondrial atp6 DNA (mit-atp6-DNA). Eighty-one taxa comprising 19 genera and 58 species were investigated, including members of the Clathraceae, Gautieriaceae, Geastraceae, Gomphaceae, Hysterangiaceae, Phallaceae, Protophallaceae, and Sphaerobolaceae. Although some nodes deep in the tree could not be fully resolved, some well-supported lineages were recovered, and the interrelationships among Gloeocantharellus, Gomphus, Phaeoclavulina, and Turbinellus, and the placement of Ramaria are better understood. Both Gomphus sensu lato and Ramaria sensu lato comprise paraphyletic lineages within the Gomphaceae. Relationships of the subgenera of Ramaria sensu lato to each other and to other members of the Gomphales were clarified. Within Gomphus sensu lato, Gomphus sensu stricto, Turbinellus, Gloeocantharellus and Phaeoclavulina are separated by the presence/absence of clamp connections, spore ornamentation (echinulate, verrucose, subreticulate or reticulate), and basidiomal morphology (fan-shaped, funnel-shaped or ramarioid). Gautieria, a sequestrate genus in the Gautieriaceae, was recovered as monophyletic and nested with members of Ramaria subgenus Ramaria. This agrees with previous observations of traits shared by these two ectomycorrhizal taxa, such as the presence of fungal mats in the soil. Clavariadelphus was recovered as a sister group to Beenakia, Kavinia, and Lentaria. The results reaffirm relationships between the Geastrales, Gomphales, Hysterangiales, and the Phallales, suggesting extensive convergence in basidiomal morphology among members of these groups. A more extensive sampling that focuses on other loci (protein-coding genes have been shown to be phylogenetically informative) may be useful to answer questions about evolutionary relationships among these fungal groups.}, }
@article {pmid20938709, year = {2011}, author = {Knoop, V}, title = {When you can't trust the DNA: RNA editing changes transcript sequences.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {68}, number = {4}, pages = {567-586}, pmid = {20938709}, issn = {1420-9071}, mesh = {Animals ; Base Sequence ; DNA/*genetics/metabolism ; Humans ; RNA/*genetics/metabolism ; *RNA Editing ; Transcription, Genetic ; }, abstract = {RNA editing describes targeted sequence alterations in RNAs so that the transcript sequences differ from their DNA template. Since the original discovery of RNA editing in trypanosomes nearly 25 years ago more than a dozen such processes of nucleotide insertions, deletions, and exchanges have been identified in evolutionarily widely separated groups of the living world including plants, animals, fungi, protists, bacteria, and viruses. In many cases gene expression in mitochondria is affected, but RNA editing also takes place in chloroplasts and in nucleocytosolic genetic environments. While some RNA editing systems largely seem to repair defect genes (cryptogenes), others have obvious functions in modulating gene activities. The present review aims for an overview on the current states of research in the different systems of RNA editing by following a historic timeline along the respective original discoveries.}, }
@article {pmid20937353, year = {2011}, author = {Usmanova, N and Tomilin, N and Zhivotovsky, B and Kropotov, A}, title = {Transcription factor GABP/NRF-2 controlling biogenesis of mitochondria regulates basal expression of peroxiredoxin V but the mitochondrial function of peroxiredoxin V is dispensable in the dog.}, journal = {Biochimie}, volume = {93}, number = {2}, pages = {306-313}, doi = {10.1016/j.biochi.2010.10.002}, pmid = {20937353}, issn = {1638-6183}, mesh = {Animals ; Base Sequence ; Binding Sites ; Dogs/*metabolism ; GA-Binding Protein Transcription Factor/genetics/*metabolism ; *Gene Expression Regulation, Enzymologic ; Genes, Reporter/genetics ; HEK293 Cells ; Humans ; Mitochondria/*metabolism ; Molecular Sequence Data ; Mutagenesis ; Peroxiredoxins/genetics/*metabolism ; Promoter Regions, Genetic/genetics ; Protein Transport ; }, abstract = {Peroxiredoxins (PRDXs) represent a conserved family of six antioxidant proteins which are widely expressed in different organisms. Human PRDX5 is detected in the cytosol and nucleus and can also target peroxisomes and mitochondria. However, it remains unknown if mitochondrial localization of PRDX5 is essential for its functions. Here we studied whether the known regulator of mitochondrial biogenesis, transcription factor GABP/NRF-2, is required for the basal expression of the human PRDX5 gene and what the significance is of the mitochondrial targeting of the PRDX5 protein. It was found that mutation-mediated inactivation of all potential binding sites for GAPB in the PRDX5 promoter lead to ∼80% inhibition of its basal activity in a reporter gene assay. Co-transfection of plasmids expressing GABP-alpha and GABP-beta stimulated activity of the non-mutated PRDX5 promoter but had no effect on the mutated promoter, suggesting that basal expression of the human PRDX5 gene is regulated by GABP. We found that the dog c-Myc-tagged PRDX5 did not target the mitochondria of human cells. Endogenously expressed PRDX5 also showed no association with mitochondria in the dog cells. It appears, therefore, that during evolution the dog PRDX5 gene lost its upstream ATG codon and mitochondrial targeting signal without major functional consequences.}, }
@article {pmid20935050, year = {2011}, author = {Vlcek, C and Marande, W and Teijeiro, S and Lukes, J and Burger, G}, title = {Systematically fragmented genes in a multipartite mitochondrial genome.}, journal = {Nucleic acids research}, volume = {39}, number = {3}, pages = {979-988}, pmid = {20935050}, issn = {1362-4962}, support = {MOP-79309//Canadian Institutes of Health Research/Canada ; }, mesh = {Chromosomes/chemistry ; DNA, Mitochondrial/chemistry ; Euglenozoa/genetics ; *Genes, Mitochondrial ; *Genome, Mitochondrial ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; Sequence Analysis, DNA ; *Trans-Splicing ; Transcription, Genetic ; }, abstract = {Arguably, the most bizarre mitochondrial DNA (mtDNA) is that of the euglenozoan eukaryote Diplonema papillatum. The genome consists of numerous small circular chromosomes none of which appears to encode a complete gene. For instance, the cox1 coding sequence is spread out over nine different chromosomes in non-overlapping pieces (modules), which are transcribed separately and joined to a contiguous mRNA by trans-splicing. Here, we examine how many genes are encoded by Diplonema mtDNA and whether all are fragmented and their transcripts trans-spliced. Module identification is challenging due to the sequence divergence of Diplonema mitochondrial genes. By employing most sensitive protein profile search algorithms and comparing genomic with cDNA sequence, we recognize a total of 11 typical mitochondrial genes. The 10 protein-coding genes are systematically chopped up into three to 12 modules of 60-350 bp length. The corresponding mRNAs are all trans-spliced. Identification of ribosomal RNAs is most difficult. So far, we only detect the 3'-module of the large subunit ribosomal RNA (rRNA); it does not trans-splice with other pieces. The small subunit rRNA gene remains elusive. Our results open new intriguing questions about the biochemistry and evolution of mitochondrial trans-splicing in Diplonema.}, }
@article {pmid20929672, year = {2010}, author = {Sauvanet, C and Arnauné-Pelloquin, L and David, C and Belenguer, P and Rojo, M}, title = {[Mitochondrial morphology and dynamics: actors, mechanisms and functions].}, journal = {Medecine sciences : M/S}, volume = {26}, number = {10}, pages = {823-829}, doi = {10.1051/medsci/20102610823}, pmid = {20929672}, issn = {0767-0974}, mesh = {Animals ; Biological Evolution ; Biomechanical Phenomena ; Cell Fusion ; Gene Deletion ; Gene Knockout Techniques ; Humans ; Kinetics ; Mitochondria/*physiology/*ultrastructure ; Mutation ; Nervous System Diseases/physiopathology ; Organelles/physiology/ultrastructure ; }, abstract = {Mitochondria are dynamic organelles that continuously move, fuse and divide. Their overall morphology, ranging from a filamentous network to a collection of isolated dots, is determined by fusion-fission equilibrium, which depends on the cellular and physiological context. The machineries of fusion and fission, that are conserved throughout evolution, include three large GTPases of the dynamin-superfamily: Dnm1/DRP1 - involved in fission - as well as Fzo1/MFN and Mgm1/OPA1 - required for fusion. While the activities, mecanisms and regulations of mitochondrial fusion and fission machineries continue to be unravelled, the relevance of mitochondrial dynamics is witnessed by their impact on organelle functions, cell survival and cell differenciation, their requirement for embryonic development and their involvement in neurological diseases.}, }
@article {pmid20927717, year = {2010}, author = {Md-Zain, BM and Mohamad, M and Ernie-Muneerah, MA and Ampeng, A and Jasmi, A and Lakim, M and Mahani, MC}, title = {Phylogenetic relationships of Malaysian monkeys, Cercopithecidae, based on mitochondrial cytochrome c sequences.}, journal = {Genetics and molecular research : GMR}, volume = {9}, number = {4}, pages = {1987-1996}, doi = {10.4238/vol9-4gmr942}, pmid = {20927717}, issn = {1676-5680}, mesh = {Algorithms ; Animals ; Base Sequence ; Cercopithecidae/*classification/genetics ; Cytochromes c/*genetics ; DNA Primers ; Mitochondria/*enzymology ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {Mitochondrial DNA cytochrome c oxidase II (COII) gene sequences of Malaysian Cercopithecidae were examined to ascertain their phylogenetic relationships. Colobinae were represented by the genera Presbytis, Trachypithecus and Nasalis, while the genus Macaca represented Cercopithecinae. DNA amplification and sequencing of the COII gene was performed on 16 samples. Symphalangus syndactylus (Hylobatidae) was used as the outgroup. Data were analyzed using both character (maximum parsimony) and distance (neighbor-joining) methods. Tree topologies indicated that Colobinae and Cercopithecinae have their own distinct monophyletic clade. This result was well supported by bootstrap values and genetic distances derived from the Kimura-2-parameter algorithm. Separation of Macaca nemestrina from M. fascicularis was also well supported by bootstrap values. In addition, tree topologies indicate a good resolution of the Colobinae phylogenetic relationships at the intergeneric level, but with low bootstrap support. The position of Nasalis remained problematic in both trees. Overall, COII is a good gene candidate for portraying the phylogenetic relationships of Malaysian primates at the inter- and intra-subfamily levels.}, }
@article {pmid20924083, year = {2011}, author = {Sun, YB and Shen, YY and Irwin, DM and Zhang, YP}, title = {Evaluating the roles of energetic functional constraints on teleost mitochondrial-encoded protein evolution.}, journal = {Molecular biology and evolution}, volume = {28}, number = {1}, pages = {39-44}, doi = {10.1093/molbev/msq256}, pmid = {20924083}, issn = {1537-1719}, mesh = {Animals ; Body Temperature Regulation/genetics ; Energy Metabolism/genetics ; *Evolution, Molecular ; Fishes/*genetics/*metabolism ; Genome, Mitochondrial ; Mitochondria/*genetics/*metabolism ; Mitochondrial Proteins/*genetics ; }, abstract = {Mitochondria are the power plant of cells, which play critical roles not only in energy metabolism but also in thermoregulation. These two roles have been individually suggested to influence mitochondrial DNA (mtDNA) evolution, however their relative importance is still rarely considered. Here, we conduct a comparative genomic analysis of 401 teleost complete mitochondrial genomes and test the roles of these dual functional constraints on mitochondria to provide a more complete view of mtDNA evolution. We found that mitochondrial protein-coding genes of migratory fishes have significantly smaller Ka/Ks than nonmigratory fishes. The same data set showed that the genes of fishes living in cold climates have significantly smaller Ka/Ks than tropical fishes. In contrast, these trends were not observed for two nuclear genes that are not involved in energy metabolism. The differences in selection patterns observed between mitochondrial and nuclear genes suggest that the functional constraints acting on mitochondria, due to energy metabolism and/or thermoregulation, influence the evolution of mitochondrial-encoded proteins in teleosts.}, }
@article {pmid20922212, year = {2010}, author = {Cavallaro, G}, title = {Genome-wide analysis of eukaryotic twin CX9C proteins.}, journal = {Molecular bioSystems}, volume = {6}, number = {12}, pages = {2459-2470}, doi = {10.1039/c0mb00058b}, pmid = {20922212}, issn = {1742-2051}, mesh = {Amino Acid Motifs ; Amino Acids ; Animals ; Cluster Analysis ; Eukaryotic Cells/*metabolism ; Genome/*genetics ; Humans ; Mitochondria/metabolism ; Mitochondrial Proteins/*chemistry/*metabolism ; Multiprotein Complexes/chemistry/metabolism ; Phylogeny ; Protein Structure, Secondary ; Protein Subunits/chemistry/metabolism ; Saccharomyces cerevisiae/metabolism ; }, abstract = {Twin CX(9)C proteins are eukaryotic proteins that derive their name from their characteristic motif, consisting of two pairs of cysteines that form two disulfide bonds stabilizing a coiled coil-helix-coiled coil-helix (CHCH) fold. The best characterized of these proteins are Cox17, a copper chaperone acting in cytochrome c oxidase biogenesis, and Mia40, the central component of a system for protein import into the mitochondrial inter-membrane space (IMS). However, the range of possible functions for these proteins is unclear. Here, we performed a systematic search of twin CX(9)C proteins in eukaryotic organisms, and classified them into groups of putative homologues, by combining bioinformatics methods with literature analysis. Our results suggest that the functions of most twin CX(9)C proteins vary around the common theme of playing a scaffolding role, which can tie their observed roles in mitochondrial structure and function. This study will enhance the present annotation of eukaryotic proteomes, and will provide a rational basis for future experimental work aimed at a deeper understanding of this remarkable class of proteins.}, }
@article {pmid20888427, year = {2011}, author = {Amer, S and Dar, Y and Ichikawa, M and Fukuda, Y and Tada, C and Itagaki, T and Nakai, Y}, title = {Identification of Fasciola species isolated from Egypt based on sequence analysis of genomic (ITS1 and ITS2) and mitochondrial (NDI and COI) gene markers.}, journal = {Parasitology international}, volume = {60}, number = {1}, pages = {5-12}, doi = {10.1016/j.parint.2010.09.003}, pmid = {20888427}, issn = {1873-0329}, mesh = {Animals ; Base Sequence ; Buffaloes/parasitology ; Cattle/parasitology ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; Egypt/epidemiology ; Fasciola/*classification/*genetics/*isolation &amp; purification ; Fascioliasis/*epidemiology/parasitology/*veterinary ; Genes, Mitochondrial ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sheep/parasitology ; }, abstract = {Fascioliasis has a negative impact on the farming industry in both developed and developing countries, rather than a public health challenge. This study was performed to identify Fasciola sp. from different definitive hosts (buffalo, cattle, and sheep) based on the molecular parameters and spermatogenesis. Ninety-one adult flukes were collected from livers of slaughtered animals at abattoirs in different prefectures in Egypt. Microscopic examination of the analyzed flukes showed many normal spermatozoa in the seminal vesicles (spermic), suggesting that they have the ability of spermatogenesis. This study showed that no parthenogenic Fasciola species occurred in Egypt. Molecular analysis was performed utilizing genomic (ITS1 and ITS2) and mitochondrial (NDI and COI) gene markers. Whereas 16 animals proved to have infection with a single Fasciola species, 2 were infected with both F. hepatica and F. gigantica. The results indicated that sheep were prone to F. hepatica (8 out of 10 animals) more than F. gigantica infection. Sequences of ITS1 and ITS2 ribosomal region indicated that the flukes were categorized into 3 groups F. hepatica-type (47), F. gigantica-type (42) and 2 flukes possessed sequences of both types indicating an existence of different alleles at the same loci. Unique overlapping of T/C bases were detected in both ITS1 (Position 96) and ITS2 (Position 416). Based on results of mitochondrial gene markers (NDI and COI), flukes were classified into F. hepatica-type and F. gigantica-type. Extensive intra-sequence polymorphism was detected at both markers. NDI and COI sequences of Egyptian strain of F. gigantica showed pronounced diversity compared with relevant sequences at database.}, }
@article {pmid20880891, year = {2011}, author = {Bonhomme, F and Orth, A and Cucchi, T and Rajabi-Maham, H and Catalan, J and Boursot, P and Auffray, JC and Britton-Davidian, J}, title = {Genetic differentiation of the house mouse around the Mediterranean basin: matrilineal footprints of early and late colonization.}, journal = {Proceedings. Biological sciences}, volume = {278}, number = {1708}, pages = {1034-1043}, pmid = {20880891}, issn = {1471-2954}, mesh = {Africa ; Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; Haplotypes ; Mediterranean Region ; Mice/classification/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The molecular signatures of the recent expansion of the western house mouse, Mus musculus domesticus, around the Mediterranean basin are investigated through the study of mitochondrial D-loop polymorphism on a 1313 individual dataset. When reducing the complexity of the matrilineal network to a series of haplogroups (HGs), our main results indicate that: (i) several HGs are recognized which seem to have almost simultaneously diverged from each other, confirming a recent expansion for the whole subspecies; (ii) some HGs are geographically delimited while others are widespread, indicative of multiple introductions or secondary exchanges; (iii) mice from the western and the eastern coasts of Africa harbour largely different sets of HGs; and (iv) HGs from the two shores of the Mediterranean are more similar in the west than in the east. This pattern is in keeping with the two-step westward expansion proposed by zooarchaeological data, an early one coincident with the Neolithic progression and limited to the eastern Mediterranean and a later one, particularly evident in the western Mediterranean, related to the generalization of maritime trade during the first millennium BC and onwards. The dispersal of mice along with humans, which continues until today, has for instance left complex footprints on the long ago colonized Cyprus or more simple ones on the much more recently populated Canary Islands.}, }
@article {pmid20880032, year = {2010}, author = {Park, JS and Kolisko, M and Simpson, AG}, title = {Cell morphology and formal description of Ergobibamus cyprinoides n. g., n. sp., another Carpediemonas-like relative of diplomonads.}, journal = {The Journal of eukaryotic microbiology}, volume = {57}, number = {6}, pages = {520-528}, doi = {10.1111/j.1550-7408.2010.00506.x}, pmid = {20880032}, issn = {1550-7408}, mesh = {Canada ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Diplomonadida/*classification/genetics/isolation &amp; purification/ultrastructure ; Genes, rRNA ; Geologic Sediments/*parasitology ; Microscopy ; Molecular Sequence Data ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; }, abstract = {About 20 new isolates of Carpediemonas-like organisms (CLOs) have been reported since 2006. Small subunit rRNA gene phylogenies divide CLOs into six major clades: four contain described exemplars (i.e. Carpediemonas, Dysnectes, Hicanonectes, and Kipferlia), but two include only undescribed organisms. Here we describe a representative of one of these latter clades as Ergobibamus cyprinoides n. g., n. sp., and catalogue its ultrastructure. Ergobibamus cyprinoides is a bean-shaped biflagellated cell, 7-11.5 μm long, with a conspicuous groove. Instead of classical mitochondria there are cristae-lacking rounded organelles 300-400 nm in diameter. The posterior flagellum has a broad ventral vane and small dorsal vane. There are normally four basal bodies, two non-flagellated. There is one anterior root (AR), containing six microtubules. The posterior flagellar apparatus follows the "typical excavate" pattern of a splitting right root supported by fibres "I,""B," and "A," a "composite" fibre, a singlet root, and a left root (LR) with a "C" fibre. The B fibre originates against the LR--a synapomorphy of the taxon Fornicata--supporting the assignation of Ergobibamus to Fornicata, along with diplomonads, retortamonads, and other CLOs. Distinctive features of E. cyprinoides include the complexity of the AR, which is intermediate between Hicanonectes, and Carpediemonas and Dysnectes, and a dorsal extension of the C fibre.}, }
@article {pmid20874734, year = {2010}, author = {Arnqvist, G and Dowling, DK and Eady, P and Gay, L and Tregenza, T and Tuda, M and Hosken, DJ}, title = {Genetic architecture of metabolic rate: environment specific epistasis between mitochondrial and nuclear genes in an insect.}, journal = {Evolution; international journal of organic evolution}, volume = {64}, number = {12}, pages = {3354-3363}, doi = {10.1111/j.1558-5646.2010.01135.x}, pmid = {20874734}, issn = {1558-5646}, mesh = {Animals ; Cell Nucleus/*genetics ; Coleoptera/*genetics/*metabolism ; Crosses, Genetic ; Energy Metabolism ; *Epistasis, Genetic ; Evolution, Molecular ; Female ; *Genes, Mitochondrial ; Genome, Insect ; Genotype ; Male ; Polymorphism, Genetic ; Temperature ; }, abstract = {The extent to which mitochondrial DNA (mtDNA) variation is involved in adaptive evolutionary change is currently being reevaluated. In particular, emerging evidence suggests that mtDNA genes coevolve with the nuclear genes with which they interact to form the energy producing enzyme complexes in the mitochondria. This suggests that intergenomic epistasis between mitochondrial and nuclear genes may affect whole-organism metabolic phenotypes. Here, we use crossed combinations of mitochondrial and nuclear lineages of the seed beetle Callosobruchus maculatus and assay metabolic rate under two different temperature regimes. Metabolic rate was affected by an interaction between the mitochondrial and nuclear lineages and the temperature regime. Sequence data suggests that mitochondrial genetic variation has a role in determining the outcome of this interaction. Our genetic dissection of metabolic rate reveals a high level of complexity, encompassing genetic interactions over two genomes, and genotype × genotype × environment interactions. The evolutionary implications of these results are twofold. First, because metabolic rate is at the root of life histories, our results provide insights into the complexity of life-history evolution in general, and thermal adaptation in particular. Second, our results suggest a mechanism that could contribute to the maintenance of nonneutral mtDNA polymorphism.}, }
@article {pmid20871025, year = {2011}, author = {Tsaousis, AD and Gaston, D and Stechmann, A and Walker, PB and Lithgow, T and Roger, AJ}, title = {A functional Tom70 in the human parasite Blastocystis sp.: implications for the evolution of the mitochondrial import apparatus.}, journal = {Molecular biology and evolution}, volume = {28}, number = {1}, pages = {781-791}, doi = {10.1093/molbev/msq252}, pmid = {20871025}, issn = {1537-1719}, support = {MOP-62809//Canadian Institutes of Health Research/Canada ; }, mesh = {*Biological Evolution ; Blastocystis/*genetics/*metabolism/ultrastructure ; Gene Knockdown Techniques ; Genetic Complementation Test ; Humans ; Mitochondria/genetics/*metabolism ; Mitochondrial Membrane Transport Proteins/chemistry/classification/*genetics/metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Models, Molecular ; Phylogeny ; Protein Conformation ; Protozoan Proteins/*genetics/*metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/metabolism ; }, abstract = {Core proteins of mitochondrial protein import are found in all mitochondria, suggesting a common origin of this import machinery. Despite the presence of a universal core import mechanism, there are specific proteins found only in a few groups of organisms. One of these proteins is the translocase of outer membrane 70 (Tom70), a protein that is essential for the import of preproteins with internal targeting sequences into the mitochondrion. Until now, Tom70 has only been found in animals and Fungi. We have identified a tom70 gene in the human parasitic anaerobic stramenopile Blastocystis sp. that is neither an animal nor a fungus. Using a combination of bioinformatics, genetic complementation, and immunofluorescence microscopy analyses, we demonstrate that this protein functions as a typical Tom70 in Blastocystis mitochondrion-related organelles. Additionally, we identified putative tom70 genes in the genomes of other stramenopiles and a haptophyte, that, in phylogenies, form a monophyletic group distinct from the animal and the fungal homologues. The presence of Tom70 in these lineages significantly expands the evolutionary spectrum of eukaryotes that contain this protein and suggests that it may have been part of the core mitochondrial protein import apparatus of the last common ancestral eukaryote.}, }
@article {pmid20870726, year = {2010}, author = {Guitart, T and Leon Bernardo, T and Sagalés, J and Stratmann, T and Bernués, J and Ribas de Pouplana, L}, title = {New aminoacyl-tRNA synthetase-like protein in insecta with an essential mitochondrial function.}, journal = {The Journal of biological chemistry}, volume = {285}, number = {49}, pages = {38157-38166}, pmid = {20870726}, issn = {1083-351X}, mesh = {Animals ; Cattle ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster ; Evolution, Molecular ; Gene Duplication ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; RNA Interference ; Serine-tRNA Ligase/genetics/*metabolism ; }, abstract = {Aminoacyl-tRNA synthetases (ARS) are modular enzymes that aminoacylate transfer RNAs (tRNA) for their use by the ribosome during protein synthesis. ARS are essential and universal components of the genetic code that were almost completely established before the appearance of the last common ancestor of all living species. This long evolutionary history explains the growing number of functions being discovered for ARS, and for ARS homologues, beyond their canonical role in gene translation. Here we present a previously uncharacterized paralogue of seryl-tRNA synthetase named SLIMP (seryl-tRNA synthetase-like insect mitochondrial protein). SLIMP is the result of a duplication of a mitochondrial seryl-tRNA synthetase (SRS) gene that took place in early metazoans and was fixed in Insecta. Here we show that SLIMP is localized in the mitochondria, where it carries out an essential function that is unrelated to the aminoacylation of tRNA. The knockdown of SLIMP by RNA interference (RNAi) causes a decrease in respiration capacity and an increase in mitochondrial mass in the form of aberrant mitochondria.}, }
@article {pmid20870040, year = {2011}, author = {Douglas, KC and Halbert, ND and Kolenda, C and Childers, C and Hunter, DL and Derr, JN}, title = {Complete mitochondrial DNA sequence analysis of Bison bison and bison-cattle hybrids: function and phylogeny.}, journal = {Mitochondrion}, volume = {11}, number = {1}, pages = {166-175}, doi = {10.1016/j.mito.2010.09.005}, pmid = {20870040}, issn = {1872-8278}, mesh = {Animals ; Base Sequence ; Bison/classification/*genetics ; Cattle/classification/*genetics ; DNA, Mitochondrial/chemistry/*genetics/metabolism ; Genetics, Population ; Genome, Mitochondrial ; Haplotypes ; *Hybridization, Genetic ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; *Sequence Analysis, DNA ; }, abstract = {Complete mitochondrial DNA (mtDNA) genomes from 43 bison and bison-cattle hybrids were sequenced and compared with other bovids. Selected animals reflect the historical range and current taxonomic structure of bison. This study identified regions of potential nuclear-mitochondrial incompatibilities in hybrids, provided a complete mtDNA phylogenetic tree for this species, and uncovered evidence of bison population substructure. Seventeen bison haplotypes defined by 66 polymorphic sites were discovered, whereas 728 fixed differences and 86 non-synonymous mutations were identified between bison and bison-cattle hybrid sequences. The potential roles of the mtDNA genome in the function of hybrid animals and bison taxonomy are discussed.}, }
@article {pmid20868295, year = {2011}, author = {Sevrioukova, IF}, title = {Apoptosis-inducing factor: structure, function, and redox regulation.}, journal = {Antioxidants &amp; redox signaling}, volume = {14}, number = {12}, pages = {2545-2579}, pmid = {20868295}, issn = {1557-7716}, mesh = {Amino Acid Sequence ; Animals ; Apoptosis/physiology ; Apoptosis Inducing Factor/*chemistry/classification/genetics/*metabolism ; Catalytic Domain ; Electron Transport/physiology ; Gene Expression Regulation ; Humans ; Mitochondria/metabolism/ultrastructure ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; *Protein Conformation ; Protein Folding ; Protein Isoforms/*chemistry/genetics/*metabolism ; Sequence Alignment ; Signal Transduction/physiology ; }, abstract = {Apoptosis-inducing factor (AIF) is a flavin adenine dinucleotide-containing, NADH-dependent oxidoreductase residing in the mitochondrial intermembrane space whose specific enzymatic activity remains unknown. Upon an apoptotic insult, AIF undergoes proteolysis and translocates to the nucleus, where it triggers chromatin condensation and large-scale DNA degradation in a caspase-independent manner. Besides playing a key role in execution of caspase-independent cell death, AIF has emerged as a protein critical for cell survival. Analysis of in vivo phenotypes associated with AIF deficiency and defects, and identification of its mitochondrial, cytoplasmic, and nuclear partners revealed the complexity and multilevel regulation of AIF-mediated signal transduction and suggested an important role of AIF in the maintenance of mitochondrial morphology and energy metabolism. The redox activity of AIF is essential for optimal oxidative phosphorylation. Additionally, the protein is proposed to regulate the respiratory chain indirectly, through assembly and/or stabilization of complexes I and III. This review discusses accumulated data with respect to the AIF structure and outlines evidence that supports the prevalent mechanistic view on the apoptogenic actions of the flavoprotein, as well as the emerging concept of AIF as a redox sensor capable of linking NAD(H)-dependent metabolic pathways to apoptosis.}, }
@article {pmid20862300, year = {2010}, author = {Gil Borlado, MC and Moreno Lastres, D and Gonzalez Hoyuela, M and Moran, M and Blazquez, A and Pello, R and Marin Buera, L and Gabaldon, T and Garcia Peñas, JJ and Martín, MA and Arenas, J and Ugalde, C}, title = {Impact of the mitochondrial genetic background in complex III deficiency.}, journal = {PloS one}, volume = {5}, number = {9}, pages = {}, pmid = {20862300}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Base Sequence ; Cytochromes b/genetics/metabolism ; Electron Transport Complex III/*deficiency/genetics ; Electron Transport Complex IV/genetics/metabolism ; Humans ; Infant, Newborn ; Male ; Mitochondria/*genetics/metabolism ; Mitochondrial Diseases/*genetics/metabolism ; Molecular Sequence Data ; *Point Mutation ; }, abstract = {BACKGROUND: In recent years clinical evidence has emphasized the importance of the mtDNA genetic background that hosts a primary pathogenic mutation in the clinical expression of mitochondrial disorders, but little experimental confirmation has been provided. We have analyzed the pathogenic role of a novel homoplasmic mutation (m.15533 A>G) in the cytochrome b (MT-CYB) gene in a patient presenting with lactic acidosis, seizures, mild mental delay, and behaviour abnormalities.<br><br>METHODOLOGY: Spectrophotometric analyses of the respiratory chain enzyme activities were performed in different tissues, the whole muscle mitochondrial DNA of the patient was sequenced, and the novel mutation was confirmed by PCR-RFLP. Transmitochondrial cybrids were constructed to confirm the pathogenicity of the mutation, and assembly/stability studies were carried out in fibroblasts and cybrids by means of mitochondrial translation inhibition in combination with blue native gel electrophoresis.<br><br>PRINCIPAL FINDINGS: Biochemical analyses revealed a decrease in respiratory chain complex III activity in patient's skeletal muscle, and a combined enzyme defect of complexes III and IV in fibroblasts. Mutant transmitochondrial cybrids restored normal enzyme activities and steady-state protein levels, the mutation was mildly conserved along evolution, and the proband's mother and maternal aunt, both clinically unaffected, also harboured the homoplasmic mutation. These data suggested a nuclear genetic origin of the disease. However, by forcing the de novo functioning of the OXPHOS system, a severe delay in the biogenesis of the respiratory chain complexes was observed in the mutants, which demonstrated a direct functional effect of the mitochondrial genetic background.<br><br>CONCLUSIONS: Our results point to possible pitfalls in the detection of pathogenic mitochondrial mutations, and highlight the role of the genetic mtDNA background in the development of mitochondrial disorders.}, }
@article {pmid20856815, year = {2010}, author = {Wei, SJ and Shi, M and Chen, XX and Sharkey, MJ and van Achterberg, C and Ye, GY and He, JH}, title = {New views on strand asymmetry in insect mitochondrial genomes.}, journal = {PloS one}, volume = {5}, number = {9}, pages = {e12708}, pmid = {20856815}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; Evolution, Molecular ; *Genome, Mitochondrial ; Insecta/chemistry/*genetics ; Mitochondria/chemistry/genetics ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; }, abstract = {Strand asymmetry in nucleotide composition is a remarkable feature of animal mitochondrial genomes. Understanding the mutation processes that shape strand asymmetry is essential for comprehensive knowledge of genome evolution, demographical population history and accurate phylogenetic inference. Previous studies found that the relative contributions of different substitution types to strand asymmetry are associated with replication alone or both replication and transcription. However, the relative contributions of replication and transcription to strand asymmetry remain unclear. Here we conducted a broad survey of strand asymmetry across 120 insect mitochondrial genomes, with special reference to the correlation between the signs of skew values and replication orientation/gene direction. The results show that the sign of GC skew on entire mitochondrial genomes is reversed in all species of three distantly related families of insects, Philopteridae (Phthiraptera), Aleyrodidae (Hemiptera) and Braconidae (Hymenoptera); the replication-related elements in the A+T-rich regions of these species are inverted, confirming that reversal of strand asymmetry (GC skew) was caused by inversion of replication origin; and finally, the sign of GC skew value is associated with replication orientation but not with gene direction, while that of AT skew value varies with gene direction, replication and codon positions used in analyses. These findings show that deaminations during replication and other mutations contribute more than selection on amino acid sequences to strand compositions of G and C, and that the replication process has a stronger affect on A and T content than does transcription. Our results may contribute to genome-wide studies of replication and transcription mechanisms.}, }
@article {pmid20853063, year = {2010}, author = {Kim, MI and Wan, X and Kim, MJ and Jeong, HC and Ahn, NH and Kim, KG and Han, YS and Kim, I}, title = {Phylogenetic relationships of true butterflies (Lepidoptera: Papilionoidea) inferred from COI, 16S rRNA and EF-1α sequences.}, journal = {Molecules and cells}, volume = {30}, number = {5}, pages = {409-425}, doi = {10.1007/s10059-010-0141-9}, pmid = {20853063}, issn = {0219-1032}, mesh = {Animals ; Base Sequence ; Butterflies/classification/enzymology/*genetics ; DNA Barcoding, Taxonomic ; Electron Transport Complex IV/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Peptide Elongation Factor 1/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The molecular phylogenetic relationships among true butterfly families (superfamily Papilionoidea) have been a matter of substantial controversy; this debate has led to several competing hypotheses. Two of the most compelling of those hypotheses involve the relationships of (Nymphalidae + Lycaenidae) + (Pieridae + Papilionidae) and (((Nymphalidae + Lycaenidae) + Pieridae) + Papilionidae). In this study, approximately 3,500 nucleotide sequences from cytochrome oxidase subunit I (COI), 16S ribosomal RNA (16S rRNA), and elongation factor-1 alpha (EF-1α) were sequenced from 83 species belonging to four true butterfly families, along with those of three outgroup species belonging to three lepidopteran superfamilies. These sequences were subjected to phylogenetic reconstruction via Bayesian Inference (BI), Maximum Likelihood (ML), and Maximum Parsimony (MP) algorithms. The monophyletic Pieridae and monophyletic Papilionidae evidenced good recovery in all analyses, but in some analyses, the monophylies of the Lycaenidae and Nymphalidae were hampered by the inclusion of single species of the lycaenid subfamily Miletinae and the nymphalid subfamily Danainae. Excluding those singletons, all phylogenetic analyses among the four true butterfly families clearly identified the Nymphalidae as the sister to the Lycaenidae and identified this group as a sister to the Pieridae, with the Papilionidae identified as the most basal linage to the true butterfly, thus supporting the hypothesis: (Papilionidae + (Pieridae + (Nymphalidae + Lycaenidae))).}, }
@article {pmid20840588, year = {2010}, author = {Mishra, S and Ande, SR and Nyomba, BL}, title = {The role of prohibitin in cell signaling.}, journal = {The FEBS journal}, volume = {277}, number = {19}, pages = {3937-3946}, doi = {10.1111/j.1742-4658.2010.07809.x}, pmid = {20840588}, issn = {1742-4658}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {Animals ; Biological Evolution ; Conserved Sequence ; DNA, Complementary/genetics ; Humans ; Neoplasms/genetics/physiopathology ; Prohibitins ; Protein Processing, Post-Translational/physiology ; Repressor Proteins/genetics/metabolism/*physiology ; Signal Transduction/genetics/*physiology ; }, abstract = {Prohibitin-1 (PHB, also known as PHB1), a member of the Band-7 family of proteins, is highly conserved evolutionarily, widely expressed, and present in different cellular compartments. Genetic studies with different organism models have provided strong evidence for an important biological role of PHB in mitochondrial function, cell proliferation, and development. Recent discoveries regarding the involvement of PHB in phophatidylinositol-3-kinase (PI3K)/protein kinase B (Akt) and transforming growth factor-β (TGF-β)/signal transducers and activators of transcription signaling pathways, and earlier reports on the interaction of PHB with Raf and its critical role in Ras/mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) signaling opened up the possibility that PHB has functions outside of the mitochondria (extramitochondrial) and may be a multifunctional protein. The PI3K/Akt and Ras/MAPK/ERK signaling cascades are versatile signaling processes that diverge from the same receptor tyrosine kinase root, and are involved in cell metabolism, proliferation, and development. Here, we review the emerging role of PHB and its post-translational modifications in signal transduction pathways, especially in PI3K/Akt and Ras/MAPK/ERK signaling. A recent discovery of opposing effects of PHB on longevity under different metabolic states and its potential connection with insulin/insulin-like growth factor-I signaling is also discussed.}, }
@article {pmid20838623, year = {2010}, author = {Castro, H and Romao, S and Carvalho, S and Teixeira, F and Sousa, C and Tomás, AM}, title = {Mitochondrial redox metabolism in trypanosomatids is independent of tryparedoxin activity.}, journal = {PloS one}, volume = {5}, number = {9}, pages = {e12607}, pmid = {20838623}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Animals ; Cell Survival ; Humans ; Leishmania infantum/chemistry/classification/genetics/*metabolism ; Leishmaniasis, Visceral/parasitology ; Male ; Mice ; Mice, Inbred BALB C ; Mitochondria/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; Protein Transport ; Protozoan Proteins/chemistry/genetics/*metabolism ; Sequence Alignment ; Thioredoxins/chemistry/genetics/*metabolism ; Trypanosomatina/chemistry/classification/genetics/metabolism ; }, abstract = {Tryparedoxins (TXNs) are oxidoreductases unique to trypanosomatids (including Leishmania and Trypanosoma parasites) that transfer reducing equivalents from trypanothione, the major thiol in these organisms, to sulfur-dependent peroxidases and other dithiol proteins. The existence of a TXN within the mitochondrion of trypanosomatids, capable of driving crucial redox pathways, is considered a requisite for normal parasite metabolism. Here this concept is shown not to apply to Leishmania. First, removal of the Leishmania infantum mitochondrial TXN (LiTXN2) by gene-targeting, had no significant effect on parasite survival, even in the context of an animal infection. Second, evidence is presented that no other TXN is capable of replacing LiTXN2. In fact, although a candidate substitute for LiTXN2 (LiTXN3) was found in the genome of L. infantum, this was shown in biochemical assays to be poorly reduced by trypanothione and to be unable to reduce sulfur-containing peroxidases. Definitive conclusion that LiTXN3 cannot directly reduce proteins located within inner mitochondrial compartments was provided by analysis of its subcellular localization and membrane topology, which revealed that LiTXN3 is a tail-anchored (TA) mitochondrial outer membrane protein presenting, as characteristic of TA proteins, its N-terminal end (containing the redox-active domain) exposed to the cytosol. This manuscript further proposes the separation of trypanosomatid TXN sequences into two classes and this is supported by phylogenetic analysis: i) class I, encoding active TXNs, and ii) class II, coding for TA proteins unlikely to function as TXNs. Trypanosoma possess only two TXNs, one belonging to class I (which is cytosolic) and the other to class II. Thus, as demonstrated for Leishmania, the mitochondrial redox metabolism in Trypanosoma may also be independent of TXN activity. The major implication of these findings is that mitochondrial functions previously thought to depend on the provision of electrons by a TXN enzyme must proceed differently.}, }
@article {pmid20836765, year = {2010}, author = {Zeth, K and Thein, M}, title = {Porins in prokaryotes and eukaryotes: common themes and variations.}, journal = {The Biochemical journal}, volume = {431}, number = {1}, pages = {13-22}, doi = {10.1042/BJ20100371}, pmid = {20836765}, issn = {1470-8728}, mesh = {Bacterial Proteins/*chemistry/metabolism ; Eukaryota/metabolism ; Mitochondria/metabolism ; Models, Biological ; Porins/*chemistry/metabolism ; Protein Conformation ; Voltage-Dependent Anion Channel 1/chemistry/metabolism ; Voltage-Dependent Anion Channels/*chemistry/metabolism ; }, abstract = {Gram-negative bacteria and mitochondria are both covered by two distinct biological membranes. These membrane systems have been maintained during the course of evolution from an early evolutionary precursor. Both outer membranes accommodate channels of the porin family, which are designed for the uptake and exchange of metabolites, including ions and small molecules, such as nucleosides or sugars. In bacteria, the structure of the outer membrane porin protein family of β-barrels is generally characterized by an even number of β-strands; usually 14, 16 or 18 strands are observed forming the bacterial porin barrel wall. In contrast, the recent structures of the mitochondrial porin, also known as VDAC (voltage-dependent anion channel), show an uneven number of 19 β-strands, but a similar molecular architecture. Despite the lack of a clear evolutionary link between these protein families, their common principles and differences in assembly, architecture and function are summarized in the present review.}, }
@article {pmid20829360, year = {2010}, author = {Carrie, C and Giraud, E and Duncan, O and Xu, L and Wang, Y and Huang, S and Clifton, R and Murcha, M and Filipovska, A and Rackham, O and Vrielink, A and Whelan, J}, title = {Conserved and novel functions for Arabidopsis thaliana MIA40 in assembly of proteins in mitochondria and peroxisomes.}, journal = {The Journal of biological chemistry}, volume = {285}, number = {46}, pages = {36138-36148}, pmid = {20829360}, issn = {1083-351X}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/classification/genetics/metabolism/*physiology ; Blotting, Western ; Conserved Sequence ; DNA, Bacterial/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genes, Essential/genetics ; Green Fluorescent Proteins/genetics/metabolism ; Mitochondria/*metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/genetics/metabolism/*physiology ; Molecular Sequence Data ; Multienzyme Complexes/genetics/metabolism ; Mutagenesis, Insertional ; Mutation ; Oligonucleotide Array Sequence Analysis ; Peroxisomes/*metabolism ; Phylogeny ; Protein Transport ; Sequence Homology, Amino Acid ; Superoxide Dismutase/genetics/metabolism ; }, abstract = {The disulfide relay system of the mitochondrial intermembrane space has been extensively characterized in Saccharomyces cerevisiae. It contains two essential components, Mia40 and Erv1. The genome of Arabidopsis thaliana contains a single gene for each of these components. Although insertional inactivation of Erv1 leads to a lethal phenotype, inactivation of Mia40 results in no detectable deleterious phenotype. A. thaliana Mia40 is targeted to and accumulates in mitochondria and peroxisomes. Inactivation of Mia40 results in an alteration of several proteins in mitochondria, an absence of copper/zinc superoxide dismutase (CSD1), the chaperone for superoxide dismutase (Ccs1) that inserts copper into CSD1, and a decrease in capacity and amount of complex I. In peroxisomes the absence of Mia40 leads to an absence of CSD3 and a decrease in abnormal inflorescence meristem 1 (Aim1), a β-oxidation pathway enzyme. Inactivation of Mia40 leads to an alteration of the transcriptome of A. thaliana, with genes encoding peroxisomal proteins, redox functions, and biotic stress significantly changing in abundance. Thus, the mechanistic operation of the mitochondrial disulfide relay system is different in A. thaliana compared with other systems, and Mia40 has taken on new roles in peroxisomes and mitochondria.}, }
@article {pmid20820906, year = {2010}, author = {Wang, CM and Way, TD and Chang, YC and Yen, NT and Hu, CL and Nien, PC and Jea, YS and Chen, LR and Kao, JY}, title = {The origin of the white Roman goose.}, journal = {Biochemical genetics}, volume = {48}, number = {11-12}, pages = {938-943}, doi = {10.1007/s10528-010-9374-8}, pmid = {20820906}, issn = {1573-4927}, mesh = {Animals ; Base Sequence ; China ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Geese/*genetics ; Models, Statistical ; Molecular Sequence Data ; *Phylogeny ; Phylogeography ; Sequence Analysis ; }, abstract = {In order to avoid interference from nuclear copies of mitochondrial DNA (numts), mtDNA of the white Roman goose (domestic goose) was extracted from liver mitochondria. The mtDNA control region was amplified using a long PCR strategy and then sequenced. Neighbor-joining, maximum parsimony, and maximum-likelihood approaches were implemented using the 1,177 bp mtDNA control region sequences to compute the phylogenetic relationships of the domestic goose with other geese. The resulting identity values for the white Roman geese were 99.1% (1,166/1,177) with western graylag geese and 98.8% (1,163/1,177) with eastern graylag geese. In molecular phylogenetic trees, the white Roman goose was grouped in the graylag lineage, indicating that the white Roman goose came from the graylag goose (Anser anser). Thus, the scientific name of the white Roman goose should be Anser anser 'White Roman.'}, }
@article {pmid20819906, year = {2011}, author = {Leclercq, S and Giraud, I and Cordaux, R}, title = {Remarkable abundance and evolution of mobile group II introns in Wolbachia bacterial endosymbionts.}, journal = {Molecular biology and evolution}, volume = {28}, number = {1}, pages = {685-697}, doi = {10.1093/molbev/msq238}, pmid = {20819906}, issn = {1537-1719}, mesh = {Animals ; Base Sequence ; DNA Transposable Elements/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Bacterial ; *Introns ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Symbiosis/*genetics ; Wolbachia/classification/*genetics ; }, abstract = {The streamlined genomes of ancient obligate endosymbionts generally lack transposable elements, as a consequence of their intracellular confinement. Yet, the genomes of Wolbachia, one of the most abundant bacterial endosymbionts on Earth, are littered with transposable elements, in particular insertion sequences (ISs). This paradox raises the question of whether or not such a mobile DNA proliferation reflects a special feature of ISs. In this study, we focused on another class of transposable elements, group II introns, and conducted an in-depth analysis of their content and the microevolutionary processes responsible for their dynamics within Wolbachia genomes. We report an exceptionally high intron abundance and striking differences in copy numbers between Wolbachia strains as well as between intron families. Our bioinformatics and experimental results provide strong evidence that intron diversity is mainly caused by recent (and perhaps ongoing) mobility and horizontal transfers. Our data also support several temporally independent intron invasions during Wolbachia evolution. Furthermore, group II intron spread in some Wolbachia strains may be regulated through gene conversion-mediated inactivation of intron copies. Finally, we found introns to be involved in numerous genomic rearrangements. This underscores the high recombinogenic potential of group II introns, contrary to general expectations. Overall, our study represents the first comprehensive analysis of group II intron evolutionary dynamics in obligate intracellular bacteria. Our results show that bacterial endosymbionts with reduced genomes can sustain high loads of mobile group II introns, as hypothesized for the endosymbiont ancestor of mitochondria during early eukaryote evolution.}, }
@article {pmid20819227, year = {2010}, author = {Zhao, W and Yu, H and Li, S and Huang, Y}, title = {Identification and analysis of candidate fungal tRNA 3'-end processing endonucleases tRNase Zs, homologs of the putative prostate cancer susceptibility protein ELAC2.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {272}, pmid = {20819227}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Endoribonucleases/*chemistry/*genetics ; Fungal Proteins/*chemistry/*genetics ; Humans ; Male ; Molecular Sequence Data ; Neoplasm Proteins/*chemistry/genetics ; Phylogeny ; Prostatic Neoplasms/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: tRNase Z is the endonuclease that is responsible for the 3'-end processing of tRNA precursors, a process essential for tRNA 3'-CCA addition and subsequent tRNA aminoacylation. Based on their sizes, tRNase Zs can be divided into the long (tRNase ZL) and short (tRNase ZS) forms. tRNase ZL is thought to have arisen from a tandem gene duplication of tRNase ZS with further sequence divergence. The species distribution of tRNase Z is complex. Fungi represent an evolutionarily diverse group of eukaryotes. The recent proliferation of fungal genome sequences provides an opportunity to explore the structural and functional diversity of eukaryotic tRNase Zs.<br><br>RESULTS: We report a survey and analysis of candidate tRNase Zs in 84 completed fungal genomes, spanning a broad diversity of fungi. We find that tRNase ZL is present in all fungi we have examined, whereas tRNase ZS exists only in the fungal phyla Basidiomycota, Chytridiomycota and Zygomycota. Furthermore, we find that unlike the Pezizomycotina and Saccharomycotina, which contain a single tRNase ZL, Schizosaccharomyces fission yeasts (Taphrinomycotina) contain two tRNase ZLs encoded by two different tRNase ZL genes. These two tRNase ZLs are most likely localized to the nucleus and mitochondria, respectively, suggesting partitioning of tRNase Z function between two different tRNase ZLs in fission yeasts. The fungal tRNase Z phylogeny suggests that tRNase ZSs are ancestral to tRNase ZLs. Additionally, the evolutionary relationship of fungal tRNase ZLs is generally consistent with known phylogenetic relationships among the fungal species and supports tRNase ZL gene duplication in certain fungal taxa, including Schizosaccharomyces fission yeasts. Analysis of tRNase Z protein sequences reveals putative atypical substrate binding domains in most fungal tRNase ZSs and in a subset of fungal tRNase ZLs. Finally, we demonstrate the presence of pseudo-substrate recognition and catalytic motifs at the N-terminal halves of tRNase ZLs.<br><br>CONCLUSIONS: This study describes the first comprehensive identification and sequence analysis of candidate fungal tRNase Zs. Our results support the proposal that tRNase ZL has evolved as a result of duplication and diversification of the tRNase ZS gene.}, }
@article {pmid20816580, year = {2010}, author = {Rubinstein, WS}, title = {Endocrine cancer predisposition syndromes: hereditary paraganglioma, multiple endocrine neoplasia type 1, multiple endocrine neoplasia type 2, and hereditary thyroid cancer.}, journal = {Hematology/oncology clinics of North America}, volume = {24}, number = {5}, pages = {907-937}, doi = {10.1016/j.hoc.2010.06.008}, pmid = {20816580}, issn = {1558-1977}, mesh = {Diagnosis, Differential ; *Genetic Predisposition to Disease ; Genetic Testing ; Genomic Imprinting ; Humans ; Multiple Endocrine Neoplasia Type 1/*genetics/therapy ; Multiple Endocrine Neoplasia Type 2a/*genetics/therapy ; Thyroid Neoplasms/*genetics/therapy ; }, abstract = {The hereditary paraganglioma, MEN1, MEN2, and hereditary thyroid cancer syndromes are clinically discernable and genetically distinct. The first 3 syndromes have been well characterized in the past 10 to 15 years. Recognizing these 3 syndromes and using a multidisciplinary team approach creates valuable opportunities for early diagnosis, reduction of morbidity and mortality, and avoidance of surgical misadventures. Hereditary paraganglioma has parent-of-origin effects and gene-environment interactions that indicate its evolution, and the syndrome sheds light on the role of mitochondria and energy metabolism in cancer. This article delineates the clinical presentation and practical management issues and summarizes the history, gene discovery, and molecular insights for each syndrome.}, }
@article {pmid20816094, year = {2010}, author = {Nouws, J and Nijtmans, L and Houten, SM and van den Brand, M and Huynen, M and Venselaar, H and Hoefs, S and Gloerich, J and Kronick, J and Hutchin, T and Willems, P and Rodenburg, R and Wanders, R and van den Heuvel, L and Smeitink, J and Vogel, RO}, title = {Acyl-CoA dehydrogenase 9 is required for the biogenesis of oxidative phosphorylation complex I.}, journal = {Cell metabolism}, volume = {12}, number = {3}, pages = {283-294}, doi = {10.1016/j.cmet.2010.08.002}, pmid = {20816094}, issn = {1932-7420}, mesh = {Acyl-CoA Dehydrogenase, Long-Chain/chemistry/classification/genetics/metabolism ; Acyl-CoA Dehydrogenases/chemistry/classification/genetics/*metabolism ; Adaptor Proteins, Signal Transducing/genetics/metabolism ; Amino Acid Sequence ; Animals ; Cells, Cultured ; Electron Transport Complex I/*biosynthesis ; Fatty Acids/metabolism ; Female ; Fibroblasts/cytology/physiology ; Humans ; Infant ; Male ; Mitochondria/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; NADH Dehydrogenase/genetics/metabolism ; Oxidation-Reduction ; *Oxidative Phosphorylation ; Phylogeny ; Pregnancy ; Protein Structure, Tertiary ; RNA Interference ; Sequence Analysis ; Sequence Analysis, DNA ; }, abstract = {Acyl-CoA dehydrogenase 9 (ACAD9) is a recently identified member of the acyl-CoA dehydrogenase family. It closely resembles very long-chain acyl-CoA dehydrogenase (VLCAD), involved in mitochondrial beta oxidation of long-chain fatty acids. Contrary to its previously proposed involvement in fatty acid oxidation, we describe a role for ACAD9 in oxidative phosphorylation. ACAD9 binds complex I assembly factors NDUFAF1 and Ecsit and is specifically required for the assembly of complex I. Furthermore, ACAD9 mutations result in complex I deficiency and not in disturbed long-chain fatty acid oxidation. This strongly contrasts with its evolutionary ancestor VLCAD, which we show is not required for complex I assembly and clearly plays a role in fatty acid oxidation. Our results demonstrate that two closely related metabolic enzymes have diverged at the root of the vertebrate lineage to function in two separate mitochondrial metabolic pathways and have clinical implications for the diagnosis of complex I deficiency.}, }
@article {pmid20814239, year = {2010}, author = {Martinez-Outschoorn, UE and Balliet, RM and Rivadeneira, DB and Chiavarina, B and Pavlides, S and Wang, C and Whitaker-Menezes, D and Daumer, KM and Lin, Z and Witkiewicz, AK and Flomenberg, N and Howell, A and Pestell, RG and Knudsen, ES and Sotgia, F and Lisanti, MP}, title = {Oxidative stress in cancer associated fibroblasts drives tumor-stroma co-evolution: A new paradigm for understanding tumor metabolism, the field effect and genomic instability in cancer cells.}, journal = {Cell cycle (Georgetown, Tex.)}, volume = {9}, number = {16}, pages = {3256-3276}, pmid = {20814239}, issn = {1551-4005}, support = {R01 CA075503/CA/NCI NIH HHS/United States ; R01 CA098779/CA/NCI NIH HHS/United States ; R01-CA-120876/CA/NCI NIH HHS/United States ; R01 CA120876/CA/NCI NIH HHS/United States ; R01-CA-70896/CA/NCI NIH HHS/United States ; R01-CA-098779/CA/NCI NIH HHS/United States ; R01-CA-86072/CA/NCI NIH HHS/United States ; R01-AR-055660/AR/NIAMS NIH HHS/United States ; R01-CA-080250/CA/NCI NIH HHS/United States ; R01 CA070896/CA/NCI NIH HHS/United States ; R01 CA107382/CA/NCI NIH HHS/United States ; P30 CA056036/CA/NCI NIH HHS/United States ; P30-CA-56036/CA/NCI NIH HHS/United States ; R01-CA-107382/CA/NCI NIH HHS/United States ; R01 AR055660/AR/NIAMS NIH HHS/United States ; R01-CA-75503/CA/NCI NIH HHS/United States ; R01 CA080250/CA/NCI NIH HHS/United States ; R01 CA086072/CA/NCI NIH HHS/United States ; }, mesh = {Autophagy ; Biological Evolution ; Breast Neoplasms/genetics/*metabolism ; Caveolin 1/genetics/*metabolism ; Cell Line ; Coculture Techniques ; DNA Damage ; Down-Regulation ; Female ; Fibroblasts/*metabolism ; *Genomic Instability ; Histones/metabolism ; Humans ; Lactic Acid/pharmacology ; Mitochondria/metabolism/physiology ; Nitric Oxide/metabolism ; Nitric Oxide Synthase Type III/metabolism ; *Oxidative Stress ; RNA Interference ; RNA, Small Interfering/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {Loss of stromal fibroblast caveolin-1 (Cav-1) is a powerful single independent predictor of poor prognosis in human breast cancer patients, and is associated with early tumor recurrence, lymph node metastasis and tamoxifen-resistance. We developed a novel co-culture system to understand the mechanism(s) by which a loss of stromal fibroblast Cav-1 induces a "lethal tumor micro-environment." Here, we propose a new paradigm to explain the powerful prognostic value of stromal Cav-1. In this model, cancer cells induce oxidative stress in cancer-associated fibroblasts, which then acts as a "metabolic" and "mutagenic" motor to drive tumor-stroma co-evolution, DNA damage and aneuploidy in cancer cells. More specifically, we show that an acute loss of Cav-1 expression leads to mitochondrial dysfunction, oxidative stress and aerobic glycolysis in cancer associated fibroblasts. Also, we propose that defective mitochondria are removed from cancer-associated fibroblasts by autophagy/mitophagy that is induced by oxidative stress. As a consequence, cancer associated fibroblasts provide nutrients (such as lactate) to stimulate mitochondrial biogenesis and oxidative metabolism in adjacent cancer cells (the "Reverse Warburg Effect"). We provide evidence that oxidative stress in cancer-associated fibroblasts is sufficient to induce genomic instability in adjacent cancer cells, via a bystander effect, potentially increasing their aggressive behavior. Finally, we directly demonstrate that nitric oxide (NO) over-production, secondary to Cav-1 loss, is the root cause for mitochondrial dysfunction in cancer associated fibroblasts. In support of this notion, treatment with anti-oxidants (such as N-acetyl-cysteine, metformin and quercetin) or NO inhibitors (L-NAME) was sufficient to reverse many of the cancer-associated fibroblast phenotypes that we describe. Thus, cancer cells use "oxidative stress" in adjacent fibroblasts (i) as an "engine" to fuel their own survival via the stromal production of nutrients and (ii) to drive their own mutagenic evolution towards a more aggressive phenotype, by promoting genomic instability. We also present evidence that the "field effect" in cancer biology could also be related to the stromal production of ROS and NO species. eNOS-expressing fibroblasts have the ability to downregulate Cav-1 and induce mitochondrial dysfunction in adjacent fibroblasts that do not express eNOS. As such, the effects of stromal oxidative stress can be laterally propagated, amplified and are effectively "contagious"--spread from cell-to-cell like a virus--creating an "oncogenic/mutagenic" field promoting widespread DNA damage.}, }
@article {pmid20812788, year = {2011}, author = {Xu, XM and Møller, SG}, title = {Iron-sulfur clusters: biogenesis, molecular mechanisms, and their functional significance.}, journal = {Antioxidants &amp; redox signaling}, volume = {15}, number = {1}, pages = {271-307}, doi = {10.1089/ars.2010.3259}, pmid = {20812788}, issn = {1557-7716}, mesh = {Animals ; Bacteria/metabolism ; Humans ; Iron-Sulfur Proteins/genetics/*metabolism ; Plants/metabolism ; Yeasts/metabolism ; }, abstract = {Iron-sulfur clusters [Fe-S] are small, ubiquitous inorganic cofactors representing one of the earliest catalysts during biomolecule evolution and are involved in fundamental biological reactions, including regulation of enzyme activity, mitochondrial respiration, ribosome biogenesis, cofactor biogenesis, gene expression regulation, and nucleotide metabolism. Although simple in structure, [Fe-S] biogenesis requires complex protein machineries and pathways for assembly. [Fe-S] are assembled from cysteine-derived sulfur and iron onto scaffold proteins followed by transfer to recipient apoproteins. Several predominant iron-sulfur biogenesis systems have been identified, including nitrogen fixation (NIF), sulfur utilization factor (SUF), iron-sulfur cluster (ISC), and cytosolic iron-sulfur protein assembly (CIA), and many protein components have been identified and characterized. In eukaryotes ISC is mainly localized to mitochondria, cytosolic iron-sulfur protein assembly to the cytosol, whereas plant sulfur utilization factor is localized mainly to plastids. Because of this spatial separation, evidence suggests cross-talk mediated by organelle export machineries and dual targeting mechanisms. Although research efforts in understanding iron-sulfur biogenesis has been centered on bacteria, yeast, and plants, recent efforts have implicated inappropriate [Fe-S] biogenesis to underlie many human diseases. In this review we detail our current understanding of [Fe-S] biogenesis across species boundaries highlighting evolutionary conservation and divergence and assembling our knowledge into a cellular context.}, }
@article {pmid20811767, year = {2010}, author = {Singh, A and Grover, A}, title = {Plant Hsp100/ClpB-like proteins: poorly-analyzed cousins of yeast ClpB machine.}, journal = {Plant molecular biology}, volume = {74}, number = {4-5}, pages = {395-404}, pmid = {20811767}, issn = {1573-5028}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/metabolism ; Heat-Shock Proteins/genetics/*physiology ; Heat-Shock Response ; Molecular Sequence Data ; Oryza/genetics/metabolism ; Phylogeny ; Plant Proteins/genetics/*physiology ; Sequence Alignment ; Yeasts/genetics/metabolism ; }, abstract = {ClpB/Hsp100 proteins act as chaperones, mediating disaggregation of denatured proteins. Recent work shows that apart from cytoplasm, these proteins are localized to nuclei, chloroplasts, mitochondria and plasma membrane. While ClpB/Hsp100 genes are essentially stress-induced (mainly heat stress) in vegetative organs of the plant body, expression of ClpB/Hsp100 proteins is noted to be constitutive in plant reproductive structures like pollen grains, developing embryos, seeds etc. With global warming looming large on the horizon, ways to genetically engineer plants against high temperature stress are urgently needed. Yeast mutants unable to synthesize active ClpB/Hsp100 protein show a clear thermosensitive phenotype. ClpB/Hsp100 proteins are implicated in high temperature stress tolerance in plants. We herein highlight the selected important facets of this protein family in plants.}, }
@article {pmid20807553, year = {2011}, author = {Castanier, C and Arnoult, D}, title = {Mitochondrial localization of viral proteins as a means to subvert host defense.}, journal = {Biochimica et biophysica acta}, volume = {1813}, number = {4}, pages = {575-583}, doi = {10.1016/j.bbamcr.2010.08.009}, pmid = {20807553}, issn = {0006-3002}, mesh = {Animals ; Humans ; *Immunity, Innate ; Mitochondria/*metabolism/*virology ; Viral Proteins/*metabolism ; Viruses/*pathogenicity ; }, abstract = {Viruses have developed a battery of distinct strategies to overcome the very sophisticated defense mechanisms of the infected host. Throughout the process of pathogen-host co-evolution, viruses have therefore acquired the capability to prevent host cell apoptosis because elimination of infected cells via apoptosis is one of the most ancestral defense mechanism against infection. Conversely, induction of apoptosis may favor viral dissemination as a result of the dismantlement of the infected cells. Mitochondria have been long recognized for their key role in the modulation of apoptosis but more recently, mitochondria have been shown to serve as a crucial platform for innate immune signaling as illustrated by the identification of MAVS. Thus, it is therefore not surprising that this organelle represents a recurrent target for viruses, aiming to manipulate the fate of the infected host cell or to inhibit innate immune response. In this review, we highlight the viral proteins that are specifically targeted to the mitochondria to subvert host defense. This article is part of a Special Issue entitled Mitochondria: the deadly organelle.}, }
@article {pmid20798037, year = {2010}, author = {Lemos, B and Branco, AT and Hartl, DL}, title = {Epigenetic effects of polymorphic Y chromosomes modulate chromatin components, immune response, and sexual conflict.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {36}, pages = {15826-15831}, pmid = {20798037}, issn = {1091-6490}, support = {R01 GM084236/GM/NIGMS NIH HHS/United States ; GM084236/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Chromatin/*physiology ; Drosophila/genetics/immunology/*physiology ; *Epigenesis, Genetic ; Female ; *Polymorphism, Genetic ; *Sexual Behavior, Animal ; *Y Chromosome ; }, abstract = {Genetic conflicts between sexes and generations provide a foundation for understanding the functional evolution of sex chromosomes and sexually dimorphic phenotypes. Y chromosomes of Drosophila contain multi-megabase stretches of satellite DNA repeats and a handful of protein-coding genes that are monomorphic within species. Nevertheless, polymorphic variation in heterochromatic Y chromosomes of Drosophila result in genome-wide gene expression variation. Here we show that such naturally occurring Y-linked regulatory variation (YRV) can be detected in somatic tissues and contributes to the epigenetic balance of heterochromatin/euchromatin at three distinct loci showing position-effect variegation (PEV). Moreover, polymorphic Y chromosomes differentially affect the expression of thousands of genes in XXY female genotypes in which Y-linked protein-coding genes are not transcribed. The data show a disproportionate influence of YRV on the variable expression of genes whose protein products localize to the nucleus, have nucleic-acid binding activity, and are involved in transcription, chromosome organization, and chromatin assembly. These include key components such as HP1, Trithorax-like (GAGA factor), Su(var)3-9, Brahma, MCM2, ORC2, and inner centromere protein. Furthermore, mitochondria-related genes, immune response genes, and transposable elements are also disproportionally affected by Y chromosome polymorphism. These functional clusterings may arise as a consequence of the involvement of Y-linked heterochromatin in the origin and resolution of genetic conflicts between males and females. Taken together, our results indicate that Y chromosome heterochromatin serves as a major source of epigenetic variation in natural populations that interacts with chromatin components to modulate the expression of biologically relevant phenotypic variation.}, }
@article {pmid20738684, year = {2009}, author = {França, GF and Oliveira, C and Quagio-Grassiotto, I}, title = {Spermatic cell characteristics in Gymnotiformes (Teleostei: Ostariophysi) and their phylogenetic meaning.}, journal = {Journal of fish biology}, volume = {75}, number = {9}, pages = {2226-2243}, doi = {10.1111/j.1095-8649.2009.02439.x}, pmid = {20738684}, issn = {1095-8649}, mesh = {Animals ; Gymnotiformes/genetics/*physiology ; Male ; Microscopy, Electron, Transmission ; *Phylogeny ; Spermatogenesis/*physiology ; Spermatozoa/*ultrastructure ; }, abstract = {Spermatic characteristics were studied in representatives of the families Rhamphichthyidae, Sternopygidae and Apteronotidae, and compared with pre-existent data from Gymnotidae and Hypopomidae. The spermatic characteristics found in Gymnotiformes were also compared with data from other Ostariophysi spermatic cells. The spermatic characteristics as the type of spermiogenesis and the structural pattern of the sperm, considering nuclear form, pattern of chromatin condensation, nuclear fossa and its relation with the centriolar complex, form and localization of mitochondria, form of midpiece, presence or absence of cytoplasmic canal and cytoplasmic sleeve, and flagellar fins were utilized. The comparative analysis of the spermatic cell of Gymnotiformes better support the previous proposals for the order considering Gymnotidae as a derived group, than the more recent ones that located Gymnotidae in a basal position as the sister group of the remaining Gymnotiformes. Regarding the Ostariophysi, the comparative analyses based on the spermatic cell characteristics is consistent with a recent systematic proposal that consider Gymnotiformes as a sister group of Characiformes.}, }
@article {pmid20731852, year = {2010}, author = {Gross, J and Bhattacharya, D}, title = {Uniting sex and eukaryote origins in an emerging oxygenic world.}, journal = {Biology direct}, volume = {5}, number = {}, pages = {53}, pmid = {20731852}, issn = {1745-6150}, mesh = {Animals ; *Biological Evolution ; Eukaryotic Cells/*metabolism ; Oxygen/*metabolism ; Prokaryotic Cells/*metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {BACKGROUND: Theories about eukaryote origins (eukaryogenesis) need to provide unified explanations for the emergence of diverse complex features that define this lineage. Models that propose a prokaryote-to-eukaryote transition are gridlocked between the opposing "phagocytosis first" and "mitochondria as seed" paradigms, neither of which fully explain the origins of eukaryote cell complexity. Sex (outcrossing with meiosis) is an example of an elaborate trait not yet satisfactorily addressed in theories about eukaryogenesis. The ancestral nature of meiosis and its dependence on eukaryote cell biology suggest that the emergence of sex and eukaryogenesis were simultaneous and synergic and may be explained by a common selective pressure.<br><br>We propose that a local rise in oxygen levels, due to cyanobacterial photosynthesis in ancient Archean microenvironments, was highly toxic to the surrounding biota. This selective pressure drove the transformation of an archaeal (archaebacterial) lineage into the first eukaryotes. Key is that oxygen might have acted in synergy with environmental stresses such as ultraviolet (UV) radiation and/or desiccation that resulted in the accumulation of reactive oxygen species (ROS). The emergence of eukaryote features such as the endomembrane system and acquisition of the mitochondrion are posited as strategies to cope with a metabolic crisis in the cell plasma membrane and the accumulation of ROS, respectively. Selective pressure for efficient repair of ROS/UV-damaged DNA drove the evolution of sex, which required cell-cell fusions, cytoskeleton-mediated chromosome movement, and emergence of the nuclear envelope. Our model implies that evolution of sex and eukaryogenesis were inseparable processes.<br><br>TESTING THE HYPOTHESIS: Several types of data can be used to test our hypothesis. These include paleontological predictions, simulation of ancient oxygenic microenvironments, and cell biological experiments with Archaea exposed to ROS and UV stresses. Studies of archaeal conjugation, prokaryotic DNA recombination, and the universality of nuclear-mediated meiotic activities might corroborate the hypothesis that sex and the nucleus evolved to support DNA repair.<br><br>Oxygen tolerance emerges as an important principle to investigate eukaryogenesis. The evolution of eukaryotic complexity might be best understood as a synergic process between key evolutionary innovations, of which meiosis (sex) played a central role.<br><br>REVIEWERS: This manuscript was reviewed by Eugene V. Koonin, Anthony M. Poole, and G&#xe1;sp&#xe1;r J&#xe9;kely.}, }
@article {pmid20728567, year = {2011}, author = {Dallai, R and Mercati, D and Carapelli, A and Nardi, F and Machida, R and Sekiya, K and Frati, F}, title = {Sperm accessory microtubules suggest the placement of Diplura as the sister-group of Insecta s.s.}, journal = {Arthropod structure &amp; development}, volume = {40}, number = {1}, pages = {77-92}, doi = {10.1016/j.asd.2010.08.001}, pmid = {20728567}, issn = {1873-5495}, mesh = {Animals ; Genitalia, Male/anatomy &amp; histology ; Insect Proteins ; Insecta/*anatomy &amp; histology/physiology ; Male ; Microtubules/ultrastructure ; Phylogeny ; Spermatogenesis ; Spermatozoa/ultrastructure ; }, abstract = {Sperm ultrastructure and spermiogenesis of the dipluran Japygidae (Japyx solifugus, Metajapyx braueri and Occasjapyx japonicus) and Campodeidae (Campodea sp.) were studied with the aim of looking for potential characters for the reconstruction of the phylogenetic relationships of basal hexapods. Both Japygidae and Campodeidae share a common sperm axonemal model 9+9+2, provided with nine accessory microtubules. These microtubules, however, after their formation lose the usual position around the 9+2 and migrate between the two mitochondria. In Japygidae, four of these microtubules are very short and were observed beneath the nucleus after negative staining and serial sections. Accessory microtubules have 13 protofilaments in their tubular wall. Diplura have a sperm morphology which is very different from that of the remaining Entognatha (Protura+Collembola). On the basis of the present results, the presence of accessory microtubules suggests that Diplura are the sister-group of the Insecta s.s.. Moreover, Japygidae and Campodeidae differ with regards to the relative position of the sperm components, the former having the axoneme starting from beneath the nucleus (above which sits the short acrosome), while the latter having a long apical acrosome and a nucleus running parallel with the proximal part of the axoneme. The present study also allowed to redescribe the male genital system of Japyx.}, }
@article {pmid20714705, year = {2011}, author = {Tan, Y and Li, S and Xie, H and Duan, S and Wang, T and Zhu, Y}, title = {Genetical and molecular analysis reveals a cooperating relationship between cytoplasmic male sterility- and fertility restoration-related genes in Oryza species.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {122}, number = {1}, pages = {9-19}, pmid = {20714705}, issn = {1432-2242}, mesh = {Blotting, Southern ; Cell Nucleus/genetics ; Cluster Analysis ; Crosses, Genetic ; Cytoplasm/*genetics ; DNA, Plant/genetics ; Fertility/genetics ; Genes, Mitochondrial/genetics ; Genes, Plant/*genetics ; Hybridization, Genetic ; Oryza/*genetics ; Phylogeny ; Physical Chromosome Mapping ; Plant Infertility/*genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Seeds/genetics ; Species Specificity ; Subcellular Fractions/metabolism ; }, abstract = {Although the characterization of genes associated with cytoplasmic male sterility (CMS) and fertility restoration (Rf) has been well documented, the evolutionary relationship between nuclear Rf and CMS factors in mitochondria in Oryza species is still less understood. Here, 41 accessions from 7 Oryza species with AA genome were employed for analyzing the evolutionary relationships between the CMS factors and Rf candidates on chromosome 10. The phylogenetic tree based on restriction fragment length polymorphism patterns of CMS-associated mitochondrial genes showed that these 41 Oryza accessions fell into 3 distinct groups. Another phylogenetic tree based on PCR profiles of the nuclear Rf candidates on chromosome 10 was also established, and three groups were distinctively grouped. The accessions in each subgroup/group of the two phylogenetic trees are well parallel to each other. Furthermore, the 41 investigated accessions were test-crossed with Honglian (gametophytic type) and Wild-abortive (sporophytic type) CMS, and 5 groups were classified according to their restoring ability. The accessions in the same subgroup of the two phylogenetic trees shared similar fertility restoring pattern. Therefore, we conclude that the CMS-associated mitotypes are compatible to the Rf candidate-related nucleotypes, CMS and Rf have a parallel evolutionary relation in the Oryza species.}, }
@article {pmid20714159, year = {2010}, author = {Ruiz-Garcia, M and Pinedo-Castro, MO}, title = {Molecular systematics and phylogeography of the genus Lagothrix (Atelidae, Primates) by means of the mitochondrial COII gene.}, journal = {Folia primatologica; international journal of primatology}, volume = {81}, number = {3}, pages = {109-128}, doi = {10.1159/000315070}, pmid = {20714159}, issn = {1421-9980}, mesh = {Animals ; Atelinae/classification/*genetics ; Electron Transport Complex IV/*genetics/metabolism ; *Evolution, Molecular ; Genetic Variation ; Haplotypes ; Mitochondria/*enzymology/*genetics ; Phylogeny ; Phylogeography ; Species Specificity ; }, abstract = {We propose the first molecular systematic hypothesis on the origin and evolution of Lagothrix taxa based on an analysis of 720 base pairs of the cytochrome c oxidase subunit II mitochondrial gene in 97 Lagothrix specimens. All the current Lagothrix forms probably descended from the ancestor L. poeppigii or perhaps (less probably) that of L. lugens. We detected at least 2 lineages in L. poeppigii. L. cana and L. lagotricha were determined to be monophyletic and had lower gene diversity levels compared to L. poeppigii and L. lugens. The most basal ancestors of the current L. poeppigii lineages diverged from the other Lagothrix taxa around 2.5 million years ago, at the end of the Pliocene or at the beginning of the Pleistocene. Clearly, L. cana and L. lagotricha were the 2 most recently derived Lagothrix taxa. The diversification within L. lugens and L. poeppigii may coincide with the first and second Pleistocene glacial periods, respectively, while the diversification within L. cana and L. lagotricha could have occurred in the last 400,000 years, coinciding with the climatological changes provoked by the Illinois-Riss (third) and Wisconsin-Würm (fourth) glaciations.}, }
@article {pmid20708960, year = {2011}, author = {Dunthorn, M and Foissner, W and Katz, LA}, title = {Expanding character sampling for ciliate phylogenetic inference using mitochondrial SSU-rDNA as a molecular marker.}, journal = {Protist}, volume = {162}, number = {1}, pages = {85-99}, pmid = {20708960}, issn = {1618-0941}, support = {P 20360/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ciliophora/*classification/*genetics/ultrastructure ; DNA, Ribosomal/*genetics ; Evolution, Molecular ; Genetic Markers ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Molecular systematics of ciliates, particularly at deep nodes, has largely focused on increasing taxon sampling using the nuclear small subunit rDNA (nSSU-rDNA) locus. These previous analyses have generally been congruent with morphologically-based classifications, although there is extensive non-monophyly at many levels. However, caution is needed in interpreting these results as nSSU-rDNA is just a single molecular marker. Here the mitochondrial small subunit rDNA (mtSSU-rDNA) is evaluated for deep ciliate nodes using the Colpodea as an example. Overall, well-supported nodes in the mtSSU-rDNA and concatenated topologies are well supported in the nSSU-rDNA topology; e.g., the non-monophyly of the Cyrtolophosidida. The two moderately- to well-supported incongruences between the loci are the placement of the Sorogenida andColpoda aspera.Our analyses of mtSSU-rDNA support the conclusion, originally derived from nSSU-rDNA, that the morphological characters used in taxonomic circumscriptions of the Colpodea represent a mixture of ancestral and derived states. This demonstration of the efficacy of the mtSSU-rDNA will enable phylogenetic reconstructions of deep nodes in the ciliate tree of life to move from a single-locus to a multi-locus approach.}, }
@article {pmid20704490, year = {2010}, author = {Pörtner, HO and Schulte, PM and Wood, CM and Schiemer, F}, title = {Niche dimensions in fishes: an integrative view.}, journal = {Physiological and biochemical zoology : PBZ}, volume = {83}, number = {5}, pages = {808-826}, doi = {10.1086/655977}, pmid = {20704490}, issn = {1537-5293}, mesh = {Adaptation, Biological/*physiology ; Animals ; *Biological Evolution ; Climate Change ; Ecology ; *Ecosystem ; Energy Metabolism/*physiology ; Fishes/*physiology ; Genetic Fitness/*physiology ; Mitochondria/*physiology ; Models, Theoretical ; Physiology, Comparative ; Species Specificity ; }, abstract = {Current shifts in ecosystem composition and function emphasize the need for an understanding of the links between environmental factors and organism fitness and tolerance. The examples discussed here illustrate how recent progress in the field of comparative physiology may provide a better mechanistic understanding of the ecological concepts of the fundamental and realized niches and thus provide insights into the impacts of anthropogenic disturbance. Here we argue that, as a link between physiological and ecological indicators of organismal performance, the mechanisms shaping aerobic scope and passive tolerance set the dimensions of an animal's niche, here defined as its capacity to survive, grow, behave, and interact with other species. We demonstrate how comparative studies of cod or killifish populations in a latitudinal cline have unraveled mitochondrial mechanisms involved in establishing a species' niche, performance, and energy budget. Riverine fish exemplify how the performance windows of various developmental stages follow the dynamic regimes of both seasonal temperatures and river hydrodynamics, as synergistic challenges. Finally, studies of species in extreme environments, such as the tilapia of Lake Magadi, illustrate how on evolutionary timescales functional and morphological shifts can occur, associated with new specializations. We conclude that research on the processes and time course of adaptations suitable to overcome current niche limits is urgently needed to assess the resilience of species and ecosystems to human impact, including the challenges of global climate change.}, }
@article {pmid20694140, year = {2010}, author = {Muñoz, J and Gómez, A and Green, AJ and Figuerola, J and Amat, F and Rico, C}, title = {Evolutionary origin and phylogeography of the diploid obligate parthenogen Artemia parthenogenetica (Branchiopoda: Anostraca).}, journal = {PloS one}, volume = {5}, number = {8}, pages = {e11932}, pmid = {20694140}, issn = {1932-6203}, mesh = {Animals ; Artemia/*genetics/*physiology ; *Diploidy ; *Evolution, Molecular ; Female ; Genes, Mitochondrial/genetics ; Genetic Variation ; Haplotypes ; Mitochondria/genetics ; Molecular Sequence Data ; Mothers ; *Parthenogenesis ; *Phylogeny ; }, abstract = {BACKGROUND: Understanding the evolutionary origin and the phylogeographic patterns of asexual taxa can shed light on the origin and maintenance of sexual reproduction. We assessed the geographic origin, genetic diversity, and phylogeographic history of obligate parthenogen diploid Artemia parthenogenetica populations, a widespread halophilic crustacean.<br><br>We analysed a partial sequence of the Cytochrome c Oxidase Subunit I mitochondrial gene from an extensive set of localities (including Eurasia, Africa, and Australia), and examined their phylogeographic patterns and the phylogenetic relationships of diploid A. parthenogenetica and its closest sexual relatives. Populations displayed an extremely low level of mitochondrial genetic diversity, with one widespread haplotype shared by over 79% of individuals analysed. Phylogenetic and phylogeographic analyses indicated a multiple and recent evolutionary origin of diploid A. parthenogenetica, and strongly suggested that the geographic origin of parthenogenesis in Artemia was in Central Asia. Our results indicate that the maternal sexual ancestors of diploid A. parthenogenetica were an undescribed species from Kazakhstan and A. urmiana.<br><br>CONCLUSIONS/SIGNIFICANCE: We found evidence for multiple origin of parthenogenesis in Central Asia. Our results indicated that, shortly after its origin, diploid A. parthenogenetica populations underwent a rapid range expansion from Central Asia towards the Mediterranean region, and probably to the rest of its current geographic distribution. This contrasts with the restricted geographic distribution, strong genetic structure, and regional endemism of sexual Artemia lineages and other passively dispersed sexual continental aquatic invertebrates. We hypothesize that diploid parthenogens might have reached their current distribution in historical times, with a range expansion possibly facilitated by an increased availability of suitable habitat provided by anthropogenic activities, such as the spread of solar saltworks, aided by their natural dispersal vectors (i.e., waterbirds).}, }
@article {pmid20688971, year = {2010}, author = {Gnad, F and Forner, F and Zielinska, DF and Birney, E and Gunawardena, J and Mann, M}, title = {Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {9}, number = {12}, pages = {2642-2653}, pmid = {20688971}, issn = {1535-9484}, support = {R01 GM081578/GM/NIGMS NIH HHS/United States ; R01 GM081578-02/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Line ; Eukaryotic Cells/*metabolism ; *Evolution, Molecular ; Humans ; Mice ; Mitochondria/*metabolism ; Phosphoproteins/metabolism ; Phosphorylation ; Prokaryotic Cells/*metabolism ; Proteome ; }, abstract = {High accuracy mass spectrometry has proven to be a powerful technology for the large scale identification of serine/threonine/tyrosine phosphorylation in the living cell. However, despite many described phosphoproteomes, there has been no comparative study of the extent of phosphorylation and its evolutionary conservation in all domains of life. Here we analyze the results of phosphoproteomics studies performed with the same technology in a diverse set of organisms. For the most ancient organisms, the prokaryotes, only a few hundred proteins have been found to be phosphorylated. Applying the same technology to eukaryotic species resulted in the detection of thousands of phosphorylation events. Evolutionary analysis shows that prokaryotic phosphoproteins are preferentially conserved in all living organisms, whereas-site specific phosphorylation is not. Eukaryotic phosphosites are generally more conserved than their non-phosphorylated counterparts (with similar structural constraints) throughout the eukaryotic domain. Yeast and Caenorhabditis elegans are two exceptions, indicating that the majority of phosphorylation events evolved after the divergence of higher eukaryotes from yeast and reflecting the unusually large number of nematode-specific kinases. Mitochondria present an interesting intermediate link between the prokaryotic and eukaryotic domains. Applying the same technology to this organelle yielded 174 phosphorylation sites mapped to 74 proteins. Thus, the mitochondrial phosphoproteome is similarly sparse as the prokaryotic phosphoproteomes. As expected from the endosymbiotic theory, phosphorylated as well as non-phosphorylated mitochondrial proteins are significantly conserved in prokaryotes. However, mitochondrial phosphorylation sites are not conserved throughout prokaryotes, consistent with the notion that serine/threonine phosphorylation in prokaryotes occurred relatively recently in evolution. Thus, the phosphoproteome reflects major events in the evolution of life.}, }
@article {pmid20686707, year = {2010}, author = {Kao, KC and Schwartz, K and Sherlock, G}, title = {A genome-wide analysis reveals no nuclear dobzhansky-muller pairs of determinants of speciation between S. cerevisiae and S. paradoxus, but suggests more complex incompatibilities.}, journal = {PLoS genetics}, volume = {6}, number = {7}, pages = {e1001038}, pmid = {20686707}, issn = {1553-7404}, support = {F32 GM079113/GM/NIGMS NIH HHS/United States ; R01 HG003328/HG/NHGRI NIH HHS/United States ; }, mesh = {*Genetic Speciation ; Genome, Fungal ; *Genome-Wide Association Study ; Mitochondria ; Models, Genetic ; Polymorphism, Genetic ; Saccharomyces/*genetics ; Saccharomyces cerevisiae ; }, abstract = {The Dobzhansky-Muller (D-M) model of speciation by genic incompatibility is widely accepted as the primary cause of interspecific postzygotic isolation. Since the introduction of this model, there have been theoretical and experimental data supporting the existence of such incompatibilities. However, speciation genes have been largely elusive, with only a handful of candidate genes identified in a few organisms. The Saccharomyces sensu stricto yeasts, which have small genomes and can mate interspecifically to produce sterile hybrids, are thus an ideal model for studying postzygotic isolation. Among them, only a single D-M pair, comprising a mitochondrially targeted product of a nuclear gene and a mitochondrially encoded locus, has been found. Thus far, no D-M pair of nuclear genes has been identified between any sensu stricto yeasts. We report here the first detailed genome-wide analysis of rare meiotic products from an otherwise sterile hybrid and show that no classic D-M pairs of speciation genes exist between the nuclear genomes of the closely related yeasts S. cerevisiae and S. paradoxus. Instead, our analyses suggest that more complex interactions, likely involving multiple loci having weak effects, may be responsible for their post-zygotic separation. The lack of a nuclear encoded classic D-M pair between these two yeasts, yet the existence of multiple loci that may each exert a small effect through complex interactions suggests that initial speciation events might not always be mediated by D-M pairs. An alternative explanation may be that the accumulation of polymorphisms leads to gamete inviability due to the activities of anti-recombination mechanisms and/or incompatibilities between the species' transcriptional and metabolic networks, with no single pair at least initially being responsible for the incompatibility. After such a speciation event, it is possible that one or more D-M pairs might subsequently arise following isolation.}, }
@article {pmid20685719, year = {2011}, author = {Scott, GR and Schulte, PM and Egginton, S and Scott, AL and Richards, JG and Milsom, WK}, title = {Molecular evolution of cytochrome C oxidase underlies high-altitude adaptation in the bar-headed goose.}, journal = {Molecular biology and evolution}, volume = {28}, number = {1}, pages = {351-363}, doi = {10.1093/molbev/msq205}, pmid = {20685719}, issn = {1537-1719}, mesh = {Adaptation, Physiological/*genetics ; *Altitude ; Animals ; Biological Evolution ; Coronary Vessels/metabolism ; Electron Transport Complex IV/chemistry/*genetics/metabolism ; Energy Metabolism/genetics ; *Evolution, Molecular ; Flight, Animal/physiology ; Geese/anatomy &amp; histology/classification/*genetics/*physiology ; Hypoxia/genetics ; Isoenzymes/*genetics ; Mitochondria/genetics/metabolism ; Models, Molecular ; Myocardium/cytology/enzymology ; Oxygen Consumption/physiology ; Phylogeny ; Protein Conformation ; Protein Subunits/genetics/metabolism ; }, abstract = {Bar-headed geese (Anser indicus) fly at up to 9,000 m elevation during their migration over the Himalayas, sustaining high metabolic rates in the severe hypoxia at these altitudes. We investigated the evolution of cardiac energy metabolism and O(2) transport in this species to better understand the molecular and physiological mechanisms of high-altitude adaptation. Compared with low-altitude geese (pink-footed geese and barnacle geese), bar-headed geese had larger lungs and higher capillary densities in the left ventricle of the heart, both of which should improve O(2) diffusion during hypoxia. Although myoglobin abundance and the activities of many metabolic enzymes (carnitine palmitoyltransferase, citrate synthase, 3-hydroxyacyl-coA dehydrogenase, lactate dehydrogenase, and pyruvate kinase) showed only minor variation between species, bar-headed geese had a striking alteration in the kinetics of cytochrome c oxidase (COX), the heteromeric enzyme that catalyzes O(2) reduction in oxidative phosphorylation. This was reflected by a lower maximum catalytic activity and a higher affinity for reduced cytochrome c. There were small differences between species in messenger RNA and protein expression of COX subunits 3 and 4, but these were inconsistent with the divergence in enzyme kinetics. However, the COX3 gene of bar-headed geese contained a nonsynonymous substitution at a site that is otherwise conserved across vertebrates and resulted in a major functional change of amino acid class (Trp-116 → Arg). This mutation was predicted by structural modeling to alter the interaction between COX3 and COX1. Adaptations in mitochondrial enzyme kinetics and O(2) transport capacity may therefore contribute to the exceptional ability of bar-headed geese to fly high.}, }
@article {pmid20680393, year = {2010}, author = {Bao, J and Sack, MN}, title = {Protein deacetylation by sirtuins: delineating a post-translational regulatory program responsive to nutrient and redox stressors.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {67}, number = {18}, pages = {3073-3087}, pmid = {20680393}, issn = {1420-9071}, support = {ZIA HL006047-02/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Acetylation ; Humans ; Mitochondria/enzymology ; Neoplasms/enzymology ; Neurons/enzymology ; Oxidation-Reduction ; Phylogeny ; *Protein Processing, Post-Translational ; Proteins/*metabolism ; Sirtuins/classification/*metabolism ; }, abstract = {Lysine acetylation/deacetylation is increasingly being recognized as common post-translational modification that appears to be broadly operational throughout the cell. The functional roles of these modifications, outside of the nucleus, have not been extensively studied. Moreover, as acetyl-CoA donates the acetyl group for acetylation, nutrient availability and energetic status may be pivotal in this modification. Similarly, nutrient limitation is associated with the deacetylation reaction. This modification is orchestrated by a novel family of sirtuin deacetylases that function in a nutrient and redox dependent manner and targets non-histone protein deacetylation. In compartment-specific locations, candidate target proteins undergoing lysine-residue deacetylation are being identified. Through these investigations, the functional role of this post-translational modification is being delineated. We review the sirtuin family proteins, discuss their functional effects on target proteins, and postulate on potential biological programs and disease processes that may be modified by sirtuin-mediated deacetylation of target proteins.}, }
@article {pmid20676380, year = {2010}, author = {Capra, JA and Paeschke, K and Singh, M and Zakian, VA}, title = {G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.}, journal = {PLoS computational biology}, volume = {6}, number = {7}, pages = {e1000861}, pmid = {20676380}, issn = {1553-7358}, support = {T32 GN003284//PHS HHS/United States ; R37 GM026938/GM/NIGMS NIH HHS/United States ; P50 GM071508/GM/NIGMS NIH HHS/United States ; R01 GM026938/GM/NIGMS NIH HHS/United States ; R01 GM076275/GM/NIGMS NIH HHS/United States ; GM076275/GM/NIGMS NIH HHS/United States ; T32 HG003284/HG/NHGRI NIH HHS/United States ; }, mesh = {Base Sequence ; *Conserved Sequence ; DNA Breaks, Double-Stranded ; DNA, Fungal/*chemistry ; *G-Quadruplexes ; *Genome, Fungal ; Markov Chains ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Saccharomyces cerevisiae/*genetics ; Sequence Analysis, DNA ; Yeasts/genetics ; }, abstract = {G-quadruplex DNA is a four-stranded DNA structure formed by non-Watson-Crick base pairing between stacked sets of four guanines. Many possible functions have been proposed for this structure, but its in vivo role in the cell is still largely unresolved. We carried out a genome-wide survey of the evolutionary conservation of regions with the potential to form G-quadruplex DNA structures (G4 DNA motifs) across seven yeast species. We found that G4 DNA motifs were significantly more conserved than expected by chance, and the nucleotide-level conservation patterns suggested that the motif conservation was the result of the formation of G4 DNA structures. We characterized the association of conserved and non-conserved G4 DNA motifs in Saccharomyces cerevisiae with more than 40 known genome features and gene classes. Our comprehensive, integrated evolutionary and functional analysis confirmed the previously observed associations of G4 DNA motifs with promoter regions and the rDNA, and it identified several previously unrecognized associations of G4 DNA motifs with genomic features, such as mitotic and meiotic double-strand break sites (DSBs). Conserved G4 DNA motifs maintained strong associations with promoters and the rDNA, but not with DSBs. We also performed the first analysis of G4 DNA motifs in the mitochondria, and surprisingly found a tenfold higher concentration of the motifs in the AT-rich yeast mitochondrial DNA than in nuclear DNA. The evolutionary conservation of the G4 DNA motif and its association with specific genome features supports the hypothesis that G4 DNA has in vivo functions that are under evolutionary constraint.}, }
@article {pmid20675436, year = {2010}, author = {West, JB}, title = {Did differences in mitochondrial properties influence the evolution of avian and mammalian lungs?.}, journal = {American journal of physiology. Lung cellular and molecular physiology}, volume = {299}, number = {5}, pages = {L595-6}, pmid = {20675436}, issn = {1522-1504}, support = {R01-HL-60968/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Birds/*anatomy &amp; histology/genetics ; Humans ; *Lung/cytology/physiology ; Mammals/*anatomy &amp; histology/genetics ; Mitochondria/*genetics ; Oxygen Consumption ; Reactive Oxygen Species/metabolism ; }, }
@article {pmid20672409, year = {2010}, author = {Liu, SQ and Zhang, JB and Tang, QY and Liu, HZ}, title = {[Phylogenetic relationships among Cobitoidea based on mitochondrial ND4 and ND5 gene sequences].}, journal = {Dong wu xue yan jiu = Zoological research}, volume = {31}, number = {3}, pages = {221-229}, doi = {10.3724/SP.J.1141.2010.03221}, pmid = {20672409}, issn = {0254-5853}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Cypriniformes/*classification/genetics ; DNA, Mitochondrial/classification/*genetics ; Electron Transport Complex I/genetics ; Evolution, Molecular ; Genes, RAG-1/*genetics ; Genetic Testing ; Humans ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Transfer/*genetics ; }, abstract = {In the present study, we cloned and sequenced 10 new ND4 and ND5 gene sequences of Cobitoidea. These sequences were used to reconstruct phylogenetic relationships together with those of 15 other species downloaded from GenBank. The results showed that the length of ND4 gene sequence was 1 380-1 387 bp with ATG as starting codon and incomplete termination signal as terminated codon; the length of ND5 gene sequence was 1 821-1 839 bp with ATG as starting codon and TAA or TAG as terminated codon; three tRNA genes coding tRNAs that carry hisidine, serine and leucine respectively, were inserted between ND4 and ND5 genes. A, T, C and G accounted for 30.4%, 27.3%, 14.2% and 28.1% in ND4/ND5 gene (including intervening three tRNA genes). The content of A+T (57.7%) is higher than that of G+C (42.3%). The estimated Ti/Tv ratio was 1.586. With Danio rerio and Cyprinus carpio as outgroups, the phylogenetic relationships of Cobitoidea were analyzed using maximum parsimony (MP) method, maximum likelihood (ML) method and Bayesian analyses (BI). Results of all the three methods indicated that Cobitinae, Nemacheilinae, Botiinae, Balitoridae and Vaillantellidae were all monophyletic respectively, and their interrelationships were: (Vaillantellidae + (Botiinae + (Cobitinae + (Nemacheilinae + Balitoridae)))), which was consistent with the previous studies based on the whole mitogenome and some nuclear genes sequences (eg. RAG1 gene). However, the present results differ from those based upon other mtDNA genes sequences (e.g. the cyt b and D-loop showed that Nemacheilinae grouped with Cobitinae forming sister-group, then they clustered with Balitoridae). The difference could be due to the phylogenetic information carried by different length sequence: Longer sequences carry more information and result in more reliable phylogenetic trees.}, }
@article {pmid20670295, year = {2010}, author = {Rikihisa, Y and Lin, M and Niu, H}, title = {Type IV secretion in the obligatory intracellular bacterium Anaplasma phagocytophilum.}, journal = {Cellular microbiology}, volume = {12}, number = {9}, pages = {1213-1221}, pmid = {20670295}, issn = {1462-5822}, support = {R01 AI030010/AI/NIAID NIH HHS/United States ; R01 AI054476/AI/NIAID NIH HHS/United States ; R01AI054476/AI/NIAID NIH HHS/United States ; R01AI30010/AI/NIAID NIH HHS/United States ; }, mesh = {Anaplasma phagocytophilum/chemistry/*metabolism/*pathogenicity ; Ankyrin Repeat ; Bacterial Proteins/chemistry/*metabolism ; *Bacterial Secretion Systems ; Biological Transport ; Cytoplasm/metabolism ; Ehrlichiosis/*microbiology ; Humans ; Neutrophils/microbiology ; Signal Transduction ; }, abstract = {Anaplasma phagocytophilum is an obligatory intracellular bacterium that infects neutrophils, the primary host defence cells. Consequent effects of infection on host cells result in a potentially fatal systemic disease called human granulocytic anaplasmosis. Despite ongoing reductive genome evolution and deletion of most genes for intermediary metabolism and amino acid biosynthesis, Anaplasma has also experienced expansion of genes encoding several components of the type IV secretion (T4S) apparatus. Two A. phagocytophilum T4S effector molecules are currently known; Anaplasma translocated substrate 1 (Ats-1) and ankyrin repeat domain-containing protein A (AnkA) have C-terminal positively charged amino acid residues that are recognized by the T4S coupling protein, VirD4. AnkA and Ats-1 contain eukaryotic protein motifs and are uniquely evolved in the family Anaplasmataceae; Ats-1 contains a mitochondria-targeting signal. They are abundantly produced and secreted into the host cytoplasm, are not toxic to host cells, and manipulate host cell processes to aid in the infection process. At the cellular level, the two effectors have distinct subcellular localization and signalling in host cells. Thus in this obligatory intracellular pathogen, the T4S system has evolved as a host-subversive survival factor.}, }
@article {pmid20663713, year = {2011}, author = {Moriyama, T and Terasawa, K and Sato, N}, title = {Conservation of POPs, the plant organellar DNA polymerases, in eukaryotes.}, journal = {Protist}, volume = {162}, number = {1}, pages = {177-187}, doi = {10.1016/j.protis.2010.06.001}, pmid = {20663713}, issn = {1618-0941}, mesh = {Animals ; DNA-Directed DNA Polymerase/isolation &amp; purification/*metabolism ; Mitochondria/enzymology ; Nucleic Acid Synthesis Inhibitors ; Organelles/*enzymology ; Phylogeny ; Rats ; Species Specificity ; Tetrahymena thermophila/*enzymology ; }, abstract = {POPs, plant organellar DNA polymerases, have been isolated from various photosynthetic eukaryotes. Previously, we purified the native POP of Cyanidioschyzon merolae(CmPOP) from whole cellular extracts and showed that CmPOP has DNA polymerase activity with a high processivity and a 3'-5' exonuclease activity, and its expression is related to cell proliferation. In rice, the recombinant protein of POP has activities found in CmPOP, and high fidelity of POP has also been demonstrated. These facts suggest that POPs are involved in the replication of organellar genomes. POPs are also conserved in most non-opisthokont eukaryotes, which lack DNA polymerase γ (Polγ), a mitochondrial replication enzyme in opisthokonts (fungi and animals). The ciliateTetrahymena thermophilacontains a single gene for a putative POP (TetPOP). Immunoblot analysis demonstrated that TetPOP is localized in mitochondria, and TetPOP has been purified from mitochondria through a column chromatography series. Sensitivity to phosphonoacetate and dideoxyTTP was examined in POPs (TetPOP and CmPOP) or POP-containing organelles (chloroplasts of Arabidopsis) and other polymerases (DNA polymerase I and mitochondria of rat liver, which contain Polγ), and the results suggest that high sensitivity to phosphonoacetate is unique to POPs in Family-A DNA polymerases. Finally, we propose a model for the succession of organellar DNA polymerases.}, }
@article {pmid20661438, year = {2010}, author = {Jiang, H and Guan, W and Gu, Z}, title = {Tinkering evolution of post-transcriptional RNA regulons: puf3p in fungi as an example.}, journal = {PLoS genetics}, volume = {6}, number = {7}, pages = {e1001030}, pmid = {20661438}, issn = {1553-7404}, mesh = {*Biological Evolution ; Codon ; Gene Expression Regulation, Fungal ; Genome, Fungal ; Mitochondria/genetics ; RNA, Fungal/*genetics ; RNA-Binding Proteins/*genetics ; Regulon/*genetics ; Saccharomyces cerevisiae Proteins/*genetics ; Saccharomycetales/*genetics ; Transcription, Genetic ; }, abstract = {Genome-wide studies of post-transcriptional mRNA regulation in model organisms indicate a "post-transcriptional RNA regulon" model, in which a set of functionally related genes is regulated by mRNA-binding RNAs or proteins. One well-studied post-transcriptional regulon by Puf3p functions in mitochondrial biogenesis in budding yeast. The evolution of the Puf3p regulon remains unclear because previous studies have shown functional divergence of Puf3p regulon targets among yeast, fruit fly, and humans. By analyzing evolutionary patterns of Puf3p and its targeted genes in forty-two sequenced fungi, we demonstrated that, although the Puf3p regulon is conserved among all of the studied fungi, the dedicated regulation of mitochondrial biogenesis by Puf3p emerged only in the Saccharomycotina clade. Moreover, the evolution of the Puf3p regulon was coupled with evolution of codon usage bias in down-regulating expression of genes that function in mitochondria in yeast species after genome duplication. Our results provide a scenario for how evolution like a tinker exploits pre-existing materials of a conserved post-transcriptional regulon to regulate gene expression for novel functional roles.}, }
@article {pmid20659421, year = {2011}, author = {Hewitt, V and Alcock, F and Lithgow, T}, title = {Minor modifications and major adaptations: the evolution of molecular machines driving mitochondrial protein import.}, journal = {Biochimica et biophysica acta}, volume = {1808}, number = {3}, pages = {947-954}, doi = {10.1016/j.bbamem.2010.07.019}, pmid = {20659421}, issn = {0006-3002}, mesh = {Animals ; Evolution, Molecular ; Humans ; Intracellular Membranes/*metabolism ; Membrane Proteins/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Protein Transport ; }, abstract = {Bacterial endosymbionts gave rise to mitochondria in a process that depended on the acquisition of protein import pathways. Modification and in some cases major re-tooling of the endosymbiont's cellular machinery produced these pathways, establishing mitochondria as organelles common to all eukaryotic cells. The legacy of this evolutionary tinkering can be seen in the homologies and structural similarities between mitochondrial protein import machinery and modern day bacterial proteins. Comparative analysis of these systems is revealing both possible routes for the evolution of the mitochondrial membrane translocases and a greater understanding of the mechanisms behind mitochondrial protein import. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.}, }
@article {pmid20659325, year = {2010}, author = {Syrjänen, L and Tolvanen, M and Hilvo, M and Olatubosun, A and Innocenti, A and Scozzafava, A and Leppiniemi, J and Niederhauser, B and Hytönen, VP and Gorr, TA and Parkkila, S and Supuran, CT}, title = {Characterization of the first beta-class carbonic anhydrase from an arthropod (Drosophila melanogaster) and phylogenetic analysis of beta-class carbonic anhydrases in invertebrates.}, journal = {BMC biochemistry}, volume = {11}, number = {}, pages = {28}, pmid = {20659325}, issn = {1471-2091}, mesh = {Amino Acid Sequence ; Animals ; Carbonic Anhydrases/*chemistry/*classification/genetics ; Databases, Protein ; Dimerization ; Drosophila Proteins/*chemistry/*classification/genetics ; Drosophila melanogaster/*enzymology ; Enzyme Inhibitors/chemistry/pharmacology ; Kinesics ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; Sulfonamides/chemistry/pharmacology ; }, abstract = {BACKGROUND: The beta-carbonic anhydrase (CA, EC 4.2.1.1) enzymes have been reported in a variety of organisms, but their existence in animals has been unclear. The purpose of the present study was to perform extensive sequence analysis to show that the beta-CAs are present in invertebrates and to clone and characterize a member of this enzyme family from a representative model organism of the animal kingdom, e.g., Drosophila melanogaster.<br><br>RESULTS: The novel beta-CA gene, here named DmBCA, was identified from FlyBase, and its orthologs were searched and reconstructed from sequence databases, confirming the presence of beta-CA sequences in 55 metazoan species. The corresponding recombinant enzyme was produced in Sf9 insect cells, purified, kinetically characterized, and its inhibition was investigated with a series of simple, inorganic anions. Holoenzyme molecular mass was defined by dynamic light scattering analysis and gel filtration, and the results suggested that the holoenzyme is a dimer. Double immunostaining confirmed predictions based on sequence analysis and localized DmBCA protein to mitochondria. The enzyme showed high CO2 hydratase activity, with a kcat of 9.5 x 105 s-1 and a kcat/KM of 1.1 x 108 M-1s-1. DmBCA was appreciably inhibited by the clinically-used sulfonamide acetazolamide, with an inhibition constant of 49 nM. It was moderately inhibited by halides, pseudohalides, hydrogen sulfide, bisulfite and sulfate (KI values of 0.67 - 1.36 mM) and more potently by sulfamide (KI of 0.15 mM). Bicarbonate, nitrate, nitrite and phenylarsonic/boronic acids were much weaker inhibitors (KIs of 26.9 - 43.7 mM).<br><br>CONCLUSIONS: The Drosophila beta-CA represents a highly active mitochondrial enzyme that is a potential model enzyme for anti-parasitic drug development.}, }
@article {pmid20652018, year = {2010}, author = {Chou, JY and Hung, YS and Lin, KH and Lee, HY and Leu, JY}, title = {Multiple molecular mechanisms cause reproductive isolation between three yeast species.}, journal = {PLoS biology}, volume = {8}, number = {7}, pages = {e1000432}, pmid = {20652018}, issn = {1545-7885}, mesh = {Aerobiosis/genetics ; Cell Nucleus/genetics/metabolism ; Crosses, Genetic ; Evolution, Molecular ; Gene Expression Regulation, Fungal ; Genes, Fungal/genetics ; Genome, Mitochondrial/genetics ; Haploidy ; Introns/genetics ; Mitochondria/genetics ; Mutation/genetics ; Phylogeny ; Reproduction ; Saccharomyces/*genetics ; Species Specificity ; }, abstract = {Nuclear-mitochondrial conflict (cytonuclear incompatibility) is a specific form of Dobzhansky-Muller incompatibility previously shown to cause reproductive isolation in two yeast species. Here, we identified two new incompatible genes, MRS1 and AIM22, through a systematic study of F2 hybrid sterility caused by cytonuclear incompatibility in three closely related Saccharomyces species (S. cerevisiae, S. paradoxus, and S. bayanus). Mrs1 is a nuclear gene product required for splicing specific introns in the mitochondrial COX1, and Aim22 is a ligase encoded in the nucleus that is required for mitochondrial protein lipoylation. By comparing different species, our result suggests that the functional changes in MRS1 are a result of coevolution with changes in the COX1 introns. Further molecular analyses demonstrate that three nonsynonymous mutations are responsible for the functional differences of Mrs1 between these species. Functional complementation assays to determine when these incompatible genes altered their functions show a strong correlation between the sequence-based phylogeny and the evolution of cytonuclear incompatibility. Our results suggest that nuclear-mitochondrial incompatibility may represent a general mechanism of reproductive isolation during yeast evolution.}, }
@article {pmid20646326, year = {2010}, author = {Singh, SK and Roy, S and Choudhury, SR and Sengupta, DN}, title = {DNA repair and recombination in higher plants: insights from comparative genomics of Arabidopsis and rice.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {443}, pmid = {20646326}, issn = {1471-2164}, mesh = {Amino Acid Sequence ; Arabidopsis/cytology/*genetics ; Chloroplasts/genetics ; *DNA Repair ; Evolution, Molecular ; Gene Duplication ; Genes, Plant/genetics ; Genome, Plant/*genetics ; *Genomics ; Humans ; Mitochondria/genetics ; Molecular Sequence Data ; Oryza/cytology/*genetics ; Plant Proteins/chemistry/genetics ; *Recombination, Genetic ; Species Specificity ; }, abstract = {BACKGROUND: The DNA repair and recombination (DRR) proteins protect organisms against genetic damage, caused by environmental agents and other genotoxic agents, by removal of DNA lesions or helping to abide them.<br><br>RESULTS: We identified genes potentially involved in DRR mechanisms in Arabidopsis and rice using similarity searches and conserved domain analysis against proteins known to be involved in DRR in human, yeast and E. coli. As expected, many of DRR genes are very similar to those found in other eukaryotes. Beside these eukaryotes specific genes, several prokaryotes specific genes were also found to be well conserved in plants. In Arabidopsis, several functionally important DRR gene duplications are present, which do not occur in rice. Among DRR proteins, we found that proteins belonging to the nucleotide excision repair pathway were relatively more conserved than proteins needed for the other DRR pathways. Sub-cellular localization studies of DRR gene suggests that these proteins are mostly reside in nucleus while gene drain in between nucleus and cell organelles were also found in some cases.<br><br>CONCLUSIONS: The similarities and dissimilarities in between plants and other organisms' DRR pathways are discussed. The observed differences broaden our knowledge about DRR in the plants world, and raises the potential question of whether differentiated functions have evolved in some cases. These results, altogether, provide a useful framework for further experimental studies in these organisms.}, }
@article {pmid20644710, year = {2010}, author = {Balabaskaran Nina, P and Dudkina, NV and Kane, LA and van Eyk, JE and Boekema, EJ and Mather, MW and Vaidya, AB}, title = {Highly divergent mitochondrial ATP synthase complexes in Tetrahymena thermophila.}, journal = {PLoS biology}, volume = {8}, number = {7}, pages = {e1000418}, pmid = {20644710}, issn = {1545-7885}, support = {P01 HL081427/HL/NHLBI NIH HHS/United States ; R01 AI028398/AI/NIAID NIH HHS/United States ; R01 AI053148/AI/NIAID NIH HHS/United States ; R56 AI028398/AI/NIAID NIH HHS/United States ; }, mesh = {Adenosine Diphosphate/pharmacology ; Amino Acid Sequence ; Chromatography, Liquid ; Conserved Sequence ; Evolution, Molecular ; *Genetic Variation/drug effects ; Mass Spectrometry ; Mitochondrial Proton-Translocating ATPases/chemistry/*genetics ; Models, Molecular ; Molecular Sequence Data ; Multienzyme Complexes/chemistry/*genetics ; Oxidative Phosphorylation/drug effects ; Oxygen Consumption/drug effects ; Phylogeny ; Protein Subunits/chemistry/metabolism ; Sequence Alignment ; Tetrahymena thermophila/drug effects/*enzymology/*genetics ; }, abstract = {The F-type ATP synthase complex is a rotary nano-motor driven by proton motive force to synthesize ATP. Its F(1) sector catalyzes ATP synthesis, whereas the F(o) sector conducts the protons and provides a stator for the rotary action of the complex. Components of both F(1) and F(o) sectors are highly conserved across prokaryotes and eukaryotes. Therefore, it was a surprise that genes encoding the a and b subunits as well as other components of the F(o) sector were undetectable in the sequenced genomes of a variety of apicomplexan parasites. While the parasitic existence of these organisms could explain the apparent incomplete nature of ATP synthase in Apicomplexa, genes for these essential components were absent even in Tetrahymena thermophila, a free-living ciliate belonging to a sister clade of Apicomplexa, which demonstrates robust oxidative phosphorylation. This observation raises the possibility that the entire clade of Alveolata may have invented novel means to operate ATP synthase complexes. To assess this remarkable possibility, we have carried out an investigation of the ATP synthase from T. thermophila. Blue native polyacrylamide gel electrophoresis (BN-PAGE) revealed the ATP synthase to be present as a large complex. Structural study based on single particle electron microscopy analysis suggested the complex to be a dimer with several unique structures including an unusually large domain on the intermembrane side of the ATP synthase and novel domains flanking the c subunit rings. The two monomers were in a parallel configuration rather than the angled configuration previously observed in other organisms. Proteomic analyses of well-resolved ATP synthase complexes from 2-D BN/BN-PAGE identified orthologs of seven canonical ATP synthase subunits, and at least 13 novel proteins that constitute subunits apparently limited to the ciliate lineage. A mitochondrially encoded protein, Ymf66, with predicted eight transmembrane domains could be a substitute for the subunit a of the F(o) sector. The absence of genes encoding orthologs of the novel subunits even in apicomplexans suggests that the Tetrahymena ATP synthase, despite core similarities, is a unique enzyme exhibiting dramatic differences compared to the conventional complexes found in metazoan, fungal, and plant mitochondria, as well as in prokaryotes. These findings have significant implications for the origins and evolution of a central player in bioenergetics.}, }
@article {pmid20641018, year = {2010}, author = {Feng, J and Zhao, J and Li, J and Zhang, L and Jiang, L}, title = {Functional characterization of the PP2C phosphatase CaPtc2p in the human fungal pathogen Candida albicans.}, journal = {Yeast (Chichester, England)}, volume = {27}, number = {9}, pages = {753-764}, doi = {10.1002/yea.1778}, pmid = {20641018}, issn = {1097-0061}, mesh = {Antifungal Agents/toxicity ; Azoles/toxicity ; Candida albicans/drug effects/*enzymology/genetics ; Cytoplasm/enzymology ; Fungal Proteins/genetics/*metabolism ; Gene Deletion ; Gene Expression Profiling ; Humans ; Hydroxyurea/toxicity ; Methyl Methanesulfonate/toxicity ; Mitochondria/enzymology ; Phosphoprotein Phosphatases/deficiency/*metabolism ; Phylogeny ; Protein Phosphatase 2C ; Sequence Homology, Amino Acid ; Sodium Dodecyl Sulfate/toxicity ; }, abstract = {Type 2C protein phosphatases (PP2C) are monomeric enzymes and their activities require the presence of magnesium or manganese ion. There are seven PP2C-like genes in Candida albicans. In this study, we demonstrate that CaPtc2p is a PP2C phosphatase. Surprisingly, in addition to the cytoplasmic localization, CaPtc2p is partially associated with mitochondria in yeast-form and filamentous cells of C. albicans. Expression of CaPTC2 is developmentally regulated during the serum-induced filamentation. Deletion of CaPTC2 renders C. albicans cells sensitive to SDS and azole antifungals, as well as the DNA methylation agent methylmethane sulphonate and the DNA synthesis inhibitor hydroxyurea. Therefore, CaPtc2p might fulfil multiple functions, including the regulation of mitochondrial physiology and checkpoint recovery from DNA damage in C. albicans cells.}, }
@article {pmid20640581, year = {2010}, author = {Li, A and Chen, Y and Zhao, X and Niu, Y and Cong, P and Zhang, Z and Chen, W and Jiang, W and Mo, D}, title = {Characterization and transcriptional regulation analysis of the porcine TNFAIP8L2 gene.}, journal = {Molecular genetics and genomics : MGG}, volume = {284}, number = {3}, pages = {185-195}, pmid = {20640581}, issn = {1617-4623}, mesh = {Animals ; Base Sequence ; Binding Sites/genetics ; Cell Line ; Cell Nucleus/metabolism ; Chromosomes, Mammalian/genetics ; Cloning, Molecular ; Endoplasmic Reticulum/metabolism ; *Gene Expression Profiling ; *Gene Expression Regulation ; Green Fluorescent Proteins/genetics/metabolism ; Intracellular Signaling Peptides and Proteins/classification/*genetics ; Luciferases/genetics/metabolism ; Microscopy, Confocal ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Binding ; Radiation Hybrid Mapping ; Regulatory Sequences, Nucleic Acid/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Swine/*genetics ; Tetradecanoylphorbol Acetate/pharmacology ; Transcription Factor AP-1/metabolism ; Transcription Initiation Site ; Transcription, Genetic/drug effects ; }, abstract = {Tumor necrosis factor alpha-induced protein 8-like 2 (TNFAIP8L2) is a new member of the tumor necrosis factor-alpha-induced protein 8 (TNFAIP8) family that functions as an important factor in the maintenance of immune homeostasis. In this study, we cloned the cDNA sequences and analyzed the genomic structure of porcine TNFAIP8L2. RH mapping using the IMpRH panel showed that this gene was closely linked to microsatellite marker SW512 in pig chromosome 4. Subcellular localization analysis showed GFP-TNFAIP8L2 fusion protein distributed in nucleus as well as cytoplasm including mitochondria and endoplasmic reticulum. Real-time PCR analysis revealed that porcine TNFAIP8L2 was more highly expressed in spleen than other tissues. To understand its characterization of transcriptional regulation, we cloned approximately 2 kb of 5'-regulatory region upstream to the porcine TNFAIP8L2 translational start site and generated sequential deletion constructs evaluated in dual-luciferase reporter assay. The results demonstrated that its core promoter is 435 base pairs (bp) upstream to the transcription initiation site. Then, site-directed mutation experiment combined with electrophoretic mobility shift assay (EMSA) indicated that M-CAT binding factor (MCBF) and activator protein 1 (AP-1) were important transcription factors for porcine TNFAIP8L2. These findings provide an important basis for further understanding of porcine TNFAIP8L2 regulation and function in swine.}, }
@article {pmid20638486, year = {2011}, author = {Cannon, MV and Dunn, DA and Irwin, MH and Brooks, AI and Bartol, FF and Trounce, IA and Pinkert, CA}, title = {Xenomitochondrial mice: investigation into mitochondrial compensatory mechanisms.}, journal = {Mitochondrion}, volume = {11}, number = {1}, pages = {33-39}, pmid = {20638486}, issn = {1872-8278}, support = {N01ES45533/ES/NIEHS NIH HHS/United States ; R21 RR016286/RR/NCRR NIH HHS/United States ; R21 RR016286-01/RR/NCRR NIH HHS/United States ; RR16286/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Cell Nucleus/genetics/metabolism ; Cells, Cultured ; DNA, Mitochondrial/*genetics/metabolism ; Disease Models, Animal ; Evolution, Molecular ; *Gene Expression Regulation ; Humans ; *Hybridization, Genetic ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Mitochondria/*genetics/metabolism/pathology ; Mitochondrial Proteins/genetics/*metabolism ; Neurodegenerative Diseases/genetics/*pathology ; Oligonucleotide Array Sequence Analysis ; Phenotype ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Xenomitochondrial mice, harboring evolutionarily divergent Mus terricolor mitochondrial DNA (mtDNA) on a Mus musculus domesticus nuclear background (B6NTac(129S6)-mt(M. terricolor)/Capt; line D7), were subjected to molecular and phenotypic analyses. No overt in vivo phenotype was identified in contrast to in vitro xenomitochondrial cybrid studies. Microarray analyses revealed differentially expressed genes in xenomitochondrial mice, though none were directly involved in mitochondrial function. qRT-PCR revealed upregulation of mt-Co2 in xenomitochondrial mice. These results illustrate that cellular compensatory mechanisms for mild mitochondrial dysfunction alter mtDNA gene expression at a proteomic and/or translational level. Understanding these mechanisms will facilitate the development of therapeutics for mitochondrial disorders.}, }
@article {pmid20637721, year = {2011}, author = {Yogev, O and Pines, O}, title = {Dual targeting of mitochondrial proteins: mechanism, regulation and function.}, journal = {Biochimica et biophysica acta}, volume = {1808}, number = {3}, pages = {1012-1020}, doi = {10.1016/j.bbamem.2010.07.004}, pmid = {20637721}, issn = {0006-3002}, mesh = {Animals ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Protein Transport ; }, abstract = {One solution found in evolution to increase the number of cellular functions, without increasing the number of genes, is distribution of single gene products to more than one cellular compartment. It is well documented that in eukaryotic cells, molecules of one protein can be located in several subcellular locations, a phenomenon termed dual targeting, dual localization, or dual distribution. The differently localized proteins are coined in this review "echoforms" indicating repetitious forms of the same protein (echo in Greek denotes repetition) distinctly placed in the cell. This term replaces the term to "isoproteins" or "isoenzymes" which are reserved for proteins with the same activity but different amino acid sequences. Echoforms are identical or nearly identical, even though, as referred to in this review may, in some cases, surprisingly have a totally different function in the different compartments. With regard to mitochondria, our operational definition of dual targeted proteins refers to situations in which one of the echoforms is translocated through/into a mitochondrial membrane. In this review we ask how, when and why mitochondrial proteins are dual localized in the cell. We describe mechanisms of dual targeting of proteins between mitochondria and other compartments of the eukaryotic cell. In particular, we have paid attention to situations in which dual localization is regulated in time, location or function. In addition, we have attempted to provide a broader view concerning the phenomenon of dual localization of proteins by looking at mechanisms that are beyond our simple definition of dual targeting. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.}, }
@article {pmid20637230, year = {2010}, author = {Goldfine, H}, title = {The appearance, disappearance and reappearance of plasmalogens in evolution.}, journal = {Progress in lipid research}, volume = {49}, number = {4}, pages = {493-498}, doi = {10.1016/j.plipres.2010.07.003}, pmid = {20637230}, issn = {1873-2194}, mesh = {Animals ; Bacteria/metabolism ; *Biological Evolution ; Molecular Structure ; Oxygen/metabolism ; *Plasmalogens/biosynthesis/chemistry ; Reactive Oxygen Species/metabolism ; }, abstract = {Plasmalogens, 1-O-alk-1'-enyl 2-acyl glycerol phospholipids and glycolipids, seem to have evolved first in anaerobic bacteria, but they did not persist when facultative and aerobic species appeared after the concentration of oxygen increased in the early earth's history. Later, when aerobic animal cells appeared with their mitochondria and other intracellular organelles, plasmalogen biosynthesis requiring molecular oxygen, reappeared. The possible reasons for the disappearance and reappearance of plasmalogens in the evolution of life on earth are discussed. The sensitivity of plasmalogens to reactive oxygen species may have caused their disappearance when respiration first evolved. Special features of plasmalogen structure and the resulting lipid packing may account for their reappearance.}, }
@article {pmid20637123, year = {2010}, author = {Janz, D and Behnke, K and Schnitzler, JP and Kanawati, B and Schmitt-Kopplin, P and Polle, A}, title = {Pathway analysis of the transcriptome and metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms.}, journal = {BMC plant biology}, volume = {10}, number = {}, pages = {150}, pmid = {20637123}, issn = {1471-2229}, mesh = {*Adaptation, Physiological ; *Biological Evolution ; Energy Metabolism ; *Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Metabolome ; Plant Leaves/chemistry/metabolism ; Populus/genetics/metabolism/*physiology ; Protein Transport ; Reproducibility of Results ; Sequence Homology, Nucleic Acid ; Sodium Chloride/*metabolism ; Starch/metabolism ; Stress, Physiological ; Sucrose/metabolism ; }, abstract = {BACKGROUND: Populus euphratica is a salt tolerant and Populus x canescens a salt sensitive poplar species. Because of low transcriptional responsiveness of P. euphratica to salinity we hypothesized that this species exhibits an innate activation of stress protective genes compared with salt sensitive poplars. To test this hypothesis, the transcriptome and metabolome of mature unstressed leaves of P. euphratica and P. x canescens were compared by whole genome microarray analyses and FT-ICR-MS metabolite profiling.<br><br>RESULTS: Direct cross-species comparison of the transcriptomes of the two poplar species from phylogenetically different sections required filtering of the data set. Genes assigned to the GO slim categories 'mitochondria', 'cell wall', 'transport', 'energy metabolism' and 'secondary metabolism' were significantly enriched, whereas genes in the categories 'nucleus', 'RNA or DNA binding', 'kinase activity' and 'transcription factor activity' were significantly depleted in P. euphratica compared with P. x canescens. Evidence for a general activation of stress relevant genes in P. euphratica was not detected. Pathway analyses of metabolome and transcriptome data indicated stronger accumulation of primary sugars, activation of pathways for sugar alcohol production, and faster consumption of secondary metabolites in P. euphratica compared to P. x canescens. Physiological measurements showing higher respiration, higher tannin and soluble phenolic contents as well as enrichment of glucose and fructose in P. euphratica compared to P. x canescens corroborated the results of pathway analyses.<br><br>CONCLUSION: P. euphratica does not rely on general over-expression of stress pathways to tolerate salt stress. Instead, it exhibits permanent activation of control mechanisms for osmotic adjustment (sugar and sugar alcohols), ion compartmentalization (sodium, potassium and other metabolite transporters) and detoxification of reactive oxygen species (phenolic compounds). The evolutionary adaptation of P. euphratica to saline environments is apparently linked with higher energy requirement of cellular metabolism and a loss of transcriptional regulation.}, }
@article {pmid20633537, year = {2010}, author = {Sterky, FH and Ruzzenente, B and Gustafsson, CM and Samuelsson, T and Larsson, NG}, title = {LRPPRC is a mitochondrial matrix protein that is conserved in metazoans.}, journal = {Biochemical and biophysical research communications}, volume = {398}, number = {4}, pages = {759-764}, doi = {10.1016/j.bbrc.2010.07.019}, pmid = {20633537}, issn = {1090-2104}, mesh = {Animals ; Conserved Sequence ; HeLa Cells ; Humans ; Mice ; Mice, Inbred C57BL ; Mitochondria/*metabolism ; Mitochondrial Proteins/classification/genetics/*metabolism ; Neoplasm Proteins/classification/genetics/*metabolism ; Phylogeny ; Protein Structure, Tertiary ; Protein Transport ; Repetitive Sequences, Amino Acid ; }, abstract = {LRPPRC (also called LRP130) is an RNA-binding pentatricopeptide repeat protein. LRPPRC has been recognized as a mitochondrial protein, but has also been shown to regulate nuclear gene transcription and to bind specific RNA molecules in both the nucleus and the cytoplasm. We here present a bioinformatic analysis of the LRPPRC primary sequence, which reveals that orthologs to the LRPPRC gene are restricted to metazoan cells and that all of the corresponding proteins contain mitochondrial targeting signals. To address the subcellular localization further, we have carefully analyzed LRPPRC in mammalian cells and identified a single isoform that is exclusively localized to mitochondria. The LRPPRC protein is imported to the mitochondrial matrix and its mitochondrial targeting sequence is cleaved upon entry.}, }
@article {pmid20625544, year = {2010}, author = {Tsankov, AM and Thompson, DA and Socha, A and Regev, A and Rando, OJ}, title = {The role of nucleosome positioning in the evolution of gene regulation.}, journal = {PLoS biology}, volume = {8}, number = {7}, pages = {e1000414}, pmid = {20625544}, issn = {1545-7885}, support = {R01 CA119176/CA/NCI NIH HHS/United States ; GM079205/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 GM079205-03/GM/NIGMS NIH HHS/United States ; R01 GM079205-04/GM/NIGMS NIH HHS/United States ; R01 CA119176-01/CA/NCI NIH HHS/United States ; R01 GM079205/GM/NIGMS NIH HHS/United States ; DP1 OD003958/OD/NIH HHS/United States ; }, mesh = {Alternative Splicing/genetics ; Ascomycota/enzymology/*genetics ; Chromosome Positioning/*genetics ; Conserved Sequence ; Cytoskeleton/genetics ; DNA Packaging/genetics ; DNA-Directed RNA Polymerases/metabolism ; *Evolution, Molecular ; Fungal Proteins/genetics/metabolism ; Gene Duplication ; *Gene Expression Regulation, Fungal ; Genes, Fungal/genetics ; Meiosis/genetics ; Mitochondria/genetics ; Nuclear Pore/genetics ; Nucleosomes/*genetics ; Open Reading Frames/genetics ; Peroxisomes/genetics ; Phylogeny ; Proteasome Endopeptidase Complex/genetics ; Species Specificity ; Transcription Factors/genetics/metabolism ; }, abstract = {Chromatin organization plays a major role in gene regulation and can affect the function and evolution of new transcriptional programs. However, it can be difficult to decipher the basis of changes in chromatin organization and their functional effect on gene expression. Here, we present a large-scale comparative genomic analysis of the relationship between chromatin organization and gene expression, by measuring mRNA abundance and nucleosome positions genome-wide in 12 Hemiascomycota yeast species. We found substantial conservation of global and functional chromatin organization in all species, including prominent nucleosome-free regions (NFRs) at gene promoters, and distinct chromatin architecture in growth and stress genes. Chromatin organization has also substantially diverged in both global quantitative features, such as spacing between adjacent nucleosomes, and in functional groups of genes. Expression levels, intrinsic anti-nucleosomal sequences, and trans-acting chromatin modifiers all play important, complementary, and evolvable roles in determining NFRs. We identify five mechanisms that couple chromatin organization to evolution of gene regulation and have contributed to the evolution of respiro-fermentation and other key systems, including (1) compensatory evolution of alternative modifiers associated with conserved chromatin organization, (2) a gradual transition from constitutive to trans-regulated NFRs, (3) a loss of intrinsic anti-nucleosomal sequences accompanying changes in chromatin organization and gene expression, (4) re-positioning of motifs from NFRs to nucleosome-occluded regions, and (5) the expanded use of NFRs by paralogous activator-repressor pairs. Our study sheds light on the molecular basis of chromatin organization, and on the role of chromatin organization in the evolution of gene regulation.}, }
@article {pmid20625286, year = {2010}, author = {Cioffi, F and Lanni, A and Goglia, F}, title = {Thyroid hormones, mitochondrial bioenergetics and lipid handling.}, journal = {Current opinion in endocrinology, diabetes, and obesity}, volume = {17}, number = {5}, pages = {402-407}, doi = {10.1097/MED.0b013e32833cf354}, pmid = {20625286}, issn = {1752-2978}, mesh = {Acetates/pharmacology/therapeutic use ; Adiposity/drug effects ; Anilides/pharmacology/therapeutic use ; Animals ; Atherosclerosis/drug therapy ; Cardiovascular Diseases/drug therapy ; Clinical Trials as Topic ; Diiodothyronines/pharmacology/therapeutic use ; Dyslipidemias/drug therapy ; Energy Metabolism/drug effects ; Fatty Liver/drug therapy ; Humans ; *Lipid Metabolism ; Mice ; Mitochondria/*metabolism ; Obesity/drug therapy ; Phenols/pharmacology/therapeutic use ; Rats ; Thyroid Hormones/*metabolism/pharmacology ; }, abstract = {PURPOSE OF REVIEW: The article is principally intended to describe the recent evolutions in the field of research concerned with the metabolic actions of thyroid hormones and those of some of their metabolites or derivatives. Mitochondria, as a result of their functions, represent the principal objective of scientists investigating the mechanisms underlying the effects of thyroid hormones or their metabolites/derivatives.<br><br>RECENT FINDINGS: Indeed, some important recent findings concern these organelles, and in particular mitochondrial uncoupling and its modulation by effectors. Traditionally, thyroxine (T4) and tri-iodo-L-thyronine (T3) were the only thyroid hormones considered to have metabolic effects, and they alone were considered for potential as agents that might counteract some important abnormalities such as dyslipidaemias and obesity. Several observations, however, led to a reconsideration of this idea. In recent years, studies dealing with the biological activities of some natural metabolites or structural analogues of thyroid hormones have revealed abilities to ameliorate some major worldwide medical problems, such as artherosclerosis, obesity and cardiovascular diseases. Among natural metabolites, 3,5-diiodothyronine (T2) has been shown to powerfully reduce adiposity and dyslipidaemia and to reverse hepatic steatosis without unfavourable side-effects usually observed when T3 or T4 is used. Examples of synthetic analogues are GC-1 (or sobetirome) and KB2115 (or eprotirome) which show ipolipidaemic and antiaterogenic capacities. Clinical trials are in progress for these last agents.<br><br>SUMMARY: In view of the above-mentioned actions, some of these compounds are now undergoing clinical trials and may have important implications for clinical practice or researches in the field of both endocrinology and metabolic-related abnormalities such as diabetes and dyslipidaemias.}, }
@article {pmid20624849, year = {2011}, author = {Brandão, MM and Silva-Filho, MC}, title = {Evolutionary history of Arabidopsis thaliana aminoacyl-tRNA synthetase dual-targeted proteins.}, journal = {Molecular biology and evolution}, volume = {28}, number = {1}, pages = {79-85}, doi = {10.1093/molbev/msq176}, pmid = {20624849}, issn = {1537-1719}, mesh = {Amino Acyl-tRNA Synthetases/*genetics ; Arabidopsis/*enzymology/*genetics ; Arabidopsis Proteins/classification/*genetics ; Bacterial Proteins/classification/genetics ; *Biological Evolution ; Databases, Protein ; Gene Expression ; Gene Transfer, Horizontal ; Microarray Analysis ; Molecular Sequence Data ; Phylogeny ; Protein Interaction Mapping ; }, abstract = {Aminoacyl-transfer RNA (tRNA) synthetases (aaRS) are key players in translation and act early in protein synthesis by mediating the attachment of amino acids to their cognate tRNA molecules. In plants, protein synthesis may occur in three subcellular compartments (cytosol, mitochondria, and chloroplasts), which requires multiple versions of the protein to be correctly delivered to its proper destination. The organellar aaRS are nuclear encoded and equipped with targeting information at the N-terminal sequence, which enables them to be specifically translocated to their final location. Most of the aaRS families present organellar proteins that are dual targeted to mitochondria and chloroplasts. Here, we examine the dual targeting behavior of aaRS from an evolutionary perspective. Our results show that Arabidopsis thaliana aaRS sequences are a result of a horizontal gene transfer event from bacteria. However, there is no evident bias indicating one single ancestor (Cyanobacteria or Proteobacteria). The dual-targeted aaRS phylogenetic relationship was characterized into two different categories (paralogs and homologs) depending on the state recovered for both dual-targeted and cytosolic proteins. Taken together, our results suggest that the dual-targeted condition is a gain-of-function derived from gene duplication. Selection may have maintained the original function in at least one of the copies as the additional copies diverged.}, }
@article {pmid20624744, year = {2010}, author = {McComish, BJ and Hills, SF and Biggs, PJ and Penny, D}, title = {Index-free de novo assembly and deconvolution of mixed mitochondrial genomes.}, journal = {Genome biology and evolution}, volume = {2}, number = {}, pages = {410-424}, pmid = {20624744}, issn = {1759-6653}, mesh = {Animals ; Base Composition ; Base Sequence ; Computer Simulation ; Contig Mapping ; DNA Primers/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Evolution, Molecular ; Gastropoda/genetics ; Genome, Human ; *Genome, Mitochondrial ; Humans ; Locus Control Region ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; Rats ; Sequence Alignment ; Sequence Analysis, DNA/*methods/statistics &amp; numerical data ; }, abstract = {Second-generation sequencing technology has allowed a very large increase in sequencing throughput. In order to make use of this high throughput, we have developed a pipeline for sequencing and de novo assembly of multiple mitochondrial genomes without the costs of indexing. Simulation studies on a mixture of diverse animal mitochondrial genomes showed that mitochondrial genomes could be reassembled from a high coverage of short (35 nt) reads, such as those generated by a second-generation Illumina Genome Analyzer. We then assessed this experimentally with long-range polymerase chain reaction products from mitochondria of a human, a rat, a bird, a frog, an insect, and a mollusc. Comparison with reference genomes was used for deconvolution of the assembled contigs rather than for mapping of sequence reads. As proof of concept, we report the complete mollusc mitochondrial genome of an olive shell (Amalda northlandica). It has a very unusual putative control region, which contains a structure that would probably only be detectable by next-generation sequencing. The general approach has considerable potential, especially when combined with indexed sequencing of different groups of genomes.}, }
@article {pmid20624730, year = {2010}, author = {Pérez-Brocal, V and Shahar-Golan, R and Clark, CG}, title = {A linear molecule with two large inverted repeats: the mitochondrial genome of the stramenopile Proteromonas lacertae.}, journal = {Genome biology and evolution}, volume = {2}, number = {}, pages = {257-266}, pmid = {20624730}, issn = {1759-6653}, support = {078566//Wellcome Trust/United Kingdom ; }, mesh = {Base Sequence ; Blastocystis/genetics ; Chromosome Mapping ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Gene Order ; *Genome, Mitochondrial ; Inverted Repeat Sequences ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; Stramenopiles/*genetics ; }, abstract = {Mitochondrial evolution has given rise to a complex array of organelles, ranging from classical aerobic mitochondria to mitochondrial remnants known as hydrogenosomes and mitosomes. The latter are found in anaerobic eukaryotes, and these highly derived organelles often retain only scant evidence of their mitochondrial origins. Intermediate evolutionary stages have also been reported as facultatively or even strictly anaerobic mitochondria, and hydrogenosomes that still retain some mitochondrial features. However, the diversity among these organelles with transitional features remains rather unclear and barely studied. Here, we report the sequence, structure, and gene content of the mitochondrial DNA of the anaerobic stramenopile Proteromonas lacertae. It has a linear genome with a unique central region flanked by two identical large inverted repeats containing numerous genes and "telomeres" with short inverted repeats. Comparison with the organelle genome of the strictly anaerobic human parasite Blastocystis reveals that, despite the close similarity of the sequences, features such as the genome structure display striking differences. It remains unclear whether the virtually identical gene repertoires are the result of convergence or descent.}, }
@article {pmid20621843, year = {2010}, author = {Leroy, I and Khosrobakhsh, F and Diot, A and Daloyau, M and Arnauné-Pelloquin, L and Cavelier, C and Emorine, LJ and Belenguer, P}, title = {Processing of the dynamin Msp1p in S. pombe reveals an evolutionary switch between its orthologs Mgm1p in S. cerevisiae and OPA1 in mammals.}, journal = {FEBS letters}, volume = {584}, number = {14}, pages = {3153-3157}, doi = {10.1016/j.febslet.2010.05.060}, pmid = {20621843}, issn = {1873-3468}, mesh = {Adenosine Triphosphatases/genetics/metabolism ; Animals ; Biological Evolution ; Dynamins/genetics/*metabolism ; Humans ; Mammals/genetics/metabolism ; Membrane Fusion/genetics ; Mitochondria/genetics/metabolism ; Optic Atrophy, Autosomal Dominant/genetics/metabolism ; Protein Isoforms/genetics/*metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; Schizosaccharomyces/genetics/*metabolism ; }, abstract = {Mitochondrial fusion depends on the evolutionary conserved dynamin, OPA1/Mgm1p/Msp1p, whose activity is controlled by proteolytic processing. Since processing diverges between Mgm1p (Saccharomyces cerevisiae) and OPA1 (mammals), we explored this process in another model, Msp1p in Schizosaccharomyces pombe. Generation of the short isoform of Msp1p neither results from the maturation of the long isoform nor correlates with mitochondrial ATP levels. Msp1p is processed by rhomboid and a protease of the matrix ATPase associated with various cellular activities (m-AAA) family. The former is involved in the generation of short Msp1p and the latter in the stability of long Msp1p. These results reveal that Msp1p processing may represent an evolutionary switch between Mgm1p and OPA1.}, }
@article {pmid20617318, year = {2010}, author = {Salmans, ML and Chaw, SM and Lin, CP and Shih, AC and Wu, YW and Mulligan, RM}, title = {Editing site analysis in a gymnosperm mitochondrial genome reveals similarities with angiosperm mitochondrial genomes.}, journal = {Current genetics}, volume = {56}, number = {5}, pages = {439-446}, pmid = {20617318}, issn = {1432-0983}, mesh = {Base Sequence ; Cycadopsida/*genetics ; Cycas/*genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Genes, Plant ; *Genome, Mitochondrial ; Genome, Plant ; Magnoliopsida/*genetics ; Mitochondria ; Organelles ; *RNA Editing ; RNA, Plant/genetics/metabolism ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; }, abstract = {Sequence analysis of organelle genomes and comprehensive analysis of C-to-U editing sites from flowering and non-flowering plants have provided extensive sequence information from diverse taxa. This study includes the first comprehensive analysis of RNA editing sites from a gymnosperm mitochondrial genome, and utilizes informatics analyses to determine conserved features in the RNA sequence context around editing sites. We have identified 565 editing sites in 21 full-length and 4 partial cDNAs of the 39 protein-coding genes identified from the mitochondrial genome of Cycas taitungensis. The information profiles and RNA sequence context of C-to-U editing sites in the Cycas genome exhibit similarity in the immediate flanking nucleotides. Relative entropy analyses indicate that similar regions in the 5' flanking 20 nucleotides have information content compared to angiosperm mitochondrial genomes. These results suggest that evolutionary constraints exist on the nucleotide sequences immediately adjacent to C-to-U editing sites, and similar regions are utilized in editing site recognition.}, }
@article {pmid20616281, year = {2010}, author = {Ricklefs, RE and Outlaw, DC}, title = {A molecular clock for malaria parasites.}, journal = {Science (New York, N.Y.)}, volume = {329}, number = {5988}, pages = {226-229}, doi = {10.1126/science.1188954}, pmid = {20616281}, issn = {1095-9203}, mesh = {Animals ; Birds/*genetics/*parasitology ; Cytochromes b/*genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; *Genes, Protozoan ; Genetic Speciation ; Haemosporida/classification/*genetics ; Host-Parasite Interactions ; Humans ; Malaria, Avian/parasitology ; Mitochondria/chemistry ; *Phylogeny ; Plasmodium/classification/*genetics ; Plasmodium falciparum/classification/genetics ; Species Specificity ; Time ; }, abstract = {The evolutionary origins of new lineages of pathogens are fundamental to understanding emerging diseases. Phylogenetic reconstruction based on DNA sequences has revealed the sister taxa of human pathogens, but the timing of host-switching events, including the human malaria pathogen Plasmodium falciparum, remains controversial. Here, we establish a rate for cytochrome b evolution in avian malaria parasites relative to its rate in birds. We found that the parasite cytochrome b gene evolves about 60% as rapidly as that of host cytochrome b, corresponding to approximately 1.2% sequence divergence per million years. This calibration puts the origin of P. falciparum at 2.5 million years ago (Ma), the initial radiation of mammalian Plasmodium at 12.8 Ma, and the contemporary global diversity of the Haemosporida across terrestrial vertebrates at 16.2 Ma.}, }
@article {pmid20608164, year = {2010}, author = {Gaziev, AI and Shaĭkhaev, GO}, title = {[Nuclear mitochondrial pseudogenes].}, journal = {Molekuliarnaia biologiia}, volume = {44}, number = {3}, pages = {405-417}, pmid = {20608164}, issn = {0026-8984}, mesh = {Aging/genetics ; Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genome, Human/*genetics ; Humans ; Pseudogenes/*genetics ; }, abstract = {Transfer of genetic material from mitochondria to the nucleus and their integration into the nuclear genome is a continuous and dynamic process. Fragments of mitochondrial DNA (mtDNA) in the nuclear genome are incorporated as non-encoded sequences, which are called nuclear mitochondrial pseudogenes (NUMT-pseudogenes). At present, the formation NUMT-pseudogenes in the nuclear genome is shown in many eukaryotes. They are distributed on different chromosomes, form a "library" of mtDNA fragments, migrated into the nuclear genome and provide important information on the history of the evolution of genomes. Escape of mtDNA from the mitochondria most is associated with damage and mitophagy these organelles. The integration of mtDNA fragments into the nuclear genome may occur during repair of double strand breaks of nuclear DNA (nDNA) arising under the action of endogenous and exogenous agents. Reparation of nDNA double strand breaks with "capture" fragments of mtDNA, occurs by non-homologous end joining and a similar mechanism, but with the involvement microhomology, located on the terminal sequences. Analysis of data allows us to suppose that the rate of formation NUMT-pseudogenes will depend on the rate of double strand breaks in nDNA, activity systems, their repair, as well--the number of mtDNA fragments that have emerged from the organelles, with their further migration into the nucleus. Such situations can be expected, most often after exposure to the damaging agents, in the first place--ionizing radiation. The emergence of new NUMT-pseudogenes, obviously, is changing not only the structure of the genome in the areas of their implementation, but may have a significant impact on the realization of genetic information. Integration NUMT-pseudogenes in the nuclear genome de novo may play a role in the development of various pathologies and aging. NUMT-pseudogenes can make serious errors in analyzing free mtDNA of total cellular DNA (using PCR), as a result of their co-amplification.}, }
@article {pmid20605476, year = {2010}, author = {Regina, TM and Quagliariello, C}, title = {Lineage-specific group II intron gains and losses of the mitochondrial rps3 gene in gymnosperms.}, journal = {Plant physiology and biochemistry : PPB}, volume = {48}, number = {8}, pages = {646-654}, doi = {10.1016/j.plaphy.2010.05.003}, pmid = {20605476}, issn = {1873-2690}, mesh = {Base Sequence ; Cycadopsida/classification/*genetics ; DNA, Plant/chemistry/genetics ; Evolution, Molecular ; Gnetum/genetics ; Introns/*genetics ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Pinaceae/classification/genetics ; Plant Proteins/*genetics ; Ribosomal Proteins/*genetics ; Sequence Analysis, DNA ; }, abstract = {According to PCR assays and sequencing, we now report the shared presence of two rps3 introns, namely the rps3i74 and the rps3i249, in the mitochondria of all the classes representing the surviving lineages of gymnosperms, and unveil several lineages experiencing intron loss. Interestingly, the rps3 intron gains and losses within the four groups of gymnosperms let us sort out the Pinaceae and the non-Pinaceae into intron (+)- and intron (-)-lineages, respectively. Worthy of mention is also the finding that only Gnetum within the Gnetales harbours both the rps3 introns. This intron distribution pattern is consistent with the hypothesis that the two rps3 introns were likely present in the common ancestor of the seed plants and, then, independently lost in the non-Pinaceae during gymnosperm evolution. The derived secondary structural model of the novel group IIA intron improves our understanding of the significance and origin of the extraordinary length polymorphisms observed among rps3i249 orthologs. Despite the remarkable structural plasticity to adopt and reject introns, the rps3 mRNAs undergo accurate processing by splicing and extensive editing in gymnosperm mitochondria. This study provides additional insights into the evolutionarily high dynamics of mitochondrial introns which may come and go in closely related plant species. The turnover of the mitochondrial rps3 group II introns seen among lineages of seed plants further suggests that these introns might be an additional signature to discriminate between particularly cryptical taxonomic groups for which there is a need of a further evaluation of their evolutionary affiliation.}, }
@article {pmid20600209, year = {2010}, author = {Cyran, KA and Kimmel, M}, title = {Alternatives to the Wright-Fisher model: the robustness of mitochondrial Eve dating.}, journal = {Theoretical population biology}, volume = {78}, number = {3}, pages = {165-172}, doi = {10.1016/j.tpb.2010.06.001}, pmid = {20600209}, issn = {1096-0325}, mesh = {Animals ; Chronology as Topic ; Computer Simulation ; Confidence Intervals ; DNA, Mitochondrial/*genetics ; *Extinction, Biological ; Genetic Variation ; Genetics, Population ; Hominidae/*genetics ; Humans ; Mitochondria/genetics ; *Models, Genetic ; Models, Statistical ; Mutation ; Poisson Distribution ; *Population Density ; Selection, Genetic ; }, abstract = {Methods of calculating the distributions of the time to coalescence depend on the underlying model of population demography. In particular, the models assuming deterministic evolution of population size may not be applicable to populations evolving stochastically. Therefore the study of coalescence models involving stochastic demography is important for applications. One interesting approach which includes stochasticity is the O'Connell limit theory of genealogy in branching processes. Our paper explores how many generations are needed for the limiting distributions of O'Connell to become adequate approximations of exact distributions. We perform extensive simulations of slightly supercritical branching processes and compare the results to the O'Connell limits. Coalescent computations under the Wright-Fisher model are compared with limiting O'Connell results and with full genealogy-based predictions. These results are used to estimate the age of the so-called mitochondrial Eve, i.e., the root of the mitochondrial polymorphisms of the modern humans based on the DNA from humans and Neanderthal fossils.}, }
@article {pmid20587059, year = {2010}, author = {Bendich, AJ}, title = {Mitochondrial DNA, chloroplast DNA and the origins of development in eukaryotic organisms.}, journal = {Biology direct}, volume = {5}, number = {}, pages = {42}, pmid = {20587059}, issn = {1745-6150}, mesh = {Animals ; *Biological Evolution ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; Eukaryota/*genetics ; Models, Theoretical ; Plants/genetics ; }, abstract = {BACKGROUND: Several proposals have been made to explain the rise of multicellular life forms. An internal environment can be created and controlled, germ cells can be protected in novel structures, and increased organismal size allows a "division of labor" among cell types. These proposals describe advantages of multicellular versus unicellular organisms at levels of organization at or above the individual cell. I focus on a subsequent phase of evolution, when multicellular organisms initiated the process of development that later became the more complex embryonic development found in animals and plants. The advantage here is realized at the level of the mitochondrion and chloroplast.<br><br>HYPOTHESIS: The extreme instability of DNA in mitochondria and chloroplasts has not been widely appreciated even though it was first reported four decades ago. Here, I show that the evolutionary success of multicellular animals and plants can be traced to the protection of organellar DNA. Three stages are envisioned. Sequestration allowed mitochondria and chloroplasts to be placed in "quiet" germ line cells so that their DNA is not exposed to the oxidative stress produced by these organelles in "active" somatic cells. This advantage then provided Opportunity, a period of time during which novel processes arose for signaling within and between cells and (in animals) for cell-cell recognition molecules to evolve. Development then led to the enormous diversity of animals and plants.<br><br>IMPLICATIONS: The potency of a somatic stem cell is its potential to generate cell types other than itself, and this is a systems property. One of the biochemical properties required for stemness to emerge from a population of cells might be the metabolic quiescence that protects organellar DNA from oxidative stress.}, }
@article {pmid20582567, year = {2010}, author = {Veyrunes, F and Catalan, J and Tatard, C and Cellier-Holzem, E and Watson, J and Chevret, P and Robinson, TJ and Britton-Davidian, J}, title = {Mitochondrial and chromosomal insights into karyotypic evolution of the pygmy mouse, Mus minutoides, in South Africa.}, journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology}, volume = {18}, number = {5}, pages = {563-574}, pmid = {20582567}, issn = {1573-6849}, mesh = {Animals ; Biological Evolution ; Chromosome Aberrations ; Chromosomes, Mammalian/*genetics ; *Karyotyping ; Mice/*genetics ; Mitochondria/*genetics ; Phylogeny ; Translocation, Genetic ; }, abstract = {The African pygmy mouse, Mus minutoides, displays extensive Robertsonian (Rb) diversity. The two extremes of the karyotypic range are found in South Africa, with populations carrying 2n = 34 and 2n = 18. In order to reconstruct the scenario of chromosomal evolution of M. minutoides and test the performance of Rb fusions in resolving fine-scale phylogenetic relationships, we first describe new karyotypes, and then perform phylogenetic analyses by two independent methods, using respectively mitochondrial cytochrome b sequences and chromosomal rearrangements as markers. The molecular and chromosomal phylogenies were in perfect congruence, providing strong confidence both for the tree topology and the chronology of chromosomal rearrangements. The analysis supports a division of South African specimens into two clades showing opposite trends of chromosomal evolution, one containing all specimens with 34 chromosomes (karyotypic stasis) and the other grouping all mice with 18 chromosomes that have further diversified by the fixation of different Rb fusions (extensive karyotypic reshuffling). The results confirm that Rb fusions are by far the predominant rearrangement in M. minutoides but strongly suggest that recurrent whole-arm reciprocal translocations have also shaped this genome.}, }
@article {pmid20574726, year = {2010}, author = {Smith, DR and Hua, J and Lee, RW}, title = {Evolution of linear mitochondrial DNA in three known lineages of Polytomella.}, journal = {Current genetics}, volume = {56}, number = {5}, pages = {427-438}, pmid = {20574726}, issn = {1432-0983}, mesh = {Base Sequence ; Chlamydomonas reinhardtii/genetics ; Chlorophyta/classification/*genetics ; DNA, Mitochondrial/chemistry/*genetics ; *Evolution, Molecular ; Genome, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Telomere ; Volvox/genetics ; }, abstract = {Although DNA sequences of linear mitochondrial genomes are available for a wide variety of species, sequence and conformational data from the extreme ends of these molecules (i.e., the telomeres) are limited. Data on the telomeres is important because it can provide insights into how linear genomes overcome the end-replication problem. This study explores the evolution of linear mitochondrial DNAs (mtDNAs) in the green-algal genus Polytomella (Chlorophyceae, Chlorophyta), the members of which are non-photosynthetic. Earlier works analyzed the linear and linear-fragmented mitochondrial genomes of Polytomella capuana and Polytomella parva. Here we present the mtDNA sequence for Polytomella strain SAG 63-10 [also known as Polytomella piriformis (Pringsheim 1963)], which is the only known representative of a mostly unexplored Polytomella lineage. We show that the P. piriformis mtDNA is made up of two linear fragments of 13 and 3 kb. The telomeric sequences of the large and small fragments are terminally inverted, and appear to end in vitro with either closed (hairpin-loop) or open (nicked-loop) structures as also shown here for P. parva and shown earlier for P. capuana. The structure of the P. piriformis mtDNA is more similar to that of P. parva, which is also fragmented, than to that of P. capuana, which is contained in a single chromosome. Phylogenetic analyses reveal high substitution rates in the mtDNA of all three Polytomella species relative to other chlamydomonadalean algae. These elevated rates could be the result of a greater number of vegetative cell divisions and/or small population sizes in Polytomella species as compared with other chlamydomonadalean algae.}, }
@article {pmid20571889, year = {2010}, author = {Flynn, A and Chokkalingam Mani, B and Mather, PJ}, title = {Sepsis-induced cardiomyopathy: a review of pathophysiologic mechanisms.}, journal = {Heart failure reviews}, volume = {15}, number = {6}, pages = {605-611}, pmid = {20571889}, issn = {1573-7322}, mesh = {Animals ; Cardiomyopathies/*immunology/*physiopathology ; Cytokines/blood ; Humans ; Mitochondria, Heart/immunology ; Nitric Oxide/blood ; Sepsis/*complications/immunology/*physiopathology ; Shock, Septic/complications/physiopathology ; }, abstract = {Cardiac dysfunction is a well-recognized complication of severe sepsis and septic shock. Cardiac dysfunction in sepsis is characterized by ventricular dilatation, reduction in ejection fraction and reduced contractility. Initially, cardiac dysfunction was considered to occur only during the "hypodynamic" phase of shock. But we now know that it occurs very early in sepsis even during the "hyperdynamic" phase of septic shock. Circulating blood-borne factors were suspected to be involved in the evolution of sepsis induced cardiomyopathy, but it is not until recently that the cellular and molecular events are being targeted by researchers in a quest to understand this enigmatic process. Septic cardiomyopathy has been the subject of investigation for nearly half a century now and yet controversies exist in understanding it's pathophysiology. Here, we discuss our understanding of the pathogenesis of septic cardiomyopathy and the complex roles played by nitric oxide, mitochondrial dysfunction, complements and cytokines.}, }
@article {pmid20568109, year = {2010}, author = {Monticone, M and Panfoli, I and Ravera, S and Puglisi, R and Jiang, MM and Morello, R and Candiani, S and Tonachini, L and Biticchi, R and Fabiano, A and Cancedda, R and Boitani, C and Castagnola, P}, title = {The nuclear genes Mtfr1 and Dufd1 regulate mitochondrial dynamic and cellular respiration.}, journal = {Journal of cellular physiology}, volume = {225}, number = {3}, pages = {767-776}, doi = {10.1002/jcp.22279}, pmid = {20568109}, issn = {1097-4652}, mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; *Cell Respiration/genetics ; *Energy Metabolism/genetics ; Gene Expression Regulation, Developmental ; HeLa Cells ; Humans ; In Situ Hybridization ; Leydig Cells/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Mitochondria/*metabolism ; Mitochondrial Proteins/deficiency/genetics/*metabolism ; Molecular Sequence Data ; Oxygen Consumption ; Phylogeny ; Polymerase Chain Reaction ; RNA Interference ; RNA, Messenger/metabolism ; Sertoli Cells/metabolism ; Spermatids/metabolism ; Spermatocytes/metabolism ; Testis/cytology/*metabolism ; Transfection ; }, abstract = {Dufd1 (DUF729 domain containing 1) is related to Mtfr1 (mitochondrial fission regulator 1), a gene involved in the regulation of antioxidant activity in the mouse testis. The present study was undertaken to better understand their role in regulating mitochondrial architecture and function in the mouse. We show that Dufd1 is expressed as a 2 kb mRNA and has a more specific tissue pattern compared to Mtfr1, with highest level of expression in testes, lower level in spleen, and negligible levels in other organs and/or tissues. In the male gonad, Dufd1 mRNA expression increases during postnatal development, similarly to Mtfr1. In situ hybridization and real-time PCR analyses show that Dufd1 is expressed in the seminiferous tubules by middle-late pachytene spermatocytes and spermatids. In transfected cells, the Dufd1-tagged protein is located in mitochondria, associated with the tips of mitochondrial tubules and to tubules constrictions, and induces mitochondrial fission although with a lesser efficiency than Mtfr1. We also found that both endogenous Dufd1 and Mtfr1 proteins are associated with membrane-enriched subcellular fractions, including mitochondria. Inhibition of Mtfr1 and/or Dufd1 expression, in a testicular germ cells line, severely impairs O(2) consumption and indicates that both genes are required for mitochondrial respiration. Accordingly, analysis of testes mitochondria from Mtfr1-deficient mice reveals severely reduced O(2) consumption and ATP synthesis compared to wt animals. These data show that, in murine testis, Dufd1 and Mtfr1 have redundant functions related to mitochondrial physiology and represent genes with a potential role in testicular function.}, }
@article {pmid20562347, year = {2010}, author = {Shutt, TE and Lodeiro, MF and Cotney, J and Cameron, CE and Shadel, GS}, title = {Core human mitochondrial transcription apparatus is a regulated two-component system in vitro.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {27}, pages = {12133-12138}, pmid = {20562347}, issn = {1091-6490}, support = {R01 HL059655/HL/NHLBI NIH HHS/United States ; HL-059655/HL/NHLBI NIH HHS/United States ; }, mesh = {DNA, Mitochondrial/*genetics ; DNA-Directed RNA Polymerases/genetics/metabolism ; Escherichia coli/genetics ; Humans ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Models, Genetic ; Promoter Regions, Genetic/genetics ; Recombinant Proteins/metabolism ; Transcription Factors/genetics/*metabolism ; Transcription, Genetic/*genetics ; }, abstract = {The core human mitochondrial transcription apparatus is currently regarded as an obligate three-component system comprising the bacteriophage T7-related mitochondrial RNA polymerase, the rRNA methyltransferase-related transcription factor, h-mtTFB2, and the high mobility group box transcription/DNA-packaging factor, h-mtTFA/TFAM. Using a faithful recombinant human mitochondrial transcription system from Escherichia coli, we demonstrate that specific initiation from the mtDNA promoters, LSP and HSP1, only requires mitochondrial RNA polymerase and h-mtTFB2 in vitro. When h-mtTFA is added to these basal components, LSP exhibits a much lower threshold for activation and a larger amplitude response than HSP1. In addition, when LSP and HSP1 are together on the same transcription template, h-mtTFA-independent transcription from HSP1 and h-mtTFA-dependent transcription from both promoters is enhanced and a higher concentration of h-mtTFA is required to stimulate HSP1. Promoter competition experiments revealed that, in addition to LSP competing transcription components away from HSP1, additional cis-acting signals are involved in these aspects of promoter regulation. Based on these results, we speculate that the human mitochondrial transcription system may have evolved to differentially regulate transcription initiation and transcription-primed mtDNA replication in response to the amount of h-mtTFA associated with nucleoids, which could begin to explain the heterogeneity of nucleoid structure and activity in vivo. Furthermore, this study sheds new light on the evolution of mitochondrial transcription components by showing that the human system is a regulated two-component system in vitro, and thus more akin to that of budding yeast than thought previously.}, }
@article {pmid20561244, year = {2010}, author = {Chen, F and Chen, L and Zhao, H and Korpelainen, H and Li, C}, title = {Sex-specific responses and tolerances of Populus cathayana to salinity.}, journal = {Physiologia plantarum}, volume = {140}, number = {2}, pages = {163-173}, doi = {10.1111/j.1399-3054.2010.01393.x}, pmid = {20561244}, issn = {1399-3054}, mesh = {Cell Nucleolus/drug effects/ultrastructure ; Chlorides/metabolism ; Chlorophyll/metabolism ; Chloroplasts/drug effects/ultrastructure ; Microscopy, Electron, Transmission ; Mitochondria/drug effects/ultrastructure ; Oxygen Consumption/drug effects ; Photosynthesis/drug effects ; Plant Leaves/metabolism/physiology/ultrastructure ; Plant Stems/metabolism/physiology ; Populus/metabolism/*physiology/ultrastructure ; Reproduction/physiology ; *Salinity ; Salt Tolerance/*physiology ; Salt-Tolerant Plants/metabolism/*physiology/ultrastructure ; Sodium/metabolism ; Sodium Chloride/pharmacology ; Thylakoids/drug effects/ultrastructure ; }, abstract = {Responses of males and females to salinity were studied in order to reveal sex-specific adaptation and evolution in Populus cathayana Rehd cuttings. This dioecious tree species plays an important role in maintaining ecological stability and providing commercial raw material in southwest China. Female and male cuttings of P. cathayana were treated for about 1 month with 0, 75 and 150 mM NaCl. Plant growth traits, gas exchange parameters, chlorophyll pigments, intrinsic water use efficiency (WUEi), membrane system injuries, ion transport and ultrastructural morphology were assessed and compared between sexes. Salt stress caused less negative effects on the dry matter accumulation, growth rate of height, growth rate of stem base diameter, total number of leaves and photosynthetic abilities in males than in females. Relative electrolyte leakage increased more in females than in males under salinity stress. Soil salinity reduced the amounts of leaf chlorophyll a, chlorophyll b and total chlorophyll, and the chlorophyll a/b ratio more in females than in males. WUEi decreased in both sexes under salinity. Regarding the ultrastructural morphology, thylakoid swelling in chloroplasts and degrading structures in mitochondria were more frequent in females than in males. Moreover, females exhibited significantly higher Na(+) and Cl(-) concentrations in leaves and stems, but lower concentrations in roots than did males under salinity. In all, female cuttings of P. cathayana are more sensitive to salinity stress than males, which could be partially due to males having a better ability to restrain Na(+) transport from roots to shoots than do females.}, }
@article {pmid20554689, year = {2010}, author = {Kopec, KO and Alva, V and Lupas, AN}, title = {Homology of SMP domains to the TULIP superfamily of lipid-binding proteins provides a structural basis for lipid exchange between ER and mitochondria.}, journal = {Bioinformatics (Oxford, England)}, volume = {26}, number = {16}, pages = {1927-1931}, pmid = {20554689}, issn = {1367-4811}, mesh = {Amino Acid Sequence ; Animals ; Biological Transport ; Carrier Proteins/*chemistry/classification/metabolism ; Endoplasmic Reticulum/*metabolism ; Membrane Proteins/chemistry/classification/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/*chemistry/classification/metabolism ; Molecular Sequence Data ; Phospholipids/*metabolism ; }, abstract = {Mitochondria must uptake some phospholipids from the endoplasmic reticulum (ER) for the biogenesis of their membranes. They convert one of these lipids, phosphatidylserine, to phosphatidylethanolamine, which can be re-exported via the ER to all other cellular membranes. The mechanisms underlying these exchanges between ER and mitochondria are poorly understood. Recently, a complex termed ER-mitochondria encounter structure (ERMES) was shown to be necessary for phospholipid exchange in budding yeast. However, it is unclear whether this complex is merely an inter-organelle tether or also the transporter. ERMES consists of four proteins: Mdm10, Mdm34 (Mmm2), Mdm12 and Mmm1, three of which contain the uncharacterized SMP domain common to a number of eukaryotic membrane-associated proteins. Here, we show that the SMP domain belongs to the TULIP superfamily of lipid/hydrophobic ligand-binding domains comprising members of known structure. This relationship suggests that the SMP domains of the ERMES complex mediate lipid exchange between ER and mitochondria.}, }
@article {pmid20546574, year = {2010}, author = {Gawryluk, RM and Gray, MW}, title = {Evidence for an early evolutionary emergence of gamma-type carbonic anhydrases as components of mitochondrial respiratory complex I.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {176}, pmid = {20546574}, issn = {1471-2148}, support = {MOP-4124//Canadian Institutes of Health Research/Canada ; }, mesh = {Acanthamoeba castellanii/enzymology/*genetics ; Amino Acid Sequence ; Carbonic Anhydrases/*genetics ; Computational Biology ; *Evolution, Molecular ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/*genetics/isolation &amp; purification ; Molecular Sequence Data ; *Phylogeny ; Protozoan Proteins/genetics/isolation &amp; purification ; Sequence Alignment ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: The complexity of mitochondrial complex I (CI; NADH:ubiquinone oxidoreductase) has increased considerably relative to the homologous complex in bacteria. Comparative analyses of CI composition in animals, fungi and land plants/green algae suggest that novel components of mitochondrial CI include a set of 18 proteins common to all eukaryotes and a variable number of lineage-specific subunits. In plants and green algae, several purportedly plant-specific proteins homologous to gamma-type carbonic anhydrases (gammaCA) have been identified as components of CI. However, relatively little is known about CI composition in the unicellular protists, the characterizations of which are essential to our understanding of CI evolution.<br><br>RESULTS: We have performed a tandem mass spectrometric characterization of CI from the amoeboid protozoon Acanthamoeba castellanii. Among the proteins identified were two gammaCA homologs, AcCa1 and AcCa2, demonstrating that gammaCA proteins are not specific to plants/green algae. In fact, through bioinformatics searches we detected gammaCA homologs in diverse protist lineages, and several of these homologs are predicted to possess N-terminal mitochondrial targeting peptides.<br><br>CONCLUSIONS: The detection of gammaCAs in CI of Acanthamoeba, considered to be a closer relative of animals and fungi than plants, suggests that gammaCA proteins may have been an ancestral feature of mitochondrial CI, rather than a novel, plant-specific addition. This assertion is supported by the presence of genes encoding gammaCAs in the nuclear genomes of a wide variety of eukaryotes. Together, these findings emphasize the importance of a phylogenetically broad characterization of CI for elucidating CI evolution in eukaryotes.}, }
@article {pmid20540728, year = {2010}, author = {Magnacca, KN and Brown, MJ}, title = {Mitochondrial heteroplasmy and DNA barcoding in Hawaiian Hylaeus (Nesoprosopis) bees (Hymenoptera: Colletidae).}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {174}, pmid = {20540728}, issn = {1471-2148}, mesh = {Animals ; Bees/classification/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genes, Insect ; Haplotypes ; Hawaii ; Mitochondria/genetics ; Polymorphism, Genetic ; Pseudogenes ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; Species Specificity ; }, abstract = {BACKGROUND: The past several years have seen a flurry of papers seeking to clarify the utility and limits of DNA barcoding, particularly in areas such as species discovery and paralogy due to nuclear pseudogenes. Heteroplasmy, the coexistence of multiple mitochondrial haplotypes in a single organism, has been cited as a potentially serious problem for DNA barcoding but its effect on identification accuracy has not been tested. In addition, few studies of barcoding have tested a large group of closely-related species with a well-established morphological taxonomy. In this study we examine both of these issues, by densely sampling the Hawaiian Hylaeus bee radiation.<br><br>RESULTS: Individuals from 21 of the 49 a priori morphologically-defined species exhibited coding sequence heteroplasmy at levels of 1-6% or more. All homoplasmic species were successfully identified by COI using standard methods of analysis, but only 71% of heteroplasmic species. The success rate in identifying heteroplasmic species was increased to 86% by treating polymorphisms as character states rather than ambiguities. Nuclear pseudogenes (numts) were also present in four species, and were distinguishable from heteroplasmic sequences by patterns of nucleotide and amino acid change.<br><br>CONCLUSIONS: Heteroplasmy significantly decreased the reliability of species identification. In addition, the practical issue of dealing with large numbers of polymorphisms- and resulting increased time and labor required - makes the development of DNA barcode databases considerably more complex than has previously been suggested. The impact of heteroplasmy on the utility of DNA barcoding as a bulk specimen identification tool will depend upon its frequency across populations, which remains unknown. However, DNA barcoding is still likely to remain an important identification tool for those species that are difficult or impossible to identify through morphology, as is the case for the ecologically important solitary bee fauna.}, }
@article {pmid20538757, year = {2010}, author = {Lanterbecq, D and Glaberman, S and Vitousek, MN and Steinfartz, S and Benavides, E and Wikelski, M and Caccone, A}, title = {Genetic differentiation between marine iguanas from different breeding sites on the island of Santa Fe (Galapagos Archipelago).}, journal = {The Journal of heredity}, volume = {101}, number = {6}, pages = {663-675}, doi = {10.1093/jhered/esq067}, pmid = {20538757}, issn = {1465-7333}, mesh = {Animals ; Aquatic Organisms/genetics ; Base Sequence ; Breeding ; DNA, Mitochondrial/*genetics ; Ecuador ; Evolution, Molecular ; Female ; Gene Flow ; *Genetic Drift ; *Genetic Variation ; Haplotypes ; Iguanas/*genetics ; Male ; Microsatellite Repeats/genetics ; Mitochondria ; Molecular Sequence Data ; Polymerase Chain Reaction ; }, abstract = {We studied patterns of genetic diversity within and among 5 populations (318 individuals) of Galápagos marine iguanas (Amblyrhynchus cristatus) from the island Santa Fé. Populations were separated by distances of 0.2 to 9.9 km. We sequenced 1182 base pairs of the mitochondrial control region and screened 13 microsatellite loci for variability. We also added data from 5 populations (397 individuals) sampled on 4 neighboring islands (Santa Cruz, Floreana, Espanola, and San Cristobal). The 5 Santa Fé populations, revealed as genetically distinct from populations on other islands, present relatively low levels of genetic diversity, which are similar for both microsatellite (average observed heterozygosity from 0.7686 to 0.7773) and mitochondrial DNA (mtDNA) markers (haplotypic and nucleotide diversity from 0.587 to 0.728 and from 0.00079 to 0.00293, respectively), and comparable with those observed in similar-sized sampling sites on other islands. There was frequency-based evidence of genetic structure between northern and southern sites on Santa Fé (F(st) of 0.0027-0.0115 for microsatellite and 0.0447-0.2391 for mtDNA), but the 4 southern sites showed little differentiation. Most of the intra-island genetic variation was allocated within rather than between sites. There was no evidence of sex-biased dispersal or population substructuring due to lek-mating behavior, suggesting that these 2 observed behaviors are not strong enough to leave an evolutionary signal on genetic patterns in this species.}, }
@article {pmid20538375, year = {2010}, author = {Lakatos, A and Derbeneva, O and Younes, D and Keator, D and Bakken, T and Lvova, M and Brandon, M and Guffanti, G and Reglodi, D and Saykin, A and Weiner, M and Macciardi, F and Schork, N and Wallace, DC and Potkin, SG and , }, title = {Association between mitochondrial DNA variations and Alzheimer's disease in the ADNI cohort.}, journal = {Neurobiology of aging}, volume = {31}, number = {8}, pages = {1355-1363}, pmid = {20538375}, issn = {1558-1497}, support = {R01 NS041850/NS/NINDS NIH HHS/United States ; AG16573/AG/NIA NIH HHS/United States ; U24 AG021886/AG/NIA NIH HHS/United States ; U19 AG023122/AG/NIA NIH HHS/United States ; R01 AG024373-02/AG/NIA NIH HHS/United States ; P01 HL058120-06A19005/HL/NHLBI NIH HHS/United States ; R01 AG024373-03/AG/NIA NIH HHS/United States ; U24-RR021992/RR/NCRR NIH HHS/United States ; P20 RR020837/RR/NCRR NIH HHS/United States ; R01 AG024373-01/AG/NIA NIH HHS/United States ; U01 AG024904-01/AG/NIA NIH HHS/United States ; U01 AG024904/AG/NIA NIH HHS/United States ; U19 AG010483/AG/NIA NIH HHS/United States ; UL1 RR025774/RR/NCRR NIH HHS/United States ; 3U01AG024904-03S5/AG/NIA NIH HHS/United States ; U24 RR021992-02/RR/NCRR NIH HHS/United States ; R01 NS021328-15/NS/NINDS NIH HHS/United States ; U24 RR021992-01A1/RR/NCRR NIH HHS/United States ; DK73691/DK/NIDDK NIH HHS/United States ; R01 NS041850-01/NS/NINDS NIH HHS/United States ; R01 DK073691-01/DK/NIDDK NIH HHS/United States ; P50 AG016573/AG/NIA NIH HHS/United States ; U19 AG023122-01/AG/NIA NIH HHS/United States ; NS41850/NS/NINDS NIH HHS/United States ; P20 RR020837-01/RR/NCRR NIH HHS/United States ; P50 AG016573-070005/AG/NIA NIH HHS/United States ; U24 RR021992/RR/NCRR NIH HHS/United States ; NS211328/NS/NINDS NIH HHS/United States ; AG24373/AG/NIA NIH HHS/United States ; R01 AG024373/AG/NIA NIH HHS/United States ; P01 HL058120/HL/NHLBI NIH HHS/United States ; P50 AG016573-060005/AG/NIA NIH HHS/United States ; R01 DK073691/DK/NIDDK NIH HHS/United States ; R01 NS021328/NS/NINDS NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Alzheimer Disease/diagnosis/*genetics ; Case-Control Studies ; Cohort Studies ; DNA, Mitochondrial/*genetics ; Female ; Follow-Up Studies ; Genes, Mitochondrial/genetics ; Genetic Association Studies/methods ; Genetic Variation/*genetics ; Humans ; Longitudinal Studies ; Male ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Prospective Studies ; Random Allocation ; }, abstract = {Despite the central role of amyloid deposition in the development of Alzheimer's disease (AD), the pathogenesis of AD still remains elusive at the molecular level. Increasing evidence suggests that compromised mitochondrial function contributes to the aging process and thus may increase the risk of AD. Dysfunctional mitochondria contribute to reactive oxygen species (ROS) which can lead to extensive macromolecule oxidative damage and the progression of amyloid pathology. Oxidative stress and amyloid toxicity leave neurons chemically vulnerable. Because the brain relies on aerobic metabolism, it is apparent that mitochondria are critical for the cerebral function. Mitochondrial DNA sequence changes could shift cell dynamics and facilitate neuronal vulnerability. Therefore we postulated that mitochondrial DNA sequence polymorphisms may increase the risk of AD. We evaluated the role of mitochondrial haplogroups derived from 138 mitochondrial polymorphisms in 358 Caucasian Alzheimer's Disease Neuroimaging Initiative (ADNI) subjects. Our results indicate that the mitochondrial haplogroup UK may confer genetic susceptibility to AD independently of the apolipoprotein E4 (APOE4) allele.}, }
@article {pmid20535601, year = {2010}, author = {Sapp, J}, title = {Saltational symbiosis.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {129}, number = {2-3}, pages = {125-133}, pmid = {20535601}, issn = {1611-7530}, mesh = {Animals ; Archaea/physiology ; Bacterial Physiological Phenomena/genetics ; Bacteriophages/physiology ; *Biological Evolution ; Chloroplasts/physiology ; Fungi/physiology ; Gene Transfer, Horizontal ; Humans ; Mitochondria/pathology ; Organelles/physiology ; Phylogeny ; Plant Physiological Phenomena/genetics ; Selection, Genetic/physiology ; Symbiosis/*physiology ; Virus Physiological Phenomena/genetics ; }, abstract = {Symbiosis has long been associated with saltational evolutionary change in contradistinction to gradual Darwinian evolution based on gene mutations and recombination between individuals of a species, as well as with super-organismal views of the individual in contrast to the classical one-genome: one organism conception. Though they have often been dismissed, and overshadowed by Darwinian theory, suggestions that symbiosis and lateral gene transfer are fundamental mechanisms of evolutionary innovation are borne out today by molecular phylogenetic research. It is time to treat these processes as central principles of evolution.}, }
@article {pmid20533899, year = {2010}, author = {Palmieri, F and Pierri, CL}, title = {Mitochondrial metabolite transport.}, journal = {Essays in biochemistry}, volume = {47}, number = {}, pages = {37-52}, doi = {10.1042/bse0470037}, pmid = {20533899}, issn = {1744-1358}, mesh = {Animals ; Biological Transport/physiology ; Humans ; Membrane Transport Proteins/*classification/genetics/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/classification/genetics/*metabolism ; Phylogeny ; }, abstract = {The flux of a variety of metabolites, nucleotides and coenzymes across the inner membrane of mitochondria is catalysed by a nuclear-coded superfamily of secondary transport proteins called MCs (mitochondrial carriers). The importance of MCs is demonstrated by their wide distribution in all eukaryotes, their role in numerous metabolic pathways and cell functions, and the identification of several diseases caused by alterations of their genes. MCs can easily be recognized in databases thanks to their striking sequence features. Until now, 22 MC subfamilies, which are well conserved throughout evolution, have been functionally characterized, mainly by transport assays upon heterologous gene expression, purification and reconstitution into liposomes. Given the significant sequence conservation, it is thought that all MCs use the same basic transport mechanism, although they exhibit different modes of transport and driving forces and their substrates vary in nature and size. Based on substrate specificity, sequence conservation and carrier homology models, progress has recently been made in understanding the transport mechanism of MCs by new insights concerning the existence of a substrate-binding site in the carrier cavity, of cytosolic and matrix gates and conserved proline and glycine residues in each of the six transmembrane alpha-helices. These structural properties are believed to play an important role in the conformational changes required for substrate translocation.}, }
@article {pmid20528687, year = {2010}, author = {Shiflett, AM and Johnson, PJ}, title = {Mitochondrion-related organelles in eukaryotic protists.}, journal = {Annual review of microbiology}, volume = {64}, number = {}, pages = {409-429}, pmid = {20528687}, issn = {1545-3251}, support = {T32 A1007323//PHS HHS/United States ; F32 A108004//PHS HHS/United States ; R37 A127857//PHS HHS/United States ; R01 A1069058//PHS HHS/United States ; R37 AI027857/AI/NIAID NIH HHS/United States ; }, mesh = {Eukaryota/*genetics/*metabolism/ultrastructure ; *Genes, Mitochondrial ; Iron-Sulfur Proteins/metabolism ; Metabolic Networks and Pathways ; Mitochondria/*genetics/*metabolism/ultrastructure ; Phylogeny ; Sequence Homology ; }, abstract = {The discovery of mitochondrion-type genes in organisms thought to lack mitochondria led to the demonstration that hydrogenosomes share a common ancestry with mitochondria, as well as the discovery of mitosomes in multiple eukaryotic lineages. No examples of examined eukaryotes lacking a mitochondrion-related organelle exist, implying that the endosymbiont that gave rise to the mitochondrion was present in the first eukaryote. These organelles, known as hydrogenosomes, mitosomes, or mitochondrion-like organelles, are typically reduced, both structurally and biochemically, relative to classical mitochondria. However, despite their diversification and adaptation to different niches, all appear to play a role in Fe-S cluster assembly, as observed for mitochondria. Although evidence supports the use of common protein targeting mechanisms in the biogenesis of these diverse organelles, divergent features are also apparent. This review examines the metabolism and biogenesis of these organelles in divergent unicellular microbes, with a focus on parasitic protists.}, }
@article {pmid20510218, year = {2010}, author = {Wen, JJ and Gupta, S and Guan, Z and Dhiman, M and Condon, D and Lui, C and Garg, NJ}, title = {Phenyl-alpha-tert-butyl-nitrone and benzonidazole treatment controlled the mitochondrial oxidative stress and evolution of cardiomyopathy in chronic chagasic Rats.}, journal = {Journal of the American College of Cardiology}, volume = {55}, number = {22}, pages = {2499-2508}, pmid = {20510218}, issn = {1558-3597}, support = {R01 AI054578/AI/NIAID NIH HHS/United States ; R01 AI054578-01A1/AI/NIAID NIH HHS/United States ; AI054578/AI/NIAID NIH HHS/United States ; }, mesh = {Analysis of Variance ; Animals ; Chagas Cardiomyopathy/etiology/prevention &amp; control ; Chagas Disease/complications/*drug therapy/physiopathology ; Chronic Disease ; Cyclic N-Oxides/*pharmacology ; Disease Models, Animal ; Disease Progression ; Heart Function Tests ; Hemodynamics/physiology ; Lipid Peroxidation ; Mitochondria, Heart/*drug effects/parasitology ; Nitroimidazoles/*pharmacology ; Oxidative Stress/*drug effects ; Probability ; Random Allocation ; Rats ; Rats, Sprague-Dawley ; Statistics, Nonparametric ; Trypanosoma cruzi ; }, abstract = {OBJECTIVES: The purpose of this study was to determine the pathological importance of oxidative stress-induced injurious processes in chagasic heart dysfunction.<br><br>BACKGROUND: Trypanosoma cruzi-induced inflammatory pathology and a feedback cycle of mitochondrial dysfunction and oxidative stress may contribute to Chagas disease.<br><br>METHODS: Sprague-Dawley rats were infected with T. cruzi and treated with phenyl-alpha-tert-butylnitrone (PBN), an antioxidant, and/or benzonidazole (BZ), an antiparasitic agent. We monitored myocardial parasite burden, oxidative adducts, mitochondrial complex activities, respiration, and adenosine triphosphate synthesis rates, and inflammatory and cardiac remodeling responses during disease development. The cardiac hemodynamics was determined for all rats.<br><br>RESULTS: Benzonidazole (not PBN) decreased the parasite persistence and immune adverse events (proinflammatory cytokine expression, beta-nicotinamide adenine dinucleotide phosphate oxidase and myeloperoxidase activities, and inflammatory infiltrate) in chronically infected hearts. PBN +/- BZ (not BZ alone) decreased the mitochondrial reactive oxygen species level, oxidative adducts (malonyldialdehyde, 4-hydroxynonenal, carbonyls), hypertrophic gene expression (atrial natriuretic peptide, B-type natriuretic peptide, alpha-skeletal actin), and collagen deposition and preserved the respiratory chain efficiency and energy status in chronically infected hearts. Subsequently, LV dysfunction was prevented in PBN +/- BZ-treated chagasic rats.<br><br>CONCLUSIONS: BZ treatment after the acute stage decreased the parasite persistence and inflammatory pathology. Yet, oxidative adducts, mitochondrial dysfunction, and remodeling responses persisted and contributed to declining cardiac function in chagasic rats. Combination treatment (PBN + BZ) was beneficial in arresting the T. cruzi-induced inflammatory and oxidative pathology and chronic heart failure in chagasic rats.}, }
@article {pmid20502706, year = {2010}, author = {Imanian, B and Pombert, JF and Keeling, PJ}, title = {The complete plastid genomes of the two 'dinotoms' Durinskia baltica and Kryptoperidinium foliaceum.}, journal = {PloS one}, volume = {5}, number = {5}, pages = {e10711}, pmid = {20502706}, issn = {1932-6203}, mesh = {Base Composition/genetics ; Conserved Sequence/genetics ; Dinoflagellida/*genetics ; Genes, Protozoan/genetics ; Genome, Plastid/*genetics ; Plasmids/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {BACKGROUND: In one small group of dinoflagellates, photosynthesis is carried out by a tertiary endosymbiont derived from a diatom, giving rise to a complex cell that we collectively refer to as a 'dinotom'. The endosymbiont is separated from its host by a single membrane and retains plastids, mitochondria, a large nucleus, and many other eukaryotic organelles and structures, a level of complexity suggesting an early stage of integration. Although the evolution of these endosymbionts has attracted considerable interest, the plastid genome has not been examined in detail, and indeed no tertiary plastid genome has yet been sequenced.<br><br>Here we describe the complete plastid genomes of two closely related dinotoms, Durinskia baltica and Kryptoperidinium foliaceum. The D. baltica (116470 bp) and K. foliaceum (140426 bp) plastid genomes map as circular molecules featuring two large inverted repeats that separate distinct single copy regions. The organization and gene content of the D. baltica plastid closely resemble those of the pennate diatom Phaeodactylum tricornutum. The K. foliaceum plastid genome is much larger, has undergone more reorganization, and encodes a putative tyrosine recombinase (tyrC) also found in the plastid genome of the heterokont Heterosigma akashiwo, and two putative serine recombinases (serC1 and serC2) homologous to recombinases encoded by plasmids pCf1 and pCf2 in another pennate diatom, Cylindrotheca fusiformis. The K. foliaceum plastid genome also contains an additional copy of serC1, two degenerate copies of another plasmid-encoded ORF, and two non-coding regions whose sequences closely resemble portions of the pCf1 and pCf2 plasmids.<br><br>CONCLUSIONS/SIGNIFICANCE: These results suggest that while the plastid genomes of two dinotoms share very similar gene content and genome organization with that of the free-living pennate diatom P. tricornutum, the K. folicaeum plastid genome has absorbed two exogenous plasmids. Whether this took place before or after the tertiary endosymbiosis is not clear.}, }
@article {pmid20494971, year = {2010}, author = {Jourdren, L and Delaveau, T and Marquenet, E and Jacq, C and Garcia, M}, title = {CORSEN, a new software dedicated to microscope-based 3D distance measurements: mRNA-mitochondria distance, from single-cell to population analyses.}, journal = {RNA (New York, N.Y.)}, volume = {16}, number = {7}, pages = {1301-1307}, pmid = {20494971}, issn = {1469-9001}, mesh = {Imaging, Three-Dimensional/*methods ; Microscopy/*methods ; Mitochondria ; RNA, Messenger/analysis ; *Software ; }, abstract = {Recent improvements in microscopy technology allow detection of single molecules of RNA, but tools for large-scale automatic analyses of particle distributions are lacking. An increasing number of imaging studies emphasize the importance of mRNA localization in the definition of cell territory or the biogenesis of cell compartments. CORSEN is a new tool dedicated to three-dimensional (3D) distance measurements from imaging experiments especially developed to access the minimal distance between RNA molecules and cellular compartment markers. CORSEN includes a 3D segmentation algorithm allowing the extraction and the characterization of the cellular objects to be processed--surface determination, aggregate decomposition--for minimal distance calculations. CORSEN's main contribution lies in exploratory statistical analysis, cell population characterization, and high-throughput assays that are made possible by the implementation of a batch process analysis. We highlighted CORSEN's utility for the study of relative positions of mRNA molecules and mitochondria: CORSEN clearly discriminates mRNA localized to the vicinity of mitochondria from those that are translated on free cytoplasmic polysomes. Moreover, it quantifies the cell-to-cell variations of mRNA localization and emphasizes the necessity for statistical approaches. This method can be extended to assess the evolution of the distance between specific mRNAs and other cellular structures in different cellular contexts. CORSEN was designed for the biologist community with the concern to provide an easy-to-use and highly flexible tool that can be applied for diverse distance quantification issues.}, }
@article {pmid20494640, year = {2011}, author = {Liu, C and Wang, SY and Zhao, M and Xu, ZY and Hu, YH and Chen, F and Zhang, RZ and Gao, GF and Yu, YS and Kong, QP}, title = {Mitochondrial DNA polymorphisms in Gelao ethnic group residing in Southwest China.}, journal = {Forensic science international. Genetics}, volume = {5}, number = {1}, pages = {e4-10}, doi = {10.1016/j.fsigen.2010.04.007}, pmid = {20494640}, issn = {1878-0326}, mesh = {Asian People/*genetics ; China ; Complementarity Determining Regions/genetics ; DNA Fingerprinting ; DNA, Mitochondrial/*genetics ; Databases, Factual ; Ethnicity/*genetics ; Gene Pool ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes ; Humans ; Mitochondria/genetics ; Open Reading Frames ; Phylogeny ; *Polymorphism, Genetic ; Reference Standards ; }, abstract = {Gelao ethnic group, an aboriginal population residing in southwest China, has undergone a long and complex evolutionary process. To investigate the genetic structure of this ancient ethnic group, mitochondrial DNA (mtDNA) polymorphisms of 102 Gelao individuals were collected and analyzed in this study. With the aid of the information extracted from control-region hypervariable segments (HVSs) I and II as well as some necessary coding-region segments, phylogenetic status of all mtDNAs under study were determined by means of classifying into various defined haplogroups. The southern-prevalent haplogroups B, R9, and M7 account for 45.1% of the gene pool, whereas northern-prevalent haplogroups A, D, G, N9, and M8 consist of 39.2%. Haplogroup distribution indicates that the Gelao bears signatures of southern populations and possesses some regional characters. In the PC map, Gelao clusters together with populations with Bai-Yue tribe origin as well as the local Han and the Miao. The results demonstrate the complexity of Gelao population and the data can well supplement the China mtDNA database.}, }
@article {pmid20480038, year = {2010}, author = {Roy, L and Dowling, AP and Chauve, CM and Buronfosse, T}, title = {Diversity of phylogenetic information according to the locus and the taxonomic level: an example from a parasitic mesostigmatid mite genus.}, journal = {International journal of molecular sciences}, volume = {11}, number = {4}, pages = {1704-1734}, pmid = {20480038}, issn = {1422-0067}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/chemistry/metabolism ; Gene Frequency ; *Genome, Protozoan ; Introns ; Mites/classification/*genetics ; Mitochondria/genetics ; Peptide Elongation Factor 1/genetics ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/metabolism ; Tropomyosin/genetics ; }, abstract = {Molecular markers for cladistic analyses may perform differently according to the taxonomic group considered and the historical level under investigation. Here we evaluate the phylogenetic potential of five different markers for resolving evolutionary relationships within the ectoparasitic genus Dermanyssus at the species level, and their ability to address questions about the evolution of specialization. COI provided 9-18% divergence between species (up to 9% within species), 16S rRNA 10-16% (up to 4% within species), ITS1 and 2 2-9% (up to 1% within species) and Tropomyosin intron n 8-20% (up to 6% within species). EF-1alpha revealed different non-orthologous copies within individuals of Dermanyssus and Ornithonyssus. Tropomyosin intron n was shown containing consistent phylogenetic signal at the specific level within Dermanyssus and represents a promising marker for future prospects in phylogenetics of Acari. Phylogenetic analyses revealed that the generalist condition is apomorphic and D. gallinae might represent a complex of hybridized lineages. The split into hirsutus-group and gallinae-group in Dermanyssus does not seem to be appropriate based upon these results and D. longipes appears to be composed of two different entities.}, }
@article {pmid20473316, year = {2010}, author = {Gobert, A and Gutmann, B and Taschner, A and Gössringer, M and Holzmann, J and Hartmann, RK and Rossmanith, W and Giegé, P}, title = {A single Arabidopsis organellar protein has RNase P activity.}, journal = {Nature structural &amp; molecular biology}, volume = {17}, number = {6}, pages = {740-744}, pmid = {20473316}, issn = {1545-9985}, support = {I 299/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Amino Acid Sequence ; Animals ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Aspartic Acid/chemistry ; Base Sequence ; Catalytic Domain/genetics ; Conserved Sequence ; Escherichia coli/enzymology/genetics ; Evolution, Molecular ; Genes, Plant ; Humans ; Mitochondria/metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Plastids/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Plant/chemistry/genetics/metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Ribonuclease P/chemistry/genetics/*metabolism ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {The ubiquitous endonuclease RNase P is responsible for the 5' maturation of tRNA precursors. Until the discovery of human mitochondrial RNase P, these enzymes had typically been found to be ribonucleoproteins, the catalytic activity of which is associated with the RNA component. Here we show that, in Arabidopsis thaliana mitochondria and plastids, a single protein called 'proteinaceous RNase P' (PRORP1) can perform the endonucleolytic maturation of tRNA precursors that defines RNase P activity. In addition, PRORP1 is able to cleave tRNA-like structures involved in the maturation of plant mitochondrial mRNAs. Finally, we show that Arabidopsis PRORP1 can replace the bacterial ribonucleoprotein RNase P in Escherichia coli cells. PRORP2 and PRORP3, two paralogs of PRORP1, are both localized in the nucleus.}, }
@article {pmid20470834, year = {2010}, author = {Týc, J and Long, S and Jirků, M and Lukes, J}, title = {YCF45 protein, usually associated with plastids, is targeted into the mitochondrion of Trypanosoma brucei.}, journal = {Molecular and biochemical parasitology}, volume = {173}, number = {1}, pages = {43-47}, doi = {10.1016/j.molbiopara.2010.05.002}, pmid = {20470834}, issn = {1872-9428}, mesh = {Cell Line ; Gene Transfer, Horizontal ; Humans ; Mitochondria/genetics/*metabolism ; Phylogeny ; Plastids/genetics/*metabolism ; Protein Transport ; Protozoan Proteins/genetics/*metabolism ; Trypanosoma brucei brucei/classification/genetics/*metabolism ; }, abstract = {YCF45 belongs to a family of proteins of unknown function usually located in the chloroplast of plants. Its highly conserved homologues were found in the genomes of several Trypanosoma and Leishmania species. HA(3)-tagging of the YCF45 protein with the start codon as annotated in the Gene(DB) revealed its cytosolic localization in the cultured procyclic stage of Trypanosoma brucei. However, when a more upstream located start codon was used in another HA(3)-tagged construct, the resulting protein was targeted to the mitochondrion. We propose that YCF45 was acquired by an ancestral trypanosomatid by horizontal gene transfer and in the absence of a plastid was re-targeted to the mitochondrion.}, }
@article {pmid20467212, year = {2010}, author = {Kuroiwa, T}, title = {Mechanisms of organelle division and inheritance and their implications regarding the origin of eukaryotic cells.}, journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences}, volume = {86}, number = {5}, pages = {455-471}, pmid = {20467212}, issn = {1349-2896}, mesh = {Animals ; Eukaryotic Cells/*cytology/metabolism/radiation effects ; Gene Targeting ; Genome/genetics ; Humans ; Light ; *Models, Biological ; Organelles/*genetics/*metabolism/radiation effects ; Reproduction, Asexual/genetics ; }, abstract = {Mitochondria and plastids have their own DNAs and are regarded as descendants of endosymbiotic prokaryotes. Organellar DNAs are not naked in vivo but are associated with basic proteins to form DNA-protein complexes (called organelle nuclei). The concept of organelle nuclei provides a new approach to explain the origin, division, and inheritance of organelles. Organelles divide using organelle division rings (machineries) after organelle-nuclear division. Organelle division machineries are a chimera of the FtsZ (filamentous temperature sensitive Z) ring of bacterial origin and the eukaryotic mechanochemical dynamin ring. Thus, organelle division machineries contain a key to solve the origin of organelles (eukaryotes). The maternal inheritance of organelles developed during sexual reproduction and it is also probably intimately related to the origin of organelles. The aims of this review are to describe the strategies used to reveal the dynamics of organelle division machineries, and the significance of the division machineries and maternal inheritance in the origin and evolution of eukaryotes.}, }
@article {pmid20466631, year = {2010}, author = {Chen, JN}, title = {[Progress in molecular chaperones participating in regulations of plant and animal development and evolution].}, journal = {Yi chuan = Hereditas}, volume = {32}, number = {5}, pages = {443-447}, doi = {10.3724/sp.j.1005.2010.00443}, pmid = {20466631}, issn = {0253-9772}, mesh = {Animals ; *Evolution, Molecular ; Fertility/genetics/physiology ; Gene Expression Regulation ; HSP70 Heat-Shock Proteins/genetics/physiology ; Heat-Shock Proteins/genetics/*physiology ; Molecular Chaperones/genetics/*physiology ; *Plant Development ; Plant Proteins/genetics/physiology ; Plants/genetics ; }, abstract = {Progresses have been made on the functions of molecular chaperone in folding, assemble, and transportation of the proteins synthesized in novo and the degradation of proteins. The number of mitochondria was changed in combination with the change of the expression of chaperone. Here, we would elucidate the progress in chaperone participating in regulations of plant and animal development and evolution. This review mainly focused on the regulation of plant and animal fertility, the improvement of stress resistance, and some progresses in tumor treatment of heat shock protein.}, }
@article {pmid20461407, year = {2010}, author = {Li, J and Zhao, GH and Zou, FC and Mo, XH and Yuan, ZG and Ai, L and Li, HL and Weng, YB and Lin, RQ and Zhu, XQ}, title = {Combined mitochondrial 16S and 12S rDNA sequences: an effective genetic marker for inter-species phylogenetic analysis of zoonotic trematodes.}, journal = {Parasitology research}, volume = {107}, number = {3}, pages = {561-569}, pmid = {20461407}, issn = {1432-1955}, mesh = {Animals ; China/epidemiology ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/analysis/genetics ; Female ; Genetic Markers/*genetics ; Genetic Variation ; Humans ; Male ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; Schistosoma japonicum/classification/*genetics ; Schistosomiasis japonica/epidemiology/parasitology ; Sequence Analysis, DNA ; Species Specificity ; Zoonoses/epidemiology/*parasitology ; }, abstract = {The present study studied the genetic variation among Schistosoma japonicum isolates from different endemic regions in mainland China and examined the phylogenetic relationships of zoonotic trematodes using the combined mitochondrial 16S and 12S ribosomal DNA sequences. The fragments of 16S and 12S rDNA were amplified from 22 S. japonicum isolates, and sequenced, and the relevant sequences of other nine trematode species belonging to six genera in four families were downloaded from GenBank, and their phylogenetic relationships were re-constructed by unweighted pair-group method with arithmetic averages analyses using the combined 16S and 12S rDNA sequences, with Trichinella spiralis as outgroup. The results showed that the partial sequences of mitochondrial 16S and 12S rDNA of S. japonicum were 757 and 797 bp, respectively, and they were quite conserved among the S. japonicum isolates. Phylogenetic analysis revealed that the combined 16S and 12S rDNA sequences were not able to distinguish S. japonicum isolates in mountainous areas from those in lake/marshland areas in mainland China. However, the combined sequences could distinguish different species of zoonotic trematodes. Therefore, the combined mitochondrial 16S and 12S rDNA sequences provide an effective molecular marker for the inter-species phylogenetic analysis and differential identification of zoonotic trematodes.}, }
@article {pmid20460712, year = {2010}, author = {Nakanishi, Y and Zhou, S and Kim, SW and Fushinobu, S and Maruyama, J and Kitamoto, K and Wakagi, T and Shoun, H}, title = {A eukaryotic copper-containing nitrite reductase derived from a NirK homolog gene of Aspergillus oryzae.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {74}, number = {5}, pages = {984-991}, doi = {10.1271/bbb.90844}, pmid = {20460712}, issn = {1347-6947}, mesh = {Amino Acid Sequence ; Aspergillus oryzae/cytology/*enzymology/*genetics ; Cloning, Molecular ; *Copper ; Cytochrome P-450 Enzyme System/deficiency/genetics ; Gene Deletion ; Genes, Bacterial/genetics ; Genes, Fungal/genetics ; Mitochondria/metabolism ; Molecular Sequence Data ; Nitrite Reductases/*chemistry/*genetics/isolation &amp; purification/metabolism ; Nitrogen/metabolism ; Recombinant Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Sequence Alignment ; *Sequence Homology, Nucleic Acid ; }, abstract = {We cloned a bacterial copper-containing nitrite reductase (NirK) homolog gene of Aspergillus oryzae (AonirK). Alignment showed that amino acid residues crucial for copper binding are conserved in the deduced sequence of the fungal protein. The recombinant protein exhibited distinct nitrite reductase activity, and its absorption and EPR spectra showed the presence of type 1 and type 2 copper atoms in the molecule. AonirK transcriptionally responded to denitrification conditions. Although the denitrifying activity of A. oryzae was weak under the conditions employed, high expression of the gene in the fungal cells enhanced the denitrifying activity 6-fold, accompanied by distinct cell growth. Furthermore, the highly expressed AoNirK was subcellularly localized to the mitochondria. The results demonstrated that AoNirK is responsible for fungal denitrification. Discussion is added on the novel insight concerning the origin and evolution of the mitochondrion provided by the findings for eukaryotic NirKs.}, }
@article {pmid20457275, year = {2010}, author = {Jedrzejowska, I and Kubrakiewicz, J}, title = {Yolk nucleus--the complex assemblage of cytoskeleton and ER is a site of lipid droplet formation in spider oocytes.}, journal = {Arthropod structure &amp; development}, volume = {39}, number = {5}, pages = {350-359}, doi = {10.1016/j.asd.2010.05.001}, pmid = {20457275}, issn = {1873-5495}, mesh = {Animals ; Cytoskeleton/*metabolism/ultrastructure ; Egg Yolk/*metabolism/ultrastructure ; Endoplasmic Reticulum/*metabolism/ultrastructure ; Female ; *Lipid Metabolism ; Oocytes/*metabolism/ultrastructure ; Ovary/anatomy &amp; histology ; Spiders/*metabolism/ultrastructure ; Vitellogenesis ; }, abstract = {Oocytes (future egg cells) of various animal groups often contain complex organelle assemblages (Balbiani bodies, yolk nuclei). The molecular composition and function of Balbiani bodies, such as those found in the oocytes of Xenopus laevis, have been recently recognized. In contrast, the functional significance of more complex and highly ordered yolk nuclei has not been elucidated to date. In this report we describe the structure, cytochemical content and evolution of the yolk nucleus in the oocytes of a common spider, Clubiona sp. We show that the yolk nucleus is a spherical, rather compact and persistent cytoplasmic accumulation of several different organelles. It consists predominantly of a highly elaborate cytoskeletal scaffold of condensed filamentous actin and a dense meshwork of intermediate-sized filaments. The yolk nucleus also comprises cisterns of endoplasmic reticulum, mitochondria, lipid droplets and other organelles. Nascent lipid droplets are regularly found in the cortical regions of the yolk nucleus in association with the endoplasmic reticulum. Single lipid droplets become surrounded by filamentous cages formed by intermediate filaments. Coexistence of the forming lipid droplets with the endoplasmic reticulum in the cortical zone of the yolk nucleus and their later investment by intermediate-sized filamentous cages suggest that the yolk nucleus is the birthplace of lipid droplets.}, }
@article {pmid20451940, year = {2010}, author = {Pajak, B and Pawlikowska, P and Cassar-Malek, I and Picard, B and Hocquette, JF and Orzechowski, A}, title = {Abundance of some skeletal muscle mitochondrial proteins is associated with increased blood serum insulin in bovine fetuses.}, journal = {Research in veterinary science}, volume = {89}, number = {3}, pages = {445-450}, doi = {10.1016/j.rvsc.2010.04.013}, pmid = {20451940}, issn = {1532-2661}, mesh = {Animals ; Blood Glucose/analysis ; Cattle ; Electron Transport Complex IV/metabolism/physiology ; Electrophoresis, Polyacrylamide Gel/veterinary ; Female ; Fetus/*metabolism/physiology ; Immunoblotting/veterinary ; Insulin/*blood ; Mitochondria, Muscle/enzymology/*metabolism/physiology ; Mitochondrial Proton-Translocating ATPases/metabolism/physiology ; Muscle, Skeletal/embryology ; Pregnancy ; Protein Subunits ; }, abstract = {The aim of this study was to investigate the evolution of the abundance of cytochrome oxidase c subunit IV (NCOIV) and beta subunit of ATP synthase (β-ATP) during the last third of gestation in bovine skeletal muscles. Semitendinosus, longissimus thoracis and rectus abdominis muscles were chosen for the immunoblotting of the respective protein levels. Muscle and blood samples from bovine fetuses of randomly selected breeds were collected at 180, 210, and 260 days post-conception (dpc). The muscle tissue expressions of NCOIV, β-ATP were compared to blood glucose and insulin. At 260 dpc, protein levels of NCOIV raised in skeletal muscles. Additionally, β-ATP in semitendinosus and longissimus thoracis were elevated and paralleled by higher concentrations of blood serum insulin. It corroborates our previous observations indicating that accelerated metabolic differentiation of bovine skeletal muscles is associated with elevated blood insulin and occurs during the last trimester of gestation. Our observations point to the connection between insulin-sensitivity and the molecular mechanisms of mitochondrial contribution to ontogenesis of skeletal muscles.}, }
@article {pmid20450883, year = {2010}, author = {Zeth, K}, title = {Structure and evolution of mitochondrial outer membrane proteins of beta-barrel topology.}, journal = {Biochimica et biophysica acta}, volume = {1797}, number = {6-7}, pages = {1292-1299}, doi = {10.1016/j.bbabio.2010.04.019}, pmid = {20450883}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Animals ; Conserved Sequence ; Evolution, Molecular ; Gram-Negative Bacteria/genetics/metabolism ; Humans ; Mice ; Mitochondrial Membrane Transport Proteins/chemistry/genetics ; Mitochondrial Membranes/*chemistry ; Mitochondrial Proteins/*chemistry/*genetics ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics ; Sequence Homology, Amino Acid ; Static Electricity ; Voltage-Dependent Anion Channels/chemistry/genetics ; }, abstract = {Gram-negative bacteria are the ancestors of mitochondrial organelles. Consequently, both entities contain two surrounding lipid bilayers known as the inner and outer membranes. While protein synthesis in bacteria is accomplished in the cytoplasm, mitochondria import 90-99% of their protein ensemble from the cytosol in the opposite direction. Three protein families including Sam50, VDAC and Tom40 together with Mdm10 compose the set of integral beta-barrel proteins embedded in the mitochondrial outer membrane in S. cerevisiae (MOM). The 16-stranded Sam50 protein forms part of the sorting and assembly machinery (SAM) and shows a clear evolutionary relationship to members of the bacterial Omp85 family. By contrast, the evolution of VDAC and Tom40, both adopting the same fold cannot be traced to any bacterial precursor. This finding is in agreement with the specific function of Tom40 in the TOM complex not existent in the enslaved bacterial precursor cell. Models of Tom40 and Sam50 have been developed using X-ray structures of related proteins. These models are analyzed with respect to properties such as conservation and charge distribution yielding features related to their individual functions.}, }
@article {pmid20446451, year = {2010}, author = {Tian, HF and Wen, JF}, title = {[Diversity of parasitic protozoan mitochondria and adaptive evolution].}, journal = {Dong wu xue yan jiu = Zoological research}, volume = {31}, number = {1}, pages = {35-38}, doi = {10.3724/sp.j.1141.2010.01035}, pmid = {20446451}, issn = {0254-5853}, mesh = {*Adaptation, Biological ; Animals ; *Biological Evolution ; Euglenozoa/genetics/*metabolism ; Mitochondria/genetics/*metabolism ; Parasites/genetics/*metabolism ; }, abstract = {Eukaryotic mitochondrion generally possess a definite and canonical structure and function. However, in the unicellular parasitic protozoa, various atypical mitochondria with respect to the number, structure, and function, have been discovered consecutively, revealing the variability, plasticity and rich diversity of mitochondrion. Here, we review the mitochondrial diversity in diverse parasitic protozoa, and the underlying reason for such diversity--the adaptive evolution of mitochondrion to the micro-oxygen or anaero parasitic environment of these parasites is also analyzed and discussed.}, }
@article {pmid20446039, year = {2010}, author = {Lee, TY and Lee, KC and Chang, HH}, title = {Modulation of the cannabinoid receptors by andrographolide attenuates hepatic apoptosis following bile duct ligation in rats with fibrosis.}, journal = {Apoptosis : an international journal on programmed cell death}, volume = {15}, number = {8}, pages = {904-914}, doi = {10.1007/s10495-010-0502-z}, pmid = {20446039}, issn = {1573-675X}, mesh = {Animals ; Anti-Inflammatory Agents/*pharmacology ; Apoptosis/*drug effects ; Bile Ducts/*surgery ; Diterpenes/*pharmacology ; Extracellular Signal-Regulated MAP Kinases/metabolism ; Fibrosis/metabolism/pathology ; Glutathione/metabolism ; JNK Mitogen-Activated Protein Kinases/metabolism ; Ligation ; *Liver/drug effects/metabolism/pathology ; Male ; Mitochondria/metabolism ; Molecular Sequence Data ; Proteome/analysis ; Rats ; Rats, Sprague-Dawley ; Receptor, Cannabinoid, CB1/*metabolism ; Receptor, Cannabinoid, CB2/*metabolism ; Signal Transduction/physiology ; Superoxide Dismutase/metabolism ; Thiobarbituric Acid Reactive Substances/metabolism ; p38 Mitogen-Activated Protein Kinases/metabolism ; }, abstract = {Bile acid-induced apoptosis plays an important role in the pathogenesis of cholestatic liver disease, and its prevention is of therapeutic interest. The aim of this study was to test whether the andrographolide limits the evolution of apoptosis in a murine model of bile duct ligation (BDL)-induced hepatic fibrosis. Male Sprague-Dawley rats were divided into four groups and hepatic apoptosis was induced by BDL for 2 weeks. The BDL animals were also treated with andrographolide (50, 100, and 200 mg/kg, i.p.) during the same time period. BDL-induced liver injury was associated with apoptosis and fibrosis, and the latter was significantly reduced in animals receiving andrographolide. The increase in serum alanine aminotransferase, asparate aminotransferase, tumor necrosis factor-alpha and IL-1beta levels caused by BDL were also significantly reduced by treatment with andrographolide. Andrographolide decreased the intrahepatic protein levels of cannabinoid receptor 1 (CB1), Bax, and cytochrome c, along with of alpha-smooth muscle actin (alpha-SMA) and transforming growth factor-beta (TGF-beta), two markers of fibrogenesis. This effect was mediated by the inactivation of the c-Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK1/2) phosphorylation cascade, but it did not affect the p38 mitogen-activated protein kinase pathway. Additionally, andrographolide reduced the generation of hepatic lipid peroxidation and enhance senescence marker protein-30 levels to resist the hepatic oxidative stress in the presence of BDL. In conclusion, this study has identified AP as a potent protector against cholestasis-induced apoptosis in vivo. Its anti-apoptotic action largely relies on the inhibition of the oxidative stress pathway.}, }
@article {pmid20445102, year = {2010}, author = {Wallace, DC}, title = {Colloquium paper: bioenergetics, the origins of complexity, and the ascent of man.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107 Suppl 2}, number = {Suppl 2}, pages = {8947-8953}, pmid = {20445102}, issn = {1091-6490}, support = {NS21328/NS/NINDS NIH HHS/United States ; R01 AG024373-05/AG/NIA NIH HHS/United States ; AG16573/AG/NIA NIH HHS/United States ; R01 NS021328-24/NS/NINDS NIH HHS/United States ; R01 DK073691-04/DK/NIDDK NIH HHS/United States ; DK73691/DK/NIDDK NIH HHS/United States ; P50 AG016573/AG/NIA NIH HHS/United States ; R01 AG013154-11/AG/NIA NIH HHS/United States ; AG24373/AG/NIA NIH HHS/United States ; R01 AG024373/AG/NIA NIH HHS/United States ; R01 DK073691/DK/NIDDK NIH HHS/United States ; R01 NS021328/NS/NINDS NIH HHS/United States ; R01 AG013154/AG/NIA NIH HHS/United States ; AG13154/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/metabolism ; DNA/metabolism ; Electrochemistry/methods ; *Energy Metabolism ; Humans ; Membrane Potentials ; Mitochondria/metabolism ; Mutation ; Selection, Genetic ; }, abstract = {Complex structures are generated and maintained through energy flux. Structures embody information, and biological information is stored in nucleic acids. The progressive increase in biological complexity over geologic time is thus the consequence of the information-generating power of energy flow plus the information-accumulating capacity of DNA, winnowed by natural selection. Consequently, the most important component of the biological environment is energy flow: the availability of calories and their use for growth, survival, and reproduction. Animals can exploit and adapt to available energy resources at three levels. They can evolve different anatomical forms through nuclear DNA (nDNA) mutations permitting exploitation of alternative energy reservoirs, resulting in new species. They can evolve modified bioenergetic physiologies within a species, primarily through the high mutation rate of mitochondrial DNA (mtDNA)-encoded bioenergetic genes, permitting adjustment to regional energetic environments. They can alter the epigenomic regulation of the thousands of dispersed bioenergetic genes via mitochondrially generated high-energy intermediates permitting individual accommodation to short-term environmental energetic fluctuations. Because medicine pertains to a single species, Homo sapiens, functional human variation often involves sequence changes in bioenergetic genes, most commonly mtDNA mutations, plus changes in the expression of bioenergetic genes mediated by the epigenome. Consequently, common nDNA polymorphisms in anatomical genes may represent only a fraction of the genetic variation associated with the common "complex" diseases, and the ascent of man has been the product of 3.5 billion years of information generation by energy flow, accumulated and preserved in DNA and edited by natural selection.}, }
@article {pmid20439315, year = {2010}, author = {Haen, KM and Pett, W and Lavrov, DV}, title = {Parallel loss of nuclear-encoded mitochondrial aminoacyl-tRNA synthetases and mtDNA-encoded tRNAs in Cnidaria.}, journal = {Molecular biology and evolution}, volume = {27}, number = {10}, pages = {2216-2219}, doi = {10.1093/molbev/msq112}, pmid = {20439315}, issn = {1537-1719}, mesh = {Amino Acyl-tRNA Synthetases/*genetics ; Animals ; Cell Nucleus/*genetics ; Cnidaria/*genetics ; Computational Biology ; *Evolution, Molecular ; Humans ; Mitochondrial Proteins/*genetics ; Models, Genetic ; *Phylogeny ; RNA, Transfer/*genetics ; Saccharomyces cerevisiae ; }, abstract = {Unlike most animal mitochondrial (mt) genomes, which encode a set of 22 transfer RNAs (tRNAs) sufficient for mt protein synthesis, those of cnidarians have only retained one or two tRNA genes. Whether the missing cnidarian mt-tRNA genes relocated outside the main mt chromosome or were lost remains unclear. It is also unknown what impact the loss of tRNA genes had on other components of the mt translational machinery. Here, we explored the nuclear genome of the cnidarian Nematostella vectensis for the presence of mt-tRNA genes and their corresponding mt aminoacyl-tRNA synthetases (mt-aaRS). We detected no candidates for mt-tRNA genes and only two mt-aaRS orthologs. At the same time, we found that all but one cytosolic aaRS appear to be targeted to mitochondria. These results indicate that the loss of mt-tRNAs in Cnidaria is genuine and occurred in parallel with the loss of nuclear-encoded mt-aaRS. Our phylogenetic analyses of individual aaRS revealed that although the nearly total loss of mt-aaRS is rare, aaRS gene deletion and replacement have occurred throughout the evolution of Metazoa.}, }
@article {pmid20433942, year = {2010}, author = {Mogi, T and Kita, K}, title = {Diversity in mitochondrial metabolic pathways in parasitic protists Plasmodium and Cryptosporidium.}, journal = {Parasitology international}, volume = {59}, number = {3}, pages = {305-312}, doi = {10.1016/j.parint.2010.04.005}, pmid = {20433942}, issn = {1873-0329}, mesh = {Animals ; Cryptosporidiosis/parasitology ; Cryptosporidium/enzymology/genetics/*metabolism ; DNA, Mitochondrial/genetics/metabolism ; Humans ; Malaria/parasitology ; *Metabolic Networks and Pathways ; Mitochondria/enzymology/genetics/*metabolism ; Plasmodium/enzymology/genetics/*metabolism ; }, abstract = {Apicomplexans are obligate intracellular parasites and occupy diverse niches. They have remodeled mitochondrial carbon and energy metabolism through reductive evolution. Plasmodium lacks mitochondrial pyruvate dehydrogenase and H(+)-translocating NADH dehydrogenase (Complex I, NDH1). The mitochondorion contains a minimal mtDNA (approximately 6kb) and carries out oxidative phosphorylation in the insect vector stages, by using 2-oxoglutarate as an alternative means of entry into the TCA cycle and a single-subunit flavoprotein as an alternative NADH dehydrogenase (NDH2). In the blood stages of mammalian hosts, mitochondrial enzymes are down-regulated and parasite energy metabolism relies mainly on glycolysis. Mitosomes of Cryptosporidium parvum and Cryptosporidium hominis (human intestine parasites) lack mtDNA, pyruvate dehydrogenase, TCA cycle enzymes except malate-quinone oxidoreductase (MQO), and ATP synthase subunits except alpha and beta. In contrast, mitosomes of Cryptosporidium muris (a rodent gastric parasite) retain all TCA cycle enzymes and functional ATP synthase and carry out oxidative phosphorylation with pyruvate-NADP(+) oxidoreductase (PNO) and a simple and unique respiratory chain consisting of NDH2 and alternative oxidase (AOX). Cryptosporidium and Perkinsus are early branching groups of chromoalveolates (apicomplexa and dinoflagellates, respectively), and both Cryptosporidium mitosome and Perkinsus mitochondrion use PNO, MQO, and AOX. All apicomplexan parasites and dinoflagellates share MQO, which has been acquired from epsilon-proteobacteria via lateral gene transfer. By genome data mining on Plasmodium, Cryptosporidium and Perkinsus, here we summarized their mitochondrial metabolic pathways, which are varied largely from those of mammalian hosts. We hope that our findings will help in understanding the apicomplexan metabolism and development of new chemotherapeutics with novel targets.}, }
@article {pmid20421605, year = {2010}, author = {Bentley, KE and Mandel, JR and McCauley, DE}, title = {Paternal leakage and heteroplasmy of mitochondrial genomes in Silene vulgaris: evidence from experimental crosses.}, journal = {Genetics}, volume = {185}, number = {3}, pages = {961-968}, pmid = {20421605}, issn = {1943-2631}, mesh = {DNA, Mitochondrial/*genetics ; Genome, Mitochondrial/*genetics ; Genotype ; Inheritance Patterns/*genetics ; Mitochondria/*genetics ; Polymerase Chain Reaction ; Recombination, Genetic ; Silene/*genetics ; }, abstract = {The inheritance of mitochondrial genetic (mtDNA) markers in the gynodioecious plant Silene vulgaris was studied using a series of controlled crosses between parents of known mtDNA genotype followed by quantitative PCR assays of offspring genotype. Overall, approximately 2.5% of offspring derived from crosses between individuals that were homoplasmic for different mtDNA marker genotypes showed evidence of paternal leakage. When the source population of the pollen donor was considered, however, population-specific rates of leakage varied significantly around this value, ranging from 10.3% to zero. When leakage did occur, the paternal contribution ranged from 0.5% in some offspring (i.e., biparental inheritance resulting in a low level of heteroplasmy) to 100% in others. Crosses between mothers known to be heteroplasmic for one of the markers and homoplasmic fathers showed that once heteroplasmy enters a maternal lineage it is retained by approximately 17% of offspring in the next generation, but lost from the others. The results are discussed with regard to previous studies of heteroplasmy in open-pollinated natural populations of S. vulgaris and with regard to the potential impact of mitochondrial paternal leakage and heteroplasmy on both the evolution of the mitochondrial genome and the evolution of gynodioecy.}, }
@article {pmid20421465, year = {2010}, author = {Shen, YY and Liang, L and Zhu, ZH and Zhou, WP and Irwin, DM and Zhang, YP}, title = {Adaptive evolution of energy metabolism genes and the origin of flight in bats.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {19}, pages = {8666-8671}, pmid = {20421465}, issn = {1091-6490}, mesh = {Adaptation, Physiological/*genetics ; Animals ; Chiroptera/*genetics/*physiology ; Energy Metabolism/*genetics ; *Evolution, Molecular ; Flight, Animal/*physiology ; Humans ; Molecular Sequence Data ; Phylogeny ; Rodentia/genetics ; Selection, Genetic ; }, abstract = {Bat flight poses intriguing questions about how flight independently developed in mammals. Flight is among the most energy-consuming activities. Thus, we deduced that changes in energy metabolism must be a primary factor in the origin of flight in bats. The respiratory chain of the mitochondrial produces 95% of the adenosine triphosphate (ATP) needed for locomotion. Because the respiratory chain has a dual genetic foundation, with genes encoded by both the mitochondrial and nuclear genomes, we examined both genomes to gain insights into the evolution of flight within mammals. Evidence for positive selection was detected in 23.08% of the mitochondrial-encoded and 4.90% of nuclear-encoded oxidative phosphorylation (OXPHOS) genes, but in only 2.25% of the nuclear-encoded nonrespiratory genes that function in mitochondria or 1.005% of other nuclear genes in bats. To address the caveat that the two available bat genomes are of only draft quality, we resequenced 77 OXPHOS genes from four species of bats. The analysis of the resequenced gene data are in agreement with our conclusion that a significantly higher proportion of genes involved in energy metabolism, compared with background genes, show evidence of adaptive evolution specific on the common ancestral bat lineage. Both mitochondrial and nuclear-encoded OXPHOS genes display evidence of adaptive evolution along the common ancestral branch of bats, supporting our hypothesis that genes involved in energy metabolism were targets of natural selection and allowed adaptation to the huge change in energy demand that were required during the origin of flight.}, }
@article {pmid20421194, year = {2010}, author = {Ohara, K and Sasaki, K and Yazaki, K}, title = {Two solanesyl diphosphate synthases with different subcellular localizations and their respective physiological roles in Oryza sativa.}, journal = {Journal of experimental botany}, volume = {61}, number = {10}, pages = {2683-2692}, pmid = {20421194}, issn = {1460-2431}, mesh = {Alkyl and Aryl Transferases/genetics/*metabolism ; Enzyme Assays ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Genetic Complementation Test ; Green Fluorescent Proteins/metabolism ; Intracellular Space/metabolism ; Organ Specificity/genetics ; Oryza/*enzymology/genetics ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plastoquinone/chemistry/metabolism ; Protein Transport ; RNA, Messenger/genetics/metabolism ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Subcellular Fractions/enzymology ; Substrate Specificity ; Ubiquinone/biosynthesis/chemistry ; }, abstract = {Long chain prenyl diphosphates are crucial biosynthetic precursors of ubiquinone (UQ) in many organisms, ranging from bacteria to humans, as well as precursors of plastoquinone in photosynthetic organisms. The cloning and characterization of two solanesyl diphosphate synthase genes, OsSPS1 and OsSPS2, in Oryza sativa is reported here. OsSPS1 was highly expressed in root tissue whereas OsSPS2 was found to be high in both leaves and roots. Enzymatic characterization using recombinant proteins showed that both OsSPS1 and OsSPS2 could produce solanesyl diphosphates as their final product, while OsSPS1 showed stronger activity than OsSPS2. However, an important biological difference was observed between the two genes: OsSPS1 complemented the yeast coq1 disruptant, which does not form UQ, whereas OsSPS2 only very weakly complemented the growth defect of the coq1 mutant. HPLC analyses showed that both OsSPS1 and OsSPS2 yeast transformants produced UQ9 instead of UQ6, which is the native yeast UQ. According to the complementation study, the UQ9 levels in OsSPS2 transformants were much lower than that of OsSPS1. Green fluorescent protein fusion analyses showed that OsSPS1 localized to mitochondria, while OsSPS2 localized to plastids. This suggests that OsSPS1 is involved in the supply of solanesyl diphosphate for ubiquinone-9 biosynthesis in mitochondria, whereas OsSPS2 is involved in providing solanesyl diphosphate for plastoquinone-9 formation. These findings indicate that O. sativa has a different mechanism for the supply of isoprenoid precursors in UQ biosynthesis from Arabidopsis thaliana, in which SPS1 provides a prenyl moiety for UQ9 at the endoplasmic reticulum.}, }
@article {pmid20419426, year = {2010}, author = {Vögtle, FN and Schmidt, O and Chacinska, A and Pfanner, N and Meisinger, C}, title = {Native techniques for analysis of mitochondrial protein import.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {619}, number = {}, pages = {425-436}, doi = {10.1007/978-1-60327-412-8_26}, pmid = {20419426}, issn = {1940-6029}, mesh = {Mitochondrial Proteins/*metabolism ; Models, Biological ; Protein Transport/*physiology ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; }, abstract = {During the evolution of eukaryotic cells, the majority of mitochondrial genes have been transferred to the nuclear genome with the consequence that most mitochondrial proteins have to be imported into the organelle. This process occurs usually in a post-translational manner. In order to accomplish this task elaborate protein machineries have evolved that import precursor proteins in a concerted fashion and sort them into the four mitochondrial subcompartments. Native techniques such as Blue Native Electrophoresis allow to analyze the composition of the import machineries and to characterize the cooperation of import components. The analysis has led to the discovery of new components and import pathways of mitochondria.}, }
@article {pmid20419418, year = {2010}, author = {Strittmatter, P and Soll, J and Bölter, B}, title = {The chloroplast protein import machinery: a review.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {619}, number = {}, pages = {307-321}, doi = {10.1007/978-1-60327-412-8_18}, pmid = {20419418}, issn = {1940-6029}, mesh = {Chloroplasts/*metabolism ; Genome, Plastid ; Models, Biological ; Plant Proteins/chemistry/*metabolism ; Protein Sorting Signals/physiology ; Protein Transport/*physiology ; }, abstract = {Plastids are a heterogeneous family of organelles found ubiquitously in plants and algal cells. Most prominent are the chloroplasts, which carry out such essential processes as photosynthesis and the biosynthesis of fatty acids as well as of amino acids. As mitochondria, chloroplasts are derived from a single endosymbiotic event. They are believed to have evolved from an ancient cyanobacterium, which was engulfed by an early eukaryotic ancestor. During evolution the plastid genome has been greatly reduced and most of the genes have been transferred to the host nucleus. Consequently, more than 98% of all plastid proteins are translated on cytosolic ribosomes. They have to be posttranslationally targeted to and imported into the organelle. Targeting is assisted by cytosolic proteins which interact with proteins destined for plastids and thereby keep them in an import competent state. After reaching the target organelle, many proteins have to conquer the barrier of the chloroplast outer and inner envelope. This process is mediated by complex molecular machines in the outer (Toc complex) and inner (Tic complex) envelope of chloroplasts, respectively. Most proteins destined for the compartments inside the chloroplast contain a cleavable N-terminal transit peptide, whereas most of the outer envelope components insert into the membrane without such a targeting peptide.}, }
@article {pmid20403720, year = {2010}, author = {Bauwe, H and Hagemann, M and Fernie, AR}, title = {Photorespiration: players, partners and origin.}, journal = {Trends in plant science}, volume = {15}, number = {6}, pages = {330-336}, doi = {10.1016/j.tplants.2010.03.006}, pmid = {20403720}, issn = {1878-4372}, mesh = {Animals ; Biological Evolution ; Mitochondria/*metabolism ; Nitrogen/metabolism ; *Phototrophic Processes ; Plants/genetics/*metabolism ; }, abstract = {Photorespiratory metabolism allows plants to thrive in a high-oxygen containing environment. This metabolic pathway recycles phosphoglycolate, a toxic compound, back to phosphoglycerate, when oxygen substitutes for carbon dioxide in the first reaction of photosynthetic carbon fixation. The recovery of phosphoglycerate is accompanied by considerable carbon and energy losses, making photorespiration a prime target for crop improvement. The genomics era has allowed the precise functional analysis of individual reaction steps of the photorespiratory cycle, and more links integrating photorespiration with cellular metabolism as a whole are becoming apparent. Here we review the evolutionary origins of photorespiration as well as new insights into the interaction with other metabolic processes such as nitrogen assimilation and mitochondrial respiration.}, }
@article {pmid20399914, year = {2010}, author = {Dayan, FE and Daga, PR and Duke, SO and Lee, RM and Tranel, PJ and Doerksen, RJ}, title = {Biochemical and structural consequences of a glycine deletion in the alpha-8 helix of protoporphyrinogen oxidase.}, journal = {Biochimica et biophysica acta}, volume = {1804}, number = {7}, pages = {1548-1556}, doi = {10.1016/j.bbapap.2010.04.004}, pmid = {20399914}, issn = {0006-3002}, support = {C06 RR-14503-01/RR/NCRR NIH HHS/United States ; }, mesh = {Amaranthus/metabolism ; Catalytic Domain ; Cloning, Molecular ; Crystallography, X-Ray/methods ; Evolution, Molecular ; Glycine/*chemistry ; Herbicides/chemistry ; Kinetics ; Mitochondria/metabolism ; Molecular Conformation ; Protein Conformation ; Protein Structure, Secondary ; Protoporphyrinogen Oxidase/*chemistry ; Nicotiana/metabolism ; }, abstract = {A rare Gly210 deletion in protoporphyrinogen oxidase (PPO) was recently discovered in herbicide-resistant Amaranthus tuberculatus. According to the published X-ray structure of Nicotiana tabacum PPO, Gly210 is adjacent to, not in, the PPO active site, so it is a matter of interest to determine why its deletion imparts resistance to herbicides. In our kinetic experiments, this deletion did not affect the affinity of protoporphyrinogen IX nor the FAD content, but decreased the catalytic efficiency of the enzyme. The suboptimal Kcat was compensated by a significant increase in the Kis for inhibitors and a switch in their interactions from competitive to mixed-type inhibition. In our protein modeling studies on herbicide-susceptible PPO and resistant PPO, we show that Gly210 plays a key role in the alphaL helix-capping motif at the C-terminus of the alpha-8 helix which helps to stabilize the helix. In molecular dynamics simulations, the deletion had significant architecture consequences, destabilizing the alpha-8 helix-capping region and unraveling the last turn of the helix, leading to enlargement of the active site cavity by approximately 50%. This seemingly innocuous deletion of Gly210 of the mitochondrial PPO imparts herbicide resistance to this dual-targeted protein without severely affecting its normal physiological function, which may explain why this unusual mutation was the favored evolutionary path for achieving resistance to PPO inhibitors.}, }
@article {pmid20398660, year = {2010}, author = {Azzolin, L and von Stockum, S and Basso, E and Petronilli, V and Forte, MA and Bernardi, P}, title = {The mitochondrial permeability transition from yeast to mammals.}, journal = {FEBS letters}, volume = {584}, number = {12}, pages = {2504-2509}, pmid = {20398660}, issn = {1873-3468}, support = {GGP08107/TI_/Telethon/Italy ; R01 GM069883/GM/NIGMS NIH HHS/United States ; R01 GM069883-04/GM/NIGMS NIH HHS/United States ; GM69883/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Calcium/metabolism ; Cyclophilins/metabolism ; Cyclosporine/pharmacology ; Humans ; Mammals/metabolism ; Mitochondria/drug effects/*metabolism ; Mitochondrial Membrane Transport Proteins/*metabolism ; Mitochondrial Permeability Transition Pore ; Permeability/drug effects ; Saccharomyces cerevisiae/drug effects/metabolism ; }, abstract = {Regulated permeability changes have been detected in mitochondria across species. We review here their key features, with the goal of assessing whether a "permeability transition" similar to that observed in higher eukaryotes is present in other species. The recent discoveries (i) that treatment with cyclosporin A (CsA) unmasks an inhibitory site for inorganic phosphate (Pi) [Basso, E., Petronilli, V., Forte, M.A. and Bernardi, P. (2008) Phosphate is essential for inhibition of the mitochondrial permeability transition pore by cyclosporin A and by cyclophilin D ablation. J. Biol. Chem. 283, 26307-26311], the classical inhibitor of the permeability transition of yeast and (ii) that under proper experimental conditions a matrix Ca(2+)-dependence can be demonstrated in yeast as well [Yamada, A., Yamamoto, T., Yoshimura, Y., Gouda, S., Kawashima, S., Yamazaki, N., Yamashita, K., Kataoka, M., Nagata, T., Terada, H., Pfeiffer, D.R. and Shinohara Y. (2009) Ca(2+)-induced permeability transition can be observed even in yeast mitochondria under optimized experimental conditions. Biochim. Biophys. Acta 1787, 1486-1491] suggest that the mitochondrial permeability transition has been conserved during evolution.}, }
@article {pmid20388489, year = {2010}, author = {Rial, E and Rodríguez-Sánchez, L and Gallardo-Vara, E and Zaragoza, P and Moyano, E and González-Barroso, MM}, title = {Lipotoxicity, fatty acid uncoupling and mitochondrial carrier function.}, journal = {Biochimica et biophysica acta}, volume = {1797}, number = {6-7}, pages = {800-806}, doi = {10.1016/j.bbabio.2010.04.001}, pmid = {20388489}, issn = {0006-3002}, mesh = {Animals ; Carrier Proteins/genetics/metabolism ; Fatty Acids/*metabolism/*toxicity ; Humans ; Ion Channels/genetics/metabolism ; Mitochondria/*drug effects/*metabolism ; Mitochondrial Proteins/genetics/metabolism ; Models, Biological ; Oxidative Phosphorylation ; Oxidative Stress/drug effects ; Phylogeny ; Uncoupling Agents/metabolism/toxicity ; Uncoupling Protein 1 ; }, abstract = {Diseases like obesity, diabetes or generalized lipodystrophy cause a chronic elevation of circulating fatty acids that can become cytotoxic, a condition known as lipotoxicity. Fatty acids cause oxidative stress and alterations in mitochondrial structure and function. The uncoupling of the oxidative phosphorylation is one of the most recognized deleterious fatty acid effects and several metabolite transporters are known to mediate in their action. The fatty acid interaction with the carriers leads to membrane depolarization and/or the conversion of the carrier into a pore. The result is the opening of the permeability transition pore and the initiation of apoptosis. Unlike the other members of the mitochondrial carrier superfamily, the eutherian uncoupling protein UCP1 has evolved to achieve its heat-generating capacity in the physiological context provided by the brown adipocyte and therefore it is activated by the low fatty acid concentrations generated by the noradrenaline-stimulated lipolysis.}, }
@article {pmid20381646, year = {2010}, author = {Augot, D and Sauvage, F and Jouet, D and Simphal, E and Veuille, M and Couloux, A and Kaltenbach, ML and Depaquit, J}, title = {Discrimination of Culicoides obsoletus and Culicoides scoticus, potential bluetongue vectors, by morphometrical and mitochondrial cytochrome oxidase subunit I analysis.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {10}, number = {5}, pages = {629-637}, doi = {10.1016/j.meegid.2010.03.016}, pmid = {20381646}, issn = {1567-7257}, mesh = {Animals ; Bluetongue/epidemiology/*transmission ; Bluetongue virus ; Ceratopogonidae/*anatomy &amp; histology/*classification/enzymology/genetics ; DNA, Mitochondrial/analysis ; Electron Transport Complex IV/*genetics ; Female ; Insect Vectors/*anatomy &amp; histology/*classification/enzymology/genetics ; Male ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Principal Component Analysis ; Protein Subunits/*genetics ; }, abstract = {Biting midges of the Culicoides obsoletus Meigen species complex (Diptera: Ceratopogonidae) are increasingly suspected as vectors of the recent emergence of bluetongue virus in Europe. Within this complex, identification of the C. obsoletus and Culicoides scoticus females is considered as difficult or sometimes not possible while the identification of males is easy, based on genitalia observation. Nolan et al. (2007) concluded that the distinction of C. obsoletus and C. scoticus females is not possible according to morphology but require molecular analyses. In 2010, the identification of biting midges is done under a stereomicroscope without specific identification within the C. obsoletus species complex. However, such a specific identification distinguishing C. obsoletus s. str. and C. scoticus s. str. is crucial to identify the European competent vectors of the virus, their relative abundances and then accurately assess the risk. We performed morphometric analyses of head, genitalia and thorax of females combined with sequencing of the cytochrome oxidase I barcode fragment of mitochondrial DNA on 88 specimens in order to have a molecular identification of our sampled species. As we knew the actual species of individuals thanks to molecular results, we explored the discriminant power of 15 morphometric variables to distinguish the females according to their species. Multivariate analyses were performed on the morphometric measurements to identify and validate a combination of variables leading to an accurate species identification. It appears that females of C. obsoletus and C. scoticus can be accurately distinguished based on only four variables: width between chitinous plates, length and width of spermathecae1 and length of spermatheca2. This approach should improve the accuracy of morphologically-based species identification.}, }
@article {pmid20370917, year = {2010}, author = {Mentel, M and Martin, W}, title = {Anaerobic animals from an ancient, anoxic ecological niche.}, journal = {BMC biology}, volume = {8}, number = {}, pages = {32}, pmid = {20370917}, issn = {1741-7007}, mesh = {Adaptation, Biological/genetics/*physiology ; Adenosine Triphosphate/metabolism ; Anaerobiosis ; Animals ; *Biological Evolution ; *Ecosystem ; Geologic Sediments/*analysis ; Hydrogen/metabolism ; Invertebrates/genetics/*physiology/ultrastructure ; Mediterranean Sea ; Mitochondria/metabolism ; Phylogeny ; Species Specificity ; }, abstract = {Tiny marine animals that complete their life cycle in the total absence of light and oxygen are reported by Roberto Danovaro and colleagues in this issue of BMC Biology. These fascinating animals are new members of the phylum Loricifera and possess mitochondria that in electron micrographs look very much like hydrogenosomes, the H2-producing mitochondria found among several unicellular eukaryotic lineages. The discovery of metazoan life in a permanently anoxic and sulphidic environment provides a glimpse of what a good part of Earth's past ecology might have been like in 'Canfield oceans', before the rise of deep marine oxygen levels and the appearance of the first large animals in the fossil record roughly 550-600 million years ago. The findings underscore the evolutionary significance of anaerobic deep sea environments and the anaerobic lifestyle among mitochondrion-bearing cells. They also testify that a fuller understanding of eukaryotic and metazoan evolution will come from the study of modern anoxic and hypoxic habitats.}, }
@article {pmid20370313, year = {2010}, author = {Khalyavkin, AV}, title = {The updated view concerning the possibility of growing old without senescence.}, journal = {Rejuvenation research}, volume = {13}, number = {2-3}, pages = {319-321}, doi = {10.1089/rej.2009.0962}, pmid = {20370313}, issn = {1557-8577}, mesh = {Aging/*pathology/*physiology ; Animals ; Biological Evolution ; Cellular Senescence/physiology ; Environment ; Humans ; Rejuvenation/physiology ; }, abstract = {New findings paradoxically highlight the capability of old mitochondria, precursor cells, tissues, and organs for rejuvenation during vital activity at appropriate conditions and modes. But most studies of aging are conducted in living beings situated in rather artificial conditions. Such external conditions are less adequate to the evolutionarily adjusted genetic construction of an organism and lead to the appearance of senescence due to incomplete self-maintenance processes. These arguments as well as other findings suggest that imitation of appropriate external signals or peculiar modification of control systems of an organism can lead to the state of full nonsenescence.}, }
@article {pmid20361936, year = {2010}, author = {Nikolic, I and Kastratovic, T and Zelen, I and Zivanovic, A and Arsenijevic, S and Mitrovic, M}, title = {Cytosolic pro-apoptotic SPIKE induces mitochondrial apoptosis in cancer.}, journal = {Biochemical and biophysical research communications}, volume = {395}, number = {2}, pages = {225-231}, doi = {10.1016/j.bbrc.2010.03.168}, pmid = {20361936}, issn = {1090-2104}, mesh = {Amino Acid Sequence ; *Apoptosis ; Apoptosis Regulatory Proteins/metabolism ; Caspase 3/biosynthesis ; Cell Line ; Crk-Associated Substrate Protein/metabolism ; Cytochromes c/metabolism ; Cytosol/*metabolism ; Enzyme Activation ; Humans ; Intracellular Signaling Peptides and Proteins/*metabolism ; Membrane Proteins/metabolism ; Mitochondria/*physiology ; Mitochondrial Proteins ; Molecular Sequence Data ; Neoplasms/*metabolism ; }, abstract = {Proteins of the BCL-2 family are important regulators of apoptosis. The BCL-2 family includes three main subgroups: the anti-apoptotic group, such as BCL-2, BCL-XL, BCL-W, and MCL-1; multi-domain pro-apoptotic BAX, BAK; and pro-apoptotic "BH3-only" BIK, PUMA, NOXA, BID, BAD, and SPIKE. SPIKE, a rare pro-apoptotic protein, is highly conserved throughout the evolution, including Caenorhabditis elegans, whose expression is downregulated in certain tumors, including kidney, lung, and breast. In the literature, SPIKE was proposed to interact with BAP31 and prevent BCL-XL from binding to BAP31. Here, we utilized the Position Weight Matrix method to identify SPIKE to be a BH3-only pro-apoptotic protein mainly localized in the cytosol of all cancer cell lines tested. Overexpression of SPIKE weakly induced apoptosis in comparison to the known BH3-only pro-apoptotic protein BIK. SPIKE promoted mitochondrial cytochrome c release, the activation of caspase 3, and the caspase cleavage of caspase's downstream substrates BAP31 and p130CAS. Although the informatics analysis of SPIKE implicates this protein as a member of the BH3-only BCL-2 subfamily, its role in apoptosis remains to be elucidated.}, }
@article {pmid20351097, year = {2010}, author = {Arnold, T and Zeth, K and Linke, D}, title = {Omp85 from the thermophilic cyanobacterium Thermosynechococcus elongatus differs from proteobacterial Omp85 in structure and domain composition.}, journal = {The Journal of biological chemistry}, volume = {285}, number = {23}, pages = {18003-18015}, pmid = {20351097}, issn = {1083-351X}, mesh = {Bacterial Outer Membrane Proteins/*chemistry/*genetics ; Cell Membrane/metabolism ; Cluster Analysis ; Computational Biology/methods ; Crystallography, X-Ray/methods ; Cyanobacteria/*metabolism ; Escherichia coli/metabolism ; Escherichia coli Proteins/*chemistry/*genetics ; Models, Biological ; Protein Denaturation ; Protein Folding ; Protein Structure, Tertiary ; Selenomethionine/chemistry ; }, abstract = {Omp85 proteins are essential proteins located in the bacterial outer membrane. They are involved in outer membrane biogenesis and assist outer membrane protein insertion and folding by an unknown mechanism. Homologous proteins exist in eukaryotes, where they mediate outer membrane assembly in organelles of endosymbiotic origin, the mitochondria and chloroplasts. We set out to explore the homologous relationship between cyanobacteria and chloroplasts, studying the Omp85 protein from the thermophilic cyanobacterium Thermosynechococcus elongatus. Using state-of-the art sequence analysis and clustering methods, we show how this protein is more closely related to its chloroplast homologue Toc75 than to proteobacterial Omp85, a finding supported by single channel conductance measurements. We have solved the structure of the periplasmic part of the protein to 1.97 A resolution, and we demonstrate that in contrast to Omp85 from Escherichia coli the protein has only three, not five, polypeptide transport-associated (POTRA) domains, which recognize substrates and generally interact with other proteins in bigger complexes. We model how these POTRA domains are attached to the outer membrane, based on the relationship of Omp85 to two-partner secretion system proteins, which we show and analyze. Finally, we discuss how Omp85 proteins with different numbers of POTRA domains evolved, and evolve to this day, to accomplish an increasing number of interactions with substrates and helper proteins.}, }
@article {pmid20345689, year = {2010}, author = {Ballard, JW and Melvin, RG}, title = {Linking the mitochondrial genotype to the organismal phenotype.}, journal = {Molecular ecology}, volume = {19}, number = {8}, pages = {1523-1539}, doi = {10.1111/j.1365-294X.2010.04594.x}, pmid = {20345689}, issn = {1365-294X}, mesh = {Adaptation, Biological/genetics ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Energy Metabolism ; *Evolution, Molecular ; Genes, Mitochondrial ; Genetic Variation ; *Genotype ; Mitochondria/*genetics ; Models, Molecular ; Mutation ; Oxidative Phosphorylation ; *Phenotype ; Protein Structure, Quaternary ; }, abstract = {One of the grand challenges of the postgenomics era is to mechanistically link the genotype with the phenotype. Here, we consider the link between the mitochondrial genotype and the organismal phenotype that is provided by bioenergetic studies of the electron transport chain. That linkage is pertinent for the fields of molecular ecology and phylogeography as it tests if, and potentially how, natural selection can influence the evolutionary and demographic past of both populations and species. We introduce the mitochondrial genotype in terms of mitochondrial-encoded genes, nuclear-encoded genes that produce structural proteins imported into the mitochondria, and mitochondrial DNA-nuclear interactions. We then review the potential for quaternary structure modelling to predict the functional consequence of specific naturally occurring mutations. We discuss how the energy-producing reactions of oxidative phosphorylation can be used to provide a mechanistic biochemical link between genotype and phenotype. Experimental manipulations can then be used to test the functional consequences of specific mutations in multiple genetic backgrounds. Finally, we examine how mitochondria can influence the organismal mitochondrial phenotype using the examples of lifespan, fertility and starvation resistance and discuss how mitochondria may be involved in establishing both the upper and lower thermal limits of organisms. We conclude that mitochondrial DNA mutations can be important in determining aspects of organism life history. The question that remains to be resolved is how common are these adaptive mutations?}, }
@article {pmid20336381, year = {2011}, author = {Feng, Y and Li, Q and Kong, L and Zheng, X}, title = {DNA barcoding and phylogenetic analysis of Pectinidae (Mollusca: Bivalvia) based on mitochondrial COI and 16S rRNA genes.}, journal = {Molecular biology reports}, volume = {38}, number = {1}, pages = {291-299}, pmid = {20336381}, issn = {1573-4978}, mesh = {Animals ; Bayes Theorem ; DNA Barcoding, Taxonomic/*methods ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology/*genetics ; Molecular Sequence Data ; Pectinidae/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {DNA sequence data enable not only the inference of phylogenetic relationships but also provide an efficient method for species-level identifications under the terms DNA barcoding or DNA taxonomy. In this study, we have sequenced partial sequences of mitochondrial COI and 16S rRNA genes from 63 specimens of 8 species of Pectinidae to assess whether DNA barcodes can efficiently distinguish these species. Sequences from homologous regions of four other species of this family were gathered from GenBank. Comparisons of within and between species levels of sequence divergence showed that genetic variation between species exceeds variation within species. When using neighbour-joining clustering based on COI and 16S genes, all species fell into reciprocally monophyletic clades with high bootstrap values. These evidenced that these scallop species can be efficiently identified by DNA barcoding. Evolutionary relationships of Pectinidae were also examined using the two mitochondrial genes. The results are almost consistent with Waller's classification, which was proposed on the basis of shell microstructure and the morphological characteristics of juveniles.}, }
@article {pmid20334646, year = {2010}, author = {Li, D and Guo, Y and Shao, H and Tellier, LC and Wang, J and Xiang, Z and Xia, Q}, title = {Genetic diversity, molecular phylogeny and selection evidence of the silkworm mitochondria implicated by complete resequencing of 41 genomes.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {81}, pmid = {20334646}, issn = {1471-2148}, mesh = {Animals ; Bombyx/classification/*genetics ; Comparative Genomic Hybridization ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genes, Insect ; *Genome, Insect ; *Genome, Mitochondrial ; Linkage Disequilibrium ; *Phylogeny ; Polymorphism, Single Nucleotide ; Population Density ; Selection, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Mitochondria are a valuable resource for studying the evolutionary process and deducing phylogeny. A few mitochondria genomes have been sequenced, but a comprehensive picture of the domestication event for silkworm mitochondria remains to be established. In this study, we integrate the extant data, and perform a whole genome resequencing of Japanese wild silkworm to obtain breakthrough results in silkworm mitochondrial (mt) population, and finally use these to deduce a more comprehensive phylogeny of the Bombycidae.<br><br>RESULTS: We identified 347 single nucleotide polymorphisms (SNPs) in the mt genome, but found no past recombination event to have occurred in the silkworm progenitor. A phylogeny inferred from these whole genome SNPs resulted in a well-classified tree, confirming that the domesticated silkworm, Bombyx mori, most recently diverged from the Chinese wild silkworm, rather than from the Japanese wild silkworm. We showed that the population sizes of the domesticated and Chinese wild silkworms both experience neither expansion nor contraction. We also discovered that one mt gene, named cytochrome b, shows a strong signal of positive selection in the domesticated clade. This gene is related to energy metabolism, and may have played an important role during silkworm domestication.<br><br>CONCLUSIONS: We present a comparative analysis on 41 mt genomes of B. mori and B. mandarina from China and Japan. With these, we obtain a much clearer picture of the evolution history of the silkworm. The data and analyses presented here aid our understanding of the silkworm in general, and provide a crucial insight into silkworm phylogeny.}, }
@article {pmid20333239, year = {2010}, author = {Dolezal, P and Dagley, MJ and Kono, M and Wolynec, P and Likić, VA and Foo, JH and Sedinová, M and Tachezy, J and Bachmann, A and Bruchhaus, I and Lithgow, T}, title = {The essentials of protein import in the degenerate mitochondrion of Entamoeba histolytica.}, journal = {PLoS pathogens}, volume = {6}, number = {3}, pages = {e1000812}, pmid = {20333239}, issn = {1553-7374}, mesh = {Animals ; Cytoplasmic Vesicles/metabolism ; Entamoeba histolytica/genetics/*metabolism ; Genome, Protozoan ; Markov Chains ; Mitochondria/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Phosphate Transport Proteins/genetics/metabolism ; Phosphates/metabolism ; Phylogeny ; Protein Transport/*physiology ; Protozoan Proteins/genetics/*metabolism ; Saccharomyces cerevisiae/genetics ; }, abstract = {Several essential biochemical processes are situated in mitochondria. The metabolic transformation of mitochondria in distinct lineages of eukaryotes created proteomes ranging from thousands of proteins to what appear to be a much simpler scenario. In the case of Entamoeba histolytica, tiny mitochondria known as mitosomes have undergone extreme reduction. Only recently a single complete metabolic pathway of sulfate activation has been identified in these organelles. The E. histolytica mitosomes do not produce ATP needed for the sulfate activation pathway and for three molecular chaperones, Cpn60, Cpn10 and mtHsp70. The already characterized ADP/ATP carrier would thus be essential to provide cytosolic ATP for these processes, but how the equilibrium of inorganic phosphate could be maintained was unknown. Finally, how the mitosomal proteins are translocated to the mitosomes had remained unclear. We used a hidden Markov model (HMM) based search of the E. histolytica genome sequence to discover candidate (i) mitosomal phosphate carrier complementing the activity of the ADP/ATP carrier and (ii) membrane-located components of the protein import machinery that includes the outer membrane translocation channel Tom40 and membrane assembly protein Sam50. Using in vitro and in vivo systems we show that E. histolytica contains a minimalist set up of the core import components in order to accommodate a handful of mitosomal proteins. The anaerobic and parasitic lifestyle of E. histolytica has produced one of the simplest known mitochondrial compartments of all eukaryotes. Comparisons with mitochondria of another amoeba, Dictystelium discoideum, emphasize just how dramatic the reduction of the protein import apparatus was after the loss of archetypal mitochondrial functions in the mitosomes of E. histolytica.}, }
@article {pmid20304999, year = {2010}, author = {Bullerwell, CE and Burger, G and Gott, JM and Kourennaia, O and Schnare, MN and Gray, MW}, title = {Abundant 5S rRNA-like transcripts encoded by the mitochondrial genome in amoebozoa.}, journal = {Eukaryotic cell}, volume = {9}, number = {5}, pages = {762-773}, pmid = {20304999}, issn = {1535-9786}, support = {R01 GM054663/GM/NIGMS NIH HHS/United States ; MOP-4124/CAPMC/CIHR/Canada ; GM54663/GM/NIGMS NIH HHS/United States ; }, mesh = {Amoebozoa/cytology/*genetics ; Animals ; Base Sequence ; Cell Fractionation ; Computational Biology ; Conserved Sequence ; DNA, Mitochondrial/genetics ; Dictyostelium/genetics ; Genome, Mitochondrial/*genetics ; Hartmannella/genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Physarum polycephalum/genetics ; RNA, Messenger/genetics/metabolism ; RNA, Ribosomal, 5S/chemistry/*genetics ; Ribosome Subunits, Large, Eukaryotic/genetics ; Sequence Homology, Amino Acid ; }, abstract = {5S rRNAs are ubiquitous components of prokaryotic, chloroplast, and eukaryotic cytosolic ribosomes but are apparently absent from mitochondrial ribosomes (mitoribosomes) of many eukaryotic groups including animals and fungi. Nevertheless, a clearly identifiable, mitochondrion-encoded 5S rRNA is present in Acanthamoeba castellanii, a member of Amoebozoa. During a search for additional mitochondrial 5S rRNAs, we detected small abundant RNAs in other members of Amoebozoa, namely, in the lobose amoeba Hartmannella vermiformis and in the myxomycete slime mold Physarum polycephalum. These RNAs are encoded by mitochondrial DNA (mtDNA), cosediment with mitoribosomes in glycerol gradients, and can be folded into a secondary structure similar to that of bona fide 5S rRNAs. Further, in the mtDNA of another slime mold, Didymium nigripes, we identified a region that in sequence, potential secondary structure, and genomic location is similar to the corresponding region encoding the Physarum small RNA. A mtDNA-encoded small RNA previously identified in Dictyostelium discoideum is here shown to share several characteristics with known 5S rRNAs. Again, we detected genes encoding potential homologs of this RNA in the mtDNA of three other species of the genus Dictyostelium as well as in a related genus, Polysphondylium. Taken together, our results indicate a widespread occurrence of small, abundant, mtDNA-encoded RNAs with 5S rRNA-like structures that are associated with the mitoribosome in various amoebozoan taxa. Our working hypothesis is that these novel small abundant RNAs represent radically divergent mitochondrial 5S rRNA homologs. We posit that currently unrecognized 5S-like RNAs may exist in other mitochondrial systems in which a conventional 5S rRNA cannot be identified.}, }
@article {pmid20298776, year = {2010}, author = {Chang, X and Wang, Z and Hao, P and Li, YY and Li, YX}, title = {Exploring mitochondrial evolution and metabolism organization principles by comparative analysis of metabolic networks.}, journal = {Genomics}, volume = {95}, number = {6}, pages = {339-344}, doi = {10.1016/j.ygeno.2010.03.006}, pmid = {20298776}, issn = {1089-8646}, mesh = {*Biological Evolution ; Citric Acid Cycle ; Data Collection ; Databases, Factual ; Metabolic Networks and Pathways/*genetics ; Mitochondria/*genetics ; Oxidative Phosphorylation ; Saccharomyces/genetics/metabolism ; Symbiosis/genetics ; Yeasts/genetics/*metabolism ; }, abstract = {The endosymbiotic theory proposed that mitochondrial genomes are derived from an alpha-proteobacterium-like endosymbiont, which was concluded from sequence analysis. We rebuilt the metabolic networks of mitochondria and 22 relative species, and studied the evolution of mitochondrial metabolism at the level of enzyme content and network topology. Our phylogenetic results based on network alignment and motif identification supported the endosymbiotic theory from the point of view of systems biology for the first time. It was found that the mitochondrial metabolic network were much more compact than the relative species, probably related to the higher efficiency of oxidative phosphorylation of the specialized organelle, and the network is highly clustered around the TCA cycle. Moreover, the mitochondrial metabolic network exhibited high functional specificity to the modules. This work provided insight to the understanding of mitochondria evolution, and the organization principle of mitochondrial metabolic network at the network level.}, }
@article {pmid20298449, year = {2010}, author = {Dezfuli, BS and Pironi, F and Campisi, M and Shinn, AP and Giari, L}, title = {The response of intestinal mucous cells to the presence of enteric helminths: their distribution, histochemistry and fine structure.}, journal = {Journal of fish diseases}, volume = {33}, number = {6}, pages = {481-488}, doi = {10.1111/j.1365-2761.2010.01146.x}, pmid = {20298449}, issn = {1365-2761}, mesh = {Acanthocephala/*physiology ; Animals ; Cestoda/*physiology ; Cestode Infections/pathology/*veterinary ; Fish Diseases/*parasitology/pathology ; Host-Parasite Interactions ; Intestinal Mucosa/*cytology/pathology ; Mucus ; Parasitic Diseases, Animal/parasitology/*pathology ; Trout ; }, abstract = {Histochemical and ultrastructural investigations were conducted on the mucous cells of the intestine of brown trout, Salmo trutta L., naturally infected with the cestode Cyathocephalus truncatus (Pallas, 1781) and the acanthocephalan Echinorhynchus truttae Shrank, 1788. A subpopulation of 45 S. trutta were examined of which 15 specimens harboured E. truttae, 15 of which were infected with C. truncatus and 15 fish, the control group, were uninfected. In histological sections, hyperplasia and hypertrophy of the mucous cells were evident at the site of parasite infection. Enhanced mucus secretion was also recorded in infected fish. The number of mucous cells close to the site of parasite attachment within the intestine was significantly higher than the number detected in uninfected individuals and in infected individuals at sites 1 cm or greater from the point of parasite attachment. There were no significant differences between the number of mucous cells found at the latter two sites. Alcian blue and periodic acid-Schiff's staining of representative histological sections revealed a significant increase in the number of mucous cells staining positively for acid glycoconjugates compared to the number of cells found in the intestines of uninfected S. trutta. In transmission electron microscopy sections, each mucous cell typically possessed an elongated, basally positioned nucleus. The cytoplasm was observed to possess numerous electron dense and lucent vesicles, in addition to well-developed rough endoplasmic reticulum, Golgi apparatus and a few round mitochondria.}, }
@article {pmid20233853, year = {2010}, author = {Tu, HK and Pan, KF and Zhang, Y and Li, WQ and Zhang, L and Ma, JL and Li, JY and You, WC}, title = {Manganese superoxide dismutase polymorphism and risk of gastric lesions, and its effects on chemoprevention in a Chinese population.}, journal = {Cancer epidemiology, biomarkers &amp; prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology}, volume = {19}, number = {4}, pages = {1089-1097}, doi = {10.1158/1055-9965.EPI-09-1174}, pmid = {20233853}, issn = {1538-7755}, mesh = {Adult ; Ascorbic Acid/therapeutic use ; Asian People ; *Dietary Supplements ; Female ; Garlic ; *Genetic Predisposition to Disease ; Helicobacter Infections/complications ; Humans ; Male ; Middle Aged ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single Nucleotide ; Precancerous Conditions/*genetics/microbiology/prevention &amp; control ; Selenium/therapeutic use ; Stomach Neoplasms/*genetics/microbiology/prevention &amp; control ; Superoxide Dismutase/*genetics ; Vitamin E/therapeutic use ; Vitamins/*therapeutic use ; }, abstract = {BACKGROUND: Manganese superoxide dismutase is the primary antioxidant enzyme in the mitochondria and is involved in carcinogenesis. To investigate the association between MnSOD Val(16)Ala polymorphism and risk of advanced gastric lesions, and its effects on chemoprevention, a population-based study was conducted in Linqu, a high-risk area of gastric cancer in China.<br><br>METHODS: Genotypes were determined by PCR-RFLP analysis in 3,355 subjects with the baseline histopathologic diagnosis in 1994, and 2,758 of these subjects received subsequent three interventions including vitamin supplementation for 7.3 years. Odds ratios (OR) and 95% confidence intervals (CI) were estimated by unconditional logistic regression model.<br><br>RESULTS: We found an increased risk of dysplasia in subjects with the Val/Ala+Ala/Ala genotype (OR, 1.31; 95% CI, 1.02-1.68) compared with the Val/Val genotype. Stratified analysis indicated that a significantly elevated risk of intestinal metaplasia (OR, 3.40; 95% CI, 2.64-4.38) or dysplasia (OR, 4.01; 95% CI, 2.79-5.74) was found in subjects carrying the Val/Ala+Ala/Ala genotype and Helicobacter pylori infection, and an interaction between this genotype and a high serum H. pylori IgG titer (>2.94) on the risk of dysplasia was observed (P(interaction) = 0.01). Furthermore, an elevated chance for regression of gastric lesions was observed in subjects with the Val/Ala+Ala/Ala genotype and high IgG titer in an intervention trial with vitamin supplementation (OR, 2.45; 95% CI, 1.37-4.38).<br><br>CONCLUSIONS: These findings suggest that Val(16)Ala polymorphism may play an important role in development of advanced gastric lesions and modify the effect of vitamin supplementation on the evolution of gastric lesions.<br><br>IMPACT: Val(16)Ala polymorphism is related to gastric cancer development.}, }
@article {pmid20233703, year = {2010}, author = {Liu, SP and Wang, K and Yuan, XP and Wang, DQ and Yue, XJ and Chen, DQ}, title = {[Genetic diversity and differentiation between populations of Glyptothorax zanaensis in the middle and lower reaches of the Nujiang River].}, journal = {Yi chuan = Hereditas}, volume = {32}, number = {3}, pages = {254-263}, doi = {10.3724/sp.j.1005.2010.00254}, pmid = {20233703}, issn = {0253-9772}, mesh = {Animals ; China ; Cytochromes b/genetics ; Fishes/classification/*genetics ; Genetic Variation/*genetics ; Genetics, Population ; Geography ; Haplotypes/genetics ; Phylogeny ; }, abstract = {The development of hydroelectricity in the Nujiang River would have adverse impacts on the populations of Glyptothorax zanaensis. In order to assess the genetic diversity and differentiation of this species, we sequenced the cytochrome b gene of the mitochondria in 102 individuals of the fish collected from 6 sampling sites (Gongshan, Gudeng and Lushui in the Nujiang Prefectural District and Daojie, Mengnuo and Mucheng in the Baoshan Municipal District). A total of 87 variation sites were detected in the fragment of 1 137 bp in length, with which the 102 samples were defined as 36 haplotypes. The haplotype diversity (h) and the nucleotide diversity (pi) of total samples were 0.851+/-0.028 and 0.01356+/-0.0008, respectively. Therefore, the genetic diversity of G. zanaensis was relatively low. However, the genetic diversity of the Nujiang population was significantly higher than that of the Baoshan population. The pairwise Fst value between the populations (0.475-0.846) was higher than that within the population (0.002-0.108), which implied that the Fst value was positively related to geographic distance. Analysis of molecular variance (AMOVA) showed that the genetic differentiation between the populations and within the populations were 53.65% and 46.35%, respectively. The fixation index (Fst value) was 0.5365, indicating that there existed significant differentiation between the Nujiang population and the Baoshan population. The phylogentic tree and networks of the haplotypes of G. zanaensis showed that there were two separate lineages: the Nujiang lineage and the Baoshan lineage. Each lineage represents at least one separated management unit, or belongs to an evolutionary significant unit. It was suggested that in the construction of hydroelectric projects the measures for protecting G. zanaensis should be adopted in fully considering the populations of G. zanaensis and the status quo of their population structure to avoid the occurrence of gene exchange among populations.}, }
@article {pmid20228344, year = {2010}, author = {Thompson, JT and Bartol, IK and Baksi, AE and Li, KY and Krueger, PS}, title = {The ontogeny of muscle structure and locomotory function in the long-finned squid Doryteuthis pealeii.}, journal = {The Journal of experimental biology}, volume = {213}, number = {Pt 7}, pages = {1079-1091}, doi = {10.1242/jeb.034553}, pmid = {20228344}, issn = {1477-9145}, mesh = {Animal Structures/*anatomy &amp; histology/*physiology ; Animals ; Decapodiformes/*anatomy &amp; histology/*physiology ; Gene Expression Regulation ; Larva/physiology/ultrastructure ; Locomotion/*physiology ; Models, Biological ; Muscle Contraction/physiology ; Muscle Fibers, Skeletal/physiology/ultrastructure ; Muscles/*anatomy &amp; histology/*physiology/ultrastructure ; Myosin Heavy Chains/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Time Factors ; }, abstract = {Understanding the extent to which changes in muscle form and function underlie ontogenetic changes in locomotory behaviors and performance is important in understanding the evolution of musculoskeletal systems and also the ecology of different life stages. We explored ontogenetic changes in the structure, myosin heavy chain (MHC) expression and contractile properties of the circular muscles that provide power for jet locomotion in the long-finned squid Doryteuthis pealeii. The circular muscle fibers of newly hatched paralarvae had different sizes, shapes, thick filament lengths, thin:thick filament ratio, myofilament organization and sarcoplasmic reticulum (SR) distribution than those of adults. Viewed in cross section, most circular muscle cells were roughly triangular or ovoid in shape with a core of mitochondria; however, numerous muscle cells with crescent or other unusual cross-sectional shapes and muscle cells with unequal distributions of mitochondria were present in the paralarvae. The frequency of these muscle cells relative to 'normal' circular muscle cells ranged from 1:6 to 1:10 among the 19 paralarvae we surveyed. The thick filaments of the two types of circular fibers, superficial mitochondria-rich (SMR) and central mitochondria-poor (CMP), differed slightly in length among paralarvae with thick filament lengths of 0.83+/-0.15 microm and 0.71+/-0.1 microm for the SMR and CMP fibers, respectively (P 0.05; ANOVA). During ontogeny the thick filament lengths of both the CMP and SMR fibers increased significantly to 1.78+/-0.27 microm and 3.12+/-0.56 microm, respectively, in adults (P<0.0001 for both comparisons; ANOVA with Tukey's highly significant difference post hoc tests). When sectioned parallel to their long axes, the SMR and CMP fibers of both paralarvae and adults exhibited the myofilament arrangements typical of obliquely striated muscle cells but the angle of obliquity of the dense bodies was 22.8+/-2.4 deg. and 4.6+/-0.87 deg. for paralarvae and adults, respectively. There were also differences in the distribution of the anastomosing network of SR. In paralarvae, the outer and central zones of SR were well developed but the intramyoplasmic zone was greatly reduced in some cells or was scattered non-uniformly across the myoplasm. Whereas in adults the intramyoplasmic SR region was composed primarily of flattened tubules, it was composed primarily of rounded vesicles or tubules when present in the paralarvae. The ontogenetic differences in circular muscle structure were correlated with significant differences in their contractile properties. In brief tetanus at 20 degrees C, the mean unloaded shortening velocity of the paralarval circular muscle preparations was 9.1 L(0) s(-1) (where L(0) was the preparation length that generated the peak isometric stress), nearly twice that measured in other studies for the CMP fibers of adults. The mean peak isometric stress was 119+/-15 mN mm(-2) physiological cross section, nearly half that measured for the CMP fibers of adults. Reverse transcriptase-polymerase chain reaction analysis of paralarval and adult mantle samples revealed very similar expression patterns of the two known isoforms of squid MHC. The ontogenetic differences in the structure and physiology of the circular muscles may result in more rapid mantle movements during locomotion. This prediction is consistent with jet pulse durations observed in other studies, with shorter jet pulses providing hydrodynamic advantages for paralarvae.}, }
@article {pmid20226718, year = {2010}, author = {Van Aken, O and Whelan, J and Van Breusegem, F}, title = {Prohibitins: mitochondrial partners in development and stress response.}, journal = {Trends in plant science}, volume = {15}, number = {5}, pages = {275-282}, doi = {10.1016/j.tplants.2010.02.002}, pmid = {20226718}, issn = {1878-4372}, mesh = {Animals ; Humans ; Mitochondria/*metabolism ; Phylogeny ; Plant Development ; Plants/genetics/*metabolism ; Prohibitins ; Repressor Proteins/*metabolism ; Signal Transduction ; *Stress, Physiological ; }, abstract = {Twelve years after their discovery in plants, prohibitins (PHBs) have retained their status as some of the most enigmatic mitochondrial proteins. Although the original hypothesis that PHBs act as negative cell cycle regulators has lost its impetus in plants, the essential molecular function(s) PHB complexes perform in the inner mitochondrial membrane are now beginning to be understood. We review the current state of knowledge to propose a unifying model that positions the PHB complex as a universal protein scaffold for key mitochondrial processes, including protein processing, respiratory chain function and mitochondrial DNA organization. Furthermore, recent findings indicate that PHBs play an active role in stress tolerance and are involved in triggering retrograde signals in response to stress and mitochondrial dysfunction.}, }
@article {pmid20209439, year = {2010}, author = {Golas, A and Malek, P and Piasecka, M and Styrna, J}, title = {Sperm mitochondria diaphorase activity--a gene mapping study of recombinant inbred strains of mice.}, journal = {The International journal of developmental biology}, volume = {54}, number = {4}, pages = {667-673}, doi = {10.1387/ijdb.082778ag}, pmid = {20209439}, issn = {1696-3547}, mesh = {Animals ; Animals, Laboratory/genetics ; *Chromosome Mapping ; Chromosomes/physiology ; Densitometry ; Dihydrolipoamide Dehydrogenase/*genetics ; Fertility/genetics ; Fertilization/genetics ; Male ; Mice ; Mice, Inbred CBA/*genetics ; Mitochondria/*genetics ; NAD/genetics ; Semen Analysis/methods ; Sperm Motility/genetics ; Spermatozoa/cytology/*physiology ; }, abstract = {In order to study the genetic control of semen quality parameters, we derived a set of recombinant inbred (RI) mice from crosses between two inbred strains, KE and CBA/Kw, which differ significantly in gamete quality and fertility parameters. In this work, we used male mice from the two parental strains and from ten RI strains to map genes controlling quantitative traits such as sperm mitochondrial diaphorase activity, and assessed the correlation between this trait, sperm motility and in vivo fertilization efficiency. We analyzed sperm mitochondrial dehydrogenase (diaphorase) activity (NADH-dependent NBT assay) cytochemically by means of computerized image densitometry and obtained values for four parameters: 1) integrated optical density (IOD) for all pixels of the midpiece, 2) mean optical density (MOD) for the midpiece pixels, 3) length of sperm midpiece and 4) area of sperm midpiece. Polymorphic microsatellite marker profiles were prepared for 20 mouse chromosomes in the ten RI strains. We used Map Manager QTX software to correlate the strain distribution patterns (SDPs) of the four measured parameters with the SDPs of the analyzed markers. Hypothetical genes modifying diaphorase activity were mapped to chromosomal region 19q43-19q47, containing, for example, Poll, Sfxn2, Cyp17a1 and Usmg5 genes. Chromosomal regions 18q44 and 18q49-18q80 also showed correlation with the SDPs of diaphorase activity. Katnal2, Me2 and StARD6 candidate genes were proposed from this region. Diaphorase activity in the mouse sperm midpiece did not correlate with in vivo fertilization efficiency, but was negatively correlated with the linearity and straightness of sperm movement.}, }
@article {pmid20202479, year = {2010}, author = {Wang, KC and Kondo, H and Hirono, I and Aoki, T}, title = {The Marsupenaeus japonicus voltage-dependent anion channel (MjVDAC) protein is involved in white spot syndrome virus (WSSV) pathogenesis.}, journal = {Fish &amp; shellfish immunology}, volume = {29}, number = {1}, pages = {94-103}, doi = {10.1016/j.fsi.2010.02.020}, pmid = {20202479}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Membrane Potential, Mitochondrial/immunology ; Molecular Sequence Data ; Penaeidae/genetics/immunology/*virology ; *Phylogeny ; RNA/chemistry/genetics ; RNA Interference/immunology ; Random Amplified Polymorphic DNA Technique ; Sequence Alignment ; Sequence Analysis, DNA ; Voltage-Dependent Anion Channels/genetics/*immunology ; White spot syndrome virus 1/*immunology ; }, abstract = {Voltage-dependent anion channel (VDAC) proteins abound in the outer membrane of mitochondria. They play an important role in mitochondrial membrane permeabilization (MMP), which can lead to stress-induced cellular apoptosis and necrosis. Several pathogens regulate this MMP in their host cells to benefit their replication cycle, while in other cases, the host can use the same mechanism to combat pathogenesis. In this study, the first shrimp VDAC gene was identified and characterized from Marsupenaeus japonicus (MjVDAC). Its open reading frame (ORF) contained 849 bp encoding 282 amino acids. The deduced MjVDAC protein includes the 4-element eukaryotic porin signature motif, the conserved ATP binding motif (the GLK motif) and a VKAKV-like sequence known in other organisms to be involved in the protein's incorporation in the mitochondrial outer membrane. Tissue tropism analysis indicated that MjVDAC is abundant in the heart, muscle, stomach and pleopod. MjVDAC proteins colocalized with mitochondria in transiently transfected Sf9 cells and in shrimp hemocytes. dsRNA silencing of shrimp VDAC delayed white spot syndrome virus (WSSV) infection by 1 day in different shrimp organs. Taken together, these findings suggest that MjVDAC is likely to be involved in WSSV pathogenesis.}, }
@article {pmid20198570, year = {2010}, author = {Ning, T and Xiao, H and Li, J and Hua, S and Zhang, YP}, title = {Adaptive evolution of the mitochondrial ND6 gene in the domestic horse.}, journal = {Genetics and molecular research : GMR}, volume = {9}, number = {1}, pages = {144-150}, doi = {10.4238/vol9-1gmr705}, pmid = {20198570}, issn = {1676-5680}, mesh = {Altitude ; Animals ; China ; *Evolution, Molecular ; Genes, Mitochondrial/*genetics ; Genetic Variation ; Horses/*genetics ; Likelihood Functions ; NADH Dehydrogenase/*genetics ; Phylogeny ; Selection, Genetic ; }, abstract = {Mitochondria play a crucial role in energy metabolism through oxidative phosphorylation. Organisms living at high altitudes are potentially influenced by oxygen deficits and cold temperatures. The severe environmental conditions can impact on metabolism and direct selection of mitochondrial DNA. As a wide-ranging animal, the domestic horse (Equus caballus) has developed various morphological and physiological characteristics for adapting to different altitudes. Thus, this is a good species for studying adaption to high altitudes at a molecular level. We sequenced the complete NADH dehydrogenase 6 gene (ND6) of 509 horses from 24 sampling locations. By comparative analysis of three horse populations living at different altitudes (>2200 m, 1200-1700 m, and <900 m), we found that the high-altitude population had the lowest genetic diversity and significant negative Tajima's D; both values declined with increasing elevation. Moreover, non-directional selection was identified for the ND6 gene by a tree-based relative ratio test (P = 0.007); the highest proportion of high-altitude horses was found distributed on the selected branches. We conclude that the high-altitude environment has directed adaptive evolution of the mitochondrial ND6 gene in the plateau horse.}, }
@article {pmid20196863, year = {2010}, author = {Hao, W}, title = {OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs.}, journal = {BMC bioinformatics}, volume = {11}, number = {}, pages = {114}, pmid = {20196863}, issn = {1471-2105}, support = {R01-GM-70612/GM/NIGMS NIH HHS/United States ; }, mesh = {Chloroplasts/*genetics ; Consensus Sequence/*genetics ; Databases, Genetic ; *Gene Conversion ; Genes, Mitochondrial ; Genome, Plant ; Internet ; Mitochondria/*genetics ; Sequence Alignment/methods ; *Software ; }, abstract = {BACKGROUND: The ancestry of mitochondria and chloroplasts traces back to separate endosymbioses of once free-living bacteria. The highly reduced genomes of these two organelles therefore contain very distant homologs that only recently have been shown to recombine inside the mitochondrial genome. Detection of gene conversion between mitochondrial and chloroplast homologs was previously impossible due to the lack of suitable computer programs. Recently, I developed a novel method and have, for the first time, discovered recurrent gene conversion between chloroplast mitochondrial genes. The method will further our understanding of plant organellar genome evolution and help identify and remove gene regions with incongruent phylogenetic signals for several genes widely used in plant systematics. Here, I implement such a method that is available in a user friendly web interface.<br><br>RESULTS: OrgConv (Organellar Conversion) is a computer package developed for detection of gene conversion between mitochondrial and chloroplast homologous genes. OrgConv is available in two forms; source code can be installed and run on a Linux platform and a web interface is available on multiple operating systems. The input files of the feature program are two multiple sequence alignments from different organellar compartments in FASTA format. The program compares every examined sequence against the consensus sequence of each sequence alignment rather than exhaustively examining every possible combination. Making use of consensus sequences significantly reduces the number of comparisons and therefore reduces overall computational time, which allows for analysis of very large datasets. Most importantly, with the significantly reduced number of comparisons, the statistical power remains high in the face of correction for multiple tests.<br><br>CONCLUSIONS: Both the source code and the web interface of OrgConv are available for free from the OrgConv website http://www.indiana.edu/~orgconv. Although OrgConv has been developed with main focus on detection of gene conversion between mitochondrial and chloroplast genes, it may also be used for detection of gene conversion between any two distinct groups of homologous sequences.}, }
@article {pmid20194738, year = {2010}, author = {Supekova, L and Supek, F and Greer, JE and Schultz, PG}, title = {A single mutation in the first transmembrane domain of yeast COX2 enables its allotopic expression.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {11}, pages = {5047-5052}, pmid = {20194738}, issn = {1091-6490}, support = {R01 GM062159/GM/NIGMS NIH HHS/United States ; GM62159/GM/NIGMS NIH HHS/United States ; }, mesh = {3' Untranslated Regions/genetics ; Aerobiosis/drug effects ; Amino Acid Sequence ; Amino Acid Substitution/genetics ; Cytoplasm/drug effects/enzymology ; Electron Transport Complex IV/*chemistry/*genetics/metabolism ; Fermentation/drug effects ; *Gene Expression Regulation, Fungal/drug effects ; Glycerol/pharmacology ; Mitochondrial Membranes/drug effects/enzymology ; Molecular Sequence Data ; Mutation/*genetics ; Phenotype ; Protein Sorting Signals ; Protein Structure, Tertiary ; Protein Transport/drug effects ; Saccharomyces cerevisiae/cytology/*enzymology/*genetics/growth &amp; development ; }, abstract = {During the course of evolution, a massive reduction of the mitochondrial genome content occurred that was associated with transfer of a large number of genes to the nucleus. To further characterize factors that control the mitochondrial gene transfer/retention process, we have investigated the barriers to transfer of yeast COX2, a mitochondrial gene coding for a subunit of cytochrome c oxidase complex. Nuclear-recoded Saccharomyces cerevisiae COX2 fused at the amino terminus to various alternative mitochondrial targeting sequences (MTS) fails to complement the growth defect of a yeast strain with an inactivated mitochondrial COX2 gene, even though it is expressed in cells. Through random mutagenesis of one such hybrid MTS-COX2, we identified a single mutation in the first Cox2 transmembrane domain (W56 --> R) that (i) results in the cellular expression of a Cox2 variant with a molecular mass indicative of MTS cleavage, which (ii) supports growth of a cox2 mutant on a nonfermentable carbon source, and that (iii) partially restores cytochrome c oxidase-specific respiration by the mutant mitochondria. COX2(W56R) can be allotopically expressed with an MTS derived from S. cerevisiae OXA1 or Neurospora crassa SU9, both coding for hydrophobic mitochondrial proteins, but not with an MTS derived from the hydrophilic protein Cox4. In contrast to some other previously transferred genes, allotopic COX2 expression is not enabled or enhanced by a 3'-UTR that localizes mRNA translation to the mitochondria, such as yeast ATP2(3)('-UTR). Application of in vitro evolution strategies to other mitochondrial genes might ultimately lead to yeast entirely lacking the mitochondrial genome, but still possessing functional respiratory capacity.}, }
@article {pmid20193748, year = {2010}, author = {Hirayama, M and Mukai, T and Miya, M and Murata, Y and Sekiya, Y and Yamashita, T and Nishida, M and Watabe, S and Oda, S and Mitani, H}, title = {Intraspecific variation in the mitochondrial genome among local populations of Medaka Oryzias latipes.}, journal = {Gene}, volume = {457}, number = {1-2}, pages = {13-24}, doi = {10.1016/j.gene.2010.02.012}, pmid = {20193748}, issn = {1879-0038}, mesh = {Acclimatization/genetics ; Animals ; Base Sequence ; Evolution, Molecular ; Genes, Mitochondrial ; *Genetic Variation ; Genetics, Population ; Genome, Mitochondrial/*genetics ; Geography ; Japan ; Models, Biological ; Molecular Sequence Data ; Nucleic Acid Conformation ; Organ Specificity/genetics ; Oryzias/*genetics ; Phylogeny ; RNA, Transfer/chemistry/genetics ; Tandem Repeat Sequences/genetics ; Temperature ; }, abstract = {The draft genome data of Medaka Oryzias latipes shows that it has distinct intraspecific genetic variation. To survey the genetic variations contributing to environmental adaptation, we focused on the mitochondrial DNA (mtDNA). The complete mtDNA sequences of Medaka were compared among 8 local population stocks and 4 inbred strains established from genetically divergent groups. Inbred strain HSOK, derived from the Eastern Korean group of Medaka, has a mitochondrial gene order that was distinct from other Medaka groups. Phylogenetic trees based on the mitochondrial genome sequences indicated that the mitogenome from the Shanghai stock (China) and HSOK strain were highly diverged from Japanese Medaka, and that the Japanese Medaka mitogenome was diverged into two groups; this result was fully consistent with those of the previous study using mtDNA-encode gene sequences. Among tRNA genes, the most divergent was the tRNA(Thr) gene as reported in humans previously. The number of tandemly repeated 11 nucleotide units in the Medaka mtDNA control region (CR) varied greatly among local populations. The number of repeats was more variable in the Northern Japanese group (10-34) than in the Southern group (7-12), while two other Oryzias species, inhabiting tropical regions, had no repeats. A comprehensive comparison between the number of repeat units and meteorological data indicated that the number of repeats correlated to the index data of a cold environment and seasonal climatic change. In cold (5 degrees C) acclimated fish, the mRNA levels varied among mitochondria coding genes. mRNA of the cytochrome oxidase subunit I gene in some local stocks was induced by cold temperature and seemed to be correlated with the number of repeated sequences in the CR. This study revealed that the repeated sequences in the mtDNA CR might function for mtDNA gene expression and that the number of tandem repeats in Medaka mtDNA is likely related to adaptation to a harsh habitat.}, }
@article {pmid20192696, year = {2010}, author = {Ito, M and Jiang, W and Sato, JJ and Zhen, Q and Jiao, W and Goto, K and Sato, H and Ishiwata, K and Oku, Y and Chai, JJ and Kamiya, H}, title = {Molecular phylogeny of the subfamily Gerbillinae (Muridae, Rodentia) with emphasis on species living in the Xinjiang-Uygur Autonomous Region of China and based on the mitochondrial cytochrome b and cytochrome c oxidase subunit II genes.}, journal = {Zoological science}, volume = {27}, number = {3}, pages = {269-278}, doi = {10.2108/zsj.27.269}, pmid = {20192696}, issn = {0289-0003}, mesh = {Animals ; China ; Cytochromes b/*genetics ; Electron Transport Complex IV/*genetics ; Gene Expression Regulation ; Gerbillinae/*genetics ; Mitochondria/genetics/*metabolism ; *Phylogeny ; }, abstract = {Rodents belonging to the subfamily Gerbillinae and living in the Xinjiang-Uygur autonomous region of China were collected in field surveys between 2001 and 2003. We found four Meriones species, including M. chengi M. liycus, M. meridianus, and M. tamariscinus, as well as related species from different genera, Rhombomys opimus and Brachiones przewaliskii For phylogenetic analyses of these gerbilline species, DNA sequences of parts of the mitochondrial cytochrome b (Cytb) and cytochrome c oxidase subunit II (COII) genes were examined with the neighbor Joining, maximum parsimony, maximum likelihood, and Bayesian inference methods. Our phylogenetic analyses suggest that the genus Meriones is not monophyletic and place M. tamaricinus as the sister taxon to a clade comprising Brachiones, Psammomys, Rhombomys, and the other Meriones species. The remaining Meriones species separate into three lineages: M. meridianus (including M. chengi), Meriones unguiculatus, and a clade that includes multiple Meriones species originating from Asia, the Middle East, and Africa. The phylogenetic relationships among the genera Brachines, Meriones, Psammomys, and Rhombomys remain ambiguous, probably due to the saturation of mutations that occurs in fast-evolving mitochondrial DNA. In addition, intraspecific variation was observed for M. meridianus, and this mostly correlated with collection localities, i.e., the northern and southern parts of the Xinjiang region. This variation corresponded to interspecific levels of divergence among other lineages of Meriones. Interestingly, no differences were observed in either the Cytb or COII gene sequences isolated from M. chengi collected from the Turfan Basin in the north and those from M. meridianus in the south, suggesting that M. chengi may be a synonym of M. meridianus.}, }
@article {pmid20192695, year = {2010}, author = {Nakagawa, E and Kobayashi, M and Suzuki, M and Tsubota, T}, title = {Genetic variation in the harbor seal (Phoca vitulina) and spotted seal (Phoca largha) around Hokkaido, Japan, based on mitochondrial cytochrome b sequences.}, journal = {Zoological science}, volume = {27}, number = {3}, pages = {263-268}, doi = {10.2108/zsj.27.263}, pmid = {20192695}, issn = {0289-0003}, mesh = {Animals ; Cytochromes b/*genetics/metabolism ; DNA/genetics ; *Genetic Variation ; Japan ; Mitochondria/*enzymology ; Phoca/*genetics ; Phylogeny ; }, abstract = {The harbor seal (Phoca vitulina) and spotted seal (Phoca largha) are the main seal species around Hokkaido, Japan. While some investigations have been conducted on the ecology and morphology of these two species, there is a lack of genetic information. We studied variation in mitochondrial cytochrome b sequences in the two species. Fifteen haplotypes were observed in 39 harbor seals from Erimo, Akkeshi, and Nosappu, and 23 were observed in 31 spotted seals from Erimo, Akkeshi, Nosappu, Rausu, Yagishiri Island, and Hamamasu. Phylogenetic trees showed two harbor seal lineages: Group I contained primarily haplotypes from Erimo, and Group II contained haplotypes from Akkeshi and Nosappu. Because the Erimo population had fewer haplotypes and less nucleotide diversity than the Akkeshi and Nosappu populations, we considered it to be Isolated from the others. In contrast, genetic variance within populations of spotted seals (97.3%) was far higher than that among populations (2.7%), determined by analysis of molecular variance. There were no significant difference among the spotted seal populations, indicating the absence of distinct lineages around Hokkaido. The differences in the genetic population structure between the two species could have been generated by their ecological differences. This study provides basic genetic information on these seal species and will contribute to the conservation and management of fisheries and seals throughout Hokkaido.}, }
@article {pmid20178587, year = {2010}, author = {Ahmadinejad, N and Dagan, T and Gruenheit, N and Martin, W and Gabaldón, T}, title = {Evolution of spliceosomal introns following endosymbiotic gene transfer.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {57}, pmid = {20178587}, issn = {1471-2148}, mesh = {Animals ; Diatoms/genetics ; Eukaryota/genetics ; Gene Transfer, Horizontal ; Introns ; Mitochondria/genetics ; Phylogeny ; Plant Physiological Phenomena ; Plants/genetics ; Spliceosomes/*genetics ; Symbiosis ; }, abstract = {BACKGROUND: Spliceosomal introns are an ancient, widespread hallmark of eukaryotic genomes. Despite much research, many questions regarding the origin and evolution of spliceosomal introns remain unsolved, partly due to the difficulty of inferring ancestral gene structures. We circumvent this problem by using genes originated by endosymbiotic gene transfer, in which an intron-less structure at the time of the transfer can be assumed.<br><br>RESULTS: By comparing the exon-intron structures of 64 mitochondrial-derived genes that were transferred to the nucleus at different evolutionary periods, we can trace the history of intron gains in different eukaryotic lineages. Our results show that the intron density of genes transferred relatively recently to the nuclear genome is similar to that of genes originated by more ancient transfers, indicating that gene structure can be rapidly shaped by intron gain after the integration of the gene into the genome and that this process is mainly determined by forces acting specifically on each lineage. We analyze 12 cases of mitochondrial-derived genes that have been transferred to the nucleus independently in more than one lineage.<br><br>CONCLUSIONS: Remarkably, the proportion of shared intron positions that were gained independently in homologous genes is similar to that proportion observed in genes that were transferred prior to the speciation event and whose shared intron positions might be due to vertical inheritance. A particular case of parallel intron gain in the nad7 gene is discussed in more detail.}, }
@article {pmid20167609, year = {2010}, author = {Papadopoulou, A and Anastasiou, I and Vogler, AP}, title = {Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration.}, journal = {Molecular biology and evolution}, volume = {27}, number = {7}, pages = {1659-1672}, doi = {10.1093/molbev/msq051}, pmid = {20167609}, issn = {1537-1719}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Gene Flow ; Genes, Mitochondrial/*genetics ; Genetic Variation ; Insecta/classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Phylogenetic trees in insects are frequently dated by applying a "standard" mitochondrial DNA (mtDNA) clock estimated at 2.3% My(-1), but despite its wide use reliable calibration points have been lacking. Here, we used a well-established biogeographic barrier, the mid-Aegean trench separating the western and eastern Aegean archipelago, to estimate substitution rates in tenebrionid beetles. Cytochrome oxidase I (cox1) for six codistributed genera across 28 islands (444 individuals) on both sides of the mid-Aegean trench revealed 60 independently coalescing entities delimited with a mixed Yule-coalescent model. One representative per entity was used for phylogenetic analysis of mitochondrial (cox1, 16S rRNA) and nuclear (Mp20, 28S rRNA) genes. Six nodes marked geographically congruent east-west splits whose separation was largely contemporaneous and likely to reflect the formation of the mid-Aegean trench at 9-12 Mya. Based on these "known" dates, a divergence rate of 3.54% My(-1) for the cox1 gene (2.69% when combined with the 16S rRNA gene) was obtained under the preferred partitioning scheme and substitution model selected using Bayes factors. An extensive survey suggests that discrepancies in mtDNA substitution rates in the entomological literature can be attributed to the use of different substitution models, the use of different mitochondrial gene regions, mixing of intraspecific with interspecific data, and not accounting for variance in coalescent times or postseparation gene flow. Different treatments of these factors in the literature confound estimates of mtDNA substitution rates in opposing directions and obscure lineage-specific differences in rates when comparing data from various sources.}, }
@article {pmid20167078, year = {2010}, author = {Doucet-Beaupré, H and Breton, S and Chapman, EG and Blier, PU and Bogan, AE and Stewart, DT and Hoeh, WR}, title = {Mitochondrial phylogenomics of the Bivalvia (Mollusca): searching for the origin and mitogenomic correlates of doubly uniparental inheritance of mtDNA.}, journal = {BMC evolutionary biology}, volume = {10}, number = {}, pages = {50}, pmid = {20167078}, issn = {1471-2148}, mesh = {Animals ; Bivalvia/*genetics ; DNA, Mitochondrial/*genetics ; Mitochondria/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Doubly uniparental inheritance (DUI) is an atypical system of animal mtDNA inheritance found only in some bivalves. Under DUI, maternally (F genome) and paternally (M genome) transmitted mtDNAs yield two distinct gender-associated mtDNA lineages. The oldest distinct M and F genomes are found in freshwater mussels (order Unionoida). Comparative analyses of unionoid mitochondrial genomes and a robust phylogenetic framework are necessary to elucidate the origin, function and molecular evolutionary consequences of DUI. Herein, F and M genomes from three unionoid species, Venustaconcha ellipsiformis, Pyganodon grandis and Quadrula quadrula have been sequenced. Comparative genomic analyses were carried out on these six genomes along with two F and one M unionoid genomes from GenBank (F and M genomes of Inversidens japanensis and F genome of Lampsilis ornata).<br><br>RESULTS: Compared to their unionoid F counterparts, the M genomes contain some unique features including a novel localization of the trnH gene, an inversion of the atp8-trnD genes and a unique 3'coding extension of the cytochrome c oxidase subunit II gene. One or more of these unique M genome features could be causally associated with paternal transmission. Unionoid bivalves are characterized by extreme intraspecific sequence divergences between gender-associated mtDNAs with an average of 50% for V. ellipsiformis, 50% for I. japanensis, 51% for P. grandis and 52% for Q. quadrula (uncorrected amino acid p-distances). Phylogenetic analyses of 12 protein-coding genes from 29 bivalve and five outgroup mt genomes robustly indicate bivalve monophyly and the following branching order within the autolamellibranch bivalves: ((Pteriomorphia, Veneroida) Unionoida).<br><br>CONCLUSION: The basal nature of the Unionoida within the autolamellibranch bivalves and the previously hypothesized single origin of DUI suggest that (1) DUI arose in the ancestral autolamellibranch bivalve lineage and was subsequently lost in multiple descendant lineages and (2) the mitochondrial genome characteristics observed in unionoid bivalves could more closely resemble the DUI ancestral condition. Descriptions and comparisons presented in this paper are fundamental to a more complete understanding regarding the origins and consequences of DUI.}, }
@article {pmid20163596, year = {2009}, author = {Wu, YP and Guan, WJ and Zhao, QJ and He, XH and Pu, YB and Huo, JH and Xie, JF and Han, JL and Rao, SQ and Ma, YH}, title = {A fine map for maternal lineage analysis by mitochondrial hypervariable region in 12 Chinese goat breeds.}, journal = {Animal science journal = Nihon chikusan Gakkaiho}, volume = {80}, number = {4}, pages = {372-380}, doi = {10.1111/j.1740-0929.2009.00659.x}, pmid = {20163596}, issn = {1740-0929}, mesh = {Animals ; China ; Complementarity Determining Regions/*genetics ; DNA, Mitochondrial/genetics ; Female ; Goats/*genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {As the fast pace of genomic research continues to identify mitochondrial lineages in animals, it has become apparent that many independent studies are needed to support a robust phylogenetic inference. The aim of this study was thus to further characterize the maternal lineage, proposed to originate in southwestern region of China, using a wider survey of diverse goat breeds in China. To this end, we sequenced the mitochondrial hypervariable region 1 (HVR1) of the mtDNA control region in 145 goats of 12 Chinese breeds. Phylogenetic analysis revealed that Chinese goats were classified into four distinct lineages (A, B, C and D) as previously reported. A Mantel test and the analysis of Analysis of Molecular Variance (ANOVA) indicated that there was not an obvious geographic structure among Chinese goat breeds. Population expansion analysis based on mismatch distribution and Fu's Fs statistic indicate that two expansion events in Chinese goats occurred respectively at about 11 and 29 mutational time units ago, revealing two star-like subclades in lineage B corresponding to two population expansion events. Moreover, lineage B sequences were presented only in the breeds of southwestern or surrounding regions of China. Multiple lines of evidence from this study and previous studies indicate that for Chinese goats mtDNA lineage B originated from the southwestern region of China.}, }
@article {pmid20157523, year = {2009}, author = {Blagosklonny, MV and Hall, MN}, title = {Growth and aging: a common molecular mechanism.}, journal = {Aging}, volume = {1}, number = {4}, pages = {357-362}, pmid = {20157523}, issn = {1945-4589}, mesh = {Aging/*physiology ; Animals ; *Biological Evolution ; Energy Metabolism ; Humans ; Signal Transduction/*genetics/*physiology ; }, abstract = {It is commonly assumed that growth and aging are somehow linked, but the nature of this link has been elusive. Here we review the aging process as a continuation of TOR-driven growth. TOR is absolutely essential for developmental growth, but upon completion of development it causes aging and age-related diseases. Thus, the nutrient-sensing and growth-promoting TOR signaling pathway may provide a molecular link between growth and aging that is universal from yeast to human.}, }
@article {pmid20156838, year = {2010}, author = {Lapaille, M and Escobar-Ramírez, A and Degand, H and Baurain, D and Rodríguez-Salinas, E and Coosemans, N and Boutry, M and Gonzalez-Halphen, D and Remacle, C and Cardol, P}, title = {Atypical subunit composition of the chlorophycean mitochondrial F1FO-ATP synthase and role of Asa7 protein in stability and oligomycin resistance of the enzyme.}, journal = {Molecular biology and evolution}, volume = {27}, number = {7}, pages = {1630-1644}, doi = {10.1093/molbev/msq049}, pmid = {20156838}, issn = {1537-1719}, mesh = {Adenosine Triphosphate/metabolism ; Chlamydomonas reinhardtii/genetics/metabolism ; Chlorophyta/*enzymology/genetics/growth &amp; development ; Dimerization ; *Drug Resistance ; Mitochondria/*enzymology ; Mitochondrial Proton-Translocating ATPases/chemistry/genetics/*metabolism ; Oligomycins/*pharmacology ; Phylogeny ; Protein Subunits/antagonists &amp; inhibitors/genetics/*metabolism ; Protons ; RNA, Small Interfering/pharmacology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {In yeast, mammals, and land plants, mitochondrial F(1)F(O)-ATP synthase (complex V) is a remarkable enzymatic machinery that comprises about 15 conserved subunits. Peculiar among eukaryotes, complex V from Chlamydomonadales algae (order of chlorophycean class) has an atypical subunit composition of its peripheral stator and dimerization module, with nine subunits of unknown evolutionary origin (Asa subunits). In vitro, this enzyme exhibits an increased stability of its dimeric form, and in vivo, Chlamydomonas reinhardtii cells are insensitive to oligomycins, which are potent inhibitors of proton translocation through the F(O) moiety. In this work, we showed that the atypical features of the Chlamydomonadales complex V enzyme are shared by the other chlorophycean orders. By biochemical and in silico analyses, we detected several atypical Asa subunits in Scenedesmus obliquus (Sphaeropleales) and Chlorococcum ellipsoideum (Chlorococcales). In contrast, complex V has a canonical subunit composition in other classes of Chlorophytes (Trebouxiophyceae, Prasinophyceae, and Ulvophyceae) as well as in Streptophytes (land plants), and in Rhodophytes (red algae). Growth, respiration, and ATP levels in Chlorophyceae were also barely affected by oligomycin concentrations that affect representatives of the other classes of Chlorophytes. We finally studied the function of the Asa7 atypical subunit by using RNA interference in C. reinhardtii. Although the loss of Asa7 subunit has no impact on cell bioenergetics or mitochondrial structures, it destabilizes in vitro the enzyme dimeric form and renders growth, respiration, and ATP level sensitive to oligomycins. Altogether, our results suggest that the loss of canonical components of the complex V stator happened at the root of chlorophycean lineage and was accompanied by the recruitment of novel polypeptides. Such a massive modification of complex V stator features might have conferred novel properties, including the stabilization of the enzyme dimeric form and the shielding of the proton channel. In these respects, we discuss an evolutionary scenario for F(1)F(O)-ATP synthase in the whole green lineage (i.e., Chlorophyta and Streptophyta).}, }
@article {pmid20154424, year = {2009}, author = {Hosaka, K and Sanetomo, R}, title = {Comparative differentiation in mitochondrial and chloroplast DNA among cultivated potatoes and closely related wild species.}, journal = {Genes &amp; genetic systems}, volume = {84}, number = {5}, pages = {371-378}, doi = {10.1266/ggs.84.371}, pmid = {20154424}, issn = {1341-7568}, mesh = {Chloroplasts/genetics ; DNA Primers/chemistry/genetics ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; Genetic Markers/*genetics ; Microsatellite Repeats ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Solanum tuberosum/*classification/*genetics/growth &amp; development ; }, abstract = {A total of 476 accessions of seven cultivated and 32 wild potato species previously characterized by nuclear DNA (nDNA) and chloroplast DNA (ctDNA) marker analyses were employed to the mitochondrial DNA (mtDNA) marker analysis. Fourteen simple sequence repeat (SSR) markers with mononucleotide repeat regions were developed from the potato mtDNA, although their variability was extremely low. Six mtDNA markers including three developed SSR markers disclosed 40 banding patterns that discriminated 63 different mtDNAs. For the same set of samples, 72 ctDNA banding patterns discriminated 129 different ctDNAs. Consequently, 164 haplotypes were distinguished. The correlation between ctDNA and mtDNA differentiation was positive (r = 0.226), but poor when compared with that between ctDNA and nDNA (r = 0.415), which likely lowered the utility of mtDNA polymorphisms in evaluating relationships among these species. Nevertheless, a finding of a unique mtDNA type in all T-type ctDNA holders (S. tuberosum and S. tarijense) strongly supports S. tarijense functioned as a maternal ancestor of potato.}, }
@article {pmid20153693, year = {2010}, author = {Wylezich, C and Nies, G and Mylnikov, AP and Tautz, D and Arndt, H}, title = {An evaluation of the use of the LSU rRNA D1-D5 domain for DNA-based taxonomy of eukaryotic protists.}, journal = {Protist}, volume = {161}, number = {3}, pages = {342-352}, doi = {10.1016/j.protis.2010.01.003}, pmid = {20153693}, issn = {1618-0941}, mesh = {Classification/*methods ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Eukaryota/*classification/*genetics ; Genes, rRNA ; Molecular Biology/*methods ; *Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; }, abstract = {Diagnostic signature DNA sequences are important tools for the identification of species. There is an active debate in the literature on the choice of the best markers applicable for a broad range of organisms. Protists have seldom been included in these evaluations. Mitochondrial gene sequences are inappropriate for protists since several groups do not possess mitochondria. Here we studied the application of the large subunit (LSU) rRNA gene fragments (D1-D5) regarding their usefulness to discriminate between a wide range of heterotrophic nanoflagellates. Phylogenetic analyses based on the LSU rRNA fragments showed similar results compared to phylogenetic trees based on the small subunit (SSU) rRNA. The data set indicates the power of the use of the D1-D5 region as a marker for a DNA-based taxonomy. Our results, together with the available sequences in Genbank, form a comprehensive database for unicellular eukaryotes, especially heterotrophic flagellates. It is now possible to assign new sequences to the different groups of heterotrophic flagellates which we have tested for different closely related Cercomonas and Paracercomonas strains from groundwater.}, }
@article {pmid20151817, year = {2010}, author = {Olson, JR and Cooper, SJ and Swanson, DL and Braun, MJ and Williams, JB}, title = {The relationship of metabolic performance and distribution in black-capped and Carolina chickadees.}, journal = {Physiological and biochemical zoology : PBZ}, volume = {83}, number = {2}, pages = {263-275}, doi = {10.1086/648395}, pmid = {20151817}, issn = {1537-5293}, mesh = {Animals ; Basal Metabolism/physiology ; Body Size/physiology ; Body Temperature Regulation/*physiology ; Cold Temperature ; Demography ; Environment ; Mitochondria/physiology ; Ohio ; Oxygen Consumption/physiology ; Songbirds/metabolism/*physiology ; Species Specificity ; Temperature ; }, abstract = {In endotherms, metabolic performance is associated with a wide array of ecological traits, including species distribution. Researchers have suggested that the northern boundaries of North American passerines are limited by their ability to sustain the high metabolic rates required for thermoregulation. Black-capped chickadees (Poecile atricapillus; BC) are year-round residents in most of Canada and the northern half of the United States, whereas Carolina chickadees (Poecile carolinensis; CA) are found exclusively in the southeastern United States. These species hybridize along a narrow contact zone that has been moving northward at a rate of about 1.6 km per decade, coincident with warming temperatures in Ohio. The location of the chickadee hybrid zone in Ohio closely matches air temperature isotherms, further suggesting that metabolic rate may correlate with distribution in these species. We tested the hypothesis that distribution patterns of chickadees are linked with their rate of metabolism. For populations of BC and CA chickadees, we measured basal metabolic rates (BMRs) and cold-induced peak metabolic rates from areas that differ in winter temperatures and supplemented this information with data from other studies. Although our findings suggest a general relationship between lower air temperatures and higher metabolic rate among black-capped chickadee populations, this trend was not robust across all locations. There was no significant relationship between lower air temperatures and metabolism in Carolina chickadees. Within Ohio, hybrids had a significantly higher mass-corrected BMR than either parental species. We suggest that the mtDNA-nDNA mismatch of hybrids may produce less efficient mitochondrial protein complexes, which in turn affects the efficiency of ATP production, thereby increasing rate of oxygen consumption to meet ATP demands.}, }
@article {pmid20145006, year = {2010}, author = {Karve, R and Lauria, M and Virnig, A and Xia, X and Rauh, BL and Moore, Bd}, title = {Evolutionary lineages and functional diversification of plant hexokinases.}, journal = {Molecular plant}, volume = {3}, number = {2}, pages = {334-346}, doi = {10.1093/mp/ssq003}, pmid = {20145006}, issn = {1674-2052}, mesh = {Amino Acid Sequence ; Arabidopsis/classification/*enzymology/genetics ; Arabidopsis Proteins/chemistry/*genetics ; Cytosol/enzymology ; *Evolution, Molecular ; Hexokinase/chemistry/classification/*genetics ; Microscopy, Confocal ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {Sequencing data from 10 species show that a plant hexokinase (HXK) family contains 5-11 genes. Functionally, a given family can include metabolic catalysts, glucose signaling proteins, and non-catalytic, apparent regulatory enzyme homologs. This study has two goals. The first aim is to develop a predictive method to determine which HXK proteins within a species have which type of function. The second aim is to determine whether HXK-dependent glucose signaling proteins occur among more primitive plants, as well as among angiosperms. Using a molecular phylogeny approach, combined with selective experimental testing, we found that non-catalytic HXK homologs might occur in all plants, including the relatively primitive Selaginella moellendorffi. We also found that different lineages of angiosperm HXKs have apparent conserved features for catalytic activity and for sub-cellular targeting. Most higher-plant HXKs are expressed predominantly at mitochondria, with HXKs of one lineage occurring in the plastid, and HXKs of one monocot lineage occurring in the cytosol. Using protoplast transient expression assays, we found that HXK glucose signaling proteins occur likely in all higher plants and in S. moellendorffi as well. Thus, the use of glucose by plant HXK isoforms in metabolism and/or as a regulatory metabolite occurs as widespread, conserved processes.}, }
@article {pmid20144467, year = {2010}, author = {Dallai, R and Mercati, D and Bu, Y and Yin, YW}, title = {Spermatogenesis and sperm structure of Acerella muscorum, (Ionescu, 1930) (Hexapoda, Protura).}, journal = {Tissue &amp; cell}, volume = {42}, number = {2}, pages = {97-104}, doi = {10.1016/j.tice.2010.01.001}, pmid = {20144467}, issn = {1532-3072}, mesh = {Animals ; Centrioles/physiology/ultrastructure ; Cytoplasm/physiology/ultrastructure ; Fertilization/physiology ; Invertebrates/physiology/*ultrastructure ; Male ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Mitochondria/physiology/ultrastructure ; Phylogeny ; Species Specificity ; Spermatids/physiology/ultrastructure ; Spermatocytes/physiology/ultrastructure ; Spermatogenesis/*physiology ; Spermatozoa/physiology/*ultrastructure ; Testis/physiology/*ultrastructure ; }, abstract = {The general organization of the male genital system, the spermatogenesis and the sperm structure of the proturan Acerella muscorum have been described. At the apex of testis apical huge cells are present; their cytoplasm contains a conventional centriole, a large amount of dense material and several less electron-dense masses surrounded by mitochondria. Spermatocytes have normal centrioles and are interconnected by cytoplasmic bridges. Such bridges seem to be absent between spermatid cells and justify the lack of synchronization of cell maturation. Spermatids are almost globular cells with a spheroidal nucleus and a large mass of dense material corresponding to the centriole adjunct. Within this mass a centriole is preserved. Mitochondria of normal structure are located between the nucleus and the plasma membrane. The spermatids are surrounded by a thick membrane. No flagellar structure is formed. Sperm have a compact spheroidal nucleus, a large cap of centriole adjunct material within which a centriole is still visible. A layer of mitochondria is located over the nucleus. The cytoplasm is reduced in comparison to spermatids; many dense bodies are interspersed with sperm in the testicular lumen. The sperm are small, immotile cells of about 2.5-3microm in diameter.}, }
@article {pmid20143628, year = {2009}, author = {Myl'nikov, AP}, title = {[Ultrastructure and phylogeny of colpodellids (Colpodellida, Alveolata)].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {6}, pages = {685-694}, pmid = {20143628}, issn = {1026-3470}, mesh = {Apicomplexa/*physiology/*ultrastructure ; Flagella/physiology/ultrastructure ; *Phylogeny ; }, abstract = {The structure of cells of the predatory flagellates Colpodella pseudoedax and C. unguis was studied. The cell was found to contain two heterodynamic flagellae, three-membrane pellicle, micropores, subpellicular microtubulae, microtubular open conoid, roptries, micronemes, extrusive organelles (trichocysts), and mitochondria with tubular cristae. Upon discharging, trichocysts form cross-striated bands. The thin-walled cylinder lies in the transitional zone of the flagellae. Cells reproduce by means of longitudinal binary fission. The similarities between given species and other colpodelids and such between perkinsea, sporozoans, and dinoflagellates are discussed.}, }
@article {pmid20141629, year = {2010}, author = {Singh, A and Singh, U and Mittal, D and Grover, A}, title = {Genome-wide analysis of rice ClpB/HSP100, ClpC and ClpD genes.}, journal = {BMC genomics}, volume = {11}, number = {}, pages = {95}, pmid = {20141629}, issn = {1471-2164}, mesh = {Adenosine Triphosphatases/*genetics ; Chloroplasts/genetics ; Cloning, Molecular ; DNA, Plant/genetics ; Gene Expression Regulation, Plant ; Genes, Plant ; Genetic Complementation Test ; *Genome, Plant ; Heat-Shock Proteins/*genetics ; Hot Temperature ; Molecular Chaperones/*genetics ; Multigene Family ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; Oryza/*genetics ; Phylogeny ; Plant Proteins/genetics ; Plants, Genetically Modified/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Saccharomyces cerevisiae/genetics ; Sequence Analysis, DNA ; Stress, Physiological ; }, abstract = {BACKGROUND: ClpB-cyt/HSP100 protein acts as chaperone, mediating disaggregation of denatured proteins. Previous studies have shown that ClpB-cyt/HSP100 gene belongs to the group class I Clp ATPase proteins and ClpB-cyt/HSP100 transcript is regulated by heat stress and developmental cues.<br><br>RESULTS: Nine ORFs were noted to constitute rice class I Clp ATPases in the following manner: 3 ClpB proteins (ClpB-cyt, Os05g44340; ClpB-m, Os02g08490; ClpB-c, Os03g31300), 4 ClpC proteins (ClpC1, Os04g32560; ClpC2, Os12g12580; ClpC3, Os11g16590; ClpC4, Os11g16770) and 2 ClpD proteins (ClpD1, Os02g32520; ClpD2, Os04g33210). Using the respective signal sequences cloned upstream to GFP/CFP reporter proteins and transient expression studies with onion epidermal cells, evidence is provided that rice ClpB-m and Clp-c proteins are indeed localized to their respective cell locations mitochondria and chloroplasts, respectively. Associated with their diverse cell locations, domain structures of OsClpB-c, OsClpB-m and OsClpB-cyt proteins are noted to possess a high-level conservation. OsClpB-cyt transcript is shown to be enriched at milk and dough stages of seed development. While expression of OsClpB-m was significantly less as compared to its cytoplasmic and chloroplastic counterparts in different tissues, this transcript showed highest heat-induced expression amongst the 3 ClpB proteins. OsClpC1 and OsClpC2 are predicted to be chloroplast-localized as is the case with all known plant ClpC proteins. However, the fact that OsClpC3 protein appears mitochondrial/chloroplastic with equal probability and OsClpC4 a plasma membrane protein reflects functional diversity of this class. Different class I Clp ATPase transcripts were noted to be cross-induced by a host of different abiotic stress conditions. Complementation assays of Deltahsp104 mutant yeast cells showed that OsClpB-cyt, OsClpB-m, OsClpC1 and OsClpD1 have significantly positive effects. Remarkably, OsClpD1 gene imparted appreciably high level tolerance to the mutant yeast cells.<br><br>CONCLUSIONS: Rice class I Clp ATPase gene family is constituted of 9 members. Of these 9, only 3 belonging to ClpB group are heat stress regulated. Distribution of ClpB proteins to different cell organelles indicates that their functioning might be critical in different cell locations. From the complementation assays, OsClpD1 appears to be more effective than OsClpB-cyt protein in rescuing the thermosensitive defect of the yeast ScDeltahsp104 mutant cells.}, }
@article {pmid20135105, year = {2010}, author = {Turmel, M and Otis, C and Lemieux, C}, title = {A deviant genetic code in the reduced mitochondrial genome of the picoplanktonic green alga Pycnococcus provasolii.}, journal = {Journal of molecular evolution}, volume = {70}, number = {2}, pages = {203-214}, pmid = {20135105}, issn = {1432-1432}, mesh = {Base Sequence ; Chlorophyta/*genetics ; *Codon ; DNA, Algal/chemistry/genetics ; Genes, Plant ; *Genome Size ; *Genome, Mitochondrial ; Genome, Plant ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleotides ; Phylogeny ; RNA, Transfer/chemistry/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Reduction in size of flagellated chlorophytes occurred multiple times during evolution, providing the opportunity to study the consequences of cell reduction on genome architecture. Recent investigations on the chloroplast genomes of the tiny prasinophyceans Ostreococcus tauri (Mamiellales), Micromonas sp. RCC299 (Mamiellales), and Pycnococcus provasolii (Pseudocourfieldiales) highlighted their extreme compaction and reduced gene repertoires. Genome compaction is also exemplified by the Ostreococcus and Micromonas mitochondrial DNAs (mtDNAs) although they have retained almost all of the about 65 genes presumably present in the mitochondria of ancestral prasinophyceans. In this study, the mitochondrial genome of Pycnococcus was sequenced and compared to those of previously examined chlorophytes. Our results document the first case where cellular reduction of a free-living alga was accompanied by marked reduction in gene content of both the mitochondrial and chloroplast genomes. At 24,321 bp, the intronless Pycnococcus mitochondrial genome falls within the lower size range displayed by green algal mtDNAs. The 36 conserved genes, specifying two rRNAs with conventional structures, 16 tRNAs and 18 proteins, are all encoded on the same DNA strand and represent 88% of the genome. Besides a pronounced codon bias, the protein-coding genes feature a variant genetic code characterized by the use of TGA (normally a stop codon) to code for tryptophan, and the unprecedented use of TTA and TTG (normally leucine codons) as stop codons. We conclude that substantial reduction of the mitochondrial genome occurred in at least three independent chlorophyte lineages and that this process entailed a number of convergent changes in these lineages.}, }
@article {pmid20133559, year = {2010}, author = {Alcock, F and Clements, A and Webb, C and Lithgow, T}, title = {Evolution. Tinkering inside the organelle.}, journal = {Science (New York, N.Y.)}, volume = {327}, number = {5966}, pages = {649-650}, doi = {10.1126/science.1182129}, pmid = {20133559}, issn = {1095-9203}, mesh = {Alphaproteobacteria/genetics/*metabolism ; Amino Acid Transport Systems/chemistry/metabolism ; Bacterial Proteins/chemistry/metabolism ; *Biological Evolution ; *Eukaryotic Cells/metabolism/ultrastructure ; Evolution, Molecular ; *Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins/chemistry/*metabolism ; *Protein Transport ; *Symbiosis ; }, }
@article {pmid20132446, year = {2010}, author = {Suematsu, T and Yokobori, S and Morita, H and Yoshinari, S and Ueda, T and Kita, K and Takeuchi, N and Watanabe, Y}, title = {A bacterial elongation factor G homologue exclusively functions in ribosome recycling in the spirochaete Borrelia burgdorferi.}, journal = {Molecular microbiology}, volume = {75}, number = {6}, pages = {1445-1454}, doi = {10.1111/j.1365-2958.2010.07067.x}, pmid = {20132446}, issn = {1365-2958}, mesh = {Borrelia burgdorferi/*enzymology/*metabolism ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Guanosine Triphosphate/metabolism ; Humans ; Molecular Sequence Data ; Peptide Elongation Factor G/*metabolism ; Phylogeny ; Prokaryotic Initiation Factor-3/metabolism ; *Protein Biosynthesis ; Ribosomal Proteins/metabolism ; Ribosomes/*metabolism ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Translation elongation factor G (EF-G) in bacteria plays two distinct roles in different phases of the translation system. EF-G catalyses the translocation of tRNAs on the ribosome in the elongation step, as well as the dissociation of the post-termination state ribosome into two subunits in the recycling step. In contrast to this conventional view, it has very recently been demonstrated that the dual functions of bacterial EF-G are distributed over two different EF-G paralogues in human mitochondria. In the present study, we show that the same division of roles of EF-G is also found in bacteria. Two EF-G paralogues are found in the spirochaete Borrelia burgdorferi, EF-G1 and EF-G2. We demonstrate that EF-G1 is a translocase, while EF-G2 is an exclusive recycling factor. We further demonstrate that B. burgdorferi EF-G2 does not require GTP hydrolysis for ribosome disassembly, provided that translation initiation factor 3 (IF-3) is present in the reaction. These results indicate that two B. burgdorferi EF-G paralogues are close relatives to mitochondrial EF-G paralogues rather than the conventional bacterial EF-G, in both their phylogenetic and biochemical features.}, }
@article {pmid20124349, year = {2010}, author = {Martin, W}, title = {Evolutionary origins of metabolic compartmentalization in eukaryotes.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1541}, pages = {847-855}, pmid = {20124349}, issn = {1471-2970}, mesh = {*Biological Evolution ; Chloroplasts/genetics/metabolism ; Eukaryota/*genetics/*metabolism ; Gene Transfer, Horizontal ; Mitochondria/genetics/metabolism ; Models, Biological ; Organelles/genetics/*metabolism ; Protein Transport ; Symbiosis ; }, abstract = {Many genes in eukaryotes are acquisitions from the free-living antecedents of chloroplasts and mitochondria. But there is no evolutionary 'homing device' that automatically directs the protein product of a transferred gene back to the organelle of its provenance. Instead, the products of genes acquired from endosymbionts can explore all targeting possibilities within the cell. They often replace pre-existing host genes, or even whole pathways. But the transfer of an enzymatic pathway from one compartment to another poses severe problems: over evolutionary time, the enzymes of the pathway acquire their targeting signals for the new compartment individually, not in unison. Until the whole pathway is established in the new compartment, newly routed individual enzymes are useless, and their genes will be lost through mutation. Here it is suggested that pathways attain novel compartmentation variants via a 'minor mistargeting' mechanism. If protein targeting in eukaryotic cells possesses enough imperfection such that small amounts of entire pathways continuously enter novel compartments, selectable units of biochemical function would exist in new compartments, and the genes could become selected. Dual-targeting of proteins is indeed very common within eukaryotic cells, suggesting that targeting variation required for this minor mistargeting mechanism to operate exists in nature.}, }
@article {pmid20124346, year = {2010}, author = {Lithgow, T and Schneider, A}, title = {Evolution of macromolecular import pathways in mitochondria, hydrogenosomes and mitosomes.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1541}, pages = {799-817}, pmid = {20124346}, issn = {1471-2970}, mesh = {*Biological Evolution ; Biological Transport, Active/*genetics ; Computational Biology ; Eukaryota/classification/*genetics/*metabolism ; Hydrogen/metabolism ; Leishmania/genetics/metabolism ; Macromolecular Substances/metabolism ; Mitochondria/*genetics/*metabolism ; Mitochondrial Proteins/metabolism ; Models, Biological ; Organelles/*genetics/*metabolism ; Phylogeny ; Plants/genetics/metabolism ; Protein Transport/genetics ; RNA, Transfer/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Symbiosis/genetics ; }, abstract = {All eukaryotes require mitochondria for survival and growth. The origin of mitochondria can be traced down to a single endosymbiotic event between two probably prokaryotic organisms. Subsequent evolution has left mitochondria a collection of heterogeneous organelle variants. Most of these variants have retained their own genome and translation system. In hydrogenosomes and mitosomes, however, the entire genome was lost. All types of mitochondria import most of their proteome from the cytosol, irrespective of whether they have a genome or not. Moreover, in most eukaryotes, a variable number of tRNAs that are required for mitochondrial translation are also imported. Thus, import of macromolecules, both proteins and tRNA, is essential for mitochondrial biogenesis. Here, we review what is known about the evolutionary history of the two processes using a recently revised eukaryotic phylogeny as a framework. We discuss how the processes of protein import and tRNA import relate to each other in an evolutionary context.}, }
@article {pmid20124345, year = {2010}, author = {Barbrook, AC and Howe, CJ and Kurniawan, DP and Tarr, SJ}, title = {Organization and expression of organellar genomes.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1541}, pages = {785-797}, pmid = {20124345}, issn = {1471-2970}, support = {BB/E004393/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Biological Evolution ; Gene Expression ; *Genome ; Genome, Chloroplast ; Genome, Mitochondrial ; Organelles/*genetics ; RNA/genetics ; Symbiosis/genetics ; }, abstract = {Protist mitochondrial genomes show a very wide range of gene content, ranging from three genes for respiratory chain components in Apicomplexa and dinoflagellates to nearly 100 genes in Reclinomonas americana. In many organisms the rRNA genes are fragmented, although still functional. Some protist mitochondria encode a full set of tRNAs, while others rely on imported molecules. There is similarly a wide variation in mitochondrial genome organization, even among closely related groups. Mitochondrial gene expression and control are generally poorly characterized. Transcription probably relies on a 'viral-type' RNA polymerase, although a 'bacterial-type' enzyme may be involved in some cases. Transcripts are heavily edited in many lineages. The chloroplast genome generally shows less variation in gene content and organization, although greatly reduced genomes are found in dinoflagellate algae and non-photosynthetic organisms. Genes in the former are located on small plasmids in contrast to the larger molecules found elsewhere. Control of gene expression in chloroplasts involves transcriptional and post-transcriptional regulation. Redox poise and the ATP/ADP ratio are likely to be important determinants. Some protists have an additional extranuclear genome, the nucleomorph, which is a remnant nucleus. Nucleomorphs of two separate lineages have a number of features in common.}, }
@article {pmid20124342, year = {2010}, author = {Lim, L and McFadden, GI}, title = {The evolution, metabolism and functions of the apicoplast.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1541}, pages = {749-763}, pmid = {20124342}, issn = {1471-2970}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Apicomplexa/*genetics/*metabolism/pathogenicity ; *Biological Evolution ; Chloroplasts/metabolism ; Fatty Acids/biosynthesis ; Gene Transfer, Horizontal ; Heme/biosynthesis ; Humans ; Iron-Sulfur Proteins/biosynthesis ; Mitochondria/genetics/metabolism ; Models, Biological ; Plasmodium/genetics/growth &amp; development/metabolism/pathogenicity ; Plastids/*genetics/*metabolism ; Protein Transport ; Symbiosis/genetics/physiology ; Terpenes/metabolism ; }, abstract = {The malaria parasite, Plasmodium falciparum, harbours a relict plastid known as the 'apicoplast'. The discovery of the apicoplast ushered in an exciting new prospect for drug development against the parasite. The eubacterial ancestry of the organelle offers a wealth of opportunities for the development of therapeutic interventions. Morphological, biochemical and bioinformatic studies of the apicoplast have further reinforced its 'plant-like' characteristics and potential as a drug target. However, we are still not sure why the apicoplast is essential for the parasite's survival. This review explores the origins and metabolic functions of the apicoplast. In an attempt to decipher the role of the organelle within the parasite we also take a closer look at the transporters decorating the plastid to better understand the metabolic exchanges between the apicoplast and the rest of the parasite cell.}, }
@article {pmid20124341, year = {2010}, author = {Keeling, PJ}, title = {The endosymbiotic origin, diversification and fate of plastids.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1541}, pages = {729-748}, pmid = {20124341}, issn = {1471-2970}, support = {//Canadian Institutes of Health Research/Canada ; }, mesh = {*Biological Evolution ; Chlorophyta/genetics/physiology ; Dinoflagellida/genetics/physiology ; Eukaryota/genetics/physiology ; Gene Transfer, Horizontal ; Mitochondria/genetics/physiology ; Models, Biological ; Phylogeny ; Plastids/*genetics/physiology ; Rhodophyta/genetics/physiology ; Symbiosis/*genetics/physiology ; }, abstract = {Plastids and mitochondria each arose from a single endosymbiotic event and share many similarities in how they were reduced and integrated with their host. However, the subsequent evolution of the two organelles could hardly be more different: mitochondria are a stable fixture of eukaryotic cells that are neither lost nor shuffled between lineages, whereas plastid evolution has been a complex mix of movement, loss and replacement. Molecular data from the past decade have substantially untangled this complex history, and we now know that plastids are derived from a single endosymbiotic event in the ancestor of glaucophytes, red algae and green algae (including plants). The plastids of both red algae and green algae were subsequently transferred to other lineages by secondary endosymbiosis. Green algal plastids were taken up by euglenids and chlorarachniophytes, as well as one small group of dinoflagellates. Red algae appear to have been taken up only once, giving rise to a diverse group called chromalveolates. Additional layers of complexity come from plastid loss, which has happened at least once and probably many times, and replacement. Plastid loss is difficult to prove, and cryptic, non-photosynthetic plastids are being found in many non-photosynthetic lineages. In other cases, photosynthetic lineages are now understood to have evolved from ancestors with a plastid of different origin, so an ancestral plastid has been replaced with a new one. Such replacement has taken place in several dinoflagellates (by tertiary endosymbiosis with other chromalveolates or serial secondary endosymbiosis with a green alga), and apparently also in two rhizarian lineages: chlorarachniophytes and Paulinella (which appear to have evolved from chromalveolate ancestors). The many twists and turns of plastid evolution each represent major evolutionary transitions, and each offers a glimpse into how genomes evolve and how cells integrate through gene transfers and protein trafficking.}, }
@article {pmid20124340, year = {2010}, author = {Hjort, K and Goldberg, AV and Tsaousis, AD and Hirt, RP and Embley, TM}, title = {Diversity and reductive evolution of mitochondria among microbial eukaryotes.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1541}, pages = {713-727}, pmid = {20124340}, issn = {1471-2970}, mesh = {Adenosine Triphosphate/metabolism ; *Biological Evolution ; Eukaryota/*genetics/*metabolism ; Hydrogen/metabolism ; Iron-Sulfur Proteins/biosynthesis ; Mitochondria/*genetics/*metabolism ; Organelles/genetics/metabolism ; Protein Transport ; }, abstract = {All extant eukaryotes are now considered to possess mitochondria in one form or another. Many parasites or anaerobic protists have highly reduced versions of mitochondria, which have generally lost their genome and the capacity to generate ATP through oxidative phosphorylation. These organelles have been called hydrogenosomes, when they make hydrogen, or remnant mitochondria or mitosomes when their functions were cryptic. More recently, organelles with features blurring the distinction between mitochondria, hydrogenosomes and mitosomes have been identified. These organelles have retained a mitochondrial genome and include the mitochondrial-like organelle of Blastocystis and the hydrogenosome of the anaerobic ciliate Nyctotherus. Studying eukaryotic diversity from the perspective of their mitochondrial variants has yielded important insights into eukaryote molecular cell biology and evolution. These investigations are contributing to understanding the essential functions of mitochondria, defined in the broadest sense, and the limits to which reductive evolution can proceed while maintaining a viable organelle.}, }
@article {pmid20124339, year = {2010}, author = {Nowack, EC and Melkonian, M}, title = {Endosymbiotic associations within protists.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1541}, pages = {699-712}, pmid = {20124339}, issn = {1471-2970}, mesh = {Animals ; *Biological Evolution ; Eukaryota/genetics/physiology ; Mitochondria/genetics/physiology ; Models, Biological ; Nitrogen Fixation ; Photosynthesis ; Plastids/genetics/physiology ; Prokaryotic Cells/microbiology/physiology ; *Symbiosis/genetics/physiology ; }, abstract = {The establishment of an endosymbiotic relationship typically seems to be driven through complementation of the host's limited metabolic capabilities by the biochemical versatility of the endosymbiont. The most significant examples of endosymbiosis are represented by the endosymbiotic acquisition of plastids and mitochondria, introducing photosynthesis and respiration to eukaryotes. However, there are numerous other endosymbioses that evolved more recently and repeatedly across the tree of life. Recent advances in genome sequencing technology have led to a better understanding of the physiological basis of many endosymbiotic associations. This review focuses on endosymbionts in protists (unicellular eukaryotes). Selected examples illustrate the incorporation of various new biochemical functions, such as photosynthesis, nitrogen fixation and recycling, and methanogenesis, into protist hosts by prokaryotic endosymbionts. Furthermore, photosynthetic eukaryotic endosymbionts display a great diversity of modes of integration into different protist hosts. In conclusion, endosymbiosis seems to represent a general evolutionary strategy of protists to acquire novel biochemical functions and is thus an important source of genetic innovation.}, }
@article {pmid20124190, year = {2010}, author = {Séveno, M and Séveno-Carpentier, E and Voxeur, A and Menu-Bouaouiche, L and Rihouey, C and Delmas, F and Chevalier, C and Driouich, A and Lerouge, P}, title = {Characterization of a putative 3-deoxy-D-manno-2-octulosonic acid (Kdo) transferase gene from Arabidopsis thaliana.}, journal = {Glycobiology}, volume = {20}, number = {5}, pages = {617-628}, doi = {10.1093/glycob/cwq011}, pmid = {20124190}, issn = {1460-2423}, mesh = {Amino Acid Sequence ; Arabidopsis/*enzymology/*genetics ; Gene Expression Regulation, Plant/*genetics ; Molecular Sequence Data ; Mutation ; Pectins/biosynthesis/chemistry ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Transferases/chemistry/*genetics/isolation &amp; purification ; }, abstract = {The structures of the pectic polysaccharide rhamnogalacturonan II (RG-II) pectin constituent are remarkably evolutionary conserved in all plant species. At least 12 different glycosyl residues are present in RG-II. Among them is the seldom eight-carbon sugar 3-deoxy-d-manno-octulosonic acid (Kdo) whose biosynthetic pathway has been shown to be conserved between plants and Gram-negative bacteria. Kdo is formed in the cytosol by the condensation of phosphoenol pyruvate with d-arabinose-5-P and then activated by coupling to cytidine monophosphate (CMP) prior to its incorporation in the Golgi apparatus by a Kdo transferase (KDTA) into the nascent polysaccharide RG-II. To gain new insight into RG-II biosynthesis and function, we isolated and characterized null mutants for the unique putative KDTA (AtKDTA) encoded in the Arabidopsis genome. We provide evidence that, in contrast to mutants affecting the RG-II biosynthesis, the extinction of the AtKDTA gene expression does not result in any developmental phenotype in the AtkdtA plants. Furthermore, the structure of RG-II from the null mutants was not altered and contained wild-type amount of Rha-alpha(1-5)Kdo side chain. The cellular localization of AtKDTA was investigated by using laser scanning confocal imaging of the protein fused to green fluorescent protein. In agreement with its cellular prediction, the fusion protein was demonstrated to be targeted to the mitochondria. These data, together with data deduced from sequence analyses of higher plant genomes, suggest that AtKDTA encodes a putative KDTA involved in the synthesis of a mitochondrial not yet identified lipid A-like molecule rather than in the synthesis of the cell wall RG-II.}, }
@article {pmid20118192, year = {2010}, author = {Alverson, AJ and Wei, X and Rice, DW and Stern, DB and Barry, K and Palmer, JD}, title = {Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae).}, journal = {Molecular biology and evolution}, volume = {27}, number = {6}, pages = {1436-1448}, pmid = {20118192}, issn = {1537-1719}, support = {F32 GM080079/GM/NIGMS NIH HHS/United States ; R01 GM070612/GM/NIGMS NIH HHS/United States ; 1F32GM080079-01A1/GM/NIGMS NIH HHS/United States ; R01-GM-70612/GM/NIGMS NIH HHS/United States ; }, mesh = {Citrullus/*genetics ; Cucurbita/*genetics ; *Evolution, Molecular ; *Genome, Mitochondrial ; *Genome, Plant ; Introns ; Models, Genetic ; Mutation ; RNA Editing ; RNA, Transfer ; Repetitive Sequences, Nucleic Acid ; }, abstract = {The mitochondrial genomes of seed plants are unusually large and vary in size by at least an order of magnitude. Much of this variation occurs within a single family, the Cucurbitaceae, whose genomes range from an estimated 390 to 2,900 kb in size. We sequenced the mitochondrial genomes of Citrullus lanatus (watermelon: 379,236 nt) and Cucurbita pepo (zucchini: 982,833 nt)--the two smallest characterized cucurbit mitochondrial genomes--and determined their RNA editing content. The relatively compact Citrullus mitochondrial genome actually contains more and longer genes and introns, longer segmental duplications, and more discernibly nuclear-derived DNA. The large size of the Cucurbita mitochondrial genome reflects the accumulation of unprecedented amounts of both chloroplast sequences (>113 kb) and short repeated sequences (>370 kb). A low mutation rate has been hypothesized to underlie increases in both genome size and RNA editing frequency in plant mitochondria. However, despite its much larger genome, Cucurbita has a significantly higher synonymous substitution rate (and presumably mutation rate) than Citrullus but comparable levels of RNA editing. The evolution of mutation rate, genome size, and RNA editing are apparently decoupled in Cucurbitaceae, reflecting either simple stochastic variation or governance by different factors.}, }
@article {pmid20107138, year = {2010}, author = {Ciccarelli, O and Altmann, DR and McLean, MA and Wheeler-Kingshott, CA and Wimpey, K and Miller, DH and Thompson, AJ}, title = {Spinal cord repair in MS: does mitochondrial metabolism play a role?.}, journal = {Neurology}, volume = {74}, number = {9}, pages = {721-727}, pmid = {20107138}, issn = {1526-632X}, support = {074618/Z/04/Z//Wellcome Trust/United Kingdom ; //Department of Health/United Kingdom ; }, mesh = {Adult ; Aspartic Acid/*analogs &amp; derivatives/metabolism ; Axons/pathology/physiology ; Cervical Vertebrae ; Disease Progression ; Female ; Follow-Up Studies ; Humans ; Linear Models ; Logistic Models ; Longitudinal Studies ; Magnetic Resonance Spectroscopy ; Male ; Mitochondria/*physiology ; Multiple Sclerosis, Chronic Progressive/pathology/*physiopathology ; Multiple Sclerosis, Relapsing-Remitting/pathology/*physiopathology ; Nerve Degeneration/*physiopathology ; Organ Size ; Reactive Oxygen Species/metabolism ; Spinal Cord/pathology/*physiopathology ; Time Factors ; }, abstract = {OBJECTIVE: To investigate the mechanisms of spinal cord repair and their relative contribution to clinical recovery in patients with multiple sclerosis (MS) after a cervical cord relapse, using spinal cord (1)H-magnetic resonance spectroscopy (MRS) and volumetric imaging.<br><br>METHODS: Fourteen patients with MS and 13 controls underwent spinal cord imaging at baseline and at 1, 3, and 6 months. N-acetyl-aspartate (NAA) concentration, which reflects axonal count and metabolism in mitochondria, and the cord cross-sectional area, which indicates axonal count, were measured in the affected cervical region. Mixed effect linear regression models investigated the temporal evolution of these measures and their association with clinical changes. Ordinal logistic regressions identified predictors of recovery.<br><br>RESULTS: Patients who recovered showed a sustained increase in NAA after 1 month. In the whole patient group, a greater increase of NAA after 1 month was associated with greater recovery. Patients showed a significant decline in cord area during follow-up, which did not correlate with clinical changes. A worse recovery was predicted by a longer disease duration at study entry.<br><br>CONCLUSIONS: The partial recovery of N-acetyl-aspartate levels after the acute event, which is concurrent with a decline in cord cross-sectional area, may be driven by increased axonal mitochondrial metabolism. This possible repair mechanism is associated with clinical recovery, and is less efficient in patients with longer disease duration. These insights into the mechanisms of spinal cord repair highlight the need to extend spinal cord magnetic resonance spectroscopy to other spinal cord disorders, and explore therapies that enhance recovery by modulating mitochondrial activity.}, }
@article {pmid20106904, year = {2010}, author = {Remmert, M and Biegert, A and Linke, D and Lupas, AN and Söding, J}, title = {Evolution of outer membrane beta-barrels from an ancestral beta beta hairpin.}, journal = {Molecular biology and evolution}, volume = {27}, number = {6}, pages = {1348-1358}, doi = {10.1093/molbev/msq017}, pmid = {20106904}, issn = {1537-1719}, mesh = {Bacterial Outer Membrane Proteins/*chemistry/genetics ; Cluster Analysis ; Computational Biology/*methods ; Databases, Protein ; *Evolution, Molecular ; Gram-Negative Bacteria/*chemistry/genetics ; Markov Chains ; Models, Biological ; *Protein Structure, Secondary ; Repetitive Sequences, Amino Acid ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Outer membrane beta-barrels (OMBBs) are the major class of outer membrane proteins from Gram-negative bacteria, mitochondria, and plastids. Their transmembrane domains consist of 8-24 beta-strands forming a closed, barrel-shaped beta-sheet around a central pore. Despite their obvious structural regularity, evidence for an origin by duplication or for a common ancestry has not been found. We use three complementary approaches to show that all OMBBs from Gram-negative bacteria evolved from a single, ancestral beta beta hairpin. First, we link almost all families of known single-chain bacterial OMBBs with each other through transitive profile searches. Second, we identify a clear repeat signature in the sequences of many OMBBs in which the repeating sequence unit coincides with the structural beta beta hairpin repeat. Third, we show that the observed sequence similarity between OMBB hairpins cannot be explained by structural or membrane constraints on their sequences. The third approach addresses a longstanding problem in protein evolution: how to distinguish between a very remotely homologous relationship and the opposing scenario of "sequence convergence." The origin of a diverse group of proteins from a single hairpin module supports the hypothesis that, around the time of transition from the RNA to the protein world, proteins arose by amplification and recombination of short peptide modules that had previously evolved as cofactors of RNAs.}, }
@article {pmid20106903, year = {2010}, author = {Chiu, WC and Chang, CP and Wen, WL and Wang, SW and Wang, CC}, title = {Schizosaccharomyces pombe possesses two paralogous valyl-tRNA synthetase genes of mitochondrial origin.}, journal = {Molecular biology and evolution}, volume = {27}, number = {6}, pages = {1415-1424}, doi = {10.1093/molbev/msq025}, pmid = {20106903}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Aminoacylation ; Cytoplasm/metabolism ; Gene Knockout Techniques ; *Genes, Essential ; *Genes, Fungal ; Genetic Complementation Test ; Histocytochemistry ; Microscopy, Fluorescence ; Mitochondria/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Schizosaccharomyces/cytology/*enzymology/genetics/metabolism ; Sequence Alignment ; Valine-tRNA Ligase/*genetics/metabolism ; }, abstract = {Previous studies showed that VAS1 of Saccharomyces cerevisiae encodes both cytosolic and mitochondrial forms of valyl-tRNA synthetase (ValRS) through alternative initiation of translation. We show herein that except for Schizosaccharomyces pombe, all yeast species studied contained a single ValRS gene encoding both forms, and all of the mature protein forms deduced from those genes possessed an N-terminal appended domain (Ad) that was absent from their bacterial relatives. In contrast, S. pombe contained two distinct nuclear ValRS genes, one encoding the mitochondrial form and the other its cytosolic counterpart. Although the cytosolic form closely resembles other yeast ValRS sequences (approximately 60% identity), the mitochondrial form exhibits significant divergence from others (approximately 35% identity). Both genes are active and essential for the survival of the yeast. Most conspicuously, the mitochondrial form lacks the characteristic Ad. A phylogenetic analysis further suggested that both forms of S. pombe ValRS are of mitochondrial origin, and the mitochondrial form is ancestral to the cytoplasmic form.}, }
@article {pmid20105154, year = {2010}, author = {Clarke, A and Pörtner, HO}, title = {Temperature, metabolic power and the evolution of endothermy.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {85}, number = {4}, pages = {703-727}, doi = {10.1111/j.1469-185X.2010.00122.x}, pmid = {20105154}, issn = {1469-185X}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; *Biological Evolution ; Biometry ; *Body Temperature Regulation ; *Energy Metabolism ; Humans ; Mitochondria/metabolism ; Models, Biological ; Muscles/metabolism ; Oxygen Consumption ; Thermogenesis ; }, abstract = {Endothermy has evolved at least twice, in the precursors to modern mammals and birds. The most widely accepted explanation for the evolution of endothermy has been selection for enhanced aerobic capacity. We review this hypothesis in the light of advances in our understanding of ATP generation by mitochondria and muscle performance. Together with the development of isotope-based techniques for the measurement of metabolic rate in free-ranging vertebrates these have confirmed the importance of aerobic scope in the evolution of endothermy: absolute aerobic scope, ATP generation by mitochondria and muscle power output are all strongly temperature-dependent, indicating that there would have been significant improvement in whole-organism locomotor ability with a warmer body. New data on mitochondrial ATP generation and proton leak suggest that the thermal physiology of mitochondria may differ between organisms of contrasting ecology and thermal flexibility. Together with recent biophysical modelling, this strengthens the long-held view that endothermy originated in smaller, active eurythermal ectotherms living in a cool but variable thermal environment. We propose that rather than being a secondary consequence of the evolution of an enhanced aerobic scope, a warmer body was the means by which that enhanced aerobic scope was achieved. This modified hypothesis requires that the rise in metabolic rate and the insulation necessary to retain metabolic heat arose early in the lineages leading to birds and mammals. Large dinosaurs were warm, but were not endotherms, and the metabolic status of pterosaurs remains unresolved.}, }
@article {pmid20103843, year = {2009}, author = {Hsu, SC and Inoue, K}, title = {Two evolutionarily conserved essential beta-barrel proteins in the chloroplast outer envelope membrane.}, journal = {Bioscience trends}, volume = {3}, number = {5}, pages = {168-178}, pmid = {20103843}, issn = {1881-7823}, mesh = {Chloroplasts/*metabolism ; *Evolution, Molecular ; Gene Duplication ; Membrane Proteins/chemistry/genetics/*metabolism ; Plant Proteins/chemistry/genetics/*metabolism ; Protein Conformation ; }, abstract = {Chloroplasts are organelles specific to photosynthetic eukaryotes that support the lives of most organisms on earth. Chloroplasts were derived from an ancient cyanobacterium by endosymbiosis, and one characteristic shared between them and extant cyanobacteria is the presence of beta-barrel proteins in the outer membrane. These integral membrane proteins are also found in the outer membranes of proteobacteria and mitochondria. In particular, a group of homologous beta-barrel proteins called BamA homologs are present in all Gram-negative bacteria and the endosymbiotic organelles, i.e., chloroplasts and mitochondria. It was recently revealed that, in both proteobacteria and mitochondria, there is a single essential BamA homolog that mediates beta-barrel protein assembly. In a chloroplast, there are two distinct BamA homologs, Toc75 and OEP80, which diverged early in the evolution of chloroplasts from their common ancestor with extant cyanobacteria. Recent genetic studies demonstrated that each of these proteins is indispensable for viability of plants although neither has been shown to be involved in beta-barrel protein assembly. Toc75 catalyzes import of nuclear-encoded precursor proteins, a process that is not required for bacteria, whereas the molecular function of OEP80 remains elusive. Establishment of a protein import apparatus was required to facilitate the transfer of genes from the endosymbiont to the host cell nucleus. Hence, we propose that the gene duplication giving rise to the two essential BamA homologs was a prerequisite for the successful conversion of the cyanobacterial endosymbiont into the chloroplast. Consequently, continued study of these two chloroplast proteins should advance our understanding of endosymbiosis and evolutionarily conserved proteins in general.}, }
@article {pmid20087396, year = {2010}, author = {Raychoudhury, R and Grillenberger, BK and Gadau, J and Bijlsma, R and van de Zande, L and Werren, JH and Beukeboom, LW}, title = {Phylogeography of Nasonia vitripennis (Hymenoptera) indicates a mitochondrial-Wolbachia sweep in North America.}, journal = {Heredity}, volume = {104}, number = {3}, pages = {318-326}, doi = {10.1038/hdy.2009.160}, pmid = {20087396}, issn = {1365-2540}, mesh = {Animals ; Bacterial Proteins/genetics ; Evolution, Molecular ; Genetic Variation ; Insect Proteins/genetics ; Microsatellite Repeats ; Mitochondria/*genetics/microbiology ; Models, Genetic ; Molecular Sequence Data ; Mutation ; North America ; *Phylogeny ; Wasps/*classification/genetics/microbiology ; Wolbachia/*genetics/physiology ; }, abstract = {Here we report evidence of a mitochondrial-Wolbachia sweep in North American populations of the parasitoid wasp Nasonia vitripennis, a cosmopolitan species and emerging model organism for evolutionary and genetic studies. Analysis of the genetic variation of 89 N. vitripennis specimens from Europe and North America was performed using four types of genetic markers: a portion of the mitochondrial cytochrome oxidase I gene, nine polymorphic nuclear microsatellites, sequences from 11 single-copy nuclear markers and six Wolbachia genes. The results show that the European populations have a sevenfold higher mitochondrial sequence variation than North American populations, but similar levels of microsatellite and nuclear gene sequence variation. Variation in the North American mitochondria is extremely low (pi=0.31%), despite a highly elevated mutation rate (approximately 35-40 times higher than the nuclear genes) in the mitochondria of Nasonia. The data are indicative of a mitochondrial sweep in the North American population, possibly due to Wolbachia infections that are maternally co-inherited with the mitochondria. Owing to similar levels of nuclear variation, the data could not resolve whether N. vitripennis originated in the New or the Old World.}, }
@article {pmid20086128, year = {2010}, author = {Ivanina, AV and Eilers, S and Kurochkin, IO and Chung, JS and Techa, S and Piontkivska, H and Sokolov, EP and Sokolova, IM}, title = {Effects of cadmium exposure and intermittent anoxia on nitric oxide metabolism in eastern oysters, Crassostrea virginica.}, journal = {The Journal of experimental biology}, volume = {213}, number = {3}, pages = {433-444}, doi = {10.1242/jeb.038059}, pmid = {20086128}, issn = {1477-9145}, mesh = {Amino Acid Sequence ; Anaerobiosis/drug effects ; Animals ; Cadmium/*toxicity ; Cell Respiration/drug effects ; Crassostrea/*drug effects/enzymology/genetics/*metabolism ; *Environmental Exposure ; Gene Expression Regulation, Enzymologic/drug effects ; Gills/drug effects/enzymology ; Mitochondria/drug effects/metabolism ; Molecular Sequence Data ; Nitric Oxide/*metabolism ; Nitric Oxide Synthase/chemistry/genetics/metabolism ; Oxidation-Reduction/drug effects ; Phylogeny ; Polyamines/pharmacology ; RNA, Messenger/genetics/metabolism ; S-Nitroso-N-Acetylpenicillamine/pharmacology ; Sequence Alignment ; }, abstract = {Nitric oxide (NO) is an intracellular signaling molecule synthesized by a group of enzymes called nitric oxide synthases (NOS) and involved in regulation of many cellular functions including mitochondrial metabolism and bioenergetics. In invertebrates, the involvement of NO in bioenergetics and metabolic responses to environmental stress is poorly understood. We determined sensitivity of mitochondrial and cellular respiration to NO and the effects of cadmium (Cd) and intermittent anoxia on NO metabolism in eastern oysters, Crassostrea virginica. NOS activity was strongly suppressed by exposure to 50 microg l(-1) Cd for 30 days (4.76 vs 1.19 pmol NO min(-1) mg(-1) protein in control and Cd-exposed oysters, respectively) and further decreased during anoxic exposure in Cd-exposed oysters but not in their control counterparts. Nitrate/nitrite content (indicative of NO levels) decreased during anoxic exposure to less than 10% of the normoxic values and recovered within 1 h of re-oxygenation in control oysters. In Cd-exposed oysters, the recovery of the normoxic NO levels lagged behind, reflecting their lower NOS activity. Oyster mitochondrial respiration was inhibited by exogenous NO, with sensitivity on a par with that of mammalian mitochondria, and ADP-stimulated mitochondrial respiration was significantly more sensitive to NO than resting respiration. In isolated gill cells, manipulations of endogenous NOS activity either with a specific NOS inhibitor (aminoguanidine) or a NOS substrate (L-arginine) had no effect on respiration, likely due to the fact that mitochondria in the resting state are relatively NO insensitive. Likewise, Cd-induced stimulation of cellular respiration did not correlate with decreased NOS activity in isolated gill cells. High sensitivity of phosphorylating (ADP-stimulated) oyster mitochondria to NO suggests that regulation of bioenergetics is an evolutionarily conserved function of NO and that NO-dependent regulation of metabolism may be most prominent under the conditions of high metabolic flux when the ADP-to-ATP ratio is high.}, }
@article {pmid20075606, year = {2010}, author = {Watanabe, K}, title = {Unique features of animal mitochondrial translation systems. The non-universal genetic code, unusual features of the translational apparatus and their relevance to human mitochondrial diseases.}, journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences}, volume = {86}, number = {1}, pages = {11-39}, pmid = {20075606}, issn = {1349-2896}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Evolution, Molecular ; Genetic Code/*genetics ; Humans ; Mitochondria/*genetics/*metabolism ; Mitochondrial Diseases/*genetics ; Molecular Sequence Data ; *Protein Biosynthesis ; RNA, Transfer/genetics ; }, abstract = {In animal mitochondria, several codons are non-universal and their meanings differ depending on the species. In addition, the tRNA structures that decipher codons are sometimes unusually truncated. These features seem to be related to the shortening of mitochondrial (mt) genomes, which occurred during the evolution of mitochondria. These organelles probably originated from the endosymbiosis of an aerobic eubacterium into an ancestral eukaryote. It is plausible that these events brought about the various characteristic features of animal mt translation systems, such as genetic code variations, unusually truncated tRNA and rRNA structures, unilateral tRNA recognition mechanisms by aminoacyl-tRNA synthetases, elongation factors and ribosomes, and compensation for RNA deficits by enlarged proteins. In this article, we discuss molecular mechanisms for these phenomena. Finally, we describe human mt diseases that are caused by modification defects in mt tRNAs.}, }
@article {pmid20068593, year = {2010}, author = {Bisceglia, L and Zoccolella, S and Torraco, A and Piemontese, MR and Dell'Aglio, R and Amati, A and De Bonis, P and Artuso, L and Copetti, M and Santorelli, FM and Serlenga, L and Zelante, L and Bertini, E and Petruzzella, V}, title = {A new locus on 3p23-p25 for an autosomal-dominant limb-girdle muscular dystrophy, LGMD1H.}, journal = {European journal of human genetics : EJHG}, volume = {18}, number = {6}, pages = {636-641}, pmid = {20068593}, issn = {1476-5438}, mesh = {Adolescent ; Adult ; Aged ; Child ; Chromosome Disorders/genetics ; Chromosome Mapping ; *Chromosomes, Human, Pair 3/genetics ; Family ; Female ; Genes, Dominant/genetics ; Haplotypes ; Humans ; Male ; Middle Aged ; Muscular Dystrophies, Limb-Girdle/*genetics ; Pedigree ; Young Adult ; }, abstract = {Limb-girdle muscular dystrophies (LGMDs) are a genetically heterogeneous group of neuromuscular disorders with a selective or predominant involvement of shoulder and pelvic girdles. We clinically examined 19 members in a four-generation Italian family with autosomal-dominant LGMD. A total of 11 subjects were affected. Clinical findings showed variable expressivity in terms of age at onset and disease severity. Five subjects presented with a slowly progressive proximal muscle weakness, in both upper and lower limbs, with onset during the fourth-fifth decade of life, which fulfilled the consensus diagnostic criteria for LGMD. Earlier onset of the disease was observed in a group of patients presenting with muscle weakness and/or calf hypertrophy, and/or occasionally high CK and lactate serum levels. Two muscle biopsies showed morphological findings compatible with MD associated with subsarcolemmal accumulation of mitochondria and the presence of multiple mitochondrial DNA deletions. A genome-wide scan performed using microsatellite markers mapped the disease on chromosome 3p23-p25.1 locus in a 25-cM region between markers D3S1263 and D3S3685. The highest two-point LOD score was 3.26 (theta=0) at marker D3S1286 and D3S3613, whereas non-parametric analysis reached a P-value=0.0004. Four candidate genes within the refined region were analysed but did not reveal any mutations. Our findings further expand the clinical and genetic heterogeneity of LGMDs.}, }
@article {pmid20068028, year = {2010}, author = {Omura, T}, title = {Structural diversity of cytochrome P450 enzyme system.}, journal = {Journal of biochemistry}, volume = {147}, number = {3}, pages = {297-306}, doi = {10.1093/jb/mvq001}, pmid = {20068028}, issn = {1756-2651}, mesh = {Animals ; Cytochrome P-450 Enzyme System/*chemistry/physiology ; Cytoplasm/chemistry/enzymology ; Evolution, Molecular ; Humans ; Microsomes/chemistry/enzymology ; Mitochondria/chemistry/enzymology ; NADPH-Ferrihemoprotein Reductase/chemistry/physiology ; Protein Conformation ; }, abstract = {Cytochrome P450 enzyme system consists of P450 and its NAD(P)H-linked reductase or reducing system, and catalyses monooxygenation reactions. The most prevalent type in eukaryotic organisms is 'microsomes type', which consists of membrane-bound P450 and NADPH-P450 reductase. The second type is 'mitochondria type', in which P450 is bound to the inner membrane while the reducing system consisting of an NADPH-linked flavoprotein and a ferredoxin-type iron-sulphur protein is soluble in the matrix space. The third type is 'bacteria type', in which both P450 and the reducing system are soluble in the cytoplasm. In addition to these three types, several forms of P450-reductase fusion proteins have been found in prokaryotic organisms. On the other hand, some P450s catalyse the re-arrangement of the oxygen atoms in the substrate molecules that does not require the supply of reducing equivalents for the reaction. A peculiar P450, P450nor, receives electrons directly from NADH for the reduction of nitric oxide.}, }
@article {pmid20064693, year = {2010}, author = {Dayaratne, DA}, title = {Impact of ecology on development of NIDDM.}, journal = {Medical hypotheses}, volume = {74}, number = {6}, pages = {986-988}, doi = {10.1016/j.mehy.2009.12.017}, pmid = {20064693}, issn = {1532-2777}, mesh = {Adaptation, Physiological ; Adipose Tissue, Brown/physiopathology ; Biological Evolution ; Climate ; Diabetes Mellitus, Type 2/epidemiology/*etiology/physiopathology ; Ecosystem ; Emigration and Immigration ; Epistasis, Genetic ; Ethnicity ; Female ; Humans ; Male ; Mitochondria/physiology ; Models, Biological ; Urbanization ; }, abstract = {Diabetes has become a global epidemic. The increased incidence of NIDDM is seen all over the world but there is geographical variation. Certain population groups show increased susceptibility to develop diabetes. The prevalence is lowest in Caucasian whites and highest in Pima Indians and Naurans. Iceland has a particularly low incidence whereas Bahrain is among the countries with highest prevalence. The highest prevalence of diabetes in 2000 was found in Papua New Guiana (15.5%), Mauritius (15%), Bahrain (14.8%), Mexico (14.2%), Trinidad and Tobago (14.1%). Most of the hypotheses developed to explain this trend concerned mainly on dietary and nutritional factors. Man had to struggle against harsh climatic conditions for survival. It has been observed that people who have been adapted to cold environment for generations demonstrate some resistance to develop diabetes. It is hypothesized that presence of thick subcutaneous fat, reactivation of brown adipose tissue in cold environment and effective mitochondrial enzyme systems for heat generation act as adaptive mechanisms for survival in cold environment and retard the development of visceral obesity. Mitochondrial defects have been found in patients with NIDDM and NAFLD. Changes of nuclear genes which encode mitochondrial enzyme systems involved in thermo genesis could be the cause for development of visceral obesity and NIDDM.}, }
@article {pmid20064602, year = {2010}, author = {van Diepeningen, AD and Slakhorst, SM and Koopmanschap, AB and Ikink, GJ and Debets, AJ and Hoekstra, RF}, title = {Calorie restriction in the filamentous fungus Podospora anserina.}, journal = {Experimental gerontology}, volume = {45}, number = {7-8}, pages = {516-524}, doi = {10.1016/j.exger.2010.01.002}, pmid = {20064602}, issn = {1873-6815}, mesh = {Biological Evolution ; DNA, Fungal/genetics/metabolism ; DNA, Mitochondrial/genetics/metabolism ; Genetic Variation ; Glucose/metabolism ; Lipofuscin/metabolism ; Mitochondria/metabolism ; Models, Biological ; Phenotype ; Plasmids/genetics ; Podospora/genetics/growth &amp; development/*metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {Calorie restriction (CR) is a regimen of reduced food intake that, although the underlying mechanism is unknown, in many organisms leads to life span extension. Podospora anserina is one of the few known ageing filamentous fungi and the ageing process and concomitant degeneration of mitochondria have been well-studied. CR in P. anserina increases not only life span but also forestalls the ageing-related decline in fertility. Here we review what is known about CR in P. anserina and about possibly involved mechanisms like enhanced mitochondrial stability, reduced production of reactive oxygen species and changes in the OXPHOS machinery. Additionally, we present new microscopic data on mitochondrial dynamics under rich nutritional and CR conditions at different points in life. Lines that have grown under severe CR for more than 50x the normal life span, show no accumulation of age-related damage, though fecundity is reduced in some of these lines. Finally, we discuss the possible role of CR in P. anserina in nature and the effect of CR at different points in life.}, }
@article {pmid20061302, year = {2010}, author = {Tominaga, M and Harada, A and Kinoshita, T and Shimazaki, K}, title = {Biochemical characterization of calcineurin B-like-interacting protein kinase in Vicia guard cells.}, journal = {Plant &amp; cell physiology}, volume = {51}, number = {3}, pages = {408-421}, doi = {10.1093/pcp/pcq006}, pmid = {20061302}, issn = {1471-9053}, mesh = {Amino Acid Sequence ; Calcineurin/metabolism ; Calcium/*metabolism ; Calcium-Binding Proteins/genetics/*metabolism ; DNA, Complementary/genetics ; DNA, Plant/genetics ; Gene Expression Regulation, Plant ; Mitochondrial Membranes/metabolism ; Molecular Sequence Data ; Phosphorylation ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Protein Binding ; Protein Serine-Threonine Kinases/genetics/*metabolism ; Sequence Alignment ; Vicia faba/*genetics/metabolism ; }, abstract = {Protein phosphorylation is crucial in the signaling of guard cells in response to various factors, including light, ABA and CO2, and calcium plays a central role in these signaling processes. Despite extensive studies on the functional role of Ca(2+)-regulated protein kinases in plants, relatively little is known about the biochemical properties of the kinases in guard cells. To investigate this, we isolated the VfCIPK1 [Vicia faba calcineurin B-like calcium-binding protein (CBL)-interacting protein kinase 1] cDNA from guard cells of Vicia faba L., which encodes a Ca(2+)-regulated protein kinase that belongs to the SnRK3 subgroup, and characterized VfCIPK1 at the biochemical level. VfCIPK1 genes were expressed in guard cells and roots, but not in mesophyll cells. The VfCIPK1 protein was localized on the outer membrane of mitochondria in guard cells and interacted with VfCBL1. The immunoprecipitation experiments indicated that VfCIPK1 interacted with VfCBL1 in vivo. The recombinant VfCIPK1 phosphorylated myelin basic protein as a substrate and the activity was increased by VfCBL1, and this activity showed a maximum in the absence of Ca2+ and decreased by an elevation of the Ca2+ concentration. A pull-down assay and the measurement of surface plasmon resonance indicated that the interaction between VfCIPK1 and VfCBL1 was decreased by Ca2+. These results suggest that VfCIPK1 may be negatively regulated by cytosolic Ca2+ through VfCBL1 and may be related to mitochondrial functions in guard cells. This is the first report that shows the inhibitory effect of Ca2+ on CIPK activity in the presence of CBL.}, }
@article {pmid20060994, year = {2010}, author = {Zizzari, ZV and Machida, R and Tsutsumi, K and Reynoso-Velasco, D and Lupetti, P and Dallai, R}, title = {Ultrastructural studies on euspermatozoa and paraspermatozoa in Mantispidae (Insecta, Neuroptera).}, journal = {Tissue &amp; cell}, volume = {42}, number = {2}, pages = {81-87}, doi = {10.1016/j.tice.2009.12.001}, pmid = {20060994}, issn = {1532-3072}, mesh = {Animals ; Axoneme/physiology/ultrastructure ; Biological Evolution ; Cell Differentiation/physiology ; Cell Movement/physiology ; Cell Shape/physiology ; Cell Size ; Diptera/physiology/*ultrastructure ; Female ; Fertilization/physiology ; Male ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Microtubules/physiology/ultrastructure ; Mitochondria/physiology/ultrastructure ; Phylogeny ; Species Specificity ; Sperm Tail/physiology/ultrastructure ; Spermatogenesis/*physiology ; Spermatozoa/physiology/*ultrastructure ; Testis/physiology/*ultrastructure ; }, abstract = {Previous studies have demonstrated the presence of sperm dimorphism in the Mantispidae Perlamantispa perla. We extended the study on several other mantidflies. In all the examined species the occurrence of euspermatozoa (typical) and paraspermatozoa (atypical) was established. The euspermatozoa are characterized by the presence of a cylindrical nucleus surrounded by an envelope that fans out laterally into two thin wings of different length. The acrosome seems to be missing. The nucleus is surrounded by extracellular material. The flagellum is provided with a 9+9+2 axonemal pattern; the accessory tubules contain 16 protofilaments and the intertubular material has the distribution typical of the taxon. Two elongated accessory bodies flank partially the axoneme and connect this structure with the mitochondrial derivatives. The flagellar axoneme of paraspermatozoa consists of an axoneme and two giant mitochondrial derivatives filled with large globular units. The axoneme exhibits a 9+9+2 pattern, in which the central 9+2 units have a normal structure, in that the microtubular doublets are provided with both dynein arms and radial links. On the contrary, the nine accessory microtubules have a large diameter and their tubular wall consists of 40 protofilaments. This comparative study provided evidences about the uniformity of sperm ultrastructure in Mantispidae. The function of non-fertilizing giant sperm in mantidflies is discussed.}, }
@article {pmid20056105, year = {2010}, author = {Lipinski, KA and Kaniak-Golik, A and Golik, P}, title = {Maintenance and expression of the S. cerevisiae mitochondrial genome--from genetics to evolution and systems biology.}, journal = {Biochimica et biophysica acta}, volume = {1797}, number = {6-7}, pages = {1086-1098}, doi = {10.1016/j.bbabio.2009.12.019}, pmid = {20056105}, issn = {0006-3002}, mesh = {DNA Repair ; DNA Replication ; DNA, Fungal/genetics/metabolism ; DNA, Mitochondrial/genetics/metabolism ; Evolution, Molecular ; Gene Expression Regulation, Fungal ; *Genome, Fungal ; *Genome, Mitochondrial ; Mitochondria/genetics/metabolism ; Models, Genetic ; RNA/genetics/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Fungal/genetics/metabolism ; RNA, Mitochondrial ; Recombination, Genetic ; Saccharomyces cerevisiae/*genetics/metabolism ; Systems Biology ; }, abstract = {As a legacy of their endosymbiotic eubacterial origin, mitochondria possess a residual genome, encoding only a few proteins and dependent on a variety of factors encoded by the nuclear genome for its maintenance and expression. As a facultative anaerobe with well understood genetics and molecular biology, Saccharomyces cerevisiae is the model system of choice for studying nucleo-mitochondrial genetic interactions. Maintenance of the mitochondrial genome is controlled by a set of nuclear-coded factors forming intricately interconnected circuits responsible for replication, recombination, repair and transmission to buds. Expression of the yeast mitochondrial genome is regulated mostly at the post-transcriptional level, and involves many general and gene-specific factors regulating splicing, RNA processing and stability and translation. A very interesting aspect of the yeast mitochondrial system is the relationship between genome maintenance and gene expression. Deletions of genes involved in many different aspects of mitochondrial gene expression, notably translation, result in an irreversible loss of functional mtDNA. The mitochondrial genetic system viewed from the systems biology perspective is therefore very fragile and lacks robustness compared to the remaining systems of the cell. This lack of robustness could be a legacy of the reductive evolution of the mitochondrial genome, but explanations involving selective advantages of increased evolvability have also been postulated.}, }
@article {pmid20053634, year = {2010}, author = {Matthews, GD and Gur, N and Koopman, WJ and Pines, O and Vardimon, L}, title = {Weak mitochondrial targeting sequence determines tissue-specific subcellular localization of glutamine synthetase in liver and brain cells.}, journal = {Journal of cell science}, volume = {123}, number = {Pt 3}, pages = {351-359}, doi = {10.1242/jcs.060749}, pmid = {20053634}, issn = {1477-9137}, mesh = {Alternative Splicing ; Amino Acid Sequence ; Animals ; Brain/*metabolism/ultrastructure ; Cells, Cultured ; Chickens ; Glutamate-Ammonia Ligase/*chemistry/genetics/*metabolism ; Immunoprecipitation ; Liver/*metabolism/ultrastructure ; Mass Spectrometry ; Membrane Potential, Mitochondrial/physiology ; Microscopy, Electron, Transmission ; Mitochondria/*metabolism/ultrastructure ; Molecular Sequence Data ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; }, abstract = {Evolution of the uricotelic system for ammonia detoxification required a mechanism for tissue-specific subcellular localization of glutamine synthetase (GS). In uricotelic vertebrates, GS is mitochondrial in liver cells and cytoplasmic in brain. Because these species contain a single copy of the GS gene, it is not clear how tissue-specific subcellular localization is achieved. Here we show that in chicken, which utilizes the uricotelic system, the GS transcripts of liver and brain cells are identical and, consistently, there is no difference in the amino acid sequence of the protein. The N-terminus of GS, which constitutes a 'weak' mitochondrial targeting signal (MTS), is sufficient to direct a chimeric protein to the mitochondria in hepatocytes and to the cytoplasm in astrocytes. Considering that a weak MTS is dependent on a highly negative mitochondrial membrane potential (DeltaPsi) for import, we examined the magnitude of DeltaPsi in hepatocytes and astrocytes. Our results unexpectedly revealed that DeltaPsi in hepatocytes is considerably more negative than that of astrocytes and that converting the targeting signal into 'strong' MTS abolished the capability to confer tissue-specific subcellular localization. We suggest that evolutional selection of weak MTS provided a tool for differential targeting of an identical protein by taking advantage of tissue-specific differences in DeltaPsi.}, }
@article {pmid20050804, year = {2010}, author = {Robert, KA and Bronikowski, AM}, title = {Evolution of senescence in nature: physiological evolution in populations of garter snake with divergent life histories.}, journal = {The American naturalist}, volume = {175}, number = {2}, pages = {147-159}, doi = {10.1086/649595}, pmid = {20050804}, issn = {1537-5323}, mesh = {Aging/*genetics/*physiology ; Animals ; Animals, Newborn ; *Biological Evolution ; Corticosterone ; DNA Damage ; DNA Repair ; Energy Metabolism ; Free Radicals/metabolism ; Mitochondria/physiology ; Oxidative Stress ; Snakes/classification/*genetics/*physiology ; }, abstract = {Evolutionary theories of aging are linked to life-history theory in that age-specific schedules of reproduction and survival determine the trajectory of age-specific mutation/selection balances across the life span and thus the rate of senescence. This is predicted to manifest at the organismal level in the evolution of energy allocation strategies of investing in somatic maintenance and robust stress responses in less hazardous environments in exchange for energy spent on growth and reproduction. Here we report experiments from long-studied populations of western terrestrial garter snakes (Thamnophis elegans) that reside in low and high extrinsic mortality environments, with evolved long and short life spans, respectively. Laboratory common-environment colonies of these two ecotypes were tested for a suite of physiological traits after control and stressed gestations. In offspring derived from control and corticosterone-treated dams, we measured resting metabolism; mitochondrial oxygen consumption, ATP and free radical production rates; and erythrocyte DNA damage and repair ability. We evaluated whether these aging biomarkers mirrored the evolution of life span and whether they were sensitive to stress. Neonates from the long-lived ecotype (1) were smaller, (2) consumed equal amounts of oxygen when corrected for body mass, (3) had DNA that damaged more readily but repaired more efficiently, and (4) had more efficient mitochondria and more efficient cellular antioxidant defenses than short-lived snakes. Many ecotype differences were enhanced in offspring derived from stress-treated dams, which supports the conclusion that nongenetic maternal effects may further impact the cellular stress defenses of offspring. Our findings reveal that physiological evolution underpins reptilian life histories and sheds light on the connectedness between stress response and aging pathways in wild-dwelling organisms.}, }
@article {pmid20042613, year = {2010}, author = {Horibata, Y and Sugimoto, H}, title = {StarD7 mediates the intracellular trafficking of phosphatidylcholine to mitochondria.}, journal = {The Journal of biological chemistry}, volume = {285}, number = {10}, pages = {7358-7365}, pmid = {20042613}, issn = {1083-351X}, mesh = {Amino Acid Sequence ; Animals ; Biological Transport/physiology ; Carrier Proteins/classification/genetics/*metabolism ; Cell Line ; Cytoplasmic Vesicles/metabolism ; Liver/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phosphatidylcholines/*metabolism ; Phylogeny ; Protein Isoforms/genetics/*metabolism ; Rats ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Alignment ; Subcellular Fractions/metabolism ; }, abstract = {Steroidogenic acute regulatory protein-related lipid transfer (START) domains, found in 15 mammalian proteins termed StarD1-StarD15, are lipid-binding domains implicated in the intracellular lipid transport systems. In the present study, we analyzed the lipid ligand and function of StarD7. We found two variable forms of mammalian StarD7, termed StarD7-I and StarD7-II. Unlike StarD7-II, StarD7-I contained a mitochondrial-targeting sequence in its N terminus. Overexpressed StarD7-I tagged with V5/His in HEPA-1 cells was mainly observed in the mitochondria of cells prepared at low cellular density, but it was distributed in the cytoplasm of high density cells. StarD7-II was constantly distributed in the cytoplasm at any cellular density. Endogenous StarD7 in HEPA-1 cells and rat liver was also distributed in both the cytoplasm and the mitochondria. A protease K protection assay indicated that the mitochondrial StarD7 was associated with the outer mitochondrial membrane. The purified recombinant StarD7 specifically catalyzed the transfer of PC between lipid vesicles in vitro. Furthermore, the intracellular transport of fluorescent PC that was exogenously incorporated into the mitochondria was increased in cells that overexpressed StarD7-I. These results suggest that StarD7 facilitates the delivery of PC to mitochondria in non-vesicular system.}, }
@article {pmid20042463, year = {2010}, author = {Dallabona, C and Marsano, RM and Arzuffi, P and Ghezzi, D and Mancini, P and Zeviani, M and Ferrero, I and Donnini, C}, title = {Sym1, the yeast ortholog of the MPV17 human disease protein, is a stress-induced bioenergetic and morphogenetic mitochondrial modulator.}, journal = {Human molecular genetics}, volume = {19}, number = {6}, pages = {1098-1107}, doi = {10.1093/hmg/ddp581}, pmid = {20042463}, issn = {1460-2083}, support = {GGP07019/TI_/Telethon/Italy ; }, mesh = {Alleles ; Blotting, Northern ; Blotting, Western ; Citric Acid Cycle/genetics ; *Energy Metabolism ; Gene Dosage/genetics ; Gene Expression Regulation, Fungal ; Genes, Suppressor ; Genetic Complementation Test ; Humans ; Membrane Proteins/*chemistry/genetics/*metabolism ; Mitochondria/enzymology/*metabolism/ultrastructure ; Mitochondrial Proteins/*chemistry/genetics/*metabolism ; *Morphogenesis ; Mutation/genetics ; Oxidation-Reduction ; Phenotype ; Promoter Regions, Genetic/genetics ; Saccharomyces cerevisiae/cytology/growth &amp; development/ultrastructure ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; *Sequence Homology, Amino Acid ; *Stress, Physiological ; Transcription, Genetic ; }, abstract = {A peculiar form of hepatocerebral mtDNA depletion syndrome is caused by mutations in the MPV17 gene, which encodes a small hydrophobic protein of unknown function located in the mitochondrial inner membrane. In order to define the molecular basis of MPV17 variants associated with the human disorder, we have previously taken advantage of S. cerevisiae as a model system thanks to the presence of an MPV17 ortholog gene, SYM1. We demonstrate here that the SYM1 gene product is essential to maintain OXPHOS, glycogen storage, mitochondrial morphology and mtDNA stability in stressing conditions such as high temperature and ethanol-dependent growth. To gain insight into the molecular basis of the Sym1-less phenotype, we identified and characterized multicopy suppressor genes and metabolic suppressor compounds. Our results suggest that (i) metabolic impairment and mtDNA instability occur independently from each other as a consequence of SYM1 ablation; (ii) ablation of Sym1 causes depletion of glycogen storage, possibly due to defective anaplerotic flux of tricarboxylic acid (TCA) cycle intermediates to the cytosol; (iii) flattening of mitochondrial cristae in Sym1-defective organelles suggests a role for Sym1 in the structural preservation of the inner mitochondrial membrane, which could in turn control mtDNA maintenance and stability.}, }
@article {pmid20042393, year = {2009}, author = {Cao, GL and Xue, RY and Zhu, YX and Wei, YH and Gong, CL}, title = {[Analysis of the aminoacyl-tRNA synthetase genes of silkworm (Bombyx mori)].}, journal = {Yi chuan = Hereditas}, volume = {31}, number = {12}, pages = {1248-1258}, doi = {10.3724/sp.j.1005.2009.01248}, pmid = {20042393}, issn = {0253-9772}, mesh = {Amino Acyl-tRNA Synthetases/chemistry/*genetics/metabolism ; Animals ; Bombyx/chemistry/classification/*enzymology/genetics ; Cytoplasm/chemistry/enzymology/genetics ; Insect Proteins/chemistry/*genetics/metabolism ; Mitochondria/chemistry/enzymology/genetics ; Molecular Conformation ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; }, abstract = {For further research on number, type, composition and origin of Bombyx mori aminoacyl-tRNA synthetase (BmaaRS) genes, in silico cloning was performed with Bombyx mori genomic and EST databases. There might be two different sets of aaRS nuclear gene in Bombxy nori genome, which encode mitochondrial BmaaRS and cytoplasmic BmaaRS, respectively. Among BmaaRS genes, there were 2 genes encoding mitochondrial BmSerRS, but no genes encoding cytoplasmic BmHisRS and mitochondrial BmGlnRS, BmLysRS, BmGlyRS, and BmThrRS. The functions of these absent genes could be directly replaced by other proteins with similar functions, or might undergo their distinct BmaaRS functions based on the alternative splice of one certain BmaaRS mRNA. Evidence of EST indicated that BmaaRS performed different alternative splicing patterns. The homology comparison and advanced structural analysis of BmaaRS demonstrated the existence of extended domains of BmaaRS. This is because some different BmaaRSs contained similar domain. Moreover, BmaaRSs with similar functions possessed the similar tertiary structure. Phylogenetic analysis revealed that BmaaRS encoded by two various sources of BmaaRS genes. Mitochondrial and cytoplasmic BmaaRS had different origin.}, }
@article {pmid20041252, year = {2010}, author = {Lenz, H and Rüdinger, M and Volkmar, U and Fischer, S and Herres, S and Grewe, F and Knoop, V}, title = {Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature.}, journal = {Current genetics}, volume = {56}, number = {2}, pages = {189-201}, pmid = {20041252}, issn = {1432-0983}, mesh = {*Base Sequence ; Chloroplasts/genetics/metabolism ; *Computers ; Conserved Sequence/genetics ; DNA, Complementary/genetics/metabolism ; Gene Expression Profiling ; Genes, Plant/*genetics ; Mitochondria/genetics/metabolism ; RNA/genetics/metabolism ; *RNA Editing ; RNA, Messenger/genetics/metabolism ; RNA, Plant/*genetics/metabolism ; }, abstract = {Transcripts in mitochondria and chloroplasts of land plants are modified through RNA editing, the exchanges of pyrimidines-a post-transcriptional process that may affect more than 1,000 sites in the mitochondrial transcriptomes of some plant species. RNA editing mainly acts as a correcting mechanism to re-create evolutionary conserved coding sequences on mRNA level and can be reasonably well predicted in new plant organelle gene sequence data. Identification and annotation of RNA editing sites is cumbersome and error-prone for larger data sets or organelle sequences subject to highly frequent RNA editing. We here present PREPACT, WWW-accessible at http://www.prepact.de , which allows prediction, analysis, annotation and graphical display of RNA editing sites for both directions of pyrimidine exchanges, using the recently proposed RNA editing nomenclature. PREPACT offers prediction of RNA editing, analysis of partial editing in cDNA pools and a BLASTX mode for simultaneous prediction of genes and RNA editing sites in novel sequences. Output options include (i) lists and annotations of RNA editing sites, (ii) sequence alignments with user-controlled color highlighting of editings, (iii) graphical displays of RNA editing in sequences and alignments. Finally, binary matrices of editing positions can be produced that may be used for downstream (e.g. phylogenetic) analyses.}, }
@article {pmid20038714, year = {2010}, author = {Su, LJ and Auluck, PK and Outeiro, TF and Yeger-Lotem, E and Kritzer, JA and Tardiff, DF and Strathearn, KE and Liu, F and Cao, S and Hamamichi, S and Hill, KJ and Caldwell, KA and Bell, GW and Fraenkel, E and Cooper, AA and Caldwell, GA and McCaffery, JM and Rochet, JC and Lindquist, S}, title = {Compounds from an unbiased chemical screen reverse both ER-to-Golgi trafficking defects and mitochondrial dysfunction in Parkinson's disease models.}, journal = {Disease models &amp; mechanisms}, volume = {3}, number = {3-4}, pages = {194-208}, pmid = {20038714}, issn = {1754-8411}, support = {R01 GM089903/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; NS049221/NS/NINDS NIH HHS/United States ; P50 NS038372/NS/NINDS NIH HHS/United States ; R01 NS049221/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Antiparkinson Agents/pharmacology/*therapeutic use ; Caenorhabditis elegans/drug effects/metabolism ; Disease Models, Animal ; Dopamine/metabolism ; Drug Evaluation, Preclinical ; Endoplasmic Reticulum/drug effects/*metabolism/ultrastructure ; Gene Expression Profiling ; Golgi Apparatus/drug effects/*metabolism/ultrastructure ; Mitochondria/drug effects/*pathology/ultrastructure ; Neurons/drug effects/pathology ; Parkinson Disease/*drug therapy/*metabolism ; Protein Transport/drug effects ; Rats ; Reactive Oxygen Species/metabolism ; Rotenone/toxicity ; Saccharomyces cerevisiae/drug effects ; Stress, Physiological/drug effects ; Structure-Activity Relationship ; alpha-Synuclein/toxicity ; }, abstract = {alpha-Synuclein (alpha-syn) is a small lipid-binding protein involved in vesicle trafficking whose function is poorly characterized. It is of great interest to human biology and medicine because alpha-syn dysfunction is associated with several neurodegenerative disorders, including Parkinson's disease (PD). We previously created a yeast model of alpha-syn pathobiology, which established vesicle trafficking as a process that is particularly sensitive to alpha-syn expression. We also uncovered a core group of proteins with diverse activities related to alpha-syn toxicity that is conserved from yeast to mammalian neurons. Here, we report that a yeast strain expressing a somewhat higher level of alpha-syn also exhibits strong defects in mitochondrial function. Unlike our previous strain, genetic suppression of endoplasmic reticulum (ER)-to-Golgi trafficking alone does not suppress alpha-syn toxicity in this strain. In an effort to identify individual compounds that could simultaneously rescue these apparently disparate pathological effects of alpha-syn, we screened a library of 115,000 compounds. We identified a class of small molecules that reduced alpha-syn toxicity at micromolar concentrations in this higher toxicity strain. These compounds reduced the formation of alpha-syn foci, re-established ER-to-Golgi trafficking and ameliorated alpha-syn-mediated damage to mitochondria. They also corrected the toxicity of alpha-syn in nematode neurons and in primary rat neuronal midbrain cultures. Remarkably, the compounds also protected neurons against rotenone-induced toxicity, which has been used to model the mitochondrial defects associated with PD in humans. That single compounds are capable of rescuing the diverse toxicities of alpha-syn in yeast and neurons suggests that they are acting on deeply rooted biological processes that connect these toxicities and have been conserved for a billion years of eukaryotic evolution. Thus, it seems possible to develop novel therapeutic strategies to simultaneously target the multiple pathological features of PD.}, }
@article {pmid20035036, year = {2010}, author = {Sienkiewicz-Porzucek, A and Sulpice, R and Osorio, S and Krahnert, I and Leisse, A and Urbanczyk-Wochniak, E and Hodges, M and Fernie, AR and Nunes-Nesi, A}, title = {Mild reductions in mitochondrial NAD-dependent isocitrate dehydrogenase activity result in altered nitrate assimilation and pigmentation but do not impact growth.}, journal = {Molecular plant}, volume = {3}, number = {1}, pages = {156-173}, pmid = {20035036}, issn = {1674-2052}, mesh = {Citric Acid Cycle/genetics/physiology ; Isocitrate Dehydrogenase/classification/genetics/*metabolism ; Solanum lycopersicum/*enzymology/genetics/growth &amp; development/*metabolism ; Mitochondria/*enzymology ; Nitrates/*metabolism ; Oligonucleotide Array Sequence Analysis ; Photosynthesis/genetics/physiology ; Phylogeny ; Pigmentation/genetics/physiology ; Plant Proteins/classification/genetics/*metabolism ; Plants, Genetically Modified/enzymology/genetics/growth &amp; development/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Transgenic tomato (Solanum lycopersicum) plants were generated expressing a fragment of the mitochondrial NAD-dependent isocitrate dehydrogenase gene (SlIDH1) in the antisense orientation. The transgenic plants displayed a mild reduction in the activity of the target enzyme in the leaves but essentially no visible alteration in growth from the wild-type. Fruit size and yield were, however, reduced. These plants were characterized by relatively few changes in photosynthetic parameters, but they displayed a minor decrease in maximum photosynthetic efficiency (Fv/Fm). Furthermore, a clear reduction in flux through the tricarboxylic acid (TCA) cycle was observed in the transformants. Additionally, biochemical analyses revealed that the transgenic lines exhibited considerably altered metabolism, being characterized by slight decreases in the levels of amino acids, intermediates of the TCA cycle, photosynthetic pigments, starch, and NAD(P)H levels, but increased levels of nitrate and protein. Results from these studies show that even small changes in mitochondrial NAD-dependent isocitrate dehydrogenase activity lead to noticeable alterations in nitrate assimilation and suggest the presence of different strategies by which metabolism is reprogrammed to compensate for this deficiency.}, }
@article {pmid20027611, year = {2010}, author = {Malhi, RS and Cybulski, JS and Tito, RY and Johnson, J and Harry, H and Dan, C}, title = {Brief communication: mitochondrial haplotype C4c confirmed as a founding genome in the Americas.}, journal = {American journal of physical anthropology}, volume = {141}, number = {3}, pages = {494-497}, doi = {10.1002/ajpa.21238}, pmid = {20027611}, issn = {1096-8644}, mesh = {DNA/genetics/isolation &amp; purification ; DNA, Mitochondrial/*genetics ; *Founder Effect ; Gene Amplification ; *Genome, Human ; Haplotypes/genetics ; Humans ; Indians, North American/*genetics ; Mitochondria/*genetics ; Mutation ; North America ; Phylogeny ; Saliva/chemistry ; }, abstract = {Mitochondrial DNA analysis of 31 unrelated Shuswap speakers from a previously poorly sampled region of North America revealed two individuals with haplogroups rarely found in the Americas, C4c and C1d. Comparison of the complete genomes of the two individuals with others found in the literature confirms that C4c is a founding haplotype and gives insight into the evolution of the C1d haplotype. This study demonstrates the importance of collecting and analyzing data from Native North Americans when addressing hypotheses about the peopling of the Americas.}, }
@article {pmid20026010, year = {2010}, author = {Jarmuszkiewicz, W and Woyda-Ploszczyca, A and Antos-Krzeminska, N and Sluse, FE}, title = {Mitochondrial uncoupling proteins in unicellular eukaryotes.}, journal = {Biochimica et biophysica acta}, volume = {1797}, number = {6-7}, pages = {792-799}, doi = {10.1016/j.bbabio.2009.12.005}, pmid = {20026010}, issn = {0006-3002}, mesh = {Acanthamoeba castellanii/genetics/metabolism ; Adipose Tissue, Brown/metabolism ; Animals ; Eukaryota/genetics/*metabolism ; Evolution, Molecular ; Fatty Acids, Nonesterified/metabolism ; Ion Channels/antagonists &amp; inhibitors/genetics/*metabolism ; Lipid Peroxidation ; Mitochondria/metabolism ; Mitochondrial Proteins/antagonists &amp; inhibitors/genetics/*metabolism ; Models, Biological ; Oxidoreductases/metabolism ; Plant Proteins ; Purine Nucleotides/pharmacology ; Reactive Oxygen Species/metabolism ; Species Specificity ; Ubiquinone/metabolism ; Uncoupling Protein 1 ; }, abstract = {Uncoupling proteins (UCPs) are members of the mitochondrial anion carrier protein family that are present in the mitochondrial inner membrane and mediate free fatty acid (FFA)-activated, purine nucleotide (PN)-inhibited proton conductance. Since 1999, the presence of UCPs has been demonstrated in some non-photosynthesising unicellular eukaryotes, including amoeboid and parasite protists, as well as in non-fermentative yeast and filamentous fungi. In the mitochondria of these organisms, UCP activity is revealed upon FFA-induced, PN-inhibited stimulation of resting respiration and a decrease in membrane potential, which are accompanied by a decrease in membranous ubiquinone (Q) reduction level. UCPs in unicellular eukaryotes are able to divert energy from oxidative phosphorylation and thus compete for a proton electrochemical gradient with ATP synthase. Our recent work indicates that membranous Q is a metabolic sensor that might utilise its redox state to release the PN inhibition of UCP-mediated mitochondrial uncoupling under conditions of phosphorylation and resting respiration. The action of reduced Q (QH2) could allow higher or complete activation of UCP. As this regulatory feature was demonstrated for microorganism UCPs (A. castellanii UCP), plant and mammalian UCP1 analogues, and UCP1 in brown adipose tissue, the process could involve all UCPs. Here, we discuss the functional connection and physiological role of UCP and alternative oxidase, two main energy-dissipating systems in the plant-type mitochondrial respiratory chain of unicellular eukaryotes, including the control of cellular energy balance as well as preventive action against the production of reactive oxygen species.}, }
@article {pmid20019817, year = {2009}, author = {Salas, A and Fachal, L and Marcos-Alonso, S and Vega, A and Martinón-Torres, F and , }, title = {Investigating the role of mitochondrial haplogroups in genetic predisposition to meningococcal disease.}, journal = {PloS one}, volume = {4}, number = {12}, pages = {e8347}, pmid = {20019817}, issn = {1932-6203}, mesh = {Chi-Square Distribution ; Child, Preschool ; DNA, Mitochondrial/genetics ; Demography ; Female ; *Genetic Predisposition to Disease ; Genetics, Population ; Haplotypes/*genetics ; Humans ; Male ; Meningococcal Infections/*genetics/pathology ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {BACKGROUND AND AIMS: Meningococcal disease remains one of the most important infectious causes of death in industrialized countries. The highly diverse clinical presentation and prognosis of Neisseria meningitidis infections are the result of complex host genetics and environmental interactions. We investigated whether mitochondrial genetic background contributes to meningococcal disease (MD) susceptibility.<br><br>Prospective controlled study was performed through a national research network on MD that includes 41 Spanish hospitals. Cases were 307 paediatric patients with confirmed MD, representing the largest series of MD patients analysed to date. Two independent sets of ethnicity-matched control samples (CG1 [N = 917]), and CG2 [N = 616]) were used for comparison. Cases and controls underwent mtDNA haplotyping of a selected set of 25 mtDNA SNPs (mtSNPs), some of them defining major European branches of the mtDNA phylogeny. In addition, 34 ancestry informative markers (AIMs) were genotyped in cases and CG2 in order to monitor potential hidden population stratification. Samples of known African, Native American and European ancestry (N = 711) were used as classification sets for the determination of ancestral membership of our MD patients. A total of 39 individuals were eliminated from the main statistical analyses (including fourteen gypsies) on the basis of either non-Spanish self-reported ancestry or the results of AIMs indicating a European membership lower than 95%. Association analysis of the remaining 268 cases against CG1 suggested an overrepresentation of the synonym mtSNP G11719A variant (Pearson's chi-square test; adjusted P-value = 0.0188; OR [95% CI] = 1.63 [1.22-2.18]). When cases were compared with CG2, the positive association could not be replicated. No positive association has been observed between haplogroup (hg) status of cases and CG1/CG2 and hg status of cases and several clinical variants.<br><br>CONCLUSIONS: We did not find evidence of association between mtSNPs and mtDNA hgs with MD after carefully monitoring the confounding effect of population sub-structure. MtDNA variability is particularly stratified in human populations owing to its low effective population size in comparison with autosomal markers and therefore, special care should be taken in the interpretation of seeming signals of positive associations in mtDNA case-control association studies.}, }
@article {pmid20008390, year = {2010}, author = {Cavalier-Smith, T}, title = {Deep phylogeny, ancestral groups and the four ages of life.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {365}, number = {1537}, pages = {111-132}, pmid = {20008390}, issn = {1471-2970}, mesh = {Cell Membrane/genetics ; Eukaryota/*genetics ; *Evolution, Molecular ; *Genetic Variation ; *Phylogeny ; }, abstract = {Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of life is a useful metaphor for organismal genealogical history provided we recognize that branches sometimes fuse. Hennigian cladistics emphasizes only lineage splitting, ignoring most other major phylogenetic processes. Though methodologically useful it has been conceptually confusing and harmed taxonomy, especially in mistakenly opposing ancestral (paraphyletic) taxa. The history of life involved about 10 really major innovations in cell structure. In membrane topology, there were five successive kinds of cell: (i) negibacteria, with two bounding membranes, (ii) unibacteria, with one bounding and no internal membranes, (iii) eukaryotes with endomembranes and mitochondria, (iv) plants with chloroplasts and (v) finally, chromists with plastids inside the rough endoplasmic reticulum. Membrane chemistry divides negibacteria into the more advanced Glycobacteria (e.g. Cyanobacteria and Proteobacteria) with outer membrane lipolysaccharide and primitive Eobacteria without lipopolysaccharide (deserving intenser study). It also divides unibacteria into posibacteria, ancestors of eukaryotes, and archaebacteria-the sisters (not ancestors) of eukaryotes and the youngest bacterial phylum. Anaerobic eobacteria, oxygenic cyanobacteria, desiccation-resistant posibacteria and finally neomura (eukaryotes plus archaebacteria) successively transformed Earth. Accidents and organizational constraints are as important as adaptiveness in body plan evolution.}, }
@article {pmid20003182, year = {2009}, author = {de Graaf, RM and Duarte, I and van Alen, TA and Kuiper, JW and Schotanus, K and Rosenberg, J and Huynen, MA and Hackstein, JH}, title = {The hydrogenosomes of Psalteriomonas lanterna.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {287}, pmid = {20003182}, issn = {1471-2148}, mesh = {Animals ; DNA, Protozoan/genetics ; Eukaryota/classification/genetics/*ultrastructure ; Expressed Sequence Tags ; Organelles/*ultrastructure ; Phylogeny ; }, abstract = {BACKGROUND: Hydrogenosomes are organelles that produce molecular hydrogen and ATP. The broad phylogenetic distribution of their hosts suggests that the hydrogenosomes of these organisms evolved several times independently from the mitochondria of aerobic progenitors. Morphology and 18S rRNA phylogeny suggest that the microaerophilic amoeboflagellate Psalteriomonas lanterna, which possesses hydrogenosomes and elusive "modified mitochondria", belongs to the Heterolobosea, a taxon that consists predominantly of aerobic, mitochondriate organisms. This taxon is rather unrelated to taxa with hitherto studied hydrogenosomes.<br><br>RESULTS: Electron microscopy of P. lanterna flagellates reveals a large globule in the centre of the cell that is build up from stacks of some 20 individual hydrogenosomes. The individual hydrogenosomes are surrounded by a double membrane that encloses a homogeneous, dark staining matrix lacking cristae. The "modified mitochondria" are found in the cytoplasm of the cell and are surrounded by 1-2 cisterns of rough endoplasmatic reticulum, just as the mitochondria of certain related aerobic Heterolobosea. The ultrastructure of the "modified mitochondria" and hydrogenosomes is very similar, and they have the same size distribution as the hydrogenosomes that form the central stack.The phylogenetic analysis of selected EST sequences (Hsp60, Propionyl-CoA carboxylase) supports the phylogenetic position of P. lanterna close to aerobic Heterolobosea (Naegleria gruberi). Moreover, this analysis also confirms the identity of several mitochondrial or hydrogenosomal key-genes encoding proteins such as a Hsp60, a pyruvate:ferredoxin oxidoreductase, a putative ADP/ATP carrier, a mitochondrial complex I subunit (51 KDa), and a [FeFe] hydrogenase.<br><br>CONCLUSION: Comparison of the ultrastructure of the "modified mitochondria" and hydrogenosomes strongly suggests that both organelles are just two morphs of the same organelle. The EST studies suggest that the hydrogenosomes of P. lanterna are physiologically similar to the hydrogenosomes of Trichomonas vaginalis and Trimastix pyriformis. Phylogenetic analysis of the ESTs confirms the relationship of P. lanterna with its aerobic relative, the heterolobosean amoeboflagellate Naegleria gruberi, corroborating the evolution of hydrogenosomes from a common, mitochondriate ancestor.}, }
@article {pmid19997590, year = {2009}, author = {Abhyankar, A and Park, HB and Tonolo, G and Luthman, H}, title = {Comparative sequence analysis of the non-protein-coding mitochondrial DNA of inbred rat strains.}, journal = {PloS one}, volume = {4}, number = {12}, pages = {e8148}, pmid = {19997590}, issn = {1932-6203}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames/*genetics ; RNA, Ribosomal/chemistry/genetics ; RNA, Transfer/chemistry/genetics ; Rats ; Rats, Inbred Strains/*genetics ; Selection, Genetic ; *Sequence Analysis, DNA ; }, abstract = {The proper function of mammalian mitochondria necessitates a coordinated expression of both nuclear and mitochondrial genes, most likely due to the co-evolution of nuclear and mitochondrial genomes. The non-protein coding regions of mitochondrial DNA (mtDNA) including the D-loop, tRNA and rRNA genes form a major component of this regulated expression unit. Here we present comparative analyses of the non-protein-coding regions from 27 Rattus norvegicus mtDNA sequences. There were two variable positions in 12S rRNA, 20 in 16S rRNA, eight within the tRNA genes and 13 in the D-loop. Only one of the three neutrality tests used demonstrated statistically significant evidence for selection in 16S rRNA and tRNA-Cys. Based on our analyses of conserved sequences, we propose that some of the variable nucleotide positions identified in 16S rRNA and tRNA-Cys, and the D-loop might be important for mitochondrial function and its regulation.}, }
@article {pmid19968861, year = {2010}, author = {Poliak, P and Van Hoewyk, D and Oborník, M and Zíková, A and Stuart, KD and Tachezy, J and Pilon, M and Lukes, J}, title = {Functions and cellular localization of cysteine desulfurase and selenocysteine lyase in Trypanosoma brucei.}, journal = {The FEBS journal}, volume = {277}, number = {2}, pages = {383-393}, pmid = {19968861}, issn = {1742-4658}, support = {R01 AI065935/AI/NIAID NIH HHS/United States ; R01 AI065935-05/AI/NIAID NIH HHS/United States ; AI065935/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Carbon-Sulfur Lyases/genetics/*metabolism ; Cell Compartmentation ; Cytosol/enzymology ; Genes, Protozoan ; Lyases/antagonists &amp; inhibitors/genetics/*metabolism ; Mitochondria/enzymology ; Phylogeny ; Protozoan Proteins/genetics/*metabolism ; RNA Interference ; RNA, Messenger/genetics/metabolism ; RNA, Protozoan/genetics/metabolism ; Trypanosoma brucei brucei/*enzymology/genetics ; }, abstract = {Nfs-like proteins have cysteine desulfurase (CysD) activity, which removes sulfur (S) from cysteine, and provides S for iron-sulfur cluster assembly and the thiolation of tRNAs. These proteins also have selenocysteine lyase activity in vitro, and cleave selenocysteine into alanine and elemental selenium (Se). It was shown previously that the Nfs-like protein called Nfs from the parasitic protist Trypanosoma brucei is a genuine CysD. A second Nfs-like protein is encoded in the nuclear genome of T. brucei. We called this protein selenocysteine lyase (SCL) because phylogenetic analysis reveals that it is monophyletic with known eukaryotic selenocysteine lyases. The Nfs protein is located in the mitochondrion, whereas the SCL protein seems to be present in the nucleus and cytoplasm. Unexpectedly, downregulation of either Nfs or SCL protein leads to a dramatic decrease in both CysD and selenocysteine lyase activities concurrently in the mitochondrion and the cytosolic fractions. Because loss of Nfs causes a growth phenotype but loss of SCL does not, we propose that Nfs can fully complement SCL, whereas SCL can only partially replace Nfs under our growth conditions.}, }
@article {pmid19966073, year = {2009}, author = {Gebert, M and Meschenmoser, K and Svidová, S and Weghuber, J and Schweyen, R and Eifler, K and Lenz, H and Weyand, K and Knoop, V}, title = {A root-expressed magnesium transporter of the MRS2/MGT gene family in Arabidopsis thaliana allows for growth in low-Mg2+ environments.}, journal = {The Plant cell}, volume = {21}, number = {12}, pages = {4018-4030}, pmid = {19966073}, issn = {1532-298X}, mesh = {Arabidopsis/*genetics/growth &amp; development/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Cation Transport Proteins/genetics/*metabolism ; Cloning, Molecular ; DNA, Bacterial/genetics ; Gene Expression Regulation, Plant ; Gene Knockout Techniques ; Genetic Complementation Test ; Magnesium/*metabolism ; Multigene Family ; Mutagenesis, Insertional ; Mutation ; Phylogeny ; Plant Roots/genetics/*growth &amp; development/metabolism ; Plants, Genetically Modified/genetics ; RNA, Plant/genetics ; Saccharomyces cerevisiae/metabolism ; Nicotiana/genetics ; }, abstract = {The MRS2/MGT gene family in Arabidopsis thaliana belongs to the superfamily of CorA-MRS2-ALR-type membrane proteins. Proteins of this type are characterized by a GMN tripeptide motif (Gly-Met-Asn) at the end of the first of two C-terminal transmembrane domains and have been characterized as magnesium transporters. Using the recently established mag-fura-2 system allowing direct measurement of Mg(2+) uptake into mitochondria of Saccharomyces cerevisiae, we find that all members of the Arabidopsis family complement the corresponding yeast mrs2 mutant. Highly different patterns of tissue-specific expression were observed for the MRS2/MGT family members in planta. Six of them are expressed in root tissues, indicating a possible involvement in plant magnesium supply and distribution after uptake from the soil substrate. Homozygous T-DNA insertion knockout lines were obtained for four members of the MRS2/MGT gene family. A strong, magnesium-dependent phenotype of growth retardation was found for mrs2-7 when Mg(2+) concentrations were lowered to 50 microM in hydroponic cultures. Ectopic overexpression of MRS2-7 from the cauliflower mosaic virus 35S promoter results in complementation and increased biomass accumulation. Green fluorescent protein reporter gene fusions indicate a location of MRS2-7 in the endomembrane system. Hence, contrary to what is frequently found in analyses of plant gene families, a single gene family member knockout results in a strong, environmentally dependent phenotype.}, }
@article {pmid19966069, year = {2010}, author = {Seger, J and Smith, WA and Perry, JJ and Hunn, J and Kaliszewska, ZA and Sala, LL and Pozzi, L and Rowntree, VJ and Adler, FR}, title = {Gene genealogies strongly distorted by weakly interfering mutations in constant environments.}, journal = {Genetics}, volume = {184}, number = {2}, pages = {529-545}, pmid = {19966069}, issn = {1943-2631}, mesh = {Algorithms ; Animals ; DNA, Mitochondrial/genetics ; *Environment ; Evolution, Molecular ; Female ; Genes/*genetics ; Genes, Insect/genetics ; Inheritance Patterns/*genetics ; Male ; *Models, Genetic ; *Mutation ; Phthiraptera/genetics/physiology ; Population Density ; Selection, Genetic ; Whales/parasitology ; }, abstract = {Neutral nucleotide diversity does not scale with population size as expected, and this "paradox of variation" is especially severe for animal mitochondria. Adaptive selective sweeps are often proposed as a major cause, but a plausible alternative is selection against large numbers of weakly deleterious mutations subject to Hill-Robertson interference. The mitochondrial genealogies of several species of whale lice (Amphipoda: Cyamus) are consistently too short relative to neutral-theory expectations, and they are also distorted in shape (branch-length proportions) and topology (relative sister-clade sizes). This pattern is not easily explained by adaptive sweeps or demographic history, but it can be reproduced in models of interference among forward and back mutations at large numbers of sites on a nonrecombining chromosome. A coalescent simulation algorithm was used to study this model over a wide range of parameter values. The genealogical distortions are all maximized when the selection coefficients are of critical intermediate sizes, such that Muller's ratchet begins to turn. In this regime, linked neutral nucleotide diversity becomes nearly insensitive to N. Mutations of this size dominate the dynamics even if there are also large numbers of more strongly and more weakly selected sites in the genome. A genealogical perspective on Hill-Robertson interference leads directly to a generalized background-selection model in which the effective population size is progressively reduced going back in time from the present.}, }
@article {pmid19956696, year = {2009}, author = {Norgate, M and Chamings, J and Pavlova, A and Bull, JK and Murray, ND and Sunnucks, P}, title = {Mitochondrial DNA indicates late pleistocene divergence of populations of Heteronympha merope, an emerging model in environmental change biology.}, journal = {PloS one}, volume = {4}, number = {11}, pages = {e7950}, pmid = {19956696}, issn = {1932-6203}, mesh = {Animals ; Australia ; Biological Evolution ; Butterflies/*genetics/*physiology ; *DNA, Mitochondrial ; Ecosystem ; Environmental Monitoring ; Gene Flow ; Genetic Variation ; Genetics, Population ; Glucose-6-Phosphate Isomerase/chemistry ; Glycolysis ; Mitochondria/metabolism ; Models, Biological ; Sequence Analysis, DNA ; }, abstract = {Knowledge of historical changes in species range distribution provides context for investigating adaptive potential and dispersal ability. This is valuable for predicting the potential impact of environmental change on species of interest. Butterflies are one of the most important taxa for studying such impacts, and Heteronympha merope has the potential to provide a particularly valuable model, in part due to the existence of historical data on morphological traits and glycolytic enzyme variation. This study investigates the population genetic structure and phylogeography of H. merope, comparing the relative resolution achieved through partial DNA sequences of two mitochondrial loci, COI and ND5. These data are used to define the relationship between subspecies, showing that the subspecies are reciprocally monophyletic. On this basis, the Western Australian subspecies H. m. duboulayi is genetically distinct from the two eastern subspecies. Throughout the eastern part of the range, levels of migration and the timing of key population splits of potential relevance to climatic adaptation are estimated and indicate Late Pleistocene divergence both of the Tasmanian subspecies and of an isolated northern population from the eastern mainland subspecies H. m. merope. This information is then used to revisit historical data and provides support for the importance of clinal variation in wing characters, as well as evidence for selective pressure acting on allozyme loci phosphoglucose isomerase and phosphoglucomutase in H. merope. The study has thus confirmed the value of H. merope as a model organism for measuring responses to environmental change, offering the opportunity to focus on isolated populations, as well as a latitudinal gradient, and to use historical changes to test the accuracy of predictions for the future.}, }
@article {pmid19955254, year = {2009}, author = {Wallace, DC}, title = {Mitochondria, bioenergetics, and the epigenome in eukaryotic and human evolution.}, journal = {Cold Spring Harbor symposia on quantitative biology}, volume = {74}, number = {}, pages = {383-393}, pmid = {19955254}, issn = {1943-4456}, support = {NS21328/NS/NINDS NIH HHS/United States ; R01 AG024373-05/AG/NIA NIH HHS/United States ; AG16573/AG/NIA NIH HHS/United States ; R01 NS021328-24/NS/NINDS NIH HHS/United States ; R01 DK073691-04/DK/NIDDK NIH HHS/United States ; DK73691/DK/NIDDK NIH HHS/United States ; P50 AG016573/AG/NIA NIH HHS/United States ; R01 AG013154-11/AG/NIA NIH HHS/United States ; AG24373/AG/NIA NIH HHS/United States ; R01 AG024373/AG/NIA NIH HHS/United States ; R01 DK073691/DK/NIDDK NIH HHS/United States ; R01 NS021328/NS/NINDS NIH HHS/United States ; R01 AG013154/AG/NIA NIH HHS/United States ; AG13154/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/genetics ; Disease/genetics ; Energy Metabolism/*genetics ; *Epigenesis, Genetic ; Eukaryota ; *Evolution, Molecular ; Genetic Speciation ; Humans ; Mitochondria/*genetics/*metabolism ; Models, Genetic ; Mutation ; }, abstract = {Studies on the origin of species have focused largely on anatomy, yet animal populations are generally limited by energy. Animals can adapt to available energy resources at three levels: (1) evolution of different anatomical forms between groups of animals through nuclear DNA (nDNA) mutations, permitting exploitation of alternative energy reservoirs and resulting in new species with novel niches, (2) evolution of different physiologies within intraspecific populations through mutations in mitochondrial DNA (mtDNA) and nDNA bioenergetic genes, permitting adjustment to energetic variation within a species' niche, and (3) epigenomic regulation of dispersed bioenergetic genes within an individual via mitochondrially generated high-energy intermediates, permitting individual adjustment to environmental fluctuations. Because medicine focuses on changes within our species, clinically relevant variation is more likely to involve changes in bioenergetics than anatomy. This may explain why mitochondrial diseases and epigenomic diseases frequently have similar phenotypes and why epigenomic diseases are being found to involve mitochondrial dysfunction. Therefore, common complex diseases may be the result of changes in any of a large number of mtDNA and nDNA bioenergetic genes or to altered epigenomic regulation of these bioenergetic genes. All of these changes result in similar bioenergetic failure and consequently related phenotypes.}, }
@article {pmid19948060, year = {2009}, author = {Wang, X and Huang, Y and Lavrov, DV and Gu, X}, title = {Comparative study of human mitochondrial proteome reveals extensive protein subcellular relocalization after gene duplications.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {275}, pmid = {19948060}, issn = {1471-2148}, mesh = {Animals ; *Comparative Genomic Hybridization ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; *Gene Duplication ; *Genome, Human ; *Genome, Mitochondrial ; Humans ; Likelihood Functions ; Mitochondrial Proteins/genetics ; Multigene Family ; Phylogeny ; Proteome/*genetics ; Sequence Analysis, Protein ; }, abstract = {BACKGROUND: Gene and genome duplication is the principle creative force in evolution. Recently, protein subcellular relocalization, or neolocalization was proposed as one of the mechanisms responsible for the retention of duplicated genes. This hypothesis received support from the analysis of yeast genomes, but has not been tested thoroughly on animal genomes. In order to evaluate the importance of subcellular relocalizations for retention of duplicated genes in animal genomes, we systematically analyzed nuclear encoded mitochondrial proteins in the human genome by reconstructing phylogenies of mitochondrial multigene families.<br><br>RESULTS: The 456 human mitochondrial proteins selected for this study were clustered into 305 gene families including 92 multigene families. Among the multigene families, 59 (64%) consisted of both mitochondrial and cytosolic (non-mitochondrial) proteins (mt-cy families) while the remaining 33 (36%) were composed of mitochondrial proteins (mt-mt families). Phylogenetic analyses of mt-cy families revealed three different scenarios of their neolocalization following gene duplication: 1) relocalization from mitochondria to cytosol, 2) from cytosol to mitochondria and 3) multiple subcellular relocalizations. The neolocalizations were most commonly enabled by the gain or loss of N-terminal mitochondrial targeting signals. The majority of detected subcellular relocalization events occurred early in animal evolution, preceding the evolution of tetrapods. Mt-mt protein families showed a somewhat different pattern, where gene duplication occurred more evenly in time. However, for both types of protein families, most duplication events appear to roughly coincide with two rounds of genome duplications early in vertebrate evolution. Finally, we evaluated the effects of inaccurate and incomplete annotation of mitochondrial proteins and found that our conclusion of the importance of subcellular relocalization after gene duplication on the genomic scale was robust to potential gene misannotation.<br><br>CONCLUSION: Our results suggest that protein subcellular relocalization is an important mechanism for the retention and gain of function of duplicated genes in animal genome evolution.}, }
@article {pmid19946900, year = {2009}, author = {Grienenberger, JM}, title = {Plant mitochondrial RNA editing: the Strasbourg chapter.}, journal = {IUBMB life}, volume = {61}, number = {12}, pages = {1110-1113}, doi = {10.1002/iub.277}, pmid = {19946900}, issn = {1521-6551}, mesh = {Amino Acyl-tRNA Synthetases/metabolism ; Biochemistry/history/methods ; Codon ; DNA, Complementary/metabolism ; Evolution, Molecular ; France ; Genome, Plant ; History, 20th Century ; Plants/*metabolism ; RNA/*metabolism ; *RNA Editing ; RNA, Mitochondrial ; RNA, Plant/*metabolism ; RNA, Transfer/metabolism ; }, abstract = {For 8 years, it was not understood why certain genes of plant mitochondria contain CGG (arginine) codons at positions where tryptophan codons (UGG) are present in the corresponding genes of nonplant species. Identification and sequencing of a tRNA(Trp) gene showed that it is not able to decode the CGG codon. Analysis of different discrepancies in the sequences of plant mitochondrial proteins prompted us to determine directly the corresponding RNA sequences. These experiments showed that plant mitochondrial transcripts are subject to RNA editing that changes C into U, resulting in a better phylogenetic conservation of protein sequences [Gualberto et al. (1989) Nature 341, 660-662].}, }
@article {pmid19946245, year = {2009}, author = {Kream, RM and Stefano, GB}, title = {Endogenous morphine and nitric oxide coupled regulation of mitochondrial processes.}, journal = {Medical science monitor : international medical journal of experimental and clinical research}, volume = {15}, number = {12}, pages = {RA263-8}, pmid = {19946245}, issn = {1643-3750}, mesh = {Animals ; Biological Evolution ; Cardiovascular System/metabolism ; Catecholamines/metabolism ; Humans ; Mitochondria/*metabolism ; Models, Biological ; Morphine/*metabolism ; Nitric Oxide/*metabolism ; Receptors, Opioid, mu/chemistry/metabolism ; Signal Transduction ; }, abstract = {The widespread expression of morphine by plants, invertebrate and vertebrate cells/organ systems strongly indicates a high level of evolutionary conservation of morphine and related morphinan alkaloids as essential chemical factors required for normal growth and development. The prototype catecholamine dopamine (DA) serves as an essential chemical intermediate in morphine biosynthesis both in plants and animals. We surmise primordial, multi-potential cell types, before the emergence of specialized plant and animal cells/organ systems, required selective mechanisms to limit their responsiveness to environmental noise. Accordingly, cellular systems that emerged with the potential for recruitment of the free radical gas nitric oxide (NO) as a multi-faceted autocrine/paracrine signaling molecule were provided with extremely positive evolutionary advantages. Endogenous "morphinergic" in concert with NO-coupled signaling systems have evolved as autocrine/paracrine regulators of metabolic homeostasis, energy metabolism, mitochondrial respiration and energy production. Basic physiological processes involving "morphinergic"/NO-coupled regulation of mitochondrial function, with special emphasis on the cardiovascular system, are critical to all organismic survival. Critical to this concept may be the phenomenon of mitochondrial enslavement in eukaryotic evolution via morphine.}, }
@article {pmid19944189, year = {2010}, author = {Jenner, RA}, title = {Higher-level crustacean phylogeny: consensus and conflicting hypotheses.}, journal = {Arthropod structure &amp; development}, volume = {39}, number = {2-3}, pages = {143-153}, doi = {10.1016/j.asd.2009.11.001}, pmid = {19944189}, issn = {1873-5495}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/metabolism ; Crustacea/*genetics/*physiology ; *Fossils ; Mitochondria/metabolism ; Paleontology/methods ; Phylogeny ; }, abstract = {This paper presents an overview of current hypotheses of higher-level crustacean phylogeny in order to assist and help focus further research. It concentrates on hypotheses proposed or debated in the recent literature based on morphological, molecular and combined evidence phylogenetic analyses. It can be concluded that crustacean phylogeny remains essentially unresolved. Conflict is rife, irrespective of whether one compares different morphological studies, molecular studies, or both. Using the number of recently proposed alternative sister group hypotheses for each of the major tetraconatan taxa as a rough estimate of phylogenetic uncertainty, it can be concluded that the phylogenetic position of Malacostraca remains the most problematic, closely followed by Branchiopoda, Cephalocarida, Remipedia, Ostracoda, Branchiura, Copepoda and Hexapoda. Future progress will depend upon a broader taxon sampling in molecular analyses, and the further exploration of new molecular phylogenetic markers. However, the need for continued revision and expansion of morphological datasets remains undiminished given the conspicuous lack of agreement between molecules and morphology for positioning several taxa. In view of the unparalleled morphological diversity of Crustacea, and the likely nesting of Hexapoda somewhere within Crustacea, working out a detailed phylogeny of Tetraconata is a crucial step towards understanding arthropod body plan evolution.}, }
@article {pmid19943893, year = {2010}, author = {Smith, S and Turbill, C and Suchentrunk, F}, title = {Introducing mother's curse: low male fertility associated with an imported mtDNA haplotype in a captive colony of brown hares.}, journal = {Molecular ecology}, volume = {19}, number = {1}, pages = {36-43}, doi = {10.1111/j.1365-294X.2009.04444.x}, pmid = {19943893}, issn = {1365-294X}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Female ; Fertility/genetics ; *Genetic Fitness ; Genetics, Population ; Haplotypes ; Hares/*genetics ; Infertility, Male/*genetics ; Male ; Models, Genetic ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Mitochondrial DNA mutations create variation in the efficiency of the oxidative phosphorylation pathway and therefore cellular energy production. Mildly deleterious mutations may reduce the performance of sperm cells in particular, due to their high energy requirements and low number of mitochondria, yet have little or no effect on the viability of somatic cells or ova. Mutations will be maintained in the population, despite the fitness cost for males, because mtDNA is passed down the female line. We looked for this so-called mother's curse effect in our captive colony of European brown hares. Significantly reduced male reproductive success was detected for a divergent haplotype that could be traced back to hares imported from a remote population. Median reproductive success for these hares was 0.17 compared to 0.49 for the indigenous haplotypes (Wilcoxon rank-sum, P = 0.002). No difference was detected for female reproductive success, nor were we able to find a nuclear DNA component to variation in male fertility. Our data are strong evidence for a mother's curse effect persisting despite multiple crossings over seven generations. These data raise important issues relating to the reproductive fitness of small or intermixing populations and have particular implications for the management of populations for conservation.}, }
@article {pmid19934175, year = {2010}, author = {Kubo, N and Arimura, S}, title = {Discovery of the rpl10 gene in diverse plant mitochondrial genomes and its probable replacement by the nuclear gene for chloroplast RPL10 in two lineages of angiosperms.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {17}, number = {1}, pages = {1-9}, pmid = {19934175}, issn = {1756-1663}, mesh = {Arabidopsis/genetics ; Arabidopsis Proteins ; Biodiversity ; Cell Nucleus/*genetics ; Chloroplasts/*genetics ; Conserved Sequence ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Genes, Plant/*genetics ; Genome, Mitochondrial/*genetics ; Magnoliopsida/*genetics ; Marchantia/genetics ; Mitochondria/genetics ; Open Reading Frames/genetics ; Oryza/genetics ; *Phylogeny ; Protein Transport ; RNA Editing/genetics ; Ribosomal Protein L10 ; Ribosomal Proteins/*genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; }, abstract = {Mitochondrial genomes of plants are much larger than those of mammals and often contain conserved open reading frames (ORFs) of unknown function. Here, we show that one of these conserved ORFs is actually the gene for ribosomal protein L10 (rpl10) in plant. No rpl10 gene has heretofore been reported in any mitochondrial genome other than the exceptionally gene-rich genome of the protist Reclinomonas americana. Conserved ORFs corresponding to rpl10 are present in a wide diversity of land plant and green algal mitochondrial genomes. The mitochondrial rpl10 genes are transcribed in all nine land plants examined, with five seed plant genes subject to RNA editing. In addition, mitochondrial-rpl10-like cDNAs were identified in EST libraries from numerous land plants. In three lineages of angiosperms, rpl10 is either lost from the mitochondrial genome or a pseudogene. In two of them (Brassicaceae and monocots), no nuclear copy of mitochondrial rpl10 is identifiably present, and instead a second copy of nuclear-encoded chloroplast rpl10 is present. Transient assays using green fluorescent protein indicate that this duplicate gene is dual targeted to mitochondria and chloroplasts. We infer that mitochondrial rpl10 has been functionally replaced by duplicated chloroplast counterparts in Brassicaceae and monocots.}, }
@article {pmid19930686, year = {2009}, author = {Szklarczyk, R and Huynen, MA}, title = {Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.}, journal = {Genome biology}, volume = {10}, number = {11}, pages = {R135}, pmid = {19930686}, issn = {1474-760X}, mesh = {Cell Nucleus/metabolism ; DNA, Fungal/genetics ; DNA, Mitochondrial/*genetics ; Gene Duplication ; Genes, Fungal ; Humans ; Mitochondria/genetics/*metabolism ; Models, Genetic ; Phylogeny ; Proteome/metabolism ; Proteomics/methods ; RNA/genetics ; Saccharomyces cerevisiae/genetics ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Mitochondria are highly complex, membrane-enclosed organelles that are essential to the eukaryotic cell. The experimental elucidation of organellar proteomes combined with the sequencing of complete genomes allows us to trace the evolution of the mitochondrial proteome.<br><br>RESULTS: We present a systematic analysis of the evolution of mitochondria via gene duplication in the human lineage. The most common duplications are intra-mitochondrial, in which the ancestral gene and the daughter genes encode mitochondrial proteins. These duplications significantly expanded carbohydrate metabolism, the protein import machinery and the calcium regulation of mitochondrial activity. The second most prevalent duplication, inter-compartmental, extended the catalytic as well as the RNA processing repertoire by the novel mitochondrial localization of the protein encoded by one of the daughter genes. Evaluation of the phylogenetic distribution of N-terminal targeting signals suggests a prompt gain of the novel localization after inter-compartmental duplication. Relocalized duplicates are more often expressed in a tissue-specific manner relative to intra-mitochondrial duplicates and mitochondrial proteins in general. In a number of cases, inter-compartmental duplications can be observed in parallel in yeast and human lineages leading to the convergent evolution of subcellular compartments.<br><br>CONCLUSIONS: One-to-one human-yeast orthologs are typically restricted to their ancestral subcellular localization. Gene duplication relaxes this constraint on the cellular location, allowing nascent proteins to be relocalized to other compartments. We estimate that the mitochondrial proteome expanded at least 50% since the common ancestor of human and yeast.}, }
@article {pmid19929881, year = {2010}, author = {Richter, U and Kühn, K and Okada, S and Brennicke, A and Weihe, A and Börner, T}, title = {A mitochondrial rRNA dimethyladenosine methyltransferase in Arabidopsis.}, journal = {The Plant journal : for cell and molecular biology}, volume = {61}, number = {4}, pages = {558-569}, pmid = {19929881}, issn = {1365-313X}, mesh = {Arabidopsis/*enzymology/genetics ; Arabidopsis Proteins/genetics/*metabolism ; Genetic Complementation Test ; Methyltransferases/genetics/*metabolism ; Mitochondria/*enzymology/genetics ; Mutagenesis, Insertional ; Mutation ; Phylogeny ; RNA, Plant/genetics ; RNA, Ribosomal, 18S/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Transcription Factors/genetics/metabolism ; Transcription, Genetic ; }, abstract = {S-adenosyl-L-methionine-dependent rRNA dimethylases mediate the methylation of two conserved adenosines near the 3' end of the rRNA in the small ribosomal subunits of bacteria, archaea and eukaryotes. Proteins related to this family of dimethylases play an essential role as transcription factors (mtTFBs) in fungal and animal mitochondria. Human mitochondrial rRNA is methylated and human mitochondria contain two related mtTFBs, one proposed to act as rRNA dimethylase, the other as transcription factor. The nuclear genome of Arabidopsis thaliana encodes three dimethylase/mtTFB-like proteins, one of which, Dim1B, is shown here to be imported into mitochondria. Transcription initiation by mitochondrial RNA polymerases appears not to be stimulated by Dim1B in vitro. In line with this finding, phylogenetic analyses revealed Dim1B to be more closely related to a group of eukaryotic non-mitochondrial rRNA dimethylases (Dim1s) than to fungal and animal mtTFBs. We found that Dim1B was capable of substituting the E. coli rRNA dimethylase activity of KsgA. Moreover, we observed methylation of the conserved adenines in the 18S rRNA of Arabidopsis mitochondria; this modification was not detectable in a mutant lacking Dim1B. These data provide evidence: (i) for rRNA methylation in Arabidopsis mitochondria; and (ii) that Dim1B is the enzyme catalyzing this process.}, }
@article {pmid19917118, year = {2009}, author = {Mower, JP and Bonen, L}, title = {Ribosomal protein L10 is encoded in the mitochondrial genome of many land plants and green algae.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {265}, pmid = {19917118}, issn = {1471-2148}, mesh = {Amino Acid Sequence ; Chlorophyta/*genetics ; Comparative Genomic Hybridization ; Conserved Sequence ; DNA, Algal/genetics ; DNA, Plant/genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames ; Plants/*genetics ; Ribosomal Protein L10 ; Ribosomal Proteins/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The mitochondrial genomes of plants generally encode 30-40 identified protein-coding genes and a large number of lineage-specific ORFs. The lack of wide conservation for most ORFs suggests they are unlikely to be functional. However, an ORF, termed orf-bryo1, was recently found to be conserved among bryophytes suggesting that it might indeed encode a functional mitochondrial protein.<br><br>RESULTS: From a broad survey of land plants, we have found that the orf-bryo1 gene is also conserved in the mitochondria of vascular plants and charophycean green algae. This gene is actively transcribed and RNA edited in many flowering plants. Comparative sequence analysis and distribution of editing suggests that it encodes ribosomal protein L10 of the large subunit of the ribosome. In several lineages, such as crucifers and grasses, where the rpl10 gene has been lost from the mitochondrion, we suggest that a copy of the nucleus-encoded chloroplast-derived rpl10 gene may serve as a functional replacement.<br><br>CONCLUSION: Despite the fact that there are now over 20 mitochondrial genome sequences for land plants and green algae, this gene has remained unidentified and largely undetected until now because of the unlikely coincidence that most of the earlier sequences were from the few lineages that lack the intact gene. These results illustrate the power of comparative sequencing to identify novel genomic features.}, }
@article {pmid19902250, year = {2010}, author = {Nilles-Bije, ML and Rivera, WL}, title = {Ultrastructural and molecular characterization of Balantidium coli isolated in the Philippines.}, journal = {Parasitology research}, volume = {106}, number = {2}, pages = {387-394}, pmid = {19902250}, issn = {1432-1955}, mesh = {Animals ; Balantidiasis/parasitology/*veterinary ; Balantidium/classification/*genetics/isolation &amp; purification/*ultrastructure ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Organelles/ultrastructure ; Philippines ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; Swine ; Swine Diseases/*parasitology ; }, abstract = {Balantidium coli is a ciliated protozoon inhabiting the colon of swine, rodents, horses, nonhuman primates and humans. In association with disease triggered by other infectious agents, B. coli may become a pathogenic opportunist. This study describes the isolation, cultivation, morphological as well as molecular characterization of B. coli isolated from the large intestine of a pig in the Philippines. Based on scanning and transmission electron microscopy, this protozoon presents a dense ciliation in the oral structure and somatic cilia that are arranged in a more transverse field. Oral and somatic monokinetids were identified in the cortex of the organism. The presence of heterokaryotic nuclear condition is evident, and the cell body of the ciliate shows numerous mucocysts, several food vacuoles, mitochondria, endoplasmic reticulum, and contractile vacuoles. Polymerase chain reaction and phylogenetic analysis based on the small subunit ribosomal RNA gene were performed in order to compare our isolate with other previously reported B. coli isolates. The full-length sequence of the SSU rRNA gene of the isolate showed 99% similarity to other B. coli isolates reported in the GenBank. Phylogenetic analysis revealed that the isolate clustered with previously reported B. coli isolates from gorillas, pig, and ostrich. To date, no studies on the ultrastructure and phylogeny of B. coli isolated in the Philippines have been reported. Results from this study may serve as a baseline data for further ultrastructural and phylogenetic studies on this organism. This study also suggests that morphological characteristics along with molecular identification are essential for validating and identifying species of Balantidium.}, }
@article {pmid19900409, year = {2010}, author = {Srivastava, S and Ratha, BK}, title = {Does fish represent an intermediate stage in the evolution of ureotelic cytosolic arginase I?.}, journal = {Biochemical and biophysical research communications}, volume = {391}, number = {1}, pages = {1-5}, doi = {10.1016/j.bbrc.2009.11.018}, pmid = {19900409}, issn = {1090-2104}, mesh = {Animals ; Arginase/chemistry/genetics/*metabolism ; Cytosol/*enzymology ; *Evolution, Molecular ; Fishes/*growth &amp; development/metabolism ; Isoenzymes/chemistry/genetics/metabolism ; Kidney/enzymology ; Liver/enzymology ; Mitochondria, Liver/enzymology ; Tissue Distribution ; Urea/*metabolism ; }, abstract = {Arginase catalyses the last step of the urea cycle. At least two isoenzymes of arginase are known; cytosolic ARG I and mitochondrial ARG II. ARG I is predominantly expressed in liver cytosol, as a part of urea cycle in ureotelic animals. The second isoform ARG II is primarily responsible for non-ureogenic functions, expressed in mitochondria of both hepatic and non-hepatic tissues in most vertebrates. Most micro-organisms and invertebrates are known to have only one type of arginase, whose function is unrelated to ornithine-urea cycle (OUC). However, in ureo-osmotic marine elasmobranchs arginase is localized in liver mitochondria as a part of OUC to synthesize urea for osmoregulation. An evolutionary transition occurred in arginase enzyme in terrestrial ureotelic vertebrates, with the evolution of ARG I from a pre-existing ancestral mitochondrial ARG II. This cytosolic ARG I activity is supposed to have first appeared in lung fishes, but the 40% and 60% distribution of arginase I and II activity in liver and kidney tissue of Heteropneustes fossilis indicates reconsideration of the above fact.}, }
@article {pmid19895685, year = {2009}, author = {de Graaf, RM and van Alen, TA and Dutilh, BE and Kuiper, JW and van Zoggel, HJ and Huynh, MB and Görtz, HD and Huynen, MA and Hackstein, JH}, title = {The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {514}, pmid = {19895685}, issn = {1471-2164}, mesh = {Electron Transport ; Electron Transport Complex IV/genetics ; Euplotes/*genetics/metabolism ; Genome, Mitochondrial/*genetics ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; RNA, Transfer/genetics ; Repetitive Sequences, Nucleic Acid ; Ribosomal Proteins/genetics ; }, abstract = {BACKGROUND: There are thousands of very diverse ciliate species from which only a handful mitochondrial genomes have been studied so far. These genomes are rather similar because the ciliates analysed (Tetrahymena spp. and Paramecium aurelia) are closely related. Here we study the mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus. These ciliates are only distantly related to Tetrahymena spp. and Paramecium aurelia, but more closely related to Nyctotherus ovalis, which possesses a hydrogenosomal (mitochondrial) genome.<br><br>RESULTS: The linear mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus were sequenced and compared with the mitochondrial genomes of several Tetrahymena species, Paramecium aurelia and the partially sequenced mitochondrial genome of the anaerobic ciliate Nyctotherus ovalis. This study reports new features such as long 5'gene extensions of several mitochondrial genes, extremely long cox1 and cox2 open reading frames and a large repeat in the middle of the linear mitochondrial genome. The repeat separates the open reading frames into two blocks, each having a single direction of transcription, from the repeat towards the ends of the chromosome. Although the Euplotes mitochondrial gene content is almost identical to that of Paramecium and Tetrahymena, the order of the genes is completely different. In contrast, the 33273 bp (excluding the repeat region) piece of the mitochondrial genome that has been sequenced in both Euplotes species exhibits no difference in gene order. Unexpectedly, many of the mitochondrial genes of E. minuta encoding ribosomal proteins possess N-terminal extensions that are similar to mitochondrial targeting signals.<br><br>CONCLUSION: The mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus are rather different from the previously studied genomes. Many genes are extended in size compared to mitochondrial genes from other sources.}, }
@article {pmid19888992, year = {2010}, author = {Maralikova, B and Ali, V and Nakada-Tsukui, K and Nozaki, T and van der Giezen, M and Henze, K and Tovar, J}, title = {Bacterial-type oxygen detoxification and iron-sulfur cluster assembly in amoebal relict mitochondria.}, journal = {Cellular microbiology}, volume = {12}, number = {3}, pages = {331-342}, doi = {10.1111/j.1462-5822.2009.01397.x}, pmid = {19888992}, issn = {1462-5822}, support = {BB/C507145/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/C507145/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacterial Proteins/*metabolism ; Entamoeba histolytica/*metabolism ; Hemerythrin/metabolism ; Iron/*metabolism ; Microscopy, Fluorescence ; Microscopy, Immunoelectron ; Organelles/*metabolism ; Oxygen/*antagonists &amp; inhibitors ; Peroxidase/metabolism ; Rubredoxins/metabolism ; Sulfur/*metabolism ; }, abstract = {The assembly of vital reactive iron-sulfur (Fe-S) cofactors in eukaryotes is mediated by proteins inherited from the original mitochondrial endosymbiont. Uniquely among eukaryotes, however, Entamoeba and Mastigamoeba lack such mitochondrial-type Fe-S cluster assembly proteins and possess instead an analogous bacterial-type system acquired by lateral gene transfer. Here we demonstrate, using immunomicroscopy and biochemical methods, that beyond their predicted cytosolic distribution the bacterial-type Fe-S cluster assembly proteins NifS and NifU have been recruited to function within the relict mitochondrial organelles (mitosomes) of Entamoeba histolytica. Both Nif proteins are 10-fold more concentrated within mitosomes compared with their cytosolic distribution suggesting that active Fe-S protein maturation occurs in these organelles. Quantitative immunoelectron microscopy showed that amoebal mitosomes are minute but highly abundant cellular structures that occupy up to 2% of the total cell volume. In addition, protein colocalization studies allowed identification of the amoebal hydroperoxide detoxification enzyme rubrerythrin as a mitosomal protein. This protein contains functional Fe-S centres and exhibits peroxidase activity in vitro. Our findings demonstrate the role of analogous protein replacement in mitochondrial organelle evolution and suggest that the relict mitochondrial organelles of Entamoeba are important sites of metabolic activity that function in Fe-S protein-mediated oxygen detoxification.}, }
@article {pmid19878576, year = {2009}, author = {Sloan, DB and Oxelman, B and Rautenberg, A and Taylor, DR}, title = {Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {260}, pmid = {19878576}, issn = {1471-2148}, mesh = {DNA, Chloroplast/genetics ; DNA, Mitochondrial/*genetics ; Genome, Plant ; Magnoliopsida/classification/*genetics ; Mitochondria/genetics ; *Mutation ; *Phylogeny ; }, abstract = {BACKGROUND: Recent phylogenetic studies have revealed that the mitochondrial genome of the angiosperm Silene noctiflora (Caryophyllaceae) has experienced a massive mutation-driven acceleration in substitution rate, placing it among the fastest evolving eukaryotic genomes ever identified. To date, it appears that other species within Silene have maintained more typical substitution rates, suggesting that the acceleration in S. noctiflora is a recent and isolated evolutionary event. This assessment, however, is based on a very limited sampling of taxa within this diverse genus.<br><br>RESULTS: We analyzed the substitution rates in 4 mitochondrial genes (atp1, atp9, cox3 and nad9) across a broad sample of 74 species within Silene and related genera in the tribe Sileneae. We found that S. noctiflora shares its history of elevated mitochondrial substitution rate with the closely related species S. turkestanica. Another section of the genus (Conoimorpha) has experienced an acceleration of comparable magnitude. The phylogenetic data remain ambiguous as to whether the accelerations in these two clades represent independent evolutionary events or a single ancestral change. Rate variation among genes was equally dramatic. Most of the genus exhibited elevated rates for atp9 such that the average tree-wide substitution rate for this gene approached the values for the fastest evolving branches in the other three genes. In addition, some species exhibited major accelerations in atp1 and/or cox3 with no correlated change in other genes. Rates of non-synonymous substitution did not increase proportionally with synonymous rates but instead remained low and relatively invariant.<br><br>CONCLUSION: The patterns of phylogenetic divergence within Sileneae suggest enormous variability in plant mitochondrial mutation rates and reveal a complex interaction of gene and species effects. The variation in rates across genomic and phylogenetic scales raises questions about the mechanisms responsible for the evolution of mutation rates in plant mitochondrial genomes.}, }
@article {pmid19864422, year = {2009}, author = {Song, D and Tu, Z and Lee, FS}, title = {Human ISCA1 interacts with IOP1/NARFL and functions in both cytosolic and mitochondrial iron-sulfur protein biogenesis.}, journal = {The Journal of biological chemistry}, volume = {284}, number = {51}, pages = {35297-35307}, pmid = {19864422}, issn = {1083-351X}, support = {R01 GM071459/GM/NIGMS NIH HHS/United States ; R01-GM71459/GM/NIGMS NIH HHS/United States ; }, mesh = {Aconitate Hydratase/*biosynthesis/genetics ; Animals ; COS Cells ; Chlorocebus aethiops ; Cytosol/*metabolism ; Gene Knockdown Techniques ; HeLa Cells ; Humans ; Hydrogenase/genetics/*metabolism ; Iron-Sulfur Proteins/antagonists &amp; inhibitors/genetics/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/antagonists &amp; inhibitors/*biosynthesis/genetics/metabolism ; Protein Binding/physiology ; RNA, Small Interfering ; Succinate Dehydrogenase/*biosynthesis/genetics ; }, abstract = {Iron-sulfur proteins play an essential role in many biologic processes. Hence, understanding their assembly is an important goal. In Escherichia coli, the protein IscA is a product of the isc (iron-sulfur cluster) operon and functions in the iron-sulfur cluster assembly pathway in this organism. IscA is conserved in evolution, but its function in mammalian cells is not known. Here, we provide evidence for a role for a human homologue of IscA, named IscA1, in iron-sulfur protein biogenesis. We observe that small interfering RNA knockdown of IscA1 in HeLa cells leads to decreased activity of two mitochondrial iron-sulfur enzymes, succinate dehydrogenase and mitochondrial aconitase, as well as a cytosolic iron-sulfur enzyme, cytosolic aconitase. IscA1 is observed both in cytosolic and mitochondrial fractions. We find that IscA1 interacts with IOP1 (iron-only hydrogenase-like protein 1)/NARFL (nuclear prelamin A recognition factor-like), a cytosolic protein that plays a role in the cytosolic iron-sulfur protein assembly pathway. We therefore propose that human IscA1 plays an important role in both mitochondrial and cytosolic iron-sulfur cluster biogenesis, and a notable component of the latter is the interaction between IscA1 and IOP1.}, }
@article {pmid19860891, year = {2009}, author = {Chatterjee, HJ and Ho, SY and Barnes, I and Groves, C}, title = {Estimating the phylogeny and divergence times of primates using a supermatrix approach.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {259}, pmid = {19860891}, issn = {1471-2148}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; Humans ; Mitochondria/genetics ; *Phylogeny ; Primates/*classification/*genetics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {BACKGROUND: The primates are among the most broadly studied mammalian orders, with the published literature containing extensive analyses of their behavior, physiology, genetics and ecology. The importance of this group in medical and biological research is well appreciated, and explains the numerous molecular phylogenies that have been proposed for most primate families and genera. Composite estimates for the entire order have been infrequently attempted, with the last phylogenetic reconstruction spanning the full range of primate evolutionary relationships having been conducted over a decade ago.<br><br>RESULTS: To estimate the structure and tempo of primate evolutionary history, we employed Bayesian phylogenetic methods to analyze data supermatrices comprising 7 mitochondrial genes (6,138 nucleotides) from 219 species across 67 genera and 3 nuclear genes (2,157 nucleotides) from 26 genera. Many taxa were only partially represented, with an average of 3.95 and 5.43 mitochondrial genes per species and per genus, respectively, and 2.23 nuclear genes per genus. Our analyses of mitochondrial DNA place Tarsiiformes as the sister group of Strepsirrhini. Within Haplorrhini, we find support for the primary divergence of Pitheciidae in Platyrrhini, and our results suggest a sister grouping of African and non-African colobines within Colobinae and of Cercopithecini and Papionini within Cercopthecinae. Date estimates for nodes within each family and genus are presented, with estimates for key splits including: Strepsirrhini-Haplorrhini 64 million years ago (MYA), Lemuriformes-Lorisiformes 52 MYA, Platyrrhini-Catarrhini 43 MYA and Cercopithecoidea-Hominoidea 29 MYA.<br><br>CONCLUSION: We present an up-to-date, comprehensive estimate of the structure and tempo of primate evolutionary history. Although considerable gaps remain in our knowledge of the primate phylogeny, increased data sampling, particularly from nuclear loci, will be able to provide further resolution.}, }
@article {pmid19860724, year = {2010}, author = {Agnati, LF and Guidolin, D and Baluska, F and Leo, G and Barlow, PW and Carone, C and Genedani, S}, title = {A new hypothesis of pathogenesis based on the divorce between mitochondria and their host cells: possible relevance for Alzheimer's disease.}, journal = {Current Alzheimer research}, volume = {7}, number = {4}, pages = {307-322}, doi = {10.2174/156720510791162395}, pmid = {19860724}, issn = {1875-5828}, mesh = {Alzheimer Disease/*etiology/genetics/*pathology ; Animals ; Cell Communication/genetics/*physiology ; Coculture Techniques ; Humans ; Mitochondria/genetics/*metabolism/*pathology ; *Models, Neurological ; Symbiosis/physiology ; }, abstract = {On the basis of not only the endosymbiotic theory of eukaryotic cell organization and evolution but also of observations of transcellular communication via Tunneling NanoTubes (TNTs), the hypothesis is put forward that when mitochondria, which were once independently living prokaryote-like organisms, are subjected to detrimental genetic, toxic, or environmental conditions, including age-related endogenous factors, they can regress towards their original independent state. At that point, they can become potentially pathogenic intruders within their eukaryotic host cell. Because of the protoplasmic disequilibrium caused by an altered, or mutated, mitochondral population, certain host cells with a minimal capacity for self-renewal, such as dopaminergic neurons, risk a loss of function and degenerate. It is also proposed that altered mitochondria, as well as their mutated mtDNA, can migrate, via TNTs, into adjacent cells. In this way, neurodegenerative states are propagated between cells (glia and/or neurons) of the Central Nervous System (CNS) and that this leads to conditions such as Alzheimer's and Parkinson's disease. This proposal finds indirect support from observations on rotenone-poisoned glioblastoma cells which have been co-cultured with non-poisoned cells. Immunocytochemical techniques revealed that mitochondria, moving along the TNTs, migrated from the poisoned cells towards the healthy cells. It has also been demonstrated by means of immunocytochemistry that, in glioblastoma cell cultures, Amyloid Precursor Protein (APP) is present in TNTs, hence it may migrate from one cell to neighbouring cells. This datum may be of high relevance for a better understanding of Alzheimer's Disease (AD) since molecular, cellular, and animal model studies have revealed that the formation of amyloid beta (Abeta) and other derivatives of the APP are key pathogenic factors in AD, causing mitochondrial dysfunction, free radical generation, oxidative damage, and inflammation. Furthermore, the present data demonstrate the presence of alpha-synuclein (alpha-syn) within TNTs, hence a similar pathogenic mechanism to the one surmised for AD, but centred on alpha-syn rather than on Abeta, may play a role in Parkinson's Disease (PD). As a matter of fact, alpha-syn can enter mitochondria and interact with complex I causing respiratory deficiency and increased oxygen free radical production. In agreement with this view, it has been demonstrated that, in comparison with normal subjects, PD patients show a significant accumulation of alpha-syn at Substantia Nigra and Striatal level, predominantly associated with the inner mitochondrial membrane,. These observations suggest that potentially neuropathogenic proteins, such as Abeta and alpha-syn, can not only diffuse via the extracellular space but also move from cell to cell also via TNTs where they can cause mitochondrial damage and cell degeneration. A mathematical model (see Appendix) is proposed to simulate the pathogenic consequences of the migration of altered mitochondria and/or of their mtDNA via TNTs. The results of the present simulation is compatible with the proposal that mutated mitochondrial agents behave as though they were infectious particles migrating through a continuum of interconnected cells.}, }
@article {pmid19860418, year = {2009}, author = {Laville, E and Sayd, T and Morzel, M and Blinet, S and Chambon, C and Lepetit, J and Renand, G and Hocquette, JF}, title = {Proteome changes during meat aging in tough and tender beef suggest the importance of apoptosis and protein solubility for beef aging and tenderization.}, journal = {Journal of agricultural and food chemistry}, volume = {57}, number = {22}, pages = {10755-10764}, doi = {10.1021/jf901949r}, pmid = {19860418}, issn = {1520-5118}, mesh = {Animals ; *Apoptosis ; Cattle ; Electrophoresis, Gel, Two-Dimensional ; Food Technology ; Male ; Meat/*analysis ; Mitochondria/chemistry/ultrastructure ; Muscle Proteins/*analysis ; Muscle, Skeletal/*chemistry/ultrastructure ; Postmortem Changes ; Shear Strength ; Solubility ; Time Factors ; }, abstract = {Within a population of Charolais young bulls, two extreme groups of longissimus thoracis muscle samples, classified according to Warner-Bratzler shear force (WBSF) of 55 degrees C grilled meat, were analyzed by 2D-electrophoresis. Muscle analyses were performed on 4 bulls of the "tender" group (WBSF=27.7+/-4.8 N) and 4 bulls of the "tough" group (WBSF=41.2+/-6.1 N), at 3 post-mortem times: D0, samples taken within 10 min post-mortem; D5 and D21, samples kept at 4 degrees C under vacuum during 5 and 21 days. Proteins of muscle samples were separated in two fractions based on protein solubility in Tris buffer: "soluble" and "insoluble". Proteins of both fractions were separated by 2D-electrophoresis. Evolution of spots during the 3 post-mortem times was analyzed by hierarchical classification (HCA). Three clusters of proteins presenting similar evolution profiles provided accurate classification of post-mortem times and showed the translocation of some chaperone proteins and glycolytic enzymes from the soluble fraction to the insoluble fraction between D0 and D5. Cellular structure dismantlement and proteolysis was observed at D21. Effect of group ("tender" vs "tough") on spot intensities was tested by ANOVA. At D0, higher quantity of proteins of the inner and outer membrane of mitochondria was found in the tender group suggesting a more extensive degradation of mitochondria that may be related to the apoptotic process.}, }
@article {pmid19859730, year = {2009}, author = {Ito-Inaba, Y and Hida, Y and Inaba, T}, title = {What is critical for plant thermogenesis? Differences in mitochondrial activity and protein expression between thermogenic and non-thermogenic skunk cabbages.}, journal = {Planta}, volume = {231}, number = {1}, pages = {121-130}, pmid = {19859730}, issn = {1432-2048}, mesh = {Amino Acid Sequence ; Araceae/cytology/enzymology/genetics/*physiology ; Cell Respiration ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Ion Channels/chemistry/genetics/metabolism ; Mitochondria/enzymology/*metabolism ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Organ Specificity/genetics ; Oxidoreductases/chemistry/genetics/metabolism ; Phylogeny ; Plant Proteins/chemistry/genetics/*metabolism ; Protein Isoforms/chemistry/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Sequence Alignment ; Temperature ; Uncoupling Protein 1 ; }, abstract = {Thermogenesis during the blooming of inflorescence is found in several but not all aroids. To understand what is critical for thermogenesis, we investigated the difference between thermogenic and non-thermogenic skunk cabbages (Symplocarpus renifolius and Lysichiton camtschatcensis), which are closely related in morphology and phylogeny. Critical parameters of mitochondrial biogenesis, including density, respiratory activity, and protein expression were compared between these two species. Mitochondrial density, respiratory activity, and the amount of alternative oxidase (AOX) in L. camtschatcensis spadix mitochondria were lower than in S. renifolius spadix mitochondria, while the level of uncoupling protein (UCP) was higher. AOX and UCP mRNAs in L. camtschatcensis were constitutively expressed in various tissues, such as the spadix, the spathe, the stalk, and the leaves. cDNA encoding two putative thermogenic proteins, AOX and UCP were isolated from L. camtschatcensis, and their primary structure was analyzed by multiple alignment and phylogenetic tree reconstruction. AOX and UCP protein of two the skunk cabbage species are closely related in structure, compared with other isoforms in thermogenic plants. Our results suggest that mitochondrial density, respiratory activity, and protein expression, rather than the primary structure of AOX or UCP proteins, may play critical roles in thermogenesis in plants.}, }
@article {pmid19858488, year = {2009}, author = {Polianskyte, Z and Peitsaro, N and Dapkunas, A and Liobikas, J and Soliymani, R and Lalowski, M and Speer, O and Seitsonen, J and Butcher, S and Cereghetti, GM and Linder, MD and Merckel, M and Thompson, J and Eriksson, O}, title = {LACTB is a filament-forming protein localized in mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {45}, pages = {18960-18965}, pmid = {19858488}, issn = {1091-6490}, mesh = {Amino Acid Sequence ; Animals ; Chromatography, Liquid ; Electrophoresis, Polyacrylamide Gel ; HeLa Cells ; Humans ; Immunoblotting ; Male ; Mass Spectrometry ; Membrane Proteins/*genetics/*metabolism ; Microscopy, Electron, Transmission ; Microscopy, Fluorescence ; Mitochondria/*metabolism ; Mitochondrial Proteins/*genetics/*metabolism ; *Models, Molecular ; Molecular Sequence Data ; Penicillin-Binding Proteins/*metabolism ; Plasmids/genetics ; Polymers/metabolism ; Rats ; Rats, Wistar ; beta-Lactamases/*genetics/*metabolism ; }, abstract = {LACTB is a mammalian active-site serine protein that has evolved from a bacterial penicillin-binding protein. Penicillin-binding proteins are involved in the metabolism of peptidoglycan, the major bacterial cell wall constituent, implying that LACTB has been endowed with novel biochemical properties during eukaryote evolution. Here we demonstrate that LACTB is localized in the mitochondrial intermembrane space, where it is polymerized into stable filaments with a length extending more than a hundred nanometers. We infer that LACTB, through polymerization, promotes intramitochondrial membrane organization and micro-compartmentalization. These findings have implications for our understanding of mitochondrial evolution and function.}, }
@article {pmid19857160, year = {2010}, author = {Duncan, WP and da Costa, OT and Sakuragui, MM and Fernandes, MN}, title = {Functional morphology of the gill in amazonian freshwater stingrays (chondrichthyes: potamotrygonidae): implications for adaptation to freshwater.}, journal = {Physiological and biochemical zoology : PBZ}, volume = {83}, number = {1}, pages = {19-32}, doi = {10.1086/605458}, pmid = {19857160}, issn = {1537-5293}, mesh = {Adaptation, Physiological/*physiology ; Animals ; Brazil ; Elasmobranchii/*anatomy &amp; histology/metabolism/physiology ; Epithelial Cells/enzymology/physiology ; Gills/*anatomy &amp; histology/cytology/enzymology/physiology ; Immunohistochemistry ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Mitochondria/enzymology/physiology ; Rivers ; Sodium-Potassium-Exchanging ATPase/physiology ; Water-Electrolyte Balance/physiology ; }, abstract = {The gill morphologies of six species of potamotrygonid freshwater stingrays from the Amazon basin were investigated using light and electron microscopy. Some unique features were found in the potamotrygonid gill: (1) fingerlike protuberances on the gill filament, (2) an Alcian blue/periodic acid-Schiff-positive histochemical reaction for several cell layers in the gill epithelium (except the basal ones), (3) pavement cells with numerous subapical mucous vesicles, (4) very large mucous cells, and (5) follicular Na(+)/K(+)-ATPase-rich (NKA-rich) mitochondria-rich cells (MRCs) in Potamotrygon sp. (known as the cururu ray). The fingerlike protuberances may constitute an additional resistance to water flow, helping to drive water through the lamellae. The secretion of a mucous substance by the pavement cells and mucous cells may help to protect the gills against mechanical injury and pathogens and aid in osmoregulation in the dilute water of the Amazon basin. All MRCs possess enfolded basolateral membranes and have poorly developed or absent tubular systems. NKA-rich MRCs are located high in the basolateral membrane. The cururu ray, which is endemic to the Rio Negro, has follicular NKA-rich MRCs (8-12 cells in cross section) that share the same apical pit in the filament; this may be considered to be an autapomorphy. The combination of these branchial characteristics may have favored tolerance to the freshwater environment during the evolution and diversification of potamotrygonids throughout the Amazon basin.}, }
@article {pmid19847819, year = {2009}, author = {Bodył, A and Mackiewicz, P and Stiller, JW}, title = {Early steps in plastid evolution: current ideas and controversies.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {31}, number = {11}, pages = {1219-1232}, doi = {10.1002/bies.200900073}, pmid = {19847819}, issn = {1521-1878}, mesh = {Arabidopsis/metabolism ; Biological Evolution ; Carbonic Anhydrases/*genetics ; Cell Membrane/metabolism ; Evolution, Molecular ; Glycosylation ; Mitochondria/metabolism ; Models, Biological ; Models, Theoretical ; Peptides/chemistry ; Phosphates/metabolism ; Plastids/*genetics/metabolism ; Protein Processing, Post-Translational ; Protein Transport ; Symbiosis ; }, abstract = {Some nuclear-encoded proteins are imported into higher plant plastids via the endomembrane (EM) system. Compared with multi-protein Toc and Tic translocons required for most plastid protein import, the relatively uncomplicated nature of EM trafficking led to suggestions that it was the original transport mechanism for nuclear-encoded endosymbiont proteins, and critical for the early stages of plastid evolution. Its apparent simplicity disappears, however, when EM transport is considered in light of selective constraints likely encountered during the conversion of stable endosymbionts into fully integrated organelles. From this perspective it is more parsimonious to presume the early evolution of post-translational protein import via simpler, ancestral forms of modern Toc and Tic plastid translocons, with EM trafficking arising later to accommodate glycosylation and/or protein targeting to multiple cellular locations. This hypothesis is supported by both empirical and comparative data, and is consistent with the relative paucity of EM-based transport to modern primary plastids.}, }
@article {pmid19845630, year = {2009}, author = {Bell, PJ}, title = {The viral eukaryogenesis hypothesis: a key role for viruses in the emergence of eukaryotes from a prokaryotic world environment.}, journal = {Annals of the New York Academy of Sciences}, volume = {1178}, number = {}, pages = {91-105}, doi = {10.1111/j.1749-6632.2009.04994.x}, pmid = {19845630}, issn = {1749-6632}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; Cell Nucleus/metabolism ; Cytoplasm/metabolism ; Eukaryotic Cells/cytology ; *Evolution, Molecular ; Meiosis ; Mitochondria/metabolism ; Prokaryotic Cells/cytology ; Viruses/*genetics ; }, abstract = {Understanding how the gulf between prokaryotic and eukaryotic cellular design arose is a major challenge. The viral eukaryogenesis (VE) hypothesis addresses the challenge of eukaryotic origins by suggesting the first eukaryotic cell was a multimember consortium consisting of a viral ancestor of the nucleus, an archaeal ancestor of the eukaryotic cytoplasm, and a bacterial ancestor of the mitochondria. Using only prokaryotes and their viruses, and invoking selective pressures observed in modern organisms, the VE hypothesis can explain the origins of the eukaryotic cell, sex, and meiosis. In the VE hypothesis, a cell wall-less archaeon and an alpha-proteobacterium established a syntrophic relationship, and then a complex DNA virus permanently lysogenized the archaeal syntroph to produce a consortium of three organisms that evolved into the eukaryotic cell. The mechanisms by which the virus replicated, controlled its copy number, and segregated to daughter cells led to the evolution of the asexual mitotic replication cycle and the sexual meiotic replication cycle. The VE hypothesis conceptually unifies prokaryotic and eukaryotic sex into variants of a single process.}, }
@article {pmid19842715, year = {2009}, author = {Atkinson, HJ and Babbitt, PC}, title = {Glutathione transferases are structural and functional outliers in the thioredoxin fold.}, journal = {Biochemistry}, volume = {48}, number = {46}, pages = {11108-11116}, pmid = {19842715}, issn = {1520-4995}, support = {P41 RR-01081/RR/NCRR NIH HHS/United States ; R01 GM60595/GM/NIGMS NIH HHS/United States ; T32GM67547/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Biocatalysis ; Catalytic Domain ; Cytosol/enzymology ; Databases, Protein ; Evolution, Molecular ; Glutathione/chemistry ; Glutathione Transferase/*chemistry/*classification/genetics ; Humans ; Hydrogen Bonding ; Mitochondria/enzymology ; Models, Molecular ; Molecular Sequence Data ; Plants/enzymology ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Static Electricity ; Structural Homology, Protein ; Thioredoxins/*chemistry ; }, abstract = {Glutathione transferases (GSTs) are ubiquitous scavengers of toxic compounds that fall, structurally and functionally, within the thioredoxin fold suprafamily. The fundamental catalytic capability of GSTs is catalysis of the nucleophilic addition or substitution of glutathione at electrophilic centers in a wide range of small electrophilic compounds. While specific GSTs have been studied in detail, little else is known about the structural and functional relationships between different groupings of GSTs. Through a global analysis of sequence and structural similarity, it was determined that variation in the binding of glutathione between the two major subgroups of cytosolic (soluble) GSTs results in a different mode of glutathione activation. Additionally, the convergent features of glutathione binding between cytosolic GSTs and mitochondrial GST kappa are described. The identification of these structural and functional themes helps to illuminate some of the fundamental contributions of the thioredoxin fold to catalysis in the GSTs and clarify how the thioredoxin fold can be modified to enable new functions.}, }
@article {pmid19838755, year = {2009}, author = {McLean, S and Richards, SM and Cover, SL and Brandon, S and Davies, NW and Bryant, JP and Clausen, TP}, title = {Papyriferic acid, an antifeedant triterpene from birch trees, inhibits succinate dehydrogenase from liver mitochondria.}, journal = {Journal of chemical ecology}, volume = {35}, number = {10}, pages = {1252-1261}, pmid = {19838755}, issn = {1573-1561}, mesh = {Animals ; Betula/*chemistry ; Cattle ; Enzyme Inhibitors/isolation &amp; purification/metabolism/*pharmacology ; Glycosides/metabolism ; Malonates/isolation &amp; purification/metabolism/*pharmacology ; Mitochondria, Liver/*drug effects/*enzymology/metabolism ; Rabbits ; Rats ; Succinate Dehydrogenase/*antagonists &amp; inhibitors ; Triterpenes/isolation &amp; purification/metabolism/*pharmacology ; }, abstract = {Papyriferic acid (PA) is a triterpene that is secreted by glands on twigs of the juvenile ontogenetic phase of resin producing tree birches (e.g., Betula neoalaskana, B. pendula) and that deters browsing by mammals such as the snowshoe hare (Lepus americanus). We investigated the pharmacology of PA as a first step in understanding its antifeedant effect. After oral administration to rats, PA and several metabolites were found in feces but not urine, indicating that little was absorbed systemically. Metabolism involved various combinations of hydrolysis of its acetyl and malonyl ester groups, and hydroxylation of the terpene moiety. The presence of a malonyl group suggested a possible interaction with succinate dehydrogenase (SDH), a mitochondrial enzyme known to be competitively inhibited by malonic acid. The effect of PA on the oxidation of succinate by SDH was examined in mitochondrial preparations from livers of ox, rabbit, and rat. In all three species, PA was a potent inhibitor of SDH. Kinetic analysis indicated that, unlike malonate, PA acted by an uncompetitive mechanism, meaning that it binds to the enzyme-substrate complex. The hydrolysis product of PA, betulafolienetriol oxide, was inactive on SDH. Overall, the evidence suggests that PA acts as the intact molecule and interacts at a site other than the succinate binding site, possibly binding to the ubiquinone sites on complex II. Papyriferic acid was potent (K(iEIS) ranged from 25 to 45 microM in the three species) and selective, as malate dehydrogenase was unaffected. Although rigorous proof will require further experiments, we have a plausible mechanism for the antifeedant effect of PA: inhibition of SDH in gastrointestinal cells decreases mitochondrial energy production resulting in a noxious stimulus, 5-HT release, and sensations of nausea and discomfort. There is evidence that the co-evolution of birches and hares over a large and geographically-diverse area in Northern Europe and America has produced marked differences in the formation of PA by birches, and the tolerance of hares to dietary PA. The present findings on the metabolic fate and biochemical effects of PA provide a rational basis for investigating the mechanisms underlying differences among populations of hares in their tolerance of a PA-rich diet.}, }
@article {pmid19835962, year = {2010}, author = {Lin, YC and Lee, FF and Wu, CL and Chen, JC}, title = {Molecular cloning and characterization of a cytosolic manganese superoxide dismutase (cytMnSOD) and mitochondrial manganese superoxide dismutase (mtMnSOD) from the kuruma shrimp Marsupenaeus japonicus.}, journal = {Fish &amp; shellfish immunology}, volume = {28}, number = {1}, pages = {143-150}, doi = {10.1016/j.fsi.2009.10.012}, pmid = {19835962}, issn = {1095-9947}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Cytosol/enzymology ; Gene Expression/genetics/immunology ; Hemocytes/immunology ; Mitochondria/enzymology ; Molecular Sequence Data ; Penaeidae/*genetics/immunology ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Superoxide Dismutase/*genetics ; Vibrio Infections/immunology ; Vibrio alginolyticus/immunology ; }, abstract = {A cytosolic manganese superoxide dismutase (cytMnSOD) gene and a mitochondrial manganese superoxide dismutase (mtMnSOD) gene were cloned from the kuruma shrimp Marsupenaeus japonicus using reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) method. The open reading frame (ORF) of cytMnSOD is 861 bp and encodes a 287 amino acids (aa) protein with a 61 aa leader sequence, whereas the ORF of mtMnSOD is 663 bp and encodes a 221 aa protein with a 21 aa mitochondrial-targeting sequence in the N-terminus. The calculated molecular mass of translated protein of cytMnSOD and mtMnSOD is 31.4 kDa and 24.3 kDa with an estimated pI of 5.62 and 7.27, respectively. The deduced amino acid sequence of cytMnSOD has similarity of 50.2% to that of mtMnSOD. Both cytMnSOD and mtMnSOD contain a manganese superoxide dismutase domain (DVWEHAYY), and four conserved amino acids responsible for binding manganese. Both cytMnSOD and mtMnSOD of M. japonicus were expressed in haemocytes, eyestalk, muscle, intestine, gill, and hepatopancreas. Both cytMnSOD and mtMnSOD transcripts in haemocytes of M. japonicus significantly increased 6 h after injection of Vibrio alginolyticus, and 12 h after injection of beta-glucan, indicating induction of SOD system response in a short time.}, }
@article {pmid19818876, year = {2010}, author = {Lu, J and Qian, Y and Li, Z and Yang, A and Zhu, Y and Li, R and Yang, L and Tang, X and Chen, B and Ding, Y and Li, Y and You, J and Zheng, J and Tao, Z and Zhao, F and Wang, J and Sun, D and Zhao, J and Meng, Y and Guan, MX}, title = {Mitochondrial haplotypes may modulate the phenotypic manifestation of the deafness-associated 12S rRNA 1555A&gt;G mutation.}, journal = {Mitochondrion}, volume = {10}, number = {1}, pages = {69-81}, pmid = {19818876}, issn = {1872-8278}, support = {R01 DC007696-03/DC/NIDCD NIH HHS/United States ; R03 DC004958-03/DC/NIDCD NIH HHS/United States ; R01 DC005230/DC/NIDCD NIH HHS/United States ; R01 DC005230-04/DC/NIDCD NIH HHS/United States ; R01DC07696/DC/NIDCD NIH HHS/United States ; R01DC05230/DC/NIDCD NIH HHS/United States ; R01 DC007696-02S1/DC/NIDCD NIH HHS/United States ; R01 DC007696-04/DC/NIDCD NIH HHS/United States ; R01 DC007696/DC/NIDCD NIH HHS/United States ; R01 DC005230-05/DC/NIDCD NIH HHS/United States ; R01 DC007696-01A2/DC/NIDCD NIH HHS/United States ; R03 DC004958/DC/NIDCD NIH HHS/United States ; }, mesh = {Adolescent ; Aminoglycosides/adverse effects ; Base Sequence ; Child ; Child, Preschool ; China ; DNA, Mitochondrial/*genetics ; Deafness/chemically induced/*genetics/*physiopathology ; Haplotypes/*genetics ; Hearing Loss/chemically induced/genetics/physiopathology ; Humans ; Mitochondria/genetics ; Molecular Sequence Data ; *Mutation ; Phenotype ; Phylogeny ; RNA, Ribosomal/*genetics ; }, abstract = {Mitochondrial 12S rRNA 1555A>G mutation is one of the important causes of aminoglycoside-induced and nonsyndromic deafness. Our previous investigations showed that the A1555G mutation was a primary factor underlying the development of deafness but was insufficient to produce deafness phenotype. However, it has been proposed that mitochondrial haplotypes modulate the phenotypic manifestation of the 1555A>G mutation. Here, we performed systematic and extended mutational screening of 12S rRNA gene in a cohort of 1742 hearing-impaired Han Chinese pediatric subjects from Zhejiang Province, China. Among these, 69 subjects with aminoglycoside-induced and nonsyndromic deafness harbored the homoplasmic 1555A>G mutation. These translated to a frequency of approximately 3.96% for the 1555A>G mutation in this hearing-impaired population. Clinical and genetic characterizations of 69 Chinese families carrying the 1555A>G mutation exhibited a wide range of penetrance and expressivity of hearing impairment. The average penetrances of deafness were 29.5% and 17.6%, respectively, when aminoglycoside-induced hearing loss was included or excluded. Furthermore, the average age-of-onset for deafness without aminoglycoside exposure ranged from 5 and 30years old, with the average of 14.5years. Their mitochondrial genomes exhibited distinct sets of polymorphisms belonging to ten Eastern Asian haplogroups A, B, C, D, F, G, M, N, R and Y, respectively. These indicated that the 1555A>G mutation occurred through recurrent origins and founder events. The haplogroup D accounted for 40.6% of the patient's mtDNA samples but only 25.8% of the Chinese control mtDNA samples. Strikingly, these Chinese families carrying mitochondrial haplogroup B exhibited higher penetrance and expressivity of hearing loss. In addition, the mitochondrial haplogroup specific variants: 15927G>A of haplogroup B5b, 12338T>C of haplogroup F2, 7444G>A of haplogroup B4, 5802T>C, 10454T>C, 12224C>T and 11696G>A of D4 haplogroup, 5821G>A of haplogroup C, 14693A>G of haplogroups Y2 and F, and 15908T>C of Y2 may enhance the penetrace of hearing loss in these Chinese families. Moreover, the absence of mutation in nuclear modifier gene TRMU suggested that TRMU may not be a modifier for the phenotypic expression of the 1555A>G mutation in these Chinese families. These observations suggested that mitochondrial haplotypes modulate the variable penetrance and expressivity of deafness among these Chinese families.}, }
@article {pmid19809492, year = {2009}, author = {Tomaska, L and Nosek, J and Kramara, J and Griffith, JD}, title = {Telomeric circles: universal players in telomere maintenance?.}, journal = {Nature structural &amp; molecular biology}, volume = {16}, number = {10}, pages = {1010-1015}, pmid = {19809492}, issn = {1545-9985}, support = {55005622/HHMI/Howard Hughes Medical Institute/United States ; R01 ES013773/ES/NIEHS NIH HHS/United States ; GM31819/GM/NIGMS NIH HHS/United States ; R03 TW005654/TW/FIC NIH HHS/United States ; R01 GM031819/GM/NIGMS NIH HHS/United States ; 2-R03-TW005654-04A1/TW/FIC NIH HHS/United States ; ES13773/ES/NIEHS NIH HHS/United States ; P01 CA019014/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Candida/*genetics ; Cell Nucleus/metabolism ; Chromosomes/ultrastructure ; DNA, Fungal/genetics/physiology ; Gene Deletion ; Genetic Techniques ; Genome ; Genome, Fungal ; Mitochondria/*metabolism ; Models, Biological ; Models, Genetic ; Recombination, Genetic ; Retroelements ; Telomere/genetics/*ultrastructure ; }, abstract = {To maintain linear DNA genomes, organisms have evolved numerous means of solving problems associated with DNA ends (telomeres), including telomere-associated retrotransposons, palindromes, hairpins, covalently bound proteins and the addition of arrays of simple DNA repeats. Telomeric arrays can be maintained through various mechanisms such as telomerase activity or recombination. The recombination-dependent maintenance pathways may include telomeric loops (t-loops) and telomeric circles (t-circles). The potential involvement of t-circles in telomere maintenance was first proposed for linear mitochondrial genomes. The occurrence of t-circles in a wide range of organisms, spanning yeasts, plants and animals, suggests the involvement of t-circles in many phenomena including the alternative-lengthening of telomeres (ALT) pathway and telomere rapid deletion (TRD). In this Perspective, we summarize these findings and discuss how t-circles may be related to t-loops and how t-circles may have initiated the evolution of telomeres.}, }
@article {pmid19806442, year = {2009}, author = {Atamna, H}, title = {Amino acids variations in amyloid-beta peptides, mitochondrial dysfunction, and new therapies for Alzheimer's disease.}, journal = {Journal of bioenergetics and biomembranes}, volume = {41}, number = {5}, pages = {457-464}, pmid = {19806442}, issn = {1573-6881}, mesh = {Alzheimer Disease/etiology/*metabolism/therapy ; Amino Acid Sequence ; Amyloid beta-Peptides/*chemistry/genetics/*metabolism ; Animals ; Brain/metabolism ; Electron Transport Complex IV/metabolism ; Genetic Variation ; Heme/metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {Soluble oligomers and/or aggregates of Amyloid-beta (Abeta) are viewed by many as the principal cause for neurodegeneration in Alzheimer's disease (AD). However, the mechanism by which Abeta and its aggregates cause neurodegeneration is not clear. The toxicity of Abeta has been attributed to its hydrophobicity. However, many specific mitochondrial cytopathologies e.g., loss of complex IV, loss of iron homeostasis, or oxidative damage cannot be explained by Abeta's hydrophobicity. In order to understand the role of Abeta in these cytopathologies we hypothesized that Abeta impairs specific metabolic pathways. We focused on heme metabolism because it links iron, mitochondria, and Abeta. We generated experimental evidence showing that Abeta alters heme metabolism in neuronal cells. Furthermore, we demonstrated that Abeta binds to and depletes intracellular regulatory heme (forming an Abeta-heme complex), which provides a strong molecular connection between Abeta and heme metabolism. We showed that heme depletion leads to key cytopathologies identical to those seen in AD including loss of iron homeostasis and loss of mitochondrial complex IV. Abeta-heme exhibits a peroxidase-like catalytic activity, which catalytically accelerates oxidative damage. Interestingly, the amino acids sequence of rodent Abeta (roAbeta) and human Abeta (huAbeta) is identical except for three amino acids within the hydrophilic region, which is also the heme-binding motif that we identified. We found that huAbeta, unlike roAbeta, binds heme tightly and forms a peroxidase. Although, roAbeta and huAbeta equally form fibrils and aggregates, rodents do not develop AD-like neuropathology. These findings led us to propose a new mechanism for mitochondrial dysfunction and huAbeta's neurotoxicity. This mechanism prompted the development of methylene blue (MB), which increased heme synthesis, complex IV, and mitochondrial function. Thus, MB may delay the onset and progression of AD and serve as a lead to develop novel drugs to treat AD.}, }
@article {pmid19805364, year = {2009}, author = {Hao, W and Palmer, JD}, title = {Fine-scale mergers of chloroplast and mitochondrial genes create functional, transcompartmentally chimeric mitochondrial genes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {39}, pages = {16728-16733}, pmid = {19805364}, issn = {1091-6490}, support = {R01 GM070612/GM/NIGMS NIH HHS/United States ; R01-GM-70612/GM/NIGMS NIH HHS/United States ; }, mesh = {Chloroplasts/*genetics/metabolism ; DNA, Mitochondrial/metabolism ; Evolution, Molecular ; Gene Conversion ; Genes, Mitochondrial/*genetics ; Genes, Plant ; Genome, Plant ; Phylogeny ; *Recombination, Genetic ; }, abstract = {The mitochondrial genomes of flowering plants possess a promiscuous proclivity for taking up sequences from the chloroplast genome. All characterized chloroplast integrants exist apart from native mitochondrial genes, and only a few, involving chloroplast tRNA genes that have functionally supplanted their mitochondrial counterparts, appear to be of functional consequence. We developed a novel computational approach to search for homologous recombination (gene conversion) in a large number of sequences and applied it to 22 mitochondrial and chloroplast gene pairs, which last shared common ancestry some 2 billion years ago. We found evidence of recurrent conversion of short patches of mitochondrial genes by chloroplast homologs during angiosperm evolution, but no evidence of gene conversion in the opposite direction. All 9 putative conversion events involve the atp1/atpA gene encoding the alpha subunit of ATP synthase, which is unusually well conserved between the 2 organelles and the only shared gene that is widely sequenced across plant mitochondria. Moreover, all conversions were limited to the 2 regions of greatest nucleotide and amino acid conservation of atp1/atpA. These observations probably reflect constraints operating on both the occurrence and fixation of recombination between ancient homologs. These findings indicate that recombination between anciently related sequences is more frequent than previously appreciated and creates functional mitochondrial genes of chimeric origin. These results also have implications for the widespread use of mitochondrial atp1 in phylogeny reconstruction.}, }
@article {pmid19805190, year = {2009}, author = {Stonebloom, S and Burch-Smith, T and Kim, I and Meinke, D and Mindrinos, M and Zambryski, P}, title = {Loss of the plant DEAD-box protein ISE1 leads to defective mitochondria and increased cell-to-cell transport via plasmodesmata.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {40}, pages = {17229-17234}, pmid = {19805190}, issn = {1091-6490}, support = {R56 GM045244/GM/NIGMS NIH HHS/United States ; GM45244/GM/NIGMS NIH HHS/United States ; F32 HG000205/HG/NHGRI NIH HHS/United States ; R01 GM045244/GM/NIGMS NIH HHS/United States ; HG-000205/HG/NHGRI NIH HHS/United States ; P01 HG000205/HG/NHGRI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/metabolism ; Biological Transport ; DEAD-box RNA Helicases/classification/genetics/*metabolism ; Flowers/genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Green Fluorescent Proteins/genetics/metabolism ; Microscopy, Fluorescence ; Mitochondria/*metabolism ; Molecular Sequence Data ; Mutation ; Phylogeny ; Plant Leaves/genetics/metabolism ; Plant Proteins/classification/genetics/*metabolism ; Plants, Genetically Modified ; Plasmodesmata/*metabolism ; Protons ; Reactive Oxygen Species/metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Seeds/genetics/metabolism ; Sequence Homology, Amino Acid ; Nicotiana/genetics/metabolism ; }, abstract = {Plants have intercellular channels, plasmodesmata (PD), that span the cell wall to enable cell-to-cell transport of micro- and macromolecules. We identified an Arabidopsis thaliana embryo lethal mutant increased size exclusion limit 1 (ise1) that results in increased PD-mediated transport of fluorescent tracers. The ise1 mutants have a higher frequency of branched and twinned PD than wild-type embryos. Silencing of ISE1 in mature Nicotiana benthamiana leaves also leads to increased PD transport, as monitored by intercellular movement of a GFP fusion to the tobacco mosaic virus movement protein. ISE1 encodes a putative plant-specific DEAD-box RNA helicase that localizes specifically to mitochondria. The N-terminal 100 aa of ISE1 specify mitochondrial targeting. Mitochondrial metabolism is compromised severely in ise1 mutant embryos, because their mitochondrial proton gradient is disrupted and reactive oxygen species production is increased. Although mitochondria are essential for numerous cell-autonomous functions, the present studies demonstrate that mitochondrial function also regulates the critical cell non-cell-autonomous function of PD.}, }
@article {pmid19801822, year = {2009}, author = {Handa, S and Maruyama, N and Ishigami, A}, title = {Over-expression of Senescence Marker Protein-30 decreases reactive oxygen species in human hepatic carcinoma Hep G2 cells.}, journal = {Biological &amp; pharmaceutical bulletin}, volume = {32}, number = {10}, pages = {1645-1648}, doi = {10.1248/bpb.32.1645}, pmid = {19801822}, issn = {1347-5215}, mesh = {Aging/metabolism ; Animals ; Antioxidants/*metabolism ; Ascorbic Acid/biosynthesis ; Calcium-Binding Proteins/genetics/*metabolism ; Carboxylic Ester Hydrolases/genetics/metabolism ; Carcinoma, Hepatocellular/metabolism ; *Gene Expression ; Glutathione/metabolism ; Hep G2 Cells/metabolism ; Humans ; Intracellular Signaling Peptides and Proteins/genetics/*metabolism ; *Lipid Peroxidation ; Liver/*enzymology ; Liver Neoplasms/metabolism ; Mice ; Mice, Knockout ; Mitochondria/metabolism ; *Oxidative Stress ; Reactive Oxygen Species/*metabolism ; Superoxide Dismutase/metabolism ; Transfection ; }, abstract = {Senescence Marker Protein-30 (SMP30) is an androgen-independent factor that decreases with aging. We recently characterized SMP30 as a gluconolactonase (GNL) involved in the biosynthetic pathway of vitamin C and established that SMP30 knockout mice could not synthesize vitamin C in vivo. Although mice normally synthesize vitamin C, humans are prevented from doing so by mutations that have altered the gluconolactone oxidase gene during evolution. Even the SMP30/GNL present abundantly in the human liver does not synthesize vitamin C in vivo. To clarify the functions of this SMP30/GNL, we transfected the human SMP30/GNL gene into the human liver carcinoma cell line, Hep G2. The resulting Hep G2/SMP30 cells expressed approximately 10.9-fold more SMP30/GNL than Hep G2/pcDNA3 mock-transfected control cells. Examination of SMP30/GNL's impact on the state of oxidative stress in these cells revealed that formation of the reactive oxygen species (ROS) of mitochondrial and post-mitochondrial fractions from Hep G2/SMP30 cells decreased by a significant 24.0% and 18.1%, respectively, compared to those from Hep G2/pcDNA3 cells. Lipid peroxidation levels in Hep G2/SMP30 cells similarly decreased. Moreover, levels of the antioxidants superoxide dismutase (SOD) and glutathione (GSH) in Hep G2/SMP30 cells were a significant 42.6% and 62.4% lower than those in Hep G2/pcDNA3 cells, respectively. Thus, over-expression of SMP30/GNL in Hep G2 cells contributed to a decrease of ROS formation accompanied by decreases of lipid peroxidation, SOD activity and GSH levels.}, }
@article {pmid19778425, year = {2009}, author = {Jacob, JE and Vanholme, B and Van Leeuwen, T and Gheysen, G}, title = {A unique genetic code change in the mitochondrial genome of the parasitic nematode Radopholus similis.}, journal = {BMC research notes}, volume = {2}, number = {}, pages = {192}, pmid = {19778425}, issn = {1756-0500}, abstract = {BACKGROUND: Mitochondria (mt) contain their own autonomously replicating DNA, constituted as a small circular genome encoding essential subunits of the respiratory chain. Mt DNA is characterized by a genetic code which differs from the standard one. Interestingly, the mt genome of nematodes share some peculiar features, such as small transfer RNAs, truncated ribosomal RNAs and - in the class of Chromadorean nematodes - unidirectional transcription.<br><br>FINDINGS: We present the complete mt genomic sequence (16,791 bp) of the plant-parasitic nematode Radopholus similis (class Chromadorea). Although it has a gene content similar to most other nematodes, many idiosyncrasies characterize the extremely AT-rich mt genome of R. similis (85.4% AT). The secondary structure of the large (16S) rRNA is further reduced, the gene order is unique, the large non-coding region contains two large repeats, and most interestingly, the UAA codon is reassigned from translation termination to tyrosine. In addition, 7 out of 12 protein-coding genes lack a canonical stop codon and analysis of transcriptional data showed the absence of polyadenylation. Northern blot analysis confirmed that only one strand is transcribed and processed. Furthermore, using nucleotide content bias methods, regions for the origin of replication are suggested.<br><br>CONCLUSION: The extraordinary mt genome of R. similis with its unique genetic code appears to contain exceptional features correlated to DNA decoding. Therefore the genome may provide an incentive to further elucidate these barely understood processes in nematodes. This comprehension may eventually lead to parasitic nematode-specific control targets as healthy mitochondria are imperative for organism survival. In addition, the presented genome is an interesting exceptional event in genetic code evolution.}, }
@article {pmid19775366, year = {2009}, author = {Rodust, PM and Stockfleth, E and Ulrich, C and Leverkus, M and Eberle, J}, title = {UV-induced squamous cell carcinoma--a role for antiapoptotic signalling pathways.}, journal = {The British journal of dermatology}, volume = {161 Suppl 3}, number = {}, pages = {107-115}, doi = {10.1111/j.1365-2133.2009.09458.x}, pmid = {19775366}, issn = {1365-2133}, mesh = {*Apoptosis/physiology/radiation effects ; Carcinoma, Basal Cell/etiology/genetics/pathology ; Carcinoma, Squamous Cell/*etiology/genetics/pathology ; *DNA Damage/genetics ; Humans ; Mitochondria/genetics/pathology/radiation effects ; Neoplasms, Radiation-Induced/etiology/genetics/pathology ; Signal Transduction/genetics/*radiation effects ; Skin Neoplasms/etiology/genetics/pathology ; TNF-Related Apoptosis-Inducing Ligand/metabolism ; Ultraviolet Rays/*adverse effects ; }, abstract = {The incidence of nonmelanoma skin cancer including squamous cell carcinoma (SCC) and basal cell carcinoma (BCC) has dramatically increased in the last decades, and chronic sun exposure was identified as a main etiologic agent. UV radiation may produce DNA damage either directly or through reactive oxygen species (ROS). As mutations caused by UV may lead to skin cancer due to oncogene activation and tumor suppressor gene inactivation, efficient safeguard mechanisms have been developed during evolution. These enclose induction of apoptosis and formation sunburn cells aiming at the removal of premalignant cells. The keratinocyte apoptotic machinery in response to UV consists of both intrinsic/mitochondrial and extrinsic/death receptor-mediated cell-death pathways, which are particularly regulated by mitogen-activated protein kinases (MAPKs, JNK and p38) and the tumor-suppressor protein p53. For development of skin cancer, it appears that critical steps in apoptosis control are dysregulated leading to resistance both to death ligand-mediated and intrinsic proapoptotic pathways. These particularly include inactivation of p53, as well as activation of EGFR, COX-2 and MAPKs, which result in specific regulation of Bcl-2 proteins, death ligands and death receptors. The final unravelling of apoptosis regulation in epithelial skin cancer may allow the development of new targeted therapeutic strategies.}, }
@article {pmid19768753, year = {2009}, author = {Jaroszewska, M and Dabrowski, K}, title = {The nature of exocytosis in the yolk trophoblastic layer of silver arowana (Osteoglossum bicirrhosum) juvenile, the representative of ancient teleost fishes.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {292}, number = {11}, pages = {1745-1755}, doi = {10.1002/ar.20996}, pmid = {19768753}, issn = {1932-8494}, mesh = {Animals ; Biological Evolution ; Bodily Secretions/physiology ; Embryo, Nonmammalian/cytology/*physiology ; Embryonic Development/physiology ; Energy Metabolism/physiology ; Exocytosis/*physiology ; Fishes/*embryology/physiology ; Hydrolysis ; Lipoproteins/metabolism ; Microvilli/physiology/ultrastructure ; Mitochondria/physiology/ultrastructure ; Phylogeny ; Species Specificity ; Trophoblasts/cytology/*metabolism ; Yolk Sac/cytology/*metabolism ; }, abstract = {We have chosen the silver arowana (Osteoglossum bicirrhosum), a representative of the most ancient teleost family Osteoglossidae, to address the question of yolk nutrients utilization. Silver arowana have particularly large eggs (1-1.5 cm of diameter) and a unique morphology of the yolk. We present evidence that the yolk cytoplasmic zone (ycz) in the "yolksac juveniles" is a very complex structure involved in sequential processes of yolk hydrolysis, lipoprotein particles synthesis, their transport, and exocytosis. Vacuoles filled with yolk granules in different stages of digestion move from the vitellolysis zone through the ycz to be emptied into the microvillar interspace in the process of exocytosis. The area of the ycz with the abundance of the mitochondria must play an important role in providing energy for both the transport of vacuoles and the release of their contents. Therefore, we postulate that the function of yolk syncytial layer (ysl) as the "early embryonic patterning center" transforms in fish larvae or yolksac juveniles into a predominantly specialized role as the yolk trophoblastic layer (ytl) involved in yolk nutrients utilization. In addition to discovering the mechanism of transformation of the ysl function into ytl function, we suggest that the machinery involved in nutrient mobilization and exocytosis in yolk of arowana yolksac juveniles can be very attractive system for studies of regulatory processes in almost all secretory pathways in animal cells.}, }
@article {pmid19767615, year = {2009}, author = {Messmer, M and Pütz, J and Suzuki, T and Suzuki, T and Sauter, C and Sissler, M and Catherine, F}, title = {Tertiary network in mammalian mitochondrial tRNAAsp revealed by solution probing and phylogeny.}, journal = {Nucleic acids research}, volume = {37}, number = {20}, pages = {6881-6895}, pmid = {19767615}, issn = {1362-4962}, mesh = {Base Sequence ; Databases, Nucleic Acid ; Humans ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA/*chemistry/*metabolism ; RNA, Mitochondrial ; RNA, Transfer, Asp/*chemistry/*metabolism ; Transcription, Genetic ; }, abstract = {Primary and secondary structures of mammalian mitochondrial (mt) tRNAs are divergent from canonical tRNA structures due to highly skewed nucleotide content and large size variability of D- and T-loops. The nonconservation of nucleotides involved in the expected network of tertiary interactions calls into question the rules governing a functional L-shaped three-dimensional (3D) structure. Here, we report the solution structure of human mt-tRNA(Asp) in its native post-transcriptionally modified form and as an in vitro transcript. Probing performed with nuclease S1, ribonuclease V1, dimethylsulfate, diethylpyrocarbonate and lead, revealed several secondary structures for the in vitro transcribed mt-tRNA(Asp) including predominantly the cloverleaf. On the contrary, the native tRNA(Asp) folds into a single cloverleaf structure, highlighting the contribution of the four newly identified post-transcriptional modifications to correct folding. Reactivities of nucleotides and phosphodiester bonds in the native tRNA favor existence of a full set of six classical tertiary interactions between the D-domain and the variable region, forming the core of the 3D structure. Reactivities of D- and T-loop nucleotides support an absence of interactions between these domains. According to multiple sequence alignments and search for conservation of Leontis-Westhof interactions, the tertiary network core building rules apply to all tRNA(Asp) from mammalian mitochondria.}, }
@article {pmid19767348, year = {2010}, author = {Gawryluk, RM and Gray, MW}, title = {An ancient fission of mitochondrial Cox1.}, journal = {Molecular biology and evolution}, volume = {27}, number = {1}, pages = {7-10}, doi = {10.1093/molbev/msp223}, pmid = {19767348}, issn = {1537-1719}, support = {MOP-4124//Canadian Institutes of Health Research/Canada ; }, mesh = {Acanthamoeba castellanii/enzymology/*genetics ; Amino Acid Sequence ; Electron Transport Complex IV/*genetics ; Eukaryota/genetics ; Evolution, Molecular ; *Genes, Mitochondrial ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Sequence Alignment ; }, abstract = {Many genes inherited from the alpha-proteobacterial ancestor of mitochondria have undergone evolutionary transfer to the nuclear genome in eukaryotes. In some rare cases, genes have been functionally transferred in pieces, resulting in split proteins that presumably interact in trans within mitochondria, fulfilling the same role as the ancestral, intact protein. We describe a nucleus-encoded mitochondrial protein (here named Cox1-c) in the amoeboid protist Acanthamoeba castellanii that is homologous to the C-terminal portion of conventional mitochondrial Cox1, whereas the corresponding portion of the mitochondrion-encoded A. castellanii Cox1 is absent. Bioinformatics searches retrieved nucleus-encoded Cox1-c homologs in most major eukaryotic supergroups; in these cases, also, the mitochondrion-encoded Cox1 lacks the corresponding C-terminal motif. These data constitute the first report of functional relocation of a portion of cox1 to the nucleus. This transfer event was likely ancient, with the resulting nuclear cox1-c being differentially activated across the eukaryotic domain.}, }
@article {pmid19766093, year = {2010}, author = {Luévano-Martínez, LA and Moyano, E and de Lacoba, MG and Rial, E and Uribe-Carvajal, S}, title = {Identification of the mitochondrial carrier that provides Yarrowia lipolytica with a fatty acid-induced and nucleotide-sensitive uncoupling protein-like activity.}, journal = {Biochimica et biophysica acta}, volume = {1797}, number = {1}, pages = {81-88}, doi = {10.1016/j.bbabio.2009.09.003}, pmid = {19766093}, issn = {0006-3002}, mesh = {Biological Transport ; Fatty Acids/pharmacology ; Guanosine Diphosphate/metabolism ; Ion Channels/metabolism ; Membrane Potentials/physiology ; Mitochondria/*metabolism/physiology ; Mitochondrial Proteins/metabolism ; *Oxygen Consumption ; Phylogeny ; Succinates/metabolism ; Sulfates/metabolism ; Uncoupling Protein 1 ; Vancomycin/pharmacology ; Yarrowia/*metabolism ; }, abstract = {Uncoupling proteins (UCPs) are mitochondrial carriers distributed throughout the eukaryotic kingdoms. While genes coding for UCPs have been identified in plants and animals, evidences for the presence of UCPs in fungi and protozoa are only functional. Here, it is reported that in the yeast Yarrowia lipolytica there is a fatty acid-promoted and GDP-sensitive uncoupling activity indicating the presence of a UCP. The uncoupling activity is higher in the stationary phase than in the mid-log growth phase. The in silico search on the Y. lipolytica genome led to the selection of two genes with the highest homology to the UCP family, XM_503525 and XM_500457. By phylogenetic analysis, XP_503525 was predicted to be an oxaloacetate carrier while XP_500457 would be a dicarboxylate carrier. Each of these two genes was cloned and heterologously expressed in Saccharomyces cerevisiae and the resulting phenotype was analyzed. The transport activity of the two gene products confirmed the phylogenetic predictions. In addition, only mitochondria isolated from yeasts expressing XP_503525 showed bioenergetic properties characteristic of a UCP: the proton conductance was increased by linoleic acid and inhibited by GDP. It is concluded that the XM_503525 gene from Y. lipolytica encodes for an oxaloacetate carrier although, remarkably, it also displays an uncoupling activity stimulated by fatty acids and inhibited by nucleotides.}, }
@article {pmid19759419, year = {2009}, author = {Liu, L and Xie, R and Yang, C and McKeehan, WL}, title = {Dual function microtubule- and mitochondria-associated proteins mediate mitotic cell death.}, journal = {Cellular oncology : the official journal of the International Society for Cellular Oncology}, volume = {31}, number = {5}, pages = {393-405}, doi = {10.3233/CLO-2009-0484}, pmid = {19759419}, issn = {1875-8606}, support = {R01 CA059971-17/CA/NCI NIH HHS/United States ; DK35310/DK/NIDDK NIH HHS/United States ; R01 DK035310/DK/NIDDK NIH HHS/United States ; R01 CA059971/CA/NCI NIH HHS/United States ; CA59971/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Cell Death ; Cell Line ; Chlorocebus aethiops ; Humans ; Microtubule-Associated Proteins/genetics/*metabolism ; Microtubules/*metabolism ; Mitochondria/*metabolism ; *Mitosis ; Protein Isoforms/genetics/metabolism ; RNA, Small Interfering/genetics ; }, abstract = {BACKGROUND: Survival and evolution of aneuploid cells after an asymmetric segregation of chromosomes at mitosis may be the common initiating event and underlying cause of the genetic diversity and adaptability of cancers. We hypothesize that mechanisms exist to detect impending aneuploidy and prevent it before completion of an aberrant mitosis.<br><br>METHODS: The distribution of isoforms of C19ORF5, an interactive partner with mitochondria-associated LRPPRC and tumor suppressor RASSF1A, state of spindle microtubules and mitochondrial aggregation was analyzed in synchronized mitotic cells and cells stalled in mitosis after treatment with paclitaxel.<br><br>RESULTS: C19ORF5 distributed broadly across the mitotic spindle and reversibly accumulated during reversible mitotic arrest. Prolonged stabilization of microtubules caused an accumulation of a C19ORF5 product with dual MAP and MtAP properties that caused irreversible aggregation of mitochondria and death of mitotic cells.<br><br>CONCLUSION: Dual function microtubule-associated (MAP) and mitochondria-associated (MtAP) proteins generated by prolonged mitotic arrest trigger mitochondrial-induced mitotic cell death. This is a potential mechanism to prevent minimal survivable aneuploidy resulting from an aberrant cell division and cancers in general at their earliest common origin.}, }
@article {pmid19755136, year = {2010}, author = {Seligmann, H}, title = {Mitochondrial tRNAs as light strand replication origins: similarity between anticodon loops and the loop of the light strand replication origin predicts initiation of DNA replication.}, journal = {Bio Systems}, volume = {99}, number = {2}, pages = {85-93}, doi = {10.1016/j.biosystems.2009.09.003}, pmid = {19755136}, issn = {1872-8324}, mesh = {Animals ; Anticodon/genetics ; Base Composition ; Base Sequence ; DNA Polymerase gamma ; DNA Replication/genetics ; DNA, Mitochondrial/*genetics ; DNA-Directed DNA Polymerase/metabolism ; Genes, Mitochondrial/*genetics ; Genetic Variation ; Humans ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/metabolism ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Primates/classification/genetics ; RNA, Transfer/chemistry/*genetics/metabolism ; Replication Origin/*genetics ; Species Specificity ; }, abstract = {Stem-loop hairpins formed by mitochondrial light strand replication origins (OL) and by heavy strand DNA coding for tRNAs that form OL-like structures initiate mitochondrial replication. The loops are recognized by one of the two active sites of the vertebrate mitochondrial gamma polymerase, which are homologous to the active sites of class II amino-acyl tRNA synthetases. Therefore, the polymerase site recognizing the OL loop could recognize tRNA anticodon loops and sequence similarity between anticodon and OL loops should predict initiation of DNA replication at tRNAs. Strengths of genome-wide deamination gradients starting at tRNA genes estimate extents by which replication starts at that tRNA. Deaminations (A-->G and C-->T) occur proportionally to time spent single stranded by heavy strand DNA during mitochondrial light strand replication. Results show that deamination gradients starting at tRNAs are proportional to sequence similarity between OL and tRNA loops: most for anticodon-, least D-, intermediate for TpsiC-loops, paralleling tRNA synthetase recognition interactions with these tRNA loops. Structural and sequence similarities with regular OLs predict OL function, loop similarity is dominant in most tRNAs. Analyses of sequence similarity and structure independently substantiate that DNA sequences coding for mitochondrial tRNAs sometimes function as alternative OLs. Pathogenic mutations in anticodon loops increase similarity with the human OL loop, non-pathogenic polymorphisms do not. Similarity/homology alignment hypotheses are experimentally testable in this system.}, }
@article {pmid19750009, year = {2009}, author = {Hou, Y and Lin, S}, title = {Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes.}, journal = {PloS one}, volume = {4}, number = {9}, pages = {e6978}, pmid = {19750009}, issn = {1932-6203}, mesh = {Chloroplasts/metabolism ; Dinoflagellida ; Eukaryota/genetics ; Expressed Sequence Tags ; Gene Dosage ; *Genome ; Mitochondria/metabolism ; Models, Genetic ; Phylogeny ; Proteins/genetics ; Regression Analysis ; Sequence Analysis, DNA/methods ; }, abstract = {The ability to predict gene content is highly desirable for characterization of not-yet sequenced genomes like those of dinoflagellates. Using data from completely sequenced and annotated genomes from phylogenetically diverse lineages, we investigated the relationship between gene content and genome size using regression analyses. Distinct relationships between log(10)-transformed protein-coding gene number (Y') versus log(10)-transformed genome size (X', genome size in kbp) were found for eukaryotes and non-eukaryotes. Eukaryotes best fit a logarithmic model, Y' = ln(-46.200+22.678X', whereas non-eukaryotes a linear model, Y' = 0.045+0.977X', both with high significance (p<0.001, R(2)>0.91). Total gene number shows similar trends in both groups to their respective protein coding regressions. The distinct correlations reflect lower and decreasing gene-coding percentages as genome size increases in eukaryotes (82%-1%) compared to higher and relatively stable percentages in prokaryotes and viruses (97%-47%). The eukaryotic regression models project that the smallest dinoflagellate genome (3x10(6) kbp) contains 38,188 protein-coding (40,086 total) genes and the largest (245x10(6) kbp) 87,688 protein-coding (92,013 total) genes, corresponding to 1.8% and 0.05% gene-coding percentages. These estimates do not likely represent extraordinarily high functional diversity of the encoded proteome but rather highly redundant genomes as evidenced by high gene copy numbers documented for various dinoflagellate species.}, }
@article {pmid19748458, year = {2009}, author = {Ropiquet, A and Li, B and Hassanin, A}, title = {SuperTRI: A new approach based on branch support analyses of multiple independent data sets for assessing reliability of phylogenetic inferences.}, journal = {Comptes rendus biologies}, volume = {332}, number = {9}, pages = {832-847}, doi = {10.1016/j.crvi.2009.05.001}, pmid = {19748458}, issn = {1768-3238}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; Classification/*methods ; DNA/genetics ; Decision Trees ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; Reproducibility of Results ; }, abstract = {Supermatrix and supertree are two methods for constructing a phylogenetic tree by using multiple data sets. However, these methods are not a panacea, as conflicting signals between data sets can lead to misinterpret the evolutionary history of taxa. In particular, the supermatrix approach is expected to be misleading if the species-tree signal is not dominant after the combination of the data sets. Moreover, most current supertree methods suffer from two limitations: (i) they ignore or misinterpret secondary (non-dominant) phylogenetic signals of the different data sets; and (ii) the logical basis of node robustness measures is unclear. To overcome these limitations, we propose a new approach, called SuperTRI, which is based on the branch support analyses of the independent data sets, and where the reliability of the nodes is assessed using three measures: the supertree Bootstrap percentage and two other values calculated from the separate analyses: the mean branch support (mean Bootstrap percentage or mean posterior probability) and the reproducibility index. The SuperTRI approach is tested on a data matrix including seven genes for 82 taxa of the family Bovidae (Mammalia, Ruminantia), and the results are compared to those found with the supermatrix approach. The phylogenetic analyses of the supermatrix and independent data sets were done using four methods of tree reconstruction: Bayesian inference, maximum likelihood, and unweighted and weighted maximum parsimony. The results indicate, firstly, that the SuperTRI approach shows less sensitivity to the four phylogenetic methods, secondly, that it is more accurate to interpret the relationships among taxa, and thirdly, that interesting conclusions on introgression and radiation can be drawn from the comparisons between SuperTRI and supermatrix analyses.}, }
@article {pmid19744143, year = {2009}, author = {Lei, CZ and Su, R and Bower, MA and Edwards, CJ and Wang, XB and Weining, S and Liu, L and Xie, WM and Li, F and Liu, RY and Zhang, YS and Zhang, CM and Chen, H}, title = {Multiple maternal origins of native modern and ancient horse populations in China.}, journal = {Animal genetics}, volume = {40}, number = {6}, pages = {933-944}, doi = {10.1111/j.1365-2052.2009.01950.x}, pmid = {19744143}, issn = {1365-2052}, mesh = {Animals ; China ; DNA, Mitochondrial/analysis ; Horses/classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {To obtain more knowledge of the origin and genetic diversity of domestic horses in China, this study provides a comprehensive analysis of mitochondrial DNA (mtDNA) D-loop sequence diversity from nine horse breeds in China in conjunction with ancient DNA data and evidence from archaeological and historical records. A 247-bp mitochondrial D-loop sequence from 182 modern samples revealed a total of 70 haplotypes with a high level of genetic diversity. Seven major mtDNA haplogroups (A-G) and 16 clusters were identified for the 182 Chinese modern horses. In the present study, nine 247-bp mitochondrial D-loop sequences of ancient remains of Bronze Age horse from the Chifeng region of Inner Mongolia in China (c. 4000-2000a bp) were used to explore the origin and diversity of Chinese modern horses and the phylogenetic relationship between ancient and modern horses. The nine ancient horses carried seven haplotypes with rich genetic diversity, which were clustered together with modern individuals among haplogroups A, E and F. Modern domestic horse and ancient horse data support the multiple origins of domestic horses in China. This study supports the argument that multiple successful events of horse domestication, including separate introductions of wild mares into the domestic herds, may have occurred in antiquity, and that China cannot be excluded from these events. Indeed, the association of Far Eastern mtDNA types to haplogroup F was highly significant using Fisher's exact test of independence (P = 0.00002), lending support for Chinese domestication of this haplogroup. High diversity and all seven mtDNA haplogroups (A-G) with 16 clusters also suggest that further work is necessary to shed more light on horse domestication in China.}, }
@article {pmid19737557, year = {2009}, author = {Yadavalli, SS and Klipcan, L and Zozulya, A and Banerjee, R and Svergun, D and Safro, M and Ibba, M}, title = {Large-scale movement of functional domains facilitates aminoacylation by human mitochondrial phenylalanyl-tRNA synthetase.}, journal = {FEBS letters}, volume = {583}, number = {19}, pages = {3204-3208}, doi = {10.1016/j.febslet.2009.09.008}, pmid = {19737557}, issn = {1873-3468}, mesh = {Catalysis ; Crystallography, X-Ray ; Evolution, Molecular ; Humans ; Mitochondria/*enzymology ; Models, Chemical ; Phenylalanine/*metabolism ; Phenylalanine-tRNA Ligase/chemistry/*metabolism ; Protein Structure, Tertiary ; RNA, Transfer/*metabolism ; Scattering, Small Angle ; *Transfer RNA Aminoacylation ; }, abstract = {Structural studies suggest rearrangement of the RNA-binding and catalytic domains of human mitochondrial PheRS (mtPheRS) is required for aminoacylation. Crosslinking the catalytic and RNA-binding domains resulted in a "closed" form of mtPheRS that still catalyzed ATP-dependent Phe activation, but was no longer able to transfer Phe to tRNA and complete the aminoacylation reaction. SAXS experiments indicated the presence of both the closed and open forms of mtPheRS in solution. Together, these results indicate that conformational flexibility of the two functional modules in mtPheRS is essential for its phenylalanylation activity. This is consistent with the evolution of the aminoacyl-tRNA synthetases as modular enzymes consisting of separate domains that display independent activities.}, }
@article {pmid19733603, year = {2009}, author = {Antico Arciuch, VG and Alippe, Y and Carreras, MC and Poderoso, JJ}, title = {Mitochondrial kinases in cell signaling: Facts and perspectives.}, journal = {Advanced drug delivery reviews}, volume = {61}, number = {14}, pages = {1234-1249}, doi = {10.1016/j.addr.2009.04.025}, pmid = {19733603}, issn = {1872-8294}, mesh = {Drug Delivery Systems/methods ; Humans ; Mitochondria/*enzymology/*physiology ; Models, Biological ; Myocardial Infarction/metabolism ; Neoplasms/metabolism ; Oxidation-Reduction ; Protein Kinases/*physiology ; Reactive Oxygen Species/metabolism ; Signal Transduction/*physiology ; }, abstract = {Phylogenetic studies had shown that evolution of mitochondria occurred in parallel with the maturation of kinases implicated in growth and final size of modern organisms. In the last years, different reports confirmed that MAPKs, Akt, PKA and PKC are present in mitochondria, particularly in the intermembrane space and inner membrane where they meet mitochondrial constitutive upstream activators. Although a priori phosphorylation is the apparent aim of translocation, new perspectives indicate that kinase activation depends on redox status as determined by the mitochondrial production of oxygen species. We observed that the degree of mitochondrial oxidation of ERK Cys(38) and Cys(214) discriminates the kinase to be phosphorylated and determines translocation to the nuclear compartment and proliferation, or accumulation in mitochondria and arrest. Otherwise, transcriptional gene regulation by Akt depends on Cys(60) and Cys(310) oxidation to sulfenic and sulfonic acids. It is concluded that the interactions between kinases and mitochondria control cell signaling pathways and participate in the modulation of cell proliferation and arrest, tissue protection, tumorigenesis and cancer progression.}, }
@article {pmid19732434, year = {2009}, author = {Kerdelhué, C and Zane, L and Simonato, M and Salvato, P and Rousselet, J and Roques, A and Battisti, A}, title = {Quaternary history and contemporary patterns in a currently expanding species.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {220}, pmid = {19732434}, issn = {1471-2148}, mesh = {Animals ; *Climate ; DNA, Mitochondrial/genetics ; Europe ; *Evolution, Molecular ; Genes, Insect ; *Genetic Variation ; *Genetics, Population ; Geography ; Haplotypes ; Mitochondria/genetics ; Moths/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Quaternary climatic oscillations had dramatic effects on species evolution. In northern latitudes, populations had to survive the coldest periods in refugial areas and recurrently colonized northern regions during interglacials. Such a history usually results in a loss of genetic diversity. Populations that did not experience glaciations, in contrast, probably maintained most of their ancestral genetic diversity. These characteristics dramatically affected the present-day distribution of genetic diversity and may influence the ability of species to cope with the current global changes. We conducted a range-wide study of mitochondrial genetic diversity in the pine processionary moth (Thaumetopoea pityocampa/T. wilkinsoni complex, Notodontidae), a forest pest occurring around the Mediterranean Basin and in southern Europe. This species is responding to the current climate change by rapid natural range expansion and can also be accidentally transported by humans. Our aim was to assess if Quaternary climatic oscillations had a different effect across the species' range and to determine if genetic footprints of contemporary processes can be identified in areas of recent introduction.<br><br>RESULTS: We identified three main clades that were spatially structured. In most of Europe, the genetic diversity pattern was typical for species that experienced marked glaciation cycles. Except in refugia, European populations were characterized by the occurrence of one main haplotype and by a strong reduction in genetic diversity, which is expected in regions that were rapidly re-colonized when climatic conditions improved. In contrast, all other sub-clades around the Mediterranean Basin occurred in limited parts of the range and were strongly structured in space, as is expected in regions in which the impact of glaciations was limited. In such places, genetic diversity was retained in most populations, and almost all haplotypes were endemic. This pattern was extreme on remote Mediterranean islands (Crete, Cyprus, Corsica) where highly differentiated, endemic haplotypes were found. Recent introductions were typified by the existence of closely-related haplotypes in geographically distant populations, which is difficult to detect in most of Europe because of a lack of overall genetic structure.<br><br>CONCLUSION: In regions that were not prone to marked glaciations, recent moth introductions/expansions could be detected due to the existence of a strong spatial genetic structure. In contrast, in regions that experienced the most intense Quaternary climatic oscillations, the natural populations are not genetically structured, and contemporary patterns of population expansion remain undetected.}, }
@article {pmid19732154, year = {2009}, author = {Beninati, T and Riegler, M and Vilcins, IM and Sacchi, L and McFadyen, R and Krockenberger, M and Bandi, C and O'Neill, SL and Lo, N}, title = {Absence of the symbiont Candidatus Midichloria mitochondrii in the mitochondria of the tick Ixodes holocyclus.}, journal = {FEMS microbiology letters}, volume = {299}, number = {2}, pages = {241-247}, doi = {10.1111/j.1574-6968.2009.01757.x}, pmid = {19732154}, issn = {1574-6968}, mesh = {Alphaproteobacteria/*isolation &amp; purification/*physiology ; Animals ; Australia ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Female ; Humans ; Ixodes/*microbiology/*physiology ; Male ; Microscopy, Electron, Transmission ; Mitochondria/*microbiology ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Candidatus Midichloria mitochondrii (M. mitochondrii) belongs to a novel clade of bacteria within the order Rickettsiales. Recent PCR-based screening studies indicate that it is present in a number of blood-sucking arthropods, as well as the blood of some vertebrates. Its medical and veterinary significance remains to be determined. Electron microscopic examinations of M. mitochondrii have thus far been conducted on two infected tick species. Remarkably, the bacterium was found in abundance within the mitochondria of the ovarian cells of each tick species. This makes it the only characterized bacterium able to invade the mitochondria of any multicellular organism. To examine whether mitochondrial invasion is a consistent characteristic of M. mitochondrii, we examined two tick species found in Eastern Australia. One of these species, Ixodes holocyclus, was infected with two M. mitochondrii strains; however, no bacteria were seen in the mitochondria. Comparative studies involving these strains may shed light on the unique phenomenon of mitochondrial invasion.}, }
@article {pmid19720733, year = {2009}, author = {Dalla Rosa, I and Goffart, S and Wurm, M and Wiek, C and Essmann, F and Sobek, S and Schroeder, P and Zhang, H and Krutmann, J and Hanenberg, H and Schulze-Osthoff, K and Mielke, C and Pommier, Y and Boege, F and Christensen, MO}, title = {Adaptation of topoisomerase I paralogs to nuclear and mitochondrial DNA.}, journal = {Nucleic acids research}, volume = {37}, number = {19}, pages = {6414-6428}, pmid = {19720733}, issn = {1362-4962}, mesh = {Adaptation, Physiological ; Cell Line ; Cell Nucleus/enzymology ; Chromosomes/enzymology ; DNA/chemistry/metabolism ; DNA Topoisomerases, Type I/chemistry/genetics/*metabolism ; DNA, Mitochondrial/*metabolism ; Gene Duplication ; Humans ; Mitochondria/enzymology ; Phenotype ; Protein Structure, Tertiary ; Transcription, Genetic ; }, abstract = {Topoisomerase I is essential for DNA metabolism in nuclei and mitochondria. In yeast, a single topoisomerase I gene provides for both organelles. In vertebrates, topoisomerase I is divided into nuclear and mitochondrial paralogs (Top1 and Top1mt). To assess the meaning of this gene duplication, we targeted Top1 to mitochondria or Top1mt to nuclei. Overexpression in the fitting organelle served as control. Targeting of Top1 to mitochondria blocked transcription and depleted mitochondrial DNA. This was also seen with catalytically inactive Top1 mutants, but not with Top1mt overexpressed in mitochondria. Targeting of Top1mt to the nucleus revealed that it was much less able to interact with mitotic chromosomes than Top1 overexpressed in the nucleus. Similar experiments with Top1/Top1mt hybrids assigned these functional differences to structural divergences in the DNA-binding core domains. We propose that adaptation of this domain to different chromatin environments in nuclei and mitochondria has driven evolutional development and conservation of organelle-restricted topoisomerase I paralogs in vertebrates.}, }
@article {pmid19717741, year = {2009}, author = {Rada, P and Smíd, O and Sutak, R and Dolezal, P and Pyrih, J and Zársky, V and Montagne, JJ and Hrdy, I and Camadro, JM and Tachezy, J}, title = {The monothiol single-domain glutaredoxin is conserved in the highly reduced mitochondria of Giardia intestinalis.}, journal = {Eukaryotic cell}, volume = {8}, number = {10}, pages = {1584-1591}, pmid = {19717741}, issn = {1535-9786}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Giardia lamblia/*metabolism ; Glutaredoxins/*chemistry ; Microscopy, Fluorescence ; Mitochondria/*metabolism ; Phylogeny ; Sequence Alignment ; }, abstract = {The highly reduced mitochondria (mitosomes) of Giardia intestinalis are recently discovered organelles for which, it was suggested, iron-sulfur cluster assembly was their only conserved function. However, only an incomplete set of the components required for FeS cluster biogenesis was localized to the mitosomes. Via proteomic analysis of a mitosome-rich cellular fraction together with immunofluorescence microscopy, we identified a novel mitosomal protein homologous to monothiol glutaredoxins containing a CGFS motif at the active site. Sequence analysis revealed the presence of long nonconserved N-terminal extension of 77 amino acids, which was absent in the mature protein. Expression of the complete and N-terminally truncated forms of the glutaredoxin indicated that the extension is involved in glutaredoxin import into mitosomes. However, the mechanism of preprotein processing is unclear, as the mitosomal processing peptidase is unable to cleave this type of extension. The recombinant mature protein was shown to form a homodimeric structure, which binds a labile FeS cluster. The cluster is stabilized by glutathione and dithiothreitol. Phylogenetic analysis showed that giardial glutaredoxin is related to the mitochondrial monothiol glutaredoxins involved in FeS cluster assembly. The identification of a mitochondrial-type monothiol glutaredoxin in the mitosomes of G. intestinalis thus completes the mitosomal FeS cluster biosynthetic pathway and provides further evidence for the mitochondrial origin of these organelles.}, }
@article {pmid19717453, year = {2009}, author = {Clements, A and Bursac, D and Gatsos, X and Perry, AJ and Civciristov, S and Celik, N and Likic, VA and Poggio, S and Jacobs-Wagner, C and Strugnell, RA and Lithgow, T}, title = {The reducible complexity of a mitochondrial molecular machine.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {37}, pages = {15791-15795}, pmid = {19717453}, issn = {1091-6490}, support = {R01 GM065835/GM/NIGMS NIH HHS/United States ; R01 GM076698/GM/NIGMS NIH HHS/United States ; GM076698/GM/NIGMS NIH HHS/United States ; GM065835/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins/chemistry/*genetics/*metabolism ; Carrier Proteins/genetics/metabolism ; Caulobacter crescentus/genetics/metabolism ; Humans ; Membrane Proteins/genetics/metabolism ; Mitochondrial Membrane Transport Proteins/chemistry/*genetics/*metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/genetics/metabolism ; Models, Molecular ; Protein Conformation ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Species Specificity ; }, abstract = {Molecular machines drive essential biological processes, with the component parts of these machines each contributing a partial function or structural element. Mitochondria are organelles of eukaryotic cells, and depend for their biogenesis on a set of molecular machines for protein transport. How these molecular machines evolved is a fundamental question. Mitochondria were derived from an alpha-proteobacterial endosymbiont, and we identified in alpha-proteobacteria the component parts of a mitochondrial protein transport machine. In bacteria, the components are found in the inner membrane, topologically equivalent to the mitochondrial proteins. Although the bacterial proteins function in simple assemblies, relatively little mutation would be required to convert them to function as a protein transport machine. This analysis of protein transport provides a blueprint for the evolution of cellular machinery in general.}, }
@article {pmid19716620, year = {2009}, author = {Burger, G and Yan, Y and Javadi, P and Lang, BF}, title = {Group I-intron trans-splicing and mRNA editing in the mitochondria of placozoan animals.}, journal = {Trends in genetics : TIG}, volume = {25}, number = {9}, pages = {381-386}, doi = {10.1016/j.tig.2009.07.003}, pmid = {19716620}, issn = {0168-9525}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Exons/genetics ; Introns/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Placozoa/*genetics ; RNA Editing/*genetics ; RNA, Messenger/chemistry/*genetics ; Trans-Splicing/*genetics ; }, abstract = {Placozoa - the simplest known free-living animals - have been considered primitive, early diverging metazoans based on mitochondrial genome structure and phylogeny. Here we reanalyze placozoan mitochondrial DNAs, reported to include a highly unorthodox, fragmented and incomplete cox1 gene. We discover overlooked exons and split group I introns that mediate trans-splicing of the discontinuous placozoan cox1. Furthermore, we find that cox1 expression involves U-to-C editing, reconstituting an otherwise invariant, essential histidine involved in copper binding. These atypical features qualify placozoan mitochondrial gene and genome organization as derived rather than primitive. Whether the Placozoa diverged early or late during metazoan evolution remains unresolved by mitochondrial phylogeny.}, }
@article {pmid19704884, year = {2008}, author = {Vaithilingam, A and Teixeira, JE and Huston, CD}, title = {Endoplasmic reticulum continuity in the protozoan parasite Entamoeba histolytica: Evolutionary implications and a cautionary note.}, journal = {Communicative &amp; integrative biology}, volume = {1}, number = {2}, pages = {172-174}, pmid = {19704884}, issn = {1942-0889}, support = {P20 RR021905/RR/NCRR NIH HHS/United States ; R01 AI072021/AI/NIAID NIH HHS/United States ; }, abstract = {Entamoeba histolytica has been described as an early branching eukaryotic parasite based on the lack of organelles such as mitochondria and peroxisomes, and on morphologic studies that concluded it possesses a vesicular endoplasmic reticulum (ER) and Golgi complex. However, a recent study from our laboratory showed that the E. histolytica ER is continuous by using an ER-targeted green fluorescent protein fusion protein and photobleaching experiments. We proposed that the vesicular ER seen earlier was likely an artifact of fixation. We now report data using an alternative fixation protocol that preserves the continuous ER morphology. These data confirm that the vesicular ER reported earlier was indeed a fixation artifact; furthermore, since we observed the same ER structure when staining for the native antigen HSP-70 in wild-type amebae, the data provide direct evidence that the continuous ER morphology we reported is correct. This work has important implications for cell biologists studying E. histolytica virulence, emphasizes the frequent need to reassess assumptions based on published data, and provides additional evidence that E. histolytica actually diverged relatively late in evolution and that many of its unusual features are likely due to loss of features during adaptation to its ecological niche.}, }
@article {pmid19703468, year = {2009}, author = {Longen, S and Bien, M and Bihlmaier, K and Kloeppel, C and Kauff, F and Hammermeister, M and Westermann, B and Herrmann, JM and Riemer, J}, title = {Systematic analysis of the twin cx(9)c protein family.}, journal = {Journal of molecular biology}, volume = {393}, number = {2}, pages = {356-368}, doi = {10.1016/j.jmb.2009.08.041}, pmid = {19703468}, issn = {1089-8638}, mesh = {Amino Acid Sequence ; Computational Biology ; Genome, Fungal/genetics ; Microscopy, Fluorescence ; Mitochondrial Membrane Transport Proteins/chemistry/genetics/metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/*chemistry/genetics/*metabolism ; Molecular Sequence Data ; Open Reading Frames ; Oxidoreductases Acting on Sulfur Group Donors/chemistry/genetics/metabolism ; Ribosomal Proteins/chemistry/genetics/metabolism ; Saccharomyces cerevisiae/genetics/growth &amp; development/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Sequence Homology, Amino Acid ; }, abstract = {The Mia40-Erv1 disulfide relay system is of high importance for mitochondrial biogenesis. Most so far identified substrates of this machinery contain either two cysteine-x(3)-cysteine (twin Cx(3)C) or two cysteine-x(9)-cysteine (twin Cx(9)C) motifs. While the first group is composed of well-characterized components of the mitochondrial import machinery, the molecular function of twin Cx(9)C proteins still remains unclear. To systematically characterize this protein family, we performed a database search to identify the full complement of Cx(9)C proteins in yeast. Thereby, we identified 14 potential family members, which, with one exception, are conserved among plants, fungi, and animals. Among these, three represent novel proteins, which we named Cmc2 to 4 (for Cx(9)C motif-containing protein) and which we demonstrated to be dependent for import on the Mia40-Erv1 disulfide relay. By testing deletion mutants of all 14 proteins for function of the respiratory chain, we found a critical function of most of these proteins for the assembly or stability of respiratory chain complexes. Our data suggest that already early during the evolution of eukaryotic cells, a multitude of twin Cx(9)C proteins developed, which exhibit largely nonredundant roles critical for the biogenesis of enzymes of the respiratory chain in mitochondria.}, }
@article {pmid19699241, year = {2009}, author = {de Miguel, N and Braun, N and Bepperling, A and Kriehuber, T and Kastenmüller, A and Buchner, J and Angel, SO and Haslbeck, M}, title = {Structural and functional diversity in the family of small heat shock proteins from the parasite Toxoplasma gondii.}, journal = {Biochimica et biophysica acta}, volume = {1793}, number = {11}, pages = {1738-1748}, doi = {10.1016/j.bbamcr.2009.08.005}, pmid = {19699241}, issn = {0006-3002}, mesh = {Amino Acid Motifs/physiology ; Animals ; Heat-Shock Proteins, Small/*genetics/metabolism ; *Phylogeny ; Protein Structure, Quaternary/physiology ; Protozoan Proteins/*genetics/metabolism ; Structure-Activity Relationship ; Toxoplasma/*genetics/metabolism ; }, abstract = {Small heat shock proteins (sHsps) are ubiquitous molecular chaperones which prevent the nonspecific aggregation of non-native proteins. Five potential sHsps exist in the parasite Toxoplasma gondii. They are located in different intracellular compartments including mitochondria and are differentially expressed during the parasite's life cycle. Here, we analyzed the structural and functional properties of all five proteins. Interestingly, this first in vitro characterization of sHsps from protists showed that all T. gondii sHsps exhibit the characteristic properties of sHsps such as oligomeric structure and chaperone activity. However, differences in their quaternary structure and in their specific chaperone properties exist. On the structural level, the T. gondii sHsps can be divided in small (12-18 subunits) and large (24-32 subunits) oligomers. Furthermore, they differ in their interaction with non-native proteins. While some bind substrates tightly, others interact more transiently. The chaperone activity of the three more mono-disperse T. gondii sHsps is regulated by temperature with a decrease in temperature leading to the activation of chaperone activity, suggesting an adaption to specific steps of the parasite's life cycle.}, }
@article {pmid19699094, year = {2009}, author = {Yoshida, Y and Kuroiwa, H and Hirooka, S and Fujiwara, T and Ohnuma, M and Yoshida, M and Misumi, O and Kawano, S and Kuroiwa, T}, title = {The bacterial ZapA-like protein ZED is required for mitochondrial division.}, journal = {Current biology : CB}, volume = {19}, number = {17}, pages = {1491-1497}, doi = {10.1016/j.cub.2009.07.035}, pmid = {19699094}, issn = {1879-0445}, mesh = {Algal Proteins/metabolism/*physiology ; Amino Acid Sequence ; Bacterial Proteins/metabolism/*physiology ; Evolution, Molecular ; Mitochondria/metabolism/*physiology/ultrastructure ; Mitochondrial Proteins/metabolism/*physiology ; Molecular Sequence Data ; Plastids/metabolism/physiology/ultrastructure ; Proteomics ; Rhodophyta/metabolism/*physiology/ultrastructure ; Sequence Alignment ; }, abstract = {Bacterial cell division systems that include FtsZ are found throughout prokaryotes. Mitochondria arose from an endosymbiotic alpha-proteobacterial ancestor and proliferate by division. However, how the mitochondrial division system was established from bacterial division is not clear. Here, we have isolated intact mitochondrial division (MD) machineries from the primitive red alga Cyanidioschyzon merolae and identified a bacterial ZapA-like protein, ZED, that constricts the basal structure of MD machinery with FtsZ. ZED contains a predicted mitochondrial transit signal and two coiled-coil regions and has partial homology with the bacterial division protein ZapA. Cytological studies revealed that ZED accumulates to form a ring structure that colocalizes with FtsZ beneath the inner membrane. ZED proteins are expressed just before mitochondrial division. The short-form ZED (S-ZED) then appears at the mitochondrial constriction phase. Protein-protein interaction analysis and transient expression of antisense against ZED showed that S-ZED interacts with FtsZ1 to constitute the basal structure of the MD machinery and is required for mitochondrial division. We also demonstrate compelling functional similarity between bacterial ZapA and mitochondrial ZED, suggesting that the bacterial cell division system was incorporated into the MD machinery with remodeling of bacterial division proteins during evolution.}, }
@article {pmid19691417, year = {2010}, author = {Iezhova, TA and Valkiūnas, G and Loiseau, C and Smith, TB and Sehgal, RN}, title = {Haemoproteus cyanomitrae sp. nov. (Haemosporida: Haemoproteidae) from a widespread African songbird, the olive sunbird, Cyanomitra olivacea.}, journal = {The Journal of parasitology}, volume = {96}, number = {1}, pages = {137-143}, doi = {10.1645/GE-2198.1}, pmid = {19691417}, issn = {1937-2345}, mesh = {Animals ; Bayes Theorem ; Bird Diseases/epidemiology/*parasitology ; Cameroon/epidemiology ; Cytochromes b/genetics ; DNA, Protozoan/chemistry/isolation &amp; purification ; Erythrocytes/parasitology ; Ghana/epidemiology ; Haemosporida/*classification/genetics/growth &amp; development ; Mitochondria/enzymology ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Prevalence ; Protozoan Infections, Animal/epidemiology/*parasitology ; Sequence Alignment/veterinary ; Songbirds/*parasitology ; Trees ; Tropical Climate ; }, abstract = {Haemoproteus (Parahaemoproteus) cyanomitrae n. sp. (Haemosporida: Haemoproteidae) was found in the olive sunbird, Cyanomitra olivacea (Nectariniidae), in rain forests of tropical Africa. It is described based on the morphology of its blood stages and a segment of the mitochondrial cytochrome b gene (GenBank accession FJ404696), which can be used for molecular identification and diagnosis of this species. Fully grown gametocytes of new parasite are similar to many other species of haemoproteids of passeriform birds, so are not easily distinguishable from many of them at this stage of their development. Haemoproteus cyanomitrae can be readily distinguished from the majority of described species of avian haemoproteids, primarily due to its growing dumbbell-shaped gametocytes and advanced halteridial gametocytes, both of which do not touch the envelope of infected erythrocytes along their entire margin. Pigment granules are most frequently clamped in 1, or several, groups in gametocytes, with larger group of pigment granules usually located close to one end of the gametocyte; asymmetric position of pigment granules in gametocytes a characteristic feature of this parasite. Illustrations of blood stages of the new species are given, and phylogenetic analysis identifies DNA lineages closely related to this parasite, which is widespread in African rain forests, but has been recorded only in the olive sunbird so far. It is probable that H. cyanomitrae is transmitted throughout the range of the olive sunbird in Africa.}, }
@article {pmid19688285, year = {2009}, author = {Flegr, J}, title = {A possible role of intracellular isoelectric focusing in the evolution of eukaryotic cells and multicellular organisms.}, journal = {Journal of molecular evolution}, volume = {69}, number = {5}, pages = {444-451}, pmid = {19688285}, issn = {1432-1432}, mesh = {Animals ; *Biological Evolution ; Cell Physiological Phenomena ; Cytoplasm/physiology ; *Eukaryotic Cells/cytology/physiology ; Hydrogen-Ion Concentration ; *Isoelectric Focusing ; Models, Biological ; Proteins/physiology ; }, abstract = {A new scenario of the origin of eukaryotic cell and multicellularity is presented. A concentric pH-gradient has been shown to exist in the cytosol of eukaryotic cells. The most probable source of such gradient is its self-formation in gradient of electric field between center and periphery of a cell. Theoretical analysis has shown that, for example, a cell of Saccharomyces cerevisiae has enough energy to continuously sustain such gradient of strength about 1.5 kV/cm, the value sufficient for effective isoelectric focusing of cytoplasmic proteins. Focusing of enzymes could highly increase the effectiveness of an otherwise diffusion-limited metabolism of large cells by concentrating enzymes into small and distinct parts of a cytoplasm. By taking away an important physical constraint to the volume of cytoplasm, the intracellular isoelectric focusing enabled evolution of cells 3-4 order of magnitude larger than typical prokaryotic cells. This opened the way for the origin of phagocytosis and lately for the development of different forms of endosymbiosis, some of them resulting in an endosymbiotic origin of mitochondria and plastids. The large volume of a cell-enabled separation of nuclear and cytoplasmic compartments which was a precondition for separation of transcription and translation processes and therefore also for the origin of various RNA-preprocessing mechanisms. The possibility to regulate gene expression by postprocessing RNA and to regulate metabolism by an electrophoretic translocation enzymes between different parts of cytoplasm by changing their isoelectric points opened the way for cell and tissue differentiation and therefore for the origin of complex multicellular organisms.}, }
@article {pmid19683530, year = {2010}, author = {Týc, J and Faktorová, D and Kriegová, E and Jirků, M and Vávrová, Z and Maslov, DA and Lukes, J}, title = {Probing for primary functions of prohibitin in Trypanosoma brucei.}, journal = {International journal for parasitology}, volume = {40}, number = {1}, pages = {73-83}, doi = {10.1016/j.ijpara.2009.07.008}, pmid = {19683530}, issn = {1879-0135}, mesh = {Animals ; DNA, Mitochondrial/genetics/metabolism ; Membrane Potentials ; *Mitochondria/metabolism/ultrastructure ; Phylogeny ; Prohibitins ; *Protein Biosynthesis ; Protozoan Proteins/genetics/metabolism ; RNA Interference ; RNA, Messenger/genetics/metabolism ; Repressor Proteins/genetics/*metabolism ; *Trypanosoma brucei brucei/genetics/growth &amp; development/metabolism/ultrastructure ; }, abstract = {Prohibitins (PHBs) 1 and 2 are small conserved proteins implicated in a number of functions in the mitochondrion, as well as in the nucleus of eukaryotic cells. The current understanding of PHB functions comes from studies of model organisms such as yeast, worm and mouse, but considerable debate remains with regard to the primary functions of these ubiquitous proteins. We exploit the tractable reverse genetics of Trypanosoma brucei, the causative agent of African sleeping sickness, in order to specifically analyse the function of PHB in this highly divergent eukaryote. Using inducible RNA interference (RNAi) we show that PHB1 is essential in T. brucei, where it is confined to the cell's single mitochondrion forming a high molecular weight complex. PHB1 and PHB2 appear to be indispensible for mitochondrial translation. Their ablation leads to a decrease in mitochondrial membrane potential, however no effect on the level of reactive oxygen species was observed. Flagellates lacking either PHB1 or both PHB1 and PHB2 exhibit significant morphological changes of their organelle, most notably its inflation. Even long after the loss of the PHB proteins, mtDNA was unaltered and mitochondrial cristae remained present, albeit displaced to the periphery of the mitochondrion, which is in contrast to other eukaryotes.}, }
@article {pmid19682765, year = {2009}, author = {Endicott, P and Ho, SY and Metspalu, M and Stringer, C}, title = {Evaluating the mitochondrial timescale of human evolution.}, journal = {Trends in ecology &amp; evolution}, volume = {24}, number = {9}, pages = {515-521}, doi = {10.1016/j.tree.2009.04.006}, pmid = {19682765}, issn = {0169-5347}, mesh = {*Biological Evolution ; DNA, Mitochondrial/chemistry ; Evolution, Molecular ; Fossils ; Genome, Mitochondrial ; Humans ; Mitochondria/*genetics ; Phylogeny ; Time Factors ; }, abstract = {Different methodologies and modes of calibration have produced disparate, sometimes irreconcilable, reconstructions of the evolutionary and demographic history of our species. We discuss how date estimates are affected by the choice of molecular data and methodology, and evaluate various mitochondrial estimates of the timescale of human evolution in the context of the contemporary palaeontological and archaeological evidence for key stages in human prehistory. We contend that some of the most widely-cited mitochondrial rate estimates have several significant shortcomings, including a reliance on a human-chimpanzee calibration, and highlight the pressing need for revised rate estimates.}, }
@article {pmid19679512, year = {2009}, author = {Holmes, RS and Goldberg, E}, title = {Computational analyses of mammalian lactate dehydrogenases: human, mouse, opossum and platypus LDHs.}, journal = {Computational biology and chemistry}, volume = {33}, number = {5}, pages = {379-385}, pmid = {19679512}, issn = {1476-928X}, support = {R01 HD005863/HD/NICHD NIH HHS/United States ; R01 HD005863-27/HD/NICHD NIH HHS/United States ; HD05863/HD/NICHD NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Computational Biology ; *Computer Simulation ; Databases, Genetic ; Humans ; Lactate Dehydrogenases/*genetics ; Mice ; *Models, Genetic ; Molecular Sequence Data ; *Opossums/genetics ; Phylogeny ; *Platypus/genetics ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {Computational methods were used to predict the amino acid sequences and gene locations for mammalian lactate dehydrogenase (LDH) genes and proteins using genome sequence databanks. Human LDHA, LDHC and LDH6A genes were located in tandem on chromosome 11, while LDH6B and LDH6C genes were on chromosomes 15 and 12, respectively. Opossum LDHC and LDH6B genes were located in tandem with the opossum LDHA gene on chromosome 5 and contained 7 (LDHA and LDHC) or 8 (LDH6B) exons. An amino acid sequence prediction for the opossum LDH6B subunit gave an extended N-terminal sequence, similar to the human and mouse LDH6B sequences, which may support the export of this enzyme into mitochondria. The platypus genome contained at least 3 LDH genes encoding LDHA, LDHB and LDH6B subunits. Phylogenetic studies and sequence analyses indicated that LDHA, LDHB and LDH6B genes are present in all mammalian genomes examined, including a monotreme species (platypus), whereas the LDHC gene may have arisen more recently in marsupial mammals.}, }
@article {pmid19670372, year = {2009}, author = {Li, J and Cai, T and Wu, P and Cui, Z and Chen, X and Hou, J and Xie, Z and Xue, P and Shi, L and Liu, P and Yates, JR and Yang, F}, title = {Proteomic analysis of mitochondria from Caenorhabditis elegans.}, journal = {Proteomics}, volume = {9}, number = {19}, pages = {4539-4553}, doi = {10.1002/pmic.200900101}, pmid = {19670372}, issn = {1615-9861}, mesh = {Animals ; *Caenorhabditis elegans/cytology/metabolism ; Caenorhabditis elegans Proteins/*analysis ; Chromatography, Liquid ; Humans ; Mitochondria/*chemistry/metabolism/ultrastructure ; Mitochondrial Proteins/*analysis ; Proteome/*analysis ; Tandem Mass Spectrometry ; }, abstract = {Mitochondria play essential roles in cell physiological processes including energy production, metabolism, ion homeostasis, cell growth, aging and apoptosis. Proteomic strategies have been applied to the study of mitochondria since 1998; these studies have yielded decisive information about the diverse physiological functions of the organelle. As an ideal model biological system, the nematode Caenorhabditis elegans has been widely used in the study of several diseases, such as metabolic diseases and cancer. However, the mitochondrial proteome of C. elegans remains elusive. In this study, we purified mitochondria from C. elegans and performed a comprehensive proteomic analysis using the shotgun proteomic approach. A total of 1117 proteins have been identified with at least two unique peptides. Their physicochemical and functional characteristics, subcellular locations, related biological processes, and associations with human diseases, especially Parkinson's disease, are discussed. An orthology comparison was also performed between C. elegans and four other model organisms for a general depiction of the conservation of mitochondrial proteins during evolution. This study will provide new clues for understanding the role of mitochondria in the physiological and pathological processes of C. elegans.}, }
@article {pmid19661396, year = {2009}, author = {Zimmer, C}, title = {Origins. On the origin of eukaryotes.}, journal = {Science (New York, N.Y.)}, volume = {325}, number = {5941}, pages = {666-668}, doi = {10.1126/science.325_666}, pmid = {19661396}, issn = {1095-9203}, mesh = {Animals ; *Archaea/classification/genetics/physiology ; *Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; *Biological Evolution ; Cell Nucleus/genetics/metabolism ; *Eukaryotic Cells/cytology/metabolism/physiology ; Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genes, Mitochondrial ; *Genome ; Mitochondria/physiology ; Organelles/physiology ; *Prokaryotic Cells/cytology/metabolism/physiology ; Symbiosis ; }, }
@article {pmid19657102, year = {2009}, author = {Scott, GR and Richards, JG and Milsom, WK}, title = {Control of respiration in flight muscle from the high-altitude bar-headed goose and low-altitude birds.}, journal = {American journal of physiology. Regulatory, integrative and comparative physiology}, volume = {297}, number = {4}, pages = {R1066-74}, doi = {10.1152/ajpregu.00241.2009}, pmid = {19657102}, issn = {1522-1490}, mesh = {Acclimatization ; Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; *Altitude ; *Animal Migration ; Animals ; Biological Evolution ; Cell Respiration ; Creatine/metabolism ; Creatine Kinase, Mitochondrial Form/metabolism ; Ducks/*physiology ; Electron Transport Complex IV/metabolism ; *Energy Metabolism ; *Flight, Animal ; Geese/*physiology ; Glycolysis ; Kinetics ; Mitochondria, Muscle/metabolism ; *Muscle Contraction ; Oxidative Phosphorylation ; Pectoralis Muscles/enzymology/*metabolism ; Succinic Acid/metabolism ; }, abstract = {Bar-headed geese fly at altitudes of up to 9,000 m on their biannual migration over the Himalayas. To determine whether the flight muscle of this species has evolved to facilitate exercise at high altitude, we compared the respiratory properties of permeabilized muscle fibers from bar-headed geese and several low-altitude waterfowl species. Respiratory capacities were assessed for maximal ADP stimulation (with single or multiple inputs to the electron transport system) and cytochrome oxidase excess capacity (with an exogenous electron donor) and were generally 20-40% higher in bar-headed geese when creatine was present. When respiration rates were extrapolated to the entire pectoral muscle mass, bar-headed geese had a higher mass-specific aerobic capacity. This may represent a surplus capacity that counteracts the depressive effects of hypoxia on mitochondrial respiration. However, there were no differences in activity for mitochondrial or glycolytic enzymes measured in homogenized muscle. The [ADP] leading to half-maximal stimulation (K(m)) was approximately twofold higher in bar-headed geese (10 vs. 4-6 microM), and, while creatine reduced K(m) by 30% in this species, it had no effect on K(m) in low-altitude birds. Mitochondrial creatine kinase may therefore contribute to the regulation of oxidative phosphorylation in flight muscle of bar-headed geese, which could promote efficient coupling of ATP supply and demand. However, this was not based on differences in creatine kinase activity in isolated mitochondria or homogenized muscle. The unique differences in bar-headed geese existed without prior exercise or hypoxia exposure and were not a result of phylogenetic history, and may, therefore, be important evolutionary specializations for high-altitude flight.}, }
@article {pmid19656201, year = {2009}, author = {Wriessnegger, T and Sunga, AJ and Cregg, JM and Daum, G}, title = {Identification of phosphatidylserine decarboxylases 1 and 2 from Pichia pastoris.}, journal = {FEMS yeast research}, volume = {9}, number = {6}, pages = {911-922}, doi = {10.1111/j.1567-1364.2009.00544.x}, pmid = {19656201}, issn = {1567-1364}, support = {P 21429/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Amino Acid Sequence ; Carboxy-Lyases/*genetics/*metabolism ; Cell Membrane/chemistry ; Fatty Acids/analysis ; Gene Deletion ; Metabolic Networks and Pathways/genetics ; Models, Biological ; Molecular Sequence Data ; Phosphatidylethanolamines/*metabolism ; Phylogeny ; Pichia/chemistry/*enzymology/genetics/growth &amp; development ; Saccharomyces cerevisiae/genetics ; Sequence Homology, Amino Acid ; }, abstract = {Genetic manipulation of lipid biosynthetic enzymes allows modification of cellular membranes. We made use of this strategy and constructed mutants in phospholipid metabolism of Pichia pastoris, which is widely used in biotechnology for expression of heterologous proteins. Here we describe identification of two P. pastoris phosphatidylserine decarboxylases (PSDs) encoded by genes homologous to PSD1 and PSD2 from Saccharomyces cerevisiae. Using P. pastoris psd1Delta and psd2Delta mutants we investigated the contribution of the respective gene products to phosphatidylethanolamine synthesis, membrane composition and cell growth. Deletion of PSD1 caused loss of PSD activity in mitochondria, a severe growth defect on minimal media and depletion of cellular and mitochondrial phosphatidylethanolamine levels. This defect could not be compensated by Psd2p, but by supplementation with ethanolamine, which is the substrate for the cytidine diphosphate (CDP)-ethanolamine pathway, the third route of phosphatidylethanolamine synthesis in yeast. Fatty acid analysis showed selectivity of both Psd1p and Psd2p in vivo for the synthesis of unsaturated phosphatidylethanolamine species. Phosphatidylethanolamine species containing palmitic acid (16:0), however, were preferentially assembled into mitochondria. In summary, this study provides first insight into membrane manipulation of P. pastoris, which may serve as a useful method to modify cell biological properties of this microorganism for biotechnological purposes.}, }
@article {pmid19647087, year = {2009}, author = {Tellier, F and Meynard, AP and Correa, JA and Faugeron, S and Valero, M}, title = {Phylogeographic analyses of the 30 degrees S south-east Pacific biogeographic transition zone establish the occurrence of a sharp genetic discontinuity in the kelp Lessonia nigrescens: vicariance or parapatry?.}, journal = {Molecular phylogenetics and evolution}, volume = {53}, number = {3}, pages = {679-693}, doi = {10.1016/j.ympev.2009.07.030}, pmid = {19647087}, issn = {1095-9513}, mesh = {Base Sequence ; Cell Nucleus/genetics ; DNA, Algal/genetics ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; *Genetic Speciation ; *Genetics, Population ; Geography ; Kelp/classification/*genetics ; Molecular Sequence Data ; Pacific Ocean ; *Phylogeny ; Polymorphism, Single-Stranded Conformational ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Phylogeographic studies are lacking in the Southern Hemisphere, and in particular in the south-eastern Pacific. To infer the possible scenario for the debated biogeographic transition zone located at 30-33 degrees S along the Chilean coast, we investigated whether there is a concordance between the phylogeographic pattern and the biogeographic transition in the intertidal kelp Lessonia nigrescens whose distribution is continuous across this transition zone. Using a combination of four makers located in the three genomic compartments (chloroplast, mitochondria and nucleus), we showed the presence of two main divergent lineages, possibly cryptic species. There was an exact match of the phylogeographic break with the 30 degrees S biogeographic transition zone, suggesting a common origin. The combined information given by the multilocus approach and by the population analysis suggested the occurrence of a budding speciation, with a northward range expansion.}, }
@article {pmid19643202, year = {2010}, author = {Tartakoff, AM and Tao, T}, title = {Comparative and evolutionary aspects of macromolecular translocation across membranes.}, journal = {The international journal of biochemistry &amp; cell biology}, volume = {42}, number = {2}, pages = {214-229}, doi = {10.1016/j.biocel.2009.07.013}, pmid = {19643202}, issn = {1878-5875}, mesh = {Animals ; Bacteria/cytology/metabolism ; Biological Transport ; Cell Membrane/*metabolism ; *Evolution, Molecular ; Humans ; Intracellular Space/metabolism ; Macromolecular Substances/*metabolism ; }, abstract = {Membrane barriers preserve the integrity of organelles of eukaryotic cells, yet the genesis and ongoing functions of the same organelles requires that their limiting membranes allow import and export of selected macromolecules. Multiple distinct mechanisms are used for this purpose, only some of which have been traced to prokaryotes. Some can accommodate both monomeric and also large heterooligomeric cargoes. The best characterized of these is nucleocytoplasmic transport. This synthesis compares the unidirectional and bidirectional mechanisms of macromolecular transport of the endoplasmic reticulum, mitochondria, peroxisomes and the nucleus, calls attention to the powerful experimental approaches which have been used for their elucidation, discusses their regulation and evolutionary origins, and highlights relatively unexplored areas.}, }
@article {pmid19640884, year = {2009}, author = {Scott, GR and Egginton, S and Richards, JG and Milsom, WK}, title = {Evolution of muscle phenotype for extreme high altitude flight in the bar-headed goose.}, journal = {Proceedings. Biological sciences}, volume = {276}, number = {1673}, pages = {3645-3653}, pmid = {19640884}, issn = {0962-8452}, mesh = {Adaptation, Physiological/genetics ; *Altitude ; Animals ; *Biological Evolution ; Flight, Animal/*physiology ; Geese/*genetics/*physiology ; Mitochondria, Muscle/physiology ; Muscle, Skeletal/*physiology ; Oxygen Consumption/physiology ; Species Specificity ; }, abstract = {Bar-headed geese migrate over the Himalayas at up to 9000 m elevation, but it is unclear how they sustain the high metabolic rates needed for flight in the severe hypoxia at these altitudes. To better understand the basis for this physiological feat, we compared the flight muscle phenotype of bar-headed geese with that of low altitude birds (barnacle geese, pink-footed geese, greylag geese and mallard ducks). Bar-headed goose muscle had a higher proportion of oxidative fibres. This increased muscle aerobic capacity, because the mitochondrial volume densities of each fibre type were similar between species. However, bar-headed geese had more capillaries per muscle fibre than expected from this increase in aerobic capacity, as well as higher capillary densities and more homogeneous capillary spacing. Their mitochondria were also redistributed towards the subsarcolemma (cell membrane) and adjacent to capillaries. These alterations should improve O(2) diffusion capacity from the blood and reduce intracellular O(2) diffusion distances, respectively. The unique differences in bar-headed geese were much greater than the minor variation between low altitude species and existed without prior exercise or hypoxia exposure, and the correlation of these traits to flight altitude was independent of phylogeny. In contrast, isolated mitochondria had similar respiratory capacities, O(2) kinetics and phosphorylation efficiencies across species. Bar-headed geese have therefore evolved for exercise in hypoxia by enhancing the O(2) supply to flight muscle.}, }
@article {pmid19639238, year = {2009}, author = {Swigonová, Z and Mohsen, AW and Vockley, J}, title = {Acyl-CoA dehydrogenases: Dynamic history of protein family evolution.}, journal = {Journal of molecular evolution}, volume = {69}, number = {2}, pages = {176-193}, pmid = {19639238}, issn = {1432-1432}, support = {R01 DK054936/DK/NIDDK NIH HHS/United States ; R01-DK54936/DK/NIDDK NIH HHS/United States ; }, mesh = {Acyl-CoA Dehydrogenases/chemistry/*genetics ; Amino Acid Sequence ; Bayes Theorem ; Conserved Sequence ; *Evolution, Molecular ; Glutaryl-CoA Dehydrogenase/genetics ; Humans ; Molecular Sequence Data ; Multigene Family/*genetics ; Phylogeny ; }, abstract = {The acyl-CoA dehydrogenases (ACADs) are enzymes that catalyze the alpha,beta-dehydrogenation of acyl-CoA esters in fatty acid and amino acid catabolism. Eleven ACADs are now recognized in the sequenced human genome, and several homologs have been reported from bacteria, fungi, plants, and nematodes. We performed a systematic comparative genomic study, integrating homology searches with methods of phylogenetic reconstruction, to investigate the evolutionary history of this family. Sequence analyses indicate origin of the family in the common ancestor of Archaea, Bacteria, and Eukaryota, illustrating its essential role in the metabolism of early life. At least three ACADs were already present at that time: ancestral glutaryl-CoA dehydrogenase (GCD), isovaleryl-CoA dehydrogenase (IVD), and ACAD10/11. Two gene duplications were unique to the eukaryotic domain: one resulted in the VLCAD and ACAD9 paralogs and another in the ACAD10 and ACAD11 paralogs. The overall patchy distribution of specific ACADs across the tree of life is the result of dynamic evolution that includes numerous rounds of gene duplication and secondary losses, interdomain lateral gene transfer events, alteration of cellular localization, and evolution of novel proteins by domain acquisition. Our finding that eukaryotic ACAD species are more closely related to bacterial ACADs is consistent with endosymbiotic origin of ACADs in eukaryotes and further supported by the localization of all nine previously studied ACADs in mitochondria.}, }
@article {pmid19632785, year = {2009}, author = {Wu, SG and Wang, GT and Xi, BW and Xiong, F and Liu, T and Nie, P}, title = {Population genetic structure of the parasitic nematode Camallanus cotti inferred from DNA sequences of ITS1 rDNA and the mitochondrial COI gene.}, journal = {Veterinary parasitology}, volume = {164}, number = {2-4}, pages = {248-256}, doi = {10.1016/j.vetpar.2009.04.030}, pmid = {19632785}, issn = {1873-2550}, mesh = {Animals ; Base Sequence ; DNA, Ribosomal Spacer/*genetics ; Electron Transport Complex IV/*genetics/metabolism ; Fish Diseases/epidemiology ; Fishes ; Gene Expression Regulation/physiology ; *Genetic Variation ; Mitochondria/enzymology ; Phylogeny ; Spirurida/*enzymology/*genetics ; Spirurida Infections/veterinary ; }, abstract = {The population genetic structure of fish parasitic nematode, Camallanus cotti, collected from the Yangtze River, Pearl River and Minjiang River in China was investigated. From these parasites, the approximately 730 bp of the first internal transcribed spacer of ribosomal DNA (ITS1 rDNA) and the 428bp of mitochondrial cytochrome c oxidase subunit I (COI) gene were sequenced. For the ITS1 rDNA data set, highly significant Fst values and low rates of migration were detected between the Pearl River group and both the Yangtze River (Fst=0.70, P<0.00001; Nm=0.21) and Minjiang River (Fst=0.73, P<0.00001; Nm=0.18) groups, while low Fst value (Fst=0.018, P>0.05) and high rate of migration (Nm=28.42) were found between the Minjiang and the Yangtze rivers. When different host/locality populations (subpopulations) within each river were considered, subpopulations between the Yangtze River and Minjiang River had low Fst values (<or=0.12) and high Nm values (>3.72), while Pearl River subpopulations were significantly different from the Yangtze River and Minjiang River subpopulations (Fst>or=0.59; Nm<1). The COI gene data set revealed a similar genetic structure. Both phylogenetic analyses and a statistical parsimony network grouped the Pearl River haplotypes into one phylogroup, while the Yangtze River and Minjiang River haplotypes formed a second group. These results suggested that the Yangtze River and Minjiang River subpopulations constituted a single reproductive pool that was distinct from the Pearl River subpopulations. In addition, the present study did not find host-related genetic differentiation occurring in the same drainage.}, }
@article {pmid19617425, year = {2009}, author = {Walter, I and Seebacher, F}, title = {Endothermy in birds: underlying molecular mechanisms.}, journal = {The Journal of experimental biology}, volume = {212}, number = {Pt 15}, pages = {2328-2336}, doi = {10.1242/jeb.029009}, pmid = {19617425}, issn = {0022-0949}, mesh = {Animals ; Body Temperature Regulation/*physiology ; Cell Respiration ; Chick Embryo ; Chickens/growth &amp; development/metabolism/*physiology ; Energy Metabolism ; Mitochondria/metabolism ; Oxidation-Reduction ; Thyroid Hormones/physiology ; }, abstract = {Endothermy is significant in vertebrate evolution because it changes the relations between animals and their environment. How endothermy has evolved in archosaurs (birds, crocodiles and dinosaurs) is controversial especially because birds do not possess brown adipose tissue, the specialized endothermic tissue of mammals. Internal heat production is facilitated by increased oxidative metabolic capacity, accompanied by the uncoupling of aerobic metabolism from energy (ATP) production. Here we show that the transition from an ectothermic to an endothermic metabolic state in developing chicken embryos occurs by the interaction between increased basal ATP demand (Na(+)/K(+)-ATPase activity and gene expression), increased oxidative capacity and increased uncoupling of mitochondria; this process is controlled by thyroid hormone via its effect on PGC1alpha and adenine nucleotide translocase (ANT) gene expression. Mitochondria become more uncoupled during development, but unlike in mammals, avian uncoupling protein (avUCP) does not uncouple electron transport from oxidative phosphorylation and therefore plays no role in heat production. Instead, ANT is the principal uncoupling protein in birds. The relationship between oxidative capacity and uncoupling indicates that there is a continuum of phenotypes that fall between the extremes of selection for increased heat production and increased aerobic activity, whereas increased cellular ATP demand is a prerequisite for increased oxidative capacity.}, }
@article {pmid19617397, year = {2009}, author = {Shen, YY and Shi, P and Sun, YB and Zhang, YP}, title = {Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability.}, journal = {Genome research}, volume = {19}, number = {10}, pages = {1760-1765}, pmid = {19617397}, issn = {1549-5469}, mesh = {Animals ; Birds/*genetics/*physiology ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Extinction, Biological ; *Flight, Animal/physiology ; Molecular Sequence Data ; Phylogeny ; *Selection, Genetic ; }, abstract = {The evolution of flight is the most important feature of birds, and this ability has helped them become one of the most successful groups of vertebrates. However, some species have independently lost their ability to fly. The degeneration of flight ability is a long process, and some species remain transitional locomotive models. Most of the energy required for locomotion is supplied by mitochondria via oxidative phosphorylation. Thus, rapidly flying birds should require a more energy efficient metabolism than weakly flying or flightless species. Therefore, we speculated that evolutionary constraints acted on the mtDNA of birds with different locomotive abilities. To test this hypothesis, we compared 76 complete avian mitochondrial genomes. Weakly flying and flightless birds, compared to rapidly flying birds, accumulated more nonsynonymous nucleotide substitutions relative to synonymous substitutions. Even after controlling for mutation rate, this trend remained significant. This finding was further tested for its generality by examining 214 complete mammalian mitochondrial genomes. The same as birds, a negative correlation was also found for the K(a)/K(s) ratio and locomotive speed. Our results demonstrated that, in addition to the previously described role for effective population size, functional constraints due to locomotion play an important role in the evolution of mtDNA.}, }
@article {pmid19609770, year = {2009}, author = {Cotter, CR and Blaho, JA}, title = {Detection of herpes simplex virus dependent apoptosis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {559}, number = {}, pages = {371-387}, doi = {10.1007/978-1-60327-017-5_26}, pmid = {19609770}, issn = {1064-3745}, support = {AI 07647/AI/NIAID NIH HHS/United States ; AI38873/AI/NIAID NIH HHS/United States ; AI48582/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Apoptosis ; Caspases/analysis/metabolism ; Cell Line ; Cell Nucleus/metabolism/*virology ; Cytochromes c/analysis/metabolism ; Herpesvirus 1, Human/*physiology ; *Host-Pathogen Interactions ; Humans ; Mitochondria/metabolism/*virology ; }, abstract = {Subversion of the host response to virus infection is a universal theme of virology and viral immunology. Multiple mechanisms are in place to limit virus spread on behalf of the host, yet through evolution, viruses have adapted to either weaken or eliminate the effects of these host factors. Cell death or apoptosis is one such example of a host response to viral infection. As such, experimental techniques that enable analysis of viruses (and viral genes) involved in triggering, blocking, or perhaps augmenting this process represent important tools for virologists, immunologists, and cell biologists. Presented here are a series of techniques developed in our lab for the analysis of apoptosis that occurs as a consequence of herpes simplex virus type 1 infection.}, }
@article {pmid19608767, year = {2009}, author = {Vaquero, A and Reinberg, D}, title = {Calorie restriction and the exercise of chromatin.}, journal = {Genes &amp; development}, volume = {23}, number = {16}, pages = {1849-1869}, pmid = {19608767}, issn = {1549-5477}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; *Caloric Restriction ; Chromatin/*metabolism ; Enzymes/metabolism ; Humans ; Mitochondria/metabolism ; Reactive Oxygen Species/metabolism ; Sirtuins/metabolism ; Transcription Factors/metabolism ; }, abstract = {Since the earliest stages of evolution, organisms have faced the challenge of sensing and adapting to environmental changes for their survival under compromising conditions such as food depletion or stress. Implicit in these responses are mechanisms developed during evolution that include the targeting of chromatin to allow or prevent expression of fundamental genes and to protect genome integrity. Among the different approaches to study these mechanisms, the analysis of the response to a moderate reduction of energy intake, also known as calorie restriction (CR), has become one of the best sources of information regarding the factors and pathways involved in metabolic adaptation from lower to higher eukaryotes. Furthermore, responses to CR are involved in life span regulation-conserved from yeast to mammals-and therefore have garnered major research interest. Herein we review current knowledge of responses to CR at the molecular level and their functional link to chromatin.}, }
@article {pmid19607930, year = {2009}, author = {Monteiro-Vitorello, CB and Hausner, G and Searles, DB and Gibb, EA and Fulbright, DW and Bertrand, H}, title = {The Cryphonectria parasitica mitochondrial rns gene: plasmid-like elements, introns and homing endonucleases.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {46}, number = {11}, pages = {837-848}, doi = {10.1016/j.fgb.2009.07.005}, pmid = {19607930}, issn = {1096-0937}, mesh = {Ascomycota/*genetics ; DNA, Mitochondrial/*genetics ; Endonucleases/metabolism ; *Genes, Fungal ; Introns ; Mitochondria/*genetics ; Phylogeny ; Plasmids ; *Recombination, Genetic ; Sequence Homology, Nucleic Acid ; }, abstract = {The mt-rns gene of Cryphonectria parasitica is 9872bp long and includes two group I and two group II introns. An analysis of intronic protein-encoding sequences revealed that LAGLIDADG ORFs, which usually are associated with group I introns, were transferred at least twice into group II introns. A plasmid-like mitochondrial element (plME) that appears in high amounts in previously mutagen-induced mit1 and mit2 hypovirulent mutants of the Ep155 standard virulent strain of C. parasitica was found to be derived from a short region of the mt-rns gene, including the exon 1 and most of the first intron. The plME is a 4.2-kb circular, multimeric DNA and an autonomously-replicating mtDNA fragment. Although sexual transmission experiments indicate that the plME does not directly cause hypovirulence, its emergence is one manifestation of the many complex molecular and genetic events that appear to underlie this phenotype.}, }
@article {pmid19605858, year = {2009}, author = {Ryan, FP}, title = {An alternative approach to medical genetics based on modern evolutionary biology. Part 1: mutation and symbiogenesis.}, journal = {Journal of the Royal Society of Medicine}, volume = {102}, number = {7}, pages = {272-277}, pmid = {19605858}, issn = {1758-1095}, mesh = {Animals ; *Biological Evolution ; Genes, Bacterial/physiology ; Genome/genetics ; Humans ; Mitochondria/*genetics ; Mitochondrial Diseases/genetics ; Mutation/*genetics ; Neoplasms/genetics ; Symbiosis/*genetics ; }, }
@article {pmid19602083, year = {2009}, author = {Park, JS and Kolisko, M and Heiss, AA and Simpson, AG}, title = {Light microscopic observations, ultrastructure, and molecular phylogeny of Hicanonectes teleskopos n. g., n. sp., a deep-branching relative of diplomonads.}, journal = {The Journal of eukaryotic microbiology}, volume = {56}, number = {4}, pages = {373-384}, doi = {10.1111/j.1550-7408.2009.00412.x}, pmid = {19602083}, issn = {1550-7408}, mesh = {Animals ; DNA, Protozoan/analysis/genetics ; *Diplomonadida/classification/genetics/ultrastructure ; Flagella/ultrastructure ; Genes, rRNA ; Microscopy, Electron, Transmission ; Mitochondria/ultrastructure ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {We describe Hicanonectes teleskopos n. g., n. sp., a heterotrophic flagellate isolated from low-oxygen marine sediment. Hicanonectes teleskopos has a ventral groove and two unequal flagella, and rapidly rotates during swimming. At the ultrastructural level H. teleskopos is a "typical excavate": it displays flagellar vanes, a split right microtubular root, "I,""B," and "C" fibres, a singlet microtubular root, and a possible composite fibre. Small subunit rRNA (SSU rRNA) gene phylogenies and an "arched" B fibre demonstrate that H. teleskopos belongs to Fornicata (i.e. diplomonads, retortamonads, and relatives). It forms a clade with the deep-branching fornicate Carpediemonas, with moderate-to-strong bootstrap support, although their SSU rRNA gene sequences are quite dissimilar. Hicanonectes differs from Carpediemonas in cell shape, swimming behaviour, number of basal bodies (i.e. 4 vs. 3), number of flagellar vanes (i.e. 2 vs. 3), anterior root organization, and by having a cytopharynx. Like Carpediemonas and Dysnectes, Hicanonectes has conspicuous mitochondrion-like organelles that lack cristae and superficially resemble the hydrogenosomes of parabasalids, rather than the mitosomes of their closer relatives the diplomonads (e.g. Giardia).}, }
@article {pmid19602081, year = {2009}, author = {Visvesvara, GS and Sriram, R and Qvarnstrom, Y and Bandyopadhyay, K and Da Silva, AJ and Pieniazek, NJ and Cabral, GA}, title = {Paravahlkampfia francinae n. sp. masquerading as an agent of primary amoebic meningoencephalitis.}, journal = {The Journal of eukaryotic microbiology}, volume = {56}, number = {4}, pages = {357-366}, doi = {10.1111/j.1550-7408.2009.00410.x}, pmid = {19602081}, issn = {1550-7408}, support = {5P30 NS047463/NS/NINDS NIH HHS/United States ; }, mesh = {Adolescent ; Amphotericin B/administration &amp; dosage ; Animals ; Antiprotozoal Agents/administration &amp; dosage ; Central Nervous System Protozoal Infections/*parasitology ; DNA, Protozoan/analysis/genetics ; Genes, rRNA ; Humans ; Male ; Mice ; Microscopy, Electron ; Molecular Sequence Data ; Phylogeny ; Protozoan Infections/*parasitology ; Schizopyrenida/drug effects/*pathogenicity/*physiology/*ultrastructure ; Species Specificity ; Virulence ; }, abstract = {Paravahlkampfia francinae n. sp., a new species of the free-living amoeba genus Paravahlkampfia, designated as CDC:V595, was isolated from the cerebrospinal fluid of a patient with headache, sore throat, and vomiting, typical symptoms of primary amoebic meningoencephalitis (PAM) caused by Naegleria fowleri. The isolate grew at 33 degrees C, 37 degrees C, 40 degrees C, and 42 degrees C and destroyed mammalian cell cultures. However, it did not kill young mice upon intranasal inoculation. P. francinae does not produce flagellates and does not grow on agar plates coated with Gram-negative bacteria such as Escherichia coli, the usual food source of Paravahlkampfia ustiana, the type species of the genus. The trophozoite at light microscopy exhibited eruptive locomotion and possessed a single vesicular nucleus. Ultrastructurally, the trophozoites had numerous mitochondria with discoidal cristae but did not have a Golgi apparatus. The trophozoites differentiated into cysts after consuming most of the monolayer. The cyst had an inner well-differentiated endocyst and an outer thin, wrinkled, and wavy ectocyst with no pores. During excystation trophozoites ruptured the cyst wall and emerged from the cysts. A unique feature seen in the cysts was the presence of bacterial endosymbionts, both in the endoplasm and within the cyst wall. Full-length sequencing analysis of the 18S and 5.8S RNA genes of P. francinae showed that they were distinct from those of other Paravahlkampfia species. The patient recovered within a few days indicating that some of the previously reported cases of PAM that survived may have been due to P. francinae.}, }
@article {pmid19589724, year = {2009}, author = {Bass, D and Howe, AT and Mylnikov, AP and Vickerman, K and Chao, EE and Edwards Smallbone, J and Snell, J and Cabral, C and Cavalier-Smith, T}, title = {Phylogeny and classification of Cercomonadida (Protozoa, Cercozoa): Cercomonas, Eocercomonas, Paracercomonas, and Cavernomonas gen. nov.}, journal = {Protist}, volume = {160}, number = {4}, pages = {483-521}, doi = {10.1016/j.protis.2009.01.004}, pmid = {19589724}, issn = {1618-0941}, mesh = {Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Eukaryota/*classification/cytology/genetics ; Genes, rRNA ; Microscopy, Electron, Scanning ; Microscopy, Interference ; Molecular Sequence Data ; *Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {Cercomonads (=Cercomonadida) are biflagellate gliding bacterivorous protozoa, abundant and diverse in soil and freshwater. We establish 56 new species based on 165 cultures, differential interference contrast microscopy, and 18S and ITS2 rDNA sequencing, and a new genus Cavernomonas studied by scanning electron microscopy. We fundamentally revise the phylogeny and classification of cercomonad Cercozoa. We describe 40 Cercomonas species (35 novel), six Eocercomonas (five novel), two Cavernomonas, and 18 Paracercomonas species (14 novel). We obtained additional cercomonad clade A (Cercomonas, Eocercomonas, Cavernomonas) sequences from multiple environmental DNA libraries. The most commonly cultivated genotypes are not the commonest in environmental DNA, suggesting that cercomonad ecology is far more complex than implied by laboratory cultures. Cercomonads have never been isolated from saline environments, although some species can grow in semi-saline media in the laboratory, and environmental DNA libraries regularly detect them in coastal marine sediments. The first ultrastructural study of an anaerobic cercozoan, Paracercomonas anaerobica sp. nov., a highly divergent cercomonad, shows much simpler ciliary roots than in clade A cercomonads, a ciliary hub-lattice and axosome, and mitochondria with tubular cristae, consistent with it being only facultatively anaerobic. We also describe Agitata tremulans gen. et sp. nov., previously misidentified as Cercobodo (=Dimastigamoeba) agilis Moroff.}, }
@article {pmid19586921, year = {2009}, author = {Leitch, JM and Yick, PJ and Culotta, VC}, title = {The right to choose: multiple pathways for activating copper,zinc superoxide dismutase.}, journal = {The Journal of biological chemistry}, volume = {284}, number = {37}, pages = {24679-24683}, pmid = {19586921}, issn = {1083-351X}, support = {GM 50016/GM/NIGMS NIH HHS/United States ; F32 GM 087904/GM/NIGMS NIH HHS/United States ; R01 GM050016/GM/NIGMS NIH HHS/United States ; R37 GM050016/GM/NIGMS NIH HHS/United States ; ES 007308/ES/NIEHS NIH HHS/United States ; P30 ES003819/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Disulfides/chemistry ; Evolution, Molecular ; Humans ; Mitochondria/enzymology ; Models, Biological ; Models, Molecular ; *Mutation ; Oxygen/chemistry ; Plants/genetics ; Saccharomyces cerevisiae/genetics ; Signal Transduction ; Superoxide Dismutase/chemistry/genetics/*metabolism ; }, abstract = {Since the discovery of SOD1 in 1969, there have been numerous achievements made in our understanding of the enzyme's biochemical reactivity and its role in oxidative stress protection and as a genetic determinant in amyotrophic lateral sclerosis. Many recent advances have also been made in understanding the "activation" of SOD1, i.e. the process by which an inert polypeptide is converted to a mature active enzyme through post-translational modifications. To date, two such activation pathways have been identified: one requiring the CCS copper chaperone and one that works independently of CCS to insert copper and activate SOD1 through oxidation of an intramolecular disulfide. Depending on an organism's lifestyle and complexity, different eukaryotes have evolved to favor one pathway over the other. Some organisms rely solely on CCS for activating SOD1, and others can only activate SOD1 independently of CCS, whereas the majority of eukaryotes appear to have evolved to use both pathways. In this minireview, we shall highlight recent advances made in understanding the mechanisms by which the CCS-dependent and CCS-independent pathways control the activity, structure, and intracellular localization of copper,zinc superoxide dismutase, with relevance to amyotrophic lateral sclerosis and an emphasis on evolutionary biology.}, }
@article {pmid19586729, year = {2010}, author = {De Mercado, E and Rodríguez, A and Gómez, E and Sanz, E}, title = {Cryopreservation of Iberian pig spermatozoa. Comparison of different freezing extenders based on post-thaw sperm quality.}, journal = {Animal reproduction science}, volume = {118}, number = {1}, pages = {54-61}, doi = {10.1016/j.anireprosci.2009.06.006}, pmid = {19586729}, issn = {1873-2232}, mesh = {Acrosome/drug effects/physiology ; Animals ; Cryopreservation/*methods/veterinary ; Cryoprotective Agents/*pharmacology ; Freezing ; Hot Temperature ; Male ; Mitochondria/drug effects/physiology ; Semen Analysis/veterinary ; Semen Preservation/*methods/veterinary ; Spermatozoa/cytology/*drug effects/physiology/ultrastructure ; *Swine/physiology ; }, abstract = {The aim of this study was to evaluate the cryoprotective effect of different freezing extenders against cryopreservation injuries on Iberian boar sperm. The sperm-rich fraction was collected and pooled from six sexually mature Iberian boars, and was frozen in different extenders containing glucose, lactose or fructose as sugar source and including Orvus ES Paste only in the freezing extender-2 (Glucose; Lactose and Fructose) or in both freezing extenders (Glucose2; Lactose2 and Fructose2). During the cryopreservation process, the supernatant was removed after the centrifugation step, then was extended with freezing extender-1 for the equilibration period and with freezing extender-2 immediately before freezing. Post-thaw sperm characteristics, such as plasma membrane integrity (SYBR-14/PI), mitochondrial function (Rhodamine 123) and acrosome integrity (NAR), were monitored. Overall sperm motility and the individual kinematic parameters of motile spermatozoa (assessed by the computer-aided sperm analysis system Sperm Class Analyzer [SCA]) were recorded in the different experimental treatments. Measurements were taken at 30 and 150 min post-thaw. The state of the acrosome after thawing did not show significant differences between the freezing extenders studied. Freezing-thawing caused a significant decrease (P<0.001) in plasma membrane integrity and in mitochondrial activity in the spermatozoa frozen with Orvus ES Paste in both freezing extenders. Furthermore, spermatozoa frozen with Orvus ES Paste in both freezing extenders exhibited lower (P<0.05) motility and kinematic parameters than those frozen in the absence of Orvus ES Paste in the first freezing extender. The spermatozoa frozen with the Lactose extender and with Orvus ES Paste only in the second freezing extender showed a better evolution of the motility and kinematic characteristics (P<0.05) over time. The deterioration in post-thaw sperm motility and kinematic parameters were concurrent with reduced sperm characteristics. It can be suggested that in the Iberian pig, the beneficial effects of Orvus ES Paste during the freezing process of spermatozoa is time dependent. The analysis of different sperm characteristics such as motility, plasma membrane integrity and mitochondrial function, determined that the extenders studied in the present experiment affected the quality of frozen-thawed semen in Iberian boar.}, }
@article {pmid19578062, year = {2009}, author = {Oberto, J and Breuil, N and Hecker, A and Farina, F and Brochier-Armanet, C and Culetto, E and Forterre, P}, title = {Qri7/OSGEPL, the mitochondrial version of the universal Kae1/YgjD protein, is essential for mitochondrial genome maintenance.}, journal = {Nucleic acids research}, volume = {37}, number = {16}, pages = {5343-5352}, pmid = {19578062}, issn = {1362-4962}, mesh = {Animals ; Bacterial Proteins/classification/genetics ; Caenorhabditis elegans/genetics/ultrastructure ; Caenorhabditis elegans Proteins/genetics/*physiology ; DNA, Mitochondrial/analysis ; Escherichia coli Proteins/genetics ; Ethidium/pharmacology ; Genes, Lethal ; *Genome, Mitochondrial ; Longevity ; Mitochondria/ultrastructure ; Mitochondrial Proteins/classification/genetics/*physiology ; Mutation ; Oxidative Stress ; Phylogeny ; Saccharomyces cerevisiae/genetics/ultrastructure ; Saccharomyces cerevisiae Proteins/genetics/*physiology ; }, abstract = {Yeast Qri7 and human OSGEPL are members of the orthologous Kae1(OSGEP)/YgjD protein family, the last class of universally conserved proteins without assigned function. Phylogenetic analyses indicate that the eukaryotic Qri7(OSGEPL) proteins originated from bacterial YgjD proteins. We have recently shown that the archaeal Kae1 protein is a DNA-binding protein that exhibits apurinic endonuclease activity in vitro. We show here that the Qri7/OSGEPL proteins localize in mitochondria and are involved in mitochondrial genome maintenance in two model eukaryotic organisms, Saccharomyces cerevisiae and Caenorhabditis elegans. Furthermore, S. cerevisiae Qri7 complements the loss of the bacterial YgjD protein in Escherichia coli, suggesting that Qri7/OSGEPL and YgjD proteins have retained similar functions in modern organisms. We suggest to name members of the Kae1(OSGEP)/YgjD family UGMP, for Universal Genome Maintenance Proteins.}, }
@article {pmid19576240, year = {2009}, author = {Lauksund, S and Svingerud, T and Bergan, V and Robertsen, B}, title = {Atlantic salmon IPS-1 mediates induction of IFNa1 and activation of NF-kappaB and localizes to mitochondria.}, journal = {Developmental and comparative immunology}, volume = {33}, number = {11}, pages = {1196-1204}, doi = {10.1016/j.dci.2009.06.012}, pmid = {19576240}, issn = {1879-0089}, mesh = {Adaptor Proteins, Signal Transducing/genetics/immunology/*metabolism ; Animals ; Birnaviridae Infections/genetics/*immunology ; Cell Line ; Cloning, Molecular ; Epithelial Cells/immunology/*metabolism/ultrastructure ; Humans ; Immunity, Innate/genetics ; Infectious pancreatic necrosis virus/*immunology ; Interferon Regulatory Factors/metabolism ; Interferon-alpha/genetics/immunology/*metabolism ; Interferon-beta/genetics/immunology/metabolism ; Mitochondria/metabolism ; NF-kappa B/metabolism ; Proline-Rich Protein Domains/genetics ; Promoter Regions, Genetic ; Protein Transport ; Salmo salar ; Sequence Alignment ; Sequence Deletion ; Signal Transduction/genetics/immunology ; }, abstract = {The striking difference in evolution of type I IFN genes of fish and mammals poses the question of whether these genes are induced through similar or different signalling pathways in the two vertebrate groups. Previous work has shown that expression of both Atlantic salmon (Salmo salar) IFNa1 and mammalian IFN-beta genes is dependent on IRF and NF-kappaB elements in their promoters. In mammals, IFN-beta transcription is induced through the RIG-I/MDA5 pathway where the adaptor protein IPS-1 plays a key role in the signal transduction. In this work we show that an Atlantic salmon homologue of IPS-1 (AsIPS-1) mediates activation of the salmon IFNa1 promoter and an NF-kappaB driven promoter. AsIPS-1 shares only 18% identity in amino acid sequence with human IPS-1, but possesses the CARD, proline-rich and transmembrane domains found in mammalian IPS-1. Overexpression of AsIPS-1 resulted in induction of an antiviral state in the cells apparently due to induction of IFN. Deletion of the CARD and transmembrane domains of AsIPS-1 abolished its ability to activate the IFNa1 promoter and the NF-kappaB driven promoter, and thus its ability to induce an antiviral state. AsIPS-1 is located to mitochondria similar to human IPS-1. Taken together, IPS-1 plays a key role in the induction of Atlantic salmon IFNa1, which appears to be the first and major IFN induced in host cells upon recognition of viral dsRNA.}, }
@article {pmid19575561, year = {2009}, author = {Vaidya, AB and Mather, MW}, title = {Mitochondrial evolution and functions in malaria parasites.}, journal = {Annual review of microbiology}, volume = {63}, number = {}, pages = {249-267}, doi = {10.1146/annurev.micro.091208.073424}, pmid = {19575561}, issn = {1545-3251}, support = {R01 AI028398/AI/NIAID NIH HHS/United States ; R01AI53148/AI/NIAID NIH HHS/United States ; R01AI28398/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Electron Transport ; Evolution, Molecular ; Mitochondria/genetics/*physiology ; Mitochondrial Proteins/genetics ; Models, Biological ; Plasmodium/genetics/*physiology ; RNA, Ribosomal/genetics ; }, abstract = {Mitochondria in malaria parasites have some unusual evolutionary and functional features. The drastic reduction in the size of their mitochondrial genome, encoding just three proteins, appears to have originated at the point of divergence of dinoflagellates and apicomplexan parasites from ciliates and may have accompanied the acquisition of plastids by the former. Unusual translational machinery as revealed by the highly fragmented mitochondrial ribosomal RNA genes also appears to have originated at this deflection point. Some of the biochemical properties of malarial mitochondria also appear to be unconventional. Although tricarboxylic acid cycle enzymes are encoded by the genome, they do not appear to be involved in the full oxidation of glucose to fuel mitochondrial ATP synthesis in the blood stages of malaria parasites. A critical role of the mitochondrial electron transport chain appears to be to serve pyrimidine biosynthesis. In spite of their minimal nature, Plasmodium mitochondria are attractive targets for antimalarial drugs.}, }
@article {pmid19574213, year = {2009}, author = {Chiu, WC and Chang, CP and Wang, CC}, title = {Evolutionary basis of converting a bacterial tRNA synthetase into a yeast cytoplasmic or mitochondrial enzyme.}, journal = {The Journal of biological chemistry}, volume = {284}, number = {36}, pages = {23954-23960}, pmid = {19574213}, issn = {0021-9258}, mesh = {Cytoplasm/*enzymology/genetics ; Escherichia coli/*enzymology/genetics ; Escherichia coli Proteins/genetics/*metabolism ; *Evolution, Molecular ; Mitochondria/*enzymology/genetics ; Mitochondrial Proteins/genetics/*metabolism ; Peptide Chain Initiation, Translational/physiology ; Protein Sorting Signals/physiology ; Protein Structure, Tertiary/physiology ; Protein Transport/physiology ; Saccharomyces cerevisiae/*enzymology/genetics ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Valine-tRNA Ligase/genetics/*metabolism ; }, abstract = {Previous studies showed that cytoplasmic and mitochondrial forms of yeast valyl-tRNA synthetase (ValRS) are specified by the VAS1 gene through alternative initiation of translation. Sequence comparison suggests that the yeast cytoplasmic (or mature mitochondrial) ValRS contains an N-terminal appendage that acts in cis as a nonspecific tRNA-binding domain (TRBD) and is absent from its bacterial relatives. We show here that Escherichia coli ValRS can substitute for the mitochondrial and cytoplasmic functions of VAS1 by fusion of a mitochondrial targeting signal and a TRBD, respectively. In addition, the bacterial ValRS gene can be converted into a dual functional yeast gene encoding both cytoplasmic and mitochondrial activities by fusion of a DNA sequence specifying both the mitochondrial targeting signal and TRBD. In vitro assays suggested that fusion of a nonspecific TRBD to the bacterial enzyme significantly enhanced its yeast tRNA-binding and aminoacylation activities. These results not only underscore the necessity of retaining a TRBD for functioning of a tRNA synthetase in yeast cytoplasm, but also provide insights into the evolution of tRNA synthetase genes.}, }
@article {pmid19567699, year = {2009}, author = {Kollberg, G and Tulinius, M and Melberg, A and Darin, N and Andersen, O and Holmgren, D and Oldfors, A and Holme, E}, title = {Clinical manifestation and a new ISCU mutation in iron-sulphur cluster deficiency myopathy.}, journal = {Brain : a journal of neurology}, volume = {132}, number = {Pt 8}, pages = {2170-2179}, doi = {10.1093/brain/awp152}, pmid = {19567699}, issn = {1460-2156}, mesh = {Aconitate Hydratase/deficiency ; Adolescent ; Adult ; Aged ; Base Sequence ; Biopsy ; Cells, Cultured ; Child ; Child, Preschool ; Female ; Genotype ; Humans ; Iron-Sulfur Proteins/deficiency/*genetics ; Male ; Mitochondria, Muscle/ultrastructure ; Mitochondrial Myopathies/*genetics/metabolism/pathology ; Mitochondrial Proteins/deficiency ; Molecular Sequence Data ; Muscle, Skeletal/pathology ; *Mutation ; Pedigree ; Phenotype ; Polymerase Chain Reaction/methods ; Polymorphism, Single Nucleotide ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Young Adult ; }, abstract = {Myopathy with deficiency of succinate dehydrogenase and aconitase is a recessively inherited disorder characterized by childhood-onset early fatigue, dyspnoea and palpitations on trivial exercise. The disease is non-progressive, but life-threatening episodes of widespread weakness, severe metabolic acidosis and rhabdomyolysis may occur. The disease has so far only been identified in northern Sweden. The clinical, histochemical and biochemical phenotype is very homogenous and the patients are homozygous for a deep intronic IVS5 + 382G>C splicing affecting mutation in ISCU, which encodes the differently spliced cytosolic and mitochondrial iron-sulphur cluster assembly protein IscU. Iron-sulphur cluster containing proteins are essential for iron homeostasis and respiratory chain function, with IscU being among the most conserved proteins in evolution. We identified a shared homozygous segment of only 405,000 base pair with the deep intronic mutation in eight patients with a phenotype consistent with the original description of the disease. Two other patients, two brothers, had an identical biochemical and histochemical phenotype which is probably pathognomonic for muscle iron-sulphur cluster deficiency, but they presented with a disease where the clinical phenotype was characterized by early onset of a slowly progressive severe muscle weakness, severe exercise intolerance and cardiomyopathy. The brothers were compound heterozygous for the deep intronic mutation and had a c.149 G>A missense mutation in exon 3 changing a completely conserved glycine residue to a glutamate. The missense mutation was inherited from their mother who was of Finnish descent. The intronic mutation affects mRNA splicing and results in inclusion of pseudoexons in most transcripts in muscle. The pseudoexon inclusion results in a change in the reading frame and appearance of a premature stop codon. In western blot analysis of protein extracts from fibroblasts, there was no pronounced reduction of IscU in any of the patients, but the analysis revealed that the species corresponding to mitochondrial IscU migrates slower than a species present only in whole cells. In protein extracted from isolated skeletal muscle mitochondria the western blot analysis revealed a severe deficiency of IscU in the homozygous patients and appearance of a faint new fraction that could represent a truncated protein. There was only a slight reduction of mitochondrial IscU in the compound heterozygotes, despite their severe phenotype, indicating that the IscU expressed in these patients is non-functional.}, }
@article {pmid19564920, year = {2009}, author = {Chapalain, A and Chevalier, S and Orange, N and Murillo, L and Papadopoulos, V and Feuilloley, MG}, title = {Bacterial ortholog of mammalian translocator protein (TSPO) with virulence regulating activity.}, journal = {PloS one}, volume = {4}, number = {6}, pages = {e6096}, pmid = {19564920}, issn = {1932-6203}, support = {R01 ES007747/ES/NIEHS NIH HHS/United States ; ES007747/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Bacterial Proteins/metabolism ; Benzodiazepines/pharmacology ; Cell Adhesion ; *Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Genome, Bacterial ; Mice ; Mitochondria/metabolism ; Mitochondrial Membranes/*metabolism ; Models, Biological ; Models, Genetic ; Pseudomonas fluorescens/*genetics ; Receptors, GABA/*metabolism ; Receptors, GABA-A/genetics/*physiology ; Virulence ; }, abstract = {The translocator protein (TSPO), previously designated as peripheral-type benzodiazepine receptor, is a protein mainly located in the outer mitochondrial membrane of eukaryotic cells. TSPO is implicated in major physiological functions and functionally associated with other proteins such as the voltage-dependent anionic channel, also designated as mitochondrial porin. Surprisingly, a TSPO-related protein was identified in the photosynthetic bacterium Rhodobacter sphaeroides but it was initially considered as a relict of evolution. In the present study we cloned a tspO gene in Pseudomonas fluorescens MF37, a non-photosynthetic eubacterium and we used bioinformatics tools to identify TSPO in the genome of 97 other bacteria. P. fluorescens TSPO was recognized by antibodies against mouse protein and by PK 11195, an artificial ligand of mitochondrial TSPO. As in eukaryotes, bacterial TSPO appears functionally organized as a dimer and the apparent Kd for PK 11195 is in the same range than for its eukaryotic counterpart. When P. fluorescens MF37 was treated with PK 11195 (10(-5) M) adhesion to living or artificial surfaces and biofilm formation activity were increased. Conversely, the apoptotic potential of bacteria on eukaryotic cells was significantly reduced. This effect of PK11195 was abolished in a mutant of P. fluorescens MF37 deficient for its major outer membrane porin, OprF. The present results demonstrate the existence of a bacterial TSPO that shares common structural and functional characteristics with its mammalian counterpart. This protein, apparently involved in adhesion and virulence, reveals the existence of a possible new inter kingdom signalling system and suggests that the human microbiome should be involuntarily exposed to the evolutionary pressure of benzodiazepines and related molecules. This discovery also represents a promising opportunity for the development of alternative antibacterial strategies.}, }
@article {pmid19558325, year = {2009}, author = {Alfonzo, JD and Söll, D}, title = {Mitochondrial tRNA import--the challenge to understand has just begun.}, journal = {Biological chemistry}, volume = {390}, number = {8}, pages = {717-722}, pmid = {19558325}, issn = {1437-4315}, support = {R01 GM022854/GM/NIGMS NIH HHS/United States ; R01 GM084065/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Evolution, Molecular ; Humans ; Mitochondria/*genetics/metabolism ; Mitochondrial Membranes/*metabolism ; Protein Biosynthesis ; RNA, Protozoan/metabolism ; RNA, Transfer/genetics/*metabolism ; }, abstract = {Mitochondrial translation is important for the synthesis of proteins involved in oxidative phosphorylation, which yields the bulk of the ATP made in cells. During evolution most mitochondria-containing organisms have lost tRNA genes from their mitochondrial genomes. Thus, to support the essential process of nuanced mitochondrial translation, mechanisms to actively transport tRNAs from the cytoplasm across the mitochondrial membranes into the mitochondrion have evolved. Here, we review the currently known tRNA import mechanisms, comment on recent discoveries of various import factors, and suggest a rationale for forces that lie behind the evolution of mitochondrial tRNA import.}, }
@article {pmid19555461, year = {2009}, author = {Gibellini, F and Hunter, WN and Smith, TK}, title = {The ethanolamine branch of the Kennedy pathway is essential in the bloodstream form of Trypanosoma brucei.}, journal = {Molecular microbiology}, volume = {73}, number = {5}, pages = {826-843}, pmid = {19555461}, issn = {1365-2958}, support = {/WT_/Wellcome Trust/United Kingdom ; 067441/WT_/Wellcome Trust/United Kingdom ; 083481/WT_/Wellcome Trust/United Kingdom ; 082596/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Blood/*parasitology ; DNA, Protozoan/chemistry/genetics ; Gene Knockout Techniques ; Genes, Essential ; Genes, Protozoan ; Mitochondria/ultrastructure ; Molecular Sequence Data ; Phosphatidylethanolamines/*analysis ; Phylogeny ; RNA Nucleotidyltransferases/*genetics/*metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Spectrometry, Mass, Electrospray Ionization ; Trypanosoma brucei brucei/*chemistry/cytology/isolation &amp; purification/ultrastructure ; }, abstract = {Phosphatidylethanolamine (GPEtn), a major phospholipid component of trypanosome membranes, is synthesized de novo from ethanolamine through the Kennedy pathway. Here the composition of the GPEtn molecular species in the bloodstream form of Trypanosoma brucei is determined, along with new insights into phospholipid metabolism, by in vitro and in vivo characterization of a key enzyme of the Kennedy pathway, the cytosolic ethanolamine-phosphate cytidylyltransferase (TbECT). Gene knockout indicates that TbECT is essential for growth and survival, thus highlighting the importance of the Kennedy pathway for the pathogenic stage of the African trypanosome. Phosphatiylserine decarboxylation, a potential salvage pathway, does not appear to be active in cultured bloodstream form T. brucei, and it is not upregulated even when the Kennedy pathway is disrupted. In vivo metabolic labelling and phospholipid composition analysis by ESI-MS/MS of the knockout cells confirmed a significant decrease in GPEtn species, as well as changes in the relative abundance of other phospholipid species. Reduction in GPEtn levels had a profound influence on the morphology of the mutants and it compromised mitochondrial structure and function, as well as glycosylphosphatidylinositol anchor biosynthesis. TbECT is therefore genetically validated as a potential drug target against the African trypanosome.}, }
@article {pmid19540236, year = {2009}, author = {Mattiacio, JL and Read, LK}, title = {Evidence for a degradosome-like complex in the mitochondria of Trypanosoma brucei.}, journal = {FEBS letters}, volume = {583}, number = {14}, pages = {2333-2338}, pmid = {19540236}, issn = {1873-3468}, support = {T32AI07614/AI/NIAID NIH HHS/United States ; T32 AI007614/AI/NIAID NIH HHS/United States ; R56 AI047329/AI/NIAID NIH HHS/United States ; R56AI047329/AI/NIAID NIH HHS/United States ; R01AI077520/AI/NIAID NIH HHS/United States ; R01 AI077520/AI/NIAID NIH HHS/United States ; R01 AI077520-01/AI/NIAID NIH HHS/United States ; R56 AI047329-06A2/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Biological Evolution ; Endoribonucleases/*metabolism ; Exoribonucleases/genetics/metabolism ; Humans ; Mitochondria/genetics/*metabolism ; Molecular Sequence Data ; Multienzyme Complexes/*metabolism ; Polyribonucleotide Nucleotidyltransferase/*metabolism ; Protozoan Proteins/genetics/*metabolism ; RNA Helicases/genetics/*metabolism ; RNA, Protozoan ; Sequence Alignment ; Trypanosoma brucei brucei/*cytology/metabolism ; }, abstract = {Mitochondrial RNA turnover in yeast involves the degradosome, composed of DSS-1 exoribonuclease and SUV3 RNA helicase. Here, we describe a degradosome-like complex, containing SUV3 and DSS-1 homologues, in the early branching protozoan, Trypanosoma brucei. TbSUV3 is mitochondrially localized and co-sediments with TbDSS-1 on glycerol gradients. Co-immunoprecipitation demonstrates that TbSUV3 and TbDSS-1 associate in a stable complex, which differs from the yeast degradosome in that it is not stably associated with mitochondrial ribosomes. This is the first report of a mitochondrial degradosome-like complex outside of yeast. Our data indicate an early evolutionary origin for the mitochondrial SUV3/DSS-1 containing complex.}, }
@article {pmid19536286, year = {2009}, author = {Stolzenberg, N and Nguyen The, B and Salducci, MD and Cavalli, L}, title = {Influence of environment and mitochondrial heritage on the ecological characteristics of fish in a hybrid zone.}, journal = {PloS one}, volume = {4}, number = {6}, pages = {e5962}, pmid = {19536286}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/metabolism ; Ecology/*methods ; Environment ; Female ; Fishes ; Male ; Mitochondria/metabolism/*pathology ; Models, Biological ; Models, Genetic ; Models, Theoretical ; Phenotype ; Sex Factors ; Time Factors ; }, abstract = {BACKGROUND: Ecological characteristics (growth, morphology, reproduction) arise from the interaction between environmental factors and genetics. Genetic analysis of individuals' life history traits might be used to improve our understanding of mechanisms that form and maintain a hybrid zone.<br><br>A fish hybrid zone was used to characterize the process of natural selection. Data were collected during two reproductive periods (2001 and 2002) and 1117 individuals (nase, Chondrostama nasus nasus, sofie C. toxostoma toxostoma and hybrids) were sampled. Reproductive dates of the two parental species overlapped at sympatric sites. The nase had an earlier reproductive period than the sofie; males had longer reproductive periods for both species. Hybridisation between female nase and male sofie was the most likely. Hybrids had a reproductive period similar to the inherited parental mitochondrial type. Growth and reproductive information from different environments has been synthesised following a bayesian approach of the von Bertalanffy model. Hybrid life history traits appear to link with maternal heritage. Hybrid size from the age of two and size at first maturity appeared to be closer to the size of the maternal origin species (nase or sofie). Median growth rates for hybrids were similar and intermediate between those of the parental species. We observed variable life history traits for hybrids and pure forms in the different parts of the hybrid zone. Geometrical analysis of the hybrid fish shape gave evidence of two main morphologies with a link to maternal heritage.<br><br>CONCLUSIONS/SIGNIFICANCE: Selective mating seemed to be the underlying process which, with mitochondrial heritage, could explain the evolution of the studied hybrid zone. More generally, we showed the importance of studies on hybrid zones and specifically the study of individuals' ecological characteristics, to improve our understanding of speciation.}, }
@article {pmid19535740, year = {2009}, author = {Tofanelli, S and Bertoncini, S and Castrì, L and Luiselli, D and Calafell, F and Donati, G and Paoli, G}, title = {On the origins and admixture of Malagasy: new evidence from high-resolution analyses of paternal and maternal lineages.}, journal = {Molecular biology and evolution}, volume = {26}, number = {9}, pages = {2109-2124}, doi = {10.1093/molbev/msp120}, pmid = {19535740}, issn = {1537-1719}, mesh = {Asian People ; Black People/*genetics ; Chromosomes, Human, Y/genetics ; Computer Simulation ; DNA, Mitochondrial/genetics ; *Fathers ; Female ; *Gene Pool ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes ; Humans ; Madagascar ; Male ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; *Mothers ; *Phylogeny ; Time Factors ; }, abstract = {The Malagasy have been shown to be a genetically admixed population combining parental lineages with African and South East Asian ancestry. In the present paper, we fit the Malagasy admixture history in a highly resolved phylogeographic framework by typing a large set of mitochondrial DNA and Y DNA markers in unrelated individuals from inland (Merina) and coastal (Antandroy, Antanosy, and Antaisaka) ethnic groups. This allowed performance of a multilevel analysis in which the diversity among main ethnic divisions, lineage ancestries, and modes of inheritance could be concurrently evaluated. Admixture was confirmed to result from the encounter of African and Southeast Asian people with minor recent male contributions from Europe. However, new scenarios are depicted about Malagasy admixture history. The distribution of ancestral components was ethnic and sex biased, with the Asian ancestry appearing more conserved in the female than in the male gene pool and in inland than in coastal groups. A statistic based on haplotype sharing (D(HS)), showing low sampling error and time linearity over the last 200 generations, was introduced here for the first time and helped to integrate our results with linguistic and archeological data. The focus about the origin of Malagasy lineages was enlarged in space and pushed back in time. Homelands could not be pinpointed but appeared to comprise two vast areas containing different populations from sub-Saharan Africa and South East Asia. The pattern of diffusion of uniparental lineages was compatible with at least two events: a primary admixture of proto-Malay people with Bantu speakers bearing a western-like pool of haplotypes, followed by a secondary flow of Southeastern Bantu speakers unpaired for gender (mainly male driven) and geography (mainly coastal).}, }
@article {pmid19535739, year = {2009}, author = {Ramírez, O and Ojeda, A and Tomàs, A and Gallardo, D and Huang, LS and Folch, JM and Clop, A and Sánchez, A and Badaoui, B and Hanotte, O and Galman-Omitogun, O and Makuza, SM and Soto, H and Cadillo, J and Kelly, L and Cho, IC and Yeghoyan, S and Pérez-Enciso, M and Amills, M}, title = {Integrating Y-chromosome, mitochondrial, and autosomal data to analyze the origin of pig breeds.}, journal = {Molecular biology and evolution}, volume = {26}, number = {9}, pages = {2061-2072}, doi = {10.1093/molbev/msp118}, pmid = {19535739}, issn = {1537-1719}, mesh = {Africa ; Animals ; *Breeding ; Chromosomes, Mammalian/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Europe ; Asia, Eastern ; Genetic Markers ; Geography ; Haplotypes ; Heterozygote ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; Polymorphism, Genetic ; Population Dynamics ; Sus scrofa/classification/*genetics ; Y Chromosome/*genetics ; }, abstract = {We have investigated the origin of swine breeds through the joint analysis of mitochondrial, microsatellite, and Y-chromosome polymorphisms in a sample of pigs and wild boars with a worldwide distribution. Genetic differentiation between pigs and wild boars was remarkably weak, likely as a consequence of a sustained gene flow between both populations. The analysis of nuclear markers evidenced the existence of a close genetic relationship between Near Eastern and European wild boars making it difficult to infer their relative contributions to the gene pool of modern European breeds. Moreover, we have shown that European and Far Eastern pig populations have contributed maternal and paternal lineages to the foundation of African and South American breeds. Although West African pigs from Nigeria and Benin exclusively harbored European alleles, Far Eastern and European genetic signatures of similar intensity were detected in swine breeds from Eastern Africa. This region seems to have been a major point of entry of livestock species in the African continent as a result of the Indian Ocean trade. Finally, South American creole breeds had essentially a European ancestry although Asian Y-chromosome and mitochondrial haplotypes were found in a few Nicaraguan pigs. The existence of Spanish and Portuguese commercial routes linking Asia with America might have favored the introduction of Far Eastern breeds into this continent.}, }
@article {pmid19534824, year = {2009}, author = {Zhang, YJ and Tian, HF and Wen, JF}, title = {The evolution of YidC/Oxa/Alb3 family in the three domains of life: a phylogenomic analysis.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {137}, pmid = {19534824}, issn = {1471-2148}, mesh = {Algal Proteins/genetics ; Animals ; Archaeal Proteins/genetics ; Bacterial Proteins/genetics ; *Evolution, Molecular ; Humans ; Likelihood Functions ; Membrane Transport Proteins/*genetics ; Mitochondrial Proteins/genetics ; *Phylogeny ; Plant Proteins/genetics ; Protozoan Proteins/genetics ; Sequence Alignment ; Thylakoids/genetics ; }, abstract = {BACKGROUND: YidC/Oxa/Alb3 family includes a group of conserved translocases that are essential for protein insertion into inner membranes of bacteria and mitochondria, and thylakoid membranes of chloroplasts. Because mitochondria and chloroplasts are of bacterial origin, Oxa and Alb3, like many other mitochondrial/chloroplastic proteins, are hypothetically derived from the pre-existing protein (YidC) of bacterial endosymbionts. Here, we test this hypothesis and investigate the evolutionary history of the whole YidC/Oxa/Alb3 family in the three domains of life.<br><br>RESULTS: Our comprehensive analyses of the phylogenetic distribution and phylogeny of the YidC/Oxa/Alb3 family lead to the following findings: 1) In archaea, YidC homologs are only sporadically distributed in Euryarchaeota; 2) Most bacteria contain only one YidC gene copy; some species in a few taxa (Bacillus, Lactobacillales, Actinobacteria and Clostridia) have two gene copies; 3) Eukaryotic Oxa and Alb3 have two separate prokaryotic origins, but they might not arise directly from the YidC of proteobacteria and cyanobacteria through the endosymbiosis origins of mitochondrium and chloroplast, respectively; 4) An ancient duplication occurred on both Oxa and Alb3 immediately after their origins, and thus most eukaryotes generally bear two Oxa and two Alb3. However, secondary loss, duplication or acquisition of new domain also occurred on the two genes in some lineages, especially in protists, resulting in a rich diversity or adaptive differentiation of the two translocases in these lineages.<br><br>CONCLUSION: YidC is distributed in bacteria and some Euryarchaeota. Although mitochondrial Oxa and chloroplastic Alb3 are derived from the prokaryotic YidC, their origin might be not related to the endosymbiosis events of the two organelles. In some eukaryotic lineages, especially in protists, Oxa and Alb3 have diverse evolutionary histories. Finally, a model for the evolutionary history of the entire YidC/Oxa/Alb3 family in the three domains of life is proposed.}, }
@article {pmid19531743, year = {2009}, author = {Dagley, MJ and Dolezal, P and Likic, VA and Smid, O and Purcell, AW and Buchanan, SK and Tachezy, J and Lithgow, T}, title = {The protein import channel in the outer mitosomal membrane of Giardia intestinalis.}, journal = {Molecular biology and evolution}, volume = {26}, number = {9}, pages = {1941-1947}, pmid = {19531743}, issn = {1537-1719}, support = {//Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Evolution, Molecular ; Giardia lamblia/*metabolism ; Immunoprecipitation ; Mitochondria/*metabolism ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; Molecular Sequence Data ; Protein Structure, Quaternary ; Protein Transport ; Protozoan Proteins/chemistry/*metabolism ; Sequence Alignment ; }, abstract = {The identification of mitosomes in Giardia generated significant debate on the evolutionary origin of these organelles, whether they were highly reduced mitochondria or the product of a unique endosymbiotic event in an amitochondrial organism. As the protein import pathway is a defining characteristic of mitochondria, we sought to discover a TOM (translocase in the outer mitochondrial membrane) complex in Giardia. A Hidden Markov model search of the Giardia genome identified a Tom40 homologous sequence (GiTom40), where Tom40 is the protein translocation channel of the TOM complex. The GiTom40 protein is located in the membrane of mitosomes in a approximately 200-kDa TOM complex. As Tom40 was derived in the development of mitochondria to serve as the protein import channel in the outer membrane, its presence in Giardia evidences the mitochondrial ancestry of mitosomes.}, }
@article {pmid19527349, year = {2009}, author = {van der Giezen, M}, title = {Hydrogenosomes and mitosomes: conservation and evolution of functions.}, journal = {The Journal of eukaryotic microbiology}, volume = {56}, number = {3}, pages = {221-231}, doi = {10.1111/j.1550-7408.2009.00407.x}, pmid = {19527349}, issn = {1550-7408}, support = {078566/A/05/Z//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Eukaryota/chemistry/genetics/*physiology/ultrastructure ; *Evolution, Molecular ; Metabolic Networks and Pathways ; Mitochondria/chemistry/genetics/*physiology/ultrastructure ; Models, Biological ; Protozoan Proteins/analysis ; }, abstract = {The field studying unusual mitochondria in microbial eukaryotes has come full circle. Some 10-15 years ago it had the evangelical task of informing the wider scientific community that not all eukaryotes had mitochondria. Advances in the field indicated that although some protists might not have mitochondria, the presence of genes of mitochondrial ancestry suggested their lineage once had. The subsequent discovery of mitochondrial compartments in all supposedly amitochondriate protists studied so far indicates that all eukaryotes do have mitochondria indeed. This assertion has fuelled novel eukaryotic origin theories and weakened others. But what do we know about these unusual mitochondria from anaerobic protists? Have they all converged onto similar roles? Iron-sulphur cluster assembly is often hailed as the unifying feature of these organelles. However, the iron-sulphur protein that is so important that a complete organelle is being maintained has not been identified. Is it to be expected that all unusual mitochondria perform the same physiological role? These organelles have been found in numerous protists occupying different ecological niches. Different selection pressures operate on different organisms so there is no reason to suspect that their mitochondria should all be the same.}, }
@article {pmid19523874, year = {2009}, author = {Cavalier-Smith, T and Lewis, R and Chao, EE and Oates, B and Bass, D}, title = {Helkesimastix marina n. sp. (Cercozoa: Sainouroidea superfam. n.) a gliding zooflagellate of novel ultrastructure and unusual ciliary behaviour.}, journal = {Protist}, volume = {160}, number = {3}, pages = {452-479}, doi = {10.1016/j.protis.2009.03.003}, pmid = {19523874}, issn = {1618-0941}, mesh = {Animals ; Cluster Analysis ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Eukaryota/*physiology/*ultrastructure ; Genes, rRNA ; Microscopy ; Microscopy, Electron ; Molecular Sequence Data ; Organelles/*ultrastructure ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {Unlike Helkesimastix faecicola and H. major, Helkesimastix marina is marine, ingests bacteria, is probably also a cannibal, and differs in cell cycle ciliary behaviour. Daughter kinetids have mirror symmetry; pre-division cilia beat asymmetrically. We sequenced its 18S rDNA and studied its ultrastructure to clarify its taxonomy. Helkesimastix (Helkesimastigidae fam. n.) differs unexpectedly radically from cercomonads, lacking their complex microtubular ciliary roots, grouping not with them but with Sainouridae within Pansomonadida. Longitudinal cortical microtubules emanate from a dense apical centrosomal plate, where a striated rhizoplast attaches the nucleus, and two very short subparallel centrioles attach by dense fibres. The marginally more posterior centriole, attached to the centrosomal plate by a dense forked fibre, bears the long 9+2 gliding posterior cilium and a microtubular root; the left-side, nucleus-attached, left centriole bears an immotile ciliary stump with abnormal axoneme of nine disorganized mainly singlet microtubules, unlike the sainourid anterior papilla. Both transitional regions have a proximal lattice, the posterior centriole with slender hub. Sainouroidea superfam. n. (Sainouridae; Helkesimastigidae) have homologous cytoskeletal geometry. Dorsal Golgi dictyosome and posterior microbody are attached to the nuclear envelope, which has slender micro-invaginations and probably a cortical lattice. Bacteria are digested posteriorly in association with numerous mitochondria with flat cristae.}, }
@article {pmid19518267, year = {2009}, author = {Zhang, Y}, title = {Relations between Shannon entropy and genome order index in segmenting DNA sequences.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {79}, number = {4 Pt 1}, pages = {041918}, doi = {10.1103/PhysRevE.79.041918}, pmid = {19518267}, issn = {1539-3755}, mesh = {Algorithms ; Animals ; *Base Sequence ; Biological Evolution ; DNA/*chemistry ; Entropy ; Escherichia coli ; *Genome ; Humans ; Mitochondria/genetics ; *Models, Genetic ; Molecular Sequence Data ; Sequence Homology ; beta-Globins/genetics ; }, abstract = {Shannon entropy H and genome order index S are used in segmenting DNA sequences. Zhang [Phys. Rev. E 72, 041917 (2005)] found that the two schemes are equivalent when a DNA sequence is converted to a binary sequence of S (strong H bond) and W (weak H bond). They left the mathematical proof to mathematicians who are interested in this issue. In this paper, a possible mathematical explanation is given. Moreover, we find that Chargaff parity rule 2 is the necessary condition of the equivalence, and the equivalence disappears when a DNA sequence is regarded as a four-symbol sequence. At last, we propose that S-2(-H) may be related to species evolution.}, }
@article {pmid19517116, year = {2009}, author = {Allen, PJ and Cech, JJ and Kültz, D}, title = {Mechanisms of seawater acclimation in a primitive, anadromous fish, the green sturgeon.}, journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology}, volume = {179}, number = {7}, pages = {903-920}, pmid = {19517116}, issn = {1432-136X}, mesh = {Acclimatization/*physiology ; Aging/physiology ; Analysis of Variance ; Animals ; Bicarbonates/analysis ; Body Weight ; Calcium/analysis ; California ; Carbon Dioxide/analysis ; Cell Compartmentation ; Cell Size ; Fishes/growth &amp; development/*physiology ; Fresh Water ; Gastrointestinal Contents/chemistry ; Gills/cytology/enzymology ; Hydrogen-Ion Concentration ; Intestines/chemistry/enzymology ; Kidney/enzymology ; Magnesium/analysis ; Mitochondria ; Salinity ; *Seawater ; Sodium-Potassium-Exchanging ATPase/metabolism ; Statistics, Nonparametric ; }, abstract = {Relatively little is known about salinity acclimation in the primitive groups of fishes. To test whether physiological preparative changes occur and to investigate the mechanisms of salinity acclimation, anadromous green sturgeon, Acipenser medirostris (Chondrostei) of three different ages (100, 170, and 533 dph) were acclimated for 7 weeks to three different salinities (<3, 10, and 33 ppt). Gill, kidney, pyloric caeca, and spiral intestine tissues were assayed for Na(+), K(+)-ATPase activity; and gills were analyzed for mitochondria-rich cell (MRC) size, abundance, localization and Na(+), K(+)-ATPase content. Kidneys were analyzed for Na(+), K(+)-ATPase localization and the gastro-intestinal tract (GIT) was assessed for changes in ion and base content. Na(+), K(+)-ATPase activities increased in the gills and decreased in the kidneys with increasing salinity. Gill MRCs increased in size and decreased in relative abundance with fish size/age. Gill MRC Na(+), K(+)-ATPase content (e.g., ion-pumping capacity) was proportional to MRC size, indicating greater abilities to regulate ions with size/age. Developmental/ontogenetic changes were seen in the rapid increases in gill MRC size and lamellar length between 100 and 170 dph. Na(+), K(+)-ATPase activities increased fourfold in the pyloric caeca in 33 ppt, presumably due to increased salt and water absorption as indicated by GIT fluids, solids, and ion concentrations. In contrast to teleosts, a greater proportion of base (HCO(3) (-) and 2CO(3) (2-)) was found in intestinal precipitates than fluids. Green sturgeon osmo- and ionoregulate with similar mechanisms to more-derived teleosts, indicating the importance of these mechanisms during the evolution of fishes, although salinity acclimation may be more dependent on body size.}, }
@article {pmid19515690, year = {2009}, author = {McCauley, DE and Bailey, MF}, title = {Recent advances in the study of gynodioecy: the interface of theory and empiricism.}, journal = {Annals of botany}, volume = {104}, number = {4}, pages = {611-620}, pmid = {19515690}, issn = {1095-8290}, mesh = {Biological Evolution ; Flowers/*physiology ; Inbreeding ; Mitochondria/metabolism ; *Models, Biological ; Population Dynamics ; }, abstract = {BACKGROUND: In this review we report on recent literature concerned with studies of gynodioecy, or the co-occurrence of female and hermaphrodite individuals in natural plant populations. Rather than review this literature in its entirety, our focus is on the interplay between theoretical and empirical approaches to the study of gynodioecy.<br><br>SCOPE: Five areas of active inquiry are considered. These are the cost of restoration, the influence of population structure on spatial sex-ratio variation, the influence of inbreeding on sex expression, the signature of cyto-nuclear coevolution on the mitochondrial genome, and the consequences of mitochondrial paternal leakage.<br><br>CONCLUSIONS: Recent advances in the study of gynodioecy have been made by considering both the ecology of female:hermaphrodite fitness differences and the genetics of sex expression. Indeed theory has guided empiricism and empiricism has guided theory. Future advances will require that some of the methods currently available only for model organisms be applied to a wider range of species.}, }
@article {pmid19513277, year = {2009}, author = {Agnati, LF and Barlow, PW and Baldelli, E and Baluska, F}, title = {Are maternal mitochondria the selfish entities that are masters of the cells of eukaryotic multicellular organisms?.}, journal = {Communicative &amp; integrative biology}, volume = {2}, number = {2}, pages = {194-200}, pmid = {19513277}, issn = {1942-0889}, abstract = {The Energide concept, as well as the endosymbiotic theory of eukaryotic cell organization and evolution, proposes that present-day cells of eukaryotic organisms are mosaics of specialized and cooperating units, or organelles. Some of these units were originally free-living prokaryotes, which were engulfed during evolutionary time. Mitochondria represent one of these types of previously independent organisms, the Energide, is another type. This new perspective on the organization of the cell has been further expanded to reveal the concept of a public milieu, the cytosol, in which Energides and mitochondria live, each with their own private internal milieu. The present paper discusses how the endosymbiotic theory implicates a new hypothesis about the hierarchical and communicational organization of the integrated prokaryotic components of the eukaryotic cell and provides a new angle from which to consider the theory of evolution and its bearing upon cellular complexity. Thus, it is proposed that the "selfish gene" hypothesis of Dawkins1 is not the only possible perspective for comprehending genomic and cellular evolution. Our proposal is that maternal mitochondria are the selfish "master" entities of the eukaryotic cell with respect not only to their propagation from cell-to-cell and from generation-to-generation but also to their regulation of all other cellular functions. However, it should be recognized that the concept of "master" and "servant" cell components is a metaphor; in present-day living organisms their organellar components are considered to be interdependent and inseparable.}, }
@article {pmid19513207, year = {2008}, author = {Vesteg, M and Krajcovic, J}, title = {Origin of eukaryotic cells as a symbiosis of parasitic alpha-proteobacteria in the periplasm of two-membrane-bounded sexual pre-karyotes.}, journal = {Communicative &amp; integrative biology}, volume = {1}, number = {1}, pages = {104-113}, pmid = {19513207}, issn = {1942-0889}, abstract = {The last universal common ancestor (LUCA) might have been either prokaryotic- or eukaryotic-like. Nevertheless, the universally distributed components suggest rather LUCA consistent with the pre-cell theory of Kandler. The hypotheses for the origin of eukaryotes are briefly summarized. The models under which prokaryotes or their chimeras were direct ancestors of eukaryotes are criticized. It is proposed that the pre-karyote (a host entity for alpha-proteobacteria) was a remnant of pre-cellular world, and was unlucky to have evolved fusion prohibiting cell surface, and thus could have evolved sex. The DNA damage checkpoint pathway could have represented the only pre-karyotic checkpoint control allowing division only when DNA was completely replicated without mistakes. The fusion of two partially diploid (in S-phase blocked) pre-karyotes might have represented another repair strategy. After completing replication of both haploid sets, DNA damage checkpoint would allow two subsequent rounds of fission. Alternatively, pre-karyote might have possessed two membranes inherited from LUCA. Under this hypothesis symbiotic alpha-proteobacterial ancestors of mitochondria might have ancestrally been selfish parasites of pre-karyote intermembrane space whose infection might have been analogous to infection of G(-)-bacterial periplasm by Bdellovibrio sp. It is suggested that eukaryotic plasma membrane might be derived from pre-karyote outer membrane and nuclear/ER membrane might be derived from pre-karyote inner membrane. Thus the nucleoplasm might be derived from pre-karyote cytoplasm and eukaryotic cytoplasm might be homologous to pre-karyote periplasm.}, }
@article {pmid19503808, year = {2009}, author = {Beckstead, WA and Ebbert, MT and Rowe, MJ and McClellan, DA}, title = {Evolutionary pressure on mitochondrial cytochrome b is consistent with a role of CytbI7T affecting longevity during caloric restriction.}, journal = {PloS one}, volume = {4}, number = {6}, pages = {e5836}, pmid = {19503808}, issn = {1932-6203}, mesh = {*Aging ; Binding Sites ; *Caloric Restriction ; Cytochromes b/*metabolism ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Female ; Free Radicals ; Humans ; Longevity/*genetics ; Mitochondria/*metabolism ; Models, Genetic ; Molecular Conformation ; Phylogeny ; *Polymorphism, Genetic ; }, abstract = {BACKGROUND: Metabolism of energy nutrients by the mitochondrial electron transport chain (ETC) is implicated in the aging process. Polymorphisms in core ETC proteins may have an effect on longevity. Here we investigate the cytochrome b (cytb) polymorphism at amino acid 7 (cytbI7T) that distinguishes human mitochondrial haplogroup H from haplogroup U.<br><br>PRINCIPAL FINDINGS: We compared longevity of individuals in these two haplogroups during historical extremes of caloric intake. Haplogroup H exhibits significantly increased longevity during historical caloric restriction compared to haplogroup U (p = 0.02) while during caloric abundance they are not different. The historical effects of natural selection on the cytb protein were estimated with the software TreeSAAP using a phylogenetic reconstruction for 107 mammal taxa from all major mammalian lineages using 13 complete protein-coding mitochondrial gene sequences. With this framework, we compared the biochemical shifts produced by cytbI7T with historical evolutionary pressure on and near this polymorphic site throughout mammalian evolution to characterize the role cytbI7T had on the ETC during times of restricted caloric intake.<br><br>SIGNIFICANCE: Our results suggest the relationship between caloric restriction and increased longevity in human mitochondrial haplogroup H is determined by cytbI7T which likely enhances the ability of water to replenish the Q(i) binding site and decreases the time ubisemiquinone is at the Q(o) site, resulting in a decrease in the average production rate of radical oxygen species (ROS).}, }
@article {pmid19500773, year = {2009}, author = {Soares, P and Ermini, L and Thomson, N and Mormina, M and Rito, T and Röhl, A and Salas, A and Oppenheimer, S and Macaulay, V and Richards, MB}, title = {Correcting for purifying selection: an improved human mitochondrial molecular clock.}, journal = {American journal of human genetics}, volume = {84}, number = {6}, pages = {740-759}, pmid = {19500773}, issn = {1537-6605}, mesh = {DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genetic Variation ; Genome, Human ; Humans ; Mitochondria/*genetics ; Models, Genetic ; Mutation/*genetics ; Phylogeny ; *Selection, Genetic ; }, abstract = {There is currently no calibration available for the whole human mtDNA genome, incorporating both coding and control regions. Furthermore, as several authors have pointed out recently, linear molecular clocks that incorporate selectable characters are in any case problematic. We here confirm a modest effect of purifying selection on the mtDNA coding region and propose an improved molecular clock for dating human mtDNA, based on a worldwide phylogeny of > 2000 complete mtDNA genomes and calibrating against recent evidence for the divergence time of humans and chimpanzees. We focus on a time-dependent mutation rate based on the entire mtDNA genome and supported by a neutral clock based on synonymous mutations alone. We show that the corrected rate is further corroborated by archaeological dating for the settlement of the Canary Islands and Remote Oceania and also, given certain phylogeographic assumptions, by the timing of the first modern human settlement of Europe and resettlement after the Last Glacial Maximum. The corrected rate yields an age of modern human expansion in the Americas at approximately 15 kya that-unlike the uncorrected clock-matches the archaeological evidence, but continues to indicate an out-of-Africa dispersal at around 55-70 kya, 5-20 ky before any clear archaeological record, suggesting the need for archaeological research efforts focusing on this time window. We also present improved rates for the mtDNA control region, and the first comprehensive estimates of positional mutation rates for human mtDNA, which are essential for defining mutation models in phylogenetic analyses.}, }
@article {pmid19497865, year = {2009}, author = {Liberles, SD and Horowitz, LF and Kuang, D and Contos, JJ and Wilson, KL and Siltberg-Liberles, J and Liberles, DA and Buck, LB}, title = {Formyl peptide receptors are candidate chemosensory receptors in the vomeronasal organ.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {24}, pages = {9842-9847}, pmid = {19497865}, issn = {1091-6490}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; In Situ Hybridization, Fluorescence ; Mice ; Neurons/metabolism ; Phylogeny ; Polymerase Chain Reaction ; Receptors, Formyl Peptide/classification/genetics/*metabolism ; Vomeronasal Organ/cytology/*metabolism ; }, abstract = {The identification of receptors that detect environmental stimuli lays a foundation for exploring the mechanisms and neural circuits underlying sensation. The mouse vomeronasal organ (VNO), which detects pheromones and other semiochemicals, has 2 known families of chemoreceptors, V1Rs and V2Rs. Here, we report a third family of mouse VNO receptors comprising 5 of 7 members of the formyl peptide receptor (FPR) family. Unlike other FPRs, which function in the immune system, these FPRs are selectively expressed in VNO neurons in patterns strikingly similar to those of V1Rs and V2Rs. Each FPR is expressed in a different small subset of neurons that are highly dispersed in the neuroepithelium, consistently coexpress either G alpha(i2) or G alpha(o), and lack other chemoreceptors examined. Given the presence of formylated peptides in bacteria and mitochondria, possible roles for VNO FPRs include the assessment of conspecifics or other species based on variations in normal bacterial flora or mitochondrial proteins.}, }
@article {pmid19496327, year = {2009}, author = {Savina, MV and Emel'yanova, LV and Korotkov, SM and Brailovskaya, IV and Nadeev, AD}, title = {Bioenergetics of mitochondria of the liver with biliary atresia during prolonged starvation.}, journal = {Doklady. Biochemistry and biophysics}, volume = {425}, number = {}, pages = {80-83}, pmid = {19496327}, issn = {1607-6729}, mesh = {Animals ; Biliary Atresia/*metabolism/*pathology ; *Energy Metabolism ; Female ; Fluorescence ; Humans ; Lampreys/metabolism ; Liver/metabolism/*pathology ; Male ; Mitochondria/*metabolism/pathology ; Mitochondrial Swelling/drug effects ; Phenazines/metabolism ; Rats ; Seasons ; Starvation/*metabolism/*pathology ; Time Factors ; Voltage-Dependent Anion Channels/antagonists &amp; inhibitors ; }, }
@article {pmid19494790, year = {2009}, author = {Sapag, A and González-Martínez, G and Lobos-González, L and Encina, G and Tampier, L and Israel, Y and Quintanilla, ME}, title = {Polymorphisms in mitochondrial genes encoding complex I subunits are maternal factors of voluntary alcohol consumption in the rat.}, journal = {Pharmacogenetics and genomics}, volume = {19}, number = {7}, pages = {528-537}, doi = {10.1097/FPC.0b013e32832dc12a}, pmid = {19494790}, issn = {1744-6872}, mesh = {Alcohol Drinking/*genetics ; Amino Acids/genetics ; Animals ; Base Sequence ; Cell Nucleus/genetics ; Computational Biology ; Electron Transport Complex I/chemistry/*genetics ; Exons/genetics ; Female ; Genes, Mitochondrial/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide/*genetics ; Protein Subunits/chemistry/*genetics ; Rats ; }, abstract = {OBJECTIVE: Alcohol is detoxified in the liver by oxidizing enzymes that require nicotinamide adenine dinucleotide (NAD+) such that, in the rat, the availability of NAD+ contributes to control voluntary ethanol intake. The UChA and UChB lines of Wistar rats drink low and high amounts of ethanol respectively and differ in the capacity of their mitochondria to oxidize NADH into NAD+. This function resides in complex I of the respiratory chain and its variation is linked to genes transmitted through the maternal line. The aim of this study was to identify the genetic basis for the difference in the reoxidation of NADH in these nondrinker (UChA) and drinker (UChB) rats.<br><br>METHODS: Seven mitochondrial genes and two chromosome X genes encoding complex I subunits from rats of both lineages were amplified from liver DNA and sequenced.<br><br>RESULTS: The UChA and UChB rat lines differ in their Nd2, Nd4, Nd5 and Nd6 mitochondrial genes and in the encoded proteins. Most noteworthy are ND2 and ND4 whose amino acid variations lead to changes in three-dimensional structure models. The ND2 proteins also differ in the number of predicted transmembrane domains. The Nd1 and Nd3 genes have silent substitutions, whereas Nd4L and the exonic sequences of the nuclear genes Ndufa1 and Ndufb11 show no differences between the UChA and UChB lines.<br><br>CONCLUSION: Amino acid variations in four complex I subunits encoded in the mitochondrial genome may contribute to explain the differences between UChA and UChB rats in their capacity to reoxidize NADH and in their alcohol intake, suggesting that mitochondrial genes may constitute maternal factors of alcoholism.}, }
@article {pmid19492355, year = {2009}, author = {Davidov, Y and Jurkevitch, E}, title = {Predation between prokaryotes and the origin of eukaryotes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {31}, number = {7}, pages = {748-757}, doi = {10.1002/bies.200900018}, pmid = {19492355}, issn = {1521-1878}, mesh = {*Biological Evolution ; Endocytosis ; Eukaryotic Cells/cytology/*metabolism ; Mitochondria/metabolism ; Phylogeny ; Prokaryotic Cells/cytology/*metabolism ; *Symbiosis ; }, abstract = {Accumulating data suggest that the eukaryotic cell originated from a merger of two prokaryotes, an archaeal host and a bacterial endosymbiont. However, since prokaryotes are unable to perform phagocytosis, the means by which the endosymbiont entered its host is an enigma. We suggest that a predatory or parasitic interaction between prokaryotes provides a reasonable explanation for this conundrum. According to the model presented here, the host in this interaction was an anaerobic archaeon with a periplasm-like space. The predator was a small (facultative) aerobic alpha-proteobacterium, which penetrated and replicated within the host periplasm, and later became the mitochondria. Plausible conditions under which this interaction took place and circumstances that may have led to the contemporary complex eukaryotic cell are discussed.}, }
@article {pmid19489141, year = {2008}, author = {Ujvari, B and Madsen, T}, title = {Complete mitochondrial genome of the frillneck lizard (Chlamydosaurus kingii, Reptilia; Agamidae), another squamate with two control regions.}, journal = {Mitochondrial DNA}, volume = {19}, number = {5}, pages = {465-470}, doi = {10.1080/19401730802449162}, pmid = {19489141}, issn = {1940-1736}, mesh = {Animals ; Base Composition ; Base Sequence ; DNA Primers/genetics ; DNA, Mitochondrial/chemistry/genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; Lizards/classification/*genetics ; *Locus Control Region ; Species Specificity ; }, abstract = {Using PCR, the complete mitochondrial genome was sequenced in three frillneck lizards (Chlamydosaurus kingii). The mitochondria spanned over 16,761bp. As in other vertebrates, two rRNA genes, 22 tRNA genes and 13 protein coding genes were identified. However, similar to some other squamate reptiles, two control regions (CRI and CRII) were identified, spanning 801 and 812 bp, respectively. Our results were compared with another Australian member of the family Agamidae, the bearded dragon (Pogana vitticeps). The overall base composition of the light-strand sequence largely mirrored that observed in P vitticeps. Furthermore, similar to P. vitticeps, we observed an insertion 801 bp long between the ND5 and ND6 genes. However, in contrast to P vitticeps we did not observe a conserved sequence block III region. Based on a comparison among the three frillneck lizards, we also present data on the proportion of variable sites within the major mitochondrial regions.}, }
@article {pmid19484124, year = {2009}, author = {Achilli, A and Bonfiglio, S and Olivieri, A and Malusà, A and Pala, M and Hooshiar Kashani, B and Perego, UA and Ajmone-Marsan, P and Liotta, L and Semino, O and Bandelt, HJ and Ferretti, L and Torroni, A}, title = {The multifaceted origin of taurine cattle reflected by the mitochondrial genome.}, journal = {PloS one}, volume = {4}, number = {6}, pages = {e5753}, pmid = {19484124}, issn = {1932-6203}, mesh = {Animals ; Cattle ; DNA, Mitochondrial/metabolism ; Evolution, Molecular ; Female ; Genetic Variation ; *Genome, Mitochondrial ; Haplotypes ; Likelihood Functions ; Mitochondria/metabolism ; Models, Biological ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {A Neolithic domestication of taurine cattle in the Fertile Crescent from local aurochsen (Bos primigenius) is generally accepted, but a genetic contribution from European aurochsen has been proposed. Here we performed a survey of a large number of taurine cattle mitochondrial DNA (mtDNA) control regions from numerous European breeds confirming the overall clustering within haplogroups (T1, T2 and T3) of Near Eastern ancestry, but also identifying eight mtDNAs (1.3%) that did not fit in haplogroup T. Sequencing of the entire mitochondrial genome showed that four mtDNAs formed a novel branch (haplogroup R) which, after the deep bifurcation that gave rise to the taurine and zebuine lineages, constitutes the earliest known split in the mtDNA phylogeny of B. primigenius. The remaining four mtDNAs were members of the recently discovered haplogroup Q. Phylogeographic data indicate that R mtDNAs were derived from female European aurochsen, possibly in the Italian Peninsula, and sporadically included in domestic herds. In contrast, the available data suggest that Q mtDNAs and T subclades were involved in the same Neolithic event of domestication in the Near East. Thus, the existence of novel (and rare) taurine haplogroups highlights a multifaceted genetic legacy from distinct B. primigenius populations. Taking into account that the maternally transmitted mtDNA tends to underestimate the extent of gene flow from European aurochsen, the detection of the R mtDNAs in autochthonous breeds, some of which are endangered, identifies an unexpected reservoir of genetic variation that should be carefully preserved.}, }
@article {pmid19483474, year = {2009}, author = {Rigden, DJ and Michels, PA and Ginger, ML}, title = {Autophagy in protists: Examples of secondary loss, lineage-specific innovations, and the conundrum of remodeling a single mitochondrion.}, journal = {Autophagy}, volume = {5}, number = {6}, pages = {784-794}, doi = {10.4161/auto.8838}, pmid = {19483474}, issn = {1554-8635}, mesh = {Animals ; *Autophagy ; Eukaryotic Cells/*cytology ; Humans ; Mitochondria/*metabolism ; *Phylogeny ; Reproducibility of Results ; Saccharomyces cerevisiae/cytology ; }, abstract = {Autophagy describes the process by which eukaryotes selectively and nonselectively target cytoplasm and entire organelles for lysosomal or (in yeast) vacuolar degradation. More than 30 different proteins contribute to this complex process, and it is widely recognized that the term autophagy does not describe merely a single linear pathway by which intracellular components are routed for lysosomal degradation. Yet, while autophagy has been unequivocally demonstrated in evolutionarily diverse organisms and the importance of autophagy in many aspects of human health and development is becoming ever more apparent, the extent to which autophagy in different taxa draws on a conserved cohort of readily recognizable proteins is not particularly clear. Here, we address this issue by comprehensive mapping of known autophagy components across a taxonomically diverse range of unicellular eukaryotes. Unexpectedly, our analysis points to independent examples of secondary loss of macroautophagy, the best understood of the autophagy pathways, in two parasites and one extremophile. Additionally, while our data point towards autophagy being an ancient innovation, utilizing conserved core machinery, it is also clear that lineage-specific moderation (e.g., probable loss of Atg17 in some unikonts) and elaboration (paralogue expansion) of the core macroautophagy pathway occurs readily. Finally, we also consider the interplay between autophagy and organelle turnover in protists. Here, there are likely to be intriguing issues, as exemplified by mitochondrial turnover. In contrast to the dynamic mitochondrial fusion and fission observed in many eukaryotes (including yeast), cell cycle regulated division of a single mitochondrion occurs in some protists. Yet, in these organisms mitochondrial function can often be rapidly remodeled; we contend that in these species turnover of mitochondrial proteins is the product of intraorganellar protease activity.}, }
@article {pmid19477263, year = {2009}, author = {Bodzioch, M and Lapicka-Bodzioch, K and Zapala, B and Kamysz, W and Kiec-Wilk, B and Dembinska-Kiec, A}, title = {Evidence for potential functionality of nuclearly-encoded humanin isoforms.}, journal = {Genomics}, volume = {94}, number = {4}, pages = {247-256}, doi = {10.1016/j.ygeno.2009.05.006}, pmid = {19477263}, issn = {1089-8646}, mesh = {Adult ; Amino Acid Motifs ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Apoptosis/*genetics ; Cell Nucleus/genetics ; Cells, Cultured ; Chromosomes, Human ; Chromosomes, Mammalian ; Computational Biology/methods ; Consensus Sequence ; DNA, Complementary ; Dose-Response Relationship, Drug ; Genome, Human ; Heterozygote ; Homozygote ; Humans ; Intracellular Signaling Peptides and Proteins/genetics/*metabolism ; Isoleucine/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Neuroprotective Agents/*pharmacology ; Open Reading Frames/genetics ; Pan troglodytes ; Peptide Fragments/chemistry/*genetics/*metabolism ; Peptide Mapping ; Phylogeny ; Protein Isoforms/genetics/metabolism ; Rhodamines/metabolism ; Sequence Homology, Amino Acid ; Staurosporine/pharmacology ; Time Factors ; Umbilical Veins/cytology ; beta Carotene/pharmacology ; }, abstract = {Humanin (HN) is a recently identified neuroprotective and antiapoptotic peptide derived from a portion of the mitochondrial MT-RNR2 gene. We provide bioinformatic and expression data suggesting the existence of 13 MT-RNR2-like nuclear loci predicted to maintain the open reading frames of 15 distinct full-length HN-like peptides. At least ten of these nuclear genes are expressed in human tissues, and respond to staurosporine (STS) and beta-carotene. Sequence comparisons of the nuclear HN isoforms and their homologues in other species reveal two consensus motifs, encompassing residues 5-11 (GFS/NCLLL), and 14-19 (SEIDLP/S). Proline vs serine in position 19 may determine whether the peptide is secreted or not, while threonine in position 13 may be important for cell surface receptor binding. Cytoprotection against the STS-induced apoptosis conferred by the polymorphic HN5 variant, in which threonine in position 13 is replaced with isoleucine, is reduced compared to the wild type HN5 peptide.}, }
@article {pmid19462511, year = {2008}, author = {Deng, W and Luo, K and Li, Z and Yang, Y}, title = {Molecular cloning and characterization of a mitochondrial dicarboxylate/tricarboxylate transporter gene in Citrus junos response to aluminum stress.}, journal = {Mitochondrial DNA}, volume = {19}, number = {4}, pages = {376-384}, pmid = {19462511}, issn = {1940-1736}, mesh = {Aluminum/toxicity ; Amino Acid Sequence ; Base Sequence ; Carrier Proteins/*genetics ; Citrus/drug effects/*genetics/*metabolism ; Cloning, Molecular ; DNA Primers/genetics ; DNA, Complementary/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Dicarboxylic Acid Transporters/*genetics ; Gene Expression/drug effects ; *Genes, Mitochondrial/drug effects ; *Genes, Plant/drug effects ; Mitochondria/drug effects/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {A mitochondrial dicarboxylate/tricarboxylate carrier gene, CjDTC, was isolated from Citrus junos by the rapid amplification of cDNA ends and the Y-shaped adaptor-dependent extension methods. It consisted of a 472-base pair (bp) upstream regulatory region and an 897-bp open reading frame encoding a protein of 299 amino acids. Homologous analysis revealed that CjDTC protein might be a plant dicarboxylate/tricarboxylate carrier protein involved in the mitochondria dicarboxylate/tricarboxylate transport. The putative light responsiveness and salicylic acid responsiveness regulatory elements were identified in the upstream regulatory region of CjDTC. Southern blot analysis demonstrated the presence of a single CjDTC gene located on the genome of citrus. As shown by northern hybridization, CjDTC was expressed in all plant tissues examined and the highest transcript level was observed in roots with significantly lower transcript amounts in leaves and stems. Moreover, real-time polymerase chain reaction analysis demonstrated that CjDTC expression was induced by aluminum treatment, suggesting that CjDTC protein might be involved in the excretion of organic acids and rhizotoxic aluminum tolerance.}, }
@article {pmid19459785, year = {2009}, author = {Bridges, HR and Grgic, L and Harbour, ME and Hirst, J}, title = {The respiratory complexes I from the mitochondria of two Pichia species.}, journal = {The Biochemical journal}, volume = {422}, number = {1}, pages = {151-159}, doi = {10.1042/BJ20090492}, pmid = {19459785}, issn = {1470-8728}, support = {MC_U105663141/MRC_/Medical Research Council/United Kingdom ; MC_U105663148/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Biocatalysis ; Electron Spin Resonance Spectroscopy ; Electron Transport Complex I/*isolation &amp; purification/metabolism ; Fungal Proteins/isolation &amp; purification/metabolism ; Mitochondria/*enzymology ; Mitochondrial Membranes/enzymology ; NADH Dehydrogenase/metabolism ; Phylogeny ; Pichia/*enzymology ; Protein Subunits/metabolism ; Proton Pumps/metabolism ; Species Specificity ; }, abstract = {NADH:ubiquinone oxidoreductase (complex I) is an entry point for electrons into the respiratory chain in many eukaryotes. It couples NADH oxidation and ubiquinone reduction to proton translocation across the mitochondrial inner membrane. Because complex I deficiencies occur in a wide range of neuromuscular diseases, including Parkinson's disease, there is a clear need for model eukaryotic systems to facilitate structural, functional and mutational studies. In the present study, we describe the purification and characterization of the complexes I from two yeast species, Pichia pastoris and Pichia angusta. They are obligate aerobes which grow to very high cell densities on simple medium, as yeast-like, spheroidal cells. Both Pichia enzymes catalyse inhibitor-sensitive NADH:ubiquinone oxidoreduction, display EPR spectra which match closely to those from other eukaryotic complexes I, and show patterns characteristic of complex I in SDS/PAGE analysis. Mass spectrometry was used to identify several canonical complex I subunits. Purified P. pastoris complex I has a particularly high specific activity, and incorporating it into liposomes demonstrates that NADH oxidation is coupled to the generation of a protonmotive force. Interestingly, the rate of NADH-induced superoxide production by the Pichia enzymes is more than twice as high as that of the Bos taurus enzyme. Our results both resolve previous disagreement about whether Pichia species encode complex I, furthering understanding of the evolution of complex I within dikarya, and they provide two new, robust and highly active model systems for study of the structure and catalytic mechanism of eukaryotic complexes I.}, }
@article {pmid19457430, year = {2009}, author = {Calo-Mata, P and Pascoal, A and Fernández-No, I and Böhme, K and Gallardo, JM and Barros-Velázquez, J}, title = {Evaluation of a novel 16S rRNA/tRNAVal mitochondrial marker for the identification and phylogenetic analysis of shrimp species belonging to the superfamily Penaeoidea.}, journal = {Analytical biochemistry}, volume = {391}, number = {2}, pages = {127-134}, doi = {10.1016/j.ab.2009.05.020}, pmid = {19457430}, issn = {1096-0309}, mesh = {Animals ; Mitochondria/*genetics ; Penaeidae/*classification/genetics ; Phylogeny ; Polymerase Chain Reaction/*methods ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/*analysis/genetics ; RNA, Transfer, Val/*analysis/genetics ; Species Specificity ; }, abstract = {In this study, we infer the phylogenetic relationships within commercial shrimp using sequence data from a novel mitochondrial marker consisting of an approximately 530-bp region of the 16S ribosomal RNA (rRNA)/transfer RNA (tRNA)(Val) genes compared with two other mitochondrial genes: 16S rRNA and cytochrome c oxidase I (COI). All three mitochondrial markers were considerably AT rich, exhibiting values up to 78.2% for the species Penaeus monodon in the 16S rRNA/tRNA(Val) genes, notably higher than the average among other Malacostracan mitochondrial genomes. Unlike the 16S rRNA and COI genes, the 16S rRNA/tRNA(Val) marker evidenced that Parapenaeus is more closely related to Metapenaeus than to Solenocera, a result that seems to be more in agreement with the taxonomic status of these genera. To our knowledge, our study using the 16S rRNA/tRNA(Val) gene as a marker for phylogenetic analysis offers the first genetic evidence to confirm that Pleoticus muelleri and Solenocera agassizi constitute a separate group and that they are more related to each other than to genera belonging to the family Penaeidae. The 16S rRNA/tRNA(Val) region was also found to contain more variable sites (56%) than the other two regions studied (33.4% for the 16S rRNA region and 42.7% for the COI region). The presence of more variable sites in the 16S rRNA/tRNA(Val) marker allowed the interspecific differentiation of all 19 species examined. This is especially useful at the commercial level for the identification of a large number of shrimp species, particularly when the lack of morphological characteristics prevents their differentiation.}, }
@article {pmid19457268, year = {2009}, author = {Wu, Y and Yang, J and Yang, F and Liu, T and Leng, W and Chu, Y and Jin, Q}, title = {Recent dermatophyte divergence revealed by comparative and phylogenetic analysis of mitochondrial genomes.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {238}, pmid = {19457268}, issn = {1471-2164}, support = {R01 AA020504/AA/NIAAA NIH HHS/United States ; }, mesh = {Arthrodermataceae/classification/*genetics ; Comparative Genomic Hybridization ; DNA, Fungal/genetics ; DNA, Mitochondrial/genetics ; Epidermophyton/classification/genetics ; *Evolution, Molecular ; Gene Order ; Genome, Fungal ; *Genome, Mitochondrial ; Introns ; Microsporum/classification/genetics ; Open Reading Frames ; *Phylogeny ; Sequence Analysis, DNA ; Trichophyton/classification/genetics ; }, abstract = {BACKGROUND: Dermatophytes are fungi that cause superficial infections of the skin, hair, and nails. They are the most common agents of fungal infections worldwide. Dermatophytic fungi constitute three genera, Trichophyton, Epidermophyton, and Microsporum, and the evolutionary relationships between these genera are epidemiologically important. Mitochondria are considered to be of monophyletic origin and mitochondrial sequences offer many advantages for phylogenetic studies. However, only one complete dermatophyte mitochondrial genome (E. floccosum) has previously been determined.<br><br>RESULTS: The complete mitochondrial DNA sequences of five dermatophyte species, T. rubrum (26,985 bp), T. mentagrophytes (24,297 bp), T. ajelloi (28,530 bp), M. canis (23,943 bp) and M. nanum (24,105 bp) were determined. These were compared to the E. floccosum sequence. Mitochondrial genomes of all 6 species were found to harbor the same set of genes arranged identical order indicating that these dermatophytes are closely related. Genome size differences were largely due to variable lengths of non-coding intergenic regions and the presence/absence of introns. Phylogenetic analyses based on complete mitochondrial genomes reveals that the divergence of the dermatophyte clade was later than of other groups of pathogenic fungi.<br><br>CONCLUSION: This is the first systematic comparative genomic study on dermatophytes, a highly conserved and recently-diverged lineage of ascomycota fungi. The data reported here provide a basis for further exploration of interrelationships between dermatophytes and will contribute to the study of mitochondrial evolution in higher fungi.}, }
@article {pmid19451646, year = {2009}, author = {Merker, S and Driller, C and Perwitasari-Farajallah, D and Pamungkas, J and Zischler, H}, title = {Elucidating geological and biological processes underlying the diversification of Sulawesi tarsiers.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {21}, pages = {8459-8464}, pmid = {19451646}, issn = {1091-6490}, mesh = {Animals ; Base Sequence ; *Biological Phenomena ; Evolution, Molecular ; Genetic Variation/genetics ; *Geological Phenomena ; Indonesia ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Population Dynamics ; Tarsiidae/classification/genetics ; }, abstract = {Because of their exceptionally long independent evolution, a range diminution of their Eocene relatives, and a remarkable subsequent diversification in Southeast Asia, tarsiers are of particular importance to evolutionary primatologists. Little is known, however, on the processes shaping the radiation of these small enigmatic primates-especially on the Indonesian island of Sulawesi, their center of endemism. Geological reconstructions and progress in applying DNA sequence information to divergence dating now provide us with the tools and background to comprehend tarsier dispersal. Here, we describe effects of plate-tectonic movements, Pleistocene sea level changes, and hybridization on the divergence of central Sulawesi tarsiers. We analyzed 12 microsatellites, the cytochrome b gene, the hypervariable region I of the mitochondrial control region, and the sex-determining region on the Y-chromosome from 144 specimens captured along a transect crossing a species boundary and a contact zone between 2 microplates. Based on these differentially inherited genetic markers, geographic information, and recordings of vocalizations, we demonstrate that the species boundary coincides with a tectonic suture. We estimate the most recent common ancestor of the 2 taxa to have lived 1.4 Mya, we describe asymmetrical introgressive hybridization, and we give evidence of unbiased dispersal in one species and male-biased dispersal in another species. This study exemplifies that the distribution of tarsier acoustic forms on Sulawesi is consistent with the allocation of genetic variability and that plate-tectonic and glacial events have left traceable marks in the biogeography of this island's unique fauna.}, }
@article {pmid19450731, year = {2009}, author = {Vickers, TJ and Murta, SM and Mandell, MA and Beverley, SM}, title = {The enzymes of the 10-formyl-tetrahydrofolate synthetic pathway are found exclusively in the cytosol of the trypanosomatid parasite Leishmania major.}, journal = {Molecular and biochemical parasitology}, volume = {166}, number = {2}, pages = {142-152}, pmid = {19450731}, issn = {1872-9428}, support = {R01 AI021903/AI/NIAID NIH HHS/United States ; R01 AI029646/AI/NIAID NIH HHS/United States ; R01 AI031078/AI/NIAID NIH HHS/United States ; R37 AI021903/AI/NIAID NIH HHS/United States ; R01 AI031078-16/AI/NIAID NIH HHS/United States ; AI21903/AI/NIAID NIH HHS/United States ; R01 AI029646-20/AI/NIAID NIH HHS/United States ; R01 AI021903-24/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Biological Transport ; Biosynthetic Pathways ; Cytosol/*enzymology/metabolism ; Kinetics ; Leishmania major/classification/*enzymology/genetics/metabolism ; Leishmaniasis, Cutaneous/*parasitology ; Leucovorin/*analogs &amp; derivatives/biosynthesis ; Mice ; Mice, Inbred BALB C ; Mitochondria/genetics/metabolism ; Phylogeny ; Protozoan Proteins/chemistry/genetics/*metabolism ; }, abstract = {In most organisms 10-formyl-tetrahydrofolate (10-CHO-THF) participates in the synthesis of purines in the cytosol and formylation of mitochondrial initiator methionyl-tRNA(Met). Here we studied 10-CHO-THF biosynthesis in the protozoan parasite Leishmania major, a purine auxotroph. Two distinct synthetic enzymes are known, a bifunctional methylene-tetrahydrofolate dehydrogenase/cyclohydrolase (DHCH) or formyl-tetrahydrofolate ligase (FTL), and phylogenomic profiling revealed considerable diversity for these in trypanosomatids. All species surveyed contain a DHCH1, which was shown recently to be essential in L. major. A second DHCH2 occurred only in L. infantum, L. mexicana and T. cruzi, and as a pseudogene in L. major. DHCH2s bear N-terminal extensions and we showed a LiDHCH2-GFP fusion was targeted to the mitochondrion. FTLs were found in all species except Trypanosoma brucei. L. major ftl(-) null mutants were phenotypically normal in growth, differentiation, animal infectivity and sensitivity to a panel of pteridine analogs, but grew more slowly when starved for serine or glycine, as expected for amino acids that are substrates in C1-folate metabolism. Cell fractionation and western blotting showed that both L. major DHCH1 and FTL were localized to the cytosol and not the mitochondrion. These localization data predict that in L. major cytosolic 10-formyl-tetrahydrofolate must be transported into the mitochondrion to support methionyl-tRNA(Met) formylation. The retention in all the trypanosomatids of at least one enzyme involved in 10-formyl-tetrahydrofolate biosynthesis, and the essentiality of this metabolite in L. major, suggests that this pathway represents a promising new area for chemotherapeutic attack in these parasites.}, }
@article {pmid19448273, year = {2009}, author = {Brandvain, Y and Wade, MJ}, title = {The functional transfer of genes from the mitochondria to the nucleus: the effects of selection, mutation, population size and rate of self-fertilization.}, journal = {Genetics}, volume = {182}, number = {4}, pages = {1129-1139}, pmid = {19448273}, issn = {1943-2631}, support = {R01 GM084238/GM/NIGMS NIH HHS/United States ; R01 GM084238-02/GM/NIGMS NIH HHS/United States ; R01-GM084238/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Transport ; Cell Nucleus/*genetics/metabolism ; Eukaryotic Cells ; *Genes, Mitochondrial ; Inbreeding ; Mitochondria/*genetics/metabolism ; *Models, Genetic ; Mutation ; Population Density ; Selection, Genetic ; }, abstract = {The transfer of mitochondrial genes to the nucleus is a recurrent and consistent feature of eukaryotic genome evolution. Although many theories have been proposed to explain such transfers, little relevant data exist. The observation that clonal and self-fertilizing plants transfer more mitochondrial genes to their nuclei than do outcrossing plants contradicts predictions of major theories based on nuclear recombination and leaves a gap in our conceptual understanding how the observed pattern of gene transfer could arise. Here, with a series of deterministic and stochastic simulations, we show how epistatic selection and relative mutation rates of mitochondrial and nuclear genes influence mitochondrial-to-nuclear gene transfer. Specifically, we show that when there is a benefit to having a mitochondrial gene present in the nucleus, but absent in the mitochondria, self-fertilization dramatically increases both the rate and the probability of gene transfer. However, absent such a benefit, when mitochondrial mutation rates exceed those of the nucleus, self-fertilization decreases the rate and probability of transfer. This latter effect, however, is much weaker than the former. Our results are relevant to understanding the probabilities of fixation when loci in different genomes interact.}, }
@article {pmid19439189, year = {2009}, author = {Hoyos-Carvajal, L and Orduz, S and Bissett, J}, title = {Genetic and metabolic biodiversity of Trichoderma from Colombia and adjacent neotropic regions.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {46}, number = {9}, pages = {615-631}, doi = {10.1016/j.fgb.2009.04.006}, pmid = {19439189}, issn = {1096-0937}, mesh = {*Biodiversity ; Carbon/metabolism ; Central America ; DNA, Fungal/analysis/genetics ; DNA, Ribosomal Spacer/analysis/genetics ; Genes, Fungal/genetics ; Genetic Variation ; Metabolome ; Mexico ; Mitochondria/metabolism ; Phylogeny ; Sequence Analysis, DNA ; South America ; Species Specificity ; Trichoderma/*genetics/isolation &amp; purification/*metabolism ; }, abstract = {The genus Trichoderma has been studied for production of enzymes and other metabolites, as well as for exploitation as effective biological control agents. The biodiversity of Trichoderma has seen relatively limited study over much of the neotropical region. In the current study we assess the biodiversity of 183 isolates from Mexico, Guatemala, Panama, Ecuador, Peru, Brazil and Colombia, using morphological, metabolic and genetic approaches. A comparatively high diversity of species was found, comprising 29 taxa: Trichoderma asperellum (60 isolates), Trichoderma atroviride (3), Trichoderma brevicompactum (5), Trichoderma crassum (3), Trichoderma erinaceum (3), Trichoderma gamsii (2), Trichoderma hamatum (2), Trichoderma harzianum (49), Trichoderma koningiopsis (6), Trichoderma longibrachiatum (3), Trichoderma ovalisporum (1), Trichoderma pubescens (2), Trichoderma rossicum (4), Trichoderma spirale (1), Trichoderma tomentosum (3), Trichoderma virens (8), Trichoderma viridescens (7) and Hypocrea jecorina (3) (anamorph: Trichoderma reesei), along with 11 currently undescribed species. T. asperellum was the prevalent species and was represented by two distinct genotypes with different metabolic profiles and habitat preferences. The second predominant species, T. harzianum, was represented by three distinct genotypes. The addition of 11 currently undescribed species is evidence of the considerable unresolved biodiversity of Trichoderma in neotropical regions. Sequencing of the internal transcribed spacer regions (ITS) of the ribosomal repeat could not differentiate some species, and taken alone gave several misidentifications in part due to the presence of nonorthologous copies of the ITS in some isolates.}, }
@article {pmid19438520, year = {2009}, author = {Degtyar, E and Zusman, T and Ehrlich, M and Segal, G}, title = {A Legionella effector acquired from protozoa is involved in sphingolipids metabolism and is targeted to the host cell mitochondria.}, journal = {Cellular microbiology}, volume = {11}, number = {8}, pages = {1219-1235}, doi = {10.1111/j.1462-5822.2009.01328.x}, pmid = {19438520}, issn = {1462-5822}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/*metabolism ; Cell Line ; Chlorocebus aethiops ; Eukaryota/*genetics/microbiology ; Evolution, Molecular ; Genes, Bacterial ; Host-Pathogen Interactions ; Legionella/*genetics/metabolism/*pathogenicity ; Legionellosis/microbiology ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Transport ; Sphingolipids/*metabolism ; Virulence ; }, abstract = {Legionella pneumophila infects alveolar macrophages and protozoa through establishment of an intracellular replication niche. This process is mediated by bacterial effectors translocated into the host cell via the Icm/Dot type IV secretion system. Most of the effectors identified so far are unique to L. pneumophila; however, some of the effectors are homologous to eukaryotic proteins. We performed a distribution analysis of many known L. pneumophila effectors and found that several of them, mostly eukaryotic homologous proteins, are present in different Legionella species. In-depth analysis of LegS2, a L. pneumophila homologue of the highly conserved eukaryotic enzyme sphingosine-1-phosphate lyase (SPL), revealed that it was most likely acquired from a protozoan organism early during Legionella evolution. The LegS2 protein was found to translocate into host cells using a C-terminal translocation domain absent in its eukaryotic homologues. LegS2 was found to complement the sphingosine-sensitive phenotype of a Saccharomyces serevisia SPL-null mutant and this complementation depended on evolutionary conserved residues in the LegS2 catalytic domain. Interestingly, unlike the eukaryotic SPL that localizes to the endoplasmic reticulum, LegS2 was found to be targeted mainly to host cell mitochondria. Collectively, our results demonstrate the remarkable adaptations of a eukaryotic protein to the L. pneumophila pathogenesis system.}, }
@article {pmid19429691, year = {2009}, author = {Remmert, M and Linke, D and Lupas, AN and Söding, J}, title = {HHomp--prediction and classification of outer membrane proteins.}, journal = {Nucleic acids research}, volume = {37}, number = {Web Server issue}, pages = {W446-51}, pmid = {19429691}, issn = {1362-4962}, mesh = {Bacterial Outer Membrane Proteins/chemistry/*classification ; Databases, Protein ; Escherichia coli Proteins/chemistry/classification ; Internet ; Sequence Homology, Amino Acid ; *Software ; User-Computer Interface ; }, abstract = {Outer membrane proteins (OMPs) are the transmembrane proteins found in the outer membranes of Gram-negative bacteria, mitochondria and plastids. Most prediction methods have focused on analogous features, such as alternating hydrophobicity patterns. Here, we start from the observation that almost all beta-barrel OMPs are related by common ancestry. We identify proteins as OMPs by detecting their homologous relationships to known OMPs using sequence similarity. Given an input sequence, HHomp builds a profile hidden Markov model (HMM) and compares it with an OMP database by pairwise HMM comparison, integrating OMP predictions by PROFtmb. A crucial ingredient is the OMP database, which contains profile HMMs for over 20,000 putative OMP sequences. These were collected with the exhaustive, transitive homology detection method HHsenser, starting from 23 representative OMPs in the PDB database. In a benchmark on TransportDB, HHomp detects 63.5% of the true positives before including the first false positive. This is 70% more than PROFtmb, four times more than BOMP and 10 times more than TMB-Hunt. In Escherichia coli, HHomp identifies 57 out of 59 known OMPs and correctly assigns them to their functional subgroups. HHomp can be accessed at http://toolkit.tuebingen.mpg.de/hhomp.}, }
@article {pmid19428983, year = {2009}, author = {Bókkon, I}, title = {Visual perception and imagery: a new molecular hypothesis.}, journal = {Bio Systems}, volume = {96}, number = {2}, pages = {178-184}, doi = {10.1016/j.biosystems.2009.01.005}, pmid = {19428983}, issn = {1872-8324}, mesh = {Animals ; Brain/metabolism ; Electron Transport Complex IV/metabolism ; Epigenesis, Genetic ; Luminescence ; Mitochondria/enzymology ; Oxidation-Reduction ; Retina/metabolism ; Second Messenger Systems ; *Visual Perception ; }, abstract = {Here, we put forward a redox molecular hypothesis about the natural biophysical substrate of visual perception and visual imagery. This hypothesis is based on the redox and bioluminescent processes of neuronal cells in retinotopically organized cytochrome oxidase-rich visual areas. Our hypothesis is in line with the functional roles of reactive oxygen and nitrogen species in living cells that are not part of haphazard process, but rather a very strict mechanism used in signaling pathways. We point out that there is a direct relationship between neuronal activity and the biophoton emission process in the brain. Electrical and biochemical processes in the brain represent sensory information from the external world. During encoding or retrieval of information, electrical signals of neurons can be converted into synchronized biophoton signals by bioluminescent radical and non-radical processes. Therefore, information in the brain appears not only as an electrical (chemical) signal but also as a regulated biophoton (weak optical) signal inside neurons. During visual perception, the topological distribution of photon stimuli on the retina is represented by electrical neuronal activity in retinotopically organized visual areas. These retinotopic electrical signals in visual neurons can be converted into synchronized biophoton signals by radical and non-radical processes in retinotopically organized mitochondria-rich areas. As a result, regulated bioluminescent biophotons can create intrinsic pictures (depictive representation) in retinotopically organized cytochrome oxidase-rich visual areas during visual imagery and visual perception. The long-term visual memory is interpreted as epigenetic information regulated by free radicals and redox processes. This hypothesis does not claim to solve the secret of consciousness, but proposes that the evolution of higher levels of complexity made the intrinsic picture representation of the external visual world possible by regulated redox and bioluminescent reactions in the visual system during visual perception and visual imagery.}, }
@article {pmid19423316, year = {2009}, author = {Becker, T and Gebert, M and Pfanner, N and van der Laan, M}, title = {Biogenesis of mitochondrial membrane proteins.}, journal = {Current opinion in cell biology}, volume = {21}, number = {4}, pages = {484-493}, doi = {10.1016/j.ceb.2009.04.002}, pmid = {19423316}, issn = {1879-0410}, mesh = {Bacteria/*metabolism ; Cell Nucleus/metabolism ; Cytosol/metabolism ; Fungi/metabolism ; Genome ; Mitochondria/metabolism ; Mitochondrial Membranes/*metabolism ; Models, Biological ; Organelles/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport ; Proteobacteria/*metabolism ; Signal Transduction ; }, abstract = {Mitochondria are ubiquitous, double-membrane bound organelles, which have developed from endosymbiotic alpha-proteobacteria during evolution. Outer and inner membranes of mitochondria are equipped with characteristic sets of membrane proteins required for energy conversion, metabolite and protein transport, membrane fusion and fission, and signal transduction. Mitochondrial membrane proteins are encoded by both, the nuclear and the mitochondrial genomes, and exhibit divergent transmembrane topologies. Correct targeting and membrane integration of these proteins and subsequent assembly into functional protein complexes must be tightly coordinated. This elaborate task is mediated by the cooperative functions of different protein import and export machineries of the outer and inner mitochondrial membranes.}, }
@article {pmid19420082, year = {2009}, author = {Romanova, LI and Lidsky, PV and Kolesnikova, MS and Fominykh, KV and Gmyl, AP and Sheval, EV and Hato, SV and van Kuppeveld, FJ and Agol, VI}, title = {Antiapoptotic activity of the cardiovirus leader protein, a viral "security" protein.}, journal = {Journal of virology}, volume = {83}, number = {14}, pages = {7273-7284}, pmid = {19420082}, issn = {1098-5514}, mesh = {Animals ; *Apoptosis ; Cardiovirus/genetics/metabolism ; Cardiovirus Infections/metabolism/*physiopathology/virology ; Cell Line ; Cricetinae ; Cytochromes c/metabolism ; Encephalomyocarditis virus/genetics/*metabolism ; HeLa Cells ; Humans ; Mitochondria/metabolism ; Viral Proteins/genetics/*metabolism ; }, abstract = {Apoptosis is a common antiviral defensive mechanism that potentially limits viral reproduction and spread. Many viruses possess apoptosis-suppressing tools. Here, we show that the productive infection of HeLa cells with encephalomyocarditis virus (a cardiovirus) was not accompanied by full-fledged apoptosis (although the activation of caspases was detected late in infection) but rather elicited a strong antiapoptotic state, as evidenced by the resistance of infected cells to viral and nonviral apoptosis inducers. The development of the antiapoptotic state appeared to depend on a function(s) of the viral leader (L) protein, since its mutational inactivation resulted in the efflux of cytochrome c from mitochondria, the early activation of caspases, and the appearance of morphological and biochemical signs of apoptosis in a significant proportion of infected cells. Infection with both wild-type and L-deficient viruses induced the fragmentation of mitochondria, which in the former case was not accompanied with cytochrome c efflux. Although the exact nature of the antiapoptotic function(s) of cardioviruses remains obscure, our results suggested that it includes previously undescribed mechanisms operating upstream and possibly downstream of the mitochondrial level, and that L is involved in the control of these mechanisms. We propose that cardiovirus L belongs to a class of viral proteins, dubbed here security proteins, whose roles consist solely, or largely, in counteracting host antidefenses. Unrelated L proteins of other picornaviruses as well as their highly variable 2A proteins also may be security proteins. These proteins appear to be independent acquisitions in the evolution of picornaviruses, implying multiple cases of functional (though not structural) convergence.}, }
@article {pmid19416880, year = {2009}, author = {Castoe, TA and de Koning, AP and Kim, HM and Gu, W and Noonan, BP and Naylor, G and Jiang, ZJ and Parkinson, CL and Pollock, DD}, title = {Evidence for an ancient adaptive episode of convergent molecular evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {22}, pages = {8986-8991}, pmid = {19416880}, issn = {1091-6490}, support = {R24 GM065580/GM/NIGMS NIH HHS/United States ; R33 GM065612/GM/NIGMS NIH HHS/United States ; GM065580/GM/NIGMS NIH HHS/United States ; GM065612/GM/NIGMS NIH HHS/United States ; R21 GM065612/GM/NIGMS NIH HHS/United States ; R01 GM083127/GM/NIGMS NIH HHS/United States ; LM009451/LM/NLM NIH HHS/United States ; T15 LM009451/LM/NLM NIH HHS/United States ; GM083127/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; Amino Acid Sequence/genetics ; Animals ; *Evolution, Molecular ; *Genome, Mitochondrial ; Lizards/*genetics ; Molecular Sequence Data ; Phylogeny ; Snakes/*genetics ; }, abstract = {Documented cases of convergent molecular evolution due to selection are fairly unusual, and examples to date have involved only a few amino acid positions. However, because convergence mimics shared ancestry and is not accommodated by current phylogenetic methods, it can strongly mislead phylogenetic inference when it does occur. Here, we present a case of extensive convergent molecular evolution between snake and agamid lizard mitochondrial genomes that overcomes an otherwise strong phylogenetic signal. Evidence from morphology, nuclear genes, and most sites in the mitochondrial genome support one phylogenetic tree, but a subset of mostly amino acid-altering substitutions (primarily at the first and second codon positions) across multiple mitochondrial genes strongly supports a radically different phylogeny. The relevant sites generally evolved slowly but converged between ancient lineages of snakes and agamids. We estimate that approximately 44 of 113 predicted convergent changes distributed across all 13 mitochondrial protein-coding genes are expected to have arisen from nonneutral causes-a remarkably large number. Combined with strong previous evidence for adaptive evolution in snake mitochondrial proteins, it is likely that much of this convergent evolution was driven by adaptation. These results indicate that nonneutral convergent molecular evolution in mitochondria can occur at a scale and intensity far beyond what has been documented previously, and they highlight the vulnerability of standard phylogenetic methods to the presence of nonneutral convergent sequence evolution.}, }
@article {pmid19408245, year = {2009}, author = {Gershoni, M and Templeton, AR and Mishmar, D}, title = {Mitochondrial bioenergetics as a major motive force of speciation.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {31}, number = {6}, pages = {642-650}, doi = {10.1002/bies.200800139}, pmid = {19408245}, issn = {1521-1878}, mesh = {Animals ; Biological Evolution ; DNA/genetics/metabolism ; *DNA, Mitochondrial/genetics/metabolism ; Energy Metabolism/*genetics ; Environment ; *Genetic Speciation ; Genetic Variation ; Humans ; *Mitochondria/genetics/metabolism ; Oxidative Phosphorylation ; }, abstract = {Mitochondrial bioenergetics plays a key role in multiple basic cellular processes, such as energy production, nucleotide biosynthesis, and iron metabolism. It is an essential system for animals' life and death (apoptosis) and it is required for embryo development. This, in conjunction with its being subjected to adaptive processes in multiple species and its gene products being involved in the formation of reproductive barriers in animals, raises the possibility that mitochondrial bioenergetics could be a candidate genetic mechanism of speciation. Here, we discuss genetic and biochemical evidence for the possible involvement of this unique system, encoded by two genomes (the mitochondrial and nuclear genomes), that differ by an order of magnitude in their mutation rates in processes leading to speciation events.}, }
@article {pmid19407923, year = {2009}, author = {Yin, C and Richter, U and Börner, T and Weihe, A}, title = {Evolution of phage-type RNA polymerases in higher plants: characterization of the single phage-type RNA polymerase gene from Selaginella moellendorffii.}, journal = {Journal of molecular evolution}, volume = {68}, number = {5}, pages = {528-538}, pmid = {19407923}, issn = {1432-1432}, mesh = {Amino Acid Sequence ; Blotting, Southern ; Cloning, Molecular ; DNA, Complementary/genetics ; DNA-Directed RNA Polymerases/chemistry/*genetics ; *Evolution, Molecular ; Gene Dosage ; *Genes, Plant ; Green Fluorescent Proteins/metabolism ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/genetics ; Protein Transport ; Recombinant Fusion Proteins/metabolism ; Selaginellaceae/*enzymology/*genetics ; Sequence Alignment ; Subcellular Fractions/metabolism ; }, abstract = {Selaginella moellendorfii (spikemoss) sequence trace data encoding a polypeptide highly similar to angiosperm and moss phage-type organelle RNA polymerases (RpoTs) were used to isolate a BAC clone containing the full-length gene SmRpoT as well as the corresponding cDNA. The SmRpoT mRNA comprises 3452 nt with an open reading frame of 3006 nt, encoding a putative protein of 1002 amino acids with a molecular mass of 113 kDa. The SmRpoT gene comprises 19 exons and 18 introns, conserved in their position with those of the angiosperm and Physcomitrella RpoT genes. In phylogenetic analyses, the Selaginella RpoT polymerase is in a sister position to all other phage-type polymerases of angiosperms. However, according to its conserved exon-intron structure, the Selaginella RpoT gene is representative of the molecular evolutionary lineage giving rise to the RpoT gene family of flowering plants. The N-terminal transit peptide of SmRpoT is shown to confer targeting of green fluorescent protein exclusively to mitochondria after transient expression in Arabidopsis and Selaginella protoplasts. Angiosperms and the moss P. patens possess small gene families encoding RpoTs, which include mitochondrial- and chloroplast-targeted RNA polymerases. In striking contrast, the Selaginella RpoT gene is shown to be single-copy, although Selaginella, as a lycophyte, has a phylogenetic position between Physcomitrella and angiosperms. Thus, there is no evidence that Selaginella may contain a nuclear-encoded phage-type chloroplast RNA polymerase.}, }
@article {pmid19401238, year = {2009}, author = {Garofalo, F and Pellegrino, D and Amelio, D and Tota, B}, title = {The Antarctic hemoglobinless icefish, fifty five years later: a unique cardiocirculatory interplay of disaptation and phenotypic plasticity.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {154}, number = {1}, pages = {10-28}, doi = {10.1016/j.cbpa.2009.04.621}, pmid = {19401238}, issn = {1531-4332}, mesh = {Acclimatization ; Adaptation, Physiological/*physiology ; Animals ; Biological Evolution ; Cardiovascular Physiological Phenomena ; Cold Temperature ; Heart/anatomy &amp; histology/physiology ; Hemoglobins/genetics ; Homeostasis/physiology ; Mitochondria, Heart ; Myocardium/metabolism ; Myoglobin/genetics ; Nitric Oxide/metabolism ; Nitric Oxide Synthase/physiology ; Oxygen/blood ; Perciformes/*physiology ; Phenotype ; }, abstract = {The teleostean Channichthyidae (icefish), endemic stenotherms of the Antarctic waters, perennially at or near freezing, represent a unique example of disaptation among adult vertebrates for their loss of functional traits, particularly hemoglobin (Hb) and, in some species, cardiac myoglobin (Mb), once considered to be essential-life oxygen-binding chromoproteins. Conceivably, this stably frigid, oxygen-rich habitat has permitted high tolerance of disaptation, followed by subsequent adaptive recovery based on gene expression reprogramming and compensatory responses, including an alternative cardio-circulatory design, Hb-free blood and Mb-free cardiac muscle. This review revisits the functional significance of the multilevel cardio-circulatory compensations (hypervolemia, near-zero hematocrit and low blood viscosity, large bore capillaries, increased vascularity with great capacitance, cardiomegaly with very large cardiac output, high blood flow with low systemic pressure and systemic resistance) that counteract the challenge of hypoxemic hypoxia by increasing peripheral oxygen transcellular movement for aerobic tissues, including the myocardium. Reconsidered in the context of recent knowledge on both polar cold adaptation and the new questions related to the advent of nitric oxide (NO) biology, these compensations can be interpreted either according to the "loss-without-penalty" alternative, or in the context of an excessive environmental oxygen supply at low cellular cost and oxygen requirement in the cold. Therefore, rather than reflecting oxygen limitation, several traits may indicate structural overcompensation of oxygen supply reductions at cell/tissue levels. At the multilevel cardio-circulatory adjustments, NO is revealing itself as a major integrator, compensating disaptation with functional phenotypic plasticity, as illustrated by the heart paradigm. Beside NOS-dependent NO generation, recent knowledge concerning Hb/Mb interplay with NO and nitrite has revealed unexpected functions in addition to the classical respiratory role of these proteins. In fact, nitrite, a major biologic reservoir of NO, generates it through deohyHb- and deoxyMb-dependent nitrite reduction, thereby regulating hypoxic vasodilation, cellular respiration and signalling. We suggest that both Hb and Mb are involved as nitrite reductases under hypoxic conditions in a number of cardiocirculatory processes. On the whole, this opens new horizons in environmental and evolutionary physiology.}, }
@article {pmid19400936, year = {2009}, author = {Zou, J and Chang, M and Nie, P and Secombes, CJ}, title = {Origin and evolution of the RIG-I like RNA helicase gene family.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {85}, pmid = {19400936}, issn = {1471-2148}, mesh = {Animals ; Comparative Genomic Hybridization ; Computational Biology ; Conserved Sequence ; DEAD-box RNA Helicases/*genetics ; *Evolution, Molecular ; Models, Molecular ; *Multigene Family ; Phylogeny ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, DNA ; *Synteny ; }, abstract = {BACKGROUND: The DExD/H domain containing RNA helicases such as retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5) are key cytosolic pattern recognition receptors (PRRs) for detecting nucleotide pathogen associated molecular patterns (PAMPs) of invading viruses. The RIG-I and MDA5 proteins differentially recognise conserved PAMPs in double stranded or single stranded viral RNA molecules, leading to activation of the interferon system in vertebrates. They share three core protein domains including a RNA helicase domain near the C terminus (HELICc), one or more caspase activation and recruitment domains (CARDs) and an ATP dependent DExD/H domain. The RIG-I/MDA5 directed interferon response is negatively regulated by laboratory of genetics and physiology 2 (LGP2) and is believed to be controlled by the mitochondria antiviral signalling protein (MAVS), a CARD containing protein associated with mitochondria.<br><br>RESULTS: The DExD/H containing RNA helicases including RIG-I, MDA5 and LGP2 were analysed in silico in a wide spectrum of invertebrate and vertebrate genomes. The gene synteny of MDA5 and LGP2 is well conserved among vertebrates whilst conservation of the gene synteny of RIG-I is less apparent. Invertebrate homologues had a closer phylogenetic relationship with the vertebrate RIG-Is than the MDA5/LGP2 molecules, suggesting the RIG-I homologues may have emerged earlier in evolution, possibly prior to the appearance of vertebrates. Our data suggest that the RIG-I like helicases possibly originated from three distinct genes coding for the core domains including the HELICc, CARD and ATP dependent DExD/H domains through gene fusion and gene/domain duplication. Furthermore, presence of domains similar to a prokaryotic DNA restriction enzyme III domain (Res III), and a zinc finger domain of transcription factor (TF) IIS have been detected by bioinformatic analysis.<br><br>CONCLUSION: The RIG-I/MDA5 viral surveillance system is conserved in vertebrates. The RIG-I like helicase family appears to have evolved from a common ancestor that originated from genes encoding different core functional domains. Diversification of core functional domains might be fundamental to their functional divergence in terms of recognition of different viral PAMPs.}, }
@article {pmid19399587, year = {2009}, author = {Walther, DM and Rapaport, D and Tommassen, J}, title = {Biogenesis of beta-barrel membrane proteins in bacteria and eukaryotes: evolutionary conservation and divergence.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {66}, number = {17}, pages = {2789-2804}, pmid = {19399587}, issn = {1420-9071}, mesh = {Animals ; Bacterial Outer Membrane Proteins/chemistry/genetics/metabolism ; Bacterial Proteins/*chemistry/genetics ; Cell Membrane/chemistry ; Chloroplasts/chemistry/metabolism/ultrastructure ; Eukaryotic Cells/*chemistry ; *Evolution, Molecular ; *Gram-Negative Bacteria/chemistry/cytology/genetics ; Membrane Proteins/*chemistry/genetics/metabolism ; Mitochondrial Membranes/chemistry/metabolism ; Mitochondrial Proteins/chemistry/genetics/metabolism ; Models, Molecular ; Multiprotein Complexes/chemistry/metabolism ; *Protein Structure, Secondary ; *Protein Structure, Tertiary ; }, abstract = {Membrane-embedded beta-barrel proteins span the membrane via multiple amphipathic beta-strands arranged in a cylindrical shape. These proteins are found in the outer membranes of Gram-negative bacteria, mitochondria and chloroplasts. This situation is thought to reflect the evolutionary origin of mitochondria and chloroplasts from Gram-negative bacterial endosymbionts. beta-barrel proteins fulfil a variety of functions; among them are pore-forming proteins that allow the flux of metabolites across the membrane by passive diffusion, active transporters of siderophores, enzymes, structural proteins, and proteins that mediate protein translocation across or insertion into membranes. The biogenesis process of these proteins combines evolutionary conservation of the central elements with some noticeable differences in signals and machineries. This review summarizes our current knowledge of the functions and biogenesis of this special family of proteins.}, }
@article {pmid19399544, year = {2009}, author = {Kutschera, U}, title = {Symbiogenesis, natural selection, and the dynamic Earth.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {128}, number = {3}, pages = {191-203}, pmid = {19399544}, issn = {1611-7530}, mesh = {Animals ; *Biological Evolution ; Cyanobacteria/physiology ; Earth, Planet ; Fishes ; Fossils ; Humans ; Mitochondria/physiology ; Models, Biological ; Models, Genetic ; Models, Theoretical ; Phagocytosis ; *Selection, Genetic ; Symbiosis ; }, abstract = {One century ago, Constantin S. Mereschkowsky introduced the symbiogenesis theory for the origin of chloroplasts from ancient cyanobacteria which was later supplemented by Ivan E. Wallin's proposal that mitochondria evolved from once free-living bacteria. Today, this Mereschkowsky-Wallin principle of symbiogenesis, which is also known as the serial primary endosymbiosis theory, explains the evolutionary origin of eukaryotic cells and hence the emergence of all eukaryotes (protists, fungi, animals and plants). In 1858, the concept of natural selection was described independently by Charles Darwin and Alfred R. Wallace. In the same year, Antonio Snider-Pellegrini proposed the idea of shifting continents, which was later expanded by Alfred Wegener, who published his theory of continental drift eight decades ago. Today, directional selection is accepted as the major cause of adaptive evolution within natural populations of micro- and macro-organisms and the theory of the dynamic Earth (plate tectonics) is well supported. In this article, I combine the processes and principles of symbiogenesis, natural selection and the dynamic Earth and propose an integrative 'synade-model' of macroevolution which takes into account organisms from all five Kingdoms of life.}, }
@article {pmid19387795, year = {2009}, author = {Boissan, M and Dabernat, S and Peuchant, E and Schlattner, U and Lascu, I and Lacombe, ML}, title = {The mammalian Nm23/NDPK family: from metastasis control to cilia movement.}, journal = {Molecular and cellular biochemistry}, volume = {329}, number = {1-2}, pages = {51-62}, pmid = {19387795}, issn = {1573-4919}, mesh = {Animals ; Cilia/genetics/*metabolism ; Humans ; Isoenzymes/metabolism ; Mammals/genetics/metabolism ; Mitochondria/enzymology ; NM23 Nucleoside Diphosphate Kinases/genetics/*metabolism ; Neoplasm Metastasis/genetics ; Neoplasms/*pathology ; Nucleoside-Diphosphate Kinase/genetics/*metabolism ; Phylogeny ; Protein Binding ; Signal Transduction ; }, abstract = {Nucleoside diphosphate kinases (NDPK) are encoded by the NME genes, also called NM23. They catalyze the transfer of gamma-phosphate from nucleoside triphosphates to nucleoside diphosphates by a ping-pong mechanism involving the formation of a high energy phospho-histidine intermediate [1, 2]. Besides their known functions in the control of intracellular nucleotide homeostasis, they are involved in multiple physiological and pathological cellular processes such as differentiation, development, metastastic dissemination or cilia functions. Over the past 15 years, ten human genes have been discovered encoding partial, full length, and/or tandemly repeated Nm23/NDPK domains, with or without N-or C-terminal extensions and/or additional domains. These genes encode proteins exhibiting different functions at various tissular and subcellular localizations. Most of these genes appear late in evolution with the emergence of the vertebrate lineage. This review summarizes the present knowledge on these multitalented proteins.}, }
@article {pmid19386803, year = {2009}, author = {Grant, N and Onda, Y and Kakizaki, Y and Ito, K and Watling, J and Robinson, S}, title = {Two cys or not two cys? That is the question; alternative oxidase in the thermogenic plant sacred Lotus.}, journal = {Plant physiology}, volume = {150}, number = {2}, pages = {987-995}, pmid = {19386803}, issn = {0032-0889}, mesh = {Amino Acid Sequence ; Cysteine/*metabolism ; Diamide/pharmacology ; Disulfides/metabolism ; Glyoxylates/metabolism ; Immunoblotting ; Isoenzymes/metabolism ; Mitochondria/drug effects/enzymology ; Mitochondrial Proteins/metabolism ; Molecular Sequence Data ; Nelumbo/drug effects/*enzymology ; Oxidoreductases/chemistry/*metabolism ; Oxygen/metabolism ; Phylogeny ; Plant Proteins ; Protein Multimerization/drug effects ; Pyruvic Acid/metabolism ; Succinates/metabolism ; *Temperature ; }, abstract = {Sacred lotus (Nelumbo nucifera) regulates temperature in its floral chamber to 32 degrees C to 35 degrees C across ambient temperatures of 8 degrees C to 40 degrees C with heating achieved through high alternative pathway fluxes. In most alternative oxidase (AOX) isoforms, two cysteine residues, Cys(1) and Cys(2), are highly conserved and play a role in posttranslational regulation of AOX. Further control occurs via interaction of reduced Cys(1) with alpha-keto acids, such as pyruvate. Here, we report on the in vitro regulation of AOX isolated from thermogenic receptacle tissues of sacred lotus. AOX protein was mostly present in the reduced form, and only a small fraction could be oxidized with diamide. Cyanide-resistant respiration in isolated mitochondria was stimulated 4-fold by succinate but not pyruvate or glyoxylate. Insensitivity of the alternative pathway of respiration to pyruvate and the inability of AOX protein to be oxidized by diamide suggested that AOX in these tissues may lack Cys(1). Subsequently, we isolated two novel cDNAs for AOX from thermogenic tissues of sacred lotus, designated as NnAOX1a and NnAOX1b. Deduced amino acid sequences of both confirmed that Cys(1) had been replaced by serine; however, Cys(2) was present. This contrasts with AOXs from thermogenic Aroids, which contain both Cys(1) and Cys(2). An additional cysteine was present at position 193 in NnAOX1b. The significance of the sequence data for regulation of the AOX protein in thermogenic sacred lotus is discussed and compared with AOXs from other thermogenic and nonthermogenic species.}, }
@article {pmid19386587, year = {2009}, author = {Charrière, F and O'Donoghue, P and Helgadóttir, S and Maréchal-Drouard, L and Cristodero, M and Horn, EK and Söll, D and Schneider, A}, title = {Dual targeting of a tRNAAsp requires two different aspartyl-tRNA synthetases in Trypanosoma brucei.}, journal = {The Journal of biological chemistry}, volume = {284}, number = {24}, pages = {16210-16217}, pmid = {19386587}, issn = {0021-9258}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Aspartate-tRNA Ligase/*genetics/*metabolism ; Cytosol/enzymology ; Drug Design ; Mitochondria/enzymology ; Phylogeny ; RNA, Transfer, Asp/*biosynthesis ; Substrate Specificity ; Transfer RNA Aminoacylation/physiology ; Trypanosoma brucei brucei/*enzymology/*genetics/growth &amp; development ; }, abstract = {The mitochondrion of the parasitic protozoon Trypanosoma brucei does not encode any tRNAs. This deficiency is compensated for by partial import of nearly all of its cytosolic tRNAs. Most trypanosomal aminoacyl-tRNA synthetases are encoded by single copy genes, suggesting the use of the same enzyme in the cytosol and in the mitochondrion. However, the T. brucei genome encodes two distinct genes for eukaryotic aspartyl-tRNA synthetase (AspRS), although the cell has a single tRNAAsp isoacceptor only. Phylogenetic analysis showed that the two T. brucei AspRSs evolved from a duplication early in kinetoplastid evolution and also revealed that eight other major duplications of AspRS occurred in the eukaryotic domain. RNA interference analysis established that both Tb-AspRS1 and Tb-AspRS2 are essential for growth and required for cytosolic and mitochondrial Asp-tRNAAsp formation, respectively. In vitro charging assays demonstrated that the mitochondrial Tb-AspRS2 aminoacylates both cytosolic and mitochondrial tRNAAsp, whereas the cytosolic Tb-AspRS1 selectively recognizes cytosolic but not mitochondrial tRNAAsp. This indicates that cytosolic and mitochondrial tRNAAsp, although derived from the same nuclear gene, are physically different, most likely due to a mitochondria-specific nucleotide modification. Mitochondrial Tb-AspRS2 defines a novel group of eukaryotic AspRSs with an expanded substrate specificity that are restricted to trypanosomatids and therefore may be exploited as a novel drug target.}, }
@article {pmid19383096, year = {2009}, author = {Reich, M and Göbel, C and Kohler, A and Buée, M and Martin, F and Feussner, I and Polle, A}, title = {Fatty acid metabolism in the ectomycorrhizal fungus Laccaria bicolor.}, journal = {The New phytologist}, volume = {182}, number = {4}, pages = {950-964}, doi = {10.1111/j.1469-8137.2009.02819.x}, pmid = {19383096}, issn = {1469-8137}, mesh = {Biosynthetic Pathways/genetics ; Chromatography, Thin Layer ; Fatty Acid Synthases/chemistry/genetics ; Fatty Acids/*metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Fungal ; Genes, Fungal/genetics ; Laccaria/enzymology/genetics/*metabolism ; Mycorrhizae/enzymology/genetics/*metabolism ; Phylogeny ; Protein Structure, Tertiary ; Pseudotsuga/microbiology ; }, abstract = {Here, the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolorwas explored with the aim of constructing a genome-wide inventory of genes involved in fatty acid metabolism. Sixty-three genes of the major pathways were annotated and validated by the detection of the corresponding transcripts. Seventy-one per cent belonged to multigene families of up to five members. In the mycelium of L. bicolor, 19 different fatty acids were detected, including at low concentrations palmitvaccenic acid (16:1(11Z)), which is known to be a marker for arbuscular mycorrhizal fungi. The pathways of fatty acid biosynthesis and degradation in L. bicolor were reconstructed using lipid composition, gene annotation and transcriptional analysis. Annotation results indicated that saturated fatty acids were degraded in mitochondria, whereas degradation of modified fatty acids was confined to peroxisomes. Fatty acid synthase (FAS) was the second largest protein annotated in L. bicolor. Phylogenetic analysis indicated that L. bicolor, Ustilago maydis and Coprinopsis cinerea have a vertebrate-like type I FAS encoded as a single protein, whereas in other basidiomycetes, including the human pathogenic basidiomycete Cryptococcus neoformans, and in most ascomycetes FAS is composed of the two structurally distinct subunits α and β.}, }
@article {pmid19381577, year = {2009}, author = {Plöscher, M and Granvogl, B and Reisinger, V and Masanek, A and Eichacker, LA}, title = {Organelle proteomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {519}, number = {}, pages = {65-82}, doi = {10.1007/978-1-59745-281-6_5}, pmid = {19381577}, issn = {1064-3745}, mesh = {Chloroplasts/chemistry ; Electrophoresis, Polyacrylamide Gel/instrumentation/methods ; Mass Spectrometry/instrumentation/methods ; Mitochondria/chemistry ; Organelles/*chemistry ; Proteome/*analysis ; Proteomics/instrumentation/*methods ; }, abstract = {The proteome of the cell is at the frontier of being too complex for proteomic analysis. Organelles provide a step up. Organelles compartmentalize the cell enabling a proteome, physiology and metabolism analysis in time and in space. Protein complexes separated by electrophoresis have been identified as the next natural level to characterize the organelles' compartmentalized membrane and soluble proteomes by mass spectrometry. Work on mitochondria and chloroplasts has shown where we are in the characterization of complex proteomes to understand the network of endogenous and extrinsic factors which regulate growth and development, adaptation and evolution.}, }
@article {pmid19378921, year = {2009}, author = {Zhu, JQ and Yang, WX}, title = {Ultrastructure of the mature spermatozoon of the bivalve Estellarca olivacea (Mollusca: Bivalvia: Arcidae) and its phylogenetic implications.}, journal = {Acta biologica Hungarica}, volume = {60}, number = {1}, pages = {27-34}, doi = {10.1556/ABiol.60.2009.1.3}, pmid = {19378921}, issn = {0236-5383}, mesh = {Animals ; Arcidae/genetics/*ultrastructure ; Male ; Microscopy, Electron, Transmission ; Phylogeny ; Sperm Head/*ultrastructure ; Sperm Midpiece/*ultrastructure ; }, abstract = {Ultrastructure of mature spermatozoa of Estellarca olivacea was studied by transmission electron microscopy and its phylogenetic implications are discussed for the first time in this paper. The mature spermatozoon is composed of a head which contains a cone-shaped acrosome, a round nucleus and a tail region. The subacrosomal space is less electron dense which contains a homogeneous material. No axial rod and a basal plate were observed in subacrosomal space. No anterior invagination exists in the nucleus, but an inverted shallow V-shaped posterior invagination is visible. Nuclear lacunae could be seen clearly although the nucleus is highly condensed. Within the mid-piece of the spermatozoon there exist five spherical mitochondria while the long whip-like end portion is composed of an axoneme with the typical 9+2 structure. The spermatozoon of Estellarca olivacea is a product of the evolution of the reproductive system of the family Arcidae. Whether the particular acrosome, subacrosomal space, or the highly condensed nucleus might be adaptations of high fertilization rate in the particular environment of this species is discussed.}, }
@article {pmid19378147, year = {2009}, author = {Abascal, F and Zardoya, R and Posada, D}, title = {Genetic code prediction for metazoan mitochondria with GenDecoder.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {537}, number = {}, pages = {233-242}, doi = {10.1007/978-1-59745-251-9_11}, pmid = {19378147}, issn = {1064-3745}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Evolution, Molecular ; Genetic Code/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Sequence Analysis/*methods ; *Software ; User-Computer Interface ; }, abstract = {There is a standard genetic code that is used by most organisms, but exceptions exist in which particular codons are translated with a different meaning, i.e., as a different amino acid. The characterization of the genetic code of an organism is hence a key step for properly analyzing and translating its protein-coding genes. Such characterization is particularly important in the case of metazoan mitochondrial genomes for two reasons: first, many variant codes occur in them and second, mitochondrial data is frequently used for evolutionary studies. Variant codes are usually found by comparative sequence analyses. Given a protein alignment, if a particular codon for a given species occurs at positions in which a particular amino acid is frequently found in other species, then the most likely hypothesis is that the codon is translated as that particular amino acid in that species. Previously, we have shown that this method can be very reliable provided that enough taxa and positions are included in the comparisons and have implemented it in the web-ser GenDecoder (http://darwin.uvigo.es/software/gendecoder.html). In this chapter we describe the rationale of the method used by GenDecoder and its usage through worked examples, highlighting the potential problems that can arise during the analysis.}, }
@article {pmid19376118, year = {2009}, author = {Reis, K and Fransson, A and Aspenström, P}, title = {The Miro GTPases: at the heart of the mitochondrial transport machinery.}, journal = {FEBS letters}, volume = {583}, number = {9}, pages = {1391-1398}, doi = {10.1016/j.febslet.2009.04.015}, pmid = {19376118}, issn = {1873-3468}, mesh = {Animals ; Biological Transport ; Calcium/metabolism ; GTP Phosphohydrolases/*metabolism ; Homeostasis ; Humans ; Mitochondria/*enzymology/metabolism ; Phylogeny ; }, abstract = {Mitochondria are organelles of elaborate structure that in addition to supplying cellular energy, have significant roles in calcium homeostasis and apoptosis. Failure to maintain mitochondrial dynamics results in neurodegenerative diseases and neuromuscular pathologies. The Miro GTPases, which constitute a unique subgroup of the Ras superfamily, have emerged as essential regulators of mitochondrial morphogenesis and trafficking along microtubules. Miro GTPases function as calcium-dependent sensors in the control of mitochondrial motility. Increased awareness of the biological function of Miro GTPases can contribute to elucidate the molecular mechanisms underlying diseases caused by deregulated mitochondrial dynamics.}, }
@article {pmid19369597, year = {2009}, author = {White, DJ and Gemmell, NJ}, title = {Can indirect tests detect a known recombination event in human mtDNA?.}, journal = {Molecular biology and evolution}, volume = {26}, number = {7}, pages = {1435-1439}, doi = {10.1093/molbev/msp073}, pmid = {19369597}, issn = {1537-1719}, mesh = {DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Humans ; Linkage Disequilibrium ; Mitochondria/*genetics ; *Recombination, Genetic ; }, abstract = {Whether human mitochondrial DNA (mtDNA) recombines sufficiently to influence its evolution, evolutionary analysis, and disease etiology, remains equivocal. Overall, evidence from indirect studies of population genetic data suggests that recombination is not occurring at detectable levels. This may be explained by no, or low, recombination or, alternatively, current indirect tests may be incapable of detecting recombination in human mtDNA. To investigate the latter, we have tested whether six well-established indirect tests of recombination could detect recombination in a human mtDNA data set, in which its occurrence had been empirically confirmed. Three showed statistical evidence for recombination (r(2) vs. distance, the Homoplasy test, Neighborhood Similarity Score), and three did not (D' vs. distance, Max Chi Squared, Pairwise Homoplasy Index). Possible reasons for detection failure are discussed. Further, evidence from earlier studies suggesting a lack of recombination in mtDNA in humans is reconsidered, taking into account the appropriateness of the tests used, based on our new findings.}, }
@article {pmid19368726, year = {2009}, author = {Whitaker, JW and McConkey, GA and Westhead, DR}, title = {The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes.}, journal = {Genome biology}, volume = {10}, number = {4}, pages = {R36}, pmid = {19368726}, issn = {1474-760X}, support = {BB/C52101X/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Bacteria/enzymology/genetics ; Bacterial Proteins/genetics/metabolism ; Enzymes/genetics/*metabolism ; Eukaryotic Cells/*metabolism ; *Gene Transfer, Horizontal ; Leishmania/genetics/metabolism ; Lipopolysaccharides/metabolism ; Metabolic Networks and Pathways ; Phytophthora/genetics/metabolism ; Plasmodium/genetics/metabolism ; Saccharomyces/genetics/metabolism ; Xylose/metabolism ; }, abstract = {BACKGROUND: Metabolic networks are responsible for many essential cellular processes, and exhibit a high level of evolutionary conservation from bacteria to eukaryotes. If genes encoding metabolic enzymes are horizontally transferred and are advantageous, they are likely to become fixed. Horizontal gene transfer (HGT) has played a key role in prokaryotic evolution and its importance in eukaryotes is increasingly evident. High levels of endosymbiotic gene transfer (EGT) accompanied the establishment of plastids and mitochondria, and more recent events have allowed further acquisition of bacterial genes. Here, we present the first comprehensive multi-species analysis of E/HGT of genes encoding metabolic enzymes from bacteria to unicellular eukaryotes.<br><br>RESULTS: The phylogenetic trees of 2,257 metabolic enzymes were used to make E/HGT assertions in ten groups of unicellular eukaryotes, revealing the sources and metabolic processes of the transferred genes. Analyses revealed a preference for enzymes encoded by genes gained through horizontal and endosymbiotic transfers to be connected in the metabolic network. Enrichment in particular functional classes was particularly revealing: alongside plastid related processes and carbohydrate metabolism, this highlighted a number of pathways in eukaryotic parasites that are rich in enzymes encoded by transferred genes, and potentially key to pathogenicity. The plant parasites Phytophthora were discovered to have a potential pathway for lipopolysaccharide biosynthesis of E/HGT origin not seen before in eukaryotes outside the Plantae.<br><br>CONCLUSIONS: The number of enzymes encoded by genes gained through E/HGT has been established, providing insight into functional gain during the evolution of unicellular eukaryotes. In eukaryotic parasites, genes encoding enzymes that have been gained through horizontal transfer may be attractive drug targets if they are part of processes not present in the host, or are significantly diverged from equivalent host enzymes.}, }
@article {pmid19368670, year = {2009}, author = {Mitschke, J and Fuss, J and Blum, T and Höglund, A and Reski, R and Kohlbacher, O and Rensing, SA}, title = {Prediction of dual protein targeting to plant organelles.}, journal = {The New phytologist}, volume = {183}, number = {1}, pages = {224-236}, doi = {10.1111/j.1469-8137.2009.02832.x}, pmid = {19368670}, issn = {1469-8137}, mesh = {Amino Acid Sequence ; *Artificial Intelligence ; Bryopsida/metabolism ; Chloroplasts/*metabolism ; *Computer Simulation ; *Genome, Plant ; Green Fluorescent Proteins ; Mitochondria/*metabolism ; Plant Proteins/*metabolism ; Plants/genetics/*metabolism ; ROC Curve ; Signal Transduction ; }, abstract = {* Dual targeting of proteins to more than one subcellular localization has been found in animals, in fungi and in plants. In the latter, ambiguous N-terminal targeting signals have been described that result in the protein being located in both mitochondria and plastids. We have developed ambiguous targeting predictor (ATP), a machine-learning implementation that classifies such ambiguous targeting signals. * Ambiguous targeting predictor is based on a support vector machine implementation that makes use of 12 different amino acid features. Prediction results were validated using fluorescent protein fusion. * Both in silico and in vivo evaluations demonstrate that ambiguous targeting predictor is useful for predicting dual targeting to mitochondria and plastids. Proteins that are targeted to both organelles by tandemly arrayed signals (so-called twin targeting) can be predicted by both ambiguous targeting predictor and a combination of single targeting prediction tools. Comparison of ambiguous targeting predictor with previous experimental approaches, as well as in silico approaches, shows good congruence. * Based on the prediction results, land plant genomes are expected to encode, on average, > 400 proteins that are located in mitochondria and plastids. Ambiguous targeting predictor is helpful for functional genome annotation and can be used as a tool to further our understanding about dual protein targeting and its evolution.}, }
@article {pmid19366667, year = {2009}, author = {Funes, S and Hasona, A and Bauerschmitt, H and Grubbauer, C and Kauff, F and Collins, R and Crowley, PJ and Palmer, SR and Brady, LJ and Herrmann, JM}, title = {Independent gene duplications of the YidC/Oxa/Alb3 family enabled a specialized cotranslational function.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {16}, pages = {6656-6661}, pmid = {19366667}, issn = {1091-6490}, support = {R01 DE008007/DE/NIDCR NIH HHS/United States ; DE08007/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacterial Proteins/*genetics ; Electron Transport Complex IV/*genetics ; *Gene Duplication ; Genetic Complementation Test ; Mitochondria/metabolism ; Mitochondrial Proteins/*genetics ; Models, Genetic ; Mutation/genetics ; Nuclear Proteins/*genetics ; Phylogeny ; Protein Binding ; *Protein Biosynthesis ; Ribosomes/metabolism ; Saccharomyces cerevisiae/cytology/*genetics ; Streptococcus mutans/*genetics ; Time Factors ; }, abstract = {YidC/Oxa/Alb3 family proteins catalyze the insertion of integral membrane proteins in bacteria, mitochondria, and chloroplasts, respectively. Unlike gram-negative organisms, gram-positive bacteria express 2 paralogs of this family, YidC1/SpoIIIJ and YidC2/YgjG. In Streptococcus mutans, deletion of yidC2 results in a stress-sensitive phenotype similar to that of mutants lacking the signal recognition particle (SRP) protein translocation pathway, while deletion of yidC1 has a less severe phenotype. In contrast to eukaryotes and gram-negative bacteria, SRP-deficient mutants are viable in S. mutans; however, double SRP-yidC2 mutants are severely compromised. Thus, YidC2 may enable loss of the SRP by playing an independent but overlapping role in cotranslational protein insertion into the membrane. This is reminiscent of the situation in mitochondria that lack an SRP pathway and where Oxa1 facilitates cotranslational membrane protein insertion by binding directly to translation-active ribosomes. Here, we show that OXA1 complements a lack of yidC2 in S. mutans. YidC2 also functions reciprocally in oxa1-deficient Saccharomyces cerevisiae mutants and mediates the cotranslational insertion of mitochondrial translation products into the inner membrane. YidC2, like Oxa1, contains a positively charged C-terminal extension and associates with translating ribosomes. Our results are consistent with a gene-duplication event in gram-positive bacteria that enabled the specialization of a YidC isoform that mediates cotranslational activity independent of an SRP pathway.}, }
@article {pmid19363601, year = {2009}, author = {Kim, S and Lee, YP and Lim, H and Ahn, Y and Sung, SK}, title = {Identification of highly variable chloroplast sequences and development of cpDNA-based molecular markers that distinguish four cytoplasm types in radish (Raphanus sativus L.).}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {119}, number = {1}, pages = {189-198}, pmid = {19363601}, issn = {1432-2242}, mesh = {Animals ; *Base Sequence ; Chloroplasts/*genetics ; *DNA, Plant/analysis/genetics ; *Genetic Markers ; Genetic Variation ; Genome ; Genome, Mitochondrial/genetics ; Molecular Sequence Data ; Phylogeny ; Raphanus/classification/*cytology/*genetics ; Sequence Alignment ; }, abstract = {Four types of cytoplasms (Ogura, DCGMS, DBRMF1, and DBRMF2) were identified in the previous studies using molecular markers based on mitochondrial genome variations in radish (Raphanus sativus L.). However, mtDNA markers have limitations in obtaining clear results due to complexity of radish mitochondrial genomes. To improve fidelity, molecular markers based on variation of chloroplast genome sequences were developed in this study. We searched for the sequence variations of chloroplast genome among the four cytoplasm types in 11 noncoding intergenic regions of ~8.7 kb. Highly variable intergenic regions between trnK and rps16 were identified, and a couple of 4-34 bp indels were used to develop a simple PCR-based marker that distinguished the four cytoplasm types based on the PCR product length polymorphism. Two additional cpDNA markers were developed by using a single nucleotide polymorphism and 17-bp insertion. Analysis of 90 accessions using both mtDNA and cpDNA markers showed the perfect match of results of both the markers, suggesting strict co-transmission of mitochondria and chloroplast in radish. Phylogenetic trees showed that two male-sterility inducing cytoplasms, Ogura and DCGMS, were closely related to DBRMF1 and DBRMF2, respectively. Analysis of 120 radish germplasms introduced from diverse countries showed that the frequency of male-sterility inducing mitotypes of Ogura and DCGMS was very low, and DCGMS was predominately detected in eastern European countries. Majority of accessions from Europe and Asia were shown to contain DBRMF2 and DBRMF1 mitotypes, respectively.}, }
@article {pmid19362582, year = {2009}, author = {Kutik, S and Stroud, DA and Wiedemann, N and Pfanner, N}, title = {Evolution of mitochondrial protein biogenesis.}, journal = {Biochimica et biophysica acta}, volume = {1790}, number = {6}, pages = {409-415}, doi = {10.1016/j.bbagen.2009.04.004}, pmid = {19362582}, issn = {0006-3002}, mesh = {Alphaproteobacteria/cytology/genetics/metabolism ; Bacterial Proteins/classification/genetics/metabolism ; *Biological Evolution ; Eukaryotic Cells/cytology/metabolism ; Membrane Proteins/classification/genetics/metabolism ; *Mitochondria/genetics/metabolism ; Mitochondrial Proteins/classification/genetics/*metabolism ; Protein Transport ; }, abstract = {Mitochondria and the nucleus are key features that distinguish eukaryotic cells from prokaryotic cells. Mitochondria originated from a bacterium that was endosymbiotically taken up by another cell more than a billion years ago. Subsequently, most mitochondrial genes were transferred and integrated into the host cell's genome, making the evolution of pathways for specific import of mitochondrial proteins necessary. The mitochondrial protein translocation machineries are composed of numerous subunits. Interestingly, many of these subunits are at least in part derived from bacterial proteins, although only few of them functioned in bacterial protein translocation. We propose that the primitive alpha-proteobacterium, which was once taken up by the eukaryote ancestor cell, contained a number of components that were utilized for the generation of mitochondrial import machineries. Many bacterial components of seemingly unrelated pathways were integrated to form the modern cooperative mitochondria-specific protein translocation system.}, }
@article {pmid19349646, year = {2009}, author = {Atteia, A and Adrait, A and Brugière, S and Tardif, M and van Lis, R and Deusch, O and Dagan, T and Kuhn, L and Gontero, B and Martin, W and Garin, J and Joyard, J and Rolland, N}, title = {A proteomic survey of Chlamydomonas reinhardtii mitochondria sheds new light on the metabolic plasticity of the organelle and on the nature of the alpha-proteobacterial mitochondrial ancestor.}, journal = {Molecular biology and evolution}, volume = {26}, number = {7}, pages = {1533-1548}, doi = {10.1093/molbev/msp068}, pmid = {19349646}, issn = {1537-1719}, mesh = {Alphaproteobacteria/metabolism ; Animals ; *Biological Evolution ; Chlamydomonas reinhardtii/cytology/*genetics/*metabolism ; Mitochondria/chemistry/*genetics/*metabolism ; Oxidative Phosphorylation ; Proteome ; }, abstract = {Mitochondria play a key role in the life and death of eukaryotic cells, yet the full spectrum of mitochondrial functions is far from being fully understood, especially in photosynthetic organisms. To advance our understanding of mitochondrial functions in a photosynthetic cell, an extensive proteomic survey of Percoll-purified mitochondria from the metabolically versatile, hydrogen-producing green alga Chlamydomonas reinhardtii was performed. Different fractions of purified mitochondria from Chlamydomonas cells grown under aerobic conditions were analyzed by nano-liquid chromatography-electrospray ionization-mass spectrometry after protein separation on sodium dodecyl sulfate polyacrylamide gel electrophoresis or on blue-native polyacrylamide gel electrophoresis. Of the 496 nonredundant proteins identified, 149 are known or predicted to reside in other cellular compartments and were thus excluded from the molecular and evolutionary analyses of the Chlamydomonas proteome. The mitochondrial proteome of the photosynthetic alga reveals important lineage-specific differences with other mitochondrial proteomes, reflecting the high metabolic diversity of the organelle. Some mitochondrial metabolic pathways in Chlamydomonas appear to combine typical mitochondrial enzymes and bacterial-type ones, whereas others are unknown among mitochondriate eukaryotes. The comparison of the Chlamydomonas proteins to their identifiable homologs predicted from 354 sequenced genomes indicated that Arabidopsis is the most closely related nonalgal eukaryote. Furthermore, this phylogenomic analysis shows that free-living alpha-proteobacteria from the metabolically versatile orders Rhizobiales and Rhodobacterales better reflect the gene content of the ancestor of the chlorophyte mitochondria than parasitic alpha-proteobacteria with reduced and specialized genomes.}, }
@article {pmid19339279, year = {2009}, author = {Prestele, M and Vogel, F and Reichert, AS and Herrmann, JM and Ott, M}, title = {Mrpl36 is important for generation of assembly competent proteins during mitochondrial translation.}, journal = {Molecular biology of the cell}, volume = {20}, number = {10}, pages = {2615-2625}, pmid = {19339279}, issn = {1939-4586}, mesh = {GTP Phosphohydrolases/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/*biosynthesis ; Models, Biological ; Mutation/genetics ; Protein Binding ; *Protein Biosynthesis ; Protein Stability ; Protein Structure, Tertiary ; Ribosomal Proteins/chemistry/*metabolism ; Ribosomes/metabolism ; Saccharomyces cerevisiae/cytology/growth &amp; development/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; Solubility ; }, abstract = {The complexes of the respiratory chain represent mosaics of nuclear and mitochondrially encoded components. The processes by which synthesis and assembly of the various subunits are coordinated remain largely elusive. During evolution, many proteins of the mitochondrial ribosome acquired additional domains pointing at specific properties or functions of the translation machinery in mitochondria. Here, we analyzed the function of Mrpl36, a protein associated with the large subunit of the mitochondrial ribosome. This protein, homologous to the ribosomal protein L31 from bacteria, contains a mitochondria-specific C-terminal domain that is not required for protein synthesis per se; however, its absence decreases stability of Mrpl36. Cells lacking this C-terminal domain can still synthesize proteins, but these translation products fail to be properly assembled into respiratory chain complexes and are rapidly degraded. Surprisingly, overexpression of Mrpl36 seems to even increase the efficiency of mitochondrial translation. Our data suggest that Mrpl36 plays a critical role during translation that determines the rate of respiratory chain assembly. This important function seems to be carried out by a stabilizing activity of Mrpl36 on the interaction between large and small ribosomal subunits, which could influence accuracy of protein synthesis.}, }
@article {pmid19337890, year = {2009}, author = {Jandová, A and Pokorný, J and Kobilková, J and Janousek, M and Masata, J and Trojan, S and Nedbalová, M and Dohnalová, A and Beková, A and Slavík, V and Cocek, A and Sanitrák, J}, title = {Cell-mediated immunity in cervical cancer evolution.}, journal = {Electromagnetic biology and medicine}, volume = {28}, number = {1}, pages = {1-14}, doi = {10.1080/15368370802708868}, pmid = {19337890}, issn = {1536-8386}, mesh = {Antigens, Neoplasm/metabolism ; Cell Adhesion ; Chromatography, High Pressure Liquid ; Female ; Humans ; *Immunity, Cellular ; L-Lactate Dehydrogenase/metabolism ; Lactate dehydrogenase-elevating virus/metabolism ; Leukocytes/cytology ; Mitochondria/metabolism ; Precancerous Conditions ; T-Lymphocytes/pathology/virology ; Uterine Cervical Neoplasms/*genetics/*immunology/pathology ; }, abstract = {Cell-mediated immunity (CMI) response to different antigens was examined in healthy women, in patients with cervical precancerous lesions, and in patients with cervical cancer. Cervical lesions were diagnosed by cytological (PAP) smears, from examination by colposcopy, and from "punch" biopsy material by histology. CMI response is related to specific processes in healthy and cancer cells. CMI was investigated by leukocyte adherence inhibition (LAI) assay using specific antigen (prepared from cervical carcinoma tissue) and non specific antigen (prepared from blood of mice infected by LDH--lactate dehydrogenase--virus). The CMI responses of healthy women and cancer patients to the antigens used are different: the majority of T lymphocytes display adherence and non adherence, respectively (but the CMI responses elicited by the antigens are not equal and small quantitative differences are observed). Regardless of the CIN (cervical intraepithelial neoplasia) grades, CMI responses correspond either to healthy women or to cervical carcinoma patients (at about similar ratio of cases in all the CIN groups). Effect of non specific antigen suggests that cervical carcinoma transformation may be connected with reduction of mitochondrial activity similar to processes in LDH virus infection.}, }
@article {pmid19335829, year = {2009}, author = {Ready, PD and Testa, JM and Wardhana, AH and Al-Izzi, M and Khalaj, M and Hall, MJ}, title = {Phylogeography and recent emergence of the Old World screwworm fly, Chrysomya bezziana, based on mitochondrial and nuclear gene sequences.}, journal = {Medical and veterinary entomology}, volume = {23 Suppl 1}, number = {}, pages = {43-50}, doi = {10.1111/j.1365-2915.2008.00771.x}, pmid = {19335829}, issn = {1365-2915}, mesh = {Animals ; Base Pairing ; Cell Nucleus/*genetics ; Cytochromes b/*genetics ; DNA/genetics/isolation &amp; purification ; DNA Primers ; Diptera/classification/*genetics ; Gene Amplification ; Geography ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {A previous study had identified an African and an Asian race of the Old World screwworm fly, Chrysomya bezziana Villeneuve (Diptera: Calliphoridae), based on the 3' terminal 279 basepairs (bp) of the mitochondrial cytochrome b gene. The current study improved the phylogeographic resolution of cytochrome b for this species by characterizing more of the gene (the 3' terminal 715 bp) and by sampling more geographical populations, including Oman, Iran, Hong Kong and the Indonesian islands of Sulawesi and East Sumba. Strong support was found for recognizing an African race, but not for a monophyletic Asian race. The cladistic and genealogical relationships among the Asian populations were complex. There was sufficient genetic homogeneity throughout separate regions (mainland Asia and each Indonesian island) to suggest that there are no reproductive barriers within each region that might necessitate the production of more than one strain for control by the sterile insect technique (SIT). Primers were designed for the amplification by polymerase chain reaction of two nuclear loci, the highly conserved elongation factor-1alphagene and the less conserved white gene, and the preliminary results indicated that these genes showed the same pattern of small-scale regional variation as cytochrome b. The cytochrome b haplotypes are useful markers for identifying the geographical origins of any emerging infestations of the species: the absence of Indonesian and African haplotypes in the Middle East demonstrates that the large-scale transport of livestock is not spreading Old World screwworm.}, }
@article {pmid19328849, year = {2009}, author = {Huynen, MA and de Hollander, M and Szklarczyk, R}, title = {Mitochondrial proteome evolution and genetic disease.}, journal = {Biochimica et biophysica acta}, volume = {1792}, number = {12}, pages = {1122-1129}, doi = {10.1016/j.bbadis.2009.03.005}, pmid = {19328849}, issn = {0006-3002}, mesh = {*Biological Evolution ; Humans ; Mitochondria/*metabolism ; Mitochondrial Diseases/*genetics/metabolism ; Mitochondrial Proteins/*metabolism ; *Proteome ; }, abstract = {Mitochondria are an essential organelle, not only to the human cell, but to all eukaryotic life. This essentiality is reflected in the large number of mutations in genes encoding mitochondrial proteins that lead to disease. Aside from their relevance to disease, mitochondria are, given their endosymbiotic origin, very interesting from an evolutionary point of view. Here, in the year that marks the bicentenary of Darwin's birth and the 150th anniversary of the publication of "On the origin of species" we review approaches that implicitly or explicitly use evolutionary analyses to find new genes involved in mitochondrial disease and to predict their function and involvement in pathways. We show how the phenotypic spectrum of mitochondrial disease is linked to the evolutionary origin of mitochondrial proteins, how combinations of evolutionary data and genomics data have been used to predict the mitochondrial proteome and functional links between the mitochondrial proteins and how the evolution of the mitochondrial proteome has been used to predict new mitochondrial disease genes. For the latter we review and reanalyze the eukaryotic evolution of the NADH:ubiquinone oxidoreductase (complex I) and the proteins involved in its assembly.}, }
@article {pmid19326079, year = {2009}, author = {Lee, SM and Hoang, MH and Han, HJ and Kim, HS and Lee, K and Kim, KE and Kim, DH and Lee, SY and Chung, WS}, title = {Pathogen inducible voltage-dependent anion channel (AtVDAC) isoforms are localized to mitochondria membrane in Arabidopsis.}, journal = {Molecules and cells}, volume = {27}, number = {3}, pages = {321-327}, doi = {10.1007/s10059-009-0041-z}, pmid = {19326079}, issn = {0219-1032}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; Gene Expression Regulation, Plant ; Genetic Complementation Test ; Microscopy, Confocal ; Mitochondrial Membranes/*metabolism ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Protein Isoforms ; Voltage-Dependent Anion Channels/biosynthesis/genetics/metabolism ; Yeasts/genetics/metabolism ; }, abstract = {Voltage-dependent anion channels (VDACs) are reported to be porin-type, beta-barrel diffusion pores. They are prominently localized in the outer mitochondrial membrane and are involved in metabolite exchange between the organelle and the cytosol. In this study, we have investigated a family of VDAC isoforms in Arabidopsis thaliana (AtVDAC). We have shown that the heterologous expression of AtVDAC proteins can functionally complement a yeast mutant lacking the endogenous mitochondrial VDAC gene. AtVDACs tagged with GFP were localized to mitochondria in both yeast and plant cells. We also looked at the response of AtVDACs to biotic and abiotic stresses and found that four AtVDAC transcripts were rapidly up-regulated in response to a bacterial pathogen.}, }
@article {pmid19325118, year = {2009}, author = {Takeuchi, K and Nakano, Y and Kato, U and Kaneda, M and Aizu, M and Awano, W and Yonemura, S and Kiyonaka, S and Mori, Y and Yamamoto, D and Umeda, M}, title = {Changes in temperature preferences and energy homeostasis in dystroglycan mutants.}, journal = {Science (New York, N.Y.)}, volume = {323}, number = {5922}, pages = {1740-1743}, doi = {10.1126/science.1165712}, pmid = {19325118}, issn = {1095-9203}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Animals, Genetically Modified ; Body Temperature Regulation ; Calcium/metabolism ; *Cold Temperature ; Drosophila Proteins/genetics/*physiology ; Drosophila melanogaster/genetics/*physiology ; Dystroglycans/genetics/*physiology ; *Energy Metabolism ; Homeostasis ; Mitochondria/metabolism ; Mutant Proteins ; Mutation ; Oxygen Consumption ; Phenotype ; Pyruvate Dehydrogenase Complex/metabolism ; Temperature ; }, abstract = {Temperature affects the physiology, behavior, and evolution of organisms. We conducted mutagenesis and screens for mutants with altered temperature preference in Drosophila melanogaster and identified a cryophilic (cold-seeking) mutant, named atsugari (atu). Reduced expression of the Drosophila ortholog of dystroglycan (DmDG) induced tolerance to cold as well as preference for the low temperature. A sustained increase in mitochondrial oxidative metabolism caused by the reduced expression of DmDG accounted for the cryophilic phenotype of the atu mutant. Although most ectothermic animals do not use metabolically produced heat to regulate body temperature, our results indicate that their thermoregulatory behavior is closely linked to rates of mitochondrial oxidative metabolism and that a mutation in a single gene can induce a sustained change in energy homeostasis and the thermal responses.}, }
@article {pmid19324832, year = {2009}, author = {Tieleman, BI and Versteegh, MA and Fries, A and Helm, B and Dingemanse, NJ and Gibbs, HL and Williams, JB}, title = {Genetic modulation of energy metabolism in birds through mitochondrial function.}, journal = {Proceedings. Biological sciences}, volume = {276}, number = {1662}, pages = {1685-1693}, pmid = {19324832}, issn = {0962-8452}, mesh = {Animals ; Basal Metabolism/*genetics ; Body Size ; DNA, Mitochondrial ; Female ; *Genetic Variation ; Hybridization, Genetic ; Male ; Mitochondria/genetics/*physiology ; Songbirds/*genetics/metabolism ; }, abstract = {Despite their central importance for the evolution of physiological variation, the genetic mechanisms that determine energy expenditure in animals have largely remained unstudied. We used quantitative genetics to confirm that both mass-specific and whole-organism basal metabolic rate (BMR) were heritable in a captive-bred population of stonechats (Saxicola torquata spp.) founded on birds from three wild populations (Europe, Africa and Asia) that differed in BMR. This argues that BMR is at least partially under genetic control by multiple unknown nuclear loci each with a limited effect on the phenotype. We then tested for a genetic effect on BMR based on mitochondrial-nuclear coadaptation using hybrids between ancestral populations with high and low BMR (Europe-Africa and Asia-Europe), with different parental configurations (female(high)-male(low) or female(low)-male(high)) within each combination of populations. Hybrids with different parental configurations have on average identical mixtures of nuclear DNA, but differ in mitochondrial DNA because it is inherited only from the mother. Mass-specific BMR differed between hybrids with different parental configurations, implying that the combination of mitochondrial and nuclear DNA affected metabolic rate. Therefore, our findings implicate mitochondrial function as an important regulator of energy metabolism. In combination with the substantial heritabilities of metabolic rate, and corroborated by genetic differences in the mitochondrial genome, these results set the stage for further investigations of a genetic control mechanism involving both mitochondrial and nuclear genes determining metabolic rate at the whole-organism level.}, }
@article {pmid19324807, year = {2009}, author = {Puthiyaveetil, S and Allen, JF}, title = {Chloroplast two-component systems: evolution of the link between photosynthesis and gene expression.}, journal = {Proceedings. Biological sciences}, volume = {276}, number = {1665}, pages = {2133-2145}, pmid = {19324807}, issn = {0962-8452}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Chloroplasts/*genetics/*metabolism ; *Evolution, Molecular ; Gene Expression Regulation, Plant/*physiology ; Photosynthesis/*genetics/*physiology ; }, abstract = {Two-component signal transduction, consisting of sensor kinases and response regulators, is the predominant signalling mechanism in bacteria. This signalling system originated in prokaryotes and has spread throughout the eukaryotic domain of life through endosymbiotic, lateral gene transfer from the bacterial ancestors and early evolutionary precursors of eukaryotic, cytoplasmic, bioenergetic organelles-chloroplasts and mitochondria. Until recently, it was thought that two-component systems inherited from an ancestral cyanobacterial symbiont are no longer present in chloroplasts. Recent research now shows that two-component systems have survived in chloroplasts as products of both chloroplast and nuclear genes. Comparative genomic analysis of photosynthetic eukaryotes shows a lineage-specific distribution of chloroplast two-component systems. The components and the systems they comprise have homologues in extant cyanobacterial lineages, indicating their ancient cyanobacterial origin. Sequence and functional characteristics of chloroplast two-component systems point to their fundamental role in linking photosynthesis with gene expression. We propose that two-component systems provide a coupling between photosynthesis and gene expression that serves to retain genes in chloroplasts, thus providing the basis of cytoplasmic, non-Mendelian inheritance of plastid-associated characters. We discuss the role of this coupling in the chronobiology of cells and in the dialogue between nuclear and cytoplasmic genetic systems.}, }
@article {pmid19324654, year = {2009}, author = {Galtier, N and Jobson, RW and Nabholz, B and Glémin, S and Blier, PU}, title = {Mitochondrial whims: metabolic rate, longevity and the rate of molecular evolution.}, journal = {Biology letters}, volume = {5}, number = {3}, pages = {413-416}, pmid = {19324654}, issn = {1744-9561}, mesh = {Basal Metabolism/*genetics/*physiology ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Longevity/*genetics ; Mitochondria/genetics/metabolism ; Mutation ; Oxidative Stress ; }, abstract = {The evolutionary rate of mitochondrial DNA (mtDNA) is highly variable across lineages in animals, and particularly in mammals. This variation has been interpreted as reflecting variations in metabolic rate: mitochondrial respiratory activity would tend to generate mutagenic agents, thus increasing the mutation rate. Here we review recent evidence suggesting that a direct, mechanical effect of species metabolic rate on mtDNA evolutionary rate is unlikely. We suggest that natural selection could act to reduce the (somatic) mtDNA mutation rate in long-lived species, in agreement with the mitochondrial theory of ageing.}, }
@article {pmid19324622, year = {2009}, author = {Hendy, MD and Woodhams, MD and Dodd, A}, title = {Modelling mitochondrial site polymorphisms to infer the number of segregating units and mutation rate.}, journal = {Biology letters}, volume = {5}, number = {3}, pages = {397-400}, pmid = {19324622}, issn = {1744-9561}, mesh = {DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Mitochondria/*genetics ; *Models, Genetic ; *Polymorphism, Genetic ; }, abstract = {We present a mathematical model of mitochondrial inheritance evolving under neutral evolution to interpret the heteroplasmies observed at some sites. A comparison of the levels of heteroplasmies transmitted from mother to her offspring allows us to estimate the number N(x) of inherited mitochondrial genomes (segregating units). The model demonstrates the necessity of accounting for both the multiplicity of an unknown number N(x), and the threshold , below which heteroplasmy cannot be detected reliably, in order to estimate the mitochondrial mutation rate mu(m) in the maternal line of descent. Our model is applicable to pedigree studies of any eukaryotic species where site heteroplasmies are observed in regions of the mitochondria, provided neutrality can be assumed. The model is illustrated with an analysis of site heteroplasmies in the first hypervariable region of mitochondrial sequence data sampled from Adélie penguin families, providing an estimate N(x) and mu(m). This estimate of mu(m) was found to be consistent with earlier estimates from ancient DNA analysis.}, }
@article {pmid19323823, year = {2009}, author = {Smith, DR and Lee, RW}, title = {The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {132}, pmid = {19323823}, issn = {1471-2164}, mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; Chlamydomonas reinhardtii/genetics ; DNA, Algal/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; *Genome, Mitochondrial ; *Genome, Plastid ; *Inverted Repeat Sequences ; Mitochondria/genetics ; Molecular Sequence Data ; Plastids/genetics ; Sequence Analysis, DNA ; Volvox/*genetics ; }, abstract = {BACKGROUND: The magnitude of noncoding DNA in organelle genomes can vary significantly; it is argued that much of this variation is attributable to the dissemination of selfish DNA. The results of a previous study indicate that the mitochondrial DNA (mtDNA) of the green alga Volvox carteri abounds with palindromic repeats, which appear to be selfish elements. We became interested in the evolution and distribution of these repeats when, during a cursory exploration of the V. carteri nuclear DNA (nucDNA) and plastid DNA (ptDNA) sequences, we found palindromic repeats with similar structural features to those of the mtDNA. Upon this discovery, we decided to investigate the diversity and evolutionary implications of these palindromic elements by sequencing and characterizing large portions of mtDNA and ptDNA and then comparing these data to the V. carteri draft nuclear genome sequence.<br><br>RESULTS: We sequenced 30 and 420 kilobases (kb) of the mitochondrial and plastid genomes of V. carteri, respectively -- resulting in partial assemblies of these genomes. The mitochondrial genome is the most bloated green-algal mtDNA observed to date: ~61% of the sequence is noncoding, most of which is comprised of short palindromic repeats spread throughout the intergenic and intronic regions. The plastid genome is the largest (>420 kb) and most expanded (>80% noncoding) ptDNA sequence yet discovered, with a myriad of palindromic repeats in the noncoding regions, which have a similar size and secondary structure to those of the mtDNA. We found that 15 kb (~0.01%) of the nuclear genome are homologous to the palindromic elements of the mtDNA, and 50 kb (~0.05%) are homologous to those of the ptDNA.<br><br>CONCLUSION: Selfish elements in the form of short palindromic repeats have propagated in the V. carteri mtDNA and ptDNA, resulting in the distension of these genomes. Copies of these same repeats are also found in a small fraction of the nucDNA, but appear to be inert in this compartment. We conclude that the palindromic repeats in V. carteri represent a single class of selfish DNA and speculate that the derivation of this element involved the lateral gene transfer of an organelle intron that first appeared in the mitochondrial genome, spreading to the ptDNA through mitochondrion-to-plastid DNA migrations, and eventually arrived in the nucDNA through organelle-to-nucleus DNA transfer events. The overall implications of palindromic repeats on the evolution of chlorophyte organelle genomes are discussed.}, }
@article {pmid19320977, year = {2009}, author = {Kato, T and Miyanaga, A and Kanaya, S and Morikawa, M}, title = {Alkane inducible proteins in Geobacillus thermoleovorans B23.}, journal = {BMC microbiology}, volume = {9}, number = {}, pages = {60}, pmid = {19320977}, issn = {1471-2180}, mesh = {Acyl-CoA Oxidase/metabolism ; Alkanes/*metabolism ; Amino Acid Sequence ; Bacillaceae/*enzymology/genetics ; Bacterial Proteins/*metabolism ; Catalase/metabolism ; Cloning, Molecular ; DNA, Bacterial/genetics ; Gene Library ; Genes, Bacterial ; Membrane Proteins/*metabolism ; Molecular Sequence Data ; Superoxide Dismutase/*metabolism ; }, abstract = {BACKGROUND: Initial step of beta-oxidation is catalyzed by acyl-CoA dehydrogenase in prokaryotes and mitochondria, while acyl-CoA oxidase primarily functions in the peroxisomes of eukaryotes. Oxidase reaction accompanies emission of toxic by-product reactive oxygen molecules including superoxide anion, and superoxide dismutase and catalase activities are essential to detoxify them in the peroxisomes. Although there is an argument about whether primitive life was born and evolved under high temperature conditions, thermophilic archaea apparently share living systems with both bacteria and eukaryotes. We hypothesized that alkane degradation pathways in thermophilic microorganisms could be premature and useful to understand their evolution.<br><br>RESULTS: An extremely thermophilic and alkane degrading Geobacillus thermoleovorans B23 was previously isolated from a deep subsurface oil reservoir in Japan. In the present study, we identified novel membrane proteins (P16, P21) and superoxide dismutase (P24) whose production levels were significantly increased upon alkane degradation. Unlike other bacteria acyl-CoA oxidase and catalase activities were also increased in strain B23 by addition of alkane.<br><br>CONCLUSION: We first suggested that peroxisomal beta-oxidation system exists in bacteria. This eukaryotic-type alkane degradation pathway in thermophilic bacterial cells might be a vestige of primitive living cell systems that had evolved into eukaryotes.}, }
@article {pmid19317891, year = {2009}, author = {Charlat, S and Duplouy, A and Hornett, EA and Dyson, EA and Davies, N and Roderick, GK and Wedell, N and Hurst, GD}, title = {The joint evolutionary histories of Wolbachia and mitochondria in Hypolimnas bolina.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {64}, pmid = {19317891}, issn = {1471-2148}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Butterflies/*genetics/*microbiology ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genes, Insect ; Genes, Mitochondrial ; Haplotypes ; Host-Pathogen Interactions ; Inheritance Patterns ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Wolbachia/*pathogenicity ; }, abstract = {BACKGROUND: The interaction between the Blue Moon butterfly, Hypolimnas bolina, and Wolbachia has attracted interest because of the high prevalence of male-killing achieved within the species, the ecological consequences of this high prevalence, the intensity of selection on the host to suppress the infection, and the presence of multiple Wolbachia infections inducing different phenotypes. We examined diversity in the co-inherited marker, mtDNA, and the partitioning of this between individuals of different infection status, as a means to investigate the population biology and evolutionary history of the Wolbachia infections.<br><br>RESULTS: Part of the mitochondrial COI gene was sequenced from 298 individuals of known infection status revealing ten different haplotypes. Despite very strong biological evidence that the sample represents a single species, the ten haplotypes did not fall within a monophyletic clade within the Hypolimnas genus, with one haplotype differing by 5% from the other nine. There were strong associations between infection status and mtDNA haplotype. The presence of wBol1 infection in association with strongly divergent haplotypes prompted closer examination of wBol1 genetic variation. This revealed the existence of two cryptic subtypes, wBol1a and wBol1b. The wBol1a infection, by far the most common, was in strict association with the single divergent mtDNA haplotype. The wBol1b infection was found with two haplotypes that were also observed in uninfected specimens. Finally, the wBol2 infection was associated with a large diversity of mtDNA haplotypes, most often shared with uninfected sympatric butterflies.<br><br>CONCLUSION: This data overall supports the hypothesis that high prevalence of male-killing Wolbachia (wBol1) in H. bolina is associated with very high transmission efficiency rather than regular horizontal transmission. It also suggests this infection has undergone a recent selective sweep and was introduced in this species through introgression. In contrast, the sharing of haplotypes between wBol2-infected and uninfected individuals indicates that this strain is not perfectly transmitted and/or shows a significant level of horizontal transmission.}, }
@article {pmid19307179, year = {2009}, author = {Nayak, D and Guo, Q and Sousa, R}, title = {A promoter recognition mechanism common to yeast mitochondrial and phage t7 RNA polymerases.}, journal = {The Journal of biological chemistry}, volume = {284}, number = {20}, pages = {13641-13647}, pmid = {19307179}, issn = {0021-9258}, support = {R01 GM052522/GM/NIGMS NIH HHS/United States ; GMS52522//PHS HHS/United States ; }, mesh = {Bacteriophage T7/*enzymology/genetics ; DNA-Directed RNA Polymerases/*chemistry/genetics/metabolism ; Evolution, Molecular ; Mitochondrial Proteins/*chemistry/genetics/metabolism ; Mutation ; Promoter Regions, Genetic/*physiology ; Protein Structure, Tertiary/physiology ; Saccharomyces cerevisiae/*enzymology/genetics ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/metabolism ; Viral Proteins/*chemistry/genetics/metabolism ; }, abstract = {Yeast mitochondrial (YMt) and phage T7 RNA polymerases (RNAPs) are two divergent representatives of a large family of single subunit RNAPs that are also found in the mitochondria and chloroplasts of higher eukaryotes, mammalian nuclei, and many other bacteriophage. YMt and phage T7 promoters differ greatly in sequence and length, and the YMt RNAP uses an accessory factor for initiation, whereas T7 RNAP does not. We obtain evidence here that, despite these apparent differences, both the YMt and T7 RNAPs utilize a similar promoter recognition loop to bind their respective promoters. Mutations in this element in YMt RNAP specifically disrupt mitochondrial promoter utilization, and experiments with site-specifically tethered chemical nucleases indicate that this element binds the mitochondrial promoter almost identically to how the promoter recognition loop from the phage RNAP binds its promoter. Sequence comparisons reveal that the other members of the single subunit RNAP family display loops of variable sequence and size at a position corresponding to the YMt and T7 RNAP promoter recognition loops. We speculate that these elements may be involved in promoter recognition in most or all of these enzymes and that this element's structure allows it to accommodate significant sequence and length variation to provide a mechanism for rapid evolution of new promoter specificities in this RNAP family.}, }
@article {pmid19306844, year = {2009}, author = {Mahlknecht, U and Voelter-Mahlknecht, S}, title = {Fluorescence in situ hybridization and chromosomal organization of the sirtuin 4 gene (Sirt4) in the mouse.}, journal = {Biochemical and biophysical research communications}, volume = {382}, number = {4}, pages = {685-690}, doi = {10.1016/j.bbrc.2009.03.092}, pmid = {19306844}, issn = {1090-2104}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cells, Cultured ; Chromosome Mapping ; Chromosomes/genetics ; *Gene Dosage ; Gene Expression ; In Situ Hybridization, Fluorescence ; Mice ; Mitochondrial Proteins ; Molecular Sequence Data ; Phylogeny ; Sirtuins/classification/*genetics ; }, abstract = {The sirtuins (SIRT1-7), also being referred to as class III HDACs, exert NAD-dependent deacetylase and/or ADP-ribosyltransferase activities in various cellular compartments including the cell nucleus, the cytoplasm and the mitochondria. The sirtuins play a central role in epigenetic gene silencing, DNA repair and recombination, cell-cycle, microtubule organization, and in the regulation of aging. SIRT4 is a mitochondrial protein that lacks deacetylase activities but efficiently works as an ADP-ribosyltransferase. We have isolated and characterized the murine Sirt4 genomic sequence, which spans a region of 12kb and which has one single genomic locus. Determination of the exon-intron splice junctions established that SIRT4 is encoded by 6 exons. The 1648bp murine Sirt4 transcript encodes a 418 aa protein with a predictive molecular weight of 47.3kDa. Fluorescence in situ hybridization analysis identified a single genomic locus for murine Sirt4 gene on chromosome 5F and is neighbored by the PLA2G1B and PXN genes.}, }
@article {pmid19306035, year = {2009}, author = {Bouteloup, C and Desport, JC and Clavelou, P and Guy, N and Derumeaux-Burel, H and Ferrier, A and Couratier, P}, title = {Hypermetabolism in ALS patients: an early and persistent phenomenon.}, journal = {Journal of neurology}, volume = {256}, number = {8}, pages = {1236-1242}, pmid = {19306035}, issn = {1432-1459}, mesh = {Age Distribution ; Aged ; Aging/metabolism ; Amyotrophic Lateral Sclerosis/genetics/*metabolism/physiopathology ; Basal Metabolism/*physiology ; Biomarkers/analysis/metabolism ; Dietary Proteins/metabolism ; Disease Progression ; Eating/physiology ; Energy Metabolism/*physiology ; Female ; Humans ; Male ; Metabolic Diseases/genetics/*metabolism/physiopathology ; Middle Aged ; Mitochondrial Diseases/genetics/metabolism/physiopathology ; Predictive Value of Tests ; Prognosis ; Serum Albumin/analysis/metabolism ; Time Factors ; }, abstract = {The malnutrition common among patients with ALS can be attributed in some cases to increased resting energy expenditure (REE). However, the origins and evolution of this hypermetabolism have yet to be fully elucidated. The aim of the present study was to monitor REE over time in patients with ALS and to identify factors that may explain any variation observed. ALS patients underwent nutritional, neurological and respiratory assessment every 6 months for 2 years (or until they died or became physically incapable of being examined). Sixty-one patients were studied. At inclusion, 47.5% exhibited hypermetabolism, with a mean measured REE (mREE) 19.7 +/- 6.4% higher than the mean calculated REE (cREE) (P < 0.0001). The hypermetabolism persisted when mREE was normalized for fat free mass (FFM): 35.1 +/- 4.2 versus 32.3 +/- 4.7 kcal/kg day(-1) (P = 0.02) in hypermetabolic and normometabolic patients, respectively. In univariate analysis, mREE was negatively correlated with age and positively correlated with BMI, FFM, energy and protein intakes, and albumin level. No correlation was found with neurological scores, disease characteristics, respiratory function and survival. Multivariate analysis revealed no significant factors. Only 10 of 45 patients in whom REE was measured at least twice changed their metabolic status. Neither mREE nor mREE/cREE varied significantly over time, despite deteriorating neurological, nutritional and respiratory parameters (P < 0.0001), and an increase in mREE/FFM (P = 0.01). This study confirms that about 50% of ALS patients are hypermetabolic, and 80% show no change in metabolic status over time. Thus, metabolic status (a clinically useful indicator of the need for nutritional support) can be determined early in the evolution of the disease. The origin of hypermetabolism in this context remains unknown, but growing evidence points to mitochondria as having an important role.}, }
@article {pmid19296112, year = {2009}, author = {Elleuche, S and Pöggeler, S}, title = {Evolution of carbonic anhydrases in fungi.}, journal = {Current genetics}, volume = {55}, number = {2}, pages = {211-222}, pmid = {19296112}, issn = {1432-0983}, mesh = {Carbonic Anhydrases/chemistry/*genetics/metabolism ; *Evolution, Molecular ; Fungi/classification/*enzymology/*genetics/metabolism ; Mitochondria/enzymology ; Phylogeny ; }, abstract = {The ubiquitous metalloenzyme carbonic anhydrase (CA) catalyzes the interconversion of carbon dioxide and bicarbonate. This enzyme has been investigated in mammals, plants, algae, bacteria, archaea and fungi. Based on distinct structural characteristics, CAs can be assigned to five independently evolved classes (alpha, beta, gamma, delta and zeta). beta-CAs can be further subdivided into plant-type and cab-type sub-classes. The recent characterization of CAs in fungi led us to initiate a systematic search for these enzymes in filamentous ascomycetes. The genomes of basidiomycetes and hemiascomycetous yeasts contain only beta-CAs, while the filamentous ascomycetes also possess genes encoding alpha-class CAs. Here, we present a phylogenetic analysis of 97 fungal CA sequences that addresses the diversification of fungal CAs. During evolution various gene duplication and gene loss events seem to be the cause for the multiplicity of CAs in filamentous ascomycetes. Our data revealed that during the evolution of filamentous ascomycetes, a gene encoding the plant-type beta-CA was duplicated, resulting in two closely related isoforms, one with and one without an N-terminal mitochondrial target sequence (MTS). The acquisition of the MTS most likely took place after the gene duplication event and after the evolutionary separation of the fungal orders Sordariales and Eurotiales.}, }
@article {pmid19284537, year = {2009}, author = {Nabholz, B and Glémin, S and Galtier, N}, title = {The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {54}, pmid = {19284537}, issn = {1471-2148}, mesh = {Animals ; Birds/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Longevity/genetics ; Mammals/*genetics ; Mitochondria/genetics ; Models, Genetic ; Mutation ; Polymorphism, Genetic ; Population Density ; Sequence Alignment ; }, abstract = {BACKGROUND: During the last ten years, major advances have been made in characterizing and understanding the evolution of mitochondrial DNA, the most popular marker of molecular biodiversity. Several important results were recently reported using mammals as model organisms, including (i) the absence of relationship between mitochondrial DNA diversity and life-history or ecological variables, (ii) the absence of prominent adaptive selection, contrary to what was found in invertebrates, and (iii) the unexpectedly large variation in neutral substitution rate among lineages, revealing a possible link with species maximal longevity. We propose to challenge these results thanks to the bird/mammal comparison. Direct estimates of population size are available in birds, and this group presents striking life-history trait differences with mammals (higher mass-specific metabolic rate and longevity). These properties make birds the ideal model to directly test for population size effects, and to discriminate between competing hypotheses about the causes of substitution rate variation.<br><br>RESULTS: A phylogenetic analysis of cytochrome b third-codon position confirms that the mitochondrial DNA mutation rate is quite variable in birds, passerines being the fastest evolving order. On average, mitochondrial DNA evolves slower in birds than in mammals of similar body size. This result is in agreement with the longevity hypothesis, and contradicts the hypothesis of a metabolic rate-dependent mutation rate. Birds show no footprint of adaptive selection on cytochrome b evolutionary patterns, but no link between direct estimates of population size and cytochrome b diversity. The mutation rate is the best predictor we have of within-species mitochondrial diversity in birds. It partly explains the differences in mitochondrial DNA diversity patterns observed between mammals and birds, previously interpreted as reflecting Hill-Robertson interferences with the W chromosome.<br><br>CONCLUSION: Mitochondrial DNA diversity patterns in birds are strongly influenced by the wide, unexpected variation of mutation rate across species. From a fundamental point of view, these results are strongly consistent with a relationship between species maximal longevity and mitochondrial mutation rate, in agreement with the mitochondrial theory of ageing. Form an applied point of view, this study reinforces and extends the message of caution previously expressed for mammals: mitochondrial data tell nothing about species population sizes, and strongly depart the molecular clock assumption.}, }
@article {pmid19281475, year = {2009}, author = {Bovers, M and Hagen, F and Kuramae, EE and Boekhout, T}, title = {Promiscuous mitochondria in Cryptococcus gattii.}, journal = {FEMS yeast research}, volume = {9}, number = {3}, pages = {489-503}, doi = {10.1111/j.1567-1364.2009.00494.x}, pmid = {19281475}, issn = {1567-1364}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Cluster Analysis ; Cryptococcosis/microbiology/veterinary ; Cryptococcus/classification/*genetics/isolation &amp; purification ; DNA Fingerprinting ; DNA, Fungal/*genetics ; DNA, Mitochondrial/*genetics ; Environmental Microbiology ; Genotype ; Mitochondria/classification/*genetics ; Phylogeny ; *Polymorphism, Genetic ; Recombination, Genetic ; }, abstract = {Cryptococcus gattii is a primary pathogenic basidiomycetous yeast comprising four genotypic groups. Here we present data on two mitochondrial loci (MtLrRNA and ATP6). Two of the genotypic groups, namely amplified fragment length polymorphism (AFLP)5/VGIII and AFLP6/VGII, formed monophyletic lineages. The AFLP4/VGI genotypic group, however, possessed five different mitochondrial genotypes that did not form a monophyletic lineage. The majority of these isolates contained mitochondrial genomes that are partially identical to those found in isolates belonging to AFLP6/VGII, which is causing the ongoing and expanding Vancouver Island outbreak. Two out of four AFLP7/VGIV isolates contained an AFLP4/VGI allele of MtLrRNA. These observations are best explained by assuming a process of mitochondrial recombination. If this is true, mitochondrial recombination seems possible between cells belonging to different genotypic groups of C. gattii, especially between AFLP6/VGII or AFLP7/VGIV and AFLP4/VGI. We also have to assume that mitochondria, most likely, were transferred from cells belonging to AFLP6/VGII to AFLP4/VGI. As such a process of mitochondrial recombination is only possible after cell-cell conjugation, this may also allow the further exchange of genetic material, for example nuclear or plasmid in nature, between different genotypes of C. gattii. This may be relevant as it may provide a possible mechanism contributing to the modulation of virulence attributes of isolates, such as has been observed in the ongoing Vancouver Island outbreak of C. gattii.}, }
@article {pmid19273422, year = {2009}, author = {Gu, ML and Wang, YJ and Shi, L and Zhang, YB and Chu, JY}, title = {[Comparison on mitochondrial ATP6, ATP8 and Cyt b genes between Chinese Tibetans in three different zones: detecting the signature of natural selection on mitochondrial genome].}, journal = {Yi chuan = Hereditas}, volume = {31}, number = {2}, pages = {147-152}, doi = {10.3724/sp.j.1005.2009.00147}, pmid = {19273422}, issn = {0253-9772}, mesh = {Adenosine Triphosphatases/*genetics ; Asian People ; DNA, Mitochondrial/*analysis ; Evolution, Molecular ; *Gene Expression Profiling ; Gene Frequency ; Genome, Mitochondrial ; Humans ; Mitochondria/*genetics ; Mitochondrial Proton-Translocating ATPases/*genetics ; Molecular Sequence Data ; RNA, Transfer ; *Selection, Genetic ; Sequence Analysis, DNA ; Tibet/ethnology ; }, abstract = {Mitochondrial DNA (mtDNA) differs from nuclear genome in many aspects such as lack of recombination, thus the investigation of mtDNA plays an essential role in human evolutionary history. We compared different sequences (approximately 2 kb) of ATP6, ATP8 and Cyt b genes in mtDNA among Tibetans in three different zones and found that the whole mtDNA sequences of the three genes, ATP6 and ATP 8 genes deviate gradually from neutral model with the increase of altitudes, yet no differences were observed. Also we found that the effect of purifying selection on Cyt b gene was elevated with the decrease of altitudes. Meanwhile, there was a possibility for the adaptive selection in ATP6 gene, which had an enhanced trend with the increase of altitudes. Thus, the geographic environment is the main determinant for selection, namely, different geographic environment has direct effect on selection.}, }
@article {pmid19271204, year = {2009}, author = {Keeling, PJ}, title = {Role of horizontal gene transfer in the evolution of photosynthetic eukaryotes and their plastids.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {532}, number = {}, pages = {501-515}, doi = {10.1007/978-1-60327-853-9_29}, pmid = {19271204}, issn = {1064-3745}, mesh = {Biological Evolution ; Chlamydiales/genetics ; Cyanobacteria/genetics ; Eukaryota/genetics ; Gene Flow ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Models, Genetic ; Photosynthesis/*genetics ; Plastids/*genetics ; Symbiosis/genetics ; }, abstract = {Plastids are the organelles derived from a cyanobacterium through endosymbiosis. Unlike mitochondria, plastids are not found in all eukaryotes, but their evolution has an added layer of complexity since plastids have moved between eukaryotic lineages by secondary and tertiary endosymbiotic events. This complex history, together with the genetic integration between plastids and their host, has led to many opportunities for gene flow between phylogenetically distinct lineages. Some intracellular transfers do not lead to a protein functioning in a new environment, but many others do and the protein makeup of many plastids appears to have been influenced by exogenous sources as well. Here, different evolutionary sources and cellular destinations of gene flow that has affected the plastid lineage are reviewed. Most horizontal gene transfer (HGT) affecting the modern plastid has taken place via the host nucleus, in the form of genes for plastid-targeted proteins. The impact of this varies greatly from lineage to lineage, but in some cases such transfers can be as high as one fifth of analyzed genes. More rarely, genes have also been transferred to the plastid genome itself, and plastid genes have also been transferred to other non-plant, non-algal lineages. Overall, the proteome of many plastids has emerged as a mosaic of proteins from many sources, some from within the same cell (e.g., cytosolic genes or genes left over from the replacement of an earlier plastid), some from the plastid of other algal lineages, and some from completely unrelated sources.}, }
@article {pmid19268697, year = {2009}, author = {Shen, X and Sun, M and Wu, Z and Tian, M and Cheng, H and Zhao, F and Meng, X}, title = {The complete mitochondrial genome of the ridgetail white prawn Exopalaemon carinicauda Holthuis, 1950 (Crustacean: Decapoda: Palaemonidae) revealed a novel rearrangement of tRNA genes.}, journal = {Gene}, volume = {437}, number = {1-2}, pages = {1-8}, doi = {10.1016/j.gene.2009.02.014}, pmid = {19268697}, issn = {1879-0038}, mesh = {Animals ; Chromosome Mapping ; Codon ; *Genome, Mitochondrial ; Palaemonidae/*genetics ; Phylogeny ; RNA, Transfer/*genetics ; }, abstract = {The complete mitochondrial (mt) DNA sequence was determined for a ridgetail white prawn, Exopalaemon carinicauda Holthuis, 1950 (Crustacea: Decopoda: Palaemonidae). The mt genome is 15,730 bp in length, encoding a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, which is typical for metazoans. The majority-strand consists of 33.6% A, 23.0% C, 13.4% G, and 30.0% T bases (AT skew=0.057; GC skew=-0.264). A total of 1045 bp of non-coding nucleotides were observed in 16 intergenic regions, including a major A+T rich (79.7%) noncoding region (886 bp). A novel translocation of tRNA(Pro) and tRNA(Thr) was found when comparing this genome with the pancrustacean ground pattern indicating that gene order is not conserved among caridean mitochondria. Furthermore, the rate of Ka/Ks in 13 protein-coding genes between three caridean species is much less than 1, which indicates a strong purifying selection within this group. To investigate the phylogenetic relationship within Malacostraca, phylogenetic trees based on currently available malacostracan complete mitochondrial sequences were built with the maximum likelihood and Bayesian models. All analyses based on nucleotide and amino acid data strongly support the monophyly of Decapoda. The Penaeidae, Reptantia, Caridea, and Meiura clades were also recovered as monophyletic groups with strong statistical support. However, the phylogenetic relationships within Pleocyemata are unstable, as represented by the inclusion or exclusion of Caridea.}, }
@article {pmid19267896, year = {2009}, author = {Hlaing, T and Tun-Lin, W and Somboon, P and Socheat, D and Setha, T and Min, S and Chang, MS and Walton, C}, title = {Mitochondrial pseudogenes in the nuclear genome of Aedes aegypti mosquitoes: implications for past and future population genetic studies.}, journal = {BMC genetics}, volume = {10}, number = {}, pages = {11}, pmid = {19267896}, issn = {1471-2156}, mesh = {Aedes/*genetics ; Animals ; Cell Nucleus/genetics ; Computational Biology/methods ; DNA, Mitochondrial/genetics ; Databases, Nucleic Acid ; Genes, Insect ; *Genes, Mitochondrial ; *Genetics, Population ; Genome ; Haplotypes ; Mitochondria/genetics ; *Pseudogenes ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Mitochondrial DNA (mtDNA) is widely used in population genetic and phylogenetic studies in animals. However, such studies can generate misleading results if the species concerned contain nuclear copies of mtDNA (Numts) as these may amplify in addition to, or even instead of, the authentic target mtDNA. The aim of this study was to determine if Numts are present in Aedes aegypti mosquitoes, to characterise any Numts detected, and to assess the utility of using mtDNA for population genetics studies in this species.<br><br>RESULTS: BLAST searches revealed large numbers of Numts in the Ae. aegypti nuclear genome on 146 supercontigs. Although the majority are short (80% < 300 bp), some Numts are almost full length mtDNA copies. These long Numts are not due to misassembly of the nuclear genome sequence as the Numt-nuclear genome junctions could be recovered by amplification and sequencing. Numt evolution appears to be a complex process in Ae. aegypti with ongoing genomic integration, fragmentation and mutation and the secondary movement of Numts within the nuclear genome.The PCR amplification of the putative mtDNA nicotinamide adenine dinucleotide dehydrogenase subunit 4 (ND4) gene from 166 Southeast Asian Ae. aegypti mosquitoes generated a network with two highly divergent lineages (clade 1 and clade 2). Approximately 15% of the ND4 sequences were a composite of those from each clade indicating Numt amplification in addition to, or instead of, mtDNA. Clade 1 was shown to be composed at least partially of Numts by the removal of clade 1-specific bases from composite sequences following enrichment of the mtDNA. It is possible that all the clade 1 sequences in the network were Numts since the clade 2 sequences correspond to the known mitochondrial genome sequence and since all the individuals that produced clade 1 sequences were also found to contain clade 2 mtDNA-like sequences using clade 2-specific primers. However, either or both sets of clade sequences could have Numts since the BLAST searches revealed two long Numts that match clade 2 and one long Numt that matches clade 1. The substantial numbers of mutations in cloned ND4 PCR products also suggest there are both recently-derived clade 1 and clade 2 Numt sequences.<br><br>CONCLUSION: We conclude that Numts are prevalent in Ae. aegypti and that it is difficult to distinguish mtDNA sequences due to the presence of recently formed Numts. Given this, future population genetic or phylogenetic studies in Ae. aegypti should use nuclear, rather than mtDNA, markers.}, }
@article {pmid19257899, year = {2009}, author = {Delgado, AM and Cook, JM}, title = {Effects of a sex-ratio distorting endosymbiont on mtDNA variation in a global insect pest.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {49}, pmid = {19257899}, issn = {1471-2148}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; DNA, Bacterial/genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Female ; Genes, Insect ; Genetic Variation ; *Genetics, Population ; Geography ; Haplotypes ; Male ; Mitochondria/genetics ; Moths/*genetics/microbiology ; Phenotype ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; *Sex Ratio ; Symbiosis ; *Wolbachia/genetics ; }, abstract = {BACKGROUND: Patterns of mtDNA variation within a species reflect long-term population structure, but may also be influenced by maternally inherited endosymbionts, such as Wolbachia. These bacteria often alter host reproductive biology and can drive particular mtDNA haplotypes through populations. We investigated the impacts of Wolbachia infection and geography on mtDNA variation in the diamondback moth, a major global pest whose geographic distribution reflects both natural processes and transport via human agricultural activities.<br><br>RESULTS: The mtDNA phylogeny of 95 individuals sampled from 10 countries on four continents revealed two major clades. One contained only Wolbachia-infected individuals from Malaysia and Kenya, while the other contained only uninfected individuals, from all countries including Malaysia and Kenya. Within the uninfected group was a further clade containing all individuals from Australasia and displaying very limited sequence variation. In contrast, a biparental nuclear gene phylogeny did not have infected and uninfected clades, supporting the notion that maternally-inherited Wolbachia are responsible for the mtDNA pattern. Only about 5% (15/306) of our global sample of individuals was infected with the plutWB1 isolate and even within infected local populations, many insects were uninfected. Comparisons of infected and uninfected isofemale lines revealed that plutWB1 is associated with sex ratio distortion. Uninfected lines have a 1:1 sex ratio, while infected ones show a 2:1 female bias.<br><br>CONCLUSION: The main correlate of mtDNA variation in P. xylostella is presence or absence of the plutWB1 infection. This is associated with substantial sex ratio distortion and the underlying mechanisms deserve further study. In contrast, geographic origin is a poor predictor of moth mtDNA sequences, reflecting human activity in moving the insects around the globe. The exception is a clade of Australasian individuals, which may reflect a bottleneck during their recent introduction to this region.}, }
@article {pmid19251672, year = {2009}, author = {Kroeger, TS and Watkins, KP and Friso, G and van Wijk, KJ and Barkan, A}, title = {A plant-specific RNA-binding domain revealed through analysis of chloroplast group II intron splicing.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {106}, number = {11}, pages = {4537-4542}, pmid = {19251672}, issn = {1091-6490}, mesh = {Binding Sites ; Chloroplasts/*chemistry ; *Introns ; Molecular Sequence Data ; Plant Proteins/metabolism ; *RNA Splicing ; RNA, Plant/metabolism ; RNA-Binding Proteins/*metabolism ; Ribonucleoproteins/*metabolism ; }, abstract = {Comparative genomics has provided evidence for numerous conserved protein domains whose functions remain unknown. We identified a protein harboring "domain of unknown function 860" (DUF860) as a component of group II intron ribonucleoprotein particles in maize chloroplasts. This protein, assigned the name WTF1 ("what's this factor?"), coimmunoprecipitates from chloroplast extract with group II intron RNAs, is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Both WTF1 and its resident DUF860 bind RNA in vitro, demonstrating that DUF860 is a previously unrecognized RNA-binding domain. DUF860 is found only in plants, where it is represented in a protein family comprising 14 orthologous groups in angiosperms. Most members of the DUF860 family are predicted to localize to chloroplasts or mitochondria, suggesting that proteins with this domain have multiple roles in RNA metabolism in both organelles. These findings add to emerging evidence that the coevolution of nuclear and organellar genomes spurred the evolution of diverse noncanonical RNA-binding motifs that perform organelle-specific functions.}, }
@article {pmid19250506, year = {2008}, author = {Dobbs, RJ and Dobbs, SM and Weller, C and Charlett, A and Bjarnason, IT and Curry, A and Ellis, DS and Ibrahim, MA and McCrossan, MV and O'Donohue, J and Owen, RJ and Oxlade, NL and Price, AB and Sanderson, JD and Sudhanva, M and Williams, J}, title = {Helicobacter hypothesis for idiopathic parkinsonism: before and beyond.}, journal = {Helicobacter}, volume = {13}, number = {5}, pages = {309-322}, pmid = {19250506}, issn = {1523-5378}, support = {//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Helicobacter Infections/*complications ; Humans ; Mitochondria/pathology/ultrastructure ; Models, Biological ; Parkinson Disease/*etiology/microbiology/pathology ; }, abstract = {We challenge the concept of idiopathic parkinsonism (IP) as inevitably progressive neurodegeneration, proposing a natural history of sequential microbial insults with predisposing host response. Proof-of-principle that infection can contribute to IP was provided by case studies and a placebo-controlled efficacy study of Helicobacter eradication. "Malignant" IP appears converted to "benign", but marked deterioration accompanies failure. Similar benefit on brady/hypokinesia from eradicating "low-density" infection favors autoimmunity. Although a minority of UK probands are urea breath test positive for Helicobacter, the predicted probability of having the parkinsonian label depends on the serum H. pylori antibody profile, with clinically relevant gradients between this "discriminant index" and disease burden and progression. In IP, H. pylori antibodies discriminate for persistently abnormal bowel function, and specific abnormal duodenal enterocyte mitochondrial morphology is described in relation to H. pylori infection. Slow intestinal transit manifests as constipation from the prodrome. Diarrhea may flag secondary small-intestinal bacterial overgrowth. This, coupled with genetically determined intense inflammatory response, might explain evolution from brady/hypokinetic to rigidity-predominant parkinsonism.}, }
@article {pmid19249364, year = {2009}, author = {López-Calcagno, PE and Moreno, J and Cedeño, L and Labrador, L and Concepción, JL and Avilán, L}, title = {Cloning, expression and biochemical characterization of mitochondrial and cytosolic malate dehydrogenase from Phytophthora infestans.}, journal = {Mycological research}, volume = {113}, number = {Pt 6-7}, pages = {771-781}, doi = {10.1016/j.mycres.2009.02.012}, pmid = {19249364}, issn = {1469-8102}, mesh = {Amino Acid Sequence ; *Cloning, Molecular ; Cytosol/chemistry/*enzymology ; Escherichia coli/genetics/metabolism ; *Gene Expression ; Kinetics ; Malate Dehydrogenase/*chemistry/genetics/metabolism ; Mitochondria/chemistry/*enzymology/genetics ; Molecular Sequence Data ; Oomycetes/chemistry/classification/genetics ; Phylogeny ; Phytophthora infestans/chemistry/classification/*enzymology/genetics ; Sequence Alignment ; }, abstract = {The genes of the mitochondrial and cytosolic malate dehydrogenase (mMDH and cMDH) of Phytophthora infestans were cloned and overexpressed in Escherichia coli as active enzymes. The catalytic properties of these proteins were determined: both enzymes have a similar specific activity. In addition, the natural mitochondrial isoenzyme was semi-purified from mycelia and its catalytic properties determined: the recombinant mitochondrial isoform behaved as the natural enzyme. A phylogenetic analysis indicated that mMDH, present in all stramenopiles studied, can be useful to study the relationships between these organisms. MDH with the conserved domain MDH_cytoplasmic_cytosolic is absent in some stramenopiles as well as in fungi. This enzyme seems to be less related within the stramenopile group. The Phytophthora cMDHs have an insertion of six amino acids that is also present in the stramenopile cMDHs studied, with the exception of Thalassiosira pseudonana cMDH, and is absent in other known eukaryotic cMDHs.}, }
@article {pmid19248758, year = {2009}, author = {Zutz, A and Gompf, S and Schägger, H and Tampé, R}, title = {Mitochondrial ABC proteins in health and disease.}, journal = {Biochimica et biophysica acta}, volume = {1787}, number = {6}, pages = {681-690}, doi = {10.1016/j.bbabio.2009.02.009}, pmid = {19248758}, issn = {0006-3002}, mesh = {ATP-Binding Cassette Transporters/*chemistry/genetics/*metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Heme/biosynthesis ; Homeostasis ; Humans ; Hydrolysis ; Iron/metabolism ; Mitochondrial Proteins/*chemistry/genetics/*metabolism ; Models, Molecular ; Phylogeny ; Protein Processing, Post-Translational ; }, abstract = {ABC transporters represent one of the largest families of membrane proteins that are found in all three phyla of life. Mitochondria comprise up to four ABC systems, ABCB7/ATM1, ABCB10/MDL1, ABCB8 and ABCB6. These half-transporters, which assemble into homodimeric complexes, are involved in a number of key cellular processes, e.g. biogenesis of cytosolic iron-sulfur clusters, heme biosynthesis, iron homeostasis, multidrug resistance, and protection against oxidative stress. Here, we summarize recent advances and emerging themes in our understanding of how these ABC systems in the inner and outer mitochondrial membrane fulfill their functions in important (patho) physiological processes, including neurodegenerative and hematological disorders.}, }
@article {pmid19248170, year = {2009}, author = {Dezfuli, BS and Capuano, S and Magosso, S and Giari, L and Berti, R}, title = {The lateral line system in larvae of the blind cyprinid cavefish, Phreatichthys andruzzii.}, journal = {Anatomical record (Hoboken, N.J. : 2007)}, volume = {292}, number = {3}, pages = {423-430}, doi = {10.1002/ar.20857}, pmid = {19248170}, issn = {1932-8494}, mesh = {Animals ; Cyprinidae/*anatomy &amp; histology ; Cytoplasm/metabolism ; Endoplasmic Reticulum, Rough/metabolism ; Golgi Apparatus/metabolism ; Hair Cells, Auditory/physiology ; Larva/anatomy &amp; histology ; Lateral Line System/*anatomy &amp; histology/physiology ; Mechanoreceptors/*cytology/physiology ; Mitochondria/metabolism ; }, abstract = {Scanning and transmission electron microscopic observations were made on the anterior and posterior lateral line system of larvae of the blind cavefish, Phreatichthys andruzzii. The investigations were conducted on 36 specimens belonging to three different ages of juvenile: 7, 14, and 28 days posthatching. The basic sensory unit of the mechanoreceptive system is a superficial "neuromast," which is composed of sensory hair cells (HCs) embedded in nonsensory support cells (SCs) frequently covered with a cupula. Head neuromasts had the longest cupulae. These organs presented the same structure and ultrastructure in the head and along the body of all specimens of P. andruzzii of different ages. Hair cells of neuromasts of P. andruzzii larvae were pear-shaped cells approximately 10-20 microm high and 3-5 microm in diameter. The nucleus of each hair cell was large and basally placed, the cytoplasm contained numerous mitochondria and each HC had a single long kinocilium and several short stereocilia. The majority of SCs were elongated in shape and their nuclei occupied a significant portion of the cytoplasm. The support cells at the margin of the neuromast were particularly thin. Both types of support cells possessed well-developed rough endoplasmic reticulum and Golgi apparatus. The size and number of neuromasts and their component cells increased with the age of larvae (ANOVA, P < 0.05). The dimensions of the neuromasts of the anterior lateral line (head) did not differ significantly from those of the posterior lateral line (trunk) (ANOVA, P > 0.05).}, }
@article {pmid19243582, year = {2009}, author = {Ennafaa, H and Cabrera, VM and Abu-Amero, KK and González, AM and Amor, MB and Bouhaha, R and Dzimiri, N and Elgaaïed, AB and Larruga, JM}, title = {Mitochondrial DNA haplogroup H structure in North Africa.}, journal = {BMC genetics}, volume = {10}, number = {}, pages = {8}, pmid = {19243582}, issn = {1471-2156}, mesh = {Africa, Northern ; DNA, Mitochondrial/*genetics ; Emigration and Immigration ; Ethnicity/genetics ; Evolution, Molecular ; Female ; Gene Flow ; *Genetics, Population ; Geography ; *Haplotypes ; Humans ; Male ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The Strait of Gibraltar separating the Iberian Peninsula from North Africa is thought to be a stronger barrier to gene flow for male than for female lineages. However, the recent subdivision of the haplogroup H at mitochondrial DNA (mtDNA) level has revealed greater genetic differentiation among geographic regions than previously detected. The dissection of the mtDNA haplogroup H in North Africa, and its comparison with the Iberian Peninsula and Near-East profiles would help clarify the relative affinities among these regions.<br><br>RESULTS: Like the Iberian Peninsula, the dominant mtDNA haplogroup H subgroups in North Africa are H1 (42%) and H3 (13%). The similarity between these regions is stronger in the North-West edge affecting mainly Moroccan Arabs, West Saharans and Mauritanians, and decreases eastwards probably due to gene flow from Near East as attested for the higher frequencies of H4, H5, H7, H8 and H11 subgroups. Moroccan Berbers show stronger affinities with Tunisian and Tunisian Berbers than with Moroccan Arabs. Coalescence ages for H1 (11 +/- 2 ky) and H3 (11 +/- 4 ky) in North Africa point to the possibility of a late Palaeolithic settlement for these lineages similar to those found for other mtDNA haplogroups. Total and partial mtDNA genomic sequencing unveiled stronger mtDNA differentiation among regions than previously found using HVSI mtDNA based analysis.<br><br>CONCLUSION: The subdivision of the mtDNA haplogroup H in North Africa has confirmed that the genetic differentiation found among Western and Eastern populations is mainly due to geographical rather than cultural barriers. It also shows that the historical Arabian role on the region had more a cultural than a demic effect. Whole mtDNA sequencing of identical H haplotypes based on HVSI and RFLP information has unveiled additional mtDNA differences between North African and Iberian Peninsula lineages, pointing to an older mtDNA genetic flow between regions than previously thought. Based on this new information, it seems that the Strait of Gibraltar barrier affected both male and female gene flow in a similar fashion.}, }
@article {pmid19239678, year = {2009}, author = {Forsman, ZH and Barshis, DJ and Hunter, CL and Toonen, RJ}, title = {Shape-shifting corals: molecular markers show morphology is evolutionarily plastic in Porites.}, journal = {BMC evolutionary biology}, volume = {9}, number = {}, pages = {45}, pmid = {19239678}, issn = {1471-2148}, mesh = {Animals ; Anthozoa/anatomy &amp; histology/classification/*genetics ; Bayes Theorem ; Biodiversity ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; *Evolution, Molecular ; Genetic Markers ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Corals are notoriously difficult to identify at the species-level due to few diagnostic characters and variable skeletal morphology. This 'coral species problem' is an impediment to understanding the evolution and biodiversity of this important and threatened group of organisms. We examined the evolution of the nuclear ribosomal internal transcribed spacer (ITS) and mitochondrial markers (COI, putative control region) in Porites, one of the most taxonomically challenging and ecologically important genera of reef-building corals.<br><br>RESULTS: Nuclear and mitochondrial markers were congruent, clearly resolving many traditionally recognized species; however, branching and mounding varieties were genetically indistinguishable within at least two clades, and specimens matching the description of 'Porites lutea' sorted into three genetically divergent groups. Corallite-level features were generally concordant with genetic groups, although hyper-variability in one group (Clade I) overlapped and obscured several others, and Synarea (previously thought to be a separate subgenus) was closely related to congeners despite its unique morphology. Scanning electron microscopy revealed subtle differences between genetic groups that may have been overlooked previously as taxonomic characters.<br><br>CONCLUSION: This study demonstrates that the coral skeleton can be remarkably evolutionarily plastic, which may explain some taxonomic difficulties, and obscure underlying patterns of endemism and diversity.}, }
@article {pmid19228377, year = {2009}, author = {Ren, J and Liu, X and Zhang, G and Liu, B and Guo, X}, title = {"Tandem duplication-random loss" is not a real feature of oyster mitochondrial genomes.}, journal = {BMC genomics}, volume = {10}, number = {}, pages = {84}, pmid = {19228377}, issn = {1471-2164}, mesh = {Animals ; Crassostrea/*genetics ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; *Gene Deletion ; *Gene Duplication ; Gene Order ; *Genome, Mitochondrial ; Polymorphism, Single Nucleotide ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Duplications and rearrangements of coding genes are major themes in the evolution of mitochondrial genomes, bearing important consequences in the function of mitochondria and the fitness of organisms. Yu et al. (BMC Genomics 2008, 9:477) reported the complete mt genome sequence of the oyster Crassostrea hongkongensis (16,475 bp) and found that a DNA segment containing four tRNA genes (trnK(1), trnC, trnQ(1) and trnN), a duplicated (rrnS) and a split rRNA gene (rrnL5') was absent compared with that of two other Crassostrea species. It was suggested that the absence was a novel case of "tandem duplication-random loss" with evolutionary significance. We independently sequenced the complete mt genome of three C. hongkongensis individuals, all of which were 18,622 bp and contained the segment that was missing in Yu et al.'s sequence. Further, we designed primers, verified sequences and demonstrated that the sequence loss in Yu et al.'s study was an artifact caused by placing primers in a duplicated region. The duplication and split of ribosomal RNA genes are unique for Crassostrea oysters and not lost in C. hongkongensis. Our study highlights the need for caution when amplifying and sequencing through duplicated regions of the genome.}, }
@article {pmid19226322, year = {2009}, author = {Haselkorn, TS and Markow, TA and Moran, NA}, title = {Multiple introductions of the Spiroplasma bacterial endosymbiont into Drosophila.}, journal = {Molecular ecology}, volume = {18}, number = {6}, pages = {1294-1305}, doi = {10.1111/j.1365-294X.2009.04085.x}, pmid = {19226322}, issn = {1365-294X}, mesh = {Animals ; Bacterial Typing Techniques ; Bayes Theorem ; *Biological Evolution ; DNA, Bacterial/genetics ; DNA, Mitochondrial/genetics ; Drosophila/genetics/*microbiology ; Genetic Variation ; Genetics, Population ; Haplotypes ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Spiroplasma/classification/*genetics ; *Symbiosis ; }, abstract = {Bacterial endosymbionts are common in insects and can have dramatic effects on their host's evolution. So far, the only heritable symbionts found in Drosophila have been Wolbachia and Spiroplasma. While the incidence and effects of Wolbachia have been studied extensively, the prevalence and significance of Spiroplasma infections in Drosophila are less clear. These small, gram-positive, helical bacteria infect a diverse array of plant and arthropod hosts, conferring a variety of fitness effects. Male-killing Spiroplasma are known from certain Drosophila species; however, in others, Spiroplasma appear not to affect sex ratio. Previous studies have identified different Spiroplasma haplotypes in Drosophila populations, although no extensive surveys have yet been reported. We used a multilocus sequence analysis to reconstruct a robust Spiroplasma endosymbiont phylogeny, assess genetic diversity, and look for evidence of recombination. Six loci were sequenced from over 65 Spiroplasma-infected individuals from nine different Drosophila species. Analysis of these sequences reveals at least five separate introductions of four phylogenetically distinct Spiroplasma haplotypes, indicating that more extensive sampling will likely reveal an even greater Spiroplasma endosymbiont diversity. Patterns of variation in Drosophila mitochondrial haplotypes in Spiroplasma-infected and uninfected flies imply imperfect vertical transmission in host populations and possible horizontal transmission.}, }
@article {pmid19219673, year = {2009}, author = {Yamaguchi, T and Prabowo, RE and Ohshiro, Y and Shimono, T and Jones, D and Kawai, H and Otani, M and Oshino, A and Inagawa, S and Akaya, T and Tamura, I}, title = {The introduction to Japan of the Titan barnacle, Megabalanus coccopoma (Darwin, 1854) (Cirripedia: Balanomorpha) and the role of shipping in its translocation.}, journal = {Biofouling}, volume = {25}, number = {4}, pages = {325-333}, doi = {10.1080/08927010902738048}, pmid = {19219673}, issn = {1029-2454}, mesh = {Animals ; Australia ; Biofilms/growth &amp; development ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Genetics, Population ; Haplotypes ; Japan ; Mitochondria/enzymology ; Phylogeny ; Sequence Analysis, DNA ; *Ships ; Species Specificity ; Thoracica/*classification/genetics/*physiology ; }, abstract = {The Titan Acorn barnacle, Megabalanus coccopoma, a native of the tropical eastern Pacific, has become established in the western Atlantic (Brazil and the northern Gulf of Mexico to the Carolinas), northwestern Europe and the western Indian Ocean (Mauritius), and therefore its dispersal capabilities are well known. This study reports its introduction to Japan and confirms its occurrence in Australia. In an attempt to determine the source of this introduction, phylogeographic techniques, involving cytochrome c oxidase I sequences of various widely separate populations of M. rosa and M. volcano, were utilized. No significant genetic differentiation or haplotype patterns between widely separated populations of each of the three species were found. Lack of such differentiation indicates recent geographical isolation and thus negates a null hypothesis predicting that the occurrence of one of more of these species in Australia was natural.}, }
@article {pmid19216709, year = {2008}, author = {Smirnov, AV and Entelis, NS and Krasheninnikov, IA and Martin, R and Tarassov, IA}, title = {Specific features of 5S rRNA structure - its interactions with macromolecules and possible functions.}, journal = {Biochemistry. Biokhimiia}, volume = {73}, number = {13}, pages = {1418-1437}, doi = {10.1134/s000629790813004x}, pmid = {19216709}, issn = {1608-3040}, mesh = {Animals ; Base Sequence ; Humans ; Macromolecular Substances/*metabolism ; Mitochondria/metabolism ; Proteins/metabolism ; RNA, Ribosomal, 23S/chemistry/genetics/metabolism ; RNA, Ribosomal, 5S/*chemistry/genetics/*metabolism ; }, abstract = {Small non-coding RNAs are today a topic of great interest for molecular biologists because they can be regarded as relicts of a hypothetical "RNA world" which, apparently, preceded the modern stage of organic evolution on Earth. The small molecule of 5S rRNA (approximately 120 nucleotides) is a component of large ribosomal subunits of all living beings (5S rRNAs are not found only in mitoribosomes of fungi and metazoans). This molecule interacts with various protein factors and 23S (28S) rRNA. This review contains the accumulated data to date concerning 5S rRNA structure, interactions with other biological macromolecules, intracellular traffic, and functions in the cell.}, }
@article {pmid19215950, year = {2009}, author = {Morgan, DA and Class, R and Violetta, G and Soslau, G}, title = {Cytokine mediated proliferation of cultured sea turtle blood cells: morphologic and functional comparison to human blood cells.}, journal = {Tissue &amp; cell}, volume = {41}, number = {4}, pages = {299-309}, doi = {10.1016/j.tice.2008.12.004}, pmid = {19215950}, issn = {1532-3072}, mesh = {Animals ; Blood Platelets/chemistry/drug effects/*metabolism/ultrastructure ; Cell Culture Techniques ; Cell Proliferation ; Cells, Cultured ; Cytokines/*pharmacology ; Erythrocytes/chemistry/drug effects/*metabolism/ultrastructure ; Flow Cytometry ; Globins/analysis ; Humans ; Microscopy, Electron ; P-Selectin/analysis ; Platelet Aggregation ; Turtles/*immunology ; }, abstract = {Blood cells from three different sea turtle species were cultured for approximately 3 weeks in nutrient medium supplemented with recombinant human cytokines known to induce terminal maturation of human hematological stem cells. Cultured turtle erythrocytes were translucent, approximately 10x larger than human erythrocytes, contained a single fluorescent inclusion body, contained nuclear epsilon (embryonic) globin proteins, and, absent of organelles while fresh cells contained few, but well defined mitochondria. Cells with basophilic cytoplasm and in all stages of proliferation were observed in cytokine-supplemented cultures and appeared to possess active protein synthesis. Cultured thrombocytes aggregated in response to agonists for at least 8 days, post-collection, contained P-selectin in the nucleus of 6 day cultured cells which appeared to be released after activation with collagen, and after 6 days had no organelles or open canalicular-like system (OCS) while freshly isolated cells demonstrated few, if any organelles but had a well developed OCS. The response of turtle cells to apparently homologous but unnatural human cytokines and the sustained biological properties of thrombocytes identify this suspension culture system as a powerful tool to explore the evolution of cell types and molecular components of hematopoiesis and hemostasis.}, }
@article {pmid19215778, year = {2009}, author = {Schuster, G and Stern, D}, title = {RNA polyadenylation and decay in mitochondria and chloroplasts.}, journal = {Progress in molecular biology and translational science}, volume = {85}, number = {}, pages = {393-422}, doi = {10.1016/S0079-6603(08)00810-6}, pmid = {19215778}, issn = {1877-1173}, mesh = {Chloroplasts/enzymology/*metabolism ; Mitochondria/enzymology/*metabolism ; *Polyadenylation ; RNA/*metabolism ; *RNA Stability ; }, abstract = {Mitochondria and chloroplasts were originally acquired by eukaryotic cells through endosymbiotic events and retain their own gene expression machinery. One hallmark of gene regulation in these two organelles is the predominance of posttranscriptional control, which is exerted both at the gene-specific and global levels. This review focuses on their mechanisms of RNA degradation, and therefore mainly on the polyadenylation-stimulated degradation pathway. Overall, mitochondria and chloroplasts have retained the prokaryotic RNA decay system, despite evolution in the number and character of the enzymes involved. However, several significant differences exist, of which the presence of stable poly(A) tails, and the location of PNPase in the intermembrane space in animal mitochondria, are perhaps the most remarkable. The known and predicted proteins taking part in polyadenylation-stimulated degradation pathways are described, both in chloroplasts and four mitochondrial types: plant, yeast, trypanosome, and animal.}, }
@article {pmid19214710, year = {2009}, author = {Yamaguchi, M}, title = {Novel protein RGPR-p117: its role as the regucalcin gene transcription factor.}, journal = {Molecular and cellular biochemistry}, volume = {327}, number = {1-2}, pages = {53-63}, pmid = {19214710}, issn = {1573-4919}, mesh = {Animals ; Base Sequence ; Cell Nucleus/metabolism ; DNA-Binding Proteins/*genetics/metabolism ; Gene Expression ; Humans ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; Transcription Factors/*genetics/*metabolism ; }, abstract = {RGPR-p117 was originally discovered as a novel protein that binds to a nuclear factor I (NFI) consensus motif TTGGC(N)(6)CC, which is present in the 5'-flanking region of the regucalcin gene (rgn). RGPR-p117 has been identified in human, rat, mouse, bovine, rabbit, and chicken livers. Phylogenetic analysis of six vertebrates shows that RGPR-p117 appears to form a single cluster, indicating a common evolutionary relationship of the RGPR-p117 family. The RGPR-p117 gene consists of at least 26 exons spanning approximately 4.1 kbp and is localized on human chromosome 1q25.2. RGPR-p117 mRNA is expressed in the liver, kidney, heart, spleen, and brain of rats. RGPR-p117 mRNA expression is stimulated through signaling mechanisms. Mammalian RGPR-p117 conserves a leucine zipper motif, which is present in many gene regulatory proteins. RGPR-p117 has been shown to translocate from the cytoplasm to the nucleus in NRK52E cells, a process which is mediated through protein kinase C signaling following hormonal stimulation. The phosphorylated RGPR-p117 binds to the TTGGC motif in the promoter region of the regucalcin gene and enhances regucalcin mRNA expression in the cells, indicating a role as a transcriptional factor. RGPR-p117 is also localized in the plasma membranes, nucleus, mitochondria, microsomes, and cytoplasm. Overexpression of RGPR-p117 has been found to induce a significant decrease in protein and DNA contents in cells, suggesting that RGPR-p117 may regulate the gene expression of other related proteins as well as the transcription factor. Also, overexpression of RGPR-p117 has a suppressive effect on cell death by inhibiting the gene expression of caspase-3, caspase-8, and Fas-associating death domain protein whose TTGGC motif is present in the promoter region of their genes. The novel protein RGPR-p117 has been shown to play an important role as a transcription factor.}, }
@article {pmid19214701, year = {2009}, author = {Shinozaki, A and Sato, N and Hayashi, Y}, title = {Peroxisomal targeting signals in green algae.}, journal = {Protoplasma}, volume = {235}, number = {1-4}, pages = {57-66}, pmid = {19214701}, issn = {1615-6102}, mesh = {Chlorophyta/*metabolism/ultrastructure ; Green Fluorescent Proteins/metabolism ; Microscopy, Electron, Transmission ; Mitochondria/metabolism/ultrastructure ; Organisms, Genetically Modified/genetics/metabolism ; Peroxisomal Targeting Signal 2 Receptor ; Peroxisome-Targeting Signal 1 Receptor ; Peroxisomes/*metabolism/ultrastructure ; Receptors, Cytoplasmic and Nuclear/*metabolism ; Recombinant Fusion Proteins/*metabolism ; Signal Transduction ; }, abstract = {Peroxisomal enzymatic proteins contain targeting signals (PTS) to enable their import into peroxisomes. These targeting signals have been identified as PTS1 and PTS2 in mammalian, yeast, and higher plant cells; however, no PTS2-like amino acid sequences have been observed in enzymes from the genome database of Cyanidiochyzon merolae (Bangiophyceae), a primitive red algae. In studies on the evolution of PTS, it is important to know when their sequences came to be the peroxisomal targeting signals for all living organisms. To this end, we identified a number of genes in the genome database of the green algae Chlamydomonas reinhardtii, which contains amino acid sequences similar to those found in plant PTS. In order to determine whether these sequences function as PTS in green algae, we expressed modified green fluorescent proteins (GFP) fused to these putative PTS peptides under the cauliflower mosaic virus 35S promoter. To confirm whether granular structures containing GFP-PTS fusion proteins accumulated in the peroxisomes of Closterium ehrenbergii, we observed these cells after the peroxisomes were stained with 3, 3'-diaminobenzidine. Our results confirm that the GFP-PTS fusion proteins indeed accumulated in the peroxisomes of these green algae. These findings suggest that the peroxisomal transport system for PTS1 and PTS2 is conserved in green algal cells and that our fusion proteins can be used to visualize peroxisomes in live cells.}, }
@article {pmid19213423, year = {2008}, author = {Artamonova, VS and Khaimina, OV and Makhrov, AA and Shirokov, VA and Shulman, BS and Shurov, IL}, title = {Evolutionary consequences of parasite invasion: a case study of Atlantic salmon Salmo salar L.}, journal = {Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections}, volume = {423}, number = {}, pages = {412-415}, pmid = {19213423}, issn = {0012-4966}, mesh = {Aging/physiology ; Animals ; Atlantic Ocean ; *Biological Evolution ; Haplotypes ; Mitochondria/genetics ; Salmo salar/genetics/*parasitology ; Time Factors ; }, }
@article {pmid19207251, year = {2009}, author = {Cardoso, YP and Montoya-Burgos, JI}, title = {Unexpected diversity in the catfish Pseudancistrus brevispinis reveals dispersal routes in a Neotropical center of endemism: the Guyanas Region.}, journal = {Molecular ecology}, volume = {18}, number = {5}, pages = {947-964}, doi = {10.1111/j.1365-294X.2008.04068.x}, pmid = {19207251}, issn = {1365-294X}, mesh = {*Animal Migration ; Animals ; Catfishes/*genetics ; Cell Nucleus/genetics ; *Genetic Variation ; Genetics, Population ; Geography ; Guyana ; Haplotypes/genetics ; Likelihood Functions ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; *Tropical Climate ; }, abstract = {Neotropical freshwater fishes have reached an unrivalled diversity, organized into several areas of endemism, yet the underlying processes are still largely unknown. The topographical and ecological characteristics of the Guyanas Region make it an ideal area of endemism in which to investigate the forces that have shaped this great diversity. This region is thought to be inhabited by species descending from Amazonian ancestors, which would have used two documented routes that, however, hardly explain the entrance of species adapted to running waters. Here, we investigate the evolutionary history of Pseudancistrus brevispinis, a catfish endemic to this region and exclusively found in running waters, thus making it an ideal model for investigating colonization routes and dispersal in such habitats. Our analyses, based on mitochondrial and nuclear markers, revealed an unexpected diversity consisting of six monophyletic lineages within P. brevispinis, showing a disjoint distribution pattern. The lineages endemic to Guyanas coastal rivers form a monophyletic group that originated via an ancestral colonization event from the Amazon basin. Evidence given favours a colonization pathway through river capture between an Amazonian tributary and the Upper Maroni River. Population genetic analyses of the most widespread species indicate that subsequent dispersal among Guyanas coastal rivers occurred principally by temporary connections between adjacent rivers during periods of lower sea level, yet instances of dispersal via interbasin river captures are not excluded. During high sea level intervals, the isolated populations would have diverged leading to the observed allopatric species. This evolutionary process is named the sea level fluctuation (SLF) hypothesis of diversification.}, }
@article {pmid19207245, year = {2009}, author = {Kanbe, T and Akimoto, S}, title = {Allelic and genotypic diversity in long-term asexual populations of the pea aphid, Acyrthosiphon pisum in comparison with sexual populations.}, journal = {Molecular ecology}, volume = {18}, number = {5}, pages = {801-816}, doi = {10.1111/j.1365-294X.2008.04077.x}, pmid = {19207245}, issn = {1365-294X}, mesh = {*Alleles ; Animals ; Aphids/*genetics ; Electron Transport Complex IV/genetics ; Female ; Genetic Loci/genetics ; *Genetic Variation ; Genetics, Population ; Genotype ; Geography ; Japan ; Male ; Microsatellite Repeats/genetics ; Mitochondria/enzymology ; Oviparity/genetics ; Pisum sativum/*parasitology ; Phylogeny ; Reproduction, Asexual/*genetics ; Sample Size ; Time Factors ; Viviparity, Nonmammalian/genetics ; }, abstract = {Many aphid species exhibit geographical variation in the mode of reproduction that ranges from cyclical parthenogenesis with a sexual phase to obligate parthenogenesis (asexual reproduction). Theoretical studies predict that organisms reproducing asexually should maintain higher allelic diversity per locus but lower genotypic diversity than organisms reproducing sexually. To corroborate this hypothesis, we evaluated genotypic and allelic diversities in the sexual and asexual populations of the pea aphid, Acyrthosiphon pisum (Harris). Microsatellite analysis revealed that populations in central Japan are asexual, whereas populations in northern Japan are obligatorily sexual. No mixed populations were detected in our study sites. Phylogenetic analysis using microsatellite data and mitochondrial cytochrome oxidase subunit I (COI) gene sequences revealed a long history of asexuality in central Japan and negated the possibility of the recent origin of the asexual populations from the sexual populations. Asexual populations exhibited much lower genotypic diversity but higher allelic richness per locus than did sexual populations. Asexual populations consisted of a few predominant clones that were considerably differentiated from one another. Sexual populations on alfalfa, an exotic plant in Japan, were most closely related to asexual populations associated with Vicia sativa L. The alfalfa-associated sexual populations harboured one COI haplotype that was included in the haplotype clade of the asexual populations. Available evidence suggests that the sexuality of the alfalfa-associated populations has recently been restored through the northward migration and colonization of alfalfa by V. sativa-associated lineages. Therefore, our results support the theoretical predictions and provide a new perspective on the origin of sexual populations.}, }
@article {pmid19204978, year = {2009}, author = {Waller, RF and Jackson, CJ}, title = {Dinoflagellate mitochondrial genomes: stretching the rules of molecular biology.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {31}, number = {2}, pages = {237-245}, doi = {10.1002/bies.200800164}, pmid = {19204978}, issn = {1521-1878}, mesh = {Animals ; Dinoflagellida/*genetics ; Genome, Mitochondrial/*genetics ; *Molecular Biology ; Open Reading Frames/genetics ; RNA Editing/genetics ; RNA, Ribosomal/genetics ; }, abstract = {Mitochondrial genomes represent relict bacterial genomes derived from a progenitor alpha-proteobacterium that gave rise to all mitochondria through an ancient endosymbiosis. Evolution has massively reduced these genomes, yet despite relative simplicity their organization and expression has developed considerable novelty throughout eukaryotic evolution. Few organisms have reengineered their mitochondrial genomes as thoroughly as the protist lineage of dinoflagellates. Recent work reveals dinoflagellate mitochondrial genomes as likely the most gene-impoverished of any free-living eukaryote, encoding only two to three proteins. The organization and expression of these genomes, however, is far from the simplicity their gene content would suggest. Gene duplication, fragmentation, and scrambling have resulted in an inflated and complex genome organization. Extensive RNA editing then recodes gene transcripts, and trans-splicing is required to assemble full-length transcripts for at least one fragmented gene. Even after these processes, messenger RNAs (mRNAs) lack canonical start codons and most transcripts have abandoned stop codons altogether.}, }
@article {pmid19203921, year = {2009}, author = {Neiman, M and Taylor, DR}, title = {The causes of mutation accumulation in mitochondrial genomes.}, journal = {Proceedings. Biological sciences}, volume = {276}, number = {1660}, pages = {1201-1209}, pmid = {19203921}, issn = {0962-8452}, mesh = {*Biological Evolution ; DNA, Mitochondrial/*genetics ; *Genome ; Mitochondria/*genetics ; Mutation ; Reproduction/genetics ; }, abstract = {A fundamental observation across eukaryotic taxa is that mitochondrial genomes have a higher load of deleterious mutations than nuclear genomes. Identifying the evolutionary forces that drive this difference is important to understanding the rates and patterns of sequence evolution, the efficacy of natural selection, the maintenance of sex and recombination and the mechanisms underlying human ageing and many diseases. Recent studies have implicated the presumed asexuality of mitochondrial genomes as responsible for their high mutational load. We review the current body of knowledge on mitochondrial mutation accumulation and recombination, and conclude that asexuality, per se, may not be the primary determinant of the high mutation load in mitochondrial DNA (mtDNA). Very little recombination is required to counter mutation accumulation, and recent evidence suggests that mitochondrial genomes do experience occasional recombination. Instead, a high rate of accumulation of mildly deleterious mutations in mtDNA may result from the small effective population size associated with effectively haploid inheritance. This type of transmission is nearly ubiquitous among mitochondrial genomes. We also describe an experimental framework using variation in mating system between closely related species to disentangle the root causes of mutation accumulation in mitochondrial genomes.}, }
@article {pmid19198901, year = {2009}, author = {Mirus, O and Bionda, T and von Haeseler, A and Schleiff, E}, title = {Evolutionarily evolved discriminators in the 3-TPR domain of the Toc64 family involved in protein translocation at the outer membrane of chloroplasts and mitochondria.}, journal = {Journal of molecular modeling}, volume = {15}, number = {8}, pages = {971-982}, pmid = {19198901}, issn = {0948-5023}, mesh = {Amino Acid Sequence ; Arabidopsis Proteins/*chemistry/genetics/metabolism ; Binding Sites/genetics ; Chloroplasts/*metabolism ; Computer Simulation ; Evolution, Molecular ; HSP90 Heat-Shock Proteins/chemistry/metabolism ; Intracellular Membranes/*metabolism ; Membrane Proteins/*chemistry/genetics/metabolism ; Mitochondria/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Principal Component Analysis ; Protein Binding ; Protein Structure, Secondary ; *Protein Structure, Tertiary ; Protein Transport ; }, abstract = {Transport of polypeptides across membranes is a general and essential cellular process utilised by molecular machines. At least one component of these complexes contains a domain composed of three tetratricopeptide repeat (3-TPR) motifs. We have focussed on the receptor Toc64 to elucidate the evolved functional specifications of its 3-TPR domain. Toc64 is a component of the Toc core complex and functionally replaces Tom70 at the outer membrane of mitochondria in plants. Its 3-TPR domain recognises the conserved C-terminus of precursor-bound chaperones. We built homology models of the 3-TPR domain of chloroplastic Toc64 from different species and of the mitochondrial isoform from Arabidopsis. Guided by modelling, we identified residues essential for functional discrimination of the differently located isoforms to be located almost exclusively on the convex surface of the 3-TPR domain. The only exception is at568Ser/ps557Met, which is positioned in the ligand-binding groove. The functional implications of the homology models are discussed.}, }
@article {pmid19198657, year = {2009}, author = {Piganeau, G and Eyre-Walker, A}, title = {Evidence for variation in the effective population size of animal mitochondrial DNA.}, journal = {PloS one}, volume = {4}, number = {2}, pages = {e4396}, pmid = {19198657}, issn = {1932-6203}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; DNA, Mitochondrial/*chemistry ; Evolution, Molecular ; Genes, Mitochondrial ; *Genetic Variation ; Genetics, Population ; Isoenzymes/genetics ; Mammals/genetics ; Mutation ; Phylogeny ; Population Density ; Selection, Genetic ; }, abstract = {BACKGROUND: It has recently been shown that levels of diversity in mitochondrial DNA are remarkably constant across animals of diverse census population sizes and ecologies, which has led to the suggestion that the effective population of mitochondrial DNA may be relatively constant.<br><br>RESULTS: Here we present several lines of evidence that suggest, to the contrary, that the effective population size of mtDNA does vary, and that the variation can be substantial. First, we show that levels of mitochondrial and nuclear diversity are correlated within all groups of animals we surveyed. Second, we show that the effectiveness of selection on non-synonymous mutations, as measured by the ratio of the numbers of non-synonymous and synonymous polymorphisms, is negatively correlated to levels of mitochondrial diversity. Finally, we estimate the effective population size of mitochondrial DNA in selected mammalian groups and show that it varies by at least an order of magnitude.<br><br>CONCLUSIONS: We conclude that there is variation in the effective population size of mitochondria. Furthermore we suggest that the relative constancy of DNA diversity may be due to a negative correlation between the effective population size and the mutation rate per generation.}, }
@article {pmid19196051, year = {2009}, author = {Passamonti, M and Ghiselli, F}, title = {Doubly uniparental inheritance: two mitochondrial genomes, one precious model for organelle DNA inheritance and evolution.}, journal = {DNA and cell biology}, volume = {28}, number = {2}, pages = {79-89}, doi = {10.1089/dna.2008.0807}, pmid = {19196051}, issn = {1557-7430}, mesh = {Animals ; *Evolution, Molecular ; Female ; Genome, Mitochondrial/*genetics ; Humans ; Male ; Mitochondria/physiology ; Models, Genetic ; Mollusca/*genetics ; Sex Determination Processes ; }, abstract = {Eukaryotes have exploited several mechanisms for organelle uniparental inheritance, so this feature arose and evolved independently many times in their history. Metazoans' mitochondria commonly experience strict maternal inheritance; that is, they are only transmitted by females. However, the most noteworthy exception comes from some bivalve mollusks, in which two mitochondrial lineages (together with their genomes) are inherited: one through females (F) and the other through males (M). M and F genomes show up to 30% sequence divergence. This inheritance mechanism is known as doubly uniparental inheritance (DUI), because both sexes inherit uniparentally their mitochondria. Here, we review what we know about this unusual system, and we propose a model for evolution of DUI that might account for its origin as sex determination mechanism. Moreover, we propose DUI as a choice model to address many aspects that should be of interest to a wide range of biological subfields, such as mitochondrial inheritance, mtDNA evolution and recombination, genomic conflicts, evolution of sex, and developmental biology. Actually, as research proceeds, mitochondria appear to have acquired a central role in many fundamental processes of life, which are not only in their metabolic activity as cellular power plants, such as cell signaling, fertilization, development, differentiation, ageing, apoptosis, and sex determination. A function of mitochondria in the origin and maintenance of sex has been also proposed.}, }
@article {pmid19194659, year = {2009}, author = {Balsera, M and Soll, J and Bölter, B}, title = {Protein import machineries in endosymbiotic organelles.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {66}, number = {11-12}, pages = {1903-1923}, doi = {10.1007/s00018-009-8644-2}, pmid = {19194659}, issn = {1420-9071}, mesh = {Chloroplasts/*physiology ; Cytosol/metabolism ; Membrane Transport Proteins/genetics/physiology ; Mitochondria/*physiology ; Mitochondrial Proteins/genetics/*physiology ; Phylogeny ; Plant Proteins/genetics/*physiology ; Plants/*metabolism/ultrastructure ; Protein Transport/physiology ; Ribosomes/metabolism ; }, abstract = {Chloroplast and mitochondria, the two organelles with an accepted endosymbiotic origin, have developed multiple translocation pathways to ensure the subcellular allocation of proteins synthesized by cytosolic ribosomes, and to guarantee their assembly into functional complexes in coordination also with organellar-encoded subunits. The evolution of different protein import machineries was thus essential for the development of these two organelles within cells. A general overview of the translocation machineries in chloroplast and mitochondrial membranes involved in targeting and import of nuclear-encoded proteins, with special focus on plant cells where the two organelles coexist, is expounded.}, }
@article {pmid19192181, year = {2009}, author = {Flanders, J and Jones, G and Benda, P and Dietz, C and Zhang, S and Li, G and Sharifi, M and Rossiter, SJ}, title = {Phylogeography of the greater horseshoe bat, Rhinolophus ferrumequinum: contrasting results from mitochondrial and microsatellite data.}, journal = {Molecular ecology}, volume = {18}, number = {2}, pages = {306-318}, doi = {10.1111/j.1365-294X.2008.04021.x}, pmid = {19192181}, issn = {1365-294X}, mesh = {Animals ; Asia ; Chiroptera/*genetics ; DNA, Mitochondrial/*genetics ; Europe ; Evolution, Molecular ; Genes, Mitochondrial ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes ; *Microsatellite Repeats ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Phylogeographical studies are typically based on haplotype data, occasionally on nuclear markers such as microsatellites, but rarely combine both. This is unfortunate because the use of markers with contrasting modes of inheritance and rates of evolution might provide a more accurate and comprehensive understanding of a species' history. Here we present a detailed study of the phylogeography of the greater horseshoe bat, Rhinolophus ferrumequinum, using 1098 bp of the mitochondrial ND2 gene from 45 localities from across its Palaearctic range to infer population history. In addition, we re-analysed a large microsatellite data set available for this species and compared the results of both markers to infer population relationships and the historical processes influencing them. We show that mtDNA, the most popular marker in phylogeography studies, yielded a misleading result, and would have led us to conclude erroneously that a single expansion had taken place in Europe. Only by combining the mitochondrial and microsatellite data sets are we able to reconstruct the species' history and show two colonization events in Europe, one before the Last Glacial Maximum (LGM) and one after it. Combining markers also revealed the importance of Asia Minor as an ancient refugium for this species and a source population for the expansion of the greater horseshoe bat into Europe before the LGM.}, }
@article {pmid19192035, year = {2009}, author = {Spinazzola, A and Zeviani, M}, title = {Disorders from perturbations of nuclear-mitochondrial intergenomic cross-talk.}, journal = {Journal of internal medicine}, volume = {265}, number = {2}, pages = {174-192}, doi = {10.1111/j.1365-2796.2008.02059.x}, pmid = {19192035}, issn = {1365-2796}, support = {GGP07019/TI_/Telethon/Italy ; }, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Disease Models, Animal ; *Gene Deletion ; Humans ; Mice ; Mitochondrial Diseases/classification/*genetics ; Mutation/genetics ; Oxidative Phosphorylation ; }, abstract = {In the course of evolution, mitochondria lost their independence, and mitochondrial DNA (mtDNA) became the 'slave' of nuclear DNA, depending on numerous nucleus-encoded factors for its integrity, replication and expression. Mutations in any of these factors may alter the cross-talk between the two genomes and cause Mendelian disorders characterized by qualitative (multiple deletions) or quantitative (depletion) alterations of mtDNA, or by defective translation of mtDNA-encoded respiratory chain components.}, }
@article {pmid19187247, year = {2009}, author = {Cheviron, ZA and Brumfield, RT}, title = {Migration-selection balance and local adaptation of mitochondrial haplotypes in rufous-collared sparrows (Zonotrichia capensis) along an elevational gradient.}, journal = {Evolution; international journal of organic evolution}, volume = {63}, number = {6}, pages = {1593-1605}, doi = {10.1111/j.1558-5646.2009.00644.x}, pmid = {19187247}, issn = {1558-5646}, mesh = {Acclimatization/*genetics ; *Altitude ; *Animal Migration ; Animals ; Ecosystem ; Evolution, Molecular ; Female ; Gene Flow ; Genetic Speciation ; Genetic Variation ; Genetics, Population ; *Haplotypes ; Male ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Peru ; *Selection, Genetic ; Sparrows/*genetics ; }, abstract = {Variable selection pressures across heterogeneous landscapes can lead to local adaptation of populations. The extent of local adaptation depends on the interplay between natural selection and gene flow, but the nature of this relationship is complex. Gene flow can constrain local adaptation by eroding differentiation driven by natural selection, or local adaptation can itself constrain gene flow through selection against maladapted immigrants. Here we test for evidence that natural selection constrains gene flow among populations of a widespread passerine bird (Zonotrichia capensis) that are distributed along an elevational gradient in the Peruvian Andes. Using multilocus sequences and microsatellites screened in 142 individuals collected along a series of replicate transects, we found that mitochondrial gene flow was significantly reduced along elevational transects relative to latitudinal control transects. Nuclear gene flow, however, was not similarly reduced. Clines in mitochondrial haplotype frequency were strongly associated with transitions in environmental variables along the elevational transects, but this association was not observed for the nuclear markers. These results suggest that natural selection constrains mitochondrial gene flow along elevational gradients and that the mitonuclear discrepancy may be due to local adaptation of mitochondrial haplotypes.}, }
@article {pmid19184408, year = {2009}, author = {Jeong, HC and Kim, JA and Im, HH and Jeong, HU and Hong, MY and Lee, JE and Han, YS and Kim, I}, title = {Mitochondrial DNA sequence variation of the swallowtail butterfly, Papilio xuthus, and the cabbage butterfly, Pieris rapae.}, journal = {Biochemical genetics}, volume = {47}, number = {3-4}, pages = {165-178}, doi = {10.1007/s10528-008-9214-2}, pmid = {19184408}, issn = {1573-4927}, mesh = {Animals ; Butterflies/*genetics ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Genetics, Population ; Korea ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {We analyzed a portion of mitochondrial COI gene sequences (658 bp) to investigate the genetic diversity and geographic variation of the swallowtail butterfly, Papilio xuthus L. (Lepidoptera: Papilionidae), and the cabbage butterfly, Pieris rapae L. (Lepidoptera: Pieridae). Papilio xuthus showed a moderate level of sequence divergence (0.91% at maximum) in 15 haplotypes, whereas Pi. rapae showed a moderate to high level of sequence divergence (1.67% at maximum) in 30 haplotypes, compared with other relevant studies. Analyses of population genetic structure showed that most populations are not genetically differentiated in both species. The distribution pattern of both species appears to be consistent with category IV of the phylogeographic pattern sensu Avise: a phylogenetic continuity, an absence of regional isolation of mtDNA clones, and extensive distribution of close clones. The observed pattern of genetic diversity and geographic variation of the two butterfly species seem to reflect the abundant habitats, abundant host plants, and flying abilities in connection with the lack of historical biogeographic barriers.}, }
@article {pmid19182105, year = {2009}, author = {Wamboldt, Y and Mohammed, S and Elowsky, C and Wittgren, C and de Paula, WB and Mackenzie, SA}, title = {Participation of leaky ribosome scanning in protein dual targeting by alternative translation initiation in higher plants.}, journal = {The Plant cell}, volume = {21}, number = {1}, pages = {157-167}, pmid = {19182105}, issn = {1040-4651}, mesh = {5' Untranslated Regions ; Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Base Sequence ; DNA Polymerase II/genetics/metabolism ; DNA, Plant/genetics ; Gene Expression Regulation, Plant ; Mitochondria/metabolism ; Molecular Sequence Data ; *Peptide Chain Initiation, Translational ; Plastids/metabolism ; RNA Probes ; Ribosomes/*metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Trans-Activators/genetics/metabolism ; *Transcription Initiation Site ; }, abstract = {Postendosymbiotic evolution has given rise to proteins that are multiply targeted within the cell. Various mechanisms have been identified to permit the expression of proteins encoding distinct N termini from a single gene. One mechanism involves alternative translation initiation (aTI). We previously showed evidence of aTI activity within the Arabidopsis thaliana organellar DNA polymerase gene POLgamma2. Translation initiates at four distinct sites within this gene, two non-AUG, to produce distinct plastid and mitochondrially targeted forms of the protein. To understand the regulation of aTI in higher plants, we used Polgamma2 as a model to investigate both cis- and trans-acting features of the process. Here, we show that aTI in Polgamma2 and other plant genes involves ribosome scanning dependent on sequence context at the multiple initiation sites to condition specific binding of at least one trans-acting factor essential for site recognition. Multiple active translation initiation sites appear to operate in several plant genes, often to expand protein targeting. In plants, where the mitochondrion and plastid must share a considerable portion of their proteomes and coordinate their functions, leaky ribosome scanning behavior provides adaptive advantage in the evolution of protein dual targeting and translational regulation.}, }
@article {pmid19181828, year = {2009}, author = {Mouton, L and Henri, H and Fleury, F}, title = {Interactions between coexisting intracellular genomes: mitochondrial density and Wolbachia infection.}, journal = {Applied and environmental microbiology}, volume = {75}, number = {7}, pages = {1916-1921}, pmid = {19181828}, issn = {1098-5336}, mesh = {Animals ; Drosophila/*genetics/*microbiology ; *Host-Parasite Interactions ; Mitochondria/*genetics ; *Symbiosis ; Wolbachia/*physiology ; }, abstract = {Many arthropods are infected with maternally transmitted microorganisms, leading to the coexistence of several intracellular genomes within the host cells, including their own mitochondria. As these genomes are cotransmitted, their patterns of evolution have been intimately linked, with possible consequences for the diversity and evolution of the host mitochondrial DNA. The evolutionary aspects of the situation have been thoroughly investigated, especially the selective sweep on the mitochondria as a result of Wolbachia invasion, whereas direct interactions between mitochondria and intracellular symbionts within the host cells or body have received little attention. Since endosymbionts exploit host resources but mitochondria supply energy to meet the bioenergetic demands of organisms, an unanswered question concerns the correlation between their densities. Here, we investigated the influence of Wolbachia symbiosis on mitochondrial density in two parasitic wasps of Drosophila species, both of which are naturally infected by three Wolbachia strains, but they differ in their degree of dependency on these bacteria. In Leptopilina heterotoma, all Wolbachia strains are facultative, whereas Asobara tabida requires a strain of Wolbachia for oogenesis to occur. In both species, Wolbachia infections are stable and well regulated, since the density of each strain does not depend on the presence or absence of other strains. Using lines that harbor various Wolbachia infection statuses, we found that mitochondrial density was not affected by the infection regardless of the sex and age of the host, which is strongly reminiscent of the independent regulation of specific Wolbachia strains and suggest that the protagonists coexist independently of each other as the result of a long-term coevolutionary interaction.}, }
@article {pmid19179764, year = {2008}, author = {Karanth, KP}, title = {Primate numts and reticulate evolution of capped and golden leaf monkeys (Primates: Colobinae).}, journal = {Journal of biosciences}, volume = {33}, number = {5}, pages = {761-770}, pmid = {19179764}, issn = {0250-5991}, mesh = {Amino Acid Sequence ; Animals ; Colobinae/*genetics ; Cytochromes b/chemistry/*genetics/metabolism ; *Evolution, Molecular ; Hybridization, Genetic ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {A recent phylogenetic study of langurs and leaf monkeys of South Asia suggested a reticulate evolution of capped and golden leaf monkeys through ancient hybridization between Semnopithecus and Trachypithecus .To test this hybridization scenario, I analysed nuclear copies of the mitochondrial cytochrome b gene (numts) from capped,golden and Phayre's leaf monkeys. These numts were aligned with mitochondrial cytochrome b sequences of various species belonging to the genera Semnopithecus and Trachypithecus .In the phylogenetic tree derived from this alignment,the numts fell into three distinct clades (A,B and C) suggesting three independent integration events.Clade A was basal to Semnopithecus, and clades B and C were basal to Trachypithecus. Among the numts in clades A and C were sequences derived from species not represented in their respective sister mitochondrial groups.This unusual placement of certain numts is taken as additional support for the hybridization scenario. Based on the molecular dating of these integration events,hybridization is estimated to have occurred around 7.1 to 3.4 million years ago.Capped and golden leaf monkeys might have to be assigned to a new genus to reconcile their unique evolutionary history. Additionally, northeast India appears to be a 'hot spot' for lineages that might have evolved through reticulate evolution.}, }
@article {pmid19175505, year = {2009}, author = {Cardoso, A and Serrano, A and Vogler, AP}, title = {Morphological and molecular variation in tiger beetles of the Cicindela hybrida complex: is an 'integrative taxonomy' possible?.}, journal = {Molecular ecology}, volume = {18}, number = {4}, pages = {648-664}, doi = {10.1111/j.1365-294X.2008.04048.x}, pmid = {19175505}, issn = {1365-294X}, mesh = {Animals ; Base Sequence ; Coleoptera/*anatomy &amp; histology/classification/*genetics ; DNA, Mitochondrial/genetics ; Europe ; *Evolution, Molecular ; Genetic Speciation ; Genetic Variation ; Haplotypes ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Current taxon assignments at the species level are frequently discordant with DNA-based analyses. Recent studies on tiger beetles in the Cicindela hybrida complex identified discordance between mtDNA patterns and the entities currently defined by the taxonomic literature. To test the accuracy of morphologically delimited groups, five named taxa (species) from 24 representative sampling sites across Europe were scored for 41 external morphological characters. Three of the named taxa were 'diagnosable', that is, defined by between one and three characters unique to each group. Newly sequenced ITS1 and existing mitochondrial cox1 markers established 20 and 22 different haplotypes, respectively, but only cox1 produced (four) diagnosable units. Phylogenetic analysis and statistical parsimony networks showed poor congruence of character variation with the taxonomic entities (and each other). Variation in morphological characters was therefore tested directly for association with DNA-based nesting groups at various hierarchical levels using permutational contingency analysis. Significant statistical associations of 11 (of 13 variable) morphological characters were observed with nesting groups from ITS1 and mitochondrial DNA markers, predominantly at the 4-step level. The analysis demonstrates the need for formal tests of congruence with morphological variation at the level of individual characters, a step that is omitted from recent studies of 'integrative taxonomy'. In addition, statistical correlation of particular morphological characters with DNA-based nesting groups can identify the lowest hierarchical level at which various character sets show congruence, as a means to define evolutionarily separated entities supported by diverse data sources.}, }
@article {pmid19173734, year = {2009}, author = {Yubuki, N and Edgcomb, VP and Bernhard, JM and Leander, BS}, title = {Ultrastructure and molecular phylogeny of Calkinsia aureus: cellular identity of a novel clade of deep-sea euglenozoans with epibiotic bacteria.}, journal = {BMC microbiology}, volume = {9}, number = {}, pages = {16}, pmid = {19173734}, issn = {1471-2180}, mesh = {Animals ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Euglenida/classification/*genetics/*ultrastructure ; Microscopy, Electron, Transmission ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {BACKGROUND: The Euglenozoa is a large group of eukaryotic flagellates with diverse modes of nutrition. The group consists of three main subclades - euglenids, kinetoplastids and diplonemids--that have been confirmed with both molecular phylogenetic analyses and a combination of shared ultrastructural characteristics. Several poorly understood lineages of putative euglenozoans live in anoxic environments, such as Calkinsia aureus, and have yet to be characterized at the molecular and ultrastructural levels. Improved understanding of these lineages is expected to shed considerable light onto the ultrastructure of prokaryote-eukaryote symbioses and the associated cellular innovations found within the Euglenozoa and beyond.<br><br>RESULTS: We collected Calkinsia aureus from core samples taken from the low-oxygen seafloor of the Santa Barbara Basin (580 - 592 m depth), California. These biflagellates were distinctively orange in color and covered with a dense array of elongated epibiotic bacteria. Serial TEM sections through individually prepared cells demonstrated that C. aureus shares derived ultrastructural features with other members of the Euglenozoa (e.g. the same paraxonemal rods, microtubular root system and extrusomes). However, C. aureus also possessed several novel ultrastructural systems, such as modified mitochondria (i.e. hydrogenosome-like), an "extrusomal pocket", a highly organized extracellular matrix beneath epibiotic bacteria and a complex flagellar transition zone. Molecular phylogenies inferred from SSU rDNA sequences demonstrated that C. aureus grouped strongly within the Euglenozoa and with several environmental sequences taken from low-oxygen sediments in various locations around the world.<br><br>CONCLUSION: Calkinsia aureus possesses all of the synapomorphies for the Euglenozoa, but lacks traits that are specific to any of the three previously recognized euglenozoan subgroups. Molecular phylogenetic analyses of C. aureus demonstrate that this lineage is a member of a novel euglenozoan subclade consisting of uncharacterized cells living in low-oxygen environments. Our ultrastructural description of C. aureus establishes the cellular identity of a fourth group of euglenozoans, referred to as the "Symbiontida".}, }
@article {pmid19169711, year = {2009}, author = {Rüdinger, M and Funk, HT and Rensing, SA and Maier, UG and Knoop, V}, title = {RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal.}, journal = {Molecular genetics and genomics : MGG}, volume = {281}, number = {5}, pages = {473-481}, pmid = {19169711}, issn = {1617-4623}, mesh = {Amino Acid Sequence ; Base Sequence ; Bryopsida/*genetics/*metabolism ; Conserved Sequence ; Gene Expression Profiling ; Genes, Mitochondrial ; Genes, Plant ; Molecular Sequence Data ; Plant Proteins/genetics ; RNA/*genetics/*metabolism ; *RNA Editing ; RNA, Messenger/*genetics/*metabolism ; RNA, Mitochondrial ; RNA, Plant/*genetics/*metabolism ; Sequence Homology, Amino Acid ; Terminology as Topic ; }, abstract = {RNA editing in mitochondria and chloroplasts of land plants alters the coding content of transcripts through site-specific exchanges of cytidines into uridines and vice versa. The abundance of RNA editing in model plant species such as rice or Arabidopsis with some 500 affected sites in their organelle transcripts hinders straightforward approaches to elucidate its mechanisms. The moss Physcomitrella patens is increasingly being appreciated as an alternative plant model system, enhanced by the recent availability of its complete chloroplast, mitochondrial, and nuclear genome sequences. We here report the transcriptomic analysis of Physcomitrella mitochondrial mRNAs as a prerequisite for future studies of mitochondrial RNA editing in this moss. We find a strikingly low frequency of RNA editing affecting only eleven, albeit highly important, sites of C-to-U nucleotide modification in only nine mitochondrial genes. Partial editing was seen for two of these sites but no evidence for any silent editing sites (leaving the identity of the encoded amino acid unchanged) as commonly observed in vascular plants was found in Physcomitrella, indicating a compact and efficient organization of the editing machinery. Furthermore, we here wish to propose a unifying nomenclature to clearly identify and designate RNA editing positions and to facilitate future communication and database annotation.}, }
@article {pmid19165886, year = {2009}, author = {Schuiki, I and Daum, G}, title = {Phosphatidylserine decarboxylases, key enzymes of lipid metabolism.}, journal = {IUBMB life}, volume = {61}, number = {2}, pages = {151-162}, doi = {10.1002/iub.159}, pmid = {19165886}, issn = {1521-6551}, support = {P 21429/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Biological Transport/genetics ; Carboxy-Lyases/chemistry/genetics/*metabolism ; Conserved Sequence ; Decarboxylation ; Eukaryotic Cells/metabolism ; Forecasting ; Lipid Metabolism/*genetics ; Molecular Sequence Data ; Phosphatidylethanolamines/biosynthesis/genetics ; Phylogeny ; Prokaryotic Cells/metabolism ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Substrate Specificity/genetics ; }, abstract = {Phosphatidylserine decarboxylases (PSDs) (E.C. 4.1.1.65) are enzymes which catalyze the formation of phosphatidylethanolamine (PtdEtn) by decarboxylation of phosphatidylserine (PtdSer). This enzymatic activity has been identified in both prokaryotic and eukaryotic organisms. PSDs occur as two types of proteins depending on their localization and the sequence of a conserved motif. Type I PSDs include enzymes of eukaryotic mitochondria and bacterial origin which contain the amino acid sequence LGST as a characteristic motif. Type II PSDs are found in the endomembrane system of eukaryotes and contain a typical GGST motif. These characteristic motifs are considered as autocatalytic cleavage sites where proenzymes are split into alpha- and beta-subunits. The S-residue set free by this cleavage serves as an attachment site of a pyruvoyl group which is required for the activity of the enzymes. Moreover, PSDs harbor characteristic binding sites for the substrate PtdSer. Substrate supply to eukaryotic PSDs requires lipid transport because PtdSer synthesis and decarboxylation are spatially separated. Targeting of PSDs to their proper locations requires additional intramolecular domains. Mitochondrially localized type I PSDs are directed to the inner mitochondrial membrane by N-terminal targeting sequences. Type II PSDs also contain sequences in their N-terminal extensions which might be required for subcellular targeting. Lack of PSDs causes various defects in different cell types. The physiological relevance of these findings and the central role of PSDs in lipid metabolism will be discussed in this review.}, }
@article {pmid19157810, year = {2009}, author = {Yoshida, M and Nakayama, T and Inouye, I}, title = {Nuclearia thermophila sp. nov. (Nucleariidae), a new nucleariid species isolated from Yunoko Lake in Nikko (Japan).}, journal = {European journal of protistology}, volume = {45}, number = {2}, pages = {147-155}, doi = {10.1016/j.ejop.2008.09.004}, pmid = {19157810}, issn = {1618-0429}, mesh = {Animals ; DNA, Ribosomal/genetics ; Eukaryota/*classification/cytology/*physiology/ultrastructure ; *Fresh Water ; Japan ; Molecular Sequence Data ; Phagocytosis/physiology ; Phylogeny ; }, abstract = {A new species of unicellular opisthokont protist, Nuclearia thermophila sp. nov., was isolated from the warm spring water of Yunoko Lake, Japan, and has been described using light and electron microscopy. It exists as a spherical floating form and a flattened amoeboid form showing various shapes. The cells occasionally extended as branches or knobbed filopodia. The spherical form when suspended in medium measured 20-40microm in diameter (excluding filopodia). The amoeboid form may exceed 65microm along the longest axis. A nucleus with an obvious spherical nucleolus, dictyosomes, mitochondria with flat cristae, food vacuoles, and lipid droplet-like vacuoles with homogeneous contents were observed; no extracellular matrix or bacterial endosymbionts were present. The cells ingested flour particles. No cysts were seen. The molecular phylogenetic tree constructed on the basis of the small subunit ribosomal DNA revealed the novelty of N. thermophila and its relationships with previously known nucleariids.}, }
@article {pmid19154799, year = {2009}, author = {Galtier, N and Blier, PU and Nabholz, B}, title = {Inverse relationship between longevity and evolutionary rate of mitochondrial proteins in mammals and birds.}, journal = {Mitochondrion}, volume = {9}, number = {1}, pages = {51-57}, doi = {10.1016/j.mito.2008.11.006}, pmid = {19154799}, issn = {1567-7249}, mesh = {Animals ; Bayes Theorem ; Birds ; Cytochromes b/metabolism ; *Evolution, Molecular ; Genetic Variation ; *Longevity ; Mammals ; Mitochondria/*metabolism ; Models, Genetic ; Mutation ; Oxygen/metabolism ; Phosphorylation ; Phylogeny ; Species Specificity ; }, abstract = {Recently, an unexpected, positive correlation between the rate of evolution of mitochondrial proteins and longevity was reported. Here we re-analyze this relationship in various mammalian lineages using a bayesian phylogenetic analysis of amino-acid sequences, allowing for variable evolutionary rates across sites and species. A negative relationship between protein evolutionary rate and species longevity is reported for all oxidative phosphorylation complexes. A detailed analysis of the cytochrome b in 528 mammals reinforced this result, which contradicts previous publications. Reconducting the analysis in birds yielded similar results. We explain the discrepancy between this and previous reports by our improved taxon sampling and more appropriate methodology: unlike distance-based methods, the tree-based bayesian approach can take into account the high variation of substitution rate across amino-acid sites, and the resulting multiple substitution events. We discuss how our analysis contradicts Rottenberg's rationale, but does not dismiss his proposal of a longevity-dependent selective pressure on mitochondrial mutation rate in mammals and birds. This is because his interpretation invokes adaptation as the single evolutionary force at work, disregarding the effects of mutation, genetic drift, and purifying selection.}, }
@article {pmid19154382, year = {2009}, author = {Wade, MJ and Brandvain, Y}, title = {Reversing mother's curse: selection on male mitochondrial fitness effects.}, journal = {Evolution; international journal of organic evolution}, volume = {63}, number = {4}, pages = {1084-1089}, pmid = {19154382}, issn = {1558-5646}, support = {1T32HD49336/HD/NICHD NIH HHS/United States ; R01 GM084238/GM/NIGMS NIH HHS/United States ; R01 GM084238-01/GM/NIGMS NIH HHS/United States ; R01GM084238-01/GM/NIGMS NIH HHS/United States ; T32 HD049336/HD/NICHD NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Female ; Humans ; Inbreeding ; Male ; Mitochondria/*genetics ; *Models, Biological ; Reproduction/genetics/*physiology ; Selection, Genetic ; }, abstract = {Many essential organelles and endosymbionts exhibit a strict matrilineal pattern of inheritance. The absence of paternal transmission of such extranuclear components is thought to preclude a response to selection on their effects on male viability and fertility. We overturn this dogma by showing that two mechanisms, inbreeding and kin selection, allow mitochondria to respond to selection on both male viability and fertility. Even modest levels of inbreeding allow such a response to selection when there are direct fitness effects of mitochondria on male fertility because inbreeding associates male fertility traits with mitochondrial matrilines. Male viability effects of mitochondria are also selectable whenever there are indirect fitness effects of males on the fitness of their sisters. When either of these effects is sufficiently strong, we show that there are conditions that allow the spread of mitochondria with direct effects that are harmful to females, contrary to standard expectation. We discuss the implications of our findings for the evolution of organelles and endosymbionts and genomic conflict.}, }
@article {pmid19144713, year = {2009}, author = {Van Wynsberghe, PM and Ahlquist, P}, title = {5' cis elements direct nodavirus RNA1 recruitment to mitochondrial sites of replication complex formation.}, journal = {Journal of virology}, volume = {83}, number = {7}, pages = {2976-2988}, pmid = {19144713}, issn = {1098-5514}, support = {R01 GM035072/GM/NIGMS NIH HHS/United States ; T32 GM007215/GM/NIGMS NIH HHS/United States ; GM35072/GM/NIGMS NIH HHS/United States ; R37 GM035072/GM/NIGMS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; T32 GM07215/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Line ; Drosophila ; Mitochondria/*virology ; Nodaviridae/*physiology ; Nucleic Acid Conformation ; Phylogeny ; RNA, Viral/*genetics/*metabolism ; Saccharomyces cerevisiae/virology ; Sequence Homology, Nucleic Acid ; Viral Proteins/metabolism ; *Virus Replication ; }, abstract = {Positive-strand RNA viruses replicate their genomes on intracellular membranes, usually in conjunction with virus-induced membrane rearrangements. For the nodavirus flock house virus (FHV), we recently showed that multifunctional FHV replicase protein A induces viral RNA template recruitment to a membrane-associated state, but the site(s) and function of this recruitment were not determined. By tagging viral RNA with green fluorescent protein, we show here in Drosophila cells that protein A recruits FHV RNA specifically to the outer mitochondrial membrane sites of RNA replication complex formation. Using Drosophila cells and yeast cells, which also support FHV replication, we also defined the cis-acting regions that direct replication and template recruitment for FHV genomic RNA1. RNA1 nucleotides 68 to 205 were required for RNA replication and directed efficient protein A-mediated RNA recruitment in both cell types. RNA secondary structure prediction, structure probing, and phylogenetic comparisons in this region identified two stable, conserved stem-loops with nearly identical loop sequences. Further mutational analysis showed that both stem-loops and certain flanking sequences were required for RNA1 recruitment, negative-strand synthesis, and subsequent positive-strand amplification in yeast and Drosophila cells. Thus, we have shown that protein A recruits RNA1 templates to mitochondria, as expected for RNA replication, and identified a new RNA1 cis element that is necessary and sufficient for RNA1 template recognition and recruitment to these mitochondrial membranes for negative-strand RNA1 synthesis. These results establish RNA recruitment to the sites of replication complex formation as an essential, distinct, and selective early step in nodavirus replication.}, }
@article {pmid19137387, year = {2009}, author = {Moriguchi, Y and Kang, KS and Lee, KY and Lee, SW and Kim, YY}, title = {Genetic variation of Picea jezoensis populations in South Korea revealed by chloroplast, mitochondrial and nuclear DNA markers.}, journal = {Journal of plant research}, volume = {122}, number = {2}, pages = {153-160}, pmid = {19137387}, issn = {1618-0860}, mesh = {Chloroplasts/metabolism ; DNA, Chloroplast/*chemistry ; DNA, Mitochondrial/*chemistry ; DNA, Plant/*chemistry ; Evolution, Molecular ; Genetic Markers ; *Genetic Variation ; Haplotypes ; Mitochondria/metabolism ; Picea/*genetics ; Republic of Korea ; }, abstract = {Genetic variation associated with Picea jezoensis populations of South Korea was investigated using chloroplast (cp), mitochondrial (mt) and nuclear DNA markers. In South Korea, P. jezoensis is distributed across a very restricted area, being found on the summits of three mountains: Mts. Jiri, Dokyu and Gyebang. Examination of five region restriction enzyme combinations for mtDNA and four for cpDNA revealed haplotypes endemic to South Korea. The Gyebang population, the most northerly and most isolated, was genetically distinct from the other populations. Nuclear microsatellite markers indicated, overall, a low level of genetic diversity (H (e) = 0.406) in South Korea; this could be attributed to genetic drift and/or founder effects associated with historical events. The Wilcoxon sign-rank test did not indicate a recent bottleneck in any of the populations irrespective of the model considered (infinite allele model, two-phased model of mutation, and stepwise mutation model). Microsatellite markers also demonstrated that the Gyebang population was distinct from the others. The results of this study could be used as the basis for conservation guidelines for the management of this species in South Korea.}, }
@article {pmid19130111, year = {2009}, author = {Pellon-Maison, M and Garcia, CF and Cattaneo, ER and Coleman, RA and Gonzalez-Baro, MR}, title = {Macrobrachium borellii hepatopancreas contains a mitochondrial glycerol-3-phosphate acyltransferase which initiates triacylglycerol biosynthesis.}, journal = {Lipids}, volume = {44}, number = {4}, pages = {337-344}, pmid = {19130111}, issn = {1558-9307}, support = {TW 06034/TW/FIC NIH HHS/United States ; R01 DK056598/DK/NIDDK NIH HHS/United States ; R03 TW006034/TW/FIC NIH HHS/United States ; DK 56598/DK/NIDDK NIH HHS/United States ; R01 DK056598-25/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Electrophoresis, Polyacrylamide Gel ; Esterification ; Glycerol-3-Phosphate O-Acyltransferase/*metabolism ; Hepatopancreas/*enzymology ; Microsomes, Liver/metabolism ; Mitochondria, Liver/*enzymology ; Palaemonidae ; Triglycerides/*biosynthesis ; }, abstract = {Mammals express four isoforms of glycerol-3-phosphate acyltransferase (GPAT). The mitochondrial isoform GPAT1 may have been the acyltransferase that appeared first in evolution. The hepatopancreas of the crustacean Macrobrachium borellii has a high capacity for triacylglycerol (TAG) biosynthesis and storage. In order to understand the mechanism of glycerolipid biosynthesis in M. borellii, we investigated its hepatopancreas GPAT activity. In hepatopancreas mitochondria, we identified a GPAT activity with characteristics similar to those of mammalian GPAT1. The activity was resistant to inactivation by SH-reactive N-ethylmaleimide, it was activated by polymyxin-B, and its preferred substrate was palmitoyl-CoA. The reaction products were similar to those of mammalian GPAT1. A 70-kDa protein band immunoreacted with an anti-rat liver GPAT1 antibody. Surprisingly, we did not detect high GPAT specific activity in hepatopancreas microsomes. GPAT activity in microsomes was consistent with mitochondrial contamination, and its properties were similar to those of the mitochondrial activity. In microsomes, TAG synthesis was not dependent on the presence of glycerol-3 phosphate as a substrate, and the addition of monoacylglycerol as a substrate increased TAG synthesis 2-fold. We conclude that in M. borellii the de novo triacylglycerol biosynthetic pathway can be completed in the mitochondria. In contrast, TAG synthesis in the ER may function via the monoacylglycerol pathway.}, }
@article {pmid19127329, year = {2008}, author = {Jeon, HK and Kim, KH and Chai, JY and Yang, HJ and Rim, HJ and Eom, KS}, title = {Sympatric distribution of three human Taenia tapeworms collected between 1935 and 2005 in Korea.}, journal = {The Korean journal of parasitology}, volume = {46}, number = {4}, pages = {235-241}, pmid = {19127329}, issn = {0023-4001}, mesh = {Animals ; Base Sequence ; Cestode Infections/epidemiology/parasitology ; Cyclooxygenase 1/genetics/metabolism ; DNA, Ribosomal Spacer/genetics ; Gene Expression Regulation ; Humans ; Korea/epidemiology ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Taenia/*classification/*genetics ; Time Factors ; }, abstract = {Taeniasis has been known as one of the prevalent parasitic infections in Korea. Until recently, Taenia saginata had long been considered a dominant, and widely distributed species but epidemiological profiles of human Taenia species in Korea still remain unclear. In order to better understand distribution patterns of human Taenia tapeworms in Korea, partial nucleotide sequences of mitochondrial cox1 and ITS2 (internal transcribed spacer 2) were determined, along with morphological examinations, on 68 Taenia specimens obtained from university museum collections deposited since 1935. Genomic DNA was extracted from formalin-preserved specimens. Phylogenetic relationships among the genotypes (cox1 haplotype) detected in this study were inferred using the neighbor-joining method as a tree building method. Morphological and genetic analyses identified 3 specimens as T. solium, 51 specimens as T. asiatica, and 14 specimens as T. saginata. Our results indicate that all 3 Taenia tapeworms are sympatrically distributed in Korea with T. asiatica dominating over T. saginata and T. solium.}, }
@article {pmid19121002, year = {2008}, author = {Geraldes, A and Basset, P and Gibson, B and Smith, KL and Harr, B and Yu, HT and Bulatova, N and Ziv, Y and Nachman, MW}, title = {Inferring the history of speciation in house mice from autosomal, X-linked, Y-linked and mitochondrial genes.}, journal = {Molecular ecology}, volume = {17}, number = {24}, pages = {5349-5363}, pmid = {19121002}, issn = {1365-294X}, support = {R01 GM074245/GM/NIGMS NIH HHS/United States ; R01 GM074245-03/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Animals ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Gene Flow ; *Genes, Mitochondrial ; *Genes, X-Linked ; *Genes, Y-Linked ; *Genetic Speciation ; Genetics, Population ; Likelihood Functions ; Mice/classification/*genetics ; Mitochondria/genetics ; Models, Genetic ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Species Specificity ; X Chromosome/genetics ; Y Chromosome/genetics ; }, abstract = {Patterns of genetic differentiation among taxa at early stages of divergence provide an opportunity to make inferences about the history of speciation. Here, we conduct a survey of DNA-sequence polymorphism and divergence at loci on the autosomes, X chromosome, Y chromosome and mitochondrial DNA in samples of Mus domesticus, M. musculus and M. castaneus. We analyzed our data under a divergence with gene flow model and estimate that the effective population size of M. castaneus is 200,000-400,000, of M. domesticus is 100,000-200,000 and of M. musculus is 60,000-120,000. These data also suggest that these species started to diverge approximately 500,000 years ago. Consistent with this recent divergence, we observed considerable variation in the genealogical patterns among loci. For some loci, all alleles within each species formed a monophyletic group, while at other loci, species were intermingled on the phylogeny of alleles. This intermingling probably reflects both incomplete lineage sorting and gene flow after divergence. Likelihood ratio tests rejected a strict allopatric model with no gene flow in comparisons between each pair of species. Gene flow was asymmetric: no gene flow was detected into M. domesticus, while significant gene flow was detected into both M. castaneus and M. musculus. Finally, most of the gene flow occurred at autosomal loci, resulting in a significantly higher ratio of fixed differences to polymorphisms at the X and Y chromosomes relative to autosomes in some comparisons, or just the X chromosome in others, emphasizing the important role of the sex chromosomes in general and the X chromosome in particular in speciation.}, }
@article {pmid19120997, year = {2008}, author = {Gompert, Z and Forister, ML and Fordyce, JA and Nice, CC}, title = {Widespread mito-nuclear discordance with evidence for introgressive hybridization and selective sweeps in Lycaeides.}, journal = {Molecular ecology}, volume = {17}, number = {24}, pages = {5231-5244}, doi = {10.1111/j.1365-294X.2008.03988.x}, pmid = {19120997}, issn = {1365-294X}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Animals ; Butterflies/*genetics/microbiology ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Female ; Genes, Mitochondrial ; Genetic Variation ; Genetics, Population ; Haplotypes ; *Hybridization, Genetic ; Inheritance Patterns ; Linkage Disequilibrium ; Male ; Mitochondria/genetics ; North America ; *Selection, Genetic ; Sequence Analysis, DNA ; Wolbachia/physiology ; }, abstract = {We investigated the extent and potential cause(s) of mitochondrial introgression within the polytypic North American Lycaeides species complex (Lepidoptera). By comparing population genetic structure based on mitochondrial DNA (COI and COII) and nuclear DNA (251 polymorphic amplified fragment length polymorphism markers), we detected substantial mito-nuclear discordance, primarily involving a single mitochondrial haplotype (h01), which is likely due to mitochondrial introgression between differentiated Lycaeides populations and/or species. We detected reduced mitochondrial genetic diversity relative to nuclear genetic diversity in populations where mitochondrial haplotype h01 occurs, suggesting that the spread of this haplotype was facilitated by selection. We found no evidence that haplotype h01 is associated with increased fitness (in terms of survival to eclosion, fresh adult weight, and adult longevity) in a polymorphic Lycaeides melissa population. However, we did find a positive association between mitochondrial haplotype h01 and infection by the endoparasitic bacterium Wolbachia in one out of three lineages tested. Linkage disequilibrium between mitochondrial haplotype h01 and Wolbachia infection status may have resulted in indirect selection favouring the spread of haplotype h01 in at least one lineage of North American Lycaeides. These results illustrate the potential for introgressive hybridization to produce substantial mito-nuclear discordance and demonstrate that an individual's mitochondrial and nuclear genome may have strikingly different evolutionary histories resulting from non-neutral processes and intrinsic differences in the inheritance and biology of these genomes.}, }
@article {pmid19120485, year = {2009}, author = {Delgado, M and Singh, S and De Haro, S and Master, S and Ponpuak, M and Dinkins, C and Ornatowski, W and Vergne, I and Deretic, V}, title = {Autophagy and pattern recognition receptors in innate immunity.}, journal = {Immunological reviews}, volume = {227}, number = {1}, pages = {189-202}, pmid = {19120485}, issn = {1600-065X}, support = {R01 AI042999-12/AI/NIAID NIH HHS/United States ; R01 AI045148/AI/NIAID NIH HHS/United States ; R01 AI042999/AI/NIAID NIH HHS/United States ; R01 AI069345-03/AI/NIAID NIH HHS/United States ; R01 AI069345/AI/NIAID NIH HHS/United States ; R37 AI042999/AI/NIAID NIH HHS/United States ; AI069345/AI/NIAID NIH HHS/United States ; AI45148/AI/NIAID NIH HHS/United States ; R01 AI045148-11/AI/NIAID NIH HHS/United States ; T32 AI007538/AI/NIAID NIH HHS/United States ; AI42999/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Antigen Presentation/immunology ; Autophagy/genetics/*immunology ; Crohn Disease/genetics/immunology ; Cytokines/genetics/metabolism ; Evolution, Molecular ; GTP-Binding Proteins/genetics/*immunology/metabolism ; Humans ; *Immunity, Innate ; Infections/immunology ; MAP Kinase Signaling System/immunology ; Mitochondria/immunology ; Nod Signaling Adaptor Proteins/immunology/*metabolism ; Th1 Cells/immunology/metabolism ; Th2 Cells/immunology/metabolism ; Toll-Like Receptors/immunology/*metabolism ; }, abstract = {Autophagy is a physiologically and immunologically controlled intracellular homeostatic pathway that sequesters and degrades cytoplasmic targets including macromolecular aggregates, cellular organelles such as mitochondria, and whole microbes or their products. Recent advances show that autophagy plays a role in innate immunity in several ways: (i) direct elimination of intracellular microbes by digestion in autolysosomes, (ii) delivery of cytosolic microbial products to pattern recognition receptors (PRRs) in a process referred to as topological inversion, and (iii) as an anti-microbial effector of Toll-like receptors and other PRR signaling. Autophagy eliminates pathogens in vitro and in vivo but, when aberrant due to mutations, contributes to human inflammatory disorders such as Crohn's disease. In this review, we examine these relationships and propose that autophagy is one of the most ancient innate immune defenses that has possibly evolved at the time of alpha-protobacteria-pre-eukaryote relationships, leading up to modern eukaryotic cell-mitochondrial symbiosis, and that during the metazoan evolution, additional layers of immunological regulation have been superimposed and integrated with this primordial innate immunity mechanism.}, }
@article {pmid20225020, year = {2009}, author = {Spinazzola, A and Zeviani, M}, title = {Mitochondrial diseases: a cross-talk between mitochondrial and nuclear genomes.}, journal = {Advances in experimental medicine and biology}, volume = {652}, number = {}, pages = {69-84}, doi = {10.1007/978-90-481-2813-6_6}, pmid = {20225020}, issn = {0065-2598}, mesh = {Cell Nucleus/*genetics ; Genome, Mitochondrial/*genetics ; Humans ; Mitochondrial Diseases/diagnosis/etiology/*genetics/pathology ; Mutation/genetics ; }, abstract = {More than one billion years ago, mitochondria were free-living prokaryotic organisms with their own DNA. However, during the evolution, ancestral genes have been transferred from the mitochondrial to the nuclear genome so that mtDNA became dependent on numerous nucleus-encoded factors for its integrity, replication and expression. Mutations in any of these factors may alter the cross-talk between the two genomes and cause Mendelian diseases that affect mtDNA integrity or expression.}, }
@article {pmid20403746, year = {2009}, author = {Kern, B and Ivanina, AV and Piontkivska, H and Sokolov, EP and Sokolova, IM}, title = {Molecular characterization and expression of a novel homolog of uncoupling protein 5 (UCP5) from the eastern oyster Crassostrea virginica (Bivalvia: Ostreidae).}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {4}, number = {2}, pages = {121-127}, doi = {10.1016/j.cbd.2008.12.006}, pmid = {20403746}, issn = {1878-0407}, mesh = {Amino Acid Sequence ; Animals ; Crassostrea/genetics/*metabolism ; Ion Channels/chemistry/genetics/*metabolism ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Uncoupling Protein 1 ; }, abstract = {Uncoupling proteins (UCPs) belong to the mitochondrial anion carrier gene family which has been implicated in diverse physiological functions ranging from thermoregulation to antioxidant defense. In mammals, the UCP family is well characterized and contains five members (UCP1-5). In contrast, invertebrate homologues of uncoupling proteins are much less studied both from the viewpoints of structure and function. In this study we report nucleotide and predicted protein structure of an important member of UCP family, UCP5 from eastern oysters Crassostrea virginica. UCP5 from oysters appears to be a close homolog of the mammalian brain mitochondrial carrier protein (BMCP1, or UCP5) and is the first full-length UCP described from a Lophotrochozoan invertebrate. Evolutionary analysis of UCP sequences indicates at least three monophyletic UCP branches (UCP1-3, UCP4 and UCP5) that have diverged early in the evolution, prior to the divergence of vertebrates and invertebrates. In oysters, two forms of UCP5 transcript are found (UCP5S and UCP5L) that differ by 152 bp in length due to the presence of an intron in UCP5L. UCP5 was expressed in all studied oyster tissues, unlike mammals, where UCP5 is predominantly expressed in brains and male gonads. Hypoxia-reoxygenation stress, sublethal Cd exposure (50 ?g L(?1) Cd for 56 days) and acclimation to different temperatures (12 and 20 °C) had no significant effect on UCP5 mRNA expression in oysters indicative of its relative unimportance in antioxidant defense and temperature adaptation of oyster mitochondria. These data suggest that despite the relatively high degree of evolutionary conservation of the UCP5 amino acid sequence, its functional significance in mitochondria changed in the course of evolution of mollusks and vertebrates.}, }
@article {pmid19103153, year = {2009}, author = {Houstek, J and Kmoch, S and Zeman, J}, title = {TMEM70 protein - a novel ancillary factor of mammalian ATP synthase.}, journal = {Biochimica et biophysica acta}, volume = {1787}, number = {5}, pages = {529-532}, doi = {10.1016/j.bbabio.2008.11.013}, pmid = {19103153}, issn = {0006-3002}, mesh = {Animals ; Brain Diseases/genetics/metabolism ; Cardiomyopathy, Hypertrophic, Familial/genetics/metabolism ; Cell Nucleus/genetics/pathology ; Electron Transport Complex IV/genetics/metabolism ; Genetic Complementation Test ; Humans ; Mammals ; Membrane Proteins/*genetics ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/*genetics ; Mitochondrial Proton-Translocating ATPases/genetics/*metabolism ; Mutation ; Oxidative Phosphorylation ; Phylogeny ; Species Specificity ; }, abstract = {An increasing number of patients with nuclear genetic defects of mitochondrial ATP synthase have been identified in recent years. They are characterized by early onset, lactic acidosis, 3-methylglutaconic aciduria, hypertrophic cardiomyopathy and encephalopathy and most cases have a fatal outcome. Patient tissues show isolated defect of the ATP synthase complex and its content decreases to > or =30% of normal due to altered enzyme biosynthesis and assembly. Gene mapping and complementation studies have identified mutations in TMEM70 gene encoding a 30kD mitochondrial protein of unknown function as the cause of the disease. An altered synthesis of this new ancillary factor in ATP synthase biogenesis was found in most of the known patients with decreased ATP synthase content. As revealed by phylogenetic analysis, TMEM70 is specific for higher eukaryotes.}, }
@article {pmid19101641, year = {2009}, author = {Drovetski, SV and Zink, RM and Mode, NA}, title = {Patchy distributions belie morphological and genetic homogeneity in rosy-finches.}, journal = {Molecular phylogenetics and evolution}, volume = {50}, number = {3}, pages = {437-445}, doi = {10.1016/j.ympev.2008.12.002}, pmid = {19101641}, issn = {1095-9513}, mesh = {Animals ; Asia ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Feathers/anatomy &amp; histology ; Female ; Finches/anatomy &amp; histology/classification/*genetics ; *Genetic Speciation ; *Genetic Variation ; Geography ; Haplotypes ; Male ; Mitochondria/genetics ; North America ; Phenotype ; *Phylogeny ; Pigmentation ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {DNA sequence data often appear to contradict low-level avian taxonomy, which is usually based on patterns of external phenotypic similarity. We examined such an apparent contradiction in the Nearctic rosy-finches. On the basis of several phenotypic characters the finches were divided into three species congeneric with three Asian species. When Nearctic taxa were analyzed in a principal components analysis, 66.9% of phenotypic variation was explained by differences between the Bering Sea and continental populations, sexual dimorphism and a latitudinal cline. Our phylogenetic analysis of mitochondrial ND2 sequences revealed four clades among six species of rosy-finches. Three clades corresponded to three Asian species. The fourth clade included all three Nearctic species. Their haplotypes were not reciprocally monophyletic and the combined genetic variability of all Nearctic taxa was lower than in two of their Asian congeners. A Z-specific intron (ACO1I9) and an autosomal coding locus (MC1R) provided little additional phylogenetic information, most likely because of the longer coalescence times relative to ND2. Phylogeographic analyses of ND2 data revealed significant gene flow among neighboring localities regardless of their taxonomic assignment. Our analyses showed that DNA and phenotypic data are not in conflict, but rather complement each other, and together help clarify species limits. Our data are consistent with a single species in North America, not three.}, }
@article {pmid19100849, year = {2009}, author = {Yu, G and Rao, D and Zhang, M and Yang, J}, title = {Re-examination of the phylogeny of Rhacophoridae (Anura) based on mitochondrial and nuclear DNA.}, journal = {Molecular phylogenetics and evolution}, volume = {50}, number = {3}, pages = {571-579}, doi = {10.1016/j.ympev.2008.11.023}, pmid = {19100849}, issn = {1095-9513}, mesh = {Animals ; Anura/classification/*genetics ; Bayes Theorem ; Cell Nucleus/genetics ; Cytochromes b/genetics ; *Evolution, Molecular ; Genetic Speciation ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The phylogenetic relationships among rhacophorid frogs are under dispute. We use partial sequences of three mitochondrial (12S rRNA, 16S rRNA, and cytochrome b) and three nuclear protein-coding (Rag-1, rhodopsin exon 1, and tyrosinase exon 1) genes from 57 ingroup taxa and eight outgroup taxa to propose a hypothesis for phylogenetic relationships within Rhacophoridae. Our results support recognition of the genus Feihyla, and Chiromantis is the sister taxon to the clade formed by Feihyla, Polypedates and Rhacophorus. We place Aquixalus odontotarsus within Kurixalus, and the remaining species of Aquixalus and Philautus jinxiuensis into the genus Gracixalus. We give Philautus (Kirtixalus) the rank of genus and place Philautus menglaensis within it. The division of species groups among Chinese Rhacophorus needs revision, and a cryptic species is revealed within Rhacophorus nigropunctatus. Rhacophorus pingbianensis is considered a synonym of Rhacophorus omeimontis. The validity of Rhacophorus hui is confirmed by present molecular evidence.}, }
@article {pmid19096520, year = {2008}, author = {Smíd, O and Matusková, A and Harris, SR and Kucera, T and Novotný, M and Horváthová, L and Hrdý, I and Kutejová, E and Hirt, RP and Embley, TM and Janata, J and Tachezy, J}, title = {Reductive evolution of the mitochondrial processing peptidases of the unicellular parasites trichomonas vaginalis and giardia intestinalis.}, journal = {PLoS pathogens}, volume = {4}, number = {12}, pages = {e1000243}, pmid = {19096520}, issn = {1553-7374}, support = {BB/C006143/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Down-Regulation/genetics ; *Evolution, Molecular ; Gene Dosage ; Giardia lamblia/*genetics/metabolism/ultrastructure ; Glycine/chemistry/genetics/physiology ; Hydrogen/metabolism ; Metalloendopeptidases/chemistry/*genetics/metabolism ; Mitochondria/metabolism ; Organelles/metabolism ; Phylogeny ; Proline-Rich Protein Domains/genetics/physiology ; Protein Multimerization ; Protein Processing, Post-Translational/genetics ; Protein Subunits/genetics ; Protein Transport ; Trichomonas vaginalis/*genetics/metabolism/ultrastructure ; Mitochondrial Processing Peptidase ; }, abstract = {Mitochondrial processing peptidases are heterodimeric enzymes (alpha/betaMPP) that play an essential role in mitochondrial biogenesis by recognizing and cleaving the targeting presequences of nuclear-encoded mitochondrial proteins. The two subunits are paralogues that probably evolved by duplication of a gene for a monomeric metallopeptidase from the endosymbiotic ancestor of mitochondria. Here, we characterize the MPP-like proteins from two important human parasites that contain highly reduced versions of mitochondria, the mitosomes of Giardia intestinalis and the hydrogenosomes of Trichomonas vaginalis. Our biochemical characterization of recombinant proteins showed that, contrary to a recent report, the Trichomonas processing peptidase functions efficiently as an alpha/beta heterodimer. By contrast, and so far uniquely among eukaryotes, the Giardia processing peptidase functions as a monomer comprising a single betaMPP-like catalytic subunit. The structure and surface charge distribution of the Giardia processing peptidase predicted from a 3-D protein model appear to have co-evolved with the properties of Giardia mitosomal targeting sequences, which, unlike classic mitochondrial targeting signals, are typically short and impoverished in positively charged residues. The majority of hydrogenosomal presequences resemble those of mitosomes, but longer, positively charged mitochondrial-type presequences were also identified, consistent with the retention of the Trichomonas alphaMPP-like subunit. Our computational and experimental/functional analyses reveal that the divergent processing peptidases of Giardia mitosomes and Trichomonas hydrogenosomes evolved from the same ancestral heterodimeric alpha/betaMPP metallopeptidase as did the classic mitochondrial enzyme. The unique monomeric structure of the Giardia enzyme, and the co-evolving properties of the Giardia enzyme and substrate, provide a compelling example of the power of reductive evolution to shape parasite biology.}, }
@article {pmid19096095, year = {2008}, author = {Crane, FL}, title = {The evolution of coenzyme Q.}, journal = {BioFactors (Oxford, England)}, volume = {32}, number = {1-4}, pages = {5-11}, doi = {10.1002/biof.5520320102}, pmid = {19096095}, issn = {0951-6433}, mesh = {Animals ; Cell Membrane/physiology ; Electron Transport ; Electron-Transferring Flavoproteins/physiology ; Humans ; Mitochondrial Membranes/physiology ; Ubiquinone/*analogs &amp; derivatives/physiology/therapeutic use ; }, abstract = {In the 50 years since the identification of coenzyme Q as an electron carrier in mitochondria, it has been identified with diverse and unexpected functions in cells. Its discovery came as a result of a search for electron carriers in mitochondria following the identification of flavin and cytochromes by Warburg, Keilin, Chance and others. As a result of investigation of membrane lipids at D.E. Green's laboratory at University of Wisconsin coenzyme Q was identified as the electron carrier between primary flavoprotein dehydrogenases and the cytochromes. Then Peter Mitchell identified the role of transmembrane proton transfer as a basis for ATP synthesis. The general distribution of coenzyme Q in all cell membranes then led to the recognition of a role as a primary antioxidant. The protonophoric function was extended to acidification of Golgi and lysosomal vericles. A further role in proton release through the plasma membrane and its relation to cell proliferation has not been fully developed. A role in generation of H202 as a messenger for hormone and cytokine action is indicated as well as prevention of apoptosis by inhibition of ceramide release. Identification of the genes and proteins required for coenzyme Q synthesis has led to a basis for defining deficiency. For 50 years Karl Folkers has led the search for deficiency and therapeutic application. The development of large scale production, better formulation for uptake, and better methods for analysis have furthered this search. The story isn't over yet. Questions remain about effects on membrane structure, breakdown and control of cellular synthesis and uptake and the basis for therapeutic action.}, }
@article {pmid19083240, year = {2009}, author = {Duchêne, AM and Pujol, C and Maréchal-Drouard, L}, title = {Import of tRNAs and aminoacyl-tRNA synthetases into mitochondria.}, journal = {Current genetics}, volume = {55}, number = {1}, pages = {1-18}, pmid = {19083240}, issn = {1432-0983}, mesh = {Amino Acyl-tRNA Synthetases/genetics/*metabolism ; Biological Transport/genetics ; Mitochondria/genetics/*metabolism ; RNA/genetics/metabolism ; RNA, Transfer/genetics/*metabolism ; }, abstract = {During evolution, most of the bacterial genes from the ancestral endosymbiotic alpha-proteobacteria at the origin of mitochondria have been either lost or transferred to the nuclear genome. A crucial evolutionary step was the establishment of macromolecule import systems to allow the come back of proteins and RNAs into the organelle. Paradoxically, the few mitochondria-encoded protein genes remain essential and must be translated by a mitochondrial translation machinery mainly constituted by nucleus-encoded components. Two crucial partners of the mitochondrial translation machinery are the aminoacyl-tRNA synthetases and the tRNAs. All mitochondrial aminoacyl-tRNA synthetases and many tRNAs are imported from the cytosol into the mitochondria in eukaryotic cells. During the last few years, their origin and their import into the organelle have been studied in evolutionary distinct organisms and we review here what is known in this field.}, }
@article {pmid19081542, year = {2008}, author = {Kuroiwa, T and Misumi, O and Nishida, K and Yagisawa, F and Yoshida, Y and Fujiwara, T and Kuroiwa, H}, title = {Vesicle, mitochondrial, and plastid division machineries with emphasis on dynamin and electron-dense rings.}, journal = {International review of cell and molecular biology}, volume = {271}, number = {}, pages = {97-152}, doi = {10.1016/S1937-6448(08)01203-3}, pmid = {19081542}, issn = {1937-6448}, mesh = {Animals ; Cytoplasmic Vesicles/*physiology/ultrastructure ; Dynamins/*physiology ; Eukaryotic Cells/*physiology/ultrastructure ; Mitochondria/*physiology/ultrastructure ; Plastids/*physiology/ultrastructure ; }, abstract = {The original eukaryotic cells contained at least one set of double-membrane-bounded organelles (cell nucleus and mitochondria) and single-membrane-bounded organelles [endoplasmic reticulum, Golgi apparatus, lysosomes (vacuoles), and microbodies (peroxisomes)]. An increase in the number of organelles accompanied the evolution of these cells into Amoebozoa and Opisthokonta. Furthermore, the basic cells, containing mitochondria, engulfed photosynthetic Cyanobacteria, which were converted to plastids, and the cells thereby evolved into cells characteristic of the Bikonta. How did basic single- and double-membrane-bounded organelles originate from bacteria-like cells during early eukaryotic evolution? To answer this question, the important roles of the GTPase dynamin- and electron-dense rings in the promotion of diverse cellular activities in eukaryotes, including endocytosis, vesicular transport, mitochondrial division, and plastid division, must be considered. In this review, vesicle division, mitochondrial division, and plastid division machineries, including the dynamin- and electron-dense rings, and their roles in the origin and biogenesis of organelles in eukaryote cells are summarized.}, }
@article {pmid19070685, year = {2009}, author = {Harrison, SP and Turrion-Gomez, JL}, title = {Mitochondrial DNA: an important female contribution to thoroughbred racehorse performance: amendments to nomenclature.}, journal = {Mitochondrion}, volume = {9}, number = {1}, pages = {58-9; discussion 60}, doi = {10.1016/j.mito.2008.11.002}, pmid = {19070685}, issn = {1567-7249}, mesh = {Animals ; DNA, Mitochondrial/*metabolism ; Female ; Genes, Mitochondrial ; Genetic Variation ; Haplotypes ; Horses/*genetics/*physiology ; Mitochondria/metabolism ; Pedigree ; Phylogeny ; Running ; Sex Factors ; Terminology as Topic ; }, }
@article {pmid19070577, year = {2008}, author = {Lee, HY and Chou, JY and Cheong, L and Chang, NH and Yang, SY and Leu, JY}, title = {Incompatibility of nuclear and mitochondrial genomes causes hybrid sterility between two yeast species.}, journal = {Cell}, volume = {135}, number = {6}, pages = {1065-1073}, doi = {10.1016/j.cell.2008.10.047}, pmid = {19070577}, issn = {1097-4172}, mesh = {Carbon/metabolism ; Chimera ; Fungal Proteins/genetics ; Genetic Speciation ; Genome, Fungal ; Genome, Mitochondrial ; Mitochondria/metabolism ; Mitochondrial Proton-Translocating ATPases/genetics ; Protein Biosynthesis ; Saccharomyces/*genetics ; Saccharomyces cerevisiae/*genetics/growth &amp; development/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; }, abstract = {Hybrids between species are usually unviable or sterile. One possible mechanism causing reproductive isolation is incompatibility between genes from different species. These "speciation" genes are interacting components that cannot function properly when mixed with alleles from other species. To test whether such genes exist in two closely related yeast species, we constructed hybrid lines in which one or two chromosomes were derived from Saccharomyces bayanus, and the rest were from Saccharomyces cerevisiae. We found that the hybrid line with Chromosome 13 substitution was completely sterile and identified Aep2, a mitochondrial protein encoded on Chromosome 13, to cause the sporulation defect as S. bayanus AEP2 is incompatible with S. cerevisiae mitochondria. This is caused by the inability of S. bayanus Aep2 protein to regulate the translation of the S. cerevisiae OLI1 mRNA. We speculate that AEP2 and OLI1 have evolved during the adaptation of S. bayanus to nonfermentable carbon sources, thereby driving speciation.}, }
@article {pmid19070568, year = {2008}, author = {Barbash, DA}, title = {Clash of the genomes.}, journal = {Cell}, volume = {135}, number = {6}, pages = {1002-1003}, doi = {10.1016/j.cell.2008.11.019}, pmid = {19070568}, issn = {1097-4172}, support = {R01 GM074737/GM/NIGMS NIH HHS/United States ; }, mesh = {Chimera ; *Genetic Speciation ; *Genome, Fungal ; Mitochondria ; Saccharomyces/*genetics ; }, abstract = {Full-genome sequences of multiple yeast species offer exciting possibilities for the functional analysis of yeast evolution and speciation. Lee et al. (2008) now report that hybrid sterility between two yeast species is caused by incompatibility between a nuclear-encoded mitochondrial regulatory protein and its mitochondrial-encoded target gene.}, }
@article {pmid19067526, year = {2008}, author = {McGill, AT}, title = {Malnutritive obesity ('malnubesity'): is it driven by human brain evolution?.}, journal = {Metabolic syndrome and related disorders}, volume = {6}, number = {4}, pages = {241-246}, doi = {10.1089/met.2008.0031}, pmid = {19067526}, issn = {1557-8518}, mesh = {Animals ; Antioxidants/metabolism ; Biological Evolution ; Brain/*physiology ; Diet ; Energy Metabolism ; Humans ; Immune System ; Malnutrition/*diagnosis/genetics ; *Metabolism ; Nutritional Sciences ; Obesity/*diagnosis/genetics/prevention &amp; control ; Phenotype ; Public Health ; }, abstract = {Abstract Health messages on low-energy diets for healthy weight loss are muddled and not working, and obesity rates are rising. Are there missing links? Accumulating evidence shows that humans have well developed 'self-addictive' appetite pathways to enhance the uptake of highly energy-dense food. Humans synthesize fewer co-factors and vitamins than other mammals and must ingest them. Both processes probably arose to maximize available energy for the developing, large association cortex of the human brain. The default phenotype resulting from consuming an 'addictive', westernized, highly refined, energy-dense, hypomicronutrient diet is 'malnutritive obesity' or 'malnubesity'. A relative lack of antioxidant (and other) co-factors contributes to inefficiently oxidized energy. This 'stress' leads to central fat deposition, disordered energy use by cell mitochondria, especially in muscle and liver, and malfunctioning immune, coagulation, endothelial, and other systems. The resultant problems appear to range from epigenetic reprogramming in utero to end organ damage of the metabolic syndrome and the immune failure of cancer. Treatment of 'malnubesity' may require: (1) understanding the drivers and mechanisms of addictions, (2) reprioritizing satiating, micronutrient-dense whole foods, (3) nonjudgmental general, psychological, and medical support for those at risk or affected by obesity; and (4) practical incentives/regulation for healthy food production and distribution.}, }
@article {pmid19063939, year = {2009}, author = {Chuma, S and Hosokawa, M and Tanaka, T and Nakatsuji, N}, title = {Ultrastructural characterization of spermatogenesis and its evolutionary conservation in the germline: germinal granules in mammals.}, journal = {Molecular and cellular endocrinology}, volume = {306}, number = {1-2}, pages = {17-23}, doi = {10.1016/j.mce.2008.11.009}, pmid = {19063939}, issn = {1872-8057}, mesh = {Animals ; *Biological Evolution ; Cytoplasmic Granules/*ultrastructure ; Germ Cells/cytology/*ultrastructure ; Male ; Mammals/*physiology ; RNA/metabolism ; *Spermatogenesis ; }, abstract = {Germline cells of many animals possess characteristic cytoplasmic structures termed germinal granules or nuage. Germinal granules are ribonucleoprotein (RNP) amorphous aggregates lacking limiting membranes, and their molecular composition is evolutionarily conserved in divergent species. Studies on germinal granules in several model animals, such as Drosophila, C. elegans and Xenopus, have mainly focused on the asymmetric partitioning of the structures to prospective germ cells during early embryogenesis. In mammals, on the other hand, germinal granules become discernible at later stages of germ cell differentiation, such as in spermatogenesis and oogenesis. Interestingly, recent genetic studies indicate that germinal granule components in mice function primarily in postnatal germ cell differentiation in the male, but not in early embryonic stages. While the function(s) of germinal granules shared by divergent species and at different differentiation stages of the germline remain elusive, evidence is accumulating that the characteristic RNP is associated with RNA metabolism, retrotransposon regulation and interplay with mitochondria. Here, we present a brief overview of the structural and molecular characteristics of mammalian germinal granules.}, }
@article {pmid19061489, year = {2008}, author = {Ricard, G and de Graaf, RM and Dutilh, BE and Duarte, I and van Alen, TA and van Hoek, AH and Boxma, B and van der Staay, GW and Moon-van der Staay, SY and Chang, WJ and Landweber, LF and Hackstein, JH and Huynen, MA}, title = {Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {587}, pmid = {19061489}, issn = {1471-2164}, mesh = {Animals ; Chromosomes/*genetics ; Ciliophora/*genetics ; Databases, Nucleic Acid ; Evolution, Molecular ; *Genome, Protozoan ; Introns ; Macronucleus/*genetics ; Phylogeny ; Telomere/genetics ; }, abstract = {BACKGROUND: Nyctotherus ovalis is a single-celled eukaryote that has hydrogen-producing mitochondria and lives in the hindgut of cockroaches. Like all members of the ciliate taxon, it has two types of nuclei, a micronucleus and a macronucleus. N. ovalis generates its macronuclear chromosomes by forming polytene chromosomes that subsequently develop into macronuclear chromosomes by DNA elimination and rearrangement.<br><br>RESULTS: We examined the structure of these gene-sized macronuclear chromosomes in N. ovalis. We determined the telomeres, subtelomeric regions, UTRs, coding regions and introns by sequencing a large set of macronuclear DNA sequences (4,242) and cDNAs (5,484) and comparing them with each other. The telomeres consist of repeats CCC(AAAACCCC)n, similar to those in spirotrichous ciliates such as Euplotes, Sterkiella (Oxytricha) and Stylonychia. Per sequenced chromosome we found evidence for either a single protein-coding gene, a single tRNA, or the complete ribosomal RNAs cluster. Hence the chromosomes appear to encode single transcripts. In the short subtelomeric regions we identified a few overrepresented motifs that could be involved in gene regulation, but there is no consensus polyadenylation site. The introns are short (21-29 nucleotides), and a significant fraction (1/3) of the tiny introns is conserved in the distantly related ciliate Paramecium tetraurelia. As has been observed in P. tetraurelia, the N. ovalis introns tend to contain in-frame stop codons or have a length that is not dividable by three. This pattern causes premature termination of mRNA translation in the event of intron retention, and potentially degradation of unspliced mRNAs by the nonsense-mediated mRNA decay pathway.<br><br>CONCLUSION: The combination of short leaders, tiny introns and single genes leads to very minimal macronuclear chromosomes. The smallest we identified contained only 150 nucleotides.}, }
@article {pmid19059488, year = {2009}, author = {Hemmerter, S and Slapeta, J and Beebe, NW}, title = {Resolving genetic diversity in Australasian Culex mosquitoes: incongruence between the mitochondrial cytochrome c oxidase I and nuclear acetylcholine esterase 2.}, journal = {Molecular phylogenetics and evolution}, volume = {50}, number = {2}, pages = {317-325}, doi = {10.1016/j.ympev.2008.11.016}, pmid = {19059488}, issn = {1095-9513}, mesh = {Acetylcholinesterase/*genetics ; Animals ; Australasia ; Bayes Theorem ; Culex/classification/enzymology/*genetics ; DNA, Mitochondrial/genetics ; Drosophila melanogaster/enzymology/genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Genetic Markers ; *Genetic Variation ; Geography ; Haplotypes ; Insect Proteins/genetics ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Insects that vector pathogens are under constant surveillance in Australasia although the repertoire of genetic markers to distinguish what are often cryptic mosquito species remains limited. We present a comparative assessment of the second exon-intron region of the acetylcholine esterase 2 gene (ace-2) and the mitochondrial DNA cytochrome c oxidase I (COI) using two closely related Australasia mosquitoes Culex annulirostris and Culex palpalis. The COI revealed eight divergent lineages of which four were confirmed with the ace-2. We dissect out the nuclear chromosomal haplotypes of the ace-2 as well as the exon-intron regions by assessing the protein's tertiary structure to reveal a hypervariable 5'-exon that forms part of an external protein loop and displays a higher polymorphic rate than the intron. We retrace the evolutionary history of these mosquitoes by phylogenetic inference and by testing different evolutionary hypotheses. We conclude that DNA barcoding using COI may overestimate the diversity of Culex mosquitoes in Australasia and should be applied cautiously with support from the nuclear DNA such as the ace-2. Together the COI and ace-2 provide robust evidence for distinct cryptic Culex lineages--one of which correlates exactly with the southern limit of Japanese encephalitis virus activity in Australasia.}, }
@article {pmid19059353, year = {2009}, author = {Pérez-Portela, R and Bishop, JD and Davis, AR and Turon, X}, title = {Phylogeny of the families Pyuridae and Styelidae (Stolidobranchiata, Ascidiacea) inferred from mitochondrial and nuclear DNA sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {50}, number = {3}, pages = {560-570}, doi = {10.1016/j.ympev.2008.11.014}, pmid = {19059353}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; *Evolution, Molecular ; Genetic Speciation ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Urochordata/classification/*genetics ; }, abstract = {The Order Stolidobranchiata comprises the families Pyuridae, Styelidae and Molgulidae. Early molecular data was consistent with monophyly of the Stolidobranchiata and also the Molgulidae. Internal phylogeny and relationships between Styelidae and Pyuridae were inconclusive however. In order to clarify these points we used mitochondrial and nuclear sequences from 31 species of Styelidae and 25 of Pyuridae. Phylogenetic trees recovered the Pyuridae as a monophyletic clade, and their genera appeared as monophyletic with the exception of Pyura. The Styelidae, on the other hand, appeared as a paraphyletic group split into several clades. One of them was formed by solitary oviparous species, of which the Pyuridae were a sister group. A second clade included the colonial genera Botryllus, Botrylloides and Symplegma. The remaining colonial and solitary genera formed several poorly resolved clades. One of the more species genus, Polycarpa, was shown to be polyphyletic, and the species Styela plicata grouped into two genetically distant clades suggesting the existence of two cryptic species. The internal phylogeny of Styelidae has bearings on the origin of coloniality in this family. We suggest to abandon the traditional division of colonial forms into social and compound species and use instead the categories of aggregated colonies that do not have common vascular systems, and integrated colonies, that do possess such systems. Our molecular results indicate that there have been several independent acquisitions of coloniality in the Styelidae, and that viviparity may be a pre-adaptation for a colonial life-style.}, }
@article {pmid19057927, year = {2009}, author = {Iorio, R and Slapeta, J and Otranto, D and Paoletti, B and Giangaspero, A and Traversa, D}, title = {Phylogenetic relationships of Habronema microstoma and Habronema muscae (Spirurida: Habronematidae) within the order Spirurida inferred using mitochondrial cytochrome c oxidase subunit 1 (cox1) gene analysis.}, journal = {Parasitology research}, volume = {104}, number = {5}, pages = {979-984}, pmid = {19057927}, issn = {1432-1955}, mesh = {Amino Acid Substitution/genetics ; Animals ; DNA, Mitochondrial/chemistry/genetics ; Electron Transport Complex IV/*genetics ; Haplotypes ; Horse Diseases/parasitology ; Horses ; Italy ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Sequence Homology ; Spirurida Infections/veterinary ; Spiruroidea/*classification/*genetics/isolation &amp; purification ; }, abstract = {The present study investigated genetic variability within a population of Habronema microstoma and Habronema muscae (Spirurida: Habronematidae) affecting horses in an endemic area of central Italy using polymerase chain reaction (PCR)-coupled sequencing of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1). No different cox1 sequences were detected in any of the H. muscae individual, while two haplotypes representing H. microstoma individuals differed for one substitution. The pairwise distance between the H. muscae and H. microstoma was 11%, coding for five amino acid changes. The sequence of an informative region within the cox1 gene of H. microstoma and H. muscae was analyzed by Maximum Likelihood and Bayesian phylogenetic methods using available mitochondrial sequences spirurid taxa belonging to Filarioidea, Thelazioidea, and Habronematoidea. Phylogenetic analysis supported the split of the tree into two sister spirurid groups, Habronematoidea and Filarioidea + Thelazioidea. The phylogenetic and evolutionary implications of Habronema with Filaroidea and Thelazioidea are discussed.}, }
@article {pmid19056502, year = {2009}, author = {Linares, MC and Soto-Calderón, ID and Lees, DC and Anthony, NM}, title = {High mitochondrial diversity in geographically widespread butterflies of Madagascar: a test of the DNA barcoding approach.}, journal = {Molecular phylogenetics and evolution}, volume = {50}, number = {3}, pages = {485-495}, doi = {10.1016/j.ympev.2008.11.008}, pmid = {19056502}, issn = {1095-9513}, support = {BBS/B/04358//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Butterflies/classification/*genetics/microbiology ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Gene Flow ; *Genetic Variation ; Genetics, Population ; Geography ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Wolbachia/genetics ; }, abstract = {The standardized use of mitochondrial cytochrome c oxidase subunit I (COI) gene sequences as DNA barcodes has been widely promoted as a high-throughput method for species identification and discovery. Species delimitation has been based on the following criteria: (1) monophyletic association and less frequently (2) a minimum 10x greater divergence between than within species. Divergence estimates, however, can be inflated if sister species pairs are not included and the geographic extent of variation within any given taxon is not sampled comprehensively. This paper addresses both potential biases in DNA divergence estimation by sampling range-wide variation in several morphologically distinct, endemic butterfly species in the genus Heteropsis, some of which are sister taxa. We also explored the extent to which mitochondrial DNA from the barcode region can be used to assess the effects of historical rainforest fragmentation by comparing genetic variation across Heteropsis populations with an unrelated forest-associated taxon Saribia tepahi. Unexpectedly, generalized primers led to the inadvertent amplification of the endosymbiont Wolbachia, undermining the use of universal primers and necessitating the design of genus-specific COI primers alongside a Wolbachia-specific PCR assay. Regardless of the high intra-specific genetic variation observed, most species satisfy DNA barcoding criteria and can be differentiated in the nuclear phylogeny. Nevertheless, two morphologically distinguishable candidate species fail to satisfy the barcoding 10x genetic distance criterion, underlining the difficulties of applying a standard distance threshold to species delimitation. Phylogeographic analysis of COI data suggests that forest fragmentation may have played an important role in the recent evolutionary diversification of these butterflies. Further work on other Malagasy taxa using both mitochondrial and nuclear data will provide better insight into the role of historical habitat fragmentation in species diversification and may potentially contribute to the identification of priority areas for conservation.}, }
@article {pmid19048493, year = {2008}, author = {Khan, HA and Arif, IA and Al Farhan, AH and Al Homaidan, AA}, title = {Phylogenetic analysis of oryx species using partial sequences of mitochondrial rRNA genes.}, journal = {Genetics and molecular research : GMR}, volume = {7}, number = {4}, pages = {1150-1155}, doi = {10.4238/vol7-4gmr490}, pmid = {19048493}, issn = {1676-5680}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Genes, Mitochondrial ; Mitochondria/*genetics ; *Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; Ruminants/classification/*genetics ; Species Specificity ; }, abstract = {We conducted a comparative evaluation of 12S rRNA and 16S rRNA genes of the mitochondrial genome for molecular differentiation among three oryx species (Oryx leucoryx, Oryx dammah and Oryx gazella) with respect to two closely related outgroups, addax and roan. Our findings showed the failure of 12S rRNA gene to differentiate between the genus Oryx and addax, whereas a 342-bp partial sequence of 16S rRNA accurately grouped all five taxa studied, suggesting the utility of 16S rRNA segment for molecular phylogeny of oryx at the genus and possibly species levels.}, }
@article {pmid19037013, year = {2009}, author = {Yu, X and Gimsa, U and Wester-Rosenlöf, L and Kanitz, E and Otten, W and Kunz, M and Ibrahim, SM}, title = {Dissecting the effects of mtDNA variations on complex traits using mouse conplastic strains.}, journal = {Genome research}, volume = {19}, number = {1}, pages = {159-165}, pmid = {19037013}, issn = {1088-9051}, mesh = {Animals ; Anxiety/genetics ; Behavior, Animal ; DNA, Mitochondrial/*genetics ; Encephalomyelitis, Autoimmune, Experimental/genetics ; Female ; *Genetic Variation ; Mice ; Mice, Congenic ; Mice, Inbred C57BL ; Mice, Inbred Strains ; Mutation ; Phenotype ; Phylogeny ; }, abstract = {Previous reports have demonstrated that the mtDNA of mouse common inbred strains (CIS) originated from a single female ancestor and that mtDNA mutations occurred during CIS establishment. This situation provides a unique opportunity to investigate the impact of individual mtDNA variations on complex traits in mammals. In this study, we compiled the complete mtDNA sequences of 52 mouse CIS. Phylogenetic analysis demonstrated that 50 of the 52 CIS descended from a single female Mus musculus domesticus mouse, and mtDNA mutations have accumulated in 26 of the CIS. We then generated conplastic strains on the C57BL/6J background for 12 mtDNA variants with one to three functional mtDNA mutations. We also generated conplastic strains for mtDNA variants of the four M. musculus subspecies, each of which contains hundreds of mtDNA variations. In total, a panel of conplastic strains was generated for 16 mtDNA variants. Phenotypic analysis of the conplastic strains demonstrated that mtDNA variations affect susceptibility to experimental autoimmune encephalomyelitis and anxiety-related behavior, which confirms that mtDNA variations affect complex traits. Thus, we have developed a unique genetic resource that will facilitate exploration of the biochemical and physiological roles of mitochondria in complex traits.}, }
@article {pmid19033259, year = {2009}, author = {Pearl, SA and Welch, ME and McCauley, DE}, title = {Mitochondrial heteroplasmy and paternal leakage in natural populations of Silene vulgaris, a gynodioecious plant.}, journal = {Molecular biology and evolution}, volume = {26}, number = {3}, pages = {537-545}, doi = {10.1093/molbev/msn273}, pmid = {19033259}, issn = {1537-1719}, mesh = {*Genes, Mitochondrial ; Genes, Plant ; *Genetic Heterogeneity ; *Genetics, Population ; *Inheritance Patterns ; Mitochondria ; Polymerase Chain Reaction/methods ; Recombination, Genetic ; Silene/*genetics ; }, abstract = {It is currently thought that most angiosperms transmit their mitochondrial genomes maternally. Maternal transmission limits opportunities for genetic heterogeneity (heteroplasmy) of the mitochondrial genome within individuals. Recent studies of the gynodioecious species Silene vulgaris and Silene acaulis, however, document both direct and indirect evidence of mitochondrial heteroplasmy, suggesting that the mitochondrial genome is at times transmitted via paternal leakage. This heteroplasmy allows the generation of multi-locus recombinants, as documented in recent studies of both species. A prior study that employed quantitative PCR (q-PCR) on a limited sample provided direct evidence of heteroplasmy in the mitochondrial gene atp1 in S. vulgaris. Here, we apply the q-PCR methods to a much larger sample and extend them to incorporate the study of an additional atp1 haplotype along with two other haplotypes of the mitochondrial gene cox1 to evaluate the origin, extent, and transmission of mitochondrial genome heteroplasmy in S. vulgaris. We first calibrate our q-PCR methods experimentally and then use them to quantify heteroplasmy in 408 S. vulgaris individuals sampled from 22 natural populations located in Virginia, New York, and Tennessee. Sixty-one individuals exhibit heteroplasmy, including five that exhibited the joint heteroplasmy at both loci that is a prerequisite for effective recombination. The heteroplasmic individuals were distributed among 18 of the populations studied, demonstrating that heteroplasmy is a widespread phenomenon in this species. Further, we compare mother and offspring from 71 families to determine the rate of heteroplasmy gained and lost via paternal leakage and vegetative sorting across generations. Of 17 sibships exhibiting cox1 heteroplasmy and 14 sibships exhibiting atp1 heteroplasmy, more than half of the observations of heteroplasmy are generated via paternal leakage at the time of fertilization, with the rest being inherited from a heteroplasmic mother. Moreover, we show that the average paternal contribution during paternal leakage is about 12%. These findings are surprising, given that the current understanding of gynodioecy assumes that mitochondrial cytoplasmic male sterility elements are strictly maternally inherited. Knowledge of the dynamics of mitochondrial populations within individuals plays an important role in understanding the evolution of gynodioecy, and we discuss our findings within this context.}, }
@article {pmid19033201, year = {2008}, author = {Rostovtseva, TK and Sheldon, KL and Hassanzadeh, E and Monge, C and Saks, V and Bezrukov, SM and Sackett, DL}, title = {Tubulin binding blocks mitochondrial voltage-dependent anion channel and regulates respiration.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {48}, pages = {18746-18751}, pmid = {19033201}, issn = {1091-6490}, support = {//Intramural NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Cell Respiration/*physiology ; Electrophysiology ; Evolution, Molecular ; Humans ; Ion Channel Gating ; Lipid Bilayers/chemistry ; Mitochondria/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxidative Phosphorylation ; Peptides/chemistry/genetics/metabolism ; Protein Binding ; Protein Conformation ; Rats ; Sequence Alignment ; Tubulin/chemistry/genetics/*metabolism ; Voltage-Dependent Anion Channels/genetics/*metabolism ; }, abstract = {Regulation of mitochondrial outer membrane (MOM) permeability has dual importance: in normal metabolite and energy exchange between mitochondria and cytoplasm and thus in control of respiration, and in apoptosis by release of apoptogenic factors into the cytosol. However, the mechanism of this regulation, dependent on the voltage-dependent anion channel (VDAC), the major channel of MOM, remains controversial. A long-standing puzzle is that in permeabilized cells, adenine nucleotide translocase (ANT) is less accessible to cytosolic ADP than in isolated mitochondria. We solve this puzzle by finding a missing player in the regulation of MOM permeability: the cytoskeletal protein tubulin. We show that nanomolar concentrations of dimeric tubulin induce voltage-sensitive reversible closure of VDAC reconstituted into planar phospholipid membranes. Tubulin strikingly increases VDAC voltage sensitivity and at physiological salt conditions could induce VDAC closure at <10 mV transmembrane potentials. Experiments with isolated mitochondria confirm these findings. Tubulin added to isolated mitochondria decreases ADP availability to ANT, partially restoring the low MOM permeability (high apparent K(m) for ADP) found in permeabilized cells. Our findings suggest a previously unknown mechanism of regulation of mitochondrial energetics, governed by VDAC and tubulin at the mitochondria-cytosol interface. This tubulin-VDAC interaction requires tubulin anionic C-terminal tail (CTT) peptides. The significance of this interaction may be reflected in the evolutionary conservation of length and anionic charge in CTT throughout eukaryotes, despite wide changes in the exact sequence. Additionally, tubulins that have lost significant length or anionic character are only found in cells that do not have mitochondria.}, }
@article {pmid19030769, year = {2008}, author = {Russell, RD and Beckenbach, AT}, title = {Recoding of translation in turtle mitochondrial genomes: programmed frameshift mutations and evidence of a modified genetic code.}, journal = {Journal of molecular evolution}, volume = {67}, number = {6}, pages = {682-695}, pmid = {19030769}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Conserved Sequence ; Electron Transport Complex I/chemistry/genetics/metabolism ; Frameshift Mutation/*genetics ; Genetic Code/*genetics ; Genome, Mitochondrial/*genetics ; Molecular Sequence Data ; Phylogeny ; Protein Biosynthesis/*genetics ; Sequence Alignment ; Turtles/*genetics/metabolism ; }, abstract = {A +1 frameshift insertion has been documented in the mitochondrial gene nad3 in some birds and reptiles. By sequencing polyadenylated mRNA of the chicken (Gallus gallus), we have shown that the extra nucleotide is transcribed and is present in mature mRNA. Evidence from other animal mitochondrial genomes has led us to hypothesize that certain mitochondrial translation systems have the ability to tolerate frameshift insertions using programmed translational frameshifting. To investigate this, we sequenced the mitochondrial genome of the red-eared slider turtle (Trachemys scripta), where both the widespread nad3 frameshift insertion and a novel site in nad4l were found. Sequencing the region surrounding the insertion in nad3 in a number of other turtles and tortoises reveal general mitochondrial +1 programmed frameshift site features as well as the apparent redefinition of a stop codon in Parker's snake-neck turtle (Chelodina parkeri), the first known example of this in vertebrate mitochondria.}, }
@article {pmid19023087, year = {2009}, author = {Catania, F and Wurmser, F and Potekhin, AA and Przybos, E and Lynch, M}, title = {Genetic diversity in the Paramecium aurelia species complex.}, journal = {Molecular biology and evolution}, volume = {26}, number = {2}, pages = {421-431}, pmid = {19023087}, issn = {1537-1719}, mesh = {Animals ; Cell Nucleus/genetics ; Evolution, Molecular ; Genetic Speciation ; *Genetic Variation ; Mitochondria/genetics ; Paramecium aurelia/classification/*genetics ; Phylogeny ; }, abstract = {Current understanding of the population genetics of free-living unicellular eukaryotes is limited, and the amount of genetic variability in these organisms is still a matter of debate. We characterized-reproductively and genetically-worldwide samples of multiple Paramecium species belonging to a cryptic species complex, Paramecium aurelia, whose species have been shown to be reproductively isolated. We found that levels of genetic diversity both in the nucleus and in the mitochondrion are substantial within groups of reproductively compatible P. aurelia strains but drop considerably when strains are partitioned according to their phylogenetic groupings. Our study reveals the existence of discrepancies between the mating behavior of a number of P. aurelia strains and their multilocus genetic profile, a controversial finding that has major consequences for both the current methods of species assignment and the species problem in the P. aurelia complex.}, }
@article {pmid19014580, year = {2008}, author = {Kubo, N and Fujimoto, M and Arimura, S and Hirai, M and Tsutsumi, N}, title = {Transfer of rice mitochondrial ribosomal protein L6 gene to the nucleus: acquisition of the 5'-untranslated region via a transposable element.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {314}, pmid = {19014580}, issn = {1471-2148}, mesh = {*5' Untranslated Regions ; Amino Acid Sequence ; Biological Transport ; Cell Nucleus/chemistry/genetics/*metabolism ; Conserved Sequence ; *DNA Transposable Elements ; DNA, Mitochondrial/chemistry/genetics/*metabolism ; Genome, Plant ; Molecular Sequence Data ; Multigene Family ; Oryza/chemistry/*genetics/metabolism ; Plant Proteins/chemistry/*genetics/metabolism ; Ribosomal Proteins/chemistry/*genetics/metabolism ; Sequence Alignment ; }, abstract = {BACKGROUND: The mitochondria of contemporary organisms contain fewer genes than the ancestral bacteria are predicted to have contained. Because most of the mitochondrial proteins are encoded in the nucleus, the genes would have been transferred from the mitochondrion to the nucleus at some stage of evolution and they must have acquired cis-regulatory elements compatible with eukaryotic gene expression. However, most of such processes remain unknown.<br><br>RESULTS: The ribosomal protein L6 gene (rpl6) has been lost in presently-known angiosperm mitochondrial genomes. We found that each of the two rice rpl6 genes (OsRpl6-1 and OsRpl6-2) has an intron in an identical position within the 5'-untranslated region (UTR), which suggests a duplication of the rpl6 gene after its transfer to the nucleus. Each of the predicted RPL6 proteins lacks an N-terminal extension as a mitochondrial targeting signal. Transient assays using green fluorescent protein indicated that their mature N-terminal coding regions contain the mitochondrial targeting information. Reverse transcription-PCR analysis showed that OsRpl6-2 expresses considerably fewer transcripts than OsRpl6-1. This might be the result of differences in promoter regions because the 5'-noncoding regions of the two rpl6 genes differ at a point close to the center of the intron. There are several sequences homologous to the region around the 5'-UTR of OsRpl6-1 in the rice genome. These sequences have characteristics similar to those of the transposable elements (TE) belonging to the PIF/Harbinger superfamily.<br><br>CONCLUSION: The above evidences suggest a novel mechanism in which the 5'-UTR of the transferred mitochondrial gene was acquired via a TE. Since the 5'-UTRs and introns within the 5'-UTRs often contain transcriptional and posttranscriptional cis-elements, the transferred rice mitochondrial rpl6 gene may have acquired its cis-element from a TE.}, }
@article {pmid19014347, year = {2009}, author = {Kleine, T and Maier, UG and Leister, D}, title = {DNA transfer from organelles to the nucleus: the idiosyncratic genetics of endosymbiosis.}, journal = {Annual review of plant biology}, volume = {60}, number = {}, pages = {115-138}, doi = {10.1146/annurev.arplant.043008.092119}, pmid = {19014347}, issn = {1545-2123}, mesh = {Cell Nucleus/*genetics/*metabolism ; DNA, Mitochondrial/genetics/metabolism ; DNA, Plant/*genetics/metabolism ; *Evolution, Molecular ; Exons ; Genes, Plant ; Mitochondria/*genetics/metabolism ; Plastids/*genetics/metabolism ; Symbiosis ; }, abstract = {In eukaryotes, DNA is exchanged between endosymbiosis-derived compartments (mitochondria and chloroplasts) and the nucleus. Organelle-to-nucleus DNA transfer involves repair of double-stranded breaks by nonhomologous end-joining, and resulted during early organelle evolution in massive relocation of organelle genes to the nucleus. A large fraction of the products of the nuclear genes so acquired are retargeted to their ancestral compartment; many others now function in new subcellular locations. Almost all present-day nuclear transfers of mitochondrial or plastid DNA give rise to noncoding sequences, dubbed nuclear mitochondrial DNAs (NUMTs) and nuclear plastid DNAs (NUPTs). Some of these sequences were recruited as exons, thus introducing new coding sequences into preexisting nuclear genes by a novel mechanism. In organisms derived from secondary or tertiary endosymbiosis, serial gene transfers involving nucleus-to-nucleus migration of DNA have also occurred. Intercompartmental DNA transfer therefore represents a significant driving force for gene and genome evolution, relocating and refashioning genes and contributing to genetic diversity.}, }
@article {pmid19013103, year = {2009}, author = {Ota, S and Vaulot, D and Le Gall, F and Yabuki, A and Ishida, K}, title = {Partenskyella glossopodia gen. et sp. nov., the first report of a Chlorarachniophyte that lacks a pyrenoid.}, journal = {Protist}, volume = {160}, number = {1}, pages = {137-150}, doi = {10.1016/j.protis.2008.09.003}, pmid = {19013103}, issn = {1434-4610}, mesh = {Chloroplasts/ultrastructure ; DNA, Algal/genetics ; DNA, Ribosomal/genetics ; Eukaryota/*genetics/*ultrastructure ; Flagella/ultrastructure ; Mediterranean Sea ; Phylogeny ; Plankton/*ultrastructure ; }, abstract = {A new chlorarachniophyte, Partenskyella glossopodia gen. et sp. nov., is described from a culture isolated from the Mediterranean Sea pelagic waters and maintained as strain RCC365 at the Roscoff Culture Collection (France). Vegetative cells of P. glossopodia are non-motile naked spherical cells. However, flagellate and amoeboid stages are also present in its life cycle. The cells are 2-4mum in diameter containing a pale-green, cup-shaped chloroplast, 1-2 mitochondria, a nucleus, and a Golgi apparatus. Vesicles containing storage product-like material are also present. The chloroplast is surrounded by four membranes possessing a nucleomorph in the periplastidal compartment. The minute cell size and the absence of a pyrenoid at any stage of the life cycle are unique characteristics among the chlorarachniophytes, which justifies our proposition for a new genus for strain RCC365.}, }
@article {pmid19007762, year = {2009}, author = {Porté, S and Crosas, E and Yakovtseva, E and Biosca, JA and Farrés, J and Fernández, MR and Parés, X}, title = {MDR quinone oxidoreductases: the human and yeast zeta-crystallins.}, journal = {Chemico-biological interactions}, volume = {178}, number = {1-3}, pages = {288-294}, doi = {10.1016/j.cbi.2008.10.018}, pmid = {19007762}, issn = {1872-7786}, mesh = {Base Sequence ; Blotting, Western ; DNA Primers ; Electrophoretic Mobility Shift Assay ; Humans ; Phylogeny ; Quinone Reductases/*metabolism ; RNA/metabolism ; Saccharomyces cerevisiae/*metabolism ; Subcellular Fractions/enzymology ; Transcription, Genetic ; zeta-Crystallins/chemistry/*metabolism ; }, abstract = {The medium-chain dehydrogenase/reductase (MDR) superfamily can be divided into Zn-containing and Zn-lacking proteins. Zn-containing MDRs are generally well-known enzymes, mostly acting as dehydrogenases. The non-Zn MDR are much less studied, and classified in several families of NADP(H)-dependent reductases, including quinone oxidoreductases (QOR). zeta-Crystallins are the best studied group of QOR, have a structural function in the lens of several mammals, exhibit ortho-quinone reductase activity, and bind to specific adenine-uracil-rich elements (ARE) in RNA. In the present work, we have further characterized human zeta-crystallin and Saccharomyces cerevisiae Zta1p, the only QOR in yeast. Subcellular localization using a fluorescent protein tag indicates that zeta-crystallin is distributed in the cytoplasm but not in nucleus. The protein may also be present in mitochondria. Zta1p localizes in both cytoplasm and nucleus. NADPH, but not NADH, competitively prevents binding of zeta-crystallin to RNA, suggesting that the cofactor-binding site is involved in RNA binding. Interference of NADPH on Zta1p binding to RNA is much lower, consistent with a weaker binding of NADPH to the yeast enzyme. Disruption of the yeast ZTA1 gene does not affect cell growth under standard conditions but makes yeast more sensitive to oxidative stress agents. Sequence alignments, phylogenetic tree analysis and kinetic properties reveal a close relationship between zeta-crystallin and Zta1p. Amino acid conservation, between the substrate-binding sites of the two proteins and that of an E. coli QOR, indicates that zeta-crystallins maintained their kinetic function throughout evolution. Quinones are toxic compounds and a relevant step in their detoxification is reduction to their corresponding hydroquinones. Many enzymes of several superfamilies can reduce quinones, including NAD(P)H:quinone oxidoreductase 1 (NQO1 or DT-diaphorase), aldo-keto reductases and short-chain dehydrogenases/reductases. In this context, the physiological role of zeta-crystallins is discussed.}, }
@article {pmid19004874, year = {2008}, author = {Papp, LV and Wang, J and Kennedy, D and Boucher, D and Zhang, Y and Gladyshev, VN and Singh, RN and Khanna, KK}, title = {Functional characterization of alternatively spliced human SECISBP2 transcript variants.}, journal = {Nucleic acids research}, volume = {36}, number = {22}, pages = {7192-7206}, pmid = {19004874}, issn = {1362-4962}, support = {R01NS055925/NS/NINDS NIH HHS/United States ; R21NS055149/NS/NINDS NIH HHS/United States ; }, mesh = {*Alternative Splicing ; Cell Line ; Evolution, Molecular ; Gene Expression Regulation ; Humans ; Mitochondrial Proteins/analysis/genetics ; Oligonucleotides, Antisense/pharmacology ; Open Reading Frames ; Protein Biosynthesis ; Protein Isoforms/genetics/metabolism ; RNA-Binding Proteins/*genetics/metabolism ; Transcription, Genetic ; Ultraviolet Rays ; }, abstract = {Synthesis of selenoproteins depends on decoding of the UGA stop codon as the amino acid selenocysteine (Sec). This process requires the presence of a Sec insertion sequence element (SECIS) in the 3'-untranslated region of selenoprotein mRNAs and its interaction with the SECIS binding protein 2 (SBP2). In humans, mutations in the SBP2-encoding gene Sec insertion sequence binding protein 2 (SECISBP2) that alter the amino acid sequence or cause splicing defects lead to abnormal thyroid hormone metabolism. Herein, we present the first in silico and in vivo functional characterization of alternative splicing of SECISBP2. We report a complex splicing pattern in the 5'-region of human SECISBP2, wherein at least eight splice variants encode five isoforms with varying N-terminal sequence. One of the isoforms, mtSBP2, contains a mitochondrial targeting sequence and localizes to mitochondria. Using a minigene-based in vivo splicing assay we characterized the splicing efficiency of several alternative transcripts, and show that the splicing event that creates mtSBP2 can be modulated by antisense oligonucleotides. Moreover, we show that full-length SBP2 and some alternatively spliced variants are subject to a coordinated transcriptional and translational regulation in response to ultraviolet type A irradiation-induced stress. Overall, our data broadens the functional scope of a housekeeping protein essential to selenium metabolism.}, }
@article {pmid19004754, year = {2009}, author = {Minge, MA and Silberman, JD and Orr, RJ and Cavalier-Smith, T and Shalchian-Tabrizi, K and Burki, F and Skjaeveland, A and Jakobsen, KS}, title = {Evolutionary position of breviate amoebae and the primary eukaryote divergence.}, journal = {Proceedings. Biological sciences}, volume = {276}, number = {1657}, pages = {597-604}, pmid = {19004754}, issn = {0962-8452}, mesh = {Animals ; Eukaryotic Cells/*classification/ultrastructure ; Expressed Sequence Tags ; Gene Library ; Genes, Mitochondrial ; Genomics ; Mitochondria/genetics/physiology ; *Phylogeny ; RNA, Ribosomal, 18S/chemistry ; Sequence Analysis, DNA ; }, abstract = {Integration of ultrastructural and molecular sequence data has revealed six supergroups of eukaryote organisms (excavates, Rhizaria, chromalveolates, Plantae, Amoebozoa and opisthokonts), and the root of the eukaryote evolutionary tree is suggested to lie between unikonts (Amoebozoa, opisthokonts) and bikonts (the other supergroups). However, some smaller lineages remain of uncertain affinity. One of these unassigned taxa is the anaerobic, free-living, amoeboid flagellate Breviata anathema, which is of key significance as it is unclear whether it is a unikont (i.e. possibly the deepest branching amoebozoan) or a bikont. To establish its evolutionary position, we sequenced thousands of Breviata genes and calculated trees using 78 protein sequences. Our trees and specific substitutions in the 18S RNA sequence indicate that Breviata is related to other Amoebozoa, thereby significantly increasing the cellular diversity of this phylum and establishing Breviata as a deep-branching unikont. We discuss the implications of these results for the ancestral state of Amoebozoa and eukaryotes generally, demonstrating that phylogenomics of phylogenetically 'nomadic' species can elucidate key questions in eukaryote evolution. Furthermore, mitochondrial genes among the Breviata ESTs demonstrate that Breviata probably contains a modified anaerobic mitochondrion. With these findings, remnants of mitochondria have been detected in all putatively deep-branching amitochondriate organisms.}, }
@article {pmid19002206, year = {2009}, author = {Pérez-Espona, S and Pérez-Barbería, FJ and Goodall-Copestake, WP and Jiggins, CD and Gordon, IJ and Pemberton, JM}, title = {Genetic diversity and population structure of Scottish Highland red deer (Cervus elaphus) populations: a mitochondrial survey.}, journal = {Heredity}, volume = {102}, number = {2}, pages = {199-210}, doi = {10.1038/hdy.2008.111}, pmid = {19002206}, issn = {1365-2540}, mesh = {Animal Migration ; Animal Population Groups/*genetics ; Animals ; DNA, Mitochondrial/genetics ; Deer/classification/*genetics ; *Genetic Variation ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; Population Dynamics ; Scotland ; }, abstract = {The largest population of red deer (Cervus elaphus) in Europe is found in Scotland. However, human impacts through hunting and introduction of foreign deer stock have disturbed the population's genetics to an unknown extent. In this study, we analysed mitochondrial control region sequences of 625 individuals to assess signatures of human and natural historical influence on the genetic diversity and population structure of red deer in the Scottish Highlands. Genetic diversity was high with 74 haplotypes found in our study area (115 x 87 km). Phylogenetic analyses revealed that none of the individuals had introgressed mtDNA from foreign species or subspecies of deer and only suggested a very few localized red deer translocations among British localities. A haplotype network and population analyses indicated significant genetic structure (Phi(ST)=0.3452, F(ST)=0.2478), largely concordant with the geographical location of the populations. Mismatch distribution analysis and neutrality tests indicated a significant population expansion for one of the main haplogroups found in the study area, approximately dated c. 8200 or 16 400 years ago when applying a fast or slow mutation rate, respectively. Contrary to general belief, our results strongly suggest that native Scottish red deer mtDNA haplotypes have persisted in the Scottish Highlands and that the population retains a largely natural haplotype diversity and structure in our study area.}, }
@article {pmid18998587, year = {2008}, author = {Rodríguez, F and Feist, SW and Guillou, L and Harkestad, LS and Bateman, K and Renault, T and Mortensen, S}, title = {Phylogenetic and morphological characterisation of the green algae infesting blue mussel Mytilus edulis in the North and South Atlantic oceans.}, journal = {Diseases of aquatic organisms}, volume = {81}, number = {3}, pages = {231-240}, doi = {10.3354/dao01956}, pmid = {18998587}, issn = {0177-5103}, mesh = {Animals ; Atlantic Ocean ; Chlorophyta/*classification/cytology/physiology/*ultrastructure ; Microscopy, Electron, Transmission ; Mytilus edulis/*parasitology ; *Phylogeny ; Pigments, Biological/chemistry ; }, abstract = {Blue mussels Mytilus edulis with shell deformations and green pustules containing parasitic algae were collected at 3 coastal sites (Burøy, Norway; Bockholm, Denmark; Goose Green, Falkland Islands). A comparative study, including mussel histopathology, algal morphology, ultrastructure and phylogenetic position was performed. Green pustules were mainly located in the posterior portion of the mantle and gonad tissues and the posterior adductor muscle. Electron microscopy confirmed the presence of algal cells with similar morphology to Coccomyxa parasitica. Algae were oval shaped with a single nucleus and chloroplast, 1 or 2 mitochondria and a dense granular cytoplasm with a lipid inclusion body, Golgi apparatus and small vesicles. Partial small subunit (SSU) rRNA phylogeny confirmed the inclusion of parasitic algae into the Coccomyxa clade. However, the sequence identity between almost full SSU rRNA sequences of parasitic algae and others in this clade yielded an unexpected result. Green algae from mussels were distant from C. parasitica Culture Collection of Algae and Protozoa (CCAP) strain 216/18 (94% identity), but very similar (99% identity) to C. glaronensis (a lichen endosymbiont) and green endophytes from the tree Ginkgo biloba. The CCAP strain 216/18 was a sister sequence to Nannochloris algae, far from the Coccomyxa clade. These results suggest a misidentification or outgrowth of the original CCAP strain 216/18 by a different 'Nannochloris-like' trebouxiophycean organism. In contrast, our sequences directly obtained from infested mussels could represent the true C. parasitica responsible for the green pustules in blue mussels.}, }
@article {pmid18992827, year = {2009}, author = {Che, J and Hu, JS and Zhou, WW and Murphy, RW and Papenfuss, TJ and Chen, MY and Rao, DQ and Li, PP and Zhang, YP}, title = {Phylogeny of the Asian spiny frog tribe Paini (Family Dicroglossidae) sensu Dubois.}, journal = {Molecular phylogenetics and evolution}, volume = {50}, number = {1}, pages = {59-73}, doi = {10.1016/j.ympev.2008.10.007}, pmid = {18992827}, issn = {1095-9513}, mesh = {Animals ; Anura/anatomy &amp; histology/*classification/*genetics ; Asia ; Base Sequence ; Cell Nucleus/genetics ; DNA/genetics ; Databases, Nucleic Acid ; Mitochondria/genetics ; *Phylogeny ; }, abstract = {The anuran tribe Paini, family Dicroglossidae, is known in this group only from Asia. The phylogenetic relationships and often the taxonomic recognition of species are controversial. In order to stabilize the classification, we used approximately 2100 bp of nuclear (rhodopsin, tyrosinase) and mitochondrial (12S, 16S rRNA) DNA sequence data to infer the phylogenetic relationships of these frogs. Phylogenetic trees reconstructed using Bayesian inference and maximum parsimony methods supported a monophyletic tribe Paini. Two distinct groups (I,II) were recovered with the mtDNA alone and the total concatenated data (mtDNA+nuDNA). The recognition of two genera, Quasipaa and Nanorana, was supported. Group I, Quasipaa, is widespread east of the Hengduan Mountain Ranges and consists of taxa from relatively low elevations in southern China, Vietnam and Laos. Group II, Nanorana, contains a mix of species occurring from high to low elevation predominantly in the Qinghai-Tibetan Plateau and Hengduan Mountain Ranges. The occurrence of frogs at high elevations appears to be a derived ecological condition. The composition of some major species groups based on morphological characteristics strongly conflicts with the molecular analysis. Some possible cryptic species are indicated by the molecular analyses. The incorporation of genetic data from type localities helped to resolve some of the taxonomic problems, although further combined analyses of morphological data from type specimens are required. The two nuDNA gene segments proved to be very informative for resolving higher phylogenetic relationships and more nuclear data should be explored to be more confident in the relationships.}, }
@article {pmid18992008, year = {2008}, author = {King, RA and Tibble, AL and Symondson, WO}, title = {Opening a can of worms: unprecedented sympatric cryptic diversity within British lumbricid earthworms.}, journal = {Molecular ecology}, volume = {17}, number = {21}, pages = {4684-4698}, doi = {10.1111/j.1365-294X.2008.03931.x}, pmid = {18992008}, issn = {1365-294X}, support = {BB/D001188/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amplified Fragment Length Polymorphism Analysis ; Animals ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; *Genetic Speciation ; Genetics, Population ; Haplotypes ; Mitochondria/genetics ; Oligochaeta/*genetics ; *Phylogeny ; *Polymorphism, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; United Kingdom ; }, abstract = {Earthworms play a major role in many aspects of soil fertility, food web ecology and ecosystem functioning, and hence are frequently the subjects of, for example, ecological and toxicological research. Our aim was to examine the genetic structure of common earthworm species, to identify cryptic lineages or species that may be distinct ecotypes or biotypes (and hence confound current research based upon morphotypes) and to try to explain the massive cryptic diversity that eventually emerged. We demonstrated that species such as Allolobophora chlorotica, Aporrectodea longa, Aporrectodea rosea and Lumbricus rubellus all comprise highly divergent lineages with species-level divergence at the mitochondrial cytochrome oxidase I (COI) gene. In Allo. chlorotica alone, we found 55 haplotypes for COI, with 35 of these being found in pink and 20 in green morph worms. There were no cases of the two colour morphs sharing COI haplotypes. Phylogenetic analyses of mitochondrial COI and 16S genes showed the presence of five highly divergent lineages, suggesting the presence of multiple cryptic species within Allo. chlorotica. There was no clear geographical pattern to lineage distribution and many populations were polymorphic for both mitochondrial DNA lineage and colour morph. Amplified fragment length polymorphism results, based on two primer combinations, were broadly congruent with mitochondrial DNA results with one significant exception. Despite showing over 14% divergence at COI, amplified fragment length polymorphism markers showed that the two green morph lineages may be interbreeding and therefore represent a single taxon. The cryptic diversity revealed by these results has profound consequences for all areas of earthworm research.}, }
@article {pmid18991723, year = {2008}, author = {Santos, C and Martínez, M and Lima, M and Hao, YJ and Simões, N and Montiel, R}, title = {Mitochondrial DNA mutations in cancer: a review.}, journal = {Current topics in medicinal chemistry}, volume = {8}, number = {15}, pages = {1351-1366}, doi = {10.2174/156802608786141151}, pmid = {18991723}, issn = {1873-4294}, mesh = {Aging/genetics/physiology ; Animals ; Apoptosis/genetics/physiology ; Base Sequence ; DNA, Mitochondrial/*genetics ; Humans ; Hybrid Cells/pathology ; Mutation/*genetics ; Neoplasms/*genetics/pathology ; Phylogeny ; }, abstract = {As mitochondria participate in fundamental process of the cellular metabolism, recent research has addressed the role of mitochondria, and of mitochondrial DNA (mtDNA), in apoptosis, aging, and complex diseases. The association between mtDNA and cancer has been discussed since the beginning of the last century, and more recently, it has gained attention due to the observation of many somatic mutations in several types of cancers. In this review we describe those germinal mutations that have been associated to cancer, and present a compilation of somatic mutations that have been observed in different cancer tissues, describing relevant characteristics among them in a phylogenetic context. We also summarize the drawbacks and criticisms made towards the studies that report an association between mtDNA mutations and cancer, and discuss the experimental models used to analyse this relationship. Although many reported somatic mutations may actually be the outcome of laboratory artefacts, a considerable number could be authentic and may have a relationship with cancer development. In our compilation, we have observed 271 cancer mutations occurring in conserved positions of mtDNA, 70 of them appearing in more than one tumour. These mutations may be candidates to be used as cancer biomarkers, and deserve further investigation, perhaps through the use of experimental models and by an analysis of tumours of distinct grade to determine if the mutations arose early during tumourigenesis. Experiments with cybrids have been successfully used; however, models are needed in which specific mtDNA variants may be introduced into the same mitochondrial and cellular background.}, }
@article {pmid18991553, year = {2008}, author = {Samuilov, VD and Kiselevsky, DB and Shestak, AA and Nesov, AV and Vasil'ev, LA}, title = {Reactive oxygen species in programmed death of pea guard cells.}, journal = {Biochemistry. Biokhimiia}, volume = {73}, number = {10}, pages = {1076-1084}, doi = {10.1134/s0006297908100039}, pmid = {18991553}, issn = {1608-3040}, mesh = {*Apoptosis ; Cell Nucleus/metabolism ; Chloroplasts/metabolism ; Cyanides/pharmacology ; Hydrogen Peroxide/metabolism ; Mitochondria/metabolism ; Pisum sativum/*metabolism ; Plant Epidermis/drug effects/*metabolism ; Reactive Oxygen Species/*metabolism ; Time Factors ; }, abstract = {Hydrogen peroxide potentiates CN(-)-induced apoptosis of guard cells recorded as destruction of cell nuclei in the epidermis from pea leaves. A still stronger effect was exerted by the addition of H2O2 and NADH, which are the substrates of the plant cell wall peroxidase producing O2*- coupled to the oxidation of NADH. The CN(-)-or (CN(-) + H2O2)-induced destruction of guard cell nuclei was completely removed by nitroblue tetrazolium (NBT) oxidizing O2*- and preventing there-by the subsequent generation of H2O2. The reduced NBT was deposited in the cells as formazan crystals. Cyanide-induced apoptosis was diminished by mannitol and ethanol, which are OH* traps. The dyes Rose Bengal (RB) and tetramethylrhodamine ethyl ester (TMRE) photosensitizing singlet oxygen production suppressed the CN(-)-induced destruction of the cell nuclei in the light. This suppression was removed by exogenous NADH, which reacts with 1O2 yielding O2*-. Incubation of leaf slices with RB in the light lowered the photosynthetic O2 evolution rate and induced the permeability of guard cells for propidium iodide, which cannot pass across intact membranes. Inhibition of photosynthetic O2 evolution by 3-(3',4'-dichlorophenyl)-1,1-dimethylurea or bromoxynil prevented CN(-)-induced apoptosis of guard cells in the light but not in the dark. RB in combination with exogenous NADH caused H2O2 production that was sensitive to NBT and estimated from dichlorofluorescein (DCF) fluorescence. Data on NBT reduction and DCF and TMRE fluorescence obtained using a confocal microscope and data on the NADH-dependent H2O2 production are indicative of generation of reactive oxygen species in the chloroplasts, mitochondria, and nuclear region of guard cells as well as with participation of apoplastic peroxidase. Cyanide inhibited generation of reactive oxygen species in mitochondria and induced their generation in chloroplasts. The results show that H2O2, OH*, and O2*- resources utilized for H2O2 production are involved in apoptosis of guard cells. It is likely that singlet oxygen generated by RB in the light, judging from the permeability of the plasmatic membrane for propidium iodide, makes Photosystem II of chloroplasts inoperative and induces necrosis of the guard cells.}, }
@article {pmid18986973, year = {2009}, author = {Krosby, M and Rohwer, S}, title = {A 2000 km genetic wake yields evidence for northern glacial refugia and hybrid zone movement in a pair of songbirds.}, journal = {Proceedings. Biological sciences}, volume = {276}, number = {1657}, pages = {615-621}, pmid = {18986973}, issn = {0962-8452}, mesh = {Animals ; California ; DNA, Mitochondrial/chemistry ; Extinction, Biological ; Female ; Genetic Speciation ; Geography ; Haplotypes ; *Hybridization, Genetic ; Male ; Population Dynamics ; Sequence Analysis, DNA ; *Sexual Behavior, Animal ; Songbirds/classification/genetics/*physiology ; Washington ; }, abstract = {Hybrid zones are natural experiments that expose the forces maintaining species differences. But for cases where a trait of one of the hybridizing pair appears shifted into the range of the other, the underlying mechanism can be difficult to infer. For example, hybridization between hermit warbler (Dendroica occidentalis) and Townsend's warbler (Dendroica townsendi) is restricted to narrow hybrid zones in Washington and Oregon, yet hermit mtDNA can be found in phenotypically pure Townsend's populations up to 2000 km north along the Pacific coast. This could reflect introgression of selectively favoured hermit mitochondria north across the hybrid zones, or a neutral genetic wake left behind following southern zone movement. Hermit mitochondrial haplotypes in populations of coastal Townsend's exhibit relatively high genetic diversity and significant divergence from those found in populations of hermit warblers. This contradicts the predictions of selective introgression, but is consistent with a northern population of hermits diverging in a glacial refugium before being replaced by Townsend's via aggressive hybridization. Previous field studies showing Townsend's males to be competitively superior to hermit males support this scenario, and suggest that the extreme hybrid zone movement evidenced by the hermit mitochondrial wake represents an extinction in progress.}, }
@article {pmid18986493, year = {2008}, author = {Nunes, MD and Neumeier, H and Schlötterer, C}, title = {Contrasting patterns of natural variation in global Drosophila melanogaster populations.}, journal = {Molecular ecology}, volume = {17}, number = {20}, pages = {4470-4479}, doi = {10.1111/j.1365-294X.2008.03944.x}, pmid = {18986493}, issn = {1365-294X}, mesh = {Alleles ; Animals ; Bayes Theorem ; Cluster Analysis ; DNA, Mitochondrial/genetics ; Drosophila melanogaster/*genetics ; *Evolution, Molecular ; Genes, Insect ; Genes, Mitochondrial ; *Genetic Variation ; *Genetics, Population ; *Geography ; Haplotypes ; Microsatellite Repeats ; Mitochondria/genetics ; Species Specificity ; }, abstract = {Despite the popularity of Drosophila melanogaster in functional and evolutionary genetics, the global pattern of natural variation has not yet been comprehensively described in this species. For the first time, we report a combined survey using neutral microsatellites and mitochondrial sequence variation jointly. Thirty-five populations originating from five continents were compared. In agreement with previous microsatellite studies, sub-Saharan African populations were the most variable ones. Consistent with previous reports of a single 'out of Africa' habitat expansion, we found that non-African populations contained a subset of the African alleles. The pattern of variation detected for the mitochondrial sequences differed substantially. The most divergent haplotypes were detected in the Mediterranean region while Africa harboured most haplotypes, which were all closely related. In the light of the well-established African origin of D. melanogaster, our results cast severe doubts about the suitability of mtDNA for biogeographic inference in this model organism.}, }
@article {pmid18984158, year = {2008}, author = {Holzmann, J and Frank, P and Löffler, E and Bennett, KL and Gerner, C and Rossmanith, W}, title = {RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme.}, journal = {Cell}, volume = {135}, number = {3}, pages = {462-474}, doi = {10.1016/j.cell.2008.09.013}, pmid = {18984158}, issn = {1097-4172}, mesh = {Animals ; Cell Line ; Escherichia coli/genetics/metabolism ; Evolution, Molecular ; Female ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Mitochondria/*enzymology ; RNA, Catalytic/*analysis ; RNA, Transfer/metabolism ; Recombinant Proteins/genetics/metabolism ; Ribonuclease P/*chemistry/genetics/isolation &amp; purification/metabolism ; }, abstract = {tRNAs are synthesized as immature precursors, and on their way to functional maturity, extra nucleotides at their 5' ends are removed by an endonuclease called RNase P. All RNase P enzymes characterized so far are composed of an RNA plus one or more proteins, and tRNA 5' end maturation is considered a universal ribozyme-catalyzed process. Using a combinatorial purification/proteomics approach, we identified the components of human mitochondrial RNase P and reconstituted the enzymatic activity from three recombinant proteins. We thereby demonstrate that human mitochondrial RNase P is a protein enzyme that does not require a trans-acting RNA component for catalysis. Moreover, the mitochondrial enzyme turns out to be an unexpected type of patchwork enzyme, composed of a tRNA methyltransferase, a short-chain dehydrogenase/reductase-family member, and a protein of hitherto unknown functional and evolutionary origin, possibly representing the enzyme's metallonuclease moiety. Apparently, animal mitochondria lost the seemingly ubiquitous RNA world remnant after reinventing RNase P from preexisting components.}, }
@article {pmid18984152, year = {2008}, author = {Walker, SC and Engelke, DR}, title = {A protein-only RNase P in human mitochondria.}, journal = {Cell}, volume = {135}, number = {3}, pages = {412-414}, pmid = {18984152}, issn = {1097-4172}, support = {R01 GM034869/GM/NIGMS NIH HHS/United States ; R01 GM034869-20/GM/NIGMS NIH HHS/United States ; }, mesh = {Evolution, Molecular ; Humans ; Mitochondria/*enzymology ; RNA, Catalytic/*analysis ; Ribonuclease P/*chemistry/metabolism ; }, abstract = {In bacteria, archaea, and the eukaryote nucleus, the endonuclease ribonuclease P (RNase P) is composed of a catalytic RNA that is assisted by protein subunits. Holzmann et al. (2008) now provide evidence that the human mitochondrial RNase P is an entirely protein-based enzyme.}, }
@article {pmid18979193, year = {2008}, author = {Trézéguet, V and Pélosi, L and Lauquin, GJ and Brandolin, G}, title = {The mitochondrial ADP/ATP carrier: functional and structural studies in the route of elucidating pathophysiological aspects.}, journal = {Journal of bioenergetics and biomembranes}, volume = {40}, number = {5}, pages = {435-443}, pmid = {18979193}, issn = {0145-479X}, mesh = {Animals ; Conserved Sequence ; Evolution, Molecular ; Humans ; Mitochondria/enzymology/genetics ; Mitochondrial ADP, ATP Translocases/*chemistry/deficiency/genetics/*physiology ; Mitochondrial Diseases/enzymology/genetics ; Models, Molecular ; Mutation ; Oxidative Phosphorylation ; Protein Structure, Quaternary ; }, abstract = {The mitochondrial ADP/ATP carrier plays a central role in aerobic cell energetics by providing to the cytosol the ATP generated by oxidative phosphorylation. Though discovered around 40 years ago owing to the existence of unique inhibitors and in spite of numerous experimental approaches, this carrier, which stands as a model of the mitochondrial solute carriers keeps some long-standing mystery. There are still open challenging questions among them the precise ADP/ATP transport mechanism, the functional oligomeric state of the carrier and relationships between human ADP/ATP carrier dysfunctioning and pathologies. Deciphering the 3D structure of this carrier afforded a considerable progress of the knowledge but requires now additional data focused on molecular dynamics from this static picture. State of the art in this topic is reviewed and debated in this paper in view of better comprehending origin of the discrepancies in these questions and, finally, the multiple physiological roles of this carrier in eukaryotic cell economy.}, }
@article {pmid18976726, year = {2008}, author = {Wonnapinij, P and Chinnery, PF and Samuels, DC}, title = {The distribution of mitochondrial DNA heteroplasmy due to random genetic drift.}, journal = {American journal of human genetics}, volume = {83}, number = {5}, pages = {582-593}, pmid = {18976726}, issn = {1537-6605}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Drosophila ; *Genetic Drift ; Humans ; Mice ; Mitochondria/*genetics ; Physiological Phenomena/*genetics ; }, abstract = {Cells containing pathogenic mutations in mitochondrial DNA (mtDNA) generally also contain the wild-type mtDNA, a condition called heteroplasmy. The amount of mutant mtDNA in a cell, called the heteroplasmy level, is an important factor in determining the amount of mitochondrial dysfunction and therefore the disease severity. mtDNA is inherited maternally, and there are large random shifts in heteroplasmy level between mother and offspring. Understanding the distribution in heteroplasmy levels across a group of offspring is an important step in understanding the inheritance of diseases caused by mtDNA mutations. Previously, our understanding of the heteroplasmy distribution has been limited to just the mean and variance of the distribution. Here we give equations, adapted from the work of Kimura on random genetic drift, for the full mtDNA heteroplasmy distribution. We describe how to use the Kimura distribution in mitochondrial genetics, and we test the Kimura distribution against human, mouse, and Drosophila data sets.}, }
@article {pmid18959795, year = {2008}, author = {O'Farrell, HC and Xu, Z and Culver, GM and Rife, JP}, title = {Sequence and structural evolution of the KsgA/Dim1 methyltransferase family.}, journal = {BMC research notes}, volume = {1}, number = {}, pages = {108}, pmid = {18959795}, issn = {1756-0500}, support = {R01 GM062432/GM/NIGMS NIH HHS/United States ; R01 GM066900/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: One of the 60 or so genes conserved in all domains of life is the ksgA/dim1 orthologous group. Enzymes from this family perform the same post-transcriptional nucleotide modification in ribosome biogenesis, irrespective of organism. Despite this common function, divergence has enabled some family members to adopt new and sometimes radically different functions. For example, in S. cerevisiae Dim1 performs two distinct functions in ribosome biogenesis, while human mtTFB is not only an rRNA methyltransferase in the mitochondria but also a mitochondrial transcription factor. Thus, these proteins offer an unprecedented opportunity to study evolutionary aspects of structure/function relationships, especially with respect to our recently published work on the binding mode of a KsgA family member to its 30S subunit substrate. Here we compare and contrast KsgA orthologs from bacteria, eukaryotes, and mitochondria as well as the paralogous ErmC enzyme.<br><br>RESULTS: By using structure and sequence comparisons in concert with a unified ribosome binding model, we have identified regions of the orthologs that are likely related to gains of function beyond the common methyltransferase function. There are core regions common to the entire enzyme class that are associated with ribosome binding, an event required in rRNA methylation activity, and regions that are conserved in subgroups that are presumably related to non-methyltransferase functions.<br><br>CONCLUSION: The ancient protein KsgA/Dim1 has adapted to cellular roles beyond that of merely an rRNA methyltransferase. These results provide a structural foundation for analysis of multiple aspects of ribosome biogenesis and mitochondrial transcription.}, }
@article {pmid18957325, year = {2009}, author = {Palero, F and Crandall, KA and Abelló, P and Macpherson, E and Pascual, M}, title = {Phylogenetic relationships between spiny, slipper and coral lobsters (Crustacea, Decapoda, Achelata).}, journal = {Molecular phylogenetics and evolution}, volume = {50}, number = {1}, pages = {152-162}, doi = {10.1016/j.ympev.2008.10.003}, pmid = {18957325}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/genetics ; DNA/genetics ; Decapoda/anatomy &amp; histology/classification/*genetics ; Mitochondria/genetics ; *Phylogeny ; }, abstract = {Molecular data can aid in the resolution of conflicting hypotheses generated through difficulties in the interpretation of morphological data and/or an incomplete fossil record. Moreover, the reconstruction of phylogenetic relationships using molecular data may help to trace back the origin of morphological innovations which had a major impact on the radiation of a taxonomical group. In this work, different nuclear (18S, 28S, and H3) and mitochondrial (16S and COI) gene regions were sequenced in a total of 35 Achelatan species to test conflicting hypotheses of evolutionary relationships within the Achelata infraorder and solve the taxonomic disagreements in the group. The combined molecular dataset strongly supports the hypothesis that Achelata is a monophyletic group composed of two main families: Palinuridae and Scyllaridae. Synaxidae is found to be a polyphyletic group, which should be included within Palinuridae. Consequently, our results indicate that the origin of the stridulating organ occurred only once during Achelata evolution. Finally, the two main clades found within the Scyllaridae are in agreement with previous inferences based on adult morphological data. The dating of divergence of Achelata obtained with a relaxed-clock model is compatible with previous hypotheses of a Triassic origin of the Achelata.}, }
@article {pmid18957137, year = {2008}, author = {He, DQ and Zhu, Q and Chen, SY and Wang, HY and Liu, YP and Yao, YG}, title = {A homogenous nature of native Chinese duck matrilineal pool.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {298}, pmid = {18957137}, issn = {1471-2148}, mesh = {Animals ; Animals, Domestic/genetics ; Animals, Wild/genetics ; China ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Ducks/*genetics ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Haplotypes ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: China, with around 30 unique breeds, has a diverse duck genetic pool. Currently, there is no systematic report which investigates the genetic diversity, phylogenetic relationship, and matrilineal genetic structure of these domestic breeds and wild mallards (Anas platyrhynchos).<br><br>RESULTS: In this study, we sequenced the mitochondrial DNA (mtDNA) control region segments in 278 domestic ducks (Anas platyrhynchos domestica) from 19 indigenous breeds/populations and 70 wild mallard samples and analyzed them together with the 101 control region sequences from published sources. Fifty-two samples were then sequenced for a cytochrome b (Cyt b) gene fragment to solidify the pattern emerged from the control region sequences. All domestic duck and wild mallard haplotypes were essentially indistinguishable and were clustered together in the phylogenetic tree. There was no geographic differentiation and breed/population-specific distribution of duck lineages.<br><br>CONCLUSION: Our results showed that unlike other domesticated farm animals in China such as chicken, cattle, goat, and yak with multiple matrilineal components, the matrilineal pool of Chinese ducks was homogenous.}, }
@article {pmid18946048, year = {2008}, author = {Bender, A and Hajieva, P and Moosmann, B}, title = {Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {43}, pages = {16496-16501}, pmid = {18946048}, issn = {1091-6490}, mesh = {Animals ; Antioxidants ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Databases, Nucleic Acid ; *Electron Transport ; Fungi ; *Genetic Code ; Genome ; Isoleucine/genetics ; Methionine/genetics/*metabolism ; Mitochondrial Membranes/chemistry ; Oxidative Stress/genetics ; Plants ; }, abstract = {Humans and most other animals use 2 different genetic codes to translate their hereditary information: the standard code for nuclear-encoded proteins and a modern variant of this code in mitochondria. Despite the pivotal role of the genetic code for cell biology, the functional significance of the deviant mitochondrial code has remained enigmatic since its first description in 1979. Here, we show that profound and functionally beneficial alterations on the encoded protein level were causative for the AUA codon reassignment from isoleucine to methionine observed in most mitochondrial lineages. We demonstrate that this codon reassignment leads to a massive accumulation of the easily oxidized amino acid methionine in the highly oxidative inner mitochondrial membrane. This apparently paradoxical outcome can yet be smoothly settled if the antioxidant surface chemistry of methionine is taken into account, and we present direct experimental evidence that intramembrane accumulation of methionine exhibits antioxidant and cytoprotective properties in living cells. Our results unveil that methionine is an evolutionarily selected antioxidant building block of respiratory chain complexes. Collective protein alterations can thus constitute the selective advantage behind codon reassignments, which authenticates the "ambiguous decoding" hypothesis of genetic code evolution. Oxidative stress has shaped the mitochondrial genetic code.}, }
@article {pmid18941287, year = {2008}, author = {Ohama, T and Inagaki, Y and Bessho, Y and Osawa, S}, title = {Evolving genetic code.}, journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences}, volume = {84}, number = {2}, pages = {58-74}, pmid = {18941287}, issn = {1349-2896}, mesh = {Amino Acid Sequence ; Base Sequence ; Codon ; *Evolution, Molecular ; Genes, Bacterial ; *Genetic Code ; Mycoplasma capricolum/genetics ; RNA, Messenger/genetics ; }, abstract = {In 1985, we reported that a bacterium, Mycoplasma capricolum, used a deviant genetic code, namely UGA, a "universal" stop codon, was read as tryptophan. This finding, together with the deviant nuclear genetic codes in not a few organisms and a number of mitochondria, shows that the genetic code is not universal, and is in a state of evolution. To account for the changes in codon meanings, we proposed the codon capture theory stating that all the code changes are non-disruptive without accompanied changes of amino acid sequences of proteins. Supporting evidence for the theory is presented in this review. A possible evolutionary process from the ancient to the present-day genetic code is also discussed.}, }
@article {pmid18938252, year = {2008}, author = {Shi, H and Fong, JJ and Parham, JF and Pang, J and Wang, J and Hong, M and Zhang, YP}, title = {Mitochondrial variation of the "eyed" turtles (Sacalia) based on known-locality and trade specimens.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {1025-1029}, doi = {10.1016/j.ympev.2008.10.001}, pmid = {18938252}, issn = {1095-9513}, mesh = {Algorithms ; Animals ; Bayes Theorem ; China ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genetic Variation ; Geography ; Likelihood Functions ; Mitochondria/genetics ; Models, Anatomic ; *Phylogeny ; Turtles/classification/*genetics ; }, }
@article {pmid18935970, year = {2009}, author = {Cavalier-Smith, T}, title = {Predation and eukaryote cell origins: a coevolutionary perspective.}, journal = {The international journal of biochemistry &amp; cell biology}, volume = {41}, number = {2}, pages = {307-322}, doi = {10.1016/j.biocel.2008.10.002}, pmid = {18935970}, issn = {1357-2725}, mesh = {Animals ; *Biological Evolution ; Eukaryotic Cells/cytology/*physiology ; Phylogeny ; }, abstract = {Cells are of only two kinds: bacteria, with DNA segregated by surface membrane motors, dating back approximately 3.5Gy; and eukaryotes, which evolved from bacteria, possibly as recently as 800-850My ago. The last common ancestor of eukaryotes was a sexual phagotrophic protozoan with mitochondria, one or two centrioles and cilia. Conversion of bacteria (=prokaryotes) into a eukaryote involved approximately 60 major innovations. Numerous contradictory ideas about eukaryogenesis fail to explain fundamental features of eukaryotic cell biology or conflict with phylogeny. Data are best explained by the intracellular coevolutionary theory, with three basic tenets: (1) the eukaryotic cytoskeleton and endomembrane system originated through cooperatively enabling the evolution of phagotrophy; (2) phagocytosis internalised DNA-membrane attachments, unavoidably disrupting bacterial division; recovery entailed the evolution of the nucleus and mitotic cycle; (3) the symbiogenetic origin of mitochondria immediately followed the perfection of phagotrophy and intracellular digestion, contributing greater energy efficiency and group II introns as precursors of spliceosomal introns. Eukaryotes plus their archaebacterial sisters form the clade neomura, which evolved from a radically modified derivative of an actinobacterial posibacterium that had replaced the ancestral eubacterial murein peptidoglycan by N-linked glycoproteins, radically modified its DNA-handling enzymes, and evolved cotranslational protein secretion, but not the isoprenoid-ether lipids of archaebacteria. I focus on this phylogenetic background and on explaining how in response to novel phagotrophic selective pressures and ensuing genome internalisation this prekaryote evolved efficient digestion of prey proteins by retrotranslocation and 26S proteasomes, then internal digestion by phagocytosis, lysosomes, and peroxisomes, and eukaryotic vesicle trafficking and intracellular compartmentation.}, }
@article {pmid18931454, year = {2008}, author = {Saruhashi, S and Hamada, K and Miyata, D and Horiike, T and Shinozawa, T}, title = {Comprehensive analysis of the origin of eukaryotic genomes.}, journal = {Genes &amp; genetic systems}, volume = {83}, number = {4}, pages = {285-291}, doi = {10.1266/ggs.83.285}, pmid = {18931454}, issn = {1341-7568}, mesh = {Animals ; Eukaryotic Cells/classification/metabolism/physiology ; *Evolution, Molecular ; *Genome/physiology ; Humans ; Phylogeny ; Prokaryotic Cells/metabolism ; }, abstract = {There is currently no consensus on the evolutionary origin of eukaryotes. In the search of the ancestors of eukaryotes, we analyzed the phylogeny of 46 genomes, including those of 2 eukaryotes, 8 archaea, and 36 eubacteria. To avoid the effects of gene duplications, we used inparalog pairs of genes with orthologous relationships. First, we grouped these inparalogs into the functional categories of the nucleus, cytoplasm, and mitochondria. Next, we counted the sister groups of eukaryotes in prokaryotic phyla and plotted them on a standard phylogenetic tree. Finally, we used Pearson's chi-square test to estimate the origin of the genomes from specific prokaryotic ancestors. The results suggest the eukaryotic nuclear genome descends from an archaea that was neither euryarchaeota nor crenarchaeota and that the mitochondrial genome descends from alpha-proteobacteria. In contrast, genes related to the cytoplasm do not appear to originate from a specific group of prokaryotes.}, }
@article {pmid18930831, year = {2008}, author = {Dolman, G and Hugall, AF}, title = {Combined mitochondrial and nuclear data enhance resolution of a rapid radiation of Australian rainbow skinks (Scincidae: Carlia).}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {782-794}, doi = {10.1016/j.ympev.2008.09.021}, pmid = {18930831}, issn = {1095-9513}, mesh = {Animals ; Australia ; Bayes Theorem ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Fructose-Bisphosphate Aldolase/genetics ; Genes, Mitochondrial ; Genes, rRNA ; Genetic Speciation ; Likelihood Functions ; Lizards/classification/*genetics ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal, 16S ; Sequence Alignment ; Sequence Analysis, DNA ; beta-Globins/genetics ; }, abstract = {In contrast to low diversity seen in many Australian rainforest squamate genera, sclerophyll adapted groups--such as Carlia--show signs of faster diversification. Here we expand upon a previous single-locus mitochondrial DNA phylogenetic study of Carlia which described a major polytomy at an intermediate level of divergence. With additional mtDNA data, two nuclear intron loci and comprehensive taxonomic coverage, we provide support, congruent across loci, for the existence of three major clades. In doing so we recognise three genera for the 'Carlia group of skinks': clade 1, Carlia Gray, 1845; 2, Lygisaurus De Vis, 1884 (includes all species formerly known as Lygisaurus, and also includes C. parrhasius); 3, Liburnascincus Wells and Wellington, 1984 (consisting of three boulder-dwelling species). Remaining regions of low bootstrap and posterior probability support are associated with short internodes and apparent conflict among loci, as inferred by Partition Branch Support. Likelihood-based diversification-rate analysis rejects constant rate models, and indicates that Carlia underwent a period of relatively rapid diversification early in the evolution of the group, a rate 3-4 times faster than subsequent rates, and faster than comparable wet forest skinks.}, }
@article {pmid18930705, year = {2009}, author = {Bandeiras, TM and Refojo, PN and Todorovic, S and Murgida, DH and Hildebrandt, P and Bauer, C and Pereira, MM and Kletzin, A and Teixeira, M}, title = {The cytochrome ba complex from the thermoacidophilic crenarchaeote Acidianus ambivalens is an analog of bc(1) complexes.}, journal = {Biochimica et biophysica acta}, volume = {1787}, number = {1}, pages = {37-45}, doi = {10.1016/j.bbabio.2008.09.009}, pmid = {18930705}, issn = {0006-3002}, mesh = {Acidianus/*metabolism ; Archaeal Proteins/*chemistry/genetics ; Cytochrome b Group/*chemistry/genetics ; Cytochromes c1/*chemistry ; Electron Transport Complex III/*chemistry/genetics ; Electrophoresis, Polyacrylamide Gel ; Operon ; Oxidation-Reduction ; Phylogeny ; Spectrum Analysis, Raman ; }, abstract = {A novel cytochrome ba complex was isolated from aerobically grown cells of the thermoacidophilic archaeon Acidianus ambivalens. The complex was purified with two subunits, which are encoded by the cbsA and soxN genes. These genes are part of the pentacistronic cbsAB-soxLN-odsN locus. The spectroscopic characterization revealed the presence of three low-spin hemes, two of the b and one of the a(s)-type with reduction potentials of +200, +400 and +160 mV, respectively. The SoxN protein is proposed to harbor the heme b of lower reduction potential and the heme a(s), and CbsA the other heme b. The soxL gene encodes a Rieske protein, which was expressed in E. coli; its reduction potential was determined to be +320 mV. Topology predictions showed that SoxN, CbsB and CbsA should contain 12, 9 and one transmembrane alpha-helices, respectively, with SoxN having a predicted fold very similar to those of the cytochromes b in bc(1) complexes. The presence of two quinol binding motifs was also predicted in SoxN. Based on these findings, we propose that the A. ambivalens cytochrome ba complex is analogous to the bc(1) complexes of bacteria and mitochondria, however with distinct subunits and heme types.}, }
@article {pmid18929672, year = {2008}, author = {Chantangsi, C and Lynn, DH}, title = {Phylogenetic relationships within the genus Tetrahymena inferred from the cytochrome c oxidase subunit 1 and the small subunit ribosomal RNA genes.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {979-987}, doi = {10.1016/j.ympev.2008.09.017}, pmid = {18929672}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; DNA, Protozoan/genetics ; Electron Transport Complex IV/*genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genes, Protozoan/genetics ; Genes, rRNA/genetics ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Tetrahymena/classification/*genetics ; }, abstract = {Details of the phylogenetic relationships among tetrahymenine ciliates remain unresolved despite a rich history of investigation with nuclear gene sequences and other characters. We examined all available species of Tetrahymena and three other tetrahymenine ciliates, and inferred their phylogenetic relationships using nearly complete mitochondrial cytochrome c oxidase subunit 1 (cox1) and small subunit (SSU) rRNA gene sequences. The inferred phylogenies showed the genus Tetrahymena to be monophyletic. The three "classical" morphology-and-ecology-based groupings are paraphyletic. The SSUrRNA phylogeny confirmed the previously established australis and borealis groupings, and nine ribosets. However, these nine ribosets were not well supported. Using cox1 gene, the deduced phylogenies based on this gene revealed 12 well supported groupings, called coxisets, which mostly corresponded to the nine ribosets. This study demonstrated the utility of cox1 for resolving the recent phylogeny of Tetrahymena, whereas the SSU rRNA gene provided resolution of deeper phylogenetic relationships within the genus.}, }
@article {pmid18929671, year = {2008}, author = {Dumbacher, JP and Deiner, K and Thompson, L and Fleischer, RC}, title = {Phylogeny of the avian genus Pitohui and the evolution of toxicity in birds.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {774-781}, doi = {10.1016/j.ympev.2008.09.018}, pmid = {18929671}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Feathers ; Genes, Mitochondrial ; Likelihood Functions ; Markov Chains ; Mitochondria/genetics ; Monte Carlo Method ; Neurotoxins/*genetics ; New Guinea ; Palau ; Passeriformes/classification/*genetics ; *Phylogeny ; Pigmentation ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Bird species in the avian genus Pitohui contain potent neurotoxic alkaloids that may be used for defense. The genus comprises multiple species that are endemic to New Guinea and were presumed to belong to the family Pachycephalidae or Colluricinclidae, within the core corvoidea, an ancient Australasian radiation of crow-like birds. In order to understand the evolution of toxicity within the genus Pitohui, we sequenced three mitochondrial and two nuclear gene segments and reconstructed a phylogeny of the genus Pitohui and its putative relatives. We show that the genus Pitohui is polyphyletic, and consists of five different lineages. Using Bayesian ancestral state reconstruction, we estimate that toxicity likely evolved multiple times within this group. Furthermore, because the morphological and behavioral similarity among these poisonous birds appears to have evolved convergently, we hypothesize that this may be a possible example of Müllerian mimicry in birds. The Morningbird of Palau, Micronesia, that has often been included in the genus Pitohui, actually belongs in the genus Pachycephala and offers an intriguing case of pronounced evolution on a remote oceanic island.}, }
@article {pmid18928449, year = {2009}, author = {Traba, J and Satrústegui, J and del Arco, A}, title = {Characterization of SCaMC-3-like/slc25a41, a novel calcium-independent mitochondrial ATP-Mg/Pi carrier.}, journal = {The Biochemical journal}, volume = {418}, number = {1}, pages = {125-133}, doi = {10.1042/BJ20081262}, pmid = {18928449}, issn = {1470-8728}, mesh = {Adenosine Triphosphate/*metabolism ; Amino Acid Sequence ; Animals ; Anion Transport Proteins/chemistry/genetics/*metabolism ; Brain/metabolism ; Calcium/metabolism ; Cell Line ; Chlorocebus aethiops ; Gene Expression Regulation ; Humans ; Magnesium/*metabolism ; Male ; Mice ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/genetics/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Organ Specificity ; Phosphorus/*metabolism ; Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Homology, Amino Acid ; Testis/metabolism ; }, abstract = {The SCaMCs (small calcium-binding mitochondrial carriers) constitute a subfamily of mitochondrial carriers responsible for the ATP-Mg/P(i) exchange with at least three paralogues in vertebrates. SCaMC members are proteins with two functional domains, the C-terminal transporter domain and the N-terminal domain which harbours calcium-binding EF-hands and faces the intermembrane space. In the present study, we have characterized a shortened fourth paralogue, SCaMC-3L (SCaMC-3-like; also named slc25a41), which lacks the calcium-binding N-terminal extension. SCaMC-3L orthologues are found exclusively in mammals, showing approx. 60% identity to the C-terminal half of SCaMC-3, its closest paralogue. In mammalian genomes, SCaMC-3 and SCaMC-3L genes are adjacent on the same chromosome, forming a head-to-tail tandem array, and show identical exon-intron boundaries, indicating that SCaMC-3L could have arisen from an SCaMC-3 ancestor by a partial duplication event which occurred prior to mammalian radiation. Expression and functional data suggest that, following the duplication event, SCaMC-3L has acquired more restrictive functions. Unlike the broadly expressed longer SCaMCs, mouse SCaMC-3L shows a limited expression pattern; it is preferentially expressed in testis and, at lower levels, in brain. SCaMC-3L transport activity was studied in yeast deficient in Sal1p, the calcium-dependent mitochondrial ATP-Mg/P(i) carrier, co-expressing SCaMC-3L and mitochondrial-targeted luciferase, and it was found to perform ATP-Mg/P(i) exchange, in a similar manner to Sal1p or other ATP-Mg/P(i) carriers. However, metabolite transport through SCaMC-3L is calcium-independent, representing a novel mechanism involved in adenine nucleotide transport across the inner mitochondrial membrane, different to ADP/ATP translocases or long SCaMC paralogues.}, }
@article {pmid18926914, year = {2008}, author = {Velazco, PM and Patterson, BD}, title = {Phylogenetics and biogeography of the broad-nosed bats, genus Platyrrhinus (Chiroptera: Phyllostomidae).}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {749-759}, doi = {10.1016/j.ympev.2008.09.015}, pmid = {18926914}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Central America ; Chiroptera/classification/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genetic Speciation ; Geography ; Likelihood Functions ; Mitochondria/genetics ; NADH Dehydrogenase/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; South America ; }, abstract = {The Neotropical broad-nosed bats, genus Platyrrhinus, represent a well-defined monophyletic group of 14 recognized species. A recent study of morphological characters confirmed Platyrrhinus monophyly and species diagnosis, but offered little support to their intra-specific relationships. We conducted phylogenetic analyses of the genus, using dense taxonomic sampling in combination with four gene sequences representing both mitochondrial and nuclear DNA transmission systems. Our aim was to elucidate the phylogenetic structure among species, using the resulting 3341 bp of DNA. Maximum parsimony, maximum likelihood, and Bayesian inference analyses produced similar topologies that confirm the monophyly of the genus Platyrrhinus and strongly support many previously unrecognized groups. Paraphyly of Platyrrhinus helleri and the unclear position of P. brachycephalus in the clades were also apparent in the data. Our biogeographical analysis suggests a Brazilian Shield origin for Platyrrhinus, followed by subsequent radiations of lineages in the Amazon Basin and Andes. Secondary dispersal from Amazonian and Andean centers is responsible for the Platyrrhinus inhabiting the Guianan Shield and the Pacific lowlands and Central America, respectively.}, }
@article {pmid18922764, year = {2009}, author = {Goremykin, VV and Salamini, F and Velasco, R and Viola, R}, title = {Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer.}, journal = {Molecular biology and evolution}, volume = {26}, number = {1}, pages = {99-110}, doi = {10.1093/molbev/msn226}, pmid = {18922764}, issn = {1537-1719}, mesh = {Chloroplasts/genetics ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Mitochondria/genetics ; Mutagenesis, Insertional ; Protein Biosynthesis ; Vitis/cytology/*genetics ; }, abstract = {The mitochondrial genome of grape (Vitis vinifera), the largest organelle genome sequenced so far, is presented. The genome is 773,279 nt long and has the highest coding capacity among known angiosperm mitochondrial DNAs (mtDNAs). The proportion of promiscuous DNA of plastid origin in the genome is also the largest ever reported for an angiosperm mtDNA, both in absolute and relative terms. In all, 42.4% of chloroplast genome of Vitis has been incorporated into its mitochondrial genome. In order to test if horizontal gene transfer (HGT) has also contributed to the gene content of the grape mtDNA, we built phylogenetic trees with the coding sequences of mitochondrial genes of grape and their homologs from plant mitochondrial genomes. Many incongruent gene tree topologies were obtained. However, the extent of incongruence between these gene trees is not significantly greater than that observed among optimal trees for chloroplast genes, the common ancestry of which has never been in doubt. In both cases, we attribute this incongruence to artifacts of tree reconstruction, insufficient numbers of characters, and gene paralogy. This finding leads us to question the recent phylogenetic interpretation of Bergthorsson et al. (2003, 2004) and Richardson and Palmer (2007) that rampant HGT into the mtDNA of Amborella best explains phylogenetic incongruence between mitochondrial gene trees for angiosperms. The only evidence for HGT into the Vitis mtDNA found involves fragments of two coding sequences stemming from two closteroviruses that cause the leaf roll disease of this plant. We also report that analysis of sequences shared by both chloroplast and mitochondrial genomes provides evidence for a previously unknown gene transfer route from the mitochondrion to the chloroplast.}, }
@article {pmid18849002, year = {2008}, author = {Cabanne, GS and d'Horta, FM and Sari, EH and Santos, FR and Miyaki, CY}, title = {Nuclear and mitochondrial phylogeography of the Atlantic forest endemic Xiphorhynchus fuscus (Aves: Dendrocolaptidae): biogeography and systematics implications.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {760-773}, doi = {10.1016/j.ympev.2008.09.013}, pmid = {18849002}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Biodiversity ; Brazil ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Gene Flow ; *Genes, Mitochondrial ; *Genetic Speciation ; Genetics, Population ; Geography ; Haplotypes ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; Passeriformes/classification/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {We studied the intraspecific evolutionary history of the South American Atlantic forest endemic Xiphorhynchusfuscus (Aves: Dendrocolaptidae) to address questions such as: Was the diversification of this bird's populations associated to areas of avian endemism? Which models of speciation (i.e., refuges, river as barriers or geotectonism) explain the diversification within X. fuscus? Does the genetic data support subspecies as independent evolutionary units (species)? We used mitochondrial (n=34) and nuclear (n=68) DNA sequences of X. fuscus to study temporal and spatial relationships within and between populations. We described four main monophyletic lineages that diverged during the Pleistocene. The subspecies taxonomy did not match all the evolutionary lineages; subspecies atlanticus was the only one that represented a monophyletic and isolated lineage. The distribution of these lineages coincided with some areas of endemism for passerines, suggesting that those areas could be regions of biotic differentiation. The ancestor of X. fuscus diverged approximately 3 million years ago from Amazonian taxa and the phylogeographic pattern suggested that X. fuscus radiated from northeastern Brazil. Neither the riverine nor the geotectonic vicariance models are supported as the primary cause for diversification of geographic lineages, but rainforest contractions and expansions (ecological vicariance) can explain most of the spatial divergence observed in this species. Finally, analyses of gene flow and divergence time estimates suggest that the endangered subspecies atlanticus (from northeastern Brazil) can be considered a full species under the general lineage species concept.}, }
@article {pmid18848978, year = {2008}, author = {Akihito,  and Fumihito, A and Ikeda, Y and Aizawa, M and Makino, T and Umehara, Y and Kai, Y and Nishimoto, Y and Hasegawa, M and Nakabo, T and Gojobori, T}, title = {Evolution of Pacific Ocean and the Sea of Japan populations of the gobiid species, Pterogobius elapoides and Pterogobius zonoleucus, based on molecular and morphological analyses.}, journal = {Gene}, volume = {427}, number = {1-2}, pages = {7-18}, doi = {10.1016/j.gene.2008.09.026}, pmid = {18848978}, issn = {0378-1119}, mesh = {Animals ; Evolution, Molecular ; Japan ; Likelihood Functions ; Mitochondria/metabolism ; Models, Genetic ; Pacific Ocean ; Perciformes/*genetics/*physiology ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Pterogobius elapoides and Pterogobius zonoleucus are common free-swimming gobies found in rocky and weedy shores along the temperate coast of Japan. We collected individuals of both species from 23 locations around the coast of Japan and compared the mitochondrial nucleotide sequences of two gene regions, CytB and ND2. Phylogenetic trees constructed using the neighbor-joining, maximum parsimony, and maximum likelihood methods consistently indicated that all 125 samples of the two species, which are collected from a variety of locations in Japan, can be clearly divided into the following four clades: "Pacific P. elapoides" (Pa-ela), "Sea of Japan P. elapoides" (SJ-ela), "Pacific P. zonoleucus" (Pa-zon), and "Sea of Japan P. zonoleucus" (SJ-zon). These four monophyletic clades were supported with very high bootstrap values. Although Pa-ela and SJ-ela composed a monophyletic clade, it is noteworthy that the two clades of P. elapoides also formed a monophyletic group together with SJ-zon with a bootstrap value of 95% and 97% by the maximum likelihood and neighbor-joining methods, respectively. We observed several morphological differences between Pa-ela and SJ-ela, including; 1) six dark bands on the body in the former versus seven dark bands in the latter and 2) more pectoral-fin rays numbering 21-24 (mode 22) in the latter compared to the former (19-22, mode 21). Furthermore, the scatter plots of scores on principal components 1 and 2 based on the morphometric characters roughly separated the populations from each other. Moreover, we documented the following morphological differences between Pa-zon and SJ-zon for the first time; 1) six light bands on the body in the former versus five light bands in the latter and 2) the light bands from both eyes forming a complete U-shaped marking on the occipital region occurred in 55% of the specimens in the former versus 16% in the latter. However, no significant differences were found in the morphometric characters between the two populations of P. zonoleucus. The estimated divergence time of the two P. zonoleucus populations was 15.06+/-2.72 (mean+/-1 S.E.) times earlier than that of the two P. elapoides populations. However, the morphological differences between the two populations of the former were much smaller than those of the latter. An explanation for this obvious discrepancy between morphological and molecular features is proposed from an evolutionary point of view.}, }
@article {pmid18848634, year = {2008}, author = {Hull, JM and Strobel, BN and Boal, CW and Hull, AC and Dykstra, CR and Irish, AM and Fish, AM and Ernest, HB}, title = {Comparative phylogeography and population genetics within Buteo lineatus reveals evidence of distinct evolutionary lineages.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {988-996}, doi = {10.1016/j.ympev.2008.09.010}, pmid = {18848634}, issn = {1095-9513}, mesh = {Alleles ; Animals ; Bayes Theorem ; Computational Biology ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Gene Frequency ; *Genetic Speciation ; Genetic Variation ; *Genetics, Population ; *Geography ; Haplotypes ; Hawks/classification/*genetics ; Microsatellite Repeats ; Mitochondria/genetics ; North America ; Phylogeny ; Population Dynamics ; Sequence Analysis, DNA ; }, abstract = {Traditional subspecies classifications may suggest phylogenetic relationships that are discordant with evolutionary history and mislead evolutionary inference. To more accurately describe evolutionary relationships and inform conservation efforts, we investigated the genetic relationships and demographic histories of Buteo lineatus subspecies in eastern and western North America using 21 nuclear microsatellite loci and 375-base pairs of mitochondrial control region sequence. Frequency based analyses of mitochondrial sequence data support significant population distinction between eastern (B. l. lineatus/alleni/texanus) and western (B. l.elegans) subspecies of B. lineatus. This distinction was further supported by frequency and Bayesian analyses of the microsatellite data. We found evidence of differing demographic histories between regions; among eastern sites, mitochondrial data suggested that rapid population expansion occurred following the end of the last glacial maximum, with B. l. texanus population expansion preceding that of B. l. lineatus/alleni. No evidence of post-glacial population expansion was detected among western samples (B. l.elegans). Rather, microsatellite data suggest that the western population has experienced a recent bottleneck, presumably associated with extensive anthropogenic habitat loss during the 19th and 20th centuries. Our data indicate that eastern and western populations of B. lineatus are genetically distinct lineages, have experienced very different demographic histories, and suggest management as separate conservation units may be warranted.}, }
@article {pmid18848633, year = {2008}, author = {Mengual, X and Ståhls, G and Rojo, S}, title = {Molecular phylogeny of Allograpta (Diptera, Syrphidae) reveals diversity of lineages and non-monophyly of phytophagous taxa.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {715-727}, doi = {10.1016/j.ympev.2008.09.011}, pmid = {18848633}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Diptera/classification/*genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Feeding Behavior ; Genes, Insect ; Genes, Mitochondrial ; Genes, rRNA ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Phylogenetic relationships of genera Allograpta, Sphaerophoria and Exallandra (Diptera, Syrphidae) were analyzed based on sequence data from the mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) and the nuclear 28S and 18S ribosomal RNA genes. The three genera are members of the subfamily Syrphinae, where nearly all members feed as larvae on soft-bodied Hemiptera and other arthropods. Phytophagous species have recently been discovered in two subgenera of Allograpta, sg Fazia and a new subgenus from Costa Rica. Phylogenetic analyses of the combined datasets were performed using parsimony, under static alignment and direct optimization, maximum likelihood and Bayesian inference. Congruent topologies obtained from all the analyses indicate paraphyly of the genus Allograpta with respect to Sphaerophoria and Exallandra. Exallandra appears embedded in the genus Sphaerophoria, and both genera are placed within Allograpta. The distribution of phytophagous taxa in Allograpta indicates that plant feeding evolved at least twice in this group.}, }
@article {pmid18848545, year = {2008}, author = {Báez, AL and Lo Presti, MS and Rivarola, HW and Pons, P and Fretes, R and Paglini-Oliva, P}, title = {Trypanosoma cruzi: Cardiac mitochondrial alterations produced by different strains in the acute phase of the infection.}, journal = {Experimental parasitology}, volume = {120}, number = {4}, pages = {397-402}, doi = {10.1016/j.exppara.2008.09.014}, pmid = {18848545}, issn = {1090-2449}, mesh = {Acute Disease ; Animals ; Chagas Disease/*pathology ; Citrate (si)-Synthase/*metabolism ; Disease Models, Animal ; Female ; Male ; Mice ; Mitochondria, Heart/*metabolism/*pathology/ultrastructure ; Multienzyme Complexes/*metabolism ; Parasitemia/pathology ; Trypanosoma cruzi/classification/pathogenicity ; }, abstract = {The parasite Trypanosoma cruzi is the causative agent of Chagas disease. T. cruzi invasion and replication in cardiomyocytes induce cellular injuries and cytotoxic reactions, with the production of inflammatory cytokines and nitric oxide, both source of reactive oxygen species. The myocyte response to oxidative stress involves the progression of cellular changes primarily targeting mitochondria. We studied the cardiac mitochondrial structure and the enzymatic activity of citrate synthase and respiratory chain CI-CIV complexes, in Albino Swiss mice infected with T. cruzi, Tulahuen strain and SGO Z12 isolate, in two periods of the acute infection. Changes in the mitochondrial structure were detected in both infected groups, reaching values of 71% for Tulahuen and 88% for SGO Z12 infected mice, 30 days post infection. The citrate synthase activity was different according to the evolution of the infection and the parasite strain, but the respiratory chain alterations were similar with either strain.}, }
@article {pmid18845547, year = {2008}, author = {Pereira, F and Soares, P and Carneiro, J and Pereira, L and Richards, MB and Samuels, DC and Amorim, A}, title = {Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region.}, journal = {Molecular biology and evolution}, volume = {25}, number = {12}, pages = {2759-2770}, doi = {10.1093/molbev/msn225}, pmid = {18845547}, issn = {1537-1719}, mesh = {Animals ; Base Composition ; DNA, Mitochondrial/chemistry/*genetics ; Gene Deletion ; Humans ; *Locus Control Region ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Primates ; Selection, Genetic ; }, abstract = {A combined effect of functional constraints and random mutational events is responsible for the sequence evolution of the human mitochondrial DNA (mtDNA) control region. Most studies targeting this noncoding segment usually focus on its primary sequence information disregarding other informative levels such as secondary or tertiary DNA conformations. In this work, we combined the most recent developments in DNA folding calculations with a phylogenetic comparative approach in order to investigate the formation of intrastrand secondary structures in the human mtDNA control region. Our most striking results are those regarding a new cloverleaf-like secondary structure predicted for a 93-bp stretch of the control region 5'-peripheral domain. Randomized sequences indicated that this structure has a more negative folding energy than the average of random sequences with the same nucleotide composition. In addition, a sliding window scan across the complete mitochondrial genome revealed that it stands out as having one of the highest folding potential. Moreover, we detected several lines of evidence of both negative and positive selection on this structure with high levels of conservation at the structure-relevant stem regions and the occurrence of compensatory base changes in the primate lineage. In the light of previous data, we discuss the possible involvement of this structure in mtDNA replication and/or transcription. We conclude that maintenance of this structure is responsible for the observed heterogeneity in the rate of substitution among sites in part of the human hypervariable region I and that it is a hot spot for the 3' end of human mtDNA deletions.}, }
@article {pmid18845277, year = {2009}, author = {Nakazawa, F and Alev, C and Shin, M and Nakaya, Y and Jakt, LM and Sheng, G}, title = {PBRL, a putative peripheral benzodiazepine receptor, in primitive erythropoiesis.}, journal = {Gene expression patterns : GEP}, volume = {9}, number = {2}, pages = {114-121}, doi = {10.1016/j.gep.2008.09.005}, pmid = {18845277}, issn = {1567-133X}, mesh = {Amino Acid Sequence ; Animals ; COS Cells ; Cells, Cultured ; Chick Embryo ; Chickens/genetics ; Chlorocebus aethiops ; Erythropoiesis/*genetics/physiology ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Enzymologic ; Heme/biosynthesis ; Models, Biological ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Receptors, GABA-A/*genetics/isolation &amp; purification/metabolism ; Sequence Homology ; }, abstract = {Benzodiazepines are a class of psychoactive drugs widely used for their anxiolytic, anticonvulsant, muscle relaxant and hypnotic properties. Although the benzodiazepine receptor in the central nervous system has been well studied, the role of peripheral type benzodiazepine receptor, PBR, remains elusive. Here, we show that there are two PBR homologous genes in amniotes, PBR and PBRL, based on phylogenetic analysis. In chickens, PBRL is exclusively expressed during early development in differentiating primitive erythrocytes and this expression is tightly correlated with that of hemoglobin genes. PBR is not expressed in hematopoietic system during this period and is weakly expressed in developing central nervous system. Because one of PBRs' known functions is to regulate heme transport between the mitochondria and cytoplasm, we investigated expression profiles of heme biosynthesis genes. Seven of the eight enzymes involved in heme biosynthesis, with the exception of protoporphyrinogen oxidase, are present in chicken genome. Five of them, delta-aminolevulinate synthase, delta-aminolevulinic acid dehydrogenase, porphobilinogen deaminase, coproporphyrinogen decarboxylase and ferrochelatase, show stage-specific increase in gene expression correlated with primitive hematopoiesis, but not with primitive erythrocyte differentiation. PBRL protein is localized to the mitochondria in culture cells, and pharmacological inhibition of PBRL activity results in a decrease in globin protein levels during primitive erythropoiesis. Our data suggest a developmental role of PBRs in erythropoiesis in chickens, possibly via the regulation of heme availability for the assembly of functional hemoglobins.}, }
@article {pmid18838124, year = {2008}, author = {Drouin, G and Daoud, H and Xia, J}, title = {Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {827-831}, doi = {10.1016/j.ympev.2008.09.009}, pmid = {18838124}, issn = {1095-9513}, mesh = {Chloroplasts/genetics ; Cycadopsida/classification/*genetics ; DNA, Chloroplast/genetics ; DNA, Complementary/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; *Evolution, Molecular ; Genes, Plant ; Genome, Chloroplast ; Genome, Mitochondrial ; *Genome, Plant ; Magnoliopsida/classification/*genetics ; Mitochondria/genetics ; Models, Genetic ; Mutation ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Previous studies have estimated that, in angiosperms, the synonymous substitution rate of chloroplast genes is three times higher than that of mitochondrial genes and that of nuclear genes is twelve times higher than that of mitochondrial genes. Here we used 12 genes in 27 seed plant species to investigate whether these relative rates of substitutions are common to diverse seed plant groups. We find that the overall relative rate of synonymous substitutions of mitochondrial, chloroplast and nuclear genes of all seed plants is 1:3:10, that these ratios are 1:2:4 in gymnosperms but 1:3:16 in angiosperms and that they go up to 1:3:20 in basal angiosperms. Our results show that the mitochondrial, chloroplast and nuclear genomes of seed plant groups have different synonymous substitutions rates, that these rates are different in different seed plant groups and that gymnosperms have smaller ratios than angiosperms.}, }
@article {pmid18836526, year = {2008}, author = {Kitazoe, Y and Kishino, H and Hasegawa, M and Nakajima, N and Thorne, JL and Tanaka, M}, title = {Adaptive threonine increase in transmembrane regions of mitochondrial proteins in higher primates.}, journal = {PloS one}, volume = {3}, number = {10}, pages = {e3343}, pmid = {18836526}, issn = {1932-6203}, mesh = {Animals ; Evolution, Molecular ; Membrane Proteins/chemistry/*genetics ; Mitochondria/*genetics ; Mitochondrial Proteins/chemistry/*genetics ; Phylogeny ; Primates/*genetics ; Protein Structure, Secondary/genetics ; Threonine/*genetics ; }, abstract = {BACKGROUND: The mitochondrial (mt) gene tree of placental mammals reveals a very strong acceleration of the amino acid (AA) replacement rate and a change in AA compositional bias in the lineage leading to the higher primates (simians), in contrast to the nuclear gene tree. Whether this acceleration and compositional bias were caused by adaptive evolution at the AA level or directional mutation pressure at the DNA level has been vigorously debated.<br><br>Our phylogenetic analysis indicates that the rate acceleration in the simian lineage is accompanied by a marked increase in threonine (Thr) residues in the transmembrane helix regions of mt DNA-encoded proteins. This Thr increase involved the replacement of hydrophobic AAs in the membrane interior. Even after accounting for lack of independence due to phylogeny, a regression analysis reveals a statistical significant positive correlation between Thr composition and longevity in primates.<br><br>CONCLUSION/SIGNIFICANCE: Because crucial roles of Thr and Ser in membrane proteins have been proposed to be the formation of hydrogen bonds enhancing helix-helix interactions, the Thr increase detected in the higher primates might be adaptive by serving to reinforce stability of mt proteins in the inner membrane. The correlation between Thr composition in the membrane interior and the longevity of animals is striking, especially because some mt functions are thought to be involved in aging.}, }
@article {pmid18833571, year = {2009}, author = {Torriani, SF and Brunner, PC and McDonald, BA and Sierotzki, H}, title = {QoI resistance emerged independently at least 4 times in European populations of Mycosphaerella graminicola.}, journal = {Pest management science}, volume = {65}, number = {2}, pages = {155-162}, doi = {10.1002/ps.1662}, pmid = {18833571}, issn = {1526-498X}, mesh = {Ascomycota/classification/drug effects/*genetics/physiology ; Cytochromes b/genetics/metabolism ; DNA, Mitochondrial/genetics ; *Drug Resistance, Fungal ; Europe ; Fungal Proteins/genetics/metabolism ; Fungicides, Industrial/*pharmacology ; Haplotypes ; Mutation, Missense ; Phylogeny ; Plant Diseases/*microbiology ; }, abstract = {BACKGROUND: QoI fungicides or quinone outside inhibitors (also called strobilurins) have been widely used to control agriculturally important fungal pathogens since their introduction in 1996. Strobilurins block the respiration pathway by inhibiting the cytochrome bc1 complex in mitochondria. Several plant pathogenic fungi have developed field resistance. The first QoI resistance in Mycosphaerella graminicola (Fuckel) Schroter was detected retrospectively in UK in 2001 at a low frequency in QoI-treated plots. During the following seasons, resistance reached high frequencies across northern Europe. The aim of this study was to identify the main evolutionary forces driving the rapid emergence and spread of QoI resistance in M. graminicola populations.<br><br>RESULTS: The G143A mutation causing QoI resistance was first detected during 2002 in all tested populations and in eight distinct mtDNA sequence haplotypes. By 2004, 24 different mtDNA haplotypes contained the G143A mutation. Phylogenetic analysis showed that strobilurin resistance was acquired independently through at least four recurrent mutations at the same site of cytochrome b. Estimates of directional migration rates showed that the majority of gene flow in Europe had occurred in a west-to-east direction.<br><br>CONCLUSION: This study demonstrated that recurring mutations independently introduced the QoI resistance allele into different genetic and geographic backgrounds. The resistant haplotypes then increased in frequency owing to the strong fungicide selection and spread eastward through wind dispersal of ascospores.}, }
@article {pmid18832039, year = {2008}, author = {Macey, JR and Kuehl, JV and Larson, A and Robinson, MD and Ugurtas, IH and Ananjeva, NB and Rahman, H and Javed, HI and Osman, RM and Doumma, A and Papenfuss, TJ}, title = {Socotra Island the forgotten fragment of Gondwana: unmasking chameleon lizard history with complete mitochondrial genomic data.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {1015-1018}, doi = {10.1016/j.ympev.2008.08.024}, pmid = {18832039}, issn = {1095-9513}, mesh = {Africa ; Animals ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genetic Speciation ; *Genome, Mitochondrial ; Geography ; India ; Lizards/classification/*genetics ; Middle East ; Mitochondria/genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, }
@article {pmid18826668, year = {2008}, author = {Hoshizaki, S and Washimori, R and Kubota, S and Ohno, S and Huang, Y and Tatsuki, S and Ishikawa, Y}, title = {Two mitochondrial lineages occur in the Asian corn borer, Ostrinia furnacalis (Lepidoptera: Crambidae), in Japan.}, journal = {Bulletin of entomological research}, volume = {98}, number = {5}, pages = {519-526}, doi = {10.1017/S0007485308005841}, pmid = {18826668}, issn = {0007-4853}, mesh = {Animals ; DNA, Mitochondrial/*chemistry ; Electron Transport Complex IV/*chemistry/genetics ; Haplotypes ; Japan ; Moths/classification/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The genealogy and diversity of the mitochondrial cytochrome oxidase subunit II (COII) gene were investigated for Ostrinia furnacalis in Japan. A preliminary examination of mitochondrial lineages in China and the Philippines was also made. Two lineages (A and B) were found in the COII gene. Lineage A was frequent throughout the Japanese main islands (Hokkaido, Honshu, Shikoku and Kyushu), while the frequency of lineage B varied among these islands. No clear patterns of geographical population structure were found. Population genetic features suggested that the O. furnacalis population harboring the lineage A mitochondria expanded in the recent past, while lineage B showed weak signals of a population expansion. It is not clear whether the two lineages of mtDNA evolved in separate or identical geographical regions. We discuss two hypotheses regarding the two lineages of mtDNA: a cryptic race/species hypothesis and a selective sweep hypothesis.}, }
@article {pmid18824237, year = {2008}, author = {Spellman, GM and Cibois, A and Moyle, RG and Winker, K and Keith Barker, F}, title = {Clarifying the systematics of an enigmatic avian lineage: what is a bombycillid?.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {1036-1040}, pmid = {18824237}, issn = {1095-9513}, support = {P20 RR016479/RR/NCRR NIH HHS/United States ; P20 RR016479-077360/RR/NCRR NIH HHS/United States ; 2 P20 RR016479/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Exons ; Genes, Mitochondrial ; Genes, RAG-1 ; Likelihood Functions ; Markov Chains ; Mitochondria/genetics ; Models, Genetic ; Passeriformes/*classification/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, }
@article {pmid18824110, year = {2008}, author = {Anducho-Reyes, MA and Cognato, AI and Hayes, JL and Zúñiga, G}, title = {Phylogeography of the bark beetle Dendroctonus mexicanus Hopkins (Coleoptera: Curculionidae: Scolytinae).}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {930-940}, doi = {10.1016/j.ympev.2008.09.005}, pmid = {18824110}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Coleoptera/classification/*genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Genes, Insect ; Genes, Mitochondrial ; Genetic Variation ; Genetics, Population ; Genome, Insect ; Geography ; Guatemala ; Haplotypes ; Mexico ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Dendroctonus mexicanus is polyphagous within the Pinus genus and has a wide geographical distribution in Mexico and Guatemala. We examined the pattern of genetic variation across the range of this species to explore its demographic history and its phylogeographic pattern. Analysis of the mtDNA sequences of 173 individuals from 25 Mexican populations allowed to us identify 53 geographically structured haplotypes. High haplotype and low nucleotide diversities and Tajima's D indicate that D. mexicanus experienced rapid population expansion during its dispersal across mountain systems within its current range. The nested clade phylogeographic analysis indicates that the phylogeographic pattern of D. mexicanus is explained by continuous dispersion among lineages from the Sierra Madre Occidental, the Sierra Madre Oriental and the Trans-Mexican Volcanic Belt. However, we also observed isolation events among haplotypes from the Cofre de Perote/Trans-Mexican Volcanic Belt/Sierra Madre Oriental and the Trans-Mexican Volcanic Belt/Sierra Madre del Sur, which is consistent with the present conformation of mountain systems in Mexico and the emergence of geographical barriers during the Pleistocene.}, }
@article {pmid18822791, year = {2008}, author = {Menzorov, AG and Matveeva, NM and Larkin, DM and Zaykin, DV and Serov, OL}, title = {[Fate of parental mitochondria in embryonic stem hybrid cells].}, journal = {Tsitologiia}, volume = {50}, number = {8}, pages = {711-718}, pmid = {18822791}, issn = {0041-3771}, support = {//Wellcome Trust/United Kingdom ; Z01 ES101866-03//Intramural NIH HHS/United States ; }, mesh = {Animals ; Cell Fusion ; Cells, Cultured ; DNA, Mitochondrial/*genetics ; Embryonic Stem Cells/metabolism/*ultrastructure ; Fibroblasts/metabolism/ultrastructure ; Genetic Drift ; Genetic Markers ; Hybrid Cells/metabolism/*ultrastructure ; Mice ; *Mitochondria/genetics/metabolism ; Polymorphism, Restriction Fragment Length ; Species Specificity ; Spleen/metabolism/ultrastructure ; }, abstract = {When hybrid cells are created, not only the nuclear genomes of parental cells unite but their cytoplasm as well. Mitochondrial DNA (mtDNA) is a convenient marker of cytoplasm allowing one to gain insight into the organization of hybrid cell cytoplasm. We analyzed the parental mtDNAs in hybrid cells resulting from fusion of Mus musculus embryonic stem (ES) cells with splenocytes and fetal fibroblasts of DD/c mice or with splenocytes of M. caroli. Identification of the parental mtDNAs in hybrid cells was based on polymorphism among the parental mtDNAs for certain restrictases. We found that intra- and inter-specific ES cell-splenocyte hybrid cells lost entirely or partially mtDNA derived from the somatic partner, whereas ES cell-fibroblast hybrids retained mtDNAs from both parents in similar ratios with a slight bias. The lost of the “somatic” mitochondria by ES-splenocyte hybrids implies non-random segregation of the parental mitochondria as supported by a computer simulation of genetic drift. In contrast, ES cell-fibroblast hybrids show bilateral random segregation of the parental mitochondria judging from analysis of mtDNA in single cells. Preferential segregation of “somatic” mitochondria does not depend on the differences in sequences of the parental mtDNAs but depends on replicative state of the parental cells.}, }
@article {pmid18819574, year = {2008}, author = {Ling, H}, title = {Sequence analysis of GDSL lipase gene family in Arabidopsis thaliana.}, journal = {Pakistan journal of biological sciences : PJBS}, volume = {11}, number = {5}, pages = {763-767}, doi = {10.3923/pjbs.2008.763.767}, pmid = {18819574}, issn = {1028-8880}, mesh = {Amino Acid Motifs ; Arabidopsis/*enzymology/*genetics ; Arabidopsis Proteins/genetics ; DNA, Complementary/metabolism ; DNA, Plant/genetics ; Gene Expression Regulation, Plant ; Introns ; Lipase/chemistry/*genetics ; Models, Genetic ; Multigene Family ; Phylogeny ; Protein Sorting Signals ; Protein Structure, Tertiary ; Sequence Analysis, DNA ; }, abstract = {To analyze sequence characters of GDSL lipase gene family in Arabidopsis thaliana, 108 members of GDSL lipases were analyzed using data mining. The gene structures display remarkable diversity, consisting of zero to 13 introns. And the genes are asymmetrically distributed in chromosome 1-5, some of which are arranged in tandem. Phylogenetically, they were classified into three groups. Lipase-GDSL domain (PF00478) is housed at or close to N-terminus, or in the middle of amino acid sequences, additionally in which other domains and replicates were also found. Most GDSL lipases contain a signal peptide for conducting the secretary pathway. They are predicted to be extracellularly secreted, or target to mitochondria, chloroplast or any other parts of the cells. Functionally, these lipases are potentially involved in multiple physiological roles including seed germination, flowering and defense reactions. This study will help further understand the sequences and functions of Arabidopsis GDSL lipases.}, }
@article {pmid18814852, year = {2008}, author = {Stöck, M and Dubey, S and Klütsch, C and Litvinchuk, SN and Scheidt, U and Perrin, N}, title = {Mitochondrial and nuclear phylogeny of circum-Mediterranean tree frogs from the Hyla arborea group.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {1019-1024}, doi = {10.1016/j.ympev.2008.08.029}, pmid = {18814852}, issn = {1095-9513}, mesh = {Animals ; Anura/classification/*genetics ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genes, RAG-1 ; Genetic Speciation ; Likelihood Functions ; Mediterranean Region ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, }
@article {pmid18814021, year = {2008}, author = {Mather, MW and Vaidya, AB}, title = {Mitochondria in malaria and related parasites: ancient, diverse and streamlined.}, journal = {Journal of bioenergetics and biomembranes}, volume = {40}, number = {5}, pages = {425-433}, pmid = {18814021}, issn = {0145-479X}, support = {R01 AI028398/AI/NIAID NIH HHS/United States ; AI028398/AI/NIAID NIH HHS/United States ; AI053148/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Antimalarials/pharmacology ; Apicomplexa/genetics/*physiology/*ultrastructure ; Biological Evolution ; Citric Acid Cycle ; Cryptosporidium/genetics/physiology/ultrastructure ; Electron Transport Chain Complex Proteins/physiology ; Host-Parasite Interactions ; Humans ; Microscopy, Electron, Transmission ; Mitochondria/drug effects/genetics/*physiology/*ultrastructure ; Models, Biological ; Plasmodium/drug effects/genetics/physiology/ultrastructure ; Proton-Motive Force ; Toxoplasma/genetics/physiology/ultrastructure ; }, abstract = {Parasitic organisms have emerged from nearly every corner of the eukaryotic kingdom and hence display tremendous diversity of form and function. This diversity extends to their mitochondria and mitochondrion-derived organelles. While the principles of the chemiosmotic theory apply to all these pathogens, the differences from their hosts provide opportunities for therapeutic development. In this review we discuss examples of mitochondrial systems from a deep-branching phylum, Apicomplexa. Many important human pathogens, such as malaria parasites, belong to this phylum. Unique features of their mitochondria are validated targets for drugs that are selectively toxic to the parasites.}, }
@article {pmid18812322, year = {2008}, author = {Massey, SE}, title = {The proteomic constraint and its role in molecular evolution.}, journal = {Molecular biology and evolution}, volume = {25}, number = {12}, pages = {2557-2565}, doi = {10.1093/molbev/msn210}, pmid = {18812322}, issn = {1537-1719}, mesh = {Animals ; *Evolution, Molecular ; Mitochondria/chemistry ; Mutation ; Protein Biosynthesis ; Proteins/*chemistry ; Proteome/chemistry ; Recombination, Genetic ; Transcription, Genetic ; }, abstract = {Recently, the concept of a "Proteomic Constraint" was introduced to explain the frequency of genetic code deviations in mitochondrial genomes. The Proteomic Constraint was proposed to be proportional to the size of the mitochondrially encoded proteome, hence small proteomes are expected to experience smaller total numbers of errors resulting from genetic code deviations, leading to less likelihood of causing lethality. The concept is now extended to encompass several other aspects of the genetic information system. When the Proteomic Constraint is small, it is proposed that there is little selective pressure to evolve or maintain error correction mechanisms, as a result of the smaller total number of errors that accumulate. Conversely, a large Proteomic Constraint is proposed to result in a correspondingly large selective pressure to evolve or maintain error correction mechanisms. Differences in the size of the Proteomic Constraint can help to explain differences in replicational, transcriptional, and translational fidelities between genomes. A key piece of evidence is the existence of negative power law relationships between proteome size and error rates; these are demonstrated to be diagnostic of the action of the Proteomic Constraint. The Proteomic Constraint is argued to be a major factor determining mutation rates in a diverse range of DNA genomes, implying that mutation rates are clock like. A small Proteomic Constraint partly explains why RNA viruses possess high mutation rates. A reduced Proteomic Constraint in intracellular pathogenic bacteria predicts a drift upwards in mutation rates. Differences in the Proteomic Constraint also appear to be linked to differences in recombination rates between eukaryotes. In addition, a reduced Proteomic Constraint may explain features of resident genomes, such as loss of DNA repair pathways, increased substitution rates, and AT biases, in addition to the occurrence of genetic code deviations. Thus, it is argued that the Proteomic Constraint is a universal factor that influences a wide range of properties of the genetic information system.}, }
@article {pmid18809504, year = {2008}, author = {Chang, CH and Lin, SM and Chen, JH}, title = {Molecular systematics and phylogeography of the gigantic earthworms of the Metaphire formosae species group (Clitellata, Megascolecidae).}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {958-968}, doi = {10.1016/j.ympev.2008.08.025}, pmid = {18809504}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genes, rRNA ; *Genetic Speciation ; Likelihood Functions ; Markov Chains ; Mitochondria/genetics ; Models, Genetic ; Monte Carlo Method ; NADH Dehydrogenase/genetics ; Oligochaeta/classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Taiwan ; }, abstract = {The earthworms of the Metaphire formosae species group distributed in Taiwan are members of the Pheretima complex within the Megascolecidae. In this study, the systematics and phylogeography of this species group were investigated using DNA sequences of mitochondrial cytochrome c oxidase subunit I (COI), 16S ribosomal (r)RNA, and NADH dehydrogenase subunit 1 (ND1). The results indicated that the 13 taxa of the M. formosae species group form a clade, including a cryptic species discovered in this study. In addition, Metaphire hengchunensis (James, S.W., Shih, H.-T., Chang, H.-W., 2005. Seven new species of Amynthas (Clitellata: Megascolecidae) and new earthworm records from Taiwan. J. Nat. Hist. 39, 1007-1028) should be regarded as a subspecies of Metaphire paiwanna Tsai, C.-F., Shen, H.-P., Tsai, S.-C., 2000a. Native and exotic species of terrestrial earthworm (Oligochaeta) in Taiwan with reference to Northeast Asia. Zool. Stud. 39, 285-294, Tsai, C.-F., Tsai, S.-C., Liaw, G.-J., 2000b. Two new species of pontandric pheretimoid earthworms belonging to the genus Metaphire (Megascolecidae: Oligochaeta) from Taiwan. J. Nat. Hist. 34, 1731-1741, and Metaphire bununa glareosa Tsai et al. 2000 should be elevated to specific status. Phylogeographical inferences showed that allopatric speciation occurred in this species group during the rapid uplift of the main island of Taiwan between 5.0 and 2.5 million years ago. Our analysis exposes non-monophyly within each of the genera Amynthas and Metaphire, and more generally within the Pheretima complex. Further revisions of this speciose complex are urgently needed.}, }
@article {pmid18807925, year = {2008}, author = {Piechota, J and Jańska, H}, title = {[Evolution of the mitochondrial DNA and its expression system--comparison between animal and plant kingdom].}, journal = {Postepy biochemii}, volume = {54}, number = {2}, pages = {142-150}, pmid = {18807925}, issn = {0032-5422}, mesh = {Animals ; DNA, Mitochondrial/*genetics/*metabolism ; DNA, Plant/*genetics ; Eukaryotic Cells/*metabolism ; Evolution, Molecular ; Gene Expression/genetics ; Gene Expression Regulation, Developmental/genetics ; Gene Expression Regulation, Plant/*genetics ; Genome ; Plants/*genetics ; }, abstract = {The information about features of the Eukaryotic cells is maintained not only in the nucleus, but also in the extranuclear genomes localized in mitochondria and chloroplasts. Comparison between plant and animal mitochondrial genomes allows to perceive two extremely distinct evolution strategies. Animals clearly tend to reduce the size of the mitochondrial genome to the minimum. In accordance with this, the simplification in decoding of genetic information present in the genome is observed. On the contrary, plant mitochondrial genomes tend to increase their size. Accumulation of extraordinary solutions for maintaining and expression of genetic information present in the genome is the second distinctive feature of plant mitochondria.}, }
@article {pmid18805497, year = {2008}, author = {Kodama, Y and Yanagimoto, T and Shinohara, G and Hayashi, I and Kojima, S}, title = {Deviation age of a deep-sea demersal fish, Bothrocara hollandi, between the Japan Sea and the Okhotsk Sea.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {682-687}, doi = {10.1016/j.ympev.2008.08.022}, pmid = {18805497}, issn = {1095-9513}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Genes, Mitochondrial ; *Genetics, Population ; Haplotypes ; Japan ; Mitochondria/genetics ; Perciformes/*classification/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, }
@article {pmid18804544, year = {2008}, author = {Wüster, W and Peppin, L and Pook, CE and Walker, DE}, title = {A nesting of vipers: Phylogeny and historical biogeography of the Viperidae (Squamata: Serpentes).}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {445-459}, doi = {10.1016/j.ympev.2008.08.019}, pmid = {18804544}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Genes, rRNA ; Genetic Speciation ; Geography ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Venoms/genetics ; Viperidae/*classification/*genetics ; }, abstract = {Despite their medical interest, the phylogeny of the snake family Viperidae remains inadequately understood. Previous studies have generally focused either on the pitvipers (Crotalinae) or on the Old World vipers (Viperinae), but there has been no comprehensive molecular study of the Viperidae as a whole, leaving the affinities of key taxa unresolved. Here, we infer the phylogenetic relationships among the extant genera of the Viperidae from the sequences of four mitochondrial genes (cytochrome b, NADH subunit 4, 16S and 12S rRNA). The results confirm Azemiops as the sister group of the Crotalinae, whereas Causus is nested within the Viperinae, and thus not a basal viperid or viperine. Relationships among the major clades of Viperinae remain poorly resolved despite increased sequence information compared to previous studies. Bayesian molecular dating in conjunction with dispersal-vicariance analysis suggests an early Tertiary origin in Asia for the crown group Viperidae, and rejects suggestions of a relatively recent, early to mid-Tertiary origin of the Caenophidia.}, }
@article {pmid18804543, year = {2008}, author = {Kyriazi, P and Poulakakis, N and Parmakelis, A and Crochet, PA and Moravec, J and Rastegar-Pouyani, N and Tsigenopoulos, CS and Magoulas, A and Mylonas, M and Lymberakis, P}, title = {Mitochondrial DNA reveals the genealogical history of the snake-eyed lizards (Ophisops elegans and O. occidentalis) (Sauria: Lacertidae).}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {795-805}, doi = {10.1016/j.ympev.2008.08.021}, pmid = {18804543}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genes, rRNA ; Genetic Speciation ; Geography ; Likelihood Functions ; Lizards/classification/*genetics ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal, 16S ; Sequence Alignment ; Sequence Analysis, DNA ; Statistics, Nonparametric ; }, abstract = {The snake-eyed lizards of the genus Ophisops (Lacertidae) have been through a series of taxonomical revisions, but still their phylogenetic relationships remain uncertain. In the present study we estimate the phylogeographic structure of O. elegans across its distributional range and we evaluate the relationships between O. elegans and the sympatric, in North Africa, species O. occidentalis, using partial mtDNA sequences (16S rRNA, COI, and cyt b). All phylogenetic analyses produced topologically identical trees where extant populations of O. elegans and O. occidentalis were found polyphyletic. Taking into account all the potential causes of polyphyly (introgressive hybridization, incomplete lineage sorting, and imperfect taxonomy) we suggest the inaccurate taxonomy as the most likely explanation for the observed pattern. Our results stress the need for re-evaluation of the current taxonomical status of these species and their subspecies. Furthermore, our biogeographic analyses and the estimated time of divergences suggest a late Miocene diversification within these species, where the present distribution of O. elegans and O. occidentalis was the result of several dispersal and vicariant events, which are associated with climatic oscillations (the late Miocene aridification of Asia and northern Africa) and paleogeographic barriers of late Miocene and Pliocene period.}, }
@article {pmid18804542, year = {2008}, author = {Horne, JB and van Herwerden, L and Choat, JH and Robertson, DR}, title = {High population connectivity across the Indo-Pacific: Congruent lack of phylogeographic structure in three reef fish congeners.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {629-638}, doi = {10.1016/j.ympev.2008.08.023}, pmid = {18804542}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Female ; Gene Flow ; Genetic Speciation ; Genetic Variation ; *Genetics, Population ; Geography ; Likelihood Functions ; Markov Chains ; Mitochondria/genetics ; Models, Genetic ; Monte Carlo Method ; Pacific Ocean ; Perciformes/*classification/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {We used the mitochondrial control region and a comparative approach to study the genetic population structure of two surgeonfishes, Naso brevirostris and Naso unicornis, across their Indo-central Pacific ranges. Our purpose was to compare our results with those of a previous study of Naso vlamingii [Klanten, S.O., van Herwerden, L., Choat J.H., 2007. Extreme genetic diversity and temporal rather than spatial partitioning in a widely distributed coral reef fish. Mar. Biol. 150, 659-670] another widely distributed Indo-central Pacific Naso species. We found no evidence of a barrier to gene flow between the Indian and Pacific Oceans for either species, consistent with what was shown for N. vlamingii. Overall, both target species lacked spatial population partitions and probably have complex patterns of gene flow on several spatial scales. Despite the lack of geographic population structure distinct clades were observed in N. brevirostris, similar to those found in N. vlamingii. Coalescence times for intraspecific clades of N. brevirostris and N. vlamingii approximate each other, suggesting parallel evolutionary histories. A bimodal mismatch distribution in N. brevirostris indicates that a biogeographic barrier separated N. brevirostris populations sometime during its species history. Naso unicornis, in contrast, lacked genetic structure of any kind, although it has what could represent a single surviving clade. Congruent lack of spatial population structure among all three species suggest that such patterns are not due to stochastic processes of DNA mutation and are most likely driven by ecological and environmental factors.}, }
@article {pmid18804169, year = {2008}, author = {Blackburn, DC}, title = {Biogeography and evolution of body size and life history of African frogs: phylogeny of squeakers (Arthroleptis) and long-fingered frogs (Cardioglossa) estimated from mitochondrial data.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {806-826}, doi = {10.1016/j.ympev.2008.08.015}, pmid = {18804169}, issn = {1095-9513}, mesh = {Africa ; Animals ; Anura/classification/*genetics ; Bayes Theorem ; Body Size/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genes, rRNA ; Genetic Speciation ; Geography ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The evolutionary history of living African amphibians remains poorly understood. This study estimates the phylogeny within the frog genera Arthroleptis and Cardioglossa using approximately 2400 bases of mtDNA sequence data (12S, tRNA-Valine, and 16S genes) from half of the described species. Analyses are conducted using parsimony, maximum likelihood, and Bayesian methods. The effect of alignment on phylogeny estimation is explored by separately analyzing alignments generated with different gap costs and a consensus alignment. The consensus alignment results in species paraphyly, low nodal support, and incongruence with the results based on other alignments, which produced largely similar results. Most nodes in the phylogeny are highly supported, yet several topologies are inconsistent with previous hypotheses. The monophyly of Cardioglossa and of miniature species previously assigned to Schoutedenella was further examined using Templeton and Shimodaira-Hasegawa tests. Cardioglossa monophyly is rejected and C. aureoli is transferred to Arthroleptis. These tests do not reject Schoutedenella monophyly, but this hypothesis receives no support from non-parametric bootstrapping or Bayesian posterior probabilities. This phylogeny provides a framework for reconstructing historical biogeography and analyzing the evolution of body size and life history. Direct development and miniaturization appear at the base of Arthroleptis phylogeny concomitant with a range expansion from Central Africa to throughout most of sub-Saharan Africa.}, }
@article {pmid18801447, year = {2008}, author = {Zhang, P and Papenfuss, TJ and Wake, MH and Qu, L and Wake, DB}, title = {Phylogeny and biogeography of the family Salamandridae (Amphibia: Caudata) inferred from complete mitochondrial genomes.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {586-597}, doi = {10.1016/j.ympev.2008.08.020}, pmid = {18801447}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genetic Speciation ; *Genome, Mitochondrial ; Geography ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; Salamandridae/*classification/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Phylogenetic relationships of members of the salamander family Salamandridae were examined using complete mitochondrial genomes collected from 42 species representing all 20 salamandrid genera and five outgroup taxa. Weighted maximum parsimony, partitioned maximum likelihood, and partitioned Bayesian approaches all produce an identical, well-resolved phylogeny; most branches are strongly supported with greater than 90% bootstrap values and 1.0 Bayesian posterior probabilities. Our results support recent taxonomic changes in finding the traditional genera Mertensiella, Euproctus, and Triturus to be non-monophyletic species assemblages. We successfully resolved the current polytomy at the base of the salamandrid tree: the Italian newt genus Salamandrina is sister to all remaining salamandrids. Beyond Salamandrina, a clade comprising all remaining newts is separated from a clade containing the true salamanders. Among these newts, the branching orders of well-supported clades are: primitive newts (Echinotriton, Pleurodeles, and Tylototriton), New World newts (Notophthalmus-Taricha), Corsica-Sardinia newts (Euproctus), and modern European newts (Calotriton, Lissotriton, Mesotriton, Neurergus, Ommatotriton, and Triturus) plus modern Asian newts (Cynops, Pachytriton, and Paramesotriton).Two alternative sets of calibration points and two Bayesian dating methods (BEAST and MultiDivTime) were used to estimate timescales for salamandrid evolution. The estimation difference by dating methods is slight and we propose two sets of timescales based on different calibration choices. The two timescales suggest that the initial diversification of extant salamandrids took place in Europe about 97 or 69Ma. North American salamandrids were derived from their European ancestors by dispersal through North Atlantic Land Bridges in the Late Cretaceous (approximately 69Ma) or Middle Eocene (approximately 43Ma). Ancestors of Asian salamandrids most probably dispersed to the eastern Asia from Europe, after withdrawal of the Turgai Sea (approximately 29Ma).}, }
@article {pmid18799135, year = {2008}, author = {Schwaninger, HR}, title = {Global mitochondrial DNA phylogeography and biogeographic history of the antitropically and longitudinally disjunct marine bryozoan Membranipora membranacea L. (Cheilostomata): another cryptic marine sibling species complex?.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {893-908}, doi = {10.1016/j.ympev.2008.08.016}, pmid = {18799135}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Bryozoa/classification/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Gene Flow ; Genes, Mitochondrial ; *Genetic Speciation ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The origin of disjunct distributions in high dispersal marine taxa remains an important evolutionary question as it relates to the formation of new species in an environment where barriers to gene flow are not always obvious. To reconstruct the relationships and phylogeographic history of the antitropically and longitudinally disjunct bryozoan Membranipora membranacea populations were surveyed with mtDNA cytochrome oxidase 1 (COI) sequences across its cosmopolitan range. Maximum parsimony, maximum likelihood and Bayesian genealogies revealed three deep clades in the North Pacific and one monophyletic clade each in the southeast Pacific (Chile), southwest Pacific (Australia/New Zealand), North Atlantic and southeast Atlantic (South Africa). Human-mediated dispersal has not impacted M. membranacea's large-scale genetic structure. M. membranacea did not participate in the trans-arctic interchange. Episodic long-distance dispersal, combined with climatic vicariance can explain the disjunct distribution. Dispersal led southward across the tropics perhaps 13 mya in the East Pacific and again northwards perhaps 6 mya in the Eastern Atlantic to colonize the North Atlantic from the south, and along the West Wind Drift to colonize Australia. The clades differentiated over evolutionary time in their respective ocean region, potentially forming a sibling species complex. The taxonomic status of the clades is discussed.}, }
@article {pmid18795352, year = {2009}, author = {Shen, YQ and Burger, G}, title = {Plasticity of a key metabolic pathway in fungi.}, journal = {Functional &amp; integrative genomics}, volume = {9}, number = {2}, pages = {145-151}, pmid = {18795352}, issn = {1438-7948}, mesh = {Evolution, Molecular ; Fatty Acids/*metabolism ; Fungal Proteins/genetics/metabolism ; Fungi/classification/genetics/*metabolism ; Genome, Fungal ; Mitochondria/metabolism ; Oxidation-Reduction ; Peroxisomes/metabolism ; Phylogeny ; }, abstract = {Beta oxidation is the principal metabolic pathway for fatty acid degradation. The pathway is virtually universally present throughout eukaryotes yet displays different forms in enzyme architecture, substrate specificity, and subcellular location. In this review, we examine beta oxidation across the fungal kingdom by conducting a large-scale in silico screen and localization prediction for all relevant enzymes in >50 species. The survey reveals that fungi exhibit an astounding diversity of beta oxidation pathways and shows that the combined presence of distinct mitochondrial and peroxisomal pathways is the prevailing and likely ancestral type of beta oxidation in fungi. In addition, the available information indicates that the mitochondrial pathway was lost in the common ancestor of Saccharomycetes. Finally, we infer the existence of a hybrid peroxisomal pathway in several Sordariomycetes, including Neurospora crassa. In these cases, a typically mitochondrion-located enzyme compensates for the lack of a peroxisomal one.}, }
@article {pmid18795098, year = {2008}, author = {Fukami, H and Chen, CA and Budd, AF and Collins, A and Wallace, C and Chuang, YY and Chen, C and Dai, CF and Iwao, K and Sheppard, C and Knowlton, N}, title = {Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria).}, journal = {PloS one}, volume = {3}, number = {9}, pages = {e3222}, pmid = {18795098}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*genetics/*physiology ; Bayes Theorem ; Cell Nucleus/*metabolism ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; Evolution, Molecular ; Fossils ; Genes, Mitochondrial ; Mitochondria/metabolism ; Models, Statistical ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ss-tubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent "robust" and "complex" clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils.}, }
@article {pmid18794572, year = {2009}, author = {Diz, AP and Dudley, E and MacDonald, BW and Piña, B and Kenchington, EL and Zouros, E and Skibinski, DO}, title = {Genetic variation underlying protein expression in eggs of the marine mussel Mytilus edulis.}, journal = {Molecular &amp; cellular proteomics : MCP}, volume = {8}, number = {1}, pages = {132-144}, pmid = {18794572}, issn = {1535-9484}, mesh = {Analysis of Variance ; Animals ; Confidence Intervals ; Databases, Protein ; Electrophoresis, Gel, Two-Dimensional ; Female ; *Genetic Variation ; Mass Spectrometry ; Mytilus edulis/*metabolism ; Ovum/*metabolism ; Proteins/chemistry/*genetics/*metabolism ; Proteome/analysis ; }, abstract = {Study of the genetic basis of gene expression variation is central to attempts to understand the causes of evolutionary change. Although there are many transcriptomics studies estimating genetic variance and heritability in model organisms such as humans there is a lack of equivalent proteomics studies. In the present study, the heritability underlying egg protein expression was estimated in the marine mussel Mytilus. We believe this to be the first such measurement of genetic variation for gene expression in eggs of any organism. The study of eggs is important in evolutionary theory and life history analysis because maternal effects might have profound effects on the rate of evolution of offspring traits. Evidence is presented that the egg proteome varies significantly between individual females and that heritability of protein expression in mussel eggs is moderate to high suggesting abundant genetic variation on which natural selection might act. The study of the mussel egg proteome is also important because of the unusual system of mitochondrial DNA inheritance in mussels whereby different mitochondrial genomes are transmitted independently through female and male lineages (doubly uniparental inheritance). It is likely that the mechanism underlying this system involves the interaction of specific egg factors with sperm mitochondria following fertilization, and its elucidation might be advanced by study of the proteome in females having different progeny sex ratios. Putative identifications are presented here for egg proteins using MS/MS in Mytilus lines differing in sex ratio. Ontology terms relating to stress response and protein folding occur more frequently for proteins showing large expression differences between the lines. The distribution of ontology terms in mussel eggs was compared with those for previous mussel proteomics studies (using other tissues) and with mammal eggs. Significant differences were observed between mussel eggs and mussel tissues but not between the two types of eggs.}, }
@article {pmid18794174, year = {2008}, author = {Zhu, Y and Saraike, T and Yamamoto, Y and Hagita, H and Takumi, S and Murai, K}, title = {orf260cra, a novel mitochondrial gene, is associated with the homeotic transformation of stamens into pistil-like structures (pistillody) in alloplasmic wheat.}, journal = {Plant &amp; cell physiology}, volume = {49}, number = {11}, pages = {1723-1733}, doi = {10.1093/pcp/pcn143}, pmid = {18794174}, issn = {1471-9053}, mesh = {Amino Acid Sequence ; Cytoplasm/genetics/metabolism ; DNA, Complementary/genetics ; DNA, Mitochondrial/genetics ; Flowers/genetics/*growth &amp; development ; Gene Expression Regulation, Plant ; Genes, Mitochondrial ; Genes, Plant ; Mitochondria/genetics ; Mitochondrial Proteins/genetics/*metabolism ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Plant Proteins/genetics/*metabolism ; RNA, Plant/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, Protein ; Triticum/*genetics/growth &amp; development ; }, abstract = {Homeotic transformation of stamens into pistil-like structures (pistillody) can occur in cytoplasmic substitution (alloplasmic) lines of bread wheat (Triticum aestivum) that have the cytoplasm of the related species, Aegilops crassa. Previously we showed that pistillody results from altered patterns of expression of class B MADS-box genes mediated by mitochondrial gene(s) in the Ae. crassa cytoplasm. The wheat cultivar Chinese Spring does not show pistillody when Ae. crassa cytoplasm is introduced. The absence of an effect is due to a single dominant gene (designated Rfd1) located on the long arm of chromosome 7B. To identify the mitochondrial gene involved in pistillody induction, we performed a subtraction analysis using cDNAs derived from young spikes of a pistillody line and a normal line. We found that mitochondrial cDNA clone R04 was abundant in the young spikes of the pistillody line but was down-regulated in the normal line that carried nuclear Rfd1. Sequencing of the full-length cDNA corresponding to clone R04 showed that two genes were present, cox I (cytochrome c oxidase subunit I) and orf260(cra). orf260(cra) shows high sequence similarity to orf256, the T. timopheevii mitochondrial gene responsible for cytoplasmic male sterility (CMS). orf260(cra) was also present in the cytoplasms of Ae. juvenalis and Ae. vavilovii, which induce pistillody, but not in the cytoplasms of other species not associated with pistillody. Furthermore, Western blot analysis revealed that the ORF260cra protein was more abundant in the pistillody line than in the normal line. We suggest therefore that orf260(cra) is associated with pistillody induction.}, }
@article {pmid18793735, year = {2008}, author = {Kutty, SN and Pape, T and Pont, A and Wiegmann, BM and Meier, R}, title = {The Muscoidea (Diptera: Calyptratae) are paraphyletic: Evidence from four mitochondrial and four nuclear genes.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {639-652}, doi = {10.1016/j.ympev.2008.08.012}, pmid = {18793735}, issn = {1095-9513}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Diptera/*classification/*genetics ; *Evolution, Molecular ; Genes, Insect ; Genes, Mitochondrial ; Genetic Speciation ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Approximately 5% of the known species-level diversity of Diptera belongs to the Muscoidea with its approximately 7000 described species. Despite including some of the most abundant and well known flies, the phylogenetic relationships within this superfamily are poorly understood. Previous attempts at reconstructing the relationships based on morphology and relatively small molecular data sets were only moderately successful. Here, we use molecular data for 127 exemplar species of the Muscoidea, two species from the Hippoboscoidea, ten species representing the Oestroidea and seven outgroup species from four acalyptrate superfamilies. Four mitochondrial genes 12S, 16S, COI, and Cytb, and four nuclear genes 18S, 28S, Ef1a, and CAD are used to reconstruct the relationships within the Muscoidea. The length-variable genes were aligned using a guide tree that was based on the protein-encoding genes and the indel-free sections of the ribosomal genes. We found that, based on topological considerations, this guide tree was a significant improvement over the default guide trees generated by ClustalX. The data matrix was analyzed using maximum parsimony (MP) and maximum likelihood (ML) and yielded very similar tree topologies. The Calyptratae are monophyletic and the Hippoboscoidea are the sister group to the remaining calyptrates (MP). The Muscoidea are paraphyletic with a monophyletic Oestroidea nested within the Muscoidea as sister group to Anthomyiidae+Scathophagidae. The monophyly of three of the four recognized families in the Muscoidea is confirmed: the Fanniidae, Muscidae, and Scathophagidae. However, the Anthomyiidae are possibly paraphyletic. Within the Oestroidea, the Sarcophagidae and Tachinidae are sister groups and the Calliphoridae are paraphyletic.}, }
@article {pmid18792899, year = {2008}, author = {Gochhait, S and Bhatt, A and Sharma, S and Singh, YP and Gupta, P and Bamezai, RN}, title = {Concomitant presence of mutations in mitochondrial genome and p53 in cancer development - a study in north Indian sporadic breast and esophageal cancer patients.}, journal = {International journal of cancer}, volume = {123}, number = {11}, pages = {2580-2586}, doi = {10.1002/ijc.23817}, pmid = {18792899}, issn = {1097-0215}, mesh = {Breast Neoplasms/epidemiology/*genetics/pathology ; Esophageal Neoplasms/epidemiology/*genetics/pathology ; Genome, Mitochondrial/*genetics ; Humans ; India/epidemiology ; Mutation/genetics ; Neoplasm Staging ; Phylogeny ; Tumor Suppressor Protein p53/*genetics ; }, abstract = {Mitochondrial DNA alterations in recent years have been suggested as modifier events, providing a possible proliferative advantage to the tumor cells. In order to provide further insight into the process of tumorigenesis, a study of whole mitochondria genome was conducted in 134 tissue samples obtained from 2 unrelated cancers (tumor and adjacent normal tissues from 36 breast cancer and 31 esophageal squamous cell carcinoma (ESCC) patients) with known p53 somatic mutation background. Fifteen of 36 (41.66%) breast and 12 of 31 (38.71%) ESCC tumors were found to contain at least 1 mtDNA somatic mutation, which correlated significantly with the concomitant presence of somatic mutation in DNA binding domain of the p53 gene (Breast cancer, p = 0.006; ESCC, p = 0.002). Interestingly, mutations in the non D-loop region of the mtDNA contributed significantly (Breast cancer, p = 0.004; ESCC, p = 0.032) in comparison to the hotspot-D-Loop-region. The concomitant presence of mutations in p53 and mtDNA were also predominant in breast cancer tumors with poor prognosis, that is, with the advanced stage, grade and the ER/PR negativity. Also, the observation made was apparently well explained in 10398A bearing N haplogroup genetic background with increased presence of novel and pathogenic germline mutation in mtDNA. Our study suggests that the concomitant presence of somatic alteration in mtDNA and the DNA binding domain of the p53 gene facilitates cell survival and tumorigenesis, requiring specialized therapeutic intervention because of a possible resistance to conventional chemotherapy.}, }
@article {pmid18789390, year = {2008}, author = {Möller, LM and Bilgmann, K and Charlton-Robb, K and Beheregaray, L}, title = {Multi-gene evidence for a new bottlenose dolphin species in southern Australia.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {674-681}, doi = {10.1016/j.ympev.2008.08.011}, pmid = {18789390}, issn = {1095-9513}, mesh = {Alleles ; Animals ; Australia ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Dolphins/*classification/*genetics ; Evolution, Molecular ; Gene Flow ; Genes, Mitochondrial ; Genetic Markers ; *Genetic Speciation ; Haplotypes ; Microsatellite Repeats ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, }
@article {pmid18784206, year = {2008}, author = {Lluís, M and Nogué, S and Miró, O}, title = {Severe acute poisoning due to a glufosinate containing preparation without mitochondrial involvement.}, journal = {Human &amp; experimental toxicology}, volume = {27}, number = {6}, pages = {519-524}, doi = {10.1177/0960327108092291}, pmid = {18784206}, issn = {0960-3271}, mesh = {Adult ; Aminobutyrates/blood/*poisoning ; Electrocardiography ; Female ; Gastric Lavage ; Heart/drug effects/physiopathology ; Herbicides/blood/*poisoning ; Humans ; Lymphocytes/drug effects/enzymology ; Mitochondria/drug effects/enzymology ; Poisoning/blood/*etiology/therapy ; Respiration, Artificial ; Suicide, Attempted ; Treatment Outcome ; }, abstract = {Glufosinate is a non-selective herbicide widely used in domestic gardens and agriculture. Few cases of glufosinate poisoning have been reported although there has been an increase in recent years, particularly in Japan. Glufosinate toxicity is related to its capacity to inhibit glutamine synthetase and glutamate decarboxylase, which may lead to a potentially fatal multiorgan failure. We report the case of a 41-year-old woman who ingested between 30 and 50 mL of a herbicide (Finale) containing glufosinate (14%) in a suicide attempt. One hour after ingestion, the patient attended the Emergency Department of her own volition. Her overall status was good, and the physical examination was unremarkable. Gastric lavage was carried out, 25 g of activated charcoal was administered, and the patient was admitted for observation. Seventeen hours later, the patient presented drowsiness and a sinus bradycardia of 40 bpm. Thirty-two hours after ingestion, the Glasgow Coma Score was 8, and orotracheal intubation and mechanical ventilation were begun. At 3 days, the patient presented a self-limiting episode of ventricular tachycardia. She recovered consciousness progressively and was extubated without complications. The evolution was favorable, but the sinus bradycardia persisted up to 8 days after the ingestion. A study of lymphocyte mitochondrial function showed no alteration in mitochondrial oxidative capacity or the enzymatic activity of the complexes of the electron transport chain. A small ingestion of glufosinate can cause severe poisoning, whose manifestations predominantly involve the central nervous system and heart rhythm. Signs and symptoms may not appear for several hours and may persist for several days. In spite of these multi-organ manifestations, no alteration in lymphocyte mitochondrial function has been reported.}, }
@article {pmid18783734, year = {2008}, author = {Duda, TF and Bolin, MB and Meyer, CP and Kohn, AJ}, title = {Hidden diversity in a hyperdiverse gastropod genus: discovery of previously unidentified members of a Conus species complex.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {867-876}, doi = {10.1016/j.ympev.2008.08.009}, pmid = {18783734}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Conotoxins/genetics ; Conus Snail/anatomy &amp; histology/classification/*genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genes, rRNA ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Molecular sequence data are a powerful tool for delimiting species, particularly in cases where morphological differences are obscure. Distinguishing species in the Conus sponsalis complex of tropical marine gastropods has long been difficult, because descriptions and identification has relied exclusively on shell characters, primarily color patterns, and these often appear to intergrade among putative species. Here we use molecular sequence data from two mitochondrial gene regions (16S rRNA and cytochrome oxidase subunit I) and one nuclear locus (a four-loop conotoxin gene) to characterize the genetic discontinuity of the nominal species of this group currently accepted as valid: the Indo-West Pacific C. sponsalis, C. nanus, C. ceylanensis, C. musicus and C. parvatus, and the eastern Pacific C. nux. In these analyses C. nanus and C. sponsalis resolve quite well and appear to represent distinct evolutionary units that are mostly congruent with morphology-based distinctions. We also identified several cryptic entities whose genetic uniqueness suggests species-level distinctions. Two of these fit the original description of C. sponsalis; three forms appear to represent C. nanus but differ in adult shell size or possess a unique shell color pattern.}, }
@article {pmid18779329, year = {2008}, author = {Chacinska, A and Guiard, B and Müller, JM and Schulze-Specking, A and Gabriel, K and Kutik, S and Pfanner, N}, title = {Mitochondrial biogenesis, switching the sorting pathway of the intermembrane space receptor Mia40.}, journal = {The Journal of biological chemistry}, volume = {283}, number = {44}, pages = {29723-29729}, pmid = {18779329}, issn = {0021-9258}, mesh = {Animals ; Humans ; Membrane Potentials ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/*chemistry ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/genetics ; Models, Biological ; Oxidation-Reduction ; Phylogeny ; Protein Structure, Tertiary ; Protein Transport/genetics ; Recombinant Proteins/chemistry ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/*chemistry ; Temperature ; }, abstract = {Mitochondrial precursor proteins are directed into the intermembrane space via two different routes, the presequence pathway and the redox-dependent MIA pathway. The pathways were assumed to be independent and transport different proteins. We report that the intermembrane space receptor Mia40 can switch between both pathways. In fungi, Mia40 is synthesized as large protein with an N-terminal presequence, whereas in metazoans and plants, Mia40 consists only of the conserved C-terminal domain. Human MIA40 and the C-terminal domain of yeast Mia40 (termed Mia40(core)) rescued the viability of Mia40-deficient yeast independently of the presence of a presequence. Purified Mia40(core) was imported into mitochondria via the MIA pathway. With cells expressing both full-length Mia40 and Mia40(core), we demonstrate that yeast Mia40 contains dual targeting information, directing the large precursor onto the presequence pathway and the smaller Mia40(core) onto the MIA pathway, raising interesting implications for the evolution of mitochondrial protein sorting.}, }
@article {pmid18779178, year = {2008}, author = {Hao, RC and Zan, LS and Liu, CS and Wang, ZG and Zhang, GX and Han, X and Hao, HZ and Wang, J and DU, XY}, title = {[Genetic diversity and origin of mitochondrial DNA D-loop region for some domestic goat breeds of China].}, journal = {Yi chuan = Hereditas}, volume = {30}, number = {9}, pages = {1187-1194}, doi = {10.3724/sp.j.1005.2008.01187}, pmid = {18779178}, issn = {0253-9772}, mesh = {Animals ; Animals, Domestic/genetics ; China ; DNA, Mitochondrial/analysis/chemistry/*genetics ; Evolution, Molecular ; Genetic Variation ; Goats/*genetics ; Haplotypes ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Sequence Analysis, DNA ; }, abstract = {The complete sequences of mitochondrial DNA D-loop of 140 individuals in 10 Chinese goat (Capra hiruc) breeds were analyzed by DNA sequencing technology. The results showed that the length of mtDNA D-loop in Chinese goats was 1 211-1 213 bp. There were 84 different haplotypes and 171 polymorphic sites. The mean nucleotide diversity (Pi) and haplotype diversity (Hd) were 0.02063+/+0.00225 and 0.988+/-0.003, respectively, and the average number of nucleotide differences (k) was 24.896. The results showed an abundant genetic diversity in domestic goats of China. The NJ tree indicated that there were two main branches in Chinese domestic goats, thereinto, one branch was clustered with Capra aegagrus, and Capra falconeri was clustered alone, which indicated that Capra aegagrus had more contribution to Chinese domestic goat breeds.}, }
@article {pmid18778782, year = {2008}, author = {Barth, D and Przyboś, E and Fokin, SI and Schlegel, M and Berendonk, TU}, title = {Cytochrome b sequence data suggest rapid speciation within the Paramecium aurelia species complex.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {669-673}, doi = {10.1016/j.ympev.2008.08.007}, pmid = {18778782}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cytochromes b/*genetics ; DNA, Mitochondrial/genetics ; DNA, Protozoan/genetics ; *Evolution, Molecular ; Fluorides ; Genes, Mitochondrial ; Genes, Protozoan ; *Genetic Speciation ; Likelihood Functions ; Methacrylates ; Mitochondria/genetics ; Models, Genetic ; Paramecium aurelia/*genetics ; *Phylogeny ; Polyurethanes ; Sequence Analysis, DNA ; }, abstract = {We investigated mitochondrial Cytochrome b sequences from all 15 members of the enigmatic Paramecium aurelia species complex (Ciliophora). The analysis revealed high genetic distances between the different P. aurelia species (6.1-19.8%) and a largely unresolved, star-like phylogenetic tree. This result strongly supports a rapid radiation in the evolutionary history of this species complex and it correlates well with the hypothesis that the extant species diversity may have originated from the neutral consequences of a whole genome duplication in the common ancestor of P. aurelia.}, }
@article {pmid18765437, year = {2008}, author = {Pérez-Brocal, V and Clark, CG}, title = {Analysis of two genomes from the mitochondrion-like organelle of the intestinal parasite Blastocystis: complete sequences, gene content, and genome organization.}, journal = {Molecular biology and evolution}, volume = {25}, number = {11}, pages = {2475-2482}, pmid = {18765437}, issn = {1537-1719}, support = {/WT_/Wellcome Trust/United Kingdom ; 078566/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Blastocystis/classification/*genetics ; Chromosome Mapping ; DNA, Protozoan ; Evolution, Molecular ; Genes, Protozoan ; *Genome, Protozoan ; Humans ; Intestines/parasitology ; Mitochondria/genetics ; Organelles/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Acquisition of mitochondria by the ancestor of all living eukaryotes represented a crucial milestone in the evolution of the eukaryotic cell. Nevertheless, a number of anaerobic unicellular eukaryotes have secondarily discarded certain mitochondrial features, leading to modified organelles such as hydrogenosomes and mitosomes via degenerative evolution. These mitochondrion-derived organelles have lost many of the typical characteristics of aerobic mitochondria, including certain metabolic pathways, morphological traits, and, in most cases, the organellar genome. So far, the evolutionary pathway leading from aerobic mitochondria to anaerobic degenerate organelles has remained unclear due to the lack of examples representing intermediate stages. The human parasitic stramenopile Blastocystis is a rare example of an anaerobic eukaryote with organelles that have retained some mitochondrial characteristics, including a genome, whereas they lack others, such as cytochromes. Here we report the sequence and comparative analysis of the organellar genome from two different Blastocystis isolates as well as a comparison to other genomes from stramenopile mitochondria. Analysis of the characteristics displayed by the unique Blastocystis organelle genome gives us an insight into the initial evolutionary steps that may have led from mitochondria to hydrogenosomes and mitosomes.}, }
@article {pmid18765231, year = {2008}, author = {Xiong, AS and Peng, RH and Zhuang, J and Gao, F and Zhu, B and Fu, XY and Xue, Y and Jin, XF and Tian, YS and Zhao, W and Yao, QH}, title = {Gene duplication and transfer events in plant mitochondria genome.}, journal = {Biochemical and biophysical research communications}, volume = {376}, number = {1}, pages = {1-4}, doi = {10.1016/j.bbrc.2008.08.116}, pmid = {18765231}, issn = {1090-2104}, mesh = {*Evolution, Molecular ; *Gene Duplication ; *Genes, Mitochondrial ; *Genome, Plant ; }, abstract = {Gene or genome duplication events increase the amount of genetic material available to increase the genomic, and thereby phenotypic, complexity of organisms during evolution. Gene duplication and transfer events have been important to molecular evolution in all three domains of life, and may be the first step in the emergence of new gene functions. Gene transfer events have been proposed as another accelerator of evolution. The duplicated gene or genome, mainly nuclear, has been the subject of several recent reviews. In addition to the nuclear genome, organisms have organelle genomes, including mitochondrial genome. In this review, we briefly summarize gene duplication and transfer events in the plant mitochondrial genome.}, }
@article {pmid18762435, year = {2008}, author = {Farias, IP and Hrbek, T}, title = {Patterns of diversification in the discus fishes (Symphysodon spp. Cichlidae) of the Amazon basin.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {32-43}, doi = {10.1016/j.ympev.2008.05.033}, pmid = {18762435}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cichlids/*classification/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genes, RAG-1 ; Genetic Speciation ; Genetics, Population ; Haplotypes ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; Phenotype ; *Phylogeny ; Rivers ; Sequence Alignment ; Sequence Analysis, DNA ; South America ; Species Specificity ; }, abstract = {We carried out a phylogeograhic and population genetic analysis of fishes of the taxonomically contentious genus Symphysodon from the Amazon basin in order to test hypotheses of relationships among taxonomic units, and potential processes driving diversification within this genus. We sampled 334 individuals of the genus Symphysodon from 24 localities that span the complete geographic distribution of this genus. The sampling scheme included all known phenotypic groups, species and subspecies. Analyses were based on 474 bp of the mitochondrial control region and 1443 bp of the exon 3 of RAG1 gene. We observed 102 mtDNA haplotypes defined by 89 segregating sites, and 5 nuDNA alleles defined by three segregating sites. Maximum-likelihood, Bayesian-inference and statistical parsimony analyses revealed three well defined monophyletic groups. These clades corresponded to the 'green' and 'blue' groups of Symphysodon aequifasciatus, and to a previously morphologically unrecognized clade from the Xingu River drainage. These three clades were nested within a paraphyletic assemblage consisting of the 'brown' group of S. aequifasciatus and of both described subspecies of S. discus, the 'Heckel' and the 'abacaxi' discus. Nuclear allele sharing was observed among groups, but there were significant differences in frequencies. We inferred several processes including past fragmentation among groups, and restricted gene flow with isolation by distance within the paraphyletic 'brown+Heckel+abacaxi' groups, and suggest that differences among the 'blue', 'Heckel' and 'brown' groups are potentially maintained by differences in water chemistry preferences. We further inferred colonization of the western Amazon basin by an ancestor of the 'green' clade. The 'green' group was the only group with a pattern of haplotype distribution consistent of a demographic expansion, and the divergence of this clade from other groups of discus was consistent with recent geologic evidence on the breach of the Purus Arch which separates western Amazon from eastern Amazon. We further hypothesized that the differentiation of the 'Xingu' clade could be due to vicariance events resulting from Pleistocene sea level, and thus Amazon River level fluctuations. We discuss the bearings of our results on the current taxonomy of this group, and on the biological reality of the different forms, subspecies and species of Symphysodon concluding that we are probably observing a process of diversification, and therefore taxonomy will remain contentious.}, }
@article {pmid18762260, year = {2008}, author = {Hourlay, F and Libois, R and D'Amico, F and Sarà, M and O'Halloran, J and Michaux, JR}, title = {Evidence of a highly complex phylogeographic structure on a specialist river bird species, the dipper (Cinclus cinclus).}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {435-444}, doi = {10.1016/j.ympev.2008.07.025}, pmid = {18762260}, issn = {1095-9513}, mesh = {Animals ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Europe ; Evolution, Molecular ; Genes, Mitochondrial ; Genetic Markers ; Genetic Variation ; *Genetics, Population ; Geography ; Likelihood Functions ; Mitochondria/genetics ; Passeriformes/*classification/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {This study details the phylogeographic pattern of the white-throated dipper (Cinclus cinclus), a Palearctic, temperate, passerine bird that is exclusively associated with flowing water. Our results reveal a complex phylogeographic structure with at least five distinct lineages for the Western Palearctic region. As for many species of the Western Palearctic fauna and flora, this genetic structure is probably linked to the isolation of populations in different southern refuges during glacial periods. Furthermore, the isolation of populations in Scandinavia and/or Eastern regions, but also in Morocco and probably in Corsica, was accentuated by ecological and biogeographic barriers during Quaternary interglacial periods. During glacial periods, Italy, Sicily and the Balkano-Carpathian region acted as major refuge zones for the dipper. At the end of the last ice age, Western Europe was repopulated by dippers from an Italian refuge, while Eastern Europe was recolonised by Balkano-Carpathian birds. A large contact zone between these two lineages was evidenced and extends from Luxembourg to Hungary. Finally, our results indicate the need to clarify the taxonomic status of the dipper, especially concerning the European subspecies whose validity appears uncertain.}, }
@article {pmid18761095, year = {2008}, author = {Phillips, CB and Vink, CJ and Blanchet, A and Hoelmer, KA}, title = {Hosts are more important than destinations: What genetic variation in Microctonus aethiopoides (Hymenoptera: Braconidae) means for foreign exploration for natural enemies.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {467-476}, doi = {10.1016/j.ympev.2008.08.005}, pmid = {18761095}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Coleoptera/*physiology ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Insect ; Genes, Mitochondrial ; Genes, rRNA ; *Genetic Variation ; Geography ; Haplotypes ; Insect Control ; Mitochondria/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; Wasps/*genetics/physiology ; }, abstract = {Nucleotide sequence data were generated from the gene regions COI, 16S, and arginine kinase to assess genetic variation within the Palearctic parasitoid, Microctonus aethiopoides, reared from Sitona discoideus, S. hispidulus, and Hypera postica collected from two proximate locations in Mediterranean France. Partitioned Bayesian phylogenetic analyses of the molecular data provided strong support for the presence of at least two M. aethiopoides biotypes, one associated with Hypera species and the other with Sitona species. These new results combined with previously published data from 14 countries show that M. aethiopoides genetic variation is much more strongly correlated with host taxon than with sampling location. This contrasts with earlier perceptions that M. aethiopoides exhibits significant geographic variation, and helps to explain the widely varying biological control outcomes that have been obtained following the introductions of M. aethiopoides to Australia, New Zealand, and North America. The results strongly suggest that success rates and environmental safety in biological control would both be improved by ensuring that parasitoids collected in the native range are reared from the same host species as the one being targeted for control in the region of introduction. The results also provided insights both on the evolution of M. aethiopoides' host range, and on its evolutionary transition between solitary and gregarious larval development.}, }
@article {pmid18760371, year = {2008}, author = {Naro-Maciel, E and Le, M and FitzSimmons, NN and Amato, G}, title = {Evolutionary relationships of marine turtles: A molecular phylogeny based on nuclear and mitochondrial genes.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {659-662}, doi = {10.1016/j.ympev.2008.08.004}, pmid = {18760371}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genetic Markers ; Markov Chains ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Turtles/*classification/*genetics ; }, }
@article {pmid18756777, year = {2008}, author = {Rudakov, NV}, title = {[Taxonometry, ecology and evolutional relation of rickettsia].}, journal = {Vestnik Rossiiskoi akademii meditsinskikh nauk}, volume = {}, number = {7}, pages = {10-15}, pmid = {18756777}, issn = {0869-6047}, mesh = {Animals ; *Biological Evolution ; *Environment ; Humans ; Rickettsia/*classification/isolation &amp; purification ; Rickettsia Infections/*parasitology ; }, abstract = {Ecology of Rickettsia is main direction of researches of RAMS academician I. V. Tarasevich and her team. Characteristics of alpha 1-Protobacteriae--parasites of eukaryotic cells--given in the work. The accent to Rickettsia characteristics in relation of their evolution relationship with eukaryote mitochondria is made. Main directions of researches in Q-fever, Tsutsugamushi fever, rickettsioses of tick-borne spotted fever (TSF) group, performed in our country under direction of RAMS academician I. V. Tarasevich, are represented. Results of study with the use of tick experimental model, monoclonal antibodies and genetical methods of TSF group Rickettsia, revealed in Siberia and Far East (focal territories of tick-born rickettsioses) and also in territories with the absence of this infection in Russia and Kazakhstan, are given.}, }
@article {pmid18755282, year = {2008}, author = {Binford, GJ and Callahan, MS and Bodner, MR and Rynerson, MR and Núñez, PB and Ellison, CE and Duncan, RP}, title = {Phylogenetic relationships of Loxosceles and Sicarius spiders are consistent with Western Gondwanan vicariance.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {538-553}, doi = {10.1016/j.ympev.2008.08.003}, pmid = {18755282}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Insect ; Genes, Mitochondrial ; Genes, rRNA ; Markov Chains ; Mitochondria/genetics ; Models, Genetic ; Monte Carlo Method ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 28S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Spiders/*classification/*genetics ; }, abstract = {The modern geographic distribution of the spider family Sicariidae is consistent with an evolutionary origin on Western Gondwana. Both sicariid genera, Loxosceles and Sicarius are diverse in Africa and South/Central America. Loxosceles are also diverse in North America and the West Indies, and have species described from Mediterranean Europe and China. We tested vicariance hypotheses using molecular phylogenetics and molecular dating analyses of 28S, COI, 16S, and NADHI sequences. We recover reciprocal monophyly of African and South American Sicarius, paraphyletic Southern African Loxosceles and monophyletic New World Loxosceles within which an Old World species group that includes L. rufescens is derived. These patterns are consistent with a sicariid common ancestor on Western Gondwana. North American Loxosceles are monophyletic, sister to Caribbean taxa, and resolved in a larger clade with South American Loxosceles. With fossil data this pattern is consistent with colonization of North America via a land bridge predating the modern Isthmus of Panama.}, }
@article {pmid18755281, year = {2008}, author = {Kawazoe, K and Kawakita, A and Kameda, Y and Kato, M}, title = {Redundant species, cryptic host-associated divergence, and secondary shift in Sennertia mites (Acari: Chaetodactylidae) associated with four large carpenter bees (Hymenoptera: Apidae: Xylocopa) in the Japanese island arc.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {503-513}, doi = {10.1016/j.ympev.2008.07.024}, pmid = {18755281}, issn = {1095-9513}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Animals ; Bayes Theorem ; Bees/*classification/genetics/*parasitology ; DNA, Mitochondrial/genetics ; Genes, Insect ; Genes, Mitochondrial ; *Genetic Speciation ; Host-Parasite Interactions/*genetics ; Japan ; Likelihood Functions ; Markov Chains ; Mites/*classification/genetics ; Mitochondria/genetics ; Monte Carlo Method ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Sennertia mites live as inquilines in the nests of carpenter bees and disperse as deutonymphs on newly emerged adult bees. Because their life cycle is tightly linked to that of the host bees, Sennertia may diverge in response to speciation in the hosts. However, the majority of Sennertia species are associated with several closely related carpenter bees, suggesting that host speciation may not be reflected in mite genetic structure. Here we investigate the extent of host-associated genetic differentiation in two Sennertia mites (S. alfkeni and S. japonica) that share four closely related, strictly allopatric large carpenter bees (Xylocopa). Analysis of the mitochondrial cytochrome oxidase subunit I (COI) gene in Sennertia unexpectedly indicates that the two species represent morphological variants of a single species, and they collectively group into four distinct, allopatric clades that are uniquely associated with a single Xylocopa host. An exception is the mites associated with X. amamensis of the northernmost populations, which have genotypes typical of those associated with neighboring X. appendiculatacircumvolans. Additional analysis using amplified fragment length polymorphism (AFLP) further corroborates the presence of four mite clades but contrary to the COI data, suggests that the mites of the southernmost population of X. appendiculatacircumvolans have genetic profiles typical of those associated with X. amamensis. These results indicate that some mites have undergone secondary host switch after the formation of the four mite lineages and further experienced mitochondrial introgression during period of lineage coexistence. Overall, our results strongly urge reappraisal of deutonymph-based mite taxonomy and illuminate the importance of host-associated divergence during incipient stage of speciation in chaetodactylid mites. Furthermore, the occurrence of host switch and introgression between genetically differentiated mites entails that two host species have co-occurred in the past, thus providing a unique source of evidence for migration and competitive exclusion between the presently allopatric Xylocopa hosts.}, }
@article {pmid18752353, year = {2008}, author = {Montooth, KL and Rand, DM}, title = {The spectrum of mitochondrial mutation differs across species.}, journal = {PLoS biology}, volume = {6}, number = {8}, pages = {e213}, pmid = {18752353}, issn = {1545-7885}, support = {R01 GM067862/GM/NIGMS NIH HHS/United States ; R01 GM067862-07/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Humans ; Mitochondria/*genetics ; *Mutation ; Species Specificity ; }, abstract = {Mitochondrial DNA mutation rates have now been measured in several model organisms. The patterns of mutation are strikingly different among species and point to modulation of mutation-selection balance in the evolution of nucleotide composition.}, }
@article {pmid18727956, year = {2008}, author = {Hoffmann, FG and Hoofer, SR and Baker, RJ}, title = {Molecular dating of the diversification of Phyllostominae bats based on nuclear and mitochondrial DNA sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {653-658}, doi = {10.1016/j.ympev.2008.08.002}, pmid = {18727956}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Chiroptera/*classification/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Fossils ; Genes, Mitochondrial ; Genes, rRNA ; Genetic Speciation ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Times of divergence among the three tribes included within the subfamily Phyllostominae were estimated using a Bayesian approach to infer dates of divergence based on mitochondrial and nuclear sequence data. The subfamily Phyllostominae is particularly attractive for such analysis, as it is one of the few groups of bats to have fossil specimens. Our molecular time analyses suggest that diversification among tribes and genera of phyllostomine bats occurred during the Early to Mid-Miocene, and was coincident with diversification events in two co distributed taxa: Caviomorph rodents and New World monkeys.}, }
@article {pmid18725306, year = {2008}, author = {Robins, JH and McLenachan, PA and Phillips, MJ and Craig, L and Ross, HA and Matisoo-Smith, E}, title = {Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {460-466}, doi = {10.1016/j.ympev.2008.08.001}, pmid = {18725306}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genetic Speciation ; *Genome, Mitochondrial ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; Rats/*classification/*genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The timing and order of divergences within the genus Rattus have, to date, been quite speculative. In order to address these important issues we sequenced six new whole mitochondrial genomes from wild-caught specimens from four species, Rattus exulans, Rattus praetor, Rattus rattus and Rattus tanezumi. The only rat whole mitochondrial genomes available previously were all from Rattus norvegicus specimens. Our phylogenetic and dating analyses place the deepest divergence within Rattus at approximately 3.5 million years ago (Mya). This divergence separates the New Guinean endemic R. praetor lineage from the Asian lineages. Within the Asian/Island Southeast Asian clade R. norvegicus diverged earliest at approximately 2.9Mya. R. exulans and the ancestor of the sister species R. rattus and R. tanezumi subsequently diverged at approximately 2.2Mya, with R. rattus and R. tanezumi separating as recently as approximately 0.4Mya. Our results give both a better resolved species divergence order and diversification dates within Rattus than previous studies.}, }
@article {pmid18725305, year = {2008}, author = {Rícan, O and Zardoya, R and Doadrio, I}, title = {Phylogenetic relationships of Middle American cichlids (Cichlidae, Heroini) based on combined evidence from nuclear genes, mtDNA, and morphology.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {3}, pages = {941-957}, doi = {10.1016/j.ympev.2008.07.022}, pmid = {18725305}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Central America ; Cichlids/anatomy &amp; histology/classification/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genes, RAG-1 ; Genetic Markers ; Geography ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; South America ; }, abstract = {Heroine cichlids are the second largest and very diverse tribe of Neotropical cichlids, and the only cichlid group that inhabits Mesoamerica. The taxonomy of heroines is complex because monophyly of most genera has never been demonstrated, and many species groups are without applicable generic names after their removal from the catch-all genus Cichlasoma (sensu Regan, 1905). Hence, a robust phylogeny for the group is largely wanting. A rather complete heroine phylogeny based on cytb sequence data is available [Concheiro Pérez, G.A., Rícan O., Ortí G., Bermingham, E., Doadrio, I., Zardoya, R. 2007. Phylogeny and biogeography of 91 species of heroine cichlids (Teleostei: Cichlidae) based on sequences of the cytochrome b gene. Mol. Phylogenet. Evol. 43, 91-110], and in the present study, we have added and analyzed independent data sets (nuclear and morphological) to further confirm and strengthen the cytb-phylogenetic hypothesis. We have analyzed a combined cytb-nuclear (RAG1 and two S7 introns) data set of 48 species representing main heroine lineages to achieve further resolution of heroine higher taxonomic levels and a combined cytb-morphological data set of 92 species to stabilize generic taxonomy. The recovered phylogenies supported the circumamazonian--CAM--Heroini (sensu Concheiro Peréz et al., 2007) as a monophyletic group, that could be divided into six main clades: (1) australoheroines (the southernmost heroine genus Australoheros), (2) nandopsines (the Antillean genus Nandopsis), (3) caquetaines (including the north western Amazonian genera Caquetaia and Heroina), (4) astatheroines (including Astatheros, Herotilapia and Rocio), (5) amphilophines (including Amphilophus and related genera), and (6) herichthyines (including Herichthyis and related genera). Nuclear and mitochondrial data partitions arrived at highly congruent topologies. Suprageneric relationships were influenced mainly by the nuclear signal, as well as the most basal phylogenetic position of Australoheros within CAM heroines. The new phylogeny of the tribe Heroini provides robust framework to stabilize the taxonomy of the group and for future comparative studies on these morphologically and ecologically diverse freshwater fishes. Morphology was mostly informative at the genus level and aid in determining the monophyly and composition of heroine genera. Upon acceptance of all putative genera, as recovered in this study, the Heroini would be with 35 genera the most genus-rich clade of Neotropical cichlids.}, }
@article {pmid18723858, year = {2008}, author = {Eisenberg, I and Novershtern, N and Itzhaki, Z and Becker-Cohen, M and Sadeh, M and Willems, PH and Friedman, N and Koopman, WJ and Mitrani-Rosenbaum, S}, title = {Mitochondrial processes are impaired in hereditary inclusion body myopathy.}, journal = {Human molecular genetics}, volume = {17}, number = {23}, pages = {3663-3674}, doi = {10.1093/hmg/ddn261}, pmid = {18723858}, issn = {1460-2083}, mesh = {Adult ; Aged ; Cells, Cultured ; Female ; Humans ; Male ; Middle Aged ; Mitochondria/*genetics/*metabolism/ultrastructure ; Molecular Sequence Data ; Muscle, Skeletal/metabolism ; Myoblasts/metabolism ; Myositis, Inclusion Body/*genetics/*metabolism ; Oligonucleotide Array Sequence Analysis ; }, abstract = {Hereditary inclusion body myopathy (HIBM) is an adult onset, slowly progressive distal and proximal myopathy. Although the causing gene, GNE, encodes for a key enzyme in the biosynthesis of sialic acid, its primary function in HIBM remains unknown. To elucidate the pathological mechanisms leading from the mutated GNE to the HIBM phenotype, we attempted to identify and characterize early occurring downstream events by analyzing the genomic expression patterns of muscle specimens from 10 HIBM patients carrying the M712T Persian Jewish founder mutation and presenting mild histological changes, compared with 10 healthy matched control individuals, using GeneChip expression microarrays. When analyzing the expression profile data sets by the intersection of three statistic methods (Student's t-test, TNoM and Info score), we found that the HIBM-specific transcriptome consists of 374 differentially expressed genes. The specificity of the HIBM transcriptome was assessed by the minimal transcript overlap found between HIBM and the transcriptome of nine additional muscle disorders including adult onset limb girdle myopathies, inflammatory myopathies and early onset conditions. A strikingly high proportion (18.6%) of the overall differentially expressed mRNAs of known function were found to encode for proteins implicated in various mitochondrial processes, revealing mitochondria pathways dysregulation. Mitochondrial morphological analysis by video-rate confocal microscopy showed a high degree of mitochondrial branching in cells of HIBM patients. The subtle involvement of mitochondrial processes identified in HIBM reveals an unexpected facet of HIBM pathophysiology which could at least partially explain the slow evolution of this disorder and give new insights in the disease mechanism.}, }
@article {pmid18723097, year = {2008}, author = {Matsui, M and Tominaga, A and Liu, WZ and Tanaka-Ueno, T}, title = {Reduced genetic variation in the Japanese giant salamander, Andrias japonicus (Amphibia: Caudata).}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {318-326}, doi = {10.1016/j.ympev.2008.07.020}, pmid = {18723097}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Ecosystem ; *Evolution, Molecular ; Genes, Mitochondrial ; *Genetic Variation ; Haplotypes ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Urodela/*classification/*genetics ; }, abstract = {The phylogenetic relationships among 46 samples from 27 populations of the Japanese giant salamander, Andriasjaponicus and its congener, A. davidianus from China was investigated, using 3664 bp sequences of the mitochondrial genes NADH1, NADH3, cyt b and CR, partial NADH6 and intervening genes. In phylogenetic trees constructed by MP, ML, and Bayesian methods, the family Cryptobranchidae and the genus Andrias both form monophyletic groups. Japanese A. japonicus and Chinese A. davidianus are sister taxa and can be regarded as separate species despite a small degree of genetic differentiation. Andriasjaponicus is divided into central and western clades, but the phylogenetic relationships within the latter clade are unresolved. As previously reported from allozyme analyses, A. japonicus exhibits little genetic differentiation, in strong contrast to salamanders of the genus Hynobius with which their distributions overlap. This reduced genetic variability in A. japonicus is attributable to a unique mating system of polygyny, delayed sexual maturity, notable longevity, life in a stable aquatic environment, and gigantism, as well as bottleneck effects following habitat fragmentation and extinction of local populations during Quaternary glaciations. The species is thus susceptible to extinction by potential environmental fluctuations, and requires extensive conservation measures.}, }
@article {pmid18722554, year = {2008}, author = {Luo, Y and Gao, W and Gao, Y and Tang, S and Huang, Q and Tan, X and Chen, J and Huang, T}, title = {Mitochondrial genome analysis of Ochotona curzoniae and implication of cytochrome c oxidase in hypoxic adaptation.}, journal = {Mitochondrion}, volume = {8}, number = {5-6}, pages = {352-357}, doi = {10.1016/j.mito.2008.07.005}, pmid = {18722554}, issn = {1567-7249}, support = {//Howard Hughes Medical Institute/United States ; }, mesh = {*Adaptation, Physiological ; Amino Acid Substitution ; Animals ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/chemistry/*genetics ; *Genome ; Hypoxia/*metabolism ; Lagomorpha/*genetics ; Male ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Pikas originated in Asia and are small lagomorphs native to cold climates. The plateau pika, Ochotona curzoniae is a keystone species on the Qinghai-Tibet Plateau and an ideal animal model for hypoxic adaptation studies. Altered mitochondrial function, especially cytochrome c oxidase activity, is an important factor in modulation of energy generation and expenditure during cold and hypoxia adaptation. In this study, we determined the complete nucleotide sequence of the O. curzoniae mitochondrial genome. The plateau pika mitochondrial DNA is 17,131bp long and encodes the complete set of 37 proteins typical for vertebrates. Phylogenetic analysis based on concatenated heavy-strand encoded protein-coding genes revealed that pikas are closer to rabbit and hare than to rat. This suggests that rabbit or hare would be a good control animal for pikas in cold and hypoxia adaptation studies. Fifteen novel mitochondrial DNA-encoded amino acid changes were identified in the pikas, including three in the subunits of cytochrome c oxidase. These amino acid substitutions potentially function in modulation of mitochondrial complexes and electron transport efficiency during cold and hypoxia adaptation.}, }
@article {pmid18713651, year = {2008}, author = {Yoshikawa, N and Matsui, M and Nishikawa, K and Kim, JB and Kryukov, A}, title = {Phylogenetic relationships and biogeography of the Japanese clawed salamander, Onychodactylus japonicus (Amphibia: Caudata: Hynobiidae), and its congener inferred from the mitochondrial cytochrome b gene.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {249-259}, doi = {10.1016/j.ympev.2008.07.016}, pmid = {18713651}, issn = {1095-9513}, mesh = {Amphibians/*classification/*genetics ; Animals ; Bayes Theorem ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; *Genes, Mitochondrial ; Genetic Speciation ; Genetics, Population ; Geography ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; Statistics, Nonparametric ; }, abstract = {Using the mitochondrial cytochrome b gene, we investigated phylogenetic relationships between and within the Japanese clawed salamander, Onychodactylus japonicus, and its close continental relative O. fischeri. Monophyly of O. japonicus was well supported, and O. japonicus was clearly distinguished from O. fischeri. However, O. fischeri comprises genetically distinct populations from Russia, NE China, and Korea that do not form a monophyletic group. Within O. japonicus, four major clades were clearly recognized: Clade I from northern Tohoku district, Clade II from southern Tohoku district and the Tsukuba Mountains, Clade III from southwestern Honshu, and Clade IV from Kinki and Chugoku districts in Honshu and from Shikoku. Although genetic distances among these clades were large (5.5-9.6%), relationships among the clades were unresolved. All clades except Clade I contained two or three distinct subclades. In several localities in Kinki and Chugoku, Clades III and IV were sympatric. The estimated divergence times and available geohistorical data suggest that O. japonicus began to differentiate in the Upper Late Miocene and that the pattern of genetic differentiation of this species has been affected strongly by climate changes and geohistorical events such as volcanic activity and mountain formation. Our results suggest that both O. fischeri and O. japonicus comprise multiple cryptic species.}, }
@article {pmid18706509, year = {2008}, author = {Ritz, MS and Millar, C and Miller, GD and Phillips, RA and Ryan, P and Sternkopf, V and Liebers-Helbig, D and Peter, HU}, title = {Phylogeography of the southern skua complex-rapid colonization of the southern hemisphere during a glacial period and reticulate evolution.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {292-303}, doi = {10.1016/j.ympev.2008.07.014}, pmid = {18706509}, issn = {1095-9513}, mesh = {Animals ; Charadriiformes/*classification/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Gene Flow ; Genes, Mitochondrial ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes ; Ice Cover ; Mitochondria/genetics ; Models, Genetic ; Models, Statistical ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Whilst we have now a good understanding how past glaciation influenced species at the northern hemisphere, our knowledge of patterns and modes of speciation is far more limited for the southern hemisphere. We provide mtDNA based data on the phylogeography of a circumpolar distributed southern hemisphere seabird group-the southern skua complex (Catharacta spp.). Diversification of southern skuas dates between 210,000 yBP and 150,000 yBP and coincides with a glacial spanning 230,000-140,000 yBP. Skuas most likely first inhabited the Antarctic continent, in the course of global cooling and increasing glaciation spread to the sub-antarctic islands and Tristan da Cunha and finally colonized Patagonia and the Falkland Islands at the glacial maximum. Despite significant differences between taxa most populations still exchange genes with neighboring populations of other taxa and speciation is incomplete.}, }
@article {pmid18703408, year = {2008}, author = {Mtango, NR and Potireddy, S and Latham, KE}, title = {Oocyte quality and maternal control of development.}, journal = {International review of cell and molecular biology}, volume = {268}, number = {}, pages = {223-290}, doi = {10.1016/S1937-6448(08)00807-1}, pmid = {18703408}, issn = {1937-6448}, support = {R24 RR015253/RR/NCRR NIH HHS/United States ; HD41440/HD/NICHD NIH HHS/United States ; RR15253/RR/NCRR NIH HHS/United States ; HD52788/HD/NICHD NIH HHS/United States ; RR18907/RR/NCRR NIH HHS/United States ; HD43092/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Cell Communication ; Cell Polarity ; Embryonic Development/*physiology ; Female ; Humans ; Male ; Mitochondria/physiology ; Models, Biological ; Mutation ; Oocytes/*cytology/*physiology ; Oogenesis ; Ovarian Follicle/cytology ; Pregnancy ; Pregnancy in Diabetics/physiopathology ; Protein Biosynthesis ; RNA, Messenger/genetics/metabolism ; }, abstract = {The oocyte is a unique and highly specialized cell responsible for creating, activating, and controlling the embryonic genome, as well as supporting basic processes such as cellular homeostasis, metabolism, and cell cycle progression in the early embryo. During oogenesis, the oocyte accumulates a myriad of factors to execute these processes. Oogenesis is critically dependent upon correct oocyte-follicle cell interactions. Disruptions in oogenesis through environmental factors and changes in maternal health and physiology can compromise oocyte quality, leading to arrested development, reduced fertility, and epigenetic defects that affect long-term health of the offspring. Our expanding understanding of the molecular determinants of oocyte quality and how these determinants can be disrupted has revealed exciting new insights into the role of oocyte functions in development and evolution.}, }
@article {pmid18703148, year = {2008}, author = {Haponski, AE and Stepien, CA}, title = {Molecular, morphological, and biogeographic resolution of cryptic taxa in the Greenside Darter Etheostoma blennioides complex.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {69-83}, doi = {10.1016/j.ympev.2008.07.013}, pmid = {18703148}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Gene Flow ; Genes, Mitochondrial ; Genetic Speciation ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes ; Introns/genetics ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; Perches/anatomy &amp; histology/*classification/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; United States ; }, abstract = {The systematic identity and genetic divergence of cryptic taxa and morphological subspecies in the Greenside Darter Etheostoma blennioides complex are analyzed from mitochondrial and nuclear DNA sequence data, along with morphological characters. We sequenced the mtDNA cytochrome b gene and control region and is the nuclear S7 intron 1 for 345 Greenside Darters from 19 locations across their distribution including areas of sympatry and allopatry, in comparison to putative sister species and relatives. Results provide the first genetic evidence that E. gutselli is a separate species and is the sister species of E. blennius, which together with E. rupestre comprise the sister group to the Greenside Darter complex; separating approximately 4.0 mya. MtDNA results show that the complex comprises 6 clades and supports only the morphological subspecies Etheostoma blennioides blennioides, distinguished by theta(ST)=0.94, approximately 1.7 my, scale counts, and ventral squamation. The former E. b. pholidotum and E. b. newmanii are polyphyletic and are invalid taxa, together comprising 5 differentiated clades that diverged approximately 0.90-1.7 mya. Nuclear DNA results recover some of the mtDNA clades, which are distinguished morphologically by subtle meristic count differences. Populations of E. b. blennioides genetically diverge, with diversity increasing to the southwest; attributed to restricted gene flow and genetic isolation with geographic distance. Samples of the former E. b. pholidotum from the Great Lakes/Wabash River clade are less divergent, with diversity increasing to the southwest, reflecting allopatric fragmentation and isolation by distance.}, }
@article {pmid18703057, year = {2008}, author = {Carrie, C and Murcha, MW and Kuehn, K and Duncan, O and Barthet, M and Smith, PM and Eubel, H and Meyer, E and Day, DA and Millar, AH and Whelan, J}, title = {Type II NAD(P)H dehydrogenases are targeted to mitochondria and chloroplasts or peroxisomes in Arabidopsis thaliana.}, journal = {FEBS letters}, volume = {582}, number = {20}, pages = {3073-3079}, doi = {10.1016/j.febslet.2008.07.061}, pmid = {18703057}, issn = {0014-5793}, mesh = {Arabidopsis/*metabolism ; Chloroplasts/*enzymology ; Green Fluorescent Proteins/genetics ; Mitochondria/*enzymology ; NADPH Dehydrogenase/classification/genetics/*metabolism ; Peroxisomes/*metabolism ; Phylogeny ; Plant Proteins/classification/*metabolism ; Sequence Analysis, Protein ; }, abstract = {We found that four type II NAD(P)H dehydrogenases (ND) in Arabidopsis are targeted to two locations in the cell; NDC1 was targeted to mitochondria and chloroplasts, while NDA1, NDA2 and NDB1 were targeted to mitochondria and peroxisomes. Targeting of NDC1 to chloroplasts as well as mitochondria was shown using in vitro and in vivo uptake assays and dual targeting of NDC1 to plastids relies on regions in the mature part of the protein. Accumulation of NDA type dehydrogenases to peroxisomes and mitochondria was confirmed using Western blot analysis on highly purified organelle fractions. Targeting of ND proteins to mitochondria and peroxisomes is achieved by two separate signals, a C-terminal signal for peroxisomes and an N-terminal signal for mitochondria.}, }
@article {pmid18701286, year = {2008}, author = {Rahaman, A and Elde, NC and Turkewitz, AP}, title = {A dynamin-related protein required for nuclear remodeling in Tetrahymena.}, journal = {Current biology : CB}, volume = {18}, number = {16}, pages = {1227-1233}, pmid = {18701286}, issn = {0960-9822}, support = {R01 GM077607/GM/NIGMS NIH HHS/United States ; R01 GM077607-01A1/GM/NIGMS NIH HHS/United States ; R01 GM077607-02/GM/NIGMS NIH HHS/United States ; GM077607/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Cell Nucleus Shape ; *Cell Nucleus Size ; Conjugation, Genetic ; Evolution, Molecular ; GTP Phosphohydrolases/genetics/*metabolism ; Multigene Family ; Starvation ; Tetrahymena thermophila/*cytology/physiology ; }, abstract = {Dynamin-related proteins (DRPs) are GTPases that reversibly assemble on cellular membranes [1]. Individual DRPs (here "DRP" includes authentic dynamins) function in fission or tubulation of the plasma membrane, trans-Golgi network, mitochondria, peroxisomes, chloroplasts, and endosomes [1] and in mitochondrial fusion [2]. Many of these functions are widespread; they are present in animals, plants, trypanosomes, Giardia, ciliates, alga, and slime molds [3-8]. Lineage-specific expansions of the gene family created specialized DRPs. In animals, such DRPs include MxB, which has been reported to regulate nuclear-pore transport [9]. Whereas many unicellular organisms possess a small number of DRPs, expansions occurred in some protist lineages. The eight DRPs in the ciliate Tetrahymena thermophila might contribute to aspects of ciliate complexity. Each ciliate cell contains distinct germline and somatic nuclei, whose differentiation and maintenance must require distinct machinery [10, 11]. Here we show that Drp6p, previously shown to be targeted to the nuclear envelope [3], is required for macronuclear development. Drp6p activity, which is distinct from that of the only other known nuclear DRP, is modulated by a combination of stage-specific subcellular targeting and assembly dynamics. This work demonstrates a novel DRP activity and presents a system in which environmental and developmental cues can be used for manipulating key aspects of regulation.}, }
@article {pmid18698356, year = {2008}, author = {Doublet, V and Souty-Grosset, C and Bouchon, D and Cordaux, R and Marcadé, I}, title = {A thirty million year-old inherited heteroplasmy.}, journal = {PloS one}, volume = {3}, number = {8}, pages = {e2938}, pmid = {18698356}, issn = {1932-6203}, mesh = {Animals ; Armadillos/*genetics ; Base Sequence ; DNA, Mitochondrial/genetics ; *Fossils ; *Genetic Heterogeneity ; Genome ; Mitochondria/genetics ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Polymorphism, Single Nucleotide ; RNA, Messenger, Stored/*genetics ; RNA, Transfer/genetics ; }, abstract = {Due to essentially maternal inheritance and a bottleneck effect during early oogenesis, newly arising mitochondrial DNA (mtDNA) mutations segregate rapidly in metazoan female germlines. Consequently, heteroplasmy (i.e. the mixture of mtDNA genotypes within an organism) is generally resolved to homoplasmy within a few generations. Here, we report an exceptional transpecific heteroplasmy (predicting an alanine/valine alloacceptor tRNA change) that has been stably inherited in oniscid crustaceans for at least thirty million years. Our results suggest that this heteroplasmy is stably transmitted across generations because it occurs within mitochondria and therefore escapes the mtDNA bottleneck that usually erases heteroplasmy. Consistently, at least two oniscid species possess an atypical trimeric mitochondrial genome, which provides an adequate substrate for the emergence of a constitutive intra-mitochondrial heteroplasmy. Persistence of a mitochondrial polymorphism on such a deep evolutionary timescale suggests that balancing selection may be shaping mitochondrial sequence evolution in oniscid crustaceans.}, }
@article {pmid18696114, year = {2008}, author = {Staiber, W}, title = {Centrosome hyperamplification with the formation of multiple asters and programmed chromosome inactivation in aberrant spermatocytes during male meiosis in Acricotopus.}, journal = {Cell and tissue research}, volume = {334}, number = {1}, pages = {81-91}, doi = {10.1007/s00441-008-0671-z}, pmid = {18696114}, issn = {1432-0878}, mesh = {Animals ; Centrosome/*metabolism/*ultrastructure ; Chironomidae/*genetics/ultrastructure ; Chromosome Pairing/physiology ; *Chromosome Segregation ; Male ; *Meiosis ; Microscopy, Electron, Transmission ; Mitosis ; Spermatocytes/physiology/*ultrastructure ; }, abstract = {In the germ line of the midge Acricotopus lucidus, an unequal chromosome segregation occurs in the last gonial mitosis prior to meiosis. This results in one daughter cell receiving only somatic chromosomes (Ss), whereas the other cell is given all the so-called germ line limited chromosomes (Ks) in addition to the Ss. The cytokinesis following this differential mitosis is incomplete and the daughter cells remain connected by a permanent cytoplasmic bridge. The cell with the Ss and Ks develops into a primary oocyte or spermatocyte, whereas the cell containing only Ss differentiates as a nurse cell in the female or as an aberrant spermatocyte in the male. When the primary spermatocyte enters meiosis, the Ss in the connected aberrant spermatocyte undergo chromosome condensation but the aberrant spermatocyte remains undivided, with the condensed metaphase status and inactivation of the Ss persisting during both meiotic divisions. These events indicate a programmed inactivation of all chromosomes in the aberrant spermatocyte at the beginning of meiosis. The alterations in the microtubule arrangements and of the distribution of mitochondria in the spermatocytes during meiosis have been followed via live-cell fluorescence labelling with the TubulinTracker and MitoTracker reagents and by transmission electron microscopy. The observations reveal a hyperamplification of the centrosomes and the formation of tetrapolar asters in the non-dividing aberrant spermatocytes containing the condensed Ss. The programmed inactivation of the Ss in the aberrant spermatocyte is suggested to have developed during evolution to inhibit the entry of the aberrant spermatocytes into meiosis, thereby preventing the formation of sperms containing only Ss but no Ks.}, }
@article {pmid18692147, year = {2008}, author = {Dyer, NA and Lawton, SP and Ravel, S and Choi, KS and Lehane, MJ and Robinson, AS and Okedi, LM and Hall, MJ and Solano, P and Donnelly, MJ}, title = {Molecular phylogenetics of tsetse flies (Diptera: Glossinidae) based on mitochondrial (COI, 16S, ND2) and nuclear ribosomal DNA sequences, with an emphasis on the palpalis group.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {227-239}, doi = {10.1016/j.ympev.2008.07.011}, pmid = {18692147}, issn = {1095-9513}, mesh = {Algorithms ; Animals ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Female ; Genes, Insect ; Genes, Mitochondrial ; Genetic Markers ; Haplotypes ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; Tsetse Flies/anatomy &amp; histology/*classification/*genetics ; }, abstract = {Relationships of 13 species of the genus Glossina (tsetse flies) were inferred from mitochondrial (cytochrome oxidase 1, NADH dehydrogenase 2 and 16S) and nuclear (internal transcribed spacer 1 of rDNA) sequences. The resulting phylogeny confirms the monophyly of the morphologically defined fusca, morsitans and palpalis subgenera. Genetic distances between palpalis and morsitans subspecies suggest that their status needs revision. In particular, cytochrome oxidase 1 sequences showed large geographical differences within G. palpalis palpalis, suggesting the existence of cryptic species within this subspecies. The morphology of palpalis group female genital plates was examined, and individuals were found varying outside the ranges specified by the standard identification keys, making definitive morphological classification impossible. A diagnostic PCR to distinguish G. palpalis palpalis, G. tachinoides and G. palpalis gambiensis based on length differences of internal transcribed spacer 1 sequences is presented.}, }
@article {pmid18692146, year = {2008}, author = {Ketmaier, V and Bianco, PG and Durand, JD}, title = {Molecular systematics, phylogeny and biogeography of roaches (Rutilus, Teleostei, Cyprinidae).}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {362-367}, doi = {10.1016/j.ympev.2008.07.012}, pmid = {18692146}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cyprinidae/*classification/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Genetic Speciation ; Genetic Variation ; Geography ; Likelihood Functions ; Mediterranean Region ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {In this study we used sequence data from the entire mtDNA cytochrome b gene to reconstruct patterns and times of diversification in the roach genus Rutilus. The genus is present with numerous endemic species in the Eastern peri-Mediterranean area and with a few widespread species in Central Europe. Our phylogenetic results do not support the subdivision into two subgenera proposed on morphological grounds. Within R. pigus and R. rutilus we identify highly divergent and allopatric mitochondrial lineages. The deeper splits in the genus phylogeny date back to the middle Miocene; the main diversification took place at the Miocene-Pliocene boundary.}, }
@article {pmid18692145, year = {2008}, author = {Bourlat, SJ and Nielsen, C and Economou, AD and Telford, MJ}, title = {Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {23-31}, doi = {10.1016/j.ympev.2008.07.008}, pmid = {18692145}, issn = {1095-9513}, support = {BB/C509866/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genes, rRNA ; Mitochondria/genetics ; *Models, Genetic ; *Phylogeny ; Ribosome Subunits, Large/genetics ; Ribosome Subunits, Small/genetics ; Sequence Alignment ; Sequence Analysis, Protein ; Statistics, Nonparametric ; }, abstract = {The new animal phylogeny inferred from ribosomal genes some years ago has prompted a number of radical rearrangements of the traditional, morphology based metazoan tree. The two main bilaterian clades, Deuterostomia and Protostomia, find strong support, but the protostomes consist of two sister groups, Ecdysozoa and Lophotrochozoa, not seen in morphology based trees. Although widely accepted, not all recent molecular phylogenetic analyses have supported the tripartite structure of the new animal phylogeny. Furthermore, even if the small ribosomal subunit (SSU) based phylogeny is correct, there is a frustrating lack of resolution of relationships between the phyla that make up the three clades of this tree. To address this issue, we have assembled a dataset including a large number of aligned sequence positions as well as a broad sampling of metazoan phyla. Our dataset consists of sequence data from ribosomal and mitochondrial genes combined with new data from protein coding genes (5139 amino acid and 3524 nucleotide positions in total) from 37 representative taxa sampled across the Metazoa. Our data show strong support for the basic structure of the new animal phylogeny as well as for the Mandibulata including Myriapoda. We also provide some resolution within the Lophotrochozoa, where we confirm support for a monophyletic clade of Echiura, Sipuncula and Annelida and surprising evidence of a close relationship between Brachiopoda and Nemertea.}, }
@article {pmid18690523, year = {2008}, author = {Zeth, K and Meins, T and Vonrhein, C}, title = {Approaching the structure of human VDAC1, a key molecule in mitochondrial cross-talk.}, journal = {Journal of bioenergetics and biomembranes}, volume = {40}, number = {3}, pages = {127-132}, pmid = {18690523}, issn = {0145-479X}, mesh = {Humans ; Mitochondria/*chemistry/metabolism ; Mitochondrial Membranes/*chemistry/metabolism ; Protein Structure, Tertiary/physiology ; Voltage-Dependent Anion Channel 1/*chemistry/metabolism ; }, abstract = {The voltage dependent anion-channel, VDAC, is the major constitutive protein of the outer membrane of mitochondria. Functionally, VDAC is involved in the exchange of small metabolites over the mitochondrial outer membrane and supports enzymes of the cytoplasm with energy precursors i.e. ATP. Moreover, the channel alone or in complex with proteins of the inner mitochondrial membrane or the intermembrane space provides a basis for docking of cytosolic proteins which can regulate outer membrane permeability in several ways. Structurally, this channel has a bacterial origin by evolution and partly resembles bacterial porin functions. However, the structure seems more complex as a variety of interactions on both channel sides can occur. Therefore, our work described is aiming to determine the structure of VDAC at atomic resolution and together with functional data to understand better how this channel can carry out such a variety of differing functions.}, }
@article {pmid18689412, year = {2008}, author = {Hiroi, J and Yasumasu, S and McCormick, SD and Hwang, PP and Kaneko, T}, title = {Evidence for an apical Na-Cl cotransporter involved in ion uptake in a teleost fish.}, journal = {The Journal of experimental biology}, volume = {211}, number = {Pt 16}, pages = {2584-2599}, doi = {10.1242/jeb.018663}, pmid = {18689412}, issn = {0022-0949}, mesh = {Acclimatization ; Amino Acid Sequence ; Animals ; Blotting, Western ; Cell Count ; *Cell Polarity ; Embryo, Nonmammalian/cytology/metabolism ; Fresh Water ; Gene Expression Profiling ; Gene Expression Regulation ; Gills/cytology/enzymology/metabolism ; Humans ; Ion Transport ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Proton-Translocating ATPases/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Seawater ; Sequence Alignment ; Sodium Chloride Symporters/chemistry/genetics/isolation &amp; purification/*metabolism ; Tilapia/*metabolism ; Time Factors ; Yolk Sac/cytology/metabolism ; }, abstract = {Cation-chloride cotransporters, such as the Na(+)/K(+)/2Cl(-) cotransporter (NKCC) and Na(+)/Cl(-) cotransporter (NCC), are localized to the apical or basolateral plasma membranes of epithelial cells and are involved in active ion absorption or secretion. The objectives of this study were to clone and identify ;freshwater-type' and ;seawater-type' cation-chloride cotransporters of euryhaline Mozambique tilapia (Oreochromis mossambicus) and to determine their intracellular localization patterns within mitochondria-rich cells (MRCs). From tilapia gills, we cloned four full-length cDNAs homologous to human cation-chloride cotransporters and designated them as tilapia NKCC1a, NKCC1b, NKCC2 and NCC. Out of the four candidates, the mRNA encoding NKCC1a was highly expressed in the yolk-sac membrane and gills (sites of the MRC localization) of seawater-acclimatized fish, whereas the mRNA encoding NCC was exclusively expressed in the yolk-sac membrane and gills of freshwater-acclimatized fish. We then generated antibodies specific for tilapia NKCC1a and NCC and conducted whole-mount immunofluorescence staining for NKCC1a and NCC, together with Na(+)/K(+)-ATPase, cystic fibrosis transmembrane conductance regulator (CFTR) and Na(+)/H(+) exchanger 3 (NHE3), on the yolk-sac membrane of tilapia embryos acclimatized to freshwater or seawater. The simultaneous quintuple-color immunofluorescence staining allowed us to classify MRCs clearly into four types: types I, II, III and IV. The NKCC1a immunoreactivity was localized to the basolateral membrane of seawater-specific type-IV MRCs, whereas the NCC immunoreactivity was restricted to the apical membrane of freshwater-specific type-II MRCs. Taking account of these data at the level of both mRNA and protein, we deduce that NKCC1a is the seawater-type cotransporter involved in ion secretion by type-IV MRCs and that NCC is the freshwater-type cotransporter involved in ion absorption by type-II MRCs. We propose a novel ion-uptake model by MRCs in freshwater that incorporates apically located NCC. We also reevaluate a traditional ion-uptake model incorporating NHE3; the mRNA was highly expressed in freshwater, and the immunoreactivity was found at the apical membrane of other freshwater-specific MRCs.}, }
@article {pmid18688271, year = {2008}, author = {Rosso, L and Marques, AC and Reichert, AS and Kaessmann, H}, title = {Mitochondrial targeting adaptation of the hominoid-specific glutamate dehydrogenase driven by positive Darwinian selection.}, journal = {PLoS genetics}, volume = {4}, number = {8}, pages = {e1000150}, pmid = {18688271}, issn = {1553-7404}, mesh = {Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Cell Line ; Chlorocebus aethiops ; Evolution, Molecular ; Gene Duplication ; Glutamate Dehydrogenase/chemistry/genetics/*physiology ; Glutamate Dehydrogenase (NADP+)/chemistry/genetics/*metabolism ; Hominidae/*genetics/metabolism ; Humans ; Hylobates ; Mice ; Mitochondria/chemistry/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Sorting Signals ; Protein Transport ; *Selection, Genetic ; Sequence Alignment ; Species Specificity ; }, abstract = {Many new gene copies emerged by gene duplication in hominoids, but little is known with respect to their functional evolution. Glutamate dehydrogenase (GLUD) is an enzyme central to the glutamate and energy metabolism of the cell. In addition to the single, GLUD-encoding gene present in all mammals (GLUD1), humans and apes acquired a second GLUD gene (GLUD2) through retroduplication of GLUD1, which codes for an enzyme with unique, potentially brain-adapted properties. Here we show that whereas the GLUD1 parental protein localizes to mitochondria and the cytoplasm, GLUD2 is specifically targeted to mitochondria. Using evolutionary analysis and resurrected ancestral protein variants, we demonstrate that the enhanced mitochondrial targeting specificity of GLUD2 is due to a single positively selected glutamic acid-to-lysine substitution, which was fixed in the N-terminal mitochondrial targeting sequence (MTS) of GLUD2 soon after the duplication event in the hominoid ancestor approximately 18-25 million years ago. This MTS substitution arose in parallel with two crucial adaptive amino acid changes in the enzyme and likely contributed to the functional adaptation of GLUD2 to the glutamate metabolism of the hominoid brain and other tissues. We suggest that rapid, selectively driven subcellular adaptation, as exemplified by GLUD2, represents a common route underlying the emergence of new gene functions.}, }
@article {pmid18678284, year = {2008}, author = {Zehrmann, A and van der Merwe, JA and Verbitskiy, D and Brennicke, A and Takenaka, M}, title = {Seven large variations in the extent of RNA editing in plant mitochondria between three ecotypes of Arabidopsis thaliana.}, journal = {Mitochondrion}, volume = {8}, number = {4}, pages = {319-327}, doi = {10.1016/j.mito.2008.07.003}, pmid = {18678284}, issn = {1567-7249}, mesh = {Arabidopsis/*genetics ; Flowers/genetics ; Mitochondria/*genetics ; Plant Leaves/genetics ; RNA Editing/*genetics ; RNA, Plant/*genetics ; }, abstract = {Most RNA editing sites in flowering plant mitochondria are located in coding regions of mRNAs and are usually essential for correct gene expression. Although accordingly little variation should be tolerated, editing sites appear and disappear even between closely related flowering plant species. To investigate whether such editing site variations also occur within species, we analyzed 379 RNA editing sites in the three ecotypes Columbia, Landsberg erecta and C24 of Arabidopsis thaliana. While all editing sites as such are conserved, we identify seven RNA editing sites with 40-60% differences in effective editing between individual ecotypes. These quantitative variations show that the extent of RNA editing in plant mitochondria is very flexible and can change even more rapidly than the evolution of species. The ecotype-specific variations of the RNA editing extent are Mendelian-inherited and can now be used to follow and identify the nuclear loci responsible for these RNA editing phenotypes.}, }
@article {pmid18678263, year = {2008}, author = {Gérard, K and Bierne, N and Borsa, P and Chenuil, A and Féral, JP}, title = {Pleistocene separation of mitochondrial lineages of Mytilus spp. mussels from Northern and Southern Hemispheres and strong genetic differentiation among southern populations.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {84-91}, doi = {10.1016/j.ympev.2008.07.006}, pmid = {18678263}, issn = {1095-9513}, mesh = {Animals ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Genes, rRNA ; Genetics, Population ; Haplotypes ; Mitochondria/*genetics ; Mytilus/*classification/*genetics ; *Phylogeny ; Polymorphism, Genetic ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Smooth-shelled mussels, Mytilus spp., have an antitropical distribution. In the Northern Hemisphere, the M. edulis complex of species is composed of three genetically well delineated taxa: M. edulis, M. galloprovincialis and M. trossulus. In the Southern Hemisphere, morphological characters, allozymes and intron length polymorphisms suggest that Mytilus spp. populations from South America and Kerguelen Islands are related to M. edulis and those from Australasia to M. galloprovincialis. On the other hand, a phylogeny of the 16S rDNA mitochondrial locus demonstrates a clear distinctiveness of southern mussels and suggests that they are related to Mediterranean M. galloprovincialis. Here, we analysed the faster-evolving cytochrome oxidase subunit I locus. The divergence between haplotypes of populations from the two hemispheres was confirmed and was found to predate the divergence between haplotypes of northern M. edulis and M. galloprovincialis. In addition, strong genetic structure was detected among the southern samples, revealing three genetic entities that correspond to (1) South America and Kerguelen Island, (2) Tasmania, (3) New Zealand. Using the trans-Arctic interchange as a molecular clock calibration, we estimated the time since divergence of populations from the two hemispheres to be between 0.5 million years (MY) and 1.3 MY (average 0.84 MY). The contrasting patterns observed for the nuclear and the organelle genomes suggested two alternative, complex scenarios: two trans-equatorial migrations and the existence of differential barriers to mitochondrial and nuclear gene flow, or a single trans-equatorial migration and a view of the composition of the nuclear genome biased by taxonomic preconception.}, }
@article {pmid18676618, year = {2008}, author = {Simon, DM and Clarke, NA and McNeil, BA and Johnson, I and Pantuso, D and Dai, L and Chai, D and Zimmerly, S}, title = {Group II introns in eubacteria and archaea: ORF-less introns and new varieties.}, journal = {RNA (New York, N.Y.)}, volume = {14}, number = {9}, pages = {1704-1713}, pmid = {18676618}, issn = {1469-9001}, mesh = {Archaea/enzymology/*genetics ; Bacteria/enzymology/*genetics ; *Introns/genetics ; Nucleic Acid Conformation ; Open Reading Frames ; Phylogeny ; RNA, Catalytic/*chemistry/*classification/genetics ; *Retroelements ; }, abstract = {Group II introns are a major class of ribozymes found in bacteria, mitochondria, and plastids. Many introns contain reverse transcriptase open reading frames (ORFs) that confer mobility to the introns and allow them to persist as selfish DNAs. Here, we report an updated compilation of group II introns in Eubacteria and Archaea comprising 234 introns. One new phylogenetic class is identified, as well as several specialized lineages. In addition, we undertake a detailed search for ORF-less group II introns in bacterial genomes in order to find undiscovered introns that either entirely lack an ORF or encode a novel ORF. Unlike organellar group II introns, we find only a handful of ORF-less introns in bacteria, suggesting that if a substantial number exist, they must be divergent from known introns. Together, these results highlight the retroelement character of bacterial group II introns, and suggest that their long-term survival is dependent upon retromobility.}, }
@article {pmid18675919, year = {2008}, author = {Duarte, JM and González, S and Maldonado, JE}, title = {The surprising evolutionary history of South American deer.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {17-22}, doi = {10.1016/j.ympev.2008.07.009}, pmid = {18675919}, issn = {1095-9513}, mesh = {Animals ; Cluster Analysis ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Deer/anatomy &amp; histology/classification/*genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; *Genetic Speciation ; Karyotyping ; Mitochondria/genetics ; Phylogeny ; South America ; Species Specificity ; }, abstract = {To clarify the systematic relationships and evolutionary history of South American deer, we conducted a comprehensive phylogenetic analysis using representative species of all of the genera of Neotropical deer. Our results revealed high levels of molecular and cytogenetic divergence between groups of morphologically similar species of brockets (Mazama), and suggest a polyphyletic origin. At least eight ancestral forms of deer invaded South America during the late Pliocene (2.5-3 MYA), and members of the red brockets had an independent early explosive diversification soon after their ancestor arrived there, giving rise to a number of morphologically cryptic species.}, }
@article {pmid18672078, year = {2008}, author = {Fenn, JD and Song, H and Cameron, SL and Whiting, MF}, title = {A preliminary mitochondrial genome phylogeny of Orthoptera (Insecta) and approaches to maximizing phylogenetic signal found within mitochondrial genome data.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {59-68}, doi = {10.1016/j.ympev.2008.07.004}, pmid = {18672078}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Gene Rearrangement ; Genes, Insect ; Genes, Mitochondrial ; *Genome, Mitochondrial ; Likelihood Functions ; Mitochondria/genetics ; Orthoptera/classification/*genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The phylogenetic utility of mitochondrial genomes (mtgenomes) is examined using the framework of a preliminary phylogeny of Orthoptera. This study presents five newly sequenced genomes from four orthopteran families. While all ensiferan and polyneopteran taxa retain the ancestral gene order, all caeliferan lineages including the newly sequenced caeliferan species contain a tRNA rearrangement from the insect ground plan tRNA(Lys)(K)-tRNA(Asp)(D) swapping to tRNA(Asp) (D)-tRNA(Lys) (K) confirming that this rearrangement is a possible molecular synapomorphy for this suborder. The phylogenetic signal in mtgenomes is rigorously examined under the analytical regimens of parsimony, maximum likelihood and Bayesian inference, along with how gene inclusion/exclusion, data recoding, gap coding, and different partitioning schemes influence the phylogenetic reconstruction. When all available data are analyzed simultaneously, the monophyly of Orthoptera and its two suborders, Caelifera and Ensifera, are consistently recovered in the context of our taxon sampling, regardless of the optimality criteria. When protein-coding genes are analyzed as a single partition, nearly identical topology to the combined analyses is recovered, suggesting that much of the signals of the mtgenome come from the protein-coding genes. Transfer and ribosomal RNAs perform poorly when analyzed individually, but contribute signal when analyzed in combination with the protein-coding genes. Inclusion of third codon position of the protein-coding genes does not negatively affect the phylogenetic reconstruction when all genes are analyzed together, whereas recoding of the protein-coding genes into amino acid sequences introduces artificial resolution. Over-partitioning in a Bayesian framework appears to have a negative effect in achieving convergence. Our findings suggest that the best phylogenetic inferences are made when all available nucleotide data from the mtgenome are analyzed simultaneously, and that the mtgenome data can resolve over a wide time scale from the Permian (approximately 260 MYA) to the Tertiary (approximately 50 MYA).}, }
@article {pmid18672077, year = {2008}, author = {Canfield, MR and Greene, E and Moreau, CS and Chen, N and Pierce, NE}, title = {Exploring phenotypic plasticity and biogeography in emerald moths: A phylogeny of the genus Nemoria (Lepidoptera: Geometridae).}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {2}, pages = {477-487}, doi = {10.1016/j.ympev.2008.07.003}, pmid = {18672077}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Insect ; Genes, Mitochondrial ; Geography ; Larva/classification/genetics ; Likelihood Functions ; Mitochondria/genetics ; Moths/*classification/*genetics ; *Phenotype ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The moth genus Nemoria (Lepidoptera: Geometridae) includes 134 described species whose larvae and adults display a considerable range of phenotypic plasticity in coloration and morphology. We reconstructed the phylogeny of 54 species of Nemoria and seven outgroups using characters from the mitochondrial genes, Cytochrome Oxidase I and II (COI and COII), and the nuclear gene, Elongation Factor-alpha (EF-1alpha). Maximum parsimony, maximum likelihood and Bayesian inference were used to infer the phylogeny. The 54 ingroup species represented 13 of the 15 recognized species groups of Nemoria [Ferguson, D.C., 1985. Fasc. 18.1, Geometroidea: Geometridae (in part). In: Dominick, R.B. (Ed.), The Moths of America North of Mexico, Fasc. 18.1. Wedge Entomological Research Foundation, Washington; Pitkin, L.M., 1993. Neotropical emerald moths of the genera Nemoria, Lissochlora and Chavarriella, with particular reference to the species of Costa Rica (Lepidoptera: Geometridae, Geometrinae). Bull. Br. Mus. Nat. Hist. 62, 39-159], and the seven outgroups came from four tribes of Geometrinae. These data support Nemoria as a monophyletic group and largely recover the species groupings proposed in previous taxonomic analyses using morphological characters. Phenotypic plasticity of larvae is not correlated with plasticity of adults among those species of Nemoria where life histories are known, and appears to be evolutionarily labile for both life history stages: Species exhibiting larval phenotypic plasticity, such as N. arizonaria and N. outina, are placed in several distinct clades, suggesting that this trait has evolved multiple times, and species displaying adult phenotypic plasticity are likewise distributed throughout the phylogeny. A comparative analysis of the biogeographic history of Nemoria supports a South American origin for the genus with multiple introductions into North America, and an application of published substitution rates to the phylogram provides an age estimate of 7.5 million years.}, }
@article {pmid18669479, year = {2008}, author = {Jiang, H and Guan, W and Pinney, D and Wang, W and Gu, Z}, title = {Relaxation of yeast mitochondrial functions after whole-genome duplication.}, journal = {Genome research}, volume = {18}, number = {9}, pages = {1466-1471}, pmid = {18669479}, issn = {1088-9051}, mesh = {Codon ; Conserved Sequence ; Evolution, Molecular ; *Gene Duplication ; Genes, Duplicate ; Genes, Fungal ; Genes, Mitochondrial ; *Genome, Fungal ; *Genome, Mitochondrial ; Kluyveromyces/genetics ; Mitochondria/*genetics/physiology ; Species Specificity ; Yeasts/classification/*genetics ; }, abstract = {Mitochondria are essential for cellular energy production in most eukaryotic organisms. However, when glucose is abundant, yeast species that underwent whole-genome duplication (WGD) mostly conduct fermentation even under aerobic conditions, and most can survive without a functional mitochondrial genome. In this study, we show that the rate of evolution for the nuclear-encoded mitochondrial genes was greater in post-WGD species than pre-WGD species. Furthermore, codon usage bias was relaxed for these genes in post-WGD yeast species. The codon usage pattern and the distribution of a particular transcription regulatory element suggest that the change to an efficient aerobic fermentation lifestyle in this lineage might have emerged after WGD between the divergence of Kluyveromyces polysporus and Saccharomyces castellii from their common ancestor. This new energy production strategy could have led to the relaxation of mitochondrial function in the relevant yeast species.}, }
@article {pmid18665223, year = {2008}, author = {Hansson, B and Hasselquist, D and Tarka, M and Zehtindjiev, P and Bensch, S}, title = {Postglacial colonisation patterns and the role of isolation and expansion in driving diversification in a passerine bird.}, journal = {PloS one}, volume = {3}, number = {7}, pages = {e2794}, pmid = {18665223}, issn = {1932-6203}, mesh = {Animal Migration ; Animals ; Base Pair Mismatch ; Birds ; *DNA, Mitochondrial ; Environment ; Evolution, Molecular ; Genetic Variation ; Geography ; Haplotypes ; Mitochondria/metabolism ; Models, Biological ; Models, Statistical ; Models, Theoretical ; Species Specificity ; }, abstract = {Pleistocene glacial cycles play a major role in diversification and speciation, although the relative importance of isolation and expansion in driving diversification remains debated. We analysed mitochondrial DNA sequence data from 15 great reed warbler (Acrocephalus arundinaceus) populations distributed over the vast Eurasian breeding range of the species, and revealed unexpected postglacial expansion patterns from two glacial refugia. There were 58 different haplotypes forming two major clades, A and B. Clade A dominated in Western Europe with declining frequencies towards Eastern Europe and the Middle East, but showed a surprising increase in frequency in Western and Central Asia. Clade B dominated in the Middle East, with declining frequencies towards north in Central and Eastern Europe and was absent from Western Europe and Central Asia. A parsimonious explanation for these patterns is independent postglacial expansions from two isolated refugia, and mismatch distribution analyses confirmed this suggestion. Gene flow analyses showed that clade A colonised both Europe and Asia from a refugium in Europe, and that clade B expanded much later and colonised parts of Europe from a refugium in the Middle East. Great reed warblers in the eastern parts of the range have slightly paler plumage than western birds (sometimes treated as separate subspecies; A. a. zarudnyi and A. a. arundinaceus, respectively) and our results suggest that the plumage diversification took place during the easterly expansion of clade A. This supports the postglacial expansion hypothesis proposing that postglacial expansions drive diversification in comparatively short time periods. However, there is no indication of any (strong) reproductive isolation between clades and our data show that the refugia populations became separated during the last glaciation. This is in line with the Pleistocene speciation hypothesis invoking that much longer periods of time in isolation are needed for speciation to occur.}, }
@article {pmid18662792, year = {2009}, author = {Goebel, AM and Ranker, TA and Corn, PS and Olmstead, RG}, title = {Mitochondrial DNA evolution in the Anaxyrus boreas species group.}, journal = {Molecular phylogenetics and evolution}, volume = {50}, number = {2}, pages = {209-225}, doi = {10.1016/j.ympev.2008.06.019}, pmid = {18662792}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Bufonidae/classification/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Genetic Variation ; Geography ; Haplotypes ; Mitochondria/genetics ; North America ; Phylogeny ; RNA, Ribosomal/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The Anaxyrus boreas species group currently comprises four species in western North America including the broadly distributed A. boreas, and three localized species, Anaxyrus nelsoni, Anaxyrusexsul and Anaxyrus canorus. Phylogenetic analyses of the mtDNA 12S rDNA, cytochrome oxidase I, control region, and restriction sites data, identified three major haplotype clades. The Northwest clade (NW) includes both subspecies of A. boreas and divergent minor clades in the middle Rocky Mountains, coastal, and central regions of the west and Pacific Northwest. The Southwest (SW) clade includes A. exsul, A. nelsoni, and minor clades in southern California. Anaxyrus canorus, previously identified as paraphyletic, has populations in both the NW and SW major clades. The Eastern major clade (E) includes three divergent lineages from southern Utah, the southern Rocky Mountains, and north of the Great Basin at the border of Utah and Nevada. These results identify new genetic variation in the eastern portion of the toad's range and are consistent with previous regional studies from the west coast. Low levels of control region sequence divergence between major clades (2.2-4.7% uncorrected pair-wise distances) are consistent with Pleistocene divergence and suggest that the phylogeographic history of the group was heavily influenced by dynamic Pleistocene glacial and climatic changes, and especially pluvial changes, in western North America. Results reported here may impact conservation plans in that the current taxonomy does not reflect the diversity in the group.}, }
@article {pmid18662791, year = {2008}, author = {Redondo, RA and Brina, LP and Silva, RF and Ditchfield, AD and Santos, FR}, title = {Molecular systematics of the genus Artibeus (Chiroptera: Phyllostomidae).}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {44-58}, doi = {10.1016/j.ympev.2008.07.001}, pmid = {18662791}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Chiroptera/*classification/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genetic Markers ; Genetic Speciation ; Haplotypes ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {A molecular phylogeny of the genus Artibeus using 19 of the 20 recognized species, many with samples from a broad geographic range, is presented. The analysis shows a clear distinction between the two subgenera (or genera), the 'large'Artibeus and the 'small'Dermanura, in both mitochondrial and nuclear genes. The placement and status of A. concolor remains inconclusive and is presented as the third subgenus Koopmania. The phylogenies and divergence time estimates show a marked influence of the Andes in the formation of the subgenera and the main lineages inside each subgenus. Nuclear genes showed a highly incomplete lineage sorting among species inside subgenera Artibeus and Dermanura. Indeed, shared alleles were also found between Artibeus and Koopmania, which are presumed to have split apart during the Miocene, showing that great care should be taken in using these markers. Cytochrome-b gene divergences and monophyly analyses suggest that A. lituratus and A. intermedius are indeed conspecifics. These analyses also suggested the existence of at least four 'new' species revealing a significant cryptic diversity inside the genus.}, }
@article {pmid18655725, year = {2008}, author = {Voigt, O and Erpenbeck, D and Wörheide, G}, title = {A fragmented metazoan organellar genome: the two mitochondrial chromosomes of Hydra magnipapillata.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {350}, pmid = {18655725}, issn = {1471-2164}, mesh = {Animals ; Base Composition ; Base Sequence ; Chromosomes/*genetics/*metabolism ; Codon/metabolism ; DNA, Mitochondrial/genetics ; Gene Order ; Genome, Mitochondrial/*genetics ; Hydra/*cytology/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Terminal Repeat Sequences ; }, abstract = {BACKGROUND: Animal mitochondrial (mt) genomes are characteristically circular molecules of approximately 16-20 kb. Medusozoa (Cnidaria excluding Anthozoa) are exceptional in that their mt genomes are linear and sometimes subdivided into two to presumably four different molecules. In the genus Hydra, the mt genome comprises one or two mt chromosomes. Here, we present the whole mt genome sequence from the hydrozoan Hydra magnipapillata, comprising the first sequence of a fragmented metazoan mt genome encoded on two linear mt chromosomes (mt1 and mt2).<br><br>RESULTS: The H. magnipapillata mt chromosomes contain the typical metazoan set of 13 genes for respiratory proteins, the two rRNA genes and two tRNA genes. All genes are unidirectionally oriented on mt1 and mt2, and several genes overlap. The gene arrangement suggests that the two mt chromosomes originated from one linear molecule that separated between nd5 and rns. Strong correlations between the AT content of rRNA genes (rns and rnl) and the AT content of protein-coding genes among 24 cnidarian genomes imply that base composition is mainly determined by mt genome-wide constraints. We show that identical inverted terminal repeats (ITR) occur on both chromosomes; these ITR contain a partial copy or part of the 3' end of cox1 (54 bp). Additionally, both mt chromosomes possess identical oriented sequences (IOS) at the 5' and 3' ends (5' and 3' IOS) adjacent to the ITR. The 5' IOS contains trnM and non-coding sequences (119 bp), whereas the 3' IOS comprises a larger part (mt2) with a larger partial copy of cox1 (243 bp).<br><br>CONCLUSION: ITR are also documented in the two other available medusozoan mt genomes (Aurelia aurita and Hydra oligactis). In H. magnipapillata, the arrangement of ITR and 5' IOS and 3' IOS suggest that these regions are crucial for mt DNA replication and/or transcription initiation. An analogous organization occurs in a highly fragmented ichthyosporean mt genome. With our data, we can reject a model of mt replication that has previously been proposed for Hydra. This raises new questions regarding replication mechanisms probably employed by all medusozoans, and also has general implications for the expected organization of fragmented linear mt chromosomes of other taxa.}, }
@article {pmid18653734, year = {2008}, author = {Oliveira, DC and Raychoudhury, R and Lavrov, DV and Werren, JH}, title = {Rapidly evolving mitochondrial genome and directional selection in mitochondrial genes in the parasitic wasp nasonia (hymenoptera: pteromalidae).}, journal = {Molecular biology and evolution}, volume = {25}, number = {10}, pages = {2167-2180}, pmid = {18653734}, issn = {1537-1719}, support = {R01 GM070026/GM/NIGMS NIH HHS/United States ; 5R01 GM070026/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Nucleus/metabolism ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Expressed Sequence Tags ; Genetic Variation ; Genome ; *Genome, Mitochondrial ; Hymenoptera/*genetics/parasitology ; Mitochondria/metabolism ; Models, Genetic ; *Mutation ; Phylogeny ; Wasps/genetics ; Wolbachia/*genetics ; }, abstract = {We sequenced the nearly complete mtDNA of 3 species of parasitic wasps, Nasonia vitripennis (2 strains), Nasonia giraulti, and Nasonia longicornis, including all 13 protein-coding genes and the 2 rRNAs, and found unusual patterns of mitochondrial evolution. The Nasonia mtDNA has a unique gene order compared with other insect mtDNAs due to multiple rearrangements. The mtDNAs of these wasps also show nucleotide substitution rates over 30 times faster than nuclear protein-coding genes, indicating among the highest substitution rates found in animal mitochondria (normally <10 times faster). A McDonald and Kreitman test shows that the between-species frequency of fixed replacement sites relative to silent sites is significantly higher compared with within-species polymorphisms in 2 mitochondrial genes of Nasonia, atp6 and atp8, indicating directional selection. Consistent with this interpretation, the Ka/Ks (nonsynonymous/synonymous substitution rates) ratios are higher between species than within species. In contrast, cox1 shows a signature of purifying selection for amino acid sequence conservation, although rates of amino acid substitutions are still higher than for comparable insects. The mitochondrial-encoded polypeptides atp6 and atp8 both occur in F0F1ATP synthase of the electron transport chain. Because malfunction in this fundamental protein severely affects fitness, we suggest that the accelerated accumulation of replacements is due to beneficial mutations necessary to compensate mild-deleterious mutations fixed by random genetic drift or Wolbachia sweeps in the fast evolving mitochondria of Nasonia. We further propose that relatively high rates of amino acid substitution in some mitochondrial genes can be driven by a "Compensation-Draft Feedback"; increased fixation of mildly deleterious mutations results in selection for compensatory mutations, which lead to fixation of additional deleterious mutations in nonrecombining mitochondrial genomes, thus accelerating the process of amino acid substitutions.}, }
@article {pmid18652904, year = {2008}, author = {Bittner, L and Payri, CE and Couloux, A and Cruaud, C and de Reviers, B and Rousseau, F}, title = {Molecular phylogeny of the Dictyotales and their position within the Phaeophyceae, based on nuclear, plastid and mitochondrial DNA sequence data.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {211-226}, doi = {10.1016/j.ympev.2008.06.018}, pmid = {18652904}, issn = {1095-9513}, mesh = {Bayes Theorem ; Chloroplasts/genetics ; DNA, Algal/genetics ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Likelihood Functions ; Mitochondria/genetics ; Phaeophyceae/*classification/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {For the first time, on the basis of nuclear, plastid and mitochondrial sequence data, the most comprehensive molecular phylogeny of the Dictyotales to date is presented, in a broad context where all brown algal orders are included (except Discosporangiales, Ascoseirales and Nemodermatales). A veto supertree approach was used here to evaluate congruency and conflicts between genes: phylogenetic signal was congruent and mainly carried by chloroplastic information. Supermatrix analyses (BI, ML and MP) revealed that Dictyotales is sister to Onslowiales, this ensemble being sister of a clade also encompassing Sphacelariales and Syringodermatales. The family Scoresbyellaceae is merged into the family Dictyotaceae. Furthermore, the current subdivision of the Dictyotaceae into two tribes was not supported. The enigmatic genus Stoechospermum was shown to belong to the same clade as Dictyota, Rugulopteryx, Scoresbyella and Canistrocarpus. Homoeostrichus and Dictyopteris did not appear monophyletic. Zonaria stipitata clustered with the Spatoglossum species; since this is consistent with its morphological features, the new combination Spatoglossum stipitatum is proposed accordingly.}, }
@article {pmid18652292, year = {2008}, author = {Hu, J and Pan, G and Xu, J and Lu, K and Dang, X and Wu, Z and Li, Y and Zhou, Z}, title = {[Characterization and analysis of mitochondrial protein frataxin in Nosema bombycis].}, journal = {Wei sheng wu xue bao = Acta microbiologica Sinica}, volume = {48}, number = {5}, pages = {608-615}, pmid = {18652292}, issn = {0001-6209}, mesh = {Amino Acid Sequence ; Animals ; Blotting, Western ; Cloning, Molecular ; DNA-Directed RNA Polymerases/metabolism ; Evolution, Molecular ; Fungal Proteins/analysis/chemistry/*genetics/metabolism ; Iron-Binding Proteins/analysis/chemistry/*genetics/*metabolism ; Mice ; Mitochondrial Proteins/analysis/chemistry/*genetics/metabolism ; Molecular Sequence Data ; *Nosema/genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; Frataxin ; }, abstract = {AIM: Frataxin protein is a component of Fe-S clusters and closely related to metabolism of mitochondria. We identified an integrity mitochondrial protein frataxin gene (Nbfra), analyzed its phylogenetic relationship, and confirmed the transcriptase activity of Nbfra in N. bombycis.<br><br>METHODS: We analyzed the sequence of the second structure, gene location in genome and construction of NJ phylogenetic tree through various bioinformatics software. We constructed recombinant vector pGEX-4T-1-Nbfra, expressed the 36.5kDa recombinant protein in E. coli BL21 (DE3), and then used the protein as antigen to produce its polyantibody in mice.<br><br>RESULTS: Nbfra was lack of targeting signal into mitochondria and part of alpha helices in functional domain, and had a synteny character between N. bombycis and E. cuniculi. Phylogenetic trees of Nbfra suggested that the evolutionary position of microsporidia was closely related to that of higher eukaryote, rather than that of other protozoa. The result of western blot suggested the expression and transcription of Nbfra gene in N. bombycis.<br><br>CONCLUSIONS: Our results offered the new evidence to analysis the conservation of Nbfra and evolutionary position of N. bombycis, and would support the hypothesis of mitosome in microsporidia.}, }
@article {pmid18644456, year = {2008}, author = {Kapli, P and Lymberakis, P and Poulakakis, N and Mantziou, G and Parmakelis, A and Mylonas, M}, title = {Molecular phylogeny of three Mesalina (Reptilia: Lacertidae) species (M. guttulata, M. brevirostris and M. bahaeldini) from North Africa and the Middle East: another case of paraphyly?.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {102-110}, doi = {10.1016/j.ympev.2008.06.016}, pmid = {18644456}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Genes, rRNA ; Geography ; Likelihood Functions ; Lizards/*classification/*genetics ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Mesalina is a widespread lacertid genus occurring throughout the Saharo-Sindian region from North Africa to Pakistan. It has been through a series of taxonomic revisions, but the phylogenetic relationships among the species remain unclear. In this study we estimate the phylogeographic structure of M. guttulata across most of its distributional range and we evaluate the relationships between M. guttulata and the sympatric species M. brevirostris and M. bahaeldini using partial mitochondrial DNA (mtDNA) sequences (cyt b and 16S). M. guttulata and M. brevirostris represent species complexes, whereas M. bahaeldini considered before as M. guttulata is a recently described species with very restricted distribution. Here we present the first evidence that M. guttulata is a paraphyletic taxon with respect to M. bahaeldini, while M. brevirostris proves to be a polytypic species or even a species complex, confirming previous studies. Although mtDNA markers have several properties that make them suitable for phylogeographic studies, they are not free of difficulties. Phylogeographic inferences within and between closely related species can be mislead by introgression and retention of ancestral polymorphism (incomplete lineage sorting). However, the present distribution pattern, the estimated times of divergence and the significant variation in morphology within M. guttulata led us to accept that the paraphyletic pattern observed, is most likely due to inaccurate taxonomy. Our hypothesis is that what has hitherto been considered as intraspecific variation, actually reflects species-level variation. Furthermore, our biogeographic analyses and the estimated time of divergences suggest that the present distribution of M. guttulata was the result of several dispersal and vicariant events, which are associated with historical changes (climatic oscillations and paleogeographic barriers) of late Miocene and Pliocene period.}, }
@article {pmid18644455, year = {2008}, author = {Maurício, GN and Mata, H and Bornschein, MR and Cadena, CD and Alvarenga, H and Bonatto, SL}, title = {Hidden generic diversity in Neotropical birds: molecular and anatomical data support a new genus for the "Scytalopus"indigoticus species-group (Aves: Rhinocryptidae).}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {125-135}, doi = {10.1016/j.ympev.2008.06.017}, pmid = {18644455}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; *Genetic Variation ; Likelihood Functions ; Mitochondria/genetics ; Passeriformes/anatomy &amp; histology/*classification/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The genus Scytalopus is a species-rich and taxonomically complicated component of the Neotropical avian family Rhinocryptidae. Probably because Scytalopus is a superficially uniform assemblage, its monophyly has not been seriously questioned. We investigated phylogenetic relationships of a representative set of species in the genus using nuclear and mitochondrial DNA sequences as well as anatomical data, and provided the first test of its presumed monophyly by including in the analyses its hypothesized closest relatives (the genera Myornis, Eugralla, and Merulaxis) as well as most rhinocryptid genera. We found strong support for the paraphyly of the genus Scytalopus, with the Scytalopus indigoticus species-group forming a clade with Merulaxis. A well-supported clade including the genera Eugralla, Myornis, and the remaining Scytalopus was also recovered. Because these results were recovered independently and with strong support using mitochondrial and nuclear data, and were entirely consistent with anatomical data, we erect a new genus for the S.indigoticus species-group. These findings illustrate the importance of formally testing hypotheses of monophyly even for well-accepted groups of Neotropical birds.}, }
@article {pmid18639642, year = {2008}, author = {Voelker, G and Klicka, J}, title = {Systematics of Zoothera thrushes, and a synthesis of true thrush molecular systematic relationships.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {377-381}, doi = {10.1016/j.ympev.2008.06.014}, pmid = {18639642}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Genetic Speciation ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Songbirds/*classification/*genetics ; Species Specificity ; }, }
@article {pmid18637481, year = {2008}, author = {Chen, JQ and Brown, TR and Yager, JD}, title = {Mechanisms of hormone carcinogenesis: evolution of views, role of mitochondria.}, journal = {Advances in experimental medicine and biology}, volume = {630}, number = {}, pages = {1-18}, pmid = {18637481}, issn = {0065-2598}, mesh = {*Concept Formation ; Energy Metabolism/physiology ; Estrogens/pharmacology ; Hormones/*physiology ; Humans ; Mitochondria/metabolism/*physiology ; Models, Biological ; Neoplasms/chemically induced/*etiology/metabolism ; Neoplasms, Hormone-Dependent/metabolism ; Receptors, Estrogen/physiology ; Signal Transduction/physiology ; }, abstract = {CumuIative and excessive exposure to estrogens is associated with increased breast cancer risk. The traditional mechanism explaining this association is that estrogens affect the rate of cell division and apoptosis and thus manifest their effect on the risk of breast cancer by affecting the growth of breast epithelial tissues. Highly proliferative cells are susceptible to genetic errors during DNA replication. The action of estrogen metabolites offers a complementary genotoxic pathway mediated by the generation of reactive estrogen quinone metabolites that can form adducts with DNA and generate reactive oxygen species through redox cycling. In this chapter, we discussed a novel mitochondrial pathway mediated by estrogens and their cognate estrogen receptors (ERs) and its potential implications in estrogen-dependent carcinogenesis. Several lines of evidence are presented to show: (1) mitochondrial localization of ERs in human breast cancer cells and other cell types; (2) a functional role for the mitochondrial ERs in regulation of the mitochondrial respiratory chain (MRC) proteins and (3) potential implications of the mitochondrial ER-mediated pathway in stimulation of cell proliferation, inhibition of apoptosis and oxidative damage to mitochondrial DNA. The possible involvement of estrogens and ERs in deregulation of mitochondrial bioenergetics, an important hallmark of cancer cells, is also described. An evolutionary view is presented to suggest that persistent stimulation by estrogens through ER signaling pathways of MRC proteins and energy metabolic pathways leads to the alterations in mitochondrial bioenergetics and contributes to the development of estrogen-related cancers.}, }
@article {pmid18629668, year = {2008}, author = {Zardoya, R and Suárez, M}, title = {Sequencing and phylogenomic analysis of whole mitochondrial genomes of animals.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {422}, number = {}, pages = {185-200}, doi = {10.1007/978-1-59745-581-7_12}, pmid = {18629668}, issn = {1064-3745}, mesh = {Animals ; Cloning, Molecular ; DNA, Mitochondrial/isolation &amp; purification ; Genome, Mitochondrial/*genetics ; Genomics/*methods ; Mitochondria/genetics ; *Phylogeny ; Polymerase Chain Reaction ; Restriction Mapping ; Sequence Analysis, DNA/*methods ; }, abstract = {Mitochondrial genomes (mtDNA) of animals are circular molecules of relatively small size, compactly organized, and generally encoding genes for 2 rRNAs, 22 tRNAs, and 13 proteins that are required for mitochondrial function. Methods of mtDNA isolation take advantage of its physical localization apart from the nuclear genome (centrifugation at low speed efficiently separates mitochondria from nuclei) and of its structure (alkaline lysis differentially precipitates linear nuclear DNA, but not circular mtDNA). Furthermore, the recent development of robust long-PCR techniques has boosted high-throughput determination of complete sequences of animal mtDNAs. The exponentially growing number of complete animal mitochondrial genomes deposited in GenBank allows a phylogenomic approach to disentangle phylogenetic relationships among main animal phyla, and provides extensive new data to gain insights on the molecular mechanisms underlying genome evolution.}, }
@article {pmid18626081, year = {2008}, author = {Ivanis, G and Esbaugh, AJ and Perry, SF}, title = {Branchial expression and localization of SLC9A2 and SLC9A3 sodium/hydrogen exchangers and their possible role in acid-base regulation in freshwater rainbow trout (Oncorhynchus mykiss).}, journal = {The Journal of experimental biology}, volume = {211}, number = {Pt 15}, pages = {2467-2477}, doi = {10.1242/jeb.017491}, pmid = {18626081}, issn = {0022-0949}, mesh = {*Acid-Base Equilibrium ; Animals ; Branchial Region/*metabolism ; Cloning, Molecular ; Fish Diseases/metabolism ; *Fresh Water ; Gene Expression Profiling ; Gene Expression Regulation ; Gills/cytology/metabolism ; Hydrocortisone/blood ; Hypercapnia/metabolism/veterinary ; Molecular Sequence Data ; Oncorhynchus mykiss/genetics/*metabolism ; Peanut Agglutinin/metabolism ; Phylogeny ; Protein Transport ; RNA, Messenger ; Sodium-Hydrogen Exchangers/genetics/*metabolism ; }, abstract = {Experiments were conducted on adult rainbow trout (Oncorhynchus mykiss) to test the hypothesis that SLC9 Na+/H+ exchangers (SLC9A2, NHE2; and SLC9A3, NHE3) on the gill epithelium are localized specifically to a subset of mitochondria-rich cells (MRCs) that are unable to bind peanut lectin agglutinin (PNA). This cell type, termed the PNA- MRC, is a sub-type of MRC believed to function in Na+ uptake and acid excretion. A technique using biotinylated PNA was used to distinguish between the PNA- and PNA+ MRCs on fixed gill sections. In contrast to expectations, both NHE2 (mRNA) and NHE3 (protein) were confined to cells enriched with Na+/K+-ATPase and capable of binding PNA. Thus, in trout, NHE2 and NHE3 are localized to PNA+ MRCs, the cells previously believed to be responsible for Cl- uptake and base excretion. Levels of mRNA for NHE2, the predominant isoform in the gill, were increased during 72 h of hypercapnic acidosis; NHE3 mRNA and protein levels were unaffected. Because plasma cortisol levels were increased during hypercapnia (from 35.3+/-9.4 to 100.1+/-30.9 ng ml(-1)), the effects of experimentally elevated cortisol levels on NHE expression were investigated. The elevation of plasma cortisol using intraperitoneal implants caused a significant increase in NHE2 mRNA expression without affecting NHE3 mRNA or protein abundance. Thus, we suggest that NHE2 contributes to acid-base regulation during hypercapnia owing to its transcriptional regulation by cortisol. The finding of NHE expression in PNA+ MRCs is discussed with reference to current models of ionic and acid-base regulation in teleost fish.}, }
@article {pmid18625327, year = {2008}, author = {Pfeiler, E and Markow, TA}, title = {Phylogenetic relationships of leopard frogs (Rana pipiens complex) from an isolated coastal mountain range in southern Sonora, Mexico.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {343-348}, doi = {10.1016/j.ympev.2008.06.011}, pmid = {18625327}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Genes, rRNA ; *Genetic Speciation ; Likelihood Functions ; Mexico ; Mitochondria/genetics ; *Phylogeny ; RNA, Ribosomal ; Rana pipiens/*classification/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Mitochondrial DNA sequence data from the control region and 12S rRNA in leopard frogs from the Sierra El Aguaje of southern Sonora, Mexico, together with GenBank sequences, were used to infer taxonomic identity and provide phylogenetic hypotheses for relationships with other members of the Rana pipiens complex. We show that frogs from the Sierra El Aguaje belong to the Rana berlandieri subgroup, or Scurrilirana clade, of the R. pipiens group, and are most closely related to Rana magnaocularis from Nayarit, Mexico. We also provide further evidence that Rana magnaocularis and R. yavapaiensis are close relatives.}, }
@article {pmid18621133, year = {2008}, author = {Smith, LL and Fessler, JL and Alfaro, ME and Streelman, JT and Westneat, MW}, title = {Phylogenetic relationships and the evolution of regulatory gene sequences in the parrotfishes.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {136-152}, pmid = {18621133}, issn = {1095-9513}, support = {R03 DE014446/DE/NIDCR NIH HHS/United States ; R03 DE014446-03/DE/NIDCR NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; *Genes, Regulator ; Genes, rRNA ; Likelihood Functions ; Mitochondria/genetics ; Perciformes/*classification/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Regulatory genes control the expression of other genes and are key components of developmental processes such as segmentation and embryonic construction of the skull in vertebrates. Here we examine the variability and evolution of three vertebrate regulatory genes, addressing issues of their utility for phylogenetics and comparing the rates of genetic change seen in regulatory loci to the rates seen in other genes in the parrotfishes. The parrotfishes are a diverse group of colorful fishes from coral reefs and seagrasses worldwide and have been placed phylogenetically within the family Labridae. We tested phylogenetic hypotheses among the parrotfishes, with a focus on the genera Chlorurus and Scarus, by analyzing eight gene fragments for 42 parrotfishes and eight outgroup species. We sequenced mitochondrial 12s rRNA (967 bp), 16s rRNA (577 bp), and cytochrome b (477 bp). From the nuclear genome, we sequenced part of the protein-coding genes rag2 (715 bp), tmo4c4 (485 bp), and the developmental regulatory genes otx1 (672 bp), bmp4 (488bp), and dlx2 (522 bp). Bayesian, likelihood, and parsimony analyses of the resulting 4903 bp of DNA sequence produced similar topologies that confirm the monophyly of the scarines and provide a phylogeny at the species level for portions of the genera Scarus and Chlorurus. Four major clades of Scarus were recovered, with three distributed in the Indo-Pacific and one containing Caribbean/Atlantic taxa. Molecular rates suggest a Miocene origin of the parrotfishes (22 mya) and a recent divergence of species within Scarus and Chlorurus, within the past 5 million years. Developmentally important genes made a significant contribution to phylogenetic structure, and rates of genetic evolution were high in bmp4, similar to other coding nuclear genes, but low in otx1 and the dlx2 exons. Synonymous and non-synonymous substitution patterns in developmental regulatory genes support the hypothesis of stabilizing selection during the history of these genes, with several phylogenetic regions of accelerated non-synonymous change detected in the phylogeny.}, }
@article {pmid18620870, year = {2008}, author = {Meraner, A and Brandstätter, A and Thaler, R and Aray, B and Unterlechner, M and Niederstätter, H and Parson, W and Zelger, R and Dalla Via, J and Dallinger, R}, title = {Molecular phylogeny and population structure of the codling moth (Cydia pomonella) in Central Europe: I. Ancient clade splitting revealed by mitochondrial haplotype markers.}, journal = {Molecular phylogenetics and evolution}, volume = {48}, number = {3}, pages = {825-837}, doi = {10.1016/j.ympev.2008.05.026}, pmid = {18620870}, issn = {1095-9513}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/genetics ; Diflubenzuron/pharmacology ; Europe ; Evolution, Molecular ; Genetic Markers ; Genotype ; *Haplotypes ; Mitochondria/*genetics ; Models, Genetic ; Moths/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The codling moth (Cydia pomonella L., Tortricidae, Lepidoptera) is an important pest of pome fruit with global distribution. It has adapted successfully to different habitats by forming various ecotypes and populations, often termed strains, which differ among each other in several morphological, developmental, and physiological features. Many strains of Cydia pomonella have developed resistance against a broad range of chemically different pesticides. Obviously, pesticide-resistant strains must have a genetic basis inherent to the gene pool of codling moth populations, and this deserves our particular attention. The primary intention of the present study was to contribute novel information regarding the evolutionary phylogeny and phylogeography of codling moth populations in Central Europe. In addition, we aimed at testing the hypothesis that differential biological traits and response patterns towards pesticides in codling moth populations may be reflected at a mitochondrial DNA level. In particular, we wanted to test if pesticide resistance in codling moths is associated repeatedly and independently with more than one mitochondrial haplotype. To this end, we analyzed mitochondrial DNA and constructed phylogenetic trees based on three mitochondrial genes: cytochrome oxidase I (COI), the A+T-rich region of the control region (CR), and the nicotinamide adenine dinucleotide dehydrogenase subunit 5 (ND5). The results indicate that Central European populations of Cydia pomonella are clearly divided in two ancient clades. As shown by means of a molecular clock approach, the splitting of the two clades can be dated to a time period between the lower and middle Pleistocene, about 1.29-0.20 million years ago. It is assumed that the cyclic changes of warm and cold periods during Pleistocene may have lead to the geographic separation of codling moth populations due to glaciation, giving rise to the formation of the two separate refugial clades, as already shown for many other European animal species. Due to their inclination towards developing novel detoxification gene variants, codling moth individuals from both clades independently and multifariously may have developed pesticide resistance, and this process may be ongoing. During their more recent evolutionary history, natural events such as the gradual disappearance of climate-specific geographic barriers, as well as human-aided dispersal in recent historic times, may have allowed codling moth haplotypes from the original clades to interbreed and completely merge again, creating a globally successful insect species with a gene pool capable of responding to novel selective challenges by rapid adaptation.}, }
@article {pmid18619978, year = {2008}, author = {Locke, BR and Kinsey, ST}, title = {Diffusional constraints on energy metabolism in skeletal muscle.}, journal = {Journal of theoretical biology}, volume = {254}, number = {2}, pages = {417-429}, doi = {10.1016/j.jtbi.2008.06.008}, pmid = {18619978}, issn = {1095-8541}, support = {R15-AR052708/AR/NIAMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/metabolism ; Animals ; *Computer Simulation ; Diffusion ; Energy Metabolism/*physiology ; Models, Biological ; *Models, Statistical ; Muscle Contraction/physiology ; Muscle, Skeletal/*metabolism ; }, abstract = {Aerobic metabolic flux depends on the diffusion of high-energy phosphate molecules (e.g., ATP and phosphocreatine) from the mitochondria to cellular ATPases, as well as the diffusion of other molecules (e.g., ADP, Pi) back to the mitochondria. Here, we develop an approach for evaluating the influence of intracellular metabolite diffusion on skeletal muscle aerobic metabolism through the application of the effectiveness factor (eta). This parameter provides an intuitive and informative means of quantifying the extent to which diffusion limits metabolic flux. We start with the classical approach assuming an infinite supply of substrate at the fiber boundary, and we expand this model to ultimately include nonlinear boundary and homogeneous reactions. Comparison of the model with experimental data from a wide range of skeletal muscle types reveals that most muscle fibers are not substantially limited by diffusion (eta close to unity), but many are on the brink of rather substantial diffusion limitation. This implies that intracellular metabolite diffusion does not dramatically limit aerobic metabolic flux in most fibers, but it likely plays a role in limiting the evolution of muscle fiber design and function.}, }
@article {pmid18619861, year = {2008}, author = {Thaler, R and Brandstätter, A and Meraner, A and Chabicovski, M and Parson, W and Zelger, R and Dalla Via, J and Dallinger, R}, title = {Molecular phylogeny and population structure of the codling moth (Cydia pomonella) in Central Europe: II. AFLP analysis reflects human-aided local adaptation of a global pest species.}, journal = {Molecular phylogenetics and evolution}, volume = {48}, number = {3}, pages = {838-849}, doi = {10.1016/j.ympev.2008.05.027}, pmid = {18619861}, issn = {1095-9513}, mesh = {Animals ; Europe ; Evolution, Molecular ; Female ; Genetic Markers ; Genetic Variation ; Geography ; Humans ; Insecticide Resistance/drug effects/genetics ; Male ; Mitochondria/genetics ; Moths/*drug effects/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Sex Factors ; }, abstract = {Originally resident in southeastern Europe, the codling moth (Cydia pomonella L.) (Tortricidae) has achieved a nearly global distribution, being one of the most successful pest insect species known today. As shown in our accompanying study, mitochondrial genetic markers suggest a Pleistocenic splitting of Cydia pomonella into two refugial clades which came into secondary contact after de-glaciation. The actual distribution pattern shows, however, that Central European codling moths have experienced a geographic splitting into many strains and locally adapted populations, which is not reflected by their mitochondrial haplotype distribution. We therefore have applied, in addition to mitochondrial markers, an approach with a higher resolution potential at the population level, based on the analysis of amplification fragment length polymorphisms (AFLPs). As shown in the present study, AFLP markers elucidate the genetic structure of codling moth strains and populations from different Central European apple orchard sites. While individual genetic diversity within codling moth strains and populations was small, a high degree of genetic differentiation was observed between the analyzed strains and populations, even at a small geographic scale. One of the main factors contributing to local differentiation may be limited gene flow among adjacent codling moth populations. In addition, microclimatic, ecological, and geographic constraints also may favour the splitting of Cydia pomonella into many local populations. Lastly, codling moths in Central European fruit orchards may experience considerable selective pressure due to pest control activities. As a consequence of all these selective forces, today in Central Europe we see a patchy distribution of many locally adapted codling moth populations, each of them having its own genetic fingerprint. Because of the complete absence of any correlation between insecticide resistance and geographic or genetic distances among populations, AFLP markers do not have a prognostic value for predicting an outbreak of pesticide resistance in the field. By combining mitochondrial genetic data and AFLP analysis it was possible, however, to track the recent evolutionary history of Cydia pomonella on three different time scales: from population splitting in Pleistocene, to interbreeding of mitochondrial haplotypes in Holocene, to human-aided complete intermixing and splitting into many locally adapted populations in very recent times. The case of Cydia pomonella is reminiscent of examples of sympatric speciation and another example of a human-induced globally successful pest species.}, }
@article {pmid18611442, year = {2008}, author = {Gifford, ME and Larson, A}, title = {In situ genetic differentiation in a Hispaniolan lizard (Ameiva chrysolaema): a multilocus perspective.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {277-291}, doi = {10.1016/j.ympev.2008.06.003}, pmid = {18611442}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Gene Flow ; Genes, Mitochondrial ; *Genetic Speciation ; Genetics, Population ; Geography ; Haplotypes ; INDEL Mutation ; Introns ; Lizards/*classification/*genetics ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {A previous phylogeographic study of mitochondrial haplotypes for the Hispaniolan lizard Ameiva chrysolaema revealed deep genetic structure associated with seawater inundation during the late Pliocene/early Pleistocene and evidence of subsequent population expansion into formerly inundated areas. We revisit hypotheses generated by our previous study using increased geographic sampling of populations and analysis of three nuclear markers (alpha-enolase intron 8, alpha-cardiac-actin intron 4, and beta-actin intron 3) in addition to mitochondrial haplotypes (ND2). Large genetic discontinuities correspond spatially and temporally with historical barriers to gene flow (sea inundations). NCPA cross-validation analysis and Bayesian multilocus analyses of divergence times (IMa and MCMCcoal) reveal two separate episodes of fragmentation associated with Pliocene and Pleistocene sea inundations, separating the species into historically separate Northern, East-Central, West-Central, and Southern population lineages. Multilocus Bayesian analysis using IMa indicates asymmetrical migration from the East-Central to the West-Central populations following secondary contact, consistent with expectations from the more pervasive sea inundation in the western region. The West-Central lineage has a genetic signature of population growth consistent with the expectation of geographic expansion into formerly inundated areas. Within each lineage, significant spatial genetic structure indicates isolation by distance at comparable temporal scales. This study adds to the growing body of evidence that vicariant speciation may be the prevailing source of lineage accumulation on oceanic islands. Thus, prior theories of island biogeography generally underestimate the role and temporal scale of intra-island vicariant processes.}, }
@article {pmid18608923, year = {2008}, author = {Jacobsen, MD and Rattray, AM and Gow, NA and Odds, FC and Shaw, DJ}, title = {Mitochondrial haplotypes and recombination in Candida albicans.}, journal = {Medical mycology}, volume = {46}, number = {7}, pages = {647-654}, doi = {10.1080/13693780801986631}, pmid = {18608923}, issn = {1369-3786}, support = {074898//Wellcome Trust/United Kingdom ; }, mesh = {Base Sequence ; Candida albicans/*genetics/isolation &amp; purification ; Candidiasis/microbiology ; Gene Frequency ; Geography ; Haplotypes/*genetics ; Linkage Disequilibrium ; Mitochondria/*genetics ; Mycological Typing Techniques ; Phylogeny ; Polymorphism, Genetic ; Recombination, Genetic/*genetics ; Sequence Alignment ; }, abstract = {Candida albicans is a common commensal and opportunistic pathogenic fungus. Although it normally reproduces clonally, several lines of evidence exist for genetic recombination and some form of sexual reproduction. We have sequenced seven regions of its mitochondrial genome in 36 strains and constructed haplotypes for the 66 polymorphic sites, which include single-nucleotide polymorphisms and insertion/deletions. Nineteen different haplotypes were observed. Strains with the same mitochondrial haplotype were found in different clades defined by nuclear multilocus sequence typing (MLST) and the UPGMA dendrograms constructed using either set of data were different in topology. There was no apparent correlation between mitochondrial haplotype and the source of the strain (geographical or anatomical). Examination of the mitochondrial haplotypes revealed substantial evidence for recombination between polymorphic sites. This suggests that the use of mitochondrial haplotypes in phylogenetic studies should be approached with caution. These results provide further evidence for recombination and genetic exchange in the biology of C. albicans.}, }
@article {pmid18606551, year = {2008}, author = {Funk, WC and Pearl, CA and Draheim, HM and Adams, MJ and Mullins, TD and Haig, SM}, title = {Range-wide phylogeographic analysis of the spotted frog complex (Rana luteiventris and Rana pretiosa) in northwestern North America.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {198-210}, doi = {10.1016/j.ympev.2008.05.037}, pmid = {18606551}, issn = {1095-9513}, mesh = {Animals ; Conservation of Natural Resources ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Genetic Speciation ; Genetic Variation ; Genetics, Population ; Geography ; Likelihood Functions ; Mitochondria/genetics ; North America ; *Phylogeny ; Ranidae/*classification/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The dynamic geological and climatic history of northwestern North America has made it a focal region for phylogeography. We conducted a range-wide phylogeographic analysis of the spotted frog complex (Rana luteiventris and Rana pretiosa) across its range in northwestern North America to understand its evolutionary history and the distribution of clades to inform conservation of R. pretiosa and Great Basin R. luteiventris, candidates for listing under the US Endangered Species Act. Mitochondrial DNA sequence data from a segment of the cytochrome b gene were obtained from 308 R. luteiventris and R. pretiosa from 96 sites. Phylogenetic analysis revealed one main R. pretiosa clade and three main R. luteiventris clades, two of which overlapped in southeastern Oregon. The three R. luteiventris clades were separated from each other by high levels of sequence divergence (average of 4.75-4.97%). Two divergent clades were also uncovered within the Great Basin. Low genetic variation in R. pretiosa and the southeastern Oregon clade of R. luteiventris suggests concern about their vulnerability to extinction.}, }
@article {pmid18603009, year = {2008}, author = {Murienne, J and Harvey, MS and Giribet, G}, title = {First molecular phylogeny of the major clades of Pseudoscorpiones (Arthropoda: Chelicerata).}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {170-184}, doi = {10.1016/j.ympev.2008.06.002}, pmid = {18603009}, issn = {1095-9513}, mesh = {Algorithms ; Animals ; Arachnida/*classification/*genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Genes, rRNA ; Mitochondria/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {The phylogenetic relationships of the major lineages of the arachnid order Pseudoscorpiones are investigated for the first time using molecular sequence data from two nuclear ribosomal genes and one mitochondrial protein-encoding gene. The data were analyzed using a dynamic homology approach with the new program POY v.4 under parsimony as the optimality criterion. The data show monophyly of Pseudoscorpiones as well as many of its superfamilies (Feaelloidea, Chthonioidea, Cheiridioidea and Sternophoroidea), but not for Neobisiodea or Garypoidea. Cheliferoidea was not monophyletic either due to the position of Neochelanops, which grouped with some garypoids. In all the analyses, Feaelloidea constituted the sister group to all other pseudoscorpions; Chthonioidea is the sister group to the remaining families, which constitute the group Iocheirata sensu Harvey--a clade including pseudoscorpions with venom glands within the pedipalpal fingers. This phylogenetic pattern suggests that venom glands evolved just once within this order of arachnids.}, }
@article {pmid18602842, year = {2008}, author = {Zhao, J and Li, C and Zhao, L and Wang, W and Cao, Y}, title = {Mitochondrial diversity and phylogeography of the Chinese perch, Siniperca chuatsi (Perciformes: Sinipercidae).}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {399-404}, doi = {10.1016/j.ympev.2008.05.031}, pmid = {18602842}, issn = {1095-9513}, mesh = {Animals ; China ; Conservation of Natural Resources ; Evolution, Molecular ; Gene Flow ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes ; Mitochondria/*genetics ; Models, Genetic ; Perches/*classification/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, }
@article {pmid18602174, year = {2008}, author = {Marciano, D and Llorente, C and Maugeri, DA and de la Fuente, C and Opperdoes, F and Cazzulo, JJ and Nowicki, C}, title = {Biochemical characterization of stage-specific isoforms of aspartate aminotransferases from Trypanosoma cruzi and Trypanosoma brucei.}, journal = {Molecular and biochemical parasitology}, volume = {161}, number = {1}, pages = {12-20}, doi = {10.1016/j.molbiopara.2008.05.005}, pmid = {18602174}, issn = {0166-6851}, mesh = {Amino Acid Sequence ; Animals ; Aspartate Aminotransferases/*genetics/isolation &amp; purification/*metabolism ; Aspartic Acid/metabolism ; Cloning, Molecular ; Escherichia coli/genetics ; Gene Expression ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Isoenzymes/genetics/isolation &amp; purification/metabolism ; Ketoglutaric Acids/metabolism ; Kinetics ; Malate Dehydrogenase/biosynthesis ; Microbodies/enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Substrate Specificity ; Succinic Acid/metabolism ; Trypanosoma brucei brucei/*enzymology ; Trypanosoma cruzi/*enzymology ; }, abstract = {Three genes encoding putative aspartate aminotransferases (ASATs) were identified in the Trypanosoma cruzi genome. Two of these ASAT genes, presumably corresponding to a cytosolic and mitochondrial isoform, were cloned and expressed as soluble His-tagged proteins in Escherichia coli. The specific activities determined for both T. cruzi isozymes were notably higher than the values previously reported for Trypanosoma brucei orthologues. To confirm these differences, T. brucei mASAT and cASAT were also expressed as His-tagged enzymes. The kinetic analysis showed that the catalytic parameters of the new recombinant T. brucei ASATs were very similar to those determined for T. cruzi orthologues. The cASATs from both parasites displayed equally broad substrate specificities, while mASATs were highly specific towards aspartate/2-oxoglutarate. The subcellular localization of the mASAT was confirmed by digitonin extraction of intact epimastigotes. At the protein level, cASAT is constitutively expressed in T. brucei, whereas mASAT is down-regulated in the bloodstream forms. By contrast in T. cruzi, mASAT is expressed along the whole life cycle, whereas cASAT is specifically induced in the mammalian stages. Similarly, the expression of malate dehydrogenases (MDHs) is developmentally regulated in T. cruzi: while glycosomal MDH is only expressed in epimastigotes and mitochondrial MDH is present in the insect and mammalian stages. Taken together, these findings provide evidence for a metabolically active mitochondrion in the mammalian stages of T. cruzi, and suggest that the succinate excreted by amastigotes more likely represents a side product of an at least partially operative Krebs cycle, than an end product of glycosomal catabolism.}, }
@article {pmid18600633, year = {2008}, author = {Vesteg, M and Krajcovic, J}, title = {On the origin of eukaryotic cytoskeleton.}, journal = {Rivista di biologia}, volume = {101}, number = {1}, pages = {109-118}, pmid = {18600633}, issn = {0035-6050}, mesh = {Animals ; Archaea/cytology/virology ; Archaeal Proteins/physiology ; Bacteria/cytology/virology ; Bacterial Proteins/physiology ; *Biological Evolution ; Cytoskeletal Proteins/genetics/physiology ; *Cytoskeleton/ultrastructure ; Escherichia coli Proteins/physiology ; Eukaryotic Cells/*ultrastructure/virology ; Evolution, Molecular ; Flagella/genetics/physiology ; Models, Biological ; Prokaryotic Cells/ultrastructure/virology ; Symbiosis ; Transduction, Genetic ; Tubulin/genetics/physiology ; Virus Replication ; }, abstract = {The origin of eukaryote-specific cytoskeletal proteins is an issue which is closely related to the origin of the domain Eukarya. As nearly all of these proteins are not found in prokaryotes, the prokaryotic origin of eukaryotic cytoskeletal network suggested by most models is questionable. Eukaryotic cytoskeletal proteins might descend from subpopulations of pre-cells co-existing with Bacteria and Archaea prior to the origin of eukaryotes. The pre-karyote (the host for a-proteobacterial ancestors of mitochondria) might have already possessed eukaryotic-like cytoskeleton. A possible role for viruses in the origin of eukaryotic cytoskeletal proteins is discussed. Viruses parasitizing on pre-cells and/or on the pre-karyote might have themselves used several eukaryotic-like cytoskeletal proteins for segregation and packing of their genomes.}, }
@article {pmid18588991, year = {2008}, author = {Osborn, KJ and Rouse, GW}, title = {Multiple origins of pelagicism within Flabelligeridae (Annelida).}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {386-392}, doi = {10.1016/j.ympev.2008.05.042}, pmid = {18588991}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Genetic Markers ; Markov Chains ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; Polychaeta/*classification/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, }
@article {pmid18588990, year = {2008}, author = {Geurgas, SR and Rodrigues, MT and Moritz, C}, title = {The genus Coleodactylus (Sphaerodactylinae, Gekkota) revisited: a molecular phylogenetic perspective.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {92-101}, doi = {10.1016/j.ympev.2008.05.043}, pmid = {18588990}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Genes, RAG-1 ; Genes, mos ; Genes, rRNA ; *Genetic Speciation ; Likelihood Functions ; Lizards/*classification/*genetics ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {Nucleotide sequence data from a mitochondrial gene (16S) and two nuclear genes (c-mos, RAG-1) were used to evaluate the monophyly of the genus Coleodactylus, to provide the first phylogenetic hypothesis of relationships among its species in a cladistic framework, and to estimate the relative timing of species divergences. Maximum Parsimony, Maximum Likelihood and Bayesian analyses of the combined data sets retrieved Coleodactylus as a monophyletic genus, although weakly supported. Species were recovered as two genetically and morphological distinct clades, with C. amazonicus populations forming the sister taxon to the meridionalis group (C. brachystoma, C. meridionalis, C. natalensis, and C. septentrionalis). Within this group, C. septentrionalis was placed as the sister taxon to a clade comprising the rest of the species, C. meridionalis was recovered as the sister species to C. brachystoma, and C. natalensis was found nested within C. meridionalis. Divergence time estimates based on penalized likelihood and Bayesian dating methods do not support the previous hypothesis based on the Quaternary rain forest fragmentation model proposed to explain the diversification of the genus. The basal cladogenic event between major lineages of Coleodactylus was estimated to have occurred in the late Cretaceous (72.6+/-1.77 Mya), approximately at the same point in time than the other genera of Sphaerodactylinae diverged from each other. Within the meridionalis group, the split between C. septentrionalis and C. brachystoma+C. meridionalis was placed in the Eocene (46.4+/-4.22 Mya), and the divergence between C. brachystoma and C. meridionalis was estimated to have occurred in the Oligocene (29.3+/-4.33 Mya). Most intraspecific cladogenesis occurred through Miocene to Pliocene, and only for two conspecific samples and for C. natalensis could a Quaternary differentiation be assumed (1.9+/-1.3 Mya).}, }
@article {pmid18586950, year = {2008}, author = {Wloga, D and Strzyzewska-Jówko, I and Gaertig, J and Jerka-Dziadosz, M}, title = {Septins stabilize mitochondria in Tetrahymena thermophila.}, journal = {Eukaryotic cell}, volume = {7}, number = {8}, pages = {1373-1386}, pmid = {18586950}, issn = {1535-9786}, mesh = {Animals ; Apoptosis/physiology ; Cytoskeletal Proteins/genetics/*metabolism ; Endoplasmic Reticulum/metabolism/ultrastructure ; Evolution, Molecular ; Green Fluorescent Proteins ; Microscopy, Electron, Transmission ; Mitochondria/*metabolism/ultrastructure ; Mitochondrial Membranes/*metabolism/ultrastructure ; Protozoan Proteins/genetics/*metabolism ; Tetrahymena thermophila/*metabolism/ultrastructure ; }, abstract = {We describe phylogenetic and functional studies of three septins in the free-living ciliate Tetrahymena thermophila. Both deletion and overproduction of septins led to vacuolization of mitochondria, destabilization of the nuclear envelope, and increased autophagy. All three green fluorescent protein-tagged septins localized to mitochondria. Specific septins localized to the outer mitochondrial membrane, to septa formed during mitochondrial scission, or to the mitochondrion-associated endoplasmic reticulum. The only other septins known to localize to mitochondria are human ARTS and murine M-septin, both alternatively spliced forms of Sep4 (S. Larisch, Cell Cycle 3:1021-1023, 2004; S. Takahashi, R. Inatome, H. Yamamura, and S. Yanagi, Genes Cells 8:81-93, 2003). It therefore appears that septins have been recruited to mitochondrial functions independently in at least two eukaryotic lineages and in both cases are involved in apoptotic events.}, }
@article {pmid18586304, year = {2008}, author = {Chung, PP and Hyne, RV and Mann, RM and Ballard, JW}, title = {Genetic and life-history trait variation of the amphipod Melita plumulosa from polluted and unpolluted waterways in eastern Australia.}, journal = {The Science of the total environment}, volume = {403}, number = {1-3}, pages = {222-229}, doi = {10.1016/j.scitotenv.2008.05.038}, pmid = {18586304}, issn = {0048-9697}, mesh = {Amphipoda/*physiology ; Animals ; Australia ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics/metabolism ; Environmental Monitoring ; Female ; Fertility/genetics ; Fresh Water/*analysis ; *Genetic Variation ; Head/anatomy &amp; histology ; Life Cycle Stages/*physiology ; Mitochondria/enzymology ; Water Pollutants, Chemical/*analysis ; *Water Pollution ; }, abstract = {To monitor genetic diversity and environmental contamination in eastern Australia, toxicity studies have employed the sensitive benthic amphipod Melita plumulosa. The goal of this study was to examine the genetic and life-history variability of natural populations of M. plumulosa from the Parramatta (polluted) and Hawkesbury (unpolluted) Rivers. The underlying genetics of the populations in these distinct waterways was examined at one mitochondrial (cytochrome c oxidase subunit I (COI)) and one nuclear (ribosomal internal transcribed spacer region 1 (ITS1)) locus. Seven unique haplotypes for COI were found amongst animals from the Parramatta River, while animals from the Hawkesbury River showed a complete absence of genetic variation at this locus. At ITS1 a total of two sequence variants were found amongst Parramatta River amphipods and three sequence variants among Hawkesbury River animals, with no common variants across the two river systems. To establish whether genetic differences were associated with organismal responses to toxicant exposure, two life-history trait variables (female head length as an estimator of amphipod size and female fecundity) were analyzed. Life-history trait analyses showed that females from the Hawkesbury River were significantly larger and more fecund. These data have critical implications for toxicity tests, the use of laboratory cultures for testing purposes, and environmental contamination in Sydney Harbor.}, }
@article {pmid18583159, year = {2008}, author = {Lavrov, DV and Wang, X and Kelly, M}, title = {Reconstructing ordinal relationships in the Demospongiae using mitochondrial genomic data.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {111-124}, doi = {10.1016/j.ympev.2008.05.014}, pmid = {18583159}, issn = {1095-9513}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Gene Order ; Genes, Mitochondrial ; Genes, rRNA ; *Genome, Mitochondrial ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; Porifera/*classification/*genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Alignment ; }, abstract = {Class Demospongiae (phylum Porifera) encompasses most of sponges' morphological and species diversity. It also represents one of the most challenging and understudied groups in animal phylogenetics, with many higher-level relationships still being unresolved. Among the unanswered questions are the most fundamental, including those about the monophyly of the Demospongiae and the relationships among the 14 recognized orders within the class. The lack of resolved phylogeny hampers progress in studies of demosponge biology, evolution and biodiversity and may interfere with the efficient conservation and economic use of this group. We addressed the question of demosponge relationships using mitochondrial genomic data. We assembled a mitochondrial genomic dataset comprising all orders of demosponges that includes 17 new and five previously published complete demosponge mitochondrial genomes. To test for the congruence between mtDNA-based and nuclear rRNA-based phylogenies, we also determined and analyzed 18S rRNA sequences for the same set of species. Our results provide strong support for five major clades within the Demospongiae: Homoscleromorpha=G0 (order Homosclerophorida), Keratosa=G1 (orders Dendroceratida, Dictyoceratida, and Verticillitida), Myxospongiae=G2 (orders Chondrosida, Halisarcida, and Verongida), marine Haplosclerida=G3 and the rest of demosponges=G4 (orders Agelasida, Astrophorida, Hadromerida, Halichondrida, Poecilosclerida, Spirophorida, and freshwater Haploscerida), and for the (G0((G1+G2)(G3+G4)) relationships among these clades. Conversely, mitochondrial genomic data do not support the monophylies of traditional subclasses Ceractinomorpha and Tetractinomorpha as well as several currently recognized orders of demosponges. Furthermore, we demonstrate that mitochondrial gene arrangements can also be informative for the inference of order-level demosponge relationships and propose a modified method for the analysis of gene order data that works well when translocation of tRNA genes are more frequent than other rearrangements.}, }
@article {pmid18582582, year = {2008}, author = {Koblmüller, S and Schliewen, UK and Duftner, N and Sefc, KM and Katongo, C and Sturmbauer, C}, title = {Age and spread of the haplochromine cichlid fishes in Africa.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {153-169}, doi = {10.1016/j.ympev.2008.05.045}, pmid = {18582582}, issn = {1095-9513}, mesh = {Africa ; Animals ; Bayes Theorem ; Cichlids/*classification/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; Likelihood Functions ; Markov Chains ; Mitochondria/genetics ; Monte Carlo Method ; NADH Dehydrogenase/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The Haplochromini are by far the most species-rich cichlid fish tribe that originated along with the so-called primary radiation of the Lake Tanganyika cichlid species flock, i.e. at the same time during which the majority of the endemic Lake Tanganyika cichlid tribes emerged. Unlike the other tribes, the haplochromines are not restricted to Lake Tanganyika but distributed throughout Africa, except for the northwestern part of the continent. Haplochromine cichlids seeded the adaptive radiation of cichlid fishes in Lakes Malawi, Kivu, Victoria, Turkana, as well as in the now extinct paleo-Lake Makgadikgadi. Here we present a comprehensive phylogenetic and phylogeographic analysis of haplochromine cichlids that is based upon DNA sequences of two mitochondrial gene segments of riverine taxa covering all major African biogeographic regions where haplochromines are found. Our analysis revealed that six lineages of haplochromines originated within a short period of time, about 5.3-4.4 MYA. These haplochromine lineages show a highly complex phylogeographic pattern, probably severely influenced by climate- and/or geology-induced changes of the environment, with river capture events most likely playing an important role for species dispersal.}, }
@article {pmid18579651, year = {2008}, author = {Richards, JG and Sardella, BA and Schulte, PM}, title = {Regulation of pyruvate dehydrogenase in the common killifish, Fundulus heteroclitus, during hypoxia exposure.}, journal = {American journal of physiology. Regulatory, integrative and comparative physiology}, volume = {295}, number = {3}, pages = {R979-90}, doi = {10.1152/ajpregu.00192.2008}, pmid = {18579651}, issn = {0363-6119}, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Cytosol/metabolism ; Energy Metabolism/physiology ; Fundulidae/genetics/*metabolism ; Hypoxia/*metabolism/*physiopathology ; Isoenzymes/genetics/metabolism ; Mitochondria/metabolism ; Muscle, Skeletal/enzymology ; NAD/metabolism ; Oxygen/metabolism ; Phylogeny ; Protein Serine-Threonine Kinases/genetics/metabolism ; Pyruvate Dehydrogenase Acetyl-Transferring Kinase ; Pyruvate Dehydrogenase Complex/*metabolism ; Pyruvic Acid/metabolism ; }, abstract = {We examined the metabolic responses of the hypoxia-tolerant killifish (Fundulus heteroclitus) to 15 h of severe hypoxia and recovery with emphasis on muscle substrate usage and the regulation of the mitochondrial protein pyruvate dehydrogenase (PDH), which controls carbohydrate oxidation. Hypoxia survival involved a transient activation of substrate-level phosphorylation in muscle (decreases in [creatine phospate] and increases in [lactate]) during which time mechanisms to reduce overall ATP consumption were initiated. This metabolic transition did not affect total cellular [ATP], but had an impact on cellular energy status as indicated by large decreases in [ATP]/[ADP(free)] and [ATP]/[AMP(free)] and a significant loss of phosphorylation potential and Gibbs free energy of ATP hydrolysis (DeltafG'). The activity of PDH was rapidly (within 3 h) decreased by approximately 50% upon hypoxia exposure and remained depressed relative to normoxic samples throughout. Inactivation of PDH was primarily mediated via posttranslational modification following the accumulation of acetyl-CoA and subsequent activation of pyruvate dehydrogenase kinase (PDK). Estimated changes in cytoplasmic and mitochondrial [NAD(+)]/[NADH] did not parallel one another, suggesting the mitochondrial NADH shuttles do not function during hypoxia exposure. Large increases in the expression of PDK (PDK isoform 2) were consistent with decreased PDH activity; however, these changes in mRNA were not associated with changes in total PDK-2 protein content assessed using mammalian antibodies. No other changes in the expression of other known hypoxia-responsive genes (e.g., lactate dehydrogenase-A or -B) were observed in either muscle or liver.}, }
@article {pmid18579173, year = {2008}, author = {Vignoli, V and Klann, AE and Michalik, P}, title = {Spermatozoa and sperm packages of the European troglophylous scorpion Belisarius xambeui Simon, 1879 (Troglotayosicidae, Scorpiones).}, journal = {Tissue &amp; cell}, volume = {40}, number = {6}, pages = {411-416}, doi = {10.1016/j.tice.2008.04.002}, pmid = {18579173}, issn = {0040-8166}, mesh = {Acrosome/ultrastructure ; Animals ; Axoneme/ultrastructure ; Cell Nucleus/ultrastructure ; Classification ; Europe ; Genitalia, Male/*cytology ; Male ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Phylogeny ; Reproduction ; Scorpions/*classification/*cytology ; Spermatozoa/*ultrastructure ; Vacuoles/ultrastructure ; }, abstract = {Studies on the sperm morphology in scorpions are rare, but the existing investigations already revealed a remarkable interfamiliar diversity. The present study reports for the first time on the spermatozoa and sperm packages of a representative of the family Troglotayosicidae, the troglophylous species Belisarius xambeui. The spermatozoa are characterized by (1) a thread-like nucleus, which is slightly bent anteriorly; (2) an asymmetrical cap-like acrosomal vacuole, which encloses the anterior tip of the nucleus; an acrosomal filament is absent; (3) an axoneme with a 9+0 microtubular pattern; (4) a midpiece consisting of elongated mitochondria coiling around the axoneme; the number can vary between 3 and 6 (mostly 4). At the end of spermiogenesis, the spermatozoa aggregate in order to form oval-shaped sperm packages in which all sperm cells show the same orientation. A single package consists of approximately 150 sperms. A secretion sheath is always absent. The present results might provide new characters for further systematic studies and their phylogenetic implications are briefly discussed.}, }
@article {pmid18574633, year = {2008}, author = {Yazawa, R and Yasuike, M and Leong, J and von Schalburg, KR and Cooper, GA and Beetz-Sargent, M and Robb, A and Davidson, WS and Jones, SR and Koop, BF}, title = {EST and mitochondrial DNA sequences support a distinct Pacific form of salmon louse, Lepeophtheirus salmonis.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {10}, number = {6}, pages = {741-749}, pmid = {18574633}, issn = {1436-2228}, mesh = {Animals ; Copepoda/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; *Expressed Sequence Tags ; Gene Library ; Genes, Mitochondrial ; Genetic Variation ; Genetics, Population ; Genome, Mitochondrial ; Mitochondria/genetics ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Nuclear deoxyribonucleic acid sequences from approximately 15,000 salmon louse expressed sequence tags (ESTs), the complete mitochondrial genome (16,148bp) of salmon louse, and 16S ribosomal ribonucleic acid (rRNA) and cytochrome oxidase subunit I (COI) genes from 68 salmon lice collected from Japan, Alaska, and western Canada support a Pacific lineage of Lepeophtheirus salmonis that is distinct from that occurring in the Atlantic Ocean. On average, nuclear genes are 3.2% different, the complete mitochondrial genome is 7.1% different, and 16S rRNA and COI genes are 4.2% and 6.1% different, respectively. Reduced genetic diversity within the Pacific form of L. salmonis is consistent with an introduction into the Pacific from the Atlantic Ocean. The level of divergence is consistent with the hypothesis that the Pacific form of L. salmonis coevolved with Pacific salmon (Onchorhynchus spp.) and the Atlantic form coevolved with Atlantic salmonids (Salmo spp.) independently for the last 2.5-11 million years. The level of genetic divergence coincides with the opportunity for migration of fish between the Atlantic and Pacific Ocean basins via the Arctic Ocean with the opening of the Bering Strait, approximately 5 million years ago. The genetic differences may help explain apparent differences in pathogenicity and environmental sensitivity documented for the Atlantic and Pacific forms of L. salmonis.}, }
@article {pmid18573842, year = {2008}, author = {Ueda, M and Fujimoto, M and Arimura, S and Tsutsumi, N and Kadowaki, K}, title = {Presence of a latent mitochondrial targeting signal in gene on mitochondrial genome.}, journal = {Molecular biology and evolution}, volume = {25}, number = {9}, pages = {1791-1793}, doi = {10.1093/molbev/msn139}, pmid = {18573842}, issn = {1537-1719}, mesh = {Arabidopsis ; Arabidopsis Proteins/genetics/metabolism ; Cell Nucleus/genetics ; *Genes, Mitochondrial ; *Genes, Plant ; Genome, Plant ; Oryza ; Plant Proteins/*genetics/metabolism ; Protein Transport/*genetics ; Recombination, Genetic ; Ribosomal Proteins/genetics/metabolism ; }, abstract = {Organelles, such as mitochondria and chloroplasts, are derived from endosymbionts. Gene transfer events from organelles to the nucleus have occurred over evolutionary time. In the case that a transferred gene in the nucleus needs to go back to the original organelle, it must obtain targeting information for sorting its protein to that organelle. Here, we reveal that the genes for the ribosomal proteins L2 and S4 in the Arabidopsis thaliana mitochondrial (mt) genome contain information for protein targeting into the mitochondria. Similarly, the genes for the ribosomal proteins L2 and S19 in the Oryza sativa mt genome contain information for protein targeting into mitochondria. These results suggest that targeting information already existed in each gene in the plant mt genome before the transfer event to the nucleus occurred. We provide new insights into the timing of the appearance of targeting signals in evolution.}, }
@article {pmid18566830, year = {2008}, author = {Huang, X and Zhu, W and Dai, S and Gai, S and Zheng, G and Zheng, C}, title = {The involvement of mitochondrial phosphate transporter in accelerating bud dormancy release during chilling treatment of tree peony (Paeonia suffruticosa).}, journal = {Planta}, volume = {228}, number = {4}, pages = {545-552}, pmid = {18566830}, issn = {0032-0935}, mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Arabidopsis/genetics ; *Cold Temperature ; DNA, Complementary ; DNA, Plant ; Flowers/anatomy &amp; histology/*growth &amp; development ; Gene Expression Regulation, Plant ; Mitochondria/*physiology ; Mitochondrial Membrane Transport Proteins/*physiology ; Molecular Sequence Data ; Paeonia/classification/metabolism/*physiology ; Phosphate Transport Proteins/chemistry/*physiology ; Phylogeny ; Plant Proteins/chemistry/*physiology ; Plants, Genetically Modified ; Up-Regulation ; }, abstract = {A cDNA clone was isolated from tree peony (Paeonia suffruticosa) subtractive cDNA library of burst buds and characterized with regard to its sequence, expression in response to chilling treatment during the release of bud dormancy, and its function in transgenic Arabidopsis thaliana. The clone, designated as PsMPT, contains 1,615 nucleotides with an open reading frame of 1,119 nucleotides, and the deduced amino acid sequence shows high homology with mitochondrial phosphate transporters (MPTs) from various organisms. The mRNA accumulation of PsMPT in tree peony was strongly induced by chilling treatment during the release of bud dormancy. When the treated plants were transferred to normal growth conditions, the level of PsMPT transcripts induced by sufficient chilling could be maintained high, whereas that induced by insufficient chilling decreased sharply. The transgenic Arabidopsis plants that overexpress PsMPT showed rapid growth and earlier flowering than wild-type plants. ATP contents in the transgenic plants were much higher than that in wild-type plants through various developmental stages. Together, these results suggest that the product of PsMPT is a MPT and might play an important role during the release of bud dormancy in tree peony.}, }
@article {pmid18558496, year = {2008}, author = {O'Neill, SB and Chapple, DG and Daugherty, CH and Ritchie, PA}, title = {Phylogeography of two New Zealand lizards: McCann's skink (Oligosoma maccanni) and the brown skink (O. zelandicum).}, journal = {Molecular phylogenetics and evolution}, volume = {48}, number = {3}, pages = {1168-1177}, doi = {10.1016/j.ympev.2008.05.008}, pmid = {18558496}, issn = {1095-9513}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genetic Speciation ; Genetic Variation ; Geography ; Lizards/*genetics ; Mitochondria/metabolism ; Models, Genetic ; New Zealand ; Phylogeny ; Reptiles/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The New Zealand skink fauna has proven to be an ideal taxonomic group in which to examine the impact of climatic and geological processes on the evolution of the New Zealand biota since the Pliocene. Here we examine the phylogeography of McCann's skink (Oligosoma maccanni) in order to gain insight into the relative contribution of Pliocene and Pleistocene processes on patterns of genetic structure in the South Island biota, and investigate the phylogeography of the brown skink (O. zelandicum) to examine whether Cook Strait landbridges facilitated geneflow between the North and South Islands in the late-Pleistocene. We obtained mitochondrial DNA sequence data (ND2 and ND4; 1282bp) from across the range of both species. We examined the phylogeographic patterns evident in each species using Neighbour-Joining, Maximum Likelihood and Bayesian methods. We found substantial phylogeographic structure within O. maccanni, with seven distinct clades identified. Divergences among clades are estimated to have occurred during the Pliocene. Populations in the Otago/Southland region (south of the Waitaki River valley) formed a well-supported lineage within O. maccanni. A substantial genetic break was evident between populations in east and west Otago, either side of the Nevis-Cardrona fault system, while north-south genetic breaks were evident within the Canterbury region. Within-clade divergences in O. maccanni appear to have occurred during the mid- to late-Pleistocene. Shimodaira-Hasegawa topology tests indicated that the 'Garston' skink is not genetically distinct from O. maccanni. There was only relatively minor phylogeographic structure within O. zelandicum, with divergences among populations occurring during the mid- to late-Pleistocene. Our genetic data supports a single colonisation of the North Island by O. zelandicum from the South Island, with the estimated timing of this event (0.46mya) consistent with the initial formation of Cook Strait.}, }
@article {pmid18558096, year = {2009}, author = {Merkwirth, C and Langer, T}, title = {Prohibitin function within mitochondria: essential roles for cell proliferation and cristae morphogenesis.}, journal = {Biochimica et biophysica acta}, volume = {1793}, number = {1}, pages = {27-32}, doi = {10.1016/j.bbamcr.2008.05.013}, pmid = {18558096}, issn = {0006-3002}, mesh = {Animals ; *Cell Proliferation ; Electron Transport/physiology ; Humans ; Mitochondria/*metabolism/ultrastructure ; Mitochondrial Membranes/*physiology ; Models, Biological ; Morphogenesis ; Phylogeny ; Prohibitins ; Repressor Proteins/analysis/*physiology ; }, abstract = {Prohibitins comprise an evolutionary conserved and ubiquitously expressed family of membrane proteins. Various roles in different cellular compartments have been proposed for prohibitin proteins. Recent experiments, however, identify large assemblies of two homologous prohibitin subunits, PHB1 and PHB2, in the inner membrane of mitochondria as the physiologically active structure. Mitochondrial prohibitin complexes control cell proliferation, cristae morphogenesis and the functional integrity of mitochondria. The processing of the dynamin-like GTPase OPA1, a core component of the mitochondrial fusion machinery, has been defined as a key process affected by prohibitins. The molecular mechanism of prohibitin function, however, remained elusive. The ring-like assembly of prohibitins and their sequence similarity with lipid raft-associated SPFH-family members suggests a scaffolding function of prohibitins, which may lead to functional compartmentalization in the inner membrane of mitochondria.}, }
@article {pmid18544552, year = {2008}, author = {Sole, CL and Bastos, AD and Scholtz, CH}, title = {Intraspecific patterns of mitochondrial variation in natural population fragments of a localized desert dung beetle species, Pachysoma gariepinum (Coleoptera: Scarabaeidae).}, journal = {The Journal of heredity}, volume = {99}, number = {5}, pages = {464-475}, doi = {10.1093/jhered/esn046}, pmid = {18544552}, issn = {1465-7333}, mesh = {Africa, Southern ; Animals ; Biological Evolution ; Coleoptera/classification/enzymology/*genetics ; Conservation of Natural Resources ; DNA, Mitochondrial ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Haplotypes ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Time ; }, abstract = {Phylogenetic, population, and coalescent methods were used to examine the genetic structuring of Pachysoma gariepinum, a flightless dung beetle species endemic to the arid west coast of southern Africa that exhibits interrupted south to north morphological clinal variation along a distributional gradient. Mitochondrial cytochrome oxidase I sequence data of 67 individuals from 5 localities revealed the presence of 3 geographically distinct evolutionary lineages (with an overall nucleotide divergence of 5.7% and a per-locality divergence of 1.9-3.8%) which display significant levels of genetic structuring. The separation of the lineages was estimated to have occurred between 2.2 and 5.7 million years ago--which is the late Miocene, early Plio-Pleistocene era--possibly in response to the ebb and flow of the Orange and Holgat River systems as well as the interactions between the moving and stable sand dune systems. Moreover the species' current range appears to have been influenced by the formation of advective fog resulting in a constant source of water in an area with low precipitation thereby allowing for the beetles to radiate to areas that were previously inhospitable. Fu's F-statistics and population parameters based on recent mutations indicated that little to no recent population growth has occurred. This together with changing anthropogenic factors and the recovery of 3 geographically discrete management units, points to a need for census data in order to monitor and conserve the genetic diversity of this species.}, }
@article {pmid18543065, year = {2008}, author = {Kmiec-Wisniewska, B and Krumpe, K and Urantowka, A and Sakamoto, W and Pratje, E and Janska, H}, title = {Plant mitochondrial rhomboid, AtRBL12, has different substrate specificity from its yeast counterpart.}, journal = {Plant molecular biology}, volume = {68}, number = {1-2}, pages = {159-171}, pmid = {18543065}, issn = {0167-4412}, mesh = {Arabidopsis/enzymology/*metabolism ; Arabidopsis Proteins/classification/genetics/*metabolism ; Chloroplasts/metabolism ; Fungal Proteins/genetics/metabolism ; GTP Phosphohydrolases/genetics/metabolism ; Green Fluorescent Proteins/chemistry/genetics/metabolism ; Mitochondrial Proteins/classification/genetics/*metabolism ; Phylogeny ; Recombinant Fusion Proteins/genetics/metabolism ; Serine Endopeptidases/genetics/*metabolism ; Substrate Specificity ; Yeasts/enzymology/*metabolism ; }, abstract = {Rhomboid proteins comprise a class of serine proteases that are conserved in all kingdoms of organisms. They contain six or seven transmembrane helices and control a wide range of cellular functions and developmental processes by intramembrane proteolysis. This paper provides experimental evidence for the existence of rhomboid proteases in plant mitochondria and chloroplasts. Among 15 putative rhomboid-like proteins in Arabidopsis thaliana, we selected five predicted as mitochondrially targeted. For these proteins we performed the GFP transient assay, and identified two homologues, AtRBL11 (At5g25752) and AtRBL12 (At1g18600) to be targeted into plastids and mitochondria, respectively. Phylogenetic analysis reveals that AtRBL12 or AtRBL11 have only one clear orthologue in plant species with completely sequenced genomes. Complementation of the yeast lacking a functional copy of mitochondrial rhomboid with AtRBL12 indicates that this plant protease, in contrast to the human orthologue, does not recognize the yeast substrates, cytochrome c peroxidase (Ccp1) or dynamin-like GTPase (Mgm1). In agreement with this, we did not observe processing of Mgm1 when labeled precursor of this protein was incubated in vitro with Arabidopsis mitochondrial extract. Our results imply that plant mitochondrial rhomboids function in a specific manner and thus differ from their yeast and mammal counterparts.}, }
@article {pmid18539524, year = {2008}, author = {Alverson, AJ}, title = {Molecular systematics and the diatom species.}, journal = {Protist}, volume = {159}, number = {3}, pages = {339-353}, pmid = {18539524}, issn = {1434-4610}, support = {F32 GM080079/GM/NIGMS NIH HHS/United States ; F32 GM080079-01A1/GM/NIGMS NIH HHS/United States ; 1F32GM080079-01A1/GM/NIGMS NIH HHS/United States ; }, mesh = {DNA, Algal/genetics ; DNA, Ribosomal/genetics ; Diatoms/*classification/*genetics ; Mitochondria/genetics ; Phylogeny ; }, }
@article {pmid18524881, year = {2008}, author = {Cosson, J and Groison, AL and Suquet, M and Fauvel, C and Dreanno, C and Billard, R}, title = {Marine fish spermatozoa: racing ephemeral swimmers.}, journal = {Reproduction (Cambridge, England)}, volume = {136}, number = {3}, pages = {277-294}, doi = {10.1530/REP-07-0522}, pmid = {18524881}, issn = {1741-7899}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Axoneme/metabolism ; Energy Metabolism ; Fishes/metabolism/*physiology ; Male ; Models, Biological ; Seawater ; Sperm Motility/*physiology ; Sperm Tail/metabolism/physiology ; Spermatozoa/metabolism/*physiology ; }, abstract = {After a long period of spermatogenesis (several weeks to months), marine fish spermatozoa are delivered at male spawning in seawater (SW) at the same time as ova. In some fish species, as the ova micropyle closes quickly after release, these minute unicells, the spermatozoa, have to accomplish their task of reaching the micropyle within a very brief period (several seconds to minutes), for delivery of the haploid male genetic information to the ova. To achieve this goal, their high-performance motile equipment, the flagellum, must fully activate immediately on contact with the SW and then propel the sperm cell at an unusually high initial velocity. The cost of such 'hyperactivity' is a very rapid consumption of intracellular ATP that outstrips the supply. The spermatozoa become rapidly exhausted because mitochondria cannot compensate for this very fast flagellar energy consumption. Therefore, any spermatozoon ends up with two possibilities: either becoming exhausted and immotile or reaching the egg micropyle within its very short period of forward motility (in the range of tens of seconds) before micropyle closure in relation to both contact of SW and cortical reaction. The aim of the present review is to present step by step the successive events occurring in marine fish spermatozoa from activation until their full arrest of motility. The present knowledge of activation mechanisms is summarized, as well as a description of the motility parameters characterizing the motility period. As a complement, in vitro results on axonemal motility obtained after demembranation of flagella bring further understanding. The description of the sperm energetic content (ATP and other high energy compounds) and its evolution during the swimming period is also discussed. A general model aiming to explain all the successive cellular events occurring immediately after the activation is presented. This model is proposed as a guideline for understanding the events governing the sperm lifespan in the marine fish species that reproduce through external fertilization.}, }
@article {pmid18524785, year = {2008}, author = {Sanchez-Puerta, MV and Cho, Y and Mower, JP and Alverson, AJ and Palmer, JD}, title = {Frequent, phylogenetically local horizontal transfer of the cox1 group I Intron in flowering plant mitochondria.}, journal = {Molecular biology and evolution}, volume = {25}, number = {8}, pages = {1762-1777}, pmid = {18524785}, issn = {1537-1719}, support = {F32 GM080079/GM/NIGMS NIH HHS/United States ; R01 GM070612/GM/NIGMS NIH HHS/United States ; R01-GM-70612/GM/NIGMS NIH HHS/United States ; 1F32GM080079/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Cyclooxygenase 1/*genetics ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Introns/*genetics ; Likelihood Functions ; Magnoliopsida/*genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Horizontal gene transfer is surprisingly common among plant mitochondrial genomes. The first well-established case involves a homing group I intron in the mitochondrial cox1 gene shown to have been frequently acquired via horizontal transfer in angiosperms. Here, we report extensive additional sampling of angiosperms, including 85 newly sequenced introns from 30 families. Analysis of all available data leads us to conclude that, among the 640 angiosperms (from 212 families) whose cox1 intron status has been characterized thus far, the intron has been acquired via roughly 70 separate horizontal transfer events. We propose that the intron was originally seeded into angiosperms by a single transfer from fungi, with all subsequent inferred transfers occurring from one angiosperm to another. The pattern of angiosperm-to-angiosperm transfer is biased toward exchanges between plants belonging to the same family. Illegitimate pollination is proposed as one potential factor responsible for this pattern, given that aberrant, cross-species pollination is more likely between close relatives. Other potential factors include shared vectoring agents or common geographic locations. We report the first apparent cases of loss of the cox1 intron; losses are accompanied by retention of the exonic coconversion tract, which is located immediately downstream of the intron and which is a product of the intron's self-insertion mechanism. We discuss the many reasons why the cox1 intron is so frequently and detectably transferred, and rarely lost, and conclude that it should be regarded as the "canary in the coal mine" with respect to horizontal transfer in angiosperm mitochondria.}, }
@article {pmid18522807, year = {2009}, author = {Herrmann, JM and Kauff, F and Neuhaus, HE}, title = {Thiol oxidation in bacteria, mitochondria and chloroplasts: common principles but three unrelated machineries?.}, journal = {Biochimica et biophysica acta}, volume = {1793}, number = {1}, pages = {71-77}, doi = {10.1016/j.bbamcr.2008.05.001}, pmid = {18522807}, issn = {0006-3002}, mesh = {Bacterial Proteins/chemistry/*metabolism ; Chloroplasts/*metabolism ; Escherichia coli Proteins/chemistry/*metabolism ; Membrane Proteins/chemistry/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/chemistry/metabolism ; Oxidation-Reduction ; Oxidoreductases/chemistry/*metabolism ; Periplasm/metabolism ; Protein Disulfide-Isomerases/chemistry/*metabolism ; Sulfhydryl Compounds/*metabolism ; Thylakoids/metabolism ; }, abstract = {The intermembrane space of mitochondria and the thylakoid lumen of chloroplasts are evolutionary descendents of the periplasmic space of bacteria. Presumably due to their common ancestry, the active oxidation of cysteinyl thiols is used in these three compartments in order to stabilize protein folding or to regulate protein function. In contrast, compartments of the eukaryotic cell which developed from the bacterial cytosol maintain cysteine residues largely reduced. Whereas the oxidizing machinery of bacteria is well characterized, that of mitochondria was only recently discovered and that of thylakoids still awaits to be identified. In mitochondria, protein oxidation is mediated by the sulfhydryl oxidase Erv1 which is highly conserved among eukaryotes. Erv1 oxidizes its substrate protein Mia40 which serves as an import receptor for proteins destined for the intermembrane space. This review summarizes the current knowledge on the mitochondrial disulfide relay system and compares its features to those of the periplasm and the thylakoid lumen. Although the sulfhydryl oxidases in the intermembrane space, Erv1, and the bacterial periplasm, DsbA-DsbB, share key structural features their primary sequence is not related and the evolutionary origin of Erv1 is unclear. On the basis of phylogenetic analyses of Erv1 sequences we propose that the mitochondrial oxidation machinery originated from a lateral gene transfer from flavobacteria-like prokaryotes early in eukaryotic evolution.}, }
@article {pmid18522806, year = {2009}, author = {Bonnefoy, N and Fiumera, HL and Dujardin, G and Fox, TD}, title = {Roles of Oxa1-related inner-membrane translocases in assembly of respiratory chain complexes.}, journal = {Biochimica et biophysica acta}, volume = {1793}, number = {1}, pages = {60-70}, pmid = {18522806}, issn = {0006-3002}, support = {R01 GM029362/GM/NIGMS NIH HHS/United States ; R01 GM029362-27/GM/NIGMS NIH HHS/United States ; R01 GM029362-28/GM/NIGMS NIH HHS/United States ; GM29362/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Electron Transport ; Electron Transport Chain Complex Proteins/*metabolism ; Electron Transport Complex IV/*metabolism ; Escherichia coli/metabolism ; Evolution, Molecular ; Humans ; Membrane Transport Proteins/*metabolism ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/*metabolism ; Nuclear Proteins/*metabolism ; Saccharomyces cerevisiae/metabolism ; }, abstract = {Members of the family of the polytopic inner membrane proteins are related to Saccharomyces cerevisiae Oxa1 function in the assembly of energy transducing complexes of mitochondria and chloroplasts. Here we focus on the two mitochondrial members of this family, Oxa1 and Cox18, reviewing studies on their biogenesis as well as their functions, reflected in the phenotypic consequences of their absence in various organisms. In yeast, cytochrome c oxidase subunit II (Cox2) is a key substrate of these proteins. Oxa1 is required for co-translational translocation and insertion of Cox2, while Cox18 is necessary for the export of its C-terminal domain. Genetic and biochemical strategies have been used to investigate the functions of distinct domains of Oxa1 and to identify its partners in protein insertion/translocation. Recent work on the related bacterial protein YidC strongly indicates that it is capable of functioning alone as a translocase for hydrophilic domains and an insertase for TM domains. Thus, the Oxa1 and Cox18 probably catalyze these reactions directly in a co- and/or posttranslational way. In various species, Oxa1 appears to assist in the assembly of different substrate proteins, although it is still unclear how Oxa1 recognizes its substrates, and whether additional factors participate in this beyond its direct interaction with mitochondrial ribosomes, demonstrated in S. cerevisiae. Oxa1 is capable of assisting posttranslational insertion and translocation in isolated mitochondria, and Cox18 may posttranslationally translocate its only known substrate, the Cox2 C-terminal domain, in vivo. Detailed understanding of the mechanisms of action of these two proteins must await the resolution of their structure in the membrane and the development of a true in vitro mitochondrial translation system.}, }
@article {pmid18518819, year = {2008}, author = {Engel, A and Gaub, HE}, title = {Structure and mechanics of membrane proteins.}, journal = {Annual review of biochemistry}, volume = {77}, number = {}, pages = {127-148}, doi = {10.1146/annurev.biochem.77.062706.154450}, pmid = {18518819}, issn = {0066-4154}, mesh = {Archaea/*metabolism ; Bacteriorhodopsins/chemistry ; Biochemistry/*methods ; Crystallization ; Crystallography, X-Ray ; Ligands ; Magnetic Resonance Spectroscopy ; Membrane Proteins/*chemistry ; Microscopy, Atomic Force/methods ; Mitochondria/metabolism ; Peptides/chemistry ; Protein Conformation ; Protein Denaturation ; Protein Folding ; Purple Membrane/chemistry ; }, abstract = {Evolution has tuned membrane proteins to exist in a lipid bilayer, provide for cell-cell communication, transport solutes, and convert energies. These proteins exhibit a hydrophobic belt that interacts with the lipid bilayer. Detergents are therefore used to extract membrane proteins and keep them in solution for purification and subsequent analyses. However, most membrane proteins are unstable when solubilized and hence often not accessible to NMR or X-ray crystallography. The atomic force microscope (AFM) is a powerful tool for imaging and manipulating membrane proteins in their native state. Superb images of native membranes have been recorded, and a quantitative interpretation of the data acquired using the AFM tip has become possible. In addition, multifunctional probes to simultaneously acquire information on the topography and electrical properties of membrane proteins have been produced. This progress is discussed here and fosters expectations for future developments and applications of AFM and single-molecule force spectroscopy.}, }
@article {pmid18516228, year = {2008}, author = {Galluzzi, L and Brenner, C and Morselli, E and Touat, Z and Kroemer, G}, title = {Viral control of mitochondrial apoptosis.}, journal = {PLoS pathogens}, volume = {4}, number = {5}, pages = {e1000018}, pmid = {18516228}, issn = {1553-7374}, mesh = {Animals ; *Apoptosis ; Host-Pathogen Interactions ; Mitochondria/*pathology/*virology ; Mitochondrial Membranes/physiology ; Permeability ; Proto-Oncogene Proteins c-bcl-2/physiology ; Viral Proteins/*physiology ; Virus Diseases/metabolism/pathology ; *Virus Physiological Phenomena ; Viruses/*pathogenicity ; }, abstract = {Throughout the process of pathogen-host co-evolution, viruses have developed a battery of distinct strategies to overcome biochemical and immunological defenses of the host. Thus, viruses have acquired the capacity to subvert host cell apoptosis, control inflammatory responses, and evade immune reactions. Since the elimination of infected cells via programmed cell death is one of the most ancestral defense mechanisms against infection, disabling host cell apoptosis might represent an almost obligate step in the viral life cycle. Conversely, viruses may take advantage of stimulating apoptosis, either to kill uninfected cells from the immune system, or to induce the breakdown of infected cells, thereby favoring viral dissemination. Several viral polypeptides are homologs of host-derived apoptosis-regulatory proteins, such as members of the Bcl-2 family. Moreover, viral factors with no homology to host proteins specifically target key components of the apoptotic machinery. Here, we summarize the current knowledge on the viral modulation of mitochondrial apoptosis, by focusing in particular on the mechanisms by which viral proteins control the host cell death apparatus.}, }
@article {pmid18515712, year = {2008}, author = {Hand, SC and Menze, MA}, title = {Mitochondria in energy-limited states: mechanisms that blunt the signaling of cell death.}, journal = {The Journal of experimental biology}, volume = {211}, number = {Pt 12}, pages = {1829-1840}, doi = {10.1242/jeb.000299}, pmid = {18515712}, issn = {0022-0949}, support = {1-R01-GM071345-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Artemia/*physiology ; Cell Death/*physiology ; Cell Hypoxia/physiology ; Energy Metabolism/*physiology ; Mitochondria/*physiology ; Mitochondrial Membranes/metabolism ; *Models, Biological ; Permeability ; Proto-Oncogene Proteins c-bcl-2/metabolism ; Signal Transduction/*physiology ; }, abstract = {Cellular conditions experienced during energy-limited states--elevated calcium, shifts in cellular adenylate status, compromised mitochondrial membrane potential--are precisely those that trigger, at least in mammals, the mitochondrion to initiate opening of the permeability transition pore, to assemble additional protein release channels, and to release pro-apoptotic factors. These pro-apototic factors in turn activate initiator and executer caspases. How is activation of mitochondria-based pathways for the signaling of apoptotic and necrotic cell death avoided under conditions of hypoxia, anoxia, diapause, estivation and anhydrobiosis? Functional trade-offs in environmental tolerance may have occurred in parallel with the evolution of diversified pathways for the signaling of cell death in eukaryotic organisms. Embryos of the brine shrimp, Artemia franciscana, survive extended periods of anoxia and diapause, and evidence indicates that opening of the mitochondrial permeability transition pore and release of cytochrome c (cyt-c) do not occur. Further, caspase activation in this crustacean is not dependent on cyt-c. Its caspases display regulation by nucleotides that is consistent with ;applying the brakes' to cell death during energy limitation. Unraveling the mechanisms by which organisms in extreme environments avoid cell death may suggest possible interventions during disease states and biostabilization of mammalian cells.}, }
@article {pmid18513996, year = {2008}, author = {Timm, J and Figiel, M and Kochzius, M}, title = {Contrasting patterns in species boundaries and evolution of anemonefishes (Amphiprioninae, Pomacentridae) in the centre of marine biodiversity.}, journal = {Molecular phylogenetics and evolution}, volume = {49}, number = {1}, pages = {268-276}, doi = {10.1016/j.ympev.2008.04.024}, pmid = {18513996}, issn = {1095-9513}, mesh = {Animals ; *Biodiversity ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genes, Mitochondrial ; *Genetic Speciation ; Genetic Variation ; Haplotypes ; Mitochondria/genetics ; Perciformes/*classification/*genetics ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Many species of coral reef fishes are distinguished by their colour patterns, but genetic studies have shown these are not always good predictors of genetic isolation and species boundaries. The genus Amphiprion comprises several species that have very similar colouration. Additionally, morphological characters are so variable, that sibling species can show a considerable overlap, making it difficult to differentiate them. In this study, we investigated the species boundaries between the sibling species pair A. ocellaris and A. percula (Subgenus Actinicola) and three closely related species of the subgenus Phalerebus (A. akallopisos, A. perideraion, A. sandaracinos) by phylogenetic analysis of mitochondrial cytochrome b and control region sequences. These two subgenera show strong differences in their patterns of species boundaries. Within the A. ocellaris/A. percula complex, five clades were found representing different geographic regions. Two major divergences both with genetic distances of 4-7% in cty b and 17-19% in the d-loop region indicate the presence of three instead of two deep evolutionary lineages. The species of the subgenus Phalerebus show three monophyletic clades, independent of the geographical location of origin, but concordant to the morphological species classification. The genetic distances between the Phalerebus species were 2-5% in cty b and 10-12% in the control region.}, }
@article {pmid18511083, year = {2008}, author = {Du, P and Li, Y}, title = {Prediction of C-to-U RNA editing sites in plant mitochondria using both biochemical and evolutionary information.}, journal = {Journal of theoretical biology}, volume = {253}, number = {3}, pages = {579-586}, doi = {10.1016/j.jtbi.2008.04.006}, pmid = {18511083}, issn = {1095-8541}, mesh = {Algorithms ; *Evolution, Molecular ; Mitochondria/*genetics ; Online Systems ; Plants/*genetics ; *RNA Editing ; RNA, Plant/*genetics ; }, abstract = {Although cytidine-to-uridine conversions in plant mitochondria were discovered 18 years ago, it was still an enigmatic process. Since the sequencing projects of plant mitochondrial genomes are providing more and more available sequences, the requirements of computationally identifying C-to-U RNA editing sites are also increasing. By incorporating both evolutionary and biochemical information, we developed a novel algorithm for predicting C-to-U RNA editing sites in plant mitochondria. The algorithm has been implemented as an online service called CURE (Cytidine-to-Uridine Recognizing Editor). CURE performs better than other methods that are based on only biochemical or only evolutionary information. CURE also provides the ability of predicting C-to-U RNA editing sites in non-coding regions and the synonymous C-to-U RNA editing sites in coding regions that are impossible for other methods. Furthermore, CURE can carry out prediction directly on the entire mitochondria genome sequence. The prediction results of CURE suggest the functional importance of synonymous RNA editing sites, which was neglected before. The CURE service can be accessed at http://bioinfo.au.tsinghua.edu.cn/cure.}, }
@article {pmid18508749, year = {2008}, author = {Alves, PC and Melo-Ferreira, J and Freitas, H and Boursot, P}, title = {The ubiquitous mountain hare mitochondria: multiple introgressive hybridization in hares, genus Lepus.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {363}, number = {1505}, pages = {2831-2839}, pmid = {18508749}, issn = {0962-8436}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Demography ; Ecosystem ; Hares/*genetics ; Hybridization, Genetic/*genetics ; Phylogeny ; Portugal ; Spain ; }, abstract = {Climatic oscillations during the glaciations forced dramatic changes in species distributions, such that some presently temperate regions were alternately occupied by temperate and arctic species. These species could have met and hybridized during climatic transitions. This phenomenon happened for three hare species present in Iberia (Lepus granatensis, Lepus europaeus and Lepus castroviejoi), which display high frequencies of mitochondrial DNA (mtDNA) from Lepus timidus, an arctic/boreal species presently extinct in Iberia. Here, we extend our previous geographical survey to determine whether the distribution of this mtDNA lineage extends beyond the northern half of the Iberian Peninsula, where it is found at high frequencies. We also review the taxonomy, distribution and molecular phylogeny of the genus Lepus. The phylogenetic inference reveals the presence of L. timidus-like mtDNA in several other hare species in Asia and North America, suggesting that the mitochondrial introgression observed in Iberia might be generalized. Comparison with the available nuclear gene phylogenies suggests that introgression could have happened repeatedly, possibly during different climatic transitions. We discuss demographic and adaptive scenarios that could account for the repetition in time and space of this spectacular phenomenon and suggest ways to improve our understanding of its determinants and consequences. Such high levels of introgressive hybridization should discourage attempts to revise hare taxonomy based solely on mtDNA.}, }
@article {pmid18504541, year = {2008}, author = {McDermott, P and Connolly, V and Kavanagh, TA}, title = {The mitochondrial genome of a cytoplasmic male sterile line of perennial ryegrass (Lolium perenne L.) contains an integrated linear plasmid-like element.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {117}, number = {3}, pages = {459-470}, pmid = {18504541}, issn = {0040-5752}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Base Pairing ; Base Sequence ; Chromosomes, Plant/genetics ; Cytoplasm/*genetics ; Extrachromosomal Inheritance ; Fungi/genetics ; Gene Expression Regulation, Plant ; Genome, Mitochondrial/*genetics ; Lolium/*genetics ; Molecular Sequence Data ; Phylogeny ; Physical Chromosome Mapping ; Plant Infertility/*genetics ; Plant Proteins/chemistry/genetics ; Plasmids/*genetics ; RNA, Messenger/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The mitochondrial genome of a cytoplasmic male sterile line of perennial ryegrass (Lolium perenne L.) was shown to contain a 9.6 kb element, LpCMSi, that is absent in the mitochondrial genome of fertile lines. LpCMSi contains the previously described chimeric gene orfC9, and three additional open reading frames (orfs) encoding a unique 45 kDa predicted protein of unknown function, a family B-like DNA polymerase (LpDpo), and a phage-type single subunit RNA polymerase (LpRpo). The latter two proteins shared significant similarity with DNA and RNA polymerases encoded by extrachromosomal linear mitochondrial plasmids of plants and fungi, and also to integrated plasmid-like sequences found in various plant and fungal mitochondrial genomes. Transcripts for both LpDpo and LpRpo were detected by RT-PCR in mitochondria of the CMS line. PCR-based investigations further revealed the presence of LpCMSi-like sequences in fertile L. perenne lines that are likely maintained as low-copy number extrachromosomal replicons. The absence of integrated forms of LpCMSi in the mitochondrial genome of fertile lines suggests that LpCMSi integration adjacent to the atp9 gene may be responsible, directly or indirectly, for the sterility phenotype of the CMS line.}, }
@article {pmid18501716, year = {2009}, author = {Walther, DM and Rapaport, D}, title = {Biogenesis of mitochondrial outer membrane proteins.}, journal = {Biochimica et biophysica acta}, volume = {1793}, number = {1}, pages = {42-51}, doi = {10.1016/j.bbamcr.2008.04.013}, pmid = {18501716}, issn = {0006-3002}, mesh = {Animals ; Carrier Proteins/chemistry/genetics/metabolism ; Evolution, Molecular ; Humans ; Mitochondrial Membrane Transport Proteins/genetics/*metabolism ; Mitochondrial Membranes/chemistry/*metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Models, Biological ; Structure-Activity Relationship ; }, abstract = {Mitochondria are surrounded by two distinct membranes: the outer and the inner membrane. The mitochondrial outer membrane mediates numerous interactions between the mitochondrial metabolic and genetic systems and the rest of the eukaryotic cell. Proteins of this membrane are nuclear-encoded and synthesized as precursor proteins in the cytosol. They are targeted to the mitochondria and inserted into their target membrane via various pathways. This review summarizes our current knowledge of the sorting signals for this specific targeting and describes the mechanisms by which the mitochondrial import machineries recognize precursor proteins, mediate their membrane integration and facilitate assembly into functional complexes.}, }
@article {pmid18498001, year = {2008}, author = {Vilar, MG and Kaneko, A and Hombhanje, FW and Tsukahara, T and Hwaihwanje, I and Lum, JK}, title = {Reconstructing the origin of the Lapita Cultural Complex: mtDNA analyses of East Sepik Province, PNG.}, journal = {Journal of human genetics}, volume = {53}, number = {8}, pages = {698-708}, pmid = {18498001}, issn = {1434-5161}, mesh = {DNA, Mitochondrial/*genetics ; Genetic Variation ; *Genetics, Population ; Haplotypes ; Humans ; Mitochondria/*genetics ; Papua New Guinea ; Phylogeny ; }, abstract = {The colonization of Oceania occurred in two waves. By 32,000 BP, humans had reached New Guinea and settled all intervisible islands east to the Solomon Islands. Around 3,500 BP, a distinct intrusive group from Southeast Asia reached coastal New Guinea, integrated their components with indigenous resources, and gave rise to the Lapita Cultural Complex. Within 2,500 years, Lapita and its descendant cultures colonized the Pacific. To uncover the origin of the Lapita Cultural Complex, we analyzed the hypervariable region I of the mitochondrial deoxyribonucleic acid (mtDNA) in 219 individuals from eight East Sepik Province villages: two villages in each of four environmental zones. Same-zone villages spoke different languages: one Austronesian and three Papuan (Arapesh, Abelam, and Boiken). Our analysis examined whether language or geography better predicted gene flow. In general, language better predicted genetic affinities. Boiken villages across all four zones showed no significant genetic difference (F(ST) P value > 0.05). In contrast, the Austronesian village was significantly different to most other villages (P < 0.05). Only the mountains and coast showed zonal gene flow (P > 0.05). We interpret the data to reflect limited gene flow inland by Austronesians overshadowed by a regional displacement by inland Boiken speakers migrating seaward. These results are consistent with oral histories and ethnographic accounts.}, }
@article {pmid18497740, year = {2008}, author = {Bych, K and Kerscher, S and Netz, DJ and Pierik, AJ and Zwicker, K and Huynen, MA and Lill, R and Brandt, U and Balk, J}, title = {The iron-sulphur protein Ind1 is required for effective complex I assembly.}, journal = {The EMBO journal}, volume = {27}, number = {12}, pages = {1736-1746}, pmid = {18497740}, issn = {1460-2075}, mesh = {Cysteine/metabolism ; Electron Spin Resonance Spectroscopy ; Electron Transport Complex I/*metabolism ; Fungal Proteins/*metabolism ; Gene Deletion ; Iron/metabolism ; Iron-Sulfur Proteins/*metabolism ; Mitochondria/metabolism ; Mitochondrial Membranes/metabolism ; Mutant Proteins/metabolism ; Mutation/genetics ; Phylogeny ; Protein Transport ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Yarrowia/*metabolism ; }, abstract = {NADH:ubiquinone oxidoreductase (complex I) of the mitochondrial inner membrane is a multi-subunit protein complex containing eight iron-sulphur (Fe-S) clusters. Little is known about the assembly of complex I and its Fe-S clusters. Here, we report the identification of a mitochondrial protein with a nucleotide-binding domain, named Ind1, that is required specifically for the effective assembly of complex I. Deletion of the IND1 open reading frame in the yeast Yarrowia lipolytica carrying an internal alternative NADH dehydrogenase resulted in slower growth and strongly decreased complex I activity, whereas the activities of other mitochondrial Fe-S enzymes, including aconitase and succinate dehydrogenase, were not affected. Two-dimensional gel electrophoresis, in vitro activity tests and electron paramagnetic resonance signals of Fe-S clusters showed that only a minor fraction (approximately 20%) of complex I was assembled in the ind1 deletion mutant. Using in vivo and in vitro approaches, we found that Ind1 can bind a [4Fe-4S] cluster that was readily transferred to an acceptor Fe-S protein. Our data suggest that Ind1 facilitates the assembly of Fe-S cofactors and subunits of complex I.}, }
@article {pmid18493044, year = {2008}, author = {Cognat, V and Deragon, JM and Vinogradova, E and Salinas, T and Remacle, C and Maréchal-Drouard, L}, title = {On the evolution and expression of Chlamydomonas reinhardtii nucleus-encoded transfer RNA genes.}, journal = {Genetics}, volume = {179}, number = {1}, pages = {113-123}, pmid = {18493044}, issn = {0016-6731}, mesh = {Animals ; Base Pairing ; Base Sequence ; Blotting, Northern ; Chlamydomonas reinhardtii/*genetics/*metabolism ; Codon/genetics ; Computational Biology ; *Evolution, Molecular ; Likelihood Functions ; Models, Genetic ; Multigene Family/*genetics ; *Phylogeny ; RNA, Transfer/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Short Interspersed Nucleotide Elements/genetics ; }, abstract = {In Chlamydomonas reinhardtii, 259 tRNA genes were identified and classified into 49 tRNA isoaccepting families. By constructing phylogenetic trees, we determined the evolutionary history for each tRNA gene family. The majority of the tRNA sequences are more closely related to their plant counterparts than to animals ones. Northern experiments also permitted us to show that at least one member of each tRNA isoacceptor family is transcribed and correctly processed in vivo. A short stretch of T residues known to be a signal for termination of polymerase III transcription was found downstream of most tRNA genes. It allowed us to propose that the vast majority of the tRNA genes are expressed and to confirm that numerous tRNA genes separated by short spacers are indeed cotranscribed. Interestingly, in silico analyses and hybridization experiments show that the cellular tRNA abundance is correlated with the number of tRNA genes and is adjusted to the codon usage to optimize translation efficiency. Finally, we studied the origin of SINEs, short interspersed elements related to tRNAs, whose presence in Chlamydomonas is exceptional. Phylogenetic analysis strongly suggests that tRNA(Asp)-related SINEs originate from a prokaryotic-type tRNA either horizontally transferred from a bacterium or originally present in mitochondria or chloroplasts.}, }
@article {pmid18492476, year = {2008}, author = {Howe, CJ}, title = {Cellular evolution: what's in a mitochondrion?.}, journal = {Current biology : CB}, volume = {18}, number = {10}, pages = {R429-R431}, doi = {10.1016/j.cub.2008.04.007}, pmid = {18492476}, issn = {0960-9822}, mesh = {Aerobiosis/physiology ; Anaerobiosis/physiology ; Animals ; *Biological Evolution ; Blastocystis/*cytology/*genetics/physiology ; Eukaryota/*cytology/*genetics/physiology ; Mitochondria/*genetics/physiology ; Symbiosis/physiology ; }, abstract = {Mitochondria and their relatives constitute a wide range of organelles, only some of which function in aerobic respiration. Mitochondrial remnants from different anaerobic lineages show a striking degree of functional convergence.}, }
@article {pmid18490179, year = {2008}, author = {Matsui, M and Yoshikawa, N and Tominaga, A and Sato, T and Takenaka, S and Tanabe, S and Nishikawa, K and Nakabayashi, S}, title = {Phylogenetic relationships of two Salamandrella species as revealed by mitochondrial DNA and allozyme variation (Amphibia: Caudata: Hynobiidae).}, journal = {Molecular phylogenetics and evolution}, volume = {48}, number = {1}, pages = {84-93}, doi = {10.1016/j.ympev.2008.04.010}, pmid = {18490179}, issn = {1095-9513}, mesh = {Amphibians/*classification/*genetics ; Animals ; DNA, Mitochondrial/genetics ; Enzymes/chemistry/genetics ; Liver/enzymology ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {We conducted molecular phylogenetic analyses to confirm taxonomic relationships and to delimit distributional ranges of Siberian salamanders, Salamandrella keyserlingii and Salamandrella schrenckii, and to elucidate the origin of the isolated population of this species complex on Hokkaido, Japan. Phylogenetic trees constructed by MP, NJ, ML, and Bayesian methods, using complete sequences of mitochondrial cytochrome b genes, all indicated monophyly of Salamandrella and of each of the two species. Identical relationships were found on UPGMA, NJ, and CONTML trees derived from electrophoretic analysis of variation in 18 inferred allozyme loci. Populations from Hokkaido and northeastern China proved to be S. keyserlingii, while populations from Khabarovsk and Lazovsky are S. schrenckii. Genetic differentiations of S. keyserlingii within Sakhalin, and between Sakhalin and Hokkaido, are substantial. The Hokkaido population is hypothesized to have been isolated on the island since early Pleistocene, much earlier than isolation of sympatric anuran populations from their Sakhalin relatives. In contrast, the continental populations of S. keyserlingii are only slightly differentiated from some Sakhalin populations, and are thought to have expanded their ranges in the late Pleistocene.}, }
@article {pmid18490026, year = {2008}, author = {Riera, AR and Kaiser, E and Levine, P and Schapachnik, E and Dubner, S and Ferreira, C and Ferreira Filho, C and de Luna, AB and Zhang, L}, title = {Kearns-Sayre syndrome: electro-vectorcardiographic evolution for left septal fascicular block of the his bundle.}, journal = {Journal of electrocardiology}, volume = {41}, number = {6}, pages = {675-678}, doi = {10.1016/j.jelectrocard.2008.04.001}, pmid = {18490026}, issn = {1532-8430}, mesh = {*Bundle of His ; Bundle-Branch Block/*diagnosis ; *Heart Septum ; Humans ; Kearns-Sayre Syndrome/*diagnosis ; Male ; Vectorcardiography/*methods ; Young Adult ; }, abstract = {The Kearns-Sayre syndrome is a neuromyopathic disorder associated with mitochondrial abnormalities and characterized by the triad of chronic external ophthalmoplegia, atypical pigmentary retinopathy, and progressive conduction system disorders. Ragged red muscle fibers that seem to contain an excess of altered mitochondria are observed. The disease affects both sexes alike, during the first or the second decade of life. The following manifestations are observed: central bilateral sensorineural deafness, pyramidal signs, ataxia, asymmetrical ptosis, external ophthalmoplegia, and progressive muscular weakness secondary to myopathy associated with a significant increase of proteins of cephalorachidian liquid. A variety of endocrinopathies may occur.}, }
@article {pmid18481082, year = {2008}, author = {Karve, A and Rauh, BL and Xia, X and Kandasamy, M and Meagher, RB and Sheen, J and Moore, BD}, title = {Expression and evolutionary features of the hexokinase gene family in Arabidopsis.}, journal = {Planta}, volume = {228}, number = {3}, pages = {411-425}, pmid = {18481082}, issn = {0032-0935}, support = {R01 GM036397-21/GM/NIGMS NIH HHS/United States ; R01 GM036397-20S1/GM/NIGMS NIH HHS/United States ; R01 GM036397-19/GM/NIGMS NIH HHS/United States ; R01 GM036397-23/GM/NIGMS NIH HHS/United States ; R01 GM036397/GM/NIGMS NIH HHS/United States ; R01 GM036397-20/GM/NIGMS NIH HHS/United States ; R01 GM036397-22/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Arabidopsis/*enzymology/*genetics ; Arabidopsis Proteins/chemistry/genetics/metabolism ; Catalysis ; *Evolution, Molecular ; Gene Expression Profiling ; *Gene Expression Regulation, Enzymologic ; *Gene Expression Regulation, Plant ; Gene Order ; Glucokinase/metabolism ; Hexokinase/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Multigene Family/*genetics ; Phylogeny ; RNA, Messenger/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; Subcellular Fractions/enzymology ; }, abstract = {Arabidopsis hexokinase1 (HXK1) is a moonlighting protein that has separable functions in glucose signaling and in glucose metabolism. In this study, we have characterized expression features and glucose phosphorylation activities of the six HXK gene family members in Arabidopsis thaliana. Three of the genes encode catalytically active proteins, including a stromal-localized HXK3 protein that is expressed mostly in sink organs. We also show that three of the genes encode hexokinase-like (HKL) proteins, which are about 50% identical to AtHXK1, but do not phosphorylate glucose or fructose. Expression studies indicate that both HKL1 and HKL2 transcripts occur in most, if not all, plant tissues and that both proteins are targeted within cells to mitochondria. The HKL1 and HKL2 proteins have 6-10 amino acid insertions/deletions (indels) at the adenosine binding domain. In contrast, HKL3 transcript was detected only in flowers, the protein lacks the noted indels, and the protein has many other amino acid changes that might compromise its ability even to bind glucose or ATP. Activity measurements of HXKs modified by site-directed mutagenesis suggest that the lack of catalytic activities in the HKL proteins might be attributed to any of numerous existing changes. Sliding windows analyses of coding sequences in A. thaliana and A. lyrata ssp. lyrata revealed a differential accumulation of nonsynonymous changes within exon 8 of both HKL1 and HXK3 orthologs. We further discuss the possibility that the non-catalytic HKL proteins have regulatory functions instead of catalytic functions.}, }
@article {pmid18478535, year = {2008}, author = {Bock, R and Timmis, JN}, title = {Reconstructing evolution: gene transfer from plastids to the nucleus.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {30}, number = {6}, pages = {556-566}, doi = {10.1002/bies.20761}, pmid = {18478535}, issn = {1521-1878}, mesh = {Cell Nucleus/*genetics ; Cyanobacteria/genetics ; DNA/genetics ; *Evolution, Molecular ; Gene Expression Regulation ; Gene Transfer Techniques ; Gene Transfer, Horizontal ; Genome, Bacterial ; Genome, Plant ; Genome, Plastid ; Models, Genetic ; Plants/genetics ; Plants, Genetically Modified ; Plastids/*genetics ; RNA/genetics ; Research Design ; Symbiosis/genetics ; }, abstract = {During evolution, the genomes of eukaryotic cells have undergone major restructuring to meet the new regulatory challenges associated with compartmentalization of the genetic material in the nucleus and the organelles acquired by endosymbiosis (mitochondria and plastids). Restructuring involved the loss of dispensable or redundant genes and the massive translocation of genes from the ancestral organelles to the nucleus. Genomics and bioinformatic data suggest that the process of DNA transfer from organelles to the nucleus still continues, providing raw material for evolutionary tinkering in the nuclear genome. Recent reconstruction of these events in the laboratory has provided a unique tool to observe genome evolution in real time and to study the molecular mechanisms by which plastid genes are converted into functional nuclear genes. Here, we summarize current knowledge about plastid-to-nuclear gene transfer in the context of genome evolution and discuss new insights gained from experiments that recapitulate endosymbiotic gene transfer in the laboratory.}, }
@article {pmid18474590, year = {2008}, author = {Hauptmann, P and Lehle, L}, title = {Kex1 protease is involved in yeast cell death induced by defective N-glycosylation, acetic acid, and chronological aging.}, journal = {The Journal of biological chemistry}, volume = {283}, number = {27}, pages = {19151-19163}, doi = {10.1074/jbc.M801303200}, pmid = {18474590}, issn = {0021-9258}, mesh = {Acetic Acid/*pharmacology ; Aging/*drug effects/metabolism ; Antiviral Agents/pharmacology ; Apoptosis/*drug effects ; Biological Evolution ; Carboxypeptidases/genetics/*metabolism ; Caspases/genetics/metabolism ; DNA Fragmentation/drug effects ; Glycosylation/drug effects ; Hexosyltransferases/genetics/metabolism ; Hot Temperature ; Indicators and Reagents/*pharmacology ; Membrane Proteins/genetics/metabolism ; Mitochondria/genetics/metabolism ; Protein Modification, Translational/*drug effects ; Reactive Oxygen Species/metabolism ; Saccharomyces cerevisiae/cytology/*enzymology/genetics ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Tunicamycin/pharmacology ; }, abstract = {N-glycosylation in the endoplasmic reticulum is an essential protein modification and highly conserved in evolution from yeast to humans. The key step of this pathway is the transfer of the lipid-linked core oligosaccharide to the nascent polypeptide chain, catalyzed by the oligosaccharyltransferase complex. Temperature-sensitive oligosaccharyltransferase mutants of Saccharomyces cerevisiae at the restrictive temperature, such as wbp1-1, as well as wild-type cells in the presence of the N-glycosylation inhibitor tunicamycin display typical apoptotic phenotypes like nuclear condensation, DNA fragmentation, phosphatidylserine translocation, caspase-like activity, and reactive oxygen species accumulation. Since deletion of the yeast metacaspase YCA1 did not abrogate this death pathway, we postulated a different proteolytic process to be responsible. Here, we show that Kex1 protease is involved in the programmed cell death caused by defective N-glycosylation. Its disruption decreases caspase-like activity, production of reactive oxygen species, and fragmentation of mitochondria and, conversely, improves growth and survival of cells. Moreover, we demonstrate that Kex1 contributes also to the active cell death program induced by acetic acid stress or during chronological aging, suggesting that Kex1 plays a more general role in cellular suicide of yeast.}, }
@article {pmid18468979, year = {2008}, author = {Mentel, M and Martin, W}, title = {Energy metabolism among eukaryotic anaerobes in light of Proterozoic ocean chemistry.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {363}, number = {1504}, pages = {2717-2729}, pmid = {18468979}, issn = {0962-8436}, mesh = {Anaerobiosis ; Animals ; *Biological Evolution ; *Energy Metabolism ; Eukaryotic Cells ; Fungi/metabolism ; Mitochondria/metabolism ; Oceans and Seas ; Organelles/metabolism ; Sulfides/metabolism ; Symbiosis ; Trichomonas/metabolism ; }, abstract = {Recent years have witnessed major upheavals in views about early eukaryotic evolution. One very significant finding was that mitochondria, including hydrogenosomes and the newly discovered mitosomes, are just as ubiquitous and defining among eukaryotes as the nucleus itself. A second important advance concerns the readjustment, still in progress, about phylogenetic relationships among eukaryotic groups and the roughly six new eukaryotic supergroups that are currently at the focus of much attention. From the standpoint of energy metabolism (the biochemical means through which eukaryotes gain their ATP, thereby enabling any and all evolution of other traits), understanding of mitochondria among eukaryotic anaerobes has improved. The mainstream formulations of endosymbiotic theory did not predict the ubiquity of mitochondria among anaerobic eukaryotes, while an alternative hypothesis that specifically addressed the evolutionary origin of energy metabolism among eukaryotic anaerobes did. Those developments in biology have been paralleled by a similar upheaval in the Earth sciences regarding views about the prevalence of oxygen in the oceans during the Proterozoic (the time from ca 2.5 to 0.6 Ga ago). The new model of Proterozoic ocean chemistry indicates that the oceans were anoxic and sulphidic during most of the Proterozoic. Its proponents suggest the underlying geochemical mechanism to entail the weathering of continental sulphides by atmospheric oxygen to sulphate, which was carried into the oceans as sulphate, fueling marine sulphate reducers (anaerobic, hydrogen sulphide-producing prokaryotes) on a global scale. Taken together, these two mutually compatible developments in biology and geology underscore the evolutionary significance of oxygen-independent ATP-generating pathways in mitochondria, including those of various metazoan groups, as a watermark of the environments within which eukaryotes arose and diversified into their major lineages.}, }
@article {pmid18467455, year = {2008}, author = {Lee, S and Chappell, J}, title = {Biochemical and genomic characterization of terpene synthases in Magnolia grandiflora.}, journal = {Plant physiology}, volume = {147}, number = {3}, pages = {1017-1033}, pmid = {18467455}, issn = {0032-0889}, mesh = {Alkyl and Aryl Transferases/*genetics/metabolism ; Amino Acid Sequence ; Cycadopsida/genetics ; Cyclohexane Monoterpenes ; Cyclohexenes/metabolism ; DNA, Complementary/isolation &amp; purification ; *Evolution, Molecular ; Genome, Plant ; *Introns ; Magnolia/enzymology/*genetics ; Molecular Sequence Data ; Monoterpenes/metabolism ; Protein Sorting Signals ; RNA, Messenger/metabolism ; }, abstract = {Magnolia grandiflora (Southern Magnolia) is a primitive evergreen tree that has attracted attention because of its horticultural distinctiveness, the wealth of natural products associated with it, and its evolutionary position as a basal angiosperm. Three cDNAs corresponding to terpene synthase (TPS) genes expressed in young leaves were isolated, and the corresponding enzymes were functionally characterized in vitro. Recombinant Mg25 converted farnesyl diphosphate (C(15)) predominantly to beta-cubebene, while Mg17 converted geranyl diphosphate (C(5)) to alpha-terpineol. Efforts to functionally characterize Mg11 were unsuccessful. Transcript levels for all three genes were prominent in young leaf tissue and significantly elevated for Mg25 and Mg11 messenger RNAs in stamens. A putative amino-terminal signal peptide of Mg17 targeted the reporter green fluorescent protein to both chloroplasts and mitochondria when transiently expressed in epidermal cells of Nicotiana tabacum leaves. Phylogenetic analyses indicated that Mg25 and Mg11 belonged to the angiosperm sesquiterpene synthase subclass TPS-a, while Mg17 aligned more closely to the angiosperm monoterpene synthase subclass TPS-b. Unexpectedly, the intron-exon organizations for the three Magnolia TPS genes were different from one another and from other well-characterized TPS gene sets. The Mg17 gene consists of six introns arranged in a manner similar to many other angiosperm sesquiterpene synthases, but Mg11 contains only four introns, and Mg25 has only a single intron located near the 5' terminus of the gene. Our results suggest that the structural diversity observed in the Magnolia TPS genes could have occurred either by a rapid loss of introns from a common ancestor TPS gene or by a gain of introns into an intron-deficient progenote TPS gene.}, }
@article {pmid18462954, year = {2008}, author = {Shepherd, LD and Holland, BR and Perrie, LR}, title = {Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Asplenium ferns.}, journal = {Molecular phylogenetics and evolution}, volume = {48}, number = {1}, pages = {176-187}, doi = {10.1016/j.ympev.2008.02.023}, pmid = {18462954}, issn = {1095-9513}, mesh = {Chloroplasts/genetics ; DNA, Chloroplast/*genetics ; Ferns/*classification/*genetics ; Phylogeny ; Recombination, Genetic ; }, abstract = {A previous study of the relationships amongst three subgroups of the Austral Asplenium ferns found conflicting signal between the two chloroplast loci investigated. Because organelle genomes like those of chloroplasts and mitochondria are thought to be non-recombining, with a single evolutionary history, we sequenced four additional chloroplast loci with the expectation that this would resolve these relationships. Instead, the conflict was only magnified. Although tree-building analyses favoured one of the three possible trees, one of the alternative trees actually had one more supporting site (six versus five) and received greater support in spectral and neighbor-net analyses. Simulations suggested that chance alone was unlikely to produce strong support for two of the possible trees and none for the third. Likelihood permutation tests indicated that the concatenated chloroplast sequence data appeared to have experienced recombination. However, recombination between the chloroplast genomes of different species would be highly atypical, and corollary supporting observations, like chloroplast heteroplasmy, are lacking. Wider taxon sampling clarified the composition of the Austral group, but the conflicting signal meant analyses (e.g., morphological evolution, biogeographic) conditional on a well-supported phylogeny could not be performed.}, }
@article {pmid18459820, year = {2008}, author = {Kotaki, M and Kurabayashi, A and Matsui, M and Khonsue, W and Djong, TH and Tandon, M and Sumida, M}, title = {Genetic divergences and phylogenetic relationships among the Fejervarya limnocharis complex in Thailand and neighboring countries revealed by mitochondrial and nuclear genes.}, journal = {Zoological science}, volume = {25}, number = {4}, pages = {381-390}, doi = {10.2108/zsj.25.381}, pmid = {18459820}, issn = {0289-0003}, mesh = {Animals ; Enzymes/*genetics ; *Evolution, Molecular ; Female ; *Genetic Variation ; Haplotypes ; Male ; Mitochondria/genetics ; *Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/genetics ; Ranidae/classification/*genetics ; Species Specificity ; Thailand ; }, abstract = {To clarify the genetic divergence in the F. limnocharis complex from Thailand and neighboring countries and to elucidate the phylogenetic problems of this taxon, we analyzed partial sequences of the mitochondrial 12S and 16S rRNA genes and the nuclear CXCR4, NCX1, RAG-1, and tyrosinase genes. The F. limnocharis complex from Thailand had three distinct haplotypes for 12S and 16S rRNA genes. Nucleotide similarities and the phylogenetic relationships indicated that the haplotype 1 group corresponded to the real "F. limnocharis", the haplotype 2 group was F. orissaensis or closely related to it, and the haplotype 3 group was possibly an undescribed species. Mitochondrial gene data also showed two major clades of the genus Fejervarya, the Southeastern and South Asian groups. Although F. orissaensis is so far known only from Orissa in India, the haplotype 2 group was observed in Thailand. This distribution pattern and the phylogeny suggested that the origin of F. orissaensis and the haplotype 2 group might lie in Southeast Asia. There was also evidence suggesting that the haplotype 3 group originated in the South Asian area and has spread to northern Thailand. The nuclear gene data did not support the monophyly of the haplotypes recognized by mitochondrial genes. This incongruence between the mitochondrial and nuclear data seems to be caused by ancestral polymorphic sites contained in nuclear genes. Although neither the mitochondrial nor the nuclear data clarified intergeneric relationships, the nuclear data rejected the monophyly of the genus Fejervarya.}, }
@article {pmid18458332, year = {2008}, author = {Alliegro, MC and Alliegro, MA}, title = {Centrosomal RNA correlates with intron-poor nuclear genes in Spisula oocytes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {19}, pages = {6993-6997}, pmid = {18458332}, issn = {1091-6490}, support = {R21 GM075163/GM/NIGMS NIH HHS/United States ; GM075163/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Nucleus/*genetics ; Centrosome/*metabolism ; DNA/metabolism ; Gene Expression Regulation ; Genome ; Introns/*genetics ; Oocytes/cytology/*metabolism ; Polymerase Chain Reaction ; RNA/chemistry/*metabolism ; RNA Transport ; Spisula/*cytology/*genetics ; }, abstract = {The evolutionary origin of centriole/kinetosomes, centrosomes, and other microtubule organizing centers (MTOCs), whether by direct filiation or symbiogenesis, has been controversial for >50 years. Centrioles, like mitochondria and chloroplasts, duplicate independently of the nucleus and constitute a heritable system independent of chromosomal DNA. Nucleic acids endogenous to the MTOC would support evolutionary origin by symbiogenesis. To date, most reports of centrosome-associated nucleic acids have used generalized reagents such as RNases and nucleic acid dyes. Here, from a library of RNAs extracted from isolated surf clam (Spisula solidissima) centrosomes, we describe a group of centrosome-associated transcripts representing a structurally unique intron-poor collection of nuclear genes skewed toward nucleic acid metabolism. Thus, we resolve the debate over the existence of centrosome-associated RNA (cnRNA). A subset of cnRNAs contain functional domains that are highly conserved across distant taxa, such as nucleotide polymerase motifs. In situ localization of cnRNA65, a molecule with an RNA polymerase domain, showed it is present in the intact oocyte nucleus (germinal vesicle). Its expression, therefore, precedes the appearance of gamma-tubulin-containing centrosomes. At this stage, the in situ signal resembles the nucleolinus, a poorly understood organelle proposed to play a role in spindle formation. After oocyte activation and germinal vesicle breakdown, cnRNA65 persists as a cytoplasmic patch within which gamma-tubulin-stained centrosomes can be seen. These observations provoke the question of whether cnRNAs and the nucleolinus serve as cytological progenitors of the centrosome and may support a symbiogenetic model for its evolution.}, }
@article {pmid18456519, year = {2008}, author = {Linnen, CR and Farrell, BD}, title = {Phylogenetic analysis of nuclear and mitochondrial genes reveals evolutionary relationships and mitochondrial introgression in the sertifer species group of the genus Neodiprion (Hymenoptera: Diprionidae).}, journal = {Molecular phylogenetics and evolution}, volume = {48}, number = {1}, pages = {240-257}, doi = {10.1016/j.ympev.2008.03.021}, pmid = {18456519}, issn = {1095-9513}, mesh = {Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Genes, Mitochondrial ; Genetic Speciation ; Hymenoptera/*genetics ; Mitochondria ; North America ; Phylogeny ; }, abstract = {Neodiprion Rohwer (Hymenoptera: Diprionidae) is a Holarctic genus of conifer-feeding sawflies with a remarkable amount of inter- and intraspecific diversity in host use, behavior, and development. This variation is thought to play a central role in Neodiprion diversification, but speciation hypotheses remain untested due to a lack of a robust phylogenetic estimate. Here, we utilize sequence data from three nuclear genes (CAD, ANL43, EF1alpha) to obtain a phylogenetic estimate for the genus. These analyses suggest that: (1) North American and Eurasian Neodiprion are monophyletic sister clades, (2) the sertifer group is paraphyletic with respect to the monophyletic lecontei group, and (3) on at least two occasions, dispersal from eastern to western North America proceeded via southern host bridges. Based on these results and host biogeography, we revise a previous scenario for the evolution of Neodiprion and suggest maximum ages for the genus and for the lecontei group (25 My and 14 My, respectively). In addition, because a previous study reported rampant mitochondrial introgression in the lecontei group, we assess its prevalence in the sertifer group. Analysis of three mitochondrial genes (COI, tRNA-leucine, and COII) reveals that mito-nuclear discordance is prevalent in the sertifer group, and patterns of species monophyly are consistent with those expected under frequent mitochondrial introgression. As was the case for lecontei group species, we find that introgression appears to be most pronounced between species that occasionally share hosts, suggesting that divergent host use is an important barrier to gene flow in Neodiprion. Finally, we suggest that the lack of phylogenetic resolution and prevalence of species non-monophyly in the non-Pinus feeding Neodiprion may result from the rapid divergence (possibly with gene flow) of these species following their entry into a novel adaptive zone.}, }
@article {pmid18455442, year = {2008}, author = {Veith, M and Lipscher, E and Oz, M and Kiefer, A and Baran, I and Polymeni, RM and Steinfartz, S}, title = {Cracking the nut: geographical adjacency of sister taxa supports vicariance in a polytomic salamander clade in the absence of node support.}, journal = {Molecular phylogenetics and evolution}, volume = {47}, number = {3}, pages = {916-931}, doi = {10.1016/j.ympev.2007.11.017}, pmid = {18455442}, issn = {1055-7903}, mesh = {Adenosine Triphosphatases/genetics ; Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; *Geography ; Haplotypes ; Inbreeding ; Mitochondria/genetics ; *Phylogeny ; Urodela/*classification/*genetics ; }, abstract = {The urodelan genus Lyciasalamandra, which inhabits a relatively small area along the southern Turkish coast and some Aegean islands, provides an outstanding example of a diverse but phylogenetically unresolved taxon. Molecular trees contain a single basal polytomy that could be either soft or hard. We here use the information of nuclear (allozymes) and mitochondrial (fractions of the 16S rRNA and ATPase genes) datasets in combination with area relationships of lineages to resolve the phylogenetic relationships among Lyciasalamandra species in the absence of sufficient node support. We can show that neither random processes nor introgressive hybridization can be invoked to explain that the majority of pairs of sister taxa form geographically adjacent units and interpret that this pattern has been shaped by vicariant events. Topology discordance between mitochondrial and nuclear trees mainly refers to an affiliation of L. helverseni, a taxon restricted to the Karpathos archipelago, to the western-most and geographically proximate mainland taxon in the nuclear tree, while in the organelle tree it turns out to be the sister lineage to the geographically most distant eastern clade. As this discordance cannot be explained by long-branch attraction in either dataset we suppose that oversea dispersal may have accounted for a second colonization of the Karpathos archipelago. It may have initiated introgression and selection driven manifestation of alien eastern mitochondrial genomes on a western nuclear background. Our approach of testing for area relationships of sister taxa against the null hypothesis of random distribution of these taxa seems to be especially helpful in phylogenetic studies where traditional measures of phylogenetic branch support fail to reject the null hypothesis of a hard polytomy.}, }
@article {pmid18453549, year = {2008}, author = {Ueda, M and Nishikawa, T and Fujimoto, M and Takanashi, H and Arimura, S and Tsutsumi, N and Kadowaki, K}, title = {Substitution of the gene for chloroplast RPS16 was assisted by generation of a dual targeting signal.}, journal = {Molecular biology and evolution}, volume = {25}, number = {8}, pages = {1566-1575}, doi = {10.1093/molbev/msn102}, pmid = {18453549}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Base Sequence ; Cell Nucleus/genetics ; DNA Primers/genetics ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; Genes, Plant/*genetics ; Molecular Sequence Data ; *Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Ribosomal Proteins/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Organelle (mitochondria and chloroplasts in plants) genomes lost a large number of genes after endosymbiosis occurred. Even after this major gene loss, organelle genomes still lose their own genes, even those that are essential, via gene transfer to the nucleus and gene substitution of either different organelle origin or de novo genes. Gene transfer and substitution events are important processes in the evolution of the eukaryotic cell. Gene loss is an ongoing process in the mitochondria and chloroplasts of higher plants. The gene for ribosomal protein S16 (rps16) is encoded in the chloroplast genome of most higher plants but not in Medicago truncatula and Populus alba. Here, we show that these 2 species have compensated for loss of the rps16 from the chloroplast genome by having a mitochondrial rps16 that can target the chloroplasts as well as mitochondria. Furthermore, in Arabidopsis thaliana, Lycopersicon esculentum, and Oryza sativa, whose chloroplast genomes encode the rps16, we show that the product of the mitochondrial rps16 has dual targeting ability. These results suggest that the dual targeting of RPS16 to the mitochondria and chloroplasts emerged before the divergence of monocots and dicots (140-150 MYA). The gene substitution of the chloroplast rps16 by the nuclear-encoded rps16 in higher plants is the first report about ongoing gene substitution by dual targeting and provides evidence for an intermediate stage in the formation of this heterogeneous organelle.}, }
@article {pmid18452512, year = {2008}, author = {Hamblin, K and Standley, DM and Rogers, MB and Stechmann, A and Roger, AJ and Maytum, R and van der Giezen, M}, title = {Localization and nucleotide specificity of Blastocystis succinyl-CoA synthetase.}, journal = {Molecular microbiology}, volume = {68}, number = {6}, pages = {1395-1405}, pmid = {18452512}, issn = {1365-2958}, support = {/WT_/Wellcome Trust/United Kingdom ; 078566/WT_/Wellcome Trust/United Kingdom ; 078566/A/05/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Base Sequence ; Blastocystis/chemistry/*cytology/*enzymology/genetics ; Blastocystis Infections/parasitology ; Cytoplasmic Structures/chemistry/enzymology/genetics ; Humans ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Subunits/chemistry/genetics/metabolism ; Protozoan Proteins/chemistry/genetics/metabolism ; Purine Nucleotides/*metabolism ; Sequence Alignment ; Substrate Specificity ; Succinate-CoA Ligases/*chemistry/genetics/metabolism ; Swine/genetics ; }, abstract = {The anaerobic lifestyle of the intestinal parasite Blastocystis raises questions about the biochemistry and function of its mitochondria-like organelles. We have characterized the Blastocystis succinyl-CoA synthetase (SCS), a tricarboxylic acid cycle enzyme that conserves energy by substrate-level phosphorylation. We show that SCS localizes to the enigmatic Blastocystis organelles, indicating that these organelles might play a similar role in energy metabolism as classic mitochondria. Although analysis of residues inside the nucleotide-binding site suggests that Blastocystis SCS is GTP-specific, we demonstrate that it is ATP-specific. Homology modelling, followed by flexible docking and molecular dynamics simulations, indicates that while both ATP and GTP fit into the Blastocystis SCS active site, GTP is destabilized by electrostatic dipole interactions with Lys 42 and Lys 110, the side-chains of which lie outside the nucleotide-binding cavity. It has been proposed that residues in direct contact with the substrate determine nucleotide specificity in SCS. However, our results indicate that, in Blastocystis, an electrostatic gatekeeper controls which ligands can enter the binding site.}, }
@article {pmid18452298, year = {2008}, author = {Jérôme, M and Martinsohn, JT and Ortega, D and Carreau, P and Verrez-Bagnis, V and Mouchel, O}, title = {Toward fish and seafood traceability: anchovy species determination in fish products by molecular markers and support through a public domain database.}, journal = {Journal of agricultural and food chemistry}, volume = {56}, number = {10}, pages = {3460-3469}, doi = {10.1021/jf703704m}, pmid = {18452298}, issn = {0021-8561}, mesh = {Animals ; DNA/*analysis ; Databases, Nucleic Acid ; Fish Products/*analysis ; Fishes/*classification/*genetics ; Food Preservation ; Genetic Markers/*genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; }, abstract = {Traceability in the fish food sector plays an increasingly important role for consumer protection and confidence building. This is reflected by the introduction of legislation and rules covering traceability on national and international levels. Although traceability through labeling is well established and supported by respective regulations, monitoring and enforcement of these rules are still hampered by the lack of efficient diagnostic tools. We describe protocols using a direct sequencing method based on 212-274-bp diagnostic sequences derived from species-specific mitochondria DNA cytochrome b, 16S rRNA, and cytochrome oxidase subunit I sequences which can efficiently be applied to unambiguously determine even closely related fish species in processed food products labeled "anchovy". Traceability of anchovy-labeled products is supported by the public online database AnchovyID (http://anchovyid.jrc.ec.europa.eu), which provided data obtained during our study and tools for analytical purposes.}, }
@article {pmid18451868, year = {2008}, author = {Oberst, A and Bender, C and Green, DR}, title = {Living with death: the evolution of the mitochondrial pathway of apoptosis in animals.}, journal = {Cell death and differentiation}, volume = {15}, number = {7}, pages = {1139-1146}, pmid = {18451868}, issn = {1350-9047}, support = {R37 GM052735-18/GM/NIGMS NIH HHS/United States ; R01 AI047891/AI/NIAID NIH HHS/United States ; R01 AI044828-11/AI/NIAID NIH HHS/United States ; R37 GM052735/GM/NIGMS NIH HHS/United States ; R01 AI040646-11/AI/NIAID NIH HHS/United States ; R01 AI047891-10/AI/NIAID NIH HHS/United States ; P01 CA069381-130010/CA/NCI NIH HHS/United States ; R01 AI044828/AI/NIAID NIH HHS/United States ; P01 CA069381/CA/NCI NIH HHS/United States ; R01 AI040646/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Apoptosis ; Apoptosis Regulatory Proteins/*metabolism ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/metabolism ; Chordata, Nonvertebrate/metabolism ; Drosophila Proteins/metabolism ; Drosophila melanogaster/metabolism ; *Evolution, Molecular ; Mitochondria/*metabolism/pathology ; Mitochondrial Proteins/*metabolism ; *Signal Transduction ; }, abstract = {The mitochondrial pathway of cell death, in which apoptosis proceeds following mitochondrial outer membrane permeabilization, release of cytochrome c, and APAF-1 apoptosome-mediated caspase activation, represents the major pathway of physiological apoptosis in vertebrates. However, the well-characterized apoptotic pathways of the invertebrates C. elegans and D. melanogaster indicate that this apoptotic pathway is not universally conserved among animals. This review will compare the role of the mitochondria in the apoptotic programs of mammals, nematodes, and flies, and will survey our knowledge of the apoptotic pathways of other, less familiar model organisms in an effort to explore the evolutionary origins of the mitochondrial pathway of apoptosis.}, }
@article {pmid18449191, year = {2008}, author = {Tsaousis, AD and Kunji, ER and Goldberg, AV and Lucocq, JM and Hirt, RP and Embley, TM}, title = {A novel route for ATP acquisition by the remnant mitochondria of Encephalitozoon cuniculi.}, journal = {Nature}, volume = {453}, number = {7194}, pages = {553-556}, doi = {10.1038/nature06903}, pmid = {18449191}, issn = {1476-4687}, support = {MC_U105663139/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adenosine Triphosphate/*metabolism ; Animals ; Biological Transport ; Carrier Proteins/genetics/immunology/metabolism ; Cell Line ; Encephalitozoon cuniculi/*cytology/genetics/*metabolism ; Escherichia coli/genetics/metabolism ; Fungal Proteins/genetics/immunology/metabolism ; Genome, Fungal/genetics ; Genome, Mitochondrial/genetics ; Mitochondria/genetics/*metabolism ; Models, Biological ; Molecular Sequence Data ; Rabbits ; Rats ; Symbiosis ; }, abstract = {Mitochondria use transport proteins of the eukaryotic mitochondrial carrier family (MCF) to mediate the exchange of diverse substrates, including ATP, with the host cell cytosol. According to classical endosymbiosis theory, insertion of a host-nuclear-encoded MCF transporter into the protomitochondrion was the key step that allowed the host cell to harvest ATP from the enslaved endosymbiont. Notably the genome of the microsporidian Encephalitozoon cuniculi has lost all of its genes for MCF proteins. This raises the question of how the recently discovered microsporidian remnant mitochondrion, called a mitosome, acquires ATP to support protein import and other predicted ATP-dependent activities. The E. cuniculi genome does contain four genes for an unrelated type of nucleotide transporter used by plastids and bacterial intracellular parasites, such as Rickettsia and Chlamydia, to import ATP from the cytosol of their eukaryotic host cells. The inference is that E. cuniculi also uses these proteins to steal ATP from its eukaryotic host to sustain its lifestyle as an obligate intracellular parasite. Here we show that, consistent with this hypothesis, all four E. cuniculi transporters can transport ATP, and three of them are expressed on the surface of the parasite when it is living inside host cells. The fourth transporter co-locates with mitochondrial Hsp70 to the E. cuniculi mitosome. Thus, uniquely among eukaryotes, the traditional relationship between mitochondrion and host has been subverted in E. cuniculi, by reductive evolution and analogous gene replacement. Instead of the mitosome providing the parasite cytosol with ATP, the parasite cytosol now seems to provide ATP for the organelle.}, }
@article {pmid18442968, year = {2008}, author = {Bauerschmitt, H and Funes, S and Herrmann, JM}, title = {The membrane-bound GTPase Guf1 promotes mitochondrial protein synthesis under suboptimal conditions.}, journal = {The Journal of biological chemistry}, volume = {283}, number = {25}, pages = {17139-17146}, doi = {10.1074/jbc.M710037200}, pmid = {18442968}, issn = {0021-9258}, mesh = {Cell Membrane/*enzymology ; Electron Transport Complex IV/metabolism ; Escherichia coli Proteins/metabolism ; GTP Phosphohydrolases/chemistry/*metabolism/physiology ; *Gene Expression Regulation, Fungal ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Models, Biological ; Nuclear Proteins/metabolism ; Peptide Initiation Factors ; Peptides/chemistry ; Phylogeny ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*physiology ; Species Specificity ; Temperature ; Transcriptional Elongation Factors/metabolism ; }, abstract = {Recently, the bacterial elongation factor LepA was identified as critical for the accuracy of in vitro translation reactions. Extremely well conserved homologues of LepA are present throughout bacteria and eukaryotes, but the physiological relevance of these proteins is unclear. Here we show that the yeast counterpart of LepA, Guf1, is located in the mitochondrial matrix and tightly associated with the inner membrane. It binds to mitochondrial ribosomes in a GTP-dependent manner. Mutants lacking Guf1 show cold- and heat-sensitive growth defects on non-fermentable carbon sources that are especially pronounced under nutrient-limiting conditions. The cold sensitivity is explained by diminished rates of protein synthesis at low temperatures. At elevated temperatures, Guf1-deficient mutants exhibit defects in the assembly of cytochrome oxidase, suggesting that the polypeptides produced are not functional. Moreover, Guf1 mutants exhibit synthetic growth defects with mutations of the protein insertase Oxa1. These observations show a critical role for Guf1 in vivo. The observed defects in Guf1-deficient mitochondria are consistent with a function of Guf1 as a fidelity factor of mitochondrial protein synthesis.}, }
@article {pmid18434609, year = {2008}, author = {Carr, H and Axelsson, L}, title = {Photosynthetic utilization of bicarbonate in Zostera marina is reduced by inhibitors of mitochondrial ATPase and electron transport.}, journal = {Plant physiology}, volume = {147}, number = {2}, pages = {879-885}, pmid = {18434609}, issn = {0032-0889}, mesh = {Adenosine Triphosphatases/*antagonists &amp; inhibitors/metabolism ; Bicarbonates/*metabolism ; Electron Transport ; Enzyme Inhibitors/*pharmacology ; Mitochondria/*drug effects/enzymology ; *Photosynthesis ; Zosteraceae/enzymology/*metabolism ; }, abstract = {When Zostera marina was irradiated after a period of darkness, initiation of photosynthetic O2 evolution occurred in two phases. During a lag phase, lasting 4 to 5 min, photosynthesis was supported by a diffusive entry of CO2. Photosynthesis then rapidly increased to its full rate. Tris buffer, at a concentration of 50 mm, completely inhibited this increase without affecting CO2-supported photosynthesis during the lag phase. These results verify that the increase in photosynthesis after the lag phase depended on an activation of bicarbonate (HCO3-) utilization through acid zones generated by proton pumps located to the outer cell membrane. In similar experiments, 6.25 microm of the mitochondrial ATPase blocker oligomycin inhibited photosynthetic HCO3(-) utilization by more than 60%. Antimycin A, a selective blocker of mitochondrial electron transport, caused a similar inhibition of HCO3(-) utilization. Measurements at elevated CO2 concentrations verified that neither oligomycin nor antimycin interfered with linear photosynthetic electron transport or with CO2 fixation. Thus, a major part of the ATP used for the generation of acid zones involved in HCO3(-) utilization in Z. marina was derived from mitochondrial respiration.}, }
@article {pmid18433447, year = {2008}, author = {Long, S and Jirků, M and Mach, J and Ginger, ML and Sutak, R and Richardson, D and Tachezy, J and Lukes, J}, title = {Ancestral roles of eukaryotic frataxin: mitochondrial frataxin function and heterologous expression of hydrogenosomal Trichomonas homologues in trypanosomes.}, journal = {Molecular microbiology}, volume = {69}, number = {1}, pages = {94-109}, doi = {10.1111/j.1365-2958.2008.06260.x}, pmid = {18433447}, issn = {1365-2958}, mesh = {Amino Acid Sequence ; Animals ; Cell Line ; Eukaryotic Cells/classification/physiology ; *Evolution, Molecular ; *Gene Expression ; Humans ; Iron-Binding Proteins/chemistry/genetics/*metabolism ; Iron-Sulfur Proteins/chemistry/genetics/metabolism ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Prokaryotic Cells/classification/physiology ; Protozoan Proteins/chemistry/genetics/metabolism ; RNA Interference ; Sequence Alignment ; Trichomonas/chemistry/classification/genetics/*metabolism ; Frataxin ; }, abstract = {Frataxin is a small conserved mitochondrial protein; in humans, mutations affecting frataxin expression or function result in Friedreich's ataxia. Much of the current understanding of frataxin function comes from informative studies with yeast models, but considerable debates remain with regard to the primary functions of this ubiquitous protein. We exploit the tractable reverse genetics of Trypanosoma brucei in order to specifically consider the importance of frataxin in an early branching lineage. Using inducible RNAi, we show that frataxin is essential in T. brucei and that its loss results in reduced activity of the marker Fe-S cluster-containing enzyme aconitase in both the mitochondrion and cytosol. Activities of mitochondrial succinate dehydrogenase and fumarase also decreased, but the concentration of reactive oxygen species increased. Trypanosomes lacking frataxin also exhibited a low mitochondrial membrane potential and reduced oxygen consumption. Crucially, however, iron did not accumulate in frataxin-depleted mitochondria, and as T. brucei frataxin does not form large complexes, it suggests that it plays no role in iron storage. Interestingly, RNAi phenotypes were ameliorated by expression of frataxin homologues from hydrogenosomes of another divergent protist Trichomonas vaginalis. Collectively, the data suggest trypanosome frataxin functions primarily only in Fe-S cluster biogenesis and protection from reactive oxygen species.}, }
@article {pmid18430024, year = {2008}, author = {Moriyama, T and Terasawa, K and Fujiwara, M and Sato, N}, title = {Purification and characterization of organellar DNA polymerases in the red alga Cyanidioschyzon merolae.}, journal = {The FEBS journal}, volume = {275}, number = {11}, pages = {2899-2918}, doi = {10.1111/j.1742-4658.2008.06426.x}, pmid = {18430024}, issn = {1742-464X}, mesh = {Algal Proteins/*chemistry ; Amino Acid Sequence ; DNA Polymerase II/*chemistry/*isolation &amp; purification ; *Gene Expression Regulation, Plant ; Green Fluorescent Proteins/metabolism ; Mitochondria/metabolism ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; Plastids/metabolism ; Recombinant Fusion Proteins/chemistry ; Recombinant Proteins/chemistry ; Rhodophyta/*enzymology ; Sequence Homology, Amino Acid ; Temperature ; }, abstract = {DNA polymerase gamma, a mitochondrial replication enzyme of yeasts and animals, is not present in photosynthetic eukaryotes. Recently, DNA polymerases with distant homology to bacterial DNA polymerase I were reported in rice, Arabidopsis, and tobacco, and they were localized to both plastids and mitochondria. We call them plant organellar DNA polymerases (POPs). However, POPs have never been purified in the native form from plant tissues. The unicellular thermotrophic red alga Cyanidioschyzon merolae contains two genes encoding proteins related to Escherichia coli DNA polymerase I (PolA and PolB). Phylogenetic analysis revealed that PolB is an ortholog of POPs. Nonphotosynthetic eukaryotes also have POPs, which suggested that POPs have an ancient origin before eukaryotic photosynthesis. PolA is a homolog of bacterial DNA polymerase I and is distinct from POPs. PolB was purified from the C. merolae cells by a series of column chromatography steps. Recombinant protein of PolA was also purified. Sensitivity to inhibitors of DNA synthesis was different in PolA, PolB, and E. coli DNA polymerase I. Immunoblot analysis and targeting studies with green fluorescent protein fusion proteins demonstrated that PolA was localized in the plastids, whereas PolB was present in both plastids and mitochondria. The expression of PolB was regulated by the cell cycle. The available results suggest that PolB is involved in the replication of plastids and mitochondria.}, }
@article {pmid18428014, year = {2008}, author = {González, AM and Karadsheh, N and Maca-Meyer, N and Flores, C and Cabrera, VM and Larruga, JM}, title = {Mitochondrial DNA variation in Jordanians and their genetic relationship to other Middle East populations.}, journal = {Annals of human biology}, volume = {35}, number = {2}, pages = {212-231}, doi = {10.1080/03014460801946538}, pmid = {18428014}, issn = {1464-5033}, mesh = {Asian People/*classification/*genetics ; Commonwealth of Independent States ; DNA, Mitochondrial/*analysis/genetics ; Egypt ; Emigration and Immigration ; Europe, Eastern ; Evolution, Molecular ; Founder Effect ; Gene Flow ; Gene Pool ; Genetic Variation ; Haplotypes ; Humans ; Iran ; Jordan ; Mitochondria/genetics ; *Phylogeny ; *Polymorphism, Restriction Fragment Length ; Population Groups/genetics ; Sequence Analysis, DNA ; Sudan ; Syria ; Turkey ; }, abstract = {BACKGROUND: The Levant is a crucial region in understanding human migrations between Africa and Eurasia. Although some mitochondrial DNA (mtDNA) studies have been carried out in this region, they have not included the Jordan area. This paper deals with the mtDNA composition of two Jordan populations.<br><br>AIM: The main objectives of this article are: first, to report mtDNA sequences of an urban and an isolate sample from Jordan and, second, to compare them with each other and with other nearby populations.<br><br>SUBJECTS AND METHODS: The analyses are based on HVSI and HVSII mtDNA sequences and diagnostic RFLPs to unequivocally classify into haplogroups 101 Amman and 44 Dead Sea unrelated individuals from Jordan.<br><br>RESULTS: Statistical analysis revealed that, whereas the sample from Amman did not significantly differ from their Levantine neighbours, the Dead Sea sample clearly behaved as a genetic outlier in the region. Its outstanding Eurasian haplogroup U3 frequency (39%) and its south-Saharan Africa lineages (19%) are the highest in the Middle East. On the contrary, the lack ((preHV)1) or comparatively low frequency (J and T) of Neolithic lineages is also striking. Although strong drift by geographic isolation could explain the anomalous mtDNA pool of the Dead Sea sample, the fact that its mtDNA lineage composition mirrors, in geographic origin and haplogroup frequencies, its Y-chromosome pool, points to founder effect as the main cause. Ancestral M1 lineages detected in Jordan that have affinities with those recently found in Northwest but not East Africa question the African origin of the M1 haplogroup.<br><br>CONCLUSION: Results are in agreement with an old human settlement in the Jordan region. However, in spite of the attested migratory spreads, genetically divergent populations, such as that of the Dead Sea, still exist in the area.}, }
@article {pmid18428000, year = {2008}, author = {Nicaise, C and Coupier, J and Dabadie, MP and De Decker, R and Mangas, A and Bodet, D and Poncelet, L and Geffard, M and Pochet, R}, title = {Gemals, a new drug candidate, extends lifespan and improves electromyographic parameters in a rat model of amyotrophic lateral sclerosis.}, journal = {Amyotrophic lateral sclerosis : official publication of the World Federation of Neurology Research Group on Motor Neuron Diseases}, volume = {9}, number = {2}, pages = {85-90}, doi = {10.1080/17482960701788180}, pmid = {18428000}, issn = {1471-180X}, mesh = {Amyotrophic Lateral Sclerosis/*drug therapy/*physiopathology ; Animals ; Animals, Genetically Modified ; *Disease Models, Animal ; Dose-Response Relationship, Drug ; Drug Combinations ; Electromyography/*drug effects ; Longevity/*drug effects ; Muscle Contraction/*drug effects ; Polylysine/administration &amp; dosage/*analogs &amp; derivatives ; Rats/genetics ; Rats, Sprague-Dawley ; Treatment Outcome ; Weight Loss/*drug effects ; }, abstract = {Amyotrophic lateral sclerosis (ALS) is a fatal disease involving selective and progressive degeneration and death of motor neurons. ALS is a multifactorial disease in which oxidative stress, glutamate excitotoxicity, intracellular aggregates, neurofilamentous disorganization, zinc excitotoxicity, mitochondrial damage, neuroinflammation, abnormalities in growth factors and apoptosis play a role. Any therapeutic approach to delay or stop the evolution of ALS should therefore ideally target these multiple pathways leading to motor neuron death. We have developed a combination therapy (Gemals) composed of functional polypeptides (fatty acids, free radical scavengers and amino acids linked to poly-L-lysine), chosen according to their known potentiality for regeneration or protection of neuronal components such as myelin, axon transport and mitochondria. We found that Gemals significantly extended lifespan and improved electromyographic parameters in a SOD1(G93A) rat model. The use of two drug concentrations indicated a possible dose dependence. These initial findings open the way to further investigation necessary to validate this new drug as a candidate for ALS treatment.}, }
@article {pmid18426587, year = {2008}, author = {Mezentseva, NV and Kumaratilake, JS and Newman, SA}, title = {The brown adipocyte differentiation pathway in birds: an evolutionary road not taken.}, journal = {BMC biology}, volume = {6}, number = {}, pages = {17}, pmid = {18426587}, issn = {1741-7007}, mesh = {Adipocytes, Brown/*cytology ; Animals ; *Biological Evolution ; Birds/*anatomy &amp; histology/embryology/genetics ; Cell Differentiation/*genetics ; Cells, Cultured ; Chick Embryo ; Mice ; }, abstract = {BACKGROUND: Thermogenic brown adipose tissue has never been described in birds or other non-mammalian vertebrates. Brown adipocytes in mammals are distinguished from the more common white fat adipocytes by having numerous small lipid droplets rather than a single large one, elevated numbers of mitochondria, and mitochondrial expression of the nuclear gene UCP1, the uncoupler of oxidative phosphorylation responsible for non-shivering thermogenesis.<br><br>RESULTS: We have identified in vitro inductive conditions in which mesenchymal cells isolated from the embryonic chicken limb bud differentiate into avian brown adipocyte-like cells (ABALCs) with the morphological and many of the biochemical properties of terminally differentiated brown adipocytes. Avian, and as we show here, lizard species lack the gene for UCP1, although it is present in amphibian and fish species. While ABALCs are therefore not functional brown adipocytes, they are generated by a developmental pathway virtually identical to brown fat differentiation in mammals: both the common adipogenic transcription factor peroxisome proliferator-activated receptor-gamma (PPARgamma), and a coactivator of that factor specific to brown fat differentiation in mammals, PGC1alpha, are elevated in expression, as are mitochondrial volume and DNA. Furthermore, ABALCs induction resulted in strong transcription from a transfected mouse UCP1 promoter.<br><br>CONCLUSION: These findings strongly suggest that the brown fat differentiation pathway evolved in a common ancestor of birds and mammals and its thermogenicity was lost in the avian lineage, with the degradation of UCP1, after it separated from the mammalian lineage. Since this event occurred no later than the saurian ancestor of birds and lizards, an implication of this is that dinosaurs had neither UCP1 nor canonically thermogenic brown fat.}, }
@article {pmid18425793, year = {2008}, author = {Wong, WW and Puthalakath, H}, title = {Bcl-2 family proteins: the sentinels of the mitochondrial apoptosis pathway.}, journal = {IUBMB life}, volume = {60}, number = {6}, pages = {390-397}, doi = {10.1002/iub.51}, pmid = {18425793}, issn = {1521-6551}, mesh = {Animals ; *Apoptosis ; Autoimmune Diseases/metabolism/therapy ; Cell Transformation, Neoplastic ; *Gene Expression Regulation ; Humans ; Mitochondria/*metabolism ; Models, Biological ; Neoplasms/metabolism/therapy ; Protein Structure, Tertiary ; Proto-Oncogene Proteins c-bcl-2/*metabolism ; bcl-2 Homologous Antagonist-Killer Protein/metabolism ; bcl-2-Associated X Protein/metabolism ; }, abstract = {Bcl-2 family members are the arbiters of mitochondrial apoptotic pathway, which is conserved through evolution. The stoichiometry of pro- versus antiapoptotic Bcl-2 family members in the cell determines whether the cell lives or dies. This fine balance is regulated at the transcriptional or posttranslational level in response to various cellular cues. These signals are transmitted through the upstream molecules in the pathway, that is, the BH3-only molecules that results in the activation of the adaptor molecules, Bax and Bak, at the mitochondrial surface ensuing mitochondrial dysfunction and apoptosis. Understanding the activation process offers a great potential in the therapeutic intervention of many diseases such as cancer and autoimmune disorders.}, }
@article {pmid18423802, year = {2008}, author = {Ting, N}, title = {Mitochondrial relationships and divergence dates of the African colobines: evidence of Miocene origins for the living colobus monkeys.}, journal = {Journal of human evolution}, volume = {55}, number = {2}, pages = {312-325}, doi = {10.1016/j.jhevol.2008.02.011}, pmid = {18423802}, issn = {0047-2484}, mesh = {Africa ; Animals ; Colobus/classification/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Fossils ; Humans ; Mitochondria/*genetics ; Molecular Sequence Data ; Paleontology ; Phylogeny ; }, abstract = {The African colobines represent a neglected area of cercopithecid systematics. Resolving the phylogenetic relationships and estimating divergence dates among the living forms will provide insight into the evolution of this group and may shed light upon the evolution of other African primates as well. This is the first molecular assessment of the evolutionary relationships among the modern colobus monkeys, which are comprised of the black-and-white, olive, and red colobus groups. Over 4,000 base pairs of mitochondrial DNA were amplified and sequenced in over 40 colobus monkey individuals incorporating representatives from all commonly recognized species. Gene trees were inferred using maximum likelihood and Bayesian inference, and penalized likelihood was employed to estimate mitochondrial divergence dates among the sampled taxa. The results are congruent with some aspects of previous phylogenetic hypotheses based on morphology and vocalizations, although the relationships among several West and Central African taxa differ to some degree. The divergence date analysis suggests that the black-and-white, olive, and red colobus had diverged from one another by the end of the Miocene, and that by the Plio-Pleistocene many of the species lineages were already present. This demonstrates that the initial extant colobus monkey diversification occurred much earlier than previously thought and was likely part of the same adaptive radiation that produced the diverse colobine taxa seen in the African Plio-Pleistocene fossil record. The lack of early members from the modern lineages in fossiliferous deposits suggests that they resided in part in the forests of Central and West Africa, which also currently harbor the highest levels of colobus monkey diversity. These forests should not be ignored in models of Plio-Pleistocene human and nonhuman primate evolution.}, }
@article {pmid18387202, year = {2008}, author = {Picardi, E and Quagliariello, C}, title = {Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets.}, journal = {BMC bioinformatics}, volume = {9 Suppl 2}, number = {Suppl 2}, pages = {S14}, pmid = {18387202}, issn = {1471-2105}, mesh = {Base Sequence ; Computer Simulation ; Databases, Genetic ; *Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Single Nucleotide/*genetics ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Plant/*genetics ; Sequence Analysis, RNA/*methods ; }, abstract = {BACKGROUND: In plant mitochondria, the post-transcriptional RNA editing process converts C to U at a number of specific sites of the mRNA sequence and usually restores phylogenetically conserved codons and the encoded amino acid residues. Sites undergoing RNA editing evolve at a higher rate than sites not modified by the process. As a result, editing sites strongly affect the evolution of plant mitochondrial genomes, representing an important source of sequence variability and potentially informative characters. To date no clear and convincing evidence has established whether or not editing sites really affect the topology of reconstructed phylogenetic trees. For this reason, we investigated here the effect of RNA editing on the tree building process of twenty different plant mitochondrial gene sequences and by means of computer simulations.<br><br>RESULTS: Based on our simulation study we suggest that the editing 'noise' in tree topology inference is mainly manifested at the cDNA level. In particular, editing sites tend to confuse tree topologies when artificial genomic and cDNA sequences are generated shorter than 500 bp and with an editing percentage higher than 5.0%. Similar results have been also obtained with genuine plant mitochondrial genes. In this latter instance, indeed, the topology incongruence increases when the editing percentage goes up from about 3.0 to 14.0%. However, when the average gene length is higher than 1,000 bp (rps3, matR and atp1) no differences in the comparison between inferred genomic and cDNA topologies could be detected.<br><br>CONCLUSIONS: Our findings by the here reported in silico and in vivo computer simulation system seem to strongly suggest that editing sites contribute in the generation of misleading phylogenetic trees if the analyzed mitochondrial gene sequence is highly edited (higher than 3.0%) and reduced in length (shorter than 500 bp). In the current lack of direct experimental evidence the results presented here encourage, thus, the use of genomic mitochondrial rather than cDNA sequences for reconstructing phylogenetic events in land plants.}, }
@article {pmid18413600, year = {2008}, author = {Paukstelis, PJ and Lambowitz, AM}, title = {Identification and evolution of fungal mitochondrial tyrosyl-tRNA synthetases with group I intron splicing activity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {16}, pages = {6010-6015}, pmid = {18413600}, issn = {1091-6490}, support = {R01 GM037951/GM/NIGMS NIH HHS/United States ; R37 GM037951/GM/NIGMS NIH HHS/United States ; GM037951/GM/NIGMS NIH HHS/United States ; }, mesh = {*Alternative Splicing ; Amino Acid Sequence ; Antifungal Agents/chemistry/pharmacology ; Aspergillus nidulans/enzymology/genetics ; Coccidioides/enzymology/genetics ; Conserved Sequence ; *Evolution, Molecular ; Fungal Proteins/chemistry/genetics/*metabolism ; Histoplasma/enzymology/genetics ; Introns/*genetics ; Mitochondria/enzymology ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Mutagenesis, Insertional ; Neurospora crassa/enzymology/genetics ; Protein Conformation ; RNA, Fungal/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, Protein ; Tyrosine/metabolism ; Tyrosine-tRNA Ligase/chemistry/genetics/*metabolism ; }, abstract = {The bifunctional Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) both aminoacylates mitochondrial tRNA(Tyr) and acts as a structure-stabilizing splicing cofactor for group I introns. Previous studies showed that CYT-18 has distinct tRNA(Tyr) and group I intron-binding sites, with the latter formed by three small "insertions" in the nucleotide-binding fold and other structural adaptations compared with nonsplicing bacterial tyrosyl-tRNA synthetases. Here, analysis of genomic sequences shows that mitochondrial tyrosyl-tRNA synthetases with structural adaptations similar to CYT-18's are uniquely characteristic of fungi belonging to the subphylum Pezizomycotina, and biochemical assays confirm group I intron splicing activity for the enzymes from several of these organisms, including Aspergillus nidulans and the human pathogens Coccidioides posadasii and Histoplasma capsulatum. By combining multiple sequence alignments with a previously determined cocrystal structure of a CYT-18/group I intron RNA complex, we identify conserved features of the Pezizomycotina enzymes related to group I intron and tRNA interactions. Our results suggest that mitochondrial tyrosyl-tRNA synthetases with group I intron splicing activity evolved during or after the divergence of the fungal subphyla Pezizomycotina and Saccharomycotina by a mechanism involving the concerted differentiation of preexisting protein loop regions. The unique group I intron splicing activity of these fungal enzymes may provide a new target for antifungal drugs.}, }
@article {pmid18413355, year = {2008}, author = {Heidel, AJ and Glöckner, G}, title = {Mitochondrial genome evolution in the social amoebae.}, journal = {Molecular biology and evolution}, volume = {25}, number = {7}, pages = {1440-1450}, doi = {10.1093/molbev/msn088}, pmid = {18413355}, issn = {1537-1719}, mesh = {Amino Acid Sequence ; Animals ; DNA, Mitochondrial/*genetics ; Eukaryota/classification/*genetics/*physiology ; *Evolution, Molecular ; Genetic Code ; *Genome, Mitochondrial ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Most mitochondria contain a core set of genes required for mitochondrial function, but beyond this base there are variable genomic features. The mitochondrial genome of the model species Dictyostelium discoideum demonstrated that the social amoebae mitochondrial genomes have a size between those of metazoans and plants, but no comparative study of social amoebae mitochondria has been performed. Here, we present a comparative analysis of social amoebae mitochondrial genomes using D. discoideum, Dictyostelium citrinum, Dictyostelium fasciculatum, and Polysphondylium pallidum. The social amoebae mitochondria have similar sizes, AT content, gene content and have a high level of synteny except for one segmental rearrangement and extensive displacement of tRNAs. From the species that contain the rearrangement, it can be concluded that the event occurred late in the evolution of social amoebae. A phylogeny using 36 mitochondrial genes produced a well-supported tree suggesting that the pairs of D. discoideum/D. citrinum and D. fasciculatum/P. pallidum are sister species although the position of the root is not certain. Group I introns and endonucleases are variable in number and location in the social amoebae. Phylogenies of the introns and endonucleases suggest that there have been multiple recent duplications or extinctions and confirm that endonucleases have the ability to insert into new areas. An analysis of dN/dS ratios in mitochondrial genes revealed that among groups of genes, adenosine triphosphate synthase complex genes have the highest ratio, whereas cytochrome oxidase and nicotinamide adenine dinucleotide (NADH) dehydrogenase genes had the lowest ratio. The genetic codes of D. citrinum, P. pallidum, and D. fasciculatum are the universal code although D. fasciculatum does not use the TGA stop codon. In D. fasciculatum, we demonstrate for the first time that a mitochondrial genome without the TGA stop codon still uses the release factor RF2 that recognizes TGA. Theories of how the genetic code can change and why RF2 may be a constraint against switching codes are discussed.}, }
@article {pmid18406119, year = {2008}, author = {Sethuraman, J and Okoli, CV and Majer, A and Corkery, TL and Hausner, G}, title = {The sporadic occurrence of a group I intron-like element in the mtDNA rnl gene of Ophiostoma novo-ulmi subsp. americana.}, journal = {Mycological research}, volume = {112}, number = {Pt 5}, pages = {564-582}, doi = {10.1016/j.mycres.2007.11.017}, pmid = {18406119}, issn = {0953-7562}, mesh = {Amino Acid Sequence ; Ascomycota/chemistry/classification/*genetics/isolation &amp; purification ; Base Pairing ; DNA, Fungal/chemistry/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Fungal Proteins/chemistry/genetics ; *Introns ; Mitochondria/chemistry/genetics ; Molecular Sequence Data ; Mutagenesis, Insertional ; Open Reading Frames ; Phylogeny ; Plant Diseases/microbiology ; Sequence Alignment ; Ulmus/microbiology ; }, abstract = {The presence of group I intron-like elements within the U7 region of the mtDNA large ribosomal subunit RNA gene (rnl) was investigated in strains of Ophiostoma novo-ulmi subsp. americana from Canada, Europe and Eurasia, and in selected strains of O. ips, O. minus, O. piceae, O. ulmi, and O. himal-ulmi. This insertion is of interest as it has been linked previously to the generation of plasmid-like mtDNA elements in diseased strains of O. novo-ulmi. Among 197 O. novo-ulmi subsp. americana strains tested, 61 contained a 1.6kb insertion within the rnl-U7 region and DNA sequence analysis suggests the presence of a group I intron (IA1 type) that encodes a potential double motif LAGLIDADG homing endonuclease-like gene (HEG). Phylogenetic analysis of rnl-U7 intron encoded HEG-like elements supports the view that double motif HEGs originated from a duplication event of a single-motif HEG followed by a fusion event that combined the two copies into one open reading frame (ORF). The data also show that rnl-U7 intron encoded ORFs belong to a clade that includes ORFs inserted into different types of group I introns, e.g. IB, ID, IC3, IA1, present within a variety of different mtDNA genes, such as the small ribosomal subunit RNA gene (rns), apo-cytochrome b gene (cob), NADH dehydrogenase subunit 5 (nad5), cytochrome oxidase subunit 1 gene (coxI), and ATPase subunit 9 gene (atp9). We also compared the occurrence of the rnl-U7 intron in our collection of 227 strains with the presence of the rnl-U11 group I intron and concluded that the U7 intron appears to be an optional element and the U11 intron is probably essential among the strains tested.}, }
@article {pmid18403202, year = {2008}, author = {Stechmann, A and Hamblin, K and Pérez-Brocal, V and Gaston, D and Richmond, GS and van der Giezen, M and Clark, CG and Roger, AJ}, title = {Organelles in Blastocystis that blur the distinction between mitochondria and hydrogenosomes.}, journal = {Current biology : CB}, volume = {18}, number = {8}, pages = {580-585}, pmid = {18403202}, issn = {0960-9822}, support = {/WT_/Wellcome Trust/United Kingdom ; 078566/WT_/Wellcome Trust/United Kingdom ; 078566/A/05/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Aerobiosis/physiology ; Anaerobiosis/physiology ; Animals ; Biological Evolution ; Blastocystis/genetics/*metabolism ; Energy Metabolism/physiology ; Expressed Sequence Tags ; Genome, Mitochondrial ; Mitochondria/genetics/*metabolism ; Molecular Sequence Data ; }, abstract = {Blastocystis is a unicellular stramenopile of controversial pathogenicity in humans. Although it is a strict anaerobe, Blastocystis has mitochondrion-like organelles with cristae, a transmembrane potential and DNA. An apparent lack of several typical mitochondrial pathways has led some to suggest that these organelles might be hydrogenosomes, anaerobic organelles related to mitochondria. We generated 12,767 expressed sequence tags (ESTs) from Blastocystis and identified 115 clusters that encode putative mitochondrial and hydrogenosomal proteins. Among these is the canonical hydrogenosomal protein iron-only [FeFe] hydrogenase that we show localizes to the organelles. The organelles also have mitochondrial characteristics, including pathways for amino acid metabolism, iron-sulfur cluster biogenesis, and an incomplete tricarboxylic acid cycle as well as a mitochondrial genome. Although complexes I and II of the electron transport chain (ETC) are present, we found no evidence for complexes III and IV or F1Fo ATPases. The Blastocystis organelles have metabolic properties of aerobic and anaerobic mitochondria and of hydrogenosomes. They are convergently similar to organelles recently described in the unrelated ciliate Nyctotherus ovalis. These findings blur the boundaries between mitochondria, hydrogenosomes, and mitosomes, as currently defined, underscoring the disparate selective forces that shape these organelles in eukaryotes.}, }
@article {pmid18402996, year = {2008}, author = {Tubaro, A and Giangaspero, A and Ardizzone, M and Soranzo, MR and Vita, F and Yasumoto, T and Maucher, JM and Ramsdell, JS and Sosa, S}, title = {Ultrastructural damage to heart tissue from repeated oral exposure to yessotoxin resolves in 3 months.}, journal = {Toxicon : official journal of the International Society on Toxinology}, volume = {51}, number = {7}, pages = {1225-1235}, doi = {10.1016/j.toxicon.2008.02.011}, pmid = {18402996}, issn = {0041-0101}, mesh = {Administration, Oral ; Animals ; Body Weight/drug effects ; Dinoflagellida/*chemistry ; Eating/drug effects ; Female ; Heart/*drug effects ; Mice ; Mice, Inbred Strains ; Mitochondria, Heart/drug effects/ultrastructure ; Mollusk Venoms ; Myocardium/pathology ; Myocytes, Cardiac/*drug effects/ultrastructure ; Myofibrils/drug effects/ultrastructure ; Oxocins/blood/*toxicity ; Recovery of Function ; Toxicity Tests ; Withholding Treatment ; }, abstract = {Yessotoxin (YTX), an algal toxin contaminating edible shellfish, was previously shown to induce ultrastructural changes in some cardiac muscle cells of mice after acute (1 and 2mg/kg) or daily repeated oral exposure (1 and 2mg/kg/day, for 7 days). Therefore, the temporal evolution of the ultrastructural myocardial alterations and the development of other signs of toxicity induced by a repeated daily oral administration of YTX (1mg/kg/day, for 7 days) to mice were evaluated within 3 months after the treatment. Symptoms, food consumption, body weight, gross pathology and histopathology of the main organs and tissues were observed, and plasma levels of transaminases, lactate dehydrogenase, creatinine and creatinine phosphokinase were measured. Heart, liver, kidneys and cerebellum were also analysed by transmission electron microscopy. In addition, the blood concentration of YTX was determined by a direct enzyme linked immunosorbent assay (ELISA) 24h after the last toxin administration. No mortality or other treatment-related changes, including histological or hematoclinical parameters, were recorded in mice administered with YTX. Similarly, electron microscopy did not reveal any ultrastructural alteration in the liver, kidneys, and cerebellum associated with YTX treatment. In contrast, changes in cardiac muscle cells near to the capillaries (clusters of rounded mitochondria and disorganization of myofibrils) were observed 24h after the treatment. These changes were also noted 30 days after the toxin administration, while after 90 days no differences in cardiac muscle cells between control and YTX-treated mice were observed, which indicated a recovery of the ultrastructural alterations induced by the toxin.}, }
@article {pmid18396149, year = {2008}, author = {Klingenspor, M and Fromme, T and Hughes, DA and Manzke, L and Polymeropoulos, E and Riemann, T and Trzcionka, M and Hirschberg, V and Jastroch, M}, title = {An ancient look at UCP1.}, journal = {Biochimica et biophysica acta}, volume = {1777}, number = {7-8}, pages = {637-641}, doi = {10.1016/j.bbabio.2008.03.006}, pmid = {18396149}, issn = {0006-3002}, mesh = {Adipose Tissue, Brown/metabolism ; Amino Acid Sequence ; Animals ; Body Temperature Regulation ; Evolution, Molecular ; Female ; Ion Channels/*chemistry/genetics/*metabolism ; Lipolysis ; Mammals ; Mitochondria/*metabolism ; Mitochondrial Proteins/*chemistry/genetics/*metabolism ; Molecular Conformation ; Molecular Sequence Data ; Placenta/metabolism ; Pregnancy ; Thermogenesis ; Uncoupling Protein 1 ; Vertebrates ; }, abstract = {Brown adipose tissue serves as a thermogenic organ in placental mammals to defend body temperature in the cold by nonshivering thermogenesis. The thermogenic function of brown adipose tissue is enabled by several specialised features on the organ as well as on the cellular level, including dense sympathetic innervation and vascularisation, high lipolytic capacity and mitochondrial density and the unique expression of uncoupling protein 1 (UCP1). This mitochondrial carrier protein is inserted into the inner mitochondrial membrane and stimulates maximum mitochondrial respiration by dissipating proton-motive force as heat. Studies in knockout mice have clearly demonstrated that UCP1 is essential for nonshivering thermogenesis in brown adipose tissue. For a long time it had been presumed that brown adipose tissue and UCP1 emerged in placental mammals providing them with a unique advantage to survive in the cold. Our subsequent discoveries of UCP1 orthologues in ectotherm vertebrates and marsupials clearly refute this presumption. We can now initiate comparative studies on the structure-function relationships in UCP1 orthologues from different vertebrates to elucidate when during vertebrate evolution UCP1 gained the biochemical properties required for nonshivering thermogenesis.}, }
@article {pmid18393999, year = {2008}, author = {Allen, JW and Jackson, AP and Rigden, DJ and Willis, AC and Ferguson, SJ and Ginger, ML}, title = {Order within a mosaic distribution of mitochondrial c-type cytochrome biogenesis systems?.}, journal = {The FEBS journal}, volume = {275}, number = {10}, pages = {2385-2402}, doi = {10.1111/j.1742-4658.2008.06380.x}, pmid = {18393999}, issn = {1742-464X}, support = {BB/C508118/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/genetics/metabolism ; Computational Biology ; Cysteine/chemistry/metabolism ; Cytochromes c/*biosynthesis/chemistry/genetics ; Cytochromes c1/*biosynthesis/chemistry/genetics ; Eukaryotic Cells/classification/physiology ; Evolution, Molecular ; Heme/chemistry/metabolism ; Lyases/genetics/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Molecular Structure ; Phylogeny ; Plant Proteins/genetics/metabolism ; }, abstract = {Mitochondrial cytochromes c and c(1) are present in all eukaryotes that use oxygen as the terminal electron acceptor in the respiratory chain. Maturation of c-type cytochromes requires covalent attachment of the heme cofactor to the protein, and there are at least five distinct biogenesis systems that catalyze this post-translational modification in different organisms and organelles. In this study, we use biochemical data, comparative genomic and structural bioinformatics investigations to provide a holistic view of mitochondrial c-type cytochrome biogenesis and its evolution. There are three pathways for mitochondrial c-type cytochrome maturation, only one of which is present in prokaryotes. We analyze the evolutionary distribution of these biogenesis systems, which include the Ccm system (System I) and the enzyme heme lyase (System III). We conclude that heme lyase evolved once and, in many lineages, replaced the multicomponent Ccm system (present in the proto-mitochondrial endosymbiont), probably as a consequence of lateral gene transfer. We find no evidence of a System III precursor in prokaryotes, and argue that System III is incompatible with multi-heme cytochromes common to bacteria, but absent from eukaryotes. The evolution of the eukaryotic-specific protein heme lyase is strikingly unusual, given that this protein provides a function (thioether bond formation) that is also ubiquitous in prokaryotes. The absence of any known c-type cytochrome biogenesis system from the sequenced genomes of various trypanosome species indicates the presence of a third distinct mitochondrial pathway. Interestingly, this system attaches heme to mitochondrial cytochromes c that contain only one cysteine residue, rather than the usual two, within the heme-binding motif. The isolation of single-cysteine-containing mitochondrial cytochromes c from free-living kinetoplastids, Euglena and the marine flagellate Diplonema papillatum suggests that this unique form of heme attachment is restricted to, but conserved throughout, the protist phylum Euglenozoa.}, }
@article {pmid18392584, year = {2008}, author = {Simonet, BM and Ríos, A and Valcárcel, M}, title = {Capillary electrophoresis separation of microorganisms.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {384}, number = {}, pages = {569-590}, doi = {10.1007/978-1-59745-376-9_22}, pmid = {18392584}, issn = {1064-3745}, mesh = {Bacteria/*isolation &amp; purification ; Buffers ; Electrophoresis, Capillary/*methods ; Isoelectric Focusing ; Molecular Weight ; Polymers ; }, abstract = {Microorganisms can be considered a bio-colloid. That is, they have a characteristic outer surface that carries, or can carry, a charge. Precisely, differences in the surface can be exploited for separation by capillary electrophoresis (CE). In fact, methods based on CE seem to be very promising because they should produce rapid and high-efficiency separations. Although CE can be used to separate microbial (i.e., bacteria, virus, fungi, and whole cells) and subcellular particles (i.e., mitochondria and nuclei), this chapter is focused mainly on the determination of bacteria and virus for their interest. At difference to the separation off molecules, microorganisms are characterized as living. This makes their analysis more difficult because several aspects such as possible lysis, aggregation, evolution, growing etc. must be taken into count.}, }
@article {pmid18390807, year = {2008}, author = {Jasinski, M and Sudre, D and Schansker, G and Schellenberg, M and Constant, S and Martinoia, E and Bovet, L}, title = {AtOSA1, a member of the Abc1-like family, as a new factor in cadmium and oxidative stress response.}, journal = {Plant physiology}, volume = {147}, number = {2}, pages = {719-731}, pmid = {18390807}, issn = {0032-0889}, mesh = {Arabidopsis/enzymology/genetics/*physiology ; Arabidopsis Proteins/classification/genetics/metabolism/*physiology ; Base Sequence ; Cadmium/*pharmacology ; Chloroplasts/metabolism ; DNA Primers ; DNA, Bacterial ; *Oxidative Stress ; Phylogeny ; Polymerase Chain Reaction ; Superoxide Dismutase/genetics/metabolism ; }, abstract = {The analysis of gene expression in Arabidopsis (Arabidopsis thaliana) using cDNA microarrays and reverse transcription-polymerase chain reaction showed that AtOSA1 (A. thaliana oxidative stress-related Abc1-like protein) transcript levels are influenced by Cd2+ treatment. The comparison of protein sequences revealed that AtOSA1 belongs to the family of Abc1 proteins. Up to now, Abc1-like proteins have been identified in prokaryotes and in the mitochondria of eukaryotes. AtOSA1 is the first member of this family to be localized in the chloroplasts. However, despite sharing homology to the mitochondrial ABC1 of Saccharomyces cerevisiae, AtOSA1 was not able to complement yeast strains deleted in the endogenous ABC1 gene, thereby suggesting different function between AtOSA1 and the yeast ABC1. The atosa1-1 and atosa1-2 T-DNA insertion mutants were more affected than wild-type plants by Cd2+ and revealed an increased sensitivity toward oxidative stress (hydrogen peroxide) and high light. The mutants exhibited higher superoxide dismutase activities and differences in the expression of genes involved in the antioxidant pathway. In addition to the conserved Abc1 region in the AtOSA1 protein sequence, putative kinase domains were found. Protein kinase assays in gelo using myelin basic protein as a kinase substrate revealed that chloroplast envelope membrane fractions from the AtOSA1 mutant lacked a 70-kD phosphorylated protein compared to the wild type. Our data suggest that the chloroplast AtOSA1 protein is a new factor playing a role in the balance of oxidative stress.}, }
@article {pmid18389624, year = {2008}, author = {Tarasenko, VI and Katyshev, AI and Kobzev, VF and Konstantinov, IuM}, title = {[Comparative analysis of mitochondrial and nuclear DNA topoisomerase I from maize].}, journal = {Molekuliarnaia biologiia}, volume = {42}, number = {1}, pages = {88-95}, pmid = {18389624}, issn = {0026-8984}, mesh = {Cell Nucleus/chemistry/*enzymology/genetics ; Cloning, Molecular ; DNA Topoisomerases, Type I/chemistry/genetics/*metabolism ; DNA, Complementary/genetics ; DNA, Single-Stranded/chemistry/metabolism ; Evolution, Molecular ; Genome, Mitochondrial/physiology ; Magnesium/chemistry/metabolism ; Mitochondria/chemistry/*enzymology/genetics ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Nuclear Proteins/chemistry/genetics/*metabolism ; Plant Proteins/chemistry/genetics/*metabolism ; Zea mays/*enzymology/genetics ; }, abstract = {We conducted a comparative study of the properties of topoisomerase I isolated from maize nuclei and mitochondria. We found that nuclear and mitochondrial enzymes possess different ability to bind single stranded DNA. Study of the enzyme activity dependence on Mg2+ demonstrated an absolute dependence of the mitochondrial topoisomerase activity. Contrary, nuclear enzyme activity was not absolutely dependent but stimulated by the magnesium cation. Mitochondrial topoisomerase formed covalent bond with the 5'-end of the cleaved DNA what is unique property of prokaryotic topoisomerase I. Nuclear enzyme bound covalently to the 3'-end like all eukaryotic topoisomerases I. The search through databases revealed genes which could encode mitochondrial topoisomerase I in the genomes of higher plants. Using both cDNA sequencing and in silico methods we demonstrated an existence of the ortholog gene in the maize genome. This gene shares significant homology with prokaryotic topoisomerase I genes that may explain differences in the properties of the mitochondrial and nuclear enzyme. Data obtained is of a significant interest both from the point of view of plant organelle evolution and mitochondrial genome expression mechanisms study.}, }
@article {pmid18385219, year = {2008}, author = {Soria-Hernanz, DF and Braverman, JM and Hamilton, MB}, title = {Parallel rate heterogeneity in chloroplast and mitochondrial genomes of Brazil nut trees (Lecythidaceae) is consistent with lineage effects.}, journal = {Molecular biology and evolution}, volume = {25}, number = {7}, pages = {1282-1296}, doi = {10.1093/molbev/msn074}, pmid = {18385219}, issn = {1537-1719}, mesh = {Base Sequence ; Bertholletia/*genetics ; Chloroplasts/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; *Evolution, Molecular ; Genome, Plant ; Likelihood Functions ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {We investigated whether relative rates of divergence were correlated between the mitochondrial and chloroplast genomes as expected under lineage effects or were genome specific as expected with locus-specific effects. Five mitochondrial noncoding regions (nad1B_C, nad4exon1_2, nad7exon2_3, nad7exon3_4, and rps14-cob) for 21 samples from Lecythidaceae were sequenced. Three chloroplast regions (rpl20-5'rps12, trnS-trnG, and psbA-trnH) were sequenced to expand the taxa in an existing data set. Absolute rates of nucleotide and insertion and deletion (indel) changes were 13 times faster in the chloroplast genome than in the mitochondrial genome. Similar indel length frequency distributions for both organelles suggested that common mechanisms were responsible for generating indels. Molecular clock tests applied to phylogenetic trees estimated from mitochondrial and chloroplast sequences revealed global rate heterogeneity of nucleotide substitution. Maximum likelihood and Tajima's 1D relative rate tests show that Lecythis zabucajo exhibited a rate acceleration for both the mitochondrial and chloroplast sequences. Whereas Eschweilera romeu-cardosoi showed a significant rate slowdown for chloroplast sequences, the mitochondrial sequences for 3 Eschweilera taxa showed evidence for a rate slowdown only when compared with L. zabucajo. Significant rate heterogeneity was also observed for indel changes in the mitochondrial genome but not for the chloroplast. The lack of mitochondrial nucleotide changes for some taxa as well as chloroplast indel homoplasy may have limited the power of relative rate tests to detect rate variation. Relative ratio tests consistently indicated rate proportionality among branch lengths between the mitochondrial and chloroplast phylogenetic trees. The relative ratio tests showed that taxa possessing rate heterogeneity had parallel relative divergence rates in both mitochondrial and chloroplast sequences as expected under lineage effects. A neutral replication-dependent model of rate heterogeneity for both nucleotide and indel changes provides a simple explanation for common patterns of rate heterogeneity across the 2 organelle genomes in Lecythidaceae. The lineage effects observed here were uncoupled from annual/perennial habit because all the species from this study are perennial.}, }
@article {pmid18380897, year = {2008}, author = {Mulkidjanian, AY and Galperin, MY and Makarova, KS and Wolf, YI and Koonin, EV}, title = {Evolutionary primacy of sodium bioenergetics.}, journal = {Biology direct}, volume = {3}, number = {}, pages = {13}, pmid = {18380897}, issn = {1745-6150}, support = {Z99 LM999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Adenosine Triphosphatases/chemistry/genetics/*metabolism ; Bacteria/enzymology ; Cation Transport Proteins/chemistry/genetics/*metabolism ; Energy Metabolism/*physiology ; *Evolution, Molecular ; Phylogeny ; Protein Subunits/chemistry/genetics/*metabolism ; Sodium/*metabolism ; Sodium-Potassium-Exchanging ATPase/chemistry/genetics/*metabolism ; Structure-Activity Relationship ; Vacuolar Proton-Translocating ATPases/chemistry/genetics/*metabolism ; }, abstract = {BACKGROUND: The F- and V-type ATPases are rotary molecular machines that couple translocation of protons or sodium ions across the membrane to the synthesis or hydrolysis of ATP. Both the F-type (found in most bacteria and eukaryotic mitochondria and chloroplasts) and V-type (found in archaea, some bacteria, and eukaryotic vacuoles) ATPases can translocate either protons or sodium ions. The prevalent proton-dependent ATPases are generally viewed as the primary form of the enzyme whereas the sodium-translocating ATPases of some prokaryotes are usually construed as an exotic adaptation to survival in extreme environments.<br><br>RESULTS: We combine structural and phylogenetic analyses to clarify the evolutionary relation between the proton- and sodium-translocating ATPases. A comparison of the structures of the membrane-embedded oligomeric proteolipid rings of sodium-dependent F- and V-ATPases reveals nearly identical sets of amino acids involved in sodium binding. We show that the sodium-dependent ATPases are scattered among proton-dependent ATPases in both the F- and the V-branches of the phylogenetic tree.<br><br>CONCLUSION: Barring convergent emergence of the same set of ligands in several lineages, these findings indicate that the use of sodium gradient for ATP synthesis is the ancestral modality of membrane bioenergetics. Thus, a primitive, sodium-impermeable but proton-permeable cell membrane that harboured a set of sodium-transporting enzymes appears to have been the evolutionary predecessor of the more structurally demanding proton-tight membranes. The use of proton as the coupling ion appears to be a later innovation that emerged on several independent occasions.}, }
@article {pmid18380652, year = {2008}, author = {Otranto, D and Stevens, JR and Testini, G and Cantacessi, C and Máca, J}, title = {Molecular characterization and phylogenesis of Steganinae (Diptera, Drosophilidae) inferred by the mitochondrial cytochrome c oxidase subunit 1.}, journal = {Medical and veterinary entomology}, volume = {22}, number = {1}, pages = {37-47}, doi = {10.1111/j.1365-2915.2008.00714.x}, pmid = {18380652}, issn = {0269-283X}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; DNA/chemistry/genetics ; Drosophilidae/*classification/*enzymology ; Electron Transport Complex IV/classification/*genetics ; *Genetic Variation ; Likelihood Functions ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Species Specificity ; }, abstract = {The subfamily Steganinae (Diptera, Drosophilidae) includes flies which display zoophilic feeding behaviour in the larval and/or adult stages, some of which act as vectors of Spirurida eyeworms, which infect both carnivores and humans. To date, the taxonomy and phylogeny of the subfamily Steganinae has been studied only superficially and many aspects of their systematics remain unresolved. Thus, the present study aimed to provide a molecular dataset to facilitate the identification and phylogenetic analysis of Steganinae species based on partial (approximately 700 basepairs) mitochondrial cytochrome c oxidase subunit 1 (cox1) sequences. A total of 134 flies belonging to 13 species and eight genera of Steganinae were subjected to molecular and phylogenetic analyses. The mean nucleotide variation within the Steganinae subfamily was 8.1%, with a variation within genera for which more than one species was examined ranging from 1.6% (in Phortica spp.) to 21.8% (in Amiota spp.). Interspecific pairwise divergence ranged from 1.6% (Phortica variegata vs. Phortica semivirgo) to 24.8% (Cacoxenus indagator vs. Amiota alboguttata) and intraspecific variation ranged from 0% to 1%. Seventy of the 233 amino acids were variable, including 26 parsimony informative sites and 44 singleton sites, with some highly conserved residues identified within the genera Stegana and Amiota. Parsimony and maximum likelihood-based phylogenetic analyses provided strong support for the genus Phortica, phylogenetically distinct from the genus Amiota. Gitona distigma was placed in an unresolved position adjacent to the outgroup taxa, Drosophila yakuba and Drosophila melanogaster. The molecular data reported here represent the first molecular dataset based on cox1 of Steganinae flies and provide a base for further investigations into the evolutionary relationships among this little-studied subfamily.}, }
@article {pmid18380326, year = {2007}, author = {Gaziev, AI and Shaĭkhaev, GO}, title = {[Ionizing radiation can activate the insertion of mitochondrial DNA fragments in the nuclear genome].}, journal = {Radiatsionnaia biologiia, radioecologiia}, volume = {47}, number = {6}, pages = {673-683}, pmid = {18380326}, issn = {0869-8031}, mesh = {Animals ; Cell Nucleus/*genetics ; *DNA Damage ; *DNA Repair ; DNA, Mitochondrial/*genetics ; Humans ; Mitochondria/genetics/*radiation effects ; Radiation, Ionizing ; Recombination, Genetic ; }, abstract = {In analytical review is considered the possibility of the insertion of mitochondrial DNA (mtDNA) fragments into the nuclear genome of cells, exposed ionizing radiation (IR). Many studies show that integration fragment mtDNA in nuclear genome, as well as its fastening as NUMT-pseudogenes, proceed at ancient periods of the evolutions not only, but also at more late periods. The number of the investigations shows that under influence endogenous reactive oxygen species, chemical agent, UV-light and IR mtDNA is damaged with greater frequency, than nucleus DNA. Furthermore, the repair systems in mitochondria are low efficiency. In irradiated by IR cells mtDNA fragments can transition from the mitochondria to the cytoplasm. The binding of mtDNA fragment to a complex with proteins provides them the protection from nuclease destroying. Possibly, at such safe condition they and are carried to nucleus. At inductions of DNA double-strand breaks (under the action of IR and activated their reparation) mtDNA fragments may be inserted to nuclear genome. Such integration of mtDNA to nuclear genome, with shaping NUMT-pseudogenes de novo, may be proceed in irradiated cells in the course of the reparations DNA double-strand breaks by the nonhomologous end-joining pathway. These insertions of mtDNA can cardinally change the structure of nuclear genomes in area of their introduction and render the essential influence upon the realization of genetic information. Available information in literature also allows to suppose that integration mtDNA in nuclear genome can proceed and at raised genomic instability observed in cells at post radiation period. It in equal extent pertains and to malignant cells with raised by instability mitochondrial and nuclear genomes. As the most efficient agent, initiating insertion fragment mtDNA in nuclear genome, is considered ionizing radiation.}, }
@article {pmid18378601, year = {2008}, author = {Ljungdahl, LG}, title = {The cellulase/hemicellulase system of the anaerobic fungus Orpinomyces PC-2 and aspects of its applied use.}, journal = {Annals of the New York Academy of Sciences}, volume = {1125}, number = {}, pages = {308-321}, doi = {10.1196/annals.1419.030}, pmid = {18378601}, issn = {0077-8923}, mesh = {Anaerobiosis ; Cellulase/*metabolism ; Fungal Proteins/metabolism ; Glycoside Hydrolases/*metabolism ; Neocallimastigales/classification/*enzymology ; Phylogeny ; }, abstract = {Anaerobic fungi, first described in 1975 by Orpin, live in close contact with bacteria and other microorganisms in the rumen and caecum of herbivorous animals, where they digest ingested plant food. Seventeen distinct anaerobic fungi belonging to five different genera have been described. They have been found in at least 50 different herbivorous animals. Anaerobic fungi do not possess mitochondria, but instead have hydrogenosomes, which form hydrogen and carbon dioxide from pyruvate and malate during fermentation of carbohydrates. In addition, they are very oxygen- and temperature-sensitive, and their DNA has an unusually high AT content of from 72 to 87 mol%. My initial reason for studying anaerobic fungi was because they solubilize lignocellulose and produce all enzymes needed to efficiently hydrolyze cellulose and hemicelluloses. Although some of these enzymes are found free in the medium, most of them are associated with cellulosomal and polycellulosomal complexes, in which the enzymes are attached through fungal dockerins to scaffolding proteins; this is similar to what has been found for cellulosomes from anaerobic bacteria. Although cellulosomes from anaerobic fungi share many properties with cellulosomes of anaerobic cellulolytic bacteria and have comparable structures, their structures differ in their amino acid sequences. I discuss some features of the cellulosome of the anaerobic fungus Orpinomyces sp. PC-2 and some possible uses of its enzymes in industrial settings.}, }
@article {pmid18369739, year = {2008}, author = {Siddique, M and Gernhard, S and von Koskull-Döring, P and Vierling, E and Scharf, KD}, title = {The plant sHSP superfamily: five new members in Arabidopsis thaliana with unexpected properties.}, journal = {Cell stress &amp; chaperones}, volume = {13}, number = {2}, pages = {183-197}, pmid = {18369739}, issn = {1466-1268}, support = {R01 GM042762/GM/NIGMS NIH HHS/United States ; GM 42762/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics ; Arabidopsis Proteins/*classification/genetics/isolation &amp; purification/physiology ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Genes, Plant ; Genes, Reporter ; Heat-Shock Proteins/*classification/genetics/isolation &amp; purification/physiology ; Hot Temperature ; Mitochondria/metabolism ; Molecular Sequence Data ; *Multigene Family ; Multiprotein Complexes/chemistry ; Open Reading Frames/genetics ; Phylogeny ; Protein Folding ; Protoplasts ; Recombinant Fusion Proteins/biosynthesis ; Sequence Alignment ; Sequence Homology, Amino Acid ; Stress, Physiological/genetics ; Subcellular Fractions/metabolism ; Nicotiana ; }, abstract = {The small heat shock proteins (sHsps), which are ubiquitous stress proteins proposed to act as chaperones, are encoded by an unusually complex gene family in plants. Plant sHsps are classified into different subfamilies according to amino acid sequence similarity and localization to distinct subcellular compartments. In the whole Arabidopsis thaliana genome, 19 genes were annotated to encode sHsps, of which 14 belong to previously defined plant sHsp families. In this paper, we report studies of the five additional sHsp genes in A. thaliana, which can now be shown to represent evolutionarily distinct sHsp subfamilies also found in other plant species. While two of these five sHsps show expression patterns typical of the other 14 genes, three have unusual tissue specific and developmental profiles and do not respond to heat induction. Analysis of intracellular targeting indicates that one sHsp represents a new class of mitochondrion-targeted sHsps, while the others are cytosolic/nuclear, some of which may cooperate with other sHsps in formation of heat stress granules. Three of the five new proteins were purified and tested for chaperone activity in vitro. Altogether, these studies complete our basic understanding of the sHsp chaperone family in plants.}, }
@article {pmid18368053, year = {2008}, author = {Woodson, JD and Chory, J}, title = {Coordination of gene expression between organellar and nuclear genomes.}, journal = {Nature reviews. Genetics}, volume = {9}, number = {5}, pages = {383-395}, pmid = {18368053}, issn = {1471-0064}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Cell Nucleus/*genetics/metabolism ; Chloroplasts/*genetics/metabolism ; Eukaryotic Cells/physiology ; *Evolution, Molecular ; Gene Expression Regulation, Plant/*physiology ; Genome, Chloroplast/*physiology ; Genome, Mitochondrial/*physiology ; Genome, Plant/*physiology ; Plant Proteins/biosynthesis/genetics ; Plants/*genetics/metabolism ; Signal Transduction/physiology ; }, abstract = {Following the acquisition of chloroplasts and mitochondria by eukaryotic cells during endosymbiotic evolution, most of the genes in these organelles were either lost or transferred to the nucleus. Encoding organelle-destined proteins in the nucleus allows for host control of the organelle. In return, organelles send signals to the nucleus to coordinate nuclear and organellar activities. In photosynthetic eukaryotes, additional interactions exist between mitochondria and chloroplasts. Here we review recent advances in elucidating the intracellular signalling pathways that coordinate gene expression between organelles and the nucleus, with a focus on photosynthetic plants.}, }
@article {pmid18366542, year = {2008}, author = {Salakij, C and Salakij, J and Narkkong, NA and Sirinarumitr, T and Pattanarangsan, R}, title = {Hematologic, cytochemical, ultrastructural, and molecular findings of Hepatozoon-infected flat-headed cats (Prionailurus planiceps).}, journal = {Veterinary clinical pathology}, volume = {37}, number = {1}, pages = {31-41}, doi = {10.1111/j.1939-165X.2008.00011.x}, pmid = {18366542}, issn = {0275-6382}, mesh = {Animal Diseases/blood/*parasitology ; Animals ; Blood Cell Count/veterinary ; Blood Chemical Analysis/veterinary ; Blood Platelets/ultrastructure ; Coccidia/genetics/isolation &amp; purification ; Coccidiosis/blood/*veterinary ; Erythrocytes/ultrastructure ; Felidae/*blood ; Female ; Leukocytes/ultrastructure ; Phylogeny ; }, abstract = {BACKGROUND: The flat-headed cat (Prionailurus planiceps) is a small wild cat of Southeast Asia and is considered extremely endangered. Little is known about the hematologic values, blood cell morphology, or hemoparasites of this species in relation to other Felidae.<br><br>OBJECTIVES: The objective of this study was to report basic hematologic values and describe the light microscopic, cytochemical, and ultrastructural characteristics of blood cells in 2 wild-caught flat-headed cats. In addition, molecular analysis was done of a Hepatozoon organism found in the neutrophils of both cats.<br><br>METHODS: Blood samples were collected into EDTA from the cephalic vein. A CBC, manual differential count, manual reticulocyte count, cytochemical stains (Sudan black B [SBB], alpha-naphthyl acetate esterase [ANAE], and beta-glucuronidase), and scanning and transmission electron microscopy were done using standard methods.<br><br>RESULTS: HCT was slightly lower and reticulocyte counts and red cell distribution width were higher than the expected values for other species of cats. Hepatozoon organisms were found in the cytoplasm of neutrophils in both cats, but the number of infected neutrophils was very low (1%-2%). Neutrophils stained strongly positive for SBB, but were negative for ANAE and beta-glucuronidase. Hepatozoon-infected neutrophils were negative for SBB, but focally positive for ANAE and beta-glucuronidase. By transmission electron microscopy, gamonts of Hepatozoon sp were observed in neutrophils, and rarely free in plasma. Infected neutrophils had fewer specific granules and more mitochondria compared with noninfected neutrophils. PCR products of partial 18S rRNA revealed that the isolate of Hepatozoon in the flat-headed cats was closely related to that of the frog Hepatozoon sp.<br><br>CONCLUSIONS: These results add to our understanding of hematologic values and blood cell morphology in Hepatozoon-infected flat-headed cats as well as the molecular analysis of the Hepatozoon organism, and may be useful for the health management and evaluation of hemoparasitic disease in this species.}, }
@article {pmid18356953, year = {2008}, author = {Waters, ER and Nguyen, SL and Eskandar, R and Behan, J and Sanders-Reed, Z}, title = {The recent evolution of a pseudogene: diversity and divergence of a mitochondria-localized small heat shock protein in Arabidopsis thaliana.}, journal = {Genome}, volume = {51}, number = {3}, pages = {177-186}, doi = {10.1139/G07-114}, pmid = {18356953}, issn = {0831-2796}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics ; Arabidopsis Proteins/analysis/*genetics ; Base Sequence ; Chloroplasts/metabolism ; *Evolution, Molecular ; Gene Duplication ; *Genetic Variation ; Heat-Shock Proteins/genetics ; Heat-Shock Proteins, Small/analysis/*genetics ; Mitochondrial Proteins/analysis/*genetics ; Molecular Sequence Data ; Phylogeny ; *Pseudogenes ; }, abstract = {In this study we examined the evolution of the genes for three organelle-localized small heat shock proteins in Arabidopsis thaliana: the chloroplast-localized (CP) protein HSP21 and two mitochondria-localized (MT) proteins, HSP23.5 and HSP23.6. We found that the CP protein and one of the MT proteins, HSP23.6, are evolving under purifying selection to maintain function. In contrast, the gene for HSP23.5, the other MT protein, is highly variable within A. thaliana, and in some accessions or ecotypes this gene may be a pseudogene. HSP23.5 and HSP23.6 are related via a segmental duplication event, and the presence of orthologs of each gene in other species within the Brassicaceae indicates that the duplication generating HSP23.5 and HSP23.6 may have occurred as much as 20 million years ago. This is considerably longer than the 4 million year half-life of gene duplicates (functional genes as well as pseudogenes) reported by some studies. Our results are consistent with the prediction that after gene duplication one gene duplicate can be maintained for some time under relaxed selection while it accumulates random mutations. By capturing a pseudogene in the making our study provides important information on how pseudogenes are formed.}, }
@article {pmid18353689, year = {2008}, author = {Schaefer, H and Renner, SS}, title = {A phylogeny of the oil bee tribe Ctenoplectrini (Hymenoptera: Anthophila) based on mitochondrial and nuclear data: evidence for early Eocene divergence and repeated out-of-Africa dispersal.}, journal = {Molecular phylogenetics and evolution}, volume = {47}, number = {2}, pages = {799-811}, doi = {10.1016/j.ympev.2008.01.030}, pmid = {18353689}, issn = {1055-7903}, mesh = {Africa ; *Animal Migration ; Animals ; Base Sequence ; Bees/enzymology/*genetics ; Cell Nucleus/*genetics ; Cloning, Molecular ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Geography ; Likelihood Functions ; Mitochondria/*genetics ; *Phylogeny ; Pseudogenes ; Time Factors ; }, abstract = {The bee tribe Ctenoplectrini, with two genera, comprises nine species in tropical Africa and ten in Asia and Australia. Most of them collect floral oil, pollen, and nectar from Cucurbitaceae, but three species are thought to be cleptoparasites. The unusual morphology of Ctenoplectrini has made it difficult to infer their closest relatives, in turn preventing an understanding of these bees' geographic and temporal origin. We used two mitochondrial and two nuclear markers (4741 nucleotides) generated for most of the species to test the monophyly of the tribe, its relationships to other Apidae, and its biogeographic history. Ctenoplectrini are strongly supported as monophyletic and closest to the Long-horned bees, Eucerini. The presumably cleptoparasitic species form a clade (Ctenoplectrina) that is sister to the remaining species (Ctenoplectra), confirming the independent evolution of cleptoparasitism in this tribe. Tree topology and molecular dating together suggest that Ctenoplectrini originated in Africa in the Early Eocene and that Ctenoplectra dispersed twice from Africa to Asia, sometime in the Late Eocene, 30-40 my ago, from where one species reached the Australian continent via Indonesia and New Guinea in the mid-Miocene, c. 13 my ago. Dry and cool mid-Miocene climates also coincide with the divergence between Ctenoplectra bequaerti from West Africa and Ctenoplectra terminalis from East and South Africa, perhaps related to fragmentation of the equatorial African rainforest belt.}, }
@article {pmid18326862, year = {2008}, author = {Suga, K and Mark Welch, DB and Tanaka, Y and Sakakura, Y and Hagiwara, A}, title = {Two circular chromosomes of unequal copy number make up the mitochondrial genome of the rotifer Brachionus plicatilis.}, journal = {Molecular biology and evolution}, volume = {25}, number = {6}, pages = {1129-1137}, doi = {10.1093/molbev/msn058}, pmid = {18326862}, issn = {1537-1719}, mesh = {Animals ; Base Sequence ; Chromosome Mapping ; Codon/genetics ; Conserved Sequence ; *Evolution, Molecular ; Gene Order ; Genes, rRNA ; *Genome, Helminth ; *Genome, Mitochondrial ; Phylogeny ; RNA, Transfer/genetics ; *Ring Chromosomes ; Rotifera/classification/*genetics ; Sequence Analysis, DNA ; Untranslated Regions/genetics ; }, abstract = {The monogonont rotifer Brachionus plicatilis is an emerging model system for a diverse array of questions in limnological ecosystem dynamics, the evolution of sexual recombination, cryptic speciation, and the phylogeny of basal metazoans. We sequenced the complete mitochondrial genome of B. plicatilis sensu strictu NH1L and found that it is composed of 2 circular chromosomes, designated mtDNA-I (11,153 bp) and mtDNA-II (12,672 bp). Hybridization to DNA isolated from mitochondria demonstrated that mtDNA-I is present at 4 times the copy number of mtDNA-II. The only nucleotide similarity between the 2 chromosomes is a 4.9-kbp region of 99.5% identity including a transfer RNA (tRNA) gene and an extensive noncoding region that contains putative D-loop and control sequence. The mtDNA-I chromosome encodes 4 proteins (ATP6, COB, NAD1, and NAD2), 13 tRNAs, and the large and small subunit ribosomal RNAs; mtDNA-II encodes 8 proteins (COX1-3, NAD3-6, and NAD4L) and 9 tRNAs. Gene order is not conserved between B. plicatilis and its closest relative with a sequenced mitochondrial genome, the acanthocephalan Leptorhynchoides thecatus, or other sequenced mitochondrial genomes. Polymerase chain reaction assays and Southern hybridization to DNA from 18 strains of Brachionus suggest that the 2-chromosome structure has been stable for millions of years. The novel organization of the B. plicatilis mitochondrial genome into 2 nearly equal chromosomes of 4-fold different copy number may provide insight into the evolution of metazoan mitochondria and the phylogenetics of rotifers and other basal animal phyla.}, }
@article {pmid18326075, year = {2008}, author = {Takenaka, M and Verbitskiy, D and van der Merwe, JA and Zehrmann, A and Brennicke, A}, title = {The process of RNA editing in plant mitochondria.}, journal = {Mitochondrion}, volume = {8}, number = {1}, pages = {35-46}, doi = {10.1016/j.mito.2007.09.004}, pmid = {18326075}, issn = {1567-7249}, mesh = {Brassica/genetics ; Carbon-Nitrogen Ligases/physiology ; Cytidine Deaminase/physiology ; Deamination ; Evolution, Molecular ; *Gene Expression Regulation, Plant ; Genome, Mitochondrial/physiology ; Genome, Plant/physiology ; Mitochondria/*genetics ; Pisum sativum/genetics ; Plants/*genetics ; RNA Editing/*physiology ; RNA Helicases/physiology ; Transaminases/physiology ; Triticum/genetics ; Zea mays/genetics ; }, abstract = {RNA editing changes more than 400 cytidines to uridines in the mRNAs of mitochondria in flowering plants. In other plants such as ferns and mosses, RNA editing reactions changing C to U and U to C are observed at almost equal frequencies. Development of transfection systems with isolated mitochondria and of in vitro systems with extracts from mitochondria has considerably improved our understanding of the recognition of specific editing sites in the last few years. These assays have also yielded information about the biochemical parameters, but the enzymes involved have not yet been identified. Here we summarize our present understanding of the process of RNA editing in flowering plant mitochondria.}, }
@article {pmid18326043, year = {2008}, author = {Saito, T and Nishi, M and Lim, MI and Wu, B and Maeda, T and Hashimoto, H and Takeuchi, T and Roos, DS and Asai, T}, title = {A novel GDP-dependent pyruvate kinase isozyme from Toxoplasma gondii localizes to both the apicoplast and the mitochondrion.}, journal = {The Journal of biological chemistry}, volume = {283}, number = {20}, pages = {14041-14052}, pmid = {18326043}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Guanosine Diphosphate/*chemistry ; Kinetics ; Mitochondria/*metabolism ; Models, Biological ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Phylogeny ; Protein Binding ; Protein Isoforms ; Pyruvate Kinase/*chemistry ; Recombinant Proteins/chemistry ; Sequence Homology, Amino Acid ; Toxoplasma/*metabolism ; }, abstract = {We previously reported a cytosolic pyruvate kinase (EC 2.7.1.40) from Toxoplasma gondii (TgPyKI) that differs from most eukaryotic pyruvate kinases in being regulated by glucose 6-phosphate rather than fructose 1,6-diphosphate. Another putative pyruvate kinase (TgPyKII) was identified from parasite genome, which exhibits 32% amino acid sequence identity to TgPyKI and retains pyruvate kinase signature motifs and amino acids essential for substrate binding and catalysis. Whereas TgPyKI is most closely related to plant/algal enzymes, phylogenetic analysis suggests a proteobacterial origin for TgPyKII. Enzymatic characterization of recombinant TgPyKII shows a high pH optimum at 8.5, and a preference for GDP as a phosphate recipient. Catalytic activity is independent of K+, and no allosteric or regulatory effects were observed in the presence of fructose 1,6-diphosphate, fructose 2,6-diphosphate, glucose 6-phosphate, ribose 5-phosphate, AMP, or ATP. Unlike TgPyKI, native TgPyKII activity was exclusively associated with the membranous fraction of a T. gondii tachyzoite lysate. TgPyKII possesses a long N-terminal extension containing five putative start codons before the conserved region and localizes to both apicoplast and mitochondrion by immunofluorescence assay using native antibody and fluorescent protein fusion to the N-terminal extension. Further deletional and site-directed mutagenesis suggests that a translation product from 1st Met is responsible for the localization to the apicoplast, whereas one from 3rd Met is for the mitochondrion. This is the first study of a potential mitochondrial pyruvate kinase in any system.}, }
@article {pmid18325793, year = {2008}, author = {Nguyen, TT and Na-Nakorn, U and Sukmanomon, S and Ziming, C}, title = {A study on phylogeny and biogeography of mahseer species (Pisces: Cyprinidae) using sequences of three mitochondrial DNA gene regions.}, journal = {Molecular phylogenetics and evolution}, volume = {48}, number = {3}, pages = {1223-1231}, doi = {10.1016/j.ympev.2008.01.006}, pmid = {18325793}, issn = {1095-9513}, mesh = {Animals ; Cyprinidae/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Geography ; Likelihood Functions ; Markov Chains ; Mitochondria/*genetics ; Models, Genetic ; Monte Carlo Method ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, }
@article {pmid18318906, year = {2008}, author = {da Fonseca, RR and Johnson, WE and O'Brien, SJ and Ramos, MJ and Antunes, A}, title = {The adaptive evolution of the mammalian mitochondrial genome.}, journal = {BMC genomics}, volume = {9}, number = {}, pages = {119}, pmid = {18318906}, issn = {1471-2164}, support = {N01CO12400/CA/NCI NIH HHS/United States ; N01-CO-12400/CO/NCI NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; Aerobiosis ; Amino Acid Sequence ; Animals ; Basal Metabolism/genetics ; Cytochromes b/chemistry/genetics/metabolism ; Cytochromes c/chemistry/genetics/metabolism ; *Evolution, Molecular ; Genes, Mitochondrial ; Genome, Mitochondrial/*genetics ; Humans ; Mitochondria/enzymology/*genetics ; Mitochondrial Proton-Translocating ATPases/chemistry/genetics/metabolism ; Models, Molecular ; Mutation ; NADH Dehydrogenase/chemistry/genetics/metabolism ; Oxidative Phosphorylation ; Oxygen/metabolism ; Phylogeny ; Protein Structure, Secondary ; }, abstract = {BACKGROUND: The mitochondria produce up to 95% of a eukaryotic cell's energy through oxidative phosphorylation. The proteins involved in this vital process are under high functional constraints. However, metabolic requirements vary across species, potentially modifying selective pressures. We evaluate the adaptive evolution of 12 protein-coding mitochondrial genes in 41 placental mammalian species by assessing amino acid sequence variation and exploring the functional implications of observed variation in secondary and tertiary protein structures.<br><br>RESULTS: Wide variation in the properties of amino acids were observed at functionally important regions of cytochrome b in species with more-specialized metabolic requirements (such as adaptation to low energy diet or large body size, such as in elephant, dugong, sloth, and pangolin, and adaptation to unusual oxygen requirements, for example diving in cetaceans, flying in bats, and living at high altitudes in alpacas). Signatures of adaptive variation in the NADH dehydrogenase complex were restricted to the loop regions of the transmembrane units which likely function as protons pumps. Evidence of adaptive variation in the cytochrome c oxidase complex was observed mostly at the interface between the mitochondrial and nuclear-encoded subunits, perhaps evidence of co-evolution. The ATP8 subunit, which has an important role in the assembly of F0, exhibited the highest signal of adaptive variation. ATP6, which has an essential role in rotor performance, showed a high adaptive variation in predicted loop areas.<br><br>CONCLUSION: Our study provides insight into the adaptive evolution of the mtDNA genome in mammals and its implications for the molecular mechanism of oxidative phosphorylation. We present a framework for future experimental characterization of the impact of specific mutations in the function, physiology, and interactions of the mtDNA encoded proteins involved in oxidative phosphorylation.}, }
@article {pmid18315572, year = {2008}, author = {McCauley, DE and Olson, MS}, title = {Do recent findings in plant mitochondrial molecular and population genetics have implications for the study of gynodioecy and cytonuclear conflict?.}, journal = {Evolution; international journal of organic evolution}, volume = {62}, number = {5}, pages = {1013-1025}, doi = {10.1111/j.1558-5646.2008.00363.x}, pmid = {18315572}, issn = {0014-3820}, mesh = {Cell Nucleus/genetics ; Genes, Mitochondrial/*genetics ; Genetics, Population ; Molecular Biology ; Plant Cells ; Plants/*genetics ; Reproduction/genetics/physiology ; }, abstract = {The coexistence of females and hermaphrodites in plant populations, or gynodioecy, is a puzzle recognized by Darwin. Correns identified cytoplasmic inheritance of one component of sex expression, now known as cytoplasmic male sterility (CMS). Lewis established cytonuclear inheritance of gynodioecy as an example of genetic conflict. Although biologists have since developed an understanding of the mechanisms allowing the joint maintenance of CMS and nuclear male fertility restorer genes, puzzles remain concerning the inheritance of sex expression and mechanisms governing the origination of CMS. Much of the theory of gynodioecy rests on the assumption of maternal inheritance of the mitochondrial genome. Here we review recent studies of the genetics of plant mitochondria, and their implications for the evolution and transmission of CMS. New studies of intragenomic recombination provide a plausible origin for the chimeric ORFs that characterize CMS. Moreover, evidence suggests that nonmaternal inheritance of mitochondria may be more common than once believed. These findings may have consequences for the maintenance of cytonuclear polymorphism, mitochondrial recombination, generation of gynomonoecious phenotypes, and interpretation of experimental crosses. Finally we point out that CMS can alter the nature of the cytonuclear conflict that may have originally selected for uniparental inheritance.}, }
@article {pmid18309660, year = {2007}, author = {Kong, JQ and Wang, W and Zheng, XD and Zhu, P and Cheng, KD}, title = {[Cloning and bioinformatics analysis of P450 cDNA in Artemisia annua].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {32}, number = {21}, pages = {2227-2231}, pmid = {18309660}, issn = {1001-5302}, mesh = {Amino Acid Sequence ; Artemisia annua/enzymology/*genetics ; Base Sequence ; Cloning, Molecular ; Cytochrome P-450 Enzyme System/classification/*genetics ; DNA, Complementary/chemistry/*genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Phylogeny ; Plant Proteins/*genetics ; Plants, Medicinal/enzymology/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {OBJECTIVE: Cloning and bioinformatics analysis of P450 cDNA in Artemisia annua.<br><br>METHOD: A P450 cDNA gene was cloned from A. annua by RT-PCR. The bioinformatics analysis of the P450 gene was performed.<br><br>RESULT: The complete ORF of this P450 cDNA is 1 464 bp and encodes 488 aa. The sequence was reported to GenBank and coded as DQ667171. Bioinformatics analysis of the P450 cDNA showed it encoded an A-type P450 protein with 54. 992 kDa, it's isoelectric point was 8.83 and the possibility of export to mitochondria was 0.893 2.<br><br>CONCLUSION: The comparable analysis of the P450 with CYP71AV1 revealed that the two proteins probably performed the same function because of the similar character.}, }
@article {pmid18305157, year = {2008}, author = {Uddin, M and Goodman, M and Erez, O and Romero, R and Liu, G and Islam, M and Opazo, JC and Sherwood, CC and Grossman, LI and Wildman, DE}, title = {Distinct genomic signatures of adaptation in pre- and postnatal environments during human evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {9}, pages = {3215-3220}, pmid = {18305157}, issn = {1091-6490}, support = {R01 NS042867/NS/NINDS NIH HHS/United States ; /ImNIH/Intramural NIH HHS/United States ; NS-42867/NS/NINDS NIH HHS/United States ; }, mesh = {Adaptation, Physiological/*genetics ; *Biological Evolution ; Embryo, Mammalian ; *Environment ; *Genome, Human ; Humans ; Infant, Newborn ; Phenotype ; Placenta ; }, abstract = {The human genome evolution project seeks to reveal the genetic underpinnings of key phenotypic features that are distinctive of humans, such as a greatly enlarged cerebral cortex, slow development, and long life spans. This project has focused predominantly on genotypic changes during the 6-million-year descent from the last common ancestor (LCA) of humans and chimpanzees. Here, we argue that adaptive genotypic changes during earlier periods of evolutionary history also helped shape the distinctive human phenotype. Using comparative genome sequence data from 10 vertebrate species, we find a signature of human ancestry-specific adaptive evolution in 1,240 genes during their descent from the LCA with rodents. We also find that the signature of adaptive evolution is significantly different for highly expressed genes in human fetal and adult-stage tissues. Functional annotation clustering shows that on the ape stem lineage, an especially evident adaptively evolved biological pathway contains genes that function in mitochondria, are crucially involved in aerobic energy production, and are highly expressed in two energy-demanding tissues, heart and brain. Also, on this ape stem lineage, there was adaptive evolution among genes associated with human autoimmune and aging-related diseases. During more recent human descent, the adaptively evolving, highly expressed genes in fetal brain are involved in mediating neuronal connectivity. Comparing adaptively evolving genes from pre- and postnatal-stage tissues suggests that different selective pressures act on the development vs. the maintenance of the human phenotype.}, }
@article {pmid18304578, year = {2008}, author = {Hoffmann, B and Nickel, J and Speer, F and Schafer, B}, title = {The 3' ends of mature transcripts are generated by a processosome complex in fission yeast mitochondria.}, journal = {Journal of molecular biology}, volume = {377}, number = {4}, pages = {1024-1037}, doi = {10.1016/j.jmb.2008.01.038}, pmid = {18304578}, issn = {1089-8638}, mesh = {Carbon/metabolism/supply &amp; distribution ; DEAD-box RNA Helicases/genetics/physiology ; Exoribonucleases ; Fermentation/physiology ; Fungal Proteins/genetics/physiology ; Gene Expression Regulation, Fungal ; Gene Library ; Genetic Complementation Test ; Mitochondria/*genetics/metabolism ; Multiprotein Complexes/metabolism/physiology ; Open Reading Frames/genetics/physiology ; Organisms, Genetically Modified ; Phosphatidate Phosphatase/genetics/physiology ; Phosphoprotein Phosphatases ; RNA 3' End Processing/*physiology ; RNA, Fungal/metabolism ; Saccharomyces cerevisiae Proteins/genetics/physiology ; Schizosaccharomyces/*genetics/growth &amp; development/metabolism ; Schizosaccharomyces pombe Proteins/genetics/physiology ; Up-Regulation ; mRNA Cleavage and Polyadenylation Factors/metabolism/*physiology ; }, abstract = {In this article, we report on the genetic analysis of the Schizosaccharomyces pombe open reading frames SPCC1322.01 and SPAC637.11, respectively, which encode proteins that are similar to the exoribonuclease Dss1p and the RNA helicase Suv3p, respectively, forming the mitochondrial degradosome of Saccharomyces cerevisiae. While the helicase Suv3p is exchangeable between S. cerevisiae and S. pombe, the functions of Dss1p and the putative fission yeast RNase protein are specific for each species. Unlike S. cerevisiae mutants lacking a functional degradosome, the major defect of fission yeast knock-out strains is their inability to perform downstream processing of transcripts. In addition, the lack of pah1 results in instability of mitochondrial RNA ends. Overexpression of par1 and pah1 has no significant effect on the steady-state levels of mitochondrial RNAs. The Pet127p-stimulated RNA degradation activity is independent of Par1p/Pah1p in fission yeast mitochondria. The results presented herein indicate that both fission yeast proteins play only a minor role (if at all) in mitochondrial RNA degradation. We assume that the RNA-degrading function was taken over by other enzymes in fission yeast mitochondria, while the former degradosome proteins were recruited to new cellular pathways, for example, RNA processing in fission yeast (as discussed in this article) or mitochondrial DNA replication, apoptosis, or chromatin maintenance in eukaryotes, during evolution.}, }
@article {pmid18302691, year = {2008}, author = {Good, JM and Hird, S and Reid, N and Demboski, JR and Steppan, SJ and Martin-Nims, TR and Sullivan, J}, title = {Ancient hybridization and mitochondrial capture between two species of chipmunks.}, journal = {Molecular ecology}, volume = {17}, number = {5}, pages = {1313-1327}, doi = {10.1111/j.1365-294X.2007.03640.x}, pmid = {18302691}, issn = {1365-294X}, support = {1P20RRO16448-01//PHS HHS/United States ; }, mesh = {Animals ; Base Sequence ; Gene Flow ; *Genetic Speciation ; Geography ; Haplotypes ; *Hybridization, Genetic ; Likelihood Functions ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Phylogeny ; Polymorphism, Genetic ; Population Dynamics ; Sciuridae/*genetics ; Sequence Analysis, DNA ; }, abstract = {Models that posit speciation in the face of gene flow are replacing classical views that hybridization is rare between animal species. We use a multilocus approach to examine the history of hybridization and gene flow between two species of chipmunks (Tamias ruficaudus and T. amoenus). Previous studies have shown that these species occupy different ecological niches and have distinct genital bone morphologies, yet appear to be incompletely isolated reproductively in multiple areas of sympatry. We compared data from four sequenced nuclear loci and from seven microsatellite loci to published cytochrome b sequences. Interspecific gene flow was primarily restricted to introgression of the T. ruficaudus mitochondrial genome into a sympatric subspecies of T. amoenus, T. a. canicaudus, with the four sequenced nuclear loci showing little to no interspecific allele sharing. Microsatellite data were consistent with high levels of differentiation between the species and also showed no current gene flow between broadly sympatric populations of T. a. canicaudus and T. ruficaudus. Coalescent analyses date the mtDNA introgression event from the mid-Pleistocene to late Pliocene. Overall, these data indicate that introgression has had a minimal impact on the nuclear genomes of T. amoenus and T. ruficaudus despite multiple independent hybridization events. Our findings challenge long-standing assumptions on patterns of reproductive isolation in chipmunks and suggest that there may be other examples of hybridization among the 23 species of Tamias that occur in western North America.}, }
@article {pmid18295512, year = {2008}, author = {Albre, J and Gers, C and Legal, L}, title = {Molecular phylogeny of the Erebia tyndarus (Lepidoptera, Rhopalocera, Nymphalidae, Satyrinae) species group combining CoxII and ND5 mitochondrial genes: a case study of a recent radiation.}, journal = {Molecular phylogenetics and evolution}, volume = {47}, number = {1}, pages = {196-210}, doi = {10.1016/j.ympev.2008.01.009}, pmid = {18295512}, issn = {1055-7903}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cyclooxygenase 2/chemistry/*genetics ; DNA Primers ; Insect Proteins/chemistry/*genetics ; Lepidoptera/*classification/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; }, abstract = {The genus Erebia is one of the more controversial groups among the Holarctic Lepidoptera. In this genus, composed of around 100 mountain species, the Erebia tyndarus complex has certainly been a major source of debate for more than a century. According to the literature, between 2 and 11 species, and at least 45 subspecies or semi-species have been recognized. For the first time, we provide a complete molecular study, based on the ND5 and CoxII mitochondrial gene sequences, including all the recognized species and 60% of the subspecies of the entire group, with European, Caucasian, Siberian and North-American taxa. Our analyses led us to recognize 11 species even though there was some poor discrimination between Western Europe species. A complete study of the events of speciation is presented in the light of glacial and interglacial cycles during the Pleistocene.}, }
@article {pmid18288890, year = {2008}, author = {Rand, DM}, title = {Mitigating mutational meltdown in mammalian mitochondria.}, journal = {PLoS biology}, volume = {6}, number = {2}, pages = {e35}, pmid = {18288890}, issn = {1545-7885}, mesh = {Animals ; Mammals/*genetics ; Mitochondria/*metabolism ; *Mutation ; Polymorphism, Genetic ; }, abstract = {Animal mitochondrial genomes have high rates of sequence evolution, and should decay from the accumulation of deleterious mutations. But the purging of mutant mtDNAs in a pedigree of "mutator mice" reveals the speed and power of purifying selection to maintain mitochondrial function.}, }
@article {pmid18288187, year = {2008}, author = {Moore, RB and Oborník, M and Janouskovec, J and Chrudimský, T and Vancová, M and Green, DH and Wright, SW and Davies, NW and Bolch, CJ and Heimann, K and Slapeta, J and Hoegh-Guldberg, O and Logsdon, JM and Carter, DA}, title = {A photosynthetic alveolate closely related to apicomplexan parasites.}, journal = {Nature}, volume = {451}, number = {7181}, pages = {959-963}, doi = {10.1038/nature06635}, pmid = {18288187}, issn = {1476-4687}, mesh = {Animals ; Cell Nucleus/genetics ; Chlorophyll/metabolism ; Chlorophyll A ; Codon/genetics ; Eukaryotic Cells/*classification/cytology/*metabolism/ultrastructure ; Parasites/*classification/*cytology/genetics/ultrastructure ; *Photosynthesis ; *Phylogeny ; Plasmodium falciparum/classification ; Plastids/genetics/*metabolism ; RNA, Ribosomal/genetics ; }, abstract = {Many parasitic Apicomplexa, such as Plasmodium falciparum, contain an unpigmented chloroplast remnant termed the apicoplast, which is a target for malaria treatment. However, no close relative of apicomplexans with a functional photosynthetic plastid has yet been described. Here we describe a newly cultured organism that has ultrastructural features typical for alveolates, is phylogenetically related to apicomplexans, and contains a photosynthetic plastid. The plastid is surrounded by four membranes, is pigmented by chlorophyll a, and uses the codon UGA to encode tryptophan in the psbA gene. This genetic feature has been found only in coccidian apicoplasts and various mitochondria. The UGA-Trp codon and phylogenies of plastid and nuclear ribosomal RNA genes indicate that the organism is the closest known photosynthetic relative to apicomplexan parasites and that its plastid shares an origin with the apicoplasts. The discovery of this organism provides a powerful model with which to study the evolution of parasitism in Apicomplexa.}, }
@article {pmid18287522, year = {2008}, author = {Nakamura, N and Hirose, S}, title = {Regulation of mitochondrial morphology by USP30, a deubiquitinating enzyme present in the mitochondrial outer membrane.}, journal = {Molecular biology of the cell}, volume = {19}, number = {5}, pages = {1903-1911}, pmid = {18287522}, issn = {1939-4586}, mesh = {Amino Acid Sequence ; Animals ; COS Cells ; Chlorocebus aethiops ; Endopeptidases/chemistry/genetics/*metabolism ; Gene Expression Profiling ; HeLa Cells ; Humans ; Membrane Proteins/chemistry/metabolism ; Mice ; Mitochondria/*enzymology ; Mitochondrial Membranes/*enzymology ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; *Organelle Shape ; Phylogeny ; Protein Sorting Signals ; Protein Transport ; Rats ; Subcellular Fractions/enzymology ; Thiolester Hydrolases/chemistry/genetics/*metabolism ; }, abstract = {Recent studies have suggested that ubiquitination of mitochondrial proteins participates in regulating mitochondrial dynamics in mammalian cells, but it is unclear whether deubiquitination is involved in this process. Here, we identify human ubiquitin-specific protease 30 (USP30) as a deubiquitinating enzyme that is embedded in the mitochondrial outer membrane. Depletion of USP30 expression by RNA interference induced elongated and interconnected mitochondria, depending on the activities of the mitochondrial fusion factors mitofusins, without changing the expression levels of the key regulators for mitochondrial dynamics. Mitochondria were rescued from this abnormal phenotype by ectopic expression of USP30 in a manner dependent on its enzymatic activity. Our findings reveal that USP30 participates in the maintenance of mitochondrial morphology, a finding that provides new insight into the cellular function of deubiquitination.}, }
@article {pmid18272380, year = {2008}, author = {Perry, AJ and Rimmer, KA and Mertens, HD and Waller, RF and Mulhern, TD and Lithgow, T and Gooley, PR}, title = {Structure, topology and function of the translocase of the outer membrane of mitochondria.}, journal = {Plant physiology and biochemistry : PPB}, volume = {46}, number = {3}, pages = {265-274}, doi = {10.1016/j.plaphy.2007.12.012}, pmid = {18272380}, issn = {0981-9428}, mesh = {Membrane Transport Proteins/chemistry/*metabolism/physiology ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/chemistry/*metabolism/physiology ; Models, Biological ; Models, Molecular ; Protein Structure, Tertiary ; }, abstract = {Proteins destined for the mitochondria required the evolution of specific and efficient molecular machinery for protein import. The subunits of the import translocases of the inner membrane (TIM) appear homologous and conserved amongst species, however the components of the translocase of the outer membrane (TOM) show extensive differences between species. Recently, bioinformatic and structural analysis of Tom20, an important receptor subunit of the TOM complex, suggests that this protein complex arose from different ancestors for plants compared to animals and fungi, but has subsequently converged to provide similar functions and analogous structures. Here we review the current knowledge of the TOM complex, the function and structure of the various subunits that make up this molecular machine.}, }
@article {pmid18266987, year = {2008}, author = {Hedtke, SM and Stanger-Hall, K and Baker, RJ and Hillis, DM}, title = {All-male asexuality: origin and maintenance of androgenesis in the Asian clam Corbicula.}, journal = {Evolution; international journal of organic evolution}, volume = {62}, number = {5}, pages = {1119-1136}, doi = {10.1111/j.1558-5646.2008.00344.x}, pmid = {18266987}, issn = {0014-3820}, mesh = {Animals ; Cell Nucleus/genetics ; Corbicula/classification/genetics/parasitology/*physiology ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Male ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/genetics ; Reproduction, Asexual/genetics/*physiology ; }, abstract = {Androgenesis is a rare form of asexual male reproduction found in disparate taxa across the Tree of Life. Phylogenetic analyses of mitochondrial genes suggest that androgenesis has arisen repeatedly in the Asian clam genus Corbicula. Two of these androgenetic species have been introduced to North America. Multiple lines of genetic evidence suggest that although nuclear recombination between these two species is rare, mitochondrial genome capture is a frequent consequence of androgenetic parasitism of heterospecific eggs. Egg parasitism may also rarely result in partial nuclear genome capture between closely related species of Corbicula, which provides a mechanism for the otherwise clonal species to avoid the deleterious effects of asexuality. Egg parasitism among congeners may explain why androgenesis has been maintained in Corbicula after fixation and has not yet led to population extinction. This mechanism also provides an explanation for the apparent multiple origins of androgenesis in Corbicula as seen on the mitochondrial DNA phylogeny. We suggest that a single androgenetic lineage may have repeatedly captured mitochondrial genomes (as well as portions of nuclear genomes) from various sexual species, resulting in several distinct androgenetic species with distantly related mtDNA genomes and divergent morphologies.}, }
@article {pmid18266629, year = {2008}, author = {Duron, O and Hurst, GD and Hornett, EA and Josling, JA and Engelstädter, J}, title = {High incidence of the maternally inherited bacterium Cardinium in spiders.}, journal = {Molecular ecology}, volume = {17}, number = {6}, pages = {1427-1437}, doi = {10.1111/j.1365-294X.2008.03689.x}, pmid = {18266629}, issn = {1365-294X}, mesh = {Animals ; Bacterial Infections/microbiology ; Bacteroidetes/*physiology ; *Biological Evolution ; DNA, Ribosomal/genetics ; Female ; Inheritance Patterns/*genetics ; Male ; Mitochondria/genetics ; Phylogeny ; Sex Ratio ; Spiders/genetics/*microbiology/*physiology ; Wolbachia/physiology ; }, abstract = {Inherited bacteria are now recognized as important players in arthropod evolution and ecology. Here, we test spiders, a group recently identified as possessing inherited bacteria commonly, for the presence of two reproductive parasites, Cardinium hertigii (Bacteroidetes group) and Wolbachia (alpha-proteobacteria), estimating incidence, prevalence, any sex bias in infection, and infection diversity, for a panel of field-collected specimens. We identify spiders as a hotspot for Cardinium. Present in 22% of the sampled species, incidence was significantly higher than that previously recorded in insects. Where present, Cardinium infection occurred at medium prevalence without evidence of sex bias in prevalence that would indicate sex-ratio distortion activity. Wolbachia was present in 37% of species, but revealed a gradation from being rare to very common. In one case, Wolbachia was found significantly more commonly in females than males, indicating it may act as a sex-ratio distorter in some species. Breeding work conducted on two species confirmed that Wolbachia and Cardinium were transmitted maternally, which represents the first proof of inheritance of these symbionts in spiders. Overall, this study demonstrates that the majority of spider species are infected with inherited bacteria, and their role in host biology clearly requires determination.}, }
@article {pmid18266623, year = {2008}, author = {Hellgren, O and Bensch, S and Malmqvist, B}, title = {Bird hosts, blood parasites and their vectors--associations uncovered by molecular analyses of blackfly blood meals.}, journal = {Molecular ecology}, volume = {17}, number = {6}, pages = {1605-1613}, doi = {10.1111/j.1365-294X.2007.03680.x}, pmid = {18266623}, issn = {1365-294X}, mesh = {Animals ; Birds/*blood/genetics/*parasitology ; DNA, Mitochondrial/genetics ; Disease Vectors ; Electron Transport Complex IV/genetics ; Eukaryota/*genetics/*physiology ; Feeding Behavior ; Geography ; *Host-Parasite Interactions ; Mitochondria/enzymology/genetics ; Parasites/genetics/*physiology ; Phylogeny ; Simuliidae/*physiology ; Species Specificity ; Sweden ; }, abstract = {The level of host specificity of blood-sucking invertebrates may have both ecological and evolutionary implications for the parasites they are transmitting. We used blood meals from wild-caught blackflies for molecular identification of parasites and hosts to examine patterns of host specificity and how these may affect the transmission of avian blood parasites of the genus Leucocytozoon. We found that five different species of ornithophilic blackflies preferred different species of birds when taking their blood meals. Of the blackflies that contained avian blood meals, 62% were infected with Leucocytozoon parasites, consisting of 15 different parasite lineages. For the blackfly species, there was a significant association between the host width (measured as the genetic differentiation between the used hosts) and the genetic similarity of the parasites in their blood meals. The absence of similar parasite in blood meals from blackflies with different host preferences is interpreted as a result of the vector-host associations. The observed associations between blackfly species and host species are therefore likely to hinder parasites to be transmitted between different host-groups, resulting in ecologically driven associations between certain parasite lineages and hosts species.}, }
@article {pmid18263605, year = {2008}, author = {Kurabayashi, A and Sumida, M and Yonekawa, H and Glaw, F and Vences, M and Hasegawa, M}, title = {Phylogeny, recombination, and mechanisms of stepwise mitochondrial genome reorganization in mantellid frogs from Madagascar.}, journal = {Molecular biology and evolution}, volume = {25}, number = {5}, pages = {874-891}, doi = {10.1093/molbev/msn031}, pmid = {18263605}, issn = {1537-1719}, mesh = {Animals ; Anura/classification/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/chemistry/genetics ; Evolution, Molecular ; Gene Rearrangement ; *Genome ; Madagascar ; Mitochondria/*genetics ; Nucleosides/chemistry ; Phylogeny ; RNA, Transfer/genetics ; Recombination, Genetic ; Regulatory Sequences, Nucleic Acid ; }, abstract = {In Malagasy frogs of the family Mantellidae, the genus Mantella is known to possess highly reorganized mitochondrial (mt) genomes with the following characteristics: 1) some rearranged gene positions, 2) 2 distinct genes and a pseudogene corresponding to the transfer RNA gene for methionine (trnM), and 3) 2 control regions (CRs) with almost identical nucleotide sequences. These unique genomic features were observed concentrated between the duplicated CRs surrounding cytochrome b (cob) and nicotinamide adenine dinucleotide dehydrogenase subunit 2 (cnad2) genes. To elucidate the mechanisms and evolutionary pathway that yielded the derived genome condition, we surveyed the reorganized genomic portion for all 12 mantellid genera. Our results show that the mt genomes of 7 genera retain the ancestral condition. In contrast, adding to Mantella, 4 genera of the subfamily Mantellinae, Blommersia, Guibemantis, Wakea, and Spinomantis, share several derived genomic characters. Furthermore, mt genomes of these mantellines showed additional structural divergences, resulting in different genome conditions between them. The high frequency of genomic reorganization does not correlate with nucleotide substitution rate. The encountered mt genomic conditions also suggest the occurrences of stepwise gene duplication and deletion events during the evolution of mantellines. Simultaneously, the majority of duplication events seems to be mediated by general (homologous) or illegitimate recombination, and general recombination also plays a role in concerted sequence evolution between multiple CRs. Considering our observations and recent conditional evidences, the following outlines can be expected for recombination processes in mt genome reorganization. 1) The CR is the "hot spot" of recombination; 2) highly frequent recombination between CRs may be mediated by a replication fork barrier lying in the CR; 3) general recombination has a potential to cause gene rearrangement in upstream regions of multiple CRs as the results of gene conversion and unequal crossing over processes. Our results also suggest that recombination activity is not a direct cause of convergent gene rearrangement; rather, homoplasious gene rearrangement seems to be mediated by persistence of a copied genomic condition through several lineage splits and subsequent parallel deletions.}, }
@article {pmid18262354, year = {2008}, author = {De Simoni, S and Goemaere, J and Knoops, B}, title = {Silencing of peroxiredoxin 3 and peroxiredoxin 5 reveals the role of mitochondrial peroxiredoxins in the protection of human neuroblastoma SH-SY5Y cells toward MPP+.}, journal = {Neuroscience letters}, volume = {433}, number = {3}, pages = {219-224}, doi = {10.1016/j.neulet.2007.12.068}, pmid = {18262354}, issn = {0304-3940}, mesh = {1-Methyl-4-phenylpyridinium/toxicity ; Apoptosis/drug effects/genetics ; Cell Survival/drug effects/genetics ; Cytoprotection/drug effects/*genetics ; Down-Regulation/genetics ; Electron Transport Chain Complex Proteins/drug effects/genetics/metabolism ; Energy Metabolism/drug effects/genetics ; Gene Silencing/physiology ; Humans ; Mitochondria/drug effects/*metabolism ; Neuroblastoma ; Neurons/drug effects/*metabolism ; Neurotoxins/toxicity ; Oxidative Stress/drug effects/genetics ; Peroxiredoxin III ; Peroxiredoxins/drug effects/genetics/*metabolism ; RNA, Small Interfering/genetics ; Substantia Nigra/drug effects/*metabolism/physiopathology ; Tumor Cells, Cultured ; }, abstract = {Peroxiredoxins (PRDXs) are a family of peroxidases well conserved throughout evolution. Human PRDX3 and PRDX5, two mitochondrial PRDXs, have been implicated in several pathologies associated with oxidative stress. However, the individual role of PRDX3 and PRDX5 in cellular antioxidant defense has never been well established due to their overlapping peroxidatic activities. We investigated the expression and function of mitochondrial PRDXs in human neuroblastoma SH-SY5Y cells. Our results show that PRDX3 and PRDX5 are expressed constitutively in these neuronal cells. To examine further the function of mitochondrial PRDXs, we silenced the expression of PRDX3 and/or PRDX5 using small hairpin RNAs. Our results show that mitochondrial PRDX-depleted cells are more prone to oxidative damages and apoptosis induced by MPP(+), a complex I inhibitor which provides an experimental paradigm of Parkinson's disease.}, }
@article {pmid18259800, year = {2008}, author = {Huang, D and Meier, R and Todd, PA and Chou, LM}, title = {Slow mitochondrial COI sequence evolution at the base of the metazoan tree and its implications for DNA barcoding.}, journal = {Journal of molecular evolution}, volume = {66}, number = {2}, pages = {167-174}, pmid = {18259800}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; Cnidaria/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Electronic Data Processing/*methods ; *Evolution, Molecular ; Genetic Variation ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Porifera/*genetics ; Species Specificity ; }, abstract = {The evolution rates of mtDNA in early metazoans hold important implications for DNA barcoding. Here, we present a comprehensive analysis of intra- and interspecific COI variabilities in Porifera and Cnidaria (separately as Anthozoa, Hydrozoa, and Scyphozoa) using a data set of 619 sequences from 224 species. We found variation within and between species to be much lower in Porifera and Anthozoa compared to Medusozoa (Hydrozoa and Scyphozoa), which has divergences similar to typical metazoans. Given that recent evidence has shown that fungi also exhibit limited COI divergence, slow-evolving mtDNA is likely to be plesiomorphic for the Metazoa. Higher rates of evolution could have originated independently in Medusozoa and Bilateria or been acquired in the Cnidaria + Bilateria clade and lost in the Anthozoa. Low identification success and substantial overlap between intra- and interspecific COI distances render the Anthozoa unsuitable for DNA barcoding. Caution is also advised for Porifera and Hydrozoa because of relatively low identification success rates as even threshold divergence that maximizes the "barcoding gap" does not improve identification success.}, }
@article {pmid18255328, year = {2008}, author = {De Zoysa, M and Pushpamali, WA and Whang, I and Kim, SJ and Lee, J}, title = {Mitochondrial thioredoxin-2 from disk abalone (Haliotis discus discus): molecular characterization, tissue expression and DNA protection activity of its recombinant protein.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {149}, number = {4}, pages = {630-639}, doi = {10.1016/j.cbpb.2007.12.009}, pmid = {18255328}, issn = {1096-4959}, mesh = {Amino Acid Sequence ; Animals ; Antioxidants/chemistry/isolation &amp; purification/metabolism ; Cloning, Molecular ; *DNA Damage ; DNA, Complementary/genetics ; DNA, Superhelical/genetics/metabolism ; Gastropoda/*genetics/metabolism ; *Gene Expression Regulation ; Hydrogen Peroxide/pharmacology ; Mitochondria/*genetics/metabolism ; Molecular Sequence Data ; Organ Specificity ; *Oxidative Stress ; Phylogeny ; RNA, Messenger/genetics ; Recombinant Fusion Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Sequence Alignment ; Thioredoxins/chemistry/*genetics/isolation &amp; purification/*metabolism ; Up-Regulation/drug effects ; }, abstract = {Thioredoxin-2 is a mitochondria-specific member of the thioredoxin (TRx) super-family that plays an important role as a component of the mitochondrial antioxidant system. The gene coding mitochondrial TRx-2 was isolated from the disk abalone (Haliotis discus discus) cDNA library, denoted as AbTRx-2. It contains 1214-bp full length with 519-bp open reading frame, encoding 173 amino acids. AbTRx-2 showed characteristic TRx active site at (96)WCGPC(100) and mitochondrial targeting peptide at the N-terminal amino acid sequence. The deduced amino acid comparison showed that AbTRx-2 shares 43 and 42% identity with Xenopus laevis and human TRx-2, respectively. Purified recombinant AbTRx-2 fusion protein was shown to catalyze insulin reduction and protect supercoiled plasmid DNA from damages induced by metal-catalyzed generation of reactive oxygen species. Constitutive AbTRx-2 mRNA was detected in gill, mantle, gonad, abductor muscle, digestive tract, and hemocytes, in a tissue specific manner. The AbTRx-2 mRNA was up-regulated in gill and digestive tract tissues initially at 3 h post-injection of H(2)O(2) and maintained higher level at 6 h. Our results suggest that abalone TRx-2 may play an important role in regulating oxidative stress in mitochondria by catalyzing protein disulfide reduction, scavenging of ROS, and minimizing the DNA damage.}, }
@article {pmid18255319, year = {2008}, author = {Slechtová, V and Bohlen, J and Perdices, A}, title = {Molecular phylogeny of the freshwater fish family Cobitidae (Cypriniformes: Teleostei): delimitation of genera, mitochondrial introgression and evolution of sexual dimorphism.}, journal = {Molecular phylogenetics and evolution}, volume = {47}, number = {2}, pages = {812-831}, doi = {10.1016/j.ympev.2007.12.018}, pmid = {18255319}, issn = {1055-7903}, mesh = {Animals ; Asia ; Bayes Theorem ; Consensus Sequence ; Cypriniformes/*classification/*genetics ; Cytochromes b/genetics ; Europe ; *Evolution, Molecular ; *Fresh Water ; Geography ; *Inbreeding ; Mitochondria/*genetics ; *Phylogeny ; *Sex Characteristics ; }, abstract = {The family Cobitidae represents a characteristic element of the Eurasian ichthyofauna. Despite diverse features of sexual dimorphism, comparably few morphological characters have been utilized for taxonomic studies resulting in many unresolved puzzles. Here we present the phylogenetic relationships of Cobitidae as inferred from the mitochondrial cytochrome b gene and the nuclear gene RAG-1. Analyses of both markers show a group of eight nominal genera, which all occur in Europe and eastern, northern and western Asia, forming a monophyletic lineage (northern clade) while all other clades inhabit South and Southeast Asia (southern lineages). While all eight southern lineages correspond to genera as defined by morphological studies, only four lineages were reliably recovered within the northern clade, and of these only one (Sabanejewia) corresponds to a formerly considered genus. The genera Cobitis, Iksookimia and Niwaëlla were polyphyletic. A comparison of the two markers shows several incongruities within the northern clade and mitochondrial introgression at least in the genus Misgurnus. Mapping the characters of sexual dimorphism on our cladogram, we identified five character states that are diagnostic for certain lineages. Estimations of the divergence times dated the separation of the northern clade from the southern lineages to the middle Eocene (46 MYA) and the origin of "Cobitis"misgurnoides, the basal taxon of the northern clade, during early Oligocene (30-35 MYA). The geographic distribution of the major clades supports recently developed hypotheses about the river history of East Asia and further suggests that a range expansion of the northern clade in late Miocene (15 MYA) led to the colonisation of Europe by three already distinct genera.}, }
@article {pmid18251919, year = {2007}, author = {Laisk, A and Oja, V and Eichelmann, H}, title = {Kinetics of leaf oxygen uptake represent in planta activities of respiratory electron transport and terminal oxidases.}, journal = {Physiologia plantarum}, volume = {131}, number = {1}, pages = {1-9}, doi = {10.1111/j.1399-3054.2007.00910.x}, pmid = {18251919}, issn = {1399-3054}, mesh = {Carbon Dioxide/metabolism ; Cell Respiration/physiology ; Electron Transport ; Kinetics ; Oxidoreductases/*metabolism ; Oxygen/*metabolism ; Photosynthesis/physiology ; Plant Leaves/enzymology/metabolism/*physiology ; Plant Proteins/*metabolism ; Populus/enzymology/metabolism/physiology ; }, abstract = {We present, for the first time, the oxygen response kinetics of mitochondrial respiration measured in intact leaves (sunflower and aspen). Low O(2) concentrations in N(2) (9-1500 ppm) were preset in a flow-through gas exchange measurement system, and the decrease in O(2) concentration and the increase in CO(2) concentration as result of leaf respiration were measured by a zirconium cell O(2) analyser and infrared-absorption CO(2) analyser, respectively. The low O(2) concentrations little influenced the rate of CO(2) evolution during the 60-s exposure. The initial slope of the O(2) uptake curve on the dissolved O(2) concentration basis was relatively constant in leaves of a single species, 1.5 mm s(-1) in sunflower and 1.8 mm s(-1) in aspen. The apparent K(0.5)(O(2)) values ranged from 0.33 to 0.67 microM in sunflower and from 0.33 to 1.1 microM in aspen, mainly because of the variation of the maximum rate, V(max) (leaf temperature 22 degrees C). The initial slope of the O(2) response of respiration characterizes the catalytic efficiency of terminal oxidases, an important parameter of the respiratory machinery in leaves. The plateau of the response characterizes the activity of the mitochondrial electron transport chain and is subject to regulations in accordance with the necessity for ATP production. The relatively low oxygen conductivity of terminal oxidases means that in leaves, less than 10% of the photosynthetic oxygen can be reassimilated by mitochondria.}, }
@article {pmid18249075, year = {2008}, author = {Stamatis, C and Giannouli, S and Suchentrunk, F and Sert, H and Stathopoulos, C and Mamuris, Z}, title = {Recruitment of mitochondrial tRNA genes as auxiliary variability markers for both intra- and inter-species analysis: The paradigm of brown hare (Lepus europaeus).}, journal = {Gene}, volume = {410}, number = {1}, pages = {154-164}, doi = {10.1016/j.gene.2007.12.010}, pmid = {18249075}, issn = {0378-1119}, mesh = {Animals ; Base Sequence ; DNA Primers ; Hares ; Mitochondria/*genetics ; Molecular Sequence Data ; RNA, Transfer/*genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {We sequenced and analyzed the mitochondrial tRNA(Thr) and tRNA(Pro) genes from brown hare (Lepus europaeus) individuals of different geographic distribution and we investigated the role of various nucleotide substitutions that were detected. We compared these tRNAs with the respective available mitochondrial tRNA genes sequences within Lepus species and among mammals. The mutations that were detected represent specific and conserved polymorphisms that do not seem to affect the structural and functional features that are required for participation of tRNA molecules in mitochondrial protein synthesis. These changes however, possibly reflect on the evolutionary background of the species, which is based on the high intra-genomic variability and the evolutionary dynamic of the mitochondrial DNA. In an attempt to compare the phylogeny that is based on these specific tRNA genes with the phylogeny that is produced from sequencing data of the mitochondrial variable loop, we came up with results that indicate similar phylogeographic clusters. This observation implies that the tRNA mutations that were used for the present study have been well tolerated during evolution and they define an additional genetic and biochemical tag that can be used for such studies. Based on this notion and according to our results, we propose that mitochondrial tRNA genes can be used as valuable auxiliary molecular markers for contemporaneous and linked biochemical and genetic analyses.}, }
@article {pmid18248682, year = {2008}, author = {Patron, NJ and Durnford, DG and Kopriva, S}, title = {Sulfate assimilation in eukaryotes: fusions, relocations and lateral transfers.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {39}, pmid = {18248682}, issn = {1471-2148}, support = {//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adenosine Triphosphate/metabolism ; Cyanobacteria/genetics ; Eukaryotic Cells/*metabolism ; Gene Transfer, Horizontal/genetics ; Microscopy, Electron, Transmission ; Oxidoreductases/classification/genetics/metabolism ; Oxidoreductases Acting on Sulfur Group Donors/classification/genetics/metabolism ; Phylogeny ; Plastids/metabolism ; Protein Isoforms/genetics/metabolism ; Sulfate Adenylyltransferase/classification/genetics/metabolism ; Sulfates/*metabolism ; }, abstract = {BACKGROUND: The sulfate assimilation pathway is present in photosynthetic organisms, fungi, and many bacteria, providing reduced sulfur for the synthesis of cysteine and methionine and a range of other metabolites. In photosynthetic eukaryotes sulfate is reduced in the plastids whereas in aplastidic eukaryotes the pathway is cytosolic. The only known exception is Euglena gracilis, where the pathway is localized in mitochondria. To obtain an insight into the evolution of the sulfate assimilation pathway in eukaryotes and relationships of the differently compartmentalized isoforms we determined the locations of the pathway in lineages for which this was unknown and performed detailed phylogenetic analyses of three enzymes involved in sulfate reduction: ATP sulfurylase (ATPS), adenosine 5'-phosphosulfate reductase (APR) and sulfite reductase (SiR).<br><br>RESULTS: The inheritance of ATPS, APR and the related 3'-phosphoadenosine 5'-phosphosulfate reductase (PAPR) are remarkable, with multiple origins in the lineages that comprise the opisthokonts, different isoforms in chlorophytes and streptophytes, gene fusions with other enzymes of the pathway, evidence a eukaryote to prokaryote lateral gene transfer, changes in substrate specificity and two reversals of cellular location of host- and endosymbiont-originating enzymes. We also found that the ATPS and APR active in the mitochondria of Euglena were inherited from its secondary, green algal plastid.<br><br>CONCLUSION: Our results reveal a complex history for the enzymes of the sulfate assimilation pathway. Whilst they shed light on the origin of some characterised novelties, such as a recently described novel isoform of APR from Bryophytes and the origin of the pathway active in the mitochondria of Euglenids, the many distinct and novel isoforms identified here represent an excellent resource for detailed biochemical studies of the enzyme structure/function relationships.}, }
@article {pmid18248575, year = {2008}, author = {Chen, G and Hare, MP}, title = {Cryptic ecological diversification of a planktonic estuarine copepod, Acartia tonsa.}, journal = {Molecular ecology}, volume = {17}, number = {6}, pages = {1451-1468}, doi = {10.1111/j.1365-294X.2007.03657.x}, pmid = {18248575}, issn = {1365-294X}, mesh = {Animals ; Base Sequence ; *Biodiversity ; Cell Nucleus/genetics ; Copepoda/cytology/genetics/*physiology ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/genetics ; *Ecology ; Electron Transport Complex IV/genetics ; Geography ; Haplotypes ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Plankton/genetics/*physiology ; Polymorphism, Restriction Fragment Length ; *Rivers ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The recent discovery of cryptic species in marine holoplankton, organisms that 'drift' in oceanic currents throughout their life cycle, contrasts with their potential for long-distance passive dispersal and presumably high gene flow. These observations suggest that holoplankton species are adapting to surprisingly small-scale oceanographic features and imply either limited dispersal or strong selection gradients. Acartia tonsa is a widespread and numerically dominant estuarine copepod containing deep mitochondrial lineages within and among populations along the northwestern Atlantic coast. In this study, we intensively investigated A. tonsa populations in Chesapeake Bay with the goals of testing species status for the deep lineages and testing for their association with environmental features over space and time. Phylogenetic analyses of DNA sequences from mitochondrial cytochrome c oxidase I (mtCOI) and the nuclear ribosomal internal transcribed spacer (nITS) resolved two concordant monophyletic clades. Deep divergence between the two clades (13.7% uncorrected sequence divergence for mtCOI and 32.2% for nITS) and genealogical concordance within sympatric populations strongly suggest that the two clades represent reproductively isolated cryptic species. Based on restriction fragment length polymorphisms of mtCOI, representatives from the two clades were found consistently associated with contrasting salinity regimes (oligohaline vs. meso-polyhaline) with an overlap between 2 and 12 PSU in samples from 1995 to 2005. Finding these patterns in one of the best-known estuarine copepods reinforces the conclusion that marine biodiversity is underestimated, not only in terms of species numbers, but also with respect to niche partitioning and the potential importance of ecological divergence in marine holoplankton.}, }
@article {pmid18245356, year = {2008}, author = {Bolnick, DI and Turelli, M and López-Fernández, H and Wainwright, PC and Near, TJ}, title = {Accelerated mitochondrial evolution and "Darwin's corollary": asymmetric viability of reciprocal F1 hybrids in Centrarchid fishes.}, journal = {Genetics}, volume = {178}, number = {2}, pages = {1037-1048}, pmid = {18245356}, issn = {0016-6731}, mesh = {Animals ; Crosses, Genetic ; *Evolution, Molecular ; Female ; Male ; Mitochondria/*genetics ; *Models, Genetic ; Perciformes/classification/*genetics ; Phylogeny ; Survival ; }, abstract = {Reciprocal crosses between species can yield hybrids with different viabilities. The high frequency of this asymmetric hybrid viability ("Darwin's corollary") places it alongside Haldane's rule and the "large-X effect" as a general feature of postmating reproductive isolation. Recent theory suggests that reciprocal cross asymmetries can arise from stochastic substitutions in uniparentally inherited loci such as mitochondrial genomes, although large systematic differences in mitochondrial substitution rates can also contribute to asymmetries. Although the magnitude of asymmetry will be relatively insensitive to unequal rates of mitochondrial evolution in diverging species, we show here that rate asymmetries can have a large effect on the direction of viability asymmetries. In reciprocal crosses between species, the maternal parent with faster mitochondrial evolution will tend to produce less viable F(1) hybrids owing to an increased probability of mito-nuclear incompatibilities. We test this prediction using data on reciprocal hybrid viability and molecular evolution rates from a clade of freshwater fishes, Centrarchidae. As predicted, species with accelerated mitochondrial evolution tend to be the worse maternal parent for F(1) hybrids, providing the first comparative evidence for a systematic basis to Darwin's corollary. This result is consistent with the hypothesis that mito-nuclear incompatibilities can play an important role in reproductive isolation. Such asymmetrical reproductive isolation may help explain the asymmetrical mitochondrial introgression observed between many hybridizing species. However, as with any comparative study, we cannot rule out the possibility that our results arise from a mutual correlation with a third variable such as body size.}, }
@article {pmid18244907, year = {2008}, author = {Niu, BL and Weng, HB and He, LH and Shen, WF and Qi, XP and Liu, Y and Meng, ZQ}, title = {[Cloning and analysis of adenine nucleotide translocase gene in Helicoverpa armigera].}, journal = {Yi chuan = Hereditas}, volume = {30}, number = {1}, pages = {81-86}, doi = {10.3724/sp.j.1005.2008.00081}, pmid = {18244907}, issn = {0253-9772}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Conserved Sequence ; DNA, Complementary/genetics ; Lepidoptera/classification/*enzymology/*genetics ; Mitochondrial ADP, ATP Translocases/chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {A cDNA clone encoding the ADP/ATP translocase in Helicoverpa armigera has been identified by RT-PCR, 5'and 3'RACE methods. Sequence analysis shows that it is 1,190 bp long and contains a single open reading frame (ORF, 133-1,033 bp) encoding a protein of 300 amino acids (GenBank submission number, AY253868). The protein has a 22 aa signal peptide on its N-terminal, which leads the protein locating onto the inner membrane of the mitochondria. It also has three conserved domains of the mitochondrial carrier protein forming a channel to exchange ATP and ADP energy molecule through the inner membrane of the mitochondria. It shows extensive similarities to the known ADP/ATP translocase poly-peptides. The ADP/ATP translocase similarity was up to 90% in the Lepidoptera.}, }
@article {pmid18241806, year = {2008}, author = {Gérard, K and Roby, C and Chevalier, N and Thomassin, B and Chenuil, A and Féral, JP}, title = {Assessment of three mitochondrial loci variability for the crown-of-thorns starfish: a first insight into Acanthaster phylogeography.}, journal = {Comptes rendus biologies}, volume = {331}, number = {2}, pages = {137-143}, doi = {10.1016/j.crvi.2007.11.005}, pmid = {18241806}, issn = {1768-3238}, mesh = {Animals ; Australia ; Ecosystem ; Genetics, Population ; Geography ; Indian Ocean ; Kenya ; Madagascar ; Mitochondria/*genetics ; Phylogeny ; Population Density ; Starfish/classification/*genetics/ultrastructure ; }, abstract = {Acanthaster planci (L.) is one of the major threats to coral reefs, whose genetic diversity has been mainly studied with allozymes. Allozymes revealed the low genetic differentiation between A. planci populations in the Indo-Pacific area. We obtained sequences of A. planci from Kenya, Mayotte and Madagascar at the three loci cytochrome oxydase subunit I (COI), 16S rDNA (16S) and five tRNAs, analysed together with available sequences of Acanthaster from the Pacific Ocean. The level of genetic diversity varied among the three loci, tRNAs being on average three times less divergent than COI and 16S genes. The genus Acanthaster appeared monophyletic, the two species A. brevispinus (Fisher) and A. planci forming distinct clades in agreement with data from morphology and systematics. The A. planci clade split into a West Indian Ocean group and a Pacific group, in agreement with allozyme data on population differentiation.}, }
@article {pmid18231851, year = {2008}, author = {Suzuki, H and Filippucci, MG and Chelomina, GN and Sato, JJ and Serizawa, K and Nevo, E}, title = {A biogeographic view of Apodemus in Asia and Europe inferred from nuclear and mitochondrial gene sequences.}, journal = {Biochemical genetics}, volume = {46}, number = {5-6}, pages = {329-346}, doi = {10.1007/s10528-008-9149-7}, pmid = {18231851}, issn = {0006-2928}, mesh = {Animals ; Asia ; Cell Nucleus/*genetics ; Cytochromes b/*genetics ; Europe ; Eye Proteins/*genetics ; Homeodomain Proteins/*genetics ; Mitochondria/*genetics ; Murinae/classification/*genetics ; Phylogeny ; Receptors, Odorant/*genetics ; Retinol-Binding Proteins/*genetics ; von Willebrand Factor/*genetics ; }, abstract = {Sequences of the mitochondrial cyt b gene and nuclear IRBP, RAGI, 17, and vWF genes were used to assess the evolutionary history of major lineages of Apodemus, in particular to better understand dispersal between Asia and Europe. Our data show eight extant lineages of Late Tertiary origin: Apodemus agrarius, A. semotus, A. peninsulae, A. speciosus, A. argenteus, A. gurkha, A. mystacinus, and A. sylvaticus. Monophyly of two European lineages (A. mystacinus and A. sylvaticus) and four Asian lineages (A. agrarius, A. semotus, A. peninsulae, and A. speciosus) was confirmed with high bootstrap support. Together with literature data, the available molecular data depict three crucial evolutionary events: (1) initial wide dispersal and subsequent radiation around 6 million years ago, (2) region-specific radiations in Europe and southern China around 2 million years ago, and (3) westward dispersal of A. agrarius to Europe in the Late Quaternary.}, }
@article {pmid18227871, year = {2008}, author = {Khrapko, K}, title = {Two ways to make an mtDNA bottleneck.}, journal = {Nature genetics}, volume = {40}, number = {2}, pages = {134-135}, pmid = {18227871}, issn = {1546-1718}, support = {R01 AG019787/AG/NIA NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Cell Lineage ; Chromosomal Proteins, Non-Histone ; Computer Simulation ; DNA Replication ; DNA, Mitochondrial/*chemistry/*genetics ; Female ; Gene Dosage ; Gene Frequency ; Genetic Drift ; Green Fluorescent Proteins/metabolism ; Mice ; Mice, Inbred Strains ; Mitochondria/*chemistry ; Models, Biological ; Models, Genetic ; Mutation ; Oocytes/chemistry ; Oogenesis ; Repressor Proteins/metabolism ; Time Factors ; }, abstract = {Rapid changes in mitochondrial DNA allele frequency between generations have been explained by an ‘mtDNA bottleneck’ in the germ line, and mtDNA aggregates, or nucleoids have been recently proposed to drive such a bottleneck. Now, a new study finds a sharp reduction in mtDNA content in the germ line and suggests that such reduction alone may account for the bottleneck effect.}, }
@article {pmid18224322, year = {2008}, author = {Ikuta, K and Kawai, H and Müller, DG and Ohama, T}, title = {Recurrent invasion of mitochondrial group II introns in specimens of Pylaiella littoralis (brown alga), collected worldwide.}, journal = {Current genetics}, volume = {53}, number = {4}, pages = {207-216}, pmid = {18224322}, issn = {0172-8083}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Genes, Mitochondrial/*genetics ; Geography ; Introns/*genetics ; Mitochondria/enzymology/*genetics ; Mitochondrial Proteins/chemistry/genetics ; Molecular Sequence Data ; Phaeophyceae/cytology/enzymology/*genetics ; Phylogeny ; Polymorphism, Genetic ; Sequence Alignment ; }, abstract = {The mitochondrial genome of a filamentous brown alga Pylaiella littoralis (strain CCMP 1907) has been reported to contain four group IIB introns in the LSU rRNA gene and three group IIA introns in the cox1 gene. We found extreme variability in the number of group II introns for these two genes by analyzing eight P. littoralis specimens collected at worldwide habitats. The first intron of the LSU rRNA gene from a specimen collected in France and the fourth intron from a specimen harvested in Japan exhibited an exceptionally long evolutionary distance when compared with the cognate introns found in P. littoralis specimens. Moreover, these introns harbored an intact or nearly intact tripartite ORF, suggesting they are the result of a recent invasion of cognate introns. Based on the fact that many of the target sites were intronless, we propose that opportunity of intron infection is the bottleneck step of the group II intron cycle which consists of invasion, degeneration, and complete loss from the target site.}, }
@article {pmid18223516, year = {2007}, author = {Tafanelli, L and Avierinos, JF and Thuny, F and Pelissier, JF and Jacquier, A and Renard, S and Amabile, N and Gaubert, JY and Habib, G}, title = {[Mitochondrial cardiomyopathy in an adult: a case history].}, journal = {Archives des maladies du coeur et des vaisseaux}, volume = {100}, number = {12}, pages = {1021-1024}, pmid = {18223516}, issn = {0003-9683}, mesh = {Adult ; Biopsy ; Cardiomyopathy, Hypertrophic/*diagnosis ; Echocardiography ; Female ; Humans ; Hyperplasia ; Magnetic Resonance Imaging ; Mitochondria, Heart/*pathology ; Myocardium/pathology ; }, abstract = {We report an original case of mitochondrial cardiomyopathy discovered in a young woman during an episode of cardiac decompensation. The diagnosis was suspected from the echocardiographic appearances of granite-like heterogeneous hypertrophic cardiomyopathy. It was confirmed by endomyocardial biopsies. The clinical evolution was favourable with classical treatment. Mitochondrial cardiomyopathy is a rare cause of cardiomyopathy, generally observed in children, with multisystemic localisation. The pathophysiology and genetics are complex. Cardiac involvement is observed in 25% of cases, with the principal manifestation being hypertrophic cardiomyopathy. In the absence of any specific clinical or paraclinical signs, echocardiography and MRI are the techniques of choice for morphological evaluation. Diagnosis relies upon myocardial biopsy, which should be readily advocated in every unexplained case of cardiomyopathy in a young subject. The prognosis is poor and no specific treatment is available.}, }
@article {pmid18221556, year = {2008}, author = {Liu, SL and Adams, K}, title = {Molecular adaptation and expression evolution following duplication of genes for organellar ribosomal protein S13 in rosids.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {25}, pmid = {18221556}, issn = {1471-2148}, mesh = {Adaptation, Physiological ; Amino Acid Sequence ; Arabidopsis/*genetics ; Bayes Theorem ; DNA, Plant/genetics ; Evolution, Molecular ; Fabaceae/*genetics ; *Gene Duplication ; Gene Expression Regulation, Plant ; *Genes, Plant ; Gossypium/*genetics ; Likelihood Functions ; Phylogeny ; Protein Array Analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Ribosomal Proteins/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: Gene duplication has been a fundamental process in the evolution of eukaryotic genomes. After duplication one copy (or both) can undergo divergence in sequence, expression pattern, and function. Two divergent copies of the ribosomal protein S13 gene (rps13) of chloroplast origin are found in the nucleus of the rosids Arabidopsis, Gossypium, and Glycine. One encodes chloroplast-imported RPS13 (nucp rps13), while the other encodes mitochondria-imported RPS13 (numit rps13). The rps13 gene has been lost from mitochondrial DNA (mt rps13) of many rosids.<br><br>RESULTS: We studied sequence evolution of numit rps13 in comparison with nucp rps13 in seven rosid genera. Ka/Ks analysis and likelihood ratio tests showed considerably higher Ka values and Ka/Ks ratios in numit rps13 than in nucp rps13, indicating increased amino acid sequence divergence in numit rps13. Two positively selected codons were detected in numit RPS13 in regions that are inferred to interact with the 16S rRNA. Several amino acids in numit RPS13 have changed from the one present in nucp RPS13 to the one present in mt RPS13, showing that numit rps13 is becoming more like mt rps13. Comparison of expression patterns and levels of numit rps13 and nucp rps13 in Arabidopsis using microarray data indicated divergence in gene expression. We discovered that in addition to numit rps13, Malus (apple) contains a transcribed mt rps13 gene. To determine if partitioning of expression takes place between numit rps13 and mt rps13, expression of both copies and RNA editing of mt rps13 were examined by RT-PCR, qRT-PCR, and sequencing from 14 different organ types plus seedlings subjected to five different abiotic stresses. Co-expression of numit rps13 and mt rps13 was observed in all the organs and various stress treatments. We determined that purifying selection is acting on both numit rps13 and mt rps13 in Malus.<br><br>CONCLUSION: Our data provide evidence that numit rps13 genes in rosids have experienced adaptive sequence evolution and convergent evolution with mt rps13. Co-expression of numit rps13 and mt rps13 and purifying selection on both genes in Malus suggest that both are functional. The three organellar rps13 genes in rosids provide a distinctive case of gene duplication involving the co-evolution of the nuclear and cytoplasmic genomes.}, }
@article {pmid18219313, year = {2008}, author = {Tattoli, I and Carneiro, LA and Jéhanno, M and Magalhaes, JG and Shu, Y and Philpott, DJ and Arnoult, D and Girardin, SE}, title = {NLRX1 is a mitochondrial NOD-like receptor that amplifies NF-kappaB and JNK pathways by inducing reactive oxygen species production.}, journal = {EMBO reports}, volume = {9}, number = {3}, pages = {293-300}, pmid = {18219313}, issn = {1469-221X}, mesh = {Amino Acid Sequence ; HeLa Cells ; Humans ; JNK Mitogen-Activated Protein Kinases/*metabolism ; Mitochondria/drug effects/*enzymology ; Mitochondrial Proteins/chemistry/*metabolism ; Molecular Sequence Data ; NF-kappa B/*metabolism ; Phylogeny ; Reactive Oxygen Species/*metabolism ; Shigella/drug effects/physiology ; Signal Transduction/drug effects ; Tumor Necrosis Factor-alpha/pharmacology ; }, abstract = {NOD-like receptors (NLRs) are a family of intracellular sensors of microbial- or danger-associated molecular patterns. Here, we report the identification of NLRX1, which is a new member of the NLR family that localizes to the mitochondria. NLRX1 alone failed to trigger most of the common signalling pathways, including nuclear factor-kappaB (NF)-kappaB- and type I interferon-dependent cascades, but could potently trigger the generation of reactive oxygen species (ROS). Importantly, NLRX1 synergistically potentiated ROS production induced by tumour necrosis factor alpha, Shigella infection and double-stranded RNA, resulting in amplified NF-kappaB-dependent and JUN amino-terminal kinases-dependent signalling. Together, these results identify NLRX1 as a NLR that contributes to the link between ROS generation at the mitochondria and innate immune responses.}, }
@article {pmid18219224, year = {2007}, author = {Alesci, S and Abu-Asab, M and Perera, SM and Tsokos, M and Morris, JC and Pacak, K}, title = {Mitochondrial localization of human recombinant adenovirus: from evolution to gene therapy.}, journal = {Neuroimmunomodulation}, volume = {14}, number = {5}, pages = {221-223}, pmid = {18219224}, issn = {1423-0216}, support = {Z99 CA999999/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Adenoviridae Infections/*genetics ; Adenoviruses, Human/*genetics/ultrastructure ; Animals ; Cattle ; Cell Line ; Cells, Cultured ; DNA, Mitochondrial/*genetics ; Defective Viruses/genetics/ultrastructure ; Evolution, Molecular ; Gene Transfer Techniques ; Genetic Therapy/adverse effects/methods ; Genetic Vectors/*genetics/ultrastructure ; Humans ; Mice ; Microscopy, Electron, Transmission ; Mitochondria/*genetics/ultrastructure/*virology ; Mitochondrial Diseases/genetics/therapy ; Recombinant Fusion Proteins/genetics ; Vaccines, DNA/genetics ; Virus Diseases/genetics ; }, abstract = {Mitochondrial research has influenced concepts in anthropology, human physiology and pathophysiology. We present here direct evidence that human recombinant viruses can localize in mitochondria to disrupt their integrity. This finding, while opening new perspectives in viral gene therapy, may provide new insights into the pathogenesis, prevention and treatment of viral diseases. In addition, it may advance the current understanding of cell evolution.}, }
@article {pmid18211861, year = {2008}, author = {Olsson, M and Wilson, M and Uller, T and Mott, B and Isaksson, C and Healey, M and Wanger, T}, title = {Free radicals run in lizard families.}, journal = {Biology letters}, volume = {4}, number = {2}, pages = {186-188}, pmid = {18211861}, issn = {1744-9561}, mesh = {Aging/*metabolism ; Animals ; *Biological Evolution ; Carbonyl Cyanide m-Chlorophenyl Hydrazone/metabolism ; Flow Cytometry ; Fluorescent Dyes ; Free Radicals/metabolism ; Lizards/*metabolism ; Mitochondria/metabolism ; Reactive Oxygen Species/*metabolism ; Species Specificity ; }, abstract = {In the ageing individual, the production of reactive oxygen species (ROS) accelerates with cell senescence. Depending on the heritability of the underlying processes that determine net ROS levels, this may influence ageing per se and its evolutionary direction and rate of change. In order to understand the inheritance and evolution of net ROS levels in free-ranging lizards, we used flow cytometry together with ROS-sensitive fluorogenic probes to measure ROS in lizard blood cells. We measured basal levels of (i) non-specific ROS (superoxide, singlet oxygen, H2O2 and peroxynitrite), (ii) superoxide specifically and (iii) superoxide after CCCP treatment, which elevated ROS production in the mitochondria. The cumulative level of non-specific ROS was higher in adults than juveniles and superoxide level showed high heritability and variability among families. We suggest that the evolution of ROS dynamics may be ROS species specific and perhaps depend on the relative degree of uni- or biparental inheritance of ROS main regulatory pathways.}, }
@article {pmid18205982, year = {2008}, author = {Epis, S and Sassera, D and Beninati, T and Lo, N and Beati, L and Piesman, J and Rinaldi, L and McCoy, KD and Torina, A and Sacchi, L and Clementi, E and Genchi, M and Magnino, S and Bandi, C}, title = {Midichloria mitochondrii is widespread in hard ticks (Ixodidae) and resides in the mitochondria of phylogenetically diverse species.}, journal = {Parasitology}, volume = {135}, number = {4}, pages = {485-494}, doi = {10.1017/S0031182007004052}, pmid = {18205982}, issn = {1469-8161}, mesh = {Alphaproteobacteria/genetics/*isolation &amp; purification/ultrastructure ; Animals ; Base Sequence ; DNA, Bacterial/genetics ; DNA, Mitochondrial/genetics ; Ixodes/*microbiology ; Microscopy, Electron, Transmission ; Mitochondria/*microbiology ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Symbiosis ; }, abstract = {The hard tick Ixodes ricinus (Ixodidae) is the sole animal thus far shown to harbour an intra-mitochondrial bacterium, which has recently been named Midichloria mitochondrii. The objectives of this work were (i) to screen ixodid ticks for Midichloria-related bacteria and (ii) to determine whether these bacteria exploit the intra-mitochondrial niche in other tick species. Our main goal was to discover further models of this peculiar form of symbiosis. We have thus performed a PCR screening for Midichloria-related bacteria in samples of ixodid ticks collected in Italy, North America and Iceland. A total of 7 newly examined species from 5 genera were found positive for bacteria closely related to M. mitochondrii. Samples of the tick species Rhipicephalus bursa, found positive in the PCR screening, were analysed with transmission electron microscopy, which revealed the presence of bacteria both in the cytoplasm and in the mitochondria of the oocytes. There is thus evidence that bacteria invade mitochondria in at least 2 tick species. Phylogenetic analysis on the bacterial 16S rRNA gene sequences generated from positive specimens revealed that the bacteria form a monophyletic group within the order Rickettsiales. The phylogeny of Midichloria symbionts and related bacteria does not appear completely congruent with the phylogeny of the hosts.}, }
@article {pmid18202374, year = {2008}, author = {Hamaji, T and Ferris, PJ and Coleman, AW and Waffenschmidt, S and Takahashi, F and Nishii, I and Nozaki, H}, title = {Identification of the minus-dominance gene ortholog in the mating-type locus of Gonium pectorale.}, journal = {Genetics}, volume = {178}, number = {1}, pages = {283-294}, pmid = {18202374}, issn = {0016-6731}, mesh = {Algal Proteins/chemistry/genetics ; Alleles ; Amino Acid Sequence ; Cell Nucleus/metabolism ; Chlorophyta/*genetics ; Conserved Sequence ; Exons/genetics ; Gene Expression Regulation ; *Genes, Dominant ; Genetic Markers ; Inheritance Patterns/genetics ; Introns/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Reproduction ; Sequence Alignment ; *Sequence Homology, Nucleic Acid ; }, abstract = {The evolution of anisogamy/oogamy in the colonial Volvocales might have occurred in an ancestral isogamous colonial organism like Gonium pectorale. The unicellular, close relative Chlamydomonas reinhardtii has a mating-type (MT) locus harboring several mating-type-specific genes, including one involved in mating-type determination and another involved in the function of the tubular mating structure in only one of the two isogametes. In this study, as the first step in identifying the G. pectorale MT locus, we isolated from G. pectorale the ortholog of the C. reinhardtii mating-type-determining minus-dominance (CrMID) gene, which is localized only in the MT- locus. 3'- and 5'-RACE RT-PCR using degenerate primers identified a CrMID-orthologous 164-amino-acid coding gene (GpMID) containing a leucine-zipper RWP-RK domain near the C-terminal, as is the case with CrMID. Genomic Southern blot analysis showed that GpMID was coded only in the minus strain of G. pectorale. RT-PCR revealed that GpMID expression increased during nitrogen starvation. Analysis of F1 progeny suggested that GpMID and isopropylmalate dehydratase LEU1S are tightly linked, suggesting that they are harbored in a chromosomal region under recombinational suppression that is comparable to the C. reinhardtii MT locus. However, two other genes present in the C. reinhardtii MT locus are not linked to the G. pectorale LEU1S/MID, suggesting that the gene content of the volvocalean MT loci is not static over time. Inheritance of chloroplast and mitochondria genomes in G. pectorale is uniparental from the plus and minus parents, respectively, as is also the case in C. reinhardtii.}, }
@article {pmid18199803, year = {2008}, author = {Hu, K and Lin, L and Tan, X and Yang, J and Bu, G and Mars, WM and Liu, Y}, title = {tPA protects renal interstitial fibroblasts and myofibroblasts from apoptosis.}, journal = {Journal of the American Society of Nephrology : JASN}, volume = {19}, number = {3}, pages = {503-514}, pmid = {18199803}, issn = {1533-3450}, support = {R01 DK064005/DK/NIDDK NIH HHS/United States ; R01 DK071040/DK/NIDDK NIH HHS/United States ; DK061408/DK/NIDDK NIH HHS/United States ; R01 DK061408/DK/NIDDK NIH HHS/United States ; DK071040/DK/NIDDK NIH HHS/United States ; DK064005/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Apoptosis/*physiology ; Extracellular Signal-Regulated MAP Kinases/metabolism ; Fibroblasts/*physiology ; Hydrogen Peroxide ; Kidney/*metabolism ; Low Density Lipoprotein Receptor-Related Protein-1 ; MAP Kinase Signaling System/physiology ; Mice ; Mice, Knockout ; Oxidative Stress/physiology ; Phosphorylation ; Receptors, LDL/metabolism ; Ribosomal Protein S6 Kinases, 90-kDa/metabolism ; Staurosporine ; Tissue Plasminogen Activator/*metabolism ; Tumor Suppressor Proteins/metabolism ; bcl-Associated Death Protein/metabolism ; }, abstract = {Activation and expansion of interstitial fibroblasts and myofibroblasts play an essential role in the evolution of renal fibrosis. After obstructive injury, mice lacking tissue-type plasminogen activator (tPA) have fewer myofibroblasts and less interstitial fibrosis than wild-type controls. This suggests that tPA controls the size of the fibroblast/myofibroblast population in vivo, and this study sought to determine the underlying mechanism. In vitro, tPA inhibited staurosporine or H(2)O(2)-induced caspase-3 activation, prevented cellular DNA fragmentation, and suppressed the release of cytochrome C from mitochondria into the cytosol in a rat interstitial fibroblast cell line (NRK-49F). tPA also protected TGF-beta1-activated myofibroblasts from apoptosis. This antiapoptotic effect of tPA was independent of its protease activity but required its membrane receptor, the LDL receptor-related protein 1 (LRP-1). Deletion or knockdown of LRP-1 abolished tPA-mediated cell survival, whereas re-introduction of an LRP-1 minigene in a mouse LRP-1-deficient fibroblast cell line (PEA-13) restored the cytoprotective ability of tPA. tPA triggered a cascade of survival signaling involving extracellular signal-regulated kinase 1/2 (Erk1/2), p90RSK, and phosphorylation of Bad. Blockade of Erk1/2 activation abrogated the antiapoptotic effect of tPA, whereas expression of constitutively active MEK1 promoted cell survival similar to tPA. In vivo, compared with wild-type controls, apoptosis of interstitial myofibroblasts was increased in tPA(-/-) mice after obstructive injury, and myofibroblasts were completely depleted 4 wk after relief of the obstruction. Together, these findings illustrate that tPA is a survival factor that prevents apoptosis of renal interstitial fibroblasts and myofibroblasts through an LRP-1-, Erk1/2-, p90RSK-, and Bad-dependent mechanism.}, }
@article {pmid18197981, year = {2008}, author = {Uddin, M and Opazo, JC and Wildman, DE and Sherwood, CC and Hof, PR and Goodman, M and Grossman, LI}, title = {Molecular evolution of the cytochrome c oxidase subunit 5A gene in primates.}, journal = {BMC evolutionary biology}, volume = {8}, number = {}, pages = {8}, pmid = {18197981}, issn = {1471-2148}, support = {AG14308/AG/NIA NIH HHS/United States ; P30 AG13854/AG/NIA NIH HHS/United States ; R01 DK56927/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Electron Transport Complex IV/*genetics ; *Evolution, Molecular ; Gene Expression Regulation, Enzymologic ; Humans ; Immunohistochemistry ; Mitochondria/enzymology ; Neocortex/enzymology ; Open Reading Frames ; Prefrontal Cortex/enzymology ; Primates/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Species Specificity ; Tissue Distribution ; }, abstract = {BACKGROUND: Many electron transport chain (ETC) genes show accelerated rates of nonsynonymous nucleotide substitutions in anthropoid primate lineages, yet in non-anthropoid lineages the ETC proteins are typically highly conserved. Here, we test the hypothesis that COX5A, the ETC gene that encodes cytochrome c oxidase subunit 5A, shows a pattern of anthropoid-specific adaptive evolution, and investigate the distribution of this protein in catarrhine brains.<br><br>RESULTS: In a dataset comprising 29 vertebrate taxa, including representatives from all major groups of primates, there is nearly 100% conservation of the COX5A amino acid sequence among extant, non-anthropoid placental mammals. The most recent common ancestor of these species lived about 100 million years (MY) ago. In contrast, anthropoid primates show markedly elevated rates of nonsynonymous evolution. In particular, branch site tests identify five positively selected codons in anthropoids, and ancestral reconstructions infer that substitutions in these codons occurred predominantly on stem lineages (anthropoid, ape and New World monkey) and on the human terminal branch. Examination of catarrhine brain samples by immunohistochemistry characterizes for the first time COX5A protein distribution in the primate neocortex, and suggests that the protein is most abundant in the mitochondria of large-size projection neurons. Real time quantitative PCR supports previous microarray results showing COX5A is expressed in cerebral cortical tissue at a higher level in human than in chimpanzee or gorilla.<br><br>CONCLUSION: Taken together, these results suggest that both protein structural and gene regulatory changes contributed to COX5A evolution during humankind's ancestry. Furthermore, these findings are consistent with the hypothesis that adaptations in ETC genes contributed to the emergence of the energetically expensive anthropoid neocortex.}, }
@article {pmid18192190, year = {2008}, author = {Boore, JL and Fuerstenberg, SI}, title = {Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {363}, number = {1496}, pages = {1445-1451}, pmid = {18192190}, issn = {0962-8436}, mesh = {Animals ; DNA/genetics ; Evolution, Molecular ; Genome, Mitochondrial ; Genomics/*methods ; *Phylogeny ; Sequence Alignment ; }, abstract = {The first whole genomes to be compared for phylogenetic inference were those of mitochondria, which provided the first sets of genome-level characters for phylogenetic reconstruction. Most powerful among these characters has been the comparisons of the relative arrangements of genes, which has convincingly resolved numerous branch points, including those that had remained recalcitrant even to very large molecular sequence comparisons. Now the world faces a tsunami of complete nuclear genome sequences. In addition to the tremendous amount of DNA sequence that is becoming available for comparison, there is also a potential for many more genome-level characters to be developed, including the relative positions of introns, the domain structures of proteins, gene family membership, the presence of particular biochemical pathways, aspects of DNA replication or transcription, and many others. These characters can be especially convincing owing to their low likelihood of reverting to a primitive condition or occurring independently in separate lineages, thereby reducing the occurrence of homoplasy. The comparisons of organelle genomes pioneered the way for using such features for phylogenetic reconstructions, and it is almost certainly true, as ever more genomic sequence becomes available, that further use of genome-level characters will play a big role in outlining the relationships among major animal groups.}, }
@article {pmid18187503, year = {2008}, author = {Cymerman, IA and Chung, I and Beckmann, BM and Bujnicki, JM and Meiss, G}, title = {EXOG, a novel paralog of Endonuclease G in higher eukaryotes.}, journal = {Nucleic acids research}, volume = {36}, number = {4}, pages = {1369-1379}, pmid = {18187503}, issn = {1362-4962}, support = {R33 CA097899/CA/NCI NIH HHS/United States ; 1R33CA97899-01A/CA/NCI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Catalytic Domain ; Cell Line ; Dimerization ; Endodeoxyribonucleases/chemistry ; Endonucleases/*chemistry/genetics/metabolism ; Exonucleases/metabolism ; Histidine/genetics ; Humans ; Hydrophobic and Hydrophilic Interactions ; Mitochondrial Membranes/*enzymology ; Mitochondrial Proteins/*chemistry/genetics/metabolism ; Molecular Sequence Data ; Mutation ; Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Alignment ; Substrate Specificity ; }, abstract = {Evolutionary conserved mitochondrial nucleases are involved in programmed cell death and normal cell proliferation in lower and higher eukaryotes. The endo/exonuclease Nuc1p, also termed 'yeast Endonuclease G (EndoG)', is a member of this class of enzymes that differs from mammalian homologs by the presence of a 5'-3' exonuclease activity in addition to its broad spectrum endonuclease activity. However, this exonuclease activity is thought to be essential for a function of the yeast enzyme in DNA recombination and repair. Here we show that higher eukaryotes in addition to EndoG contain its paralog 'EXOG', a novel EndoG-like mitochondrial endo/exonuclease. We find that during metazoan evolution duplication of an ancestral nuclease gene obviously generated the paralogous EndoG- and EXOG-protein subfamilies in higher eukaryotes, thereby maintaining the full endo/exonuclease activity found in mitochondria of lower eukaryotes. We demonstrate that human EXOG is a dimeric mitochondrial enzyme that displays 5'-3' exonuclease activity and further differs from EndoG in substrate specificity. We hypothesize that in higher eukaryotes the complementary enzymatic activities of EndoG and EXOG probably together account for both, the lethal and vital functions of conserved mitochondrial endo/exonucleases.}, }
@article {pmid18183306, year = {2008}, author = {Kroth, PG and Chiovitti, A and Gruber, A and Martin-Jezequel, V and Mock, T and Parker, MS and Stanley, MS and Kaplan, A and Caron, L and Weber, T and Maheswari, U and Armbrust, EV and Bowler, C}, title = {A model for carbohydrate metabolism in the diatom Phaeodactylum tricornutum deduced from comparative whole genome analysis.}, journal = {PloS one}, volume = {3}, number = {1}, pages = {e1426}, pmid = {18183306}, issn = {1932-6203}, support = {P50 ES012762/ES/NIEHS NIH HHS/United States ; }, mesh = {*Carbohydrate Metabolism ; Carbon Dioxide/metabolism ; Diatoms/*metabolism ; *Genome ; *Models, Biological ; }, abstract = {BACKGROUND: Diatoms are unicellular algae responsible for approximately 20% of global carbon fixation. Their evolution by secondary endocytobiosis resulted in a complex cellular structure and metabolism compared to algae with primary plastids.<br><br>The whole genome sequence of the diatom Phaeodactylum tricornutum has recently been completed. We identified and annotated genes for enzymes involved in carbohydrate pathways based on extensive EST support and comparison to the whole genome sequence of a second diatom, Thalassiosira pseudonana. Protein localization to mitochondria was predicted based on identified similarities to mitochondrial localization motifs in other eukaryotes, whereas protein localization to plastids was based on the presence of signal peptide motifs in combination with plastid localization motifs previously shown to be required in diatoms. We identified genes potentially involved in a C4-like photosynthesis in P. tricornutum and, on the basis of sequence-based putative localization of relevant proteins, discuss possible differences in carbon concentrating mechanisms and CO(2) fixation between the two diatoms. We also identified genes encoding enzymes involved in photorespiration with one interesting exception: glycerate kinase was not found in either P. tricornutum or T. pseudonana. Various Calvin cycle enzymes were found in up to five different isoforms, distributed between plastids, mitochondria and the cytosol. Diatoms store energy either as lipids or as chrysolaminaran (a beta-1,3-glucan) outside of the plastids. We identified various beta-glucanases and large membrane-bound glucan synthases. Interestingly most of the glucanases appear to contain C-terminal anchor domains that may attach the enzymes to membranes.<br><br>CONCLUSIONS/SIGNIFICANCE: Here we present a detailed synthesis of carbohydrate metabolism in diatoms based on the genome sequences of Thalassiosira pseudonana and Phaeodactylum tricornutum. This model provides novel insights into acquisition of dissolved inorganic carbon and primary metabolic pathways of carbon in two different diatoms, which is of significance for an improved understanding of global carbon cycles.}, }
@article {pmid18179429, year = {2008}, author = {Cameron, EK and Bayne, EM and Coltman, DW}, title = {Genetic structure of invasive earthworms Dendrobaena octaedra in the boreal forest of Alberta: insights into introduction mechanisms.}, journal = {Molecular ecology}, volume = {17}, number = {5}, pages = {1189-1197}, doi = {10.1111/j.1365-294X.2007.03603.x}, pmid = {18179429}, issn = {1365-294X}, mesh = {Alberta ; Animals ; Base Sequence ; Genetic Variation ; Geography ; Haplotypes ; Mitochondria/genetics ; Molecular Sequence Data ; Oligochaeta/*genetics ; *Trees ; }, abstract = {Population genetic studies can help to determine whether invasive species are established via single vs. multiple introduction events and also to distinguish among various colonization scenarios. We used this approach to investigate the introduction of Dendrobaena octaedra, a non-native earthworm species, to the boreal forest of northern Alberta. The spread of non-native earthworms in forested systems is not well understood, although bait abandonment and vehicular transport are believed to be important. Mitochondrial DNA sequencing revealed that multiple introductions of this species have occurred in northern Alberta, although individual populations may have been established by either single or multiple invaders introduced on one or more occasions. There was no relationship between genetic distances and either geographical distances or distances along road networks, suggesting that human-mediated jump dispersal is more common than diffusive spread via road networks or via active dispersal. As well, genetic diversity was significantly greater at boat launches than roads, indicating that multiple introductions may be more likely to occur at those locations. Focusing management efforts on areas where multiple introductions are likely to occur may help to reduce invasive species' potential for adaptive evolution and subsequent rapid spread.}, }
@article {pmid18179422, year = {2008}, author = {Scocca, JR and Shapiro, TA}, title = {A mitochondrial topoisomerase IA essential for late theta structure resolution in African trypanosomes.}, journal = {Molecular microbiology}, volume = {67}, number = {4}, pages = {820-829}, doi = {10.1111/j.1365-2958.2007.06087.x}, pmid = {18179422}, issn = {0950-382X}, support = {R01 AI028855/AI/NIAID NIH HHS/United States ; R01AI28855/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; DNA Topoisomerases, Type I/genetics/*metabolism ; DNA, Kinetoplast/*chemistry/*metabolism ; Mitochondria/*enzymology/metabolism ; Phylogeny ; RNA Interference ; Trypanosoma brucei brucei/cytology/enzymology/*genetics/metabolism ; }, abstract = {Trypanosomes and Leishmania, protozoans that cause major human diseases, have a topologically intricate mitochondrial DNA (kinetoplast or kDNA) in the form of a network of thousands of interlocked circles. This unusual system provides a useful reporter for studying topoisomerase functions in vivo. We now find that these organisms have three type IA topoisomerases, one of which is phylogenetically distinctive and which we designate topoisomerase IA(mt). In Trypanosoma brucei topoisomerase IA(mt) immunolocalizes within the mitochondrion close to the kDNA disk in patterns that vary with the cell cycle. When expression of TOPIA(mt) is silenced by RNAi there is a striking accumulation of kDNA late theta structure replication intermediates, with subsequent loss of kDNA networks and halt in cell growth. This essential enzyme provides clear molecular evidence for the obligatory role of a type IA enzyme in the resolution of late theta structures in vivo. With no close orthologue in humans it also offers a target for the rational development of selectively toxic new antiprotozoal therapies.}, }
@article {pmid18178670, year = {2008}, author = {Avisar, D and Prokhnevsky, AI and Makarova, KS and Koonin, EV and Dolja, VV}, title = {Myosin XI-K Is required for rapid trafficking of Golgi stacks, peroxisomes, and mitochondria in leaf cells of Nicotiana benthamiana.}, journal = {Plant physiology}, volume = {146}, number = {3}, pages = {1098-1108}, pmid = {18178670}, issn = {0032-0889}, support = {GM 053190/GM/NIGMS NIH HHS/United States ; }, mesh = {Actins/metabolism ; DNA, Complementary ; Eukaryota/genetics ; Light ; Molecular Sequence Data ; Movement/*physiology ; Myosins/genetics/*metabolism ; Organelles/*physiology ; Phylogeny ; Plant Leaves/*physiology ; RNA Interference ; Nicotiana/*metabolism/physiology ; }, abstract = {A prominent feature of plant cells is the rapid, incessant movement of the organelles traditionally defined as cytoplasmic streaming and attributed to actomyosin motility. We sequenced six complete Nicotiana benthamiana cDNAs that encode class XI and class VIII myosins. Phylogenetic analysis indicates that these two classes of myosins diverged prior to the radiation of green algae and land plants from a common ancestor and that the common ancestor of land plants likely possessed at least seven myosins. We further report here that movement of Golgi stacks, mitochondria, and peroxisomes in the leaf cells of N. benthamiana is mediated mainly by myosin XI-K. Suppression of myosin XI-K function using dominant negative inhibition or RNA interference dramatically reduced movement of each of these organelles. When similar approaches were used to inhibit functions of myosin XI-2 or XI-F, only moderate to marginal effects were observed. Organelle trafficking was virtually unaffected in response to inhibition of each of the three class VIII myosins. Interestingly, none of the tested six myosins appears to be involved in light-induced movements of chloroplasts. Taken together, these data strongly suggest that myosin XI-K has a major role in trafficking of Golgi stacks, mitochondria, and peroxisomes, whereas myosins XI-2 and XI-F might perform accessory functions in this process. In addition, our analysis of thousands of individual organelles revealed independent movement patterns for Golgi stacks, mitochondria, and peroxisomes, indicating that the notion of coordinated cytoplasmic streaming is not generally applicable to higher plants.}, }
@article {pmid18167542, year = {2008}, author = {Hampl, V and Silberman, JD and Stechmann, A and Diaz-Triviño, S and Johnson, PJ and Roger, AJ}, title = {Genetic evidence for a mitochondriate ancestry in the 'amitochondriate' flagellate Trimastix pyriformis.}, journal = {PloS one}, volume = {3}, number = {1}, pages = {e1383}, pmid = {18167542}, issn = {1932-6203}, mesh = {Amino Acid Sequence ; Amino Acids/metabolism ; Animals ; DNA, Mitochondrial/*genetics ; Energy Metabolism ; Eukaryota/classification/*genetics/metabolism ; Expressed Sequence Tags ; Molecular Sequence Data ; Phylogeny ; Protein Transport ; Sequence Homology, Amino Acid ; }, abstract = {Most modern eukaryotes diverged from a common ancestor that contained the alpha-proteobacterial endosymbiont that gave rise to mitochondria. The 'amitochondriate' anaerobic protist parasites that have been studied to date, such as Giardia and Trichomonas harbor mitochondrion-related organelles, such as mitosomes or hydrogenosomes. Yet there is one remaining group of mitochondrion-lacking flagellates known as the Preaxostyla that could represent a primitive 'pre-mitochondrial' lineage of eukaryotes. To test this hypothesis, we conducted an expressed sequence tag (EST) survey on the preaxostylid flagellate Trimastix pyriformis, a poorly-studied free-living anaerobe. Among the ESTs we detected 19 proteins that, in other eukaryotes, typically function in mitochondria, hydrogenosomes or mitosomes, 12 of which are found exclusively within these organelles. Interestingly, one of the proteins, aconitase, functions in the tricarboxylic acid cycle typical of aerobic mitochondria, whereas others, such as pyruvate:ferredoxin oxidoreductase and [FeFe] hydrogenase, are characteristic of anaerobic hydrogenosomes. Since Trimastix retains genetic evidence of a mitochondriate ancestry, we can now say definitively that all known living eukaryote lineages descend from a common ancestor that had mitochondria.}, }
@article {pmid18160177, year = {2008}, author = {Röhlk, C and Rohlfs, M and Leier, S and Schliwa, M and Liu, X and Parsch, J and Woehlke, G}, title = {Properties of the Kinesin-1 motor DdKif3 from Dictyostelium discoideum.}, journal = {European journal of cell biology}, volume = {87}, number = {4}, pages = {237-249}, doi = {10.1016/j.ejcb.2007.11.001}, pmid = {18160177}, issn = {0171-9335}, mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Dictyostelium/genetics/*metabolism ; Escherichia coli ; Kinesins/chemistry/genetics/*metabolism ; Microtubules/metabolism ; Molecular Motor Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Protein Structure, Tertiary ; Protozoan Proteins/genetics/*metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {The amoeba Dictyostelium discoideum possesses genes for 13 different kinesins. Here we characterize DdKif3, a member of the Kinesin-1 family. Kinesin-1 motors form homodimers that can move micrometer-long distances on microtubules using the energy derived from ATP hydrolysis. We expressed recombinant motors in Escherichia coli and tested them in different in vitro assays. Full-length and truncated Kif3 motors were active in gliding and ATPase assays. They showed a strong dependence on ionic strength. Like the full-length motor, the truncated DdKif3-592 motor (aa 1-592; comprising motor domain, neck, and partial stalk) reached its maximum speed of around 2.0micrcom s(-1) at a potassium acetate concentration of 200mM. The shortened DdKif3-342 motor (aa 1-342; comprising motor domain, partial neck) showed a high ATP turnover, comparable to that of the fungal Kinesin-1, Nkin. Results from the duty cycle calculations and gliding assays indicate that DdKif3 is a processive motor. A GFP-fusion protein revealed a mainly cytoplasmic localization of DdKif3. Immunofluorescence staining makes an association with the endoplasmic reticulum or mitochondria unlikely. Despite a similar phylogenetic distance to both metazoa and fungi, in terms of its biochemical properties DdKif3 revealed a closer similarity to fungal than animal kinesins.}, }
@article {pmid18157077, year = {2007}, author = {Sanchez, S and Hourdez, S and Lallier, FH}, title = {[Chemoautotrophic endosymbioses: contemporary models for symbiogenesis?].}, journal = {Journal de la Societe de biologie}, volume = {201}, number = {3}, pages = {247-257}, doi = {10.1051/jbio:2007036}, pmid = {18157077}, issn = {1295-0661}, mesh = {Animals ; Biological Evolution ; Cyanobacteria/physiology ; Earth, Planet ; Eukaryotic Cells/physiology ; Geography ; Models, Biological ; Photosynthesis ; Symbiosis/*physiology ; Time ; }, abstract = {Oxygen appears to be one of the key factors in understanding the evolution of life on Earth. Almost absent during more than 2 billion years, its subsequent increase is correlated with the emergence of oxygenic photosynthesis by Cyanobacteria, followed by aerobic Prokaryotes and eventually Eukaryotes, all primitively aerobic, and more recently, the development of complex multicellular organisms. However, in some reduced environments, still present at the surface of the Earth and even more so in ocean depths (hydrothermal vents, cold seeps, massive organic falls,...), anaerobic or micro-aerobic Prokaryotes continue to grow, including some chemoautotrophic bacteria deriving energy from sulfide oxidation for instance. A few Metazoa have managed to collaborate with such chemoautotroph Prokaryotes, the most abundant species forming endosymbiotic associations. The most studied of these endosymbioses (the mussels Bathymodiolus, the vestimentiferan tubeworm Riftia pachyptila, or the clams Calyptogena) have revealed important differences in the degree of interdependence between host and symbionts, and in the mode of symbiont transmission. The evolutive process of these symbioses is reminiscent of the primary endosymbioses which have given rise to the organelles of heterotrophic Eukaryotes (mitochondria) and phototrophic Eukaryotes (chloroplasts). The study of these modern days biological models could shed light on symbiogenesis itself and also potentially reveal thiotrophic Eukaryotes as a new lineage.}, }
@article {pmid18097445, year = {2008}, author = {Youle, RJ and Strasser, A}, title = {The BCL-2 protein family: opposing activities that mediate cell death.}, journal = {Nature reviews. Molecular cell biology}, volume = {9}, number = {1}, pages = {47-59}, doi = {10.1038/nrm2308}, pmid = {18097445}, issn = {1471-0080}, mesh = {Animals ; Apoptosis/*physiology ; Humans ; Mitochondria/physiology ; Models, Molecular ; Phylogeny ; Protein Structure, Tertiary/physiology ; Proto-Oncogene Proteins c-bcl-2/*physiology ; }, abstract = {BCL-2 family proteins, which have either pro- or anti-apoptotic activities, have been studied intensively for the past decade owing to their importance in the regulation of apoptosis, tumorigenesis and cellular responses to anti-cancer therapy. They control the point of no return for clonogenic cell survival and thereby affect tumorigenesis and host-pathogen interactions and regulate animal development. Recent structural, phylogenetic and biological analyses, however, suggest the need for some reconsideration of the accepted organizational principles of the family and how the family members interact with one another during programmed cell death. Although these insights into interactions among BCL-2 family proteins reveal how these proteins are regulated, a unifying hypothesis for the mechanisms they use to activate caspases remains elusive.}, }
@article {pmid18096186, year = {2008}, author = {Mohr, G and Del Campo, M and Mohr, S and Yang, Q and Jia, H and Jankowsky, E and Lambowitz, AM}, title = {Function of the C-terminal domain of the DEAD-box protein Mss116p analyzed in vivo and in vitro.}, journal = {Journal of molecular biology}, volume = {375}, number = {5}, pages = {1344-1364}, pmid = {18096186}, issn = {1089-8638}, support = {F32 GM076961-02/GM/NIGMS NIH HHS/United States ; F32 GM76961/GM/NIGMS NIH HHS/United States ; R37 GM037951/GM/NIGMS NIH HHS/United States ; R01 GM037951/GM/NIGMS NIH HHS/United States ; R01 GM067700/GM/NIGMS NIH HHS/United States ; R01 GM037951-23/GM/NIGMS NIH HHS/United States ; F32 GM076961/GM/NIGMS NIH HHS/United States ; R01 GM06770/GM/NIGMS NIH HHS/United States ; R01 GM067700-05/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphatases/antagonists &amp; inhibitors/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Amino Acids, Basic/chemistry ; Binding Sites ; Computational Biology/methods ; Conserved Sequence ; Crystallography, X-Ray ; DEAD-box RNA Helicases/*chemistry/genetics/isolation &amp; purification/metabolism ; Drosophila Proteins/chemistry ; Escherichia coli/genetics ; Evolution, Molecular ; Gene Silencing ; Genetic Complementation Test ; Hydrophobic and Hydrophilic Interactions ; In Vitro Techniques ; Introns ; Isoelectric Point ; Kinetics ; Mitochondria/metabolism ; Molecular Chaperones/metabolism ; Molecular Sequence Data ; Mutation, Missense ; Plasmids ; Protein Binding ; Protein Biosynthesis ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA/metabolism ; RNA Splicing ; RNA, Catalytic/metabolism ; RNA, Fungal/metabolism ; Saccharomyces cerevisiae/chemistry/genetics/metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/isolation &amp; purification/metabolism ; Sequence Homology, Amino Acid ; Temperature ; }, abstract = {The DEAD-box proteins CYT-19 in Neurospora crassa and Mss116p in Saccharomyces cerevisiae are general RNA chaperones that function in splicing mitochondrial group I and group II introns and in translational activation. Both proteins consist of a conserved ATP-dependent RNA helicase core region linked to N and C-terminal domains, the latter with a basic tail similar to many other DEAD-box proteins. In CYT-19, this basic tail was shown to contribute to non-specific RNA binding that helps tether the core helicase region to structured RNA substrates. Here, multiple sequence alignments and secondary structure predictions indicate that CYT-19 and Mss116p belong to distinct subgroups of DEAD-box proteins, whose C-terminal domains have a defining extended alpha-helical region preceding the basic tail. We find that mutations or C-terminal truncations in the predicted alpha-helical region of Mss116p strongly inhibit RNA-dependent ATPase activity, leading to loss of function in both translational activation and RNA splicing. These findings suggest that the alpha-helical region may stabilize and/or regulate the activity of the RNA helicase core. By contrast, a truncation that removes only the basic tail leaves high RNA-dependent ATPase activity and causes only a modest reduction in translation and RNA splicing efficiency in vivo and in vitro. Biochemical analysis shows that deletion of the basic tail leads to weaker non-specific binding of group I and group II intron RNAs, and surprisingly, also impairs RNA-unwinding at saturating protein concentrations and nucleotide-dependent tight binding of single-stranded RNAs by the RNA helicase core. Together, our results indicate that the two sub-regions of Mss116p's C-terminal domain act in different ways to support and modulate activities of the core helicase region, whose RNA-unwinding activity is critical for both the translation and RNA splicing functions.}, }
@article {pmid18081717, year = {2008}, author = {Ellison, CK and Burton, RS}, title = {Interpopulation hybrid breakdown maps to the mitochondrial genome.}, journal = {Evolution; international journal of organic evolution}, volume = {62}, number = {3}, pages = {631-638}, doi = {10.1111/j.1558-5646.2007.00305.x}, pmid = {18081717}, issn = {0014-3820}, mesh = {Adenosine Triphosphate/biosynthesis ; Analysis of Variance ; Animals ; Copepoda/*genetics ; Crosses, Genetic ; DNA, Mitochondrial/*genetics ; *Epistasis, Genetic ; *Genetics, Population ; *Hybridization, Genetic ; }, abstract = {Hybrid breakdown, or outbreeding depression, is the loss of fitness observed in crosses between genetically divergent populations. The role of maternally inherited mitochondrial genomes in hybrid breakdown has not been widely examined. Using laboratory crosses of the marine copepod Tigriopus californicus, we report that the low fitness of F(3) hybrids is completely restored in the offspring of maternal backcrosses, where parental mitochondrial and nuclear genomic combinations are reassembled. Paternal backcrosses, which result in mismatched mitochondrial and nuclear genomes, fail to restore hybrid fitness. These results suggest that fitness loss in T. californicus hybrids is completely attributable to nuclear-mitochondrial genomic interactions. Analyses of ATP synthetic capacity in isolated mitochondria from hybrid and backcross animals found that reduced ATP synthesis in hybrids was also largely restored in backcrosses, again with maternal backcrosses outperforming paternal backcrosses. The strong fitness consequences of nuclear-mitochondrial interactions have important, and often overlooked, implications for evolutionary and conservation biology.}, }
@article {pmid18078956, year = {2008}, author = {Williams, BA and Haferkamp, I and Keeling, PJ}, title = {An ADP/ATP-specific mitochondrial carrier protein in the microsporidian Antonospora locustae.}, journal = {Journal of molecular biology}, volume = {375}, number = {5}, pages = {1249-1257}, doi = {10.1016/j.jmb.2007.11.005}, pmid = {18078956}, issn = {1089-8638}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Base Sequence ; Escherichia coli/genetics ; Green Fluorescent Proteins/metabolism ; Membrane Transport Proteins/*genetics/metabolism ; Microsporidia/*genetics/metabolism ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/chemistry/*genetics/metabolism ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/metabolism ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {The mitochondrion is one of the defining characteristics of eukaryotic cells, and to date, no eukaryotic lineage has been shown to have lost mitochondria entirely. In certain anaerobic or microaerophilic lineages, however, the mitochondrion has become severely reduced that it lacks a genome and no longer synthesizes ATP. One example of such a reduced organelle, called the mitosome, is found in microsporidian parasites. Only a handful of potential mitosomal proteins were found to be encoded in the complete genome of the microsporidian Encephalitozoon cuniculi, and significantly no proteins of the mitochondrial carrier family were identified. These carriers facilitate the transport of solutes across the inner mitochondrial membrane, are a means of communication between the mitochondrion and cytosol, and are abundant in organisms with aerobic mitochondria. Here, we report the characterization of a mitochondrial carrier protein in the microsporidian Antonospora locustae and demonstrate that the protein is heterologously targeted to mitochondria in Saccharomyces cerevisiae. The protein is phylogenetically allied to the NAD(+) transporter of S. cerevisiae, but we show that it has high specificity for ATP and ADP when expressed in Escherichia coli. An ADP/ATP carrier may provide ATP for essential ATP-dependent mitosomal processes such as Hsp70-dependent protein import and export of iron-sulfur clusters to the cytosol.}, }
@article {pmid18075112, year = {2007}, author = {Iwahashi, H and Ishidou, E and Kitagawa, E and Momose, Y}, title = {Combined cadmium and thiuram show synergistic toxicity and induce mitochondrial petite mutants.}, journal = {Environmental science &amp; technology}, volume = {41}, number = {22}, pages = {7941-7946}, doi = {10.1021/es071313y}, pmid = {18075112}, issn = {0013-936X}, mesh = {Biological Assay ; Cadmium/*analysis/chemistry ; Cluster Analysis ; DNA, Mitochondrial/chemistry ; Dose-Response Relationship, Drug ; *Gene Expression Profiling ; Mitochondria/*metabolism ; *Mutation ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; Phylogeny ; RNA, Messenger/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Saccharomyces cerevisiae/genetics ; Thiram/*analysis ; }, abstract = {A bioassay is a system for monitoring toxicity of chemicals in the environment via the biological responses of experimental organisms. These responses can be detected by analysis of genome-wide changes in mRNA expression levels using DNA microarrays. We applied this system for evaluation of synergistic toxicity by cadmium and thiuram, as this combination showed mutual growth inhibition in yeast. Hierarchical cluster analysis using mRNA expression profiles suggested the response of yeast to this combination is similar to that seen with cadmium treatment alone. Functional characterization of genes induced by this combinational treatment also suggests that the toxicity of cadmium was enhanced. This toxicity was observed as the damage to mitochondrial functions, which were not observed with either cadmium or thiuram treatments alone. The potential toxicity to mitochondria by this combinational treatment was confirmed as the result of deletion of mitochondria with petite colony formation frequency. We could evaluate synergistic toxicity by cadmium and thiuram and show the possible use of transcriptome bioassay for synergistic toxicity.}, }
@article {pmid18074191, year = {2008}, author = {Zhang, SW and Zhang, YL and Yang, HF and Zhao, CH and Pan, Q}, title = {Using the concept of Chou's pseudo amino acid composition to predict protein subcellular localization: an approach by incorporating evolutionary information and von Neumann entropies.}, journal = {Amino acids}, volume = {34}, number = {4}, pages = {565-572}, doi = {10.1007/s00726-007-0010-9}, pmid = {18074191}, issn = {1438-2199}, mesh = {Algorithms ; Amino Acid Sequence ; Amino Acids/*chemistry ; Computational Biology/*methods ; Computer Simulation ; Databases, Protein ; *Entropy ; Evolution, Molecular ; Intracellular Space/chemistry ; Proteins/*chemistry ; Sequence Analysis, Protein ; }, abstract = {The rapidly increasing number of sequence entering into the genome databank has called for the need for developing automated methods to analyze them. Information on the subcellular localization of new found protein sequences is important for helping to reveal their functions in time and conducting the study of system biology at the cellular level. Based on the concept of Chou's pseudo-amino acid composition, a series of useful information and techniques, such as residue conservation scores, von Neumann entropies, multi-scale energy, and weighted auto-correlation function were utilized to generate the pseudo-amino acid components for representing the protein samples. Based on such an infrastructure, a hybridization predictor was developed for identifying uncharacterized proteins among the following 12 subcellular localizations: chloroplast, cytoplasm, cytoskeleton, endoplasmic reticulum, extracell, Golgi apparatus, lysosome, mitochondria, nucleus, peroxisome, plasma membrane, and vacuole. Compared with the results reported by the previous investigators, higher success rates were obtained, suggesting that the current approach is quite promising, and may become a useful high-throughput tool in the relevant areas.}, }
@article {pmid18073380, year = {2008}, author = {Nikoh, N and Tanaka, K and Shibata, F and Kondo, N and Hizume, M and Shimada, M and Fukatsu, T}, title = {Wolbachia genome integrated in an insect chromosome: evolution and fate of laterally transferred endosymbiont genes.}, journal = {Genome research}, volume = {18}, number = {2}, pages = {272-280}, pmid = {18073380}, issn = {1088-9051}, mesh = {Animals ; Base Sequence ; Blotting, Southern ; Chromosome Mapping ; Chromosomes/*genetics ; Coleoptera/genetics/*microbiology ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genome/*genetics ; In Situ Hybridization, Fluorescence ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Pseudogenes/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; *Symbiosis ; Wolbachia/*genetics ; }, abstract = {Recent accumulation of microbial genome data has demonstrated that lateral gene transfers constitute an important and universal evolutionary process in prokaryotes, while those in multicellular eukaryotes are still regarded as unusual, except for endosymbiotic gene transfers from mitochondria and plastids. Here we thoroughly investigated the bacterial genes derived from a Wolbachia endosymbiont on the nuclear genome of the beetle Callosobruchus chinensis. Exhaustive PCR detection and Southern blot analysis suggested that approximately 30% of Wolbachia genes, in terms of the gene repertoire of wMel, are present on the insect nuclear genome. Fluorescent in situ hybridization located the transferred genes on the proximal region of the basal short arm of the X chromosome. Molecular evolutionary and other lines of evidence indicated that the transferred genes are probably derived from a single lateral transfer event. The transferred genes were, for the length examined, structurally disrupted, freed from functional constraints, and transcriptionally inactive. Hence, most, if not all, of the transferred genes have been pseudogenized. Notwithstanding this, the transferred genes were ubiquitously detected from Japanese and Taiwanese populations of C. chinensis, while the number of the transferred genes detected differed between the populations. The transferred genes were not detected from congenic beetle species, indicating that the transfer event occurred after speciation of C. chinensis, which was estimated to be one or several million years ago. These features of the laterally transferred endosymbiont genes are compared with the evolutionary patterns of mitochondrial and plastid genome fragments acquired by nuclear genomes through recent endosymbiotic gene transfers.}, }
@article {pmid18056078, year = {2008}, author = {Haque, ME and Grasso, D and Spremulli, LL}, title = {The interaction of mammalian mitochondrial translational initiation factor 3 with ribosomes: evolution of terminal extensions in IF3mt.}, journal = {Nucleic acids research}, volume = {36}, number = {2}, pages = {589-597}, pmid = {18056078}, issn = {1362-4962}, support = {R01 GM032734/GM/NIGMS NIH HHS/United States ; GM 32734/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cattle ; Eukaryotic Initiation Factors/*chemistry/genetics/*metabolism ; Evolution, Molecular ; Guanosine Triphosphate/analogs &amp; derivatives/metabolism ; Humans ; Kinetics ; Mitochondria/genetics ; Mitochondrial Proteins/*chemistry/genetics/*metabolism ; Prokaryotic Initiation Factor-3/chemistry ; Protein Binding ; RNA, Transfer, Met/metabolism ; Ribosome Subunits, Large, Eukaryotic/*metabolism ; Ribosome Subunits, Small, Eukaryotic/*metabolism ; Sequence Deletion ; Surface Plasmon Resonance ; }, abstract = {Mammalian mitochondrial initiation factor 3 (IF3(mt)) has a central region with homology to bacterial IF3. This homology region is preceded by an N-terminal extension and followed by a C-terminal extension. The role of these extensions on the binding of IF3(mt) to mitochondrial small ribosomal subunits (28S) was studied using derivatives in which the extensions had been deleted. The K(d) for the binding of IF3(mt) to 28S subunits is approximately 30 nM. Removal of either the N- or C-terminal extension has almost no effect on this value. IF3(mt) has very weak interactions with the large subunit of the mitochondrial ribosome (39S) (K(d) = 1.5 muM). However, deletion of the extensions results in derivatives with significant affinity for 39S subunits (K(d) = 0.12-0.25 muM). IF3(mt) does not bind 55S monosomes, while the deletion derivative binds slightly to these particles. IF3(mt) is very effective in dissociating 55S ribosomes. Removal of the N-terminal extension has little effect on this activity. However, removal of the C-terminal extension leads to a complex dissociation pattern due to the high affinity of this derivative for 39S subunits. These data suggest that the extensions have evolved to ensure the proper dissociation of IF3(mt) from the 28S subunits upon 39S subunit joining.}, }
@article {pmid18054044, year = {2008}, author = {Uyttewaal, M and Mireau, H and Rurek, M and Hammani, K and Arnal, N and Quadrado, M and Giegé, P}, title = {PPR336 is associated with polysomes in plant mitochondria.}, journal = {Journal of molecular biology}, volume = {375}, number = {3}, pages = {626-636}, doi = {10.1016/j.jmb.2007.11.011}, pmid = {18054044}, issn = {1089-8638}, mesh = {Amino Acid Motifs ; Amino Acid Substitution ; Arabidopsis/cytology/genetics/metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Binding Sites ; Escherichia coli/genetics ; Homozygote ; Mitochondria/*metabolism ; Mitochondrial Membranes/chemistry ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Molecular Weight ; Phylogeny ; Plant Proteins/*metabolism ; Polyribosomes/*metabolism ; Protein Binding ; Repetitive Sequences, Amino Acid/genetics ; }, abstract = {The function of pentatricopeptide repeat (PPR) proteins has been associated with various post-transcriptional steps of organelle gene expression. Among them, translation and its regulation are essential processes. However, in plant mitochondria, they are also the steps of gene expression that are the least understood. In this study, PPR336 was identified as part of a high-molecular-weight complex in Arabidopsis mitochondria. PPR336 is an unusual representative of the large PPR family because it is relatively short and is characterised by a high expression level compared with other PPR proteins. PPR336 defines a small subgroup of eight class P PPR proteins that are similar in terms of motif organization. Among them, PPR336-like is the closest homolog of PPR336. Biochemical analysis has indicated that PPR336 is a strictly mitochondrial protein, extrinsically attached to the inner mitochondrial membrane and part of an RNase-sensitive complex. Sucrose gradients and polysome destabilisation experiments show that PPR336 is associated with ribosomes in plant mitochondria. Moreover, in Ppr336/336-like mutants, mitochondrial polysomes of lower molecular weight accumulate compared with wild-type plants. Polysome association and these unusual features suggest that PPR336 could be involved in a distinctive process, possibly translation in plant mitochondria.}, }
@article {pmid18048402, year = {2008}, author = {Jia, W and Higgs, PG}, title = {Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection.}, journal = {Molecular biology and evolution}, volume = {25}, number = {2}, pages = {339-351}, doi = {10.1093/molbev/msm259}, pmid = {18048402}, issn = {1537-1719}, mesh = {Animals ; Codon/*genetics ; *Evolution, Molecular ; *Genetic Code ; *Genetic Variation ; *Genome, Mitochondrial ; Mutation/genetics ; Open Reading Frames/genetics ; }, abstract = {We analyze the frequencies of synonymous codons in animal mitochondrial genomes, focusing particularly on mammals and fish. The frequencies of bases at 4-fold degenerate sites are found to be strongly influenced by context-dependent mutation, which causes correlations between pairs of neighboring bases. There is a pattern of excess of certain dinucleotides and deficit of others that is consistent across large numbers of species, despite the wide variation of single-nucleotide frequencies among species. In many bacteria, translational selection is an important influence on codon usage. In order to test whether translational selection also plays a role in mitochondria, we need to control for context-dependent mutation. Selection for translational accuracy can be detected by comparison of codon usage in conserved and variable sites in the same genes. We give a test of this type that works in the presence of context-dependent mutation. There is very little evidence for translational accuracy selection in the mitochondrial genes considered here. Selection for translational efficiency might lead to preference for codons that match the limited repertoire of anticodons on the mitochondrial tRNAs. This is difficult to detect because the effect would usually be in the same direction in comparable to codon families and so would not cause an observable difference in codon usage between families. Several lines of evidence suggest that this type of selection is weak in most cases. However, we found several cases where unusual bases occur at the wobble position of the tRNA, and in these cases, some evidence for selection on codon usage was found. We discuss the way that these unusual cases are associated with codon reassignments in the mitochondrial genetic code.}, }
@article {pmid18048316, year = {2007}, author = {Chamala, S and Beckstead, WA and Rowe, MJ and McClellan, DA}, title = {Evolutionary selective pressure on three mitochondrial SNPs is consistent with their influence on metabolic efficiency in Pima Indians.}, journal = {International journal of bioinformatics research and applications}, volume = {3}, number = {4}, pages = {504-522}, doi = {10.1504/IJBRA.2007.015418}, pmid = {18048316}, issn = {1744-5485}, mesh = {ATP Synthetase Complexes/chemistry ; Amino Acids/chemistry ; DNA, Mitochondrial/*genetics ; Ethnicity ; Evolution, Molecular ; Humans ; Metabolism ; Mitochondria/*metabolism ; Models, Molecular ; Phylogeny ; Polymorphism, Genetic ; *Polymorphism, Single Nucleotide ; Population Groups ; Pressure ; Software ; }, abstract = {We investigated whether the effect of evolutionary selection on three recent Single Nucleotide Polymorphisms (SNPs) in the mitochondrial sub-haplogroups of Pima Indians is consistent with their effects on metabolic efficiency. The mitochondrial SNPs impact metabolic rate and respiratory quotient, and may be adaptations to caloric restriction in a desert habitat. Using TreeSAAP software, we examined evolutionary selection in 107 mammalian species at these SNPs, characterising the biochemical shifts produced by the amino acid substitutions. Our results suggest that two SNPs were affected by selection during mammalian evolution in a manner consistent with their effects on metabolic efficiency in Pima Indians.}, }
@article {pmid18048312, year = {2007}, author = {Baer, KK and McClellan, DA}, title = {Molecular coevolution of the vertebrate cytochrome c(1) and Rieske iron sulphur protein in the cytochrome bc(1) complex.}, journal = {International journal of bioinformatics research and applications}, volume = {3}, number = {4}, pages = {456-470}, doi = {10.1504/IJBRA.2007.015414}, pmid = {18048312}, issn = {1744-5485}, mesh = {Amino Acids/chemistry ; Animals ; Biochemistry/methods ; Computational Biology ; Cytochromes c1/*chemistry ; Electron Transport ; Electron Transport Complex III/*chemistry ; Electrons ; Humans ; Iron-Sulfur Proteins/*chemistry ; Molecular Conformation ; Phylogeny ; Protein Conformation ; Protons ; Ubiquinone/chemistry ; }, abstract = {Cytochrome c(1) (cyt-c(1)) and the Rieske Iron Sulphur Protein (ISP) are subunits of the cytochrome bc(1) complex located in the mitochondria functioning both as a proton pump and an electron transporter. Vertebrate model organism phylogenies were used in conjunction with existing 3D protein structures to evaluate the biochemical evolution of cyt-c(1) and ISP in terms of selection on amino acid properties. We found selection acting on the exterior surfaces of both proteins and specifically the core region of cyt-c(1). There is evidence supporting coevolution of these proteins relative to alpha helical tendencies, compressibility and equilibrium constant.}, }
@article {pmid18047198, year = {2007}, author = {Marquez, JG and Cummings, MA and Krafsur, ES}, title = {Phylogeography of stable fly (Diptera: Muscidae) estimated by diversity at ribosomal 16S and cytochrome oxidase I mitochondrial genes.}, journal = {Journal of medical entomology}, volume = {44}, number = {6}, pages = {998-1008}, doi = {10.1603/0022-2585(2007)44[998:posfdm]2.0.co;2}, pmid = {18047198}, issn = {0022-2585}, mesh = {Animals ; Demography ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Haplotypes/genetics ; Mitochondria/*enzymology ; Muscidae/*genetics/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The blood-feeding cosmopolitan stable fly, Stomoxys calcitrans L. (Diptera: Muscidae), is thought to disperse rapidly and widely, and earlier studies of allozyme variation were consistent with high vagility in this species. The geographic origins of New World populations are unknown. Diversity at mitochondrial loci r16S and cytochrome oxidase I was examined in 277 stable flies from 11 countries, including five zoogeographical regions. Of 809 nucleotides, 174 were polymorphic and 133 were parsimony informative. Seventy-six haplotypes were found in frequencies consistent with the Wright-Fisher infinite allele model. None were shared among four or more zoogeographical regions. The null hypothesis of mutation neutrality was not rejected, thereby validating the observed distribution. Fifty-nine haplotypes were singular, eight were private and confined to the Old World, and three of 76 haplotypes were shared between the Old and New World. Only 19 haplotypes were found in the New World, 14 of which were singletons. Haplotype and nucleotide diversities were heterogeneous among countries and regions. The most diversity was observed in sub-Saharan Africa. Regional differentiation indices were C(RT) = 0.26 and N(RT) = 0.31, indicating populations were highly structured macrogeographically. Palearctic and New World flies were the least differentiated from each other. There were strong genetic similarities among populations in the Nearctic, Neotropical, and Palearctic regions, and it is most likely that New World populations were derived from the Palearctic after 1492 CE, in the colonial era.}, }
@article {pmid18047017, year = {2007}, author = {Chelomina, GN and Atopkin, DM and Bogdanov, AS}, title = {Phylogenetic relationships between species and intraspecific forms of forest mice from the genus Sylvaemus as determined by partial sequencing of the cytochrome b gene of mitochondrial DNA.}, journal = {Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections}, volume = {416}, number = {}, pages = {356-359}, pmid = {18047017}, issn = {0012-4966}, mesh = {Animals ; Cluster Analysis ; Cytochromes b/*genetics ; DNA/metabolism ; *DNA, Mitochondrial ; Genetic Variation ; Karyotyping ; Mice ; Mitochondria/metabolism ; Models, Biological ; Models, Statistical ; Phylogeny ; Species Specificity ; }, }
@article {pmid18045382, year = {2007}, author = {Gill, EE and Diaz-Triviño, S and Barberà, MJ and Silberman, JD and Stechmann, A and Gaston, D and Tamas, I and Roger, AJ}, title = {Novel mitochondrion-related organelles in the anaerobic amoeba Mastigamoeba balamuthi.}, journal = {Molecular microbiology}, volume = {66}, number = {6}, pages = {1306-1320}, doi = {10.1111/j.1365-2958.2007.05979.x}, pmid = {18045382}, issn = {0950-382X}, mesh = {Amoeba/genetics/*metabolism/ultrastructure ; Anaerobiosis ; Animals ; Chaperonin 60/genetics/metabolism ; Cloning, Molecular ; Electrophoresis, Gel, Two-Dimensional ; Immunoblotting ; Iron-Sulfur Proteins/metabolism ; Microscopy, Electron, Transmission ; Microscopy, Fluorescence ; Mitochondria/*metabolism/ultrastructure ; Organelles/*metabolism/ultrastructure ; Phylogeny ; Protozoan Proteins/classification/genetics/metabolism ; }, abstract = {Unicellular eukaryotes that lack mitochondria typically contain related organelles such as hydrogenosomes or mitosomes. To characterize the evolutionary diversity of these organelles, we conducted an expressed sequence tag (EST) survey on the free-living amoeba Mastigamoeba balamuthi, a relative of the human parasite Entamoeba histolytica. From 19 182 ESTs, we identified 21 putative mitochondrial proteins implicated in protein import, amino acid interconversion and carbohydrate metabolism, two components of the iron-sulphur cluster (Fe-S) assembly apparatus as well as two enzymes characteristic of hydrogenosomes. By immunofluorescence microscopy and subcellular fractionation, we show that mitochondrial chaperonin 60 is targeted to small abundant organelles within Mastigamoeba. In transmission electron micrographs, we identified double-membraned compartments that likely correspond to these mitochondrion-derived organelles, The predicted organellar proteome of the Mastigamoeba organelle indicates a unique spectrum of functions that collectively have never been observed in mitochondrion-related organelles. However, like Entamoeba, the Fe-S cluster assembly proteins in Mastigamoeba were acquired by lateral gene transfer from epsilon-proteobacteria and do not possess obvious organellar targeting peptides. These data indicate that the loss of classical aerobic mitochondrial functions and acquisition of anaerobic enzymes and Fe-S cluster assembly proteins occurred in a free-living member of the eukaryote super-kingdom Amoebozoa.}, }
@article {pmid18044191, year = {2007}, author = {Tosato, M and Zamboni, V and Ferrini, A and Cesari, M}, title = {The aging process and potential interventions to extend life expectancy.}, journal = {Clinical interventions in aging}, volume = {2}, number = {3}, pages = {401-412}, pmid = {18044191}, issn = {1176-9092}, mesh = {Aging/*drug effects/genetics/immunology/metabolism ; Animals ; Antioxidants/*pharmacology ; Biological Evolution ; *Caloric Restriction ; DNA Damage ; DNA, Mitochondrial/metabolism ; Free Radicals/metabolism ; Gene Expression Regulation/drug effects ; Humans ; Immune System/drug effects/metabolism ; Inflammation/genetics/metabolism ; *Life Expectancy ; Longevity/*drug effects/genetics/immunology ; Mitochondria/drug effects/metabolism ; Neurosecretory Systems/drug effects/metabolism ; Oxidative Stress/drug effects ; Telomere/metabolism ; }, abstract = {Aging is commonly defined as the accumulation of diverse deleterious changes occurring in cells and tissues with advancing age that are responsible for the increased risk of disease and death. The major theories of aging are all specific of a particular cause of aging, providing useful and important insights for the understanding of age-related physiological changes. However, a global view of them is needed when debating of a process which is still obscure in some of its aspects. In this context, the search for a single cause of aging has recently been replaced by the view of aging as an extremely complex, multifactorial process. Therefore, the different theories of aging should not be considered as mutually exclusive, but complementary of others in the explanation of some or all the features of the normal aging process. To date, no convincing evidence showing the administration of existing "anti-aging" remedies can slow aging or increase longevity in humans is available. Nevertheless, several studies on animal models have shown that aging rates and life expectancy can be modified. The present review provides an overlook of the most commonly accepted theories of aging, providing current evidence of those interventions aimed at modifying the aging process.}, }
@article {pmid18036550, year = {2008}, author = {Morales-Sainz, L and Escobar-Ramírez, A and Cruz-Torres, V and Reyes-Prieto, A and Vázquez-Acevedo, M and Lara-Martínez, R and Jiménez-García, LF and González-Halphen, D}, title = {The polypeptides COX2A and COX2B are essential components of the mitochondrial cytochrome c oxidase of Toxoplasma gondii.}, journal = {Biochimica et biophysica acta}, volume = {1777}, number = {2}, pages = {202-210}, doi = {10.1016/j.bbabio.2007.10.013}, pmid = {18036550}, issn = {0006-3002}, support = {HL59646/HL/NHLBI NIH HHS/United States ; TW01176/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Dimerization ; Electron Transport Complex IV/*chemistry ; Evolution, Molecular ; Microscopy, Electron ; Mitochondria/*enzymology ; Protein Subunits/*chemistry ; Toxoplasma/*enzymology ; }, abstract = {Two genes encoding cytochrome c oxidase subunits, Cox2a and Cox2b, are present in the nuclear genomes of apicomplexan parasites and show sequence similarity to corresponding genes in chlorophycean algae. We explored the presence of COX2A and COX2B subunits in the cytochrome c oxidase of Toxoplasma gondii. Antibodies were raised against a synthetic peptide containing a 14-residue fragment of the COX2A polypeptide and against a hexa-histidine-tagged recombinant COX2B protein. Two distinct immunochemical stainings localized the COX2A and COX2B proteins in the parasite's mitochondria. A mitochondria-enriched fraction exhibited cyanide-sensitive oxygen uptake in the presence of succinate. T. gondii mitochondria were solubilized and subjected to Blue Native Electrophoresis followed by second dimension electrophoresis. Selected protein spots from the 2D gels were subjected to mass spectrometry analysis and polypeptides of mitochondrial complexes III, IV and V were identified. Subunits COX2A and COX2B were detected immunochemically and found to co-migrate with complex IV; therefore, they are subunits of the parasite's cytochrome c oxidase. The apparent molecular mass of the T. gondii mature COX2A subunit differs from that of the chlorophycean alga Polytomella sp. The data suggest that during its biogenesis, the mitochondrial targeting sequence of the apicomplexan COX2A precursor protein may be processed differently than the one from its algal counterpart.}, }
@article {pmid18033741, year = {2008}, author = {Giegé, P and Grienenberger, JM and Bonnard, G}, title = {Cytochrome c biogenesis in mitochondria.}, journal = {Mitochondrion}, volume = {8}, number = {1}, pages = {61-73}, doi = {10.1016/j.mito.2007.10.001}, pmid = {18033741}, issn = {1567-7249}, mesh = {ATP-Binding Cassette Transporters/*genetics/physiology ; Bacteria/enzymology ; Cytochromes c/biosynthesis/*genetics ; Evolution, Molecular ; Genome, Bacterial ; Genome, Fungal ; Genome, Plant ; Heme/metabolism ; Lyases/genetics/physiology ; Mitochondria/*enzymology ; Plants/enzymology/*genetics ; }, abstract = {As part of the respiratory chain, c-type cytochromes are essential electron transporters. They are characterized by the covalent attachment of a heme prosthetic group. The biogenesis of these proteins includes all the processes leading to this fixation. Yeast and animals have evolved a comparatively simple mechanism relying on cytochrome c heme lyases. In contrast, plant mitochondria have kept a maturation pathway inherited from their prokaryote ancestor. It involves Ccm proteins encoded in both the nuclear and the mitochondrial genomes of plants. These proteins compose a heme delivery pathway, include an ABC transporter, a redox protein and a putative heme lyase.}, }
@article {pmid18028257, year = {2008}, author = {Moosmann, B and Behl, C}, title = {Mitochondrially encoded cysteine predicts animal lifespan.}, journal = {Aging cell}, volume = {7}, number = {1}, pages = {32-46}, doi = {10.1111/j.1474-9726.2007.00349.x}, pmid = {18028257}, issn = {1474-9726}, mesh = {Aging ; Animals ; Computational Biology ; Cysteine/*analysis/genetics/metabolism ; DNA, Mitochondrial/genetics ; Free Radicals/metabolism ; Humans ; Longevity/*genetics ; Mitochondria/*genetics ; Mitochondrial Proteins/*chemistry/genetics ; Models, Molecular ; Phylogeny ; }, abstract = {The role of genetic factors in the determination of lifespan is undisputed. However, numerous successful efforts to identify individual genetic modulators of longevity have not yielded yet a quantitative measure to estimate the lifespan of a species from scratch, merely based on its genomic constitution. Here, we report on a meta-examination of genome sequences from 248 animal species with known maximum lifespan, including mammals, birds, fish, insects, and helminths. Our analysis reveals that the frequency with which cysteine is encoded by mitochondrial DNA is a specific and phylogenetically ubiquitous molecular indicator of aerobic longevity: long-lived species synthesize respiratory chain complexes which are depleted of cysteine. Cysteine depletion was also found on a proteome-wide scale in aerobic versus anaerobic bacteria, archaea, and unicellular eukaryotes; in mitochondrial versus hydrogenosomal sequences; and in the mitochondria of free-living, aerobic versus anaerobic-parasitic worms. The association of longevity with mitochondrial cysteine depletion persisted after correction for body mass and phylogenetic interdependence, but it was uncoupled in helminthic species with predominantly anaerobic lifestyle. We conclude that protein-coding genes on mitochondrial DNA constitute a quantitative trait locus for aerobic longevity, wherein the oxidation of mitochondrially translated cysteine mediates the coupling of trait and locus. These results provide distinct support for the free radical theory of aging.}, }
@article {pmid18027391, year = {2007}, author = {Bhattacharya, D and Archibald, JM and Weber, AP and Reyes-Prieto, A}, title = {How do endosymbionts become organelles? Understanding early events in plastid evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {29}, number = {12}, pages = {1239-1246}, doi = {10.1002/bies.20671}, pmid = {18027391}, issn = {0265-9247}, mesh = {*Biological Evolution ; Models, Biological ; Plant Proteins/chemistry ; Plastids/*physiology ; Protein Transport ; *Symbiosis ; }, abstract = {What factors drove the transformation of the cyanobacterial progenitor of plastids (e.g. chloroplasts) from endosymbiont to bona fide organelle? This question lies at the heart of organelle genesis because, whereas intracellular endosymbionts are widespread in both unicellular and multicellular eukaryotes (e.g. rhizobial bacteria, Chlorella cells in ciliates, Buchnera in aphids), only two canonical eukaryotic organelles of endosymbiotic origin are recognized, the plastids of algae and plants and the mitochondrion. Emerging data on (1) the discovery of non-canonical plastid protein targeting, (2) the recent origin of a cyanobacterial-derived organelle in the filose amoeba Paulinella chromatophora, and (3) the extraordinarily reduced genomes of psyllid bacterial endosymbionts begin to blur the distinction between endosymbiont and organelle. Here we discuss the use of these terms in light of new data in order to highlight the unique aspects of plastids and mitochondria and underscore their central role in eukaryotic evolution.}, }
@article {pmid18021395, year = {2007}, author = {Boxma, B and Ricard, G and van Hoek, AH and Severing, E and Moon-van der Staay, SY and van der Staay, GW and van Alen, TA and de Graaf, RM and Cremers, G and Kwantes, M and McEwan, NR and Newbold, CJ and Jouany, JP and Michalowski, T and Pristas, P and Huynen, MA and Hackstein, JH}, title = {The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {230}, pmid = {18021395}, issn = {1471-2148}, mesh = {Animals ; Chimera/*genetics ; Ciliophora/*enzymology/genetics ; Electron Transport Complex I/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genome, Mitochondrial ; Genome, Protozoan ; Hydrogenase/*genetics ; Iron-Sulfur Proteins/*genetics ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: The hydrogenosomes of the anaerobic ciliate Nyctotherus ovalis show how mitochondria can evolve into hydrogenosomes because they possess a mitochondrial genome and parts of an electron-transport chain on the one hand, and a hydrogenase on the other hand. The hydrogenase permits direct reoxidation of NADH because it consists of a [FeFe] hydrogenase module that is fused to two modules, which are homologous to the 24 kDa and the 51 kDa subunits of a mitochondrial complex I.<br><br>RESULTS: The [FeFe] hydrogenase belongs to a clade of hydrogenases that are different from well-known eukaryotic hydrogenases. The 24 kDa and the 51 kDa modules are most closely related to homologous modules that function in bacterial [NiFe] hydrogenases. Paralogous, mitochondrial 24 kDa and 51 kDa modules function in the mitochondrial complex I in N. ovalis. The different hydrogenase modules have been fused to form a polyprotein that is targeted into the hydrogenosome.<br><br>CONCLUSION: The hydrogenase and their associated modules have most likely been acquired by independent lateral gene transfer from different sources. This scenario for a concerted lateral gene transfer is in agreement with the evolution of the hydrogenosome from a genuine ciliate mitochondrion by evolutionary tinkering.}, }
@article {pmid18007659, year = {2007}, author = {Bos, MP and Robert, V and Tommassen, J}, title = {Functioning of outer membrane protein assembly factor Omp85 requires a single POTRA domain.}, journal = {EMBO reports}, volume = {8}, number = {12}, pages = {1149-1154}, pmid = {18007659}, issn = {1469-221X}, mesh = {Bacterial Outer Membrane Proteins/classification/genetics/*metabolism ; Binding Sites/genetics ; Cell Membrane/metabolism ; Electrophoresis, Polyacrylamide Gel ; Immunoblotting ; Mutation ; Neisseria meningitidis/genetics/*metabolism ; Phylogeny ; }, abstract = {beta-Barrel proteins are present in the outer membranes of Gram-negative bacteria, mitochondria and chloroplasts. The central component of their assembly machinery is called Omp85 in bacteria. Omp85 is predicted to consist of an integral membrane domain and an amino-terminal periplasmic extension containing five polypeptide-transport-associated (POTRA) domains. We have addressed the function of these domains by creating POTRA domain deletions in Omp85 of Neisseria meningitidis. Four POTRA domains could be deleted with only slight defects in Omp85 function. Only the most carboxy-terminal POTRA domain was essential, as was the membrane domain. Thus, similar to the mitochondrial Omp85 homologue, the functional core of bacterial Omp85 consists of its membrane domain and a single POTRA domain, that is, POTRA5.}, }
@article {pmid18006386, year = {2008}, author = {Bonen, L}, title = {Cis- and trans-splicing of group II introns in plant mitochondria.}, journal = {Mitochondrion}, volume = {8}, number = {1}, pages = {26-34}, doi = {10.1016/j.mito.2007.09.005}, pmid = {18006386}, issn = {1567-7249}, mesh = {Base Sequence ; Evolution, Molecular ; Genes, Plant ; Introns/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Plants/*genetics ; *RNA Splicing ; *Trans-Splicing ; }, abstract = {Group II-type introns in the mitochondrial genes of flowering plants belong to the ribozymic, mobile retroelement family, but not all exhibit conventional structural features and some follow unusual splicing pathways. Moreover, several introns have been disrupted by DNA rearrangements, so that separately-transcribed precursors undergo splicing in trans. RNA processing in plant mitochondria has the added complexity of C-to-U RNA editing which also sometimes occurs within core intron structures or at exon sites very close to introns. It appears that mitochondrial introns in flowering plants have followed quite different evolutionary pathways than other group II introns.}, }
@article {pmid17999954, year = {2008}, author = {Xu, Y and Johansson, M and Karlsson, A}, title = {Human UMP-CMP kinase 2, a novel nucleoside monophosphate kinase localized in mitochondria.}, journal = {The Journal of biological chemistry}, volume = {283}, number = {3}, pages = {1563-1571}, doi = {10.1074/jbc.M707997200}, pmid = {17999954}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Cloning, Molecular ; DNA, Complementary ; Electrophoresis, Polyacrylamide Gel ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Neoplastic ; HeLa Cells ; Humans ; Isoelectric Point ; Kinetics ; Mitochondria/*enzymology ; Models, Biological ; Molecular Sequence Data ; Neoplasms/enzymology/genetics ; Nucleoside-Phosphate Kinase/chemistry/genetics/*isolation &amp; purification/*metabolism ; Nucleotides/metabolism ; Phylogeny ; Protein Transport ; RNA, Messenger/genetics/metabolism ; Recombinant Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Subcellular Fractions/enzymology ; Substrate Specificity ; }, abstract = {Enzyme deficiency in the salvage pathway of deoxyribonucleotide synthesis in mitochondria can cause mtDNA depletion syndromes. We have identified a human mitochondrial UMP-CMP kinase (UMP-CMPK, cytidylate kinase; EC 2.7.4.14), designated as UMP-CMP kinase 2 (UMP-CMPK2). The C-terminal domain of this 449-amino acid protein contains all consensus motifs of a nucleoside monophosphate kinase. Phylogenetic analysis showed that UMP-CMPK2 belonged to a novel nucleoside monophosphate kinase family, which was closer to thymidylate kinase than to cytosolic UMP-CMP kinase. Subcellular localization with green fluorescent protein fusion proteins illustrated that UMP-CMPK2 was localized in the mitochondria of HeLa cells and that the mitochondrial targeting signal was included in the N-terminal 22 amino acids. The enzyme was able to phosphorylate dUMP, dCMP, CMP, and UMP with ATP as phosphate donor, but the kinetic properties were different compared with the cytosolic UMP-CMPK. Its efficacy to convert dUMP was highest, followed by dCMP, whereas CMP and UMP were the poorest substrates. It also phosphorylated the monophosphate forms of the nucleoside analogs ddC, dFdC, araC, BVDU, and FdUrd, which suggests that UMP-CMPK2 may be involved in mtDNA depletion caused by long term treatment with ddC or other pyrimidine analogs. UMP-CMPK2 mRNA expression was exclusively detected in chronic myelogenous leukemia K-562 and lymphoblastic leukemia MOLT-4 among eight studied cancer cell lines. Particular high expression in leukemia cells, dominant expression in bone marrow, and tight correlation with macrophage activation and inflammatory response suggest that UMP-CMPK2 may have other functions in addition to the supply of substrates for mtDNA synthesis.}, }
@article {pmid17999208, year = {2007}, author = {Szolnoki, Z and Kondacs, A and Mandi, Y and Somogyvari, F}, title = {A cytoskeleton motor protein genetic variant may exert a protective effect on the occurrence of multiple sclerosis: the janus face of the kinesin light-chain 1 56836CC genetic variant.}, journal = {Neuromolecular medicine}, volume = {9}, number = {4}, pages = {335-339}, pmid = {17999208}, issn = {1535-1084}, mesh = {Alternative Splicing ; DNA/blood/genetics/isolation &amp; purification ; *Genetic Variation ; Genotype ; Humans ; Introns ; Janus Kinase 1/genetics ; Kinesins ; Microtubule-Associated Proteins/*genetics ; Models, Genetic ; Multiple Sclerosis, Relapsing-Remitting/*genetics/prevention &amp; control ; *Polymorphism, Single Nucleotide ; RNA, Messenger/genetics ; Reference Values ; }, abstract = {Although the main pathomechanism of multiple sclerosis (MS) is not known, an autoimmune response is presumed to involve its evolution and propagation. In this study, we examined how the kinesin light-chain 1 (KLC1) G56836C (rs8702) single nucleotide polymorphism (SNP) in intron 13 affects the occurrence of MS. This genetic variant was found to be associated with cognitive disturbances and neurodegeneration, and it was presumed to affect the kinesin function. Kinesin serves as a main cytoskeleton motor protein by carrying mitochondria and the molecular apparatus of myelin basic protein synthesis. The present association analysis of this genetic variant was performed in 102 relapsing-remitting MS patients and in 207 neuroimaging alteration-free controls. The KLC1 56836CC variant proved to exert a significant protective effect on the occurrence of MS (2.0% vs. 9.7%, P < 0.02; crude OR: 0.19, 95% CI: 0.04-0.82, P < 0.05; adjusted OR: 0.21, 95% CI: 0.018-0.88, P < 0.05). Our results draw attention to possible roles of the cytoskeleton in MS.}, }
@article {pmid17983265, year = {2007}, author = {Gabaldón, T and Huynen, MA}, title = {From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism.}, journal = {PLoS computational biology}, volume = {3}, number = {11}, pages = {e219}, pmid = {17983265}, issn = {1553-7358}, mesh = {Biological Evolution ; Computer Simulation ; DNA Mutational Analysis/methods ; *Evolution, Molecular ; Fungal Proteins/*physiology ; Genetic Variation/genetics ; Humans ; Mitochondria/*physiology ; Mitochondrial Proteins/*physiology ; *Models, Genetic ; Organelles/physiology ; Protein Biosynthesis/*genetics ; Symbiosis/*genetics ; }, abstract = {Mitochondria are eukaryotic organelles that originated from the endosymbiosis of an alpha-proteobacterium. To gain insight into the evolution of the mitochondrial proteome as it proceeded through the transition from a free-living cell to a specialized organelle, we compared a reconstructed ancestral proteome of the mitochondrion with the proteomes of alpha-proteobacteria as well as with the mitochondrial proteomes in yeast and man. Overall, there has been a large turnover of the mitochondrial proteome during the evolution of mitochondria. Early in the evolution of the mitochondrion, proteins involved in cell envelope synthesis have virtually disappeared, whereas proteins involved in replication, transcription, cell division, transport, regulation, and signal transduction have been replaced by eukaryotic proteins. More than half of what remains from the mitochondrial ancestor in modern mitochondria corresponds to translation, including post-translational modifications, and to metabolic pathways that are directly, or indirectly, involved in energy conversion. Altogether, the results indicate that the eukaryotic host has hijacked the proto-mitochondrion, taking control of its protein synthesis and metabolism.}, }
@article {pmid17981466, year = {2007}, author = {Kucej, M and Butow, RA}, title = {Evolutionary tinkering with mitochondrial nucleoids.}, journal = {Trends in cell biology}, volume = {17}, number = {12}, pages = {586-592}, doi = {10.1016/j.tcb.2007.08.007}, pmid = {17981466}, issn = {1879-3088}, support = {GM22525/GM/NIGMS NIH HHS/United States ; GM33510/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/*metabolism/ultrastructure ; *Evolution, Molecular ; Gene Expression Regulation ; Genome, Mitochondrial ; Humans ; Mitochondria/*metabolism/ultrastructure ; Mitochondrial Proteins/*metabolism ; }, abstract = {Mitochondrial DNA (mtDNA) is organized in nucleoprotein particles called nucleoids. Each nucleoid, which is considered a heritable unit of mtDNA, might contain several copies of the mitochondrial genome and several different proteins. Some nucleoid-associated proteins, such as the high mobility group (HMG) box family, have well defined functions in mtDNA maintenance and packaging; others, such as Aco1 and IIv5, are bifunctional, fulfilling their roles in nucleoids in addition to well established metabolic functions. The fact that the HMG box mtDNA packaging proteins are of eukaryotic rather than bacterial origin and also that every organism seems to have a unique set of nucleoid-associated proteins suggests that evolutionary tinkering occurred to reinvent mitochondrial nucleoprotein during the evolution of mitochondrial genomes.}, }
@article {pmid17980591, year = {2007}, author = {Cooper, MA and Adam, RD and Worobey, M and Sterling, CR}, title = {Population genetics provides evidence for recombination in Giardia.}, journal = {Current biology : CB}, volume = {17}, number = {22}, pages = {1984-1988}, doi = {10.1016/j.cub.2007.10.020}, pmid = {17980591}, issn = {0960-9822}, support = {TW00036/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Evolution, Molecular ; Genes, Protozoan ; *Genetics, Population ; Giardia lamblia/*genetics ; Humans ; *Recombination, Genetic ; Reproduction/genetics ; }, abstract = {Giardia lamblia (syn. Giardia intestinalis, Giardia duodenalis) is an enteric protozoan parasite with two nuclei, and it might be one of the earliest branching eukaryotes. However, the discovery of at least rudimentary forms of certain features, such as Golgi and mitochondria, has refuted the proposal that its emergence from the eukaryotic lineage predated the development of certain eukaryotic features. The recent recognition of many of the genes known to be required for meiosis in the genome has also cast doubt on the idea that Giardia is primitively asexual, but so far there has been no direct evidence of sexual reproduction in Giardia, and population data have suggested clonal reproduction. We did a multilocus sequence evaluation of the genotype A2 reference strain, JH, and five genotype A2 isolates from a highly endemic area in Peru. Loci from different chromosomes yielded significantly different phylogenetic trees, indicating that they do not share the same evolutionary history; within individual loci, tests for recombination yielded significant statistical support for meiotic recombination. These observations provide genetic data supportive of sexual reproduction in Giardia.}, }
@article {pmid17977456, year = {2007}, author = {Brinkmann, H and Philippe, H}, title = {The diversity of eukaryotes and the root of the eukaryotic tree.}, journal = {Advances in experimental medicine and biology}, volume = {607}, number = {}, pages = {20-37}, doi = {10.1007/978-0-387-74021-8_2}, pmid = {17977456}, issn = {0065-2598}, mesh = {*Eukaryotic Cells ; *Evolution, Molecular ; *Genetic Variation ; Models, Biological ; Phylogeny ; Time Factors ; }, abstract = {More than 15 years ago, on the basis of phylogenetic analyses of a handful of anciently duplicated genes and of rRNA, Carl Woese proposed both a eubacterial rooting of the Tree of Life and a stepwise evolution of the eukaryotic cell. An important part of Woese's paradigm was the assumption that the so-called Archezoa were considered to be genuinely primitive because they were lacking mitochondria and several other organelles characteristic for most eukaryotes. Since then, enormous progress have been accomplished in sequencing technology and in phylogenetic reconstruction. In particular, it is now clear that a tree reconstruction artefact, known as Long Branch Attraction, is responsible for the early emergence of the fast evolving Archezoa in the eukaryotic tree. The corollary hypothesis that all extant eukaryotes are ancestrally mitochondrial is strongly supported by the discovery of rudimentary mitochondrial organelles in all analysed Archezoa. Today a consensus that divides the extant eukaryotes into six major groups is replacing Woese's paradigm, which needs, however, further confirmation. Recently, a molecular dating study based on a large phylogenomic dataset with a relaxed molecular clock and multiple time intervals yielded in a surprisingly recent time estimate of 1085 Mya for the origin of the extant eukaryotic diversity. Therefore, extant eukaryotes seem to be the product of a massive radiation that happened rather late, at least in terms of prokaryotic diversity. In multiple cases evolution has proceeded via secondary simplification of a complex ancestor, instead of the constant march towards rising complexity generally assumed. Therefore it is time to reevaluate the origin and evolution of eukaryotes, in light of the newly established phylogeny, by further integrating secondary simplification as an equal partner to complexification.}, }
@article {pmid17967180, year = {2007}, author = {Shen, YQ and Burger, G}, title = {'Unite and conquer': enhanced prediction of protein subcellular localization by integrating multiple specialized tools.}, journal = {BMC bioinformatics}, volume = {8}, number = {}, pages = {420}, pmid = {17967180}, issn = {1471-2105}, mesh = {Algorithms ; Amino Acid Motifs ; Arabidopsis Proteins/chemistry ; Computational Biology/*instrumentation/*methods ; Databases, Protein ; False Positive Reactions ; Internet ; Mitochondria/metabolism ; Peptides/chemistry ; Phylogeny ; Protein Structure, Tertiary ; Protein Transport ; Proteins/*chemistry ; Reproducibility of Results ; Sequence Alignment ; Sequence Analysis, Protein ; Software ; }, abstract = {BACKGROUND: Knowing the subcellular location of proteins provides clues to their function as well as the interconnectivity of biological processes. Dozens of tools are available for predicting protein location in the eukaryotic cell. Each tool performs well on certain data sets, but their predictions often disagree for a given protein. Since the individual tools each have particular strengths, we set out to integrate them in a way that optimally exploits their potential. The method we present here is applicable to various subcellular locations, but tailored for predicting whether or not a protein is localized in mitochondria. Knowledge of the mitochondrial proteome is relevant to understanding the role of this organelle in global cellular processes.<br><br>RESULTS: In order to develop a method for enhanced prediction of subcellular localization, we integrated the outputs of available localization prediction tools by several strategies, and tested the performance of each strategy with known mitochondrial proteins. The accuracy obtained (up to 92%) surpasses by far the individual tools. The method of integration proved crucial to the performance. For the prediction of mitochondrion-located proteins, integration via a two-layer decision tree clearly outperforms simpler methods, as it allows emphasis of biologically relevant features such as the mitochondrial targeting peptide and transmembrane domains.<br><br>CONCLUSION: We developed an approach that enhances the prediction accuracy of mitochondrial proteins by uniting the strength of specialized tools. The combination of machine-learning based integration with biological expert knowledge leads to improved performance. This approach also alleviates the conundrum of how to choose between conflicting predictions. Our approach is easy to implement, and applicable to predicting subcellular locations other than mitochondria, as well as other biological features. For a trial of our approach, we provide a webservice for mitochondrial protein prediction (named YimLOC), which can be accessed through the AnaBench suite at http://anabench.bcm.umontreal.ca/anabench/. The source code is provided in the Additional File 2.}, }
@article {pmid17965091, year = {2007}, author = {Lin, Z and Nei, M and Ma, H}, title = {The origins and early evolution of DNA mismatch repair genes--multiple horizontal gene transfers and co-evolution.}, journal = {Nucleic acids research}, volume = {35}, number = {22}, pages = {7591-7603}, pmid = {17965091}, issn = {1362-4962}, support = {R01 GM020293/GM/NIGMS NIH HHS/United States ; R01 GM063871/GM/NIGMS NIH HHS/United States ; GM020293/GM/NIGMS NIH HHS/United States ; GM63871/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *DNA Mismatch Repair ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Genes, Archaeal ; Genes, Bacterial ; Genes, Plant ; Genomics ; Models, Genetic ; *Multigene Family ; MutS DNA Mismatch-Binding Protein/classification/*genetics ; MutS Homolog 2 Protein/classification/genetics ; Phylogeny ; }, abstract = {To understand the evolutionary process of the DNA mismatch repair system, we conducted systematic phylogenetic analysis of its key components, the bacterial MutS and MutL genes and their eukaryotic homologs. Based on genome-wide homolog searches, we identified three new MutS subfamilies (MutS3-5) in addition to the previously studied MutS1 and MutS2 subfamilies. Detailed evolutionary analysis strongly suggests that frequent ancient horizontal gene transfer (HGT) occurred with both MutS and MutL genes from bacteria to eukaryotes and/or archaea. Our results further imply that the origins of mismatch repair system in eukaryotes and archaea are largely attributed to ancient HGT from bacteria instead of vertical evolution. Specifically, the eukaryotic MutS and MutL homologs likely originated from endosymbiotic ancestors of mitochondria or chloroplasts, indicating that not only archaea, but also bacteria are important sources of eukaryotic DNA metabolic genes. The archaeal MutS1 and MutL homologs were also acquired from bacteria simultaneously through HGT. Moreover, the distribution and evolution profiles of the MutS1 and MutL genes suggest that they have undergone long-term coevolution. Our work presents an overall portrait of the evolution of these important genes in DNA metabolism and also provides further understanding about the early evolution of cellular organisms.}, }
@article {pmid17961221, year = {2007}, author = {Fahrein, K and Talarico, G and Braband, A and Podsiadlowski, L}, title = {The complete mitochondrial genome of Pseudocellus pearsei (Chelicerata: Ricinulei) and a comparison of mitochondrial gene rearrangements in Arachnida.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {386}, pmid = {17961221}, issn = {1471-2164}, mesh = {Animals ; Arachnida/classification/*genetics ; DNA, Mitochondrial/genetics ; *Gene Order ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer/chemistry/genetics ; }, abstract = {BACKGROUND: Mitochondrial genomes are widely utilized for phylogenetic and population genetic analyses among animals. In addition to sequence data the mitochondrial gene order and RNA secondary structure data are used in phylogenetic analyses. Arachnid phylogeny is still highly debated and there is a lack of sufficient sequence data for many taxa. Ricinulei (hooded tickspiders) are a morphologically distinct clade of arachnids with uncertain phylogenetic affinities.<br><br>RESULTS: The first complete mitochondrial DNA genome of a member of the Ricinulei, Pseudocellus pearsei (Arachnida: Ricinulei) was sequenced using a PCR-based approach. The mitochondrial genome is a typical circular duplex DNA molecule with a size of 15,099 bp, showing the complete set of genes usually present in bilaterian mitochondrial genomes. Five tRNA genes (trnW, trnY, trnN, trnL(CUN), trnV) show different relative positions compared to other Chelicerata (e.g. Limulus polyphemus, Ixodes spp.). We propose that two events led to this derived gene order: (1) a tandem duplication followed by random deletion and (2) an independent translocation of trnN. Most of the inferred tRNA secondary structures show the common cloverleaf pattern except tRNA-Glu where the TpsiC-arm is missing. In phylogenetic analyses (maximum likelihood, maximum parsimony, Bayesian inference) using concatenated amino acid and nucleotide sequences of protein-coding genes the basal relationships of arachnid orders remain unresolved.<br><br>CONCLUSION: Phylogenetic analyses (ML, MP, BI) of arachnid mitochondrial genomes fail to resolve interordinal relationships of Arachnida and remain in a preliminary stage because there is still a lack of mitogenomic data from important taxa such as Opiliones and Pseudoscorpiones. Gene order varies considerably within Arachnida - only eight out of 23 species have retained the putative arthropod ground pattern. Some gene order changes are valuable characters in phylogenetic analysis of intraordinal relationships, e.g. in Acari.}, }
@article {pmid17959393, year = {2007}, author = {Meixner, MJ and Lüter, C and Eckert, C and Itskovich, V and Janussen, D and von Rintelen, T and Bohne, AV and Meixner, JM and Hess, WR}, title = {Phylogenetic analysis of freshwater sponges provide evidence for endemism and radiation in ancient lakes.}, journal = {Molecular phylogenetics and evolution}, volume = {45}, number = {3}, pages = {875-886}, doi = {10.1016/j.ympev.2007.09.007}, pmid = {17959393}, issn = {1055-7903}, mesh = {Animals ; Electron Transport Complex IV/genetics/metabolism ; Evolution, Molecular ; *Fresh Water ; Mitochondria/enzymology/genetics ; *Phylogeny ; Population Dynamics ; Porifera/classification/genetics/*physiology ; RNA, Ribosomal, 18S/genetics ; Time Factors ; }, abstract = {Morphologic and phylogenetic analysis of freshwater sponges endemic to lakes in Central Sulawesi, Siberia and South-East Europe is presented. We also analyzed several cosmopolitan sponge species from Eurasia and North America and included sponge sequences from public databases. In agreement with previous reports [Addis, J.S., Peterson, K.J., 2005. Phylogenetic relationships of freshwater sponges (Porifera, Spongillina) inferred from analyses of 18S rDNA, COI mtDNA, and ITS2 rDNA sequences. Zool. Scr. 34, 549-557], the metaniid sponge Corvomeyenia sp. was the most deeply branching species within a monophyletic lineage of the suborder Spongillina. Pachydictyum globosum (Malawispongiidae) and Nudospongilla vasta (Spongillidae), two morphologically quite distinct species from Sulawesi were found in a joint clade with Trochospongilla (Spongillidae) rendering Trochospongilla paraphyletic. Furthermore, Ochridaspongia sp., another Malawispongiidae, clustered far away from that clade, together with Ephydatia fluviatilis, making the latter family polyphyletic. The Lubomirskiidae endemic to Lake Baikal, Lubomirskia abietina, Baikalospongia bacillifera, B. intermedia, and Swartschewskia papyracea formed a well-supported clade that was most closely linked to the genus Ephydatia (99.9% identity over a total length of 2169 concatenated nucleotide positions). Our study indicates the frequent and independent origin of sponge species endemic to different freshwater ecosystems from a few cosmopolitan founder species. The highly specific primer sets newly developed here facilitate work on the molecular phylogeny and DNA barcoding of sponges.}, }
@article {pmid17959197, year = {2007}, author = {Smith, DG and Gawryluk, RM and Spencer, DF and Pearlman, RE and Siu, KW and Gray, MW}, title = {Exploring the mitochondrial proteome of the ciliate protozoon Tetrahymena thermophila: direct analysis by tandem mass spectrometry.}, journal = {Journal of molecular biology}, volume = {374}, number = {3}, pages = {837-863}, doi = {10.1016/j.jmb.2007.09.051}, pmid = {17959197}, issn = {1089-8638}, mesh = {Animals ; Chromatography, Liquid ; Mitochondria/*chemistry ; *Proteome ; Tandem Mass Spectrometry/*methods ; Tetrahymena thermophila/*chemistry ; }, abstract = {To date, direct analysis of mitochondrial proteomes has largely been limited to animals, fungi and plants. To broaden our knowledge of mitochondrial structure and function, and to provide additional insight into the evolution of this key eukaryotic organelle, we have undertaken the first comprehensive analysis of the mitochondrial proteome of a protist. Highly purified mitochondria from Tetrahymena thermophila, a ciliated protozoon, were digested exhaustively with trypsin and the resulting peptides subjected to tandem liquid chromatography-tandem mass spectrometry (LC/LC-MS/MS). In this way, we directly identified a total of 573 mitochondrial proteins, 545 of which are encoded by the nuclear genome and 28 by the mitochondrial genome. The latter number includes a novel, 44 residue protein (which we designate Ymf78) that had not been recognized during annotation of the T. thermophila mtDNA sequence. The corresponding gene, ymf78, is highly conserved in genomic position, size and sequence within the genus Tetrahymena. Our analysis has provided broad coverage of both membrane-bound and soluble proteins from the various submitochondrial compartments, with prominent representatives including components of the tricarboxylic acid cycle, Complexes I-IV of the electron transport chain and Complex V (ATP synthase), the mitochondrial transcription and translation machinery, the TOM and TIM protein translocases, various mitochondrial transporters, chaperonins (Cpn60, Hsp70, Hsp90), at least four FtsH family ATP-dependent metalloproteases implicated in m-AAA and i-AAA protease function, and enzymes involved in lipid, amino acid and coenzyme metabolism, as well as iron-sulfur cluster formation. Unexpectedly, six of the ten enzymes of glycolysis were found by MS analysis of purified T. thermophila mitochondria, whereas no hits were seen to any cytosolic ribosomal proteins. At least one of the glycolytic proteins, enolase, has an evident N-terminal extension that exhibits characteristics of a typical mitochondrial targeting peptide. As in other organisms, phylogenetic analysis of functionally annotated mitochondrial proteins demonstrates that <20% can be traced confidently to the alpha-proteobacterial lineage of Bacteria, emphasizing the chimeric evolutionary nature of the mitochondrial proteome. Notably, about 45% of the proteins identified in our analysis have no known function, and most of these do not have obvious homologs outside of the ciliate lineage. About two-thirds of these ORFan proteins have putative homologs in another ciliate, Paramecium tetraurelia, whereas the remainder appear to be Tetrahymena-specific. These results emphasize the power and importance of direct MS-based analysis of mitochondria in revealing novel mitochondrial proteins in different eukaryotic lineages. Our observations reinforce an emerging view of the mitochondrion as an evolutionarily flexible organelle, with novel proteins (and presumably functions) being added in a lineage-specific fashion to an ancient, highly conserved functional core, much of which was contributed by the presumptive alpha-proteobacterial symbiont from which the mitochondrial genome was derived.}, }
@article {pmid17951706, year = {2007}, author = {Foth, BJ}, title = {Phylogenetic analysis to uncover organellar origins of nuclear-encoded genes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {390}, number = {}, pages = {467-488}, doi = {10.1007/1-59745-466-4_30}, pmid = {17951706}, issn = {1064-3745}, mesh = {Cell Nucleus/*genetics/metabolism ; Computational Biology ; *Evolution, Molecular ; *Genes ; Genetic Techniques ; Mitochondria/genetics/metabolism ; Organelles/*genetics/metabolism ; *Phylogeny ; Plastids/genetics/metabolism ; Software ; Symbiosis ; }, abstract = {Most proteins that are located in mitochondria or plastids are encoded by the nuclear genome, because the organellar genomes have undergone severe reduction during evolution. In many cases, although not all, the nuclear genes encoding organelle-targeted proteins actually originated from the respective organellar genome and thus carry the phylogenetic fingerprint that still bespeaks their evolutionary origin. Phylogenetic analysis is a powerful in silico method that can yield important insights into the evolutionary history or molecular kinship of any gene or protein and that can thus also be used more specifically in the context of organellar targeting as one means to recognize protein candidates (e.g., from genome data) that may be targeted to mitochondria or plastids. This chapter provides protocols for creating multiple sequence alignments and carrying out phylogenetic analysis with the robust and comprehensive software packages Clustal and PHYLIP, which are both available free of charge for multiple computer platforms. Besides presenting step-by-step instructions on how to run these computer programs, this chapter also covers topics such as data collection and presentation of phylogenetic trees.}, }
@article {pmid17951689, year = {2007}, author = {Bölter, B and Soll, J}, title = {Import of plastid precursor proteins into pea chloroplasts.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {390}, number = {}, pages = {195-206}, doi = {10.1007/978-1-59745-466-7_13}, pmid = {17951689}, issn = {1064-3745}, mesh = {Chloroplasts/*metabolism ; Membrane Proteins/metabolism ; Pisum sativum/*metabolism ; Plant Proteins/*metabolism ; Protein Precursors/*metabolism ; Protein Transport ; }, abstract = {Plastids are a heterogeneous family of organelles found ubiquitously in plant and algal cells (1) Most prominent are the chloroplasts, which carry out such essential processes as photosynthesis and the biosynthesis of fatty acids as well as of amino acids. As mitochondria, chloroplasts derived from a single endosymbiotic even (2). They are believed to have evolved from an ancient cyanobacterium, which had been engulfed by an early eukaryotic ancestor. During evolution the plastid genome has been greatly reduced, and most of the genes have been transferred to the host nucleus. Consequently, more than 98% of all plastid proteins are translated onto cytosolic ribosomes. They have to be posttranslationally targeted to and imported into the organelle. Targeting is assisted by cytosolic proteins, which interact with proteins destined for plastids and thereby keep them in an import-competent state. After reaching the target organelle, many proteins have to conquer the barrier of the chloroplast outer and inner envelopes. This process is mediated by complex molecular machines in the outer (Toc complex) and inner (Tic complex) envelope of chloroplasts, respectively (3). Most proteins, destined for compartments inside the chloroplast contain a cleavable N-terminal transit peptide (4), whereas most of the outer envelope components insert into the membrane without such a targeting peptide (5).}, }
@article {pmid17951688, year = {2007}, author = {Hörmann, F and Soll, J and Bölter, B}, title = {The chloroplast protein import machinery: a review.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {390}, number = {}, pages = {179-193}, doi = {10.1007/978-1-59745-466-7_12}, pmid = {17951688}, issn = {1064-3745}, mesh = {Chloroplasts/*physiology/ultrastructure ; Membrane Proteins/metabolism ; Models, Biological ; *Plant Physiological Phenomena ; Plant Proteins/*metabolism ; Protein Transport ; }, abstract = {Plastids are a heterogeneous family of organelles found ubiquitously in plant and algal cells. Most prominent are the chloroplasts, which carry out such essential processes as photosynthesis and the biosynthesis of fatty acids as well as of amino acids. As mitochondria, chloroplasts derived from a single endosymbiotic event. They are believed to have evolved from an ancient cyanobacterium, which was engulfed by an early eukaryotic ancestor. During evolution the plastid genome has been greatly reduced and most of the genes have been transferred to the host nucleus. Consequently, more than 98% of all plastid proteins are translated on cytosolic ribosomes. They have to be posttranslationally targeted to and imported into the organelle. Targeting is assisted by cytosolic proteins, which interact with proteins destined for plastids and thereby keep them in an import-competent state. After reaching the target organelle, many proteins have to conquer the barrier of the chloroplast outer and inner envelopes. This process is mediated by complex molecular machines in the outer (Toc complex) and inner (Tic complex) envelope of chloroplasts, respectively. Most proteins destined for compartments inside the chloroplast contain a cleavable N-terminal transit peptide, whereas most of the outer envelope components insert into the membrane without such a targeting peptide.}, }
@article {pmid17951687, year = {2007}, author = {Tovar, J and Cox, SS and van der Giezen, M}, title = {A mitosome purification protocol based on percoll density gradients and its use in validating the mitosomal nature of Entamoeba histolytica mitochondrial Hsp70.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {390}, number = {}, pages = {167-177}, doi = {10.1007/978-1-59745-466-7_11}, pmid = {17951687}, issn = {1064-3745}, support = {078566/A/05/Z//Wellcome Trust/United Kingdom ; //Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Biochemistry/*methods ; Cell Fractionation ; Centrifugation, Density Gradient ; Entamoeba histolytica/genetics/*metabolism ; HSP70 Heat-Shock Proteins/*analysis ; Humans ; Mitochondria/*metabolism ; Organelles/*metabolism ; Povidone/*chemistry ; Silicon Dioxide/*chemistry ; }, abstract = {Mitochondria are indispensable for aerobic respiration, but many microbial eukaryotes have lost this function through reductive evolution. Their modified mitochondria are known as hydrogenosomes or mitosomes depending on whether or not they produce molecular hydrogen. The intestinal parasite Entamoeba histolytica contains mitosomes whose role in cellular metabolism is unclear. Only three proteins have been shown thus far to reside in these organelles: the molecular chaperones Hsp10 and Hsp60 and an unusual ADP/ATP carrier. Here we describe the isolation of E. histolytica mitosomes by cellular fractionation and density gradient centrifugation and show that the mitochondrial-type chaperone Hsp70 is also housed in Entamoeba mitosomes.}, }
@article {pmid17950289, year = {2007}, author = {Chakrabarti, R and Walker, JM and Chapman, EG and Shepardson, SP and Trdan, RJ and Curole, JP and Watters, GT and Stewart, DT and Vijayaraghavan, S and Hoeh, WR}, title = {Reproductive function for a C-terminus extended, male-transmitted cytochrome c oxidase subunit II protein expressed in both spermatozoa and eggs.}, journal = {FEBS letters}, volume = {581}, number = {27}, pages = {5213-5219}, pmid = {17950289}, issn = {0014-5793}, support = {R01 HD038520/HD/NICHD NIH HHS/United States ; R01 HD038520-01A1/HD/NICHD NIH HHS/United States ; HD38520/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/genetics/metabolism ; Electron Transport Complex IV/chemistry/*genetics/*physiology ; Evolution, Molecular ; Female ; Male ; Microscopy, Electron ; Ovum/*enzymology ; Reproduction/genetics/physiology ; Seasons ; Spermatozoa/*enzymology ; Tissue Distribution ; Unionidae/*genetics/*physiology ; }, abstract = {Our previous study documented expression of a male-transmitted cytochrome c oxidase subunit II protein (MCOX2), with a C-terminus extension (MCOX2e), in unionoidean bivalve testes and sperm mitochondria. Here, we present evidence demonstrating that MCOX2 is seasonally expressed in testis, with a peak shortly before fertilization that is independent of sperm density. MCOX2 is localized to the inner and outer sperm mitochondrial membranes and the MCOX2 antibody's epitope is conserved across >65 million years of evolution. We also demonstrate the presence of male-transmitted mtDNA and season-specific MCOX2 spatial variation in ovaries. We hypothesize that MCOX2 plays a role in reproduction through gamete maturation, fertilization and/or embryogenesis.}, }
@article {pmid17947572, year = {2007}, author = {Landweber, LF}, title = {Genetics. Why genomes in pieces?.}, journal = {Science (New York, N.Y.)}, volume = {318}, number = {5849}, pages = {405-407}, doi = {10.1126/science.1150280}, pmid = {17947572}, issn = {1095-9203}, support = {GM59708/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Eukaryota/*genetics/metabolism ; Evolution, Molecular ; *Genome ; *Genome, Protozoan ; Mitochondria/*genetics ; RNA Editing ; RNA Processing, Post-Transcriptional ; RNA, Transfer/chemistry/*genetics/metabolism ; Rhodophyta/*genetics/metabolism ; }, }
@article {pmid17947421, year = {2007}, author = {Sun, S and Xu, J}, title = {Genetic analyses of a hybrid cross between serotypes A and D strains of the human pathogenic fungus Cryptococcus neoformans.}, journal = {Genetics}, volume = {177}, number = {3}, pages = {1475-1486}, pmid = {17947421}, issn = {0016-6731}, mesh = {Base Sequence ; Chromosome Mapping ; Chromosomes, Fungal/genetics ; Crosses, Genetic ; Cryptococcus neoformans/classification/*genetics/pathogenicity ; DNA Primers/genetics ; DNA, Fungal/genetics ; Gene Rearrangement ; Genetic Markers ; Genome, Fungal ; Genotype ; Humans ; Hybridization, Genetic ; Polymorphism, Restriction Fragment Length ; Recombination, Genetic ; Serotyping ; }, abstract = {Cryptococcus neoformans has two varieties, var. grubii and var. neoformans, that correspond to serotypes A and D, respectively. Molecular phylogenetic analyses suggest that these two varieties have diverged from each other for approximately 18 million years. The discovery of pathogenic serotype AD hybrid strains in nature indicates that intervariety mating in C. neoformans occurs in the natural environment. However, little is known about the genetic consequences of hybridization in C. neoformans. Here, we analyzed a hybrid population of 163 progeny from a cross between strains of serotypes A (CDC15) and D (JEC20), using 114 codominant nuclear PCR-RFLP markers and 1 direct PCR marker. These markers were distributed on all 14 chromosomes of the sequenced strain JEC21 that was isogenic to one of the parents (JEC20) in our cross. Our analyses identified that of the 163 progeny, 5 were heterozygous at all 115 loci, 1 was completely homozygous and identical to one of the parents (CDC15), and the remaining 157 each contained at least 1 heterozygous locus. Because all 163 progeny inherited mitochondria from the MATa parent JEC20, none of the progeny had a genotype identical to either of the two parents or to a composite of the two parents. All 115 nuclear loci showed three different genotypes in the progeny population, consistent with Mendelian segregation during meiosis. While the linkage analysis showed independent reassortment among loci on different linkage groups, there were significant differences in recombination frequencies among chromosomes and among regions within certain chromosomes. Overall, the linkage-map length from this hybrid cross was much shorter and the recombination frequency much lower than those constructed using serotype D strains, consistent with suppressed recombination in the intervariety cross between strains of serotypes A and D. We discuss the implications of our results in our understanding of the speciation and evolution of the C. neoformans species complex.}, }
@article {pmid17945343, year = {2008}, author = {Giari, L and Simoni, E and Manera, M and Dezfuli, BS}, title = {Histo-cytological responses of Dicentrarchus labrax (L.) following mercury exposure.}, journal = {Ecotoxicology and environmental safety}, volume = {70}, number = {3}, pages = {400-410}, doi = {10.1016/j.ecoenv.2007.08.013}, pmid = {17945343}, issn = {1090-2414}, mesh = {Animals ; Bass/*anatomy &amp; histology/physiology ; Behavior, Animal/drug effects ; Biomarkers ; Gills/drug effects/pathology/ultrastructure ; Intestines/drug effects/pathology/ultrastructure ; Kidney/drug effects/pathology/ultrastructure ; Liver/drug effects/pathology/ultrastructure ; Mercury/*toxicity ; Water Pollutants, Chemical/*toxicity ; }, abstract = {This work deals with the damaging effects of mercury (Hg concentrations 251, 355, 501 microgl(-1)) on the structure and ultrastructure of gills, liver, intestine and kidney of farmed European sea bass (Dicentrarchus labrax L., 1758) acutely treated for 24 and 48 h. The histoarchitecture of the gills of exposed fish was highly modified due to severe oedema, telangiectasia and secondary lamellar fusion. In hepatocytes and enterocytes hydropic cell swelling, alterations to the endoplasmic reticulum and mitochondria were noted, in addition to an abundance of myelinoid bodies which were frequently encountered following treatment. In the intestine and renal tubules of exposed European sea bass, rodlet cells (RCs) displayed ultrastructural modifications. Statistical analyses were conducted on the number and the size of selected cell types and structures. Following exposure to mercury for 24 and 48 h, the number of chloride cells, RCs and macrophage aggregates were found to have increased significantly in the gills, the intestine and the head kidney.}, }
@article {pmid17942449, year = {2007}, author = {Ono, Y and Sakai, A and Takechi, K and Takio, S and Takusagawa, M and Takano, H}, title = {NtPolI-like1 and NtPolI-like2, bacterial DNA polymerase I homologs isolated from BY-2 cultured tobacco cells, encode DNA polymerases engaged in DNA replication in both plastids and mitochondria.}, journal = {Plant &amp; cell physiology}, volume = {48}, number = {12}, pages = {1679-1692}, doi = {10.1093/pcp/pcm140}, pmid = {17942449}, issn = {0032-0781}, mesh = {Amino Acid Sequence ; Base Sequence ; Cells, Cultured ; DNA Polymerase I/chemistry/isolation &amp; purification/*metabolism ; DNA Primers ; *DNA Replication ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Plastids/*metabolism ; Sequence Homology, Amino Acid ; Nicotiana/*enzymology ; }, abstract = {Two cDNAs encoding homologs of bacterial DNA polymerase I were isolated from cultured tobacco (Nicotiana tabacum) BY-2 cells, and the corresponding genes were named NtPolI-like1 and NtPolI-like2. High sequence similarity suggested that they are orthologous genes each derived from respective parental species of N. tabacum, an allotetraploid plant. Each of the NtPolI-like1/2 gene products had a putative transit peptide for plastid localization at the N-terminus, followed by a 3'-5' exonuclease domain in the internal region, and a DNA polymerase domain in the C-terminal region. Among family A DNA polymerases, NtPolI-like proteins formed, together with other plant DNA polymerase I homologs, a phylogenetic group distinct from mitochondrial DNA polymerase gamma in animals and fungi, as well as eukaryotic cell nuclear-localized repair enzymes. In contrast to computer predictions, experiments with green fluorescent protein (GFP) fusion protein and Western blotting analysis suggested dual targeting of the gene products to both plastids and mitochondria. The recombinant NtPolI-like2 protein exhibited DNA polymerase activity in vitro. Their biochemical character roughly coincided with those of the 116 kDa DNA polymerases found in the plastid and mitochondrial nuclei (nucleoids) isolated from BY-2 cells. Pre-treatment of the organelle nuclear extracts with anti-NtPolI-like antibody removed most of the DNA polymerase activity. Reverse transcription-PCR (RT-PCR) and Western blotting analyses demonstrated transient activation of NtPolI-like gene expression in the initial phase of cell proliferation, exactly when the 116 kDa DNA polymerases in the isolated organelle nuclei were activated and preferential synthesis of organelle DNAs occurred. Taken together, our results suggest that NtPolI-like1/2 genes encode DNA polymerases engaged in DNA replication in both plastids and mitochondria.}, }
@article {pmid17941840, year = {2007}, author = {McGuire, JA and Linkem, CW and Koo, MS and Hutchison, DW and Lappin, AK and Orange, DI and Lemos-Espinal, J and Riddle, BR and Jaeger, JR}, title = {Mitochondrial introgression and incomplete lineage sorting through space and time: phylogenetics of crotaphytid lizards.}, journal = {Evolution; international journal of organic evolution}, volume = {61}, number = {12}, pages = {2879-2897}, doi = {10.1111/j.1558-5646.2007.00239.x}, pmid = {17941840}, issn = {0014-3820}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/*chemistry ; Geographic Information Systems ; Geography ; Hybridization, Genetic ; Lizards/*classification/genetics ; Models, Biological ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {We investigate the roles of mitochondrial introgression and incomplete lineage sorting during the phylogenetic history of crotaphytid lizards. Our Bayesian phylogenetic estimate for Crotaphytidae is based on analysis of mitochondrial DNA sequence data for 408 individuals representing the 12 extant species of Crotaphytus and Gambelia. The mitochondrial phylogeny disagrees in several respects with a previously published morphological tree, as well as with conventional species designations, and we conclude that some of this disagreement stems from hybridization-mediated mitochondrial introgression, as well as from incomplete lineage sorting. Unidirectional introgression of Crotaphytus collaris (western collared lizard) mitochondria into C. reticulatus (reticulate collared lizard) populations in the Rio Grande Valley of Texas has resulted in the replacement of ancestral C. reticulatus mitochondria over approximately two-thirds of the total range of the species, a linear distance of approximately 270 km. Introgression of C. collaris mitochondria into C. bicinctores (Great Basin collared lizard) populations in southwestern Arizona requires a more complex scenario because at least three temporally separated and superimposed introgression events appear to have occurred in this region. We propose an "introgression conveyor" model to explain this unique pattern of mitochondrial variation in this region. We show with ecological niche modeling that the predicted geographical ranges of C. collaris, C. bicinctores, and C. reticulatus during glacial maxima could have provided enhanced opportunities for past hybridization. Our analyses suggest that incomplete lineage sorting and/or introgression has further confounded the phylogenetic placements of additional species including C. nebrius, C. vestigium, C. insularis, C. grismeri, and perhaps G. copei. Despite many independent instances of interspecific hybridization among crotaphytid lizards, the species continue to maintain morphological and geographic cohesiveness throughout their ranges.}, }
@article {pmid17940211, year = {2008}, author = {Mower, JP}, title = {Modeling sites of RNA editing as a fifth nucleotide state reveals progressive loss of edited sites from angiosperm mitochondria.}, journal = {Molecular biology and evolution}, volume = {25}, number = {1}, pages = {52-61}, doi = {10.1093/molbev/msm226}, pmid = {17940211}, issn = {1537-1719}, mesh = {Magnoliopsida/*genetics/metabolism ; Mitochondria/*genetics/metabolism ; *Models, Genetic ; Plastids/genetics/metabolism ; RNA Editing/*physiology ; RNA, Plant/*genetics/metabolism ; }, abstract = {RNA editing is a type of nucleic acid modification found in many eukaryotic lineages. In plants, RNA editing occurs by the site-specific conversion of cytidines to uridines in mitochondrial and plastid transcripts. To quantify the rates of edit site gain and loss in angiosperm mitochondrial genes, a nonreversible maximum likelihood model was developed that treats sites of RNA editing as a fifth nucleotide state. The rate of loss of editing, either by genomic replacement with a thymidine or by loss of recognition by the editing complex, was found to be significantly higher than the rate of gain. Furthermore, the frequency of editing is not at equilibrium in angiosperm mitochondrial sequences; there is a strong tendency for the number of edited sites to decrease over time. These results indicate that selection plays a key role in driving the higher rate of edit site loss relative to gain and suggest that the strength of selection against editing has become increasingly stringent over the course of angiosperm evolution. The model described here should be easily adaptable to other systems that involve nucleic acid modifications.}, }
@article {pmid17936020, year = {2007}, author = {Bergamaschi, S and Dawes-Gromadzki, TZ and Luchetti, A and Marini, M and Mantovani, B}, title = {Molecular taxonomy and phylogenetic relationships among Australian Nasutitermes and Tumulitermes genera (Isoptera, Nasutitermitinae) inferred from mitochondrial COII and 16S sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {45}, number = {3}, pages = {813-821}, doi = {10.1016/j.ympev.2007.07.014}, pmid = {17936020}, issn = {1055-7903}, mesh = {Animals ; Australia ; Electron Transport Complex IV/classification/*genetics/metabolism ; *Evolution, Molecular ; Isoptera/*classification/*genetics ; Mitochondria/classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/classification/*genetics ; }, abstract = {The subfamily Nasutitermitinae Hare (1937) is a tropical and subtropical group, generally considered as the most specialised subfamily of Termitidae. To highlight some taxonomic inconsistencies, the phylogenetic relationships among seven Australian species, morphologically ascribed to the genera Nasutitermes and Tumulitermes, were studied through the analyses of the mitochondrial markers cytochrome oxidase II and 16S ribosomal RNA genes. In our trees, N. longipennis samples clearly pertain to two different specific entities with an apparently parapatric distribution. Further, the phylogenetic analysis performed on separated and combined data sets shows the placement of Tumulitermes species within a clade grouping Nasutitermes ones, and vice versa. Tests for alternative topologies do not support the monophyly of the genera Nasutitermes and Tumulitermes. Our results confirm the hypothesis that the morphological features used to establish relationships among these species are not phylogenetically decisive.}, }
@article {pmid17935214, year = {2007}, author = {Schrader, M and Yoon, Y}, title = {Mitochondria and peroxisomes: are the 'big brother' and the 'little sister' closer than assumed?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {29}, number = {11}, pages = {1105-1114}, doi = {10.1002/bies.20659}, pmid = {17935214}, issn = {0265-9247}, support = {R01 DK061991/DK/NIDDK NIH HHS/United States ; R21 DK073858/DK/NIDDK NIH HHS/United States ; DK061991/DK/NIDDK NIH HHS/United States ; DK073858/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Humans ; Mitochondria/*metabolism/physiology/ultrastructure ; Models, Biological ; Peroxisomes/*metabolism/physiology/ultrastructure ; }, abstract = {Mitochondria and peroxisomes are essential subcellular organelles in mammals. Despite obvious differences, both organelles display certain morphological and functional similarities. Recent studies have elucidated that these highly dynamic and plastic organelles share components of their division machinery. Mitochondria and peroxisomes are metabolically linked organelles, which are cooperating and cross-talking. This review addresses the dynamics and division of mitochondria and peroxisomes as well as their functional similarities to provide insight as to why these organelles share the fission machinery in evolutionary aspects.}, }
@article {pmid17934206, year = {2008}, author = {Podsiadlowski, L and Braband, A and Mayer, G}, title = {The complete mitochondrial genome of the onychophoran Epiperipatus biolleyi reveals a unique transfer RNA set and provides further support for the ecdysozoa hypothesis.}, journal = {Molecular biology and evolution}, volume = {25}, number = {1}, pages = {42-51}, doi = {10.1093/molbev/msm223}, pmid = {17934206}, issn = {1537-1719}, mesh = {Animals ; Codon/*genetics ; *Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Invertebrates/*genetics ; Mitochondria/*genetics ; RNA, Transfer/*genetics ; Species Specificity ; }, abstract = {Onychophora (velvet worms) play a crucial role in current discussions on position of arthropods. The ongoing Articulata/Ecdysozoa debate is in need of additional ground pattern characters for Panarthropoda (Arthropoda, Tardigrada, and Onychophora). Hence, Onychophora is an important outgroup taxon in resolving the relationships among arthropods, irrespective of whether morphological or molecular data are used. To date, there has been a noticeable lack of mitochondrial genome data from onychophorans. Here, we present the first complete mitochondrial genome sequence of an onychophoran, Epiperipatus biolleyi (Peripatidae), which shows several characteristic features. Specifically, the gene order is considerably different from that in other arthropods and other bilaterians. In addition, there is a lack of 9 tRNA genes usually present in bilaterian mitochondrial genomes. All these missing tRNAs have anticodon sequences corresponding to 4-fold degenerate codons, whereas the persisting 13 tRNAs all have anticodons pairing with 2-fold degenerate codons. Sequence-based phylogenetic analysis of the mitochondrial protein-coding genes provides a robust support for a clade consisting of Onychophora, Priapulida, and Arthropoda, which confirms the Ecdysozoa hypothesis. However, resolution of the internal ecdysozoan relationships suffers from a cluster of long-branching taxa (including Nematoda and Platyhelminthes) and a lack of data from Tardigrada and further nemathelminth taxa in addition to nematodes and priapulids.}, }
@article {pmid17932618, year = {2007}, author = {Tanaka, K and Uda, K and Shimada, M and Takahashi, K and Gamou, S and Ellington, WR and Suzuki, T}, title = {Evolution of the cytoplasmic and mitochondrial phosphagen kinases unique to annelid groups.}, journal = {Journal of molecular evolution}, volume = {65}, number = {5}, pages = {616-625}, pmid = {17932618}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Cytoplasm/*enzymology ; *Evolution, Molecular ; Exons/genetics ; Humans ; Introns/genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phosphotransferases/chemistry/*genetics/metabolism ; Phylogeny ; Polychaeta/*enzymology/*genetics ; Sequence Alignment ; }, abstract = {Creatine kinase (CK) is a member of a group of phosphoryl transfer enzymes called phosphagen kinases that play a key role in cellular energy transactions in animals. Three CK isoform gene families are known-cytoplasmic CK (CK), flagellar CK (fCK), and mitochondrial CK (MiCK). Each of the isoforms has a unique gene structure (intron/exon organization). A broad array of other phosphagen kinases is present in animals. Some of these enzymes are found only in annelids and closely related groups including glyocyamine kinase (GK), lombricine kinase (LK), taurocyamine kinase (TK), and a unique arginine kinase (AK) restricted to annelids. Phylogenetic analyses of these annelid phosphagen kinases indicate that they appear to have evolved from a CK-like ancestor. To gain a greater understanding of the relationship of the CK isoforms to the annelid enzymes, we have determined the intron/exon organization of the genes for the following phosphagen kinases: Eisenia LK, Sabellastarte AK, and Arenicola mitochondrial TK (MiTK). Analysis of genomic database for the polychaete Capitella sp. yielded two putative LK genes [cytoplasmic LK and mitochondrial LK (MiLK)]. The intron/exon organization of these genes was compared with available data for cytoplasmic and mitochondrial CKs, and an annelid GK. Surprisingly, these annelid genes, irrespective of whether they are cytoplasmic (LK, AK, and GK) or mitochondrial (MiTK and MiLK), had the same 8-intron/9-exon organization and were strikingly similar to MiCK genes sharing seven of eight splice junctions. These results support the view that the MiCK gene is basal and ancestral to the phosphagen kinases unique to annelids.}, }
@article {pmid17930289, year = {2007}, author = {Sample, C and Golovin, AA}, title = {Nonlinear dynamics of a double bilipid membrane.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {76}, number = {3 Pt 1}, pages = {031925}, doi = {10.1103/PhysRevE.76.031925}, pmid = {17930289}, issn = {1539-3755}, abstract = {The nonlinear dynamics of a biological double membrane that consists of two coupled lipid bilayers, typical of some intracellular organelles such as mitochondria or nuclei, is studied. A phenomenological free-energy functional is formulated in which the curvatures of the two parts of the double membrane and the distance between them are coupled to the lipid chemical composition. The derived nonlinear evolution equations for the double-membrane dynamics are studied analytically and numerically. A linear stability analysis is performed, and the domains of parameters are found in which the double membrane is stable. For the parameter values corresponding to an unstable membrane, numerical simulations are performed that reveal various types of complex dynamics, including the formation of stationary, spatially periodic patterns.}, }
@article {pmid17925860, year = {2007}, author = {Naderi, S and Rezaei, HR and Taberlet, P and Zundel, S and Rafat, SA and Naghash, HR and el-Barody, MA and Ertugrul, O and Pompanon, F and , }, title = {Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity.}, journal = {PloS one}, volume = {2}, number = {10}, pages = {e1012}, pmid = {17925860}, issn = {1932-6203}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Genetic Variation ; Genetics, Population ; Goats/*genetics ; Haplotypes ; Mitochondria ; Models, Biological ; Models, Genetic ; Phylogeny ; Polymorphism, Genetic ; Species Specificity ; }, abstract = {BACKGROUND: From the beginning of domestication, the transportation of domestic animals resulted in genetic and demographic processes that explain their present distribution and genetic structure. Thus studying the present genetic diversity helps to better understand the history of domestic species.<br><br>The genetic diversity of domestic goats has been characterized with 2430 individuals from all over the old world, including 946 new individuals from regions poorly studied until now (mainly the Fertile Crescent). These individuals represented 1540 haplotypes for the HVI segment of the mitochondrial DNA (mtDNA) control region. This large-scale study allowed the establishment of a clear nomenclature of the goat maternal haplogroups. Only five of the six previously defined groups of haplotypes were divergent enough to be considered as different haplogroups. Moreover a new mitochondrial group has been localized around the Fertile Crescent. All groups showed very high haplotype diversity. Most of this diversity was distributed among groups and within geographic regions. The weak geographic structure may result from the worldwide distribution of the dominant A haplogroup (more than 90% of the individuals). The large-scale distribution of other haplogroups (except one), may be related to human migration. The recent fragmentation of local goat populations into discrete breeds is not detectable with mitochondrial markers. The estimation of demographic parameters from mismatch analyses showed that all groups had a recent demographic expansion corresponding roughly to the period when domestication took place. But even with a large data set it remains difficult to give relative dates of expansion for different haplogroups because of large confidence intervals.<br><br>CONCLUSIONS/SIGNIFICANCE: We propose standard criteria for the definition of the different haplogroups based on the result of mismatch analysis and on the use of sequences of reference. Such a method could be also applied for clarifying the nomenclature of mitochondrial haplogroups in other domestic species.}, }
@article {pmid17921152, year = {2007}, author = {Kinsey, ST and Hardy, KM and Locke, BR}, title = {The long and winding road: influences of intracellular metabolite diffusion on cellular organization and metabolism in skeletal muscle.}, journal = {The Journal of experimental biology}, volume = {210}, number = {Pt 20}, pages = {3505-3512}, doi = {10.1242/jeb.000331}, pmid = {17921152}, issn = {0022-0949}, support = {R15-AR052708/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Cell Size ; Diffusion ; Energy Metabolism ; Humans ; Muscle Fibers, Skeletal/cytology/metabolism ; Muscle, Skeletal/*cytology/*metabolism ; }, abstract = {A fundamental principle of physiology is that cells are small in order to minimize diffusion distances for O(2) and intracellular metabolites. In skeletal muscle, it has long been recognized that aerobic fibers that are used for steady state locomotion tend to be smaller than anaerobic fibers that are used for burst movements. This tendency reflects the interaction between diffusion distances and aerobic ATP turnover rates, since maximal intracellular diffusion distances are ultimately limited by fiber size. The effect of diffusion distance on O(2) flux in muscle has been the subject of quantitative analyses for a century, but the influence of ATP diffusion from mitochondria to cellular ATPases on aerobic metabolism has received much less attention. The application of reaction-diffusion mathematical models to experimental measurements of aerobic metabolic processes has revealed that the extreme diffusion distances between mitochondria found in some muscle fibers do not necessarily limit the rates of aerobic processes per se, as long as the metabolic process is sufficiently slow. However, skeletal muscle fibers from a variety of animals appear to have intracellular diffusion distances and/or fiber sizes that put them on the brink of diffusion limitation. Thus, intracellular metabolite diffusion likely influences the evolution of muscle design and places limits on muscle function.}, }
@article {pmid17920936, year = {2007}, author = {Nikulina, EA and Hanel, R and Schäfer, P}, title = {Cryptic speciation and paraphyly in the cosmopolitan bryozoan Electra pilosa--impact of the Tethys closing on species evolution.}, journal = {Molecular phylogenetics and evolution}, volume = {45}, number = {3}, pages = {765-776}, doi = {10.1016/j.ympev.2007.07.016}, pmid = {17920936}, issn = {1055-7903}, mesh = {Animals ; Bryozoa/*classification/*genetics ; Cell Nucleus/genetics ; DNA/genetics ; Europe ; Mitochondria/genetics ; New Zealand ; *Phylogeny ; }, abstract = {Cosmopolitan nature of the marine bryozoan Electra pilosa was studied to clarify geographic structure and to outline evolution and phylogeography of the species. Several local populations from the Northeast Atlantic (North Sea and Baltic Sea), Arctic (Barents Sea and White Sea) and Indo-West Pacific (New Zealand) were compared. In addition, we examined the closely related species E. posidoniae from the Mediterranean Sea. Phylogenetic analysis based on both 16S and 18S rDNA indicate that the Indo-West Pacific E. pilosa is a sister species to the Atlantic-Mediterranean clade, with the latter including the species E. posidoniae and the Atlantic population of E. pilosa. The topology of the phylogenetic tree leads us to conclude that E. pilosa is a paraphyletic species group relative to E. posidoniae, and a molecular dating of its divergence is consistent to geologic events associated with the closure of the Tethys Sea.}, }
@article {pmid17920299, year = {2007}, author = {Boumans, L and Vieites, DR and Glaw, F and Vences, M}, title = {Geographical patterns of deep mitochondrial differentiation in widespread Malagasy reptiles.}, journal = {Molecular phylogenetics and evolution}, volume = {45}, number = {3}, pages = {822-839}, doi = {10.1016/j.ympev.2007.05.028}, pmid = {17920299}, issn = {1055-7903}, mesh = {Animals ; Madagascar ; Mitochondria/classification/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reptiles/classification/*genetics ; }, abstract = {Using sequences of the mitochondrial 16S rRNA gene, we reconstructed the phylogeography of six widely distributed Malagasy reptiles: two gekkonid lizard species, Phelsuma lineata and Hemidactylus mercatorius; two chameleons, the Calumma brevicorne complex, and Furcifer lateralis; and two skinks, Trachylepis gravenhorstii and Trachylepis elegans. Genetic differentiation among major haplotype lineages was high and in some cases indicates or confirms species status of the divergent populations. Maximum uncorrected sequence divergences were between 2.2% and 8.3% within the various species or species complexes. Haplotype lineages were exclusive to geographic regions, except in the commensal H. mercatorius where in three anthropogenic habitats coexistence of haplotype lineages was observed, possibly due to human translocation. The eastward flowing rivers Mangoro and Mananara may represent barriers to gene flow in the case of three species each. Some species sampled from humid eastern and arid western Madagascar showed no differentiation between populations from these two regions; instead the pattern observed was in several cases more concordant with a differentiation along a north-south axis.}, }
@article {pmid17918371, year = {2007}, author = {Hellgren, O and Krizanauskiene, A and Valkĭunas, G and Bensch, S}, title = {Diversity and phylogeny of mitochondrial cytochrome B lineages from six morphospecies of avian Haemoproteus (Haemosporida: Haemoproteidae).}, journal = {The Journal of parasitology}, volume = {93}, number = {4}, pages = {889-896}, doi = {10.1645/GE-1051R1.1}, pmid = {17918371}, issn = {0022-3395}, mesh = {Animals ; Bird Diseases/*parasitology ; Birds ; Cytochromes b/*genetics ; *Genetic Variation ; Haemosporida/classification/*genetics ; Mitochondria/enzymology ; *Phylogeny ; Protozoan Infections, Animal/*parasitology ; }, abstract = {Species of Haemoproteus (Haemosporida: Haemoproteidae), avian haemosporidians, have traditionally been described based on morphology of their gametocytes and on limited experimental information on their vertebrate host specificity. We investigated to what extent the morphological species are represented by monophyletic groups based on DNA sequence data using 2 different fragment lengths of the cytochrome b (cyt. b) gene. Phylogenetic reconstructions of obtained cyt. b lineages from 6 morphospecies of Haemoproteus showed that all lineages formed monophyletic clusters matching the morphospecies. Comparing our data with a recently published study showed that this is not always the case; the morphospecies H. belopolskyi consists of 2 distinct clusters of lineages that apparently have converged in morphology. However, the overall broad congruence between the molecular and morphological clustering of lineages will facilitate the integration of the knowledge obtained by traditional and molecular parasitology. Mean between morphospecies variation was 10-fold higher than the within species variation (5.5% vs. 0.54%), suggesting that Haemoproteus lineages with a genetic differentiation >5% are expected to be morphologically differentiated in most cases. When investigate the utility of 2 different fragment sizes of the cyt. b gene, the partial, 479-bp, cyt. b protocol picked up all mitochondrial (mt)DNA lineages that are found when using the full cyt. b gene, 1073 bp, suggesting that this protocol is sufficient for identification of most mtDNA lineages. All of the mtDNA lineages were associated with unique alleles when amplification was possible at a nuclear locus, strengthening the hypothesis that the designation of lineages based on mtDNA is largely genome-wide representative. We, therefore, propose the use of a cyt. b fragment of this length as a standard gene fragment for a DNA bar-coding system for avian Haemoproteus species.}, }
@article {pmid17917076, year = {2007}, author = {Szolnoki, Z and Kondacs, A and Mandi, Y and Somogyvari, F}, title = {A genetic variant in cytoskeleton motors amplifies susceptibility to leukoaraiosis in hypertensive smokers: gene-environmental interactions behind vascular white matter demyelinization.}, journal = {Journal of molecular neuroscience : MN}, volume = {33}, number = {2}, pages = {173-179}, pmid = {17917076}, issn = {0895-8696}, mesh = {Aged ; Aged, 80 and over ; Cytoskeleton/*metabolism ; Female ; Genetic Predisposition to Disease ; Humans ; *Hypertension ; Kinesins/*genetics ; *Leukoaraiosis/genetics/pathology ; Male ; Middle Aged ; Models, Theoretical ; *Polymorphism, Single Nucleotide ; Risk Factors ; *Smoking ; }, abstract = {One of the most frequent causes of an age-associated cognitive decline is the vascular white matter demyelinization of the brain referred to as leukoaraiosis (LA). The wide range of severity of the cognitive decline caused by LA can have numerous deleterious effects on the quality of life, leading overall to far-reaching public health problems. Besides clinical risk factors such as hypertension and advanced age, genetic susceptibility factors are presumed to be of great importance in the development of LA. The protein kinesin, which is the main motor protein in the trafficking system of the mitochondria, can undergo functional damage under the circumstances of chronic hypoxia. This may give rise to a slowly developing metabolic crisis in the glia cells, a phenomenon hypothesized to account for the evolution of LA. Setting out from this assumption, we examined how the kinesin light-chain 1 (KNS2) G56836C single nucleotide polymorphism in intron 13 affects the susceptibility to LA. This genetic variant was found to be associated with cognitive disturbances and neurodegeneration, and it was presumed to affect the function of kinesin. The association analysis of the above genetic variant was performed in 229 patients with LA and 264 neuroimaging alteration-free controls. The KNS2 56836CC variant increased the risk of LA 7.76-fold in hypertensive smokers as compared with those not carrying this variant. This finding may be useful in everyday clinical practice by indicating the need for stricter preventive measures in CC carriers.}, }
@article {pmid17916323, year = {2007}, author = {Yount, NY and Andrés, MT and Fierro, JF and Yeaman, MR}, title = {The gamma-core motif correlates with antimicrobial activity in cysteine-containing kaliocin-1 originating from transferrins.}, journal = {Biochimica et biophysica acta}, volume = {1768}, number = {11}, pages = {2862-2872}, doi = {10.1016/j.bbamem.2007.07.024}, pmid = {17916323}, issn = {0006-3002}, support = {AI39001/AI/NIAID NIH HHS/United States ; AI48031/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Antimicrobial Cationic Peptides/*chemistry/pharmacology ; Lactoferrin/*chemistry/*pharmacology ; Models, Molecular ; Models, Theoretical ; Molecular Sequence Data ; Phylogeny ; Transferrin/*chemistry ; Two-Hybrid System Techniques ; }, abstract = {Kaliocin-1 is a 31-residue peptide derived from human lactoferrin, and with antimicrobial properties that recapitulate those of its 611 amino acid parent holoprotein. As kaliocin-1 is a cysteine-stabilized peptide, it was of interest to determine whether it contained a multidimensional gamma-core signature recently identified as common to virtually all classes of disulfide-stabilized antimicrobial peptides. Importantly, sequence and structural analyses identified an iteration of this multidimensional antimicrobial signature in kaliocin-1. Further, the gamma-core motif was found to be highly conserved in the transferrin family of proteins across the phylogenetic spectrum. Previous studies suggested that the mechanism by which kaliocin-1 exerts anti-candidal efficacy depends on mitochondrial perturbation without cell membrane permeabilization. Interestingly, results of a yeast two-hybrid screening analysis identified an interaction between kaliocin-1 and mitochondrial initiation factor 2 in a Saccharomyces cerevisiae model system. Taken together, these data extend the repertoire of antimicrobial peptides that contain gamma-core motifs, and suggest that the motif is conserved within large native as well as antimicrobial peptide subcomponents of transferrin family proteins. Finally, these results substantiate the hypothesis that antimicrobial activity associated with host defense effector proteins containing a gamma-core motif may correspond to targets common to fungal mitochondria or their bacterial ancestors.}, }
@article {pmid17912611, year = {2008}, author = {Bogorad, L}, title = {Evolution of early eukaryotic cells: genomes, proteomes, and compartments.}, journal = {Photosynthesis research}, volume = {95}, number = {1}, pages = {11-21}, pmid = {17912611}, issn = {0166-8595}, mesh = {Animals ; *Biological Evolution ; *Cell Compartmentation ; Eukaryotic Cells/*cytology/*metabolism ; Genome/*genetics ; Mitochondria/metabolism ; Proteome/*metabolism ; }, abstract = {Eukaryotes arose from an endosymbiotic association of an alpha-proteobacterium-like organism (the ancestor of mitochondria) with a host cell (lacking mitochondria or plastids). Plants arose by the addition of a cyanobacterium-like endosymbiont (the ancestor of plastids) to the two-member association. Each member of the association brought a unique internal environment and a unique genome. Analyses of recently acquired genomic sequences with newly developed algorithms have revealed (a) that the number of endosymbiont genes that remain in eukaryotic cells-principally in the nucleus-is surprisingly large, (b) that protein products of a large number of genes (or their descendents) that entered the association in the genome of the host are now directed to an organelle derived from an endosymbiont, and (c) that protein products of genes traceable to endosymbiont genomes are directed to the nucleo-cytoplasmic compartment. Consideration of these remarkable findings has led to the present suggestion that contemporary eukaryotic cells evolved through continual chance relocation and testing of genes as well as combinations of gene products and biochemical processes in each unique cell compartment derived from a member of the eukaryotic association. Most of these events occurred during about 300 million years, or so, before contemporary forms of eukaryotic cells appear in the fossil record; they continue today.}, }
@article {pmid17906827, year = {2007}, author = {Marcadé, I and Cordaux, R and Doublet, V and Debenest, C and Bouchon, D and Raimond, R}, title = {Structure and evolution of the atypical mitochondrial genome of Armadillidium vulgare (Isopoda, Crustacea).}, journal = {Journal of molecular evolution}, volume = {65}, number = {6}, pages = {651-659}, pmid = {17906827}, issn = {0022-2844}, mesh = {Animals ; Base Composition ; Base Sequence ; DNA, Mitochondrial/chemistry/genetics ; *Evolution, Molecular ; Genome, Mitochondrial/*genetics ; Isopoda/*genetics ; Models, Genetic ; Molecular Sequence Data ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {The crustacean isopod Armadillidium vulgare is characterized by an unusual approximately 42-kb-long mitochondrial genome consisting of two molecules co-occurring in mitochondria: a circular approximately 28-kb dimer formed by two approximately 14-kb monomers fused in opposite polarities and a linear approximately 14-kb monomer. Here we determined the nucleotide sequence of the fundamental monomeric unit of A. vulgare mitochondrial genome, to gain new insight into its structure and evolution. Our results suggest that the junction zone between monomers of the dimer structure is located in or near the control region. Direct sequencing indicated that the nucleotide sequences of the different monomer units are virtually identical. This suggests that gene conversion and/or replication processes play an important role in shaping nucleotide sequence variation in this mitochondrial genome. The only heteroplasmic site we identified predicts an alloacceptor tRNA change from tRNA(Ala) to tRNA(Val). Therefore, in A. vulgare, tRNA(Ala) and tRNA(Val) are found at the same locus in different monomers, ensuring that both tRNAs are present in mitochondria. The presence of this heteroplasmic site in all sequenced individuals suggests that the polymorphism is selectively maintained, probably because of the necessity of both tRNAs for maintaining proper mitochondrial functions. Thus, our results provide empirical evidence for the tRNA gene recruitment model of tRNA evolution. Moreover, interspecific comparisons showed that the A. vulgare mitochondrial gene order is highly derived compared to the putative ancestral arthropod type. By contrast, an overall high conservation of mitochondrial gene order is observed within crustacean isopods.}, }
@article {pmid17905998, year = {2007}, author = {Schlegel, T and Mirus, O and von Haeseler, A and Schleiff, E}, title = {The tetratricopeptide repeats of receptors involved in protein translocation across membranes.}, journal = {Molecular biology and evolution}, volume = {24}, number = {12}, pages = {2763-2774}, doi = {10.1093/molbev/msm211}, pmid = {17905998}, issn = {0737-4038}, mesh = {Cell Membrane/*metabolism ; Evolution, Molecular ; Humans ; Likelihood Functions ; Models, Genetic ; Pisum sativum/chemistry ; Phylogeny ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport ; Receptors, Cell Surface/*chemistry/*metabolism ; *Repetitive Sequences, Amino Acid ; Saccharomyces cerevisiae/chemistry ; }, abstract = {Transport of polypeptides across membranes is a general and essential process in every cell. This process is utilized by molecular machines composed of soluble and membrane-inserted proteins. At least one component of the molecular transport machines present in different membranes contains a subunit with a domain composed of 3 tetratricopeptide repeat (TPR) motifs. These domains are important for protein-protein interaction, for example, recognition of chaperones. To understand the evolution of these TPR domain-containing receptors involved in protein translocation, we inferred their phylogenetic relationships. We show that the evolutionary rate of these TPR domains is reduced when compared with the remaining sequence. The reduction is explained by the interaction of the TPR domains with their substrates. Based on the TPR tree, we propose that Sec72 recognizes Hsp70 and that Tom34 recognizes Hsp90. The phylogeny can further be used to assign the localization of the Toc64 isoforms to mitochondria or chloroplasts. Our findings are discussed in the context of the evolutionary development of translocation systems with focus on the occurrence of Hsp70/Hsp90-recognizing TPR domains in these machineries.}, }
@article {pmid17898086, year = {2008}, author = {Autio, KJ and Kastaniotis, AJ and Pospiech, H and Miinalainen, IJ and Schonauer, MS and Dieckmann, CL and Hiltunen, JK}, title = {An ancient genetic link between vertebrate mitochondrial fatty acid synthesis and RNA processing.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {22}, number = {2}, pages = {569-578}, doi = {10.1096/fj.07-8986}, pmid = {17898086}, issn = {1530-6860}, mesh = {Amino Acid Sequence ; Animals ; Conserved Sequence ; DNA, Complementary/genetics ; Fatty Acids/*biosynthesis ; Gene Expression Regulation, Enzymologic ; Genome/genetics ; Humans ; Hydro-Lyases/chemistry/genetics/isolation &amp; purification/metabolism ; Mitochondria/*genetics/*metabolism ; Mitochondrial Proteins ; Molecular Sequence Data ; Mutation/genetics ; Open Reading Frames/genetics ; Phylogeny ; RNA/*genetics ; Ribonuclease P/genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Sequence Alignment ; Transcription, Genetic/genetics ; Vertebrates/*genetics/*metabolism ; }, abstract = {In bacteria, functionally related gene products are often encoded by a common transcript. Such polycistronic transcripts are rare in eukaryotes. Here we isolated several clones from human cDNA libraries, which rescued the respiratory-deficient phenotype of a yeast mitochondrial 3-hydroxyacyl thioester dehydratase 2 (htd2) mutant strain. All complementing cDNAs were derived from the RPP14 transcript previously described to encode the RPP14 subunit of the human ribonuclease P (RNase P) complex. We identified a second, 3' open reading frame (ORF) on the RPP14 transcript encoding a protein showing similarity to known dehydratases and hydratase 2 enzymes. The protein was localized in mitochondria, and the recombinant enzyme exhibited (3R)-specific hydratase 2 activity. Based on our results, we named the protein human 3-hydroxyacyl-thioester dehydratase 2 (HsHTD2), which is involved in mitochondrial fatty acid synthesis. The bicistronic arrangement of RPP14 and HsHTD2, as well as the general exon structure of the gene, is conserved in vertebrates from fish to humans, indicating a genetic link conserved for 400 million years between RNA processing and mitochondrial fatty acid synthesis.}, }
@article {pmid17897476, year = {2007}, author = {Jackson, CJ and Norman, JE and Schnare, MN and Gray, MW and Keeling, PJ and Waller, RF}, title = {Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria.}, journal = {BMC biology}, volume = {5}, number = {}, pages = {41}, pmid = {17897476}, issn = {1741-7007}, mesh = {Animals ; Blotting, Southern ; Codon, Initiator ; Codon, Terminator ; DNA, Mitochondrial/genetics ; Dinoflagellida/*genetics ; *Genome, Mitochondrial ; Genome, Protozoan ; Phylogeny ; Polymerase Chain Reaction ; RNA Editing ; RNA, Ribosomal/genetics ; Terminal Repeat Sequences ; Trans-Splicing ; *Transcription, Genetic ; }, abstract = {BACKGROUND: Dinoflagellates comprise an ecologically significant and diverse eukaryotic phylum that is sister to the phylum containing apicomplexan endoparasites. The mitochondrial genome of apicomplexans is uniquely reduced in gene content and size, encoding only three proteins and two ribosomal RNAs (rRNAs) within a highly compacted 6 kb DNA. Dinoflagellate mitochondrial genomes have been comparatively poorly studied: limited available data suggest some similarities with apicomplexan mitochondrial genomes but an even more radical type of genomic organization. Here, we investigate structure, content and expression of dinoflagellate mitochondrial genomes.<br><br>RESULTS: From two dinoflagellates, Crypthecodinium cohnii and Karlodinium micrum, we generated over 42 kb of mitochondrial genomic data that indicate a reduced gene content paralleling that of mitochondrial genomes in apicomplexans, i.e., only three protein-encoding genes and at least eight conserved components of the highly fragmented large and small subunit rRNAs. Unlike in apicomplexans, dinoflagellate mitochondrial genes occur in multiple copies, often as gene fragments, and in numerous genomic contexts. Analysis of cDNAs suggests several novel aspects of dinoflagellate mitochondrial gene expression. Polycistronic transcripts were found, standard start codons are absent, and oligoadenylation occurs upstream of stop codons, resulting in the absence of termination codons. Transcripts of at least one gene, cox3, are apparently trans-spliced to generate full-length mRNAs. RNA substitutional editing, a process previously identified for mRNAs in dinoflagellate mitochondria, is also implicated in rRNA expression.<br><br>CONCLUSION: The dinoflagellate mitochondrial genome shares the same gene complement and fragmentation of rRNA genes with its apicomplexan counterpart. However, it also exhibits several unique characteristics. Most notable are the expansion of gene copy numbers and their arrangements within the genome, RNA editing, loss of stop codons, and use of trans-splicing.}, }
@article {pmid17892581, year = {2007}, author = {Imanian, B and Keeling, PJ}, title = {The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum retain functionally overlapping mitochondria from two evolutionarily distinct lineages.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {172}, pmid = {17892581}, issn = {1471-2148}, mesh = {Animals ; DNA Primers ; DNA, Complementary ; DNA, Mitochondrial/*genetics ; DNA, Protozoan/*genetics ; Dinoflagellida/classification/enzymology/*genetics/ultrastructure ; Electron Transport Complex IV/genetics ; *Genome, Mitochondrial ; Likelihood Functions ; Mitochondria/*ultrastructure ; Phylogeny ; RNA, Protozoan ; Sequence Analysis, DNA ; Symbiosis ; Transcription, Genetic ; }, abstract = {BACKGROUND: The dinoflagellates Durinskia baltica and Kryptoperidinium foliaceum are distinguished by the presence of a tertiary plastid derived from a diatom endosymbiont. The diatom is fully integrated with the host cell cycle and is so altered in structure as to be difficult to recognize it as a diatom, and yet it retains a number of features normally lost in tertiary and secondary endosymbionts, most notably mitochondria. The dinoflagellate host is also reported to retain mitochondrion-like structures, making these cells unique in retaining two evolutionarily distinct mitochondria. This redundancy raises the question of whether the organelles share any functions in common or have distributed functions between them.<br><br>RESULTS: We show that both host and endosymbiont mitochondrial genomes encode genes for electron transport proteins. We have characterized cytochrome c oxidase 1 (cox1), cytochrome oxidase 2 (cox2), cytochrome oxidase 3 (cox3), cytochrome b (cob), and large subunit of ribosomal RNA (LSUrRNA) of endosymbiont mitochondrial ancestry, and cox1 and cob of host mitochondrial ancestry. We show that all genes are transcribed and that those ascribed to the host mitochondrial genome are extensively edited at the RNA level, as expected for a dinoflagellate mitochondrion-encoded gene. We also found evidence for extensive recombination in the host mitochondrial genes and that recombination products are also transcribed, as expected for a dinoflagellate.<br><br>CONCLUSION: Durinskia baltica and K. foliaceum retain two mitochondria from evolutionarily distinct lineages, and the functions of these organelles are at least partially overlapping, since both express genes for proteins in electron transport.}, }
@article {pmid17889652, year = {2007}, author = {Yang, H and Yang, T and Baur, JA and Perez, E and Matsui, T and Carmona, JJ and Lamming, DW and Souza-Pinto, NC and Bohr, VA and Rosenzweig, A and de Cabo, R and Sauve, AA and Sinclair, DA}, title = {Nutrient-sensitive mitochondrial NAD+ levels dictate cell survival.}, journal = {Cell}, volume = {130}, number = {6}, pages = {1095-1107}, pmid = {17889652}, issn = {0092-8674}, support = {P01 AG027916-030003/AG/NIA NIH HHS/United States ; P01 AG027916-020003/AG/NIA NIH HHS/United States ; P01 AG027916-010003/AG/NIA NIH HHS/United States ; P01 AG027916-04S20003/AG/NIA NIH HHS/United States ; R01AG028730/AG/NIA NIH HHS/United States ; R01 AG019719-06A1/AG/NIA NIH HHS/United States ; R01 GM068072/GM/NIGMS NIH HHS/United States ; P01 AG027916/AG/NIA NIH HHS/United States ; P01 AG027916-04S10003/AG/NIA NIH HHS/United States ; R01 AG028730/AG/NIA NIH HHS/United States ; //Intramural NIH HHS/United States ; R01 AG019719-07/AG/NIA NIH HHS/United States ; R01 AG028730-02/AG/NIA NIH HHS/United States ; R01 DK073466/DK/NIDDK NIH HHS/United States ; R01 AG028730-01A1/AG/NIA NIH HHS/United States ; R01GM068072/GM/NIGMS NIH HHS/United States ; P01 AG027916-040003/AG/NIA NIH HHS/United States ; R01 AG019719/AG/NIA NIH HHS/United States ; R01 DK 073466/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Apoptosis/drug effects ; Cell Hypoxia ; Cell Line ; Cell Nucleus/metabolism ; Cell Survival ; Cells, Cultured ; Cytokines/*biosynthesis/*metabolism ; Cytoplasm/metabolism ; Fasting/*metabolism ; Food Deprivation ; Humans ; Methyl Methanesulfonate/toxicity ; Mice ; Mitochondria/drug effects/enzymology/*metabolism/pathology ; Mitochondrial Proteins/genetics/metabolism ; Mutagens/toxicity ; NAD/*metabolism ; Nicotinamide Phosphoribosyltransferase ; RNA Interference ; RNA, Small Interfering/metabolism ; Rats ; Sirtuin 3 ; Sirtuins/genetics/metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Transfection ; Up-Regulation ; }, abstract = {A major cause of cell death caused by genotoxic stress is thought to be due to the depletion of NAD(+) from the nucleus and the cytoplasm. Here we show that NAD(+) levels in mitochondria remain at physiological levels following genotoxic stress and can maintain cell viability even when nuclear and cytoplasmic pools of NAD(+) are depleted. Rodents fasted for 48 hr show increased levels of the NAD(+) biosynthetic enzyme Nampt and a concomitant increase in mitochondrial NAD(+). Increased Nampt provides protection against cell death and requires an intact mitochondrial NAD(+) salvage pathway as well as the mitochondrial NAD(+)-dependent deacetylases SIRT3 and SIRT4. We discuss the relevance of these findings to understanding how nutrition modulates physiology and to the evolution of apoptosis.}, }
@article {pmid17884500, year = {2007}, author = {Esser, C and Martin, W}, title = {Supertrees and symbiosis in eukaryote genome evolution.}, journal = {Trends in microbiology}, volume = {15}, number = {10}, pages = {435-437}, doi = {10.1016/j.tim.2007.09.001}, pmid = {17884500}, issn = {0966-842X}, mesh = {Bacteria/genetics ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; *Genome ; Mitochondria/genetics ; *Models, Genetic ; *Phylogeny ; Plastids/genetics ; *Symbiosis ; }, abstract = {If we took all of the single copy genes in all sequenced genomes, made phylogenetic trees from them individually, and then made the supertree of those trees, what would we get? Recently, David Pisani and colleagues did that experiment and their results are likely to spark much discussion. Their prokaryote tree looks very familiar, but the genome history of eukaryotes appears dominated by genes of cyanobacterial (plastid) and alpha-proteobacterial (mitochondrial) origin, while the host component branches within the archaebacteria.}, }
@article {pmid17880942, year = {2008}, author = {Aguilera, P and Barry, T and Tovar, J}, title = {Entamoeba histolytica mitosomes: organelles in search of a function.}, journal = {Experimental parasitology}, volume = {118}, number = {1}, pages = {10-16}, doi = {10.1016/j.exppara.2007.08.004}, pmid = {17880942}, issn = {0014-4894}, support = {BB/C507145/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Aerobiosis ; Anaerobiosis ; Animals ; Entamoeba histolytica/classification/physiology/*ultrastructure ; Entamoebiasis/parasitology ; Genome, Protozoan ; Humans ; Intestine, Large/parasitology ; Iron-Sulfur Proteins/biosynthesis/physiology ; Mitochondria/physiology ; Organelles/genetics/*physiology/ultrastructure ; Oxygen Consumption ; Phylogeny ; Protozoan Proteins/metabolism ; Pyruvic Acid/metabolism ; Symbiosis ; }, abstract = {It has been more than eight years since the discovery of mitosomes (mitochondrial remnant organelles) in the intestinal human pathogen Entamoeba histolytica. Despite detailed knowledge about the biochemistry of this parasite and the completion of the E. histolytica genome sequencing project no physiological function has yet been unequivocally assigned to these organelles. Entamoeba mitosomes seem to be the most degenerate of all endosymbiosis-derived organelles studied to date. They do not appear to participate in energy metabolism and may have dispensed completely with the proteins required for iron-sulphur cluster biosynthesis. However, the large number of mitosomes found in E. histolytica trophozoites hints at a significant biological role for these organelles in their natural environment. Identifying the protein complement of mitosomes will provide answers as to their biological significance and the reason(s) for their retention in this parasite.}, }
@article {pmid17878306, year = {2007}, author = {Elrod, JW and Calvert, JW and Morrison, J and Doeller, JE and Kraus, DW and Tao, L and Jiao, X and Scalia, R and Kiss, L and Szabo, C and Kimura, H and Chow, CW and Lefer, DJ}, title = {Hydrogen sulfide attenuates myocardial ischemia-reperfusion injury by preservation of mitochondrial function.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {39}, pages = {15560-15565}, pmid = {17878306}, issn = {0027-8424}, support = {R01 HL060849/HL/NHLBI NIH HHS/United States ; 2R01 HL060849-07/HL/NHLBI NIH HHS/United States ; R21 GM073049/GM/NIGMS NIH HHS/United States ; R01 DK064344/DK/NIDDK NIH HHS/United States ; 1F32 DK077380-01/DK/NIDDK NIH HHS/United States ; R21 GM73049-01/GM/NIGMS NIH HHS/United States ; F32 DK077380/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Apoptosis ; Echocardiography/methods ; Heart Ventricles/pathology ; Hydrogen Sulfide/chemistry/*pharmacology ; Inflammation ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Mitochondria/metabolism/*pathology ; Myocardium/chemistry/*pathology ; Myocytes, Cardiac/metabolism ; Neutrophils/metabolism ; Oxygen Consumption ; *Reperfusion Injury ; Troponin I/metabolism ; }, abstract = {The recent discovery that hydrogen sulfide (H(2)S) is an endogenously produced gaseous second messenger capable of modulating many physiological processes, much like nitric oxide, prompted us to investigate the potential of H(2)S as a cardioprotective agent. In the current study, we demonstrate that the delivery of H(2)S at the time of reperfusion limits infarct size and preserves left ventricular (LV) function in an in vivo model of myocardial ischemia-reperfusion (MI-R). This observed cytoprotection is associated with an inhibition of myocardial inflammation and a preservation of both mitochondrial structure and function after I-R injury. Additionally, we show that modulation of endogenously produced H(2)S by cardiac-specific overexpression of cystathionine gamma-lyase (alpha-MHC-CGL-Tg mouse) significantly limits the extent of injury. These findings demonstrate that H(2)S may be of value in cytoprotection during the evolution of myocardial infarction and that either administration of H(2)S or the modulation of endogenous production may be of clinical benefit in ischemic disorders.}, }
@article {pmid17875217, year = {2007}, author = {Kessler, D and Papatheodorou, P and Stratmann, T and Dian, EA and Hartmann-Fatu, C and Rassow, J and Bayer, P and Mueller, JW}, title = {The DNA binding parvulin Par17 is targeted to the mitochondrial matrix by a recently evolved prepeptide uniquely present in Hominidae.}, journal = {BMC biology}, volume = {5}, number = {}, pages = {37}, pmid = {17875217}, issn = {1741-7007}, mesh = {Animals ; Base Sequence ; Blotting, Western ; Cell Fractionation ; DNA-Binding Proteins/*genetics/metabolism ; *Evolution, Molecular ; HeLa Cells ; Hominidae/*genetics ; Humans ; Mitochondria/metabolism ; Mitochondrial Proteins/*genetics/metabolism ; Molecular Sequence Data ; NIMA-Interacting Peptidylprolyl Isomerase ; Peptidylprolyl Isomerase/*genetics/metabolism ; Protein Interaction Domains and Motifs ; Protein Structure, Secondary ; Protein Transport ; Sequence Alignment ; }, abstract = {BACKGROUND: The parvulin-type peptidyl prolyl cis/trans isomerase Par14 is highly conserved in all metazoans. The recently identified parvulin Par17 contains an additional N-terminal domain whose occurrence and function was the focus of the present study.<br><br>RESULTS: Based on the observation that the human genome encodes Par17, but bovine and rodent genomes do not, Par17 exon sequences from 10 different primate species were cloned and sequenced. Par17 is encoded in the genomes of Hominidae species including humans, but is absent from other mammalian species. In contrast to Par14, endogenous Par17 was found in mitochondrial and membrane fractions of human cell lysates. Fluorescence of EGFP fusions of Par17, but not Par14, co-localized with mitochondrial staining. Par14 and Par17 associated with isolated human, rat and yeast mitochondria at low salt concentrations, but only the Par17 mitochondrial association was resistant to higher salt concentrations. Par17 was imported into mitochondria in a time and membrane potential-dependent manner, where it reached the mitochondrial matrix. Moreover, Par17 was shown to bind to double-stranded DNA under physiological salt conditions.<br><br>CONCLUSION: Taken together, the DNA binding parvulin Par17 is targeted to the mitochondrial matrix by the most recently evolved mitochondrial prepeptide known to date, thus adding a novel protein constituent to the mitochondrial proteome of Hominidae.}, }
@article {pmid17868468, year = {2007}, author = {Chu, Z and Li, J and Eshaghi, M and Karuturi, RK and Lin, K and Liu, J}, title = {Adaptive expression responses in the Pol-gamma null strain of S. pombe depleted of mitochondrial genome.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {323}, pmid = {17868468}, issn = {1471-2164}, mesh = {Aniline Compounds/metabolism ; Cell Wall/metabolism ; DNA Polymerase gamma ; DNA, Mitochondrial/*genetics ; DNA-Directed DNA Polymerase/*genetics ; Fluorescent Dyes/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Fungal ; *Genes, Fungal ; Indoles/metabolism ; Models, Genetic ; Phylogeny ; Schizosaccharomyces/*genetics/metabolism/ultrastructure ; }, abstract = {BACKGROUND: DNA polymerase gamma(Pol-gamma) has been shown to be essential for maintenance of the mitochondrial genome (mtDNA) in the petite-positive budding yeast Saccharomyces cerevisiae. Budding yeast cells lacking mitochondria exhibit a slow-growing or petite-colony phenotype. Petite strains fail to grow on non-fermentable carbon sources. However, it is not clear whether the Pol-gamma is required for mtDNA maintenance in the petite-negative fission yeast Schizosaccharomyces pombe.<br><br>RESULTS: We show that disruption of the nuclear gene pog1+ that encodes Pol-gamma is sufficient to deplete mtDNA in S. pombe. Cells bearing pog1Delta allele require substantial growth periods to form petite colonies. Mitotracker assays indicate that pog1Delta cells are defective in mitochondrial function and EM analyses suggest that pog1Delta cells lack normal mitochondrial structures. Depletion of mtDNA in pog1Delta cells is evident from quantitative real-time PCR assays. Genome-wide expression profiles of pog1Delta and other mtDNA-less cells reveal that many genes involved in response to stimulus, energy derivation by oxidation of organic compounds, cellular carbohydrate metabolism, and energy reserve metabolism are induced. Conversely, many genes encoding proteins involved in amino acid metabolism and oxidative phosphorylation are repressed.<br><br>CONCLUSION: By showing that Pol-gamma is essential for mtDNA maintenance and disruption of pog1+ alters the genome-wide expression profiles, we demonstrated that cells lacking mtDNA exhibit adaptive nuclear gene expression responses in the petite-negative S. pombe.}, }
@article {pmid17855023, year = {2007}, author = {Burton, RS and Byrne, RJ and Rawson, PD}, title = {Three divergent mitochondrial genomes from California populations of the copepod Tigriopus californicus.}, journal = {Gene}, volume = {403}, number = {1-2}, pages = {53-59}, doi = {10.1016/j.gene.2007.07.026}, pmid = {17855023}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; California ; Copepoda/*genetics ; DNA/chemistry/genetics ; DNA Primers ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Gene Order ; *Genetics, Population ; *Genome ; Locus Control Region/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; }, abstract = {Previous work on the harpacticoid copepod Tigriopus californicus has focused on the extensive population differentiation in three mtDNA protein coding genes (COXI, COXII, Cytb). In order to get a more complete understanding of mtDNA evolution in this species, we sequenced three complete mitochondrial genomes (one from each of three California populations) and compared them to two published mtDNA genomes from an Asian congener, Tigriopus japonicus. Several features of the mtDNA genome appear to be conserved within the genus: 1) the unique order of the protein coding genes, rRNA genes and most of the tRNA genes, 2) the genome is compact, varying between 14.3 and 14.6 kb, and 3) all genes are encoded on the same strand of the mtDNA. Within T. californicus, extremely high levels of nucleotide divergence (>20%) are observed across much of the mitochondrial genome. Inferred amino acid sequences of the proteins encoded in the mtDNAs also show high levels of divergence; at the extreme, the three ND3 variants in T. californicus showed >25% amino acid substitutions, compared with <3% amino acid divergence at the previously studied COXI locus. Unusual secondary structures make functional assignments of some tRNAs difficult. The only apparent tRNA(trp) in these genomes completely overlaps the 5' end of the 16S rRNA in all three T. californicus mtDNAs. Although not previously noted, this feature is also conserved in T. japonicus mtDNAs; whether this sequence is processed into a functional tRNA has not been determined. The putative control region contains a duplicated segment of different length (from 88 to 155 bp) in each of the T. californicus sequences. In each case, the duplicated segments are not tandem repeats; despite their different lengths, the distance between the start of the first and the start of the second repeat is conserved (520 bp). The functional significance, if any, of this repeat structure remains unknown.}, }
@article {pmid17824774, year = {2007}, author = {Miyazaki, J and Nakao, K and Mihara, M and Sakai, T and Gunji, Y and Tojo, K and Muraoka, K and Hosoya, K}, title = {Incongruence between mtDNA phylogeny and morphologial and ecological characters in loaches of the genus Lefua (Balitoridae, Cypriniformes).}, journal = {Zoological science}, volume = {24}, number = {7}, pages = {666-675}, doi = {10.2108/zsj.24.666}, pmid = {17824774}, issn = {0289-0003}, mesh = {Animals ; Base Sequence ; Cypriniformes/anatomy &amp; histology/*classification/genetics/*physiology ; DNA, Mitochondrial/analysis/*chemistry/genetics ; Ecology ; *Evolution, Molecular ; Genetic Variation/*genetics ; Japan ; Molecular Sequence Data ; *Phylogeny ; Random Amplified Polymorphic DNA Technique/veterinary ; Sequence Alignment/veterinary ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {To elucidate the phylogenetic position of Lefua loaches from Aichi and Shizuoka Prefectures of Honshu Island, Japan, we determined their nucleotide sequences for the mitochondrial D-loop region and compared these to sequences from four other Lefua species: L. costata, L. nikkonis, L. echigonia, and L. sp. Loaches identified as L. sp. on the basis of morphology comprised a clade (the L. sp. Tokai population) that grouped together with L. echigonia; hence, the processes involved in evolution within the genus Lefua were unclear. We performed randomly amplified polymorphic DNA (RAPD) analyses to obtain genetic information on nuclear DNA. The RAPD patterns of the L. sp. Tokai population differed from those of the local L. echigonia and L. sp. populations. The L. sp. Tokai population was similar to L. echigonia with regard to mitochondrial DNA but differed from L. echigonia and L. sp. with respect to nuclear DNA; this indicated that the evolutionary background of the L. sp. Tokai population was unique. We suggest that introgression of mitochondria occurred from L. echigonia to the L. sp. Tokai population, and speculate on the process of evolution of the latter population of Lefua. As with six L. echigonia populations and two L. sp. populations, we regard the L. sp. Tokai population as an evolutionary significant unit (ESU) that qualifies for protection as an endangered loach.}, }
@article {pmid17786631, year = {2007}, author = {Orrenius, S}, title = {Reactive oxygen species in mitochondria-mediated cell death.}, journal = {Drug metabolism reviews}, volume = {39}, number = {2-3}, pages = {443-455}, doi = {10.1080/03602530701468516}, pmid = {17786631}, issn = {0360-2532}, mesh = {Animals ; Antioxidants/metabolism ; Apoptosis/physiology ; Cardiolipins/metabolism ; Cell Death/*physiology ; Cytochromes c/metabolism ; Humans ; Mitochondria/*physiology ; Oxidation-Reduction ; Reactive Oxygen Species/*metabolism ; }, abstract = {In addition to the well-established role of the mitochondria in energy metabolism, regulation of cell death has recently emerged as a second major function of these organelles. This, in turn, seems to be intimately linked to their role as the major intracellular source of reactive oxygen species (ROS) which are mainly, generated at Complex I and III of the respiratory chain. Excessive ROS production can lead to oxidation of macromolecules and has been implicated in mtDNA mutations, ageing, and cell death. Although mitochondrial dysfunction can cause ATP depletion and necrosis, these organelles are also involved in the regulation of apoptotic cell death by mechanisms, which have been conserved through evolution. Thus, many lethal agents target the mitochondria and cause release of cytochrome c and other pro-apoptotic proteins, which can trigger caspase activation and apoptosis. Taken together, these findings have placed the mitochondria in the focus of current cell death research.}, }
@article {pmid17765203, year = {2007}, author = {Azuma, K and Kobayashi, M and Nakamura, M and Suzuki, N and Yashima, S and Iwamuro, S and Ikegame, M and Yamamoto, T and Hattori, A}, title = {Two osteoclastic markers expressed in multinucleate osteoclasts of goldfish scales.}, journal = {Biochemical and biophysical research communications}, volume = {362}, number = {3}, pages = {594-600}, doi = {10.1016/j.bbrc.2007.08.010}, pmid = {17765203}, issn = {0006-291X}, mesh = {Acid Phosphatase/*biosynthesis ; Amino Acid Sequence ; Animals ; Bone and Bones/metabolism ; Cathepsin K ; Cathepsins/*biosynthesis/metabolism ; Cloning, Molecular ; DNA, Complementary/metabolism ; Gene Expression Regulation ; Goldfish ; In Situ Hybridization ; Isoenzymes/*biosynthesis ; Molecular Sequence Data ; Osteoclasts/*metabolism ; Phylogeny ; RNA, Messenger/metabolism ; Sequence Homology, Amino Acid ; Tartrate-Resistant Acid Phosphatase ; }, abstract = {Complementary DNAs encoding two major osteoclastic markers, tartrate-resistant acid phosphatase (TRAP) and cathepsin K (Cath K) were cloned from the scales of a teleost, the goldfish. This is the first report of the full coding sequence of TRAP and Cath K molecules in fish. In the goldfish scale both TRAP and Cath K mRNAs were expressed in the multinucleate osteoclasts, which showed large numbers of mitochondria and lysosomes, and a well developed ruffled border. These characteristic features of osteoclasts in the scales are similar to those in mammals. Most teleosts use the scale as an internal calcium reservoir during the reproductive season. The expression of TRAP and Cath K mRNAs in the scale significantly increased in April, which is a reproductive season, compared with that in October, a non-reproductive season. Thus, both of these molecular markers should be useful for the study of osteoclasts in the teleost scale.}, }
@article {pmid17764966, year = {2007}, author = {Goyal, A}, title = {Osmoregulation in Dunaliella, Part I: Effects of osmotic stress on photosynthesis, dark respiration and glycerol metabolism in Dunaliella tertiolecta and its salt-sensitive mutant (HL 25/8).}, journal = {Plant physiology and biochemistry : PPB}, volume = {45}, number = {9}, pages = {696-704}, doi = {10.1016/j.plaphy.2007.05.008}, pmid = {17764966}, issn = {0981-9428}, mesh = {Chlorophyta/genetics/*metabolism ; Darkness ; Gene Expression Regulation, Plant ; Glycerol/*metabolism ; *Oxygen Consumption ; Photosynthesis/drug effects/*physiology ; Sodium Chloride/*pharmacology ; Time Factors ; Water/metabolism ; Water-Electrolyte Balance ; }, abstract = {The photosynthetic oxygen evolution increased by about 30% over control when Dunaliella tertiolecta and its salt-sensitive mutant (HL 25/8) were stressed by raising NaCl concentration from 0.17 to 0.4M, however, during the dilution stress the photosynthetic oxygen evolution was progressively decreased with increasing dilution (decreasing the salinity). The photosynthetic oxygen evolution is affected by the water potential of the medium rather than by the ionic strength. Mitochondrial dark respiration was unaffected by salt stress, however, it was increased by about 50% (parent strain) and 35% (the mutant) upon dilution as if reduced pyridine nucleotide generated during glycerol dissimilation reaction were continuously oxidized by the mitochondria. The salt stress-induced changes in photosynthetic (14)CO(2) fixation were consistent with the observed rates of photosynthetic oxygen evolution. The mutant strain showed about one-half the capability for photosynthesis, and glycerol synthesis compared to the parent strain. However, the proportion of photosynthetically newly fixed carbon during salt stress in glycerol was similar in both strains. The glycerol dissimilation capabilities of both strains were also similar. It is suggested that the salt sensitivity of the mutant is probably due to its reduced dissolved inorganic carbon transport, photosynthetic and starch metabolism capabilities to provide carbon for glycerol synthesis in the time frame of adaptation process.}, }
@article {pmid17728076, year = {2007}, author = {Ueda, M and Fujimoto, M and Arimura, S and Murata, J and Tsutsumi, N and Kadowaki, K}, title = {Loss of the rpl32 gene from the chloroplast genome and subsequent acquisition of a preexisting transit peptide within the nuclear gene in Populus.}, journal = {Gene}, volume = {402}, number = {1-2}, pages = {51-56}, doi = {10.1016/j.gene.2007.07.019}, pmid = {17728076}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Cell Nucleus/genetics/metabolism ; *Genes, Plant ; *Genome, Chloroplast ; *Genome, Plant ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/analysis/*genetics ; Populus/*genetics ; Protein Sorting Signals ; Recombinant Fusion Proteins/genetics/metabolism ; Ribosomal Proteins/analysis/chemistry/*genetics ; Sequence Alignment ; Superoxide Dismutase/genetics/metabolism ; Superoxide Dismutase-1 ; }, abstract = {Gene transfer events from organelle genomes (mitochondria and chloroplasts in plants) to the nuclear genome are important processes in the evolution of the eukaryotic cell. It is highly likely that the gene transfer event is still an ongoing process in higher plant mitochondria and chloroplasts. The number and order of genes encoded in the chloroplast genome of higher plants are highly conserved. Recently, several exceptional cases of gene loss from the chloroplast genome have been discovered as the number of complete chloroplast genome sequences has increased. The Populus chloroplast genome has lost the rpl32 gene, while the corresponding the chloroplast rpl32 (cp rpl32) gene has been identified in the nuclear genome. Nuclear genes transferred from the chloroplast genome need to gain a sequence that encodes a transit peptide. Here, we revealed that the nuclear cp rpl32 gene has acquired the exon sequence, which is highly homologous to a transit peptide derived from the chloroplast Cu-Zn superoxide dismutase (cp sod-1) gene. The cp rpl32 gene has acquired the sequence that encodes not only for the transit peptide, but also for the conserved N-terminal portion of the mature SOD protein from the cp sod-1 gene, suggesting the occurrence of DNA sequence duplication. Unlike cp SOD-1, cp RPL32 did not show biased localization in the chloroplasts. This difference may be caused by mutations accumulated in the sequence of the SOD domain on the cp rpl32 gene. We provide new insight into the fate of the inherent sequence derived from a transit peptide.}, }
@article {pmid17724133, year = {2007}, author = {Kim, Y and Zhou, P and Qian, L and Chuang, JZ and Lee, J and Li, C and Iadecola, C and Nathan, C and Ding, A}, title = {MyD88-5 links mitochondria, microtubules, and JNK3 in neurons and regulates neuronal survival.}, journal = {The Journal of experimental medicine}, volume = {204}, number = {9}, pages = {2063-2074}, pmid = {17724133}, issn = {0022-1007}, support = {R01 NS034179/NS/NINDS NIH HHS/United States ; NS 34179/NS/NINDS NIH HHS/United States ; AI 30165/AI/NIAID NIH HHS/United States ; R01 NS035806/NS/NINDS NIH HHS/United States ; R01 AI030165/AI/NIAID NIH HHS/United States ; R01 GM061710/GM/NIGMS NIH HHS/United States ; GM 61710/GM/NIGMS NIH HHS/United States ; R37 NS034179/NS/NINDS NIH HHS/United States ; NS 35806/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Cell Compartmentation ; Cell Death ; Cell Survival ; Conserved Sequence ; Evolution, Molecular ; Glucose/deficiency ; Hippocampus/cytology/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Microtubules/*metabolism ; Mitochondria/enzymology/*metabolism ; Mitogen-Activated Protein Kinase 10/*metabolism ; Myeloid Cells/metabolism ; Myeloid Differentiation Factor 88/deficiency/*metabolism ; Neurons/*cytology/*enzymology ; Oxygen ; Protein Binding ; Protein Transport ; }, abstract = {The innate immune system relies on evolutionally conserved Toll-like receptors (TLRs) to recognize diverse microbial molecular structures. Most TLRs depend on a family of adaptor proteins termed MyD88s to transduce their signals. Critical roles of MyD88-1-4 in host defense were demonstrated by defective immune responses in knockout mice. In contrast, the sites of expression and functions of vertebrate MyD88-5 have remained elusive. We show that MyD88-5 is distinct from other MyD88s in that MyD88-5 is preferentially expressed in neurons, colocalizes in part with mitochondria and JNK3, and regulates neuronal death. We prepared MyD88-5/GFP transgenic mice via a bacterial artificial chromosome to preserve its endogenous expression pattern. MyD88-5/GFP was detected chiefly in the brain, where it associated with punctate structures within neurons and copurified in part with mitochondria. In vitro, MyD88-5 co-immunoprecipitated with JNK3 and recruited JNK3 from cytosol to mitochondria. Hippocampal neurons from MyD88-5-deficient mice were protected from death after deprivation of oxygen and glucose. In contrast, MyD88-5-null macrophages behaved like wild-type cells in their response to microbial products. Thus, MyD88-5 appears unique among MyD88s in functioning to mediate stress-induced neuronal toxicity.}, }
@article {pmid17719785, year = {2007}, author = {Westermann, B}, title = {Focus on mitochondria: introducing a new series in Trends in Cell Biology.}, journal = {Trends in cell biology}, volume = {17}, number = {9}, pages = {417-418}, doi = {10.1016/j.tcb.2007.07.006}, pmid = {17719785}, issn = {1879-3088}, mesh = {Animals ; Biological Evolution ; Cell Physiological Phenomena ; Eukaryotic Cells/*cytology ; Humans ; *Mitochondria/genetics/metabolism ; Symbiosis ; }, }
@article {pmid17716375, year = {2007}, author = {Beraldo, FH and Garcia, CR}, title = {Divergent calcium signaling in RBCs from Tropidurus torquatus (Squamata--Tropiduridae) strengthen classification in lizard evolution.}, journal = {BMC physiology}, volume = {7}, number = {}, pages = {7}, pmid = {17716375}, issn = {1472-6793}, mesh = {Animals ; *Biological Evolution ; Calcium Signaling/*physiology ; Erythrocytes/classification/cytology/*physiology ; Lizards/*classification/*physiology ; Mitochondria/classification/physiology ; }, abstract = {BACKGROUND: We have previously reported that a Teiid lizard red blood cells (RBCs) such as Ameiva ameiva and Tupinambis merianae controls intracellular calcium levels by displaying multiple mechanisms. In these cells, calcium stores could be discharged not only by: thapsigargin, but also by the Na+/H+ ionophore monensin, K+/H+ ionophore nigericin and the H+ pump inhibitor bafilomycin as well as ionomycin. Moreover, these lizards possess a P2Y-type purinoceptors that mobilize Ca2+ from intracellular stores upon ATP addition.<br><br>RESULTS: Here we report, that RBCs from the tropidurid lizard Tropidurus torquatus store Ca2+ in endoplasmic reticulum (ER) pool but unlike in the referred Teiidae, these cells do not store calcium in monensin-nigericin sensitive pools. Moreover, mitochondria from T. torquatus RBCs accumulate Ca2+. Addition of ATP to a calcium-free medium does not increase the [Ca2+]c levels, however in a calcium medium we observe an increase in cytosolic calcium. This is an indication that purinergic receptors in these cells are P2X-like.<br><br>CONCLUSION: T. torquatus RBCs present different mechanisms from Teiid lizard red blood cells (RBCs), for controlling its intracellular calcium levels. At T. torquatus the ion is only stored at endoplasmic reticulum and mitochondria. Moreover activation of purinergic receptor, P2X type, was able to induce an influx of calcium from extracellular medium. These studies contribute to the understanding of the evolution of calcium homeostasis and signaling in nucleated RBCs.}, }
@article {pmid17567455, year = {2007}, author = {Sato, N}, title = {Central role of mitochondria in metabolic regulation of liver pathophysiology.}, journal = {Journal of gastroenterology and hepatology}, volume = {22 Suppl 1}, number = {}, pages = {S1-6}, doi = {10.1111/j.1440-1746.2007.04963.x}, pmid = {17567455}, issn = {0815-9319}, mesh = {Animals ; Biological Evolution ; Cytochromes/physiology ; Electron Transport ; Energy Metabolism/*physiology ; Humans ; Liver Diseases/metabolism/*physiopathology ; Mitochondria, Liver/*physiology ; Oxidative Phosphorylation ; Reactive Oxygen Species ; }, abstract = {Mitochondria play a central role in cellular energy metabolism. Oxidative phosphorylation occurs in the electron transport system of the inner mitochondrial membrane. Cytochrome aa3, b and c1 are encoded by mitochondrial DNA whereas cytochrome c is encoded by the nuclear gene, and these mitochondrial-DNA dependent cytochromes are decreased and electron transport at complex II, III and IV is disturbed in liver carcinomas and during carcinogenesis. The more the decreased cytochrome and oxidase activity are seen, the more significant is the increase in reactive oxygen species (ROS) production. ROS produced in mitochondria may be the main cause of nuclear-gene mutation in carcinogenesis. The mitochondrial dysfunction and overproduction of ROS plays a key role in progression of chronic hepatitis C and ethanol-induced liver injury. Ethanol also causes bacterial translocation in the intestine and the resulting lipopolysaccharides (LPS) activates Kupffer cells to produce pro-inflammatory cytokines. We suspect that non-alcoholic steatohepatitis (NASH) also is the result of increased ROS production in Kupffer cells and hepatocytes.}, }
@article {pmid17715154, year = {2007}, author = {Dacks, JB and Field, MC}, title = {Evolution of the eukaryotic membrane-trafficking system: origin, tempo and mode.}, journal = {Journal of cell science}, volume = {120}, number = {Pt 17}, pages = {2977-2985}, doi = {10.1242/jcs.013250}, pmid = {17715154}, issn = {0021-9533}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Biological Evolution ; Biological Transport/physiology ; Eukaryotic Cells/cytology/*metabolism ; Genomics ; Humans ; Intracellular Membranes/*metabolism ; Phylogeny ; }, abstract = {The emergence of an endomembrane system was a crucial stage in the prokaryote-to-eukaryote evolutionary transition. Recent genomic and molecular evolutionary analyses have provided insight into how this critical system arrived at its modern configuration. The apparent relative absence of prokaryotic antecedents for the endomembrane machinery contrasts with the situation for mitochondria, plastids and the nucleus. Overall, the evidence suggests an autogenous origin for the eukaryotic membrane-trafficking machinery. The emerging picture is that early eukaryotic ancestors had a complex endomembrane system, which implies that this cellular system evolved relatively rapidly after the proto-eukaryote diverged away from the other prokaryotic lines. Many of the components of the trafficking system are the result of gene duplications that have produced proteins that have similar functions but differ in their subcellular location. A proto-eukaryote possessing a very simple trafficking system could thus have evolved to near modern complexity in the last common eukaryotic ancestor (LCEA) via paralogous gene family expansion of the proteins encoding organelle identity. The descendents of this common ancestor have undergone further modification of the trafficking machinery; unicellular simplicity and multicellular complexity are the prevailing trend, but there are some remarkable counter-examples.}, }
@article {pmid17711486, year = {2007}, author = {Montes-Cano, MA and de la Horra, C and Dapena, FJ and Mateos, I and Friaza, V and Respaldiza, N and Muñoz-Lobato, F and Medrano, FJ and Calderon, EJ and Varela, JM}, title = {Dynamic colonisation by different Pneumocystis jirovecii genotypes in cystic fibrosis patients.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {13}, number = {10}, pages = {1008-1011}, doi = {10.1111/j.1469-0691.2007.01789.x}, pmid = {17711486}, issn = {1198-743X}, mesh = {Adolescent ; Adult ; Carrier State/*epidemiology/microbiology ; Child ; Child, Preschool ; Cystic Fibrosis/*complications ; Female ; Genotype ; Humans ; Infant ; Male ; Mitochondria/genetics ; *Molecular Epidemiology ; Pneumocystis carinii/classification/*genetics ; Pneumonia, Pneumocystis/*epidemiology/microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; Spain/epidemiology ; }, abstract = {Although asymptomatic carriers of Pneumocystis jirovecii with cystic fibrosis (CF) have been described previously, the molecular epidemiology of P. jirovecii in CF patients has not yet been clarified. This study identified the distribution and dynamic evolution of P. jirovecii genotypes based on the mitochondrial large-subunit (mt LSU) rRNA gene. The mt LSU rRNA genotypes of P. jirovecii isolates in 33 respiratory samples from CF patients were investigated using nested PCR and direct sequencing. Three different genotypes were detected: 36.3% genotype 1 (85C/248C); 15.1% genotype 2 (85A/248C); 42.4% genotype 3 (85T/248C); and 6% mixed genotypes. Patients studied during a 1-year follow-up period showed a continuous colonisation/clearance cycle involving P. jirovecii and an accumulative tendency to be colonised with genotype 3.}, }
@article {pmid17705058, year = {2008}, author = {Zeh, JA and Zeh, DW}, title = {Maternal inheritance, epigenetics and the evolution of polyandry.}, journal = {Genetica}, volume = {134}, number = {1}, pages = {45-54}, pmid = {17705058}, issn = {0016-6707}, mesh = {Animals ; *Biological Evolution ; *Epigenesis, Genetic ; Female ; Genetic Variation ; Humans ; Inheritance Patterns/*genetics ; Male ; Mating Preference, Animal/physiology ; Pregnancy ; Reproduction/*genetics/physiology ; Selection, Genetic ; Sexual Behavior, Animal/physiology ; Spermatozoa/physiology ; }, abstract = {Growing evidence indicates that females actively engage in polyandry either to avoid genetic incompatibility or to bias paternity in favor of genetically superior males. Despite empirical support for the intrinsic male quality hypothesis, the maintenance of variation in male fitness remains a conundrum for traditional "good genes" models of sexual selection. Here, we discuss two mechanisms of non-Mendelian inheritance, maternal inheritance of mitochondria and epigenetic regulation of gene expression, which may explain the persistence of variation in male fitness traits important in post-copulatory sexual selection. The inability of males to transmit mitochondria precludes any direct evolutionary response to selection on mitochondrial mutations that reduce or enhance male fitness. Consequently, mitochondrial-based variation in sperm traits is likely to persist, even in the face of intense sperm competition. Indeed, mitochondrial nucleotide substitutions, deletions and insertions are now known to be a primary cause of low sperm count and poor sperm motility in humans. Paradoxically, in the field of sexual selection, female-limited response to selection has been largely overlooked. Similarly, the contribution of epigenetics (e.g., DNA methylation, histone modifications and non-coding RNAs) to heritable variation in male fitness has received little attention from evolutionary theorists. Unlike DNA sequence based variation, epigenetic variation can be strongly influenced by environmental and stochastic effects experienced during the lifetime of an individual. Remarkably, in some cases, acquired epigenetic changes can be stably transmitted to offspring. A recent study indicates that sperm exhibit particularly high levels of epigenetic variation both within and between individuals. We suggest that such epigenetic variation may have important implications for post-copulatory sexual selection and may account for recent findings linking sperm competitive ability to offspring fitness.}, }
@article {pmid17704138, year = {2007}, author = {Sarnowska, E and Grzybowska, EA and Sobczak, K and Konopinski, R and Wilczynska, A and Szwarc, M and Sarnowski, TJ and Krzyzosiak, WJ and Siedlecki, JA}, title = {Hairpin structure within the 3'UTR of DNA polymerase beta mRNA acts as a post-transcriptional regulatory element and interacts with Hax-1.}, journal = {Nucleic acids research}, volume = {35}, number = {16}, pages = {5499-5510}, pmid = {17704138}, issn = {1362-4962}, mesh = {3' Untranslated Regions/*chemistry ; Animals ; Base Sequence ; Binding Sites ; Carrier Proteins/analysis/*metabolism ; Cell Line, Tumor ; DNA Polymerase beta/*genetics ; Dimerization ; Evolution, Molecular ; *Gene Expression Regulation ; Genes, Reporter ; Intracellular Signaling Peptides and Proteins ; Mitochondria/chemistry ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Nuclear Matrix/chemistry ; Nucleic Acid Conformation ; Rats ; *Regulatory Sequences, Ribonucleic Acid ; Ultraviolet Rays ; }, abstract = {Aberrant expression of DNA polymerase beta, a key enzyme involved in base excision repair, leads to genetic instability and carcinogenesis. Pol beta expression has been previously shown to be regulated at the level of transcription, but there is also evidence of post-transcriptional regulation, since rat transcripts undergo alternative polyadenylation, and the resulting 3'UTR contain at least one regulatory element. Data presented here indicate that RNA of the short 3'UTR folds to form a strong secondary structure (hairpin). Its regulatory role was established utilizing a luciferase-based reporter system. Further studies led to the identification of a protein factor, which binds to this element-the anti-apoptotic, cytoskeleton-related protein Hax-1. The results of in vitro binding analysis indicate that the formation of the RNA-protein complex is significantly impaired by disruption of the hairpin motif. We demonstrate that Hax-1 binds to Pol beta mRNA exclusively in the form of a dimer. Biochemical analysis revealed the presence of Hax-1 in mitochondria, but also in the nuclear matrix, which, along with its transcript-binding properties, suggests that Hax-1 plays a role in post-transcriptional regulation of expression of Pol beta.}, }
@article {pmid17697939, year = {2007}, author = {Stöckl, P and Zankl, C and Hütter, E and Unterluggauer, H and Laun, P and Heeren, G and Bogengruber, E and Herndler-Brandstetter, D and Breitenbach, M and Jansen-Dürr, P}, title = {Partial uncoupling of oxidative phosphorylation induces premature senescence in human fibroblasts and yeast mother cells.}, journal = {Free radical biology &amp; medicine}, volume = {43}, number = {6}, pages = {947-958}, doi = {10.1016/j.freeradbiomed.2007.06.005}, pmid = {17697939}, issn = {0891-5849}, support = {S 9302/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Acetylcysteine/metabolism ; Aging, Premature/chemically induced/*etiology/metabolism ; Carbonyl Cyanide p-Trifluoromethoxyphenylhydrazone/pharmacology ; Cell Proliferation ; Cell Respiration ; Cells, Cultured ; *Cellular Senescence ; Fibroblasts/drug effects/metabolism ; Humans ; *Oxidative Phosphorylation/drug effects ; Reactive Oxygen Species/metabolism ; Saccharomyces cerevisiae/drug effects/metabolism ; Uncoupling Agents/pharmacology ; }, abstract = {The mitochondrial theory of aging predicts that functional alterations in mitochondria leading to reactive oxygen species (ROS) production contribute to the aging process in most if not all species. Using cellular senescence as a model for human aging, we have recently reported partial uncoupling of the respiratory chain in senescent human fibroblasts. In the present communication, we address a potential cause-effect relationship between impaired mitochondrial coupling and premature senescence. Chronic exposure of human fibroblasts to the chemical uncoupler carbonylcyanide p-trifluoromethoxyphenylhydrazone (FCCP) led to a temporary, reversible uncoupling of oxidative phosphorylation. FCCP inhibited cell proliferation in a dose-dependent manner, and a significant proportion of the cells entered premature senescence within 12 days. Unexpectedly, chronic exposure of cells to FCCP led to a significant increase in ROS production, and the inhibitory effect of FCCP on cell proliferation was eliminated by the antioxidant N-acetyl-cysteine. However, antioxidant treatment did not prevent premature senescence, suggesting that a reduction in the level of oxidative phosphorylation contributes to phenotypical changes characteristic of senescent human fibroblasts. To assess whether this mechanism might be conserved in evolution, the influence of mitochondrial uncoupling on replicative life span of yeast cells was also addressed. Similar to our findings in human fibroblasts, partial uncoupling of oxidative phsophorylation in yeast cells led to a substantial decrease in the mother-cell-specific life span and a concomitant incrase in ROS, indicating that life span shortening by mild mitochondrial uncoupling may represent a "public" mechanism of aging.}, }
@article {pmid17696778, year = {2007}, author = {Santamaria, M and Lanave, C and Vicario, S and Saccone, C}, title = {Variability of the mitochondrial genome in mammals at the inter-species/intra-species boundary.}, journal = {Biological chemistry}, volume = {388}, number = {9}, pages = {943-946}, doi = {10.1515/BC.2007.121}, pmid = {17696778}, issn = {1431-6730}, mesh = {Animals ; Base Sequence/genetics ; Cattle/*genetics ; Dogs/*genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; Genetic Variation ; *Genome, Mitochondrial ; Humans ; Mitochondria/*genetics ; Species Specificity ; Sus scrofa/*genetics ; }, abstract = {Genomic variations represent the molecular basis of the biodiversity of living organisms on which selection operates to generate evolution. In eukaryotes, genomic variability can be experienced in both nuclear and organellar, i.e. mitochondrial and plastid (where present), genomes, which can follow completely different evolution pathways, as revealed by comparative genomics analyses. In Metazoa, for which a substantial number of complete genome sequences are available (nuclear, but mainly mitochondrial), we are just starting to grasp the selective pressures operating on some basic features of the genome as a whole. In this brief review, we discuss the variability of the mitochondrial metazoan genome, with particular reference to mitochondrial DNA in mammals. In light of the recent assumption that a small segment of mitochondrial DNA may be used, particularly in Metazoa, as a species marker, some data on mitochondrial gene variability at the inter-species/intra-species boundary are reported. Intra-species variability has been evaluated in four mammalian species, Homo sapiens, Bos taurus, Sus scrofa and Canis familiaris, whereas the relationship between intra- and inter-species variability has been investigated in Bos taurus and Bos indicus.}, }
@article {pmid17696775, year = {2007}, author = {Merz, S and Hammermeister, M and Altmann, K and Dürr, M and Westermann, B}, title = {Molecular machinery of mitochondrial dynamics in yeast.}, journal = {Biological chemistry}, volume = {388}, number = {9}, pages = {917-926}, doi = {10.1515/BC.2007.110}, pmid = {17696775}, issn = {1431-6730}, mesh = {Mitochondria/metabolism/*physiology/ultrastructure ; Mitochondrial Proteins/*metabolism ; Saccharomyces cerevisiae/*physiology/ultrastructure ; Saccharomyces cerevisiae Proteins/metabolism ; }, abstract = {Mitochondria are amazingly dynamic organelles. They continuously move along cytoskeletal tracks and frequently fuse and divide. These processes are important for maintenance of mitochondrial functions, for inheritance of the organelles upon cell division, for cellular differentiation and for apoptosis. As the machinery of mitochondrial behavior has been highly conserved during evolution, it can be studied in simple model organisms, such as yeast. During the past decade, several key components of mitochondrial dynamics have been identified and functionally characterized in Saccharomyces cerevisiae. These include the mitochondrial fusion and fission machineries and proteins required for maintenance of tubular shape and mitochondrial motility. Taken together, these findings reveal a comprehensive picture that shows the cellular processes and molecular components required for mitochondrial inheritance and morphogenesis in a simple eukaryotic cell.}, }
@article {pmid17686885, year = {2007}, author = {Nakada, T and Hoshijima, K and Esaki, M and Nagayoshi, S and Kawakami, K and Hirose, S}, title = {Localization of ammonia transporter Rhcg1 in mitochondrion-rich cells of yolk sac, gill, and kidney of zebrafish and its ionic strength-dependent expression.}, journal = {American journal of physiology. Regulatory, integrative and comparative physiology}, volume = {293}, number = {4}, pages = {R1743-53}, doi = {10.1152/ajpregu.00248.2007}, pmid = {17686885}, issn = {0363-6119}, support = {R01-GM-069382/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Animals, Genetically Modified ; Base Sequence ; Cation Transport Proteins/chemistry/*genetics/*metabolism ; Gene Expression Regulation ; Gills/*cytology ; Green Fluorescent Proteins ; Kidney/*cytology ; Mitochondria/*metabolism ; Osmolar Concentration ; Phylogeny ; Protein Transport ; RNA, Messenger/genetics/metabolism ; Water/chemistry ; Yolk Sac/*cytology ; Zebrafish ; Zebrafish Proteins/chemistry/*genetics/*metabolism ; }, abstract = {Members of the Rh glycoprotein family have been shown to be involved in ammonia transport in a variety of species. Here we show that zebrafish Rhcg1, a member of the Rh glycoprotein family, is highly expressed in the yolk sac, gill, and renal tubules. Molecular cloning and characterization indicate that zebrafish Rhcg1 shares 82% sequence identity with the pufferfish ortholog fRhcg1. RT-PCR, combined with in situ hybridization, revealed that Rhcg1 is first expressed in vacuolar-type H(+)-ATPase/mitochondrion-rich cells (vH-MRC) on the yolk sac of larvae at 3 days postfertilization (dpf) and later in vH-MRC-like cells in the gill at 4-5 dpf. Ammonia excretion from zebrafish larvae increased in parallel with the expression of Rhcg1. At larval stages, Rhcg1 mRNA was detected only on the yolk sac and gill; however, the kidney, as well as the gill, becomes a major site of Rhcg1 expression in adults. Using a zebrafish Tol2 transgenic line whose vH-MRC are labeled with green fluorescent protein (GFP) and an antibody against zebrafish Rhcg1, we demonstrate that Rhcg1 is located in the apical regions of 1) vH-MRC on the yolk sac and vH-MRC-like cells (cell population with the expression of Rhcg1 and GFP) in the gill and 2) cells in the renal distal tubule and intercalated cell-like cells in the collecting duct of the kidney. Remarkably, expression of Rhcg1 mRNA at the larval stage was changed by environmental ionic strength. These results suggest that roles of zebrafish Rhcg1 are not solely ammonia secretion to eliminate nitrogen from the gill.}, }
@article {pmid17684698, year = {2007}, author = {Waters, ER and Rioflorido, I}, title = {Evolutionary analysis of the small heat shock proteins in five complete algal genomes.}, journal = {Journal of molecular evolution}, volume = {65}, number = {2}, pages = {162-174}, pmid = {17684698}, issn = {0022-2844}, mesh = {Algal Proteins/*genetics ; Amino Acid Sequence ; Animals ; Chlamydomonas reinhardtii/genetics ; Chlorophyta/genetics ; Diatoms/genetics ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; *Genome ; Heat-Shock Proteins, Small/*genetics ; Molecular Sequence Data ; Phylogeny ; Rhodophyta/genetics ; Sequence Alignment ; Sequence Analysis, Protein ; Species Specificity ; }, abstract = {Small heat shock proteins (sHSPs) are chaperones that are crucial in the heat shock response but also have important nonstress roles within the cell. sHSPs are found in all three domains of life (Bacteria, Archaea, and Eukarya). These proteins are particularly diverse within land plants and the evolutionary origin of the land plant sHSP families is still an open question. Here we describe the identification of 17 small sHSPs from the complete genome sequences of five diverse algae: Chlamydomonas reinhardtii, Cyanidioschyzon merolae, Ostreococcus lucimarinus, Ostreococcus tauri, and Thalassiosira pseudonana. Our analysis indicates that the number and diversity of algal sHSPs are not correlated with adaptation to extreme conditions. While all of the algal sHSPs identified are members of this large and important superfamily, none of these sHSPs are members of the diverse land plant sHSP families. The evolutionary relationships among the algal sHSPs and homologues from bacteria and other eukaryotes are consistent with the hypothesis that the land plant chloroplast and mitochondrion sHSPs did not originate from the endosymbionts of the chloroplast and mitochondria. In addition the evolutionary history of the sHSPs is very different from that of the HSP70s. Finally, our analysis of the algal sHSPs sequences in light of the known sHSP crystal structures and functional data suggests that the sHSPs possess considerable structural and functional diversity.}, }
@article {pmid17681397, year = {2007}, author = {Breton, S and Beaupré, HD and Stewart, DT and Hoeh, WR and Blier, PU}, title = {The unusual system of doubly uniparental inheritance of mtDNA: isn't one enough?.}, journal = {Trends in genetics : TIG}, volume = {23}, number = {9}, pages = {465-474}, doi = {10.1016/j.tig.2007.05.011}, pmid = {17681397}, issn = {0168-9525}, mesh = {Adaptation, Biological/genetics ; Animals ; Bivalvia/*genetics ; Evolution, Molecular ; Female ; *Genes, Mitochondrial ; Genome ; Male ; Models, Biological ; Models, Genetic ; Phylogeny ; Sex Factors ; }, abstract = {Mitochondria possess their own genetic material (mitochondrial DNA or mtDNA), whose gene products are involved in mitochondrial respiration and oxidative phosphorylation, transcription, and translation. In animals, mitochondrial DNA is typically transmitted to offspring by the mother alone. The discovery of 'doubly uniparental inheritance' (DUI) of mtDNA in some bivalves has challenged the paradigm of strict maternal inheritance (SMI). In this review, we survey recent advances in our understanding of DUI, which is a peculiar system of cytoplasmic DNA inheritance that involves distinct maternal and paternal routes of mtDNA transmission, a novel extension of a mitochondrial gene (cox2), recombination, and periodic 'role-reversals' of the normally male and female-transmitted mitochondrial genomes. DUI provides a unique opportunity for studying nuclear-cytoplasmic genome interactions and the evolutionary significance of different modes of mitochondrial inheritance.}, }
@article {pmid17679693, year = {2007}, author = {Popadin, K and Polishchuk, LV and Mamirova, L and Knorre, D and Gunbin, K}, title = {Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large versus small mammals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {33}, pages = {13390-13395}, pmid = {17679693}, issn = {0027-8424}, mesh = {Animals ; Biological Evolution ; Mammals/classification/*genetics ; Mitochondria/genetics ; Models, Theoretical ; *Mutation ; Proteins/*genetics ; }, abstract = {After the effective size of a population, N(e), declines, some slightly deleterious amino acid replacements which were initially suppressed by purifying selection become effectively neutral and can reach fixation. Here we investigate this phenomenon for a set of all 13 mitochondrial protein-coding genes from 110 mammalian species. By using body mass as a proxy for N(e), we show that large mammals (i.e., those with low N(e)) as compared with small ones (in our sample these are, on average, 369.5 kg and 275 g, respectively) have a 43% higher rate of accumulation of nonsynonymous nucleotide substitutions relative to synonymous substitutions, and an 8-40% higher rate of accumulation of radical amino acid substitutions relative to conservative substitutions, depending on the type of amino acid classification. These higher rates result in a 6% greater amino acid dissimilarity between modern species and their most recent reconstructed ancestors in large versus small mammals. Because nonsynonymous substitutions are likely to be more harmful than synonymous substitutions, and radical amino acid substitutions are likely to be more harmful than conservative ones, our results suggest that large mammals experience less efficient purifying selection than small mammals. Furthermore, because in the course of mammalian evolution body size tends to increase and, consequently, N(e) tends to decline, evolution of mammals toward large body size may involve accumulation of slightly deleterious mutations in mitochondrial protein-coding genes, which may contribute to decline or extinction of large mammals.}, }
@article {pmid17676874, year = {2007}, author = {Hemp, J and Han, H and Roh, JH and Kaplan, S and Martinez, TJ and Gennis, RB}, title = {Comparative genomics and site-directed mutagenesis support the existence of only one input channel for protons in the C-family (cbb3 oxidase) of heme-copper oxygen reductases.}, journal = {Biochemistry}, volume = {46}, number = {35}, pages = {9963-9972}, doi = {10.1021/bi700659y}, pmid = {17676874}, issn = {0006-2960}, support = {R01 HL016101/HL/NHLBI NIH HHS/United States ; GM15590-37/GM/NIGMS NIH HHS/United States ; HL16101/HL/NHLBI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Amino Acid Substitution/genetics ; Copper/chemistry ; Electron Transport Complex IV/*genetics ; Heme/analogs &amp; derivatives/chemistry/*metabolism ; Ion Channels/chemistry/metabolism ; Ion Transport ; Models, Molecular ; Molecular Sequence Data ; *Mutagenesis, Site-Directed ; Oxidation-Reduction ; Phylogeny ; Proton Pumps/*genetics/metabolism ; *Protons ; Rhodobacter sphaeroides/*enzymology/genetics ; Sequence Analysis, DNA ; Vibrio cholerae/*enzymology/genetics ; }, abstract = {Oxygen reductase members of the heme-copper superfamily are terminal respiratory oxidases in mitochondria and many aerobic bacteria and archaea, coupling the reduction of molecular oxygen to water to the translocation of protons across the plasma membrane. The protons required for catalysis and pumping in the oxygen reductases are derived from the cytoplasmic side of the membrane, transferred via proton-conducting channels comprised of hydrogen bond chains containing internal water molecules along with polar amino acid side chains. Recent analyses identified eight oxygen reductase families in the superfamily: the A-, B-, C-, D-, E-, F-, G-, and H-families of oxygen reductases. Two proton input channels, the K-channel and the D-channel, are well established in the A-family of oxygen reductases (exemplified by the mitochondrial cytochrome c oxidases and by the respiratory oxidases from Rhodobacter sphaeroides and Paracoccus denitrificans). Each of these channels can be identified by the pattern of conserved polar amino acid residues within the protein. The C-family (cbb3 oxidases) is the second most abundant oxygen reductase family after the A-family, making up more than 20% of the sequences of the heme-copper superfamily. In this work, sequence analyses and structural modeling have been used to identify likely proton channels in the C-family. The pattern of conserved polar residues supports the presence of only one proton input channel, which is spatially analogous to the K-channel in the A-family. There is no pattern of conserved residues that could form a D-channel analogue or an alternative proton channel. The functional importance of the residues proposed to be part of the K-channel was tested by site-directed mutagenesis using the cbb3 oxidases from R. sphaeroides and Vibrio cholerae. Several of the residues proposed to be part of the putative K-channel had significantly reduced catalytic activity upon mutation: T219V, Y227F/Y228F, N293D, and Y321F. The data strongly suggest that in the C-family only one channel functions for the delivery of both catalytic and pumped protons. In addition, it is also proposed that a pair of acidic residues, which are totally conserved among the C-family, may be part of a proton-conducting exit channel for pumped protons. The residues homologous to these acidic amino acids are highly conserved in the cNOR family of nitric oxide reductases and have previously been implicated as part of a proton-conducting channel delivering protons from the periplasmic side of the membrane to the enzyme active site in the cNOR family. It is possible that the C-family contains a homologous proton-conducting channel that delivers pumped protons in the opposite direction, from the active site to the periplasm.}, }
@article {pmid17674076, year = {2007}, author = {Gibson, T and Blok, VC and Dowton, M}, title = {Sequence and characterization of six mitochondrial subgenomes from Globodera rostochiensis: multipartite structure is conserved among close nematode relatives.}, journal = {Journal of molecular evolution}, volume = {65}, number = {3}, pages = {308-315}, pmid = {17674076}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; *Conserved Sequence ; Cytochromes b/genetics ; DNA, Helminth/analysis ; *Genome, Mitochondrial ; Molecular Sequence Data ; Mosaicism ; Nematoda/*genetics ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Recently, a multipartite mitochondrial genome was characterized in the potato cyst nematode, Globodera pallida. Six subgenomic circles were detectable by PCR, while full-length genomes were not. We investigate here whether this subgenomic organization occurs in a close relative of G. pallida. We amplified and sequenced one entire mitochondrial subgenome from the cyst-forming nematode, Globodera rostochiensis. Comparison of the noncoding region of this subgenome with those reported previously for G. pallida facilitated the design of amplification primers for a range of subgenomes from G. rostochiensis. We then randomly sequenced five subgenomic fragments, each representative of a unique subgenome. This study indicates that the multipartite structure reported for G. pallida is conserved in G. rostochiensis. A comparison of subgenomic organization between these two Globodera species indicates a considerable degree of overlap between them. Indeed, we identify two subgenomes with an organization identical with that reported for G. pallida. However, other subgenomes are unique to G. rostochiensis, although some of these have blocks of genes comparable to those in G. pallida. Dot-plot comparisons of pairs of subgenomes from G. rostochiensis indicate that the different subgenomes share fragments with high sequence identity. We interpret this as evidence that recombination is operating in the mitochondria of G. rostochiensis.}, }
@article {pmid17662842, year = {2007}, author = {Krishnan, U and Barsamian, A and Miller, DL}, title = {Evolution of RNA editing sites in the mitochondrial small subunit rRNA of the Myxomycota.}, journal = {Methods in enzymology}, volume = {424}, number = {}, pages = {197-220}, doi = {10.1016/S0076-6879(07)24009-1}, pmid = {17662842}, issn = {0076-6879}, mesh = {Animals ; Base Sequence ; Binding Sites ; Biochemistry/*methods ; Cloning, Molecular ; DNA Primers/chemistry ; *Genetic Techniques ; Molecular Sequence Data ; Myxomycetes/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA/metabolism ; *RNA Editing ; RNA, Mitochondrial ; RNA, Ribosomal/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Because of their unique and unprecedented character, it is often difficult to imagine how and why the different, diverse types of RNA editing have evolved. Information about the evolution of a particular RNA editing system can be obtained by comparing RNA editing characteristics in contemporary organisms whose phylogenetic relationships are known so that editing patterns in ancestral organisms can be inferred. This information can then be used to build models of the origins, constraints, variability, and mechanisms of RNA editing. As an example of the types of information that can be obtained from these analyses, we describe how we have used cDNA, covariation, and phylogenetic analyses to study the evolution of the variation in RNA editing site location in the core region of the small subunit rRNA gene in the mtDNA of seven myxomycetes, including Physarum polycephalum. We find that the unique type of insertional RNA editing present in mitochondria of P. polycephalum is also present in the mitochondrial small subunit (SSU) rRNA of the other six myxomycetes. As in Physarum, this editing predominantly consists of cytidine insertions, but also includes uridine insertions and certain dinucleotide insertions such that any of the four canonical ribonucleotides can be inserted. Although the characteristics of RNA editing in these organisms are the same as in Physarum, the location of the insertion sites varies among the seven organisms relative to the conserved primary sequence and secondary structure of the rRNA. Nucleotide insertions have been identified at 29 different sites within this core region of the rRNA, but no one organism has more than 10 of these insertion sites, suggesting that editing sites have been created and/or eliminated since the divergence of these organisms. To determine the order in which editing sites have been created or eliminated, the sequences of the mitochondrial SSU rRNA have been aligned and this alignment has been used to produce phylogenetic trees showing the sequence relationship of these organisms. These phylogenetic trees are congruent with phylogenetic trees predicted by alignment of nuclear rDNA sequences. These trees indicate that editing sites change rapidly relative to mtDNA sequence divergence and suggest that some editing sites have been created more than once during the evolution of the Myxomycota.}, }
@article {pmid17662054, year = {2007}, author = {Fekete, V and Cierna, M and Poláková, S and Piskur, J and Sulo, P}, title = {Transition of the ability to generate petites in the Saccharomyces/Kluyveromyces complex.}, journal = {FEMS yeast research}, volume = {7}, number = {8}, pages = {1237-1247}, doi = {10.1111/j.1567-1364.2007.00287.x}, pmid = {17662054}, issn = {1567-1356}, mesh = {DNA, Fungal/drug effects/genetics ; DNA, Mitochondrial/drug effects/genetics ; Ethidium/pharmacology ; Genome, Fungal/drug effects ; Kluyveromyces/classification/drug effects/*genetics/*growth &amp; development ; Mitochondria/drug effects/genetics ; Mutagenesis ; Mutagens/pharmacology ; Phenotype ; Phylogeny ; Saccharomyces/classification/drug effects/*genetics/*growth &amp; development ; }, abstract = {Petite-positivity - the ability to tolerate the loss of mtDNA - was examined after the treatment with ethidium bromide (EB) in over hundred isolates from the Saccharomyces/Kluyveromyces complex. The identity of petite mutants was confirmed by the loss of specific mtDNA DAPI staining patterns. Besides unequivocal petite-positive and petite-negative phenotypes, a few species exhibited temperature sensitive petite positive phenotype and petiteness of a few other species could be observed only at the elevated EB concentrations. Several yeast species displayed a mixed 'moot' phenotype, where a major part of the population did not tolerate the loss of mtDNA but several cells did. The genera from postwhole-genome duplication lineages (Saccharomyces, Kazachstania, Naumovia, Nakaseomyces) were invariably petite-positive. However, petite-positive traits could also be observed among the prewhole-genome duplication species.}, }
@article {pmid17655860, year = {2007}, author = {Slamovits, CH and Saldarriaga, JF and Larocque, A and Keeling, PJ}, title = {The highly reduced and fragmented mitochondrial genome of the early-branching dinoflagellate Oxyrrhis marina shares characteristics with both apicomplexan and dinoflagellate mitochondrial genomes.}, journal = {Journal of molecular biology}, volume = {372}, number = {2}, pages = {356-368}, doi = {10.1016/j.jmb.2007.06.085}, pmid = {17655860}, issn = {0022-2836}, mesh = {Animals ; Base Sequence ; Codon, Initiator/genetics ; Codon, Terminator/genetics ; DNA, Complementary/genetics ; DNA, Mitochondrial/*genetics ; Dinoflagellida/classification/cytology/enzymology/*genetics ; *Evolution, Molecular ; Gene Expression Regulation ; Genes, Protozoan/*genetics ; Genome, Protozoan/*genetics ; Mitochondria/enzymology/*genetics ; Molecular Sequence Data ; *Phylogeny ; RNA Caps/chemistry ; RNA Editing ; RNA, Protozoan/genetics/metabolism ; Transcription, Genetic ; }, abstract = {The mitochondrial genome and the expression of the genes within it have evolved to be highly unusual in several lineages. Within alveolates, apicomplexans and dinoflagellates share the most reduced mitochondrial gene content on record, but differ from one another in organisation and function. To clarify how these characteristics originated, we examined mitochondrial genome form and expression in a key lineage that arose close to the divergence of apicomplexans and dinoflagellates, Oxyrrhis marina. We show that Oxyrrhis is a basal member of the dinoflagellate lineage whose mitochondrial genome has some unique characteristics while sharing others with apicomplexans or dinoflagellates. Specifically, Oxyrrhis has the smallest gene complement known, with several rRNA fragments and only two protein coding genes, cox1 and a cob-cox3 fusion. The genome appears to be highly fragmented, like that of dinoflagellates, but genes are frequently arranged as tandem copies, reminiscent of the repeating nature of the Plasmodium genome. In dinoflagellates and Oxyrrhis, genes are found in many arrangements, but the Oxyrrhis genome appears to be more structured, since neighbouring genes or gene fragments are invariably the same: cox1 and the cob-cox3 fusion were never found on the same genomic fragment. Analysing hundreds of cDNAs for both genes and circularized mRNAs from cob-cox3 showed that neither uses canonical start or stop codons, although a UAA terminator is created in the cob-cox3 fusion mRNA by post-transcriptional oligoadenylation. mRNAs from both genes also use a novel 5' oligo(U) cap. Extensive RNA editing is characteristic of dinoflagellates, but we find no editing in Oxyrrhis. Overall, the combination of characteristics found in the Oxyrrhis genome allows us to plot the sequence of many events that led to the extreme organisation of apicomplexan and dinoflalgellate mitochondrial genomes.}, }
@article {pmid17655768, year = {2007}, author = {Jiang, ZJ and Castoe, TA and Austin, CC and Burbrink, FT and Herron, MD and McGuire, JA and Parkinson, CL and Pollock, DD}, title = {Comparative mitochondrial genomics of snakes: extraordinary substitution rate dynamics and functionality of the duplicate control region.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {123}, pmid = {17655768}, issn = {1471-2148}, support = {R24 GM065580/GM/NIGMS NIH HHS/United States ; R33 GM065612/GM/NIGMS NIH HHS/United States ; GM065580-01/GM/NIGMS NIH HHS/United States ; GM065612-01/GM/NIGMS NIH HHS/United States ; R21 GM065612/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial/chemistry/*genetics ; *Evolution, Molecular ; Gene Duplication ; Genes, Mitochondrial/genetics ; Genomics/*methods ; Mutation ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Snakes/classification/*genetics ; Species Specificity ; }, abstract = {BACKGROUND: The mitochondrial genomes of snakes are characterized by an overall evolutionary rate that appears to be one of the most accelerated among vertebrates. They also possess other unusual features, including short tRNAs and other genes, and a duplicated control region that has been stably maintained since it originated more than 70 million years ago. Here, we provide a detailed analysis of evolutionary dynamics in snake mitochondrial genomes to better understand the basis of these extreme characteristics, and to explore the relationship between mitochondrial genome molecular evolution, genome architecture, and molecular function. We sequenced complete mitochondrial genomes from Slowinski's corn snake (Pantherophis slowinskii) and two cottonmouths (Agkistrodon piscivorus) to complement previously existing mitochondrial genomes, and to provide an improved comparative view of how genome architecture affects molecular evolution at contrasting levels of divergence.<br><br>RESULTS: We present a Bayesian genetic approach that suggests that the duplicated control region can function as an additional origin of heavy strand replication. The two control regions also appear to have different intra-specific versus inter-specific evolutionary dynamics that may be associated with complex modes of concerted evolution. We find that different genomic regions have experienced substantial accelerated evolution along early branches in snakes, with different genes having experienced dramatic accelerations along specific branches. Some of these accelerations appear to coincide with, or subsequent to, the shortening of various mitochondrial genes and the duplication of the control region and flanking tRNAs.<br><br>CONCLUSION: Fluctuations in the strength and pattern of selection during snake evolution have had widely varying gene-specific effects on substitution rates, and these rate accelerations may have been functionally related to unusual changes in genomic architecture. The among-lineage and among-gene variation in rate dynamics observed in snakes is the most extreme thus far observed in animal genomes, and provides an important study system for further evaluating the biochemical and physiological basis of evolutionary pressures in vertebrate mitochondria.}, }
@article {pmid17655652, year = {2007}, author = {Aronsson, H and Boij, P and Patel, R and Wardle, A and Töpel, M and Jarvis, P}, title = {Toc64/OEP64 is not essential for the efficient import of proteins into chloroplasts in Arabidopsis thaliana.}, journal = {The Plant journal : for cell and molecular biology}, volume = {52}, number = {1}, pages = {53-68}, doi = {10.1111/j.1365-313X.2007.03207.x}, pmid = {17655652}, issn = {0960-7412}, mesh = {Arabidopsis/metabolism/*physiology ; Arabidopsis Proteins/genetics/*physiology ; Base Sequence ; Chloroplasts/*metabolism ; DNA Primers ; DNA, Bacterial/genetics ; Membrane Proteins/genetics/*physiology ; Microscopy, Electron, Transmission ; Mutagenesis, Insertional ; Phylogeny ; Protein Transport ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Toc64/OEP64 was identified biochemically in pea as a putative component of the chloroplast protein import apparatus. In Arabidopsis, three paralogous genes (atTOC64-III, atTOC64-V and atTOC64-I) encode Toc64-related proteins, and these have been reported to localize in chloroplasts, mitochondria and the cytosol, respectively. To assess the role of the atToc64-III protein in chloroplast protein import in an in vivo context, we identified and characterized Arabidopsis knockout mutants. The absence of detectable defects in toc64-III single mutants raised the possibility of redundancy, and prompted us to also identify toc64-V and toc64-I mutants, cross them to toc64-III, and generate double- and triple-mutant combinations. The toc64 mutants were analysed carefully with respect to a variety of criteria, including chlorophyll accumulation, photosynthetic performance, organellar ultrastructure and chloroplast protein accumulation. In each case, the mutant plants were indistinguishable from wild type. Furthermore, the efficiency of chloroplast protein import was not affected by the toc64 mutations, even when a putative substrate of the atToc64-III protein (wheatgerm-translated precursor of the 33 kDa subunit of the oxygen-evolving complex, OE33) was examined. Moreover, under various stress conditions (high light, osmotic stress and cold), the toc64 triple-mutant plants were not significantly different from wild type. These results demonstrate that Toc64/OEP64 is not essential for the efficient import of proteins into chloroplasts in Arabidopsis, and draw into question the functional significance of this component.}, }
@article {pmid17653277, year = {2007}, author = {Moradian, MM and Beglaryan, D and Skozylas, JM and Kerikorian, V}, title = {Complete mitochondrial genome sequence of three Tetrahymena species reveals mutation hot spots and accelerated nonsynonymous substitutions in Ymf genes.}, journal = {PloS one}, volume = {2}, number = {7}, pages = {e650}, pmid = {17653277}, issn = {1932-6203}, mesh = {Amino Acids/genetics ; Animals ; Base Sequence ; Codon/genetics ; Conserved Sequence ; DNA, Mitochondrial/chemistry/*genetics ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Genetic Variation ; *Genome, Protozoan ; Introns/genetics ; Mitochondria/*genetics ; Protozoan Proteins/genetics ; Replication Origin ; Species Specificity ; Tetrahymena/classification/*genetics ; Transcription, Genetic ; }, abstract = {The ciliate Tetrahymena, a model organism, contains divergent mitochondrial (Mt) genome with unusual properties, where half of its 44 genes still remain without a definitive function. These genes could be categorized into two major groups of KPC (known protein coding) and Ymf (genes without an identified function). To gain insights into the mechanisms underlying gene divergence and molecular evolution of Tetrahymena (T.) Mt genomes, we sequenced three Mt genomes of T.paravorax, T.pigmentosa, and T.malaccensis. These genomes were aligned and the analyses were carried out using several programs that calculate distance, nucleotide substitution (dn/ds), and their rate ratios (omega) on individual codon sites and via a sliding window approach. Comparative genomic analysis indicated a conserved putative transcription control sequence, a GC box, in a region where presumably transcription and replication initiate. We also found distinct features in Mt genome of T.paravorax despite similar genome organization among these approximately 47 kb long linear genomes. Another significant finding was the presence of at least one or more highly variable regions in Ymf genes where majority of substitutions were concentrated. These regions were mutation hotspots where elevated distances and the dn/ds ratios were primarily due to an increase in the number of nonsynonymous substitutions, suggesting relaxed selective constraint. However, in a few Ymf genes, accelerated rates of nonsynonymous substitutions may be due to positive selection. Similarly, on protein level the majority of amino acid replacements occurred in these regions. Ymf genes comprise half of the genes in Tetrahymena Mt genomes, so understanding why they have not been assigned definitive functions is an important aspect of molecular evolution. Importantly, nucleotide substitution types and rates suggest possible reasons for not being able to find homologues for Ymf genes. Additionally, comparative genomic analysis of complete Mt genomes is essential in identifying biologically significant motifs such as control regions.}, }
@article {pmid17652520, year = {2007}, author = {Wei, W and McCusker, JH and Hyman, RW and Jones, T and Ning, Y and Cao, Z and Gu, Z and Bruno, D and Miranda, M and Nguyen, M and Wilhelmy, J and Komp, C and Tamse, R and Wang, X and Jia, P and Luedi, P and Oefner, PJ and David, L and Dietrich, FS and Li, Y and Davis, RW and Steinmetz, LM}, title = {Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {31}, pages = {12825-12830}, pmid = {17652520}, issn = {0027-8424}, support = {HG 000205/HG/NHGRI NIH HHS/United States ; GM 068717/GM/NIGMS NIH HHS/United States ; HG 02052/HG/NHGRI NIH HHS/United States ; P01 HG000205/HG/NHGRI NIH HHS/United States ; R01 GM068717/GM/NIGMS NIH HHS/United States ; F32 HG000205/HG/NHGRI NIH HHS/United States ; }, mesh = {Base Sequence ; Chromosome Inversion/genetics ; Gene Transfer, Horizontal/genetics ; Genome, Fungal/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Phenotype ; Phylogeny ; Polymorphism, Genetic/genetics ; Saccharomyces cerevisiae/*genetics ; Translocation, Genetic/genetics ; }, abstract = {We sequenced the genome of Saccharomyces cerevisiae strain YJM789, which was derived from a yeast isolated from the lung of an AIDS patient with pneumonia. The strain is used for studies of fungal infections and quantitative genetics because of its extensive phenotypic differences to the laboratory reference strain, including growth at high temperature and deadly virulence in mouse models. Here we show that the approximately 12-Mb genome of YJM789 contains approximately 60,000 SNPs and approximately 6,000 indels with respect to the reference S288c genome, leading to protein polymorphisms with a few known cases of phenotypic changes. Several ORFs are found to be unique to YJM789, some of which might have been acquired through horizontal transfer. Localized regions of high polymorphism density are scattered over the genome, in some cases spanning multiple ORFs and in others concentrated within single genes. The sequence of YJM789 contains clues to pathogenicity and spurs the development of more powerful approaches to dissecting the genetic basis of complex hereditary traits.}, }
@article {pmid17635416, year = {2007}, author = {Lambert, AJ and Brand, MD}, title = {Research on mitochondria and aging, 2006-2007.}, journal = {Aging cell}, volume = {6}, number = {4}, pages = {417-420}, doi = {10.1111/j.1474-9726.2007.00316.x}, pmid = {17635416}, issn = {1474-9718}, support = {MC_U105663137/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Aging/*physiology ; Animals ; DNA Damage ; DNA, Mitochondrial/genetics/metabolism ; Electron Transport Complex I/*metabolism ; Energy Metabolism ; Humans ; Longevity/physiology ; Mice ; Mitochondria/*physiology ; Oxidation-Reduction ; Oxidative Stress/physiology ; Reactive Oxygen Species/*metabolism ; }, abstract = {This review focuses on some of the 'hot topics' that fall under the general heading 'mitochondria and aging'. For each selected topic, we highlight recent publications that have either addressed specific problems within the field or presented novel findings of interest regarding the links between mitochondria and aging. These include studies on the structure of complex I and the mechanisms of superoxide production by this complex; work showing a novel site of hydrogen peroxide production within mitochondria that is modulated by caloric restriction; explorations of the relationship between the rate of evolution of mitochondrial DNA and lifespan; a demonstration that mitochondrial DNA mutations do not limit lifespan in mice; and investigations of the effects of mitochondrial fission on aging. We also list other relevant articles of interest and suggest some key challenges for the field in the near future.}, }
@article {pmid17626375, year = {2007}, author = {Mitani, H and Takahashi, M and Masuyama, M and Fukunaga, M}, title = {Ixodes philipi (Acari: Ixodidae): phylogenetic status inferred from mitochondrial cytochrome oxidase subunit I gene sequence comparison.}, journal = {The Journal of parasitology}, volume = {93}, number = {3}, pages = {719-722}, doi = {10.1645/GE-953R.1}, pmid = {17626375}, issn = {0022-3395}, mesh = {Animals ; Base Sequence ; Bird Diseases/parasitology ; Birds ; DNA, Mitochondrial/*chemistry ; Electron Transport Complex IV/*genetics ; Female ; *Genes, Mitochondrial ; Ixodes/*classification/enzymology/genetics ; Japan ; Male ; Mitochondria/enzymology ; *Phylogeny ; Polymerase Chain Reaction/veterinary ; Sequence Alignment/veterinary ; Tick Infestations/parasitology/veterinary ; }, abstract = {Ixodes philipi ticks were collected from the nest burrows of streaked shearwaters, Calonectris luecomelas, on 3 different islands of Japan (Awashima: 38 degrees 45'N, 139 degrees 24'E; Mikurajima: 33 degrees 52'N, 139 degrees 36'E; and Omorijima: 36 degrees 8'N, 133 degrees 10'E). The mitochondrial cytochrome oxidase subunit I (COI) gene sequence was determined for each tick. The COI sequences of 9 other ixodid tick species also were determined, and they were used for taxonomic positioning of I. philipi. A metastriata tick, Amblyomma triguttatum, was used as an outgroup reference for the analysis. Phylogenetic examination indicated that the I. philipi ticks are on the branch with Ixodes turdus and Ixodes acutitarsus weakly, and the bootstrap value of this branching was low. Three different analyses, maximum parsimony, genetic distance, and maximum likelihood, support this conclusion. To further refine this analysis, 2761 base pairs (bp) of sequence, which included the genes for tRNA(Met), NADH dehydrogenase subunit 2 (ND2), tRNA(Trp), tRNA(Cys), tRNA(Tyr), and COI, were determined and compared for 6 I. philipi ticks from the 3 different collection sites. Although a base substitution (T to C in the ND2 gene for an Awashima tick) and 2 transitions (G to A in the COI gene for 1 Omorijima tick) have occurred, the overall sequences were highly conserved. Preserved mitochondrial sequences in the ticks from 3 widely separated locations suggest the possibility of gene flow, which was probably accomplished by migratory seabirds.}, }
@article {pmid17625545, year = {2007}, author = {Davidov, Y and Jurkevitch, E}, title = {How incompatibilities may have led to eukaryotic cell.}, journal = {Nature}, volume = {448}, number = {7150}, pages = {130}, doi = {10.1038/448130a}, pmid = {17625545}, issn = {1476-4687}, mesh = {Archaea/*genetics/metabolism ; Bacteria/*genetics/metabolism ; *Biological Evolution ; Energy Metabolism ; Eukaryotic Cells/*cytology/metabolism ; Mitochondria ; }, }
@article {pmid17621670, year = {2007}, author = {Erol, A}, title = {Insulin resistance is an evolutionarily conserved physiological mechanism at the cellular level for protection against increased oxidative stress.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {29}, number = {8}, pages = {811-818}, doi = {10.1002/bies.20618}, pmid = {17621670}, issn = {0265-9247}, mesh = {Animals ; *Biological Evolution ; Cytoprotection/*physiology ; Glucose/physiology ; Humans ; Insulin/metabolism ; Insulin Resistance/*physiology ; Insulin Secretion ; Mitochondria/drug effects ; Models, Biological ; Oxidative Stress/*physiology ; Reactive Oxygen Species/pharmacology ; }, abstract = {Several protective cellular mechanisms protect against the accumulation of reactive oxygen species (ROS) and the concomitant oxidative stress. Therefore, any reduction in glucose or fatty acid flux into cells leading to a decrease in the production of reducing equivalents would also lead to a decreased ROS production and protect cells against oxidative stress. In the presence of insulin, FOXO proteins are localized from the nucleus to the cytoplasm and degraded. An increase in cellular glucose uptake will lead to increased production of ROS. This in turn activates the stress-responsive Jun-N-terminal kinase (JNK), which promotes nuclear translocation of FOXO proteins, upregulating some important target genes including stress resistance. Consequently, insulin resistance should result in decreased cellular ROS production. For this reason, insulin resistance could be a physiological mechanism activated at the cellular level in response to conditions stimulating ROS production and leading to the prevention of oxidative stress, and extension of life. Concerning the whole organism, however, IR is a maladaptive process in the long term causing a diabetic state.}, }
@article {pmid17621274, year = {2008}, author = {Alcalá, S and Klee, M and Fernández, J and Fleischer, A and Pimentel-Muiños, FX}, title = {A high-throughput screening for mammalian cell death effectors identifies the mitochondrial phosphate carrier as a regulator of cytochrome c release.}, journal = {Oncogene}, volume = {27}, number = {1}, pages = {44-54}, doi = {10.1038/sj.onc.1210600}, pmid = {17621274}, issn = {1476-5594}, mesh = {Apoptosis/*physiology ; Apoptosis Regulatory Proteins/*physiology ; Cloning, Molecular/methods ; Cytochromes c/*metabolism ; HCT116 Cells ; HeLa Cells ; Humans ; Mitochondria/*enzymology/metabolism ; Mitochondrial Membrane Transport Proteins/*physiology ; Mitochondrial Proteins/*physiology ; Oligonucleotide Array Sequence Analysis ; Phosphate Transport Proteins/*physiology ; }, abstract = {Functional annotation of complex genomes requires the development of novel experimental platforms with increased capacity. Here, we describe a high-throughput system designed to identify cDNAs whose overexpression induces morphologically distinct cell death modalities. The methodology incorporates two robotized steps, and relies on coexpression of library clones with GFP to reveal the morphological features presented by the dying cells. By using this system we screened 135 000 cDNA clones and obtained 90 independent molecules. Interestingly, three death categories were identified, namely; apoptotic, vacuolated and autophagic. Among the pro-apoptotic clones, we found four members of the mitochondrial carrier family: the phosphate and adenine nucleotide (type 3) transporters, and the mitochondrial carrier homologs (MTCHs) 1 and 2. Expression of these molecules induced cytochrome c release and caspase-9-dependent death. One of them, the phosphate carrier, was able to interact with members of the permeability transition pore complex ANT1 and VDAC1, and its binding to ANT1 was stabilized in the presence of apoptotic activators. Depletion of this carrier by siRNA delayed cytochrome c mobilization and apoptosis. These results attribute a previously undescribed apoptotic function to the phosphate carrier and, more generally, suggest that a common property of various mitochondrial transporters was exploited during evolution to regulate apoptosis.}, }
@article {pmid17611770, year = {2007}, author = {Graier, WF and Frieden, M and Malli, R}, title = {Mitochondria and Ca(2+) signaling: old guests, new functions.}, journal = {Pflugers Archiv : European journal of physiology}, volume = {455}, number = {3}, pages = {375-396}, pmid = {17611770}, issn = {0031-6768}, support = {F 3010/FWF_/Austrian Science Fund FWF/Austria ; P 16860/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Calcium/*metabolism ; Calcium Channels/drug effects/physiology ; Calcium Signaling/*physiology ; Cell Membrane/physiology ; Cytosol/physiology ; Endoplasmic Reticulum/physiology ; Homeostasis/physiology ; Humans ; Ion Channels/physiology ; Membrane Potential, Mitochondrial/physiology ; Mitochondria/*physiology/ultrastructure ; Mitochondrial Membranes/physiology ; Mitochondrial Proteins/physiology ; Phosphoproteins/metabolism ; Protein Folding ; Reactive Oxygen Species/metabolism ; Second Messenger Systems/physiology ; Uncoupling Protein 2 ; Uncoupling Protein 3 ; }, abstract = {Mitochondria are ancient endosymbiotic guests that joined the cells in the evolution of complex life. While the unique ability of mitochondria to produce adenosine triphosphate (ATP) and their contribution to cellular nutrition metabolism received condign attention, our understanding of the organelle's contribution to Ca(2+) homeostasis was restricted to serve as passive Ca(2+) sinks that accumulate Ca(2+) along the organelle's negative membrane potential. This paradigm has changed radically. Nowadays, mitochondria are known to respond to environmental Ca(2+) and to contribute actively to the regulation of spatial and temporal patterns of intracellular Ca(2+) signaling. Accordingly, mitochondria contribute to many signal transduction pathways and are actively involved in the maintenance of capacitative Ca(2+) entry, the accomplishment of Ca(2+) refilling of the endoplasmic reticulum and Ca(2+)-dependent protein folding. Mitochondrial Ca(2+) homeostasis is complex and regulated by numerous, so far, genetically unidentified Ca(2+) channels, pumps and exchangers that concertedly accomplish the organelle's Ca(2+) demand. Notably, mitochondrial Ca(2+) homeostasis and functions are crucially influenced by the organelle's structural organization and motility that, in turn, is controlled by matrix/cytosolic Ca(2+). This review intends to provide a condensed overview on the molecular mechanisms of mitochondrial Ca(2+) homeostasis (uptake, buffering and storage, extrusion), its modulation by other ions, kinases and small molecules, and its contribution to cellular processes as fundamental basis for the organelle's contribution to signaling pathways. Hence, emphasis is given to the structure-to-function and mobility-to-function relationship of the mitochondria and, thereby, bridging our most recent knowledge on mitochondria with the best-established mitochondrial function: metabolism and ATP production.}, }
@article {pmid17611493, year = {2007}, author = {Aldrich, BT and Kambhampati, S}, title = {Population structure and colony composition of two Zootermopsis nevadensis subspecies.}, journal = {Heredity}, volume = {99}, number = {4}, pages = {443-451}, doi = {10.1038/sj.hdy.6801022}, pmid = {17611493}, issn = {0018-067X}, mesh = {Animals ; California ; DNA/genetics ; Evolution, Molecular ; Genetic Variation ; Genetics, Population ; Genotype ; Geography ; Haplotypes ; Isoptera/*genetics ; Linkage Disequilibrium ; Microsatellite Repeats/genetics ; Mitochondria/genetics ; Models, Genetic ; Polymorphism, Genetic ; }, abstract = {Understanding the origin and maintenance of eusociality in termites has proved problematic, in part, due to a lack of knowledge concerning the variability and evolutionary changes in termite breeding structure. One way to address this is to compare the population genetics of a broad range of termite species. However, few studies have investigated the population genetics of basal termite taxa. We used 12 polymorphic microsatellite loci to characterize and compare the colony genetic structure of 18 colonies of two basal termite subspecies, Zootermopsis nevadensis nevadensis and Zootermopsis nevadensis nuttingi. The average relatedness (r) among individuals within a colony was high (0.59) and similar to values reported for other termite species. Average relatedness between colony founders was lower (0.21) suggesting the alates outbreed. Genotypes of workers and soldiers in 4 out of the 18 colonies were consistent with reproduction by a single pair of primary reproductives and the remaining colonies were inferred to have been derived from more than two reproductives. Eleven colonies with three or more reproductives were consistent with replacement reproductives (neotenics) and the remaining three colonies included genetic contribution from three or more primary reproductives. Comparisons between the subspecies revealed significant differences in breeding structure, specifically in the number and types of reproductives (that is, primaries or neotenics). Furthermore, we observed a larger proportion of colonies with greater than three primary reproductives compared to more derived termite lineages. Thus, our results suggest that breeding structure can vary significantly among termite taxa.}, }
@article {pmid17604309, year = {2007}, author = {Smits, P and Smeitink, JA and van den Heuvel, LP and Huynen, MA and Ettema, TJ}, title = {Reconstructing the evolution of the mitochondrial ribosomal proteome.}, journal = {Nucleic acids research}, volume = {35}, number = {14}, pages = {4686-4703}, pmid = {17604309}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry/classification/genetics ; *Evolution, Molecular ; Fungal Proteins/chemistry/classification/genetics ; Gene Duplication ; Genomics ; Humans ; Mitochondrial Proteins/chemistry/classification/*genetics ; Molecular Sequence Data ; Proteome/chemistry/classification/*genetics ; Ribosomal Proteins/chemistry/classification/*genetics ; Sequence Alignment ; }, abstract = {For production of proteins that are encoded by the mitochondrial genome, mitochondria rely on their own mitochondrial translation system, with the mitoribosome as its central component. Using extensive homology searches, we have reconstructed the evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, revealing an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. We observe large variations in the protein content of mitoribosomes between different eukaryotes, with mammalian mitoribosomes sharing only 74 and 43% of its proteins with yeast and Leishmania mitoribosomes, respectively. We detected many previously unidentified mitochondrial ribosomal proteins (MRPs) and found that several have increased in size compared to their bacterial ancestral counterparts by addition of functional domains. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome. Using sensitive profile-profile homology searches, we found hitherto undetected homology between bacterial and eukaryotic ribosomal proteins, as well as between fungal and mammalian ribosomal proteins, detecting two novel human MRPs. These newly detected MRPs constitute, along with evolutionary conserved MRPs, excellent new screening targets for human patients with unresolved mitochondrial oxidative phosphorylation disorders.}, }
@article {pmid17600515, year = {2007}, author = {Sullivan, PG and Krishnamurthy, S and Patel, SP and Pandya, JD and Rabchevsky, AG}, title = {Temporal characterization of mitochondrial bioenergetics after spinal cord injury.}, journal = {Journal of neurotrauma}, volume = {24}, number = {6}, pages = {991-999}, doi = {10.1089/neu.2006.0242}, pmid = {17600515}, issn = {0897-7151}, support = {NS 048191/NS/NINDS NIH HHS/United States ; }, mesh = {Aldehydes/analysis/metabolism ; Animals ; Disease Models, Animal ; Disease Progression ; Energy Metabolism/*physiology ; Female ; Free Radicals/analysis/metabolism ; Lipid Peroxidation/physiology ; Mitochondria/*metabolism ; Oxidative Stress/physiology ; Rats ; Rats, Sprague-Dawley ; Reactive Oxygen Species/analysis/metabolism ; Spinal Cord/*metabolism/*physiopathology ; Spinal Cord Injuries/drug therapy/*metabolism/*physiopathology ; Time Factors ; Tyrosine/analogs &amp; derivatives/analysis/metabolism ; }, abstract = {Mitochondrial dysfunction following spinal cord injury (SCI) may be critical for the development of secondary pathophysiology and neuronal cell death. Previous studies have demonstrated a loss of mitochondrial bioenergetics at 24 h following SCI. To begin to understand the evolution and study the contribution of mitochondrial dysfunction in pathophysiology of SCI, we investigated mitochondrial bioenergetics in the mid-thoracic region at 6, 12, and 24 h following contusion SCI. It is widely accepted that increased free radical generation plays a critical role in neuronal damage after SCI. Hence, to ascertain the role of free radicals in SCI-induced mitochondrial dysfunction, markers for oxidative damage, including nitrotyrosine (3-NT), lipid peroxidation byproduct (4-hydroxynonenal [HNE]), and protein oxidation (protein carbonyls) were quantified in the same samples of isolated mitochondria during the 24-h time course. The results demonstrate that a significant decline in mitochondrial function begins to occur 12 h post-injury and persists for a least 24 h following SCI. Furthermore, there was a progressive increase in mitochondrial oxidative damage that preceded the loss of mitochondrial bioenergetics, suggesting that free radical damage may be a major mitochondrial secondary injury process. Based on the present results, the temporal profile of mitochondrial dysfunction indicates that interventions targeting mitochondrial oxidative damage and dysfunction may serve as a beneficial pharmacological treatment for acute SCI.}, }
@article {pmid17598752, year = {2007}, author = {Ballard, JW and Melvin, RG and Katewa, SD and Maas, K}, title = {Mitochondrial DNA variation is associated with measurable differences in life-history traits and mitochondrial metabolism in Drosophila simulans.}, journal = {Evolution; international journal of organic evolution}, volume = {61}, number = {7}, pages = {1735-1747}, doi = {10.1111/j.1558-5646.2007.00133.x}, pmid = {17598752}, issn = {0014-3820}, support = {R01 GM067862-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Drosophila/*metabolism ; Electron Transport Complex IV/genetics ; Female ; Fertility ; *Life Cycle Stages ; Mitochondria/*metabolism ; Ovum ; }, abstract = {Recent studies have used a variety of theoretical arguments to show that mitochondrial (mt) DNA rarely evolves as a strictly neutral marker and that selection operates on the mtDNA of many species. However, the vast majority of researchers are not convinced by these arguments because data linking mtDNA variation with phenotypic differences are limited. We investigated sequence variation in the three mtDNA and nine nuclear genes (including all isoforms) that encode the 12 subunits of cytochrome c oxidase of the electron transport chain in Drosophila. We then studied cytochrome c oxidase activity as a key aspect of mitochondrial bioenergetics and four life-history traits. In Drosophila simulans, sequence data from the three mtDNA encoded cytochrome c oxidase genes show that there are 76 synonymous and two nonsynonymous fixed differences among flies harboring siII compared with siIII mtDNA. In contrast, 13 nuclear encoded genes show no evidence of genetic subdivision associated with the mtDNA. Flies with siIII mtDNA had higher cytochrome c oxidase activity and were more starvation resistant. Flies harboring siII mtDNA had greater egg size and fecundity, and recovered faster from cold coma. These data are consistent with a causative role for mtDNA variation in these phenotypic differences, but we cannot completely rule out the involvement of nuclear genes. The results of this study have significant implications for the use of mtDNA as an assumed neutral marker and show that evolutionary shifts can involve changes in mtDNA despite the small number of genes encoded in the organelle genome.}, }
@article {pmid17596970, year = {2007}, author = {Yokobori, S and Lindsay, DJ and Yoshida, M and Tsuchiya, K and Yamagishi, A and Maruyama, T and Oshima, T}, title = {Mitochondrial genome structure and evolution in the living fossil vampire squid, Vampyroteuthis infernalis, and extant cephalopods.}, journal = {Molecular phylogenetics and evolution}, volume = {44}, number = {2}, pages = {898-910}, doi = {10.1016/j.ympev.2007.05.009}, pmid = {17596970}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Cephalopoda/*genetics ; *Fossils ; Genome/*genetics ; Mitochondria/*genetics ; *Phylogeny ; }, abstract = {Complete nucleotide sequences of mitochondrial (mt) genomes of the "living fossil" cephalopod Vampyroteuthis infernalis (Vampyromorpha) and the cuttlefish Sepia esculenta (Sepiida) were determined. The V. infernalis mt genome structure is identical to the incirrate octopod Octopus vulgaris mt genome structure, and is therefore more similar to that of the polyplacophoran Katharina tunicata, than to that of the other "living fossil" cephalopod Nautilus macromphalus. The mt genome structure of S. esculenta is identical to that of Sepia officinalis. Molecular phylogenetic analyses based on the mt protein genes from the completely sequenced cephalopod mt genomes suggested the monophyletic relationship of two myopsid squids Loligo bleekeri and Sepiotheuthis lessoniana, and the monophyletic relationship of two oegopsid squids Watasenia scintillans, and Todarodes pacificus. Sepiida appeared as the sister group of Teuthida (Myopsida + Oegopsida). The phylogenetic position of Vampyromorpha appeared as the sister group of Octopoda, although the monophyly of Vampyromorpha and Decapodiformes cannot be rejected outright by our phylogenetic analyses. The hypothesis that Vampyromorpha is basal among the coleoid cephalopods can be rejected because of low statistical support. Therefore, it is reasonable to recognize three major groups in Coleoidea--Vampyromorpha, Octopoda, and Decapodiformes.}, }
@article {pmid17595195, year = {2007}, author = {Niessen, M and Thiruveedhi, K and Rosenkranz, R and Kebeish, R and Hirsch, HJ and Kreuzaler, F and Peterhänsel, C}, title = {Mitochondrial glycolate oxidation contributes to photorespiration in higher plants.}, journal = {Journal of experimental botany}, volume = {58}, number = {10}, pages = {2709-2715}, doi = {10.1093/jxb/erm131}, pmid = {17595195}, issn = {0022-0957}, mesh = {Alcohol Oxidoreductases/genetics/*metabolism ; Arabidopsis/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Carbon Dioxide/metabolism ; Glycolates/*metabolism ; Mitochondria/*metabolism ; Mutagenesis, Insertional ; *Oxidation-Reduction ; *Photosynthesis ; RNA, Messenger/metabolism ; }, abstract = {The oxidation of glycolate to glyoxylate is an important reaction step in photorespiration. Land plants and charophycean green algae oxidize glycolate in the peroxisome using oxygen as a co-factor, whereas chlorophycean green algae use a mitochondrial glycolate dehydrogenase (GDH) with organic co-factors. Previous analyses revealed the existence of a GDH in the mitochondria of Arabidopsis thaliana (AtGDH). In this study, the contribution of AtGDH to photorespiration was characterized. Both RNA abundance and mitochondrial GDH activity were up-regulated under photorespiratory growth conditions. Labelling experiments indicated that glycolate oxidation in mitochondrial extracts is coupled to CO(2) release. This effect could be enhanced by adding co-factors for aminotransferases, but is inhibited by the addition of glycine. T-DNA insertion lines for AtGDH show a drastic reduction in mitochondrial GDH activity and CO(2) release from glycolate. Furthermore, photorespiration is reduced in these mutant lines compared with the wild type, as revealed by determination of the post-illumination CO(2) burst and the glycine/serine ratio under photorespiratory growth conditions. The data show that mitochondrial glycolate oxidation contributes to photorespiration in higher plants. This indicates the conservation of chlorophycean photorespiration in streptophytes despite the evolution of leaf-type peroxisomes.}, }
@article {pmid17594435, year = {2007}, author = {Scheffer, SJ and Hawthorne, DJ}, title = {Molecular evidence of host-associated genetic divergence in the holly leafminer Phytomyza glabricola (Diptera: Agromyzidae): apparent discordance among marker systems.}, journal = {Molecular ecology}, volume = {16}, number = {13}, pages = {2627-2637}, doi = {10.1111/j.1365-294X.2007.03303.x}, pmid = {17594435}, issn = {0962-1083}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Ilex/classification/enzymology/*genetics ; Mitochondria/enzymology ; North Carolina ; Phylogeny ; Plant Leaves/*parasitology ; Plants/*parasitology ; South Carolina ; }, abstract = {Host races play a central part in understanding the role of host plant mediated divergence and speciation of phytophagous insects. Of greatest interest are host-associated populations that have recently diverged; however, finding genetic evidence for very recent divergences is difficult because initially only a few loci are expected to evolve diagnostic differences. The holly leafminer Phytomyza glabricola feeds on two hollies, Ilex glabra and I. coriacea, that are broadly sympatric throughout most of their ranges. The leafminer is often present on both host plants and exhibits a dramatic life history difference on the two hosts, suggesting that host races may be present. We collected 1393 bp of mitochondrial cytochrome oxidase I (COI) sequence and amplified fragment length polymorphism (AFLP) data (45 polymorphic bands) from sympatric populations of flies reared from the two hosts. Phylogenetic and frequency analysis of mitochondrial COI sequence data uncovered considerable variation but no structuring by the host plant, and only limited differentiation among geographical locations. In contrast, analysis of AFLP frequency data found a significant effect with host plant, and a much smaller effect with geographical location. Likewise, neighbour-joining analysis of AFLP data resulted in clustering by host plant. The AFLP data indicate that P. glabricola is most likely comprised of two host races. Because there were no fixed differences in mitochondrial or AFLP data, this host-associated divergence is likely to have occurred very recently. P. glabricola therefore provides a new sympatric system for exploring the role of geography and ecological specialization in the speciation of phytophagous insects.}, }
@article {pmid17591603, year = {2007}, author = {Mulligan, RM and Chang, KL and Chou, CC}, title = {Computational analysis of RNA editing sites in plant mitochondrial genomes reveals similar information content and a sporadic distribution of editing sites.}, journal = {Molecular biology and evolution}, volume = {24}, number = {9}, pages = {1971-1981}, doi = {10.1093/molbev/msm125}, pmid = {17591603}, issn = {0737-4038}, mesh = {Arabidopsis/genetics ; Base Sequence ; Brassica napus/genetics ; Codon/genetics ; Computer Simulation ; Cytidine/genetics ; DNA, Mitochondrial/*genetics ; Genes, Mitochondrial/genetics ; *Genome, Plant ; Models, Genetic ; Oryza/genetics ; Plants/*genetics ; *RNA Editing ; RNA, Plant/genetics ; }, abstract = {A computational analysis of RNA editing sites was performed on protein-coding sequences of plant mitochondrial genomes from Arabidopsis thaliana, Beta vulgaris, Brassica napus, and Oryza sativa. The distribution of nucleotides around edited and unedited cytidines was compared in 41 nucleotide segments and included 1481 edited cytidines and 21,390 unedited cytidines in the 4 genomes. The distribution of nucleotides was examined in 1, 2, and 3 nucleotide windows by comparison of nucleotide frequency ratios and relative entropy. The relative entropy analyses indicate that information is encoded in the nucleotide sequences in the 5 prime flank (-18 to -14, -13 to -10, -6 to -4, -2/-1) and the immediate 3 prime flanking nucleotide (+1), and these regions may be important in editing site recognition. The relative entropy was large when 2 or 3 nucleotide windows were analyzed, suggesting that several contiguous nucleotides may be involved in editing site recognition. RNA editing sites were frequently preceded by 2 pyrimidines or AU and followed by a guanidine (HYCG) in the monocot and dicot mitochondrial genomes, and rarely preceded by 2 purines. Analysis of chloroplast editing sites from a dicot, Nicotiana tabacum, and a monocot, Zea mays, revealed a similar distribution of nucleotides around editing sites (HYCA). The similarity of this motif around editing sites in monocots and dicots in both mitochondria and chloroplasts suggests that a mechanistic basis for this motif exists that is common in these different organelle and phylogenetic systems. The preferred sequence distribution around RNA editing sites may have an important impact on the acquisition of editing sites in evolution because the immediate sequence context of a cytidine residue may render a cytidine editable or uneditable, and consequently determine whether a T to C mutation at a specific position may be corrected by RNA editing. The distribution of editing sites in many protein-coding sequences is shown to be non-random with editing sites clustered in groups separated by regions with no editing sites. The sporadic distribution of editing sites could result from a mechanism of editing site loss by gene conversion utilizing edited sequence information, possibly through an edited cDNA intermediate.}, }
@article {pmid17588779, year = {2007}, author = {Makokha, JS and Bauer, AM and Mayer, W and Matthee, CA}, title = {Nuclear and mtDNA-based phylogeny of southern African sand lizards, Pedioplanis (Sauria: Lacertidae).}, journal = {Molecular phylogenetics and evolution}, volume = {44}, number = {2}, pages = {622-633}, doi = {10.1016/j.ympev.2007.04.021}, pmid = {17588779}, issn = {1055-7903}, mesh = {Africa ; Animals ; Cell Nucleus/*genetics ; DNA/*genetics ; Databases, Nucleic Acid ; Lizards/*genetics ; Mitochondria/*genetics ; *Phylogeny ; *Silicon Dioxide ; Time Factors ; }, abstract = {The diversity of lacertid lizards in Africa is highest in the southern African subcontinent, where over two-thirds of the species are endemic. With eleven currently recognized species, Pedioplanis is the most diverse among the southern African genera. In this study we use 2200 nucleotide positions derived from two mitochondrial markers (ND2 and 16S rRNA) and one nuclear gene (RAG-1) to (i) assess the phylogeny of Pedioplanis and (ii) estimate divergence time among lineages using the relaxed molecular clock method. Individual analyses of each gene separately supported different nodes in the phylogeny and the combined analysis yielded more well supported relationships. We present the first, well-resolved gene tree for the genus Pedioplanis and this is largely congruent with a phylogeny derived from morphology. Contrary to previous suggestions Heliobolus/Nucras are sister to Pedioplanis. The genus Pedioplanis is monophyletic, with P. burchelli/P. laticeps forming a clade that is sister to all the remaining congeners. Two distinct geographic lineages can be identified within the widespread P. namaquensis; one occurs in Namibia, while the other occurs in South Africa. The P. undata species complex is monophyletic, but one of its constituent species, P. inornata, is paraphyletic. Relationships among the subspecies of P. lineoocellata are much more complex than previously documented. An isolated population previously assigned to P. l. pulchella is paraphyletic and sister to the three named subspecies. The phylogeny identifies two biogeographical clades that probably diverged during the mid-Miocene, after the development of the Benguella Current. This probably led to habitat changes associated with climate and, in conjunction with physical barriers (Great Escarpment), contributed towards speciation within the genus Pedioplanis.}, }
@article {pmid17587513, year = {2007}, author = {Wang, X and Wang, J and He, S and Mayden, RL}, title = {The complete mitochondrial genome of the Chinese hook snout carp Opsariichthys bidens (Actinopterygii: Cypriniformes) and an alternative pattern of mitogenomic evolution in vertebrate.}, journal = {Gene}, volume = {399}, number = {1}, pages = {11-19}, doi = {10.1016/j.gene.2007.04.019}, pmid = {17587513}, issn = {0378-1119}, mesh = {Animals ; Carps/classification/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genome/*genetics ; Mitochondria/genetics ; Mitochondrial Proteins/*genetics ; Nucleic Acid Conformation ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The complete mitochondrial genome sequence of the Chinese hook snout carp, Opsariichthys bidens, was newly determined using the long and accurate polymerase chain reaction method. The 16,611-nucleotide mitogenome contains 13 protein-coding genes, two rRNA genes (12S, 16S), 22 tRNA genes, and a noncoding control region. We use these data and homologous sequence data from multiple other ostariophysan fishes in a phylogenetic evaluation to test hypothesis pertaining to codon usage pattern of O. bidens mitochondrial protein genes as well as to re-examine the ostariophysan phylogeny. The mitochondrial genome of O. bidens reveals an alternative pattern of vertebrate mitochondrial evolution. For the mitochondrial protein genes of O. bidens, the most frequently used codon generally ends with either A or C, with C preferred over A for most fourfold degenerate codon families; the relative synonymous codon usage of G-ending codons is greatly elevated in all categories. The codon usage pattern of O. bidens mitochondrial protein genes is remarkably different from the general pattern found previously in the relatively closely related zebrafish and most other vertebrate mitochondria. Nucleotide bias at third codon positions is the main cause of codon bias in the mitochondrial protein genes of O. bidens, as it is biased particularly in favor of C over A. Bayesian analysis of 12 concatenated mitochondrial protein sequences for O. bidens and 46 other teleostean taxa supports the monophyly of Cypriniformes and Otophysi and results in a robust estimate of the otophysan phylogeny.}, }
@article {pmid17586602, year = {2007}, author = {Hulett, JM and Walsh, P and Lithgow, T}, title = {Domain stealing by receptors in a protein transport complex.}, journal = {Molecular biology and evolution}, volume = {24}, number = {9}, pages = {1909-1911}, doi = {10.1093/molbev/msm126}, pmid = {17586602}, issn = {0737-4038}, mesh = {Binding Sites ; Biological Transport ; Membrane Transport Proteins/genetics/*metabolism ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins ; Protein Binding ; Receptors, Cytoplasmic and Nuclear/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {The mitochondrion is an essential cellular compartment in eukaryotes. The mitochondrial proteins Tom20 and Tom22 are receptors that ensure recognition and binding of proteins imported for mitochondrial biogenesis. Comparison of the sequence for the Tom20 and Tom22 subunits in the yeasts Saccharomyces cerevisiae and Saccharomyces castellii, show a rare case of domain stealing, where in Saccharomyces castellii Tom22 has lost an acidic domain, and Tom20 has gained one. This example of domain stealing is a snapshot of evolution in action and provides excellent evidence that Tom20 and Tom22 are subunits of a single, composite receptor that binds precursor proteins for import into mitochondria.}, }
@article {pmid17584253, year = {2007}, author = {Natcheva, R and Cronberg, N}, title = {Maternal transmission of cytoplasmic DNA in interspecific hybrids of peat mosses, Sphagnum (Bryophyta).}, journal = {Journal of evolutionary biology}, volume = {20}, number = {4}, pages = {1613-1616}, doi = {10.1111/j.1420-9101.2007.01341.x}, pmid = {17584253}, issn = {1010-061X}, mesh = {DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; *Extrachromosomal Inheritance ; Hybridization, Genetic ; Sphagnopsida/*genetics ; }, abstract = {The progeny of spontaneous interspecific hybrid sporophytes of Sphagnum were used to analyse the inheritance of cytoplasmic DNA. The analysis showed that only the female parent donated chloroplasts and mitochondria in Sphagnum hybrids. Thus, this is the first study demonstrating maternal cytoplasmic inheritance in a nonvascular land plant. This finding has important implications for phylogenetic reconstructions utilizing chloroplast and mitochondrial DNA sequences as well as for the evolution of cytoplasmic inheritance in relation to the life cycle of land plants.}, }
@article {pmid17582999, year = {2007}, author = {Shemarova, IV}, title = {[Pathways of transduction of apoptotic signals in unicellular eukaryotes].}, journal = {Tsitologiia}, volume = {49}, number = {3}, pages = {229-242}, pmid = {17582999}, issn = {0041-3771}, mesh = {Animals ; *Apoptosis ; Biological Evolution ; Caspases/metabolism ; Eukaryota/*physiology ; Fas-Associated Death Domain Protein/metabolism ; Fungal Proteins/metabolism ; Fungi/*physiology ; Mitochondria/metabolism ; Protozoan Proteins/metabolism ; *Signal Transduction ; }, abstract = {The review summarizes current data about transduction mechanism of apoptotic signals by caspase-like enzymes and mitochondrial apoptogenic proteins in unicellular eukaryotes. The role of receptor-dependent and receptor-independent caspase cascades is rewieved. The special attention is given to evolution aspects of problem of apoptosis.}, }
@article {pmid17581566, year = {2007}, author = {Poole, A and Penny, D}, title = {Eukaryote evolution: engulfed by speculation.}, journal = {Nature}, volume = {447}, number = {7147}, pages = {913}, doi = {10.1038/447913a}, pmid = {17581566}, issn = {1476-4687}, mesh = {Archaea/cytology/metabolism ; Bacteria/cytology/metabolism ; *Biological Evolution ; Endocytosis ; Eukaryotic Cells/*cytology/metabolism ; Mitochondria/metabolism ; *Models, Biological ; }, }
@article {pmid17574602, year = {2007}, author = {de Bivort, BL and Chen, CC and Perretti, F and Negro, G and Philip, TM and Bar-Yam, Y}, title = {Metabolic implications for the mechanism of mitochondrial endosymbiosis and human hereditary disorders.}, journal = {Journal of theoretical biology}, volume = {248}, number = {1}, pages = {26-36}, doi = {10.1016/j.jtbi.2007.04.017}, pmid = {17574602}, issn = {0022-5193}, mesh = {*Biological Evolution ; *Computer Simulation ; Eukaryotic Cells/*parasitology/ultrastructure ; Female ; *Game Theory ; Genetic Diseases, Inborn/*metabolism ; Humans ; Male ; Mitochondria/*physiology ; Selection, Genetic ; Symbiosis ; }, abstract = {The endosymbiosis of proto-mitochondrial prokaryotes (PMP) into proto-eukaryotic host-cells was a major advance in eukaryotic evolution. The nature of the initial relationship remains the subject of controversy. Various conceptual models have been proposed, but none has definitive support. We construct a model of inter-species interactions based upon well-established respiratory pathways, describing the respective energy gain of host-cell and PMP resulting from varying levels of cooperation. The model demonstrates conflicting evolutionary strategies ("Prisoner's Dilemmas") in the interspecies molecular transfers. Nevertheless, we show that coercion and iterated, multilevel selection on both species encourage endosymbiosis. Mutualism is favored if host-cells are significantly more effective than PMPs at gathering food. Otherwise, an unambiguous asymmetry between host-cell and PMP benefits implies that the initial relationship consisted of the host-cell deriving a reproductive advantage at the PMPs' expense-a cellular version of farming. Other initial relationships such as oxygen-detoxification mutualism and parasitism are not strongly supported by the model. We compare the model behavior with experiments on mutant human mitochondria and find the model predicts proliferation rates consistent with that data. We derive from the evolutionary dynamics counter-intuitive therapeutic targets for two human hereditary mitochondrial disorders that reflect the ongoing effect of short-term selection at the mitochondrial level.}, }
@article {pmid17569023, year = {2007}, author = {Zhang, SC and Barclay, C and Alexander, LA and Geldenhuys, L and Porter, GA and Casson, AG and Murphy, PR}, title = {Alternative splicing of the FGF antisense gene: differential subcellular localization in human tissues and esophageal adenocarcinoma.}, journal = {Journal of molecular medicine (Berlin, Germany)}, volume = {85}, number = {11}, pages = {1215-1228}, pmid = {17569023}, issn = {0946-2716}, mesh = {Adenocarcinoma/*genetics/pathology ; Alternative Splicing/*genetics ; Amino Acid Sequence ; Animals ; COS Cells ; Cell Proliferation ; Chlorocebus aethiops ; Computational Biology ; Disease-Free Survival ; Esophageal Neoplasms/*genetics/pathology ; Fibroblast Growth Factor 2/chemistry/*genetics/*metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Genetic Complementation Test ; Humans ; Molecular Sequence Data ; Phylogeny ; Protein Isoforms/genetics/metabolism ; Protein Transport ; *RNA Transport ; RNA, Messenger/genetics/metabolism ; Sequence Deletion ; Subcellular Fractions/metabolism ; }, abstract = {Overexpression of FGF-2 is associated with tumor recurrence and reduced survival after surgical resection of esophageal cancer, and these risks are reduced in tumors co-expressing the FGF antisense (FGF-AS) RNA. The aim of this study was to characterize the expression of alternatively spliced FGF-AS transcripts and encoded nudix-motif proteins in normal human tissues and in esophageal adenocarcinoma, and to correlate their expression with clinicopathologic findings and outcome. Three alternatively spliced FGF-AS transcripts encoding GFG/NUDT6 isoforms with distinct N termini were detected in various human tissues including esophageal adenocarcinoma. Expression of each isoform as a fusion protein with enhanced green fluorescent protein revealed differential subcellular trafficking: hGFGa is localized to mitochondria by an N-terminal targeting sequence (MTS), whereas hGFGb and hGFGc were localized in the cytoplasm and nucleus. Mutation/deletion analysis confirmed that the predicted MTS was necessary and sufficient for mitochondrial compartmentalization. The predominant FGF-AS mRNA expressed in esophageal tumors was splice variant b. GFG immunoreactivity was detected in the cytoplasm of all esophageal adenocarcinomas and in 88% of tumor cell nuclei. Although we found a trend towards reduced disease-free survival in patients with FGF-2 overexpressing esophageal adenocarcinomas, significantly worse disease-free survival was noted among patients whose tumors did not also overexpress the FGF-AS b isoform (p = 0.03). Tetracycline-inducible FGF-AS b expression in stably transfected human Seg-1 esophageal adenocarcinoma cells resulted in a significant suppression of steady state FGF-2 mRNA content and cell proliferation. Our data implicate the FGF-AS b isoform in modulation of FGF-2 expression and clinical outcome in esophageal adenocarcinoma.}, }
@article {pmid17567998, year = {2007}, author = {Xi, H and Yu, Y and Fu, Y and Foley, J and Halees, A and Weng, Z}, title = {Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1.}, journal = {Genome research}, volume = {17}, number = {6}, pages = {798-806}, pmid = {17567998}, issn = {1088-9051}, support = {R01 HG003110/HG/NHGRI NIH HHS/United States ; R01HG03110/HG/NHGRI NIH HHS/United States ; }, mesh = {5' Untranslated Regions/*genetics ; *Evolution, Molecular ; Gene Expression Profiling ; *Genome, Human ; Humans ; Mitochondrial Proteins/genetics ; Oligonucleotide Array Sequence Analysis ; *Response Elements ; Ribosomal Proteins/genetics ; TATA Box ; *Transcription, Genetic ; }, abstract = {A set of 723 high-quality human core promoter sequences were compiled and analyzed for overrepresented motifs. Beside the two well-characterized core promoter motifs (TATA and Inr), several known motifs (YY1, Sp1, NRF-1, NRF-2, CAAT, and CREB) and one potentially new motif (motif8) were found. Interestingly, YY1 and motif8 mostly reside immediately downstream from the TSS. In particular, the YY1 motif occurs primarily in genes with 5'-UTRs shorter than 40 base pairs (bp) and its locations coincide with the translation start site. We verified that the YY1 motif is bound by YY1 in vitro. We then performed detailed analysis on YY1 chromatin immunoprecipitation data with a whole-genome human promoter microarray (ChIP-chip) and revealed that the thus identified promoters in HeLa cells were highly enriched with the YY1 motif. Moreover, the motif overlapped with the translation start sites on the plus strand of a group of genes, many with short 5'-UTRs, and with the transcription start sites on the minus strand of another distinct group of genes; together, the two groups of genes accounted for the majority of the YY1-bound promoters in the ChIP-chip data. Furthermore, the first group of genes was highly enriched in the functional categories of ribosomal proteins and nuclear-encoded mitochondria proteins. We suggest that the YY1 motif plays a dual role in both transcription and translation initiation of these genes. We also discuss the evolutionary advantages of housing a transcriptional element inside the transcript in terms of the migration of these genes in the human genome.}, }
@article {pmid17566373, year = {2007}, author = {Mitsuhara, I and Ohashi, Y}, title = {[Cell death and acquired resistance in pathogen-infected plants].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {52}, number = {6 Suppl}, pages = {673-679}, pmid = {17566373}, issn = {0039-9450}, mesh = {*Cell Death/immunology ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Genes, Plant/genetics/physiology ; Immunity, Innate/genetics/immunology ; MAP Kinase Signaling System/physiology ; Mitochondria/physiology ; Mitogen-Activated Protein Kinases/physiology ; Plant Proteins/physiology ; Plants/*immunology/microbiology/parasitology/virology ; }, }
@article {pmid17565672, year = {2007}, author = {Kiraga, J and Mackiewicz, P and Mackiewicz, D and Kowalczuk, M and Biecek, P and Polak, N and Smolarczyk, K and Dudek, MR and Cebrat, S}, title = {The relationships between the isoelectric point and: length of proteins, taxonomy and ecology of organisms.}, journal = {BMC genomics}, volume = {8}, number = {}, pages = {163}, pmid = {17565672}, issn = {1471-2164}, mesh = {Base Composition/genetics ; Computational Biology ; *Ecosystem ; Isoelectric Point ; Mutation/genetics ; *Phylogeny ; Proteins/*chemistry ; Proteomics/*methods ; Species Specificity ; }, abstract = {BACKGROUND: The distribution of isoelectric point (pI) of proteins in a proteome is universal for all organisms. It is bimodal dividing the proteome into two sets of acidic and basic proteins. Different species however have different abundance of acidic and basic proteins that may be correlated with taxonomy, subcellular localization, ecological niche of organisms and proteome size.<br><br>RESULTS: We have analysed 1784 proteomes encoded by chromosomes of Archaea, Bacteria, Eukaryota, and also mitochondria, plastids, prokaryotic plasmids, phages and viruses. We have found significant correlation in more than 95% of proteomes between the protein length and pI in proteomes--positive for acidic proteins and negative for the basic ones. Plastids, viruses and plasmids encode more basic proteomes while chromosomes of Archaea, Bacteria, Eukaryota, mitochondria and phages more acidic ones. Mitochondrial proteomes of Viridiplantae, Protista and Fungi are more basic than Metazoa. It results from the presence of basic proteins in the former proteomes and their absence from the latter ones and is related with reduction of metazoan genomes. Significant correlation was found between the pI bias of proteomes encoded by prokaryotic chromosomes and proteomes encoded by plasmids but there is no correlation between eukaryotic nuclear-coded proteomes and proteomes encoded by organelles. Detailed analyses of prokaryotic proteomes showed significant relationships between pI distribution and habitat, relation to the host cell and salinity of the environment, but no significant correlation with oxygen and temperature requirements. The salinity is positively correlated with acidicity of proteomes. Host-associated organisms and especially intracellular species have more basic proteomes than free-living ones. The higher rate of mutations accumulation in the intracellular parasites and endosymbionts is responsible for the basicity of their tiny proteomes that explains the observed positive correlation between the decrease of genome size and the increase of basicity of proteomes. The results indicate that even conserved proteins subjected to strong selectional constraints follow the global trend in the pI distribution.<br><br>CONCLUSION: The distribution of pI of proteins in proteomes shows clear relationships with length of proteins, subcellular localization, taxonomy and ecology of organisms. The distribution is also strongly affected by mutational pressure especially in intracellular organisms.}, }
@article {pmid17562131, year = {2007}, author = {Kakkar, P and Singh, BK}, title = {Mitochondria: a hub of redox activities and cellular distress control.}, journal = {Molecular and cellular biochemistry}, volume = {305}, number = {1-2}, pages = {235-253}, pmid = {17562131}, issn = {0300-8177}, mesh = {Aging/physiology ; Animals ; Antioxidants/metabolism/physiology ; Biological Evolution ; Calcium Signaling/physiology ; Cell Death/physiology ; Drug Delivery Systems ; Energy Metabolism/physiology ; Humans ; Ion Channels/physiology ; Mitochondria/drug effects/*metabolism/*physiology ; Mitochondrial Diseases/etiology ; Mitochondrial Proteins/physiology ; Models, Biological ; Oxidation-Reduction ; Oxidative Stress/*physiology ; Reactive Nitrogen Species/metabolism ; Reactive Oxygen Species/metabolism ; Uncoupling Protein 1 ; }, abstract = {In their reductionist approach in unraveling phenomena inside the cell, scientists in recent times have focused attention to mitochondria. An organelle with peculiar evolutionary history and organization, it is turning out to be an important cell survival switch. Besides controlling bioenergetics of a cell it also has its own genetic machinery which codes 37 genes. It is a major source of generation of reactive oxygen species, acts as a safety device against toxic increases of cytosolic Ca2+ and its membrane permeability transition is a critical control point in cell death. Redox status of mitochondria is important in combating oxidative stress and maintaining membrane permeability. Importance of mitochondria in deciding the response of cell to multiplicity of physiological and genetic stresses, inter-organelle communication, and ultimate cell survival is constantly being unraveled and discussed in this review. Mitochondrial events involved in apoptosis and necrotic cell death, such as activation of Bcl-2 family proteins, formation of permeability transition pore, release of cytochrome c and apoptosis inducing factors, activation of caspase cascade, and ultimate cell death is the focus of attention not only for cell biologists, but also for toxicologists in unraveling stress responses. Mutations caused by ROS to mitochondrial DNA, its inability to repair it completely and creation of a vicious cycle of mutations along with role of Bcl-2 family genes and proteins has been implicated in many diseases where mitochondrial dysfunctions play a key role. New therapeutic approaches toward targeting low molecular weight compounds to mitochondria, including antioxidants is a step toward nipping the stress in the bud.}, }
@article {pmid17547748, year = {2007}, author = {Huang, J and Gogarten, JP}, title = {Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?.}, journal = {Genome biology}, volume = {8}, number = {6}, pages = {R99}, pmid = {17547748}, issn = {1474-760X}, mesh = {Biological Evolution ; Chlamydia/*genetics/physiology ; Cyanobacteria/genetics ; Gene Transfer, Horizontal ; Genes, Bacterial ; Phylogeny ; Plastids/*genetics ; Rhodophyta/*genetics/physiology ; *Symbiosis ; }, abstract = {BACKGROUND: Ancient endosymbioses are responsible for the origins of mitochondria and plastids, and they contribute to the divergence of several major eukaryotic groups. Although chlamydiae, a group of obligate intracellular bacteria, are not found in plants, an unexpected number of chlamydial genes are most similar to plant homologs, which, interestingly, often contain a plastid-targeting signal. This observation has prompted several hypotheses, including gene transfer between chlamydiae and plant-related groups and an ancestral relationship between chlamydiae and cyanobacteria.<br><br>RESULTS: We conducted phylogenomic analyses of the red alga Cyanidioschyzon merolae to identify genes specifically related to chlamydial homologs. We show that at least 21 genes were transferred between chlamydiae and primary photosynthetic eukaryotes, with the donor most similar to the environmental Protochlamydia. Such an unusually high number of transferred genes suggests an ancient chlamydial endosymbiosis with the ancestral primary photosynthetic eukaryote. We hypothesize that three organisms were involved in establishing the primary photosynthetic lineage: the eukaryotic host cell, the cyanobacterial endosymbiont that provided photosynthetic capability, and a chlamydial endosymbiont or parasite that facilitated the establishment of the cyanobacterial endosymbiont.<br><br>CONCLUSION: Our findings provide a glimpse into the complex interactions that were necessary to establish the primary endosymbiotic relationship between plastid and host cytoplasms, and thereby explain the rarity with which long-term successful endosymbiotic relationships between heterotrophs and photoautotrophs were established. Our data also provide strong and independent support for a common origin of all primary photosynthetic eukaryotes and of the plastids they harbor.}, }
@article {pmid17546088, year = {2007}, author = {Handa, H}, title = {Investigation of the origin and transmission of linear mitochondrial plasmid based on phylogenetic analysis in Japanese rapeseed varieties.}, journal = {Genome}, volume = {50}, number = {2}, pages = {234-240}, doi = {10.1139/g06-150}, pmid = {17546088}, issn = {0831-2796}, mesh = {Brassica rapa/*genetics ; Cell Nucleus/metabolism ; Chromosomes, Plant/*genetics ; DNA Primers/chemistry ; DNA, Mitochondrial/*genetics ; Genome, Plant ; Models, Genetic ; Oligonucleotides/chemistry ; Phylogeny ; Plant Proteins/*genetics ; Plasmids/metabolism ; Polymerase Chain Reaction ; }, abstract = {A linear mitochondrial plasmid is present in some varieties of rapeseed. To elucidate its origin and transmission the author investigated types of mitochondrial genome and the presence of plasmid in 78 rapeseed varieties and landraces in Japan and carried out a comparative analysis using the breeding history of Japanese rapeseed varieties. The mitochondrial genome of rapeseed was classified roughly into 2 types, type I (nap) and type II (cam). Type II rapeseed mitochondria closely resembles that of Brassica rapa, which is a related species of rapeseed. In this study, the author found that all varieties with type II mitochondria originated from interspecific crosses between rapeseed (B. napus) and B. rapa. This indicates that type II cytoplasm was introduced to rapeseed through a breeding program. The presence of plasmid was limited to B. rapa landraces and rapeseed varieties that arose by interspecific crosses between B. napus and B. rapa. The results suggest that mitochondrial plasmid is of B. rapa origin and that it has been introduced into rapeseed by interspecific crosses in a modern breeding program, as in the case of the mitochondrial genome. Phylogenetic study of Japanese rapeseed varieties suggests the participation not of the mitochondrial genome but, rather, the nuclear genome for the perpetuation of plasmid in progeny varieties.}, }
@article {pmid17544704, year = {2007}, author = {Lane, CE and Lindstrom, SC and Saunders, GW}, title = {A molecular assessment of northeast Pacific Alaria species (Laminariales, Phaeophyceae) with reference to the utility of DNA barcoding.}, journal = {Molecular phylogenetics and evolution}, volume = {44}, number = {2}, pages = {634-648}, doi = {10.1016/j.ympev.2007.03.016}, pmid = {17544704}, issn = {1055-7903}, mesh = {Base Sequence ; Chloroplasts/genetics ; Cloning, Molecular ; DNA/*classification/*genetics ; Databases, Nucleic Acid ; Genetic Markers ; Mitochondria/genetics ; Pacific Ocean ; Phaeophyceae/*classification/*genetics ; Phylogeny ; Transcription, Genetic/genetics ; }, abstract = {Despite their relatively complex morphologies, species in the genus Alaria Greville are notoriously difficult to identify with certainty. Morphological characters, often influenced by environmental factors, make individuals in similar habitats artificially appear related. Species identification would, therefore, benefit greatly from the application of molecular tools. We applied DNA barcoding, using the 5' end of the cytochrome c oxidase I (coxI-5') gene from the mitochondrial genome, to define species limits and relationships in northeast Pacific populations of Alaria. This emerging technique is being employed to catalogue species diversity worldwide, particularly among animals, and it has been shown to be sensitive enough to discriminate between closely related species. However, the utility of this marker for identifying or categorizing the majority of life remains unclear. We compared the resolution obtained with this marker to two other molecular systems commonly used in algal research: the nuclear internal transcribed spacer (ITS) of the ribosomal cistron, and the plastid Rubisco operon spacer (rbcSp). In agreement with previous results, Alaria fistulosa Postels &amp; Ruprecht, with its distinct morphological, ecological and molecular features, stands apart from the other species in the genus and we establish Druehlia gen. nov. to accommodate it. For the remaining isolates, distinct mitochondrial haplotypes resolved with the barcode data indicate a period of genetic isolation for at least three incipient species in the northeast Pacific, whereas unexpected levels and patterns of ITS variation, as well as the extreme morphological plasticity found among these isolates, have most probably resulted from a recent collapse in species barriers. The cloning of ITS amplicons revealed multiple ITS copies in several individuals, further supporting this hypothesis.}, }
@article {pmid17542912, year = {2007}, author = {Brown, MT and Goldstone, HM and Bastida-Corcuera, F and Delgadillo-Correa, MG and McArthur, AG and Johnson, PJ}, title = {A functionally divergent hydrogenosomal peptidase with protomitochondrial ancestry.}, journal = {Molecular microbiology}, volume = {64}, number = {5}, pages = {1154-1163}, doi = {10.1111/j.1365-2958.2007.05719.x}, pmid = {17542912}, issn = {0950-382X}, support = {2-T32-AI-007323/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Endopeptidases/chemistry/genetics/*metabolism ; Escherichia coli/genetics ; Evolution, Molecular ; Gene Duplication ; Genes, Protozoan ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Molecular Weight ; Peptide Hydrolases/chemistry/genetics/*metabolism ; Phylogeny ; Protein Precursors/genetics/*metabolism ; Protein Subunits/chemistry/genetics ; Recombinant Proteins/chemistry/isolation &amp; purification/metabolism ; Trichomonas vaginalis/enzymology/genetics ; }, abstract = {Matrix proteins of mitochondria, hydrogenosomes and mitosomes are typically targeted and translocated into their respective organelles using N-terminal presequences that are subsequently cleaved by a peptidase. Here we characterize a approximately 47 kDa metallopeptidase, from the hydrogenosome-bearing, unicellular eukaryote Trichomonas vaginalis, that contains the active site motif (HXXEHX(76)E) characteristic of the beta subunit of the mitochondrial processing peptidase (MPP) and localizes to hydrogenosomes. The purified recombinant protein, named hydrogenosomal processing peptidase (HPP), is capable of cleaving a hydrogenosomal presequence in vitro, in contrast to MPP which requires both an alpha and beta subunit for activity. T. vaginalis HPP forms an approximately 100 kDa homodimer in vitro and also exists in an approximately 100 kDa complex in vivo. Our phylogenetic analyses support a common origin for HPP and betaMPP and demonstrate that gene duplication gave rise to alphaMPP and betaMPP before the divergence of T. vaginalis and mitochondria-bearing lineages. These data, together with published analyses of MPPs and putative mitosomal processing peptidases, lead us to propose that the length of targeting presequences and the subunit composition of organellar processing peptidases evolved in concert. Specifically, longer mitochondrial presequences may have evolved to require an alpha/beta heterodimer for accurate cleavage, while shorter hydrogenosomal and mitosomal presequences did not.}, }
@article {pmid17542850, year = {2007}, author = {Linnen, CR and Farrell, BD}, title = {Mitonuclear discordance is caused by rampant mitochondrial introgression in Neodiprion (Hymenoptera: Diprionidae) sawflies.}, journal = {Evolution; international journal of organic evolution}, volume = {61}, number = {6}, pages = {1417-1438}, doi = {10.1111/j.1558-5646.2007.00114.x}, pmid = {17542850}, issn = {0014-3820}, mesh = {Animals ; Bayes Theorem ; DNA, Mitochondrial ; Evolution, Molecular ; Gene Flow ; *Hybridization, Genetic ; Hymenoptera/classification/*genetics ; Mitochondria/*genetics ; Models, Genetic ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {We investigate the pervasiveness of hybridization and mitochondrial introgression in Neodiprion Rohwer (Hymenoptera; Diprionidae), a Holarctic genus of conifer-feeding sawflies. A phylogenetic analysis of the lecontei species group revealed extensive discordance between a contiguous mitochondrial region spanning three genes (COI, tRNA-leucine, and COII) and three nuclear loci (EF1alpha, CAD, and an anonymous nuclear locus). Bayesian tests of monophyly and Shimodaira-Hasegawa (SH) tests of topological congruence were consistent with mitochondrial introgression; however, these patterns could also be explained by lineage sorting (i.e., deep coalescence). Therefore, to explicitly test the mitochondrial introgression hypothesis, we used a novel application of coalescent-based isolation with migration (IM) models to measure interspecific gene flow at each locus. In support of our hypothesis, mitochondrial gene flow was consistently higher than nuclear gene flow across 120 pairwise species comparisons (P < 1 x 10(-12)). We combine phylogenetic and coalescent evidence to identify likely cases of recent and ancient introgression in Neodiprion, and based on these observations, we hypothesize that shared hosts and/or pheromones facilitate hybridization, whereas disparate abundances between hybridizing species promote mitochondrial introgression. Our results carry implications for phylogenetic analysis, and we advocate the separation of high and low gene flow regions to inform analyses of hybridization and speciational history, respectively.}, }
@article {pmid17537638, year = {2007}, author = {Bodył, A and Mackiewicz, P and Stiller, JW}, title = {The intracellular cyanobacteria of Paulinella chromatophora: endosymbionts or organelles?.}, journal = {Trends in microbiology}, volume = {15}, number = {7}, pages = {295-296}, doi = {10.1016/j.tim.2007.05.002}, pmid = {17537638}, issn = {0966-842X}, mesh = {Amoeba/cytology/*microbiology/physiology ; Animals ; Biological Evolution ; Cyanobacteria/classification/*physiology ; Organelles/classification/*physiology ; Symbiosis/*physiology ; }, abstract = {Endosymbiotic relationships are common across the tree of life and have had profound impacts on cellular evolution and diversity. Recent molecular investigations of the amoeba Paulinella chromatophora have raised a timely and important question: should obligatory intracellular cyanobacteria in Paulinella be considered new organelles, or do plastids and mitochondria hold a unique stature in the history of endosymbiotic events? We argue that drawing a sharp distinction between these two organelles and all other endosymbionts is not supported by accumulating data, neither is it a productive framework for investigating organelle evolution.}, }
@article {pmid17533174, year = {2007}, author = {Barr, CM and Keller, SR and Ingvarsson, PK and Sloan, DB and Taylor, DR}, title = {Variation in mutation rate and polymorphism among mitochondrial genes of Silene vulgaris.}, journal = {Molecular biology and evolution}, volume = {24}, number = {8}, pages = {1783-1791}, doi = {10.1093/molbev/msm106}, pmid = {17533174}, issn = {0737-4038}, mesh = {Base Sequence ; DNA, Plant/genetics ; Evolution, Molecular ; Genes, Mitochondrial/*genetics ; Genes, Plant/*genetics ; *Genetic Variation ; Models, Genetic ; Molecular Sequence Data ; Mutation/*genetics ; Phylogeny ; Polymorphism, Genetic/*genetics ; Recombination, Genetic ; Sequence Homology, Nucleic Acid ; Silene/*genetics ; }, abstract = {The prevailing wisdom of the plant mitochondrial genome is that it has very low substitution rates, thus it is generally assumed that nucleotide diversity within species will also be low. However, recent evidence suggests plant mitochondrial genes may harbor variable and sometimes high levels of within-species polymorphism, a result attributed to variance in the influence of selection. However, insufficient attention has been paid to the effect of among-gene variation in mutation rate on varying levels of polymorphism across loci. We measured levels of polymorphism in seven mitochondrial gene regions across a geographically wide sample of the plant Silene vulgaris to investigate whether individual mitochondrial genes accumulate polymorphisms equally. We found that genes vary significantly in polymorphism. Tests based on coalescence theory show that the genes vary significantly in their scaled mutation rate, which, in the absence of differences among genes in effective population size, suggests these genes vary in their underlying mutation rate. Further evidence that among-gene variance in polymorphism is due to variation in the underlying mutation rate comes from a significant positive relationship between the number of segregating sites and silent site divergence from an outgroup. Contrary to recent studies, we found unconvincing evidence of recombination in the mitochondrial genome, and generally confirm the standard model of plant mitochondria characterized by low substitution rates and no recombination. We also show no evidence of significant variation in the strength or direction of selection among genes; this result may be expected if there is no recombination. The present study provides some of the most thorough data on plant mitochondrial polymorphism, and provides compelling evidence for mutation rate variation among genes. The study also demonstrates the difficulty in establishing a null model of mitochondrial genome polymorphism, and thus the difficulty, in the absence of a comparative approach, in testing the assumption that low substitution rates in plant mitochondria lead to low polymorphism.}, }
@article {pmid17517886, year = {2007}, author = {Chen, S and Sánchez-Fernández, R and Lyver, ER and Dancis, A and Rea, PA}, title = {Functional characterization of AtATM1, AtATM2, and AtATM3, a subfamily of Arabidopsis half-molecule ATP-binding cassette transporters implicated in iron homeostasis.}, journal = {The Journal of biological chemistry}, volume = {282}, number = {29}, pages = {21561-21571}, doi = {10.1074/jbc.M702383200}, pmid = {17517886}, issn = {0021-9258}, support = {DK53953/DK/NIDDK NIH HHS/United States ; }, mesh = {ATP-Binding Cassette Transporters/chemistry/*physiology ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/chemistry/*physiology ; Cloning, Molecular ; Cytochromes c/metabolism ; Cytosol/metabolism ; Iron/chemistry/metabolism ; Microscopy, Fluorescence ; Models, Biological ; Models, Genetic ; Mutation ; Phenotype ; Phylogeny ; Plant Roots/metabolism ; Protein Transport ; }, abstract = {The functional capabilities of one of the smallest subfamilies of ATP-binding cassette transporters from Arabidopsis thaliana, the AtATMs, are described. Designated AtATM1, AtAATM2, and AtATM3, these half-molecule ABC proteins are homologous to the yeast mitochondrial membrane protein ATM1 (ScATM1), which is clearly implicated in the export of mitochondrially synthesized iron/sulfur clusters. Yeast ATM1-deficient (atm1) mutants grow very slowly (have a petite phenotype), are respiration-deficient, accumulate toxic levels of iron in their mitochondria, and show enhanced compensatory high affinity iron uptake. Of the three Arabidopsis ATMs, AtATM3 bears the closest functional resemblance to ScATM1. Heterologously expressed AtATM3 is not only able to complement the yeast atm1 petite phenotype but is also able to suppress the constitutively high capacity for high affinity iron uptake associated with loss of the chromosomal copy of ScATM1, abrogate intra-mitochondrial iron hyperaccumulation, and restore mitochondrial respiratory function and cytochrome c levels. By comparison, AtATM1 only weakly suppresses the atm1 phenotype, and AtATM2 exerts little or no suppressive action but instead is toxic when expressed in this system. The differences between AtATM3 and AtATM1 are maintained after exchanging their target peptides, and these proteins as well as AtATM2 colocalize with the mitochondrial fluor MitoTracker Red when expressed in yeast as GFP fusions. Although its toxicity when heterologously expressed in yeast, except when fused with GFP, precludes the functional analysis of native AtATM2, a common function, mitochondrial export of Fe/S clusters or their precursors for the assembly of cytosolic Fe/S proteins, is inferred for AtATM3 and AtATM1.}, }
@article {pmid17517155, year = {2007}, author = {Combadão, J and Campos, PR and Dionisio, F and Gordo, I}, title = {Small-world networks decrease the speed of Muller's ratchet.}, journal = {Genetical research}, volume = {89}, number = {1}, pages = {7-18}, doi = {10.1017/S0016672307008658}, pmid = {17517155}, mesh = {Animals ; *Biological Evolution ; Evolution, Molecular ; *Extinction, Biological ; Genetics, Population ; *Models, Genetic ; Population Dynamics ; Population Growth ; Reproduction, Asexual/physiology ; *Selection, Genetic ; Time Factors ; }, abstract = {Muller's ratchet is an evolutionary process that has been implicated in the extinction of asexual species, the evolution of non-recombining genomes, such as the mitochondria, the degeneration of the Y chromosome, and the evolution of sex and recombination. Here we study the speed of Muller's ratchet in a spatially structured population which is subdivided into many small populations (demes) connected by migration, and distributed on a graph. We studied different types of networks: regular networks (similar to the stepping-stone model), small-world networks and completely random graphs. We show that at the onset of the small-world network - which is characterized by high local connectivity among the demes but low average path length - the speed of the ratchet starts to decrease dramatically. This result is independent of the number of demes considered, but is more pronounced the larger the network and the stronger the deleterious effect of mutations. Furthermore, although the ratchet slows down with increasing migration between demes, the observed decrease in speed is smaller in the stepping-stone model than in small-world networks. As migration rate increases, the structured populations approach, but never reach, the result in the corresponding panmictic population with the same number of individuals. Since small-world networks have been shown to describe well the real contact networks among people, we discuss our results in the light of the evolution of microbes and disease epidemics.}, }
@article {pmid17514372, year = {2008}, author = {Kerscher, S and Dröse, S and Zickermann, V and Brandt, U}, title = {The three families of respiratory NADH dehydrogenases.}, journal = {Results and problems in cell differentiation}, volume = {45}, number = {}, pages = {185-222}, doi = {10.1007/400_2007_028}, pmid = {17514372}, issn = {0080-1844}, mesh = {Amino Acid Sequence ; Bacteria/metabolism ; Bacterial Physiological Phenomena ; Catalysis ; *Electron Transport ; Electron Transport Complex I ; Mitochondria/*metabolism ; Models, Biological ; Models, Molecular ; Molecular Conformation ; Molecular Sequence Data ; NADH Dehydrogenase/*chemistry/*physiology ; Phylogeny ; Sequence Homology, Amino Acid ; Sodium/chemistry ; }, abstract = {Most reducing equivalents extracted from foodstuffs during oxidative metabolism are fed into the respiratory chains of aerobic bacteria and mitochondria by NADH:quinone oxidoreductases. Three families of enzymes can perform this task and differ remarkably in their complexity and role in energy conversion. Alternative or NDH-2-type NADH dehydrogenases are simple one subunit flavoenzymes that completely dissipate the redox energy of the NADH/quinone couple. Sodium-pumping NADH dehydrogenases (Nqr) that are only found in procaryotes contain several flavins and are integral membrane protein complexes composed of six different subunits. Proton-pumping NADH dehydrogenases (NDH-1 or complex I) are highly complicated membrane protein complexes, composed of up to 45 different subunits, that are found in bacteria and mitochondria. This review gives an overview of the origin, structural and functional properties and physiological significance of these three types of NADH dehydrogenase.}, }
@article {pmid17510790, year = {2007}, author = {Spinazzola, A and Zeviani, M}, title = {Disorders of nuclear-mitochondrial intergenomic communication.}, journal = {Bioscience reports}, volume = {27}, number = {1-3}, pages = {39-51}, doi = {10.1007/s10540-007-9036-1}, pmid = {17510790}, issn = {0144-8463}, mesh = {Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Genomic Instability ; Humans ; Mitochondrial Diseases/*genetics/pathology ; Mutation ; Protein Biosynthesis ; }, abstract = {In the course of evolution, mitochondria lost their independence, and mtDNA became "slave" of nDNA, depending on numerous nucleus-encoded factors for its integrity, replication and expression. Mutations in any of these factors may alter the cross-talk between the two genomes and cause diseases that affect mtDNA integrity or expression, being inherited as mendelian traits.}, }
@article {pmid17510656, year = {2007}, author = {Mukherjee, S and Basu, S and Home, P and Dhar, G and Adhya, S}, title = {Necessary and sufficient factors for the import of transfer RNA into the kinetoplast mitochondrion.}, journal = {EMBO reports}, volume = {8}, number = {6}, pages = {589-595}, pmid = {17510656}, issn = {1469-221X}, mesh = {Animals ; Leishmania tropica/*metabolism ; Mitochondria/*genetics ; Protein Subunits/metabolism ; Protozoan Proteins/*metabolism ; *RNA Transport ; RNA, Transfer/genetics/*metabolism ; Recombinant Proteins/metabolism ; }, abstract = {The mechanism of active transport of transfer RNA (tRNA) across membranes is largely unknown. Factors mediating the import of tRNA into the kinetoplast mitochondrion of the protozoon Leishmania tropica are organized into a multiprotein RNA import complex (RIC) at the inner membrane. Here, we present the complete characterization of the identities and functions of the subunits of this complex. The complex contains three mitochondrion- and eight nuclear-encoded subunits; six of the latter are necessary and sufficient for import. Antisense-mediated knockdown of essential subunits resulted in the depletion of mitochondrial tRNAs and inhibition of organellar translation. Functional complexes were reconstituted with recombinant subunits expressed in Escherichia coli. Several essential RIC subunits are identical to specific subunits of respiratory complexes. These findings provide new information on the evolution of tRNA import and the foundation for detailed structural and mechanistic studies.}, }
@article {pmid17510655, year = {2007}, author = {Kozjak-Pavlovic, V and Ross, K and Benlasfer, N and Kimmig, S and Karlas, A and Rudel, T}, title = {Conserved roles of Sam50 and metaxins in VDAC biogenesis.}, journal = {EMBO reports}, volume = {8}, number = {6}, pages = {576-582}, pmid = {17510655}, issn = {1469-221X}, mesh = {Animals ; Cell Cycle Proteins ; *Evolution, Molecular ; HeLa Cells ; Humans ; Ion Channel Gating ; Membrane Proteins/*metabolism ; Mice ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Membranes/metabolism ; Proteins/*metabolism ; RNA, Small Interfering/metabolism ; Rats ; Voltage-Dependent Anion Channels/*biosynthesis ; }, abstract = {Voltage-dependent anion-selective channel (VDAC) is a beta-barrel protein in the outer mitochondrial membrane that is necessary for metabolite exchange with the cytosol and is proposed to be involved in certain forms of apoptosis. We studied the biogenesis of VDAC in human mitochondria by depleting the components of the mitochondrial import machinery by using RNA interference. Here, we show the importance of the translocase of the outer mitochondrial membrane (TOM) complex in the import of the VDAC precursor. The deletion of Sam50, the central component of the sorting and assembly machinery (SAM), led to both a strong defect in the assembly of VDAC and a reduction in the steady-state level of VDAC. Metaxin 2-depleted mitochondria had reduced levels of metaxin 1 and were deficient in import and assembly of VDAC and Tom40, but not of three matrix-targeted precursors. We also observed a reduction in the levels of metaxin 1 and metaxin 2 in Sam50-depleted mitochondria, implying a connection between these three proteins, although Sam50 and metaxins seemed to be in different complexes. We conclude that the pathway of VDAC biogenesis in human mitochondria involves the TOM complex, Sam50 and metaxins, and that it is evolutionarily conserved.}, }
@article {pmid17509845, year = {2007}, author = {Kageyama, K and Senda, M and Asano, T and Suga, H and Ishiguro, K}, title = {Intra-isolate heterogeneity of the ITS region of rDNA in Pythium helicoides.}, journal = {Mycological research}, volume = {111}, number = {Pt 4}, pages = {416-423}, doi = {10.1016/j.mycres.2007.01.019}, pmid = {17509845}, issn = {0953-7562}, mesh = {DNA, Fungal/genetics ; DNA, Ribosomal/genetics ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Genes, Fungal ; Genetic Variation ; Phylogeny ; Plant Diseases/microbiology ; Plant Roots/microbiology ; Polymorphism, Restriction Fragment Length ; Pythium/*genetics ; Sequence Analysis, DNA ; }, abstract = {Heterogeneity of the rDNA ITS region in Pythium helicoides and the phylogenetic relationship between P. helicoides and closely related species were investigated. In PCR-RFLP analysis of the rDNA ITS region of six P. helicoides isolates investigated, including the type culture, intraspecific variation was found at the HhaI site. The total length of fragments was longer than before cutting, indicating sequence heterogeneity within isolates. Digestion of the cloned rDNA ITS region derived from seven isolates with HhaI revealed polymorphisms among and within single zoospore isolates, and variability of the region was also present among the clones derived from the same isolate. To test whether the rDNA ITS region of closely related species and other regions in the genome of P. helicoides are also variable, the rDNA ITS region of P. ultimum and the cytochrome oxydase II (cox II) gene encoded in mitochondria were sequenced. P. ultimum had little variation in the rDNA ITS region. The cox II gene sequences of both species revealed only a low intraspecific variability and no intra-isolate variation. In the phylogenic tree based on the rDNA ITS sequences, all clones of P. helicoides formed one large clade that was distinct from the clades comprising morphologically similar species, such as P. oedochilum and P. ostracodes, and was closely related to P. chamaehyphon rather than the other species.}, }
@article {pmid17508407, year = {2007}, author = {Davidov, Y and Jurkevitch, E}, title = {Comments of Poole and Penny's essay "Evaluating hypotheses for the origin of eukaryotes", BioEssays 29:74-84.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {29}, number = {6}, pages = {615-616}, doi = {10.1002/bies.20587}, pmid = {17508407}, issn = {0265-9247}, mesh = {Archaea/*physiology ; *Biological Evolution ; Eukaryotic Cells/*physiology ; *Mitochondria ; Phagocytosis ; Phylogeny ; }, }
@article {pmid17508406, year = {2007}, author = {Poole, AM and Penny, D}, title = {Response to Dagan and Martin.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {29}, number = {6}, pages = {611-614}, doi = {10.1002/bies.20577}, pmid = {17508406}, issn = {0265-9247}, mesh = {Archaea/*physiology ; *Biological Evolution ; Eukaryotic Cells/*physiology ; Gene Transfer, Horizontal ; *Mitochondria ; *Phagocytosis ; Phylogeny ; }, }
@article {pmid17506638, year = {2007}, author = {Wallace, DC}, title = {Why do we still have a maternally inherited mitochondrial DNA? Insights from evolutionary medicine.}, journal = {Annual review of biochemistry}, volume = {76}, number = {}, pages = {781-821}, doi = {10.1146/annurev.biochem.76.081205.150955}, pmid = {17506638}, issn = {0066-4154}, support = {AG13154/AG/NIA NIH HHS/United States ; AG24373/AG/NIA NIH HHS/United States ; HL64017/HL/NHLBI NIH HHS/United States ; NS21328/NS/NINDS NIH HHS/United States ; NS41650/NS/NINDS NIH HHS/United States ; TW01366/TW/FIC NIH HHS/United States ; }, mesh = {Biological Evolution ; *DNA, Mitochondrial ; *Genes, Mitochondrial ; Genomics ; Humans ; Mitochondrial Proteins/genetics/metabolism ; Oxidative Phosphorylation ; Phylogeny ; Protein Subunits/genetics/metabolism ; }, abstract = {The human cell is a symbiosis of two life forms, the nucleus-cytosol and the mitochondrion. The nucleus-cytosol emphasizes structure and its genes are Mendelian, whereas the mitochondrion specializes in energy and its mitochondrial DNA (mtDNA) genes are maternal. Mitochondria oxidize calories via oxidative phosphorylation (OXPHOS) to generate a mitochondrial inner membrane proton gradient (DeltaP). DeltaP then acts as a source of potential energy to produce ATP, generate heat, regulate reactive oxygen species (ROS), and control apoptosis, etc. Interspecific comparisons of mtDNAs have revealed that the mtDNA retains a core set of electron and proton carrier genes for the proton-translocating OXPHOS complexes I, III, IV, and V. Human mtDNA analysis has revealed these genes frequently contain region-specific adaptive polymorphisms. Therefore, the mtDNA with its energy controlling genes may have been retained to permit rapid adaptation to new environments.}, }
@article {pmid17504772, year = {2007}, author = {Pisani, D and Cotton, JA and McInerney, JO}, title = {Supertrees disentangle the chimerical origin of eukaryotic genomes.}, journal = {Molecular biology and evolution}, volume = {24}, number = {8}, pages = {1752-1760}, doi = {10.1093/molbev/msm095}, pmid = {17504772}, issn = {0737-4038}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; DNA, Mitochondrial/genetics ; Eukaryotic Cells/classification/*physiology ; *Evolution, Molecular ; Genes, Archaeal ; *Genome, Archaeal ; *Genome, Bacterial ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; }, abstract = {Eukaryotes are traditionally considered to be one of the three natural divisions of the tree of life and the sister group of the Archaebacteria. However, eukaryotic genomes are replete with genes of eubacterial ancestry, and more than 20 mutually incompatible hypotheses have been proposed to account for eukaryote origins. Here we test the predictions of these hypotheses using a novel supertree-based phylogenetic signal-stripping method, and recover supertrees of life based on phylogenies for up to 5,741 single gene families distributed across 185 genomes. Using our signal-stripping method, we show that there are three distinct phylogenetic signals in eukaryotic genomes. In order of strength, these link eukaryotes with the Cyanobacteria, the Proteobacteria, and the Thermoplasmatales, an archaebacterial (euryarchaeotes) group. These signals correspond to distinct symbiotic partners involved in eukaryote evolution: plastids, mitochondria, and the elusive host lineage. According to our whole-genome data, eukaryotes are hardly the sister group of the Archaebacteria, because up to 83% of eukaryotic genes with a prokaryotic homolog have eubacterial, not archaebacterial, origins. The results reject all but two of the current hypotheses for the origin of eukaryotes: those assuming a sulfur-dependent or hydrogen-dependent syntrophy for the origin of mitochondria.}, }
@article {pmid17503387, year = {2006}, author = {Vinh, le S and Varón, A and Wheeler, WC}, title = {Pairwise alignment with rearrangements.}, journal = {Genome informatics. International Conference on Genome Informatics}, volume = {17}, number = {2}, pages = {141-151}, pmid = {17503387}, issn = {0919-9454}, mesh = {Algorithms ; Animals ; Base Sequence ; DNA, Mitochondrial/genetics ; Databases, Genetic ; Evolution, Molecular ; Gene Order ; *Gene Rearrangement ; *Genome ; Mitochondria/genetics ; Models, Genetic ; Mutagenesis, Insertional ; *Phylogeny ; *Recombination, Genetic ; *Sequence Alignment ; Software ; }, abstract = {The increase of available genomes poses new optimization problems in genome comparisons. A genome can be considered as a sequence of characters (loci) which are genes or segments of nucleotides. Genomes are subject to both nucleotide transformation and character order rearrangement processes. In this context, we define a problem of so-called pairwise alignment with rearrangements (PAR) between two genomes. The PAR generalizes the ordinary pairwise alignment by allowing the rearrangement of character order. The objective is to find the optimal PAR that minimizes the total cost which is composed of three factors: the edit cost between characters, the deletion/insertion cost of characters, and the rearrangement cost between character orders. To this end, we propose simple and effective heuristic methods: character moving and simultaneous character swapping. The efficiency of the methods is tested on Metazoa mitochondrial genomes. Experiments show that, pairwise alignments with rearrangements give better performance than ordinary pairwise alignments without rearrangements. The best proposed method, simultaneous character swapping, is implemented as an essential subroutine in our software POY version 4.0 to reconstruct genome-based phylogenies.}, }
@article {pmid17499024, year = {2007}, author = {Fisher, N and Bray, PG and Ward, SA and Biagini, GA}, title = {The malaria parasite type II NADH:quinone oxidoreductase: an alternative enzyme for an alternative lifestyle.}, journal = {Trends in parasitology}, volume = {23}, number = {7}, pages = {305-310}, doi = {10.1016/j.pt.2007.04.014}, pmid = {17499024}, issn = {1471-4922}, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Evolution, Molecular ; Mitochondria/*enzymology ; Models, Molecular ; Molecular Sequence Data ; NADH, NADPH Oxidoreductases/chemistry/*metabolism ; Oxidation-Reduction ; Plasmodium falciparum/*enzymology ; Quinones/*metabolism ; }, abstract = {The operation of a type II NADH:quinone oxidoreductase (PfNDH2), also known as alternative Complex I, in the mitochondrion of the human malaria parasite, Plasmodium falciparum, has recently been described. Unlike the Complex I of typical mitochondria, type II NADH:quinone oxidoreductases do not have transmembrane domains and are not involved directly in proton (H(+)) pumping. Here, we present a predictive model of PfNDH2, describing putative NADH-, flavin- and quinone-binding sites, as well as a possible membrane 'anchoring' region. In addition, we hypothesize that the alternative Complex I is an evolutionary adaptation to a microaerophilic lifestyle enabling (proton) uncoupled oxidation of NADH. This adaptive feature has several advantages, including: (i) a reduction of proton 'back-pressure' in the absence of extensive ATP synthesis; (ii) a reduction of mitochondrial superoxide generation; and (iii) a mechanism for the deregulated oxidation of cytosolic NADH.}, }
@article {pmid17498627, year = {2007}, author = {Huo, G and Jiang, G and Sun, Z and Liu, D and Zhang, Y and Lu, L}, title = {Phylogenetic reconstruction of the family Acrypteridae (Orthoptera: Acridoidea) based on mitochondrial cytochrome B gene.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {34}, number = {4}, pages = {294-306}, doi = {10.1016/S1673-8527(07)60031-9}, pmid = {17498627}, issn = {1673-8527}, mesh = {Animals ; Codon ; Cytochromes b/*genetics ; DNA, Mitochondrial/genetics ; Mitochondria/*genetics ; Orthoptera/*classification/cytology/*genetics ; *Phylogeny ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {Sequences from the mitochondrial cytochrome b gene (Cyt b) were determined for 25 species from the superfamily Acridoidae and the homologous sequences of 19 species of grasshoppers were downloaded from the GenBank data library. The purpose was to develop a molecular phylogeny of the Acrypteridae, and to interpret the phylogenetic position of the family within the superfamily Acridoidea. Phylogeny was reconstructed by Maximum-parsimony (MP) and Bayesian criteria using Yunnanites coriacea and Tagasta marginella as outgroups. The alignment length of the fragments was 384 bp after excluding ambiguous sites, including 167 parsimony informative sites. In the fragments, the percentages of A + T and G + C were 70.7% and 29.3%, respectively. The monophyly of Arcypteridae is not supported by phylogenetic trees. Within the Arcypteridae, neither Arcypterinae nor Ceracrinae is supported as a monophyletic group. The current genus Chorthippus is not a monophyletic group, and should be a polyphyletic group. The present results are significantly different from the classification scheme of Arcypteridae, which is based on morphology.}, }
@article {pmid17485854, year = {2007}, author = {Lertwattanasakul, N and Sootsuwan, K and Limtong, S and Thanonkeo, P and Yamada, M}, title = {Comparison of the gene expression patterns of alcohol dehydrogenase isozymes in the thermotolerant yeast Kluyveromyces marxianus and their physiological functions.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {71}, number = {5}, pages = {1170-1182}, doi = {10.1271/bbb.60622}, pmid = {17485854}, issn = {0916-8451}, mesh = {Alcohol Dehydrogenase/genetics/isolation &amp; purification/*metabolism ; Amino Acid Sequence ; Base Sequence ; Binding Sites ; Blotting, Southern ; Carbon/metabolism ; Cloning, Molecular ; Conserved Sequence ; Cytoplasm/enzymology ; Ethanol/analysis ; *Gene Expression Regulation, Fungal ; Genes, Fungal ; Glucose/analysis ; Isoenzymes/genetics/metabolism ; Kluyveromyces/*enzymology/genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; TATA Box ; Temperature ; }, abstract = {Four genes encoding alcohol dehydrogenase (Adh) isozymes in the thermotolerant yeast Kluyveromyces marxianus, a potent candidate for ethanol production at high temperatures, were investigated. Of these, KmADH3 and KmADH4 were cloned and sequenced, and their deduced amino acid sequences were compared with those of KmAdh1 and KmAdh2 and other Adhs of Kluyveromyces lactis and Saccharomyces cerevisiae. The four KmAdhs had high sequence similarity, though KmAdh3 and KmAdh4 possessed an amino-terminal extension as a mitochondrial targeting sequence, and appear to belong to the zinc-containing Adh family. These results and the results of Southern blot experiments suggest that there are at least four Adh isozymes in K. marxianus, two cytoplasmic enzymes and two mitochondrial enzymes. The expression profile revealed that KmADH genes are differently expressed depending on growth phase and carbon source, suggesting that these highly homologous Adhs play distinctive roles in cells.}, }
@article {pmid17483224, year = {2007}, author = {Williams, KP and Sobral, BW and Dickerman, AW}, title = {A robust species tree for the alphaproteobacteria.}, journal = {Journal of bacteriology}, volume = {189}, number = {13}, pages = {4578-4586}, pmid = {17483224}, issn = {0021-9193}, mesh = {Alphaproteobacteria/classification/*genetics ; Computational Biology ; Evolution, Molecular ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Rickettsiaceae/classification/genetics ; Software ; }, abstract = {The branching order and coherence of the alphaproteobacterial orders have not been well established, and not all studies have agreed that mitochondria arose from within the Rickettsiales. A species tree for 72 alphaproteobacteria was produced from a concatenation of alignments for 104 well-behaved protein families. Coherence was upheld for four of the five orders with current standing that were represented here by more than one species. However, the family Hyphomonadaceae was split from the other Rhodobacterales, forming an expanded group with Caulobacterales that also included Parvularcula. The three earliest-branching alphaproteobacterial orders were the Rickettsiales, followed by the Rhodospirillales and then the Sphingomonadales. The principal uncertainty is whether the expanded Caulobacterales group is more closely associated with the Rhodobacterales or the Rhizobiales. The mitochondrial branch was placed within the Rickettsiales as a sister to the combined Anaplasmataceae and Rickettsiaceae, all subtended by the Pelagibacter branch. Pelagibacter genes will serve as useful additions to the bacterial outgroup in future evolutionary studies of mitochondrial genes, including those that have transferred to the eukaryotic nucleus.}, }
@article {pmid17483207, year = {2007}, author = {Taylor, CT and Pouyssegur, J}, title = {Oxygen, hypoxia, and stress.}, journal = {Annals of the New York Academy of Sciences}, volume = {1113}, number = {}, pages = {87-94}, doi = {10.1196/annals.1391.004}, pmid = {17483207}, issn = {0077-8923}, mesh = {Adaptation, Physiological ; Animals ; Humans ; Hypoxia/*metabolism ; Oxidative Stress/physiology ; Oxygen/metabolism/*physiology ; }, abstract = {Since cyanobacteria began to photosynthesize and introduce the colorless and odorless gas oxygen into the earth's atmosphere some 2.5 billion years ago, human evolution has been intrinsically linked to this critical molecule. Initially, the electrophilic chemical properties of oxygen rendered it a formidable toxic challenge to organisms; however, eukaryotic cells, following the incorporation of bacterial-derived mitochondria, evolved to make beneficial use of the chemical properties of molecular oxygen as the final electron acceptor in the highly efficient production of cellular energy supplies in the form of adenosine triphosphate. Because of both its necessity for eukaryotic life and its reactive chemical nature, however, a delicate balance exists between the supply of oxygen to a cell/tissue/organism and the beneficial or harmful outcome. In this minireview, we shall discuss the role of oxygen in metabolism with a particular emphasis on outcomes when oxygen supply is significantly altered. Furthermore, we will describe endogenous mechanisms that have evolved to protect cells and tissues during such adverse conditions and may prove useful as novel therapeutic targets in a range of disease states where oxygen-related stress occurs.}, }
@article {pmid17478548, year = {2007}, author = {Ostersetzer, O and Kato, Y and Adam, Z and Sakamoto, W}, title = {Multiple intracellular locations of Lon protease in Arabidopsis: evidence for the localization of AtLon4 to chloroplasts.}, journal = {Plant &amp; cell physiology}, volume = {48}, number = {6}, pages = {881-885}, doi = {10.1093/pcp/pcm052}, pmid = {17478548}, issn = {0032-0781}, mesh = {Arabidopsis/*cytology/*enzymology ; Arabidopsis Proteins/*metabolism ; Chloroplasts/*enzymology/metabolism ; Mitochondria/metabolism ; Protease La/*metabolism ; Protein Transport ; Serine Endopeptidases/*metabolism ; Thylakoids/metabolism ; }, abstract = {Arabidopsis contains four Lon protease-like proteins (AtLon1-AtLon4), predicted to be localized in different cellular organelles, including mitochondria, peroxisomes and plastids. A notable question is whether Lon is present in chloroplasts, since it is absent from cyanobacteria and thus appears to have been lost during the evolution of photosynthetic organisms. Based on in vivo transient assays, we found that AtLon4 is dually targeted to both mitochondria and chloroplasts. Furthermore, immunoblot analysis localized AtLon4 to the thylakoids. Thus, in spite of its absence from basal photosynthetic organisms, our results suggest the presence of Lon in plant plastids.}, }
@article {pmid17478060, year = {2007}, author = {Nolan, DV and Carpenter, S and Barber, J and Mellor, PS and Dallas, JF and Mordue Luntz, AJ and Piertney, SB}, title = {Rapid diagnostic PCR assays for members of the Culicoides obsoletus and Culicoides pulicaris species complexes, implicated vectors of bluetongue virus in Europe.}, journal = {Veterinary microbiology}, volume = {124}, number = {1-2}, pages = {82-94}, doi = {10.1016/j.vetmic.2007.03.019}, pmid = {17478060}, issn = {0378-1135}, mesh = {Animals ; Bluetongue/*transmission ; Bluetongue virus ; Ceratopogonidae/*classification/genetics/virology ; Electron Transport Complex IV/*genetics ; Female ; Insect Vectors/*classification/genetics/virology ; Likelihood Functions ; Male ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction/methods/veterinary ; Sequence Alignment/veterinary ; Species Specificity ; }, abstract = {Biting midges of the Culicoides obsoletus Meigen and Culicoides pulicaris L. species complexes (Diptera: Ceratopogonidae) are increasingly implicated as vectors of bluetongue virus in Palearctic regions. However, predicting epidemiological risk and the spread of disease is hampered because whilst vector competence of Culicoides is expressed only in adult females, morphological identification of constituent species is only readily applicable to adult males and some species distinguishing traits have overlapping character states. Furthermore, adult males are typically rare in field collections, making characterisation of Culicoides communities impossible. Here we highlight the utility of mitochondrial cytochrome oxidase subunit I (COI) DNA sequences for taxonomic resolution and species identification of all species within C. obsoletus and C. pulicarus complexes. Culicoides were collected from 18 sites in the UK and Continental Europe, and identified to species level, or species complex level, based on morphological characters. The sample comprised four species from the C. obsoletus complex (n = 88) and five species from the C. pulicaris complex (n = 39). The DNA sequence of the 5' end of the COI gene was obtained from all individuals. Each member species formed a well-supported reciprocally monophyletic clade in a maximum likelihood phylogeny. Levels of DNA sequence divergence were sufficiently high between species to allow the design of species-specific PCR primers that can be used in PCR for identification of members of the C. pulicaris complex or in a multiplex PCR to identify members of the C. obsoletus complex. This approach provides a valuable diagnostic tool for monitoring species composition in mixed field collections of Culicoides.}, }
@article {pmid17472911, year = {2007}, author = {Whitworth, TL and Dawson, RD and Magalon, H and Baudry, E}, title = {DNA barcoding cannot reliably identify species of the blowfly genus Protocalliphora (Diptera: Calliphoridae).}, journal = {Proceedings. Biological sciences}, volume = {274}, number = {1619}, pages = {1731-1739}, pmid = {17472911}, issn = {0962-8452}, mesh = {Animals ; Classification/*methods ; Diptera/classification/*genetics/microbiology ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Hybridization, Genetic ; Likelihood Functions ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; United States ; Wolbachia/genetics ; }, abstract = {In DNA barcoding, a short standardized DNA sequence is used to assign unknown individuals to species and aid in the discovery of new species. A fragment of the mitochondrial gene cytochrome c oxidase subunit 1 is emerging as the standard barcode region for animals. However, patterns of mitochondrial variability can be confounded by the spread of maternally transmitted bacteria that cosegregate with mitochondria. Here, we investigated the performance of barcoding in a sample comprising 12 species of the blow fly genus Protocalliphora, known to be infected with the endosymbiotic bacteria Wolbachia. We found that the barcoding approach showed very limited success: assignment of unknown individuals to species is impossible for 60% of the species, while using the technique to identify new species would underestimate the species number in the genus by 75%. This very low success of the barcoding approach is due to the non-monophyly of many of the species at the mitochondrial level. We even observed individuals from four different species with identical barcodes, which is, to our knowledge, the most extensive case of mtDNA haplotype sharing yet described. The pattern of Wolbachia infection strongly suggests that the lack of within-species monophyly results from introgressive hybridization associated with Wolbachia infection. Given that Wolbachia is known to infect between 15 and 75% of insect species, we conclude that identification at the species level based on mitochondrial sequence might not be possible for many insects. However, given that Wolbachia-associated mtDNA introgression is probably limited to very closely related species, identification at the genus level should remain possible.}, }
@article {pmid17466066, year = {2007}, author = {Kolokotronis, SO and Macphee, RD and Greenwood, AD}, title = {Detection of mitochondrial insertions in the nucleus (NuMts) of Pleistocene and modern muskoxen.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {67}, pmid = {17466066}, issn = {1471-2148}, mesh = {Animals ; Cloning, Molecular ; Complementarity Determining Regions/*genetics ; DNA Transposable Elements/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Haplotypes ; Paleontology ; Phylogeny ; Polymerase Chain Reaction ; Ruminants/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Nuclear insertions of mitochondrial sequences (NuMts) have been identified in a wide variety of organisms. Trafficking of genetic material from the mitochondria to the nucleus has occurred frequently during mammalian evolution and can lead to the production of a large pool of sequences with varying degrees of homology to organellar mitochondrial DNA (mtDNA) sequences. This presents both opportunities and challenges for forensics, population genetics, evolutionary genetics, conservation biology and the study of DNA from ancient samples. Here we present a case in which difficulties in ascertaining the organellar mtDNA sequence from modern samples hindered their comparison to ancient DNA sequences.<br><br>RESULTS: We obtained mitochondrial hypervariable region (HVR) sequences from six ancient samples of tundra muskox (Ovibos moschatus) that were reproducible but distinct from modern muskox sequences reported previously. Using the same PCR primers applied to the ancient specimens and the primers used to generate the modern muskox DNA sequences in a previous study, we failed to definitively identify the organellar sequence from the two modern muskox samples tested. Instead of anticipated sequence homogeneity, we obtained multiple unique sequences from both hair and blood of one modern specimen. Sequencing individual clones of a >1 kb PCR fragment from modern samples did not alleviate the problem as there was not a consistent match across the entire length of the sequences to Ovibos when compared to sequences in GenBank.<br><br>CONCLUSION: In specific taxa, due to nuclear insertions some regions of the mitochondrial genome may not be useful for the characterization of modern or ancient DNA.}, }
@article {pmid17464328, year = {2007}, author = {Pellegrini, L and Scorrano, L}, title = {A cut short to death: Parl and Opa1 in the regulation of mitochondrial morphology and apoptosis.}, journal = {Cell death and differentiation}, volume = {14}, number = {7}, pages = {1275-1284}, doi = {10.1038/sj.cdd.4402145}, pmid = {17464328}, issn = {1350-9047}, support = {TCP02016/TI_/Telethon/Italy ; }, mesh = {Animals ; Apoptosis/*physiology ; Cell Shape/physiology ; Evolution, Molecular ; GTP Phosphohydrolases/genetics/*metabolism ; Humans ; Metalloproteases/genetics/*metabolism ; Mitochondria/*metabolism/ultrastructure ; Mitochondrial Membranes/*metabolism/ultrastructure ; Mitochondrial Proteins/genetics/*metabolism ; Peptide Hydrolases/metabolism ; Phosphorylation ; }, abstract = {Mitochondria are crucial amplifiers of death signals. They release cytochrome c and other pro-apoptotic factors required to fully activate effector caspases. This release is accompanied by fragmentation of the mitochondrial reticulum and by remodelling of the internal structure of the organelle. Here we review data supporting the existence of a regulatory network in the inner mitochondrial membrane that includes optic atrophy 1 (Opa1), a dynamin-related protein, and presenilin-associated rhomboid-like (Parl), a rhomboid protease. Opa1 regulates remodelling of the cristae independent of its effect on fusion. Cristae remodelling conversely requires Parl, which participates in the production of a soluble form of Opa1 retrieved together with the integral membrane one in oligomers that are disrupted early during apoptosis. Parl itself is regulated by proteolysis to generate a cleaved form, which in turn modulates the shape of the mitochondrial reticulum. Cleavage of Parl depends on its phosphorylation state around the cleavage site, implicating mitochondrial kinases and phosphatases in the regulation of mitochondrial shape.}, }
@article {pmid17463271, year = {2007}, author = {Martin, W and Dagan, T and Koonin, EV and Dipippo, JL and Gogarten, JP and Lake, JA}, title = {The evolution of eukaryotes.}, journal = {Science (New York, N.Y.)}, volume = {316}, number = {5824}, pages = {542-3; author reply 542-3}, doi = {10.1126/science.316.5824.542c}, pmid = {17463271}, issn = {1095-9203}, mesh = {Archaeal Proteins/chemistry ; Bacterial Proteins/chemistry ; *Biological Evolution ; *Eukaryotic Cells ; Evolution, Molecular ; Fungal Proteins/chemistry ; Genomics ; Humans ; Mitochondria ; Phagocytosis ; Prokaryotic Cells ; Proteins/*chemistry ; }, }
@article {pmid17454297, year = {2007}, author = {Ohtsuki, T and Watanabe, Y}, title = {T-armless tRNAs and elongated elongation factor Tu.}, journal = {IUBMB life}, volume = {59}, number = {2}, pages = {68-75}, doi = {10.1080/15216540701218722}, pmid = {17454297}, issn = {1521-6543}, mesh = {Animals ; Base Sequence ; Caenorhabditis elegans/*genetics ; Evolution, Molecular ; Mitochondria/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Peptide Elongation Factor Tu/*chemistry/genetics/metabolism ; RNA, Transfer/*chemistry/metabolism ; }, abstract = {Most tRNAs share a common secondary structure containing a T arm, a D arm, an anticodon arm and an acceptor stem. However, there are some exceptions. Most nematode mitochondrial tRNAs and some animal mitochondrial tRNAs lack the T arm, which is necessary for binding to canonical elongation factor Tu (EF-Tu). The mitochondria of the nematode Caenorhabditis elegans have a unique EF-Tu, named EF-Tu1, whose structure has supplied clues as to how truncated tRNAs can work in translation. EF-Tu1 has a C-terminal extension of about 60 aa that is absent in canonical EF-Tu. Recent data from our laboratory strongly suggests that EF-Tu1 recognizes the D-arm instead of the T arm by a mechanism involving this C-terminal region. Further biochemical analysis of mitochondrial tRNAs and EF-Tu from the distantly related nematode Trichinella spp. and sequence information on nuclear and mitochondrial DNA in arthropods suggest that T-armless tRNAs may have arisen as a result of duplication of the EF-Tu gene. These studies provide valuable insights into the co-evolution of RNA and RNA-binding proteins.}, }
@article {pmid17451987, year = {2007}, author = {Rombough, P}, title = {The functional ontogeny of the teleost gill: which comes first, gas or ion exchange?.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {148}, number = {4}, pages = {732-742}, doi = {10.1016/j.cbpa.2007.03.007}, pmid = {17451987}, issn = {1531-4332}, mesh = {Animals ; Biological Evolution ; Fishes/*physiology ; Gases ; Gills/embryology/*physiology ; Ion Exchange ; Larva/metabolism ; Mitochondria/metabolism ; Models, Biological ; Oxygen/*metabolism ; *Oxygen Consumption ; Physiology, Comparative ; }, abstract = {For most of the last century, the need to obtain sufficient oxygen to meet the respiratory requirements of the tissues was viewed as the primary selective pressure driving gill development in teleost fish. Recently, however, it has been suggested that ionoregulatory pressures may actually be more important. This manuscript reviews the theoretical and empirical evidence dealing with the functional ontogeny of the gill in the context of the oxygen and ionoregulatory hypotheses. Gas and ion exchange are subject to similar geometric constraints in developing fish. Both initially are exclusively cutaneous but shift to the gill with tissue growth because of declining surface-to-volume ratios. Based on the appearance of mitochondria-rich cells (MRCs), ionoregulatory activity shifts to the gill in advance of gas exchange. In every species examined to date, MRCs appear on the developing gill in advance of secondary lamellae, the definitive gas exchange structure of the adult gill. Biochemical and histochemical studies indicate that these early branchial MRCs are actively involved in ion exchange. In some cases, the specific activity is many times greater than in the adult gill. In contrast, O2 microelectrode and hemoglobin ablation experiments suggest that the early gill contributes little O2 to the general systemic circulation. Any oxygen taken up appears to be consumed locally. Functional ablation experiments with zebrafish indicated that the larval gill became essential for ion balance well before it was needed for O2 uptake. Similar experiments with rainbow trout, however, found that the gill became essential in terms of gas and ion exchange at about the same time. On balance, the evidence appears to favour the ionoregulatory hypothesis but the oxygen hypothesis cannot be absolutely rejected without more information. Some of the major deficiencies in our knowledge regarding the transition from cutaneous to branchial gas and ion exchange are highlighted and potential implications of the ionoregulatory hypothesis are discussed.}, }
@article {pmid17450603, year = {2007}, author = {Dagan, T and Martin, W}, title = {Testing hypotheses without considering predictions.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {29}, number = {5}, pages = {500-503}, doi = {10.1002/bies.20566}, pmid = {17450603}, issn = {0265-9247}, mesh = {Animals ; Mitochondria/metabolism ; Phylogeny ; *Research Design ; Symbiosis ; }, }
@article {pmid17445713, year = {2007}, author = {Pinkert, CA and Trounce, IA}, title = {Generation of transmitochondrial mice: development of xenomitochondrial mice to model neurodegenerative diseases.}, journal = {Methods in cell biology}, volume = {80}, number = {}, pages = {549-569}, doi = {10.1016/S0091-679X(06)80027-0}, pmid = {17445713}, issn = {0091-679X}, mesh = {Animals ; Cells, Cultured ; DNA, Mitochondrial/genetics ; *Disease Models, Animal ; Embryonic Stem Cells/transplantation ; Hybrid Cells/transplantation ; *Mice ; Mice, Transgenic ; Mitochondria/genetics/*transplantation ; Models, Biological ; Mutation ; Neurodegenerative Diseases/*pathology ; Phylogeny ; Transfection ; }, }
@article {pmid17438362, year = {2007}, author = {Scherz-Shouval, R and Shvets, E and Elazar, Z}, title = {Oxidation as a post-translational modification that regulates autophagy.}, journal = {Autophagy}, volume = {3}, number = {4}, pages = {371-373}, doi = {10.4161/auto.4214}, pmid = {17438362}, issn = {1554-8627}, mesh = {Animals ; Autophagy/*physiology ; Cysteine/metabolism ; Cysteine Endopeptidases/metabolism ; Food Deprivation ; Humans ; Hydrogen Peroxide/pharmacology ; Models, Chemical ; Oxidation-Reduction ; *Protein Processing, Post-Translational ; Reactive Oxygen Species/metabolism ; }, abstract = {The toxicity associated with accumulation of reactive oxygen species (ROS) has led to the evolution of various defense strategies to overcome oxidative stress, including autophagy. This pathway is involved in the removal and degradation of damaged mitochondria and oxidized proteins. At low levels, however, ROS act as signal transducers in various intracellular pathways. In a recent study we described the role of ROS as signaling molecules in starvation-induced autophagy. We showed that starvation stimulates formation of ROS, specifically H(2)O(2), in the mitochondria. Furthermore, we identified the cysteine protease HsAtg4 as a direct target for oxidation by H(2)O(2), and specified a cysteine residue located near the HsAtg4 catalytic site as critical for this regulation. Here we focus on Atg4, the target of regulation, and discuss possible mechanisms for the regulation of this enzyme in the autophagic process.}, }
@article {pmid17437148, year = {2007}, author = {Fukami, H and Chen, CA and Chiou, CY and Knowlton, N}, title = {Novel group I introns encoding a putative homing endonuclease in the mitochondrial cox1 gene of Scleractinian corals.}, journal = {Journal of molecular evolution}, volume = {64}, number = {5}, pages = {591-600}, pmid = {17437148}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Anthozoa/*genetics ; Base Sequence ; Electron Transport Complex IV/chemistry/*genetics/metabolism ; Endonucleases/*genetics ; Evolution, Molecular ; Gene Expression Regulation ; Genes, Mitochondrial/*genetics ; Introns/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; }, abstract = {Analyses of mitochondrial sequences revealed the existence of a group I intron in the cytochrome oxidase subunit 1 (cox1) gene in 13 of 41 genera (20 out of 73 species) of corals conventionally assigned to the suborder Faviina. With one exception, phylogenies of the coral cox1 gene and its intron were concordant, suggesting at most two insertions and many subsequent losses. The coral introns were inferred to encode a putative homing endonuclease with a LAGLI-DADG motif as reported for the cox1 group I intron in the sea anemone Metridium senile. However, the coral and sea anemone cox1 group I introns differed in several aspects, such as the intron insertion site and sequence length. The coral cox1 introns most closely resemble the mitochondrial cox1 group I introns of a sponge species, which also has the same insertion site. The coral introns are also more similar to the introns of several fungal species than to that of the sea anemone (although the insertion site differs in the fungi). This suggests either a horizontal transfer between a sponge and a coral or independent transfers from a similar fungal donor (perhaps one with an identical insertion site that has not yet been discovered). The common occurrence of this intron in corals strengthens the evidence for an elevated abundance of group I introns in the mitochondria of anthozoans.}, }
@article {pmid17429433, year = {2007}, author = {de Duve, C}, title = {The origin of eukaryotes: a reappraisal.}, journal = {Nature reviews. Genetics}, volume = {8}, number = {5}, pages = {395-403}, doi = {10.1038/nrg2071}, pmid = {17429433}, issn = {1471-0056}, mesh = {Animals ; *Biological Evolution ; Cell Membrane/physiology ; Cell Nucleus/physiology ; Chimerism ; Cytoskeleton/physiology ; Eukaryotic Cells/*physiology ; Humans ; Hydrogen/metabolism ; Mitochondria/metabolism/physiology ; Models, Biological ; Time Factors ; }, abstract = {Ever since the elucidation of the main structural and functional features of eukaryotic cells and subsequent discovery of the endosymbiotic origin of mitochondria and plastids, two opposing hypotheses have been proposed to account for the origin of eukaryotic cells. One hypothesis postulates that the main features of these cells, including their ability to capture food by endocytosis and to digest it intracellularly, were developed first, and later had a key role in the adoption of endosymbionts; the other proposes that the transformation was triggered by an interaction between two typical prokaryotic cells, one of which became the host and the other the endosymbiont. Re-examination of this question in the light of cell-biological and phylogenetic data leads to the conclusion that the first model is more likely to be the correct one.}, }
@article {pmid17428608, year = {2007}, author = {Traversa, D and Costanzo, F and Iorio, R and Aroch, I and Lavy, E}, title = {Mitochondrial cytochrome c oxidase subunit 1 (cox1) gene sequence of Spirocerca lupi (Nematoda, Spirurida): avenues for potential implications.}, journal = {Veterinary parasitology}, volume = {146}, number = {3-4}, pages = {263-270}, doi = {10.1016/j.vetpar.2007.03.015}, pmid = {17428608}, issn = {0304-4017}, mesh = {Animals ; Base Sequence ; Cloning, Molecular ; Dog Diseases/parasitology ; Dogs ; Electron Transport Complex IV/*genetics/*metabolism ; Mitochondria/*enzymology ; Phylogeny ; Spirurida Infections/parasitology/veterinary ; Thelazioidea/*enzymology/*genetics ; }, abstract = {Canine spirocercosis is a life-threatening parasitosis caused by Spirocerca lupi (Nematoda, Spirurida) that is presently emerging in several countries. This study characterised an informative region within the mitochondrial (mtDNA) gene encoding for the cytochrome c oxidase subunit 1 (cox1) of S. lupi by Polymerase Chain Reaction (PCR)-coupled sequencing. Specimens from five different countries in Europe, Asia and Africa were examined and two different sequence variants of cox1 (i.e. haplotypes) were determined, displaying nucleotidic variation at 6 of 689 positions. All of these positions were invariable among all the parasite individuals from Europe (haplotype 1) and among the African and Asian individuals (haplotype 2), but differed between Europe and Asia/Africa. The S. lupi cox1 sequences were consistent with those of other common Spirurida previously reported at both nucleotidic and phylogenetic levels. This study provides molecular information essential for identification of the nematode, irrespective of its life cycle stage. Crucial implications for the specific molecular diagnosis of clinical spirocercosis and investigation of the evolution, population genetics, ecology and epidemiology of S. lupi are discussed.}, }
@article {pmid17426763, year = {2006}, author = {Kubo, N and Arimura, S and Tsutsumi, N and Kadowaki, K and Hirai, M}, title = {Isolation and characterization of the pea cytochrome c oxidase Vb gene.}, journal = {Genome}, volume = {49}, number = {11}, pages = {1481-1489}, doi = {10.1139/g06-105}, pmid = {17426763}, issn = {0831-2796}, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Conserved Sequence ; DNA, Complementary/isolation &amp; purification ; Electron Transport Complex IV/*genetics/isolation &amp; purification/*metabolism ; Evolution, Molecular ; Gene Duplication ; Gene Expression Regulation, Plant ; Genome, Plant ; Green Fluorescent Proteins/genetics/metabolism ; Introns ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Pisum sativum/*genetics ; Phylogeny ; Plant Proteins/*genetics/isolation &amp; purification ; Protein Subunits ; Sequence Homology, Amino Acid ; Zinc Fingers ; }, abstract = {Three copies of the gene that encodes cytochrome c oxidase subunit Vb were isolated from the pea (PscoxVb-1, PscoxVb-2, and PscoxVb-3). Northern Blot and reverse transcriptase-PCR analyses suggest that all 3 genes are transcribed in the pea. Each pea coxVb gene has an N-terminal extended sequence that can encode a mitochondrial targeting signal, called a presequence. The localization of green fluorescent proteins fused with the presequence strongly suggests the targeting of pea COXVb proteins to mitochondria. Each pea coxVb gene has 5 intron sites within the coding region. These are similar to Arabidopsis and rice, although the intron lengths vary greatly. A phylogenetic analysis of coxVb suggests the occurrence of gene duplication events during angiosperm evolution. In particular, 2 duplication events might have occurred in legumes, grasses, and Solanaceae. A comparison of amino acid sequences in COXVb or its counterpart shows the conservation of several amino acids within a zinc finger motif. Interestingly, a homology search analysis showed that bacterial protein COG4391 and a mitochondrial complex I 13 kDa subunit also have similar amino acid compositions around this motif. Such similarity might reflect evolutionary relationships among the 3 proteins.}, }
@article {pmid17425940, year = {2007}, author = {Kiefer, D and Kuhn, A}, title = {YidC as an essential and multifunctional component in membrane protein assembly.}, journal = {International review of cytology}, volume = {259}, number = {}, pages = {113-138}, doi = {10.1016/S0074-7696(06)59003-5}, pmid = {17425940}, issn = {0074-7696}, mesh = {Amino Acid Sequence ; Animals ; Arabidopsis Proteins/metabolism ; Cell Membrane/*metabolism ; Chloroplasts/metabolism ; Electron Transport Complex IV/metabolism ; Escherichia coli/*metabolism ; Escherichia coli Proteins/chemistry/*metabolism ; Eukaryotic Cells/*metabolism ; Evolution, Molecular ; Humans ; Membrane Transport Proteins/chemistry/*metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins/metabolism ; Molecular Sequence Data ; Nuclear Proteins/metabolism ; Protein Conformation ; Protein Transport ; }, abstract = {Membrane proteins fulfill a number of vital functions in prokaryotic and eukaryotic cells. They are often organized in multicomponent complexes, folded within the membrane bilayer and interacting with the cytoplasmic and periplasmic or external soluble compartments. For the biogenesis of integral membrane proteins, the essential biochemical steps are (1) the insertion and topogenesis of the transmembrane protein segments into the lipid bilayer, (2) the three-dimensional folding of the translocated hydrophilic domains, and (3) the assembly into multimeric complexes. Intensive research has elucidated the basic mechanisms of membrane protein insertion in the homologous translocation machineries of different cellular systems. Whereas the Sec translocation system is found in the endoplasmic reticulum of eukaryotic cells and in the prokaryotic plasma membrane, the YidC-Oxa1 membrane insertase is present in prokaryotic and organellar membranes. This review focuses on the discoveries of the YidC system in bacterial as well as the Oxa1/Alb3 protein family of eukaryotic cells and will particularly emphasize evolutionary aspects.}, }
@article {pmid17411345, year = {2007}, author = {Curran, SP and Ruvkun, G}, title = {Lifespan regulation by evolutionarily conserved genes essential for viability.}, journal = {PLoS genetics}, volume = {3}, number = {4}, pages = {e56}, pmid = {17411345}, issn = {1553-7404}, support = {R01 AG016636/AG/NIA NIH HHS/United States ; F32 AG026207-02/AG/NIA NIH HHS/United States ; F32-AG026207/AG/NIA NIH HHS/United States ; R01-AG016636/AG/NIA NIH HHS/United States ; R00 AG032308/AG/NIA NIH HHS/United States ; F32 AG026207/AG/NIA NIH HHS/United States ; F32 AG026207-03/AG/NIA NIH HHS/United States ; F32 AG026207-01/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Caenorhabditis elegans/*genetics/growth &amp; development/*physiology ; Caenorhabditis elegans Proteins/metabolism ; Clone Cells ; Conserved Sequence/*genetics ; *Evolution, Molecular ; Forkhead Transcription Factors ; Gene Expression Regulation ; *Genes, Essential ; *Genes, Helminth ; Insulin/metabolism ; Larva ; Longevity/*genetics ; Mitochondria/metabolism ; Phenotype ; RNA Interference ; Signal Transduction ; Survival Analysis ; Transcription Factors/metabolism ; }, abstract = {Evolutionarily conserved mechanisms that control aging are predicted to have prereproductive functions in order to be subject to natural selection. Genes that are essential for growth and development are highly conserved in evolution, but their role in longevity has not previously been assessed. We screened 2,700 genes essential for Caenorhabditis elegans development and identified 64 genes that extend lifespan when inactivated postdevelopmentally. These candidate lifespan regulators are highly conserved from yeast to humans. Classification of the candidate lifespan regulators into functional groups identified the expected insulin and metabolic pathways but also revealed enrichment for translation, RNA, and chromatin factors. Many of these essential gene inactivations extend lifespan as much as the strongest known regulators of aging. Early gene inactivations of these essential genes caused growth arrest at larval stages, and some of these arrested animals live much longer than wild-type adults. daf-16 is required for the enhanced survival of arrested larvae, suggesting that the increased longevity is a physiological response to the essential gene inactivation. These results suggest that insulin-signaling pathways play a role in regulation of aging at any stage in life.}, }
@article {pmid17408485, year = {2007}, author = {Kneip, C and Lockhart, P and Voss, C and Maier, UG}, title = {Nitrogen fixation in eukaryotes--new models for symbiosis.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {55}, pmid = {17408485}, issn = {1471-2148}, mesh = {Animals ; Bacteria/*genetics/metabolism ; Diatoms/genetics/metabolism/physiology ; Fungi/genetics/metabolism/physiology ; Invertebrates/genetics/microbiology/physiology ; *Models, Biological ; Nitrogen Fixation/*genetics ; *Phylogeny ; Plants/genetics/metabolism ; *Symbiosis ; }, abstract = {BACKGROUND: Nitrogen, a component of many bio-molecules, is essential for growth and development of all organisms. Most nitrogen exists in the atmosphere, and utilisation of this source is important as a means of avoiding nitrogen starvation. However, the ability to fix atmospheric nitrogen via the nitrogenase enzyme complex is restricted to some bacteria. Eukaryotic organisms are only able to obtain fixed nitrogen through their symbiotic interactions with nitrogen-fixing prokaryotes. These symbioses involve a variety of host organisms, including animals, plants, fungi and protists.<br><br>RESULTS: We have compared the morphological, physiological and molecular characteristics of nitrogen fixing symbiotic associations of bacteria and their diverse hosts. Special features of the interaction, e.g. vertical transmission of symbionts, grade of dependency of partners and physiological modifications have been considered in terms of extent of co-evolution and adaptation. Our findings are that, despite many adaptations enabling a beneficial partnership, most symbioses for molecular nitrogen fixation involve facultative interactions. However, some interactions, among them endosymbioses between cyanobacteria and diatoms, show characteristics that reveal a more obligate status of co-evolution.<br><br>CONCLUSION: Our review emphasises that molecular nitrogen fixation, a driving force for interactions and co-evolution of different species, is a widespread phenomenon involving many different organisms and ecosystems. The diverse grades of symbioses, ranging from loose associations to highly specific intracellular interactions, might themselves reflect the range of potential evolutionary fates for symbiotic partnerships. These include the extreme evolutionary modifications and adaptations that have accompanied the formation of organelles in eukaryotic cells: plastids and mitochondria. However, age and extensive adaptation of plastids and mitochondria complicate the investigation of processes involved in the transition of symbionts to organelles. Extant lineages of symbiotic associations for nitrogen fixation show diverse grades of adaptation and co-evolution, thereby representing different stages of symbiont-host interaction. In particular cyanobacterial associations with protists, like the Rhopalodia gibba-spheroid body symbiosis, could serve as important model systems for the investigation of the complex mechanisms underlying organelle evolution.}, }
@article {pmid17408359, year = {2007}, author = {Falkenberg, M and Larsson, NG and Gustafsson, CM}, title = {DNA replication and transcription in mammalian mitochondria.}, journal = {Annual review of biochemistry}, volume = {76}, number = {}, pages = {679-699}, doi = {10.1146/annurev.biochem.76.060305.152028}, pmid = {17408359}, issn = {0066-4154}, mesh = {Aging/physiology ; Animals ; DNA Helicases/genetics/metabolism ; DNA Polymerase gamma ; *DNA Replication ; *DNA, Mitochondrial/genetics/metabolism ; DNA-Directed DNA Polymerase/metabolism ; DNA-Directed RNA Polymerases/metabolism ; Humans ; Mitochondria/*physiology ; Mitochondrial Proteins/genetics/metabolism ; Mutation ; Transcription Factors/genetics/metabolism ; *Transcription, Genetic ; }, abstract = {The mitochondrion was originally a free-living prokaryotic organism, which explains the presence of a compact mammalian mitochondrial DNA (mtDNA) in contemporary mammalian cells. The genome encodes for key subunits of the electron transport chain and RNA components needed for mitochondrial translation. Nuclear genes encode the enzyme systems responsible for mtDNA replication and transcription. Several of the key components of these systems are related to proteins replicating and transcribing DNA in bacteriophages. This observation has led to the proposition that some genes required for DNA replication and transcription were acquired together from a phage early in the evolution of the eukaryotic cell, already at the time of the mitochondrial endosymbiosis. Recent years have seen a rapid development in our molecular understanding of these machineries, but many aspects still remain unknown.}, }
@article {pmid17404397, year = {2007}, author = {Behura, SK}, title = {Analysis of nuclear copies of mitochondrial sequences in honeybee (Apis mellifera) genome.}, journal = {Molecular biology and evolution}, volume = {24}, number = {7}, pages = {1492-1505}, doi = {10.1093/molbev/msm068}, pmid = {17404397}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; Bees/*genetics ; Cell Nucleus/*genetics ; Chromosomes/genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Genes, Mitochondrial ; Genome ; NADH Dehydrogenase/genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {At least 0.08% of the Apis mellifera nuclear genome contains sequences that originated from mitochondria. These nuclear copies of mitochondrial sequences (numts) are scattered all over the honeybee chromosomes and have originated by multiple independent insertions of mitochondrial DNA (mtDNA) as evident by phylogenetic analysis. Apart from original insertions, moderate duplications of numts also contributed to the present pattern and distribution of mitochondrial sequences in honeybee chromosomes. Assimilation of mitochondrial genes in the nuclear genome is mediated by extensive fragmentations of the original inserts. Replication slippage seems to be a major mechanism by which small sequences are inserted or deleted from mtDNA destined to nucleus. Most of the honeybee numts (84%) are located in the nongenic regions. The majority (94%) of the numts that are located in predicted nuclear genes have originated from mitochondrial genes coding for cytochrome oxidase and NADH dehydrogenase subunits. On the other hand, the mitochondrial rRNA or tRNA gene sequences are predominantly (88%) located in nongenic regions of the genome. Evidences also support for exertion of purifying selection on numts located in specific genes. Comparative analysis of numts of European, African, and Africanized honeybees suggests that numt evolution in A. mellifera is probably not demarked by speciation time frame but may be a continuous and dynamic process.}, }
@article {pmid17403155, year = {2007}, author = {Imanian, B and Carpenter, KJ and Keeling, PJ}, title = {Mitochondrial genome of a tertiary endosymbiont retains genes for electron transport proteins.}, journal = {The Journal of eukaryotic microbiology}, volume = {54}, number = {2}, pages = {146-153}, doi = {10.1111/j.1550-7408.2007.00245.x}, pmid = {17403155}, issn = {1066-5234}, mesh = {Animals ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; DNA, Protozoan/chemistry/genetics ; Dinoflagellida/classification/*genetics/*ultrastructure ; Electron Transport/genetics ; Electron Transport Complex IV/genetics ; Microscopy, Electron, Transmission ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/*genetics ; Sequence Analysis, DNA ; Symbiosis/genetics ; }, abstract = {Mitochondria and plastids originated through endosymbiosis, and subsequently became reduced and integrated with the host in similar ways. Plastids spread between lineages through further secondary or even tertiary endosymbioses, but mitochondria appear to have originated once and have not spread between lineages. Mitochondria are also generally lost in secondary and tertiary endosymbionts, with the single exception of the diatom tertiary endosymbiont of dinoflagellates like Kryptoperidinium foliaceum, where both host and endosymbiont are reported to contain mitochondria. Here we describe the first mitochondrial genes from this system: cytochrome c oxidase 1 (cox1), cytochrome oxidase 3 (cox3), and cytochrome b (cob). Phylogenetic analyses demonstrated that all characterized genes were derived from the pennate diatom endosymbiont, and not the host. We also demonstrated that all three genes are expressed, that cox1 contains spliced group II introns, and that cob and cox3 form an operon, all like their diatom relatives. The endosymbiont mitochondria not only retain a genome, but also express their genes, and are therefore likely involved in electron transport. Ultrastructural examination confirmed the endosymbiont mitochondria retain normal tubular cristae. Overall, these data suggest the endosymbiont mitochondria have not reduced at the genomic or functional level.}, }
@article {pmid20021090, year = {2005}, author = {Seiça, R and Santos, DL and Palmeira, CM and Moreno, AJ and Sena, C and Cunha, MF and Santos, MS}, title = {Mitochondrial function is not affected by renal morphological changes in diabetic goto-kakizaki rat.}, journal = {Toxicology mechanisms and methods}, volume = {15}, number = {4}, pages = {253-261}, doi = {10.1080/15376520590968806}, pmid = {20021090}, issn = {1537-6524}, abstract = {Renal disease is a common complication of diabetes mellitus. The pathogenesis of diabetic nephropathy is not well understood, but hyperglycemia seems to be a crucial factor. Recent evidence indicates that the overproduction of reactive oxygen species, observed in both clinical and experimental diabetes, and mitochondrial dysfunction are key factors in pathogenic process. The objective of this investigation was to test the hypothesis of whether hyperglycemia could affect kidney morphology and mitochondrial bioenergetics as well as susceptibility to oxidative stress in 12-month-old diabetic Goto-Kakizaki (GK) rats, a model of type 2 diabetes mellitus. We observed that there were no significant differences in the kidney respiratory function and phosphorylation capacity between GK and age-matched control Wistar rats. Mitochondria from kidneys of diabetic rats were equally susceptible to in vitro oxidative damage as those from normal rats, while coenzyme Q and alpha -tocopherol concentrations were similar in both types of preparations. However, the kidney of GK rats presented in most glomerulus a capillary basement membrane thickening with mesangial widening, in evolution to segmental glomerular sclerosis, and, in some interlobular arteries, excessive deposition of PAS-positive material at the tunica intima. The results show that the mild prolonged hyperglycemia and the kidney structural changes observed in GK rats are not sufficient to cause renal dysfunction and were not associated with functional and biochemical alterations in mitochondria.}, }
@article {pmid21238406, year = {1998}, author = {Katz, LA}, title = {Changing perspectives on the origin of eukaryotes.}, journal = {Trends in ecology &amp; evolution}, volume = {13}, number = {12}, pages = {493-497}, doi = {10.1016/s0169-5347(98)01490-6}, pmid = {21238406}, issn = {0169-5347}, abstract = {From the initial application of molecular techniques to the study of microbial organisms, three domains of life emerged, with eukaryotes and archaea as sister taxa. However, recent analyses of an expanding molecular data set reveal that the eukaryotic genome is chimeric with respect to archaea and bacteria. Moreover, there is now evidence that the primitive eukaryotic group `Archezoa' once harbored mitochondia. These discoveries have challenged the traditional stepwise model of the evolution of eukaryotes, in which the nucleus and microtubules evolve before the acquisition of mitochondria, and consequently compel a revision of existing models of the origin of eukaryotic cells.}, }
@article {pmid21238143, year = {1997}, author = {Embley, TM and Horner, DA and Hirt, RP}, title = {Anaerobic eukaryote evolution: hydrogenosomes as biochemically modified mitochondria?.}, journal = {Trends in ecology &amp; evolution}, volume = {12}, number = {11}, pages = {437-441}, doi = {10.1016/s0169-5347(97)01208-1}, pmid = {21238143}, issn = {0169-5347}, abstract = {Hydrogenosomes are energy generating organelles which are found in a variety of anaerobic microbial eukaryotes. Recent data suggest that some of these hydrogenosomes may be bichemically modified mithochondria, subverting the conventional role of this compartment from one of oxidative phosphorylation, to one of hydrogen evolving fermentation. The origins of the key enzymes which are responsible for hydrogen porduction are currently obscure but they are not considered to be typical of most eukaryotes.}, }
@article {pmid21237113, year = {1995}, author = {Ballard, JW and Kreitman, M}, title = {Is mitochondrial DNA a strictly neutral marker?.}, journal = {Trends in ecology &amp; evolution}, volume = {10}, number = {12}, pages = {485-488}, doi = {10.1016/s0169-5347(00)89195-8}, pmid = {21237113}, issn = {0169-5347}, abstract = {Variation and change in mitochondrial DNA (mtDNA) is often assumed to conform to a constant mutation rate equilibrium neutral model of molecular evolution. Recent evidence, however, indicates that the assumptions underlying this model are frequently violated. The mitochondria) genome may be subject to the same suite of forces known to be acting in the nuclear genome, including hitchhiking and selection, as well as forces that do not affect nuclear variation. Wherever possible, evolutionary studies involving mtDNA should incorporate statistical tests to investigate the forces shaping sequence variation and evolution.}, }
@article {pmid21236913, year = {1994}, author = {Saumitou-Laprade, P and Cuguen, J and Vernet, P}, title = {Cytoplasmic male sterility in plants: molecular evidence and the nucleocytoplasmic conflict.}, journal = {Trends in ecology &amp; evolution}, volume = {9}, number = {11}, pages = {431-435}, doi = {10.1016/0169-5347(94)90126-0}, pmid = {21236913}, issn = {0169-5347}, abstract = {A much-debated issue in plant evolutionary biology concerns the maintenance of a high frequency of male sterility in natural populations. For the past decade, a theoretical framework has been provided by the concept of nucleocytoplasmic conflict. Recent molecular studies on cytoplasmic male sterility indicate that novel chimeric genes, resulting from duplications and rearrangements of mitochondrial DNA sequences, are involved In its control. Thus, male sterility, which is phenotypically the loss of the male function, is encoded by a new mitochondrial function at the molecular level. Molecular data are in agreement with theoretical models that consider cytoplasmic male sterility as a stage in the coevolution between nucleus and mitochondria, and not simply as a deleterious mitochondrial mutation.}, }
@article {pmid18620157, year = {1986}, author = {Paz, P and Chamorro, CA and Fernandez, JG and Villar, JM}, title = {Quantitative ultrastructural changes of the endodermal cells in the early chick embryo analysed by stereological methods.}, journal = {Tissue &amp; cell}, volume = {18}, number = {1}, pages = {63-70}, doi = {10.1016/0040-8166(86)90007-8}, pmid = {18620157}, issn = {0040-8166}, abstract = {The ultrastructure of endoderm cells of the area pellucida has been analysed in the chick embryo by stereological methods. These cells show a specific subcellular evolution which can be correlated with several aspects of morphogenetic behaviour. The cell form coefficient (CFc) changes notably from stage 5 (0.683) to stage 8 (0.446) accompanying the transformation of this layer into a squamous epithelium. An increase of the nuclear surface density is observed and is discussed in relation to the control of nucleocytoplasmic interchange. The mitochondrial volume and surface densities remain constant (3.12% of cellular volume and 0.727 mitochondria/mu(3) respectively). The endodermal cells possess higher levels of vitelline reserves (lipid bodies, 6.97% and yolk droplets, 8.90%) than other cellular types of the chick embryo. This fact is discussed with respect to the role of the endoderm in the phagocytosis of yolk. The RER length density shows an increase that could be related to some specific changes of the extracellular matrix during this period, but this fact remains to be demonstrated in relation to changes of Golgi membranes.}, }
@article {pmid17400896, year = {2007}, author = {Kühn, K and Bohne, AV and Liere, K and Weihe, A and Börner, T}, title = {Arabidopsis phage-type RNA polymerases: accurate in vitro transcription of organellar genes.}, journal = {The Plant cell}, volume = {19}, number = {3}, pages = {959-971}, pmid = {17400896}, issn = {1040-4651}, mesh = {Arabidopsis/*enzymology/*genetics ; Base Sequence ; Chloroplasts/enzymology/*genetics ; Conserved Sequence ; DNA Mutational Analysis ; DNA-Directed RNA Polymerases/isolation &amp; purification/*metabolism ; Genes, Plant ; Mitochondria/enzymology/*genetics ; Molecular Sequence Data ; Promoter Regions, Genetic/genetics ; *Transcription, Genetic ; Viral Proteins/*metabolism ; }, abstract = {The T7 bacteriophage RNA polymerase (RNAP) performs all steps of transcription, including promoter recognition, initiation, and elongation as a single-polypeptide enzyme. Arabidopsis thaliana possesses three nuclear-encoded T7 phage-type RNAPs that localize to mitochondria (RpoTm), plastids (RpoTp), or presumably both organelles (RpoTmp). Their specific functions are as yet unresolved. We have established an in vitro transcription system to examine the abilities of the three Arabidopsis phage-type RNAPs to synthesize RNA and to recognize organellar promoters. All three RpoT genes were shown to encode transcriptionally active RNAPs. RpoTmp displayed no significant promoter specificity, whereas RpoTm and RpoTp were able to accurately initiate transcription from overlapping subsets of mitochondrial and plastidial promoters without the aid of protein cofactors. Our study strongly suggests RpoTm to be the enzyme that transcribes most, if not all, mitochondrial genes in Arabidopsis. Intrinsic promoter specificity, a feature that RpoTm and RpoTp share with the T7 RNAP, appears to have been conserved over the long period of evolution of nuclear-encoded mitochondrial and plastidial RNAPs. Selective promoter recognition by the Arabidopsis phage-type RNAPs in vitro implies that auxiliary factors are required for efficient initiation of transcription in vivo.}, }
@article {pmid17397804, year = {2007}, author = {Igaki, T and Suzuki, Y and Tokushige, N and Aonuma, H and Takahashi, R and Miura, M}, title = {Evolution of mitochondrial cell death pathway: Proapoptotic role of HtrA2/Omi in Drosophila.}, journal = {Biochemical and biophysical research communications}, volume = {356}, number = {4}, pages = {993-997}, doi = {10.1016/j.bbrc.2007.03.079}, pmid = {17397804}, issn = {0006-291X}, mesh = {Animals ; Apoptosis/*physiology ; Apoptosis Regulatory Proteins/*metabolism ; Cells, Cultured ; Drosophila ; Drosophila Proteins/*metabolism ; High-Temperature Requirement A Serine Peptidase 2 ; Inhibitor of Apoptosis Proteins/*metabolism ; Mitochondria/*physiology/ultrastructure ; Mitochondrial Proteins/*metabolism ; Serine Endopeptidases/*metabolism ; Signal Transduction/physiology ; }, abstract = {Despite the essential role of mitochondria in a variety of mammalian cell death processes, the involvement of mitochondrial pathway in Drosophila cell death has remained unclear. To address this, we cloned and characterized DmHtrA2, a Drosophila homolog of a mitochondrial serine protease HtrA2/Omi. We show that DmHtrA2 normally resides in mitochondria and is up-regulated by UV-irradiation. Upon receipt of apoptotic stimuli, DmHtrA2 is translocated to extramitochondrial compartment; however, unlike its mammalian counterpart, the extramitochondrial DmHtrA2 does not diffuse throughout the cytosol but stays near the mitochondria. RNAi-mediated knock-down of DmHtrA2 in larvae or adult flies results in a resistance to stress stimuli. DmHtrA2 specifically cleaves Drosophila inhibitor-of-apoptosis protein 1 (DIAP1), a cellular caspase inhibitor, and induces cell death both in vitro and in vivo as potent as other fly cell death proteins. Our observations suggest that DmHtrA2 promotes cell death through a cleavage of DIAP1 in the vicinity of mitochondria, which may represent a prototype of mitochondrial cell death pathway in evolution.}, }
@article {pmid17396019, year = {2007}, author = {Odahara, M and Inouye, T and Fujita, T and Hasebe, M and Sekine, Y}, title = {Involvement of mitochondrial-targeted RecA in the repair of mitochondrial DNA in the moss, Physcomitrella patens.}, journal = {Genes &amp; genetic systems}, volume = {82}, number = {1}, pages = {43-51}, doi = {10.1266/ggs.82.43}, pmid = {17396019}, issn = {1341-7568}, mesh = {Amino Acid Sequence ; Bryopsida/*enzymology/genetics ; *DNA Repair ; DNA, Mitochondrial/*metabolism ; Microscopy, Fluorescence ; Mitochondria/*enzymology ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/analysis/*metabolism ; Rec A Recombinases/analysis/*metabolism ; Recombination, Genetic ; Sequence Alignment ; Time Factors ; }, abstract = {Homologous recombination is a universal process that contributes to genetic diversity and genomic integrity. Bacterial-type RecA generally exists in all bacteria and plays a crucial role in homologous recombination. Although RecA homologues also exist in plant mitochondria, there have been few reports about the in vivo functions of these homologues. We identified a recA gene orthologue (named PprecA1) in a cDNA library of the moss, Physcomitrella patens. N-terminal fusion of the putative organellar targeting sequence of PpRecA1 to GFP caused a targeting of PpRecA1 to mitochondria. PprecA1 partially complemented the effects of a DNA damaging agent in an Escherichia coli recA deficient strain. Additionally, the expression of PprecA1 was induced by treating the plants with DNA damaging agents. Disruption of PprecA1 by targeted replacement resulted lower rate of the recovery of the mitochondrial DNA from methyl methan sulfonate damage. This is the first report about the characteristics of a null mutant of bacterial-type recA gene in plant. The data suggest that PprecA1 participates in the repair of mitochondrial DNA in P. patens.}, }
@article {pmid17393186, year = {2007}, author = {Hagner, SC and Misof, B and Maier, WA and Kampen, H}, title = {Bayesian analysis of new and old malaria parasite DNA sequence data demonstrates the need for more phylogenetic signal to clarify the descent of Plasmodium falciparum.}, journal = {Parasitology research}, volume = {101}, number = {3}, pages = {493-503}, pmid = {17393186}, issn = {0932-0113}, mesh = {Animals ; *Base Sequence ; *Bayes Theorem ; Computational Biology ; Cytochromes b/*genetics ; DNA, Protozoan/genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Peptide Hydrolases/*genetics ; *Phylogeny ; Plasmodium/classification/enzymology/genetics ; Plasmodium falciparum/classification/enzymology/*genetics ; Plastids ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA ; Software ; }, abstract = {Molecular systematic studies published during the last 15 years to clarify the phylogenetic relationships among the malaria parasites have led to two major hypotheses on the descent of Plasmodium falciparum: One supports an avian origin as a result of a relatively recent host switch, and another one favours the evolutionary development of P. falciparum together with its human host from primate ancestors. In this paper, we present phylogenetic analyses of three different Plasmodium genes, the nuclear 18 small sub-unit (SSU) ribosomal ribonucleic acid (rRNA), the mitochondrial cytochrome b (cyt b) and the plastid caseinolytic protease C (ClpC) gene, using numerous haemosporidian parasite DNA sequences obtained from the GenBank as well as several new sequences for major malaria parasites including the avian one Plasmodium cathemerium, which has never been considered in molecular phylogenetic analyses before. Most modern and sophisticated DNA substitution models based on Bayesian inference analysis were applied to estimate the cyt b and ClpC phylogenetic trees, whereas the 18 SSU rRNA gene was examined with regards to its secondary structure using PHASE software. Our results indicate that the data presently available are generally neither sufficient in number nor in information to solve the problem of the phylogenetic origin of P. falciparum.}, }
@article {pmid17390094, year = {2007}, author = {Massey, SE and Garey, JR}, title = {A comparative genomics analysis of codon reassignments reveals a link with mitochondrial proteome size and a mechanism of genetic code change via suppressor tRNAs.}, journal = {Journal of molecular evolution}, volume = {64}, number = {4}, pages = {399-410}, pmid = {17390094}, issn = {0022-2844}, mesh = {Animals ; Codon/*genetics ; Codon, Nonsense/genetics ; Genetic Code/*genetics ; Genome/genetics ; *Genomics ; Mitochondria/*chemistry/*genetics ; Phylogeny ; Proteome/*genetics ; RNA, Transfer/*genetics ; }, abstract = {Using a comparative genomics approach we demonstrate a negative correlation between the number of codon reassignments undergone by 222 mitochondrial genomes and the mitochondrial genome size, the number of mitochondrial ORFs, and the sizes of the large and small subunit mitochondrial rRNAs. In addition, we show that the TGA-to-tryptophan codon reassignment, which has occurred 11 times in mitochondrial genomes, is found in mitochondrial genomes smaller than those which have not undergone the reassignment. We therefore propose that mitochondrial codon reassignments occur in a wide range of phyla, particularly in Metazoa, due to a reduced "proteomic constraint" on the mitochondrial genetic code, compared to the nuclear genetic code. The reduced proteomic constraint reflects the small size of the mitochondrial-encoded proteome and allows codon reassignments to occur with less likelihood of lethality. In addition, we demonstrate a striking link between nonsense codon reassignments and the decoding properties of naturally occurring nonsense suppressor tRNAs. This suggests that natural preexisting nonsense suppression facilitated nonsense codon reassignments and constitutes a novel mechanism of genetic code change. These findings explain for the first time the identity of the stop codons and amino acids reassigned in mitochondrial and nuclear genomes. Nonsense suppressor tRNAs provided the raw material for nonsense codon reassignments, implying that the properties of the tRNA anticodon have dictated the identity of nonsense codon reassignments.}, }
@article {pmid17381550, year = {2007}, author = {Robert, KA and Brunet-Rossinni, A and Bronikowski, AM}, title = {Testing the 'free radical theory of aging' hypothesis: physiological differences in long-lived and short-lived colubrid snakes.}, journal = {Aging cell}, volume = {6}, number = {3}, pages = {395-404}, doi = {10.1111/j.1474-9726.2007.00287.x}, pmid = {17381550}, issn = {1474-9718}, mesh = {*Aging ; Animals ; Biological Evolution ; Cellular Senescence ; Colubridae/*physiology ; *Free Radicals ; Locomotion ; Longevity ; Mitochondria/metabolism ; Models, Biological ; Oxidative Stress ; Oxygen Consumption ; Reactive Oxygen Species ; Species Specificity ; Temperature ; }, abstract = {We test the 'free radical theory of aging' using six species of colubrid snakes (numerous, widely distributed, non-venomous snakes of the family Colubridae) that exhibit long (> 15 years) or short (< 10 years) lifespans. Because the 'rate of living theory' predicts metabolic rates to be correlated with rates of aging and oxidative damage results from normal metabolic processes we sought to answer whether physiological parameters and locomotor performance (which is a good predictor of survival in juvenile snakes) mirrored the evolution of lifespans in these colubrid snakes. We measured whole animal metabolic rate (oxygen consumption Vo2), locomotor performance, cellular metabolic rate (mitochondrial oxygen consumption), and oxidative stress potential (hydrogen peroxide production by mitochondria). Longer-lived colubrid snakes have greater locomotor performance and reduced hydrogen peroxide production than short-lived species, while whole animal metabolic rates and mitochondrial efficiency did not differ with lifespan. We present the first measures testing the 'free radical theory of aging' using reptilian species as model organisms. Using reptiles with different lifespans as model organisms should provide greater insight into mechanisms of aging.}, }
@article {pmid17380892, year = {2007}, author = {Emel'ianov, VV}, title = {[Suggested mitochondrial ancestry of non-mitochondrial ATP/ADP].}, journal = {Molekuliarnaia biologiia}, volume = {41}, number = {1}, pages = {59-70}, pmid = {17380892}, issn = {0026-8984}, mesh = {Alphaproteobacteria/enzymology/genetics ; Animals ; Bacterial Proteins/genetics ; Eukaryota/genetics ; *Evolution, Molecular ; Mitochondria/*genetics ; Mitochondrial ADP, ATP Translocases/*genetics ; *Phylogeny ; Plants/genetics ; Plastids/genetics ; Symbiosis/genetics ; }, abstract = {One of the major evolutionary events that transformed endosymbiotic bacterium into mitochondrion was an acquisition of ATP/ADP carrier in order to supply the host with respiration-derived ATP. Along with mitochondrial carrier, unrelated carrier is known which is characteristic of intracellular chlamydiae, plastids, parasitic intracellular eukaryote Encephalitozoon cuniculi, and the genus Rickettsia of obligate endosymbiotic alpha-Proteobacteria. This non-mitochondrial ATP/ADP carrier was recently described in rickettsia-like endosymbionts - a group of obligate intracellular bacteria, classified with the order Rickettsiales, which have diverged after free-living alpha-Proteobacteria but before sister groups of the Rickettsiaceae assemblage (true rickettsiae) and mitochondria. Published controversial phylogenetic data on the non-mitochondrial carrier were reanalysed in the present work using both DNA and protein sequences, and various methods including Bayesian analysis. The data presented are consistent with classic endosymbiont theory for the origin of mitochondria and also suggest that even last but one common ancestor of rickettsiae and organelles may have been an endosymbiotic bacterium in which ATP/ADP carrier has first originated.}, }
@article {pmid17374133, year = {2007}, author = {Toro, N and Jiménez-Zurdo, JI and García-Rodríguez, FM}, title = {Bacterial group II introns: not just splicing.}, journal = {FEMS microbiology reviews}, volume = {31}, number = {3}, pages = {342-358}, doi = {10.1111/j.1574-6976.2007.00068.x}, pmid = {17374133}, issn = {0168-6445}, mesh = {Bacteria/classification/genetics ; Genes, Bacterial/genetics ; Introns/*genetics ; Phylogeny ; RNA Splicing/*genetics/physiology ; RNA, Catalytic/classification/*physiology ; Retroelements/physiology ; }, abstract = {Group II introns are both catalytic RNAs (ribozymes) and mobile retroelements that were discovered almost 14 years ago. It has been suggested that eukaryotic mRNA introns might have originated from the group II introns present in the alphaproteobacterial progenitor of the mitochondria. Bacterial group II introns are of considerable interest not only because of their evolutionary significance, but also because they could potentially be used as tools for genetic manipulation in biotechnology and for gene therapy. This review summarizes what is known about the splicing mechanisms and mobility of bacterial group II introns, and describes the recent development of group II intron-based gene-targetting methods. Bacterial group II intron diversity, evolutionary relationships, and behaviour in bacteria are also discussed.}, }
@article {pmid17368752, year = {2007}, author = {Halabe Bucay, A}, title = {The biological significance of cancer: mitochondria as a cause of cancer and the inhibition of glycolysis with citrate as a cancer treatment.}, journal = {Medical hypotheses}, volume = {69}, number = {4}, pages = {826-828}, doi = {10.1016/j.mehy.2007.02.002}, pmid = {17368752}, issn = {0306-9877}, mesh = {Antineoplastic Agents/therapeutic use ; Cell Transformation, Neoplastic ; Citrates/*therapeutic use ; Glycolysis/drug effects/*physiology ; Humans ; Mitochondria/drug effects/*physiology ; Models, Biological ; Neoplasms/drug therapy/*physiopathology ; }, abstract = {In this article, I present the hypothesis that cancer presents due to the domination of the cell by mitochondria, which, from an evolution viewpoint, appeared in multi-cellular living being with the incorporation of a bacteria into a primitive cell, the bacteria sustained itself as mitochondria and these conserved their identity and bacterial characteristics, based on this, the hypothesis is suggested of the biological competition between the cell and the mitochondria; the mitochondria, on establishing itself as an independent entity within the cell, created the need to permanently remain in the cytoplasm of the cell, thus, from an energy viewpoint, when a cell becomes malignant, the mitochondria are the sole beneficiaries, as there is an ideal environment at the cellular level for the mitochondria to sustain their functions, and from this hypothesis, the treatment for fighting cancer consists of inhibiting glycolysis, being the principal source of energy for the mitochondria, this is achieved by administering citrate to cancer patients, as the citrate inhibits the phosphofructokinase enzyme, the pyruvate dehydrogenase complex and the succinate dehydrogenase enzyme of Krebs cycle, thus, the mitochondria will be forced to limit their metabolism and, secondarily, will lower the reproduction capacity of the cell in general.}, }
@article {pmid17363967, year = {2007}, author = {Lee, SH and Stephens, JL and Englund, PT}, title = {A fatty-acid synthesis mechanism specialized for parasitism.}, journal = {Nature reviews. Microbiology}, volume = {5}, number = {4}, pages = {287-297}, doi = {10.1038/nrmicro1617}, pmid = {17363967}, issn = {1740-1534}, mesh = {Acetyltransferases/genetics/*metabolism ; Animals ; Biological Evolution ; Biosynthetic Pathways ; Eukaryota/enzymology/genetics/metabolism ; Fatty Acid Elongases ; Fatty Acid Synthases/genetics/metabolism ; Fatty Acids/*biosynthesis ; Fatty Acids, Unsaturated/biosynthesis ; Glycosylphosphatidylinositols/chemistry/metabolism ; Leishmania major/enzymology/genetics ; Life Cycle Stages ; Microsomes/*enzymology ; Mitochondria/enzymology ; Trypanosoma brucei brucei/enzymology/genetics/growth &amp; development/*metabolism ; Trypanosoma cruzi/enzymology/genetics ; }, abstract = {Most cells use either a type I or type II synthase to make fatty acids. Trypanosoma brucei, the sleeping sickness parasite, provides the first example of a third mechanism for this process. Trypanosomes use microsomal elongases to synthesize fatty acids de novo, whereas other cells use elongases to make long-chain fatty acids even longer. The modular nature of the pathway allows synthesis of different fatty-acid end products, which have important roles in trypanosome biology. Indeed, this newly discovered mechanism seems ideally suited for the parasitic lifestyle.}, }
@article {pmid17363285, year = {2007}, author = {Yamamoto, S and Sota, T}, title = {Phylogeny of the Geometridae and the evolution of winter moths inferred from a simultaneous analysis of mitochondrial and nuclear genes.}, journal = {Molecular phylogenetics and evolution}, volume = {44}, number = {2}, pages = {711-723}, doi = {10.1016/j.ympev.2006.12.027}, pmid = {17363285}, issn = {1055-7903}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/*genetics ; Databases, Nucleic Acid ; Lepidoptera/*genetics ; Mitochondria/*genetics ; *Seasons ; Time Factors ; }, abstract = {Geometridae is one of the most diverse families within the Lepidoptera, comprising nine subfamilies. Winter moths, which have a unique life history, are found in three subfamilies. To examine the phylogeny of the Geometridae at the subfamily level and determine the evolutionary history of winter moths, we constructed phylogenetic trees for all nine geometrid subfamilies using two mitochondrial and two nuclear gene sequences. Specimens of all subfamilies were sampled from Japan. Simultaneous analyses of the combined data from all genes revealed that the Geometridae comprised two major clades: one with subfamilies Larentiinae and Sterrhinae, and the other with the remaining seven subfamilies. The second clade included the largest subfamily, Ennominae, and the subfamily Archiearinae, which is traditionally considered to be an ancestral lineage of the Geometridae. The Larentiinae+Sterrhinae clade contained one winter moth lineage, and the second major clade consisted of three winter moth lineages, including Alsophilinae, which contains winter moths exclusively. Using a Bayesian inference of divergence times, we estimated that geometrids began to diverge 54 Mya (62-48 Mya), whereas winter moth lineages differentiated from non-winter moth lineages 34-12 Mya, during the global cooling events in the Oligocene and the early Miocene. The adaptation to cool climates may have been a preadaptation that facilitated the winter moth life cycle.}, }
@article {pmid17362337, year = {2006}, author = {Thulin, CG and Fang, M and Averianov, AO}, title = {Introgression from Lepus europaeus to L. timidus in Russia revealed by mitochondrial single nucleotide polymorphisms and nuclear microsatellites.}, journal = {Hereditas}, volume = {143}, number = {2006}, pages = {68-76}, doi = {10.1111/j.2006.0018-0661.01952.x}, pmid = {17362337}, issn = {1601-5223}, mesh = {Animals ; Cell Nucleus/genetics ; Cytochrome b Group/genetics ; DNA, Mitochondrial/*chemistry ; Haplotypes ; Hares/classification/*genetics ; *Hybridization, Genetic ; *Microsatellite Repeats ; Mitochondria/genetics ; Polymorphism, Restriction Fragment Length ; *Polymorphism, Single Nucleotide ; Russia ; Species Specificity ; }, abstract = {Hybridisation among wild mammal populations may lead to introgression of genes and genomes over the species barrier. In Sweden, in northern Europe, and on the Iberian Peninsula in southern Europe, mitochondrial DNA from L. timidus occurs among L. europaeus specimens, presumably as a result of interspecific hybridisation. In Russia, the species are believed to hybridise as well, but no investigations have confirmed introgression. Here we develop species diagnostic single nucleotide polymorphisms in the mitochondrial genomes and combine them with analysis of nuclear microsatellite markers to investigate hybridisation and introgression in 71 Lepus specimens from Russia. A total of 58 specimens are typical representatives of either species. An additional nine specimens have slightly intermediate genotypes, potentially as a result of introgression of nuclear genes. Finally, we find three specimens with L. europaeus mitochondrial genome and apparent L. timidus nuclear genome. This indicates that the reciprocal transfer of mtDNA occur among Russian populations of these species. Our observation differs from previous observations of mtDNA introgression in Sweden and Iberia, and provides further support for a reticulated mode of introgression within the genus Lepus.}, }
@article {pmid17355904, year = {2007}, author = {Passardi, F and Bakalovic, N and Teixeira, FK and Margis-Pinheiro, M and Penel, C and Dunand, C}, title = {Prokaryotic origins of the non-animal peroxidase superfamily and organelle-mediated transmission to eukaryotes.}, journal = {Genomics}, volume = {89}, number = {5}, pages = {567-579}, doi = {10.1016/j.ygeno.2007.01.006}, pmid = {17355904}, issn = {0888-7543}, mesh = {Animals ; Ascorbate Peroxidases ; Bacteria/*enzymology ; Cytochrome-c Peroxidase/classification/genetics ; Eukaryotic Cells/enzymology ; *Evolution, Molecular ; Fungi/*enzymology ; Peroxidases/*classification/genetics ; Phylogeny ; Plants/*enzymology ; }, abstract = {Members of the superfamily of plant, fungal, and bacterial peroxidases are known to be present in a wide variety of living organisms. Extensive searching within sequencing projects identified organisms containing sequences of this superfamily. Class I peroxidases, cytochrome c peroxidase (CcP), ascorbate peroxidase (APx), and catalase peroxidase (CP), are known to be present in bacteria, fungi, and plants, but have now been found in various protists. CcP sequences were detected in most mitochondria-possessing organisms except for green plants, which possess only ascorbate peroxidases. APx sequences had previously been observed only in green plants but were also found in chloroplastic protists, which acquired chloroplasts by secondary endosymbiosis. CP sequences that are known to be present in prokaryotes and in Ascomycetes were also detected in some Basidiomycetes and occasionally in some protists. Class II peroxidases are involved in lignin biodegradation and are found only in the Homobasidiomycetes. In fact class II peroxidases were identified in only three orders, although degenerate forms were found in different Pezizomycota orders. Class III peroxidases are specific for higher plants, and their evolution is thought to be related to the emergence of the land plants. We have found, however, that class III peroxidases are present in some green algae, which predate land colonization. The presence of peroxidases in all major phyla (except vertebrates) makes them powerful marker genes for understanding the early evolutionary events that led to the appearance of the ancestors of each eukaryotic group.}, }
@article {pmid17355224, year = {2007}, author = {Amo, T and Brand, MD}, title = {Were inefficient mitochondrial haplogroups selected during migrations of modern humans? A test using modular kinetic analysis of coupling in mitochondria from cybrid cell lines.}, journal = {The Biochemical journal}, volume = {404}, number = {2}, pages = {345-351}, pmid = {17355224}, issn = {1470-8728}, support = {MC_U105663137/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Arctic Regions ; Biological Evolution ; Catalase/metabolism ; Cell Line, Tumor ; DNA, Mitochondrial/*genetics/metabolism ; *Haplotypes ; Humans ; Hybrid Cells ; Kinetics ; Membrane Potentials ; Mice ; Oxidative Phosphorylation ; *Travel ; }, abstract = {We introduce a general test of the bioenergetic importance of mtDNA (mitochondrial DNA) variants: modular kinetic analysis of oxidative phosphorylation in mitochondria from cybrid cells with constant nuclear DNA but different mtDNA. We have applied this test to the hypothesis [Ruiz-Pesini, Mishmar, Brandon, Procaccio and Wallace (2004) Science 303, 223-226] that particular mtDNA haplogroups (specific combinations of polymorphisms) that cause lowered coupling efficiency, leading to generation of less ATP and more heat, were positively selected during radiations of modern humans into colder climates. Contrary to the predictions of this hypothesis, mitochondria from Arctic haplogroups had similar or even greater coupling efficiency than mitochondria from tropical haplogroups.}, }
@article {pmid17349998, year = {2007}, author = {Kimura, M and Okano, Y}, title = {Human Misato regulates mitochondrial distribution and morphology.}, journal = {Experimental cell research}, volume = {313}, number = {7}, pages = {1393-1404}, doi = {10.1016/j.yexcr.2007.02.004}, pmid = {17349998}, issn = {0014-4827}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; COS Cells ; Cell Cycle Proteins/genetics/*metabolism ; Cell Survival ; Chlorocebus aethiops ; Cytoskeletal Proteins/genetics/*metabolism ; Drosophila Proteins/genetics ; Extrachromosomal Inheritance ; Gene Expression Regulation ; HeLa Cells ; Humans ; Immunohistochemistry ; Mitochondria/genetics/*metabolism/physiology ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/genetics/*metabolism/physiology ; Molecular Sequence Data ; Phylogeny ; RNA Interference ; Sequence Homology, Amino Acid ; Transfection ; }, abstract = {Misato of Drosophila melanogaster and Saccharomyces cerevisiae DML1 are conserved proteins having a homologous region with a part of the GTPase family that includes eukaryotic tubulin and prokaryotic FtsZ. We characterized human Misato sharing homology with Misato of D. melanogaster and S. cerevisiae DML1. Tissue distribution of Misato exhibited ubiquitous distribution. Subcellular localization of the protein studied using anti-Misato antibody suggested that it is localized to the mitochondria. Further experiments of fractionating mitochondria revealed that Misato was localized to the outer membrane. The transfection of Misato siRNA led to growth deficiencies compared with control siRNA transfected HeLa cells, and the Misato-depleted HeLa cells showed apoptotic nuclear fragmentation resulting in cell death. After silencing of Misato, the filamentous mitochondrial network disappeared and fragmented mitochondria were observed, indicating human Misato has a role in mitochondrial fusion. To examine the effects of overexpression, COS-7 cells were transfected with cDNA encoding EGFP-Misato. Its overexpression resulted in the formation of perinuclear aggregations of mitochondria in these cells. The Misato-overexpressing cells showed low viability and had no nuclei or a small and structurally unusual ones. These results indicated that human Misato has a role(s) in mitochondrial distribution and morphology and that its unregulated expression leads to cell death.}, }
@article {pmid17347008, year = {2007}, author = {Li, X and Zhu, Z and Mo, D and Wang, H and Yang, S and Zhao, S and Li, K}, title = {Comparative molecular characterization of ADSS1 and ADSS2 genes in pig (Sus scrofa).}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {147}, number = {2}, pages = {271-277}, doi = {10.1016/j.cbpb.2007.01.013}, pmid = {17347008}, issn = {1096-4959}, mesh = {Adenylosuccinate Synthase/*genetics ; Animals ; Base Sequence ; Chromosome Mapping ; Cloning, Molecular ; Cluster Analysis ; DNA Primers ; *Gene Expression ; Gene Expression Profiling ; Isoenzymes/genetics ; Molecular Sequence Data ; Muscle, Skeletal/metabolism ; *Phylogeny ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Sus scrofa/*genetics ; }, abstract = {Adenylosuccinate synthetase (ADSS) catalyzes the key step of AMP synthesis. Vertebrates have two isozymes of ADSS, which are named ADSS1 and ADSS2, respectively. In this study, we cloned porcine ADSS1 and ADSS2 genes and comparatively analyzed their sequence, chromosome mapping, mRNA distribution and subcellular localization. According to our results, the ADSS1 gene was predominantly expressed in the striated muscle tissues, while ADSS2 gene distributed widely in all the tissues detected. Additionally, ADSS1 gene was up-regulated significantly along with porcine muscle growth, and ADSS2 gene expression was more constant during the muscle development. Porcine ADSS1 gene was assigned to SSC7q and the linked marker was SSC12B09, ADSS2 gene was mapped on SSC10p and the linked marker was SW497, and porcine ADSS2 protein was subcellular localized in mitochondria. Moreover, we found that one single nucleotide polymorphism (SNP, T/C(70)) in the ninth intron of ADSS2 gene was significantly associated with average daily gain trait (ADG, P<0.05) and loin muscle area trait (P<0.05).}, }
@article {pmid17336467, year = {2007}, author = {Montesanti, A and Deignan, K and Hensey, C}, title = {Cloning and characterization of Xenopus laevis Smac/DIABLO.}, journal = {Gene}, volume = {392}, number = {1-2}, pages = {187-195}, doi = {10.1016/j.gene.2006.12.010}, pmid = {17336467}, issn = {0378-1119}, support = {057990/Z/99/Z//Wellcome Trust/United Kingdom ; 061410/GM/SP/JAT//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Conserved Sequence ; Embryo, Nonmammalian ; Evolution, Molecular ; Inhibitor of Apoptosis Proteins/*genetics ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Homology ; Xenopus Proteins/*genetics ; Xenopus laevis/*genetics ; }, abstract = {Mitochondria-mediated apoptosis plays a central role in animal development and tissue homeostasis, and mitochondria contain several pro-apoptotic proteins that have key roles in apoptosis. Smac/DIABLO was identified as a mitochondrial protein that is released into the cytosol following apoptotic stimuli, subsequently blocking the anti-apoptotic activity of inhibitor of apoptosis proteins. Through expressed sequence tag (EST) analysis we detected evidence for the presence of a number of Xenopus counterparts to mammalian mitochondrial pro-apoptotic proteins. EST and genome sequencing provides evidence for the presence of endonuclease G, AIF, HtrA/Omi and Smac/DIABLO in Xenopus laevis and tropicalis. Here we report the cloning and characterization of X. laevis Smac/DIABLO (XSmac/DIABLO). In this study degenerate primers based on conserved regions of human, mouse and an EST predicted Smac from X. tropicalis were used to amplify cDNA templates from X. laevis. The full length cDNA of Xenopus Smac contained a complete open reading frame of 732 bp, encoding 244 amino acids, that when expressed is observed to be approximately 27 kDa in size. The protein sequence is 49% identical and 71% similar to human Smac, and includes the motifs involved in mitochondrial targeting, and IAP-binding (AIPV). Smac expression was detected throughout early development with multiple transcripts being detected by Northern blot analysis, suggesting the presence of alternatively spliced isoforms. Exogenous expression of Xenopus Smac enhances gamma-irradiation-induced apoptosis in HeLa cells, demonstrating its functional equivalence with mammalian forms. Our study has identified the third vertebrate homologue of Smac/DIABLO, with its structural and functional similarities to mammalian Smac/DIABLO further illustrating the evolutionary conservation of apoptotic pathways across vertebrate species.}, }
@article {pmid17328740, year = {2007}, author = {Goffrini, P}, title = {A respiratory-deficient mutation associated with high salt sensitivity in Kluyveromyces lactis.}, journal = {FEMS yeast research}, volume = {7}, number = {2}, pages = {180-187}, doi = {10.1111/j.1567-1364.2006.00148.x}, pmid = {17328740}, issn = {1567-1356}, mesh = {ATPases Associated with Diverse Cellular Activities ; Electron Transport Complex III/metabolism ; Fungal Proteins/genetics ; Genetic Complementation Test ; Kluyveromyces/*drug effects/genetics/*physiology ; Membrane Proteins ; Mitochondria/physiology ; Mitochondrial Proteins/*genetics ; Molecular Chaperones ; Molecular Sequence Data ; *Mutation ; Oxygen Consumption/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Sequence Analysis, DNA ; Sodium Chloride/*pharmacology ; Vacuolar Proton-Translocating ATPases/chemistry/*genetics/metabolism ; }, abstract = {A salt-sensitive mutant of Kluyveromyces lactis was isolated that was unable to grow in high-salt media. This mutant was also respiratory-deficient and temperature-sensitive for growth. The mutation mapped in a single nuclear gene that is the ortholog of BCS1 of Saccharomyces cerevisiae. The BCS1 product is a mitochondrial protein required for the assembly of respiratory complex III. The bcs1 mutation of S. cerevisiae leads to a loss of respiration, but, unlike in K. lactis, it is not accompanied by salt sensitivity. All the respiratory-deficient K. lactis mutants tested were found to be salt-sensitive compared to their isogenic wild-type strains. In the presence of the respiratory inhibitor antimycin A, the wild-type strain also became salt-sensitive. By contrast, none of the S. cerevisiae respiratory-deficient mutants tested showed increased salt sensitivity. The salt sensitivity of the Klbcs1 mutant, but not its respiratory deficiency, was suppressed by the multicopy KlVMA13 gene, a homolog of the S. cerevisiae VMA13 gene encoding a subunit of the vacuolar H(+)-ATPase. These results suggest that cellular salt homeostasis in K. lactis is strongly dependent on mitochondrial respiratory activity, and/or that the ion homeostasis of mitochondria themselves could be a primary target of salt stress.}, }
@article {pmid17321123, year = {2007}, author = {Nobukuni, T and Kozma, SC and Thomas, G}, title = {hvps34, an ancient player, enters a growing game: mTOR Complex1/S6K1 signaling.}, journal = {Current opinion in cell biology}, volume = {19}, number = {2}, pages = {135-141}, doi = {10.1016/j.ceb.2007.02.019}, pmid = {17321123}, issn = {0955-0674}, support = {R01 CA-120475-01/CA/NCI NIH HHS/United States ; R01 DK-73802-01/DK/NIDDK NIH HHS/United States ; U01 CA84292-06/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Autophagy ; Endosomes/metabolism ; Humans ; Models, Biological ; Phosphatidylinositol 3-Kinases/*metabolism ; Protein Kinases/*metabolism ; Ribosomal Protein S6 Kinases, 70-kDa/*metabolism ; *Signal Transduction ; TOR Serine-Threonine Kinases ; }, abstract = {Recent studies have shown that the nutrient input to the mTOR Complex1/S6K1 signaling pathway is mediated by class 3 PI3K or hVps34, the oldest member of the PI3K family. Moreover, studies to date would suggest that during the evolution of multicellular organisms this ancient branch of the pathway was merged with the growth-factor-hormone-controlled class 1 PI3K pathway at the level of mTOR Complex1 to control the development and growth of the organism. However, hVps34 also plays a role in the regulation of macroautophagy - the mechanism by which cells generate nutrients, such as amino acids, through the degradation of intracellular complexes, including mitochondria and ribosomes. These functions of hVps34 initially appear contradictory, since increased mTOR Complex1 activation is triggered by increased amino acid levels, while autophagy is triggered when cells are faced with amino acid deprivation.}, }
@article {pmid17312024, year = {2007}, author = {Herrmann, JM and Köhl, R}, title = {Catch me if you can! Oxidative protein trapping in the intermembrane space of mitochondria.}, journal = {The Journal of cell biology}, volume = {176}, number = {5}, pages = {559-563}, pmid = {17312024}, issn = {0021-9525}, mesh = {Mitochondria/*metabolism/ultrastructure ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; *Models, Biological ; Oxidation-Reduction ; Oxidoreductases/chemistry/physiology ; Protein Folding ; Protein Transport/physiology ; }, abstract = {The intermembrane space (IMS) of mitochondria, the compartment that phylogenetically originated from the periplasm of bacteria, contains machinery to catalyze the oxidative folding of proteins (Mesecke, N., N. Terziyska, C. Kozany, F. Baumann, W. Neupert, K. Hell, and J.M. Herrmann. 2005. Cell. 121:1059-1069; Rissler, M., N. Wiedemann, S. Pfannschmidt, K. Gabriel, B. Guiard, N. Pfanner, and A. Chacinska. 2005. J. Mol. Biol. 353: 485-492; Tokatlidis, K. 2005. Cell. 121:965-96). This machinery introduces disulfide bonds into newly imported precursor proteins, thereby locking them in a folded conformation. Because folded proteins cannot traverse the translocase of the outer membrane, this stably traps the proteins in the mitochondria. The principle of protein oxidation in the IMS presumably has been conserved from the bacterial periplasm and has been adapted during evolution to drive the vectorial translocation of proteins from the cytosol into the mitochondria.}, }
@article {pmid17311591, year = {2007}, author = {Zuo, X and Xue, D and Li, N and Clark-Walker, GD}, title = {A functional core of the mitochondrial genome maintenance protein Mgm101p in Saccharomyces cerevisiae determined with a temperature-conditional allele.}, journal = {FEMS yeast research}, volume = {7}, number = {1}, pages = {131-140}, doi = {10.1111/j.1567-1364.2006.00141.x}, pmid = {17311591}, issn = {1567-1356}, mesh = {*Alleles ; Amino Acid Sequence ; Amino Acid Substitution ; DNA-Binding Proteins ; Dimerization ; *Gene Expression Regulation, Fungal ; Mitochondria/metabolism ; Mitochondrial Proteins ; Molecular Sequence Data ; Mutagenesis ; Nuclear Proteins/*chemistry/genetics/metabolism ; Point Mutation ; *Protein Sorting Signals ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/metabolism ; *Temperature ; }, abstract = {Analysis of Mgm101p isolated from mitochondria shows that the mature protein of 27.6 kDa lacks 22 amino acids from the N-terminus. This mitochondrial targeting sequence has been incorporated in the design of oligonucleotides used to determine a functional core of Mgm101p. Progressive deletions, although retaining the targeting sequence, reveal that 76 N-terminal and six C-terminal amino acids of Mgm101p can be removed without altering the ability to complement an mgm101-1(ts) temperature-sensitive mutant. However, this active core is unable to complement mgm101 null mutants, suggesting that the Mgm101p might need to form a dimer or multimer to be functional in vivo. The active core, enriched in basic residues, contains 165 amino acids with a pI of 9.2. Alignment with 22 Mgm101p sequences from other lower eukaryotes shows that a number of amino acids are highly conserved in this region. Random mutagenesis confirms that certain critical amino acids required for function are invariant across the 23 proteins. Searches in the PFAM database revealed a low level of structural similarity between the active core and the Rad52 protein family.}, }
@article {pmid17304745, year = {2004}, author = {Elenga, N and Msellati, P and Fassinou, P and Viho, I and Dabis, F}, title = {[Zidovudine-associated mitochondriopathy: three possible observations in Abidjan, Côte d'Ivoire].}, journal = {Bulletin de la Societe de pathologie exotique (1990)}, volume = {97}, number = {4}, pages = {253-256}, pmid = {17304745}, issn = {0037-9085}, mesh = {Adult ; Anemia, Hypochromic/complications ; Anti-HIV Agents/*adverse effects/pharmacology ; Cohort Studies ; Comorbidity ; Cote d'Ivoire/epidemiology ; Epilepsy, Generalized/*chemically induced ; Failure to Thrive/*chemically induced ; Female ; Fetus/*drug effects ; Growth Disorders/chemically induced ; HIV Infections/drug therapy ; Humans ; Infant ; Male ; Mitochondria/*drug effects ; Muscle Hypotonia/chemically induced ; Pregnancy ; Pregnancy Complications, Infectious/drug therapy ; *Prenatal Exposure Delayed Effects ; Protein-Energy Malnutrition/complications ; Psychomotor Disorders/*chemically induced ; Randomized Controlled Trials as Topic ; Zidovudine/*adverse effects/pharmacology ; }, abstract = {In Africa, prevention of mother-to-child transmission of HIV (PMTCT) with antiretrovirals is becoming a key component of the response to the pandemic. Toxicity issues remain however a concern and require careful monitoring. We report here three observations of mild neurological deterioration among children for whom a diagnosis of mitochondrial dysfunction was considered possible. These children were identified within a PMTCT research program (ANRS 049) conducted in Abidjan, Côte d'Ivoire, and evaluating a short regimen of maternal zidovudine monotherapy for PMTCT of HIV type 1. Maternal HIV-1 infection was diagnosed during pregnancy before enrolment in the randomised trial (two cases) or in the subsequent open cohort (one case). These three women had been allocated to the ZDV group and had no particular medical history. Pregnancy check-up was negative except the diagnosis of HIV-1 infection. The three children were diagnosed as uninfected by HIV-1. Symptoms developed by the age of six months (two cases) and 13 months (one case): growth failure, anthropometric abnormalities, impaired psycho-motor development, generalised and repeated seizures. The evolution of these three HIV-uninfected children was favourable after 12 to 18 months. The transient nature of these abnormalities is compatible with mild complications of mitochondrial dysfunction. We conclude however that the anticipated benefits of PMTCT with antiretrovirals in Africa greatly outweigh the potential risks and should not lead to reconsider their public health interest}, }
@article {pmid17299702, year = {2006}, author = {Vesteg, M and Krajcovic, J and Ebringer, L}, title = {On the origin of eukaryotic cells and their endomembranes.}, journal = {Rivista di biologia}, volume = {99}, number = {3}, pages = {499-519}, pmid = {17299702}, issn = {0035-6050}, mesh = {Animals ; Archaea ; Bacteria ; *Eukaryotic Cells ; Evolution, Molecular ; Genome ; Humans ; *Intracellular Membranes ; Mitochondria ; Models, Biological ; Phagocytosis ; Phylogeny ; Plants ; Prokaryotic Cells ; *Symbiosis ; }, abstract = {A novel hypothesis for the origin of eukaryotic cells is presented. It is assumed that the universal ancestor was bounded by two membranes of heterochiral lipid composition. We propose that the prokaryotic cells (the hypothetical host entity for alpha proteic-bacteria), though sharing a common ancestor with Archaea, was bounded by two membranes. The hypothesis suggests that an alpha proteic-bacterial symbiont was enclosed in the prokaryotic cells intermembrane space. In this view, the eukaryotic nuclear membrane and endomembrane system arose from the prokaryotic cells inner membrane while the eukaryotic plasma membrane arose from the prokaryotic cells outer membrane. The outlined scenario agrees with the view that engulfment of an alpha-proteic-bacterial cell by a host entity and its transformation to a mitochondrion was the driving force leading to the appearance of the first eukaryotic cell. The hypothesis seems to be consistent with the pre-cell theory, theory of membrane heredity, and the phagocytosis-late scenario.}, }
@article {pmid17295908, year = {2007}, author = {Mamirova, L and Popadin, K and Gelfand, MS}, title = {Purifying selection in mitochondria, free-living and obligate intracellular proteobacteria.}, journal = {BMC evolutionary biology}, volume = {7}, number = {}, pages = {17}, pmid = {17295908}, issn = {1471-2148}, mesh = {Animals ; Base Sequence ; *Evolution, Molecular ; *Genes, Bacterial ; *Genes, Mitochondrial ; Lagomorpha ; Likelihood Functions ; Mitochondria/*genetics ; Models, Genetic ; Proteobacteria/*genetics ; Retroelements ; Rodentia ; *Selection, Genetic ; }, abstract = {BACKGROUND: The effectiveness of elimination of slightly deleterious mutations depends mainly on drift and recombination frequency. Here we analyze the influence of these two factors on the strength of the purifying selection in mitochondrial and proteobacterial orthologous genes taking into account the differences in the organism lifestyles.<br><br>RESULTS: (I) We found that the probability of fixation of nonsynonymous substitutions (Kn/Ks) in mitochondria is significantly lower compared to obligate intracellular bacteria and even marginally significantly lower compared to free-living bacteria. The comparison of bacteria of different lifestyles demonstrates more effective elimination of slightly deleterious mutations in (II) free-living bacteria as compared to obligate intracellular species and in (III) obligate intracellular parasites as compared to obligate intracellular symbionts. (IV) Finally, we observed that the level of the purifying selection (i.e. 1-Kn/Ks) increases with the density of mobile elements in bacterial genomes.<br><br>CONCLUSION: This study shows that the comparison of patterns of molecular evolution of orthologous genes between ecologically different groups of organisms allow to elucidate the genetic consequences of their various lifestyles. Comparing the strength of the purifying selection among proteobacteria with different lifestyles we obtained results, which are in concordance with theoretical expectations: (II) low effective population size and level of recombination in obligate intracellular proteobacteria lead to less effective elimination of mutations compared to free-living relatives; (III) rare horizontal transmissions, i.e. effectively zero recombination level in symbiotic obligate intracellular bacteria leads to less effective purifying selection than in parasitic obligate intracellular bacteria; (IV) the increased frequency of recombination in bacterial genomes with high mobile element density leads to a more effective elimination of slightly deleterious mutations. At the same time, (I) more effective purifying selection in relatively small populations of nonrecombining mitochondria as compared to large populations of recombining proteobacteria was unexpected. We hypothesize that additional features such as the high number of protein-protein interactions or female germ-cell atresia increase evolutionary constraints and maintain the effective purifying selection in mitochondria, but more work is needed to definitely establish these additional features.}, }
@article {pmid17295027, year = {2007}, author = {Schwacke, R and Fischer, K and Ketelsen, B and Krupinska, K and Krause, K}, title = {Comparative survey of plastid and mitochondrial targeting properties of transcription factors in Arabidopsis and rice.}, journal = {Molecular genetics and genomics : MGG}, volume = {277}, number = {6}, pages = {631-646}, pmid = {17295027}, issn = {1617-4615}, mesh = {Arabidopsis/*metabolism ; Arabidopsis Proteins/chemistry/*metabolism ; Cell Nucleus/metabolism ; Chloroplasts/chemistry/*metabolism ; DNA-Binding Proteins/chemistry/genetics ; Green Fluorescent Proteins/metabolism ; Mitochondria/chemistry/metabolism ; Oryza/*metabolism ; Phylogeny ; Plant Proteins/chemistry/genetics/*metabolism ; Protein Sorting Signals ; Transcription Factors/chemistry/*metabolism ; }, abstract = {A group of nuclear transcription factors, the Whirly proteins, were recently shown to be targeted also to chloroplasts and mitochondria. In order to find out whether other proteins might share this feature, an in silico-based screening of transcription factors from Arabidopsis and rice was carried out with the aim of identifying putative N-terminal chloroplast and mitochondrial targeting sequences. For this, the individual predictions of several independent programs were combined to a consensus prediction using a naïve Bayes method. This consensus prediction shows a higher specificity at a given sensitivity value than each of the single programs. In both species, transcription factors from a variety of protein families that possess putative N-terminal plastid or mitochondrial target peptides as well as nuclear localization sequences, were found. A search for homologues within members of the AP2/EREBP protein family revealed that target peptide-containing proteins are conserved among monocotyledonous and dicotyledonous species. Fusion of one of these proteins to GFP revealed, indeed, a dual targeting activity of this protein. We propose that dually targeted transcription factors might be involved in the communication between the nucleus and the organelles in plant cells. We further discuss how recent results on the physical interaction between the organelles and the nucleus could have significance for the regulation of the localization of these proteins.}, }
@article {pmid17293371, year = {2007}, author = {Bichet, A and Hannemann, F and Rekowski, M and Bernhardt, R}, title = {A new application of the yeast two-hybrid system in protein engineering.}, journal = {Protein engineering, design &amp; selection : PEDS}, volume = {20}, number = {3}, pages = {117-123}, doi = {10.1093/protein/gzm002}, pmid = {17293371}, issn = {1741-0126}, mesh = {Adrenodoxin/chemistry/genetics/metabolism ; Coenzymes/metabolism ; Directed Molecular Evolution ; *Protein Engineering ; Saccharomyces cerevisiae ; *Two-Hybrid System Techniques ; }, abstract = {Cytochromes P450 are involved in the biosynthesis of steroid hormones in mitochondria of the adrenal gland. The electrons required for these reactions are provided via a redox chain consisting of adrenodoxin reductase (AdR) and adrenodoxin (Adx). A prerequisite for a fast and efficient electron transfer as well as high catalytic activity is the formation of functional complexes between the different redox partners. To improve the protein-protein interactions by directed evolution, we developed a new in vivo selection system. This high-throughput screening method is based on the yeast two-hybrid system. It enables a background-free screening for increased protein-protein interactions between stable and functional species including cofactor-containing proteins (FAD, [2Fe-2S], heme). The method was successfully applied for the directed evolution of Adx and selected variants were analyzed biochemically and biophysically. All analyzed proteins exhibit typical characteristics of [2Fe-2S]-cluster-type ferredoxins. Adx-dependent substrate conversion assays with different cytochromes demonstrated that the improved ability of the mutants to form complexes results in an enhanced catalytic efficiency of the cytochrome P450 system.}, }
@article {pmid17292632, year = {2007}, author = {Wood, AR and Apte, S and MacAvoy, ES and Gardner, JP}, title = {A molecular phylogeny of the marine mussel genus Perna (Bivalvia: Mytilidae) based on nuclear (ITS1&amp;2) and mitochondrial (COI) DNA sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {44}, number = {2}, pages = {685-698}, doi = {10.1016/j.ympev.2006.12.019}, pmid = {17292632}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Bivalvia/classification/*genetics ; Cell Nucleus/*genetics ; DNA/*genetics ; DNA, Ribosomal Spacer/*genetics ; Databases, Nucleic Acid ; Electron Transport Complex IV/*genetics ; Mitochondria/*genetics ; *Phylogeny ; }, abstract = {A molecular phylogeny is presented for marine mussels of the genus Perna, based on nuclear (ITS1,ITS2) and mitochondrial (COI) DNA sequence data. The three generally recognised species (Perna viridis, Perna perna and Perna canaliculus) and one putative species (Perna picta) were each sampled from several locations within their known geographic distributions. A range of phylogenetic analyses was used to investigate the current taxonomic assignments, evolutionary relationships and the biogeographical history of the genus. The different analyses produced similar, well supported topologies and verified the monophyly of the genus with respect to five mytilid outgroup species. P. perna (Atlantic), P. viridis (Indo-West Pacific), and P. canaliculus (New Zealand) each formed distinct clades, confirming their specific status. Putative P. picta from North Africa clustered within the P. perna clade and is not regarded as a separate species. P. perna and P. canaliculus were the most closely related of the three species. Possible biogeographic explanations for the present species distributions are evaluated.}, }
@article {pmid17291829, year = {2007}, author = {Kamikawa, R and Inagaki, Y and Sako, Y}, title = {Fragmentation of mitochondrial large subunit rRNA in the dinoflagellate Alexandrium catenella and the evolution of rRNA structure in alveolate mitochondria.}, journal = {Protist}, volume = {158}, number = {2}, pages = {239-245}, doi = {10.1016/j.protis.2006.12.002}, pmid = {17291829}, issn = {1434-4610}, mesh = {Animals ; DNA, Mitochondrial/chemistry/*genetics ; DNA, Ribosomal/chemistry/genetics ; Dinoflagellida/*genetics ; *Evolution, Molecular ; *Genome, Mitochondrial ; Genome, Protozoan ; RNA, Protozoan/genetics ; Ribosome Subunits, Large, Eukaryotic/*chemistry ; }, abstract = {Extensive investigations on apicomplexan mitochondria, such as those of Plasmodium falciparum, revealed that ribosomal RNAs (rRNAs) are fragmented into multiple short pieces. In this study, we isolated three mitochondrial large subunit rRNA (mtLSU rRNA) fragments from the dinoflagellate Alexandrium catenella. A piece of mtLSU rRNA that possesses high sequence similarity to the P. falciparum LSU rRNA E fragment was identified in a 1.7-kbp mitochondrial (mt) DNA clone. We further confirmed that the A. catenella "E-like" fragment is indeed transcriptionally active and that the transcript could form appropriate RNA secondary structures. In addition, we identified expression of two additional rRNA fragments with sequence similarities to P. falciparum F and G fragments. Notably, the 1.7-kbp mt DNA clone contains only one of the three rRNA fragments identified in this study, suggesting that the rRNA fragments are separately encoded in the A. catenella mt genome. Given the sister relationship between apicomplexa and dinoflagellates in eukaryote phylogeny, it is most parsimonious to assume that the mt rRNA fragmentation was established prior to the separation of the two protist groups. However, current sequence data on dinoflagellate mitochondria are insufficient to reject the alternative scenario, in which the rRNA fragmentation evolved independently in apicomplexan and dinoflagellate mitochondria.}, }
@article {pmid17286560, year = {2007}, author = {Clark-Walker, GD}, title = {The F1-ATPase inhibitor Inh1 (IF1) affects suppression of mtDNA loss-lethality in Kluyveromyces lactis.}, journal = {FEMS yeast research}, volume = {7}, number = {5}, pages = {665-674}, doi = {10.1111/j.1567-1364.2006.00201.x}, pmid = {17286560}, issn = {1567-1356}, mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Base Sequence ; DNA, Mitochondrial/drug effects/*genetics ; *Enzyme Inhibitors/chemistry/metabolism/pharmacology ; Kinetics ; Kluyveromyces/drug effects/enzymology/*genetics/growth &amp; development ; Mitochondria/enzymology ; Molecular Sequence Data ; Mutation ; *Proteins/chemistry/genetics/metabolism/pharmacology ; Proton-Translocating ATPases/*antagonists &amp; inhibitors/genetics/metabolism ; *Suppression, Genetic/drug effects ; ATPase Inhibitory Protein ; }, abstract = {Loss of mtDNA by the petite-negative yeast Kluyveromyces lactis is lethal (rho(o)-lethality). However, mutations in the alpha, beta and gamma subunits of F(1)-ATPase can suppress lethality by increasing intramitochondrial hydrolysis of ATP. Increased hydrolysis of ATP can also occur on inactivation of Inh1, the natural inhibitor of F(1)-ATPase. However, not all strains of K. lactis show suppression of rho(o)-lethality on inactivation of INH1. Genetic analysis indicates that one or more alleles of modifying factors are required for suppression. Papillae showing enhanced resistance to ethidium bromide (EB) in INH1 disruptants have mutations in the alpha, beta and gamma subunits of F(1)-ATPase. Increased growth of double mutants on EB has been investigated by disruption of INH1 in previously characterized atp suppressor mutants. Inactivation of Inh1, with one exception, results in better growth on EB and increased F(1)-ATPase activity, indicating that suppression of rho(o)-lethality is not due to atp mutations preventing Inh1 from interacting with the F(1)-complex. By contrast, in suppressor mutants altered in Arg435 of the beta subunit, disruption of INH1 did not change the kinetic properties of F(1)-ATPase or alter growth on EB. Consequently, Arg435 appears to be required for interaction of Inh1 with the beta subunit. In a previous study, a mex1-1 allele was found to enhance mgi(atp) expression. In accord with results from double mutants, it has been found that mex1-1 is a frameshift mutation in INH1 causing inactivation of Inh1p.}, }
@article {pmid17273918, year = {2007}, author = {Tian, X and Zheng, J and Hu, S and Yu, J}, title = {The discriminatory transfer routes of tRNA genes among organellar and nuclear genomes in flowering plants: a genome-wide investigation of indica rice.}, journal = {Journal of molecular evolution}, volume = {64}, number = {3}, pages = {299-307}, pmid = {17273918}, issn = {0022-2844}, mesh = {Cell Nucleus/*genetics/metabolism ; Evolution, Molecular ; Flowers/*genetics/metabolism ; Genes, Plant/genetics ; Genome, Plant ; Mitochondria/*genetics/metabolism ; Oryza/*genetics/metabolism ; Phylogeny ; Plastids/genetics ; RNA, Transfer/*genetics/metabolism ; *Recombination, Genetic ; }, abstract = {The transfer and integration of tRNA genes from organellar genomes to the nuclear genome and between organellar genomes occur extensively in flowering plants. The routes of the genetic materials flowing from one genome to another are biased, limited largely by compatibility of DNA replication and repair systems differing among the organelles and nucleus. After thoroughly surveying the tRNA gene transfer among organellar genomes and the nuclear genome of a domesticated rice (Oryza sativa L. ssp. indica), we found that (i) 15 mitochondrial tRNA genes originate from the plastid; (ii) 43 and 80 nuclear tRNA genes are mitochondrion-like and plastid-like, respectively; and (iii) 32 nuclear tRNA genes have both mitochondrial and plastid counterparts. Besides the native (or genuine) tRNA gene sets, the nuclear genome contains organelle-like tRNA genes that make up a complete set of tRNA species capable of transferring all amino acids. More than 97% of these organelle-like nuclear tRNA genes flank organelle-like sequences over 20 bp. Nearly 40% of them colocalize with two or more other organelle-like tRNA genes. Twelve of the 15 plastid-like mitochondrial tRNA genes possess 5'- and 3'-flanking sequences over 20 bp, and they are highly similar to their plastid counterparts. Phylogenetic analyses of the migrated tRNA genes and their original copies suggest that intergenomic tRNA gene transfer is an ongoing process with noticeable discriminatory routes among genomes in flowering plants.}, }
@article {pmid17268189, year = {2007}, author = {Volker, M and Sonnenberg, R and Ráb, P and Kullmann, H}, title = {Karyotype differentiation in Chromaphyosemion killifishes (Cyprinodontiformes, Nothobranchiidae). III: extensive karyotypic variability associated with low mitochondrial haplotype differentiation in C. bivittatum.}, journal = {Cytogenetic and genome research}, volume = {116}, number = {1-2}, pages = {116-126}, doi = {10.1159/000097429}, pmid = {17268189}, issn = {1424-859X}, mesh = {Africa ; Animals ; Chromosome Banding ; Cyprinodontiformes ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genetic Variation ; *Haplotypes ; Heterochromatin/metabolism ; *Karyotyping ; Mitochondria/*metabolism ; Models, Genetic ; Phenotype ; Phylogeny ; Translocation, Genetic ; }, abstract = {We investigated chromosomal evolution in the African killifish species Chromaphyosemion bivittatum using a combination of cytogenetic and phylogenetic methods. Specimens from five populations were examined by conventional Giemsa staining as well as sequential chromosome banding with 4',6-diamidino-2-phenylindole (DAPI), chromomycin A(3) (CMA(3)), AgNO(3)-staining and C-banding. The cytogenetic analysis revealed variability in 2n ranging from 2n = 29 to 2n = 36 and in NF ranging from NF = 38 to NF = 44. Two populations showed an extensive chromosomal polymorphism (2n = 29-34, NF = 44 and 2n = 32-34, NF = 38-42, respectively). Karyotypic variability within and among populations was mainly due to Robertsonian translocations and heterochromatin additions, and chromosome banding patterns suggested that both types of chromosomal rearrangements were related to the presence of AT-rich heterochromatin. A phylogenetic analysis of the partial mitochondrial (mt) cytochrome b gene, using specimens from eleven populations, revealed a low degree of haplotype differentiation, which suggested a relatively recent divergence of the populations examined. This finding conformed to the low degree of morphological differentiation observed among C. bivittatum populations and might indicate fast chromosomal evolution. The high karyotypic variability may be caused by an elevated chromosomal mutation rate as well as certain aspects of the mating system and population dynamics of C. bivittatum facilitating the fixation of new chromosomal variants.}, }
@article {pmid17265184, year = {2007}, author = {Kirschning, J and Zachos, FE and Cirovic, D and Radovic, IT and Hmwe, SS and Hartl, GB}, title = {Population Genetic Analysis of Serbian Red Foxes (Vulpes vulpes) by Means of Mitochondrial Control Region Sequences.}, journal = {Biochemical genetics}, volume = {45}, number = {5-6}, pages = {409-420}, doi = {10.1007/s10528-007-9082-1}, pmid = {17265184}, issn = {0006-2928}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Foxes/*genetics ; Genetic Drift ; Genetic Variation ; *Genetics, Population ; Haplotypes ; Mitochondria/*genetics ; Yugoslavia/epidemiology ; }, abstract = {A population genetic analysis based on sequences of the mitochondrial control region in 110 red foxes from five sampling localities in northern Serbia was carried out. The analysis yielded nine different haplotypes. Neither haplotype phylogeny nor their distribution was in accordance with the geographic location of the populations. In particular, the data failed to detect an unequivocal influence of the two big rivers, the Danube and the Tisza, separating the populations studied. Population differentiation was altogether low, without any relationship to the rivers as possible migration barriers. Although the possibility of foxes crossing the rivers over bridges or by swimming, thus keeping up gene flow, cannot be ruled out, it is most probable that the control region sequences are not sensitive enough to resolve small-scale population relationships but rather show patterns determined by stochastic processes such as genetic drift or lineage sorting.}, }
@article {pmid17252246, year = {2007}, author = {Russo, J and Madec, L}, title = {Haemocyte apoptosis as a general cellular immune response of the snail, Lymnaea stagnalis, to a toxicant.}, journal = {Cell and tissue research}, volume = {328}, number = {2}, pages = {431-441}, doi = {10.1007/s00441-006-0353-7}, pmid = {17252246}, issn = {0302-766X}, mesh = {Animals ; Annexin A5/metabolism ; Apoptosis/*drug effects ; Benzamides/*toxicity ; Blood Cell Count ; Flow Cytometry ; Hemocytes/*cytology ; Immunity/*drug effects ; Lymnaea/*drug effects/*immunology ; Membrane Potential, Mitochondrial/drug effects ; Oxidative Stress/drug effects ; Reactive Oxygen Species/metabolism ; }, abstract = {The effects of a xenobiotic on the circulating haemocytes of Lymnaea stagnalis were investigated after short-term (24 h, 96 h) and long-term (504 h) exposure of snails to environmental concentrations. Fomesafen, a pro-oxidant generator led to the activation of the haemocyte apoptotic program by promoting reactive oxygen species (ROS). Cells entering apoptosis underwent a series of events, both on the plasma membrane and in the mitochondria; these events were quantified by flow cytofluorometry. The data showed a loss of mitochondrial transmembrane potential (Deltapsim), which was dose-dependent and time-dependent and related to an increased release of superoxide anions. The phosphatidylserine that was exposed at the outer plasma membrane was not related to the disruption of either ROS or Deltapsim but was strongly correlated with the haemocyte concentration (total haemocyte count). This cascade of apoptotic processes occurred in a dose-independent manner and was not strengthened over time. The increase of circulating haemocytes depended upon the life span of the cells and might have reflected either facilitated cell turn-over or the accompanying presence of haemocytes phagocytosing apoptotic cells.}, }
@article {pmid17252245, year = {2007}, author = {Miyamoto-Kikuta, S and Komuro, T}, title = {Ultrastructural observations of the tunica muscularis in the small intestine of Xenopus laevis, with special reference to the interstitial cells of Cajal.}, journal = {Cell and tissue research}, volume = {328}, number = {2}, pages = {271-279}, doi = {10.1007/s00441-006-0363-5}, pmid = {17252245}, issn = {0302-766X}, mesh = {Animals ; Intestine, Small/*cytology/*ultrastructure ; Muscle, Smooth/*ultrastructure ; Neuroglia/ultrastructure ; *Xenopus laevis ; }, abstract = {The distribution and ultrastructure of the interstitial cells of Cajal (ICC) has been examined in the small intestine of the frog Xenopus laevis, as the physiological significance of these cells remains obscure in amphibians and other lower vertebrates. The present study has revealed the existence of a special type of interstitial cell in the tunica muscularis of the small intestine of Xenopus; this cell is characterized by the presence of numerous caveolae, many small mitochondria, and the formation of intercellular connections with the same type of cell. Since these ultrastructural features are shared with mammalian ICC, the cells in the small intestine of Xenopus probably correspond to ICC. These cells also form close contacts with neighboring smooth muscle cells and with nerve varicosities containing accumulations of synaptic vesicles. These cellular networks are likely to be involved in the transmission of nerve impulses to muscle cells, as has been suggested for mammalian tissues. However, true gap junctions have not been detected; they occur neither between the same type of cells nor between the putative ICC and smooth muscle cells. The widespread distribution of ICC or equivalent cells in different groups of vertebrates, together with the conservation of their ultrastructural features, suggests that they differentiated early in vertebrate evolution to play key regulatory roles in gastrointestinal movement.}, }
@article {pmid17251121, year = {2007}, author = {Ujvari, B and Dowton, M and Madsen, T}, title = {Mitochondrial DNA recombination in a free-ranging Australian lizard.}, journal = {Biology letters}, volume = {3}, number = {2}, pages = {189-192}, pmid = {17251121}, issn = {1744-9561}, mesh = {Animals ; Australia ; Base Sequence ; DNA, Mitochondrial/chemistry/*genetics ; Genes, Mitochondrial/genetics ; Geography ; Haplotypes/genetics ; Lizards/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Recombination, Genetic/*genetics ; }, abstract = {Mitochondrial DNA (mtDNA) is the traditional workhorse for reconstructing evolutionary events. The frequent use of mtDNA in such analyses derives from the apparent simplicity of its inheritance: maternal and lacking bi-parental recombination. However, in hybrid zones, the reproductive barriers are often not completely developed, resulting in the breakdown of male mitochondrial elimination mechanisms, leading to leakage of paternal mitochondria and transient heteroplasmy, resulting in an increased possibility of recombination. Despite the widespread occurrence of heteroplasmy and the presence of the molecular machinery necessary for recombination, we know of no documented example of recombination of mtDNA in any terrestrial wild vertebrate population. By sequencing the entire mitochondrial genome (16761bp), we present evidence for mitochondrial recombination in the hybrid zone of two mitochondrial haplotypes in the Australian frillneck lizard (Chlamydosaurus kingii).}, }
@article {pmid17251118, year = {2007}, author = {Esser, C and Martin, W and Dagan, T}, title = {The origin of mitochondria in light of a fluid prokaryotic chromosome model.}, journal = {Biology letters}, volume = {3}, number = {2}, pages = {180-184}, pmid = {17251118}, issn = {1744-9561}, mesh = {Alphaproteobacteria/genetics ; Bacterial Proteins/genetics ; Chromosomes/*genetics ; *Evolution, Molecular ; Genome, Bacterial/genetics ; Mitochondria/*genetics ; Phylogeny ; *Prokaryotic Cells ; RNA, Ribosomal, 16S/analysis ; }, abstract = {Biologists agree that the ancestor of mitochondria was an alpha-proteobacterium. But there is no consensus as to what constitutes an alpha-proteobacterial gene. Is it a gene found in all or several alpha-proteobacteria, or in only one? Here, we examine the proportion of alpha-proteobacterial genes in alpha-proteobacterial genomes by means of sequence comparisons. We find that each alpha-proteobacterium harbours a particular collection of genes and that, depending upon the lineage examined, between 97 and 33% are alpha-proteobacterial by the nearest-neighbour criterion. Our findings bear upon attempts to reconstruct the mitochondrial ancestor and upon inferences concerning the collection of genes that the mitochondrial ancestor possessed at the time that it became an endosymbiont.}, }
@article {pmid17250838, year = {2007}, author = {Burri, L and Keeling, PJ}, title = {Protein targeting in parasites with cryptic mitochondria.}, journal = {International journal for parasitology}, volume = {37}, number = {3-4}, pages = {265-272}, doi = {10.1016/j.ijpara.2006.12.004}, pmid = {17250838}, issn = {0020-7519}, mesh = {Animals ; Membrane Transport Proteins/metabolism ; Mitochondria/*metabolism ; Organelles/*metabolism ; Parasites/*metabolism ; Protein Transport/physiology ; }, abstract = {Many highly specialised parasites have adapted to their environments by simplifying different aspects of their morphology or biochemistry. One interesting case is the mitochondrion, which has been subject to strong reductive evolution in parallel in several different parasitic groups. In extreme cases, mitochondria have degenerated so much in physical size and functional complexity that they were not immediately recognised as mitochondria, and are now referred to as 'cryptic'. Cryptic mitochondrion-derived organelles can be classified as either hydrogenosomes or mitosomes. In nearly all cases they lack a genome and all organellar proteins are nucleus-encoded and expressed in the cytosol. The same is true for the majority of proteins in canonical mitochondria, where the proteins are directed to the organelle by specific targeting sequences (transit peptides) that are recognised by translocases in the mitochondrial membrane. In this review, we compare targeting sequences of different parasitic systems with highly reduced mitochondria and give an overview of how the import machinery has been modified in hydrogenosomes and mitosomes.}, }
@article {pmid17240176, year = {2007}, author = {Miotto, G and Tessaro, S and Rotta, GA and Bonatto, D}, title = {In silico analyses of Fsf1 sequences, a new group of fungal proteins orthologous to the metazoan sideroblastic anemia-related sideroflexin family.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {44}, number = {8}, pages = {740-753}, doi = {10.1016/j.fgb.2006.12.004}, pmid = {17240176}, issn = {1087-1845}, mesh = {Amino Acid Sequence ; Cation Transport Proteins/*genetics ; Computational Biology ; Conserved Sequence ; Fungal Proteins/*genetics ; Fungi/*genetics ; Hydrophobic and Hydrophilic Interactions ; Iron/metabolism ; Membrane Proteins/*genetics ; Mitochondrial Proteins/*genetics ; Phylogeny ; *Sequence Homology, Amino Acid ; }, abstract = {Sideroblastic anemias are pathologies observed in metazoan species characterized by accumulation of iron in the mitochondria (sideroblasts), defective erythropoiesis, and iron overload. Some genes have been associated with sideroblastic anemia, e.g. delta-aminolevulinic acid synthase gene (e-ALAS2). Recently, a new sideroblastic-associated protein family was discovered in metazoans and termed sideroflexin (Sfxn). The metazoan Sfxn family comprises five groups of paralogous proteins, present in mitochondria and whose functions are unknown. Using an in silico approach, we have identified and characterized new sideroflexin sequences from the genomes of different fungal species. An in-depth phylogenetic analysis of these new fungal Sfxn sequences (termed Fsf1p) showed that they form a distinct clade within the metazoan Sfxn family. Hydrophobic cluster analysis and transmembrane topological mapping allowed us to compare conserved regions among Fsf1 and Sfxn proteins. The results indicate that Fsf1 probably belongs to an ancient, mitochondrial group of proteins, necessary to maintain the homeostasis of iron within this organelle.}, }
@article {pmid17235548, year = {2007}, author = {Valkiūnas, G and Zehtindjiev, P and Hellgren, O and Ilieva, M and Iezhova, TA and Bensch, S}, title = {Linkage between mitochondrial cytochrome b lineages and morphospecies of two avian malaria parasites, with a description of Plasmodium (Novyella) ashfordi sp. nov.}, journal = {Parasitology research}, volume = {100}, number = {6}, pages = {1311-1322}, pmid = {17235548}, issn = {0932-0113}, mesh = {Animals ; Cytochromes b/*genetics ; Malaria, Avian/*parasitology ; Mitochondria/*enzymology ; Passeriformes/*parasitology ; Phylogeny ; Plasmodium/*classification/enzymology/*genetics ; }, abstract = {Numerous lineages of avian malaria parasites of the genus Plasmodium have been deposited in GenBank. However, only seven morphospecies have been linked to these lineages. This study linked two molecular sequences with morphospecies of malaria parasites. Two species of Plasmodium (mitochondrial cytochrome b gene lineages P-GRW2 and P-GRW4) were isolated from naturally infected adult great reed warblers (Acrocephalus arundinaceus) and inoculated to naive juvenile individuals of the same host species. Heavy parasitemia developed in the subinoculated birds, which enable identification of the species and deposition of their voucher specimens. Parasites of the lineage P-GRW2 were described as a new species, Plasmodium (Novyella) ashfordi, which is characterized primarily by the fan-like mature erythrocytic meronts containing seven to eight merozoites and the terminal position of clumped pigment granules in the gametocytes. Illustrations of the blood stages of the new species and Plasmodium (Haemamoeba) relictum (lineage P-GRW4) are given. The parasites of both lineages are transmitted in Africa and probably not in northern Europe. Other lineages closely related to P. ashfordi and P. relictum are identified. This study establishes the value of PCR-based identification of avian malaria parasites.}, }
@article {pmid17234378, year = {2007}, author = {Albrecht-Buehler, G}, title = {The three classes of triplet profiles of natural genomes.}, journal = {Genomics}, volume = {89}, number = {5}, pages = {596-601}, doi = {10.1016/j.ygeno.2006.12.009}, pmid = {17234378}, issn = {0888-7543}, mesh = {Animals ; Classification/*methods ; Codon/*classification ; Evolution, Molecular ; *Genome ; Genomics/*classification ; Mitochondria/genetics ; Organelles/genetics ; *Phylogeny ; Plants/genetics ; }, abstract = {Based on the huge variety of different genomes, one may expect a correspondingly large variety of the frequency distribution of their trinucleotides ("triplet profiles"). Yet, this article reports the unexpected finding that there are essentially only three kinds of triplet profiles among the large number of genomes examined here. None of the classes included random profiles, all of them contained members from vastly different taxa and species. Since the three classes of genomes do not reflect the phylogeny of their member organisms, I propose that these classes may reflect species-independent mechanisms of genome evolution.}, }
@article {pmid17226040, year = {2007}, author = {Rymaszewska, A}, title = {Symbiotic bacteria in oocyte and ovarian cell mitochondria of the tick Ixodes ricinus: biology and phylogenetic position.}, journal = {Parasitology research}, volume = {100}, number = {5}, pages = {917-920}, pmid = {17226040}, issn = {0932-0113}, mesh = {Animals ; Bacteria/*classification/genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Ixodes/*microbiology/physiology ; Mitochondria/*microbiology ; Oocytes/*microbiology ; Phylogeny ; Symbiosis ; }, abstract = {Under natural conditions, eukaryote cells may contain bacteria. Arthropods such as ticks, insects or mites are a group particularly favoured by the obligate intracellular bacteria. While arthropods are vectors for some of them, other bacteria inhabit invertebrate host cells having entered mutualistic interactions. Such endosymbionts dwell usually in the host cell vacuoles or cytoplasm but have been also reported from tick oocyte mitochondria. The microorganisms contribute to mitochondria degradation, but their colonies are not eliminated from the tick cells affected. So far, such bacteria have been detected in three research centres. The Italian centre has reported on results of microscope and molecular analyses, while the Polish centre published molecular data. The Danish centre registered a 16S rRNA gene fragment in GenBank. Independent comparisons of the 16S rRNA gene sequences, carried out in the Italian and Polish centres, confirmed that the nucleotide sequences of the Ixodes ricinus endosymbionts formed a single clade with certain non-identified tick bacterium species isolated from the tick Haemaphysalis wellingtoni. On the other hand, pathogenic species of the genera Anaplasma, Ehrlichia and Rickettsia detected in I. ricinus as well as symbionts of the genus Wolbachia present in Culex pipiens and Drosophila simulans have been placed at a different site on the phylogenetic tree.}, }
@article {pmid17222063, year = {2007}, author = {Signorovitch, AY and Buss, LW and Dellaporta, SL}, title = {Comparative genomics of large mitochondria in placozoans.}, journal = {PLoS genetics}, volume = {3}, number = {1}, pages = {e13}, pmid = {17222063}, issn = {1553-7404}, support = {R21 AI066242/AI/NIAID NIH HHS/United States ; T32 GM007499/GM/NIGMS NIH HHS/United States ; 5 T32 GM07499-28/GM/NIGMS NIH HHS/United States ; R21-AI066242-01A1/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Chromosome Mapping ; DNA, Mitochondrial/genetics ; Exons/genetics ; Genome/genetics ; *Genomics ; Introns/genetics ; Invertebrates/*cytology/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Proteins/chemistry ; }, abstract = {The first sequenced mitochondrial genome of a placozoan, Trichoplax adhaerens, challenged the conventional wisdom that a compact mitochondrial genome is a common feature among all animals. Three additional placozoan mitochondrial genomes representing highly divergent clades have been sequenced to determine whether the large Trichoplax mtDNA is a shared feature among members of the phylum Placozoa or a uniquely derived condition. All three mitochondrial genomes were found to be very large, 32- to 37-kb, circular molecules, having the typical 12 respiratory chain genes, 24 tRNAs, rnS, and rnL. They share with the Trichoplax mitochondrial genome the absence of atp8, atp9, and all ribosomal protein genes, the presence of several cox1 introns, and a large open reading frame containing an intron group I LAGLIDADG endonuclease domain. The differences in mtDNA size within Placozoa are due to variation in intergenic spacer regions and the presence or absence of long open reading frames of unknown function. Phylogenetic analyses of the 12 respiratory chain genes support the monophyly of Placozoa. The similarities in composition and structure between the three mitochondrial genomes reported here and that of Trichoplax's mtDNA suggest that their uncompacted state is a shared ancestral feature to other nonmetazoans while their gene content is a derived feature shared only among the Metazoa.}, }
@article {pmid17216240, year = {2007}, author = {Hansen, H and Bakke, TA and Bachmann, L}, title = {Mitochondrial haplotype diversity of Gyrodactylus thymalli (Platyhelminthes; Monogenea): extended geographic sampling in United Kingdom, Poland, and Norway reveals further lineages.}, journal = {Parasitology research}, volume = {100}, number = {6}, pages = {1389-1394}, pmid = {17216240}, issn = {0932-0113}, mesh = {Animals ; *Genetic Variation ; Haplotypes ; Mitochondria/*genetics ; Norway ; Phylogeny ; Platyhelminths/*classification/*genetics ; Poland ; Salmonidae/parasitology ; United Kingdom ; }, abstract = {In recent years, the mitochondrial haplotype diversity of the monogenean ectoparasites Gyrodactylus salaris Malmberg, 1957 on Atlantic salmon and G. thymalli Zitnan, 1960 on grayling has been studied intensively to understand the taxonomy and phylogeography of the two species. According to these studies, neither species can be considered monophyletic, but unfortunately, the geographic sampling has mostly been restricted to Fennoscandia. Only few samples from continental Europe have been analysed, and samples from the United Kingdom have not been included at all. Gyrodactylosis is a notifiable disease in Europe and is in the UK considered the most important exotic disease threat to wild Atlantic salmon populations. In this study, we report six new mitochondrial haplotypes of G. thymalli from England, Poland, and Norway detected by sequencing 745 bp of the cytochrome oxidase I gene. The six new haplotypes add five new clades to a neighbor-joining dendrogram deduced on the basis of the currently known 44 mitochondrial haplotypes for G. thymalli and G. salaris. We conclude that G. thymalli established in the UK along with the immigration of grayling. There is currently no reason to suspect that this parasite is a threat to Atlantic salmon in the UK, although its infectivity to salmon stocks in the UK has not been tested.}, }
@article {pmid17216232, year = {2007}, author = {Yang, KS and Kim, HS and Jin, UH and Lee, SS and Park, JA and Lim, YP and Pai, HS}, title = {Silencing of NbBTF3 results in developmental defects and disturbed gene expression in chloroplasts and mitochondria of higher plants.}, journal = {Planta}, volume = {225}, number = {6}, pages = {1459-1469}, pmid = {17216232}, issn = {0032-0935}, mesh = {Amino Acid Sequence ; Chloroplasts/*metabolism ; *Gene Expression Regulation, Plant ; *Gene Silencing ; Mitochondria/*metabolism ; Molecular Sequence Data ; Nuclear Proteins/chemistry/*deficiency/genetics/metabolism ; Phenotype ; Phylogeny ; Plant Leaves/metabolism ; Plant Proteins/chemistry/genetics/metabolism ; Reactive Oxygen Species/metabolism ; Nicotiana/*cytology/*genetics ; Transcription Factors/chemistry/*deficiency/genetics/metabolism ; }, abstract = {BTF3 (betaNAC) was originally isolated as a general transcription factor required for RNA polymerase II-dependent transcription, and later found to be a beta-subunit of nascent-polypeptide-associated complex that has been implicated in regulating protein localization during translation. In this study, virus-induced gene silencing of NbBTF3 encoding a Nicotiana benthamiana homolog of human BTF3 caused leaf yellowing and abnormal leaf morphology without altering the overall growth of the plant. The NbBTF3 gene is constitutively expressed and the NbBTF3-GFP fusion protein is primarily targeted to the nucleus. At the cellular level, downregulation of NbBTF3 expression reduced the chloroplast sizes and chlorophyll contents. The affected cells produced excessive amounts of reactive oxygen species. Furthermore, the transcript level of various plastid- and mitochondria-encoded genes was severely reduced in the NbBTF3-depleted leaf cells. These findings indicate that depletion of NbBTF3 activity preferentially affected development and/or physiology of chloroplasts and mitochondria in plants, possibly by hampering efficient translocation of the nascent organellar proteins into the organelles.}, }
@article {pmid17211549, year = {2007}, author = {Sinniger, F and Chevaldonné, P and Pawlowski, J}, title = {Mitochondrial genome of Savalia savaglia (Cnidaria, Hexacorallia) and early metazoan phylogeny.}, journal = {Journal of molecular evolution}, volume = {64}, number = {2}, pages = {196-203}, pmid = {17211549}, issn = {0022-2844}, mesh = {Animals ; Anthozoa/*classification/*genetics ; Bayes Theorem ; DNA, Mitochondrial/genetics ; Genome ; Likelihood Functions ; Mitochondria/*genetics ; Molecular Sequence Data ; Mutation ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {Mitochondrial genomes have recently become widely used in animal phylogeny, mainly to infer the relationships between vertebrates and other bilaterians. However, only 11 of 723 complete mitochondrial genomes available in the public databases are of early metazoans, including cnidarians (Anthozoa, mainly Scleractinia) and sponges. Although some cnidarians (Medusozoa) are known to possess atypical linear mitochondrial DNA, the anthozoan mitochondrial genome is circular and its organization is similar to that of other metazoans. Because the phylogenetic relationships among Anthozoa as well as their relation to other early metazoans still need to be clarified, we tested whether sequencing the complete mitochondrial genome of Savalia savaglia, an anthozoan belonging to the order Zoantharia (=Zoanthidea), could be useful to infer such relationships. Compared to other anthozoans, S. savaglia's genome is unusually long (20,766 bp) due to the presence of several noncoding intergenic regions (3691 bp). The genome contains all 13 protein coding genes commonly found in metazoans, but like other Anthozoa it lacks most of the tRNAs. Phylogenetic analyses of S. savaglia mitochondrial sequences show Zoantharia branching closely to other Hexacorallia, either as a sister group to Actiniaria or as a sister group to Actiniaria and Scleractinia. The close relationships suggested between Zoantharia and Actiniaria are reinforced by strong similarities in their gene order and the presence of similar introns in the COI and ND5 genes. Our study suggests that mitochondrial genomes can be a source of potentially valuable information on the phylogeny of Hexacorallia and may provide new insights into the evolution of early metazoans.}, }
@article {pmid17207937, year = {2007}, author = {Lyu, BN and Lyu, MB and Ismailov, BI and Ismailov, SB}, title = {Four hypotheses on mitochondria's role in the development and regulation of oxidative stress in the normal state, cell pathology and reversion of tumor cells.}, journal = {Medical hypotheses}, volume = {69}, number = {1}, pages = {186-194}, doi = {10.1016/j.mehy.2006.10.055}, pmid = {17207937}, issn = {0306-9877}, mesh = {Animals ; Humans ; Mitochondria/*metabolism ; *Models, Biological ; Neoplasms/*metabolism ; *Oxidative Stress ; Oxygen/*metabolism ; *Oxygen Consumption ; }, abstract = {The biological evolution has resulted in adaptation of both unicellular and multicellular organisms to negative effect of excessive O2 in reply to gradual increase of free oxygen (O2) contents in the earth atmosphere. This adaptation has led to formation of various antioxidant systems in the organism. Such system within the cell has hierarchic structure and is represented by at least than three levels of protection: antioxygene, antiradical and antiperoxide. The first and most effective antioxidant level is represented as mitochondrial respiration able to perform several functions. One of these functions is antioxygene since the very the mitochondria's capability to be a main O2 consumer in the cell provides for low but sufficient for respiration and energy supply levels of O2 partial pressure and dependent concentrations of active O2 forms. The latters, being signal molecules at certain values, modify regular and synthetic processes in the cells either directly or indirectly. This is the possibility for mitochondria to more extensively affect the intracellular processes than simply produce ATP. In case of defective of the cell first protection line the hyperoxia starts due to poor utilization of the incoming O2. Change in mitochondria's "capacity" (quantity, size and maturity level of mitochondria) anyway occurring in the cells are an efficient way of regulation of the oxy-peroxide condition (oxidative stress) and related signal channels. The relationship between changes in the condition of cells, i.e. from their normal state to different pathologic forms, and growing disbalance Delta(PO-AO) between its pro-oxygen (PO) and anti-oxygen (AO) components has been assumed. It is expected that during the evolution the cell could have supposedly acquired a sequence of "specialized" Delta(PO-AO) disbalances. Each sequence needs to implement a certain set of biochemical processes. The probability of Delta(PO-AO) disbalance gradation with specification of their value ranges has been determined. These ranges identify or impact certain cell state, namely proliferation of normal cell (oxidative mitogenesis), ageing, A1 apoptosis, carcinogenesis, A2 apoptosis, and oxidative cytolysis. The cited assumption allows us to: (1) explain reverse dependence of cell proliferation due to the level of their differentiation, increase in the amount and activity of mitochondria as an indispensable condition for the disbalance shift towards differentiation, (2) bring up the idea that regress of the cells, and in particular tumour cells, directly results from the Delta(PO-AO) disbalance decrease to certain levels under the influence of reverse inductors, (3) explain relatively easy and frequent embryonic and stem cells malignancy, and also their reversal normalization. These phenomena occur due to small number and/or size of mitochondria in the designated cells. To verify the above mentioned hypotheses it is primarily necessary to be able to stimulate and slow down the mitochondria biogenesis in the embryonic, stem, ageing, cancer and other cells.}, }
@article {pmid17203877, year = {2006}, author = {Szilágyi, G and Nagy, Z}, title = {[New methods in the investigation of brain hypoxia].}, journal = {Ideggyogyaszati szemle}, volume = {59}, number = {11-12}, pages = {411-415}, pmid = {17203877}, issn = {0019-1442}, mesh = {Animals ; *Apoptosis ; Biological Assay/*methods ; Cells, Cultured ; Drug Evaluation, Preclinical ; Humans ; Hypoxia, Brain/*metabolism/pathology/physiopathology ; Membrane Potential, Mitochondrial ; Microscopy, Confocal ; Neuroprotective Agents/pharmacology ; *Oxidative Stress ; Rats ; Reactive Oxygen Species/metabolism ; }, abstract = {The main challenge is the investigation of mechanism for apoptosis research and the drug development. Mitochondria have a key position in the production of reactive oxygen species and in the evolution of apoptosis. More possible pathway will be known with the apoptosis investigation. For development of neuroprotective molecules could give strategies the investigation of apoptosis. Exact knowledge of apoptosis provides the possibility to screen new neuroprotective molecules. We developed a research assay, that could provide quantitative and qualitative data about the free radical production and the mitochondrial transmembrane potential using confocal microscopy. Thus, we could screen drug candidate, neuroprotective molecules.}, }
@article {pmid17190825, year = {2007}, author = {Pannebakker, BA and Loppin, B and Elemans, CP and Humblot, L and Vavre, F}, title = {Parasitic inhibition of cell death facilitates symbiosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {104}, number = {1}, pages = {213-215}, pmid = {17190825}, issn = {0027-8424}, mesh = {Animals ; *Apoptosis ; Female ; *Oogenesis ; *Symbiosis ; Wasps/*parasitology ; Wolbachia/*physiology ; }, abstract = {Symbiotic microorganisms have had a large impact on eukaryotic evolution, with effects ranging from parasitic to mutualistic. Mitochondria and chloroplasts are prime examples of symbiotic microorganisms that have become obligate for their hosts, allowing for a dramatic extension of suitable habitats for life. Out of the extraordinary diversity of bacterial endosymbionts in insects, most are facultative for their hosts, such as the ubiquitous Wolbachia, which manipulates host reproduction. Some endosymbionts, however, have become obligatory for host reproduction and/or survival. In the parasitoid wasp Asobara tabida the presence of Wolbachia is necessary for host oogenesis, but the mechanism involved is yet unknown. We show that Wolbachia influences programmed cell death processes (a host regulatory feature typically targeted by pathogens) in A. tabida, making its presence essential for the wasps' oocytes to mature. This suggests that parasite strategies, such as bacterial regulation of host apoptosis, can drive the evolution of host dependence, allowing for a swift transition from parasitism to mutualism.}, }
@article {pmid17187354, year = {2007}, author = {Poole, AM and Penny, D}, title = {Evaluating hypotheses for the origin of eukaryotes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {29}, number = {1}, pages = {74-84}, doi = {10.1002/bies.20516}, pmid = {17187354}, issn = {0265-9247}, mesh = {Archaea ; Bacteria ; *Biological Evolution ; *Eukaryotic Cells ; Mitochondria ; *Models, Biological ; Phylogeny ; Symbiosis ; }, abstract = {Numerous scenarios explain the origin of the eukaryote cell by fusion or endosymbiosis between an archaeon and a bacterium (and sometimes a third partner). We evaluate these hypotheses using the following three criteria. Can the data be explained by the null hypothesis that new features arise sequentially along a stem lineage? Second, hypotheses involving an archaeon and a bacterium should undergo standard phylogenetic tests of gene distribution. Third, accounting for past events by processes observed in modern cells is preferable to postulating unknown processes that have never been observed. For example, there are many eukaryote examples of bacteria as endosymbionts or endoparasites, but none known in archaea. Strictly post-hoc hypotheses that ignore this third criterion should be avoided. Applying these three criteria significantly narrows the number of plausible hypotheses. Given current knowledge, our conclusion is that the eukaryote lineage must have diverged from an ancestor of archaea well prior to the origin of the mitochondrion. Significantly, the absence of ancestrally amitochondriate eukaryotes (archezoa) among extant eukaryotes is neither evidence for an archaeal host for the ancestor of mitochondria, nor evidence against a eukaryotic host.}, }
@article {pmid17185738, year = {2007}, author = {Alkhalfioui, F and Renard, M and Montrichard, F}, title = {Unique properties of NADP-thioredoxin reductase C in legumes.}, journal = {Journal of experimental botany}, volume = {58}, number = {5}, pages = {969-978}, doi = {10.1093/jxb/erl248}, pmid = {17185738}, issn = {0022-0957}, mesh = {Amino Acid Sequence ; Gene Expression Regulation, Plant ; Medicago truncatula/*enzymology ; Molecular Sequence Data ; NAD/metabolism ; NADP/metabolism ; Phylogeny ; Plant Proteins/chemistry/genetics/metabolism ; Thioredoxin-Disulfide Reductase/chemistry/genetics/*metabolism ; }, abstract = {NADP-thioredoxin reductases (NTRs) reduce thioredoxins (Trxs), using NADPH as a reductant, together constituting complete redox systems (NTS). Beside NTRA and NTRB targeted to both cytosol and mitochondria of plant cells, there is in chloroplasts an unusual NTR (NTRC) harbouring a Trx domain in a C-terminal extension, as recently reported in Oryza sativa. Although NTRC may constitute a complete NTS, it was described as a bifunctional enzyme. Because the gene is only present in photosynthetic organisms and the protein in green tissues, NTRC was thought to have a role restricted to photosynthetic cells. To determine whether NTRC from dicot plants is a bifunctional enzyme or a complete NTS, as well as to identify its putative target, NTRC from Medicago truncatula was cloned and NTRA was cloned for comparison. Here evidence is presented that MtNTRC (i) acts as an NTS and reduces dithiobisnitrobenzoate (DTNB) with a turnover (0.62 s(-1)) similar to that measured with MtNTRA in the presence of a Trxh (0.81 s(-1)); (ii) is able to use both NADPH (k(M)=2.4 microM) and NADH (k(M)=11 microM) as cofactors; (iii) efficiently reduces BAS1, a plastidial peroxiredoxin; and (iv) is expressed in both leaves and stems but unexpectedly is even more abundant in cotyledons from dry and germinating seeds. Because BAS1 is also present in both green tissues and seeds, NTRC/BAS1 may be involved in the scavenging of peroxides produced in green tissues during the day or the night and in seeds during germination. These results suggest different roles for NTRC in monocot and dicot plants.}, }
@article {pmid17183657, year = {2006}, author = {Goddard, MR and Leigh, J and Roger, AJ and Pemberton, AJ}, title = {Invasion and persistence of a selfish gene in the Cnidaria.}, journal = {PloS one}, volume = {1}, number = {1}, pages = {e3}, pmid = {17183657}, issn = {1932-6203}, mesh = {Animals ; Bayes Theorem ; Cnidaria/classification/*enzymology/*genetics ; DNA Restriction Enzymes/*genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Gene Conversion ; Gene Transfer, Horizontal ; Genes, Mitochondrial ; Genetics, Population ; Models, Genetic ; Phylogeny ; Sea Anemones/enzymology/genetics ; Species Specificity ; United Kingdom ; }, abstract = {BACKGROUND: Homing endonuclease genes (HEGs) are superfluous, but are capable of invading populations that mix alleles by biasing their inheritance patterns through gene conversion. One model suggests that their long-term persistence is achieved through recurrent invasion. This circumvents evolutionary degeneration, but requires reasonable rates of transfer between species to maintain purifying selection. Although HEGs are found in a variety of microbes, we found the previous discovery of this type of selfish genetic element in the mitochondria of a sea anemone surprising.<br><br>METHODS/PRINCIPAL FINDINGS: We surveyed 29 species of Cnidaria for the presence of the COXI HEG. Statistical analyses provided evidence for HEG invasion. We also found that 96 individuals of Metridium senile, from five different locations in the UK, had identical HEG sequences. This lack of sequence divergence illustrates the stable nature of Anthozoan mitochondria. Our data suggests this HEG conforms to the recurrent invasion model of evolution.<br><br>CONCLUSIONS: Ordinarily such low rates of HEG transfer would likely be insufficient to enable major invasion. However, the slow rate of Anthozoan mitochondrial change lengthens greatly the time to HEG degeneration: this significantly extends the periodicity of the HEG life-cycle. We suggest that a combination of very low substitution rates and rare transfers facilitated metazoan HEG invasion.}, }
@article {pmid17182897, year = {2007}, author = {Brindefalk, B and Viklund, J and Larsson, D and Thollesson, M and Andersson, SG}, title = {Origin and evolution of the mitochondrial aminoacyl-tRNA synthetases.}, journal = {Molecular biology and evolution}, volume = {24}, number = {3}, pages = {743-756}, doi = {10.1093/molbev/msl202}, pmid = {17182897}, issn = {0737-4038}, mesh = {Alphaproteobacteria/genetics ; Amino Acyl-tRNA Synthetases/*genetics ; Bayes Theorem ; Cluster Analysis ; Computational Biology ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; *Models, Genetic ; *Phylogeny ; }, abstract = {Many theories favor a fusion of 2 prokaryotic genomes for the origin of the Eukaryotes, but there are disagreements on the origin, timing, and cellular structures of the cells involved. Equally controversial is the source of the nuclear genes for mitochondrial proteins, although the alpha-proteobacterial contribution to the mitochondrial genome is well established. Phylogenetic inferences show that the nuclearly encoded mitochondrial aminoacyl-tRNA synthetases (aaRSs) occupy a position in the tree that is not close to any of the currently sequenced alpha-proteobacterial genomes, despite cohesive and remarkably well-resolved alpha-proteobacterial clades in 12 of the 20 trees. Two or more alpha-proteobacterial clusters were observed in 8 cases, indicative of differential loss of paralogous genes or horizontal gene transfer. Replacement and retargeting events within the nuclear genomes of the Eukaryotes was indicated in 10 trees, 4 of which also show split alpha-proteobacterial groups. A majority of the mitochondrial aaRSs originate from within the bacterial domain, but none specifically from the alpha-Proteobacteria. For some aaRS, the endosymbiotic origin may have been erased by ongoing gene replacements on the bacterial as well as the eukaryotic side. For others that accurately resolve the alpha-proteobacterial divergence patterns, the lack of affiliation with mitochondria is more surprising. We hypothesize that the ancestral eukaryotic gene pool hosted primordial "bacterial-like" genes, to which a limited set of alpha-proteobacterial genes, mostly coding for components of the respiratory chain complexes, were added and selectively maintained.}, }
@article {pmid17166769, year = {2007}, author = {Walker, G}, title = {Meeting Report: 16th Meeting of the International Society for Evolutionary Protistology; Wrocław, Poland, August 2-5, 2006 (ISEP XVI).}, journal = {Protist}, volume = {158}, number = {1}, pages = {5-19}, doi = {10.1016/j.protis.2006.11.001}, pmid = {17166769}, issn = {1434-4610}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/genetics/physiology/ultrastructure ; *Eukaryota/classification/genetics/ultrastructure ; Genome, Protozoan ; Mitochondria/genetics/physiology/ultrastructure ; Phylogeny ; Plastids/genetics/physiology/ultrastructure ; }, }
@article {pmid17161897, year = {2007}, author = {Zhang, H and Meng, LH and Pommier, Y}, title = {Mitochondrial topoisomerases and alternative splicing of the human TOP1mt gene.}, journal = {Biochimie}, volume = {89}, number = {4}, pages = {474-481}, doi = {10.1016/j.biochi.2006.11.002}, pmid = {17161897}, issn = {0300-9084}, support = {//Intramural NIH HHS/United States ; }, mesh = {*Alternative Splicing ; Catalysis ; DNA Replication ; DNA Topoisomerases, Type I/chemistry/*genetics/*metabolism ; DNA, Mitochondrial/*genetics ; Humans ; Mitochondria/*enzymology ; Phylogeny ; Transcription, Genetic ; }, abstract = {Mitochondria are the only organelles containing metabolically active DNA besides nuclei. By analogy with the nuclear topoisomerases, mitochondrial topoisomerase activities are probably critical for maintaining the topology of mitochondrial DNA during replication, transcription, and repair. Mitochondrial diseases include a wide range of defects including neurodegeneracies, myopathies, metabolic abnormalities and premature aging. Vertebrates only have one known specific mitochondrial topoisomerase gene (TOP1mt), coding for a type IB topoisomerase. Like the mitochondrial DNA and RNA polymerase, the TOP1mt gene is encoded in the nuclear genome. The TOP1mt gene possesses the 13 exon Top1B signature motif and codes for a mitochondrial targeting signals at the N-terminus of the Top1mt polypeptide. This review summarizes our current knowledge of mitochondrial topoisomerases (type IA, IB and type II) in eukaryotes including budding and fission yeasts (Saccharomyces cerevisiae and Schizosaccharomyces pombe) and protozoan parasites (kinetoplastidiae and plasmodium). It also includes new data showing alternative splice variants of human TOP1mt.}, }
@article {pmid17158739, year = {2006}, author = {Mukherjee, M and Brown, MT and McArthur, AG and Johnson, PJ}, title = {Proteins of the glycine decarboxylase complex in the hydrogenosome of Trichomonas vaginalis.}, journal = {Eukaryotic cell}, volume = {5}, number = {12}, pages = {2062-2071}, pmid = {17158739}, issn = {1535-9778}, support = {/WT_/Wellcome Trust/United Kingdom ; T32 AI007323/AI/NIAID NIH HHS/United States ; 2-T32-AI-07323/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Dihydrolipoamide Dehydrogenase/genetics/metabolism ; Genes, Protozoan ; Glycine Decarboxylase Complex/genetics/*metabolism ; Glycine Decarboxylase Complex H-Protein/genetics/metabolism ; Kinetics ; Molecular Sequence Data ; Organelles/enzymology ; Phylogeny ; Protozoan Proteins/genetics/*metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/*enzymology/genetics ; }, abstract = {Trichomonas vaginalis is a unicellular eukaryote that lacks mitochondria and contains a specialized organelle, the hydrogenosome, involved in carbohydrate metabolism and iron-sulfur cluster assembly. We report the identification of two glycine cleavage H proteins and a dihydrolipoamide dehydrogenase (L protein) of the glycine decarboxylase complex in T. vaginalis with predicted N-terminal hydrogenosomal presequences. Immunofluorescence analyses reveal that both H and L proteins are localized in hydrogenosomes, providing the first evidence for amino acid metabolism in this organelle. All three proteins were expressed in Escherichia coli and purified to homogeneity. The experimental Km of L protein for the two H proteins were 2.6 microM and 3.7 microM, consistent with both H proteins serving as substrates of L protein. Analyses using purified hydrogenosomes showed that endogenous H proteins exist as monomers and endogenous L protein as a homodimer in their native states. Phylogenetic analyses of L proteins revealed that the T. vaginalis homologue shares a common ancestry with dihydrolipoamide dehydrogenases from the firmicute bacteria, indicating its acquisition via a horizontal gene transfer event independent of the origins of mitochondria and hydrogenosomes.}, }
@article {pmid17158683, year = {2007}, author = {Kitada, S and Uchiyama, T and Funatsu, T and Kitada, Y and Ogishima, T and Ito, A}, title = {A protein from a parasitic microorganism, Rickettsia prowazekii, can cleave the signal sequences of proteins targeting mitochondria.}, journal = {Journal of bacteriology}, volume = {189}, number = {3}, pages = {844-850}, pmid = {17158683}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/*metabolism ; Kinetics ; Metalloendopeptidases/chemistry/genetics/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Molecular Sequence Data ; Peptides/chemistry/metabolism ; Phylogeny ; Protein Sorting Signals ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport ; Recombinant Fusion Proteins/genetics/metabolism ; Rickettsia prowazekii/genetics/*metabolism ; Sequence Alignment ; Mitochondrial Processing Peptidase ; }, abstract = {The obligate intracellular parasitic bacteria rickettsiae are more closely related to mitochondria than any other microbes investigated to date. A rickettsial putative peptidase (RPP) was found to resemble the alpha and beta subunits of mitochondrial processing peptidase (MPP), which cleaves the transport signal sequences of mitochondrial preproteins. RPP showed completely conserved zinc-binding and catalytic residues compared with beta-MPP but barely contained any of the glycine-rich loop region characteristic of alpha-MPP. When the biochemical activity of RPP purified from a recombinant source was analyzed, RPP specifically hydrolyzed basic peptides and presequence peptides with frequent cleavage at their MPP-processing sites. Moreover, RPP appeared to activate yeast beta-MPP so that it processed preproteins with shorter presequences. Thus, RPP behaves as a bifunctional protein that could act as a basic peptide peptidase and a somewhat regulatory protein for other protein activities in rickettsiae. These are the first biological and enzymological studies to report that a protein from a parasitic microorganism can cleave the signal sequences of proteins targeted to mitochondria.}, }
@article {pmid17158073, year = {2007}, author = {Guha, S and Goyal, SP and Kashyap, VK}, title = {Molecular phylogeny of musk deer: a genomic view with mitochondrial 16S rRNA and cytochrome b gene.}, journal = {Molecular phylogenetics and evolution}, volume = {42}, number = {3}, pages = {585-597}, doi = {10.1016/j.ympev.2006.06.020}, pmid = {17158073}, issn = {1055-7903}, mesh = {Animals ; Cytochromes b/*genetics ; Deer/*genetics ; *Evolution, Molecular ; Mitochondria/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Ruminants/genetics ; }, abstract = {The phylogenetic status of the infra order Pecora is controversial, even though it is supported by paleontological, morphological, and molecular evidence. We analyzed two mitochondrial genes (i.e., 16S rRNA and cytochrome b) to resolve the phylogenetic position of pecoran species, i.e., the Bovidae, Cervidae, and Moschidae endemic to the Indian subcontinent. We used phylogenetic analysis based on different algorithms, including neighbor joining, maximum parsimony, Bayesian inference, maximum likelihood, minimum evolution, median joining network, along with multidimensional scaling, and DNA word analysis. Our results established the basal position of Tragulidae and the monophyly of the infra order Pecora within the Suborder Ruminantia. Our results also demonstrated that Bovidae, Cervidae, and Moschidae are allied with the placement of musk deer as more closely related to bovids than to cervids. Molecular dating based on sequence analysis shows that the radiation of Pecora occurred during the early Oligocene and that the majority of the pecoran families radiated and dispersed rapidly during the Oligocene/Miocene transition.}, }
@article {pmid17156084, year = {2007}, author = {Harper, JM and Salmon, AB and Leiser, SF and Galecki, AT and Miller, RA}, title = {Skin-derived fibroblasts from long-lived species are resistant to some, but not all, lethal stresses and to the mitochondrial inhibitor rotenone.}, journal = {Aging cell}, volume = {6}, number = {1}, pages = {1-13}, pmid = {17156084}, issn = {1474-9718}, support = {T32 AG000114/AG/NIA NIH HHS/United States ; U19 AG023122/AG/NIA NIH HHS/United States ; AG023122/AG/NIA NIH HHS/United States ; P30 AG024824-019003/AG/NIA NIH HHS/United States ; P30 AG024824/AG/NIA NIH HHS/United States ; AG024824/AG/NIA NIH HHS/United States ; GM07315/GM/NIGMS NIH HHS/United States ; Z01 AG000114/ImNIH/Intramural NIH HHS/United States ; T32 GM007315/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cadmium/toxicity ; Cells, Cultured ; Cellular Senescence/drug effects/*physiology/radiation effects ; Chiroptera ; Energy Metabolism/drug effects/physiology ; Fibroblasts/drug effects/*metabolism/radiation effects ; Glucose/metabolism ; Heat Stress Disorders/metabolism/physiopathology ; Hydrogen Peroxide/toxicity ; Immunity, Innate/drug effects/physiology ; Linear Models ; Longevity/*physiology ; Mice ; Mitochondria/drug effects/*metabolism ; Oxidative Stress/physiology ; Rodentia ; Rotenone/*toxicity ; Skin/*cytology ; Species Specificity ; Ultraviolet Rays ; Uncoupling Agents/toxicity ; }, abstract = {Fibroblast cell lines were developed from skin biopsies of eight species of wild-trapped rodents, one species of bat, and a group of genetically heterogeneous laboratory mice. Each cell line was tested in vitro for their resistance to six varieties of lethal stress, as well as for resistance to the nonlethal metabolic effects of the mitochondrial inhibitor rotenone and of culture at very low glucose levels. Standard linear regression of species-specific lifespan against each species mean stress resistance showed that longevity was associated with resistance to death induced by cadmium and hydrogen peroxide, as well as with resistance to rotenone inhibition. A multilevel regression method supported these associations, and suggested a similar association for resistance to heat stress. Regressions for resistance to cadmium, peroxide, heat, and rotenone remained significant after various statistical adjustments for body weight. In contrast, cells from longer-lived species did not show significantly greater resistance to ultraviolet light, paraquat, or the DNA alkylating agent methylmethanesulfonate. There was a strong correlation between species longevity and resistance to the metabolic effects of low-glucose medium among the rodent cell lines, but this test did not distinguish mice and rats from the much longer-lived little brown bat. These results are consistent with the idea that evolution of long-lived species may require development of cellular resistance to several forms of lethal injury, and provide justification for evaluation of similar properties in a much wider range of mammals and bird species.}, }
@article {pmid17155115, year = {2006}, author = {Campos, PR and Combadão, J and Dionisio, F and Gordo, I}, title = {Muller's ratchet in random graphs and scale-free networks.}, journal = {Physical review. E, Statistical, nonlinear, and soft matter physics}, volume = {74}, number = {4 Pt 1}, pages = {042901}, doi = {10.1103/PhysRevE.74.042901}, pmid = {17155115}, issn = {1539-3755}, mesh = {*Algorithms ; *Biological Evolution ; Computer Simulation ; *Extinction, Biological ; *Genetics, Population ; *Models, Biological ; Mutation ; *Population Growth ; Reproduction, Asexual/*genetics ; }, abstract = {Muller's ratchet is an evolutionary process that has been implicated in the extinction of asexual species, the evolution of mitochondria, the degeneration of the Y chromosome, the evolution of sex and recombination and the evolution of microbes. Here we study the speed of Muller's ratchet in a population subdivided into many small subpopulations connected by migration, and distributed on a network. We compare the speed of the ratchet in two distinct types of topologies: scale free networks and random graphs. The difference between the topologies is noticeable when the average connectivity of the network and the migration rate is large. In this situation we observe that the ratchet clicks faster in scale free networks than in random graphs. So contrary to intuition, scale free networks are more prone to loss of genetic information than random graphs. On the other hand, we show that scale free networks are more robust to the random extinction than random graphs. Since these complex networks have been shown to describe well real-life systems, our results open a framework for studying the evolution of microbes and disease epidemics.}, }
@article {pmid17152948, year = {2006}, author = {Kimura, M and Dhondt, AA and Irby J, L}, title = {Phylogeographic structuring of Plasmodium lineages across the North American range of the house finch (Carpodacus Mexicanus).}, journal = {The Journal of parasitology}, volume = {92}, number = {5}, pages = {1043-1049}, doi = {10.1645/GE-639R.1}, pmid = {17152948}, issn = {0022-3395}, mesh = {Animals ; Cytochromes b/genetics ; DNA, Protozoan/blood/chemistry/isolation &amp; purification ; Finches/*parasitology ; Haplotypes ; Malaria, Avian/epidemiology/*parasitology ; Mitochondria/enzymology/genetics ; Phylogeny ; Plasmodium/*classification/genetics ; Polymerase Chain Reaction/veterinary ; Prevalence ; United States/epidemiology ; }, abstract = {The determinants of the geographic distribution of avian hematozoa are poorly understood. Sampling parasites from one avian host species across a wide geographic range is an accepted approach to separate the potential influence of host species distribution from geographic effects not directly related to host species biology. We used polymerase chain reaction to screen samples for hematozoan infection from 490 house finches (Carpodacus mexicanus) collected at 8 sites spanning continental North America. To explore geographic patterns of parasite lineage distributions, we sequenced a portion of the mitochondrial cytochrome b gene of Plasmodium species infecting 77 house finches. We identified 5 distinct Plasmodium haplotypes representing 3 lineages that likely represent 3 species. One lineage was common at all sites where we detected Plasmodium species. The second lineage contained 3 haplotypes that showed phylogeographic structuring on a continent-wide scale, with 1 haplotype common in eastern North America and 2 common in western North America. The third divergent lineage was recovered from 1 individual host. Considered together, the partial phylogeographic structuring of Plasmodium cytochrome b lineages over the range of the house finch suggests that parasite lineage distribution is not solely dependent on host species distribution, and other factors such as arthropod vector competence and distribution may be important.}, }
@article {pmid17151253, year = {2007}, author = {Popescu, CE and Lee, RW}, title = {Mitochondrial genome sequence evolution in Chlamydomonas.}, journal = {Genetics}, volume = {175}, number = {2}, pages = {819-826}, pmid = {17151253}, issn = {0016-6731}, mesh = {Animals ; Base Composition/genetics ; Base Sequence ; Cell Nucleus/metabolism ; Chlamydomonas/*genetics ; Codon/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genes, Protozoan ; Genome, Protozoan/*genetics ; Mitochondrial Proteins/genetics ; Mutation/genetics ; Nucleotides/genetics ; }, abstract = {The mitochondrial genomes of the Chlorophyta exhibit significant diversity with respect to gene content and genome compactness; however, quantitative data on the rates of nucleotide substitution in mitochondrial DNA, which might help explain the origin of this diversity, are lacking. To gain insight into the evolutionary forces responsible for mitochondrial genome diversification, we sequenced to near completion the mitochondrial genome of the chlorophyte Chlamydomonas incerta, estimated the evolutionary divergence between Chlamydomonas reinhardtii and C. incerta mitochondrial protein-coding genes and rRNA-coding regions, and compared the relative evolutionary rates in mitochondrial and nuclear genes. Synonymous and nonsynonymous substitution rates do not differ significantly between the mitochondrial and nuclear protein-coding genes. The mitochondrial rRNA-coding regions, however, are evolving much faster than their nuclear counterparts, and this difference might be explained by relaxed functional constraints on the mitochondrial translational apparatus due to the small number of proteins synthesized in Chlamydomonas mitochondria. Substitution rates at synonymous sites in a nonstandard mitochondrial gene (rtl) and at intronic and synonymous sites in nuclear genes expressed at low levels suggest that the mutation rate is similar in these two genetic compartments. Potential evolutionary forces shaping mitochondrial genome evolution in Chlamydomonas are discussed.}, }
@article {pmid17150537, year = {2004}, author = {Sekito, T and Okamoto, K and Kitano, H and Yoshida, K}, title = {Up-to-dating of complete sequenced DNA data of Hansenula wingei yeast mitochondria.}, journal = {Nucleic acids symposium series (2004)}, volume = {}, number = {48}, pages = {179-180}, doi = {10.1093/nass/48.1.179}, pmid = {17150537}, issn = {1746-8272}, mesh = {Base Sequence ; DNA, Mitochondrial/*genetics ; Genes, Fungal ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Open Reading Frames/genetics ; Phylogeny ; Pichia/*genetics ; RNA Processing, Post-Transcriptional ; RNA, Ribosomal/chemistry/metabolism ; *Sequence Analysis, DNA ; }, abstract = {To update sequenced data, we determined the 5' and 3' termini of yeast Hansenula wingei (Pichia canadensis) mitochondrial (mt) large subunit ribosomal RNA (LSU) which is encoded in the mt genome. The 5' end position was mapped downstream from a putative transcription starting site which is homologous to a Saccharomyces cerevisiae mitochondrial promoter sequence. This suggests that the primary transcript of LSU is processed from 5' end and then mature transcript is formed. This processing is different from that of S. cerevisiae mt LSU in which processing on its 5' end does not occur. Based on the sequence data of H. wingei mt LSU, we constructed its secondary structure, and compared it with those of the other fungal organisms. Conserved regions of H. wingei LSU were identified and used for subsequent phylogenetic analysis. In genome structure and gene content, H. wingei mt genome has several characteristics similar to those in filamentous fungi, but the phylogenetic analysis indicates closer kinship to yeast S. cerevisiae. This agrees with previous non-sequencing phylogenies and suggests that extraordinary rearrangements have occurred in yeast mt genomes during divergent evolution.}, }
@article {pmid17148377, year = {2006}, author = {Tokuda, G and Yamada, A and Nakano, K and Arita, N and Yamasaki, H}, title = {Occurrence and recent long-distance dispersal of deep-sea hydrothermal vent shrimps.}, journal = {Biology letters}, volume = {2}, number = {2}, pages = {257-260}, pmid = {17148377}, issn = {1744-9561}, mesh = {Animals ; Decapoda/*classification/genetics ; Electron Transport Complex IV/genetics ; *Environment ; Japan ; Mitochondria/enzymology ; Phylogeny ; Population Dynamics ; RNA, Ribosomal, 18S/genetics ; Seawater ; }, abstract = {Deep-sea hydrothermal vents and methane seeps are extreme environments that have a high concentration of hydrogen sulphide. However, abundant unique invertebrates including shrimps of the family Bresiliidae have been found in such environments. The bresiliid shrimps are believed to have radiated in the Miocene (less than 20 Myr); however, the period when and the mechanisms by which they dispersed across the hydrothermal vents and cold seeps in oceans worldwide have not been clarified. In the present study, we collected the deep-sea blind shrimp Alvinocaris longirostris from the hydrothermal vent site in the Okinawa Trough and carried out the first investigation of the 18S rRNA gene of a bresiliid shrimp. The phylogenetic analysis revealed that the bresiliid shrimp is situated at an intermediate lineage within the infraorder Caridea and shows monophyly with palaemonid shrimps, which live in shallow sea and freshwater. Furthermore, the mitochondrial cytochrome oxidase I (COI) gene sequences were analysed to determine the phylogenetic relationship with known bresiliid shrimps. A. longirostris of the Okinawa Trough had two haplotypes of the COI gene, one of which was identical to the Alvinocaris sp. of the cold seeps in Sagami Bay. These results indicate that a long-distance dispersal of A. longirostris occurred possibly within the last 100,000 years.}, }
@article {pmid17147999, year = {2006}, author = {Kiefel, BR and Gilson, PR and Beech, PL}, title = {Cell biology of mitochondrial dynamics.}, journal = {International review of cytology}, volume = {254}, number = {}, pages = {151-213}, doi = {10.1016/S0074-7696(06)54004-5}, pmid = {17147999}, issn = {0074-7696}, mesh = {Animals ; Apoptosis ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/metabolism ; Phylogeny ; }, abstract = {Mitochondria are the product of an ancient endosymbiotic event between an alpha-proteobacterium and an archael host. An early barrier to overcome in this relationship was the control of the bacterium's proliferation within the host. Undoubtedly, the bacterium (or protomitochondrion) would have used its own cell division apparatus to divide at first and, today a remnant of this system remains in some "ancient" and diverse eukaryotes such as algae and amoebae, the most conserved and widespread of all bacterial division proteins, FtsZ. In many of the eukaryotes that still use FtsZ to constrict the mitochondria from the inside, the mitochondria still resemble bacteria in shape and size. Eukaryotes, however, have a mitochondrial morphology that is often highly fluid, and in their tubular networks of mitochondria, division is clearly complemented by mitochondrial fusion. FtsZ is no longer used by these complex eukaryotes, and may have been replaced by other proteins better suited to sustaining complex mitochondrial networks. Although proteins that divide mitochondria from the inside are just beginning to be characterized in higher eukaryotes, many division proteins are known to act on the outside of the organelle. The most widespread of these are the dynamin-like proteins, which appear to have been recruited very early in the evolution of mitochondria. The essential nature of mitochondria dictates that their loss is intolerable to human cells, and that mutations disrupting mitochondrial division are more likely to be fatal than result in disease. To date, only one disease (Charcot-Marie-Tooth disease 2A) has been mapped to a gene that is required for mitochondrial division, whereas two other diseases can be attributed to mutations in mitochondrial fusion genes. Apart from playing a role in regulating the morphology, which might be important for efficient ATP production, research has indicated that the mitochondrial division and fusion proteins can also be important during apoptosis; mitochondrial fragmentation is an early triggering (and under many stimuli, essential) step in the pathway to cell suicide.}, }
@article {pmid17143541, year = {2007}, author = {Paquet, P and Pierard, GE}, title = {Toxic epidermal necrolysis: revisiting the tentative link between early apoptosis and late necrosis (review).}, journal = {International journal of molecular medicine}, volume = {19}, number = {1}, pages = {3-10}, pmid = {17143541}, issn = {1107-3756}, mesh = {Apoptosis ; Humans ; Keratinocytes/metabolism/*pathology ; Mitochondria/*metabolism ; Models, Biological ; Molecular Structure ; Necrosis/metabolism ; Oxidation-Reduction ; Phosphorylation ; Signal Transduction ; Stevens-Johnson Syndrome/etiology/metabolism/*pathology/physiopathology ; }, abstract = {Toxic epidermal necrolysis (TEN) is a dramatic drug-induced reaction that may lead to full destruction of the epidermis and epithelial mucosae. The keratinocytes themselves seem to play a major role in the pathogenic mechanism. Biochemical and morphological studies performed on early epidermal lesions demonstrated that keratinocytes undergo apoptosis, but histological and clinical data show evidence of necrosis of the epidermis later in the disease evolution. Based on the limited information currently available about TEN pathomechanism, we present a 'mitochondrial hypothesis' that may explain both early apoptosis and late necrosis in TEN epidermis. Strong electrophilic drug metabolites are generated in TEN-affected keratinocytes due to an impaired detoxication pathway. These compounds presumably disrupt the electron transfer chain in the mitochondriae resulting in a decline in ATP production, loss of electrochemical gradient across the inner membrane (Deltapsim), and partial reduction in O2 with production of reactive oxygen species (ROS). The latter compounds directly damage cell membranes and act as intracellular chemical messengers stimulating proapoptotic systems such as CD95 and TNF-alpha, which in turn can activate nitric oxide (NO) metabolism. NO interacts with ROS to enhance their toxic effects. These proapoptotic events represent swift processes in the involved cells. The loss of Deltapsim and the opening of permeability transition pores in the mitochondrial membrane lead to osmotic swelling and rupture of these organelles with subsequent necrosis of the cell. The necrotic events follow apoptosis when both phenomena are present.}, }
@article {pmid17133864, year = {2006}, author = {Maklakov, AA and Friberg, U and Dowling, DK and Arnqvist, G}, title = {Within-population variation in cytoplasmic genes affects female life span and aging in Drosophila melanogaster.}, journal = {Evolution; international journal of organic evolution}, volume = {60}, number = {10}, pages = {2081-2086}, pmid = {17133864}, issn = {0014-3820}, mesh = {Aging/*genetics ; Animals ; Crosses, Genetic ; Cytoplasm/genetics ; *DNA, Mitochondrial ; Drosophila melanogaster ; Female ; Founder Effect ; Genetic Variation ; Longevity/*genetics ; Male ; Mitochondria/genetics/physiology ; }, abstract = {It has been suggested that mitochondrial DNA (mtDNA) may play an important role in aging. Yet, few empirical studies have tested this hypothesis, partly because the degree of sequence polymorphism in mtDNA is assumed to be low. However, low sequence variation may not necessarily translate into low phenotypic variation. Here, we report an experiment that tests whether there is within-population variation in cytoplasmic genes for female longevity and senescence. To achieve this, we randomly selected 25 "mitochondrial founders" from a single, panmictic population of Drosophila melanogaster and used these founders to generate distinct "mt" lines in which we controlled for the nuclear background by successive backcrossing. Potential confounding effects of cytoplasmically transmitted bacteria were eliminated by tetracycline treatment. The mt lines were then assayed for differences in longevity, Gompertz intercept (frailty), and demographic rate of change in mortality with age (rate-of-senescence) in females. We found significant cytoplasmic effects on all three variables. This provides evidence that genetic variation in cytoplasmic genes, presumably mtDNA, contributes to variation in female mortality and aging.}, }
@article {pmid17123444, year = {2006}, author = {Roy, V and Demanche, C and Livet, A and Harry, M}, title = {Genetic differentiation in the soil-feeding termite Cubitermes sp. affinis subarquatus: occurrence of cryptic species revealed by nuclear and mitochondrial markers.}, journal = {BMC evolutionary biology}, volume = {6}, number = {}, pages = {102}, pmid = {17123444}, issn = {1471-2148}, mesh = {Animals ; Base Sequence ; DNA, Intergenic/analysis ; DNA, Mitochondrial/analysis ; Gabon ; *Genetic Drift ; Genetic Markers ; *Genetic Variation ; Isoptera/*genetics ; Microsatellite Repeats ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {BACKGROUND: Soil-feeding termites are particularly interesting models for studying the effects of fragmentation, a natural or anthropic phenomenon described as promoting genetic differentiation. However, studying the link between fragmentation and genetics requires a method for identifying species unambiguously, especially when morphological diagnostic characters are lacking. In humivorous termites, which contribute to the fertility of tropical soils, molecular taxonomy and phylogenetic relationships are rarely studied, though mitochondrial and nuclear molecular markers are widely used in studies of pest termites. Here, we attempt to clarify the taxonomy of soil-feeding colonies collected throughout the naturally fragmented Lopé Reserve area (Gabon) and morphologically affiliated to Cubitermes sp. affinis subarquatus. The mitochondrial gene of cytochrome oxidase II (COII), the second nuclear rDNA internal transcribed spacer (ITS2) and five microsatellites were analyzed in 19 colonies.<br><br>RESULTS: Bayesian Inference, Maximum Likelihood and Maximum Parsimony phylogenetic analyses, which were applied to the COII and ITS2 sequences, and Neighbor-Joining reconstructions, applied to the microsatellite data, reveal four major lineages in the Cubitermes sp. affinis subarquatus colonies. The concordant genealogical pattern of these unlinked markers strongly supports the existence of four cryptic species. Three are sympatric in the Reserve and are probably able to disperse within a mosaic of forests of variable ages and savannahs. One is limited to a very restricted gallery forest patch located in the North, outside the Reserve.<br><br>CONCLUSION: Our survey highlights the value of combined mitochondrial and nuclear markers for exploring unknown groups such as soil-feeding termites, and their relevance for resolving the taxonomy of organisms with ambiguous morphological diagnostic characters.}, }
@article {pmid17120136, year = {2007}, author = {Carrie, C and Murcha, MW and Millar, AH and Smith, SM and Whelan, J}, title = {Nine 3-ketoacyl-CoA thiolases (KATs) and acetoacetyl-CoA thiolases (ACATs) encoded by five genes in Arabidopsis thaliana are targeted either to peroxisomes or cytosol but not to mitochondria.}, journal = {Plant molecular biology}, volume = {63}, number = {1}, pages = {97-108}, pmid = {17120136}, issn = {0167-4412}, mesh = {Acetyl-CoA C-Acetyltransferase/genetics/*metabolism ; Acetyl-CoA C-Acyltransferase/genetics/*metabolism ; Amino Acid Sequence ; Arabidopsis Proteins/genetics/metabolism ; Cluster Analysis ; Cytosol/*metabolism ; Gene Expression Regulation, Plant ; Green Fluorescent Proteins/genetics/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Peroxisomes/*metabolism ; Phylogeny ; Protein Transport ; Recombinant Fusion Proteins/genetics/metabolism ; }, abstract = {The sub-cellular location of enzymes of fatty acid beta-oxidation in plants is controversial. In the current debate the role and location of particular thiolases in fatty acid degradation, fatty acid synthesis and isoleucine degradation are important. The aim of this research was to determine the sub-cellular location and hence provide information about possible functions of all the putative 3-ketoacyl-CoA thiolases (KAT) and acetoacetyl-CoA thiolases (ACAT) in Arabidopsis. Arabidopsis has three genes predicted to encode KATs, one of which encodes two polypeptides that differ at the N-terminal end. Expression in Arabidopsis cells of cDNAs encoding each of these KATs fused to green fluorescent protein (GFP) at their C-termini showed that three are targeted to peroxisomes while the fourth is apparently cytosolic. The four KATs are also predicted to have mitochondrial targeting sequences, but purified mitochondria were unable to import any of the proteins in vitro. Arabidopsis also has two genes encoding a total of five different putative ACATs. One isoform is targeted to peroxisomes as a fusion with GFP, while the others display no targeting in vivo as GFP fusions, or import into isolated mitochondria. Analysis of gene co-expression clusters in Arabidopsis suggests a role for peroxisomal KAT2 in beta-oxidation, while KAT5 co-expresses with genes of the flavonoid biosynthesis pathway and cytosolic ACAT2 clearly co-expresses with genes of the cytosolic mevalonate biosynthesis pathway. We conclude that KATs and ACATs are present in the cytosol and peroxisome, but are not found in mitochondria. The implications for fatty acid beta-oxidation and for isoleucine degradation in mitochondria are discussed.}, }
@article {pmid17120123, year = {2006}, author = {Travers, A}, title = {The evolution of the genetic code revisited.}, journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life}, volume = {36}, number = {5-6}, pages = {549-555}, pmid = {17120123}, issn = {0169-6149}, support = {MC_U105184288/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anticodon/genetics ; Base Sequence ; Codon/genetics ; DNA/genetics ; *Evolution, Molecular ; Genetic Code/*genetics ; }, abstract = {The evolution of the genetic code in terms of the adoption of new codons has previously been related to the relative thermostability of codon-anticodon interactions such that the most stable interactions have been hypothesised to represent the most ancient coding capacity. This derivation is critically dependent on the accuracy of the experimentally determined stability parameters. A new set of parameters recently determined for B-DNA reveals that the codon-anticodon pairs for the codes in non-plant mitochondria on the one hand and prokaryotic and eukaryotic organisms on the other can be unequivocally divided into two classes - the most stable base steps define a common code specified by the first two bases in a codon while the less stable base steps correlate with divergent usage and the adoption of a 3-letter code. This pattern suggests that the fixation of codons for A, G, P, V, S, T, D/E, R may have preceded the divergence of the non-plant mitochondrial line from other organisms. Other variations in the code correlate with the least stable codon-anticodon pairs.}, }
@article {pmid17116872, year = {2006}, author = {Jeyaraju, DV and Xu, L and Letellier, MC and Bandaru, S and Zunino, R and Berg, EA and McBride, HM and Pellegrini, L}, title = {Phosphorylation and cleavage of presenilin-associated rhomboid-like protein (PARL) promotes changes in mitochondrial morphology.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {49}, pages = {18562-18567}, pmid = {17116872}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Apoptosis/physiology ; Cell Line ; HeLa Cells ; Humans ; Hydrolysis ; Metalloproteases/*chemistry/*metabolism/physiology ; Mitochondria/*chemistry/*physiology ; Mitochondrial Proteins/*chemistry/*metabolism/physiology ; Molecular Sequence Data ; Phosphorylation ; Presenilins/metabolism ; }, abstract = {Remodeling of mitochondria is a dynamic process coordinated by fusion and fission of the inner and outer membranes of the organelle, mediated by a set of conserved proteins. In metazoans, the molecular mechanism behind mitochondrial morphology has been recruited to govern novel functions, such as development, calcium signaling, and apoptosis, which suggests that novel mechanisms should exist to regulate the conserved membrane fusion/fission machinery. Here we show that phosphorylation and cleavage of the vertebrate-specific Pbeta domain of the mammalian presenilin-associated rhomboid-like (PARL) protease can influence mitochondrial morphology. Phosphorylation of three residues embedded in this domain, Ser-65, Thr-69, and Ser-70, impair a cleavage at position Ser(77)-Ala(78) that is required to initiate PARL-induced mitochondrial fragmentation. Our findings reveal that PARL phosphorylation and cleavage impact mitochondrial dynamics, providing a blueprint to study the molecular evolution of mitochondrial morphology.}, }
@article {pmid17113597, year = {2007}, author = {Facey, SJ and Neugebauer, SA and Krauss, S and Kuhn, A}, title = {The mechanosensitive channel protein MscL is targeted by the SRP to the novel YidC membrane insertion pathway of Escherichia coli.}, journal = {Journal of molecular biology}, volume = {365}, number = {4}, pages = {995-1004}, doi = {10.1016/j.jmb.2006.10.083}, pmid = {17113597}, issn = {0022-2836}, mesh = {Adenosine Triphosphatases/metabolism ; Bacterial Proteins/metabolism ; Cell Membrane/*metabolism ; Chloroplasts/metabolism ; Electrochemistry/methods ; Escherichia coli/metabolism ; Escherichia coli Proteins/chemistry/*metabolism/*physiology ; Evolution, Molecular ; Ion Channels/chemistry/*physiology ; Membrane Potentials ; Membrane Transport Proteins/*metabolism ; Mitochondria/metabolism ; Plasmids/metabolism ; Protein Transport ; Proton-Motive Force ; SEC Translocation Channels ; SecA Proteins ; *Signal Recognition Particle ; }, abstract = {The mechanosensitive channel MscL in the inner membrane of Escherichia coli is a homopentameric complex involved in homeostasis when cells are exposed to hypo-osmotic conditions. The E. coli MscL protein is synthesized as a polypeptide of 136 amino acid residues and uses the bacterial signal recognition particle (SRP) for membrane targeting. The protein is inserted into the membrane independently of the Sec translocon. Mutants affected in the Sec-components are competent for MscL assembly. Translocation of the periplasmic domain was detected using a membrane-impermeant, sulfhydryl-specific gel-shift reagent. The modification of a single cysteine residue at position 68 indicated its translocation across the inner membrane. From these in vivo experiments, it is concluded that the electrical chemical membrane potential is not necessary for membrane insertion of MscL. However, depletion of the membrane insertase YidC inhibits translocation of the protein across the membrane. We show here that YidC is essential for efficient membrane insertion of the MscL protein. YidC is a component of a recently identified membrane insertion pathway that is evolutionarily conserved in bacteria, mitochondria and chloroplasts.}, }
@article {pmid17110464, year = {2007}, author = {Doron-Faigenboim, A and Pupko, T}, title = {A combined empirical and mechanistic codon model.}, journal = {Molecular biology and evolution}, volume = {24}, number = {2}, pages = {388-397}, doi = {10.1093/molbev/msl175}, pmid = {17110464}, issn = {0737-4038}, mesh = {Amino Acid Substitution ; Animals ; Anti-HIV Agents/therapeutic use ; Carbamates/therapeutic use ; Chloroplasts/genetics ; *Codon ; Drug Resistance, Viral ; Evolution, Molecular ; Furans ; Genes, Mitochondrial ; Genes, Viral ; HIV Infections/drug therapy ; HIV Protease/chemistry/genetics ; HIV-1/enzymology ; Humans ; Markov Chains ; *Models, Genetic ; *Models, Statistical ; Mutation ; Selection, Genetic ; Sulfonamides/therapeutic use ; }, abstract = {The evolutionary selection forces acting on a protein are commonly inferred using evolutionary codon models by contrasting the rate of synonymous to nonsynonymous substitutions. Most widely used models are based on theoretical assumptions and ignore the empirical observation that distinct amino acids differ in their replacement rates. In this paper, we develop a general method that allows assimilation of empirical amino acid replacement probabilities into a codon-substitution matrix. In this way, the resulting codon model takes into account not only the transition-transversion bias and the nonsynonymous/synonymous ratio, but also the different amino acid replacement probabilities as specified in empirical amino acid matrices. Different empirical amino acid replacement matrices, such as secondary structure-specific matrices or organelle-specific matrices (e.g., mitochondria and chloroplasts), can be incorporated into the model, making it context dependent. Using a diverse set of coding DNA sequences, we show that the novel model better fits biological data as compared with either mechanistic or empirical codon models. Using the suggested model, we further analyze human immunodeficiency virus type 1 protease sequences obtained from drug-treated patients and reveal positive selection in sites that are known to confer drug resistance to the virus.}, }
@article {pmid17110332, year = {2006}, author = {Qin, Y and Polacek, N and Vesper, O and Staub, E and Einfeldt, E and Wilson, DN and Nierhaus, KH}, title = {The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome.}, journal = {Cell}, volume = {127}, number = {4}, pages = {721-733}, doi = {10.1016/j.cell.2006.09.037}, pmid = {17110332}, issn = {0092-8674}, mesh = {Amino Acid Sequence ; Computational Biology ; *Conserved Sequence ; Escherichia coli/*metabolism ; Escherichia coli Proteins/chemistry/*metabolism ; GTP Phosphohydrolases/metabolism ; Green Fluorescent Proteins/metabolism ; Models, Genetic ; Molecular Sequence Data ; Peptide Elongation Factor G/chemistry ; Peptide Elongation Factors/*metabolism ; Peptide Initiation Factors ; Phylogeny ; Protein Biosynthesis/*genetics ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Ribosomes/*metabolism ; Transcription, Genetic ; Transcriptional Elongation Factors/chemistry/*metabolism ; }, abstract = {The ribosomal elongation cycle describes a series of reactions prolonging the nascent polypeptide chain by one amino acid and driven by two universal elongation factors termed EF-Tu and EF-G in bacteria. Here we demonstrate that the extremely conserved LepA protein, present in all bacteria and mitochondria, is a third elongation factor required for accurate and efficient protein synthesis. LepA has the unique function of back-translocating posttranslocational ribosomes, and the results suggest that it recognizes ribosomes after a defective translocation reaction and induces a back-translocation, thus giving EF-G a second chance to translocate the tRNAs correctly. We suggest renaming LepA as elongation factor 4 (EF4).}, }
@article {pmid17109325, year = {2006}, author = {Burton, RS and Ellison, CK and Harrison, JS}, title = {The sorry state of F2 hybrids: consequences of rapid mitochondrial DNA evolution in allopatric populations.}, journal = {The American naturalist}, volume = {168 Suppl 6}, number = {}, pages = {S14-24}, doi = {10.1086/509046}, pmid = {17109325}, issn = {1537-5323}, mesh = {Animals ; Copepoda/*genetics/growth &amp; development/physiology ; Cytochromes c/genetics/metabolism ; DNA, Mitochondrial/*chemistry ; Electron Transport Complex IV/genetics/metabolism ; *Evolution, Molecular ; Genetic Variation ; Genotype ; *Hybridization, Genetic ; Mitochondria/physiology ; Transcription, Genetic ; }, abstract = {Through the processes of natural selection and genetic drift, allopatric populations diverge genetically and may ultimately become reproductively incompatible. In cases of prezygotic reproductive isolation, candidate systems for speciation genes logically include genes involved in mate or gamete recognition. However, where only postzygotic isolation exists, candidate speciation genes could include any genes that affect hybrid performance. We hypothesize that because mitochondrial genes frequently evolve more rapidly than the nuclear genes with which they interact, interpopulation hybridization might be particularly disruptive to mitochondrial function. Understanding the potential impact of intergenomic (nuclear and mitochondrial) coadaptation on the evolution of allopatric populations of the intertidal copepod Tigriopus californicus has required a broadly integrative research program; here we present the results of experiments spanning the spectrum of biological organization in order to demonstrate the consequences of molecular evolution on physiological performance and organismal fitness. We suggest that disruption of mitochondrial function, known to result in a diverse set of human diseases, may frequently underlie reduced fitness in interpopulation and interspecies hybrids in animals.}, }
@article {pmid17108184, year = {2007}, author = {Khachane, AN and Timmis, KN and Martins dos Santos, VA}, title = {Dynamics of reductive genome evolution in mitochondria and obligate intracellular microbes.}, journal = {Molecular biology and evolution}, volume = {24}, number = {2}, pages = {449-456}, doi = {10.1093/molbev/msl174}, pmid = {17108184}, issn = {0737-4038}, mesh = {Base Composition ; Biological Evolution ; Buchnera/*genetics ; DNA, Mitochondrial ; DNA, Ribosomal/genetics ; *Evolution, Molecular ; Extrachromosomal Inheritance ; Genome ; *Genome, Bacterial ; Mitochondria/*genetics ; Models, Genetic ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Reductive evolution in mitochondria and obligate intracellular microbes has led to a significant reduction in their genome size and guanine plus cytosine content (GC). We show that genome shrinkage during reductive evolution in prokaryotes follows an exponential decay pattern and provide a method to predict the extent of this decay on an evolutionary timescale. We validated predictions by comparison with estimated extents of genome reduction known to have occurred in mitochondria and Buchnera aphidicola, through comparative genomics and by drawing on available fossil evidences. The model shows how the mitochondrial ancestor would have quickly shed most of its genome, shortly after its incorporation into the protoeukaryotic cell and prior to codivergence subsequent to the split of eukaryotic lineages. It also predicts that the primary rickettsial parasitic event would have occurred between 180 and 425 million years ago (MYA), an event of relatively recent evolutionary origin considering the fact that Rickettsia and mitochondria evolved from a common alphaproteobacterial ancestor. This suggests that the symbiotic events of Rickettsia and mitochondria originated at different time points. Moreover, our model results predict that the ancestor of Wigglesworthia glossinidia brevipalpis, dated around the time of origin of its symbiotic association with the tsetse fly (50-100 MYA), was likely to have been an endosymbiont itself, thus supporting an earlier proposition that Wigglesworthia, which is currently a maternally inherited primary endosymbiont, evolved from a secondary endosymbiont.}, }
@article {pmid17107559, year = {2006}, author = {Davidov, Y and Huchon, D and Koval, SF and Jurkevitch, E}, title = {A new alpha-proteobacterial clade of Bdellovibrio-like predators: implications for the mitochondrial endosymbiotic theory.}, journal = {Environmental microbiology}, volume = {8}, number = {12}, pages = {2179-2188}, doi = {10.1111/j.1462-2920.2006.01101.x}, pmid = {17107559}, issn = {1462-2912}, mesh = {Alphaproteobacteria/classification/genetics/*isolation &amp; purification ; Bdellovibrio/classification/genetics/*isolation &amp; purification ; *Biological Evolution ; DNA, Mitochondrial/*physiology ; Mitochondria/*classification/physiology ; Molecular Sequence Data ; Phylogeny ; Prokaryotic Cells/cytology ; RNA, Ribosomal, 16S ; *Soil Microbiology ; Symbiosis/*physiology ; }, abstract = {Bdellovibrio-and-like organisms (BALOs) are peculiar, ubiquitous, small-sized, highly motile Gram-negative bacteria that are obligatory predators of other bacteria. Typically, these predators invade the periplasm of their prey where they grow and replicate. To date, BALOs constitute two highly diverse families affiliated with the delta-proteobacteria class. In this study, Micavibrio spp., a BALO lineage of epibiotic predators, were isolated from soil. These bacteria attach to digest and grow at the expense of other prokaryotes, much like other BALOs. Multiple phylogenetic analyses based on six genes revealed that they formed a deep branch within the alpha-proteobacteria, not affiliated with any of the alpha-proteobacterial orders. The presence of BALOs deep among the alpha-proteobacteria suggests that their peculiar mode of parasitism maybe an ancestral character in this proteobacterial class. The origin of the mitochondrion from an alpha-proteobacterium endosymbiont is strongly supported by molecular phylogenies. Accumulating data suggest that the endosymbiont's host was also a prokaryote. As prokaryotes are unable to phagocytose, the means by which the endosymbiont gained access into its host remains mysterious. We here propose a scenario based on the BALO feeding-mode to hypothesize a mechanism at play at the origin of the mitochondrial endosymbiosis.}, }
@article {pmid17105386, year = {2006}, author = {Bokori-Brown, M and Holt, IJ}, title = {Expression of algal nuclear ATP synthase subunit 6 in human cells results in protein targeting to mitochondria but no assembly into ATP synthase.}, journal = {Rejuvenation research}, volume = {9}, number = {4}, pages = {455-469}, doi = {10.1089/rej.2006.9.455}, pmid = {17105386}, issn = {1549-1684}, support = {MC_U105663140/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Algal Proteins/*physiology ; Animals ; Cell Culture Techniques ; Cells, Cultured ; *Chlamydomonas reinhardtii ; DNA, Mitochondrial/*physiology ; Eukaryotic Cells/*enzymology ; *Gene Transfer Techniques ; Humans ; Mitochondrial Proton-Translocating ATPases/*metabolism ; Protein Transport/physiology ; }, abstract = {Artificial transfer of mitochondrial genes to the nucleus has implications for the understanding of mitochondrial function, evolution, and human health. Therefore, we created nuclear compatible versions of human subunit a (A6) of ATP synthase, linked to a mitochondrial targeting signal. Expression and targeting of human nuclear subunit a were compared to subunit a of Chlamydomonas reinhardtii, which naturally occurs in the nucleus. Algal subunit a was targeted to mitochondria more efficiently than human nuclear subunit a variants. However, there was no evidence of improved mitochondrial function in cultured cells; on the contrary, long-term expression of algal subunit a was associated with poor survival and intolerance of growth conditions that demand heavy reliance on oxidative phosphorylation. Analysis of enriched mitochondrial membrane fractions on native gels revealed a high-molecular- weight complex containing FLAG-tagged subunit a; however, this complex did not colocalize with ATP synthase. Thus, there was no evidence of assembly of algal subunit a into holoenzyme, nor did human nuclear subunit a colocalize with ATP synthase holoenzyme. In conclusion, obstacles remain to functional expression of mitochondrial genes transferred to the nucleus.}, }
@article {pmid17101959, year = {2006}, author = {Ames, BN}, title = {Low micronutrient intake may accelerate the degenerative diseases of aging through allocation of scarce micronutrients by triage.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {47}, pages = {17589-17594}, pmid = {17101959}, issn = {0027-8424}, support = {R21 AT001918/AT/NCCIH NIH HHS/United States ; K05 AT001323/AT/NCCIH NIH HHS/United States ; K95 AT001323/AT/NCCIH NIH HHS/United States ; P60 MD00222/MD/NIMHD NIH HHS/United States ; P60 MD000222/MD/NIMHD NIH HHS/United States ; }, mesh = {Aging/*physiology ; Animals ; Cellular Senescence ; DNA Damage ; Diet ; Dietary Supplements ; Disease/*etiology ; Energy Intake ; Heme/metabolism ; Humans ; *Malnutrition ; Micronutrients/*metabolism ; Mitochondria/metabolism ; Neoplasms/physiopathology ; Nutrition Policy ; Nutritional Requirements ; Nutritional Status ; Trace Elements ; }, abstract = {Inadequate dietary intakes of vitamins and minerals are widespread, most likely due to excessive consumption of energy-rich, micronutrient-poor, refined food. Inadequate intakes may result in chronic metabolic disruption, including mitochondrial decay. Deficiencies in many micronutrients cause DNA damage, such as chromosome breaks, in cultured human cells or in vivo. Some of these deficiencies also cause mitochondrial decay with oxidant leakage and cellular aging and are associated with late onset diseases such as cancer. I propose DNA damage and late onset disease are consequences of a triage allocation response to micronutrient scarcity. Episodic shortages of micronutrients were common during evolution. Natural selection favors short-term survival at the expense of long-term health. I hypothesize that short-term survival was achieved by allocating scarce micronutrients by triage, in part through an adjustment of the binding affinity of proteins for required micronutrients. If this hypothesis is correct, micronutrient deficiencies that trigger the triage response would accelerate cancer, aging, and neural decay but would leave critical metabolic functions, such as ATP production, intact. Evidence that micronutrient malnutrition increases late onset diseases, such as cancer, is discussed. A multivitamin-mineral supplement is one low-cost way to ensure intake of the Recommended Dietary Allowance of micronutrients throughout life.}, }
@article {pmid17098851, year = {2007}, author = {Murcha, MW and Elhafez, D and Lister, R and Tonti-Filippini, J and Baumgartner, M and Philippar, K and Carrie, C and Mokranjac, D and Soll, J and Whelan, J}, title = {Characterization of the preprotein and amino acid transporter gene family in Arabidopsis.}, journal = {Plant physiology}, volume = {143}, number = {1}, pages = {199-212}, pmid = {17098851}, issn = {0032-0889}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/ultrastructure ; Arabidopsis Proteins/analysis/classification/*genetics ; Carrier Proteins/analysis/classification/*genetics ; Chloroplasts/metabolism ; Genetic Complementation Test ; Genome, Plant ; Membrane Transport Proteins/genetics ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Precursor Protein Import Complex Proteins ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; RNA, Messenger/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Sequence Alignment ; }, abstract = {Seventeen loci encode proteins of the preprotein and amino acid transporter family in Arabidopsis (Arabidopsis thaliana). Some of these genes have arisen from recent duplications and are not in annotated duplicated regions of the Arabidopsis genome. In comparison to a number of other eukaryotic organisms, this family of proteins has greatly expanded in plants, with 24 loci in rice (Oryza sativa). Most of the Arabidopsis and rice genes are orthologous, indicating expansion of this family before monocot and dicot divergence. In vitro protein uptake assays, in vivo green fluorescent protein tagging, and immunological analyses of selected proteins determined either mitochondrial or plastidic localization for 10 and six proteins, respectively. The protein encoded by At5g24650 is targeted to both mitochondria and chloroplasts and, to our knowledge, is the first membrane protein reported to be targeted to mitochondria and chloroplasts. Three genes encoded translocase of the inner mitochondrial membrane (TIM)17-like proteins, three TIM23-like proteins, and three outer envelope protein16-like proteins in Arabidopsis. The identity of Arabidopsis TIM22-like proteins is most likely a protein encoded by At3g10110/At1g18320, based on phylogenetic analysis, subcellular localization, and complementation of a yeast (Saccharomyces cerevisiae) mutant and coexpression analysis. The lack of a preprotein and amino acid transporter domain in some proteins, localization in mitochondria, plastids, or both, variation in gene structure, and the differences in expression profiles indicate that the function of this family has diverged in plants beyond roles in protein translocation.}, }
@article {pmid17095273, year = {2007}, author = {Bagnaresi, P and Rodrigues, MT and Garcia, CRS}, title = {Calcium signaling in lizard red blood cells.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {147}, number = {3}, pages = {779-787}, doi = {10.1016/j.cbpa.2006.09.015}, pmid = {17095273}, issn = {1095-6433}, mesh = {Animals ; *Calcium Signaling ; Erythrocytes/*metabolism ; Homeostasis ; Lizards/*metabolism ; Mitochondria/metabolism ; Receptors, Purinergic/metabolism ; }, abstract = {The ion calcium is a ubiquitous second messenger, present in all eukaryotic cells. It modulates a vast number of cellular events, such as cell division and differentiation, fertilization, cell volume, decodification of external stimuli. To process this variety of information, the cells display a number of calcium pools, which are capable of mobilization for signaling purposes. Here we review the calcium signaling on lizards red blood cells, an interesting model that has been receiving an increasing notice recently. These cells possess a complex machinery to regulate calcium, and display calcium responses to extracellular agonists. Interestingly, the pattern of calcium handling and response are divergent in different lizard families, which enforces the morphological data to their phylogenetic classification, and suggest the radiation of different calcium signaling models in lizards evolution.}, }
@article {pmid17092626, year = {2007}, author = {Lopez, L and Picardi, E and Quagliariello, C}, title = {RNA editing has been lost in the mitochondrial cox3 and rps13 mRNAs in Asparagales.}, journal = {Biochimie}, volume = {89}, number = {1}, pages = {159-167}, doi = {10.1016/j.biochi.2006.09.011}, pmid = {17092626}, issn = {0300-9084}, mesh = {Amino Acid Sequence ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Liliaceae/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics ; Polymerase Chain Reaction ; *RNA Editing ; RNA, Plant/*genetics ; Ribosomal Proteins/*genetics ; }, abstract = {RNA editing in plant mitochondria alters the RNA sequence by converting C-to-U or U-to-C at a specific site. We investigated the requirement for RNA editing in the complete genomic sequences of the gene encoding the cytochrome oxidase subunit III (cox3) and the ribosomal protein S13 (rps13) in 59 closely related species within the Asparagales and Liliales (monocots). To obtain a comprehensive picture of the degree of variation in editing we explored the non-synonymous RNA editing sites within the newly sequenced cox3 and rps13 genes by a comparative phylogenetic approach. RNA editing is predicted to occur in all the surveyed species, but to different extents. Zero to one non-synonymous editing site is inferred in the cox3 mRNA in species from Amaryllidaceae and Iridaceae. No RNA editing of rps13 mRNAs is required in Amaryllidaceae, because all respective genomic sequences resemble the edited version of the mRNAs of other analysed land plants. The observed absence of cox3 and rps13 RNA editing in Iridaceae and Amaryllidaceae and the striking RNA editing reduction of ccb2 in the latter family is likely generated by recombination and reverse transcription mediated events involving edited mitochondrial transcripts.}, }
@article {pmid17090413, year = {2006}, author = {de Grey, AD}, title = {Free radicals in aging: causal complexity and its biomedical implications.}, journal = {Free radical research}, volume = {40}, number = {12}, pages = {1244-1249}, doi = {10.1080/10715760600913176}, pmid = {17090413}, issn = {1071-5762}, mesh = {Aging/*physiology ; Animals ; DNA Damage ; DNA, Mitochondrial/metabolism ; Free Radicals/*metabolism ; Glycation End Products, Advanced/metabolism ; Humans ; Mitochondria/drug effects/metabolism ; }, abstract = {Superoxide generated adventitiously by the mitochondrial respiratory chain can give rise to much more reactive radicals, resulting in random oxidation of all classes of macromolecules. Harman's 1956 suggestion that this process might drive aging has been a leading strand of biogerontological thinking since the discovery of superoxide dismutase. However, it has become apparent that the many downstream consequences of free radical damage can also be caused by processes not involving oxidation. Moreover, free radicals have been put to use by evolution to such an extent that their wholesale elimination would certainly be fatal. This multiplicity of parallel pathways and side-effects illustrates why attempts to postpone aging by "cleaning up" metabolism will surely fail for the foreseeable future: we simply understand metabolism too poorly. This has led me to pursue the alternative, "repair and maintenance" approach that sidesteps our ignorance of metabolism and may be feasible relatively soon.}, }
@article {pmid17088246, year = {2007}, author = {Bredemeier, R and Schlegel, T and Ertel, F and Vojta, A and Borissenko, L and Bohnsack, MT and Groll, M and von Haeseler, A and Schleiff, E}, title = {Functional and phylogenetic properties of the pore-forming beta-barrel transporters of the Omp85 family.}, journal = {The Journal of biological chemistry}, volume = {282}, number = {3}, pages = {1882-1890}, doi = {10.1074/jbc.M609598200}, pmid = {17088246}, issn = {0021-9258}, mesh = {Animals ; Bacterial Outer Membrane Proteins/*chemistry/*physiology ; Cross-Linking Reagents/pharmacology ; Drosophila Proteins/chemistry ; Drosophila melanogaster ; Electrophysiology ; Escherichia coli Proteins/chemistry ; Evolution, Molecular ; *Gene Expression Regulation, Bacterial ; Models, Biological ; Nostoc/*metabolism ; Phylogeny ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA-Binding Proteins/chemistry ; }, abstract = {beta-Barrel-shaped channels of the Omp85 family are involved in the translocation or assembly of proteins of bacterial, mitochondrial, and plastidic outer membranes. We have compared these proteins to understand the evolutionary development of the translocators. We have demonstrated that the proteins from proteobacteria and mitochondria have a pore diameter that is at least five times smaller than found for the Omp85 in cyanobacteria and plastids. This finding can explain why Omp85 from cyanobacteria (but not the homologous protein from proteobacteria) was remodeled to become the protein translocation pore after endosymbiosis. Further, the pore-forming region of the Omp85 proteins is restricted to the C terminus. Based on a phylogenetic analysis we have shown that the pore-forming domain displays a different evolutionary relationship than the N-terminal domain. In line with this, the affinity of the N-terminal domain to the C-terminal region of the Omp85 from plastids and cyanobacteria differs, even though the N-terminal domain is involved in gating of the pore in both groups. We have further shown that the N-terminal domain of nOmp85 takes part in homo-oligomerization. Thereby, the differences in the phylogeny of the two domains are explained by different functional constraints acting on the regions. The pore-forming domain, however, is further divided into two functional regions, where the distal C terminus itself forms a dimeric pore. Based on functional and phylogenetic analysis, we suggest an evolutionary scenario that explains the origin of the contemporary translocon.}, }
@article {pmid17086397, year = {2007}, author = {Murayama, S and Handa, H}, title = {Genes for alkaline/neutral invertase in rice: alkaline/neutral invertases are located in plant mitochondria and also in plastids.}, journal = {Planta}, volume = {225}, number = {5}, pages = {1193-1203}, pmid = {17086397}, issn = {0032-0935}, mesh = {Arabidopsis/classification/genetics ; Cloning, Molecular ; DNA Primers ; DNA, Complementary/genetics ; DNA, Plant/genetics ; Hydrogen-Ion Concentration ; Mitochondria/*enzymology ; Oryza/classification/*enzymology/genetics ; Phylogeny ; Plant Proteins/genetics/metabolism ; Plastids/*enzymology ; Recombinant Fusion Proteins/metabolism ; beta-Fructofuranosidase/*genetics/metabolism ; }, abstract = {Two cDNA clones (OsNIN1 and OsNIN3) encoding an alkaline/neutral invertase localized in organelles were identified from rice. The deduced amino acid sequences of these cDNA clones showed high homology to other plant alkaline/neutral invertases. Semi-quantitative reverse transcription polymerase chain reaction revealed that the expression of OsNIN1 was constitutive and independent of organ difference, although its expression level was low. Analyses using five types of web software for the prediction of protein localization in the cell, Predotar, PSORT, Mitoprot, TargetP, and ChloroP, strongly supported the possibility that OsNIN1 is transported into the mitochondria and that OsNIN3 is transported into plastids. Transient expression of fusion proteins combining the amino terminal region of these two proteins with sGFP demonstrated that N-OsNIN1::GFP and N-OsNIN3::GFP fusion proteins were transported into the mitochondria and plastids, respectively. We expressed the OsNIN1 protein in vitro and revealed that the translated protein had an invertase activity. These results clearly indicate that some of alkaline/neutral invertases are located in plant organelles, mitochondria and plastids, and that they might have a novel physiological function in plant organelles.}, }
@article {pmid17085684, year = {2006}, author = {Stegemann, S and Bock, R}, title = {Experimental reconstruction of functional gene transfer from the tobacco plastid genome to the nucleus.}, journal = {The Plant cell}, volume = {18}, number = {11}, pages = {2869-2878}, pmid = {17085684}, issn = {1040-4651}, mesh = {Base Sequence ; Cell Nucleus/*metabolism ; Chromosome Segregation ; Chromosomes, Plant/metabolism ; Crosses, Genetic ; Drug Resistance ; Gene Rearrangement ; *Gene Transfer Techniques ; *Genes, Plant ; Genome, Plant/*genetics ; Molecular Sequence Data ; Plastids/*metabolism ; RNA 3' End Processing/genetics ; RNA, Messenger/genetics/metabolism ; Selection, Genetic ; Nicotiana/*genetics ; Transcriptional Activation ; }, abstract = {Eukaryotic cells arose through the uptake of free-living bacteria by endosymbiosis and their gradual conversion into organelles (plastids and mitochondria). Capture of the endosymbionts was followed by massive translocation of their genes to the genome of the host cell. How genes were transferred from the (prokaryotic) organellar genome to the (eukaryotic) nuclear genome and how the genes became functional in their new eukaryotic genetic environment is largely unknown. Here, we report the successful experimental reconstruction of functional gene transfer between an organelle and the nucleus, a process that normally occurs only on large evolutionary timescales. In consecutive genetic screens, we first transferred a chloroplast genome segment to the nucleus and then selected for gene activation in the nuclear genome. We show that DNA-mediated gene transfer can give rise to functional nuclear genes if followed by suitable rearrangements in the nuclear genome. Acquisition of gene function involves (1) transcriptional activation by capture of the promoter of an upstream nuclear gene and (2) utilization of AT-rich noncoding sequences downstream of the plastid gene as RNA cleavage and polyadenylation sites. Our results reveal the molecular mechanisms of how organellar DNA transferred to the nucleus gives rise to functional genes and reproduce in the laboratory a key process in the evolution of eukaryotic cells.}, }
@article {pmid17082386, year = {2006}, author = {Sassera, D and Beninati, T and Bandi, C and Bouman, EAP and Sacchi, L and Fabbi, M and Lo, N}, title = {'Candidatus Midichloria mitochondrii', an endosymbiont of the tick Ixodes ricinus with a unique intramitochondrial lifestyle.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {56}, number = {Pt 11}, pages = {2535-2540}, doi = {10.1099/ijs.0.64386-0}, pmid = {17082386}, issn = {1466-5026}, mesh = {Alphaproteobacteria/*classification/*isolation &amp; purification/physiology/ultrastructure ; Animals ; Cytoplasm/microbiology ; DNA Gyrase/genetics ; DNA, Bacterial/chemistry/genetics ; Female ; In Situ Hybridization ; Ixodes/*microbiology/ultrastructure ; Male ; Microscopy, Electron, Transmission ; Mitochondria/*microbiology ; Mitochondrial Membranes/microbiology ; Molecular Sequence Data ; Ovary/cytology/microbiology ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; *Symbiosis ; }, abstract = {An intracellular bacterium with the unique ability to enter mitochondria exists in the European vector of Lyme disease, the hard tick Ixodes ricinus. Previous phylogenetic analyses based on 16S rRNA gene sequences suggested that the bacterium formed a divergent lineage within the Rickettsiales (Alphaproteobacteria). Here, we present additional phylogenetic evidence, based on the gyrB gene sequence, that confirms the phylogenetic position of the bacterium. Based on these data, as well as electron microscopy (EM), in situ hybridization and other observations, we propose the name 'Candidatus Midichloria mitochondrii' for this bacterium. The symbiont appears to be ubiquitous in females of I. ricinus across the tick's distribution, while lower prevalence is observed in males (44%). Based on EM and in situ hybridization studies, the presence of 'Candidatus M. mitochondrii' in females appears to be restricted to ovarian cells. The bacterium was found to be localized both in the cytoplasm and in the intermembrane space of the mitochondria of ovarian cells. 'Candidatus M. mitochondrii' is the first bacterium to be identified that resides within animal mitochondria.}, }
@article {pmid17080938, year = {2006}, author = {Li, WY and Wong, FL and Tsai, SN and Phang, TH and Shao, G and Lam, HM}, title = {Tonoplast-located GmCLC1 and GmNHX1 from soybean enhance NaCl tolerance in transgenic bright yellow (BY)-2 cells.}, journal = {Plant, cell &amp; environment}, volume = {29}, number = {6}, pages = {1122-1137}, doi = {10.1111/j.1365-3040.2005.01487.x}, pmid = {17080938}, issn = {0140-7791}, mesh = {Amino Acid Sequence ; Bacterial Proteins/analysis/genetics ; Chloride Channels/chemistry/*genetics/physiology ; Cloning, Molecular ; Intracellular Membranes/drug effects/*metabolism/ultrastructure ; Luminescent Proteins/analysis/genetics ; Mitochondria/drug effects/metabolism/ultrastructure ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/*genetics/physiology ; Plants, Genetically Modified/drug effects/metabolism ; Polyethylene Glycols/pharmacology ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/analysis ; Sequence Alignment ; Sodium Chloride/*pharmacology ; Sodium-Hydrogen Exchangers/chemistry/*genetics/physiology ; Glycine max/drug effects/*genetics/ultrastructure ; Surface-Active Agents/pharmacology ; Nicotiana/genetics ; Vacuoles/drug effects/metabolism/ultrastructure ; }, abstract = {Genes encoding ion transporters that regulate ion homeostasis in soybean have not been carefully investigated. Using degenerate primers, we cloned a putative chloride channel gene (GmCLC1) and a putative Na+/H+ antiporter gene (GmNHX1) from soybean. Confocal microscopic studies using yellow fluorescent fusion proteins revealed that GmCLC1 and GmNHX1 were both localized on tonoplast. The expressions of GmCLC1 and GmNHX1 were both induced by NaCl or dehydration stress imposed by polyethylene glycol (PEG). Using mitochondrial integrity and cell death as the damage indicators, a clear alleviation under NaCl stress (but not PEG stress) was observed in both GmCLC1 and GmNHX1 transgenic cells. Using fluorescent dye staining and quenching, respectively, a higher concentration of chloride ion (Cl-) or sodium ion (Na+) was observed in isolated vacuoles in the cells of GmCLC1 and of GmNHX1 transgenic lines. Our result suggested that these vacuolar-located ion transporters function to sequester ions from cytoplasm into vacuole to reduce its toxic effects.}, }
@article {pmid17078501, year = {2006}, author = {Wojtczak, L}, title = {[Two faces of cytochrome c].}, journal = {Postepy biochemii}, volume = {52}, number = {2}, pages = {122-128}, pmid = {17078501}, issn = {0032-5422}, mesh = {Apoptosis/physiology ; Caspases/metabolism ; Cytochromes c/*history/*metabolism ; Evolution, Molecular ; History, 19th Century ; History, 20th Century ; Mitochondria/*metabolism ; Mitochondrial Membranes/metabolism ; Oxidation-Reduction ; Phylogeny ; bcl-2-Associated X Protein/metabolism ; }, abstract = {This is an outline of the history of research on cytochrome c. Cytochromes were first discovered by Charles A. MacMunn (1886) and re-discovered by David Keilin (1925) who also identified their function in cell respiration. The role of cytochrome c in the mitochondrial electron transport chain has been well established, thus pointing to a vital role of this haemoprotein in cell function. Yet, towards the end of the last century, a novel role of cytochrome c, namely as a signal molecule for the programmed cell death (apoptosis), has been described. Differences in aminoacid composition of cytochrome c have also been used as markers of biochemical evolution. The article ends with a short biographic note on David Keilin.}, }
@article {pmid17073796, year = {2006}, author = {Feyereisen, R}, title = {Evolution of insect P450.}, journal = {Biochemical Society transactions}, volume = {34}, number = {Pt 6}, pages = {1252-1255}, doi = {10.1042/BST0341252}, pmid = {17073796}, issn = {0300-5127}, mesh = {Amino Acid Sequence ; Animals ; Conserved Sequence ; Cytochrome P-450 Enzyme System/chemistry/*genetics ; Evolution, Molecular ; Genome ; Insecta/classification/*enzymology ; Mitochondria/enzymology ; Phylogeny ; }, abstract = {The first fully sequenced insect genomes were those of the fruitfly and the mosquito, both from the order Diptera. Now, with an increasing number and diversity of insect genomes becoming available, the diversity of insect P450 genes can be better appreciated and tentative ideas about the evolution of the CYP (cytochrome P450) superfamily in insects can be proposed. There are four large clades of insect P450 genes that existed before the divergence of the class Insecta and that are also represented by CYP families in vertebrates: the CYP2 clade, the CYP3 clade, the CYP4 clade and the mitochondrial P450 clade. P450s with known or suspected physiological functions are present in each of these clades and only a dozen genes appear to have orthologues or very close paralogues in each insect genome. P450 enzymes from each of these clades have been linked to insecticide resistance or to the metabolism of natural products and xenobiotics. In particular, insects appear to maintain a repertoire of mitochondrial P450 paralogues devoted to the response to environmental challenges.}, }
@article {pmid17072079, year = {2006}, author = {Zhang, W and Zhang, Z and Shen, F and Hou, R and Lv, X and Yue, B}, title = {Highly conserved D-loop-like nuclear mitochondrial sequences (Numts) in tiger (Panthera tigris).}, journal = {Journal of genetics}, volume = {85}, number = {2}, pages = {107-116}, pmid = {17072079}, issn = {0022-1333}, mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; Complementarity Determining Regions ; Conserved Sequence ; DNA, Mitochondrial/*chemistry ; Evolution, Molecular ; Genetic Variation ; Mitochondria/genetics ; Molecular Sequence Data ; NADH Dehydrogenase/genetics ; Phylogeny ; Sequence Alignment ; Tigers/classification/*genetics ; }, abstract = {Using oligonucleotide primers designed to match hypervariable segments I (HVS-1) of Panthera tigris mitochondrial DNA (mtDNA), we amplified two different PCR products (500 bp and 287 bp) in the tiger (Panthera tigris), but got only one PCR product (287 bp) in the leopard (Panthera pardus). Sequence analyses indicated that the sequence of 287 bp was a D-loop-like nuclear mitochondrial sequence (Numts), indicating a nuclear transfer that occurred approximately 4.8-17 million years ago in the tiger and 4.6-16 million years ago in the leopard. Although the mtDNA D-loop sequence has a rapid rate of evolution, the 287-bp Numts are highly conserved; they are nearly identical in tiger subspecies and only 1.742% different between tiger and leopard. Thus, such sequences represent molecular 'fossils' that can shed light on evolution of the mitochondrial genome and may be the most appropriate outgroup for phylogenetic analysis. This is also proved by comparing the phylogenetic trees reconstructed using the D-loop sequence of snow leopard and the 287-bp Numts as outgroup.}, }
@article {pmid17071643, year = {2006}, author = {Navrot, N and Collin, V and Gualberto, J and Gelhaye, E and Hirasawa, M and Rey, P and Knaff, DB and Issakidis, E and Jacquot, JP and Rouhier, N}, title = {Plant glutathione peroxidases are functional peroxiredoxins distributed in several subcellular compartments and regulated during biotic and abiotic stresses.}, journal = {Plant physiology}, volume = {142}, number = {4}, pages = {1364-1379}, pmid = {17071643}, issn = {0032-0889}, mesh = {Amino Acid Sequence ; Binding Sites ; Gene Expression Regulation, Plant ; Genome, Plant ; Glutathione Peroxidase/analysis/chemistry/*physiology ; Green Fluorescent Proteins/analysis ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidative Stress ; Peroxides/metabolism ; Phylogeny ; Plant Proteins/analysis/chemistry/*physiology ; Populus/chemistry/*enzymology/genetics ; Protein Isoforms/analysis/chemistry/physiology ; Recombinant Fusion Proteins/analysis ; Sequence Alignment ; Substrate Specificity ; Thioredoxins/metabolism ; }, abstract = {We provide here an exhaustive overview of the glutathione (GSH) peroxidase (Gpx) family of poplar (Populus trichocarpa). Although these proteins were initially defined as GSH dependent, in fact they use only reduced thioredoxin (Trx) for their regeneration and do not react with GSH or glutaredoxin, constituting a fifth class of peroxiredoxins. The two chloroplastic Gpxs display a marked selectivity toward their electron donors, being exclusively specific for Trxs of the y type for their reduction. In contrast, poplar Gpxs are much less specific with regard to their electron-accepting substrates, reducing hydrogen peroxide and more complex hydroperoxides equally well. Site-directed mutagenesis indicates that the catalytic mechanism and the Trx-mediated recycling process involve only two (cysteine [Cys]-107 and Cys-155) of the three conserved Cys, which form a disulfide bridge with an oxidation-redox midpoint potential of -295 mV. The reduction/formation of this disulfide is detected both by a shift on sodium dodecyl sulfate-polyacrylamide gel electrophoresis or by measuring the intrinsic tryptophan fluorescence of the protein. The six genes identified coding for Gpxs are expressed in various poplar organs, and two of them are localized in the chloroplast, with one colocalizing in mitochondria, suggesting a broad distribution of Gpxs in plant cells. The abundance of some Gpxs is modified in plants subjected to environmental constraints, generally increasing during fungal infection, water deficit, and metal stress, and decreasing during photooxidative stress, showing that Gpx proteins are involved in the response to both biotic and abiotic stress conditions.}, }
@article {pmid17070766, year = {2006}, author = {Searcy, DG}, title = {Rapid hydrogen sulfide consumption by Tetrahymena pyriformis and its implications for the origin of mitochondria.}, journal = {European journal of protistology}, volume = {42}, number = {3}, pages = {221-231}, doi = {10.1016/j.ejop.2006.06.001}, pmid = {17070766}, issn = {0932-4739}, mesh = {Animals ; Azides/pharmacology ; Biological Evolution ; Cell Fractionation ; Chemical Precipitation ; Hydrogen Cyanide/pharmacology ; Hydrogen Sulfide/administration &amp; dosage/*metabolism ; Mitochondria/drug effects/*metabolism ; Oxygen Consumption/drug effects ; Quinone Reductases/metabolism ; Silver Compounds/chemistry ; Silver Nitrate/administration &amp; dosage/chemistry ; Symbiosis ; Tetrahymena pyriformis/drug effects/*metabolism/ultrastructure ; }, abstract = {Although sulfide is typically regarded as toxic to eukaryotic cells, it is avidly consumed by Tetrahymena pyriformis. That was observed only when the sulfide concentration was kept below 1 microM. Previously concentrations that were too high had been tested. A new device (Sulfidostat) was used to measure sulfide consumption in steady-state concentrations as low as 10(-12)M. The technique was validated non-biologically by slowly injecting AgNO(3) into buffer and using Ag(2)S precipitation to mimic sulfide consumption, confirming that rates of sulfide consumption could be measured independently of sulfide concentrations. With T. pyriformis, sulfide consumption was 0.25 micromol (gprotein)(-1)s(-1) in 0.5 microM sulfide. Sulfide consumption required O(2) and was inhibited by HCN or by too much sulfide. When cells were separated into fractions, sulfide consumption occurred in the particulate (mitochondrial) fraction. Unexpectedly, the soluble cytosolic fraction slowly produced sulfide even when aerated. The observations are consistent with the conjecture that mitochondria evolved from sulfidotrophic symbionts in a sulfidogenic host cell.}, }
@article {pmid17061145, year = {2007}, author = {Canestrelli, D and Verardi, A and Nascetti, G}, title = {Genetic differentiation and history of populations of the Italian treefrog Hyla intermedia: lack of concordance between mitochondrial and nuclear markers.}, journal = {Genetica}, volume = {130}, number = {3}, pages = {241-255}, doi = {10.1007/s10709-006-9102-9}, pmid = {17061145}, issn = {0016-6707}, mesh = {Alleles ; Animals ; Anura/*genetics ; Cell Nucleus/*metabolism ; Cytochromes b/metabolism ; Cytoplasm/metabolism ; DNA, Mitochondrial/genetics ; Enzymes/chemistry ; Gene Frequency ; *Genetic Variation ; Geography ; Italy ; Mitochondria/*metabolism ; Models, Genetic ; Phylogeny ; }, abstract = {The genetic differentiation among 33 populations of the Italian treefrog, Hyla intermedia (Anura: Hylidae), was investigated using both biparentally (23 allozyme loci) and maternally (partial mitochondrial cytochrome b gene) inherited markers. Two main population groups were evidenced by both markers, located north and south of the northern Apennines. However, the pattern of differentiation between these two groups was much less pronounced at allozymes than at mtDNA, leading to gene flow estimates that were 25 times lower at mitochondrial than at nuclear level. Also, the mtDNA divergence between the two groups was particularly marked for two cospecific lineages of anuran amphibians (the P-distance being on average 9.04%), while their average genetic distance at allozymes was comparatively low (D (NEI) = 0.07). This contrasting pattern of nuclear versus mitochondrial genetic variation is discussed in the context of: (1) marker specific selection, (2) secondary contact and sex-biased gene flow and (3) ancestral polymorphism and colonization from north to south. Finally we emphasize how, for population genetic studies, the use of multiple markers having distinct evolutionary properties can help unravel the existence of more complex evolutionary histories.}, }
@article {pmid17058107, year = {2007}, author = {Luchetti, A and Trentini, M and Pampiglione, S and Fioravanti, ML and Mantovani, B}, title = {Genetic variability of Tunga penetrans (Siphonaptera, Tungidae) sand fleas across South America and Africa.}, journal = {Parasitology research}, volume = {100}, number = {3}, pages = {593-598}, pmid = {17058107}, issn = {0932-0113}, mesh = {Africa ; Animals ; Base Sequence ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Female ; *Genetic Variation ; Mitochondria/enzymology ; Phylogeny ; Siphonaptera/*genetics ; South America ; }, abstract = {Tunga penetrans is a widely distributed sand flea, infecting men and domestic animals. It originated in South America, but it is now also endemic of Sub-Saharan Africa due to a recent accidental introduction. Previous genetic analyses indicated a very limited variability in the Ecuadorian populations; on the other hand, samples from Madagascar resulted to be genetically isolated. To better examine the genetic variability of T. penetrans, a wider sampling was analysed for mitochondrial (cytochrome oxidase II) and nuclear (ribosomal internal transcribed spacer [ITS] 2) DNA sequences. The mitochondrial marker confirms the low genetic variability, with few haplotypes characterizing the majority of individuals from different populations. Haplotype distribution is in agreement with a recent colonization of Africa and with a rapid spreading across this continent. Moreover, a consistent gene flow between the Pacific and Atlantic South American populations emerges, possibly due to human and/or animal cross-Andean dispersal. On the other hand, the ITS2 marker depicts a sharply diverging pattern with samples collected in Ecuador unequivocally distinguished from the Brazilian and African ones. On the whole, taking into account also the molecular features of the marker used, data here presented are better interpreted in the light of a high dispersal ability of T. penetrans, probably reducing the phylogeographic signal.}, }
@article {pmid17054726, year = {2006}, author = {Hirano, Y and Ohniwa, RL and Wada, C and Yoshimura, SH and Takeyasu, K}, title = {Human small G proteins, ObgH1, and ObgH2, participate in the maintenance of mitochondria and nucleolar architectures.}, journal = {Genes to cells : devoted to molecular &amp; cellular mechanisms}, volume = {11}, number = {11}, pages = {1295-1304}, doi = {10.1111/j.1365-2443.2006.01017.x}, pmid = {17054726}, issn = {1356-9597}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Base Sequence ; Cell Nucleolus/*metabolism ; Conserved Sequence ; Escherichia coli/genetics/metabolism ; Escherichia coli Proteins/genetics/metabolism ; Evolution, Molecular ; GTP-Binding Proteins/genetics ; Genetic Complementation Test ; HeLa Cells ; Humans ; Mitochondria/*metabolism ; Molecular Sequence Data ; Monomeric GTP-Binding Proteins/antagonists &amp; inhibitors/genetics/*metabolism ; Phylogeny ; RNA Interference ; RNA, Small Interfering/genetics ; Sequence Homology, Amino Acid ; }, abstract = {The Obg subfamily protein is one of the P-loop small G proteins and is highly conserved in many organisms from bacteria to human. Two obg genes, obgH1 and obgH2, exist in the human genome. Both ObgH1 and ObgH2 showed similar GTPase activities (0.014 +/- 0.005 and 0.010 +/- 0.002/min for ObgH1 and ObgH2, respectively) to those of the bacterial Obg proteins and complemented the Obg function in Escherichia coli ribosome maturation, suggesting that the functions of Obg proteins are well conserved through evolution. Immunofluorescence microscopy of HeLa cells revealed that ObgH1 localizes in mitochondria, and ObgH2 in the dense fibrillar compartment region of the nucleolus. Knock-down of ObgH1 by RNAi induced mitochondria elongation, whereas knock-down of ObgH2 resulted in the disorganization of the nucleolar architecture. In conclusion, the two human Obg proteins have similar enzymatic activities that can complement bacterial Obg function, but show different cellular function(s) with different intracellular localizations.}, }
@article {pmid17054397, year = {2006}, author = {Perocchi, F and Jensen, LJ and Gagneur, J and Ahting, U and von Mering, C and Bork, P and Prokisch, H and Steinmetz, LM}, title = {Assessing systems properties of yeast mitochondria through an interaction map of the organelle.}, journal = {PLoS genetics}, volume = {2}, number = {10}, pages = {e170}, pmid = {17054397}, issn = {1553-7404}, mesh = {Disease Susceptibility ; Evolution, Molecular ; Gene Expression Regulation, Fungal ; Gene Regulatory Networks ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Mutation/genetics ; Phenotype ; Protein Binding ; Protein Interaction Mapping ; Protein Transport ; Saccharomyces cerevisiae/*cytology ; Saccharomyces cerevisiae Proteins/metabolism ; Sequence Homology ; }, abstract = {Mitochondria carry out specialized functions; compartmentalized, yet integrated into the metabolic and signaling processes of the cell. Although many mitochondrial proteins have been identified, understanding their functional interrelationships has been a challenge. Here we construct a comprehensive network of the mitochondrial system. We integrated genome-wide datasets to generate an accurate and inclusive mitochondrial parts list. Together with benchmarked measures of protein interactions, a network of mitochondria was constructed in their cellular context, including extra-mitochondrial proteins. This network also integrates data from different organisms to expand the known mitochondrial biology beyond the information in the existing databases. Our network brings together annotated and predicted functions into a single framework. This enabled, for the entire system, a survey of mutant phenotypes, gene regulation, evolution, and disease susceptibility. Furthermore, we experimentally validated the localization of several candidate proteins and derived novel functional contexts for hundreds of uncharacterized proteins. Our network thus advances the understanding of the mitochondrial system in yeast and identifies properties of genes underlying human mitochondrial disorders.}, }
@article {pmid17051209, year = {2006}, author = {James, TY and Kauff, F and Schoch, CL and Matheny, PB and Hofstetter, V and Cox, CJ and Celio, G and Gueidan, C and Fraker, E and Miadlikowska, J and Lumbsch, HT and Rauhut, A and Reeb, V and Arnold, AE and Amtoft, A and Stajich, JE and Hosaka, K and Sung, GH and Johnson, D and O'Rourke, B and Crockett, M and Binder, M and Curtis, JM and Slot, JC and Wang, Z and Wilson, AW and Schüssler, A and Longcore, JE and O'Donnell, K and Mozley-Standridge, S and Porter, D and Letcher, PM and Powell, MJ and Taylor, JW and White, MM and Griffith, GW and Davies, DR and Humber, RA and Morton, JB and Sugiyama, J and Rossman, AY and Rogers, JD and Pfister, DH and Hewitt, D and Hansen, K and Hambleton, S and Shoemaker, RA and Kohlmeyer, J and Volkmann-Kohlmeyer, B and Spotts, RA and Serdani, M and Crous, PW and Hughes, KW and Matsuura, K and Langer, E and Langer, G and Untereiner, WA and Lücking, R and Büdel, B and Geiser, DM and Aptroot, A and Diederich, P and Schmitt, I and Schultz, M and Yahr, R and Hibbett, DS and Lutzoni, F and McLaughlin, DJ and Spatafora, JW and Vilgalys, R}, title = {Reconstructing the early evolution of Fungi using a six-gene phylogeny.}, journal = {Nature}, volume = {443}, number = {7113}, pages = {818-822}, doi = {10.1038/nature05110}, pmid = {17051209}, issn = {1476-4687}, mesh = {Chytridiomycota/classification/genetics ; *Evolution, Molecular ; Fungi/classification/*genetics ; Genes, Fungal/*genetics ; Microsporidia/classification/genetics ; *Phylogeny ; }, abstract = {The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.}, }
@article {pmid17046345, year = {2005}, author = {Kutschera, U and Niklas, KJ}, title = {Endosymbiosis, cell evolution, and speciation.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {124}, number = {1}, pages = {1-24}, pmid = {17046345}, issn = {1431-7613}, mesh = {Animals ; *Biological Evolution ; Endocytosis/*physiology ; History, 19th Century ; History, 20th Century ; History, 21st Century ; *Models, Biological ; Organelles/*physiology ; Species Specificity ; Symbiosis/*physiology ; }, abstract = {In 1905, the Russian biologist C. Mereschkowsky postulated that plastids (e.g., chloroplasts) are the evolutionary descendants of endosymbiotic cyanobacteria-like organisms. In 1927, I. Wallin explicitly postulated that mitochondria likewise evolved from once free-living bacteria. Here, we summarize the history of these endosymbiotic concepts to their modern-day derivative, the "serial endosymbiosis theory", which collectively expound on the origin of eukaryotic cell organelles (plastids, mitochondria) and subsequent endosymbiotic events. Additionally, we review recent hypotheses about the origin of the nucleus. Model systems for the study of "endosymbiosis in action" are also described, and the hypothesis that symbiogenesis may contribute to the generation of new species is critically assessed with special reference to the secondary and tertiary endosymbiosis (macroevolution) of unicellular eukaryotic algae.}, }
@article {pmid17043242, year = {2006}, author = {Burri, L and Williams, BA and Bursac, D and Lithgow, T and Keeling, PJ}, title = {Microsporidian mitosomes retain elements of the general mitochondrial targeting system.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {43}, pages = {15916-15920}, pmid = {17043242}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Fungal Proteins/chemistry/metabolism ; Glycerolphosphate Dehydrogenase/genetics/metabolism ; Intracellular Membranes/*metabolism ; Microsporidia/*metabolism ; Mitochondria/chemistry/*metabolism ; Molecular Sequence Data ; Signal Transduction ; }, abstract = {Microsporidia are intracellular parasites that infect a variety of animals, including humans. As highly specialized parasites, they are characterized by a number of unusual adaptations, many of which are manifested as extreme reduction at the molecular, biochemical, and cellular levels. One interesting aspect of reduction is the mitochondrion. Microsporidia were long considered to be amitochondriate, but recently a tiny mitochondrion-derived organelle called the mitosome was detected. The molecular function of this organelle remains poorly understood. The mitosome has no genome, so it must import all its proteins from the cytosol. In other fungi, the mitochondrial protein import machinery consists of a network series of heterooligomeric translocases and peptidases, but in microsporidia, only a few subunits of some of these complexes have been identified to date. Here, we look at targeting sequences of the microsporidian mitosomal import system and show that mitosomes do in some cases still use N-terminal and internal targeting sequences that are recognizable by import systems of mitochondria in yeast. Furthermore, we have examined the function of the inner membrane peptidase processing enzyme and demonstrate that mitosomal substrates of this enzyme are processed to mature proteins in one species with a simplified processing complex, Antonospora locustae. However, in Encephalitozoon cuniculi, the processing complex is lost altogether, and the preprotein substrate functions with the targeting leader still attached. This report provides direct evidence for presequencing processing in mitosomes and also shows how a complex molecular system has continued to degenerate throughout the evolution of microsporidia.}, }
@article {pmid17035181, year = {2006}, author = {Wang, HJ and Zhang, ZM and Liu, ZL and Xiong, GM}, title = {[A molecular phylogeny of Shennongjia white bear based on mitochondrial cytochrome b gene sequence].}, journal = {Yi chuan = Hereditas}, volume = {28}, number = {10}, pages = {1237-1241}, doi = {10.1360/yc-006-1237}, pmid = {17035181}, issn = {0253-9772}, mesh = {Animals ; Base Sequence ; China ; Cytochromes b/*genetics ; Databases, Genetic ; Mitochondria/*genetics ; Mutation ; *Phylogeny ; Ursidae/*classification/*genetics ; }, abstract = {The phylogenetic relationship of Shennongjia white bear has been an open question. Total DNA was extracted and sequenced from hair and feces of Shennongjia white bear. Based on the partial Cyt b gene sequence obtained from the samples, the authors aligned them using the Clustal W software program. The MEGA software was used to analyze the divergences and base substitutions of the partial Cyt b gene among the 11 species: Shennongjia white bear, Selenarctos thibetanus, Euarctos americanus, Helarctos malayanus, Ursus arctos, Thalarctos maritimus, Melursus ursinus, Procyon lotor, Ailuropoda melanoleuca, Ailurus fulgens and Tremarctos ornatus. The phylogenetic trees constructed by multiple methods (NJ and MP) supported nearly the same topology. Our molecular results show that the sequence divergence between Shennongjia white bear and Asiatic black bear (Selenarctos thibetanus) is lower than that between other species.}, }
@article {pmid17032475, year = {2007}, author = {Shao, R and Barker, SC}, title = {Mitochondrial genomes of parasitic arthropods: implications for studies of population genetics and evolution.}, journal = {Parasitology}, volume = {134}, number = {Pt 2}, pages = {153-167}, doi = {10.1017/S0031182006001429}, pmid = {17032475}, issn = {0031-1820}, mesh = {Animals ; Arthropods/classification/*genetics ; Base Sequence ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genetics, Population/methods ; *Genome ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Over 39000 species of arthropods parasitize humans, domestic animals and wildlife. Despite their medical, veterinary and economic importance, most aspects of the population genetics and evolution of the vast majority of parasitic arthropods are poorly understood. Mitochondrial genomes are a rich source of markers for studies of population genetics and evolution. These markers include (1) nucleotide sequences of each of the 37 mitochondrial genes and non-coding regions; (2) concatenated nucleotide sequences of 2 or more genes; and (3) genomic features, such as gene duplications, gene rearrangements, and changes in gene content and secondary structures of RNAs. To date, the mitochondrial genomes of over 700 species of multi-cellular animals have been sequenced entirely, however, only 24 of these species are parasitic arthropods. Of the mitochondrial genome markers, only the nucleotide sequences of 4 mitochondrial genes, cox1, cob, rrnS and rrnL, have been well explored in population genetic and evolutionary studies of parasitic arthropods whereas the sequences of the other 33 genes, and various genomic features have not. We review current knowledge of the mitochondrial genomes of parasitic arthropods, summarize applications of mitochondrial genes and genomic features in population genetic and evolutionary studies, and highlight prospects for future research.}, }
@article {pmid17031549, year = {2006}, author = {Pasdois, P and Beauvoit, B and Tariosse, L and Vinassa, B and Bonoron-Adèle, S and Santos, PD}, title = {MitoK(ATP)-dependent changes in mitochondrial volume and in complex II activity during ischemic and pharmacological preconditioning of Langendorff-perfused rat heart.}, journal = {Journal of bioenergetics and biomembranes}, volume = {38}, number = {2}, pages = {101-112}, pmid = {17031549}, issn = {0145-479X}, mesh = {Adenosine Diphosphate/metabolism ; Animals ; Antihypertensive Agents/pharmacology ; Cell Respiration/physiology ; Decanoic Acids/pharmacology ; Diazoxide/pharmacology ; Electron Transport Complex II/*physiology ; Hydroxy Acids/pharmacology ; In Vitro Techniques ; *Ischemic Preconditioning, Myocardial ; Male ; Mitochondria, Heart/drug effects/*physiology ; *Mitochondrial Size ; Myocardial Ischemia/*metabolism ; Myocardial Reperfusion ; Myofibrils/drug effects/physiology ; Potassium Channels/*metabolism ; Rats ; Rats, Sprague-Dawley ; Succinic Acid/metabolism ; }, abstract = {It has been proposed that activation of the mitochondrial ATP-sensitive potassium channel (mitoK(ATP)) is part of signaling pathways triggering the cardioprotection afforded by ischemic preconditioning of the heart. This work was to analyze the mitochondrial function profile of Langendorff-perfused rat hearts during the different phases of various ischemia-reperfusion protocols. Specifically, skinned fibers of ischemic preconditioned hearts exhibit a decline in the succinate-supported respiration and complex II activity during ischemia, followed by a recovery during reperfusion. Meanwhile, the apparent affinity of respiration for ADP (which reflects the matrix volume expansion) is increased during preconditioning stimulus and, to a larger extent, during prolonged ischemia. This evolution pattern is mimicked by diazoxide and abolished by 5-hydroxydecanoate. It is concluded that opening the mitoK(ATP) channel mediates the preservation of mitochondrial structure-function via a mitochondrial matrix shrinkage and a reversible inactivation of complex II during prolonged ischemic insult.}, }
@article {pmid17030538, year = {2007}, author = {Lunn, JE}, title = {Compartmentation in plant metabolism.}, journal = {Journal of experimental botany}, volume = {58}, number = {1}, pages = {35-47}, doi = {10.1093/jxb/erl134}, pmid = {17030538}, issn = {0022-0957}, mesh = {Arabidopsis/cytology/metabolism ; Cell Compartmentation ; Chloroplasts/metabolism ; Coenzymes/biosynthesis ; Cytosol/metabolism ; Gene Expression Regulation, Plant ; Gluconeogenesis ; Glycolysis ; *Metabolic Networks and Pathways ; Photosynthesis ; *Plant Cells ; Plant Proteins/chemistry ; Plants/*metabolism ; Proteome/analysis ; Terpenes/metabolism ; Vitamins/biosynthesis ; }, abstract = {Cell fractionation and immunohistochemical studies in the last 40 years have revealed the extensive compartmentation of plant metabolism. In recent years, new protein mass spectrometry and fluorescent-protein tagging technologies have accelerated the flow of information, especially for Arabidopsis thaliana, but the intracellular locations of the majority of proteins in the plant proteome are still not known. Prediction programs that search for targeting information within protein sequences can be applied to whole proteomes, but predictions from different programs often do not agree with each other or, indeed, with experimentally determined results. The compartmentation of most pathways of primary metabolism is generally covered in plant physiology textbooks, so the focus here is mainly on newly discovered metabolic pathways in plants or pathways that have recently been revised. Ultimately, all of the pathways of plant metabolism are interconnected, and a major challenge facing plant biochemists is to understand the regulation and control of metabolic networks. One of the best-characterized networks links sucrose synthesis in the cytosol with photosynthetic CO(2) fixation and starch synthesis in the chloroplasts. One of the key features of this network is how the transport of pathway intermediates and signal metabolites across the chloroplast envelope conveys information between the two compartments, influencing the regulation of several enzymes to co-ordinate fluxes through the different pathways. It is widely accepted that chloroplasts and mitochondria originated from prokaryotic endosymbionts, and that new transporters and regulatory networks evolved to integrate metabolism in these organelles with the rest of the cell. Curiously, the present-day locations of many metabolic pathways within the cell often do not reflect their evolutionary origin, and there is evidence of extensive shuffling of enzymes and whole pathways between compartments during the evolution of plants.}, }
@article {pmid17029566, year = {2007}, author = {Orrenius, S and Gogvadze, V and Zhivotovsky, B}, title = {Mitochondrial oxidative stress: implications for cell death.}, journal = {Annual review of pharmacology and toxicology}, volume = {47}, number = {}, pages = {143-183}, doi = {10.1146/annurev.pharmtox.47.120505.105122}, pmid = {17029566}, issn = {0362-1642}, mesh = {Apoptosis/*physiology ; Cardiolipins/physiology ; Mitochondria/*physiology ; Necrosis ; Oxidative Stress/*physiology ; *Reactive Oxygen Species ; }, abstract = {In addition to the established role of the mitochondria in energy metabolism, regulation of cell death has emerged as a second major function of these organelles. This seems to be intimately linked to their generation of reactive oxygen species (ROS), which have been implicated in mtDNA mutations, aging, and cell death. Mitochondrial regulation of apoptosis occurs by mechanisms, which have been conserved through evolution. Thus, many lethal agents target the mitochondria and cause release of cytochrome c and other pro-apoptotic proteins into the cytoplasm. Cytochrome c release is initiated by the dissociation of the hemoprotein from its binding to the inner mitochondrial membrane. Oxidation of cardiolipin reduces cytochrome c binding and increases the level of soluble cytochrome c in the intermembrane space. Subsequent release of the hemoprotein occurs by pore formation mediated by pro-apoptotic Bcl-2 family proteins, or by Ca(2+) and ROS-triggered mitochondrial permeability transition, although the latter pathway might be more closely associated with necrosis. Taken together, these findings have placed the mitochondria in the focus of current cell death research.}, }
@article {pmid17028054, year = {2007}, author = {Delph, LF and Touzet, P and Bailey, MF}, title = {Merging theory and mechanism in studies of gynodioecy.}, journal = {Trends in ecology &amp; evolution}, volume = {22}, number = {1}, pages = {17-24}, doi = {10.1016/j.tree.2006.09.013}, pmid = {17028054}, issn = {0169-5347}, mesh = {Alleles ; Biological Evolution ; Crops, Agricultural/genetics ; Genes, Mitochondrial ; Genes, Plant ; Models, Biological ; Plants/*genetics ; Polymorphism, Genetic ; *Sex Determination Processes ; Suppression, Genetic ; }, abstract = {In gynodioecious species, females and hermaphrodites coexist and the genetics of sex determination is usually nuclear cytoplasmic. Maintaining nuclear-cytoplasmic gynodioecy requires polymorphism for the feminizing genes (contained in the mitochondria) and the genes that restore male fertility (contained in the nucleus). This complex polymorphism depends, in part, on there being negative pleiotropic effects (i.e. costs) of the nuclear restorer alleles. Here, we combine information from theoretical studies and studies on the molecular action of restorer alleles in crops to interpret the probable costs of such alleles, and suggest how various aspects of the theoretical models could be tested. In doing so, we highlight how crops can be used to address evolutionary questions about the maintenance of nuclear-cytoplasmic gynodioecy.}, }
@article {pmid17024226, year = {2007}, author = {Olichon, A and Elachouri, G and Baricault, L and Delettre, C and Belenguer, P and Lenaers, G}, title = {OPA1 alternate splicing uncouples an evolutionary conserved function in mitochondrial fusion from a vertebrate restricted function in apoptosis.}, journal = {Cell death and differentiation}, volume = {14}, number = {4}, pages = {682-692}, doi = {10.1038/sj.cdd.4402048}, pmid = {17024226}, issn = {1350-9047}, mesh = {Alternative Splicing/*genetics ; Animals ; Apoptosis/genetics/*physiology ; Evolution, Molecular ; GTP Phosphohydrolases/*chemistry/*metabolism ; HeLa Cells/*metabolism ; Humans ; Microscopy, Fluorescence ; Mitochondrial Membranes/physiology ; Mitochondrial Proteins/*metabolism ; Protein Interaction Mapping ; Protein Isoforms/genetics ; Sequence Analysis, Protein ; Tumor Cells, Cultured ; Yeasts/*metabolism ; }, abstract = {In most eucaryote cells, release of apoptotic proteins from mitochondria involves fission of the mitochondrial network and drastic remodelling of the cristae structures. The intramitochondrial dynamin OPA1, as a potential central actor of these processes, exists as eight isoforms resulting from the alternate splicing combinations of exons (Ex) 4, 4b and 5b, which functions remain undetermined. Here, we show that Ex4 that is conserved throughout evolution confers functions to OPA1 involved in the maintenance of the DeltaPsi(m) and in the fusion of the mitochondrial network. Conversely, Ex4b and Ex5b, which are vertebrate specific, define a function involved in cytochrome c release, an apoptotic process also restricted to vertebrates. The drastic changes of OPA1 variant abundance in different organs suggest that nuclear splicing can control mitochondrial dynamic fate and susceptibility to apoptosis and pathologies.}, }
@article {pmid17021930, year = {2006}, author = {Ruiz-González, MX and Marín, I}, title = {Proteasome-related HslU and HslV genes typical of eubacteria are widespread in eukaryotes.}, journal = {Journal of molecular evolution}, volume = {63}, number = {4}, pages = {504-512}, pmid = {17021930}, issn = {0022-2844}, mesh = {ATP-Dependent Proteases/chemistry/genetics ; Amino Acid Sequence ; Bacteria/*genetics ; Cell Lineage ; Escherichia coli Proteins/chemistry/genetics ; Eukaryotic Cells/*metabolism ; Genes, Bacterial/*genetics ; Mitochondria ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Proteasome Endopeptidase Complex/*genetics ; Sequence Alignment ; }, abstract = {Many eubacteria contain an ATP-dependent protease complex, which is built by multiple copies of the HslV and HslU proteins and is therefore called HslVU. HslU proteins are AAA + ATPases, while HslV proteins are proteases that show highly significant similarity to beta subunits of proteasomes. Therefore, the HslVU complex has been envisaged as a precursor or ancestral type of proteasome. Here we show that species of most of the main eukaryotic lineages have HslU and HslV genes very similar to those found in proteobacteria. We have detected them in amoebozoa, plantae, chromoalveolata, rhizaria, and excavata species. Phylogenetic analyses suggest that these genes have been obtained by endosymbiosis from the proteobacterial ancestor that gave rise to eukaryotic mitochondria. The products encoded by these eukaryotic genes adopt, according to modeling based on the known crystal structures of prokaryotic HslU and HslV proteins, conformations that are compatible with their being fully active, suggesting that functional HslVU complexes may be present in many eukaryotic species.}, }
@article {pmid17018628, year = {2006}, author = {Ansiaux, R and Baudelet, C and Jordan, BF and Crokart, N and Martinive, P and DeWever, J and Grégoire, V and Feron, O and Gallez, B}, title = {Mechanism of reoxygenation after antiangiogenic therapy using SU5416 and its importance for guiding combined antitumor therapy.}, journal = {Cancer research}, volume = {66}, number = {19}, pages = {9698-9704}, doi = {10.1158/0008-5472.CAN-06-1854}, pmid = {17018628}, issn = {1538-7445}, mesh = {Angiogenesis Inhibitors/pharmacology/*therapeutic use ; Animals ; Antineoplastic Combined Chemotherapy Protocols/*therapeutic use ; Cell Hypoxia/*drug effects ; Combined Modality Therapy ; Cyclophosphamide/administration &amp; dosage ; Drug Resistance, Neoplasm/drug effects ; Drug Screening Assays, Antitumor ; Fibrosarcoma/blood supply/*drug therapy/metabolism/radiotherapy ; Indoles/administration &amp; dosage/pharmacology/*therapeutic use ; Liver Neoplasms, Experimental/blood supply/*drug therapy/metabolism/radiotherapy ; Mice ; Mice, Inbred C3H ; Mitochondria/drug effects/metabolism ; Oxygen/*metabolism ; Oxygen Consumption/drug effects ; Pyrroles/administration &amp; dosage/pharmacology/*therapeutic use ; Radiation-Sensitizing Agents/pharmacology/therapeutic use ; }, abstract = {Emerging preclinical studies support the concept of a transient "normalization" of tumor vasculature during the early stage of antiangiogenic treatment, with possible beneficial effects on associated radiotherapy or chemotherapy. One key issue in this area of research is to determine whether this feature is common to all antiangiogenic drugs and whether the phenomenon occurs in all types of tumors. In the present study, we characterized the evolution of the tumor oxygenation (in transplantable liver tumor and FSAII tumor models) after administration of SU5416, an antagonist of the vascular endothelial growth factor receptor. SU5416 induced an early increase in tumor oxygenation [measured by electronic paramagnetic resonance (EPR)], which did not correlate with remodeling of the tumor vasculature (assessed by CD31 labeling using immunohistochemistry) or with tumor perfusion (measured by dynamic contrast enhanced-magnetic resonance imaging). Inhibition of mitochondrial respiration (measured by EPR) was responsible for this early reoxygenation. Consistent with these unique findings in the tumor microenvironment, we found that SU5416 potentiated tumor response to radiotherapy but not to chemotherapy. In addition to the fact that the characterization of the tumor oxygenation is essential to enable correct application of combined therapies, our results show that the long-term inhibition of oxygen consumption is a potential novel target in this class of compounds.}, }
@article {pmid17012285, year = {2006}, author = {Arita, M and Suematsu, T and Osanai, A and Inaba, T and Kamiya, H and Kita, K and Sisido, M and Watanabe, Y and Ohtsuki, T}, title = {An evolutionary 'intermediate state' of mitochondrial translation systems found in Trichinella species of parasitic nematodes: co-evolution of tRNA and EF-Tu.}, journal = {Nucleic acids research}, volume = {34}, number = {18}, pages = {5291-5299}, pmid = {17012285}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Caenorhabditis elegans Proteins/chemistry ; *Evolution, Molecular ; Helminth Proteins/chemistry/metabolism ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Peptide Elongation Factor Tu/*chemistry/metabolism ; *Protein Biosynthesis ; RNA/chemistry/metabolism ; RNA, Helminth/chemistry/metabolism ; RNA, Mitochondrial ; RNA, Transfer/*chemistry/metabolism ; RNA, Transfer, Ala/chemistry/metabolism ; RNA, Transfer, Ser/chemistry/metabolism ; RNA, Transfer, Trp/chemistry/metabolism ; Sequence Alignment ; Trichinella/*genetics ; }, abstract = {EF-Tu delivers aminoacyl-tRNAs to ribosomes in the translation system. However, unusual truncations found in some animal mitochondrial tRNAs seem to prevent recognition by a canonical EF-Tu. We showed previously that the chromadorean nematode has two distinct EF-Tus, one of which (EF-Tu1) binds only to T-armless aminoacyl-tRNAs and the other (EF-Tu2) binds to D-armless Ser-tRNAs. Neither of the EF-Tus can bind to canonical cloverleaf tRNAs. In this study, by analyzing the translation system of enoplean nematode Trichinella species, we address how EF-Tus and tRNAs have evolved from the canonical structures toward those of the chromadorean translation system. Trichinella mitochondria possess three types of tRNAs: cloverleaf tRNAs, which do not exist in chromadorean nematode mitochondria; T-armless tRNAs; and D-armless tRNAs. We found two mitochondrial EF-Tu species, EF-Tu1 and EF-Tu2, in Trichinella britovi. T.britovi EF-Tu2 could bind to only D-armless Ser-tRNA, as Caenorhabditis elegans EF-Tu2 does. In contrast to the case of C.elegans EF-Tu1, however, T.britovi EF-Tu1 bound to all three types of tRNA present in Trichinella mitochondria. These results suggest that Trichinella mitochondrial translation system, and particularly the tRNA-binding specificity of EF-Tu1, could be an intermediate state between the canonical system and the chromadorean nematode mitochondrial system.}, }
@article {pmid17011109, year = {2006}, author = {Diffels, JF and Seret, ML and Goffeau, A and Baret, PV}, title = {Heavy metal transporters in Hemiascomycete yeasts.}, journal = {Biochimie}, volume = {88}, number = {11}, pages = {1639-1649}, doi = {10.1016/j.biochi.2006.08.008}, pmid = {17011109}, issn = {0300-9084}, mesh = {Ascomycota/classification/*metabolism ; Biological Transport ; Cell Membrane/metabolism ; Metals, Heavy/*pharmacokinetics ; Phylogeny ; Yeasts/*metabolism ; }, abstract = {We have compiled all known heavy metal transporters of the yeast Saccharomyces cerevisiae and identified their orthologs in four other species spanning the entire Hemiascomycete phylum. The 213 transporters belong to 27 distinct phylogenetic families distributed within the three classes: channels, secondary porters (permeases) and transport ATPases. They are present in all cellular membranes: plasma membranes, vacuoles, mitochondria, endoplasmic reticulum, nucleus, Golgi and various cytoplasmic vesicles. The major physiological heavy metals transported are: iron, manganese, zinc, copper, arsenite and cadmium. The major subfamilies that comprise the highest number of transporters are Siderophore-Iron Transporters (SIT) and CT2 (conjugated ABC transporters). They transport heavy metals (iron or cadmium, respectively) conjugated to organic chelators such as siderophores or glutathione. Both subfamilies are considerably amplified in the yeast Yarrowia lipolytica. The pattern of expansion and restriction of the subfamilies during the evolution of the different species is highly variable. The phylogenetic trees of the major transporters subfamilies distinguish homogenous clusters of transporters suggesting that possible different physiological or mechanistic functions evolved independently. We also validated the use of the Hemiascomycetes heavy metal transporters for identification of orthologs transporters in the pathogenic Basidiomycetes Cryptococcus neoformans.}, }
@article {pmid16990491, year = {2007}, author = {Nishimoto, G and Sasaki, G and Yaoita, E and Nameta, M and Li, H and Furuse, K and Fujinaka, H and Yoshida, Y and Mitsudome, A and Yamamoto, T}, title = {Molecular characterization of water-selective AQP (EbAQP4) in hagfish: insight into ancestral origin of AQP4.}, journal = {American journal of physiology. Regulatory, integrative and comparative physiology}, volume = {292}, number = {1}, pages = {R644-51}, doi = {10.1152/ajpregu.00362.2006}, pmid = {16990491}, issn = {0363-6119}, mesh = {Amino Acid Sequence ; Animals ; Biological Transport, Active/physiology ; Blotting, Western ; Cell Membrane/metabolism ; DNA, Complementary/biosynthesis/genetics ; Freeze Fracturing ; Gills/metabolism ; Hagfishes/*metabolism ; Immunohistochemistry ; Mercury/pharmacology ; Microscopy, Electron ; Molecular Sequence Data ; Multigene Family/genetics ; Oocytes/metabolism ; Permeability ; Phylogeny ; RNA/biosynthesis/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Water/metabolism ; Xenopus ; }, abstract = {Hagfish (Eptatretus burgeri) are agnathous and are the earliest vertebrates still in existence. Pavement cells adjacent to the mitochondria-rich cells show orthogonal arrays of particles (OAPs) in the gill of hagfish, a known ultrastructural morphology of aquaporin (AQP) in mammalian freeze-replica studies, suggesting that an AQP homolog exists in pavement cells. We therefore cloned water channels from hagfish gill and examined their molecular characteristics. The cloned AQP [E. burgeri AQP4 (EbAQP4)] encodes 288 amino acids, including two NPA motifs and six transmembrane regions. The deduced amino acid sequence of EbAQP4 showed high homology to mammalian and avian AQP4 (rat, 44%; quail, 43%) and clustered with AQP4 subsets by the molecular phylogenetic tree. The osmotic water permeability of Xenopus oocytes injected with EbAQP4 cRNA increased eightfold compared with water-injected controls and was not reversibly inhibited by 0.3 mM HgCl(2). EbAQP4 mRNA expression in the gill was demonstrated by the RNase protection assay; antibody raised against the COOH terminus of EbAQP4 also detected (by Western blot analysis) a major approximately 31-kDa band in the gill. Immunohistochemistry and immunoelectron microscopy showed EbAQP4 localized along the basolateral membranes of gill pavement cells. In freeze-replica studies, OAPs were detected on the protoplasmic face of the split membrane comprising particles 5-6 nm long on the basolateral side of the pavement cells. These observations suggest that EbAQP4 is an ancestral water channel of mammalian AQP4 and plays a role in basolateral water transport in the gill pavement cells.}, }
@article {pmid16989663, year = {2006}, author = {Yue, GH and Liew, WC and Orban, L}, title = {The complete mitochondrial genome of a basal teleost, the Asian arowana (Scleropages formosus, Osteoglossidae).}, journal = {BMC genomics}, volume = {7}, number = {}, pages = {242}, pmid = {16989663}, issn = {1471-2164}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry ; Fishes/classification/*genetics ; *Genes, Mitochondrial ; Genes, rRNA ; *Genome ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Transfer/genetics ; Regulatory Sequences, Nucleic Acid ; Repetitive Sequences, Nucleic Acid ; }, abstract = {BACKGROUND: Mitochondrial DNA-derived sequences have become popular markers for evolutionary studies, as their comparison may yield significant insights into the evolution of both the organisms and their genomes. From the more than 24,000 teleost species, only 254 complete mtDNA sequences are available (GenBank status on 06 Sep 2006). In this paper, we report the complete mitochondrial genome sequence of Asian arowana, a basal bonytongue fish species, which belongs to the order of Osteoglossiformes.<br><br>RESULTS: The complete mitochondrial genomic sequence (mtDNA) of Asian arowana (Scleropages formosus) was determined by using shotgun sequencing method. The length of Asian arowana mtDNA is ca. 16,650 bp (its variation is due to polymorphic repeats in the control region), containing 13 protein-coding genes, 22 tRNA and 2 rRNA genes. Twelve of the thirteen protein coding genes were found to be encoded by the heavy strand in the order typically observed for vertebrate mitochondrial genomes, whereas only nad6 was located on the light strand. An interesting feature of Asian arowana mitogenome is that two different repeat arrays were identified in the control region: a 37 bp tandem repeat at the 5' end and an AT-type dinucleotide microsatellite at the 3' end. Both repeats show polymorphism among the six individuals tested; moreover the former one is present in the mitochondrial genomes of several other teleost groups. The TACAT motif described earlier only from mammals and lungfish was found in the tandem repeat of several osteoglossid and eel species. Phylogenetic analysis of fish species representing Actinopterygii and Sarcopterygii taxa has shown that the Asian arowana is located near the baseline of the teleost tree, confirming its status among the ancestral teleost lineages.<br><br>CONCLUSION: The mitogenome of Asian arowana is very similar to the typical vertebrate mitochondrial genome in terms of gene arrangements, codon usage and base composition. However its control region contains two different types of repeat units at both ends, an interesting feature that to our knowledge has never been reported before for other vertebrate mitochondrial control regions. Phylogenetic analysis using the complete mtDNA sequence of Asian arowana confirmed that it belongs to an ancestral teleost lineage.}, }
@article {pmid16987107, year = {2006}, author = {Willkomm, DK and Hartmann, RK}, title = {Intricacies and surprises of nuclear-mitochondrial co-evolution.}, journal = {The Biochemical journal}, volume = {399}, number = {2}, pages = {e7-9}, pmid = {16987107}, issn = {1470-8728}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/*metabolism ; Mitochondria/*metabolism ; Peptide Elongation Factor Tu/metabolism ; Protein Biosynthesis/genetics ; }, abstract = {In this issue of the Biochemical Journal, Watanabe and colleagues disclose another fascinating facet of the mitochondrial protein synthesis machinery: one of the two nematode mitochondrial elongation factors Tu, EF-Tu1, specifically recognizes the D-arm of T-armless tRNAs via a 57-amino-acid C-terminal extension that compensates for the reduction in tRNA structure. This principle provides a paradigm for the evolutionary events thought to have ignited the transition from an ancient 'RNA world' to the 'protein world' of today.}, }
@article {pmid16984813, year = {2006}, author = {Shepherd, VA}, title = {The cytomatrix as a cooperative system of macromolecular and water networks.}, journal = {Current topics in developmental biology}, volume = {75}, number = {}, pages = {171-223}, doi = {10.1016/S0070-2153(06)75006-2}, pmid = {16984813}, issn = {0070-2153}, mesh = {Animals ; Cytoplasm/chemistry/*physiology ; Humans ; Macromolecular Substances/chemistry/*metabolism ; Water/chemistry/*physiology ; }, abstract = {Water was called by Szent-Gyorgi "life's mater and matrix, mother and medium." This chapter considers both aspects of his statement. Many astrobiologists argue that some, if not all, of Earth's water arrived during cometary bombardments. Amorphous water ices of comets possibly facilitated organization of complex organic molecules, kick-starting prebiotic evolution. In Gaian theory, Earth retains its water as a consequence of biological activity. The cell cytomatrix is a proteinaceous matrix/lattice incorporating the cytoskeleton, a pervasive, holistic superstructural network that integrates metabolic pathways. Enzymes of metabolic pathways are ordered in supramolecular clusters (metabolons) associated with cytoskeleton and/or membranes. Metabolic intermediates are microchanneled through metabolons without entering a bulk aqueous phase. Rather than being free in solution, even major signaling ions are probably clustered in association with the cytomatrix. Chloroplasts and mitochondria, like bacteria and archaea, also contain a cytoskeletal lattice, metabolons, and channel metabolites. Eukaryotic metabolism is mathematically a scale-free or small-world network. Enzyme clusters of bacterial origin are incorporated at a pathway level that is architecturally archaean. The eucaryotic cell may be a product of serial endosymbiosis, a chimera. Cell cytoplasm is approximately 80% water. Water is indisputably a conserved structural element of proteins, essential to their folding, specificity, ligand binding, and to enzyme catalysis. The vast literature of organized cell water has long argued that the cytomatrix and cell water are an entire system, a continuum, or gestalt. Alternatives are offered to mainstream explanations of cell electric potentials, ion channel, enzyme, and motor protein function, in terms of high-order cooperative systems of ions, water, and macromolecules. This chapter describes some prominent concepts of organized cell water, including vicinal water network theory, the association-induction hypothesis, wave-cluster theory, phase-gel transition theories, and theories of low- and high-density water polymorphs.}, }
@article {pmid16982216, year = {2006}, author = {D'Elia, D and Catalano, D and Licciulli, F and Turi, A and Tripoli, G and Porcelli, D and Saccone, C and Caggese, C}, title = {The MitoDrome database annotates and compares the OXPHOS nuclear genes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae.}, journal = {Mitochondrion}, volume = {6}, number = {5}, pages = {252-257}, doi = {10.1016/j.mito.2006.07.001}, pmid = {16982216}, issn = {1567-7249}, mesh = {Animals ; Anopheles/*genetics ; Biological Evolution ; *Databases, Nucleic Acid ; Drosophila/*genetics ; Drosophila melanogaster/genetics ; *Genes, Insect ; Humans ; Mitochondria/genetics ; *Oxidative Phosphorylation ; User-Computer Interface ; }, abstract = {The oxidative phosphorylation (OXPHOS) is the primary energy-producing process of all aerobic organisms and the only cellular function under the dual control of both the mitochondrial and the nuclear genomes. Functional characterization and evolutionary study of the OXPHOS system is of great importance for the understanding of many as yet unclear aspects of nucleus-mitochondrion genomic co-evolution and co-regulation gene networks. The MitoDrome database is a web-based database which provides genomic annotations about nuclear genes of Drosophila melanogaster encoding for mitochondrial proteins. Recently, MitoDrome has included a new section annotating genomic information about OXPHOS genes in Drosophila pseudoobscura and Anopheles gambiae and their comparative analysis with their Drosophila melanogaster and human counterparts. The introduction of this new comparative annotation section into MitoDrome is expected to be a useful resource for both functional and structural genomics related to the OXPHOS system.}, }
@article {pmid16980398, year = {2006}, author = {Houliston, GJ and Olson, MS}, title = {Nonneutral evolution of organelle genes in Silene vulgaris.}, journal = {Genetics}, volume = {174}, number = {4}, pages = {1983-1994}, pmid = {16980398}, issn = {0016-6731}, mesh = {Base Sequence ; Chloroplasts/*genetics ; *Evolution, Molecular ; Genes, Plant/*genetics ; *Genetic Variation ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; Silene/*genetics ; }, abstract = {Knowledge of mitochondrial gene evolution in angiosperms has taken a dramatic shift within the past decade, from universal slow rates of nucleotide change to a growing realization of high variation in rates among lineages. Additionally, evidence of paternal inheritance of plant mitochondria and recombination among mitochondrial genomes within heteroplasmic individuals has led to speculation about the potential for independent evolution of organellar genes. We report intraspecific mitochondrial and chloroplast sequence variation in a cosmopolitan sample of 42 Silene vulgaris individuals. There was remarkably high variation in two mitochondrial genes (atp1, atp9) and additional variation within a third gene (cob). Tests for patterns of nonneutral evolution were significant for atp1 and atp9, indicative of the maintenance of balanced polymorphisms. Two chloroplast genes (matK, ndhF) possessed less, but still high, variation and no divergence from neutral expectations. Phylogenetic patterns of organelle genes in both the chloroplast and mitochondria were incongruent, indicating the potential for independent evolutionary trajectories. Evidence indicated reassociation among cytoplasmic genomes and recombination between mitochondrial genes and within atp1, implying transient heteroplasmy in ancestral lineages. Although the mechanisms for long-term maintenance of mitochondrial polymorphism are currently unknown, frequency-dependent selection on linked cytoplasmic male sterility genes is a potential candidate.}, }
@article {pmid16978258, year = {2006}, author = {Bouzenzana, J and Pelosi, L and Briolay, A and Briolay, J and Bulone, V}, title = {Identification of the first Oomycete annexin as a (1--&gt;3)-beta-D-glucan synthase activator.}, journal = {Molecular microbiology}, volume = {62}, number = {2}, pages = {552-565}, doi = {10.1111/j.1365-2958.2006.05389.x}, pmid = {16978258}, issn = {0950-382X}, mesh = {Amino Acid Sequence ; Annexins/analysis/genetics/*metabolism ; Blotting, Western/methods ; Calcium Chloride/pharmacology ; Catalysis/drug effects ; DNA, Complementary/chemistry/genetics/isolation &amp; purification ; Egtazic Acid/pharmacology ; Electrophoresis, Gel, Two-Dimensional/methods ; Electrophoresis, Polyacrylamide Gel/methods ; Glucosyltransferases/genetics/*metabolism ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Molecular Weight ; Oomycetes/enzymology/genetics ; Phylogeny ; Saprolegnia/*enzymology/genetics ; Sequence Analysis, DNA ; Sequence Analysis, Protein/methods ; Sequence Homology, Amino Acid ; }, abstract = {(1-->3)-beta-D-Glucans are major components of the cell walls of Oomycetes and as such they play an essential role in the morphogenesis and growth of these microorganisms. Despite the biological importance of (1-->3)-beta-D-glucans, their mechanisms of biosynthesis are poorly understood. Previous studies on (1-->3)-beta-D-glucan synthases from Saprolegnia monoica have shown that three protein bands of an apparent molecular weight of 34, 48 and 50 kDa co-purify with enzyme activity. However, none of the corresponding proteins have been identified. Here we have identified, purified, sequenced and characterized a protein from the 34 kDa band and clearly shown that it has all the biochemical properties of proteins from the annexin family. In addition, we have unequivocally demonstrated that the purified protein is an activator of (1-->3)-beta-D-glucan synthase. This represents a new type of function for proteins belonging to the annexin family. Two other proteins from the 48 and 50 kDa bands were identified as ATP synthase subunits, which most likely arise from contaminations by mitochondria during membrane preparation. The results, which are discussed in relation with the possible regulation mechanisms of (1-->3)-beta-D-glucan synthases, represent a first step towards a better understanding of cell wall polysaccharide biosynthesis in Oomycetes.}, }
@article {pmid16977376, year = {2006}, author = {Chowdhury, I and Tharakan, B and Bhat, GK}, title = {Current concepts in apoptosis: the physiological suicide program revisited.}, journal = {Cellular &amp; molecular biology letters}, volume = {11}, number = {4}, pages = {506-525}, pmid = {16977376}, issn = {1689-1392}, mesh = {Animals ; Apoptosis/*physiology ; Caspases/physiology ; Cell Death/physiology ; Humans ; Intracellular Membranes/enzymology/physiology ; }, abstract = {Apoptosis, or programmed cell death (PCD), involves a complex network of biochemical pathways that normally ensure a homeostatic balance between cellular proliferation and turnover in nearly all tissues. Apoptosis is essential for the body, as its deregulation can lead to several diseases. It plays a major role in a variety of physiological events, including embryonic development, tissue renewal, hormone-induced tissue atrophy, removal of inflammatory cells, and the evolution of granulation tissue into scar tissue. It also has an essential role in wound repair. The various cellular and biochemical mechanisms involved in apoptosis are not fully understood. However, there are two major pathways, the extrinsic pathway (receptor-mediated apoptotic pathway) and the intrinsic pathway (mitochondria-mediated apoptotic pathway), which are both well established. The key component in both is the activation of the caspase cascade. Caspases belong to the family of proteases that ultimately, by cleaving a set of proteins, cause disassembly of the cell. Although the caspase-mediated proteolytic cascade represents a central point in the apoptotic response, its initiation is tightly regulated by a variety of other factors. Among them, Bcl-2 family proteins, TNF and p53 play pivotal roles in the regulation of caspase activation and in the regulation of apoptosis. This review summarizes the established concepts in apoptosis as a physiological cell suicide program, highlighting the recent and significant advances in its study.}, }
@article {pmid16972986, year = {2006}, author = {Rot, C and Goldfarb, I and Ilan, M and Huchon, D}, title = {Putative cross-kingdom horizontal gene transfer in sponge (Porifera) mitochondria.}, journal = {BMC evolutionary biology}, volume = {6}, number = {}, pages = {71}, pmid = {16972986}, issn = {1471-2148}, mesh = {Animals ; Base Sequence ; Ecosystem ; Electron Transport Complex IV/genetics ; Fungi/*genetics/physiology ; *Gene Transfer, Horizontal ; *Genes, Mitochondrial ; Introns ; Molecular Sequence Data ; Phylogeny ; Porifera/classification/*genetics/*microbiology ; RNA/chemistry/genetics ; RNA, Mitochondrial ; Sequence Alignment ; Symbiosis/*genetics ; }, abstract = {BACKGROUND: The mitochondrial genome of Metazoa is usually a compact molecule without introns. Exceptions to this rule have been reported only in corals and sea anemones (Cnidaria), in which group I introns have been discovered in the cox1 and nad5 genes. Here we show several lines of evidence demonstrating that introns can also be found in the mitochondria of sponges (Porifera).<br><br>RESULTS: A 2,349 bp fragment of the mitochondrial cox1 gene was sequenced from the sponge Tetilla sp. (Spirophorida). This fragment suggests the presence of a 1143 bp intron. Similar to all the cnidarian mitochondrial introns, the putative intron has group I intron characteristics. The intron is present in the cox1 gene and encodes a putative homing endonuclease. In order to establish the distribution of this intron in sponges, the cox1 gene was sequenced from several representatives of the demosponge diversity. The intron was found only in the sponge order Spirophorida. A phylogenetic analysis of the COI protein sequence and of the intron open reading frame suggests that the intron may have been transmitted horizontally from a fungus donor.<br><br>CONCLUSION: Little is known about sponge-associated fungi, although in the last few years the latter have been frequently isolated from sponges. We suggest that the horizontal gene transfer of a mitochondrial intron was facilitated by a symbiotic relationship between fungus and sponge. Ecological relationships are known to have implications at the genomic level. Here, an ecological relationship between sponge and fungus is suggested based on the genomic analysis.}, }
@article {pmid16971498, year = {2007}, author = {Chen, Q and Camara, AK and Stowe, DF and Hoppel, CL and Lesnefsky, EJ}, title = {Modulation of electron transport protects cardiac mitochondria and decreases myocardial injury during ischemia and reperfusion.}, journal = {American journal of physiology. Cell physiology}, volume = {292}, number = {1}, pages = {C137-47}, doi = {10.1152/ajpcell.00270.2006}, pmid = {16971498}, issn = {0363-6143}, support = {1K01 HL 73246/HL/NHLBI NIH HHS/United States ; 2P01 AG 15885/AG/NIA NIH HHS/United States ; }, mesh = {Aging ; Animals ; *Electron Transport ; Humans ; Ischemic Preconditioning, Myocardial ; Mitochondria, Heart/*metabolism ; Myocardial Reperfusion Injury/*metabolism/*pathology ; Oxidative Phosphorylation ; Protons ; Reactive Oxygen Species/metabolism ; }, abstract = {Mitochondria are increasingly recognized as lynchpins in the evolution of cardiac injury during ischemia and reperfusion. This review addresses the emerging concept that modulation of mitochondrial respiration during and immediately following an episode of ischemia can attenuate the extent of myocardial injury. The blockade of electron transport and the partial uncoupling of respiration are two mechanisms whereby manipulation of mitochondrial metabolism during ischemia decreases cardiac injury. Although protection by inhibition of electron transport or uncoupling of respiration initially appears to be counterintuitive, the continuation of mitochondrial oxidative phosphorylation in the pathological milieu of ischemia generates reactive oxygen species, mitochondrial calcium overload, and the release of cytochrome c. The initial target of these deleterious mitochondrial-driven processes is the mitochondria themselves. Consequences to the cardiomyocyte, in turn, include oxidative damage, the onset of mitochondrial permeability transition, and activation of apoptotic cascades, all favoring cardiomyocyte death. Ischemia-induced mitochondrial damage carried forward into reperfusion further amplifies these mechanisms of mitochondrial-driven myocyte injury. Interruption of mitochondrial respiration during early reperfusion by pharmacologic blockade of electron transport or even recurrent hypoxia or brief ischemia paradoxically decreases cardiac injury. It increasingly appears that the cardioprotective paradigms of ischemic preconditioning and postconditioning utilize modulation of mitochondrial oxidative metabolism as a key effector mechanism. The initially counterintuitive approach to inhibit mitochondrial respiration provides a new cardioprotective paradigm to decrease cellular injury during both ischemia and reperfusion.}, }
@article {pmid16968450, year = {2006}, author = {Hoppenrath, M and Leander, BS}, title = {Dinoflagellate, Euglenid, or Cercomonad? The ultrastructure and molecular phylogenetic position of Protaspis grandis n. sp.}, journal = {The Journal of eukaryotic microbiology}, volume = {53}, number = {5}, pages = {327-342}, doi = {10.1111/j.1550-7408.2006.00110.x}, pmid = {16968450}, issn = {1066-5234}, mesh = {Animals ; Cell Nucleus/ultrastructure ; Cell Wall/ultrastructure ; Cytoplasm/ultrastructure ; DNA, Ribosomal/genetics ; Dinoflagellida/classification/*genetics/ultrastructure ; Euglenida/classification/*genetics/ultrastructure ; Eukaryota/classification/genetics/ultrastructure ; Microscopy, Electron, Scanning/methods ; Microscopy, Electron, Transmission/methods ; *Phylogeny ; }, abstract = {Protaspis is an enigmatic genus of marine phagotrophic biflagellates that have been tentatively classified with several different groups of eukaryotes, including dinoflagellates, euglenids, and cercomonads. This uncertainty led us to investigate the phylogenetic position of Protaspis grandis n. sp. with ultrastructural and small subunit (SSU) rDNA sequence data. Our results demonstrated that the cells were dorsoventrally flattened, shaped like elongated ovals with parallel lateral sides, 32.5-55.0 mum long and 20.0-35.0 mum wide. Moreover, two heterodynamic flagella emerged through funnels that were positioned subapically, each within a depression and separated by a distinctive protrusion. A complex multilayered wall surrounded the cell. Like dinoflagellates and euglenids, the nucleus contained permanently condensed chromosomes and a large nucleolus throughout the cell cycle. Pseudopodia containing numerous mitochondria with tubular cristae emerged from a ventral furrow through a longitudinal slit that was positioned posterior to the protrusion and flagellar apparatus. Batteries of extrusomes were present within the cytoplasm and had ejection sites through pores in the cell wall. The SSU rDNA phylogeny demonstrated a very close relationship between the benthic P. grandis n. sp. and the planktonic Cryothecomonas longipes. These ultrastructural and molecular phylogenetic data for Protaspis indicated that the current taxonomy of Protaspis and Crythecomonas is in need of re-evaluation. The composition and identity of Protaspis is reviewed and suggestions for future taxonomic changes are presented. Problems within the genus Cryothecomonas are highlighted as well, and the missing data needed to resolve ambiguities between the two genera are clarified.}, }
@article {pmid16968273, year = {2006}, author = {Peijnenburg, KT and Fauvelot, C and Breeuwer, JA and Menken, SB}, title = {Spatial and temporal genetic structure of the planktonic Sagitta setosa (Chaetognatha) in European seas as revealed by mitochondrial and nuclear DNA markers.}, journal = {Molecular ecology}, volume = {15}, number = {11}, pages = {3319-3338}, doi = {10.1111/j.1365-294X.2006.03002.x}, pmid = {16968273}, issn = {0962-1083}, mesh = {Atlantic Ocean ; Base Sequence ; DNA, Mitochondrial/chemistry/*genetics ; *Ecosystem ; Electron Transport Complex IV/chemistry/genetics ; Europe ; Genetic Markers/genetics ; Genetic Variation ; Haplotypes ; Mediterranean Sea ; Microsatellite Repeats/*genetics ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Plankton/enzymology/*genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; }, abstract = {Little is known about the spatial and temporal scales at which planktonic organisms are genetically structured. A previous study of mitochondrial DNA (mtDNA) in the holoplanktonic chaetognath Sagitta setosa revealed strong phylogeographic structuring suggesting that Northeast (NE) Atlantic, Mediterranean and Black Sea populations are genetically disjunct. The present study used a higher sampling intensity and a combination of mitochondrial and four microsatellite markers to reveal population structuring between and within basins. Between basins, both marker sets indicated significant differentiation confirming earlier results that gene flow is probably absent between the respective S. setosa populations. At the within-basin scale, we found no evidence of spatial or temporal structuring within the NE Atlantic. In the Mediterranean basin, both marker sets indicated significant structuring, but only the mtDNA data indicated a sharp genetic division between Adriatic and all other Mediterranean populations. Data were inconclusive about population structuring in the Black Sea. The levels of differentiation indicated by the two marker sets differed substantially, with far less pronounced structure detected by microsatellite than mtDNA data. This study also uncovered the presence of highly divergent mitochondrial lineages that were discordant with morphology, geography and nuclear DNA. We thus propose the hypothesis that highly divergent mitochondrial lineages may be present within interbreeding S. setosa populations.}, }
@article {pmid16968271, year = {2006}, author = {Audzijonyte, A and Väinölä, R}, title = {Phylogeographic analyses of a circumarctic coastal and a boreal lacustrine mysid crustacean, and evidence of fast postglacial mtDNA rates.}, journal = {Molecular ecology}, volume = {15}, number = {11}, pages = {3287-3301}, doi = {10.1111/j.1365-294X.2006.02998.x}, pmid = {16968271}, issn = {0962-1083}, mesh = {Africa, Northern ; Animals ; Arctic Regions ; Base Sequence ; Crustacea/*genetics ; DNA, Mitochondrial/chemistry/genetics ; *Ecosystem ; Electron Transport Complex IV/chemistry/genetics ; Europe ; *Evolution, Molecular ; Genetic Variation ; Haplotypes ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Phylogeographic structures of two weakly dispersing Mysis sibling species, one with a circumarctic coastal, the other with a boreal lacustrine-Baltic distribution, were studied from mitochondrial cytochrome c oxidase subunit I (COI) gene sequences. Mysis segerstralei showed high overall diversity and little phylogeographic structure across the Arctic, indicating late-glacial dispersal among coastal and lake populations from Alaska, Siberia and the north of Europe. A strongly divergent refugial lineage was however identified in Beringia. The boreal 'glacial relict'Mysis salemaai in turn displayed clear structuring among postglacially isolated Scandinavian lake populations. The inferred pattern of intralake mitochondrial DNA (mtDNA) monophyly in Scandinavia suggested relatively small population sizes and a remarkably fast postglacial mtDNA divergence rate (0.27% per 10 000 years). Nevertheless, the broader phylogeographic pattern did not support distinct eastern and western glacial refugia in Northern Europe, unlike in some other aquatic taxa. In all, the two species comprised three equidistant mitochondrial lineages (approximately 2% divergence), corresponding to M. salemaai, to the bulk of M. segerstralei, and to the Beringian M. segerstralei lineage. The lack of reciprocal monophyly of the two species in respect to their mitochondrial genealogy could indicate postspeciation mitochondrial introgression, also exemplified by an evidently more recent capture of M. segerstralei mitochondria in a Karelian population of M. salemaai. Overall, the data suggest that the continental boreal M. salemaai has a relatively recent ancestry in arctic coastal waters, whereas two other boreal 'glacial relict'Mysis sibling species in Europe (Mysis relicta) and North America (Mysis diluviana) have colonized inland waters much earlier (approximately 8% COI divergence).}, }
@article {pmid16968258, year = {2006}, author = {Dalebout, ML and Ruzzante, DE and Whitehead, H and Oien, NI}, title = {Nuclear and mitochondrial markers reveal distinctiveness of a small population of bottlenose whales (Hyperoodon ampullatus) in the western North Atlantic.}, journal = {Molecular ecology}, volume = {15}, number = {11}, pages = {3115-3129}, doi = {10.1111/j.1365-294X.2006.03004.x}, pmid = {16968258}, issn = {0962-1083}, mesh = {Animals ; Atlantic Ocean ; Bayes Theorem ; Cell Nucleus/*genetics ; Cluster Analysis ; DNA, Mitochondrial/chemistry/*genetics ; Evolution, Molecular ; Female ; Genetic Markers/genetics ; Genetic Variation ; Genetics, Population ; Male ; Microsatellite Repeats/genetics ; Mitochondria/*genetics ; Polymerase Chain Reaction/veterinary ; Polymorphism, Single-Stranded Conformational ; Sequence Analysis, DNA ; Sex Factors ; Whales/*genetics ; }, abstract = {Small populations at the edge of a species' distribution can represent evolutionary relics left behind after range contractions due to climate change or human exploitation. The distinctiveness and genetic diversity of a small population of bottlenose whales in the Gully, a submarine canyon off Nova Scotia, was quantified by comparison to other North Atlantic populations using 10 microsatellites and mitrochondrial DNA (mtDNA) control region sequences (434 bp). Both markers confirmed the distinctiveness of the Gully (n = 34) from the next nearest population, off Labrador (n = 127; microsatellites -F(ST)= 0.0243, P < 0.0001; mtDNA -Phi(ST) = 0.0456, P < 0.05). Maximum likelihood microsatellite estimates suggest that less than two individuals per generation move between these areas, refuting the hypothesis of population links through seasonal migration. Both males and females appear to be philopatric, based on significant differentiation at both genomes and similar levels of structuring among the sexes for microsatellites. mtDNA diversity was very low in all populations (h = 0.51, pi = 0.14%), a pattern which may be due to selective sweeps associated with this species' extreme deep-diving ecology. Whaling had a substantial impact on bottlenose whale abundance, with over 65 000 animals killed before the hunt ceased in the early 1970s. Genetic diversity was similar among all populations, however, and no signal for bottlenecks was detected, suggesting that the Gully is not a relic of a historically wider distribution. Instead, this unique ecosystem appears to have long provided a stable year-round habitat for a distinct population of bottlenose whales.}, }
@article {pmid16966406, year = {2006}, author = {Jia, J and Wang, Y and Zhou, L and Jin, S}, title = {Expression of Pseudomonas aeruginosa toxin ExoS effectively induces apoptosis in host cells.}, journal = {Infection and immunity}, volume = {74}, number = {12}, pages = {6557-6570}, pmid = {16966406}, issn = {0019-9567}, mesh = {ADP Ribose Transferases/analysis/genetics/*metabolism ; ADP-Ribosylation Factors/analysis/genetics/*metabolism ; Animals ; *Apoptosis ; Bacterial Toxins/analysis/genetics/*metabolism ; Cell Line ; Drosophila melanogaster/cytology ; Evolution, Molecular ; Genetic Vectors/genetics ; Green Fluorescent Proteins/analysis/genetics ; HeLa Cells ; Humans ; MAP Kinase Kinase 4/metabolism ; Mitochondria/metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Signal Transduction ; Transfection ; Transgenes ; }, abstract = {Pseudomonas aeruginosa is an opportunistic bacterial pathogen that primarily infects immunocompromised individuals and patients with cystic fibrosis. Invasive strains of P. aeruginosa are known to induce apoptosis at a high frequency in HeLa cells and in many other cell lines, a process that is dependent on the ADP-ribosylation (ADPRT) activity of a type III secreted protein ExoS. In our previous report, it was proposed that P. aeruginosa secreting ExoS, upon infection, shuts down host cell survival signal pathways by inhibiting ERK1/2 and p38 activation, and it activates proapoptotic pathways through activation of JNK1/2, leading ultimately to cytochrome c release and activation of caspases. In this study, we demonstrate that the expression of ExoS in HeLa cells by eukaryotic expression vector effectively caused apoptosis in an ADPRT activity-dependent manner, indicating that ExoS alone is sufficient to trigger apoptotic death of host cells independent of any other bacterial factors. By expressing an EGFP-ExoS fusion protein, we were able to directly correlate the death of HeLa cells with the presence of intracellular ExoS and further proved the dependence of this process on both JNK activation and mitochondrial proapoptotic event. The cellular pathway responsible for the ExoS-induced cytotoxicity appears to be well conserved, since the expression of the ADPRT-competent ExoS also induced rapid cell death in the Drosophila melanogaster S2 cell lines. The presented study not only highlights the ability of ExoS ADPRT to modulate host cell signaling, eventually leading to apoptosis, but also establishes ExoS as a valuable tool, in principle, for the elucidation of apoptosis mechanisms.}, }
@article {pmid16950510, year = {2007}, author = {Fabbro, A and Pastore, B and Nistri, A and Ballerini, L}, title = {Activity-independent intracellular Ca2+ oscillations are spontaneously generated by ventral spinal neurons during development in vitro.}, journal = {Cell calcium}, volume = {41}, number = {4}, pages = {317-329}, doi = {10.1016/j.ceca.2006.07.006}, pmid = {16950510}, issn = {0143-4160}, mesh = {Animals ; Calcium/*metabolism/pharmacology ; Calcium Channels/metabolism ; *Calcium Signaling ; Ganglia, Spinal/*metabolism ; Gap Junctions/metabolism ; Glutamic Acid/pharmacology ; Immunohistochemistry ; In Vitro Techniques ; Mice ; Mice, Inbred C57BL ; Neurons/*metabolism ; Spinal Cord/*metabolism ; Time Factors ; gamma-Aminobutyric Acid/metabolism ; }, abstract = {Within the CNS, distinct neurons may rely on different processes to modulate cytosolic Ca2+ depending on the network developmental phase. In particular, in the immature spinal cord, synchronous electrical discharges are coupled with biochemical signals triggered by intracellular Ca2+ waves. Nevertheless, the presence of neuronal-specific Ca2+ elevations independent from synaptic activity within mammalian spinal networks has not yet been described. The present report is the first description of repetitive calcium events generated by discrete ventral spinal neurons maintained in organotypic culture during in vitro maturation stages crucial for network evolution. Ventral interneurons in one-third of slices displayed spontaneous intracellular calcium transients suppressed by calcium-free extracellular solution or by application of cobalt, and resistant to blockers of network activity like TTX, CNQX, APV, strychnine or bicuculline. Our data suggest a primary role for mitochondria in intracellular calcium oscillations, because CCCP, that selectively collapses the mitochondrial electrochemical gradient, eliminated the ability of these neurons to show activity-independent calcium oscillations. Likewise, CGP-37157, a blocker of mitochondrial Na+/Ca2+ exchanger, inhibited oscillations in the majority of neurons. We propose that spontaneous Ca2+ transients, dynamically regulated by mitochondria, occurred in a discrete cluster of interneurons possibly to guide the development of synaptic connections.}, }
@article {pmid16950266, year = {2006}, author = {Troell, K and Engström, A and Morrison, DA and Mattsson, JG and Höglund, J}, title = {Global patterns reveal strong population structure in Haemonchus contortus, a nematode parasite of domesticated ruminants.}, journal = {International journal for parasitology}, volume = {36}, number = {12}, pages = {1305-1316}, doi = {10.1016/j.ijpara.2006.06.015}, pmid = {16950266}, issn = {0020-7519}, mesh = {Animals ; Base Sequence ; DNA, Helminth/*genetics ; DNA, Mitochondrial/*genetics ; Gene Amplification/genetics ; Genes, Helminth/genetics ; Genetic Markers/genetics ; Genetics, Population ; Genotype ; Goats/parasitology ; Haemonchus/classification/*genetics ; Mitochondria/genetics ; NADH Dehydrogenase/genetics ; Phylogeny ; Polymorphism, Genetic/*genetics ; Ruminants/*parasitology ; Sheep/parasitology ; }, abstract = {We have examined the global population genetic structure of Haemonchus contortus. The genetic variability was studied using both amplified fragment length polymorphism (AFLP) and nad4 sequences of the mitochondrial genome. To examine the performance and information content of the two different marker systems, comparative assessment of population genetic diversity was undertaken in 19 isolates of H. contortus, a parasitic nematode of small ruminants. A total of 150 individual adult worms representing 14 countries from all inhabited continents were analysed. Altogether 1,429 informative AFLP markers were generated using four different primer combinations. Also, the genetic variation was high, which agrees with results from previous AFLP studies of nematode parasites of livestock. The genetic structure was high, indicating limited gene flow between the different isolates and populations from each continent mostly formed monophyletic groups in the phylogenetic analysis. However, for isolates representing Australia, Greece and one laboratory strain that originated from South Africa (WRS), there was no clear genetic relationship between the isolates and the distance between their geographical origins. Basically the same pattern was observed for the mitochondrial marker, although the phylogenetic analysis was less resolved than for AFLP. In contrast with previous findings on the population genetic structure of H. contortus, the calculation of population structure gave high values (Nst=0.59). The strong structure was present also for the four Swedish isolates (Nst=0.16) representing a small geographical area.}, }
@article {pmid16949352, year = {2006}, author = {Faure, E and Casanova, JP}, title = {Comparison of chaetognath mitochondrial genomes and phylogenetical implications.}, journal = {Mitochondrion}, volume = {6}, number = {5}, pages = {258-262}, doi = {10.1016/j.mito.2006.07.004}, pmid = {16949352}, issn = {1567-7249}, mesh = {Animals ; Base Sequence ; *DNA, Mitochondrial ; Genes, Mitochondrial ; *Genome ; Invertebrates/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Transfer/genetics ; Sequence Alignment ; }, abstract = {Two complete mitochondrial genomes (mtDNAs) of chaetognaths, Spadella cephaloptera and Paraspadella gotoi, have been recently published. These genomes are highly unusual. They are the smallest metazoan mtDNAs so far known; atp6 and atp8 genes are missing; lastly, our reanalysis has evidenced that, contrarily to what has been previously published for one sequence, both contain a unique transfer RNA (tRNA(Met)) evidencing that both have the same gene content. Indeed, even if the gene order seems very different, two gene blocks are conserved. In addition, comparison of gene arrangement suggests phylogenetical relationships between chaetognaths and some lophotrochozoa like annelids and molluscs.}, }
@article {pmid16949250, year = {2006}, author = {Haitina, T and Lindblom, J and Renström, T and Fredriksson, R}, title = {Fourteen novel human members of mitochondrial solute carrier family 25 (SLC25) widely expressed in the central nervous system.}, journal = {Genomics}, volume = {88}, number = {6}, pages = {779-790}, doi = {10.1016/j.ygeno.2006.06.016}, pmid = {16949250}, issn = {0888-7543}, mesh = {Animals ; *Biological Transport ; Brain/metabolism ; Central Nervous System/*metabolism ; Computational Biology/methods ; Female ; Humans ; Male ; Markov Chains ; Membrane Transport Proteins/*genetics/*metabolism ; Mice ; Mitochondria/*metabolism ; *Multigene Family ; Phylogeny ; Polymerase Chain Reaction/methods ; Rats ; Rats, Sprague-Dawley ; Synteny ; }, abstract = {Members of the solute carrier family 25 (SLC25) are known to transport molecules over the mitochondrial membrane. In this paper we present 14 novel members of SLC25 family in human. These were provided with following gene symbols by the HGNC: SLC25A32, SLC25A33, SLC25A34, SLC25A35, SLC25A37, SLC25A38, SLC25A39, SLC25A40, SLC25A41, SLC25A42, SLC25A43, SLC25A44, SLC25A45, and SLC25A46. We also identified the orthologues for these genes in rat and mouse. Moreover, we found yeast orthologues for 9 of these genes and show that the predicted substrate binding residues are highly conserved in the human and yeast proteins. We performed a comprehensive tissue localization study for 9 of these genes on a panel of 30 rat tissues with quantitative real-time polymerse chain reaction. We detected their mRNA in a wide number of tissues, both in brain and in periphery. This study provides an overall roadmap of the repertoire of the SLC25 family in mammals, showing that there are at least 46 genes in the human genome coding for mitochondrial transporters.}, }
@article {pmid16948501, year = {2006}, author = {Morel, F and Renoux, M and Alziari, S}, title = {Mitochondrial biochemical activities and heteroplasmy evolution in established D. subobscura cell line.}, journal = {In vitro cellular &amp; developmental biology. Animal}, volume = {42}, number = {7}, pages = {201-207}, pmid = {16948501}, issn = {1071-2690}, mesh = {Animals ; Cell Culture Techniques ; *Cell Line ; Culture Media ; Drosophila/*cytology/genetics/metabolism ; Energy Metabolism/physiology ; *Evolution, Molecular ; Gene Deletion ; Genes, Mitochondrial ; Genome, Insect ; Glycolysis ; Mitochondria/genetics/*metabolism ; }, abstract = {A mutant strain of drosophila (D. subobscura) has two types of mitochondrial genomes: a small population (20%) identical to that of the wild strain (15.9 kb) and a predominant population (80%) which has undergone a 5-kb deletion affecting more than 30% of the coding zone. Two cell lines were established from homogenates of embryos from mutant and wild strains. The activities of the respiratory complexes measured in the different cell lines are much lower than in the flies, indicating a glycolytic metabolism. Various modifications of the medium composition did not change this metabolic pathway. The mutant cell line has two types of populations of mitochondrial genomes and the heteroplasmy is equivalent to that measured in the mutant strain. However, the biochemical characteristics differ from those observed in the flies (i.e., the decrease of complex I and III activities), and the various systems of compensation for the consequences of the deletion that are showed in the mutant strain are no longer observed. Furthermore, in contrast with observations made on mutant flies, the heteroplasmy appears unstable in the mutant cell lines: after 60 or so generations, it progressively decreases until it disappears completely. The limited importance of mitochondrial energy metabolism in cells may explain the low impact of the mutation on the established cell line, in contrast to what is seen in the mutant strain.}, }
@article {pmid16940310, year = {2006}, author = {Baruffini, E and Lodi, T and Dallabona, C and Puglisi, A and Zeviani, M and Ferrero, I}, title = {Genetic and chemical rescue of the Saccharomyces cerevisiae phenotype induced by mitochondrial DNA polymerase mutations associated with progressive external ophthalmoplegia in humans.}, journal = {Human molecular genetics}, volume = {15}, number = {19}, pages = {2846-2855}, doi = {10.1093/hmg/ddl219}, pmid = {16940310}, issn = {0964-6906}, support = {GGP030039/TI_/Telethon/Italy ; }, mesh = {Base Sequence ; DNA Polymerase I/genetics ; DNA Polymerase gamma ; DNA, Fungal/genetics ; DNA, Mitochondrial/genetics ; DNA-Directed DNA Polymerase/*genetics ; Deoxyribonucleotides/metabolism ; Humans ; Mitochondria/enzymology ; Mutation ; Ophthalmoplegia, Chronic Progressive External/*enzymology/*genetics ; Phenotype ; Reactive Oxygen Species/metabolism ; Saccharomyces cerevisiae/*enzymology/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; Trefoil Factor-2 ; }, abstract = {The human POLG gene encodes the catalytic subunit of mitochondrial DNA polymerase gamma (pol gamma). Mutations in pol gamma are associated with a spectrum of disease phenotypes including autosomal dominant and recessive forms of progressive external ophthalmoplegia, spino-cerebellar ataxia and epilepsy, and Alpers-Huttenlocher hepatocerebral poliodystrophy. Multiple deletions, or depletion of mtDNA in affected tissues, are the molecular hallmarks of pol gamma mutations. To shed light on the pathogenic mechanisms leading to these phenotypes, we have introduced in MIP1, the yeast homologue of POLG, two mutations equivalent to the human Y955C and G268A mutations, which are associated with dominant and recessive PEO, respectively. Both mutations induced the generation of petite colonies, carrying either rearranged (rho-) or no (rho0) mtDNA. Mutations in genes that control the mitochondrial supply of deoxynucleotides (dNTP) affect the mtDNA integrity in both humans and yeast. To test whether the manipulation of the dNTP pool can modify the effects of pol gamma mutations in yeast, we have overexpressed a dNTP checkpoint enzyme, ribonucleotide reductase, RNR1, or deleted its inhibitor, SML1. In both mutant strains, the petite mutability was dramatically reduced. The same result was obtained by exposing the mutant strains to dihydrolipoic acid, an anti-oxidant agent. Therefore, an increase of the mitochondrial dNTP pool and/or a decrease of reactive oxygen species can prevent the mtDNA damage induced by pol gamma mutations in yeast and, possibly, in humans.}, }
@article {pmid16940157, year = {2006}, author = {Hunt, MC and Rautanen, A and Westin, MA and Svensson, LT and Alexson, SE}, title = {Analysis of the mouse and human acyl-CoA thioesterase (ACOT) gene clusters shows that convergent, functional evolution results in a reduced number of human peroxisomal ACOTs.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {20}, number = {11}, pages = {1855-1864}, doi = {10.1096/fj.06-6042com}, pmid = {16940157}, issn = {1530-6860}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA Primers ; *Evolution, Molecular ; Humans ; Mice ; Molecular Sequence Data ; *Multigene Family ; Open Reading Frames ; Palmitoyl-CoA Hydrolase/genetics ; Peroxisomes/*enzymology ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Sequence Homology, Amino Acid ; Thiolester Hydrolases/*genetics ; Transcription, Genetic ; }, abstract = {The maintenance of cellular levels of free fatty acids and acyl-CoAs, the activated form of free fatty acids, is extremely important, as imbalances in lipid metabolism have serious consequences for human health. Acyl-coenzyme A (CoA) thioesterases (ACOTs) hydrolyze acyl-CoAs to the free fatty acid and CoASH, and thereby have the potential to regulate intracellular levels of these compounds. We previously identified and characterized a mouse ACOT gene cluster comprised of six genes that apparently arose by gene duplications encoding acyl-CoA thioesterases with localizations in cytosol (ACOT1), mitochondria (ACOT2), and peroxisomes (ACOT3-6). However, the corresponding human gene cluster contains only three genes (ACOT1, ACOT2, and ACOT4) coding for full-length thioesterase proteins, of which only one is peroxisomal (ACOT4). We therefore set out to characterize the human genes, and we show here that the human ACOT4 protein catalyzes the activities of three mouse peroxisomal ACOTs (ACOT3, 4, and 5), being active on succinyl-CoA and medium to long chain acyl-CoAs, while ACOT1 and ACOT2 carry out similar functions to the corresponding mouse genes. These data strongly suggest that the human ACOT4 gene has acquired the functions of three mouse genes by a functional convergent evolution that also provides an explanation for the unexpectedly low number of human genes.}, }
@article {pmid16938841, year = {2006}, author = {Margulis, L and Chapman, M and Guerrero, R and Hall, J}, title = {The last eukaryotic common ancestor (LECA): acquisition of cytoskeletal motility from aerotolerant spirochetes in the Proterozoic Eon.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {35}, pages = {13080-13085}, pmid = {16938841}, issn = {0027-8424}, mesh = {Cell Movement ; Cell Nucleus/physiology ; Cytoskeleton/*physiology ; Eukaryotic Cells/*cytology/*physiology ; History, Ancient ; Microtubules/metabolism ; Mitochondria/physiology ; *Models, Biological ; *Phylogeny ; Spirochaetales/*cytology/physiology ; Sulfides/metabolism ; Symbiosis ; Time Factors ; }, abstract = {We develop a symbiogenetic concept of the origin of eukaryotic intracellular motility systems from anaerobic but aerotolerant spirochetes in sulfide-rich environments. The last eukaryotic common ancestors (LECAs) have extant archaeprotist descendants: motile nucleated cells with Embden-Meyerhof glycolysis and substrate-level phosphorylation that lack the alpha-proteobacterial symbiont that became the mitochondrion. Swimming and regulated O(2)-tolerance via sulfide oxidation already had been acquired by sulfidogenic wall-less archaebacteria (thermoplasmas) after aerotolerant cytoplasmic-tubule-containing spirochetes (eubacteria) attached to them. Increasing stability of sulfide-oxidizing/sulfur-reducing consortia analogous to extant sulfur syntrophies (Thiodendron) led to fusion. The eubacteria-archaebacteria symbiosis became permanent as the nucleus evolved by prokaryotic recombination with membrane hypertrophy, analogous to Gemmata obscuriglobus and other delta-proteobacteria with membrane-bounded nucleoids. Histone-coated DNA, protein-synthetic RNAs, amino-acylating, and other enzymes were contributed by the sulfidogen whereas most intracellular motility derives from the spirochete. From this redox syntrophy in anoxic and microoxic Proterozoic habitats LECA evolved. The nucleus originated by recombination of eu- and archaebacterial DNA that remained attached to eubacterial motility structures and became the microtubular cytoskeleton, including the mitotic apparatus. Direct LECA descendants include free-living archaeprotists in anoxic environments: archamoebae, metamonads, parabasalids, and some mammalian symbionts with mitosomes. LECA later acquired the fully aerobic Krebs cycle-oxidative phosphorylation-mitochondrial metabolism by integration of the protomitochondrion, a third alpha-proteobacterial symbiont from which the ancestors to most protoctists, all fungi, plants, and animals evolved. Secondarily anaerobic eukaryotes descended from LECA after integration of this oxygen-respiring eubacterium. Explanatory power and experimental predictions for molecular biology of the LECA concept are stated.}, }
@article {pmid16937356, year = {2006}, author = {Das, J}, title = {The role of mitochondrial respiration in physiological and evolutionary adaptation.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {28}, number = {9}, pages = {890-901}, doi = {10.1002/bies.20463}, pmid = {16937356}, issn = {0265-9247}, mesh = {*Adaptation, Physiological ; Animals ; *Biological Evolution ; Cell Respiration/*physiology ; Energy Metabolism ; Mitochondria/*metabolism ; Selection, Genetic ; }, abstract = {Aerobic mitochondria serve as the power sources of eukaryotes by producing ATP through oxidative phosphorylation (OXPHOS). The enzymes involved in OXPHOS are multisubunit complexes encoded by both nuclear and mitochondrial DNA. Thus, regulation of respiration is necessarily a highly coordinated process that must organize production, assembly and function of mitochondria to meet an organism's energetic needs. Here I review the role of OXPHOS in metabolic adaptation and diversification of higher animals. On a physiological timescale, endocrine-initiated signaling pathways allow organisms to modulate respiratory enzyme concentration and function under changing environmental conditions. On an evolutionary timescale, mitochondrial enzymes are targets of natural selection, balancing cytonuclear coevolutionary constraints against physiological innovation. By synthesizing our knowledge of biochemistry, physiology and evolution of respiratory regulation, I propose that we can now explore questions at the interface of these fields, from molecular translation of environmental cues to selection on mitochondrial haplotype variation.}, }
@article {pmid16936790, year = {2006}, author = {Stewart, JB and Beckenbach, AT}, title = {Insect mitochondrial genomics 2: The complete mitochondrial genome sequence of a giant stonefly, Pteronarcys princeps, asymmetric directional mutation bias, and conserved plecopteran A+T-region elements.}, journal = {Genome}, volume = {49}, number = {7}, pages = {815-824}, doi = {10.1139/g06-037}, pmid = {16936790}, issn = {0831-2796}, mesh = {Animals ; Base Composition ; Base Sequence ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; *Genome, Insect ; Insecta/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; *Mutation ; Phylogeny ; }, abstract = {Mitochondrial (mt) genome sequences of insects are receiving renewed attention in molecular phylogentic studies, studies of mt-genome rearrangement, and other unusual molecular phenomena, such as translational frameshifting. At present, the basal neopteran lineages are poorly represented by mt-genome sequences. Complete mt-genome sequences are available in the databases for only the Orthoptera and Blatteria; 9 orders are unrepresented. Here, we present the complete mt-genome sequence of a giant stonefly, Pteronarcys princeps (Plecoptera; Pteronarcyidae). The 16,004 bp genome is typical in its genome content, gene organisation, and nucleotide composition. The genome shows evidence of strand-specific mutational biases, correlated with the time between the initiation of leading and the initiation of lagging strand replication. Comparisons with other insects reveal that this trend is seen in other insect groups, but is not universally consistent among sampled mt-genomes. The A+T region is compared with that of 2 stoneflies in the family Peltoperlidae. Conserved stem-loop structures and sequence blocks are noted between these distantly related families.}, }
@article {pmid16935874, year = {2006}, author = {Boulé, JB and Zakian, VA}, title = {Roles of Pif1-like helicases in the maintenance of genomic stability.}, journal = {Nucleic acids research}, volume = {34}, number = {15}, pages = {4147-4153}, pmid = {16935874}, issn = {1362-4962}, support = {GM43265/GM/NIGMS NIH HHS/United States ; R01 GM043265/GM/NIGMS NIH HHS/United States ; GM26938/GM/NIGMS NIH HHS/United States ; R37 GM026938/GM/NIGMS NIH HHS/United States ; R01 GM026938/GM/NIGMS NIH HHS/United States ; }, mesh = {Conserved Sequence ; DNA Helicases/chemistry/*physiology ; DNA Replication/*physiology ; Evolution, Molecular ; Genomic Instability/*physiology ; Humans ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/chemistry ; }, abstract = {The Pif1p family of DNA helicases is conserved from yeast to humans. To date, four members of this family have been analyzed in some detail by in vitro and in vivo assays: the two baker's yeast helicases, ScPif1p and Rrm3p, the fission yeast Pfh1p and the human enzyme hPif1p. In vitro, these enzymes are 5' to 3' DNA helicase and show little processivity. In vivo, ScPif1p, Rrm3p and probably Pfh1p, function in both the nucleus at specific genomic loci and in mitochondria, where they are needed for the stable maintenance of the genome as accessory helicases to the replication machinery. Interestingly, they act on common DNA substrates but appear to have largely non-overlapping cellular functions, ranging from Okazaki fragment processing, telomerase inhibition, to helping the replication fork progress through non-nucleosomal protein-DNA complexes. For example, both ScPif1p and Rrm3p affect the replication of telomeres, but in a different way: Pif1p inhibits telomerase-mediated telomere elongation by directly removing telomerase from a DNA end, whereas Rrm3p facilitates replication through telomeric DNA. Here we review the current knowledge on the Pif1-like helicases, as a first step towards understanding the basis of their functional specialization and mechanism of action.}, }
@article {pmid16930655, year = {2006}, author = {Israelsson, O}, title = {Observations on some unusual cell types in the enigmatic worm Xenoturbella (phylum uncertain).}, journal = {Tissue &amp; cell}, volume = {38}, number = {4}, pages = {233-242}, doi = {10.1016/j.tice.2006.05.002}, pmid = {16930655}, issn = {0040-8166}, mesh = {Animals ; Cell Differentiation/physiology ; Cilia/physiology/ultrastructure ; Helminths/physiology/*ultrastructure ; Intestines/physiology/ultrastructure ; Muscle Cells/physiology/ultrastructure ; Phagocytes/physiology/ultrastructure ; Regeneration/physiology ; }, abstract = {The inner epithelially organized gastrodermis of the enigmatic simple worms of the genus Xenoturbella contains numerous partly phagocytized cells of two kinds, ciliated cells (PCCs) and muscle cells (PMCs). PCCs and PMCs have features of undifferentiated cells and do not derive from differentiated adult cells. Homology of phagocytized cells to pulsatile bodies in acoel and nemertodermatid flatworms is therefore rejected. The phagocytized cells might represent an hitherto unknown process of regeneration in Xenoturbella. The phagocytized material contains as much DNA as in all mitochondria and nuclei of the living cells. This is probably caused by lack of digestion of nucleic acids. The genome size of Xenoturbella bocki was determined. It has a C-value of about 0.55 pg.}, }
@article {pmid16929655, year = {2006}, author = {Ellison, CK and Burton, RS}, title = {Disruption of mitochondrial function in interpopulation hybrids of Tigriopus californicus.}, journal = {Evolution; international journal of organic evolution}, volume = {60}, number = {7}, pages = {1382-1391}, pmid = {16929655}, issn = {0014-3820}, mesh = {Adaptation, Biological ; Adenosine Triphosphate/metabolism ; Biological Evolution ; Cell Nucleus/genetics ; Citrate (si)-Synthase/metabolism ; Copepoda/enzymology/genetics/*metabolism ; DNA-Directed RNA Polymerases/metabolism ; Electron Transport ; Genotype ; Hybridization, Genetic ; Inbreeding ; Mitochondria/enzymology/genetics/*metabolism ; Species Specificity ; }, abstract = {Electron transport system (ETS) function in mitochondria is essential for the aerobic production of energy. Because ETS function requires extensive interactions between mitochondrial and nuclear gene products, coadaptation between mitochondrial and nuclear genomes may evolve within populations. Hybridization between allopatric populations may then expose functional incompatibilities between genomes that have not coevolved. The intertidal copepod Tigriopus californicus has high levels of nucleotide divergence among populations at mitochondrial loci and suffers F2 hybrid breakdown in interpopulation hybrids. We hypothesize that hybridization results in incompatibilities among subunits in ETS enzyme complexes and that these incompatibilities result in diminished mitochondrial function and fitness. To test this hypothesis, we measured fitness, mitochondrial function, and ETS enzyme activity in inbred recombinant hybrid lines of Tigriopus californicus. We found that (1) both fitness and mitochondrial function are reduced in hybrid lines, (2) only those ETS enzymes with both nuclear and mitochondrial subunits show a loss of activity in hybrid lines, and (3) positive relationships exist between ETS enzyme activity and mitochondrial function and between mitochondrial function and fitness. We also present evidence that hybrid lines harboring mitochondrial DNA (mtDNA) and mitochondrial RNA polymerase (mtRPOL) from the same parental source population have higher fitness than those with mtDNA and mtRPOL from different populations, suggesting that mitochondrial gene regulation may play a role in disruption of mitochondrial performance and fitness of hybrids. These results suggest that disruption of coadaptation between nuclear and mitochondrial genes contributes to the phenomenon of hybrid breakdown.}, }
@article {pmid16923830, year = {2006}, author = {Terada, LS}, title = {Specificity in reactive oxidant signaling: think globally, act locally.}, journal = {The Journal of cell biology}, volume = {174}, number = {5}, pages = {615-623}, pmid = {16923830}, issn = {0021-9525}, support = {R01 HL061897/HL/NHLBI NIH HHS/United States ; R01 HL067256/HL/NHLBI NIH HHS/United States ; R01-HL61897/HL/NHLBI NIH HHS/United States ; R01-HL67256/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Calcium Signaling ; Cytosol/*metabolism ; Evolution, Molecular ; Homeostasis ; Humans ; Mitochondria/*metabolism ; NADPH Oxidases/genetics/metabolism ; *Oxidative Stress ; Reactive Oxygen Species/*metabolism ; *Signal Transduction ; Tyrosine/metabolism ; rac1 GTP-Binding Protein/metabolism ; }, abstract = {Although reactive oxidants have long been stigmatized as unwanted metabolic byproducts, the expression of oxidases specifically functioning to produce these same molecules in a regulated fashion is surprisingly pervasive throughout metazoan and plant evolution. Although the involvement of oxidants in many signaling pathways is well documented, the cellular strategies for conferring pathway specificity to such reactive molecules have remained more recondite. Recent studies now suggest that cells may spatially restrict oxidant production to allow microdomain-specific signaling.}, }
@article {pmid16923211, year = {2006}, author = {Lo, N and Eldridge, RH and Lenz, M}, title = {Phylogeny of Australian Coptotermes (Isoptera: Rhinotermitidae) species inferred from mitochondrial COII sequences.}, journal = {Bulletin of entomological research}, volume = {96}, number = {4}, pages = {433-437}, pmid = {16923211}, issn = {0007-4853}, mesh = {Animals ; Australia ; Electron Transport Complex IV/*genetics ; Isoptera/*enzymology/*genetics ; Mitochondria/*enzymology ; *Phylogeny ; }, abstract = {Six Australian species of Coptotermes are traditionally recognized, but recent cuticular hydrocarbon studies suggest that some of these may represent more than one species. An understanding of the phylogenetic diversity of Australian Coptotermes, particularly the pest species, is likely to be important for the improvement of termite management strategies. A study of phylogenetic relationships among species of this genus was performed, based on the mitochondrial cytochrome oxidase (COII) gene, comparing the data with recent data from Asian species. Representatives of the species C. lacteus (Froggatt), C. frenchi Hill and C. michaelseni Silvestri were each found to form closely related monophyletic groups, however representatives of C. acinaciformis (Froggatt) were not. For C. acinaciformis, representatives from northern mound-building populations were found to form a distinct group to southern, tree-nesting forms. Among southern C. acinaciformis, two Western Australian representatives were found to be divergent from other populations. The results suggest that C. acinaciformis probably represents a complex of species rather than one, as has been suggested previously. One unidentified Coptotermes sp. taxon from Melbourne was found to be divergent from other taxa. Notably, some Australian species were more closely related to Asian species than other Australian species.}, }
@article {pmid16920629, year = {2006}, author = {Schilke, B and Williams, B and Knieszner, H and Pukszta, S and D'Silva, P and Craig, EA and Marszalek, J}, title = {Evolution of mitochondrial chaperones utilized in Fe-S cluster biogenesis.}, journal = {Current biology : CB}, volume = {16}, number = {16}, pages = {1660-1665}, doi = {10.1016/j.cub.2006.06.069}, pmid = {16920629}, issn = {0960-9822}, support = {2P04 A 00530//PHS HHS/United States ; R01 GM 27870/GM/NIGMS NIH HHS/United States ; }, mesh = {Computational Biology ; Escherichia coli ; *Evolution, Molecular ; Gene Duplication ; HSP70 Heat-Shock Proteins/metabolism ; Iron-Sulfur Proteins/genetics/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins ; Molecular Chaperones/genetics/*metabolism ; Phylogeny ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; }, abstract = {Biogenesis of Fe-S clusters is an essential process [1]. In both Escherichia coli and Saccharomyces cerevisiae, insertion of clusters into an apoprotein requires interaction between a scaffold protein on which clusters are assembled and a molecular chaperone system--an unusually specialized mitochondrial Hsp70 (mtHsp70) and its J protein cochaperone [2]. It is generally assumed that mitochondria inherited their Fe-S cluster assembly machinery from prokaryotes via the endosymbiosis of a bacterium that led to formation of mitochondria. Indeed, phylogenetic analyses demonstrated that the S. cerevisiae J protein, Jac1, and the scaffold, Isu, are orthologous to their bacterial counterparts [3, 4]. However, our analyses indicate that the specialized mtHsp70, Ssq1, is only present in a subset of fungi; most eukaryotes have a single mtHsp70, Ssc1. We propose that an Hsp70 having a role limited to Fe-S cluster biogenesis arose twice during evolution. In the fungal lineage, the gene encoding multifunctional mtHsp70, Ssc1, was duplicated, giving rise to specialized Ssq1. Therefore, Ssq1 is not orthologous to the specialized Hsp70 from E. coli (HscA), but shares a striking level of convergence at the biochemical level. Thus, in the vast majority of eukaryotes, Jac1 and Isu function with the single, multifunctional mtHsp70 in Fe-S cluster biogenesis.}, }
@article {pmid16919404, year = {2006}, author = {Podsiadlowski, L and Carapelli, A and Nardi, F and Dallai, R and Koch, M and Boore, JL and Frati, F}, title = {The mitochondrial genomes of Campodea fragilis and Campodea lubbocki (Hexapoda: Diplura): High genetic divergence in a morphologically uniform taxon.}, journal = {Gene}, volume = {381}, number = {}, pages = {49-61}, doi = {10.1016/j.gene.2006.06.009}, pmid = {16919404}, issn = {0378-1119}, mesh = {Animals ; Base Composition ; Base Sequence ; *DNA, Mitochondrial ; Evolution, Molecular ; *Genetic Drift ; *Genome, Insect ; Insecta/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Polymerase Chain Reaction ; RNA, Transfer/genetics ; }, abstract = {Complete mitochondrial genome sequences are presented from two dipluran hexapods (i.e., a group of "primarily wingless insects") of the genus Campodea and compared to those of other arthropods. Their gene order is the same as in most other hexapods and crustaceans. Structural changes have occurred in tRNA-C, tRNA-R, tRNA-S1 and tRNA-S2 as well as in both ribosomal RNAs. These mtDNAs have striking biases in nucleotide and amino acid composition. Although the two Campodea species are morphologically highly similar, their genetic divergence is larger than expected, suggesting a long evolutionary history, perhaps under stable ecological conditions.}, }
@article {pmid16918441, year = {2006}, author = {Salvioli, S and Capri, M and Valensin, S and Tieri, P and Monti, D and Ottaviani, E and Franceschi, C}, title = {Inflamm-aging, cytokines and aging: state of the art, new hypotheses on the role of mitochondria and new perspectives from systems biology.}, journal = {Current pharmaceutical design}, volume = {12}, number = {24}, pages = {3161-3171}, doi = {10.2174/138161206777947470}, pmid = {16918441}, issn = {1381-6128}, mesh = {Aging/*physiology ; Animals ; Cytokines/genetics/*physiology ; Humans ; Inflammation/genetics/*physiopathology ; Mitochondria/*physiology ; Phylogeny ; Polymorphism, Genetic/genetics ; Systems Biology/methods ; }, abstract = {In this article we summarise present knowledge on the role of pro-inflammatory cytokines on chronic inflammation leading to organismal aging, a phenomenon we proposed to call "inflamm-aging". In particular, we review genetic data regarding polymorphisms of genes encoding for cytokines and proteins involved in natural immunity (such as Toll-like Receptors and Heat Shock Proteins) obtained from large population studies including young, old and very old people in good health status or affected by age-related diseases such as Alzheimer's Disease and Type II Diabetes. On the whole, despite some controversial results, the available data are in favour of the hypothesis that pro-inflammatory cytokines play an important role in aging and longevity. Further, we present a possible hypothesis to reconcile energetic dysfunction, including mitochondria, and inflamm-aging. New perspectives for future studies, including phylogenetic studies in animal models and in silico studies on mathematical and bioinformatic models inspired by the systems biology approach, are also proposed.}, }
@article {pmid16911214, year = {2006}, author = {Audzijonyte, A and Daneliya, ME and Väinölä, R}, title = {Comparative phylogeography of Ponto-Caspian mysid crustaceans: isolation and exchange among dynamic inland sea basins.}, journal = {Molecular ecology}, volume = {15}, number = {10}, pages = {2969-2984}, doi = {10.1111/j.1365-294X.2006.03018.x}, pmid = {16911214}, issn = {0962-1083}, mesh = {Animals ; Crustacea/*genetics ; Ecology ; Genetic Variation ; *Geography ; Haplotypes ; Mitochondria/metabolism ; Oceans and Seas ; *Phylogeny ; Species Specificity ; }, abstract = {The distributions of many endemic Ponto-Caspian brackish-water taxa are subdivided among the Black, Azov and Caspian Sea basins and further among river estuaries. Of the two alternative views to explain the distributions, the relict school has claimed Tertiary fragmentation of the once contiguous range by emerging geographical and salinity barriers, whereas the immigration view has suggested recolonization of the westerly populations from the Caspian Sea after extirpation during Late Pleistocene environmental perturbations. A study of mitochondrial (COI) phylogeography of seven mysid crustacean taxa from the genera Limnomysis and Paramysis showed that both scenarios can be valid for different species. Four taxa had distinct lineages related to the major basin subdivision, but the lineage distributions and depths of divergence were not concordant. The data do not support a hypothesis of Late Miocene (10-5 Myr) vicariance; rather, range subdivisions and dispersal from and to the Caspian Sea seem to have occurred at different times throughout the Pleistocene. For example, in Paramysis lacustris each basin had an endemic clade 2-5% diverged from the others, whereas Paramysis kessleri from the southern Caspian and the western Black Sea were nearly identical. Species-specific ecological characteristics such as vagility and salinity tolerance seem to have played important roles in shaping the phylogeographic patterns. The mitochondrial data also suggested recent, human-mediated cryptic invasions of P. lacustris and Limnomysis benedeni from the Caspian to the Sea of Azov basin via the Volga-Don canal. Cryptic species-level subdivisions were recorded in populations attributed to Paramysis baeri, and possibly in P. lacustris.}, }
@article {pmid16907971, year = {2006}, author = {Koonin, EV}, title = {The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?.}, journal = {Biology direct}, volume = {1}, number = {}, pages = {22}, pmid = {16907971}, issn = {1745-6150}, abstract = {BACKGROUND: Ever since the discovery of 'genes in pieces' and mRNA splicing in eukaryotes, origin and evolution of spliceosomal introns have been considered within the conceptual framework of the 'introns early' versus 'introns late' debate. The 'introns early' hypothesis, which is closely linked to the so-called exon theory of gene evolution, posits that protein-coding genes were interrupted by numerous introns even at the earliest stages of life's evolution and that introns played a major role in the origin of proteins by facilitating recombination of sequences coding for small protein/peptide modules. Under this scenario, the absence of spliceosomal introns in prokaryotes is considered to be a result of "genome streamlining". The 'introns late' hypothesis counters that spliceosomal introns emerged only in eukaryotes, and moreover, have been inserted into protein-coding genes continuously throughout the evolution of eukaryotes. Beyond the formal dilemma, the more substantial side of this debate has to do with possible roles of introns in the evolution of eukaryotes.<br><br>RESULTS: I argue that several lines of evidence now suggest a coherent solution to the introns-early versus introns-late debate, and the emerging picture of intron evolution integrates aspects of both views although, formally, there seems to be no support for the original version of introns-early. Firstly, there is growing evidence that spliceosomal introns evolved from group II self-splicing introns which are present, usually, in small numbers, in many bacteria, and probably, moved into the evolving eukaryotic genome from the alpha-proteobacterial progenitor of the mitochondria. Secondly, the concept of a primordial pool of 'virus-like' genetic elements implies that self-splicing introns are among the most ancient genetic entities. Thirdly, reconstructions of the ancestral state of eukaryotic genes suggest that the last common ancestor of extant eukaryotes had an intron-rich genome. Thus, it appears that ancestors of spliceosomal introns, indeed, have existed since the earliest stages of life's evolution, in a formal agreement with the introns-early scenario. However, there is no evidence that these ancient introns ever became widespread before the emergence of eukaryotes, hence, the central tenet of introns-early, the role of introns in early evolution of proteins, has no support. However, the demonstration that numerous introns invaded eukaryotic genes at the outset of eukaryotic evolution and that subsequent intron gain has been limited in many eukaryotic lineages implicates introns as an ancestral feature of eukaryotic genomes and refutes radical versions of introns-late. Perhaps, most importantly, I argue that the intron invasion triggered other pivotal events of eukaryogenesis, including the emergence of the spliceosome, the nucleus, the linear chromosomes, the telomerase, and the ubiquitin signaling system. This concept of eukaryogenesis, in a sense, revives some tenets of the exon hypothesis, by assigning to introns crucial roles in eukaryotic evolutionary innovation.<br><br>CONCLUSION: The scenario of the origin and evolution of introns that is best compatible with the results of comparative genomics and theoretical considerations goes as follows: self-splicing introns since the earliest stages of life's evolution--numerous spliceosomal introns invading genes of the emerging eukaryote during eukaryogenesis--subsequent lineage-specific loss and gain of introns. The intron invasion, probably, spawned by the mitochondrial endosymbiont, might have critically contributed to the emergence of the principal features of the eukaryotic cell. This scenario combines aspects of the introns-early and introns-late views.<br><br>REVIEWERS: this article was reviewed by W. Ford Doolittle, James Darnell (nominated by W. Ford Doolittle), William Martin, and Anthony Poole.}, }
@article {pmid16905875, year = {2006}, author = {Ishii, T and Takahashi, C and Ikeda, N and Kamijima, O and Mori, N}, title = {Mitochondrial microsatellite variability in common wheat and its ancestral species.}, journal = {Genes &amp; genetic systems}, volume = {81}, number = {3}, pages = {211-214}, doi = {10.1266/ggs.81.211}, pmid = {16905875}, issn = {1341-7568}, mesh = {DNA, Mitochondrial/genetics ; Evolution, Molecular ; *Genetic Variation ; Microsatellite Repeats/*genetics ; Mitochondria/*genetics ; Triticum/*genetics ; }, abstract = {On the basis of the entire mitochondrial DNA sequence of common wheat, Triticum aestivum, 21 mitochondrial microsatellite loci having more than ten mononucleotide repeats were identified. The mitochondrial microsatellite variability at all loci was examined with 43 accessions from 11 Triticum and Aegilops species involved in wheat polyploidy evolution. Polymorphic banding patterns were obtained at 15 out of 21 mitochondrial microsatellite loci. The number of alleles per polymorphic microsatellite ranged from 2 to 5 with an average of 3.07, and the diversity values (H) ranged from 0.09 to 0.50 with an average of 0.29. These values are almost two third of wheat chloroplast microsatellite values, indicating that variability of mitochondrial microsatellite is much less than that of chloroplast microsatellite. Based on the allele variation at all loci, a total of seven mitochondrial haplotypes were identified among common wheat and its ancestral species. Three diploid species showed their own specific haplotypes and timopheevi group (11 accessions) had three types, whereas 29 accessions of emmer and common wheat groups shared the same haplotype. These results indicate that a single mitochondrial haplotype determined by microsatellite analysis has conservatively been maintained in the evolutionary lineage from wild tetraploid to cultivated hexaploid species.}, }
@article {pmid16905872, year = {2006}, author = {Munemasa, M and Nikaido, M and Donnellan, S and Austin, CC and Okada, N and Hasegawa, M}, title = {Phylogenetic analysis of diprotodontian marsupials based on complete mitochondrial genomes.}, journal = {Genes &amp; genetic systems}, volume = {81}, number = {3}, pages = {181-191}, doi = {10.1266/ggs.81.181}, pmid = {16905872}, issn = {1341-7568}, mesh = {Animals ; *DNA, Mitochondrial ; *Genome ; Likelihood Functions ; Marsupialia/*genetics ; Mitochondria/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; }, abstract = {Australidelphia is the cohort, originally named by Szalay, of all Australian marsupials and the South American Dromiciops. A lot of mitochondria and nuclear genome studies support the hypothesis of a monophyly of Australidelphia, but some familial relationships in Australidelphia are still unclear. In particular, the familial relationships among the order Diprotodontia (koala, wombat, kangaroos and possums) are ambiguous. These Diprotodontian families are largely grouped into two suborders, Vombatiformes, which contains Phascolarctidae (koala) and Vombatidae (wombat), and Phalangerida, which contains Macropodidae, Potoroidae, Phalangeridae, Petauridae, Pseudocheiridae, Acrobatidae, Tarsipedidae and Burramyidae. Morphological evidence and some molecular analyses strongly support monophyly of the two families in Vombatiformes. The monophyly of Phalangerida as well as the phylogenetic relationships of families in Phalangerida remains uncertain, however, despite searches for morphological synapomorphy and mitochondrial DNA sequence analyses. Moreover, phylogenetic relationships among possum families (Phalangeridae, Petauridae, Pseudocheiridae, Acrobatidae, Tarsipedidae and Burramyidae) as well as a sister group of Macropodoidea (Macropodidae and Potoroidae) remain unclear. To evaluate familial relationships among Dromiciops and Australian marsupials as well as the familial relationships in Diprotodontia, we determined the complete mitochondrial sequence of six Diprotodontian species. We used Maximum Likelihood analyses with concatenated amino acid and codon sequences of 12 mitochondrial protein genomes. Our analysis of mitochondria amino acid sequence supports monophyly of Australian marsupials+Dromiciops and monophyly of Phalangerida. The close relatedness between Macropodidae and Phalangeridae is also weakly supported by our analysis.}, }
@article {pmid16905154, year = {2006}, author = {Seligmann, H and Krishnan, NM and Rao, BJ}, title = {Mitochondrial tRNA sequences as unusual replication origins: pathogenic implications for Homo sapiens.}, journal = {Journal of theoretical biology}, volume = {243}, number = {3}, pages = {375-385}, doi = {10.1016/j.jtbi.2006.06.028}, pmid = {16905154}, issn = {0022-5193}, mesh = {Aging/genetics ; *DNA Replication ; Genome ; Humans ; Mitochondria/*genetics ; Mitochondrial Diseases/*genetics ; *Models, Genetic ; Mutation ; RNA, Transfer/*genetics ; Sequence Homology ; Transcription, Genetic ; }, abstract = {The heavy strand of vertebrate mitochondrial genomes accumulates deaminations proportionally to the time it spends single-stranded during replication. A previous study showed that the strength of genome-wide deamination gradients originating from tRNA gene's locations increases with their capacities to form secondary structures resembling mitochondrial origins of light strand replication (OL), suggesting an alternative function for tRNA sequences. We hypothesize that this function is frequently pathogenic for those tRNA genes that normally do not form OL-like structures, because this could cause excess mutations in genome regions unadapted to tolerate them. In human mitochondrial genomes, pathogenic tRNA variants usually form less OL-like structures than non-pathogenic ones in cases where the normal non-pathogenic tRNA variant can function as OL, as evolutionary analyses reveal. For tRNAs lacking the putative OL-like functioning capacity, pathogenic variants form more OL-like secondary structures, particularly structures that might invoke bi-directional replication (true for 14 among 21 tRNA species, p<0.05, sign test; significantly at p<0.05 (1 tailed test) for 7 tRNA species), but not more unidirectional replication invoking structures. Accounting for the functional cloverleaf-like structure-forming capacities of tRNAs yields similar results. Rare, non-pathogenic tRNA mutants tend to form more OL-like structures than the common, non-pathogenic ones, suggesting weak directional selection also among non-pathogenic variants. The duration spent single stranded by a region of the heavy strand (D(ssH)) during replication, estimated by integrating over all regions that can function as OL in Homo sapiens mitochondrial genomes, increases with distance of that region from the Dloop. This suggests convergence of single-strandedness during replication and transcription, and explains conserved locations of tRNA species in mitochondrial genomes and bacterial operons. These locations minimize deamination costs only in anticodons and not in other tRNA regions, during replication and transcription. Therefore, putative functioning as OLs by tRNA sequences is normal at some locations and pathogenic at others.}, }
@article {pmid16897469, year = {2006}, author = {Arnal, N and Alban, C and Quadrado, M and Grandjean, O and Mireau, H}, title = {The Arabidopsis Bio2 protein requires mitochondrial targeting for activity.}, journal = {Plant molecular biology}, volume = {62}, number = {3}, pages = {471-479}, pmid = {16897469}, issn = {0167-4412}, mesh = {Arabidopsis/genetics/*metabolism ; Base Sequence ; Cytosol/metabolism ; DNA Primers ; DNA, Bacterial/genetics ; Mitochondria/*metabolism ; Mutation ; Sulfurtransferases/genetics/*metabolism ; }, abstract = {Mitochondria are involved in the production of various vitamins, such as biotin, in plants. It is unclear why these biosynthetic pathways have been maintained partly or entirely within the mitochondria throughout evolution. The last step in biotin biosynthesis occurs within the mitochondria and is catalyzed by the biotin synthase complex containing the BIO2 gene product. We investigated whether the Arabidopsis Bio2 enzyme could function outside mitochondria, by trying to complement a bio2 mutant with a truncated version of BIO2 lacking the region encoding the mitochondrial targeting sequence. We describe the characterization of a new T-DNA allele of bio2, with the sole phenotype of an absence of biotin production, in contrast to the previously characterized EMS bio2 allele (Patton et al. 1998, Plant Physiol 116(3):935-946). We found that a cytosolic version of the Bio2 protein could not complement this mutant. Supplementation with the substrate dethiobiotin (DTB) also failed to rescue the mutant phenotype. Thus, the lack of availability of DTB in the cytosol is not the only factor preventing this reaction from occurring outside mitochondria. Bio2 requires mitochondrial targeting for activity, enabling it to fulfill its role in biotin synthesis. The reaction catalyzed by Bio2 may be subject to biochemical constraints, and the apparent close connection with the mitochondrial Fe-S machinery may account for the reaction being retained within the organelle.}, }
@article {pmid16897087, year = {2006}, author = {Hackstein, JH and Tjaden, J and Huynen, M}, title = {Mitochondria, hydrogenosomes and mitosomes: products of evolutionary tinkering!.}, journal = {Current genetics}, volume = {50}, number = {4}, pages = {225-245}, pmid = {16897087}, issn = {0172-8083}, mesh = {Animals ; Eukaryota/genetics/metabolism ; *Evolution, Molecular ; Mitochondria/*genetics/physiology ; Organelles/genetics/physiology ; Phylogeny ; Protozoan Proteins/metabolism ; }, }
@article {pmid16896205, year = {2006}, author = {Colasante, C and Alibu, VP and Kirchberger, S and Tjaden, J and Clayton, C and Voncken, F}, title = {Characterization and developmentally regulated localization of the mitochondrial carrier protein homologue MCP6 from Trypanosoma brucei.}, journal = {Eukaryotic cell}, volume = {5}, number = {8}, pages = {1194-1205}, pmid = {16896205}, issn = {1535-9778}, mesh = {Animals ; Base Sequence ; Escherichia coli/genetics ; Gene Expression Regulation, Developmental ; Humans ; Mitochondrial Membranes/*chemistry ; Mitochondrial Proteins/*chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/*chemistry/*genetics ; RNA, Messenger/biosynthesis ; Sequence Alignment ; Sequence Homology, Amino Acid ; Trypanosoma brucei brucei/*genetics/growth &amp; development ; }, abstract = {Proteins of the mitochondrial carrier family (MCF) are located mainly in the inner mitochondrial membrane and mediate the transport of a large range of metabolic intermediates. The genome of Trypanosoma brucei harbors 29 genes encoding different MCF proteins. We describe here the characterization of MCP6, a novel T. brucei MCF protein. Sequence comparison and phylogenetic reconstruction revealed that MCP6 is closely related to different mitochondrial ADP/ATP and calcium-dependent solute carriers, including the ATP-Mg/Pi carrier of Homo sapiens. However, MCP6 lacks essential amino acids and sequence motifs conserved in these metabolite transporters, and functional reconstitution and transport assays with E. coli suggested that this protein indeed does not function as an ADP/ATP or ATP-Mg/Pi carrier. The subcellular localization of MCP6 is developmentally regulated: in bloodstream-form trypanosomes, the protein is predominantly glycosomal, whereas in the procyclic form, it is found mainly in the mitochondria. Depletion of MCP6 in procyclic trypanosomes resulted in growth inhibition, an increased cell size, aberrant numbers of nuclei and kinetoplasts, and abnormal kinetoplast morphology, suggesting that depletion of MCP6 inhibits division of the kinetoplast.}, }
@article {pmid16893615, year = {2006}, author = {Nikolaou, C and Almirantis, Y}, title = {Deviations from Chargaff's second parity rule in organellar DNA Insights into the evolution of organellar genomes.}, journal = {Gene}, volume = {381}, number = {}, pages = {34-41}, doi = {10.1016/j.gene.2006.06.010}, pmid = {16893615}, issn = {0378-1119}, mesh = {Animals ; Bacteria/genetics ; Caenorhabditis elegans/genetics ; Chloroplasts/*genetics ; DNA, Single-Stranded/chemistry/*genetics ; *Evolution, Molecular ; *Genome ; Humans ; Mitochondria/*genetics ; Rhizopus/genetics ; }, abstract = {Chargaff' s second parity rule (PR2) states that complementary nucleotides are met with almost equal frequencies in single stranded DNA. This is indeed the case for all bacterial and eukaryotic genomes studied, although the genomic patterns may differ among genomes in terms of local deviations. The behaviour of organellar genomes regarding the second parity rule has not been studied in detail up to now. We tested all available organellar genomes and found that a large number of mitochondrial genomes significantly deviate from the 2nd parity rule in contrast to the eubacterial ones, although mitochondria are believed to have evolved from proteobacteria. Moreover, mitochondria may be divided into three distinct sub-groups according to their overall deviation from the aforementioned parity rule. On the other hand, chloroplast genomes share the pattern of eubacterial genomes and, interestingly, so do mitochondrial genomes originating from plants and some fungi. The deviation from the second parity is found to be weakly correlated with the overall excess of purines against pyrimidines. The behaviour of the large majority of the mitochondrial genomes may be attributed to their distinct mode of replication, which is fundamentally different from the one of the eubacteria. Differences between chloroplast and mitochondrial genomes might also be explained on the basis of different replication mechanisms and correlated to differences in the genome size and compaction. The results presented herein may provide some insight into different modes of evolution of genome structure between chloroplasts and mitochondria.}, }
@article {pmid16891155, year = {2006}, author = {Okamoto, N and Inouye, I}, title = {Hatena arenicola gen. et sp. nov., a katablepharid undergoing probable plastid acquisition.}, journal = {Protist}, volume = {157}, number = {4}, pages = {401-419}, doi = {10.1016/j.protis.2006.05.011}, pmid = {16891155}, issn = {1434-4610}, mesh = {Animals ; Eukaryota/*classification/genetics/physiology/ultrastructure ; *Evolution, Molecular ; Microscopy, Electron ; Phylogeny ; Plastids/*ultrastructure ; *Symbiosis ; }, abstract = {Hatena arenicola gen. et sp. nov., an enigmatic flagellate of the katablepharids, is described. It shows ultrastructural affinities to the katablepharids, including large and small ejectisomes, cell covering, and a feeding apparatus. Although molecular phylogenies of the 18S ribosomal DNA support its classification into the katablepharids, the cell is characterized by a dorsiventrally compressed cell shape and a crawling motion, both of which are unusual within this group. The most distinctive feature of Hatena arenicola is that it harbors a Nephroselmis symbiont. This symbiosis is distinct from previously reported cases of ongoing symbiosis in that the symbiont plastid is selectively enlarged, while other structures such as the mitochondria, Golgi body, cytoskeleton, and endomembrane system are degraded; the host and symbiont have developed a morphological association, i.e., the eyespot of the symbiont is always at the cell apex of Hatena arenicola; and only one daughter cell inherits the symbiont during cell division, resulting in a symbiont-bearing green cell and a symbiont-lacking colorless cell. Interestingly, the colorless cells have a feeding apparatus that corresponds to the location of the eyespot in symbiont-bearing cells, and they are able to feed on prey cells. This indicates that the morphology of the host depends on the presence or absence of the symbiont. These observations suggest that Hatena arenicola has a unique "half-plant, half-predator" life cycle; one cell divides into an autotrophic cell possessing a symbiotic Nephroselmis species, and a symbiont-lacking colorless cell, which later develops a feeding apparatus de novo. The evolutionary implications of Hatena arenicola as an intermediate step in plastid acquisition are discussed in the context of other examples of ongoing endosymbioses in dinoflagellates.}, }
@article {pmid16884501, year = {2006}, author = {Bernard, L and Desplats, C and Mus, F and Cuiné, S and Cournac, L and Peltier, G}, title = {Agrobacterium tumefaciens type II NADH dehydrogenase. Characterization and interactions with bacterial and thylakoid membranes.}, journal = {The FEBS journal}, volume = {273}, number = {15}, pages = {3625-3637}, doi = {10.1111/j.1742-4658.2006.05370.x}, pmid = {16884501}, issn = {1742-464X}, mesh = {Agrobacterium tumefaciens/*enzymology ; Amino Acid Sequence ; Bacteria/classification/*metabolism ; Cell Membrane/metabolism ; Electrophoresis, Polyacrylamide Gel ; Genetic Complementation Test ; Molecular Sequence Data ; Mutation ; NADH Dehydrogenase/chemistry/genetics/*metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; Thylakoids/*metabolism ; }, abstract = {Type II NADH dehydrogenases (NDH-2) are monomeric enzymes that catalyse quinone reduction and allow electrons to enter the respiratory chain in different organisms including higher plant mitochondria, bacteria and yeasts. In this study, an Agrobacterium tumefaciens gene encoding a putative alternative NADH dehydrogenase (AtuNDH-2) was isolated and expressed in Escherichia coli as a (His)6-tagged protein. The purified 46 kDa protein contains FAD as a prosthetic group and oxidizes both NADH and NADPH with similar Vmax values, but with a much higher affinity for NADH than for NADPH. AtuNDH-2 complements the growth (on a minimal medium) of an E. coli mutant strain deficient in both NDH-1 and NDH-2, and is shown to supply electrons to the respiratory chain when incubated with bacterial membranes prepared from this mutant. By measuring photosystem II chlorophyll fluorescence on thylakoid membranes prepared from the green alga Chlamydomonas reinhardtii, we show that AtuNDH-2 is able to stimulate NADH-dependent reduction of the plastoquinone pool. We discuss the possibility of using heterologous expression of NDH-2 enzymes to improve nonphotochemical reduction of plastoquinones and H2 production in C. reinhardtii.}, }
@article {pmid16876233, year = {2006}, author = {Rottenberg, H}, title = {Longevity and the evolution of the mitochondrial DNA-coded proteins in mammals.}, journal = {Mechanisms of ageing and development}, volume = {127}, number = {9}, pages = {748-760}, doi = {10.1016/j.mad.2006.06.001}, pmid = {16876233}, issn = {0047-6374}, mesh = {Animals ; DNA, Mitochondrial/chemistry/*genetics ; Databases, Genetic ; *Evolution, Molecular ; Linear Models ; Longevity/*genetics ; Mammals/*genetics/physiology ; Mitochondria/genetics/physiology ; Mitochondrial Proteins/*genetics/physiology ; Phylogeny ; Reactive Oxygen Species ; Sequence Alignment ; }, abstract = {The amino acids sequences of the mitochondrial DNA-coded peptides of placental mammals evolved at different rates in different branches of the mammalian phylogenetic tree. Adaptive selection was suggested to account for the faster evolution of some mitochondrial DNA-coded proteins in several branches of the mammalian tree, but the driving force(s) for the accelerated evolution has not been elucidated. Mitochondria generate reactive oxygen species (ROS) that appear to constrain the life span of many species. Therefore, I tested the hypothesis that the evolution of mammalian longevity drives the accelerated evolution of mitochondrial DNA-coded peptides. Using rodents as an outgroup for a clad that included most placental mammals (excluding rodents and hedgehogs) the computed rates of amino acid substitution per site were positively correlated with genus longevity (maximal observed averaged life span) for most of the mitochondrial DNA-coded peptides. The substitution per site of ATP6, the proton conducting subunit of ATPsynthase, CYTB, the core subunit of ubiquinone oxidoreductase that participate in both electron and proton transport, and ND3, a subunit of NADH dehydrogenase, showed the strongest correlations with longevity. Additional confirmation for the hypothesis was obtained by the observation that the genetic distances between placental mammals species that belong to different orders are positively correlated with the sum of longevities of the species pairs. The substitutions per site for the entire amino acid sequence coded by the heavy strand mtDNA were also positively correlated with the average longevities of the placental mammals orders. These results support the hypothesis that the evolution of longevity in mammals drove the accelerated evolution of mtDNA-coded peptide. It is suggested that, in mammals, adaptive selection of mutations that decrease the rate of production of reactive oxygen species, directly or indirectly (e.g. by increasing proton leak), increases longevity.}, }
@article {pmid16874468, year = {2006}, author = {Park, JS and Cho, BC and Simpson, AG}, title = {Halocafeteria seosinensis gen. et sp. nov. (Bicosoecida), a halophilic bacterivorous nanoflagellate isolated from a solar saltern.}, journal = {Extremophiles : life under extreme conditions}, volume = {10}, number = {6}, pages = {493-504}, pmid = {16874468}, issn = {1431-0651}, mesh = {Animals ; *DNA, Protozoan ; Eukaryota/*classification/genetics/growth &amp; development/isolation &amp; purification/metabolism/ultrastructure ; Flagella/ultrastructure ; Korea ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; *Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Ribotyping ; Seawater/chemistry/*parasitology ; Sodium Chloride/analysis/*metabolism ; Temperature ; }, abstract = {Recently, heterotrophic nanoflagellates (HNF) have been reported to actively ingest prokaryotes in high salinity waters. We report the isolation and culture of an HNF from a Korean saltern pond of 300 per thousand salinity. The organism is biflagellated with an acronematic anterior flagellum and never glides on surfaces. The mitochondria have tubular cristae. Neither transitional helix nor spiral fiber were observed in the transition zones of the flagella. The cell has a cytostome supported by an arc of eight microtubules, suggesting that our isolate is a bicosoecid. Our isolate had neither mastigonemes, lorica, body scales, nor cytopharynx and thus could not be placed in any of the presently described bicosoecid genera. Phylogenetic analysis of 18S rRNA gene sequences from stramenopiles confirmed the bicosoecid affinities of our isolate, but did not place it within any established genus or family. Its closest relatives include Caecitellus and Cafeteria. The optimal range of growth temperature was 30-35 degrees C. The isolated HNF grew optimally at 150 per thousand salinity and tolerated up to 363 per thousand salinity, but it failed to grow below 75 per thousand salinity, indicating that it could be a borderline extreme halophile. On the basis of its morphological features and position in 18S rRNA trees we propose a novel genus for our isolate; Halocafeteria, n. gen. The species name Halocafeteria seosinensis sp. nov. is proposed.}, }
@article {pmid16872524, year = {2006}, author = {Alvarez, N and Benrey, B and Hossaert-McKey, M and Grill, A and McKey, D and Galtier, N}, title = {Phylogeographic support for horizontal gene transfer involving sympatric bruchid species.}, journal = {Biology direct}, volume = {1}, number = {}, pages = {21}, pmid = {16872524}, issn = {1745-6150}, support = {V 169/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {BACKGROUND: We report on the probable horizontal transfer of a mitochondrial gene, cytb, between species of Neotropical bruchid beetles, in a zone where these species are sympatric. The bruchid beetles Acanthoscelides obtectus, A. obvelatus, A. argillaceus and Zabrotes subfasciatus develop on various bean species in Mexico. Whereas A. obtectus and A. obvelatus develop on Phaseolus vulgaris in the Mexican Altiplano, A. argillaceus feeds on P. lunatus in the Pacific coast. The generalist Z. subfasciatus feeds on both bean species, and is sympatric with A. obtectus and A. obvelatus in the Mexican Altiplano, and with A. argillaceus in the Pacific coast. In order to assess the phylogenetic position of these four species, we amplified and sequenced one nuclear (28S rRNA) and two mitochondrial (cytb, COI) genes.<br><br>RESULTS: Whereas species were well segregated in topologies obtained for COI and 28S rRNA, an unexpected pattern was obtained in the cytb phylogenetic tree. In this tree, individuals from A. obtectus and A. obvelatus, as well as Z. subfasciatus individuals from the Mexican Altiplano, clustered together in a unique little variable monophyletic unit. In contrast, A. argillaceus and Z. subfasciatus individuals from the Pacific coast clustered in two separated clades, identically to the pattern obtained for COI and 28S rRNA. An additional analysis showed that Z. subfasciatus individuals from the Mexican Altiplano also possessed the cytb gene present in individuals of this species from the Pacific coast. Zabrotes subfasciatus individuals from the Mexican Altiplano thus demonstrated two cytb genes, an "original" one and an "infectious" one, showing 25% of nucleotide divergence. The "infectious" cytb gene seems to be under purifying selection and to be expressed in mitochondria.<br><br>CONCLUSION: The high degree of incongruence of the cytb tree with patterns for other genes is discussed in the light of three hypotheses: experimental contamination, hybridization, and pseudogenisation. However, none of these seem able to explain the patterns observed. A fourth hypothesis, involving recent horizontal gene transfer (HGT) between A. obtectus and A. obvelatus, and from one of these species to Z. subfasciatus in the Mexican Altiplano, seems the only plausible explanation. The HGT between our study species seems to have occurred recently, and only in a zone where the three beetles are sympatric and share common host plants. This suggests that transfer could have been effected by some external vector such as a eukaryotic or viral parasite, which might still host the transferred fragment.<br><br>REVIEWERS: This article was reviewed by Eric Bapteste, Adam Eyre-Walker and Alexey Kondrashov.}, }
@article {pmid16872296, year = {2006}, author = {Leander, BS and Ramey, PA}, title = {Cellular identity of a novel small subunit rDNA sequence clade of apicomplexans: description of the marine parasite Rhytidocystis polygordiae n. sp. (host: Polygordius sp., Polychaeta).}, journal = {The Journal of eukaryotic microbiology}, volume = {53}, number = {4}, pages = {280-291}, doi = {10.1111/j.1550-7408.2006.00109.x}, pmid = {16872296}, issn = {1066-5234}, mesh = {Animals ; Apicomplexa/*classification/*cytology/genetics ; DNA, Protozoan/genetics ; DNA, Ribosomal/*genetics ; Genes, rRNA ; Intestines/parasitology ; Microscopy, Electron, Transmission ; Phylogeny ; Polychaeta/*parasitology ; RNA, Ribosomal/*genetics ; Seawater/*parasitology ; }, abstract = {A new species of Rhytidocystis (Apicomplexa) is characterized from North American waters of the Atlantic Ocean using electron microscopy and phylogenetic analyses of small subunit (SSU) rDNA sequences. Rhytidocystis polygordiae n. sp. is a parasite of the polychaete Polygordius sp. and becomes the fourth described species within this genus. The trophozoites of R. polygordiae were relatively small oblong cells (L=35-55 microm; W=20-25 microm) and distinctive in possessing subterminal indentations at both ends of the cell. The surface of the trophozoites had six to eight longitudinal series of small transverse folds and several micropores arranged in short linear rows. The trophozoites of R. polygordiae were positioned beneath the brush border of the intestinal epithelium but appeared to reside between the epithelial cells within the extracellular matrix rather than within the cells. The trophozoites possessed a uniform distribution of paraglycogen granules, putative apicoplasts, mitochondria with tubular cristae, and a centrally positioned nucleus. The trophozoites were non-motile and lacked a mucron and an apical complex. Intracellular sporozoites of R. polygordiae had a conoid, a few rhoptries, micronemes, dense granules, and a posteriorly positioned nucleus. Phylogenies inferred from SSU rDNA sequences demonstrated a close relationship between R. polygordiae and the poorly known parasite reported from the hemolymph of the giant clam Tridacna crocea. The rhytidocystid clade diverged early in the apicomplexan radiation and showed a weak affinity to a clade consisting of cryptosporidian parasites, monocystids, and neogregarines.}, }
@article {pmid16859488, year = {2006}, author = {Sakurai, M and Watanabe, Y and Watanabe, K and Ohtsuki, T}, title = {A protein extension to shorten RNA: elongated elongation factor-Tu recognizes the D-arm of T-armless tRNAs in nematode mitochondria.}, journal = {The Biochemical journal}, volume = {399}, number = {2}, pages = {249-256}, pmid = {16859488}, issn = {1470-8728}, mesh = {Amino Acid Sequence ; Animals ; *Ascaris suum/cytology/genetics ; Base Sequence ; Binding Sites ; Caenorhabditis elegans/metabolism ; Cross-Linking Reagents ; Ethylnitrosourea ; Mitochondria/*genetics/*metabolism ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Nucleic Acid Conformation ; Peptide Elongation Factor Tu/chemistry/*metabolism ; RNA, Helminth/chemistry/genetics/*metabolism ; RNA, Transfer, Met/*chemistry/genetics/*metabolism ; Sequence Alignment ; Sequence Deletion ; }, abstract = {Nematode mitochondria possess extremely truncated tRNAs. Of 22 tRNAs, 20 lack the entire T-arm. The T-arm is necessary for the binding of canonical tRNAs and EF (elongation factor)-Tu (thermo-unstable). The nematode mitochondrial translation system employs two different EF-Tu factors named EF-Tu1 and EF-Tu2. Our previous study showed that nematode Caenorhabditis elegans EF-Tu1 binds specifically to T-armless tRNA. C. elegans EF-Tu1 has a 57-amino acid C-terminal extension that is absent from canonical EF-Tu, and the T-arm-binding residues of canonical EF-Tu are not conserved. In this study, the recognition mechanism of T-armless tRNA by EF-Tu1 was investigated. Both modification interference assays and primer extension analysis of cross-linked ternary complexes revealed that EF-Tu1 interacts not only with the tRNA acceptor stem but also with the D-arm. This is the first example of an EF-Tu recognizing the D-arm of a tRNA. The binding activity of EF-Tu1 was impaired by deletion of only 14 residues from the C-terminus, indicating that the C-terminus of EF-Tu1 is required for its binding to T-armless tRNA. These results suggest that C. elegans EF-Tu1 recognizes the D-arm instead of the T-arm by a mechanism involving its C-terminal region. This study sheds light on the co-evolution of RNA and RNA-binding proteins in nematode mitochondria.}, }
@article {pmid16857931, year = {2006}, author = {Dolezal, P and Likic, V and Tachezy, J and Lithgow, T}, title = {Evolution of the molecular machines for protein import into mitochondria.}, journal = {Science (New York, N.Y.)}, volume = {313}, number = {5785}, pages = {314-318}, doi = {10.1126/science.1127895}, pmid = {16857931}, issn = {1095-9203}, mesh = {Bacterial Proteins/chemistry/metabolism ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Intracellular Membranes/metabolism ; Membrane Proteins/metabolism ; Membrane Transport Proteins/chemistry/*genetics/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Molecular Chaperones/metabolism ; *Protein Transport ; Serine Endopeptidases/metabolism ; Symbiosis ; }, abstract = {In creating mitochondria some 2 billion years ago, the first eukaryotes needed to establish protein import machinery in the membranes of what was a bacterial endosymbiont. Some of the preexisting protein translocation apparatus of the endosymbiont appears to have been commandeered, including molecular chaperones, the signal peptidase, and some components of the protein-targeting machinery. However, the protein translocases that drive protein import into mitochondria have no obvious counterparts in bacteria, making it likely that these machines were created de novo. The presence of similar translocase subunits in all eukaryotic genomes sequenced to date suggests that all eukaryotes can be considered descendants of a single ancestor species that carried an ancestral "protomitochondria."}, }
@article {pmid16857679, year = {2006}, author = {Coustou, V and Biran, M and Besteiro, S and Rivière, L and Baltz, T and Franconi, JM and Bringaud, F}, title = {Fumarate is an essential intermediary metabolite produced by the procyclic Trypanosoma brucei.}, journal = {The Journal of biological chemistry}, volume = {281}, number = {37}, pages = {26832-26846}, doi = {10.1074/jbc.M601377200}, pmid = {16857679}, issn = {0021-9258}, mesh = {Animals ; Cytosol/enzymology ; Electrons ; Fumarates/*chemistry ; Glucose/metabolism ; Green Fluorescent Proteins/metabolism ; Microbodies/metabolism ; Mitochondria/enzymology ; Mutation ; Phylogeny ; Protein Isoforms ; RNA Interference ; Time Factors ; Trypanosoma brucei brucei/*metabolism ; }, abstract = {The procyclic stage of Trypanosoma brucei, a parasitic protist responsible for sleeping sickness in humans, converts most of the consumed glucose into excreted succinate, by succinic fermentation. Succinate is produced by the glycosomal and mitochondrial NADH-dependent fumarate reductases, which are not essential for parasite viability. To further explore the role of the succinic fermentation pathways, we studied the trypanosome fumarases, the enzymes providing fumarate to fumarate reductases. The T. brucei genome contains two class I fumarase genes encoding cytosolic (FHc) and mitochondrial (FHm) enzymes, which account for total cellular fumarase activity as shown by RNA interference. The growth arrest of a double RNA interference mutant cell line showing no fumarase activity indicates that fumarases are essential for the parasite. Interestingly, addition of fumarate to the medium rescues the growth phenotype, indicating that fumarate is an essential intermediary metabolite of the insect stage trypanosomes. We propose that trypanosomes use fumarate as an essential electron acceptor, as exemplified by the fumarate dependence previously reported for an enzyme of the essential de novo pyrimidine synthesis (Takashima, E., Inaoka, D. K., Osanai, A., Nara, T., Odaka, M., Aoki, T., Inaka, K., Harada, S., and Kita, K. (2002) Mol. Biochem. Parasitol. 122, 189-200).}, }
@article {pmid16855218, year = {2006}, author = {Schlick, NE and Jensen-Seaman, MI and Orlebeke, K and Kwitek, AE and Jacob, HJ and Lazar, J}, title = {Sequence analysis of the complete mitochondrial DNA in 10 commonly used inbred rat strains.}, journal = {American journal of physiology. Cell physiology}, volume = {291}, number = {6}, pages = {C1183-92}, doi = {10.1152/ajpcell.00234.2006}, pmid = {16855218}, issn = {0363-6143}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*analysis/chemistry/classification ; Evolution, Molecular ; Humans ; Mice ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Polymorphism, Single Nucleotide ; RNA, Transfer/genetics ; Rats ; Rats, Inbred Strains/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Rat remains a major biomedical model system for common, complex diseases. The rat continues to gain importance as a model system with the completion of its full genomic sequence. Although the genomic sequence has generated much interest, only three complete sequences of the rat mitochondria exist. Therefore, to increase the knowledge of the rat genome, the entire mitochondrial genomes (16,307-16,315 bp) from 10 inbred rat strains (that are standard laboratory models around the world) and 2 wild rat strains were sequenced. We observed a total of 195 polymorphisms, 32 of which created an amino acid change (nonsynonymous substitutions) in 12 of the 13 protein coding genes within the mitochondrial genome. There were 11 single nucleotide polymorphisms within the tRNA genes, six in the 12S rRNA, and 12 in the 16S rRNA including 3 insertions/deletions. We found 14 single nucleotide polymorphisms and 2 insertion/deletion polymorphisms in the D-loop. The inbred rat strains cluster phylogenetically into three distinct groups. The wild rat from Tokyo grouped closely with five inbred strains in the phylogeny, whereas the wild rat from Milwaukee was not closely related to any inbred strain. These data will enable investigators to rapidly assess the potential impact of the mitochondria in these rats on the physiology and the pathophysiology of phenotypes studied in these strains. Moreover, these data provide information that may be useful as new animal models, which result in novel combinations of nuclear and mitochondrial genomes, are developed.}, }
@article {pmid16854241, year = {2006}, author = {Boore, JL}, title = {The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda).}, journal = {BMC genomics}, volume = {7}, number = {}, pages = {182}, pmid = {16854241}, issn = {1471-2164}, mesh = {Animals ; Base Composition ; Base Sequence ; Codon, Initiator ; Codon, Terminator ; *Genes, Mitochondrial ; Models, Genetic ; Molecular Sequence Data ; Nautilus/*genetics ; RNA, Transfer ; RNA, Untranslated ; Regulatory Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Signal Transduction ; }, abstract = {BACKGROUND: Mitochondria contain small genomes that are physically separate from those of nuclei. Their comparison serves as a model system for understanding the processes of genome evolution. Although complete mitochondrial genome sequences have been reported for more than 600 animals, the taxonomic sampling is highly biased toward vertebrates and arthropods, leaving much of the diversity yet uncharacterized.<br><br>RESULTS: The mitochondrial genome of the bellybutton nautilus, Nautilus macromphalus, a cephalopod mollusk, is 16,258 nts in length and 59.5% A+T, both values that are typical of animal mitochondrial genomes. It contains the 37 genes that are almost universally found in animal mtDNAs, with 15 on one DNA strand and 22 on the other. The arrangement of these genes can be derived from that of the distantly related Katharina tunicata (Mollusca: Polyplacophora) by a switch in position of two large blocks of genes and transpositions of four tRNA genes. There is strong skew in the distribution of nucleotides between the two strands, and analysis of this yields insight into modes of transcription and replication. There is an unusual number of non-coding regions and their function, if any, is not known; however, several of these demark abrupt shifts in nucleotide skew, and there are several identical sequence elements at these junctions, suggesting that they may play roles in transcription and/or replication. One of the non-coding regions contains multiple repeats of a tRNA-like sequence. Some of the tRNA genes appear to overlap on the same strand, but this could be resolved if the polycistron were cleaved at the beginning of the downstream gene, followed by polyadenylation of the product of the upstream gene to form a fully paired structure.<br><br>CONCLUSION: Nautilus macromphalus mtDNA contains an expected gene content that has experienced few rearrangements since the evolutionary split between cephalopods and polyplacophorans. It contains an unusual number of non-coding regions, especially considering that these otherwise often are generated by the same processes that produce gene rearrangements. The skew in nucleotide composition between the two strands is strong and associated with the direction of transcription in various parts of the genomes, but a comparison with K. tunicata implies that mutational bias during replication also plays a role. This appears to be yet another case where polyadenylation of mitochondrial tRNAs restores what would otherwise be an incomplete structure.}, }
@article {pmid16847554, year = {2006}, author = {Kasprzak, A and Safár, J and Janda, J and Dolezel, J and Wolko, B and Naganowska, B}, title = {The bacterial artificial chromosome (BAC) library of the narrow-leafed lupin (Lupinus angustifolius L.).}, journal = {Cellular &amp; molecular biology letters}, volume = {11}, number = {3}, pages = {396-407}, pmid = {16847554}, issn = {1689-1392}, mesh = {Chromosomes, Artificial, Bacterial/*genetics ; Clone Cells ; Electrophoresis, Gel, Pulsed-Field ; *Gene Library ; Lupinus/*genetics ; Mitochondria/metabolism ; }, abstract = {The narrow-leafed lupin possesses valuable traits for environment-friendly agriculture and for the production of unconventional agricultural products. Despite various genetic and environmental studies, the breeding of improved cultivars has been slow due to the limited knowledge of its genomic structure. Further advances in genomics require, among other things, the availability of a genomic DNA library with large inserts. We report here on the construction of the first DNA library cloned in a BAC (bacterial artificial chromosome) vector from diploid Lupinus angustifolius L. cv. Sonet. The high molecular weight DNA used for its preparation was isolated from interphase nuclei that were purified by flow cytometry. The library comprises 55,296 clones and is ordered in 144x384-well microtitre plates. With an average insert size of 100 kb, the library represents six haploid genome equivalents. Thanks to the purification of the nuclei by flow cytometry, contamination with chloroplast DNA and mitochondrial DNA was negligible. The availability of a BAC library opens avenues for the development of a physical contig map and positional gene cloning, as well as for the analysis of the plant's genome structure and evolution.}, }
@article {pmid16846615, year = {2006}, author = {Bell, PJ}, title = {Sex and the eukaryotic cell cycle is consistent with a viral ancestry for the eukaryotic nucleus.}, journal = {Journal of theoretical biology}, volume = {243}, number = {1}, pages = {54-63}, doi = {10.1016/j.jtbi.2006.05.015}, pmid = {16846615}, issn = {0022-5193}, mesh = {Animals ; Cell Cycle/*physiology ; Cell Nucleus/physiology ; DNA Viruses/*physiology ; Eukaryotic Cells/*cytology ; Evolution, Molecular ; Lysogeny/physiology ; Meiosis/physiology ; Mitosis/physiology ; *Sex ; }, abstract = {The origin of the eukaryotic cell cycle, including mitosis, meiosis, and sex are as yet unresolved aspects of the evolution of the eukaryotes. The wide phylogenetic distribution of both mitosis and meiosis suggest that these processes are integrally related to the origin of the earliest eukaryotic cells. According to the viral eukaryogenesis (VE) hypothesis, the eukaryotes are a composite of three phylogenetically unrelated organisms: a viral lysogen that evolved into the nucleus, an archaeal cell that evolved into the eukaryotic cytoplasm, and an alpha-proteobacterium that evolved into the mitochondria. In the extended VE hypothesis presented here, the eukaryotic cell cycle arises as a consequence of the derivation of the nucleus from a lysogenic DNA virus.}, }
@article {pmid16845034, year = {2006}, author = {Abascal, F and Zardoya, R and Posada, D}, title = {GenDecoder: genetic code prediction for metazoan mitochondria.}, journal = {Nucleic acids research}, volume = {34}, number = {Web Server issue}, pages = {W389-93}, pmid = {16845034}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Codon ; Conserved Sequence ; Evolution, Molecular ; *Genes, Mitochondrial ; Internet ; Protein Biosynthesis ; Sequence Alignment ; Sequence Analysis/*methods ; *Software ; User-Computer Interface ; }, abstract = {Although the majority of the organisms use the same genetic code to translate DNA, several variants have been described in a wide range of organisms, both in nuclear and organellar systems, many of them corresponding to metazoan mitochondria. These variants are usually found by comparative sequence analyses, either conducted manually or with the computer. Basically, when a particular codon in a query-species is linked to positions for which a specific amino acid is consistently found in other species, then that particular codon is expected to translate as that specific amino acid. Importantly, and despite the simplicity of this approach, there are no available tools to help predicting the genetic code of an organism. We present here GenDecoder, a web server for the characterization and prediction of mitochondrial genetic codes in animals. The analysis of automatic predictions for 681 metazoans aimed us to study some properties of the comparative method, in particular, the relationship among sequence conservation, taxonomic sampling and reliability of assignments. Overall, the method is highly precise (99%), although highly divergent organisms such as platyhelminths are more problematic. The GenDecoder web server is freely available from http://darwin.uvigo.es/software/gendecoder.html.}, }
@article {pmid16844075, year = {2006}, author = {Palmieri, F and Agrimi, G and Blanco, E and Castegna, A and Di Noia, MA and Iacobazzi, V and Lasorsa, FM and Marobbio, CM and Palmieri, L and Scarcia, P and Todisco, S and Vozza, A and Walker, J}, title = {Identification of mitochondrial carriers in Saccharomyces cerevisiae by transport assay of reconstituted recombinant proteins.}, journal = {Biochimica et biophysica acta}, volume = {1757}, number = {9-10}, pages = {1249-1262}, doi = {10.1016/j.bbabio.2006.05.023}, pmid = {16844075}, issn = {0006-3002}, support = {MC_U105663150/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Biological Transport ; Mitochondrial ADP, ATP Translocases/*metabolism ; Phylogeny ; Recombinant Proteins/*metabolism ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/*metabolism ; }, abstract = {The inner membranes of mitochondria contain a family of carrier proteins that are responsible for the transport in and out of the mitochondrial matrix of substrates, products, co-factors and biosynthetic precursors that are essential for the function and activities of the organelle. This family of proteins is characterized by containing three tandem homologous sequence repeats of approximately 100 amino acids, each folded into two transmembrane alpha-helices linked by an extensive polar loop. Each repeat contains a characteristic conserved sequence. These features have been used to determine the extent of the family in genome sequences. The genome of Saccharomyces cerevisiae contains 34 members of the family. The identity of five of them was known before the determination of the genome sequence, but the functions of the remaining family members were not. This review describes how the functions of 15 of these previously unknown transport proteins have been determined by a strategy that consists of expressing the genes in Escherichia coli or Saccharomyces cerevisiae, reconstituting the gene products into liposomes and establishing their functions by transport assay. Genetic and biochemical evidence as well as phylogenetic considerations have guided the choice of substrates that were tested in the transport assays. The physiological roles of these carriers have been verified by genetic experiments. Various pieces of evidence point to the functions of six additional members of the family, but these proposals await confirmation by transport assay. The sequences of many of the newly identified yeast carriers have been used to characterize orthologs in other species, and in man five diseases are presently known to be caused by defects in specific mitochondrial carrier genes. The roles of eight yeast mitochondrial carriers remain to be established.}, }
@article {pmid16842408, year = {2006}, author = {Spaulding, AW and Mock, KE and Schroeder, MA and Warheit, KI}, title = {Recency, range expansion, and unsorted lineages: implications for interpreting neutral genetic variation in the sharp-tailed grouse (Tympanuchus phasianellus).}, journal = {Molecular ecology}, volume = {15}, number = {9}, pages = {2317-2332}, doi = {10.1111/j.1365-294X.2006.02935.x}, pmid = {16842408}, issn = {0962-1083}, mesh = {Animals ; Canada ; Cell Nucleus/genetics ; Galliformes/*genetics/*physiology ; Genetic Variation/*genetics ; Mitochondria/genetics ; Phylogeny ; Population Dynamics ; United States ; }, abstract = {Both current and historical patterns of variation are relevant to understanding and managing ecological diversity. Recently derived species present a challenge to the reconstruction of historical patterns because neutral molecular data for these taxa are more likely to exhibit effects of recent and ongoing demographic processes. We studied geographical patterns of neutral molecular variation in a species thought to be of relatively recent origin, Tympanuchus phasianellus (sharp-tailed grouse), using mitochondrial control region sequences (CR-I), amplified fragment length polymorphisms (AFLP), and microsatellites. For historical context, we also analysed CR-I in all species of Tympanuchus. Within T. phasianellus, we found evidence for restricted gene flow between eastern and western portions of the species range, generally corresponding with the range boundary of T. p. columbianus and T. p. jamesi. The mismatch distribution and molecular clock estimates from the CR-I data suggested that all Tympanuchus underwent a range expansion prior to sorting of mitotypes among the species, and that sorting may have been delayed as a result of mutation-drift disequilibrium. This study illustrates the challenge of using genetic data to detect historical divergence in groups that are of relatively recent origin, or that have a history dominated by nonequilibrium conditions. We suggest that in such cases, morphological, ecological, and behavioural data may be particularly important adjuncts to molecular data for the recognition of historically or adaptively divergent groups.}, }
@article {pmid16838214, year = {2006}, author = {Xu, W and Jameson, D and Tang, B and Higgs, PG}, title = {The relationship between the rate of molecular evolution and the rate of genome rearrangement in animal mitochondrial genomes.}, journal = {Journal of molecular evolution}, volume = {63}, number = {3}, pages = {375-392}, pmid = {16838214}, issn = {0022-2844}, mesh = {Amino Acids ; Animals ; Cytochromes b/genetics ; DNA, Mitochondrial ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; *Gene Rearrangement ; *Genes, Mitochondrial ; Genome ; Hemiptera/genetics ; Lepidoptera/genetics ; Models, Theoretical ; Phthiraptera/genetics ; Phylogeny ; Selection, Genetic ; Statistics as Topic ; }, abstract = {Evolution of mitochondrial genes is far from clock-like. The substitution rate varies considerably between species, and there are many species that have a significantly increased rate with respect to their close relatives. There is also considerable variation among species in the rate of gene order rearrangement. Using a set of 55 complete arthropod mitochondrial genomes, we estimate the evolutionary distance from the common ancestor to each species using protein sequences, tRNA sequences, and breakpoint distances (a measure of the degree of genome rearrangement). All these distance measures are correlated. We use relative rate tests to compare pairs of related species in several animal phyla. In the majority of cases, the species with the more highly rearranged genome also has a significantly higher rate of sequence evolution. Species with higher amino acid substitution rates in mitochondria also have more variable amino acid composition in response to mutation pressure. We discuss the possible causes of variation in rates of sequence evolution and gene rearrangement among species and the possible reasons for the observed correlation between the two rates.}, }
@article {pmid16837213, year = {2006}, author = {Ropiquet, A and Hassanin, A}, title = {Hybrid origin of the Pliocene ancestor of wild goats.}, journal = {Molecular phylogenetics and evolution}, volume = {41}, number = {2}, pages = {395-404}, doi = {10.1016/j.ympev.2006.05.033}, pmid = {16837213}, issn = {1055-7903}, mesh = {Altitude ; Animals ; Cell Nucleus/genetics ; DNA ; Gene Flow ; Genes, Mitochondrial ; Genetic Speciation ; Genome ; Goats/*genetics ; *Hybridization, Genetic ; Phylogeny ; Selection, Genetic ; Sheep/genetics ; Spectrin/genetics ; }, abstract = {Recent theories on speciation suggest that interspecific hybridization is an important mechanism for explaining adaptive radiation. According to this view, hybridization can promote the rapid transfer of adaptations between different species; the hybrid population thus invades new habitats and diversifies into a variety of new species. Although hybridization is well accepted as a fairly common mechanism for diversification in plants, its role in the evolution of animals is more controversial, because reduced fitness would typically condemn animal hybrids to an evolutionary dead-end. Here, we examine DNA sequences of four mitochondrial and four nuclear genes selected for resolving phylogenetic relationships between goats, sheep, and their allies. Our analyses provide evidence of strong discordance for the position of Capra between mitochondrial and nuclear phylogenies. We suggest that the common ancestor of wild goats arose from interspecific hybridization, and that the mitochondrial genome of a species better adapted to life at high altitudes was transferred via this route into the common ancestor of Capra. We propose that the acquisition of more efficient mitochondria has conferred a selective advantage on goats, allowing their rapid adaptive radiation during the Plio-Pleistocene epoch. Our study therefore agrees with theories that predict an important role for interspecific hybridization in the evolution and diversification of animal species.}, }
@article {pmid16835291, year = {2006}, author = {Tillich, M and Lehwark, P and Morton, BR and Maier, UG}, title = {The evolution of chloroplast RNA editing.}, journal = {Molecular biology and evolution}, volume = {23}, number = {10}, pages = {1912-1921}, doi = {10.1093/molbev/msl054}, pmid = {16835291}, issn = {0737-4038}, mesh = {Adiantum/genetics/metabolism ; Anthocerotophyta/genetics/metabolism ; Arabidopsis/genetics/metabolism ; DNA, Chloroplast/genetics ; *Evolution, Molecular ; Mitochondria/genetics/metabolism ; Models, Genetic ; Mutation ; Pinus/genetics/metabolism ; RNA Editing/*genetics ; RNA, Chloroplast/*genetics/*metabolism ; Species Specificity ; Nicotiana/genetics/metabolism ; Zea mays/genetics/metabolism ; }, abstract = {RNA editing alters the nucleotide sequence of an RNA molecule so that it deviates from the sequence of its DNA template. Different RNA-editing systems are found in the major eukaryotic lineages, and these systems are thought to have evolved independently. In this study, we provide a detailed analysis of data on C-to-U editing sites in land plant chloroplasts and propose a model for the evolution of RNA editing in land plants. First, our data suggest that the limited RNA-editing system of seed plants and the much more extensive systems found in hornworts and ferns are of monophyletic origin. Further, although some eukaryotic editing systems appear to have evolved to regulate gene expression, or at least are now involved in gene regulation, there is no evidence that RNA editing plays a role in gene regulation in land plant chloroplasts. Instead, our results suggest that land plant chloroplast C-to-U RNA editing originated as a mechanism to generate variation at the RNA level, which could complement variation at the DNA level. Under this model, many of the original sites, particularly in seed plants, have been subsequently lost due to mutation at the DNA level, and the function of extant sites is merely to conserve certain codons. This is the first comprehensive model for the evolution of the chloroplast RNA-editing system of land plants and may also be applicable to the evolution of RNA editing in plant mitochondria.}, }
@article {pmid16835267, year = {2006}, author = {Browman, DT and Resek, ME and Zajchowski, LD and Robbins, SM}, title = {Erlin-1 and erlin-2 are novel members of the prohibitin family of proteins that define lipid-raft-like domains of the ER.}, journal = {Journal of cell science}, volume = {119}, number = {Pt 15}, pages = {3149-3160}, doi = {10.1242/jcs.03060}, pmid = {16835267}, issn = {0021-9533}, mesh = {Amino Acid Sequence ; Animals ; Cell Line ; Cholesterol/metabolism ; Endoplasmic Reticulum/chemistry/*metabolism ; Humans ; Membrane Microdomains/chemistry/*metabolism ; Membrane Proteins/classification/genetics/*metabolism ; Mice ; Molecular Sequence Data ; Monocytes/chemistry/cytology/metabolism ; Nerve Tissue Proteins/classification/genetics/*metabolism ; Phylogeny ; Prohibitins ; Recombinant Fusion Proteins/genetics/metabolism ; Repressor Proteins/genetics/*metabolism ; Sequence Alignment ; Subcellular Fractions/chemistry/metabolism ; }, abstract = {Our laboratory was interested in characterizing the molecular composition of non-caveolar lipid rafts. Thus, we generated monoclonal antibodies to lipid raft proteins of human myelomonocytic cells. Two of these proteins, KE04p and C8orf2, were found to be highly enriched in the detergent-insoluble, buoyant fraction of sucrose gradients in a cholesterol-dependent manner. They contain an evolutionarily conserved domain placing them in the prohibitin family of proteins. In contrast to other family members, these two proteins localized to the ER. Furthermore, the extreme N-termini of KE04p and C8orf2 were found to be sufficient for heterologous targeting of GFP to the ER in the absence of classical ER retrieval motifs. We also demonstrate that all prohibitin family members rely on sequences in their extreme N-termini for their distinctive subcellular distributions including the mitochondria, plasma membrane and Golgi vesicles. Owing to their subcellular localization and their presence in lipid rafts, we have named KE04p and C8orf2, ER lipid raft protein (erlin)-1 and erlin-2, respectively. Interestingly, the ER contains relatively low levels of cholesterol and sphingolipids compared with other organelles. Thus, our data support the existence of lipid-raft-like domains within the membranes of the ER.}, }
@article {pmid16830098, year = {2006}, author = {Abdelnoor, RV and Christensen, AC and Mohammed, S and Munoz-Castillo, B and Moriyama, H and Mackenzie, SA}, title = {Mitochondrial genome dynamics in plants and animals: convergent gene fusions of a MutS homologue.}, journal = {Journal of molecular evolution}, volume = {63}, number = {2}, pages = {165-173}, pmid = {16830098}, issn = {0022-2844}, mesh = {Adenosine Triphosphatases/genetics/metabolism ; Amino Acid Sequence ; Animals ; Cloning, Molecular ; DNA Repair Enzymes/chemistry/*genetics/metabolism ; DNA, Mitochondrial/*genetics ; Endonucleases/genetics/metabolism ; *Evolution, Molecular ; Gene Fusion/genetics ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/chemistry/genetics/metabolism ; Molecular Sequence Data ; MutS DNA Mismatch-Binding Protein/chemistry/*genetics/metabolism ; Phylogeny ; Plant Proteins/chemistry/genetics/metabolism ; Plants/*genetics/metabolism ; Protein Structure, Tertiary ; Protein Transport ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Mitochondrial processes influence a broad spectrum of physiological and developmental events in higher eukaryotes, and their aberrant function can lead to several familiar disease phenotypes in mammals. In plants, mitochondrial genes directly influence pollen development and the occurrence of male sterility in natural plant populations. Likewise, in animal systems evidence accumulates to suggest important mitochondrial functions in spermatogenesis and reproduction. Here we present evidence for a convergent gene fusion involving a MutS-homologous gene functioning within the mitochondrion and designated Msh1. In only plants and soft corals, the MutS homologue has fused with a homing endonuclease sequence at the carboxy terminus of the protein. However, the endonuclease domains in the plants and the soft corals are members of different groups. In plants, Msh1 can influence mitochondrial genome organization and male sterility expression. Based on parallels in Msh1 gene structure shared by plants and corals, and their similarities in reproductive behavior, we postulate that this convergent gene fusion might have occurred in response to coincident adaptive pressures on reproduction.}, }
@article {pmid16825195, year = {2006}, author = {Chatterjee, S and Home, P and Mukherjee, S and Mahata, B and Goswami, S and Dhar, G and Adhya, S}, title = {An RNA-binding respiratory component mediates import of type II tRNAs into Leishmania mitochondria.}, journal = {The Journal of biological chemistry}, volume = {281}, number = {35}, pages = {25270-25277}, doi = {10.1074/jbc.M604126200}, pmid = {16825195}, issn = {0021-9258}, mesh = {Allosteric Site ; Animals ; Biological Transport ; Cloning, Molecular ; Cross-Linking Reagents/pharmacology ; Gene Expression Regulation ; Guanine Nucleotide Exchange Factors/*chemistry/physiology ; Humans ; Leishmania tropica/*metabolism ; Membrane Transport Proteins/*chemistry/physiology ; Mitochondria/*metabolism ; Models, Molecular ; Protein Structure, Tertiary ; RNA/*metabolism ; RNA, Transfer/*chemistry ; Recombinant Proteins/chemistry ; }, abstract = {Transport of tRNAs across the inner mitochondrial membrane of the kinetoplastid protozoon Leishmania requires interactions with specific binding proteins (receptors) in a multi-subunit complex. The allosteric model of import regulation proposes cooperative and antagonistic interactions between two or more receptors with binding specificities for distinct tRNA families (types I and II, respectively). To identify the type II receptor, the gene encoding RIC8A, a subunit of the complex, was cloned. The C-terminal region of RIC8A is homologous to subunit 6b of ubiquinol cytochrome c reductase (respiratory complex III), while the N-terminal region has intrinsic affinity for type II, but not for type I, tRNAs. RIC8A is shared by the import complex and complex III, indicating its bi-functionality, but is assembled differently in the two complexes. Knockdown of RIC8A in Leishmania lowered the mitochondrial content of type II tRNAs but raised that of type I tRNAs, with downstream effects on mitochondrial translation and respiration, and cell death. In RIC8A knockdown cells, a subcomplex was formed that interacted with type I tRNA, but the negative regulation by type II tRNA was lost. Mitochondrial extracts from these cells were defective for type II, but not type I, import; import and regulation were restored by purified RIC8A. These results provide evidence for the relevance of allosteric regulation in vivo and indicate that acquisition of new tRNA-binding domains by ancient respiratory components have played a key role in the evolution of mitochondrial tRNA import.}, }
@article {pmid16824191, year = {2006}, author = {Kominami, K and Takagi, C and Kurata, T and Kitayama, A and Nozaki, M and Sawasaki, T and Kuida, K and Endo, Y and Manabe, N and Ueno, N and Sakamaki, K}, title = {The initiator caspase, caspase-10beta, and the BH-3-only molecule, Bid, demonstrate evolutionary conservation in Xenopus of their pro-apoptotic activities in the extrinsic and intrinsic pathways.}, journal = {Genes to cells : devoted to molecular &amp; cellular mechanisms}, volume = {11}, number = {7}, pages = {701-717}, doi = {10.1111/j.1365-2443.2006.00983.x}, pmid = {16824191}, issn = {1356-9597}, mesh = {Amino Acid Sequence ; Animals ; Apoptosis Regulatory Proteins/genetics/*metabolism ; BH3 Interacting Domain Death Agonist Protein/biosynthesis/genetics/*metabolism ; Caspase 10 ; Caspases/biosynthesis/genetics/*metabolism ; Chickens ; Evolution, Molecular ; Green Fluorescent Proteins/genetics/metabolism ; HeLa Cells ; Humans ; Mice ; Mitochondria/metabolism ; Molecular Sequence Data ; Peptide Hydrolases/metabolism ; RNA, Messenger/biosynthesis/genetics ; Sequence Alignment ; Transfection ; Xenopus/embryology/*genetics/metabolism ; }, abstract = {Two major apoptotic signaling pathways have been defined in mammals, the extrinsic pathway, initiated by ligation of death receptors, and the intrinsic pathway, triggered by cytochrome c release from mitochondria. Here, we identified and characterized the Xenopus homologs of caspase-10 (xCaspase-10beta), a novel initiator caspase, and Bid (xBid), a BH3-only molecule of the Bcl-2 family involved in both the extrinsic and intrinsic pathways. Exogenous expression of these molecules induced apoptosis of mammalian cells. By biochemical and cytological analyses, we clarified that xCaspase-10beta and xBid exhibit structural and functional similarities to their mammalian orthologues. We also detected xCaspase-10beta and xBid transcripts during embryogenesis by whole-mount in situ hybridization and RT-PCR analysis. Microinjection of mRNA encoding a protease-defect xCaspase-10beta mutant into embryos resulted in irregular development. Enforced expression of active xBid induced cell death in developing embryos. Using transgenic frogs established to allow monitoring of caspase activation in vivo, we confirmed that this form of cell death is caspase-dependent apoptosis. Thus, we demonstrated that the machinery governing the extrinsic and intrinsic apoptotic pathways are already established in Xenopus embryos. Additionally, we propose that the functions of the initiator caspase and BH3-only molecule are evolutionarily conserved in vertebrates, functioning during embryonic development.}, }
@article {pmid16824008, year = {2006}, author = {Lill, R and Mühlenhoff, U}, title = {Iron-sulfur protein biogenesis in eukaryotes: components and mechanisms.}, journal = {Annual review of cell and developmental biology}, volume = {22}, number = {}, pages = {457-486}, doi = {10.1146/annurev.cellbio.22.010305.104538}, pmid = {16824008}, issn = {1081-0706}, mesh = {Animals ; Bacteria/metabolism ; Eukaryotic Cells/*metabolism ; Ferredoxin-NADP Reductase/metabolism ; Iron-Sulfur Proteins/*biosynthesis/metabolism ; Mitochondria/metabolism ; Saccharomyces cerevisiae/metabolism ; }, abstract = {Iron-sulfur (Fe/S) clusters require a complex set of proteins to become assembled and incorporated into apoproteins in a living cell. Researchers have described three distinct assembly systems in eukaryotes that are involved in the maturation of cellular Fe/S proteins. Mitochondria are central for biogenesis. They contain the ISC-the iron-sulfur cluster assembly machinery that was inherited from a similar system of eubacteria in evolution and is involved in biogenesis of all cellular Fe/S proteins. The basic principle of mitochondrial (and bacterial) Fe/S protein maturation is the synthesis of the Fe/S cluster on a scaffold protein before the cluster is transferred to apoproteins. Biogenesis of cytosolic and nuclear Fe/S proteins is facilitated by the cytosolic iron-sulfur protein assembly (CIA) apparatus. This process requires the participation of mitochondria that export a still unknown component via the ISC export machinery, including an ABC transporter.}, }
@article {pmid16822756, year = {2006}, author = {Cavalier-Smith, T}, title = {Origin of mitochondria by intracellular enslavement of a photosynthetic purple bacterium.}, journal = {Proceedings. Biological sciences}, volume = {273}, number = {1596}, pages = {1943-1952}, pmid = {16822756}, issn = {0962-8452}, mesh = {Bacterial Proteins/classification/metabolism/physiology ; *Biological Evolution ; Eukaryotic Cells/ultrastructure ; Gene Transfer, Horizontal ; Genome ; Membrane Proteins/classification/metabolism/physiology ; Mitochondria/genetics/*metabolism/ultrastructure ; Mitochondrial Membrane Transport Proteins/classification/genetics/metabolism ; Mitochondrial Membranes/metabolism/ultrastructure ; Mitochondrial Proteins/classification/metabolism/physiology ; Models, Biological ; Phagocytosis ; Photosynthesis ; Proteobacteria/genetics/*metabolism/ultrastructure ; Symbiosis ; }, abstract = {Mitochondria originated by permanent enslavement of purple non-sulphur bacteria. These endosymbionts became organelles through the origin of complex protein-import machinery and insertion into their inner membranes of protein carriers for extracting energy for the host. A chicken-and-egg problem exists: selective advantages for evolving import machinery were absent until inner membrane carriers were present, but this very machinery is now required for carrier insertion. I argue here that this problem was probably circumvented by conversion of the symbiont protein-export machinery into protein-import machinery, in three phases. I suggest that the first carrier entered the periplasmic space via pre-existing beta-barrel proteins in the bacterial outer membrane that later became Tom40, and inserted into the inner membrane probably helped by a pre-existing inner membrane protein, thereby immediately providing the protoeukaryote host with photosynthesate. This would have created a powerful selective advantage for evolving more efficient carrier import by inserting Tom70 receptors. Massive gene transfer to the nucleus inevitably occurred by mutation pressure. Finally, pressure from harmful, non-selected gene transfer to the nucleus probably caused evolution of the presequence mechanism, and photosynthesis was lost.}, }
@article {pmid16817936, year = {2006}, author = {Lo, N and Beninati, T and Sassera, D and Bouman, EA and Santagati, S and Gern, L and Sambri, V and Masuzawa, T and Gray, JS and Jaenson, TG and Bouattour, A and Kenny, MJ and Guner, ES and Kharitonenkov, IG and Bitam, I and Bandi, C}, title = {Widespread distribution and high prevalence of an alpha-proteobacterial symbiont in the tick Ixodes ricinus.}, journal = {Environmental microbiology}, volume = {8}, number = {7}, pages = {1280-1287}, doi = {10.1111/j.1462-2920.2006.01024.x}, pmid = {16817936}, issn = {1462-2912}, mesh = {Alphaproteobacteria/*genetics/growth &amp; development ; Animals ; Europe/epidemiology ; Female ; Infectious Disease Transmission, Vertical ; Ixodes/*microbiology ; Male ; Mitochondria/*microbiology ; Ovary/cytology/microbiology ; Phylogeny ; Prevalence ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {The tick Ixodes ricinus is responsible for the transmission of a number of bacterial, protozoan and viral diseases to humans and animals in Europe and Northern Africa. Female I. ricinus from England, Switzerland and Italy have been found to harbour an intracellular alpha-proteobacterium, designated IricES1, within the cells of the ovary. IricES1 is the only prokaryote known to exist within the mitochondria of any animal or multicellular organism. To further examine the distribution, prevalence and mode of transmission of IricES1, we performed polymerase chain reaction screening of I. ricinus adults from 12 countries across its geographic distribution, including tick colonies that have been maintained in the laboratory for varying periods of time. IricES1 was detected in 100% of field-collected female ticks from all countries examined (n = 128), while 44% of males were found to be infected (n = 108). Those males that are infected appear to harbour fewer bacteria than females. Sequencing of fragments of the 16S rRNA and gyrB genes revealed very low nucleotide diversity among various populations of IricES1. Transmission of IricES1 from engorged adult females to eggs was found to be 100% (n = 31). In tick colonies that had been maintained in the laboratory for several years, a relatively low prevalence was found in females (32%; n = 25). To our knowledge, IricES1 is the most widespread and highly prevalent of any tick-associated symbiont.}, }
@article {pmid16810325, year = {2007}, author = {Laporte, C and Kosta, A and Klein, G and Aubry, L and Lam, D and Tresse, E and Luciani, MF and Golstein, P}, title = {A necrotic cell death model in a protist.}, journal = {Cell death and differentiation}, volume = {14}, number = {2}, pages = {266-274}, doi = {10.1038/sj.cdd.4401994}, pmid = {16810325}, issn = {1350-9047}, mesh = {Animals ; Cell Death/drug effects ; Cell Membrane/drug effects/metabolism ; Dictyostelium/*cytology/drug effects ; Fluoresceins/pharmacology ; Fluorescence ; Glucose/pharmacology ; Hexanones/pharmacology ; Hydrocarbons, Chlorinated/pharmacology ; Mitochondria/drug effects/metabolism ; *Models, Biological ; *Necrosis ; Uncoupling Agents/pharmacology ; }, abstract = {While necrotic cell death is attracting considerable interest, its molecular bases are still poorly understood. Investigations in simple biological models, taken for instance outside the animal kingdom, may benefit from less interference from other cell death mechanisms and from better experimental accessibility, while providing phylogenetic information. Can necrotic cell death occur outside the animal kingdom? In the protist Dictyostelium, developmental stimuli induced in an autophagy mutant a stereotyped sequence of events characteristic of necrotic cell death. This sequence included swift mitochondrial uncoupling with mitochondrial 2',7'-dichlorofluorescein diacetate fluorescence, ATP depletion and increased oxygen consumption. This was followed by perinuclear clustering of dilated mitochondria. Rapid plasma membrane rupture then occurred, which was evidenced by time-lapse videos and quantified by FACS. Of additional interest, developmental stimuli and classical mitochondrial uncouplers triggered a similar sequence of events, and exogenous glucose delayed plasma membrane rupture in a nonglycolytic manner. The occurrence of necrotic cell death in the protist Dictyostelium (1) provides a very favorable model for further study of this type of cell death, and (2) strongly suggests that the mechanism underlying necrotic cell death was present in an ancestor common to the Amoebozoa protists and to animals and has been conserved in evolution.}, }
@article {pmid16806990, year = {2006}, author = {van Herwerden, L and Choat, JH and Dudgeon, CL and Carlos, G and Newman, SJ and Frisch, A and van Oppen, M}, title = {Contrasting patterns of genetic structure in two species of the coral trout Plectropomus (Serranidae) from east and west Australia: introgressive hybridisation or ancestral polymorphisms.}, journal = {Molecular phylogenetics and evolution}, volume = {41}, number = {2}, pages = {420-435}, doi = {10.1016/j.ympev.2006.04.024}, pmid = {16806990}, issn = {1055-7903}, mesh = {Animals ; Australia ; Bass/classification/*genetics ; DNA, Mitochondrial/genetics ; Female ; Genetic Markers ; Geography ; *Hybridization, Genetic ; Locus Control Region/genetics ; Male ; Microsatellite Repeats ; Phylogeny ; *Polymorphism, Genetic ; Sequence Analysis, DNA ; }, abstract = {Inter-specific genetic relationships among regional populations of two species of grouper (Plectropomus maculatus and Plectropomus leopardus) were examined using mitochondrial and nuclear markers. mtDNA revealed contrasting regional inter-specific patterns whilst nuclear markers revealed contrasting patterns among markers, irrespective of region. In eastern Australia (EA) the species form a single mtDNA lineage, but the two species are reciprocally monophyletic in Western Australia (WA). This supports previous evidence for hybridisation between these species on the east coast. WA P. leopardus forms a sister relationship with the EA P. leopardus-maculatus clade while WA P. maculatus is more basal and sister to the P. leopardus lineages, indicating mtDNA does not suffer from incomplete lineage sorting for these species. In contrast, one of three nuclear markers (locus 7-90TG) differentiated the species into two reciprocally monophyletic clades, with no evidence of hybridisation or ancestral polymorphism. The remaining two nuclear markers (2-22 and ETS-2) did not separate these two species, while distinguishing other plectropomid species, suggesting incomplete lineage sorting at these nuclear loci. These results together with coalescence analyses suggest that P. leopardus females have hybridised historically with P. maculatus males and that P. maculatus mitochondria were displaced through introgressive hybridisation and fixation in the P. maculatus founder population on the Great Barrier Reef. The contrasting regional patterns of mtDNA structure may be attributed to Quaternary sea-level changes and shelf width differences driving different reef configurations on each coast. These reef configurations have provided opportunities for local scale interaction and reproduction among species on the narrower EA continental shelves, but not on the broader WA continental shelves.}, }
@article {pmid16804921, year = {2006}, author = {Tripepi, S and Jamieson, BG and Brunelli, E}, title = {Ultrastructure of the spermatid of Caprimulgus europaeus Linnaeus 1758, the European nightjar (Aves; Caprimulgidae), with phylogenetic implications.}, journal = {Journal of morphology}, volume = {267}, number = {10}, pages = {1157-1164}, doi = {10.1002/jmor.10466}, pmid = {16804921}, issn = {0362-2525}, mesh = {Acrosome/ultrastructure ; Animals ; Birds/*classification ; Cell Nucleus/ultrastructure ; Centrioles/ultrastructure ; Europe ; Male ; *Phylogeny ; Sperm Midpiece/ultrastructure ; Spermatids/cytology/*ultrastructure ; Spermatogenesis/physiology ; }, abstract = {The sperm of Caprimulgus europaeus is typical of other nonpasserines in many respects. Features shared with Paleognathae and Galloanserae are the conical acrosome, shorter than the nucleus; the presence of a perforatorium and endonuclear canal; the presence of a proximal as well as distal centriole; the elongate midpiece with mitochondria grouped around a central axis (here maximally six mitochondria in approximately 10 tiers); and the presence of a fibrous or amorphous sheath around the principal piece of the axoneme. A major (apomorphic) difference from paleognaths and galloanserans is the short distal centriole, the midpiece being penetrated for most of its length by the axoneme and for only a very short proximal portion by the centriole. Nonpasserines differ from paleognaths in that the latter have a transversely ribbed fibrous sheath, whereas in nonpasserines it is amorphous, as in Caprimulgus, or absent. The absence of an annulus is an apomorphic feature of Caprimulgus, apodiform, psittaciform, gruiform, and passerine sperm, homoplastic in at least some of these. In contrast to passerines, in Caprimulgus the cytoplasmic microtubules in the spermatid are restricted to a transient longitudinal manchette. The structure of the spermatid and spermatozoon is consistent with placement of the Caprimulgidae near the Psittacidae, but is less supportive of close proximity to the Apodidae, from DNA-DNA hybridization and some other analyses.}, }
@article {pmid16798872, year = {2006}, author = {Lin, Z and Kong, H and Nei, M and Ma, H}, title = {Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {27}, pages = {10328-10333}, pmid = {16798872}, issn = {0027-8424}, support = {R01 GM020293/GM/NIGMS NIH HHS/United States ; R01 GM063871/GM/NIGMS NIH HHS/United States ; GM020293/GM/NIGMS NIH HHS/United States ; GM63871-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Endocytosis ; *Evolution, Molecular ; *Gene Duplication ; Gene Transfer, Horizontal/*genetics ; Humans ; Multigene Family/*genetics ; Rad51 Recombinase/classification/*genetics/metabolism ; Rec A Recombinases/classification/*genetics/metabolism ; Symbiosis/genetics ; Time Factors ; }, abstract = {The bacterial recA gene and its eukaryotic homolog RAD51 are important for DNA repair, homologous recombination, and genome stability. Members of the recA/RAD51 family have functions that have differentiated during evolution. However, the evolutionary history and relationships of these members remains unclear. Homolog searches in prokaryotes and eukaryotes indicated that most eubacteria contain only one recA. However, many archaeal species have two recA/RAD51 homologs (RADA and RADB), and eukaryotes possess multiple members (RAD51, RAD51B, RAD51C, RAD51D, DMC1, XRCC2, XRCC3, and recA). Phylogenetic analyses indicated that the recA/RAD51 family can be divided into three subfamilies: (i) RADalpha, with highly conserved functions; (ii) RADbeta, with relatively divergent functions; and (iii) recA, functioning in eubacteria and eukaryotic organelles. The RADalpha and RADbeta subfamilies each contain archaeal and eukaryotic members, suggesting that a gene duplication occurred before the archaea/eukaryote split. In the RADalpha subfamily, eukaryotic RAD51 and DMC1 genes formed two separate monophyletic groups when archaeal RADA genes were used as an outgroup. This result suggests that another duplication event occurred in the early stage of eukaryotic evolution, producing the DMC1 clade with meiosis-specific genes. The RADbeta subfamily has a basal archaeal clade and five eukaryotic clades, suggesting that four eukaryotic duplication events occurred before animals and plants diverged. The eukaryotic recA genes were detected in plants and protists and showed strikingly high levels of sequence similarity to recA genes from proteobacteria or cyanobacteria. These results suggest that endosymbiotic transfer of recA genes occurred from mitochondria and chloroplasts to nuclear genomes of ancestral eukaryotes.}, }
@article {pmid16797512, year = {2006}, author = {Kagan, VE and Tyurina, YY and Bayir, H and Chu, CT and Kapralov, AA and Vlasova, II and Belikova, NA and Tyurin, VA and Amoscato, A and Epperly, M and Greenberger, J and Dekosky, S and Shvedova, AA and Jiang, J}, title = {The "pro-apoptotic genies" get out of mitochondria: oxidative lipidomics and redox activity of cytochrome c/cardiolipin complexes.}, journal = {Chemico-biological interactions}, volume = {163}, number = {1-2}, pages = {15-28}, doi = {10.1016/j.cbi.2006.04.019}, pmid = {16797512}, issn = {0009-2797}, support = {HL70755/HL/NHLBI NIH HHS/United States ; OH00828/OH/NIOSH CDC HHS/United States ; U19 AIO68021//PHS HHS/United States ; }, mesh = {Animals ; Apoptosis/*physiology ; Cardiolipins/*metabolism ; Cytochromes c/*metabolism ; Humans ; Mitochondria, Heart/metabolism/*physiology ; Mitochondrial Membranes/metabolism ; Oxidation-Reduction ; Signal Transduction/*physiology ; }, abstract = {One of the prominent consequences of the symbiogenic origin of eukaryotic cells is the unique presence of one particular class of phospholipids, cardiolipin (CL), in mitochondria. As the product originated from the evolution of symbiotic bacteria, CL is predominantly confined to the inner mitochondrial membrane in normally functioning cells. Recent findings identified CL and its oxidation products as important participants and signaling molecules in the apoptotic cell death program. Early in apoptosis, massive membrane translocations of CL take place resulting in its appearance in the outer mitochondrial membrane. Consequently, significant amounts of CL become available for the interactions with cyt c, one of the major proteins of the intermembrane space. Binding of CL with cytochrome c (cyt c) yields the cyt c/CL complex that acts as a potent CL-specific peroxidase and generates CL hydroperoxides. In this review, we discuss the catalytic mechanisms of CL oxidation by the peroxidase activity of cyt c as well as the role of oxidized CL (CLox) in the release of pro-apoptotic factors from mitochondria into the cytosol. Potential implications of cyt c/CL peroxidase intracellular complexes in disease conditions (cancer, neurodegeneration) are also considered. The discovery of the new role of cyt c/CL complexes in early mitochondrial apoptosis offers interesting opportunities for new targets in drug discovery programs. Finally, exit of cyt c from damaged and/or dying (apoptotic) cells into extracellular compartments and its accumulation in biofluids is discussed in lieu of the formation of its peroxidase complexes with negatively charged lipids and their significance in the development of systemic oxidative stress in circulation.}, }
@article {pmid16794377, year = {2006}, author = {Manfredi, R and Calza, L and Chiodo, F}, title = {[Hyperlactacidemia during antiretroviral therapy: frequency and clinical-therapeutic correlations].}, journal = {Le infezioni in medicina}, volume = {14}, number = {1}, pages = {33-36}, pmid = {16794377}, issn = {1124-9390}, mesh = {Adult ; Anti-HIV Agents/*adverse effects/pharmacology/therapeutic use ; Antiretroviral Therapy, Highly Active/adverse effects ; Case-Control Studies ; Comorbidity ; Dyslipidemias/blood ; Female ; HIV Infections/*blood/drug therapy ; HIV-Associated Lipodystrophy Syndrome/blood ; Humans ; Lactic Acid/*blood ; Male ; Middle Aged ; Mitochondria, Heart/drug effects ; RNA, Viral/blood ; Reverse Transcriptase Inhibitors/adverse effects/pharmacology/therapeutic use ; }, abstract = {While asymptomatic hyperlactacidemia is quite a frequent phenomenon among HIV-infected patients treated with highly active antiretroviral therapy (HAART), lactic acidosis is a rare, but potentially life-threatening occurrence. Epidemiology, clinical and laboratory presentation, evolution, and outcome of this phenomenon are currently under intensive investigation, and the most likely pathogenetic pathways seem to involve mitochondrial toxicity prompted by the administration of nucleoside reverse transcriptase inhibitors. Our case-control study on an extensive, single centre population treated for HIV infection provides novel insights on these emerging issues, reported and discussed on the basis of the most recently published findings.}, }
@article {pmid16790414, year = {2006}, author = {Fang, M and Andersson, L}, title = {Mitochondrial diversity in European and Chinese pigs is consistent with population expansions that occurred prior to domestication.}, journal = {Proceedings. Biological sciences}, volume = {273}, number = {1595}, pages = {1803-1810}, pmid = {16790414}, issn = {0962-8452}, mesh = {Animals ; China ; Cytochromes b/genetics ; DNA, Mitochondrial/*analysis ; Europe ; *Genetic Variation ; Geography ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; Swine/*genetics ; }, abstract = {Mitochondrial DNA (mtDNA) diversity in European and Asian pigs was assessed using 1536 samples representing 45 European and 21 Chinese breeds. Diagnostic nucleotide differences in the cytochrome b (Cytb) gene between the European and Asian mtDNA variants were determined by pyrosequencing as a rapid screening method. Subsequently, 637bp of the hypervariable control region was sequenced to further characterize mtDNA diversity. All sequences belonged to the D1 and D2 clusters of pig mtDNA originating from ancestral wild boar populations in Europe and Asia, respectively. The average frequency of Asian mtDNA haplotypes was 29% across European breeds, but varied from 0 to 100% within individual breeds. A neighbour-joining (NJ) tree of control region sequences showed that European and Asian haplotypes form distinct clusters consistent with the independent domestication of pigs in Asia and Europe. The Asian haplotypes found in the European pigs were identical or closely related to those found in domestic pigs from Southeast China. The star-like pattern detected by network analysis for both the European and Asian haplotypes was consistent with a previous demographic expansion. Mismatch analysis supported this notion and suggested that the expansion was initiated before domestication.}, }
@article {pmid16790030, year = {2006}, author = {Sunderland, PA and West, CE and Waterworth, WM and Bray, CM}, title = {An evolutionarily conserved translation initiation mechanism regulates nuclear or mitochondrial targeting of DNA ligase 1 in Arabidopsis thaliana.}, journal = {The Plant journal : for cell and molecular biology}, volume = {47}, number = {3}, pages = {356-367}, doi = {10.1111/j.1365-313X.2006.02791.x}, pmid = {16790030}, issn = {0960-7412}, mesh = {Arabidopsis/*enzymology/genetics/ultrastructure ; Arabidopsis Proteins/chemistry/*genetics/*metabolism ; Base Sequence ; Cell Nucleus/metabolism ; Chloroplasts/metabolism ; Codon, Initiator ; DNA Ligase ATP ; DNA Ligases/chemistry/*genetics/*metabolism ; Evolution, Molecular ; Green Fluorescent Proteins/analysis ; Mitochondria/*metabolism ; Molecular Sequence Data ; Nuclear Localization Signals/physiology ; *Peptide Chain Initiation, Translational ; Protein Isoforms/biosynthesis/chemistry/metabolism ; Protein Sorting Signals/physiology ; Protein Structure, Secondary ; Protein Transport ; RNA, Messenger/metabolism ; Recombinant Fusion Proteins/analysis ; }, abstract = {The Arabidopsis DNA ligase 1 gene (AtLIG1) is indispensable for cell viability. AtLIG1 expresses one major and two minor mRNA transcripts differing only in the length of the 5' untranslated leader sequences preceding a common ORF. Control of AtLIG1 isoform production and intracellular targeting depends upon mechanisms controlling the choice of translation initiation site within the AtLIG1 ORF. Confocal laser scanning microscopy of green fluorescent protein-tagged AtLIG1 isoforms expressed in Arabidopsis revealed that translation of AtLIG1 mRNA transcripts from the first in-frame start codon produces an AtLIG1 isoform that is targeted exclusively to the mitochondria. Translation initiation from the second in-frame start codon produces an AtLIG1 isoform targeted only to the nucleus. There is no evidence for AtLIG1-GFP being targeted to chloroplasts. The mitochondrial AtLIG1 isoform possesses both an N-terminal mitochondrial-targeting signal and an internal bipartite nuclear localization signal (NLS) yet is targeted only to mitochondria, demonstrating a hierarchical dominance of the mitochondrial presequence over the NLS. The length of the 5'-UTR and more significantly the nucleotide context around alternative start codons in the AtLIG1 transcripts affect translation initiation to ensure a balanced synthesis of both nuclear and mitochondrial AtLIG1 isoforms, probably via a context-dependent leaky ribosome scanning mechanism.}, }
@article {pmid16788047, year = {2006}, author = {Nomura, H and Athauda, SB and Wada, H and Maruyama, Y and Takahashi, K and Inoue, H}, title = {Identification and reverse genetic analysis of mitochondrial processing peptidase and the core protein of the cytochrome bc1 complex of Caenorhabditis elegans, a model parasitic nematode.}, journal = {Journal of biochemistry}, volume = {139}, number = {6}, pages = {967-979}, doi = {10.1093/jb/mvj114}, pmid = {16788047}, issn = {0021-924X}, mesh = {Amino Acid Motifs/genetics ; Amino Acid Sequence ; Animals ; Blotting, Western ; Caenorhabditis elegans/*genetics/metabolism ; Caenorhabditis elegans Proteins/chemistry/*genetics/metabolism ; DNA, Complementary/genetics ; Electron Transport Complex III/chemistry/*genetics/metabolism ; Humans ; Metalloendopeptidases/chemistry/*genetics/metabolism ; Mitochondrial Proteins/chemistry/genetics/metabolism ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Nematoda/genetics/metabolism ; Phylogeny ; Protein Structure, Quaternary ; RNA Interference ; Recombinant Proteins/chemistry/metabolism ; Sequence Homology, Amino Acid ; Substrate Specificity ; Mitochondrial Processing Peptidase ; }, abstract = {Mitochondria could be a good target for anti-parasitic drugs. The alpha and beta subunits of mitochondrial processing peptidase (MPP) and the core subunits of the cytochrome bc1 complex, UCR-1 and UCR-2, are homologous to one another and are important for mitochondrial functions. However, our knowledge of these proteins in nematodes is very limited. Caenorhabditis elegans, a free-living nematode, has six genes coding for proteins homologous to these subunits. On primary structure comparison, and immunochemical and enzymological analyses, the gene products were assigned as follows: Y71G12B.24, alpha-MPP; ZC410.2, beta-MPP; F56D2.1, UCR-1; VW06B3R.1, T10B10.2; and T24C4.1, UCR-2. The primary structures of beta-MPP and UCR-1 from Brugia malayi, a parasitic nematode causing human filariasis, were deduced from their cDNA structures. Phylogenetic analysis showed that the UCR-1s from both C. elegans and B. malayi were less related to mammalian UCR-1s than to MPPs from various organisms. MPP and the bc1 complex are essential for the life cycle of C. elegans, because their reverse genetic inhibition is lethal. This suggests the possibility that these proteins are also essential for the viability of B. malayi and other parasitic nematodes, and are potential targets for anti-parasitic agents.}, }
@article {pmid16782050, year = {2006}, author = {Rodríguez-Roldán, V and García-Heredia, JM and Navarro, JA and Hervás, M and De la Cerda, B and Molina-Heredia, FP and De la Rosa, MA}, title = {A comparative kinetic analysis of the reactivity of plant, horse, and human respiratory cytochrome c towards cytochrome c oxidase.}, journal = {Biochemical and biophysical research communications}, volume = {346}, number = {3}, pages = {1108-1113}, doi = {10.1016/j.bbrc.2006.06.022}, pmid = {16782050}, issn = {0006-291X}, mesh = {Animals ; Arabidopsis/*enzymology ; Chemical Phenomena ; Chemistry, Physical ; Cytochromes c/*metabolism ; Electron Transport Complex IV/*metabolism ; Flavins/metabolism ; *Horses ; Humans ; Kinetics ; Mitochondria/*enzymology ; Oxidation-Reduction/drug effects ; Potassium Chloride/pharmacology ; }, abstract = {Two synthetic genes coding for human and Arabidopsis cytochrome c, respectively, have been designed and constructed, and the recombinant proteins have been over-expressed in Escherichia coli cells. Thus a comparative analysis of the two heme proteins, including horse cytochrome c as a reference, has been performed. In addition to their physico-chemical properties, the redox behavior of the three proteins has been analyzed by following the kinetics of both their reduction by flavin semiquinones (lumiflavin, riboflavin, and FMN) and oxidation by cytochrome c oxidase. The resulting data indicate that the accessibility and electrostatic charge of the active site do not differ in a significant way among the three proteins, but human cytochrome c exhibits some intriguing differences when interacting with cytochrome c oxidase that could be related to the amino acid changes underwent by the latter along evolution.}, }
@article {pmid16780520, year = {2006}, author = {Olson, MS and Graf, AV and Niles, KR}, title = {Fine scale spatial structuring of sex and mitochondria in Silene vulgaris.}, journal = {Journal of evolutionary biology}, volume = {19}, number = {4}, pages = {1190-1201}, doi = {10.1111/j.1420-9101.2006.01103.x}, pmid = {16780520}, issn = {1010-061X}, mesh = {DNA, Mitochondrial/*genetics ; Genes, Plant ; Genetic Markers ; *Sex Ratio ; *Silene/genetics ; }, abstract = {Fine scale spatial structure (FSSS) of cytoplasmic genes in plants is thought to be generated via founder events and can be amplified when seeds germinate close to their mother. In gynodioecious species these processes are expected to generate FSSS in sex ratio because maternally inherited cytoplasmic male sterility genes partially influence sex expression. Here we document a striking example of FSSS in both mitochondrial genetic markers and sex in roadside populations of Silene vulgaris. We show that in one population FSSS of sexes influences relative fruit production of females compared to hermaphrodites. Furthermore, FSSS in sex ratio is expected to persist into future generations because offspring sex ratios from females are female-biased whereas offspring sex ratios from hermaphrodites are hermaphrodite-biased. Earlier studies indicated that pollen limitation is the most likely mechanism underlying negative frequency dependent fitness of females. Our results support the theoretical predictions that FSSS in sex ratio can reduce female fitness by decreasing the frequency at which females experience hermaphrodites. We argue that the influence of FSSS on female fitness is complementary to the influence of larger scale population structure on female fitness, and that population structure at both scales will act to decrease female frequencies in gynodioecious species. Better comprehension of the spatial structure of genders and genes controlling sex expression at a local scale is required for future progress toward understanding sex ratio evolution in gynodioecious plants.}, }
@article {pmid16778769, year = {2006}, author = {Crawford, MJ and Thomsen-Zieger, N and Ray, M and Schachtner, J and Roos, DS and Seeber, F}, title = {Toxoplasma gondii scavenges host-derived lipoic acid despite its de novo synthesis in the apicoplast.}, journal = {The EMBO journal}, volume = {25}, number = {13}, pages = {3214-3222}, pmid = {16778769}, issn = {0261-4189}, support = {F32 AI010482/AI/NIAID NIH HHS/United States ; AI05093/AI/NIAID NIH HHS/United States ; //Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Caprylates/pharmacology ; Cell Survival ; Mitochondria/metabolism ; Organelles/*metabolism ; Phylogeny ; Protozoan Proteins/*metabolism ; Thioctic Acid/*metabolism ; Toxoplasma/growth &amp; development/*metabolism/ultrastructure ; }, abstract = {In contrast to other eukaryotes, which manufacture lipoic acid, an essential cofactor for several vital dehydrogenase complexes, within the mitochondrion, we show that the plastid (apicoplast) of the obligate intracellular protozoan parasite Toxoplasma gondii is the only site of de novo lipoate synthesis. However, antibodies specific for protein-attached lipoate reveal the presence of lipoylated proteins in both, the apicoplast and the mitochondrion of T. gondii. Cultivation of T. gondii-infected cells in lipoate-deficient medium results in substantially reduced lipoylation of mitochondrial (but not apicoplast) proteins. Addition of exogenous lipoate to the medium can rescue this effect, showing that the parasite scavenges this cofactor from the host. Exposure of T. gondii to lipoate analogues in lipoate-deficient medium leads to growth inhibition, suggesting that T. gondii might be auxotrophic for this cofactor. Phylogenetic analyses reveal the secondary loss of the mitochondrial lipoate synthase gene after the acquisition of the plastid. Our studies thus reveal an unexpected metabolic deficiency in T. gondii and raise the question whether the close interaction of host mitochondria with the parasitophorous vacuole is connected to lipoate supply by the host.}, }
@article {pmid16774921, year = {2006}, author = {Hsu, JL and Rho, SB and Vannella, KM and Martinis, SA}, title = {Functional divergence of a unique C-terminal domain of leucyl-tRNA synthetase to accommodate its splicing and aminoacylation roles.}, journal = {The Journal of biological chemistry}, volume = {281}, number = {32}, pages = {23075-23082}, doi = {10.1074/jbc.M601606200}, pmid = {16774921}, issn = {0021-9258}, support = {GM63107/GM/NIGMS NIH HHS/United States ; GM63789/GM/NIGMS NIH HHS/United States ; }, mesh = {Alternative Splicing ; Amino Acid Sequence ; Crystallography, X-Ray ; DNA-Directed RNA Polymerases/chemistry ; Escherichia coli/genetics/metabolism ; Leucine-tRNA Ligase/*chemistry ; Mitochondria/metabolism ; Molecular Sequence Data ; Protein Structure, Tertiary ; RNA Splicing ; Sequence Homology, Amino Acid ; Two-Hybrid System Techniques ; Viral Proteins/chemistry ; Yeasts/metabolism ; }, abstract = {Leucyl-tRNA synthetase (LeuRS) performs dual essential roles in group I intron RNA splicing as well as protein synthesis within the yeast mitochondria. Deletions of the C terminus differentially impact the two functions of the enzyme in splicing and aminoacylation in vivo. Herein, we determined that a fiveamino acid C-terminal deletion of LeuRS, which does not complement a null strain, can form a ternary complex with the bI4 intron and its maturase splicing partner. However, the complex fails to stimulate splicing activity. The x-ray co-crystal structure of LeuRS showed that a C-terminal extension of about 60 amino acids forms a discrete domain, which is unique among the LeuRSs and interacts with the corner of the L-shaped tRNALeu. Interestingly, deletion of the entire yeast mitochondrial LeuRS C-terminal domain enhanced its aminoacylation and amino acid editing activities. In striking contrast, deletion of the corresponding C-terminal domain of Escherichia coli LeuRS abolished aminoacylation of tRNALeu and also amino acid editing of mischarged tRNA molecules. These results suggest that the role of the leucine-specific C-terminal domain in tRNA recognition for aminoacylation and amino acid editing has adapted differentially and with surprisingly opposite effects. We propose that the secondary role of yeast mitochondrial LeuRS in RNA splicing has impacted the functional evolution of this critical C-terminal domain.}, }
@article {pmid16773565, year = {2006}, author = {Saxena, R and de Bakker, PI and Singer, K and Mootha, V and Burtt, N and Hirschhorn, JN and Gaudet, D and Isomaa, B and Daly, MJ and Groop, L and Ardlie, KG and Altshuler, D}, title = {Comprehensive association testing of common mitochondrial DNA variation in metabolic disease.}, journal = {American journal of human genetics}, volume = {79}, number = {1}, pages = {54-61}, pmid = {16773565}, issn = {0002-9297}, mesh = {Body Mass Index ; Case-Control Studies ; DNA, Mitochondrial/*genetics ; Diabetes Mellitus, Type 2/*genetics ; Humans ; Metabolic Diseases/*genetics ; Polymorphism, Single Nucleotide ; }, abstract = {Many lines of evidence implicate mitochondria in phenotypic variation: (a) rare mutations in mitochondrial proteins cause metabolic, neurological, and muscular disorders; (b) alterations in oxidative phosphorylation are characteristic of type 2 diabetes, Parkinson disease, Huntington disease, and other diseases; and (c) common missense variants in the mitochondrial genome (mtDNA) have been implicated as having been subject to natural selection for adaptation to cold climates and contributing to "energy deficiency" diseases today. To test the hypothesis that common mtDNA variation influences human physiology and disease, we identified all 144 variants with frequency >1% in Europeans from >900 publicly available European mtDNA sequences and selected 64 tagging single-nucleotide polymorphisms that efficiently capture all common variation (except the hypervariable D-loop). Next, we evaluated the complete set of common mtDNA variants for association with type 2 diabetes in a sample of 3,304 diabetics and 3,304 matched nondiabetic individuals. Association of mtDNA variants with other metabolic traits (body mass index, measures of insulin secretion and action, blood pressure, and cholesterol) was also tested in subsets of this sample. We did not find a significant association of common mtDNA variants with these metabolic phenotypes. Moreover, we failed to identify any physiological effect of alleles that were previously proposed to have been adaptive for energy metabolism in human evolution. More generally, this comprehensive association-testing framework can readily be applied to other diseases for which mitochondrial dysfunction has been implicated.}, }
@article {pmid16772046, year = {2006}, author = {Patron, NJ and Rogers, MB and Keeling, PJ}, title = {Comparative rates of evolution in endosymbiotic nuclear genomes.}, journal = {BMC evolutionary biology}, volume = {6}, number = {}, pages = {46}, pmid = {16772046}, issn = {1471-2148}, mesh = {Bacterial Proteins/genetics ; Cell Nucleus/*genetics ; Cryptophyta/*cytology/*genetics ; Eukaryotic Cells/*metabolism ; *Evolution, Molecular ; Genome/*genetics ; Phylogeny ; Plant Proteins/genetics ; Plastids/genetics ; Proteobacteria/genetics ; Symbiosis/*genetics ; }, abstract = {BACKGROUND: The nucleomorphs associated with secondary plastids of cryptomonads and chlorarachniophytes are the sole examples of organelles with eukaryotic nuclear genomes. Although not as widespread as their prokaryotic equivalents in mitochondria and plastids, nucleomorph genomes share similarities in terms of reduction and compaction. They also differ in several aspects, not least in that they encode proteins that target to the plastid, and so function in a different compartment from that in which they are encoded.<br><br>RESULTS: Here, we test whether the phylogenetically distinct nucleomorph genomes of the cryptomonad, Guillardia theta, and the chlorarachniophyte, Bigelowiella natans, have experienced similar evolutionary pressures during their transformation to reduced organelles. We compared the evolutionary rates of genes from nuclear, nucleomorph, and plastid genomes, all of which encode proteins that function in the same cellular compartment, the plastid, and are thus subject to similar selection pressures. Furthermore, we investigated the divergence of nucleomorphs within cryptomonads by comparing G. theta and Rhodomonas salina.<br><br>CONCLUSION: Chlorarachniophyte nucleomorph genes have accumulated errors at a faster rate than other genomes within the same cell, regardless of the compartment where the gene product functions. In contrast, most nucleomorph genes in cryptomonads have evolved faster than genes in other genomes on average, but genes for plastid-targeted proteins are not overly divergent, and it appears that cryptomonad nucleomorphs are not presently evolving rapidly and have therefore stabilized. Overall, these analyses suggest that the forces at work in the two lineages are different, despite the similarities between the structures of their genomes.}, }
@article {pmid16769251, year = {2006}, author = {Rewitz, KF and Styrishave, B and Løbner-Olsen, A and Andersen, O}, title = {Marine invertebrate cytochrome P450: emerging insights from vertebrate and insects analogies.}, journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP}, volume = {143}, number = {4}, pages = {363-381}, doi = {10.1016/j.cbpc.2006.04.001}, pmid = {16769251}, issn = {1532-0456}, mesh = {Animals ; Annelida/enzymology ; Crustacea/enzymology ; *Cytochrome P-450 Enzyme System/genetics ; Echinodermata/enzymology ; Gene Expression Regulation ; Invertebrates/*enzymology/genetics ; Microsomes/enzymology ; Mitochondria/enzymology ; Mollusca/enzymology ; Phylogeny ; Tissue Distribution ; Xenobiotics/metabolism ; }, abstract = {Cytochrome P450 enzymes (P450s) are responsible for the oxidative metabolism of a plethora of endogenous and exogenous substrates. P450s and associated activities have been demonstrated in numerous marine invertebrates belonging to the phyla Cnidaria, Annelida (Polychaeta), Mollusca, Arthropoda (Crustacea) and Echinodermata. P450s of marine invertebrates and vertebrates show considerable sequence divergence and the few orthologs reveal the selective constraint on physiologically significant enzymes. P450s are present in virtually all tissues of marine invertebrates, although high levels usually are found in hepatic-like organs and steroidogenic tissues. High-throughput technologies result in the rapid acquisition of new marine invertebrate P450 sequences; however, the understanding of their function is poor. Based on analogy to vertebrates and insects, it is likely that P450s play a pivotal role in the physiology of marine invertebrates by catalyzing the biosynthesis of signal molecules including steroids such as 20-hydroxyecdysone (the molting hormone of crustaceans). The metabolism of many exogenous compounds including benzo(a)pyrene (BaP), pyrene, ethoxyresorufin, ethoxycoumarin and aniline is mediated by P450 enzymes in tissues of marine invertebrates. P450 gene expression, protein levels and P450 mediated metabolism of xenobiotics are induced by PAHs in some marine invertebrate species. Thus, regulation of P450 enzyme activity may play a central role in the adaptation of animals to environmental pollutants. Emphasis should be put on the elucidation of the function and regulation of the ever-increasing number of marine invertebrate P450s.}, }
@article {pmid16764907, year = {2006}, author = {Tower, J}, title = {Sex-specific regulation of aging and apoptosis.}, journal = {Mechanisms of ageing and development}, volume = {127}, number = {9}, pages = {705-718}, doi = {10.1016/j.mad.2006.05.001}, pmid = {16764907}, issn = {0047-6374}, support = {AG11644/AG/NIA NIH HHS/United States ; AG11833/AG/NIA NIH HHS/United States ; }, mesh = {Aging/*genetics ; Animals ; Apoptosis/genetics ; Cell Nucleus/genetics/metabolism ; Chromosomes, Human, X ; Female ; Gene Expression Regulation, Developmental ; Humans ; Longevity/*genetics ; Male ; Mitochondria/genetics/microbiology ; Oxidative Stress ; Quantitative Trait Loci ; *Sex Characteristics ; Species Specificity ; X Chromosome ; }, abstract = {Genetic analysis of Drosophila, mice and humans indicates that gene alleles, mutations and transgenes that affect life span tend to do so differently depending on the sex of the organism. The likely reason for this is that the sexes are different genotypes (e.g., X/X vs. X/Y) and face quite different environments: e.g., to reproduce, males have to mate with females while females have to mate with males. Genes are subject to different genetic interactions and different gene-by-environment effects in male vs. female. The consequence is that through evolution certain genes are differently selected and optimized for each sex. Both the mitochondrial genome and the X chromosome are asymmetrically inherited in Drosophila and mammals; through evolution these genes spend relatively more time under selection in females and are therefore expected to be better optimized for function in the female than in the male. Consistent with this the Drosophila X chromosome has been found to be a hotspot for sexually antagonistic fitness variation. Old Drosophila and old mammals exhibit apoptosis-an observation consistent with the idea that the mitochondria are less functional during aging due to maternal-only inheritance. One feature of aging that is common to Drosophila and mammals is that females tend to live longer than males, and this may be due in part to sub-optimal mitochondrial function in males. The data support the conclusion that a significant part of the aging phenotype is due to antagonistic pleiotropy of gene function between the sexes. Liberal application of Occam's razor yields a molecular model for the co-regulation of sex, apoptosis and life span based on the on/off status of a single gene: Sxl in Drosophila melanogaster and Xist in humans. Aging may simply represent an ancient and conserved mechanism by which genes re-assort.}, }
@article {pmid16762445, year = {2006}, author = {Boore, JL}, title = {The use of genome-level characters for phylogenetic reconstruction.}, journal = {Trends in ecology &amp; evolution}, volume = {21}, number = {8}, pages = {439-446}, doi = {10.1016/j.tree.2006.05.009}, pmid = {16762445}, issn = {0169-5347}, mesh = {*Genome ; Mitochondria/genetics ; *Phylogeny ; }, abstract = {Now that large-scale genome-sequencing projects are sampling many organismal lineages, it is becoming possible to compare large data sets of not only DNA and protein sequences, but also genome-level features, such as gene arrangements and the positions of mobile genetic elements. Although it is unlikely that comparisons of such features will address a large number of evolutionary branch points across the broad tree of life owing to the infeasibility of such sampling, they have great potential for resolving many crucial, contested relationships for which no other data seem promising. Here, I discuss the advancements, advantages, methods, and problems of the use of genome-level characters for reconstructing evolutionary relationships.}, }
@article {pmid16758930, year = {2006}, author = {Watanabe, K and Suzuki, T}, title = {[Universality and evolutional deviation of the genetic code].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {51}, number = {7}, pages = {844-852}, pmid = {16758930}, issn = {0039-9450}, mesh = {Amino Acids/genetics ; Animals ; Candida/genetics ; Codon/genetics/physiology ; *Evolution, Molecular ; *Genetic Code ; Humans ; Mitochondria/genetics ; RNA, Messenger/genetics ; }, }
@article {pmid16757556, year = {2006}, author = {Liu, Z and Lin, H and Ye, S and Liu, QY and Meng, Z and Zhang, CM and Xia, Y and Margoliash, E and Rao, Z and Liu, XJ}, title = {Remarkably high activities of testicular cytochrome c in destroying reactive oxygen species and in triggering apoptosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {24}, pages = {8965-8970}, pmid = {16757556}, issn = {0027-8424}, mesh = {Animals ; Apoptosis/*physiology ; Ascorbic Acid/metabolism ; Crystallography, X-Ray ; Cytochromes c/chemistry/classification/genetics/*metabolism ; DNA Damage ; Electron Transport Complex IV/metabolism ; Erythrocytes/cytology/metabolism ; Humans ; Hydrogen Peroxide/metabolism ; Male ; Mice ; Models, Molecular ; Oocytes/physiology ; Oxidants/metabolism ; Phylogeny ; Protein Conformation ; Protein Isoforms/*metabolism ; Reactive Oxygen Species/*metabolism ; Spermatozoa/physiology ; Testis/*enzymology/*metabolism ; Water/chemistry ; Xenopus laevis ; }, abstract = {Hydrogen peroxide (H(2)O(2)) is the major reactive oxygen species (ROS) produced in sperm. High concentrations of H(2)O(2) in sperm induce nuclear DNA fragmentation and lipid peroxidation and result in cell death. The respiratory chain of the mitochondrion is one of the most productive ROS generating systems in sperm, and thus the destruction of ROS in mitochondria is critical for the cell. It was recently reported that H(2)O(2) generated by the respiratory chain of the mitochondrion can be efficiently destroyed by the cytochrome c-mediated electron-leak pathway where the electron of ferrocytochrome c migrates directly to H(2)O(2) instead of to cytochrome c oxidase. In our studies, we found that mouse testis-specific cytochrome c (T-Cc) can catalyze the reduction of H(2)O(2) three times faster than its counterpart in somatic cells (S-Cc) and that the T-Cc heme has the greater resistance to being degraded by H(2)O(2). Together, these findings strongly imply that T-Cc can protect sperm from the damages caused by H(2)O(2). Moreover, the apoptotic activity of T-Cc is three to five times greater than that of S-Cc in a well established apoptosis measurement system using Xenopus egg extract. The dramatically stronger apoptotic activity of T-Cc might be important for the suicide of male germ cells, considered a physiological mechanism that regulates the number of sperm produced and eliminates those with damaged DNA. Thus, it is very likely that T-Cc has evolved to guarantee the biological integrity of sperm produced in mammalian testis.}, }
@article {pmid16756507, year = {2006}, author = {Nordlund, P and Reichard, P}, title = {Ribonucleotide reductases.}, journal = {Annual review of biochemistry}, volume = {75}, number = {}, pages = {681-706}, doi = {10.1146/annurev.biochem.75.103004.142443}, pmid = {16756507}, issn = {0066-4154}, mesh = {Allosteric Regulation ; Animals ; Binding Sites ; Evolution, Molecular ; Free Radicals/metabolism ; Fungal Proteins/chemistry/classification/genetics/metabolism ; Gene Expression Regulation, Enzymologic ; Humans ; Mitochondria/metabolism ; Models, Molecular ; Molecular Structure ; Protein Conformation ; *Ribonucleotide Reductases/chemistry/classification/genetics/metabolism ; Substrate Specificity ; Transcriptional Activation ; }, abstract = {Ribonucleotide reductases (RNRs) transform RNA building blocks to DNA building blocks by catalyzing the substitution of the 2'OH-group of a ribonucleotide with a hydrogen by a mechanism involving protein radicals. Three classes of RNRs employ different mechanisms for the generation of the protein radical. Recent structural studies of members from each class have led to a deeper understanding of their catalytic mechanism and allosteric regulation by nucleoside triphosphates. The main emphasis of this review is on regulation of RNR at the molecular and cellular level. Conformational transitions induced by nucleotide binding determine the regulation of substrate specificity. An intricate interplay between gene activation, enzyme inhibition, and protein degradation regulates, together with the allosteric effects, enzyme activity and provides the appropriate amount of deoxynucleotides for DNA replication and repair. In spite of large differences in the amino acid sequences, basic structural features are remarkably similar and suggest a common evolutionary origin for the three classes.}, }
@article {pmid16754862, year = {2006}, author = {Alliegro, MC and Alliegro, MA and Palazzo, RE}, title = {Centrosome-associated RNA in surf clam oocytes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {24}, pages = {9034-9038}, pmid = {16754862}, issn = {0027-8424}, support = {R01 GM043264/GM/NIGMS NIH HHS/United States ; R21 GM075163/GM/NIGMS NIH HHS/United States ; GM043264/GM/NIGMS NIH HHS/United States ; GM075163/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bivalvia/cytology/*genetics/metabolism ; Centrosome/*metabolism ; Cytoplasm/metabolism ; Humans ; In Situ Hybridization ; Molecular Sequence Data ; Oocytes/cytology/*physiology ; RNA/genetics/*metabolism ; Sequence Alignment ; }, abstract = {Centrosomes are the major microtubule-organizing center in animal cells. They are composed of a pair of [9(3) + 0] centrioles surrounded by a relatively ill-defined pericentriolar matrix, provide the ciliary centriole-kinetosome (basal body) progenitor, and organize the assembly of microtubules into the mitotic spindle during cell division. Despite >100 years of microscopic observation and their obvious significance, our understanding of centrosome composition, dynamic organization, and mechanism of action is limited when compared with that of other cellular organelles. Centrosomes duplicate only once per cell cycle to ensure development of a normal bipolar spindle. The initial event in centrosome duplication is centriole replication, which is generative, semiconservative, and independent of the nucleus. Such observations led to the proposal that centrosomes contain their own complement of nucleic acids, possibly representative of an organellar genome comparable with those described for mitochondria and chloroplasts. The consensus in the field is that centrosomes lack DNA but may contain RNA. We isolated centrosomes from oocytes of the surf clam, Spisula solidissima, and purified from them a unique set of RNAs. We show here by biochemical means and subcellular in situ hybridization that the first transcript we analyzed is intimately associated with centrosomes. Sequence analysis reveals that this centrosome-associated RNA encodes a conserved RNA-directed polymerase domain. The hypothesis that centrosomes contain an intrinsic complement of specific RNAs suggests new opportunities to address the century-old problem of centrosome function, heredity, and evolution.}, }
@article {pmid16754614, year = {2006}, author = {Embley, TM}, title = {Multiple secondary origins of the anaerobic lifestyle in eukaryotes.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {361}, number = {1470}, pages = {1055-1067}, pmid = {16754614}, issn = {0962-8436}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Anaerobiosis/*physiology ; *Biological Evolution ; Eukaryotic Cells/enzymology/*physiology ; Hydrogenase/genetics ; Iron-Sulfur Proteins/genetics ; Mitochondria/genetics/metabolism ; Phylogeny ; Pyruvate Synthase/genetics ; }, abstract = {Classical ideas for early eukaryotic evolution often posited a period of anaerobic evolution producing a nucleated phagocytic cell to engulf the mitochondrial endosymbiont, whose presence allowed the host to colonize emerging aerobic environments. This idea was given credence by the existence of contemporary anaerobic eukaryotes that were thought to primitively lack mitochondria, thus providing examples of the type of host cell needed. However, the groups key to this hypothesis have now been shown to contain previously overlooked mitochondrial homologues called hydrogenosomes or mitosomes; organelles that share common ancestry with mitochondria but which do not carry out aerobic respiration. Mapping these data on the unfolding eukaryotic tree reveals that secondary adaptation to anaerobic habitats is a reoccurring theme among eukaryotes. The apparent ubiquity of mitochondrial homologues bears testament to the importance of the mitochondrial endosymbiosis, perhaps as a founding event, in eukaryotic evolution. Comparative study of different mitochondrial homologues is needed to determine their fundamental importance for contemporary eukaryotic cells.}, }
@article {pmid16750865, year = {2006}, author = {Szabadkai, G and Simoni, AM and Bianchi, K and De Stefani, D and Leo, S and Wieckowski, MR and Rizzuto, R}, title = {Mitochondrial dynamics and Ca2+ signaling.}, journal = {Biochimica et biophysica acta}, volume = {1763}, number = {5-6}, pages = {442-449}, doi = {10.1016/j.bbamcr.2006.04.002}, pmid = {16750865}, issn = {0006-3002}, support = {GGP05284/TI_/Telethon/Italy ; }, mesh = {Animals ; Biological Evolution ; *Calcium Signaling ; Endoplasmic Reticulum/metabolism ; Humans ; Mitochondria/*metabolism ; }, abstract = {Recent data shed light on two novel aspects of the mitochondria-Ca2+ liaison. First, it was extensively investigated how Ca2+ handling is controlled by mitochondrial shape, and positioning; a playground also of cell death and survival regulation. On the other hand, significant progress has been made to explore how intra- and near-mitochondrial Ca2+ signals modify mitochondrial morphology and cellular distribution. Here, we shortly summarize these advances and provide a model of Ca2+-mitochondria interactions.}, }
@article {pmid16714384, year = {2006}, author = {Goswami, S and Dhar, G and Mukherjee, S and Mahata, B and Chatterjee, S and Home, P and Adhya, S}, title = {A bifunctional tRNA import receptor from Leishmania mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {22}, pages = {8354-8359}, pmid = {16714384}, issn = {0027-8424}, mesh = {Animals ; Biological Transport ; Leishmania tropica/*cytology/genetics/*metabolism ; Mitochondria/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Structure, Tertiary ; Protein Subunits/chemistry/genetics/metabolism ; Protozoan Proteins/chemistry/genetics/*metabolism ; RNA, Transfer/*metabolism ; Structural Homology, Protein ; }, abstract = {In kinetoplastid protozoa, import of cytosolic tRNAs into mitochondria occurs through tRNAs interacting with membrane-bound proteins, the identities of which are unknown. The inner membrane RNA import complex of Leishmania tropica contains multiple proteins and is active for import in vitro. RIC1, the largest subunit of this complex, is structurally homologous to the conserved alpha subunit of F1 ATP synthase. The RIC1 gene complemented an atpA mutation in Escherichia coli. Antisense-mediated knockdown of RIC1/F1alpha in Leishmania resulted in depletion of several mitochondrial tRNAs belonging to distinct subsets (types I and II) that interact cooperatively or antagonistically within the import complex. The knockdown-induced defect in import of type I tRNAs was rectified in a reconstituted system by purified RIC1/F1alpha alone, but recovery of type II tRNA import additionally required a type I tRNA. RIC1/F1alpha formed stable complexes with type I, but not type II, tRNAs through the cooperation of its nucleotide binding and C-terminal domains. Thus, RIC1/F1alpha is a type I tRNA import receptor. As expected of a bifunctional protein, RIC1/F1alpha is shared by both the import complex and by respiratory complex V. Alternative use of ancient respiratory proteins may have been an important step in the evolution of tRNA import.}, }
@article {pmid16710701, year = {2007}, author = {Herget, M and Tampé, R}, title = {Intracellular peptide transporters in human--compartmentalization of the "peptidome".}, journal = {Pflugers Archiv : European journal of physiology}, volume = {453}, number = {5}, pages = {591-600}, pmid = {16710701}, issn = {0031-6768}, mesh = {ATP Binding Cassette Transporter 1 ; ATP Binding Cassette Transporter, Subfamily B, Member 2 ; ATP Binding Cassette Transporter, Subfamily B, Member 3 ; *ATP-Binding Cassette Transporters/antagonists &amp; inhibitors/genetics/physiology ; Antigen Presentation ; Humans ; Immediate-Early Proteins/physiology ; Lysosomes/physiology ; Models, Biological ; Phylogeny ; Protein Structure, Tertiary ; Protein Transport/*physiology ; RNA-Binding Proteins/physiology ; Substrate Specificity ; Viral Proteins/physiology ; }, abstract = {In the human genome, the five adenosine triphosphate (ATP)-binding cassette (ABC) half transporters ABCB2 (TAP1), ABCB3 (TAP2), ABCB9 (TAP-like), and in part, also ABCB8 and ABCB10 are closely related with regard to their structural and functional properties. Although targeted to different cellular compartments such as the endoplasmic reticulum (ER), lysosomes, and mitochondria, they are involved in intracellular peptide trafficking across membranes. The transporter associated with antigen processing (TAP1 and TAP2) constitute a key machinery in the major histocompatibility complex (MHC) class I-mediated cellular immune defense against infected or malignantly transformed cells. TAP translocates the cellular "peptidome" derived primarily from cytosolic proteasomal degradation into the ER lumen for presentation by MHC class I molecules. The homodimeric ABCB9 (TAP-like) complex located in lysosomal compartments shares structural and functional similarities to TAP; however, its biological role seems to be different from the MHC I antigen processing. ABCB8 and ABCB10 are targeted to the inner mitochondrial membrane. MDL1, the yeast homologue of ABCB10, is involved in the export of peptides derived from proteolysis of inner-membrane proteins into the intermembrane space. As such peptides are presented as minor histocompatibility antigens on the surface of mammalian cells, a physiological role of ABCB10 in the antigen processing can be accounted.}, }
@article {pmid16706173, year = {2005}, author = {Galitskiĭ, VA}, title = {[The origin of eukaryotic cells and origination of apoptosis].}, journal = {Tsitologiia}, volume = {47}, number = {2}, pages = {103-120}, pmid = {16706173}, issn = {0041-3771}, mesh = {Animals ; Apoptosis/*physiology ; *Biological Evolution ; Chloroplasts ; Cytoplasm/physiology ; Cytoskeleton ; Eukaryotic Cells/cytology/*physiology ; Intracellular Membranes/physiology ; Mitochondria/physiology ; Oncogene Proteins ; Prokaryotic Cells/physiology ; Proto-Oncogene Proteins c-bcl-2/metabolism ; Signal Transduction ; Spindle Apparatus ; Symbiosis ; Tumor Suppressor Protein p53/metabolism ; Viral Proteins ; }, abstract = {The unified conception of the origin of eukaryotic cells has been proposed. In the author's opinion, evolutionary transformation of prokaryotic cell into eukaryotic cell took place 3.3-1.4 billion years ago and involved the next four stages: 1) the appearance of intracellular membranes due to prokaryotic cell plasmalemma invaginating into its cytoplasm; 2) the cell nucleus formation by the double sheet of intracellular membrane surrounding and sequestrating genetic material of the cell; 3) the appearance of cytoskeleton in parallel with mitotic spindle formation and gradual transition from prokaryotic way of cell division to mitosis; 4) the establishment of symbiosis between the evolving nucleated cell and prokaryotic microorganicsms that subsequently transform into mitochondria and chloroplasts. Apoptosis of cells of the present day multicellular eukaryotic organisms is supposed to be an evolutionary altered response of mitochondrian predecessors to the influence of factors, which are able to damage eukaryotic host cell. The initial biological significance of this reaction pertained to attempts of endosymbionts to leave the host cell as soon as possible, if the probability of its irreversible injury was very high, and by this to escape from their death. It is possible that numerous proteins, known as sensors or transducers of proapoptotic signals in Bcl-2--p53-dependent apoptotic pathway, were initially encoded by mitochondrial genome, whereas antiapoptotic factors and also components of receptor-mediated and granzyme B perforin dependent apoptotic pathways have cellular origin.}, }
@article {pmid16701327, year = {2004}, author = {Rand, DM and Haney, RA and Fry, AJ}, title = {Cytonuclear coevolution: the genomics of cooperation.}, journal = {Trends in ecology &amp; evolution}, volume = {19}, number = {12}, pages = {645-653}, doi = {10.1016/j.tree.2004.10.003}, pmid = {16701327}, issn = {0169-5347}, abstract = {Without mitochondria we would be in big trouble, and there would be a global biological energy crisis if it were not for chloroplasts. Fortunately, genomic evolution over the past two billion years has ensured that the functions of these key organelles are with us to stay. Whole-genome analyses have not only proven that mitochondria and chloroplasts are descended from formerly free-living bacteria, but have also shown that it is difficult to define eukaryotes without reference to the fusion and coevolution of host and endosymbiont genomes. Here, we review how the macro- and microevolutionary insights that follow from the genomics of cytonuclear interactions are uniting molecular evolution, structural proteomics, population genetics and problems in aging and disease. Our goals are to clarify the coevolutionary events that have governed nuclear and organelle evolution, and to encourage further critical analyses of these interactions as problems in the study of co-adapted gene complexes.}, }
@article {pmid16701262, year = {2004}, author = {Gemmell, NJ and Metcalf, VJ and Allendorf, FW}, title = {Mother's curse: the effect of mtDNA on individual fitness and population viability.}, journal = {Trends in ecology &amp; evolution}, volume = {19}, number = {5}, pages = {238-244}, doi = {10.1016/j.tree.2004.02.002}, pmid = {16701262}, issn = {0169-5347}, abstract = {The mitochondrial genome is considered generally to be an innocent bystander in adaptive evolution; however, there is increasing evidence that mitochondrial DNA (mtDNA) is an important contributor to viability and fecundity. Some of this evidence is now well documented, with mtDNA mutations having been shown to play a causal role in degenerative diseases, ageing, and cancer. However, most research on mtDNA has ignored the possibility that other instances exist where mtDNA mutations could have profound fitness consequences. Recent work in humans and other species now indicates that mtDNA mutations play an important role in sperm function, male fertility, and male fitness. Ironically, deleterious mtDNA mutations that affect only males, such as those that impair sperm function, will not be subject to natural selection because mitochondria are generally maternally inherited and could reach high frequencies in populations if the mutations are not disadvantageous in females. Here, we review how such mtDNA mutations might affect the viability of natural populations. We consider factors that increase or decrease the strength of the effect of mtDNA mutations on population viability and discuss what mechanisms exist to mitigate deleterious mtDNA effects.}, }
@article {pmid16690143, year = {2006}, author = {Kuroiwa, T and Nishida, K and Yoshida, Y and Fujiwara, T and Mori, T and Kuroiwa, H and Misumi, O}, title = {Structure, function and evolution of the mitochondrial division apparatus.}, journal = {Biochimica et biophysica acta}, volume = {1763}, number = {5-6}, pages = {510-521}, doi = {10.1016/j.bbamcr.2006.03.007}, pmid = {16690143}, issn = {0006-3002}, mesh = {Animals ; *Biological Evolution ; Dynamins/metabolism ; Endocytosis ; Mitochondria/*physiology/ultrastructure ; Plastids/metabolism ; }, abstract = {Mitochondria are derived from free-living alpha-proteobacteria that were engulfed by eukaryotic host cells through the process of endosymbiosis, and therefore have their own DNA which is organized using basic proteins to form organelle nuclei (nucleoids). Mitochondria divide and are split amongst the daughter cells during cell proliferation. Their division can be separated into two main events: division of the mitochondrial nuclei and division of the matrix (the so-called mitochondrial division, or mitochondriokinesis). In this review, we first focus on the cytogenetical relationships between mitochondrial nuclear division and mitochondriokinesis. Mitochondriokinesis occurs after mitochondrial nuclear division, similar to bacterial cytokinesis. We then describe the fine structure and dynamics of the mitochondrial division ring (MD ring) as a basic morphological background for mitochondriokinesis. Electron microscopy studies first identified a small electron-dense MD ring in the cytoplasm at the constriction sites of dividing mitochondria in the slime mold Physarum polycephalum, and then two large MD rings (with outer cytoplasmic and inner matrix sides) in the red alga Cyanidioschyzon merolae. Now MD rings have been found in all eukaryotes. In the third section, we describe the relationships between the MD ring and the FtsZ ring descended from ancestral bacteria. Other than the GTPase, FtsZ, mitochondria have lost most of the proteins required for bacterial cytokinesis as a consequence of endosymbiosis. The FtsZ protein forms an electron transparent ring (FtsZ or Z ring) in the matrix inside the inner MD ring. For the fourth section, we describe the dynamic association between the outer MD ring with a ring composed of the eukaryote-specific GTPase dynamin. Recent studies have revealed that eukaryote-specific GTPase dynamins form an electron transparent ring between the outer membrane and the MD ring. Thus, mitochondriokinesis is thought to be controlled by a mitochondrial division (MD) apparatus including a dynamic trio, namely the FtsZ, MD and dynamin rings, which consist of a chimera of rings from bacteria and eukaryotes in primitive organisms. Since the genes for the MD ring and dynamin rings are not found in the prokaryotic genome, the host genomes may make these rings to actively control mitochondrial division. In the fifth part, we focus on the dynamic changes in the formation and disassembly of the FtsZ, MD and dynamin rings. FtsZ rings are digested during a later period of mitochondrial division and then finally the MD and dynamin ring apparatuses pinched off the daughter mitochondria, supporting the idea that the host genomes are responsible for the ultimate control of mitochondrial division. We discuss the evolution, from the original vesicle division (VD) apparatuses to VD apparatuses including classical dynamin rings and MD apparatuses. It is likely that the MD apparatuses involving the dynamic trio evolved into the plastid division (PD) apparatus in Bikonta, while in Opisthokonta, the MD apparatus was simplified during evolution and may have branched into the mitochondrial fusion apparatus. Finally, we describe the possibility of intact isolation of large MD/PD apparatuses, the identification of all their proteins and their related genes using C. merolae genome information and TOF-MS analyses. These results will assist in elucidating the universal mechanism and evolution of MD, PD and VD apparatuses.}, }
@article {pmid16685148, year = {2006}, author = {Noblesse, E and Nizard, C and Cario-André, M and Lepreux, S and Pain, C and Schnebert, S and Taïeb, A and Kurfurst, R}, title = {Skin ultrastructure in senile lentigo.}, journal = {Skin pharmacology and physiology}, volume = {19}, number = {2}, pages = {95-100}, doi = {10.1159/000091976}, pmid = {16685148}, issn = {1660-5527}, mesh = {Aged ; Aged, 80 and over ; Biopsy ; Cell Count ; Dermis/pathology/ultrastructure ; Female ; Hand/pathology ; Humans ; Immunohistochemistry ; Lentigo/diagnosis/*pathology ; Male ; Melanocytes/pathology/ultrastructure ; Microscopy, Electron ; Middle Aged ; Skin/*pathology/*ultrastructure ; Tissue Embedding ; }, abstract = {Senile lentigo is a common component of photoaged skin. It is characterized by hyperpigmented macules which affect chronically irradiated skin mostly after the age of 50. This study was undertaken to assess the morphology of senile lentigo on the dorsum of the hands. A systematic comparison between lesional and perilesional skin using histology and transmission electron microscopy was done to determine whether melanocytes or keratinocytes are affected in the evolution of lesions and which tissue structure is modified. The histology study showed that lesional skin is characterized by a hyperpigmented basal layer and an elongation of the rete ridges, which seem to drive deeply into the dermis. The epidermis contained clusters of keratinocytes, which retained and accumulated the melanin pigment. Electron microscopy studies showed important modifications in the lesional skin ultrastructure in comparison with perilesional skin. In melanocytes from perilesional and lesional skin, we observed normal size melanosomes at all stages of maturation in the cytoplasm and in migration within dendrites. No pigment accumulation was observed. However, the morphology of melanocytes in lesional skin revealed an activated status with numerous mitochondria and a well-developed endoplasmic reticulum, which could reflect intense protein synthesis. In basal keratinocytes from lesional skin, we observed numerous melanosome complexes called polymelanosomes, which formed massive caps on the nuclei. Observations in colored semi-thin sections also revealed perturbed structures in the basal layer region, which could explain the skin perturbation. Indeed, we observed keratinocytes that presented important microinvaginations and pendulum melanocytes, which sank into the dermis, beneath the basal layer of keratinocytes. These cell modifications seemed to be due to a perturbation of the dermal-epidermal junction, which appeared disorganized and disrupted and could directly disturb the basal support of the cells.}, }
@article {pmid16684995, year = {2006}, author = {Kosa, P and Valach, M and Tomaska, L and Wolfe, KH and Nosek, J}, title = {Complete DNA sequences of the mitochondrial genomes of the pathogenic yeasts Candida orthopsilosis and Candida metapsilosis: insight into the evolution of linear DNA genomes from mitochondrial telomere mutants.}, journal = {Nucleic acids research}, volume = {34}, number = {8}, pages = {2472-2481}, pmid = {16684995}, issn = {1362-4962}, support = {R03 TW005654/TW/FIC NIH HHS/United States ; }, mesh = {Base Sequence ; Candida/classification/*genetics/metabolism ; Conserved Sequence ; DNA, Circular/chemistry ; DNA, Mitochondrial/*chemistry ; *Evolution, Molecular ; Gene Order ; *Genome, Fungal ; Mitochondria/*genetics ; Mutation ; Phylogeny ; RNA/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Messenger/metabolism ; RNA, Mitochondrial ; RNA, Transfer/metabolism ; Telomere/*chemistry/genetics ; }, abstract = {We determined complete mitochondrial DNA sequences of the two yeast species, Candida orthopsilosis and Candida metapsilosis, and compared them with the linear mitochondrial genome of their close relative, C.parapsilosis. Mitochondria of all the three species harbor compact genomes encoding the same set of genes arranged in the identical order. Differences in the length of these genomes result mainly from the presence/absence of introns. Multiple alterations were identified also in the sequences of the ribosomal and transfer RNAs, and proteins. However, the most striking feature of C.orthopsilosis and C.metapsilosis is the existence of strains differing in the molecular form of the mitochondrial genome (circular-mapping versus linear). Their analysis opens a unique window for understanding the role of mitochondrial telomeres in the stability and evolution of molecular architecture of the genome. Our results indicate that the circular-mapping mitochondrial genome derived from the linear form by intramolecular end-to-end fusions. Moreover, we suggest that the linear mitochondrial genome evolved from a circular-mapping form present in a common ancestor of the three species and, at the same time, the emergence of mitochondrial telomeres enabled the formation of linear monomeric DNA forms. In addition, comparison of isogenic C.metapsilosis strains differing in the form of the organellar genome suggests a possibility that, under some circumstances, the linearity and/or the presence of telomeres provide a competitive advantage over a circular-mapping mitochondrial genome.}, }
@article {pmid16679012, year = {2006}, author = {Aravind, L and Iyer, LM and Koonin, EV}, title = {Comparative genomics and structural biology of the molecular innovations of eukaryotes.}, journal = {Current opinion in structural biology}, volume = {16}, number = {3}, pages = {409-419}, doi = {10.1016/j.sbi.2006.04.006}, pmid = {16679012}, issn = {0959-440X}, support = {//Intramural NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/*methods ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; Gene Duplication ; Genomics/*methods ; Humans ; Protein Folding ; Protein Structure, Tertiary ; Proteins/chemistry/genetics ; }, abstract = {Eukaryotes encode numerous proteins that either have no detectable homologs in prokaryotes or have only distant homologs. These molecular innovations of eukaryotes may be classified into three categories: proteins and domains inherited from prokaryotic precursors without drastic changes in biochemical function, but often recruited for novel roles in eukaryotes; new superfamilies or distinct biochemical functions emerging within pre-existing protein folds; and domains with genuinely new folds, apparently 'invented' at the outset of eukaryotic evolution. Most new folds emerging in eukaryotes are either alpha-helical or stabilized by metal chelation. Comparative genomics analyses point to an early phase of rapid evolution, and dramatic changes between the origin of the eukaryotic cell and the advent of the last common ancestor of extant eukaryotes. Extensive duplication of numerous genes, with subsequent functional diversification, is a distinctive feature of this turbulent era. Evolutionary analysis of ancient eukaryotic proteins is generally compatible with a two-symbiont scenario for eukaryotic origin, involving an alpha-proteobacterium (the ancestor of the mitochondria) and an archaeon, as well as key contributions from their selfish elements.}, }
@article {pmid16678772, year = {2006}, author = {Schafer, ZT and Kornbluth, S}, title = {The apoptosome: physiological, developmental, and pathological modes of regulation.}, journal = {Developmental cell}, volume = {10}, number = {5}, pages = {549-561}, doi = {10.1016/j.devcel.2006.04.008}, pmid = {16678772}, issn = {1534-5807}, support = {R01 CA102702/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Apoptosis/genetics/*physiology ; Biological Evolution ; *Disease ; Gene Expression Regulation, Developmental ; Humans ; }, abstract = {Apoptosis, a form of programmed cell death, is executed by a family of zymogenic proteases known as caspases, which cleave an array of intracellular substrates in the dying cell. Many proapoptotic stimuli trigger cytochrome c release from mitochondria, promoting the formation of a complex between Apaf-1 and caspase-9 in a caspase-activating structure known as the apoptosome. In this review, we describe knockout and knockin studies of apoptosome components, elegant structural and biochemical experiments, and analyses of the apoptosome in various cancers and other disease states, all of which have provided new insight into this critical locus of apoptotic control.}, }
@article {pmid16651558, year = {2006}, author = {Shahsavarani, A and McNeill, B and Galvez, F and Wood, CM and Goss, GG and Hwang, PP and Perry, SF}, title = {Characterization of a branchial epithelial calcium channel (ECaC) in freshwater rainbow trout (Oncorhynchus mykiss).}, journal = {The Journal of experimental biology}, volume = {209}, number = {Pt 10}, pages = {1928-1943}, doi = {10.1242/jeb.02190}, pmid = {16651558}, issn = {0022-0949}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Calcium Channels/chemistry/genetics/*metabolism ; Epithelial Cells/cytology ; Epithelium/*metabolism ; Female ; Gills/*metabolism ; Immunohistochemistry ; Male ; Molecular Sequence Data ; Oncorhynchus mykiss/*metabolism ; Phylogeny ; }, abstract = {The entry of calcium (Ca2+) through an apical membrane epithelial calcium channel (ECaC) is thought to a key step in piscine branchial Ca2+ uptake. In mammals, ECaC is a member of the transient receptor potential (TRP) gene family of which two sub-families have been identified, TRPV5 and TPRV6. In the present study we have identified a single rainbow trout (Oncorhynchus mykiss) ECaC (rtECaC) that is similar to the mammalian TRPV5 and TRPV6. Phylogenetic analysis of the protein sequence suggests that an ancestral form of the mammalian genes diverged from those in the lower vertebrates prior to the gene duplication event that gave rise to TRPV5 and TRPV6. The putative model for Ca2+ uptake in fish proposes that the mitochondria-rich cell (also termed ionocyte or chloride cell) is the predominant or exclusive site of transcellular Ca2+ movements owing to preferential localisation of ECaC to the apical membrane of these cells. However, the results of real-time PCR performed on enriched gill cell populations as well as immunocytochemistry and in situ hybridisation analysis of enriched cells, cell cultures and whole gill sections strongly suggest that ECaC is not exclusive to mitochondria-rich cells but that it is also found in pavement cells. Not only was ECaC protein localized to areas of the gill normally having few mitochondria-rich cells, but there was also no consistent co-localization of ECaC- and Na+/K+-ATPase-positive (a marker of mitochondria rich cells) cells. Taken together, the results of the present study suggest that although ECaC (mRNA and protein) does exist in trout gill, its cellular distribution is more extensive than previously thought, thus suggesting that Ca2+ uptake may not be restricted to mitochondria-rich cells as was proposed in previous models.}, }
@article {pmid16648156, year = {2006}, author = {Richards, TA and van der Giezen, M}, title = {Evolution of the Isd11-IscS complex reveals a single alpha-proteobacterial endosymbiosis for all eukaryotes.}, journal = {Molecular biology and evolution}, volume = {23}, number = {7}, pages = {1341-1344}, doi = {10.1093/molbev/msl001}, pmid = {16648156}, issn = {0737-4038}, mesh = {Alphaproteobacteria/*genetics/growth &amp; development ; Amino Acid Sequence ; Carbon-Sulfur Lyases/genetics ; Eukaryotic Cells/*metabolism/microbiology ; *Evolution, Molecular ; Iron-Sulfur Proteins/*genetics ; Mitochondrial Proteins/*genetics ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; Saccharomyces cerevisiae Proteins/*genetics ; Sequence Homology, Amino Acid ; Symbiosis/*genetics ; }, abstract = {Giardia and Trichomonas are eukaryotes without standard mitochondria but contain mitochondrial-type alpha-proteobacterium-derived iron-sulfur cluster (ISC) assembly proteins, located to mitosomes in Giardia and hydrogenosomes in Trichomonas. Although these data suggest a single common endosymbiotic ancestry for mitochondria, mitosomes, and hydrogenosomes, separate origins are still being proposed. Here, we present a bioinformatic analysis of Isd11, a recently described essential component of the mitochondrial ISC assembly pathway. Isd11 is unique to eukaryotes but functions closely with the alpha-proteobacterium-derived cysteine desulfurase IscS. We demonstrate the presence of homologues of Isd11 in all 5 eukaryotic supergroups sampled, including hydrogenosomal and mitosomal lineages. The eukaryotic invention of Isd11 as a functional partner to IscS directly implies a single shared alpha-proteobacterial endosymbiotic ancestry for all eukaryotes. This pinpoints the alpha-proteobacterial endosymbiosis to before the last common ancestor of all eukaryotes without ambiguity.}, }
@article {pmid16640602, year = {2006}, author = {Ahn, CS and Lee, JH and Reum Hwang, A and Kim, WT and Pai, HS}, title = {Prohibitin is involved in mitochondrial biogenesis in plants.}, journal = {The Plant journal : for cell and molecular biology}, volume = {46}, number = {4}, pages = {658-667}, doi = {10.1111/j.1365-313X.2006.02726.x}, pmid = {16640602}, issn = {0960-7412}, mesh = {DNA, Complementary ; Gene Silencing ; Homeostasis/genetics ; Membrane Potentials ; Mitochondria/chemistry/*metabolism/ultrastructure ; Mitochondrial Membranes/physiology ; Oxidative Stress ; Oxygen/metabolism ; Phylogeny ; Plant Proteins/analysis/genetics/*physiology ; Prohibitins ; Protein Subunits/analysis/genetics/physiology ; Reactive Oxygen Species/metabolism ; Repressor Proteins/analysis/genetics/*physiology ; Sequence Analysis, DNA ; Nicotiana/genetics/metabolism/ultrastructure ; }, abstract = {Prohibitin, which consists of two subunits PHB1 and PHB2, plays a role in cell-cycle progression, senescence, apoptosis, and maintenance of mitochondrial function in mammals and yeast. In this study, we examined the role of prohibitins in plants by using virus-induced gene silencing (VIGS) of two prohibitin subunit genes of Nicotiana benthamiana, designated NbPHB1 and NbPHB2. NbPHB1 and NbPHB2 were targeted to the mitochondria, and their gene expression was suppressed during senescence. VIGS of NbPHB2 caused severe growth inhibition, leaf yellowing and symptoms of cell death, whereas VIGS of NbPHB1 resulted in a milder phenotype. At the cellular level, depletion of these subunits affected mitochondria by severely reducing their number and/or mass, and by causing morphological and physiological abnormalities. Suppression of prohibitin function resulted in a 10- to 20-fold higher production of reactive oxygen species and induced premature leaf senescence. Finally, disruption of prohibitin function rendered the plants more susceptible to various oxidative stress-inducing reagents, including H(2)O(2), paraquat, antimycin A and salicylic acid. These results suggest that prohibitins play a crucial role in mitochondrial biogenesis and protection against stress and senescence in plant cells.}, }
@article {pmid16636268, year = {2006}, author = {Charrière, F and Helgadóttir, S and Horn, EK and Söll, D and Schneider, A}, title = {Dual targeting of a single tRNA(Trp) requires two different tryptophanyl-tRNA synthetases in Trypanosoma brucei.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {18}, pages = {6847-6852}, pmid = {16636268}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Animals ; Isoenzymes/classification/genetics/*metabolism ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Organisms, Genetically Modified ; Phylogeny ; RNA Interference ; RNA, Transfer, Trp/*metabolism ; Trypanosoma brucei brucei/cytology/*enzymology/genetics ; Tryptophan-tRNA Ligase/classification/genetics/*metabolism ; }, abstract = {The mitochondrion of Trypanosoma brucei does not encode any tRNAs. This deficiency is compensated for by the import of a small fraction of nearly all of its cytosolic tRNAs. Most trypanosomal aminoacyl-tRNA synthetases are encoded by single-copy genes, suggesting the use of the same enzyme in the cytosol and mitochondrion. However, the T. brucei genome contains two distinct genes for eukaryotic tryptophanyl-tRNA synthetase (TrpRS). RNA interference analysis established that both TrpRS1 and TrpRS2 are essential for growth and required for cytosolic and mitochondrial tryptophanyl-tRNA formation, respectively. Decoding the mitochondrial tryptophan codon UGA requires mitochondria-specific C-->U RNA editing in the anticodon of the imported tRNA(Trp). In vitro charging assays with recombinant TrpRS enzymes demonstrated that the edited anticodon and the mitochondria-specific thiolation of U33 in the imported tRNA(Trp) act as antideterminants for the cytosolic TrpRS1. The existence of two TrpRS enzymes, therefore, can be explained by the need for a mitochondrial synthetase with extended substrate specificity to achieve aminoacylation of the imported thiolated and edited tRNA(Trp). Thus, the notion that, in an organism, all nuclear-encoded tRNAs assigned to a given amino acid are charged by a single aminoacyl-tRNA synthetase, is not universally valid.}, }
@article {pmid16628009, year = {2006}, author = {Brown, TA and Clayton, DA}, title = {Genesis and wanderings: origins and migrations in asymmetrically replicating mitochondrial DNA.}, journal = {Cell cycle (Georgetown, Tex.)}, volume = {5}, number = {9}, pages = {917-921}, doi = {10.4161/cc.5.9.2710}, pmid = {16628009}, issn = {1551-4005}, mesh = {Animals ; DNA Replication/*physiology ; DNA, Mitochondrial/*metabolism/ultrastructure ; Electrophoresis, Gel, Two-Dimensional ; *Evolution, Molecular ; Microscopy, Atomic Force ; Models, Genetic ; }, abstract = {Mammalian mitochondria maintain a small circular genome that encodes RNA and polypeptides that are essential for the generation of ATP through oxidative phosphorylation. The mechanism of replication of mammalian mitochondrial DNA (mtDNA) has recently been a topic of controversy. New evidence has led to a modified strand-displacement model that reconciles much of the current data. This revision stems from a new appreciation for alternative light-strand origins. We consider here some of the potential mechanisms for light-strand origin initiation. We also consider further the susceptibility of branch migration within replicating mtDNA molecules. The existence of alternative light-strand origins and a propensity for branch migration in replicating mtDNA molecules exposes a new array of possible configurations of mtDNA. The assortment and assignment of these forms is relevant to the interpretation of experimental data and may also yield insight into the molecular basis of replication errors.}, }
@article {pmid16624922, year = {2006}, author = {Willett, CS}, title = {Deleterious epistatic interactions between electron transport system protein-coding loci in the copepod Tigriopus californicus.}, journal = {Genetics}, volume = {173}, number = {3}, pages = {1465-1477}, pmid = {16624922}, issn = {0016-6731}, mesh = {Animals ; Cell Nucleus/metabolism ; Copepoda/cytology/*genetics/metabolism ; Crosses, Genetic ; Electron Transport Complex III/*genetics/metabolism ; *Epistasis, Genetic ; Genetic Markers ; Heterozygote ; Homozygote ; Mitochondria/metabolism ; Models, Biological ; }, abstract = {The nature of epistatic interactions between genes encoding interacting proteins in hybrid organisms can have important implications for the evolution of postzygotic reproductive isolation and speciation. At this point very little is known about the fitness differences caused by specific closely interacting but evolutionarily divergent proteins in hybrids between populations or species. The intertidal copepod Tigriopus californicus provides an excellent model in which to study such interactions because the species range includes numerous genetically divergent populations that are still capable of being crossed in the laboratory. Here, the effect on fitness due to the interactions of three complex III proteins of the electron transport system in F2 hybrid copepods resulting from crosses of a pair of divergent populations is examined. Significant deviations from Mendelian inheritance are observed for each of the three genes in F2 hybrid adults but not in nauplii (larvae). The two-way interactions between these genes also have a significant impact upon the viability of these hybrid copepods. Dominance appears to play an important role in mediating the interactions between these loci as deviations are caused by heterozygote/homozygote deleterious interactions. These results suggest that the fitness consequences of the interactions of these three complex III-associated genes could influence reproductive isolation in this system.}, }
@article {pmid16623392, year = {2006}, author = {Hackstein, JH and Yarlett, N}, title = {Hydrogenosomes and symbiosis.}, journal = {Progress in molecular and subcellular biology}, volume = {41}, number = {}, pages = {117-142}, doi = {10.1007/3-540-28221-1_7}, pmid = {16623392}, issn = {0079-6484}, mesh = {Animals ; Hydrogen/*metabolism ; Mitochondria/metabolism/ultrastructure ; Organelles/*metabolism/ultrastructure ; Phylogeny ; *Symbiosis ; Trichomonas vaginalis/cytology/ultrastructure ; }, }
@article {pmid16621606, year = {2006}, author = {Cheng, W and Tung, YH and Chiou, TT and Chen, JC}, title = {Cloning and characterisation of mitochondrial manganese superoxide dismutase (mtMnSOD) from the giant freshwater prawn Macrobrachium rosenbergii.}, journal = {Fish &amp; shellfish immunology}, volume = {21}, number = {4}, pages = {453-466}, doi = {10.1016/j.fsi.2006.02.005}, pmid = {16621606}, issn = {1050-4648}, mesh = {Actins/biosynthesis ; Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA Primers/chemistry ; DNA, Complementary/chemistry ; Gene Expression Regulation, Enzymologic/*physiology ; Hemolymph/enzymology ; Hepatopancreas/enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; Palaemonidae/enzymology/*genetics ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Sequence Alignment ; Sequence Homology, Amino Acid ; Superoxide Dismutase/*biosynthesis/*genetics ; Time Factors ; }, abstract = {A cDNA encoding a mitochondrial manganese superoxide dismutase (mtMnSOD) was cloned from the hepatopancreas of giant freshwater prawn Macrobrachium rosenbergii using reverse transcription polymerase chain reaction (RT-PCR) by degenerate primers. Both 3'- and 5'-regions were isolated by rapid amplification of cDNA end (RACE) PCR method. Analysis of nucleotide sequence revealed that the mtMnSOD full-length cDNA consists of 1202bp containing an open reading frame of 654bp, which encodes a protein consisting of 218 amino acids including a signal peptide of 16 amino acid residues. The calculated molecular mass of the mature proteins (202 amino acids) is 24kDa with an estimated pI of 7.12. Two putative N-glycosylation sites, NXT and NXS were observed in the mtMnSOD. Manganese superoxide dismutase signatures from 180 to 187 (DVWEHAYY), and four conserved amino acids responsible for binding manganese were observed (H48, H96, D180 and H184). Sequence comparison showed that the mtMnSOD deduced amino acid sequence of Macrobrachium rosenbergii has similarity of 88%, 78%, 56%, 54% and 46% to that of blue crab Callinectes sapidus, crucifix crab Charybdis feriatus, brown shrimp Farfantepenaeus aztecus, European lobster Palinurus vulgaris, and grass shrimp Palaemontes pugio, respectively, and has similarity of 45%, 44%, 43%, 26% and 25% to cytMnSOD (cytosolic MnSOD) deduced amino acid sequence of blue crab C. sapidus, prawn M. rosenbergii, tiger shrimp Penaeus monodon, grass shrimp P. pugio and brown shrimp F. aztecus, respectively. Quantitative real-time RT-PCR analysis showed that levels of mtMn-SOD transcripts in hepatopancreas and haemocytes were not significantly different between the M. rosenbergii injected with Lactococcus garvieae, and that injected with saline after 3h to 24h.}, }
@article {pmid16620376, year = {2006}, author = {Tan, DJ and Chang, J and Liu, LL and Bai, RK and Wang, YF and Yeh, KT and Wong, LJ}, title = {Significance of somatic mutations and content alteration of mitochondrial DNA in esophageal cancer.}, journal = {BMC cancer}, volume = {6}, number = {}, pages = {93}, pmid = {16620376}, issn = {1471-2407}, support = {R01 CA100023/CA/NCI NIH HHS/United States ; R01CA100023/CA/NCI NIH HHS/United States ; R21CA87327/CA/NCI NIH HHS/United States ; }, mesh = {Adenocarcinoma/genetics ; Adult ; Aged ; Amino Acid Sequence ; Base Sequence ; Carcinoma, Adenosquamous/genetics ; Carcinoma, Squamous Cell/genetics ; DNA/genetics ; DNA Mutational Analysis ; DNA, Mitochondrial/*genetics ; Electrophoresis ; Esophageal Neoplasms/*genetics ; Evolution, Molecular ; Female ; Frameshift Mutation ; Genetic Predisposition to Disease ; Germ-Line Mutation ; Humans ; Male ; Middle Aged ; Molecular Sequence Data ; *Mutation ; Mutation, Missense ; Reactive Oxygen Species ; Sequence Analysis, DNA ; Temperature ; }, abstract = {BACKGROUND: The roles of mitochondria in energy metabolism, the generation of ROS, aging, and the initiation of apoptosis have implicated their importance in tumorigenesis. In this study we aim to establish the mutation spectrum and to understand the role of somatic mtDNA mutations in esophageal cancer.<br><br>METHODS: The entire mitochondrial genome was screened for somatic mutations in 20 pairs (18 esophageal squamous cell carcinomas, one adenosquamous carcinoma and one adenocarcinoma) of tumor/surrounding normal tissue of esophageal cancers, using temporal temperature gradient gel electrophoresis (TTGE), followed by direct DNA sequencing to identify the mutations.<br><br>RESULTS: Fourteen somatic mtDNA mutations were identified in 55% (11/20) of tumors analyzed, including 2 novel missense mutations and a frameshift mutation in ND4L, ATP6 subunit, and ND4 genes respectively. Nine mutations (64%) were in the D-loop region. Numerous germline variations were found, at least 10 of them were novel and five were missense mutations, some of them occurred in evolutionarily conserved domains. Using real-time quantitative PCR analysis, the mtDNA content was found to increase in some tumors and decrease in others. Analysis of molecular and other clinicopathological findings does not reveal significant correlation between somatic mtDNA mutations and mtDNA content, or between mtDNA content and metastatic status.<br><br>CONCLUSION: Our results demonstrate that somatic mtDNA mutations in esophageal cancers are frequent. Some missense and frameshift mutations may play an important role in the tumorigenesis of esophageal carcinoma. More extensive biochemical and molecular studies will be necessary to determine the pathological significance of these somatic mutations.}, }
@article {pmid16620150, year = {2006}, author = {Abascal, F and Posada, D and Knight, RD and Zardoya, R}, title = {Parallel evolution of the genetic code in arthropod mitochondrial genomes.}, journal = {PLoS biology}, volume = {4}, number = {5}, pages = {e127}, pmid = {16620150}, issn = {1545-7885}, mesh = {Animals ; Arthropods/*genetics ; Codon ; Computer Simulation ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genes, Mitochondrial/*genetics ; Genetic Code/*genetics ; Models, Genetic ; Phylogeny ; RNA, Transfer/genetics ; }, abstract = {The genetic code provides the translation table necessary to transform the information contained in DNA into the language of proteins. In this table, a correspondence between each codon and each amino acid is established: tRNA is the main adaptor that links the two. Although the genetic code is nearly universal, several variants of this code have been described in a wide range of nuclear and organellar systems, especially in metazoan mitochondria. These variants are generally found by searching for conserved positions that consistently code for a specific alternative amino acid in a new species. We have devised an accurate computational method to automate these comparisons, and have tested it with 626 metazoan mitochondrial genomes. Our results indicate that several arthropods have a new genetic code and translate the codon AGG as lysine instead of serine (as in the invertebrate mitochondrial genetic code) or arginine (as in the standard genetic code). We have investigated the evolution of the genetic code in the arthropods and found several events of parallel evolution in which the AGG codon was reassigned between serine and lysine. Our analyses also revealed correlated evolution between the arthropod genetic codes and the tRNA-Lys/-Ser, which show specific point mutations at the anticodons. These rather simple mutations, together with a low usage of the AGG codon, might explain the recurrence of the AGG reassignments.}, }
@article {pmid16615858, year = {2006}, author = {Samuilov, VD and Kiselevsky, DB and Sinitsyn, SV and Shestak, AA and Lagunova, EM and Nesov, AV}, title = {H2O2 intensifies CN(-)-induced apoptosis in pea leaves.}, journal = {Biochemistry. Biokhimiia}, volume = {71}, number = {4}, pages = {384-394}, doi = {10.1134/s0006297906040067}, pmid = {16615858}, issn = {0006-2979}, mesh = {*Apoptosis/drug effects ; Ascorbic Acid/metabolism/pharmacology ; Cell Membrane/metabolism ; Cell Nucleus/drug effects/metabolism ; Chloroplasts/drug effects/metabolism ; Cyanides/metabolism/*toxicity ; Diuron/metabolism/pharmacology ; Drug Synergism ; Electron Transport/drug effects ; Enzyme Inhibitors/metabolism/pharmacology ; Hydrogen Peroxide/metabolism/*toxicity ; Microscopy, Fluorescence ; NADPH Oxidases/metabolism ; Pisum sativum/cytology/metabolism ; Photosystem I Protein Complex/metabolism ; Plant Epidermis/cytology/metabolism ; Plant Leaves/*drug effects/metabolism ; Reactive Oxygen Species ; Trinitrobenzenes/metabolism/pharmacology ; }, abstract = {H2O2 intensifies CN(-)-induced apoptosis in stoma guard cells and to lesser degree in basic epidermal cells in peels of the lower epidermis isolated from pea leaves. The maximum effect of H2O2 on guard cells was observed at 10(-4) M. By switching on non-cyclic electron transfer in chloroplasts menadione and methyl viologen intensified H2O2 generation in the light, but prevented the CN--induced apoptosis in guard cells. The light stimulation of CN- effect on guard cell apoptosis cannot be caused by disturbance of the ribulose-1,5-bisphosphate carboxylase function and associated OH* generation in chloroplasts with participation of free transition metals in the Fenton or Haber-Weiss type reactions as well as with participation of the FeS clusters of the electron acceptor side of Photosystem I. Menadione and methyl viologen did not suppress the CN(-)-induced apoptosis in epidermal cells that, unlike guard cells, contain mitochondria only, but not chloroplasts. Quinacrine and diphenylene iodonium, inhibitors of NAD(P)H oxidase of cell plasma membrane, had no effect on the respiration and photosynthetic O2 evolution by leaf slices, but prevented the CN(-)-induced guard cell death. The data suggest that NAD(P)H oxidase of guard cell plasma membrane is a source of reactive oxygen species (ROS) needed for execution of CN(-)-induced programmed cell death. Chloroplasts and mitochondria were inefficient as ROS sources in the programmed death of guard cells. When ROS generation is insufficient, exogenous H2O2 exhibits a stimulating effect on programmed cell death. H2O2 decreased the inhibitory effects of DCMU and DNP-INT on the CN(-)-induced apoptosis of guard cells. Quinacrine, DCMU, and DNP-INT had no effect on CN(-)-induced death of epidermal cells.}, }
@article {pmid16611603, year = {2006}, author = {Sota, T and Sasabe, M}, title = {Utility of nuclear allele networks for the analysis of closely related species in the genus Carabus, subgenus Ohomopterus.}, journal = {Systematic biology}, volume = {55}, number = {2}, pages = {329-344}, doi = {10.1080/10635150500541607}, pmid = {16611603}, issn = {1063-5157}, mesh = {*Alleles ; Animals ; Coleoptera/anatomy &amp; histology/*classification/*genetics ; DNA/*genetics ; Genetic Speciation ; Genetic Variation ; Male ; Phylogeny ; Recombination, Genetic ; Species Specificity ; }, abstract = {Nuclear DNA sequence data for diploid organisms are potentially a rich source of phylogenetic information for disentangling the evolutionary relationships of closely related organisms, but present special phylogenetic problems owing to difficulties arising from heterozygosity and recombination. We analyzed allelic relationships for two nuclear gene regions (phosphoenolpyruvate carboxykinase and elongation factor-1a), along with a mitochondrial gene region (NADH dehydrogenase subunit 5), for an assemblage of closely related species of carabid beetles (Carabus subgenus Ohomopterus). We used a network approach to examine whether the nuclear gene sequences provide substantial phylogenetic information on species relationships and evolutionary history. The mitochondrial gene genealogy strongly contradicted the morphological species boundary as a result of introgression of heterospecific mitochondria. Two nuclear gene regions showed high allelic diversity within species, and this diversity was partially attributable to recombination between various alleles and high variability in the intron region. Shared nuclear alleles among species were rare and were considered to represent shared ancestral polymorphism. Despite the presence of recombination, nuclear allelic networks recovered species monophyly more often and presented genetic differentiation patterns (low to high) among species more clearly. Overall, nuclear gene networks provide clear evidence for separate biological species and information on the phylogenetic relationships among closely related carabid beetles.}, }
@article {pmid16611600, year = {2006}, author = {Mueller, RL}, title = {Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis.}, journal = {Systematic biology}, volume = {55}, number = {2}, pages = {289-300}, doi = {10.1080/10635150500541672}, pmid = {16611600}, issn = {1063-5157}, mesh = {Animals ; Bayes Theorem ; *Evolution, Molecular ; Genes, Mitochondrial/*genetics ; Mitochondria/*genetics ; *Phylogeny ; Urodela/genetics ; }, abstract = {The mitochondrial genome is one of the most frequently used loci in phylogenetic and phylogeographic analyses, and it is becoming increasingly possible to sequence and analyze this genome in its entirety from diverse taxa. However, sequencing the entire genome is not always desirable or feasible. Which genes should be selected to best infer the evolutionary history of the mitochondria within a group of organisms, and what properties of a gene determine its phylogenetic performance? The current study addresses these questions in a Bayesian phylogenetic framework with reference to a phylogeny of plethodontid and related salamanders derived from 27 complete mitochondrial genomes; this topology is corroborated by nuclear DNA and morphological data. Evolutionary rates for each mitochondrial gene and divergence dates for all nodes in the plethodontid mitochondrial genome phylogeny were estimated in both Bayesian and maximum likelihood frameworks using multiple fossil calibrations, multiple data partitions, and a clock-independent approach. Bayesian analyses of individual genes were performed, and the resulting trees compared against the reference topology. Ordinal logistic regression analysis of molecular evolution rate, gene length, and the G-shape parameter a demonstrated that slower rate of evolution and longer gene length both increased the probability that a gene would perform well phylogenetically. Estimated rates of molecular evolution vary 84-fold among different mitochondrial genes and different salamander lineages, and mean rates among genes vary 15-fold. Despite having conserved amino acid sequences, cox1, cox2, cox3, and cob have the fastest mean rates of nucleotide substitution, and the greatest variation in rates, whereas rrnS and rrnL have the slowest rates. Reasons underlying this rate variation are discussed, as is the extensive rate variation in cox1 in light of its proposed role in DNA barcoding.}, }
@article {pmid16610321, year = {2006}, author = {Bachtrog, D and Thornton, K and Clark, A and Andolfatto, P}, title = {Extensive introgression of mitochondrial DNA relative to nuclear genes in the Drosophila yakuba species group.}, journal = {Evolution; international journal of organic evolution}, volume = {60}, number = {2}, pages = {292-302}, pmid = {16610321}, issn = {0014-3820}, support = {GM64590/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Chromosomes/genetics ; DNA, Mitochondrial/*genetics ; Drosophila/*classification/*genetics ; Female ; Genetic Variation ; Male ; Molecular Sequence Data ; Phylogeny ; Selection, Genetic ; }, abstract = {Studies of gene flow between recently diverged species can illuminate the role of natural selection in the formation of new species. Drosophila santomea and D. yakuba are recently diverged, partially reproductively isolated species that continue to hybridize in the wild, and appear to be reproductively isolated from the more distantly related species D. teissieri. We examine patterns of nucleotide polymorphism and divergence in these three species at multiple X-linked, Y-linked, and mitochondrial markers. All three species harbor drastically reduced variability on the Y chromosome relative to the X, as expected for a nonrecombining chromosome subject to variation-reducing selection. The three species are generally well differentiated at the nuclear markers, with little evidence for recent introgression for either the X- or Y-linked genes. Based on the nuclear genes, we estimate that D. santomea and D. yakuba diverged about one-half million years ago and split from D. teissieri about one million years ago. In contrast to the pattern at nuclear loci, all three species share a very similar mtDNA haplotype. We show that the mtDNA must have recently introgressed across species boundaries in the D. yakuba subgroup and that its fixation was driven by either selection on the mitochondria itself or other cytoplasmic factors. These results demonstrate that different regions of the genome can have distinct evolutionary dynamics in the context of species formation. Although natural selection is usually thought of as accentuating divergence between species, our results imply that it can also act as a homogenizing force.}, }
@article {pmid16607039, year = {2006}, author = {Yamanoue, Y and Miya, M and Inoue, JG and Matsuura, K and Nishida, M}, title = {The mitochondrial genome of spotted green pufferfish Tetraodon nigroviridis (Teleostei: Tetraodontiformes) and divergence time estimation among model organisms in fishes.}, journal = {Genes &amp; genetic systems}, volume = {81}, number = {1}, pages = {29-39}, doi = {10.1266/ggs.81.29}, pmid = {16607039}, issn = {1341-7568}, mesh = {Animals ; *DNA, Mitochondrial ; *Evolution, Molecular ; *Genome ; Mitochondria/*genetics ; Phylogeny ; Tetraodontiformes/*genetics ; }, abstract = {We determined the whole mitochondrial genome sequence for spotted green pufferfish, Tetraodon nigroviridis (Teleostei: Tetraodontiformes). The genome (16,488 bp) contained 37 genes (two ribosomal RNA genes, 22 transfer RNA genes, and 13 protein-coding genes) plus control region as found in other vertebrates, with the gene order identical to that of typical vertebrates. The sequence was used to estimate phylogenetic relationships and divergence times among major lineages of fishes, including representative model organisms in fishes. We employed partitioned Bayesian approaches for these two analyses using two datasets that comprised concatenated amino acid sequences from 12 protein-coding genes (excluding the ND6 gene) and concatenated nucleotide sequences from the 12 protein-coding genes (without 3rd codon positions), 22 transfer RNA genes, and two ribosomal RNA genes. The resultant trees from the two datasets were well resolved and largely congruent with those from previous studies, with spotted green pufferfish being placed in a reasonable phylogenetic position. The approximate divergence times between spotted green pufferfish and model organisms in fishes were 85 million years ago (MYA) vs. torafugu, 183 MYA vs. three-spined stickleback, 191 MYA vs. medaka, and 324 MYA vs. zebrafish, all of which were about twice as old as the divergence times estimated by their earliest occurrences in fossil records.}, }
@article {pmid16607038, year = {2006}, author = {Sugihara, K and Yui, R and Ibaragi, Y and Matsuura, ET}, title = {Complete nucleotide sequence of the A+T-rich region of Drosophila mauritiana mitochondrial DNA.}, journal = {Genes &amp; genetic systems}, volume = {81}, number = {1}, pages = {21-28}, doi = {10.1266/ggs.81.21}, pmid = {16607038}, issn = {1341-7568}, mesh = {*AT Rich Sequence ; Animals ; Base Sequence ; *DNA, Mitochondrial ; Drosophila/*genetics ; Female ; Mitochondria/*genetics ; Molecular Sequence Data ; *Repetitive Sequences, Nucleic Acid ; }, abstract = {We determined the complete nucleotide sequence of the A+T-rich region of the maII type of mtDNA in D. mauritiana. The nucleotide sequence was found to contain 3,206 bp. Three types of conserved element, i.e., type I element, type II element, and T-stretch, were included in this sequence, as reported for D. melanogaster. Comparison between the two species revealed that the type I elements were less conserved than the type II elements. However, each of these type I elements contained a G-stretch within a loop of a putative stem-loop-forming sequence, which has also been observed in D. melanogaster. Moreover, in both type I and type II repeat arrays, the elements closest to the T-stretch diverged the most, due to nucleotide substitution and/or the insertion of short repeats. Sequence comparison of the two complete sequences of the A+T-rich region of D. melanogaster and the maII type of D. mauritiana, as well as comparison of partial sequences in other types of mtDNA within the melanogaster complex, suggested that the A+T-rich region in this complex has been maintained by concerted evolution after the duplication of two types of element, i.e., type I and type II.}, }
@article {pmid16607026, year = {2006}, author = {de Andrade Rosa, I and Einicker-Lamas, M and Roney Bernardo, R and Previatto, LM and Mohana-Borges, R and Morgado-Díaz, JA and Benchimol, M}, title = {Cardiolipin in hydrogenosomes: evidence of symbiotic origin.}, journal = {Eukaryotic cell}, volume = {5}, number = {4}, pages = {784-787}, pmid = {16607026}, issn = {1535-9778}, mesh = {Animals ; Biological Evolution ; Cardiolipins/*analysis ; Chromatography, High Pressure Liquid ; Mitochondria/chemistry/metabolism ; Organelles/*chemistry/metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Symbiosis ; Trichomonas/*chemistry ; }, abstract = {Hydrogenosomes are found in organisms that lack typical mitochondria. Cardiolipin is a phospholipid located exclusively in bacterial membranes and the inner membrane of mitochondria. Here we show, by cell fractionation, thin-layer chromatography, high-pressure liquid chromatography, and matrix-assisted laser desorption ionization-time of flight mass spectrometry that hydrogenosomes of Tritrichomonas foetus, a cattle vaginal parasite, contain cardiolipin, which is strong evidence for its endosymbiotic origin.}, }
@article {pmid16606596, year = {2006}, author = {Pan, D and Fu, YX and Zhang, YP}, title = {[Population genetics of Rhinopithecus bieti: a study of the mitochondrial control region].}, journal = {Yi chuan = Hereditas}, volume = {28}, number = {4}, pages = {432-436}, pmid = {16606596}, issn = {0253-9772}, mesh = {Animals ; Cercopithecidae/*genetics ; China ; DNA, Mitochondrial/*genetics/physiology ; Evolution, Molecular ; *Genetics, Population ; Haplorhini ; }, abstract = {Yunnan snub-nose monkey (Rhinopithecus bieti) is a famous endangered primate in China. So far, however, studies on its population genetics based on DNA sequences are not available. In this paper, the whole mitochondria control region of the samples from Weixi, Yunan Province as well as the whole cytochrome b gene in some individuals were sequenced. A deep divergence was observed within the Weixi population, which was confirmed after excluding the possibility of it being a nuclear pseudogene. Nonetheless, if the effects of population structure and migration are considered, the true level of polymorphism of the Weixi population may be not as high as observed.}, }
@article {pmid16603388, year = {2006}, author = {Domingues, VS and Santos, RS and Brito, A and Almada, VC}, title = {Historical population dynamics and demography of the Eastern Atlantic pomacentrid Chromis limbata (Valenciennes, 1833).}, journal = {Molecular phylogenetics and evolution}, volume = {40}, number = {1}, pages = {139-147}, doi = {10.1016/j.ympev.2006.02.009}, pmid = {16603388}, issn = {1055-7903}, mesh = {Animals ; Atlantic Ocean ; DNA, Mitochondrial/genetics ; Geography ; History, Ancient ; Ice Cover ; Mitochondria/genetics ; Perciformes/classification/*genetics/*physiology ; *Phylogeny ; Population Dynamics ; }, abstract = {Recent studies have focused on the relationship between the marine fauna of the Eastern Atlantic and the Mediterranean Sea, but within the Atlantic, little is known about genetic relationships between populations of the Macaronesian islands. In this study, we tested whether the paleo-climatology and paleo-oceanography of the region could predict the genetic relationships among three Eastern Atlantic populations (Azores, Madeira, and Canaries) of a damselfish, Chromis limbata, and compared our results with its Mediterranean and adjacent Atlantic sister species, Chromis chromis. We combined phylogeographic and coalescent approaches using the fast evolving mitochondrial control region gene. No population structure was found for the three archipelagos. The coalescence time estimated for C. limbata (0.857-1.17 Mya) was much greater than that estimated for C. chromis. We propose that this difference reflects differences in glaciating extents in the Northeastern Atlantic and the Mediterranean. Diversity indexes (Hd and genetic distances) together with historical demographic parameters of C. limbata (Theta and g) revealed a more stable population history when compared to C. chromis. Our results suggest that the Macaronesian populations of C. limbata have probably been less affected by the last glaciation than the Mediterranean populations of C. chromis. Migration across the three archipelagos was estimated and a prevailing northwest trend was detected. This result supports the idea of a colonization of the Azores by warm water fish from Madeira or the westernmost Canary islands which acted as major glacial refugia for the tropical and subtropical marine fauna during the glaciations.}, }
@article {pmid16597625, year = {2006}, author = {Fender, A and Sauter, C and Messmer, M and Pütz, J and Giegé, R and Florentz, C and Sissler, M}, title = {Loss of a primordial identity element for a mammalian mitochondrial aminoacylation system.}, journal = {The Journal of biological chemistry}, volume = {281}, number = {23}, pages = {15980-15986}, doi = {10.1074/jbc.M511633200}, pmid = {16597625}, issn = {0021-9258}, mesh = {Acylation ; Base Sequence ; Humans ; Kinetics ; Mutagenesis ; Nucleic Acid Conformation ; Plasmids ; RNA, Transfer, Asp/chemistry/genetics/*metabolism ; }, abstract = {In mammalian mitochondria the translational machinery is of dual origin with tRNAs encoded by a simplified and rapidly evolving mitochondrial (mt) genome and aminoacyl-tRNA synthetases (aaRS) coded by the nuclear genome, and imported. Mt-tRNAs are atypical with biased sequences, size variations in loops and stems, and absence of residues forming classical tertiary interactions, whereas synthetases appear typical. This raises questions about identity elements in mt-tRNAs and adaptation of their cognate mt-aaRSs. We have explored here the human mt-aspartate system in which a prokaryotic-type AspRS, highly similar to the Escherichia coli enzyme, recognizes a bizarre tRNA(Asp). Analysis of human mt-tRNA(Asp) transcripts confirms the identity role of the GUC anticodon as in other aspartylation systems but reveals the non-involvement of position 73. This position is otherwise known as the site of a universally conserved major aspartate identity element, G73, also known as a primordial identity signal. In mt-tRNA(Asp), position 73 can be occupied by any of the four nucleotides without affecting aspartylation. Sequence alignments of various AspRSs allowed placing Gly-269 at a position occupied by Asp-220, the residue contacting G73 in the crystallographic structure of E. coli AspRS-tRNA(Asp) complex. Replacing this glycine by an aspartate renders human mt-AspRS more discriminative to G73. Restriction in the aspartylation identity set, driven by a rapid mutagenic rate of the mt-genome, suggests a reverse evolution of the mt-tRNA(Asp) identity elements in regard to its bacterial ancestor.}, }
@article {pmid16581267, year = {2006}, author = {Yaakub, SM and Bellwood, DR and Herwerden, Lv and Walsh, FM}, title = {Hybridization in coral reef fishes: introgression and bi-directional gene exchange in Thalassoma (family Labridae).}, journal = {Molecular phylogenetics and evolution}, volume = {40}, number = {1}, pages = {84-100}, doi = {10.1016/j.ympev.2006.02.012}, pmid = {16581267}, issn = {1055-7903}, mesh = {Animals ; Anthozoa ; Asia ; Australia ; Cytochromes/genetics ; Ecology ; Female ; Fishes/*classification/*genetics ; *Hybridization, Genetic ; Inbreeding ; Introns/*genetics ; Male ; Mitochondria/genetics ; Oxidoreductases/genetics ; Phylogeny ; Ribosomes/genetics ; }, abstract = {Hybrids in coral reef fishes have traditionally been described based on external features using meristic characters and colouration to identify putative parental contributors. This study utilised molecular genetic techniques to verify hybrid status and identify putative parental species for five hybrid specimens (Labridae: Thalassoma) collected from Holmes Reef in the Coral Sea. Phylogenetic analyses support hybrid origins of the specimens. Mitochondrial COI gene, nuclear S7 (intron 1) and nuclear copy of mitochondrial (NUMT) D-loop region corroborate the identity of T. quinquevittatum as the maternal and T. jansenii as the paternal contributor. Backcrossing to parental species by hybrids and bi-directional gene exchange between the Holmes Reef populations of T. jansenii and T. quinquevittatum was detected, suggesting that hybrids are fertile and able to reproduce successfully. F(1) hybrids display a mixture of the colouration attributes of the two parental species, but subsequent backcrossed individuals were unrecognisable as hybrids and displayed colouration of either parental species. A large numerical imbalance exists between the putative parental species at Holmes Reef, with T. quinquevittatum outnumbering T. jansenii by approximately 25:1. In this case study, hybridization appears to be driven by ecological rather than evolutionary factors.}, }
@article {pmid16572163, year = {2006}, author = {Embley, TM and Martin, W}, title = {Eukaryotic evolution, changes and challenges.}, journal = {Nature}, volume = {440}, number = {7084}, pages = {623-630}, doi = {10.1038/nature04546}, pmid = {16572163}, issn = {1476-4687}, mesh = {*Biological Evolution ; Eukaryotic Cells/*cytology/metabolism ; Hydrogen/metabolism ; Mitochondria/metabolism ; Phylogeny ; Prokaryotic Cells/cytology/metabolism ; }, abstract = {The idea that some eukaryotes primitively lacked mitochondria and were true intermediates in the prokaryote-to-eukaryote transition was an exciting prospect. It spawned major advances in understanding anaerobic and parasitic eukaryotes and those with previously overlooked mitochondria. But the evolutionary gap between prokaryotes and eukaryotes is now deeper, and the nature of the host that acquired the mitochondrion more obscure, than ever before.}, }
@article {pmid16566938, year = {2006}, author = {Chan, NC and Likić, VA and Waller, RF and Mulhern, TD and Lithgow, T}, title = {The C-terminal TPR domain of Tom70 defines a family of mitochondrial protein import receptors found only in animals and fungi.}, journal = {Journal of molecular biology}, volume = {358}, number = {4}, pages = {1010-1022}, doi = {10.1016/j.jmb.2006.02.062}, pmid = {16566938}, issn = {0022-2836}, mesh = {Animals ; Base Sequence ; Binding Sites ; Conserved Sequence ; DNA/genetics ; DNA, Fungal/genetics ; Evolution, Molecular ; In Vitro Techniques ; Membrane Proteins/*chemistry/*genetics/metabolism ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/*chemistry/*genetics/metabolism ; Phylogeny ; Protein Structure, Tertiary ; Protein Transport ; Rats ; Receptors, Cytoplasmic and Nuclear/*chemistry/*genetics/metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/*genetics/metabolism ; }, abstract = {In fungi and animals the translocase in the outer mitochondrial membrane (TOM complex) consists of multiple components including the receptor subunit Tom70. Genome sequence analyses suggest no Tom70 receptor subunit exists in plants or protozoans, raising questions about its ancestry, function and the importance of its activity. Here we characterise the relationships within the Tom70 family of proteins. We find that in both fungi and animals, a conserved domain structure exists within the Tom70 family, with a transmembrane segment followed by 11 tetratricopeptide repeat motifs organised in three distinct domains. The C-terminal domain of Tom70 is highly conserved, and crucial for the import of hydrophobic substrate proteins, including those with and those without N-terminal presequences. Tom70 likely arose after fungi and animals diverged from other eukaryote lineages including plants, and subsequent gene duplication gave rise to a paralogue specific to the Saccharomyces group of yeasts. In animals and in fungi, Tom70 plays a fundamental role in the import of precursor proteins, by assisting relatively hydrophobic regions of substrate proteins into the translocation channel in the outer mitochondrial membrane. Proteins that function equivalently to Tom70 may have arisen independently in plants and protists.}, }
@article {pmid16566929, year = {2006}, author = {Molina-Navarro, MM and Casas, C and Piedrafita, L and Bellí, G and Herrero, E}, title = {Prokaryotic and eukaryotic monothiol glutaredoxins are able to perform the functions of Grx5 in the biogenesis of Fe/S clusters in yeast mitochondria.}, journal = {FEBS letters}, volume = {580}, number = {9}, pages = {2273-2280}, doi = {10.1016/j.febslet.2006.03.037}, pmid = {16566929}, issn = {0014-5793}, mesh = {Animals ; Bacterial Proteins/genetics/*metabolism ; Chick Embryo/cytology/enzymology ; Chickens/*genetics/metabolism ; Escherichia coli/*enzymology/genetics ; Evolution, Molecular ; Gene Expression/genetics ; Gene Expression Regulation, Developmental/physiology ; Glutaredoxins ; Mitochondria/*enzymology/genetics ; Mutation ; Organ Specificity/physiology ; Oxidoreductases/genetics/*metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; Synechocystis/*enzymology/genetics ; }, abstract = {The Saccharomyces cerevisiae monothiol glutaredoxin Grx5 participates in the mitochondrial biogenesis of iron-sulfur clusters. Grx5 homologues exist in organisms from bacteria to humans. Chicken (cGRX5) and human (hGRX5) homologues contain a mitochondrial targeting sequence, suggesting a mitochondrial localization for these two proteins. We have compartmentalized the Escherichia coli and Synechocystis sp. homologues, and also cGRX5 and hGRX5, in the mitochondrial matrix of a yeast grx5 mutant. All four heterologous proteins rescue the defects of the mutant. The chicken cGRX5 gene was significantly expressed throughout the embryo stages in different tissues. These results underline the functional conservation of Grx5 homologues throughout evolution.}, }
@article {pmid16563428, year = {2006}, author = {Azevedo, C and Balseiro, P and Casal, G and Gestal, C and Aranguren, R and Stokes, NA and Carnegie, RB and Novoa, B and Burreson, EM and Figueras, A}, title = {Ultrastructural and molecular characterization of Haplosporidium montforti n. sp., parasite of the European abalone Haliotis tuberculata.}, journal = {Journal of invertebrate pathology}, volume = {92}, number = {1}, pages = {23-32}, doi = {10.1016/j.jip.2006.02.002}, pmid = {16563428}, issn = {0022-2011}, mesh = {Animals ; Base Sequence ; Haplosporida/*genetics/*ultrastructure ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Mollusca/*parasitology ; Phylogeny ; Polymerase Chain Reaction ; RNA, Protozoan/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; Spores, Protozoan/ultrastructure ; }, abstract = {A new member of the parasitic phylum Haplosporidia, which was found infecting the connective tissue, gill, digestive gland, and foot muscle of Haliotis tuberculata imported from Ireland and experimentally grown in Galicia (NW Spain), is described. Scanning electron microscopy, transmission electron microscopy, and molecular characterization of the small subunit ribosomal RNA (SSU rRNA) gene were carried out to confirm the description of this species. The ultrastructural morphology of the spores and their surrounding ornaments attached to the spore wall was described from light, scanning, and transmission electron microscopy observations. Systemic infection with uninucleated and multinucleated plasmodia containing spherical nuclei was observed among several sporocysts containing the different spore maturation stages. The spores were spherical to slightly ellipsoidal (2.42 +/- 0.5 x 2.31 +/- 0.6 microm). The apical zone of the spore wall was modified into a complex opercular system covering a circular orifice that measured about 0.5 microm in diameter. The operculum was connected to the spore wall by a hinge. The spore wall was about 110 nm thick, with 4 filaments (20-28 microm long). The filaments were composed of the same material that formed the wall. The cross-sections through the base of these filaments showed T-like and X-like sections. Internally, the uninucleated endosporoplasm contained typical haplosporidian structures, such as, haplosporosomes, a spherulosome, and mitochondria with vesicular cristae. The SSU rRNA gene sequence was different from previously reported haplosporidian SSU rRNA gene sequences, corroborating morphological data that this was an undescribed species. Based on differences from previously described haplosporidians in ultrastructural characteristics of the spore and SSU rRNA gene sequence, we describe the abalone haplosporidian as Haplosporidium montforti n. sp.}, }
@article {pmid16556832, year = {2006}, author = {Lynch, M and Koskella, B and Schaack, S}, title = {Mutation pressure and the evolution of organelle genomic architecture.}, journal = {Science (New York, N.Y.)}, volume = {311}, number = {5768}, pages = {1727-1730}, doi = {10.1126/science.1118884}, pmid = {16556832}, issn = {1095-9203}, support = {R01 GM036827/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Chloroplasts/genetics ; DNA, Intergenic ; *Evolution, Molecular ; *Genes, Mitochondrial ; *Genetic Drift ; *Genome ; Genome, Plant ; Humans ; Mitochondria/*genetics ; *Mutation ; Phylogeny ; Plants/*genetics ; RNA Editing ; }, abstract = {The nuclear genomes of multicellular animals and plants contain large amounts of noncoding DNA, the disadvantages of which can be too weak to be effectively countered by selection in lineages with reduced effective population sizes. In contrast, the organelle genomes of these two lineages evolved to opposite ends of the spectrum of genomic complexity, despite similar effective population sizes. This pattern and other puzzling aspects of organelle evolution appear to be consequences of differences in organelle mutation rates. These observations provide support for the hypothesis that the fundamental features of genome evolution are largely defined by the relative power of two nonadaptive forces: random genetic drift and mutation pressure.}, }
@article {pmid16556314, year = {2006}, author = {Gabaldón, T and Snel, B and van Zimmeren, F and Hemrika, W and Tabak, H and Huynen, MA}, title = {Origin and evolution of the peroxisomal proteome.}, journal = {Biology direct}, volume = {1}, number = {}, pages = {8}, pmid = {16556314}, issn = {1745-6150}, abstract = {BACKGROUND: Peroxisomes are ubiquitous eukaryotic organelles involved in various oxidative reactions. Their enzymatic content varies between species, but the presence of common protein import and organelle biogenesis systems support a single evolutionary origin. The precise scenario for this origin remains however to be established. The ability of peroxisomes to divide and import proteins post-translationally, just like mitochondria and chloroplasts, supports an endosymbiotic origin. However, this view has been challenged by recent discoveries that mutant, peroxisome-less cells restore peroxisomes upon introduction of the wild-type gene, and that peroxisomes are formed from the Endoplasmic Reticulum. The lack of a peroxisomal genome precludes the use of classical analyses, as those performed with mitochondria or chloroplasts, to settle the debate. We therefore conducted large-scale phylogenetic analyses of the yeast and rat peroxisomal proteomes.<br><br>RESULTS: Our results show that most peroxisomal proteins (39-58%) are of eukaryotic origin, comprising all proteins involved in organelle biogenesis or maintenance. A significant fraction (13-18%), consisting mainly of enzymes, has an alpha-proteobacterial origin and appears to be the result of the recruitment of proteins originally targeted to mitochondria. Consistent with the findings that peroxisomes are formed in the Endoplasmic Reticulum, we find that the most universally conserved Peroxisome biogenesis and maintenance proteins are homologous to proteins from the Endoplasmic Reticulum Assisted Decay pathway.<br><br>CONCLUSION: Altogether our results indicate that the peroxisome does not have an endosymbiotic origin and that its proteins were recruited from pools existing within the primitive eukaryote. Moreover the reconstruction of primitive peroxisomal proteomes suggests that ontogenetically as well as phylogenetically, peroxisomes stem from the Endoplasmic Reticulum.<br><br>REVIEWERS: This article was reviewed by Arcady Mushegian, G&#xe1;sp&#xe1;r J&#xe9;kely and John Logsdon.<br><br>OPEN PEER REVIEW: Reviewed by Arcady Mushegian, G&#xe1;spar J&#xe9;kely and John Logsdon. For the full reviews, please go to the Reviewers' comments section.}, }
@article {pmid16553897, year = {2006}, author = {Khakhlova, O and Bock, R}, title = {Elimination of deleterious mutations in plastid genomes by gene conversion.}, journal = {The Plant journal : for cell and molecular biology}, volume = {46}, number = {1}, pages = {85-94}, doi = {10.1111/j.1365-313X.2006.02673.x}, pmid = {16553897}, issn = {0960-7412}, mesh = {Base Sequence ; Biological Evolution ; Chloroplasts/*genetics ; Codon, Initiator ; DNA, Chloroplast/genetics ; Gene Conversion/*physiology ; *Genome, Plant ; Molecular Sequence Data ; *Mutation ; Plant Proteins/genetics ; Plants, Genetically Modified/genetics ; Polyploidy ; Reproduction, Asexual/genetics ; Sequence Analysis, DNA ; Nicotiana/genetics ; }, abstract = {Asexual reproduction is believed to be detrimental, mainly because of the accumulation of deleterious mutations over time, a hypothesis known as Muller's ratchet. In seed plants, most asexually reproducing genetic systems are polyploid, with apomictic species (plants forming seeds without fertilization) as well as plastids and mitochondria providing prominent examples. Whether or not polyploidy helps asexual genetic systems to escape Muller's ratchet is unknown. Gene conversion, particularly when slightly biased, represents a potential mechanism that could allow asexual genetic systems to reduce their mutation load in a genome copy number-dependent manner. However, direct experimental evidence for the operation of gene conversion between genome molecules to correct mutations is largely lacking. Here we describe an experimental system based on transgenic tobacco chloroplasts that allows us to analyze gene conversion events in higher plant plastid genomes. We provide evidence for gene conversion acting as a highly efficient mechanism by which the polyploid plastid genetic system can correct deleterious mutations and make one good genome out of two bad ones. Our finding that gene conversion can be biased may provide a molecular link between asexual reproduction, high genome copy numbers and low mutation rates.}, }
@article {pmid16553311, year = {2006}, author = {Ginger, ML}, title = {Niche metabolism in parasitic protozoa.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {361}, number = {1465}, pages = {101-118}, pmid = {16553311}, issn = {0962-8436}, mesh = {Animals ; Biological Evolution ; *Energy Metabolism ; Eukaryota/genetics/*metabolism ; Genome, Protozoan ; Host-Parasite Interactions ; Parasitic Diseases/metabolism/*parasitology ; }, abstract = {Complete or partial genome sequences have recently become available for several medically and evolutionarily important parasitic protozoa. Through the application of bioinformatics complete metabolic repertoires for these parasites can be predicted. For experimentally intractable parasites insight provided by metabolic maps generated in silico has been startling. At its more extreme end, such bioinformatics reckoning facilitated the discovery in some parasites of mitochondria remodelled beyond previous recognition, and the identification of a non-photosynthetic chloroplast relic in malarial parasites. However, for experimentally tractable parasites, mapping of the general metabolic terrain is only a first step in understanding how the parasite modulates its streamlined, yet still often puzzlingly complex, metabolism in order to complete life cycles within host, vector, or environment. This review provides a comparative overview and discussion of metabolic strategies used by several different parasitic protozoa in order to subvert and survive host defences, and illustrates how genomic data contribute to the elucidation of parasite metabolism.}, }
@article {pmid16547870, year = {2006}, author = {Ueno, O and Wada, Y and Wakai, M and Bang, SW}, title = {Evidence from photosynthetic characteristics for the hybrid origin of Diplotaxis muralis from a C3-C4 intermediate and a C3 species.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {8}, number = {2}, pages = {253-259}, doi = {10.1055/s-2005-873050}, pmid = {16547870}, issn = {1435-8603}, mesh = {Brassicaceae/*genetics/*metabolism ; Carbon/*metabolism ; Crosses, Genetic ; *Evolution, Molecular ; Glycine Dehydrogenase (Decarboxylating)/metabolism ; *Hybridization, Genetic ; Photosynthesis/genetics/*physiology ; Plant Leaves/cytology/metabolism ; Protein Transport ; }, abstract = {Artificial hybridization studies have been carried out between plants with different photosynthetic types to study the genetic mechanism of photosynthetic types. However, there are only few reports describing the possibility of natural hybridization between plants with different photosynthetic types. A previous cytological and morphological study suggested that a cruciferous allotetraploid species, Diplotaxis muralis (L.) DC. (2n = 42), originated from natural hybridization between D. tenuifolia (L.) DC. (2n = 22) and D. viminea (L.) DC. (2n = 20). These putative parents have recently been reported to be a C (3)-C (4) intermediate and a C (3) species, respectively. If this hybridization occurred, D. muralis should have characteristics intermediate between those of the C (3)-C (4) intermediate and C (3) types. We compared leaf structures and photosynthetic characteristics of the three species. The bundle sheath (BS) cells in D. tenuifolia included many centripetally located chloroplasts and mitochondria, but those of D. viminea had only a few organelles. The BS cells in D. muralis displayed intermediate features between the putative parents. Glycine decarboxylase P protein was confined to the BS mitochondria in D. tenuifolia, but accumulated mainly in the mesophyll mitochondria in D. viminea. In D. muralis, it accumulated in both the BS and the mesophyll mitochondria. Values of CO (2) compensation point and its response to changing light intensity were also intermediate between the putative parents. These data support the theory that D. muralis was created by natural hybridization between species with different photosynthetic types.}, }
@article {pmid16546069, year = {2006}, author = {Lister, R and Whelan, J}, title = {Mitochondrial protein import: convergent solutions for receptor structure.}, journal = {Current biology : CB}, volume = {16}, number = {6}, pages = {R197-9}, doi = {10.1016/j.cub.2006.02.024}, pmid = {16546069}, issn = {0960-9822}, mesh = {Animals ; *Evolution, Molecular ; Fungal Proteins/chemistry/physiology ; Fungi/metabolism ; Membrane Proteins/*chemistry/physiology ; Mitochondria/metabolism ; Mitochondrial Membranes/*metabolism ; Mitochondrial Proteins/*chemistry/*metabolism ; Plant Proteins/chemistry/physiology ; Plants/metabolism ; Protein Structure, Tertiary ; Protein Transport ; }, abstract = {Complex machinery has evolved to recognise and import nuclear-encoded proteins into mitochondria. Recent work now shows that the plant Tom20 mitochondrial protein import receptor has a similar tertiary structure to animal Tom20, although the proteins are evolutionarily distinct, representing an elegant example of convergent evolution.}, }
@article {pmid16545471, year = {2006}, author = {Logan, DC}, title = {Plant mitochondrial dynamics.}, journal = {Biochimica et biophysica acta}, volume = {1763}, number = {5-6}, pages = {430-441}, doi = {10.1016/j.bbamcr.2006.01.003}, pmid = {16545471}, issn = {0006-3002}, mesh = {Biological Evolution ; Cell Death ; Mitochondria/*metabolism/ultrastructure ; Mutation/genetics ; Plant Cells ; Plants/*metabolism/ultrastructure ; }, abstract = {Higher plant mitochondria are dynamic, pleomorphic organelles. The higher plant chondriome (all mitochondria in a cell collectively) is typically composed of numerous, physically discrete, mitochondria. However, frequent inter-mitochondrial fusion, enabling the mixing and recombination of mtDNA, ensures that the higher plant chondriome functions, at least genetically, as a discontinuous whole. Nothing is known about the genes controlling mitochondrial fusion in plants; there are no plant homologues of most of the genes known to be involved in fusion in other organisms. In contrast, the mitochondrial fission apparatus is generally conserved. Higher plant mitochondria use dynamin-like and Fis-type proteins for division; like yeast and animals, higher plants have lost the mitochondrial-specific form of the prokaryote-derived protein, FtsZ. In addition to being providers of energy for life, mitochondria provide a trigger for death. The role of mitochondrial dynamics in the initiation and promulgation of cell death is conserved in higher plants although there are specific differences in the genes and mechanisms involved relative to other higher eukaryotes.}, }
@article {pmid16545376, year = {2006}, author = {Lloyd, D and Murray, DB}, title = {The temporal architecture of eukaryotic growth.}, journal = {FEBS letters}, volume = {580}, number = {12}, pages = {2830-2835}, doi = {10.1016/j.febslet.2006.02.066}, pmid = {16545376}, issn = {0014-5793}, mesh = {Biological Evolution ; Chromosomes, Fungal ; Mitochondria/physiology ; Oxidative Stress ; Oxygen/metabolism ; Reactive Oxygen Species ; Saccharomyces cerevisiae/*growth &amp; development/physiology ; Signal Transduction ; }, abstract = {Coherence of the time structure of growing organisms depends on a metronome-like orchestration. In a continuously perfused culture of Saccharomyces cerevisiae the redox state of the cell shows a temperature-compensated oscillation manifest in respiratory cycles, which are measured by continuous and non-invasive electrodes of probes such as dissolved oxygen and probes such as fluorometric NAD(P)H. Although the entire transcriptome exhibits low-amplitude oscillatory behaviour, transcripts involved in the vast majority of metabolism, stress response, cellular structure, protein turnover, mRNA turnover, and DNA synthesis are amongst the top oscillators and their orchestration occurs by an intricate network of transcriptional regulators. Therefore cellular auto-dynamism is a function of a large ensemble of excitable intracellular components of that self-organized temporally and spatially that encompasses mitochondrial, nuclear, transcriptional and metabolic dynamics, coupled by cellular redox state.}, }
@article {pmid16540393, year = {2006}, author = {Chen, Q and Lesnefsky, EJ}, title = {Depletion of cardiolipin and cytochrome c during ischemia increases hydrogen peroxide production from the electron transport chain.}, journal = {Free radical biology &amp; medicine}, volume = {40}, number = {6}, pages = {976-982}, doi = {10.1016/j.freeradbiomed.2005.10.043}, pmid = {16540393}, issn = {0891-5849}, support = {1PO1AG15885/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; Antimycin A/pharmacology ; Cardiolipins/*metabolism ; Cytochromes c/*metabolism ; Electron Transport/drug effects ; Electron Transport Complex IV/antagonists &amp; inhibitors ; Hydrogen Peroxide/metabolism ; Mitochondria, Heart/drug effects ; Myocardial Ischemia/*physiopathology ; Myocardial Reperfusion Injury/*physiopathology ; Rabbits ; Rotenone/pharmacology ; Sodium Azide/pharmacology ; }, abstract = {Mitochondrial electron transport is a major source of reactive oxygen species (ROS) during cardiac ischemia and reperfusion. In the isolated rabbit heart, 30 and 45 min of ischemia decrease the contents of cardiolipin and cytochrome c in subsarcolemmal mitochondria (SSM) located beneath the plasma membrane. In contrast, interfibrillar mitochondria (IFM) in the interior of the myocyte do not sustain a decrease in cardiolipin. We proposed that the depletion of cardiolipin and the accompanying cytochrome c loss during ischemia were critical events that amplified ROS production by mitochondria. The total production of H2O2 was measured in submitochondrial particles (SMP) prepared from rabbit heart SSM and IFM after 0, 15, 30, and 45 min of ischemia. With NADH as substrate, total H2O2 production was increased only in SMP from SSM after 30 and 45 min ischemia, when ischemia decreased the content of cardiolipin and cytochrome c. In contrast, ischemia did not augment H2O2 generation in SMP from IFM with preserved cardiolipin and cytochrome c content. Thus, during the evolution of ischemic injury, H2O2 production from the electron transport chain increased after depletion of cardiolipin and the loss of cytochrome c.}, }
@article {pmid16539155, year = {2005}, author = {Otranto, D and Traversa, D and Milillo, P and De Luca, F and Stevens, J}, title = {Utility of mitochondrial and ribosomal genes for differentiation and phylogenesis of species of gastrointestinal bot flies.}, journal = {Journal of economic entomology}, volume = {98}, number = {6}, pages = {2235-2245}, doi = {10.1093/jee/98.6.2235}, pmid = {16539155}, issn = {0022-0493}, mesh = {Animals ; Base Sequence ; DNA/chemistry/*genetics ; Diptera/classification/*genetics ; *Genetic Variation ; Larva/genetics ; Mitochondria/*genetics ; Phylogeny ; Ribosomes/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {Larvae of Gasterophilus spp. (Diptera: Oestridae) cause gastrointestinal myiasis of equids. However, their identification may be problematic due to morphological similarities between species infesting identical regions of the digestive tract. In this study, genes encoding for mitochondrial cytochrome oxidase I (COI) and for the 16S and 28S ribosomal subunits of the most commonly encountered Gasterophilinae subfamily species [i.e., Gasterophilus haemorrhoidalis (L.), Gasterophilus inermis (Brauer), Gasterophilus intestinalis (De Geer), Gasterophilus nasalis (L.), and Gasterophilus pecorum (F.)] were studied, together with Gyrostigma pavesii (Corti), a rhinoceros parasite, and Hypoderma lineatum (De Villers), as outgroup taxa. Analysis identified interspecific differences that allowed their unequivocal identification. The high genetic homology among the sequences of G. haemorrhoidalis and G. intestinalis (i.e., 100, 99.86, and 99.46% in the 28S, COI, and 16S genes, respectively) strongly support the hypothesis that they are morphotypes of the same species. Phylogenetic analyses (maximum-likelihood and parsimony) were performed using PAUP; all analyses supported monophyly of subfamily Gasterophilinae. This study confirms the utility of the COI and 16S and 28S rRNA genes to address diagnostic and phylogenetic questions in Gasterophilus species.}, }
@article {pmid16537127, year = {2006}, author = {Seebacher, F and Schwartz, TS and Thompson, MB}, title = {Transition from ectothermy to endothermy: the development of metabolic capacity in a bird (Gallus gallus).}, journal = {Proceedings. Biological sciences}, volume = {273}, number = {1586}, pages = {565-570}, pmid = {16537127}, issn = {0962-8452}, mesh = {Aerobiosis/physiology ; Animals ; Basal Metabolism/*physiology ; Body Temperature Regulation/physiology ; Chick Embryo/enzymology/*metabolism ; Citrate (si)-Synthase/genetics/metabolism ; Electron Transport Complex IV/genetics/metabolism ; L-Lactate Dehydrogenase/genetics/metabolism ; Mitochondria, Liver/metabolism ; Oxygen Consumption/physiology ; Phosphofructokinase-1/genetics/metabolism ; }, abstract = {The evolution of endothermy is one of the most significant events in vertebrate evolution. Adult mammals and birds are delineated from their early ontogenetic stages, as well as from other vertebrates, by high resting metabolic rates and consequent internal heat production. We used the embryonic development of a bird (Gallus gallus) as a model to investigate the metabolic transition between ectothermy and endothermy. Increases in aerobic capacity occur at two functional levels that are regulated independently from each other: (i) upregulation of gene expression; and (ii) significant increases in the catalytic activity of the main oxidative control enzymes. Anaerobic capacity, measured as lactate dehydrogenase activity, is extremely high during early development, but diminishes at the same time as aerobic capacity increases. Changes in lactate dehydrogenase activity are independent from its gene expression. The regulatory mechanisms that lead to endothermic metabolic capacity are similar to those of ectotherms in their response to environmental change. We suggest that the phylogenetic occurrence of endothermy is restricted by its limited selective advantages rather than by evolutionary innovation.}, }
@article {pmid16534508, year = {2006}, author = {Alesci, S and Manoli, I and Michopoulos, VJ and Brouwers, FM and Le, H and Gold, PW and Blackman, MR and Rennert, OM and Su, YA and Chrousos, GP}, title = {Development of a human mitochondria-focused cDNA microarray (hMitChip) and validation in skeletal muscle cells: implications for pharmaco- and mitogenomics.}, journal = {The pharmacogenomics journal}, volume = {6}, number = {5}, pages = {333-342}, doi = {10.1038/sj.tpj.6500377}, pmid = {16534508}, issn = {1470-269X}, support = {//Intramural NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Cells, Cultured ; Databases, Genetic ; Dexamethasone/pharmacology ; *Gene Expression Profiling ; *Gene Expression Regulation ; Glucocorticoids/pharmacology ; Humans ; Male ; Mitochondrial Proteins/genetics/*metabolism ; Muscle, Skeletal/drug effects/*metabolism ; Oligonucleotide Array Sequence Analysis/*methods ; Pharmacogenetics ; Polymerase Chain Reaction ; RNA, Messenger/metabolism ; Reproducibility of Results ; }, abstract = {Mitochondrial research has influenced our understanding of human evolution, physiology and pathophysiology. Mitochondria, intracellular organelles widely known as 'energy factories' of the cell, also play fundamental roles in intermediary metabolism, steroid hormone and heme biosyntheses, calcium signaling, generation of radical oxygen species, and apoptosis. Mitochondria possess a distinct DNA (mitochondrial DNA); yet, the vast majority of mitochondrial proteins are encoded by the nuclear DNA. Mitochondria-related genetic defects have been described in a variety of mostly rare, often fatal, primary mitochondrial disorders; furthermore, they are increasingly reported in association with many common morbid conditions, such as cancer, obesity, diabetes and neurodegenerative disorders, although their role remains unclear. This study describes the creation of a human mitochondria-focused cDNA microarray (hMitChip) and its validation in human skeletal muscle cells treated with glucocorticoids. We suggest that hMitChip is a reliable and novel tool that will prove useful for systematically studying the contribution of mitochondrial genomics to human health and disease.}, }
@article {pmid16533820, year = {2006}, author = {Shutt, TE and Gray, MW}, title = {Homologs of mitochondrial transcription factor B, sparsely distributed within the eukaryotic radiation, are likely derived from the dimethyladenosine methyltransferase of the mitochondrial endosymbiont.}, journal = {Molecular biology and evolution}, volume = {23}, number = {6}, pages = {1169-1179}, doi = {10.1093/molbev/msk001}, pmid = {16533820}, issn = {0737-4038}, mesh = {Acanthamoeba castellanii/genetics ; Alphaproteobacteria/genetics ; Amino Acid Sequence ; Animals ; DNA-Binding Proteins/genetics ; Dictyostelium/genetics ; Eukaryota/*genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Hartmannella/genetics ; Humans ; Introns ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Nucleic Acid ; Symbiosis ; Transcription Factors/*genetics ; }, abstract = {Mitochondrial transcription factor B (mtTFB), an essential component in regulating the expression of mitochondrial DNA-encoded genes in both yeast and humans, is a dimethyladenosine methyltransferase (DMT) that has acquired a secondary role in mitochondrial transcription. So far, mtTFB has only been well studied in Opisthokonta (metazoan animals and fungi). Here we investigate the phylogenetic distribution of mtTFB homologs throughout the domain Eucarya, documenting the first examples of this protein outside of the opisthokonts. Surprisingly, we identified putative mtTFB homologs only in amoebozoan protists and trypanosomatids. Phylogenetic analysis together with conservation of intron positions in amoebozoan and human genes supports the grouping of the putative mtTFB homologs as a distinct clade. Phylogenetic analysis further demonstrates that the mtTFB is most likely derived from the DMT of the mitochondrial endosymbiont.}, }
@article {pmid16528519, year = {2006}, author = {Yao, YG and Salas, A and Bravi, CM and Bandelt, HJ}, title = {A reappraisal of complete mtDNA variation in East Asian families with hearing impairment.}, journal = {Human genetics}, volume = {119}, number = {5}, pages = {505-515}, pmid = {16528519}, issn = {0340-6717}, mesh = {DNA, Mitochondrial/*genetics ; Asia, Eastern ; *Genetic Variation ; Hearing Loss/*genetics ; Humans ; Mitochondria/*genetics ; Polymorphism, Single Nucleotide ; Selection Bias ; }, abstract = {In a number of recent studies, we summarized the obvious errors and shortcomings that can be spotted in many (if not most) mitochondrial DNA (mtDNA) data sets published in medical genetics. We have reanalyzed here the complete mtDNA genome data published in various recent reports of East Asian families with hearing impairment, using a phylogenetic approach, in order to demonstrate the persistence of lab-specific mistakes in mtDNA genome sequencing in cases where those caveats were (deliberately) neglected. A phylogenetic reappraisal of complete mtDNAs with mutation A1555G (or G11778A) indeed supports the suggested lack of association between haplogroup background and phenotypic presentation of these mutations in East Asians. In contrast, the claimed pathogenicity of mutation T1095C in Chinese families with hearing impairment seems unsupported, basically because this mutation is rather basal in the mtDNA phylogeny, being specific to haplogroup M11 in East Asia. The roles of other haplogroup specific or associated variants, such as A827G, T961C, T1005C, in East Asian subjects with aminoglycoside-induced and non-syndromic hearing loss are also unclear in view of the known mtDNA phylogeny.}, }
@article {pmid16525920, year = {2006}, author = {Ribacoba, R and Salas-Puig, J and González, C and Astudillo, A}, title = {[Characteristics of status epilepticus in MELAS. Analysis of four cases].}, journal = {Neurologia (Barcelona, Spain)}, volume = {21}, number = {1}, pages = {1-11}, pmid = {16525920}, issn = {0213-4853}, mesh = {Adult ; Autopsy ; Electroencephalography ; Female ; Humans ; MELAS Syndrome/complications/diagnosis/pathology/*physiopathology ; Male ; Status Epilepticus/etiology/*physiopathology ; Tomography, Emission-Computed, Single-Photon ; }, abstract = {INTRODUCTION: Clinical characteristics of status epilepticus (SE) as a first manifestation in patients with MELAS who had not previously epileptic episode has been studied little in the literature.<br><br>OBJECTIVES: Our aim was to analyse precipitating factors, clinical characteristics, EEG and difficulties in the treatment of SE in MELAS.<br><br>PATIENTS AND METHODS: We studied four cases with ages between 27 an 41 years who began with SE and they had been diagnosed with MELAS during the episode. Case 3 was confirmed by autopsy. Cases 1, 2 and 4 showed a 3243 mtDNA mutation in the lymphocytes. Epileptic seizures had not been present in any previous status case. The precipitating factor in cases 1 and 3 was fever and in case 2 and 4 stress by headache. Moreover in case 2 second status was caused by stress in hyperglycaemic ketoacidosis. All cases were studied with EEG and a brain CT or MRI.<br><br>RESULTS: All patients started with epilepsia partialis continua that began with partial motor simple seizures, but sometimes progressed to partial complex seizures or secondary tonic clonic seizures. In two cases the initial symptom was migraine with aura, in two cases fever with cephalalgia and in one case diabetes mellitus decompensation. The EEG during a seizure presented a complex pseudoperiodic complex in the temporal-occipital contralateral region that spread to all hemisphere when myoclonus was increased.<br><br>CONCLUSIONS: SE in MELAS appears in cell stress situation precipitated by hypermetabolic conditions and it provokes claudication in ill mitochondria. In fact, events such as fever, glycemic alterations, hypoxemia or headache that could change the normal mechanism of sequester mitochondrial calcium in the neuron are able to trigger SE. Optimal evolution depends on an improvement of basal metabolic conditions that could precipitate the status. Supplementary folic acid, riboflavin and coenzyme Q 10 can be useful.}, }
@article {pmid16515848, year = {2006}, author = {Dacks, JB and Dyal, PL and Embley, TM and van der Giezen, M}, title = {Hydrogenosomal succinyl-CoA synthetase from the rumen-dwelling fungus Neocallimastix patriciarum; an energy-producing enzyme of mitochondrial origin.}, journal = {Gene}, volume = {373}, number = {}, pages = {75-82}, doi = {10.1016/j.gene.2006.01.012}, pmid = {16515848}, issn = {0378-1119}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Mitochondria/*enzymology ; Models, Biological ; Molecular Sequence Data ; Neocallimastix/*enzymology/genetics ; Organelles/*enzymology ; Phylogeny ; Sequence Homology, Amino Acid ; Succinate-CoA Ligases/*genetics ; }, abstract = {Hydrogenosomes are hydrogen-producing organelles that are related to mitochondria and found in a variety of evolutionarily unrelated anaerobic microbial eukaryotes. Similar to classic mitochondria, hydrogenosomes contain the enzyme catalyzing the only reaction of the citric acid cycle directly producing energy; succinyl-CoA synthetase. We have isolated and characterized the genes encoding both subunits of this enzyme from the anaerobic chytrid fungus Neocallimastix patriciarum, a model organism in hydrogenosome research. Both subunits contain all characteristic features of this enzyme, including predicted hydrogenosomal targeting signals. Phylogenetic analyses of succinyl-CoA synthetase clearly indicate its mitochondrial ancestry, both by affiliation with mitochondrially localized fungal homologues and by the sisterhood of the eukaryotic succinyl-CoA synthetase clade with alpha-proteobacteria. Our analyses of the Trichomonas vaginalis SCS sequences also confirmed the mitochondrial affiliation of these hydrogenosomal enzymes, in contrast to previous results. While both hydrogenosomal and mitochondrial succinyl-CoA synthetase homologues have been identified, no succinyl-CoA synthetase proteins were identifiable in taxa possessing another mitochondrially derived organelle, the mitosome. Our analyses further confirm the mitochondrial ancestry of the Neocallimastix hydrogenosome and sheds light upon the stepwise process by which mitochondria evolve into alternate forms of the organelle.}, }
@article {pmid16515731, year = {2006}, author = {Höglund, J and Morrison, DA and Mattsson, JG and Engström, A}, title = {Population genetics of the bovine/cattle lungworm (Dictyocaulus viviparus) based on mtDNA and AFLP marker techniques.}, journal = {Parasitology}, volume = {133}, number = {Pt 1}, pages = {89-99}, doi = {10.1017/S0031182006009991}, pmid = {16515731}, issn = {0031-1820}, mesh = {Animals ; Base Sequence ; Cattle ; Cattle Diseases/*parasitology ; DNA, Helminth/*chemistry ; DNA, Mitochondrial/*chemistry ; Dictyocaulus/classification/*genetics ; Dictyocaulus Infections/*parasitology ; Genes, Helminth ; Genetic Markers ; Genetics, Population ; Genotype ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; *Polymorphism, Genetic ; Sequence Analysis, DNA ; Sweden ; }, abstract = {Mitochondrial DNA (mtDNA) sequence data and amplified fragment length polymorphism (AFLP) patterns were compared for the lungworm Dictyocaulus viviparus, a nematode parasite of cattle. Eight individual D. viviparus samples from each of 8 herds in Sweden and 1 laboratory isolate were analysed, with the aim of describing the diversity and genetic structure in populations using different genetic markers on exactly the same DNA samples. There was qualitative agreement between the whole-genome AFLP data and the mtDNA sequence data, both indicating relatively strong genetic differentiation among the Swedish farms. However, the AFLP data detected much more genetic variation than did the mtDNA data, even after allowing for the different inheritance patterns of the markers, and indicated that there was much less differentiation among the populations. The mtDNA data therefore seemed to be more informative about the most recent history of the parasite populations, as the general patterns were less obscured by detailed inter-relationships among individual worms. The 4 mtDNA genes sequenced (1542 bp) showed consistent patterns, although there was more genetic variation in the protein-coding genes than in the structural RNA genes. Furthermore, there appeared to be at least 3 distinct genetic groups of D. viviparus infecting Swedish cattle, 1 of which was predominant and showed considerable differentiation between farms, but not necessarily within farms. Second, the 2 smaller genetic groups occurred on farms where the predominant group also occurred, suggesting that these farms have had multiple introductions of D. viviparus.}, }
@article {pmid16511496, year = {2006}, author = {Shaw, GC and Cope, JJ and Li, L and Corson, K and Hersey, C and Ackermann, GE and Gwynn, B and Lambert, AJ and Wingert, RA and Traver, D and Trede, NS and Barut, BA and Zhou, Y and Minet, E and Donovan, A and Brownlie, A and Balzan, R and Weiss, MJ and Peters, LL and Kaplan, J and Zon, LI and Paw, BH}, title = {Mitoferrin is essential for erythroid iron assimilation.}, journal = {Nature}, volume = {440}, number = {7080}, pages = {96-100}, doi = {10.1038/nature04512}, pmid = {16511496}, issn = {1476-4687}, support = {P01 HL032262/HL/NHLBI NIH HHS/United States ; R01 DK070838/DK/NIDDK NIH HHS/United States ; R01 HL075714/HL/NHLBI NIH HHS/United States ; }, mesh = {Anemia/blood/metabolism ; Animals ; Cation Transport Proteins/genetics/metabolism ; Cell Differentiation ; Conserved Sequence ; Erythroblasts/cytology/*metabolism/pathology ; Gene Expression Regulation ; Genetic Complementation Test ; Heme/metabolism ; Homeostasis ; Humans ; Iron/*metabolism ; Iron Overload ; Iron-Sulfur Proteins/biosynthesis/genetics ; Membrane Transport Proteins/genetics/*metabolism ; Mice ; Mitochondria/*metabolism ; Mitochondrial Proteins ; Molecular Sequence Data ; Mutation/genetics ; Phylogeny ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Stem Cells/cytology/metabolism ; Zebrafish/genetics/metabolism ; Zebrafish Proteins/genetics/*metabolism ; }, abstract = {Iron has a fundamental role in many metabolic processes, including electron transport, deoxyribonucleotide synthesis, oxygen transport and many essential redox reactions involving haemoproteins and Fe-S cluster proteins. Defective iron homeostasis results in either iron deficiency or iron overload. Precise regulation of iron transport in mitochondria is essential for haem biosynthesis, haemoglobin production and Fe-S cluster protein assembly during red cell development. Here we describe a zebrafish mutant, frascati (frs), that shows profound hypochromic anaemia and erythroid maturation arrest owing to defects in mitochondrial iron uptake. Through positional cloning, we show that the gene mutated in the frs mutant is a member of the vertebrate mitochondrial solute carrier family (SLC25) that we call mitoferrin (mfrn). mfrn is highly expressed in fetal and adult haematopoietic tissues of zebrafish and mouse. Erythroblasts generated from murine embryonic stem cells null for Mfrn (also known as Slc25a37) show maturation arrest with severely impaired incorporation of 55Fe into haem. Disruption of the yeast mfrn orthologues, MRS3 and MRS4, causes defects in iron metabolism and mitochondrial Fe-S cluster biogenesis. Murine Mfrn rescues the defects in frs zebrafish, and zebrafish mfrn complements the yeast mutant, indicating that the function of the gene may be highly conserved. Our data show that mfrn functions as the principal mitochondrial iron importer essential for haem biosynthesis in vertebrate erythroblasts.}, }
@article {pmid16511485, year = {2006}, author = {Martin, W and Koonin, EV}, title = {Introns and the origin of nucleus-cytosol compartmentalization.}, journal = {Nature}, volume = {440}, number = {7080}, pages = {41-45}, doi = {10.1038/nature04531}, pmid = {16511485}, issn = {1476-4687}, support = {//Intramural NIH HHS/United States ; }, mesh = {*Biological Evolution ; Cell Compartmentation/*physiology ; Cell Nucleus/genetics/*metabolism ; Chromosomes/genetics/metabolism ; Cytosol/*metabolism ; Eukaryotic Cells/cytology/metabolism ; Introns/*genetics/*physiology ; Mitochondria/genetics/metabolism ; *Models, Biological ; Nuclear Envelope/physiology ; Protein Biosynthesis/genetics ; RNA/genetics/metabolism ; Ribosomes/metabolism ; }, abstract = {The origin of the eukaryotic nucleus marked a seminal evolutionary transition. We propose that the nuclear envelope's incipient function was to allow mRNA splicing, which is slow, to go to completion so that translation, which is fast, would occur only on mRNA with intact reading frames. The rapid, fortuitous spread of introns following the origin of mitochondria is adduced as the selective pressure that forged nucleus-cytosol compartmentalization.}, }
@article {pmid16510155, year = {2006}, author = {Mears, JA and Sharma, MR and Gutell, RR and McCook, AS and Richardson, PE and Caulfield, TR and Agrawal, RK and Harvey, SC}, title = {A structural model for the large subunit of the mammalian mitochondrial ribosome.}, journal = {Journal of molecular biology}, volume = {358}, number = {1}, pages = {193-212}, pmid = {16510155}, issn = {0022-2836}, support = {GM 61576/GM/NIGMS NIH HHS/United States ; R01 GM061576/GM/NIGMS NIH HHS/United States ; R01 GM053827/GM/NIGMS NIH HHS/United States ; R01 GM067317-03/GM/NIGMS NIH HHS/United States ; R01 GM067317/GM/NIGMS NIH HHS/United States ; GM 67317/GM/NIGMS NIH HHS/United States ; GM 53827/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Cattle ; Mitochondria/*chemistry/*genetics ; *Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; RNA/chemistry/genetics ; RNA, Mitochondrial ; RNA, Ribosomal, 16S/chemistry/genetics ; RNA, Transfer/genetics ; Reproducibility of Results ; Ribosomal Proteins/chemistry ; Ribosomes/*chemistry/*genetics ; Structural Homology, Protein ; }, abstract = {Protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. Evolutionary changes in protein and RNA sequences can affect the 3D organization of structural features in ribosomes in different species. The most dramatic changes occur in animal mitochondria, whose genomes have been reduced and altered significantly. The RNA component of the mitochondrial ribosome (mitoribosome) is reduced in size, with a compensatory increase in protein content. Until recently, it was unclear how these changes affect the 3D structure of the mitoribosome. Here, we present a structural model of the large subunit of the mammalian mitoribosome developed by combining molecular modeling techniques with cryo-electron microscopic data at 12.1A resolution. The model contains 93% of the mitochondrial rRNA sequence and 16 mitochondrial ribosomal proteins in the large subunit of the mitoribosome. Despite the smaller mitochondrial rRNA, the spatial positions of RNA domains known to be involved directly in protein synthesis are essentially the same as in bacterial and archaeal ribosomes. However, the dramatic reduction in rRNA content necessitates evolution of unique structural features to maintain connectivity between RNA domains. The smaller rRNA sequence also limits the likelihood of tRNA binding at the E-site of the mitoribosome, and correlates with the reduced size of D-loops and T-loops in some animal mitochondrial tRNAs, suggesting co-evolution of mitochondrial rRNA and tRNA structures.}, }
@article {pmid16502095, year = {2006}, author = {de Moraes-Barros, N and Silva, JA and Miyaki, CY and Morgante, JS}, title = {Comparative phylogeography of the Atlantic forest endemic sloth (Bradypus torquatus) and the widespread three-toed sloth (Bradypus variegatus) (Bradypodidae, Xenarthra).}, journal = {Genetica}, volume = {126}, number = {1-2}, pages = {189-198}, doi = {10.1007/s10709-005-1448-x}, pmid = {16502095}, issn = {0016-6707}, mesh = {Animals ; Brazil ; DNA, Mitochondrial ; Genetic Variation ; Geography ; Locus Control Region/genetics ; Mitochondria/genetics ; *Phylogeny ; Sloths/*genetics ; }, abstract = {The comparative phylogeographic study of the maned sloth (Bradypus torquatus) and the three-toed sloth (Bradypus variegatus) was performed using a segment of mitochondrial DNA (mtDNA) control region. We examined 19 B. torquatus from two regions and 47 B. variegatus from three distant regions of Atlantic forest. This first characterization of molecular diversity indicates a great diversity (B. torquatus: h = 0.901 +/- 0.039 and pi = 0.012 +/- 0.007; B. variegatus: h = 0.699 +/- 0.039 and pi = 0.010 +/- 0.006) and very divergent mitochondrial lineages within each sloth species. The different sampled regions carry distinct and non-overlapping sets of mtDNA haplotypes and are genetically divergent. This phylogeographic pattern may be characteristic of sloth species. In addition, we infer that two main phylogeographic groups exist in the Atlantic forest representing a north and south distinct divergence.}, }
@article {pmid16502089, year = {2006}, author = {de Azeredo-Espin, AM and Lessinger, AC}, title = {Genetic approaches for studying myiasis-causing flies: molecular markers and mitochondrial genomics.}, journal = {Genetica}, volume = {126}, number = {1-2}, pages = {111-131}, doi = {10.1007/s10709-005-1439-y}, pmid = {16502089}, issn = {0016-6707}, mesh = {Animals ; Diptera/*genetics ; Genetic Markers ; *Genomics ; Mitochondria/*genetics ; Myiasis/*genetics/metabolism/parasitology ; Screw Worm Infection/genetics/parasitology ; }, abstract = {"Myiasis-causing flies" is a generic term that includes species from numerous dipteran families, mainly Calliphoridae and Oestridae, of which blowflies, screwworm flies and botflies are among the most important. This group of flies is characterized by the ability of their larvae to develop in animal flesh. When the host is a live vertebrate, such parasitism by dipterous larvae is known as primary myiasis. Myiasis-causing flies can be classified as saprophagous (free-living species), facultative or obligate parasites. Many of these flies are of great medical and veterinary importance in Brazil because of their role as key livestock insect-pests and vectors of pathogens, in addition to being considered important legal evidence in forensic entomology. The characterization of myiasis-causing flies using molecular markers to study mtDNA (by RFLP) and nuclear DNA (by RAPD and microsatellite) has been used to identify the evolutionary mechanisms responsible for specific patterns of genetic variability. These approaches have been successfully used to analyze the population structures of the New World screwworm fly Cochliomyia hominivorax and the botfly Dermatobia hominis. In this review, various aspects of the organization, evolution and potential applications of the mitochondrial genome of myiasis-causing flies in Brazil, and the analysis of nuclear markers in genetic studies of populations, are discussed.}, }
@article {pmid16498697, year = {2006}, author = {Miranda, I and Silva, R and Santos, MA}, title = {Evolution of the genetic code in yeasts.}, journal = {Yeast (Chichester, England)}, volume = {23}, number = {3}, pages = {203-213}, doi = {10.1002/yea.1350}, pmid = {16498697}, issn = {0749-503X}, mesh = {Base Sequence ; Candida/*genetics ; Codon/genetics ; *Evolution, Molecular ; *Genetic Code ; Models, Molecular ; Molecular Sequence Data ; Saccharomycetales/*genetics ; }, abstract = {During the last 30 years, a number of genetic code alterations have been uncovered in bacteria and in the mitochondria and cytoplasm of various eukaryotes, invalidating the hypothesis that the genetic code is universal and frozen. In the mitochondria of most yeasts, the UGA stop codon is decoded as tryptophan and the four leucine codons of the CUN family (N = any nucleotide) are decoded as threonine. Recently, a unique genetic code change involving the decoding of the leucine CUG codon as serine was discovered in the cytoplasm of Candida and Debaryomyces species, indicating that the genetic code of yeasts may be under specific evolutionary pressures whose molecular nature is not yet fully understood. This genetic code alteration is mediated by a novel serine-tRNA that acquired a leucine 5'-CAG-3' anticodon (ser-tRNACAG) through insertion of an adenosine in the intron of its gene. This event, which occurred 272 +/- 25 million years ago, reprogrammed the identity of approximately 30 000 CUG codons existent in the ancestor of these yeasts and had a profound impact on the evolution of the genus Candida and of other species. Here, we review the most recent results and concepts arising from the study of this genetic code change and highlight how its study is changing our views of the evolution of the genetic code.}, }
@article {pmid16497363, year = {2006}, author = {Yu, BP and Chung, HY}, title = {Adaptive mechanisms to oxidative stress during aging.}, journal = {Mechanisms of ageing and development}, volume = {127}, number = {5}, pages = {436-443}, doi = {10.1016/j.mad.2006.01.023}, pmid = {16497363}, issn = {0047-6374}, mesh = {*Aging ; Animals ; Evolution, Molecular ; Exercise ; Gene Expression Regulation ; Humans ; Inflammation ; Mitochondria/metabolism/pathology ; NF-kappa B/metabolism ; *Oxidative Stress ; Oxygen/metabolism ; Transcription, Genetic ; }, abstract = {Whether or not oxidative stress is the cause of the aging process, as proposed by the oxidative stress theory of aging remains unknown; but accumulated evidence overwhelmingly identifies increased oxidative stress with age as a source of damage to cellular structure and function. From an evolutionary perspective, the utilization of oxygen as a life supporting means makes oxidative stress an inescapable part of an organism's biological system. The inseparability of oxidative stress from the biological system can be viewed as an adaptive response that all aerobic organisms undergo to ward-off the potentially harmful effects of oxygen and its derivatives, including free radicals. The organism's adaptive mechanisms include an intricate network of defenses that regulate and guard against any over-acting oxidative reactions to ensure its survival. This review discusses and illustrates several adaptive responses at various levels (from gene regulation to physical exercise) that organisms use as part of their survival strategy.}, }
@article {pmid16488430, year = {2006}, author = {Celebi, N and Yi, L and Facey, SJ and Kuhn, A and Dalbey, RE}, title = {Membrane biogenesis of subunit II of cytochrome bo oxidase: contrasting requirements for insertion of N-terminal and C-terminal domains.}, journal = {Journal of molecular biology}, volume = {357}, number = {5}, pages = {1428-1436}, doi = {10.1016/j.jmb.2006.01.030}, pmid = {16488430}, issn = {0022-2836}, support = {GM63862-05/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphatases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Cell Membrane/*metabolism ; *Electron Transport Complex IV/biosynthesis/chemistry/genetics ; Escherichia coli/enzymology ; Escherichia coli Proteins/genetics/*metabolism ; Evolution, Molecular ; Membrane Transport Proteins/genetics/*metabolism ; Mitochondria/enzymology ; *Protein Conformation ; Protein Precursors/chemistry/genetics/metabolism ; Protein Sorting Signals ; *Protein Subunits/biosynthesis/chemistry/genetics ; SEC Translocation Channels ; SecA Proteins ; }, abstract = {The membrane assembly of the respiratory complexes requires the membrane insertases Oxa1 in mitochondria and YidC in bacteria. Oxa1 is responsible for the insertion of the mitochondrial cytochrome c oxidase subunit II (CoxII). Here, we investigated whether YidC, the bacterial Oxa1 homolog, plays a crucial role in the assembly of the bacterial subunit II (CyoA) of cytochrome bo oxidase. CyoA spans the membrane twice and is made with a cleavable signal peptide. We find that translocation of the short N-terminal domain of CyoA is YidC-dependent. In contrast, both the SecA/SecYEG complex and YidC are required for translocation of the large C-terminal domain. By studying the N-terminal domain of CyoA alone, we find that translocation is unaffected when SecE is depleted, suggesting that the YidC insertase on its own catalyzes membrane insertion of the N-terminal region of CyoA. Strikingly, we find that the translocation of the N-terminal domain is a prerequisite for translocation of the C-terminal domain in the full-length CyoA protein because translocation of the large C-terminal domain alone in a truncated CyoA derivative was observed in the absence of YidC. This work shows that the distinct domains of CyoA have different translocation requirements (YidC only and Sec/YidC) and confirms that the membrane biogenesis of subunit II of cytochrome oxidase in bacteria and mitochondria have conserved features.}, }
@article {pmid16487606, year = {2006}, author = {Schrader, M}, title = {Shared components of mitochondrial and peroxisomal division.}, journal = {Biochimica et biophysica acta}, volume = {1763}, number = {5-6}, pages = {531-541}, doi = {10.1016/j.bbamcr.2006.01.004}, pmid = {16487606}, issn = {0006-3002}, mesh = {Animals ; Biological Evolution ; Humans ; Mitochondria/*metabolism ; Mitochondrial Proteins/metabolism ; Peroxisomes/*metabolism ; }, abstract = {Mitochondria and peroxisomes are ubiquitous subcellular organelles, which are highly dynamic and display large plasticity. Recent studies have led to the surprising finding that both organelles share components of their division machinery, namely the dynamin-related protein DLP1/Drp1 and hFis1, which recruits DLP1/Drp1 to the organelle membranes. This review addresses the current state of knowledge concerning the dynamics and fission of peroxisomes, especially in relation to mitochondrial morphology and division in mammalian cells.}, }
@article {pmid16483135, year = {2005}, author = {He, D and Dong, J and Wen, J and Xin, D and Lu, S}, title = {Phylogenetic positions of several amitochondriate protozoa--evidence from phylogenetic analysis of DNA topoisomerase II.}, journal = {Science in China. Series C, Life sciences}, volume = {48}, number = {6}, pages = {565-573}, doi = {10.1360/04yc0111}, pmid = {16483135}, issn = {1006-9305}, mesh = {Animals ; Base Sequence ; DNA Topoisomerases, Type II/*genetics ; DNA, Protozoan/chemistry/isolation &amp; purification ; Encephalitozoon cuniculi/classification/enzymology/genetics ; Entamoeba histolytica/classification/enzymology/genetics ; Eukaryota/*classification/enzymology/*genetics ; Genes, Protozoan ; Giardia lamblia/classification/enzymology/genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Protozoan/isolation &amp; purification ; Trichomonas vaginalis/classification/enzymology/genetics ; }, abstract = {Several groups of parasitic protozoa, as represented by Giardia, Trichomonas, Entamoeba and Microsporida, were once widely considered to be the most primitive extant eukaryotic group--Archezoa. The main evidence for this is their 'lacking mitochondria' and possessing some other primitive features between prokaryotes and eukaryotes, and being basal to all eukaryotes with mitochondria in phylogenies inferred from many molecules. Some authors even proposed that these organisms diverged before the endosymbiotic origin of mitochondria within eukaryotes. This view was once considered to be very significant to the study of origin and evolution of eukaryotic cells (eukaryotes). However, in recent years this has been challenged by accumulating evidence from new studies. Here the sequences of DNA topoisomerase II in G lamblia, T. vaginalis and E. histolytica were identified first by PCR and sequencing, then combining with the sequence data of the microsporidia Encephalitozoon cunicul and other eukaryotic groups of different evolutionary positions from GenBank, phylogenetic trees were constructed by various methods to investigate the evolutionary positions of these amitochondriate protozoa. Our results showed that since the characteristics of DNA topoisomerase II make it avoid the defect of 'long-branch attraction' appearing in the previous phylogenetic analyses, our trees can not only reflect effectively the relationship of different major eukaryotic groups, which is widely accepted, but also reveal phylogenetic positions for these amitochondriate protozoa, which is different from the previous phylogenetic trees. They are not the earliest-branching eukaryotes, but diverged after some mitochondriate organisms such as kinetoplastids and mycetozoan; they are not a united group but occupy different phylogenetic positions. Combining with the recent cytological findings of mitochondria-like organelles in them, we think that though some of them (e.g. diplomonads, as represented by Giardia) may occupy a very low evolutionary position, generally these organisms are not as extremely primitive as was thought before; they should be polyphyletic groups diverging after the endosymbiotic origin of mitochondrion to adapt themselves to anaerobic parasitic life.}, }
@article {pmid16475111, year = {2005}, author = {Voloch, CM and Freire, PR and Russo, CA}, title = {Molecular phylogeny of penaeid shrimps inferred from two mitochondrial markers.}, journal = {Genetics and molecular research : GMR}, volume = {4}, number = {4}, pages = {668-674}, pmid = {16475111}, issn = {1676-5680}, mesh = {Algorithms ; Animals ; Bayes Theorem ; Electron Transport Complex I/genetics ; *Evolution, Molecular ; Genetic Markers ; Genetic Variation/*genetics ; Likelihood Functions ; Mitochondria/*genetics ; Penaeidae/classification/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment/methods ; }, abstract = {Penaeid shrimps are an important resource in crustacean fisheries, representing more than the half of the gross production of shrimp worldwide. In the present study, we used a sample of wide-ranging diversity (41 shrimp species) and two mitochondrial markers (758 bp) to clarify the evolutionary relationships among Penaeidae genera. Three different methodologies of tree reconstruction were employed in the study: maximum likelihood, neighbor joining and Bayesian analysis. Our results suggest that the old Penaeus genus is monophyletic and that the inclusion of the Solenocera genus within the Penaeidae family remains uncertain. With respect to Metapenaeopsis monophyly, species of this genus appeared clustered, but with a nonsignificant bootstrap value. These results elucidate some features of the unclear evolution of Penaeidae and may contribute to the taxonomic characterization of this family.}, }
@article {pmid16475085, year = {2005}, author = {Criscuolo, F and Gonzalez-Barroso, Mdel M and Bouillaud, F and Ricquier, D and Miroux, B and Sorci, G}, title = {Mitochondrial uncoupling proteins: new perspectives for evolutionary ecologists.}, journal = {The American naturalist}, volume = {166}, number = {6}, pages = {686-699}, doi = {10.1086/497439}, pmid = {16475085}, issn = {1537-5323}, mesh = {Aging/*physiology ; Amino Acids/analysis ; Animals ; *Biological Evolution ; Birds ; Ecosystem ; Ion Channels/*genetics/*physiology ; Mitochondrial Membranes/physiology ; Mitochondrial Proteins/*genetics/*physiology ; Oxygen Consumption ; Reactive Oxygen Species/metabolism ; Thermodynamics ; Uncoupling Protein 1 ; }, abstract = {Reactive oxygen species (ROS)-induced damage on host cells and molecules has been considered the most likely proximal mechanism responsible for the age-related decline in organismal performance. Organisms have two possible ways to reduce the negative effect of ROS: disposing of effective antioxidant defenses and minimizing ROS production. The unbalance between the amount of ROS produced and the availability of antioxidant defenses determines the intensity of so-called oxidative stress. Interestingly, most studies that deal with the effect of oxidative stress on organismal performance have focused on the antioxidant defense compartment and, surprisingly, have neglected the mechanisms that control ROS production within mitochondria. Uncoupling proteins (UCPs), mitochondrial transporters of the inner membrane, are involved in the control of redox state of cells and in the production of mitochondrial ROS. Given their function, UCPs might therefore represent a major mechanistic link between metabolic activity and fitness. We suggest that by exploring the role of expression and function of UCPs both in experimental as well as in comparative studies, evolutionary biologists may gain better insight into this link.}, }
@article {pmid16473895, year = {2006}, author = {Borecky, J and Nogueira, FT and de Oliveira, KA and Maia, IG and Vercesi, AE and Arruda, P}, title = {The plant energy-dissipating mitochondrial systems: depicting the genomic structure and the expression profiles of the gene families of uncoupling protein and alternative oxidase in monocots and dicots.}, journal = {Journal of experimental botany}, volume = {57}, number = {4}, pages = {849-864}, doi = {10.1093/jxb/erj070}, pmid = {16473895}, issn = {0022-0957}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/metabolism ; Carrier Proteins/*genetics/metabolism ; Cold Temperature ; Computational Biology ; Gene Expression Profiling ; Genome, Plant ; Ion Channels ; Membrane Proteins/*genetics/metabolism ; Mitochondria/enzymology/*genetics/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; Multigene Family/*genetics/physiology ; Oxidoreductases/*genetics/metabolism ; Phylogeny ; Plant Proteins/*genetics/metabolism ; RNA, Messenger/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Saccharum/*genetics/metabolism ; Sequence Alignment ; Sequence Analysis, Protein ; Uncoupling Protein 1 ; }, abstract = {The simultaneous existence of alternative oxidases and uncoupling proteins in plants has raised the question as to why plants need two energy-dissipating systems with apparently similar physiological functions. A probably complete plant uncoupling protein gene family is described and the expression profiles of this family compared with the multigene family of alternative oxidases in Arabidopsis thaliana and sugarcane (Saccharum sp.) employed as dicot and monocot models, respectively. In total, six uncoupling protein genes, AtPUMP1-6, were recognized within the Arabidopsis genome and five (SsPUMP1-5) in a sugarcane EST database. The recombinant AtPUMP5 protein displayed similar biochemical properties as AtPUMP1. Sugarcane possessed four Arabidopsis AOx1-type orthologues (SsAOx1a-1d); no sugarcane orthologue corresponding to Arabidopsis AOx2-type genes was identified. Phylogenetic and expression analyses suggested that AtAOx1d does not belong to the AOx1-type family but forms a new (AOx3-type) family. Tissue-enriched expression profiling revealed that uncoupling protein genes were expressed more ubiquitously than the alternative oxidase genes. Distinct expression patterns among gene family members were observed between monocots and dicots and during chilling stress. These findings suggest that the members of each energy-dissipating system are subject to different cell or tissue/organ transcriptional regulation. As a result, plants may respond more flexibly to adverse biotic and abiotic conditions, in which oxidative stress is involved.}, }
@article {pmid16469879, year = {2006}, author = {Sazanov, LA and Hinchliffe, P}, title = {Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus.}, journal = {Science (New York, N.Y.)}, volume = {311}, number = {5766}, pages = {1430-1436}, doi = {10.1126/science.1123809}, pmid = {16469879}, issn = {1095-9203}, support = {MC_U105674180/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Bacterial Proteins/*chemistry ; Binding Sites ; Crystallography, X-Ray ; Electron Transport Complex I/*chemistry ; Iron-Binding Proteins/chemistry ; Oxidation-Reduction ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Protein Subunits ; Thermus thermophilus/*chemistry ; Frataxin ; }, abstract = {Respiratory complex I plays a central role in cellular energy production in bacteria and mitochondria. Its dysfunction is implicated in many human neurodegenerative diseases, as well as in aging. The crystal structure of the hydrophilic domain (peripheral arm) of complex I from Thermus thermophilus has been solved at 3.3 angstrom resolution. This subcomplex consists of eight subunits and contains all the redox centers of the enzyme, including nine iron-sulfur clusters. The primary electron acceptor, flavin-mononucleotide, is within electron transfer distance of cluster N3, leading to the main redox pathway, and of the distal cluster N1a, a possible antioxidant. The structure reveals new aspects of the mechanism and evolution of the enzyme. The terminal cluster N2 is coordinated, uniquely, by two consecutive cysteines. The novel subunit Nqo15 has a similar fold to the mitochondrial iron chaperone frataxin, and it may be involved in iron-sulfur cluster regeneration in the complex.}, }
@article {pmid16467478, year = {2006}, author = {Batista, WL and Matsuo, AL and Ganiko, L and Barros, TF and Veiga, TR and Freymüller, E and Puccia, R}, title = {The PbMDJ1 gene belongs to a conserved MDJ1/LON locus in thermodimorphic pathogenic fungi and encodes a heat shock protein that localizes to both the mitochondria and cell wall of Paracoccidioides brasiliensis.}, journal = {Eukaryotic cell}, volume = {5}, number = {2}, pages = {379-390}, pmid = {16467478}, issn = {1535-9778}, mesh = {Cell Wall/*metabolism/ultrastructure ; *Conserved Sequence ; Flow Cytometry ; Genome, Fungal ; HSP40 Heat-Shock Proteins/chemistry/*genetics/*metabolism ; Humans ; Introns/genetics ; Mitochondria/*metabolism/ultrastructure ; Paracoccidioides/*cytology/*genetics/metabolism/pathogenicity ; Paracoccidioidomycosis ; Phylogeny ; Protein Transport ; Recombinant Fusion Proteins ; }, abstract = {J-domain (DnaJ) proteins, of the Hsp40 family, are essential cofactors of their cognate Hsp70 chaperones, besides acting as independent chaperones. In the present study, we have demonstrated the presence of Mdj1, a mitochondrial DnaJ member, not only in the mitochondria, where it is apparently sorted, but also in the cell wall of Paracoccidioides brasiliensis, a thermodimorphic pathogenic fungus. The molecule (PbMdj1) was localized to fungal yeast cells using both confocal and electron microscopy and also flow cytometry. The anti-recombinant PbMdj1 antibodies used in the reactions specifically recognized a single 55-kDa mitochondrial and cell wall (alkaline beta-mercaptoethanol extract) component, compatible with the predicted size of the protein devoid of its matrix peptide-targeting signal. Labeling was abundant throughout the cell wall and especially in the budding regions; however, anti-PbMdj1 did not affect fungal growth in the concentrations tested in vitro, possibly due to the poor access of the antibodies to their target in growing cells. Labeled mitochondria stood preferentially close to the plasma membrane, and gold particles were detected in the thin space between them, toward the cell surface. We show that Mdj1 and the mitochondrial proteinase Lon homologues are heat shock proteins in P. brasiliensis and that their gene organizations are conserved among thermodimorphic fungi and Aspergillus, where the genes are adjacent and have a common 5' region. This is the first time a DnaJ member has been observed on the cell surface, where its function is speculative.}, }
@article {pmid16465445, year = {2006}, author = {Shikanai, T}, title = {RNA editing in plant organelles: machinery, physiological function and evolution.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {63}, number = {6}, pages = {698-708}, doi = {10.1007/s00018-005-5449-9}, pmid = {16465445}, issn = {1420-682X}, mesh = {Chloroplasts/*genetics ; *Evolution, Molecular ; Mitochondria/*genetics ; Plant Proteins/*genetics/metabolism ; Plants/genetics ; *RNA Editing ; }, abstract = {In plants, RNA editing is a process for converting a specific nucleotide of RNA from C to U and less frequently from U to C in mitochondria and plastids. To specify the site of editing, the cis-element adjacent to the editing site functions as a binding site for the trans-acting factor. Genetic approaches using Arabidopsis thaliana have clarified that a member of the protein family with pentatricopeptide repeat (PPR) motifs is essential for RNA editing to generate a translational initiation codon of the chloroplast ndhD gene. The PPR motif is a highly degenerate unit of 35 amino acids and appears as tandem repeats in proteins that are involved in RNA maturation steps in mitochondria and plastids. The Arabidopsis genome encodes approximately 450 members of the PPR family, some of which possibly function as trans-acting factors binding the cis-elements of the RNA editing sites to facilitate access of an unidentified RNA editing enzyme. Based on this breakthrough in the research on plant RNA editing, I would like to discuss the possible steps of co-evolution of RNA editing events and PPR proteins.}, }
@article {pmid16464263, year = {2006}, author = {Parham, JF and Feldman, CR and Boore, JL}, title = {The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA.}, journal = {BMC evolutionary biology}, volume = {6}, number = {}, pages = {11}, pmid = {16464263}, issn = {1471-2148}, mesh = {Animals ; Cell Nucleus/genetics ; DNA/chemistry ; DNA, Mitochondrial/*chemistry ; Gene Order ; *Genes, Mitochondrial ; Genome ; Genomics ; Mitochondria/*genetics ; Models, Genetic ; *Phylogeny ; Turtles/anatomy &amp; histology/*classification/genetics ; }, abstract = {BACKGROUND: The big-headed turtle (Platysternon megacephalum) from east Asia is the sole living representative of a poorly-studied turtle lineage (Platysternidae). It has no close living relatives, and its phylogenetic position within turtles is one of the outstanding controversies in turtle systematics. Platysternon was traditionally considered to be close to snapping turtles (Chelydridae) based on some studies of its morphology and mitochondrial (mt) DNA, however, other studies of morphology and nuclear (nu) DNA do not support that hypothesis.<br><br>RESULTS: We sequenced the complete mt genome of Platysternon and the nearly complete mt genomes of two other relevant turtles and compared them to turtle mt genomes from the literature to form the largest molecular dataset used to date to address this issue. The resulting phylogeny robustly rejects the placement of Platysternon with Chelydridae, but instead shows that it is a member of the Testudinoidea, a diverse, nearly globally-distributed group that includes pond turtles and tortoises. We also discovered that Platysternon mtDNA has large-scale gene rearrangements and possesses two, nearly identical, control regions, features that distinguish it from all other studied turtles.<br><br>CONCLUSION: Our study robustly determines the phylogenetic placement of Platysternon and provides a well-resolved outline of major turtle lineages, while demonstrating the significantly greater resolving power of comparing large amounts of mt sequence over that of short fragments. Earlier phylogenies placing Platysternon with chelydrids required a temporal gap in the fossil record that is now unnecessary. The duplicated control regions and gene rearrangements of the Platysternon mtDNA probably resulted from the duplication of part of the genome and then the subsequent loss of redundant genes. Although it is possible that having two control regions may provide some advantage, explaining why the control regions would be maintained while some of the duplicated genes were eroded, examples of this are rare. So far, duplicated control regions have been reported for mt genomes from just 12 clades of metazoans, including Platysternon.}, }
@article {pmid16463378, year = {2006}, author = {Seligmann, H and Krishnan, NM}, title = {Mitochondrial replication origin stability and propensity of adjacent tRNA genes to form putative replication origins increase developmental stability in lizards.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {306}, number = {5}, pages = {433-449}, doi = {10.1002/jez.b.21095}, pmid = {16463378}, issn = {1552-5007}, mesh = {Animals ; *DNA Replication/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genetic Variation/*genetics ; Lizards/classification/*genetics/growth &amp; development ; Mitochondria ; RNA, Transfer/*genetics ; Transcription, Genetic ; }, abstract = {Secondary structure stability of mitochondrial origins of light-strand replication (OL) presumably reduces delayed formation of light-strand initiating replication forks on the heavy strand. Delayed replication initiation prolongs single strandedness of the heavy strand. More mutations accumulate during the prolonged time spent single stranded. Presumably, delayed replication initiation and excess mutations affect mitochondrial biochemical processes and ultimately morphological outcomes of development at the whole-organism level. This predicts that developmental stability increases with OL secondary structure stability and with formation of OL-like structures by the five tRNA genes flanking recognized OLs. Stable OLs and high percentages of OL-resembling secondary structures of adjacent tRNA genes (predicted by Mfold) correlate positively with developmental stability in three lizard families (Anguidae, Amphisbaenidae, and Polychrotidae). Accounting for effects of the regular OL, Sfold-predicted OL-like propensity of the entire tRNA gene cluster (not of individual genes) correlates with increased developmental stability in Anguidae, also across the entire free-energy range of Boltzmann's distribution of secondary structures. In the fossorial Amphisbaenidae, the OL-like structure-forming propensity of tRNA genes correlates positively with developmental stability for the distribution's sub-optimally stable regions, and negatively for its optimally stable regions, suggesting the thermoregulated functioning of OL vs. flanking tRNA genes as replication origins. Results for polychrotid tRNA genes are intermediate. Anguid tRNA genes possibly function in addition to the regular OL. Mitochondrial tRNA genes may thus frequently acquire and lose the alternative OL function, without sequence (gene) duplication and loss of their primary function.}, }
@article {pmid16461358, year = {2006}, author = {Won, YJ and Wang, Y and Sivasundar, A and Raincrow, J and Hey, J}, title = {Nuclear gene variation and molecular dating of the cichlid species flock of Lake Malawi.}, journal = {Molecular biology and evolution}, volume = {23}, number = {4}, pages = {828-837}, doi = {10.1093/molbev/msj101}, pmid = {16461358}, issn = {0737-4038}, mesh = {Animals ; Cell Nucleus/*genetics ; Cichlids/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Fish Proteins/genetics ; Fresh Water ; *Genetic Variation ; *Genetics, Population ; Malawi ; Nuclear Proteins/genetics ; Sequence Homology, Nucleic Acid ; Tilapia/genetics ; }, abstract = {The cichlid fishes of Lake Malawi are famously diverse. However, evolutionary studies have been difficult because of their recent and uncertain phylogenetic history. Portions of 12 nuclear loci were sequenced in nine rock-dwelling species (mbuna) and three representatives of pelagic nonmbuna species. In contrast to the pattern of variation at mitochondrial genes, which do provide phylogenetic resolution at the level of mbuna versus nonmbuna, and among some genera, the nuclear loci were virtually devoid of phylogenetic signal. Only a small minority of variable positions were phylogenetically informative, and no phylogenetic branches are supported by more than one site. From the nuclear gene perspective the Malawian radiation appears to be a star phylogeny, as if the founding of the lake was accompanied by a partial bottleneck. The pattern is different from that found in Lake Victoria, in which nuclear loci share large amounts of ancestral variation. In the case of nuclear genes of Lake Malawi, the absence of phylogenetically informative variation suggests a relative absence of ancestral variation. Nuclear genes also differed from the mitochondria in having nearly twice the amount of divergence from Oreochromis (tilapia). An approximate splitting time between mbuna and nonmbuna lineages was estimated as 0.7 Myr. Oreochromis is estimated to have diverged from the cichlids in Lake Malawi and Lake Tanganyika about 18 MYA.}, }
@article {pmid16461275, year = {2006}, author = {Perry, AJ and Hulett, JM and Likić, VA and Lithgow, T and Gooley, PR}, title = {Convergent evolution of receptors for protein import into mitochondria.}, journal = {Current biology : CB}, volume = {16}, number = {3}, pages = {221-229}, doi = {10.1016/j.cub.2005.12.034}, pmid = {16461275}, issn = {0960-9822}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics ; Base Sequence ; Binding Sites/genetics ; Carrier Proteins/*genetics ; Computational Biology ; *Evolution, Molecular ; Gene Components ; Mitochondria/*genetics ; Mitochondrial Precursor Protein Import Complex Proteins ; *Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Protein Structure, Tertiary ; Protein Transport/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {BACKGROUND: Mitochondria evolved from intracellular bacterial symbionts. Establishing mitochondria as organelles required a molecular machine to import proteins across the mitochondrial outer membrane. This machinery, the TOM complex, is composed of at least seven component parts, and its creation and evolution represented a sizeable challenge. Although there is good evidence that a core TOM complex, composed of three subunits, was established in the protomitochondria, we suggest that the receptor component of the TOM complex arose later in the evolution of this machine.<br><br>RESULTS: We have solved by nuclear magnetic resonance the structure of the presequence binding receptor from the TOM complex of the plant Arabidopsis thaliana. The protein fold suggests that this protein, AtTom20, belongs to the tetratricopeptide repeat (TPR) superfamily, but it is unusual in that it contains insertions lengthening the helices of each TPR motif. Peptide titrations map the presequence binding site to a groove of the concave surface of the receptor. In vitro functional assays and peptide titrations suggest that the plant Tom20 is functionally equivalent to fungal and animal Tom20s.<br><br>CONCLUSIONS: Comparison of the sequence and structure of Tom20 from plants and animals suggests that these two presequence binding receptors evolved from two distinct ancestral genes following the split of the animal and plant lineages. The need to bind equivalent mitochondrial targeting sequences and to make similar interactions within an equivalent protein translocation machine has driven the convergent evolution of two distinct proteins to a common structure and function.}, }
@article {pmid16460507, year = {2006}, author = {Williams, P and Hardeman, K and Fowler, J and Rivin, C}, title = {Divergence of duplicated genes in maize: evolution of contrasting targeting information for enzymes in the porphyrin pathway.}, journal = {The Plant journal : for cell and molecular biology}, volume = {45}, number = {5}, pages = {727-739}, doi = {10.1111/j.1365-313X.2005.02632.x}, pmid = {16460507}, issn = {0960-7412}, mesh = {Amino Acid Sequence ; Base Sequence ; Coproporphyrinogen Oxidase/*genetics ; *Evolution, Molecular ; Gene Duplication ; Gene Expression ; *Genes, Plant ; Green Fluorescent Proteins ; Mitochondria/enzymology ; Molecular Sequence Data ; Mutagenesis, Insertional ; Porphyrins/metabolism ; Protein Transport ; Zea mays/enzymology/*genetics ; }, abstract = {The divergence of sequence and expression pattern of duplicated genes provides a means for genetic innovation to occur without sacrificing an essential function. The cpx1 and cpx2 genes of maize are a singular example of duplicated genes that have diverged by deletion and creation of protein targeting information. The cpx genes encode coproporphyrinogen III oxidase ('coprogen oxidase'), which catalyzes a step in the synthesis of chlorophyll and heme. In plants, this enzyme has been found exclusively in the plastids. The cpx1 and cpx2 genes encode almost identical, catalytically active enzymes with distinctive N-terminal peptide sequences. The cpx1 gene encodes the expected plastid transit peptide, but this region is deleted from the cpx2 gene. While the 5' regions of both messenger RNAs are highly similar, the cpx2 gene has an open-reading frame that could encode a new targeting signal. GFP fused with CPX1 localized to the plastids. In contrast, the GFP fusion with CPX2 did not target plastids and appeared to localize to mitochondria. Both cpx genes are expressed ubiquitously but, based on mutant phenotype, they seem to have discrete biological roles. Seedlings homozygous for a null mutation in the cpx1 gene completely lack chlorophyll and develop necrotic lesions in the light. However, the mutant seedlings and callus cultures will grow in tissue culture in the dark, implying that they retain a capacity to produce heme. We discuss models for the evolution of the cpx genes and possible roles of mitochondrion-localized coprogen oxidase activity in maize.}, }
@article {pmid16452484, year = {2006}, author = {Atteia, A and van Lis, R and Gelius-Dietrich, G and Adrait, A and Garin, J and Joyard, J and Rolland, N and Martin, W}, title = {Pyruvate formate-lyase and a novel route of eukaryotic ATP synthesis in Chlamydomonas mitochondria.}, journal = {The Journal of biological chemistry}, volume = {281}, number = {15}, pages = {9909-9918}, doi = {10.1074/jbc.M507862200}, pmid = {16452484}, issn = {0021-9258}, mesh = {Acetylesterase/metabolism ; Acetyltransferases/*physiology ; Adenosine Triphosphate/*chemistry ; Amino Acid Sequence ; Animals ; Chlamydomonas reinhardtii/*metabolism ; Chloroplasts/metabolism ; DNA, Complementary/metabolism ; Expressed Sequence Tags ; Gene Library ; Immunoblotting ; Mass Spectrometry ; Mitochondria/*metabolism ; Models, Biological ; Models, Chemical ; Molecular Sequence Data ; Peptides/chemistry ; Phylogeny ; Proteomics/methods ; Pyruvate Dehydrogenase Complex/chemistry ; Pyruvate Synthase/metabolism ; RNA/chemistry/metabolism ; RNA, Messenger/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Pyruvate formate-lyase (PFL) catalyzes the non-oxidative conversion of pyruvate to formate and acetyl-CoA. PFL and its activating enzyme (PFL-AE) are common among strict anaerobic and microaerophilic prokaryotes but are very rare among eukaryotes. In a proteome survey of isolated Chlamydomonas reinhardtii mitochondria, we found several PFL-specific peptides leading to the identification of cDNAs for PFL and PFL-AE, establishing the existence of a PFL system in this photosynthetic algae. Anaerobiosis and darkness led to increased PFL transcripts but had little effect on protein levels, as determined with antiserum raised against C. reinhardtii PFL. Protein blots revealed the occurrence of PFL in both chloroplast and mitochondria purified from aerobically grown cells. Mass spectrometry sequencing of C. reinhardtii mitochondrial proteins, furthermore, identified peptides for phosphotransacetylase and acetate kinase. The phosphotransacetylase-acetate kinase pathway is a common route of ATP synthesis or acetate assimilation among prokaryotes but is novel among eukaryotes. In addition to PFL and pyruvate dehydrogenase, the algae also expresses pyruvate:ferredoxin oxidoreductase and bifunctional aldehyde/alcohol dehydrogenase. Among eukaryotes, the oxygen producer C. reinhardtii has the broadest repertoire of pyruvate-, ethanol-, and acetate-metabolizing enzymes described to date, many of which were previously viewed as specific to anaerobic eukaryotic lineages.}, }
@article {pmid16452116, year = {2006}, author = {Schlüter, A and Fourcade, S and Ripp, R and Mandel, JL and Poch, O and Pujol, A}, title = {The evolutionary origin of peroxisomes: an ER-peroxisome connection.}, journal = {Molecular biology and evolution}, volume = {23}, number = {4}, pages = {838-845}, doi = {10.1093/molbev/msj103}, pmid = {16452116}, issn = {0737-4038}, mesh = {Animals ; *Biological Evolution ; Endoplasmic Reticulum/enzymology/*genetics ; Eukaryota/enzymology/genetics ; Fungi/enzymology/genetics ; Genetic Markers ; Humans ; Peroxisomes/enzymology/*genetics ; Phylogeny ; *Proteome ; }, abstract = {The peroxisome is an essential eukaryotic organelle, crucial for lipid metabolism and free radical detoxification, development, differentiation, and morphogenesis from yeasts to humans. Loss of peroxisomes invariably leads to fatal peroxisome biogenesis disorders in man. The evolutionary origin of peroxisomes remains unsolved; proposals for either a symbiogenetic or cellular membrane invagination event are unconclusive. To address this question, we have probed with a peroxisomal proteome, an "ensemble" of 19 representative eukaryotic complete genomes. Molecular phylogenetic and sequence comparison tools allowed us to identify four proteins as peroxisomal markers for unequivocal in silico peroxisome detection. We have then detected the Apicomplexa phylum as the first group of organisms devoid of peroxisomes, in the presence of mitochondria. Finally, we deliver evidence against a prokaryotic ancestor of peroxisomes: (1) the peroxisomal membrane is composed of purely eukaryotic bricks and is thus useful to trace the eukaryotes in their evolutionary paths and (2) the peroxisomal matrix protein import system shares mechanistic similarities with the endoplasmic reticulum/proteasome degradation process, indicating a common evolutionary history.}, }
@article {pmid16449389, year = {2006}, author = {Zagorski, N}, title = {Profile of Alan M. Lambowitz.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {103}, number = {6}, pages = {1669-1671}, pmid = {16449389}, issn = {0027-8424}, mesh = {Evolution, Molecular ; History, 20th Century ; History, 21st Century ; Humans ; Microbiology/history ; Mitochondria/*genetics/*physiology ; Mycology/history ; United States ; }, }
@article {pmid16441579, year = {2006}, author = {Barth, D and Krenek, S and Fokin, SI and Berendonk, TU}, title = {Intraspecific genetic variation in Paramecium revealed by mitochondrial cytochrome C oxidase I sequences.}, journal = {The Journal of eukaryotic microbiology}, volume = {53}, number = {1}, pages = {20-25}, doi = {10.1111/j.1550-7408.2005.00068.x}, pmid = {16441579}, issn = {1066-5234}, mesh = {Animals ; DNA Primers ; DNA, Mitochondrial/analysis/genetics ; DNA, Ribosomal Spacer/analysis ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Mitochondria/*enzymology ; Molecular Sequence Data ; Paramecium/*classification/enzymology/*genetics ; Paramecium caudatum/classification/enzymology/genetics ; RNA, Ribosomal, 5.8S/genetics ; *Sequence Analysis, DNA ; }, abstract = {Studies of intraspecific genetic diversity of ciliates, such as population genetics and biogeography, are particularly hampered by the lack of suitable DNA markers. For example, sequences of the non-coding ribosomal internal transcribed spacer (ITS) regions are often too conserved for intraspecific analyses. We have therefore identified primers for the mitochondrial cytochrome c oxidase I (COI) gene and applied them for intraspecific investigations in Paramecium caudatum and Paramecium multimicronucleatum. Furthermore, we obtained sequences of the ITS regions from the same strains and carried out comparative sequence analyses of both data sets. The mitochondrial sequences revealed substantially higher variation in both Paramecium species, with intraspecific divergences up to 7% in P. caudatum and 9.5% in P. multimicronucleatum. Moreover, an initial survey of the population structure discovered different mitochondrial haplotypes of P. caudatum in one pond, thereby demonstrating the potential of this genetic marker for population genetic analyses. Our primers successfully amplified the COI gene of other Paramecium. This is the first report of intraspecific variation in free-living protozoans based on mitochondrial sequence data. Our results show that the high variation in mitochondrial DNA makes it a suitable marker for intraspecific and population genetic studies.}, }
@article {pmid16438643, year = {2006}, author = {López, S and Negredo, E and Garrabou, G and Puig, J and Ruiz, L and Sanjurjo, E and Ramos, X and Infante, AB and Casademont, J and Cardellach, F and Clotet, B and Miró, O}, title = {Longitudinal study on mitochondrial effects of didanosine-tenofovir combination.}, journal = {AIDS research and human retroviruses}, volume = {22}, number = {1}, pages = {33-39}, doi = {10.1089/aid.2006.22.33}, pmid = {16438643}, issn = {0889-2229}, mesh = {Adenine/*analogs &amp; derivatives/pharmacology/therapeutic use ; Anti-HIV Agents/pharmacology/*therapeutic use ; *Antiretroviral Therapy, Highly Active ; DNA, Mitochondrial/blood/*drug effects ; Didanosine/pharmacology/*therapeutic use ; Drug Therapy, Combination ; Electron Transport Complex IV/drug effects ; HIV Infections/*drug therapy/physiopathology ; HIV-1/immunology ; Humans ; Longitudinal Studies ; Organophosphonates/pharmacology/*therapeutic use ; Oxidative Phosphorylation/drug effects ; Prospective Studies ; Retrospective Studies ; Tenofovir ; }, abstract = {Tenofovir disoproxil fumarate (TDF) has been reported to be free of adverse effects on mitochondria. We evaluate the effects of the introduction of TDF in a didanosine (ddI)-based highly active antiretroviral therapy (HAART) on mitochondrial DNA (mtDNA) content, mitochondrial mass (MM), and cytochrome c oxidase (COX) activity of the oxidative phosphorylation (OXPHOS) system over a 12-month period. Forty-four asymptomatic HIV patients with undetectable viral load receiving a ddI-based HAART were recruited and switched to ddI plus TDF (ddI + TDF) and nevirapine (n = 22) or maintained with the same baseline ddIbased HAART scheme (n = 22). Peripheral blood mononuclear cells were obtained at 0, 6, and 12 months. COX activity and MM were determined by spectrophotometry and the mtDNA content by quantitative realtime PCR. The mtDNA content showed a progressive decrease over the 12-month period of the study for the two groups with respect to baseline, with such a decrease statistically significant only in the ddI + TDF group (55% decrease, p < 0.001). In addition, the decrease of mtDNA content over time was statistically different between both groups (p < 0.001). Consistently, MM and COX activity decreased significantly at 12 months with respect to baseline only in the ddI < TDF group (28% decrease for MM, p < 0.05; 47% decrease for COX activity, p < 0.001). We conclude that switching to a HAART regimen containing ddI + TDF is associated with evolutive mitochondrial damage expressed as mtDNA depletion, loss of MM, and decrease in COX efficiency. The particular relevance of either ddI, TDF, or any interaction between them in such a mitochondrial dysfunction remains to be established.}, }
@article {pmid16436509, year = {2006}, author = {Li, W and Sun, L and Liang, Q and Wang, J and Mo, W and Zhou, B}, title = {Yeast AMID homologue Ndi1p displays respiration-restricted apoptotic activity and is involved in chronological aging.}, journal = {Molecular biology of the cell}, volume = {17}, number = {4}, pages = {1802-1811}, pmid = {16436509}, issn = {1059-1524}, mesh = {*Apoptosis ; Electron Transport ; Electron Transport Complex I ; Gene Deletion ; Mitochondria/*metabolism ; NADH Dehydrogenase/classification/genetics/*metabolism ; Phylogeny ; Reactive Oxygen Species/*metabolism ; Saccharomyces cerevisiae/enzymology/*growth &amp; development/ultrastructure ; Saccharomyces cerevisiae Proteins/classification/genetics/*metabolism ; Superoxide Dismutase/genetics ; Time Factors ; Transcriptional Activation ; }, abstract = {Apoptosis-inducing factor (AIF) and AIF-homologous mitochondrion-associated inducer of death (AMID) are both mitochondrial flavoproteins that trigger caspase-independent apoptosis. Phylogenetic analysis suggests that these two proteins evolutionarily diverge back from their common prokaryote ancestor. Compared with AIF, the proapoptotic nature of AMID and its mode of action are much less clarified. Here, we show that overexpression of yeast AMID homologue internal NADH dehydrogenase (NDI1), but not external NADH dehydrogenase (NDE1), can cause apoptosis-like cell death, and this effect can be repressed by increased respiration on glucose-limited media. This result indicates that the regulatory network of energy metabolism, in particular the cross-talk between mitochondria and the rest of the cell, is involved in Ndi1p-induced yeast cell apoptosis. The apoptotic effect of NDI1 overexpression is associated with increased production of reactive oxygen species (ROS) in mitochondria. In addition, NDI1 overexpression in sod2 background causes cell lethality in both fermentable and semifermentable media. Interruption of certain components in the electron transport chain can suppress the growth inhibition from Ndi1p overexpression. We finally show that disruption of NDI1 or NDE1 decreases ROS production and elongates the chronological life span of yeast, accompanied by the loss of survival fitness. Implication of these findings for Ndi1p-induced apoptosis is discussed.}, }
@article {pmid16433928, year = {2006}, author = {Catalano, D and Licciulli, F and Turi, A and Grillo, G and Saccone, C and D'Elia, D}, title = {MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa.}, journal = {BMC bioinformatics}, volume = {7}, number = {}, pages = {36}, pmid = {16433928}, issn = {1471-2105}, mesh = {Animals ; Anopheles/*genetics ; Cell Nucleus/*metabolism ; Chromosome Mapping ; Cluster Analysis ; Computational Biology/methods ; *DNA, Mitochondrial ; Databases, Factual ; Databases, Genetic ; Databases, Nucleic Acid ; Databases, Protein ; Drosophila/*genetics ; Drosophila melanogaster/*genetics ; Evolution, Molecular ; Exons ; Genome ; Internet ; Introns ; Mitochondria/*metabolism ; Mitochondrial Proteins ; Models, Biological ; Protein Sorting Signals ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Mitochondria are sub-cellular organelles that have a central role in energy production and in other metabolic pathways of all eukaryotic respiring cells. In the last few years, with more and more genomes being sequenced, a huge amount of data has been generated providing an unprecedented opportunity to use the comparative analysis approach in studies of evolution and functional genomics with the aim of shedding light on molecular mechanisms regulating mitochondrial biogenesis and metabolism. In this context, the problem of the optimal extraction of representative datasets of genomic and proteomic data assumes a crucial importance. Specialised resources for nuclear-encoded mitochondria-related proteins already exist; however, no mitochondrial database is currently available with the same features of MitoRes, which is an update of the MitoNuc database extensively modified in its structure, data sources and graphical interface. It contains data on nuclear-encoded mitochondria-related products for any metazoan species for which this type of data is available and also provides comprehensive sequence datasets (gene, transcript and protein) as well as useful tools for their extraction and export.<br><br>DESCRIPTION: MitoRes http://www2.ba.itb.cnr.it/MitoRes/ consolidates information from publicly external sources and automatically annotates them into a relational database. Additionally, it also clusters proteins on the basis of their sequence similarity and interconnects them with genomic data. The search engine and sequence management tools allow the query/retrieval of the database content and the extraction and export of sequences (gene, transcript, protein) and related sub-sequences (intron, exon, UTR, CDS, signal peptide and gene flanking regions) ready to be used for in silico analysis.<br><br>CONCLUSION: The tool we describe here has been developed to support lab scientists and bioinformaticians alike in the characterization of molecular features and evolution of mitochondrial targeting sequences. The way it provides for the retrieval and extraction of sequences allows the user to overcome the obstacles encountered in the integrative use of different bioinformatic resources and the completeness of the sequence collection allows intra- and interspecies comparison at different biological levels (gene, transcript and protein).}, }
@article {pmid16430924, year = {2006}, author = {Seligmann, H and Krishnan, NM and Rao, BJ}, title = {Possible multiple origins of replication in primate mitochondria: Alternative role of tRNA sequences.}, journal = {Journal of theoretical biology}, volume = {241}, number = {2}, pages = {321-332}, doi = {10.1016/j.jtbi.2005.11.035}, pmid = {16430924}, issn = {0022-5193}, mesh = {Animals ; Computational Biology ; DNA Replication/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Mitochondria/*genetics ; Models, Genetic ; Multigene Family/genetics ; Mutation ; Primates/*genetics ; RNA, Transfer/*genetics ; Species Specificity ; }, abstract = {DNA replication in vertebrate mitochondria is usually directional, leaving different portions of the genome single-stranded for different periods of time. During this time, mutations resulting from deaminations of cytosines to thymines and adenines to guanines accumulate on the heavy strand. Therefore, T/C and G/A ratios increase along mitochondrial genomes, proportionally to the time spent single-stranded during replication. Such trends exist at third codon positions for base ratios averaged across genes in individual genomes as well as for gene-specific and site-specific substitution frequencies estimated using phylogenetic methods. We use multiple regressions to test for the potential functioning of all 12 tRNA clusters in 19 primate mitochondrial genomes as alternative origins of light strand replication (OL). We provide a general algorithm for calculating time spent single stranded by a given site for any possible locations of the site and OL. For codon positions 1, 2, and 3, respectively, 23%, 9% and 35% of tRNA gene clusters have significant (p < 0.05) deamination gradients originating from them. The strength of the deamination gradient originating from tRNA gene clusters varies among species, and for five clusters, correlates with the tendency of tRNA genes in each of these clusters to form secondary structures that resemble the OL's structure. This is notably true for all codon positions for tRNA-Lys, which in absence of nuclear regulation, forms secondary structures resembling the hairpin structure of OL. For two tRNA gene clusters, correlations were statistically significant, but opposite to the direction expected by the known unidirectional replication, putatively compatible with bi-directional replication. Few substitutions in tRNA sequences can be neutral at the level of cloverleaf structure and function, yet significantly alter capacities to form OL-like structures, causing sudden evolution of genome-wide nucleotide contents.}, }
@article {pmid16429263, year = {2006}, author = {Lunde, C and Baumann, U and Shirley, NJ and Drew, DP and Fincher, GB}, title = {Gene structure and expression pattern analysis of three monodehydroascorbate reductase (Mdhar) genes in Physcomitrella patens: implications for the evolution of the MDHAR family in plants.}, journal = {Plant molecular biology}, volume = {60}, number = {2}, pages = {259-275}, pmid = {16429263}, issn = {0167-4412}, mesh = {Amino Acid Sequence ; Base Sequence ; Bryopsida/enzymology/*genetics ; DNA, Plant ; *Evolution, Molecular ; *Gene Expression Regulation, Enzymologic ; *Gene Expression Regulation, Plant ; Molecular Sequence Data ; NADH, NADPH Oxidoreductases/chemistry/*genetics ; Phylogeny ; Promoter Regions, Genetic ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {The ascorbate-glutathione pathway plays a major role in the detoxification of reactive oxygen species (ROS) in vascular plants. One of the key enzymes in this pathway is monodehydroascorbate reductase (MDHAR), a FAD enzyme that catalyses the reduction of the monodehydroascorbate radical. To elucidate the evolution and functional role of MDHAR we identified and characterised MDHARs from the moss Physcomitrella patens. Expressed sequence tag (EST) databases containing approximately 100.000 ESTs from Physcomitrella were searched and three isoforms of monodehydroascorbate reductase (PpMDHAR1, PpMDHAR2 and PpMDHAR3) were identified. In vascular plants MDHAR is found in the cytosol, chloroplast, mitochondria and peroxisome. Surprisingly, all three PpMDHARs resembled the cytosolic isoforms from vascular plants lacking the NH(2)-terminal or COOH-terminal extension found in organelle targeted MDHARs. The number and position of introns was also conserved between PpMDHARs and cytosolic MDHARs from vascular plants. Phylogenetic analysis revealed that cytosolic MDHARs are monophyletic in origin and the ancestral gene evolved before the divergence of bryophytes more than 400 million years ago. Transcript analyses showed that expression of PpMdhar1 and PpMdhar3 was increased up to 5-fold under salt stress, osmotic stress or upon exposure to abscisic acid. In contrast, PpMdhar transcription levels were unchanged upon chilling, UV-B exposure or oxidative stress. The conservation of cytosolic MDHAR in the land-plant lineage and the transcriptional upregulation under water deficiency suggest that the evolution of cytosolic MDHAR played an essential role in stress protection for land plants when they inhabited the dry terrestrial environment.}, }
@article {pmid16416317, year = {2006}, author = {Igamberdiev, AU and Shen, T and Gardeström, P}, title = {Function of mitochondria during the transition of barley protoplasts from low light to high light.}, journal = {Planta}, volume = {224}, number = {1}, pages = {196-204}, pmid = {16416317}, issn = {0032-0935}, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Carbon Dioxide/metabolism ; Electron Transport/physiology ; Hordeum/cytology/*metabolism ; *Light ; Malate Dehydrogenase (NADP+)/metabolism ; Mitochondria/drug effects/*metabolism ; NADP/metabolism ; Oligomycins/pharmacology ; Oxidative Phosphorylation ; Oxygen/metabolism ; Photosynthesis/physiology ; Plant Leaves/cytology/metabolism/physiology ; Protoplasts/drug effects/*metabolism/ultrastructure ; Ribulosephosphates/metabolism ; }, abstract = {Mitochondrial contribution to photosynthetic metabolism during the transition from low light (25-100 micromol quanta m(-2) s(-1), limiting photosynthesis) to high light (500 micromol quanta m(-2) s(-1), saturating photosynthesis) was investigated in protoplasts from barley (Hordeum vulgare) leaves. After the light shift, photosynthetic oxygen evolution rate increased rapidly during the first 30-40 s and then declined up to 60-70 s after which the rate increased to a new steady-state after 80-110 s. Rapid fractionation of protoplasts was used to follow changes in sub-cellular distribution of key metabolites during the light shift and the activation state of chloroplastic NADP-dependent malate dehydrogenase (EC 1.1.1.82) was measured. Although oligomycin (an inhibitor of the mitochondrial ATP synthase) affected the metabolite content of protoplasts following the light shift, the first oxygen burst was not affected. However, the transition to the new steady-state was delayed. Rotenone (an inhibitor of mitochondrial complex I) had similar, but less pronounced effect as oligomycin. From the analysis of metabolite content and sub-cellular distribution we suggest that the decrease in oxygen evolution following the first oxygen burst is due to phosphate limitation in the chloroplast stroma. For the recovery the control protoplasts can utilize ATP supplied by mitochondrial oxidative phosphorylation to quickly overcome the limitation in stromal phosphate and to increase the content of Calvin cycle metabolites. The oligomycin-treated protoplasts were deficient in cytosolic ATP and thereby unable to support Calvin cycle operation. This resulted in a delayed capacity to adjust to a sudden increase in light intensity.}, }
@article {pmid16410965, year = {2005}, author = {Giordano, R and Cortez, JC and Paulk, S and Stevens, L}, title = {Genetic diversity of Triatoma infestans (Hemiptera: Reduviidae) in Chuquisaca, Bolivia based on the mitochondrial cytochrome b gene.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {100}, number = {7}, pages = {753-760}, doi = {10.1590/s0074-02762005000700014}, pmid = {16410965}, issn = {0074-0276}, mesh = {Animals ; Bolivia ; Cytochromes b/analysis/*genetics ; DNA, Protozoan/genetics ; *Genetic Variation ; Haplotypes/*genetics ; Mitochondria/*chemistry ; Phylogeny ; Sequence Analysis, DNA ; Triatoma/chemistry/*genetics ; }, abstract = {Partial cytochrome b DNA sequences for 62 Triatoma infestans were analyzed to determine the degree of genetic variation present in populations of this insect in the northwest region of Chuquisaca, Bolivia. A total of seven haplotypes were detected in the localities sampled. The phylogenetic relationship and population genetic structure of the haplotypes found in this region, indicate that there is greater variation in this relatively small region of Bolivia than what has been previously reported by studies using the same gene fragment, for more distant geographic areas of this country. In addition, a comparison of rural and peri-urban localities, indicate that there is no difference in the genetic variation of T. infestans between these two environments.}, }
@article {pmid16406301, year = {2006}, author = {Barbrook, AC and Howe, CJ and Purton, S}, title = {Why are plastid genomes retained in non-photosynthetic organisms?.}, journal = {Trends in plant science}, volume = {11}, number = {2}, pages = {101-108}, doi = {10.1016/j.tplants.2005.12.004}, pmid = {16406301}, issn = {1360-1385}, mesh = {Animals ; Apicomplexa/genetics/metabolism ; Genes, Plant ; Genes, rRNA ; *Genome ; Heme/biosynthesis ; Mitochondria/metabolism ; *Photosynthesis/genetics ; Plastids/*genetics ; Protein Biosynthesis ; RNA, Transfer/physiology ; RNA, Transfer, Glu/physiology ; RNA, Transfer, Met/physiology ; }, abstract = {The evolution of the plastid from a photosynthetic bacterial endosymbiont involved a dramatic reduction in the complexity of the plastid genome, with many genes either discarded or transferred to the nucleus of the eukaryotic host. However, this evolutionary process has not gone to completion and a subset of genes remains in all plastids examined to date. The various hypotheses put forward to explain the retention of the plastid genome have tended to focus on the need for photosynthetic organisms to retain a genetic system in the chloroplast, and they fail to explain why heterotrophic plants and algae, and the apicomplexan parasites all retain a genome in their non-photosynthetic plastids. Here we consider two additional explanations: the 'essential tRNAs' hypothesis and the 'transfer-window' hypothesis.}, }
@article {pmid16404737, year = {2006}, author = {Blier, PU and Breton, S and Desrosiers, V and Lemieux, H}, title = {Functional conservatism in mitochondrial evolution: insight from hybridization of arctic and brook charrs.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {306}, number = {5}, pages = {425-432}, doi = {10.1002/jez.b.21089}, pmid = {16404737}, issn = {1552-5007}, mesh = {*Adaptation, Physiological ; Animals ; Arctic Regions ; *Biological Evolution ; Chimera/*genetics ; DNA, Mitochondrial/*physiology ; Electron Transport Complex I/metabolism ; Electron Transport Complex IV/metabolism ; Enzyme Stability ; Female ; Male ; Mitochondria/enzymology/*genetics ; Mitochondrial Membranes/enzymology ; Muscle Fibers, Fast-Twitch/enzymology ; Muscle, Skeletal/enzymology ; Temperature ; Trout/classification/*genetics/growth &amp; development ; }, abstract = {To assess the potential adaptive value of mtDNA, we evaluated functional properties and thermal sensitivity of key mitochondrial enzymes in two species that have originally evolved in different thermal environments (arctic charr, Salvelinus alpinus, and brook charr, S. fontinalis), as well as in their hybrids. We measured the activity of two enzymes of the electron transport system (cytochrome c oxidase and NADH-ubiquinone oxidoreductase), one enzyme of the mitochondrial matrix (citrate synthase), and one enzyme of the anaerobic glycolysis (lactate dehydrogenase) in the red muscle at three temperatures (6 degrees C, 12 degrees C and 18 degrees C). Surprisingly, the species presented no significant differences in enzyme activity, thermal sensitivity or thermostability of key metabolic enzymes even though they evolved in different thermal environments and present important differences in amino acid sequences. It seems that amino acid substitutions between those species have minor impact on the functional properties of mitochondrial enzymes studied. The thermal sensitivity results (Q(10)) obtained for inner-membrane mitochondrial enzymes differed somewhat from those of mitochondrial matrix or cytosolic enzymes. This result indicates the modulation of thermal sensitivity of all mitochondrial inner-membrane processes by a common parameter, which could be the structural and functional properties of membrane phospholipids.}, }
@article {pmid16400175, year = {2006}, author = {Oli, MW and Cotlin, LF and Shiflett, AM and Hajduk, SL}, title = {Serum resistance-associated protein blocks lysosomal targeting of trypanosome lytic factor in Trypanosoma brucei.}, journal = {Eukaryotic cell}, volume = {5}, number = {1}, pages = {132-139}, pmid = {16400175}, issn = {1535-9778}, support = {R01 AI039033/AI/NIAID NIH HHS/United States ; R21 AI039033/AI/NIAID NIH HHS/United States ; AI39033/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cell Nucleus/metabolism ; Genotype ; Humans ; Lipoproteins, HDL/*metabolism ; Lysosomes/*metabolism ; Membrane Glycoproteins/chemistry/genetics/*metabolism ; Mitochondria/metabolism ; Phenotype ; Protein Binding ; Protein Transport ; Protozoan Proteins/chemistry/genetics/*metabolism ; RNA, Messenger/genetics/metabolism ; Transfection ; Trypanosoma brucei brucei/*cytology/*metabolism ; }, abstract = {Trypanosoma brucei brucei is the causative agent of nagana in cattle and can infect a wide range of mammals but is unable to infect humans because it is susceptible to the innate cytotoxic activity of normal human serum. A minor subfraction of human high-density lipoprotein (HDL) containing apolipoprotein A-I (apoA-I), apolipoprotein L-I (apoL-I), and haptoglobin-related protein (Hpr) provides this innate protection against T. b. brucei infection. This HDL subfraction, called trypanosome lytic factor (TLF), kills T. b. brucei following receptor binding, endocytosis, and lysosomal localization. Trypanosoma brucei rhodesiense, which is morphologically and physiologically indistinguishable from T. b. brucei, is resistant to TLF-mediated killing and causes human African sleeping sickness. Human infectivity by T. b. rhodesiense correlates with the evolution of a resistance-associated protein (SRA) that is able to ablate TLF killing. To examine the mechanism of TLF resistance, we transfected T. b. brucei with an epitope-tagged SRA gene. Transfected T. b. brucei expressed SRA mRNA at levels comparable to those in T. b. rhodesiense and was highly resistant to TLF. In the SRA-transfected cells, intracellular trafficking of TLF was altered, with TLF being mainly localized to a subset of SRA-containing cytoplasmic vesicles but not to the lysosome. These results indicate that the cellular distribution of TLF is influenced by SRA expression and may directly determine the organism's susceptibility to TLF.}, }
@article {pmid16399892, year = {2005}, author = {Skulachev, VP and Longo, VD}, title = {Aging as a mitochondria-mediated atavistic program: can aging be switched off?.}, journal = {Annals of the New York Academy of Sciences}, volume = {1057}, number = {}, pages = {145-164}, doi = {10.1196/annals.1356.009}, pmid = {16399892}, issn = {0077-8923}, mesh = {Aging/*physiology ; Animals ; Apoptosis/*physiology ; Biological Evolution ; Hormones/metabolism ; Humans ; Mitochondria/*metabolism ; Mutation ; Reactive Oxygen Species/metabolism ; Tumor Suppressor Protein p53/metabolism ; Yeasts/physiology ; }, abstract = {Programmed death phenomena have been demonstrated on subcellular (mitoptosis), cellular (apoptosis), and supracellular (collective apoptosis) levels. There are numerous examples of suicide mechanisms at the organismal level (phenoptosis). In yeast, it was recently shown that the death of aging cells is programmed. Many of the steps of programmed cell death are shown to be common for yeast and animals, including mammals. In particular, generation of the mitochondrial reactive oxygen species (ROS) is involved in the suicide programs. Aging of higher animals is accompanied by an increase in damage induced by mitochondrial ROS. Perhaps prevention of such damage by scavenging of mitochondrial ROS might slow down or even switch off the aging programs.}, }
@article {pmid16395585, year = {2006}, author = {Dorion, S and Matton, DP and Rivoal, J}, title = {Characterization of a cytosolic nucleoside diphosphate kinase associated with cell division and growth in potato.}, journal = {Planta}, volume = {224}, number = {1}, pages = {108-124}, pmid = {16395585}, issn = {0032-0935}, mesh = {Amino Acid Sequence ; Cell Division/genetics ; Cell Enlargement ; Cells, Cultured ; DNA, Complementary/analysis ; Escherichia coli/genetics ; Kinetics ; Meristem/enzymology/growth &amp; development ; Molecular Sequence Data ; Nucleoside-Diphosphate Kinase/genetics/metabolism/*physiology ; Phylogeny ; Plant Proteins/genetics/metabolism/*physiology ; Plant Roots/cytology/enzymology/growth &amp; development ; Plant Shoots/cytology/enzymology/growth &amp; development ; Protein Isoforms/genetics/metabolism/physiology ; Sequence Alignment ; Sequence Analysis, DNA ; Solanum tuberosum/cytology/*enzymology/growth &amp; development ; Uridine Triphosphate/metabolism ; }, abstract = {A cDNA encoding Solanum chacoense cytosolic NDPK (NDPK1, EC 2.7.4.6) was isolated. The open reading frame encoded a 148 amino acid protein that shares homology with other cytosolic NDPKs including a conserved N-terminal domain. S. chacoense NDPK1 was expressed in Escherichia coli as a 6xHis-tagged protein and purified by affinity chromatography. The recombinant protein exhibited a pattern of abortive complex formation suggesting that the enzyme is strongly regulated by the NTP/NDP ratio. A polyclonal antibody generated against recombinant NDPK1 was specific for the cytosolic isoform in Solanum tuberosum as shown from immunoprecipitation experiments and immunoblot analysis of chloroplasts and mitochondria preparations. NDPK activity and NDPK1 protein were found at different levels in various vegetative and reproductive tissues. DEAE fractogel analyses of NDPK activity in root tips, leaves, tubers and cell cultures suggest that NDPK1 constitutes the bulk of extractable NDPK activity in all these organs. NDPK activity and NDPK1 protein levels raised during the exponential growth phase of potato cell cultures whereas no rise in activity or NDPK1 protein was observed when sucrose concentration in the culture was manipulated to limit growth. Activity measurements, immunoblot analysis as well as immunolocalization experiments performed on potato root tips and shoot apical buds demonstrated that NDPK1 was predominantly localized in the meristematic zones and provascular tissues of the apical regions. These data suggest that NDPK1 plays a specific role in the supply of UTP during early growth of plant meristematic and provascular tissues.}, }
@article {pmid16391670, year = {2005}, author = {Oliver, P and Balanyà, J and Ramon, MM and Picornell, A and Serra, L and Moya, A and Castro, JA}, title = {Population dynamics of the 2 major mitochondrial DNA haplotypes in experimental populations of Drosophila subobscura.}, journal = {Genome}, volume = {48}, number = {6}, pages = {1010-1018}, doi = {10.1139/g05-077}, pmid = {16391670}, issn = {0831-2796}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Drosophila/*genetics ; Female ; Genetic Drift ; *Haplotypes ; Male ; Mitochondria/genetics ; *Population Dynamics ; Selection, Genetic ; }, abstract = {The evolution of Drosophila subobscura mitochondrial DNA has been studied in experimental populations, founded with flies from a natural population from Calvià (Majorca, Balearic Islands, Spain). This population, like others founded in Europe, is characterized by the presence of 2 very common (>95%) mitochondrial haplotypes (named I and II) and rare and endemic haplotypes that appear at very low frequencies. Four experimental populations were established with flies having a heterogeneous nuclear genetic background, which was representative of the composition of the natural population. The populations were started with haplotypes I and II at an initial frequency of 50% each. After 33 generations, the 2 haplotypes coexisted. Random drift could be rejected as the only force responsible for the observed changes in haplotype frequencies. A slight but significant linear trend favouring a mtDNA (haploid) fitness effect has been detected, with a nonlinear deviation that could be due to a nuclear component. An analysis of chromosomal arrangements was made before the foundations of the cages and at generation 23. Our results indicated that the hypothesis that the maintenance of the frequencies of haplotypes I and II in natural populations could be due to their association with chromosomal arrangements remains controversial.}, }
@article {pmid16388691, year = {2006}, author = {Paramá, A and Arranz, JA and Alvarez, MF and Sanmartín, ML and Leiro, J}, title = {Ultrastructure and phylogeny of Philasterides dicentrarchi (Ciliophora, Scuticociliatia) from farmed turbot in NW Spain.}, journal = {Parasitology}, volume = {132}, number = {Pt 4}, pages = {555-564}, doi = {10.1017/S0031182005009534}, pmid = {16388691}, issn = {0031-1820}, mesh = {Animals ; Ciliophora Infections/parasitology/*veterinary ; DNA Primers/chemistry ; DNA, Protozoan/chemistry ; DNA, Ribosomal/genetics ; Fish Diseases/*parasitology ; Fisheries ; Flatfishes/*parasitology ; Microscopy, Electron, Transmission/veterinary ; Molecular Sequence Data ; Oligohymenophorea/*classification/*ultrastructure ; *Phylogeny ; Polymerase Chain Reaction/veterinary ; }, abstract = {Several species of opportunistic histophagous scuticociliates have been implicated in systemic infections of farmed fish. In turbot, scuticociliatosis is an emerging disease, and the identification of the parasite species involved is controversial. We have previously isolated Philasterides dicentrarchi from farmed turbot scuticociliatosis outbreaks in northwest Spain. In the present study, we report detailed ultrastructural studies of this parasite, and investigate phylogenetic relations with other members of the order Philasterida on the basis of sequence comparison of the small-subunit rRNA (SSUrRNA) gene. Ultrastructural study indicates the presence of dikinetids in the anterior two-thirds of the body; micronucleus closely associated with the macronucleus, though not physically connected; numerous mitochondria located below the cell cortex, parallel to the surface; numerous spherical and fusiform extrusomes located close to the plasma membrane. We consider that these characteristics are useful for diagnosis of infections by this parasite. A nested 350-bp nucleotide sequence of the SSUrRNA gene of the turbot P. dicentrachi isolate showed high identity with previously reported SSUrRNA gene sequences from 2 scuticociliates isolated from olive flounder Paralichthys olivaceus in Korea, namely P. dicentrarchi (98%) and Miamiensis avidus (99%); conversely, our P. dicentrarchi sequence showed low identity (86%) with that of Uronema marinum, a scuticociliate that has also been implicated in scuticociliatosis outbreaks in turbot in Europe and olive flounder in Asia. Phylogenetic tree construction on the basis of the SSUrRNA gene sequences, using the neighbour-joining method, confirm that the different P. dicentrarchi isolates and M. avidus are closely related and a possible synonymy between both ciliates species should be considered.}, }
@article {pmid16382169, year = {2005}, author = {Marotta, R and Melone, G and Bright, M and Ferraguti, M}, title = {Spermatozoa and sperm aggregates in the vestimentiferan Lamellibrachia luymesi compared with those of Riftia pachyptila (Polychaeta: Siboglinidae: Vestimentifera).}, journal = {The Biological bulletin}, volume = {209}, number = {3}, pages = {215-226}, doi = {10.2307/3593111}, pmid = {16382169}, issn = {0006-3185}, mesh = {Acrosome/ultrastructure ; Anatomy, Comparative ; Animals ; Annelida/*ultrastructure ; Cell Nucleus/ultrastructure ; Centrioles/ultrastructure ; Flagella/ultrastructure ; Male ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Microscopy, Fluorescence ; Mitochondria/ultrastructure ; Phylogeny ; Spermatozoa/ultrastructure ; }, abstract = {The spermatozoa and the sperm bundles of the vestimentiferans Riftia pachyptila and Lamellibrachia luymesi (Annelida: Siboglinidae) were studied using several microscopical techniques (transmission and scanning electron microscopy, and confocal microscopy) and compared with some other annelid sperm. The spermatozoa and sperm bundles of both species show a similar structure, but they differ in the dimensions of the components of individual cells and in the number of spermatozoa forming each sperm bundle. The spermatozoa of R. pachyptila and L. luymesi are filiform cells composed, in sequence, by an acrosome in the form of a thread-like helical vesicle, an elongated coiled nucleus surrounded by two helical mitochondria, and a long flagellum. In the spermatozoa of both species, the apical portion of the nucleus is completely devoid of chromatin and is delimited by a thickened nuclear envelope with a fibrillar appearance. Both species have sperm bundles that resemble buds, having a calyx-like portion formed by the helical heads, and a stalk-like portion formed by the tightly packed flagella. A parsimony analysis based on spermatozoal characters showed monophyly of the Siboglinidae and the Vestimentifera. We propose a new set of autapomorphies characterizing vestimentiferan spermatozoa. Our analysis suggests that spermatozoal characters are useful to the understanding of the phylogeny of the group.}, }
@article {pmid16381962, year = {2006}, author = {O'Brien, EA and Zhang, Y and Yang, L and Wang, E and Marie, V and Lang, BF and Burger, G}, title = {GOBASE--a database of organelle and bacterial genome information.}, journal = {Nucleic acids research}, volume = {34}, number = {Database issue}, pages = {D697-9}, pmid = {16381962}, issn = {1362-4962}, mesh = {Chloroplasts/*genetics ; *Databases, Genetic ; Evolution, Molecular ; *Genome, Bacterial ; Genomics ; Internet ; Mitochondria/*genetics ; Rickettsia prowazekii/genetics ; User-Computer Interface ; }, abstract = {The organelle genome database GOBASE is now in its twelfth release, and includes 350,000 mitochondrial sequences and 118,000 chloroplast sequences, roughly a 3-fold expansion since previously documented. GOBASE also includes a fully reannotated genome sequence of Rickettsia prowazekii, one of the closest bacterial relatives of mitochondria, and will shortly expand to contain more data from bacteria from which organelles originated. All these sequences are now accessible through a single unified interface. Enhancements to the functionality of GOBASE include addition of pages for RNA structures and a page compiling data about the taxonomic distribution of organelle-encoded genes; incorporation of Gene Ontology terms; addition of features deduced from incomplete annotations to sequences in GenBank; marking of type examples in cases where single genes in single species are oversampled within GenBank; and addition of graphics illustrating gene structure and the position of neighbouring genes on a sequence. The database has been reimplemented in PostgreSQL to facilitate development and maintenance, and structural modifications have been made to speed up queries, particularly those related to taxonomy. The GOBASE database can be queried at http://gobase.bcm.umontreal.ca/ and inquiries should be directed to gobase@bch.umontreal.ca.}, }
@article {pmid16380372, year = {2006}, author = {Guo, K and Lukacik, P and Papagrigoriou, E and Meier, M and Lee, WH and Adamski, J and Oppermann, U}, title = {Characterization of human DHRS6, an orphan short chain dehydrogenase/reductase enzyme: a novel, cytosolic type 2 R-beta-hydroxybutyrate dehydrogenase.}, journal = {The Journal of biological chemistry}, volume = {281}, number = {15}, pages = {10291-10297}, doi = {10.1074/jbc.M511346200}, pmid = {16380372}, issn = {0021-9258}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Arginine/chemistry ; Binding Sites ; Cloning, Molecular ; Crystallography, X-Ray ; Cytosol/*enzymology/metabolism ; Dose-Response Relationship, Drug ; Exons ; Green Fluorescent Proteins/metabolism ; HeLa Cells ; Humans ; Hydrogen-Ion Concentration ; Hydroxybutyrate Dehydrogenase/*chemistry/genetics ; Kinetics ; Lipids/chemistry ; Mitochondria/metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxidoreductases/*chemistry ; Phylogeny ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Substrate Specificity ; Sulfates/chemistry ; }, abstract = {Human DHRS6 is a previously uncharacterized member of the short chain dehydrogenases/reductase family and displays significant homologies to bacterial hydroxybutyrate dehydrogenases. Substrate screening reveals sole NAD(+)-dependent conversion of (R)-hydroxybutyrate to acetoacetate with K(m) values of about 10 mm, consistent with plasma levels of circulating ketone bodies in situations of starvation or ketoacidosis. The structure of human DHRS6 was determined at a resolution of 1.8 A in complex with NAD(H) and reveals a tetrameric organization with a short chain dehydrogenases/reductase-typical folding pattern. A highly conserved triad of Arg residues ("triple R" motif consisting of Arg(144), Arg(188), and Arg(205)) was found to bind a sulfate molecule at the active site. Docking analysis of R-beta-hydroxybutyrate into the active site reveals an experimentally consistent model of substrate carboxylate binding and catalytically competent orientation. GFP reporter gene analysis reveals a cytosolic localization upon transfection into mammalian cells. These data establish DHRS6 as a novel, cytosolic type 2 (R)-hydroxybutyrate dehydrogenase, distinct from its well characterized mitochondrial type 1 counterpart. The properties determined for DHRS6 suggest a possible physiological role in cytosolic ketone body utilization, either as a secondary system for energy supply in starvation or to generate precursors for lipid and sterol synthesis.}, }
@article {pmid16377245, year = {2006}, author = {Hu, M and Gasser, RB}, title = {Mitochondrial genomes of parasitic nematodes--progress and perspectives.}, journal = {Trends in parasitology}, volume = {22}, number = {2}, pages = {78-84}, doi = {10.1016/j.pt.2005.12.003}, pmid = {16377245}, issn = {1471-4922}, mesh = {Animals ; Biological Evolution ; DNA, Helminth/genetics ; Databases, Nucleic Acid ; Genetics, Population/methods ; Genome, Helminth/*genetics ; Genomics/*trends ; Mitochondria/*genetics ; Nematoda/classification/*genetics ; Phylogeny ; }, abstract = {Mitochondria are subcellular organelles in which oxidative phosphorylation and other important biochemical functions take place within the cell. Within these organelles is a mitochondrial (mt) genome, which is distinct from, but cooperates with, the nuclear genome of the cell. Studying mt genomes has implications for various fundamental areas, including mt biochemistry, physiology and molecular biology. Importantly, the mt genome is a rich source of markers for population genetic and systematic studies. To date, more than 696 mt genomes have been sequenced for a range of metazoan organisms. However, few of these are from parasitic nematodes, despite their socioeconomic importance and the need for fundamental investigations into areas such as nematode genetics, systematics and ecology. In this article, we review knowledge and recent progress in mt genomics of parasitic nematodes, summarize applications of mt gene markers to the study of population genetics, systematics, epidemiology and evolution of key nematodes, and highlight some prospects and opportunities for future research.}, }
@article {pmid16369939, year = {2006}, author = {Blackstone, NW}, title = {Multicellular redox regulation: integrating organismal biology and redox chemistry.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {28}, number = {1}, pages = {72-77}, doi = {10.1002/bies.20337}, pmid = {16369939}, issn = {0265-9247}, mesh = {Animals ; Biological Evolution ; Humans ; *Metabolism ; Mitochondria/*metabolism ; Oxidation-Reduction ; Reactive Oxygen Species/metabolism ; }, abstract = {Early in the 20th century, Charles Manning Child attributed organismal gradients in metabolism to interactions among groups of cells. Metabolic gradients are now firmly grounded in redox chemistry, yet modern work on metabolic signaling has consistently focused on the cellular level. Multicellular redox regulation, however, may occur when redox state is determined by the behavior of a group of cells. For instance, typically an abundance of substrate will shift the redox state of mitochondria in the direction of reduction, leading to increased reactive oxygen species (ROS). These ROS, in turn, may modify the conformation and activity of proteins involved in signaling pathways, resulting in phenotypic changes. In contrast, if substrate triggers the contractions of a muscular structure comprising mitochondrion-rich cells, the resulting metabolic demand may shift the redox state in the direction of oxidation, with a corresponding decrease of ROS and different phenotypic effects. Indeed, colonial hydroids exemplify this process. Parallel examples may occur whenever mitochondria are concentrated in cells of structures that can respond to environmental perturbations with increased metabolic demand. In these circumstances, predicting the direction of metabolic signaling may require an understanding of events at the organismal level.}, }
@article {pmid16368144, year = {2006}, author = {Czömpöly, T and Olasz, K and Simon, D and Nyárády, Z and Pálinkás, L and Czirják, L and Berki, T and Németh, P}, title = {A possible new bridge between innate and adaptive immunity: Are the anti-mitochondrial citrate synthase autoantibodies components of the natural antibody network?.}, journal = {Molecular immunology}, volume = {43}, number = {11}, pages = {1761-1768}, doi = {10.1016/j.molimm.2005.11.004}, pmid = {16368144}, issn = {0161-5890}, mesh = {Adult ; Amino Acid Sequence ; Autoantibodies/*immunology ; Autoimmune Diseases/immunology ; Autoimmunity/immunology ; Case-Control Studies ; Child ; Chromatography, Affinity ; Citrate (si)-Synthase/chemistry/*immunology/*metabolism ; Cross Reactions ; Female ; Humans ; Immune Sera/immunology ; Immunity, Active/*immunology ; Immunity, Innate/*immunology ; Male ; Mitochondria/*enzymology/*immunology ; Molecular Sequence Data ; Peptide Library ; }, abstract = {Natural antibody (nAb) producing B-1 B cells are considered an intermediate stage of evolution between innate and adaptive immunity. nAbs are immunoglobulins that are produced without antigen priming. nAbs can recognize foreign targets and may serve in the first line of immune defense during an infection. Natural autoantibodies (nAAbs) present in the serum of both healthy humans and patients suffering from systemic autoimmune diseases recognize a set of evolutionarily conserved self-structures. Because of their endosymbiotic evolutionary origin, proteins compartmentalized into mitochondria represent an interesting transition from prokaryotic foreign (non-self) to essential (self) molecules. We investigated the possible overlap in recognized epitopes of innate and self-reactive nAbs and surveyed changes in physiological autoreactivity under pathological autoimmune conditions. Epitope mapping analysis of a mitochondrial inner membrane enzyme, citrate synthase (CS) (EC 2.3.3.1) by synthetic overlapping peptides and phage display libraries using sera from healthy individuals and from patients having systemic autoimmune disease revealed CS recognizing nAAbs with IgM isotype. We analyzed cross reactive epitopes on human CS, bacterial CS, and various standard autoantigens. The anti-CS nAAbs by participating in the nAb network, could function in innate defense mechanisms and at the same time recognize a target antigen (nucleosome) in a systemic autoimmune disease. Thus, at the level of recognized epitopes there is a possible new link between the innate like component and the adaptive-autoimmune arm of the humoral immune system.}, }
@article {pmid16368004, year = {2005}, author = {Parkinson, CL and Mower, JP and Qiu, YL and Shirk, AJ and Song, K and Young, ND and DePamphilis, CW and Palmer, JD}, title = {Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae.}, journal = {BMC evolutionary biology}, volume = {5}, number = {}, pages = {73}, pmid = {16368004}, issn = {1471-2148}, support = {GM-35087/GM/NIGMS NIH HHS/United States ; R01 GM070612/GM/NIGMS NIH HHS/United States ; GM-19225/GM/NIGMS NIH HHS/United States ; F32 GM017923/GM/NIGMS NIH HHS/United States ; F32 GM019225/GM/NIGMS NIH HHS/United States ; GM-17923/GM/NIGMS NIH HHS/United States ; GM-70612/GM/NIGMS NIH HHS/United States ; R01 GM035087/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Chloroplasts/genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; *Evolution, Molecular ; Genetic Variation ; Genome, Plant ; Geraniaceae/classification/*genetics ; Mitochondria/genetics ; Pelargonium/genetics ; Phylogeny ; Plantago/genetics ; Polymerase Chain Reaction ; }, abstract = {BACKGROUND: Rates of synonymous nucleotide substitutions are, in general, exceptionally low in plant mitochondrial genomes, several times lower than in chloroplast genomes, 10-20 times lower than in plant nuclear genomes, and 50-100 times lower than in many animal mitochondrial genomes. Several cases of moderate variation in mitochondrial substitution rates have been reported in plants, but these mostly involve correlated changes in chloroplast and/or nuclear substitution rates and are therefore thought to reflect whole-organism forces rather than ones impinging directly on the mitochondrial mutation rate. Only a single case of extensive, mitochondrial-specific rate changes has been described, in the angiosperm genus Plantago.<br><br>RESULTS: We explored a second potential case of highly accelerated mitochondrial sequence evolution in plants. This case was first suggested by relatively poor hybridization of mitochondrial gene probes to DNA of Pelargonium hortorum (the common geranium). We found that all eight mitochondrial genes sequenced from P. hortorum are exceptionally divergent, whereas chloroplast and nuclear divergence is unexceptional in P. hortorum. Two mitochondrial genes were sequenced from a broad range of taxa of variable relatedness to P. hortorum, and absolute rates of mitochondrial synonymous substitutions were calculated on each branch of a phylogenetic tree of these taxa. We infer one major, approximately 10-fold increase in the mitochondrial synonymous substitution rate at the base of the Pelargonium family Geraniaceae, and a subsequent approximately 10-fold rate increase early in the evolution of Pelargonium. We also infer several moderate to major rate decreases following these initial rate increases, such that the mitochondrial substitution rate has returned to normally low levels in many members of the Geraniaceae. Finally, we find unusually little RNA editing of Geraniaceae mitochondrial genes, suggesting high levels of retroprocessing in their history.<br><br>CONCLUSION: The existence of major, mitochondrial-specific changes in rates of synonymous substitutions in the Geraniaceae implies major and reversible underlying changes in the mitochondrial mutation rate in this family. Together with the recent report of a similar pattern of rate heterogeneity in Plantago, these findings indicate that the mitochondrial mutation rate is a more plastic character in plants than previously realized. Many molecular factors could be responsible for these dramatic changes in the mitochondrial mutation rate, including nuclear gene mutations affecting the fidelity and efficacy of mitochondrial DNA replication and/or repair and--consistent with the lack of RNA editing--exceptionally high levels of "mutagenic" retroprocessing. That the mitochondrial mutation rate has returned to normally low levels in many Geraniaceae raises the possibility that, akin to the ephemerality of mutator strains in bacteria, selection favors a low mutation rate in plant mitochondria.}, }
@article {pmid16367838, year = {2006}, author = {Bensch, S and Irwin, DE and Irwin, JH and Kvist, L and Akesson, S}, title = {Conflicting patterns of mitochondrial and nuclear DNA diversity in Phylloscopus warblers.}, journal = {Molecular ecology}, volume = {15}, number = {1}, pages = {161-171}, doi = {10.1111/j.1365-294X.2005.02766.x}, pmid = {16367838}, issn = {0962-1083}, mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; DNA Primers ; DNA, Mitochondrial/genetics ; *Demography ; *Evolution, Molecular ; *Genetic Variation ; *Genetics, Population ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Siberia ; Songbirds/*genetics ; Species Specificity ; Sweden ; United Kingdom ; }, abstract = {Molecular variation is often used to infer the demographic history of species, but sometimes the complexity of species history can make such inference difficult. The willow warbler, Phylloscopus trochilus, shows substantially less geographical variation than the chiffchaff, Phylloscopus collybita, both in morphology and in mitochondrial DNA (mtDNA) divergence. We therefore predicted that the willow warbler should harbour less nuclear DNA diversity than the chiffchaff. We analysed sequence data obtained from multiple samples of willow warblers and chiffchaffs for the mtDNA cytochrome b gene and four nuclear genes. We confirmed that the mtDNA diversity among willow warblers is low (pi = 0.0021). Sequence data from three nuclear genes (CHD-Z, AFLP-WW1 and MC1R) not linked to the mitochondria demonstrated unexpectedly high nucleotide diversity (pi values of 0.0172, 0.0141 and 0.0038) in the willow warbler, on average higher than the nucleotide diversity for the chiffchaff (pi values of 0.0025, 0.0017 and 0.0139). In willow warblers, Tajima's D analyses showed that the mtDNA diversity, but not the nuclear DNA diversity, has been reduced relative to the neutral expectation of molecular evolution, suggesting the action of a selective sweep affecting the maternally inherited genes. The large nuclear diversity seen within willow warblers is not compatible with processes of neutral evolution occurring in a population with a constant population size, unless the long-term effective population size has been very large (N(e) > 10(6)). We suggest that the contrasting patterns of genetic diversity in the willow warbler may reflect a more complex evolutionary history, possibly including historical demographic fluctuations or historical male-biased introgression of nuclear genes from a differentiated population of Phylloscopus warblers.}, }
@article {pmid16364493, year = {2006}, author = {Shutt, TE and Gray, MW}, title = {Bacteriophage origins of mitochondrial replication and transcription proteins.}, journal = {Trends in genetics : TIG}, volume = {22}, number = {2}, pages = {90-95}, doi = {10.1016/j.tig.2005.11.007}, pmid = {16364493}, issn = {0168-9525}, mesh = {Bacteriophage T7/*genetics ; DNA Replication ; DNA, Mitochondrial/*genetics ; DNA-Directed RNA Polymerases ; Mitochondria/*metabolism ; Replication Origin ; *Transcription, Genetic ; }, abstract = {Mounting evidence suggests that key components of the mitochondrial transcription and replication apparatus are derived from the T-odd lineage of bacteriophage rather than from an alpha-Proteobacterium, as the endosymbiont hypothesis would predict. We propose that several mitochondrial replication genes were acquired together from an ancestor of T-odd phage early in the evolution of the eukaryotic cell, at the time of the mitochondrial endosymbiosis. We further propose that at a later stage the single-subunit RNA polymerase, originally acquired for mitochondrial DNA replication, was co-opted to serve in mitochondrial transcription.}, }
@article {pmid16351843, year = {2001}, author = {Prechtl, J and Maier, UG}, title = {Zoology meets Botany: establishing intracellular organelles by endosymbiosis.}, journal = {Zoology (Jena, Germany)}, volume = {104}, number = {3-4}, pages = {284-289}, doi = {10.1078/0944-2006-00034}, pmid = {16351843}, issn = {0944-2006}, abstract = {One of the most citated characteristics of eukaryotic cells are mitochondria and in the case of phototrophic cells, the plastids. These organelles are of eubacterial origin and contain a remnant genome. Here, we present hypotheses concerning the origin of the first mitochondrium-harboring cell and show the evolution of primary, secondary and tertiary plastids. Furthermore we discuss models explaining why plastids have to maintain their own genome.}, }
@article {pmid16336009, year = {2005}, author = {Hansen, D and Dendale, P and Berger, J and Meeusen, R}, title = {Rehabilitation in cardiac patients:what do we know about training modalities?.}, journal = {Sports medicine (Auckland, N.Z.)}, volume = {35}, number = {12}, pages = {1063-1084}, pmid = {16336009}, issn = {0112-1642}, mesh = {*Cardiac Rehabilitation ; Cardiovascular Diseases/diagnosis ; Exercise Therapy/*methods ; Exercise Tolerance/*physiology ; Female ; Heart Function Tests ; Humans ; Male ; Oxygen Consumption/physiology ; Prognosis ; Recovery of Function ; Risk Assessment ; Severity of Illness Index ; }, abstract = {This article discusses the effects of training in cardiac rehabilitation and describes the influence of various training modalities on the evolution of exercise capacity in cardiac patients. Both home- and hospital-based studies are analysed separately. From the collected studies, a very heterogeneous character of the content of the rehabilitation programmes appears. Direct comparison of the effects of the training programmes on exercise capacity remains difficult. Baseline factors for predicting a better training outcome are: low exercise capacity and peripheral oxygen extraction; presence of hibernating myocardium; high myocardial perfusion; low degree of coronary vessel occlusion; working status; and improved feelings of wellbeing. The increased work capacity as a result of rehabilitation is associated with: an increased volume density of skeletal muscle mitochondria; peripheral muscular vasodilatory capacity; cardiac output and a decreased left ventricular end-diastolic pressure; depletion of muscular phosphocreatine levels; and degree of restenosis. Home- and hospital-based interventions induce comparable training effects. More research is needed concerning the training modalities in cardiac rehabilitation. There is an influence of weekly training frequency and programme duration on the training outcome. A higher training frequency and/or duration might induce greater training effects. The evolution of the anaerobic threshold is sensitive to the training intensity and inclusion of strength training, which remains to be established for maximal exercise capacity. However, insufficient information is available on the influence of training session duration on the evolution of exercise capacity.}, }
@article {pmid16333326, year = {2005}, author = {Bleackley, RC}, title = {A molecular view of cytotoxic T lymphocyte induced killing.}, journal = {Biochemistry and cell biology = Biochimie et biologie cellulaire}, volume = {83}, number = {6}, pages = {747-751}, doi = {10.1139/o05-146}, pmid = {16333326}, issn = {0829-8211}, mesh = {Animals ; Cysteine Endopeptidases/metabolism ; Cytotoxicity, Immunologic/physiology ; Granzymes ; Humans ; Mitochondria/metabolism ; Serine Endopeptidases/metabolism ; T-Lymphocytes, Cytotoxic/*physiology ; }, abstract = {Cytotoxic T lymphocytes (CTLs) search out and destroy pathogenic cells, such as those infected with viruses. The biochemistry laboratory at the University of Alberta (Edmonton, Alta.) studies the molecular mechanisms used by these effectors, and this review covers research on this topic primarily from this group. Research there began with the discovery of the granzyme genes and the realization that granzyme B (GrB) had an unusual substrate specificity. Cleavage at aspartate residues gave us the clue that caspases, key regulators of apoptosis, were important substrates. However, it is now clear that mitochondria are also important in controlling granzyme-induced apoptosis. This led to the discovery that the proapoptotic member of the Bcl2 family, Bid, is also activated by GrB. Cleaved Bid then translocates to the mitochondria, resulting in the release of antagonists of inhibitors of apoptosis proteins. The evolution of our understanding of the molecular basis of CTL killing is presented.}, }
@article {pmid16327803, year = {2006}, author = {Hayashi, M and Imanaka-Yoshida, K and Yoshida, T and Wood, M and Fearns, C and Tatake, RJ and Lee, JD}, title = {A crucial role of mitochondrial Hsp40 in preventing dilated cardiomyopathy.}, journal = {Nature medicine}, volume = {12}, number = {1}, pages = {128-132}, doi = {10.1038/nm1327}, pmid = {16327803}, issn = {1078-8956}, support = {CA079871/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Aorta/pathology ; Cardiomyopathy, Dilated/*pathology/prevention &amp; control ; Cell Line ; DNA/metabolism ; DNA Polymerase gamma ; DNA, Mitochondrial/metabolism ; DNA-Directed DNA Polymerase/*metabolism ; Electron Transport ; Electron Transport Complex IV/metabolism ; Evolution, Molecular ; Green Fluorescent Proteins/metabolism ; HSP40 Heat-Shock Proteins/*chemistry/genetics/metabolism/*physiology ; Humans ; Immunoblotting ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Mice, Transgenic ; Microscopy, Fluorescence ; Mitochondria/metabolism ; Myocytes, Cardiac/metabolism ; Protein Binding ; Protein Denaturation ; Protein Folding ; Protein Renaturation ; Protein Structure, Tertiary ; Reverse Transcriptase Polymerase Chain Reaction ; Time Factors ; Transfection ; }, abstract = {Many heat-shock proteins (Hsp) are members of evolutionarily conserved families of chaperone proteins that inhibit the aggregation of unfolded polypeptides and refold denatured proteins, thereby remedying phenotypic effects that may result from protein aggregation or protein instability. Here we report that the mitochondrial chaperone Hsp40, also known as Dnaja3 or Tid1, is differentially expressed during cardiac development and pathological hypertrophy. Mice deficient in Dnaja3 developed dilated cardiomyopathy (DCM) and died before 10 weeks of age. Progressive respiratory chain deficiency and decreased copy number of mitochondrial DNA were evident in cardiomyocytes lacking Dnaja3. Profiling of Dnaja3-interacting proteins identified the alpha-subunit of DNA polymerase gamma (Polga) as a client protein. These findings suggest that Dnaja3 is crucial for mitochondrial biogenesis, at least in part, through its chaperone activity on Polga and provide genetic evidence of the necessity for mitochondrial Hsp40 in preventing DCM.}, }
@article {pmid16325371, year = {2006}, author = {Hawthorne, SK and Goodarzi, G and Bagarova, J and Gallant, KE and Busanelli, RR and Olend, WJ and Kleene, KC}, title = {Comparative genomics of the sperm mitochondria-associated cysteine-rich protein gene.}, journal = {Genomics}, volume = {87}, number = {3}, pages = {382-391}, doi = {10.1016/j.ygeno.2005.09.010}, pmid = {16325371}, issn = {0888-7543}, mesh = {3' Untranslated Regions/genetics ; 5' Untranslated Regions/genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Northern ; Cattle ; Chromosome Mapping ; Chromosomes, Human, Pair 1/genetics ; Cricetinae ; Databases, Nucleic Acid ; Dogs ; Epithelium/metabolism ; Female ; Gene Expression Profiling ; Genomics/*methods ; Humans ; Male ; Mesocricetus ; Mice ; Molecular Sequence Data ; Peromyscus ; Pseudogenes/genetics ; RNA, Messenger/genetics/metabolism ; Rats ; Reverse Transcriptase Polymerase Chain Reaction ; Selenoproteins/*genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Testis/metabolism ; Transcription Initiation Site ; }, abstract = {The sperm mitochondrial cysteine-rich protein (SMCP) is a rapidly evolving cysteine- and proline-rich protein that is localized in the mitochondrial capsule and enhances sperm motility. The sequences of the SMCP protein, gene, and mRNA in a variety of mammals have been compared to understand their evolution and regulation. SMCP can now be reliably identified by its tripartite structure including a short amino-terminal segment; a central segment containing short tandem repeats rich in cysteine, proline, glutamine, and lysine; and a C-terminal segment containing no repeats, few cysteines, and a C-terminal lysine. The SMCP gene is located in the epidermal differentiation complex (EDC), a large gene cluster that functions in forming epithelial barriers. Similarities in chromosomal location, molecular function, intron-exon structure, and protein organization argue that SMCP originated from an EDC gene and acquired spermatogenic cell-specific transcriptional and translational regulation and a novel cellular function in sperm motility. The SMCP 5' UTR and 3' UTR contain conserved elements and uORFs that may function in cytoplasmic regulation of gene expression, and the levels of SMCP mRNA in human are much lower than in other mammals, a feature of male-biased expression. The evolution of SMCP has been accompanied by changes in the sequence, number, and length of repeat units, including three alleles in dogs. The major proteins associated with the mitochondrial capsule, SMCP and phospholipid hydroperoxide glutathione peroxidase, provide outstanding examples of changes in cellular function driven by selective pressures on sperm motility, an important determinant of male reproductive success.}, }
@article {pmid16322521, year = {2006}, author = {Breton, S and Burger, G and Stewart, DT and Blier, PU}, title = {Comparative analysis of gender-associated complete mitochondrial genomes in marine mussels (Mytilus spp.).}, journal = {Genetics}, volume = {172}, number = {2}, pages = {1107-1119}, pmid = {16322521}, issn = {0016-6731}, mesh = {Animals ; Base Sequence ; Cell Nucleus/metabolism ; Cytoplasm/metabolism ; Electron Transport Complex IV/genetics ; Female ; *Genome ; Male ; Mitochondria/*genetics ; Molecular Sequence Data ; Mytilus/*genetics ; Nucleic Acid Conformation ; Protein Subunits/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Recombination, Genetic ; *Sequence Analysis, DNA ; }, abstract = {Marine mussels of the genus Mytilus have an unusual mode of mitochondrial DNA (mtDNA) transmission termed doubly uniparental inheritance (DUI). Female mussels are homoplasmic for the F mitotype, which is inherited maternally, while males are usually heteroplasmic, carrying a mixture of the maternal F mitotype and the paternally inherited M genome. Two classes of M genomes have been observed: "standard" M genomes and "recently masculinized" M genomes. The latter are more similar to F genomes at the sequence level but are transmitted paternally like standard M genomes. In this study we report the complete sequences of two standard male M. edulis and one recently masculinized male M. trossulus mitochondrial genome. A comparative analysis, including the previously sequenced M. edulis F and M. galloprovincialis F and M mtDNAs, reveals that these genomes are identical in gene order, but highly divergent in nucleotide and amino acid sequence. The large amount (>20%) of nucleotide substitutions that fall in coding regions implies that there are several amino acid replacements between the F and M genomes, which likely have an impact on the structural and functional properties of the mitochondrial proteome. Correlation of the divergence rate of different protein-coding genes indicates that mtDNA-encoded proteins of the M genome are still under selective constraints, although less highly than genes of the F genome. The mosaic F/M control region of the masculinized F genome provides evidence for lineage-specific sequences that may be responsible for the different mode of transmission genetics. This analysis shows the value of comparative genomics to better understand the mechanisms of maintenance and segregation of mtDNA sequence variants in mytilid mussels.}, }
@article {pmid16321390, year = {2006}, author = {Aranda, A and Maugeri, D and Uttaro, AD and Opperdoes, F and Cazzulo, JJ and Nowicki, C}, title = {The malate dehydrogenase isoforms from Trypanosoma brucei: subcellular localization and differential expression in bloodstream and procyclic forms.}, journal = {International journal for parasitology}, volume = {36}, number = {3}, pages = {295-307}, doi = {10.1016/j.ijpara.2005.09.013}, pmid = {16321390}, issn = {0020-7519}, mesh = {Amino Acid Sequence ; Animals ; Chromatography, Agarose/methods ; Cross Reactions/immunology ; Cytosol/enzymology ; Gene Expression Regulation, Developmental/genetics ; Genes, Protozoan/genetics ; Isoenzymes/analysis/immunology ; Malate Dehydrogenase/*analysis/genetics/immunology ; Microbodies/enzymology/genetics/immunology ; Mitochondria/enzymology/genetics/immunology ; Oxaloacetic Acid/metabolism ; Phenylpyruvic Acids/metabolism ; Phylogeny ; Protozoan Proteins/metabolism ; Rabbits ; Recombinant Proteins/metabolism ; Sequence Alignment/methods ; Trypanosoma brucei brucei/*enzymology/immunology ; }, abstract = {Trypanosoma brucei procyclic forms possess three different malate dehydrogenase isozymes that could be separated by hydrophobic interaction chromatography and were recognized as the mitochondrial, glycosomal and cytosolic malate dehydrogenase isozymes. The latter is the only malate dehydrogenase expressed in the bloodstream forms, thus confirming that the expression of malate dehydrogenase isozymes is regulated during the T. brucei life cycle. To achieve further biochemical characterization, the genes encoding mitochondrial and glycosomal malate dehydrogenase were cloned on the basis of previously reported nucleotide sequences and the recombinant enzymes were functionally expressed in Escherichia coli cultures. Mitochondrial malate dehydrogenase showed to be more active than glycosomal malate dehydrogenase in the reduction of oxaloacetate; nearly 80% of the total activity in procyclic crude extracts corresponds to the former isozyme which also catalyzes, although less efficiently, the reduction of p-hydroxyphenyl-pyruvate. The rabbit antisera raised against each of the recombinant isozymes showed that the three malate dehydrogenases do not cross-react immunologically. Immunofluorescence experiments using these antisera confirmed the glycosomal and mitochondrial localization of glycosomal and mitochondrial malate dehydrogenase, as well as a cytosolic localization for the third malate dehydrogenase isozyme. These results clearly distinguish Trypanosoma brucei from Trypanosoma cruzi, since in the latter parasite a cytosolic malate dehydrogenase is not present and mitochondrial malate dehydrogenase specifically reduces oxaloacetate.}, }
@article {pmid16318324, year = {2005}, author = {Ueshima, R}, title = {[Evolution of metazoan mitochondrial genome].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {50}, number = {14 Suppl}, pages = {1813-1814}, pmid = {16318324}, issn = {0039-9450}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genetic Code ; Genome/*genetics ; Introns/genetics ; Mitochondria/*genetics ; RNA/chemistry/genetics ; RNA, Mitochondrial ; RNA, Ribosomal/chemistry/genetics ; RNA, Transfer/chemistry/genetics ; }, }
@article {pmid16318319, year = {2005}, author = {Sodmergen,  and Sakamoto, W}, title = {[Maternal inheritance of mitochondria in higher plants].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {50}, number = {14 Suppl}, pages = {1795-1798}, pmid = {16318319}, issn = {0039-9450}, mesh = {Biological Evolution ; DNA, Mitochondrial/*genetics/metabolism ; Eukaryotic Cells ; Genes, Mitochondrial/*genetics ; Genome, Plant/*genetics ; Plants/*genetics ; Plastids/genetics ; Pollen/*genetics ; }, }
@article {pmid16318316, year = {2005}, author = {Kadowaki, K}, title = {[Structure, replication and evolution of plant mitochondrial genomes].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {50}, number = {14 Suppl}, pages = {1782-1785}, pmid = {16318316}, issn = {0039-9450}, mesh = {*DNA Replication ; *DNA, Mitochondrial/chemistry/genetics ; *DNA, Plant ; *Evolution, Molecular ; *Genome, Plant/genetics ; Mitochondria/*genetics ; }, }
@article {pmid16318315, year = {2005}, author = {Sugiyama, Y}, title = {[Inheritance and evolution of plant mtDNA: Overview].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {50}, number = {14 Suppl}, pages = {1780-1781}, pmid = {16318315}, issn = {0039-9450}, mesh = {DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; *Evolution, Molecular ; *Genes, Mitochondrial ; Genome, Plant/*genetics ; Mitochondria/*genetics/physiology ; Mutation ; Plants/*genetics ; }, }
@article {pmid16318303, year = {2005}, author = {Shigi, N and Suzuki, T}, title = {[Unique translation system and mitochondrial genome evolution].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {50}, number = {14 Suppl}, pages = {1732-1736}, pmid = {16318303}, issn = {0039-9450}, mesh = {Animals ; Anticodon/genetics ; Escherichia coli/genetics ; *Evolution, Molecular ; Genetic Code/genetics ; Genome/*genetics ; Humans ; Mitochondria/*genetics ; Protein Biosynthesis/*genetics ; RNA/genetics ; RNA, Mitochondrial ; RNA, Ribosomal ; RNA, Transfer/genetics ; Ribosomal Proteins ; Transcription, Genetic ; }, }
@article {pmid16316982, year = {2006}, author = {Kulikowicz, T and Shapiro, TA}, title = {Distinct genes encode type II Topoisomerases for the nucleus and mitochondrion in the protozoan parasite Trypanosoma brucei.}, journal = {The Journal of biological chemistry}, volume = {281}, number = {6}, pages = {3048-3056}, doi = {10.1074/jbc.M505977200}, pmid = {16316982}, issn = {0021-9258}, support = {AI28855/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Blotting, Northern ; Blotting, Southern ; Blotting, Western ; Cell Nucleus/*enzymology/metabolism ; Crithidia/metabolism ; DNA Topoisomerases, Type II/*genetics ; DNA, Kinetoplast/genetics ; Escherichia coli/metabolism ; Flow Cytometry ; *Gene Expression Regulation, Enzymologic ; Immunoblotting ; Leishmania/metabolism ; Mitochondria/*enzymology ; Models, Genetic ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Plasmids/metabolism ; RNA Interference ; RNA, Messenger/metabolism ; Transfection ; Trypanosoma brucei brucei/*enzymology ; }, abstract = {Topoisomerases are essential for orderly nucleic acid metabolism and cell survival and are proven targets for clinically useful antimicrobial and anticancer drugs. Interest in the topologically intricate mitochondrial DNA (kinetoplast or kDNA) of Trypanosoma brucei brucei and related kinetoplastid protozoan parasites has led to many reports of type II topoisomerases that participate in kDNA metabolism (we term the T. brucei brucei gene TbTOP2mt). We have now identified and characterized two new genes for type II topoisomerases in T. brucei brucei, termed TbTOP2alpha and TbTOP2beta. Phylogenetically, they share a common node with other nuclear topoisomerases, clearly distinct from a clade that includes the previously reported kinetoplastid genes, all of which are homologs of TbTOP2mt. Southern blot analysis reveals the new genes are single copy and positioned approximately 1.7 kb apart. Cognate mRNAs are expressed in African trypanosomes, but only a single message is detected in Leishmania or Crithidia. TbTOP2alpha encodes an ATP-dependent topoisomerase that appears as a single approximately 170-kDa band on immunoblots and localizes to the nucleus; RNA interference leads to pleomorphic nuclear (but not kDNA) abnormalities and early growth arrest. The role of TbTOP2beta is unclear. Although transcribed in trypanosomes, TbTOP2beta is not detected by beta-specific antiserum, and RNAi silencing results in no obvious phenotype. These studies indicate that African trypanosomes and related kinetoplastid human pathogens are unusual in having independent topoisomerase II genes to service their nuclear and mitochondrial genomes, and they highlight TbTOP2alpha as a promising target for the development of much-needed new therapies.}, }
@article {pmid16313611, year = {2005}, author = {Gentle, IE and Burri, L and Lithgow, T}, title = {Molecular architecture and function of the Omp85 family of proteins.}, journal = {Molecular microbiology}, volume = {58}, number = {5}, pages = {1216-1225}, doi = {10.1111/j.1365-2958.2005.04906.x}, pmid = {16313611}, issn = {0950-382X}, mesh = {*Bacterial Outer Membrane Proteins/chemistry/genetics/metabolism ; Cell Membrane/*metabolism ; Gram-Negative Bacteria/chemistry/genetics/*metabolism ; }, abstract = {Omp85 is a protein found in Gram-negative bacteria where it serves to integrate proteins into the bacterial outer membrane. Members of the Omp85 family of proteins are defined by the presence of two domains: an N-terminal, periplasmic domain rich in POTRA repeats and a C-terminal beta-barrel domain embedded in the outer membrane. The widespread distribution of Omp85 family members together with their fundamental role in outer membrane assembly suggests the ancestral Omp85 arose early in the evolution of prokaryotic cells. Mitochondria, derived from an ancestral bacterial endosymbiont, also use a member of the Omp85 family to assemble proteins in their outer membranes. More distant relationships are seen between the Omp85 family and both the core proteins in two-partner secretion systems and the Toc75 family of protein translocases found in plastid outer envelopes. Aspects of the ancestry and molecular architecture of the Omp85 family of proteins is providing insight into the mechanism by which proteins might be integrated and assembled into bacterial outer membranes.}, }
@article {pmid16313565, year = {2005}, author = {van Opijnen, T and Baudry, E and Baldo, L and Bartos, J and Werren, JH}, title = {Genetic variability in the three genomes of Nasonia: nuclear, mitochondrial and Wolbachia.}, journal = {Insect molecular biology}, volume = {14}, number = {6}, pages = {653-663}, doi = {10.1111/j.1365-2583.2005.00595.x}, pmid = {16313565}, issn = {0962-1075}, mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; *Genome, Bacterial ; *Genome, Insect ; Phylogeny ; Wasps/cytology/*genetics/microbiology ; Wolbachia/*genetics ; }, abstract = {Nasonia consists of three closely related species of parasitoid wasps that are all infected with the endosymbiotic bacteria Wolbachia, a reproductive parasite common in arthropods. This situation presents the opportunity to compare patterns of variation in three associated genomes, Wolbachia and the nuclear and mitochondrial genomes of its host. Furthermore, although Nasonia wasps are emerging as a model for evolutionary and genetic studies, little is known about their genetic variability. Using amplified fragment length polymorphisms (AFLPs), all three species present a relatively high level of nuclear polymorphism and have different patterns of variation, with one of the species, Nasonia giraulti, being divided into two divergent subgroups. In each species, the mitochondrial pattern of variation is different from the nuclear pattern, possibly due to genetic hitchhiking of the mitochondria during (cytoplasmically inherited) Wolbachia sweeps. Mitochondria in Nasonia show a synonymous substitution rate approximately 10-15-fold higher than nuclear genes, probably reflecting an elevated mitochondrial mutation rate that is among the highest found in insects. Finally, all three species are doubly infected with their own strains of Wolbachia, one each from the two major supergroups (A and B). Sequence analysis reveals that each of the three Nasonia species acquired their A and B bacteria independently by horizontal transfer events from other insects with the exception of B type Wolbachia in N. longicornis and N. giraulti, which were acquired prior to speciation and then codiverged with the host. This represents one of the few clear-cut examples of codivergence of Wolbachia during host speciation.}, }
@article {pmid16313447, year = {2005}, author = {Zhang, H and Lin, S}, title = {Mitochondrial cytochrome b mRNA editing in dinoflagellates: possible ecological and evolutionary associations?.}, journal = {The Journal of eukaryotic microbiology}, volume = {52}, number = {6}, pages = {538-545}, doi = {10.1111/j.1550-7408.2005.00060.x}, pmid = {16313447}, issn = {1066-5234}, mesh = {Animals ; Base Sequence ; Cloning, Molecular ; Cytochromes b/*genetics/metabolism ; Dinoflagellida/classification/*enzymology/genetics ; *Ecosystem ; *Evolution, Molecular ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; *RNA Editing ; RNA, Messenger/*genetics ; RNA, Mitochondrial ; Sequence Analysis, DNA ; }, abstract = {To verify the hypothesis that mt mRNA editing is widespread in dinoflagellates, we analyzed cytochrome b (cob) mRNA editing for six species representing distinct ecotypes and taxonomic classes of Dinophyceae. Editing is detected in all, which is similar to the three other species studied previously in that edited sites appear to aggregate in four clusters and occur predominantly at first and second positions of codons (93%), overwhelmingly involving A --> G, U --> C, or C --> U substitutions with a smaller number of G --> C, G --> A changes. Comparative analyses on editing characteristics reveal interesting trends related to phylogenetic relatedness and ecological features. Editing density (percentage of nucleotide that is affected by editing) increases from early to derived lineages. Higher editing densities also map to red tide-forming lineages. Furthermore, similarity of location of edited codons (LOE) and the type of nucleotide changes (TOE) in different lineages mirror the taxonomic affinity of the lineages. Phylogenetic trees constructed from LOE and TOE resemble those inferred from cob sequences. The results bolster our earlier hypothesis that cob editing is widespread in dinoflagellates and suggest that density, location, and type of editing may bear yet-to-be-defined evolutionary and ecological significance.}, }
@article {pmid16313445, year = {2005}, author = {Visvesvara, GS and De Jonckheere, JF and Marciano-Cabral, F and Schuster, FL}, title = {Morphologic and molecular identification of Naegleria dunnebackei n. sp. isolated from a water sample.}, journal = {The Journal of eukaryotic microbiology}, volume = {52}, number = {6}, pages = {523-531}, doi = {10.1111/j.1550-7408.2005.00061.x}, pmid = {16313445}, issn = {1066-5234}, mesh = {Animal Husbandry ; Animals ; Cattle ; DNA, Ribosomal Spacer/*analysis ; Fresh Water/*parasitology ; Mice ; Microscopy, Electron ; Molecular Sequence Data ; Naegleria/*classification/isolation &amp; purification/*ultrastructure/virology ; Phylogeny ; RNA, Ribosomal, 5.8S/*genetics ; Sequence Analysis, DNA ; *Water Supply ; }, abstract = {Naegleria dunnebackei n. sp., a new species of the free-living amoeboflagellate Naegleria, is described in this report. The organism was isolated from a water sample taken from drinking troughs associated with cases of primary amoebic meningoencephalitis in cattle at a ranch in southern California. The isolate grew at, but not above 37 degrees C, and did not kill young mice upon intranasal inoculation suggesting that it was not pathogenic. The new species combines morphological features of non-pathogenic Naegleria gruberi and pathogenic Naegleria fowleri. The trophic amoeba resembled other members of the genus, with a prominent vesicular nucleus and mitochondria with discoidal cristae; a Golgi apparatus was not observed by electron microscopy. The cyst stage had pores in the wall typical of those seen in pathogenic N. fowleri. Upon suspension in distilled water, amoebae transformed into temporary, non-feeding flagellates, mostly with two anterior flagella but occasionally with four. The rationale for its description as a new species was based upon sequencing of the 5.8S rDNA and internal transcribed spacers of the amoeba, which is similar to but not identical to that of Naegleria gallica, differing from that organism's DNA by six base pairs. Virus-like elements were found in the cytoplasm of trophic amoebae, often in association with crystalloids, and may be the cause of lysis of amoebae in culture.}, }
@article {pmid16307849, year = {2006}, author = {Gissi, C and San Mauro, D and Pesole, G and Zardoya, R}, title = {Mitochondrial phylogeny of Anura (Amphibia): a case study of congruent phylogenetic reconstruction using amino acid and nucleotide characters.}, journal = {Gene}, volume = {366}, number = {2}, pages = {228-237}, doi = {10.1016/j.gene.2005.07.034}, pmid = {16307849}, issn = {0378-1119}, mesh = {Amphibian Proteins/*genetics ; Animals ; Anura/*genetics ; Codon/genetics ; DNA, Mitochondrial/*genetics ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; *Phylogeny ; Sequence Analysis, DNA/methods ; Sequence Analysis, Protein/methods ; }, abstract = {We explore whether phylogenetic analyses of the same sequence data set at the amino acid and nucleotide level are able to recover congruent topologies, as well as the advantages and limitations of both alternative approaches. As a case study, mitochondrial protein-coding genes were used to discern among competing hypotheses on the phylogenetic relationships of major anuran amphibian lineages. To properly address this phylogenetic question, the complete nucleotide sequences of the mitochondrial genomes of two archaeobatrachian species, Ascaphus truei and Pelobates cultripes, were determined anew. Bayesian and maximum likelihood phylogenetic inferences of the same sequence data set were performed based on both amino acid and nucleotide characters, with the latter analysed either as codons or as a reduced data set of first+second (P12) codon positions. In addition, likelihood-based ratio tests were performed to evaluate the support of alternative topologies. The different data sets arrived at congruent and highly supported topologies, suggesting a similar phylogenetic resolving power of the two character types provided that correctly selected sites and appropriate evolutionary models are used. The reconstructed anuran mitochondrial phylogeny supports the paraphyly of Archaeobatrachia, with Ascaphus as sister group to all the remaining anurans, and Pelobates as sister group of Neobatrachia. However, the employed tree reconstruction methods and likelihood-based ratio tests seemed to be negatively affected by the fast evolving sequences of neobatrachians, suggesting that the phylogeny of Anura here presented is not definitive, and needs further investigation using an extended taxon sampling.}, }
@article {pmid16306143, year = {2005}, author = {van Lis, R and Atteia, A and Nogaj, LA and Beale, SI}, title = {Subcellular localization and light-regulated expression of protoporphyrinogen IX oxidase and ferrochelatase in Chlamydomonas reinhardtii.}, journal = {Plant physiology}, volume = {139}, number = {4}, pages = {1946-1958}, pmid = {16306143}, issn = {0032-0889}, mesh = {Amino Acid Sequence ; Animals ; Chlamydomonas reinhardtii/*enzymology/genetics/radiation effects ; DNA, Algal/genetics ; DNA, Complementary/genetics ; DNA, Protozoan/genetics ; Escherichia coli/genetics ; Ferrochelatase/genetics/*metabolism ; Gene Dosage ; Gene Expression Regulation, Enzymologic/radiation effects ; Genes, Protozoan ; Light ; Molecular Sequence Data ; Phylogeny ; Protoporphyrinogen Oxidase/genetics/*metabolism ; RNA, Algal/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Protozoan/genetics/metabolism ; Sequence Homology, Amino Acid ; Subcellular Fractions/enzymology ; }, abstract = {Protoporphyrinogen IX oxidase (PPO) catalyzes the last common step in chlorophyll and heme synthesis, and ferrochelatase (FeC) catalyzes the last step of the heme synthesis pathway. In plants, each of these two enzymes is encoded by two or more genes, and the enzymes have been reported to be located in the chloroplasts or in the mitochondria. We report that in the green alga Chlamydomonas reinhardtii, PPO and FeC are each encoded by a single gene. Phylogenetic analysis indicates that C. reinhardtii PPO and FeC are most closely related to plant counterparts that are located only in chloroplasts. Immunoblotting results suggest that C. reinhardtii PPO and FeC are targeted exclusively to the chloroplast, where they are associated with membranes. These results indicate that cellular needs for heme in this photosynthetic eukaryote can be met by heme that is synthesized in the chloroplast. It is proposed that the multiplicity of genes for PPO and FeC in higher plants could be related to differential expression in differently developing tissues rather than to targeting of different gene products to different organelles. The FeC content is higher in C. reinhardtii cells growing in continuous light than in cells growing in the dark, whereas the content of PPO does not significantly differ in light- and dark-grown cells. In cells synchronized to a light/dark cycle, the level of neither enzyme varied significantly with the phase of the cycle. These results indicate that heme synthesis is not directly regulated by the levels of PPO and FeC in C. reinhardtii.}, }
@article {pmid16300765, year = {2006}, author = {Benesh, DP and Hasu, T and Suomalainen, LR and Valtonen, ET and Tiirola, M}, title = {Reliability of mitochondrial DNA in an acanthocephalan: the problem of pseudogenes.}, journal = {International journal for parasitology}, volume = {36}, number = {2}, pages = {247-254}, doi = {10.1016/j.ijpara.2005.09.008}, pmid = {16300765}, issn = {0020-7519}, mesh = {Acanthocephala/*genetics ; Animals ; Base Sequence ; *Biological Evolution ; DNA Primers ; DNA, Mitochondrial/*analysis ; Electron Transport Complex IV/*genetics ; Genotype ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/methods ; *Pseudogenes ; }, abstract = {The utility of mitochondrial DNA as a molecular marker for evolutionary studies is well recognized. However, several problems can arise when using mitochondrial DNA, one of which is the presence of nuclear mitochondrial pseudogenes, or Numts. Pseudogenes of cytochrome oxidase I were preferentially amplified from Acanthocephalus lucii (Acanthocephala) using a universal PCR approach. To verify the presence and abundance of pseudogenes, length heterogeneity analysis of the PCR fragments was performed. PCR products obtained with universal primers often contained fragments of different sizes. Cloned sequences from universal PCR products nearly always contained sequence abnormalities such as indels and/or stop codons. Based on these sequences, new primers were developed to specifically target mitochondrial DNA. Sequences obtained with these specific primers lacked abnormalities. Phylogenetic analysis produced a single most parsimonious tree in which pseudogenes obtained with universal primers grouped together as did putative mitochondrial DNA sequences obtained with specific primers. The pattern of codon bias observed in the pseudogenes suggests a single nuclear integration event from the mitochondria. This is the first reported occurrence of pseudogenes in an acanthocephalan, and it demonstrates the potential dangers associated with the use of universal primers.}, }
@article {pmid16295658, year = {2005}, author = {Kovacević, G and Kalafatić, M and Ljubesić, N}, title = {Endosymbiotic alga from green hydra under the influence of cinoxacin.}, journal = {Folia microbiologica}, volume = {50}, number = {3}, pages = {205-208}, pmid = {16295658}, issn = {0015-5632}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Biological Evolution ; Chlorella/*drug effects/isolation &amp; purification/physiology/ultrastructure ; Chloroplasts/drug effects ; Cinoxacin/*pharmacology ; Hydra/*drug effects/physiology/ultrastructure ; Microscopy, Electron ; Mitochondria/drug effects ; Symbiosis/drug effects ; }, abstract = {Cinoxacin (Cxn) showed a strong effect on the endosymbiotic alga Chlorella; it was significantly damaged. Changes in algal color, position, structure and ultrastructure were found. In some algal cells ultrastructures were completely destroyed. The antichloroplastal and antimitochondrial effect was especially expressed. Damage to the thylakoid system of chloroplasts was more pronounced with increasing Cxn concentration. Some of the mitochondria were swollen and some of them were completely destroyed. From the evolutionary point of view, the correlation between antibacterial, and antichloroplastal and antimitochondrial effect of Cxn points to the evolutionary connection of chloroplasts and mitochondria with eubacteria.}, }
@article {pmid16286717, year = {2005}, author = {Maekawa, K and Kon, M and Matsumoto, T and Araya, K and Lo, N}, title = {Phylogenetic analyses of fat body endosymbionts reveal differences in invasion times of blaberid wood-feeding cockroaches (Blaberidae: Panesthiinae) into the Japanese archipelago.}, journal = {Zoological science}, volume = {22}, number = {10}, pages = {1061-1067}, doi = {10.2108/zsj.22.1061}, pmid = {16286717}, issn = {0289-0003}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; Cockroaches/*microbiology/*physiology ; *Demography ; Evolution, Molecular ; Fat Body/*microbiology ; Flavobacteriaceae/*genetics ; Geography ; Japan ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Cockroaches have endosymbiotic bacteria in their fat bodies. Recent molecular phylogenetic analyses on both hosts and endosymbionts have revealed that co-evolution has occurred throughout the history of cockroaches and termites. Co-cladogenesis was also shown among closely related taxa (woodroach genus Cryptocercus; Cryptocercidae), and thus endosymbiont data are likely to be useful for biogeographical analyses. To test the possibility of co-cladogenesis among inter-and intraspecific taxa, as well as the utility of endosymbiont data for inferring biogeographical scenarios, we analyzed rRNA genes of endosymbionts of Japanese and Taiwanese Panesthiinae (Salganea and Panesthia; Blaberidae), on which phylogenetic analyses previously had been performed based on the mitochondrial genes. Statistical analyses on the topologies inferred from both endosymbiont and host mitochondria genes showed that co-cladogenesis has occurred. The endosymbiont sequences examined appear to have evolved in a clock-like manner, and their rate of evolution based on the host fossil data showed a major difference in the time of invasion of the two Japanese genera, that is congruent with the recent analyses of their mitochondrial genes.}, }
@article {pmid16286090, year = {2005}, author = {Salducci, MD and Marty, C and Fouquet, A and Gilles, A}, title = {Phylogenetic relationships and biodiversity in Hylids (Anura: Hylidae) from French Guiana.}, journal = {Comptes rendus biologies}, volume = {328}, number = {10-11}, pages = {1009-1024}, doi = {10.1016/j.crvi.2005.07.005}, pmid = {16286090}, issn = {1631-0691}, mesh = {Animals ; Anura/classification/*physiology ; Biomarkers ; Cell Nucleus/genetics ; DNA/genetics ; DNA Primers ; DNA, Recombinant/genetics ; Databases, Genetic ; French Guiana ; Mitochondria/metabolism ; Monophenol Monooxygenase/genetics ; Phylogeny ; RNA/genetics ; RNA, Ribosomal, 18S/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {We evaluated two biodiversity criteria, higher taxonomic diversity and phylogenetic diversity in French Guiana. For this, we used a recent assessment of the knowledge accumulated since 30 years of study on the amphibian species currently known in French Guiana. We focused on two well-represented genera, Hyla and Scinax, belonging to the subfamily Hylinae. We used partial sequences of two mitochondrial genes (16S rDNA and 12S rDNA, 813 bp) and two nuclear genes (tyrosinase and 18S rRNA, 1590 bp) covering a total of 2403 bp. According to the high bootstrap support in phylogenetic analysis of the complete dataset, the genus Scinax is a homophyletic clade formed by two species groups (rubra and rostrata) in French Guiana. The genus Hyla was confirmed to be a paraphyletic group formed by two species groups as well (30 chromosomes and the 'gladiator frogs'). We confirmed that these genera should be taxonomically reconsidered. Moreover, at the genus, subfamily and family levels, the use of only morphological characters or only molecular DNA markers would hamper estimations of biodiversity. Thus, we strongly advise the combined use of both morphology and molecular data (nuclear and mitochondrial markers).}, }
@article {pmid16283555, year = {2005}, author = {Mozo, J and Emre, Y and Bouillaud, F and Ricquier, D and Criscuolo, F}, title = {Thermoregulation: what role for UCPs in mammals and birds?.}, journal = {Bioscience reports}, volume = {25}, number = {3-4}, pages = {227-249}, doi = {10.1007/s10540-005-2887-4}, pmid = {16283555}, issn = {0144-8463}, mesh = {Acclimatization ; Adipose Tissue, Brown/metabolism ; Animals ; Birds/*physiology ; Body Temperature Regulation/*physiology ; Carrier Proteins/chemistry/classification/genetics/*metabolism ; Cold Temperature ; Energy Metabolism/physiology ; Hormones/metabolism ; Humans ; Ion Channels ; Mammals/*physiology ; Membrane Proteins/chemistry/classification/genetics/*metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins ; Obesity/genetics/metabolism ; Phylogeny ; Protein Isoforms/chemistry/genetics/*metabolism ; Reactive Oxygen Species/metabolism ; Uncoupling Protein 1 ; }, abstract = {Mammals and birds are endotherms and respond to cold exposure by the means of regulatory thermogenesis, either shivering or non-shivering. In this latter case, waste of cell energy as heat can be achieved by uncoupling of mitochondrial respiration. Uncoupling proteins, which belong to the mitochondrial carrier family, are able to transport protons and thus may assume a thermogenic function. The mammalian UCP1 physiological function is now well understood and gives to the brown adipose tissue the capacity for heat generation. But is it really the case for its more recently discovered isoforms UCP2 and UCP3? Additionally, whereas more and more evidence suggests that non-shivering also exists in birds, is the avian UCP also involved in response to cold exposure? In this review, we consider the latest advances in the field of UCP biology and present putative functions for UCP1 homologues.}, }
@article {pmid16283554, year = {2005}, author = {Nogueira, FT and Borecký, J and Vercesi, AE and Arruda, P}, title = {Genomic structure and regulation of mitochondrial uncoupling protein genes in mammals and plants.}, journal = {Bioscience reports}, volume = {25}, number = {3-4}, pages = {209-226}, doi = {10.1007/s10540-005-2886-5}, pmid = {16283554}, issn = {0144-8463}, mesh = {Animals ; Carrier Proteins/classification/*genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Membrane Proteins/classification/*genetics/metabolism ; Mitochondrial Proteins/classification/*genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Plant Proteins/classification/*genetics/metabolism ; Protein Isoforms/classification/genetics/metabolism ; Transcription, Genetic ; }, abstract = {Uncoupling mitochondrial proteins (UCPs) belong to a discrete family within the mitochondrial anion carrier superfamily. Several uncoupling protein types have been found in mitochondria from mammals and plants, as well as in fishes, fungi, and protozoa. Mammalian UCPs and plant uncoupling proteins (PUMPs) form five distinct subfamilies. Only subfamily III contains both plant and animal uncoupling proteins, as well as UCPs from primitive eukaryotic organisms, which suggest that this group may represent an ancestral cluster from which other UCPs/PUMPs may have evolved. Genetic data indicate that UCPs/PUMPs are regulated at the transcriptional, post-transcriptional, and translational levels. Tissue/organ- and stress-specific gene expression suggests that UCPs/PUMPs are involved in the general balance of basic energy expenditure, protection against reactive oxygen species, and thermogenesis. Finally, the simultaneous occurrence of PUMP and alternative oxidase, another energy-dissipating system in plant mitochondria, raises the question of their response to biotic and abiotic stress at the transcriptional and functional levels.}, }
@article {pmid16282285, year = {2005}, author = {Rand, DM}, title = {Mitochondrial genetics of aging: intergenomic conflict resolution.}, journal = {Science of aging knowledge environment : SAGE KE}, volume = {2005}, number = {45}, pages = {re5}, doi = {10.1126/sageke.2005.45.re5}, pmid = {16282285}, issn = {1539-6150}, mesh = {Aging/*genetics/*physiology ; Archaea ; Cell Nucleus/physiology ; *DNA, Mitochondrial ; Epistasis, Genetic ; Eubacterium ; Evolution, Molecular ; Gene Transfer, Horizontal ; Genetics, Population ; Humans ; Mitochondria/*genetics ; Reactive Oxygen Species ; Symbiosis ; }, abstract = {Mitochondria are the organelles of aerobic respiration. They consume the oxygen we breathe to stay alive and generate energy for cells to function. But oxygen can be dangerous. Indeed, mitochondria generate the majority of reactive oxygen species that are prime suspects among the causes of aging. Mitochondria have been influential elements of evolving eukaryotic cells for perhaps 2 billion years, since a eubacterium fused with an archaebacterium. The picture that has emerged from this long history of genomic fusion is that of a complex network of nuclear-mitochondrial cross-talk. Here, we discuss the biochemical and genetic conflicts between mitochondria and nucleus, which have shaped the role of mitochondria in aging, and point to new paths for further investigations.}, }
@article {pmid16274729, year = {2006}, author = {Hipkiss, AR}, title = {On the mechanisms of ageing suppression by dietary restriction-is persistent glycolysis the problem?.}, journal = {Mechanisms of ageing and development}, volume = {127}, number = {1}, pages = {8-15}, doi = {10.1016/j.mad.2005.09.006}, pmid = {16274729}, issn = {0047-6374}, mesh = {Aging/*physiology ; Animals ; Biological Evolution ; *Caloric Restriction ; Glycolysis/*physiology ; Glyoxal/analogs &amp; derivatives/metabolism ; Humans ; Stress, Physiological/physiopathology ; }, abstract = {The mechanism(s) by which dietary restriction (DR) suppresses ageing and onset of age-related pathologies are discussed in relation to frequency of glycolysis, and the reactivity of glycolytic intermediates. Most glycolytic intermediates are potentially toxic and readily modify (i.e. glycate) proteins and other macromolecules non-enzymically. Attention is drawn to the reactivity of methyglyoxal (MG) which is formed predominantly from the glycolytic intermediates dihydroxyacetone- and glyceraldehyde-3-phosphates. MG rapidly glycates proteins, damages mitochondria and induces a pro-oxidant state, similar to that observed in aged cells. It is suggested that because DR animals' energy metabolism is less glycolytic than in those fed ad libitum, intracellular MG levels are lowered by DR The decreased glycolysis during DR may delay senescence by lowering intracellular MG concentration compared to ad libitum-fed animals. Because of the reactivity MG and glycolytic intermediates, occasional glycolysis could be hormetic where glyoxalase, carnosine synthetase and ornithine decarboxylase are upregulated to control cellular MG concentration. It is suggested that in ad libitum-fed animals persistent glycolysis permanently raises MG levels which progressively overwhelm protective processes, particularly in non-mitotic tissues, to create the senescent state earlier than in DR animals. The possible impact of diet and intracellular glycating agents on age-related mitochondrial dysfunction is also discussed.}, }
@article {pmid16274719, year = {2006}, author = {Ferraguti, M and Garbelli, C}, title = {The spermatozoon of a 'living fossil': Tubiluchus troglodytes (Priapulida).}, journal = {Tissue &amp; cell}, volume = {38}, number = {1}, pages = {1-6}, doi = {10.1016/j.tice.2005.05.001}, pmid = {16274719}, issn = {0040-8166}, mesh = {Acrosome/ultrastructure ; Animals ; Biological Evolution ; Cell Nucleus/ultrastructure ; Fossils ; Invertebrates/anatomy &amp; histology/*ultrastructure ; Male ; Mediterranean Sea ; Microscopy, Electron ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Spermatozoa/cytology/*ultrastructure ; }, abstract = {The spermatozoon of Tubiluchus troglodytes, the first priapulid formally described from the Mediterranean Sea has a head composed of an acrosome and a nucleus. The acrosome is divided in two branches coiled around the nucleus. The nucleus is basally columnar, but apically generates two rods helically coiled one around the other. The midpiece is formed by an axoneme with 27 accessory microtubules, surrounded by three mitochondria. An annulus separates the midpiece from the tail that contains a 9 + 2 axoneme surrounded by nine accessory microtubules. The spermatozoon of T. troglodytes is similar to that of the other two species known from the genus, and completely different from the 'primitive' one of the other priapulids. Since Tubiluchus is considered the most basal of the extant priapulids, and the only genus with an internal fertilization, it may be that in priapulids the external fertilization is a derived character.}, }
@article {pmid16269741, year = {2005}, author = {Zhang, H and Lin, S}, title = {Development of a cob-18S rRNA gene real-time PCR assay for quantifying Pfiesteria shumwayae in the natural environment.}, journal = {Applied and environmental microbiology}, volume = {71}, number = {11}, pages = {7053-7063}, pmid = {16269741}, issn = {0099-2240}, mesh = {Animals ; Base Sequence ; Boston ; Chile ; Cytochromes b/*genetics ; DNA, Protozoan/analysis ; DNA, Ribosomal/analysis ; Dinoflagellida/genetics/*isolation &amp; purification ; Genes, rRNA ; Maine ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 18S/*genetics ; Rivers/*parasitology ; Seawater/*parasitology ; }, abstract = {Despite the fact that the heterotrophic dinoflagellate Pfiesteria shumwayae is an organism of high interest due to alleged toxicity, its abundance in natural environments is poorly understood. To address this inadequacy, a real-time quantitative PCR assay based on mitochondrial cytochrome b (cob) and 18S rRNA gene was developed and P. shumwayae abundance was investigated in several geographic locations. First, cob and its 5'-end region were isolated from a P. shumwayae culture, revealing three different copies, each consisting of an identical cob coding region and an unidentified region (X) of variable length and sequence. The unique sequences in cob and the X region were then used to develop a P. shumwayae-specific primer set. This primer set was used with reported P. shumwayae-specific 18S primers in parallel real-time PCRs to investigate P. shumwayae abundance from Maine to North Carolina along the U.S. east coast and along coasts in Chile, Hawaii, and China. Both genes generally gave similar results, indicating that this species was present, but at low abundance (mostly <10 cells x ml(-1)), in all the American coast locations investigated (with the exception of Long Island Sound, where which both genes gave negative results). Genetic variation was detected by use of both genes in most of the locations, and while cob consistently detected P. shumwayae or close genetic variants, some of the 18S PCR products were unrelated to P. shumwayae. We conclude that (i) the real-time PCR assay developed is useful for specific quantification of P. shumwayae, and (ii) P. shumwayae is distributed widely at the American coasts, but normally only as a minor component of plankton even in high-risk estuaries (Neuse River and the Chesapeake Bay).}, }
@article {pmid16262695, year = {2005}, author = {Majeran, W and Friso, G and van Wijk, KJ and Vallon, O}, title = {The chloroplast ClpP complex in Chlamydomonas reinhardtii contains an unusual high molecular mass subunit with a large apical domain.}, journal = {The FEBS journal}, volume = {272}, number = {21}, pages = {5558-5571}, doi = {10.1111/j.1742-4658.2005.04951.x}, pmid = {16262695}, issn = {1742-464X}, mesh = {Amino Acid Sequence ; Animals ; Cell Nucleus/genetics ; Chlamydomonas reinhardtii/chemistry/*enzymology/genetics ; Chloroplasts/chemistry/*enzymology/genetics ; Endopeptidase Clp/*chemistry/genetics/*metabolism ; Enzyme Stability ; Molecular Sequence Data ; Molecular Weight ; Phylogeny ; Protein Binding ; Protein Structure, Tertiary ; Protein Subunits/chemistry/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {The composition of the chloroplast-localized protease complex, ClpP, from the green alga Chlamydomonas reinhardtii was characterized by nondenaturing electrophoresis, immunoblotting and MS. The detected ClpP complex has a native mass of approximately 540 kDa, which is approximately 200 kDa higher than ClpP complexes in higher plant chloroplasts, mitochondria or bacteria. The 540-kDa ClpP complex contains two nuclear-encoded ClpP proteins (ClpP3 and P5) and five ClpR (R1, R2, R3, R4 and R6) proteins, as well two proteins, ClpP1L and ClpP1H, both probably derived from the plastid clpP1 gene. ClpP1H is 59 kDa and contains a approximately 30-kDa insertion sequence (IS1) not found in other ClpP proteins, responsible for the high MW of the complex. Based on comparison with other sequences, IS1 protrudes as an additional domain on the apical surface of the ClpP/R complex, probably preventing interaction with the HSP100 chaperone. ClpP1L is a 25-kDa protein similar in size to other ClpP proteins and could arise by post-translational processing of ClpP1H. Chloramphenicol-chase experiments show that ClpP1L and ClpP1H have a similar half-life, indicating that both are stable components of the complex. The structure of the ClpP complex is further discussed in conjunction with a phylogenetic analysis of the ClpP/R genes. A model is proposed for the evolution of the algal and plant complex from its cyanobacterial ancestor.}, }
@article {pmid16262260, year = {2005}, author = {Cowley, AB and Sun, N and Rivera, M and Benson, DR}, title = {Divergence in nonspecific hydrophobic packing interactions in the apo state, and its possible role in functional specialization of mitochondrial and microsomal cytochrome b5.}, journal = {Biochemistry}, volume = {44}, number = {44}, pages = {14606-14615}, doi = {10.1021/bi051337m}, pmid = {16262260}, issn = {0006-2960}, mesh = {Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; Cytochromes b5/*chemistry ; Microsomes/*chemistry ; Mitochondria/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Denaturation ; Protein Isoforms/chemistry ; *Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry ; Sequence Alignment ; }, abstract = {The outer mitochondrial membrane isoform of mammalian cytochrome b(5) (OM b(5)) is distinguished from the microsomal isoform (Mc b(5)) by its considerably greater stability. In contrast, OM and Mc apocytochrome b(5) (apo-b(5)) exhibit similar thermodynamic stability. Contributing substantially to the greater stability of OM b(5) relative to that of Mc b(5) is the presence of Leu at position 71. Replacing Leu-71 in OM b(5) with the corresponding Mc b(5) residue (Ser) not only diminishes holoprotein stability but also markedly compromises apoprotein stability. The studies reported herein were undertaken to clarify the role played by Leu-71 in stabilizing OM b(5)s relative to Mc b(5)s, and were motivated by the possibility that stability is related to other differences in OM and Mc b(5) properties that are important for their specialized subcellular roles. The results of these studies show that Leu-71 plays an essential role in maintaining the structural integrity of the heme-independent folding core of OM apo-b(5) (core 2), despite its location in the disordered empty heme-binding pocket (core 1). The conformational integrity of core 2 in Mc apo-b(5)s is not similarly dependent on the presence of a hydrophobic residue at position 71, providing new evidence for evolution of compensating structural features not present in OM b(5)s. We propose that Leu-71 achieves its effect on OM apo-b(5) core 2 structure by participating in a nonspecific hydrophobic collapse of disordered core 1, templated by more conformationally restricted side chains of residues in the beta-sheet that separates the two cores. We hypothesize that this has the added effect of maintaining core 1 of OM apo-b(5)s in a state more compact than that which occurs in Mc apo-b(5)s, possibly contributing to stronger heme binding by limiting the number of non-native conformations that the empty heme-binding pocket can populate.}, }
@article {pmid16260473, year = {2005}, author = {Ogihara, Y and Yamazaki, Y and Murai, K and Kanno, A and Terachi, T and Shiina, T and Miyashita, N and Nasuda, S and Nakamura, C and Mori, N and Takumi, S and Murata, M and Futo, S and Tsunewaki, K}, title = {Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome.}, journal = {Nucleic acids research}, volume = {33}, number = {19}, pages = {6235-6250}, pmid = {16260473}, issn = {1362-4962}, mesh = {Base Sequence ; Chromosome Mapping ; DNA Shuffling ; DNA, Chloroplast/chemistry ; DNA, Mitochondrial/*chemistry ; Evolution, Molecular ; *Genome, Plant ; Mitochondria/*genetics ; Molecular Sequence Data ; Recombination, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; Triticum/*genetics ; }, abstract = {The application of a new gene-based strategy for sequencing the wheat mitochondrial genome shows its structure to be a 452 528 bp circular molecule, and provides nucleotide-level evidence of intra-molecular recombination. Single, reciprocal and double recombinant products, and the nucleotide sequences of the repeats that mediate their formation have been identified. The genome has 55 genes with exons, including 35 protein-coding, 3 rRNA and 17 tRNA genes. Nucleotide sequences of seven wheat genes have been determined here for the first time. Nine genes have an exon-intron structure. Gene amplification responsible for the production of multicopy mitochondrial genes, in general, is species-specific, suggesting the recent origin of these genes. About 16, 17, 15, 3.0 and 0.2% of wheat mitochondrial DNA (mtDNA) may be of genic (including introns), open reading frame, repetitive sequence, chloroplast and retro-element origin, respectively. The gene order of the wheat mitochondrial gene map shows little synteny to the rice and maize maps, indicative that thorough gene shuffling occurred during speciation. Almost all unique mtDNA sequences of wheat, as compared with rice and maize mtDNAs, are redundant DNA. Features of the gene-based strategy are discussed, and a mechanistic model of mitochondrial gene amplification is proposed.}, }
@article {pmid16252476, year = {2005}, author = {Putignani, L}, title = {The unusual architecture and predicted function of the mitochondrion organelle in Cryptosporidium parvum and hominis species: the strong paradigm of the structure-function relationship.}, journal = {Parassitologia}, volume = {47}, number = {2}, pages = {217-225}, pmid = {16252476}, issn = {0048-2951}, mesh = {Adenosine Triphosphate/biosynthesis ; Animals ; Chaperonins/genetics ; Cryptophyta/ultrastructure ; Cryptosporidium/genetics/growth &amp; development/physiology/*ultrastructure ; Cryptosporidium parvum/genetics/growth &amp; development/physiology/*ultrastructure ; DNA, Mitochondrial/analysis ; DNA, Protozoan/analysis ; Eimeria tenella/ultrastructure ; Genomics ; Humans ; Mitochondria/*physiology/*ultrastructure ; Mitochondrial Membranes/ultrastructure ; Mitochondrial Proteins ; Models, Biological ; Oxidative Phosphorylation ; Oxidoreductases/genetics ; Phylogeny ; Plant Proteins ; Proteomics ; Protozoan Proteins/analysis/genetics ; Species Specificity ; Structure-Activity Relationship ; Superoxide Dismutase/genetics ; Toxoplasma/ultrastructure ; }, abstract = {Cryptosporidium spp. is a protozoan parasite that causes widespread diarrhoeal disease in humans and other animals and is responsible for large waterborne outbreaks of cryptosporidiosis. Unlike many organisms belonging to the phylum Apicomplexa, such as Plasmodium spp. and Toxoplasma gondii, there is no clinically proven drug treatment against this parasite. Some aspects of the basic biology of Cryptosporidium spp. such as the understanding of key metabolic pathways or the full description of the organellar compartment are still lacking. Here I present evidence of the anomalous shape and substructure of the mitochondrion organelle in C. parvum and C. hominis, which is closer to the Guillardia theta nucleomorph structure rather than to the canonical mitochondrion of the proximate apicomplexan T gondii. The atypical architecture is accomplished by an altered organellar metabolone, inferred by in silico conceptual prediction and characterized by unusual, partial and/or reduced pathways. However, phylogeneticanalyses of the mitochondrion and mitochondrion-related loci hsp60, hsp70 (dnaK), alternative oxidase (AOX) and superoxide dismutase (SOD) in C. parvum show diversiform evolutionary pathways, suggesting a "chimera" derived organelle. Taken together these data depict peculiar and intriguing aspects of the C. parvum and C. hominis anomalous mitochondrion framework for further comparative analysis of the organelle within the Cryptosporidium spp. order.}, }
@article {pmid16251277, year = {2005}, author = {Duchêne, AM and Giritch, A and Hoffmann, B and Cognat, V and Lancelin, D and Peeters, NM and Zaepfel, M and Maréchal-Drouard, L and Small, ID}, title = {Dual targeting is the rule for organellar aminoacyl-tRNA synthetases in Arabidopsis thaliana.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {45}, pages = {16484-16489}, pmid = {16251277}, issn = {0027-8424}, mesh = {Amino Acyl-tRNA Synthetases/*analysis/genetics ; Arabidopsis/*enzymology/genetics ; Chloroplasts/enzymology ; Genome, Plant ; Mitochondria/enzymology ; Phylogeny ; }, abstract = {In plants, protein synthesis occurs in the cytosol, mitochondria, and plastids. Each compartment requires a full set of tRNAs and aminoacyl-tRNA synthetases. We have undertaken a systematic analysis of the targeting of organellar aminoacyl-tRNA synthetases in the model plant Arabidopsis thaliana. Dual targeting appeared to be a general rule. Among the 24 identified organellar aminoacyl-tRNA synthetases (aaRSs), 15 (and probably 17) are shared between mitochondria and plastids, and 5 are shared between cytosol and mitochondria (one of these aaRSs being present also in chloroplasts). Only two were shown to be uniquely chloroplastic and none to be uniquely mitochondrial. Moreover, there are no examples where the three aaRS genes originating from the three ancestral genomes still coexist. These results indicate that extensive exchange of aaRSs has occurred during evolution and that many are now shared between two or even three compartments. The findings have important implications for studies of the translation machinery in plants and on protein targeting and gene transfer in general.}, }
@article {pmid16247555, year = {2005}, author = {Urantowka, A and Knorpp, C and Olczak, T and Kolodziejczak, M and Janska, H}, title = {Plant mitochondria contain at least two i-AAA-like complexes.}, journal = {Plant molecular biology}, volume = {59}, number = {2}, pages = {239-252}, pmid = {16247555}, issn = {0167-4412}, mesh = {Amino Acid Sequence ; Arabidopsis/*enzymology ; Arabidopsis Proteins/chemistry/genetics/metabolism ; DNA, Bacterial/genetics ; Intracellular Membranes/metabolism ; Metalloproteases/*chemistry/genetics/*metabolism ; Mitochondria/*enzymology ; Molecular Sequence Data ; Molecular Weight ; Multienzyme Complexes/chemistry/genetics/metabolism ; Mutagenesis, Insertional/genetics ; Mutation ; Phylogeny ; Protein Transport ; Saccharomyces cerevisiae/genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {The FtsH proteases, also called AAA proteases, are membrane-bound ATP-dependent metalloproteases. The Arabidopsis genome contains a total of 12 FtsH-like genes. Two of them, AtFtsH4 and AtFtsH11, encode proteins with a high similarity to Yme1p, a subunit of the i-AAA complex in yeast mitochondria. Phylogenetic analysis groups the AtFtsH4, AtFtsH11 and Yme1 proteins together, with AtFtsH4 being the most similar to Yme1. Using immunological method we demonstrate here that AtFtsH4 is an exclusively mitochondrial protein while AtFtsH11 is found in both chloroplasts and mitochondria. AtFtsH4 and AtFtsH11 proteases are integral parts of the inner mitochondrial membrane and expose their catalytic sites towards the intermembrane space, same as yeast i-AAA. Database searches revealed that orthologs of AtFtsH4 and AtFtsH11 are present in both monocotyledonous and dicotyledonous plants. The two plant i-AAA proteases differ significantly in their termini: the FtsH4 proteins have a characteristic alanine stretch at the C-terminal end while FtsH11s have long N-terminal extensions. Blue-native gel electrophoresis revealed that AtFtsH4 and AtFtsH11 form at least two complexes with apparent molecular masses of about 1500 kDa. This finding implies that plants, in contrast to fungi and metazoa, have more than one complex with a topology similar to that of yeast i-AAA.}, }
@article {pmid16245569, year = {2005}, author = {Provorov, NA}, title = {[Molecular basis of symbiogenic evolution: from free-living bacteria towards organelles].}, journal = {Zhurnal obshchei biologii}, volume = {66}, number = {5}, pages = {371-388}, pmid = {16245569}, issn = {0044-4596}, mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena ; Eukaryotic Cells/*cytology ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; Genetic Drift ; Genome, Bacterial ; Organelles ; Plasmids ; Symbiosis ; }, abstract = {Molecular mechanisms of the bacteria evolution are addressed in the context of the theory of symbiogenic origin of eukaryotic cells. In the evolution of symbiotic bacteria two strategies are implemented: (a) combinative, resulted in the formation of symbiotic (sym) gene systems from the genes previously involved in the autonomous life (facultative and ecologically obligatory symbioses); (b) reductive, related to the loss of genes for the autonomous life (genetically obligatory symbioses). Both strategies are based on the increase in genomic plasticity leading: (a) during combinative evolution--to the segregation of sym gene systems into the special plasmids or "islands" (the genome size and complexity increase); (b) during the reductive evolution--to the losses of many metabolic pathways (genome size decreases). These processes are continued during the evolution of mitochondria, hydrogenosomes and plastids in which many genes for the transcription and translation were lost, while the genomes of organelles and nuclei recombined. These reorganizations are related to the peculiarities of the bacteria population dynamics within the symbiotic systems. The bacteria which combine the abilities for symbiotic and autonomous lifestyles are characterized by ecotypic polymorphism (stable coexistence of symbiotic and asymbiotic genotypes). A key role in their evolution is implemented by horizontal transfer of sym genes that in combination with different forms of natural selection (individual, frequency-dependent and group selection) are responsible for the combinative evolution of bacteria genome. In the populations of obligatory symbionts, the genetic drift and group selection dominate that ensure bacteria genome reduction, loss of their biological identity and transformation into organelles.}, }
@article {pmid16242992, year = {2005}, author = {Martin, W}, title = {Archaebacteria (Archaea) and the origin of the eukaryotic nucleus.}, journal = {Current opinion in microbiology}, volume = {8}, number = {6}, pages = {630-637}, doi = {10.1016/j.mib.2005.10.004}, pmid = {16242992}, issn = {1369-5274}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; Cell Nucleus/*genetics ; Eukaryotic Cells/*ultrastructure ; }, abstract = {The eukaryotic nucleus is a unique structure. Because it lacks an obvious homologue or precursor among prokaryotes, ideas about its evolutionary origin are diverse. Current attempts to derive the nuclear membrane focus on invaginations of the plasma membrane in a prokaryote, endosymbiosis of an archaebacterium within a eubacterial host, or the origin of a genuinely new membrane system following the origin of mitochondria in an archaebacterial host. Recent reports point to ways in which different ideas regarding the origin of the nucleus might someday be discriminated.}, }
@article {pmid16240629, year = {2005}, author = {Odintsova, MS and Iurina, NP}, title = {[Genomics and evolution of cellular organelles].}, journal = {Genetika}, volume = {41}, number = {9}, pages = {1170-1182}, pmid = {16240629}, issn = {0016-6758}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; Genome/*genetics ; *Genomics/methods ; Organelles/*genetics ; Plants ; Symbiosis/genetics ; }, abstract = {The structure, functions, and evolution of cellular organelles are reviewed. The mitochondrial genomes of eukaryotes differ considerably in size and structural organization mainly due to the length variation in noncoding regions and the presence of introns. The mitochondrial genomes of angiosperms are the largest and most complicated. Gene content in eukaryotic mitochondrial genomes is similar. They usually encode all types of rRNA, a complete or partial complement of tRNA, and a limited number of proteins essential for mitochondrial functions. In all eukaryotes studied, mitochondrial genomes code for two highly hydrophobic proteins involved in respiration, cytochrome b and subunit 1 of cytochrome oxidase. Genome structure and gene content in plastids, mainly in higher plant chloroplasts, are highly conserved. Plastid genomes of algae are more variable in gene composition and contain several unique genes absent in the chloroplast DNA of higher plants. Plastid genomes encode proteins involved in transcription and translation, as well as proteins of the photosynthetic apparatus. Both types of cellular organelles are supposed to be of endosymbiotic origin. Modern plastids originate from a cyanobacterial ancestor. Alpha-proteobacteria, especially the most mitochondrion-like rickettsia, gave rise to mitochondria. The origin of plastids of higher plants and green algae as a result of primary endosymbiosis and that of other algal lineages by secondary endosymbiosis are briefly discussed.}, }
@article {pmid16239307, year = {2006}, author = {Yoshida, K and Terashima, I and Noguchi, K}, title = {Distinct roles of the cytochrome pathway and alternative oxidase in leaf photosynthesis.}, journal = {Plant &amp; cell physiology}, volume = {47}, number = {1}, pages = {22-31}, doi = {10.1093/pcp/pci219}, pmid = {16239307}, issn = {0032-0781}, mesh = {Antimycin A/pharmacology ; Chlorophyll/metabolism ; Cytochromes/*metabolism ; Electron Transport/drug effects ; Kinetics ; Mitochondrial Proteins ; Models, Biological ; Oxidoreductases/*metabolism ; Oxygen Consumption/drug effects ; Photosynthesis/drug effects/*physiology ; Photosystem II Protein Complex/metabolism ; Plant Leaves/drug effects/*metabolism/radiation effects ; Plant Proteins ; Salicylamides/pharmacology ; Vicia faba/drug effects/metabolism/radiation effects ; }, abstract = {In illuminated leaves, mitochondria are thought to play roles in optimizing photosynthesis. However, the roles of the cytochrome pathway (CP) and alternative oxidase (AOX) in photosynthesis, in particular in the redox state of the photosynthetic electron transport chain, are not separately characterized. We examined the effects of specific inhibition of two respiratory pathways, CP and AOX, on photosynthetic oxygen evolution and the redox state of the photosynthetic electron transport chain in broad bean (Vicia faba L.) leaves under various light intensities. Under saturating photosynthetic photon flux density (PPFD; 700 micromol photon m(-2) s(-1)), inhibition of either pathway caused a decrease in the steady-state levels of the photosynthetic O(2) evolution rate and the PSII operating efficiency, Phi(II). Because these inhibitors, at the concentrations applied to the leaves, had little effect on photosynthesis in the intact chloroplasts, two respiratory pathways are essential for maintenance of high photosynthetic rates at saturating PPFD. CP or AOX inhibition affected to Chl fluorescence parameters (e.g. photochemical quenching and non-photochemical quenching) differently, suggesting that CP and AOX contribute to photosynthesis in different ways. At low PPFD (100 micromol photon m(-2) s(-1)), only the inhibition of AOX, not CP, lowered the photosynthetic rate and Phi(II). AOX inhibition also decreased the Phi(II)/Phi(I) ratio even at low PPFD levels. These data suggest that AOX inhibition caused the over-reduction of the photosynthetic electron transport chain and induced the cyclic electron flow around PSI (CEF-PSI) even at the low PPFD. Based on these results, we discuss possible roles for CP and AOX in the light.}, }
@article {pmid16234795, year = {2005}, author = {Kapel'ko, VI}, title = {[Evolution of concept and metabolic basis of ischemic dysfunction of the myocardium].}, journal = {Kardiologiia}, volume = {45}, number = {9}, pages = {55-61}, pmid = {16234795}, issn = {0022-9040}, mesh = {Humans ; Mitochondria, Heart/metabolism/pathology ; Myocardial Ischemia/*metabolism/pathology/*physiopathology ; Myocardial Stunning/metabolism/pathology/physiopathology ; Reactive Oxygen Species/metabolism ; Terminology as Topic ; }, abstract = {Myocardial contractile function during acute as well as chronic ischemia is reduced due to activation of a number of metabolic energy protecting mechanisms. Their abolition during reperfusion, associated with oxidative stress and incomplete restoration of function may cause cellular apoptosis due to impairment of aerobic ATP resynthesis. Strategy of postischemic reperfusion of the heart should be based on the use of natural protective mechanisms providing preferential restoration of high energy phosphates. The state of mitochondria is decisive for survival or restoration of function of cells.}, }
@article {pmid16228120, year = {2006}, author = {Lin, G and Lo, LC and Zhu, ZY and Feng, F and Chou, R and Yue, GH}, title = {The complete mitochondrial genome sequence and characterization of single-nucleotide polymorphisms in the control region of the Asian seabass (Lates calcarifer).}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {8}, number = {1}, pages = {71-79}, pmid = {16228120}, issn = {1436-2228}, mesh = {Animals ; Base Composition/genetics ; Base Sequence/genetics ; Biological Evolution ; DNA, Mitochondrial/*chemistry ; Gene Order/genetics ; Genes, rRNA ; Genome/*genetics ; Locus Control Region/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Perciformes/classification/*genetics ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Polymorphism, Single Nucleotide/*genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/veterinary ; }, abstract = {We determined the complete mtDNA nucleotide sequence of Lates calcarifer using the shotgun sequencing method. The mitochondrial DNA (mtDNA) was 16,535 base pairs (bp) in length, and contained 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and one major noncoding control region (CR). The CR was unusually short at only 768 bp. A striking feature of the mitochondrial genome was the high G+C content (46.1%), which is among the highest in fish. The gene order was identical to that of a typical vertebrate. Phylogenetic analyses using concatenated amino acid sequences of 12 protein-coding genes of 30 fish species representing 14 suborders clearly showed Lates calcarifer was located in the cluster of fish species from the order Perciformes, supporting the traditional systematic classification. We characterized single-nucleotide polymorphisms (SNPs) in the CR by sequencing the complete CR of 25 individuals obtained from Australia and Singapore. A total of 68 SNPs were detected. Eighteen SNPs were fixed with alternative nucleotides in Australian and Singapore seabass, and these SNPs could be used for differentiating fish from the two countries.}, }
@article {pmid16216380, year = {2005}, author = {Leister, D}, title = {Origin, evolution and genetic effects of nuclear insertions of organelle DNA.}, journal = {Trends in genetics : TIG}, volume = {21}, number = {12}, pages = {655-663}, doi = {10.1016/j.tig.2005.09.004}, pmid = {16216380}, issn = {0168-9525}, mesh = {Cell Nucleus/*genetics/metabolism ; Chloroplasts/*genetics/metabolism ; DNA/genetics/*metabolism ; *Evolution, Molecular ; Humans ; Mitochondria/*genetics/metabolism ; Phylogeny ; Plants/genetics/metabolism ; }, abstract = {In eukaryotes, nuclear genomes are subject to an influx of DNA from mitochondria and plastids. The nuclear insertion of organellar sequences can occur during the illegitimate repair of double-stranded breaks. After integration, nuclear organelle DNA is modified by point mutations, and by deletions. Insertion of organelle DNA into nuclear genes is not rare and can potentially have harmful effects. In humans, some insertions of nuclear mitochondrial DNA are associated with heritable diseases. It remains to be determined whether nuclear organelle DNA can contribute beneficially to gene evolution.}, }
@article {pmid16215758, year = {2005}, author = {Lukes, J and Hashimi, H and Zíková, A}, title = {Unexplained complexity of the mitochondrial genome and transcriptome in kinetoplastid flagellates.}, journal = {Current genetics}, volume = {48}, number = {5}, pages = {277-299}, pmid = {16215758}, issn = {0172-8083}, support = {5R03TW6445-2/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; DNA, Kinetoplast/chemistry ; Gene Expression ; *Genes, Mitochondrial ; *Genome, Protozoan ; Kinetoplastida/*genetics ; Mitochondria/genetics ; RNA Editing ; RNA, Messenger/metabolism ; RNA, Protozoan/metabolism ; Transcription, Genetic ; }, abstract = {Kinetoplastids are flagellated protozoans, whose members include the pathogens Trypanosoma brucei, T. cruzi and Leishmania species, that are considered among the earliest diverging eukaryotes with a mitochondrion. This organelle has become famous because of its many unusual properties, which are unique to the order Kinetoplastida, including an extensive kinetoplast DNA network and U-insertion/deletion type RNA editing of its mitochondrial transcripts. In the last decade, considerable progress has been made in elucidating the complex machinery of RNA editing. Moreover, our understanding of the structure and replication of kinetoplast DNA has also dramatically improved. Much less however, is known, about the developmental regulation of RNA editing, its integration with other RNA maturation processes, stability of mitochondrial mRNAs, or evolution of the editing process itself. Yet the profusion of genomic data recently made available by sequencing consortia, in combination with methods of reverse genetics, hold promise in understanding the complexity of this exciting organelle, knowledge of which may enable us to fight these often medically important protozoans.}, }
@article {pmid16212260, year = {2005}, author = {Markov, AV and Kulikov, AM}, title = {[Homologous protein domains in superkingdoms Archaea, Bacteria, and Eukaryota and the problem of the origin of eukaryotes].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {4}, pages = {389-400}, pmid = {16212260}, issn = {1026-3470}, mesh = {Animals ; Archaea/*genetics/metabolism ; Archaeal Proteins/*genetics/metabolism ; Bacteria/*genetics/metabolism ; Bacterial Proteins/*genetics/metabolism ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; Mitochondria/genetics/metabolism ; Plastids/genetics/metabolism ; Protein Structure, Tertiary/physiology ; }, abstract = {The distribution of protein domains was analyzed in superkingdoms Archaea, Bacteria, and Eukaryota. About a half of eukaryotic domains have prokaryotic origin. Many domains related to information processing in the nucleocytoplasm were inherited from archaea. Sets of domains associated with metabolism and regulatory and signaling systems were inherited from bacteria. Many signaling and regulatory domains common for bacteria and eukaryotes were responsible for the cellular interaction of bacteria with other components of the microbial community but were involved in coordination of the activity of eukaryotic organelles and cells in multicellular organisms. Many eukaryotic domains of bacterial origin could not originate from ancestral mitochondria and plastids but rather were adopted from other bacteria. An archaeon with the induced incorporation of alien genetic material could be the ancestor of the eukaryotic nucleocytoplasm.}, }
@article {pmid16207980, year = {2005}, author = {Biswas, SK and Wang, L and Yokoyama, K and Nishimura, K}, title = {Molecular phylogenetics of the genus trichosporon inferred from mitochondrial cytochrome B gene sequences.}, journal = {Journal of clinical microbiology}, volume = {43}, number = {10}, pages = {5171-5178}, pmid = {16207980}, issn = {0095-1137}, mesh = {Amino Acid Sequence ; Cytochromes b/chemistry/*genetics ; DNA, Fungal/analysis ; Mitochondria/*enzymology ; Molecular Sequence Data ; Mycological Typing Techniques ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; Trichosporon/*classification/*genetics ; }, abstract = {Mitochondrial cytochrome b (cyt b) genes of 42 strains representing 23 species of the genus Trichosporon were partially sequenced to determine their molecular phylogenetic relationships. Almost half of the 22 strains investigated (from 11 different species) contained introns in their sequences. Analysis of a 396-bp coding sequence from each strain of Trichosporon under investigation showed a total of 141 (35.6%) variable nucleotide sites. A phylogenetic tree based on the cyt b gene sequences revealed that all species of Trichosporon except Trichosporon domesticum and Trichosporon montevideense had species-specific cyt b genes. Trichosporon sp. strain CBS 5581 was identified as Trichosporon pullulans, and one clinical isolate, IFM 48794, was identified as Trichosporon faecale. Analysis of 132-bp deduced amino acid sequences showed a total of 34 (25.75%) variable amino acid sites. T. domesticum and T. montevideense, Trichosporon asahii and Trichosporon asteroides, and Trichosporon gracile and Trichosporon guehoae had identical amino acid sequences. A phylogenetic tree constructed with the ascomycetes Saccharomyces douglasii and Candida glabrata taken as outgroup species and including representative species from closely related genera species of Trichosporon clustered with other basidiomycetous yeasts that contain xylose in their cell wall compositions. These results indicate the effectiveness of mitochondrial cyt b gene sequences for both species identification and the phylogenetic analysis of Trichosporon species.}, }
@article {pmid16204094, year = {2005}, author = {Gabaldón, T and Huynen, MA}, title = {Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes.}, journal = {Bioinformatics (Oxford, England)}, volume = {21 Suppl 2}, number = {}, pages = {ii144-50}, doi = {10.1093/bioinformatics/bti1124}, pmid = {16204094}, issn = {1367-4811}, mesh = {Animals ; Chromosome Mapping/*methods ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; *Gene Deletion ; Genetic Variation/genetics ; Humans ; Linkage Disequilibrium/*genetics ; Mitochondrial Proteins/*genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; Symbiosis/*genetics ; }, abstract = {The endosymbiotic origin of mitochondria has resulted in a massive horizontal transfer of genetic material from an alpha-proteobacterium to the early eukaryotes. Using large-scale phylogenetic analysis we have previously identified 630 orthologous groups of proteins derived from this event. Here we show that this proto-mitochondrial protein set has undergone extensive lineage-specific gene loss in the eukaryotes, with an average of three losses per orthologous group in a phylogeny of nine species. This gene loss has resulted in a high variability of the alphaproteobacterial-derived gene content of present-day eukaryotic genomes that might reflect functional adaptation to different environments. Proteins functioning in the same biochemical pathway tend to have a similar history of gene loss events, and we use this property to predict functional interactions among proteins in our set.}, }
@article {pmid16197560, year = {2005}, author = {Monti, MM and Nappo, AG and Giorgini, M}, title = {Molecular characterization of closely related species in the parasitic genus Encarsia (Hymenoptera: Aphelinidae) based on the mitochondrial cytochrome oxidase subunit I gene.}, journal = {Bulletin of entomological research}, volume = {95}, number = {5}, pages = {401-408}, doi = {10.1079/ber2005371}, pmid = {16197560}, issn = {0007-4853}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation/genetics ; Hymenoptera/*classification/*genetics ; Mitochondria/*enzymology/*genetics ; Parasites/classification/genetics ; Phylogeny ; Protein Subunits ; }, abstract = {The genus Encarsia Förster includes parasitoid species that are effective natural enemies of whitefly and armoured scale insect agricultural pests. Within this genus, several species groups have been recognized on the basis of morphological similarity, although their monophyly appears uncertain. It is often difficult to separate morphologically similar species, and there is evidence that some species could in fact be complexes of cryptic species. Their correct identification is fundamental for biological control purposes. Recently, due to unreliability of morphological characters, molecular techniques have been investigated to identify markers that differentiate closely related species. In this study, DNA variation in an approximately 900 bp segment of the mitochondrial cytochrome oxidase subunit I (COI) gene was examined by both sequencing and PCR-RFLP. Two pairs of species that are difficult to distinguish morphologically were analysed: Encarsia formosa Gahan and Encarsialuteola Howard, belonging to the luteola group, and two populations of Encarsiasophia (Girault &amp; Dodd) from Pakistan and Spain, belonging to the strenua group, recently characterized as cryptic species. High sequence divergence and species-specific restriction patterns clearly differentiate both species pairs. Parsimony analysis of the nucleotide sequences was also performed, including Encarsiahispida De Santis (luteola group) and Encarsia protransvena Viggiani (strenua group). Two monophyletic clades supporting the two groups of species considered were resolved. The results of this study support the use of the COI gene as a useful marker in separating species of Encarsia, for which morphological differences are subtle. Moreover, the COI gene appears potentially useful for understanding phylogenetic relationships in this genus.}, }
@article {pmid16188880, year = {2005}, author = {Chen, W and Li, N and Chen, T and Han, Y and Li, C and Wang, Y and He, W and Zhang, L and Wan, T and Cao, X}, title = {The lysosome-associated apoptosis-inducing protein containing the pleckstrin homology (PH) and FYVE domains (LAPF), representative of a novel family of PH and FYVE domain-containing proteins, induces caspase-independent apoptosis via the lysosomal-mitochondrial pathway.}, journal = {The Journal of biological chemistry}, volume = {280}, number = {49}, pages = {40985-40995}, doi = {10.1074/jbc.M502190200}, pmid = {16188880}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Apoptosis/*physiology ; Apoptosis Regulatory Proteins ; Blotting, Northern ; Caspases/*metabolism ; Cathepsin D/metabolism ; Cathepsin L ; Cathepsins/metabolism ; Cell Line, Tumor ; Cell Membrane Permeability ; Cloning, Molecular ; Cysteine Endopeptidases/metabolism ; DNA, Complementary/genetics ; Fibrosarcoma ; Gene Expression ; Humans ; Lysosomes/*metabolism ; Mice ; Microscopy, Electron ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Proteins/*chemistry/genetics/*physiology ; RNA, Messenger/antagonists &amp; inhibitors ; RNA, Small Interfering/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Transfection ; Tumor Necrosis Factor-alpha/pharmacology ; }, abstract = {Lysosomes have recently been identified as important apoptotic signal integrators in response to various stimuli. Here we report the functional characterization of LAPF, a novel lysosome-associated apoptosis-inducing protein containing PH and FYVE domains. LAPF is a representative of a new protein family, the Phafins (protein containing both PH and FYVE domains), which consists of 14 unidentified proteins from various species. Overexpression of LAPF in L929 cells induces apoptosis and also increases cell sensitivity to TNFalpha-induced apoptosis, concomitant with its translocation to lysosomes. Two mutants of LAPF, either lacking the PH or FYVE domain, failed to induce cell death and translocate to lysosomes, suggesting that both domains are required for its apoptosis-inducing activity and relocation. We demonstrate that LAPF may induce apoptosis via the following steps: LAPF translocation to lysosomes, lysosomal membrane permeabilization (LMP), release of cathepsin (cath) D and L, mitochondrial membrane permeabilization (MMP), release of apoptosis-inducing factor (AIF), and caspase-independent apoptosis. The cath D-specific inhibitor attenuates LAPF-induced apoptosis, indicating a pivotal role of lysosomes in LAPF-initiated apoptosis. We also demonstrate that the lysosomal pathway was employed in the typical apoptotic model in which high dose TNFalpha was used to stimulate L929 cells. Silencing of LAPF expression by small RNA interference protected L929 cells from hTNFalpha-induced apoptosis by impairing hTNFalpha-triggered LMP and MMP. Therefore, LAPF may launch caspase-independent apoptosis through the lysosomal-mitochondrial pathway.}, }
@article {pmid16188310, year = {2005}, author = {Uda, K and Tanaka, K and Bailly, X and Zal, F and Suzuki, T}, title = {Phosphagen kinase of the giant tubeworm Riftia pachyptila. Cloning and expression of cytoplasmic and mitochondrial isoforms of taurocyamine kinase.}, journal = {International journal of biological macromolecules}, volume = {37}, number = {1-2}, pages = {54-60}, doi = {10.1016/j.ijbiomac.2005.08.009}, pmid = {16188310}, issn = {0141-8130}, mesh = {Amino Acid Sequence ; Animals ; Annelida ; Arginine/chemistry ; Catalysis ; Cloning, Molecular ; Creatine/chemistry ; Cytoplasm/*metabolism ; DNA, Complementary/metabolism ; Evolution, Molecular ; Gene Library ; Glycine/analogs &amp; derivatives/chemistry ; Helminths ; Kinetics ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phosphotransferases (Nitrogenous Group Acceptor)/biosynthesis/*chemistry/*genetics ; Phylogeny ; Protein Isoforms ; Recombinant Proteins/chemistry ; Sequence Homology, Amino Acid ; Serine/analogs &amp; derivatives/chemistry ; Temperature ; }, abstract = {The giant tubeworm Riftia pachyptila lives at deep-sea hydrothermal vents along the East Pacific Rise and the Galapagos Rift. The large size and high growth rate of R. pachyptila is supported by an endosymbiotic relationship with a chemosynthetic bacterium. Elucidation of the regulation of energy metabolism of the giant tubeworm remains an interesting problem. The purpose of this study is to determine the cDNA sequence of phosphagen kinase, one of the most important enzymes in energy metabolism, and to characterize its function. Two phosphagen kinase cDNA sequences amplified from the cDNA library of R. pachyptila showed high derived amino acid sequence identity (74%) with those of cytoplasmic taurocyamine kinase (TK) and mitochondrial TK from an annelid Arenicola brasiliensis. The cytoplasmic form of the Riftia recombinant enzyme showed stronger activity for the substrates taurocyamine and also considerable activity for lombricine (21% that of taurocyamine). The mitochondrial form, which was structurally similar to mitochondrial creatine kinase, showed stronger activity for taurocyamine, and a broader activity for various guanidine compounds: glycocyamine (35% that of taurocyamine), lombricine (31%) and arginine (3%). Both forms showed no activity for creatine. The difference in substrate specificities between the cytoplasmic and mitochondrial forms might be attributable to the large difference in the amino acid sequence of the GS region and/or several key amino acid residues for establishing guanidine substrate specificity. Based on these results, we conclude that Riftia contains at least two forms of TK as phosphagen kinase. We also report the kinetic parameters, Km and kcat, of Arenicola and Riftia TKs for the first time. The Km values for taurocyamine of Arenicola and Riftia TKs ranged from 0.9 to 4.0 mM and appear to be comparable to those of other annelid-specific enzymes, lombricine kinase and glycocyamine kinase, but are significantly lower than those of Neanthes cytoplasmic and mitochondrial creatine kinases. Comparison of kcat/Km value in various annelid phosphagen kinases indicates that Arenicola mitochondrial TK has the highest catalytic efficiency (16.2 s-1 mM-1). In Arenicola TKs, the mitochondrial form has seven-fold higher efficiency than the cytoplasmic form.}, }
@article {pmid16187796, year = {2005}, author = {Salas, A and Yao, YG and Macaulay, V and Vega, A and Carracedo, A and Bandelt, HJ}, title = {A critical reassessment of the role of mitochondria in tumorigenesis.}, journal = {PLoS medicine}, volume = {2}, number = {11}, pages = {e296}, pmid = {16187796}, issn = {1549-1676}, mesh = {Artifacts ; Biomarkers, Tumor/*genetics ; DNA Mutational Analysis ; DNA, Mitochondrial/*genetics/metabolism ; Databases, Nucleic Acid ; Diagnostic Errors ; Genetics, Medical ; Haplotypes ; Humans ; Mutation/genetics ; Neoplasms/diagnosis/*genetics/metabolism ; Phylogeny ; Reproducibility of Results ; Research Design ; }, abstract = {BACKGROUND: Mitochondrial DNA (mtDNA) is being analyzed by an increasing number of laboratories in order to investigate its potential role as an active marker of tumorigenesis in various types of cancer. Here we question the conclusions drawn in most of these investigations, especially those published in high-rank cancer research journals, under the evidence that a significant number of these medical mtDNA studies are based on obviously flawed sequencing results.<br><br>METHODS AND FINDINGS: In our analyses, we take a phylogenetic approach and employ thorough database searches, which together have proven successful for detecting erroneous sequences in the fields of human population genetics and forensics. Apart from conceptual problems concerning the interpretation of mtDNA variation in tumorigenesis, in most cases, blocks of seemingly somatic mutations clearly point to contamination or sample mix-up and, therefore, have nothing to do with tumorigenesis.<br><br>CONCLUSION: The role of mitochondria in tumorigenesis remains unclarified. Our findings of laboratory errors in many contributions would represent only the tip of the iceberg since most published studies do not provide the raw sequence data for inspection, thus hindering a posteriori evaluation of the results. There is no precedent for such a concatenation of errors and misconceptions affecting a whole subfield of medical research.}, }
@article {pmid16185363, year = {2005}, author = {Bradshaw, PC and Rathi, A and Samuels, DC}, title = {Mitochondrial-encoded membrane protein transcripts are pyrimidine-rich while soluble protein transcripts and ribosomal RNA are purine-rich.}, journal = {BMC genomics}, volume = {6}, number = {}, pages = {136}, pmid = {16185363}, issn = {1471-2164}, mesh = {Adenosine Triphosphate/chemistry ; Codon ; Computational Biology/*methods ; DNA, Mitochondrial/genetics/metabolism ; Databases, Genetic ; Evolution, Molecular ; Humans ; Membrane Proteins/*chemistry ; Mitochondria/*metabolism ; Open Reading Frames ; Oxygen/metabolism ; Phosphorylation ; Purines/*chemistry/metabolism ; Pyrimidines/*chemistry ; RNA, Messenger/metabolism ; RNA, Ribosomal/*chemistry ; RNA, Transfer/chemistry ; }, abstract = {BACKGROUND: Eukaryotic organisms contain mitochondria, organelles capable of producing large amounts of ATP by oxidative phosphorylation. Each cell contains many mitochondria with many copies of mitochondrial DNA in each organelle. The mitochondrial DNA encodes a small but functionally critical portion of the oxidative phosphorylation machinery, a few other species-specific proteins, and the rRNA and tRNA used for the translation of these transcripts. Because the microenvironment of the mitochondrion is unique, mitochondrial genes may be subject to different selectional pressures than those affecting nuclear genes.<br><br>RESULTS: From an analysis of the mitochondrial genomes of a wide range of eukaryotic species we show that there are three simple rules for the pyrimidine and purine abundances in mitochondrial DNA transcripts. Mitochondrial membrane protein transcripts are pyrimidine rich, rRNA transcripts are purine-rich and the soluble protein transcripts are purine-rich. The transitions between pyrimidine and purine-rich regions of the genomes are rapid and are easily visible on a pyrimidine-purine walk graph. These rules are followed, with few exceptions, independent of which strand encodes the gene. Despite the robustness of these rules across a diverse set of species, the magnitude of the differences between the pyrimidine and purine content is fairly small. Typically, the mitochondrial membrane protein transcripts have a pyrimidine richness of 56%, the rRNA transcripts are 55% purine, and the soluble protein transcripts are only 53% purine.<br><br>CONCLUSION: The pyrimidine richness of mitochondrial-encoded membrane protein transcripts is partly driven by U nucleotides in the second codon position in all species, which yields hydrophobic amino acids. The purine-richness of soluble protein transcripts is mainly driven by A nucleotides in the first codon position. The purine-richness of rRNA is also due to an abundance of A nucleotides. Possible mechanisms as to how these trends are maintained in mtDNA genomes of such diverse ancestry, size and variability of A-T richness are discussed.}, }
@article {pmid16183216, year = {2005}, author = {Dávila, S and Piñero, D and Bustos, P and Cevallos, MA and Dávila, G}, title = {The mitochondrial genome sequence of the scorpion Centruroides limpidus (Karsch 1879) (Chelicerata; Arachnida).}, journal = {Gene}, volume = {360}, number = {2}, pages = {92-102}, doi = {10.1016/j.gene.2005.06.008}, pmid = {16183216}, issn = {0378-1119}, mesh = {Animals ; Arachnida/*genetics ; Base Composition/genetics ; Base Sequence ; DNA, Mitochondrial/chemistry/*genetics ; *Genome ; Mitochondria/genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer/*genetics/metabolism ; }, abstract = {The mitochondrial genome of the scorpion Centruroides limpidus (Chelicerata; Arachnida) has been completely sequenced and is 14519 bp long. The genome contains 13 protein-encoding genes, two ribosomal RNA genes, 21 transfer RNA genes and a large non-coding region related to the control region. The overall A+T composition is the lowest among the complete mitochondrial sequences published within the Chelicerata subphylum. Gene order and gene content differ slightly from that of Limulus polyphemus (Chelicerata: Xiphosura): i.e., the lack of the trnD gene, and the translocation-inversion of the trnI gene. Preliminary phylogenetic analysis of some Chelicerata shows that scorpions (C. limpidus and Mesobuthus gibbosus) make a tight cluster with the spiders (Arachnida; Araneae). Our analysis does not support that Scorpiones order is the sister group to all Arachnida Class, since it is closer to Araneae than to Acari orders.}, }
@article {pmid16180344, year = {2005}, author = {Riva, C and Longuet, M and Lucciano, M and Magnan, J and Lavieille, JP}, title = {[Implication of mitochondrial apoptosis in neural degeneration of cochlea in a murine model for presbycusis].}, journal = {Revue de laryngologie - otologie - rhinologie}, volume = {126}, number = {2}, pages = {67-74}, pmid = {16180344}, issn = {0035-1334}, mesh = {Adaptor Proteins, Signal Transducing/metabolism ; Animals ; Apoptosis/*physiology ; Cochlea/metabolism/*ultrastructure ; *Disease Models, Animal ; Mice ; Mice, Inbred C57BL ; Mitochondria/metabolism/*ultrastructure ; Nerve Degeneration/metabolism/*pathology ; Presbycusis/metabolism/*pathology ; Tumor Suppressor Protein p53/metabolism ; }, abstract = {HYPOTHESIS: Pathologies of senescence, in particular those of neurosensory organs represent an important health problem. The improvement of the life expectation entails the fast increase of the frequency of the presbyacusis in the population. The biological and molecular causes of this degenerative pathology of the inner ear are linked to the disappearance of the sensory cells (inner and outer hair cells) and are associated to nervous damages of the spiral ganglion in the cochlea. We were interested in mechanisms causing the cochlear degeneration in a model of mouse CD 1 presenting prematurely auditive losses.<br><br>MATERIALS AND METHODS: We tried to correlate the evolution of the hearing and the appearance of apoptotic phenomena by marking with specific antibody, activated anti-caspase-3, in the cochlea during time. We studied the role and the involvement of proteins controlling the apoptosis as the P53 protein and from an energy point of view at the level of the mitochondria such as proteins of the Bcl-2 family and the cytochrome c in the various structures of the cochlea.<br><br>RESULTS: After implantation of electrodes for auditory nerve acoustic thresholds measurements, the audition of mice CD 1 presented a characteristic profile of hearing losses which begins in the high frequencies from the age of 1 month and which quickly evolves towards the low frequencies. The observation (between the 1st and 3rd month of age) of spiral ganglion cells revealed an unchanged number of cellular bodies of type 1 neurons, on the other hand a characteristic morphology of apoptosis of glial cells with the formation of apoptotic body was noted. Indeed, glial cells expressed activated caspase-3. Furthermore, this phenomenon seems to be under the control of the pro-apoptotic protein Bax by its overexpression and a increased release of the cytochrome c. This phenomenon was followed at 3 and 6 months by the disappearance of the outer hair cells by 9 and 48% respectively.<br><br>CONCLUSION: The apparition of the deafness in the murin model CD 1 allowed us to demonstrate that the degeneration of cochlear structure begins at the level of glial cells of the spiral ganglion from 3 months, followed thereafter by the deterioration of the nervous conduction between the spiral ganglion and the sensory cells. As a consequence, because of the impoverishment in nervous signals, the outer hair cells would begin to disappear during the 6th month. In conclusion, the understanding of the sequence and the cause of these mechanisms responsible for the neural degeneration and the loss of hearing could eventually, allow us to optimize the various treatments of the presbyacusis.}, }
@article {pmid16172508, year = {2006}, author = {Kivisild, T and Shen, P and Wall, DP and Do, B and Sung, R and Davis, K and Passarino, G and Underhill, PA and Scharfe, C and Torroni, A and Scozzari, R and Modiano, D and Coppa, A and de Knijff, P and Feldman, M and Cavalli-Sforza, LL and Oefner, PJ}, title = {The role of selection in the evolution of human mitochondrial genomes.}, journal = {Genetics}, volume = {172}, number = {1}, pages = {373-387}, pmid = {16172508}, issn = {0016-6731}, support = {R01 GM063883/GM/NIGMS NIH HHS/United States ; P01 GM028428/GM/NIGMS NIH HHS/United States ; GM28428/GM/NIGMS NIH HHS/United States ; GM55273/GM/NIGMS NIH HHS/United States ; GM63883/GM/NIGMS NIH HHS/United States ; E.0890/TI_/Telethon/Italy ; }, mesh = {Amino Acid Substitution ; Base Pairing ; Base Sequence ; Codon/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; *Genome, Human ; Humans ; Mitochondria/*genetics ; Molecular Sequence Data ; Mutation/genetics ; Phylogeny ; RNA, Ribosomal/genetics ; *Selection, Genetic ; }, abstract = {High mutation rate in mammalian mitochondrial DNA generates a highly divergent pool of alleles even within species that have dispersed and expanded in size recently. Phylogenetic analysis of 277 human mitochondrial genomes revealed a significant (P < 0.01) excess of rRNA and nonsynonymous base substitutions among hotspots of recurrent mutation. Most hotspots involved transitions from guanine to adenine that, with thymine-to-cytosine transitions, illustrate the asymmetric bias in codon usage at synonymous sites on the heavy-strand DNA. The mitochondrion-encoded tRNAThr varied significantly more than any other tRNA gene. Threonine and valine codons were involved in 259 of the 414 amino acid replacements observed. The ratio of nonsynonymous changes from and to threonine and valine differed significantly (P = 0.003) between populations with neutral (22/58) and populations with significantly negative Tajima's D values (70/76), independent of their geographic location. In contrast to a recent suggestion that the excess of nonsilent mutations is characteristic of Arctic populations, implying their role in cold adaptation, we demonstrate that the surplus of nonsynonymous mutations is a general feature of the young branches of the phylogenetic tree, affecting also those that are found only in Africa. We introduce a new calibration method of the mutation rate of synonymous transitions to estimate the coalescent times of mtDNA haplogroups.}, }
@article {pmid16169894, year = {2005}, author = {Christensen, AC and Lyznik, A and Mohammed, S and Elowsky, CG and Elo, A and Yule, R and Mackenzie, SA}, title = {Dual-domain, dual-targeting organellar protein presequences in Arabidopsis can use non-AUG start codons.}, journal = {The Plant cell}, volume = {17}, number = {10}, pages = {2805-2816}, pmid = {16169894}, issn = {1040-4651}, mesh = {5' Untranslated Regions/genetics ; Amino Acid Sequence/genetics ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/genetics/*metabolism ; Base Sequence/genetics ; Codon, Initiator/*genetics ; Codon, Terminator/genetics ; DNA-Directed DNA Polymerase/genetics/metabolism ; Eukaryotic Initiation Factors/genetics/*metabolism ; Gene Expression Regulation, Plant/genetics ; Mitochondrial Proteins/genetics/metabolism ; Organelles/genetics/*metabolism ; Plastids/genetics/metabolism ; Protein Biosynthesis/*genetics ; Protein Structure, Tertiary/genetics ; Protein Transport/genetics ; Recombination, Genetic/genetics ; }, abstract = {The processes accompanying endosymbiosis have led to a complex network of interorganellar protein traffic that originates from nuclear genes encoding mitochondrial and plastid proteins. A significant proportion of nucleus-encoded organellar proteins are dual targeted, and the process by which a protein acquires the capacity for both mitochondrial and plastid targeting may involve intergenic DNA exchange coupled with the incorporation of sequences residing upstream of the gene. We evaluated targeting and sequence alignment features of two organellar DNA polymerase genes from Arabidopsis thaliana. Within one of these two loci, protein targeting appeared to be plastidic when the 5' untranslated leader region (UTR) was deleted and translation could only initiate at the annotated ATG start codon but dual targeted when the 5' UTR was included. Introduction of stop codons at various sites within the putative UTR demonstrated that this region is translated and influences protein targeting capacity. However, no ATG start codon was found within this upstream, translated region, suggesting that translation initiates at a non-ATG start. We identified a CTG codon that likely accounts for much of this initiation. Investigation of the 5' region of other nucleus-encoded organellar genes suggests that several genes may incorporate upstream sequences to influence targeting capacity. We postulate that a combination of intergenic recombination and some relaxation of constraints on translation initiation has acted in the evolution of protein targeting specificity for those proteins capable of functioning in both plastids and mitochondria.}, }
@article {pmid16167181, year = {2005}, author = {Wojtkowska, M and Szczech, N and Stobienia, O and Jarmuszkiewicz, W and Budzinska, M and Kmita, H}, title = {An inception report on the TOM complex of the Amoeba Acanthamoeba castellanii, a simple model protozoan in mitochondria studies.}, journal = {Journal of bioenergetics and biomembranes}, volume = {37}, number = {4}, pages = {261-268}, pmid = {16167181}, issn = {0145-479X}, mesh = {Acanthamoeba castellanii/*genetics/metabolism/ultrastructure ; Amino Acid Sequence ; Animals ; Carrier Proteins/*genetics/metabolism ; DNA, Protozoan/genetics ; Evolution, Molecular ; Mass Spectrometry ; Membrane Proteins/genetics/metabolism ; Mitochondria/genetics/*metabolism ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Precursor Protein Import Complex Proteins ; Molecular Sequence Data ; Protein Binding ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; }, abstract = {It is suggested that in the course of the TOM complex evolution at least two lineages have appeared: the animal-fungal and green plant ones. The latter involves also the TOM complexes of algae and protozoans. The amoeba Acanthamoeba castellanii is a free-living non-photosynthetic soil protozoan, whose mitochondria share many bioenergetic properties with mitochondria of plants, animals and fungi. Here, we report that a protein complex, identified electrophysiologically as the A. castellanii TOM complex, contains a homologue of yeast/animal Tom 70. Further, molecular weight of the complex (about 500 kDa) also points to A. castellanii evolutionary relation with fungi and animal. Thus, the data indicates that the TOM complex of A. castellanii is not a typical example of the protozoan TOM complex.}, }
@article {pmid16162501, year = {2005}, author = {Roy, H and Ling, J and Alfonzo, J and Ibba, M}, title = {Loss of editing activity during the evolution of mitochondrial phenylalanyl-tRNA synthetase.}, journal = {The Journal of biological chemistry}, volume = {280}, number = {46}, pages = {38186-38192}, doi = {10.1074/jbc.M508281200}, pmid = {16162501}, issn = {0021-9258}, mesh = {Adenosine Triphosphate/chemistry ; Amino Acid Sequence ; Binding Sites ; Cytosol/metabolism ; DNA-Directed RNA Polymerases/chemistry ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/metabolism ; Evolution, Molecular ; Kinetics ; Mitochondria/*enzymology/metabolism ; Models, Biological ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phenylalanine/chemistry ; Phenylalanine-tRNA Ligase/*chemistry ; Phosphates/chemistry ; Phylogeny ; Plasmids/metabolism ; Point Mutation ; Protein Biosynthesis ; *RNA Editing ; RNA, Transfer/chemistry ; Ribosomes/*physiology ; Saccharomyces cerevisiae/metabolism ; Sequence Homology, Amino Acid ; Substrate Specificity ; Time Factors ; Transcription, Genetic ; Tyrosine/chemistry ; Viral Proteins/chemistry ; }, abstract = {Accurate selection of amino acids is essential for faithful translation of the genetic code. Errors during amino acid selection are usually corrected by the editing activity of aminoacyl-tRNA synthetases such as phenylalanyl-tRNA synthetases (PheRS), which edit misactivated tyrosine. Comparison of cytosolic and mitochondrial PheRS from the yeast Saccharomyces cerevisiae suggested that the organellar protein might lack the editing activity. Yeast cytosolic PheRS was found to contain an editing site, which upon disruption abolished both cis and trans editing of Tyr-tRNA(Phe). Wild-type mitochondrial PheRS lacked cis and trans editing and could synthesize Tyr-tRNA(Phe), an activity enhanced in active site variants with improved tyrosine recognition. Possible trans editing was investigated in isolated mitochondrial extracts, but no such activity was detected. These data indicate that the mitochondrial protein synthesis machinery lacks the tyrosine proofreading activity characteristic of cytosolic translation. This difference between the mitochondria and the cytosol suggests that either organellar protein synthesis quality control is focused on another step or that translation in this compartment is inherently less accurate than in the cytosol.}, }
@article {pmid16162288, year = {2005}, author = {Liang, P and Nair, JR and Song, L and McGuire, JJ and Dolnick, BJ}, title = {Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.}, journal = {BMC genomics}, volume = {6}, number = {}, pages = {125}, pmid = {16162288}, issn = {1471-2164}, support = {CA101515/CA/NCI NIH HHS/United States ; EB002116/EB/NIBIB NIH HHS/United States ; P30 CA016056/CA/NCI NIH HHS/United States ; CA16056/CA/NCI NIH HHS/United States ; R01 EB002116/EB/NIBIB NIH HHS/United States ; R03 CA101515/CA/NCI NIH HHS/United States ; CA43500/CA/NCI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Western ; Cell Line ; Codon ; Computational Biology/*methods ; Genome ; Genomics/*methods ; Humans ; Mitochondria/*metabolism ; Models, Biological ; Molecular Sequence Data ; Phylogeny ; Protein Isoforms ; Protein Structure, Tertiary ; Subcellular Fractions ; Thymidylate Synthase/*genetics/metabolism ; }, abstract = {BACKGROUND: The rTS gene (ENOSF1), first identified in Homo sapiens as a gene complementary to the thymidylate synthase (TYMS) mRNA, is known to encode two protein isoforms, rTSalpha and rTSbeta. The rTSbeta isoform appears to be an enzyme responsible for the synthesis of signaling molecules involved in the down-regulation of thymidylate synthase, but the exact cellular functions of rTS genes are largely unknown.<br><br>RESULTS: Through comparative genomic sequence analysis, we predicted the existence of a novel protein isoform, rTS, which has a 27 residue longer N-terminus by virtue of utilizing an alternative start codon located upstream of the start codon in rTSbeta. We observed that a similar extended N-terminus could be predicted in all rTS genes for which genomic sequences are available and the extended regions are conserved from bacteria to human. Therefore, we reasoned that the protein with the extended N-terminus might represent an ancestral form of the rTS protein. Sequence analysis strongly predicts a mitochondrial signal sequence in the extended N-terminal of human rTSgamma, which is absent in rTSbeta. We confirmed the existence of rTS in human mitochondria experimentally by demonstrating the presence of both rTSgamma and rTSbeta proteins in mitochondria isolated by subcellular fractionation. In addition, our comprehensive analysis of rTS orthologous sequences reveals an unusual phylogenetic distribution of this gene, which suggests the occurrence of one or more horizontal gene transfer events.<br><br>CONCLUSION: The presence of two rTS isoforms in mitochondria suggests that the rTS signaling pathway may be active within mitochondria. Our report also presents an example of identifying novel protein isoforms and for improving gene annotation through comparative genomic analysis.}, }
@article {pmid16159319, year = {2005}, author = {Barr, CM and Neiman, M and Taylor, DR}, title = {Inheritance and recombination of mitochondrial genomes in plants, fungi and animals.}, journal = {The New phytologist}, volume = {168}, number = {1}, pages = {39-50}, doi = {10.1111/j.1469-8137.2005.01492.x}, pmid = {16159319}, issn = {0028-646X}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Fungi/*genetics ; *Genome ; Mitochondria/*genetics ; Mutation ; Plants/*genetics ; Recombination, Genetic ; }, abstract = {It is generally assumed that mitochondrial genomes are uniparentally transmitted, homoplasmic and nonrecombining. However, these assumptions draw largely from early studies on animal mitochondrial DNA (mtDNA). In this review, we show that plants, animals and fungi are all characterized by episodes of biparental inheritance, recombination among genetically distinct partners, and selfish elements within the mitochondrial genome, but that the extent of these phenomena may vary substantially across taxa. We argue that occasional biparental mitochondrial transmission may allow organisms to achieve the best of both worlds by facilitating mutational clearance but continuing to restrict the spread of selfish genetic elements. We also show that methodological biases and disproportionately allocated study effort are likely to have influenced current estimates of the extent of biparental inheritance, heteroplasmy and recombination in mitochondrial genomes from different taxa. Despite these complications, there do seem to be discernible similarities and differences in transmission dynamics and likelihood of recombination of mtDNA in plant, animal and fungal taxa that should provide an excellent opportunity for comparative investigation of the evolution of mitochondrial genome dynamics.}, }
@article {pmid16159315, year = {2005}, author = {Mauricio, R}, title = {The 'bricolage' of the genome elucidated through evolutionary genomics.}, journal = {The New phytologist}, volume = {168}, number = {1}, pages = {1-4}, doi = {10.1111/j.1469-8137.2005.01554.x}, pmid = {16159315}, issn = {0028-646X}, mesh = {*Biological Evolution ; DNA, Intergenic/genetics ; Gene Duplication ; *Genome, Plant ; Mitochondria/genetics ; Multigene Family ; Plants/*genetics ; }, }
@article {pmid16157484, year = {2005}, author = {Filée, J and Forterre, P}, title = {Viral proteins functioning in organelles: a cryptic origin?.}, journal = {Trends in microbiology}, volume = {13}, number = {11}, pages = {510-513}, doi = {10.1016/j.tim.2005.08.012}, pmid = {16157484}, issn = {0966-842X}, mesh = {Alphaproteobacteria/*genetics ; Bacteriophages/genetics ; Chloroplasts/genetics ; Computational Biology ; DNA Primase/genetics ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed RNA Polymerases/genetics ; Genome, Bacterial/genetics ; Mitochondria/chemistry/*physiology ; Prophages/genetics ; Viral Proteins/genetics/*physiology ; }, abstract = {Although mitochondria derive from alpha-proteobacteria, many proteins acting in this organelle did not originate from bacteria. In particular, phylogenetic evidence indicates that RNA polymerase, DNA polymerase and DNA primase--with homologues encoded by T3/T7-like bacteriophages--have replaced the ancestral proteins of bacterial origin. To date, there was no clear explanation for this puzzling observation. Bacterial genomics has now revealed the presence of cryptic prophages that are related to T3/T7 in several genomes of proteobacteria. We propose that such a prophage was present in the ancestral alpha-proteobacterium at the origin of mitochondria and that RNA polymerase, DNA polymerase and DNA primase encoded by this prophage replaced the original bacterial enzymes to function in mitochondria. Another T3/T7 viral-like RNA polymerase is functional in the chloroplast, indicating that a strong selection pressure has favored replacement of some cellular proteins by viral proteins in organelle evolution.}, }
@article {pmid16155230, year = {2005}, author = {Darveau, CA and Hochachka, PW and Roubik, DW and Suarez, RK}, title = {Allometric scaling of flight energetics in orchid bees: evolution of flux capacities and flux rates.}, journal = {The Journal of experimental biology}, volume = {208}, number = {Pt 18}, pages = {3593-3602}, doi = {10.1242/jeb.01777}, pmid = {16155230}, issn = {0022-0949}, mesh = {Animals ; Bees/metabolism/*physiology ; *Biological Evolution ; Cell Respiration/physiology ; Energy Metabolism/*physiology ; Enzymes/*metabolism ; Flight, Animal/*physiology ; Mitochondria/metabolism ; Muscles/enzymology/*physiology ; Panama ; Spectrophotometry, Ultraviolet ; }, abstract = {The evolution of metabolic pathways involved in energy production was studied in the flight muscles of 28 species of orchid bees. Previous work revealed that wingbeat frequencies and mass-specific metabolic rates decline in parallel by threefold as body mass increases interspecifically over a 20-fold range. We investigated the correlated evolution of metabolic rates during hovering flight and the flux capacities, i.e. V(max) values, of flight muscle enzymes involved in substrate catabolism, the Krebs cycle and the electron transport chain. V(max) at the hexokinase (HK) step scales allometrically with an exponent almost identical to those obtained for wingbeat frequency and mass-specific metabolic rate. Analysis of this relationship using phylogenetically independent contrasts supports the hypothesis of correlated evolution between HK activity and mass-specific metabolic rate. Although other enzymes scale allometrically with respect to body mass, e.g. trehalase, glycogen phosphorylase and citrate synthase, no other enzyme activities were correlated with metabolic rate after controlling for phylogenetic relatedness. Pathway flux rates were used with enzyme V(max) values to estimate fractional velocities (fraction of V(max) at which enzymes operate) for various reactions to gain insights into enzyme function and how this varies with body mass. Fractional velocity is highly conserved across species at the HK step, but varied at all other steps examined. These results are discussed in the context of the regulation and evolution of pathways of energy metabolism.}, }
@article {pmid16155228, year = {2005}, author = {Suarez, RK and Darveau, CA and Welch, KC and O'Brien, DM and Roubik, DW and Hochachka, PW}, title = {Energy metabolism in orchid bee flight muscles: carbohydrate fuels all.}, journal = {The Journal of experimental biology}, volume = {208}, number = {Pt 18}, pages = {3573-3579}, doi = {10.1242/jeb.01775}, pmid = {16155228}, issn = {0022-0949}, mesh = {3-Hydroxyacyl CoA Dehydrogenases/metabolism ; Animals ; Bees/enzymology/*physiology ; Carbohydrate Metabolism/*physiology ; Carbon Dioxide/metabolism ; Energy Metabolism/*physiology ; Flight, Animal/*physiology ; Glycogen Phosphorylase/metabolism ; Hexokinase/metabolism ; Mitochondria/metabolism ; Muscles/enzymology/*physiology ; Oxygen Consumption/physiology ; Panama ; Species Specificity ; Spectrophotometry, Ultraviolet ; Trehalase/metabolism ; }, abstract = {The widely accepted idea that bees fuel flight through the oxidation of carbohydrate is based on studies of only a few species. We tested this hypothesis as part of our research program to investigate the size-dependence of flight energetics in Panamanian orchid bees. We succeeded in measuring rates of O(2) consumption and CO(2) production in vivo during hovering flight, as well as maximal activities (V(max) values) in vitro of key enzymes in flight muscle energy metabolism in nine species belonging to four genera. Respiratory quotients (ratios of rates of CO(2) production to O(2) consumption) in all nine species are close to 1.0. This indicates that carbohydrate is the main fuel used for flight. Trehalase, glycogen phosphorylase and hexokinase activities are sufficient to account for the glycolytic flux rates estimated from rates of CO(2) production. High activities of other glycolytic enzymes, as well as high activities of mitochondrial oxidative enzymes, are consistent with the estimated rates of carbohydrate-fueled oxidative metabolism. In contrast, hydroxyacylCoA dehydrogenase, an enzyme involved in fatty acid oxidation, was not detectable in any species. Thoracic homogenates displayed ADP-stimulated oxidition of pyruvate + proline, but did not oxidize palmitoyl l-carnitine + proline as substrates. A metabolic map, based on data reported herein and information from the literature, is presented. The evidence available supports the hypothesis that carbohydrate serves as the main fuel for flight in bees.}, }
@article {pmid16151221, year = {2005}, author = {van der Giezen, M and León-Avila, G and Tovar, J}, title = {Characterization of chaperonin 10 (Cpn10) from the intestinal human pathogen Entamoeba histolytica.}, journal = {Microbiology (Reading, England)}, volume = {151}, number = {Pt 9}, pages = {3107-3115}, doi = {10.1099/mic.0.28068-0}, pmid = {16151221}, issn = {1350-0872}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Chaperonin 10/chemistry/genetics/*metabolism ; DNA, Protozoan/analysis ; Entamoeba histolytica/genetics/*metabolism ; Heat-Shock Response ; Humans ; Intestines/*parasitology ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Entamoeba histolytica is the causative agent of amoebiasis, a poverty-related disease that kills an estimated 100 000 people each year. E. histolytica does not contain "standard mitochondria", but harbours mitochondrial remnant organelles called mitosomes. These organelles are characterized by the presence of mitochondrial chaperonin Cpn60, but little else is known about the functions and molecular composition of mitosomes. In this study, a gene encoding molecular chaperonin Cpn10--the functional partner of Cpn60--was cloned, and its structure and expression were characterized, as well as the cellular localization of its encoded protein. The 5' untranslated region of the gene contains all of the structural promoter elements required for transcription in this organism. The amoebic Cpn10, like Cpn60, is not significantly upregulated upon heat-shock treatment. Computer-assisted protein modelling, and specific antibodies against Cpn10 and Cpn60, suggest that both proteins interact with each other, and that they function in the same intracellular compartment. Thus, E. histolytica appears to have retained at least two of the key molecular components required for the refolding of imported mitosomal proteins.}, }
@article {pmid16151187, year = {2006}, author = {Fitzpatrick, DA and Creevey, CJ and McInerney, JO}, title = {Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales.}, journal = {Molecular biology and evolution}, volume = {23}, number = {1}, pages = {74-85}, doi = {10.1093/molbev/msj009}, pmid = {16151187}, issn = {0737-4038}, mesh = {Alphaproteobacteria/*genetics ; Base Sequence ; Bayes Theorem ; Computational Biology ; *Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Genome, Bacterial/*genetics ; Mitochondria/*genetics ; Models, Genetic ; *Phylogeny ; Sequence Alignment ; Species Specificity ; }, abstract = {Placement of the mitochondrial branch on the tree of life has been problematic. Sparse sampling, the uncertainty of how lateral gene transfer might overwrite phylogenetic signals, and the uncertainty of phylogenetic inference have all contributed to the issue. Here we address this issue using a supertree approach and completed genomic sequences. We first determine that a sensible alpha-proteobacterial phylogenetic tree exists and that it can confidently be inferred using orthologous genes. We show that congruence across these orthologous gene trees is significantly better than might be expected by random chance. There is some evidence of horizontal gene transfer within the alpha-proteobacteria, but it appears to be restricted to a minority of genes (approximately 23%) most of whom (approximately 74%) can be categorized as operational. This means that placement of the mitochondrion should not be excessively hampered by interspecies gene transfer. We then show that there is a consistently strong signal for placement of the mitochondrion on this tree and that this placement is relatively insensitive to methodological approach or data set. A concatenated alignment was created consisting of 15 mitochondrion-encoded proteins that are unlikely to have undergone any lateral gene transfer in the timeline under consideration. This alignment infers that the sister group of the mitochondria, for the taxa that have been sampled, is the order Rickettsiales.}, }
@article {pmid16144518, year = {2005}, author = {Xu, SQ and Yang, YZ and Zhou, J and Jing, GE and Chen, YT and Wang, J and Yang, HM and Wang, J and Yu, J and Zheng, XG and Ge, RL}, title = {A mitochondrial genome sequence of the Tibetan antelope (Pantholops hodgsonii).}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {3}, number = {1}, pages = {5-17}, pmid = {16144518}, issn = {1672-0229}, mesh = {Amino Acid Sequence ; Animals ; Antelopes/*genetics ; Cyclooxygenase 1 ; Cytochromes b/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Evolution, Molecular ; Genome ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; Prostaglandin-Endoperoxide Synthases/genetics ; RNA, Transfer/genetics ; Sequence Homology, Amino Acid ; Tibet ; }, abstract = {To investigate genetic mechanisms of high altitude adaptations of native mammals on the Tibetan Plateau, we compared mitochondrial sequences of the endangered Pantholops hodgsonii with its lowland distant relatives Ovis aries and Capra hircus, as well as other mammals. The complete mitochondrial genome of P. hodgsonii (16,498 bp) revealed a similar gene order as of other mammals. Because of tandem duplications, the control region of P. hodgsonii mitochondrial genome is shorter than those of O. aries and C. hircus, but longer than those of Bos species. Phylogenetic analysis based on alignments of the entire cytochrome b genes suggested that P. hodgsonii is more closely related to O. aries and C. hircus, rather than to species of the Antilopinae subfamily. The estimated divergence time between P. hodgsonii and O. aries is about 2.25 million years ago. Further analysis on natural selection indicated that the COXI (cytochrome c oxidase subunit I) gene was under positive selection in P. hodgsonii and Bos grunniens. Considering the same climates and environments shared by these two mammalian species, we proposed that the mitochondrial COXI gene is probably relevant for these native mammals to adapt the high altitude environment unique to the Tibetan Plateau.}, }
@article {pmid16143878, year = {2005}, author = {Miyagishima, SY}, title = {Origin and evolution of the chloroplast division machinery.}, journal = {Journal of plant research}, volume = {118}, number = {5}, pages = {295-306}, pmid = {16143878}, issn = {0918-9440}, mesh = {*Biological Evolution ; *Chloroplasts ; Cyanobacteria/ultrastructure ; Eukaryotic Cells ; Mitochondria ; Plastids ; Symbiosis ; }, abstract = {Chloroplasts were originally established in eukaryotes by the endosymbiosis of a cyanobacterium; they then spread through diversification of the eukaryotic hosts and subsequent engulfment of eukaryotic algae by previously nonphotosynthetic eukaryotes. The continuity of chloroplasts is maintained by division of preexisting chloroplasts. Like their ancestors, chloroplasts use a bacterial division system based on the FtsZ ring and some associated factors, all of which are now encoded in the host nuclear genome. The majority of bacterial division factors are absent from chloroplasts and several new factors have been added by the eukaryotic host. For example, the ftsZ gene has been duplicated and modified, plastid-dividing (PD) rings were most likely added by the eukaryotic host, and a member of the dynamin family of proteins evolved to regulate chloroplast division. The identification of several additional proteins involved in the division process, along with data from diverse lineages of organisms, our current knowledge of mitochondrial division, and the mining of genomic sequence data have enabled us to begin to understand the universality and evolution of the division system. The principal features of the chloroplast division system thus far identified are conserved across several lineages, including those with secondary chloroplasts, and may reflect primeval features of mitochondrial division.}, }
@article {pmid16131591, year = {2005}, author = {Neuwirt, J and Takenaka, M and van der Merwe, JA and Brennicke, A}, title = {An in vitro RNA editing system from cauliflower mitochondria: editing site recognition parameters can vary in different plant species.}, journal = {RNA (New York, N.Y.)}, volume = {11}, number = {10}, pages = {1563-1570}, pmid = {16131591}, issn = {1355-8382}, mesh = {5' Untranslated Regions ; Arabidopsis Proteins ; Base Sequence ; Brassica/cytology/*genetics ; Cell Extracts ; Cell-Free System/chemistry/metabolism ; Conserved Sequence ; Evolution, Molecular ; Genetic Variation ; In Vitro Techniques ; Mitochondrial Proton-Translocating ATPases ; Molecular Sequence Data ; Pisum sativum/cytology/genetics ; Point Mutation ; RNA/*chemistry/metabolism ; *RNA Editing ; RNA, Mitochondrial ; RNA, Plant/*chemistry/metabolism ; Regulatory Sequences, Nucleic Acid/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Deletion ; Sequence Homology, Nucleic Acid ; Species Specificity ; Templates, Genetic ; }, abstract = {Most of the 400 RNA editing sites in flowering plant mitochondria are found in mRNAs. Consequently, the sequence vicinities of homologous sites are highly conserved between different species and are presumably recognized by likewise conserved trans-factors. To investigate the evolutionary adaptation to sequence variation, we have now analyzed the recognition elements of an editing site with divergent upstream sequences in the two species pea and cauliflower. This variation is tolerated at the site selected, because the upstream cis-elements reach into the 5'-UTR of the mRNA. To compare cis-recognition features in pea and cauliflower mitochondria, we developed a new in vitro RNA editing system for cauliflower. In vitro editing assays with deleted and mutated template RNAs show that the major recognition elements for both species are located within the conserved sequence. In cauliflower, however, the essential upstream nucleotides extend further upstream than they do in pea. In-depth analysis of single-nucleotide mutations reveals critical spacing of the editing site and the specific recognition elements, and shows that the +1 nucleotide identity is important in cauliflower, but not in pea.}, }
@article {pmid16126389, year = {2005}, author = {Paschen, SA and Neupert, W and Rapaport, D}, title = {Biogenesis of beta-barrel membrane proteins of mitochondria.}, journal = {Trends in biochemical sciences}, volume = {30}, number = {10}, pages = {575-582}, doi = {10.1016/j.tibs.2005.08.009}, pmid = {16126389}, issn = {0968-0004}, mesh = {Bacterial Proteins/genetics/physiology ; Evolution, Molecular ; Gram-Negative Bacteria/genetics/physiology ; Mitochondria/*physiology ; Mitochondrial Membrane Transport Proteins/genetics/*physiology ; Organelles ; *Origin of Life ; }, abstract = {beta-Barrel membrane proteins have several important functions in outer membranes of Gram-negative bacteria and in the organelles of endosymbiotic origin, mitochondria and chloroplasts. The biogenesis of beta-barrel membrane proteins was, until recently, an unresolved process. A breakthrough was achieved when a specific pathway for the insertion of beta-barrel outer-membrane proteins was identified in both mitochondria and Gram-negative bacteria. The key component of this pathway is Tob55 (also known as Sam50) in mitochondria and Omp85 in bacteria, both beta-barrel membrane proteins themselves. Tob55 is part of the hetero-oligomeric TOB (topogenesis of mitochondrial outer-membrane beta-barrel proteins) or SAM (sorting and assembly of mitochondria) complex, which is present in the mitochondrial outer membrane. Tob55 belongs to an evolutionarily conserved protein family, the members of which are present in almost all eukaryotes and in Gram-negative bacteria and chloroplasts. Thus, is it emphasized that the insertion pathway of mitochondrial beta-barrel membrane proteins was conserved during evolution of mitochondria from endosymbiotic bacterial ancestors.}, }
@article {pmid16121172, year = {2005}, author = {Richards, TA and Cavalier-Smith, T}, title = {Myosin domain evolution and the primary divergence of eukaryotes.}, journal = {Nature}, volume = {436}, number = {7054}, pages = {1113-1118}, doi = {10.1038/nature03949}, pmid = {16121172}, issn = {1476-4687}, mesh = {Animals ; Bayes Theorem ; Classification ; Computational Biology ; Eukaryotic Cells/chemistry/classification/*cytology/*metabolism ; *Evolution, Molecular ; Genomics ; Humans ; Myosins/*chemistry/*classification/genetics ; Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; }, abstract = {Eukaryotic cells have two contrasting cytoskeletal and ciliary organizations. The simplest involves a single cilium-bearing centriole, nucleating a cone of individual microtubules (probably ancestral for unikonts: animals, fungi, Choanozoa and Amoebozoa). In contrast, bikonts (plants, chromists and all other protozoa) were ancestrally biciliate with a younger anterior cilium, converted every cell cycle into a dissimilar posterior cilium and multiple ciliary roots of microtubule bands. Here we show by comparative genomic analysis that this fundamental cellular dichotomy also involves different myosin molecular motors. We found 37 different protein domain combinations, often lineage-specific, and many previously unidentified. The sequence phylogeny and taxonomic distribution of myosin domain combinations identified five innovations that strongly support unikont monophyly and the primary bikont/unikont bifurcation. We conclude that the eukaryotic cenancestor (last common ancestor) had a cilium, mitochondria, pseudopodia, and myosins with three contrasting domain combinations and putative functions.}, }
@article {pmid16120285, year = {2002}, author = {Terkeltaub, R and Johnson, K and Murphy, A and Ghosh, S}, title = {Invited review: the mitochondrion in osteoarthritis.}, journal = {Mitochondrion}, volume = {1}, number = {4}, pages = {301-319}, doi = {10.1016/s1567-7249(01)00037-x}, pmid = {16120285}, issn = {1567-7249}, abstract = {In a variety of tissues, cumulative oxidative stress, disrupted mitochondrial respiration, and mitochondrial damage promote aging, cell death, and ultimately, functional failure and degeneration. Because articular cartilage chondroyctes are highly glycolytic, mitochondrially mediated pathogenesis has not been previously applied in models for pathogenesis of osteoarthritis (OA), a cartilage degenerative disease that increases markedly in aging. However, chondrocyte mitochondria respire in vitro and they demonstrate swelling and changes in number in situ in the course of OA. Normal chondrocyte mitochondrial function is hypothesized to critically support adenosine triphosphate (ATP) reserves in functional stressed chondrocytes during OA evolution. In this model, disruption of chondrocyte respiration by nitric oxide, a mediator markedly up-regulated in OA cartilage, is centrally involved in chondrocyte functional compromise. Furthermore, mitochondrial dysfunction can mediate several specific pathogenic pathways implicated in OA. These include oxidative stress, inadequacy of chondrocyte biosynthetic and growth responses, up-regulated chondrocyte cytokine-induced inflammation and matrix catabolism, increased chondrocyte apoptosis, and pathologic cartilage matrix calcification. In addition, the direct, sublethal impairment of chondrocyte mitochondrial ATP synthesis in vitro decreases matrix synthesis and increases matrix calcification ('disease in a dish'). The weight of evidence reviewed herein strongly supports chondrocyte mitochondrial impairment as a mediator of the establishment and progression of OA.}, }
@article {pmid16118182, year = {2006}, author = {De Hertogh, B and Hancy, F and Goffeau, A and Baret, PV}, title = {Emergence of species-specific transporters during evolution of the hemiascomycete phylum.}, journal = {Genetics}, volume = {172}, number = {2}, pages = {771-781}, pmid = {16118182}, issn = {0016-6731}, mesh = {Ascomycota/*genetics ; Candida albicans/genetics/metabolism ; Candida glabrata ; Carrier Proteins/*genetics/*metabolism ; *Evolution, Molecular ; Genome, Fungal ; Kluyveromyces/genetics/metabolism ; Membrane Transport Proteins/genetics/metabolism ; Mitochondria/metabolism ; Multigene Family ; Proteome ; Saccharomyces cerevisiae/genetics/metabolism ; Species Specificity ; Yarrowia/genetics/metabolism ; }, abstract = {We have traced the evolution patterns of 2480 transmembrane transporters from five complete genome sequences spanning the entire Hemiascomycete phylum: Saccharomyces cerevisiae, Candida glabrata, Kluyveromyces lactis, Debaryomyces hansenii, and Yarrowia lipolytica. The use of nonambiguous functional and phylogenetic criteria derived from the TCDB classification system has allowed the identification within the Hemiascomycete phylum of 97 small phylogenetic transporter subfamilies comprising a total of 355 transporters submitted to four distinct evolution patterns named "ubiquitous," "species specific," "phylum gains and losses," or "homoplasic." This analysis identifies the transporters that contribute to the emergence of species during the evolution of the Hemiascomycete phylum and may aid in establishing novel phylogenetic criteria for species classification.}, }
@article {pmid16115016, year = {2005}, author = {Zeevalk, GD and Bernard, LP and Song, C and Gluck, M and Ehrhart, J}, title = {Mitochondrial inhibition and oxidative stress: reciprocating players in neurodegeneration.}, journal = {Antioxidants &amp; redox signaling}, volume = {7}, number = {9-10}, pages = {1117-1139}, doi = {10.1089/ars.2005.7.1117}, pmid = {16115016}, issn = {1523-0864}, mesh = {Animals ; Antioxidants/metabolism/pharmacology ; Electron Transport Chain Complex Proteins/chemistry/*physiology ; Glutathione/metabolism ; Humans ; Lipid Bilayers ; Mitochondria/*metabolism/pathology ; Models, Biological ; Nerve Degeneration/pathology ; Neurodegenerative Diseases/*pathology ; *Oxidative Stress ; Rats ; Reactive Oxygen Species ; Time Factors ; }, abstract = {Although the etiology for many neurodegenerative diseases is unknown, the common findings of mitochondrial defects and oxidative damage posit these events as contributing factors. The temporal conundrum of whether mitochondrial defects lead to enhanced reactive oxygen species generation, or conversely, if oxidative stress is the underlying cause of the mitochondrial defects remains enigmatic. This review focuses on evidence to show that either event can lead to the evolution of the other with subsequent neuronal cell loss. Glutathione is a major antioxidant system used by cells and mitochondria for protection and is altered in a number of neurodegenerative and neuropathological conditions. This review also addresses the multiple roles for glutathione during mitochondrial inhibition or oxidative stress. Protein aggregation and inclusions are hallmarks of a number of neurodegenerative diseases. Recent evidence that links protein aggregation to oxidative stress and mitochondrial dysfunction will also be examined. Lastly, current therapies that target mitochondrial dysfunction or oxidative stress are discussed.}, }
@article {pmid16112882, year = {2005}, author = {Wiklund, H and Nygren, A and Pleijel, F and Sundberg, P}, title = {Phylogeny of Aphroditiformia (Polychaeta) based on molecular and morphological data.}, journal = {Molecular phylogenetics and evolution}, volume = {37}, number = {2}, pages = {494-502}, doi = {10.1016/j.ympev.2005.07.005}, pmid = {16112882}, issn = {1055-7903}, mesh = {Animals ; Cell Nucleus/genetics ; Cytochromes b/*genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/*genetics ; Mitochondria/enzymology ; *Phylogeny ; Polychaeta/*anatomy &amp; histology/*classification/genetics ; RNA, Ribosomal, 18S/*genetics ; }, abstract = {The phylogeny of Aphroditiformia, benthic polychaetes carrying dorsal elytra, is assessed from nuclear 18S rDNA, mitochondrial cytochrome c oxidase subunit I (COI), and 31 morphological characters. Two non-elytrabearing taxa, Palmyra and Pisione, are included to assess their relationship to the elytrabearers. The data are analysed both separately and combined, with parsimony, maximum likelihood and Bayesian analyses. In total, 19 terminal taxa are examined, including 12 elytrabearing taxa from all scale-worm groups, Palmyra, Pisione, and five outgroup taxa. The results show that Palmyra and Pisione are nested within Aphroditiformia. Palmyra is sister to Aphrodita, and both Pisione and Pholoe are positioned within Sigalionidae, suggesting that both family names Pisionidae and Pholoidae should be treated as junior synonyms of Sigalionidae.}, }
@article {pmid16109924, year = {2005}, author = {Gutterman, DD}, title = {Mitochondria and reactive oxygen species: an evolution in function.}, journal = {Circulation research}, volume = {97}, number = {4}, pages = {302-304}, doi = {10.1161/01.RES.0000179773.18195.12}, pmid = {16109924}, issn = {1524-4571}, mesh = {Animals ; Biological Factors/physiology ; Calcium/*metabolism ; Humans ; Ischemic Preconditioning, Myocardial ; Mitochondria/*physiology ; Nitric Oxide Synthase/physiology ; Nitric Oxide Synthase Type III ; Potassium Channels/*physiology ; *Reactive Oxygen Species ; *Vasodilation ; }, }
@article {pmid16109488, year = {2005}, author = {Martin, W}, title = {The missing link between hydrogenosomes and mitochondria.}, journal = {Trends in microbiology}, volume = {13}, number = {10}, pages = {457-459}, doi = {10.1016/j.tim.2005.08.005}, pmid = {16109488}, issn = {0966-842X}, mesh = {Animals ; *Biological Evolution ; Ciliophora/metabolism/*ultrastructure ; Hydrogen/*metabolism ; Mitochondria/genetics/physiology ; Organelles/*genetics/*physiology ; }, abstract = {Mitochondria typically respire oxygen and possess a small DNA genome. But among various groups of oxygen-shunning eukaryotes, typical mitochondria are often lacking, organelles called hydrogenosomes being found instead. Like mitochondria, hydrogenosomes are surrounded by a double-membrane, produce ATP and sometimes even have cristae. In contrast to mitochondria, hydrogenosomes produce molecular hydrogen through fermentations, lack cytochromes and usually lack DNA. Hydrogenosomes do not fit into the conceptual mold cast by the classical endosymbiont hypothesis about the nature of mitochondria. Accordingly, ideas about their evolutionary origins have focussed on the differences between the two organelles instead of their commonalities. Are hydrogenosomes fundamentally different from mitochondria, the result of a different endosymbiosis? Or are our concepts about the mitochondrial archetype simply too narrow? A new report has uncovered DNA in the hydrogenosomes of anaerobic ciliates. The sequences show that these hydrogenosomes are, without a doubt, mitochondria in the evolutionary sense, even though they differ from typical mitochondria in various biochemical properties. The new findings are a benchmark for our understanding of hydrogenosome origins.}, }
@article {pmid16094287, year = {2005}, author = {Yokoyama, K}, title = {[Phylogenetic relationship of the genus Malassezia based on mitochondrial cytochrome B gene].}, journal = {Nihon Ishinkin Gakkai zasshi = Japanese journal of medical mycology}, volume = {46}, number = {3}, pages = {151-156}, doi = {10.3314/jjmm.46.151}, pmid = {16094287}, issn = {0916-4804}, mesh = {Cytochromes b/*genetics ; Malassezia/*classification/enzymology ; Mitochondria/*enzymology ; Phylogeny ; }, abstract = {Mitochondrial cytochrome b genes of pathogenic yeasts and fungi were analyzed for identification and phylogenetic relationship. The species of genus Malassezia also were analyzed and each sequence was specific in the same domain of cytochrome b gene. Some species represented intraspecies variation. The structure and function of cytochrome b protein was retained and its substitution rates may be in proportion to the evolutionary period. The deduced amino acid sequence was encoded by each nucleotide sequence of cytochrome b gene, and the phylogenetic tree of eukaryote and basidiomycetous yeast was obtained using this sequence. The species of genus Malassezia formed one cluster in this tree, meaning that the concepts of this genus reflect its evolution. The mitochondrial cytochrome b gene analysis was valuable for the identification and phylogenetic analysis of the genus.}, }
@article {pmid16092527, year = {2005}, author = {Lister, R and Hulett, JM and Lithgow, T and Whelan, J}, title = {Protein import into mitochondria: origins and functions today (review).}, journal = {Molecular membrane biology}, volume = {22}, number = {1-2}, pages = {87-100}, doi = {10.1080/09687860500041247}, pmid = {16092527}, issn = {0968-7688}, mesh = {Bacterial Physiological Phenomena ; Bacterial Proteins/metabolism ; *Evolution, Molecular ; Fungal Proteins/metabolism ; Membrane Proteins/physiology ; Membrane Transport Proteins/*physiology ; Mitochondria/*metabolism ; Mitochondrial Proteins/*metabolism ; Protein Transport ; Yeasts/physiology ; }, abstract = {Mitochondria are organelles derived from alpha-proteobacteria over the course of one to two billion years. Mitochondria from the major eukaryotic lineages display some variation in functions and coding capacity but sequence analysis demonstrates them to be derived from a single common ancestral endosymbiont. The loss of assorted functions, the transfer of genes to the nucleus, and the acquisition of various 'eukaryotic' proteins have resulted in an organelle that contains approximately 1000 different proteins, with most of these proteins imported into the organelle across one or two membranes. A single translocase in the outer membrane and two translocases in the inner membrane mediate protein import. Comparative sequence analysis and functional complementation experiments suggest some components of the import pathways to be directly derived from the eubacterial endosymbiont's own proteins, and some to have arisen 'de novo' at the earliest stages of 'mitochondrification' of the endosymbiont. A third class of components appears lineage-specific, suggesting they were incorporated into the process of protein import long after mitochondria was established as an organelle and after the divergence of the various eukaryotic lineages. Protein sorting pathways inherited from the endosymbiont have been co-opted and play roles in intraorganelle protein sorting after import. The import apparatus of animals and fungi show significant similarity to one another, but vary considerably to the plant apparatus. Increasing complexity in the eukaryotic lineage, i.e., from single celled to multi-cellular life forms, has been accompanied by an expansion in genes encoding each component, resulting in small gene families encoding many components. The functional differences in these gene families remain to be elucidated, but point to a mosaic import apparatus that can be regulated by a variety of signals.}, }
@article {pmid16091132, year = {2005}, author = {Cook, CE}, title = {The complete mitochondrial genome of the stomatopod crustacean Squilla mantis.}, journal = {BMC genomics}, volume = {6}, number = {}, pages = {105}, pmid = {16091132}, issn = {1471-2164}, mesh = {Animals ; Base Composition ; Base Sequence ; Codon ; Computational Biology/*methods ; Crustacea/*genetics ; DNA Primers/chemistry ; *DNA, Mitochondrial ; Evolution, Molecular ; Gene Order ; Genetic Techniques ; *Genetics ; *Genome ; Histidine/chemistry ; Least-Squares Analysis ; Mitochondria/genetics ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleotides/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA/genetics ; RNA, Ribosomal/chemistry/genetics ; RNA, Transfer/genetics ; Regression Analysis ; Sequence Analysis, DNA ; Serine/chemistry ; Translocation, Genetic ; }, abstract = {BACKGROUND: Animal mitochondrial genomes are physically separate from the much larger nuclear genomes and have proven useful both for phylogenetic studies and for understanding genome evolution. Within the phylum Arthropoda the subphylum Crustacea includes over 50,000 named species with immense variation in body plans and habitats, yet only 23 complete mitochondrial genomes are available from this subphylum.<br><br>RESULTS: I describe here the complete mitochondrial genome of the crustacean Squilla mantis (Crustacea: Malacostraca: Stomatopoda). This 15994-nucleotide genome, the first described from a hoplocarid, contains the standard complement of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding AT-rich region that is found in most other metazoans. The gene order is identical to that considered ancestral for hexapods and crustaceans. The 70% AT base composition is within the range described for other arthropods. A single unusual feature of the genome is a 230 nucleotide non-coding region between a serine transfer RNA and the nad1 gene, which has no apparent function. I also compare gene order, nucleotide composition, and codon usage of the S. mantis genome and eight other malacostracan crustaceans. A translocation of the histidine transfer RNA gene is shared by three taxa in the order Decapoda, infraorder Brachyura; Callinectes sapidus, Portunus trituberculatus and Pseudocarcinus gigas. This translocation may be diagnostic for the Brachyura. For all nine taxa nucleotide composition is biased towards AT-richness, as expected for arthropods, and is within the range reported for other arthropods. Codon usage is biased, and much of this bias is probably due to the skew in nucleotide composition towards AT-richness.<br><br>CONCLUSION: The mitochondrial genome of Squilla mantis contains one unusual feature, a 230 base pair non-coding region has so far not been described in any other malacostracan. Comparisons with other Malacostraca show that all nine genomes, like most other mitochondrial genomes, share a bias toward AT-richness and a related bias in codon usage. The nine malacostracans included in this analysis are not representative of the diversity of the class Malacostraca, and additional malacostracan sequences would surely reveal other unusual genomic features that could be useful in understanding mitochondrial evolution in this taxon.}, }
@article {pmid16089034, year = {2005}, author = {Kopp, A and Barmina, O}, title = {Evolutionary history of the Drosophila bipectinata species complex.}, journal = {Genetical research}, volume = {85}, number = {1}, pages = {23-46}, doi = {10.1017/s0016672305007317}, pmid = {16089034}, mesh = {Alleles ; Animals ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; Drosophila/*genetics ; *Evolution, Molecular ; Female ; Gene Frequency ; Genetic Variation ; Genetics, Population ; Geography ; Haplotypes ; Male ; Mitochondria/genetics ; Phenotype ; Phylogeny ; Pigmentation ; Polymorphism, Genetic ; Recombination, Genetic ; Sex Factors ; Species Specificity ; Temperature ; }, abstract = {Groups of recently diverged species offer invaluable glimpses into the history and genetic basis of speciation and phenotypic evolution. In this report, we combine phylogenetic and population-genetic approaches to reconstruct the evolutionary history of the Drosophila bipectinata species complex. This complex is a group of four closely related, largely sympatric species--D. bipectinata, D. parabipectinata, D. malerkotliana and D. pseudoananassae. Using the sequences of one mitochondrial and six nuclear loci, we show that D. bipectinata and D. parabipectinata are the two most closely related species, and that together with D. malerkotliana they form a monophyletic clade to which D. pseudoananassae is a relatively distant outgroup. Genetic divergence among D. bipectinata, D. parabipectinata and D. malerkotliana is extremely low, and we estimate that these species diverged only 283,000-385,000 years ago. We also find that mitochondrial DNA shows evidence of recent gene flow across species boundaries. Despite the low genetic divergence, species of the bipectinata complex show an unusually high degree of morphological differentiation. This contrast underscores the importance of understanding the genetic basis of functional differentiation among closely related species.}, }
@article {pmid16086405, year = {2005}, author = {Liana, M and Witaliński, W}, title = {Sperm structure and phylogeny of Astigmata.}, journal = {Journal of morphology}, volume = {265}, number = {3}, pages = {318-324}, doi = {10.1002/jmor.10361}, pmid = {16086405}, issn = {0362-2525}, mesh = {Acari/*anatomy &amp; histology ; Animals ; Male ; Microscopy, Electron ; Models, Biological ; *Phylogeny ; Species Specificity ; Spermatozoa/*ultrastructure ; }, abstract = {The Astigmata, a large and variable group, is still a subject of taxonomic dispute. Particularly, their origin from ancestors of the lower oribatid mites (e.g., Malaconothroidea) seems well documented by many lines of evidence. The structure of spermatozoa has been successfully applied to phylogenetic investigations in many animal groups. The aim of our study was to provide new data on spermatozoon structure in Astigmata and to consider its appropriateness in phylogenetic studies. The study reveals information on spermatozoa in 17 species of Astigmata (11 species studied for the first time) extending our knowledge to 18 species (one species known only from the literature) representing 12 families and 7 superfamilies. Spermatozoa have the same basic structure in all species: cells are multiform and the chromatin forms thin threads embedded directly in the cytoplasm; the acrosome is absent. The cytoplasm in most species contains electron-dense lamellae, varying in both number and arrangement within the cell. In Sarcoptoidea, electron-dense tubules in contact with lamellae margins were also observed in Psoroptidae (Psoroptes equi), whereas in two representatives of Sarcoptidae (Notoedres cati and Sarcoptes scabiei), only electron-dense tubules were found. In two species, Canestrinia sellnicki (Canestrinioidea: Canestriniidae) and Scutulanyssus obscurus (Analgoidea: Pteronyssidae), neither lamellae nor tubules were present. The mitochondria in a spermatozoon are usually gathered at the cell periphery and their structure is usually modified to form so-called mitochondrial derivatives. The chromatin threads are an autapomorphy strongly supporting the monophyly of Astigmata. As spermatozoa vary considerably between species in Astigmata, we deduce that sperm structure may be useful for phylogenetic analyses within the group. Several conclusions concerning the affinities within Astigmata are presented. Spermatology seems to be unhelpful, however, in questions on the origin of Astigmata (particularly for Astigmata-Oribatida relationships), since their sperm do not possess synapomorphies with sperm of the remaining groups of Acariformes, i.e., Endeostigmata, Prostigmata, and Oribatida.}, }
@article {pmid16082564, year = {2005}, author = {Mayer, F and Kerth, G}, title = {Microsatellite evolution in the mitochondrial genome of Bechstein's bat (Myotis bechsteinii).}, journal = {Journal of molecular evolution}, volume = {61}, number = {3}, pages = {408-416}, pmid = {16082564}, issn = {0022-2844}, mesh = {Animals ; Chiroptera/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genetic Variation/genetics ; *Genome ; Microsatellite Repeats/*genetics ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Being highly polymorphic, microsatellites are widely used genetic markers. They are abundant throughout the nuclear genomes of eukaryotes but rare in the mitochondrial genomes (mtDNA) of animals. We describe a short but highly polymorphic AT microsatellite in the mtDNA control region of Bechstein's bat and discuss the role of mutation, genetic drift, and selection in maintaining its variability. As heteroplasmy and hence mutation rate were positively correlated with repeat number, a simple mutation model cannot explain the observed frequency distribution of AT copy numbers. Because of the unimodal distribution of repeat numbers found in heteroplasmic individuals, single step mutations are likely to be the predominant mechanism of copy number alternations. Above a certain copy number (seven repeats), deletions of single dinucleotide repeats seem to be more common than additions, which results in a decrease in frequency of long alleles. Heteroplasmy was inherited from mothers to their offspring and no evidence of paternal inheritance of mitochondria was found. Genetic differences accumulated with more distant ancestry, which suggests that microsatellites can be useful genetic markers in population genetics.}, }
@article {pmid16079242, year = {2005}, author = {Yamauchi, A}, title = {Rate of gene transfer from mitochondria to nucleus: effects of cytoplasmic inheritance system and intensity of intracellular competition.}, journal = {Genetics}, volume = {171}, number = {3}, pages = {1387-1396}, pmid = {16079242}, issn = {0016-6731}, mesh = {Cell Nucleus/*genetics/metabolism ; DNA, Mitochondrial/*metabolism ; Data Interpretation, Statistical ; Evolution, Molecular ; Extrachromosomal Inheritance/*genetics ; Intracellular Fluid/*metabolism ; Mitochondria/*genetics/metabolism ; Models, Genetic ; }, abstract = {Endosymbiotic theory states that mitochondria originated as bacterial intracellular symbionts, the size of the mitochondrial genome gradually reducing over a long period owing to, among other things, gene transfer from the mitochondria to the nucleus. Such gene transfer was observed in more genes in animals than in plants, implying a higher transfer rate of animals. The evolution of gene transfer may have been affected by an intensity of intracellular competition among organelle strains and the organelle inheritance system of the organism concerned. This article reveals a relationship between those factors and the gene transfer rate from organelle to nuclear genomes, using a mathematical model. Mutant mitochondria that lose a certain gene by deletion are considered to replicate more rapidly than normal ones, resulting in an advantage in intracellular competition. If the competition is intense, heteroplasmic individuals possessing both types of mitochondria change to homoplasmic individuals including mutant mitochondria only, with high probability. According to the mathematical model, it was revealed that the rate of gene transfer from mitochondria to the nucleus can be affected by three factors, the intensity of intracellular competition, the probability of paternal organelle transmission, and the effective population size. The gene transfer rate tends to increase with decreasing intracellular competition, increasing paternal organelle transmission, and decreasing effective population size. Intense intracellular competition tends to suppress gene transfer because it is likely to exclude mutant mitochondria that lose the essential gene due to the production of lethal individuals.}, }
@article {pmid16064055, year = {2005}, author = {Nuss, DL}, title = {Hypovirulence: mycoviruses at the fungal-plant interface.}, journal = {Nature reviews. Microbiology}, volume = {3}, number = {8}, pages = {632-642}, doi = {10.1038/nrmicro1206}, pmid = {16064055}, issn = {1740-1526}, mesh = {Ascomycota/pathogenicity/*virology ; Basidiomycota/pathogenicity/*virology ; Genome, Viral ; Mitochondria/virology ; Plant Diseases/*microbiology/virology ; Plants/microbiology/virology ; RNA Viruses/*genetics ; Signal Transduction ; Transcription, Genetic ; Virulence ; }, abstract = {Whereas most mycoviruses lead 'secret lives', some reduce the ability of their fungal hosts to cause disease in plants. This property, known as hypovirulence, has attracted attention owing to the importance of fungal diseases in agriculture and the limited strategies that are available for the control of these diseases. Using one pathogen to control another is appealing, both intellectually and ecologically. The recent development of an infectious cDNA-based reverse genetics system for members of the Hypoviridae mycovirus family has enabled the analysis of basic aspects of this fascinating virus-fungus-plant interaction, including virus-host interactions, the mechanisms underlying fungal pathogenesis, fungal signalling pathways and the evolution of RNA silencing. Such systems also provide a means for engineering mycoviruses for enhanced biocontrol potential.}, }
@article {pmid16055441, year = {2005}, author = {Bedhomme, M and Hoffmann, M and McCarthy, EA and Gambonnet, B and Moran, RG and Rébeillé, F and Ravanel, S}, title = {Folate metabolism in plants: an Arabidopsis homolog of the mammalian mitochondrial folate transporter mediates folate import into chloroplasts.}, journal = {The Journal of biological chemistry}, volume = {280}, number = {41}, pages = {34823-34831}, doi = {10.1074/jbc.M506045200}, pmid = {16055441}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Arabidopsis/*metabolism ; Arabidopsis Proteins/*chemistry/physiology ; Blotting, Western ; CHO Cells ; Catalysis ; Chlorophyll/chemistry ; Chloroplasts/chemistry/*metabolism ; Cloning, Molecular ; Cricetinae ; DNA, Complementary/metabolism ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/metabolism ; Folic Acid/metabolism ; Genetic Complementation Test ; Glycine/chemistry ; Green Fluorescent Proteins/metabolism ; Immunoblotting ; Membrane Transport Proteins/*chemistry/metabolism/physiology ; Mitochondria/metabolism ; Models, Biological ; Molecular Sequence Data ; Mutation ; Nucleic Acids/chemistry ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Time Factors ; Transfection ; }, abstract = {The distribution of folates in plant cells suggests a complex traffic of the vitamin between the organelles and the cytosol. The Arabidopsis thaliana protein AtFOLT1 encoded by the At5g66380 gene is the closest homolog of the mitochondrial folate transporters (MFTs) characterized in mammalian cells. AtFOLT1 belongs to the mitochondrial carrier family, but GFP-tagging experiments and Western blot analyses indicated that it is targeted to the envelope of chloroplasts. By using the glycine auxotroph Chinese hamster ovary glyB cell line, which lacks a functional MFT and is deficient in folates transport into mitochondria, we showed by complementation that AtFOLT1 functions as a folate transporter in a hamster background. Indeed, stable transfectants bearing the AtFOLT1 cDNA have enhanced levels of folates in mitochondria and can support growth in glycine-free medium. Also, the expression of AtFOLT1 in Escherichia coli allows bacterial cells to uptake exogenous folate. Disruption of the AtFOLT1 gene in Arabidopsis does not lead to phenotypic alterations in folate-sufficient or folate-deficient plants. Also, the atfolt1 null mutant contains wild-type levels of folates in chloroplasts and preserves the enzymatic capacity to catalyze folate-dependent reactions in this subcellular compartment. These findings suggest strongly that, despite many common features shared by chloroplasts and mitochondria from mammals regarding folate metabolism, the folate import mechanisms in these organelles are not equivalent: folate uptake by mammalian mitochondria is mediated by a unique transporter, whereas there are alternative routes for folate import into chloroplasts.}, }
@article {pmid16050982, year = {2005}, author = {Itoi, S and Misaki, R and Hirayama, M and Nakaniwa, M and Liang, CS and Kondo, H and Watabe, S}, title = {Identification of three isoforms for mitochondrial adenine nucleotide translocator in the pufferfish Takifugu rubripes.}, journal = {Mitochondrion}, volume = {5}, number = {3}, pages = {162-172}, doi = {10.1016/j.mito.2005.01.003}, pmid = {16050982}, issn = {1567-7249}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Computational Biology ; Conserved Sequence ; DNA, Complementary ; Genome ; Isoenzymes/*chemistry/*genetics/isolation &amp; purification ; Mitochondria, Heart/enzymology ; Mitochondria, Muscle/enzymology ; Mitochondrial ADP, ATP Translocases/*chemistry/*genetics/isolation &amp; purification ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques ; Phylogeny ; Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Takifugu/*genetics ; Tissue Distribution ; Transcription, Genetic ; }, abstract = {Three adenine nucleotide translocator (ANT) genes were identified through in silico data mining of the Fugu genome database along with isolation of their corresponding cDNAs in vivo from the pufferfish (Takifugu rubripes). As a result of phylogenetic analysis, the ANT gene on scaffold_254 corresponded to mammalian ANT1, whereas both of those on scaffold_6 and scaffold_598 to mammalian ANT3. The ANT gene encoded by scaffold_6 was expressed ubiquitously in various tissues, whereas the ANT genes encoded by scaffold_254 and scaffold_598 were predominantly expressed in skeletal muscle and heart, respectively.}, }
@article {pmid16042377, year = {2005}, author = {Huang, YS and Karashima, T and Yamamoto, M and Hamaguchi, HO}, title = {Molecular-level investigation of the structure, transformation, and bioactivity of single living fission yeast cells by time- and space-resolved Raman spectroscopy.}, journal = {Biochemistry}, volume = {44}, number = {30}, pages = {10009-10019}, doi = {10.1021/bi050179w}, pmid = {16042377}, issn = {0006-2960}, mesh = {*Cell Cycle/genetics ; Cell Division ; Cell Nucleus/chemistry/genetics/metabolism ; G1 Phase ; G2 Phase ; Green Fluorescent Proteins/metabolism ; Microscopy, Fluorescence ; Mitochondria/chemistry/genetics/metabolism ; Organelles/*chemistry/genetics/metabolism ; S Phase ; Schizosaccharomyces/*chemistry/*cytology/genetics/metabolism ; Spectrum Analysis, Raman/methods ; }, abstract = {The structure, transformation, and bioactivity of single living Schizosaccharomyces pombe cells at the molecular level have been studied in vivo by time- and space-resolved Raman spectroscopy. A time resolution of 100 s and a space resolution of 250 nm have been achieved with the use of a confocal Raman microspectrometer. The space-resolved Raman spectra of living S. pombe cells at different cell cycle stages were recorded in an effort to elucidate the molecular compositions of organelles, including nuclei, cytoplasm, mitochondria, and septa. The time- and space-resolved measurement of the central part of a dividing yeast cell showed continuous spectral evolution from that of the nucleus to those of the cytoplasm and mitochondria and finally to that of the septum, in accordance with the transformation during the cell cycle. A strong Raman band was observed at 1602 cm(-)(1) only when cells were under good nutrient conditions. The effect of a respiration inhibitor, KCN, on a living yeast cell was studied by measuring the Raman spectra of its mitochondria. A sudden disappearance of the 1602 cm(-)(1) band followed by the change in the shape and intensity of the phospholipid bands was observed, indicating a strong relationship between the cell activity and the intensity of this band. We therefore call this band "the Raman spectroscopic signature of life". The Raman mapping of a living yeast cell was also carried out. Not only the distributions of molecular species but also those of active mitochondria in the cell were successfully visualized in vivo.}, }
@article {pmid16040811, year = {2005}, author = {Dolezal, P and Smíd, O and Rada, P and Zubácová, Z and Bursać, D and Suták, R and Nebesárová, J and Lithgow, T and Tachezy, J}, title = {Giardia mitosomes and trichomonad hydrogenosomes share a common mode of protein targeting.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {31}, pages = {10924-10929}, pmid = {16040811}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Animals ; Biological Transport, Active ; Evolution, Molecular ; Ferredoxins/genetics/metabolism ; Giardia lamblia/genetics/*metabolism/ultrastructure ; Iron-Sulfur Proteins/genetics/metabolism ; Molecular Sequence Data ; Organelles/metabolism ; Protein Processing, Post-Translational ; Protozoan Proteins/genetics/*metabolism ; Recombinant Proteins/genetics/metabolism ; Trichomonas vaginalis/genetics/*metabolism/ultrastructure ; }, abstract = {Mitochondria are archetypal organelles of endosymbiotic origin in eukaryotic cells. Some unicellular eukaryotes (protists) were considered to be primarily amitochondrial organisms that diverged from the eukaryotic lineage before the acquisition of the premitochondrial endosymbiont, but their amitochondrial status was recently challenged by the discovery of mitochondria-like double membrane-bound organelles called mitosomes. Here, we report that proteins targeted into mitosomes of Giardia intestinalis have targeting signals necessary and sufficient to be recognized by the mitosomal protein import machinery. Expression of these mitosomal proteins in Trichomonas vaginalis results in targeting to hydrogenosomes, a hydrogen-producing form of mitochondria. We identify, in Giardia and Trichomonas, proteins related to the component of the translocase in the inner membrane from mitochondria and the processing peptidase. A shared mode of protein targeting supports the hypothesis that mitosomes, hydrogenosomes, and mitochondria represent different forms of the same fundamental organelle having evolved under distinct selection pressures.}, }
@article {pmid16040665, year = {2005}, author = {Yu, F and Park, S and Rodermel, SR}, title = {Functional redundancy of AtFtsH metalloproteases in thylakoid membrane complexes.}, journal = {Plant physiology}, volume = {138}, number = {4}, pages = {1957-1966}, pmid = {16040665}, issn = {0032-0889}, mesh = {Arabidopsis/*enzymology/genetics ; Gene Duplication ; Gene Expression Regulation, Plant ; Metalloproteases/genetics/*metabolism ; Multigene Family ; Mutation ; Oryza/enzymology ; Pisum sativum/enzymology ; Phylogeny ; Plants, Genetically Modified ; Thylakoids/*enzymology ; }, abstract = {FtsH is an ATP-dependent metalloprotease found in bacteria, mitochondria, and plastids. Arabidopsis (Arabidopsis thaliana) contains 12 AtFtsH proteins, three in the mitochondrion and nine in the chloroplast. Four of the chloroplast FtsH proteins are encoded by paired members of closely related genes (AtFtsH1 and 5, and AtFtsH2 and 8). We have previously reported that AtFtsH2 and 8 are interchangeable components of AtFtsH complexes in the thylakoid membrane. In this article, we show that the var1 variegation mutant, which is defective in AtFtsH5, has a coordinate reduction in the AtFtsH2 and 8 pair, and that the levels of both pairs are restored to normal in var1 plants that overexpress AtFtsH1. Overexpression of AtFtsH1, but not AtFtsH2/VAR2, normalizes the pattern of var1 variegation, restoring a nonvariegated phenotype. We conclude that AtFtsH proteins within a pair, but not between pairs, are interchangeable and functionally redundant, at least in part. We further propose that the abundance of each pair is matched with that of the other pair, with excess subunits being turned over. The variegation phenotype of var1 (as well as var2, which is defective in AtFtsH2) suggests that a threshold concentration of subunits is required for normal chloroplast function. AtFtsH1, 2, 5, and 8 do not show evidence of tissue or developmental specific expression. Phylogenetic analyses revealed that rice (Oryza sativa) and Arabidopsis share a conserved core of seven FtsH subunit genes, including the AtFtsH1 and 5 and AtFtsH2 and 8 pairs, and that the structure of the present-day gene families can be explained by duplication events in each species following the monocot/dicot divergence.}, }
@article {pmid16039600, year = {2005}, author = {Shepherd, M and Dailey, HA}, title = {A continuous fluorimetric assay for protoporphyrinogen oxidase by monitoring porphyrin accumulation.}, journal = {Analytical biochemistry}, volume = {344}, number = {1}, pages = {115-121}, pmid = {16039600}, issn = {0003-2697}, support = {R01 DK032303/DK/NIDDK NIH HHS/United States ; R56 DK032303/DK/NIDDK NIH HHS/United States ; DK032303/DK/NIDDK NIH HHS/United States ; }, mesh = {Bacteria/enzymology ; Fluorometry ; Humans ; Kinetics ; Mitochondria, Liver/enzymology ; Myxococcus xanthus/enzymology ; Nitrobenzoates/pharmacology ; Protoporphyrins/*biosynthesis ; Sensitivity and Specificity ; Spectrometry, Fluorescence ; }, abstract = {A continuous spectrofluorimetric assay for protoporphyrinogen oxidase (PPO, EC 1.3.3.4) activity has been developed using a 96-well plate reader. Protoporphyrinogen IX, the tetrapyrrole substrate, is a colorless nonfluorescent compound. The evolution of the fluorescent tetrapyrrole product, protoporphyrin IX, was detected using a fluorescence plate reader. The apparent Km (Kapp) values for protoporphyrinogen IX were measured as 3.8+/-0.3, 3.6+/-0.5, and 1.0+/-0.1 microM for the enzymes from human, Myxococcus xanthus, and Aquifex aeolicus, respectively. The Ki for acifluorfen, a diphenylether herbicide, was measured as 0.53 microM for the human enzyme. Also, the specific activity of mouse liver mitochondrial PPO was measured as 0.043 nmol h-1/mg mitochondria, demonstrating that this technique is useful for monitoring low-enzyme activities. This method can be used to accurately measure activities as low as 0.5 nM min-1, representing a 50-fold increase in sensitivity over the currently used discontinuous assay. Furthermore, this continuous assay may be used to monitor up to 96 samples simultaneously. These obvious advantages over the discontinuous assay will be of importance for both the kinetic characterization of recombinant PPOs and the detection of low concentrations of this enzyme in biological samples.}, }
@article {pmid16024781, year = {2005}, author = {Slomovic, S and Laufer, D and Geiger, D and Schuster, G}, title = {Polyadenylation and degradation of human mitochondrial RNA: the prokaryotic past leaves its mark.}, journal = {Molecular and cellular biology}, volume = {25}, number = {15}, pages = {6427-6435}, pmid = {16024781}, issn = {0270-7306}, mesh = {3' Untranslated Regions ; Cell Line, Tumor ; Cells, Cultured ; Computational Biology ; Cyclooxygenase 1 ; *Evolution, Molecular ; Expressed Sequence Tags ; Humans ; Membrane Proteins ; Mitochondria/*genetics ; Polyadenylation/*physiology ; Prokaryotic Cells/*metabolism ; Prostaglandin-Endoperoxide Synthases/genetics ; RNA/*metabolism ; RNA, Antisense ; RNA, Messenger/metabolism ; RNA, Mitochondrial ; RNA, Ribosomal, 16S/genetics ; RNA, Transfer, Ser/genetics ; }, abstract = {RNA polyadenylation serves a purpose in bacteria and organelles opposite from the role it plays in nuclear systems. The majority of nucleus-encoded transcripts are characterized by stable poly(A) tails at their mature 3' ends, which are essential for stabilization and translation initiation. In contrast, in bacteria, chloroplasts, and plant mitochondria, polyadenylation is a transient feature which promotes RNA degradation. Surprisingly, in spite of their prokaryotic origin, human mitochondrial transcripts possess stable 3'-end poly(A) tails, akin to nucleus-encoded mRNAs. Here we asked whether human mitochondria retain truncated and transiently polyadenylated transcripts in addition to stable 3'-end poly(A) tails, which would be consistent with the preservation of the largely ubiquitous polyadenylation-dependent RNA degradation mechanisms of bacteria and organelles. To this end, using both molecular and bioinformatic methods, we sought and revealed numerous examples of such molecules, dispersed throughout the mitochondrial genome. The broad distribution but low abundance of these polyadenylated truncated transcripts strongly suggests that polyadenylation-dependent RNA degradation occurs in human mitochondria. The coexistence of this system with stable 3'-end polyadenylation, despite their seemingly opposite effects, is so far unprecedented in bacteria and other organelles.}, }
@article {pmid16021339, year = {2005}, author = {Wong, CE and Li, Y and Whitty, BR and Díaz-Camino, C and Akhter, SR and Brandle, JE and Golding, GB and Weretilnyk, EA and Moffatt, BA and Griffith, M}, title = {Expressed sequence tags from the Yukon ecotype of Thellungiella reveal that gene expression in response to cold, drought and salinity shows little overlap.}, journal = {Plant molecular biology}, volume = {58}, number = {4}, pages = {561-574}, pmid = {16021339}, issn = {0167-4412}, mesh = {Algorithms ; Arabidopsis/genetics ; Brassicaceae/*genetics ; Cold Temperature ; DNA, Complementary/chemistry/genetics ; Disasters ; *Expressed Sequence Tags ; *Gene Expression Profiling ; Gene Expression Regulation, Plant/drug effects ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Sodium Chloride/pharmacology ; Water/pharmacology ; }, abstract = {Thellungiella salsuginea (also known as T. halophila) is a close relative of Arabidopsis that is very tolerant of drought, freezing, and salinity and may be an appropriate model to identify the molecular mechanisms underlying abiotic stress tolerance in plants. We produced 6578 ESTs, which represented 3628 unique genes (unigenes), from cDNA libraries of cold-, drought-, and salinity-stressed plants from the Yukon ecotype of Thellungiella. Among the unigenes, 94.1% encoded products that were most similar in amino acid sequence to Arabidopsis and 1.5% had no match with a member of the family Brassicaceae. Unigenes from the cold library were more similar to Arabidopsis sequences than either drought- or salinity-induced sequences, indicating that latter responses may be more divergent between Thellungiella and Arabidopsis. Analysis of gene ontology using the best matched Arabidopsis locus showed that the Thellungiella unigenes represented all biological processes and all cellular components, with the highest number of sequences attributed to the chloroplast and mitochondria. Only 140 of the unigenes were found in all three abiotic stress cDNA libraries. Of these common unigenes, 70% have no known function, which demonstrates that Thellungiella can be a rich resource of genetic information about environmental responses. Some of the ESTs in this collection have low sequence similarity with those in Genbank suggesting that they may encode functions that may contribute to Thellungiella's high degree of stress tolerance when compared with Arabidopsis. Moreover, Thellungiella is a closer relative of agriculturally important Brassica spp. than Arabidopsis, which may prove valuable in transferring information to crop improvement programs.}, }
@article {pmid16014637, year = {2005}, author = {Kondrashov, FA}, title = {Prediction of pathogenic mutations in mitochondrially encoded human tRNAs.}, journal = {Human molecular genetics}, volume = {14}, number = {16}, pages = {2415-2419}, doi = {10.1093/hmg/ddi243}, pmid = {16014637}, issn = {0964-6906}, mesh = {Base Sequence ; Humans ; Mitochondria/*genetics ; Molecular Sequence Data ; Mutation/*genetics ; RNA, Transfer/chemistry/*genetics/metabolism ; }, abstract = {Some mutations in human mitochondrial tRNAs are severely pathogenic. The available computational methods have a poor record of predicting the impact of a tRNA mutation on the phenotype and fitness. Here patterns of evolution at tRNA sites that harbor pathogenic mutations and at sites that harbor phenotypically cryptic polymorphisms were compared. Mutations that are pathogenic to humans occupy more conservative sites, are only rarely fixed in closely related species, and, when located in stem structures, often disrupt Watson-Crick pairing and display signs of compensatory evolution. These observations make it possible to classify approximately 90% of all known pathogenic mutations as deleterious together with only approximately 30% of polymorphisms. These polymorphisms segregate at frequencies that are more than two times lower than frequencies of polymorphisms classified as benign, indicating that at least approximately 30% of known polymorphisms in mitochondrial tRNAs affect fitness negatively.}, }
@article {pmid16011000, year = {2005}, author = {Smith, EJ and Shi, L and Tu, Z}, title = {Gallus gallus aggrecan gene-based phylogenetic analysis of selected avian taxonomic groups.}, journal = {Genetica}, volume = {124}, number = {1}, pages = {23-32}, doi = {10.1007/s10709-004-5184-4}, pmid = {16011000}, issn = {0016-6707}, mesh = {Aggrecans ; Animals ; Birds/*genetics ; Cell Nucleus ; Chickens/*genetics ; *Classification ; Extracellular Matrix Proteins/*genetics ; Lectins, C-Type ; *Phylogeny ; Proteoglycans/*genetics ; Sequence Analysis, DNA ; }, abstract = {Mitochondrial DNA (mtDNA) sequences remain the most widely used for phylogenetic analysis in birds. A major limitation of mtDNA sequences, however, is that mitochondria genes are inherited as a single linkage group. Here we describe the use of a 540-bp DNA sequence corresponding to the G3 domain of Gallus gallus nuclear aggrecan gene (AGCI) for phylogenetic analysis of the main groups of Galliformes including Phasianidae, Numididae, and Odontophoridae. We also included species from Cracidae and Megapodiidae which are considered by some as Craciformes and others, including here as Galliformes. The uncorrected sequence divergence of the G3 fragments ranges from 1% among the grouses to 36% between some of the distant groups within Galliformes. These sequences contain 39-48% AT nucleotides and the ratios of transition versus transversion are above 1.5 in majority of the comparisons. Using G3 sequences from an Anseriform, Oxyura jamaicensis, as out-groups, phylogenetic trees were obtained using maximum parsimony and distance algorithms and bootstrap analyses. These trees were consistent with those described using Avian sarcoma and leucosis virus gag genes and those from amino acid sequences of hemoglobin and lysozyme c. Our data also support relationships among Galliformes which were defined using mtDNA sequences. In addition to the general support of the five main families of Galliformes, our data are also consistent with previous work that showed Francolinus africanus and Gallus gallus are in the same clade and that Tetraoninae is a well-supported monophyletic subfamily within Phasianidae. The results presented here suggest that the AGC1 sequences meet the criterion of novel nuclear DNA sequences that can be used to help resolve the relationships among Galliformes.}, }
@article {pmid16008553, year = {2005}, author = {Uda, K and Saishoji, N and Ichinari, S and Ellington, WR and Suzuki, T}, title = {Origin and properties of cytoplasmic and mitochondrial isoforms of taurocyamine kinase.}, journal = {The FEBS journal}, volume = {272}, number = {14}, pages = {3521-3530}, doi = {10.1111/j.1742-4658.2005.04767.x}, pmid = {16008553}, issn = {1742-464X}, mesh = {Amino Acid Sequence ; Animals ; Catalysis ; Creatine Kinase/chemistry/metabolism ; Cytoplasm/*enzymology ; Evolution, Molecular ; Humans ; Mitochondria/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Phosphotransferases (Nitrogenous Group Acceptor)/chemistry/genetics/*metabolism ; Phylogeny ; Polychaeta/*enzymology/genetics ; Protein Isoforms/chemistry/genetics/metabolism ; Protein Structure, Tertiary ; Sequence Alignment ; }, abstract = {Taurocyamine kinase (TK) is a member of the highly conserved family of phosphagen kinases that includes creatine kinase (CK) and arginine kinase. TK is found only in certain marine annelids. In this study we used PCR to amplify two cDNAs coding for TKs from the polychaete Arenicola brasiliensis, cloned these cDNAs into the pMAL plasmid and expressed the TKs as fusion proteins with the maltose-binding protein. These are the first TK cDNA and deduced amino acid sequences to be reported. One of the two cDNA-derived amino acid sequences of TKs shows a high amino acid identity to lombricine kinase, another phosphagen kinase unique to annelids, and appears to be a cytoplasmic isoform. The other sequence appears to be a mitochondrial isoform; it has a long N-terminal extension that was judged to be a mitochondrial targeting peptide by several on-line programs and shows a higher similarity in amino acid sequence to mitochondrial creatine kinases from both vertebrates and invertebrates. The recombinant cytoplasmic TK showed activity for the substrates taurocyamine and lombricine (9% of that of taurocyamine). However, the mitochondrial TK showed activity for taurocyamine, lombricine (30% of that of taurocyamine) and glycocyamine (7% of that of taurocyamine). Neither TK catalyzed the phosphorylation of creatine. Comparison of the deduced amino acid sequences of mitochondrial CK and TK indicated that several key residues required for CK activity are lacking in the mitochondrial TK sequence. Homology models for both cytoplasmic and mitochondrial TK, constructed using CK templates, provided some insight into the structural correlation of differences in substrate specificity between the two TKs. A phylogenetic analysis using amino acid sequences from a broad spectrum of phosphagen kinases showed that annelid-specific phosphagen kinases (lombricine kinase, glycocyamine kinase and cytoplasmic and mitochondrial TKs) are grouped in one cluster, and form a sister-group with CK sequences from vertebrate and invertebrate groups. It appears that the annelid-specific phosphagen kinases, including cytoplasmic and mitochondrial TKs, evolved from a CK-like ancestor(s) early in the divergence of the protostome metazoans. Furthermore, our results suggest that the cytoplasmic and mitochondrial isoforms of TK evolved independently.}, }
@article {pmid16007699, year = {2005}, author = {Prado, M and Calo, P and Cepeda, A and Barros-Velázquez, J}, title = {Genetic evidence of an Asian background in heteroplasmic Iberian cattle (Bos taurus): effect on food authentication studies based on polymerase chain reaction-restriction fragment length polymorphism analysis.}, journal = {Electrophoresis}, volume = {26}, number = {15}, pages = {2918-2926}, doi = {10.1002/elps.200500011}, pmid = {16007699}, issn = {0173-0835}, mesh = {Animals ; Base Pair Mismatch ; Base Sequence ; Cattle/*genetics ; Cytochromes b/*genetics ; DNA Primers ; DNA, Mitochondrial/genetics ; Genotype ; Mitochondria/genetics ; Muscle, Skeletal/enzymology ; Phylogeny ; Polymerase Chain Reaction ; *Polymorphism, Restriction Fragment Length ; Species Specificity ; }, abstract = {This work was aimed at identifying nucleotide polymorphic sites in a 359 bp region of the cytochrome b (cytb) mitochondrial gene of Iberian cattle (Bos taurus). This region is widely used as target in polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) species identification studies in foodstuffs destined for human and animal consumption. Two different coexisting restriction patterns were observed in four of the six animals studied when the 359 bp DNA fragment was cleaved with PalI, HinfI, MvaI, RsaI, or MboI. The amplification of both genotypes with the mitochondrial-specific primers L14735 and H15149 revealed the absence of nuclear pseudo-cytb genes, confirming the existence of mitochondrial heteroplasmy. The two coexisting mtDNA fragments were selectively sequenced in PCR extracts in which one genotype predominated over the other, both exhibiting a sequence variation of 10.4%. From the 37 nucleotide mismatches observed between genotypes, 32 were transitions and five were transversions. While 31 of the nucleotide mismatches between genotypes resulted to be conservative at the amino acid level, six changes implied amino acid substitutions, five of them being located in the variable transmembrane region. Genetic analysis suggests the presence of an Asian background in the mitochondria of Iberian cattle: while one of the genotypes matched the published sequence for Bos taurus, the other genotype clustered with a B. primigenius indicus animal and close to an Asian Bos taurus animal. These results also suggest that a number of current PCR-RFLP species identification methods based on cytb sequences may not be reliable for the accurate detection and identification of bovine material: an alternative battery of enzymes consisting of MmeI, NlaIV, and AluI is proposed.}, }
@article {pmid16007490, year = {2005}, author = {Schmitz, J and Piskurek, O and Zischler, H}, title = {Forty million years of independent evolution: a mitochondrial gene and its corresponding nuclear pseudogene in primates.}, journal = {Journal of molecular evolution}, volume = {61}, number = {1}, pages = {1-11}, pmid = {16007490}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Humans ; Molecular Sequence Data ; Primates ; *Pseudogenes ; }, abstract = {Sequences from nuclear mitochondrial pseudogenes (numts) that originated by transfer of genetic information from mitochondria to the nucleus offer a unique opportunity to compare different regimes of molecular evolution. Analyzing a 1621-nt-long numt of the rRNA specifying mitochondrial DNA residing on human chromosome 3 and its corresponding mitochondrial gene in 18 anthropoid primates, we were able to retrace about 40 MY of primate rDNA evolutionary history. The results illustrate strengths and weaknesses of mtDNA data sets in reconstructing and dating the phylogenetic history of primates. We were able to show the following. In contrast to numt-DNA, (1) the nucleotide composition of mtDNA changed dramatically in the different primate lineages. This is assumed to lead to significant misinterpretations of the mitochondrial evolutionary history. (2) Due to the nucleotide compositional plasticity of primate mtDNA, the phylogenetic reconstruction combining mitochondrial and nuclear sequences is unlikely to yield reliable information for either tree topologies or branch lengths. This is because a major part of the underlying sequence evolution model--the nucleotide composition--is undergoing dramatic change in different mitochondrial lineages. We propose that this problem is also expressed in the occasional unexpected long branches leading to the "common ancestor" of orthologous numt sequences of different primate taxa. (3) The heterogeneous and lineage-specific evolution of mitochondrial sequences in primates renders molecular dating based on primate mtDNA problematic, whereas the numt sequences provide a much more reliable base for dating.}, }
@article {pmid15996831, year = {2005}, author = {Toler, S}, title = {The plasmodial apicoplast was retained under evolutionary selective pressure to assuage blood stage oxidative stress.}, journal = {Medical hypotheses}, volume = {65}, number = {4}, pages = {683-690}, doi = {10.1016/j.mehy.2005.05.011}, pmid = {15996831}, issn = {0306-9877}, mesh = {Animals ; Antioxidants/metabolism ; Antiprotozoal Agents/metabolism ; *Biological Evolution ; Organelles/metabolism/*physiology ; Oxidative Stress/*physiology ; Plasmodium/*physiology ; *Selection, Genetic ; *Symbiosis ; Thioctic Acid/metabolism ; }, abstract = {Malaria, the clinical disease resulting from infection with Plasmodium, has haunted mankind with illness and death for thousands of years. As Plasmodia's ancient ancestor evolved from a mixotroph to an intracellular parasite, subsiding on amino acids obtained from hemoglobin, it encountered increased oxidative stress. To compensate for this oxidative stress, Plasmodia reduced its own production of reactive oxygen species by becoming largely fermentative and adapted novel methods to assuage oxidative injury. One such method appears to have been accomplished through the acquisition, retention and exploitation of an ancient red algal endosymbiote, now denoted the apicoplast. The apicoplast, located in close proximity to mitochondria, appears to synthesize the potent antioxidant lipoic acid. Lipoic acid may be utilized by Plasmodium as an antioxidant, a shuttle for reducing potentials and as a mitochondrial cofactor. Inhibition or alteration of the apicoplast leads to a curious phenomena known as "delayed death", whereby parasites die not in the present generation but in the ensuing one. Apicoplast inhibition may produce lipoic acid "starvation", increasing oxidative stress/mitochondrial injury during the subsequent asexual reproductive cycle. Collectively, data available to date indicate that the apicoplast was retained as an obligate endosymbiote, under evolutionary selective pressure, to assuage oxidative stress and plays a critical role in maintaining parasite viability during the Plasmodial shizont blood stage.}, }
@article {pmid15993645, year = {2005}, author = {Bullerwell, CE and Lang, BF}, title = {Fungal evolution: the case of the vanishing mitochondrion.}, journal = {Current opinion in microbiology}, volume = {8}, number = {4}, pages = {362-369}, doi = {10.1016/j.mib.2005.06.009}, pmid = {15993645}, issn = {1369-5274}, mesh = {DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Fungi/*genetics ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; }, abstract = {Mitochondria, the energy-producing organelles of the eukaryotic cell, are derived from an ancient endosymbiotic alpha-Proteobacterium. These organelles contain their own genetic system, a remnant of the endosymbiont's genome, which encodes only a fraction of the mitochondrial proteome. The majority of mitochondrial proteins are translated from nuclear genes and are imported into mitochondria. Recent studies of phylogenetically diverse representatives of Fungi reveal that their mitochondrial DNAs are among the most highly derived, encoding only a limited set of genes. Much of the reduction in the coding content of the mitochondrial genome probably occurred early in fungal evolution. Nevertheless, genome reduction is an ongoing process. Fungi in the chytridiomycete order Neocallimastigales and in the pathogenic Microsporidia have taken mitochondrial reduction to the extreme and have permanently lost a mitochondrial genome. These organisms have organelles derived from mitochondria that retain traces of their mitochondrial ancestry.}, }
@article {pmid15992863, year = {2005}, author = {Samuels, DC}, title = {Life span is related to the free energy of mitochondrial DNA.}, journal = {Mechanisms of ageing and development}, volume = {126}, number = {10}, pages = {1123-1129}, doi = {10.1016/j.mad.2005.05.003}, pmid = {15992863}, issn = {0047-6374}, mesh = {*Aging/genetics ; Animals ; DNA, Mitochondrial/*chemistry/genetics ; *Evolution, Molecular ; Humans ; *Mutation ; Thermodynamics ; }, abstract = {Broadly speaking, the mitochondrial theory of aging relates aging to the rate of damage to mitochondria. In this work, I concentrate on a DNA sequence property, the free energy, which can be interpreted as a factor in the susceptibility of mitochondrial DNA (mtDNA) to mutation. I show that life spans across a broad range of species are a function of the mtDNA free energy and are proportional to the probability of opening of bubbles of single-stranded mtDNA of approximately 20 base pairs in length, in agreement with the measured nucleation size of these bubbles. These transient separations of the mtDNA strands are a possible aging mechanism, through increased mtDNA mutations. In comparisons of species with similar life spans, avian mtDNA has more negative free energy than does mammalian mtDNA, suppressing the predicted probability of mtDNA bubble formation in birds by over 80% and thus protecting them against mutation. Based on these results I propose three hypotheses about the conflicting evolutionary forces that have acted on the free energy of mtDNA.}, }
@article {pmid15989955, year = {2005}, author = {Mesecke, N and Terziyska, N and Kozany, C and Baumann, F and Neupert, W and Hell, K and Herrmann, JM}, title = {A disulfide relay system in the intermembrane space of mitochondria that mediates protein import.}, journal = {Cell}, volume = {121}, number = {7}, pages = {1059-1069}, doi = {10.1016/j.cell.2005.04.011}, pmid = {15989955}, issn = {0092-8674}, mesh = {Amino Acid Motifs/physiology ; Binding Sites/physiology ; Cation Transport Proteins/metabolism ; Copper Transport Proteins ; Cysteine/chemistry ; Disulfides/*metabolism ; Evolution, Molecular ; Intracellular Membranes/drug effects/*metabolism ; Mitochondria/drug effects/*metabolism ; Mitochondrial Membrane Transport Proteins/*metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/*metabolism ; Molecular Chaperones ; Oxidation-Reduction/drug effects ; Oxidoreductases Acting on Sulfur Group Donors ; Prokaryotic Cells/metabolism ; Protein Binding/physiology ; Protein Folding ; Protein Transport/drug effects/physiology ; Reducing Agents/pharmacology ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism ; }, abstract = {We describe here a pathway for the import of proteins into the intermembrane space (IMS) of mitochondria. Substrates of this pathway are proteins with conserved cysteine motifs, which are critical for import. After passage through the TOM channel, these proteins are covalently trapped by Mia40 via disulfide bridges. Mia40 contains cysteine residues, which are oxidized by the sulfhydryl oxidase Erv1. Depletion of Erv1 or conditions reducing Mia40 prevent protein import. We propose that Erv1 and Mia40 function as a disulfide relay system that catalyzes the import of proteins into the IMS by an oxidative folding mechanism. The existence of a disulfide exchange system in the IMS is unexpected in view of the free exchange of metabolites between IMS and cytosol via porin channels. We suggest that this process reflects the evolutionary origin of the IMS from the periplasmic space of the prokaryotic ancestors of mitochondria.}, }
@article {pmid15987606, year = {2005}, author = {He, D and Wen, JF and Chen, WQ and Lu, SQ and Xin, DD}, title = {Identification, characteristic and phylogenetic analysis of type II DNA topoisomerase gene in Giardia lamblia.}, journal = {Cell research}, volume = {15}, number = {6}, pages = {474-482}, doi = {10.1038/sj.cr.7290316}, pmid = {15987606}, issn = {1001-0602}, mesh = {Animals ; DNA Topoisomerases, Type II/classification/*genetics ; *Genes, Protozoan ; Giardia lamblia/*enzymology ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {The genes encoding type II DNA topoisomerases were investigated in Giardia lamblia genome, and a type IIA gene, GlTop 2 was identified. It is a single copy gene with a 4476 bp long ORF without intron. The deduced amino acid sequence shows strong homology to eukaryotic DNA Top 2. However, some distortions were found, such as six insertions in the ATPase domain and the central domain, a approximately 100 aa longer central domain; a approximately 200 aa shorter C-terminal domain containing rich charged residues. These features revealed by comparing with Top 2 of the host, human, might be helpful in exploiting drug selectivity for antigiardial therapy. Phylogenetic analysis of eukaryotic enzymes showed that kinetoplastids, plants, fungi, and animals were monophyletic groups, and the animal and fungi lineages shared a more recent common ancestor than either did with the plant lineage; microsporidia grouped with fungi. However, unlike many previous phylogenetic analyses, the "amitochondriate"G. lamblia was not the earliest branch but diverged after mitochondriate kinetoplastids in our trees. Both the finding of typical eukaryotic type IIA topoisomerase and the phylogenetic analysis suggest G. lamblia is not possibly as primitive as was regarded before and might diverge after the acquisition of mitochondria. This is consistent with the recent discovery of mitochondrial remnant organelles in G. lamblia.}, }
@article {pmid15986834, year = {2005}, author = {Gupta, RS}, title = {Protein signatures distinctive of alpha proteobacteria and its subgroups and a model for alpha-proteobacterial evolution.}, journal = {Critical reviews in microbiology}, volume = {31}, number = {2}, pages = {101-135}, doi = {10.1080/10408410590922393}, pmid = {15986834}, issn = {1040-841X}, mesh = {Alphaproteobacteria/chemistry/*classification/*genetics ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/*genetics ; *Biological Evolution ; Genes, rRNA ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {Alpha (alpha) proteobacteria comprise a large and metabolically diverse group. No biochemical or molecular feature is presently known that can distinguish these bacteria from other groups. The evolutionary relationships among this group, which includes numerous pathogens and agriculturally important microbes, are also not understood. Shared conserved inserts and deletions (i.e., indels or signatures) in molecular sequences provide a powerful means for identification of different groups in clear terms, and for evolutionary studies (see www.bacterialphylogeny.com). This review describes, for the first time, a large number of conserved indels in broadly distributed proteins that are distinctive and unifying characteristics of either all alpha-proteobacteria, or many of its constituent subgroups (i.e., orders, families, etc.). These signatures were identified by systematic analyses of proteins found in the Rickettsia prowazekii (RP) genome. Conserved indels that are unique to alpha-proteobacteria are present in the following proteins: Cytochrome c oxidase assembly protein Ctag, PurC, DnaB, ATP synthase alpha-subunit, exonuclease VII, prolipoprotein phosphatidylglycerol transferase, RP-400, FtsK, puruvate phosphate dikinase, cytochrome b, MutY, and homoserine dehydrogenase. The signatures in succinyl-CoA synthetase, cytochrome oxidase I, alanyl-tRNA synthetase, and MutS proteins are found in all alpha-proteobacteria, except the Rickettsiales, indicating that this group has diverged prior to the introduction of these signatures. A number of proteins contain conserved indels that are specific for Rickettsiales (XerD integrase and leucine aminopeptidase), Rickettsiaceae (Mfd, ribosomal protein L19, FtsZ, Sigma 70 and exonuclease VII), or Anaplasmataceae (Tgt and RP-314), and they distinguish these groups from all others. Signatures in DnaA, RP-057, and DNA ligase A are commonly shared by various Rhizobiales, Rhodobacterales, and Caulobacter, suggesting that these groups shared a common ancestor exclusive of other alpha-proteobacteria. A specific relationship between Rhodobacterales and Caulobacter is indicated by a large insert in the Asn-Gln amidotransferase. The Rhizobiales group of species are distinguished from others by a large insert in the Trp-tRNA synthetase. Signature sequences in a number of other proteins (viz. oxoglutarate dehydogenase, succinyl-CoA synthase, LytB, DNA gyrase A, LepA, and Ser-tRNA synthetase) serve to distinguish the Rhizobiaceae, Brucellaceae, and Phyllobacteriaceae families from Bradyrhizobiaceae and Methylobacteriaceae. Based on the distribution patterns of these signatures, it is now possible to logically deduce a model for the branching order among alpha-proteobacteria, which is as follows: Rickettsiales --> Rhodospirillales-Sphingomonadales --> Rhodobacterales-Caulobacterales --> Rhizobiales (Rhizobiaceaea-Brucellaceae-Phyllobacteriaceae, and Bradyrhizobiaceae). The deduced branching order is also consistent with the topologies in the 16 rRNA and other phylogenetic trees. Signature sequences in a number of other proteins provide evidence that alpha-proteobacteria is a late branching taxa within Bacteria, which branched after the delta,epsilon-subdivisions but prior to the beta,gamma-proteobacteria. The shared presence of many of these signatures in the mitochondrial (eukaryotic) homologs also provides evidence of the alpha-proteobacterial ancestry of mitochondria.}, }
@article {pmid15985435, year = {2005}, author = {Regoes, A and Zourmpanou, D and León-Avila, G and van der Giezen, M and Tovar, J and Hehl, AB}, title = {Protein import, replication, and inheritance of a vestigial mitochondrion.}, journal = {The Journal of biological chemistry}, volume = {280}, number = {34}, pages = {30557-30563}, doi = {10.1074/jbc.M500787200}, pmid = {15985435}, issn = {0021-9258}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Cell Cycle ; Cell Line ; Cytoskeleton/metabolism ; DNA/chemistry ; Databases, Genetic ; Genetic Vectors ; Giardia/metabolism ; Giardia lamblia/metabolism ; Humans ; Microscopy, Confocal ; Microscopy, Fluorescence ; Mitochondria/*metabolism ; Models, Biological ; Octoxynol/pharmacology ; Peptides/chemistry ; Protein Transport ; Stochastic Processes ; Symbiosis ; Transfection ; }, abstract = {Mitochondrial remnant organelles (mitosomes) that exist in a range of "amitochondrial" eukaryotic organisms represent ideal models for the study of mitochondrial evolution and for the establishment of the minimal set of proteins required for the biogenesis of an endosymbiosis-derived organelle. Giardia intestinalis, often described as the earliest branching eukaryote, contains double membrane-bounded structures involved in iron-sulfur cluster biosynthesis, an essential function of mitochondria. Here we present evidence that Giardia mitosomes also harbor Cpn60, mtHsp70, and ferredoxin and that despite their advanced state of reductive evolution they have retained vestiges of presequence-dependent and -independent protein import pathways akin to those that operate in mammalian mitochondria. Although import of IscU and ferredoxin is still reliant on their amino-terminal presequences, targeting of Giardia Cpn60, IscS, or mtHsp70 into mitosomes no longer requires cleavable presequences, a derived feature from their mitochondrial homologues. In addition, we found that division and segregation of a single centrally positioned mitosome tightly associated with the microtubular cytoskeleton is coordinated with the cell cycle, whereas peripherally located mitosomes are inherited into daughter cells stochastically.}, }
@article {pmid15984936, year = {2005}, author = {Peng, J and Huang, CH and Short, MK and Jubinsky, PT}, title = {Magmas gene structure and evolution.}, journal = {In silico biology}, volume = {5}, number = {3}, pages = {251-263}, pmid = {15984936}, issn = {1386-6338}, support = {DK62704/DK/NIDDK NIH HHS/United States ; HL66274/HL/NHLBI NIH HHS/United States ; }, mesh = {Alternative Splicing ; Amino Acid Sequence ; Animals ; *Evolution, Molecular ; Gene Duplication ; Granulocyte-Macrophage Colony-Stimulating Factor/metabolism ; Humans ; Introns ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/chemistry/*genetics/physiology ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; Signal Transduction/physiology ; Species Specificity ; }, abstract = {Magmas is a nuclear encoded protein found in the mitochondria of mammalian cells. It participates in granulocyte-macrophage-colony stimulating factor (GM-CSF) signaling in hematopoietic cells and has an essential role in invertebrate development. In order to characterize the protein structural features and gene evolution of Magmas, a dataset containing 61 Magmas homologs from 52 species distributed among animals, plants and fungi was analyzed. All Magmas members were found to possess three novel sequence motifs in addition to a conserved leader peptide. Phylogenetic tree and dN/dS rate ratios showed that Magmas was evolutionarily conserved. Analysis of Magmas gene organization demonstrated incremental intron acquisition in plants and vertebrates. Significant genetic diversity in Magmas was observed from kingdom specific amino acid signatures, the presence of predicted signal peptides that target the protein to other intracellular locations besides the mitochondria, and the detection of multiple isoforms in higher animals. These studies demonstrate that Magmas members constitute an important family of conserved proteins having multifunctional activities, and provide a basis for future experiments.}, }
@article {pmid15980957, year = {2005}, author = {Peretó, J and López-García, P and Moreira, D}, title = {Phylogenetic analysis of eukaryotic thiolases suggests multiple proteobacterial origins.}, journal = {Journal of molecular evolution}, volume = {61}, number = {1}, pages = {65-74}, pmid = {15980957}, issn = {0022-2844}, mesh = {Acetyl-CoA C-Acyltransferase/*genetics ; Animals ; Databases, Nucleic Acid ; Eukaryota/genetics ; *Evolution, Molecular ; Fungi/genetics ; Humans/genetics ; Mitochondria/enzymology/genetics ; Peroxisomes/enzymology/genetics ; *Phylogeny ; Plants/genetics ; Proteobacteria/*genetics ; Sequence Alignment ; }, abstract = {Eukaryotic thiolases are essential enzymes located in three different compartments (peroxisome, mitochondrion, and cytosol) that can display catabolic or anabolic functions. They are responsible for the thiolytic cleavage of oxidized acyl-CoA (thiolase I; EC 2.3.1.16) and the synthesis or degradation of acetoacetyl-CoA (thiolase II; EC 2.3.1.9). Phylogenetic analysis of eukaryotic thiolase sequences showed that they form six distinct clusters, one of them highly divergent, which are in good correlation with their class and subcellular location. When analyzed together with a representative sample of prokaryotic thiolases, all eukaryotic thiolase groups emerged close to proteobacterial sequences. Metazoan cytosolic thiolase II was related to alpha-proteobacterial sequences, suggesting a mitochondrial origin. Unexpectedly, cytosolic thiolases from green plants and fungi as well as at least one member of all eukaryotic peroxisomal and mitochondrial thiolases had delta-proteobacteria as closest relatives. Our analysis suggests that these eukaryotic peroxisomal and mitochondrial thiolases may have been acquired from delta-proteobacteria prior to the ancestor of all known eukaryotes.}, }
@article {pmid15979254, year = {2005}, author = {Margeot, A and Garcia, M and Wang, W and Tetaud, E and di Rago, JP and Jacq, C}, title = {Why are many mRNAs translated to the vicinity of mitochondria: a role in protein complex assembly?.}, journal = {Gene}, volume = {354}, number = {}, pages = {64-71}, doi = {10.1016/j.gene.2005.04.022}, pmid = {15979254}, issn = {0378-1119}, mesh = {3' Untranslated Regions/chemistry/genetics ; Base Sequence ; Electron Transport Complex IV/genetics/metabolism ; Mitochondria/genetics/metabolism/*physiology ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Polyribosomes/metabolism ; Protein Biosynthesis/*genetics ; Proton-Translocating ATPases/genetics/metabolism ; RNA, Messenger/*genetics ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Signal Transduction/physiology ; }, abstract = {The longstanding question of the presence of mitochondria-bound polysomes has been recently revisited using new approaches. Genome-wide analyses provided evidence that many genes are actually translated on mitochondria-bound polysomes and GFP-labeling techniques have shown that, in vivo, the 3'UTR sequence of these genes contains signals which can target hybrid RNA molecules to the proximity of mitochondria. Evolutionary conservation of some of these signals will be presented. Interestingly, class I mRNA which are translated on free polysomes and class II mRNA which are translated on mitochondria-bound polysomes have, mostly, eukaryotic and prokaryotic origins respectively. Using ATP2, a typical prokaryotic-derived gene, as a model for class II mRNA, we showed that its 3'UTR sequence is essential both for a correct addressing of mRNA to mitochondria proximity and to a proper production of functional ATP synthases. These different observations suggest that prokaryotic-derived genes are, like the contemporary mitochondrial genes, translated near mitochondrial membranes. In both cases this locus specific translation process might be connected to a correct complex assembly program and the cases of ATP synthase and cytochrome c oxidase complexes will be considered in this respect.}, }
@article {pmid15977827, year = {2005}, author = {Kondrashov, FA}, title = {[The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus].}, journal = {Biofizika}, volume = {50}, number = {3}, pages = {396-403}, pmid = {15977827}, issn = {0006-3029}, mesh = {Animals ; Armadillos/*genetics ; Base Sequence ; *Evolution, Molecular ; Mitochondria/*genetics ; Molecular Sequence Data ; *Nucleic Acid Conformation ; RNA, Transfer, Cys/*genetics ; }, abstract = {The case of the convergent loss of the D-hairpin in mitochondrial cysteine tRNA of the nine-banded armadillo Dasypus novemcinctus is described. This evolutionary event sheds light on the molecular structure-function relationship and on the effect of this relationship on the processes of evolution of biopolymers and macromolecules.}, }
@article {pmid15975737, year = {2005}, author = {De Grassi, A and Caggese, C and D'Elia, D and Lanave, C and Pesole, G and Saccone, C}, title = {Evolution of nuclearly encoded mitochondrial genes in Metazoa.}, journal = {Gene}, volume = {354}, number = {}, pages = {181-188}, doi = {10.1016/j.gene.2005.03.046}, pmid = {15975737}, issn = {0378-1119}, mesh = {Animals ; Cell Nucleus/*genetics ; Ciona intestinalis ; Cytochromes c/genetics ; Databases, Protein ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Fishes ; Genome ; Humans ; Insecta ; Mice ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/*genetics ; Nuclear Proteins/*genetics ; Oxidative Phosphorylation ; Pan troglodytes ; Protein Subunits/genetics ; Rats ; }, abstract = {All Metazoan nuclear genomes underwent a continuous process of both complete and partial genetic material gain and loss. The forces modulating these events are also subject to the strict interaction between nuclear and mitochondrial (mt) genome. In this context we investigate the evolution of nuclear genes encoding proteins which target the mitochondrion, with a particular attention to genes involved in oxidative phosphorylation (OXPHOS), one of the most ancient and conserved functions. To examine thoroughly the evolutionary strategies that preserve OXPHOS and coordinate the two cellular genomes, a comparative analysis has been carried out for 78 OXPHOS gene families in several Metazoa (insects, tunicates, fishes and mammals). We demonstrate that the duplication rate of OXPHOS genes increases passing from invertebrates to vertebrates consistently with the total increase in genome size, but all species are prone to negatively select OXPHOS duplicates compared to the general trend of nuclear gene families. These results are consistent with the 'balance hypothesis' and, at least in insects, the expression of duplicate genes is low and strongly testis-biased.}, }
@article {pmid15970444, year = {2005}, author = {Robe, LJ and Valente, VL and Budnik, M and Loreto, EL}, title = {Molecular phylogeny of the subgenus Drosophila (Diptera, Drosophilidae) with an emphasis on Neotropical species and groups: a nuclear versus mitochondrial gene approach.}, journal = {Molecular phylogenetics and evolution}, volume = {36}, number = {3}, pages = {623-640}, doi = {10.1016/j.ympev.2005.05.005}, pmid = {15970444}, issn = {1055-7903}, mesh = {Animals ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Drosophila/*classification/enzymology/*genetics ; Drosophila Proteins/genetics ; Drug Resistance/genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Methyldopa/pharmacology ; Mitochondria/enzymology/genetics ; *Phylogeny ; Tropical Climate ; }, abstract = {The genus Drosophila has played an essential role in many biological studies during the last 100 years but much controversy and many incompletely addressed issues still remain to be elucidated regarding the phylogeny of this genus. Because information on the Neotropical species contained in the subgenus Drosophila is particularly incomplete, with this taxonomic group being underrepresented in many studies, we designed a study to answer some evolutionary questions related to these species. We subjected at least 41 Drosophilidae taxa to a phylogenetic analysis using a 516-base pair (bp) fragment of the alpha-methyldopa (Amd) nuclear gene and a 672 bp fragment of the mitochondrial cytochrome oxidase subunit II (COII) gene both individually and in combination. We found that the subgenus Drosophila is paraphyletic and subdivided into two main clusters: the first containing species traditionally placed in the virilis-repleta radiation and the second assembling species of the immigrans-Hirtodrosophila radiation. Inside the first of these clusters we could detect the monophyly of both the flavopilosa (the sister-clade of the annulimana group) and the mesophragmatica (closely related to the repleta group) species groups. Concerning the immigrans-Hirtodrosophila lineage, Zaprionus, Liodrosophila, Samoaia, and Hirtodrosophila were the early offshoots, followed by the immigrans, quinaria, testacea, and funebris species groups. The tripunctata radiation appears to be a derived clade, composed of a paraphyletic tripunctata group, intimately interposed with members of the cardini, guarani, and guaramunu species groups. Overall, the COII gene yielded a poor phylogenetic performance when compared to the Amd gene, the evolutionary hypothesis of which agreed with the total evidence tree. This phenomenon can be explained by the fast saturation of transitional substitutions in COII, due to strong biases in both base composition and substitution patterns, as also by its great among-site rate variation heterogeneity.}, }
@article {pmid15969755, year = {2005}, author = {Nickrent, DL and Der, JP and Anderson, FE}, title = {Discovery of the photosynthetic relatives of the "Maltese mushroom" Cynomorium.}, journal = {BMC evolutionary biology}, volume = {5}, number = {}, pages = {38}, pmid = {15969755}, issn = {1471-2148}, mesh = {Bayes Theorem ; Botany/methods ; Cynomorium/classification/*physiology ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/chemistry ; Evolution, Molecular ; Genome, Plant ; Mitochondria/metabolism ; Models, Statistical ; *Photosynthesis ; Phylogeny ; Plant Physiological Phenomena ; Software ; }, abstract = {BACKGROUND: Although recent molecular phylogenetic studies have identified the photosynthetic relatives of several enigmatic holoparasitic angiosperms, uncertainty remains for the last parasitic plant order, Balanophorales, often considered to include two families, Balanophoraceae and Cynomoriaceae. The nonphotosynthetic (holoparasitic) flowering plant Cynomorium coccineum has long been known to the Muslim world as "tarthuth" and to Europeans as the "Maltese mushroom"; C. songaricum is known in Chinese medicine as "suo yang." Interest in these plants is increasing and they are being extensively collected from wild populations for use in herbal medicines.<br><br>RESULTS: Here we report molecular phylogenetic analyses of nuclear ribosomal DNA and mitochondrial matR sequence data that strongly support the independent origin of Balanophoraceae and Cynomoriaceae. Analyses of single gene and combined gene data sets place Cynomorium in Saxifragales, possibly near Crassulaceae (stonecrop family). Balanophoraceae appear related to Santalales (sandalwood order), a position previously suggested from morphological characters that are often assumed to be convergent.<br><br>CONCLUSION: Our work shows that Cynomorium and Balanophoraceae are not closely related as indicated in all past and present classifications. Thus, morphological features, such as inflorescences bearing numerous highly reduced flowers, are convergent and were attained independently by these two holoparasite lineages. Given the widespread harvest of wild Cynomorium species for herbal medicines, we here raise conservation concerns and suggest that further molecular phylogenetic work is needed to identify its photosynthetic relatives. These relatives, which will be easier to cultivate, should then be examined for phytochemical activity purported to be present in the more sensitive Cynomorium.}, }
@article {pmid15967446, year = {2005}, author = {Tang, WK and Chan, CB and Cheng, CH and Fong, WP}, title = {Seabream antiquitin: molecular cloning, tissue distribution, subcellular localization and functional expression.}, journal = {FEBS letters}, volume = {579}, number = {17}, pages = {3759-3764}, doi = {10.1016/j.febslet.2005.05.070}, pmid = {15967446}, issn = {0014-5793}, mesh = {Aldehyde Dehydrogenase/analysis/*genetics/*metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Fish Proteins/analysis/*genetics/*metabolism ; Kidney/chemistry/metabolism ; Liver/chemistry/metabolism ; Mitochondria/chemistry ; Molecular Sequence Data ; Phylogeny ; Recombinant Proteins/biosynthesis/genetics ; Sea Bream/genetics/*metabolism ; Tissue Distribution ; }, abstract = {Subsequent to our earlier report on the first purification of antiquitin protein from seabream liver and demonstration of its enzymatic activity [FEBS Letters 516 (2002) 183-186], we report herein the cloning of its full-length cDNA sequence. The open reading frame encodes a protein of 511 amino acids. Results of RT-PCR indicate that antiquitin is highly expressed in both the seabream liver and kidney. Transfection studies in cultured eukaryotic cells provided further evidence that it is a cytosolic protein. Bacterial expression of the enzyme was also performed. The purified recombinant protein was demonstrated to exhibit similar kinetic properties as the native enzyme.}, }
@article {pmid15967440, year = {2005}, author = {Krause, K and Kilbienski, I and Mulisch, M and Rödiger, A and Schäfer, A and Krupinska, K}, title = {DNA-binding proteins of the Whirly family in Arabidopsis thaliana are targeted to the organelles.}, journal = {FEBS letters}, volume = {579}, number = {17}, pages = {3707-3712}, doi = {10.1016/j.febslet.2005.05.059}, pmid = {15967440}, issn = {0014-5793}, mesh = {Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/analysis/classification/*metabolism ; Chloroplasts/chemistry/metabolism ; DNA-Binding Proteins/analysis/classification/*metabolism ; Mitochondria/chemistry/metabolism ; Organelles/chemistry/metabolism ; Phylogeny ; Protein Transport ; }, abstract = {Arabidopsis thaliana contains three genes with high homology to potato p24 which was described as a member of the Whirly family of nuclear transcriptional activators. Computer-based analysis revealed that all Arabidopsis Whirly (Why) proteins contain targeting sequences for either plastids or mitochondria. The functionality of these sequences was demonstrated by in vitro import assays into isolated organelles. Transient expression of GFP fusion proteins in protoplasts and onion epidermal cells confirmed the localisation of these proteins in plastids or mitochondria, respectively. The possession of organellar targeting sequences seems to be conserved among Why proteins of higher plant species, including potato p24.}, }
@article {pmid15965040, year = {2005}, author = {Lee, HK and Park, KS and Cho, YM and Lee, YY and Pak, YK}, title = {Mitochondria-based model for fetal origin of adult disease and insulin resistance.}, journal = {Annals of the New York Academy of Sciences}, volume = {1042}, number = {}, pages = {1-18}, doi = {10.1196/annals.1338.001}, pmid = {15965040}, issn = {0077-8923}, mesh = {Aging/*physiology ; Animals ; *Disease ; Fetus/*physiology ; Humans ; Insulin Resistance/*physiology ; Mitochondria/*metabolism ; *Models, Biological ; }, abstract = {Insulin resistance has been recognized as the fundamental underlying metabolic defect in the pathogenesis of metabolic syndrome, a clustering of cardiovascular risk factors such as diabetes, hypertension, dyslipidemia, and obesity. Recent studies established that mitochondrial dysfunction is involved in insulin resistance in general and fetal origin of this state in particular. Because genes are the fundamental molecular basis of inheritance--and thus the cornerstones of evolution--a model explaining insulin resistance is based at the gene level at best. Since a certain mtDNA polymorphism, 16189T>C, is associated with insulin resistance, mtDNA has to be a basic component of the gene-based model. We developed a mitochondria-based model that explains insulin resistance in terms of quantitative and qualitative change of the mitochondrion and its DNA. This model can accommodate several important hypotheses, such as thrifty genotype hypothesis, thrifty phenotype hypothesis, fetal insulin hypothesis, contribution of metabolic imprinting by epigenetic changes, and many other features associated with insulin resistance. We will discuss mechanisms that indicate why the perturbed initial condition of mitochondrial function should lead to the reduced insulin sensitivity.}, }
@article {pmid15964980, year = {2005}, author = {Dawson, MN and Hamner, WM}, title = {Rapid evolutionary radiation of marine zooplankton in peripheral environments.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {102}, number = {26}, pages = {9235-9240}, pmid = {15964980}, issn = {0027-8424}, mesh = {Animals ; Biodiversity ; Biological Evolution ; Electron Transport Complex IV/genetics ; Environment ; Evolution, Molecular ; Founder Effect ; Genetic Variation ; Genetics, Population ; Geography ; Mitochondria/metabolism ; Models, Molecular ; Models, Statistical ; Molecular Sequence Data ; Oceans and Seas ; Palau ; Phylogeny ; Zooplankton/*genetics/*physiology ; }, abstract = {Populations of jellyfish, Mastigias sp., landlocked in tropical marine lakes during the Holocene, show extreme genetic isolation (0.74 < or = phiST < or = 1.00), founder effects (genetic diversity: 0.000 < or = pi < or = 0.001), rapid morphological evolution, and behavioral adaptation. These results demonstrate incipient speciation in what we propose may be modern analogues of Plio-Pleistocene populations isolated in ocean basins by glacially lowered sea level and counterparts to modern marine populations isolated on archipelagos and other distant shores. Geographic isolation in novel environments, even if geologically brief, may contribute much to marine biodiversity because evolutionary rates in marine plankton can rival the most rapid speciation seen for limnetic species, such as cichlids and sticklebacks. Marine lakes present situations rare in their clarity for studying evolution in marine taxa.}, }
@article {pmid15951934, year = {2005}, author = {Prieto, I and Jiménez, F and Aller, MA and Nava, MP and Vara, E and Garcia, C and Arias, J}, title = {Tumor necrosis factor-alpha, interleukin-1beta and nitric oxide: induction of liver megamitochondria in prehepatic portal hypertensive rats.}, journal = {World journal of surgery}, volume = {29}, number = {7}, pages = {903-908}, pmid = {15951934}, issn = {0364-2313}, mesh = {Animals ; Fatty Liver/etiology/*physiopathology ; Hypertension, Portal/complications/*physiopathology ; Interleukin-1/*analysis/physiology ; Male ; Mitochondria, Liver/*physiology ; Models, Animal ; Nitric Oxide/*analysis/physiology ; Rats ; Rats, Wistar ; Tumor Necrosis Factor-alpha/*analysis/physiology ; }, abstract = {It has been shown that portal hypertension in the rat causes microvesicular hepatocytic fatty infiltration. Formation of megamitochondria (MG) is one of the most prominent alterations in steatosis. Because nitric oxide (NO), tumor necrosis factor-alpha (TNFalpha), and interleukin-1beta (IL-1beta) impair mitochondrial function, these mediators have been studied in prehepatic portal hypertensive rats to verify their coexistence with MG and therefore with steatosis. Male Wistar rats were divided into two groups: a control group (n = 7) and a group with partial portal vein hgation (n = 19) at 6 weeks of evolution. TNFalpha and IL-1beta were quantified in liver by enzyme-linked immunosorbent assay, and NO was measured in the portal vein, suprahepatic inferior vena cava, and infrahepatic inferior vena cava by the Griess reaction. In portal hypertensive rats, the serum concentration of NO of hepatic origin increases (132.10 +/- 34.72 vs. 52.44 +/- 11.32 nmol/ml; p < 0.001), as do TNFalpha (2.02 +/- 0.20 vs. 1.12 +/- 0.43 micromol/mg protein) and IL-1beta (18.95 +/- 2.59 vs. 5.48 +/- 1.70 micromol/mg protein) (p = 0.005) in the liver. The most frequent hepatic histologic findings are the presence of MG (p < 0.001), steatosis, and hyperplasia. An increase in hepatic release of NO, TNFalpha and IL-1beta with MG formation is produced in rats with portal hypertension. Therefore these proinflammatory mediators and this morphologic mitochondrial alteration could both be involved in the etiopathogenesis of steatosis.}, }
@article {pmid15949981, year = {2005}, author = {van Lis, R and González-Halphen, D and Atteia, A}, title = {Divergence of the mitochondrial electron transport chains from the green alga Chlamydomonas reinhardtii and its colorless close relative Polytomella sp.}, journal = {Biochimica et biophysica acta}, volume = {1708}, number = {1}, pages = {23-34}, doi = {10.1016/j.bbabio.2004.12.010}, pmid = {15949981}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Animals ; Chlamydomonas reinhardtii/*genetics/growth &amp; development/*metabolism ; Cytochrome c Group/chemistry ; Electron Transport Chain Complex Proteins/*genetics ; Electron Transport Complex III/chemistry ; Electrophoresis, Polyacrylamide Gel ; Eukaryota/*genetics/growth &amp; development/*metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Protein Structure, Quaternary ; Proteome/chemistry ; Sequence Alignment ; }, abstract = {Compelling evidence exists that the colorless algae of the genus Polytomella arose from a green Chlamydomonas-like ancestor by losing its functional photosynthetic apparatus. Due to the close relationship between the colorless and the green chlorophyte, Polytomella sp. appeared as a useful indicative framework for structural studies of Chlamydomonas reinhardtii mitochondria. However, comparative studies reported here unexpectedly revealed significant differences between the mitochondrial respiratory systems of the two algae. Two-dimensional blue native/SDS-PAGE of isolated mitochondria indicated that cytochrome-containing respiratory complexes III and IV in the two chlorophytes contrast in size, subunit composition and relative abundance. Complex IV in Polytomella is smaller than its counterpart in C. reinhardtii and occurs in two forms that differ presumably in the presence of subunit COXIII. The cytochrome c and the iron-sulfur Rieske protein of both chlorophytes revealed structural differences on the amino acid sequence level. Under comparable culture conditions, the colorless alga exhibits lower levels of cytochrome c and complex IV but a higher respiratory activity than the green alga. Cytochrome c levels were also found to be differently regulated by the growth conditions in both algae. The divergence between the respiratory systems in the two related chlorophytes can be viewed as a consequence of the loss of photosynthetic activity and/or of the adaptation to the environment via the acquisition of a more flexible, heterotrophic metabolism. Our understanding of mitochondrial function and evolution is expected to be greatly enhanced via further parallel studies of photosynthetic/non-photosynthetic algae, for which this study forms an incentive.}, }
@article {pmid15947205, year = {2005}, author = {Marande, W and Lukes, J and Burger, G}, title = {Unique mitochondrial genome structure in diplonemids, the sister group of kinetoplastids.}, journal = {Eukaryotic cell}, volume = {4}, number = {6}, pages = {1137-1146}, pmid = {15947205}, issn = {1535-9778}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry/ultrastructure ; Electrophoresis, Agar Gel ; Euglenida/*genetics/ultrastructure ; Evolution, Molecular ; Genes, rRNA ; *Genome, Protozoan ; Kinetoplastida/classification/*genetics/ultrastructure ; Microscopy, Electron ; Microscopy, Fluorescence ; Mitochondria/*genetics/*ultrastructure ; Phylogeny ; RNA Editing ; RNA Splicing ; RNA, Guide, Kinetoplastida/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {Kinetoplastid flagellates are characterized by uniquely massed mitochondrial DNAs (mtDNAs), the kinetoplasts. Kinetoplastids of the trypanosomatid group possess two types of mtDNA molecules: maxicircles bearing protein and mitoribosomal genes and minicircles specifying guide RNAs, which mediate uridine insertion/deletion RNA editing. These circles are interlocked with one another to form dense networks. Whether these peculiar mtDNA features are restricted to kinetoplastids or prevail throughout Euglenozoa (euglenids, diplonemids, and kinetoplastids) is unknown. Here, we describe the mitochondrial genome and the mitochondrial ultrastructure of Diplonema papillatum, a member of the diplonemid flagellates, the sister group of kinetoplastids. Fluorescence and electron microscopy show a single mitochondrion per cell with an ultrastructure atypical for Euglenozoa. In addition, DNA is evenly distributed throughout the organelle rather than compacted. Molecular and electron microscopy studies distinguish numerous 6- and 7-kbp-sized mitochondrial chromosomes of monomeric circular topology and relaxed conformation in vivo. Remarkably, the cox1 gene (and probably other mitochondrial genes) is fragmented, with separate gene pieces encoded on different chromosomes. Generation of the contiguous cox1 mRNA requires trans-splicing, the precise mechanism of which remains to be determined. Taken together, the mitochondrial gene/genome structure of Diplonema is not only different from that of kinetoplastids but unique among eukaryotes as a whole.}, }
@article {pmid15940286, year = {2005}, author = {van der Giezen, M and Tovar, J}, title = {Degenerate mitochondria.}, journal = {EMBO reports}, volume = {6}, number = {6}, pages = {525-530}, pmid = {15940286}, issn = {1469-221X}, mesh = {*Biological Evolution ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; Mitochondria/*genetics/*physiology/ultrastructure ; }, abstract = {Mitochondria are the main sites of biological energy generation in eukaryotes. These organelles are remnants of a bacterial endosymbiont that took up residence inside a host cell over 1,500 million years ago. Comparative genomics studies suggest that the mitochondrion is monophyletic in origin. Thus, the original mitochondrial endosymbiont has evolved independently in anaerobic and aerobic environments that are inhabited by diverse eukaryotic lineages. This process has resulted in a collection of morphologically, genetically and functionally heterogeneous organelle variants that include anaerobic and aerobic mitochondria, hydrogenosomes and mitosomes. Current studies aim to determine whether a central common function drives the retention of mitochondrial organelles in different eukaryotic organisms.}, }
@article {pmid15936981, year = {2005}, author = {Agatsuma, T and Iwagami, M and Uni, S and Takaoka, H and Katsumi, A and Kimura, E and Bain, O}, title = {Molecular phylogenetic relationships among seven Japanese species of Cercopithifilaria.}, journal = {Parasitology international}, volume = {54}, number = {3}, pages = {195-199}, doi = {10.1016/j.parint.2005.04.002}, pmid = {15936981}, issn = {1383-5769}, mesh = {Animals ; Antelopes/*parasitology ; DNA, Helminth/analysis ; DNA, Mitochondrial/analysis ; Deer/*parasitology ; Electron Transport Complex IV/genetics ; Filariasis/parasitology/*veterinary ; Filarioidea/*classification/*genetics/isolation &amp; purification/physiology ; Host-Parasite Interactions ; Japan ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {DNA sequences from a portion of the mitochondrial COI gene were used to clarify phylogenetic relationships among Japanese species in the genus Cercopithifilaria. Sequences were determined from seven Japanese species, five (C. shohoi, C. multicauda, C. minuta, C. tumidicervicata and C. bulboidea) from the serow (Capricornis crispus F. Bovidae) and two (C. longa and C. crassa) from the sika deer (Cervus nippon nippon F. Cervidae). No base substitutions were observed between C. bulboidea and C. longa, suggesting that recent host switching of a lineage of C. bulboidea between bovid and cervid hosts gave rise to C. longa. In phylogenetic trees inferred using a variety of methods, the morphologically ancestral type, C. bulboidea, appeared as a derived species. C. multicauda was found to be basal in the analyses. It seems therefore that C. multicauda is the most primitive out of the seven species.}, }
@article {pmid15931495, year = {2005}, author = {Shao, R and Mitani, H and Barker, SC and Takahashi, M and Fukunaga, M}, title = {Novel mitochondrial gene content and gene arrangement indicate illegitimate inter-mtDNA recombination in the chigger mite, Leptotrombidium pallidum.}, journal = {Journal of molecular evolution}, volume = {60}, number = {6}, pages = {764-773}, pmid = {15931495}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; Cell Nucleus/metabolism ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genome ; Humans ; Mites ; Mitochondria/*genetics ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; *Recombination, Genetic ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; }, abstract = {To better understand the evolution of mitochondrial (mt) genomes in the Acari (mites and ticks), we sequenced the mt genome of the chigger mite, Leptotrombidium pallidum (Arthropoda: Acari: Acariformes). This genome is highly rearranged relative to that of the hypothetical ancestor of the arthropods and the other species of Acari studied. The mt genome of L. pallidum has two genes for large subunit rRNA, a pseudogene for small subunit rRNA, and four nearly identical large noncoding regions. Nineteen of the 22 tRNAs encoded by this genome apparently lack either a T-arm or a D-arm. Further, the mt genome of L. pallidum has two distantly separated sections with identical sequences but opposite orientations of transcription. This arrangement cannot be accounted for by homologous recombination or by previously known mechanisms of mt gene rearrangement. The most plausible explanation for the origin of this arrangement is illegitimate inter-mtDNA recombination, which has not been reported previously in animals. In light of the evidence from previous experiments on recombination in nuclear and mt genomes of animals, we propose a model of illegitimate inter-mtDNA recombination to account for the novel gene content and gene arrangement in the mt genome of L. pallidum.}, }
@article {pmid15930151, year = {2005}, author = {Pombert, JF and Otis, C and Lemieux, C and Turmel, M}, title = {The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages.}, journal = {Molecular biology and evolution}, volume = {22}, number = {9}, pages = {1903-1918}, doi = {10.1093/molbev/msi182}, pmid = {15930151}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; Chlorophyta/classification/*genetics ; Chromosome Mapping ; DNA, Chloroplast/*genetics ; *Evolution, Molecular ; Gene Order ; *Genome, Plant ; Molecular Sequence Data ; Multigene Family ; Nucleic Acid Conformation ; *Phylogeny ; Repetitive Sequences, Nucleic Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {One major lineage of green plants, the Chlorophyta, is represented by the green algal classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae, and Chlorophyceae. The Prasinophyceae occupies the most basal position in the Chlorophyta, but the branching order of the Ulvophyceae, Trebouxiophyceae, and Chlorophyceae remains unresolved. The chloroplast genome sequences currently available for representatives of three chlorophyte classes have revealed that this genome is highly plastic, with Chlamydomonas (Chlorophyceae) and Chlorella (Trebouxiophyceae) showing fewer ancestral features than Nephroselmis (Prasinophyceae). We report the 195,867-bp chloroplast DNA (cpDNA) sequence of Pseudendoclonium akinetum (Ulvophyceae), a member of the class that has not been previously examined for detailed cpDNA analysis. This genome shares common evolutionary trends with its Chlorella and Chlamydomonas homologs. The gene content, number of ancestral gene clusters, and abundance of short dispersed repeats in Pseudendoclonium cpDNA are intermediate between those observed for Chlorella and Chlamydomonas cpDNAs. Although Pseudendoclonium cpDNA features a large inverted repeat, its quadripartite structure is unusual in displaying an rRNA operon transcribed toward the large single-copy (LSC) region and a small single-copy region containing 14 genes that are normally found in the LSC region. Twenty-seven group I introns lie in nine genes and fall within four subgroups (IA1, IA2, IA3, and IB); 19 encode putative homing endonucleases, and 7 have homologs at identical insertion sites in other chlorophyte or streptophyte organelle genomes. The high similarity observed among the 14 IA1 and 7 IA2 introns and their encoded endonucleases suggests that many introns arose from intragenomic proliferation of a few founding introns in the lineage leading to Pseudendoclonium. Interestingly, one intron (in atpA) and some of the dispersed repeats also reside in Pseudendoclonium mitochondria, providing strong evidence for interorganellar lateral transfer of these genetic elements. Phylogenetic analyses of 58 cpDNA-encoded proteins and genes support the hypothesis that the Ulvophyceae is sister to the Trebouxiophyceae but cannot eliminate the hypothesis that the Ulvophyceae is sister to the Chlorophyceae. We favor the latter hypothesis because it is strongly supported by phylogenetic analyses of gene order data and by independent structural evidence based on shared gene losses and rearrangement break points within ancestrally conserved gene clusters.}, }
@article {pmid15927004, year = {2005}, author = {Williams, BA and Keeling, PJ}, title = {Microsporidian mitochondrial proteins: expression in Antonospora locustae spores and identification of genes coding for two further proteins.}, journal = {The Journal of eukaryotic microbiology}, volume = {52}, number = {3}, pages = {271-276}, doi = {10.1111/j.1550-7408.2005.05-00036.x}, pmid = {15927004}, issn = {1066-5234}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Blotting, Western ; Gene Expression ; Glycerolphosphate Dehydrogenase/isolation &amp; purification ; Membrane Transport Proteins/genetics ; Microsporidia/chemistry/*genetics ; Mitochondria/*chemistry ; Mitochondrial Proteins/biosynthesis/*genetics ; Monocarboxylic Acid Transporters ; Peptide Hydrolases/genetics ; Phylogeny ; Protozoan Proteins/biosynthesis/*genetics ; Pyruvate Dehydrogenase (Lipoamide)/isolation &amp; purification ; RNA, Messenger/analysis ; RNA, Protozoan/analysis ; Sequence Homology, Amino Acid ; Spores, Protozoan/genetics/*metabolism ; }, abstract = {Microsporidia are obligate intracellular parasites, phylogenetically allied to the fungi. Once considered amitochondriate, now a number of mitochondrion-derived genes have been described from various species, and the relict organelle was recently identified in Trachipleistophora hominis. We have investigated the expression of potential mitochondrial targeted proteins in the spore stage to determine whether the organelle is likely to have a role in the spore or early infection stage. To investigate whether the Antonospora locustae genome codes for a different complement of mitochondrial proteins than Encephalitozoon cuniculi an EST library was searched for putative mitochondrial genes that have not been identified in the E. cuniculi genome project. The spore is the infectious stage of microsporidia, but is generally considered to be metabolically dormant. Fourteen genes for putatively mitochondrion-targeted proteins were shown to be present in purified spore mRNA by 3'-rapid amplification of cDNA ends and EST sequencing. Pyruvate dehydrogenase E1alpha and mitochondrial glycerol-3-phosphate dehydrogenase proteins were also shown to be present in A. locustae and E. cuniculi spores, respectively, suggesting a role for these proteins in the early stages of infection, or within the spore itself. EST sequencing also revealed two mitochondrial protein-encoding genes in A. locustae that are not found in the genome of E. cuniculi. One encodes a possible pyruvate transporter, the other a subunit of the mitochondrial inner membrane peptidase. In yeast mitochondria, this protein is part of a trimeric complex that processes proteins targeted to the inner membrane and the intermembrane space, and its substrate in A. locustae is presently unknown.}, }
@article {pmid15926202, year = {2005}, author = {Sato, S and Wilson, RJ}, title = {Organelle-specific cochaperonins in apicomplexan parasites.}, journal = {Molecular and biochemical parasitology}, volume = {141}, number = {2}, pages = {133-143}, doi = {10.1016/j.molbiopara.2005.01.010}, pmid = {15926202}, issn = {0166-6851}, mesh = {Amino Acid Sequence ; Animals ; Apicomplexa/chemistry/*genetics/metabolism ; Chaperonins/*analysis/chemistry/*genetics ; Cloning, Molecular ; DNA, Protozoan/chemistry ; Genes, Protozoan ; Green Fluorescent Proteins/analysis/genetics ; Mitochondria/chemistry ; Molecular Sequence Data ; Organelles/*chemistry ; Phylogeny ; Plasmodium falciparum/chemistry/*genetics/ultrastructure ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Protein maturation in eukaryotic organelles requires the type I chaperonin system; this comprises chaperonin 60 (Cpn60) and its cochaperonin. We have re-examined and revised the sequence of the nuclear genes specifying organellar cochaperonins in Plasmodium falciparum (Pf). One gene encodes a typical cochaperonin (PfCpn10) whereas the other (encoding PfCpn20) specifies two Cpn10 domains arranged in tandem as in plant chloroplasts. Transfection experiments using fluorescent reporters showed specific localization of PfCpn10 to the mitochondrion and PfCpn20 to the plastid. As P. falciparum also has two Cpn60s, one of which is targeted specifically to the mitochondrion and the other exclusively to the plastid, each organelle has a distinct type I chaperonin system. Comparative sequence analysis extended these findings to several other apicomplexan parasites that have both a mitochondrion and a plastid. Phylogenetic analysis suggests the Cpn10s and Cpn20s of apicomplexans are independently monophyletic. The apicomplexan Cpn10 is phylogenetically related to other mitochondrial versions but a significant relationship between apicomplexan Cpn20s and other cochaperonins was not established.}, }
@article {pmid15923129, year = {2005}, author = {Fischer, WM and Palmer, JD}, title = {Evidence from small-subunit ribosomal RNA sequences for a fungal origin of Microsporidia.}, journal = {Molecular phylogenetics and evolution}, volume = {36}, number = {3}, pages = {606-622}, doi = {10.1016/j.ympev.2005.03.031}, pmid = {15923129}, issn = {1055-7903}, support = {R01 GM-35087/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Fungi/*classification/*genetics ; Genes, Fungal/genetics ; Microsporidia/*classification/*genetics ; *Phylogeny ; RNA, Ribosomal/*genetics ; }, abstract = {The phylum Microsporidia comprises a species-rich group of minute, single-celled, and intra-cellular parasites. Lacking normal mitochondria and with unique cytology, microsporidians have sometimes been thought to be a lineage of ancient eukaryotes. Although phylogenetic analyses using small-subunit ribosomal RNA (SSU-rRNA) genes almost invariably place the Microsporidia among the earliest branches on the eukaryotic tree, many other molecules suggest instead a relationship with fungi. Using maximum likelihood methods and a diverse SSU-rRNA data set, we have re-evaluated the phylogenetic affiliations of Microsporidia. We demonstrate that tree topologies used to estimate likelihood model parameters can materially affect phylogenetic searches. We present a procedure for reducing this bias: "tree-based site partitioning," in which a comprehensive set of alternative topologies is used to estimate sequence data partitions based on inferred evolutionary rates. This hypothesis-driven approach appears to be capable of utilizing phylogenetic information that is not available to standard likelihood implementations (e.g., approximation to a gamma distribution); we have employed it in maximum likelihood and Bayesian analysis. Applying our method to a phylogenetically diverse SSU-rRNA data set revealed that the early diverging ("deep") placement of Microsporidia typically found in SSU-rRNA trees is no better than a fungal placement, and that the likeliest placement of Microsporidia among non-long-branch eukaryotic taxa is actually within fungi. These results illustrate the importance of hypothesis testing in parameter estimation, provide a way to address certain problems in difficult data sets, and support a fungal origin for the Microsporidia.}, }
@article {pmid15914576, year = {2005}, author = {Jolly, RA and Goldstein, KM and Wei, T and Gao, H and Chen, P and Huang, S and Colet, JM and Ryan, TP and Thomas, CE and Estrem, ST}, title = {Pooling samples within microarray studies: a comparative analysis of rat liver transcription response to prototypical toxicants.}, journal = {Physiological genomics}, volume = {22}, number = {3}, pages = {346-355}, doi = {10.1152/physiolgenomics.00260.2004}, pmid = {15914576}, issn = {1531-2267}, mesh = {Animals ; Clofibrate/toxicity ; Cluster Analysis ; Diethylhexyl Phthalate/toxicity ; Fatty Acids/metabolism ; Gene Expression ; Gene Expression Profiling ; Gene Expression Regulation ; Liver/*drug effects/*metabolism ; Liver Extracts/*metabolism ; Male ; Mitochondria/metabolism ; Models, Biological ; Models, Statistical ; Oligonucleotide Array Sequence Analysis/*methods ; Organ Size ; Phenotype ; Phylogeny ; Principal Component Analysis ; RNA/metabolism ; RNA, Messenger/metabolism ; Rats ; Rats, Sprague-Dawley ; Reverse Transcriptase Polymerase Chain Reaction ; Transcription, Genetic ; Valproic Acid/toxicity ; }, abstract = {Combining or pooling individual samples when carrying out transcript profiling using microarrays is a fairly common means to reduce both the cost and complexity of data analysis. However, pooling does not allow for statistical comparison of changes between samples and can result in a loss of information. Because a rigorous comparison of the identified expression changes from the two approaches has not been reported, we compared the results for hepatic transcript profiles from pooled vs. individual samples. Hepatic transcript profiles from a single-dose time-course rat study in response to the prototypical toxicants clofibrate, diethylhexylphthalate, and valproic acid were evaluated. Approximately 50% more transcript expression changes were observed in the individual (statistical) analysis compared with the pooled analysis. While the majority of these changes were less than twofold in magnitude (approximately 80%), a substantial number were greater than twofold (approximately 20%). Transcript changes unique to the individual analysis were confirmed by quantitative RT-PCR, while all the changes unique to the pooled analysis did not confirm. The individual analysis identified more hits per biological pathway than the pooled approach. Many of the transcripts identified by the individual analysis were novel findings and may contribute to a better understanding of molecular mechanisms of these compounds. Furthermore, having individual animal data provided the opportunity to correlate changes in transcript expression to phenotypes (i.e., histology) observed in toxicology studies. The two approaches were similar when clustering methods were used despite the large difference in the absolute number of transcripts changed. In summary, pooling reduced resource requirements substantially, but the individual approach enabled statistical analysis that identified more gene expression changes to evaluate mechanisms of toxicity. An individual animal approach becomes more valuable when the overall expression response is subtle and/or when associating expression data to variable phenotypic responses.}, }
@article {pmid15909226, year = {2005}, author = {Steinauer, ML and Nickol, BB and Broughton, R and Ortí, G}, title = {First sequenced mitochondrial genome from the phylum Acanthocephala (Leptorhynchoides thecatus) and its phylogenetic position within Metazoa.}, journal = {Journal of molecular evolution}, volume = {60}, number = {6}, pages = {706-715}, pmid = {15909226}, issn = {0022-2844}, mesh = {Acanthocephala/*genetics ; Animals ; Codon ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Evolution, Molecular ; Genome ; Likelihood Functions ; Mitochondria/genetics ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Analysis, DNA/*methods ; }, abstract = {The complete sequence of the mitochondrial genome of Leptorhynchoides thecatus (Acanthocephala) was determined, and a phylogenetic analysis was carried out to determine its placement within Metazoa. The genome is circular, 13,888 bp, and contains at least 36 of the 37 genes typically found in animal mitochondrial genomes. The genes for the large and small ribosomal RNA subunits are shorter than those of most metazoans, and the structures of most of the tRNA genes are atypical. There are two significant noncoding regions (377 and 294 bp), which are the best candidates for a control region; however, these regions do not appear similar to any of the control regions of other animals studied to date. The amino acid and nucleotide sequences of the protein coding genes of L. thecatus and 25 other metazoan taxa were used in both maximum likelihood and maximum parsimony phylogenetic analyses. Results indicate that among taxa with available mitochondrial genome sequences, Platyhelminthes is the closest relative to L. thecatus, which together are the sister taxon of Nematoda; however, long branches and/or base composition bias could be responsible for this result. The monophyly of Ecdysozoa, molting organisms, was not supported by any of the analyses. This study represents the first mitochondrial genome of an acanthocephalan to be sequenced and will allow further studies of systematics, population genetics, and genome evolution.}, }
@article {pmid15908143, year = {2005}, author = {Leister, D}, title = {Genomics-based dissection of the cross-talk of chloroplasts with the nucleus and mitochondria in Arabidopsis.}, journal = {Gene}, volume = {354}, number = {}, pages = {110-116}, doi = {10.1016/j.gene.2005.03.039}, pmid = {15908143}, issn = {0378-1119}, mesh = {Arabidopsis/*genetics ; Cell Nucleus/*genetics ; Cluster Analysis ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; Gene Expression Regulation, Plant/genetics ; *Genomics ; Models, Biological ; Signal Transduction/*genetics ; }, abstract = {Post-endosymbiotic evolution of chloroplasts was characterized by a massive transfer of cyanobacterial genes to the nucleus, followed by re-routing of many of their encoded proteins. In consequence, most plastid proteins are nucleus-encoded, enabling an anterograde (nucleus-to-plastid) control of the organelle. The regulation of chloroplast functions includes also cross-talk between chloroplasts and mitochondria, as well as retrograde (plastid-to-nucleus) signalling. Genetic analyses reveal that redox state, flux through the chlorophyll biosynthetic pathway, sugar sensing and reactive oxygen species contribute to retrograde signalling. However, the identity of the messenger molecule(s) remains largely unknown. Novel facets of the chloroplast-mitochondrion cross-talk have been revealed by the characterization of mitochondrial mutants affected in chloroplast properties. Studies of the nuclear chloroplast transcriptome imply the existence of at least three distinct types of transcriptional regulation: a master switch, acting in a binary mode by either inducing or repressing the same large set of genes; a "mixed response" with about equal numbers of up- and down-regulated genes; and mechanisms supporting the specific co-regulation of nuclear genes for photosynthesis and for plastid gene expression. The recent discovery of the latter mode of control highlights a possibly ancient route to co-ordinate chloroplast and nuclear genome expression.}, }
@article {pmid15904985, year = {2005}, author = {Pütz, S and Gelius-Dietrich, G and Piotrowski, M and Henze, K}, title = {Rubrerythrin and peroxiredoxin: two novel putative peroxidases in the hydrogenosomes of the microaerophilic protozoon Trichomonas vaginalis.}, journal = {Molecular and biochemical parasitology}, volume = {142}, number = {2}, pages = {212-223}, doi = {10.1016/j.molbiopara.2005.04.003}, pmid = {15904985}, issn = {0166-6851}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins ; Ferredoxins ; Hemerythrin ; Hydrogen/*metabolism ; Molecular Sequence Data ; Organelles/*enzymology ; Oxidative Stress ; Oxygen/pharmacology ; Peroxidases/chemistry/genetics/*metabolism ; Peroxiredoxins ; Phylogeny ; Proteome ; Protozoan Proteins/chemistry/genetics/*metabolism ; Rubredoxins ; Sequence Alignment ; Trichomonas vaginalis/*enzymology/genetics/physiology ; }, abstract = {The parasitic flagellate Trichomonas vaginalis contains hydrogenosomes, anaerobic organelles related to mitochondria, that generate ATP from the fermentative conversion of pyruvate to acetate, CO2 and molecular hydrogen. Although an essentially anaerobic organism, Trichomonas encounters low oxygen concentrations in its natural habitat and has to protect itself, and especially the oxygen-sensitve enzymes of hydrogenosomal metabolism, from oxidative damage. We have identified two novel proteins in the hydrogenosomal proteome with strong similarity to two putative prokaryotic peroxidases, rubrerythrin and periplasmic thiol peroxidase. Both proteins have previously been found in many prokaryotes but were not known from eukaryotes, suggesting a significant prokaryotic component in the oxygen-detoxification system of trichomonad hydrogenosomes.}, }
@article {pmid15901574, year = {2002}, author = {Hu, K and Wu, QS}, title = {[The basic outline of the evolution of single cell life-form].}, journal = {Yi chuan = Hereditas}, volume = {24}, number = {1}, pages = {104-110}, pmid = {15901574}, issn = {0253-9772}, abstract = {In 1960s, kingdoms of organisms were charted generally in a five branching form. Later, the endosymbiont hypothesis for the mitochondria and the chloroplast was proposed. The life-form is divided into two forms, the prokaryotes (bacteria) and the eukaryotes. The study of the molecular biology made the progress faster. In 1980s, Woese, CR.asserted that two-domain view of life was no longer true, a three-domain construct, the Bacteria, the Archaea, and the Eukaryotes had to take its place. At first, phylogeny trees based on differences in the amino acid sequences, then among ribosomal RNAs and also nuclear gene from hundreds of microbial species were depicted and many mini phylogenetic trees grouped the species according to their differences in the sequences. It was found that they shared genes between their contemporaries and across the species barriers. At the root of the phylogeny tree, there was not a single common cell, it was replaced by a common ancestral community of primitive cells. Genes transfered rather freely as the transposons swapping between those cells. There was no last universal common ancestor of single cell that could be found in the revised Tree of Life, It was not easy to represent the genealogical patterns of thousands of different families of genes, in one systematic map, therefor there was no trunk at all.}, }
@article {pmid15892877, year = {2005}, author = {Daley, DO and Whelan, J}, title = {Why genes persist in organelle genomes.}, journal = {Genome biology}, volume = {6}, number = {5}, pages = {110}, pmid = {15892877}, issn = {1474-760X}, mesh = {Chloroplasts/genetics ; *Evolution, Molecular ; Genes, Mitochondrial ; *Genome ; Hydrophobic and Hydrophilic Interactions ; Mitochondria/*genetics ; Models, Genetic ; Plastids/*genetics ; }, abstract = {Mitochondria and plastids (including chloroplasts) have a small but vital genetic coding capacity, but what are the properties of some genes that dictate that they must remain encoded in organelles?}, }
@article {pmid15890885, year = {2005}, author = {Macaulay, V and Hill, C and Achilli, A and Rengo, C and Clarke, D and Meehan, W and Blackburn, J and Semino, O and Scozzari, R and Cruciani, F and Taha, A and Shaari, NK and Raja, JM and Ismail, P and Zainuddin, Z and Goodwin, W and Bulbeck, D and Bandelt, HJ and Oppenheimer, S and Torroni, A and Richards, M}, title = {Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes.}, journal = {Science (New York, N.Y.)}, volume = {308}, number = {5724}, pages = {1034-1036}, doi = {10.1126/science.1109792}, pmid = {15890885}, issn = {1095-9203}, mesh = {Africa ; Asia ; Australasia ; DNA, Mitochondrial/*genetics ; Emigration and Immigration ; Ethnicity/*genetics ; Europe ; Founder Effect ; Genetic Drift ; *Genetic Variation ; Genetics, Population ; *Genome, Human ; Haplotypes ; History, Ancient ; Humans ; India ; Malaysia ; Mitochondria/*genetics ; Mutation ; Phylogeny ; *Population Dynamics ; Time ; }, abstract = {A recent dispersal of modern humans out of Africa is now widely accepted, but the routes taken across Eurasia are still disputed. We show that mitochondrial DNA variation in isolated "relict" populations in southeast Asia supports the view that there was only a single dispersal from Africa, most likely via a southern coastal route, through India and onward into southeast Asia and Australasia. There was an early offshoot, leading ultimately to the settlement of the Near East and Europe, but the main dispersal from India to Australia approximately 65,000 years ago was rapid, most likely taking only a few thousand years.}, }
@article {pmid15888416, year = {2005}, author = {Birdsey, GM and Lewin, J and Holbrook, JD and Simpson, VR and Cunningham, AA and Danpure, CJ}, title = {A comparative analysis of the evolutionary relationship between diet and enzyme targeting in bats, marsupials and other mammals.}, journal = {Proceedings. Biological sciences}, volume = {272}, number = {1565}, pages = {833-840}, pmid = {15888416}, issn = {0962-8452}, mesh = {Alanine Transaminase/*metabolism ; Animals ; Chiroptera/*metabolism ; *Diet ; Glyoxylates/*metabolism ; Immunohistochemistry ; Linear Models ; Liver/*metabolism ; Marsupialia/*metabolism ; Mitochondria/metabolism ; Peroxisomes/metabolism ; Phylogeny ; }, abstract = {The subcellular distribution of the enzyme alanine:glyoxylate aminotransferase (AGT) in the livers of different mammals appears to be related to their natural diets. Thus, AGT tends to be mitochondrial in carnivores, peroxisomal in herbivores, and both mitochondrial and peroxisomal in omnivores. To what extent this relationship is an incidental consequence of phylogenetic structure or an evolutionarily meaningful adaptive response to changes in dietary selection pressure is unknown. In order to distinguish between these two possibilities, we have determined the subcellular distribution of AGT in the livers of 22 new mammalian species, including members of three orders not studied before. In addition, we have analysed the statistical relationship between AGT distribution and diet in all 77 mammalian species, from 12 different orders, for which the distribution is currently known. Our analysis shows that there is a highly significant correlation between AGT distribution and diet, independent of phylogeny. This finding is compatible with the suggestion that the variable intracellular targeting of AGT is an adaptive response to episodic changes in dietary selection pressure. To our knowledge, this is the first example of such a response being manifested at the molecular and cellular levels across the breadth of Mammalia.}, }
@article {pmid15880893, year = {2004}, author = {Belyavskaya, NA}, title = {Biological effects due to weak magnetic field on plants.}, journal = {Advances in space research : the official journal of the Committee on Space Research (COSPAR)}, volume = {34}, number = {7}, pages = {1566-1574}, doi = {10.1016/j.asr.2004.01.021}, pmid = {15880893}, issn = {0273-1177}, mesh = {Calcium/metabolism ; Cell Differentiation/physiology ; Cell Division/physiology ; Germination/physiology ; Life Support Systems ; *Magnetics ; Meristem/cytology/*physiology/ultrastructure ; Plant Cells ; *Plant Physiological Phenomena ; Plant Roots/cytology/physiology/ultrastructure ; Plants/ultrastructure ; Seeds/growth &amp; development/physiology ; Space Flight ; }, abstract = {Throughout the evolution process, Earth's magnetic field (MF, about 50 microT) was a natural component of the environment for living organisms. Biological objects, flying on planned long-term interplanetary missions, would experience much weaker magnetic fields, since galactic MF is known to be 0.1-1 nT. However, the role of weak magnetic fields and their influence on functioning of biological organisms are still insufficiently understood, and is actively studied. Numerous experiments with seedlings of different plant species placed in weak magnetic field have shown that the growth of their primary roots is inhibited during early germination stages in comparison with control. The proliferative activity and cell reproduction in meristem of plant roots are reduced in weak magnetic field. Cell reproductive cycle slows down due to the expansion of G1 phase in many plant species (and of G2 phase in flax and lentil roots), while other phases of cell cycle remain relatively stable. In plant cells exposed to weak magnetic field, the functional activity of genome at early pre-replicate period is shown to decrease. Weak magnetic field causes intensification of protein synthesis and disintegration in plant roots. At ultrastructural level, changes in distribution of condensed chromatin and nucleolus compactization in nuclei, noticeable accumulation of lipid bodies, development of a lytic compartment (vacuoles, cytosegresomes and paramural bodies), and reduction of phytoferritin in plastids in meristem cells were observed in pea roots exposed to weak magnetic field. Mitochondria were found to be very sensitive to weak magnetic field: their size and relative volume in cells increase, matrix becomes electron-transparent, and cristae reduce. Cytochemical studies indicate that cells of plant roots exposed to weak magnetic field show Ca2+ over-saturation in all organelles and in cytoplasm unlike the control ones. The data presented suggest that prolonged exposures of plants to weak magnetic field may cause different biological effects at the cellular, tissue and organ levels. They may be functionally related to systems that regulate plant metabolism including the intracellular Ca2+ homeostasis. However, our understanding of very complex fundamental mechanisms and sites of interactions between weak magnetic fields and biological systems is still incomplete and still deserve strong research efforts.}, }
@article {pmid15878829, year = {2005}, author = {Matsubara, M and Komatsu, M and Araki, T and Asakawa, S and Yokobori, S and Watanabe, K and Wada, H}, title = {The phylogenetic status of Paxillosida (Asteroidea) based on complete mitochondrial DNA sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {36}, number = {3}, pages = {598-605}, doi = {10.1016/j.ympev.2005.03.018}, pmid = {15878829}, issn = {1055-7903}, mesh = {Animals ; Base Composition ; Base Sequence ; Codon, Initiator/genetics ; Codon, Terminator/genetics ; DNA, Mitochondrial/*genetics ; Echinodermata/*classification/*genetics ; Genome ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; }, abstract = {One of the most important issues in asteroid phylogeny is the phylogenetic status of Paxillosida. This group lacks an anus and suckers on the tube feet in adults and does not develop the brachiolaria stage in early development. Two controversial hypotheses have been proposed for the phylogenetic status of Paxillosida, i.e., Paxillosida is primitive or rather specialized in asteroids. In this study, we determined the complete mitochondrial DNA nucleotide sequences from two paxillosidans (Astropecten polyacanthus and Luidia quinaria) and one forcipulatidan (Asterias amurensis). The mitochondrial genomes of the three asteroids were identical with respect to gene order and transcription direction, and were identical to the previously reported mitochondrial genomes of Asterina pectinifera (Valvatida) and Pisaster ochraceus (Forcipulatida) in this respect. Therefore, the comparison of genome structures was uninformative for the purposes of asteroid phylogeny. However, molecular phylogenetic analyses based on the amino acid sequences and the nucleotide sequences from the five asteroids supported the monophyly of the clade that included the two paxillosidans and Asterina. This suggests that the paxillosidan characters are secondarily derived ones.}, }
@article {pmid15867426, year = {2005}, author = {Noutsos, C and Richly, E and Leister, D}, title = {Generation and evolutionary fate of insertions of organelle DNA in the nuclear genomes of flowering plants.}, journal = {Genome research}, volume = {15}, number = {5}, pages = {616-628}, pmid = {15867426}, issn = {1088-9051}, mesh = {Arabidopsis/*genetics ; Base Composition ; Base Sequence ; Cell Nucleus/*genetics ; Chromosome Mapping ; Chromosomes, Plant/genetics ; DNA, Chloroplast/genetics/*metabolism ; DNA, Mitochondrial/genetics/*metabolism ; *Evolution, Molecular ; *Genome, Plant ; Molecular Sequence Data ; Mutation/genetics ; Oryza/*genetics ; }, abstract = {Nuclear genomes are exposed to a continuous influx of DNA from mitochondria and plastids. We have characterized the structure of approximately 750 kb of organelle DNA, distributed among 13 loci, in the nuclear genomes of Arabidopsis and rice. These segments are large and migrated to the nucleus quite recently, allowing us to reconstruct their evolution. Two general types of nuclear insertions coexist; one is characterized by long sequence stretches that are colinear with organelle DNA, the other type consists of mosaics of organelle DNA, often derived from both plastids and mitochondria. The levels of sequence divergence of the two types exclude their common descent, implying that at least two independent modes of DNA transfer from organelle to nucleus operate. The post-integration fate of organelle DNA is characterized by a predominance of transition mutations, associated with the gradual amelioration of the integrated sequence to the nucleotide composition of the host chromosome. Deletion of organelle DNA at these loci is essentially balanced by insertions of nonorganelle DNA. Deletions are associated with the removal of DNA between perfect repeats, indicating that they originate by replication slippage.}, }
@article {pmid15861250, year = {2004}, author = {Coates, BS and Sumerford, DV and Hellmich, RL}, title = {Geographic and voltinism differentiation among North American Ostrinia nubilalis (European corn borer) mitochondrial cytochrome c oxidase haplotypes.}, journal = {Journal of insect science (Online)}, volume = {4}, number = {}, pages = {35}, pmid = {15861250}, issn = {1536-2442}, mesh = {Animals ; Demography ; Ecosystem ; Electron Transport Complex IV/*genetics ; Gene Expression Regulation, Enzymologic ; Genetic Variation ; Haplotypes ; Insect Proteins/genetics ; Mitochondria/*enzymology ; Moths/*enzymology/genetics ; Phylogeny ; }, abstract = {DNA sequence of European corn borer, Ostrinia nubilalis (Hubner) (Lepidoptera: Crambidae), mitochondrial cytochrome c oxidase I (cox1) and II (cox2) genes were characterized and used for population genetic analysis. Twenty-six point mutations were identified from a 2,156 bp DNA sequence alignment. The frequency of polymorphic cox1DdeI and HaeIII, and cox2 Sau3AI and MspI restriction sites were determined from 1,414 individuals by polymerase chain reaction restriction fragment length polymorphism. Ten haplotypes were observed. A single haplotype was present among 90% of individuals examined, and a HaeIII haplotype was not present in samples from the Atlantic coast. Significant genetic differentiation existed between Atlantic coast and midwestern United States samples, and between sympatric uni- and bivoltine ecotypes. These genetic markers identify regional and ecotype differences in the North American O. nubilalis population.}, }
@article {pmid15855395, year = {2005}, author = {Weibel, ER and Hoppeler, H}, title = {Exercise-induced maximal metabolic rate scales with muscle aerobic capacity.}, journal = {The Journal of experimental biology}, volume = {208}, number = {Pt 9}, pages = {1635-1644}, doi = {10.1242/jeb.01548}, pmid = {15855395}, issn = {0022-0949}, mesh = {Animals ; Capillaries/*anatomy &amp; histology ; Energy Metabolism/*physiology ; Fractals ; Mammals/*physiology ; Mitochondria/*physiology ; *Models, Biological ; Muscle, Skeletal/blood supply/*physiology ; Oxygen Consumption/physiology ; Physical Exertion/*physiology ; Species Specificity ; }, abstract = {The logarithmic nature of the allometric equation suggests that metabolic rate scaling is related to some fractal properties of the organism. Two universal models have been proposed, based on (1) the fractal design of the vasculature and (2) the fractal nature of the 'total effective surface' of mitochondria and capillaries. According to these models, basal and maximal metabolic rates must scale as M3/4. This is not what we find. In 34 eutherian mammalian species (body mass Mb ranging from 7 g to 500 kg) we found VO2max to scale with the 0.872 (+/-0.029) power of body mass, which is significantly different from 3/4 power scaling. Integrated structure-function studies on a subset of eleven species (Mb 20 g to 450 kg) show that the variation of VO2max with body size is tightly associated with the total volume of mitochondria and of the locomotor musculature capillaries. In athletic species the higher VO2max is linked to proportionally larger mitochondrial and capillary volumes. As a result, VO2max is linearly related to both total mitochondrial and capillary erythrocyte volumes, as well as to their surface areas. Consequently, the allometric variation of maximal metabolic rate is directly related to the scaling of the total effective surfaces of mitochondria and capillaries, thus confirming the basic conjecture of the second fractal models but refuting the arguments for 3/4 power scaling. We conclude that the scaling of maximal metabolic rate is determined by the energy needs of the cells active during maximal work. The vascular supply network is adapted to the needs of the cells at their working limit. We conjecture that the optimization of the arterial tree by fractal design is the result rather than the cause of the evolution of metabolic rate scaling. The remaining question is why the energy needs of locomotion scale with the 0.872 or 7/8 power of body mass.}, }
@article {pmid15854906, year = {2005}, author = {Chan, KW and Slotboom, DJ and Cox, S and Embley, TM and Fabre, O and van der Giezen, M and Harding, M and Horner, DS and Kunji, ER and León-Avila, G and Tovar, J}, title = {A novel ADP/ATP transporter in the mitosome of the microaerophilic human parasite Entamoeba histolytica.}, journal = {Current biology : CB}, volume = {15}, number = {8}, pages = {737-742}, doi = {10.1016/j.cub.2005.02.068}, pmid = {15854906}, issn = {0960-9822}, support = {MC_U105663139/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Bayes Theorem ; Blotting, Western ; Cell Fractionation ; Computational Biology ; DNA, Complementary/genetics ; Electrophoresis, Polyacrylamide Gel ; Entamoeba histolytica/genetics/*metabolism ; Humans ; Lactococcus lactis ; Mitochondrial ADP, ATP Translocases/*genetics/metabolism ; Models, Genetic ; Molecular Sequence Data ; Organelles/*metabolism ; *Phylogeny ; Protein Conformation ; Saccharomyces cerevisiae ; Sequence Analysis, DNA ; Transport Vesicles/metabolism ; }, abstract = {Recent data suggest that microaerophilic and parasitic protozoa, which lack oxidative phosphorylation, nevertheless contain mitochondrial homologs [1-6], organelles that share common ancestry with mitochondria. Such widespread retention suggests there may be a common function for mitochondrial homologs that makes them essential for eukaryotic cells. We determined the mitochondrial carrier family (MCF) complement of the Entamoeba histolytica mitochondrial homolog, also known as a crypton [5] or more commonly as a mitosome [3]. MCF proteins support mitochondrial metabolic energy generation, DNA replication, and amino-acid metabolism by linking biochemical pathways in the mitochondrial matrix with those in the cytosol [7]. MCF diversity thus closely mirrors important facets of mitochondrial metabolic diversity. The Entamoeba histolytica mitosome has lost all but a single type of MCF protein, which transports ATP and ADP via a novel mechanism that is not reliant on a membrane potential. Phylogenetic analyses confirm that the Entamoeba ADP/ATP carrier is distinct from archetypal mitochondrial ADP/ATP carriers, an observation that is supported by its different substrate and inhibitor specificity. Because many functions of yeast and human mitochondria rely on solutes transported by specialized members of this family, the Entamoeba mitosome must contain only a small subset of these processes requiring adenine nucleotide exchange.}, }
@article {pmid15851064, year = {2005}, author = {Zeh, JA and Zeh, DW}, title = {Maternal inheritance, sexual conflict and the maladapted male.}, journal = {Trends in genetics : TIG}, volume = {21}, number = {5}, pages = {281-286}, doi = {10.1016/j.tig.2005.03.006}, pmid = {15851064}, issn = {0168-9525}, mesh = {*Adaptation, Biological ; Animals ; Biological Evolution ; Cell Nucleus/*genetics ; *Conflict, Psychological ; Extrachromosomal Inheritance/*genetics ; Female ; Fertility ; Humans ; Male ; Maternal Behavior/*physiology ; Models, Biological ; Selection, Genetic ; *Sexual Behavior ; }, abstract = {Females differ from males in transmitting not only nuclear genes but also cytoplasmic genetic elements (CGEs), including DNA in mitochondria, chloroplasts and microorganisms that are present in the cell. Until recently, evolutionary research has adopted a nucleocentric approach in which organelles have been viewed as subservient energy suppliers. In this article, we propose that a more equitable view of nuclear genes and organelle genomes will lead to a better understanding of the dynamics of sexual selection and the constraints on male adaptation. Maternal inheritance of CGEs intensifies sexually-antagonistic coevolution and provides a parsimonious explanation for the relatively high frequency in males of such apparently maladaptive traits as infertility, homosexuality and baldness.}, }
@article {pmid15846094, year = {2005}, author = {Robey, RB and Hay, N}, title = {Mitochondrial hexokinases: guardians of the mitochondria.}, journal = {Cell cycle (Georgetown, Tex.)}, volume = {4}, number = {5}, pages = {654-658}, doi = {10.4161/cc.4.5.1678}, pmid = {15846094}, issn = {1551-4005}, support = {AG016927/AG/NIA NIH HHS/United States ; CA090764/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Apoptosis ; Biological Evolution ; Cell Survival ; Energy Metabolism ; Gene Expression Regulation, Enzymologic ; Glucose/metabolism ; Hexokinase/genetics/*physiology ; *Homeostasis ; Humans ; Mitochondria/*enzymology/*physiology ; Models, Biological ; Proto-Oncogene Proteins c-akt/*physiology ; }, abstract = {There is accumulating evidence that cell survival and energy metabolism are inexorably linked. As a major mediator of both the metabolic and anti-apoptotic effects of growth factors, the serine/threonine kinase Akt (also known as protein kinase B or PKB) is particularly well-suited to coordinate the regulation of these interrelated processes. Recent demonstrations that growth factors and Akt require glucose (Glc) to prevent apoptosis and promote cell survival are compatible with this contention, as is a positive correlation between Akt-regulated mitochondrial hexokinase (mtHK) association and apoptotic resistance. From a phylogenetic perspective, the ability of Akt to regulate cellular energy metabolism apparently preceded the capacity to control cell survival, suggesting an evolutionary basis for the Glc dependent anti-apoptotic effects of Akt. We speculate that, somewhere in the course of evolution, the metabolic regulatory function of Akt evolved into an adaptive sensing system involving mtHK that ensures mitochondrial homeostasis, thereby coupling metabolism to cell survival. We also propose that this "guardian" function of mtHK may be specifically exploited for therapeutic purposes.}, }
@article {pmid15845582, year = {2005}, author = {Isaeva, EV and Shkryl, VM and Shirokova, N}, title = {Mitochondrial redox state and Ca2+ sparks in permeabilized mammalian skeletal muscle.}, journal = {The Journal of physiology}, volume = {565}, number = {Pt 3}, pages = {855-872}, pmid = {15845582}, issn = {0022-3751}, support = {R01 AR045690/AR/NIAMS NIH HHS/United States ; R01 AR45690/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Calcium/metabolism ; Calcium Signaling/*physiology ; Cell Membrane Permeability ; Cytoplasm/metabolism ; Female ; Homeostasis/physiology ; Mammals ; Mice ; Mitochondria/*metabolism ; Muscle Fibers, Skeletal/*metabolism ; Muscle, Skeletal/cytology/*metabolism ; Oxidation-Reduction ; Rats ; Rats, Sprague-Dawley ; Sarcoplasmic Reticulum/metabolism ; }, abstract = {Intact skeletal muscle fibres from adult mammals exhibit neither spontaneous nor stimulated Ca(2+) sparks. Mechanical or chemical skinning procedures have been reported to unmask sparks. The present study investigates the mechanisms that determine the development of Ca(2+) spark activity in permeabilized fibres dissected from muscles with different metabolic capacity. Spontaneous Ca(2+) sparks were detected with fluo-3 and single photon confocal microscopy; mitochondrial redox potential was evaluated from mitochondrial NADH signals recorded with two-photon confocal microscopy, and Ca(2+) load of the sarcoplasmic reticulum (SR) was estimated from the amplitude of caffeine-induced Ca(2+) transients recorded with fura-2 and digital photometry. In three fibre types studied, there was a time lag between permeabilization and spark development. Under all experimental conditions, the delay was the longest in slow-twitch oxidative fibres, intermediate in fast-twitch glycolytic-oxidative fibres, and the shortest in fast-twitch glycolytic cells. The temporal evolution of Ca(2+) spark frequencies was bell-shaped, and the maximal spark frequency was reached slowly in mitochondria-rich oxidative cells but quickly in mitochondria-poor glycolytic fibres. The development of spontaneous Ca(2+) sparks did not correlate with the SR Ca(2+) content of the fibre, but did correlate with the redox potential of their mitochondria. Treatment of fibres with scavengers of reactive oxygen species (ROS), such as superoxide dismutase (SOD) and catalase, dramatically and reversibly reduced the spark frequency and also delayed their appearance. In contrast, incubation of fibres with 50 microm H(2)O(2) sped up the development of Ca(2+) sparks and increased their frequency. These results indicate that the appearance of Ca(2+) sparks in permeabilized skeletal muscle cells depends on the fibre's oxidative strength and that misbalance between mitochondrial ROS production and the fibre's ability to fight oxidative stress is likely to be responsible for unmasking Ca(2+) sparks in skinned preparations. They also suggest that under physiological and pathophysiological conditions the appearance of Ca(2+) sparks may be, at least in part, limited by the fine-tuned equilibrium between mitochondrial ROS production and cellular ROS scavenging mechanisms.}, }
@article {pmid15843018, year = {2005}, author = {Gabaldón, T and Rainey, D and Huynen, MA}, title = {Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I).}, journal = {Journal of molecular biology}, volume = {348}, number = {4}, pages = {857-870}, doi = {10.1016/j.jmb.2005.02.067}, pmid = {15843018}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Animals ; Computational Biology ; Electron Transport Complex I/*chemistry/*genetics/metabolism ; Eukaryotic Cells/*enzymology ; *Evolution, Molecular ; Humans ; Molecular Sequence Data ; Photosynthesis ; Phylogeny ; Plastids/enzymology ; Protein Binding ; Protein Subunits/chemistry/genetics/metabolism ; Sequence Alignment ; Structural Homology, Protein ; }, abstract = {The increasing availability of sequenced genomes enables the reconstruction of the evolutionary history of large protein complexes. Here, we trace the evolution of NADH:ubiquinone oxidoreductase (Complex I), which has increased in size, by so-called supernumary subunits, from 14 subunits in the bacteria to 30 in the plants and algae, 37 in the fungi and 46 in the mammals. Using a combination of pair-wise and profile-based sequence comparisons at the levels of proteins and the DNA of the sequenced eukaryotic genomes, combined with phylogenetic analyses to establish orthology relationships, we were able to (1) trace the origin of six of the supernumerary subunits to the alpha-proteobacterial ancestor of the mitochondria, (2) detect previously unidentified homology relations between subunits from fungi and mammals, (3) detect previously unidentified subunits in the genomes of several species and (4) document several cases of gene duplications among supernumerary subunits in the eukaryotes. One of these, a duplication of N7BM (B17.2), is particularly interesting as it has been lost from genomes that have also lost Complex I proteins, making it a candidate for a Complex I interacting protein. A parsimonious reconstruction of eukaryotic Complex I evolution shows an initial increase in size that predates the separation of plants, fungi and metazoa, followed by a gradual adding and incidental losses of subunits in the various evolutionary lineages. This evolutionary scenario is in contrast to that for Complex I in the prokaryotes, for which the combination of several separate, and previously independently functioning modules into a single complex has been proposed.}, }
@article {pmid15836787, year = {2005}, author = {van der Kuyl, AC and Ballasina, DL and Zorgdrager, F}, title = {Mitochondrial haplotype diversity in the tortoise species Testudo graeca from North Africa and the Middle East.}, journal = {BMC evolutionary biology}, volume = {5}, number = {}, pages = {29}, pmid = {15836787}, issn = {1471-2148}, mesh = {Africa, Northern ; Animals ; Binding Sites ; Computer Simulation ; DNA/metabolism ; DNA, Mitochondrial/*genetics/metabolism ; Genetic Variation ; Genetics, Population ; Haploidy ; *Haplotypes ; Likelihood Functions ; Middle East ; Mitochondria/metabolism ; Models, Statistical ; Nucleotides/*genetics ; Phylogeny ; RNA, Ribosomal/*genetics ; Turtles ; }, abstract = {BACKGROUND: To help conservation programs of the endangered spur-thighed tortoise and to gain better insight into its systematics, genetic variation and evolution in the tortoise species Testudo graeca (Testudines: Testudinidae) was investigated by sequence analysis of a 394-nucleotide fragment of the mitochondrial 12S rRNA gene for 158 tortoise specimens belonging to the subspecies Testudo graeca graeca, Testudo graeca ibera, Testudo graeca terrestris, and a newly recognized subspecies Testudo graeca whitei. A 411-nucleotide fragment of the mitochondrial D-loop was additionally sequenced for a subset of 22 T. graeca, chosen because of their 12S gene haplotype and/or geographical origin.<br><br>RESULTS: Haplotype networks generated by maximum-likelihood and neighbor-joining analyses of both the separate and the combined sequence data sets suggested the existence of two main clades of Testudo graeca, comprising Testudo graeca from northern Africa and Testudo graeca from the Turkey and the Middle East, respectively.<br><br>CONCLUSION: Mitochondrial DNA haplotyping suggests that the tortoise subspecies of T. g. graeca and T. g. ibera are genetically distinct, with a calculated divergence time in the early or middle Pleistocene. Other proposed subspecies could not clearly be recognized based upon their mt haplotypes and phylogenetic position, and were either part of the T. g. graeca or of the T. g. ibera clade, suggesting that genetic evidence for the existence of most of the 15 proposed subspecies of T. graeca is weak.}, }
@article {pmid15831942, year = {2005}, author = {Pavesi, A}, title = {Utility of JC polyomavirus in tracing the pattern of human migrations dating to prehistoric times.}, journal = {The Journal of general virology}, volume = {86}, number = {Pt 5}, pages = {1315-1326}, doi = {10.1099/vir.0.80650-0}, pmid = {15831942}, issn = {0022-1317}, mesh = {Biological Evolution ; DNA, Mitochondrial/*genetics ; DNA, Viral/*genetics ; Emigration and Immigration/*history ; *Genetic Drift ; History, Ancient ; Humans ; JC Virus/*genetics/isolation &amp; purification ; Mitochondria/genetics ; Polyomavirus Infections/virology ; Selection, Genetic ; Sequence Homology, Nucleic Acid ; }, abstract = {JC virus (JCV) is a double-stranded DNA polyomavirus co-evolving with humans since the time of their origin in Africa. JCV seems to provide new insights into the history of human populations, as it suggests an expansion of humans from Africa via two distinct migrations, each carrying a different lineage of the virus. A possible alternative to this interpretation could be that the divergence between the two lineages is due to selective pressures favouring adaptation of JCV to different climates, thus making any inference about human history debatable. In the present study, the evolution of JCV was investigated by applying correspondence analysis to a set of 273 fully sequenced strains. The first and more important axis of ordination led to the detection of 61 nt positions as the main determinants of the divergence between the two virus lineages. One lineage includes strains of types 1 and 4, the other strains of types 2, 3, 7 and 8. The distinctiveness of the Caucasian lineage (types 1 and 4), largely diffused in the northern areas of the world, was almost entirely ascribed to synonymous substitutions. The findings provided by the subsequent axes of ordination supported the view of an evolutionary history of JCV characterized by genetic drift and migration, rather than by natural selection. Correspondence analysis was also applied to a set of 156 human mitochondrial genome sequences. A detailed comparison between the substitution patterns in JCV and mitochondria brought to light some relevant advantages of the use of the virus in tracing human migrations.}, }
@article {pmid15830887, year = {2004}, author = {Guo, KW and Niu, AO}, title = {[Studies on the genetic variation of two mitochondrial DNA molecules of Schistosoma japonicum].}, journal = {Zhongguo ji sheng chong xue yu ji sheng chong bing za zhi = Chinese journal of parasitology &amp; parasitic diseases}, volume = {22}, number = {5}, pages = {300-302}, pmid = {15830887}, issn = {1000-7423}, mesh = {Animals ; Base Sequence ; DNA, Helminth/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex I/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Schistosoma japonicum/*genetics ; }, abstract = {OBJECTIVE: To study the variation of Schistosoma japonicum through two mitochondrial DNA molecules.<br><br>METHODS: Genomic DNA was isolated with kit, and the mitochondrial NADH dehydrogenase 1 (ND1) and cytochrome c oxidase I (COI) gene fragments were amplified by polymerase chain reaction (PCR) and sequenced. The gene trees were constructed and the acquired data were analyzed with the help of bioinformatics.<br><br>RESULTS: The gene trees showed that the Taiwan isolate and the mainland isolates can be divided in two groups: a group from the hilly region (Yunnan and Sichuan), another group from the lake region (Hunan, Jiangxi and Anhui); isolates from Hubei are at a different position on the gene trees.<br><br>CONCLUSION: There are variations among the geographic isolates of Schistosoma japonicum in China, nevertheless, they have close kinship.}, }
@article {pmid15828011, year = {2005}, author = {Loong, AM and Hiong, KC and Lee, SM and Wong, WP and Chew, SF and Ip, YK}, title = {Ornithine-urea cycle and urea synthesis in African lungfishes, Protopterus aethiopicus and Protopterus annectens, exposed to terrestrial conditions for six days.}, journal = {Journal of experimental zoology. Part A, Comparative experimental biology}, volume = {303}, number = {5}, pages = {354-365}, doi = {10.1002/jez.a.147}, pmid = {15828011}, issn = {1548-8969}, mesh = {*Air ; Animals ; Arginase/*metabolism ; Carbamoyl-Phosphate Synthase (Ammonia)/*metabolism ; Evolution, Molecular ; Fishes/*metabolism ; Liver/metabolism ; Mitochondria/metabolism ; Ornithine/*metabolism ; Species Specificity ; Urea/*metabolism ; }, abstract = {The objectives of this study were (1) to determine the type of carbamoyl phosphate synthetase (CPS) present, and the compartmentalization of arginase, in the livers of the African lungfishes, Protopterus aethiopicus and Protopterus annectens, and (2) to elucidate if these two lungfishes were capable of increasing the rates of urea synthesis and capacities of the ornithine-urea cycle (OUC) during 6 days of aerial exposure without undergoing aestivation. Like another African lungfish, Protopterus dolloi, reported elsewhere, the CPS activities from the livers of P. aethiopicus and P. annectens had properties similar to that of the marine ray (Taeniura lymma), but dissimilar to that of the mouse (Mus musculus). Hence, they possessed CPS III, and not CPS I as reported previously. CPS III was present exclusively in the liver mitochondria of both lungfishes, but the majority of the arginase activities were present in the cytosolic fractions of their livers. Glutamine synthetase (GS) activity was also detected in the hepatic mitochondria of both specimens. Therefore, our results suggest that the evolution of CPS III to CPS I might not have occurred before the evolution of extant lungfishes as suggested previously, prompting an examination of the current view on the evolution of CPS and OUC in vertebrates. Aerial exposure led to significant decreases in rates of ammonia excretion in P. aethiopicus and P. annectens, but there were no accumulations of ammonia in their tissues. However, urea contents in their tissues increased significantly after 6 days of aerial exposure. The estimated rates of urea synthesis in P. aethiopicus and P. annectens increased 1.2- and 1.47-fold, respectively, which were smaller than that in P. dolloi (8.6-fold) reported elsewhere. In addition, unlike P. dolloi, 6 days of aerial exposure had no significant effects on the hepatic CPS III activities of P. aethiopicus and P. annectens. In contrast, aerial exposure induced relatively greater degrees of reductions in ammonia production in P. aethiopicus (34%) and P. annectens (37%) than P. dolloi (28%) as previously reported. Thus, our results suggest that various species of African lungfishes respond to aerial exposure differently with respect to nitrogen metabolism and excretion, and it can be concluded that P. aethiopicus and P. annectens depended more on reductions in ammonia production than on increases in urea synthesis to ameliorate ammonia toxicity when exposed to terrestrial conditions.}, }
@article {pmid15827031, year = {2005}, author = {Bhushan, S and Ståhl, A and Nilsson, S and Lefebvre, B and Seki, M and Roth, C and McWilliam, D and Wright, SJ and Liberles, DA and Shinozaki, K and Bruce, BD and Boutry, M and Glaser, E}, title = {Catalysis, subcellular localization, expression and evolution of the targeting peptides degrading protease, AtPreP2.}, journal = {Plant &amp; cell physiology}, volume = {46}, number = {6}, pages = {985-996}, doi = {10.1093/pcp/pci107}, pmid = {15827031}, issn = {0032-0781}, mesh = {Amino Acid Sequence ; Arabidopsis/*enzymology/*genetics ; Base Sequence ; Biological Transport, Active ; Catalysis ; Chloroplasts/enzymology ; DNA, Complementary/genetics ; DNA, Plant/genetics ; Evolution, Molecular ; Gene Expression ; Genes, Plant ; Mass Spectrometry ; Metalloproteases/*genetics/*metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Peptides/chemistry ; Plants, Genetically Modified ; Subcellular Fractions/enzymology ; Substrate Specificity ; Nicotiana/enzymology/genetics ; }, abstract = {We have previously identified a zinc metalloprotease involved in the degradation of mitochondrial and chloroplast targeting peptides, the presequence protease (PreP). In the Arabidopsis thaliana genomic database, there are two genes that correspond to the protease, the zinc metalloprotease (AAL90904) and the putative zinc metalloprotease (AAG13049). We have named the corresponding proteins AtPreP1 and AtPreP2, respectively. AtPreP1 and AtPreP2 show significant differences in their targeting peptides and the proteins are predicted to be localized in different compartments. AtPreP1 was shown to degrade both mitochondrial and chloroplast targeting peptides and to be dual targeted to both organelles using an ambiguous targeting peptide. Here, we have overexpressed, purified and characterized proteolytic and targeting properties of AtPreP2. AtPreP2 exhibits different proteolytic subsite specificity from AtPreP1 when used for degradation of organellar targeting peptides and their mutants. Interestingly, AtPreP2 precursor protein was also found to be dual targeted to both mitochondria and chloroplasts in a single and dual in vitro import system. Furthermore, targeting peptide of the AtPreP2 dually targeted green fluorescent protein (GFP) to both mitochondria and chloroplasts in tobacco protoplasts and leaves using an in vivo transient expression system. The targeting of both AtPreP1 and AtPreP2 proteases to chloroplasts in A. thaliana in vivo was confirmed via a shotgun mass spectrometric analysis of highly purified chloroplasts. Reverse transcription-polymerase chain reaction (RT-PCR) analysis revealed that AtPreP1 and AtPreP2 are differentially expressed in mature A. thaliana plants. Phylogenetic evidence indicated that AtPreP1 and AtPreP2 are recent gene duplicates that may have diverged through subfunctionalization.}, }
@article {pmid15826309, year = {2005}, author = {Mower, JP}, title = {PREP-Mt: predictive RNA editor for plant mitochondrial genes.}, journal = {BMC bioinformatics}, volume = {6}, number = {}, pages = {96}, pmid = {15826309}, issn = {1471-2105}, support = {R01 GM035087/GM/NIGMS NIH HHS/United States ; R01-GM-35087/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Binding Sites ; Chloroplasts ; Computational Biology/*methods ; Conserved Sequence ; Cytidine/chemistry ; DNA/chemistry ; DNA, Plant ; Databases, Protein ; *Genes, Plant ; *Genome, Plant ; Mitochondrial Proteins ; Models, Statistical ; Molecular Sequence Data ; Phylogeny ; Plant Proteins ; Protein Binding ; RNA/*chemistry ; *RNA Editing ; RNA, Chloroplast ; RNA, Mitochondrial ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Homology, Amino Acid ; Software ; }, abstract = {BACKGROUND: In plants, RNA editing is a process that converts specific cytidines to uridines and uridines to cytidines in transcripts from virtually all mitochondrial protein-coding genes. There are thousands of plant mitochondrial genes in the sequence databases, but sites of RNA editing have not been determined for most. Accurate methods of RNA editing site prediction will be important in filling in this information gap and could reduce or even eliminate the need for experimental determination of editing sites for many sequences. Because RNA editing tends to increase protein conservation across species by "correcting" codons that specify unconserved amino acids, this principle can be used to predict editing sites by identifying positions where an RNA editing event would increase the conservation of a protein to homologues from other plants. PREP-Mt takes this approach to predict editing sites for any protein-coding gene in plant mitochondria.<br><br>RESULTS: To test the general applicability of the PREP-Mt methodology, RNA editing sites were predicted for 370 full-length or nearly full-length DNA sequences and then compared to the known sites of RNA editing for these sequences. Of 60,263 cytidines in this test set, PREP-Mt correctly classified 58,994 as either an edited or unedited site (accuracy = 97.9%). PREP-Mt properly identified 3,038 of the 3,698 known sites of RNA editing (sensitivity = 82.2%) and 55,956 of the 56,565 known unedited sites (specificity = 98.9%). Accuracy and sensitivity increased to 98.7% and 94.7%, respectively, after excluding the 489 silent editing sites (which have no effect on protein sequence or function) from the test set.<br><br>CONCLUSION: These results indicate that PREP-Mt is effective at identifying C to U RNA editing sites in plant mitochondrial protein-coding genes. Thus, PREP-Mt should be useful in predicting protein sequences for use in molecular, biochemical, and phylogenetic analyses. In addition, PREP-Mt could be used to determine functionality of a mitochondrial gene or to identify particular sequences with unusual editing properties. The PREP-Mt methodology should be applicable to any system where RNA editing increases protein conservation across species.}, }
@article {pmid15821992, year = {2004}, author = {Perales, M and Parisi, G and Fornasari, MS and Colaneri, A and Villarreal, F and González-Schain, N and Echave, J and Gómez-Casati, D and Braun, HP and Araya, A and Zabaleta, E}, title = {Gamma carbonic anhydrase like complex interact with plant mitochondrial complex I.}, journal = {Plant molecular biology}, volume = {56}, number = {6}, pages = {947-957}, pmid = {15821992}, issn = {0167-4412}, mesh = {Arabidopsis/cytology/genetics/metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Binding Sites/genetics ; Biological Transport ; Carbonic Anhydrases/genetics/*metabolism ; Cells, Cultured ; Dimerization ; Electron Transport Complex I/genetics/*metabolism ; Electrophoresis, Gel, Two-Dimensional ; Genetic Variation ; Isoenzymes/genetics/metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Models, Molecular ; Oligopeptides/genetics ; Phylogeny ; Protein Binding ; Protein Structure, Tertiary ; Repetitive Sequences, Amino Acid/genetics ; Two-Hybrid System Techniques ; Yeasts/genetics ; }, abstract = {We report the identification by two hybrid screens of two novel similar proteins, called Arabidopsis thaliana gamma carbonic anhydrase like1 and 2 (AtgammaCAL1 and AtgammaCAL2), that interact specifically with putative Arabidopsis thaliana gamma Carbonic Anhydrase (AtgammaCA) proteins in plant mitochondria. The interaction region that was located in the N-terminal 150 amino acids of mature AtgammaCA and AtgammaCA like proteins represents a new interaction domain. In vitro experiments indicate that these proteins are imported into mitochondria and are associated with mitochondrial complex I as AtgammaCAs. All plant species analyzed contain both AtgammaCA and AtgammaCAL sequences indicating that these genes were conserved throughout plant evolution. Structural modeling of AtgammaCAL sequences show a deviation of functionally important active site residues with respect to gammaCAs but could form active interfaces in the interaction with AtgammaCAs. We postulate a CA complex tightly associated to plant mitochondrial complex.}, }
@article {pmid15817482, year = {2005}, author = {Puri, N and Lai-Zhang, J and Meier, S and Mueller, DM}, title = {Expression of bovine F1-ATPase with functional complementation in yeast Saccharomyces cerevisiae.}, journal = {The Journal of biological chemistry}, volume = {280}, number = {23}, pages = {22418-22424}, doi = {10.1074/jbc.M411113200}, pmid = {15817482}, issn = {0021-9258}, support = {R01 GM 066223/GM/NIGMS NIH HHS/United States ; R01 GM 067091/GM/NIGMS NIH HHS/United States ; }, mesh = {ATP Synthetase Complexes/chemistry ; Animals ; Carbon/metabolism ; Cattle ; Gene Deletion ; *Genetic Complementation Test ; Genetic Techniques ; Mitochondria, Heart/metabolism ; Models, Genetic ; Mutagenesis ; Mutation ; Myocardium/metabolism ; Plasmids/metabolism ; Proton-Translocating ATPases/*chemistry/metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; }, abstract = {The mitochondrial F(1)F(0)-ATP synthase is a multimeric enzyme complex composed of at least 16 unique peptides with an overall molecular mass of approximately 600 kDa. F(1)-ATPase is composed of alpha(3)beta(3)gammadeltaepsilon with an overall molecular mass of 370 kDa. The genes encoding bovine F(1)-ATPase have been expressed in a quintuple yeast Saccharomyces cerevisiae deletion mutant (DeltaalphaDeltabetaDeltagammaDeltadeltaDeltaepsilon). This strain expressing bovine F(1) is unable to grow on medium containing a non-fermentable carbon source (YPG), indicating that the enzyme is non-functional. However, daughter strains were easily selected for growth on YPG medium and these were evolved for improved growth on YPG medium. The evolution of the strains was presumably due to mutations, but mutations in the genes encoding the subunits of the bovine F(1)-ATPase were not required for the ability of the cell to grow on YPG medium. The bovine enzyme expressed in yeast was partially purified to a specific activity of about half of that of the enzyme purified from bovine heart mitochondria. These results indicate that the molecular machinery required for the assembly of the mitochondrial ATP synthase is conserved from bovine and yeast and suggest that yeast may be useful for the expression, mutagenesis, and analysis of the mammalian F(1)- or F(1)F(0)-ATP synthase.}, }
@article {pmid15817118, year = {2005}, author = {Keithly, JS and Langreth, SG and Buttle, KF and Mannella, CA}, title = {Electron tomographic and ultrastructural analysis of the Cryptosporidium parvum relict mitochondrion, its associated membranes, and organelles.}, journal = {The Journal of eukaryotic microbiology}, volume = {52}, number = {2}, pages = {132-140}, doi = {10.1111/j.1550-7408.2005.04-3317.x}, pmid = {15817118}, issn = {1066-5234}, support = {P41 RR001219/RR/NCRR NIH HHS/United States ; AI-40320/AI/NIAID NIH HHS/United States ; TWO 0915-051/TW/FIC NIH HHS/United States ; RR01219/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Cryptosporidium parvum/*ultrastructure ; Intracellular Membranes/ultrastructure ; Microscopy, Electron, Transmission ; Mitochondria/*ultrastructure ; Organelles/ultrastructure ; Sporozoites/*ultrastructure ; Tomography, X-Ray Computed/*methods ; }, abstract = {Sporozoites of the apicomplexan Cryptosporidium parvum possess a small, membranous organelle sandwiched between the nucleus and crystalloid body. Based upon immunolabelling data, this organelle was identified as a relict mitochondrion. Transmission electron microscopy and tomographic reconstruction reveal the complex arrangement of membranes in the vicinity of this organelle, as well as its internal organization. The mitochondrion is enveloped by multiple segments of rough endoplasmic reticulum that extend from the outer nuclear envelope. In tomographic reconstructions of the mitochondrion, there is either a single, highly-folded inner membrane or multiple internal subcompartments (which might merge outside the reconstructed volume). The infoldings of the inner membrane lack the tubular "crista junctions" found in typical metazoan, fungal, and protist mitochondria. The absence of this highly conserved structural feature is congruent with the loss, through reductive evolution, of the normal oxidative phosphorylation machinery in C. parvum. It is proposed that the retention of a relict mitochondrion in C. parvum is a strategy for compartmentalizing away from the cytosol toxic ferrous iron and sulfide, which are needed for iron sulfur cluster biosynthesis, an essential function of mitochondria in all eukaryotes.}, }
@article {pmid15814826, year = {2005}, author = {Ho, SY and Phillips, MJ and Cooper, A and Drummond, AJ}, title = {Time dependency of molecular rate estimates and systematic overestimation of recent divergence times.}, journal = {Molecular biology and evolution}, volume = {22}, number = {7}, pages = {1561-1568}, doi = {10.1093/molbev/msi145}, pmid = {15814826}, issn = {0737-4038}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bayes Theorem ; Birds/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genetic Variation ; *Genetics, Population ; Hominidae/genetics ; Humans/genetics ; Mutation ; *Phylogeny ; Primates/genetics ; Species Specificity ; Time Factors ; }, abstract = {Studies of molecular evolutionary rates have yielded a wide range of rate estimates for various genes and taxa. Recent studies based on population-level and pedigree data have produced remarkably high estimates of mutation rate, which strongly contrast with substitution rates inferred in phylogenetic (species-level) studies. Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (< 1-2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222-705 ka), Neandertals (108 ka; 70-156 ka), and modern humans (76 ka; 47-110 ka). If the rate curve for a particular taxonomic group can be accurately estimated, it can be a useful tool for correcting divergence date estimates by taking the rate decay into account. Our results show that it is invalid to extrapolate molecular rates of change across different evolutionary timescales, which has important consequences for studies of populations, domestication, conservation genetics, and human evolution.}, }
@article {pmid15809292, year = {2005}, author = {Haguenauer, A and Raimbault, S and Masscheleyn, S and Gonzalez-Barroso, Mdel M and Criscuolo, F and Plamondon, J and Miroux, B and Ricquier, D and Richard, D and Bouillaud, F and Pecqueur, C}, title = {A new renal mitochondrial carrier, KMCP1, is up-regulated during tubular cell regeneration and induction of antioxidant enzymes.}, journal = {The Journal of biological chemistry}, volume = {280}, number = {23}, pages = {22036-22043}, doi = {10.1074/jbc.M412136200}, pmid = {15809292}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Antioxidants/*pharmacology ; Blotting, Northern ; Blotting, Western ; Brain/metabolism ; COS Cells ; Carrier Proteins/*biosynthesis/*chemistry/metabolism/*physiology ; Cloning, Molecular ; DNA, Complementary/metabolism ; Glutamine/chemistry ; Glycerol/chemistry/metabolism ; Immunoprecipitation ; Ion Channels ; Kidney/*metabolism ; Kidney Tubules/*physiology ; Membrane Potentials ; Membrane Proteins/metabolism ; Mice ; Mice, Inbred C57BL ; Mitochondria/*metabolism ; Mitochondrial Proteins/*biosynthesis/*physiology ; Molecular Sequence Data ; Oxidants/pharmacology ; Oxidation-Reduction ; Oxidative Stress ; Oxygen/metabolism ; Oxygen Consumption ; Phylogeny ; RNA/chemistry/metabolism ; *Regeneration ; Superoxide Dismutase/metabolism ; Time Factors ; Tissue Distribution ; Uncoupling Protein 1 ; *Up-Regulation ; }, abstract = {The mitochondrial carrier family transports a variety of metabolites across the inner mitochondrial membrane. We identified and cloned a new member of this family, KMCP1 (kidney mitochondrial carrier protein-1), that is highly homologous to the previously identified protein BMCP1 (brain mitochondrial carrier protein-1). Western blotting and in situ experiments showed that this carrier is expressed predominantly within the kidney cortex in the proximal and distal tubules. KMCP1 was increased during fasting and during the regenerative phase of glycerol-induced renal failure. We show that both situations are associated with transiently increased expression of superoxide-generating enzymes, followed by increased mitochondrial metabolism and antioxidant defenses. Given that KMCP1 expression occurs simultaneously with these latter events, we propose that KMCP1 is involved in situations in which mitochondrial metabolism is increased, in particular when the cellular redox balance tends toward a pro-oxidant status.}, }
@article {pmid15804833, year = {2004}, author = {Fago, A and Hundahl, C and Malte, H and Weber, RE}, title = {Functional properties of neuroglobin and cytoglobin. Insights into the ancestral physiological roles of globins.}, journal = {IUBMB life}, volume = {56}, number = {11-12}, pages = {689-696}, doi = {10.1080/15216540500037299}, pmid = {15804833}, issn = {1521-6543}, mesh = {Animals ; Biological Evolution ; Cytoglobin ; Globins/*physiology ; Humans ; Mice ; Nerve Tissue Proteins/*physiology ; Neuroglobin ; Nuclear Proteins/*physiology ; Oxidation-Reduction ; Oxygen/metabolism ; Reactive Nitrogen Species/metabolism ; Reactive Oxygen Species/metabolism ; Sulfhydryl Compounds/metabolism ; }, abstract = {Neuroglobin and cytoglobin are two recently discovered vertebrate globins, which are expressed at low levels in neuronal tissues and in all tissues investigated so far, respectively. Based on their amino acid sequences, these globins appear to be phylogenetically ancient and to have mutated less during evolution in comparison to the other vertebrate globins, myoglobin and hemoglobin. As with some plant and bacterial globins, neuroglobin and cytoglobin hemes are hexacoordinate in the absence of external ligands, in that the heme iron atom coordinates both a proximal and a distal His residue. While the physiological role of hexacoordinate globins is still largely unclear, neuroglobin appears to participate in the cellular defence against hypoxia. We present the current knowledge on the functional properties of neuroglobin and cytoglobin, and describe a mathematical model to evaluate the role of mammalian retinal neuroglobin in supplying O2 supply to the mitochondria. As shown, the model argues against a significant such role for neuroglobin, that more likely plays a role to scavenge reactive oxygen and nitrogen species that are generated following brain hypoxia. The O2 binding properties of cytoglobin, which is upregulated upon hypoxia, are consistent with a role for this protein in O2-requiring reactions, such as those catalysed by hydroxylases.}, }
@article {pmid15804829, year = {2004}, author = {Pesce, A and De Sanctis, D and Nardini, M and Dewilde, S and Moens, L and Hankeln, T and Burmester, T and Ascenzi, P and Bolognesi, M}, title = {Reversible hexa- to penta-coordination of the heme Fe atom modulates ligand binding properties of neuroglobin and cytoglobin.}, journal = {IUBMB life}, volume = {56}, number = {11-12}, pages = {657-664}, doi = {10.1080/15216540500078830}, pmid = {15804829}, issn = {1521-6543}, mesh = {Animals ; Cytoglobin ; Globins/*metabolism ; Heme/*metabolism ; Humans ; Iron/*metabolism ; Mice ; Nerve Tissue Proteins/*metabolism ; Neuroglobin ; Nuclear Proteins/*metabolism ; Protein Structure, Tertiary ; }, abstract = {Neuroglobin (Ngb) and cytoglobin (Cygb) are two recently discovered intracellular members of the vertebrate hemoglobin (Hb) family. Ngb, predominantly expressed in nerve cells, is of ancient evolutionary origin and is homologous to nerve-globins of invertebrates. Cygb, present in many different tissues, shares common ancestry with myoglobin (Mb) and can be traced to early vertebrate evolution. Ngb is held to facilitate O2 diffusion to the mitochondria and to protect neuronal cells from hypoxic-ischemic insults, may be an oxidative stress-responsive sensor protein for signal transduction, and may carry out enzymatic activities, such as NO/O2 scavenging. Cygb is linked to collagen synthesis, may provide O2 for enzymatic reactions, and may be involved in a ROS(NO)-signaling pathway(s). Ngb and Cgb display the classical three-over-three alpha-helical fold of Hb and Mb, and are endowed with a hexa-coordinate heme-Fe atom, in their ferrous and ferric forms, having the heme distal HisE7 residue as the endogenous ligand. Reversible hexa- to penta-coordination of the heme Fe atom modulates ligand binding properties of Ngb and Cygb. Moreover, Ngb and Cygb display a tunnel/cavity system within the protein matrix held to facilitate ligand channeling to/from the heme, multiple ligand copies storage, multi-ligand reactions, and conformational transitions supporting ligand binding.}, }
@article {pmid15803417, year = {2004}, author = {Woloszynska, M and Bocer, T and Mackiewicz, P and Janska, H}, title = {A fragment of chloroplast DNA was transferred horizontally, probably from non-eudicots, to mitochondrial genome of Phaseolus.}, journal = {Plant molecular biology}, volume = {56}, number = {5}, pages = {811-820}, pmid = {15803417}, issn = {0167-4412}, mesh = {Base Sequence ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/genetics ; *Gene Transfer, Horizontal ; Molecular Sequence Data ; Phaseolus/*genetics ; Phylogeny ; Plant Proteins/genetics ; RNA, Transfer, Ala/genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {The mitochondrial genomes of some Phaseolus species contain a fragment of chloroplast trnA gene intron, named pvs-trnA for its location within the Phaseolus vulgaris sterility sequence (pvs). The purpose of this study was to determine the type of transfer (intracellular or horizontal) that gave rise to pvs-trnA. Using a PCR approach we could not find the respective portion of the trnA gene as a part of pvs outside the Phaseolus genus. However, a BLAST search revealed longer fragments of trnA present in the mitochondrial genomes of some Citrus species, Helianthus annuus and Zea mays. Basing on the identity or near-identity between these mitochondrial sequences and their chloroplast counterparts we concluded that they had relocated from chloroplasts to mitochondria via recent, independent, intracellular DNA transfers. In contrast, pvs-trnA displayed a relatively higher sequence divergence when compared with its chloroplast counterpart from Phaseolus vulgaris. Alignment of pvs-trnA with corresponding trnA fragments from 35 plant species as well as phylogenetic analysis revealed that pvs-trnA grouped with non-eudicot sequences and was well separated from all Fabales sequences. In conclusion, we propose that pvs-trnA arose via horizontal transfer of a trnA intron fragment from chloroplast of a non-eudicot plant to Phaseolus mitochondria. This is the first example of horizontal transfer of a chloroplast sequence to the mitochondrial genome in higher plants.}, }
@article {pmid15803323, year = {2005}, author = {Purnell, MP and Skopelitis, DS and Roubelakis-Angelakis, KA and Botella, JR}, title = {Modulation of higher-plant NAD(H)-dependent glutamate dehydrogenase activity in transgenic tobacco via alteration of beta subunit levels.}, journal = {Planta}, volume = {222}, number = {1}, pages = {167-180}, pmid = {15803323}, issn = {0032-0935}, mesh = {Amino Acids/metabolism ; Cloning, Molecular ; Gene Expression Regulation, Enzymologic ; *Gene Expression Regulation, Plant ; Genotype ; Glutamate Dehydrogenase (NADP+)/*chemistry/genetics/*metabolism ; Isoenzymes/chemistry/genetics/metabolism ; Mitochondria/enzymology ; Phylogeny ; Plants, Genetically Modified ; Protein Processing, Post-Translational ; Protein Subunits/biosynthesis/genetics/metabolism ; Quaternary Ammonium Compounds/metabolism ; RNA, Messenger/genetics/metabolism ; Nicotiana/*enzymology/*genetics ; Transformation, Genetic ; }, abstract = {Glutamate dehydrogenase (GDH; EC 1.4.1.2-1.4.1.4) catalyses in vitro the reversible amination of 2-oxoglutarate to glutamate. In vascular plants the in vivo direction(s) of the GDH reaction and hence the physiological role(s) of this enzyme remain obscure. A phylogenetic analysis identified two clearly separated groups of higher-plant GDH genes encoding either the alpha- or beta-subunit of the GDH holoenzyme. To help clarify the physiological role(s) of GDH, tobacco (Nicotiana tabacum L.) was transformed with either an antisense or sense copy of a beta-subunit gene, and transgenic plants recovered with between 0.5- and 34-times normal leaf GDH activity. This large modulation of GDH activity (shown to be via alteration of beta-subunit levels) had little effect on leaf ammonium or the leaf free amino acid pool, except that a large increase in GDH activity was associated with a significant decrease in leaf Asp (~51%, P=0.0045). Similarly, plant growth and development were not affected, suggesting that a large modulation of GDH beta-subunit titre does not affect plant viability under the ideal growing conditions employed. Reduction of GDH activity and protein levels in an antisense line was associated with a large increase in transcripts of a beta-subunit gene, suggesting that the reduction in beta-subunit levels might have been due to translational inhibition. In another experiment designed to detect post-translational up-regulation of GDH activity, GDH over-expressing plants were subjected to prolonged dark-stress. GDH activity increased, but this was found to be due more likely to resistance of the GDH protein to stress-induced proteolysis, rather than to post-translational up-regulation.}, }
@article {pmid15803140, year = {2005}, author = {Rouault, TA and Tong, WH}, title = {Iron-sulphur cluster biogenesis and mitochondrial iron homeostasis.}, journal = {Nature reviews. Molecular cell biology}, volume = {6}, number = {4}, pages = {345-351}, doi = {10.1038/nrm1620}, pmid = {15803140}, issn = {1471-0072}, mesh = {Anemia, Sideroblastic ; Animals ; Evolution, Molecular ; Friedreich Ataxia/pathology/therapy ; Homeostasis ; Humans ; Iron/*metabolism ; Iron Overload/metabolism ; Iron-Sulfur Proteins/genetics/*metabolism ; Mice ; Mitochondria/*metabolism ; Protein Structure, Tertiary ; Yeasts/metabolism ; }, abstract = {Iron-sulphur clusters are important cofactors for proteins that are involved in many cellular processes, including electron transport, enzymatic catalysis and regulation. The enzymes that catalyse the formation of iron-sulphur clusters are widely conserved from bacteria to humans. Recent studies in model systems and humans reveal that iron-sulphur proteins have important roles in mitochondrial iron homeostasis and in the pathogenesis of the human disease Friedreich ataxia.}, }
@article {pmid15793838, year = {2005}, author = {Gonzalez, IL}, title = {Barth syndrome: TAZ gene mutations, mRNAs, and evolution.}, journal = {American journal of medical genetics. Part A}, volume = {134}, number = {4}, pages = {409-414}, doi = {10.1002/ajmg.a.30661}, pmid = {15793838}, issn = {1552-4825}, mesh = {Abnormalities, Multiple/*genetics/pathology ; Acyltransferases ; Alternative Splicing ; Animals ; Base Sequence ; Cardiomyopathy, Dilated/*pathology ; DNA/chemistry/genetics ; *Evolution, Molecular ; Humans ; Molecular Sequence Data ; *Mutation ; Neutropenia/pathology ; Phylogeny ; Primates/genetics ; Proteins/*genetics ; RNA, Messenger/*genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Syndrome ; Transcription Factors/*genetics ; }, abstract = {Barth syndrome (MIM 302060) is an X-linked condition that includes dilated cardiomyopathy, neutropenia, failure to thrive, abnormal mitochondria, and 3-methylglutaconic aciduria. The mutated gene, TAZ, first described in 1996, appeared to produce a large set of alternatively spliced mRNAs with initiations of transcription upstream of exons 1 and 3. Since then, disease-causing mutations have been found in all exons including, most recently, a missense mutation in the controversial exon 5. Because of the initially described second initiation of transcription in intron 2, with in-frame initiation of translation in exon 3, we hypothesized that subjects with mutations in exons 1 and 2 would produce more normal "short product" that might attenuate their phenotype. Moreover, it was of interest to determine which splice variants were potentially functional as exon 5 is not present in yeast and rodents, and the variant lacking this exon is the most abundant. Using RT-PCR, we characterized TAZ mRNAs in cultured lymphocytes from nine subjects with Barth syndrome and two healthy controls. The TAZ genes and mRNAs of primates were also included. We found the following: (1) there is only one site for initiation of transcription, and the normal alternatively spliced assortment is limited to full-length, delta5, delta7, delta5delta7; (2) there are two alternative splice sites within introns 1 and 2 that could potentially produce an in-frame product; (3) exon 5 evolved into "exonhood" in the primate lineage after the split between Old World monkeys and hominoid primates; and (4) our results suggest that only two functional protein variants exist in lymphocytes: delta5 and full-length. Although exon 5 does not appear to be required for TAZ function in yeast and monkeys, its evolution to a highly conserved spliced exon in hominoid primates and the recent finding of an exon 5 mutation in a patient with Barth syndrome suggest that the full-length variant is important to TAZ function.}, }
@article {pmid15791267, year = {2005}, author = {Schuster, J and Betat, H and Mörl, M}, title = {Is yeast on its way to evolving tRNA editing?.}, journal = {EMBO reports}, volume = {6}, number = {4}, pages = {367-372}, pmid = {15791267}, issn = {1469-221X}, mesh = {Base Sequence ; DNA Primers ; Escherichia coli ; *Evolution, Molecular ; Genes, Overlapping/*genetics ; *Models, Biological ; Molecular Sequence Data ; RNA 3' End Processing/*genetics/physiology ; RNA Editing/*genetics/physiology ; RNA, Transfer, Amino Acid-Specific/*genetics ; RNA, Transfer, Tyr/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Yeasts ; }, abstract = {In human mitochondria, genes for tRNA(Tyr) and tRNA(Cys) overlap by a single nucleotide. From polycistronic precursors, a 3'-truncated upstream tRNA(Tyr) is released, missing the overlapping position. A subsequent editing reaction restores this position. Similar mitochondrial tRNA gene overlaps exist in all metazoans, but not in organisms such as yeast or Escherichia coli. Therefore, we asked whether tRNA overlaps are processed in these organisms. Corresponding constructs were introduced and transcripts tested for processing and editing in E. coli and yeast. E. coli produces only one functional tRNA from these precursors, indicating that tRNA overlaps are incompatible with its processing pathway. In contrast, yeast processes overlapping tRNAs similar to human mitochondria, releasing a 3'-truncated upstream tRNA. This tRNA is restored in an editing-like event, although yeast does not carry a corresponding endogenous editing substrate. These findings support the hypothesis of the evolution of editing by recruitment of a pre-existing and promiscuous editing enzyme.}, }
@article {pmid15785848, year = {2005}, author = {Regina, TM and Picardi, E and Lopez, L and Pesole, G and Quagliariello, C}, title = {A novel additional group II intron distinguishes the mitochondrial rps3 gene in gymnosperms.}, journal = {Journal of molecular evolution}, volume = {60}, number = {2}, pages = {196-206}, pmid = {15785848}, issn = {0022-2844}, mesh = {Base Sequence ; Cycas/*genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Evolution, Molecular ; *Genes, Plant ; Genome, Plant ; Helianthus/genetics ; Introns ; Magnolia/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Plant Proteins/*genetics ; RNA Editing ; RNA, Messenger/genetics/metabolism ; RNA, Plant/chemistry/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Ribosomal Proteins/*genetics ; Species Specificity ; }, abstract = {Comparative analysis of the ribosomal protein S3 gene (rps3) in the mitochondrial genome of Cycas with newly sequenced counterparts from Magnolia and Helianthus and available sequences from higher plants revealed that the positional clustering with the genes for ribosomal protein S19 (rps19) and L16 (rpl16) is preserved in gymnosperms. However, in contrast to the other land plant species, the rps3 gene in Cycas mitochondria is unique in possessing a second intron: rps3i2. Reverse transcription-polymerase chain reaction (RT-PCR) analysis of the transcripts generated from the rps19-rps3-rpl16 cluster in Cycas mitochondria demonstrated that the genes are cotranscribed and extensively modified by RNA editing and that both introns are efficiently spliced. Despite remarkable size heterogeneity, the Cycas rps3i1 can be shown to be homologous to the group IIA introns present within the rps3 gene of algae and land plants, including Magnolia and Helianthus. Conversely, sequences similar to the rps3i2 have not been reported previously. On the basis of conserved primary and secondary structure the second intervening sequence interrupting the Cycas rps3 gene has been classified as a group II intron. The close relationship of the rps3i2 to a group of different plant mitochondrial introns is intriguing and suggestive of a mitochondrial derivation for this novel intervening sequence. Interestingly, the rps3i2 appears to be conserved at the same gene location in other gymnosperms. Furthermore, the pattern of the rps3i2 distribution among algae and land plants provides evidence for the evolutionary acquisition of this novel intron in gymnosperms via intragenomic transposition or retrotransposition.}, }
@article {pmid15780502, year = {2005}, author = {Parris, GE}, title = {The role of viruses in cell fusion and its importance to evolution, invasion and metastasis of cancer clones.}, journal = {Medical hypotheses}, volume = {64}, number = {5}, pages = {1011-1014}, doi = {10.1016/j.mehy.2004.11.012}, pmid = {15780502}, issn = {0306-9877}, mesh = {Aneuploidy ; *Cell Fusion ; Mitosis ; *Neoplasm Invasiveness ; *Neoplasm Metastasis ; Papillomaviridae/physiology ; *Virus Physiological Phenomena ; }, abstract = {The hypothesis described here is a logical extension of two areas of observation: First, it has been discovered that viruses (and perhaps other intracellular parasites) catalyze cell fusion as a means of cell-to-cell transmission. Effective cell-to-cell transmission appears to require: (i) induced expression of adhesion molecules on the cell surface; (ii) suppression of p53-dependent apoptosis; (iii) arrest of the cell cycle that would otherwise lead to cell death by "mitotic catastrophe". Suppression of apoptosis and cell death through "mitotic catastrophe" are important for formation of stable syncytia. Expression of Bcl-2 or a viral analogue of Bcl-2 (vBcl-2) is particularly useful to viruses because Bcl-2 both suppresses (p53-dependent) apoptosis and arrests the cell cycle through p27. Bcl-2 may also block any p53-independent cell death (e.g., mitotic catastrophe) that is initiated at the mitochondria. Second, it has been found that cell fusion plays a role in cancer clone evolution, invasion of normal cells in tissue adjacent to tumors and metastasis to remote normal tissues. Thus, it can be hypothesized that infection of cancer cells with viruses that spread by cell-to-cell transmission may coincidentally contribute to development of aggressive aneuploid clones and facilitate both invasion and metastasis of tumors. Regardless of the role of viruses, suppression of Bcl-2 may be an approach to preventing successful formation of syncytia and limiting the invasion and metastasis of tumors, thus, making surgical removal and radiation treatment more feasible.}, }
@article {pmid15770678, year = {2005}, author = {de Grey, AD}, title = {Forces maintaining organellar genomes: is any as strong as genetic code disparity or hydrophobicity?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {27}, number = {4}, pages = {436-446}, doi = {10.1002/bies.20209}, pmid = {15770678}, issn = {0265-9247}, mesh = {Animals ; *DNA, Chloroplast ; *DNA, Mitochondrial ; Evolution, Molecular ; *Genetic Code ; Genome ; Humans ; *Hydrophobic and Hydrophilic Interactions ; Proteins/chemistry/genetics ; }, abstract = {It remains controversial why mitochondria and chloroplasts retain the genes encoding a small subset of their constituent proteins, despite the transfer of so many other genes to the nucleus. Two candidate obstacles to gene transfer, suggested long ago, are that the genetic code of some mitochondrial genomes differs from the standard nuclear code, such that a transferred gene would encode an incorrect amino acid sequence, and that the proteins most frequently encoded in mitochondria are generally very hydrophobic, which may impede their import after synthesis in the cytosol. More recently it has been suggested that both these interpretations suffer from serious "false positives" and "false negatives": genes that they predict should be readily transferred but which have never (or seldom) been, and genes whose transfer has occurred often or early, even though this is predicted to be very difficult. Here I consider the full known range of ostensibly problematic such genes, with particular reference to the sequences of events that could have led to their present location. I show that this detailed analysis of these cases reveals that they are in fact wholly consistent with the hypothesis that code disparity and hydrophobicity are much more powerful barriers to functional gene transfer than any other. The popularity of the contrary view has led to the search for other barriers that might retain genes in organelles even more powerfully than code disparity or hydrophobicity; one proposal, concerning the role of proteins in redox processes, has received widespread support. I conclude that this abandonment of the original explanations for the retention of organellar genomes has been premature. Several other, relatively minor, obstacles to gene transfer certainly exist, contributing to the retention of relatively many organellar genes in most lineages compared to animal mtDNA, but there is no evidence for obstacles as severe as code disparity or hydrophobicity. One corollary of this conclusion is that there is currently no reason to suppose that engineering nuclear versions of the remaining mammalian mitochondrial genes, a feat that may have widespread biomedical relevance, should require anything other than sequence alterations obviating code disparity and causing modest reductions in hydrophobicity without loss of enzymatic function.}, }
@article {pmid15769290, year = {2005}, author = {Garrow, AG and Agnew, A and Westhead, DR}, title = {TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins.}, journal = {BMC bioinformatics}, volume = {6}, number = {}, pages = {56}, pmid = {15769290}, issn = {1471-2105}, mesh = {Algorithms ; Bacterial Outer Membrane Proteins/chemistry ; Calibration ; Cell Membrane/*metabolism ; Chloroplasts/metabolism ; Computational Biology/*methods ; Databases, Protein ; Escherichia coli/metabolism ; Evolution, Molecular ; Genome ; Markov Chains ; Membrane Proteins/*chemistry ; Models, Molecular ; Models, Statistical ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins ; *Proteome ; Proteomics/*methods ; Reproducibility of Results ; Sequence Alignment ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; Software ; User-Computer Interface ; }, abstract = {BACKGROUND: Beta-barrel transmembrane (bbtm) proteins are a functionally important and diverse group of proteins expressed in the outer membranes of bacteria (both gram negative and acid fast gram positive), mitochondria and chloroplasts. Despite recent publications describing reasonable levels of accuracy for discriminating between bbtm proteins and other proteins, screening of entire genomes remains troublesome as these molecules only constitute a small fraction of the sequences screened. Therefore, novel methods are still required capable of detecting new families of bbtm protein in diverse genomes.<br><br>RESULTS: We present TMB-Hunt, a program that uses a k-Nearest Neighbour (k-NN) algorithm to discriminate between bbtm and non-bbtm proteins on the basis of their amino acid composition. By including differentially weighted amino acids, evolutionary information and by calibrating the scoring, an accuracy of 92.5% was achieved, with 91% sensitivity and 93.8% positive predictive value (PPV), using a rigorous cross-validation procedure. A major advantage of this approach is that because it does not rely on beta-strand detection, it does not require resolved structures and thus larger, more representative, training sets could be used. It is therefore believed that this approach will be invaluable in complementing other, physicochemical and homology based methods. This was demonstrated by the correct reassignment of a number of proteins which other predictors failed to classify. We have used the algorithm to screen several genomes and have discussed our findings.<br><br>CONCLUSION: TMB-Hunt achieves a prediction accuracy level better than other approaches published to date. Results were significantly enhanced by use of evolutionary information and a system for calibrating k-NN scoring. Because the program uses a distinct approach to that of other discriminators and thus suffers different liabilities, we believe it will make a significant contribution to the development of a consensus approach for bbtm protein detection.}, }
@article {pmid15754208, year = {2005}, author = {Spooner, DM and Nuñez, J and Rodríguez, F and Naik, PS and Ghislain, M}, title = {Nuclear and chloroplast DNA reassessment of the origin of Indian potato varieties and its implications for the origin of the early European potato.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {110}, number = {6}, pages = {1020-1026}, pmid = {15754208}, issn = {0040-5752}, mesh = {Cluster Analysis ; DNA Primers ; DNA, Chloroplast/genetics ; Electrophoresis, Polyacrylamide Gel ; *Evolution, Molecular ; *Genetic Variation ; Geography ; India ; Microsatellite Repeats/genetics ; Models, Genetic ; Solanum tuberosum/*genetics ; Species Specificity ; }, abstract = {The modern cultivated potato was first recorded in Europe in 1562, but its area(s) of exportation has long been in dispute. Two competing hypotheses have proposed an "Andean" area (somewhere from upland Venezuela to northern Argentina) or a lowland south central "Chilean" area. Potato landraces from these two areas can be distinguished, although sometimes with difficulty, by (1) cytoplasmic sterility factors, (2) morphological traits, (3) daylength adaptation, (4) microsatellite markers, and (5) co-evolved chloroplast (cp) and mitochondria (mt) DNA. The Chilean introduction hypothesis originally was proposed because of similarities among Chilean landraces and modern "European" cultivars with respect to traits 2 and 3. Alternatively, the Andean introduction hypothesis suggests that (1) traits 2 and 3 of European potato evolved rapidly, in parallel, from Andean landraces to a Chilean type through selection following import to Europe, and (2) the worldwide late blight epidemics beginning in 1845 in the United Kingdom displaced most existing European cultivars and the potato was subsequently improved by importations of Chilean landraces. We reassess these two competing hypotheses with nuclear microsatellite and cpDNA analyses of (1) 32 Indian cultivars, some of which are thought to preserve putatively remnant populations of Andean landraces, (2) 12 Andean landraces, and (3) five Chilean landraces. Our microsatellite results cluster all Indian cultivars, including putatively remnant Andean landrace populations, with the Chilean landraces, and none with the "old Andigenum" landraces. Some of these Indian landraces, however, lack the cpDNA typical of Chilean landraces and advanced cultivars, indicating they likely are hybrids of Andean landraces with Chilean clones or more advanced cultivars. These results lead us to reexamine the hypothesis that early introductions of potato to Europe were solely from the Andes.}, }
@article {pmid15752985, year = {2005}, author = {Lill, R and Mühlenhoff, U}, title = {Iron-sulfur-protein biogenesis in eukaryotes.}, journal = {Trends in biochemical sciences}, volume = {30}, number = {3}, pages = {133-141}, doi = {10.1016/j.tibs.2005.01.006}, pmid = {15752985}, issn = {0968-0004}, mesh = {Animals ; Bacteria/genetics/metabolism ; Biological Evolution ; Cell Nucleus/metabolism ; Cytosol/metabolism ; Eukaryotic Cells ; Humans ; Iron-Sulfur Proteins/*biosynthesis/genetics ; Mitochondria/metabolism ; Models, Biological ; Mutation ; }, abstract = {Iron-sulfur (Fe-S) clusters (ISCs) are versatile, ancient co-factors of proteins that are involved in electron transport, enzyme catalysis and regulation of gene expression. The synthesis of ISCs and their insertion into apoproteins involves the function of complex cellular machineries. In eukaryotes, the mitochondrial ISC-assembly machinery is involved in the maturation of all cellular iron-sulfur proteins. A mitochondrial export machinery and a recently discovered cytosolic assembly system specifically participate in the maturation of cytosolic and nuclear iron-sulfur proteins. Of the approximately 20 assembly components, more than ten are encoded by essential genes, which indicates that the process is indispensable for life. Mutations in two of the assembly components lead to neurological diseases. The essential character of Fe-S-protein biogenesis in eukaryotes and its importance for human disease identifies this evolutionary ancient process as one of the most important biosynthetic pathways of life.}, }
@article {pmid15752446, year = {2005}, author = {Chua, PK and Corkill, JE and Hooi, PS and Cheng, SC and Winstanley, C and Hart, CA}, title = {Isolation of Waddlia malaysiensis, a novel intracellular bacterium, from fruit bat (Eonycteris spelaea).}, journal = {Emerging infectious diseases}, volume = {11}, number = {2}, pages = {271-277}, pmid = {15752446}, issn = {1080-6040}, mesh = {3T3 Cells ; Acetylmuramyl-Alanyl-Isoglutamine/*analogs &amp; derivatives/chemistry/genetics ; Animals ; Anti-Bacterial Agents/pharmacology ; Base Sequence ; Chiroptera/*microbiology/urine ; Chlamydiales/drug effects/genetics/*isolation &amp; purification/ultrastructure ; Chlorocebus aethiops ; Cricetinae ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Humans ; Mice ; Microbial Sensitivity Tests ; Microscopy, Electron ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics ; RNA, Ribosomal, 23S/chemistry/genetics ; Sequence Alignment ; Vero Cells ; }, abstract = {An obligate intracellular bacterium was isolated from urine samples from 7 (3.5%) of 202 fruit bats (Eonycteris spelaea) in peninsular Malaysia. The bacterium produced large membrane-bound inclusions in human, simian, and rodent cell lines, including epithelial, fibroblastlike, and lymphoid cells. Thin-section electron microscopy showed reticulate bodies dividing by binary fission and elementary bodies in the inclusions; mitochondria surrounded the inclusions. The inclusions were positive for periodic acid-Schiff stain but could not be stained by fluorescein-labeled anti-Chlamydia trachomatis major outer membrane protein monoclonal antibody. The bacterium was resistant to penicillin and streptomycin (MICs > 256 mg/L) but susceptible to tetracycline (MIC = 0.25 mg/L) and chloramphenicol (MIC = 0.5 mg/L). Sequence analysis of the 16SrRNA gene indicated that it was most closely related to 2 isolates of Waddlia chondrophila (94% and 96% identity). The 16S and 23S rRNA gene signatures were only 91% identical. We propose this novel bacterium be called W. malaysiensis.}, }
@article {pmid15744502, year = {2005}, author = {Edmondson, AC and Song, D and Alvarez, LA and Wall, MK and Almond, D and McClellan, DA and Maxwell, A and Nielsen, BL}, title = {Characterization of a mitochondrially targeted single-stranded DNA-binding protein in Arabidopsis thaliana.}, journal = {Molecular genetics and genomics : MGG}, volume = {273}, number = {2}, pages = {115-122}, pmid = {15744502}, issn = {1617-4615}, support = {BBS/E/J/00000201/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics ; Biolistics ; Computational Biology ; DNA-Binding Proteins/*genetics ; Escherichia coli ; Gene Components ; Green Fluorescent Proteins ; Likelihood Functions ; Mitochondria/*metabolism ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Rec A Recombinases/metabolism ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {A gene encoding a predicted mitochondrially targeted single-stranded DNA binding protein (mtSSB) was identified in the Arabidopsis thaliana genome sequence. This gene (At4g11060) codes for a protein of 201 amino acids, including a 28-residue putative mitochondrial targeting transit peptide. Protein sequence alignment shows high similarity between the mtSSB protein and single-stranded DNA binding proteins (SSB) from bacteria, including residues conserved for SSB function. Phylogenetic analysis indicates a close relationship between this protein and other mitochondrially targeted SSB proteins. The predicted targeting sequence was fused with the GFP coding region, and the organellar localization of the expressed fusion protein was determined. Specific targeting to mitochondria was observed in in-vitro import experiments and by transient expression of a GFP fusion construct in Arabidopsis leaves after microprojectile bombardment. The mature mtSSB coding region was overexpressed in Escherichia coli and the protein was purified for biochemical characterization. The purified protein binds single-stranded, but not double-stranded, DNA. MtSSB stimulates the homologous strand-exchange activity of E. coli RecA. These results indicate that mtSSB is a functional homologue of the E. coli SSB, and that it may play a role in mitochondrial DNA recombination.}, }
@article {pmid15744302, year = {2005}, author = {Boxma, B and de Graaf, RM and van der Staay, GW and van Alen, TA and Ricard, G and Gabaldón, T and van Hoek, AH and Moon-van der Staay, SY and Koopman, WJ and van Hellemond, JJ and Tielens, AG and Friedrich, T and Veenhuis, M and Huynen, MA and Hackstein, JH}, title = {An anaerobic mitochondrion that produces hydrogen.}, journal = {Nature}, volume = {434}, number = {7029}, pages = {74-79}, doi = {10.1038/nature03343}, pmid = {15744302}, issn = {1476-4687}, mesh = {*Anaerobiosis ; Animals ; Ciliophora/*cytology/genetics/*metabolism/ultrastructure ; Cockroaches/parasitology ; DNA, Mitochondrial/genetics ; Electron Transport ; Electron Transport Complex I/antagonists &amp; inhibitors/metabolism ; Genome ; Glucose/metabolism ; Hydrogen/*metabolism ; Mitochondria/enzymology/genetics/*metabolism/ultrastructure ; Molecular Sequence Data ; Open Reading Frames/genetics ; Organelles/drug effects/genetics/metabolism/ultrastructure ; Phylogeny ; Proteome ; }, abstract = {Hydrogenosomes are organelles that produce ATP and hydrogen, and are found in various unrelated eukaryotes, such as anaerobic flagellates, chytridiomycete fungi and ciliates. Although all of these organelles generate hydrogen, the hydrogenosomes from these organisms are structurally and metabolically quite different, just like mitochondria where large differences also exist. These differences have led to a continuing debate about the evolutionary origin of hydrogenosomes. Here we show that the hydrogenosomes of the anaerobic ciliate Nyctotherus ovalis, which thrives in the hindgut of cockroaches, have retained a rudimentary genome encoding components of a mitochondrial electron transport chain. Phylogenetic analyses reveal that those proteins cluster with their homologues from aerobic ciliates. In addition, several nucleus-encoded components of the mitochondrial proteome, such as pyruvate dehydrogenase and complex II, were identified. The N. ovalis hydrogenosome is sensitive to inhibitors of mitochondrial complex I and produces succinate as a major metabolic end product--biochemical traits typical of anaerobic mitochondria. The production of hydrogen, together with the presence of a genome encoding respiratory chain components, and biochemical features characteristic of anaerobic mitochondria, identify the N. ovalis organelle as a missing link between mitochondria and hydrogenosomes.}, }
@article {pmid15744282, year = {2005}, author = {Gray, MW}, title = {Evolutionary biology: the hydrogenosome's murky past.}, journal = {Nature}, volume = {434}, number = {7029}, pages = {29-31}, doi = {10.1038/434029a}, pmid = {15744282}, issn = {1476-4687}, mesh = {Animals ; Ciliophora/*cytology/*genetics/metabolism ; DNA, Mitochondrial/genetics ; Electron Transport ; Electron Transport Complex I/chemistry/metabolism ; Genome ; Hydrogen/*metabolism ; Isoptera/parasitology ; Mitochondria/enzymology/*genetics/*metabolism ; Organelles/enzymology/*genetics/*metabolism ; *Phylogeny ; Trichomonas vaginalis/cytology/genetics ; }, }
@article {pmid15744251, year = {2005}, author = {Matsumori, Y and Hong, SM and Aoyama, K and Fan, Y and Kayama, T and Sheldon, RA and Vexler, ZS and Ferriero, DM and Weinstein, PR and Liu, J}, title = {Hsp70 overexpression sequesters AIF and reduces neonatal hypoxic/ischemic brain injury.}, journal = {Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism}, volume = {25}, number = {7}, pages = {899-910}, doi = {10.1038/sj.jcbfm.9600080}, pmid = {15744251}, issn = {0271-678X}, support = {NS35902/NS/NINDS NIH HHS/United States ; R01 NS35902/NS/NINDS NIH HHS/United States ; R01 NS40469/NS/NINDS NIH HHS/United States ; R01 NS44025/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Animals, Newborn ; Apoptosis Inducing Factor ; Apoptosis Regulatory Proteins ; Blood Volume ; Brain Injuries/metabolism/pathology ; Carrier Proteins/metabolism ; Cytochromes c/metabolism ; Disease Progression ; Flavoproteins/*metabolism ; HSP70 Heat-Shock Proteins/*genetics/*metabolism ; Hypoxia-Ischemia, Brain/genetics/*metabolism/*pathology ; Membrane Proteins/*metabolism ; Mice ; Mice, Transgenic ; Mitochondria/metabolism ; Mitochondrial Proteins/metabolism ; Protein Binding ; Protein Transport ; Rats ; Time Factors ; }, abstract = {Apoptosis is implicated in neonatal hypoxic/ischemic (H/I) brain injury among various forms of cell death. Here we investigate whether overexpression of heat shock protein (Hsp) 70, an antiapoptotic protein, protects the neonatal brain from H/I injury and the pathways involved in the protection. Postnatal day 7 (P7) transgenic mice overexpressing rat Hsp70 (Tg) and their wild-type littermates (Wt) underwent unilateral common carotid artery ligation followed by 30 mins exposure to 8% O(2). Significant neuroprotection was observed in Tg versus Wt mice on both P12 and P21, correlating with a high level of constitutive but not inducible Hsp70 in the Tg. More prominent injury was observed in Wt and Tg mice on P21, suggesting its continuous evolution after P12. Western blot analysis showed that translocation of cytochrome c, but not the second mitochondria-derived activator of caspase (Smac)/DIABLO and apoptosis-inducing factor (AIF), from mitochondria into cytosol was significantly reduced in Tg 24 h after H/I compared with Wt mice. Coimmunoprecipitation detected more Hsp70 bound to AIF in Tg than Wt mice 24 h after H/I, inversely correlating with the amount of nuclear, but not cytosolic, AIF translocation. Our results suggest that interaction between Hsp70 and AIF might have reduced downstream events leading to cell death, including the reduction of nuclear AIF translocation in the neonatal brains of Hsp70 Tg mice after H/I.}, }
@article {pmid15737729, year = {2005}, author = {Aguirre, J and Ríos-Momberg, M and Hewitt, D and Hansberg, W}, title = {Reactive oxygen species and development in microbial eukaryotes.}, journal = {Trends in microbiology}, volume = {13}, number = {3}, pages = {111-118}, doi = {10.1016/j.tim.2005.01.007}, pmid = {15737729}, issn = {0966-842X}, mesh = {Antioxidants/metabolism ; Cell Differentiation/physiology ; DNA, Fungal/chemistry/genetics ; FMN Reductase/genetics/metabolism ; Fungi/cytology/enzymology/genetics/*metabolism ; Mitochondria/metabolism ; NADPH Oxidases/genetics/metabolism ; Phylogeny ; Reactive Oxygen Species/*metabolism ; }, abstract = {Reactive oxygen species (ROS) have been regarded as inevitable harmful by-products of aerobic metabolism. Growing evidence, however, suggests that ROS play important physiological roles. This raises questions about the pathways that different groups of organisms use to produce and sense ROS. In microbial eukaryotes, recent data show (i) increased ROS levels during cell differentiation, (ii) the existence of ROS-producing enzymes, such as NADPH oxidases (NOX), (iii) the involvement of NOX in developmental processes, and (iv) a conservation in the signal-transduction mechanisms used to detect ROS. This shows that manipulation of reactive species, as strategy to regulate cell differentiation, is ubiquitous in eukaryotes and suggests that such strategy was selected early in evolution.}, }
@article {pmid15737601, year = {2005}, author = {Arnason, U}, title = {Comments on the paper "Phylogeny of mysticete whales based on mitochondrial and nuclear data" by Amanda L. Rychel, Tod W. Reeder, and Annalisa Berta [Mol. Phylogenet. Evol. 32 (2004) 892-901].}, journal = {Molecular phylogenetics and evolution}, volume = {35}, number = {1}, pages = {309-10; author reply 311-2}, doi = {10.1016/j.ympev.2004.11.013}, pmid = {15737601}, issn = {1055-7903}, mesh = {Animals ; Cell Nucleus/*genetics ; Mitochondria/*genetics ; *Phylogeny ; Whales/*classification/*genetics ; }, }
@article {pmid15737587, year = {2005}, author = {Martínez-Navarro, EM and Galián, J and Serrano, J}, title = {Phylogeny and molecular evolution of the tribe Harpalini (Coleoptera, Carabidae) inferred from mitochondrial cytochrome-oxidase I.}, journal = {Molecular phylogenetics and evolution}, volume = {35}, number = {1}, pages = {127-146}, doi = {10.1016/j.ympev.2004.11.009}, pmid = {15737587}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Coleoptera/classification/*genetics ; DNA Primers ; Electron Transport Complex IV/*genetics ; *Evolution, Molecular ; Mitochondria/*enzymology ; *Phylogeny ; }, abstract = {The tribe Harpalini is a group of ground beetles with a world-wide distribution that comprises approximately 2000 species and about 238 genera and subgenera. Hypotheses about the phylogenetic relationships of the subtribes of Harpalini are implicit within the systematic criteria put forward by different authors. A 759 bp fragment of the mitochondrial COI was sequenced in 119 specimens (107 species) of 52 genera and subgenera that represent the main lineages of Harpalines, and 3 species of other tribes used as outgroups. A hierarchical study of sequence divergence (under uncorrected and corrected models) and ts:tv ratio pattern analyses were carried out at different taxonomic levels. A low saturation rate was detected at first and second codon positions, whereas A+T richness causes a low transitions:transversions ratio, which suggests--a priori--a high rate of saturation at the third codon position. A progressive accumulation of sequence divergence and a decreasing ts:tv ratio were found from lower to higher taxonomic levels. MP strict consensus, ML, and minimum evolution distance (under ts+tv and tv only schemes) trees showed similar major clades within the tribe. The subtribe Ditomina is a monophyletic lineage with close affinities to the subtribe Harpalina. Harpalina is a polyphyletic lineage as the genus Daptus is always related to members of the subtribe Stenolophina, and the Selenophorines resulted a polyphyletic group related to the subtribe Anisodactylina. Main lineages proposed by Noonan [Quaest. Entomol. 9 (1973) 266] within the subtribe Anisodactylina have been corroborated in this study. The Australian genus Phorticosomus is not related to Ditomina but to the Australian Notiobioids lineage. Most taxa of the subtribe Stenolophina are always included in the same clade, together with taxa of the subtribe Pelmatellina, which might be considered as a lineage of Stenolophina related to Bradycellus and Dicheirotrichus. The subtribe Amblystomina lacks a well-supported relationship to the other subtribes of Harpalini and could not be consistently related to any of them.}, }
@article {pmid15734678, year = {2005}, author = {Kenyon, C}, title = {The plasticity of aging: insights from long-lived mutants.}, journal = {Cell}, volume = {120}, number = {4}, pages = {449-460}, doi = {10.1016/j.cell.2005.02.002}, pmid = {15734678}, issn = {0092-8674}, mesh = {Animals ; Biological Evolution ; Disease Susceptibility ; Insulin/genetics/physiology ; Insulin-Like Growth Factor I/genetics/physiology ; Longevity/*genetics/physiology ; Mitochondria/*genetics/physiology ; *Mutation/physiology ; Oxidative Stress/genetics/physiology ; Reproduction/*genetics/physiology ; Telomere/*genetics/physiology ; }, abstract = {Mutations in genes affecting endocrine signaling, stress responses, metabolism, and telomeres can all increase the life spans of model organisms. These mutations have revealed evolutionarily conserved pathways for aging, some of which appear to extend life span in response to sensory cues, caloric restriction, or stress. Many mutations affecting longevity pathways delay age-related disease, and the molecular analysis of these pathways is leading to a mechanistic understanding of how these two processes--aging and disease susceptibility--are linked.}, }
@article {pmid15734677, year = {2005}, author = {Kirkwood, TB}, title = {Understanding the odd science of aging.}, journal = {Cell}, volume = {120}, number = {4}, pages = {437-447}, doi = {10.1016/j.cell.2005.01.027}, pmid = {15734677}, issn = {0092-8674}, support = {BEP17042/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Aging/*physiology ; Animals ; *Biological Evolution ; Diet ; Energy Intake/physiology ; Humans ; Mitochondria/physiology ; Models, Biological ; Mutation/genetics/*physiology ; Reproduction/*physiology ; Telomere/physiology ; }, abstract = {Evolutionary considerations suggest aging is caused not by active gene programming but by evolved limitations in somatic maintenance, resulting in a build-up of damage. Ecological factors such as hazard rates and food availability influence the trade-offs between investing in growth, reproduction, and somatic survival, explaining why species evolved different life spans and why aging rate can sometimes be altered, for example, by dietary restriction. To understand the cell and molecular basis of aging is to unravel the multiplicity of mechanisms causing damage to accumulate and the complex array of systems working to keep damage at bay.}, }
@article {pmid15734655, year = {2005}, author = {Graczyk, TK}, title = {Is Giardia a living fossil?.}, journal = {Trends in parasitology}, volume = {21}, number = {3}, pages = {104-107}, doi = {10.1016/j.pt.2005.01.002}, pmid = {15734655}, issn = {1471-4922}, mesh = {Animals ; Eukaryotic Cells/physiology ; *Evolution, Molecular ; Giardia/*genetics ; Host-Parasite Interactions ; Mitochondria/metabolism ; Oxygen/metabolism ; Phylogeny ; Prokaryotic Cells/physiology ; Symbiosis/physiology ; }, abstract = {Despite enormous efforts, the patterns of the rise of eukaryotic life on Earth are not clearly defined. The ability of eukaryotes to produce energy using oxygen and sugars was a key factor in advancing life on Earth towards complex multicellular organisms. However, this was not the only way to produce energy and survive. Mitochondria probably appeared soon after the oxygen increase in the Earth's atmosphere but many microaerophilic protists require little or no oxygen to survive. New ultrastructural, biochemical and molecular phylogeny data about structures and processes involved in the generation of energy by currently known protists have forced the revision of understanding of the "tree of life".}, }
@article {pmid15733919, year = {2005}, author = {Likić, VA and Perry, A and Hulett, J and Derby, M and Traven, A and Waller, RF and Keeling, PJ and Koehler, CM and Curran, SP and Gooley, PR and Lithgow, T}, title = {Patterns that define the four domains conserved in known and novel isoforms of the protein import receptor Tom20.}, journal = {Journal of molecular biology}, volume = {347}, number = {1}, pages = {81-93}, doi = {10.1016/j.jmb.2004.12.057}, pmid = {15733919}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Evolution, Molecular ; Humans ; Markov Chains ; Mitochondrial Membrane Transport Proteins ; Models, Molecular ; Molecular Sequence Data ; Peptides/metabolism ; Phylogeny ; *Protein Conformation ; *Protein Isoforms/chemistry/classification/genetics/metabolism ; *Receptors, Cytoplasmic and Nuclear/chemistry/classification/genetics/metabolism ; *Saccharomyces cerevisiae Proteins/chemistry/classification/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Tom20 is the master receptor for protein import into mitochondria. Analysis of motifs present in Tom20 sequences from fungi and animals found several highly conserved regions, including features of the transmembrane segment, the ligand-binding domain and functionally important flexible segments at the N terminus and the C terminus of the protein. Hidden Markov model searches of genome sequence data revealed novel isoforms of Tom20 in vertebrate and invertebrate animals. A three-dimensional comparative model of the novel type I Tom20, based on the structurally characterized type II isoform, shows important differences in the amino acid residues lining the ligand-binding groove, where the type I protein from animals is more similar to the fungal form of Tom20. Given that the two receptor types from mouse interact with the same set of precursor protein substrates, comparative analysis of the substrate-binding site provides unique insight into the mechanism of substrate recognition. No Tom20-related protein was found in genome sequence data from plants or protozoans, suggesting the receptor Tom20 evolved after the split of animals and fungi from the main lineage of eukaryotes.}, }
@article {pmid15729396, year = {2005}, author = {Stewart, JB and Beckenbach, AT}, title = {Insect mitochondrial genomics: the complete mitochondrial genome sequence of the meadow spittlebug Philaenus spumarius (Hemiptera: Auchenorrhyncha: Cercopoidae).}, journal = {Genome}, volume = {48}, number = {1}, pages = {46-54}, doi = {10.1139/g04-090}, pmid = {15729396}, issn = {0831-2796}, mesh = {Animals ; Base Sequence ; Biological Evolution ; DNA, Mitochondrial/*genetics ; *Genome ; Genomics ; Hemiptera/classification/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames/genetics ; *Phylogeny ; RNA, Transfer/chemistry/genetics ; Sequence Analysis, DNA ; }, abstract = {We present the complete mitochondrial genome sequence of the meadow spittlebug Philaenus spumarius (Auchenorrhyncha: Cercopoidae). This contribution represents the second mitochondrial genome from the Hemiptera and the second of the three hemipteran suborders sampled. The genome is a circular molecule of 16 324 bp with a total A+T content of 77.0% and 76.7% for coding regions only. The gene content, order, and structure are consistent with the Drosophila yakuba genome structure (Clary and Wolstenholme 1985) and the hypothesized ancestral arthropod genome arrangement (Crease 1999). Nucleotide composition and codon usage are near the means observed in other insect mitochondria sequenced to date but have a higher A+T richness compared with the other hemipteran example, the kissing bug Triatoma dimidiata (Dotson and Beard. 2001. Insect Mol. Biol. 10: 205-215). The major noncoding region (the A+T rich region or putative control region) between the small ribosomal subunit and the tRNAIle gene includes two extensive repeat regions. The first repeat region includes 19 tandem repeats of a 46-bp sequence, whereas the second contains a longer sequence (146 bp) tandemly repeated four times.}, }
@article {pmid15721031, year = {2005}, author = {Kunisawa, T}, title = {Branching orders among alpha-proteobacteria and mitochondria inferred from gene transpositions.}, journal = {Journal of theoretical biology}, volume = {234}, number = {1}, pages = {1-5}, doi = {10.1016/j.jtbi.2004.11.004}, pmid = {15721031}, issn = {0022-5193}, mesh = {Alphaproteobacteria/*genetics ; Gene Rearrangement ; *Genes, Bacterial ; Mitochondria/*genetics ; Phylogeny ; }, }
@article {pmid15720402, year = {2005}, author = {Riemenschneider, A and Wegele, R and Schmidt, A and Papenbrock, J}, title = {Isolation and characterization of a D-cysteine desulfhydrase protein from Arabidopsis thaliana.}, journal = {The FEBS journal}, volume = {272}, number = {5}, pages = {1291-1304}, doi = {10.1111/j.1742-4658.2005.04567.x}, pmid = {15720402}, issn = {1742-464X}, mesh = {Amino Acids, Cyclic/metabolism ; Arabidopsis/*enzymology ; Binding Sites ; Cell Nucleus/metabolism ; Cystathionine gamma-Lyase/chemistry/*isolation &amp; purification/*metabolism ; Cysteine/*metabolism ; Escherichia coli/metabolism ; Green Fluorescent Proteins/metabolism ; Mitochondria/metabolism ; Phylogeny ; Pyridoxal Phosphate/*metabolism ; Pyruvic Acid/metabolism ; RNA, Plant/metabolism ; Recombinant Proteins/metabolism ; Subcellular Fractions ; }, abstract = {In several organisms D-cysteine desulfhydrase (D-CDes) activity (EC 4.1.99.4) was measured; this enzyme decomposes D-cysteine into pyruvate, H2S, and NH3. A gene encoding a putative D-CDes protein was identified in Arabidopsis thaliana (L) Heynh. based on high homology to an Escherichia coli protein called YedO that has D-CDes activity. The deduced Arabidopsis protein consists of 401 amino acids and has a molecular mass of 43.9 kDa. It contains a pyridoxal-5'-phosphate binding site. The purified recombinant mature protein had a Km for D-cysteine of 0.25 mm. Only D-cysteine but not L-cysteine was converted by D-CDes to pyruvate, H2S, and NH3. The activity was inhibited by aminooxy acetic acid and hydroxylamine, inhibitors specific for pyridoxal-5'-phosphate dependent proteins, at low micromolar concentrations. The protein did not exhibit 1-aminocyclopropane-1-carboxylate deaminase activity (EC 3.5.99.7) as homologous bacterial proteins. Western blot analysis of isolated organelles and localization studies using fusion constructs with the green fluorescent protein indicated an intracellular localization of the nuclear encoded D-CDes protein in the mitochondria. D-CDes RNA levels increased with proceeding development of Arabidopsis but decreased in senescent plants; D-CDes protein levels remained almost unchanged in the same plants whereas specific D-CDes activity was highest in senescent plants. In plants grown in a 12-h light/12-h dark rhythm D-CDes RNA levels were highest in the dark, whereas protein levels and enzyme activity were lower in the dark period than in the light indicating post-translational regulation. Plants grown under low sulfate concentration showed an accumulation of D-CDes RNA and increased protein levels, the D-CDes activity was almost unchanged. Putative in vivo functions of the Arabidopsisd-CDes protein are discussed.}, }
@article {pmid15713237, year = {2005}, author = {Young, ND and dePamphilis, CW}, title = {Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function.}, journal = {BMC evolutionary biology}, volume = {5}, number = {}, pages = {16}, pmid = {15713237}, issn = {1471-2148}, mesh = {Cell Nucleus/metabolism ; DNA/metabolism ; DNA, Chloroplast ; DNA, Plant ; Evolution, Molecular ; *Gene Expression Regulation, Plant ; Genes, Plant ; Genetic Variation ; Genome, Plant ; Likelihood Functions ; Mitochondria/metabolism ; Models, Genetic ; Mutation ; Orobanchaceae/genetics ; Photosynthesis ; Phylogeny ; Plant Proteins ; Plastids/*genetics ; Selection, Genetic ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The analysis of synonymous and nonsynonymous rates of DNA change can help in the choice among competing explanations for rate variation, such as differences in constraint, mutation rate, or the strength of genetic drift. Nonphotosynthetic plants of the Orobanchaceae have increased rates of DNA change. In this study 38 taxa of Orobanchaceae and relatives were used and 3 plastid genes were sequenced for each taxon.<br><br>RESULTS: Phylogenetic reconstructions of relative rates of sequence evolution for three plastid genes (rbcL, matK and rps2) show significant rate heterogeneity among lineages and among genes. Many of the non-photosynthetic plants have increases in both synonymous and nonsynonymous rates, indicating that both (1) selection is relaxed, and (2) there has been a change in the rate at which mutations are entering the population in these species. However, rate increases are not always immediate upon loss of photosynthesis. Overall there is a poor correlation of synonymous and nonsynonymous rates. There is, however, a strong correlation of synonymous rates across the 3 genes studied and the lineage-speccific pattern for each gene is strikingly similar. This indicates that the causes of synonymous rate variation are affecting the whole plastid genome in a similar way. There is a weaker correlation across genes for nonsynonymous rates. Here the picture is more complex, as could be expected if there are many causes of variation, differing from taxon to taxon and gene to gene.<br><br>CONCLUSIONS: The distinctive pattern of rate increases in Orobanchaceae has at least two causes. It is clear that there is a relaxation of constraint in many (though not all) non-photosynthetic lineages. However, there is also some force affecting synonymous sites as well. At this point, it is not possible to tell whether it is generation time, speciation rate, mutation rate, DNA repair efficiency or some combination of these factors.}, }
@article {pmid15712112, year = {2004}, author = {Hoshiyama, D and Kuma, K and Miyata, T}, title = {Markedly reduced evolutionary rates of transcription factors and cytoplasmic ribosomal RNAs and proteins in higher vertebrates and their evolutionary implications.}, journal = {Genome informatics. International Conference on Genome Informatics}, volume = {15}, number = {1}, pages = {82-92}, pmid = {15712112}, issn = {0919-9454}, mesh = {Animals ; Cytoplasm/genetics ; *Evolution, Molecular ; Mammals/genetics ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal/*genetics ; Ribosomes/genetics ; Takifugu/genetics ; Time ; Transcription Factors/*genetics ; Vertebrates/*genetics ; }, abstract = {To reveal the relationship between organismal evolution and the molecular evolutionary rate, the temporal pattern of evolutionary rates were investigated for various genes during the course of deuterostome evolution. Deuterostome lineage leading to extant mammals was tentatively divided into two periods (the First and the Latter periods) by the time of divergence of bony fishes and mammals. For each of the First and the Latter period, evolutionary rates of 207 gene sets were calculated. In the Latter period, the evolutionary rate was significantly reduced in such informational genes as transcription factors and cytoplasmic ribosomal RNAs and proteins. In contrast, a variety of enzymes and mitochondrial ribosomal proteins evolve at nearly constant rate throughout the First and the Latter periods. The present result suggests that the increase of gene number by extensive gene duplications in the early evolution of vertebrates is responsible for the decrease of evolutionary rate.}, }
@article {pmid15711972, year = {2005}, author = {Fallahi, M and Crosthwait, J and Calixte, S and Bonen, L}, title = {Fate of mitochondrially located S19 ribosomal protein genes after transfer of a functional copy to the nucleus in cereals.}, journal = {Molecular genetics and genomics : MGG}, volume = {273}, number = {1}, pages = {76-83}, pmid = {15711972}, issn = {1617-4615}, mesh = {Amino Acid Sequence ; Base Sequence ; Cell Nucleus/*genetics ; DNA Primers ; Edible Grain/*genetics ; *Evolution, Molecular ; Expressed Sequence Tags ; Gene Expression Regulation, Plant/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Pseudogenes/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Ribosomal Proteins/*metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Mitochondrial genes for ribosomal proteins undergo relatively frequent transfer to the nucleus during plant evolution, and when migration is successful the mitochondrial copy becomes redundant and can be lost. We have examined the status of the mitochondrial rps19 gene for ribosomal protein S19 in closely related cereals. In oat, the mitochondrial rps19 reading frame is blocked by a premature termination codon and lacks abundant transcripts, whereas in the mitochondria of wheat and rye rps19 is a 5'-truncated pseudogene which is co-transcribed with the downstream nad4L gene. In barley and maize, rps19 sequences are completely absent from the mitochondrion. All five of these cereals differ from rice, in which an intact, transcriptionally active mitochondrial rps19 gene is found, and this is preceded by rpl2 in an organization reminiscent of that seen in bacteria. Based on EST sequence data for maize, barley and wheat, it can be inferred that a functional rps19 gene was transferred to the nucleus prior to the divergence of the maize and rice lineages (approximately 50 million years ago), and the present-day nuclear copies encode an N-terminal sequence related to the mitochondrial targeting signal of Hsp70 (heat shock protein) in cereals. Subsequent evolutionary events have included independent losses of the mitochondrial copies in the barley and maize lineages. In the rice lineage, on the other hand, the nuclear copy was lost. This is reflected in the persistence of the mitochondrial rps19 after a period during which rps19 genes coexisted in both compartments. These observations illustrate the dynamic nature of the location and structure of genes for mitochondrial ribosomal proteins in flowering plants.}, }
@article {pmid15708540, year = {2005}, author = {Portincasa, P and Grattagliano, I and Palmieri, VO and Palasciano, G}, title = {Nonalcoholic steatohepatitis: recent advances from experimental models to clinical management.}, journal = {Clinical biochemistry}, volume = {38}, number = {3}, pages = {203-217}, doi = {10.1016/j.clinbiochem.2004.10.014}, pmid = {15708540}, issn = {0009-9120}, mesh = {Animals ; Diagnosis, Differential ; *Disease Models, Animal ; Fatty Liver/*metabolism/pathology/*therapy ; Hepatitis/metabolism/pathology/therapy ; Humans ; Insulin Resistance ; Microsomes, Liver/metabolism ; Mitochondria, Liver/metabolism/pathology ; Oxidation-Reduction ; Oxidative Stress ; Peroxisomes/metabolism ; }, abstract = {A condition defined as nonalcoholic fatty liver disease (NAFLD) is frequently found in humans. Deemed as a benign condition until recently, more emphasis is now put on the potential harmful evolution of the inflammatory form, that is, nonalcoholic steatohepatitis (NASH), toward end-stage liver disease. This review highlights the major morphologic and pathophysiological features of NASH. The link between experimental biochemical findings in animal models and clinical and therapeutic approaches in humans is discussed. Once all the other causes of persistent elevation of serum transaminase levels have been excluded, the diagnosis of NASH can be only confirmed by liver histology. Other noninvasive diagnostic tools, however, are being investigated to assess specific subcellular functions and to allow the follow-up of patients at higher risk for major liver dysfunction. A better understanding of various pathogenic aspects of NASH will help in identifying potential therapeutic approaches in these patients.}, }
@article {pmid15707358, year = {2005}, author = {Arnesano, F and Banci, L and Bertini, I and Martinelli, M}, title = {Ortholog search of proteins involved in copper delivery to cytochrome C oxidase and functional analysis of paralogs and gene neighbors by genomic context.}, journal = {Journal of proteome research}, volume = {4}, number = {1}, pages = {63-70}, doi = {10.1021/pr049862f}, pmid = {15707358}, issn = {1535-3893}, mesh = {Animals ; Bacterial Proteins ; Carrier Proteins ; Cation Transport Proteins/genetics/*physiology ; Copper/*metabolism ; Copper Transport Proteins ; Databases, Protein ; Electron Transport Chain Complex Proteins ; Electron Transport Complex IV/*biosynthesis/genetics ; Genomics/*methods ; Humans ; Membrane Proteins/genetics/physiology ; Mitochondria/genetics ; Mitochondrial Proteins ; Molecular Chaperones ; Phylogeny ; Proteins/genetics/physiology ; }, abstract = {Cytochrome c oxidase (COX) is a multi-subunit enzyme of the mitochondrial respiratory chain. Delivery of metal cofactors to COX is essential for assembly, which represents a long-standing puzzle. The proteins Cox17, Sco1/2, and Cox11 are necessary for copper insertion into CuA and CuB redox centers of COX in eukaryotes. A genome-wide search in all prokaryotic genomes combined with genomic context reveals that only Sco and Cox11 have orthologs in prokaryotes. However, while Cox11 function is confined to COX assembly, Sco acts as a multifunctional linker connecting a variety of biological processes. Multifunctionality is achieved by gene duplication and paralogs. Neighbor genes of Sco paralogs often encode cuproenzymes and cytochrome c domains and, in some cases, Sco is fused to cytochrome c. This led us to suggest that cytochrome c might be relevant to Sco function and the two proteins might jointly be involved in COX assembly. Sco is also related, in terms of gene neighborhood and phylogenetic occurrence, to a newly detected protein involved in copper trafficking in bacteria and archaea, but with no sequence similarity to the mitochondrial copper chaperone Cox17. By linking the assembly system to the copper uptake system, Sco allows COX to face alternative copper trafficking pathways.}, }
@article {pmid15706032, year = {2005}, author = {Rinehart, J and Krett, B and Rubio, MA and Alfonzo, JD and Söll, D}, title = {Saccharomyces cerevisiae imports the cytosolic pathway for Gln-tRNA synthesis into the mitochondrion.}, journal = {Genes &amp; development}, volume = {19}, number = {5}, pages = {583-592}, pmid = {15706032}, issn = {0890-9369}, mesh = {Amino Acyl-tRNA Synthetases/genetics/*metabolism ; Biological Transport, Active/genetics/physiology ; Gene Expression Regulation, Fungal/genetics/physiology ; Mitochondria/genetics/*physiology ; Protein Biosynthesis/genetics/*physiology ; Protein Transport/genetics/physiology ; RNA, Transfer, Amino Acyl/genetics/*metabolism ; RNA, Transfer, Gln/genetics/*metabolism ; Saccharomyces cerevisiae/genetics/*physiology ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; }, abstract = {Aminoacyl-tRNA (aa-tRNA) formation, an essential process in protein biosynthesis, is generally achieved by direct attachment of an amino acid to tRNA by the aa-tRNA synthetases. An exception is Gln-tRNA synthesis, which in eukaryotes is catalyzed by glutaminyl-tRNA synthetase (GlnRS), while most bacteria, archaea, and chloroplasts employ the transamidation pathway, in which a tRNA-dependent glutamate modification generates Gln-tRNA. Mitochondrial protein synthesis is carried out normally by mitochondrial enzymes and organelle-encoded tRNAs that are different from their cytoplasmic counterparts. Early work suggested that mitochondria use the transamidation pathway for Gln-tRNA formation. We found no biochemical support for this in Saccharomyces cerevisiae mitochondria, but demonstrated the presence of the cytoplasmic GlnRS in the organelle and its involvement in mitochondrial Gln-tRNA synthesis. In addition, we showed in vivo localization of cytoplasmic tRNAGln in mitochondria and demonstrated its role in mitochondrial translation. We furthermore reconstituted in vitro cytoplasmic tRNAGln import into mitochondria by a novel mechanism. This tRNA import mechanism expands our knowledge of RNA trafficking in the eukaryotic cell. These findings change our view of the evolution of organellar protein synthesis.}, }
@article {pmid15703239, year = {2005}, author = {Lavrov, DV and Forget, L and Kelly, M and Lang, BF}, title = {Mitochondrial genomes of two demosponges provide insights into an early stage of animal evolution.}, journal = {Molecular biology and evolution}, volume = {22}, number = {5}, pages = {1231-1239}, doi = {10.1093/molbev/msi108}, pmid = {15703239}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; Genetic Code ; *Genome ; Introns ; Invertebrates/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Porifera/*genetics ; RNA, Ribosomal/*genetics ; RNA, Transfer/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {Mitochondrial DNA (mtDNA) of multicellular animals (Metazoa) is typically a small (approximately 16 kbp), circular-mapping molecule that encodes 37 tightly packed genes. The structures of mtDNA-encoded transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs) are usually highly unorthodox, and proteins are translated with multiple deviations from the standard genetic code. In contrast, mtDNA of the choanoflagellate Monosiga brevicollis, the closest unicellular relative of animals, is four times larger, contains 1.5 times as many genes, and lacks mentioned peculiarities of animal mtDNA. To investigate the evolutionary transition that led to the specific organization of metazoan mtDNA, we determined complete mitochondrial sequences from the demosponges Geodia neptuni and Tethya actinia, two representatives of the most basal animal phylum, the Porifera. We found that poriferan mtDNAs resemble those of other animals in their compact organization, lack of introns, and a well-conserved animal-like gene order. Yet, they contain several extra genes, encode bacterial-like rRNAs and tRNAs, and use a minimally derived genetic code. Our findings suggest that the evolution of the typical metazoan mtDNA has been a multistep process in which the compact genome organization and the reduced gene content were established prior to the reduction of tRNA and rRNA structures and the introduction of multiple changes of the translation code.}, }
@article {pmid15703189, year = {2005}, author = {Srivastava, S and Moraes, CT}, title = {Double-strand breaks of mouse muscle mtDNA promote large deletions similar to multiple mtDNA deletions in humans.}, journal = {Human molecular genetics}, volume = {14}, number = {7}, pages = {893-902}, pmid = {15703189}, issn = {0964-6906}, support = {R01 EY010804/EY/NEI NIH HHS/United States ; EY 10804/EY/NEI NIH HHS/United States ; GM 55766/GM/NIGMS NIH HHS/United States ; R01 MH085801/MH/NIMH NIH HHS/United States ; R56 NS041777/NS/NINDS NIH HHS/United States ; NS 041777/NS/NINDS NIH HHS/United States ; R01 NS041777/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Blotting, Southern ; *DNA Damage ; DNA Primers/chemistry ; DNA, Mitochondrial/*genetics/metabolism ; Disease Models, Animal ; Electron Transport ; *Gene Deletion ; Humans ; Immunohistochemistry ; Mice ; Mice, Transgenic ; Microscopy, Electron ; Mitochondria/metabolism ; *Models, Genetic ; Molecular Sequence Data ; Muscle, Skeletal/metabolism ; Muscles/*metabolism ; Muscular Diseases ; Phylogeny ; Polymerase Chain Reaction ; Protein Structure, Tertiary ; Sequence Analysis, DNA ; Transgenes ; }, abstract = {Mitochondrial DNA (mtDNA) deletions are a common cause of mitochondrial disorders and have been found to accumulate during normal aging. Despite the fact that hundreds of deletions have been characterized at the molecular level, their mechanisms of genesis are unknown. We tested the effect of double-strand breaks of muscle mtDNA by developing a mouse model in which a mitochondrially targeted restriction endonuclease (PstI) was expressed in skeletal muscle of mice. Because mouse mtDNA harbors two PstI sites, transgenic founders developed a mitochondrial myopathy associated with mtDNA depletion. The founders showed a chimeric pattern of transgene expression and their residual level of wild-type mtDNA in muscle was approximately 40% of controls. We were able to identify the formation of large mtDNA deletions in muscle of transgenic mice. A family of mtDNA deletions was identified, and most of these rearrangements involved one of the PstI sites and the 3' end of the D-loop region. The deletions had no or small direct repeats at the breakpoint region. These features are essentially identical to the ones observed in humans with multiple mtDNA deletions in muscle, suggesting that double-strand DNA breaks mediate the formation of large mtDNA deletions.}, }
@article {pmid15700763, year = {2005}, author = {Hu, M and Gasser, RB and Chilton, NB and Beveridge, I}, title = {Genetic variation in the mitochondrial cytochrome c oxidase subunit 1 within three species of Progamotaenia (Cestoda: Anoplocephalidae) from macropodid marsupials.}, journal = {Parasitology}, volume = {130}, number = {Pt 1}, pages = {117-129}, doi = {10.1017/s0031182004006377}, pmid = {15700763}, issn = {0031-1820}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cestoda/*enzymology/*genetics ; Cestode Infections/parasitology/veterinary ; Electron Transport Complex IV/*genetics ; *Genetic Variation ; Macropodidae/*parasitology ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {Sequence variation within 3 morphologically defined species of the anoplocephalid cestode genus Progamotaenia (P. ewersi, P. macropodis and P. zschokkei) was investigated using the cytochrome c oxidase subunit 1 gene. The magnitude of genetic variation detected within each morphospecies suggests that, in each instance, several cryptic species are present. Within P. ewersi, 5 genetically distict groups of cestodes were detected, 1 shared by Macropus robustus and M. parryi in Queensland, 1 in M. agilis from Queensland, 1 in Petrogale assimilis from Queensland, 1 in Macropus fuliginosus from South Australia and 1 in Wallabia bicolor from Victoria. In P. macropodis, cestodes from M. robustus from Queensland, Western Australia and the Northern Territory, M. parryi from Queensland and M. eugenii from South Australia were genetically distinct from those in Wallabia bicolor from Queensland and Victoria and from M. fuliginosus from South Australia. P. zschokkei consisted of a number of genetically distinct groups of cestodes, 1 in Lagorchestes conspicillatus and L. hirsutus from Queensland and the Northern Territory respectively, 1 in Petrogale herberti, P. assimilis and M. dorsalis from Queensland, 1 in Onychogalea fraenata from Queensland, 1 in M. agilis from Queensland and 1 in Thylogale stigmatica and T. thetis from Queensland. In general, genetic groups within each morphospecies were host specific and occurred predominantly in a particular macropodid host clade. Comparison of genetic relationships of cestodes with the phylogeny of their hosts revealed examples of colonization (P. zschokkei in M. agilis) and of host switching (P. zschokkei in M. dorsalis).}, }
@article {pmid15700158, year = {2005}, author = {Dee, CT and Moffat, KG}, title = {A novel family of mitochondrial proteins is represented by the Drosophila genes slmo, preli-like and real-time.}, journal = {Development genes and evolution}, volume = {215}, number = {5}, pages = {248-254}, pmid = {15700158}, issn = {0949-944X}, mesh = {Adaptor Proteins, Signal Transducing/genetics/*metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Drosophila/embryology/*genetics ; Drosophila Proteins/*genetics/*metabolism ; Drosophila melanogaster ; Gene Expression Regulation, Developmental ; Homeodomain Proteins/*genetics ; Intestinal Mucosa/metabolism ; Intestines/embryology ; Membrane Proteins ; Mice ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; NIH 3T3 Cells ; Nervous System/embryology/metabolism ; Nuclear Proteins/*genetics ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; Transfection ; }, abstract = {Mitochondria play essential roles in development and disease. The characterisation of mitochondrial proteins is therefore of particular importance. The slowmo (slmo) gene of Drosophila melanogaster has been shown to encode a novel type of mitochondrial protein, and is essential in the developing central nervous system. The Slmo protein contains a conserved PRELI/MSF1p' domain, found in proteins from a wide variety of eukaryotic organisms. However, the function of the proteins of this family is currently unknown. In this study, the evolutionary relationships between members of the PRELI/MSF1p' family are described, and we present the first analysis of two novel Drosophila genes predicted to encode proteins of this type. The first of these, preli-like (prel), is expressed ubiquitously during embryonic development, whilst the second, real-time (retm), is expressed dynamically in the developing gut and central nervous system. retm encodes a member of a novel conserved subclass of larger PRELI/MSF1p' domain proteins, which also contain the CRAL-TRIO motif thought to mediate the transport of small hydrophobic ligands. Here we provide evidence that, like Slmo, both the Prel and Retm proteins are localised to the mitochondria, indicating that the function of the PRELI/MSF1p' domain is specific to this organelle.}, }
@article {pmid15696375, year = {2005}, author = {Swire, J and Judson, OP and Burt, A}, title = {Mitochondrial genetic codes evolve to match amino acid requirements of proteins.}, journal = {Journal of molecular evolution}, volume = {60}, number = {1}, pages = {128-139}, pmid = {15696375}, issn = {0022-2844}, mesh = {Amino Acids/*genetics ; Animals ; Base Sequence ; Codon/*genetics ; DNA, Mitochondrial/*genetics ; Databases, Nucleic Acid ; *Evolution, Molecular ; Humans ; Mitochondrial Proteins/*genetics ; Models, Genetic ; Mutation ; Phylogeny ; Selection, Genetic ; }, abstract = {Mitochondria often use genetic codes different from the standard genetic code. Now that many mitochondrial genomes have been sequenced, these variant codes provide the first opportunity to examine empirically the processes that produce new genetic codes. The key question is: Are codon reassignments the sole result of mutation and genetic drift? Or are they the result of natural selection? Here we present an analysis of 24 phylogenetically independent codon reassignments in mitochondria. Although the mutation-drift hypothesis can explain reassignments from stop to an amino acid, we found that it cannot explain reassignments from one amino acid to another. In particular--and contrary to the predictions of the mutation-drift hypothesis--the codon involved in such a reassignment was not rare in the ancestral genome. Instead, such reassignments appear to take place while the codon is in use at an appreciable frequency. Moreover, the comparison of inferred amino acid usage in the ancestral genome with the neutral expectation shows that the amino acid gaining the codon was selectively favored over the amino acid losing the codon. These results are consistent with a simple model of weak selection on the amino acid composition of proteins in which codon reassignments are selected because they compensate for multiple slightly deleterious mutations throughout the mitochondrial genome. We propose that the selection pressure is for reduced protein synthesis cost: most reassignments give amino acids that are less expensive to synthesize. Taken together, our results strongly suggest that mitochondrial genetic codes evolve to match the amino acid requirements of proteins.}, }
@article {pmid15689432, year = {2005}, author = {Seif, E and Leigh, J and Liu, Y and Roewer, I and Forget, L and Lang, BF}, title = {Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms.}, journal = {Nucleic acids research}, volume = {33}, number = {2}, pages = {734-744}, pmid = {15689432}, issn = {1362-4962}, mesh = {Bacteria/enzymology/genetics ; Base Sequence ; Conserved Sequence ; DNA Transposable Elements ; DNA, Mitochondrial/*chemistry ; Endonucleases/genetics ; Fungi/classification/*genetics ; Gene Transfer, Horizontal ; Genes, Fungal ; Genetic Code ; *Genome, Fungal ; Introns ; Magnoliopsida/genetics ; Mitochondria/enzymology/*genetics ; Mitochondrial Proteins/classification/genetics ; Molecular Sequence Data ; Phylogeny ; RNA/*chemistry/genetics/metabolism ; RNA, Fungal/chemistry/genetics/metabolism ; RNA, Messenger/chemistry ; RNA, Mitochondrial ; RNA, Ribosomal/chemistry ; Ribonuclease P/*genetics ; }, abstract = {To generate data for comparative analyses of zygomycete mitochondrial gene expression, we sequenced mtDNAs of three distantly related zygomycetes, Rhizopus oryzae, Mortierella verticillata and Smittium culisetae. They all contain the standard fungal mitochondrial gene set, plus rnpB, the gene encoding the RNA subunit of the mitochondrial RNase P (mtP-RNA) and rps3, encoding ribosomal protein S3 (the latter lacking in R.oryzae). The mtP-RNAs of R.oryzae and of additional zygomycete relatives have the most eubacteria-like RNA structures among fungi. Precise mapping of the 5' and 3' termini of the R.oryzae and M.verticillata mtP-RNAs confirms their expression and processing at the exact sites predicted by secondary structure modeling. The 3' RNA processing of zygomycete mitochondrial mRNAs, SSU-rRNA and mtP-RNA occurs at the C-rich sequence motifs similar to those identified in fission yeast and basidiomycete mtDNAs. The C-rich motifs are included in the mature transcripts, and are likely generated by exonucleolytic trimming of RNA 3' termini. Zygomycete mtDNAs feature a variety of insertion elements: (i) mtDNAs of R.oryzae and M.verticillata were subject to invasions by double hairpin elements; (ii) genes of all three species contain numerous mobile group I introns, including one that is closest to an intron that invaded angiosperm mtDNAs; and (iii) at least one additional case of a mobile element, characterized by a homing endonuclease insertion between partially duplicated genes [Paquin,B., Laforest,M.J., Forget,L., Roewer,I., Wang,Z., Longcore,J. and Lang,B.F. (1997) Curr. Genet., 31, 380-395]. The combined mtDNA-encoded proteins contain insufficient phylogenetic signal to demonstrate monophyly of zygomycetes.}, }
@article {pmid15683935, year = {2005}, author = {Daniels, SR and Heideman, NJ and Hendricks, MG and Mokone, ME and Crandall, KA}, title = {Unraveling evolutionary lineages in the limbless fossorial skink genus Acontias (Sauria: Scincidae): are subspecies equivalent systematic units?.}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {3}, pages = {645-654}, doi = {10.1016/j.ympev.2004.11.011}, pmid = {15683935}, issn = {1055-7903}, mesh = {Animals ; *Biological Evolution ; Cytochromes b/genetics ; Electron Transport Complex IV/genetics ; Lizards/*classification/*genetics ; Mitochondria/genetics ; *Phylogeny ; RNA, Ribosomal ; RNA, Ribosomal, 16S ; }, abstract = {Subspecies in the limbless, endemic African fossorial skink genus Acontias constitute ill-defined operational taxonomic units, consequently considerable systematic debate has lingered on the systematic diversity within Acontias. In the present study, the systematic affinities among acontine taxa are explored with the utility of partial sequence data from two mitochondrial gene loci (16S rRNA and cytochrome oxidase subunit 1 (COI)) for all taxa, while two additional loci (12S rRNA, cytochrome b) were used to investigate relationships within the Acontias meleagris complex. Phylogenetic results, derived from the combined analysis, revealed two monophyletic clades. Clade 1 is comprised of small-bodied skinks while clade 2 comprised the medium bodied skinks. Within clade 2 none of the traditionally recognized subspecies formed reciprocally monophyletic groups. Furthermore, constraining the topology and enforcing sister taxa relationships between the assumed subspecies, consistently recovered a topology that was statistically significant worse, indicating that the traditionally designated subspecies groupings probably represent invalid taxonomic units, thus clearly reflecting considerable discord with current taxonomy. The burrowing life style of these lizards has probably led to marked convergent evolution and constrained the development of diagnostic morphological characters among these species. Morphological similarities in color as well as scale architecture within Acontias are labile and highly homoplaseous and do not reflect the evolutionary history of the group. Taxonomic implications of these results are discussed.}, }
@article {pmid15683934, year = {2005}, author = {Mallarino, R and Bermingham, E and Willmott, KR and Whinnett, A and Jiggins, CD}, title = {Molecular systematics of the butterfly genus Ithomia (Lepidoptera: Ithomiinae): a composite phylogenetic hypothesis based on seven genes.}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {3}, pages = {625-644}, doi = {10.1016/j.ympev.2004.10.021}, pmid = {15683934}, issn = {1055-7903}, mesh = {Animals ; Butterflies/classification/*genetics ; DNA, Mitochondrial ; Microtubule Proteins/genetics ; Mitochondria/genetics ; *Phylogeny ; }, abstract = {Butterflies in the nymphalid subfamily Ithomiinae are brightly colored and involved in mimicry. Here we present a phylogenetic hypothesis for 23 of the 24 species in the genus Ithomia, based on seven different gene regions, representing 5 linkage groups and 4469 bp. We sequenced varying length regions of the following genes: (1) elongation factor 1alpha (Ef1alpha; 1028 bp); (2) tektin (tektin; 715 bp); (3) wingless (wg; 405 bp); (4) ribosomal protein L5 (RpL5; 722 bp, exons 1, 2, 3, and introns 1 and 2); and (5) mitochondrial cytochrome oxidase I, II (Co1 and Co2 and intervening leucine tRNA; 1599 bp). The results show incongruence between some genetic loci, although when alternate topologies are compared statistically it was generally true that one topology was supported by a majority of loci sampled. This highlights the need to sample widely across the genome in order to obtain a well-supported phylogenetic hypothesis. A combined evidence topology is presented based on a Bayesian analysis of all the gene regions, except the fast-evolving RpL5. The resulting hypothesis is concordant with the most probable relationships determined from our topological comparisons, although in some parts of the tree relationships remain weakly supported. The tree suggests diversification has largely occurred within biogeographic regions such as Central America, the Amazon, the southern and northern Andes, with only occasional dispersal (or vicariance) between such regions. This phylogenetic hypothesis can now be used to investigate patterns of diversification across the genus, such as the potential role of color pattern changes in speciation.}, }
@article {pmid15683933, year = {2005}, author = {Trontelj, P and Utevsky, SY}, title = {Celebrity with a neglected taxonomy: molecular systematics of the medicinal leech (genus Hirudo).}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {3}, pages = {616-624}, doi = {10.1016/j.ympev.2004.10.012}, pmid = {15683933}, issn = {1055-7903}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/genetics ; Hirudo medicinalis/*classification/*genetics ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; RNA, Ribosomal ; }, abstract = {The medicinal leech is the most famous representative of the Hirudinea. It is one of few invertebrates widely used in medicine and as a scientific model object. It has recently been given considerable conservation effort. Despite all attention there is confusion regarding the taxonomic status of different morphological forms, with many different species described in the past, but only two generally accepted at present. The results of the phylogenetic analysis of a nuclear (ITS2+5.8S rRNA) and two mitochondrial gene sequences (12S rRNA, COI) suggest that the genus Hirudo is monophyletic. It consists, apart form the type Hirudo medicinalis and the East Asian Hirudo nipponia, of three other, neglected species. All of them have already been described either as species or morphological variety, and can readily be identified by their coloration pattern. The type species is in weakly supported sister relation with Hirudo sp. n. (described as variety orientalis) from Transcaucasia and Iran. Sister to them stands Hirudo verbana from southeastern Europe and Turkey, which is nowadays predominantly bred in leech farms and used as 'medicinal leech.' The North African Hirudo troctina is the sister taxon to this group of Western Eurasian species, whereas the basal split is between H. nipponia and the Western Palaearctic clade.}, }
@article {pmid15683930, year = {2005}, author = {Iglésias, SP and Lecointre, G and Sellos, DY}, title = {Extensive paraphylies within sharks of the order Carcharhiniformes inferred from nuclear and mitochondrial genes.}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {3}, pages = {569-583}, doi = {10.1016/j.ympev.2004.10.022}, pmid = {15683930}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Genes, RAG-1 ; Likelihood Functions ; Mitochondria/*genetics ; Phylogeny ; Polymorphism, Genetic ; RNA, Ribosomal, 16S ; Sequence Alignment ; Sharks/classification/*genetics ; }, abstract = {Using nuclear coding and mitochondrial ribosomal genes we try to clarify relationships within Carcharhiniformes with special focus on the two most problematic groups: scyliorhinids and triakids. The mitochondrial aligned sequences are 1542 bp long, and include principally portion of 16S rRNA gene. They are obtained for two outgroup species and 43 Carcharhiniformes species, covering 5 of the 8 families and 15 of the 48 genera of the order. The nuclear RAG1 sequences are 1454 bp long, and are obtained for 17 species representative of the diversity of all species sampled. We used Maximum Parsimony and Maximum Likelihood criteria for tree reconstruction. Paraphylies within the family Scyliorhinidae was proposed for the first time by Maisey [Zool. J. Linn. Soc. 82, 33, 1984] in a morphological cladistic analysis. This result has never been proposed again until recently from molecular phylogenies [Mol. Phylogenet. Evol. 31, 214, 2004]. Here, independent and simultaneous analyses of nuclear and mitochondrial data are congruent in supporting the paraphyly of scyliorhinids. Two groups of scyliorhinids are obtained, thoroughly in line with discrimination proposed by previous authors, based on presence/absence of supraorbital crests on the chondrocranium. The first group (Scyliorhinus+Cephaloscyllium) is basal within carcharhiniforms and the second group (Apristurus+Asymbolus+Cephalurus+Galeus+Parmaturus) is sister group of all the other families investigated (Carcharhinidae, Proscyllidae, Pseudotriakidae, and Triakidae). The paraphyly of triakids appeared probable but more investigations are needed. In conclusion several independent morphological and molecular phylogenetic studies support paraphyly within scyliorhinids. So we propose a new classification for the group, with the redefinition of the family Scyliorhinidae sensu stricto and the resurrection of the family Pentanchidae with a new definition.}, }
@article {pmid15683927, year = {2005}, author = {Holcroft, NI}, title = {A molecular analysis of the interrelationships of tetraodontiform fishes (Acanthomorpha: Tetraodontiformes).}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {3}, pages = {525-544}, doi = {10.1016/j.ympev.2004.11.003}, pmid = {15683927}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Bayes Theorem ; *Evolution, Molecular ; Homeodomain Proteins/genetics ; Mitochondria/genetics ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Tetraodontiformes/*genetics ; }, abstract = {Tetraodontiform fishes (e.g., triggerfishes, boxfishes, pufferfishes, and giant ocean sunfishes) have long been recognized as a monophyletic group. Morphological analyses have resulted in conflicting hypotheses of relationships among the tetraodontiform families. Molecular data from the single-copy nuclear gene RAG1 and from two mitochondrial ribosomal genes, 12S and 16S, were used to test these morphology-based hypotheses. Total evidence (RAG1+12S+16S), RAG1-only, and mitochondrial-only analyses were performed using both maximum parsimony and Bayesian criteria. Total evidence and RAG1-only analyses recover a monophyletic Tetraodontiformes. However, the relationships recovered within the order differ, and none completely conform to previous hypotheses. Analysis of mitochondrial data alone fails to recover a monophyletic Tetraodontiformes and therefore does not support any of the morphology-based topologies. The RAG1 data appear to give the best estimate of tetraodontiform phylogeny, resulting in many strongly supported nodes and showing a high degree of congruence between both parsimony and Bayesian analyses. All analyses recover every tetraodontiform family for which more than one representative is included as a strongly supported monophyletic group. Balistidae and Monacanthidae are recovered as sister groups with robust support in every analysis, and all analyses except the Bayesian analyses of the mitochondrial data alone recover a strongly supported sister-group relationship between Tetraodontidae and Diodontidae. Many of the intrafamilial relationships recovered from the molecular data presented here corroborate previous morphological hypotheses.}, }
@article {pmid15683923, year = {2005}, author = {Jesus, J and Brehm, A and Harris, DJ}, title = {Phylogenetic relationships of Hemidactylus geckos from the Gulf of Guinea islands: patterns of natural colonizations and anthropogenic introductions estimated from mitochondrial and nuclear DNA sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {3}, pages = {480-485}, doi = {10.1016/j.ympev.2004.11.006}, pmid = {15683923}, issn = {1055-7903}, mesh = {Africa, Western ; Animals ; Cytochromes b/genetics ; *Genes, mos ; Lizards/*genetics ; Mitochondria/*genetics ; Phosphopyruvate Hydratase/*genetics ; *Phylogeny ; RNA, Ribosomal ; RNA, Ribosomal, 16S ; }, abstract = {Mitochondrial DNA (12S rRNA, 16S rRNA, and cytochrome b) sequences and nuclear sequences (C-mos and alpha-Enolase) were analyzed within all known Hemidactylus species from all three volcanic islands in the Gulf of Guinea that have never been connected to the continent. These comprise both endemic and widespread species. Our aim was to determine if the widespread species was introduced anthropogenically, to determine the number of distinct genetic lineages within the islands, and to determine if the endemic forms constituted a monophyletic group. Our results suggest that a previously undescribed species on São Tomé is the sister taxon to Hemidactylus newtoni, endemic to Annobon. Genetic variation between populations of Hemidactylus greefii from São Tomé and Principe is very high based on mtDNA sequences, but the forms cannot be distinguished using the nuclear DNA sequences. Hemidactylus mabouia appears to have been anthropogenically introduced to all three islands. The island endemics do not form a monophyletic group, suggesting multiple independent colonizations of the islands.}, }
@article {pmid15683922, year = {2005}, author = {Castro, LR and Dowton, M}, title = {The position of the Hymenoptera within the Holometabola as inferred from the mitochondrial genome of Perga condei (Hymenoptera: Symphyta: Pergidae).}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {3}, pages = {469-479}, doi = {10.1016/j.ympev.2004.11.005}, pmid = {15683922}, issn = {1055-7903}, mesh = {Amino Acid Sequence ; Animals ; Evolution, Molecular ; Hymenoptera/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {We sequenced most of the mitochondrial genome of the sawfly Perga condei (Insecta: Hymenoptera: Symphyta: Pergidae) and tested different models of phylogenetic reconstruction in order to resolve the position of the Hymenoptera within the Holometabola, using mitochondrial genomes. The mitochondrial genome sequenced for P. condei had less compositional bias and slower rates of molecular evolution than the honeybee, as well as a less rearranged genome organization. Phylogenetic analyses showed that, when using mitochondrial genomes, both adequate taxon sampling and more realistic models of analysis are necessary to resolve relationships among insect orders. Both parsimony and Bayesian analyses performed better when nucleotide instead of amino acid sequences were used. In particular, this study supports the placement of the Hymenoptera as sister group to the Mecopterida.}, }
@article {pmid15674770, year = {2004}, author = {Portner, HO}, title = {Climate variability and the energetic pathways of evolution: the origin of endothermy in mammals and birds.}, journal = {Physiological and biochemical zoology : PBZ}, volume = {77}, number = {6}, pages = {959-981}, doi = {10.1086/423742}, pmid = {15674770}, issn = {1522-2152}, mesh = {Adaptation, Physiological ; Animals ; *Biological Evolution ; Birds/*physiology ; Cell Membrane/physiology ; *Climate ; Environment ; Invertebrates/physiology ; Mammals/*physiology ; Mitochondria/physiology ; Oxygen ; Reptiles/physiology ; Thermogenesis/*genetics/*physiology ; }, abstract = {Large-scale climate oscillations in earth's history have influenced the directions of evolution, last but not least, through mass extinction events. This analysis tries to identify some unifying forces behind the course of evolution that favored an increase in organismic complexity and performance, paralleled by an increase in energy turnover, and finally led to endothermy. The analysis builds on the recent concept of oxygen-limited thermal tolerance and on the hypothesis that unifying principles exist in the temperature-dependent biochemical design of the eukaryotic cell in animals. The comparison of extant water-breathing and air-breathing animal species from various climates provides a cause-and-effect understanding of the trade-offs and constraints in thermal adaptation and their energetic consequences. It is hypothesized that the high costs of functional adaptation to fluctuating temperatures, especially in the cold (cold eurythermy), cause an increase in energy turnover and, at the same time, mobility and agility. These costs are associated with elevated mitochondrial capacities at minimized levels of activation enthalpies for proton leakage. Cold eurythermy is seen as a precondition for the survival of evolutionary crises elicited by repeated cooling events during extreme climate fluctuations. The costs of cold eurythermy appear as the single most important reason why metazoan evolution led to life forms with high energy turnover. They also explain why dinosaurs were able to live in subpolar climates. Finally, they give insight into the pathways, benefits, and trade-offs involved in the evolution of constant, elevated body temperature maintained by endothermy. Eurythermy, which encompasses cold tolerance, is thus hypothesized to be the "missing link" between ectothermy and endothermy. Body temperatures between 32 degrees and 42 degrees C in mammals and birds then result from trade-offs between the limiting capacities of ventilation and circulation and the evolutionary trend to maximize performance at the warm end of the thermal tolerance window.}, }
@article {pmid15674769, year = {2004}, author = {Else, PL and Turner, N and Hulbert, AJ}, title = {The evolution of endothermy: role for membranes and molecular activity.}, journal = {Physiological and biochemical zoology : PBZ}, volume = {77}, number = {6}, pages = {950-958}, doi = {10.1086/422767}, pmid = {15674769}, issn = {1522-2152}, mesh = {Animals ; Basal Metabolism/*physiology ; Biological Clocks ; *Biological Evolution ; Membranes/physiology ; Mitochondria/physiology ; Sodium-Potassium-Exchanging ATPase ; Thermogenesis/*genetics/*physiology ; }, abstract = {On the basis of the comparative approach and three models of metabolism (endothermic and ectothermic vertebrates, body mass, and mammalian development), we suggest that a few common cellular processes, linked either directly or indirectly to membranes, consume the majority of energy used by most organisms; that membranes act as pacemakers of metabolism through changes in lipid composition, altering membrane characteristics and the working environment of membrane proteins--specifically, that changes in the membrane environment similarly affect the molecular activities (specific rates of activity) of membrane-bound proteins; and that polyunsaturation of membranes increases whereas monounsaturation decreases the activity of membrane proteins. Experiments designed to test this theory using the sodium pump support this supposition. Potential mechanisms considered include fluidity, electrical fields, and related surface area requirements of lipids. In considering the evolution of endothermy in mammals, for example, if the first mammals were small, possibly nocturnal and active organisms, all these factors would favour increased polyunsaturation of membranes. Such changes (from monounsaturated to polyunsaturated membranes) would allow membranes to set the pace of metabolism in the evolution of endothermy.}, }
@article {pmid15672664, year = {2004}, author = {Hejli, AM and Koster, KL}, title = {The allelochemical sorgoleone inhibits root H+-ATPase and water uptake.}, journal = {Journal of chemical ecology}, volume = {30}, number = {11}, pages = {2181-2191}, pmid = {15672664}, issn = {0098-0331}, mesh = {Benzoquinones/chemistry/*pharmacology ; Chloroplasts/drug effects/metabolism ; Edible Grain/chemistry/metabolism ; Electron Transport/drug effects/physiology ; Enzyme Inhibitors/pharmacology ; Lipids/chemistry/*pharmacology ; Mitochondria/drug effects/metabolism ; Pheromones/chemistry/*pharmacology ; Plant Roots/drug effects/metabolism ; Proton-Translocating ATPases/antagonists &amp; inhibitors/*metabolism ; Seedlings/drug effects/metabolism ; Glycine max/chemistry/metabolism ; Water/*metabolism ; }, abstract = {Sorghum plants inhibit the growth of some adjacent species. Root exudates from grain sorghum (Sorghum bicolor), consisting primarily of the quinone sorgoleone, are phytotoxic to several plant species, yet the mechanisms of growth inhibition remain to be fully explained. Disruption of electron transport functions in isolated mitochondria and chloroplasts has been reported as one explanation for growth inhibition. In the studies reported here, however, soybean seedlings grown in nutrient solution with 10, 50, or 100 microM sorgoleone showed no disruption of photosynthesis, as measured by leaf fluorescence and oxygen evolution, yet their mean leaf surface area was less when grown in 100 microM sorgoleone. Furthermore, in the presence of these same concentrations of sorgoleone, decreased nutrient solution use by soybean seedlings and decreased H+-ATPase activity in corn root microsomal membranes were observed. This suggests that impairment of essential plant processes, such as solute and water uptake, driven by proton-pumping across the root cell plasmalemma should also be considered as a mechanism contributing to observed plant growth inhibition by sorgoleone.}, }
@article {pmid15671040, year = {2005}, author = {van Bloois, E and Nagamori, S and Koningstein, G and Ullers, RS and Preuss, M and Oudega, B and Harms, N and Kaback, HR and Herrmann, JM and Luirink, J}, title = {The Sec-independent function of Escherichia coli YidC is evolutionary-conserved and essential.}, journal = {The Journal of biological chemistry}, volume = {280}, number = {13}, pages = {12996-13003}, doi = {10.1074/jbc.M414094200}, pmid = {15671040}, issn = {0021-9258}, support = {DK5113109/DK/NIDDK NIH HHS/United States ; }, mesh = {Adenosine Triphosphatases/*physiology ; Bacterial Proteins/*physiology ; Cell Membrane/metabolism ; Cell Proliferation ; Chloroplasts/metabolism ; Cross-Linking Reagents/pharmacology ; Electron Transport Complex IV/genetics ; Endopeptidase K/chemistry ; Escherichia coli/*metabolism ; Escherichia coli Proteins/metabolism/*physiology ; Evolution, Molecular ; Genetic Complementation Test ; Membrane Transport Proteins/chemistry/metabolism/*physiology ; Mitochondria/metabolism ; Mitochondrial Proteins/genetics ; Models, Biological ; Mutation ; Nuclear Proteins/genetics ; Plasmids/metabolism ; Protein Biosynthesis ; Protein Folding ; Protein Transport ; SEC Translocation Channels ; SecA Proteins ; Thylakoids/metabolism ; Transcription, Genetic ; }, abstract = {YidC plays a role in the integration and assembly of many (if not all) Escherichia coli inner membrane proteins. Strikingly, YidC operates in two distinct pathways: one associated with the Sec translocon that also mediates protein translocation across the inner membrane and one independent from the Sec translocon. YidC is homologous to Alb3 and Oxa1 that function in the integration of proteins into the thylakoid membrane of chloroplasts and inner membrane of mitochondria, respectively. Here, we have expressed the conserved region of yeast Oxa1 in a conditional E. coli yidC mutant. We find that Oxa1 restores growth upon depletion of YidC. Data obtained from in vivo protease protection assays and in vitro cross-linking and folding assays suggest that Oxa1 complements the insertion of Sec-independent proteins but is unable to take over the Sec-associated function of YidC. Together, our data indicate that the Sec-independent function of YidC is conserved and essential for cell growth.}, }
@article {pmid15668256, year = {2005}, author = {Zhang, L and Joshi, AK and Hofmann, J and Schweizer, E and Smith, S}, title = {Cloning, expression, and characterization of the human mitochondrial beta-ketoacyl synthase. Complementation of the yeast CEM1 knock-out strain.}, journal = {The Journal of biological chemistry}, volume = {280}, number = {13}, pages = {12422-12429}, doi = {10.1074/jbc.M413686200}, pmid = {15668256}, issn = {0021-9258}, support = {DK 16073/DK/NIDDK NIH HHS/United States ; GM 69717/GM/NIGMS NIH HHS/United States ; }, mesh = {3-Oxoacyl-(Acyl-Carrier-Protein) Synthase/*biosynthesis/chemistry/*genetics ; Amino Acid Sequence ; Animals ; Cell Nucleus/metabolism ; Cerulenin/chemistry ; Cloning, Molecular ; DNA Primers/chemistry ; DNA, Complementary/metabolism ; Dose-Response Relationship, Drug ; Esters/chemistry ; Genetic Complementation Test ; Humans ; Kinetics ; Mass Spectrometry ; Mice ; Mitochondria/*enzymology/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Substrate Specificity ; Thioctic Acid/chemistry ; Tissue Distribution ; }, abstract = {A human beta-ketoacyl synthase implicated in a mitochondrial pathway for fatty acid synthesis has been identified, cloned, expressed, and characterized. Sequence analysis indicates that the protein is more closely related to freestanding counterparts found in prokaryotes and chloroplasts than it is to the beta-ketoacyl synthase domain of the human cytosolic fatty acid synthase. The full-length nuclear-encoded 459-residue protein includes an N-terminal sequence element of approximately 38 residues that functions as a mitochondrial targeting sequence. The enzyme can elongate acyl-chains containing 2-14 carbon atoms with malonyl moieties attached in thioester linkage to the human mitochondrial acyl carrier protein and is able to restore growth to the respiratory-deficient yeast mutant cem1 that lacks the endogenous mitochondrial beta-ketoacyl synthase and exhibits lowered lipoic acid levels. To date, four components of a putative type II mitochondrial fatty acid synthase pathway have been identified in humans: acyl carrier protein, malonyl transferase, beta-ketoacyl synthase, and enoyl reductase. The substrate specificity and complementation data for the beta-ketoacyl synthase suggest that, as in plants and fungi, in humans this pathway may play an important role in the generation of octanoyl-acyl carrier protein, the lipoic acid precursor, as well as longer chain fatty acids that are required for optimal mitochondrial function.}, }
@article {pmid15667261, year = {2005}, author = {Hackstein, JH}, title = {Eukaryotic Fe-hydrogenases -- old eukaryotic heritage or adaptive acquisitions?.}, journal = {Biochemical Society transactions}, volume = {33}, number = {Pt 1}, pages = {47-50}, doi = {10.1042/BST0330047}, pmid = {15667261}, issn = {0300-5127}, mesh = {Eukaryotic Cells/*enzymology ; Hydrogenase/*metabolism ; Iron-Sulfur Proteins/*metabolism ; Phylogeny ; }, abstract = {All eukaryotes seem to possess proteins that most probably evolved from an ancestral Fe-hydrogenase. These proteins, known as NARF or Nar, do not produce hydrogen. Notably, a small group of rather unrelated unicellular anaerobes and a few algae possess Fe-hydrogenases, which produce hydrogen. In most, but not all organisms, hydrogen production occurs in membrane-bounded organelles, i.e. hydrogenosomes or plastids. Whereas plastids are monophyletic, hydrogenosomes evolved repeatedly and independently from mitochondria or mitochondria-like organelles. A systematic analysis of the various hydrogenosomes and their hydrogenases will contribute to an understanding of the evolution of the eukaryotic cell, and provide clues to the evolutionary origin(s) of the Fe-hydrogenase.}, }
@article {pmid15666722, year = {2004}, author = {McEwan, ML and Keeling, PJ}, title = {HSP90, tubulin and actin are retained in the tertiary endosymbiont genome of Kryptoperidinium foliaceum.}, journal = {The Journal of eukaryotic microbiology}, volume = {51}, number = {6}, pages = {651-659}, doi = {10.1111/j.1550-7408.2004.tb00604.x}, pmid = {15666722}, issn = {1066-5234}, mesh = {Actins/*genetics ; Animals ; Base Composition ; DNA, Protozoan/chemistry/isolation &amp; purification ; Diatoms/genetics ; Dinoflagellida/*genetics ; Evolution, Molecular ; Genome, Protozoan ; HSP90 Heat-Shock Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/*genetics ; Sequence Analysis, DNA ; Sequence Homology ; Symbiosis/genetics ; Tubulin/*genetics ; }, abstract = {The dinoflagellate Kryptoperidinium foliaceum has replaced its ancestral peridinin-containing plastid with a fucoxanthin-containing diatom plastid via tertiary endosymbiosis. The diatom endosymbiont of K. foliaceum is much less reduced than well-studied endosymbiotic intermediates, such as cryptophytes and chlorarachniophytes, where relict nuclear genomes are retained in secondary endosymbionts. The K. foliaceum endosymbiont retains a prominent nucleus, multiple four-membrane plastids, and mitochondria, all within a relatively large volume of cytoplasm that is separated from the host cytoplasm by a single membrane. Here we report the first protein-coding gene sequences from the K. foliaceum endosymbiont and host nuclear genomes. We have characterised genes for nucleus-encoded cytosolic proteins, actin (from endosymbiont), alpha-tubulin (from both), beta-tubulin (from host), and HSP90 (from both), in addition to homologues from pennate diatoms Nitzschia thermalis and Phaeodactylum tricornutum. Phylogenetic reconstruction shows that the actin is diatom-derived, the beta-tubulin dinoflagellate-derived, while both diatom- and dinoflagellate-derived alpha-tubulin and HSP90 genes were found. The base composition biases of these genes co-varied with their phylogenetic position, suggesting that the genes still reside in their respective genomes. The presence of these genes implies they are still functional and more generally indicates that the endosymbiont is less genetically reduced than those of cryptophytes or chlorarachniophytes, raising the interesting question of whether any genes have transferred between the two nuclear genomes.}, }
@article {pmid15665243, year = {2005}, author = {Nunes-Nesi, A and Carrari, F and Lytovchenko, A and Smith, AM and Loureiro, ME and Ratcliffe, RG and Sweetlove, LJ and Fernie, AR}, title = {Enhanced photosynthetic performance and growth as a consequence of decreasing mitochondrial malate dehydrogenase activity in transgenic tomato plants.}, journal = {Plant physiology}, volume = {137}, number = {2}, pages = {611-622}, pmid = {15665243}, issn = {0032-0889}, mesh = {Ascorbic Acid/metabolism ; Chloroplasts/metabolism ; DNA, Complementary/genetics/physiology ; Electron Transport ; Solanum lycopersicum/enzymology/*genetics/growth &amp; development ; Malate Dehydrogenase/genetics/*metabolism ; Mitochondria/*enzymology ; Molecular Sequence Data ; Oxygen Consumption ; Phenotype ; Photosynthesis/*physiology ; Phylogeny ; Plants, Genetically Modified ; }, abstract = {Transgenic tomato (Solanum lycopersicum) plants expressing a fragment of the mitochondrial malate dehydrogenase gene in the antisense orientation and exhibiting reduced activity of this isoform of malate dehydrogenase show enhanced photosynthetic activity and aerial growth under atmospheric conditions (360 ppm CO2). In comparison to wild-type plants, carbon dioxide assimilation rates and total plant dry matter were up to 11% and 19% enhanced in the transgenics, when assessed on a whole-plant basis. Accumulation of carbohydrates and redox-related compounds such as ascorbate was also markedly elevated in the transgenics. Also increased in the transgenic plants was the capacity to use L-galactono-lactone, the terminal precursor of ascorbate biosynthesis, as a respiratory substrate. Experiments in which ascorbate was fed to isolated leaf discs also resulted in increased rates of photosynthesis providing strong indication for an ascorbate-mediated link between the energy-generating processes of respiration and photosynthesis. This report thus shows that the repression of this mitochondrially localized enzyme improves both carbon assimilation and aerial growth in a crop species.}, }
@article {pmid15664623, year = {2005}, author = {Landis, GN and Tower, J}, title = {Superoxide dismutase evolution and life span regulation.}, journal = {Mechanisms of ageing and development}, volume = {126}, number = {3}, pages = {365-379}, doi = {10.1016/j.mad.2004.08.012}, pmid = {15664623}, issn = {0047-6374}, support = {AG011644/AG/NIA NIH HHS/United States ; AG011833/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; *Evolution, Molecular ; Humans ; Longevity/genetics/*physiology ; Phylogeny ; Superoxide Dismutase/genetics/*metabolism ; }, abstract = {Superoxide is among the most abundant reactive oxygen species (ROS) produced by the mitochondria, and is involved in cellular signaling pathways. Superoxide and other ROS can damage cellular macromolecules and levels of oxidative damage products are positively correlated with aging. Superoxide dismutase (SOD) enzymes catalyze the breakdown of superoxide into hydrogen peroxide and water and are therefore central regulators of ROS levels. Genetic and transgenic manipulation of SOD activities in model systems such as S. cereviseae, mouse and Drosophila are consistent with a central role for SOD enzymes in regulating oxidative stress resistance. Over-expression of SOD in S. cereviseae and Drosophila can reduce oxidative damage and extend life span, but the mechanism(s) are not yet clear. A phylogenetic analysis of publicly available SOD protein sequences suggests several additional conserved gene families. For example, in addition to the well-characterized soluble Cu/Zn enzyme (Sod) and mitochondrial manganese-containing form (Sod2), Drosophila melanogaster is found to contain a putative copper chaperone (CCS), an extracellular Cu/Zn enzyme (Sod3), and an extracellular protein distantly related to the Cu/Zn forms (Sodq). C. elegans and blue crab are unusual in having two Mn-containing SODs, and A. gambiae contains an unusual internally repeated SOD. The most parsimonius conclusion from the analysis of the extracellular SODs is that they evolved independently multiple times by addition of a signal peptide to cytoplasmic SOD.}, }
@article {pmid15661357, year = {2005}, author = {Haugen, P and Simon, DM and Bhattacharya, D}, title = {The natural history of group I introns.}, journal = {Trends in genetics : TIG}, volume = {21}, number = {2}, pages = {111-119}, doi = {10.1016/j.tig.2004.12.007}, pmid = {15661357}, issn = {0168-9525}, mesh = {Alternative Splicing ; Bacteriophages/*genetics ; Catalysis ; DNA, Ribosomal/chemistry ; Evolution, Molecular ; *Genes, Bacterial ; *Introns ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer/chemistry ; }, abstract = {There are four major classes of introns: self-splicing group I and group II introns, tRNA and/or archaeal introns and spliceosomal introns in nuclear pre-mRNA. Group I introns are widely distributed in protists, bacteria and bacteriophages. Group II introns are found in fungal and land plant mitochondria, algal plastids, bacteria and Archaea. Group II and spliceosomal introns share a common splicing pathway and might be related to each other. The tRNA and/or archaeal introns are found in the nuclear tRNA of eukaryotes and in archaeal tRNA, rRNA and mRNA. The mechanisms underlying the self-splicing and mobility of a few model group I introns are well understood. By contrast, the role of these highly distinct processes in the evolution of the 1500 group I introns found thus far in nature (e.g. in algae and fungi) has only recently been clarified. The explosion of new sequence data has facilitated the use of comparative methods to understand group I intron evolution in a broader context and to generate hypotheses about intron insertion, splicing and spread that can be tested experimentally.}, }
@article {pmid15660955, year = {2005}, author = {Fontanillas, P and Dépraz, A and Giorgi, MS and Perrin, N}, title = {Nonshivering thermogenesis capacity associated to mitochondrial DNA haplotypes and gender in the greater white-toothed shrew, Crocidura russula.}, journal = {Molecular ecology}, volume = {14}, number = {2}, pages = {661-670}, doi = {10.1111/j.1365-294X.2004.02414.x}, pmid = {15660955}, issn = {0962-1083}, mesh = {Acclimatization/*genetics ; Altitude ; Animals ; Basal Metabolism ; Base Sequence ; Body Composition ; Body Weight ; DNA Primers ; DNA, Mitochondrial/genetics ; *Genetic Variation ; Haplotypes/genetics ; Molecular Sequence Data ; Mutation/genetics ; *Seasons ; Sequence Analysis, DNA ; Sex Factors ; Shrews/genetics/*physiology ; Switzerland ; Thermogenesis/genetics/*physiology ; }, abstract = {A selection gradient was recently suggested as one possible cause for a clinal distribution of mitochondrial DNA (mtDNA) haplotypes along an altitudinal transect in the greater white-toothed shrew, Crocidura russula (Ehinger et al. 2002). One mtDNA haplotype (H1) rare in lowland, became widespread when approaching the altitudinal margin of the distribution. As H1 differs from the main lowland haplotype by several nonsynonymous mutations (including on ATP6), and as mitochondria play a crucial role in metabolism and thermogenesis, distribution patterns might stem from differences in the thermogenic capacity of different mtDNA haplotypes. In order to test this hypothesis, we measured the nonshivering thermogenesis (NST) associated with different mtDNA haplotypes. Sixty-two shrews, half of which had the H1 haplotype, were acclimated in November at semioutdoor conditions and measured for NST throughout winter. Our results showed the crucial role of NST for winter survival in C. russula. The individuals that survived winter displayed a higher significant increase in NST during acclimation, associated with a significant gain in body mass, presumably from brown fat accumulation. The NST capacity (ratio of NST to basal metabolic rate) was exceptionally high for such a small species. NST was significantly affected by a gender x haplotype interaction after winter-acclimation: females bearing the H1 haplotype displayed a better thermogenesis at the onset of the breeding season, while the reverse was true for males. Altogether, our results suggest a sexually antagonistic cyto-nuclear selection on thermogenesis.}, }
@article {pmid15657051, year = {2005}, author = {Nosek, J and Rycovska, A and Makhov, AM and Griffith, JD and Tomaska, L}, title = {Amplification of telomeric arrays via rolling-circle mechanism.}, journal = {The Journal of biological chemistry}, volume = {280}, number = {11}, pages = {10840-10845}, doi = {10.1074/jbc.M409295200}, pmid = {15657051}, issn = {0021-9258}, support = {1-R03-TW05654-01/TW/FIC NIH HHS/United States ; GM31819/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Candida/*metabolism ; Cell Nucleus/metabolism ; DNA/chemistry ; DNA, Mitochondrial/chemistry ; DNA, Single-Stranded/chemistry ; Genes, Fungal ; Genes, Plant ; Microscopy, Electron ; Mitochondria/*metabolism ; Models, Genetic ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Oligonucleotides/chemistry ; Plasmids/metabolism ; Propidium/pharmacology ; Recombination, Genetic ; Sequence Homology, Nucleic Acid ; Subcellular Fractions/metabolism ; Telomere/*chemistry/ultrastructure ; Xenopus laevis ; }, abstract = {Alternative (telomerase-independent) lengthening of telomeres mediated through homologous recombination is often accompanied by a generation of extrachromosomal telomeric circles (t-circles), whose role in direct promotion of recombinational telomere elongation has been recently demonstrated. Here we present evidence that t-circles in a natural telomerase-deficient system of mitochondria of the yeast Candida parapsilosis replicate independently of the linear chromosome via a rolling-circle mechanism. This is supported by an observation of (i) single-stranded DNA consisting of concatameric arrays of telomeric sequence, (ii) lasso-shaped molecules representing rolling-circle intermediates, and (iii) preferential incorporation of deoxyribonucleotides into telomeric fragments and t-circles. Analysis of naturally occurring variant t-circles revealed conserved motifs with potential function in driving the rolling-circle replication. These data indicate that extrachromosomal t-circles observed in a wide variety of organisms, including yeasts, plants, Xenopus laevis, and certain human cell lines, may represent independent replicons generating telomeric sequences and, thus, actively participating in telomere dynamics. Moreover, because of the promiscuous occurrence of t-circles across phyla, the results from yeast mitochondria have implications related to the primordial system of telomere maintenance, providing a paradigm for evolution of telomeres in nuclei of early eukaryotes.}, }
@article {pmid15654078, year = {2005}, author = {Preuss, M and Ott, M and Funes, S and Luirink, J and Herrmann, JM}, title = {Evolution of mitochondrial oxa proteins from bacterial YidC. Inherited and acquired functions of a conserved protein insertion machinery.}, journal = {The Journal of biological chemistry}, volume = {280}, number = {13}, pages = {13004-13011}, doi = {10.1074/jbc.M414093200}, pmid = {15654078}, issn = {0021-9258}, mesh = {Cross-Linking Reagents/pharmacology ; Dose-Response Relationship, Drug ; Escherichia coli/metabolism ; Escherichia coli Proteins/chemistry/*physiology ; Evolution, Molecular ; Gene Deletion ; Genetic Complementation Test ; Immunoprecipitation ; Macromolecular Substances ; Membrane Proteins/chemistry ; Membrane Transport Proteins/chemistry/*physiology ; Mitochondria/*metabolism ; Mitochondrial Proteins/chemistry ; Models, Biological ; Models, Genetic ; Mutation ; Protein Binding ; Protein Biosynthesis ; Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Protein Transport ; Ribosomes/chemistry ; Subcellular Fractions ; Time Factors ; beta-Lactamases/chemistry ; }, abstract = {Members of the Oxa1/YidC family are involved in the biogenesis of membrane proteins. In bacteria, YidC catalyzes the insertion and assembly of proteins of the inner membrane. Mitochondria of animals, fungi, and plants harbor two distant homologues of YidC, Oxa1 and Cox18/Oxa2. Oxa1 plays a pivotal role in the integration of mitochondrial translation products into the inner membrane of mitochondria. It contains a C-terminal ribosome-binding domain that physically interacts with mitochondrial ribosomes to facilitate the co-translational insertion of nascent membrane proteins. The molecular function of Cox18/Oxa2 is not well understood. Employing a functional complementation approach with mitochondria-targeted versions of YidC we show that YidC is able to functionally replace both Oxa1 and Cox18/Oxa2. However, to integrate mitochondrial translation products into the inner membrane of mitochondria, the ribosome-binding domain of Oxa1 has to be appended onto YidC. On the contrary, the fusion of the ribosome-binding domain onto YidC prevents its ability to complement COX18 mutants suggesting an indispensable post-translational activity of Cox18/Oxa2. Our observations suggest that during evolution of mitochondria from their bacterial ancestors the two descendents of YidC functionally segregated to perform two distinct activities, one co-translational and one post-translational.}, }
@article {pmid15653464, year = {2005}, author = {Zhu, G and Golding, GB and Dean, AM}, title = {The selective cause of an ancient adaptation.}, journal = {Science (New York, N.Y.)}, volume = {307}, number = {5713}, pages = {1279-1282}, doi = {10.1126/science.1106974}, pmid = {15653464}, issn = {1095-9203}, support = {GM060611/GM/NIGMS NIH HHS/United States ; }, mesh = {3-Isopropylmalate Dehydrogenase ; Acetates/metabolism ; *Adaptation, Physiological ; Alcohol Oxidoreductases/chemistry/metabolism ; Bacteria/*genetics/growth &amp; development/*metabolism ; Binding Sites ; Biological Evolution ; Escherichia coli/enzymology/genetics/metabolism ; Isocitrate Dehydrogenase/chemistry/genetics/*metabolism ; Isocitrate Lyase/genetics/metabolism ; Kinetics ; NAD/*metabolism ; NADP/*metabolism ; Oxidation-Reduction ; Phylogeny ; Protein Engineering ; *Selection, Genetic ; }, abstract = {Phylogenetic analysis reveals that the use of nicotinamide adenine dinucleotide phosphate (NADP) by prokaryotic isocitrate dehydrogenase (IDH) arose around the time eukaryotic mitochondria first appeared, about 3.5 billion years ago. We replaced the wild-type gene that encodes the NADP-dependent IDH of Escherichia coli with an engineered gene that possesses the ancestral NAD-dependent phenotype. The engineered enzyme is disfavored during competition for acetate. The selection intensifies in genetic backgrounds where other sources of reduced NADP have been removed. A survey of sequenced prokaryotic genomes reveals that those genomes that encode isocitrate lyase, which is essential for growth on acetate, always have an NADP-dependent IDH. Those with only an NAD-dependent IDH never have isocitrate lyase. Hence, the NADP dependence of prokaryotic IDH is an ancient adaptation to anabolic demand for reduced NADP during growth on acetate.}, }
@article {pmid15652223, year = {2005}, author = {Sherman, F}, title = {The importance of mutation, then and now: studies with yeast cytochrome c.}, journal = {Mutation research}, volume = {589}, number = {1}, pages = {1-16}, doi = {10.1016/j.mrrev.2004.07.001}, pmid = {15652223}, issn = {0027-5107}, support = {R01 GM12702/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Cloning, Molecular ; Cytochromes c/*genetics ; Gene Expression Regulation, Fungal/genetics ; Molecular Sequence Data ; Mutagenesis, Site-Directed/genetics ; Mutation/*genetics ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/*genetics ; Sequence Analysis, Protein ; Transcription, Genetic/genetics ; }, abstract = {The development of a genetic system based on the CYC1 gene was initiated over 40 years ago, primarily because of the anticipated ease of sequencing of the corresponding encoded protein, iso-1-cytochrome c from Saccharomyces cerevisiae. The success of the iso-cytochrome c system was dependent on the early development of methods for detecting and selecting cyc1 defective mutants and CYC1 functional revertants, and of methods for fine-structure genetic mapping using deletions and single-site mutations. The nonsense codons TAA and TAG, and the initiation codon ATG, were determined from the amino acid alterations of iso-1-cytochromes c from intragenic revertants; this represented the first assignments of such codons in a eukaryotic organism. The types of desired sequences were expanded by selecting recombinants from cyc1 x cyc1 nonfunctional mutants or CYC1 x CYC1 functional mutants, permitting the early determination of the rules of translation, which differed from those of prokaryotes by use of the most 5' AUG codon for initiation of translation. The sequence of 44 base pairs of CYC1 was determined with altered iso-1-cytochromes c from revertants of frameshift and initiation mutants, allowing the early cloning of the gene. A method was developed for transforming yeast directly with synthetic oligonucleotides, resulting in the convenient production of CYC1 mutants with defined sequences. At this point in time, Sherman and colleagues have published approximately 240 papers on or using the iso-cytochrome c system, dealing with such diverse topics as translation, informational suppressors, transcription and transcription termination, recombination, ectopic recombination, mutagen specificity, regulation by Ty1 elements, evolution of duplicated chromosomal segments, structure-function relationships of cytochrome c, protein stability and degradation, biosynthesis and mitochondrial import of cytochrome c, mitochondrial proteases, co- and post-translational modifications, and mRNA degradation. Current work on degradation of proteins in mitochondria, on degradation of mRNA in the nucleus, and on N-terminal acetylation stems from properties of CYC1 mutants isolated in early screens more than a decade ago.}, }
@article {pmid15652179, year = {2005}, author = {Tsoneva, I and Nikolova, B and Georgieva, M and Guenova, M and Tomov, T and Rols, MP and Berger, MR}, title = {Induction of apoptosis by electrotransfer of positively charged proteins as Cytochrome C and Histone H1 into cells.}, journal = {Biochimica et biophysica acta}, volume = {1721}, number = {1-3}, pages = {55-64}, doi = {10.1016/j.bbagen.2004.10.002}, pmid = {15652179}, issn = {0006-3002}, mesh = {Animals ; Apoptosis/*drug effects ; Cell Survival/drug effects ; Cytochromes c/*pharmacology ; DNA Fragmentation ; *Electroporation ; Histones/*pharmacology ; Humans ; K562 Cells ; Mitochondria, Liver/enzymology ; Rats ; Serum Albumin, Bovine/pharmacology ; }, abstract = {Cytochrome C (Cyt. C) is a mitochondrial protein inducing apoptosis when it is accumulated in the cytosol by a currently unknown mechanism, but regulated by the bcl-2 family of proteins. The linker Histone H1 is another basic protein with highly conservative structure, composition, and equal molecular weight, not changed during the evolution. An attempt was made to understand better the apoptotic processes by electroloading of leukemic cells, such as K562, HL-60, and SKW3, and human lymphocytes with positively charged proteins, such as Cyt. C, Histone H1, and methylated BSA albumin (mBSA). The triggering apoptotic processes followed by MTT test, FACS analysis, and DNA fragmentation after the electrotransfer of these proteins into the cells were observed. Histone H1 and mBSA induce the release of Cyt. C from rat liver mitochondria. Cytochrome C release was higher when mitochondria were in "high-energy" state. It is supposed that release of Cyt. C from mitochondria is due to the mechanical rupture of the outer mitochondrial membrane, rich in negatively charged groups, predominately due to cardiolipin. The reason for the morphological rupture of the outer mitochondial membrane could be the rigidification and segregation of the membrane and the destroyed membrane asymmetries of both monolayers in the presence of positively charged proteins at higher linear charges such as Histone H1. We suggested that Histone H1, at a given moment of activated signaling for apoptosis, could be not transported to the nucleus and could lead to the release of Cyt. C from the mitochondria in the cytoplasm. It is temping to speculate that Histone H1 has other physiological extranuclear functions involved in apoptosis.}, }
@article {pmid15650813, year = {2005}, author = {Nishikawa, T and Vaughan, DA and Kadowaki, K}, title = {Phylogenetic analysis of Oryza species, based on simple sequence repeats and their flanking nucleotide sequences from the mitochondrial and chloroplast genomes.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {110}, number = {4}, pages = {696-705}, pmid = {15650813}, issn = {0040-5752}, mesh = {Base Sequence ; Chloroplasts/*genetics ; DNA, Mitochondrial ; DNA, Plant ; *Genome, Plant ; *Minisatellite Repeats ; Mitochondria/*genetics ; Oryza/*classification/genetics ; Phylogeny ; Polyploidy ; }, abstract = {Simple sequence repeats (SSR) and their flanking regions in the mitochondrial and chloroplast genomes were sequenced in order to reveal DNA sequence variation. This information was used to gain new insights into phylogenetic relationships among species in the genus Oryza. Seven mitochondrial and five chloroplast SSR loci equal to or longer than ten mononucleotide repeats were chosen from known rice mitochondrial and chloroplast genome sequences. A total of 50 accessions of Oryza that represented six different diploid genomes and three different allopolyploid genomes of Oryza species were analyzed. Many base substitutions and deletions/insertions were identified in the SSR loci as well as their flanking regions. Of mononucleotide SSR, G (or C) repeats were more variable than A (or T) repeats. Results obtained by chloroplast and mitochondrial SSR analyses showed similar phylogenetic relationships among species, although chloroplast SSR were more informative because of their higher sequence diversity. The CC genome is suggested to be the maternal parent for the two BBCC genome species (O. punctata and O. minuta) and the CCDD species O. latifolia, based on the high level of sequence conservation between the diploid CC genome species and these allotetraploid species. This is the first report of phylogenetic analysis among plant species, based on mitochondrial and chloroplast SSR and their flanking sequences.}, }
@article {pmid15648215, year = {2004}, author = {Davolos, D and Maclean, N and Pietrangeli, B}, title = {A molecular phylogenetic study of the freshwater talitrid amphipod Orchestia cavimana (Crustacea).}, journal = {Rivista di biologia}, volume = {97}, number = {1}, pages = {161-168}, pmid = {15648215}, issn = {0035-6050}, mesh = {Amino Acid Sequence ; Amphipoda/*genetics ; Animals ; Electron Transport Complex IV/genetics ; Mitochondria/genetics ; *Phylogeny ; Poisson Distribution ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {In this paper we performed a molecular phylogenetic study of Orchestia cavimana, the sole talitrid amphipod inhabiting beaches of European freshwater lakes and rivers. For that purpose, we have PCR amplified and sequenced regions of the mitochondrial cytochrome oxidase subunit I (COI) gene, basing our analysis on both nucleotide and amino acid sequences and considering also structural classes of the COI enzyme. Phylogenetic analyses were conducted by neighbour-joining (NJ) and maximum-parsimony (MP) methods comparing homologous sequences of talitrids and other Crustacea. In both NJ and MP trees, O. cavimana shows a basal placement with respect to other talitrid amphipods.}, }
@article {pmid15644465, year = {2005}, author = {Vandepoele, K and Van de Peer, Y}, title = {Exploring the plant transcriptome through phylogenetic profiling.}, journal = {Plant physiology}, volume = {137}, number = {1}, pages = {31-42}, pmid = {15644465}, issn = {0032-0889}, mesh = {Arabidopsis/genetics ; Biological Evolution ; Chloroplasts/genetics ; *Databases, Genetic ; Expressed Sequence Tags ; *Gene Expression Profiling ; Mitochondria/genetics ; Multigene Family ; Oryza/genetics ; *Phylogeny ; Plants/*genetics ; Proteomics ; }, abstract = {Publicly available protein sequences represent only a small fraction of the full catalog of genes encoded by the genomes of different plants, such as green algae, mosses, gymnosperms, and angiosperms. By contrast, an enormous amount of expressed sequence tags (ESTs) exists for a wide variety of plant species, representing a substantial part of all transcribed plant genes. Integrating protein and EST sequences in comparative and evolutionary analyses is not straightforward because of the heterogeneous nature of both types of sequence data. By combining information from publicly available EST and protein sequences for 32 different plant species, we identified more than 250,000 plant proteins organized in more than 12,000 gene families. Approximately 60% of the proteins are absent from current sequence databases but provide important new information about plant gene families. Analysis of the distribution of gene families over different plant species through phylogenetic profiling reveals interesting insights into plant gene evolution, and identifies species- and lineage-specific gene families, orphan genes, and conserved core genes across the green plant lineage. We counted a similar number of approximately 9,500 gene families in monocotyledonous and eudicotyledonous plants and found strong evidence for the existence of at least 33,700 genes in rice (Oryza sativa). Interestingly, the larger number of genes in rice compared to Arabidopsis (Arabidopsis thaliana) can partially be explained by a larger amount of species-specific single-copy genes and species-specific gene families. In addition, a majority of large gene families, typically containing more than 50 genes, are bigger in rice than Arabidopsis, whereas the opposite seems true for small gene families.}, }
@article {pmid15634957, year = {2005}, author = {Kurtzman, CP and Robnett, CJ and Ward, JM and Brayton, C and Gorelick, P and Walsh, TJ}, title = {Multigene phylogenetic analysis of pathogenic candida species in the Kazachstania (Arxiozyma) telluris complex and description of their ascosporic states as Kazachstania bovina sp. nov., K. heterogenica sp. nov., K. pintolopesii sp. nov., and K. slooffiae sp. nov.}, journal = {Journal of clinical microbiology}, volume = {43}, number = {1}, pages = {101-111}, pmid = {15634957}, issn = {0095-1137}, support = {N01-CO-56000/CO/NCI NIH HHS/United States ; }, mesh = {Animals ; Candida/*classification/genetics/*pathogenicity/physiology ; Candidiasis/microbiology/pathology ; Fungal Proteins/*genetics ; Genes, rRNA ; Humans ; Mice ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; RNA Polymerase II/genetics ; RNA, Ribosomal/genetics ; Rats ; Saccharomycetales/*classification/genetics ; Sequence Analysis, DNA ; Spores, Fungal/physiology ; }, abstract = {A yeast causing widespread infection of laboratory mice was identified from 26S rRNA gene sequences as Candida pintolopesii. To determine the relationship of C. pintolopesii with other members of the Kazachstania (Arxiozyma) telluris species complex, nucleotide sequences from domains 1 and 2 of the 26S rRNA gene, the mitochondrial small-subunit rRNA gene, and the RNA polymerase II gene were phylogenetically analyzed. That analysis resolved the 48 strains examined into five closely related species: K. telluris, Candida bovina, C. pintolopesii, Candida slooffiae, and a previously unknown species. One or more strains of each of the last four species formed an ascosporic state much like that of K. telluris. To place these ascosporogenous strains taxonomically, it is proposed that they be assigned to the teleomorphic genus Kazachstania as K. bovina (type strain NRRL Y-7283, CBS 9732, from the nasal passage of a pigeon), K. heterogenica (type strain NRRL Y-27499, CBS 2675, from rodent feces), K. pintolopesii (type strain NRRL Y-27500, CBS 2985, from the peritoneal fluid of a dead guinea pig), and K. slooffiae (type strain NRRL YB-4349, CBS 9733, from the cecum of a horse). On the basis of multigene sequence analyses, K. heterogenica appears to be a hybrid of K. pintolopesii and a presently unknown species. With the exception of K. bovina, the phylogenetically defined species show a moderate degree of host specificity.}, }
@article {pmid15631992, year = {2005}, author = {Dimmer, KS and Jakobs, S and Vogel, F and Altmann, K and Westermann, B}, title = {Mdm31 and Mdm32 are inner membrane proteins required for maintenance of mitochondrial shape and stability of mitochondrial DNA nucleoids in yeast.}, journal = {The Journal of cell biology}, volume = {168}, number = {1}, pages = {103-115}, pmid = {15631992}, issn = {0021-9525}, mesh = {Actins/metabolism ; DNA, Mitochondrial/*metabolism ; Epistasis, Genetic ; Genomic Instability ; Green Fluorescent Proteins/genetics/metabolism ; Humans ; Intracellular Membranes/*metabolism ; Membrane Proteins/classification/genetics/*metabolism ; Mitochondria/*metabolism/ultrastructure ; Mitochondrial Proteins/classification/genetics/*metabolism ; Multiprotein Complexes ; Phenotype ; Phylogeny ; Saccharomyces cerevisiae/cytology/metabolism ; Saccharomyces cerevisiae Proteins/classification/genetics/*metabolism ; }, abstract = {The MDM31 and MDM32 genes are required for normal distribution and morphology of mitochondria in the yeast Saccharomyces cerevisiae. They encode two related proteins located in distinct protein complexes in the mitochondrial inner membrane. Cells lacking Mdm31 and Mdm32 harbor giant spherical mitochondria with highly aberrant internal structure. Mitochondrial DNA (mtDNA) is instable in the mutants, mtDNA nucleoids are disorganized, and their association with Mmm1-containing complexes in the outer membrane is abolished. Mutant mitochondria are largely immotile, resulting in a mitochondrial inheritance defect. Deletion of either one of the MDM31 and MDM32 genes is synthetically lethal with deletion of either one of the MMM1, MMM2, MDM10, and MDM12 genes, which encode outer membrane proteins involved in mitochondrial morphogenesis and mtDNA inheritance. We propose that Mdm31 and Mdm32 cooperate with Mmm1, Mmm2, Mdm10, and Mdm12 in maintenance of mitochondrial morphology and mtDNA.}, }
@article {pmid15619454, year = {2005}, author = {Hart, MW and Podolsky, RD}, title = {Mitochondrial DNA phylogeny and rates of larval evolution in Macrophiothrix brittlestars.}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {2}, pages = {438-447}, doi = {10.1016/j.ympev.2004.09.011}, pmid = {15619454}, issn = {1055-7903}, mesh = {Animals ; *Biological Evolution ; *DNA, Mitochondrial ; Echinodermata/*genetics ; Larva/genetics ; Mitochondria/genetics ; *Phylogeny ; }, abstract = {Phylogenetic analysis has led to significant insights into the evolution of early life-history stages of marine invertebrates. Although echinoderms have been a major focus, developmental and phylogenetic information are relatively poor for ophiuroids, the most species-rich echinoderm class. We used DNA sequences from two mitochondrial genes to develop a phylogenetic hypothesis for 14 brittlestar species in the genus Macrophiothrix (Family Ophiotrichidae). Species are similar in adult form and ecology, but have diverse egg sizes and modes of larval development. In particular, two species have rare larval forms with characteristics that are intermediate between more common modes of feeding and non-feeding development. We use the phylogeny to address whether intermediate larval forms are rare because the evolution of a simplified morphology is rapid once food is no longer required for development. In support of this hypothesis, branch lengths for intermediate forms were short relative to those for species with highly derived non-feeding forms. The absolute rarity of such forms makes robust tests of the hypothesis difficult.}, }
@article {pmid15619452, year = {2005}, author = {Han, HY and Ro, KE}, title = {Molecular phylogeny of the superfamily Tephritoidea (Insecta: Diptera): new evidence from the mitochondrial 12S, 16S, and COII genes.}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {2}, pages = {416-430}, doi = {10.1016/j.ympev.2004.10.017}, pmid = {15619452}, issn = {1055-7903}, mesh = {Animals ; Diptera/classification/*genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Mitochondria/genetics ; Multigene Family ; *Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, RNA ; }, abstract = {The phylogeny of the superfamily Tephritoidea (Diptera: Muscomorpha) was reconstructed from three mitochondrial gene fragments (12S, 16S, and COII) using 49 species representing 19 tephritoid and related families. Phylogenetic signal present in different gene fragments as well as combinations of gene fragments was examined using the interior branch and bootstrap test values from minimum evolution method. The minimum evolution, maximum likelihood, and maximum parsimony trees based on a combined dataset of all three gene fragments provided insight concerning the following phylogenetic relationships: (1) two monophyletic groups (Group-1 and -2) within the superfamily Tephritoidea were clearly recognized; they are compatible with Willi Hennig's Pallopteroidea and Otitoidea that are not used in the contemporary higher classification; (2) the non-monophyletic nature of the family Platystomatidae; and (3) a sister group relationship of Conopidae to Tephritoidea was not supported; instead, our result suggested that Conopidae and Diopsidae might be the basal most groups among the schizophoran families included in this study. The combined data of 12S, 16S, and COII genes was found, therefore, to be a viable genetic marker to resolve divergences among families of the Tephritoidea and other related superfamilies.}, }
@article {pmid15619449, year = {2005}, author = {Brandstätter, A and Salzburger, W and Sturmbauer, C}, title = {Mitochondrial phylogeny of the Cyprichromini, a lineage of open-water cichlid fishes endemic to Lake Tanganyika, East Africa.}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {2}, pages = {382-391}, doi = {10.1016/j.ympev.2004.10.019}, pmid = {15619449}, issn = {1055-7903}, mesh = {Africa, Eastern ; Animals ; Cichlids/classification/*genetics ; *DNA, Mitochondrial ; Likelihood Functions ; Mitochondria/*genetics ; *Phylogeny ; }, abstract = {We present a phylogeny of the Cyprichromini, a lineage of cichlid fishes from Lake Tanganyika, showing progressive adaptation towards pelagic life style. Our study is based upon three mitochondrial gene segments, 443 bp of the control region, 402 bp of the cytochrome b gene and the entire NADH dehydrogenase subunit 2 gene (1047 bp). The topologies obtained by different tree building methods subdivide the Cyprichromini into four distinct lineages: the Paracyprichromis-, the Cyprichromis zonatus-, the Cyprichromis microlepidotus-lineage, and a lineage comprising Cyprichromis pavo and Cyprichromis leptosoma. Our study thus corroborates the distinctness of C. zonatus which was recently described formally. Concerning ecology and mating behavior, a clear evolutionary trend towards progressive adaptation to the pelagic zone emerges during the evolution of the Cyprichromini. The linearized tree analysis further shows that the four lineages have split almost contemporaneously. The mean Kimura-2-parameter distance among the four lineages emerging from the primary radiation of the Cyprichromini amounts to 7.21% and is in close agreement to that previously found for the primary radiation of the tribe Tropheini (7.01%), a lineage of rock-dwelling cichlids endemic to Lake Tanganyika. To date, the influence of lake level fluctuations as promoters of diversification has been demonstrated only for rock-dwelling cichlids. Based on the agreement in temporary patterns of diversification, we suggest that Pleistocene lake level changes have left a similar genetic imprint in a group of cichlid fishes that progressively colonized the open water during their radiation.}, }
@article {pmid15619441, year = {2005}, author = {Yokobori, S and Oshima, T and Wada, H}, title = {Complete nucleotide sequence of the mitochondrial genome of Doliolum nationalis with implications for evolution of urochordates.}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {2}, pages = {273-283}, doi = {10.1016/j.ympev.2004.10.002}, pmid = {15619441}, issn = {1055-7903}, mesh = {Animals ; *DNA, Mitochondrial ; *Evolution, Molecular ; Genome ; Mitochondria/*genetics ; RNA, Ribosomal ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Urochordata/*genetics ; }, abstract = {The evolutionary history of the diverse lifestyles adopted by urochordates has attracted intense interest because it may effect the evolutionary history of vertebrates. Here, we report the complete mitochondrial (mt) DNA sequence of the pelagic thaliacean doliolid Doliolum nationalis. The doliolid mt genome shares the unusual tRNAs of trnM(uau) and trnG(ucu) with other ascidians, such as Halocynthia and Ciona. On the other hand, the gene order of the doliolid mt genome is significantly different from that of any ascidian species or vertebrate reported to date. Phylogenetic analyses of the amino acid sequences of 12 protein-coding genes strongly support the sister-grouping of doliolids and the Phlebobranch ascidian Ciona, with the Stolidobranch ascidian alocynthia as the outgroup, thereby providing strong support for the paraphyly of ascidians, as has been suggested by 18S rDNA studies. Given the paraphyletic nature of ascidians, it seems likely that the common ancestor of ascidians and thaliaceans was sessile, as are the present-day ascidians, and that the thaliaceans subsequently evolved a pelagic lifestyle.}, }
@article {pmid15619004, year = {2005}, author = {Gelhaye, E and Rouhier, N and Navrot, N and Jacquot, JP}, title = {The plant thioredoxin system.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {62}, number = {1}, pages = {24-35}, doi = {10.1007/s00018-004-4296-4}, pmid = {15619004}, issn = {1420-682X}, mesh = {Amino Acid Sequence ; Arabidopsis Proteins/classification/genetics/metabolism ; Chloroplasts/metabolism ; Genetic Variation/genetics ; Mitochondria/metabolism ; Molecular Sequence Data ; *Phylogeny ; Plant Proteins/*classification/*metabolism ; Protein Isoforms/genetics/metabolism ; Sequence Homology, Amino Acid ; Thioredoxins/*classification/genetics/*metabolism ; }, abstract = {Thioredoxins are small proteins catalyzing thiol-disulfide interchange and are involved in the regulation of the redox environment of the cell. In plants, the thioredoxin system is particularly complex since at least 20 thioredoxin isoforms are found in the plant model Arabidopsis thaliana. Based upon primary sequence analysis and subcellular localization, thioredoxins can be classified into different groups and subgroups. Different pathways allowing thioredoxin reduction also coexist in the plant involving ferredoxin-thioredoxin reductase, thioredoxin reductases and the glutathione/glutaredoxin system. This review discusses the literature of plant thioredoxins with emphasis on recent findings in the field.}, }
@article {pmid15611174, year = {2004}, author = {Shoemaker, DD and Dyer, KA and Ahrens, M and McAbee, K and Jaenike, J}, title = {Decreased diversity but increased substitution rate in host mtDNA as a consequence of Wolbachia endosymbiont infection.}, journal = {Genetics}, volume = {168}, number = {4}, pages = {2049-2058}, pmid = {15611174}, issn = {0016-6731}, mesh = {Animals ; *DNA, Mitochondrial ; Drosophila/*genetics/*microbiology ; *Evolution, Molecular ; Genetic Variation ; Mitochondria/genetics ; Molecular Sequence Data ; Wolbachia/*metabolism ; }, abstract = {A substantial fraction of insects and other terrestrial arthropods are infected with parasitic, maternally transmitted endosymbiotic bacteria that manipulate host reproduction. In addition to imposing direct selection on the host to resist these effects, endosymbionts may also have indirect effects on the evolution of the mtDNA with which they are cotransmitted. Patterns of mtDNA diversity and evolution were examined in Drosophila recens, which is infected with the endosymbiont Wolbachia, and its uninfected sister species D. subquinaria. The level of mitochondrial, but not nuclear, DNA diversity is much lower in D. recens than in D. subquinaria, consistent with the hypothesized diversity-purging effects of an evolutionarily recent Wolbachia sweep. The d(N)/d(S) ratio in mtDNA is significantly greater in D. recens, suggesting that Muller's ratchet has brought about an increased rate of substitution of slightly deleterious mutations. The data also reveal elevated rates of synonymous substitutions in D. recens, suggesting that these sites may experience weak selection. These findings show that maternally transmitted endosymbionts can severely depress levels of mtDNA diversity within an infected host species, while accelerating the rate of divergence among mtDNA lineages in different species.}, }
@article {pmid15604675, year = {2004}, author = {Parisi, G and Perales, M and Fornasari, MS and Colaneri, A and González-Schain, N and Gómez-Casati, D and Zimmermann, S and Brennicke, A and Araya, A and Ferry, JG and Echave, J and Zabaleta, E}, title = {Gamma carbonic anhydrases in plant mitochondria.}, journal = {Plant molecular biology}, volume = {55}, number = {2}, pages = {193-207}, pmid = {15604675}, issn = {0167-4412}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics ; Arabidopsis Proteins/genetics/metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Binding Sites/genetics ; Carbonic Anhydrases/chemistry/*genetics/metabolism ; Green Fluorescent Proteins/genetics/metabolism ; Isoenzymes/chemistry/genetics/metabolism ; Methanosarcina/genetics ; Microscopy, Confocal ; Mitochondria/metabolism ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; *Phylogeny ; Plant Proteins/chemistry/*genetics/metabolism ; Plants, Genetically Modified ; Protein Conformation ; Protein Structure, Tertiary ; Protein Transport ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Three genes from Arabidopsis thaliana with high sequence similarity to gamma carbonic anhydrase (gammaCA), a Zn containing enzyme from Methanosarcina thermophila (CAM), were identified and characterized. Evolutionary and structural analyses predict that these genes code for active forms of gammaCA. Phylogenetic analyses reveal that these Arabidopsis gene products cluster together with CAM and related sequences from alpha and gamma proteobacteria, organisms proposed as the mitochondrial endosymbiont ancestor. Indeed, in vitro and in vivo experiments indicate that these gene products are transported into the mitochondria as occurs with several mitochondrial protein genes transferred, during evolution, from the endosymbiotic bacteria to the host genome. Moreover, putative CAM orthologous genes are detected in other plants and green algae and were predicted to be imported to mitochondria. Structural modeling and sequence analysis performed in more than a hundred homologous sequences show a high conservation of functionally important active site residues. Thus, the three histidine residues involved in Zn coordination (His 81, 117 and 122), Arg 59, Asp 61, Gin 75, and Asp 76 of CAM are conserved and properly arranged in the active site cavity of the models. Two other functionally important residues (Glu 62 and Glu 84 of CAM) are lacking, but alternative amino acids that might serve to their roles are postulated. Accordingly, we propose that photosynthetic eukaryotic organisms (green algae and plants) contain gammaCAs and that these enzymes codified by nuclear genes are imported into mitochondria to accomplish their biological function.}, }
@article {pmid15599510, year = {2004}, author = {Thomarat, F and Vivarès, CP and Gouy, M}, title = {Phylogenetic analysis of the complete genome sequence of Encephalitozoon cuniculi supports the fungal origin of microsporidia and reveals a high frequency of fast-evolving genes.}, journal = {Journal of molecular evolution}, volume = {59}, number = {6}, pages = {780-791}, pmid = {15599510}, issn = {0022-2844}, mesh = {Animals ; Classification/methods ; Cluster Analysis ; Computational Biology ; *Evolution, Molecular ; Fungal Proteins/genetics ; *Genome, Fungal ; Likelihood Functions ; Microsporidia/classification/*genetics ; Models, Genetic ; *Phylogeny ; }, abstract = {Microsporidia are unicellular eukaryotes living as obligate intracellular parasites. Lacking mitochondria, they were initially considered as having diverged before the endosymbiosis at the origin of mitochondria. That microsporidia were primitively amitochondriate was first questioned by the discovery of microsporidial sequences homologous to genes encoding mitochondrial proteins and then refuted by the identification of remnants of mitochondria in their cytoplasm. Various molecular phylogenies also cast doubt on the early divergence of microsporidia, these organisms forming a monophyletic group with or within the fungi. The 2001 proteins putatively encoded by the complete genome of Encephalitozoon cuniculi provided powerful data to test this hypothesis. Phylogenetic analysis of 99 proteins selected as adequate phylogenetic markers indicated that the E. cuniculi sequences having the lowest evolutionary rates preferentially clustered with fungal sequences or, more rarely, with both animal and fungal sequences. Because sequences with low evolutionary rates are less sensitive to the long-branch attraction artifact, we concluded that microsporidia are evolutionarily related to fungi. This analysis also allowed comparing the accuracy of several phylogenetic algorithms for a fast-evolving lineage with real rather than simulated sequences.}, }
@article {pmid15598738, year = {2004}, author = {Cho, Y and Mower, JP and Qiu, YL and Palmer, JD}, title = {Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {51}, pages = {17741-17746}, pmid = {15598738}, issn = {0027-8424}, support = {R01 GM035087/GM/NIGMS NIH HHS/United States ; R01-GM-35087/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Nucleus/genetics ; Chloroplasts/genetics ; Cyclooxygenase 1 ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Flowers/classification/cytology/*genetics ; Genes, Plant/*genetics ; Genetic Variation/*genetics ; Isoenzymes/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Mutation/genetics ; Phylogeny ; Plantago/classification/*cytology/*genetics ; Prostaglandin-Endoperoxide Synthases/genetics ; Time Factors ; Trees/genetics ; }, abstract = {Plant mitochondrial (mt) genomes have long been known to evolve slowly in sequence. Here we show remarkable departure from this pattern of conservative evolution in a genus of flowering plants. Substitution rates at synonymous sites vary substantially among lineages within Plantago. At the extreme, rates in Plantago exceed those in exceptionally slow plant lineages by approximately 4,000-fold. The fastest Plantago lineages set a new benchmark for rapid evolution in a DNA genome, exceeding even the fastest animal mt genome by an order of magnitude. All six mt genes examined show similarly elevated divergence in Plantago, implying that substitution rates are highly accelerated throughout the genome. In contrast, substitution rates show little or no elevation in Plantago for each of four chloroplast and three nuclear genes examined. These results, combined with relatively modest elevations in rates of nonsynonymous substitutions in Plantago mt genes, indicate that major, reversible changes in the mt mutation rate probably underlie the extensive variation in synonymous substitution rates. These rate changes could be caused by major changes in any number of factors that control the mt mutation rate, from the production and detoxification of oxygen free radicals in the mitochondrion to the efficacy of mt DNA replication and/or repair.}, }
@article {pmid15592871, year = {2004}, author = {Souto-Padrón, T and Labriola, CA and de Souza, W}, title = {Immunocytochemical localisation of calreticulin in Trypanosoma cruzi.}, journal = {Histochemistry and cell biology}, volume = {122}, number = {6}, pages = {563-569}, pmid = {15592871}, issn = {0948-6143}, mesh = {Animals ; Calreticulin/immunology/*metabolism ; Cell Nucleus/metabolism ; Cytosol/metabolism ; DNA, Kinetoplast/metabolism ; Endoplasmic Reticulum/metabolism ; Golgi Apparatus/metabolism ; Immunohistochemistry ; Microscopy, Immunoelectron ; Mitochondria/metabolism ; Transport Vesicles/metabolism ; Trypanosoma cruzi/*metabolism/ultrastructure ; }, abstract = {Calreticulin, a Ca(2+) chaperone, is found in many different locations in various eukaryotic cells, including lumen of the endoplasmic reticulum, the cell surface, perinuclear areas and cytosolic granules. In the present study, a polyclonal antibody against calreticulin was used for the immunocytochemical localisation of the protein in Trypanosoma cruzi. Labelling was observed in the endoplasmic reticulum, Golgi complex, reservosomes, flagellar pocket, cell surface, cytosol, nucleus and kinetoplast. Significant differences in labelling were observed among the three evolutive forms of the protozoan. The functional role of calreticulin in T. cruzi is discussed.}, }
@article {pmid15592471, year = {2005}, author = {Roca, AL and Georgiadis, N and O'Brien, SJ}, title = {Cytonuclear genomic dissociation in African elephant species.}, journal = {Nature genetics}, volume = {37}, number = {1}, pages = {96-100}, doi = {10.1038/ng1485}, pmid = {15592471}, issn = {1061-4036}, mesh = {Africa South of the Sahara ; Animals ; DNA, Mitochondrial ; Elephants/*genetics ; Female ; *Gene Frequency ; *Genetics, Population ; Haplotypes ; Male ; Molecular Sequence Data ; Phylogeny ; }, abstract = {African forest and savanna elephants are distinct species separated by a hybrid zone. Because hybridization can affect the systematic and conservation status of populations, we examined gene flow between forest and savanna elephants at 21 African locations. We detected cytonuclear dissociation, indicative of different evolutionary histories for nuclear and mitochondrial genomes. Both paternally (n = 205 males) and biparentally (n = 2,123 X-chromosome segments) inherited gene sequences indicated that there was deep genetic separation between forest and savanna elephants. Yet in some savanna locales distant from present-day forest habitats, many individuals with savanna-specific nuclear genotypes carried maternally transmitted forest elephant mitochondrial DNA. This extreme cytonuclear dissociation implies that there were ancient episodes of hybridization between forest females and savanna males, which are larger and reproductively dominant to forest or hybrid males. Recurrent backcrossing of female hybrids to savanna bulls replaced the forest nuclear genome. The persistence of residual forest elephant mitochondria in savanna elephant herds renders evolutionary interpretations based on mitochondrial DNA alone misleading and preserves a genomic record of ancient habitat changes.}, }
@article {pmid15588583, year = {2004}, author = {Mizumoto, K and Murai, K and Nakamura, C and Takumi, S}, title = {Preferential expression of a HLP homolog encoding a mitochondrial L14 ribosomal protein in stamens of common wheat.}, journal = {Gene}, volume = {343}, number = {2}, pages = {281-289}, doi = {10.1016/j.gene.2004.09.005}, pmid = {15588583}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Arabidopsis Proteins/*genetics ; Cell Nucleus/genetics ; Flowers/*genetics/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Recombinant Fusion Proteins/genetics/metabolism ; Recombinant Proteins/*genetics ; Ribosomal Proteins/*genetics/metabolism ; Sequence Homology, Amino Acid ; Triticum/*genetics ; }, abstract = {Interaction between nucleus and cytoplasm has essential roles in plant development, including that of floral organs. We isolated a wheat homolog Whlp of Arabidopsis HUELLENLOS PARALOG (HLP) gene encoding a mitochondrial (mt) ribosomal protein L14. Transient expression analysis using the green fluorescent protein (GFP) fusion protein showed that 50 amino residues located on the N-terminal of the wheat HLP homolog (WHLP) protein acted as a mt-targeting signal (MTS). Expression patterns of the Whlp gene were compared among floral organs of alloplasmic lines of wheat, in which intrinsic cytoplasms were replaced by the cytoplasm of a wild relative Aegilops crassa. In these alloplasmic lines, pistillody (homeotic transformation of stamens into pistil-like organs) is induced by the alien cytoplasm in the absence of nuclear restorer genes. The Whlp transcripts preferentially accumulated in stamens compared with pistils, leaves, and roots. The expression level of Whlp in the pistillate stamens of the alloplasmic lines was similar to that in genuine pistils of both euplasmic lines and fertile alloplasmic lines. The result suggested that the elevated expression of the Whlp gene plays a role in aiding the development of male reproductive organ but not in the determination of its whorl identity. A comparable expression pattern was observed in another nuclear-encoded mt ribosomal protein gene but not in a mt-encoded gene. The different expression patterns of different mt ribosomal protein genes suggest that the abundance of mt ribosomal proteins is differentially regulated in the organ/tissue development in wheat.}, }
@article {pmid15585129, year = {2004}, author = {Krishnan, NM and Seligmann, H and Raina, SZ and Pollock, DD}, title = {Detecting gradients of asymmetry in site-specific substitutions in mitochondrial genomes.}, journal = {DNA and cell biology}, volume = {23}, number = {10}, pages = {707-714}, pmid = {15585129}, issn = {1044-5498}, support = {R24 GM065580/GM/NIGMS NIH HHS/United States ; R33 GM065612/GM/NIGMS NIH HHS/United States ; GM065580-01/GM/NIGMS NIH HHS/United States ; GM065612-01/GM/NIGMS NIH HHS/United States ; R21 GM065612/GM/NIGMS NIH HHS/United States ; R33 GM065612-03/GM/NIGMS NIH HHS/United States ; }, mesh = {*Genome ; Markov Chains ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Messenger/chemistry/genetics ; }, abstract = {During mitochondrial replication, spontaneous mutations occur and accumulate asymmetrically during the time spent single stranded by the heavy strand (DssH). The predominant mutations appear to be deaminations from adenine to hypoxanthine (A --> H, which leads to an A --> G substitution) and cytosine to thymine (C --> T). Previous findings indicated that C --> T substitutions accumulate rapidly and then saturate at high DssH, suggesting protection or repair, whereas A --> G accumulates linearly with DssH. We describe here the implementation of a simple hidden Markov model (HMM) of among-site rate correlations to provide an almost continuous profile of the asymmetry in substitution response for any particular substitution type. We implement this model using a phylogeny-based Bayesian Markov chain Monte Carlo (MCMC) approach. We compare and contrast the relative asymmetries in all 12 possible substitution types, and find that the observed transition substitution responses determined using our new method agree quite well with previous predictions of a saturating curve for C --> T transition substitutions and a linear accumulation of A --> G transitions. The patterns seen in transversion substitutions show much lower among-site variation, and are nonlinear and more complex than those seen in transitions. We also find that, after accounting for the principal linear effect, some of the residual variation in A --> G/G --> A response ratios is explained by the average predicted nucleic acid secondary structure propensity at a site, possibly due to protection from mutation when secondary structure forms.}, }
@article {pmid15583938, year = {2005}, author = {Sugiyama, Y and Watase, Y and Nagase, M and Makita, N and Yagura, S and Hirai, A and Sugiura, M}, title = {The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants.}, journal = {Molecular genetics and genomics : MGG}, volume = {272}, number = {6}, pages = {603-615}, pmid = {15583938}, issn = {1617-4615}, mesh = {Base Sequence ; Contig Mapping ; DNA, Mitochondrial/*genetics ; Gene Order/*genetics ; Genes, rRNA ; *Genome, Plant ; Magnoliopsida/classification/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Nicotiana/classification/*genetics ; }, abstract = {Tobacco is a valuable model system for investigating the origin of mitochondrial DNA (mtDNA) in amphidiploid plants and studying the genetic interaction between mitochondria and chloroplasts in the various functions of the plant cell. As a first step, we have determined the complete mtDNA sequence of Nicotiana tabacum. The mtDNA of N. tabacum can be assumed to be a master circle (MC) of 430,597 bp. Sequence comparison of a large number of clones revealed that there are four classes of boundaries derived from homologous recombination, which leads to a multipartite organization with two MCs and six subgenomic circles. The mtDNA of N. tabacum contains 36 protein-coding genes, three ribosomal RNA genes and 21 tRNA genes. Among the first class, we identified the genes rps1 and psirps14, which had previously been thought to be absent in tobacco mtDNA on the basis of Southern analysis. Tobacco mtDNA was compared with those of Arabidopsis thaliana, Beta vulgaris, Oryza sativa and Brassica napus. Since repeated sequences show no homology to each other among the five angiosperms, it can be supposed that these were independently acquired by each species during the evolution of angiosperms. The gene order and the sequences of intergenic spacers in mtDNA also differ widely among the five angiosperms, indicating multiple reorganizations of genome structure during the evolution of higher plants. Among the conserved genes, the same potential conserved nonanucleotide-motif-type promoter could only be postulated for rrn18-rrn5 in four of the dicotyledonous plants, suggesting that a coding sequence does not necessarily move with the promoter upon reorganization of the mitochondrial genome.}, }
@article {pmid15579394, year = {2005}, author = {Trontelj, P and Machino, Y and Sket, B}, title = {Phylogenetic and phylogeographic relationships in the crayfish genus Austropotamobius inferred from mitochondrial COI gene sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {1}, pages = {212-226}, doi = {10.1016/j.ympev.2004.09.010}, pmid = {15579394}, issn = {1055-7903}, mesh = {Animals ; Astacoidea/*genetics ; Electron Transport Complex IV/*genetics ; Europe ; Evolution, Molecular ; Genetic Variation ; Geography ; Haplotypes ; Likelihood Functions ; Mitochondria/*genetics ; *Phylogeny ; }, abstract = {The present study explores the utility of mitochondrial COI gene sequences to reveal phylogenetic and phylogeographic relationships for the entire European freshwater crayfish genus Austropotamobius. The two traditional taxa, Austropotamobius pallipes and Austropotamobius torrentium, were monophyletic, showing similar genetic diversity, with 28 and 25 haplotypes, respectively, and an uncorrected average pairwise divergence of 0.059 and 0.041. A third distinct haplotype clade, in sister relation to A. torrentium, was discovered at the Upper Kolpa drainage in the northern Dinaric area. All populations north and west of the Alps are genetically impoverished (nucleotide diversity (pi)=0.000-0.001), while southern populations are more diverse (pi=0.001-0.034). A. pallipes reaches the highest diversity in the region of Istra, probably its primary center of radiation. The genetic diversity center for A. torrentium is the southern Balkan peninsula. Other potential glacial refugia were identified in Southern France, Northwestern Italy, the Apennine Peninsula, and in the northern Dinaric area. The Iberian Peninsula has been stocked artificially from Northern Italy. Three main periods of radiation were tentatively identified: late Miocene/early Pliocene for the divergence of species and main lineages, the Pleistocene for the divergence within populations south from Alps, and a postPleistocene expansion north and west from Alps.}, }
@article {pmid15579392, year = {2005}, author = {Moussalli, A and Hugall, AF and Moritz, C}, title = {A mitochondrial phylogeny of the rainforest skink genus Saproscincus, Wells and Wellington (1984).}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {1}, pages = {190-202}, doi = {10.1016/j.ympev.2004.08.022}, pmid = {15579392}, issn = {1055-7903}, mesh = {Animals ; Australia ; Base Sequence ; Bayes Theorem ; Genetic Variation ; Geography ; Lizards/*genetics ; Mitochondria/*genetics ; Models, Genetic ; *Phylogeny ; Sequence Alignment ; }, abstract = {The phylogenetic relationships and historical biogeography of 10 currently described rainforest skinks in the genus Saproscincus were investigated using mitochondrial protein-coding ND4 and ribosomal RNA 16S genes. A robust phylogeny is inferred using both maximum likelihood and Bayesian analysis, with all inter-specific nodes strongly supported when datasets are combined. The phylogeny supports the recognition of two major lineages (northern and southern), each of which comprises two divergent clades. Both northern and southern lineages have comparably divergent representatives in mid-east Queensland (MEQ), providing further molecular evidence for the importance of two major biogeographic breaks, the St. Lawrence gap and Burdekin gap separating MEQ from southern and northern counterparts respectively. Vicariance associated with the fragmentation and contraction of temperate rainforest during the mid-late Miocene epoch underpins the deep divergence between morphologically conservative lineages in at least three instances. In contrast, one species, Saproscincus oriarus, shows very low sequence divergence but distinct morphological and ecological differentiation from its allopatric sister clade within Saproscincus mustelinus. These results suggest that while vicariance has played a prominent role in diversification and historical biogeography of Saproscincus, divergent selection may also be important.}, }
@article {pmid15579391, year = {2005}, author = {Gongora, J and Moran, C}, title = {Nuclear and mitochondrial evolutionary analyses of Collared, White-lipped, and Chacoan peccaries (Tayassuidae).}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {1}, pages = {181-189}, doi = {10.1016/j.ympev.2004.08.021}, pmid = {15579391}, issn = {1055-7903}, mesh = {Animals ; Artiodactyla/*genetics ; Cell Nucleus/*genetics ; *Evolution, Molecular ; Locus Control Region/genetics ; Mitochondria/*genetics ; Natural History ; }, abstract = {The three extant peccary species, the Chacoan (Catagonus wagneri), the White-lipped (Tayassu pecari) and the Collared (Pecari tajacu), are morphologically and chromosomally distinct and confined to the New World. There is ongoing paleontological, cytogenetic, and molecular debate about phylogenetic relationships among them. To contribute to the understanding of Tayassuidae phylogeny, three mitochondrial (control region, cytochrome b, and 12S rRNA) and five nuclear (K-casein, thyrotropin, tyrosinase, and swine short interspersed nuclear elements PRE-1 P27 and P642) peccary DNA fragments were amplified, cloned and sequenced from Chacoan, White-lipped, and Collared peccaries. Phylogenetic analyses were performed using maximum likelihood and neighbor joining methods. K-casein, thyrotropin, and tyrosinase sequences did not resolve the phylogeny, while control region, cytochrome b, 12S rRNA, and PRE-1 P27 and P642 sequences were more informative in deciphering phylogenetic relationships. When pig and warthog were used as an outgroup, Chacoan and White-lipped peccaries clustered distinct from Collared peccaries. Furthermore, control region and cytochrome b sequence variation within Collared peccaries was as extreme as that between White-lipped and Chacoan peccaries, supporting subspecific and possibly even specific variation within the widely distributed Collared peccary. This study supports the existence of two independent genera within the Tayassuidae family consisting of Collared and Chacoan/White-lipped peccaries, in contrast with classical morphological taxonomy which clusters White-lipped and Collared peccaries in the genus Tayassu or which alternatively clusters the Collared peccary in the genus Dicotyles as a related sister clade of the Chacoan peccary (genus Catagonus).}, }
@article {pmid15579390, year = {2005}, author = {Burbrink, FT}, title = {Inferring the phylogenetic position of Boa constrictor among the Boinae.}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {1}, pages = {167-180}, doi = {10.1016/j.ympev.2004.08.017}, pmid = {15579390}, issn = {1055-7903}, mesh = {Animals ; Bayes Theorem ; Boidae/anatomy &amp; histology/classification/*genetics ; Cytochromes b/genetics ; Evolution, Molecular ; Geography ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; }, abstract = {Snakes of the subfamily Boinae are found in Madagascar, the Papuan-Pacific Islands, and the Neotropics. It has been suggested that genera within each of these particular areas do not form monophyletic groups. Further, it was proposed that the New World Boa constrictor is more closely related to boine genera in Madagascar than to boines in the Neotropics. Along with inferring the relationship of all boine genera using data from the cytochrome b gene and morphology, the placement of Boa was also examined. Phylogenetic inferences using maximum likelihood and Bayesian (BI) methods for combined data analyses and separate analyses of DNA sequence and morphological data were conducted. Priors, parametric bootstraps, and the Shimodaira-Hasegawa test were used to examine the previously proposed placement of Boa with Madagascan taxa using these DNA data. DNA data and combined data analyses strongly reject the hypothesis that Boa is more closely related to Old World genera than to other New World genera. Additionally, strong tree support suggests that all species within Madagascar, the Papuan-Pacific Islands, and the Neotropics each form a monophyletic group with respect to their geographic region.}, }
@article {pmid15579385, year = {2005}, author = {Froufe, E and Knizhin, I and Weiss, S}, title = {Phylogenetic analysis of the genus Thymallus (grayling) based on mtDNA control region and ATPase 6 genes, with inferences on control region constraints and broad-scale Eurasian phylogeography.}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {1}, pages = {106-117}, doi = {10.1016/j.ympev.2004.09.009}, pmid = {15579385}, issn = {1055-7903}, mesh = {Animals ; Asia ; Base Sequence ; *DNA, Mitochondrial ; Europe ; Geography ; *Locus Control Region ; Mitochondria/genetics ; Mitochondrial Proton-Translocating ATPases/*genetics ; *Phylogeny ; Salmonidae/*genetics ; Sequence Alignment ; }, abstract = {We present first insights into the molecular phylogeny of the grayling genus Thymallus (Salmonidae) using sequences from the mitochondrial control region and ATPase6 genes. A suite of analytical approaches were applied for each gene separately and for the combined data. The ATPase6 gene is shown to have a mean divergence rate across the genus of 2.46 times faster than the complete control region. Based on the combined data, four major (internal) clades, presumably originating in the Pliocene, were resolved with high support in all analyses and represented two distinct lineages in the Amur basin, one lineage in all remaining Siberian and Mongolian drainages, and one lineage corresponding to European grayling Thymallus thymallus. The resolution of multiple lineages, from both additional internal and terminal clades, within each major drainage basin underscores the complexity and effects that Pleistocene hydrological dynamics have had on the distribution of biodiversity in Siberia.}, }
@article {pmid15579384, year = {2005}, author = {Van der Meij, MA and de Bakker, MA and Bout, RG}, title = {Phylogenetic relationships of finches and allies based on nuclear and mitochondrial DNA.}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {1}, pages = {97-105}, doi = {10.1016/j.ympev.2004.09.006}, pmid = {15579384}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Cell Nucleus/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial ; Fibrinogen/genetics ; Finches/*genetics ; Genetic Variation ; Mitochondria/*genetics ; *Phylogeny ; Sequence Alignment ; }, abstract = {The complete mitochondrial gene cytochrome b in combination with a nuclear gene, beta-fibrinogen intron 7, is sequenced for different groups of mostly granivorous species in the superfamily Passeroidea, with a focus on the estrildids and fringillids. From our study we can conclude that within the group of granivorous finches two clades can be distinguished, the estrildid weaver clade and the cardueline, fringillid, emberizid, passerine sparrow clade. In contrast to many other studies the passerine sparrows are not placed within the weavers estrildid clade which is in agreement with other recent studies (e.g.,). Our study also shows that the estrildids do form a monophyletic group, but there is a division based on geographic origin: an African group and an Asian-Australian group. Within the Fringillidae the Fringilla species are the sister group of the carduelines.}, }
@article {pmid15579381, year = {2005}, author = {Kasapidis, P and Suchentrunk, F and Magoulas, A and Kotoulas, G}, title = {The shaping of mitochondrial DNA phylogeographic patterns of the brown hare (Lepus europaeus) under the combined influence of Late Pleistocene climatic fluctuations and anthropogenic translocations.}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {1}, pages = {55-66}, doi = {10.1016/j.ympev.2004.09.007}, pmid = {15579381}, issn = {1055-7903}, mesh = {Animals ; *DNA, Mitochondrial ; Europe ; Evolution, Molecular ; Geography ; Haplotypes ; Hares/*genetics ; Mitochondria/*genetics ; Natural History ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The phylogeographic structure of the brown hare (Lepus europaeus) was studied by analysing mtDNA control region sequences of 98 individuals from continental and insular Greece, Bulgaria, Cyprus and northern Israel, together with 44 published sequences from Italy and central Europe. We found two distinct clades separated by an average nucleotide divergence of 6.6%, which may correspond to a Balkan and to an Asia Minor refugium. The estimated time of separation of the two clades was dated back to 105,000- 490,000 years ago. These two clades coexist in the area of northeastern Greece and Bulgaria, most likely as a result of a post-glacial northward expansion. Within the southern Balkan refugium, network analyses showed geographical structuring, which supports the hypothesis of several isolated Late Pleistocene populations. The central European and Italian populations appear to have originated from a non-detected northern Balkan population that was genetically closely related to some northern Greek populations, as a result of postglacial expansion, translocations or a combination of both. Moreover, several cases of ancient and recent translocations by humans were detected, especially for some island populations, while the eastern Aegean islands off the Asia Minor coast were most likely colonized naturally through Late Pleistocene land bridge connection. The genetic analysis presented here provides a framework for designing proper conservation and management guidelines for this species.}, }
@article {pmid15579378, year = {2005}, author = {Wüster, W and Dumbrell, AJ and Hay, C and Pook, CE and Williams, DJ and Fry, BG}, title = {Snakes across the Strait: trans-Torresian phylogeographic relationships in three genera of Australasian snakes (Serpentes: Elapidae: Acanthophis, Oxyuranus, and Pseudechis).}, journal = {Molecular phylogenetics and evolution}, volume = {34}, number = {1}, pages = {1-14}, doi = {10.1016/j.ympev.2004.08.018}, pmid = {15579378}, issn = {1055-7903}, mesh = {Animals ; Australia ; DNA, Mitochondrial ; Elapidae/*genetics ; Geography ; Haplotypes ; Mitochondria/genetics ; New Guinea ; Phylogeny ; }, abstract = {We analyze the phylogeny of three genera of Australasian elapid snakes (Acanthophis-death adders; Oxyuranus-taipans; Pseudechis-blacksnakes), using parsimony, maximum likelihood, and Bayesian analysis of sequences of the mitochondrial cytochrome b and ND4 genes. In Acanthophis and Pseudechis, we find evidence of multiple trans-Torresian sister-group relationships. Analyses of the timing of cladogenic events suggest crossings of the Torres Strait on several occasions between the late Miocene and the Pleistocene. These results support a hypothesis of repeated land connections between Australia and New Guinea in the late Cenozoic. Additionally, our results reveal undocumented genetic diversity in Acanthophis and Pseudechis, supporting the existence of more species than previously believed, and provide a phylogenetic framework for a reinterpretation of the systematics of these genera. In contrast, our Oxyuranus scutellatus samples from Queensland and two localities in New Guinea share a single haplotype, suggesting very recent (late Pleistocene) genetic exchange between New Guinean and Australian populations.}, }
@article {pmid15577909, year = {2004}, author = {Hrdy, I and Hirt, RP and Dolezal, P and Bardonová, L and Foster, PG and Tachezy, J and Embley, TM}, title = {Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I.}, journal = {Nature}, volume = {432}, number = {7017}, pages = {618-622}, doi = {10.1038/nature03149}, pmid = {15577909}, issn = {1476-4687}, mesh = {Aerobiosis ; Amino Acid Sequence ; Anaerobiosis ; Animals ; Electron Transport Complex I/chemistry/*metabolism ; Hydrogen/*metabolism ; Malates/metabolism ; Mitochondria/*enzymology/metabolism ; Models, Biological ; Molecular Sequence Data ; NAD/metabolism ; NADH Dehydrogenase/chemistry/*metabolism ; Organelles/*enzymology/metabolism ; Phylogeny ; Protein Subunits/chemistry/metabolism ; Protozoan Proteins/chemistry/metabolism ; Sequence Alignment ; Symbiosis ; Trichomonas vaginalis/*cytology/*enzymology/metabolism ; }, abstract = {Hydrogenosomes are double-membraned ATP-producing and hydrogen-producing organelles of diverse anaerobic eukaryotes. In some versions of endosymbiotic theory they are suggested to be homologues of mitochondria, but alternative views suggest they arose from an anaerobic bacterium that was distinct from the mitochondrial endosymbiont. Here we show that the 51-kDa and 24-kDa subunits of the NADH dehydrogenase module in complex I, the first step in the mitochondrial respiratory chain, are active in hydrogenosomes of Trichomonas vaginalis. Like mitochondrial NADH dehydrogenase, the purified Trichomonas enzyme can reduce a variety of electron carriers including ubiquinone, but unlike the mitochondrial enzyme it can also reduce ferredoxin, the electron carrier used for hydrogen production. The presence of NADH dehydrogenase solves the long-standing conundrum of how hydrogenosomes regenerate NAD+ after malate oxidation. Phylogenetic analyses show that the Trichomonas 51-kDa homologue shares common ancestry with the mitochondrial enzyme. Recruitment of complex I subunits into a H2-producing pathway provides evidence that mitochondria and hydrogenosomes are aerobic and anaerobic homologues of the same endosymbiotically derived organelle.}, }
@article {pmid15576054, year = {2004}, author = {Gabaldón, T and Huynen, MA}, title = {Shaping the mitochondrial proteome.}, journal = {Biochimica et biophysica acta}, volume = {1659}, number = {2-3}, pages = {212-220}, doi = {10.1016/j.bbabio.2004.07.011}, pmid = {15576054}, issn = {0006-3002}, mesh = {Animals ; *Biological Evolution ; Biological Transport ; Energy Metabolism ; Eukaryotic Cells/physiology ; Humans ; Mitochondria/*physiology ; Phylogeny ; Proteome/*physiology ; }, abstract = {Mitochondria are eukaryotic organelles that originated from a single bacterial endosymbiosis some 2 billion years ago. The transition from the ancestral endosymbiont to the modern mitochondrion has been accompanied by major changes in its protein content, the so-called proteome. These changes included complete loss of some bacterial pathways, amelioration of others and gain of completely new complexes of eukaryotic origin such as the ATP/ADP translocase and most of the mitochondrial protein import machinery. This renewal of proteins has been so extensive that only 14-16% of modern mitochondrial proteome has an origin that can be traced back to the bacterial endosymbiont. The rest consists of proteins of diverse origin that were eventually recruited to function in the organelle. This shaping of the proteome content reflects the transformation of mitochondria into a highly specialized organelle that, besides ATP production, comprises a variety of functions within the eukaryotic metabolism. Here we review recent advances in the fields of comparative genomics and proteomics that are throwing light on the origin and evolution of the mitochondrial proteome.}, }
@article {pmid15574809, year = {2005}, author = {Bayona-Bafaluy, MP and Müller, S and Moraes, CT}, title = {Fast adaptive coevolution of nuclear and mitochondrial subunits of ATP synthetase in orangutan.}, journal = {Molecular biology and evolution}, volume = {22}, number = {3}, pages = {716-724}, doi = {10.1093/molbev/msi059}, pmid = {15574809}, issn = {0737-4038}, support = {GM55766/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Line ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Hominidae/*genetics ; Humans ; Mitochondria/genetics ; Mitochondrial Proton-Translocating ATPases/*genetics ; Oxidative Phosphorylation ; Phylogeny ; }, abstract = {Nuclear and mitochondrial genomes have to work in concert to generate a functional oxidative phosphorylation (OXPHOS) system. We have previously shown that we could restore partial OXPHOS function when chimpanzee or gorilla mitochondrial DNA (mtDNA) were introduced into human cells lacking mtDNA. However, we were unable to maintain orangutan mitochondrial DNA in a human cell. We have now produced chimpanzee, gorilla, orangutan, and baboon cells lacking mtDNA and attempted to introduce mtDNA from different apes into them. Surprisingly, we were able to maintain human mtDNA in an orangutan nuclear background, even though these cells showed severe OXPHOS abnormalities, including a complete absence of assembled ATP synthetase. Phylogenetic analysis of complex V mtDNA-encoded subunits showed that they are among the most evolutionarily divergent components of the mitochondrial genome between orangutan and the other apes. Our studies showed that adaptive coevolution of nuclear and mitochondrial components in apes can be fast and accelerate in recent branches of anthropoid primates.}, }
@article {pmid15574518, year = {2005}, author = {Golden, DE and Hajduk, SL}, title = {The 3'-untranslated region of cytochrome oxidase II mRNA functions in RNA editing of African trypanosomes exclusively as a cis guide RNA.}, journal = {RNA (New York, N.Y.)}, volume = {11}, number = {1}, pages = {29-37}, pmid = {15574518}, issn = {1355-8382}, support = {R01 AI021401/AI/NIAID NIH HHS/United States ; AI21401/AI/NIAID NIH HHS/United States ; }, mesh = {3' Untranslated Regions ; Animals ; Base Sequence ; Binding Sites/genetics ; Conserved Sequence ; Electron Transport Complex IV/chemistry/*genetics ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Subunits ; *RNA Editing ; RNA, Guide, Kinetoplastida/*genetics/*metabolism ; RNA, Messenger/*genetics/*metabolism ; RNA, Protozoan/*genetics/*metabolism ; Sequence Homology, Nucleic Acid ; Trypanosoma brucei brucei/*genetics/*metabolism ; }, abstract = {RNA editing in trypanosomes is a post-transcriptional process responsible for correcting the coding sequences of many mitochondrial mRNAs. Uridines are specifically added or deleted from mRNA by an enzymatic cascade in which a pre-edited mRNA is specifically cleaved, uridines are added or removed, and the corrected mRNA is ligated. The process is directed by RNA molecules, termed guide RNAs (gRNA). The ability of this class of small, noncoding RNA to function in RNA editing is essential for these organisms. Typically, gRNAs are transcribed independent of the their cognate mRNA and anneal to form a binary RNA complex . An exception for this process may be cytochrome oxidase subunit II (COII) mRNA since a gene encoding a trans acting gRNA has not been identified. Using an in vitro editing assay we find that the 3' UTR of COII, indeed, functions as a guide for both the site and number of uridines added to the coding region of the COII mRNA. We further show that the guiding sequence within the COII 3' UTR can only function in COII editing when contiguous with the editing substrate, indicating that the 3' UTR of COII lacks sequence or structure information necessary to function as a trans-acting gRNA. While other RNAs have been shown to "guide" RNA processing reactions, our discovery that the COII 3' UTR directs editing of its cognate mRNA in cis, is a unique function for a 3' UTR. The findings described here have led us to propose a new model for the evolution of gRNAs in kinetoplastids.}, }
@article {pmid15569691, year = {2005}, author = {Hoffmeister, M and Piotrowski, M and Nowitzki, U and Martin, W}, title = {Mitochondrial trans-2-enoyl-CoA reductase of wax ester fermentation from Euglena gracilis defines a new family of enzymes involved in lipid synthesis.}, journal = {The Journal of biological chemistry}, volume = {280}, number = {6}, pages = {4329-4338}, doi = {10.1074/jbc.M411010200}, pmid = {15569691}, issn = {0021-9258}, mesh = {Adenosine Triphosphate/chemistry ; Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Northern ; Blotting, Western ; Catalysis ; Chromatography ; Cloning, Molecular ; Culture Media ; DNA, Complementary/metabolism ; Electrons ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/metabolism ; Euglena gracilis/*metabolism ; Evolution, Molecular ; Fatty Acids/metabolism ; Kinetics ; *Lipid Metabolism ; Mass Spectrometry ; Mitochondria/*enzymology ; Molecular Sequence Data ; NAD/metabolism ; NADH, NADPH Oxidoreductases/metabolism/*physiology ; NADP/metabolism ; Nucleic Acid Hybridization ; Open Reading Frames ; Operon ; Oxidoreductases Acting on CH-CH Group Donors ; Peptides/chemistry ; Phylogeny ; Protein Binding ; Protein Structure, Tertiary ; Silver Staining ; Trypsin/chemistry ; }, abstract = {Under anaerobiosis, Euglena gracilis mitochondria perform a malonyl-CoA independent synthesis of fatty acids leading to accumulation of wax esters, which serve as the sink for electrons stemming from glycolytic ATP synthesis and pyruvate oxidation. An important enzyme of this unusual pathway is trans-2-enoyl-CoA reductase (EC 1.3.1.44), which catalyzes reduction of enoyl-CoA to acyl-CoA. Trans-2-enoyl-CoA reductase from Euglena was purified 1700-fold to electrophoretic homogeneity and was active with NADH and NADPH as the electron donor. The active enzyme is a monomer with molecular mass of 44 kDa. The amino acid sequence of tryptic peptides determined by electrospray ionization mass spectrometry were used to clone the corresponding cDNA, which encoded a polypeptide that, when expressed in Escherichia coli and purified by affinity chromatography, possessed trans-2-enoyl-CoA reductase activity close to that of the enzyme purified from Euglena. Trans-2-enoyl-CoA reductase activity is present in mitochondria and the mRNA is expressed under aerobic and anaerobic conditions. Using NADH, the recombinant enzyme accepted crotonyl-CoA (km=68 microm) and trans-2-hexenoyl-CoA (km=91 microm). In the crotonyl-CoA-dependent reaction, both NADH (km=109 microm) or NADPH (km=119 microm) were accepted, with 2-3-fold higher specific activities for NADH relative to NADPH. Trans-2-enoyl-CoA reductase homologues were not found among other eukaryotes, but are present as hypothetical reading frames of unknown function in sequenced genomes of many proteobacteria and a few Gram-positive eubacteria, where they occasionally occur next to genes involved in fatty acid and polyketide biosynthesis. Trans-2-enoyl-CoA reductase assigns a biochemical activity, NAD(P)H-dependent acyl-CoA synthesis from enoyl-CoA, to one member of this gene family of previously unknown function.}, }
@article {pmid15568984, year = {2004}, author = {Gray, MW and Lang, BF and Burger, G}, title = {Mitochondria of protists.}, journal = {Annual review of genetics}, volume = {38}, number = {}, pages = {477-524}, doi = {10.1146/annurev.genet.37.110801.142526}, pmid = {15568984}, issn = {0066-4197}, mesh = {Animals ; Bacteria/genetics ; *Biological Evolution ; Cell Lineage ; DNA, Mitochondrial/*genetics ; Eukaryota/genetics ; *Eukaryotic Cells ; Fungi/genetics ; Gene Expression ; Mitochondria/*genetics/metabolism/physiology ; Phylogeny ; Plants/genetics ; Proteomics ; }, abstract = {Over the past several decades, our knowledge of the origin and evolution of mitochondria has been greatly advanced by determination of complete mitochondrial genome sequences. Among the most informative mitochondrial genomes have been those of protists (primarily unicellular eukaryotes), some of which harbor the most gene-rich and most eubacteria-like mitochondrial DNAs (mtDNAs) known. Comparison of mtDNA sequence data has provided insights into the radically diverse trends in mitochondrial genome evolution exhibited by different phylogenetically coherent groupings of eukaryotes, and has allowed us to pinpoint specific protist relatives of the multicellular eukaryotic lineages (animals, plants, and fungi). This comparative genomics approach has also revealed unique and fascinating aspects of mitochondrial gene expression, highlighting the mitochondrion as an evolutionary playground par excellence.}, }
@article {pmid15568970, year = {2004}, author = {Lambowitz, AM and Zimmerly, S}, title = {Mobile group II introns.}, journal = {Annual review of genetics}, volume = {38}, number = {}, pages = {1-35}, doi = {10.1146/annurev.genet.38.072902.091600}, pmid = {15568970}, issn = {0066-4197}, support = {GM37949/GM/NIGMS NIH HHS/United States ; GM37951/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Base Sequence ; DNA Replication ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Gene Targeting ; *Introns ; Models, Genetic ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Phylogeny ; RNA Splicing ; RNA, Catalytic/*genetics ; Retroelements/genetics ; Spliceosomes/genetics ; Yeasts/genetics ; }, abstract = {Mobile group II introns, found in bacterial and organellar genomes, are both catalytic RNAs and retrotransposable elements. They use an extraordinary mobility mechanism in which the excised intron RNA reverse splices directly into a DNA target site and is then reverse transcribed by the intron-encoded protein. After DNA insertion, the introns remove themselves by protein-assisted, autocatalytic RNA splicing, thereby minimizing host damage. Here we discuss the experimental basis for our current understanding of group II intron mobility mechanisms, beginning with genetic observations in yeast mitochondria, and culminating with a detailed understanding of molecular mechanisms shared by organellar and bacterial group II introns. We also discuss recently discovered links between group II intron mobility and DNA replication, new insights into group II intron evolution arising from bacterial genome sequencing, and the evolutionary relationship between group II introns and both eukaryotic spliceosomal introns and non-LTR-retrotransposons. Finally, we describe the development of mobile group II introns into gene-targeting vectors, "targetrons," which have programmable target specificity.}, }
@article {pmid15567032, year = {2005}, author = {Osaki, H and Nakamura, H and Nomura, K and Matsumoto, N and Yoshida, K}, title = {Nucleotide sequence of a mitochondrial RNA virus from the plant pathogenic fungus, Helicobasidium mompa Tanaka.}, journal = {Virus research}, volume = {107}, number = {1}, pages = {39-46}, doi = {10.1016/j.virusres.2004.06.010}, pmid = {15567032}, issn = {0168-1702}, mesh = {Amino Acid Sequence ; Base Sequence ; Basidiomycota/genetics/*virology ; DNA, Viral/genetics ; Mitochondria/virology ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Plants/microbiology ; RNA Viruses/classification/*genetics/isolation &amp; purification ; RNA, Double-Stranded/chemistry/genetics ; RNA, Viral/chemistry/genetics ; Sequence Homology, Amino Acid ; }, abstract = {A double-stranded (ds) RNA (2411 bp) from a strain V18 of the violet root rot basidiomycetous fungus, Helicobasidium mompa was sequenced. Using the fungal mitochondrial genetic code in which UGA codes for tryptophan, the positive strand of V18 dsRNA was found to contain a long open-reading frame with the potential to encode a protein of 700 amino acids (molecular mass 79,805 Da), including conserved motifs characteristic of RNA-dependent RNA polymerase (RDRP). This putative RDRP was shown to be related to putative RDRPs of several fungal mitochondrial viruses. It is proposed that V18 dsRNA is assigned to the genus Mitovirus in the family Narnaviridae and designated as H. mompa mitovirus 1-18 (HmMV1-18). Like other mitoviruses, HmMV1-18 RNA can be folded into potentially stable stem-loop structures at both the 5'- and 3'-termini, and both terminal sequences have inverted complementarity with the potential to form panhandle structure. BLAST analysis indicates that the RDRP encoded by HmMV1-18 is more closely related to those encoded by mitochondrial viruses of some ascomycetes than to that of the unassigned RsM2-1A1 dsRNA in the basidiomycetous Rhizoctonia solani. HmMV1-18 is the first member of the genus Mitovirus from basidiomycete fungi.}, }
@article {pmid15563690, year = {2005}, author = {Ruchko, M and Gorodnya, O and LeDoux, SP and Alexeyev, MF and Al-Mehdi, AB and Gillespie, MN}, title = {Mitochondrial DNA damage triggers mitochondrial dysfunction and apoptosis in oxidant-challenged lung endothelial cells.}, journal = {American journal of physiology. Lung cellular and molecular physiology}, volume = {288}, number = {3}, pages = {L530-5}, doi = {10.1152/ajplung.00255.2004}, pmid = {15563690}, issn = {1040-0605}, mesh = {Animals ; *Apoptosis ; Caspase 3 ; Caspases/metabolism ; Cell Nucleus/ultrastructure ; Cells, Cultured ; *DNA Damage ; DNA Fragmentation ; DNA Glycosylases/metabolism ; *DNA, Mitochondrial ; Endothelial Cells/*drug effects/ultrastructure ; Enzyme Activation ; Membrane Potentials ; *Mitochondria/metabolism ; Oxidants/pharmacology ; Pulmonary Artery/*drug effects/*physiopathology/ultrastructure ; Rats ; Rats, Sprague-Dawley ; Xanthine Oxidase/*pharmacology ; }, abstract = {Oxidant-induced death and dysfunction of pulmonary vascular cells play important roles in the evolution of acute lung injury. In pulmonary artery endothelial cells (PAECs), oxidant-mediated damage to mitochondrial DNA (mtDNA) seems to be critical in initiating cytotoxicity inasmuch as overexpression of the mitochondrially targeted human DNA repair enzyme, human Ogg1 (hOgg1), prevents both mtDNA damage and cell death (Dobson AW, Grishko V, LeDoux SP, Kelley MR, Wilson GL, and Gillespie MN. Am J Physiol Lung Cell Mol Physiol 283: L205-L210, 2002). The mechanism by which mtDNA damage leads to PAEC death is unknown, and the present study tested the specific hypothesis that enhanced mtDNA repair suppresses PAEC mitochondrial dysfunction and apoptosis evoked by xanthine oxidase (XO). PAECs transfected either with an adenoviral vector encoding hOgg1 linked to a mitochondrial targeting sequence or with empty vector were challenged with ascending doses of XO plus hypoxanthine. Quantitative Southern blot analyses revealed that, as expected, hOgg1 overexpression suppressed XO-induced mtDNA damage. Mitochondrial overexpression of hOgg1 also suppressed the XO-mediated loss of mitochondrial membrane potential. Importantly, hOgg1 overexpression attenuated XO-induced apoptosis as detected by suppression of caspase-3 activation, by reduced DNA fragmentation, and by a blunted appearance of condensed, fragmented nuclei. These observations suggest that mtDNA damage serves as a trigger for mitochondrial dysfunction and apoptosis in XO-treated PAECs.}, }
@article {pmid15563621, year = {2004}, author = {Elorza, A and León, G and Gómez, I and Mouras, A and Holuigue, L and Araya, A and Jordana, X}, title = {Nuclear SDH2-1 and SDH2-2 genes, encoding the iron-sulfur subunit of mitochondrial complex II in Arabidopsis, have distinct cell-specific expression patterns and promoter activities.}, journal = {Plant physiology}, volume = {136}, number = {4}, pages = {4072-4087}, pmid = {15563621}, issn = {0032-0889}, mesh = {Arabidopsis/enzymology/*genetics/growth &amp; development ; Arabidopsis Proteins/*genetics/metabolism ; Base Sequence ; Evolution, Molecular ; Flowers/enzymology/*genetics/growth &amp; development ; Gene Expression Regulation, Plant/physiology ; Iron-Sulfur Proteins/*genetics/metabolism ; Molecular Sequence Data ; Plant Roots/genetics ; Plants, Genetically Modified ; Promoter Regions, Genetic ; Seedlings/genetics ; }, abstract = {Three different nuclear genes encode the essential iron-sulfur subunit of mitochondrial complex II (succinate dehydrogenase) in Arabidopsis (Arabidopsis thaliana), raising interesting questions about their origin and function. To find clues about their role, we have undertaken a detailed analysis of their expression. Two genes (SDH2-1 and SDH2-2) that likely arose via a relatively recent duplication event are expressed in all organs from adult plants, whereas transcripts from the third gene (SDH2-3) were not detected. The tissue- and cell-specific expression of SDH2-1 and SDH2-2 was investigated by in situ hybridization. In flowers, both genes are regulated in a similar way. Enhanced expression was observed in floral meristems and sex organ primordia at early stages of development. As flowers develop, SDH2-1 and SDH2-2 transcripts accumulate in anthers, particularly in the tapetum, pollen mother cells, and microspores, in agreement with an essential role of mitochondria during anther development. Interestingly, in contrast to the situation in flowers, only SDH2-2 appears to be expressed at a significant level in root tips. Strong labeling was observed in all cell layers of the root meristematic zone, and a cell-specific pattern of expression was found with increasing distance from the root tip, as cells attain their differentiated state. Analysis of transgenic Arabidopsis plants carrying SDH2-1 and SDH2-2 promoters fused to the beta-glucuronidase reporter gene indicate that both promoters have similar activities in flowers, driving enhanced expression in anthers and/or pollen, and that only the SDH2-2 promoter is active in root tips. These beta-glucuronidase staining patterns parallel those obtained by in situ hybridization, suggesting transcriptional regulation of these genes. Progressive deletions of the promoters identified regions important for SDH2-1 expression in anthers and/or pollen and for SDH2-2 expression in anthers and/or pollen and root tips. Interestingly, regions driving enhanced expression in anthers are differently located in the two promoters.}, }
@article {pmid15562597, year = {2004}, author = {DeJong, RJ and Emery, AM and Adema, CM}, title = {The mitochondrial genome of Biomphalaria glabrata (Gastropoda: Basommatophora), intermediate host of Schistosoma mansoni.}, journal = {The Journal of parasitology}, volume = {90}, number = {5}, pages = {991-997}, doi = {10.1645/GE-284R}, pmid = {15562597}, issn = {0022-3395}, support = {AI052363/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Biomphalaria/classification/*genetics/parasitology ; DNA, Complementary/chemistry ; DNA, Mitochondrial/*chemistry/genetics ; Disease Vectors ; *Genome ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Proteins/genetics ; RNA/genetics ; RNA, Mitochondrial ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Alignment ; }, abstract = {The complete mitochondrial (Mt) genome of the gastropod Biomphalaria glabrata, a major intermediate host for the human parasite Schistosoma mansoni, was sequenced. The circular genome, the first determined from a basommatophoran snail, is AT rich (74.6%) and the smallest Mt genome (13,670 nucleotides [nt]) characterized from mollusks to date. Sequences from 2 B. glabrata strains, M-line and 1742, differed by only 18 nt. Phylogenetic analysis of 16S and ND1 sequences confirmed the Brazilian ancestry of both B. glabrata strains. Gene predictions indicated 22 transfer RNA, 12S and 16S ribosomal RNA (rRNA), and 13 protein-encoding genes, as is typical for metazoans. Of the mollusk Mt genomes currently known, the gene order was most similar to that of stylommatophoran gastropods, concordant with the monophyly of pulmonate gastropods. Screening of GenBank (expressed sequence tags database [dbEST]) with the Mt sequence identified 108 entries from B. glabrata as Mt-derived sequences, including 12S and 16S rRNA sequences. Moreover, 11 sequences originating from the Mt genome of B. glabrata were identified among EST entries ascribed to intramolluskan stages of S. mansoni. The availability of this Mt sequence will facilitate further molecular investigations into the biology of Biomphalaria sp. and interactions between this intermediate host and intramolluskan stages of S. mansoni.}, }
@article {pmid15556293, year = {2004}, author = {Guy, L and Roten, CA}, title = {Genometric analyses of the organization of circular chromosomes: a universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication.}, journal = {Gene}, volume = {340}, number = {1}, pages = {45-52}, doi = {10.1016/j.gene.2004.06.056}, pmid = {15556293}, issn = {0378-1119}, mesh = {Base Composition/genetics ; Chromosomes, Archaeal/*genetics ; Chromosomes, Bacterial/*genetics ; DNA Replication/genetics ; DNA, Circular/genetics ; DNA, Mitochondrial/genetics ; Databases, Nucleic Acid ; *Genome, Archaeal ; *Genome, Bacterial ; Humans ; Models, Genetic ; Phylogeny ; RNA, Ribosomal/genetics ; Replication Origin/genetics ; Transcription, Genetic/genetics ; }, abstract = {Selective pressures related to gene function and chromosomal architecture are acting on genome sequences and can be revealed, for instance, by appropriate genometric methods. Cumulative nucleotide skew analyses, i.e., GC, TA, and ORF orientation skews, predict the location of the origin of DNA replication for 88 out of 100 completely sequenced bacterial chromosomes. These methods appear fully reliable for proteobacteria, Gram-positives, and spirochetes as well as for euryarchaeotes. Based on this genome architecture information, coorientation analyses reveal that in prokaryotes, ribosomal RNA (rRNA) genes encoding the small and large ribosomal subunits are all transcribed in the same direction as DNA replication; that is, they are located along the leading strand. This result offers a simple and reliable method for circumscribing the region containing the origin of the DNA replication and reveals a strong selective pressure acting on the orientation of rRNA genes similar to the weaker one acting on the orientation of ORFs. Rate of coorientation of transfer RNA (tRNA) genes with DNA replication appears to be taxon-specific. Analyzing nucleotide biases such as GC and TA skews of genes and plotting one against the other reveals a taxonomic clusterization of species. All ribosomal RNA genes are enriched in Gs and depleted in Cs, the only so far known exception being the rRNA genes of deuterostomian mitochondria. However, this exception can be explained by the fact that in the chromosome of the human mitochondrion, the model of the deuterostomian organelle genome, DNA replication, and rRNA transcription proceed in opposite directions. A general rule is deduced from prokaryotic and mitochondrial genomes: ribosomal RNA genes that are transcribed in the same direction as the DNA replication are enriched in Gs, and those transcribed in the opposite direction are depleted in Gs.}, }
@article {pmid15550228, year = {2004}, author = {Villegas-Castrejón, H and Solís-Arrieta, L and Martínez-Flores, F and Escobar-Cedillo, RE and García-Pérez, BE}, title = {[Peripheral hereditary neuropathies: Charcot-Marie-Tooth types 1 and 2].}, journal = {Cirugia y cirujanos}, volume = {72}, number = {5}, pages = {387-94; discussion 395-6}, pmid = {15550228}, issn = {0009-7411}, mesh = {Adolescent ; Adult ; Charcot-Marie-Tooth Disease/*pathology ; Female ; Humans ; Male ; }, abstract = {OBJECTIVE: We report 14 cases of patients with Charcot-Marie-Tooth types 1 (CMT) and type 2 (CMT2). The objective of this study was to determine the diagnostic value of structural studies of peripheral nerve and striated muscle biopsies and to discuss correlations with clinical symptoms and electrophysiologic findings.<br><br>MATERIAL AND METHODS: Nerve and muscle biopsies were obtained and processed according to standards methods for transmission electron microscopy. Diagnosis of CMT was based on clinical electrophysiologic findings.<br><br>RESULTS: Our results demonstrated that myelinated fibers showed moderate-to- severe demyelinization and remyelinization, folding complex, tomacula formations, and presence of moderate vacuoles into myelin. The axonal cytoskeleton shows an important decrease of neurofilaments and microtubules in myelinated and unmyelinated nerves. Striated muscle showed different degenerative changes in Z disc. One important finding was presence of crystals inclusions in mitochondrion. In 11 cases, it was possible to find relevant changes in mitochondria-like hyperplasia. In this study, we had four cases with > 20 years of evolution; these cases showed relevant degenerative changes in nerve and muscle. Nerves presented great demyelination with damage in cytoskeleton of the axon, while fibers of muscle had necrosis and hyalinization.<br><br>CONCLUSIONS: According to our results, it is possible to distinguish morphologically CMT subtypes, due to the fact that in CMT2 we found a 50% decrease of filaments and microtubules that were reduced in myelinic axons; this finding does not occur in CMT1.}, }
@article {pmid15548749, year = {2005}, author = {Xin, DD and Wen, JF and He, D and Lu, SQ}, title = {Identification of a Giardia krr1 homolog gene and the secondarily anucleolate condition of Giaridia lamblia.}, journal = {Molecular biology and evolution}, volume = {22}, number = {3}, pages = {391-394}, doi = {10.1093/molbev/msi052}, pmid = {15548749}, issn = {0737-4038}, mesh = {Animals ; Cell Nucleolus/genetics/metabolism ; *Evolution, Molecular ; Giardia lamblia/*genetics/metabolism ; Mitochondria/genetics/metabolism ; Protozoan Proteins/*genetics/metabolism ; RNA Precursors/genetics/metabolism ; RNA-Binding Proteins/*genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Giaridia lamblia was long considered to be one of the most primitive eukaryotes and to lie close to the transition between prokaryotes and eukaryotes, but several supporting features, such as lack of mitochondrion and Golgi, have been challenged recently. It was also reported previously that G. lamblia lacked nucleolus, which is the site of pre-rRNA processing and ribosomal assembling in the other eukaryotic cells. Here, we report the identification of the yeast homolog gene, krr1, in the anucleolate eukaryote, G. lamblia. The krr1 gene, encoding one of the pre-rRNA processing proteins in yeast, is actively transcribed in G. lamblia. The deduced protein sequence of G. lamblia krr1 is highly similar to yeast KRR1p that contains a single-KH domain. Our database searches indicated that krr1 genes actually present in diverse eukaryotes and also seem to present in Archaea. However, only the eukaryotic homologs, including that of G. lamblia, have the single-KH domain, which contains the conserved motif KR(K)R. Fibrillarin, another important pre-rRNA processing protein has also been identified previously in G. lamblia. Moreover, our database search shows that nearly half of the other nucleolus-localized protein genes of eukaryotic cells also have their homologs in Giardia. Therefore, we suggest that a common mechanism of pre-RNA processing may operate in the anucleolate eukaryote G. lamblia and in the other eukaryotes and that like the case of "lack of mitochondrion," "lack of nucleolus" may not be a primitive feature, but a secondarily evolutionary condition of the parasite.}, }
@article {pmid15548286, year = {2004}, author = {Smith, MA and Green, DM}, title = {Phylogeography of Bufo fowleri at its northern range limit.}, journal = {Molecular ecology}, volume = {13}, number = {12}, pages = {3723-3733}, doi = {10.1111/j.1365-294X.2004.02301.x}, pmid = {15548286}, issn = {0962-1083}, mesh = {Analysis of Variance ; Animals ; Base Sequence ; Bufonidae/*genetics ; Cluster Analysis ; DNA, Mitochondrial/genetics ; *Demography ; *Genetic Variation ; Geography ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Ohio ; Ontario ; Pennsylvania ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Many of the species that recolonized previously glaciated areas in the Great Lakes basin of North America over the past 10-12,000 years exhibit genetic evidence of multiple invasion routes and present-day secondary contact between deeply divergent lineages. With this in mind, we investigated the phylogeographical structure of genetic variability in Fowler's toads (Bufo fowleri) at the northern edge of its distribution where its range encircles the Lake Erie basin. Because B. fowleri is so closely tied to habitats along the Lake Erie shoreline, we would expect to find clear evidence of the number of invasions leading to the species' colonization of the northern shore. A 540 bp sequence from the mitochondrial control region was amplified and analysed for 158 individuals from 21 populations. Interpopulation sequence variation ranged from 0% to 6%. Phylogenetic analysis of p-distance using the neighbor-joining method revealed two deeply divergent (6% sequence divergence) mtDNA lineages (Phylogroup 1 and 2), possibly arising as a result of secondary contact of populations that entered the region from two separate glacial refugia. However, the phylogeographical pattern was not simple. The populations at Long Point, on the north shore of Lake Erie, clustered with the population from Indiana Dunes on Lake Michigan to form Phylogroup 2 whereas all other B. fowleri populations examined from both sides of Lake Erie constituted Phylogroup 1. Furthermore, mtDNA sequences from the related species Bufo americanus, obtained from populations outside the range of B. fowleri, clustered with mtDNA haplotypes of B. fowleri Phylogroup 1, indicating the possibility of partial introgression of mitochondria from one species to the other.}, }
@article {pmid15546859, year = {2005}, author = {Bullerwell, CE and Gray, MW}, title = {In vitro characterization of a tRNA editing activity in the mitochondria of Spizellomyces punctatus, a Chytridiomycete fungus.}, journal = {The Journal of biological chemistry}, volume = {280}, number = {4}, pages = {2463-2470}, doi = {10.1074/jbc.M411273200}, pmid = {15546859}, issn = {0021-9258}, mesh = {Adenosine Triphosphate/chemistry/metabolism ; Base Pairing ; Base Sequence ; Chromatography, Thin Layer ; Chytridiomycota/*metabolism ; Cytoplasm/metabolism ; Evolution, Molecular ; *Genes, Fungal ; In Vitro Techniques ; Mitochondria/*metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligonucleotides/chemistry ; Periodic Acid/pharmacology ; RNA/*chemistry/metabolism ; *RNA Editing ; RNA Processing, Post-Transcriptional ; RNA, Fungal/*chemistry ; RNA, Messenger/metabolism ; RNA, Mitochondrial ; RNA, Transfer/*chemistry/metabolism ; }, abstract = {In the chytridiomycete fungus, Spizellomyces punctatus, all eight of the mitochondrially encoded tRNAs are predicted to have one or more base pair mismatches at the first three positions of their aminoacyl acceptor stems. These tRNAs are edited post-transcriptionally by replacement of the 5'-nucleotide in each mismatched pair with a nucleotide that can form a standard Watson-Crick base pair with its counterpart in the 3'-half of the stem. The type of mitochondrial tRNA editing found in S. punctatus also occurs in Acanthamoeba castellanii, a distantly related amoeboid protist. Using an S. punctatus mitochondrial extract, we have developed an in vitro assay of tRNA editing in which nucleotides are incorporated into various tRNA substrates. Experiments employing synthetic transcripts revealed that the S. punctatus tRNA editing activity incorporates nucleotides on the 5'-side of substrate tRNAs, uses the 3'-sequence as a template for incorporation, and adds nucleotides in a 3'-to-5' direction. This activity can add nucleotides to a triphosphorylated 5'-end in the absence of ATP but requires ATP to add nucleotides to a monophosphorylated 5'-end; moreover, it functions independently of the state of tRNA 3' processing. These data parallel results obtained in a previous in vitro study of A. castellanii tRNA editing, suggesting that remarkably similar activities function in the mitochondria of these two organisms. The evolutionary origins of these activities are discussed.}, }
@article {pmid15544974, year = {2004}, author = {Suarez, RK and Darveau, CA and Childress, JJ}, title = {Metabolic scaling: a many-splendoured thing.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {139}, number = {3}, pages = {531-541}, doi = {10.1016/j.cbpc.2004.05.001}, pmid = {15544974}, issn = {1096-4959}, mesh = {Animals ; *Basal Metabolism ; Exercise ; Humans ; Mitochondria/*metabolism ; Oxygen Consumption/*physiology ; }, abstract = {Animals at rest and during exercise display rates of aerobic metabolism, VO2, that represent mainly the sum of mitochondrial respiration rates in various organs. The relative contributions of these organs change with physiological state such that internal organs such as liver, kidney and brain account for most of the whole-body VO2 at rest, while locomotory muscles account for >90% of the maximum rate, VO2max, during maximal aerobic exercise. Mechanisms that regulate VO2 are complex and the relative importance of each step in a series, estimated by metabolic control analysis, depends upon the level of biological organization under consideration as well as physiological state. Despite this complexity, prominent single-cause models propose that metabolic rates are supply-limited and that the scaling of supply systems provides a sufficient explanation for the allometric scaling of metabolism. We argue that some assumptions, as well as current interpretations of the meaning (or consequences) of these constraints are flawed, i.e., elephants do not have lower mass-specific basal or maximal rates of aerobic metabolism because their mitochondria are more supply-limited than those of shrews. Animals do not violate the laws of physics, and the allometric scaling of supply systems would be expected, to some extent, to be matched by capacities for (and rates of) energy expenditure. But life is not so simple. Animals are so diverse that to do justice to metabolic scaling, it is also necessary to consider the scaling of energy expenditure. It is by doing so that models of metabolic scaling can be consistent with current paradigms in metabolic regulation and accommodate the range of inter- and intraspecific exponents found in nature. The "allometric cascade," a first attempt at such an accounting, was a source of great satisfaction to Peter Hochachka. It was the last door that he helped open to comparative physiologists before he said goodbye.}, }
@article {pmid15533048, year = {2004}, author = {Allen, A and Kwagh, J and Fang, J and Stanley, CA and Smith, TJ}, title = {Evolution of glutamate dehydrogenase regulation of insulin homeostasis is an example of molecular exaptation.}, journal = {Biochemistry}, volume = {43}, number = {45}, pages = {14431-14443}, doi = {10.1021/bi048817i}, pmid = {15533048}, issn = {0006-2960}, support = {DK53012/DK/NIDDK NIH HHS/United States ; GM10704/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Diphosphate/*analogs &amp; derivatives/chemistry/metabolism ; Alanine/genetics ; Allosteric Regulation/genetics ; Animals ; Arginine/genetics ; Cattle ; Deamination ; *Evolution, Molecular ; Glutamate Dehydrogenase/antagonists &amp; inhibitors/*chemistry/genetics/metabolism ; *Homeostasis/genetics ; Humans ; Insulin/*metabolism ; Insulin Secretion ; Kinetics ; Lipid Peroxidation ; Palmitoyl Coenzyme A/chemistry ; Protein Binding ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; Tetrahymena thermophila/enzymology/genetics ; }, abstract = {Glutamate dehydrogenase (GDH) is found in all organisms and catalyzes the oxidative deamination of glutamate to 2-oxoglutarate. While this enzyme does not exhibit allosteric regulation in plants, bacteria, or fungi, its activity is tightly controlled by a number of compounds in mammals. We have previously shown that this regulation plays an important role in insulin homeostasis in humans and evolved concomitantly with a 48-residue "antenna" structure. As shown here, the antenna and some of the allosteric regulation first appears in the Ciliates. This primitive regulation is mediated by fatty acids and likely reflects the gradual movement of fatty acid oxidation from the peroxisomes to the mitochondria as the Ciliates evolved away from plants, fungi, and other protists. Mutagenesis studies where the antenna is deleted support this contention by demonstrating that the antenna is essential for fatty acid regulation. When the antenna from the Ciliates is spliced onto human GDH, it was found to fully communicate all aspects of mammalian regulation. Therefore, we propose that glutamate dehydrogenase regulation of insulin secretion is a example of exaptation at the molecular level where the antenna and associated fatty acid regulation was created to accommodate the changes in organelle function in the Ciliates and then later used to link amino acid catabolism and/or regulation of intracellular glutamate/glutamine levels in the pancreatic beta cells with insulin homeostasis in mammals.}, }
@article {pmid15527405, year = {2004}, author = {Gordeeva, AV and Labas, YA and Zvyagilskaya, RA}, title = {Apoptosis in unicellular organisms: mechanisms and evolution.}, journal = {Biochemistry. Biokhimiia}, volume = {69}, number = {10}, pages = {1055-1066}, doi = {10.1023/b:biry.0000046879.54211.ab}, pmid = {15527405}, issn = {0006-2979}, mesh = {Animals ; Apoptosis/genetics/*physiology ; *Bacterial Physiological Phenomena ; Biological Evolution ; Caenorhabditis elegans/physiology ; Calcium/metabolism ; Caspases/physiology ; Cytochromes c/physiology ; Eukaryota/*physiology ; Mitochondria/physiology ; Nitric Oxide/metabolism ; Proto-Oncogene Proteins c-bcl-2/physiology ; Reactive Oxygen Species/metabolism ; Yeasts/physiology ; }, abstract = {Data about the programmed death (apoptosis) in unicellular organisms, from bacteria to ciliates, are discussed. Firstly apoptosis appeared in lower eukaryotes, but its mechanisms in these organisms are different from the classical apoptosis. During evolution, the apoptotic process has been improving gradually, with reactive oxygen species and Ca2+ playing an essential role in triggering apoptosis. All eukaryotic organisms have apoptosis inhibitors, which might be introduced by viruses. In the course of evolution, caspases and apoptosis-inducing factor appeared before other apoptotic proteins, with so-called death receptors being the last among them. The functional analogs of eukaryotic apoptotic proteins take parts in the programmed death of bacteria.}, }
@article {pmid15526035, year = {2004}, author = {Vahsen, N and Candé, C and Brière, JJ and Bénit, P and Joza, N and Larochette, N and Mastroberardino, PG and Pequignot, MO and Casares, N and Lazar, V and Feraud, O and Debili, N and Wissing, S and Engelhardt, S and Madeo, F and Piacentini, M and Penninger, JM and Schägger, H and Rustin, P and Kroemer, G}, title = {AIF deficiency compromises oxidative phosphorylation.}, journal = {The EMBO journal}, volume = {23}, number = {23}, pages = {4679-4689}, pmid = {15526035}, issn = {0261-4189}, mesh = {Adenosine Triphosphate/biosynthesis ; Animals ; Apoptosis ; Apoptosis Inducing Factor ; Brain/metabolism ; Cells, Cultured ; Electron Transport Complex I/biosynthesis ; Electron Transport Complex III/biosynthesis ; Flavoproteins/genetics/metabolism ; Glucose/metabolism ; Humans ; Lactic Acid/biosynthesis ; Membrane Proteins/*deficiency/genetics/metabolism ; Mice ; Mice, Transgenic ; Mitochondria/metabolism ; Myocardium/metabolism ; Organ Specificity ; Oxidative Phosphorylation ; Phylogeny ; RNA, Small Interfering/metabolism ; Retina/metabolism ; Yeasts/genetics/growth &amp; development/metabolism ; }, abstract = {Apoptosis-inducing factor (AIF) is a mitochondrial flavoprotein that, after apoptosis induction, translocates to the nucleus where it participates in apoptotic chromatinolysis. Here, we show that human or mouse cells lacking AIF as a result of homologous recombination or small interfering RNA exhibit high lactate production and enhanced dependency on glycolytic ATP generation, due to severe reduction of respiratory chain complex I activity. Although AIF itself is not a part of complex I, AIF-deficient cells exhibit a reduced content of complex I and of its components, pointing to a role of AIF in the biogenesis and/or maintenance of this polyprotein complex. Harlequin mice with reduced AIF expression due to a retroviral insertion into the AIF gene also manifest a reduced oxidative phosphorylation (OXPHOS) in the retina and in the brain, correlating with reduced expression of complex I subunits, retinal degeneration, and neuronal defects. Altogether, these data point to a role of AIF in OXPHOS and emphasize the dual role of AIF in life and death.}, }
@article {pmid15523480, year = {2004}, author = {Pfanner, N and Wiedemann, N and Meisinger, C and Lithgow, T}, title = {Assembling the mitochondrial outer membrane.}, journal = {Nature structural &amp; molecular biology}, volume = {11}, number = {11}, pages = {1044-1048}, doi = {10.1038/nsmb852}, pmid = {15523480}, issn = {1545-9993}, mesh = {Adenosine Triphosphate/metabolism ; Apoptosis ; Cytosol/metabolism ; Fungal Proteins/physiology ; Humans ; Intracellular Membranes/*metabolism ; Mitochondria/metabolism/*pathology ; Mitochondrial Proteins/chemistry/metabolism ; Models, Biological ; Molecular Chaperones/metabolism ; Plant Proteins/metabolism ; Protein Transport ; }, abstract = {The general preprotein translocase of the outer mitochondrial membrane (TOM complex) transports virtually all mitochondrial precursor proteins, but cannot assemble outer-membrane precursors into functional complexes. A recently discovered sorting and assembly machinery (SAM complex) is essential for integration and assembly of outer-membrane proteins, revealing unexpected connections to mitochondrial evolution and morphology.}, }
@article {pmid15522848, year = {2004}, author = {Aharoni, A and Giri, AP and Verstappen, FW and Bertea, CM and Sevenier, R and Sun, Z and Jongsma, MA and Schwab, W and Bouwmeester, HJ}, title = {Gain and loss of fruit flavor compounds produced by wild and cultivated strawberry species.}, journal = {The Plant cell}, volume = {16}, number = {11}, pages = {3110-3131}, pmid = {15522848}, issn = {1040-4651}, mesh = {Acyclic Monoterpenes ; Alkyl and Aryl Transferases/*genetics/metabolism ; Amino Acid Sequence ; Bicyclic Monoterpenes ; Catalysis ; Cloning, Molecular ; Cytochrome P-450 Enzyme System/genetics ; Cytosol/metabolism ; Fragaria/*enzymology/*genetics/growth &amp; development ; Gene Expression Regulation, Plant/physiology ; Green Fluorescent Proteins/genetics/metabolism ; Hydroxylation ; Intramolecular Lyases/genetics/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Monoterpenes/metabolism ; Plastids/metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Sesquiterpenes/metabolism ; Terpenes/*metabolism ; }, abstract = {The blends of flavor compounds produced by fruits serve as biological perfumes used to attract living creatures, including humans. They include hundreds of metabolites and vary in their characteristic fruit flavor composition. The molecular mechanisms by which fruit flavor and aroma compounds are gained and lost during evolution and domestication are largely unknown. Here, we report on processes that may have been responsible for the evolution of diversity in strawberry (Fragaria spp) fruit flavor components. Whereas the terpenoid profile of cultivated strawberry species is dominated by the monoterpene linalool and the sesquiterpene nerolidol, fruit of wild strawberry species emit mainly olefinic monoterpenes and myrtenyl acetate, which are not found in the cultivated species. We used cDNA microarray analysis to identify the F. ananassa Nerolidol Synthase1 (FaNES1) gene in cultivated strawberry and showed that the recombinant FaNES1 enzyme produced in Escherichia coli cells is capable of generating both linalool and nerolidol when supplied with geranyl diphosphate (GPP) or farnesyl diphosphate (FPP), respectively. Characterization of additional genes that are very similar to FaNES1 from both the wild and cultivated strawberry species (FaNES2 and F. vesca NES1) showed that only FaNES1 is exclusively present and highly expressed in the fruit of cultivated (octaploid) varieties. It encodes a protein truncated at its N terminus. Green fluorescent protein localization experiments suggest that a change in subcellular localization led to the FaNES1 enzyme encountering both GPP and FPP, allowing it to produce linalool and nerolidol. Conversely, an insertional mutation affected the expression of a terpene synthase gene that differs from that in the cultivated species (termed F. ananassa Pinene Synthase). It encodes an enzyme capable of catalyzing the biosynthesis of the typical wild species monoterpenes, such as alpha-pinene and beta-myrcene, and caused the loss of these compounds in the cultivated strawberries. The loss of alpha-pinene also further influenced the fruit flavor profile because it was no longer available as a substrate for the production of the downstream compounds myrtenol and myrtenyl acetate. This phenomenon was demonstrated by cloning and characterizing a cytochrome P450 gene (Pinene Hydroxylase) that encodes the enzyme catalyzing the C10 hydroxylation of alpha-pinene to myrtenol. The findings shed light on the molecular evolutionary mechanisms resulting in different flavor profiles that are eventually selected for in domesticated species.}, }
@article {pmid15522815, year = {2004}, author = {Doan, JW and Schmidt, TR and Wildman, DE and Uddin, M and Goldberg, A and Hüttemann, M and Goodman, M and Weiss, ML and Grossman, LI}, title = {Coadaptive evolution in cytochrome c oxidase: 9 of 13 subunits show accelerated rates of nonsynonymous substitution in anthropoid primates.}, journal = {Molecular phylogenetics and evolution}, volume = {33}, number = {3}, pages = {944-950}, doi = {10.1016/j.ympev.2004.07.016}, pmid = {15522815}, issn = {1055-7903}, support = {GM 65580/GM/NIGMS NIH HHS/United States ; GM48517/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Humans ; Mitochondria/genetics ; Phylogeny ; Primates ; }, }
@article {pmid15522786, year = {2004}, author = {Uit de Weerd, DR and Piel, WH and Gittenberger, E}, title = {Widespread polyphyly among Alopiinae snail genera: when phylogeny mirrors biogeography more closely than morphology.}, journal = {Molecular phylogenetics and evolution}, volume = {33}, number = {3}, pages = {533-548}, doi = {10.1016/j.ympev.2004.07.010}, pmid = {15522786}, issn = {1055-7903}, mesh = {Animals ; Bayes Theorem ; Cell Nucleus/metabolism ; DNA, Ribosomal Spacer/genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Geography ; Mitochondria/metabolism ; Models, Anatomic ; Phylogeny ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; Snails/anatomy &amp; histology/*genetics ; Species Specificity ; }, abstract = {Consider a group of species that is evenly divided by an easily identifiable complex morphological character. Most biologists would assume that this character should provide better phylogenetic information than, say, the spatial distribution of these species over a fairly continuous 500-km radius area. Paradoxically, this is not the case among terrestrial snail genera in the clausiliid subfamily Alopiinae. Phylogenetic analysis using the nuclear markers ITS1/ITS2 and mitochondrial markers COI/12S reveals widespread homoplasy in the clausilial apparatus (a complex aperture-closing mechanism), and concomitant extensive polyphyly among Carinigera, Isabellaria, and Sericata. In contrast, phylogenetic relationships as revealed by molecular data are closely congruent with biogeography at a relatively small scale. A combination of extremely low vagility and extremely high morphological convergence has conspired to produce this unexpected result. Implications as to the function of the clausilial apparatus are discussed.}, }
@article {pmid15520290, year = {2004}, author = {Johnson, ZI and Chisholm, SW}, title = {Properties of overlapping genes are conserved across microbial genomes.}, journal = {Genome research}, volume = {14}, number = {11}, pages = {2268-2272}, pmid = {15520290}, issn = {1088-9051}, mesh = {Computational Biology ; Databases, Nucleic Acid ; *Evolution, Molecular ; Gene Order/*genetics ; Genes, Bacterial/*genetics ; Genes, Overlapping/*genetics ; *Genome, Bacterial ; Open Reading Frames/*genetics ; }, abstract = {There are numerous examples from the genomes of viruses, mitochondria, and chromosomes that adjacent genes can overlap, sharing at least one nucleotide. Overlaps have been hypothesized to be involved in genome size minimization and as a regulatory mechanism of gene expression. Here we show that overlapping genes are a consistent feature (approximately one-third of all genes) across all microbial genomes sequenced to date, have homologs in more microbes than do non-overlapping genes, and are therefore likely more conserved. In addition, the size, phase (reading frame offset), and distribution, among other characteristics, of overlapping genes are most consistent with the hypothesis that overlaps function in the regulation of gene expression. The upstream sequences and conservation of overlapping orthologs of two model organisms from the genus Prochlorococcus that have significantly different GC-content, and therefore different nucleotide sequences for orthologs, are also consistent with small overlapping sequence regions and programmed shifts in reading frame as a common mechanism in the regulation of microbial gene expression.}, }
@article {pmid15516736, year = {2004}, author = {Zhou, C and Zhou, K and Zhang, S}, title = {Molecular authentication of the animal crude drug Sailonggu (bone of Myospalax baileyi).}, journal = {Biological &amp; pharmaceutical bulletin}, volume = {27}, number = {11}, pages = {1850-1858}, doi = {10.1248/bpb.27.1850}, pmid = {15516736}, issn = {0918-6158}, mesh = {Alleles ; Animals ; Bone and Bones/*chemistry ; Cytochromes c/genetics ; DNA Primers ; Medicine, Chinese Traditional ; Mitochondria/chemistry ; Pharmaceutical Preparations/*analysis ; Phylogeny ; Polymerase Chain Reaction ; Rodentia/*genetics ; Sequence Alignment ; }, abstract = {Two pairs of allele-specific diagnostic primers (SL1L/SL1H and SL2L/SL2H) for distinguishing the Chinese crude drug Sailonggu (bone of plateau zokor, Myospalax baileyi) from its substitutes were designed based on complete sequences of mitochondrial 12S rRNA and cytochrome b genes of the original animals of Myospalacinae, bamboo rat Rhizomys sinensis and black lipped pika Ochotona curzoniae. Total DNA was extracted from crude drug samples and original animals. Allele-specific diagnostic PCRs were performed using these primers with the total DNA as a template annealing at 65 degrees C. Positive amplifications were obtained from all DNA templates of Sailonggu and M. baileyi, whereas negative amplifications resulted from those of other zokors, the bamboo rat and black lipped pika. These results indicate that Sailonggu samples can be definitely distinguished from their substitutes by diagnostic PCR, and no incorrect discrimination was found under the same reaction conditions. Each of the two diagnostic primer pairs can be used to distinguish crude drug Sailonggu from its substitutes or adulterants. The three Sailonggu samples studied were diagnosed as genuine Sailonggu. In addition, the results of sequence alignment and phylogenetic analysis are congruent with that of the allele-specific diagnostic PCR.}, }
@article {pmid15510149, year = {2004}, author = {Dyall, SD and Yan, W and Delgadillo-Correa, MG and Lunceford, A and Loo, JA and Clarke, CF and Johnson, PJ}, title = {Non-mitochondrial complex I proteins in a hydrogenosomal oxidoreductase complex.}, journal = {Nature}, volume = {431}, number = {7012}, pages = {1103-1107}, doi = {10.1038/nature02990}, pmid = {15510149}, issn = {1476-4687}, mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Biological Evolution ; Carbohydrate Metabolism ; Electron Transport Complex I/chemistry/*metabolism ; Fermentation ; Hydrogen/*metabolism ; Hydrogenase/metabolism ; Iron-Sulfur Proteins/metabolism ; Ketone Oxidoreductases/metabolism ; Mitochondrial Proteins/chemistry ; Models, Biological ; Molecular Sequence Data ; NADH Dehydrogenase/chemistry/*metabolism ; Organelles/*enzymology/metabolism ; Oxidation-Reduction ; Phosphorylation ; Phylogeny ; Protein Binding ; Pyruvate Synthase ; Pyruvic Acid/metabolism ; Symbiosis ; Trichomonas vaginalis/*cytology/*enzymology/metabolism ; }, abstract = {Trichomonas vaginalis is a unicellular microaerophilic eukaryote that lacks mitochondria yet contains an alternative organelle, the hydrogenosome, involved in pyruvate metabolism. Pathways between the two organelles differ substantially: in hydrogenosomes, pyruvate oxidation is catalysed by pyruvate:ferredoxin oxidoreductase (PFOR), with electrons donated to an [Fe]-hydrogenase which produces hydrogen. ATP is generated exclusively by substrate-level phosphorylation in hydrogenosomes, as opposed to oxidative phosphorylation in mitochondria. PFOR and hydrogenase are found in eubacteria and amitochondriate eukaryotes, but not in typical mitochondria. Analyses of mitochondrial genomes indicate that mitochondria have a single endosymbiotic origin from an alpha-proteobacterial-type progenitor. The absence of a genome in trichomonad hydrogenosomes precludes such comparisons, leaving the endosymbiotic history of this organelle unclear. Although phylogenetic reconstructions of a few proteins indicate that trichomonad hydrogenosomes share a common origin with mitochondria, others do not. Here we describe a novel NADH dehydrogenase module of respiratory complex I that is coupled to the central hydrogenosomal fermentative pathway to form a hydrogenosomal oxidoreductase complex that seems to function independently of quinones. Phylogenetic analyses of hydrogenosomal complex I-like proteins Ndh51 and Ndh24 reveal that neither has a common origin with mitochondrial homologues. These studies argue against a vertical origin of trichomonad hydrogenosomes from the proto-mitochondrial endosymbiont.}, }
@article {pmid15507320, year = {2004}, author = {Tone, Y and Kawai-Yamada, M and Uchimiya, H}, title = {Isolation and characterization of Arabidopsis thaliana ISU1 gene.}, journal = {Biochimica et biophysica acta}, volume = {1680}, number = {3}, pages = {171-175}, doi = {10.1016/j.bbaexp.2004.09.005}, pmid = {15507320}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/*genetics/*metabolism ; Blotting, Northern ; Cloning, Molecular ; DNA, Plant/genetics/*isolation &amp; purification ; Gene Expression Regulation, Plant ; *Genes, Plant ; Genetic Complementation Test ; Green Fluorescent Proteins/metabolism ; Mitochondrial Proteins ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Plant Proteins/*genetics/isolation &amp; purification ; Plasmids ; Saccharomyces cerevisiae/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {We describe the isolation of a cDNA encoding Arabidopsis thaliana ISU1 (AtISU1), which regulates iron homeostasis in the mitochondria. The AtISU1 gene contained an open reading frame that encoded 167 amino acid residues. Northern blot analysis demonstrated that AtISU1 gene was ubiquitously expressed in plant tissues examined. The yeast seo5-1, which harbors a single base-pair deletion in ScISU1, is a suppressor of oxidative damage in sod1-deficient mutant. Based on comparative expression analyses using yeast ISU1 gene (ScISU1) in seo5-1 mutant, we found that AtISU1 acts as a counterpart of ScISU1.}, }
@article {pmid15500440, year = {2004}, author = {Allen, JW and Ginger, ML and Ferguson, SJ}, title = {Maturation of the unusual single-cysteine (XXXCH) mitochondrial c-type cytochromes found in trypanosomatids must occur through a novel biogenesis pathway.}, journal = {The Biochemical journal}, volume = {383}, number = {Pt. 3}, pages = {537-542}, pmid = {15500440}, issn = {1470-8728}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Motifs/genetics ; Animals ; Cysteine/*genetics ; Cytochrome c Group/biosynthesis/*chemistry/*genetics ; *Evolution, Molecular ; Genetic Variation/genetics ; Mitochondria/*enzymology ; Mitochondrial Proteins/biosynthesis/chemistry/genetics ; Recombinant Proteins/biosynthesis/genetics ; Trypanosoma brucei brucei/*enzymology ; }, abstract = {The c-type cytochromes are characterized by the covalent attachment of haem to the polypeptide via thioether bonds formed from haem vinyl groups and, normally, the thiols of two cysteines in a CXXCH motif. Intriguingly, the mitochondrial cytochromes c and c1 from two euglenids and the Trypanosomatidae contain only a single cysteine within the haem-binding motif (XXXCH). There are three known distinct pathways by which c-type cytochromes are matured post-translationally in different organisms. The absence of genes encoding any of these c-type cytochrome biogenesis machineries is established here by analysis of six trypanosomatid genomes, and correlates with the presence of single-cysteine cytochromes c and c1. In contrast, we have identified a comprehensive catalogue of proteins required for a typical mitochondrial oxidative phosphorylation apparatus. Neither spontaneous nor catalysed maturation of the single-cysteine Trypanosoma brucei cytochrome c occurred in Escherichia coli. However, a CXXCH variant was matured by the E. coli cytochrome c maturation machinery, confirming the proposed requirement of the latter for two cysteines in the haem-binding motif and indicating that T. brucei cytochrome c can accommodate a second cysteine in a CXXCH motif. The single-cysteine haem attachment conserved in cytochromes c and c1 of the trypanosomatids is suggested to be related to their cytochrome c maturation machinery, and the environment in the mitochondrial intermembrane space. Our genomic and biochemical studies provide very persuasive evidence that the trypanosomatid mitochondrial cytochromes c are matured by a novel biogenesis system.}, }
@article {pmid15498771, year = {2004}, author = {Andreau, K and Castedo, M and Perfettini, JL and Roumier, T and Pichart, E and Souquere, S and Vivet, S and Larochette, N and Kroemer, G}, title = {Preapoptotic chromatin condensation upstream of the mitochondrial checkpoint.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {53}, pages = {55937-55945}, doi = {10.1074/jbc.M406411200}, pmid = {15498771}, issn = {0021-9258}, mesh = {Amino Acid Chloromethyl Ketones/pharmacology ; *Apoptosis ; Caspase Inhibitors ; Caspases/metabolism ; Cell Nucleus/metabolism ; Chromatin/*chemistry/metabolism ; Cisplatin/pharmacology ; Cytochromes c/metabolism ; DNA/chemistry ; DNA Damage ; DNA Fragmentation ; DNA Repair ; Dactinomycin/pharmacology ; Enzyme Activation ; Flow Cytometry ; HeLa Cells ; Histones/chemistry ; Humans ; Matrix Metalloproteinases/metabolism ; Membrane Potentials ; Microscopy, Electron, Transmission ; Microscopy, Fluorescence ; Mitochondria/*metabolism ; Phosphatidylserines/chemistry ; Phosphorylation ; Protein Binding ; RNA, Small Interfering/metabolism ; Staurosporine/*pharmacology ; Time Factors ; Transcription, Genetic ; Transfection ; Tumor Suppressor Protein p53/metabolism ; }, abstract = {When added for a short period (2-4 h) to cells, the kinase inhibitor staurosporine (STS), can trigger double strand breaks, the formation of nuclear foci containing phosphorylated H2AX, Chk2, and p53, a decrease in transcription, and a minor degree of peripheral chromatin condensation. This "preapoptotic chromatin condensation" (PACC) occurs before mitochondrial membrane permeabilization (MMP) and caspase activation become detectable and is not inhibited by Z-VAD-fmk or Bcl-2. PACC is followed by classical apoptosis, when cells are cultured overnight, even when STS is removed from the system. After overnight incubation, STS-pretreated cells manifest mitochondrial cytochrome c release, caspase activation, phosphatidylserine exposure, and apoptotic DNA fragmentation. Caspase or MMP inhibitors did not influence the advent of PACC yet did suppress the evolution of PACC toward apoptosis. Importantly, two unrelated MMP inhibitors (viral mitochondrial inhibitor of apoptosis (vMIA) from cytomegalovirus and mitochondrion-targeted Bcl-2) had a larger range of effects than the pan-caspase inhibitor Z-VAD-fmk. Caspase inhibition simply prevented the transition from PACC to apoptosis yet did not reverse PACC and did not restore transcription. In contrast, Bcl-2 and vMIA allowed for the repair of the DNA lesions, correlating with the reestablishment of active transcription. PACC could also be induced by a gross perturbation of RNA synthesis or primary DNA damage. Again, inhibition of MMP (but not that of caspases) reversed PACC induced by these stimuli. In synthesis, our data reveal the unexpected capacity of STS to induce DNA lesions and suggest qualitative differences in the cytoprotective and DNA repair-inducing potential of different apoptosis inhibitors.}, }
@article {pmid15498761, year = {2004}, author = {Spence, E and Bailey, S and Nenninger, A and Møller, SG and Robinson, C}, title = {A homolog of Albino3/OxaI is essential for thylakoid biogenesis in the cyanobacterium Synechocystis sp. PCC6803.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {53}, pages = {55792-55800}, doi = {10.1074/jbc.M411041200}, pmid = {15498761}, issn = {0021-9258}, mesh = {Arabidopsis Proteins/metabolism/*physiology ; Blotting, Southern ; Cell Membrane/metabolism ; Chlorophyll/chemistry ; Chloroplasts/metabolism ; Cyanobacteria/*metabolism ; Electron Transport ; Electrophoresis, Polyacrylamide Gel ; Glucose/metabolism ; Light ; Microscopy, Confocal ; Microscopy, Electron ; Microscopy, Electron, Transmission ; Mitochondria/metabolism ; Models, Genetic ; Mutation ; Open Reading Frames ; Oxygen/metabolism ; Photosynthesis ; Plasmids/metabolism ; Pressure ; Synechocystis/*metabolism ; Thylakoids/metabolism ; Time Factors ; }, abstract = {YidC/OxaI play essential roles in the insertion of a wide range of membrane proteins in Eschericha coli and mitochondria, respectively. In contrast, the chloroplast thylakoid homolog Albino3 (Alb3) facilitates the insertion of only a specialized subset of proteins, and the vast majority insert into thylakoids by a pathway that is so far unique to chloroplasts. In this study, we have analyzed the role of Alb3 in the cyanobacterium Synechocystis sp. PCC6803, which contains internal thylakoids that are similar in some respects to those of chloroplasts. The single alb3 gene (slr1471) was disrupted by the introduction of an antibiotic cassette, and photoautotrophic growth resulted in the generation of a merodiploid species (but not full segregation), indicating an essential role for Alb3 in maintaining the photosynthetic apparatus. Thylakoid organization is lost under these conditions, and the levels of photosynthetic pigments fall to approximately 40% of wild-type levels. Photosynthetic electron transport and oxygen evolution are reduced by a similar extent. Growth on glucose relieves the selective pressure to maintain photosynthetic competence, and under these conditions, the cells become completely bleached, again indicating that Alb3 is essential for thylakoid biogenesis. Full segregation could not be achieved under any growth regime, strongly suggesting that the slr1471 open reading frame is essential for cell viability.}, }
@article {pmid15496432, year = {2004}, author = {D'Aurelio, M and Gajewski, CD and Lin, MT and Mauck, WM and Shao, LZ and Lenaz, G and Moraes, CT and Manfredi, G}, title = {Heterologous mitochondrial DNA recombination in human cells.}, journal = {Human molecular genetics}, volume = {13}, number = {24}, pages = {3171-3179}, doi = {10.1093/hmg/ddh326}, pmid = {15496432}, issn = {0964-6906}, support = {EY10804/EY/NEI NIH HHS/United States ; GM55766/GM/NIGMS NIH HHS/United States ; NS02179/NS/NINDS NIH HHS/United States ; }, mesh = {Blotting, Southern ; Cloning, Molecular ; *DNA, Mitochondrial ; Haplotypes ; Humans ; Hybrid Cells ; Mitochondria/*genetics ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; *Recombination, Genetic ; }, abstract = {Inter-molecular heterologous mitochondrial DNA (mtDNA) recombination is known to occur in yeast and plants. Nevertheless, its occurrence in human cells is still controversial. To address this issue we have fused two human cytoplasmic hybrid cell lines, each containing a distinct pathogenic mtDNA mutation and specific sets of genetic markers. In this hybrid model, we found direct evidence of recombination between these two mtDNA haplotypes. Recombinant mtDNA molecules in the hybrid cells were identified using three independent experimental approaches. First, recombinant molecules containing genetic markers from both parental alleles were demonstrated with restriction fragment length polymorphism of polymerase chain reaction products, by measuring the relative frequencies of each marker. Second, fragments of recombinant mtDNA were cloned and sequenced to identify the regions involved in the recombination events. Finally, recombinant molecules were demonstrated directly by Southern blot using appropriate combinations of polymorphic restriction sites and probes. This combined approach confirmed the existence of heterogeneous species of recombinant mtDNA molecules in the hybrid cells. These findings have important implications for mtDNA-related diseases, the interpretation of human evolution and population genetics and forensic analyses based on mtDNA genotyping.}, }
@article {pmid15496229, year = {2004}, author = {Nickrent, DL and Blarer, A and Qiu, YL and Vidal-Russell, R and Anderson, FE}, title = {Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer.}, journal = {BMC evolutionary biology}, volume = {4}, number = {}, pages = {40}, pmid = {15496229}, issn = {1471-2148}, mesh = {Bayes Theorem ; Cell Nucleus/genetics ; Chloroplasts/genetics ; *Gene Transfer, Horizontal ; *Genes, Plant ; Likelihood Functions ; Magnoliopsida/*classification/*genetics ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: The phylogenetic relationships among the holoparasites of Rafflesiales have remained enigmatic for over a century. Recent molecular phylogenetic studies using the mitochondrial matR gene placed Rafflesia, Rhizanthes and Sapria (Rafflesiaceae s. str.) in the angiosperm order Malpighiales and Mitrastema (Mitrastemonaceae) in Ericales. These phylogenetic studies did not, however, sample two additional groups traditionally classified within Rafflesiales (Apodantheaceae and Cytinaceae). Here we provide molecular phylogenetic evidence using DNA sequence data from mitochondrial and nuclear genes for representatives of all genera in Rafflesiales.<br><br>RESULTS: Our analyses indicate that the phylogenetic affinities of the large-flowered clade and Mitrastema, ascertained using mitochondrial matR, are congruent with results from nuclear SSU rDNA when these data are analyzed using maximum likelihood and Bayesian methods. The relationship of Cytinaceae to Malvales was recovered in all analyses. Relationships between Apodanthaceae and photosynthetic angiosperms varied depending upon the data partition: Malvales (3-gene), Cucurbitales (matR) or Fabales (atp1). The latter incongruencies suggest that horizontal gene transfer (HGT) may be affecting the mitochondrial gene topologies. The lack of association between Mitrastema and Ericales using atp1 is suggestive of HGT, but greater sampling within eudicots is needed to test this hypothesis further.<br><br>CONCLUSIONS: Rafflesiales are not monophyletic but composed of three or four independent lineages (families): Rafflesiaceae, Mitrastemonaceae, Apodanthaceae and Cytinaceae. Long-branch attraction appears to be misleading parsimony analyses of nuclear small-subunit rDNA data, but model-based methods (maximum likelihood and Bayesian analyses) recover a topology that is congruent with the mitochondrial matR gene tree, thus providing compelling evidence for organismal relationships. Horizontal gene transfer appears to be influencing only some taxa and some mitochondrial genes, thus indicating that the process is acting at the single gene (not whole genome) level.}, }
@article {pmid15493148, year = {2004}, author = {Hu, WG and Duan, ZY and Wang, JF and Sheng, JL and Ma, RL}, title = {[Divergence and systematical evolution of three Leuciscus species in Xinjiang based on mitochondrial DNA control region sequences].}, journal = {Yi chuan xue bao = Acta genetica Sinica}, volume = {31}, number = {9}, pages = {970-975}, pmid = {15493148}, issn = {0379-4172}, mesh = {Animals ; Base Sequence ; Cyprinidae/classification/*genetics ; DNA, Mitochondrial/*chemistry ; Haploidy ; Molecular Sequence Data ; Phylogeny ; *Regulatory Sequences, Nucleic Acid ; }, abstract = {Nucleotide sequence of fish mitochondria DNA (mtDNA) D-loop region from Leuciscus leuciscus baicalensis, L. merzbacheri, and L. idus in Xinjiang, China, were examined by sequencing 667 - 669 bp length of homological fragments in the D-loop from 24 individuals of the three fish species. DNA divergence ranged from 6.39% - 9.89% among the three fish species in the genius of Leuciscus cuvier. The sequence similarity is high and the variation is low between L. Leuciscus baicalensis and L. idus. In contract, the genetic distance is larger between L. Leuciscus baicalensis and L. merzbacheri. The average nucleotide variation within each of the two geographical populations (Sailimu lake and E' erqis river) of L. leuciscus baicalensis is 1.07% and 1.08%, respectively, and such variation is 1.07% between the two populations. These results demonstrate that the two geographic populations of L. leuciscus baicalensis do not appear to have significant genetic differentiation. Sequencing data showed the existence of sufficient genetic variations among three species of fish, as illustrated by distinct haplotypes for each species. The phylogenetic trees built with MEGA1.02 pointed out that the relationship between L. leuciscus baicalensis and L. idus is close, and L. merzbacheri is ancient among three Leuciscus.}, }
@article {pmid15492359, year = {2004}, author = {Noguera, A and Fortuny, C and Muñoz-Almagro, C and Sanchez, E and Vilaseca, MA and Artuch, R and Pou, J and Jimenez, R}, title = {Hyperlactatemia in human immunodeficiency virus-uninfected infants who are exposed to antiretrovirals.}, journal = {Pediatrics}, volume = {114}, number = {5}, pages = {e598-603}, doi = {10.1542/peds.2004-0955}, pmid = {15492359}, issn = {1098-4275}, mesh = {Alanine/blood ; Antiretroviral Therapy, Highly Active/*adverse effects ; Didanosine/adverse effects/therapeutic use ; Female ; HIV Infections/drug therapy ; *HIV Seronegativity ; Humans ; Infant ; Infant, Newborn ; Infectious Disease Transmission, Vertical/prevention &amp; control ; Lactic Acid ; Logistic Models ; Male ; Mitochondria/*drug effects ; Pregnancy ; Pregnancy Complications, Infectious/drug therapy ; Prospective Studies ; Reverse Transcriptase Inhibitors/*adverse effects/therapeutic use ; Zidovudine/*adverse effects/therapeutic use ; }, abstract = {OBJECTIVE: Exposure to nucleoside analogues in fetal or early life has been associated with rare clinically significant mitochondrial toxic effects, mainly neurologic symptoms. Lactate (LA) measurements have been used to monitor nucleoside-related mitochondrial toxicity. Our aim was to determine the prevalence, clinical evolution, and risk factors for hyperlactatemia in our cohort of human immunodeficiency virus (HIV)-uninfected children who were exposed to antiretrovirals.<br><br>METHODS: We conducted a prospective observational study of 127 HIV-uninfected infants who were born to HIV-infected women. Clinical symptoms suggesting mitochondrial dysfunction were analyzed in routine follow-up, and LA and alanine plasma levels were obtained at 6 weeks, 3 months, 6 months, and 12 months in all patients. Elevated alanine levels, together with hyperlactatemia, suggest chronic mitochondrial injury.<br><br>RESULTS: Most (85%) women received highly active antiretroviral therapy (HAART) during pregnancy (mean duration: 31 weeks) and zidovudine during labor (93%). Most (96%) children received zidovudine alone. Hyperlactatemia with hyperalaninemia was detected in 63 children in at least 1 of the measurements. Mean LA levels were significantly higher in children who were exposed to nucleoside analogue reverse transcriptase inhibitors than in control subjects (2.88 vs 1.61 at 6 weeks, 2.78 vs 1.49 at 3 months, 1.89 vs 1.39 at 6 months, and 1.71 vs 1.24 at 12 months; peak levels: 8.06, 10.1, 7.28, and 4.48 mmol/L, respectively). In 44 patients, LA levels progressed spontaneously to normality within the first year of life. Three girls presented a slight and self-limited delay in psychomotor development, with LA peak levels of 7.3, 4.0, and 4.6 mmol/L. Only the gestational use of didanosine was associated with a higher risk of hyperlactatemia.<br><br>CONCLUSIONS: In our series, almost half of the children (63 of 127) who were exposed to nucleoside analogues developed benign and self-limited hyperlactatemia. When symptomatic, nucleoside analogue-induced toxicity affected neurologic development.}, }
@article {pmid15486695, year = {2004}, author = {Suzuki, T and Mizuta, C and Uda, K and Ishida, K and Mizuta, K and Sona, S and Compaan, DM and Ellington, WR}, title = {Evolution and divergence of the genes for cytoplasmic, mitochondrial, and flagellar creatine kinases.}, journal = {Journal of molecular evolution}, volume = {59}, number = {2}, pages = {218-226}, pmid = {15486695}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Creatine Kinase/*genetics ; Cytoplasm/genetics/metabolism ; DNA, Complementary/genetics ; *Evolution, Molecular ; Flagella/genetics/metabolism ; Gene Components ; *Genetic Variation ; Invertebrates/*genetics ; Likelihood Functions ; Mitochondria/genetics/metabolism ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Amplification Techniques ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Creatine kinase (CK) plays a central role in energy homeostasis in cells that display high and variable rates of energy turnover. A number of CK genes exist, each being targeted to particular intracellular compartments. In the vertebrates, two genes code for proteins which form homo- and heterodimers targeted to the cytoplasm, while two additional genes code for primarily octameric proteins targeted to the mitochondrial intermembrane space. Yet another gene is present in certain groups which codes for three fused, complete CK domains and is typically targeted to the flagellar membrane of primitive-type spermatozoa. CK is widely distributed in protochordates and both protostome and deuterostome invertebrate groups. The evolutionary relationships of these CK genes have not been fully elucidated. The present communication reports new cDNA-derived deduced amino acid sequences for four cytoplasmic and three mitochondrial CKs and one flagellar CK from lophotrochozoan, protostome invertebrates as well as a new cytoplasmic CK sequence from a protochordate tunicate. These new sequences, coupled with available sequences in the databases and sequences extracted from genome sequencing projects, provide revealing insights into the evolution and divergence of CK genes. Phylogenetic analyses showed that single cytoplasmic, mitochondrial, and flagellar CK genes were present prior to the divergence of the protostomes and deuterostomes. The flagellar CK gene may have evolved within the cytoplasmic gene clade, although the evidence is somewhat equivocal. The two cytoplasmic genes in the vertebrates, and most likely the two mitochondrial genes, evolved after the divergence of the craniates from the protochordates. Comparison of the structure of the genes for selected cytoplasmic, mitochondrial, and flagellar CKs revealed two identical intron boundaries, further reinforcing the notion of a common evolutionary origin, but also showed patterns of changes in structure consistent with each gene type. These studies show that the cytoplasmic, mitochondrial, and flagellar CK genes are rather ancient and that there has been a systematic pattern of duplication and divergence consistent with changing nature of energy demands and physicochemical environment in the cells where they are expressed.}, }
@article {pmid15486098, year = {2004}, author = {Hwang, YT and Pelitire, SM and Henderson, MP and Andrews, DW and Dyer, JM and Mullen, RT}, title = {Novel targeting signals mediate the sorting of different isoforms of the tail-anchored membrane protein cytochrome b5 to either endoplasmic reticulum or mitochondria.}, journal = {The Plant cell}, volume = {16}, number = {11}, pages = {3002-3019}, pmid = {15486098}, issn = {1040-4651}, mesh = {Aleurites/*genetics/*metabolism ; Amino Acid Motifs/genetics ; Amino Acid Sequence ; Cytochromes b5/chemistry/genetics/isolation &amp; purification/*metabolism ; Endoplasmic Reticulum/*metabolism ; Gene Expression Regulation, Plant/physiology ; Intracellular Membranes/metabolism ; Membrane Proteins/chemistry/genetics/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/genetics/metabolism ; Protein Isoforms/chemistry/genetics/metabolism ; Protein Sorting Signals/*genetics ; Protein Structure, Tertiary ; Protein Transport/physiology ; Signal Transduction/genetics ; }, abstract = {Tail-anchored membrane proteins are a class of proteins that are targeted posttranslationally to various organelles and integrated by a single segment of hydrophobic amino acids located near the C terminus. Although the localization of tail-anchored proteins in specific subcellular compartments in plant cells is essential for their biological function, the molecular targeting signals responsible for sorting these proteins are not well defined. Here, we describe the biogenesis of four closely related tung (Aleurites fordii) cytochrome b5 isoforms (Cb5-A, -B, -C, and -D), which are small tail-anchored proteins that play an essential role in many cellular processes, including lipid biosynthesis. Using a combination of in vivo and in vitro assays, we show that Cb5-A, -B, and -C are targeted exclusively to the endoplasmic reticulum (ER), whereas Cb5-D is targeted specifically to mitochondrial outer membranes. Comprehensive mutational analyses of ER and mitochondrial Cb5s revealed that their C termini, including transmembrane domains (TMD) and tail regions, contained several unique physicochemical and sequence-specific characteristics that defined organelle-specific targeting motifs. Mitochondrial targeting of Cb5 was mediated by a combination of hydrophilic amino acids along one face of the TMD, an enrichment of branched beta-carbon-containing residues in the medial portion of the TMD, and a dibasic -R-R/K/H-x motif in the C-terminal tail. By contrast, ER targeting of Cb5 depended primarily upon the overall length and hydrophobicity of the TMD, although an -R/H-x-Y/F- motif in the tail was also a targeting determinant. Collectively, the results presented provide significant insight into the early biogenetic events required for entry of tail-anchored proteins into either the ER or mitochondrial targeting pathways.}, }
@article {pmid15483054, year = {2005}, author = {Fuchs, F and Westermann, B}, title = {Role of Unc104/KIF1-related motor proteins in mitochondrial transport in Neurospora crassa.}, journal = {Molecular biology of the cell}, volume = {16}, number = {1}, pages = {153-161}, pmid = {15483054}, issn = {1059-1524}, mesh = {Animals ; Biological Transport ; Caenorhabditis elegans Proteins/metabolism/*physiology ; Cell Movement ; Cell Proliferation ; Microscopy ; Microtubules/metabolism/ultrastructure ; Mitochondria/*metabolism ; Mutation ; Nerve Tissue Proteins/metabolism/*physiology ; Neurospora crassa/*metabolism ; Phylogeny ; Plasmids/metabolism ; Protein Binding ; Subcellular Fractions ; Time Factors ; Up-Regulation ; }, abstract = {Eukaryotic cells use diverse cytoskeleton-dependent machineries to control inheritance and intracellular positioning of mitochondria. In particular, microtubules play a major role in mitochondrial motility in the filamentous fungus Neurospora crassa and in mammalian cells. We examined the role of two novel Unc104/KIF1-related members of the kinesin family, Nkin2 and Nkin3, in mitochondrial motility in Neurospora. The Nkin2 protein is required for mitochondrial interactions with microtubules in vitro. Mutant hyphae lacking Nkin2 show mitochondrial motility defects in vivo early after germination of conidiospores. Nkin3, a member of a unique fungal-specific subgroup of small Unc104/KIF1-related proteins, is not associated with mitochondria in wild-type cells. However, it is highly expressed and recruited to mitochondria in Deltankin-2 mutants. Mitochondria lacking Nkin2 require Nkin3 for binding to microtubules in vitro, and mitochondrial motility defects in Deltankin-2 mutants disappear with up-regulation of Nkin3 in vivo. We propose that mitochondrial transport is mediated by Nkin2 in Neurospora, and organelle motility defects in Deltankin-2 mutants are rescued by Nkin3. Apparently, a highly versatile complement of organelle motors allows the cell to efficiently respond to exogenous challenges, a process that might also account for the great variety of different mitochondrial transport systems that have evolved in eukaryotic cells.}, }
@article {pmid15481813, year = {2004}, author = {Carafoli, E}, title = {The ambivalent nature of the calcium signal.}, journal = {Journal of endocrinological investigation}, volume = {27}, number = {6 Suppl}, pages = {134-136}, pmid = {15481813}, issn = {0391-4097}, mesh = {Animals ; Apoptosis/physiology ; Calcium Signaling/*physiology ; Cell Communication/physiology ; Cell Death/physiology ; Energy Metabolism/physiology ; Humans ; Necrosis ; }, abstract = {In the couse of evolution, calcium has emerged as the most versatile intracellular messenger. Its concentration within cells is controlled by reversible binding to specific protein acting as sensors to decode its information. The decoding operation is based on specific conformational changes in these sensor proteins. Other proteins intrinsic to membranes (plasma membrane, endosarcoplasmic reticulum, mitochondria, nuclear envelope) simply control calcium concentration by transporting it across membrane boundaries. Calcium is an ambivalent signaling agent. It carries information to all processes important to cell life, including excitation-contraction coupling, secretion, gene transcription and enzyme activity through protein phosphorylation-dephosphorylation. However, it also transmits signals that promote programmed demise of cells and, when escaping control, it may also precipitate toxic cell death.}, }
@article {pmid15480793, year = {2004}, author = {Caldwell, EF and Mayor, LR and Thomas, MG and Danpure, CJ}, title = {Diet and the frequency of the alanine:glyoxylate aminotransferase Pro11Leu polymorphism in different human populations.}, journal = {Human genetics}, volume = {115}, number = {6}, pages = {504-509}, pmid = {15480793}, issn = {0340-6717}, mesh = {Alleles ; Asian People ; Biological Evolution ; Black People ; Catalysis ; Cheek ; DNA/genetics ; *Diet ; Diet, Vegetarian ; Genetics, Population ; Genotype ; Humans ; Mouth Mucosa/metabolism ; *Polymorphism, Genetic ; Statistics as Topic ; Transaminases/*genetics ; White People ; }, abstract = {The intermediary metabolic enzyme alanine:glyoxylate aminotransferase (AGT) contains a Pro11Leu polymorphism that decreases its catalytic activity by a factor of three and causes a small proportion to be mistargeted from its normal intracellular location in the peroxisomes to the mitochondria. These changes are predicted to have significant effects on the synthesis and excretion of the metabolic end-product oxalate and the deposition of insoluble calcium oxalate in the kidney and urinary tract. Based on the evolution of AGT targeting in mammals, we have previously hypothesised that this polymorphism would be advantageous for individuals who have a meat-rich diet, but disadvantageous for those who do not. If true, the frequency distribution of Pro11Leu in different extant human populations should have been shaped by their dietary history so that it should be more common in populations with predominantly meat-eating ancestral diets than it is in populations in which the ancestral diets were predominantly vegetarian. In the present study, we have determined frequency of Pro11Leu in 11 different human populations with divergent ancestral dietary lifestyles. We show that the Pro11Leu allelic frequency varies widely from 27.9% in the Saami, a population with a very meat-rich ancestral diet, to 2.3% in Chinese, who are likely to have had a more mixed ancestral diet. FST analysis shows that the differences in Pro11Leu frequency between some populations (particularly Saami vs Chinese) was very high when compared with neutral loci, suggesting that its frequency might have been shaped by dietary selection pressure.}, }
@article {pmid15475391, year = {2004}, author = {Dalebout, ML and Baker, CS and Mead, JG and Cockcroft, VG and Yamada, TK}, title = {A comprehensive and validated molecular taxonomy of beaked whales, family Ziphiidae.}, journal = {The Journal of heredity}, volume = {95}, number = {6}, pages = {459-473}, doi = {10.1093/jhered/esh054}, pmid = {15475391}, issn = {0022-1503}, mesh = {Actins/genetics ; Animals ; Cytochromes b/genetics ; DNA, Mitochondrial ; Databases, Genetic ; Evolution, Molecular ; Genetic Variation ; Mitochondria/genetics ; Phylogeny ; Polymerase Chain Reaction ; Reference Values ; Species Specificity ; Whales/*classification/genetics ; }, abstract = {DNA sequences from orthologous loci can provide universal characters for taxonomic identification. Molecular taxonomy is of particular value for groups in which distinctive morphological features are difficult to observe or compare. To assist in species identification for the little known family Ziphiidae (beaked whales), we compiled a reference database of mitochondrial DNA (mtDNA) control region (437 bp) and cytochrome b (384 bp) sequences for all 21 described species in this group. This mtDNA database is complemented by a nuclear database of actin intron sequences (925 bp) for 17 of the 21 species. All reference sequences were derived from specimens validated by diagnostic skeletal material or other documentation, and included four holotypes. Phylogenetic analyses of mtDNA sequences confirmed the genetic distinctiveness of all beaked whale species currently recognized. Both mitochondrial loci were well suited for species identification, with reference sequences for all known ziphiids forming robust species-specific clades in phylogenetic reconstructions. The majority of species were also distinguished by nuclear alleles. Phylogenetic comparison of sequence data from "test" specimens to these reference databases resulted in three major taxonomic discoveries involving animals previously misclassified from morphology. Based on our experience with this family and the order Cetacea as a whole, we suggest that a molecular taxonomy should consider the following components: comprehensiveness, validation, locus sensitivity, genetic distinctiveness and exclusivity, concordance, and universal accessibility and curation.}, }
@article {pmid15475345, year = {2004}, author = {Nevo, Y and Nelson, N}, title = {The mutation F227I increases the coupling of metal ion transport in DCT1.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {51}, pages = {53056-53061}, doi = {10.1074/jbc.M408398200}, pmid = {15475345}, issn = {0021-9258}, mesh = {Animals ; Biological Transport ; Cation Transport Proteins/*genetics/*physiology ; Cobalt/chemistry ; Electrophysiology ; Evolution, Molecular ; Fungal Proteins/chemistry ; Genetic Complementation Test ; Hydrogen-Ion Concentration ; Ions ; Iron/chemistry/metabolism ; Iron-Binding Proteins/*genetics/*physiology ; Macrophages/metabolism ; Manganese/chemistry ; Mutagenesis, Site-Directed ; *Mutation ; Oocytes/metabolism ; Protons ; RNA, Complementary/metabolism ; RNA, Messenger/metabolism ; Time Factors ; Xenopus ; Zinc/chemistry/pharmacokinetics ; }, abstract = {Metal ion transport by DCT1, a member of the natural resistance-associated macrophage protein family, is driven by protons. The stoichiometry of the proton to metal ion is variable, and under optimal transport conditions, more than 10 protons are co-transported with a single metal ion. To understand this phenomenon better, we used site-directed mutagenesis of DCT1 and analyzed the mutants by complementation of yeast suppressor of mitochondria import function-null mutants and electrophysiology with Xenopus oocytes. The mutation F227I resulted in an increase of up to 14-fold in the ratio between metal ions to protons transported. This observation suggests that low metal ion to proton transport of DCT1 resulting from a proton slippage is not a necessity of the transport mechanism in which positively charged protons are driving two positive charges of the metal ion in the same direction. It supports the idea that the proton slippage has a physiological advantage, and the proton slip was positively selected during the evolution of DCT1.}, }
@article {pmid15475118, year = {2004}, author = {Grossman, LI and Wildman, DE and Schmidt, TR and Goodman, M}, title = {Accelerated evolution of the electron transport chain in anthropoid primates.}, journal = {Trends in genetics : TIG}, volume = {20}, number = {11}, pages = {578-585}, doi = {10.1016/j.tig.2004.09.002}, pmid = {15475118}, issn = {0168-9525}, mesh = {Animals ; Electron Transport Chain Complex Proteins/*genetics/physiology ; Electron Transport Complex III/genetics/physiology ; Electron Transport Complex IV/genetics/physiology ; Evolution, Molecular ; Haplorhini/*genetics/physiology ; Humans ; Phylogeny ; }, abstract = {Mitochondria are both the power plant of the cell and a central integrator of signals that govern the lifespan, replication and death of the cell. Perhaps as a consequence, genes that encode components of the mitochondrial electron transport chain (ETC) are generally conserved. Therefore, it is surprising that many of these genes in anthropoid primates (New World monkeys, Old World monkeys and apes, including humans) have been major targets of darwinian positive selection. Sequence comparisons have provided evidence that marked increases of non-synonymous substitution rates occurred in anthropoid ETC genes that encode subunits of Complex III and IV, and the electron carrier molecule cytochrome c (CYC). Two important questions are: (i) how has evolution altered ETC function? and; (ii) how might functional changes in the ETC be linked to evolution of an expanded neocortical brain?}, }
@article {pmid15475115, year = {2004}, author = {Reichert, AS and Neupert, W}, title = {Mitochondriomics or what makes us breathe.}, journal = {Trends in genetics : TIG}, volume = {20}, number = {11}, pages = {555-562}, doi = {10.1016/j.tig.2004.08.012}, pmid = {15475115}, issn = {0168-9525}, mesh = {Animals ; Biological Evolution ; Computational Biology ; Humans ; Mitochondria/*physiology ; Mitochondrial Proteins/genetics/physiology ; *Proteomics ; RNA/physiology ; Saccharomyces cerevisiae/genetics/physiology ; }, abstract = {Mitochondria perform several fundamental cellular processes in higher eukaryotes including oxidative phosphorylation, Fe/S cluster formation and apoptosis. Dysfunction of the organelle is associated with a wide range of human diseases. To gain a better understanding of mitochondrial function, several recent proteomic, genetic, transcriptomic and bioinformatic approaches have set out to determine the complete set of mitochondrially located proteins in yeast, plants and mammals. Here, we review these studies and discuss the advances and limitations of individual strategies. Integration of various approaches proves to be a successful and useful way to identify the mitochondrial proteome with high sensitivity and specificity. The most comprehensive dataset is available for Saccharomyces cerevisiae, giving an estimated number of 700 different proteins located in mitochondria.}, }
@article {pmid15474311, year = {2004}, author = {Krücken, J and Schroetel, RM and Müller, IU and Saïdani, N and Marinovski, P and Benten, WP and Stamm, O and Wunderlich, F}, title = {Comparative analysis of the human gimap gene cluster encoding a novel GTPase family.}, journal = {Gene}, volume = {341}, number = {}, pages = {291-304}, doi = {10.1016/j.gene.2004.07.005}, pmid = {15474311}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Animals ; Blotting, Northern ; CHO Cells ; Cricetinae ; Cricetulus ; Exons ; Female ; GTP-Binding Proteins/*genetics/metabolism ; Gene Expression Profiling ; Gene Order ; Genes/genetics ; Humans ; Introns ; Jurkat Cells ; Luminescent Proteins/genetics/metabolism ; Male ; Membrane Proteins/*genetics/metabolism ; Microscopy, Confocal ; Molecular Sequence Data ; Multigene Family/*genetics ; Phylogeny ; Plasmids/genetics ; Protein Isoforms/genetics ; RNA, Messenger/genetics/metabolism ; Sequence Homology, Amino Acid ; Tissue Array Analysis ; Transfection ; }, abstract = {There is a growing family of novel GTPases conserved among higher plants and vertebrates, abbreviated as AIG1, IAP, IMAP, and IAN, respectively. Here, we comparatively analyze the human gene family encoding GTPases of the immunity-associated protein family recently re-termed GIMAP. Chromosome 7q36.1 contains, within 300 kb, a gimap gene cluster with seven functional genes and one pseudogene (hgimap3). The six genes hgimap1, hgimap2, hgimap4, hgimap5, hgimap6, and hgimap7 encode 33-46 kDa proteins with one GTP-binding domain, whereas hgimap8 encodes a very unusual 75-kDa protein with three GTP-binding domains. All hgimap genes except hgimap2 have orthologs in the mouse. Major expression sites of hgimap mRNAs are the spleen and lymph nodes, but also other organs such as muscle, heart, placenta, and digestive tract display detectable hgimap mRNA levels. The proteins hGIMAP4 and hGIMAP7 can be localized at ER and Golgi apparatus, but not in mitochondria, lysosomes and nuclei. All hgimap genes were expressed at very low levels-if at all-in diverse cancer cell lines. Our data support the view that the GIMAP proteins are involved in the control of cell survival not only in cells of the immune system as commonly anticipated.}, }
@article {pmid15474026, year = {2004}, author = {Busi, MV and Zabaleta, EJ and Araya, A and Gomez-Casati, DF}, title = {Functional and molecular characterization of the frataxin homolog from Arabidopsis thaliana.}, journal = {FEBS letters}, volume = {576}, number = {1-2}, pages = {141-144}, doi = {10.1016/j.febslet.2004.09.003}, pmid = {15474026}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/growth &amp; development/*metabolism ; Arabidopsis Proteins/*chemistry/genetics/metabolism ; Cloning, Molecular ; Evolution, Molecular ; Gene Expression ; *Genes, Plant ; Genetic Complementation Test ; Iron-Binding Proteins/*chemistry/genetics ; Mitochondria/chemistry/metabolism ; Mitochondrial Proteins/*chemistry/metabolism ; Molecular Sequence Data ; Mutation ; Oxidative Stress ; Phylogeny ; Protein Structure, Secondary ; Saccharomyces cerevisiae/genetics ; Sensitivity and Specificity ; Sequence Homology, Amino Acid ; Transcription, Genetic ; Frataxin ; }, abstract = {Frataxin is a highly conserved protein from bacteria to mammals that has been proposed to participate in iron-sulfur cluster assembly and mitochondrial iron homeostasis. In higher organisms, the frataxin gene is nuclear-encoded and the protein is required for maintenance of normal mitochondrial iron levels and respiration. We describe here AtFH, a plant gene with significant homology to other members of the frataxin family. Plant frataxin has five segments of beta regions and two alpha helices, which are characteristics of human frataxin, as well as a potential N-terminal targeting peptide for the mitochondrial localization. Transcription analysis showed that AtFH is ubiquitously expressed with high levels in flowers. Complementation of a Saccharomyces cerevisiae mutant (Deltayfh) lacking the frataxin gene proved that AtFH is a functional protein, because it restored normal rates of respiration, growth and sensitivity to H2O2 of the null mutant. Our results support the involvement of AtFH in mitochondrial respiration and survival during oxidative stress in plants. This is the first report of a functional frataxin gene in plants.}, }
@article {pmid15466869, year = {2004}, author = {Behm-Ansmant, I and Grosjean, H and Massenet, S and Motorin, Y and Branlant, C}, title = {Pseudouridylation at position 32 of mitochondrial and cytoplasmic tRNAs requires two distinct enzymes in Saccharomyces cerevisiae.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {51}, pages = {52998-53006}, doi = {10.1074/jbc.M409581200}, pmid = {15466869}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Aminohydrolases/chemistry/*physiology ; Aspartic Acid/chemistry ; Catalysis ; Cell-Free System ; Cytoplasm/*metabolism ; Dose-Response Relationship, Drug ; Gene Deletion ; Genetic Complementation Test ; Intramolecular Transferases/chemistry ; Mitochondria/*metabolism ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Open Reading Frames ; Plasmids/metabolism ; Protein Structure, Tertiary ; RNA/chemistry ; RNA, Transfer/*chemistry/metabolism ; Recombinant Proteins/chemistry ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/*physiology ; Sequence Homology, Amino Acid ; Uridine/*chemistry ; }, abstract = {Cytoplasmic and mitochondrial tRNAs contain several pseudouridylation sites, and the tRNA:Psi-synthase acting at position 32 had not been identified in Saccharomyces cerevisiae. By combining genetic and biochemical analyses, we demonstrate that two enzymes, Rib2/Pus8p and Pus9p, are required for Psi32 formation in cytoplasmic and mitochondrial tRNAs, respectively. Pus9p acts mostly in mitochondria, and Rib2/Pus8p is strictly cytoplasmic. This is the first case reported so far of two distinct tRNA modification enzymes acting at the same position but present in two different compartments. This peculiarity may be the consequence of a gene fusion that occurred during yeast evolution. Indeed, Rib2/Pus8p displays two distinct catalytic activities involved in completely unrelated metabolism: its C-terminal domain has a DRAP-deaminase activity required for riboflavin biogenesis in the cytoplasm, whereas its N-terminal domain carries the tRNA:Psi32-synthase activity. Pus9p has only a tRNA:Psi32-synthase activity and contains a characteristic mitochondrial targeting sequence at its N terminus. These results are discussed in terms of RNA:Psi-synthase evolution.}, }
@article {pmid15465027, year = {2004}, author = {Da Pozzo, P and Cardaioli, E and Radi, E and Federico, A}, title = {Sequence analysis of the complete mitochondrial genome in patients with mitochondrial encephaloneuromyopathies lacking the common pathogenic DNA mutations.}, journal = {Biochemical and biophysical research communications}, volume = {324}, number = {1}, pages = {360-364}, doi = {10.1016/j.bbrc.2004.09.058}, pmid = {15465027}, issn = {0006-291X}, mesh = {Adult ; Aged ; Amino Acid Sequence ; DNA, Mitochondrial/*analysis ; Evolution, Molecular ; Female ; Genome ; Humans ; Male ; Middle Aged ; Mitochondria/*genetics ; Mitochondrial Encephalomyopathies/*genetics/physiopathology ; *Mutation ; Polymorphism, Genetic ; *Sequence Analysis, DNA ; }, abstract = {The purpose of this study was to identify novel mitochondrial deoxyribonucleic acid (mtDNA) mutations in a series of patients with clinical and/or morphological features of mitochondrial dysfunction, but still no genetic diagnosis. A heterogeneous group of clinical disorders is caused by mutations in mtDNA that damage respiratory chain function of cell energy production. We developed a method to systematically screen the entire mitochondrial genome. The sequence-data were obtained with a rapid automated system. In the six mitochondrial genomes analysed we found 20 variants of the revised Cambridge reference sequence [Nat. Genet. 23 (1999) 147]. In skeletal muscle nineteen novel mtDNA variants were homoplasmic, suggesting secondary pathogenicity or co-responsibility in determination of the disease. In one patient we identified a novel heteroplasmic mtDNA mutation which presumably has a pathogenic role. This screening is therefore useful to extend the mtDNA polymorphism database and should facilitate definition of disease-related mutations in human mtDNA.}, }
@article {pmid15459382, year = {2004}, author = {Armbrust, EV and Berges, JA and Bowler, C and Green, BR and Martinez, D and Putnam, NH and Zhou, S and Allen, AE and Apt, KE and Bechner, M and Brzezinski, MA and Chaal, BK and Chiovitti, A and Davis, AK and Demarest, MS and Detter, JC and Glavina, T and Goodstein, D and Hadi, MZ and Hellsten, U and Hildebrand, M and Jenkins, BD and Jurka, J and Kapitonov, VV and Kröger, N and Lau, WW and Lane, TW and Larimer, FW and Lippmeier, JC and Lucas, S and Medina, M and Montsant, A and Obornik, M and Parker, MS and Palenik, B and Pazour, GJ and Richardson, PM and Rynearson, TA and Saito, MA and Schwartz, DC and Thamatrakoln, K and Valentin, K and Vardi, A and Wilkerson, FP and Rokhsar, DS}, title = {The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism.}, journal = {Science (New York, N.Y.)}, volume = {306}, number = {5693}, pages = {79-86}, doi = {10.1126/science.1101156}, pmid = {15459382}, issn = {1095-9203}, mesh = {Adaptation, Physiological ; Algal Proteins/chemistry/genetics/physiology ; Animals ; *Biological Evolution ; Cell Nucleus/genetics ; Chromosomes ; DNA/genetics ; Diatoms/chemistry/cytology/*genetics/metabolism ; *Ecosystem ; Energy Metabolism ; *Genome ; Iron/metabolism ; Light ; Light-Harvesting Protein Complexes/chemistry/genetics/metabolism ; Mitochondria/genetics ; Molecular Sequence Data ; Nitrogen/metabolism ; Photosynthesis ; Plastids/genetics ; Restriction Mapping ; Sequence Alignment ; *Sequence Analysis, DNA ; Silicic Acid/metabolism ; Symbiosis ; Urea/metabolism ; }, abstract = {Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for approximately 20% of global carbon fixation. We report the 34 million-base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand-base pair plastid and 44 thousand-base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.}, }
@article {pmid15459356, year = {2004}, author = {Pennisi, E}, title = {Genetics. DNA reveals diatom's complexity.}, journal = {Science (New York, N.Y.)}, volume = {306}, number = {5693}, pages = {31}, doi = {10.1126/science.306.5693.31a}, pmid = {15459356}, issn = {1095-9203}, mesh = {Algal Proteins/genetics/physiology ; Animals ; Biological Evolution ; Chloroplasts/genetics ; DNA/genetics ; Diatoms/*genetics/physiology ; Ecosystem ; *Genome ; Mitochondria/genetics ; Photosynthesis/genetics ; *Sequence Analysis, DNA ; Silicon/metabolism ; }, }
@article {pmid15452701, year = {2004}, author = {Korpelainen, H}, title = {The evolutionary processes of mitochondrial and chloroplast genomes differ from those of nuclear genomes.}, journal = {Die Naturwissenschaften}, volume = {91}, number = {11}, pages = {505-518}, pmid = {15452701}, issn = {0028-1042}, mesh = {Animals ; Cell Nucleus/*genetics ; Chloroplasts/*genetics ; Cytoplasm/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Female ; Genetic Drift ; Genome ; Humans ; Male ; Mitochondria/*genetics ; }, abstract = {This paper first introduces our present knowledge of the origin of mitochondria and chloroplasts, and the organization and inheritance patterns of their genomes, and then carries on to review the evolutionary processes influencing mitochondrial and chloroplast genomes. The differences in evolutionary phenomena between the nuclear and cytoplasmic genomes are highlighted. It is emphasized that varying inheritance patterns and copy numbers among different types of genomes, and the potential advantage achieved through the transfer of many cytoplasmic genes to the nucleus, have important implications for the evolution of nuclear, mitochondrial and chloroplast genomes. Cytoplasmic genes transferred to the nucleus have joined the more strictly controlled genetic system of the nuclear genome, including also sexual recombination, while genes retained within the cytoplasmic organelles can be involved in selection and drift processes both within and among individuals. Within-individual processes can be either intra- or intercellular. In the case of heteroplasmy, which is attributed to mutations or biparental inheritance, within-individual selection on cytoplasmic DNA may provide a mechanism by which the organism can adapt rapidly. The inheritance of cytoplasmic genomes is not universally maternal. The presence of a range of inheritance patterns indicates that different strategies have been adopted by different organisms. On the other hand, the variability occasionally observed in the inheritance mechanisms of cytoplasmic genomes reduces heritability and increases environmental components in phenotypic features and, consequently, decreases the potential for adaptive evolution.}, }
@article {pmid15451509, year = {2004}, author = {Bullerwell, CE and Gray, MW}, title = {Evolution of the mitochondrial genome: protist connections to animals, fungi and plants.}, journal = {Current opinion in microbiology}, volume = {7}, number = {5}, pages = {528-534}, doi = {10.1016/j.mib.2004.08.008}, pmid = {15451509}, issn = {1369-5274}, mesh = {Animals ; Chlorophyta/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; Fungi/classification/*genetics ; Gene Order ; Genes ; *Genome ; Mitochondria/*genetics ; Phylogeny ; Plants/classification/*genetics ; }, abstract = {The past decade has seen the determination of complete mitochondrial genome sequences from a taxonomically diverse set of organisms. These data have allowed an unprecedented understanding of the evolution of the mitochondrial genome in terms of gene content and order, as well as genome size and structure. In addition, phylogenetic reconstructions based on mitochondrial DNA (mtDNA)-encoded protein sequences have firmly established the identities of protistan relatives of the animal, fungal and plant lineages. Analysis of the mtDNAs of these protists has provided insight into the structure of the mitochondrial genome at the origin of these three, mainly multicellular, eukaryotic groups. Further research into mtDNAs of taxa ancestral and intermediate to currently characterized organisms will help to refine pathways and modes of mtDNA evolution, as well as provide valuable phylogenetic characters to assist in unraveling the deep branching order of all eukaryotes.}, }
@article {pmid15450001, year = {2005}, author = {Austin, AD and Johnson, NF and Dowton, M}, title = {Systematics, evolution, and biology of scelionid and platygastrid wasps.}, journal = {Annual review of entomology}, volume = {50}, number = {}, pages = {553-582}, doi = {10.1146/annurev.ento.50.071803.130500}, pmid = {15450001}, issn = {0066-4170}, mesh = {Animals ; Biological Evolution ; Chromosome Mapping ; Mitochondria/genetics ; Phylogeny ; Reproduction ; *Wasps/classification/genetics/physiology ; }, abstract = {The Platygastroidea comprises two families of parasitoids, Scelionidae and Platygastridae, and nearly 4500 described species. They parasitize a diverse array of insects as well as spiders. Idiobiont endoparasitism of eggs is the putative ground plan biology, as reflected by all scelionids, but most Platygastridae are koinobiont endoparasitoids of immature Auchenorrhyncha, Sternorrhyncha, and Cecidomyiidae. The superfamily is demonstrably monophyletic but its phylogenetic position remains uncertain. Relationships within the Platygastroidea are also poorly known and the group is in need of comprehensive phylogenetic study. Significant information is available on host relationships and biology, although much of this is biased to a few genera of Telenominae that are employed as biocontrol agents. Hosts for many genera are unknown, in particular those that inhabit leaf litter or parasitize solitary host eggs. The Trissolcus basalis-Nezara viridula parasitoid-host association has become a favored model system in ecological, behavioral, and physiological research on insects.}, }
@article {pmid15385674, year = {2004}, author = {Gelhaye, E and Rouhier, N and Gérard, J and Jolivet, Y and Gualberto, J and Navrot, N and Ohlsson, PI and Wingsle, G and Hirasawa, M and Knaff, DB and Wang, H and Dizengremel, P and Meyer, Y and Jacquot, JP}, title = {A specific form of thioredoxin h occurs in plant mitochondria and regulates the alternative oxidase.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {40}, pages = {14545-14550}, pmid = {15385674}, issn = {0027-8424}, mesh = {Base Sequence ; DNA, Recombinant/genetics ; Glutathione Peroxidase/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins ; Oxidation-Reduction ; Oxidoreductases/*metabolism ; Phylogeny ; Plant Proteins/genetics/*metabolism ; Plants/genetics/*metabolism ; Plants, Genetically Modified ; Populus/genetics/metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Thioredoxin h ; }, abstract = {The plant mitochondrial thioredoxin (Trx) system has been described as containing an NADPH-dependent Trx reductase and Trx o. In addition to the mitochondrial isoform, Trx o, plants are known to contain several chloroplastic Trx isoforms and the cytosolic Trx h isoforms. We report here the presence in plant mitochondria of a Trx isoform (PtTrxh2) belonging to the Trx h group. Western blot analyses with mitochondrial proteins isolated from both poplar and GFP fusion constructs indicate that PtTrxh2 is targeted to plant mitochondria. The recombinant protein, PtTrxh2, has been shown to be reduced efficiently by the mitochondrial Trx reductase AtNTRA. PtTrxh2 is also able to reduce alternative oxidase homodimers and to allow its activation by pyruvate. In contrast, neither PtTrxh2 nor AtTrxo1 exhibits activity with several poplar glutathione peroxidases and especially a putative mitochondrial isoform. Incubation of PtTrxh2 with glutathione disulfide led to the formation of glutathionylated Trx, identified by mass spectrometry. The formation of a glutathione adduct increases the redox potential of PtTrxh2 from -290 to -225 mV. In addition to Trx o, this study shows that Trx h could also be present in mitochondria. This previously unrecognized complexity is not unexpected, considering the multiple redox-regulated processes found in plant mitochondria.}, }
@article {pmid15383911, year = {2004}, author = {Schneider, A and Ebert, D}, title = {Covariation of mitochondrial genome size with gene lengths: evidence for gene length reduction during mitochondrial evolution.}, journal = {Journal of molecular evolution}, volume = {59}, number = {1}, pages = {90-96}, pmid = {15383911}, issn = {0022-2844}, mesh = {Bacteria/*genetics ; Base Composition ; Computational Biology ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; *Evolution, Molecular ; *Genome ; Selection, Genetic ; Statistics, Nonparametric ; }, abstract = {Reduction of genome size and gene shortening have been observed in a number of parasitic and mutualistic intracellular symbionts. Reduction of coding capacity is also a unifying principle in the evolutionary history of mitochondria, but little is known about the evolution of gene length in mitochondria. The genes for cytochrome c oxidase subunits I-III, cytochrome b, and the large and small subunit rRNAs are, with very few exceptions, always found on the mitochondrial genome. These resident mitochondrial genes can therefore be used to test whether the reduction in gene lengths observed in a number of intracellular symbionts is also seen in mitochondria. Here we show that resident mitochondrial gene products are shorter than their corresponding counterparts in alpha-proteobacteria and, furthermore, that the reduction of mitochondrial genome size is correlated with a reduction in the length of the corresponding resident gene products. We show that relative genomic AT content, which has been identified as a factor influencing gene lengths in other systems, cannot explain gene length/genome size covariance observed in mitochondria. Our data are therefore in agreement with the idea that gene length evolves as a consequence of selection for smaller genomes, either to avoid accumulation of deleterious mutations or triggered by selection for a replication advantage.}, }
@article {pmid15375767, year = {2004}, author = {Maricchiolo, G and Genovese, L and Laurà, R and Micale, V and Muglia, U}, title = {Fine structure of spermatozoa in the common pandora (Pagellus erythrinus Linnaeus, 1758) (Perciformes, Sparidae).}, journal = {Histology and histopathology}, volume = {19}, number = {4}, pages = {1237-1240}, doi = {10.14670/HH-19.1237}, pmid = {15375767}, issn = {0213-3911}, mesh = {Animals ; Biological Evolution ; Male ; Microscopy, Electron ; Microscopy, Electron, Scanning ; Mitochondria/ultrastructure ; Perciformes/*anatomy &amp; histology/classification ; Sperm Head/ultrastructure ; Sperm Midpiece/ultrastructure ; Sperm Tail/ultrastructure ; Spermatozoa/*ultrastructure ; }, abstract = {Scanning and transmission electron microscopy were used to investigate the fine structure of the sperm of the Sparid fish Pagellus erythrinus L. The spermatozoon of pandora has a spherical head lacking an acrosome, a cone-shaped midpiece and a long tail. The midpiece houses a single mitochondrion. The centriolar complex lies inside the nuclear fossa and is composed of a proximal and a distal centriole which are arranged at right angles to each other. The flagellum is inserted medio-laterally into the head, contains the conventional 9+2 axoneme and possesses one pair of lateral fins. On the basis of its ultrastructural organization, the pandora sperm can be regarded as an evolved form of the primitive spermatozoon found in Teleosts. According to the morphological classification proposed by Mattei (1970), the sperm of pandora belongs to a "type I" designation, like that of the other Sparid fish.}, }
@article {pmid15374817, year = {2005}, author = {Dalziel, AC and Moore, SE and Moyes, CD}, title = {Mitochondrial enzyme content in the muscles of high-performance fish: evolution and variation among fiber types.}, journal = {American journal of physiology. Regulatory, integrative and comparative physiology}, volume = {288}, number = {1}, pages = {R163-72}, doi = {10.1152/ajpregu.00152.2004}, pmid = {15374817}, issn = {0363-6119}, mesh = {Amino Acid Sequence ; Animals ; Citrate (si)-Synthase/genetics/*metabolism ; DNA/metabolism ; Gene Expression Regulation, Enzymologic/physiology ; Genetic Variation ; Mitochondria, Muscle/*enzymology ; Molecular Sequence Data ; Perciformes/*metabolism ; RNA Processing, Post-Transcriptional/physiology ; RNA, Messenger/metabolism ; Sequence Alignment ; Species Specificity ; Transcription, Genetic/physiology ; Tuna/metabolism ; }, abstract = {Muscle mitochondrial content varies widely among fiber types and species. We investigated the origins of variation in the activity of the mitochondrial enzyme citrate synthase (CS), an index of mitochondrial abundance, among fiber types and species of high-performance fish (tunas and billfishes). CS activities varied up to 30-fold among muscles: lowest in billfish white muscle and highest in billfish heater organ. Among species, CS activities of red, white, and cardiac muscles of three tuna species were twofold greater than the homologous muscles of two billfish species. Because comparisons of CS amino acid sequences deduced from a combination of PCR methods argue against clade-specific differences in catalytic properties, CS activity reflects CS content among these five species. To assess the bases of these differences in CS activity, we looked at the relationship between CS activity (U/g muscle), nuclear content (DNA/g muscle), and CS transcript levels (CS mRNA/g RNA). Muscle CS activity differed by 10- to 30-fold when expressed per gram of muscle but only threefold when expressed per milligram of DNA. Thus it is nuclear DNA content, not fiber-type differences, in CS gene expression that may be the main determinant of CS activity in muscle. Conversely, evolutionary (tunas vs. billfishes) differences in CS arise from differences in posttranscriptional regulation, based on relationships between CS enzyme levels and CS mRNA assessed by quantitative competitive RT-PCR. These data argue that fiber-type differences can arise without major differences in fiber-type-specific regulation of the CS gene, whereas evolutionary differences may be largely due to posttranscriptional regulation.}, }
@article {pmid15371928, year = {2004}, author = {Hervé, S and Riachi, G and Noblet, C and Guillement, N and Tanasescu, S and Goria, O and Thuillez, C and Tranvouez, JL and Ducrotte, P and Lerebours, E}, title = {Acute hepatitis due to buprenorphine administration.}, journal = {European journal of gastroenterology &amp; hepatology}, volume = {16}, number = {10}, pages = {1033-1037}, doi = {10.1097/00042737-200410000-00013}, pmid = {15371928}, issn = {0954-691X}, mesh = {Acute Disease ; Administration, Sublingual ; Adult ; Buprenorphine/*adverse effects/therapeutic use ; Causality ; Female ; Hepatitis C/*chemically induced/complications ; Humans ; Injections, Intravenous ; Male ; Mitochondria, Liver/drug effects ; Narcotic Antagonists/*adverse effects/therapeutic use ; Substance-Related Disorders/complications/drug therapy ; }, abstract = {BACKGROUND: Buprenorphine, a synthetic molecule derived from thebaine, has been commercialized in France since 1987 as a substitute treatment for pharmacodependence on opiates. Hepatotoxicity is poorly documented, since only few cases of hepatic injury have been reported.<br><br>METHODS: We report seven cases of acute cytolytic hepatitis due to buprenorphine. All patients were former drug addicts by the parenteral route and had been receiving withdrawal therapy with buprenorphine for an average of 91 days at a daily dosage ranging from 2 to 12 mg. Liver tests, complete viral screening and an abdominal computerized tomography scan were performed in each patient.<br><br>RESULTS: Five out of seven subjects presented with acute icteric hepatitis without abdominal pain or fever. Average alanine aminotransferase levels were 39 times the normal rate. There was no sign of liver failure. All patients had anti-hepatitis C virus-positive serology and two had positive hepatitis C virus-RNA. Although no specific treatment was administered, buprenorphine doses were reduced whenever possible. Cytolysis and jaundice resolved rapidly in all cases, although treatment was continued at the same doses in four cases and the dosage was reduced by 50% in three other cases.<br><br>CONCLUSIONS: Although buprenorphine hepatitis is uncommon and has spontaneously good evolution, we suggest better monitoring of hepatic profiles in patients whose mitochondrial function is already impaired by viral infections or other toxic factors.}, }
@article {pmid15370881, year = {2004}, author = {McDonald, A and Vanlerberghe, G}, title = {Branched mitochondrial electron transport in the Animalia: presence of alternative oxidase in several animal phyla.}, journal = {IUBMB life}, volume = {56}, number = {6}, pages = {333-341}, doi = {10.1080/1521-6540400000876}, pmid = {15370881}, issn = {1521-6543}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Ciona intestinalis/enzymology/genetics ; Electron Transport ; Humans ; Mitochondria/*enzymology ; Mitochondrial Proteins ; Oxidoreductases/*classification/*genetics/metabolism ; Phylogeny ; Plant Proteins ; Sequence Alignment ; Tylenchoidea/enzymology/genetics ; }, abstract = {The mitochondrion of most eukaryotes has multiple electron transport components that increase the points of entry and/or exit of electrons, thus giving a branched nature to the respiratory chain. In plants and many other organisms, a prominent example is alternative oxidase, a non-energy conserving branch in the respiratory chain and an additional terminal oxidase for the exit of electrons. Our genome database searches have now revealed the presence of alternative oxidase in four animal species from three different phyla (Mollusca, Nematoda and Chordata), consistent with frequent reports of cyanide-resistant respiration in the Animalia. In Ciona intestinalis and Crassostrea gigas, alternative oxidase is expressed in several different tissues. Phylogenetic analysis is consistent with the animal proteins having originated by vertical inheritance. We hypothesize that alternative oxidase is likely widespread in the Animalia and discuss some of the potential role(s) for such a branched respiratory chain.}, }
@article {pmid15369601, year = {2004}, author = {Boore, JL}, title = {Complete mitochondrial genome sequence of Urechis caupo, a representative of the phylum Echiura.}, journal = {BMC genomics}, volume = {5}, number = {}, pages = {67}, pmid = {15369601}, issn = {1471-2164}, mesh = {Amino Acid Sequence/genetics ; Animals ; Annelida/*genetics ; Base Composition/genetics ; Base Sequence/genetics ; Codon/genetics ; Codon, Terminator/genetics ; DNA, Intergenic/genetics ; DNA, Mitochondrial/*genetics ; Genes/genetics ; *Genome ; Mitochondria/*genetics ; Molecular Sequence Data ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Transcription Initiation Site ; }, abstract = {BACKGROUND: Mitochondria contain small genomes that are physically separate from those of nuclei. Their comparison serves as a model system for understanding the processes of genome evolution. Although hundreds of these genome sequences have been reported, the taxonomic sampling is highly biased toward vertebrates and arthropods, with many whole phyla remaining unstudied. This is the first description of a complete mitochondrial genome sequence of a representative of the phylum Echiura, that of the fat innkeeper worm, Urechis caupo.<br><br>RESULTS: This mtDNA is 15,113 nts in length and 62% A+T. It contains the 37 genes that are typical for animal mtDNAs in an arrangement somewhat similar to that of annelid worms. All genes are encoded by the same DNA strand which is rich in A and C relative to the opposite strand. Codons ending with the dinucleotide GG are more frequent than would be expected from apparent mutational biases. The largest non-coding region is only 282 nts long, is 71% A+T, and has potential for secondary structures.<br><br>CONCLUSIONS: Urechis caupo mtDNA shares many features with those of the few studied annelids, including the common usage of ATG start codons, unusual among animal mtDNAs, as well as gene arrangements, tRNA structures, and codon usage biases.}, }
@article {pmid15364197, year = {2004}, author = {Sakai, A and Takano, H and Kuroiwa, T}, title = {Organelle nuclei in higher plants: structure, composition, function, and evolution.}, journal = {International review of cytology}, volume = {238}, number = {}, pages = {59-118}, doi = {10.1016/S0074-7696(04)38002-2}, pmid = {15364197}, issn = {0074-7696}, mesh = {Cell Nucleus/metabolism ; DNA Replication ; DNA, Mitochondrial/isolation &amp; purification/*metabolism ; DNA, Plant/isolation &amp; purification/*metabolism ; DNA-Binding Proteins/isolation &amp; purification/*metabolism ; DNA-Directed DNA Polymerase/classification/genetics/metabolism ; DNA-Directed RNA Polymerases/metabolism ; Genome, Plant ; Macromolecular Substances ; Microscopy, Fluorescence ; Mitochondria/*ultrastructure ; Phylogeny ; Plant Proteins/isolation &amp; purification/*metabolism ; Plants/metabolism/*ultrastructure ; Plastids/*ultrastructure ; Transcription, Genetic ; }, abstract = {Plant cells have two distinct types of energy-converting organelles: plastids and mitochondria. These organelles have their own DNAs and are regarded as descendants of endosymbiotic prokaryotes. The organelle DNAs associate with various proteins to form compact DNA-protein complexes, which are referred to as organelle nuclei or nucleoids. Various functions of organelle genomes, such as DNA replication and transcription, are performed within these compact structures. Fluorescence microscopy using the DNA-specific fluorochrome 4',6-diamidino-2-phenylindole has played a pivotal role in establishing the concept of "organelle nuclei." This fluorochrome has also facilitated the isolation of morphologically intact organelle nuclei, which is indispensable for understanding their structure and composition. Moreover, development of an in vitro transcription?DNA synthesis system using isolated organelle nuclei has provided us with a means of measuring and analyzing the function of organelle nuclei. In addition to these morphological and biochemical approaches, genomics has also had a great impact on our ability to investigate the components of organelle nuclei. These analyses have revealed that organelle nuclei are not a vestige of the bacterial counterpart, but rather are a complex system established through extensive interaction between organelle and cell nuclear genomes during evolution. Extensive diversion or exchange during evolution is predicted to have occurred for several important structural proteins, such as major DNA-compacting proteins, and functional proteins, such as RNA and DNA polymerases, resulting in complex mechanisms to control the function of organelle genomes. Thus, organelle nuclei represent the most dynamic front of interaction between the three genomes (cell nuclear, plastid, and mitochondrial) constituting eukaryotic plant cells.}, }
@article {pmid15356283, year = {2005}, author = {Groth-Malonek, M and Pruchner, D and Grewe, F and Knoop, V}, title = {Ancestors of trans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosses with vascular plants.}, journal = {Molecular biology and evolution}, volume = {22}, number = {1}, pages = {117-125}, doi = {10.1093/molbev/msh259}, pmid = {15356283}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Base Sequence ; Bryophyta/*genetics ; *Evolution, Molecular ; Ferns/*genetics ; Genes, Plant/genetics ; Introns/*genetics ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics ; RNA Editing ; RNA, Plant/chemistry/genetics ; Sequence Homology, Amino Acid ; *Trans-Splicing ; }, abstract = {Some group II introns in the organelle genomes of plants and algae are disrupted and require trans-splicing of the affected exons from independent transcripts. A peculiar mitochondrial nad5 gene structure is universally conserved in flowering plants where two trans-splicing introns frame a tiny exon of only 22 nucleotides, and two additional conventional group II introns interrupt the nad5 reading frame at other sites. These four introns are absent in the liverwort Marchantia polymorpha, which carries a group I intron at an unrelated site in nad5. To determine how intron gains and losses have sculptured mitochondrial gene structures in early land-plant evolution, we have investigated the full nad5 gene structures in the three bryophyte classes and the fern Asplenium nidus. We find the single Marchantia group I intron nad5i753 present as the only intervening sequence in both closely (Corsinia and Monoclea) and distantly related (Noteroclada, Bazzania, and Haplomitrium) liverwort genera. In a taxonomically wide spectrum of mosses (Sphagnum, Encalypta, Timmia, Ulota, and Rhacocarpus); however, we additionally identify the angiosperm-type group II introns nad5i230 and nad5i1455. The latter is a cis-arranged homolog to one of the two angiosperm trans-splicing introns, notably the first of its kind in mosses. In the hornwort Anthoceros, the "moss and liverwort-type" group I intron nad5i753 is absent, and, besides nad5i230 and nad5i1455, intron nad5i1477 is present as the second ancestral group II intron which has evolved into a trans-splicing arrangement in angiosperms. The influence of highly frequent RNA editing, most notably in the genera Haplomitrium, Anthoceros, and Asplenium, on phylogenetic tree construction is investigated and discussed. Taken together, the data (1) support a sister group relationship of liverworts as a whole to all other embryophytes, (2) indicate loss of a group I and serial entries of group II introns in the nad5 gene during early evolution of the nonliverwort lineage, and (3) propose a placement of hornworts as sister group to tracheophytes.}, }
@article {pmid15342796, year = {2004}, author = {Piganeau, G and Gardner, M and Eyre-Walker, A}, title = {A broad survey of recombination in animal mitochondria.}, journal = {Molecular biology and evolution}, volume = {21}, number = {12}, pages = {2319-2325}, doi = {10.1093/molbev/msh244}, pmid = {15342796}, issn = {0737-4038}, mesh = {Analysis of Variance ; Animals ; Base Sequence ; Computational Biology ; DNA, Mitochondrial/*genetics ; Databases, Nucleic Acid ; Invertebrates/*genetics ; Linkage Disequilibrium ; *Models, Genetic ; Molecular Sequence Data ; *Recombination, Genetic ; Sequence Alignment ; Vertebrates/*genetics ; }, abstract = {Recombination in mitochondrial DNA (mtDNA) remains a controversial topic. Here we present a survey of 279 animal mtDNA data sets, of which 12 were from asexual species. Using four separate tests, we show that there is widespread evidence of recombination; for one test as many as 14.2% of the data sets reject a model of clonal inheritance and in several data sets, including primates, the recombinants can be identified visually. We show that none of the tests give significant results for obligate clonal species (apomictic pathogens) and that the sexual species show significantly greater evidence of recombination than asexual species. For some data sets, such as Macaca nemestrina, additional data sets suggest that the recombinants are not artifacts. For others, it cannot be determined whether the recombinants are real or produced by laboratory error. Either way, the results have important implications for how mtDNA is sequenced and used.}, }
@article {pmid15341915, year = {2004}, author = {Kouvelis, VN and Ghikas, DV and Typas, MA}, title = {The analysis of the complete mitochondrial genome of Lecanicillium muscarium (synonym Verticillium lecanii) suggests a minimum common gene organization in mtDNAs of Sordariomycetes: phylogenetic implications.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {41}, number = {10}, pages = {930-940}, doi = {10.1016/j.fgb.2004.07.003}, pmid = {15341915}, issn = {1087-1845}, mesh = {Codon ; DNA, Intergenic ; DNA, Mitochondrial/chemistry/*genetics ; Gene Order ; Genes, Fungal ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Transfer/genetics ; Regulatory Sequences, Nucleic Acid ; *Sequence Analysis, DNA ; Synteny ; Verticillium/*genetics ; }, abstract = {The mitochondrial genome (mtDNA) of the entomopathogenic fungus Lecanicillium muscarium (synonym Verticillium lecanii) with a total size of 24,499-bp has been analyzed. So far, it is the smallest known mitochondrial genome among Pezizomycotina, with an extremely compact gene organization and only one group-I intron in its large ribosomal RNA (rnl) gene. It contains the 14 typical genes coding for proteins related to oxidative phosphorylation, the two rRNA genes, one intronic ORF coding for a possible ribosomal protein (rps), and a set of 25 tRNA genes which recognize codons for all amino acids, except alanine and cysteine. All genes are transcribed from the same DNA strand. Gene order comparison with all available complete fungal mtDNAs-representatives of all four Phyla are included-revealed some characteristic common features like uninterrupted gene pairs, overlapping genes, and extremely variable intergenic regions, that can all be exploited for the study of fungal mitochondrial genomes. Moreover, a minimum common mtDNA gene order could be detected, in two units, for all known Sordariomycetes namely nad1-nad4-atp8-atp6 and rns-cox3-rnl, which can be extended in Hypocreales, to nad4L-nad5-cob-cox1-nad1-nad4-atp8-atp6 and rns-cox3-rnl nad2-nad3, respectively. Phylogenetic analysis of all fungal mtDNA essential protein-coding genes as one unit, clearly demonstrated the superiority of small genome (mtDNA) over single gene comparisons.}, }
@article {pmid15317874, year = {2004}, author = {Wilder, JA and Mobasher, Z and Hammer, MF}, title = {Genetic evidence for unequal effective population sizes of human females and males.}, journal = {Molecular biology and evolution}, volume = {21}, number = {11}, pages = {2047-2057}, doi = {10.1093/molbev/msh214}, pmid = {15317874}, issn = {0737-4038}, support = {GM-52566/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; *Chromosomes, Human, Y ; DNA/genetics ; DNA Mutational Analysis ; *DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Female ; Genetics, Population ; Humans ; Male ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; Sex Factors ; }, abstract = {The time to the most recent common ancestor (TMRCA) of the human mitochondria (mtDNA) is estimated to be older than that of the nonrecombining portion of the Y chromosome (NRY). Surveys of variation in globally distributed humans typically result in mtDNA TMRCA values just under 200 thousand years ago (kya), whereas those for the NRY range between 46 and 110 kya. A favored hypothesis for this finding is that natural selection has acted on the NRY, leading to a recent selective sweep. An alternate hypothesis is that sex-biased demographic processes are responsible. Here, we re-examine the disparity between NRY and mtDNA TMRCAs using data collected from individual human populations--a sampling strategy that minimizes the confounding influence of population subdivision in global data sets. We survey variation at 782 bp of the mitochondrial cytochrome c oxidase subunit 3 gene as well as at 26.5 kb of noncoding DNA from the NRY in a sample of 25 Khoisan, 24 Mongolians, and 24 Papua New Guineans. Data from both loci in all populations are best described by a model of constant population size, with the exception of Mongolian mtDNA, which appears to be experiencing rapid population growth. Taking these demographic models into account, we estimate the TMRCAs for each locus in each population. A pattern that is remarkably consistent across all three populations is an approximately twofold deeper coalescence for mtDNA than for the NRY. The oldest TMRCAs are observed for the Khoisan (73.6 kya for the NRY and 176.5 kya for mtDNA), whereas those in the non-African populations are consistently lower (averaging 47.7 kya for the NRY and 92.8 kya for mtDNA). Our data do not suggest that differential natural selection is the cause of this difference in TMRCAs. Rather, these results are most consistent with a higher female effective population size.}, }
@article {pmid15317750, year = {2004}, author = {Ugalde, C and Vogel, R and Huijbens, R and Van Den Heuvel, B and Smeitink, J and Nijtmans, L}, title = {Human mitochondrial complex I assembles through the combination of evolutionary conserved modules: a framework to interpret complex I deficiencies.}, journal = {Human molecular genetics}, volume = {13}, number = {20}, pages = {2461-2472}, doi = {10.1093/hmg/ddh262}, pmid = {15317750}, issn = {0964-6906}, mesh = {DNA, Mitochondrial/genetics ; Doxycycline/pharmacology ; Electron Transport Complex I/deficiency/genetics/*metabolism ; Evolution, Molecular ; Humans ; Intracellular Membranes/metabolism ; Mitochondria/metabolism ; Mitochondrial Diseases/*enzymology/genetics ; Models, Biological ; Osteosarcoma ; Protein Transport/drug effects ; Tumor Cells, Cultured ; }, abstract = {With 46 subunits, human mitochondrial complex I is the largest enzyme of the oxidative phosphorylation system. We have studied the assembly of complex I in cultured human cells. This will provide essential information about the nature of complex I deficiencies and will enhance our understanding of mitochondrial disease mechanisms. We have found that 143B206 rho zero cells, not containing mitochondrial DNA, are still able to form complex I subcomplexes. To further address the nature of these subcomplexes, we depleted 143B osteosarcoma cells of complex I by inhibiting mitochondrial protein translation with doxycycline. After removing this drug, complex I formation resumes and assembly intermediates were observed by two-dimensional blue native electrophoresis. Analysis of the observed subcomplexes indicates that assembly of human complex I is a semi-sequential process in which different preassembled subcomplexes are joined to form a fully assembled complex. The membrane part of the complex is formed in distinct steps. The B17 subunit is part of a subcomplex to which ND1, ND6 and PSST are subsequently added. This is bound to a hydrophilic subcomplex containing the 30 and 49 kDa subunits, to which a subcomplex including the 39 kDa subunit is incorporated, and later on the 18 and 24 kDa subunits. At a later stage more subunits, including the 15 kDa, are added and holo-complex I is formed. Our results suggest that human complex I assembly resembles that of Neurospora crassa, in which a membrane arm is formed and assembled to a preformed peripheral arm, and support ideas about modular evolution.}, }
@article {pmid15306347, year = {2004}, author = {Aanen, DK and Kuyper, TW and Debets, AJ and Hoekstra, RF}, title = {The evolution of non-reciprocal nuclear exchange in mushrooms as a consequence of genomic conflict.}, journal = {Proceedings. Biological sciences}, volume = {271}, number = {1545}, pages = {1235-1241}, pmid = {15306347}, issn = {0962-8452}, mesh = {Agaricales/*genetics ; *Biological Evolution ; Cell Nucleus/genetics/*physiology ; Extrachromosomal Inheritance/genetics ; *Genome, Fungal ; Mitochondria/genetics/physiology ; *Models, Biological ; Reproduction/genetics ; }, abstract = {Heterothallic mushrooms accomplish sex by exchanging nuclei without cytoplasm. Hyphal fusions occur between haploid mycelia resulting from germinated spores and subsequent reciprocal nuclear exchange without cytoplasmic mixing. The resulting dikaryon is therefore a cytoplasmic mosaic with uniformly distributed nuclei (two in each cell). Cytoplasmic inheritance is doubly uniparental: both mated monokaryons can potentially transmit their cytoplasm to the sexual spores, but normally only a single type per spore is found. Intracellular competition between mitochondria is thus limited, but at the dikaryon level, the two types of mitochondria compete over transmission. This creates the conditions for genomic conflict: within the dikaryon, a selfish mitochondrial mutant with increased relative transmission can be favoured, but selection between dikaryons will act against such a mitochondrial mutant. Moreover, because nuclear fitness is directly dependent on dikaryon fitness, a reduction in dikaryon fitness directly conflicts with nuclear interests. We propose that genomic conflict explains the frequent occurrence of non-reciprocal nuclear exchange in mushrooms. With non-reciprocal exchange, one monokaryon donates a nucleus and the other accepts it, but not vice versa as in the typical life cycle. We propose a model where non-reciprocal nuclear exchange is primarily driven by mitochondria inducing male sterility and the evolution of nuclear suppressors.}, }
@article {pmid15305681, year = {2004}, author = {Sacchi, L}, title = {[Ultrastructural basis of interactions between prokaryotes and eukaryotes in different symbiotic models].}, journal = {Parassitologia}, volume = {46}, number = {1-2}, pages = {19-24}, pmid = {15305681}, issn = {0048-2951}, mesh = {Animals ; *Bacterial Physiological Phenomena ; Bdellovibrio/physiology/ultrastructure ; Biological Evolution ; Brugia pahangi/microbiology/ultrastructure ; Cockroaches/cytology/embryology/microbiology ; Eggs/microbiology ; Eukaryotic Cells/*ultrastructure ; Fat Body/microbiology ; Female ; Filarioidea/cytology/*microbiology ; Hemocytes/microbiology ; Insecta/cytology/*microbiology ; Isoptera/cytology/microbiology ; Models, Biological ; Ovary/microbiology ; Prokaryotic Cells/*ultrastructure ; *Symbiosis ; Ticks/cytology/*microbiology ; Wolbachia/physiology/ultrastructure ; }, abstract = {This paper reviews the Author's contribution to the knowledge of the ultrastructural basis of the prokaryote-eukaryote interactions in different models assessed by an ultrastructural approach. In agreement with the hypothesis of the origin of eukaryotic cells, which are chimeras of several prokaryotes with different morpho-functional specializations, symbiosis had major consequence for evolution of life. In Arthropods, one of the most successful lifestyles, the presence of endosymbiotic prokaryotes, plays an important role in their metabolism. In some cases, genome integration has occurred in the endosymbiotic relationships with the host, proving that intracellular symbiosis is not merely a nutritional supplement. Intracellular symbiotic bacteria are also described in nematodes. In particular, the presence of intracellular Wolbachia in filariae, even if its function is not yet completely known, influences positively the reproductive biology and the survival of the host, as proved by antibiotic treatment against this bacterium. The ultrastructural images reported in this review were obtained using different species of cockroaches, termites, ticks and filarial nematodes. The traditional methods of transmission (TEM), scansion (SEM) and immuno electron microscopy were used. In addition, also freeze-fracture and deep-etching techniques were employed. The cockroaches and the primitive termite Mastotermes darwiniensis host symbiotic bacteria in the ovary and in specialized cells (bacteriocytes) of the fat body. These bacteria have the typical cell boundary profile of gram-negative bacteria and are enveloped in a vacuolar membrane produced by the host cell. Molecular sequence data of 16S rDNA of endosymbionts of five species of cockroaches and M. darwiniensis indicate that they are members of the Flavobacteria-bacteroides group and that the infection occurred in an ancestor common to cockroaches and termites probably after the end of the Paleozoic (250 Ma BP). The symbiotic bacteria are transmitted transovarially and, during embryogenesis, they are integrated into the morphogenetic processes. In particular, we were able to demonstrate that the origin of the bacteriocyte should be looked for in the cells of the haemocyte line (embryonic plasmatocytes). The eggs are infected by the bacteria emerging from the bacteriocytes of the ovaric fat body and, at the end of the vitellogenesis, they are actively phagocytized by the egg membrane. In filarial nematodes, intracellular bacteria belonging to the genus Wolbachia have been described: they have evolved an obligatory mutualistic association with their host. In fact, antibiotic treatments lead to the clearance of bacteria and this loss produces a negative impact on reproduction and survival of the filarial host. We evidenced, by TEM, the degenerative events occurring during the embriogenesis of Brugia pahangi and Dirofilaria immitis after tetracycline treatment. The data suggest that the Wolbachia play a direct role in worm metabolism. Finally, a new additional model of the prokaryote-eukaryote interaction has been described: we have recently discovered a new intracellular alpha-proteobacterium, named Iric ES1, which resides in the ovarian tissues of the tick Ixodes ricinus. The intriguing characteristic of this bacterium is its ability to invade and consume the ovaric mitochondria. From an evolutionary perspective, it is interesting to note that Iric ES1 enters mitochondria in a similar way to that employed by the "predatory" bacterium Bdellovibrio bacteriovorus.}, }
@article {pmid15305173, year = {2005}, author = {Jolly, MT and Jollivet, D and Gentil, F and Thiébaut, E and Viard, F}, title = {Sharp genetic break between Atlantic and English Channel populations of the polychaete Pectinaria koreni, along the North coast of France.}, journal = {Heredity}, volume = {94}, number = {1}, pages = {23-32}, doi = {10.1038/sj.hdy.6800543}, pmid = {15305173}, issn = {0018-067X}, mesh = {Animals ; Atlantic Ocean ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; England ; *Evolution, Molecular ; France ; *Genetic Drift ; *Genetic Variation ; Geography ; Haplotypes/genetics ; Mitochondria/enzymology/genetics ; Phylogeny ; Polychaeta/*classification/*genetics ; }, abstract = {This study uses enzymatic and mitochondrial genes to infer the relative importance of historical processes and contemporary hydrodynamic features on the observed patterns of genetic structure in subdivided populations of Pectinaria koreni (Polychaeta: Pectinariidae) along the coasts of Brittany and the English Channel. Nucleotide sequence variation of a 603-bp fragment of the mtDNA cytochrome oxidase subunit I gene revealed a surprisingly deep phylogeographic break of about 16% divergence separating the Brittany and Channel populations, which coincides with a biogeographic boundary along the western coast of Brittany. Deep sequence divergence with fixed haplotype differences and the inversion of allele frequencies at two enzyme loci suggests the occurrence of potential cryptic or sibling species of P. koreni. The two clades showed opposite features. Channel populations exhibited bimodal match-mismatch curves due to two highly divergent haplotypes occurring at high frequencies and no overall heterozygote deficiencies at enzyme loci, suggesting respectively, a historic secondary contact between two differentiated populations followed by contemporary panmixia. On the contrary, Brittany populations displayed unimodal curves with low nucleotide diversity and highly significant heterozygote deficiencies, probably reminiscent of a recent population expansion and recolonisation of Brittany with contemporary admixture of divergent populations.}, }
@article {pmid15300404, year = {2004}, author = {Knoop, V}, title = {The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective.}, journal = {Current genetics}, volume = {46}, number = {3}, pages = {123-139}, pmid = {15300404}, issn = {0172-8083}, mesh = {DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Gene Components ; Gene Expression Regulation, Plant ; Gene Order ; *Genetic Variation ; Multigene Family/genetics ; *Phylogeny ; Plants/*genetics ; Recombination, Genetic/genetics ; }, abstract = {Land plants exhibit a significant evolutionary plasticity in their mitochondrial DNA (mtDNA), which contrasts with the more conservative evolution of their chloroplast genomes. Frequent genomic rearrangements, the incorporation of foreign DNA from the nuclear and chloroplast genomes, an ongoing transfer of genes to the nucleus in recent evolutionary times and the disruption of gene continuity in introns or exons are the hallmarks of plant mtDNA, at least in flowering plants. Peculiarities of gene expression, most notably RNA editing and trans-splicing, are significantly more pronounced in land plant mitochondria than in chloroplasts. At the same time, mtDNA is generally the most slowly evolving of the three plant cell genomes on the sequence level, with unique exceptions in only some plant lineages. The slow sequence evolution and a variable occurrence of introns in plant mtDNA provide an attractive reservoir of phylogenetic information to trace the phylogeny of older land plant clades, which is as yet not fully resolved. This review attempts to summarize the unique aspects of land plant mitochondrial evolution from a phylogenetic perspective.}, }
@article {pmid15297626, year = {2004}, author = {Meeusen, S and McCaffery, JM and Nunnari, J}, title = {Mitochondrial fusion intermediates revealed in vitro.}, journal = {Science (New York, N.Y.)}, volume = {305}, number = {5691}, pages = {1747-1752}, doi = {10.1126/science.1100612}, pmid = {15297626}, issn = {1095-9203}, support = {S10 RR019409-01/RR/NCRR NIH HHS/United States ; R01-GM62942A/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/metabolism ; Energy Metabolism ; GTP Phosphohydrolases/genetics/metabolism ; Green Fluorescent Proteins ; Guanosine Triphosphate/metabolism ; Intracellular Membranes/*physiology/ultrastructure ; Luminescent Proteins/metabolism ; *Membrane Fusion ; Membrane Potentials ; Membrane Proteins/genetics/metabolism ; Microscopy, Fluorescence ; Mitochondria/*physiology/*ultrastructure ; Mitochondrial Proteins ; Models, Biological ; Saccharomyces cerevisiae/genetics/*physiology/ultrastructure ; Saccharomyces cerevisiae Proteins ; Red Fluorescent Protein ; }, abstract = {The events that occur during the fusion of double-membraned mitochondria are unknown. As an essential step toward determining the mechanism of mitochondrial fusion, we have captured this event in vitro. Mitochondrial outer and inner membrane fusion events were separable and mechanistically distinct, but both required guanosine 5'-triphosphate hydrolysis. Homotypic trans interactions of the ancient outer transmembrane guanosine triphosphatase, Fzo1, were required to promote the fusion of mitochondrial outer membranes, whereas electrical potential was also required for fusion of inner membranes. Our conclusions provide fundamental insights into the molecular events driving mitochondrial fusion and advance our understanding of the evolution of mitochondrial fusion in eukaryotic cells.}, }
@article {pmid15297602, year = {2004}, author = {Yokobori, S and Fukuda, N and Nakamura, M and Aoyama, T and Oshima, T}, title = {Long-term conservation of six duplicated structural genes in cephalopod mitochondrial genomes.}, journal = {Molecular biology and evolution}, volume = {21}, number = {11}, pages = {2034-2046}, doi = {10.1093/molbev/msh227}, pmid = {15297602}, issn = {0737-4038}, mesh = {Animals ; Blotting, Southern ; Cloning, Molecular ; DNA Primers/genetics ; *DNA, Mitochondrial ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; *Genome ; Mitochondrial Proton-Translocating ATPases/genetics ; Models, Genetic ; Mollusca/*genetics ; Octopodiformes/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {The complete nucleotide sequences of the mitochondrial (mt) genomes of three cephalopods, Octopus vulgaris (Octopodiformes, Octopoda, Incirrata), Todarodes pacificus (Decapodiformes, Oegopsida, Ommastrephidae), and Watasenia scintillans (Decapodiformes, Oegopsida, Enoploteuthidae), were determined. These three mt genomes encode the standard set of metazoan mt genes. However, W. scintillans and T. pacificus mt genomes share duplications of the longest noncoding region, three cytochrome oxidase subunit genes and two ATP synthase subunit genes, and the tRNA(Asp) gene. Southern hybridization analysis of the W. scintillans mt genome shows that this single genome carries both duplicated regions. The near-identical sequence of the duplicates suggests that there are certain concerted evolutionary mechanisms, at least in cephalopod mitochondria. Molecular phylogenetic analyses of mt protein genes are suggestive, although not statistically significantly so, of a monophyletic relationship between W. scintillans and T. pacificus.}, }
@article {pmid15295112, year = {2004}, author = {Cowley, AB and Rivera, M and Benson, DR}, title = {Stabilizing roles of residual structure in the empty heme binding pockets and unfolded states of microsomal and mitochondrial apocytochrome b5.}, journal = {Protein science : a publication of the Protein Society}, volume = {13}, number = {9}, pages = {2316-2329}, pmid = {15295112}, issn = {0961-8368}, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Cattle ; Circular Dichroism ; Cytochromes b5/*chemistry/*metabolism ; Evolution, Molecular ; Heme/*metabolism ; Hydrophobic and Hydrophilic Interactions ; Light ; Microsomes/*chemistry ; Mitochondria/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Denaturation ; Protein Folding ; Rats ; Scattering, Radiation ; Sequence Homology, Amino Acid ; }, abstract = {The microsomal (Mc) and mitochondrial (OM) isoforms of mammalian cytochrome b5 are the products of different genes, which likely arose via duplication of a primordial gene and subsequent functional divergence. Despite sharing essentially identical folds, heme-polypeptide interactions are stronger in OM b5s than in Mc b5s due to the presence of two conserved patches of hydrophobic amino acid side chains in the OM heme binding pockets. This is of fundamental interest in terms of understanding heme protein structure-function relationships, because stronger heme-polypeptide interactions in OM b5s in comparison to Mc b5s may represent a key source of their more negative reduction potentials. Herein we provide evidence that interactions amongst the amino acid side chains contributing to the hydrophobic patches in rat OM (rOM) b5 persist when heme is removed, rendering the empty heme binding pocket of rOM apo-b5 more compact and less conformationally dynamic than that in bovine Mc (bMc) apo-b5. This may contribute to the stronger heme binding by OM apo-b5 by reducing the entropic penalty associated with polypeptide folding. We also show that when bMc apo-b5 unfolds it adopts a structure that is more compact and contains greater nonrandom secondary structure content than unfolded rOM apo-b5. We propose that a more robust beta-sheet in Mc apo-b5s compensates for the absence of the hydrophobic packing interactions that stabilize the heme binding pocket in OM apo-b5s.}, }
@article {pmid15291971, year = {2004}, author = {Thao, ML and Baumann, L and Baumann, P}, title = {Organization of the mitochondrial genomes of whiteflies, aphids, and psyllids (Hemiptera, Sternorrhyncha).}, journal = {BMC evolutionary biology}, volume = {4}, number = {}, pages = {25}, pmid = {15291971}, issn = {1471-2148}, mesh = {Animals ; Anticodon/genetics ; Aphids/*genetics ; Chromosome Deletion ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Gene Order/genetics ; Genes, Insect/genetics ; *Genome ; Hemiptera/*genetics ; Mitochondria/*genetics ; NADH Dehydrogenase/genetics ; Polymerase Chain Reaction/methods ; Protein Subunits/genetics ; RNA, Transfer, Ala/genetics ; RNA, Transfer, Arg/genetics ; RNA, Transfer, Asn/genetics ; RNA, Transfer, Gly/genetics ; RNA, Untranslated/genetics ; Recombination, Genetic/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: With some exceptions, mitochondria within the class Insecta have the same gene content, and generally, a similar gene order allowing the proposal of an ancestral gene order. The principal exceptions are several orders within the Hemipteroid assemblage including the order Thysanoptera, a sister group of the order Hemiptera. Within the Hemiptera, there are available a number of completely sequenced mitochondrial genomes that have a gene order similar to that of the proposed ancestor. None, however, are available from the suborder Sternorryncha that includes whiteflies, psyllids and aphids.<br><br>RESULTS: We have determined the complete nucleotide sequence of the mitochondrial genomes of six species of whiteflies, one psyllid and one aphid. Two species of whiteflies, one psyllid and one aphid have mitochondrial genomes with a gene order very similar to that of the proposed insect ancestor. The remaining four species of whiteflies had variations in the gene order. In all cases, there was the excision of a DNA fragment encoding for cytochrome oxidase subunit III(COIII)-tRNAgly-NADH dehydrogenase subunit 3(ND3)-tRNAala-tRNAarg-tRNAasn from the ancestral position between genes for ATP synthase subunit 6 and NADH dehydrogenase subunit 5. Based on the position in which all or part of this fragment was inserted, the mitochondria could be subdivided into four different gene arrangement types. PCR amplification spanning from COIII to genes outside the inserted region and sequence determination of the resulting fragments, indicated that different whitefly species could be placed into one of these arrangement types. A phylogenetic analysis of 19 whitefly species based on genes for mitochondrial cytochrome b, NADH dehydrogenase subunit 1, and 16S ribosomal DNA as well as cospeciating endosymbiont 16S and 23S ribosomal DNA indicated a clustering of species that corresponded to the gene arrangement types.<br><br>CONCLUSIONS: In whiteflies, the region of the mitochondrial genome consisting of genes encoding for COIII-tRNAgly-ND3-tRNAala-tRNAarg-tRNAasn can be transposed from its ancestral position to four different locations on the mitochondrial genome. Related species within clusters established by phylogenetic analysis of host and endosymbiont genes have the same mitochondrial gene arrangement indicating a transposition in the ancestor of these clusters.}, }
@article {pmid15287975, year = {2004}, author = {Gutiérrez, RA and Green, PJ and Keegstra, K and Ohlrogge, JB}, title = {Phylogenetic profiling of the Arabidopsis thaliana proteome: what proteins distinguish plants from other organisms?.}, journal = {Genome biology}, volume = {5}, number = {8}, pages = {R53}, pmid = {15287975}, issn = {1474-760X}, mesh = {Animals ; Arabidopsis/*chemistry/genetics/metabolism ; Arabidopsis Proteins/*chemistry/genetics/*metabolism ; Evolution, Molecular ; Expressed Sequence Tags ; Gene Expression Regulation, Plant ; Genomics ; Humans ; Metabolism/genetics ; Organ Specificity ; *Phylogeny ; Proteome/chemistry/genetics/*metabolism ; Proteomics ; Species Specificity ; Transcription Factors/chemistry/genetics/metabolism ; }, abstract = {BACKGROUND: The availability of the complete genome sequence of Arabidopsis thaliana together with those of other organisms provides an opportunity to decipher the genetic factors that define plant form and function. To begin this task, we have classified the nuclear protein-coding genes of Arabidopsis thaliana on the basis of their pattern of sequence similarity to organisms across the three domains of life.<br><br>RESULTS: We identified 3,848 Arabidopsis proteins that are likely to be found solely within the plant lineage. More than half of these plant-specific proteins are of unknown function, emphasizing the general lack of knowledge of processes unique to plants. Plant-specific proteins that are membrane-associated and/or targeted to the mitochondria or chloroplasts are the most poorly characterized. Analyses of microarray data indicate that genes coding for plant-specific proteins, but not evolutionarily conserved proteins, are more likely to be expressed in an organ-specific manner. A large proportion (13%) of plant-specific proteins are transcription factors, whereas other basic cellular processes are under-represented, suggesting that evolution of plant-specific control of gene expression contributed to making plants different from other eukaryotes.<br><br>CONCLUSIONS: We identified and characterized the Arabidopsis proteins that are most likely to be plant-specific. Our results provide a genome-wide assessment that supports the hypothesis that evolution of higher plant complexity and diversity is related to the evolution of regulatory mechanisms. Because proteins that are unique to the green plant lineage will not be studied in other model systems, they should be attractive priorities for future studies.}, }
@article {pmid15284954, year = {2004}, author = {Bortolini, MC and Da Silva, WA and Zago, MA and Elion, J and Krishnamoorthy, R and Goncalves, VF and Pena, SD}, title = {The phylogeography of mitochondrial DNA haplogroup L3g in Africa and the Atlantic slave trade.}, journal = {American journal of human genetics}, volume = {75}, number = {3}, pages = {522-4; author reply 524-6}, doi = {10.1086/423823}, pmid = {15284954}, issn = {0002-9297}, mesh = {Black People/*genetics ; *DNA, Mitochondrial ; *Data Interpretation, Statistical ; Haplotypes ; History, 17th Century ; History, 18th Century ; History, 19th Century ; Humans ; Mitochondria/genetics ; Mutation ; Phylogeny ; Social Problems/history ; }, }
@article {pmid15283236, year = {2004}, author = {Kawasaki, M and Mochizuki, T and Ishizaki, H and Fujihiro, M}, title = {Ascospore-derived isolate of Arthroderma benhamiae with morphology suggestive of Trichophyton verrucosum.}, journal = {Medical mycology}, volume = {42}, number = {3}, pages = {223-228}, doi = {10.1080/13693780310001644699}, pmid = {15283236}, issn = {1369-3786}, mesh = {Arthrodermataceae/*classification/*genetics/growth &amp; development/metabolism ; DNA Fingerprinting ; DNA, Fungal/analysis/chemistry/isolation &amp; purification ; DNA, Ribosomal Spacer/chemistry/isolation &amp; purification ; Glucose/metabolism ; Inositol/metabolism ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Sequence Homology ; Thiamine/metabolism ; Trichophyton/*classification/*genetics/growth &amp; development ; }, abstract = {Sixty-one ascospores were isolated from an ascocarp produced by the mating of two Arthroderma benhamiae strains, RV 26678 and KMU4169, that differed in their mitochondrial DNA (mtDNA) restriction fragment length polymorphism (RFLP) patterns and in the sequences of their nuclear ribosomal internal transcribed spacer (ITS) regions. RV 26678 is a genetically typical A. benhamiae isolate, while KMU4169, though morphologically indistinguishable from A. benhamiae, is an isolate with a deviating ITS sequence and with a mtDNA RFLP profile identical to that of T. verrucosum. One of the 61 progeny ascospores formed a colony, KMU5-46, that was quite different from both parental isolates. KMU5-46 is a faviform colony morphologically similar to Trichophyton verrucosum, although its mtDNA RFLP patterns and ITS sequences were identical to those of A. benhamiae parental strain RV 26678. The morphological alteration manifested in KMU5-46, as well as this isolate's complete loss of sexual response, indicates the possibility that the asexual T. verrucosum and the sexual A. benhamiae are conspecific.}, }
@article {pmid15279958, year = {2004}, author = {Sienkiewicz, N and Daher, W and Dive, D and Wrenger, C and Viscogliosi, E and Wintjens, R and Jouin, H and Capron, M and Müller, S and Khalife, J}, title = {Identification of a mitochondrial superoxide dismutase with an unusual targeting sequence in Plasmodium falciparum.}, journal = {Molecular and biochemical parasitology}, volume = {137}, number = {1}, pages = {121-132}, doi = {10.1016/j.molbiopara.2004.05.005}, pmid = {15279958}, issn = {0166-6851}, mesh = {Adaptation, Psychological ; Amino Acid Sequence ; Animals ; Cytoplasm/enzymology ; DNA, Complementary ; DNA, Protozoan/chemistry ; Erythrocytes/parasitology ; Fluorescent Antibody Technique, Indirect ; Gene Duplication ; Gene Expression Regulation ; Introns/genetics ; Mitochondria/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Oxidative Stress ; Phylogeny ; Plasmodium falciparum/*enzymology/genetics/growth &amp; development ; *Protein Sorting Signals ; *Protein Transport ; RNA, Messenger/analysis ; RNA, Protozoan/analysis ; Recombinant Fusion Proteins/metabolism ; Sequence Analysis, DNA ; Sequence Homology ; Superoxide Dismutase/*chemistry/*genetics/metabolism ; Superoxide Dismutase-1 ; }, abstract = {The intraerythrocytic stages of Plasmodium falciparum are exposed to oxidative stress and require functional anti-oxidant systems to survive. In addition to the parasite's known iron-dependent superoxide dismutase PfSOD1, a second SOD gene (PfSOD2) interrupted by 8 introns was identified on chromosome 6. Molecular modelling shows that the structure of PfSOD2 is similar to other iron-dependent SODs and phylogenetic analysis suggests PfSOD1 and PfSOD2 are the result of an ancestral gene duplication. The deduced amino acid sequence of PfSOD2 is similar to PfSOD1 but has a long N-terminal extension. Immunofluorescence studies show that PfSOD1 is cytosolic, whereas the N-terminal extension of PfSOD2 targets a green fluorescent protein fusion into the parasite's mitochondrion. Both SOD genes are transcribed during the erythrocytic cycle with PfSOD1 mRNA levels up to 35-fold higher than those of PfSOD2. Northern blots demonstrated that the mRNA levels of both SOD genes are up-regulated upon exposure to oxidative stress.}, }
@article {pmid15273991, year = {2004}, author = {Armstrong, JS and Whiteman, M and Yang, H and Jones, DP}, title = {The redox regulation of intermediary metabolism by a superoxide-aconitase rheostat.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {26}, number = {8}, pages = {894-900}, doi = {10.1002/bies.20071}, pmid = {15273991}, issn = {0265-9247}, mesh = {Aconitate Hydratase/*metabolism ; Animals ; Citric Acid/metabolism ; Evolution, Molecular ; Hydrogen Peroxide/metabolism ; Mice ; Mice, Knockout ; Mitochondria/*metabolism ; Oxidants/metabolism ; Oxidation-Reduction ; Reactive Oxygen Species/metabolism ; Signal Transduction/physiology ; Superoxide Dismutase/genetics/metabolism ; Superoxides/*metabolism ; }, abstract = {In this article, we discuss a hypothesis to explain the preferential synthesis of the superoxide sensitive form of aconitase in mitochondria and the phenotype observed in manganese superoxide dismutase mutant mice, which show a gross over accumulation of stored fat in liver. The model proposes that intermediary metabolism is redox regulated by mitochondrial superoxide generated during mitochondrial respiration. This regulates the level of reducing equivalents (NADH) entering the electron transport chain (ETC) through the reversible inactivation of mitochondrial aconitase. This control mechanism has a dual function; firstly, it regulates levels of superoxide generated by the ETC and, secondly, it fine-tunes metabolism by channeling citrate either for the production of NADH for energy metabolism or diverting it for the synthesis of fats. In this setting, the mitochondrial redox state influences metabolic decisions via a superoxide-aconitase rheostat.}, }
@article {pmid15269332, year = {2004}, author = {Lurin, C and Andrés, C and Aubourg, S and Bellaoui, M and Bitton, F and Bruyère, C and Caboche, M and Debast, C and Gualberto, J and Hoffmann, B and Lecharny, A and Le Ret, M and Martin-Magniette, ML and Mireau, H and Peeters, N and Renou, JP and Szurek, B and Taconnat, L and Small, I}, title = {Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis.}, journal = {The Plant cell}, volume = {16}, number = {8}, pages = {2089-2103}, pmid = {15269332}, issn = {1040-4651}, mesh = {Amino Acid Motifs ; Animals ; Arabidopsis/cytology/*genetics/metabolism ; Arabidopsis Proteins/*genetics ; Computational Biology ; DNA, Bacterial/genetics ; Evolution, Molecular ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Genome, Plant ; Humans ; Molecular Sequence Data ; Multigene Family ; Oligonucleotide Array Sequence Analysis ; Organelles/*physiology ; Phylogeny ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; *Tandem Repeat Sequences ; }, abstract = {The complete sequence of the Arabidopsis thaliana genome revealed thousands of previously unsuspected genes, many of which cannot be ascribed even putative functions. One of the largest and most enigmatic gene families discovered in this way is characterized by tandem arrays of pentatricopeptide repeats (PPRs). We describe a detailed bioinformatic analysis of 441 members of the Arabidopsis PPR family plus genomic and genetic data on the expression (microarray data), localization (green fluorescent protein and red fluorescent protein fusions), and general function (insertion mutants and RNA binding assays) of many family members. The basic picture that arises from these studies is that PPR proteins play constitutive, often essential roles in mitochondria and chloroplasts, probably via binding to organellar transcripts. These results confirm, but massively extend, the very sparse observations previously obtained from detailed characterization of individual mutants in other organisms.}, }
@article {pmid15267107, year = {2004}, author = {Putignani, L and Tait, A and Smith, HV and Horner, D and Tovar, J and Tetley, L and Wastling, JM}, title = {Characterization of a mitochondrion-like organelle in Cryptosporidium parvum.}, journal = {Parasitology}, volume = {129}, number = {Pt 1}, pages = {1-18}, doi = {10.1017/s003118200400527x}, pmid = {15267107}, issn = {0031-1820}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Carrier Proteins/chemistry/genetics ; Chaperonin 60/metabolism ; Cloning, Molecular ; Cryptosporidium parvum/genetics/metabolism/*ultrastructure ; DNA, Protozoan/chemistry/genetics ; Fluorescent Dyes/chemistry ; Indoles/chemistry ; Microscopy, Electron ; Microscopy, Fluorescence ; Mitochondria/metabolism/*ultrastructure ; Models, Biological ; Molecular Sequence Data ; Organic Chemicals ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; }, abstract = {Cryptosporidium parvum is a protozoan parasite that causes widespread diarrhoeal disease in humans and other animals and is responsible for large waterborne outbreaks of cryptosporidiosis. Unlike many organisms belonging to the phylum Apicomplexa, such as Plasmodium spp. and Toxoplasma gondii, there is no clinically proven drug treatment against this parasite. Aspects of the basic biology of C. parvum remain poorly understood, including a detailed knowledge of key metabolic pathways, its genome organization and organellar complement. Previous studies have proposed that C. parvum lacks a relic plastid organelle, or 'apicoplast', but that it may possess a mitochondrion. Here we characterize a mitochondrion-like organelle in C. parvum by (i) ultrastructural and morphological description (ii) localization of heterologous mitochondrial chaperonin antibody probes (iii) phylogenetic analysis of genes encoding mitochondrial transport proteins (iv) identification and analysis of mitochondrion-associated gene sequences. Our descriptive morphological analysis was performed by energy-filtering transmission electron microscopy (EFTEM) of C. hominis and C. parvum. The 'mitochondrion-like' organelle was characterized by labelling the structure with a heterologous mitochondrial chaperonin probe (hsp60) both in immunoelectron microscopy (IMEM) and immunofluorescence (IMF). Phylogenetic analysis of the mitochondrial import system and housekeeping components (hsp60 and hsp70-dnaK) suggested that the C. parvum mitochondrion-like organelle is likely to have descended from a common ancestral apicomplexan mitochondrion. We also identified a partial cDNA sequence coding for an alternative oxidase (AOX) gene, a component of the electron transport chain which can act as an alternative to the terminal mitochondrial respiratory complexes III and IV, which has not yet been reported in any other member of this phylum. Degenerate primers developed to identify selected mitochondrial genes failed to identify either cytochrome oxidase subunit I, or cytochrome b. Taken together, our data aim to provide new insights into the characterization of this Cryptosporidium organelle and a logical framework for future functional investigation.}, }
@article {pmid15260141, year = {2004}, author = {Aldrich, BT and Krafsur, E and Kambhampati, S}, title = {Species-specific allozyme markers for Appalachian wood-feeding cockroaches (Dictyoptera: Cryptocercidae).}, journal = {Biochemical genetics}, volume = {42}, number = {5-6}, pages = {149-164}, doi = {10.1023/b:bigi.0000026631.46010.ca}, pmid = {15260141}, issn = {0006-2928}, mesh = {Alleles ; Animals ; Appalachian Region ; Cockroaches/*enzymology/*genetics ; Genetic Markers/genetics ; Heterozygote ; Hybridization, Genetic ; Isoenzymes/analysis/*genetics ; Mitochondria/genetics ; Phylogeny ; Polymorphism, Genetic ; Population Dynamics ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Members of the genus Cryptocercus are wood-feeding cockroaches that live in the temperate forests. Nine species are recognized in the genus worldwide: two in eastern Eurasia, two in China, and five in the United States. Within the United States, one species occurs in the Pacific Northwest and four occur in the Appalachian Mountains. Previous studies have revealed the presence of potential zones of overlap in distribution among the Appalachian species, raising the possibility of hybridization among them. Differences in mitochondrial DNA have previously been identified for the Appalachian species. However, to identify hybrid individuals one or more species-specific, codominant nuclear markers are required. Therefore, our objective was to undertake allozyme analysis of enzymatic loci to identify fixed, species-specific alleles for the four Appalachian species. We assayed a mean of 42 individuals each from 16 sites for allozyme variation for the four species. At 6 of the 33 loci examined, fixed alternate alleles were identified; a combination of 2 loci enabled the identification of all four species. To identify hybrids in the field, we examined 42 individuals each from 13 sites in which two or more of the above species occur in close proximity for presence of heterozygous individuals at one or more of the six fixed loci. No heterozygous individuals were found suggesting the lack of hybridization among the Appalachian species.}, }
@article {pmid15259434, year = {2003}, author = {Monro, JA}, title = {Treatment of cancer with mushroom products.}, journal = {Archives of environmental health}, volume = {58}, number = {8}, pages = {533-537}, doi = {10.3200/AEOH.58.8.533-537}, pmid = {15259434}, issn = {0003-9896}, mesh = {Adjuvants, Immunologic/pharmacology/*therapeutic use ; *Agaricales/chemistry/immunology ; Aggrecans ; Basement Membrane/physiology ; Biological Evolution ; Combined Modality Therapy ; Decorin ; *Extracellular Matrix Proteins ; Fungal Proteins/therapeutic use ; Humans ; Lectins, C-Type ; Neoplasms/epidemiology/etiology/*therapy ; Phytotherapy/*methods/standards ; Polysaccharides/physiology ; Proteoglycans/chemistry/physiology/therapeutic use ; Ribonucleases/physiology ; Risk Factors ; Treatment Outcome ; }, abstract = {Cancer has been attributed to 3 causes: pollution, infection, and poor nutrition. Conventional treatments include surgery, chemotherapy, and radiotherapy. The author proposes that immunotherapy also be considered. Among other environmental influences, dietary deficiencies and carcinogenic viral infections must be investigated and treated wherever possible. It has been suggested that mushrooms, in particular, have a structure that is immunomodulatory because it resembles the proteoglycan structure in the human extracellular matrix, and both are metabolically active. Inasmuch as mitochondria have a bacterial origin, proteoglycans may have a mushroom origin. The author describes a study which shows that natural killer cells can double in number with 8 wk of treatment with Coriolus versicolor. Also described is an epidemiological survey of cancer deaths among Flammulina velutipes farmers in Japan, which found that the mushroom farmers had lower rates of cancer deaths than controls who were not involved in mushroom farming.}, }
@article {pmid15258168, year = {2004}, author = {Wirtz, M and Droux, M and Hell, R}, title = {O-acetylserine (thiol) lyase: an enigmatic enzyme of plant cysteine biosynthesis revisited in Arabidopsis thaliana.}, journal = {Journal of experimental botany}, volume = {55}, number = {404}, pages = {1785-1798}, doi = {10.1093/jxb/erh201}, pmid = {15258168}, issn = {0022-0957}, mesh = {Arabidopsis/*enzymology ; Carbon-Oxygen Lyases/*chemistry/isolation &amp; purification/metabolism ; Cysteine/*biosynthesis ; Cytosol/enzymology ; Enzyme Stability ; Escherichia coli/genetics ; Gene Expression Regulation, Plant ; Isoenzymes ; Kinetics ; Mitochondria/enzymology ; Phylogeny ; Plastids/enzymology ; Protein Binding ; Recombinant Proteins/*chemistry/isolation &amp; purification/metabolism ; Substrate Specificity ; }, abstract = {The synthesis of cysteine is positioned at a decisive stage of assimilatory sulphate reduction, marking the fixation of inorganic sulphide into a carbon skeleton. O-acetylserine (thiol) lyase (OAS-TL) catalyses the reaction of inorganic sulphide with O-acetylserine (OAS). Despite its prominent position in the pathway OAS-TL is generally regarded as a non-limiting enzyme without regulatory function, due to low substrate affinities and semi-constitutive expression patterns. To resolve this apparent contradiction, the kinetic properties of three OAS-TLs from Arabidopsis thaliana, localized in the cytosol (A), plastids (B), and mitochondria (C), were analysed. The recombinant expressed OAS-TLs were purified to apparent homogeneity without any fusion tag to maintain their native forms. The proteins displayed high specific activities of 550-900 micromol min(-1) mg(-1). Using an improved and highly sensitive assay method for cysteine determination, the apparent K(m)(sulphide) was 3-6 microM for OAS-TL A, B, and C and thus 10-100 times lower than previously reported for plant OAS-TLs. K(m)(OAS) was between 310 microM and 690 microM for OAS-TL isoform A, B, and C, whereas the apparent dissociation binding constant for OAS was much lower (K(d)<1 microM OAS). A HPLC method was developed for OAS quantification that revealed fast increases of the cellular OAS concentration in response to sulphate deprivation. The observed fluctuations of intracellular OAS concentrations, combined with the OAS dissociation constant and the catalytic properties of OAS-TL, support the model of a dynamic cysteine synthesis system with regulatory function as can be expected from the position of the reaction in the sulphur assimilation pathway.}, }
@article {pmid15256617, year = {2004}, author = {Davis, CC and Wurdack, KJ}, title = {Host-to-parasite gene transfer in flowering plants: phylogenetic evidence from Malpighiales.}, journal = {Science (New York, N.Y.)}, volume = {305}, number = {5684}, pages = {676-678}, doi = {10.1126/science.1100671}, pmid = {15256617}, issn = {1095-9203}, mesh = {Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Flowers ; *Gene Transfer, Horizontal ; Genes, Plant ; Magnoliopsida/*classification/*genetics ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Phylogeny ; Plant Proteins/genetics ; Vitaceae/*classification/*genetics/parasitology ; }, abstract = {Horizontal gene transfer (HGT) between sexually unrelated species has recently been documented for higher plants, but mechanistic explanations for HGTs have remained speculative. We show that a parasitic relationship may facilitate HGT between flowering plants. The endophytic parasites Rafflesiaceae are placed in the diverse order Malpighiales. Our multigene phylogenetic analyses of Malpighiales show that mitochondrial (matR) and nuclear loci (18S ribosomal DNA and PHYC) place Rafflesiaceae in Malpighiales, perhaps near Ochnaceae/Clusiaceae. Mitochondrial nad1B-C, however, groups them within Vitaceae, near their obligate host Tetrastigma. These discordant phylogenetic hypotheses strongly suggest that part of the mitochondrial genome in Rafflesiaceae was acquired via HGT from their hosts.}, }
@article {pmid15255480, year = {2004}, author = {Bonhomme, F and Orth, A and Cucchi, T and Hadjisterkotis, E and Vigne, JD and Auffray, JC}, title = {[A new species of wild mice on the Island of Cyprus].}, journal = {Comptes rendus biologies}, volume = {327}, number = {5}, pages = {501-507}, doi = {10.1016/j.crvi.2004.03.001}, pmid = {15255480}, issn = {1631-0691}, mesh = {Animals ; Climate ; Cyprus ; Geography ; Mitochondria/genetics ; Muridae/*classification/genetics ; Phylogeny ; }, abstract = {A mitochondrial and nuclear gene analysis allowed us to precise the taxonomical position of the two sympatric species of mice known to be present on Cyprus. One of them is the commensal house mouse M. m. domesticus, and the other revealed to be a new taxon that is a sister species of M. spicilegus and M. macedonicus. The new species is equidistant from each of these, the divergence dating around 0.5-1 Myr. Its origin either results from an ancient accidental colonisation of the island or from a recent transportation by the first epipalaeolithic settlers. In this last eventuality, the new species would also exist somewhere else in Asia Minor.}, }
@article {pmid15252706, year = {2004}, author = {Seo, D and Kamino, K and Inoue, K and Sakurai, H}, title = {Purification and characterization of ferredoxin-NADP+ reductase encoded by Bacillus subtilis yumC.}, journal = {Archives of microbiology}, volume = {182}, number = {1}, pages = {80-89}, doi = {10.1007/s00203-004-0701-5}, pmid = {15252706}, issn = {0302-8933}, mesh = {Bacillus subtilis/*enzymology/genetics ; Ferredoxin-NADP Reductase/chemistry/genetics/*isolation &amp; purification ; Ferredoxins/*metabolism ; Phylogeny ; }, abstract = {From Bacillus subtilis cell extracts, ferredoxin-NADP+ reductase (FNR) was purified to homogeneity and found to be the yumC gene product by N-terminal amino acid sequencing. YumC is a approximately 94-kDa homodimeric protein with one molecule of non-covalently bound FAD per subunit. In a diaphorase assay with 2,6-dichlorophenol-indophenol as electron acceptor, the affinity for NADPH was much higher than that for NADH, with Km values of 0.57 microM vs >200 microM. Kcat values of YumC with NADPH were 22.7 s(-1) and 35.4 s(-1) in diaphorase and in a ferredoxin-dependent NADPH-cytochrome c reduction assay, respectively. The cell extracts contained another diaphorase-active enzyme, the yfkO gene product, but its affinity for ferredoxin was very low. The deduced YumC amino acid sequence has high identity to that of the recently identified Chlorobium tepidum FNR. A genomic database search indicated that there are more than 20 genes encoding proteins that share a high level of amino acid sequence identity with YumC and which have been annotated variously as NADH oxidase, thioredoxin reductase, thioredoxin reductase-like protein, etc. These genes are found notably in gram-positive bacteria, except Clostridia, and less frequently in archaea and proteobacteria. We propose that YumC and C. tepidum FNR constitute a new group of FNR that should be added to the already established plant-type, bacteria-type, and mitochondria-type FNR groups.}, }
@article {pmid15247432, year = {2004}, author = {Laforest, MJ and Bullerwell, CE and Forget, L and Lang, BF}, title = {Origin, evolution, and mechanism of 5' tRNA editing in chytridiomycete fungi.}, journal = {RNA (New York, N.Y.)}, volume = {10}, number = {8}, pages = {1191-1199}, pmid = {15247432}, issn = {1355-8382}, mesh = {Chytridiomycota/*genetics/physiology ; *Evolution, Molecular ; Nucleic Acid Conformation ; Phylogeny ; RNA Editing/genetics/*physiology ; RNA, Transfer/*metabolism ; }, abstract = {5' tRNA editing has been demonstrated to occur in the mitochondria of the distantly related rhizopod amoeba Acanthamoeba castellanii and the chytridiomycete fungus Spizellomyces punctatus. In these organisms, canonical tRNA structures are restored by removing mismatched nucleotides at the first three 5' positions and replacing them with nucleotides capable of forming Watson-Crick base pairs with their 3' counterparts. This form of editing seems likely to occur in members of Amoebozoa other than A. castellanii, as well as in members of Heterolobosea. Evidence for 5' tRNA editing has not been found to date, however, in any other fungus including the deeply branching chytridiomycete Allomyces macrogynus. We predicted that a similar form of tRNA editing would occur in members of the chytridiomycete order Monoblepharidales based on the analysis of complete mitochondrial tRNA complements. This prediction was confirmed by analysis of tRNA sequences using a tRNA circularization/RT-PCR-based approach. The presence of partially and completely unedited tRNAs in members of the Monoblepharidales suggests the involvement of a 5'-to-3' exonuclease rather than an endonuclease in removing the three 5' nucleotides from a tRNA substrate. Surprisingly, analysis of the mtDNA of the chytridiomycete Rhizophydium brooksianum, which branches as a sister group to S. punctatus in molecular phylogenies, did not suggest the presence of editing. This prediction was also confirmed experimentally. The absence of tRNA editing in R. brooksianum raises the possibility that 5' tRNA editing may have evolved twice independently within Chytridiomycota, once in the lineage leading to S. punctatus and once in the lineage leading to the Monoblepharidales.}, }
@article {pmid15247091, year = {2004}, author = {Ross, IK}, title = {Mitochondria, sex, and mortality.}, journal = {Annals of the New York Academy of Sciences}, volume = {1019}, number = {}, pages = {581-584}, doi = {10.1196/annals.1297.109}, pmid = {15247091}, issn = {0077-8923}, mesh = {*Aging ; Animals ; Biological Evolution ; Cell Nucleus/*metabolism ; DNA, Mitochondrial/metabolism ; Humans ; Mitochondria/*pathology ; *Reproduction ; Sex Factors ; }, abstract = {It has been proposed that prior to the evolution of sex, the endosymbiotic relationship between mitochondria and nuclear genomes would have selected mechanisms that maintained the optimum interaction between the two genomes. Once sex evolved, mating would introduce different, competitive, mtDNA and/or nDNA gene products that could well upset the balance. Mechanisms, such as the specific degradation of one mitochondrial genome that is known to occur, could have been selected to prevent part of such competition. Unlike most protein complexes in the cell, the proteins of the multienzyme complexes of the ox-phos system are derived from both nuclear-genome-coded genes and mitochondrial-genome-coded genes. Minor mutations in either mtDNA or nDNA coding for these proteins are known to lead to major and catastrophic diseases of humans, suggesting that very tight and precise interactions are required. To maintain the evolutionarily established balance after mating, monoallelic expression of the nuclear-coded genes would be advantageous and prevent subtly different competitive proteins from interacting with the resident mitochondria. This would require regulation of the expression of those specific nuclear genes, possibly under the control of the resident mitochondria. It is possible that aging cells could lose the requisite tight regulation and allow expression of proteins derived from the formerly repressed nuclear alleles that would compete for mitochondrial complex sites. With age, random failure of this control could lead to increasingly inefficient mitochondria in different tissues and organs and eventually to senescence and death.}, }
@article {pmid15247075, year = {2004}, author = {Brunet Rossinni, AK}, title = {Testing the free radical theory of aging in bats.}, journal = {Annals of the New York Academy of Sciences}, volume = {1019}, number = {}, pages = {506-508}, doi = {10.1196/annals.1297.093}, pmid = {15247075}, issn = {0077-8923}, mesh = {*Aging ; Animals ; Chiroptera/*metabolism ; *Free Radicals ; Hydrogen Peroxide/pharmacology ; Oxidative Stress ; Oxygen/metabolism ; Oxygen Consumption ; Shrews ; Time Factors ; }, abstract = {The extended longevity of bats, despite their high metabolic rates, may provide insight to patterns and mechanisms of aging. I tested the free radical theory of aging as an explanation for the extreme longevity of the little brown bat, Myotis lucifugus (maximum life span potential [MLSP] = 34 years). In a comparative study, I measured whole-organism oxygen consumption and mitochondrial hydrogen peroxide production in brain, heart, and kidney tissues from M. lucifugus and short-tailed shrews, Blarina brevicauda (MLSP = 2 years). As predicted by the free radical theory of aging, M. lucifugus produced approximately half the amount of hydrogen peroxide as B. brevicauda. In addition, I compared oxygen consumption and hydrogen peroxide production of adult (approximately 1 year) and juvenile (fully developed and fledged young of the year) M. lucifugus to assess oxidative damage to mitochondria (measured as an increase in hydrogen peroxide production) due to the high metabolic rate associated with flight. Contrary to my prediction, juveniles had significantly higher levels of hydrogen peroxide production than adults. I propose that the decreased free radical production in adults is the result of within-individual selection of efficient mitochondria due to selective pressure created by the high energetic demands of flight.}, }
@article {pmid15235010, year = {2004}, author = {Dawson, TJ and Mifsud, B and Raad, MC and Webster, KN}, title = {Aerobic characteristics of red kangaroo skeletal muscles: is a high aerobic capacity matched by muscle mitochondrial and capillary morphology as in placental mammals?.}, journal = {The Journal of experimental biology}, volume = {207}, number = {Pt 16}, pages = {2811-2821}, doi = {10.1242/jeb.01115}, pmid = {15235010}, issn = {0022-0949}, mesh = {Analysis of Variance ; Animals ; Biological Evolution ; Blood Volume ; Body Constitution ; Body Weights and Measures ; Capillaries/*anatomy &amp; histology ; Macropodidae/*anatomy &amp; histology/*physiology ; Microscopy, Electron ; Mitochondria, Muscle/*physiology ; Muscle, Skeletal/*physiology/ultrastructure ; Oxygen Consumption/*physiology ; }, abstract = {Marsupials and placentals together comprise the Theria, the advanced mammals, but they have had long independent evolutionary histories, with the last common ancestor occurring more than 125 million years ago. Although in the past the marsupials were considered to be metabolically 'primitive', the red kangaroo Macropus rufus has been reported to have an aerobic capacity (VO2max) comparable to that of the most 'athletic' of placentals such as dogs. However, kangaroos travel at moderate speeds with lower relative cost than quadrupedal placentals. Given the long independent evolution of the two therian groups, and their unusual locomotor energetics, do kangaroos achieve their high aerobic capacity using the same structural and functional mechanisms used by (athletic) placentals? Red kangaroo skeletal muscle morphometry matched closely the general aerobic characteristics of placental mammals. The relationship between total mitochondrial volume in skeletal muscle and VO2max during exercise was identical to that in quadrupedal placentals, and differed from that in bipedal humans. As for placentals generally, red kangaroo mitochondrial oxygen consumption at VO2max was 4.7 ml O2 min(-1) ml(-1) of mitochondria. Also, the inner mitochondrial membrane densities were 35.8 +/- 0.7 m2 ml(-1) of mitochondria, which is the same as for placental mammals, and the same pattern of similarity was seen for capillary densities and volumes. The overall data for kangaroos was equivalent to that seen in athletic placentals such as dogs and pronghorns. Total skeletal muscle mass was high, being around 50% of body mass, and was concentrated around the pelvis and lower back. The majority of the muscles sampled had relatively high mitochondrial volume densities, in the range 8.8-10.6% in the major locomotor muscles. Again, capillary densities and capillary blood volumes followed the pattern seen for mitochondria. Our results indicate that the red kangaroo, despite its locomotion and extreme body form, shows fundamental aerobic/muscular relationships that appear common to both marsupials and placentals. The evolution of such metabolic relationships apparently predates the divergence of the therian groups in the early Cretaceous, and perhaps evolved in the mammal-like reptiles during the Triassic (220 million years ago) before the actual evolution of the mammals.}, }
@article {pmid15232219, year = {2004}, author = {Kim, YJ and Kweon, HS and Kim, IC and Lee, YM and Kim, JM and Lee, JS}, title = {The complete mitochondrial genome of the floating goby, Gymnogobius petschiliensis (Perciformes, Gobiidae).}, journal = {Molecules and cells}, volume = {17}, number = {3}, pages = {446-453}, pmid = {15232219}, issn = {1016-8478}, mesh = {Animals ; Base Sequence ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Fishes/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Perciformes/*genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {We isolated floating goby Gymnogobius petschiliensis mitochondrial DNA by long-polymerase chain reaction (Long-PCR) with conserved primers, and sequenced the mitogenome by primer walking using flanking sequences. The G. petschiliensis mitochondrial DNA has 16,424 bp and its structural organization is similar to the mitochondrial DNAs of other fish, and mammals. We analyzed phylogenetic relationships derived from the mitochondrial cytochrome b gene. We report the basic characteristics of the G. petschiliensis mitochondrial genome including its structural organization and the base composition of the rRNAs, tRNAs and protein-coding genes as well as characteristics of tRNAs. These features are used to analyze phylogenetic relationship among the 60 species of the genus Gymnogobius.}, }
@article {pmid15232214, year = {2004}, author = {Park, JK and Choe, BL and Eom, KS}, title = {Two mitochondrial lineages in Korean freshwater Corbicula (Corbiculidae: bivalvia).}, journal = {Molecules and cells}, volume = {17}, number = {3}, pages = {410-414}, pmid = {15232214}, issn = {1016-8478}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Genetics, Population ; Haplotypes/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Mollusca/*genetics ; Mutation ; Species Specificity ; }, abstract = {The Korean freshwater Corbicula was surveyed genetically by sequencing 614-bp homologous fragment of mitochondrial cytochrome oxidase I subunit. Among a total of 127 individuals collected from 12 Korean freshwater localities we found only two COI haplotypes and these differed by a total of 9 base substitutions. Although the sequence divergence between the two haplotypes is moderate (p = 1.47%), placing the two mitotypic sequences in the context of Asian mtDNA phylogeny reveals that Korean freshwater Corbicula is comprised of two independent freshwater mitochondrial lineages. These results are in serious disagreement with the long-standing conclusions of earlier conchology-based taxonomic work on Korean Corbicula in which a number of species names (a minimum of 10 nominal species) have been used. This indicates that morphological characteristics alone are poor criteria for species-level identification in this group. In addition, our COI dataset shows that there is an extremely low level of genetic variation in Korean freshwater populations, suggesting that these populations have passed through a severe population bottleneck that greatly reduced their genetic variability. Our data also provide new information on the biogeographic distribution of Korean freshwater Corbicula. When haplotypic frequencies were compared, it was evident that the two Korean freshwater mitochondrial lineages have achieved very different distribution ranges: the predominant lineage (FWKR1) is widely distributed in Korean freshwater systems, whereas the minor lineage (FWKR2) is restricted to a relatively narrow range.}, }
@article {pmid15229290, year = {2004}, author = {Krishnan, NM and Seligmann, H and Stewart, CB and De Koning, AP and Pollock, DD}, title = {Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference.}, journal = {Molecular biology and evolution}, volume = {21}, number = {10}, pages = {1871-1883}, doi = {10.1093/molbev/msh198}, pmid = {15229290}, issn = {0737-4038}, support = {R01-GM06076004/GM/NIGMS NIH HHS/United States ; R33 GM065612-05/GM/NIGMS NIH HHS/United States ; GM065580/GM/NIGMS NIH HHS/United States ; R21 GM065612-02/GM/NIGMS NIH HHS/United States ; R33 GM065612-04/GM/NIGMS NIH HHS/United States ; R21 GM065612-01/GM/NIGMS NIH HHS/United States ; GM065612/GM/NIGMS NIH HHS/United States ; R33 GM065612-03/GM/NIGMS NIH HHS/United States ; R24-GM65580/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; *DNA, Mitochondrial ; Data Interpretation, Statistical ; *Evolution, Molecular ; Humans ; Likelihood Functions ; Mitochondria/*genetics ; Phylogeny ; Primates/*genetics ; }, abstract = {Reconstruction of ancestral DNA and amino acid sequences is an important means of inferring information about past evolutionary events. Such reconstructions suggest changes in molecular function and evolutionary processes over the course of evolution and are used to infer adaptation and convergence. Maximum likelihood (ML) is generally thought to provide relatively accurate reconstructed sequences compared to parsimony, but both methods lead to the inference of multiple directional changes in nucleotide frequencies in primate mitochondrial DNA (mtDNA). To better understand this surprising result, as well as to better understand how parsimony and ML differ, we constructed a series of computationally simple "conditional pathway" methods that differed in the number of substitutions allowed per site along each branch, and we also evaluated the entire Bayesian posterior frequency distribution of reconstructed ancestral states. We analyzed primate mitochondrial cytochrome b (Cyt-b) and cytochrome oxidase subunit I (COI) genes and found that ML reconstructs ancestral frequencies that are often more different from tip sequences than are parsimony reconstructions. In contrast, frequency reconstructions based on the posterior ensemble more closely resemble extant nucleotide frequencies. Simulations indicate that these differences in ancestral sequence inference are probably due to deterministic bias caused by high uncertainty in the optimization-based ancestral reconstruction methods (parsimony, ML, Bayesian maximum a posteriori). In contrast, ancestral nucleotide frequencies based on an average of the Bayesian set of credible ancestral sequences are much less biased. The methods involving simpler conditional pathway calculations have slightly reduced likelihood values compared to full likelihood calculations, but they can provide fairly unbiased nucleotide reconstructions and may be useful in more complex phylogenetic analyses than considered here due to their speed and flexibility. To determine whether biased reconstructions using optimization methods might affect inferences of functional properties, ancestral primate mitochondrial tRNA sequences were inferred and helix-forming propensities for conserved pairs were evaluated in silico. For ambiguously reconstructed nucleotides at sites with high base composition variability, ancestral tRNA sequences from Bayesian analyses were more compatible with canonical base pairing than were those inferred by other methods. Thus, nucleotide bias in reconstructed sequences apparently can lead to serious bias and inaccuracies in functional predictions.}, }
@article {pmid15225610, year = {2004}, author = {Chloupková, M and Reaves, SK and LeBard, LM and Koeller, DM}, title = {The mitochondrial ABC transporter Atm1p functions as a homodimer.}, journal = {FEBS letters}, volume = {569}, number = {1-3}, pages = {65-69}, doi = {10.1016/j.febslet.2004.05.051}, pmid = {15225610}, issn = {0014-5793}, support = {P01HD08315/HD/NICHD NIH HHS/United States ; }, mesh = {ATP-Binding Cassette Transporters/*chemistry/genetics/*metabolism ; Amino Acid Sequence ; Base Sequence ; Conserved Sequence ; DNA Primers ; Dimerization ; Genetic Complementation Test ; Mitochondria/*metabolism ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Plasmids ; Recombinant Proteins/chemistry/metabolism ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism ; Sequence Alignment ; }, abstract = {The ATP-binding cassette (ABC) transporters constitute one of the largest families of proteins in evolution. The ATM1 gene of the yeast Saccharomyces cerevisiae encodes an ABC protein, which is localized to the mitochondrial inner membrane. A deletion of ATM1 results in the accumulation of up to a 30-fold excess of mitochondrial iron, loss of mitochondrial cytochromes and abnormalities of cytosolic iron metabolism. In this study, we have evaluated the role of conserved sequence elements in Atm1p in its function and dimerization in vivo. We report that conserved residues in the Walker A and B motifs of the nucleotide binding domain, which are required for ATP binding and hydrolysis, are essential for Atm1p function. In addition, we provide evidence that ATP binding is important for Atm1p dimerization.}, }
@article {pmid15219233, year = {2004}, author = {Pereira, SL and Baker, AJ}, title = {Low number of mitochondrial pseudogenes in the chicken (Gallus gallus) nuclear genome: implications for molecular inference of population history and phylogenetics.}, journal = {BMC evolutionary biology}, volume = {4}, number = {}, pages = {17}, pmid = {15219233}, issn = {1471-2148}, mesh = {Animals ; Cell Nucleus/*genetics ; Chickens/*genetics ; Computational Biology/methods ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; *Evolution, Molecular ; *Genome ; Genome, Human ; Humans ; Mitochondria/genetics ; *Phylogeny ; Pseudogenes/*genetics ; }, abstract = {BACKGROUND: Mitochondrial DNA has been detected in the nuclear genome of eukaryotes as pseudogenes, or Numts. Human and plant genomes harbor a large number of Numts, some of which have high similarity to mitochondrial fragments and thus may have been inadvertently included in population genetic and phylogenetic studies using mitochondrial DNA. Birds have smaller genomes relative to mammals, and the genome-wide frequency and distribution of Numts is still unknown. The release of a preliminary version of the chicken (Gallus gallus) genome by the Genome Sequencing Center at Washington University, St. Louis provided an opportunity to search this first avian genome for the frequency and characteristics of Numts relative to those in human and plants.<br><br>RESULTS: We detected at least 13 Numts in the chicken nuclear genome. Identities between Numts and mitochondrial sequences varied from 58.6 to 88.8%. Fragments ranged from 131 to 1,733 nucleotides, collectively representing only 0.00078% of the nuclear genome. Because fewer Numts were detected in the chicken nuclear genome, they do not represent all regions of the mitochondrial genome and are not widespread in all chromosomes. Nuclear integrations in chicken seem to occur by a DNA intermediate and in regions of low gene density, especially in macrochromosomes.<br><br>CONCLUSION: The number of Numts in chicken is low compared to those in human and plant genomes, and is within the range found for most sequenced eukaryotic genomes. For chicken, PCR amplifications of fragments of about 1.5 kilobases are highly likely to represent true mitochondrial amplification. Sequencing of these fragments should expose the presence of unusual features typical of pseudogenes, unless the nuclear integration is very recent and has not yet been mutated. Metabolic selection for compact genomes with reduced repetitive DNA and gene-poor regions where Numts occur may explain their low incidence in birds.}, }
@article {pmid15215507, year = {2004}, author = {Lindemann, P and Koch, A and Degenhardt, B and Hause, G and Grimm, B and Papadopoulos, V}, title = {A novel Arabidopsis thaliana protein is a functional peripheral-type benzodiazepine receptor.}, journal = {Plant &amp; cell physiology}, volume = {45}, number = {6}, pages = {723-733}, doi = {10.1093/pcp/pch088}, pmid = {15215507}, issn = {0032-0781}, support = {ES-07747/ES/NIEHS NIH HHS/United States ; }, mesh = {Arabidopsis/*drug effects/genetics/*metabolism ; Arabidopsis Proteins/genetics/isolation &amp; purification/*metabolism ; Benzodiazepines/metabolism ; Binding, Competitive/genetics ; Carrier Proteins/genetics/isolation &amp; purification/metabolism ; Cholesterol/metabolism ; DNA, Complementary/genetics/isolation &amp; purification ; Escherichia coli/genetics/metabolism ; Evolution, Molecular ; Heme/*biosynthesis ; Ligands ; Microscopy, Electron ; Mitochondria/genetics/metabolism/ultrastructure ; Molecular Sequence Data ; Phylogeny ; Protoporphyrins/metabolism ; Radioligand Assay ; Receptors, GABA-A/genetics/isolation &amp; purification/*metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Steroids/*metabolism ; }, abstract = {A key element in the regulation of mammalian steroid biosynthesis is the 18 kDa peripheral-type benzodiazepine receptor (PBR), which mediates mitochondrial cholesterol import. PBR also possess an affinity to the tetrapyrrole metabolite protoporphyrin. The bacterial homolog to the mammalian PBR, the Rhodobacter TspO (CrtK) protein, was shown to be involved in the bacterial tetrapyrrole metabolism. Looking for a similar mitochondrial import mechanism in plants, protein sequences from Arabidopsis and several other plants were found with significant similarities to the mammalian PBR and to the Rhodobacter TspO protein. A PBR-homologous Arabidopsis sequence was cloned and expressed in E. coli. The recombinant gene product showed specific high affinity benzodiazepine ligand binding. Moreover, the protein applied to E. coli protoplasts caused an equal benzodiazepine-stimulated uptake of cholesterol and protoporphyrin IX. These results suggest that the PBR like protein is involved in steroid import and is directing protoporphyrinogen IX to the mitochondrial site of protoheme formation.}, }
@article {pmid15210995, year = {2004}, author = {Boussau, B and Karlberg, EO and Frank, AC and Legault, BA and Andersson, SG}, title = {Computational inference of scenarios for alpha-proteobacterial genome evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {26}, pages = {9722-9727}, pmid = {15210995}, issn = {0027-8424}, mesh = {Alphaproteobacteria/classification/*genetics/metabolism ; Animals ; Chromosomes, Bacterial/genetics ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Genes, Bacterial/*genetics ; *Genome, Bacterial ; Humans ; Mitochondria/genetics/physiology ; Phylogeny ; Plants/microbiology ; }, abstract = {The alpha-proteobacteria, from which mitochondria are thought to have originated, display a 10-fold genome size variation and provide an excellent model system for studies of genome size evolution in bacteria. Here, we use computational approaches to infer ancestral gene sets and to quantify the flux of genes along the branches of the alpha-proteobacterial species tree. Our study reveals massive gene expansions at branches diversifying plant-associated bacteria and extreme losses at branches separating intracellular bacteria of animals and humans. Alterations in gene numbers have mostly affected functional categories associated with regulation, transport, and small-molecule metabolism, many of which are encoded by paralogous gene families located on auxiliary chromosomes. The results suggest that the alpha-proteobacterial ancestor contained 3,000-5,000 genes and was a free-living, aerobic, and motile bacterium with pili and surface proteins for host cell and environmental interactions. Approximately one third of the ancestral gene set has no homologs among the eukaryotes. More than 40% of the genes without eukaryotic counterparts encode proteins that are conserved among the alpha-proteobacteria but for which no function has yet been identified. These genes that never made it into the eukaryotes but are widely distributed in bacteria may represent bacterial drug targets and should be prime candidates for future functional characterization.}, }
@article {pmid15197470, year = {2004}, author = {Giglione, C and Boularot, A and Meinnel, T}, title = {Protein N-terminal methionine excision.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {61}, number = {12}, pages = {1455-1474}, doi = {10.1007/s00018-004-3466-8}, pmid = {15197470}, issn = {1420-682X}, mesh = {Amidohydrolases/*chemistry ; Aminopeptidases/chemistry ; Animals ; Cations ; Cell Nucleus/metabolism ; Cytoplasm/metabolism ; Humans ; Metalloproteases/metabolism ; Methionine/*chemistry ; Mitochondria/metabolism ; Models, Chemical ; Phylogeny ; Plastids/metabolism ; Protein Structure, Tertiary ; Proteins/*chemistry ; Proteome/chemistry ; }, abstract = {N-terminal methionine excision (NME) is the major proteolytic pathway responsible for the diversity of N-terminal amino acids in proteins. Dedicated NME components have been identified in all organisms, in all compartments in which protein synthesis occurs: cytoplasm, plastids and mitochondria. Recent studies have revealed that NME is regulated at various levels and plays an important role in controlling protein turnover. NME is essential in Eubacteria and lower eukaryotes and is the target of many natural and synthetic inhibitors. Such inhibitors have considerable potential for use in the treatment of various human diseases, from cancer to bacterial and parasitic infections.}, }
@article {pmid15190127, year = {2004}, author = {Howell, N and Elson, JL and Turnbull, DM and Herrnstadt, C}, title = {African Haplogroup L mtDNA sequences show violations of clock-like evolution.}, journal = {Molecular biology and evolution}, volume = {21}, number = {10}, pages = {1843-1854}, doi = {10.1093/molbev/msh184}, pmid = {15190127}, issn = {0737-4038}, mesh = {*Black or African American ; *DNA, Mitochondrial ; *Evolution, Molecular ; Genetic Markers ; Haplotypes ; Humans ; Likelihood Functions ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {A set of 96 complete mtDNA sequences that belong to the three major African haplogroups (L1, L2, and L3) was analyzed to determine if mtDNA has evolved as a molecular clock. Likelihood ratio tests (LRTs) were carried out with each of the haplogroups and with combined haplogroup sequence sets. Evolution has not been clock-like, neither for the coding region nor for the control region, in combined sets of African haplogroup L mtDNA sequences. In tests of individual haplogroups, L2 mtDNAs showed violations of a molecular clock under all conditions and in both the control and coding regions. In contrast, haplogroup L1 and L3 sequences, both for the coding and control regions, show clock-like evolution. In clock tests of individual L2 subclades, the L2a sequences showed a marked violation of clock-like evolution within the coding region. In addition, the L2a and L2c branch lengths of both the coding and control regions were shorter relative to those of the L2b and L2d sequences, a result that indicates lower levels of sequence divergence. Reduced median network analyses of the L2a sequences indicated the occurrence of marked homoplasy at multiple sites in the control region. After exclusion of the L2a and L2c sequences, African mtDNA coding region evolution has not significantly departed from a molecular clock, despite the results of neutrality tests that indicate the mitochondrial coding region has evolved under nonneutral conditions. In contrast, control region evolution is clock-like only at the haplogroup level, and it thus appears to have evolved essentially independently from the coding region. The results of the clock tests, the network analyses, and the branch length comparisons all caution against the use of simple mtDNA clocks.}, }
@article {pmid15186824, year = {2004}, author = {Kojima, S and Fujikura, K and Okutani, T}, title = {Multiple trans-Pacific migrations of deep-sea vent/seep-endemic bivalves in the family Vesicomyidae.}, journal = {Molecular phylogenetics and evolution}, volume = {32}, number = {1}, pages = {396-406}, doi = {10.1016/j.ympev.2004.02.016}, pmid = {15186824}, issn = {1055-7903}, mesh = {Animals ; *Biological Evolution ; DNA Primers/chemistry ; Ecosystem ; Environment ; Geography ; Geologic Sediments ; Mitochondria/genetics ; Mollusca/classification/*genetics ; Oceans and Seas ; Pacific Ocean ; Phylogeny ; Polymerase Chain Reaction ; *Seawater ; Sequence Analysis, DNA ; Temperature ; }, }
@article {pmid15186803, year = {2004}, author = {Favret, C and Voegtlin, DJ}, title = {Speciation by host-switching in pinyon Cinara (Insecta: Hemiptera: Aphididae).}, journal = {Molecular phylogenetics and evolution}, volume = {32}, number = {1}, pages = {139-151}, doi = {10.1016/j.ympev.2003.12.005}, pmid = {15186803}, issn = {1055-7903}, mesh = {Animals ; Aphids/*genetics ; Cell Nucleus/metabolism ; DNA/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Host-Parasite Interactions ; Mitochondria/metabolism ; Peptide Elongation Factor 1/genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Trees ; }, abstract = {Parasite-host cospeciation has received much attention as an important mechanism in the diversification of phytophagous insects. However, studies have shown that for certain taxa, it is not host fidelity but host-switching that plays the critical role in speciation. Cinara are aphids (Insecta: Hemiptera: Aphididae: Lachninae) that feed exclusively on the woody parts of conifers of the Cupressaceae and Pinaceae. They are unusual aphids because most Pinaceae play host to several species of Cinara. The aphids show relatively strong host fidelity, and as a consequence historically have been treated based on the taxonomy of their hosts. The historical paradigm of aphid evolution implies that Cinara species have radiated to different parts of the same host species and/or speciated with their host. Using mitochondrial cytochrome oxidase 1 and nuclear elongation factor 1-alpha DNA sequences, we performed molecular phylogenetic analysis of Cinara species, concentrating on those associated with pinyon pines in the southwestern USA. We determined that switching hosts has played a key role in the speciation of the genus, reflected in the polyphyly of pinyon-feeding Cinara. Furthermore, species sharing a common feeding site on different hosts were more closely related to each other than to those sharing the same host but at different feeding sites, suggesting that feeding site fidelity plays a more important role in speciation than does host fidelity in general. This study also elucidated the primary taxonomy of various species: it suggested that Cinara rustica Hottes is a junior synonym of C. edulis (Wilson) and that C. wahtolca Hottes represents two species on the two different pinyon pine species, Pinus edulis Englem. and P. monophylla Torr. &amp; Frem.}, }
@article {pmid15186801, year = {2004}, author = {Schwarz, MP and Tierney, SM and Cooper, SJ and Bull, NJ}, title = {Molecular phylogenetics of the allodapine bee genus Braunsapis: A-T bias and heterogeneous substitution parameters.}, journal = {Molecular phylogenetics and evolution}, volume = {32}, number = {1}, pages = {110-122}, doi = {10.1016/j.ympev.2003.11.017}, pmid = {15186801}, issn = {1055-7903}, mesh = {Animals ; Bayes Theorem ; Bees/*genetics ; Cell Nucleus/metabolism ; Codon ; DNA/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Likelihood Functions ; Mitochondria/genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Extreme AT bias in Hymenopteran mitochondrial genes have created difficulties for molecular phylogenetic analyses, especially for older divergences where multiple substitutions can erode signal. Heterogeneity in the evolutionary rates of different codon positions and different genes also appears to have been a major problem in resolving ancient divergences in allodapine bees. Here we examine the phylogeny of relatively recent divergences in the allodapine bee genus Braunsapis. We examined heterogeneity in nucleotide substitution parameters for one nuclear gene and codon positions in two mitochondrial genes, exploring various phylogenetic analyses for recovering relationships among species from Africa, Madagascar, southern Asia, and Australia. We explored maximum parsimony, maximum likelihood, Log determinant and Bayesian analyses. Broad topological features of best fit trees tended to be similar for equivalent data sets (e.g., total, or with 3rd mt positions excluded), regardless of the analytic method used (e.g., maximum likelihood or Bayesian). Analyses that used the total data set without modelling partitions separately gave unlikely results, indicating that the Malagasy species was most closely related to Australian species. However, analyses that excluded 3rd mitochondrial positions, or modelled partitions separately, suggested that the Malagasy species falls within the African clade. The unlikely topologies apparently result from long branch attraction, and this problem is ameliorated where modelling allows more realistic estimates of base composition and evolutionary rates for 3rd mitochondrial positions. However, we found that even when codon positions are modelled separately, estimated evolutionary rates for 3rd mitochondrial positions are likely to underestimate true rates. Long branch attraction and multiple substitutions are likely to be much more difficult to circumvent in analyses that explore older, generic-level, divergences in allodapine bees where overwriting is expected to be much more extreme. Our results indicate an African origin for Braunsapis, followed by a single, very early, dispersal event into Asia and then by a later dispersal event into Australia. The Malagasy species is derived from within the African clade.}, }
@article {pmid15186796, year = {2004}, author = {Monteiro, FA and Donnelly, MJ and Beard, CB and Costa, J}, title = {Nested clade and phylogeographic analyses of the Chagas disease vector Triatoma brasiliensis in Northeast Brazil.}, journal = {Molecular phylogenetics and evolution}, volume = {32}, number = {1}, pages = {46-56}, doi = {10.1016/j.ympev.2003.12.011}, pmid = {15186796}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Chagas Disease/*parasitology/transmission ; Cytochromes b/genetics ; DNA/genetics ; DNA, Mitochondrial/genetics ; Genetic Variation ; Geography ; Haplotypes ; Mitochondria/genetics ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Species Specificity ; Triatoma/*genetics ; }, abstract = {Triatoma brasiliensis (Hemiptera: Reduviidae: Triatominae) is the most important Chagas disease vector in the semiarid areas of Northeast Brazil. We analyzed mitochondrial cytochrome b sequence variation among 136 individuals representing 16 populations from across the species' distribution. Neighbor-joining and parsimony tree-building methods were used in conjunction with nested clade analysis to describe the systematics and phylogeography of this species. Our results indicate that T. brasiliensis is composed of four genetically distinct chromatic forms (referred to as brasiliensis, macromelasoma, juazeiro, and melanica) that present inter-population divergence values (0.027-0.119, corrected K2-p) and a pattern of haplotype geographic distribution compatible with the existence of a species complex. As a consequence, such forms can be treated as isolated targets in vector control programs. We were unable to infer what is shaping the population structure of the brasiliensis form as we obtained mutually exclusive causes of structure, namely a barrier to gene flow caused by past population fragmentation, and isolation by distance between populations (which would permit gene flow). We found indication of mitochondrial DNA introgression occurring among forms in putative hybrid zones.}, }
@article {pmid15185745, year = {2004}, author = {Hornos, JE and Braggion, L and Magini, M and Forger, M}, title = {Symmetry preservation in the evolution of the genetic code.}, journal = {IUBMB life}, volume = {56}, number = {3}, pages = {125-130}, doi = {10.1080/15216540410001687838}, pmid = {15185745}, issn = {1521-6543}, mesh = {Animals ; *Evolution, Molecular ; *Genetic Code ; Humans ; Mitochondria/genetics ; Models, Molecular ; Phylogeny ; }, abstract = {The standard genetic code is found to exhibit an exact symmetry under a finite group of order 4 known in mathematics as the Klein group. The same symmetry is also present in almost all non-standard codes, mitochondrial as well as nuclear. Analysis of the phylogenetic tree for the evolution of the mitochondrial codes reveals that all changes along the main line of evolution preserve this symmetry, with a tendency towards symmetry enhancement. In the side branches of the evolutionary tree, the majority of changes also respect the symmetry. The few exceptional cases where it is broken correspond to reassignments that appear to be unstable or incomplete. Since the Klein group emerges naturally from the symplectic model for the prebiotic evolution that has led to the standard code, we interpret these results as lending support to the hypothesis that this symmetry has been selected during the evolution of the genetic code, not only before but also after establishment of the standard code.}, }
@article {pmid15179056, year = {2004}, author = {Min, MS and Okumura, H and Jo, DJ and An, JH and Kim, KS and Kim, CB and Shin, NS and Lee, MH and Han, CH and Voloshina, IV and Lee, H}, title = {Molecular phylogenetic status of the Korean goral and Japanese serow based on partial sequences of the mitochondrial cytochrome b gene.}, journal = {Molecules and cells}, volume = {17}, number = {2}, pages = {365-372}, pmid = {15179056}, issn = {1016-8478}, mesh = {Animals ; Base Sequence ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/*analysis ; Genetic Variation ; Goats/*classification/*genetics ; Haplotypes ; Japan ; Korea ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {To investigate the molecular phylogenetic status of the Korean goral, Nemorhaedus caudatus raddeanus, and Japanese serow, Capricornis crispus, we determined partial sequences of the mitochondrial cytochrome b gene of twelve Korean gorals and sixteen Japanese serows, and compared them with those of the major lineages of Rupicaprini species including two other Nemorhaedus species and two other Capricornis species. The Korean gorals examined possessed two haplotypes with only one nucleotide difference between them, while the Japanese serows showed slightly higher sequence diversity with five haplotypes. Genetic distances and molecular phylogenetic trees indicated that there is considerable genetic divergence between the Korean goral and N. caudatus (the Chinese goral) [Groves and Shields (1996)], but virtually none between Korean and Russian gorals. The Korean and Russian gorals may therefore be distinct from the Chinese goral. The data highlight the importance of conservation of the goral populations of these regions, and the need to reconsider the taxonomic status of Korean and Russian gorals. Our study also clearly demonstrated sufficient genetic distance between serows and gorals to justify their assignment to separate genera. Of the three species of Capricornis, the Formosan serow, C. swinhoei is more closely related to C. sumatraensis than to the Japanese serow, suggesting that the Formosan serow is a distinct species. Preliminary data on intraspecific genetic variation in the Japanese serow are also presented.}, }
@article {pmid15173569, year = {2004}, author = {LeClere, S and Rampey, RA and Bartel, B}, title = {IAR4, a gene required for auxin conjugate sensitivity in Arabidopsis, encodes a pyruvate dehydrogenase E1alpha homolog.}, journal = {Plant physiology}, volume = {135}, number = {2}, pages = {989-999}, pmid = {15173569}, issn = {0032-0889}, support = {R29 GM054749-04/GM/NIGMS NIH HHS/United States ; R29 GM054749-05/GM/NIGMS NIH HHS/United States ; R29-GM54749/GM/NIGMS NIH HHS/United States ; T32-GM08362/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Arabidopsis/enzymology/*genetics ; Arabidopsis Proteins/*genetics/metabolism ; Indoleacetic Acids/*metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Mutation ; Phylogeny ; Pyruvate Decarboxylase/*genetics/metabolism ; Pyruvate Dehydrogenase (Lipoamide)/genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {The formation and hydrolysis of indole-3-acetic acid (IAA) conjugates represent a potentially important means for plants to regulate IAA levels and thereby auxin responses. The identification and characterization of mutants defective in these processes is advancing the understanding of auxin regulation and response. Here we report the isolation and characterization of the Arabidopsis iar4 mutant, which has reduced sensitivity to several IAA-amino acid conjugates. iar4 is less sensitive to a synthetic auxin and low concentrations of an ethylene precursor but responds to free IAA and other hormones tested similarly to wild type. The gene defective in iar4 encodes a homolog of the E1alpha-subunit of mitochondrial pyruvate dehydrogenase, which converts pyruvate to acetyl-coenzyme A. We did not detect glycolysis or Krebs-cycle-related defects in the iar4 mutant, and a T-DNA insertion in the IAR4 coding sequence conferred similar phenotypes as the originally identified missense allele. In contrast, we found that disruption of the previously described mitochondrial pyruvate dehydrogenase E1alpha-subunit does not alter IAA-Ala responsiveness or confer any obvious phenotypes. It is possible that IAR4 acts in the conversion of indole-3-pyruvate to indole-3-acetyl-coenzyme A, which is a potential precursor of IAA and IAA conjugates.}, }
@article {pmid15170257, year = {2004}, author = {Mukai, A and Endoh, H}, title = {Presence of a bacterial-like citrate synthase gene in Tetrahymena thermophila: recent lateral gene transfers (LGT) or multiple gene losses subsequent to a single ancient LGT?.}, journal = {Journal of molecular evolution}, volume = {58}, number = {5}, pages = {540-549}, pmid = {15170257}, issn = {0022-2844}, mesh = {Amino Acid Motifs/genetics ; Amino Acid Sequence ; Animals ; Blotting, Southern ; Citrate (si)-Synthase/*genetics ; DNA/analysis ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Molecular Sequence Data ; Peroxisomal Targeting Signal 2 Receptor ; Peroxisome-Targeting Signal 1 Receptor ; Phylogeny ; Receptors, Cytoplasmic and Nuclear/genetics ; Tetrahymena thermophila/*genetics ; }, abstract = {Citrate synthase is the initial enzyme in the tricarboxylic acid cycle of mitochondria. In plants and fungi, it is the second isozyme in the glyoxylate cycle of peroxisomes (or glyoxysomes), and it is also present in bacteria. Some of the biochemical reactions in the glyoxylate cycle of the ciliated protozoan Tetrahymena pyriformis depend upon mitochondrial enzymes, as T. pyriformis lacks some glyoxysome-specific enzymes. Here we demonstrate a new citrate synthase gene from Tetrahymena thermophila that is different from the mitochondrial counterpart. A potential peroxysome-targeted signal was detected in the N-terminus, suggesting the localization of the enzyme in peroxysomes. Phylogenetic analysis placed the Tetrahymena sequence in a clade consisting of a few sequences from eukaryotes such as cellular slime molds and two land plants, near a green sulfur bacterium and many proteobacteria as a sister group but not in a mitochondrial clade. Southern blot analysis revealed that this type of gene was absent from distantly related ciliates and other species of Tetrahymena except for the closest species, T. mallaccensis. The scattered presence of the bacterial-like genes among distantly related eukaryotes suggests three alternative interpretations of acquisition of the novel glyoxysomal citrate synthase gene via lateral gene transfer (LGT). (1). Some eukaryotes independently acquired the gene from a common bacterium or closely related bacteria via LGT. (2). A hypothetical eukaryote once acquired the gene, which was thereafter independently transferred from the eukaryote to other eukaryotes. (3). A single event of LGT (or duplication) occurred in a certain common ancestor of eukaryotes, followed by multiple losses in many eukaryotic lineages during the subsequent evolution. Considering the monophyly of the bacterial-like eukaryotic citrate synthase genes, the first model is somewhat unlikely, even though it is not impossible. The second and third models can rationally explain the present observation, so these models are discussed in some detail.}, }
@article {pmid15162115, year = {2004}, author = {Lo Brutto, S and Azeuleo, M and Sarà, M}, title = {Mitochondrial simple sequence repeats and 12S-rRNA gene reveal two distinct lineages of Crocidura russula (Mammalia, Soricidae).}, journal = {Heredity}, volume = {92}, number = {6}, pages = {527-533}, doi = {10.1038/sj.hdy.6800448}, pmid = {15162115}, issn = {0018-067X}, mesh = {Africa, Northern ; Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; Europe ; Genes, rRNA/*genetics ; Genetics, Population ; Microsatellite Repeats/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/*genetics ; Sequence Alignment ; Sequence Analysis ; Sequence Homology, Nucleic Acid ; Shrews/*genetics ; }, abstract = {A short segment (135 bp) of the control region and a partial sequence (394 bp) of the 12S-rRNA gene in the mitochondrial DNA of Crocidura russula were analyzed in order to test a previous hypothesis regarding the presence of a gene flow disruption in northern Africa. This breakpoint would have separated northeast-African C. russula populations from the European (plus the northwest-African) populations. The analysis was carried out on specimens from Tunisia (C. r. cf agilis), Sardinia (C. r. ichnusae), and Pantelleria (C. r. cossyrensis), and on C. r. russula from Spain and Belgium. Two C. russula lineages were identified; they both shared R2 tandem repeated motifs of the same length (12 bp), but not the same primary structure. These simple sequence repeats were present in 12-23 copies in the right domain of the control region. Within the northeast-African populations, a polymorphism of repeat variants, not yet found in Europe, was recorded. A neighbor-join tree, which was built by sequences of the conserved 12S-rRNA gene, separated the two sister groups; it permitted us to date a divergence time of 0.5 Myr. Our data discriminated two different mitochondrial lineages in accordance with the previous morphological and karyological data. Ecoclimatic barriers formed during the Middle Pleistocene broke the range of ancestral species in the Eastern Algeria (Kabile Mountains), leading to two genetically separate and modern lineages. The northeast-African lineage can today be located in Tunisia, Pantelleria, and Sardinia. The northwest-African lineage (Morocco and West Algeria), reaching Spain by anthropogenic introduction, spread over north Europe in modern times. The Palaearctic C. russula species is monophyletic, but a taxonomical revision (ie, to provide a full species rank for the northeast taxa and to put in synonymy some insular taxa) is required.}, }
@article {pmid15158725, year = {2004}, author = {Hunter, SE and Spremulli, LL}, title = {Effects of mutagenesis of residue 221 on the properties of bacterial and mitochondrial elongation factor EF-Tu.}, journal = {Biochimica et biophysica acta}, volume = {1699}, number = {1-2}, pages = {173-182}, doi = {10.1016/j.bbapap.2004.02.015}, pmid = {15158725}, issn = {0006-3002}, support = {GM 32734/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Escherichia coli/*chemistry/genetics/metabolism ; Guanine Nucleotides/metabolism ; Mitochondria/*chemistry/metabolism ; Molecular Sequence Data ; *Mutagenesis ; Peptide Elongation Factor Tu/*chemistry/genetics/metabolism ; Protein Biosynthesis ; Protein Conformation ; RNA, Transfer, Cys/*chemistry ; RNA, Transfer, Phe/*chemistry ; Ribosomes/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {During protein biosynthesis, elongation factor Tu (EF-Tu) delivers aminoacyl-tRNA (aa-tRNA) to the A-site of ribosomes. This factor is highly conserved throughout evolution. However, several key residues differ between bacterial and mammalian mitochondrial EF-Tu (EF-Tu(mt)). One such residue is Ser221 (Escherichia coli numbering). This residue is conserved as a Ser or Thr in the bacterial factors but is present as Pro269 in EF-Tu(mt). Pro269 reorients the loop containing this residue and shifts the adjoining beta-strand in EF-Tu(mt) compared to that of E. coli EF-Tu potentially altering the binding pocket for the acceptor stem of the aa-tRNA. Pro269 was mutated to a serine residue (P269S) in EF-Tu(mt). For comparison, the complementary mutation was created at Ser221 in E. coli EF-Tu (S221P). The E. coli EF-Tu S221P variant is poorly expressed in E. coli and the majority of the molecules fail to fold into an active conformation. In contrast, EF-Tu(mt) P269S is expressed to a high level in E. coli. When corrected for the percentage of active molecules, both variants function as effectively as their respective wild-type factors in ternary complex formation using E. coli Phe-tRNA(Phe) and Cys-tRNA(Cys). They are also active in A-site binding and in vitro translation assays with E. coli Phe-tRNA(Phe). In addition, both variants are as active as their respective wild-type factors in ternary complex formation, A-site binding and in vitro translation assays using mitochondrial Phe-tRNA(Phe).}, }
@article {pmid15155803, year = {2004}, author = {Maćasev, D and Whelan, J and Newbigin, E and Silva-Filho, MC and Mulhern, TD and Lithgow, T}, title = {Tom22', an 8-kDa trans-site receptor in plants and protozoans, is a conserved feature of the TOM complex that appeared early in the evolution of eukaryotes.}, journal = {Molecular biology and evolution}, volume = {21}, number = {8}, pages = {1557-1564}, doi = {10.1093/molbev/msh166}, pmid = {15155803}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Carrier Proteins/*genetics ; Diatoms/*genetics ; Dictyostelium/*genetics ; Membrane Transport Proteins/*genetics ; Mitochondria/*genetics/metabolism ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Precursor Protein Import Complex Proteins ; Molecular Sequence Data ; Plasmodium falciparum/genetics ; Receptors, Cell Surface/*genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; }, abstract = {One of the earliest events in the evolution of mitochondria was the development a means to translocate proteins made in the cytosol into the "protomitochondrion." How this was achieved remains uncertain, and the nature of the earliest version of the protein translocation machinery is not known. Comparative sequence analysis suggests three subunits, Tom40, Tom7, and Tom22 as common elements of the protein translocase in the mitochondrial outer membrane in diverse extant eukaryotes. Tom22, the 22-kDa subunit, plays a critical role in the function of this complex in fungi and animals, and we show that an 8-kDa subunit of the plant translocase is a truncated form of Tom22. It has a single transmembrane segment conforming in sequence to the same region of Tom22 from other eukaryotic lineages and a short carboxy-terminal trans domain located in the mitochondrial intermembrane space. The trans domain from the Arabidopsis thaliana protein functions in yeast lacking their own Tom22 by complementing protein import defects and restoring cell growth. Moreover, we have identified orthologs of Tom22, Tom7, and Tom40 in diverse eukaryotes such as the diatom Phaeodactylum tricornutum, the amoebic slime Dictyostelium discoideum, and the protozoan parasite Plasmodium falciparum. This finding strongly suggests these subunits as the core of the protein translocase in the earliest mitochondria.}, }
@article {pmid15155798, year = {2004}, author = {Das, J and Miller, ST and Stern, DL}, title = {Comparison of diverse protein sequences of the nuclear-encoded subunits of cytochrome C oxidase suggests conservation of structure underlies evolving functional sites.}, journal = {Molecular biology and evolution}, volume = {21}, number = {8}, pages = {1572-1582}, doi = {10.1093/molbev/msh161}, pmid = {15155798}, issn = {0737-4038}, mesh = {Animals ; Catalytic Domain/*genetics ; Cattle ; Electron Transport Complex IV/chemistry/*genetics ; Mitochondria/*genetics ; *Models, Molecular ; Plants/genetics ; Yeasts/genetics ; }, abstract = {Interspecific comparisons of protein sequences can reveal regions of evolutionary conservation that are under purifying selection because of functional constraints. Interpreting these constraints requires combining evolutionary information with structural, biochemical, and physiological data to understand the biological function of conserved regions. We take this integrative approach to investigate the evolution and function of the nuclear-encoded subunits of cytochrome c oxidase (COX). We find that the nuclear-encoded subunits evolved subsequent to the origin of mitochondria and the subunit composition of the holoenzyme varies across diverse taxa that include animals, yeasts, and plants. By mapping conserved amino acids onto the crystal structure of bovine COX, we show that conserved residues are structurally organized into functional domains. These domains correspond to some known functional sites as well as to other uncharacterized regions. We find that amino acids that are important for structural stability are conserved at frequencies higher than expected within each taxon, and groups of conserved residues cluster together at distances of less than 5 A more frequently than do randomly selected residues. We, therefore, suggest that selection is acting to maintain the structural foundation of COX across taxa, whereas active sites vary or coevolve within lineages.}, }
@article {pmid15155797, year = {2004}, author = {Esser, C and Ahmadinejad, N and Wiegand, C and Rotte, C and Sebastiani, F and Gelius-Dietrich, G and Henze, K and Kretschmann, E and Richly, E and Leister, D and Bryant, D and Steel, MA and Lockhart, PJ and Penny, D and Martin, W}, title = {A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes.}, journal = {Molecular biology and evolution}, volume = {21}, number = {9}, pages = {1643-1660}, doi = {10.1093/molbev/msh160}, pmid = {15155797}, issn = {0737-4038}, mesh = {Alphaproteobacteria/*genetics ; Archaea/genetics ; Bacteria/*genetics ; Bacterial Proteins/genetics ; Carrier Proteins/genetics ; Evolution, Molecular ; Genes, Archaeal ; Genes, Bacterial ; *Genes, Fungal ; Genome ; Mitochondria/genetics ; Mitochondrial Proteins/genetics ; Models, Genetic ; Phylogeny ; Rhodospirillum rubrum/genetics ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Sequence Homology, Amino Acid ; }, abstract = {Analyses of 55 individual and 31 concatenated protein data sets encoded in Reclinomonas americana and Marchantia polymorpha mitochondrial genomes revealed that current methods for constructing phylogenetic trees are insufficiently sensitive (or artifact-insensitive) to ascertain the sister of mitochondria among the current sample of eight alpha-proteobacterial genomes using mitochondrially-encoded proteins. However, Rhodospirillum rubrum came as close to mitochondria as any alpha-proteobacterium investigated. This prompted a search for methods to directly compare eukaryotic genomes to their prokaryotic counterparts to investigate the origin of the mitochondrion and its host from the standpoint of nuclear genes. We examined pairwise amino acid sequence identity in comparisons of 6,214 nuclear protein-coding genes from Saccharomyces cerevisiae to 177,117 proteins encoded in sequenced genomes from 45 eubacteria and 15 archaebacteria. The results reveal that approximately 75% of yeast genes having homologues among the present prokaryotic sample share greater amino acid sequence identity to eubacterial than to archaebacterial homologues. At high stringency comparisons, only the eubacterial component of the yeast genome is detectable. Our findings indicate that at the levels of overall amino acid sequence identity and gene content, yeast shares a sister-group relationship with eubacteria, not with archaebacteria, in contrast to the current phylogenetic paradigm based on ribosomal RNA. Among eubacteria and archaebacteria, proteobacterial and methanogen genomes, respectively, shared more similarity with the yeast genome than other prokaryotic genomes surveyed.}, }
@article {pmid15154547, year = {2004}, author = {Iwanaga, A and Sasaki, A}, title = {Evolution of hierarchical cytoplasmic inheritance in the plasmodial slime mold Physarum polycephalum.}, journal = {Evolution; international journal of organic evolution}, volume = {58}, number = {4}, pages = {710-722}, doi = {10.1111/j.0014-3820.2004.tb00404.x}, pmid = {15154547}, issn = {0014-3820}, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/*metabolism ; Deoxyribonucleases/metabolism ; Extrachromosomal Inheritance/*genetics ; Linkage Disequilibrium/genetics ; Mitochondria/*genetics ; *Models, Genetic ; Myxomycetes/*genetics/metabolism ; Reproduction/genetics ; }, abstract = {A striking linear dominance relationship for uniparental mitochondrial transmission is known between many mating types of plasmodial slime mold Physarum polycephalum. We herein examine how such hierarchical cytoplasmic inheritance evolves in isogamous organisms with many self-incompatible mating types. We assume that a nuclear locus determines the mating type of gametes and that another nuclear locus controls the digestion of mitochondria DNAs (mtDNAs) of the recipient gamete after fusion. We then examine the coupled genetic dynamics for the evolution of self-incompatible mating types and biased mitochondrial transmission between them. In Physarum, a multiallelic nuclear locus matA controls both the mating type of the gametes and the selective elimination of the mtDNA in the zygotes. We theoretically examine two potential mechanisms that might be responsible for the preferential digestion of mitochondria in the zygote. In the first model, the preferential digestion of mitochondria is assumed to be the outcome of differential expression levels of a suppressor gene carried by each gamete (suppression-power model). In the second model (site-specific nuclease model), the digestion of mtDNAs is assumed to be due to their cleavage by a site-specific nuclease that cuts the mtDNA at unmethylated recognition sites. Also assumed is that the mtDNAs are methylated at the same recognition site prior to the fusion, thereby being protected against the nuclease of the same gamete, and that the suppressor alleles convey information for the recognition sequences of nuclease and methylase. In both models, we found that a linear dominance hierarchy evolves as a consequence of the buildup of a strong linkage disequilibrium between the mating-type locus and the suppressor locus, though it fails to evolve if the recombination rate between the two loci is larger than a threshold. This threshold recombination rate depends on the number of mating types and the degree of fitness reduction in the heteroplasmic zygotes. If the recombination rate is above the threshold, suppressor alleles are equally distributed in each mating type at evolutionary equilibrium. Based on the theoretical results of the site-specific nuclease model, we propose that a nested subsequence structure in the recognition sequence should underlie the linear dominance hierarchy of mitochondrial transmission.}, }
@article {pmid15152220, year = {2004}, author = {Knight, J}, title = {Giardia: not so special, after all?.}, journal = {Nature}, volume = {429}, number = {6989}, pages = {236-237}, doi = {10.1038/429236a}, pmid = {15152220}, issn = {1476-4687}, mesh = {Animals ; *Biological Evolution ; Eukaryotic Cells/cytology/physiology ; Giardia/*classification/*cytology/genetics ; Mitochondria/genetics/*physiology ; }, }
@article {pmid15144062, year = {2004}, author = {Kiefel, BR and Gilson, PR and Beech, PL}, title = {Diverse eukaryotes have retained mitochondrial homologues of the bacterial division protein FtsZ.}, journal = {Protist}, volume = {155}, number = {1}, pages = {105-115}, doi = {10.1078/1434461000168}, pmid = {15144062}, issn = {1434-4610}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/*genetics/physiology ; Biological Evolution ; Chloroplasts/genetics ; Chrysophyta/genetics ; Conserved Sequence ; Cyanophora/genetics ; Cytoskeletal Proteins/*genetics/physiology ; Diatoms/genetics ; Dictyostelium/genetics ; Eukaryota/genetics ; *Eukaryotic Cells ; Fungi/genetics ; Genes, Essential ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Phytophthora/genetics ; Plants/genetics ; Sequence Alignment ; Sequence Homology ; }, abstract = {Mitochondrial fission requires the division of both the inner and outer mitochondrial membranes. Dynamin-related proteins operate in division of the outer membrane of probably all mitochondria, and also that of chloroplasts--organelles that have a bacterial origin like mitochondria. How the inner mitochondrial membrane divides is less well established. Homologues of the major bacterial division protein, FtsZ, are known to reside inside mitochondria of the chromophyte alga Mallomonas, a red alga, and the slime mould Dictyostelium discoideum, where these proteins are likely to act in division of the organelle. Mitochondrial FtsZ is, however, absent from the genomes of higher eukaryotes (animals, fungi, and plants), even though FtsZs are known to be essential for the division of probably all chloroplasts. To begin to understand why higher eukaryotes have lost mitochondrial FtsZ, we have sampled various diverse protists to determine which groups have retained the gene. Database searches and degenerate PCR uncovered genes for likely mitochondrial FtsZs from the glaucocystophyte Cyanophora paradoxa, the oomycete Phytophthora infestans, two haptophyte algae, and two diatoms--one being Thalassiosira pseudonana, the draft genome of which is now available. From Thalassiosira we also identified two chloroplast FtsZs, one of which appears to be undergoing a C-terminal shortening that may be common to many organellar FtsZs. Our data indicate that many protists still employ the FtsZ-based ancestral mitochondrial division mechanism, and that mitochondrial FtsZ has been lost numerous times in the evolution of eukaryotes.}, }
@article {pmid15141947, year = {2004}, author = {Sánchez Puerta, MV and Bachvaroff, TR and Delwiche, CF}, title = {The complete mitochondrial genome sequence of the haptophyte Emiliania huxleyi and its relation to heterokonts (supplement).}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {11}, number = {1}, pages = {67-68}, doi = {10.1093/dnares/11.1.67}, pmid = {15141947}, issn = {1340-2838}, mesh = {Base Sequence ; DNA, Mitochondrial/*genetics ; *Genome, Plant ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; Phytoplankton/*genetics ; }, }
@article {pmid15141941, year = {2004}, author = {Sánchez Puerta, MV and Bachvaroff, TR and Delwiche, CF}, title = {The complete mitochondrial genome sequence of the haptophyte Emiliania huxleyi and its relation to heterokonts.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {11}, number = {1}, pages = {1-10}, doi = {10.1093/dnares/11.1.1}, pmid = {15141941}, issn = {1340-2838}, mesh = {Base Sequence ; DNA, Mitochondrial/*genetics ; *Genome, Plant ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; *Phylogeny ; Phytoplankton/genetics ; }, abstract = {The complete nucleotide sequence of the mitochondrial genome of Emiliania huxleyi (Haptophyta) was determined. E. huxleyi is the most abundant coccolithophorid, key in many marine ecosystems, and plays a vital role in the global carbon cycle. The mitochondrial genome contains genes encoding three subunits of cytochrome c oxidase, apocytochrome b, seven subunits of the NADH dehydrogenase complex, two ATPase subunits, two ribosomal RNAs, 25 tRNAs and five ribosomal proteins. One potentially functional open reading frame was identified, with no counterpart in any other organism so far studied. The cox1 gene transcript is apparently spliced from two distant segments in the genome. One of the most interesting features in this mtDNA is the presence of the dam gene, which codes for a DNA adenine methyltransferase. This enzyme is common in bacterial genomes, but is not present in any studied mitochondrial genome. Despite the great age of this group (ca. 300 Ma), little is known about the evolution of haptophytes or their relationship to other eukaryotes. This is the first published haptophyte organellar genome, and will improve the understanding of their biology and evolution and allow us to test the monophyly of the chromoalveolate clade.}, }
@article {pmid15137682, year = {2003}, author = {Sopott-Ehlers, B and Ehlers, U}, title = {Eyes covered by mitochondrial lenses in Petaliella spiracauda and Ptychopera purasjokii (Plathelminthes, Rhabdocoela, Trigonostominae). Ultrastructural features and phylogenetic implications.}, journal = {Journal of submicroscopic cytology and pathology}, volume = {35}, number = {4}, pages = {415-421}, pmid = {15137682}, issn = {1122-9497}, mesh = {Animals ; *Biological Evolution ; Eye/*ultrastructure ; Mitochondria/*ultrastructure ; *Phylogeny ; Platyhelminths/genetics/*ultrastructure ; }, abstract = {The submicroscopic anatomy of the eyes in Petaliella spiracauda and Ptychopera purasjokii is described. These eyes correspond in general to the basic pattern of rhabdomeric pigment-cup ocelli. This, however, does not apply to modifications of the cup cell such as the differentiation of mitochondrial lenses. Corresponding with two sensory cells two extensions of the cup cell capping the eye aperture are crowded with small unmodified mitochondria in the eyes of P. spiracauda. The eyes of P. purasjokii have three sensory cells and the lenticular element is formed by a trifoil-shaped differentiation of three giant mitochondrial derivatives. These derivatives show peripheral appendages of various configurations, all of which resemble the profiles of small mitochondria. The implication of the existence of such appendages is that the lenses in P. purasjokii are derived from many fused mitochondria, rather than from a single enlarged one. It is concluded that the unmodified or modified mitochondrial differentiations in proliferations of the pigment cell capping the opening of the eye cup serve to focalize incoming light. The evolution of mitochondrial lenses in Plathelminthes is considered.}, }
@article {pmid15136745, year = {2004}, author = {Wall, MK and Mitchenall, LA and Maxwell, A}, title = {Arabidopsis thaliana DNA gyrase is targeted to chloroplasts and mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {20}, pages = {7821-7826}, pmid = {15136745}, issn = {0027-8424}, support = {BBS/E/J/00000201/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Anti-Infective Agents/pharmacology ; Arabidopsis/drug effects/*enzymology/metabolism ; Chloroplasts/drug effects/*enzymology/metabolism ; Ciprofloxacin/pharmacology ; Cytoplasm/metabolism ; DNA/metabolism ; DNA Gyrase/drug effects/*metabolism ; Mitochondria/drug effects/*enzymology/metabolism ; Phylogeny ; Seedlings/drug effects ; Sequence Analysis, DNA ; }, abstract = {DNA gyrase is the bacterial DNA topoisomerase (topo) that supercoils DNA by using the free energy of ATP hydrolysis. The enzyme, an A(2)B(2) tetramer encoded by the gyrA and gyrB genes, catalyses topological changes in DNA during replication and transcription, and is the only topo that is able to introduce negative supercoils. Gyrase is essential in bacteria and apparently absent from eukaryotes and is, consequently, an important target for antibacterial agents (e.g., quinolones and coumarins). We have identified four putative gyrase genes in the model plant Arabidopsis thaliana; one gyrA and three gyrB homologues. DNA gyrase protein A (GyrA) has a dual translational initiation site targeting the mature protein to both chloroplasts and mitochondria, and there are individual targeting sequences for two of the DNA gyrase protein B (GyrB) homologues. N-terminal fusions of the organellar targeting sequences to GFPs support the hypothesis that one enzyme is targeted to the chloroplast and another to the mitochondrion, which correlates with supercoiling activity in isolated organelles. Treatment of seedlings and cultured cells with gyrase-specific drugs leads to growth inhibition. Knockout of A. thaliana gyrA is embryo-lethal whereas knockouts in the gyrB genes lead to seedling-lethal phenotypes or severely stunted growth and development. The A. thaliana genes have been cloned in Escherichia coli and found to complement gyrase temperature-sensitive strains. This report confirms the existence of DNA gyrase in eukaryotes and has important implications for drug targeting, organelle replication, and the evolution of topos in plants.}, }
@article {pmid15134833, year = {2004}, author = {Bratosin, D and Estaquier, J and Slomianny, C and Tissier, JP and Quatannens, B and Bulai, T and Mitrofan, L and Marinescu, A and Trandaburu, I and Ameisen, JC and Montreuil, J}, title = {On the evolution of erythrocyte programmed cell death: apoptosis of Rana esculenta nucleated red blood cells involves cysteine proteinase activation and mitochondrion permeabilization.}, journal = {Biochimie}, volume = {86}, number = {3}, pages = {183-192}, doi = {10.1016/j.biochi.2004.03.003}, pmid = {15134833}, issn = {0300-9084}, mesh = {Animals ; *Apoptosis ; Biological Evolution ; Cell Nucleus ; Cysteine Endopeptidases/*metabolism ; Enzyme Activation ; Erythrocytes/*cytology/*enzymology ; Flow Cytometry ; Intracellular Membranes/metabolism ; Kinetics ; Microscopy, Electron, Scanning ; Mitochondria/*metabolism ; Permeability ; Phosphoserine/metabolism ; Protein Transport ; Rana esculenta/*blood/*metabolism ; }, abstract = {Batracian Rana esculenta erythrocytes cell death induced by either calcium influx, or staurosporine, involves typical apoptotic phenotype. Our data reveal: (i) a drastic modification of the cell morphology with loss of the ellipsoidal form as assessed by phase contrast microscopy and scanning electron microscopy; (ii) an exposure of the phosphatidylserine residues in the outer leaflet of the cell membrane; (iii) a caspase-3-like activity; (iv) a mitochondrial membrane potential (Delta Psi m) loss; and (v) a chromatin condensation and fragmentation. Erythrocyte chromatin condensation and fragmentation are prevented by caspase and calpain peptide inhibitors. These inhibitors also prevent Delta Psi m loss supporting the idea that mitochondria is a central sensor for Rana erythrocytes cell death. Our observations highlight the conservation of the programmed cell death machinery in erythrocytes across kingdom.}, }
@article {pmid15134648, year = {2004}, author = {Ceccarelli, EA and Arakaki, AK and Cortez, N and Carrillo, N}, title = {Functional plasticity and catalytic efficiency in plant and bacterial ferredoxin-NADP(H) reductases.}, journal = {Biochimica et biophysica acta}, volume = {1698}, number = {2}, pages = {155-165}, doi = {10.1016/j.bbapap.2003.12.005}, pmid = {15134648}, issn = {0006-3002}, mesh = {Bacteria/*enzymology ; Ferredoxin-NADP Reductase/*physiology ; Mitochondria/enzymology ; Phylogeny ; Plants/*enzymology ; Protein Structure, Tertiary ; }, abstract = {Ferredoxin (flavodoxin)-NADP(H) reductases (FNRs) are ubiquitous flavoenzymes that deliver NADPH or low potential one-electron donors (ferredoxin, flavodoxin, adrenodoxin) to redox-based metabolisms in plastids, mitochondria and bacteria. Two great families of FAD-containing proteins displaying FNR activity have evolved from different and independent origins. The enzymes present in mitochondria and some bacterial genera are members of the structural superfamily of disulfide oxidoreductases whose prototype is glutathione reductase. A second group, comprising the FNRs from plastids and most eubacteria, constitutes a unique family, the plant-type FNRs, totally unrelated in sequence with the former. The two-domain structure of the plant family of FNR also provides the basic scaffold for an extended superfamily of electron transfer flavoproteins. In this article we compare FNR flavoenzymes from very different origins and describe how the natural history of these reductases shaped structure, flavin conformation and catalytic activity to face the very different metabolic demands they have to deal with in their hosts. We show that plant-type FNRs can be classified into a plastidic class, characterised by extended FAD conformation and high catalytic efficiency, and a bacterial class displaying a folded FAD molecule and low turnover rates. Sequence alignments supported this classification, providing a criterion to predict the structural and biochemical properties of newly identified members of the family.}, }
@article {pmid15133067, year = {2004}, author = {Lloyd, D}, title = {'Anaerobic protists': some misconceptions and confusions.}, journal = {Microbiology (Reading, England)}, volume = {150}, number = {Pt 5}, pages = {1115-1116}, doi = {10.1099/mic.0.26802-0}, pmid = {15133067}, issn = {1350-0872}, mesh = {Anaerobiosis ; Animals ; Biological Evolution ; Cattle ; Eukaryota/*growth &amp; development/physiology/*ultrastructure ; Eukaryotic Cells ; Giardia lamblia/growth &amp; development/physiology/ultrastructure ; Humans ; Mitochondria/*physiology/ultrastructure ; Protozoan Infections/parasitology ; }, }
@article {pmid15128508, year = {2004}, author = {Beninati, T and Lo, N and Sacchi, L and Genchi, C and Noda, H and Bandi, C}, title = {A novel alpha-Proteobacterium resides in the mitochondria of ovarian cells of the tick Ixodes ricinus.}, journal = {Applied and environmental microbiology}, volume = {70}, number = {5}, pages = {2596-2602}, pmid = {15128508}, issn = {0099-2240}, mesh = {Alphaproteobacteria/*classification/*genetics/isolation &amp; purification ; Animals ; DNA, Ribosomal/analysis ; Female ; In Situ Hybridization ; Ixodes/*microbiology ; Male ; Microscopy, Electron ; Mitochondria/*microbiology ; Molecular Sequence Data ; Ovary/cytology/microbiology/ultrastructure ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {An intracellular bacterium from Ixodes ricinus ticks collected in Italy was characterized by electron microscopy (EM), PCR sequencing of the 16S rRNA gene, molecular phylogenetic analysis, and in situ hybridization (ISH). This bacterium was shown by EM to be present in the cytoplasm, as well as in the mitochondria of ovarian cells. When universal 16S rRNA bacterial primers were used, PCR amplification of ovarian DNA followed by cloning and sequencing resulted in the same sequence being found in each sample. Phylogenetic analysis of this sequence showed that the bacterium from which it was derived, tentatively designated IricES1, is part of a novel clade in the alpha subdivision of the Proteobacterium: ISH and PCR assays of various tissues performed with oligonucleotides specific for the IricES1 16S rRNA showed that IricES1 is restricted to ovarian cells. Based on the results obtained, we inferred that the bacteria seen by EM in ovarian cells are a single type of bacteria, corresponding to IricES1. PCR screening of 166 ticks from various parts of Italy and one site in England showed that IricES1 was present in 96% of adult females and 44% of nymphs (unsexed). No adult males were found to be infected. Despite the apparent parasitism of host mitochondria by IricES1, the available information suggests that the bacterium has an obligate relationship with its host, although this must be confirmed.}, }
@article {pmid15126405, year = {2004}, author = {Arnason, E}, title = {Mitochondrial cytochrome B DNA variation in the high-fecundity atlantic cod: trans-atlantic clines and shallow gene genealogy.}, journal = {Genetics}, volume = {166}, number = {4}, pages = {1871-1885}, pmid = {15126405}, issn = {0016-6731}, mesh = {Analysis of Variance ; Animals ; Atlantic Ocean ; Base Sequence ; Cytochromes b/*genetics ; Fertility/*genetics ; Fishes/*genetics/physiology ; *Genetic Variation ; *Genetics, Population ; Geography ; Haplotypes/genetics ; Molecular Sequence Data ; *Phylogeny ; Population Density ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {An analysis of sequence variation of 250 bp of the mitochondrial cytochrome b gene of 1278 Atlantic cod Gadus morhua ranging from Newfoundland to the Baltic shows four high-frequency (>8%) haplotypes and a number of rare and singleton haplotypes. Variation is primarily synonymous mutations. Natural selection acting directly on these variants is either absent or very weak. Common haplotypes show regular trans-Atlantic clines in frequencies and each of them reaches its highest frequency in a particular country. A shallow multifurcating constellation gene genealogy implies young age and recent turnover of polymorphism. Haplotypes characterizing populations at opposite ends of the geographic distribution in Newfoundland and the Baltic are mutationally closest together. The haplotypes are young and have risen rapidly in frequency. Observed differentiation among countries is due primarily to clinal variation. Hypotheses of historical isolation and polymorphisms balanced by local selection and gene flow are unlikely. Instead the results are explained by demic selection of mitochondria carried by highly fit females winning reproductive sweepstakes. By inference the Atlantic cod, a very high-fecundity vertebrate, is characterized by a high variance of offspring number and strong natural selection that leads to very low effective to actual population sizes.}, }
@article {pmid15126279, year = {2004}, author = {Tanaka, M and Takeyasu, T and Fuku, N and Li-Jun, G and Kurata, M}, title = {Mitochondrial genome single nucleotide polymorphisms and their phenotypes in the Japanese.}, journal = {Annals of the New York Academy of Sciences}, volume = {1011}, number = {}, pages = {7-20}, doi = {10.1007/978-3-662-41088-2_2}, pmid = {15126279}, issn = {0077-8923}, mesh = {Brain/physiology ; DNA, Mitochondrial/*genetics ; Haplotypes ; Humans ; Japan ; Life Expectancy ; Male ; Mitochondria/*genetics/metabolism ; Mitochondrial Proteins/chemistry/genetics ; Nucleic Acid Conformation ; Obesity/genetics/metabolism ; Phenotype ; Phylogeny ; *Polymorphism, Single Nucleotide ; Protein Conformation ; }, abstract = {Polymorphisms in the human mitochondrial genome have been used for the elucidation of phylogenetic relationships among various ethnic groups. Because analysis by mitochondrial genetics has detected pathogenic mutations causing mitochondrial encephalomyopathy or cardiomyopathy, most of the mitochondrial single nucleotide polymorphisms (mtSNPs) found in control subjects have been regarded as merely normal variants. However, we cannot exclude the possibility that the mitochondrial functional differences among individuals are ascribable at least in part to the mtSNPs of each individual. Human lifespan in ancient history was much shorter than that at the present time. Therefore, it is reasonable to speculate that certain mtSNPs that predispose one toward susceptibility to adult- or elderly-onset diseases, such as Parkinson's disease and Alzheimer's disease, have never been a target for natural selection in the past. Similarly, thrifty mtSNPs that had been advantageous for survival under severe famine or cold climate conditions might turn out to be related to satiation-related diseases, such as diabetes mellitus and obesity. To examine these hypotheses, we have constructed a mtSNP database by sequencing the entire mitochondrial genomes of 672 subjects: 96 in each of seven groups (i.e., centenarians, young obese or non-obese subjects, diabetic patients with or without major vascular involvement, patients with Parkinson's disease, and those with Alzheimer's disease).}, }
@article {pmid15126278, year = {2004}, author = {Lee, HK}, title = {Mitochondrial pathogenesis from genes and apoptosis to aging and disease. Overview.}, journal = {Annals of the New York Academy of Sciences}, volume = {1011}, number = {}, pages = {1-6}, doi = {10.1196/annals.1293.001}, pmid = {15126278}, issn = {0077-8923}, mesh = {Apoptosis/physiology ; Biological Evolution ; DNA, Mitochondrial/genetics/metabolism ; *DNA-Binding Proteins ; Diabetes Mellitus/metabolism/physiopathology ; Humans ; *Mitochondria/genetics/metabolism ; Mitochondrial Diseases/diagnosis/physiopathology/therapy ; *Mitochondrial Proteins ; *Nuclear Proteins ; Transcription Factors/metabolism ; }, }
@article {pmid15120408, year = {2004}, author = {Megens, HJ and van Moorsel, CH and Piel, WH and Pierce, NE and de Jong, R}, title = {Tempo of speciation in a butterfly genus from the Southeast Asian tropics, inferred from mitochondrial and nuclear DNA sequence data.}, journal = {Molecular phylogenetics and evolution}, volume = {31}, number = {3}, pages = {1181-1196}, doi = {10.1016/j.ympev.2003.10.002}, pmid = {15120408}, issn = {1055-7903}, mesh = {Animals ; Asia, Southeastern ; Base Sequence ; Butterflies/*genetics ; Cell Nucleus/*genetics/metabolism ; *DNA, Mitochondrial ; Evolution, Molecular ; Likelihood Functions ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; Time Perception ; }, abstract = {Molecular systematics is frequently beset with phylogenetic results that are not fully resolved. Researchers either state that the absence of resolution is due to character conflict, explosive speciation, or some combination of the two, but seldom do they carefully examine their data to distinguish between these causes. In this study, we exhaustively analyze a set of nuclear and mitochondrial nucleotide data for the Asian tropical butterfly genus Arhopala so as to highlight the causes of polytomies in the phylogenetic trees, and, as a result, to infer important biological events in the history of this genus. We began by using non-parametric statistical methods to determine whether the ambiguously resolved regions in these trees represent hard or soft polytomies. In addition we determined how this correlated to number of inferred changes on branches, using parametric maximum likelihood estimations. Based on congruent patterns in both mitochondrial and nuclear DNA sequences, we concluded that at two stages in the history of Arhopala there have been accelerated instances of speciation. One event, at the base of the phylogeny, generated many of the groups and subgroups currently recognized in this genus, while a later event generated another major clade consisting of both Oriental and Papuan species groups. Based on comparisons of closely related taxa, the ratio of instantaneous rate of evolution between mitochondrial and nuclear DNA evolution is established at approximately 3:1. The earliest radiation is dated between 7 and 11 Ma by a molecular clock analysis, setting the events generating much of the diversity of Arhopala at well before the Pleistocene. Periodical flooding of the Sunda plateau during interglacial periods was, therefore, not responsible for generating the major divisions in the genus Arhopala. Instead, we hypothesize that large-scale climatic changes taking place in the Miocene have induced the early acceleration in speciation.}, }
@article {pmid15120404, year = {2004}, author = {Juste, J and Ibáñez, C and Muñoz, J and Trujillo, D and Benda, P and Karataş, A and Ruedi, M}, title = {Mitochondrial phylogeography of the long-eared bats (Plecotus) in the Mediterranean Palaearctic and Atlantic Islands.}, journal = {Molecular phylogenetics and evolution}, volume = {31}, number = {3}, pages = {1114-1126}, doi = {10.1016/j.ympev.2003.10.005}, pmid = {15120404}, issn = {1055-7903}, mesh = {Animals ; Atlantic Islands ; Chiroptera/*genetics ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Genetics, Population ; Geography ; Mediterranean Region ; Mitochondria/*genetics ; Paleontology ; *Phylogeny ; Species Specificity ; }, abstract = {Long-eared bats of the genus Plecotus are widespread and common over most of the western Palaearctic. Based on recent molecular evidence, they proved to represent a complex of several cryptic species, with three new species being described from Europe in 2002. Evolutionary relationships among the different lineages are still fragmentary because of the limited geographic coverage of previous studies. Here we analyze Plecotus mitochondrial DNA sequences from the entire Mediterranean region and Atlantic Islands. Phylogenetic reconstructions group these western Palaearctic Plecotus into two major clades which split at least 5 Myr ago and that are each subdivided into further subgroups. An 'auritus group' includes the traditional P. auritus species and its sister taxon P. macrobullaris (=P. alpinus) plus related specimens from the Middle East. P. auritus and P. macrobullaris have broadly overlapping distributions in Europe, although the latter is apparently more restricted to mountain ranges. The other major clade, the 'austriacus group,' includes the European species P. austriacus and at least two other related taxa from North Africa (including P. teneriffae from the Canary Islands), the Balkans and Anatolia (P. kolombatovici). The sister species of this 'austriacus group' is P. balensis, an Ethiopian endemic. Phylogenetic reconstructions further suggest that P. austriacus reached Madeira during its relatively recent westward expansion through Europe, while the Canary Islands were colonized by a North African ancestor. Although colonization of the two groups of Atlantic Islands by Plecotus bats followed very distinct routes, neither involved lineages from the 'auritus group.' Furthermore, the Strait of Gibraltar perfectly segregates the distinct lineages, which confirms its key role as a geographic barrier. This study also stresses the biogeographical importance of the Mediterranean region, and particularly of North Africa, in understanding the evolution of the western Palaearctic biotas.}, }
@article {pmid15120395, year = {2004}, author = {Peng, Z and He, S and Zhang, Y}, title = {Phylogenetic relationships of glyptosternoid fishes (Siluriformes: Sisoridae) inferred from mitochondrial cytochrome b gene sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {31}, number = {3}, pages = {979-987}, doi = {10.1016/j.ympev.2003.10.023}, pmid = {15120395}, issn = {1055-7903}, mesh = {Animals ; Bayes Theorem ; Catfishes/*genetics ; Cytochromes b/*genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Likelihood Functions ; Mitochondria/*metabolism ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {To explore phylogenetic relationships among glyptosternoid fishes, we determined nucleotide sequences of the complete mitochondrial cytochrome b gene region (1138 base pair). Thirteen species of glyptosternoid fishes and six species of non-glyptosternoids represent 10 sisorid genera were examined. Molecular phylogenetic trees were constructed using the maximum parsimony, minimum evolution, maximum likelihood, and Bayesian methods. Bayesian and maximum likelihood analyses support the monophyly of glyptosternoids, but our hypothesis of internal relationships differs from previous hypothesis. Results indicated that glyptosternoid is a monophyletic group and genera Glyptosternum and Exostoma are two basal species having a primitive position among it. Genera Euchiloglanis and Pareuchiloglanis form a sister-group. Then they form a sister-group with Pseudexostoma plus Oreoglanis. Our result also found that Pareuchiloglanis anteanalis might be considered as the synonyms of Parechiloglanis sinensis, and genus Euchiloglanis might have only one valid species, Euchiloglanis davidi.}, }
@article {pmid15120393, year = {2004}, author = {Hodges, WL and Zamudio, KR}, title = {Horned lizard (Phrynosoma) phylogeny inferred from mitochondrial genes and morphological characters: understanding conflicts using multiple approaches.}, journal = {Molecular phylogenetics and evolution}, volume = {31}, number = {3}, pages = {961-971}, doi = {10.1016/j.ympev.2003.11.005}, pmid = {15120393}, issn = {1055-7903}, mesh = {Animals ; Cytochromes b/genetics ; DNA, Mitochondrial/*genetics ; Lizards/*genetics ; Mitochondria/metabolism ; NADH Dehydrogenase/genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The genus Phrynosoma includes 13 species of North American lizards characterized by unique and highly derived morphologies and ecologies. Understanding interspecific relationships within this genus is essential for testing hypotheses about character evolution in this group. We analyzed mitochondrial ND4 and cytochrome b gene sequence data from all species of Phrynosoma in conjunction with a previously published dataset including 12S and 16S rRNA gene sequences and morphological characters. We used multiple phylogenetic methods and diagnostic tests for data combinability and taxonomic congruence to investigate the data in separate and combined analyses. Separate data partitions resulted in several well-supported lineages, but taxonomic congruence was lacking between topologies from separate and combined analyses. Partitioned Bremer support analyses also reveals conflict between data partitions in certain tree regions. When taxa associated with well-supported clades were removed from analyses, phylogenetic signal was lost. Combined, our results initially suggest conflict between data partitions, but further tests show the data are only appropriate for phylogenetic reconstruction of those parts of the topology that were well resolved. Nonetheless, our data analyses reveal five well-supported clades: (1) Phrynosoma ditmarsi and Phrynosoma hernandesi, (2) P. ditmarsi, P. hernandesi, and Phrynosoma douglasii, (3) P. ditmarsi, P. hernandesi, P. douglasii, and Phrynosoma orbiculare, (4) Phrynosoma mcallii and Phrynosoma platyrhinos, and (5) Phrynosoma braconnieri and Phrynosoma taurus.}, }
@article {pmid15120381, year = {2004}, author = {Lumbsch, HT and Schmitt, I and Palice, Z and Wiklund, E and Ekman, S and Wedin, M}, title = {Supraordinal phylogenetic relationships of Lecanoromycetes based on a Bayesian analysis of combined nuclear and mitochondrial sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {31}, number = {3}, pages = {822-832}, doi = {10.1016/j.ympev.2003.11.001}, pmid = {15120381}, issn = {1055-7903}, mesh = {Ascomycota/genetics/*metabolism ; Bayes Theorem ; Cell Nucleus/*metabolism ; DNA/chemistry ; DNA, Ribosomal/chemistry ; Databases as Topic ; Mitochondria/*metabolism ; Monte Carlo Method ; Phylogeny ; Species Specificity ; }, abstract = {Phylogenetic relationships of lichen-forming discomycetes and their relatives in the class Lecanoromycetes were examined by using nuclear large subunit and mitochondrial small subunit ribosomal DNA sequences. Ninety-eight partial sequences of 53 ascomycetes were generated and aligned with the corresponding sequences retrieved from GenBank resulting in an alignment of 100 taxa that was analyzed using a Bayesian approach with Markov chain Monte Carlo (B/MCMC) methods. The analysis revealed the monophyly of the Lecanoromycetes with two major clades: one clade including the monophyletic orders Graphidales and Ostropales and the paraphyletic Gyalectales, the other clade including the monophyletic Lecanorales (incl. Caliciales, Peltigerales, and Teloschistales) and a clade containing the polyphyletic Agyriales, a yet undescribed order Umbilicariales (including Elixiaceae and Umbilicariaceae), and Pertusariales. The monophyly of the Pertusariales was not resolved. Testing of alternative hypotheses revealed that a placement of Chaetothyriomycetes and Eurotiomycetes within Lecanoromycetes and the monophyly of Agyriales s. lat. (incl. Elixiaceae and Schaereriaceae) and Ostropales s. lat. (incl. Graphidales) can be rejected, while monophyly of Gyalectales and the Pertusariales and placement of Umbilicariales on the Lecanorales branch cannot be rejected with the current data set.}, }
@article {pmid15120112, year = {2004}, author = {Hourton-Cabassa, C and Rita Matos, A and Zachowski, A and Moreau, F}, title = {The plant uncoupling protein homologues: a new family of energy-dissipating proteins in plant mitochondria.}, journal = {Plant physiology and biochemistry : PPB}, volume = {42}, number = {4}, pages = {283-290}, doi = {10.1016/j.plaphy.2004.01.007}, pmid = {15120112}, issn = {0981-9428}, mesh = {Carrier Proteins/chemistry/genetics/metabolism ; Energy Metabolism ; Ion Channels ; Membrane Proteins/chemistry/genetics/metabolism ; Mitochondrial Proteins/chemistry/*genetics/*metabolism ; Phylogeny ; Plant Proteins/chemistry/*genetics/*metabolism ; Uncoupling Protein 1 ; }, abstract = {Uncoupling proteins (UCPs) form a subfamily within the mitochondrial carrier protein family, which catalyze a free fatty acid-mediated proton recycling and can modulate the tightness of coupling between mitochondrial respiration and ATP synthesis. As in mammalian tissues, UCPs are rather ubiquitous in the plant kingdom and widespread in plant tissues in which they could have various physiological roles, such as heat production or protection against free oxygen radicals. The simultaneous occurrence in plant mitochondria of two putative energy-dissipating systems, namely UCP which dissipates the proton motive force, and alternative oxidase (AOX) which dissipates the redox potential, raises the question of their functional interactions.}, }
@article {pmid15115550, year = {2004}, author = {Bukovsky, A and Caudle, MR and Svetlikova, M and Upadhyaya, NB}, title = {Origin of germ cells and formation of new primary follicles in adult human ovaries.}, journal = {Reproductive biology and endocrinology : RB&amp;E}, volume = {2}, number = {}, pages = {20}, pmid = {15115550}, issn = {1477-7827}, mesh = {Adult ; *Cell Differentiation ; Cell Movement ; Epithelial Cells/cytology/enzymology/metabolism ; Female ; Humans ; Immunohistochemistry ; Mesoderm/cytology/enzymology/metabolism ; Mitogen-Activated Protein Kinases/metabolism ; Models, Biological ; Oocytes/*cytology/enzymology/metabolism ; Oogenesis ; Ovarian Follicle/*cytology/*growth &amp; development/pathology ; Thy-1 Antigens/analysis ; }, abstract = {Recent reports indicate that functional mouse oocytes and sperm can be derived in vitro from somatic cell lines. We hypothesize that in adult human ovaries, mesenchymal cells in the tunica albuginea (TA) are bipotent progenitors with a commitment for both primitive granulosa and germ cells. We investigated ovaries of twelve adult women (mean age 32.8 +/- 4.1 SD, range 27-38 years) by single, double, and triple color immunohistochemistry. We show that cytokeratin (CK)+ mesenchymal cells in ovarian TA differentiate into surface epithelium (SE) cells by a mesenchymal-epithelial transition. Segments of SE directly associated with ovarian cortex are overgrown by TA, forming solid epithelial cords, which fragment into small (20 micron) epithelial nests descending into the lower ovarian cortex, before assembling with zona pellucida (ZP)+ oocytes. Germ cells can originate from SE cells which cover the TA. Small (10 micron) germ-like cells showing PS1 meiotically expressed oocyte carbohydrate protein are derived from SE cells via asymmetric division. They show nuclear MAPK immunoexpression, subsequently divide symmetrically, and enter adjacent cortical vessels. During vascular transport, the putative germ cells increase to oocyte size, and are picked-up by epithelial nests associated with the vessels. During follicle formation, extensions of granulosa cells enter the oocyte cytoplasm, forming a single paranuclear CK+ Balbiani body supplying all the mitochondria of the oocyte. In the ovarian medulla, occasional vessels show an accumulation of ZP+ oocytes (25-30 microns) or their remnants, suggesting that some oocytes degenerate. In contrast to males, adult human female gonads do not preserve germline type stem cells. This study expands our previous observations on the formation of germ cells in adult human ovaries. Differentiation of primitive granulosa and germ cells from the bipotent mesenchymal cell precursors of TA in adult human ovaries represents a most sophisticated adaptive mechanism created during the evolution of female reproduction. Our data indicate that the pool of primary follicles in adult human ovaries does not represent a static but a dynamic population of differentiating and regressing structures. An essential mission of such follicular turnover might be elimination of spontaneous or environmentally induced genetic alterations of oocytes in resting primary follicles.}, }
@article {pmid15112735, year = {2004}, author = {Hejl, AM and Koster, KL}, title = {Juglone disrupts root plasma membrane H+-ATPase activity and impairs water uptake, root respiration, and growth in soybean (Glycine max) and corn (Zea mays).}, journal = {Journal of chemical ecology}, volume = {30}, number = {2}, pages = {453-471}, pmid = {15112735}, issn = {0098-0331}, mesh = {Enzyme Inhibitors/*pharmacology ; Naphthoquinones/*pharmacology ; Oxygen/metabolism ; Peptidylprolyl Isomerase/antagonists &amp; inhibitors ; Plant Roots/physiology ; Potassium Channel Blockers ; Proton-Translocating ATPases/antagonists &amp; inhibitors/*pharmacology ; Glycine max/*growth &amp; development/physiology ; Water-Electrolyte Balance ; Zea mays/physiology ; }, abstract = {Juglone is phytotoxic, but the mechanisms of growth inhibition have not been fully explained. Previous studies have proposed that disruption of electron transport functions in mitochondria and chloroplasts contribute to observed growth reduction in species exposed to juglone. In studies reported here, corn and soybean seedlings grown in nutrient solution amended with 10, 50, or 100 microM juglone showed significant decreases in root and shoot dry weights and lengths with increasing concentrations. However, no significant differences in leaf chlorophyll fluorescence or CO2-dependent leaf oxygen evolution were observed, even in seedlings that were visibly affected. Disruption of root oxygen uptake was positively correlated with increasing concentrations of juglone, suggesting that juglone may reach mitochondria in root cells. Water uptake and acid efflux also decreased for corn and soybean seedlings treated with juglone, suggesting that juglone may affect metabolism of root cells by disrupting root plasma membrane function. Therefore, the effect of juglone on H+-ATPase activity in corn and soybean root microsomes was tested. Juglone treatments from 10 to 1000 microM significantly reduced H+-ATPase activity compared to controls. This inhibition of H+-ATPase activity and observed reduction of water uptake offers a logical explanation for previously documented phytotoxicity of juglone. Impairment of this enzyme's activity could affect plant growth in a number of ways because proton-pumping in root cells drives essential plant processes such as solute uptake and, hence, water uptake.}, }
@article {pmid15112236, year = {2004}, author = {Bazinet, C}, title = {Endosymbiotic origins of sex.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {26}, number = {5}, pages = {558-566}, doi = {10.1002/bies.20023}, pmid = {15112236}, issn = {0265-9247}, support = {HD36498-01/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Gene Transfer, Horizontal ; Germ Cells/physiology ; Mitochondria/metabolism ; *Reproduction ; Reproduction, Asexual ; Sperm Motility ; Spermatogenesis/physiology ; *Symbiosis ; }, abstract = {Understanding how complex sexual reproduction arose, and why sexual organisms have been more successful than otherwise similar asexual organisms, is a longstanding problem in evolutionary biology. Within this problem, the potential role of endosymbionts or intracellular pathogens in mediating primitive genetic transfers is a continuing theme. In recent years, several remarkable activities of mitochondria have been observed in the germline cells of complex eukaryotes, and it has been found that bacterial endosymbionts related to mitochondria are capable of manipulating diverse aspects of metazoan gametogenesis. An attempt is made here to rationalize these observations with an endosymbiotic model for the evolutionary origins of sex. It is hypothesized that the contemporary life cycle of germline cells has descended from the life cycle of the endosymbiotic ancestor of the mitochondrion. Through an actin-based motility that drove it from one cell to another, the rickettsial ancestor of mitochondria may have functioned as a primitive transducing particle, the evolutionary progenitor of sperm.}, }
@article {pmid15096574, year = {2004}, author = {Zhang, H and Meng, LH and Zimonjic, DB and Popescu, NC and Pommier, Y}, title = {Thirteen-exon-motif signature for vertebrate nuclear and mitochondrial type IB topoisomerases.}, journal = {Nucleic acids research}, volume = {32}, number = {7}, pages = {2087-2092}, pmid = {15096574}, issn = {1362-4962}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cell Nucleus/*enzymology ; Cluster Analysis ; Conserved Sequence/genetics ; DNA Topoisomerases, Type I/*genetics ; *Evolution, Molecular ; Exons/*genetics ; Gene Duplication ; Humans ; In Situ Hybridization, Fluorescence ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Vertebrates/genetics ; }, abstract = {DNA topoisomerases contribute to various cellular activities that involve DNA. We previously identified a human nuclear gene that encodes a mitochondrial DNA topoisomerase. Here we show that genes for mitochondrial DNA topoisomerases (type IB) exist only in vertebrates. A 13-exon topoisomerase motif was identified as a characteristic of genes for both nuclear and mitochondrial type IB topoisomerases. The presence of this signature motif is thus an indicator of the coexistence of nuclear and mitochondrial type IB DNA topoisomerases. We hypothesize that the prototype topoisomerase IB with the 13-exon structure formed first, and then duplicated. One topoisomerase specialized for nuclear DNA and the other for mitochondrial DNA.}, }
@article {pmid15094398, year = {2004}, author = {Sona, S and Suzuki, T and Ellington, WR}, title = {Cloning and expression of mitochondrial and protoflagellar creatine kinases from a marine sponge: implications for the origin of intracellular energy transport systems.}, journal = {Biochemical and biophysical research communications}, volume = {317}, number = {4}, pages = {1207-1214}, doi = {10.1016/j.bbrc.2004.03.176}, pmid = {15094398}, issn = {0006-291X}, mesh = {Amino Acid Sequence ; Animals ; Biological Transport ; Ciona intestinalis/enzymology ; Cloning, Molecular ; Creatine Kinase/*biosynthesis/chemistry/*genetics ; Cytoplasm/*enzymology ; Dimerization ; Energy Metabolism ; Escherichia coli/metabolism ; Isoenzymes ; Mice ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Polychaeta/enzymology ; Porifera/*enzymology ; Recombinant Proteins/biosynthesis/chemistry/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Creatine kinase (CK) plays a central role in energy transactions in cells displaying high and variable rates of ATP turnover. Cytoplasmic and mitochondrial CK genes code for isoforms which are targeted to distinct intracellular compartments often in close physical proximity to sites of ATP hydrolysis or synthesis. In certain lower groups a third CK gene is present which codes for a flagellar CK isoform consisting of three complete, fused CK domains. Recent work has shown that cytoplasmic, mitochondrial, and flagellar CKs are present in protochordates and in deuterostome and protostome invertebrates. We report here that the marine sponge Tethya aurantia, a representative of the oldest of all multi-cellular animal groups, expresses three unique CK transcripts. One of these CK transcripts codes for protein that has a mitochondrial targeting sequence and in a phylogenetic analysis is positioned at the base of the cluster containing mitochondrial CK sequences from invertebrates, protochordates, and vertebrates; it is clearly a mitochondrial CK. When expressed in Escherichia coli the mitochondrial form from T. aurantia was found to be dimeric unlike all other mitochondrial CKs which are typically octameric. The other two T. aurantia transcripts code for proteins that appear to be more closely related to flagellar CKs. These protoflagellar CKs were found to be dimers when expressed in Escherichia coli. Sponges last shared a common ancestor with higher animals as long as one billion years ago. The antiquity of intracellular localization, as evidenced by the presence of a true mitochondrial CK and protoflagellar CKs in the sponge T. aurantia, indicates that physical constraints on cellular energy transport were key, early driving forces in the evolution of this key enzyme system.}, }
@article {pmid15093244, year = {2004}, author = {Orrenius, S}, title = {Mitochondrial regulation of apoptotic cell death.}, journal = {Toxicology letters}, volume = {149}, number = {1-3}, pages = {19-23}, doi = {10.1016/j.toxlet.2003.12.017}, pmid = {15093244}, issn = {0378-4274}, mesh = {Adenosine Triphosphate/physiology ; Animals ; Apoptosis/*physiology ; Caspases/physiology ; Environmental Pollutants/toxicity ; Humans ; Mitochondria/*physiology ; }, abstract = {Although it has long been known that impairment of mitochondrial function may lead to ATP depletion and necrotic cell death, recent work has revealed that these organelles also play an important role in the regulation of apoptotic cell death by mechanisms which have been conserved through evolution. Thus, it seems that a number of toxicants target the mitochondria and promote their release of cytochrome c and other pro-apoptotic proteins, which can trigger caspase activation and other parts of the apoptotic process. Cytochrome c release is governed by the Bcl-2 family of proteins, whereas subsequent caspase activation is modulated by other proteins, including inhibitor of apoptosis proteins (IAPs) and heat shock proteins. Recent findings indicate that cytochrome c extrusion occurs by a two-step process, which is initiated by a disruption of the association of the hemoprotein with cardiolipin, the phospholipid that anchors it to the outer surface of the inner mitochondrial membrane. Release of the solubilized pool of cytochrome c into the cytosol may then occur by permeabilization of the outer mitochondrial membrane mediated by pro-apoptotic Bcl-2 family proteins, notably Bax and Bak, or by Ca2+-triggered mitochondrial permeability transition. Taken together, these findings have placed the mitochondria in the focus of apoptosis research and further underlined the important function of these organelles in cell life and death.}, }
@article {pmid15087133, year = {2004}, author = {Atteia, A and van Lis, R and van Hellemond, JJ and Tielens, AG and Martin, W and Henze, K}, title = {Identification of prokaryotic homologues indicates an endosymbiotic origin for the alternative oxidases of mitochondria (AOX) and chloroplasts (PTOX).}, journal = {Gene}, volume = {330}, number = {}, pages = {143-148}, doi = {10.1016/j.gene.2004.01.015}, pmid = {15087133}, issn = {0378-1119}, mesh = {Alphaproteobacteria/enzymology/genetics ; Amino Acid Sequence ; Animals ; Chloroplasts/drug effects/*enzymology ; Cyanobacteria/enzymology/genetics ; *Evolution, Molecular ; Mitochondria/*enzymology ; Mitochondrial Proteins ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Phylogeny ; Plant Proteins ; Prokaryotic Cells/enzymology/*metabolism ; Salicylamides/pharmacology ; Sequence Homology, Amino Acid ; Symbiosis/*genetics ; }, abstract = {The alternative oxidase is a ubiquinol oxidase that has been found to date in the mitochondrial respiratory chain of plants, some fungi and protists. Because of its sparse distribution among eukaryotic lineages and because of its diversity in regulatory mechanisms, the origin of AOX has been a mystery, particularly since no prokaryotic homologues have previously been identified. Here we report the identification of a gene encoding a clear homologue of the mitochondrial alternative oxidase in an alpha-proteobacterium, and the identification of three cyanobacterial genes that encode clear homologues of the plastid-specific alternative oxidase of plants and algae. These findings suggest that the eukaryotic nuclear genes for the alternative oxidases of mitochondria and chloroplasts were acquired via endosymbiotic gene transfer from the eubacterial ancestors of these two organelles, respectively.}, }
@article {pmid15086795, year = {2004}, author = {Emanuel, C and Weihe, A and Graner, A and Hess, WR and Börner, T}, title = {Chloroplast development affects expression of phage-type RNA polymerases in barley leaves.}, journal = {The Plant journal : for cell and molecular biology}, volume = {38}, number = {3}, pages = {460-472}, doi = {10.1111/j.0960-7412.2004.02060.x}, pmid = {15086795}, issn = {0960-7412}, mesh = {Amino Acid Sequence ; Chloroplasts/*enzymology/genetics/physiology ; Cloning, Molecular ; DNA, Complementary/chemistry/genetics ; DNA, Plant/chemistry/genetics ; DNA-Directed RNA Polymerases/*genetics/metabolism ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Hordeum/*enzymology/genetics/growth &amp; development ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Plant Leaves/*enzymology/genetics/growth &amp; development ; Plant Proteins/genetics/metabolism ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Transcription Factors/genetics/metabolism ; }, abstract = {We have identified the barley gene and cDNA encoding the plastid phage-type RNA polymerase (RNAP), nuclear-encoded plastid RNAP (RpoTp), and the nearly full-length cDNA of the mitochondrial RNAP, nuclear-encoded mitochondrial RNAP (RpoTm). RpoTp spans more than 9000 nt, consists of 19 exons and 18 introns, gives rise to a 3632-nt mRNA and is localized to the long arm of chromosome 1 (7H). The length of the deduced polypeptide is 948 residues. The mRNA levels of RpoTp and RpoTm were determined in roots and primary leaf sections of 7-day-old barley seedlings of the albostrians mutant, which were either phenotypically normal and exhibited a gradient of chloroplast development, or contained ribosome-deficient undifferentiated plastids. Transcript levels of RpoTp and RpoTm in almost all sections reached higher concentrations in plastid ribosome-deficient leaves than in the wild-type material, except in the most basal part of the leaf. These data indicate a role of plastid-to-nucleus signalling in the expression of the two RpoT genes. The mRNA levels of the plastid genes, beta-subunit of plastid-encoded RNAP (rpoB), proteolytic subunit of the Clp protease (clpP) and ribosomal protein Rpl2 (rpl2), all known to be transcribed by the nuclear-encoded RNAP (NEP), followed closely the pattern of RpoTp mRNA accumulation, strongly suggesting that RpoTp and NEP are identical. Transcripts of RpoTm and RpoTm-transcribed mitochondrial genes cytochrome oxidase subunit 2 (coxII) and ATPase subunit 9 (atp9) accumulated to the highest levels in the most basal parts of the leaf and declined considerably towards the leaf tip with a pronounced reduction in green versus white leaves. Our data revealed a marked influence of the developmental stage of the plastid on the expression and activity of organellar phage-type RNAPs and their target genes. Thus, interorganellar cross-talk in the regulated expression of nuclear-encoded plastid and mitochondrial RNAP genes might be a key element governing the concerted expression of genes located within plastids, mitochondria and the nucleus of the plant cell.}, }
@article {pmid15084303, year = {2004}, author = {Jarvis, P}, title = {Organellar proteomics: chloroplasts in the spotlight.}, journal = {Current biology : CB}, volume = {14}, number = {8}, pages = {R317-9}, doi = {10.1016/j.cub.2004.03.054}, pmid = {15084303}, issn = {0960-9822}, mesh = {Arabidopsis/genetics/*physiology ; Arabidopsis Proteins/*metabolism ; *Biological Evolution ; Chloroplasts/*genetics ; Mitochondria/genetics ; Protein Sorting Signals/physiology ; *Proteomics ; }, }
@article {pmid15082931, year = {2003}, author = {McDonald, AE and Amirsadeghi, S and Vanlerberghe, GC}, title = {Prokaryotic orthologues of mitochondrial alternative oxidase and plastid terminal oxidase.}, journal = {Plant molecular biology}, volume = {53}, number = {6}, pages = {865-876}, pmid = {15082931}, issn = {0167-4412}, mesh = {Amino Acid Sequence ; Anabaena/enzymology/*genetics ; Arabidopsis Proteins/genetics ; Blotting, Northern ; Blotting, Southern ; Conserved Sequence/genetics ; DNA, Bacterial/genetics ; Eukaryotic Cells/enzymology ; Gene Expression Regulation, Enzymologic ; Mitochondria/enzymology ; Mitochondrial Proteins ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Phylogeny ; Plant Proteins ; Prokaryotic Cells/enzymology ; RNA, Bacterial/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {The mitochondrial alternative oxidase (AOX) and the plastid terminal oxidase (PTOX) are two similar members of the membrane-bound diiron carboxylate group of proteins. AOX is a ubiquinol oxidase present in all higher plants, as well as some algae, fungi, and protists. It may serve to dampen reactive oxygen species generation by the respiratory electron transport chain. PTOX is a plastoquinol oxidase in plants and some algae. It is required in carotenoid biosynthesis and may represent the elusive oxidase in chlororespiration. Recently, prokaryotic orthologues of both AOX and PTOX proteins have appeared in sequence databases. These include PTOX orthologues present in four different cyanobacteria as well as an AOX orthologue in an alpha-proteobacterium. We used PCR, RT-PCR and northern analyses to confirm the presence and expression of the PTOX gene in Anabaena variabilis PCC 7120. An extensive phylogeny of newly found prokaryotic and eukaryotic AOX and PTOX proteins supports the idea that AOX and PTOX represent two distinct groups of proteins that diverged prior to the endosymbiotic events that gave rise to the eukaryotic organelles. Using multiple sequence alignment, we identified residues conserved in all AOX and PTOX proteins. We also provide a scheme to readily distinguish PTOX from AOX proteins based upon differences in amino acid sequence in motifs around the conserved iron-binding residues. Given the presence of PTOX in cyanobacteria, we suggest that this acronym now stand for plastoquinol terminal oxidase. Our results have implications for the photosynthetic and respiratory metabolism of these prokaryotes, as well as for the origin and evolution of eukaryotic AOX and PTOX proteins.}, }
@article {pmid15077304, year = {2004}, author = {Johnson, K and Svensson, CI and Etten, DV and Ghosh, SS and Murphy, AN and Powell, HC and Terkeltaub, R}, title = {Mediation of spontaneous knee osteoarthritis by progressive chondrocyte ATP depletion in Hartley guinea pigs.}, journal = {Arthritis and rheumatism}, volume = {50}, number = {4}, pages = {1216-1225}, doi = {10.1002/art.20149}, pmid = {15077304}, issn = {0004-3591}, support = {3-R01-NS-18715/NS/NINDS NIH HHS/United States ; AR-47347/AR/NIAMS NIH HHS/United States ; P01-AG-07996/AG/NIA NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/*metabolism ; Aging/metabolism/pathology ; Animals ; Cells, Cultured ; Chondrocalcinosis/*metabolism ; Chondrocytes/cytology/*metabolism ; Disease Models, Animal ; Glycosaminoglycans/metabolism ; Guinea Pigs ; Male ; Microscopy, Electron ; Mitochondria/metabolism/ultrastructure ; Nitric Oxide/metabolism ; Osteoarthritis, Knee/*metabolism ; Phosphoric Diester Hydrolases/metabolism ; Pyrophosphatases/metabolism ; Transglutaminases/metabolism ; }, abstract = {OBJECTIVE: Because articular chondrocytes reside in a hypoxic milieu, anaerobic glycolysis is central in generating ATP to support chondrocyte matrix synthesis and viability, with mitochondrial oxidative phosphorylation possibly providing physiologic reserve ATP generation. Nitric oxide (NO) potently suppresses mitochondrial oxidative phosphorylation. Because enhanced cartilage NO generation occurs in osteoarthritis (OA), we systematically tested for mitochondrial dysfunction in the pathogenesis of OA.<br><br>METHODS: We assessed chondrocytes for ATP depletion and for in situ changes in mitochondrial ultrastructure prior to and during the evolution of spontaneous knee OA in male Hartley guinea pigs, a model in which chondrocalcinosis also supervenes.<br><br>RESULTS: Spontaneous NO release from knee cartilage samples in organ culture doubled between ages 2 months and 8 months as knee OA developed. Concomitantly, chondrocyte intracellular ATP levels declined by approximately 50%, despite a lack of mitochondrial ultrastructure abnormalities in knee chondrocytes. As ATP depletion progressed with aging in knee chondrocytes, an increased ratio of lactate to pyruvate was observed, consistent with an adaptive augmentation of glycolysis to mitochondrial dysfunction. Furthermore, we observed progressive elevation of chondrocyte ATP-scavenging nucleotide pyrophosphatase/phosphodiesterase (NPP) activity and extracellular levels of the NPP enzymatic end product inorganic pyrophosphate (PPi), which stimulate chondrocalcinosis.<br><br>CONCLUSION: Profound chondrocyte ATP depletion develops in association with heightened NO generation in guinea pig knee OA. Increased NPP activity and concordant increases in extracellular PPi, which are strongly associated with human aging-associated degenerative arthropathy and directly stimulate chondrocalcinosis, may be primarily driven by chondrocyte ATP depletion. Our findings implicate a decreased mitochondrial bioenergetic reserve as a pathogenic factor in both degenerative arthropathy and chondrocalcinosis in aging.}, }
@article {pmid15075277, year = {2004}, author = {Slapeta, J and Keithly, JS}, title = {Cryptosporidium parvum mitochondrial-type HSP70 targets homologous and heterologous mitochondria.}, journal = {Eukaryotic cell}, volume = {3}, number = {2}, pages = {483-494}, pmid = {15075277}, issn = {1535-9778}, support = {D43 TW000915/TW/FIC NIH HHS/United States ; TW00915-05/TW/FIC NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Cryptosporidium parvum/genetics/*metabolism/ultrastructure ; Escherichia coli Proteins/genetics ; Gene Expression ; HSP70 Heat-Shock Proteins/chemistry/genetics/*metabolism ; Microscopy, Electron, Transmission ; Microscopy, Fluorescence ; Mitochondria/genetics/*metabolism/ultrastructure ; Molecular Sequence Data ; Phylogeny ; Protein Sorting Signals ; Protein Structure, Secondary ; Protein Transport ; Sequence Alignment ; Sporozoites/ultrastructure ; }, abstract = {A mitochondrial HSP70 gene (Cp-mtHSP70) is described for the apicomplexan Cryptosporidium parvum, an agent of diarrhea in humans and animals. Mitochondrial HSP70 is known to have been acquired from the proto-mitochondrial endosymbiont. The amino acid sequence of Cp-mtHSP70 shares common domains with mitochondrial and proteobacterial homologues, including 34 amino acids of an NH2-terminal mitochondrion-like targeting presequence. Phylogenetic reconstruction places Cp-mtHSP70 within the mitochondrial clade of HSP70 homologues. Using reverse transcription-PCR, Cp-mtHSP70 mRNA was observed in C. parvum intracellular stages cultured in HCT-8 cells. Polyclonal antibodies to Cp-mtHSP70 recognize a approximately 70-kDa protein in Western blot analysis of sporozoite extracts. Both fluorescein- and immunogold-labeled anti-Cp-mtHSP70 localize to a single mitochondrial compartment in close apposition to the nucleus. Furthermore, the NH2-terminal presequence of Cp-mtHSP70 can correctly target green fluorescent protein to the single mitochondrion of the apicomplexan Toxoplasma gondii and the mitochondrial network of the yeast Saccharomyces cerevisiae. When this presequence was truncated, the predicted amphiphilic alpha-helix was shown to be essential for import into the yeast mitochondrion. These data further support the presence of a secondarily reduced relict mitochondrion in C. parvum.}, }
@article {pmid15073369, year = {2004}, author = {Dyall, SD and Brown, MT and Johnson, PJ}, title = {Ancient invasions: from endosymbionts to organelles.}, journal = {Science (New York, N.Y.)}, volume = {304}, number = {5668}, pages = {253-257}, doi = {10.1126/science.1094884}, pmid = {15073369}, issn = {1095-9203}, support = {AI27857/AI/NIAID NIH HHS/United States ; }, mesh = {Alphaproteobacteria/genetics/physiology ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Chloroplasts/physiology ; Cyanobacteria/genetics/physiology ; Evolution, Molecular ; Genome ; Genome, Bacterial ; Mitochondria/*physiology ; Organelles/*physiology ; Origin of Life ; Plastids/*physiology ; Proteins/chemistry/metabolism ; *Symbiosis ; }, abstract = {The acquisitions of mitochondria and plastids were important events in the evolution of the eukaryotic cell, supplying it with compartmentalized bioenergetic and biosynthetic factories. Ancient invasions by eubacteria through symbiosis more than a billion years ago initiated these processes. Advances in geochemistry, molecular phylogeny, and cell biology have offered insight into complex molecular events that drove the evolution of endosymbionts into contemporary organelles. In losing their autonomy, endosymbionts lost the bulk of their genomes, necessitating the evolution of elaborate mechanisms for organelle biogenesis and metabolite exchange. In the process, symbionts acquired many host-derived properties, lost much of their eubacterial identity, and were transformed into extraordinarily diverse organelles that reveal complex histories that we are only beginning to decipher.}, }
@article {pmid15071595, year = {2004}, author = {Matsuzaki, M and Misumi, O and Shin-I, T and Maruyama, S and Takahara, M and Miyagishima, SY and Mori, T and Nishida, K and Yagisawa, F and Nishida, K and Yoshida, Y and Nishimura, Y and Nakao, S and Kobayashi, T and Momoyama, Y and Higashiyama, T and Minoda, A and Sano, M and Nomoto, H and Oishi, K and Hayashi, H and Ohta, F and Nishizaka, S and Haga, S and Miura, S and Morishita, T and Kabeya, Y and Terasawa, K and Suzuki, Y and Ishii, Y and Asakawa, S and Takano, H and Ohta, N and Kuroiwa, H and Tanaka, K and Shimizu, N and Sugano, S and Sato, N and Nozaki, H and Ogasawara, N and Kohara, Y and Kuroiwa, T}, title = {Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D.}, journal = {Nature}, volume = {428}, number = {6983}, pages = {653-657}, doi = {10.1038/nature02398}, pmid = {15071595}, issn = {1476-4687}, mesh = {Actins/genetics ; Algal Proteins/classification/genetics ; Cell Nucleus/genetics ; Chromosomes/genetics ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/genetics ; Evolution, Molecular ; *Genome ; Genomics ; Introns/genetics ; Molecular Sequence Data ; Plastids/genetics/physiology ; Rhodophyta/cytology/*genetics ; Sequence Analysis, DNA ; }, abstract = {Small, compact genomes of ultrasmall unicellular algae provide information on the basic and essential genes that support the lives of photosynthetic eukaryotes, including higher plants. Here we report the 16,520,305-base-pair sequence of the 20 chromosomes of the unicellular red alga Cyanidioschyzon merolae 10D as the first complete algal genome. We identified 5,331 genes in total, of which at least 86.3% were expressed. Unique characteristics of this genomic structure include: a lack of introns in all but 26 genes; only three copies of ribosomal DNA units that maintain the nucleolus; and two dynamin genes that are involved only in the division of mitochondria and plastids. The conserved mosaic origin of Calvin cycle enzymes in this red alga and in green plants supports the hypothesis of the existence of single primary plastid endosymbiosis. The lack of a myosin gene, in addition to the unexpressed actin gene, suggests a simpler system of cytokinesis. These results indicate that the C. merolae genome provides a model system with a simple gene composition for studying the origin, evolution and fundamental mechanisms of eukaryotic cells.}, }
@article {pmid15065427, year = {2004}, author = {Palenko, MV and Mukha, DV and Zakharov, IA}, title = {[Variability of the mitochondrial gene for cytochrome oxidase I within the Adalia bipunctata species and within species of ladybird beetles (Coleoptera: Coccinellidae)].}, journal = {Genetika}, volume = {40}, number = {2}, pages = {205-209}, pmid = {15065427}, issn = {0016-6758}, mesh = {Animals ; Base Sequence ; Coleoptera/classification/*genetics ; DNA ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Intergeneric, interspecific, and intraspecific genetic variation of the 310-bp 3'-end region of the mitochondrial gene of cytochrome oxidase I (COI) has been assessed in ladybirds (Coleoptera: Coccinnellidae). The phylogenetic distances between eight species of ladybirds have been determined. Mitochondrial DNA (mtDNA) nucleotide sequences have been compared in Adalia bipunctata L. differing in the elytron and pronotum colors that have been sampled from several geographically remote populations. The taxonomic statuses of two morphs from the genus Adalia, A. bipunctata bipunctata and A. bipunctata fasciatopunctata, have been identified.}, }
@article {pmid15062797, year = {2004}, author = {Dreyer, H and Steiner, G}, title = {The complete sequence and gene organization of the mitochondrial genome of the gadilid scaphopod Siphonondentalium lobatum (Mollusca).}, journal = {Molecular phylogenetics and evolution}, volume = {31}, number = {2}, pages = {605-617}, doi = {10.1016/j.ympev.2003.08.007}, pmid = {15062797}, issn = {1055-7903}, mesh = {Amino Acid Sequence ; Animals ; Codon/genetics ; DNA, Mitochondrial/*genetics ; Gene Order/genetics ; *Genome ; Mitochondria/genetics ; Molecular Sequence Data ; Mollusca/*classification/*genetics ; *Phylogeny ; Proteins/genetics ; RNA, Transfer/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; }, abstract = {Comparisons of mitochondrial gene sequences and gene arrangements can be informative for reconstructing high-level phylogenetic relationships. We determined the complete sequence of the mitochondrial genome of Siphonodentalium lobatum, (Mollusca, Scaphopoda). With only 13,932 bases, it is the shortest molluscan mitochondrial genome reported so far. The genome contains the usual 13 protein-coding genes, two rRNA and 22 tRNA genes. The ATPase subunit 8 gene is exceptionally short. Several transfer RNAs show truncated TpsiC arms or DHU arms. The gene arrangement of S. lobatum is markedly different from all other known molluscan mitochondrial genomes and shows low similarity even to an unpublished gene order of a dentaliid scaphopod. Phylogenetic analyses of all available complete molluscan mitochondrial genomes based on amino acid sequences of 11 protein-coding genes yield trees with low support for the basal branches. None of the traditionally accepted molluscan taxa and phylogenies are recovered in all analyses, except for the euthyneuran Gastropoda. S. lobatum appears as the sister taxon to two of the three bivalve species. We conclude that the deep molluscan phylogeny is probably beyond the resolution of mitochondrial protein sequences. Moreover, assessing the phylogenetic signal in gene order data requires a much larger taxon sample than is currently available, given the exceptional diversity of this character set in the Mollusca.}, }
@article {pmid15054102, year = {2004}, author = {del Arco, A and Satrústegui, J}, title = {Identification of a novel human subfamily of mitochondrial carriers with calcium-binding domains.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {23}, pages = {24701-24713}, doi = {10.1074/jbc.M401417200}, pmid = {15054102}, issn = {0021-9258}, mesh = {Alternative Splicing ; Amino Acid Motifs ; Amino Acid Sequence ; Amino Acid Transport Systems ; Amino Acid Transport Systems, Acidic ; Animals ; Antiporters ; Blotting, Northern ; Blotting, Western ; COS Cells ; Calcium/*chemistry/metabolism ; Calcium-Binding Proteins/*chemistry/physiology ; Calmodulin/chemistry ; Cell Line ; DNA, Complementary/metabolism ; Databases as Topic ; Dexamethasone/pharmacology ; Exons ; Expressed Sequence Tags ; Genome, Human ; Humans ; Immunoblotting ; Introns ; Lung/metabolism ; Membrane Transport Proteins/*chemistry/physiology ; Microscopy, Fluorescence ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Proteins/physiology ; Molecular Sequence Data ; Multigene Family ; Organic Anion Transporters/physiology ; Peptides/chemistry ; Peroxisomes/metabolism ; Phylogeny ; Plasmids/metabolism ; Promoter Regions, Genetic ; Protein Isoforms ; Protein Structure, Tertiary ; Rats ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Tissue Distribution ; Up-Regulation ; }, abstract = {Aralar1 and citrin were identified as calcium binding aspartate/glutamate carriers (AGC) in mitochondria. The presence of calcium binding motifs facing the extramitochondrial space allows the regulation of the transport activity of these carriers by cytosolic calcium and provides a new mechanism to transduce calcium signals in mitochondria without the requirement of calcium entry in the organelle. We now report the complete characterization of a second subfamily of human calcium binding mitochondrial carriers named SCaMC (short calcium-binding mitochondrial carriers). We have identified three SCaMC genes in the human genome. All code for highly conserved proteins (about 70-80% identity), of about 500 amino acids with a characteristic mitochondrial carrier domain at the C terminus, and an N-terminal extension harboring four EF-hand binding motifs with high similarity to calmodulin. All SCaMC proteins were found to be located exclusively in mitochondria, and their N-terminal extensions were dispensable for the correct mitochondrial targeting of the polypeptides. SCaMC-1 is the human orthologue of the rabbit Efinal protein, which was reported to be located in peroxisomes, and SCaMC-2 is the human orthologue of the rat MCSC protein, described as up-regulated by dexamethasone in AR42J cells. One of the SCaMC genes, SCaMC-2, has four variants generated by alternative splicing, resulting in proteins with a common C terminus but with variations in their N-terminal halves, including the loss of one to three EF-hand motifs. These results make SCaMC one of most complex subfamilies of mitochondrial carriers and suggest that the large number of isoforms and splice variants may confer different calcium sensitivity to the transport activity of these carriers.}, }
@article {pmid15051864, year = {2004}, author = {Romano, PG and Horton, P and Gray, JE}, title = {The Arabidopsis cyclophilin gene family.}, journal = {Plant physiology}, volume = {134}, number = {4}, pages = {1268-1282}, pmid = {15051864}, issn = {0032-0889}, mesh = {Amino Acid Sequence ; Arabidopsis/enzymology/*genetics ; Arabidopsis Proteins/*genetics/metabolism ; Cyclophilin A/chemistry/genetics/metabolism ; Cyclophilins/*genetics/metabolism ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Molecular Sequence Data ; Multigene Family ; Photosynthetic Reaction Center Complex Proteins/*genetics/metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {Database searching has allowed the identification of a number of previously unreported single and multidomain isoform members of the Arabidopsis cyclophilin gene family. In addition to the cyclophilin-like peptidyl-prolyl cis-trans isomerase domain, the latter contain a variety of other domains with characterized functions. Transcriptional analysis showed they are expressed throughout the plant, and different isoforms are present in all parts of the cell including the cytosol, nucleus, mitochondria, secretory pathway, and chloroplast. The abundance and diversity of cyclophilin isoforms suggests that, like their animal counterparts, plant cyclophilins are likely to be important proteins involved in a wide variety of cellular processes. As well as fulfilling the basic role of protein folding, they may also play important roles in mRNA processing, protein degradation, and signal transduction and thus may be crucial during both development and stress responsiveness.}, }
@article {pmid15047880, year = {2004}, author = {Sakaguchi, S and Fukuda, T and Takano, H and Ono, K and Takio, S}, title = {Photosynthetic electron transport differentially regulates the expression of superoxide dismutase genes in liverwort, Marchantia paleacea var. diptera.}, journal = {Plant &amp; cell physiology}, volume = {45}, number = {3}, pages = {318-324}, doi = {10.1093/pcp/pch039}, pmid = {15047880}, issn = {0032-0781}, mesh = {Amino Acid Sequence ; Deoxyadenosines/pharmacology ; Dibromothymoquinone/pharmacology ; Diuron/pharmacology ; Electron Transport/drug effects/radiation effects ; Gene Expression Regulation, Enzymologic/drug effects/radiation effects ; Gene Expression Regulation, Plant/drug effects/radiation effects ; Hepatophyta/enzymology/genetics/*physiology ; Light ; Molecular Sequence Data ; Photosynthesis/drug effects/radiation effects ; Photosynthetic Reaction Center Complex Proteins/*genetics/physiology ; Phylogeny ; Sequence Homology, Amino Acid ; Superoxide Dismutase/*genetics/metabolism ; Transcription Factors/genetics/physiology ; }, abstract = {Liverwort, Marchantia paleacea var. diptera, contains Mn-superoxide dismutase (Mn-SOD) in mitochondria, Fe-SOD in chloroplast and CuZn-SOD in cytosol. An Mn-SOD gene (MpMnSOD) was isolated from the liverwort. Using this clone together with the liverwort Fe-SOD and CuZn-SOD genes as probes, the expression of three SOD genes was investigated. Under heterotrophic conditions, the transcript of three SOD genes was accumulated light independently. On the other hand, under photoautotrophic conditions, the transcript levels of Fe-SOD and Mn-SOD increased in the light while that of CuZn-SOD decreased. The reverse occurred in the dark. In contrast to the transcript level, the activity of the three SODs was barely affected by light. The transcription inhibitor, cordycepin, inhibited either the light-promoted accumulation of Fe-SOD and Mn-SOD transcript or the light-induced reduction of the CuZn-SOD transcript. Photosynthetic electron transport inhibitors, DCMU and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone, inhibited the photo-response in three SOD genes. These results suggest that the transcript abundance of three SOD genes in liverwort is regulated by photosynthetic electron transport but the mechanism regulating the transcript abundance of the CuZn-SOD gene is different from that of the Fe-SOD and Mn-SOD genes.}, }
@article {pmid15045487, year = {2004}, author = {García, MA and Nicholson, EH and Nickrent, DL}, title = {Extensive intraindividual variation in plastid rDNA sequences from the holoparasite Cynomorium coccineum (Cynomoriaceae).}, journal = {Journal of molecular evolution}, volume = {58}, number = {3}, pages = {322-332}, pmid = {15045487}, issn = {0022-2844}, mesh = {Base Composition ; Base Pairing ; Base Sequence ; Cynomorium/*genetics ; DNA Primers ; DNA, Ribosomal/*genetics ; *Genetic Variation ; Molecular Sequence Data ; Mutation/genetics ; *Phylogeny ; Plastids/*genetics ; Sequence Analysis, DNA ; Spain ; }, abstract = {Ribosomal genes are considered to have a high degree of sequence conservation between species and also at higher taxonomic levels. In this paper we document a case where a single individual of Cynomorium coccineum (Cynomoriaceae), a nonphotosynthetic holoparasitic plant, contains highly divergent plastid ribosomal genes. PCR amplification a nearly complete ribosomal DNA cistron was performed using genomic DNA, the products cloned, and the 23S rDNA genes were sequenced from 19 colonies. Of these, five distinct types were identified. Fifteen of the sequences were nearly identical (11 or fewer differences) and these were designated Type I. The remaining types (II-V) were each represented by a single clone and differed from Type I by 93 to 255 changes. Compared with green vascular plants, we found that there are more substitutional differences in the 23S rDNA sequences within a single individual of Cynomorium than among all sequenced photosynthetic vascular plants. Several trends of molecular evolution observed in 16S rDNA from other holoparasitic angiosperms and heterotrophic green algae have been also observed in Cynomorium 23S rDNA. Higher-order structures were constructed for representatives of the five clone types, and in all cases these possessed complete complements of the major structural elements present in functional plastid 23S rRNAs. These data indicate that such molecules may be subject to purifying selection, thus providing indirect evidence that they have retained some degree of functionality. This intraindividual polymorphism is probably a case of plastid heteroplasmy but translocation of ribosomal cistrons to the nucleus or mitochondria has not been tested and therefore cannot be ruled out.}, }
@article {pmid15045484, year = {2004}, author = {Miyagishima, SY and Nozaki, H and Nishida, K and Nishida, K and Matsuzaki, M and Kuroiwa, T}, title = {Two types of FtsZ proteins in mitochondria and red-lineage chloroplasts: the duplication of FtsZ is implicated in endosymbiosis.}, journal = {Journal of molecular evolution}, volume = {58}, number = {3}, pages = {291-303}, pmid = {15045484}, issn = {0022-2844}, mesh = {Algal Proteins/*genetics ; Amino Acid Sequence ; Bacterial Proteins/genetics ; Base Sequence ; Cluster Analysis ; Cytoskeletal Proteins/genetics ; DNA Primers ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/genetics ; Diatoms/*genetics ; Evolution, Molecular ; Gene Components ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Multigene Family/genetics ; Organelles/genetics ; *Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; Rhodophyta/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The ancestors of plastids and mitochondria were once free-living bacteria that became organelles as a result of endosymbiosis. According to this theory, a key bacterial division protein, FtsZ, plays a role in plastid division in algae and plants as well as in mitochondrial division in lower eukaryotes. Recent studies have shown that organelle division is a process that combines features derived from the bacterial division system with features contributed by host eukaryotic cells. Two nonredundant versions of FtsZ, FtsZ1 and FtsZ2, have been identified in green-lineage plastids, whereas most bacteria have a single ftsZ gene. To examine whether there is also more than one type of FtsZ in red-lineage chloroplasts (red algal chloroplasts and chloroplasts that originated from the secondary endosymbiosis of red algae) and in mitochondria, we obtained FtsZ sequences from the complete sequence of the primitive red alga Cyanidioschyzon merolae and the draft sequence of the stramenopile (heterokont) Thalassiosira pseudonana. Phylogenetic analyses that included known FtsZ proteins identified two types of chloroplast FtsZ in red algae (FtsZA and FtsZB) and stramenopiles (FtsZA and FtsZC). These analyses also showed that FtsZB emerged after the red and green lineages diverged, while FtsZC arose by the duplication of an ftsZA gene that in turn descended from a red alga engulfed by the ancestor of stramenopiles. A comparison of the predicted proteins showed that like bacterial FtsZ and green-lineage FtsZ2, FtsZA has a short conserved C-termmal sequence (the C-terminal core domain), whereas FtsZB and FtsZC, like the green-lineage FtsZ1, lack this sequence. In addition, the Cyanidioschyzon and Dictyostelium genomes encode two types of mitochondrial FtsZ proteins, one of which lacks the C-terminal variable domain. These results suggest that the acquisition of an additional FtsZ protein with a modified C terminus was common to the primary and secondary endosymbioses that produced plastids and that this also occurred during the establishment of mitochondria, presumably to regulate the multiplication of these organelles.}, }
@article {pmid15041416, year = {2004}, author = {Gwo, JC and Kuo, MC and Chiu, JY and Cheng, HY}, title = {Ultrastructure of Pagrus major and Rhabdosargus sarba spermatozoa (Perciformes: Sparidae: Sparinae).}, journal = {Tissue &amp; cell}, volume = {36}, number = {2}, pages = {141-147}, doi = {10.1016/j.tice.2003.11.003}, pmid = {15041416}, issn = {0040-8166}, mesh = {Animals ; Cell Nucleus/*ultrastructure ; Male ; Mitochondria/*ultrastructure ; Perciformes/*anatomy &amp; histology ; Phylogeny ; Sperm Head/*ultrastructure ; Sperm Midpiece/*ultrastructure ; }, abstract = {Transmission and scanning electron microscopy were used to investigate the ultrastructure of spermatozoa in two Sparinae species Pagrus major and Rhabdosargus sarba. Ultrastructurally, the spermatozoa of P. major and R. sarba both consist of a spherical, homogeneously electron-dense nucleus with a deep axial nuclear fossa, and an unusual notch, in the nuclear region. The midpiece contains two spherical mitochondria in R. sarba and one in P. major. The comparison of spermatozoal ultrastructure of these two species of Sparidae shows that they closely resemble one another and suggests that they are closely related. Variation in the geometry and dimensions of the mitochondrion and nucleus is substantial in these two Sparidae species. It is concluded that the spermatozoa of both species are of primitive type, and they are distinguished by several unique features which may provide useful systematic characteristics.}, }
@article {pmid15040816, year = {2004}, author = {van der Giezen, M and Cox, S and Tovar, J}, title = {The iron-sulfur cluster assembly genes iscS and iscU of Entamoeba histolytica were acquired by horizontal gene transfer.}, journal = {BMC evolutionary biology}, volume = {4}, number = {}, pages = {7}, pmid = {15040816}, issn = {1471-2148}, mesh = {5' Flanking Region/genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; DNA, Protozoan/chemistry/genetics ; Entamoeba histolytica/*genetics ; *Gene Transfer, Horizontal ; Iron-Sulfur Proteins/chemistry/*genetics ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Protozoan Proteins/chemistry/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: Iron-sulfur (FeS) proteins are present in all living organisms and play important roles in electron transport and metalloenzyme catalysis. The maturation of FeS proteins in eukaryotes is an essential function of mitochondria, but little is known about this process in amitochondriate eukaryotes. Here we report on the identification and analysis of two genes encoding critical FeS cluster (Isc) biosynthetic proteins from the amitochondriate human pathogen Entamoeba histolytica.<br><br>RESULTS: E. histolytica IscU and IscS were found to contain all features considered essential for their biological activity, including amino acid residues involved in substrate and/or co-factor binding. The IscU protein differs significantly from other eukaryotic homologs and resembles the long type isoforms encountered in some bacteria. Phylogenetic analyses of E. histolytica IscS and IscU showed a close relationship with homologs from Helicobacter pylori and Campylobacter jejuni, to the exclusion of mitochondrial isoforms.<br><br>CONCLUSIONS: The bacterial-type FeS cluster assembly genes of E. histolytica suggest their lateral acquisition from epsilon proteobacteria. This is a clear example of horizontal gene transfer (HGT) from eubacteria to unicellular eukaryotic organisms, a phenomenon known to contribute significantly to the evolution of eukaryotic genomes.}, }
@article {pmid15037763, year = {2004}, author = {Williams, K}, title = {Evolutionary resealing of a split RNA: Reversal of gene permutation.}, journal = {RNA (New York, N.Y.)}, volume = {10}, number = {4}, pages = {555-557}, pmid = {15037763}, issn = {1355-8382}, mesh = {Alphaproteobacteria/genetics ; Animals ; Eukaryota/genetics ; *Evolution, Molecular ; Mitochondria/genetics ; RNA/*genetics/metabolism ; RNA, Bacterial ; Spliceosomes/*genetics/metabolism ; }, }
@article {pmid15037637, year = {2004}, author = {Brauner, CJ and Matey, V and Wilson, JM and Bernier, NJ and Val, AL}, title = {Transition in organ function during the evolution of air-breathing; insights from Arapaima gigas, an obligate air-breathing teleost from the Amazon.}, journal = {The Journal of experimental biology}, volume = {207}, number = {Pt 9}, pages = {1433-1438}, doi = {10.1242/jeb.00887}, pmid = {15037637}, issn = {0022-0949}, mesh = {Animals ; *Biological Evolution ; Fishes/anatomy &amp; histology/*physiology ; Gills/cytology/physiology/*ultrastructure ; Immunohistochemistry ; Kidney/*anatomy &amp; histology/physiology ; Microscopy, Electron, Scanning ; Mitochondria/physiology ; *Respiration ; Sodium-Potassium-Exchanging ATPase/physiology ; }, abstract = {The transition from aquatic to aerial respiration is associated with dramatic physiological changes in relation to gas exchange, ion regulation, acid-base balance and nitrogenous waste excretion. Arapaima gigas is one of the most obligate extant air-breathing fishes, representing a remarkable model system to investigate (1) how the transition from aquatic to aerial respiration affects gill design and (2) the relocation of physiological processes from the gills to the kidney during the evolution of air-breathing. Arapaima gigas undergoes a transition from water- to air-breathing during development, resulting in striking changes in gill morphology. In small fish (10 g), the gills are qualitatively similar in appearance to another closely related water-breathing fish (Osteoglossum bicirrhosum); however, as fish grow (100-1000 g), the inter-lamellar spaces become filled with cells, including mitochondria-rich (MR) cells, leaving only column-shaped filaments. At this stage, there is a high density of MR cells and strong immunolocalization of Na(+)/K(+)-ATPase along the outer cell layer of the gill filament. Despite the greatly reduced overall gill surface area, which is typical of obligate air-breathing fish, the gills may remain an important site for ionoregulation and acid-base regulation. The kidney is greatly enlarged in A. gigas relative to that in O. bicirrhosum and may comprise a significant pathway for nitrogenous waste excretion. Quantification of the physiological role of the gill and the kidney in A. gigas during development and in adults will yield important insights into developmental physiology and the evolution of air-breathing.}, }
@article {pmid15033531, year = {2004}, author = {Dolezal, P and Vanácová, S and Tachezy, J and Hrdý, I}, title = {Malic enzymes of Trichomonas vaginalis: two enzyme families, two distinct origins.}, journal = {Gene}, volume = {329}, number = {}, pages = {81-92}, doi = {10.1016/j.gene.2003.12.022}, pmid = {15033531}, issn = {0378-1119}, support = {1 R03 TW05536-01/TW/FIC NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Cytosol/enzymology ; DNA, Protozoan/chemistry/genetics ; Isoenzymes/genetics/isolation &amp; purification/metabolism ; Kinetics ; Malate Dehydrogenase/*genetics/isolation &amp; purification/metabolism ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/enzymology/*genetics ; }, abstract = {The cytosolic malic enzyme of the amitochondriate protist Trichomonas vaginalis was purified to homogeneity and characterized. The corresponding gene was sequenced and compared with its hydrogenosomal homologue from the same organism. The enzymes were found to differ in coenzyme specificity, molecular mass and physiological role. The cytosolic malic enzyme is a dimer consisting of two 42-kDa subunits with strict specificity for nicotinamide adenine dinucleotide phosphate (NADP(+)), and has a presumed function of pyruvate and NADPH production. The hydrogenosomal malic enzyme is a tetramer of 60-kDa subunits that preferentially utilizes nicotinamide adenine dinucleotide (NAD(+)) to NADP(+). The hydrogenosomal enzyme supplies the hydrogenosome with pyruvate for further catabolic processes linked with substrate-level phosphorylation. Phylogenetic analysis of malic enzymes showed the existence of two distinct families of these enzymes in nature, which differ in subunit size. The trichomonad cytosolic malic enzyme belongs to the small subunit-type family that occurs almost exclusively in prokaryotes. In contrast, the hydrogenosomal malic enzyme displays a close relationship with the large subunit-type family of the enzyme, which is found in mitochondria, plastids and the cytosol of eukaryotes. The eubacterial origin of trichomonad cytosolic malic enzyme suggests an occurrence of horizontal gene transfer from a eubacterium to the ancestor of T. vaginalis. The presence of both prokaryotic and eukaryotic type of malic enzyme in different compartments of a single eukaryotic cell appears to be unique in nature.}, }
@article {pmid15032872, year = {2004}, author = {Wheeler, GL and Grant, CM}, title = {Regulation of redox homeostasis in the yeast Saccharomyces cerevisiae.}, journal = {Physiologia plantarum}, volume = {120}, number = {1}, pages = {12-20}, doi = {10.1111/j.0031-9317.2004.0193.x}, pmid = {15032872}, issn = {1399-3054}, abstract = {An increasingly important area of research is based on sulphydryl chemistry, since the oxidation of -SH groups is one of the earliest observable events during oxidant-mediated damage and -SH groups play a critical role in the function of many macromolecular structures including enzymes, transcription factors and membrane proteins. Glutaredoxins and thioredoxins are small heat-stable oxidoreductases, conserved throughout evolution, which play key roles in maintaining the cellular redox balance. Much progress has been made in analysing these systems in the yeast Saccharomyces cerevisiae which is a very useful model eukaryote due to its ease of genetic manipulation, its compact genome, the availability of the entire genome sequence, and the current rate of progress in gene function research. Yeast, like all eukaryotes, contains a number of glutaredoxin and thioredoxin isoenzymes located in both the cytoplasm and the mitochondria. This review describes recent findings made in yeast that are leading to a better understanding of the regulation and role of redox homeostasis in eukaryotic cell metabolism.}, }
@article {pmid15028287, year = {2004}, author = {Onishi, M and Yasunaga, T and Tanaka, H and Nishimune, Y and Nozaki, M}, title = {Gene structure and evolution of testicular haploid germ cell-specific genes, Oxct2a and Oxct2b.}, journal = {Genomics}, volume = {83}, number = {4}, pages = {647-657}, doi = {10.1016/j.ygeno.2003.09.018}, pmid = {15028287}, issn = {0888-7543}, mesh = {Animals ; Base Sequence ; Blotting, Southern ; Bone Morphogenetic Proteins/metabolism ; Chromosomes, Human, Pair 4/metabolism ; Coenzyme A-Transferases/*genetics ; CpG Islands ; DNA Primers/chemistry ; DNA, Complementary/metabolism ; Evolution, Molecular ; Genome ; Haploidy ; Humans ; Introns ; Male ; Mice ; Models, Genetic ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Poly A/metabolism ; RNA/chemistry ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; Spermatids/metabolism ; Testis/*metabolism ; Transcription, Genetic ; }, abstract = {OXCT/SCOT is the rate-determining enzyme in ketolysis in mitochondria of many extrahepatic organs. Two testicular isoforms, Oxct2a and Oxct2b, are highly homologous and specifically expressed in haploid spermatids of the mouse. In this report, we analyzed the structure and evolution of Oxct2a and Oxct2b. Both Oxct2's are single-copy intronless genes, of which nucleotide sequences are conserved with Oxct, indicating that these genes are transposons generated from Oxct. A CpG island was found within both Oxct2's. Oxct2a and Oxct2b are located in the third introns of Bmp8a and Bmp8b, and they are positioned within a 240-kb region in a tail-to-tail orientation on chromosome 4. This structural feature was also conserved in a syntenic region of human 1p34.3. Structural similarity between mice and humans indicated that these two sets of genes were generated by a segmental gene duplication, which occurred before the primate-rodent split. Dot matrix and phylogenetic tree analyses demonstrated that multiple rounds of intrachromosomal gene conversion between the two loci occurred in each species independently.}, }
@article {pmid15024419, year = {2004}, author = {Wu, M and Sun, LV and Vamathevan, J and Riegler, M and Deboy, R and Brownlie, JC and McGraw, EA and Martin, W and Esser, C and Ahmadinejad, N and Wiegand, C and Madupu, R and Beanan, MJ and Brinkac, LM and Daugherty, SC and Durkin, AS and Kolonay, JF and Nelson, WC and Mohamoud, Y and Lee, P and Berry, K and Young, MB and Utterback, T and Weidman, J and Nierman, WC and Paulsen, IT and Nelson, KE and Tettelin, H and O'Neill, SL and Eisen, JA}, title = {Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements.}, journal = {PLoS biology}, volume = {2}, number = {3}, pages = {E69}, pmid = {15024419}, issn = {1545-7885}, support = {UO1-AI47409-01/AI/NIAID NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/chemistry ; Animals ; Cell Lineage ; DNA/chemistry/genetics ; DNA Primers/chemistry ; Drosophila melanogaster/microbiology ; Evolution, Molecular ; Gene Deletion ; Gene Duplication ; Gene Library ; Genes, Bacterial ; Genome ; Genome, Bacterial ; Genomics/*methods ; Glycolysis ; Interspersed Repetitive Sequences ; Models, Genetic ; Molecular Sequence Data ; Open Reading Frames ; Parasites ; Phylogeny ; Polymerase Chain Reaction ; Protein Structure, Tertiary ; Purines/chemistry ; Wolbachia/*genetics ; }, abstract = {The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the alpha-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel-D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections.}, }
@article {pmid15024005, year = {2004}, author = {Ravanel, S and Block, MA and Rippert, P and Jabrin, S and Curien, G and Rébeillé, F and Douce, R}, title = {Methionine metabolism in plants: chloroplasts are autonomous for de novo methionine synthesis and can import S-adenosylmethionine from the cytosol.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {21}, pages = {22548-22557}, doi = {10.1074/jbc.M313250200}, pmid = {15024005}, issn = {0021-9258}, mesh = {Arabidopsis/metabolism ; Blotting, Western ; Chloroplasts/*metabolism ; Cloning, Molecular ; Cytosol/*metabolism ; DNA, Complementary/metabolism ; Diffusion ; Dose-Response Relationship, Drug ; Escherichia coli/metabolism ; Green Fluorescent Proteins ; Homocysteine/chemistry ; Immunoblotting ; Kinetics ; Luminescent Proteins/metabolism ; Methionine/*chemistry/*metabolism ; Mitochondria/metabolism ; Models, Biological ; Molecular Sequence Data ; Pisum sativum ; Phylogeny ; Plastids/metabolism ; Protein Isoforms ; S-Adenosylmethionine/*chemistry ; Time Factors ; Vitamin B 12/metabolism ; }, abstract = {The subcellular distribution of Met and S-adenosylmethionine (AdoMet) metabolism in plant cells discloses a complex partition between the cytosol and the organelles. In the present work we show that Arabidopsis contains three functional isoforms of vitamin B(12)-independent methionine synthase (MS), the enzyme that catalyzes the methylation of homocysteine to Met with 5-methyltetrahydrofolate as methyl group donor. One MS isoform is present in chloroplasts and is most likely required to methylate homocysteine that is synthesized de novo in this compartment. Thus, chloroplasts are autonomous and are the unique site for de novo Met synthesis in plant cells. The additional MS isoforms are present in the cytosol and are most probably involved in the regeneration of Met from homocysteine produced in the course of the activated methyl cycle. Although Met synthesis can occur in chloroplasts, there is no evidence that AdoMet is synthesized anywhere but the cytosol. In accordance with this proposal, we show that AdoMet is transported into chloroplasts by a carrier-mediated facilitated diffusion process. This carrier is able to catalyze the uniport uptake of AdoMet into chloroplasts as well as the exchange between cytosolic AdoMet and chloroplastic AdoMet or S-adenosylhomocysteine. The obvious function for the carrier is to sustain methylation reactions and other AdoMet-dependent functions in chloroplasts and probably to remove S-adenosylhomocysteine generated in the stroma by methyltransferase activities. Therefore, the chloroplastic AdoMet carrier serves as a link between cytosolic and chloroplastic one-carbon metabolism.}, }
@article {pmid15022766, year = {2004}, author = {Su, ZH and Imura, Y and Okamoto, M and Kim, CG and Zhou, HZ and Paik, JC and Osawa, S}, title = {Phylogeny and evolution of Digitulati ground beetles (Coleoptera, Carabidae) inferred from mitochondrial ND5 gene sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {30}, number = {1}, pages = {152-166}, doi = {10.1016/s1055-7903(03)00163-5}, pmid = {15022766}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; China ; Coleoptera/*classification/*genetics ; DNA/genetics/isolation &amp; purification ; DNA Primers ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Geography ; Mitochondria/genetics ; Mitochondria, Muscle/genetics ; Muscle Proteins/*genetics ; Muscle, Skeletal/chemistry ; *Phylogeny ; }, abstract = {Genealogical trees have been constructed using mitochondrial ND5 gene sequences of 87 specimens consisting of 32 species which have been believed to belong to the division Digitulati (one of the lineages of the subtribe Carabina) of the world. There have been recognized six lineages, which are well separated from each other. Each lineage contains the following genus: (1) the lineage A: Ohomopterus from Japan; (2) the lineage B: Isiocarabus from eastern Eurasian Continent; (3) the lineage C: Carabus from China which are further subdivided into three sublineages; (4) the lineage D: Carabus from USA; (5) the lineage E: Carabus from the Eurasian Continent, Japan and North America; and (6) the lineage F: Eucarabus from the Eurasian Continent. Additionally, the genus Acrocarabus which had been treated as a constituent of the division Archicarabomorphi has been recognized to be the 7th lineage of the division Digitulati from the ND5 genealogical analysis as well as morphology. These lineages are assumed to have radiated within a short period and are largely linked to their geographic distribution.}, }
@article {pmid15014982, year = {2004}, author = {Gojković, Z and Knecht, W and Zameitat, E and Warneboldt, J and Coutelis, JB and Pynyaha, Y and Neuveglise, C and Møller, K and Löffler, M and Piskur, J}, title = {Horizontal gene transfer promoted evolution of the ability to propagate under anaerobic conditions in yeasts.}, journal = {Molecular genetics and genomics : MGG}, volume = {271}, number = {4}, pages = {387-393}, pmid = {15014982}, issn = {1617-4615}, mesh = {*Anaerobiosis ; *Biological Evolution ; Cell Division ; Cytoplasm/enzymology ; DNA, Fungal/genetics/isolation &amp; purification ; Dihydroorotate Dehydrogenase ; Electron Transport ; *Gene Transfer, Horizontal ; Mitochondria/enzymology ; Oxidoreductases Acting on CH-CH Group Donors/metabolism ; Oxygen/metabolism ; Phylogeny ; Pyrimidines/*biosynthesis ; Saccharomyces cerevisiae/*enzymology/genetics/*growth &amp; development ; Subcellular Fractions/enzymology ; }, abstract = {The ability to propagate under anaerobic conditions is an essential and unique trait of brewer's or baker's yeast (Saccharomyces cervisiae). To understand the evolution of facultative anaerobiosis we studied the dependence of de novo pyrimidine biosynthesis, more precisely the fourth enzymic activity catalysed by dihydroorotate dehydrogenase (DHODase), on the enzymes of the respiratory chain in several yeast species. While the majority of yeasts possess a mitochondrial DHODase, Saccharomyces cerevisiae has a cytoplasmatic enzyme, whose activity is independent of the presence of oxygen. From the phylogenetic point of view, this enzyme is closely related to a bacterial DHODase from Lactococcus lactis. Here we show that S. kluyveri, which separated from the S. cerevisiae lineage more than 100 million years ago, represents an evolutionary intermediate, having both cytoplasmic and mitochondrial DHODases. We show that these two S. kluyveri enzymes, and their coding genes, differ in their dependence on the presence of oxygen. Only the cytoplasmic DHODase promotes growth in the absence of oxygen. Apparently a Saccharomyces yeast progenitor which had a eukaryotic-like mitochondrial DHODase acquired a bacterial gene for DHODase, which subsequently allowed cell growth gradually to become independent of oxygen.}, }
@article {pmid15014167, year = {2004}, author = {Masta, SE and Boore, JL}, title = {The complete mitochondrial genome sequence of the spider Habronattus oregonensis reveals rearranged and extremely truncated tRNAs.}, journal = {Molecular biology and evolution}, volume = {21}, number = {5}, pages = {893-902}, doi = {10.1093/molbev/msh096}, pmid = {15014167}, issn = {0737-4038}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Genome ; Horseshoe Crabs/genetics ; Mitochondria/genetics ; Models, Genetic ; Nucleic Acid Conformation ; Phylogeny ; Plasmids/metabolism ; RNA Editing ; RNA, Transfer/*genetics/metabolism ; Spiders/*genetics ; }, abstract = {We sequenced the entire mitochondrial genome of the jumping spider Habronattus oregonensis of the arachnid order Araneae (Arthropoda: Chelicerata). A number of unusual features distinguish this genome from other chelicerate and arthropod mitochondrial genomes. Most of the transfer RNA (tRNA) gene sequences are greatly reduced in size and cannot be folded into typical cloverleaf-shaped secondary structures. At least nine of the tRNA sequences lack the potential to form TPsiC arm stem pairings and instead are inferred to have TV-replacement loops. Furthermore, sequences that could encode the 3' aminoacyl acceptor stems in at least 10 tRNAs appear to be lacking, because fully paired acceptor stems are not possible and because the downstream sequences instead encode adjacent genes. Hence, these appear to be among the smallest known tRNA genes. We postulate that an RNA editing mechanism must exist to restore the 3' aminoacyl acceptor stems to allow the tRNAs to function. At least seven tRNAs are rearranged with respect to the chelicerate Limulus polyphemus, although the arrangement of the protein-coding genes is identical. Most mitochondrial protein-coding genes of H. oregonensis have ATN as initiation codons, as commonly found in arthropod mtDNAs, but cytochrome oxidase subunits 2 and 3 genes apparently use TTG as an initiation codon. Finally, many of the gene sequences overlap one another and are truncated. This 14,381-bp genome, the first mitochondrial genome of a spider yet sequenced, is one of the smallest arthropod mitochondrial genomes known. We suggest that posttranscriptional RNA editing can likely maintain function of the tRNAs, while permitting the accumulation of mutations that would otherwise be deleterious. Such mechanisms may have allowed for the minimization of the spider mitochondrial genome.}, }
@article {pmid15014143, year = {2004}, author = {Richly, E and Leister, D}, title = {NUMTs in sequenced eukaryotic genomes.}, journal = {Molecular biology and evolution}, volume = {21}, number = {6}, pages = {1081-1084}, doi = {10.1093/molbev/msh110}, pmid = {15014143}, issn = {0737-4038}, mesh = {Cell Nucleus/*genetics ; Computational Biology ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; *Evolution, Molecular ; *Genome ; Species Specificity ; }, abstract = {Mitochondrial DNA sequences are frequently transferred to the nucleus giving rise to the so-called nuclear mitochondrial DNA (NUMT). Analysis of 13 eukaryotic species with sequenced mitochondrial and nuclear genomes reveals a large interspecific variation of NUMT number and size. Copy number ranges from none or few copies in Anopheles, Caenorhabditis, Plasmodium, Drosophila, and Fugu to more than 500 in human, rice, and Arabidopsis. The average size is between 62 (baker's yeast) and 647 bps (Neurospora), respectively. A correlation between the abundance of NUMTs and the size of the nuclear or the mitochondrial genomes, or of the nuclear gene density, is not evident. Other factors, such as the number and/or stability of mitochondria in the germline, or species-specific mechanisms controlling accumulation/loss of nuclear DNA, might be responsible for the interspecific diversity in NUMT accumulation.}, }
@article {pmid15014069, year = {2004}, author = {Hoffmeister, M and van der Klei, A and Rotte, C and van Grinsven, KW and van Hellemond, JJ and Henze, K and Tielens, AG and Martin, W}, title = {Euglena gracilis rhodoquinone:ubiquinone ratio and mitochondrial proteome differ under aerobic and anaerobic conditions.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {21}, pages = {22422-22429}, doi = {10.1074/jbc.M400913200}, pmid = {15014069}, issn = {0021-9258}, mesh = {Animals ; Biochemistry/methods ; Cloning, Molecular ; DNA, Complementary/metabolism ; Databases as Topic ; Electron Transport ; Electrophoresis, Gel, Two-Dimensional ; Euglena gracilis/*metabolism ; Expressed Sequence Tags ; Gene Expression Regulation, Bacterial ; Hydrogen/chemistry ; Mitochondria/enzymology/*metabolism ; Models, Chemical ; Molecular Sequence Data ; Oxygen/*metabolism ; Peptides/chemistry ; Phylogeny ; Protein Structure, Tertiary ; Proteome ; Pyruvic Acid/chemistry ; Trypsin/chemistry ; Ubiquinone/*analogs &amp; derivatives/*chemistry ; }, abstract = {Euglena gracilis cells grown under aerobic and anaerobic conditions were compared for their whole cell rhodoquinone and ubiquinone content and for major protein spots contained in isolated mitochondria as assayed by two-dimensional gel electrophoresis and mass spectrometry sequencing. Anaerobically grown cells had higher rhodoquinone levels than aerobically grown cells in agreement with earlier findings indicating the need for fumarate reductase activity in anaerobic wax ester fermentation in Euglena. Microsequencing revealed components of complex III and complex IV of the respiratory chain and the E1beta subunit of pyruvate dehydrogenase to be present in mitochondria of aerobically grown cells but lacking in mitochondria from anaerobically grown cells. No proteins were identified as specific to mitochondria from anaerobically grown cells. cDNAs for the E1alpha, E2, and E3 subunits of mitochondrial pyruvate dehydrogenase were cloned and shown to be differentially expressed under aerobic and anaerobic conditions. Their expression patterns differed from that of mitochondrial pyruvate:NADP(+) oxidoreductase, the N-terminal domain of which is pyruvate:ferredoxin oxidoreductase, an enzyme otherwise typical of hydrogenosomes, hydrogen-producing forms of mitochondria found among anaerobic protists. The Euglena mitochondrion is thus a long sought intermediate that unites biochemical properties of aerobic and anaerobic mitochondria and hydrogenosomes because it contains both pyruvate:ferredoxin oxidoreductase and rhodoquinone typical of hydrogenosomes and anaerobic mitochondria as well as pyruvate dehydrogenase and ubiquinone typical of aerobic mitochondria. Our data show that under aerobic conditions Euglena mitochondria are prepared for anaerobic function and furthermore suggest that the ancestor of mitochondria was a facultative anaerobe, segments of whose physiology have been preserved in the Euglena lineage.}, }
@article {pmid15012752, year = {2004}, author = {Ballard, JW and Whitlock, MC}, title = {The incomplete natural history of mitochondria.}, journal = {Molecular ecology}, volume = {13}, number = {4}, pages = {729-744}, doi = {10.1046/j.1365-294x.2003.02063.x}, pmid = {15012752}, issn = {0962-1083}, mesh = {DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Genetics, Population ; Geography ; Mitochondria/metabolism/*physiology ; Mutation/genetics ; *Phylogeny ; Reactive Oxygen Species/metabolism ; Selection, Genetic ; }, abstract = {Mitochondrial DNA (mtDNA) has been used to study molecular ecology and phylogeography for 25 years. Much important information has been gained in this way, but it is time to reflect on the biology of the mitochondrion itself and consider opportunities for evolutionary studies of the organelle itself and its ecology, biochemistry and physiology. This review has four sections. First, we review aspects of the natural history of mitochondria and their DNA to show that it is a unique molecule with specific characteristics that differ from nuclear DNA. We do not attempt to cover the plethora of differences between mitochondrial and nuclear DNA; rather we spotlight differences that can cause significant bias when inferring demographic properties of populations and/or the evolutionary history of species. We focus on recombination, effective population size and mutation rate. Second, we explore some of the difficulties in interpreting phylogeographical data from mtDNA data alone and suggest a broader use of multiple nuclear markers. We argue that mtDNA is not a sufficient marker for phylogeographical studies if the focus of the investigation is the species and not the organelle. We focus on the potential bias caused by introgression. Third, we show that it is not safe to assume a priori that mtDNA evolves as a strictly neutral marker because both direct and indirect selection influence mitochondria. We outline some of the statistical tests of neutrality that can, and should, be applied to mtDNA sequence data prior to making any global statements concerning the history of the organism. We conclude with a critical examination of the neglected biology of mitochondria and point out several surprising gaps in the state of our knowledge about this important organelle. Here we limelight mitochondrial ecology, sexually antagonistic selection, life-history evolution including ageing and disease, and the evolution of mitochondrial inheritance.}, }
@article {pmid15008420, year = {2003}, author = {Ota, R and Penny, D}, title = {Estimating changes in mutational mechanisms of evolution.}, journal = {Journal of molecular evolution}, volume = {57 Suppl 1}, number = {}, pages = {S233-40}, pmid = {15008420}, issn = {0022-2844}, mesh = {Animals ; Codon ; DNA Repair ; *Evolution, Molecular ; Humans ; Mammals/genetics ; *Markov Chains ; Mitochondria/genetics ; *Models, Genetic ; *Mutation ; Purines ; Pyrimidines ; }, abstract = {By considering three DNA sequences simultaneously there is sufficient information to recover a full Markov model with three transition matrices from the root to each of the sequences. It is necessary to have relatively long sequences because, for nucleotides, the full model requires 39 parameters that are estimated from 63 observable values. This triplet Markov method is evaluated for the protein coding genes of mammalian vertebrate mitochondrial genomes, and, in addition, version for two-state-characters (such as R/Y coding) is implemented. A key finding is that some changes in mutational mechanism differentially affect the mutation rate between pairs of nucleotides: there does not appear to be a universal change in "rate" of evolution. It remains to be explored whether detecting changes in certain nucleotide interchanges can be localized to a particular part of the DNA replication/repair system. In order to estimate divergence dates it may eventually be advantageous to use the nucleotide interchanges that show little rate change.}, }
@article {pmid15005799, year = {2004}, author = {Hedges, SB and Blair, JE and Venturi, ML and Shoe, JL}, title = {A molecular timescale of eukaryote evolution and the rise of complex multicellular life.}, journal = {BMC evolutionary biology}, volume = {4}, number = {}, pages = {2}, pmid = {15005799}, issn = {1471-2148}, mesh = {Animals ; Eukaryotic Cells/*metabolism ; *Evolution, Molecular ; Fungi/genetics ; Genetic Variation ; Phylogeny ; Plants/genetics ; Proteins/genetics ; Rhodophyta/genetics ; Time Factors ; Vertebrates/genetics ; }, abstract = {BACKGROUND: The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time.<br><br>RESULTS: Our phylogenetic analyses revealed that (i) animals are more closely related to fungi than to plants, (ii) red algae are closer to plants than to animals or fungi, (iii) choanoflagellates are closer to animals than to fungi or plants, (iv) diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v) diplomonads are basal to other eukaryotes (including alveolates and euglenozoans). Divergence times were estimated from global and local clock methods using 20-188 proteins per node, with data treated separately (multigene) and concatenated (supergene). Different time estimation methods yielded similar results (within 5%): vertebrate-arthropod (964 million years ago, Ma), Cnidaria-Bilateria (1,298 Ma), Porifera-Eumetozoa (1,351 Ma), Pyrenomycetes-Plectomycetes (551 Ma), Candida-Saccharomyces (723 Ma), Hemiascomycetes-filamentous Ascomycota (982 Ma), Basidiomycota-Ascomycota (968 Ma), Mucorales-Basidiomycota (947 Ma), Fungi-Animalia (1,513 Ma), mosses-vascular plants (707 Ma), Chlorophyta-Tracheophyta (968 Ma), Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma), Plantae-Animalia (1,609 Ma), Alveolata-plants+animals+fungi (1,973 Ma), Euglenozoa-plants+animals+fungi (1,961 Ma), and Giardia-plants+animals+fungi (2,309 Ma). By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to approximately 10 types at 1500 Ma and 50 cell types at approximately 1000 Ma.<br><br>CONCLUSIONS: The results suggest that oxygen levels in the environment, and the ability of eukaryotes to extract energy from oxygen, as well as produce oxygen, were key factors in the rise of complex multicellular life. Mitochondria and organisms with more than 2-3 cell types appeared soon after the initial increase in oxygen levels at 2300 Ma. The addition of plastids at 1500 Ma, allowing eukaryotes to produce oxygen, preceded the major rise in complexity.}, }
@article {pmid15003491, year = {2004}, author = {Roberts, CW and Roberts, F and Henriquez, FL and Akiyoshi, D and Samuel, BU and Richards, TA and Milhous, W and Kyle, D and McIntosh, L and Hill, GC and Chaudhuri, M and Tzipori, S and McLeod, R}, title = {Evidence for mitochondrial-derived alternative oxidase in the apicomplexan parasite Cryptosporidium parvum: a potential anti-microbial agent target.}, journal = {International journal for parasitology}, volume = {34}, number = {3}, pages = {297-308}, doi = {10.1016/j.ijpara.2003.11.002}, pmid = {15003491}, issn = {0020-7519}, support = {N01 AI25466/AI/NIAID NIH HHS/United States ; R01 AI-43228/AI/NIAID NIH HHS/United States ; R01 AI-50471/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Coccidiostats/*pharmacology ; Cryptosporidium parvum/*drug effects/enzymology/growth &amp; development ; Dose-Response Relationship, Drug ; Enzyme Inhibitors/pharmacology ; Genes, Protozoan ; Genome ; Mitochondria/*enzymology ; Mitochondrial Proteins ; Molecular Sequence Data ; Oxidoreductases/*antagonists &amp; inhibitors/genetics/metabolism ; Oxyquinoline/pharmacology ; Phylogeny ; Plant Proteins ; Plasmodium falciparum/drug effects/growth &amp; development ; Salicylamides/pharmacology ; Sequence Alignment ; Toxoplasma/drug effects/growth &amp; development ; }, abstract = {The observation that Plasmodium falciparum possesses cyanide insensitive respiration that can be inhibited by salicylhydroxamic acid (SHAM) and propyl gallate is consistent with the presence of an alternative oxidase (AOX). However, the completion and annotation of the P. falciparum genome project did not identify any protein with convincing similarity to the previously described AOXs from plants, fungi or protozoa. We undertook a survey of the available apicomplexan genome projects in an attempt to address this anomaly. Putative AOX sequences were identified and sequenced from both type 1 and 2 strains of Cryptosporidium parvum. The gene encodes a polypeptide of 336 amino acids and has a predicted N-terminal transit sequence similar to that found in proteins targeted to the mitochondria of other species. The potential of AOX as a target for new anti-microbial agents for C. parvum is evident by the ability of SHAM and 8-hydroxyquinoline to inhibit in vitro growth of C. parvum. In spite of the lack of a good candidate for AOX in either the P. falciparum or Toxoplasma gondii genome projects, SHAM and 8-hydroxyquinoline were found to inhibit the growth of these parasites. Phylogenetic analysis suggests that AOX and the related protein immutans are derived from gene transfers from the mitochondrial endosymbiont and the chloroplast endosymbiont, respectively. These data are consistent with the functional localisation studies conducted thus far, which demonstrate mitochondrial localisation for some AOX and chloroplastidic localization for immutans. The presence of a mitochondrial compartment is further supported by the prediction of a mitochondrial targeting sequence at the N-terminus of the protein and MitoTracker staining of a subcellular compartment in trophozoite and meront stages. These results give insight into the evolution of AOX and demonstrate the potential of targeting the alternative pathway of respiration in apicomplexans.}, }
@article {pmid15003237, year = {2004}, author = {Picault, N and Hodges, M and Palmieri, L and Palmieri, F}, title = {The growing family of mitochondrial carriers in Arabidopsis.}, journal = {Trends in plant science}, volume = {9}, number = {3}, pages = {138-146}, doi = {10.1016/j.tplants.2004.01.007}, pmid = {15003237}, issn = {1360-1385}, mesh = {Arabidopsis/*genetics/metabolism ; Carrier Proteins/*genetics/metabolism ; Gene Expression Regulation, Plant ; Genome, Plant ; Genomics/methods ; Mitochondria/genetics/metabolism ; Mitochondrial Proteins/*genetics/metabolism ; Phylogeny ; }, }
@article {pmid14998395, year = {2004}, author = {Yamada, Y and Makimura, K and Uchida, K and Yamaguchi, H and Osumi, M}, title = {Phylogenetic relationships among medically important yeasts based on sequences of mitochondrial large subunit ribosomal RNA gene.}, journal = {Mycoses}, volume = {47}, number = {1-2}, pages = {24-28}, doi = {10.1046/j.0933-7407.2003.00942.x}, pmid = {14998395}, issn = {0933-7407}, mesh = {Base Sequence ; Candida/classification/genetics/isolation &amp; purification ; Cluster Analysis ; Cryptococcus/classification/genetics/isolation &amp; purification ; DNA, Fungal/chemistry/isolation &amp; purification ; DNA, Ribosomal/chemistry/isolation &amp; purification ; Genes, Fungal ; *Genes, rRNA ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Yeasts/*classification/*genetics/isolation &amp; purification ; }, abstract = {Sequences of the mitochondrial large subunit ribosomal RNA (mtLsurRNA) gene of medically important yeasts were analysed. Sixteen strains of eight species including two varieties were subjected to sequencing. Sequencing enabled us to recognize the differences between all the species and varieties. Alignment analysis revealed that these sequences consisted of three clusters: the Candida albicans group, the C. glabrata group, and the basidiomycetous group. It is possible, therefore, that the mtLsurRNA gene is one of the targets not only for species identification but also for phylogenetic analysis of closely related yeasts. The dendrogram of each group, obtained from this gene, supports the previous study of yeasts based upon the chromosomal genes.}, }
@article {pmid14996492, year = {2004}, author = {Igaki, T and Miura, M}, title = {Role of Bcl-2 family members in invertebrates.}, journal = {Biochimica et biophysica acta}, volume = {1644}, number = {2-3}, pages = {73-81}, doi = {10.1016/j.bbamcr.2003.09.007}, pmid = {14996492}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Animals ; Apoptosis ; Biological Evolution ; Caenorhabditis elegans Proteins/physiology ; Drosophila Proteins/physiology ; Invertebrates/cytology/genetics/*metabolism ; Molecular Sequence Data ; Proto-Oncogene Proteins c-bcl-2/genetics/*physiology ; Sequence Alignment ; Signal Transduction ; }, abstract = {Proteins belonging to the Bcl-2 family function as regulators of 'life-or-death' decisions in response to various intrinsic and extrinsic stimuli. In mammals, cell death is controlled by pro- and anti-apoptotic members of the Bcl-2 family, which function upstream of the caspase cascade. Structural and functional homologues of the Bcl-2 family proteins also exist in lower eukaryotes, such as nematodes and flies. In nematodes, an anti-apoptotic Bcl-2 family protein, CED-9, functions as a potent cell death inhibitor, and a BH3-only protein, EGL-1, acts as an inhibitor of CED-9 to facilitate the spatio-temporal regulation of programmed cell death. On the other hand, the Drosophila genome encodes two Bcl-2 family proteins, Drob-1/Debcl/dBorg-1/dBok and Buffy/dBorg-2, both of which structurally belong to the pro-apoptotic group, despite abundant similarities in the cell death mechanisms between flies and vertebrates. Drob-1 acts as a pro-apoptotic factor in vitro and in vivo, and Buffy/dBorg-2 exhibits a weak anti-apoptotic function. The ancestral role of the Bcl-2 family protein may be pro-apoptotic, and the evolution of the functions of this family of proteins may be closely linked with the contribution of mitochondria to the cell death pathway.}, }
@article {pmid14994549, year = {2003}, author = {Nikolaev, SI and Berney, S and Fahrni, J and Mylnikov, AP and Petrov, NB and Pawlowski, J}, title = {Genetic relationships between desmothoracid heliozoa and gymnophryid amoebas as evidenced by comparison of the nucleotide sequences of 18S rRNA genes.}, journal = {Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections}, volume = {393}, number = {}, pages = {553-556}, pmid = {14994549}, issn = {0012-4966}, mesh = {Amoeba ; Animals ; Base Sequence ; DNA, Complementary/metabolism ; Genes, rRNA ; Likelihood Functions ; Mitochondria/pathology ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; *Sequence Analysis, DNA ; }, }
@article {pmid14993600, year = {2004}, author = {Parker, JD and Parker, KM and Sohal, BH and Sohal, RS and Keller, L}, title = {Decreased expression of Cu-Zn superoxide dismutase 1 in ants with extreme lifespan.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {10}, pages = {3486-3489}, pmid = {14993600}, issn = {0027-8424}, mesh = {Aging/*genetics/*metabolism ; Amino Acid Sequence ; Animals ; Ants/*enzymology/*genetics ; Cloning, Molecular ; Drosophila melanogaster/enzymology/genetics ; Female ; Gene Expression ; Longevity ; Male ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; Superoxide Dismutase/*genetics/metabolism ; Superoxide Dismutase-1 ; }, abstract = {Reactive oxygen species, the by-products of oxidative energy metabolism, are considered a main proximate cause of aging. Accordingly, overexpression of the enzyme Cu-Zn superoxide dismutase 1 (SOD1) can lengthen lifespan of Drosophila melanogaster in the laboratory. However, the role of SOD1 as a main determinant of lifespan has been challenged on the grounds that overexpression might be effective only in compromised genetic backgrounds. Moreover, interspecific comparisons show lower levels of antioxidant activities in longer-lived species, suggesting that life-span extension may evolve through less reactive oxygen species generation from the mitochondria rather than higher expression of SOD1. The tremendous variation in lifespan between ant castes, ranging over 2 orders of magnitude, coupled with the fact that all individuals share the same genome, provides a system to investigate the role of SOD1 in the wild. We used the ant Lasius niger as a model system, because queens can reach the extreme age of 28 years, whereas workers and males live only 1-2 years and a few weeks, respectively. We cloned SOD1 and found that long-lived queens have a lower level of expression than workers and males. Specific enzyme-activity assays also showed higher SOD1 activity levels in males and workers compared with queens, which had SOD1 activity levels similar to that of D. melanogaster. Altogether, these data show that increased expression of SOD1 is not required for the evolution of extreme lifespan, even in a system in which differential gene expression is the only way to express phenotypes with great lifespan differences.}, }
@article {pmid14991737, year = {2004}, author = {Nayernia, K and Diaconu, M and Aumüller, G and Wennemuth, G and Schwandt, I and Kleene, K and Kuehn, H and Engel, W}, title = {Phospholipid hydroperoxide glutathione peroxidase: expression pattern during testicular development in mouse and evolutionary conservation in spermatozoa.}, journal = {Molecular reproduction and development}, volume = {67}, number = {4}, pages = {458-464}, doi = {10.1002/mrd.20039}, pmid = {14991737}, issn = {1040-452X}, mesh = {Animals ; Biological Evolution ; Fishes ; Gene Expression ; Glutathione Peroxidase/*metabolism ; Goats ; Humans ; Male ; Mice ; Phospholipid Hydroperoxide Glutathione Peroxidase ; Rats ; Spermatozoa/*metabolism/*ultrastructure ; Swine ; *Testis/cytology/growth &amp; development/metabolism ; }, abstract = {Phospholipid hydroperoxide glutathione peroxidase (PHGPx) is a selenoprotein belonging to the family of glutathione peroxidases and has been implicated in antioxidative defense and spermatogenesis. PHGPx accounts for almost the entire selenium content of mammalian testis. In an attempt to verify the expression pattern of PHGPx, testes of mouse mutants with arrest at different stages of germ cell development and testes of mice at different ages were subjected to immunostaining with a monoclonal anti-PHGPx antibody. PHGPx was detected in Leydig cells of testes in all developmental stages. In the seminiferous tubuli, the PHGPx staining was first observed in testes of 21-day-old mice which is correlated with the appearance of the first spermatids. This result was confirmed when the testes of mutant mice with defined arrest of germ cell development were used. An immunostaining was observed in the seminiferous tubuli of olt/olt and qk/qk mice which show an arrest at spermatid differentiation. In Western blot analysis of proteins extracted from testes of mutant mice and from developing testes, two signals at 19- and 22-kDa were observed which confirm the existence of two PHGPx forms in testicular cells. In mouse spermatozoa, a subcellular localization of PHGPx and sperm mitochondria-associated cysteine-rich protein (SMCP) was demonstrated, indicating the localization of PHGPx in mitochondria of spermatozoa midpiece. For verifying the midpiece localization of PHGPx in other species, spermatozoa of Drosophila melanogaster, frog, fish, cock, mouse, rat, pig, bull, and human were used in immunostaining using anti-PHGPx antibody. A localization of PHGPx was found in the midpiece of spermatozoa in all species examined. In electronmicroscopical analysis, PHGPx signals were found in the mitochondria of midpiece. These results indicate a conserved crucial role of PHGPx during sperm function and male fertility.}, }
@article {pmid14984933, year = {2004}, author = {Wang, YS and Harding, SA and Tsai, CJ}, title = {Expression of a glycine decarboxylase complex H-protein in non-photosynthetic tissues of Populus tremuloides.}, journal = {Biochimica et biophysica acta}, volume = {1676}, number = {3}, pages = {266-272}, doi = {10.1016/j.bbaexp.2003.12.004}, pmid = {14984933}, issn = {0006-3002}, mesh = {Amino Acid Oxidoreductases/biosynthesis/chemistry/*genetics ; Amino Acid Sequence ; Cloning, Molecular ; DNA, Complementary/analysis/biosynthesis/chemistry ; Gene Expression Regulation, Enzymologic ; Glycine Decarboxylase Complex ; Glycine Decarboxylase Complex H-Protein ; Glycine Dehydrogenase (Decarboxylating) ; Molecular Sequence Data ; Phylogeny ; Plant Roots/enzymology ; Populus/enzymology/growth &amp; development/*metabolism ; Protein Isoforms/genetics ; Sequence Alignment ; }, abstract = {The Gly decarboxylase complex (GDC) is abundant in mitochondria of C3 leaves and functions in photorespiratory carbon recovery. However, expression of GDC component proteins has generally been less evident in non-green tissues. Here we report an aspen (Populus tremuloides Michx.) PtgdcH1 gene, encoding a GDC subunit H-protein that is phylogenetically distinct from previously characterized photorespiratory H-proteins. Strong expression of PtgdcH1 in root tips and developing xylem suggests that GDC supports a very active C1 metabolism in non-photosynthetic tissues of aspen.}, }
@article {pmid14984837, year = {2004}, author = {Agatsuma, T and Rajapakse, RP and Kuruwita, VY and Iwagami, M and Rajapakse, RC}, title = {Molecular taxonomic position of the elephant schistosome, Bivitellobilharzia nairi, newly discovered in Sri Lanka.}, journal = {Parasitology international}, volume = {53}, number = {1}, pages = {69-75}, doi = {10.1016/j.parint.2003.11.003}, pmid = {14984837}, issn = {1383-5769}, mesh = {Animals ; Base Sequence ; DNA, Helminth/analysis ; DNA, Ribosomal Spacer/analysis ; Electron Transport Complex IV/genetics ; Elephants/*parasitology ; Male ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 28S/genetics ; Schistosomatidae/*classification/*genetics/isolation &amp; purification ; Sequence Analysis, DNA ; Sri Lanka ; Trematode Infections/parasitology/*veterinary ; }, abstract = {Bivitellobilharzia nairi (Mudaliar and Ramanujachar, 1945) Dutt and Srivastava, 1955 was first recorded in India. A number of adult worm specimens of this schistosome species were recovered from a domestic elephant, which died in 1999 in Sri Lanka. This is the first report of this schistosome from Sri Lanka. In the present study, in order to clarify the phylogenetic relationship with other species of schistosomes, sequences from the second internal transcribed spacer (ITS2) of the ribosomal gene repeat, part of the 28S ribosomal RNA gene (28S), and part of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene from B. nairi were analyzed. Two intraspecific variations were seen within 13 individuals in the ITS2 region. In the CO1 region of the mitochondrial DNA, there were four haplotypes in the nucleotide sequences and two haplotypes in the amino acid sequences. Phylogenetic analysis using the nuclear DNA showed that B. nairi was basal to all of species of the genus Schistosoma. The 28S tree also showed that the mammalian lineage was monophyletic. However, phylogenetic analysis using the mitochondrial DNA showed that B. nairi was nested within the genus Schistosoma. The taxonomical position for this species as well as the contradiction between the results from the nuclear and mitochondrial genes were discussed.}, }
@article {pmid14984742, year = {2004}, author = {Hazkani-Covo, E and Levanon, EY and Rotman, G and Graur, D and Novik, A}, title = {Evolution of multicellularity in Metazoa: comparative analysis of the subcellular localization of proteins in Saccharomyces, Drosophila and Caenorhabditis.}, journal = {Cell biology international}, volume = {28}, number = {3}, pages = {171-178}, doi = {10.1016/j.cellbi.2003.11.016}, pmid = {14984742}, issn = {1065-6995}, mesh = {Animals ; *Biological Evolution ; Caenorhabditis elegans/*metabolism ; Caenorhabditis elegans Proteins/*metabolism ; Drosophila Proteins/*metabolism ; Drosophila melanogaster/*metabolism ; Organelles/metabolism ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/*metabolism ; }, abstract = {A comparison of the subcellular assignments of proteins between the unicellular Saccharomyces cerevisiae and the multicellular Drosophila melanogaster and Caenorhabditis elegans was performed using a computational tool for the prediction of subcellular localization. Nine subcellular compartments were studied: (1) extracellular domain, (2) cell membrane, (3) cytoplasm, (4) endoplasmic reticulum, (5) Golgi apparatus, (6) lysosome, (7) peroxisome, (8) mitochondria, and (9) nucleus. The transition to multicellularity was found to be characterized by an increase in the total number of proteins encoded by the genome. Interestingly, this increase is distributed unevenly among the subcellular compartments. That is, a disproportionate increase in the number of proteins in the extracellular domain, the cell membrane, and the cytoplasm is observed in multicellular organisms, while no such increase is seen in other subcellular compartments. A possible explanation involves signal transduction. In terms of protein numbers, signal transduction pathways may be roughly described as a pyramid with an expansive base in the extracellular domain (the numerous extracellular signal proteins), progressively narrowing at the cell membrane and cytoplasmic levels, and ending in a narrow tip consisting of only a handful of transcription modulators in the nucleus. Our observations suggest that extracellular signaling interactions among metazoan cells account for the uneven increase in the numbers of proteins among subcellular compartments during the transition to multicellularity.}, }
@article {pmid14982636, year = {2004}, author = {Tjaden, J and Haferkamp, I and Boxma, B and Tielens, AG and Huynen, M and Hackstein, JH}, title = {A divergent ADP/ATP carrier in the hydrogenosomes of Trichomonas gallinae argues for an independent origin of these organelles.}, journal = {Molecular microbiology}, volume = {51}, number = {5}, pages = {1439-1446}, doi = {10.1111/j.1365-2958.2004.03918.x}, pmid = {14982636}, issn = {0950-382X}, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Anti-Bacterial Agents/metabolism ; Bongkrekic Acid/metabolism ; Escherichia coli/genetics/metabolism ; *Evolution, Molecular ; Hydrogen/metabolism ; Mitochondrial ADP, ATP Translocases/classification/genetics/*metabolism ; Molecular Sequence Data ; Organelles/*metabolism ; Phylogeny ; Plant Proteins/metabolism ; Protozoan Proteins/classification/genetics/*metabolism ; Trichomonas/*cytology/*metabolism ; }, abstract = {The evolution of mitochondrial ADP and ATP exchanging proteins (AACs) highlights a key event in the evolution of the eukaryotic cell, as ATP exporting carriers were indispensable in establishing the role of mitochondria as ATP-generating cellular organelles. Hydrogenosomes, i.e. ATP- and hydrogen-generating organelles of certain anaerobic unicellular eukaryotes, are believed to have evolved from the same ancestral endosymbiont that gave rise to present day mitochondria. Notably, the hydrogenosomes of the parasitic anaerobic flagellate Trichomonas seemed to be deficient in mitochondrial-type AACs. Instead, HMP 31, a different member of the mitochondrial carrier family (MCF) with a hitherto unknown function, is abundant in the hydrogenosomal membranes of Trichomonas vaginalis. Here we show that the homologous HMP 31 of closely related Trichomonas gallinae specifically transports ADP and ATP with high efficiency, as do genuine mitochondrial AACs. However, phylogenetic analysis and its resistance against bongkrekic acid (BKA, an efficient inhibitor of mitochondrial-type AACs) identify HMP 31 as a member of the mitochondrial carrier family that is distinct from all mitochondrial and hydrogenosomal AACs studied so far. Thus, our data support the hypothesis that the various hydrogenosomes evolved repeatedly and independently.}, }
@article {pmid14975754, year = {2004}, author = {Karlgren, M and Backlund, M and Johansson, I and Oscarson, M and Ingelman-Sundberg, M}, title = {Characterization and tissue distribution of a novel human cytochrome P450-CYP2U1.}, journal = {Biochemical and biophysical research communications}, volume = {315}, number = {3}, pages = {679-685}, doi = {10.1016/j.bbrc.2004.01.110}, pmid = {14975754}, issn = {0006-291X}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cell Line ; Cloning, Molecular ; Cytochrome P-450 Enzyme System/*genetics/*metabolism ; Cytoplasm/enzymology ; DNA, Complementary/genetics ; Humans ; Isoenzymes/genetics/metabolism ; Microsomes/enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; Oligonucleotide Probes/chemistry/genetics ; Phylogeny ; RNA, Messenger/genetics/metabolism ; Rats ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Tissue Distribution ; }, abstract = {A novel human cytochrome P450 cDNA designated CYP2U1 was identified using homology searches, and the corresponding gene is located on chromosome 4. The deduced 544 amino acid sequence displays up to 39% identity to other CYP2 family members, with closest resemblance to CYP2R1 and is highly conserved between species. CYP2U1 shows some structural differences compared to other CYP2 family members. The gene has only five exons and the enzyme harbors two insertions in the N-terminal region. Northern blot analysis revealed high mRNA expression in human thymus, with weaker expression in heart and brain, whereas in the rat similar mRNA levels were detected in thymus and brain. Western blot analysis revealed much higher CYP2U1 protein expression in rat brain than in thymus, particularly in limbic structures and in cortex. The physiological and toxicological role of this novel P450 is still unknown, but the selective tissue distribution suggests an important endogenous function.}, }
@article {pmid14975245, year = {2004}, author = {Kloc, M and Bilinski, S and Etkin, LD}, title = {The Balbiani body and germ cell determinants: 150 years later.}, journal = {Current topics in developmental biology}, volume = {59}, number = {}, pages = {1-36}, doi = {10.1016/S0070-2153(04)59001-4}, pmid = {14975245}, issn = {0070-2153}, support = {CA16672/CA/NCI NIH HHS/United States ; GM50221/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Cytoplasm/chemistry/*metabolism ; Cytoplasmic Structures/*physiology/*ultrastructure ; Germ Cells/*cytology/*physiology ; Mitochondria/ultrastructure ; Oocytes/physiology/ultrastructure ; Oogenesis/physiology ; RNA/metabolism ; }, }
@article {pmid14970379, year = {2004}, author = {Hartmann, RK and Mörl, M and Sprinzl, M}, title = {The tRNA world.}, journal = {RNA (New York, N.Y.)}, volume = {10}, number = {3}, pages = {344-349}, doi = {10.1261/rna.5240904}, pmid = {14970379}, issn = {1355-8382}, mesh = {Animals ; Computational Biology ; Evolution, Molecular ; Humans ; Mitochondria/physiology ; RNA, Transfer/*physiology ; Ribonucleases/physiology ; }, }
@article {pmid14968308, year = {2004}, author = {Akagi, H and Nakamura, A and Yokozeki-Misono, Y and Inagaki, A and Takahashi, H and Mori, K and Fujimura, T}, title = {Positional cloning of the rice Rf-1 gene, a restorer of BT-type cytoplasmic male sterility that encodes a mitochondria-targeting PPR protein.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {108}, number = {8}, pages = {1449-1457}, pmid = {14968308}, issn = {0040-5752}, mesh = {Amino Acid Sequence ; *Chromosome Mapping ; Chromosomes, Plant/genetics ; Cloning, Molecular ; Cytoplasm/*genetics ; Evolution, Molecular ; Fertility/genetics ; Genes, Duplicate/genetics ; Genes, Plant/*genetics ; Genome, Plant ; Mitochondria/genetics/*metabolism ; Molecular Sequence Data ; Oryza/*genetics ; Phenotype ; Plant Proteins/chemistry/*genetics/*metabolism ; Protein Transport ; Sequence Analysis, DNA ; }, abstract = {The combination of cytoplasmic male sterility (CMS) in one parent and a restorer gene (Rf) to restore fertility in another are indispensable for the development of hybrid varieties. We have found a rice Rf-1 gene that restores BT-type CMS by applying a positional cloning strategy. Using linkage analysis in combination with 6,104 BC(1)F(3) progeny derived from a cross between two near-isogenic lines (NILs) differing only at the Rf-1 locus, we delimited the Rf-1 gene to a 22.4-kb region in the rice genome. Duplicate open reading frames (Rf-1A and Rf-1B) with a pentatricopeptide (PPR) motif were found in this region. Since several insertions and/or deletions were found in the regions corresponding to both the Rf-1A and Rf-1B genes in the maintainer's allele, they may have lost their function. Rf-1A protein had a mitochondria-targeting signal, whereas Rf-1B did not. The Rf-1B gene encoded a shorter polypeptide that was determined by a premature stop codon. Based on the function of the Rf-1 gene, its product is expected to target mitochondria and may process the transcript from an atp6/orf79 region in the mitochondrial genome. Since the Rf-1A gene encodes a 791-amino acid protein with a signal targeting mitochondria and has 16 repeats of the PPR motif, we concluded that Rf-1A is the Rf-1 gene. Nine duplications of Rf-1A homologs were found around the Rf-1 locus in the Nipponbare genome. However, while some of them encoded proteins with the PPR motif, they do not restore BT-type CMS based on the lack of co-segregation with the restoration phenotype. These duplicates may have played diversified roles in RNA processing and/or recombination in mitochondria during the co-evolution of these genes and the mitochondrial genome.}, }
@article {pmid14959454, year = {2003}, author = {de Micheli, A and Chávez, E}, title = {[Ischemia-reperfusion myocardial injury].}, journal = {Archivos de cardiologia de Mexico}, volume = {73}, number = {4}, pages = {284-290}, pmid = {14959454}, issn = {1405-9940}, mesh = {Electrophysiology ; Humans ; Mitochondria/metabolism ; *Myocardial Reperfusion Injury/metabolism/pathology/physiopathology/therapy ; Oxidative Stress ; }, abstract = {In this article, we present some considerations on the myocardial damage due to a deficit of oxygen supply. In fact, this damage properly constitutes a partial diastolic depolarization or injury, i.e., a moderate reduction of the rest transmembrane potential. This phenomenon is characteristic of the acute phase of the myocardial infarction syndrome and is responsible for the main electrical manifestations appearing in this phase: disorders of rhythm and conduction, as well as a reduced contractility of the involved myocardial fibers. All the mentioned phenomena are due to a defect of the myocardial energetic mechanisms, owing to the mitochondrial alterations in myocytes: early reduction of the nicotinamide adenine nucleotides, accumulation of calcium ("calcium overload") into mitochondria, and a drop in oxidative phosphorylation. These changes can present again, more exaggerated, in a following phase of evolution of the myocardial infarction due to myocardial reperfusion. Its severity is related to the duration of the initial ischemia period. Moreover, consequences of the oxidative stress can add producing cellular damage by liberation of reactive oxygen species. Oxidant stress causes also alterations in the mitochondrial DNA, i.e., mutations due to oxidation of nitrogenous bases. During the initial ischemia phase, as well as during reperfusion, metabolic therapy can be very useful as, for example, glucose-insulin-potassium solutions (G-I-K). These could act as scavengers of the free radicals derived from oxygen and avoid or reduce the myocardial damage due to reperfused myocytes. Metabolic drugs, as for example trimetazidine, antioxidants, etc, can also be used in the myocardial reperfusion phase.}, }
@article {pmid14769929, year = {2004}, author = {Reinbothe, S and Quigley, F and Springer, A and Schemenewitz, A and Reinbothe, C}, title = {The outer plastid envelope protein Oep16: role as precursor translocase in import of protochlorophyllide oxidoreductase A.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {101}, number = {7}, pages = {2203-2208}, pmid = {14769929}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Chloroplast Proteins ; Cross-Linking Reagents ; Evolution, Molecular ; Intracellular Membranes/chemistry/*metabolism ; Ion Channels/chemistry/metabolism ; Membrane Transport Proteins/chemistry/*metabolism ; Molecular Sequence Data ; Molecular Weight ; Oxidoreductases Acting on CH-CH Group Donors/*metabolism ; Plant Cells ; Plant Proteins/chemistry/*metabolism ; Plants/chemistry/enzymology/*metabolism ; Plastids/chemistry/*metabolism ; Protein Binding ; Protein Precursors/chemistry/*metabolism ; Protein Transport ; }, abstract = {A 16-kDa plastid envelope protein was identified by chemical crosslinking that interacts with the precursor of NADPH:protochlorophyllide oxdidoreductase A (pPORA) during its posttranslational import into isolated barley chloroplasts. Protein purification and subsequent protein sequencing showed that the 16-kDa protein is an ortholog of a previously identified outer plastid envelope protein, Oep16. A protein of identical size was present in barley etioplasts and interacted with pPORA. Similar 16-kDa protein-dependent crosslink products of pPORA were detected in wheat, pea, and Arabidopsis chloroplasts. Database analyses revealed that the 16-kDa protein belongs to a family of preprotein and amino acid transporters found in free-living bacteria and endosymbiotic mitochondria and chloroplasts. Antibodies raised against the 16-kDa protein inhibited import of pPORA, highlighting its role in protein import.}, }
@article {pmid14767059, year = {2004}, author = {Funes, S and Nargang, FE and Neupert, W and Herrmann, JM}, title = {The Oxa2 protein of Neurospora crassa plays a critical role in the biogenesis of cytochrome oxidase and defines a ubiquitous subbranch of the Oxa1/YidC/Alb3 protein family.}, journal = {Molecular biology of the cell}, volume = {15}, number = {4}, pages = {1853-1861}, pmid = {14767059}, issn = {1059-1524}, mesh = {Amino Acid Sequence ; Blotting, Western ; Cell Division ; DNA/chemistry ; Electron Transport Complex IV/*biosynthesis/chemistry/metabolism ; Gene Deletion ; Genetic Complementation Test ; Genome, Fungal ; Membrane Proteins/chemistry/genetics/*physiology ; Mitochondria/metabolism ; Mitochondrial Proteins/chemistry/*physiology ; Molecular Sequence Data ; Multigene Family ; Mutation ; Neurospora crassa/*metabolism ; Oxidoreductases/metabolism ; Phylogeny ; Plant Proteins ; Protein Binding ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/genetics ; Subcellular Fractions ; Time Factors ; }, abstract = {Proteins of the Oxa1/YidC/Alb3 family mediate the insertion of proteins into membranes of mitochondria, bacteria, and chloroplasts. Here we report the identification of a second gene of the Oxa1/YidC/Alb3 family in the genome of Neurospora crassa, which we have named oxa2. Its gene product, Oxa2, is located in the inner membrane of mitochondria. Deletion of the oxa2 gene caused a specific defect in the biogenesis of cytochrome oxidase and resulted in induction of the alternative oxidase (AOD), which bypasses the need for complex IV of the respiratory chain. The Oxa2 protein of N. crassa complements Cox18-deficient yeast mutants suggesting a common function for both proteins. The oxa2 sequence allowed the identification of a new subfamily of Oxa1/YidC/Alb3 proteins whose members appear to be ubiquitously present in mitochondria of fungi, plants, and animals including humans.}, }
@article {pmid14763899, year = {2004}, author = {Coleman, CS and Hu, G and Pegg, AE}, title = {Putrescine biosynthesis in mammalian tissues.}, journal = {The Biochemical journal}, volume = {379}, number = {Pt 3}, pages = {849-855}, pmid = {14763899}, issn = {1470-8728}, support = {CA-18138/CA/NCI NIH HHS/United States ; }, mesh = {Agmatine/analysis/metabolism ; Animals ; Arginine/metabolism ; Carbon Dioxide/metabolism ; Carboxy-Lyases/analysis/metabolism ; Cell Extracts ; Cloning, Molecular ; Databases, Genetic ; Escherichia coli/enzymology ; Humans ; Kidney/enzymology ; Liver/enzymology ; Mammals/*metabolism ; Mice ; Mitochondria/enzymology ; Ornithine Decarboxylase/genetics/metabolism ; Phylogeny ; Putrescine/*biosynthesis/metabolism ; Rats ; }, abstract = {L-ornithine decarboxylase provides de novo putrescine biosynthesis in mammals. Alternative pathways to generate putrescine that involve ADC (L-arginine decarboxylase) occur in non-mammalian organisms. It has been suggested that an ADC-mediated pathway may generate putrescine via agmatine in mammalian tissues. Published evidence for a mammalian ADC is based on (i) assays using mitochondrial extracts showing production of 14CO2 from [1-14C]arginine and (ii) cloned cDNA sequences that have been claimed to represent ADC. We have reinvestigated this evidence and were unable to find any evidence supporting a mammalian ADC. Mitochondrial extracts prepared from freshly isolated rodent liver and kidney using a metrizamide/Percoll density gradient were assayed for ADC activity using L-[U-14C]-arginine in the presence or absence of arginine metabolic pathway inhibitors. Although 14CO2 was produced in substantial amounts, no labelled agmatine or putrescine was detected. [14C]Agmatine added to liver extracts was not degraded significantly indicating that any agmatine derived from a putative ADC activity was not lost due to further metabolism. Extensive searches of current genome databases using non-mammalian ADC sequences did not identify a viable candidate ADC gene. One of the putative mammalian ADC sequences appears to be derived from bacteria and the other lacks several residues that are essential for decarboxylase activity. These results indicate that 14CO2 release from [1-14C]arginine is not adequate evidence for a mammalian ADC. Although agmatine is a known constituent of mammalian cells, it can be transported from the diet. Therefore L-ornithine decarboxylase remains the only established route for de novo putrescine biosynthesis in mammals.}, }
@article {pmid14762207, year = {2004}, author = {Sheveleva, EV and Hallick, RB}, title = {Recent horizontal intron transfer to a chloroplast genome.}, journal = {Nucleic acids research}, volume = {32}, number = {2}, pages = {803-810}, pmid = {14762207}, issn = {1362-4962}, support = {GM35665/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Chloroplasts/*genetics ; Cyanobacteria/*genetics ; Euglena/enzymology/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal/*genetics ; Genes, Bacterial/genetics ; Genes, Protozoan/genetics ; *Genome ; Introns/*genetics ; Molecular Sequence Data ; Photosystem II Protein Complex/genetics ; Phylogeny ; RNA Splicing/genetics ; RNA-Directed DNA Polymerase/genetics ; Time Factors ; }, abstract = {Evidence is presented for the recent, horizontal transfer of a self-splicing, homing group II intron from a cyanobacteria to the chloroplast genome of Euglena myxocylindracea. The psbA gene of E.myxocylindracea was found to contain a single 2566 nt group II intron with a gene in domain 4 for a 575 amino acid maturase. The predicted secondary structure and tertiary interactions of the group II intron, as well as the derived maturase primary sequence, most closely resemble the homing intron of the cyanobacterium Calothrix and the rnl introns of Porphyra purpurea mitochondria, while being only distantly related to all other Euglena plastid introns and maturases. All main functional domains of the intron-encoded proteins of known homing introns are conserved, including reverse transcriptase domains 1-7, the zinc finger domain and domain X. The close relationship with cyanobacterial introns was confirmed by phylogenetic analysis. Both the full-length psbA intron and a Delta-maturase variant self-splice in vitro in two independent assays. The psbA intron is the first example of a self-splicing chloroplast group II intron from any organism. These results support the conclusion that the psbA intron is the result of a recent horizontal transfer into the E.myxocylindracea chloroplast genome from a cyanobacterial donor and should prompt a reconsideration of horizontal transfer mechanisms to account for the origin of other chloroplast genetic elements.}, }
@article {pmid14756315, year = {2003}, author = {Atteia, A and van Lis, R and Mendoza-Hernández, G and Henze, K and Martin, W and Riveros-Rosas, H and González-Halphen, D}, title = {Bifunctional aldehyde/alcohol dehydrogenase (ADHE) in chlorophyte algal mitochondria.}, journal = {Plant molecular biology}, volume = {53}, number = {1-2}, pages = {175-188}, pmid = {14756315}, issn = {0167-4412}, support = {TW01176/TW/FIC NIH HHS/United States ; }, mesh = {Alcohol Dehydrogenase/*genetics/metabolism ; Aldehyde Dehydrogenase/*genetics/metabolism ; Amino Acid Sequence ; Blotting, Northern ; Chlorophyta/enzymology/*genetics ; DNA, Complementary/chemistry/genetics/isolation &amp; purification ; Electrophoresis, Gel, Two-Dimensional ; Gene Expression Regulation, Enzymologic ; Hydrogen-Ion Concentration ; Mitochondria/*enzymology ; Mitochondrial Proteins/metabolism ; Molecular Sequence Data ; Multienzyme Complexes/genetics/metabolism ; Oxidative Phosphorylation ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Solubility ; }, abstract = {Protein profiles of mitochondria isolated from the heterotrophic chlorophyte Polytomella sp. grown on ethanol at pH 6.0 and pH 3.7 were analyzed by Blue Native and denaturing polyacrylamide gel electrophoresis. Steady-state levels of oxidative phosphorylation complexes were influenced by external pH. Levels of an abundant, soluble, mitochondrial protein of 85 kDa and its corresponding mRNA increased at pH 6.0 relative to pH 3.7. N-terminal and internal sequencing of the 85 kDa mitochondrial protein together with the corresponding cDNA identified it as a bifunctional aldehyde/alcohol dehydrogenase (ADHE) with strong similarity to homologues from eubacteria and amitochondriate protists. A mitochondrial targeting sequence of 27 amino acids precedes the N-terminus of the mature mitochondrial protein. A gene encoding an ADHE homologue was also identified in the genome of Chlamydomonas reinhardtii, a photosynthetic relative of Polytomella. ADHE reveals a complex picture of sequence similarity among homologues. The lack of ADHE from archaebacteria indicates a eubacterial origin for the eukaryotic enzyme. Among eukaryotes, ADHE has hitherto been characteristic of anaerobes since it is essential to cytosolic energy metabolism of amitochondriate protists such as Giardia intestinalis and Entamoeba histolytica. Its abundance and expression pattern suggest an important role for ADHE in mitochondrial metabolism of Polytomella under the conditions studied. The current data are compatible with the view that Polytomella ADHE could be involved either in ethanol production or assimilation, or both, depending upon environmental conditions. Presence of ADHE in an oxygen-respiring algal mitochondrion and co-expression at ambient oxygen levels with respiratory chain components is unexpected with respect to the view that eukaryotes acquired ADHE genes specifically as an adaptation to an anaerobic lifestyle.}, }
@article {pmid14750528, year = {2003}, author = {Benichou, M and Li, Z and Tournier, B and Chaves, A and Zegzouti, H and Jauneau, A and Delalande, C and Latché, A and Bouzayen, M and Spremulli, LL and Pech, JC}, title = {Tomato EF-Ts(mt), a functional mitochondrial translation elongation factor from higher plants.}, journal = {Plant molecular biology}, volume = {53}, number = {3}, pages = {411-422}, pmid = {14750528}, issn = {0167-4412}, support = {GM32734/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Dimerization ; Escherichia coli/genetics/metabolism ; Green Fluorescent Proteins ; Guanine Nucleotide Exchange Factors/metabolism ; Luminescent Proteins/genetics/metabolism ; Solanum lycopersicum/*genetics ; Microscopy, Confocal ; Mitochondria/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Peptide Elongation Factors/chemistry/*genetics/metabolism ; Phylogeny ; Plants/*genetics ; Poly U/metabolism ; Protein Binding ; Protein Conformation ; Protein Transport ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Ethylene-induced ripening in tomato (Lycopersicon esculentum) resulted in the accumulation of a transcript designated LeEF-Ts(mt) that encodes a protein with significant homology to bacterial Ts translational elongation factor (EF-Ts). Transient expression in tobacco and sunflower protoplasts of full-length and truncated LeEF-Ts(mt)-GFP fusion constructs and confocal microscopy observations clearly demonstrated the targeting of LeEF-Ts(mt) to mitochondria and not to chloroplasts and the requirement for a signal peptide for the proper sorting of the protein. Escherichia coli recombinant LeEF-Ts(mt) co-eluted from Ni-NTA resins with a protein corresponding to the molecular weight of the elongation factor EF-Tu of E. coli, indicating an interaction with bacterial EF-Tu. Increasing the GDP concentration in the extraction buffer reduced the amount of EF-Tu in the purified LeEF-Ts(mt) fraction. The purified LeEF-Ts(mt) stimulated the poly(U)-directed polymerization of phenylalanine 10-fold in the presence of EF-Tu. Furthermore, LeEF-Ts(mt) was capable of catalysing the nucleotide exchange reaction with E. coli EF-Tu. Altogether, these data demonstrate that LeEF-Ts(mt) encodes a functional mitochondrial EF-Ts. LeEF-Ts(mt) represents the first mitochondrial elongation factor to be isolated and functionally characterized in higher plants.}, }
@article {pmid14749485, year = {2004}, author = {Nomata, T and Kabeya, Y and Sato, N}, title = {Cloning and characterization of glycine-rich RNA-binding protein cDNAs in the moss Physcomitrella patens.}, journal = {Plant &amp; cell physiology}, volume = {45}, number = {1}, pages = {48-56}, doi = {10.1093/pcp/pch005}, pmid = {14749485}, issn = {0032-0781}, mesh = {Amino Acid Sequence/genetics ; Base Sequence/genetics ; Bryopsida/*genetics/*metabolism ; Cell Nucleus/genetics/metabolism ; DNA, Complementary/genetics/*isolation &amp; purification ; Gene Expression Regulation, Plant/genetics ; Glycine/metabolism ; Introns/genetics ; Mitochondria/genetics/metabolism ; Molecular Biology ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics/isolation &amp; purification/*metabolism ; Protein Structure, Tertiary/genetics ; RNA/metabolism ; RNA-Binding Proteins/genetics/isolation &amp; purification/*metabolism ; Recombinant Fusion Proteins/genetics ; Sequence Homology, Amino Acid ; }, abstract = {We isolated three cDNAs for the genes PpGRP1, PpGRP2 and PpGRP3 that encode glycine-rich RNA-binding proteins (GRPs) from Physcomitrella patens. Three full-length cDNA clones were isolated from a cDNA library prepared from poly(A)(+) RNA from 7-day-old protonemata of P. patens. They were named PpGRP1, PpGRP2 and PpGRP3, which encode putative polypeptides of 162, 178 and 155 residues, respectively. Preliminary genomic sequencing suggested that the positions of the three introns in the PpGRP3 gene are similar to those of introns in Arabidopsis GRP genes. PpGRP3 had a putative transit sequence. The PpGRP1-sGFP and PpGRP2-sGFP fusions were targeted to the cell nucleus, while PpGRP3-sGFP fusion was targeted to mitochondria. The level of these PpGRP transcripts as well as that of PpGRP proteins increased after cold treatment. Homoribopolymer RNA assay revealed that PpGRP3 protein show high affinity for poly(U) and poly(G). Results of phylogenetic analysis suggest that the nuclear and mitochondrial forms of GRP have been established early during the evolution of green plants.}, }
@article {pmid14746448, year = {2004}, author = {Deubel, DV}, title = {From evolution to green chemistry: rationalization of biomimetic oxygen-transfer cascades.}, journal = {Journal of the American Chemical Society}, volume = {126}, number = {4}, pages = {996-997}, doi = {10.1021/ja039234j}, pmid = {14746448}, issn = {0002-7863}, mesh = {Biological Evolution ; Biomimetic Materials/*chemistry ; Hydrogen Peroxide/chemistry ; Oxidation-Reduction ; Oxides/chemistry ; Oxygen/*chemistry/metabolism ; Thermodynamics ; }, abstract = {Thermodynamic electron-transfer potentials from biology textbooks elucidate the sequence of electron-transfer events in the respiratory chain in mitochondria. In this study, thermodynamic and kinetic oxygen-transfer potentials have been defined and predicted for oxidants and substrates using density functional theory, aiming to rationalize multiple oxygen-transfer events in chemical catalysis, particularly in current developments of the Sharpless dihydroxylation. Key transition states for competing mechanisms in a recent dihydroxylation method containing the olefin, osmium tetraoxide, methyltrioxorhenium(VII), a chiral tertiary amine, and the green terminal oxidant hydrogen peroxide have been investigated rigorously. The calculations show the amine to function as an oxygen-transfer mediator between rhenium peroxides and osma-2,5-dioxolanes, in addition to its role as a carrier of chiral information. Unique mechanistic and stereoelectronic patterns in this oxygen-transfer cascade explain the unexpected failure of reactivity predictions using simpler models such as Marcus theory.}, }
@article {pmid14742662, year = {2004}, author = {Ichinoe, A and Behmanesh, M and Tominaga, Y and Ushijima, Y and Hirano, S and Sakai, Y and Tsuchimoto, D and Sakumi, K and Wake, N and Nakabeppu, Y}, title = {Identification and characterization of two forms of mouse MUTYH proteins encoded by alternatively spliced transcripts.}, journal = {Nucleic acids research}, volume = {32}, number = {2}, pages = {477-487}, pmid = {14742662}, issn = {1362-4962}, mesh = {Adenine/metabolism ; Alternative Splicing/*genetics ; Amino Acid Sequence ; Animals ; Cell Line ; Cell Nucleus/enzymology ; DNA Glycosylases/*chemistry/*genetics/isolation &amp; purification/metabolism ; DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism ; Gene Deletion ; Guanine/*analogs &amp; derivatives/metabolism ; Isoenzymes/chemistry/genetics/isolation &amp; purification/metabolism ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Mice, Knockout ; Mitochondria/enzymology ; Molecular Sequence Data ; Protein Transport ; RNA, Messenger/genetics/metabolism ; Recombinant Fusion Proteins ; Solubility ; Stem Cells/enzymology ; Thymus Gland/cytology/enzymology ; }, abstract = {There are three types of mouse Mutyh mRNAs (type a, b and c) generated by alternative splicing, and type b mRNA is a major form among the three in most of the tissues examined. The level of type c mRNA is relatively high in brain. Type a and b mRNAs were expected to encode 57.7 kDa protein (MUTYHalpha), while type c mRNA had a partly different open reading frame encoding a 50.2 kDa protein (MUTYHbeta). An in vitro translation of type b and c mRNAs produced a 50 kDa MUTYHalpha and 47 kDa MUTYHbeta, respectively. MUTYHalpha and MUTYHbeta were detected in wild-type embryonic stem (ES) cells or thymocytes prepared from wild-type mice, but neither MUTYH-null ES cells nor thymocytes prepared from MUTYH-null mice. Both MUTYHalpha and MUTYHbeta were mainly localized in the nuclei and some in mitochondria in wild-type ES cells. Recombinant MUTYHalpha and beta were expressed as fusion proteins with thioredoxin in Escherichia coli, but only MUTYHalpha was partly soluble and thus could be purified. Recombinant MUTYHalpha possessed DNA glycosylase activities to excise adenine opposite 8-oxoguanine and guanine but not AP lyase activity.}, }
@article {pmid14741580, year = {2004}, author = {Friedrich, T and Böttcher, B}, title = {The gross structure of the respiratory complex I: a Lego System.}, journal = {Biochimica et biophysica acta}, volume = {1608}, number = {1}, pages = {1-9}, doi = {10.1016/j.bbabio.2003.10.002}, pmid = {14741580}, issn = {0006-3002}, mesh = {Electron Transport ; Electron Transport Complex I/*chemistry/metabolism/ultrastructure ; Escherichia coli/*chemistry/enzymology ; Models, Molecular ; Protein Conformation ; Proton-Motive Force ; }, abstract = {The proton-pumping NADH:ubiquinone oxidoreductase, also called complex I, is the entry point for electrons into the respiratory chains of many bacteria and mitochondria of most eucaryotes. It couples electron transfer with the translocation of protons across the membrane, thus providing the proton motive force essential for energy-consuming processes. Electron microscopy revealed the 'L'-shaped structure of the bacterial and mitochondrial complex with two arms arranged perpendicular to each other. Recently, we showed that the Escherichia coli complex I takes on another stable conformation with the two arms arranged side by side resulting in a horseshoe-shaped structure. This model reflects the evolution of complex I from pre-existing modules for electron transfer and proton translocation.}, }
@article {pmid14739601, year = {2004}, author = {Fumarola, C and Guidotti, GG}, title = {Stress-induced apoptosis: toward a symmetry with receptor-mediated cell death.}, journal = {Apoptosis : an international journal on programmed cell death}, volume = {9}, number = {1}, pages = {77-82}, doi = {10.1023/B:APPT.0000012124.30095.09}, pmid = {14739601}, issn = {1360-8185}, mesh = {Animals ; *Apoptosis ; Caspase Inhibitors ; Caspases/metabolism ; Evolution, Molecular ; Humans ; Mitochondria/pathology ; Models, Biological ; Signal Transduction ; }, abstract = {Apoptosis is a form of programmed cell death executed by caspases activated along signalling pathways initiated by ligation of cell-surface death receptors (extrinsic pathway) or by perturbation of the mithocondrial membrane promoted by physical or chemical stress agents (intrinsic pathway). In metazoans, this evolutionary conserved, genetically controlled process has a role in a variety of physiological settings, as development, homeostasis of tissues and maintenance of the organism integrity. When deranged by impaired regulation or inappropriate activation apoptosis contributes to the pathogenesis of diseases as autoimmunity, cancer, restenosis, ischaemia, heart failure and neurodegenerative disorders. In this review we will present a survey of the stress-induced intrinsic, mithochondrial, pathway and, based on recent experimental data, we will propose a view compatible with an emergent conceptual symmetry between the two apoptogenic extrinsic and intrinsic pathways. Elements of symmetry present in both the apoptogenic signalling pathways include: early activation of initiator caspases (feed-forwarded by a direct or post-mitocondrial effector caspase-mediated amplification loop in some cell types) and mitochondrial membrane permeabilization with required release of antagonists of active caspase inhibitors (IAPs) in high-level IAPs-expressing cells and apoptosome-mediated amplification of the caspase cascade more or less needed in different cell types.}, }
@article {pmid14739251, year = {2004}, author = {Birdsey, GM and Lewin, J and Cunningham, AA and Bruford, MW and Danpure, CJ}, title = {Differential enzyme targeting as an evolutionary adaptation to herbivory in carnivora.}, journal = {Molecular biology and evolution}, volume = {21}, number = {4}, pages = {632-646}, doi = {10.1093/molbev/msh054}, pmid = {14739251}, issn = {0737-4038}, mesh = {Adaptation, Biological/*genetics ; Amino Acid Sequence ; Animals ; Carnivora/classification/*genetics/metabolism ; *Evolution, Molecular ; *Food Preferences ; Green Fluorescent Proteins/analysis/genetics ; Microscopy, Immunoelectron ; Mitochondria/ultrastructure ; Molecular Sequence Data ; Peroxisomes/ultrastructure ; Phylogeny ; Sequence Alignment ; Transaminases/analysis/*genetics/metabolism ; }, abstract = {Not all members of the order Carnivora are carnivorous. Some are omnivorous, and a few, such as the giant panda, Ailuropoda melanoleuca, are almost exclusively herbivorous. Although a number of adaptations to increased plant-eating are recognized within Carnivora, few have been studied at the molecular level. One molecular adaptation to diet that is spread widely across Mammalia is the differential intracellular targeting of the intermediary metabolic enzyme alanine:glyoxylate aminotransferase (AGT), which tends to be mitochondrial in carnivores, peroxisomal in herbivores, and both mitochondrial and peroxisomal in omnivores. In the present study, we have analyzed the targeting of AGT in Carnivora in relation to species' natural diets. We show not only that there has been an adaptive shift in AGT targeting from the mitochondrion toward the peroxisome as diets have shifted from being mainly carnivorous to ones that are more omnivorous and herbivorous but also that in one lineage, namely that of the giant panda, there is evidence for positive selection pressure at the molecular level on the AGT mitochondrial targeting sequence to decrease its efficiency, thereby allowing more AGT to be targeted to the peroxisomes.}, }
@article {pmid14739247, year = {2004}, author = {Lucattini, R and Likic, VA and Lithgow, T}, title = {Bacterial proteins predisposed for targeting to mitochondria.}, journal = {Molecular biology and evolution}, volume = {21}, number = {4}, pages = {652-658}, doi = {10.1093/molbev/msh058}, pmid = {14739247}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics/metabolism ; Computational Biology ; Escherichia coli Proteins/*genetics/metabolism ; *Evolution, Molecular ; Mitochondria/*metabolism ; Mitochondrial Proteins/*genetics/metabolism ; Models, Biological ; Molecular Sequence Data ; Protein Transport/genetics ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Sequence Alignment ; }, abstract = {Mitochondria evolved from an endosymbiotic proteobacterium in a process that required the transfer of genes from the bacterium to the host cell nucleus, and the translocation of proteins thereby made in the host cell cytosol into the internal compartments of the organelle. According to current models for this evolution, two highly improbable events are required to occur simultaneously: creation of a protein translocation machinery to import proteins back into the endosymbiont and creation of targeting sequences on the protein substrates themselves. Using a combination of two independent prediction methods, validated through tests on simulated genomes, we show that at least 5% of proteins encoded by an extant proteobacterium are predisposed for targeting to mitochondria, and propose we that mitochondrial targeting information was preexisting for many proteins of the endosymbiont. We analyzed a family of proteins whose members exist both in bacteria and in mitochondria of eukaryotes and show that the amino-terminal extensions occasionally found in bacterial family members can function as a crude import sequence when the protein is presented to isolated mitochondria. This activity leaves the development of a primitive translocation channel in the outer membrane of the endosymbiont as a single hurdle to initiating the evolution of mitochondria.}, }
@article {pmid14738316, year = {2003}, author = {Yokobori, S and Watanabe, Y and Oshima, T}, title = {Mitochondrial genome of Ciona savignyi (Urochordata, Ascidiacea, Enterogona): comparison of gene arrangement and tRNA genes with Halocynthia roretzi mitochondrial genome.}, journal = {Journal of molecular evolution}, volume = {57}, number = {5}, pages = {574-587}, pmid = {14738316}, issn = {0022-2844}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Genetic Code ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer/*genetics ; Sequence Analysis, DNA ; *Synteny ; Urochordata/*genetics ; }, abstract = {The complete nucleotide sequence of the urochordate Ciona savignyi (Ascidiacea, Enterogona) mitochondrial (mt) genome (14,737 bp) was determined. The Ciona mt genome does not encode a gene for ATP synthetase subunit 8 but encodes an additional tRNAGly gene (anticodon UCU), as is the case in another urochordate, Halocynthia roretzi (Ascidiacea, Pleurogona), mt genome. In addition, the Ciona mt genome encodes two tRNAMet genes; anticodon CAT and anticodon TAT. The tRNACys gene is thought to lack base pairs at the D-stem. Thus, the Ciona mt genome encodes 12 protein, 2 rRNA, and 24 tRNA genes. The gene arrangement of the Ciona mt genome differs greatly from those of any other metazoan mt genomes reported to date. Only three gene boundaries are shared between the Halocynthia and the Ciona mt genomes. Molecular phylogenetic analyses based on amino acid sequences of mt protein genes failed to demonstrate the monophyly of the chordates.}, }
@article {pmid14736150, year = {2003}, author = {Zhou, L and Sriram, R and Visvesvara, GS and Xiao, L}, title = {Genetic variations in the internal transcribed spacer and mitochondrial small subunit rRNA gene of Naegleria spp.}, journal = {The Journal of eukaryotic microbiology}, volume = {50 Suppl}, number = {}, pages = {522-526}, doi = {10.1111/j.1550-7408.2003.tb00617.x}, pmid = {14736150}, issn = {1066-5234}, mesh = {Animals ; Base Sequence ; DNA Primers ; DNA, Protozoan/genetics ; DNA, Ribosomal/*genetics ; *Genetic Variation ; Mitochondria/*genetics ; Molecular Sequence Data ; Naegleria/classification/*genetics/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; *Transcription, Genetic ; }, abstract = {Naegleria spp. are widely distributed free-living amebas, but one species in the genus, N. fowleri, causes acute fulminant primary amebic meningoencephalitis in humans and other animals. Thus, it is important to differentiate N. fowleri from the rest in the genus of Naegleria, and to develop tools for the detection of intra-specific genetic variations. In this study, one isolate each of N. australiensis, N. gruberi, N. jadini, and N. lovaniensis and 22 isolates of N. fowleri were characterized at the internal transcribed spacers (ITS) and mitochondrial small subunit rRNA (mtSSU rRNA) gene. The mtSSU rRNA primers designed amplified DNA of all isolates, with distinct sequences obtained from all species examined. In contrast, the ITS primers only amplified DNA from N. lovaniensis and N. fowleri, with minor sequence differences between the two. Three genotypes of N. fowleri were found among the isolates analyzed in both the mtSSU rRNA gene and ITS. The extent of sequence variation was greater in the mtSSU rRNA gene, but the ITS had the advantage of length polymorphism. These data should be useful in the development of molecular tools for rapid species differentiation and genotyping of Naegleria spp.}, }
@article {pmid14735123, year = {2004}, author = {Timmis, JN and Ayliffe, MA and Huang, CY and Martin, W}, title = {Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes.}, journal = {Nature reviews. Genetics}, volume = {5}, number = {2}, pages = {123-135}, doi = {10.1038/nrg1271}, pmid = {14735123}, issn = {1471-0056}, mesh = {Biological Evolution ; Biological Transport ; Cell Nucleus/genetics/metabolism ; Chloroplasts/genetics/metabolism ; Chromosomes/*genetics ; Cytoplasm/genetics/metabolism ; DNA/*metabolism ; Eukaryotic Cells ; Extrachromosomal Inheritance/*genetics ; Mitochondria/metabolism ; Organelles/*genetics/metabolism ; }, }
@article {pmid14729454, year = {2004}, author = {Gwo, JC and Yang, WT and Kuo, MC and Takemura, A and Cheng, HY}, title = {Spermatozoal ultrastructures of two marine perciform teleost fishes, the goatfish, Paraupeneus spilurus (Mullidae) and the rabbitfish, Siganus fuscescens (Siganidae) from Taiwan.}, journal = {Tissue &amp; cell}, volume = {36}, number = {1}, pages = {63-69}, doi = {10.1016/j.tice.2003.10.001}, pmid = {14729454}, issn = {0040-8166}, mesh = {Animals ; Male ; Microscopy, Electron ; Microscopy, Electron, Scanning ; *Perciformes ; Phylogeny ; Species Specificity ; Spermatozoa/*ultrastructure ; Taiwan ; }, abstract = {Mature spermatozoa of two perciform teleost fishes, Paraupeneus spilurus (Mullidae) and Siganus fuscescens (Siganidae) from Taiwan were examined using transmission and scanning electron microscopy. Despite the fact that spermatozoa of both species are of the primitive type, the results of the present study highlight the potential application of spermatozoal morphology in studies of fish phylogenetic relationships. To our knowledge, the flattened nucleus observed in P. spilurus spermatozoa is reported for the first time. Several features common to Sigandae spermatozoa-the unusual almost parallel situation of the centrioles, the arrangement of mitochondria and the near absence of shallow nuclear fossa-are significantly different from other common teleost sperm types. These unique features may be synapomorphies for the Siganidae and Mullidae and evidently contribute to the study of phylogenetic relationships in teleosts.}, }
@article {pmid14729451, year = {2004}, author = {Zama, U and Lino-Neto, J and Dolder, H}, title = {Structure and ultrastructure of spermatozoa in Meliponini (stingless bees) (Hymenoptera: Apidae).}, journal = {Tissue &amp; cell}, volume = {36}, number = {1}, pages = {29-41}, doi = {10.1016/j.tice.2003.08.003}, pmid = {14729451}, issn = {0040-8166}, mesh = {Acrosome/ultrastructure ; Animals ; Bees/classification/*cytology ; Centrioles/ultrastructure ; Male ; Microscopy, Electron ; Mitochondria/ultrastructure ; Phylogeny ; Seminal Vesicles/cytology ; Sperm Head/ultrastructure ; Sperm Tail/ultrastructure ; Spermatozoa/*ultrastructure ; }, abstract = {In spite of their importance in the reproduction of phanerograms, few bees have received an adequate description of their sperm ultrastructure. In this study, we concluded that it was possible to define a characteristic pattern for Meliponini spermatozoa. However, we have also found species-specific differences that could be used, for example, in a taxonomic or phylogenetic evaluation. Meliponini spermatozoa are made up of a head and a flagellar region. The head includes an acrosome containing the perforatorium, covered by the acrosomal vesicle and a nucleus. In transverse sections, the acrosome is circular at the tip but becomes triangular as it nears the nucleus. The perforatorium base penetrates into a small cavity in the nuclear tip. The flagellum consists of an axoneme, a pair of mitochondrial derivatives, a centriolar adjunct and a pair of accessory bodies. The axoneme has a typical 9+9+2 microtubule pattern. In the final portion, the axoneme becomes gradually disorganized with the accessory microtubules terminating last. The mitochondrial derivatives are asymmetric in length and diameter. In cross-section, they are ellipsoidal and the larger one has a paracrystalline region. The centriolar adjunct begins at the nuclear base and extends parallel to the axoneme up to the anterior end of the smaller mitochondrial derivative.}, }
@article {pmid14726512, year = {2004}, author = {Mühlenbein, N and Hofmann, S and Rothbauer, U and Bauer, MF}, title = {Organization and function of the small Tim complexes acting along the import pathway of metabolite carriers into mammalian mitochondria.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {14}, pages = {13540-13546}, doi = {10.1074/jbc.M312485200}, pmid = {14726512}, issn = {0021-9258}, mesh = {Animals ; Biological Transport ; Evolution, Molecular ; HeLa Cells ; Humans ; Mammals ; Membrane Transport Proteins/*metabolism ; Mice ; Mitochondria, Liver/*metabolism ; Mitochondrial Proteins/*metabolism ; Yeasts/metabolism ; }, abstract = {Tim9, Tim10a, and Tim10b are members of the family of small Tim proteins located in the intermembrane space of mammalian mitochondria. In yeast, members of this family act along the TIM22 import pathway during import of metabolite carriers and other integral inner membrane proteins. Here, we show that the human small proteins form two distinct hetero-oligomeric complexes. A 70-kDa complex that contains Tim9 and Tim10a and a Tim9-10a-10b that is part of a higher molecular weight assembly of 450 kDa. This distribution among two complexes suggests Tim10b to be the functional homologue of yeast Tim12. Both human complexes are tightly associated with the inner membrane and, compared with yeast, soluble 70-kDa complexes appear to be completely absent in the intermembrane space. Thus, the function of soluble 70-kDa complexes as trans-site receptors for incoming carrier proteins is not conserved from lower to higher eukaryotes. During import, the small Tim complexes directly interact with human adenine nucleotide translocator (ANT) in transit in a metal-dependent manner. For insertion of carrier preproteins into the inner membrane, the human small Tim proteins directly interact with human Tim22, the putative insertion pore of the TIM22 translocase. However, in contrast to yeast, only a small fraction of Tim9-Tim10a-Tim10b complex is in a stable association with Tim22. We conclude that different mechanisms and specific requirements for import and insertion of mammalian carrier preproteins have evolved in higher eukaryotes.}, }
@article {pmid14717597, year = {2004}, author = {Bowman, MK and Berry, EA and Roberts, AG and Kramer, DM}, title = {Orientation of the g-tensor axes of the Rieske subunit in the cytochrome bc1 complex.}, journal = {Biochemistry}, volume = {43}, number = {2}, pages = {430-436}, doi = {10.1021/bi034620z}, pmid = {14717597}, issn = {0006-2960}, support = {GM61904/GM/NIGMS NIH HHS/United States ; R01DK44842/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Catalysis ; Cattle ; Crystallization ; Dimerization ; Electron Spin Resonance Spectroscopy ; Electron Transport ; Electron Transport Complex III/antagonists &amp; inhibitors/*chemistry ; Enzyme Inhibitors/chemistry ; Iron-Sulfur Proteins/antagonists &amp; inhibitors/*chemistry ; Ligands ; Mitochondria/*enzymology ; Polyenes/chemistry ; Protein Subunits/antagonists &amp; inhibitors/*chemistry ; }, abstract = {The orientation of the g-tensors of the Rieske iron-sulfur protein subunit was determined in a single crystal of the bovine mitochondrial cytochrome bc1 complex with stigmatellin in the Qo quinol binding site. The g-tensor principal axes are skewed with respect to the Fe-Fe and S-S atom direction in the 2Fe2S cluster, which is allowed by the lack of rigorous symmetry of the cluster. The asymmetric unit in the crystal is the active dimer, and the g-tensor axes have slightly different orientations relative to the iron-sulfur cluster in the two halves of the dimer. The g approximately 1.79 axis makes an average angle of 30 degrees with respect to the Fe-Fe direction and the g approximately 2.024 axis an average angle of 26 degrees with respect to the S-S direction. This assignment of the g-tensor axis directions indicates that conformations of the Rieske protein are likely the same in the cytochrome bc1 and b6f complexes and that the extent of motion of the Rieske head domain during the catalytic cycle has been highly conserved during evolution of these distantly related complexes.}, }
@article {pmid14717589, year = {2004}, author = {Ladner, JE and Parsons, JF and Rife, CL and Gilliland, GL and Armstrong, RN}, title = {Parallel evolutionary pathways for glutathione transferases: structure and mechanism of the mitochondrial class kappa enzyme rGSTK1-1.}, journal = {Biochemistry}, volume = {43}, number = {2}, pages = {352-361}, doi = {10.1021/bi035832z}, pmid = {14717589}, issn = {0006-2960}, support = {P30 ES00267/ES/NIEHS NIH HHS/United States ; R01 GM30910/GM/NIGMS NIH HHS/United States ; RR07707/RR/NCRR NIH HHS/United States ; T32 ES07028/ES/NIEHS NIH HHS/United States ; T32 GM08320/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Substitution/genetics ; Animals ; Binding Sites ; Catalysis ; Crystallography, X-Ray ; Dimerization ; *Evolution, Molecular ; Glutathione/chemistry/metabolism ; Glutathione Transferase/*chemistry/genetics/*metabolism ; Isoenzymes/chemistry/metabolism ; Kinetics ; Mitochondria/*enzymology ; Protein Binding ; Protein Subunits/chemistry/metabolism ; Rats ; Serine/genetics ; Structure-Activity Relationship ; }, abstract = {The class kappa glutathione (GSH) transferase is an enzyme that resides in the mitochondrial matrix. Its relationship to members of the canonical GSH transferase superfamily has remained an enigma. The three-dimensional structure of the class kappa enzyme from rat (rGSTK1-1) in complex with GSH has been solved by single isomorphous replacement with anomalous scattering at a resolution of 2.5 A. The structure reveals that the enzyme is more closely related to the protein disulfide bond isomerase, dsbA, from Escherichia coli than it is to members of the canonical superfamily. The structures of rGSTK1-1 and the canonical superfamily members indicate that the proteins folds have diverged from a common thioredoxin/glutaredoxin progenitor but did so by different mechanisms. The mitochondrial enzyme, therefore, represents a fourth protein superfamily that supports GSH transferase activity. The thioredoxin domain functions in a manner that is similar to that seen in the canonical enzymes by providing key structural elements for the recognition of GSH. The hydroxyl group of S16 is within hydrogen-bonding distance of the sulfur of bound GSH and is, in part, responsible for the ionization of the thiol in the E*GSH complex (pKa = 6.4 +/- 0.1). Preequilibrium kinetic experiments indicate that the k(on) for GSH is 1 x 10(5) M(-1) s(-1) and k(off) for GS- is approximately 8 s(-1) and relatively slow with respect to turnover with 1-chloro-2, 4-dinitrobenzene (CDNB). As a result, the KM(GSH) (11 mM) is much larger than the apparent Kd(GSH) (90 microM). The active site has a relatively open access channel that is flanked by disordered loops that may explain the relatively high turnover number (280 s(-1) at pH 7.0) toward CDNB. The disordered loops form an extensive contiguous patch on one face of the dimeric enzyme, a fact that suggests that the protein surface may interact with a membrane or other protein partner.}, }
@article {pmid14716012, year = {2004}, author = {Ruiz-Pesini, E and Mishmar, D and Brandon, M and Procaccio, V and Wallace, DC}, title = {Effects of purifying and adaptive selection on regional variation in human mtDNA.}, journal = {Science (New York, N.Y.)}, volume = {303}, number = {5655}, pages = {223-226}, doi = {10.1126/science.1088434}, pmid = {14716012}, issn = {1095-9203}, support = {AG13154/AG/NIA NIH HHS/United States ; HL64017/HL/NHLBI NIH HHS/United States ; NS21328/NS/NINDS NIH HHS/United States ; NS37167/NS/NINDS NIH HHS/United States ; }, mesh = {*Adaptation, Physiological ; Africa ; Arctic Regions ; Asia ; *Climate ; Cold Climate ; Conserved Sequence ; DNA, Mitochondrial/*genetics ; Emigration and Immigration ; Energy Metabolism ; Europe ; Genetic Predisposition to Disease ; *Genetic Variation ; Haplotypes ; Humans ; Longevity ; Metabolic Diseases/genetics ; Mitochondria/metabolism ; Mutation ; Neurodegenerative Diseases/genetics ; Phenotype ; Phylogeny ; Racial Groups/genetics ; *Selection, Genetic ; Siberia ; }, abstract = {A phylogenetic analysis of 1125 global human mitochondrial DNA (mtDNA) sequences permitted positioning of all nucleotide substitutions according to their order of occurrence. The relative frequency and amino acid conservation of internal branch replacement mutations was found to increase from tropical Africa to temperate Europe and arctic northeastern Siberia. Particularly highly conserved amino acid substitutions were found at the roots of multiple mtDNA lineages from higher latitudes. These same lineages correlate with increased propensity for energy deficiency diseases as well as longevity. Thus, specific mtDNA replacement mutations permitted our ancestors to adapt to more northern climates, and these same variants are influencing our health today.}, }
@article {pmid14715441, year = {2003}, author = {Rapoport, SI}, title = {Coupled reductions in brain oxidative phosphorylation and synaptic function can be quantified and staged in the course of Alzheimer disease.}, journal = {Neurotoxicity research}, volume = {5}, number = {6}, pages = {385-398}, pmid = {14715441}, issn = {1029-8428}, mesh = {Alzheimer Disease/*metabolism/pathology/physiopathology ; Brain/pathology ; Brain Chemistry/*physiology ; Diagnostic Imaging ; Disease Progression ; Humans ; *Oxidative Phosphorylation ; Synapses/pathology/*physiology ; }, abstract = {In vivo, post-mortem and biopsy data suggest that coupled declines occur in brain synaptic activity and brain energy consumption during the evolution of Alzheimer disease. In the first stage of these declines, changes in synaptic structure and function reduce neuronal energy demand and lead to potentially reversible downregulation of oxidative phosphorylation (OXPHOS) within neuronal mitochondria. At this stage, measuring brain glucose metabolism or brain blood flow in patients, using positron emission tomography (PET), shows that the brain can be almost normally activated in response to stimulation. Thus, therapy at this stage should be designed to re-establish synaptic integrity or prevent its further deterioration. As disease progresses, neurofibrillary tangles with abnormally phosphorylated tau protein accumulate within neuronal cytoplasm, to the point that they co-opt the nonphosphorylated tau necessary for axonal transport of mitochondria between the cell nucleus and the synapse. In this second stage, severe energy depletion and other pathological processes associated with irreversibly downregulated OXPHOS lead to cell death, and the brain cannot normally respond to functional stimulation.}, }
@article {pmid14715231, year = {2004}, author = {Hardman, M}, title = {The phylogenetic relationships among Noturus catfishes (Siluriformes: Ictaluridae) as inferred from mitochondrial gene cytochrome b and nuclear recombination activating gene 2.}, journal = {Molecular phylogenetics and evolution}, volume = {30}, number = {2}, pages = {395-408}, doi = {10.1016/s1055-7903(03)00203-3}, pmid = {14715231}, issn = {1055-7903}, mesh = {Animals ; Catfishes ; Cell Nucleus/metabolism ; Cytochromes b/*genetics ; DNA, Mitochondrial/*genetics ; DNA-Binding Proteins/*genetics ; Mitochondria/metabolism ; Phylogeny ; *Recombination, Genetic ; }, abstract = {Madtom catfishes of the genus Noturus are a well-known component of the North American ichthyofauna. Original nucleotide sequence data were collected from mitochondrial (cytochrome b) and nuclear (recombination activating gene 2) genes and used to estimate genetic variation and infer phylogenetic relationships among and within species of Noturus. Mitochondrial sequences were variable among species and several species were found to contain considerable genetic diversity. Relationships among members of the subgenus Rabida were resolved and in many cases well supported. Relationships among members of the subgenus Schilbeodes were poorly resolved. Previous phylogenetic hypotheses and the traditional classification (except the furiosus species group) were rejected in their explicit form according to the Kishino-Hasegawa and Shimodaira-Hasegawa tests of tree score difference.}, }
@article {pmid14715228, year = {2004}, author = {Mattern, MY}, title = {Molecular phylogeny of the Gasterosteidae: the importance of using multiple genes.}, journal = {Molecular phylogenetics and evolution}, volume = {30}, number = {2}, pages = {366-377}, doi = {10.1016/s1055-7903(03)00190-8}, pmid = {14715228}, issn = {1055-7903}, mesh = {Adenosine Triphosphatases/metabolism ; Animals ; Cytochromes b/metabolism ; DNA/metabolism ; DNA Primers/genetics ; DNA, Mitochondrial/*metabolism ; Fishes/*genetics ; Likelihood Functions ; Mitochondria ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Gasterosteidae is an important model system in evolutionary biology. Phylogenetic relationships have previously been constructed based upon morphological and behavioral data, but to date no one has investigated those relationships using molecular characters. This paper reports the results of an analysis using sequences from five mitochondrial genes (12S rRNA, 16S rRNA, cytochrome b, ATPase 6, and control region). Phylogenetic analysis of 2879 bp produced a single most parsimonious tree with a consistency index of 72.6%. That tree agrees with the behavior+morphology topology, with one exception: Apeltes is placed as the sister group to Pungitius+Culaea, rather than as the sister-group of (Pungitius+Culaea)+Gasterosteus. This study highlights the importance of using multiple mitochondrial genes in a phylogenetic analysis. Separately, the five genes produced four significantly different topologies, and might have given different versions of gasterosteid relationships had only one or two genes been sequenced. It is thus imperative that comparative biologists choose only trees that contain multiple mitochondrial genes as the basis for studies of evolutionary patterns and processes.}, }
@article {pmid14715222, year = {2004}, author = {Vences, M and Chiari, Y and Raharivololoniaina, L and Meyer, A}, title = {High mitochondrial diversity within and among populations of Malagasy poison frogs.}, journal = {Molecular phylogenetics and evolution}, volume = {30}, number = {2}, pages = {295-307}, doi = {10.1016/s1055-7903(03)00217-3}, pmid = {14715222}, issn = {1055-7903}, mesh = {Animals ; Anura ; Cytochromes b/genetics ; DNA, Mitochondrial/metabolism ; Haplotypes ; Madagascar ; Mitochondria/*metabolism ; Multigene Family ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Rhodopsin/genetics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The diurnal, brightly colored, and toxic frogs of the genus Mantella are among the most prominent representatives of the endemic anuran fauna of Madagascar. Especially three closely related species, M. aurantiaca, M. crocea, and M. milotympanum, are intensively collected for the pet trade, although basic data on their natural history and genetic diversity are still lacking. Our phylogenetic analyses based on 2.8 kbp of partial 16S rRNA, 12S rRNA, cytochrome b, and rhodopsin DNA sequences confirmed that these species belong to one of the five major clades in Mantella, the M. madagascariensis group. A haplotype network constructed using 830 bp of cytochrome b in 49 individuals from seven populations revealed that M. milotympanum and M. crocea have largely similar haplotypes sharing, confirming doubts about the species validity of M. milotympanum and indicating independent evolution of bright orange pattern in M. milotympanum and M. aurantiaca. Further, clustering of four individuals of M. aurantiaca from Andranomena with M. crocea suggests incomplete lineage sorting or introgression resulting from secondary contact of refugial populations. AMOVA confirmed significant intrapopulation nucleotide diversity (>20%). These diversity patterns and our field observations indicate relatively large population sizes. Hence, overcollecting is probably a minor problem and conservation efforts should rather focus on saving some large populations from habitat destruction through logging and forest fires.}, }
@article {pmid14715220, year = {2004}, author = {Teske, PR and Cherry, MI and Matthee, CA}, title = {The evolutionary history of seahorses (Syngnathidae: Hippocampus): molecular data suggest a West Pacific origin and two invasions of the Atlantic Ocean.}, journal = {Molecular phylogenetics and evolution}, volume = {30}, number = {2}, pages = {273-286}, doi = {10.1016/s1055-7903(03)00214-8}, pmid = {14715220}, issn = {1055-7903}, mesh = {Animals ; Atlantic Ocean ; Bayes Theorem ; Cell Nucleus/metabolism ; Evolution, Molecular ; Genetic Markers ; Mitochondria/metabolism ; Pacific Ocean ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/chemistry/genetics ; Smegmamorpha/*genetics ; Species Specificity ; }, abstract = {Sequence data derived from four markers (the nuclear RP1 and Aldolase and the mitochondrial 16S rRNA and cytochrome b genes) were used to determine the phylogenetic relationships among 32 species belonging to the genus Hippocampus. There were marked differences in the rate of evolution among these gene fragments, with Aldolase evolving the slowest and the mtDNA cytochrome b gene the fastest. The RP1 gene recovered the highest number of nodes supported by >70% bootstrap values from parsimony analysis and >95% posterior probabilities from Bayesian inference. The combined analysis based on 2317 nucleotides resulted in the most robust phylogeny. A distinct phylogenetic split was identified between the pygmy seahorse, Hippocampus bargibanti, and a clade including all other species. Three species from the western Pacific Ocean included in our study, namely H. bargibanti, H. breviceps, and H. abdominalis occupy basal positions in the phylogeny. This and the high species richness in the region suggests that the genus evolved somewhere in the West Pacific. There is also fairly strong molecular support for the remaining species being subdivided into three main evolutionary lineages: two West Pacific clades and a clade of species present in both the Indo-Pacific and the Atlantic Ocean. The phylogeny obtained herein suggests at least two independent colonization events of the Atlantic Ocean, once before the closure of the Tethyan seaway, and once afterwards.}, }
@article {pmid14713334, year = {2004}, author = {Miranda-Vizuete, A and Sadek, CM and Jiménez, A and Krause, WJ and Sutovsky, P and Oko, R}, title = {The mammalian testis-specific thioredoxin system.}, journal = {Antioxidants &amp; redox signaling}, volume = {6}, number = {1}, pages = {25-40}, doi = {10.1089/152308604771978327}, pmid = {14713334}, issn = {1523-0864}, support = {OH07324-01/OH/NIOSH CDC HHS/United States ; }, mesh = {Animals ; Humans ; Male ; Oxidation-Reduction ; Phylogeny ; Spermatids/chemistry/metabolism ; Spermatozoa/ultrastructure ; Testis/chemistry/*metabolism ; Thioredoxin-Disulfide Reductase/chemistry/genetics/*metabolism ; Thioredoxins/chemistry/*metabolism ; }, abstract = {Redox control of cell physiology is one of the most important regulatory mechanisms in all living organisms. The thioredoxin system, composed of thioredoxin and thioredoxin reductase, has emerged as a key player in cellular redox-mediated reactions. For many years, only one thioredoxin system had been described in higher organisms, ubiquitously expressed in the cytoplasm of eukaryotic cells. However, during the last decade, we and others have identified and characterized novel thioredoxin systems with unique properties, such as organelle-specific localization in mitochondria or endoplasmic reticulum, tissue-specific distribution mostly in the testis, and features novel for thioredoxins, such as microtubule-binding properties. In this review, we will focus on the mammalian testis-specific thioredoxin system that comprises three thioredoxins exclusively expressed in spermatids (named Sptrx-1, Sptrx-2, and Sptrx-3) and an additional thioredoxin highly expressed in testis, but also present in lung and other ciliated tissues (Txl-2). The implications of these findings in the context of male fertility and testicular cancer, as well as evolutionary aspects, will be discussed.}, }
@article {pmid14711083, year = {2003}, author = {Williams, BA and Keeling, PJ}, title = {Cryptic organelles in parasitic protists and fungi.}, journal = {Advances in parasitology}, volume = {54}, number = {}, pages = {9-68}, doi = {10.1016/s0065-308x(03)54001-5}, pmid = {14711083}, issn = {0065-308X}, mesh = {Animals ; Eukaryota/*physiology ; Fungi/*physiology ; Organelles/*physiology ; Parasites/*physiology ; Phylogeny ; }, abstract = {A number of parasitic protists and fungi have adopted extremely specialised characteristics of morphology, biochemistry, and molecular biology, sometimes making it difficult to discern their evolutionary origins. One aspect of several parasitic groups that reflects this is their metabolic organelles, mitochondria and plastids. These organelles are derived from endosymbiosis with an alpha-proteobacterium and a cyanobacterium respectively, and are home to a variety of core metabolic processes. As parasites adapted, new demands, or perhaps a relaxation of demands, frequently led to significant changes in these organelles. At the extreme, the organelles are degenerated and transformed beyond recognition, and are referred to as "cryptic". Generally, there is no prior cytological evidence for a cryptic organelle, and its presence is only discovered through phylogenetic analysis of molecular relicts followed by their localisation to organelle-like structures. Since the organelles are derived from eubacteria, the genes for proteins and RNAs associated with them are generally easily recognisable, and since the metabolic activities retained in these organelles are prokaryotic, or at least very unusual, they often serve as an important target for therapeutics. Cryptic mitochondria are now known in several protist and fungal parasites. In some cases (e.g., Trichomonas), well characterised but evolutionarily enigmatic organelles called hydrogenosomes were shown to be derived from mitochondria. In other cases (e.g., Entamoeba and microsporidia), "amitochondriate" parasites have been shown to harbour a previously undetected mitochondrial organelle. Typically, little is known about the functions of these newly discovered organelles, but recent progress in several groups has revealed a number of potential functions. Cryptic plastids have now been found in a small number of parasites that were not previously suspected to have algal ancestors. One recent case is the discovery that helicosporidian parasites are really highly adapted green alga, but the most spectacular case is the discovery of a plastid in the Apicomplexa. Apicomplexa are very well-studied parasites that include the malaria parasite, Plasmodium, so the discovery of a cryptic plastid in Apicomplexa came as quite a surprise. The apicomplexan plastid is now very well characterised and has been shown to function in the biosynthesis of fatty acids, isopentenyl diphosphate and heme, activities also found in photosynthetic plastids.}, }
@article {pmid14710997, year = {2004}, author = {Hu, M and Chilton, NB and Gasser, RB}, title = {The mitochondrial genomics of parasitic nematodes of socio-economic importance: recent progress, and implications for population genetics and systematics.}, journal = {Advances in parasitology}, volume = {56}, number = {}, pages = {133-212}, doi = {10.1016/s0065-308x(03)56003-1}, pmid = {14710997}, issn = {0065-308X}, mesh = {Animals ; Classification/methods ; Genetic Markers ; *Genetics, Population ; *Genomics ; Mitochondria/classification/*genetics ; *Nematoda/classification/genetics ; Parasites/classification/*genetics ; Socioeconomic Factors ; }, abstract = {Mitochondria are subcellular organelles in which oxidative phosphorylation and other important biochemical functions take place within the cell. Within these organelles is a genome, called the mitochondrial (mt) genome, which is distinct from, but cooperates closely with the nuclear genome of the cell. Investigating mt genomes has significant implications for various fundamental research areas, including mt biochemistry and physiology, and, importantly, such genomes provide a rich source of markers for population genetic and systematic studies. While approximately 250 complete mt genome sequences have been determined for a range of metazoan organisms from various phyla, few of these represent parasitic helminths. Until 1998, only two mt genome sequences had been determined for parasitic nematodes, in spite of their socio-economic importance and the need for investigations into their population genetics, taxonomy and evolution. However, since that time, there has been some progress. The main focus of the present chapter is to review the state of knowledge of the mt genomics for parasitic nematodes, to describe recent technological improvements to mt genome sequencing, to summarize applications of mt gene markers for studying the systematics and population genetics of parasitic nematodes, and to emphasize prospects and opportunities for future research in these areas.}, }
@article {pmid14708572, year = {2003}, author = {Barroso, G and Sirand-Pugnet, P and Mouhamadou, B and Labarère, J}, title = {Secondary structure and molecular evolution of the mitochondrial small subunit ribosomal RNA in Agaricales (Euagarics clade, Homobasidiomycota).}, journal = {Journal of molecular evolution}, volume = {57}, number = {4}, pages = {383-396}, pmid = {14708572}, issn = {0022-2844}, mesh = {Agaricales/*genetics ; Base Sequence ; DNA, Ribosomal/genetics ; *Evolution, Molecular ; Gene Deletion ; Lentinula/genetics ; Molecular Sequence Data ; Mutagenesis, Insertional ; *Nucleic Acid Conformation ; RNA/*chemistry/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/*chemistry/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {The complete sequences and secondary structures of the mitochondrial small subunit (SSU) ribosomal RNAs of both mostly cultivated mushrooms Agaricus bisporus (1930 nt) and Lentinula edodes (2164 nt) were achieved. These secondary structures and that of Schizophyllum commune (1872 nt) were compared to that previously established for Agrocybe aegerita. The four structures are near the model established for Archae, Bacteria, plastids, and mitochondria; particularly the helices 23 and 37, described as specific to bacteria, are present. Within the four Agaricales (Homobasidiomycota), the SSU-rRNA "core" is conserved in size (966 to 1009 nt) with the exception of an unusual extension of 40 nt in the H17 helix of S. commune. The four core sequences possess 76% of conserved positions and a cluster of C in their 3' end, which could constitute a signal involved in the RNA maturation process. Among the nine putative variable domains, three (V3, V5, V7) do not show significant length variations and possess similar percentages of conserved positions (69%) than the core. The other six variable domains show important length variations, due to independent large size inserted/deleted sequences, and higher rates of nucleotide substitutions than the core (only 31% of conserved positions between the four species). Interestingly, the inserted/deleted sequences are located in few preferential sites (hot spots for insertion/deletion) where they seem to arise or disappear haphazardly during evolution. These sites are located on the surface of the tertiary structure of the 30S ribosomal subunit, at the beginning of hairpin loops; the insertions lead to a lengthening of existing hairpins or to branching loops bearing up to five additional helices.}, }
@article {pmid14706648, year = {2004}, author = {Suzuki, T and Hashimoto, T and Yabu, Y and Kido, Y and Sakamoto, K and Nihei, C and Hato, M and Suzuki, S and Amano, Y and Nagai, K and Hosokawa, T and Minagawa, N and Ohta, N and Kita, K}, title = {Direct evidence for cyanide-insensitive quinol oxidase (alternative oxidase) in apicomplexan parasite Cryptosporidium parvum: phylogenetic and therapeutic implications.}, journal = {Biochemical and biophysical research communications}, volume = {313}, number = {4}, pages = {1044-1052}, doi = {10.1016/j.bbrc.2003.12.038}, pmid = {14706648}, issn = {0006-291X}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Cryptosporidiosis/drug therapy ; Cryptosporidium parvum/drug effects/*enzymology/genetics ; DNA, Protozoan/genetics ; Enzyme Inhibitors/pharmacology ; Humans ; Mitochondria/enzymology ; Molecular Sequence Data ; Oxidoreductases/antagonists &amp; inhibitors/chemistry/genetics/*metabolism ; Phylogeny ; Recombinant Proteins/antagonists &amp; inhibitors/chemistry/genetics/metabolism ; Sequence Homology, Amino Acid ; Sesquiterpenes/pharmacology ; }, abstract = {Cryptosporidium parvum is a parasitic protozoan that causes the diarrheal disease cryptosporidiosis, for which no satisfactory chemotherapy is currently available. Although the presence of mitochondria in this parasite has been suggested, its respiratory system is poorly understood due to difficulties in performing biochemical analyses. In order to better understand the respiratory chain of C. parvum, we surveyed its genomic DNA database in GenBank and identified a partial sequence encoding cyanide-insensitive alternative oxidase (AOX). Based on this sequence, we cloned C. parvum AOX (CpAOX) cDNA from the phylum apicomplexa for the first time. The deduced amino acid sequence (335 a.a.) of CpAOX contains diiron coordination motifs (-E-, -EXXH-) that are conserved among AOXs. Phylogenetic analysis suggested that CpAOX is a mitochondrial-type AOX, possibly derived from mitochondrial endosymbiont gene transfer. The recombinant enzyme expressed in Escherichia coli showed quinol oxidase activity. This activity was insensitive to cyanide and highly sensitive to ascofuranone, a specific inhibitor of trypanosome AOX.}, }
@article {pmid14706454, year = {2004}, author = {Schlickum, S and Moghekar, A and Simpson, JC and Steglich, C and O'Brien, RJ and Winterpacht, A and Endele, SU}, title = {LETM1, a gene deleted in Wolf-Hirschhorn syndrome, encodes an evolutionarily conserved mitochondrial protein.}, journal = {Genomics}, volume = {83}, number = {2}, pages = {254-261}, doi = {10.1016/j.ygeno.2003.08.013}, pmid = {14706454}, issn = {0888-7543}, mesh = {Abnormalities, Multiple/*genetics ; Animals ; Calcium-Binding Proteins/analysis/*genetics ; Craniofacial Abnormalities/genetics ; Databases, Protein ; *Evolution, Molecular ; *Gene Deletion ; Heart Defects, Congenital/genetics ; Humans ; Intellectual Disability/*genetics ; Membrane Proteins/analysis/*genetics ; Mitochondrial Diseases/genetics ; Mitochondrial Proteins/*analysis/*genetics ; Rats ; Seizures/genetics ; Sequence Homology, Amino Acid ; Syndrome ; }, abstract = {The leucine zipper-, EF-hand-containing transmembrane protein 1 (LETM1) has recently been cloned in an attempt to identify genes deleted in Wolf-Hirschhorn syndrome (WHS), a microdeletion syndrome characterized by severe growth and mental retardation, hypotonia, seizures, and typical facial dysmorphic features. LETM1 is deleted in almost all patients with the full phenotype and has recently been suggested as an excellent candidate gene for the seizures in WHS patients. We have shown that LETM1 is evolutionarily conserved throughout the eukaryotic kingdom and exhibits homology to MDM38, a putative yeast protein involved in mitochondrial morphology. Using LETM1-EGFP fusion constructs and an anti-rat LetM1 polyclonal antibody we have demonstrated that LETM1 is located in the mitochondria. The present study presents information about a possible function for LETM1 and suggests that at least some (neuromuscular) features of WHS may be caused by mitochondrial dysfunction.}, }
@article {pmid14706233, year = {2004}, author = {Brunet-Rossinni, AK}, title = {Reduced free-radical production and extreme longevity in the little brown bat (Myotis lucifugus) versus two non-flying mammals.}, journal = {Mechanisms of ageing and development}, volume = {125}, number = {1}, pages = {11-20}, doi = {10.1016/j.mad.2003.09.003}, pmid = {14706233}, issn = {0047-6374}, mesh = {Animals ; Brain/metabolism ; Chiroptera/metabolism/*physiology ; Female ; Free Radicals ; Kidney/metabolism ; *Longevity ; Male ; Mitochondria/metabolism ; Mitochondrial Proteins/metabolism ; Myocardium/metabolism ; Oxygen Consumption ; Peromyscus/metabolism/*physiology ; Shrews/metabolism/*physiology ; Superoxide Dismutase/metabolism ; }, abstract = {The extended longevity of bats, despite their high metabolic rate, may provide insight to patterns and mechanisms of aging. Here I test predictions of the free radical or oxidative stress theory of aging as an explanation for differences in lifespan between the little brown bat, Myotis lucifugus (maximum lifespan potential MLSP=34 years), the short-tailed shrew, Blarina brevicauda (MLSP=2 years), and the white-footed mouse, Peromyscus leucopus (MLSP=8 years) by comparing whole-organism oxygen consumption, hydrogen peroxide production, and superoxide dismutase activity in heart, kidney, and brain tissue. Mitochondria from M. lucifugus produced half to one-third the amount of hydrogen peroxide per unit of oxygen consumed compared to mitochondria from B. brevicauda and P. leucopus, respectively. Superoxide dismutase (SOD) activity did not differ among the three species. These results are similar to those found for birds, which like bats have high metabolic rates and extended longevities, and provide support for the free radical theory of aging as an at least partial explanation for the extreme longevity of bats.}, }
@article {pmid14699844, year = {2003}, author = {Kitada, S}, title = {[Molecular recognition and cleavage of presequence by mitochondrial processing peptidase].}, journal = {Seikagaku. The Journal of Japanese Biochemical Society}, volume = {75}, number = {11}, pages = {1439-1444}, pmid = {14699844}, issn = {0037-1017}, mesh = {Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; Evolution, Molecular ; Metalloendopeptidases/chemistry/genetics/*physiology ; Mitochondria/chemistry/*metabolism ; Mitochondrial Proteins/chemistry/*metabolism ; Protein Transport ; Mitochondrial Processing Peptidase ; }, }
@article {pmid14699090, year = {2004}, author = {Gentle, I and Gabriel, K and Beech, P and Waller, R and Lithgow, T}, title = {The Omp85 family of proteins is essential for outer membrane biogenesis in mitochondria and bacteria.}, journal = {The Journal of cell biology}, volume = {164}, number = {1}, pages = {19-24}, pmid = {14699090}, issn = {0021-9525}, mesh = {Bacteria/genetics ; Cell Survival/genetics ; Energy Metabolism/genetics ; Eukaryotic Cells/*metabolism/ultrastructure ; Gene Expression Regulation, Fungal/genetics ; Immunohistochemistry ; Intracellular Membranes/*metabolism/ultrastructure ; Microscopy, Electron ; Mitochondria/*metabolism/ultrastructure ; Mitochondrial Membrane Transport Proteins/genetics/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Molecular Sequence Data ; Mutation/genetics ; Phylogeny ; Porins/genetics/metabolism ; Protein Transport/genetics ; Saccharomyces cerevisiae/genetics/*metabolism/ultrastructure ; Saccharomyces cerevisiae Proteins/biosynthesis/genetics/*metabolism ; Sequence Homology, Amino Acid ; Voltage-Dependent Anion Channels ; }, abstract = {Integral proteins in the outer membrane of mitochondria control all aspects of organelle biogenesis, being required for protein import, mitochondrial fission, and, in metazoans, mitochondrial aspects of programmed cell death. How these integral proteins are assembled in the outer membrane had been unclear. In bacteria, Omp85 is an essential component of the protein insertion machinery, and we show that members of the Omp85 protein family are also found in eukaryotes ranging from plants to humans. In eukaryotes, Omp85 is present in the mitochondrial outer membrane. The gene encoding Omp85 is essential for cell viability in yeast, and conditional omp85 mutants have defects that arise from compromised insertion of integral proteins like voltage-dependent anion channel (VDAC) and components of the translocase in the outer membrane of mitochondria (TOM) complex into the mitochondrial outer membrane.}, }
@article {pmid14696258, year = {2002}, author = {Frolov, AO and Malysheva, MN}, title = {[Ultrastructure of the flagellate Cruzella marina (Kinetoplastidea)].}, journal = {Tsitologiia}, volume = {44}, number = {5}, pages = {477-484}, pmid = {14696258}, issn = {0041-3771}, mesh = {Animals ; Kinetoplastida/classification/*ultrastructure ; Microscopy, Electron ; Mitochondria/*ultrastructure ; Phylogeny ; }, abstract = {The ultrastructure of a marine, free-living heterotrophic kinetoplastid Cruzella marina was investigated with special attention being paid to the mitochondrion and flagellar organization. The flagellates have a polykinetoplastidal mitochondrion. Two flagella emerge from the pocket; one of these turns anteriorly being forward-directed, while the other is posteriorly directed to be adjacent to the ventral cell surface. The transition zone of both the flagella includes central filaments. The cytostome opens on the tip of the rostrum. The cytostome leads to the channel of cytopharynx, which penetrates the rostrum and proceeds into the flagellate body cytoplasm. The comparison of the relevant morphological and molecular data suggest that C. marina may arise early in the Kinetoplastidea lineage, before divergence of the majority taxa of the kinetoplastid flagellates.}, }
@article {pmid14694072, year = {2004}, author = {Nikolaidis, N and Nei, M}, title = {Concerted and nonconcerted evolution of the Hsp70 gene superfamily in two sibling species of nematodes.}, journal = {Molecular biology and evolution}, volume = {21}, number = {3}, pages = {498-505}, doi = {10.1093/molbev/msh041}, pmid = {14694072}, issn = {0737-4038}, support = {GM20293/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Caenorhabditis/classification/*genetics ; Chromosome Mapping ; *Evolution, Molecular ; HSP110 Heat-Shock Proteins ; HSP70 Heat-Shock Proteins/*genetics ; *Multigene Family ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {We have identified the Hsp70 gene superfamily of the nematode Caenorhabditis briggsae and investigated the evolution of these genes in comparison with Hsp70 genes from C. elegans, Drosophila, and yeast. The Hsp70 genes are classified into three monophyletic groups according to their subcellular localization, namely, cytoplasm (CYT), endoplasmic reticulum (ER), and mitochondria (MT). The Hsp110 genes can be classified into the polyphyletic CYT group and the monophyletic ER group. The different Hsp70 and Hsp110 groups appeared to evolve following the model of divergent evolution. This model can also explain the evolution of the ER and MT genes. On the other hand, the CYT genes are divided into heat-inducible and constitutively expressed genes. The constitutively expressed genes have evolved more or less following the birth-and-death process, and the rates of gene birth and gene death are different between the two nematode species. By contrast, some heat-inducible genes show an intraspecies phylogenetic clustering. This suggests that they are subject to sequence homogenization resulting from gene conversion-like events. In addition, the heat-inducible genes show high levels of sequence conservation in both intra-species and inter-species comparisons, and in most cases, amino acid sequence similarity is higher than nucleotide sequence similarity. This indicates that purifying selection also plays an important role in maintaining high sequence similarity among paralogous Hsp70 genes. Therefore, we suggest that the CYT heat-inducible genes have been subjected to a combination of purifying selection, birth-and-death process, and gene conversion-like events.}, }
@article {pmid14688256, year = {2004}, author = {Davis, CA and Hearn, AS and Fletcher, B and Bickford, J and Garcia, JE and Leveque, V and Melendez, JA and Silverman, DN and Zucali, J and Agarwal, A and Nick, HS}, title = {Potent anti-tumor effects of an active site mutant of human manganese-superoxide dismutase. Evolutionary conservation of product inhibition.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {13}, pages = {12769-12776}, doi = {10.1074/jbc.M310623200}, pmid = {14688256}, issn = {0021-9258}, mesh = {Animals ; Antioxidants/metabolism ; Binding Sites ; Blotting, Northern ; Catalase/metabolism ; Catalysis ; Cell Division ; Cell Line ; Crystallography, X-Ray ; DNA, Complementary/metabolism ; Evolution, Molecular ; Genetic Vectors ; Green Fluorescent Proteins ; Histidine/chemistry ; Humans ; Hydrogen Peroxide/pharmacology ; Immunoblotting ; Luminescent Proteins/metabolism ; Mice ; Mice, SCID ; Mitochondria/metabolism ; Models, Chemical ; Models, Genetic ; Models, Molecular ; Mutagenesis, Site-Directed ; *Mutation ; Oxygen/*metabolism ; Phylogeny ; Plasmids/metabolism ; Retroviridae/genetics ; Signal Transduction ; Superoxide Dismutase/*genetics ; Time Factors ; Transfection ; }, abstract = {Mn-SOD serves as the primary cellular defense against oxidative damage by converting superoxide radicals (O(2)(-)) to O(2) and H(2)O(2). A unique characteristic of this mitochondrial anti-oxidant enzyme is the conservation from bacteria to man of a rapidly formed product inhibited state. Using site-directed mutagenesis, we have generated an active site mutant (H30N) of human Mn-SOD, which exhibits significantly reduced product inhibition and increased enzymatic efficiency. Overexpression of the H30N enzyme causes anti-proliferative effects in vitro and anti-tumor effects in vivo. Our results provide a teleological basis for the phylogenetically invariant nature of position His-30 and the evolutionary conservation of product inhibition. These data also provide more direct intracellular evidence for the signaling role associated with H(2)O(2).}, }
@article {pmid14685243, year = {2003}, author = {Paschen, SA and Waizenegger, T and Stan, T and Preuss, M and Cyrklaff, M and Hell, K and Rapaport, D and Neupert, W}, title = {Evolutionary conservation of biogenesis of beta-barrel membrane proteins.}, journal = {Nature}, volume = {426}, number = {6968}, pages = {862-866}, doi = {10.1038/nature02208}, pmid = {14685243}, issn = {1476-4687}, mesh = {Circular Dichroism ; *Evolution, Molecular ; Fungal Proteins/*biosynthesis/*chemistry/genetics/metabolism ; Lipid Bilayers/metabolism ; Macromolecular Substances ; Membrane Proteins/*biosynthesis/*chemistry/genetics/metabolism ; Microscopy, Electron ; Mitochondrial Proteins/biosynthesis/chemistry/genetics/metabolism ; Neurospora crassa/chemistry/cytology/*metabolism ; Protein Binding ; Protein Structure, Secondary ; Protein Transport ; Recombinant Fusion Proteins/biosynthesis/chemistry/genetics/metabolism ; }, abstract = {The outer membranes of mitochondria and chloroplasts are distinguished by the presence of beta-barrel membrane proteins. The outer membrane of Gram-negative bacteria also harbours beta-barrel proteins. In mitochondria these proteins fulfil a variety of functions such as transport of small molecules (porin/VDAC), translocation of proteins (Tom40) and regulation of mitochondrial morphology (Mdm10). These proteins are encoded by the nucleus, synthesized in the cytosol, targeted to mitochondria as chaperone-bound species, recognized by the translocase of the outer membrane, and then inserted into the outer membrane where they assemble into functional oligomers. Whereas some knowledge has been accumulated on the pathways of insertion of proteins that span cellular membranes with alpha-helical segments, very little is known about how beta-barrel proteins are integrated into lipid bilayers and assembled into oligomeric structures. Here we describe a protein complex that is essential for the topogenesis of mitochondrial outer membrane beta-barrel proteins (TOB). We present evidence that important elements of the topogenesis of beta-barrel membrane proteins have been conserved during the evolution of mitochondria from endosymbiotic bacterial ancestors.}, }
@article {pmid14675758, year = {2003}, author = {Woo, PC and Zhen, H and Cai, JJ and Yu, J and Lau, SK and Wang, J and Teng, JL and Wong, SS and Tse, RH and Chen, R and Yang, H and Liu, B and Yuen, KY}, title = {The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts.}, journal = {FEBS letters}, volume = {555}, number = {3}, pages = {469-477}, doi = {10.1016/s0014-5793(03)01307-3}, pmid = {14675758}, issn = {0014-5793}, mesh = {Base Sequence ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; Gene Components/genetics ; Genes/genetics ; Genes, rRNA/genetics ; *Genome, Fungal ; Humans ; Likelihood Functions ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Penicillium/*genetics ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Yeasts/*genetics ; }, abstract = {We report the complete sequence of the mitochondrial genome of Penicillium marneffei, the first complete mitochondrial DNA sequence of a thermal dimorphic fungus. This 35 kb mitochondrial genome contains the genes encoding ATP synthase subunits 6, 8, and 9 (atp6, atp8, and atp9), cytochrome oxidase subunits I, II, and III (cox1, cox2, and cox3), apocytochrome b (cob), reduced nicotinamide adenine dinucleotide ubiquinone oxireductase subunits (nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), ribosomal protein of the small ribosomal subunit (rps), 28 tRNAs, and small and large ribosomal RNAs. Analysis of gene contents, gene orders, and gene sequences revealed that the mitochondrial genome of P. marneffei is more closely related to those of molds than yeasts.}, }
@article {pmid14675750, year = {2003}, author = {Finnegan, PM and Umbach, AL and Wilce, JA}, title = {Prokaryotic origins for the mitochondrial alternative oxidase and plastid terminal oxidase nuclear genes.}, journal = {FEBS letters}, volume = {555}, number = {3}, pages = {425-430}, doi = {10.1016/s0014-5793(03)01309-7}, pmid = {14675750}, issn = {0014-5793}, mesh = {Alphaproteobacteria/enzymology/genetics ; Amino Acid Sequence ; Binding Sites ; Cyanobacteria/enzymology/genetics ; Mitochondria/*enzymology ; Mitochondrial Proteins ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Phylogeny ; Plant Proteins ; Plastids/*enzymology ; Prokaryotic Cells/*enzymology/physiology ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {The mitochondrial alternative oxidase is a diiron carboxylate quinol oxidase (Dox) found in plants and some fungi and protists, but not animals. The plastid terminal oxidase is distantly related to alternative oxidase and is most likely also a Dox protein. Database searches revealed that the alpha-proteobacterium Novosphingobium aromaticivorans and the cyanobacteria Nostoc sp. PCC7120, Synechococcus sp. WH8102 and Prochlorococcus marinus subsp. pastoris CCMP1378 each possess a Dox homolog. Each prokaryotic protein conforms to the current structural models of the Dox active site and phylogenetic analyses suggest that the eukaryotic Dox genes arose from an ancestral prokaryotic gene.}, }
@article {pmid14674884, year = {2004}, author = {Agrimi, G and Di Noia, MA and Marobbio, CM and Fiermonte, G and Lasorsa, FM and Palmieri, F}, title = {Identification of the human mitochondrial S-adenosylmethionine transporter: bacterial expression, reconstitution, functional characterization and tissue distribution.}, journal = {The Biochemical journal}, volume = {379}, number = {Pt 1}, pages = {183-190}, pmid = {14674884}, issn = {1470-8728}, mesh = {Amino Acid Sequence ; Amino Acid Transport Systems ; Animals ; Biological Transport/drug effects ; Brain Chemistry ; Bromcresol Purple/pharmacology ; CHO Cells ; Calcium-Binding Proteins/antagonists &amp; inhibitors/*genetics/isolation &amp; purification/physiology ; Cloning, Molecular ; Cricetinae ; Cytosol/metabolism ; DNA, Complementary/genetics ; Escherichia coli ; Expressed Sequence Tags ; *Genes ; Humans ; Hydrolyzable Tannins/pharmacology ; Membrane Transport Modulators ; Membrane Transport Proteins/antagonists &amp; inhibitors/*genetics/isolation &amp; purification/physiology ; Mitochondria/*metabolism ; Mitochondrial Proteins/antagonists &amp; inhibitors/*genetics/isolation &amp; purification/physiology ; Molecular Sequence Data ; Nerve Tissue Proteins/genetics/isolation &amp; purification ; Organ Specificity ; Phylogeny ; RNA, Messenger/biosynthesis ; Recombinant Fusion Proteins/metabolism ; S-Adenosylhomocysteine/*metabolism ; S-Adenosylmethionine/*metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {The mitochondrial carriers are a family of transport proteins that, with a few exceptions, are found in the inner membranes of mitochondria. They shuttle metabolites and cofactors through this membrane, and connect cytoplasmic functions with others in the matrix. SAM (S-adenosylmethionine) has to be transported into the mitochondria where it is converted into S-adenosylhomocysteine in methylation reactions of DNA, RNA and proteins. The transport of SAM has been investigated in rat liver mitochondria, but no protein has ever been associated with this activity. By using information derived from the phylogenetically distant yeast mitochondrial carrier for SAM and from related human expressed sequence tags, a human cDNA sequence was completed. This sequence was overexpressed in bacteria, and its product was purified, reconstituted into phospholipid vesicles and identified from its transport properties as the human mitochondrial SAM carrier (SAMC). Unlike the yeast orthologue, SAMC catalysed virtually only countertransport, exhibited a higher transport affinity for SAM and was strongly inhibited by tannic acid and Bromocresol Purple. SAMC was found to be expressed in all human tissues examined and was localized to the mitochondria. The physiological role of SAMC is probably to exchange cytosolic SAM for mitochondrial S-adenosylhomocysteine. This is the first report describing the identification and characterization of the human SAMC and its gene.}, }
@article {pmid14670954, year = {2004}, author = {Morgan, GW and Goulding, D and Field, MC}, title = {The single dynamin-like protein of Trypanosoma brucei regulates mitochondrial division and is not required for endocytosis.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {11}, pages = {10692-10701}, doi = {10.1074/jbc.M312178200}, pmid = {14670954}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Blotting, Northern ; Blotting, Western ; Cloning, Molecular ; DNA/chemistry ; Databases as Topic ; Dynamins/*biosynthesis/*chemistry/*physiology ; *Endocytosis ; Evolution, Molecular ; Fluorescent Antibody Technique, Indirect ; Genome ; Leishmania major/metabolism ; Microscopy, Electron ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Protein Structure, Tertiary ; RNA Interference ; Time Factors ; Trypanosoma brucei brucei/*metabolism ; Trypanosoma vivax/metabolism ; }, abstract = {Members of the evolutionarily conserved dynamin-related GTPase family mediate numerous cellular membrane remodeling events. Dynamin family functions include the scission of clathrin-coated pits from the plasma membrane, mitochondrial fission, and chloroplast division. Here we report that the divergent eukaryote Trypanosoma brucei possesses a single dynamin family gene, which we have designated TbDLP. Furthermore, a single dynamin family gene is also found in the Leishmania major and Trypanosoma vivax genomes, indicating that this is a conserved feature among the kinetoplastida. TbDLP is most homologous to the DMN/DRP family of dynamin-like proteins. Indirect immunofluorescence microscopy reveals that TbDLP is distributed in punctate structures within the cell that partially co-localize with the mitochondrion when labeled with MitoTracker. To define TbDLP function, we have used RNA interference to silence the TbDLP gene. Reduction of TbDLP protein levels causes a profound alteration in mitochondrial morphology without affecting the structure of other membrane-bound compartments, including the endocytic and exocytic apparatus. The mitochondrial profiles present in wild type trypanosomes fuse and collapse in the mutant cells, and by electron microscopy the mitochondria are found to contain an accumulation of constriction sites. These findings demonstrate TbDLP functions in division of the mitochondrial membrane. Most significantly, as TbDLP is the sole member of the dynamin family in this organism, scission of clathrin-coated pits involved in protein trafficking through the highly active endocytic system in trypanosomes must function in the absence of dynamin. The evolutionary implications of these findings are discussed.}, }
@article {pmid14666125, year = {2004}, author = {Donnelly, MJ and Pinto, J and Girod, R and Besansky, NJ and Lehmann, T}, title = {Revisiting the role of introgression vs shared ancestral polymorphisms as key processes shaping genetic diversity in the recently separated sibling species of the Anopheles gambiae complex.}, journal = {Heredity}, volume = {92}, number = {2}, pages = {61-68}, doi = {10.1038/sj.hdy.6800377}, pmid = {14666125}, issn = {0018-067X}, support = {A140631-01//PHS HHS/United States ; }, mesh = {Africa ; Animals ; Anopheles/classification/*genetics ; DNA, Mitochondrial/analysis ; *Genetic Variation ; Haplotypes ; Hybridization, Genetic/*genetics ; Insect Vectors/classification/*genetics ; Phylogeny ; *Polymorphism, Genetic ; Sequence Analysis, DNA ; }, abstract = {The role of interspecific hybridisation in the evolution of pest species is poorly understood. In mosquito disease vectors this is of particular importance due to the evolution of insecticide resistance and the proposed release of transgenic strains that are refractory to the malaria parasite. In this study, we apply population genetic methods in a novel manner to determine whether mitochondrial DNA sequences have introgressed between the closely related African malaria vectors Anopheles gambiae and A. arabiensis. Our results suggest that speciation was geologically recent and ancestral haplotypes at the ND5 locus are retained in both species. In addition, comparing haplotype frequencies in allopatric and sympatric populations, suggest locale specific unidirectional introgression of mitochondria from A. arabiensis into A. gambiae.}, }
@article {pmid14663084, year = {2003}, author = {LaGier, MJ and Tachezy, J and Stejskal, F and Kutisova, K and Keithly, JS}, title = {Mitochondrial-type iron-sulfur cluster biosynthesis genes (IscS and IscU) in the apicomplexan Cryptosporidium parvum.}, journal = {Microbiology (Reading, England)}, volume = {149}, number = {Pt 12}, pages = {3519-3530}, doi = {10.1099/mic.0.26365-0}, pmid = {14663084}, issn = {1350-0872}, support = {1D43 TWO 0091/TW/FIC NIH HHS/United States ; 5R03-TWO 1507-02/TW/FIC NIH HHS/United States ; 5R03-TWO 5536-02/TW/FIC NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Cryptosporidium parvum/*genetics/metabolism ; DNA, Protozoan/genetics ; Gene Expression ; *Genes, Protozoan ; Green Fluorescent Proteins ; Iron-Sulfur Proteins/biosynthesis/*genetics ; Luminescent Proteins/genetics/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Sorting Signals/genetics ; Protozoan Proteins/biosynthesis/*genetics ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Several reports have indicated that the iron-sulfur cluster [Fe-S] assembly machinery in most eukaryotes is confined to the mitochondria and chloroplasts. The best-characterized and most highly conserved [Fe-S] assembly proteins are a pyridoxal-5'-phosphate-dependent cysteine desulfurase (IscS), and IscU, a protein functioning as a scaffold for the assembly of [Fe-S] prior to their incorporation into apoproteins. In this work, genes encoding IscS and IscU homologues have been isolated and characterized from the apicomplexan parasite Cryptosporidium parvum, an opportunistic pathogen in AIDS patients, for which no effective treatment is available. Primary sequence analysis (CpIscS and CpIscU) and phylogenetic studies (CpIscS) indicate that both genes are most closely related to mitochondrial homologues from other organisms. Moreover, the N-terminal signal sequences of CpIscS and CpIscU predicted in silico specifically target green fluorescent protein to the mitochondrial network of the yeast Saccharomyces cerevisiae. Overall, these findings suggest that the previously identified mitochondrial relict of C. parvum may have been retained by the parasite as an intracellular site for [Fe-S] assembly.}, }
@article {pmid14662942, year = {2003}, author = {Biswas, SK and Wang, L and Yokoyama, K and Nishimura, K}, title = {Molecular analysis of Cryptococcus neoformans mitochondrial cytochrome b gene sequences.}, journal = {Journal of clinical microbiology}, volume = {41}, number = {12}, pages = {5572-5576}, pmid = {14662942}, issn = {0095-1137}, mesh = {Base Sequence ; Cryptococcus neoformans/classification/*genetics/isolation &amp; purification ; Cytochromes b/*genetics ; DNA Primers ; Genes, Fungal ; Humans ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/methods ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Serotyping/methods ; }, abstract = {Mitochondrial cytochrome b genes (cyt b) of 40 strains of Cryptococcus neoformans were partially sequenced to determine the genetic relations. With the exception of the type strain of C. neoformans var. neoformans, all strains contained introns in their sequences. Analysis of 386 bp of coding sequence from each strain under investigation revealed a total of 27 (6.99%) variable nucleotide sites and categorized isolates of C. neoformans into nine cyt b types. C. neoformans var. gattii included cyt b types I to V, and C. neoformans var. neoformans comprised types VI to IX. cyt b types were correlated with serotypes. All strains with cyt b types I, IV, and V were serotype B. All other strains except IFM 5878 (serotype B) with cyt b types II and III were serotype C. Serotype D strains had cyt b types VI and IX, and serotype A strains were cyt b type VIII. Of four serotype AD strains, one was cyt b type VII and the remaining three were type VIII. The phylogenetic tree based on deduced amino acid sequences divided the strains only into C. neoformans var. neoformans and C. neoformans var. gattii. These results indicate that cyt b sequences are effective for DNA typing as well as phylogenetic analysis of C. neoformans.}, }
@article {pmid14662316, year = {2003}, author = {Leyens, G and Donnay, I and Knoops, B}, title = {Cloning of bovine peroxiredoxins-gene expression in bovine tissues and amino acid sequence comparison with rat, mouse and primate peroxiredoxins.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {136}, number = {4}, pages = {943-955}, doi = {10.1016/s1096-4959(03)00290-2}, pmid = {14662316}, issn = {1096-4959}, mesh = {Amino Acid Sequence ; Animals ; Cattle/*genetics ; Cloning, Molecular ; DNA, Complementary/genetics ; *Gene Expression Profiling ; Isoenzymes/genetics ; Liver/enzymology ; Mice ; Molecular Sequence Data ; Organ Specificity ; Peroxidases/*chemistry/*genetics ; Peroxiredoxin VI ; Peroxiredoxins ; Phylogeny ; *Primates ; Rats ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {The peroxiredoxin (PRDX) family is a recently identified family of peroxidases found in organisms ranging from bacteria to mammals. In mammals, six PRDX isoforms have been characterized in human (Homo sapiens), rat (Rattus norvegicus) and mouse (Mus musculus). PRDXs are cytosolic, secreted or targeted to organelles such as peroxisomes, mitochondria and the nucleus. Some PRDXs are synthesized as larger precursor proteins with a presequence that is cleaved to produce the mature form. To study the expression of the six PRDXs in bovine (Bos taurus), we first cloned cDNAs coding for PRDX1, PRDX2, PRDX4 and PRDX5. PRDX3 and PRDX6 had previously been cloned and characterized in bovine. The comparison of bovine PRDXs with their rat, mouse and primate orthologues reveals a minimum of 95% similarity of mature proteins. Even though mitochondrial or export signal presequences are normally less conserved, the unprocessed proteins still present a minimum of 84% similarity. Nevertheless, a major divergence lies at the N-terminus of bovine PRDX2, where a Cys-Val-Cys motif was identified. The expression of the six PRDXs in 22 bovine tissues has been studied by RT-PCR. Our results point out the ubiquity of the different PRDX transcripts in bovine tissues. The important conservation of the different PRDXs, the multiple processes they have been associated with, as well as the ubiquity of all the members of the family analyzed in this study for the first time altogether, suggest that they play a major role in the basal metabolism of mammalian cells.}, }
@article {pmid14662295, year = {2003}, author = {Johnston, IA}, title = {Muscle metabolism and growth in Antarctic fishes (suborder Notothenioidei): evolution in a cold environment.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {136}, number = {4}, pages = {701-713}, doi = {10.1016/s1096-4959(03)00258-6}, pmid = {14662295}, issn = {1096-4959}, mesh = {Animals ; Antarctic Regions ; *Biological Evolution ; *Cold Temperature ; Fishes/*metabolism ; Muscle, Skeletal/*growth &amp; development/*metabolism ; Oxygen Consumption ; Phylogeny ; }, abstract = {The radiation of notothenioid fishes (order Perciformes) in the Southern Ocean provides a model system for investigating evolution and adaptation to a low temperature environment. The Notothenioid fishes comprising eight families, 43 genera and 122 species dominate the fish fauna in Antarctica. The diversification of the clade probably began 15-20 million years ago after the formation of the Antarctic Polar Front. The radiation was, therefore, associated with climatic cooling down to the present day temperature of -1.86 degrees C. Origins and Evolution of the Antarctic Biota Geological Society Special Publication No. 47, Geological Society of London. pp. 253-268). The success of the group has been closely linked with the evolution of glycopeptide and peptide antifreezes, which are amongst the most abundant proteins in blood and interstitial fluid. The radiation of the clade has been associated with disaptation (evolutionary loss of function) and recovery. For example, it is thought that the icefishes (Channichyidae) lost haemoglobin through a single mutational event leading to the deletion of the entire beta-globin gene and the 5' end of the linked alpha-globin gene, resulting in compensatory adaptations of the cardiovascular system. Phylogenetically based statistical methods also indicate a progressive and dramatic reduction in the number of skeletal muscle fibres (FN(max)) at the end of the recruitment phase of growth in basal compared to derived families. The reduction in FN(max) is associated with a compensatory increase in the maximum fibre diameter, which can reach 100 microm in slow and 600 microm in fast muscle fibres. At -1 to 0 degrees C, the oxygen consumption of isolated mitochondria per mg mitochondrial protein shows no evidence of up-regulation relative to mitochondria from temperate and tropical Perciform fishes. The mitochondria content of slow muscle fibres in Antarctic notothenioids is towards the upper end of the range reported for teleosts with similar lifestyles, reaching 50% in Channichthyids. High mitochondrial densities facilitate ATP production and oxygen diffusion through the membrane lipid compartment of the fibre. Modelling studies suggest that adequate oxygen flux in the large diameter muscle fibres of notothenioids is possible because of the reduced metabolic demand and enhanced solubility of oxygen associated with low temperature. At the whole animal level size-corrected resting metabolic rate fits on the same temperature relationship as for Perciformes from warmer climates. It seems likely that the additional energetic costs associated with antifreeze synthesis and high mitochondrial densities are compensated for by reductions in other energy requiring processes: a hypothesis that could be tested with detailed energy budget studies. One plausible candidate is a reduction in membrane leak pathways linked to the loss of muscle fibres, which would serve to minimise the cost of maintaining ionic gradients.}, }
@article {pmid14660687, year = {2004}, author = {Willett, CS and Burton, RS}, title = {Evolution of interacting proteins in the mitochondrial electron transport system in a marine copepod.}, journal = {Molecular biology and evolution}, volume = {21}, number = {3}, pages = {443-453}, doi = {10.1093/molbev/msh031}, pmid = {14660687}, issn = {0737-4038}, mesh = {Adaptation, Biological ; Animals ; Crustacea/*genetics/metabolism ; Cytochromes b/genetics ; Cytochromes c/genetics ; DNA, Mitochondrial/genetics ; *Electron Transport ; Electron Transport Complex III/genetics ; *Evolution, Molecular ; Genetic Variation ; Iron-Sulfur Proteins/genetics ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Genetic ; }, abstract = {The extensive interaction between mitochondrial-encoded and nuclear-encoded subunits of electron transport system (ETS) enzymes in mitochondria is expected to lead to intergenomic coadaptation. Whether this coadaptation results from adaptation to the environment or from fixation of deleterious mtDNA mutations followed by compensatory nuclear gene evolution is unknown. The intertidal copepod Tigriopus californicus shows extreme divergence in mtDNA sequence and provides an excellent model system for study of intergenomic coadaptation. Here, we examine genes encoding subunits of complex III of the ETS, including the mtDNA-encoded cytochrome b (CYTB), the nuclear-encoded rieske iron-sulfur protein (RISP), and cytochrome c(1) (CYC1). We compare levels of polymorphism within populations and divergence between populations in these genes to begin to untangle the selective forces that have shaped evolution in these genes. CYTB displays dramatic divergence between populations, but sequence analysis shows no evidence for positive selection driving this divergence. CYC1 and RISP have lower levels of sequence divergence between populations than CYTB, but, again, sequence analysis gives no evidence for positive selection acting on them. However, an examination of variation at cytochrome c (CYC), a nuclear-encoded protein that transfers electrons between complex III and complex IV provides evidence for selective divergence. Hence, it appears that rapid evolution in mitochondrial-encoded subunits is not always associated with rapid divergence in interacting subunits (CYC1 and RISP), but can be in some cases (CYC). Finally, a comparison of nuclear-encoded and mitochondrial-encoded genes from T. californicus suggests that substitution rates in the mitochondrial-encoded genes are dramatically increased relative to nuclear genes.}, }
@article {pmid14660680, year = {2004}, author = {Goh, CH and Jung, KH and Roberts, SK and McAinsh, MR and Hetherington, AM and Park, YI and Suh, K and An, G and Nam, HG}, title = {Mitochondria provide the main source of cytosolic ATP for activation of outward-rectifying K+ channels in mesophyll protoplast of chlorophyll-deficient mutant rice (OsCHLH) seedlings.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {8}, pages = {6874-6882}, doi = {10.1074/jbc.M309071200}, pmid = {14660680}, issn = {0021-9258}, support = {P18229/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adenosine Triphosphate/*chemistry ; Carbon Dioxide/chemistry ; Cell Membrane/metabolism ; Chlorophyll/chemistry/*genetics ; Cytosol/*metabolism ; Genotype ; Glucose/metabolism ; Homozygote ; Light ; Membrane Potentials ; Mitochondria/*metabolism ; Models, Genetic ; *Mutation ; Oryza/*genetics ; Oxygen/metabolism ; Oxygen Consumption ; Patch-Clamp Techniques ; Phenotype ; Photosynthesis ; Polymerase Chain Reaction ; Potassium/chemistry ; Potassium Channels/*chemistry ; *Potassium Channels, Tandem Pore Domain ; Protoplasts/metabolism ; Time Factors ; }, abstract = {The role of mitochondria in providing intracellular ATP that controls the activity of plasma membrane outward-rectifying K+ channels was evaluated. The OsCHLH rice mutant, which lacks chlorophyll in the thylakoids, was isolated by T-DNA gene trapping (Jung, K.-H., Hur, J., Ryu, C.-H., Choi, Y., Chung, Y.-Y., Miyao, A., Hirochika, H., and An, G. (2003) Plant Cell Physiol. 44, 463-472). The OsCHLH mutant is unable to fix CO2 and exhibits reduced growth. Wild type and mutant plants exhibit similar rates of respiratory O2 uptake in the dark, whereas the rate of photosynthetic O2 evolution by the mutant was negligible during illumination. During dark respiration the wild type and mutant exhibited similar levels of cytoplasmic ATP. In the mutant oligomycin treatment (an inhibitor of mitochondrial F1F0-ATPase) drastically reduced ATP production. The fact that this was reversed by the addition of glucose suggested that the mutant produced ATP exclusively from mitochondria but not from chloroplasts. In whole cell patch clamp experiments, the activity of outward-rectifying K+ channels of rice mesophyll cells showed ATP-dependent currents, which were 1.5-fold greater in wild type than in mutant cells. Channels in both wild type and mutant cells were deactivated by the removal of cytosolic ATP, whereas in the presence of ATP the channels remained active. We conclude that mesophyll cells in the OsCHLH rice mutant derive ATP from mitochondrial respiration, and that this is critical for the normal function of plasma membrane outward-rectifying K+ channels.}, }
@article {pmid14660674, year = {2004}, author = {Yasuno, R and von Wettstein-Knowles, P and Wada, H}, title = {Identification and molecular characterization of the beta-ketoacyl-[acyl carrier protein] synthase component of the Arabidopsis mitochondrial fatty acid synthase.}, journal = {The Journal of biological chemistry}, volume = {279}, number = {9}, pages = {8242-8251}, doi = {10.1074/jbc.M308894200}, pmid = {14660674}, issn = {0021-9258}, mesh = {3-Oxoacyl-(Acyl-Carrier-Protein) Synthase/chemistry/*genetics/*metabolism ; Amino Acid Sequence ; Arabidopsis/*enzymology ; Blotting, Western ; Cerulenin/pharmacology ; Cloning, Molecular ; DNA, Complementary/isolation &amp; purification ; DNA, Plant/isolation &amp; purification ; Enzyme Inhibitors/pharmacology ; Escherichia coli/enzymology/genetics ; Fatty Acid Synthases/*chemistry/genetics/metabolism ; Fatty Acids/biosynthesis ; Gene Deletion ; Gene Expression ; Green Fluorescent Proteins ; Isoenzymes/genetics/metabolism ; Luminescent Proteins/genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Phylogeny ; Recombinant Fusion Proteins ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Transfection ; }, abstract = {Substrate specificity of condensing enzymes is a predominant factor determining the nature of fatty acyl chains synthesized by type II fatty acid synthase (FAS) enzyme complexes composed of discrete enzymes. The gene (mtKAS) encoding the condensing enzyme, beta-ketoacyl-[acyl carrier protein] (ACP) synthase (KAS), constituent of the mitochondrial FAS was cloned from Arabidopsis thaliana, and its product was purified and characterized. The mtKAS cDNA complemented the KAS II defect in the E. coli CY244 strain mutated in both fabB and fabF encoding KAS I and KAS II, respectively, demonstrating its ability to catalyze the condensation reaction in fatty acid synthesis. In vitro assays using extracts of CY244 containing all E. coli FAS components, except that KAS I and II were replaced by mtKAS, gave C(4)-C(18) fatty acids exhibiting a bimodal distribution with peaks at C(8) and C(14)-C(16). Previously observed bimodal distributions obtained using mitochondrial extracts appear attributable to the mtKAS enzyme in the extracts. Although the mtKAS sequence is most similar to that of bacterial KAS IIs, sensitivity of mtKAS to the antibiotic cerulenin resembles that of E. coli KAS I. In the first or priming condensation reaction of de novo fatty acid synthesis, purified His-tagged mtKAS efficiently utilized malonyl-ACP, but not acetyl-CoA as primer substrate. Intracellular targeting using green fluorescent protein, Western blot, and deletion analyses identified an N-terminal signal conveying mtKAS into mitochondria. Thus, mtKAS with its broad chain length specificity accomplishes all condensation steps in mitochondrial fatty acid synthesis, whereas in plastids three KAS enzymes are required.}, }
@article {pmid14658756, year = {2003}, author = {O'Brien, TW}, title = {Properties of human mitochondrial ribosomes.}, journal = {IUBMB life}, volume = {55}, number = {9}, pages = {505-513}, doi = {10.1080/15216540310001626610}, pmid = {14658756}, issn = {1521-6543}, mesh = {Escherichia coli/chemistry/physiology ; GTP-Binding Proteins/physiology ; Humans ; Mitochondria/chemistry/*physiology ; RNA, Ribosomal/physiology ; Ribosomal Proteins/physiology ; Ribosomes/chemistry/*physiology ; }, abstract = {Mammalian mitochondrial ribosomes (55S) differ unexpectedly from bacterial (70S) and cytoplasmic ribosomes (80S), as well as other kinds of mitochondrial ribosomes. Typical of mammalian mitochondrial ribosomes, the bovine mitochondrial ribosome has been developed as a model system for the study of human mitochondrial ribosomes, to address several questions related to the structure, function, biosynthesis and evolution of these interesting ribosomes. Bovine mitochondrial ribosomal proteins (MRPs) from each subunit have been identified and characterized with respect to individuality and electrophoretic properties, amino acid sequence, topographic disposition, RNA binding properties, evolutionary relationships and reaction with affinity probes of ribosomal functional domains. Several distinctive properties of these ribosomes are being elucidated, including their antibiotic susceptibility and composition. Human mitochondrial ribosomes lack several of the major RNA stem structures of bacterial ribosomes but they contain a correspondingly higher protein content (as many as 80 proteins), suggesting a model where proteins have replaced RNA structural elements during the evolution of these ribosomes. Despite their lower RNA content they are physically larger than bacterial ribosomes, because of the 'extra' proteins they contain. The extra proteins in mitochondrial ribosomes are 'new' in the sense that they are not homologous to proteins in bacterial or cytoplasmic ribosomes. Some of the new proteins appear to be bifunctional. All of the mammalian MRPs are encoded in nuclear genes (a separate set from those encoding cytoplasmic ribosomal proteins) which are evolving more rapidly than those encoding cytoplasmic ribosomal proteins. The MRPs are imported into mitochondria where they assemble coordinately with mitochondrially transcribed rRNAs into ribosomes that are responsible for translating the 13 mRNAs for essential proteins of the oxidative phosphorylation system.}, }
@article {pmid14657485, year = {2003}, author = {Osteryoung, KW and Nunnari, J}, title = {The division of endosymbiotic organelles.}, journal = {Science (New York, N.Y.)}, volume = {302}, number = {5651}, pages = {1698-1704}, doi = {10.1126/science.1082192}, pmid = {14657485}, issn = {1095-9203}, support = {R01GM62942A/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Arabidopsis Proteins ; Bacteria/cytology/metabolism ; Bacterial Proteins/chemistry/metabolism ; Biological Evolution ; Cell Division ; Chloroplasts/*physiology/ultrastructure ; *Cytoskeletal Proteins ; Dynamins/metabolism ; GTP Phosphohydrolases/chemistry/metabolism ; Mitochondria/*physiology/ultrastructure ; Plant Proteins/chemistry/metabolism ; *Symbiosis ; }, abstract = {Mitochondria and chloroplasts are essential eukaryotic organelles of endosymbiotic origin. Dynamic cellular machineries divide these organelles. The mechanisms by which mitochondria and chloroplasts divide were thought to be fundamentally different because chloroplasts use proteins derived from the ancestral prokaryotic cell division machinery, whereas mitochondria have largely evolved a division apparatus that lacks bacterial cell division components. Recent findings indicate, however, that both types of organelles universally require dynamin-related guanosine triphosphatases to divide. This mechanistic link provides fundamental insights into the molecular events driving the division, and possibly the evolution, of organelles in eukaryotes.}, }
@article {pmid14657408, year = {2004}, author = {Wandrey, M and Trevaskis, B and Brewin, N and Udvardi, MK}, title = {Molecular and cell biology of a family of voltage-dependent anion channel porins in Lotus japonicus.}, journal = {Plant physiology}, volume = {134}, number = {1}, pages = {182-193}, pmid = {14657408}, issn = {0032-0889}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Complementary/genetics/isolation &amp; purification ; DNA, Plant/genetics/isolation &amp; purification ; Gene Expression ; Genes, Plant ; Genetic Complementation Test ; Ion Channels/*genetics/*metabolism ; Lotus/*genetics/*metabolism ; Molecular Sequence Data ; Mutation ; Phylogeny ; Plant Proteins/*genetics/*metabolism ; Porins/*genetics/*metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; Sequence Homology, Amino Acid ; Glycine max/genetics/metabolism ; Subcellular Fractions/metabolism ; Voltage-Dependent Anion Channel 1 ; Voltage-Dependent Anion Channels ; }, abstract = {Voltage-dependent anion channels (VDACs) are generally considered as the main pathway for metabolite transport across the mitochondrial outer membrane. Recent proteomic studies on isolated symbiosome membranes from legume nodules indicated that VDACs might also be involved in transport of nutrients between plants and rhizobia. In an attempt to substantiate this, we carried out a detailed molecular and cellular characterization of VDACs in Lotus japonicus and soybean (Glycine max). Database searches revealed at least five genes encoding putative VDACs in each of the legumes L. japonicus, Medicago truncatula, and soybean. We obtained and sequenced cDNA clones from L. japonicus encoding five full-length VDAC proteins (LjVDAC1.1-1.3, LjVDAC2.1, and LjVDAC3.1). Complementation of a yeast (Saccharomyces cerevisiae) mutant impaired in VDAC1, a porin of the mitochondrial outer membrane, showed that LjVDAC1.1, LjVDAC1.2, LjVDAC2.1, and LjVDAC3.1, but not LjVDAC1.3, are functional and targeted to the mitochondrial outer membrane in yeast. Studies of the expression pattern of the five L. japonicus VDAC genes revealed largely constitutive expression of each throughout the plant, including nodules. Antibodies to LjVDAC1.1 of L. japonicus and the related POM36 protein of potato (Solanum tuberosum) recognized several proteins between 30 and 36 kD on western blots, including LjVDAC1.1, LjVDAC1.2, LjVDAC1.3, and LjVDAC2.1. Immunolocalization of VDACs in L. japonicus and soybean root nodules demonstrated their presence on not only mitochondria but also on numerous, small vesicles at the cell periphery. No evidence was found for the presence of VDACs on the symbiosome membrane. Nonetheless, the data indicate that VDACs may play more diverse roles in plants than suspected previously.}, }
@article {pmid14657102, year = {2003}, author = {Cavalier-Smith, T}, title = {The excavate protozoan phyla Metamonada Grassé emend. (Anaeromonadea, Parabasalia, Carpediemonas, Eopharyngia) and Loukozoa emend. (Jakobea, Malawimonas): their evolutionary affinities and new higher taxa.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {53}, number = {Pt 6}, pages = {1741-1758}, doi = {10.1099/ijs.0.02548-0}, pmid = {14657102}, issn = {1466-5026}, mesh = {Animals ; *Biological Evolution ; Eukaryota/*classification/*genetics ; Molecular Sequence Data ; Paleontology ; *Phylogeny ; RNA, Ribosomal/genetics ; Terminology as Topic ; }, abstract = {It is argued here that the anaerobic protozoan zooflagellate Parabasalia, Carpediemonas and Eopharyngia (diplomonads, enteromonads, retortamonads) constitute a holophyletic group, for which the existing name Trichozoa is adopted as a new subphylum. Ancestrally, Trichozoa probably had hydrogenosomes, stacked Golgi dictyosomes, three anterior centrioles and one posterior centriole: the typical tetrakont pattern. It is also argued that the closest relatives of Trichozoa are Anaeromonada (Trimastix, oxymonads), and the two groups are classified as subphyla of a revised phylum Metamonada. Returning Parabasalia and Anaeromonadea to Metamonada, as in Grassé's original classification, simplifies classification of the kingdom Protozoa by reducing the number of phyla within infrakingdom Excavata from five to four. Percolozoa (Heterolobosea plus Percolatea classis nov.) and Metamonada are probably both ancestrally quadriciliate with a kinetid of four centrioles attached to the nucleus; the few biciliates among them are probably secondarily derived. Metamonada ancestrally probably had two divergent centriole pairs, whereas, in Percolozoa, all four centrioles are parallel. It is suggested that Discicristata (Percolozoa, Euglenozoa) are holophyletic, ancestrally with two parallel centrioles. In the phylum Loukozoa, Malawimonadea classis nov. is established for Malawimonas (with a new family and order also) and Diphyllatea classis nov., for Diphylleida (Diphylleia, Collodictyon), is transferred back to Apusozoa. A new class, order and family are established for the anaerobic, biciliate, tricentriolar Carpediemonas, transferring it from Loukozoa to Trichozoa because of its triply flanged cilia; like Retortamonas, it may be secondarily biciliate--its unique combination of putative hydrogenosomes and flanged cilia agree with molecular evidence that Carpediemonas is sister to Eopharyngia, diverging before their ancestor lost hydrogenosomes and acquired a cytopharynx. Removal of anaeromonads and Carpediemonas makes Loukozoa more homogeneous, being basically biciliate, aerobic and free-living, in contrast to Metamonada. A new taxon-rich rRNA tree supports holophyly of Discicristata and Trichozoa strongly, holophyly of Metamonada and Excavata and paraphyly of Loukozoa weakly. Mitochondria were probably transformed into hydrogenosomes independently in the ancestors of lyromonad Percolozoa and Metamonada and further reduced in the ancestral eopharyngian. Evidence is briefly discussed that Metamonada and all other excavates share a photosynthetic ancestry with Euglenozoa and are secondarily non-photosynthetic, as predicted by the cabozoan hypothesis for a single secondary symbiogenetic acquisition of green algal plastids by the last common ancestor of Euglenozoa and Cercozoa. Excavata plus core Rhizaria (Cercozoa, Retaria) probably form an ancestrally photophagotrophic clade. The origin from a benthic loukozoan ancestor of the characteristic cellular features of Percolozoa and Euglenozoa through divergent adaptations for feeding on or close to surfaces is also discussed.}, }
@article {pmid14651648, year = {2003}, author = {Parvizi, P and Benlarbi, M and Ready, PD}, title = {Mitochondrial and Wolbachia markers for the sandfly Phlebotomus papatasi: little population differentiation between peridomestic sites and gerbil burrows in Isfahan province, Iran.}, journal = {Medical and veterinary entomology}, volume = {17}, number = {4}, pages = {351-362}, doi = {10.1111/j.1365-2915.2003.00451.x}, pmid = {14651648}, issn = {0269-283X}, mesh = {Animals ; Base Sequence ; Cytochromes b/genetics ; Disease Reservoirs/veterinary ; Female ; Gene Transfer Techniques ; *Gerbillinae/parasitology ; Haplotypes ; Host-Parasite Interactions ; Humans ; Insect Vectors/classification/*microbiology/parasitology ; Iran ; Leishmania major/pathogenicity/physiology ; Leishmaniasis, Cutaneous/*prevention &amp; control/transmission ; Male ; Mitochondria/chemistry ; Phlebotomus/classification/*microbiology/parasitology ; Phylogeny ; Polymerase Chain Reaction/veterinary ; Population Dynamics ; Sequence Analysis, DNA ; Sex Factors ; Species Specificity ; Transgenes ; Wolbachia/*genetics/growth &amp; development ; }, abstract = {In Iran, Phlebotomus papatasi (Scopoli) (Diptera: Psychodidae) is the main vector of Leishmania major Yakimoff &amp; Schokhor (Kinetoplastida: Trypanosomatidae), the causative agent of rural zoonotic cutaneous leishmaniasis. This sandfly is abundant both in villages and in the burrows of the main reservoir host, the gerbil Rhombomys opimus (Licht.) (Rodentia: Gerbillidae). Populations of P. papatasi were sampled from the edges of villages in Isfahan province, using CDC miniature light traps in peridomestic sites and sticky papers placed at the entrances to gerbil burrows. Single peridomestic sites in two northern provinces were also sampled. Individual sandflies were characterized by PCR amplification and sequencing of fragments of their mitochondrial cytochrome b gene and of the wsp gene of endosymbiotic Wolbachia pipientis Hertig (alpha-Proteobacteria: Rickettsiaceae). The distributions of the haplotypes of these two maternally inherited genes were analysed to assess the population differentiation of P. papatasi, knowledge of which will be needed for planning control measures. For the first time these markers were used to characterize P. papatasi from gerbil burrows, and they indicated the absence not only of sympatric cryptic species but also of any long-term differentiation of lineages in different habitats. A single lineage of cytochrome b haplotypes was found, and both sexes in all populations had a high infection rate of the same A-group strain of Wolbachia (wPap). The distributions of cytochrome b haplotypes were consistent with females dispersing more than males, which has been reported for P. papatasi in other countries. The widespread distribution of wPap suggests that Wolbachia could be used to spread transgenes between populations of P. papatasi in different habitats.}, }
@article {pmid14648296, year = {2003}, author = {Tuomivirta, TT and Hantula, J}, title = {Gremmeniella abietina mitochondrial RNA virus S1 is phylogenetically related to the members of the genus Mitovirus.}, journal = {Archives of virology}, volume = {148}, number = {12}, pages = {2429-2436}, doi = {10.1007/s00705-003-0195-5}, pmid = {14648296}, issn = {0304-8608}, mesh = {Amino Acid Sequence ; Fungi/*virology ; Genome, Viral ; Mitochondria/*virology ; Molecular Sequence Data ; Phylogeny ; RNA Viruses/*classification/genetics ; RNA, Double-Stranded/chemistry ; RNA, Viral/chemistry ; RNA-Dependent RNA Polymerase/genetics ; }, abstract = {A double stranded (ds) RNA genome of Gremmeniella abietina mitochondrial RNA virus S1 (GaMRV-S1) was sequenced. The length of the genome was 2572 base pairs, it had a very low GC content (30.6%), and sequence and length variations occurred in both ends of it. The genome coded for a putative 741 amino acid long RNA-dependent RNA polymerase (RdRp) using a mitochondrial translation code. Comparison of the putative amino acid sequences suggested that GaMRV-S1 is a putative member of the genus Mitovirus.}, }
@article {pmid14644195, year = {2003}, author = {Bossy-Wetzel, E and Barsoum, MJ and Godzik, A and Schwarzenbacher, R and Lipton, SA}, title = {Mitochondrial fission in apoptosis, neurodegeneration and aging.}, journal = {Current opinion in cell biology}, volume = {15}, number = {6}, pages = {706-716}, doi = {10.1016/j.ceb.2003.10.015}, pmid = {14644195}, issn = {0955-0674}, support = {P01HD29587/HD/NICHD NIH HHS/United States ; R01EY05477/EY/NEI NIH HHS/United States ; R01EY09024/EY/NEI NIH HHS/United States ; R01NS41207/NS/NINDS NIH HHS/United States ; R01NS44314/NS/NINDS NIH HHS/United States ; }, mesh = {*Aging ; Animals ; *Apoptosis ; Caenorhabditis elegans ; DNA/chemistry ; Drosophila ; GTP Phosphohydrolases/metabolism ; Humans ; Mitochondria/metabolism/*pathology ; Models, Biological ; Models, Genetic ; Mutation ; Neurodegenerative Diseases/pathology ; Protein Structure, Tertiary ; }, abstract = {A decline in mitochondrial function is well recognized in neurodegenerative diseases and aging, and is thought to play a causal role in their biology. Unfortunately, the molecular basis underlying this detrimental loss in mitochondrial function remains mysterious. Interestingly, mitochondria undergo frequent fission and fusion. This process is regulated by molecular machinery that has been highly conserved during evolution, including dynamin-related GTPases that manifest opposing effects. A balance between mitochondrial fission and fusion events is required for normal mitochondrial and cellular function. Emerging evidence indicates that mitochondria undergo rapid and extensive fission at an early stage during apoptosis. A clue that these new findings are of significance for the pathogenesis of neurodegenerative disease is provided by the observation that OPA-1, a dynamin-related GTPase regulating mitochondrial fusion, is mutated in humans with dominant optic atrophy, which is characterized by degeneration of retinal ganglion cells and childhood blindness. Loss of function of OPA-1, analogous to deficiency of its yeast homologue, Mgm1p, is expected to lead to mitochondrial fission, loss of mitochondrial DNA, respiratory deficits and an increase in reactive oxygen species. Here we review the molecular mediators controlling mitochondrial fission and fusion, and how death effector molecules may hijack this ancient machinery. A shift in the rate of mitochondrial fission or fusion may provide a new mechanistic explanation for the mitochondrial dysfunction in neurodegenerative diseases and normal aging, and may offer a new target for therapeutic intervention.}, }
@article {pmid14642660, year = {2003}, author = {Cotta, C and Moscato, P}, title = {A memetic-aided approach to hierarchical clustering from distance matrices: application to gene expression clustering and phylogeny.}, journal = {Bio Systems}, volume = {72}, number = {1-2}, pages = {75-97}, doi = {10.1016/s0303-2647(03)00136-9}, pmid = {14642660}, issn = {0303-2647}, mesh = {*Algorithms ; Animals ; Artificial Intelligence ; *Biological Evolution ; Chromosome Mapping/methods ; *Cluster Analysis ; Gene Expression Profiling/*methods ; Humans ; Mitochondria/*genetics ; Oligonucleotide Array Sequence Analysis/*methods ; Pattern Recognition, Automated ; Phylogeny ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Alignment/*methods ; Sequence Analysis, DNA/*methods ; Software ; }, abstract = {We propose a heuristic approach to hierarchical clustering from distance matrices based on the use of memetic algorithms (MAs). By using MAs to solve some variants of the Minimum Weight Hamiltonian Path Problem on the input matrix, a sequence of the individual elements to be clustered (referred to as patterns) is first obtained. While this problem is also NP-hard, a probably optimal sequence is easy to find with the current advances for this problem and helps to prune the space of possible solutions and/or to guide the search performed by an actual clustering algorithm. This technique has been successfully applied to both a Branch-and-Bound algorithm, and to evolutionary algorithms and MAs. Experimental results are given in the context of phylogenetic inference and in the hierarchical clustering of gene expression data.}, }
@article {pmid14642765, year = {2003}, author = {Chose, O and Sarde, CO and Gerbod, D and Viscogliosi, E and Roseto, A}, title = {Programmed cell death in parasitic protozoans that lack mitochondria.}, journal = {Trends in parasitology}, volume = {19}, number = {12}, pages = {559-564}, doi = {10.1016/j.pt.2003.09.016}, pmid = {14642765}, issn = {1471-4922}, mesh = {Animals ; Apoptosis/*physiology ; *Biological Evolution ; Eukaryota/*physiology ; Mitochondria/physiology ; Necrosis ; Symbiosis/physiology ; Trichomonas vaginalis/physiology ; }, }
@article {pmid14642752, year = {2003}, author = {Burger, G and Gray, MW and Lang, BF}, title = {Mitochondrial genomes: anything goes.}, journal = {Trends in genetics : TIG}, volume = {19}, number = {12}, pages = {709-716}, doi = {10.1016/j.tig.2003.10.012}, pmid = {14642752}, issn = {0168-9525}, mesh = {Animals ; Biological Evolution ; Cell Nucleus ; DNA, Mitochondrial/*genetics ; Eukaryota/genetics ; Genes ; *Genome ; Humans ; Invertebrates/genetics ; Mitochondria/*genetics ; Models, Biological ; Phylogeny ; Plants/genetics ; Vertebrates/*genetics ; Yeasts/genetics ; }, }
@article {pmid14640972, year = {2004}, author = {Fox, EJ and Stubbs, SA and Kyaw Tun, J and Leek, JP and Markham, AF and Wright, SC}, title = {PRELI (protein of relevant evolutionary and lymphoid interest) is located within an evolutionarily conserved gene cluster on chromosome 5q34-q35 and encodes a novel mitochondrial protein.}, journal = {The Biochemical journal}, volume = {378}, number = {Pt 3}, pages = {817-825}, pmid = {14640972}, issn = {1470-8728}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cell Cycle ; Cell Differentiation ; Cell Line ; Chromosome Mapping ; *Chromosomes, Mammalian ; Evolution, Molecular ; Gene Expression Regulation ; Humans ; Mice ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Multigene Family ; Promoter Regions, Genetic ; Protein Sorting Signals ; Repressor Proteins/genetics ; rab GTP-Binding Proteins/genetics ; }, abstract = {The characterization of mitochondrial proteins is important for the understanding of both normal cellular function and mitochondrial disease. In the present study we identify a novel mitochondrial protein, PRELI (protein of relevant evolutionary and lymphoid interest), that is encoded within the evolutionarily conserved MAD3/PRELI/RAB24 gene cluster located at chromosome 5q34-q35. Mouse Preli is expressed at high levels in all settings analysed; it is co-expressed with Rab24 from a strong bi-directional promoter, and is regulated independently from the S-phase-specific Mad3 gene located at its 3' end. PRELI contains a stand-alone 170 amino acid PRELI/MSF1p' motif at its N-terminus. This domain is found in a variety of proteins from diverse eukaryotes including yeast, Drosophila and mammals, but its function is unknown, and the subcellular location of higher eukaryotic PRELI/MSF1P' proteins has not been determined previously. We show here that PRELI is located in the mitochondria, and by using green-fluorescent-protein fusion proteins we identify a mitochondrial targeting signal at its N-terminus.}, }
@article {pmid14635898, year = {2003}, author = {Gómez-Zurita, J and Vogler, AP}, title = {Incongruent nuclear and mitochondrial phylogeographic patterns in the Timarcha goettingensis species complex (Coleoptera, Chrysomelidae).}, journal = {Journal of evolutionary biology}, volume = {16}, number = {5}, pages = {833-843}, doi = {10.1046/j.1420-9101.2003.00599.x}, pmid = {14635898}, issn = {1010-061X}, mesh = {Animals ; Coleoptera/*genetics ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; Female ; *Genetic Markers ; *Genetics, Population ; Geography ; Hybridization, Genetic ; Male ; Mitochondria ; *Phylogeny ; Population Dynamics ; }, abstract = {Phylogeographic analyses have mostly been based on single-gene genealogies but it is unclear how conclusions from such studies depend on the choice of gene markers. We conducted a nested geographical clade analysis [A.R. Templeton, E. Routman and C.A. Phillips (1995) Genetics 140: 767-782] based on nuclear rDNA internal transcribed spacer region 2 (ITS2) sequences in the Timarcha goettingensis species complex (Coleoptera, Chrysomelidae), and compared the inferences with an updated version of previously published results using mitochondrial cytochrome oxidase II (COIl) sequences. Inferences from ITS2 suggest that patterns of marker distribution are mostly explained by restricted gene flow with isolation by distance. In contrast, COII revealed a history of geographical structure resulting from episodic population contiguous-range expansions. Both markers also show different genealogical patterns, which are associated to the effects of genetic introgression in a putative hybrid zone between two major lineages in the complex. Altogether, these differences are attributed to distinct population and/or evolutionary dynamics of the markers, and offer a more accurate phylogeographic description for the T. goettingensis complex.}, }
@article {pmid14630958, year = {2003}, author = {Cardol, P and Gloire, G and Havaux, M and Remacle, C and Matagne, R and Franck, F}, title = {Photosynthesis and state transitions in mitochondrial mutants of Chlamydomonas reinhardtii affected in respiration.}, journal = {Plant physiology}, volume = {133}, number = {4}, pages = {2010-2020}, pmid = {14630958}, issn = {0032-0889}, mesh = {Animals ; Chlamydomonas reinhardtii/*genetics/metabolism ; Darkness ; Energy Metabolism ; Kinetics ; Light ; Mitochondria/*genetics ; Oxygen Consumption/*genetics ; Photosynthesis/*physiology ; }, abstract = {Photosynthetic activities were analyzed in Chlamydomonas reinhardtii mitochondrial mutants affected in different complexes (I, III, IV, I + III, and I + IV) of the respiratory chain. Oxygen evolution curves showed a positive relationship between the apparent yield of photosynthetic linear electron transport and the number of active proton-pumping sites in mitochondria. Although no significant alterations of the quantitative relationships between major photosynthetic complexes were found in the mutants, 77 K fluorescence spectra showed a preferential excitation of photosystem I (PSI) compared with wild type, which was indicative of a shift toward state 2. This effect was correlated with high levels of phosphorylation of light-harvesting complex II polypeptides, indicating the preferential association of light-harvesting complex II with PSI. The transition to state 1 occurred in untreated wild-type cells exposed to PSI light or in 3-(3,4-dichlorophenyl)-1,1-dimethylureatreated cells exposed to white light. In mutants of the cytochrome pathway and in double mutants, this transition was only observed in white light in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea. This suggests higher rates of nonphotochemical plastoquinone reduction through the chlororespiratory pathway, which was confirmed by measurements of the complementary area above the fluorescence induction curve in dark-adapted cells. Photo-acoustic measurements of energy storage by PSI showed a stimulation of PSI-driven cyclic electron flow in the most affected mutants. The present results demonstrate that in C. reinhardtii mutants, permanent defects in the mitochondrial electron transport chain stabilize state 2, which favors cyclic over linear electron transport in the chloroplast.}, }
@article {pmid14628919, year = {2003}, author = {Sackton, TB and Haney, RA and Rand, DM}, title = {Cytonuclear coadaptation in Drosophila: disruption of cytochrome c oxidase activity in backcross genotypes.}, journal = {Evolution; international journal of organic evolution}, volume = {57}, number = {10}, pages = {2315-2325}, doi = {10.1111/j.0014-3820.2003.tb00243.x}, pmid = {14628919}, issn = {0014-3820}, mesh = {Adaptation, Biological/*genetics ; Analysis of Variance ; Animals ; Base Sequence ; Biological Assay ; Crosses, Genetic ; DNA Primers ; Drosophila/*enzymology/*genetics ; Electron Transport Complex IV/*genetics/*metabolism ; Evolution, Molecular ; Hybridization, Genetic/genetics ; Microsatellite Repeats ; Mitochondria/genetics/*physiology ; *Models, Genetic ; Molecular Sequence Data ; Sequence Analysis, DNA ; }, abstract = {The cytochrome c oxidase enzyme (COX) is comprised of 10 nuclear-encoded subunits and three mitochondrial-encoded subunits in close physical association in the inner mitochondrial membrane. COX passes electrons from cytochrome c to molecular oxygen and pumps protons into the inner mitochondrial space for ATP production. Selection on nuclear-mitochondrial interactions within species should lead to coadaptation of the proteins comprising this important enzyme. Under this model, there should be relatively little disruption of COX activity when mitochondrial genomes are crossed among strains within species. A more pronounced disruption of activity is expected when the mitochondrial genome is expressed in the nuclear background of a different species. We test these hypotheses in Drosophila using hybridization and backcrossing among lines of D. simulans and D. mauritiana. Disrupted cytonuclear genotypes were constructed using backcrosses between two lines of D. simulans (siI and siII) that introduced each divergent mitochondrial DNA (mtDNA) into each nuclear background due to maternal inheritance of mtDNA. Similar crosses were used to introduce each D. simulans mtDNA into the D. mauritiana maI nuclear background. Reconstituted cytonuclear control genotypes were constructed by backcrossing the initial F1 females to males of the maternal genotype. COX enzyme activities were compared among these disrupted and reconstituted backcross genotypes within and between species. The disruption effect on COX activity was restricted to males of interspecific genotypes. These data support the coadaptation hypothesis and are consistent with predictions that the evolution of modifiers of male mitochondrial dysfunction is hindered by the maternal inheritance of mtDNA. New sequence data for nuclear encoded subunits of COX identified amino acids that may play a role in the disruption effect.}, }
@article {pmid14623864, year = {2003}, author = {Atorino, L and Silvestri, L and Koppen, M and Cassina, L and Ballabio, A and Marconi, R and Langer, T and Casari, G}, title = {Loss of m-AAA protease in mitochondria causes complex I deficiency and increased sensitivity to oxidative stress in hereditary spastic paraplegia.}, journal = {The Journal of cell biology}, volume = {163}, number = {4}, pages = {777-787}, pmid = {14623864}, issn = {0021-9525}, support = {F.1/TI_/Telethon/Italy ; TGM03S01/TI_/Telethon/Italy ; TGM06S01/TI_/Telethon/Italy ; R01 NS38713-01/NS/NINDS NIH HHS/United States ; }, mesh = {ATP-Dependent Proteases ; ATPases Associated with Diverse Cellular Activities ; Adenosine Triphosphatases/genetics/metabolism ; Cell Respiration/genetics ; Cells, Cultured ; Down-Regulation/genetics ; Electron Transport Complex I/deficiency/*metabolism ; Fibroblasts ; Humans ; Intracellular Membranes/metabolism ; Macromolecular Substances ; Metalloendopeptidases/*deficiency/genetics/*metabolism ; Mitochondria/*enzymology ; Oxidative Stress/genetics ; Phylogeny ; Reactive Oxygen Species/pharmacology ; Saccharomyces cerevisiae/enzymology/genetics ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Sequence Homology, Nucleic Acid ; Spastic Paraplegia, Hereditary/*enzymology/genetics ; }, abstract = {Mmutations in paraplegin, a putative mitochondrial metallopeptidase of the AAA family, cause an autosomal recessive form of hereditary spastic paraplegia (HSP). Here, we analyze the function of paraplegin at the cellular level and characterize the phenotypic defects of HSP patients' cells lacking this protein. We demonstrate that paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane. These two proteins form a high molecular mass complex, which we show to be aberrant in HSP fibroblasts. The loss of this complex causes a reduced complex I activity in mitochondria and an increased sensitivity to oxidant stress, which can both be rescued by exogenous expression of wild-type paraplegin. Furthermore, complementation studies in yeast demonstrate functional conservation of the human paraplegin-AFG3L2 complex with the yeast m-AAA protease and assign proteolytic activity to this structure. These results shed new light on the molecular pathogenesis of HSP and functionally link AFG3L2 to this neurodegenerative disease.}, }
@article {pmid14622983, year = {2003}, author = {Emelyanov, VV}, title = {Common evolutionary origin of mitochondrial and rickettsial respiratory chains.}, journal = {Archives of biochemistry and biophysics}, volume = {420}, number = {1}, pages = {130-141}, doi = {10.1016/j.abb.2003.09.031}, pmid = {14622983}, issn = {0003-9861}, mesh = {Alphaproteobacteria/enzymology/genetics ; Amino Acid Sequence ; Biological Evolution ; Cell Respiration/*genetics ; Coxiellaceae/*enzymology/*genetics ; Electron Transport Chain Complex Proteins/classification/*genetics ; Electron Transport Complex I ; Electron Transport Complex II ; Electron Transport Complex III ; *Evolution, Molecular ; Gene Expression Profiling/methods ; Gene Expression Regulation, Enzymologic/genetics ; Mitochondria/*enzymology/*genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Comprehensive phylogenetic analysis of the subunits of respiratory chain was carried out using a variety of mitochondrial and bacterial sequences including those from all unfinished alpha-proteobacterial genomes known to date. Maximum likelihood, neighbor-joining, and maximum parsimony consensus trees, based on four proton-translocating complexes, placed mitochondria as a sister group to the order Rickettsiales of obligate endosymbiotic bacteria to the exclusion of free-living alpha-proteobacteria. Thus, phylogenetic relationship of most eukaryotic respiratory enzymes conforms to canonical pattern of mitochondrial ancestry, prior established in analyses of ribosomal RNAs, which are encoded by residual mitochondrial genomes. These data suggest that mitochondria may have derived from a reduced intracellular bacterium and that respiration may be the only evolutionary novelty brought into eukaryotes by mitochondrial endosymbiont.}, }
@article {pmid14619972, year = {2003}, author = {Lohia, A}, title = {The cell cycle of Entamoeba histolytica.}, journal = {Molecular and cellular biochemistry}, volume = {253}, number = {1-2}, pages = {217-222}, pmid = {14619972}, issn = {0300-8177}, mesh = {Animals ; CDC28 Protein Kinase, S cerevisiae/metabolism ; Cell Cycle/*physiology ; Cell Cycle Proteins/metabolism ; Cell Nucleus/*metabolism ; Dysentery, Amebic/*parasitology ; Entamoeba histolytica/*physiology ; Genes, Protozoan/genetics ; Humans ; Mitochondria/metabolism ; *Saccharomyces cerevisiae Proteins ; Tubulin/metabolism ; }, abstract = {Entamoeba histolytica, is a microaerophilic protist, which causes amoebic dysentery in humans. This unicellular organism proliferates in the human intestine as the motile trophozoite and survives the hostile environment outside the human host as the dormant quadri-nucleate cyst. Lack of organelles--such as mitochondria and Golgi bodies--and an unequal mode of cell division, led to the popular belief, that this organism preceded other eukaryotes during evolution. However, data from several laboratories have shown that, contrary to this belief, E. histolytica is remarkable in its divergence from other eukaryotes. This uniqueness is witnessed in many aspects of its biochemical pathways, cellular biology and genetic diversity. In this context, I have analysed the cell division cycle of this organism and compared it to that of other eukaryotes. Studies on E. histolytica, suggest that in its proliferative phase, this organism may accumulate polyploid cells. Thus 'checkpoints' regulating alternation of genome duplication and cell division appear to be absent in this unicellular protist. Sequence homologs of several cell cycle regulating proteins have been identified in amoeba, but their structural divergence suggests that they may not have equivalent function in this organism. The regulation of cell proliferation in E. histolytica, may be ideally suited to survival of a parasite in a complex host. Analysis of these molecular details may offer solutions for eradicating the pathogen by hitherto unknown methods.}, }
@article {pmid14615181, year = {2003}, author = {Adams, KL and Palmer, JD}, title = {Evolution of mitochondrial gene content: gene loss and transfer to the nucleus.}, journal = {Molecular phylogenetics and evolution}, volume = {29}, number = {3}, pages = {380-395}, doi = {10.1016/s1055-7903(03)00194-5}, pmid = {14615181}, issn = {1055-7903}, mesh = {Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genes/genetics ; *Genetic Variation ; Magnoliopsida/genetics ; Mitochondria/*genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {Mitochondrial gene content is highly variable across extant eukaryotes. The number of mitochondrial protein genes varies from 3 to 67, while tRNA gene content varies from 0 to 27. Moreover, these numbers exclude the many diverse lineages of non-respiring eukaryotes that lack a mitochondrial genome yet still contain a mitochondrion, albeit one often highly derived in ultrastructure and metabolic function, such as the hydrogenosome. Diversity in tRNA gene content primarily reflects differential usage of imported tRNAs of nuclear origin. In the case of protein genes, most of this diversity reflects differential degrees of functional gene transfer to the nucleus, with more minor contributions resulting from gene loss from the cell as a consequence of either substitution via a functional nuclear homolog or the cell's dispensation of the function of the gene product. The tempo and pattern of mitochondrial gene loss is highly episodic, both across the broad sweep of eukaryotes and within such well-studied groups as angiosperms. All animals, some plants, and certain other groups of eukaryotes are mired in profound stases in mitochondrial gene content, whereas other lineages have experienced relatively frequent gene loss. Loss and transfer to the nucleus of ribosomal protein and succinate dehydrogenase genes has been especially frequent, sporadic, and episodic during angiosperm evolution. Potential mechanisms for activation of transferred genes have been inferred, and intermediate stages in the process have been identified by comparative studies. Several hypotheses have been proposed for why mitochondrial genes are transferred to the nucleus, why mitochondria retain genomes, and why functional gene transfer is almost exclusively unidirectional.}, }
@article {pmid14614504, year = {2003}, author = {Tovar, J and León-Avila, G and Sánchez, LB and Sutak, R and Tachezy, J and van der Giezen, M and Hernández, M and Müller, M and Lucocq, JM}, title = {Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation.}, journal = {Nature}, volume = {426}, number = {6963}, pages = {172-176}, doi = {10.1038/nature01945}, pmid = {14614504}, issn = {1476-4687}, mesh = {Amino Acid Sequence ; Animals ; Biological Evolution ; Cloning, Molecular ; Fluorescent Antibody Technique ; Genes, Protozoan/genetics ; Giardia/*cytology/genetics/*metabolism ; Iron-Sulfur Proteins/*biosynthesis/metabolism ; Microscopy, Immunoelectron ; Mitochondria/*metabolism ; Molecular Sequence Data ; Protein Transport ; Protozoan Proteins/*biosynthesis/metabolism ; Symbiosis ; }, abstract = {Giardia intestinalis (syn. lamblia) is one of the most widespread intestinal protozoan pathogens worldwide, causing hundreds of thousands of cases of diarrhoea each year. Giardia is a member of the diplomonads, often described as an ancient protist group whose primitive nature is suggested by the lack of typical eukaryotic organelles (for example, mitochondria, peroxisomes), the presence of a poorly developed endomembrane system and by their early branching in a number of gene phylogenies. The discovery of nuclear genes of putative mitochondrial ancestry in Giardia and the recent identification of mitochondrial remnant organelles in amitochondrial protists such as Entamoeba histolytica and Trachipleistophora hominis suggest that the eukaryotic amitochondrial state is not a primitive condition but is rather the result of reductive evolution. Using an in vitro protein reconstitution assay and specific antibodies against IscS and IscU--two mitochondrial marker proteins involved in iron-sulphur cluster biosynthesis--here we demonstrate that Giardia contains mitochondrial remnant organelles (mitosomes) bounded by double membranes that function in iron-sulphur protein maturation. Our results indicate that Giardia is not primitively amitochondrial and that it has retained a functional organelle derived from the original mitochondrial endosymbiont.}, }
@article {pmid14614484, year = {2003}, author = {Henze, K and Martin, W}, title = {Evolutionary biology: essence of mitochondria.}, journal = {Nature}, volume = {426}, number = {6963}, pages = {127-128}, doi = {10.1038/426127a}, pmid = {14614484}, issn = {1476-4687}, mesh = {Adenosine Triphosphate/metabolism ; Anaerobiosis ; Animals ; *Biological Evolution ; Eukaryotic Cells/cytology/metabolism ; Giardia/*cytology/*metabolism ; Humans ; Iron-Sulfur Proteins/*biosynthesis/metabolism ; Mitochondria/*metabolism ; Prokaryotic Cells/cytology/metabolism ; Protozoan Proteins/*biosynthesis/metabolism ; }, }
@article {pmid14613618, year = {2003}, author = {Parmentier, E and Gennotte, V and Focant, B and Goffinet, G and Vandewalle, P}, title = {Characterization of the primary sonic muscles in Carapus acus (Carapidae): a multidisciplinary approach.}, journal = {Proceedings. Biological sciences}, volume = {270}, number = {1530}, pages = {2301-2308}, pmid = {14613618}, issn = {0962-8452}, mesh = {Air Sacs/anatomy &amp; histology/physiology ; Animals ; Electrophoresis, Polyacrylamide Gel ; Fishes/*anatomy &amp; histology ; Histocytochemistry ; Muscle Proteins/chemistry ; Muscles/*anatomy &amp; histology/*chemistry/physiology ; Parvalbumins/chemistry ; }, abstract = {Sound production in carapid fishes results from the action of extrinsic muscles that insert into the swim bladder. Biochemical, histochemical and morphological techniques were used to examine the sonic muscles and compare them with epaxial muscles in Carapus acus. Sonic fibres are thicker than red and thinner than white epaxial fibres, and sonic fibres and myofibrils exhibit an unusual helicoidal organization: the myofibrils of the centre are in a straight line whereas they are more and more twisted towards the periphery. Sonic muscles have both features of red (numerous mitochondria, high glycogen content) and white (alkali-stable ATPase) fibres. They differ also in the isoforms of the light chain (LC3) and heavy chain (HC), in having T tubules at both the Z-line and the A-I junction and in a unique parvalbumin isoform (PAI) that may aid relaxation. All these features lead to the expression of two assumptions about sound generation: the sonic muscle should be able to perform fast and powerful contractions that provoke the forward movement of the forepart of the swim bladder and the stretching and "flapping" of the swim bladder fenestra; the helicoidal organization allows progressive drawing of the swim bladder fenestra which emits a sound when rapidly released in a spring-like manner.}, }
@article {pmid14613499, year = {2003}, author = {Hannaert, V and Bringaud, F and Opperdoes, FR and Michels, PA}, title = {Evolution of energy metabolism and its compartmentation in Kinetoplastida.}, journal = {Kinetoplastid biology and disease}, volume = {2}, number = {1}, pages = {11}, pmid = {14613499}, issn = {1475-9292}, abstract = {Kinetoplastida are protozoan organisms that probably diverged early in evolution from other eukaryotes. They are characterized by a number of unique features with respect to their energy and carbohydrate metabolism. These organisms possess peculiar peroxisomes, called glycosomes, which play a central role in this metabolism; the organelles harbour enzymes of several catabolic and anabolic routes, including major parts of the glycolytic and pentosephosphate pathways. The kinetoplastid mitochondrion is also unusual with regard to both its structural and functional properties.In this review, we describe the unique compartmentation of metabolism in Kinetoplastida and the metabolic properties resulting from this compartmentation. We discuss the evidence for our recently proposed hypothesis that a common ancestor of Kinetoplastida and Euglenida acquired a photosynthetic alga as an endosymbiont, contrary to the earlier notion that this event occurred at a later stage of evolution, in the Euglenida lineage alone. The endosymbiont was subsequently lost from the kinetoplastid lineage but, during that process, some of its pathways of energy and carbohydrate metabolism were sequestered in the kinetoplastid peroxisomes, which consequently became glycosomes. The evolution of the kinetoplastid glycosomes and the possible selective advantages of these organelles for Kinetoplastida are discussed. We propose that the possession of glycosomes provided metabolic flexibility that has been important for the organisms to adapt easily to changing environmental conditions. It is likely that metabolic flexibility has been an important selective advantage for many kinetoplastid species during their evolution into the highly successful parasites today found in many divergent taxonomic groups.Also addressed is the evolution of the kinetoplastid mitochondrion, from a supposedly pluripotent organelle, attributed to a single endosymbiotic event that resulted in all mitochondria and hydrogenosomes of extant eukaryotes. Furthermore, indications are presented that Kinetoplastida may have acquired other enzymes of energy and carbohydrate metabolism by various lateral gene transfer events different from those that involved the algal- and alpha-proteobacterial-like endosymbionts responsible for the respective formation of the glycosomes and mitochondria.}, }
@article {pmid14610025, year = {2003}, author = {Moyes, CD}, title = {Controlling muscle mitochondrial content.}, journal = {The Journal of experimental biology}, volume = {206}, number = {Pt 24}, pages = {4385-4391}, doi = {10.1242/jeb.00699}, pmid = {14610025}, issn = {0022-0949}, mesh = {Animals ; Evolution, Molecular ; *Gene Expression Regulation ; Mitochondria/*enzymology ; *Models, Biological ; Muscle, Skeletal/*cytology ; Transcription Factors ; }, abstract = {Mitochondrial content, a chief determinant of aerobic capacity, varies widely among muscle types and species. Mitochondrial enzyme levels in vertebrate skeletal muscles vary more than 100-fold, from fish white muscle to bird flight muscles. Recent studies have shed light on the transcriptional regulators that control mitochondrial gene expression in muscle fiber differentiation and development, and in the context of pathological conditions such as neuromuscular disease and obesity. While the transcriptional co-activator PGC-1alpha (peroxisome proliferator-activated receptor gamma co-activator 1) has emerged as a master controller of mitochondrial gene expression, it is important to consider other mechanisms by which coordinated changes in mitochondrial content could arise. These studies, largely using biomedical models, provide important information for comparative biologists interested in the mechanistic basis of inter-species variation in muscle aerobic capacity.}, }
@article {pmid14604008, year = {2003}, author = {Anant, S and Blanc, V and Davidson, NO}, title = {Molecular regulation, evolutionary, and functional adaptations associated with C to U editing of mammalian apolipoproteinB mRNA.}, journal = {Progress in nucleic acid research and molecular biology}, volume = {75}, number = {}, pages = {1-41}, doi = {10.1016/s0079-6603(03)75001-6}, pmid = {14604008}, issn = {0079-6603}, support = {DK-52574/DK/NIDDK NIH HHS/United States ; DK-56260/DK/NIDDK NIH HHS/United States ; DK-62265/DK/NIDDK NIH HHS/United States ; HL-38180/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Apolipoproteins B/*genetics ; Cytidine/*genetics/metabolism ; *Evolution, Molecular ; *RNA Editing ; RNA, Messenger/*genetics/metabolism ; Uridine/*genetics/metabolism ; }, abstract = {RNA editing encompasses an important class of co- or posttranscriptional nucleic acid modification that has expanded our understanding of the range of mechanisms that facilitate genetic plasticity. Since the initial description of RNA editing in trypanosome mitochondria, a model of gene regulation has emerged that now encompasses a diverse range of biochemical and genetic mechanisms by which nuclear, mitochondrial, and t-RNA sequences are modified from templated versions encoded in the genome. RNA editing is genetically and biochemically distinct from other RNA modifications such as splicing, capping, and polyadenylation although, as discussed in Section I, these modifications may have relevance to the regulation of certain types of mammalian RNA editing. This review will focus on C to U RNA editing, in particular, the biochemical and genetic mechanisms that regulate this process in mammals. These mechanisms will be examined in the context of the prototype model of C to U RNA editing, namely the posttranscriptional cytidine deamination targeting a single nucleotide in mammalian apolipoproteinB (apoB). Other examples of C to U RNA editing will be discussed and the molecular mechanisms--where known--contrasted with those regulating apoB RNA editing.}, }
@article {pmid14602641, year = {2003}, author = {Won, YJ and Hallam, SJ and O'Mullan, GD and Pan, IL and Buck, KR and Vrijenhoek, RC}, title = {Environmental acquisition of thiotrophic endosymbionts by deep-sea mussels of the genus bathymodiolus.}, journal = {Applied and environmental microbiology}, volume = {69}, number = {11}, pages = {6785-6792}, pmid = {14602641}, issn = {0099-2240}, mesh = {Animals ; Atlantic Ocean ; Bacteria/classification/genetics/isolation &amp; purification ; DNA, Mitochondrial/genetics ; DNA, Ribosomal Spacer/analysis ; Endocytosis/*physiology ; Gills/cytology/*microbiology/ultrastructure ; Microscopy, Electron ; Molecular Sequence Data ; Mollusca/*microbiology ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Sulfur/metabolism ; *Symbiosis ; }, abstract = {Deep-sea Bathymodiolus mussels, depending on species and location, have the capacity to host sulfur-oxidizing (thiotrophic) and methanotrophic eubacteria in gill bacteriocytes, although little is known about the mussels' mode of symbiont acquisition. Previous studies of Bathymodiolus host and symbiont relationships have been based on collections of nonoverlapping species across wide-ranging geographic settings, creating an apparent model for vertical transmission. We present genetic and cytological evidence for the environmental acquisition of thiotrophic endosymbionts by vent mussels from the Mid-Atlantic Ridge. Open pit structures in cell membranes of the gill surface revealed likely sites for endocytosis of free-living bacteria. A population genetic analysis of the thiotrophic symbionts exploited a hybrid zone where two Bathymodiolus species intergrade. Northern Bathymodiolus azoricus and southern Bathymodiolus puteoserpentis possess species-specific DNA sequences that identify both their symbiont strains (internal transcribed spacer regions) and their mitochondria (ND4). However, the northern and southern symbiont-mitochondrial pairs were decoupled in the hybrid zone. Such decoupling of symbiont-mitochondrial pairs would not occur if the two elements were transmitted strictly vertically through the germ line. Taken together, these findings are consistent with an environmental source of thiotrophic symbionts in Bathymodiolus mussels, although an environmentally "leaky" system of vertical transmission could not be excluded.}, }
@article {pmid14596274, year = {2003}, author = {Arrivillaga, J and Mutebi, JP and Piñango, H and Norris, D and Alexander, B and Feliciangeli, MD and Lanzaro, GC}, title = {The taxonomic status of genetically divergent populations of Lutzomyia longipalpis (Diptera: Psychodidae) based on the distribution of mitochondrial and isozyme variation.}, journal = {Journal of medical entomology}, volume = {40}, number = {5}, pages = {615-627}, doi = {10.1603/0022-2585-40.5.615}, pmid = {14596274}, issn = {0022-2585}, support = {AI39540/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; DNA Primers ; DNA, Mitochondrial/*genetics ; *Genetic Variation ; Genetics, Population ; Isoenzymes/*genetics ; Mitochondria/enzymology/genetics ; *Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Single-Stranded Conformational ; Psychodidae/classification/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {The sand fly, Lutzomyia longipalpis (Lutz &amp; Neiva) reputedly is a complex of cryptic species; however, there is currently no consensus as to the number of species in the complex or their geographic distributions. We conducted phylogenetic analyses of 31 populations from throughout the species range, using seven isozyme loci and genes in the mitochondrial genome. Analyses of these two independent sets of markers were largely concordant and revealed four distinct clades that support the existence of four species. The four clades have distinct geographic ranges: (1) Brazil (Species A = Lu. longipalpis sensu stricto), (2) Laran (Species B = Lu. pseudolongipalpis), (3) cis-Andean (Species C), and (4) trans-Andean (Species D). The cis-Andean clade may be subdivided further into two groups, one in Colombia and one in northwestern Venezuela, but their taxonomic status remains unresolved. Knowledge that Lu. longipalpis is a complex of species may ultimately shed light on anomalies in the epidemiology of visceral leishmaniasis in the New World.}, }
@article {pmid14594718, year = {2003}, author = {Otu, HH and Sayood, K}, title = {A new sequence distance measure for phylogenetic tree construction.}, journal = {Bioinformatics (Oxford, England)}, volume = {19}, number = {16}, pages = {2122-2130}, doi = {10.1093/bioinformatics/btg295}, pmid = {14594718}, issn = {1367-4803}, mesh = {*Algorithms ; Animals ; Chromosome Mapping/*methods ; Evolution, Molecular ; Gene Expression Profiling/*methods ; Humans ; Mitochondria/*genetics ; *Phylogeny ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Analysis, DNA/*methods ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {MOTIVATION: Most existing approaches for phylogenetic inference use multiple alignment of sequences and assume some sort of an evolutionary model. The multiple alignment strategy does not work for all types of data, e.g. whole genome phylogeny, and the evolutionary models may not always be correct. We propose a new sequence distance measure based on the relative information between the sequences using Lempel-Ziv complexity. The distance matrix thus obtained can be used to construct phylogenetic trees.<br><br>RESULTS: The proposed approach does not require sequence alignment and is totally automatic. The algorithm has successfully constructed consistent phylogenies for real and simulated data sets.<br><br>AVAILABILITY: Available on request from the authors.}, }
@article {pmid14584589, year = {2003}, author = {Embley, TM and van der Giezen, M and Horner, DS and Dyal, PL and Bell, S and Foster, PG}, title = {Hydrogenosomes, mitochondria and early eukaryotic evolution.}, journal = {IUBMB life}, volume = {55}, number = {7}, pages = {387-395}, doi = {10.1080/15216540310001592834}, pmid = {14584589}, issn = {1521-6543}, mesh = {Adenosine Triphosphate/*metabolism ; Animals ; Biological Evolution ; COS Cells ; Eukaryotic Cells/pathology ; Ferritins/metabolism ; Hydrogen/chemistry/*metabolism ; Mitochondria/metabolism/*pathology ; Organelles ; Oxidoreductases/metabolism ; Phylogeny ; Saccharomyces cerevisiae/metabolism ; Time Factors ; Transfection ; }, abstract = {Available data suggest that unusual organelles called hydrogenosomes, that make ATP and hydrogen, and which are found in diverse anaerobic eukaryotes, were once mitochondria. The evolutionary origins of the enzymes used to make hydrogen, pyruvate:ferredoxin oxidoreductase (PFO) and hydrogenase, are unresolved, but it seems likely that both were present at an early stage of eukaryotic evolution. Once thought to be restricted to a few unusual anaerobes, these proteins are found in diverse eukaryotic cells, including our own, where they are targeted to different cell compartments. Organelles related to mitochondria and hydrogenosomes have now been found in species of anaerobic and parasitic protozoa that were previously thought to have separated from other eukaryotes before the mitochondrial endosymbiosis. Thus it is possible that all eukaryotes may eventually be shown to contain an organelle of mitochondrial ancestry, bearing testimony to the important role that the mitochondrial endosymbiosis has played in eukaryotic evolution. It remains to be seen if members of this family of organelles share a common function essential to the eukaryotic cell, that provides the underlying selection pressure for organelle retention under different living conditions.}, }
@article {pmid14579253, year = {2003}, author = {Jékely, G}, title = {Small GTPases and the evolution of the eukaryotic cell.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {25}, number = {11}, pages = {1129-1138}, doi = {10.1002/bies.10353}, pmid = {14579253}, issn = {0265-9247}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus ; Eukaryotic Cells/cytology/*physiology ; GTP Phosphohydrolases/classification/*genetics/*metabolism ; Intracellular Membranes/metabolism ; Mitosis ; Molecular Sequence Data ; Phagocytosis ; Phylogeny ; ras Proteins/classification/genetics/metabolism ; }, abstract = {The origin of eukaryotes is one of the major challenges of evolutionary cell biology. Other than the endosymbiotic origin of mitochondria and chloroplasts, the steps leading to eukaryotic endomembranes and endoskeleton are poorly understood. Ras-family small GTPases are key regulators of cytoskeleton dynamics, vesicular trafficking and nuclear function. They are specific for eukaryotes and their expansion probably traces the evolution of core eukaryote features. The phylogeny of small GTPases suggests that the first endomembranes to evolve during eukaryote evolution had secretory, and not phagocytic, function. Based on the reconstruction of putative roles for ancestral small GTPases, a hypothetical scenario on the origins of the first endomembranes, the nucleus, and phagocytosis is presented.}, }
@article {pmid14575317, year = {2003}, author = {Donato, M and Gelpi, RJ}, title = {Adenosine and cardioprotection during reperfusion--an overview.}, journal = {Molecular and cellular biochemistry}, volume = {251}, number = {1-2}, pages = {153-159}, pmid = {14575317}, issn = {0300-8177}, mesh = {Adenosine/physiology/*therapeutic use ; Animals ; Blood Pressure/drug effects ; Humans ; Myocardial Ischemia/drug therapy/*physiopathology ; Myocardial Reperfusion/adverse effects ; Myocardial Reperfusion Injury/*drug therapy/physiopathology ; Myocardial Stunning/physiopathology/*prevention &amp; control ; Receptors, Purinergic P1/drug effects ; Time Factors ; }, abstract = {Ischemic heart disease includes a number of entities that have been grouped in accordance with physiopathology and evolutive criteria. In recent years 'new' ischemic syndromes have been described. Within the 'new' ischemic syndromes, ventricular post-ischemic dysfunction--also known as 'stunned myocardium'--is worth mentioning. In this route, several studies have suggested that reperfusion per se could cause cellular injury (reperfusion injury). In previous years, a protective effect on the injury caused by ischemia and reperfusion in the heart has been attributed to adenosine. These effects have been documented in different experimental in vivo and in vitro models. Thus, the administration of exogenous adenosine, or agonists of adenosine receptors prior to ischemia reduces the size of the infarction, improves the recovery of the ventricular function during reperfusion (attenuating stunning) and prolongs the time period to the ischemic contracture. However, focusing on a potential therapeutic application, it is of the utmost importance to find this protection and learn the mechanisms involved when procedures are applied during early reperfusion. We showed that adenosine, administered from the beginning of reperfusion, attenuated systolic and diastolic (myocardial stiffness) alterations of the stunned myocardium. This protective effect was mediated by the activation of A1 adenosine receptors, and without modification on infarct size. According to some authors, adenosine can decrease the release of endothelin, during early reperfusion, and reduce an overload of Ca2+ that could cause a cellular lesion. Finally, ischemic preconditioning involves a series of intracellular events that are initiated with the activation of the A1 receptor, and end at the sensitive K+ ATP channels of the mitochondria. The phosphorylation and opening of these channels would cause the protective effect. Activation of this specific mechanism during reperfusion has not been studied extensively.}, }
@article {pmid14573484, year = {2003}, author = {Faith, JJ and Pollock, DD}, title = {Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes.}, journal = {Genetics}, volume = {165}, number = {2}, pages = {735-745}, pmid = {14573484}, issn = {0016-6731}, support = {GM-65612/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Data Interpretation, Statistical ; *Genome ; *Likelihood Functions ; Linear Models ; Mitochondria/*genetics ; *Mutation ; Phylogeny ; Vertebrates/*genetics ; }, abstract = {Protein-coding genes in mitochondrial genomes have varying degrees of asymmetric skew in base frequencies at the third codon position. The variation in skew among genes appears to be caused by varying durations of time that the heavy strand spends in the mutagenic single-strand state during replication (D(ssH)). The primary data used to study skew have been the gene-by-gene base frequencies in individual taxa, which provide little information on exactly what kinds of mutations are responsible for the base frequency skew. To assess the contribution of individual mutation components to the ancestral vertebrate substitution pattern, here we analyze a large data set of complete vertebrate mitochondrial genomes in a phylogeny-based likelihood context. This also allows us to evaluate the change in skew continuously along the mitochondrial genome and to directly estimate relative substitution rates. Our results indicate that different types of mutation respond differently to the D(ssH) gradient. A primary role for hydrolytic deamination of cytosines in creating variance in skew among genes was not supported, but rather linearly increasing rates of mutation from adenine to hypoxanthine with D(ssH) appear to drive regional differences in skew. Substitutions due to hydrolytic deamination of cytosines, although common, appear to quickly saturate, possibly due to stabilization by the mitochondrial DNA single-strand-binding protein. These results should form the basis of more realistic models of DNA and protein evolution in mitochondria.}, }
@article {pmid14562965, year = {2003}, author = {Schmidt, TR and Doan, JW and Goodman, M and Grossman, LI}, title = {Retention of a duplicate gene through changes in subcellular targeting: an electron transport protein homologue localizes to the golgi.}, journal = {Journal of molecular evolution}, volume = {57}, number = {2}, pages = {222-228}, pmid = {14562965}, issn = {0022-2844}, support = {GM48517/GM/NIGMS NIH HHS/United States ; P30CA22453/CA/NCI NIH HHS/United States ; P30E506639//PHS HHS/United States ; }, mesh = {Electron Transport Complex IV/chemistry/*genetics ; Evolution, Molecular ; Genes, Duplicate ; Golgi Apparatus/*genetics ; HeLa Cells ; Humans ; Mitochondria/enzymology ; Organ Specificity ; Protein Isoforms ; Recombinant Fusion Proteins/genetics ; Sequence Homology, Amino Acid ; }, abstract = {Cytochrome c oxidase (COX), the terminal enzyme complex of the electron transport chain, contains 13 subunits, 3 encoded by mitochondrial DNA and 10 by nuclear. Several of the nuclear subunits, including subunit VIIa, are known to have two tissue- and development-specific isoforms in mammals. A recently identified third member of the gene family, COX7AR, encodes a protein previously thought to function in mitochondria. However, observation of fluorescent pCOX7AR C-terminal fusion proteins in HeLa cells showed that pCOX7AR is localized to the Golgi apparatus. Sequence analyses indicate that the duplication of COX7AR occurred prior to the origin of the Euteleostomi (bony vertebrates) and that pCOX7AR is more highly conserved than the two other isoforms. These results indicate that, after gene duplication and modification of the mitochondrial targeting signal, pCOX7AR was evolutionarily altered to a new and apparently important function in the Golgi. These results also suggest that predictions of function from homology can be misleading and show that specialization and modification of subcellular localization are similar to cis-element subfunctionalization. In cis-element subfunctionalization, complementary null mutations occur to the cis-elements of the descendents of a gene duplication, causing both descendent genes to be obligate. In the process described in this paper, which could be termed subcellular subfunctionalization, complementary null mutations can occur to the subcellular localization signals of the descendants of a gene duplication, causing both descendent genes to be similarly obligate. Noncomplementary null mutations could also uncover an alternate localization, which is the more likely case for pCOX7AR.}, }
@article {pmid14557390, year = {2003}, author = {Yang, J and Wang, J and Kijas, J and Liu, B and Han, H and Yu, M and Yang, H and Zhao, S and Li, K}, title = {Genetic diversity present within the near-complete mtDNA genome of 17 breeds of indigenous Chinese pigs.}, journal = {The Journal of heredity}, volume = {94}, number = {5}, pages = {381-385}, doi = {10.1093/jhered/esg077}, pmid = {14557390}, issn = {0022-1503}, mesh = {Animals ; China ; *DNA, Mitochondrial ; Europe ; *Genetic Variation ; Mitochondria/*genetics ; Phylogeny ; Point Mutation ; Swine/classification/*genetics ; }, abstract = {The genetic diversity present within the near-complete mitochondrial genome (15,982 bp) was determined from 17 indigenous Chinese pig breeds and 3 European breeds. Animals were selected from 17 Chinese breeds that reflect the large phenotypic diversity of Chinese pigs and represent each of the six breed types, which are grouped based on morphological characteristics. Analysis of nucleotide diversity confirmed a high level of divergence between animals of European versus Asian origin; however, much more limited variation was observed between the 17 indigenous Chinese breeds. Each had a unique haplotype, but the lowest pairwise sequence divergence was only 0.01 +/- 0.01%, observed between the Tongcheng and Yushan Black. Comparison of control region sequence diversity revealed the 17 Chinese breeds contain a lower average pairwise distance (0.61 +/- 0.19%) than a group of European commercial breeds (0.91 +/- 0.21%). The dendrogram constructed from the near-complete mtDNA sequences showed the Chinese sequences loosely clustering into two groups. Although some correspondence with geographic origin was present, notable differences between the dendrogram and the traditional pig breed grouping system were observed.}, }
@article {pmid14556468, year = {2003}, author = {Desnuelle, C}, title = {[Evolution of the concept of mitochondrial disease].}, journal = {Bulletin de l'Academie nationale de medecine}, volume = {187}, number = {3}, pages = {537-55; discussion 555-7}, pmid = {14556468}, issn = {0001-4079}, mesh = {Chromosomes, Human/genetics ; DNA, Mitochondrial/genetics ; Electron Transport/genetics ; Female ; Humans ; Male ; *Mitochondrial Diseases/classification/diagnosis/genetics/pathology ; Mutation ; Oxidative Phosphorylation ; Phenotype ; }, abstract = {The concept of mitochondrial disease originated in 1962 when Luft and co-workers described a patient with non thyroidal hypermetabolism related to loose coupling of oxidation-phosphorylation in muscle mitochondria. Over the following quarter of century, with the routine use of the Engel-Gomory staining on muscle biopsy revealing ragged-red fibres as a convenient markers for mitochondrial pathology, numerous papers described clinical, biochemical and morphological aspects of mitochondrial encephalomyopathies. With the discovery in 1988 of mutations in mitochondrial DNA, the concept of mitochondrial disease with maternal transmission led to an explosive expansion of research in the field. Throughout the 1990's the rapid identification of multiple mitochondrial gene defects associated with clinically diverse disorders has left practitioners puzzled about diagnosing such heterogeneous and complexes syndromes. The great complexity of the system and the ubiquitous repartition of mitochondria explain the wide variety of clinical phenotypes associated with primary mitochondrial diseases due to mutations in the mitochondrial genome, in the nuclear genome or in the cross-talk between the two genomes and regulations. In the past few years, the pivotal role of mitochondria in drug sensitivity, their key role in aging, apoptosis or neurodegeneration lead to a mitochondial medicine. Here the term of mitochondrial disease is limited to genetic defect in the respiratory chain where advance were recently especially significant for the evolution of the concept and updated classification.}, }
@article {pmid14556388, year = {2003}, author = {Debruyne, R and Van Holt, A and Barriel, V and Tassy, P}, title = {Status of the so-called African pygmy elephant (Loxodonta pumilio (NOACK 1906)): phylogeny of cytochrome b and mitochondrial control region sequences.}, journal = {Comptes rendus biologies}, volume = {326}, number = {7}, pages = {687-697}, doi = {10.1016/s1631-0691(03)00158-6}, pmid = {14556388}, issn = {1631-0691}, mesh = {Africa ; Animals ; Cytochromes b/*genetics ; Elephants/*classification/*genetics ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; Trees ; }, abstract = {Among the African elephants, it has been unanimously acknowledged that the forest elephants (cyclotis form) are peculiar, so that they have been elevated to the specific rank. The development of molecular analyses of extant Loxodonta has only focused on two forms yet: the savannah form (africana) and the forest form (cyclotis), disregarding the so-called pygmy elephants (pumilio or fransseni) the systematic status of which has been debated since their discovery. Therefore, we have sampled nine dwarfed-labelled specimens in collection and eight specimens of typical forest elephants that we compared to three savannah elephants and two Asian elephants. Because of the degraded nature of the nuclear DNA content in bone samples of old specimens, we assayed mitochondrial markers; 1961 bp of the mitochondrial genome were sequenced (over a continuous range spanning the cytochrome b gene, tRNA Thr, tRNA Pro, hypervariable region 1 and central conserved region of the control region). Pumilio and cyclotis are not sister-taxa: the phylogenetic analyses rather account for the inclusion of the so-called pygmy elephants within a monophyletic group of forest elephants sensu lato. The internal structure of this clade reveals to depend on isolation and remoteness between populations, characteristics that may have been extensively influenced by climatic variations during the Quaternary period. We conclude that the specific taxon Loxodonta pumilio (or Loxodonta fransseni) should be abandoned.}, }
@article {pmid14555490, year = {2003}, author = {Fast, NM and Law, JS and Williams, BA and Keeling, PJ}, title = {Bacterial catalase in the microsporidian Nosema locustae: implications for microsporidian metabolism and genome evolution.}, journal = {Eukaryotic cell}, volume = {2}, number = {5}, pages = {1069-1075}, pmid = {14555490}, issn = {1535-9778}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Bacteria/enzymology/genetics ; Catalase/*genetics ; *Evolution, Molecular ; Gene Library ; Gene Transfer, Horizontal ; *Genome ; Nosema/enzymology/*genetics ; Phylogeny ; Spores, Protozoan/enzymology/genetics ; }, abstract = {Microsporidia constitute a group of extremely specialized intracellular parasites that infect virtually all animals. They are highly derived, reduced fungi that lack several features typical of other eukaryotes, including canonical mitochondria, flagella, and peroxisomes. Consistent with the absence of peroxisomes in microsporidia, the recently completed genome of the microsporidian Encephalitozoon cuniculi lacks a gene for catalase, the major enzymatic marker for the organelle. We show, however, that the genome of the microsporidian Nosema locustae, in contrast to that of E. cuniculi, encodes a group II large-subunit catalase. Surprisingly, phylogenetic analyses indicate that the N. locustae catalase is not specifically related to fungal homologs, as one would expect, but is instead closely related to proteobacterial sequences. This finding indicates that the N. locustae catalase is derived by lateral gene transfer from a bacterium. The catalase gene is adjacent to a large region of the genome that appears to be far less compact than is typical of microsporidian genomes, a characteristic which may make this region more amenable to the insertion of foreign genes. The N. locustae catalase gene is expressed in spores, and the protein is detectable by Western blotting. This type of catalase is a particularly robust enzyme that has been shown to function in dormant cells, indicating that the N. locustae catalase may play some functional role in the spore. There is no evidence that the N. locustae catalase functions in a cryptic peroxisome.}, }
@article {pmid14553920, year = {2003}, author = {Emelyanov, VV}, title = {Phylogenetic affinity of a Giardia lamblia cysteine desulfurase conforms to canonical pattern of mitochondrial ancestry.}, journal = {FEMS microbiology letters}, volume = {226}, number = {2}, pages = {257-266}, doi = {10.1016/S0378-1097(03)00598-6}, pmid = {14553920}, issn = {0378-1097}, mesh = {Amino Acid Sequence ; Animals ; *Carbon-Sulfur Lyases ; Cytochromes b/genetics ; Electron Transport Complex IV/genetics ; Giardia lamblia/classification/*enzymology/*genetics ; Lyases/chemistry/*genetics ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; }, abstract = {Among a few potential archezoan groups, only the Metamonada (diplomonads, retortamonads, and oxymonads) still retain the status of amitochondriate protists that diverged before the acquisition or retention of mitochondria. Indeed, finding that diplomonad genomes harbor a gene encoding a mitochondrial type chaperonin 60, the most compelling evidence for their secondarily amitochondriate nature, may be interpreted as an acquisition of this important general chaperone during some transient alpha-proteobacterial endosymbiosis. Recently published data on the cysteine desulfurase IscS demonstrated an alpha-proteobacterial origin of mitochondrial enzymes including a diplomonad Giardia lamblia homolog. An extended phylogenetic analysis of IscS is reported here that revealed a full canonical pattern of mitochondrial ancestry for the giardial enzyme. The above canonical pattern, a sister group relationship of mitochondria and rickettsiae exclusive of free-living alpha-proteobacteria, was robustly confirmed by a comprehensive analysis of Cob and Cox1 subunits of the respiratory chain encoded by resident mitochondrial genes. Given that Fe-S cluster assembly involving IscS represents an essential mitochondrial function, these data strongly suggest that diplomonads once harbored bona fide mitochondria.}, }
@article {pmid14535340, year = {2003}, author = {Dyková, I and Veverková, M and Fiala, I and Machácková, B and Pecková, H}, title = {Nuclearia pattersoni sp. n. (Filosea), a new species of amphizoic amoeba isolated from gills of roach (Rutilus rutilus), and its rickettsial endosymbiont.}, journal = {Folia parasitologica}, volume = {50}, number = {3}, pages = {161-170}, pmid = {14535340}, issn = {0015-5683}, mesh = {Amoeba/classification/genetics/*isolation &amp; purification/ultrastructure ; Animals ; Base Sequence ; Cyprinidae/*microbiology/*parasitology ; DNA/genetics ; DNA, Bacterial/genetics ; Gills/microbiology/parasitology ; Microscopy, Electron ; Phylogeny ; Rickettsia/classification/genetics/*isolation &amp; purification ; Symbiosis ; }, abstract = {A new species of amphizoic amoeba, Nuclearia pattersoni sp. n., isolated from gills of Rutilus rutilus L. is described. It is characterised by elongate flattened trophozoites of irregular shape. The longer dimension of their bodies is 13.2 (11.0-15.7) microm. Filopodia radiating mostly from the poles are 2 to 2.5 times longer than the body. The diameter of less frequently observed spherical trophozoites is 8.2-10.8 microm; their filopodia radiate to all directions. Cyst-like stages have shorter pseudopodia that arise from one pole only. The surface of locomotive forms from agar plate cultures has a thin amorphous glycocalyx, while most cells are covered by two layers of extracellular matrix. Mitochondria have flattened cristae, dictyosomes are located in the perinuclear zone. A conspicuous ultrastructural feature of the morphologically similar N. simplex, perinuclear striated band, is not present. Light microscopic and ultrastructural data are completed with the sequence of SSU rRNA gene and phylogenetic analysis including sequences of related taxa. The bacterial endosymbiont found in N. pattersoni type strain RR2G2 is assigned to the genus Rickettsia.}, }
@article {pmid14533692, year = {2003}, author = {Li, J and Liao, X}, title = {The taxonomic status of Digramma (Pseudophyllidea: Ligulidae) inferred from DNA sequences.}, journal = {The Journal of parasitology}, volume = {89}, number = {4}, pages = {792-799}, doi = {10.1645/GE-3078}, pmid = {14533692}, issn = {0022-3395}, mesh = {Animals ; Base Sequence ; Cestoda/*classification/genetics ; Cestode Infections/parasitology/*veterinary ; China ; Cluster Analysis ; DNA, Helminth/*chemistry ; DNA, Ribosomal/chemistry ; DNA, Ribosomal Spacer/chemistry ; Electron Transport Complex IV/genetics ; Fish Diseases/*parasitology ; Fishes ; Mitochondria/enzymology ; Molecular Sequence Data ; NADH Dehydrogenase/genetics ; Phylogeny ; RNA, Ribosomal, 28S/genetics ; Sequence Alignment/veterinary ; Sequence Analysis, DNA/veterinary ; }, abstract = {The traditional classification of the ligulid tapeworms into 2 genera, Ligula Bloch, 1782 and Digramma Cholodkovsky, 1914, remains controversial. Molecular data of sequences for the 5' end of the nuclear 28S ribosomal ribonucleic acid (rRNA) gene, the mitochondrial cytochrome c oxidase subunit I (COI) gene, and the nicotinamide adenine dinucleotide dehydrogenase subunit 1 (ND1) gene, as well as the first internal transcribed spacer (ITS1) of the nuclear ribosomal deoxyribonucleic acid (DNA), were used to characterize Digramma and to investigate its relationship with Ligula. Digramma spp. exhibited identical sequences with Ligula intestinalis both in the 28S rRNA and the COI gene and differed from L. intestinalis by 0.7% in the ITS1 region and 7.4% in the ND1 gene, respectively. A high degree of genetic conservation within 28S ribosomal DNA, COI, ITS1, and even ND1 genes, was found in Ligula and Digramma. The low genetic divergence in the 4 genes between Ligula and Digramma indicates that Digramma is probably not an independent genus. Therefore, it is proposed that Ligula and Digramma should be considered as 2 species within the genus Ligula and the tapeworms of Digramma collected from diverse localities in China belong to the same species. The present study also suggests that ITS1 and ND1 sequences can act as useful genetic markers to distinguish Ligula and Digramma.}, }
@article {pmid14532271, year = {2003}, author = {Serero, A and Giglione, C and Sardini, A and Martinez-Sanz, J and Meinnel, T}, title = {An unusual peptide deformylase features in the human mitochondrial N-terminal methionine excision pathway.}, journal = {The Journal of biological chemistry}, volume = {278}, number = {52}, pages = {52953-52963}, doi = {10.1074/jbc.M309770200}, pmid = {14532271}, issn = {0021-9258}, mesh = {Amidohydrolases/*chemistry ; Amino Acid Motifs ; Amino Acid Sequence ; Aminopeptidases/chemistry ; Animals ; Catalysis ; DNA/chemistry ; DNA, Complementary/metabolism ; Escherichia coli/metabolism ; Gene Expression Regulation ; Genetic Complementation Test ; Genetic Variation ; Green Fluorescent Proteins ; Humans ; Ions ; Kinetics ; Luminescent Proteins/metabolism ; Solanum lycopersicum/metabolism ; Methionine/*chemistry ; Methionyl Aminopeptidases ; Mitochondria/*metabolism ; Models, Genetic ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Open Reading Frames ; Phylogeny ; Plant Proteins/metabolism ; Plasmids/metabolism ; Plastids/chemistry ; Protein Structure, Tertiary ; RNA, Messenger/metabolism ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {Dedicated machinery for N-terminal methionine excision (NME) was recently identified in plant organelles and shown to be essential in plastids. We report here the existence of mitochondrial NME in mammals, as shown by the identification of cDNAs encoding specific peptide deformylases (PDFs) and new methionine aminopeptidases (MAP1D). We cloned the two full-length human cDNAs and showed that the N-terminal domains of the encoded enzymes were specifically involved in targeting to mitochondria. In contrast to mitochondrial MAP1D, the human PDF sequence differed from that of known PDFs in several key features. We characterized the human PDF fully in vivo and in vitro. Comparison of the processed human enzyme with the plant mitochondrial PDF1A, to which it is phylogenetically related, showed that the human enzyme had an extra N-terminal domain involved in both mitochondrial targeting and enzyme stability. Mammalian PDFs also display non-random substitutions in the conserved motifs important for activity. Human PDF site-directed mutagenesis variants were studied and compared with the corresponding plant PDF1A variants. We found that amino acid substitutions in human PDF specifically altered its catalytic site, resulting in an enzyme intermediate between bacterial PDF1Bs and plant PDF1As. Because (i) human PDF was found to be active both in vitro and in vivo, (ii) the entire machinery is conserved and expressed in most animals, (iii) the mitochondrial genome expresses substrates for these enzymes, and (iv) mRNA synthesis is regulated, we conclude that animal mitochondria have a functional NME machinery that can be regulated.}, }
@article {pmid14531549, year = {2003}, author = {Müller, W and Mennel, HD and Bewermeyer, K and Bewermeyer, H}, title = {Is there a final common pathway in mitochondrial encephalomyopathies? Considerations based on an autopsy case of Kearns-Sayre syndrome.}, journal = {Clinical neuropathology}, volume = {22}, number = {5}, pages = {240-245}, pmid = {14531549}, issn = {0722-5091}, mesh = {Adult ; Atrophy ; Brain/pathology/physiopathology ; Cerebellum/pathology/physiopathology ; Cerebral Infarction/pathology/physiopathology ; Disease Progression ; Dominance, Cerebral/physiology ; Energy Metabolism/*physiology ; Female ; Gliosis/pathology/physiopathology ; Humans ; Kearns-Sayre Syndrome/*pathology/physiopathology ; Mitochondria/pathology/physiology ; Mitochondrial Encephalomyopathies/*pathology/physiopathology ; Neurologic Examination ; Tomography, X-Ray Computed ; }, abstract = {A case of Kearns-Sayre syndrome (KSS) diagnosed 18 years prior to death due to stroke and heart failure with postnatal onset was followed over 15 years and confirmed by postmortem examination. Within the brain, an old cystic infarction of the left hemisphere was found. Other features included white matter gliosis and cerebellar atrophy. Equal or similar features were observed in other conditions thought to be due to failure of mitochondrial metabolism, therefore, a common evolution of neuropathological changes must be discussed.}, }
@article {pmid14520869, year = {2003}, author = {Ladygin, VG and Semenova, GA and Smolov, AP}, title = {[The influence of ammonium and nitrate of nutrient medium on ultrastructural organization and photosynthesis of callus cells in Glycine max L].}, journal = {Tsitologiia}, volume = {45}, number = {4}, pages = {380-386}, pmid = {14520869}, issn = {0041-3771}, mesh = {Cells, Cultured ; Chlorophyll/analysis/biosynthesis ; Chloroplasts/*drug effects/metabolism/ultrastructure ; Culture Media ; Microscopy, Electron ; Nitrates/*pharmacology ; Oxygen/metabolism ; Photosynthesis/*drug effects ; Quaternary Ammonium Compounds/*pharmacology ; Ribosomes/metabolism ; Glycine max/*drug effects/metabolism/ultrastructure ; Thylakoids/metabolism ; Time Factors ; }, abstract = {We studied the influence of exogenic ammonium on the functional activity and ultrastructural organization of cells of the mixotrophic soybean callus (Glycine max L.). Ammonium available in the nutrient medium increased the chlorophyll content, accelerating the rate of photosynthetic O2 evolution per unit of biomass. The presence of ammonium in the medium promoted formation of the protein-synthesizing system, which manifested itself as increased numbers of ribosomes, and thylakoids of chloroplasts, and higher electron density of the stroma in mitochondria and cytoplasm of mixotrophic cells. It has been concluded that the use of ammonium may lead to activation of protein synthesis, thus rising photosynthetic activity and favouring formation and development of membrane structures in chloroplasts.}, }
@article {pmid14518011, year = {2003}, author = {Scheltinga, DM and Wilkinson, M and Jamieson, BG and Oommen, OV}, title = {Ultrastructure of the mature spermatozoa of caecilians (Amphibia: Gymnophiona).}, journal = {Journal of morphology}, volume = {258}, number = {2}, pages = {179-192}, doi = {10.1002/jmor.10139}, pmid = {14518011}, issn = {0362-2525}, mesh = {Acrosome/ultrastructure ; Amphibians/*anatomy &amp; histology ; Anatomy, Comparative ; Animals ; Biological Evolution ; Cell Nucleus/ultrastructure ; India ; Male ; Microscopy ; Microscopy, Electron ; Sperm Head/ultrastructure ; Sperm Midpiece/ultrastructure ; Sperm Tail/ultrastructure ; Spermatozoa/cytology/*ultrastructure ; }, abstract = {The spermatozoa of Gymnophiona show the following autapomorphies: 1) penetration of the distal centriole by the axial fiber; 2) presence of an acrosomal baseplate; 3) presence of an acrosome seat (flattened apical end of nucleus); and 4) absence of juxta-axonemal fibers. The wide separation of the plasma membrane bounding the undulating membrane is here also considered to be apomorphic. Three plesiomorphic spermatozoal characters are recognized that are not seen in other Amphibia but occur in basal amniotes: 1) presence of mitochondria with a delicate array of concentric cristae (concentric cristae of salamander spermatozoa differ in lacking the delicate array); 2) presence of peripheral dense fibers associated with the triplets of the distal centriole; and 3) presence of a simple annulus (a highly modified, elongate annulus is present in salamander sperm). The presence of an endonuclear canal containing a perforatorium is a plesiomorphic feature of caecilian spermatozoa that is shared with urodeles, some basal anurans, sarcopterygian fish, and some amniotes. Spermatozoal synapomorphies are identified for 1) the Uraeotyphlidae and Ichthyophiidae, and 2) the Caeciliidae and Typhlonectidae, suggesting that the members of each pair of families are more closely related to each other than to other caecilians. Although caecilian spermatozoa exhibit the clear amphibian synapomorphy of the unilateral location of the undulating membrane and its axial fiber, they have no apomorphic characters that suggest a closer relationship to either the Urodela or Anura.}, }
@article {pmid14507740, year = {2003}, author = {Duckett, JG and Ligrone, R}, title = {The structure and development of haustorial placentas in leptosporangiate ferns provide a clear-cut distinction between euphyllophytes and lycophytes.}, journal = {Annals of botany}, volume = {92}, number = {4}, pages = {513-521}, pmid = {14507740}, issn = {0305-7364}, mesh = {Cell Differentiation/physiology ; Culture Techniques ; Ferns/classification/*growth &amp; development/ultrastructure ; Fertility/physiology ; Microscopy, Electron ; Mitochondria/physiology/ultrastructure ; Plastids/physiology/ultrastructure ; Pteridium/growth &amp; development/ultrastructure ; Spores/*growth &amp; development/ultrastructure ; }, abstract = {This light and electron microscope study revealed that leptosporangiate ferns have highly distinctive gametophyte-sporophyte junctions characterized by sporophytic haustoria, the absence of intraplacental spaces and degenerating cells, and the early appearance of wall ingrowths in both generations. Other notable cytological features are highly pleomorphic plastids and mitochondrial aggregates in the gametophytic placental cells. Close similarities with the gametophyte-sporophyte junctions in Tmesipteris and major differences from those of homosporous lycophytes are in line with the placement of psilophytes and ferns in the same clade and distance both from lycophytes. A smooth interface between the two generations in Azolla suggests a clear-cut discontinuity between homosporous and heterosporous ferns, although this is the only heterosporous fern investigated to date. Similarities between the gametophyte-sporophyte junctions of leptosporangiate ferns and hornworts, when balanced against differences between them, are considered more likely the result of parallel evolution rather than homology.}, }
@article {pmid13678910, year = {2003}, author = {Miyagishima, SY and Nishida, K and Kuroiwa, T}, title = {An evolutionary puzzle: chloroplast and mitochondrial division rings.}, journal = {Trends in plant science}, volume = {8}, number = {9}, pages = {432-438}, doi = {10.1016/S1360-1385(03)00193-6}, pmid = {13678910}, issn = {1360-1385}, mesh = {Animals ; *Biological Evolution ; Cell Division ; Chloroplasts/genetics/*ultrastructure ; GTP Phosphohydrolases/metabolism ; Humans ; Mitochondria/genetics/*ultrastructure ; Phylogeny ; Plants/classification/*genetics/ultrastructure ; }, abstract = {Consistent with their bacterial origin, chloroplasts and primitive mitochondria retain a FtsZ ring for division. However, chloroplasts and mitochondria have lost most of the proteins required for bacterial division other than FtsZ and certain homologues of the Min proteins, but they do contain plastid and mitochondrion dividing rings, which were recently shown to be distinct from the FtsZ ring. Moreover, recent studies have revealed that rings of the eukaryote-specific dynamin-related family of GTPases regulate the division of chloroplasts and mitochondria, and these proteins emerged early in eukaryotic evolution. These findings suggest that the division of chloroplasts and primitive mitochondria involve very similar systems, consisting of an amalgamation of rings from bacteria and eukaryotes.}, }
@article {pmid13678684, year = {2003}, author = {Rest, JS and Ast, JC and Austin, CC and Waddell, PJ and Tibbetts, EA and Hay, JM and Mindell, DP}, title = {Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome.}, journal = {Molecular phylogenetics and evolution}, volume = {29}, number = {2}, pages = {289-297}, doi = {10.1016/s1055-7903(03)00108-8}, pmid = {13678684}, issn = {1055-7903}, support = {T32-HG00040/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Cell Lineage ; DNA/chemistry/genetics ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics/metabolism ; Genome ; Mitochondria/*genetics ; Phylogeny ; RNA, Transfer/metabolism ; Reptiles ; Species Specificity ; Turtles/genetics ; Vertebrates ; }, abstract = {We provide phylogenetic analyses for primary Reptilia lineages including, for the first time, Sphenodon punctatus (tuatara) using data from whole mitochondrial genomes. Our analyses firmly support a sister relationship between Sphenodon and Squamata, which includes lizards and snakes. Using Sphenodon as an outgroup for select squamates, we found evidence indicating a sister relationship, among our study taxa, between Serpentes (represented by Dinodon) and Varanidae. Our analyses support monophyly of Archosauria, and a sister relationship between turtles and archosaurs. This latter relationship is congruent with a growing set of morphological and molecular analyses placing turtles within crown Diapsida and recognizing them as secondarily anapsid (lacking a skull fenestration). Inclusion of Sphenodon, as the only surviving member of Sphenodontia (with fossils from the mid-Triassic), helps to fill a sampling gap within previous analyses of reptilian phylogeny. We also report a unique configuration for the mitochondrial genome of Sphenodon, including two tRNA(Lys) copies and an absence of ND5, tRNA(His), and tRNA(Thr) genes.}, }
@article {pmid13677454, year = {2003}, author = {O'Kelly, CJ and Silberman, JD and Amaral Zettler, LA and Nerad, TA and Sogin, ML}, title = {Monopylocystis visvesvarai n. gen., n. sp. and Sawyeria marylandensis n. gen., n. sp.: two new amitochondrial heterolobosean amoebae from anoxic environments.}, journal = {Protist}, volume = {154}, number = {2}, pages = {281-290}, doi = {10.1078/143446103322166563}, pmid = {13677454}, issn = {1434-4610}, mesh = {Amoebida/*classification/genetics/physiology/ultrastructure ; Anaerobiosis ; Animals ; DNA, Protozoan/analysis ; DNA, Ribosomal/analysis ; Fresh Water/*parasitology ; Microscopy, Electron ; Mitochondria/*ultrastructure ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/genetics ; Sequence Analysis, DNA ; }, abstract = {Two new species of heterolobosean amoebae from anoxic environments, Monopylocystis visvesvarai and Sawyeria marylandensis, are described on the basis of light microscopy, electron microscopy, and their phylogenetic affiliation based on analyses of nuclear small-subunit ribosomal RNA gene sequences. Both species lack mitochondria but have organelles provisionally interpreted as hydrogenosomes, and neither can tolerate aerobic conditions. As their conditions of culture do not exclude all oxygen, they may be microaerophiles rather than strict anaerobes. Both species have unusual nucleolar morphologies. Monopylocystis visvesvarai, from a marine sediment, has nucleolar material distributed around the nuclear periphery. It is the first non-aerobic heterolobosean protist for which a cyst is known; the cyst is unmineralized and unornamented except for a single, raised, plugged pore. Sawyeria marylandensis, from an iron-rich freshwater stream, has nucleolar material distributed in one or two parietal masses, which persist during mitosis. In phylogenetic analyses of small-subunit rRNA gene sequences, Monopylocystis visvesvarai, Sawyeria marylandensis and Psalteriomonas lanterna converge to form a single clade of non-aerobic (anaerobic/microaerophilic) heteroloboseans.}, }
@article {pmid12974613, year = {2003}, author = {Searcy, DG}, title = {Metabolic integration during the evolutionary origin of mitochondria.}, journal = {Cell research}, volume = {13}, number = {4}, pages = {229-238}, doi = {10.1038/sj.cr.7290168}, pmid = {12974613}, issn = {1001-0602}, mesh = {Bacteria/metabolism ; *Biological Evolution ; Eukaryotic Cells/cytology/metabolism/microbiology ; Humans ; Methane/metabolism ; Mitochondria/classification/*metabolism ; Phylogeny ; Reactive Oxygen Species/metabolism ; Sulfur/metabolism ; Symbiosis ; }, abstract = {Although mitochondria provide eukaryotic cells with certain metabolic advantages, in other ways they may be disadvantageous. For example, mitochondria produce reactive oxygen species that damage both nucleocytoplasm and mitochondria, resulting in mutations, diseases, and aging. The relationship of mitochondria to the cytoplasm is best understood in the context of evolutionary history. Although it is clear that mitochondria evolved from symbiotic bacteria, the exact nature of the initial symbiosis is a matter of continuing debate. The exchange of nutrients between host and symbiont may have differed from that between the cytoplasm and mitochondria in modern cells. Speculations about the initial relationships include the following. (1) The pre-mitochondrion may have been an invasive, parasitic bacterium. The host did not benefit. (2) The relationship was a nutritional syntrophy based upon transfer of organic acids from host to symbiont. (3) The relationship was a syntrophy based upon H2 transfer from symbiont to host, where the host was a methanogen. (4) There was a syntrophy based upon reciprocal exchange of sulfur compounds. The last conjecture receives support from our detection in eukaryotic cells of substantial H2S-oxidizing activity in mitochondria, and sulfur-reducing activity in the cytoplasm.}, }
@article {pmid12972666, year = {2003}, author = {Michalecka, AM and Svensson, AS and Johansson, FI and Agius, SC and Johanson, U and Brennicke, A and Binder, S and Rasmusson, AG}, title = {Arabidopsis genes encoding mitochondrial type II NAD(P)H dehydrogenases have different evolutionary origin and show distinct responses to light.}, journal = {Plant physiology}, volume = {133}, number = {2}, pages = {642-652}, pmid = {12972666}, issn = {0032-0889}, mesh = {Amino Acid Sequence ; Animals ; Arabidopsis/classification/*enzymology/*genetics ; Arabidopsis Proteins/chemistry/genetics ; Base Sequence ; Conserved Sequence ; DNA Primers ; *Evolution, Molecular ; Exons ; FMN Reductase/chemistry/*genetics ; Gene Expression Regulation, Enzymologic/genetics ; Gene Expression Regulation, Plant/genetics ; *Genes, Plant ; Introns ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {In addition to proton-pumping complex I, plant mitochondria contain several type II NAD(P)H dehydrogenases in the electron transport chain. The extra enzymes allow the nonenergy-conserving electron transfer from cytoplasmic and matrix NAD(P)H to ubiquinone. We have investigated the type II NAD(P)H dehydrogenase gene families in Arabidopsis. This model plant contains two and four genes closely related to potato (Solanum tuberosum) genes nda1 and ndb1, respectively. A novel homolog, termed ndc1, with a lower but significant similarity to potato nda1 and ndb1, is also present. All genes are expressed in several organs of the plant. Among the nda genes, expression of nda1, but not nda2, is dependent on light and circadian regulation, suggesting separate roles in photosynthesis-associated and other respiratory NADH oxidation. Genes from all three gene families encode proteins exclusively targeted to mitochondria, as revealed by expression of green fluorescent fusion proteins and by western blotting of fractionated cells. Phylogenetic analysis indicates that ndc1 affiliates with cyanobacterial type II NADH dehydrogenase genes, suggesting that this gene entered the eukaryotic cell via the chloroplast progenitor. The ndc1 should then have been transferred to the nucleus and acquired a signal for mitochondrial targeting of the protein product. Although they are of different origin, the nda, ndb, and ndc genes carry an identical intron position.}, }
@article {pmid12972568, year = {2003}, author = {Sylvestre, J and Margeot, A and Jacq, C and Dujardin, G and Corral-Debrinski, M}, title = {The role of the 3' untranslated region in mRNA sorting to the vicinity of mitochondria is conserved from yeast to human cells.}, journal = {Molecular biology of the cell}, volume = {14}, number = {9}, pages = {3848-3856}, pmid = {12972568}, issn = {1059-1524}, mesh = {Electron Transport Complex IV ; Evolution, Molecular ; HeLa Cells ; Humans ; Microscopy, Fluorescence ; Mitochondria/genetics/*metabolism ; Mitochondrial Proteins ; Nuclear Proteins/genetics/*metabolism ; Polyribosomes/metabolism ; RNA Transport/physiology ; RNA, Messenger/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Saccharomyces cerevisiae/genetics/metabolism ; Untranslated Regions ; }, abstract = {We recently demonstrated, using yeast DNA microarrays, that mRNAs of polysomes that coisolate with mitochondria code for a subset of mitochondrial proteins. The majority of these mRNAs encode proteins of prokaryotic origin. Herein, we show that a similar association occurs between polysomes and mitochondria in human cells. To determine whether mRNA transport machinery is conserved from yeast to human cells, we examined the subcellular localization of human OXA1 mRNA in yeast. Oxa1p is a key component in the biogenesis of mitochondrial inner membrane and is conserved from bacteria to eukaryotic organelles. The expression of human OXA1 cDNA partially restores the respiratory capacity of yeast oxa1- cells. In this study, we demonstrate that 1) OXA1 mRNAs are remarkably enriched in mitochondrion-bound polysomes purified from yeast and human cells; 2) the presence of the human OXA1 3' untranslated region (UTR) is required for the function of the human Oxa1p inside yeast mitochondria; and 3) the accurate sorting of the human OXA1 mRNA to the vicinity of yeast mitochondria is due to the recognition by yeast proteins of the human 3' UTR. Therefore, it seems that the recognition mechanism of OXA1 3' UTR is conserved throughout evolution and is necessary for Oxa1p function.}, }
@article {pmid12972297, year = {2003}, author = {Godbole, A and Varghese, J and Sarin, A and Mathew, MK}, title = {VDAC is a conserved element of death pathways in plant and animal systems.}, journal = {Biochimica et biophysica acta}, volume = {1642}, number = {1-2}, pages = {87-96}, doi = {10.1016/s0167-4889(03)00102-2}, pmid = {12972297}, issn = {0006-3002}, mesh = {Animals ; Apoptosis/*physiology ; Cotyledon/drug effects/metabolism ; Cucumis sativus/metabolism ; Energy Metabolism/physiology ; Enzyme Inhibitors/pharmacology ; Eukaryotic Cells/*metabolism ; Evolution, Molecular ; Gene Expression Regulation, Plant/drug effects/physiology ; HeLa Cells ; Humans ; Intracellular Membranes/metabolism ; Jurkat Cells ; Mitochondria/*metabolism ; Oryza/genetics ; Plant Proteins/genetics/metabolism ; Plants/genetics/*metabolism ; Porins/genetics/*metabolism ; Proto-Oncogene Proteins c-bcl-2/antagonists &amp; inhibitors/metabolism ; Voltage-Dependent Anion Channels ; }, abstract = {Programmed cell death (PCD) is very much a part of plant life, although the underlying mechanisms are not so well understood as in animals. In animal cells, the voltage-dependent anion channel (VDAC), a major mitochondrial outer membrane transporter, plays an important role in apoptosis by participating in the release of intermembrane space proteins. To characterize plant PCD pathways by investigating the function of putative components in a mammalian apoptotic context, we have overexpressed a rice VDAC (osVDAC4) in the Jurkat T-cell line. Overexpression of osVDAC4 induces apoptosis, which can be blocked by Bcl-2 and the VDAC inhibitor DIDS. Modifying endogenous VDAC function by DIDS and hexokinase II (HxKII) in Jurkat cells inhibits mitochondria-mediated apoptotic pathways. Finally, we show that DIDS also abrogates heat-induced PCD in cucumber cotyledons. Our data suggest that VDAC is a conserved mitochondrial element of the death machinery in both plant and animal cells.}, }
@article {pmid12971274, year = {2003}, author = {Sakamoto, J and Sone, N}, title = {[Diversity of the respiratory chain in gram-positive bacteria--its position in the whole life].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {48}, number = {12}, pages = {1712-1721}, pmid = {12971274}, issn = {0039-9450}, mesh = {*Electron Transport/genetics ; Electron Transport Complex IV/genetics/*physiology ; *Evolution, Molecular ; *Genome, Bacterial ; Gram-Positive Bacteria/*genetics/*physiology ; Mitochondria/enzymology ; NADH Dehydrogenase/genetics/*physiology ; }, }
@article {pmid12970547, year = {2003}, author = {Delsuc, F and Phillips, MJ and Penny, D}, title = {Comment on "Hexapod origins: monophyletic or paraphyletic?".}, journal = {Science (New York, N.Y.)}, volume = {301}, number = {5639}, pages = {1482; author reply 1482}, doi = {10.1126/science.1086558}, pmid = {12970547}, issn = {1095-9203}, mesh = {Amino Acid Sequence ; Animals ; Arthropods/classification/*genetics ; Base Composition ; Base Sequence ; Bayes Theorem ; Insecta/classification/genetics ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; Proteins/chemistry/genetics ; }, }
@article {pmid12963738, year = {2003}, author = {Kaser, M and Kambacheld, M and Kisters-Woike, B and Langer, T}, title = {Oma1, a novel membrane-bound metallopeptidase in mitochondria with activities overlapping with the m-AAA protease.}, journal = {The Journal of biological chemistry}, volume = {278}, number = {47}, pages = {46414-46423}, doi = {10.1074/jbc.M305584200}, pmid = {12963738}, issn = {0021-9258}, mesh = {Electron Transport Complex IV ; Fungal Proteins/genetics/metabolism ; Metalloendopeptidases/*metabolism ; Metalloproteases/genetics/*metabolism ; Mitochondrial Proteins/genetics/metabolism ; Mutation ; Nuclear Proteins/genetics/*metabolism ; Phenotype ; Phylogeny ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Sequence Alignment ; Temperature ; }, abstract = {The integrity of the inner membrane of mitochondria is maintained by a membrane-embedded quality control system that ensures the removal of misfolded membrane proteins. Two ATP-dependent AAA proteases with catalytic sites at opposite membrane surfaces are key components of this proteolytic system. Here we describe the identification of a novel conserved metallopeptidase that exerts activities overlapping with the m-AAA protease and was therefore termed Oma1. Both peptidases are integral parts of the inner membrane and mediate the proteolytic breakdown of a misfolded derivative of the polytopic inner membrane protein Oxa1. The m-AAA protease cleaves off the matrix-exposed C-terminal domain of Oxa1 and processively degrades its transmembrane domain. In the absence of the m-AAA protease, proteolysis of Oxa1 is mediated in an ATP-independent manner by Oma1 and a yet unknown peptidase resulting in the accumulation of N- and C-terminal proteolytic fragments. Oma1 exposes its proteolytic center to the matrix side; however, mapping of Oma1 cleavage sites reveals clipping of Oxa1 in loop regions at both membrane surfaces. These results identify Oma1 as a novel component of the quality control system in the inner membrane of mitochondria. Proteins homologous to Oma1 are present in higher eukaryotic cells, eubacteria and archaebacteria, suggesting that Oma1 is the founding member of a conserved family of membrane-embedded metallopeptidases.}, }
@article {pmid12949150, year = {2003}, author = {Serb, JM and Lydeard, C}, title = {Complete mtDNA sequence of the North American freshwater mussel, Lampsilis ornata (Unionidae): an examination of the evolution and phylogenetic utility of mitochondrial genome organization in Bivalvia (Mollusca).}, journal = {Molecular biology and evolution}, volume = {20}, number = {11}, pages = {1854-1866}, doi = {10.1093/molbev/msg218}, pmid = {12949150}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; Bivalvia/*genetics ; Chromosome Mapping ; Codon ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genome ; Mitochondria/*genetics/metabolism ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Plasmids/metabolism ; RNA, Transfer/genetics ; Recombination, Genetic ; }, abstract = {Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. Two factors inhibiting our understanding the evolution of gene rearrangement in bivalves are inadequate taxonomic sampling and failure to examine gene order in a phylogenetic framework. Here, we report the first complete nucleotide sequence (16,060 bp) of the mitochondrial (mt) genome of a North American freshwater bivalve, Lampsilis ornata (Mollusca: Paleoheterodonta: Unionidae). Gene order and mt genome content is examined in a comparative phylogenetic framework for Lampsilis and five other bivalves, representing five families. Mitochondrial genome content is shown to vary by gene duplication and loss among taxa and between male and female mitotypes within a species. Although mt gene arrangement is highly variable among bivalves, when optimized on an independently derived phylogenetic hypothesis, it allows for the reconstruction of ancestral gene order states and indicates the potential phylogenetic utility of the data. However, the interpretation of reconstructed ancestral gene order states must take in to account both the accuracy of the phylogenetic estimation and the probability of character state change across the topology, such as the presence/absence of atp8 in bivalve lineages. We discuss what role, if any, doubly uniparental inheritance (DUI) and recombination between sexual mitotypes may play in influencing gene rearrangement of the mt genome in some bivalve lineages.}, }
@article {pmid12949122, year = {2003}, author = {Aris-Brosou, S and Yang, Z}, title = {Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa.}, journal = {Molecular biology and evolution}, volume = {20}, number = {12}, pages = {1947-1954}, doi = {10.1093/molbev/msg226}, pmid = {12949122}, issn = {0737-4038}, mesh = {Algorithms ; Animals ; *Bayes Theorem ; Cell Nucleus/genetics ; Computer Simulation ; *Evolution, Molecular ; Fossils ; Invertebrates/*genetics ; Mitochondria/genetics ; Models, Genetic ; Phylogeny ; Time Factors ; }, abstract = {Multicellular animals, or Metazoa, appear in the fossil records between 575 and 509 million years ago (MYA). At odds with paleontological evidence, molecular estimates of basal metazoan divergences have been consistently older than 700 MYA. However, those date estimates were based on the molecular clock hypothesis, which is almost always violated. To relax this hypothesis, we have implemented a Bayesian approach to describe the change of evolutionary rate over time. Analysis of 22 genes from the nuclear and the mitochondrial genomes under the molecular clock assumption produced old date estimates, similar to those from previous studies. However, by allowing rates to vary in time and by taking small species-sampling fractions into account, we obtained much younger estimates, broadly consistent with the fossil records. In particular, the date of protostome-deuterostome divergence was on average 582 +/- 112 MYA. These results were found to be robust to specification of the model of rate change. The clock assumption thus had a dramatic effect on date estimation. However, our results appeared sensitive to the prior model of cladogenesis, although the oldest estimates (791 +/- 246 MYA) were obtained under a suboptimal model. Bayes posterior estimates of evolutionary rates indicated at least one major burst of molecular evolution at the end of the Precambrian when protostomes and deuterostomes diverged. We stress the importance of assumptions about rates on date estimation and suggest that the large discrepancies between the molecular and fossil dates of metazoan divergences might partly be due to biases in molecular date estimation.}, }
@article {pmid12947037, year = {2003}, author = {Nesbø, CL and Doolittle, WF}, title = {Active self-splicing group I introns in 23S rRNA genes of hyperthermophilic bacteria, derived from introns in eukaryotic organelles.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {19}, pages = {10806-10811}, pmid = {12947037}, issn = {0027-8424}, mesh = {Bacteria/*genetics ; Base Sequence ; DNA Primers ; Evolution, Molecular ; *Introns ; Likelihood Functions ; Molecular Sequence Data ; Nucleic Acid Conformation ; Organelles/*genetics ; *RNA Splicing ; RNA, Ribosomal, 23S/chemistry/*genetics ; Reverse Transcriptase Polymerase Chain Reaction ; }, abstract = {Group I introns are common in the 23 rRNA genes of mitochondria and chloroplasts. Often, they encode "homing endonucleases," which target highly conserved gene sequences and drive interorganellar intron mobility, even across species and genus lines. Most bacterial 23S rRNA genes show these same endonuclease-sensitive target sequences. However, only two bacterial 23S rRNA genes are known to contain group I introns: that of Simkania negevensis [Everett, K. D., Kahane, S., Bush, R. M. &amp; Friedman, M. G. (1999) J. Bacteriol. 181, 4734-4740], where the intron is not spliced and probably limits growth, and that of Coxiella burnetii [Seshadri, R., et al. (2003) Proc. Natl. Acad. Sci. USA 100, 5455-5460], where no direct evidence of splicing exists. Both bacteria are intracellular parasites and might have acquired introns from eukaryotic hosts. Here we provide direct evidence for splicing, and evolutionary evidence for mobility, of group I introns in the 23S rRNA genes of several free-living hyperthermophilic bacteria of the genus Thermotoga. These bacteria do not live closely with eukaryotes, but phylogenetic analyses suggest that their introns were also acquired from eukaryotic (probably algal) organelles. In vivo, their introns must be spliced at temperatures approaching 90 degrees C, making them the most thermostable natural ribozymes so far described. We demonstrate that at least some of these introns can also self-splice in vitro.}, }
@article {pmid12945496, year = {2002}, author = {Arvelo, F}, title = {[Mitochondria and apoptosis].}, journal = {Acta cientifica venezolana}, volume = {53}, number = {4}, pages = {297-306}, pmid = {12945496}, issn = {0001-5504}, mesh = {Apoptosis/*physiology ; Bacteria, Aerobic/physiology ; Biological Evolution ; Heat-Shock Proteins/physiology ; Mitochondria/*physiology ; }, abstract = {It is now accepted that mitochondria are endosymbionts, originated in aerobic bacteria which were integrated by the ancestor of eukaryotic cells. A part of the apoptotic machinery could exist in unicellular eukaryotic and some controlling apoptosis components might be present in prokaryotes. It is therefore possible that the mechanism originally involved in the maintenance of the symbiosis between the bacterial ancestor of the mitochondria and the host cell precursor of eukaryotes, provided the basis for the actual mechanism controlling cell survival. Metazoans would have improved this possibility by connecting to the mitochondria as principal effector of cellular death to the pathways of signal transduction. A variety of events appoint to the mitochondria as principal effector of the apoptosis. This including the release caspase activators (cytochrome c), changes in electron transport, loss of mitochondrial transmembrane potential, altered cellular oxidation-reduction, and participation of pro and antiapoptotic Bcl-2 proteins. The different signals that converge on mitochondria for activation or inhibition of these events, delineate several pathways in the physiology of the cellular death.}, }
@article {pmid12942637, year = {2003}, author = {Kolesnikov, AA and Merzliak, EM and Bessolitsyna, EA and Fediakov, AV and Shoenian, G}, title = {[Reduction of the edited domain of the mitochondrial A6 gene for ATPase subunit 6 in Trypanosomatidae].}, journal = {Molekuliarnaia biologiia}, volume = {37}, number = {4}, pages = {637-642}, pmid = {12942637}, issn = {0026-8984}, mesh = {Adenosine Triphosphatases/*genetics/metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Mitochondria/enzymology/*genetics ; Mitochondrial Proton-Translocating ATPases ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; *RNA Editing ; RNA, Ribosomal, 18S ; Sequence Homology, Amino Acid ; Trypanosomatina/enzymology/*genetics ; }, abstract = {The sequence of mitochondrial A6 (MURF4) was compared for several trypanosomatids in order to assess the reduction of the edited domain (ED). The association between the ED reduction and the phylogenetic position of a species proved to be less tight than believed earlier. Compared with digenetic species, monogenetic ones more often displayed ED reduction and had smaller ED.}, }
@article {pmid12941016, year = {2003}, author = {Otranto, D and Traversa, D and Guida, B and Tarsitano, E and Fiorente, P and Stevens, JR}, title = {Molecular characterization of the mitochondrial cytochrome oxidase I gene of Oestridae species causing obligate myiasis.}, journal = {Medical and veterinary entomology}, volume = {17}, number = {3}, pages = {307-315}, doi = {10.1046/j.1365-2915.2003.00442.x}, pmid = {12941016}, issn = {0269-283X}, mesh = {Animals ; Base Sequence ; Codon/genetics ; DNA/genetics/isolation &amp; purification ; DNA Primers ; Diptera/classification/*enzymology/genetics ; Electron Transport Complex IV/*genetics ; Genes ; Larva ; Mitochondria/enzymology/genetics ; Myiasis/*veterinary ; Phylogeny ; Polymerase Chain Reaction/methods ; Polymorphism, Genetic ; }, abstract = {A 688-bp region of the mitochondrial cytochrome oxidase I gene was sequenced from larvae of 18 species of Oestridae causing obligate myiasis. Larvae belonged to the four Oestridae subfamilies (Cuterebrinae, Gasterophilinae, Hypodermatinae and Oestrinae), which are commonly found throughout the world. Analysis of both nucleotide and amino acid data was performed. Nucleotide sequences included 385 conserved sites and 303 variable sites; mean nucleotide variation between all species was 18.1% and variation within each subfamily ranged from 5.3% to 13.34%. Intraspecific pairwise divergences ranged from 0.14% to 1.59%, and interspecific variation ranged from 0.7% to 27%. Of the 229 amino acids, 76 were variable (60 of which were phylogenetically informative), with some highly conserved residues identified within each subfamily. Phylogenetic analysis showed a strong divergence among the four subfamilies, concordant with classical taxonomy based on morphological and biological features. This study provides the first molecular data set for myiasis-causing Oestridae species, providing an essential database for the molecular identification of these parasites and the assessment of phylogenetic relationships within family Oestridae.}, }
@article {pmid12924944, year = {2003}, author = {Nguyen, KT and Hu, X and Colton, C and Chakrabarti, R and Zhu, MX and Pei, D}, title = {Characterization of a human peptide deformylase: implications for antibacterial drug design.}, journal = {Biochemistry}, volume = {42}, number = {33}, pages = {9952-9958}, doi = {10.1021/bi0346446}, pmid = {12924944}, issn = {0006-2960}, support = {AI40575/AI/NIAID NIH HHS/United States ; }, mesh = {*Amidohydrolases ; Amino Acid Sequence ; Aminopeptidases/*chemistry/genetics/metabolism ; Anti-Bacterial Agents/pharmacology ; Cell Division/drug effects ; Cells, Cultured ; Cloning, Molecular ; DNA, Complementary/metabolism ; Dose-Response Relationship, Drug ; *Drug Design ; Enzyme Inhibitors/pharmacology ; Escherichia coli/*enzymology ; Green Fluorescent Proteins ; Humans ; Kidney/enzymology ; Kinetics ; Leucine/chemistry ; Luminescent Proteins/metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Peptides/chemistry ; Protein Binding ; Protein Transport ; Recombinant Fusion Proteins/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Ribosomal protein synthesis in eubacteria and eukaryotic organelles initiates with an N-formylmethionyl-tRNA(i), resulting in N-terminal formylation of all nascent polypeptides. Peptide deformylase (PDF) catalyzes the subsequent removal of the N-terminal formyl group from the majority of bacterial proteins. Deformylation was for a long time thought to be a feature unique to the prokaryotes, making PDF an attractive target for designing novel antibiotics. However, recent genomic sequencing has revealed PDF-like sequences in many eukaryotes, including man. In this work, the cDNA encoding Homo sapiens PDF (HsPDF) has been cloned and a truncated form that lacks the N-terminal 58-amino-acid targeting sequence was overexpressed in Escherichia coli. The recombinant, Co(2+)-substituted protein is catalytically active in deformylating N-formylated peptides, shares many of the properties of bacterial PDF, and is strongly inhibited by specific PDF inhibitors. Expression of HsPDF fused to the enhanced green fluorescence protein in human embryonic kidney cells revealed its location in the mitochondrion. However, HsPDF is much less active than its bacterial counterpart, providing a possible explanation for the apparent lack of deformylation in the mammalian mitochondria. The lower catalytic activity is at least partially due to mutation of a highly conserved residue (Leu-91 in E. coli PDF) in mammalian PDF. PDF inhibitors had no detectable effect on two different human cell lines. These results suggest that HsPDF is likely an evolutional remnant without any functional role in protein formylation/deformylation and validates PDF as an excellent target for antibacterial drug design.}, }
@article {pmid12924155, year = {2003}, author = {Chen, XF and Wang, X and Yuan, XD and Tang, MQ and Li, YX and Guo, YM and Li, QW}, title = {[Sequence variation of mitochondrial cytochrome b gene and phylogenetic relationships among twelve species of Charadriiformes].}, journal = {Yi chuan xue bao = Acta genetica Sinica}, volume = {30}, number = {5}, pages = {419-424}, pmid = {12924155}, issn = {0379-4172}, mesh = {Animals ; Base Sequence ; Birds/*classification/*genetics ; Cytochromes b/*genetics ; DNA, Mitochondrial/*chemistry ; Genetic Variation ; Mitochondria/*enzymology ; Phylogeny ; }, abstract = {Studies of the phylogenetic relationships of the Charadriiformes have been largely based on conservative morphological characters. During the past 10 years, many studies on the evolutionary biology of birds adopted phylogenetic information obtained from mitochondrial DNA, but few work on the Charadriiformes has been reported to date. Therefore, phylogenetic relationships and classification of the Charadriiformes remains controversial. In this study, we try to shed light on these relationships via DNA sequence analysis of the mitochondrial Cyt b gene in 12 species of Charadriiformes. It was a preliminary study of the origin and evolution of the species by using nucleotide sequence data. Using the well-known PCR techniques, the complete mitochondrial Cyt b gene sequences were amplified and sequenced respectively from Charadrius mongolus, Charadrius alexandrinus, Numenius madagascariensis, Numenius arquat, Numenius phaeopus, Tringa totanus, Tringa glareola, Xenus cineres, Arenaria interpres, Calidris tenuirostris, Recurvirostra avosetts and Haematopus ostralensis. The 1143 bp long DNA sequences of the gene from these species were obtained, in which 381 variable sites were identified without insertions or deletions. The nucleic acid sequence variation of the mitochondrial Cyt b gene was 5.16%-16.01% among these species. Phylogenetic trees constructed using the NJ method, MP method and ML method with Ciconia ciconia as the outgroup indicate that the 12 species of Charadriiformes examined in this study are clustered in two major clades. The first clade includes T. totanus, T. glareola, A. interpres, C. tenuirostris, X. cineres, N. madagascariensis, N. arquata and N. phaeopus. The second one includes C. mongolus, C. alexandrinus, R. avosetts and H. ostralensis. Our molecular data show that the phylogenetic relationships among species of Scolopacidae are consistent with the classification based on morphological studies; R. avosetts and H. ostralensis are relatively closer, and form a sister group, and then form paraphyletic group with a sister group which comprised of C. mongolus and C. alexandrinus. The results support Sibley's opinion of assigning R. avosetts and H. ostralensis which form Recurvirostrinae as a taxon of the Charadriidae, and the Charadriidae dividing into two subfamilies: Recurvirostrinae and Charadriinae respectively.}, }
@article {pmid12923659, year = {2003}, author = {Senapin, S and Chen, XJ and Clark-Walker, GD}, title = {Transcription of TIM9, a new factor required for the petite-positive phenotype of Saccharomyces cerevisiae, is defective in spt7 mutants.}, journal = {Current genetics}, volume = {44}, number = {4}, pages = {202-210}, pmid = {12923659}, issn = {0172-8083}, mesh = {Alleles ; Amino Acid Sequence ; Blotting, Northern ; DNA Mutational Analysis ; DNA Primers ; Membrane Transport Proteins/*genetics ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Precursor Protein Import Complex Proteins ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Mutation, Missense/genetics ; *Phenotype ; Point Mutation/genetics ; Saccharomyces cerevisiae/cytology/*genetics ; Saccharomyces cerevisiae Proteins/*genetics/*metabolism ; Sequence Analysis, DNA ; Temperature ; Transcription Factors/genetics/*metabolism ; Transcription, Genetic/*genetics/physiology ; }, abstract = {TIM9 has been identified as an additional novel gene required for the petite-positive phenotype in Saccharomyces cerevisiae. tim9-1 was obtained through a screen for respiratory-deficient strains that are unable to survive in the absence of mitochondrial DNA. A point mutation found in the tim9-1 coding region converts codon 71 from Gly to Arg. Examination of genes encoding other Tim components indicated that the temperature-conditional alleles of essential genes for the viability of S. cerevisiae, TIM9, TIM10 and TIM12, are required for petite survival, while deletion of TIM8 and TIM13 has no notable effect on petite cell viability. Northern hybridization results suggested that the Spt7 transcription factor is strictly involved in transcription of TIM9 and that the synergistic lethality of tim9-1/spt7Delta dual mutations is due to the deficiency of TIM9 transcription together with defective function of the tim9-1 protein.}, }
@article {pmid12923256, year = {2003}, author = {Seif, ER and Forget, L and Martin, NC and Lang, BF}, title = {Mitochondrial RNase P RNAs in ascomycete fungi: lineage-specific variations in RNA secondary structure.}, journal = {RNA (New York, N.Y.)}, volume = {9}, number = {9}, pages = {1073-1083}, pmid = {12923256}, issn = {1355-8382}, mesh = {Ascomycota/*genetics/metabolism ; Base Sequence ; Endoribonucleases/*genetics ; Evolution, Molecular ; Mitochondria/*genetics/metabolism ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Phylogeny ; RNA/*metabolism ; RNA, Catalytic/*genetics ; Ribonuclease P ; }, abstract = {The RNA subunit of mitochondrial RNase P (mtP-RNA) is encoded by a mitochondrial gene (rnpB) in several ascomycete fungi and in the protists Reclinomonas americana and Nephroselmis olivacea. By searching for universally conserved structural elements, we have identified previously unknown rnpB genes in the mitochondrial DNAs (mtDNAs) of two fission yeasts, Schizosaccharomyces pombe and Schizosaccharomyces octosporus; in the budding yeast Pichia canadensis; and in the archiascomycete Taphrina deformans. The expression of mtP-RNAs of the predicted size was experimentally confirmed in the two fission yeasts, and their precise 5' and 3' ends were determined by sequencing of cDNAs generated from circularized mtP-RNAs. Comparative RNA secondary structure modeling shows that in contrast to mtP-RNAs of the two protists R. americana and N. olivacea, those of ascomycete fungi all have highly reduced secondary structures. In certain budding yeasts, such as Saccharomycopsis fibuligera, we find only the two most conserved pairings, P1 and P4. A P18 pairing is conserved in Saccharomyces cerevisiae and its close relatives, whereas nearly half of the minimum bacterial consensus structure is retained in the RNAs of fission yeasts, Aspergillus nidulans and Taphrina deformans. The evolutionary implications of the reduction of mtP-RNA structures in ascomycetes will be discussed.}, }
@article {pmid12910371, year = {2003}, author = {Guidi, C and Zeppa, S and Barbieri, E and Zambonelli, A and Polidori, E and Potenza, L and Stocchi, V}, title = {A putative mitochondrial fission gene from the ectomycorrhizal ascomycete Tuber borchii Vittad.: cloning, characterisation and phylogeny.}, journal = {Current genetics}, volume = {44}, number = {3}, pages = {148-154}, pmid = {12910371}, issn = {0172-8083}, mesh = {Amino Acid Sequence ; Ascomycota/*genetics ; Base Sequence ; Blotting, Northern ; Blotting, Southern ; DNA Primers ; Gene Components ; *Gene Expression ; Introns/genetics ; Likelihood Functions ; Membrane Proteins/*genetics ; Mitochondria/*genetics/physiology ; Mitochondrial Proteins/genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Saccharomyces cerevisiae Proteins/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Mitochondrial binary division is a complex process occurring in multiple steps, mediated by several proteins. In Saccharomyces cerevisiae, a mitochondrial membrane protein, Fis1p, is required for the proper assembly of the mitochondrial division apparatus. In this study, we report the cloning, characterisation and phylogenetic analysis of Tbfis1, a gene from the ectomycorrhizal ascomycetous truffle Tuber borchii, encoding for an orthologue of S. cerevisiae Fis1p. The Tbfis1 coding region consists of a 468-nucleotide open reading frame interrupted by four introns, which encodes for a polypeptide of 155 amino acids, having a predicted transmembrane domain structure typical of the Fis1p Family. Southern blot analysis revealed that Tbfis1 is a single-copy gene in the T. borchii genome. Tbfis1 is highly expressed during the first stages of T. borchii fruit body ripening, while its expression decreases during T. borchii mycelium ageing. Also, Virtual Northern blot analysis revealed Tbfis1 expression in the symbiotic phase of the fungus life cycle. Phylogenetic analysis allowed the identification of Tbfis1 orthologues in filamentous fungi, yeasts, plants, worms, flies and mammals, indicating that the function of the protein coded by this gene has been conserved during evolution.}, }
@article {pmid12909344, year = {2003}, author = {Hüttemann, M and Schmidt, TR and Grossman, LI}, title = {A third isoform of cytochrome c oxidase subunit VIII is present in mammals.}, journal = {Gene}, volume = {312}, number = {}, pages = {95-102}, doi = {10.1016/s0378-1119(03)00604-8}, pmid = {12909344}, issn = {0378-1119}, support = {GM48517/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; DNA, Complementary/chemistry/genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Gene Expression Regulation, Enzymologic ; HeLa Cells ; Humans ; Isoenzymes/genetics ; Lemur/*genetics ; Male ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Protein Subunits/genetics ; Rats ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {The terminal enzyme of the mitochondrial respiratory chain, cytochrome c oxidase (COX), contains three mitochondrial and ten nuclear encoded subunits in mammals. Three of the nuclear subunits (VIa, VIIa, and VIII) have muscle and non-muscle-specific isoforms, subunit IV contains a lung-specific isoform, and subunit VIb contains a testes-specific isoform. For subunit VIII, the smallest nuclear encoded COX polypeptide, we have now found a third gene (COX 8-3), which has been identified in human, lemur, rat, and mouse, suggesting that it is present in a broad range of Eutherian mammals. Sequence similarity and gene structure support the homology of COX8-3 to the other subunit VIII isoforms, indicating that all three are the product of gene duplications. COX VIII-3 protein is mitochondrially-targeted, as shown by a fluorescent COX VIII3/DsRed fusion protein. Both the mitochondrial targeting and its sequence conservation suggest that COXVIII-3 functions as part of the COX holoenzyme and could have a tissue-specific role, as is the case for the other two isoforms. Questions remain about where COX8-3 is predominantly expressed. However, detection of full-length cDNAs, lower levels of sequence divergence at the first and second codon positions compared to the third, and a conserved gene structure indicate that COX VIII-3 is an expressed gene whose origin dates to at least 91 million years ago.}, }
@article {pmid12898180, year = {2003}, author = {Nosek, J and Tomáska, L}, title = {Mitochondrial genome diversity: evolution of the molecular architecture and replication strategy.}, journal = {Current genetics}, volume = {44}, number = {2}, pages = {73-84}, pmid = {12898180}, issn = {0172-8083}, mesh = {DNA Replication/*genetics ; DNA, Circular/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; *Genetic Variation ; Recombinases/genetics ; Telomere/*genetics ; }, abstract = {Mitochondrial genomes in organisms from diverse phylogenetic groups vary in both size and molecular form. Although the types of mitochondrial genome appear very dissimilar, several lines of evidence argue that they do not differ radically. This would imply that interconversion between different types of mitochondrial genome might have occurred via relatively simple mechanisms. We exemplify this scenario on patterns accompanying evolution of mitochondrial telomeres. We propose that mitochondrial telomeres are derived from mobile elements (transposons or plasmids) that invaded mitochondria, integrated into circular or polydisperse linear mitochondrial DNAs (mtDNAs) and subsequently enabled precise resolution of the linear genophore. Simply, the selfish elements generated a problem - how to maintain the ends of a linear DNA - and, at the same time, made themselves essential by providing its solution. This scenario implies that insertion or deletion of such resolution elements may represent relatively simple routes for interconversion between different forms of the mitochondrial genome.}, }
@article {pmid12897260, year = {2003}, author = {Turmel, M and Otis, C and Lemieux, C}, title = {The mitochondrial genome of Chara vulgaris: insights into the mitochondrial DNA architecture of the last common ancestor of green algae and land plants.}, journal = {The Plant cell}, volume = {15}, number = {8}, pages = {1888-1903}, pmid = {12897260}, issn = {1040-4651}, mesh = {Base Sequence ; Chlorophyta/*genetics ; Chromosome Mapping ; DNA, Intergenic/genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; Evolution, Molecular ; Genome, Plant ; Hepatophyta/genetics ; Introns ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Plants/*genetics ; RNA, Plant/chemistry/genetics ; Species Specificity ; }, abstract = {Mitochondrial DNA (mtDNA) has undergone radical changes during the evolution of green plants, yet little is known about the dynamics of mtDNA evolution in this phylum. Land plant mtDNAs differ from the few green algal mtDNAs that have been analyzed to date by their expanded size, long spacers, and diversity of introns. We have determined the mtDNA sequence of Chara vulgaris (Charophyceae), a green alga belonging to the charophycean order (Charales) that is thought to be the most closely related alga to land plants. This 67,737-bp mtDNA sequence, displaying 68 conserved genes and 27 introns, was compared with those of three angiosperms, the bryophyte Marchantia polymorpha, the charophycean alga Chaetosphaeridium globosum (Coleochaetales), and the green alga Mesostigma viride. Despite important differences in size and intron composition, Chara mtDNA strikingly resembles Marchantia mtDNA; for instance, all except 9 of 68 conserved genes lie within blocks of colinear sequences. Overall, our genome comparisons and phylogenetic analyses provide unequivocal support for a sister-group relationship between the Charales and the land plants. Only four introns in land plant mtDNAs appear to have been inherited vertically from a charalean algar ancestor. We infer that the common ancestor of green algae and land plants harbored a tightly packed, gene-rich, and relatively intron-poor mitochondrial genome. The group II introns in this ancestral genome appear to have spread to new mtDNA sites during the evolution of bryophytes and charalean green algae, accounting for part of the intron diversity found in Chara and land plant mitochondria.}, }
@article {pmid12893934, year = {2003}, author = {Gabaldón, T and Huynen, MA}, title = {Reconstruction of the proto-mitochondrial metabolism.}, journal = {Science (New York, N.Y.)}, volume = {301}, number = {5633}, pages = {609}, doi = {10.1126/science.1085463}, pmid = {12893934}, issn = {1095-9203}, mesh = {Aerobiosis ; Algorithms ; Alphaproteobacteria/chemistry/genetics/*metabolism ; Amino Acids/metabolism ; Animals ; Bacterial Proteins/chemistry/*metabolism ; Genome ; Genome, Bacterial ; Glycerol/metabolism ; Humans ; Lipid Metabolism ; Mitochondria/chemistry/genetics/*metabolism ; Phylogeny ; *Proteome ; Symbiosis ; Yeasts/metabolism ; }, }
@article {pmid12887014, year = {2003}, author = {Navet, R and Jarmuszkiewicz, W and Almeida, AM and Sluse-Goffart, C and Sluse, FE}, title = {Energy conservation and dissipation in mitochondria isolated from developing tomato fruit of ethylene-defective mutants failing normal ripening: the effect of ethephon, a chemical precursor of ethylene.}, journal = {Journal of bioenergetics and biomembranes}, volume = {35}, number = {2}, pages = {157-168}, pmid = {12887014}, issn = {0145-479X}, mesh = {Carrier Proteins/genetics/*metabolism ; Cell Respiration/*physiology ; Cells, Cultured ; Energy Transfer/*physiology ; Ethylenes/*metabolism ; Fruit/genetics/growth &amp; development/metabolism ; Ion Channels ; Solanum lycopersicum/genetics/*growth &amp; development/*metabolism ; Membrane Proteins/genetics/*metabolism ; Mitochondria/*physiology ; Mitochondrial Proteins ; Mutation ; Oxidoreductases/genetics/*metabolism ; Plant Proteins ; Plants, Genetically Modified/genetics/growth &amp; development/metabolism ; Uncoupling Protein 1 ; }, abstract = {Alternative oxidase (AOX) and uncoupling protein (UCP) are present simultaneously in tomato fruit mitochondria. In a previous work, it has been shown that protein expression and activity of these two energy-dissipating systems exhibit large variations during tomato fruit development and ripening on the vine. It has been suggested that AOX and UCP could be responsible for the respiration increase at the end of ripening and that the cytochrome pathway could be implicated in the climacteric respiratory burst before the onset of ripening. In this study, the use of tomato mutants that fail normal ripening because of deficiencies in ethylene perception or production as well as the treatment of one selected mutant with a chemical precursor of ethylene have revealed that the bioenergetics of tomato fruit development and ripening is under the control of this plant hormone. Indeed, the evolution pattern of bioenergetic features changes with the type of mutation and with the introduction of ethylene into an ethylene-synthesis-deficient tomato fruit mutant during its induced ripening.}, }
@article {pmid12885964, year = {2003}, author = {Harper, JT and Keeling, PJ}, title = {Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids.}, journal = {Molecular biology and evolution}, volume = {20}, number = {10}, pages = {1730-1735}, doi = {10.1093/molbev/msg195}, pmid = {12885964}, issn = {0737-4038}, mesh = {*Biological Evolution ; Cell Nucleus/genetics ; Cytosol/enzymology ; Eukaryota/genetics ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics/metabolism ; Mitochondria/enzymology ; *Phylogeny ; Plants/genetics ; Plastids/*enzymology ; }, abstract = {Plastids (the photosynthetic organelles of plants and algae) originated through endosymbiosis between a cyanobacterium and a eukaryote and subsequently spread to other eukaryotes by secondary endosymbioses between two eukaryotes. Mounting evidence favors a single origin for plastids of apicomplexans, cryptophytes, dinoflagellates, haptophytes, and heterokonts (together with their nonphotosynthetic relatives, termed chromalveolates), but so far, no single molecular marker has been described that supports this common origin. One piece of evidence comes from plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which originated by a gene duplication of the cytosolic form. However, no plastid GAPDH has been characterized from haptophytes, leaving an important piece of the puzzle missing. We have sequenced genes encoding cytosolic, mitochondrion-targeted, and plastid-targeted GAPDH proteins from a number of haptophytes and heterokonts and found haptophyte homologs that branch within a strongly supported clade of chromalveolate plastid-targeted genes, being more closely related to an apicomplexan homolog than was expected. The evolution of plastid-targeted GAPDH supports red algal ancestry of apicomplexan plastids and raises a number of questions about the importance of plastid loss and the possibility of cryptic plastids in nonphotosynthetic lineages such as ciliates.}, }
@article {pmid12884584, year = {2003}, author = {Wang, ZR and Bao, HE}, title = {[Identification of Taenia saginata by mtCO I in four areas of Yunnan and Guizhou provinces].}, journal = {Zhongguo ji sheng chong xue yu ji sheng chong bing za zhi = Chinese journal of parasitology &amp; parasitic diseases}, volume = {21}, number = {1}, pages = {20-23}, pmid = {12884584}, issn = {1000-7423}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; China ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Taenia/*classification/genetics/isolation &amp; purification ; }, abstract = {OBJECTIVE: To identify the types of Taenia saginata isolated from Dali of Yunnan Province, and from Duyun and Congjiang of Guizhou Province.<br><br>METHODS: Genomic DNA was isolated, and the mitochondrial cytochrome C oxidase subunit I (mtCO I) genes were amplified by polymerase chain reaction(PCR) and analyzed by PHYLIP software package.<br><br>RESULTS: The mtCO I gene sequences of Lanping sample were identical to that of T. saginata asiatica known in Taiwan, and the samples obtained from Dali and Duyun showed the same mtCO I gene sequences, while the sample from Congjiang had the same mtCO I gene sequences as T. saginata. The homology between these two groups of gene sequences was 97.44%, while the homology of amino acid sequences reached to 99.16%. The constructed phylogenetic tree revealed that the relationship between T. saginata asiatica and T. saginata is closer, both are distant relative to T. solium and other species of cestodes.<br><br>CONCLUSION: The Taenia prevalent in Lanping, Dali and Duyun is identified as T. saginata asiatica, while that isolated in Congjiang is the typical T. saginata.}, }
@article {pmid12882974, year = {2003}, author = {Zhang, L and Joshi, AK and Smith, S}, title = {Cloning, expression, characterization, and interaction of two components of a human mitochondrial fatty acid synthase. Malonyltransferase and acyl carrier protein.}, journal = {The Journal of biological chemistry}, volume = {278}, number = {41}, pages = {40067-40074}, doi = {10.1074/jbc.M306121200}, pmid = {12882974}, issn = {0021-9258}, support = {DK 16073/DK/NIDDK NIH HHS/United States ; }, mesh = {Acyl Carrier Protein/chemistry/genetics/metabolism ; Acyl-Carrier Protein S-Malonyltransferase ; Acyltransferases/chemistry/genetics/metabolism ; Animals ; Base Sequence ; Cell Line ; Cloning, Molecular ; DNA, Complementary/genetics ; Fatty Acid Synthases/chemistry/*genetics/*metabolism ; Green Fluorescent Proteins ; HeLa Cells ; Humans ; In Vitro Techniques ; Luminescent Proteins/genetics/metabolism ; Malonyl Coenzyme A/metabolism ; Mitochondria/enzymology ; Phylogeny ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; }, abstract = {The possibility that human cells contain, in addition to the cytosolic type I fatty acid synthase complex, a mitochondrial type II malonyl-CoA-dependent system for the biosynthesis of fatty acids has been examined by cloning, expressing, and characterizing two putative components. Candidate coding sequences for a malonyl-CoA:acyl carrier protein transacylase (malonyltransferase) and its acyl carrier protein substrate, identified by BLAST searches of the human sequence data base, were located on nuclear chromosomes 22 and 16, respectively. The encoded proteins localized exclusively in mitochondria only when the putative N-terminal mitochondrial targeting sequences were present as revealed by confocal microscopy of HeLa cells infected with appropriate green fluorescent protein fusion constructs. The mature, processed forms of the mitochondrial proteins were expressed in Sf9 cells and purified, the acyl carrier protein was converted to the holoform in vitro using purified human phosphopantetheinyltransferase, and the functional interaction of the two proteins was studied. Compared with the dual specificity malonyl/acetyltransferase component of the cytosolic type I fatty acid synthase, the type II mitochondrial counterpart exhibits a relatively narrow substrate specificity for both the acyl donor and acyl carrier protein acceptor. Thus, it forms a covalent acyl-enzyme complex only when incubated with malonyl-CoA and transfers exclusively malonyl moieties to the mitochondrial holoacyl carrier protein. The type II acyl carrier protein from Bacillus subtilis, but not the acyl carrier protein derived from the human cytosolic type I fatty acid synthase, can also function as an acceptor for the mitochondrial transferase. These data provide compelling evidence that human mitochondria contain a malonyl-CoA/acyl carrier protein-dependent fatty acid synthase system, distinct from the type I cytosolic fatty acid synthase, that resembles the type II system present in prokaryotes and plastids. The final products of this system, yet to be identified, may play an important role in mitochondrial function.}, }
@article {pmid12880203, year = {2003}, author = {Gray, MW}, title = {Diversity and evolution of mitochondrial RNA editing systems.}, journal = {IUBMB life}, volume = {55}, number = {4-5}, pages = {227-233}, doi = {10.1080/1521654031000119425}, pmid = {12880203}, issn = {1521-6543}, mesh = {Amino Acid Sequence ; Animals ; Dinoflagellida/classification/genetics ; *Evolution, Molecular ; Kinetoplastida/classification/genetics ; Molecular Sequence Data ; Myxomycetes/classification/genetics ; Phylogeny ; RNA/chemistry/classification/*metabolism ; *RNA Editing ; RNA, Mitochondrial ; }, abstract = {'RNA editing' describes the programmed alteration of the nucleotide sequence of an RNA species, relative to the sequence of the encoding DNA. The phenomenon encompasses two generic patterns of nucleotide change, 'insertion/deletion' and 'substitution', defined on the basis of whether the sequence of the edited RNA is colinear with the DNA sequence that encodes it. RNA editing is mediated by a variety of pathways that are mechanistically and evolutionarily unrelated. Messenger, ribosomal, transfer and viral RNAs all undergo editing in different systems, but well-documented cases of this phenomenon have so far been described only in eukaryotes, and most often in mitochondria. Editing of mRNA changes the identity of encoded amino acids and may create translation initiation and termination codons. The existence of RNA editing violates one of the long-accepted tenets of genetic information flow, namely, that the amino acid sequence of a protein can be directly predicted from the corresponding gene sequence. Particular RNA editing systems display a narrow phylogenetic distribution, which argues that such systems are derived within specific eukaryotic lineages, rather than representing traits that ultimately trace to a common ancestor of eukaryotes, or even further back in evolution. The derived nature of RNA editing raises intriguing questions about how and why RNA editing systems arise, and how they become fixed as additional, essential steps in genetic information transfer.}, }
@article {pmid12880200, year = {2003}, author = {Burger, G and Lang, BF}, title = {Parallels in genome evolution in mitochondria and bacterial symbionts.}, journal = {IUBMB life}, volume = {55}, number = {4-5}, pages = {205-212}, doi = {10.1080/1521654031000137380}, pmid = {12880200}, issn = {1521-6543}, mesh = {Animals ; DNA, Mitochondrial/classification/genetics ; Eukaryotic Cells/classification ; *Evolution, Molecular ; Genes, Bacterial ; *Genome ; *Genome, Bacterial ; Mitochondria/classification/*genetics ; Symbiosis/*genetics ; }, abstract = {Mitochondria, the energy-producing organelles of the eukaryotic cell, originate from an endosymbiotic alpha-proteobacterium. These organelles are believed to have arisen only once in evolutionary history, but despite their common ancestry, mitochondrial DNAs vary extensively throughout eukaryotes in genome architecture and gene content. New insights into early mitochondrial genome evolution come from the investigation of primitive mitochondriate eukaryotes, as well as the comparison between mitochondria and intracellular bacterial symbionts.}, }
@article {pmid12880199, year = {2003}, author = {Martin, W and Rotte, C and Hoffmeister, M and Theissen, U and Gelius-Dietrich, G and Ahr, S and Henze, K}, title = {Early cell evolution, eukaryotes, anoxia, sulfide, oxygen, fungi first (?), and a tree of genomes revisited.}, journal = {IUBMB life}, volume = {55}, number = {4-5}, pages = {193-204}, doi = {10.1080/1521654031000141231}, pmid = {12880199}, issn = {1521-6543}, mesh = {Animals ; Atmosphere/chemistry ; *Biological Evolution ; Eukaryotic Cells/*classification ; Fungi/*classification/genetics ; Fungi, Unclassified/classification/genetics ; *Genome ; Mitochondria/classification/genetics ; Oxygen/chemistry ; *Phylogeny ; Plastids/classification/genetics ; Prokaryotic Cells/*classification ; Sulfides/chemistry ; Sulfur/analysis ; Time Factors ; }, abstract = {Genomes contain evidence for the history of life and furthermore contain evidence for lateral gene transfer, which was an important part of that history. The geological record also contains evidence for the history of life, and newer findings indicates that the Earth's oceans were largely anoxic and highly sulfidic up until about 0.6 billion years ago. Eukaryotes, which fossil data indicate to have been in existence for at least 1.5 billion years, must have therefore spent much of their evolutionary history in oxygen-poor and sulfide-rich environments. Many eukaryotes still inhabit such environments today. Among eukaryotes, organelles also contain evidence for the history of life and have preserved abundant traces of their anaerobic past in the form of energy metabolic pathways. New views of eukaryote phylogeny suggest that fungi may be among the earliest-branching eukaryotes. From the standpoint of the fungal feeding habit (osmotrophy rather than phagotrophy) and from the standpoint of the diversity in their ATP-producing pathways, a eukaryotic tree with fungi first would make sense. Because of lateral gene transfer and endosymbiosis, branches in the tree of genomes intermingle and occasionally fuse, but the overall contours of cell history nonetheless seem sketchable and roughly correlateable with geological time.}, }
@article {pmid12871231, year = {2003}, author = {Hoffmeister, M and Martin, W}, title = {Interspecific evolution: microbial symbiosis, endosymbiosis and gene transfer.}, journal = {Environmental microbiology}, volume = {5}, number = {8}, pages = {641-649}, doi = {10.1046/j.1462-2920.2003.00454.x}, pmid = {12871231}, issn = {1462-2912}, mesh = {Animals ; Archaea/*physiology ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Chlorophyta/genetics/physiology/ultrastructure ; Chloroplasts/physiology ; *Gene Transfer, Horizontal ; Genes, Bacterial ; Invertebrates/genetics/microbiology/*physiology ; Mitochondria/physiology ; *Symbiosis ; }, abstract = {Microbial symbioses are interesting in their own right and also serve as exemplary models to help biologists to understand two important symbioses in the evolutionary past of eukaryotic cells: the origins of chloroplasts and mitochondria. Most, if not all, microbial symbioses have a chemical basis: compounds produced by one partner are useful for the other. But symbioses can also entail the transfer of genes from one partner to the other, which in some cases cements two cells into a bipartite, co-evolving unit. Here, we discuss some microbial symbioses in which progress is being made in uncovering the nature of symbiotic interactions: anaerobic methane-oxidizing consortia, marine worms that possess endosymbionts instead of a digestive tract, amino acid-producing endosymbionts of aphids, prokaryotic endosymbionts living within a prokaryotic host within mealybugs, endosymbionts of an insect vector of human disease and a photosynthetic sea slug that steals chloroplasts from algae. In the case of chloroplasts and mitochondria, examples of recent and ancient gene transfer to the chromosomes of their host cell illustrate the process of genetic merger in the wake of organelle origins.}, }
@article {pmid12868056, year = {2003}, author = {Gray, CH and Ines Borges-Walmsley, M and Evans, GJ and Walmsley, AR}, title = {The pfr1 gene from the human pathogenic fungus Paracoccidioides brasiliensis encodes a half-ABC transporter that is transcribed in response to treatment with fluconazole.}, journal = {Yeast (Chichester, England)}, volume = {20}, number = {10}, pages = {865-880}, doi = {10.1002/yea.1013}, pmid = {12868056}, issn = {0749-503X}, mesh = {ATP-Binding Cassette Transporters/biosynthesis/*genetics ; Adenosine Triphosphatases/metabolism ; Amino Acid Sequence ; Antifungal Agents/*pharmacology ; Base Sequence ; Cloning, Molecular ; Drug Resistance, Fungal ; Fluconazole/*pharmacology ; Fungal Proteins/biosynthesis/*genetics ; Genes, Fungal/drug effects/*genetics/physiology ; Humans ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; Paracoccidioides/drug effects/*genetics/metabolism ; Phylogeny ; RNA, Fungal/chemistry/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; Transcription, Genetic/drug effects/genetics/physiology ; Up-Regulation/drug effects ; }, abstract = {We have isolated a gene that encodes a half-ABC-transporter, designated Pfr1, from the dimorphic human pathogenic fungus Paracoccidioides brasiliensis, which has high identity with members of the ABC-superfamily involved in multidrug resistance. The pfr1 gene is predicted to encode a 827 amino acid protein that, in common with mammalian Mdr1, has a TM-NBD topology. The transcription of the pfr1 gene is induced by the triazole drug fluconazole but not by amphotericin B, suggesting a role in transport-mediated azole resistance. However, Pfr1 has greatest identity to the mitochondrial ABC transporters Mdl1 and Mdl2 from Saccharomyces cerevisiae and mammalian ABC-me, with identities of 47.2%, 40.6% and 39.5%, respectively, over the length of these proteins. Furthermore, the N-terminus of Pfr1 is rich in positively charged residues, a feature of mitochondrial targeting sequences. Considering these features, it seems likely that Pfr1 is a mitochondrial protein. Previous studies have revealed that the acquisition of azole resistance in S. cerevisiae is linked to mitochondrial loss and, conversely, that mitochondrial dysfunction can lead to the upregulation of PDR transporters mediated by the transcription factor Pdr3. Our studies suggest that a mitochondrial ABC transporter is induced as part of the cellular response to drug treatment. The promoter region of pfr1 contains a PDRE-like consensus sequence to which Pdr3 binds, which may be the element responsible for the upregulation of Pfr1 in response to fluconazole. The nucleotide binding domain of Pfr1 was expressed and purified from Escherichia coli and shown to retain ATPase activity, consistent with Pfr1 functioning as a homodimeric transport ATPase.}, }
@article {pmid12862482, year = {2003}, author = {Ashur, I and Brandis, A and Greenwald, M and Vakrat-Haglili, Y and Rosenbach-Belkin, V and Scheer, H and Scherz, A}, title = {Control of redox transitions and oxygen species binding in Mn centers by biologically significant ligands; model studies with [Mn]-bacteriochlorophyll a.}, journal = {Journal of the American Chemical Society}, volume = {125}, number = {29}, pages = {8852-8861}, doi = {10.1021/ja030170m}, pmid = {12862482}, issn = {0002-7863}, mesh = {Bacteriochlorophyll A/*chemistry/metabolism ; Circular Dichroism ; Hydroxyl Radical/chemistry/metabolism ; Kinetics ; Ligands ; Manganese/*chemistry/metabolism ; Oxidation-Reduction ; Reactive Oxygen Species/*chemistry/metabolism ; Spectrometry, Mass, Electrospray Ionization ; Spin Trapping ; Superoxide Dismutase/*chemistry/metabolism ; }, abstract = {Mn-superoxide dismutase (Mn-SOD), which protects the cell from the toxic potential of superoxide radicals (O(2)(-*)), is the only type of SOD which resides in eukaryotic mitochondria. Up-to-date, the exact catalytic mechanism of the enzyme and the relationship between substrate moieties and the ligands within the active site microenvironment are still not resolved. Here, we set out to explore the possible involvement of hydroperoxyl radicals ((*)OOH) in the catalytic dismutaion by following the interplay of Mn(III)/Mn(II) redox transitions, ligands binding, and evolution or consumption of superoxide radical, using a new model system. The model system encompassed an Mn atom chelated by a bacteriochlorophyll allomer macrocycle (BChl) in aerated aprotic media that contain residual water. The redox states of the Mn ion were monitored by the Q(y) electronic transitions at 774 and 825 nm for [Mn(II)]- and [Mn(III)]-BChl, respectively (Geskes, C.; Hartwich, G.; Scheer, H.; Mantele, W.; Heinze, J. J. Am. Chem. Soc. 1995, 117, 7776) and confirmed by electron spin resonance spectroscopy. Evolution of (*)OOH radicals was monitored by the ESR spin-trap technique using 5,5-dimethyl-1-pyrroline-N-oxide (DMPO). The experimental data suggest that the [Mn]-BChl forms a (HO(-))[Mn(III)]-BChl(OOH) complex upon solvation. Spectrophotometeric titrations with tetrabutylamonnium acetate (TBAA) and 1-methylimidazole (1-MeIm) together with ESI-MS measurements indicated the formation of a 1:1 complex with [Mn]-BChl for both ligands. The coordination of ligands at low concentrations to [Mn(III)]-BChl induced a release of a (*)OOH radical and a [Mn(III)]-BChl --> [Mn(II)]-BChl transition at higher concentrations. The estimated equilibrium constants for the total redox reaction ()()are 1.9 x 10(4) +/- 1 x 10(3) M(-)(1) and 12.3 +/- 0.6 M(-)(1) for TBAA and 1-MeIm, respectively. The profound difference between the equilibrium constants agrees with the suggested key role of the ligand's basicity in the process. A direct interaction of superoxide radicals with [Mn(III)]-BChl in a KO(2) acetonitrile (AN) solution also resulted in [Mn(III)]-BChl --> [Mn(II)]-BChl transition. Cumulatively, our data show that the Mn(III) center encourages the protonation of the O(2)(-)(*) radical in an aprotic environment containing residual water molecules, while promoting its oxidation in the presence of basic ligands. Similar coordination and stabilization of the (*)OOH radical by the Mn center may be key steps in the enzymatic dismutation of superoxide radicals by Mn-SOD.}, }
@article {pmid12857827, year = {2003}, author = {Forti, G and Furia, A and Bombelli, P and Finazzi, G}, title = {In vivo changes of the oxidation-reduction state of NADP and of the ATP/ADP cellular ratio linked to the photosynthetic activity in Chlamydomonas reinhardtii.}, journal = {Plant physiology}, volume = {132}, number = {3}, pages = {1464-1474}, pmid = {12857827}, issn = {0032-0889}, mesh = {Adenosine Diphosphate/*metabolism ; Adenosine Triphosphate/*metabolism ; Animals ; Chlamydomonas reinhardtii/cytology/*metabolism ; Chloroplasts/metabolism ; Darkness ; Electron Transport ; Hordeum/metabolism/radiation effects ; Ionophores/metabolism ; Light ; Mitochondria/metabolism ; NADP/*metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; *Photosynthesis ; Plant Leaves/metabolism/radiation effects ; }, abstract = {The ATP/ADP and NADP/NADPH ratios have been measured in whole-cell extract of the green alga Chlamydomonas reinhardtii, to understand their availability for CO(2) assimilation by the Calvin cycle in vivo. Measurements were performed during the dark-light transition of both aerobic and anaerobic cells, under illumination with saturating or low light intensity. Two different patterns of behavior were observed: (a) In anaerobic cells, during the lag preceding O(2) evolution, ATP was synthesized without changes in the NADP/NADPH ratio, consistently with the operation of cyclic electron flow. (b) In aerobiosis, illumination increased the ATP/ADP ratio independently of the intensity used, whereas the amount of NADPH was decreased at limiting photon flux and regained the dark-adapted level under saturating photon flux. Moreover, under these conditions, the addition of low concentrations of uncouplers stimulated photosynthetic O(2) evolution. These observations suggest that the photosynthetic generation of reducing equivalents rather than the rate of ATP formation limits the photosynthetic assimilation of CO(2) in C. reinhardtii cells. This situation is peculiar to C. reinhardtii, because neither NADPH nor ATP limited this process in plant leaves, as shown by their increase upon illumination in barley (Hordeum vulgare) leaves, independent of light intensity. Experiments are presented and were designed to evaluate the contribution of different physiological processes that might increase the photosynthetic ATP/NADPH ratio-the Mehler reaction, respiratory ATP supply following the transfer of reducing equivalents via the malate/oxaloacetate shuttle, and cyclic electron flow around PSI-to this metabolic situation.}, }
@article {pmid12853958, year = {2003}, author = {Bergthorsson, U and Adams, KL and Thomason, B and Palmer, JD}, title = {Widespread horizontal transfer of mitochondrial genes in flowering plants.}, journal = {Nature}, volume = {424}, number = {6945}, pages = {197-201}, doi = {10.1038/nature01743}, pmid = {12853958}, issn = {1476-4687}, mesh = {Base Sequence ; DNA, Mitochondrial ; DNA, Plant ; *Gene Transfer, Horizontal ; *Genes, Plant ; Magnoliopsida/classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics ; Ribosomal Proteins/genetics ; }, abstract = {Horizontal gene transfer--the exchange of genes across mating barriers--is recognized as a major force in bacterial evolution. However, in eukaryotes it is prevalent only in certain phagotrophic protists and limited largely to the ancient acquisition of bacterial genes. Although the human genome was initially reported to contain over 100 genes acquired during vertebrate evolution from bacteria, this claim was immediately and repeatedly rebutted. Moreover, horizontal transfer is unknown within the evolution of animals, plants and fungi except in the special context of mobile genetic elements. Here we show, however, that standard mitochondrial genes, encoding ribosomal and respiratory proteins, are subject to evolutionarily frequent horizontal transfer between distantly related flowering plants. These transfers have created a variety of genomic outcomes, including gene duplication, recapture of genes lost through transfer to the nucleus, and chimaeric, half-monocot, half-dicot genes. These results imply the existence of mechanisms for the delivery of DNA between unrelated plants, indicate that horizontal transfer is also a force in plant nuclear genomes, and are discussed in the contexts of plant molecular phylogeny and genetically modified plants.}, }
@article {pmid12850438, year = {2003}, author = {Richly, E and Chinnery, PF and Leister, D}, title = {Evolutionary diversification of mitochondrial proteomes: implications for human disease.}, journal = {Trends in genetics : TIG}, volume = {19}, number = {7}, pages = {356-362}, doi = {10.1016/S0168-9525(03)00137-9}, pmid = {12850438}, issn = {0168-9525}, mesh = {Animals ; Arabidopsis/genetics ; *Biological Evolution ; Humans ; Mitochondria/*genetics ; Mitochondrial Diseases/*genetics ; Parasites/genetics ; Phylogeny ; Proteome/*genetics ; Yeasts/genetics ; }, }
@article {pmid12847252, year = {2003}, author = {Doyle, CK and Davis, BK and Cook, RG and Rich, RR and Rodgers, JR}, title = {Hyperconservation of the N-formyl peptide binding site of M3: evidence that M3 is an old eutherian molecule with conserved recognition of a pathogen-associated molecular pattern.}, journal = {Journal of immunology (Baltimore, Md. : 1950)}, volume = {171}, number = {2}, pages = {836-844}, doi = {10.4049/jimmunol.171.2.836}, pmid = {12847252}, issn = {0022-1767}, support = {R01 AI30036/AI/NIAID NIH HHS/United States ; R01AI7897/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Amino Acid Substitution/immunology ; Animals ; Bacterial Proteins/genetics/*metabolism ; Binding Sites/immunology ; Cell Line ; *Conserved Sequence ; Cytochrome b Group/genetics/metabolism ; *Evolution, Molecular ; Histocompatibility Antigens Class I/genetics/*metabolism ; Mice ; Mice, Inbred C57BL ; Models, Immunological ; Molecular Sequence Data ; Muridae ; N-Formylmethionine Leucyl-Phenylalanine/*metabolism ; Peromyscus ; Phylogeny ; Protein Binding/immunology ; Rats ; Rats, Inbred F344 ; Rats, Wistar ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {The mouse MHC class I-b molecule H2-M3 has unique specificity for N-formyl peptides, derived from bacteria (and mitochondria), and is thus a pathogen-associated molecular pattern recognition receptor (PRR). To test whether M3 was selected for this PRR function, we studied M3 sequences from diverse murid species of murine genera Mus, Rattus, Apodemus, Diplothrix, Hybomys, Mastomys, and Tokudaia and of sigmodontine genera Sigmodon and PEROMYSCUS: We found that M3 is highly conserved, and the 10 residues coordinating the N-formyl group are almost invariant. The ratio of nonsynonymous and synonymous substitution rates suggests the Ag recognition site of M3, unlike the Ag recognition site of class I-a molecules, is under strong negative (purifying) selection and has been for at least 50-65 million years. Consistent with this, M3 alpha1alpha2 domains from Rattus norvegicus and Sigmodon hispidus and from the "null" allele H2-M3(b) specifically bound N-formyl peptides. The pattern of nucleotide substitution in M3 suggests M3 arose rapidly from murid I-a precursors by an evolutionary leap ("saltation"), perhaps involving intense selective pressure from bacterial pathogens. Alternatively, M3 arose more slowly but prior to the radiation of eutherian (placental) mammals. Older dates for the emergence of M3, and the accepted antiquity of CD1, suggest that primordial class I MHC molecules could have evolved originally as monomorphic PRR, presenting pathogen-associated molecular patterns. Such MHC PRR molecules could have been preadaptations for the evolution of acquired immunity during the early vertebrate radiation.}, }
@article {pmid12844360, year = {2003}, author = {Sylvestre, J and Vialette, S and Corral Debrinski, M and Jacq, C}, title = {Long mRNAs coding for yeast mitochondrial proteins of prokaryotic origin preferentially localize to the vicinity of mitochondria.}, journal = {Genome biology}, volume = {4}, number = {7}, pages = {R44}, pmid = {12844360}, issn = {1474-760X}, mesh = {Biological Transport ; Genes, Fungal ; Intracellular Membranes/chemistry ; Mitochondria/*chemistry/metabolism ; Mitochondrial Proteins/*genetics ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; Polyribosomes/chemistry ; Prokaryotic Cells ; RNA, Fungal/analysis ; RNA, Messenger/*analysis/chemistry/metabolism ; Saccharomyces cerevisiae/chemistry/*genetics ; Saccharomyces cerevisiae Proteins/*genetics ; Subcellular Fractions/chemistry ; }, abstract = {BACKGROUND: Subcellular messenger RNA localization is important in most eukaryotic cells, even in unicellular organisms like yeast for which this process has been underestimated. Microarrays are rarely used to study subcellular mRNA localization at whole-genome level, but can be adapted to that purpose. This work focuses on studying the repartition of yeast nuclear transcripts encoding mitochondrial proteins between free cytosolic polysomes and polysomes bound to the mitochondrial outer membrane.<br><br>RESULTS: Combining biochemical fractionations with oligonucleotide array analyses permits clustering of genes on the basis of the subcellular sites of their mRNA translation. A large fraction of yeast nuclear transcripts known to encode mitochondrial proteins is found in mitochondrial outer-membrane-bound fractions. These results confirm and extend a previous analysis conducted with partial genomic microarrays. Interesting statistical relations among mRNA localization, gene origin and mRNA lengths were found: longer and older mRNAs are more prone to be localized to the vicinity of mitochondria. These observations are included in a refined model of mitochondrial protein import.<br><br>CONCLUSIONS: Mitochondrial biogenesis requires concerted expression of the many genes whose products make up the organelle. In the absence of any clear transcriptional program, coordinated mRNA localization could be an important element of the time-course of organelle construction. We have built a 'MitoChip' localization database from our results which allows us to identify interesting genes whose mRNA localization might be essential for mitochondrial biogenesis in most eukaryotic cells. Moreover, many components of the experimental and data-analysis strategy implemented here are of general relevance in global transcription studies.}, }
@article {pmid12843377, year = {2003}, author = {Waller, RF and Keeling, PJ and van Dooren, GG and McFadden, GI}, title = {Comment on "A green algal apicoplast ancestor".}, journal = {Science (New York, N.Y.)}, volume = {301}, number = {5629}, pages = {49; author reply 49}, doi = {10.1126/science.1084684}, pmid = {12843377}, issn = {1095-9203}, mesh = {Amino Acid Sequence ; Animals ; Apicomplexa/enzymology/*genetics/ultrastructure ; *Biological Evolution ; Chlorophyta/enzymology/*genetics ; Ciliophora/enzymology/genetics/ultrastructure ; Electron Transport Complex IV/chemistry/*genetics ; Gene Transfer, Horizontal ; Genes, Protozoan ; Hydrophobic and Hydrophilic Interactions ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; Plastids/*genetics ; Rhodophyta/enzymology/*genetics ; }, }
@article {pmid12840076, year = {2003}, author = {Bloomfield, G and Pears, C}, title = {Superoxide signalling required for multicellular development of Dictyostelium.}, journal = {Journal of cell science}, volume = {116}, number = {Pt 16}, pages = {3387-3397}, doi = {10.1242/jcs.00649}, pmid = {12840076}, issn = {0021-9533}, mesh = {Animals ; Cell Communication ; Dictyostelium/growth &amp; development/*metabolism ; Mitochondria/drug effects/*metabolism ; Reactive Oxygen Species/metabolism ; Rotenone/pharmacology ; Signal Transduction ; Superoxide Dismutase/metabolism ; Superoxides/*metabolism ; Uncoupling Agents/pharmacology ; }, abstract = {Reactive oxygen species are known to have a signalling role in many organisms. In bacteria and yeast various response systems have evolved to combat oxidative stress which are triggered by reactive oxygen species. Mammals and plants are known to actively generate reactive oxygen species such as superoxide during signalling responses to a variety of extracellular factors. We report here the generation of superoxide as a signalling molecule in early development of Dictyostelium discoideum. Dictyostelium grows as single amoebae but, on starvation, the single cells aggregate to form a multicellular organism. Superoxide is generated in response to a secreted factor during the transition to the multicellular phase of development. Scavenging superoxide, either pharmacologically or by overexpressing the enzyme superoxide dismutase, inhibits the formation of the aggregate. This report of the use of superoxide as a signalling molecule in a lower eukaryote as it switches to a multicellular phase suggests that this signalling mechanism arose early in the evolution of multicellular organisms, perhaps as a necessary consequence of the need to diversify the number and type of signalling pathways available to facilitate intercellular communication.}, }
@article {pmid12840039, year = {2003}, author = {Ingman, M and Gyllensten, U}, title = {Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines.}, journal = {Genome research}, volume = {13}, number = {7}, pages = {1600-1606}, pmid = {12840039}, issn = {1088-9051}, mesh = {Africa ; Asia ; Australia ; DNA, Mitochondrial/*genetics ; Europe ; *Evolution, Molecular ; Genetic Variation/*genetics ; Genetics, Population/methods ; *Genome, Human ; Humans ; India ; Melanesia ; Mitochondria/*genetics ; Molecular Sequence Data ; Native Hawaiian or Other Pacific Islander/*genetics ; New Guinea ; Phylogeny ; Polynesia ; }, abstract = {To study the evolutionary history of the Australian and New Guinean indigenous peoples, we analyzed 101 complete mitochondrial genomes including populations from Australia and New Guinea as well as from Africa, India, Europe, Asia, Melanesia, and Polynesia. The genetic diversity of the Australian mitochondrial sequences is remarkably high and is similar to that found across Asia. This is in contrast to the pattern seen in previously described Y-chromosome data where an Australia-specific haplotype was found at high frequency. The mitochondrial genome data indicate that Australia was colonized between 40 and 70 thousand years ago, either by a single migration from a heterogeneous source population or by multiple movements of smaller groups occurring over a period of time. Some Australian and New Guinea sequences form clades, suggesting the possibility of a joint colonization and/or admixture between the two regions.}, }
@article {pmid12838413, year = {2003}, author = {Giese, H and Lyngkjaer, MF and Stummann, BM and Grell, MN and Christiansen, SK}, title = {Analysis of the structure and inheritance of a linear plasmid from the obligate biotrophic fungus Blumeria graminis f. sp. hordei.}, journal = {Molecular genetics and genomics : MGG}, volume = {269}, number = {5}, pages = {699-705}, pmid = {12838413}, issn = {1617-4615}, mesh = {Ascomycota/*genetics ; Base Sequence ; DNA, Mitochondrial/genetics ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed RNA Polymerases/genetics ; Gene Expression ; Phylogeny ; *Plasmids ; Transcription, Genetic ; }, abstract = {A linear plasmid is widespread among isolates of the obligate biotrophic fungus Blumeria graminis f.sp. hordei (synonym Erysiphe graminis) (Bgh), the organism that causes the disease powdery mildew on barley. We cloned and sequenced the entire plasmid of 7965 bp. The plasmid contains two identical terminal inverted repeats (TIR) of 610 bp. Two ORFs are present on opposite strands, one encoding a phage-type DNA polymerase and the other a phage-type RNA polymerase. Two large transcripts of approximately 4.2 and 5.6 kb were identified in conidia, germinating conidia and Bgh -infected barley leaves, indicating that the polymerases are transcribed at most stages of the lifecycle. The transcription start sites were localised within the TIR regions, where a putative 11-bp ARS consensus sequence was also identified. To follow the sexual transmission of the plasmid we screened 27 Bgh isolates for mitochondrial polymorphisms. One polymorphism allowed us to carry out a cross between two isolates that differed in both mitochondrial genotype and presence/absence of the Bgh plasmid. The plasmid was transmitted independently of the origin of the mitochondria. No transfer of the plasmid was observed between two Bgh isolates that were co-cultivated for 1.5 years on a common susceptible barley variety. The plasmid appears to be an autonomous replicon with no phenotypic effect on Bgh.}, }
@article {pmid12837951, year = {2003}, author = {Elo, A and Lyznik, A and Gonzalez, DO and Kachman, SD and Mackenzie, SA}, title = {Nuclear genes that encode mitochondrial proteins for DNA and RNA metabolism are clustered in the Arabidopsis genome.}, journal = {The Plant cell}, volume = {15}, number = {7}, pages = {1619-1631}, pmid = {12837951}, issn = {1040-4651}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/metabolism ; Cell Nucleus/genetics ; Chromosome Mapping ; Chromosomes, Plant ; DNA, Mitochondrial/genetics/*metabolism ; Evolution, Molecular ; Gene Duplication ; *Genome, Plant ; Mitochondrial Proteins/*genetics/metabolism ; Molecular Sequence Data ; Multigene Family/*genetics ; Phylogeny ; Plastids/genetics ; RNA/genetics/*metabolism ; RNA, Mitochondrial ; Rickettsia/genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {The plant mitochondrial genome is complex in structure, owing to a high degree of recombination activity that subdivides the genome and increases genetic variation. The replication activity of various portions of the mitochondrial genome appears to be nonuniform, providing the plant with an ability to modulate its mitochondrial genotype during development. These and other interesting features of the plant mitochondrial genome suggest that adaptive changes have occurred in DNA maintenance and transmission that will provide insight into unique aspects of plant mitochondrial biology and mitochondrial-chloroplast coevolution. A search in the Arabidopsis genome for genes involved in the regulation of mitochondrial DNA metabolism revealed a region of chromosome III that is unusually rich in genes for mitochondrial DNA and RNA maintenance. An apparently similar genetic linkage was observed in the rice genome. Several of the genes identified within the chromosome III interval appear to target the plastid or to be targeted dually to the mitochondria and the plastid, suggesting that the process of endosymbiosis likely is accompanied by an intimate coevolution of these two organelles for their genome maintenance functions.}, }
@article {pmid12836878, year = {2003}, author = {Bakatselou, C and Beste, D and Kadri, AO and Somanath, S and Clark, CG}, title = {Analysis of genes of mitochondrial origin in the genus Entamoeba.}, journal = {The Journal of eukaryotic microbiology}, volume = {50}, number = {3}, pages = {210-214}, doi = {10.1111/j.1550-7408.2003.tb00119.x}, pmid = {12836878}, issn = {1066-5234}, mesh = {Animals ; DNA, Mitochondrial/genetics ; DNA, Protozoan/analysis ; Entamoeba/*genetics/metabolism ; *Genes, Protozoan ; Heat-Shock Response ; Hot Temperature ; Mitochondria/*genetics/metabolism ; Molecular Sequence Data ; Organelles/genetics/metabolism ; Phylogeny ; RNA, Messenger/analysis/genetics ; Sequence Analysis, DNA ; }, abstract = {The amitochondriate protistan parasite Entamoeba histolytica has lost most mitochondrial functions secondarily but has retained a reduced organelle of mitochondrial origin, the mitosome. We here investigate the presence, origins, and expression in other species of Entamoeba of three genes of mitochondrial origin--pyridine nucleotide transhydrogenase and the mitochondrial-type chaperonins cpn60 and hsp70. The genes appear to be present in all species and specifically related, confirming that the E. histolytica mitosomal genes were not acquired recently by lateral transfer from another organism. Detection of expression was not possible in all cases under the culture conditions used, but several genes were induced during recovery from exposure to a heat shock. This includes the transhydrogenase, which to our knowledge has not been shown previously to be a heat-shock protein.}, }
@article {pmid12836681, year = {2003}, author = {Spring, J}, title = {Major transitions in evolution by genome fusions: from prokaryotes to eukaryotes, metazoans, bilaterians and vertebrates.}, journal = {Journal of structural and functional genomics}, volume = {3}, number = {1-4}, pages = {19-25}, pmid = {12836681}, issn = {1345-711X}, mesh = {Animals ; *Biological Evolution ; Eukaryotic Cells/*metabolism ; Gene Duplication ; *Genome ; Humans ; Prokaryotic Cells/*metabolism ; Vertebrates/*metabolism ; }, abstract = {The major transitions in human evolution from prokaryotes to eukaryotes, from protozoans to metazoans, from the first animals to bilaterians and finally from a primitive chordate to vertebrates were all accompanied by increases in genome complexity. Rare fusion of divergent genomes rather than continuous single gene duplications could explain these jumps in evolution. The origin of eukaryotes was proposed to be due to a symbiosis of Archaea and Bacteria. Symbiosis is clearly seen as the source for mitochondria. A fundamental difference of higher eukaryotes is the cycle from haploidy to diploidy, a well-regulated genome duplication. Of course, self-fertilization exists, but the potential of sex increases with the difference of the haploid stages, such as the sperm and the egg. What should be the advantage of having two identical copies of a gene? Still, genes duplicate all the time and even genomes duplicate rather often. In plants, polyploidy is well recognized, but seems to be abundant in fungi and even in animals, too. However, hybridization, rather than autopolyploidy, seems to be the potential mechanism for creating something new. The problem with chimaeric, symbiotic or reticulate evolution events is that they blur phylogenetic lineages. Unrecognized paralogous genes or random loss of one of the paralogs in different lineages can lead to false conclusions. Horizontal genome transfer, genome fusion or hybridization might be only truly innovative combined with rare geological transitions such as change to an oxygen atmosphere, snowball Earth events or the Cambrian explosion, but correlates well with the major transitions in evolution.}, }
@article {pmid12834405, year = {2003}, author = {Kleine, T and Lockhart, P and Batschauer, A}, title = {An Arabidopsis protein closely related to Synechocystis cryptochrome is targeted to organelles.}, journal = {The Plant journal : for cell and molecular biology}, volume = {35}, number = {1}, pages = {93-103}, doi = {10.1046/j.1365-313x.2003.01787.x}, pmid = {12834405}, issn = {0960-7412}, mesh = {Amino Acid Sequence ; Arabidopsis/cytology/genetics/*metabolism ; Arabidopsis Proteins/*chemistry/*metabolism ; Chloroplasts/*metabolism ; Cryptochromes ; Cyanobacteria/*chemistry ; DNA/metabolism ; DNA-Binding Proteins/chemistry/metabolism ; Deoxyribodipyrimidine Photo-Lyase/*chemistry/*metabolism ; *Drosophila Proteins ; *Eye Proteins ; Flavin-Adenine Dinucleotide/metabolism ; Flavoproteins/*chemistry/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; *Photoreceptor Cells, Invertebrate ; Phylogeny ; Protein Transport ; Receptors, G-Protein-Coupled ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Cryptochromes (CRYs) are blue/UV-A photoreceptors related to the DNA repair enzyme DNA photolyase. They have been found in plants, animals and most recently in the cyanobacterium Synechocystis. Closely related to the Synechocystis cryptochrome is the Arabidopsis gene At5g24850. Here, we show that the encoded protein of At5g24850 binds flavin adenine dinucleotide (FAD). It has no photolyase activity, and is likely to function as a photoreceptor. We have named it At-cry3 to distinguish it from the other Arbabidopsis cryptochrome homologues At-cry1 and At-cry2. At-cry3 carries an N-terminal sequence, which mediates import into chloroplasts and mitochondria. Furthermore, we show that At-cry3 binds DNA. DNA binding was also demonstrated for the Synechocystis cryptochrome, indicating that both photoreceptors could have similar modes of action. Based on the finding of a new cryptochrome class in bacteria and plants, it has been suggested that cryptochromes evolved before the divergence of eukaryotes and prokaryotes. However, our phylogenetic analyses are also consistent with an alternative explanation that the presence of cryptochromes in the plant nuclear genome is the result of dual horizontal gene transfer. That is, CRY1 and CRY2 genes may originate from an endosymbiotic ancestor of modern-day alpha-proteobacteria, while the CRY3 gene may originate from an endosymbiotic ancestor of modern-day cyanobacteria.}, }
@article {pmid12833378, year = {2003}, author = {Müller, G}, title = {Male genital system and spermiogenesis of Nanorchestes amphibius (Acari: Endeostigmata: Nanorchestidae): anatomy, histology, and evolutionary implications.}, journal = {Journal of morphology}, volume = {257}, number = {2}, pages = {171-180}, doi = {10.1002/jmor.10117}, pmid = {12833378}, issn = {0362-2525}, mesh = {Animals ; Genitalia, Male/*anatomy &amp; histology/ultrastructure ; Histological Techniques ; Male ; Microscopy, Electron ; Mites/*anatomy &amp; histology/*physiology ; Phylogeny ; *Spermatogenesis ; }, abstract = {In the present article the anatomy and histology of the male genital system of an endeostigmatid mite are described for the first time. The Endeostigmata probably are a paraphyletic group supposed to include the most primitive actinotrichid mites. In Nanorchestes amphibius, the testis comprises a paired germinal region connected with an unpaired glandular region. In the germinal region, spermiogenesis takes place in cysts of a somatic cell containing germ cells representing the same developmental stage. In the lumen of the glandular region, the spermatozoa are stored together with secretions of the glandular epithelium. These secretions are probably involved in the formation of spermatophores. From the glandular region, spermatozoa and secretions are released into the vasa deferentia that histologically can be divided into three sections, beginning with a short paired region with strong circular muscles serving as a sphincter, continuing with a paired proximal zone, followed by a short unpaired distal section. The distal vas deferens leads into the chitinous, unpaired ductus ejaculatorius which is followed by the progenital chamber. The ductus ejaculatorius is composed of a proximal section and a proximal, central, and anterior chamber. It is accompanied by a complex system of muscles and sclerites probably involved in the formation and ejaculation of the spermatophore. A similar organization can also be found in Prostigmata, but not in Oribatida. Anterior to the progenital chamber is located a paired accessory gland that probably produces a lipid secretion. Spermiogenesis is characterized by disintegration of the nuclear envelope, condensation of chromatin, and extensive reduction of the amount of sperm cell cytoplasm. The mature aflagellate, U-shaped spermatozoa are simple in structure and lack mitochondria and an acrosome complex. The results do not support the current view that Nanorchestidae are more closely related to Sarcoptiformes, i.e., Oribatida and Astigmata, than to Prostigmata.}, }
@article {pmid12832653, year = {2003}, author = {Schrago, CG and Russo, CA}, title = {Timing the origin of New World monkeys.}, journal = {Molecular biology and evolution}, volume = {20}, number = {10}, pages = {1620-1625}, doi = {10.1093/molbev/msg172}, pmid = {12832653}, issn = {0737-4038}, mesh = {Animals ; Cebidae/*genetics ; Cercopithecidae/*genetics ; DNA, Mitochondrial ; *Evolution, Molecular ; Hominidae/genetics ; Humans ; Mitochondria/genetics ; Molecular Sequence Data ; }, abstract = {The origin of New World monkeys (Infraorder Platyrrhini) has been an extensively debated issue. In this study, we analyzed mitochondrial genomes from Cebus (Platyrrhini), Homo, Hylobates, Pan, Pongo (Hominoids), Macaca, Papio (Cercopithecoids), and Tarsius (outgroup) to investigate this matter. Two distinct methodologies were employed on mitochondrial genes to estimate divergence times: the traditional likelihood ratio test performed in ML analyses of individual and concatenated gene sequences and the recent multigene Bayesian approach. Using the Cercopithecoid-Hominoid split as calibration point (25 MYA), our results show consistently that Platyrrhines split from Catarrhines at around 35 MYA. Although the main focus of the study is New World monkey origins, we have also estimated other primate divergence times: Homo-Pan at 5-7 MYA; Pongo-(Homo/Pan) at 13-16 MYA; Hylobates-(Pongo/Homo/Pan) at 15-19 MYA; and Macaca-Papio at 10-12 MYA. Our estimate for the origin of New World monkeys is in agreement with the hypothesis of a transatlantic journey from Africa to South America, as suggested by the fossil record.}, }
@article {pmid12832626, year = {2003}, author = {Shao, R and Dowton, M and Murrell, A and Barker, SC}, title = {Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects.}, journal = {Molecular biology and evolution}, volume = {20}, number = {10}, pages = {1612-1619}, doi = {10.1093/molbev/msg176}, pmid = {12832626}, issn = {0737-4038}, mesh = {Animals ; *DNA, Mitochondrial ; *Evolution, Molecular ; Insecta/*genetics ; Mitochondria/*genetics ; *Point Mutation ; }, abstract = {A number of studies indicated that lineages of animals with high rates of mitochondrial (mt) gene rearrangement might have high rates of mt nucleotide substitution. We chose the hemipteroid assemblage and the Insecta to test the idea that rates of mt gene rearrangement and mt nucleotide substitution are correlated. For this purpose, we sequenced the mt genome of a lepidopsocid from the Psocoptera, the only order of hemipteroid insects for which an entire mtDNA sequence is not available. The mt genome of this lepidopsocid is circular, 16,924 bp long, and contains 37 genes and a putative control region; seven tRNA genes and a protein-coding gene in this genome have changed positions relative to the ancestral arrangement of mt genes of insects. We then compared the relative rates of nucleotide substitution among species from each of the four orders of hemipteroid insects and among the 20 insects whose mt genomes have been sequenced entirely. All comparisons among the hemipteroid insects showed that species with higher rates of gene rearrangement also had significantly higher rates of nucleotide substitution statistically than did species with lower rates of gene rearrangement. In comparisons among the 20 insects, where the mt genomes of the two species differed by more than five breakpoints, the more rearranged species always had a significantly higher rate of nucleotide substitution than the less rearranged species. However, in comparisons where the mt genomes of two species differed by five or less breakpoints, the more rearranged species did not always have a significantly higher rate of nucleotide substitution than the less rearranged species. We tested the statistical significance of the correlation between the rates of mt gene rearrangement and mt nucleotide substitution with nine pairs of insects that were phylogenetically independent from one another. We found that the correlation was positive and statistically significant (R2 = 0.73, P = 0.01; Rs = 0.67, P < 0.05). We propose that increased rates of nucleotide substitution may lead to increased rates of gene rearrangement in the mt genomes of insects.}, }
@article {pmid12832624, year = {2003}, author = {Theissen, U and Hoffmeister, M and Grieshaber, M and Martin, W}, title = {Single eubacterial origin of eukaryotic sulfide:quinone oxidoreductase, a mitochondrial enzyme conserved from the early evolution of eukaryotes during anoxic and sulfidic times.}, journal = {Molecular biology and evolution}, volume = {20}, number = {9}, pages = {1564-1574}, doi = {10.1093/molbev/msg174}, pmid = {12832624}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Anaerobiosis ; Animals ; Bacteria/enzymology/genetics ; Conserved Sequence ; DNA, Mitochondrial/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Gene Duplication ; Humans ; Mitochondria/*enzymology/genetics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Quinone Reductases/*genetics ; Sequence Homology, Amino Acid ; Sulfides/metabolism ; }, abstract = {Mitochondria occur as aerobic, facultatively anaerobic, and, in the case of hydrogenosomes, strictly anaerobic forms. This physiological diversity of mitochondrial oxygen requirement is paralleled by that of free-living alpha-proteobacteria, the group of eubacteria from which mitochondria arose, many of which are facultative anaerobes. Although ATP synthesis in mitochondria usually involves the oxidation of reduced carbon compounds, many alpha-proteobacteria and some mitochondria are known to use sulfide (H2S) as an electron donor for the respiratory chain and its associated ATP synthesis. In many eubacteria, the oxidation of sulfide involves the enzyme sulfide:quinone oxidoreductase (SQR). Nuclear-encoded homologs of SQR are found in several eukaryotic genomes. Here we show that eukaryotic SQR genes characterized to date can be traced to a single acquisition from a eubacterial donor in the common ancestor of animals and fungi. Yet, SQR is not a well-conserved protein, and our analyses suggest that the SQR gene has furthermore undergone some lateral transfer among prokaryotes during evolution, leaving the precise eubacterial lineage from which eukaryotes obtained their SQR difficult to discern with phylogenetic methods. Newer geochemical data and microfossil evidence indicate that major phases of early eukaryotic diversification occurred during a period of the Earth's history from 1 to 2 billion years before present in which the subsurface ocean waters contained almost no oxygen but contained high concentrations of sulfide, suggesting that the ability to deal with sulfide was essential for prokaryotes and eukaryotes during that time. Notwithstanding poor resolution in deep SQR phylogeny and lack of a specifically alpha-protebacterial branch for the eukaryotic enzyme on the basis of current lineage sampling, a single eubacterial origin of eukaryotic SQR and the evident need of ancient eukaryotes to deal with sulfide, a process today germane to mitochondrial quinone reduction, are compatible with the view that eukaryotic SQR was an acquisition from the mitochondrial endosymbiont.}, }
@article {pmid12823454, year = {2003}, author = {Bazinet, C and Rollins, JE}, title = {Rickettsia-like mitochondrial motility in Drosophila spermiogenesis.}, journal = {Evolution &amp; development}, volume = {5}, number = {4}, pages = {379-385}, doi = {10.1046/j.1525-142x.2003.03045.x}, pmid = {12823454}, issn = {1520-541X}, support = {R01 HD36498-01/HD/NICHD NIH HHS/United States ; }, mesh = {Actins/metabolism ; Animals ; Drosophila melanogaster/*physiology ; Male ; Mitochondria/*physiology ; *Phylogeny ; Rickettsia/*cytology/genetics/metabolism ; *Sperm Motility ; Spermatogenesis/*physiology ; Testis/ultrastructure ; }, abstract = {Although it is generally accepted that mitochondria and chloroplasts are descended in evolution from bacteria, the potential contributions of their endosymbiont ancestors to specialized cellular pathways in development remain largely unexplored. Here we show that a motile behavior of mitochondria in Drosophila spermiogenesis is strikingly similar to the actin-based "comet tail" motility of several bacteria. A combination of electron and fluorescence microscopy demonstrates major reorganization and movement of mitochondria ahead of, and in close association with, dense conical arrays of actin filaments in the sperm individualization complex, which mediates the resolution of male germline syncytia into separate gametes. Because of several other parallels between the movement of the individualization complex and the motility behavior of some rickettsiae, the bacterial family from which mitochondria are most likely descended, this motility phenomenon is a strong candidate for a true vestige of endosymbiont behavior in contemporary mitochondria. The potential conservation of an ancient endosymbiont motility mechanism within a highly conserved feature of gametogenesis, the resolution of germline syncytia, may indicate a formative role for the endosymbiotic ancestor of mitochondria in the evolution of this developmental pathway.}, }
@article {pmid12820399, year = {2003}, author = {Solakidi, S and Sekeris, CE}, title = {Oligonucleotide sequences similar to transcription factor consensi of nuclear genes are present in the human mitochondrial genome.}, journal = {Anticancer research}, volume = {23}, number = {2B}, pages = {1389-1393}, pmid = {12820399}, issn = {0250-7005}, mesh = {Binding Sites ; Consensus Sequence ; DNA, Mitochondrial/*metabolism ; DNA-Binding Proteins/metabolism ; Evolution, Molecular ; Gene Expression Regulation ; Humans ; Sequence Homology, Nucleic Acid ; Transcription Factors/*metabolism ; }, abstract = {Screening the mitochondrial genome for binding sites for known nuclear transcription factors revealed oligonucleotide sequences identical or with over 85% similarity to consensi sequences for twenty-one transcription factors, modulating nuclear genes involved, among others, in cell proliferation, inflammation and synthesis of ribosomal and mitochondrial proteins. Two of these sequences were found in the D-loop, the others dispersed among structural genes for respiratory enzyme subunits, for t-RNAs and for rRNAs. We hypothesize that the transcription factors corresponding to the detected mitochondrial binding sites and the agents controlling the availability of these factors could play a regulatory role in the diverse functions of mitochondria, such as energy production, differentiation and apoptosis.}, }
@article {pmid12820379, year = {2003}, author = {Peters, U and Preisler-Adams, S and Lanvers-Kaminsky, C and Jürgens, H and Lamprecht-Dinnesen, A}, title = {Sequence variations of mitochondrial DNA and individual sensitivity to the ototoxic effect of cisplatin.}, journal = {Anticancer research}, volume = {23}, number = {2B}, pages = {1249-1255}, pmid = {12820379}, issn = {0250-7005}, mesh = {Adolescent ; Adult ; Antineoplastic Agents/*adverse effects ; Bone Neoplasms/drug therapy ; Brain Neoplasms/drug therapy ; Child ; Child, Preschool ; Cisplatin/*adverse effects ; DNA Mutational Analysis ; DNA, Mitochondrial/*genetics ; Dose-Response Relationship, Drug ; Genetic Linkage ; Genetic Predisposition to Disease ; Germinoma/drug therapy ; Hair Cells, Auditory, Outer/drug effects ; Haplotypes/genetics ; Hearing Loss, Sensorineural/*chemically induced/genetics ; Humans ; Medulloblastoma/drug therapy ; Mutagenesis, Insertional ; Mutation, Missense ; Neuroblastoma/drug therapy ; Optic Atrophy, Hereditary, Leber/genetics ; Osteosarcoma/drug therapy ; Phenotype ; Phylogeny ; Point Mutation ; Polymorphism, Genetic ; Sequence Deletion ; }, abstract = {BACKGROUND: Since mutations in the mitochondrial genome are associated with hearing loss, we analyzed whether sequence variations of mtDNA are associated with individual sensitivity to cisplatin-induced ototoxicity.<br><br>MATERIALS AND METHODS: The mtDNA of 20 patients with and 19 patients without hearing impairment under therapeutic doses of cisplatin was sequenced for mutations and characterized for haplotype by restriction analysis.<br><br>RESULTS: Neither the A7445G mutation, nor the 7472insC insertion or the A1555G mutation were identified in any of the patients. Nucleotide variations in the variable D-loop region did not correlate with cisplatin-induced hearing loss. However, these patients clustered more frequently (5 out of 20) in the rare European haplogroup J, than those with normal hearing after therapy (1 out of 19).<br><br>CONCLUSION: The linkage of cisplatin-induced hearing impairment to the mitochondrial haplogroup J, which is also associated with the mitochondrially-mediated Leber's Hereditary Optic Neuropathy, might act as a predisponsing genetic background for biochemical differences in mitochondria.}, }
@article {pmid12815198, year = {2003}, author = {Isashiki, Y and Sonoda, S and Izumo, S and Sakamoto, T and Tachikui, H and Inoue, I}, title = {Phylogenetic assessment of the mitochondrial DNA displacement loop haplotype in Japanese patients with Leber's hereditary optic neuropathy harboring the mitochondrial DNA G11778A mutation.}, journal = {Ophthalmic research}, volume = {35}, number = {4}, pages = {224-231}, doi = {10.1159/000071174}, pmid = {12815198}, issn = {0030-3747}, mesh = {Base Sequence ; DNA Mutational Analysis ; DNA, Mitochondrial/*genetics ; Haplotypes ; Humans ; Japan ; Mitochondria/genetics ; Molecular Sequence Data ; Optic Atrophy, Hereditary, Leber/*genetics ; *Phylogeny ; *Point Mutation ; Polymorphism, Genetic/genetics ; }, abstract = {To investigate the anthropological background and the association of mitochondrial DNA (mtDNA) haplotype with the disease phenotype, the nucleotide sequence in the hypervariable segment of the displacement loop (D-loop) region of mtDNA was determined in Japanese patients with Leber's hereditary optic neuropathy (LHON) harboring the G11778A mutation. Genetic polymorphism of mtDNA was examined in 36 unrelated Japanese LHON patients who presented with bilateral optic nerve disease and had the mtDNA G11778A mutation. DNA was extracted from the peripheral blood after having obtained informed consent. The nucleotide sequence of the D-loop region (np 16,002-16,490) was directly determined. The intergenic deletion of the COII/tRNA(Lys) gene of mtDNA was also examined. From the data set of nucleotide alignments, the phylogeny of the mtDNA sequence and phenotypic diversity within the examined population were evaluated. One-base polymorphism was present at 37 different sites. The estimated value of nucleotide diversity was 0.69%. D-loop sequences were classified into 13 monophyletic clusters (CA to CM). There was not any definite ancestral haplotype of the D-loop sequence in the examined LHON population. Thus, the mutational event of G11778A appears to be independent of the evolutionary course in the D-loop haplotype. Patients with a CD plus CH cluster had a significantly older age at onset (p = 0.006), and had a family history being significantly lower as compared with patients with other clusters (p = 0.05). The mtDNA D-loop haplotype characterized by the presence of T16362C or C16290T, lacking G16129A and G16390A, may be a risk for older age at onset and other unusual clinical features in Japanese LHON patients with the G11778A mutation.}, }
@article {pmid12815048, year = {2003}, author = {Joshi, AK and Zhang, L and Rangan, VS and Smith, S}, title = {Cloning, expression, and characterization of a human 4'-phosphopantetheinyl transferase with broad substrate specificity.}, journal = {The Journal of biological chemistry}, volume = {278}, number = {35}, pages = {33142-33149}, doi = {10.1074/jbc.M305459200}, pmid = {12815048}, issn = {0021-9258}, support = {DK 16073/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Cell Line ; Chromatography, Gel ; Cloning, Molecular ; Coenzyme A/metabolism ; Cytosol/enzymology/metabolism ; DNA Primers/chemistry ; DNA, Complementary/metabolism ; Databases, Genetic ; Dose-Response Relationship, Drug ; Electrophoresis, Polyacrylamide Gel ; Fatty Acid Synthases/metabolism ; Humans ; Insecta ; Kinetics ; Lysine/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Binding ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Serine/chemistry ; Substrate Specificity ; Time Factors ; Tissue Distribution ; Transferases (Other Substituted Phosphate Groups)/biosynthesis/*chemistry/*genetics ; }, abstract = {A single candidate 4'-phosphopantetheine transferase, identified by BLAST searches of the human genome sequence data base, has been cloned, expressed, and characterized. The human enzyme, which is expressed mainly in the cytosolic compartment in a wide range of tissues, is a 329-residue, monomeric protein. The enzyme is capable of transferring the 4'-phosphopantetheine moiety of coenzyme A to a conserved serine residue in both the acyl carrier protein domain of the human cytosolic multifunctional fatty acid synthase and the acyl carrier protein associated independently with human mitochondria. The human 4'-phosphopantetheine transferase is also capable of phosphopantetheinylation of peptidyl carrier and acyl carrier proteins from prokaryotes. The same human protein also has recently been implicated in phosphopantetheinylation of the alpha-aminoadipate semialdehyde dehydrogenase involved in lysine catabolism (Praphanphoj, V., Sacksteder, K. A., Gould, S. J., Thomas, G. H., and Geraghty, M. T. (2001) Mol. Genet. Metab. 72, 336-342). Thus, in contrast to yeast, which utilizes separate 4'-phosphopantetheine transferases to service each of three different carrier protein substrates, humans appear to utilize a single, broad specificity enzyme for all posttranslational 4'-phosphopantetheinylation reactions.}, }
@article {pmid12814433, year = {2003}, author = {Lujan, HD and Touz, MC}, title = {Protein trafficking in Giardia lamblia.}, journal = {Cellular microbiology}, volume = {5}, number = {7}, pages = {427-434}, doi = {10.1046/j.1462-5822.2003.00284.x}, pmid = {12814433}, issn = {1462-5814}, mesh = {Animals ; Giardia lamblia/growth &amp; development/*metabolism ; Giardiasis/parasitology ; Humans ; Protein Transport ; Protozoan Proteins/*metabolism ; }, abstract = {Giardia, a protozoan parasite of humans and other vertebrates, is a common cause of intestinal disease worldwide. Besides its medical importance, Giardia is considered an excellent system to study the evolution of fundamental cellular processes because it belongs to the earliest branches of the eukaryotic lineage of descent. Giardia trophozoites lack organelles typical of higher eukaryotes such mitochondria, peroxisomes and compartments involved in intracellular protein trafficking and secretion, such as the Golgi apparatus and secretory granules. Nevertheless, the minimal machinery for protein transport and sorting is present in this parasite. When Giardia undergoes encystation, the biogenesis of secretory organelles necessary to transport cyst wall constituents to the cell surface takes place. Recent studies in both vegetative and encysting trophozoites have provided interesting information regarding the secretory pathway of this important human pathogen.}, }
@article {pmid12803385, year = {2003}, author = {Cochennec-Laureau, N and Reece, KS and Berthe, FC and Hine, PM}, title = {Mikrocytos roughleyi taxonomic affiliation leads to the genus Bonamia (Haplosporidia).}, journal = {Diseases of aquatic organisms}, volume = {54}, number = {3}, pages = {209-217}, doi = {10.3354/dao054209}, pmid = {12803385}, issn = {0177-5103}, mesh = {Animals ; Base Sequence ; DNA, Ribosomal/analysis/chemistry ; Eukaryota/*classification/genetics/ultrastructure ; Host-Parasite Interactions ; Microscopy, Electron ; Molecular Sequence Data ; Ostreidae/*parasitology ; Phylogeny ; Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal/analysis/*chemistry/genetics ; Sequence Alignment/veterinary ; Sequence Analysis, DNA/veterinary ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {Microcell-type parasites of oysters are associated with a complex of diseases in different oyster species around the world. The etiological agents are protists of very small size that are very difficult to characterize taxonomically. Associated lesions may vary according to the host species, and their occurrence may be related to variations in tissue structure. Lesion morphology cannot be used to distinguish the different agents involved. Ultrastructural observations on Mikrocytos roughleyi revealed similarities with Bonamia spp., particularly in regard to the presence of electron-dense haplosporosomes and mitochondria, whose absence from M. mackini also indicate that M. roughleyi and M. mackini are not congeneric. A partial small subunit (ssu) rRNA gene sequence of M. roughleyi was determined. This partial sequence, 951 nucleotides in length, has 95.2 and 98.4% sequence similarities with B. ostreae and B. exitiosus ssu rDNA sequences, respectively. Polymorphisms among the ssu rDNA sequences of B. ostreae, B. exitiosus and M. roughleyi allowed identification of restriction enzyme digestion patterns diagnostic for each species. Phylogenetic analysis based on the ssu rDNA data suggested that M. roughleyi belongs in the phylum Haplosporidia and that it is closely related to Bonamia spp. On the basis of ultrastructural and molecular considerations, M. roughleyi should be considered a putative member of the genus Bonamia.}, }
@article {pmid12801406, year = {2003}, author = {Heazlewood, JL and Millar, AH and Day, DA and Whelan, J}, title = {What makes a mitochondrion?.}, journal = {Genome biology}, volume = {4}, number = {6}, pages = {218}, pmid = {12801406}, issn = {1474-760X}, mesh = {Evolution, Molecular ; Humans ; Mitochondria/*genetics ; Mitochondrial Proteins/classification/genetics ; }, abstract = {Experimental analyses of the proteins found in the mitochondria of yeast, humans and Arabidopsis have confirmed some expectations but given some surprises and some insights into the evolutionary origins of mitochondrial proteins.}, }
@article {pmid12797979, year = {2003}, author = {Brisse, S and Henriksson, J and Barnabé, C and Douzery, EJ and Berkvens, D and Serrano, M and De Carvalho, MR and Buck, GA and Dujardin, JC and Tibayrenc, M}, title = {Evidence for genetic exchange and hybridization in Trypanosoma cruzi based on nucleotide sequences and molecular karyotype.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {2}, number = {3}, pages = {173-183}, doi = {10.1016/s1567-1348(02)00097-7}, pmid = {12797979}, issn = {1567-1348}, mesh = {Animals ; Base Sequence ; Chromosomes/genetics/ultrastructure ; Cytochrome b Group/genetics ; DNA Probes ; Humans ; *Hybridization, Genetic ; Karyotyping ; Mitochondria/genetics ; Phylogeny ; Promoter Regions, Genetic ; RNA, Ribosomal/genetics ; Trypanosoma cruzi/classification/*genetics ; }, abstract = {Trypanosoma cruzi is thought to undergo predominant clonal evolution, as determined by population genetics studies. However, this model does not exclude occasional recombination, which existence is strongly suggested by several recent studies. We sequenced a portion of the maxicircle cytochrome b (CYb) gene and of the nuclear rRNA promoter region from representative strains of six T. cruzi genetic lineages isolated from anthroponotic environments and man (lineages IIb, IId and IIe), sylvatic environments (lineages IIa and IIc) or both (lineage I). Phylogenetic analyses based on the two genes were incongruent. Remarkably, in lineage IIe, CYb and rRNA sequences were very closely related to those of lineages IIc and IIb, respectively. One stock of lineage IId showed rRNA sequence heterogeneity, with both IIb-like and IIc-like copies. Analysis of the size variation of six distinct pairs of putative homologous chromosomes revealed a bimodal distribution of chromosomal sizes across T. cruzi. Notably, stocks of lineages IId and IIe had several chromosomal pairs distributed in distinct modes, with the corresponding modes individually found in lineages IIb and IIc. Together, these data indicate the origin of lineages IId and IIe by hybridization between representatives of lineages IIb and IIc. CYb and rRNA sequences clustered into three and four major lineages, respectively. Data were in agreement with the distinction of six genetic lineages, but not with their proposed grouping into two primary lineages, as lineage II was not monophyletic. Based on a CYb substitution rate of 1% per million years (Myr), the major lineages are estimated to have diverged around 10 million years ago.}, }
@article {pmid12787815, year = {2003}, author = {Huettenbrenner, S and Maier, S and Leisser, C and Polgar, D and Strasser, S and Grusch, M and Krupitza, G}, title = {The evolution of cell death programs as prerequisites of multicellularity.}, journal = {Mutation research}, volume = {543}, number = {3}, pages = {235-249}, doi = {10.1016/s1383-5742(02)00110-2}, pmid = {12787815}, issn = {0027-5107}, mesh = {Animals ; Apoptosis ; *Biological Evolution ; Humans ; Mitochondria/physiology ; Necrosis ; }, abstract = {One of the hallmarks of multicellularity is that the individual cellular fate is sacrificed for the benefit of a higher order of life-the organism. The accidental death of cells in a multicellular organism results in swelling and membrane-rupture and inevitably spills cell contents into the surrounding tissue with deleterious effects for the organism. To avoid this form of necrotic death the cells of metazoans have developed complex self-destruction mechanisms, collectively called programmed cell death, which see to an orderly removal of superfluous cells. Since evolution never invents new genes but plays variations on old themes by DNA mutations, it is not surprising, that some of the genes involved in metazoan death pathways apparently have evolved from homologues in unicellular organisms, where they originally had different functions. Interestingly some unicellular protozoans have developed a primitive form of non-necrotic cell death themselves, which could mean that the idea of an altruistic death for the benefit of genetically identical cells predated the invention of multicellularity. The cell death pathways of protozoans, however, show no homology to those in metazoans, where several death pathways seem to have evolved in parallel. Mitochondria stands at the beginning of several death pathways and also determines, whether a cell has sufficient energy to complete a death program. However, the endosymbiotic bacterial ancestors of mitochondria are unlikely to have contributed to the recent mitochondrial death machinery and therefore, these components may derive from mutated eukaryotic precursors and might have invaded the respective mitochondrial compartments. Although there is no direct evidence, it seems that the prokaryotic-eukaryotic symbiosis created the space necessary for sophisticated death mechanisms on command, which in their distinct forms are major factors for the evolution of multicellular organisms.}, }
@article {pmid12781743, year = {2003}, author = {Otsuka, J and Sugaya, N}, title = {Advanced formulation of base pair changes in the stem regions of ribosomal RNAs; its application to mitochondrial rRNAs for resolving the phylogeny of animals.}, journal = {Journal of theoretical biology}, volume = {222}, number = {4}, pages = {447-460}, doi = {10.1016/s0022-5193(03)00057-2}, pmid = {12781743}, issn = {0022-5193}, mesh = {Animals ; Base Composition ; Evolution, Molecular ; *Models, Genetic ; *Phylogeny ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/*genetics ; Selection, Genetic ; }, abstract = {The ribosomal RNAs (rRNAs) of animal mitochondria, especially those of arthropod mitochondria, have a higher content of G:U and U:G base pairs in their stem regions than the nuclear rRNAs. Thus, the theoretical formulation of base pair changes is extended to incorporate the faster base pair changes A:U<-->G:U<-->G:C and U:A<-->U:G<-->C:G into the previous formulation of the slower base pair changes between A:U, G:C, C:G and U:A. The relative base pair change probability containing the faster and slower base pair changes is theoretically derived to estimate the divergence time of rRNAs under the influence of selection for these base pairs. Using the cartilaginous fish-teleost fish divergence and the crustacean-insect divergence as calibration points, the present method successfully predicts the divergence times of the main branches of animals: Deuterostomia and Protostomia diverged 9.2 x 10(8) years ago, the divergence of Echinodermata, Hemichordata and Cephalochordata succeedingly occurred during the period from 8 x 10(8) to 6 x 10(8) years ago, while Arthropoda, Annelida and Mollusca diverged almost concomitantly about 7 x 10(8) years ago. The dating for the divergence of Platyhelminthes and Cnidaria is traced back to 1.2 x 10(9) years ago. This result is consistent with the fossil records in the Stirling Range Formation of southwestern Australia, the Ediacara and Avalon faunas and the Cambrian Burgess Shale. Thus, the present method may be useful for estimating the divergence times of animals ranging from 10(8) to 10(9) years ago, resolving the difficult problems, e.g. deviation from rate constancy and large sampling variances, in the usual methods of treating apparent change rates between individual bases and/or base pairs.}, }
@article {pmid12777531, year = {2003}, author = {McKenzie, M and Chiotis, M and Pinkert, CA and Trounce, IA}, title = {Functional respiratory chain analyses in murid xenomitochondrial cybrids expose coevolutionary constraints of cytochrome b and nuclear subunits of complex III.}, journal = {Molecular biology and evolution}, volume = {20}, number = {7}, pages = {1117-1124}, doi = {10.1093/molbev/msg132}, pmid = {12777531}, issn = {0737-4038}, support = {N01DE12634/DE/NIDCR NIH HHS/United States ; R21RR16286/RR/NCRR NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Cell Line ; Cell Nucleus/*metabolism ; Cytochromes b/*physiology ; DNA, Mitochondrial/metabolism ; Electron Transport/*physiology ; Electron Transport Complex III/*physiology ; Evolution, Molecular ; Genotype ; Lactic Acid/metabolism ; Mice ; Mitochondria/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidative Phosphorylation ; Oxygen/metabolism ; Phylogeny ; Rats ; Respiration ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {The large number of extant Muridae species provides the opportunity of investigating functional limits of nuclear/mitochondrial respiratory chain (RC) subunit interactions by introducing mitochondrial genomes from progressively more divergent species into Mus musculus domesticus mtDNA-less (rho0) cells. We created a panel of such xenomitochondrial cybrids, using as mitochondrial donors cells from six murid species with divergence from M. m. domesticus estimated at 2 to 12 Myr before present. Species used were Mus spretus, Mus caroli, Mus dunni, Mus pahari, Otomys irroratus, and Rattus norvegicus. Parsimony analysis of partial mtDNA sequences showed agreement with previous molecular phylogenies, with the exception that Otomys did not nest within the murinae as suggested by some recent nuclear gene analyses. Cellular production of lactate, a sensitive indicator of decreased respiratory chain ATP production, correlated with divergence. Functional characterization of the chimeric RC complexes in isolated mitochondria using enzymological analyses demonstrated varying decreases in activities of complexes I, III, and IV, which have subunits encoded in both mitochondrial and nuclear genomes. Complex III showed a striking decline in electron transfer function in the most divergent xenocybrids, being greatly reduced in the Rattus xenocybrid and virtually absent in the Otomys xenocybrid. This suggests that nuclear subunits interacting with cytochrome b face the greatest constraints in the coevolution of murid RC subunits. We sequenced the cytochrome b gene from the species used to identify potential amino acid substitutions involved in such interactions. The greater sensitivity of complex III to xenocybrid dysfunction may result from the encoding of redox center apoproteins in both nuclear and mitochondrial genomes, a unique feature of this RC complex.}, }
@article {pmid12777056, year = {2003}, author = {Koga, R and Horiuchi, H and Fukuhara, T}, title = {Double-stranded RNA replicons associated with chloroplasts of a green alga, Bryopsis cinicola.}, journal = {Plant molecular biology}, volume = {51}, number = {6}, pages = {991-999}, pmid = {12777056}, issn = {0167-4412}, mesh = {Amino Acid Sequence ; Chlorophyta/*genetics ; Chloroplasts/*genetics ; DNA, Complementary/chemistry/genetics/isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; RNA Viruses/enzymology/genetics ; RNA, Double-Stranded/*genetics/metabolism ; RNA-Dependent RNA Polymerase/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {Double-stranded RNAs (dsRNAs) associated with chloroplasts and mitochondria have been found in the coenocytic green alga Bryopsis cinicola. In this study we report molecular properties of the four chloroplast-associated dsRNAs (BDRC1 to BDRC4). The longest dsRNA molecule (BDRC1) was sequenced entirely (1959 bp) and a single large ORF of 1722 bp was found within it. Database searches revealed similarities between the deduced amino acid sequence of this ORF and RNA-dependent RNA polymerase (RdRp) sequences from several RNA viruses. The most similar sequence in the database was the RdRp of beet cryptic virus 3. Phylogenetic analysis revealed that the RdRp-like sequence of BDRC1 can be placed in the Partitiviridae clade. To detect autonomous replication of these dsRNAs, RdRp assays were carried out with actinomycin D, which is an inhibitor of DNA-dependent RNA synthesis. Incorporation of [alpha-32P]UTP was detected specifically in the chloroplast and mitochondrial dsRNAs, indicating that both the chloroplast dsRNAs (BDRCs) and the mitochondrial dsRNA (BDRM) of B. cinicola are RNA replicons. The green alga B. cinicola harbors different dsRNA replicons in its chloroplasts and mitochondria.}, }
@article {pmid12774122, year = {2003}, author = {McQuibban, GA and Saurya, S and Freeman, M}, title = {Mitochondrial membrane remodelling regulated by a conserved rhomboid protease.}, journal = {Nature}, volume = {423}, number = {6939}, pages = {537-541}, doi = {10.1038/nature01633}, pmid = {12774122}, issn = {0028-0836}, mesh = {Amino Acid Sequence ; Cell Division ; Cell Respiration ; *Conserved Sequence ; Cytochrome-c Peroxidase/metabolism ; GTP-Binding Proteins/genetics/metabolism ; Gene Deletion ; Intracellular Membranes/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/genetics/metabolism ; Molecular Sequence Data ; Phenotype ; Protein Processing, Post-Translational ; Saccharomyces cerevisiae/*cytology/*enzymology/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Serine Endopeptidases/*chemistry/genetics/*metabolism ; }, abstract = {Rhomboid proteins are intramembrane serine proteases that activate epidermal growth factor receptor (EGFR) signalling in Drosophila. Rhomboids are conserved throughout evolution, and even in eukaryotes their existence in species with no EGFRs implies that they must have additional roles. Here we report that Saccharomyces cerevisiae has two rhomboids, which we have named Rbd1p and Rbd2p. RBD1 deletion results in a respiratory defect; consistent with this, Rbd1p is localized in the inner mitochondrial membrane and mutant cells have disrupted mitochondria. We have identified two substrates of Rbd1p: cytochrome c peroxidase (Ccp1p); and a dynamin-like GTPase (Mgm1p), which is involved in mitochondrial membrane fusion. Rbd1p mutants are indistinguishable from Mgm1p mutants, indicating that Mgm1p is a key substrate of Rbd1p and explaining the rbd1Delta mitochondrial phenotype. Our data indicate that mitochondrial membrane remodelling is regulated by cleavage of Mgm1p and show that intramembrane proteolysis by rhomboids controls cellular processes other than signalling. In addition, mitochondrial rhomboids are conserved throughout eukaryotes and the mammalian homologue, PARL, rescues the yeast mutant, suggesting that these proteins represent a functionally conserved subclass of rhomboid proteases.}, }
@article {pmid12773543, year = {2003}, author = {Teoh, ML and Walasek, PJ and Evans, DH}, title = {Leporipoxvirus Cu,Zn-superoxide dismutase (SOD) homologs are catalytically inert decoy proteins that bind copper chaperone for SOD.}, journal = {The Journal of biological chemistry}, volume = {278}, number = {35}, pages = {33175-33184}, doi = {10.1074/jbc.M300644200}, pmid = {12773543}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Blotting, Western ; Catalysis ; Copper/*metabolism ; Electrophoresis, Polyacrylamide Gel ; Fibroma Virus, Rabbit/enzymology ; Glutathione Transferase/metabolism ; Humans ; Leporipoxvirus/*enzymology ; Metals/pharmacology ; Microscopy, Confocal ; Mitochondria/metabolism ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Mutation ; Myxoma/metabolism ; Myxoma virus/enzymology ; Phylogeny ; Plasmids/metabolism ; Precipitin Tests ; Protein Binding ; Recombinant Proteins/metabolism ; Sequence Homology, Amino Acid ; Superoxide Dismutase/*chemistry/metabolism ; Zinc/metabolism ; }, abstract = {Many Chordopoxviruses encode catalytically inactive homologs of cellular Cu-Zn superoxide dismutase (SOD). The biological function of these proteins is unknown, although the proteins encoded by Leporipoxviruses have been shown to promote a slow decline in the level of superoxide dismutase activity in virus-infected cells. To gain more insights into their function, we have further characterized the enzymatic and biochemical properties of a SOD homolog encoded by Shope fibroma virus. Shope fibroma virus SOD has retained the zinc binding properties of its cellular homolog, but cannot bind copper. Site-directed mutagenesis showed that it requires at least four amino acid substitutions to partially restore copper binding activity, but even these changes still did not restore catalytic activity. Reciprocal co-immunoprecipitation experiments showed that recombinant Shope fibroma virus SOD forms very stable complexes with cellular copper chaperones for SOD and these observations were confirmed using glutathione-S-transferase tagged proteins. Similar viral SOD/chaperone complexes were formed in cells infected with a closely related myxoma virus, where we also noted that some of the SOD antigen co-localizes with mitochondrial markers using confocal fluorescence microscopy. About 2% of the viral SOD was subsequently detected in gradient-purified mitochondria extracted from virus-infected cells. These poxviral SOD homologs do not form stable complexes with cellular Cu,Zn-SOD or affect its concentration. We suggest that Leporipoxvirus SOD homologs are catalytically inert decoy proteins that are designed to interfere in the proper metallation and activation of cellular Cu,Zn-SOD. This reaction might be advantageous for tumorigenic poxviruses, since higher levels of superoxide have been proposed to have anti-apoptotic and tumorigenic activity.}, }
@article {pmid12769817, year = {2003}, author = {Brouwer, M and Hoexum Brouwer, T and Grater, W and Brown-Peterson, N}, title = {Replacement of a cytosolic copper/zinc superoxide dismutase by a novel cytosolic manganese superoxide dismutase in crustaceans that use copper (haemocyanin) for oxygen transport.}, journal = {The Biochemical journal}, volume = {374}, number = {Pt 1}, pages = {219-228}, pmid = {12769817}, issn = {0264-6021}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Copper/*metabolism ; Crustacea/classification/*enzymology ; Cytosol/enzymology ; Digestive System/enzymology ; Hemocyanins/*metabolism ; Humans ; Isoenzymes/metabolism ; Molecular Sequence Data ; Oxygen Consumption ; Peptide Fragments/chemistry ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Homology, Amino Acid ; Superoxide Dismutase/chemistry/genetics/*metabolism ; }, abstract = {The blue crab, Callinectes sapidus, which uses the copper-dependent protein haemocyanin for oxygen transport, lacks the ubiquitous cytosolic copper-dependent enzyme copper/zinc superoxide dismutase (Cu,ZnSOD) as evidenced by undetectable levels of Cu,ZnSOD activity, protein and mRNA in the hepatopancreas (the site of haemocyanin synthesis) and gills. Instead, the crab has an unusual cytosolic manganese SOD (cytMnSOD), which is retained in the cytosol, because it lacks a mitochondrial transit peptide. A second familiar MnSOD is present in the mitochondria (mtMnSOD). This unique phenomenon occurs in all Crustacea that use haemocyanin for oxygen transport. Molecular phylogeny analysis suggests the MnSOD gene duplication is as old as the origin of the arthropod phylum. cytMnSOD activity in the hepatopancreas changes during the moulting cycle of the crab. Activity is high in intermoult crabs and non-detectable in postmoult papershell crabs. mtMnSOD is present in all stages of the moulting cycle. Despite the lack of cytCu,ZnSOD, crabs have an extracellular Cu,ZnSOD (ecCu,ZnSOD) that is produced by haemocytes, and is part of a large, approx. 160 kDa, covalently-linked protein complex. ecCu,ZnSOD is absent from the hepatopancreas of intermoult crabs, but appears in this tissue at premoult. However, no ecCu,ZnSOD mRNA can be detected, suggesting that the protein is recruited from the haemolymph. Screening of different taxa of the arthropod phylum for Cu,ZnSOD activity shows that those crustaceans that use haemoglobin for oxygen transport have retained cytCu,ZnSOD. It appears, therefore, that the replacement of cytCu,ZnSOD with cytMnSOD is part of an adaptive response to the dynamic, haemocyanin-linked, fluctuations in copper metabolism that occur during the moulting cycle of the crab.}, }
@article {pmid12769656, year = {2002}, author = {Rivarola, HW and Paglini-Oliva, PA}, title = {Trypanosoma cruzi trypanothione reductase inhibitors: phenothiazines and related compounds modify experimental Chagas' disease evolution.}, journal = {Current drug targets. Cardiovascular &amp; haematological disorders}, volume = {2}, number = {1}, pages = {43-52}, doi = {10.2174/1568006023337745}, pmid = {12769656}, issn = {1568-0061}, mesh = {Animals ; Antiprotozoal Agents/pharmacology/*therapeutic use ; Chagas Disease/*drug therapy/enzymology ; Enzyme Inhibitors/pharmacology/*therapeutic use ; Humans ; NADH, NADPH Oxidoreductases/*antagonists &amp; inhibitors/metabolism ; Phenothiazines/pharmacology/*therapeutic use ; Trypanosoma cruzi/drug effects/*enzymology ; }, abstract = {Chagas' disease affects about 18 million people and 25% of the population of Latin America is at risk of acquiring Chagas' disease. The chemotherapy of Chagas' disease is still an open field and remains as an unsolved problem. Nifurtimox and benznidazole are currently used to treat this disease, however, both drugs have high toxicity and are mutagenic with the result that the patients frequently fail to follow treatment. T. cruzi enzimes such as trypanothione reductase, represent potential drug targets because they play an essential role in the life of this organism. This enzyme has been isolated, purified and studied by X ray crystallography. Phenothiazines and related compounds inhibit trypanothione reductase and a specially favoured fit is a phenothiazine with a 2- substitued with 2- chloro and 2- trifluoromethyl with a remote hydrophobic patch. The essential phenothiazine nucleus can adopt more than one inhibitory orientation in its binding site. Phenothiazines and related compounds are drugs used in psychiatric treatments. These anti-depressants inhibit trypanothione reductase through the peroxidase/ H2O2/ system, and also exert other trypanocidal effects upon epimastigotes and tripomastigotes forms: clomipramine through an anticalmodulin action; trifluopherazine and thioridazine induced disruption of mitochondria and prometazine provoked serious cell membrane disorganization. Clomipramine and thioridazine were also effective in treatment of mice with experimental Chagas' disease, significantly modifying the natural evolution of the infection; cardiac function and survival of infected and treated animals were not different from non infected animals. Phenothiazines and related compounds are promising trypanocidal agents for treatment of Chagas' disease. Other trypanocidal agents as nifurtimox, benznidazol,Allopurinol, cystein protease inhibitors and others, are also discussed.}, }
@article {pmid12768414, year = {2003}, author = {Khazi, FR and Edmondson, AC and Nielsen, BL}, title = {An Arabidopsis homologue of bacterial RecA that complements an E. coli recA deletion is targeted to plant mitochondria.}, journal = {Molecular genetics and genomics : MGG}, volume = {269}, number = {4}, pages = {454-463}, pmid = {12768414}, issn = {1617-4615}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics ; Blotting, Western ; Escherichia coli/genetics ; Gene Transfer Techniques ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Rec A Recombinases/*genetics ; Sequence Alignment ; Sequence Deletion ; }, abstract = {Homologous recombination results in the exchange and rearrangement of DNA, and thus generates genetic variation in living organisms. RecA is known to function in all bacteria as the central enzyme catalyzing strand transfer and has functional homologues in eukaryotes. Most of our knowledge of homologous recombination in eukaryotes is limited to processes in the nucleus. The mitochondrial genomes of higher plants contain repeated sequences that are known to undergo frequent rearrangements and recombination events. However, very little is known about the proteins involved or the biochemical mechanisms of DNA recombination in plant mitochondria. We provide here the first report of an Arabidopsis thaliana homologue of Escherichia coli RecA that is targeted to mitochondria. The mt recA gene has a putative mitochondrial presequence identified from the A. thaliana genome database. This nuclear gene encodes a predicted product that shows highest sequence homology to chloroplast RecA and RecA proteins from proteobacteria. When fused to the GFP coding sequence, the predicted presequence was able to target the fusion protein to isolated mitochondria but not to chloroplasts. The mitochondrion-specific localization of the mt recA gene product was confirmed by Western analysis using polyclonal antibodies raised against a synthetic peptide from a unique region of the mature mtRecA. The Arabidopsis mt recA gene partially complemented a recA deletion in E. coli, enhancing survival after exposure to DNA-damaging agents. These results suggest a possible role for mt recA in homologous recombination and/or repair in Arabidopsis mitochondria.}, }
@article {pmid12765765, year = {2003}, author = {Kadenbach, B}, title = {Intrinsic and extrinsic uncoupling of oxidative phosphorylation.}, journal = {Biochimica et biophysica acta}, volume = {1604}, number = {2}, pages = {77-94}, doi = {10.1016/s0005-2728(03)00027-6}, pmid = {12765765}, issn = {0006-3002}, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Biological Evolution ; Electron Transport Complex IV/metabolism ; Energy Metabolism ; Fatty Acids/metabolism ; Intracellular Membranes/metabolism ; Membrane Potentials ; Membrane Proteins/metabolism ; Mitochondria/drug effects/metabolism ; Models, Biological ; *Oxidative Phosphorylation/drug effects ; Proton Pumps/drug effects/metabolism ; Proton-Translocating ATPases/metabolism ; Protons ; Reactive Oxygen Species/metabolism ; Thyroid Hormones/metabolism ; Uncoupling Agents/*metabolism/pharmacology ; }, abstract = {This article reviews parameters of extrinsic uncoupling of oxidative phosphorylation (OxPhos) in mitochondria, based on induction of a proton leak across the inner membrane. The effects of classical uncouplers, fatty acids, uncoupling proteins (UCP1-UCP5) and thyroid hormones on the efficiency of OxPhos are described. Furthermore, the present knowledge on intrinsic uncoupling of cytochrome c oxidase (decrease of H(+)/e(-) stoichiometry=slip) is reviewed. Among the three proton pumps of the respiratory chain of mitochondria and bacteria, only cytochrome c oxidase is known to exhibit a slip of proton pumping. Intrinsic uncoupling was shown after chemical modification, by site-directed mutagenesis of the bacterial enzyme, at high membrane potential DeltaPsi, and in a tissue-specific manner to increase thermogenesis in heart and skeletal muscle by high ATP/ADP ratios, and in non-skeletal muscle tissues by palmitate. In addition, two mechanisms of respiratory control are described. The first occurs through the membrane potential DeltaPsi and maintains high DeltaPsi values (150-200 mV). The second occurs only in mitochondria, is suggested to keep DeltaPsi at low levels (100-150 mV) through the potential dependence of the ATP synthase and the allosteric ATP inhibition of cytochrome c oxidase at high ATP/ADP ratios, and is reversibly switched on by cAMP-dependent phosphorylation. Finally, the regulation of DeltaPsi and the production of reactive oxygen species (ROS) in mitochondria at high DeltaPsi values (150-200 mV) are discussed.}, }
@article {pmid12765685, year = {2003}, author = {Minke, B and Agam, K}, title = {TRP gating is linked to the metabolic state and maintenance of the Drosophila photoreceptor cells.}, journal = {Cell calcium}, volume = {33}, number = {5-6}, pages = {395-408}, doi = {10.1016/s0143-4160(03)00052-6}, pmid = {12765685}, issn = {0143-4160}, support = {EY 03529/EY/NEI NIH HHS/United States ; }, mesh = {Animals ; Calcium Channels/*physiology ; Calmodulin-Binding Proteins/*physiology ; Drosophila Proteins/*physiology ; Drosophila melanogaster/metabolism ; *Ion Channel Gating ; Membrane Potentials/physiology ; Membrane Proteins/*physiology ; Mitochondria/physiology ; Oxidative Stress/drug effects/*physiology ; Photoreceptor Cells, Invertebrate/chemistry/physiology ; Transient Receptor Potential Channels ; Vision, Ocular/*physiology ; }, abstract = {The Drosophila light-activated channel TRP is the founding member of a large and diverse family of channel proteins that is conserved throughout evolution. In spite of much progress, the gating mechanism of TRP channels is still unknown. However, recent studies have shown multi-faceted functions of the Drosophila light-sensitive TRP channel that may shed light on TRP gating. Accordingly, metabolic stress, which leads to depletion of cellular ATP, reversibly activates the Drosophila TRP and TRPL channels in the dark in a constitutive manner. In several Drosophila mutants, constitutive activity of TRP channels lead to a rapid retinal degeneration in the dark, while genetic elimination of TRP protects the cells from degeneration. Additional studies have shown that TRPL translocates in a light-dependent manner between the signaling membranes and the cell body. This light-activated translocation is accompanied by reversible morphological changes leading to partial and reversible collapse of the microvillar signaling membranes into the cytosol, which allows turnover of signaling molecules. These morphological changes are also blocked by genetic elimination of TRP channels. The link of TRP gating to the metabolic state and maintenance of cells makes cells expressing TRP extremely vulnerable to metabolic stress via a mechanism that may underlie retinal degeneration and neuronal cell death upon malfunction.}, }
@article {pmid12762649, year = {2003}, author = {Formichi, P and Battisti, C and Bianchi, S and Cardaioli, E and Federico, A}, title = {Evidence of apoptosis via TUNEL staining in muscle biopsy from patients with mitochondrial encephaloneuromyopathies.}, journal = {Journal of submicroscopic cytology and pathology}, volume = {35}, number = {1}, pages = {29-34}, pmid = {12762649}, issn = {1122-9497}, mesh = {Adult ; Aged ; *Apoptosis ; Biomarkers ; Biopsy ; DNA Fragmentation ; DNA, Mitochondrial/genetics ; Female ; Humans ; *In Situ Nick-End Labeling ; Male ; Middle Aged ; Mitochondrial Encephalomyopathies/genetics/*pathology ; Muscle, Skeletal/*pathology ; Mutation ; }, abstract = {Apoptosis is an evolution-conserved form of cell death essential for development and maintenance of tissue homeostasis. Dysregulation of apoptosis has been implicated in several pathological conditions, including neurodegenerative disorders. The crucial role of mitochondria in regulation of the apoptotic pathway prompted us to investigate the pattern of apoptosis in muscle biopsies from 17 patients with mitochondrial encephaloneuromyopathies caused by mtDNA defects. The results were compared with muscle biopsies from controls and from patients with myopathies without mitochondrial impairment. The terminal deoxynucleotidyl transferase-mediated dUTP nick and labelling (TUNEL) reaction was used as marker of apoptosis. Our findings were very heterogeneous, even between patients with the same mtDNA mutations, suggesting that tissue evaluation of apoptotic process is less useful than in vitro techniques, for investigating the role of apoptosis in mitochondrial pathologies.}, }
@article {pmid12755702, year = {2003}, author = {Genu, V and Gödecke, S and Hollenberg, CP and Pereira, GG}, title = {The Hansenula polymorpha MOX gene presents two alternative transcription start points differentially utilized and sensitive to respiratory activity.}, journal = {European journal of biochemistry}, volume = {270}, number = {11}, pages = {2467-2475}, doi = {10.1046/j.1432-1033.2003.03618.x}, pmid = {12755702}, issn = {0014-2956}, mesh = {Alcohol Oxidoreductases/*metabolism ; Antifungal Agents/pharmacology ; Antimycin A/pharmacology ; Blotting, Northern ; Gene Deletion ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Fungal ; Genes, Fungal ; Genes, Reporter ; Glucose/metabolism ; Glycerol/metabolism ; Kinetics ; Methanol/metabolism ; Mitochondria/metabolism ; Mutation ; Oxygen Consumption ; Peroxisomes/metabolism ; Pichia/*metabolism ; Plasmids/metabolism ; Promoter Regions, Genetic ; RNA, Messenger/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; *Transcription, Genetic ; }, abstract = {The peroxisomal methanol metabolism of Hansenula polymorpha depends on a group of genes that are coordinately regulated. Methanol oxidase (Mox) plays a key role in this pathway and its synthesis has been shown to be regulated at the transcriptional level. MOX expression is strongly repressed on glucose and activated on glycerol or methanol. In this study we have identified two MOX transcripts that are differentially expressed along MOX derepression. The first one, named l-MOX (for longer MOX), starts at position -425, is only weakly and transiently transcribed and is not translated into the Mox protein. The other is the true MOX mRNA, which initiates around position -25. Using a strain bearing multiple copies of MOX(Q1N) and a reporter gene fused to the MOX promoter, regulation of the two transcripts was investigated. Initiation of the true MOX correlates with repression of l-MOX and conditions that are repressive for MOX transcription, such as the inhibition of mitochondrial activity, lead to higher levels of l-MOX expression. This effect was first observed in a mox mutant (Q1N-M8) unable to grow on nonfermentable carbon sources. No function was detected for l-MOX, but its regulation follows a pattern similar to that of catalase, which is essential for methanol metabolism. This suggests that, l-MOX, although precisely regulated, seems to be a remnant of the evolution of the methanol metabolism network.}, }
@article {pmid12750393, year = {2003}, author = {Brenner, C and Kroemer, G}, title = {The mitochondriotoxic domain of Vpr determines HIV-1 virulence.}, journal = {The Journal of clinical investigation}, volume = {111}, number = {10}, pages = {1455-1457}, pmid = {12750393}, issn = {0021-9738}, mesh = {Apoptosis ; Cell Cycle/drug effects ; Gene Products, vpr/genetics/*toxicity ; HIV Infections/*physiopathology ; HIV Long-Term Survivors ; HIV-1/*pathogenicity ; Humans ; Mitochondria/*drug effects/metabolism ; T-Lymphocytes/virology ; Virulence/genetics ; vpr Gene Products, Human Immunodeficiency Virus ; }, }
@article {pmid12750316, year = {2003}, author = {Jiggins, FM}, title = {Male-killing Wolbachia and mitochondrial DNA: selective sweeps, hybrid introgression and parasite population dynamics.}, journal = {Genetics}, volume = {164}, number = {1}, pages = {5-12}, pmid = {12750316}, issn = {0016-6731}, mesh = {Animals ; Butterflies/*genetics/microbiology ; *DNA, Mitochondrial ; Female ; Genetic Variation ; *Hybridization, Genetic ; Likelihood Functions ; Male ; Molecular Sequence Data ; Phylogeny ; Population Dynamics ; Selection, Genetic ; Wolbachia/*genetics ; }, abstract = {Mitochondrial DNA (mtDNA) sequences are widely used as neutral genetic markers in insects. However, patterns of mtDNA variability are confounded by the spread of maternally transmitted parasites, which are genetically linked to the mitochondria. We have investigated these effects in the butterflies Acraea encedon (which is host to two strains of male-killing Wolbachia bacteria) and A. encedana (which is host to one strain). Within a population, the mitochondria are in linkage disequilibrium with the different male-killers. Furthermore, there has been a recent selective sweep of the mtDNA, which has led to the loss of mitochondrial variation within populations and erased any geographical structure. We also found that one of the male-killers, together with the associated mtDNA, has introgressed from A. encedana into A. encedon within the last 16,000 years. Interestingly, because butterflies are female heterogametic, this will presumably have also led to the introgression of genes on the W sex chromosome. Finally, in A. encedon the mitochondria in uninfected females are unaltered by the spread of the male-killer and have diverse, geographically structured mtDNA. This means we can reject the hypothesis that the male-killer is at a stable equilibrium maintained by imperfect transmission of the bacterium. Instead, some other form of balancing selection may be maintaining uninfected females in the population and preventing the species from going extinct due to a shortage of males.}, }
@article {pmid12742584, year = {2003}, author = {Amino, H and Osanai, A and Miyadera, H and Shinjyo, N and Tomitsuka, E and Taka, H and Mineki, R and Murayama, K and Takamiya, S and Aoki, T and Miyoshi, H and Sakamoto, K and Kojima, S and Kita, K}, title = {Isolation and characterization of the stage-specific cytochrome b small subunit (CybS) of Ascaris suum complex II from the aerobic respiratory chain of larval mitochondria.}, journal = {Molecular and biochemical parasitology}, volume = {128}, number = {2}, pages = {175-186}, doi = {10.1016/s0166-6851(03)00074-4}, pmid = {12742584}, issn = {0166-6851}, mesh = {Aerobiosis ; Amino Acid Sequence ; Animals ; Ascaris suum/cytology/*enzymology/*growth &amp; development ; Cloning, Molecular ; Cytochrome b Group/*chemistry/genetics/isolation &amp; purification/*metabolism ; Electron Transport ; Kinetics ; Larva/enzymology ; Mitochondria/*enzymology ; Molecular Sequence Data ; Multienzyme Complexes/metabolism ; Peptide Mapping ; Phylogeny ; Sequence Alignment ; Species Specificity ; }, abstract = {We recently reported that Ascaris suum mitochondria express stage-specific isoforms of complex II: the flavoprotein subunit and the small subunit of cytochrome b (CybS) of the larval complex II differ from those of adult enzyme, while two complex IIs share a common iron-sulfur cluster subunit (Ip). In the present study, A. suum larval complex II was highly purified to characterize the larval cytochrome b subunits in more detail. Peptide mass fingerprinting and N-terminal amino acid sequencing showed that the larval and adult cytochrome b (CybL) proteins are identical. In contrast, cDNA sequences revealed that the small subunit of larval cytochrome b (CybS(L)) is distinct from the adult CybS (CybS(A)). Furthermore, Northern analysis and immunoblotting showed stage-specific expression of CybS(L) and CybS(A) in larval and adult mitochondria, respectively. Enzymatic assays revealed that the ratio of rhodoquinol-fumarate reductase (RQFR) to succinate-ubiquinone reductase (SQR) activities and the K(m) values for quinones are almost identical for the adult and larval complex IIs, but that the fumarate reductase (FRD) activity is higher for the adult form than for the larval form. These results indicate that the adult and larval A. suum complex IIs have different properties than the complex II of the mammalian host and that the larval complex II is able to function as a RQFR. Such RQFR activity of the larval complex II would be essential for rapid adaptation to the dramatic change of oxygen availability during infection of the host.}, }
@article {pmid12740605, year = {2003}, author = {Desloire, S and Gherbi, H and Laloui, W and Marhadour, S and Clouet, V and Cattolico, L and Falentin, C and Giancola, S and Renard, M and Budar, F and Small, I and Caboche, M and Delourme, R and Bendahmane, A}, title = {Identification of the fertility restoration locus, Rfo, in radish, as a member of the pentatricopeptide-repeat protein family.}, journal = {EMBO reports}, volume = {4}, number = {6}, pages = {588-594}, pmid = {12740605}, issn = {1469-221X}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics ; Cell Nucleus/metabolism ; Chloroplasts/metabolism ; Chromosome Mapping ; Cloning, Molecular ; Cytoplasm/metabolism ; Databases as Topic ; *Genes, Plant ; Genetic Markers ; Mitochondria/metabolism ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Physical Chromosome Mapping ; Plant Proteins/metabolism ; Raphanus/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {Ogura cytoplasmic male sterility (CMS) in radish (Raphanus sativus) is caused by an aberrant mitochondrial gene, Orf138, that prevents the production of functional pollen without affecting female fertility. Rfo, a nuclear gene that restores male fertility, alters the expression of Orf138 at the post-transcriptional level. The Ogura CMS/Rfo two-component system is a useful model for investigating nuclear-cytoplasmic interactions, as well as the physiological basis of fertility restoration. Using a combination of positional cloning and microsynteny analysis of Arabidopsis thaliana and radish, we genetically and physically delimited the Rfo locus to a 15-kb DNA segment. Analysis of this segment shows that Rfo is a member of the pentatricopeptide repeat (PPR) family. In Arabidopsis, this family contains more than 450 members of unknown function, although most of them are predicted to be targeted to mitochondria and chloroplasts and are thought to have roles in organellar gene expression.}, }
@article {pmid12739049, year = {2003}, author = {Schäfer, B}, title = {Genetic conservation versus variability in mitochondria: the architecture of the mitochondrial genome in the petite-negative yeast Schizosaccharomyces pombe.}, journal = {Current genetics}, volume = {43}, number = {5}, pages = {311-326}, pmid = {12739049}, issn = {0172-8083}, mesh = {DNA Replication/*genetics ; DNA, Mitochondrial/*genetics ; Endonucleases/genetics/metabolism ; *Gene Expression ; Genetic Variation ; Introns/genetics ; Mitochondria/*physiology ; Retroelements/genetics ; Schizosaccharomyces/*genetics ; }, abstract = {The great amount of molecular information and the many molecular genetic techniques available make Schizosaccharomyces pombe an ideal model eukaryote, complementary to the budding yeast Saccharomyces cerevisiae. In particular, mechanisms involved in mitochiondrial (mt) biogenesis in fission yeast are more similar to higher eukaryotes than to budding yeast. In this review, recent findings on mt morphogenesis, DNA replication and gene expression in this model organism are summarised. A second aspect is the organisation of the mt genome in fission yeast. On the one hand, fission yeast has a strong tendency to maintain mtDNA intact; and, on the other hand, the mt genomes of naturally occurring strains show a great variability. Therefore, the molecular mechanisms behind the susceptibility to mutations in the mtDNA and the mechanisms that promote sequence variations during the evolution of the genome in fission yeast mitochondria are discussed.}, }
@article {pmid12730263, year = {2003}, author = {Bauwe, H and Kolukisaoglu, U}, title = {Genetic manipulation of glycine decarboxylation.}, journal = {Journal of experimental botany}, volume = {54}, number = {387}, pages = {1523-1535}, doi = {10.1093/jxb/erg171}, pmid = {12730263}, issn = {0022-0957}, mesh = {Amino Acid Oxidoreductases/*genetics/metabolism ; Arabidopsis/genetics ; Glycine/*metabolism ; Glycine Dehydrogenase (Decarboxylating) ; Glycine Hydroxymethyltransferase/*genetics/metabolism ; Hordeum/genetics ; Mutation ; Photosynthetic Reaction Center Complex Proteins/classification/genetics/metabolism ; Serine/biosynthesis ; }, abstract = {The glycine-serine interconversion, catalysed by glycine decarboxylase and serine hydroxymethyltransferase, is an important reaction of primary metabolism in all organisms including plants, by providing one-carbon units for many biosynthetic reactions. In plants, in addition, it is an integral part of the photorespiratory metabolic pathway and produces large amounts of photorespiratory CO(2) within mitochondria. Although controversial, there is significant evidence that this process, by the relocation of glycine decarboxylase within the leaves from the mesophyll to the bundle-sheath, contributed to the evolution of C(4) photosynthesis. In this review, some aspects of current knowledge about glycine decarboxylase and serine hydroxymethyltransferase and the role of these enzymes in metabolism, about the corresponding genes and their expression as well as about mutants and anti-sense plants related to these genes or processes will be summarized and discussed. From a comparison of the available information about the number and organization of GDC and SHMT genes in the genomes of Arabidopsis thaliana and Oryza sativa it appears that these and, possibly, other genes related to photorespiration, are similarly organized even in only very distantly related angiosperms.}, }
@article {pmid12729588, year = {2003}, author = {Clavería, C and Torres, M}, title = {Mitochondrial apoptotic pathways induced by Drosophila programmed cell death regulators.}, journal = {Biochemical and biophysical research communications}, volume = {304}, number = {3}, pages = {531-537}, doi = {10.1016/s0006-291x(03)00626-0}, pmid = {12729588}, issn = {0006-291X}, mesh = {Amino Acid Sequence ; Animals ; *Apoptosis ; Biological Evolution ; Drosophila Proteins/chemistry/*metabolism ; Drosophila melanogaster/cytology/*metabolism ; Mitochondria/*metabolism ; Models, Biological ; Protein Structure, Tertiary ; Signal Transduction ; }, abstract = {Multicellular organisms eliminate unwanted or damaged cells by cell death, a process essential to the maintenance of tissue homeostasis. Cell death is a tightly regulated event, whose alteration by excess or defect is involved in the pathogenesis of many diseases such as cancer, autoimmune syndromes, and neurodegenerative processes. Studies in model organisms, especially in the nematode Caenorhabditis elegans, have been crucial in identifying the key molecules implicated in the regulation and execution of programmed cell death. In contrast, the study of cell death in Drosophila melanogaster, often an excellent model organism, has identified regulators and mechanisms not obviously conserved in other metazoans. Recent molecular and cellular analyses suggest, however, that the mechanisms of action of the main programmed cell death regulators in Drosophila include a canonical mitochondrial pathway.}, }
@article {pmid12729583, year = {2003}, author = {van Gurp, M and Festjens, N and van Loo, G and Saelens, X and Vandenabeele, P}, title = {Mitochondrial intermembrane proteins in cell death.}, journal = {Biochemical and biophysical research communications}, volume = {304}, number = {3}, pages = {487-497}, doi = {10.1016/s0006-291x(03)00621-1}, pmid = {12729583}, issn = {0006-291X}, mesh = {Animals ; *Apoptosis ; Apoptosis Inducing Factor ; Apoptosis Regulatory Proteins ; Carrier Proteins/physiology ; Cytochrome c Group/physiology ; Endodeoxyribonucleases/physiology ; Flavoproteins/physiology ; High-Temperature Requirement A Serine Peptidase 2 ; Intracellular Membranes/metabolism ; Intracellular Signaling Peptides and Proteins ; Membrane Proteins/*physiology ; Mitochondria/metabolism ; Mitochondrial Proteins/*physiology ; Models, Biological ; Oxidative Phosphorylation ; Serine Endopeptidases/physiology ; }, abstract = {Apoptosis is a form of programmed cell death important in the development and tissue homeostasis of multicellular organisms. Mitochondria have, next to their function in respiration, an important role in the apoptotic-signaling pathway. Malfunctioning at any level of the cell is eventually translated in the release of apoptogenic factors from the mitochondrial intermembrane space resulting in the organized demise of the cell. Some of these factors, such as AIF and endonuclease G, appear to be highly conserved during evolution. Other factors, like cytochrome c, have gained their apoptogenic function later during evolution. In this review, we focus on the role of cytochrome c, AIF, endonuclease G, Smac/DIABLO, Omi/HtrA2, Acyl-CoA-binding protein, and polypyrimidine tract-binding protein in the initiation and modulation of cell death in different model organisms. These mitochondrial factors may contribute to both caspase-dependent and caspase-independent processes in apoptotic cell death.}, }
@article {pmid12729582, year = {2003}, author = {Frank, S and Robert, EG and Youle, RJ}, title = {Scission, spores, and apoptosis: a proposal for the evolutionary origin of mitochondria in cell death induction.}, journal = {Biochemical and biophysical research communications}, volume = {304}, number = {3}, pages = {481-486}, doi = {10.1016/s0006-291x(03)00620-x}, pmid = {12729582}, issn = {0006-291X}, mesh = {*Apoptosis ; Bacteria/ultrastructure ; Bacterial Physiological Phenomena ; Bacterial Proteins/metabolism ; *Biological Evolution ; Cell Death ; *Cytoskeletal Proteins ; Mitochondria/classification/*physiology/ultrastructure ; *Models, Biological ; Phylogeny ; Spores, Bacterial/ultrastructure ; }, abstract = {Mitochondria fragment prior to caspase activation during many pathways of apoptosis. Inhibition of the machinery that normally regulates mitochondrial morphology in healthy cells inhibits the fission that occurs during apoptosis and actually delays the process of cell death. Interestingly, there are certain parallels between mitochondrial fission and bacterial sporulation. As bacterial sporulation can be considered a stress response we suggest that a primordial stress response of endosymbiont mitochondrial progenitors may have been adopted for the stress response of early eukaryotes. Thus, the mitochondrial fission process may represent an early stress response of primitive mitochondria that could have integrated the stress signals and acted as an initial sensor for the eukaryotic response system. The fact that mitochondria fragment during apoptosis using the machinery descended from or that superceded the bacterial stress response of sporulation is consistent with this hypothesis. This hypothesis would explain why what is generally considered the "power house" of the cell came to integrate the cell death response and regulate apoptosis.}, }
@article {pmid12728281, year = {2003}, author = {Karlberg, EO and Andersson, SG}, title = {Mitochondrial gene history and mRNA localization: is there a correlation?.}, journal = {Nature reviews. Genetics}, volume = {4}, number = {5}, pages = {391-397}, doi = {10.1038/nrg1063}, pmid = {12728281}, issn = {1471-0056}, mesh = {Animals ; Humans ; Mitochondria/*genetics/metabolism ; Protein Transport ; RNA, Messenger/*genetics ; Saccharomyces cerevisiae/genetics ; }, abstract = {Phylogenetic studies of the yeast mitochondrial proteome have shown a complex evolutionary scenario, in which proteins of bacterial origin form complexes with proteins of eukaryotic origin. Exciting new results from whole-genome microarray studies of subcellular mRNA localizations have shown that mRNAs that are of putative bacterial origin are mainly translated on polysomes that are associated with the mitochondrion, whereas those of eukaryotic origin are generally translated on free cytosolic polysomes. Understanding these newly discovered relationships promises insights into old questions about organelle origins and mRNA localization in the eukaryotic cell.}, }
@article {pmid12724317, year = {2003}, author = {Soccio, RE and Breslow, JL}, title = {StAR-related lipid transfer (START) proteins: mediators of intracellular lipid metabolism.}, journal = {The Journal of biological chemistry}, volume = {278}, number = {25}, pages = {22183-22186}, doi = {10.1074/jbc.R300003200}, pmid = {12724317}, issn = {0021-9258}, support = {GM07739/GM/NIGMS NIH HHS/United States ; HL32435/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Carrier Proteins/*chemistry/*genetics/*metabolism ; Cholesterol/metabolism ; Evolution, Molecular ; Humans ; Intracellular Membranes/physiology ; Kinetics ; *Lipid Metabolism ; Mitochondria/physiology ; Neoplasm Proteins/chemistry/metabolism ; Signal Transduction ; }, }
@article {pmid12716992, year = {2003}, author = {van der Giezen, M and Birdsey, GM and Horner, DS and Lucocq, J and Dyal, PL and Benchimol, M and Danpure, CJ and Embley, TM}, title = {Fungal hydrogenosomes contain mitochondrial heat-shock proteins.}, journal = {Molecular biology and evolution}, volume = {20}, number = {7}, pages = {1051-1061}, doi = {10.1093/molbev/msg103}, pmid = {12716992}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Chaperonin 60/*genetics ; Green Fluorescent Proteins ; HSP70 Heat-Shock Proteins/*genetics ; Hydrogen/*metabolism ; Luminescent Proteins/metabolism ; Mitochondria/*genetics ; Molecular Sequence Data ; Neocallimastix/*genetics ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {At least three groups of anaerobic eukaryotes lack mitochondria and instead contain hydrogenosomes, peculiar organelles that make energy and excrete hydrogen. Published data indicate that ciliate and trichomonad hydrogenosomes share common ancestry with mitochondria, but the evolutionary origins of fungal hydrogenosomes have been controversial. We have now isolated full-length genes for heat shock proteins 60 and 70 from the anaerobic fungus Neocallimastix patriciarum, which phylogenetic analyses reveal share common ancestry with mitochondrial orthologues. In aerobic organisms these proteins function in mitochondrial import and protein folding. Homologous antibodies demonstrated the localization of both proteins to fungal hydrogenosomes. Moreover, both sequences contain amino-terminal extensions that in heterologous targeting experiments were shown to be necessary and sufficient to locate both proteins and green fluorescent protein to the mitochondria of mammalian cells. This finding, that fungal hydrogenosomes use mitochondrial targeting signals to import two proteins of mitochondrial ancestry that play key roles in aerobic mitochondria, provides further strong evidence that the fungal organelle is also of mitochondrial ancestry. The extraordinary capacity of eukaryotes to repeatedly evolve hydrogen-producing organelles apparently reflects a general ability to modify the biochemistry of the mitochondrial compartment.}, }
@article {pmid12709048, year = {2003}, author = {Carrillo, N and Ceccarelli, EA}, title = {Open questions in ferredoxin-NADP+ reductase catalytic mechanism.}, journal = {European journal of biochemistry}, volume = {270}, number = {9}, pages = {1900-1915}, doi = {10.1046/j.1432-1033.2003.03566.x}, pmid = {12709048}, issn = {0014-2956}, mesh = {Bacterial Proteins/chemistry/metabolism ; Binding Sites ; Catalysis ; Electron Transport ; Ferredoxin-NADP Reductase/chemistry/*metabolism ; Models, Molecular ; Molecular Structure ; NADP/*metabolism ; Oxidation-Reduction ; Plant Proteins/chemistry/metabolism ; Protein Conformation ; }, abstract = {Ferredoxin (flavodoxin)-NADP(H) reductases (FNR) are ubiquitous flavoenzymes that deliver NADPH or low potential one-electron donors (ferredoxin, flavodoxin) to redox-based metabolisms in plastids, mitochondria and bacteria. The plant-type reductase is also the basic prototype for one of the major families of flavin-containing electron transferases that display common functional and structural properties. Many aspects of FNR biochemistry have been extensively characterized in recent years using a combination of site-directed mutagenesis, steady-state and transient kinetic experiments, spectroscopy and X-ray crystallography. Despite these considerable advances, various key features in the enzymology of these important reductases remain yet to be explained in molecular terms. This article reviews the current status of these open questions. Measurements of electron transfer rates and binding equilibria indicate that NADP(H) and ferredoxin interactions with FNR result in a reciprocal decrease of affinity, and that this induced-fit step is a mandatory requisite for catalytic turnover. However, the expected conformational movements are not apparent in the reported atomic structures of these flavoenzymes in the free state or in complex with their substrates. The overall reaction catalysed by FNR is freely reversible, but the pathways leading to NADP+ or ferredoxin reduction proceed through entirely different kinetic mechanisms. Also, the reductases isolated from various sources undergo inactivating denaturation on exposure to NADPH and other electron donors that reduce the FAD prosthetic group, a phenomenon that might have profound consequences for FNR function in vivo. The mechanisms underlying this reductive inhibition are so far unknown. Finally, we provide here a rationale to interpret FNR evolution in terms of catalytic efficiency. Using the formalism of the Albery-Knowles theory, we identified which parameter(s) have to be modified to make these reductases even more proficient under a variety of conditions, natural or artificial. Flavoenzymes with FNR activity catalyse a number of reactions with potential importance for biotechnological processes, so that modification of their catalytic competence is relevant on both scientific and technical grounds.}, }
@article {pmid12706105, year = {2003}, author = {Zhang, Z and Gerstein, M}, title = {Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome.}, journal = {Genomics}, volume = {81}, number = {5}, pages = {468-480}, doi = {10.1016/s0888-7543(03)00004-1}, pmid = {12706105}, issn = {0888-7543}, support = {P50HG02357-01/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; *DNA, Mitochondrial ; Genome, Human ; Humans ; Mice ; Molecular Sequence Data ; Phylogeny ; *Pseudogenes ; Ribosomal Proteins/*genetics ; Sequence Analysis, DNA ; Sequence Analysis, Protein ; }, abstract = {The human (nuclear) genome encodes at least 79 mitochondrial ribosomal proteins (MRPs), which are imported into the mitochondria. Using a comprehensive approach, we find 41 of these give rise to 120 pseudogenes in the genome. The majority of the MRP pseudogenes are of processed origin and can be aligned to match the entire coding region of the functional MRP mRNAs. One processed pseudogene was found to have originated from an alternatively spliced mRNA transcript. We also found two duplicated pseudogenes that are transcribed in the cell as confirmed by screening the human EST database. We observed a significant correlation between the number of processed pseudogenes and the gene CDS length (R = -0.40; p < 0.001), i.e., the relatively shorter genes tend to have more processed pseudogenes. There is also a weaker correlation between the number of processed pseudogenes and the gene CDS GC content. Our study provides a catalogue of human MRP pseudogenes, which will be useful in the study of functional MRP genes. It also provides a molecular record of the evolution of these genes. More details are available at http://pseudogene.org/.}, }
@article {pmid12700156, year = {2003}, author = {Gast, RJ and Beaudoin, DJ and Caron, DA}, title = {Isolation of symbiotically expressed genes from the dinoflagellate symbiont of the solitary radiolarian Thalassicolla nucleata.}, journal = {The Biological bulletin}, volume = {204}, number = {2}, pages = {210-214}, doi = {10.2307/1543561}, pmid = {12700156}, issn = {0006-3185}, mesh = {Animals ; Dinoflagellida/*genetics/physiology ; Eukaryota/*microbiology ; Gene Expression/genetics/physiology ; Genomics ; Nucleic Acid Hybridization ; RNA/genetics/*isolation &amp; purification ; Symbiosis/*genetics ; }, abstract = {Symbiotic associations are fundamental to the survival of many organisms on Earth. The ability of the symbiont to perform key biochemical functions often allows the host to occupy environments that it would otherwise find inhospitable. This can have profound impacts upon the diversification and distribution of the host. Cellular organelles (chloroplasts and mitochondria) represent the final stages of integration of endosymbionts. These organelles were of critical importance to the evolution and success of eukaryotic lineages on our planet because they allowed the host cells to harness light energy and to thrive in the presence of oxygen. The marine photosymbiotic associations that we study represent an earlier stage in the process of symbiont integration-one in which the photobiont can still be removed from the host and exist on its own. These systems are of interest to us for two reasons. First, they are ecologically important in the marine environment where they occur. These organisms form zones of photosynthetic production in oceanic regions typically low in nutrients. Second, investigation of these interactions may shed light on the molecular and evolutionary mechanisms involved in the integration of cells and their genomes.}, }
@article {pmid12698290, year = {2003}, author = {Dowton, M and Castro, LR and Campbell, SL and Bargon, SD and Austin, AD}, title = {Frequent mitochondrial gene rearrangements at the hymenopteran nad3-nad5 junction.}, journal = {Journal of molecular evolution}, volume = {56}, number = {5}, pages = {517-526}, doi = {10.1007/s00239-002-2420-3}, pmid = {12698290}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; Chromosome Inversion ; DNA Shuffling ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Gene Rearrangement ; Genes, Insect ; Genes, rRNA ; Hymenoptera/*genetics ; Mitochondria/*genetics ; Mitochondrial Proteins/*genetics ; Molecular Sequence Data ; Multigene Family ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {We characterized the organization of mitochondrial genes from a diverse range of hymenopterans. Of the 21 taxa characterized, 12 had distinct, derived organizations. Some rearrangements were consistent with the duplication-random loss mechanism, while others were not. Local inversions were relatively common, i.e., rearrangements characterized by the movement of genes from one mitochondrial strand to the other, opposite or close to their ancestral position. This type of rearrangement is inconsistent with the duplication/random loss model of mitochondrial gene rearrangement. Instead, they are best explained by the operation of recombination. Taxa with derived organizations were restricted to a single, monophyletic group of wasps, the Apocrita, which comprise about 90% of all hymenopterans.}, }
@article {pmid12694174, year = {2003}, author = {Emelyanov, VV}, title = {Mitochondrial connection to the origin of the eukaryotic cell.}, journal = {European journal of biochemistry}, volume = {270}, number = {8}, pages = {1599-1618}, doi = {10.1046/j.1432-1033.2003.03499.x}, pmid = {12694174}, issn = {0014-2956}, mesh = {Amino Acid Sequence ; Animals ; Conserved Sequence ; Energy Metabolism ; Eukaryotic Cells/metabolism ; Glycolysis/genetics ; Humans ; Mitochondria/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Valine-tRNA Ligase/chemistry/genetics ; }, abstract = {Phylogenetic evidence is presented that primitively amitochondriate eukaryotes containing the nucleus, cytoskeleton, and endomembrane system may have never existed. Instead, the primary host for the mitochondrial progenitor may have been a chimeric prokaryote, created by fusion between an archaebacterium and a eubacterium, in which eubacterial energy metabolism (glycolysis and fermentation) was retained. A Rickettsia-like intracellular symbiont, suggested to be the last common ancestor of the family Rickettsiaceae and mitochondria, may have penetrated such a host (pro-eukaryote), surrounded by a single membrane, due to tightly membrane-associated phospholipase activity, as do present-day rickettsiae. The relatively rapid evolutionary conversion of the invader into an organelle may have occurred in a safe milieu via numerous, often dramatic, changes involving both partners, which resulted in successful coupling of the host glycolysis and the symbiont respiration. Establishment of a potent energy-generating organelle made it possible, through rapid dramatic changes, to develop genuine eukaryotic elements. Such sequential, or converging, global events could fill the gap between prokaryotes and eukaryotes known as major evolutionary discontinuity.}, }
@article {pmid12691300, year = {2003}, author = {Fleischer, A and Rebollo, A and Ayllón, V}, title = {BH3-only proteins: the lords of death.}, journal = {Archivum immunologiae et therapiae experimentalis}, volume = {51}, number = {1}, pages = {9-17}, pmid = {12691300}, issn = {0004-069X}, mesh = {Animals ; Apoptosis/*physiology ; Gene Expression Regulation ; Peptide Fragments/*metabolism ; Protein Processing, Post-Translational ; Proto-Oncogene Proteins c-bcl-2/genetics/*metabolism ; }, abstract = {Although the mechanisms by which Bcl-2 family proteins control the apoptotic machinery of the cell are not fully understood, it becomes clear that the role of BH3-only proteins consists in serving as sensors or sentinels of cellular damage, transducing the apoptotic stimuli to the mitochondria. For this reason, mammalian cells have developed several strategies for their strict regulation throughout evolution. This review aims to highlight the different ways by which BH3-only proteins are controlled, including transcriptional regulation, post-translational modifications and subcellular localization.}, }
@article {pmid12678440, year = {2002}, author = {Almeida, AM and Navet, R and Jarmuszkiewicz, W and Vercesi, AE and Sluse-Goffart, CM and Sluse, FE}, title = {The energy-conserving and energy-dissipating processes in mitochondria isolated from wild type and nonripening tomato fruits during development on the plant.}, journal = {Journal of bioenergetics and biomembranes}, volume = {34}, number = {6}, pages = {487-498}, pmid = {12678440}, issn = {0145-479X}, mesh = {Adenosine Triphosphate/biosynthesis ; Carrier Proteins/metabolism ; Energy Metabolism ; Fatty Acids, Nonesterified/metabolism ; Ion Channels ; Solanum lycopersicum/genetics/growth &amp; development/*metabolism ; Membrane Proteins/metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins ; Mutation ; Oxidoreductases/metabolism ; Oxygen Consumption ; Plant Proteins/metabolism ; Uncoupling Protein 1 ; }, abstract = {Bioenergetics of tomato (Lycopersicon esculentum) development on the plant was followed from the early growing stage to senescence in wild type (climacteric) and nonripening mutant (nor, non-climacteric) fruits. Fruit development was expressed in terms of evolution of chlorophyll a content allowing the assessment of a continuous time-course in both cultivars. Measured parameters: the cytochrome pathway-dependent respiration, i.e., the ATP synthesis-sustained respiration (energy-conserving), the uncoupling protein (UCP) activity-sustained respiration (energy-dissipating), the alternative oxidase(AOX)-mediated respiration (energy-dissipating), as well as the protein expression of UCP and AOX, and free fatty acid content exhibited different evolution patterns in the wild type and nor mutant that can be attributed to their climacteric/nonclimacteric properties, respectively. In the wild type, the climacteric respiratory burst observed in vitro depended totally on an increse in the cytochrome pathway activity sustained by ATP synthesis, while the second respiratory rise during the ripening stage was linked to a strong increase in AOX activity accompanied by an overexpression of AOX protein. In wild type mitochondria, the 10-microM linoleic acid-stimulated UCP-activity-dependent respiration remained constant during the whole fruit development except in senescence where general respiratory decay was observed.}, }
@article {pmid12675680, year = {2003}, author = {Punj, V and Chakrabarty, AM}, title = {Redox proteins in mammalian cell death: an evolutionarily conserved function in mitochondria and prokaryotes.}, journal = {Cellular microbiology}, volume = {5}, number = {4}, pages = {225-231}, doi = {10.1046/j.1462-5822.2003.00269.x}, pmid = {12675680}, issn = {1462-5814}, support = {ES-04050-17/ES/NIEHS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Azurin/genetics/metabolism ; Bacterial Proteins/genetics/*metabolism ; Biological Evolution ; Cell Death/*physiology ; Cytochrome c Group/metabolism ; Humans ; Mitochondria/enzymology/*metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Prokaryotic Cells/*metabolism ; Sequence Alignment ; Tumor Cells, Cultured ; }, abstract = {Mammalian cell mitochondria are believed to have prokaryotic ancestry. Mitochondria are not only the powerhouse of energy generation within the eukaryotic cell but they also play a major role in inducing apoptotic cell death through release of redox proteins such as cytochrome c and the apoptosis-inducing factor (AIF), a flavoprotein with NADH oxidase activity. Recent evidence indicates that some present day prokaryotes release redox proteins that induce apoptosis in mammalian cells through stabilization of the tumour suppressor protein p53. p53 interacts with mitochondria either directly or through activation of the genes for pro-apoptotic proteins such as Bax or NOXA or genes that encode redox enzymes responsible for the production of reactive oxygen species (ROS). The analogy between the ancient ancestors of present day bacteria, the mitochondria, and the present day bacteria with regard to their ability to release redox proteins for triggering mammalian cell death is an interesting example of functional conservation during the hundreds of millions of years of evolution. It is possible that the ancestors of the present day prokaryotes released redox proteins to kill the ancestors of the eukaryotes. During evolution of the mitochondria from prokaryotes as obligate endosymbionts, the mitochondria maintained the same functions to programme their own host cell death.}, }
@article {pmid12669803, year = {2003}, author = {Jamnongluk, W and Baimai, V and Kittayapong, P}, title = {Molecular phylogeny of tephritid fruit flies in the Bactrocera tau complex using the mitochondrial COI sequences.}, journal = {Genome}, volume = {46}, number = {1}, pages = {112-118}, doi = {10.1139/g02-113}, pmid = {12669803}, issn = {0831-2796}, mesh = {Animals ; *Evolution, Molecular ; Larva/genetics ; Mitochondria/*genetics ; *Phylogeny ; Tephritidae/*genetics ; }, abstract = {We compared sequences of the mitochondrial cytochrome oxidase I gene of eight species of the Bactrocera tau complex using Bactrocera dorsalis, Bactrocera pyrifoliae, Ceratitis capitata, Anopheles gambiae, and Locusta migratoria as outgroups. A 639-bp variable region was sequenced. The sequence divergence between species in the B. tau complex ranged from 0.06 to 28%, and up to 29% between the complex and its tephritid outgroups, B. dorsalis and C. capitata. According to the phylogenetic relationships, these members of the B. tau complex could be classified into four clades. Thus, species A and D form clades 1 and 3, respectively, while species C and I belong to clade 4. However, species B, E, and F form a distinct group, clade 2, and infested the fruits of non-cucurbit hosts. Host-plant shifts resulting in adaptive radiation and premating isolation among species might play an important role in species differentiation of the B. tau complex.}, }
@article {pmid12664168, year = {2003}, author = {Nozaki, H and Matsuzaki, M and Takahara, M and Misumi, O and Kuroiwa, H and Hasegawa, M and Shin-i, T and Kohara, Y and Ogasawara, N and Kuroiwa, T}, title = {The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids.}, journal = {Journal of molecular evolution}, volume = {56}, number = {4}, pages = {485-497}, doi = {10.1007/s00239-002-2419-9}, pmid = {12664168}, issn = {0022-2844}, mesh = {Cell Nucleus/*genetics ; Mitochondria/*genetics ; *Phylogeny ; Plastids/*genetics ; Rhodophyta/classification/*genetics ; Tubulin/genetics ; }, abstract = {Red algae are one of the main photosynthetic eukaryotic lineages and are characterized by primitive features, such as a lack of flagella and the presence of phycobiliproteins in the chloroplast. Recent molecular phylogenetic studies using nuclear gene sequences suggest two conflicting hypotheses (monophyly versus non-monophyly) regarding the relationships between red algae and green plants. Although kingdom-level phylogenetic analyses using multiple nuclear genes from a wide-range of eukaryotic lineages were very recently carried out, they used highly divergent gene sequences of the cryptomonad nucleomorph (as the red algal taxon) or incomplete red algal gene sequences. In addition, previous eukaryotic phylogenies based on nuclear genes generally included very distant archaebacterial sequences (designated as the outgroup) and/or amitochondrial organisms, which may carry unusual gene substitutions due to parasitism or the absence of mitochondria. Here, we carried out phylogenetic analyses of various lineages of mitochondria-containing eukaryotic organisms using nuclear multigene sequences, including the complete sequences from the primitive red alga Cyanidioschyzon merolae. Amino acid sequence data for two concatenated paralogous genes (alpha- and beta-tubulin) from mitochondria-containing organisms robustly resolved the basal position of the cellular slime molds, which were designated as the outgroup in our phylogenetic analyses. Phylogenetic analyses of 53 operational taxonomic units (OTUs) based on a 1525-amino-acid sequence of four concatenated nuclear genes (actin, elongation factor-1alpha, alpha-tubulin, and beta-tubulin) reliably resolved the phylogeny only in the maximum parsimonious (MP) analysis, which indicated the presence of two large robust monophyletic groups (Groups A and B) and the basal eukaryotic lineages (red algae, true slime molds, and amoebae). Group A corresponded to the Opisthokonta (Metazoa and Fungi), whereas Group B included various primary and secondary plastid-containing lineages (green plants, glaucophytes, euglenoids, heterokonts, and apicomplexans), Ciliophora, Kinetoplastida, and Heterolobosea. The red algae represented the sister lineage to Group B. Using 34 OTUs for which essentially the entire amino acid sequences of the four genes are known, MP, distance, quartet puzzling, and two types of maximum likelihood (ML) calculations all robustly resolved the monophyly of Group B, as well as the basal position of red algae within eukaryotic organisms. In addition, phylogenetic analyses of a concatenated 4639-amino-acid sequence for 12 nuclear genes (excluding the EF-2 gene) of 12 mitochondria-containing OTUs (including C. merolae) resolved a robust non-sister relationship between green plants and red algae within a robust monophyletic group composed of red algae and the eukaryotic organisms belonging to Group B. A new scenario for the origin and evolution of plastids is suggested, based on the basal phylogenetic position of the red algae within the large clade (Group B plus red algae). The primary plastid endosymbiosis likely occurred once in the common ancestor of this large clade, and the primary plastids were subsequently lost in the ancestor(s) of the Discicristata (euglenoids, Kinetoplastida, and Heterolobosea), Heterokontophyta, and Alveolata (apicomplexans and Ciliophora). In addition, a new concept of "Plantae" is proposed for phototrophic and nonphototrophic organisms belonging to Group B and red algae, on the basis of the common history of the primary plastid endosymbiosis. The Plantae include primary plastid-containing phototrophs and nonphototrophic eukaryotes that possibly contain genes of cyanobacterial origin acquired in the primary endosymbiosis.}, }
@article {pmid12657464, year = {2003}, author = {Linka, N and Hurka, H and Lang, BF and Burger, G and Winkler, HH and Stamme, C and Urbany, C and Seil, I and Kusch, J and Neuhaus, HE}, title = {Phylogenetic relationships of non-mitochondrial nucleotide transport proteins in bacteria and eukaryotes.}, journal = {Gene}, volume = {306}, number = {}, pages = {27-35}, doi = {10.1016/s0378-1119(03)00429-3}, pmid = {12657464}, issn = {0378-1119}, support = {AI-15035/AI/NIAID NIH HHS/United States ; }, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Alphaproteobacteria/*genetics ; Biological Transport ; Escherichia coli/genetics/metabolism ; Eukaryotic Cells/*metabolism ; Molecular Sequence Data ; Nucleotide Transport Proteins/*genetics/metabolism ; *Phylogeny ; Rhodophyta/genetics ; Species Specificity ; }, abstract = {Current knowledge about the nucleotide metabolism of intracellular bacteria is very limited. Here we report on the identification of nucleotide transport proteins (NTT) of two obligate endoparasites, Caedibacter caryophila and Holospora obtusa, both alpha-proteobacteria, which reside in the vegetative macronucleus of Paramecium caudatum. For comparative studies, we also identified the first nucleotide transporter in chloroplasts of a red alga, i.e. Galdieria sulphuraria, and further homologs in plant chloroplasts. Heterologous expression of the NTT proteins from C. caryophila, H. obtusa, and G. sulphuraria in Escherichia coli demonstrate that the nucleotide influx mediated by these transporters is specific for ATP and ADP. The NTT proteins of C. caryophila and H. obtusa exhibit substantial sequence identity with their counterparts in chloroplasts and intracellular bacterial pathogens of humans, but not with the nucleotide transport system of mitochondria. Comprehensive phylogenetic analyses of bacterial and chloroplast NTT proteins showed that homologs in chloroplasts from plants, and green, red, stramenopile and glaucocystophyte algae are monophyletic. In contrast, the evolutionary relationships of the bacterial counterparts appear highly complex. In the presented phylogeny, NTT proteins of C. caryophila and H. obtusa are only distantly related to one another, although these two taxa are close relatives in 16S rRNA trees. The tree topology indicates that some bacterial NTT paralogs have arisen by gene duplications and others by horizontal transfer.}, }
@article {pmid12655071, year = {2003}, author = {Whittle, CA and Johnston, MO}, title = {Male-biased transmission of deleterious mutations to the progeny in Arabidopsis thaliana.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {7}, pages = {4055-4059}, pmid = {12655071}, issn = {0027-8424}, mesh = {Arabidopsis/*genetics/radiation effects ; *Biological Evolution ; Chloroplasts/genetics ; Crosses, Genetic ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; Mitochondria/genetics ; *Mutation ; Pollen/genetics/*physiology ; *Ultraviolet Rays ; }, abstract = {The extent and cause of male-biased mutation rates, the higher number of mutations in sperm than in eggs, is currently an active and controversial subject. Recent evidence indicates that this male (sperm) bias not only occurs in animals but also in plants. The higher mutation rate in plant sperm was inferred from rates of evolution of neutral DNA regions, and the results were confined to the mitochondria and chloroplasts of gymnosperms. However, the relative transmission rates of deleterious mutations, which have substantial evolutionary consequences, have rarely been studied. Here, an investigation is described by using the hermaphroditic self-compatible flowering plant Arabidopsis thaliana, in which we artificially increased the rate of mutation in pollen (i.e., sperm donor) and maternal (i.e., egg donor) parents, by using two kinds of UV irradiation in parallel and separate experiments, and assessed the deleterious effects on fitness of the F(2) generation. The results show that more deleterious induced mutations are transmitted to the progeny by a sperm than by an egg. These findings provide the first experimental evidence that more deleterious mutations are inherited from sperm than from an egg in any organism. Possible causes underlying this male bias are discussed.}, }
@article {pmid12649480, year = {2003}, author = {Nardi, F and Spinsanti, G and Boore, JL and Carapelli, A and Dallai, R and Frati, F}, title = {Hexapod origins: monophyletic or paraphyletic?.}, journal = {Science (New York, N.Y.)}, volume = {299}, number = {5614}, pages = {1887-1889}, doi = {10.1126/science.1078607}, pmid = {12649480}, issn = {1095-9203}, mesh = {Animals ; Arthropods/anatomy &amp; histology/classification/*genetics ; Base Composition ; Biological Evolution ; Crustacea/anatomy &amp; histology/classification/*genetics ; DNA, Mitochondrial/genetics ; Insecta/anatomy &amp; histology/classification/*genetics ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Recent morphological and molecular evidence has changed interpretations of arthropod phylogeny and evolution. Here we compare complete mitochondrial genomes to show that Collembola, a wingless group traditionally considered as basal to all insects, appears instead to constitute a separate evolutionary lineage that branched much earlier than the separation of many crustaceans and insects and independently adapted to life on land. Therefore, the taxon Hexapoda, as commonly defined to include all six-legged arthropods, is not monophyletic.}, }
@article {pmid12649471, year = {2003}, author = {Thomas, RH}, title = {Evolution. Wingless insects and plucked chickens.}, journal = {Science (New York, N.Y.)}, volume = {299}, number = {5614}, pages = {1854-1855}, doi = {10.1126/science.1083465}, pmid = {12649471}, issn = {1095-9203}, mesh = {Animals ; Arthropods/classification/*genetics ; Base Composition ; Biological Evolution ; Crustacea/classification/*genetics ; DNA, Mitochondrial/genetics ; Insecta/classification/*genetics ; Mitochondria/genetics ; *Phylogeny ; Sequence Analysis, DNA ; }, }
@article {pmid12645546, year = {2003}, author = {Mashima, H and Ueda, N and Ohno, H and Suzuki, J and Ohnishi, H and Yasuda, H and Tsuchida, T and Kanamaru, C and Makita, N and Iiri, T and Omata, M and Kojima, I}, title = {A novel mitochondrial Ca2+-dependent solute carrier in the liver identified by mRNA differential display.}, journal = {The Journal of biological chemistry}, volume = {278}, number = {11}, pages = {9520-9527}, doi = {10.1074/jbc.m208398200}, pmid = {12645546}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Northern ; Blotting, Western ; Calcium/*metabolism ; Calcium-Binding Proteins/chemistry ; Cell Differentiation ; Cell Line ; Cloning, Molecular ; DNA, Complementary/metabolism ; Dexamethasone/pharmacology ; Gene Expression Profiling ; Gene Expression Regulation ; Genetic Vectors ; Glucocorticoids/pharmacology ; Hepatocytes/metabolism ; Humans ; Immunohistochemistry ; Liver/metabolism ; Membrane Transport Proteins/*chemistry/metabolism ; Mice ; Microscopy, Fluorescence ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Proteins/*chemistry/metabolism ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Protein Structure, Tertiary ; RNA, Messenger/metabolism ; Rats ; Recombinant Proteins/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Time Factors ; }, abstract = {Pancreatic AR42J cells have the feature of pluripotency of the precursor cells of the gut endoderm. Dexamethasone converts them to exocrine cells or liver cells. Using mRNA differential display techniques, we have identified a novel Ca2+-dependent member of the mitochondrial solute carrier superfamily, which is expressed during the course of differentiation, and have designated it MCSC. The corresponding cDNA comprises an open reading frame of 1407 base pairs encoding a polypeptide of 469 amino acids. The carboxyl-terminal-half of MCSC has high similarity with other mitochondrial carriers, and the amino-terminal-half has three canonical elongation factor-hand motifs and has calcium binding capacity. The deduced amino acid sequence revealed 79.1% homology to the rabbit peroxisomal Ca2+-dependent member of the mitochondrial superfamily, but the subcellular localization of the protein was exclusively mitochondrial, not peroxisomal. Northern blot and Western blot analyses revealed its predominant expression in the liver and the skeletal muscle. In the liver, the expression level of MCSC was higher in the adult stage than in the fetal stage, and MCSC was highly up-regulated in dexamethasone-treated AR42J cells before the expression of albumin. Taken together, MCSC may play an important role in regulating the function of hepatocytes rather than in differentiation in vivo.}, }
@article {pmid12644696, year = {2003}, author = {Tamasloukht, M and Séjalon-Delmas, N and Kluever, A and Jauneau, A and Roux, C and Bécard, G and Franken, P}, title = {Root factors induce mitochondrial-related gene expression and fungal respiration during the developmental switch from asymbiosis to presymbiosis in the arbuscular mycorrhizal fungus Gigaspora rosea.}, journal = {Plant physiology}, volume = {131}, number = {3}, pages = {1468-1478}, pmid = {12644696}, issn = {0032-0889}, mesh = {Cell Respiration/physiology ; Cloning, Molecular ; DNA, Complementary/chemistry/genetics ; Gene Expression Regulation, Fungal ; Hyphae/genetics/growth &amp; development/metabolism ; Mitochondria/genetics/*metabolism ; Molecular Sequence Data ; Mycorrhizae/*genetics/growth &amp; development/physiology ; Phylogeny ; Plant Roots/*metabolism/microbiology ; Pyruvate Carboxylase/genetics/metabolism ; RNA, Fungal/genetics/metabolism ; Sequence Analysis, DNA ; Spores/growth &amp; development ; Symbiosis/*genetics/physiology ; Transcriptional Activation ; }, abstract = {During spore germination, arbuscular mycorrhizal (AM) fungi show limited hyphal development in the absence of a host plant (asymbiotic). In the presence of root exudates, they switch to a new developmental stage (presymbiotic) characterized by extensive hyphal branching. Presymbiotic branching of the AM fungus Gigaspora rosea was induced in liquid medium by a semipurified exudate fraction from carrot (Daucus carota) root organ cultures. Changes in RNA accumulation patterns were monitored by differential display analysis. Differentially appearing cDNA fragments were cloned and further analyzed. Five cDNA fragments could be identified that show induced RNA accumulation 1 h after the addition of root exudate. Sequence similarities of two fragments to mammalian Nco4 and mitochondrial rRNA genes suggested that root exudates could influence fungal respiratory activity. To support this hypothesis, additional putative mitochondrial related-genes were shown to be induced by root exudates. These genes were identified after subtractive hybridization and putatively encode a pyruvate carboxylase and a mitochondrial ADP/ATP translocase. The gene GrosPyc1 for the pyruvate carboxylase was studied in more detail by cloning a cDNA and by quantifying its RNA accumulation. The hypothesis that respiratory activity of AM fungi is stimulated by root exudates was confirmed by physiological and cytological analyses in G. rosea and Glomus intraradices. Oxygen consumption and reducing activity of both fungi was induced after 3 and 2 h of exposition with the root factor, respectively, and the first respiration activation was detected in G. intraradices after approximately 90 min. In addition, changes in mitochondrial morphology, orientation, and overall biomass were detected in G. rosea after 4 h. In summary, the root-exuded factor rapidly induces the expression of certain fungal genes and, in turn, fungal respiratory activity before intense branching. This defines the developmental switch from asymbiosis to presymbiosis, first by gene activation (0.5-1 h), subsequently on the physiological level (1.5-3 h), and finally as a morphological response (after 5 h).}, }
@article {pmid12642645, year = {2002}, author = {Nishibori, M and Tsudzuki, M and Hayashi, T and Yamamoto, Y and Yasue, H}, title = {Complete nucleotide sequence of the Coturnix chinensis (blue-breasted quail) mitochondrial genome and a phylogenetic analysis with related species.}, journal = {The Journal of heredity}, volume = {93}, number = {6}, pages = {439-444}, doi = {10.1093/jhered/93.6.439}, pmid = {12642645}, issn = {0022-1503}, mesh = {Animals ; Codon/genetics ; Coturnix/*classification/*genetics ; DNA, Mitochondrial/*genetics ; Databases, Nucleic Acid ; Enzymes/genetics ; *Genome ; Mitochondria/*genetics ; *Phylogeny ; RNA, Transfer, Amino Acyl/genetics ; Species Specificity ; }, abstract = {Coturnix chinensis (blue-breasted quail) has been classically grouped in Galliformes Phasianidae Coturnix, based on morphologic features and biochemical evidence. Since the blue-breasted quail has the smallest body size among the species of Galliformes, in addition to a short generation time and an excellent reproductive performance, it is a possible model fowl for breeding and physiological studies of the Coturnix japonica (Japanese quail) and Gallus gallus domesticus (chicken), which are classified in the same family as blue-breasted quail. However, since its phylogenetic position in the family Phasianidae has not been determined conclusively, the sequence of the entire blue-breasted quail mitochondria (mt) genome was obtained to provide genetic information for phylogenetic analysis in the present study. The blue-breasted quail mtDNA was found to be a circular DNA of 16,687 base pairs (bp) with the same genomic structure as the mtDNAs of Japanese quail and chicken, though it is smaller than Japanese quail and chicken mtDNAs by 10 bp and 88 bp, respectively. The sequence identity of all mitochondrial genes, including those for 12S and 16S ribosomal RNAs, between blue-breasted quail and Japanese quail ranged from 84.5% to 93.5%; between blue-breasted quail and chicken, sequence identity ranged from 78.0% to 89.6%. In order to obtain information on the phylogenetic position of blue-breasted quail in Galliformes Phasianidae, the 2,184 bp sequence comprising NADH dehydrogenase subunit 2 and cytochrome b genes available for eight species in Galliformes [Japanese quail, chicken, Gallus varius (green junglefowl), Bambusicola thoracica (Chinese bamboo partridge), Pavo cristatus (Indian peafowl), Perdix perdix (gray partridge), Phasianus colchicus (ring-neck pheasant), and Tympanchus phasianellus (sharp-tailed grouse)] together with that of Aythya americana (redhead) were examined using a maximum likelihood (ML) method. The ML analyses on the first/second codon positions, the third codon positions, and amino acid sequence consistently demonstrated that blue-breasted quail and Japanese quail are in the same phylogenetic cluster.}, }
@article {pmid12626702, year = {2003}, author = {Bullerwell, CE and Forget, L and Lang, BF}, title = {Evolution of monoblepharidalean fungi based on complete mitochondrial genome sequences.}, journal = {Nucleic acids research}, volume = {31}, number = {6}, pages = {1614-1623}, pmid = {12626702}, issn = {1362-4962}, mesh = {Base Sequence ; Chytridiomycota/classification/*genetics ; Conserved Sequence/genetics ; DNA, Mitochondrial/chemistry/*genetics ; *Evolution, Molecular ; Gene Order ; Molecular Sequence Data ; Phylogeny ; RNA, Transfer/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {We have determined the complete mitochondrial DNA (mtDNA) sequences of three chytridiomycete fungi, Monoblepharella15, Harpochytrium94 and Harpochytrium105. Our phylogenetic analysis based on concatenated mitochondrial protein sequences confirms the placement of Mono blepharella15 together with Harpochytrium spp. and Hyaloraphidium curvatum within the taxonomic order Monoblepharidales, with overwhelming support. These four mtDNA sequences encode the standard fungal mitochondrial gene complement and, like certain other chytridiomycete fungi, encode a reduced complement of 7-9 tRNAs, some of which require 5'-tRNA editing to be functional. Highly conserved sequence elements were identified upstream of almost all protein-coding genes in the mtDNAs of Monoblepharella15 and both Harpochytrium species. Finally, a guanosine residue is conserved upstream of the predicted ATG or GTG start codons of almost every protein-coding gene in these genomes. The appearance of this G residue correlates with the presence of a non-canonical cytosine residue at position 37 in the anticodon loop of the mitochondrial initiator tRNAs. Based on the unorthodox features in these four genomes, we propose that a 4 bp interaction between the CAUC anticodon of these tRNAs and GAUG/GGUG codons is involved in translation initiation in monoblepharidalean mitochondria. Intriguingly, a similar interaction may also be involved in mitochondrial translation initiation in the sea anemone Metridium senile.}, }
@article {pmid12622195, year = {2002}, author = {Katoch, B and Sebastian, S and Sahdev, S and Padh, H and Hasnain, SE and Begum, R}, title = {Programmed cell death and its clinical implications.}, journal = {Indian journal of experimental biology}, volume = {40}, number = {5}, pages = {513-524}, pmid = {12622195}, issn = {0019-5189}, mesh = {*Apoptosis ; Biological Evolution ; Caspases/metabolism ; Mitochondria/physiology ; Necrosis ; }, abstract = {Cell death is a highly regulated process that is ubiquitous in all eukaryotes. Programmed cell death (PCD) is an integral part of both animal and plant development. Studies on apoptosis, the well characterized form of programmed cell death led to the identification of a central tripartite death switch i.e. apoptosome consisting of Apaf-1, Apaf-2 and Apaf-3. The caspases, a family of cysteine-dependent aspartate directed-proteases, constitute the central executioners of apoptosis. Much of the attention on programmed cell death is focused on caspases, however, cell death can still occur even when the caspase cascade is blocked, revealing the existence of nonapoptotic alternative pathway(s) of cell death. The mitochondrial release of cytochrome C following a PCD inducing stimulus in both plants and animals suggests the evolutionary conservation of death pathways. Dysregulation of apoptosis may be related to the development of several disease states as well as ageing. Excessive apoptosis is associated with neurodegenerative disorders, AIDS etc., whereas deficient apoptosis is associated with cancer, auto-immunity, viral infections etc. Understanding the regulation of programmed cell death would throw light in designing drugs and gene therapies that can target specific molecules in the apoptotic pathway opening the vistas for new therapeutic endeavors in many areas of medicine.}, }
@article {pmid12615939, year = {2003}, author = {Miyagishima, SY and Nishida, K and Mori, T and Matsuzaki, M and Higashiyama, T and Kuroiwa, H and Kuroiwa, T}, title = {A plant-specific dynamin-related protein forms a ring at the chloroplast division site.}, journal = {The Plant cell}, volume = {15}, number = {3}, pages = {655-665}, pmid = {12615939}, issn = {1040-4651}, mesh = {Algal Proteins/*genetics/metabolism ; Amino Acid Sequence ; Arabidopsis Proteins/genetics/metabolism ; Cell Division/genetics/physiology ; Chloroplasts/*metabolism/ultrastructure ; Cytosol/metabolism ; Dynamin II/*genetics/metabolism ; Dynamins/*genetics/metabolism ; GTP-Binding Proteins/genetics/metabolism ; Immunohistochemistry ; Microscopy, Immunoelectron ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics/metabolism ; Rhodophyta/genetics/metabolism/ultrastructure ; Sequence Homology, Amino Acid ; }, abstract = {Chloroplasts have retained the bacterial FtsZ for division, whereas mitochondria lack FtsZ except in some lower eukaryotes. Instead, mitochondrial division involves a dynamin-related protein, suggesting that chloroplasts retained the bacterial division system, whereas a dynamin-based system replaced the bacterial system in mitochondria during evolution. In this study, we identified a novel plant-specific group of dynamins from the primitive red alga Cyanidioschyzon merolae. Synchronization of chloroplast division and immunoblot analyses showed that the protein (CmDnm2) associates with the chloroplast only during division. Immunocytochemical analyses showed that CmDnm2 appears in cytoplasmic patches just before chloroplast division and is recruited to the cytosolic side of the chloroplast division site to form a ring in the late stage of division. The ring constricts until division is complete, after which it disappears. These results show that a dynamin-related protein also participates in chloroplast division and that its behavior differs from that of FtsZ and plastid-dividing rings that form before constriction at the site of division. Combined with the results of a recent study of mitochondrial division in Cyanidioschyzon, our findings led us to hypothesize that when first established in lower eukaryotes, mitochondria and chloroplasts divided using a very similar system that included the FtsZ ring, the plastid-dividing/mitochondrion-dividing ring, and the dynamin ring.}, }
@article {pmid12615497, year = {2003}, author = {Matessi, C and Saino, N}, title = {Mother's mitochondria and optimal offspring sex ratio.}, journal = {Theoretical population biology}, volume = {63}, number = {2}, pages = {147-157}, doi = {10.1016/s0040-5809(02)00059-x}, pmid = {12615497}, issn = {0040-5809}, mesh = {Animals ; Biological Evolution ; Cell Division/genetics ; Female ; *Genetic Variation ; Genetics, Population ; Italy ; Male ; Mitochondria/*genetics ; Mutation/genetics ; Reproduction/genetics ; *Sex Ratio ; }, abstract = {In certain cases, predicted by evolutionary theory of sex-allocation and confirmed by empirical evidence, animals adaptively change their progeny sex-ratio according to individual circumstances. Here we argue that a similar response of offspring sex-ratio must exist in relation to genetic variation of mothers' mitochondria, as a consequence of maternal inheritance of these organelles and of their influence on fitness resulting from their crucial role in metabolism. In fact, a mathematical analysis of evolutionary dynamics of sex-allocation mutants demonstrates that natural selection promotes an evolutionarily stable allocation policy where mothers with defective mitochondria generate only sons, while those with optimal mitochondria have female biased progenies.}, }
@article {pmid12612835, year = {2003}, author = {Creer, S and Malhotra, A and Thorpe, RS and Stöcklin, RS and Favreau, PS and Hao Chou, WS}, title = {Genetic and ecological correlates of intraspecific variation in pitviper venom composition detected using matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS) and isoelectric focusing.}, journal = {Journal of molecular evolution}, volume = {56}, number = {3}, pages = {317-329}, doi = {10.1007/s00239-002-2403-4}, pmid = {12612835}, issn = {0022-2844}, mesh = {Animals ; Crotalid Venoms/*genetics ; Cytochrome b Group/genetics ; Evolution, Molecular ; *Genetic Variation ; Isoelectric Focusing ; Mitochondria/genetics ; Phylogeny ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Taiwan ; Viperidae/*genetics ; }, abstract = {The ability to detect biochemical diversity in animal venoms has wide-ranging implications for a diverse array of scientific disciplines. Matrix-assisted laser desorption time-of-flight mass spectrometry (and, for comparative purposes, isoelectric focusing) were used to characterize venoms from a geographically diverse sample of Trimeresurus stejnegeri (n < 229) from Taiwan. Previously unrealized levels of heterogeneity were detected in venom phospholipase A(2) isoforms (PLA(2)) and in whole venom profiles. Geographic variation in venom was primarily between Taiwan and two Pacific islets. Despite the common assumption that venom variation is a product of neutral molecular evolution, statistical testing failed to link venom variation with phylogenetic descent convincingly. Instead, pronounced differences in venom composition may be the product of natural selection for regional diets or of independent founder effects. More data are required on the functional differences between the isoforms to distinguish between these alternatives.}, }
@article {pmid12612582, year = {2003}, author = {Green, P and Ewing, B and Miller, W and Thomas, PJ and ,  and Green, ED}, title = {Transcription-associated mutational asymmetry in mammalian evolution.}, journal = {Nature genetics}, volume = {33}, number = {4}, pages = {514-517}, doi = {10.1038/ng1103}, pmid = {12612582}, issn = {1061-4036}, mesh = {Animals ; Biological Evolution ; Cell Lineage ; Chromosomes, Human, Pair 22 ; CpG Islands ; *DNA Mutational Analysis ; Databases as Topic ; Humans ; Models, Genetic ; Papio ; RNA, Messenger/metabolism ; Sequence Analysis, DNA ; *Transcription, Genetic ; }, abstract = {Although mutation is commonly thought of as a random process, evolutionary studies show that different types of nucleotide substitution occur with widely varying rates that presumably reflect biases intrinsic to mutation and repair mechanisms. A strand asymmetry, the occurrence of particular substitution types at higher rates than their complementary types, that is associated with DNA replication has been found in bacteria and mitochondria. A strand asymmetry that is associated with transcription and attributable to higher rates of cytosine deamination on the coding strand has been observed in enterobacteria. Here, we describe a qualitatively different transcription-associated strand asymmetry in mammals, which may be a byproduct of transcription-coupled repair in germline cells. This mutational asymmetry has acted over long periods of time to produce a compositional asymmetry, an excess of G+T over A+C on the coding strand, in most genes. The mutational and compositional asymmetries can be used to detect the orientations and approximate extents of transcribed regions.}, }
@article {pmid12609740, year = {2003}, author = {Tsuji, H and Tsutsumi, N and Sasaki, T and Hirai, A and Nakazono, M}, title = {Organ-specific expressions and chromosomal locations of two mitochondrial aldehyde dehydrogenase genes from rice (Oryza sativa L.), ALDH2a and ALDH2b.}, journal = {Gene}, volume = {305}, number = {2}, pages = {195-204}, doi = {10.1016/s0378-1119(03)00383-4}, pmid = {12609740}, issn = {0378-1119}, mesh = {Aldehyde Dehydrogenase/*genetics/metabolism ; Amino Acid Sequence ; Blotting, Northern ; Blotting, Southern ; Blotting, Western ; Chromosome Mapping ; Chromosomes, Plant/*genetics ; DNA, Complementary/chemistry/genetics ; DNA, Plant/genetics ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Isoenzymes/genetics/metabolism ; Mitochondria/*enzymology ; Molecular Sequence Data ; Multigene Family/genetics ; Oryza/enzymology/*genetics/growth &amp; development ; Phylogeny ; Plant Leaves/enzymology/*genetics/growth &amp; development ; Recombinant Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Recent studies have suggested that mitochondrial aldehyde dehydrogenase (aldehyde:NAD(P)(+) oxidoreductase, EC 1.2.1.3) (ALDH2) plays essential roles in pollen development in plants. Rice (Oryza sativa L.) ALDH2 is encoded by at least two ALDH2 genes, one of which (ALDH2a) was previously identified. In this study, to understand the roles of ALDH2 in rice, we isolated and characterized a cDNA clone encoding another rice ALDH2 (ALDH2b). An in vitro ALDH assay indicated that ALDH2b possesses an NAD(+)-linked activity for oxidation of acetaldehyde, glycolaldehyde and propionaldehyde. Northern blot and immunoblot analyses revealed that ALDH2b was constitutively present in all the organs examined, whereas ALDH2a was expressed in leaves of dark-grown seedlings and panicles. By RFLP linkage mapping, the ALDH2a and ALDH2b genes were mapped to the long arm of chromosome 2 and the short arm of chromosome 6, respectively. We suggest that the rice ALDH2a and ALDH2b genes are orthologues of maize mitochondrial ALDH genes, rf2b and rf2a, respectively.}, }
@article {pmid12601042, year = {2003}, author = {Ledee, DR and Booton, GC and Awwad, MH and Sharma, S and Aggarwal, RK and Niszl, IA and Markus, MB and Fuerst, PA and Byers, TJ}, title = {Advantages of using mitochondrial 16S rDNA sequences to classify clinical isolates of Acanthamoeba.}, journal = {Investigative ophthalmology &amp; visual science}, volume = {44}, number = {3}, pages = {1142-1149}, doi = {10.1167/iovs.02-0485}, pmid = {12601042}, issn = {0146-0404}, support = {R01 EY009073-10/EY/NEI NIH HHS/United States ; EY09073/EY/NEI NIH HHS/United States ; }, mesh = {Acanthamoeba/*classification/*genetics/isolation &amp; purification ; Acanthamoeba Keratitis/parasitology ; Animals ; DNA, Protozoan/genetics ; DNA, Ribosomal/*genetics ; Genotype ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {PURPOSE: This work was intended to test the classification of Acanthamoeba into genotypes based on nuclear ribosomal RNA gene (18S rDNA, Rns) sequences. Nearly all Acanthamoeba keratitis (AK) isolates are genotype RnsT4. This marked phylogenetic localization is presumably either due to an innate potential for pathogenicity or to a peculiarity of the gene sequences used. To differentiate between these possibilities, relationships among isolates have been reexamined, using a second gene.<br><br>METHODS: Phylogenetic relationships among isolates of Acanthamoeba were studied, using sequences of the mitochondrial small subunit ribosomal RNA gene (16S rDNA; rns). Genotypes based on complete sequences of approximately 1540 bp were determined for 68 strains, by using multiple phylogenetic analyses.<br><br>RESULTS: Each strain's mitochondria contained a single intron-free rns sequence (allele). The 68 strains had 35 different sequences. Twenty-eight strains had unique sequences, and 40 strains each shared one of the seven remaining sequences. Eleven mitochondrial rns genotypes corresponding to 11 of 12 previously described nuclear Rns genotypes were identified. Genotype rnsT4 was subdivided into eight distinct clades, with seven including Acanthamoeba keratitis (AK) isolates.<br><br>CONCLUSIONS: The phylogenetic clustering of AK isolates was confirmed and thus is not specific to the nuclear gene. Rns and rns sequences are both suitable for genotyping of ACANTHAMOEBA: However, the mitochondrial sequences are shorter and more consistent in length, have a higher percentage of alignable bases for sequence comparisons, and have none of the complications caused by multiple alleles or introns, which are occasionally found in Rns. In addition, the more common occurrence of strains with identical rns sequences simplifies identification and clustering of isolates.}, }
@article {pmid12598691, year = {2003}, author = {Kvist, L and Martens, J and Nazarenko, AA and Orell, M}, title = {Paternal leakage of mitochondrial DNA in the great tit (Parus major).}, journal = {Molecular biology and evolution}, volume = {20}, number = {2}, pages = {243-247}, doi = {10.1093/molbev/msg025}, pmid = {12598691}, issn = {0737-4038}, mesh = {Alleles ; Animals ; *DNA, Mitochondrial ; Haplotypes ; Likelihood Functions ; Mitochondria ; Mutation ; Phylogeny ; Sequence Analysis, DNA ; Songbirds/*genetics ; }, abstract = {Animal mitochondrial DNA is normally inherited clonally from a mother to all her offspring. Mitochondrial heteroplasmy, the occurrence of more than one mitochondrial haplotype within an individual, can be generated by relatively common somatic mutations within an individual, by heteroplasmy of the oocytes, or by paternal leakage of mitochondria during fertilization of an egg. This biparental inheritance has so far been reported only in mice, mussels, Drosophila, and humans. Here we present evidence that paternal leakage occurs in a bird, the great tit Parus major. The major and minor subspecies groups of the great tit mix in the middle Amur Valley in far-eastern Siberia, where we found a bird that possessed the very distinct haplotypes of the two groups. To our knowledge this is the first report of paternal leakage in birds.}, }
@article {pmid12598689, year = {2003}, author = {Zigler, KS and Lessios, HA}, title = {Evolution of bindin in the pantropical sea urchin Tripneustes: comparisons to bindin of other genera.}, journal = {Molecular biology and evolution}, volume = {20}, number = {2}, pages = {220-231}, doi = {10.1093/molbev/msg020}, pmid = {12598689}, issn = {0737-4038}, mesh = {Alleles ; Amino Acid Sequence ; Animals ; Cloning, Molecular ; Codon ; DNA, Complementary/metabolism ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Geography ; Glycoproteins/*genetics ; Likelihood Functions ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Receptors, Cell Surface ; Sea Urchins ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {Bindin, a sea urchin sperm protein, mediates sperm-egg attachment and membrane fusion and is thus important in species recognition and speciation. Patterns of bindin variation differed among three genera that had been studied previously. In two genera of the superorder Camarodonta, Echinometra and Strongylocentrotus, both of which contain sympatric species, bindin is highly variable within and between species; a region of the molecule evolves at high rates under strong positive selection. In Arbacia, which belongs to the superorder Stirodonta and whose extant species are all allopatric, bindin variation is low, and there is no evidence of positive selection. We cloned and sequenced bindin from Tripneustes, a sea urchin that belongs to the Camarodonta but whose three species are found in different oceans. Worldwide sampling of bindin alleles shows that the bindin of Tripneustes (1) contains the highly conserved core characteristic of all other bindins characterized to date, (2) has an intron in the same position, and (3) has approximately the same length. Its structure is more like that of bindin from other camarodont sea urchins than to bindin from the stirodont ARBACIA: The resemblances to other camarodonts include a glycine-rich repeat structure upstream of the core and lack of a hydrophobic domain 3' of the core, a characteristic of Arbacia bindin. Yet the mode of evolution of Tripneustes bindin is more like that of Arbacia. Differences between bindins of the Caribbean Tripneustes ventricosus and the eastern Pacific T. depressus, separated for 3 my by the Isthmus of Panama, are limited to four amino acid changes and a single indel. There are no fixed amino acid differences or indels between T. depressus from the eastern Pacific and T. gratilla from the Indo-Pacific. Bindin of Tripneustes, like that of Arbacia, also shows no evidence of diversifying selection that would manifest itself in a higher proportion of amino acid replacements than of silent nucleotide substitutions. When the rate of intrageneric bindin divergence is standardized by dividing it by cytochrome oxidase I (COI) divergence, Tripneustes and Arbacia show a lower ratio of bindin to COI substitutions between the species of each genus than exists between the species of either Echinometra or Strongylocentrotus. Thus, mode of bindin evolution is not correlated with phylogenetic affinities or molecular structure, but rather with whether the species in a genus are allopatric or sympatric. For a molecule involved in gametic recognition, this would suggest a pattern of evolution via reinforcement. However, in bindin the process that gave rise to this pattern is not likely to have been selection to avoid hybridization, because there is no excess of amino acid replacements between species versus within species in the bindins of Echinometra and Strongylocentrotus, as would have been expected if specific recognition were the driving force in their evolution. We suggest instead that the pattern of reinforcement is a secondary effect of the ability of species with rapidly evolving bindins to coexist in sympatry.}, }
@article {pmid12598129, year = {2003}, author = {Herrmann, JM}, title = {Converting bacteria to organelles: evolution of mitochondrial protein sorting.}, journal = {Trends in microbiology}, volume = {11}, number = {2}, pages = {74-79}, doi = {10.1016/s0966-842x(02)00033-1}, pmid = {12598129}, issn = {0966-842X}, mesh = {Bacterial Proteins/chemistry/genetics/*metabolism ; *Evolution, Molecular ; Intracellular Membranes/metabolism ; Membrane Proteins/chemistry/*metabolism ; Mitochondria/*metabolism ; Models, Biological ; Protein Transport/physiology ; }, abstract = {During the evolution of mitochondria from free-living alpha-proteobacteria, many bacterial genes were transferred into the nuclear genome of eukaryotic cells. This required the development of both targeting signals on the respective polypeptides and protein translocation machineries (translocases) in the mitochondrial membranes. Most components of these translocases have no obvious homologies to bacterial proteins or proteins found in other organelles. Membrane integration of many inner membrane proteins, however, apparently occurs via a conserved sorting pathway whose components and characteristics resemble protein translocation in bacteria. Consistent with this, the topogenic signals of these mitochondrial inner membrane proteins mimic those of bacterial proteins. The requirement for post-translational transport to their final destination has placed considerable constraints on the evolution of mitochondrial protein sequences.}, }
@article {pmid12596945, year = {2002}, author = {Minke, B}, title = {The TRP calcium channel and retinal degeneration.}, journal = {Advances in experimental medicine and biology}, volume = {514}, number = {}, pages = {601-622}, doi = {10.1007/978-1-4615-0121-3_34}, pmid = {12596945}, issn = {0065-2598}, mesh = {Animals ; Calcium/metabolism ; Calcium Channels/metabolism/*physiology ; *Drosophila Proteins ; Drosophila melanogaster ; Insect Proteins/metabolism/*physiology ; Mitochondria/metabolism ; Models, Biological ; Mutation ; Photoreceptor Cells, Invertebrate/*physiology ; Protein Structure, Tertiary ; Retinal Degeneration/*metabolism/pathology ; Transient Receptor Potential Channels ; }, abstract = {The Drosophila light activated channel TRP is the founding member of a large and diverse family of channel proteins that is conserved throughout evolution. These channels are Ca2+ permeable and have been implicated as important component of cellular Ca2+ homeostasis in neuronal and non-neuronal cells. The power of the molecular genetics of Drosophila has yielded several mutants in which constitutive activity of TRP leads to a rapid retinal degeneration in the dark. Metabolic stress activates rapidly and reversibly the TRP channels in the dark in a constitutive manner by a still unknown mechanism. The link of TRP gating to the metabolic state of the cell is shared also by mammalian homologues of TRP and makes cells expressing TRP extremely vulnerable to metabolic stress, a mechanism that may underlie retinal degeneration and neuronal cell death.}, }
@article {pmid12595256, year = {2003}, author = {Gille, C and Goede, A and Schlöetelburg, C and Preissner, R and Kloetzel, PM and Göbel, UB and Frömmel, C}, title = {A comprehensive view on proteasomal sequences: implications for the evolution of the proteasome.}, journal = {Journal of molecular biology}, volume = {326}, number = {5}, pages = {1437-1448}, doi = {10.1016/s0022-2836(02)01470-5}, pmid = {12595256}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Animals ; Archaea/chemistry/*metabolism ; Bacteria/chemistry/*metabolism ; *Biological Evolution ; Catalytic Domain ; Cysteine Endopeptidases/*genetics ; Eukaryotic Cells/chemistry/*metabolism ; *Genome ; Heat-Shock Proteins/*physiology ; Humans ; Molecular Sequence Data ; Multienzyme Complexes/*genetics ; Phylogeny ; Proteasome Endopeptidase Complex ; Protein Subunits ; Sequence Alignment ; Sequence Homology, Amino Acid ; Ubiquitins/*metabolism ; }, abstract = {Proteasomes are large multimeric self-compartmentizing proteases, which play a crucial role in the clearance of misfolded proteins, breakdown of regulatory proteins, processing of proteins by specific partial proteolysis, cell cycle control as well as preparation of peptides for immune presentation. Two main types can be distinguished by their different tertiary structure: the 20S proteasome and the proteasome-like heat shock protein encoded by heat shock locus V, hslV. Usually, each biological kingdom is characterized by its specific type of proteasome. The 20S proteasomes occur in eukarya and archaea whereas hslV protease is prevalent in bacteria. To verify this rule we applied a genome-wide sequence search to identify proteasomal sequences in data of finished and yet unfinished genome projects. We found several exceptions to this paradigm: (1) Protista: in addition to the 20S proteasome, Leishmania, Trypanosoma and Plasmodium contained hslV, which may have been acquired from an alpha-proteobacterial progenitor of mitochondria. (2) Bacteria: for Magnetospirillum magnetotacticum and Enterococcus faecium we found that each contained two distinct hslVs due to gene duplication or horizontal transfer. Including unassembled data into the analyses we confirmed that a number of bacterial genomes do not contain any proteasomal sequence due to gene loss. (3) High G+C Gram-positives: we confirmed that high G+C Gram-positives possess 20S proteasomes rather than hslV proteases. The core of the 20S proteasome consists of two distinct main types of homologous monomers, alpha and beta, which differentiated into seven subtypes by further gene duplications. By looking at the genome of the intracellular pathogen Encephalitozoon cuniculi we were able to show that differentiation of beta-type subunits into different subtypes occurred earlier than that of alpha-subunits. Additionally, our search strategy had an important methodological consequence: a comprehensive sequence search for a particular protein should also include the raw sequence data when possible because proteins might be missed in the completed assembled genome. The structure-based multiple proteasomal alignment of 433 sequences from 143 organisms can be downloaded from the URL dagger and will be updated regularly.}, }
@article {pmid12594929, year = {2003}, author = {}, title = {General discussion.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {358}, number = {1429}, pages = {217-222}, pmid = {12594929}, issn = {0962-8436}, mesh = {*Biological Evolution ; Eukaryotic Cells/*cytology/*metabolism ; Mitochondria/genetics/metabolism ; *Models, Biological ; Organelles/metabolism ; Symbiosis ; Time Factors ; }, }
@article {pmid12594928, year = {2003}, author = {van Hellemond, JJ and van der Klei, A and van Weelden, SW and Tielens, AG}, title = {Biochemical and evolutionary aspects of anaerobically functioning mitochondria.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {358}, number = {1429}, pages = {205-13; discussion 213-5}, pmid = {12594928}, issn = {0962-8436}, mesh = {Acetates/metabolism ; Aerobiosis ; *Anaerobiosis ; Animals ; *Biological Evolution ; Electron Transport ; Fermentation ; Mitochondria/chemistry/enzymology/*metabolism ; Phylogeny ; Succinate Dehydrogenase/metabolism ; Ubiquinone/*analogs &amp; derivatives/metabolism ; }, abstract = {Mitochondria are usually considered to be the powerhouses of the cell and to be responsible for the aerobic production of ATP. However, many eukaryotic organisms are known to possess anaerobically functioning mitochondria, which differ significantly from classical aerobically functioning mitochondria. Recently, functional and phylogenetic studies on some enzymes involved clearly indicated an unexpected evolutionary relationship between these anaerobically functioning mitochondria and the classical aerobic type. Mitochondria evolved by an endosymbiotic event between an anaerobically functioning archaebacterial host and an aerobic alpha-proteobacterium. However, true anaerobically functioning mitochondria, such as found in parasitic helminths and some lower marine organisms, most likely did not originate directly from the pluripotent ancestral mitochondrion, but arose later in evolution from the aerobic type of mitochondria after these were already adapted to an aerobic way of life by losing their anaerobic capacities. This review will focus on some biochemical and evolutionary aspects of these fermentative mitochondria, with special attention to fumarate reductase, the synthesis of the rhodoquinone involved, and the enzymes involved in acetate production (acetate : succinate CoA-transferase and succinyl CoA-synthetase).}, }
@article {pmid12594927, year = {2003}, author = {Embley, TM and van der Giezen, M and Horner, DS and Dyal, PL and Foster, P}, title = {Mitochondria and hydrogenosomes are two forms of the same fundamental organelle.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {358}, number = {1429}, pages = {191-201; discussion 201-2}, pmid = {12594927}, issn = {0962-8436}, mesh = {Anaerobiosis ; *Biological Evolution ; Eukaryotic Cells/*cytology/enzymology/metabolism ; Hydrogen/*metabolism ; Hydrogenase/genetics/metabolism ; Mitochondria/*metabolism ; Organelles/*metabolism ; Phylogeny ; }, abstract = {Published data suggest that hydrogenosomes, organelles found in diverse anaerobic eukaryotes that make energy and hydrogen, were once mitochondria. As hydrogenosomes generally lack a genome, the conversion is probably one way. The sources of the key hydrogenosomal enzymes, pyruvate : ferredoxin oxidoreductase (PFO) and hydrogenase, are not resolved by current phylogenetic analyses, but it is likely that both were present at an early stage of eukaryotic evolution. Once thought to be restricted to a few unusual anaerobic eukaryotes, the proteins are intimately integrated into the fabric of diverse eukaryotic cells, where they are targeted to different cell compartments, and not just hydrogenosomes. There is no evidence supporting the view that PFO and hydrogenase originated from the mitochondrial endosymbiont, as posited by the hydrogen hypothesis for eukaryogenesis. Other organelles derived from mitochondria have now been described in anaerobic and parasitic microbial eukaryotes, including species that were once thought to have diverged before the mitochondrial symbiosis. It thus seems possible that all eukaryotes may eventually be shown to contain an organelle of mitochondrial ancestry, to which different types of biochemistry can be targeted. It remains to be seen if, despite their obvious differences, this family of organelles shares a common function of importance for the eukaryotic cell, other than energy production, that might provide the underlying selection pressure for organelle retention.}, }
@article {pmid12594925, year = {2003}, author = {Andersson, SG and Karlberg, O and Canbäck, B and Kurland, CG}, title = {On the origin of mitochondria: a genomics perspective.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {358}, number = {1429}, pages = {165-77; discussion 177-9}, pmid = {12594925}, issn = {0962-8436}, mesh = {Adenosine Triphosphate/metabolism ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; Eukaryotic Cells/cytology ; *Evolution, Molecular ; *Genomics ; Mitochondria/*genetics/metabolism ; Phylogeny ; Protein Transport ; }, abstract = {The availability of complete genome sequence data from both bacteria and eukaryotes provides information about the contribution of bacterial genes to the origin and evolution of mitochondria. Phylogenetic analyses based on genes located in the mitochondrial genome indicate that these genes originated from within the alpha-proteobacteria. A number of ancestral bacterial genes have also been transferred from the mitochondrial to the nuclear genome, as evidenced by the presence of orthologous genes in the mitochondrial genome in some species and in the nuclear genome of other species. However, a multitude of mitochondrial proteins encoded in the nucleus display no homology to bacterial proteins, indicating that these originated within the eukaryotic cell subsequent to the acquisition of the endosymbiont. An analysis of the expression patterns of yeast nuclear genes coding for mitochondrial proteins has shown that genes predicted to be of eukaryotic origin are mainly translated on polysomes that are free in the cytosol whereas those of putative bacterial origin are translated on polysomes attached to the mitochondrion. The strong relationship with alpha-proteobacterial genes observed for some mitochondrial genes, combined with the lack of such a relationship for others, indicates that the modern mitochondrial proteome is the product of both reductive and expansive processes.}, }
@article {pmid12594919, year = {2003}, author = {Herrmann, RG and Maier, RM and Schmitz-Linneweber, C}, title = {Eukaryotic genome evolution: rearrangement and coevolution of compartmentalized genetic information.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {358}, number = {1429}, pages = {87-97; discussion 97}, pmid = {12594919}, issn = {0962-8436}, mesh = {Atropa belladonna/cytology/genetics ; Eukaryotic Cells/cytology/*metabolism ; *Evolution, Molecular ; *Genome ; Plants/*genetics ; Plastids/genetics ; RNA Editing ; Nicotiana/cytology/genetics ; Transcription, Genetic ; }, abstract = {The plant cell operates with an integrated, compartmentalized genome consisting of nucleus/cytosol, plastids and mitochondria that, in its entirety, is regulated in time, quantitatively, in multicellular organisms and also in space. This genome, as do genomes of eukaryotes in general, originated in endosymbiotic events, with at least three cells, and was shaped phylogenetically by a massive and highly complex restructuring and intermixing of the genetic potentials of the symbiotic partners and by lateral gene transfer. This was accompanied by fundamental changes in expression signals in the entire system at almost all regulatory levels. The gross genome rearrangements contrast with a highly specific compartmental interplay, which becomes apparent in interspecific nuclear-plastid cybrids or hybrids. Organelle exchanges, even between closely related species, can greatly disturb the intracellular genetic balance ("hybrid bleaching"), which is indicative of compartmental coevolution and is of relevance for speciation processes. The photosynthetic machinery of plastids, which is embedded in that genetic machinery, is an appealing model to probe into genomic and organismic evolution and to develop functional molecular genomics. We have studied the reciprocal Atropa belladonna-Nicotiana tabacum cybrids, which differ markedly in their phenotypes, and found that transcriptional and post-transcriptional processes can contribute to genome/plastome incompatibility. Allopolyploidy can influence this phenomenon by providing an increased, cryptic RNA editing potential and the capacity to maintain the integrity of organelles of different taxonomic origins.}, }
@article {pmid12594918, year = {2003}, author = {Martin, W and Russell, MJ}, title = {On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {358}, number = {1429}, pages = {59-83; discussion 83-5}, pmid = {12594918}, issn = {0962-8436}, mesh = {Biochemical Phenomena ; Biochemistry ; *Biological Evolution ; Eukaryotic Cells/*cytology/*metabolism ; *Models, Biological ; Origin of Life ; Prokaryotic Cells/*cytology/*metabolism ; Time Factors ; }, abstract = {All life is organized as cells. Physical compartmentation from the environment and self-organization of self-contained redox reactions are the most conserved attributes of living things, hence inorganic matter with such attributes would be life's most likely forebear. We propose that life evolved in structured iron monosulphide precipitates in a seepage site hydrothermal mound at a redox, pH and temperature gradient between sulphide-rich hydrothermal fluid and iron(II)-containing waters of the Hadean ocean floor. The naturally arising, three-dimensional compartmentation observed within fossilized seepage-site metal sulphide precipitates indicates that these inorganic compartments were the precursors of cell walls and membranes found in free-living prokaryotes. The known capability of FeS and NiS to catalyse the synthesis of the acetyl-methylsulphide from carbon monoxide and methylsulphide, constituents of hydrothermal fluid, indicates that pre-biotic syntheses occurred at the inner surfaces of these metal-sulphide-walled compartments, which furthermore restrained reacted products from diffusion into the ocean, providing sufficient concentrations of reactants to forge the transition from geochemistry to biochemistry. The chemistry of what is known as the RNA-world could have taken place within these naturally forming, catalyticwalled compartments to give rise to replicating systems. Sufficient concentrations of precursors to support replication would have been synthesized in situ geochemically and biogeochemically, with FeS (and NiS) centres playing the central catalytic role. The universal ancestor we infer was not a free-living cell, but rather was confined to the naturally chemiosmotic, FeS compartments within which the synthesis of its constituents occurred. The first free-living cells are suggested to have been eubacterial and archaebacterial chemoautotrophs that emerged more than 3.8 Gyr ago from their inorganic confines. We propose that the emergence of these prokaryotic lineages from inorganic confines occurred independently, facilitated by the independent origins of membrane-lipid biosynthesis: isoprenoid ether membranes in the archaebacterial and fatty acid ester membranes in the eubacterial lineage. The eukaryotes, all of which are ancestrally heterotrophs and possess eubacterial lipids, are suggested to have arisen ca. 2 Gyr ago through symbiosis involving an autotrophic archaebacterial host and a heterotrophic eubacterial symbiont, the common ancestor of mitochondria and hydrogenosomes. The attributes shared by all prokaryotes are viewed as inheritances from their confined universal ancestor. The attributes that distinguish eubacteria and archaebacteria, yet are uniform within the groups, are viewed as relics of their phase of differentiation after divergence from the non-free-living universal ancestor and before the origin of the free-living chemoautotrophic lifestyle. The attributes shared by eukaryotes with eubacteria and archaebacteria, respectively, are viewed as inheritances via symbiosis. The attributes unique to eukaryotes are viewed as inventions specific to their lineage. The origin of the eukaryotic endomembrane system and nuclear membrane are suggested to be the fortuitous result of the expression of genes for eubacterial membrane lipid synthesis by an archaebacterial genetic apparatus in a compartment that was not fully prepared to accommodate such compounds, resulting in vesicles of eubacterial lipids that accumulated in the cytosol around their site of synthesis. Under these premises, the most ancient divide in the living world is that between eubacteria and archaebacteria, yet the steepest evolutionary grade is that between prokaryotes and eukaryotes.}, }
@article {pmid12594916, year = {2003}, author = {Allen, JF}, title = {The function of genomes in bioenergetic organelles.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {358}, number = {1429}, pages = {19-37; discussion 37-8}, pmid = {12594916}, issn = {0962-8436}, mesh = {Chloroplasts/*genetics/*metabolism ; Cytoplasm/genetics ; DNA, Chloroplast/*genetics ; Evolution, Molecular ; Gene Expression Regulation ; *Genome ; Mitochondria/*genetics/*metabolism ; Mitochondrial Proteins/biosynthesis/*genetics ; Models, Biological ; Oxidation-Reduction ; Protein Transport ; }, abstract = {Mitochondria and chloroplasts are energy-transducing organelles of the cytoplasm of eukaryotic cells. They originated as bacterial symbionts whose host cells acquired respiration from the precursor of the mitochondrion, and oxygenic photosynthesis from the precursor of the chloroplast. The host cells also acquired genetic information from their symbionts, eventually incorporating much of it into their own genomes. Genes of the eukaryotic cell nucleus now encode most mitochondrial and chloroplast proteins. Genes are copied and moved between cellular compartments with relative ease, and there is no obvious obstacle to successful import of any protein precursor from the cytosol. So why are any genes at all retained in cytoplasmic organelles? One proposal is that these small but functional genomes provide a location for genes that is close to, and in the same compartment as, their gene products. This co-location facilitates rapid and direct regulatory coupling. Redox control of synthesis de novo is put forward as the common property of those proteins that must be encoded and synthesized within mitochondria and chloroplasts. This testable hypothesis is termed CORR, for co-location for redox regulation. Principles, predictions and consequences of CORR are examined in the context of competing hypotheses and current evidence.}, }
@article {pmid12594914, year = {2003}, author = {}, title = {Chloroplasts and mitochondria: functional genomics and evolution. Proceedings of a meeting. 26-28 June 2002.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {358}, number = {1429}, pages = {3-274}, doi = {10.1098/rstb.2002.1195}, pmid = {12594914}, issn = {0962-8436}, mesh = {*Chloroplasts/genetics/physiology ; *Evolution, Molecular ; *Mitochondria/genetics/physiology ; }, }
@article {pmid12592707, year = {2002}, author = {Wang, TH and Wu, ZH and Liu, SL and Huang, W}, title = {Cloning and sequence analysis of a mitochondrial gene cluster encoding cytochrome C oxidase subunit III from Trichoderma pseudokoningii.}, journal = {DNA sequence : the journal of DNA sequencing and mapping}, volume = {13}, number = {5}, pages = {271-275}, doi = {10.1080/1042517021000019250}, pmid = {12592707}, issn = {1042-5179}, mesh = {*DNA, Mitochondrial ; Electron Transport Complex IV/*genetics ; Membrane Proteins/*genetics ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Saccharomyces cerevisiae Proteins ; Sequence Homology ; Transcription, Genetic ; Trichoderma/enzymology/*genetics ; }, abstract = {A mitochondrial gene cluster encoding cytochrome c oxidase subunit III (COX3), an ORF (called ORF250) similar to NADH dehydrogenase subunit VI (ND6), ten tRNA molecules, partial rRNA small subunit and rRNA large subunit from Trichoderma pseudokoningii S38 was cloned and sequenced. These genes are tandemly clustered on the mitochondrial genome of Trichoderma pseudokoningii S38. Phylogenetic analysis showed that cytochrome C oxidase subunits III exhibited high degree of similarity to sequences from Hypocrea jecorina, Verticillium lecanii, Podospora anserine, Neurospora crassa and Magnaporthe grisea (99, 90, 84, 82 and 79% identity, respectively). Prediction of transmembrane helices revealed that COX3 was a transmembrane protein. Northern dot blot analysis showed that the cytochrome c oxidase subunits III gene we had cloned is actively transcribed in the T. pseudokoningii mitochondria.}, }
@article {pmid12589726, year = {2003}, author = {Dallai, R and Beani, L and Kathirithamby, J and Lupetti, P and Afzelius, BA}, title = {New findings on sperm ultrastructure of Xenos vesparum (Rossi) (Strepsiptera, Insecta).}, journal = {Tissue &amp; cell}, volume = {35}, number = {1}, pages = {19-27}, doi = {10.1016/s0040-8166(02)00099-x}, pmid = {12589726}, issn = {0040-8166}, mesh = {Animals ; Cell Nucleus/ultrastructure ; Centrioles/ultrastructure ; Glycocalyx/ultrastructure ; Insecta/*ultrastructure ; Male ; Microscopy, Electron ; Microscopy, Electron, Scanning ; Microscopy, Fluorescence ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Phylogeny ; Species Specificity ; Spermatids/*ultrastructure ; }, abstract = {The systematic position of insect order Strepsiptera is still under debate. It was, therefore, thought of interest to examine the ultrastructure of a strepsipteran in a search for synapomorphies shared with Coleoptera, Diptera, or any other insect order. The fine structure of spermatozoa and the spermatid from Xenos vesparum (Rossi) was re-examined using scanning and transmission electron microscopy and a fixation technique that permits the visualization of the macromolecular organization of the organelles. The spermatozoon was shown to possess several traits that are characteristics of insects in general, such as a 9 + 9 + 2 axoneme, two mitochondrial derivatives containing a crystalline material and two 'zipper lines' present along the sperm tail. Seventeen protofilaments occurred along most of the accessory tubules, which reduced to 16 posteriorly. An acrosome is absent. The neck region contains a prominent centriolar adjunct, which gives rise to two accessory bodies which adhere to the mitochondrial derivatives, and to slender strands of the so-called intertubular material found between the accessory tubules. Of interest is the finding that the glycocalyx consists of prominent filamentous strands, similar to those found in siphonapterans, mecopterans and basal dipterans.}, }
@article {pmid12588294, year = {2003}, author = {Toro, N}, title = {Bacteria and Archaea Group II introns: additional mobile genetic elements in the environment.}, journal = {Environmental microbiology}, volume = {5}, number = {3}, pages = {143-151}, doi = {10.1046/j.1462-2920.2003.00398.x}, pmid = {12588294}, issn = {1462-2912}, mesh = {Archaea/genetics ; Archaeal Proteins/genetics ; Bacteria/*genetics ; Bacterial Proteins/genetics ; *DNA Transposable Elements ; Environmental Microbiology ; Evolution, Molecular ; Introns/*genetics ; }, abstract = {Self-splicing group II introns are present in the organelles of lower eukaryotes, plants and Bacteria and have been found recently in Archaea. It is generally accepted that group II introns originated in bacteria before spreading to mitochondria and chloroplasts. These introns are thought to be related to the progenitors of spliceosomal introns. Group II introns are also mobile genetic elements. In bacteria, they appear to spread using either other mobile genetic elements or low-expression regions as target sites. Bacteria and Archaea genome sequence annotations have revealed the diversity of group II intron classes and that they are involved in vertical and horizontal inheritance.}, }
@article {pmid12586869, year = {2003}, author = {Millar, AH and Heazlewood, JL}, title = {Genomic and proteomic analysis of mitochondrial carrier proteins in Arabidopsis.}, journal = {Plant physiology}, volume = {131}, number = {2}, pages = {443-453}, pmid = {12586869}, issn = {0032-0889}, mesh = {Arabidopsis/*genetics/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Carrier Proteins/*genetics/isolation &amp; purification/metabolism ; Gene Expression Profiling/methods ; Genomics/*methods ; Hydrophobic and Hydrophilic Interactions ; Mass Spectrometry ; Membrane Proteins/genetics/isolation &amp; purification/metabolism ; Mitochondrial Proteins/*genetics/metabolism ; Multigene Family ; Phylogeny ; Proteomics/*methods ; }, abstract = {Plant mitochondria maintain metabolic communication with the cytosol through a family of carrier proteins. In Arabidopsis, a subset of 45 putative genes encoding members of this family have been identified based on generalized mitochondrial carrier features. No gene clusters are apparent and few of the predicted protein products have mitochondrial targeting sequences recognized by bioinformatic predictors. Only nine genes are currently represented by more than 10 expressed sequence tags at The Institute for Genomic Research. Analyses of public microarray experiments reveal differential expression profiles of the more highly expressed members of this gene family in different plant organs and in response to plant hormone application and environmental stresses. A comparison of this Arabidopsis carrier subset (45) to the yeast gene family (35) reveals 10 orthologous groups between the two species. Recent surveys of the Arabidopsis mitochondrial proteome by two-dimensional gel separations have not identified any of these carrier proteins, presumably because of their hydrophobicity and basicity. Isolating integral membrane proteins from Arabidopsis mitochondria, using one-dimensional electrophoresis for protein separation and tandem mass spectrometry-based sequencing of doubly charged peptides, we have unequivocally identified specific carrier gene products located in mitochondria. This approach has identified six of the nine carriers represented highly in expressed sequence tag databases: adenine nucleotide translocator (At3g8580 and At5g13490), dicarboxylate/tricarboxylate carrier (At5g19760), phosphate carrier (At5g14040), uncoupling protein (At3g54110), and a carrier gene of unknown function (At4g01100). Overall, the combined transcript and protein expression data indicates that only a small subset of the carrier family of genes provide the majority of carrier proteins of Arabidopsis mitochondria.}, }
@article {pmid12574863, year = {2003}, author = {Hazkani-Covo, E and Sorek, R and Graur, D}, title = {Evolutionary dynamics of large numts in the human genome: rarity of independent insertions and abundance of post-insertion duplications.}, journal = {Journal of molecular evolution}, volume = {56}, number = {2}, pages = {169-174}, doi = {10.1007/s00239-002-2390-5}, pmid = {12574863}, issn = {0022-2844}, mesh = {*DNA Transposable Elements ; *Evolution, Molecular ; Gene Duplication ; *Genome, Human ; Humans ; Likelihood Functions ; Mitochondria/*genetics ; Models, Genetic ; Phylogeny ; *Pseudogenes ; }, abstract = {We determined the phylogenetic positions of 82 large nuclear pseudogenes of mitochondrial origin (numts) within the human genome. For each numt, two possibilities pertaining to its origin were considered: (1) independent insertion from the mitochondria into the nucleus, or (2) genomic duplication subsequent to the insertion. A significant increase in the rate of numt accumulation is seen after the divergence of Platyrrhini (New World monkeys) from the Catarrhini (Old World monkeys, apes and humans). By using pairwise phylogenetic analyses, we were able to demonstrate that this peak in numt accumulation is mostly the result of duplication of preexisting nuclear numts rather than the result of an increase in mitochondrial-sequence insertion. In fact, only about a third of all the numt repertoire in the human nuclear genome is due to insertions of mitochondrial sequences, the rest originated as duplications of preexisting numts. Hence, we conclude that numt insertion occurs at a much lower rate than previously reported. As expected under the assumption that genomic duplications occur at rates that are uninfluenced by content, older numts were found to be duplicated more times than recently inserted ones.}, }
@article {pmid12574861, year = {2003}, author = {Seligmann, H}, title = {Cost-minimization of amino acid usage.}, journal = {Journal of molecular evolution}, volume = {56}, number = {2}, pages = {151-161}, doi = {10.1007/s00239-002-2388-z}, pmid = {12574861}, issn = {0022-2844}, mesh = {Amino Acids/chemistry/*metabolism ; Animals ; Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Base Composition ; Codon ; Energy Metabolism/*physiology ; Eukaryotic Cells/physiology ; Genome ; *Models, Biological ; Molecular Weight ; *Protein Biosynthesis ; Proteins/chemistry ; }, abstract = {The negative correlation between the frequencies of usage of amino acids and their biosynthetic cost suggests that organisms minimize costs of protein biosynthesis. Empirical results support that: (1) free-living organisms (Archaea, Bacteria, and Eucaryota) minimize the usage of heavy amino acids more than intracellular organisms (viruses, chloroplasts, and mitochondria), a result confirmed by comparing intracellular Bacteria with other Bacteria; (2) avoidance of amino acids with low impact on protein structure (Chou-Fasman indices) is greater than for those with equal molecular weight but greater structural impact: constraints on protein function limit cost-minimization; (3) amino acid weight minimization (WM) for a protein correlates positively with the protein's expression level and with its size; (4) preliminary results suggest that for different proteins, the evolutionary rate of amino acid replacements correlates negatively with WM in these proteins; (5) results suggest that WM decreases with genome-size; and (6) developmental rates correlate positively with WM (within primates and rodents), even after confounding factors were accounted for. Effects of biosynthetic cost-minimization at whole-organism levels vary with metabolic and ecological strategies. Biosynthetic cost-minimization is an adaptive hypothesis that yields a semi-mechanistic explanation for small differences in allele fitness.}, }
@article {pmid12574860, year = {2003}, author = {Amiri, H and Karlberg, O and Andersson, SG}, title = {Deep origin of plastid/parasite ATP/ADP translocases.}, journal = {Journal of molecular evolution}, volume = {56}, number = {2}, pages = {137-150}, doi = {10.1007/s00239-002-2387-0}, pmid = {12574860}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Chlamydiaceae/enzymology/genetics ; Eukaryotic Cells/enzymology/microbiology ; Evolution, Molecular ; Gene Transfer, Horizontal ; Host-Parasite Interactions ; Mitochondria/enzymology/genetics ; Mitochondrial ADP, ATP Translocases/*genetics ; Molecular Sequence Data ; *Phylogeny ; Plastids/*enzymology/genetics ; Rickettsia/*enzymology/genetics ; Rickettsia rickettsii/enzymology/genetics ; Rickettsia typhi ; Sequence Analysis ; Sequence Homology, Amino Acid ; }, abstract = {Membrane proteins that transport ATP and ADP have been identified in mitochondria, plastids, and obligate intracellular parasites. The mitochondrial ATP/ADP transporters are derived from a broad-specificity transport family of eukaryotic origin, whereas the origin of the plastid/parasite ATP/ADP translocase is more elusive. Here we present the sequences of five genes coding for ATP/ADP translocases from four species of Rickettsia. The results are consistent with an early duplication and divergence of the five ATP/ADP translocases within the rickettsial lineage. A comparison of the phylogenetic depths of the mitochondrial and the plastid/parasite ATP/ADP translocases indicates a deep origin for both transporters. The results provide no evidence for a recent acquisition of the ATP/ADP transporters in Rickettsia via horizontal gene transfer, as previously suggested. A possible function of the two types of ATP/ADP translocases was to allow switches between glycolysis and aerobic respiration in the early eukaryotic cell and its endosymbiont.}, }
@article {pmid12572613, year = {1998}, author = {Hasegawa, M and Cao, Y and Yang, Z}, title = {Preponderance of slightly deleterious polymorphism in mitochondrial DNA: nonsynonymous/synonymous rate ratio is much higher within species than between species.}, journal = {Molecular biology and evolution}, volume = {15}, number = {11}, pages = {1499-1505}, doi = {10.1093/oxfordjournals.molbev.a025877}, pmid = {12572613}, issn = {0737-4038}, mesh = {Adenosine Triphosphatases/genetics ; Amino Acid Substitution/*genetics ; Animals ; DNA, Mitochondrial/*genetics ; Electron Transport Complex I ; Evolution, Molecular ; Genetic Variation/genetics ; Gorilla gorilla ; Humans ; Mitochondria/enzymology ; Mitochondrial Proton-Translocating ATPases ; Models, Genetic ; Models, Statistical ; Mutagenesis/*genetics ; NADH Dehydrogenase/genetics ; NADH, NADPH Oxidoreductases/genetics ; Pan troglodytes ; Polymorphism, Genetic/*genetics ; Species Specificity ; }, abstract = {We estimated synonymous (dN) and nonsynonymous (dS) substitution rates for protein-coding genes of the mitochondrial genome from two individuals each of the species human, chimpanzee, and gorilla. The genes were analyzed both separately and in a combined data set. Pairwise sequence comparisons suggest that the dN/dS rate ratios are about 5-10 times higher in within-species comparisons than in between-species comparisons. This result is confirmed by a more rigorous likelihood ratio test, which rejected the null hypothesis that the dN/dS rate ratios are identical within and between species. The likelihood models account for the genetic code structure, transition/transversion rate ratio, and codon usage bias and are expected to produce more reliable results than the commonly used contingency test. Separate analyses of different genes show that the dN/dS rate ratios are higher within species than between species for all 13 mitochondrial genes, with the difference being statistically significant for all except three small or slowly evolving genes. Furthermore, in conserved genes, nonsynonymous rates within species tend to be higher than the between-species rates by a greater proportion than in fast-changing genes. Our findings confirm and extend earlier results obtained from smaller data sets and suggest the operation of slightly deleterious mutations throughout the mitochondrial genome in the hominoids. Implications of the results for evolutionary studies and, in particular, for studies of the origin of modern humans, are discussed.}, }
@article {pmid12569423, year = {2003}, author = {Baric, S and Salzburger, W and Sturmbauer, C}, title = {Phylogeography and evolution of the Tanganyikan cichlid genus Tropheus based upon mitochondrial DNA sequences.}, journal = {Journal of molecular evolution}, volume = {56}, number = {1}, pages = {54-68}, doi = {10.1007/s00239-002-2380-7}, pmid = {12569423}, issn = {0022-2844}, mesh = {Cichlids/*genetics ; *Evolution, Molecular ; Geography ; Haplotypes ; Mitochondria/*genetics ; *Phylogeny ; Sequence Analysis, DNA ; Tanzania ; }, abstract = {Lake Tanganyika harbors the oldest and most diverse species flock of cichlid fish. Many species are subdivided into numerous genetically and phenotypically distinct populations. Their present distribution and genetic structure were shaped by a series of lake level fluctuations which caused cycles of isolation and admixis and promoted dispersal events. One of the best examples of this phenomenon is the genus Tropheus. We present a comprehensive mtDNA phylogeny based upon 365 individuals of 55 populations from all over Lake Tanganyika, which suggests an almost-contemporaneous origin of eight major mitochondrial lineages about 700 Ka ago. While the distribution of seven lineages is restricted to particular sections of the lake shore, one lineage was found to have a much more widespread distribution. This particular lineage is subdivided into four sublineages which seem to have originated from a single dispersal event about 400 Ka. By using a molecular clock estimate in combination with geological data we derived a hypothetical scenario for the colonization history of Tropheus. Thereby we show a high degree of concordance between major changes of the lake level in the recent history of Lake Tanganyika and three distinct diversification events in this genus.}, }
@article {pmid12569422, year = {2003}, author = {Brehm, A and James Harris, AD and Alves, CD and Jesus, JD and Thomarat, FD and Vicente, LD}, title = {Structure and evolution of the mitochondrial DNA complete control region in the lizard Lacerta dugesii (Lacertidae, Sauria).}, journal = {Journal of molecular evolution}, volume = {56}, number = {1}, pages = {46-53}, doi = {10.1007/s00239-002-2379-0}, pmid = {12569422}, issn = {0022-2844}, mesh = {Animals ; *Evolution, Molecular ; Lizards/*genetics ; Mitochondria/*genetics ; Nucleic Acid Conformation ; RNA, Transfer/chemistry ; }, abstract = {We sequenced the complete control region (CR) and adjacent tRNAs, partial 12S rRNA, and cytochrome b (over 3100 bp) from eight individuals of Madeiran wall lizards, Lacerta dugesii, from four distinct island populations. The tRNAs exhibit a high degree of intraspecific polymorphisms compared to other vertebrates. All CR sequences include a minisatellite that varies in length between populations but is apparently fixed within them. Variation in minisatellite length appears between populations separated by apparently very short evolutionary time spans. Many motifs identified in the CR of other vertebrates are not highly conserved, although conserved blocks are identifiable between the few published reptile CR sequences. Overall there are extensive differences in the internal organization of the reptile CR compared to the more widely studied mammals and birds. Variability in the CR is lower than in cytochrome b, but higher than in 12S rRNA. Phylogenetic analysis of these sequences produces a well-resolved estimate of relationships between populations.}, }
@article {pmid12569421, year = {2003}, author = {Mardulyn, P and Termonia, A and Milinkovitch, MC}, title = {Structure and evolution of the mitochondrial control region of leaf beetles (Coleoptera: Chrysomelidae): a hierarchical analysis of nucleotide sequence variation.}, journal = {Journal of molecular evolution}, volume = {56}, number = {1}, pages = {38-45}, doi = {10.1007/s00239-002-2378-1}, pmid = {12569421}, issn = {0022-2844}, mesh = {Animals ; Coleoptera/*genetics/metabolism ; *Evolution, Molecular ; Genetic Variation ; Mitochondria/*genetics/metabolism ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {To assess the levels of variation at different evolutionary scales in the mitochondrial (mt) control region of leaf beetles, we sequenced and compared the full mt control region in two genera (Chrysomela and Gonioctena), in two species within a genus (Gonioctena olivacea and G. pallida), in individuals from distant populations of these species in Europe, and in individuals from populations separated by moderate (10- to 100-km) to short (<5-km) distances. In all individuals, a highly repetitive section consisting of the tandem repetition of 12 to 17 imperfect copies of a 107- to 159-bp-long core sequence was observed. This repetitive fragment accounts for roughly 50% of the full control-region length. The sequence variability among repeated elements within the control region of a given individual depends on the species considered: the variability within any G. olivacea individual is much higher than that within G. pallida individuals. Comparisons of the repeated elements, in a phylogenetic framework, within and among individuals of G. olivacea and G. pallida suggests that the repetitive section of the control region experienced recurrent duplications/deletions, leading to some degree of concerted evolution. Comparisons between Chrysomela and Gonioctena control regions revealed virtually no significant sequence similarity, except for two long stretches of A's and several [T(T)A(A)] repeats, all found in the control region of other insect orders. Our analyses allowed us to identify portions of the control region with enough variation for population genetic or phylogeographic studies.}, }
@article {pmid12567563, year = {2002}, author = {Qiu, CP and Chris, S and Xia, MY and Chen, Q and Tong, XM and Gong, X and Davis, G and Feng, Z}, title = {[Study on genomic diversity among different isolates of Schistosoma japonicum in China].}, journal = {Zhongguo ji sheng chong xue yu ji sheng chong bing za zhi = Chinese journal of parasitology &amp; parasitic diseases}, volume = {20}, number = {2}, pages = {79-82}, pmid = {12567563}, issn = {1000-7423}, support = {IP50 AI 39461/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; China ; Electron Transport Complex IV/*genetics ; Genotype ; Haplotypes ; Mice ; Mitochondria/enzymology ; Molecular Sequence Data ; NADH Dehydrogenase/*genetics ; Phylogeny ; Schistosoma japonicum/enzymology/*genetics ; }, abstract = {OBJECTIVE: To study genomic diversity among the isolates of Schistosoma japonicum in China.<br><br>METHODS: Schistosome adults were collected from different endemic areas. Mitochondrial NADH dehydrogenase 1 (ND1) and cytochrome C oxidase 1 (CO1) gene fragments of the worms were amplified by PCR, cloned into plasmid, and finally sequenced. Program MEGA was used for sequence analysis.<br><br>RESULTS: The ND1 and CO1 genes amplified from different geographic strains were 476 bp and 1,033 bp, respectively. There are two distinct haplotypes, type I and II, for both ND1 and CO1 nucleotide sequences. The differences between the two types were 4.0% and 3.4%. They are considered to be two different genetypes by the phylogenetic analysis. In individual mitochondrial gene, type I of ND1 was fixedly accompanied with type I of CO1 gene, and type II of ND1 with type II of CO1.<br><br>CONCLUSION: There are two different genetypes of ND1 and CO1 genes of S. japonicum in China.}, }
@article {pmid12566758, year = {2002}, author = {Sena, L and Vallinoto, M and Sampaio, I and Schneider, H and Ferrari, SF and Schneider, MP}, title = {Mitochondrial COII gene sequences provide new insights into the phylogeny of marmoset species groups (Callitrichidae, Primates).}, journal = {Folia primatologica; international journal of primatology}, volume = {73}, number = {5}, pages = {240-251}, doi = {10.1159/000067456}, pmid = {12566758}, issn = {0015-5713}, mesh = {Amino Acid Sequence ; Animals ; Callitrichinae/*classification/*genetics ; Electron Transport Complex IV/chemistry/*genetics ; *Evolution, Molecular ; Mitochondria/*enzymology/*genetics ; Molecular Sequence Data ; *Phylogeny ; Population Dynamics ; Sequence Alignment ; }, abstract = {Mitochondrial cytochrome oxidase II (COII) gene sequences (549 base pairs) were used to investigate the taxonomic relationships among 12 marmoset (Callithrix, Cebuella and Mico) taxa. A large number of substitutions were found in the third base codon positions, providing a strong phylogenetic signal in a gene coding a conserved protein. Despite the significant affinity between the 2 Amazonian genera Cebuella and Mico, found in recent molecular studies, the analysis presented here did not resolve convincingly the phylogenetic relationships between the 3 genera. Mico nevertheless formed 3 distinct clades, reflecting a basic division of species groups based on geographic distribution (east or west of the Rio Tapajós) rather than morphology (presence or absence of auricular hair). This supports the taxonomic distinction of the allopatric emiliae forms. In Callithrix, Callithrix aurita forms a distinct clade, but the remaining morphotypes form a somewhat contradictory cluster, possibly resulting from an extremely rapid radiation.}, }
@article {pmid12565034, year = {2003}, author = {Johnson, KP and Cruickshank, RH and Adams, RJ and Smith, VS and Page, RD and Clayton, DH}, title = {Dramatically elevated rate of mitochondrial substitution in lice (Insecta: Phthiraptera).}, journal = {Molecular phylogenetics and evolution}, volume = {26}, number = {2}, pages = {231-242}, doi = {10.1016/s1055-7903(02)00342-1}, pmid = {12565034}, issn = {1055-7903}, mesh = {Animals ; Birds/parasitology ; Electron Transport Complex IV/genetics ; *Eukaryotic Initiation Factor-1 ; Evolution, Molecular ; *Genetic Variation ; Mammals/parasitology ; Mitochondria/*genetics ; Models, Genetic ; Peptide Initiation Factors/genetics ; Phthiraptera/*classification/*genetics ; *Phylogeny ; Polymerase Chain Reaction/methods ; }, abstract = {Few estimates of relative substitution rates, and the underlying mutation rates, exist between mitochondrial and nuclear genes in insects. Previous estimates for insects indicate a 2-9 times faster substitution rate in mitochondrial genes relative to nuclear genes. Here we use novel methods for estimating relative rates of substitution, which incorporate multiple substitutions, and apply these methods to a group of insects (lice, Order: Phthiraptera). First, we use a modification of copath analysis (branch length regression) to construct independent comparisons of rates, consisting of each branch in a phylogenetic tree. The branch length comparisons use maximum likelihood models to correct for multiple substitution. In addition, we estimate codon-specific rates under maximum likelihood for the different genes and compare these values. Estimates of the relative synonymous substitution rates between a mitochondrial (COI) and nuclear (EF-1alpha) gene in lice indicate a relative rate of several 100 to 1. This rapid relative mitochondrial rate (>100 times) is at least an order of magnitude faster than previous estimates for any group of organisms. Comparisons using the same methods for another group of insects (aphids) reveals that this extreme relative rate estimate is not simply attributable to the methods we used, because estimates from aphids are substantially lower. Taxon sampling affects the relative rate estimate, with comparisons involving more closely related taxa resulting in a higher estimate. Relative rate estimates also increase with model complexity, indicating that methods accounting for more multiple substitution estimate higher relative rates.}, }
@article {pmid12559567, year = {2003}, author = {Rinaldi, T and Gambadoro, A and Francisci, S and Frontali, L}, title = {Nucleo-mitochondrial interactions in Saccharomyces cerevisiae: characterization of a nuclear gene suppressing a defect in mitochondrial tRNA(Asp) processing.}, journal = {Gene}, volume = {303}, number = {}, pages = {63-68}, doi = {10.1016/s0378-1119(02)01154-x}, pmid = {12559567}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Cell Nucleus/genetics/*metabolism ; Conserved Sequence/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Gene Expression Regulation, Fungal ; Genetic Complementation Test ; Mitochondria/genetics/*metabolism ; Molecular Sequence Data ; Mutation ; Nuclear Proteins/genetics/metabolism ; Oxidoreductases ; RNA, Transfer, Asp/genetics/metabolism ; Saccharomyces cerevisiae/genetics/growth &amp; development/*metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Temperature ; }, abstract = {We utilized the heat-sensitive mutant strain (Ts932), bearing a mutation at position 61 in the mitochondrial tRNA(Asp) gene, to identify nuclear genes involved in tRNA biogenesis; this mutant is defective in 3'-end processing and consequently in the production of mature mitochondrial tRNA(Asp). We transformed this strain with a yeast nuclear library and we isolated among other suppressors, an unknown, non-essential gene (called SMM1, corresponding to open reading frame YNR015w), which restored the growth on glycerol and a normal amount of processed tRNA(Asp) in the mutant. The gene contains a domain highly conserved in evolution from bacteria to human and its product has been recently shown to have dihydrouridine synthase activity.}, }
@article {pmid12556151, year = {2003}, author = {Booton, GC and Carmichael, JR and Visvesvara, GS and Byers, TJ and Fuerst, PA}, title = {Genotyping of Balamuthia mandrillaris based on nuclear 18S and mitochondrial 16S rRNA genes.}, journal = {The American journal of tropical medicine and hygiene}, volume = {68}, number = {1}, pages = {65-69}, pmid = {12556151}, issn = {0002-9637}, support = {R01 EY009073-10/EY/NEI NIH HHS/United States ; EY09073/EY/NEI NIH HHS/United States ; }, mesh = {Adolescent ; Animals ; Base Sequence ; Brain/parasitology ; Cell Nucleus/genetics ; Child ; DNA, Ribosomal/chemistry ; Encephalitis/parasitology ; Female ; Genotype ; Horses ; Humans ; Lobosea/*classification/genetics ; Male ; Middle Aged ; Mitochondria/genetics ; Molecular Sequence Data ; Opportunistic Infections/parasitology ; Papio ; Phylogeny ; Protozoan Infections/parasitology ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 18S/*genetics ; Sequence Alignment ; }, abstract = {Balamuthia mandrillaris is an opportunistically pathogenic ameba that causes fatal granulomatous amebic encephalitis (GAE) in vertebrates. Previous phylogenetic analyses that included the sequence of a single nuclear small subunit ribosomal RNA gene (18S or ssu rDNA) from this ameba suggested that Balamuthia is closely related to Acanthamoeba, another opportunistically pathogenic amebic genus, which includes multiple ssu rDNA genotypes. We tested whether this also is true for Balamuthia. The nuclear ssu rDNA from 4 isolates and the mitochondrial ssu rDNA from 7 isolates of B. mandrillaris have been sequenced. No variation in the nuclear rDNA sequences and low levels of variation in the mitochondrial rDNA were found. Both gene sequences were consistent with a single genotype for B. mandrillaris. The mitochondrial sequences of B. mandrillaris are unique and should be useful for development of genus-specific diagnostic probes for use with clinical, environmental, and archived specimens.}, }
@article {pmid12554459, year = {2002}, author = {Drovetski, SV}, title = {Molecular phylogeny of grouse: individual and combined performance of W-linked, autosomal, and mitochondrial loci.}, journal = {Systematic biology}, volume = {51}, number = {6}, pages = {930-945}, doi = {10.1080/10635150290102500}, pmid = {12554459}, issn = {1063-5157}, mesh = {Aggrecans ; Animals ; Birds/*genetics ; Cell Nucleus/metabolism ; Chromosome Mapping ; *Evolution, Molecular ; *Extracellular Matrix Proteins ; Lectins, C-Type ; Mitochondria/genetics/metabolism ; Models, Statistical ; *Phylogeny ; Polymerase Chain Reaction ; Proteoglycans/genetics ; }, abstract = {The phylogeny of grouse (Aves: Tetraoninae) was reconstructed using four noncoding loci: two were W-linked, one was autosomal, and one was the mitochondrial control region (CR). The rapidly evolving CR provided resolution throughout the tree, whereas the slowly evolving nuclear loci failed to resolve deeper nodes. The tree based on all four loci combined was almost identical to the CR tree and did not improve resolution or bootstrap support. The stemminess and imbalance of the trees were good determinants of the quality of the phylogenetic signal. The skewness of the tree score distribution (g(1)) behaved contrary to prediction; loci that had a more symmetric tree score distribution produced trees that had greater stemminess and balance. The quality of the phylogenetic signal was related to the evolutionary rate. Four clades of grouse were discovered. Two of these clades corresponded to currently recognized genera Bonasa and Lagopus. Bonasa was the sister to other grouse and Lagopus was the sister to the other two non-Bonasa clades. The third clade included Falcipennis, Tetrao, and Lyrurus. The fourth clade included the genera Centrocercus, Dendragapus, and Tympanuchus. The data support recognition of Falcipennis canadensis franklinii and Dendragapus obscurus fuliginosus as species.}, }
@article {pmid12547920, year = {2002}, author = {Miretti, MM and Pereira, HA and Poli, MA and Contel, EP and Ferro, JA}, title = {African-derived mitochondria in South American native cattle breeds (Bos taurus): evidence of a new taurine mitochondrial lineage.}, journal = {The Journal of heredity}, volume = {93}, number = {5}, pages = {323-330}, doi = {10.1093/jhered/93.5.323}, pmid = {12547920}, issn = {0022-1503}, mesh = {Africa ; Analysis of Variance ; Animals ; Biological Evolution ; Breeding ; Cattle/*genetics ; Gene Frequency ; *Genetic Variation ; Haplotypes ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {This article reports the nucleotide diversity within the control region of 42 mitochondrial chromosomes belonging to five South American native cattle breeds (Bos taurus). Analysis of these data in conjunction with B. taurus and B. indicus sequences from Africa, Europe, the Near East, India, and Japan allowed the recognition of eight new mitochondrial haplotypes and their relative positions in a phylogenetic network. The structure of genetic variation among different hypothetical groupings was tested through the molecular variance decomposition, which was best explained by haplotype group components. Haplotypes surveyed were classified as European-related and African-related. Unexpectedly, two haplotypes within the African cluster were more divergent from the African consensus than the latter from the European consensus. A neighbor-joining tree shows the position of two haplotypes compared to European/African mitochondrial lineage splitting. This different and putatively ancestral mitochondrial lineage (AA) is supported by the calibration of sequence divergence based on the Bos-Bison separation. The European/African mitochondria divergence might be subsequent (67,100 years before present) to that between AA and Africans (84,700 years before present), also preceding domestication times. These genetic data could reflect the haplotype distribution of Iberian cattle five centuries ago.}, }
@article {pmid12532263, year = {2003}, author = {Rantanen, A and Gaspari, M and Falkenberg, M and Gustafsson, CM and Larsson, NG}, title = {Characterization of the mouse genes for mitochondrial transcription factors B1 and B2.}, journal = {Mammalian genome : official journal of the International Mammalian Genome Society}, volume = {14}, number = {1}, pages = {1-6}, doi = {10.1007/s00335-002-2218-z}, pmid = {12532263}, issn = {0938-8990}, mesh = {Animals ; Chromosome Mapping ; Mice ; Mitochondria/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Promoter Regions, Genetic ; Synteny ; Transcription Factors/*genetics/metabolism ; }, abstract = {We have recently fully reconstituted the basal human mitochondrial transcription machinery in a pure in vitro system. Surprisingly, we found two different transcription factors (TFB1M and TFB2M) that each interact with mitochondrial RNA polymerase in human mitochondria, whereas there is only one such factor in budding yeast mitochondria. This unexpected finding raised important questions concerning the regulation of mitochondrial transcription in mammals in general and in other metazoans. We have now further analyzed putative homologs to TFB1M and TFB2M in different species. We mapped the mouse homologs, Tfb1m and Tfb2m, by linkage analysis to mouse Chr 17 and Chr 1, respectively. These regions display conserved linkage synteny with human Chr 6 and Chr 1, where TFB1M and TFB2M map. The intron-exon arrangements of Tfb1m and TFB1M and of Tfb2m and TFB2M were identical, and the promoter regions had similar predicted recognition elements for transcriptional factors NRF2 and Sp1. Northern blot analyses showed that Tfb1m and Tfb2m were ubiquitously expressed and had expression patterns that were very similar to the previously reported expression patterns for TFB1M and TFB2M. These findings show that Tfb1m and Tfb2m indeed are orthologs to TFB1M and TFB2M. Bioinformatic analyses indicated that most metazoans have two TFBM genes, since putative homologs to both TFB1M and TFB2M were found in D. melanogaster. Our data thus suggest that a duplication event of the TFBM gene in early metazoan evolution has permitted a more flexible regulation of mtDNA transcription, possibly in response to the complex physiological demands of multicellular organisms.}, }
@article {pmid12529534, year = {2003}, author = {Dutilleul, C and Driscoll, S and Cornic, G and De Paepe, R and Foyer, CH and Noctor, G}, title = {Functional mitochondrial complex I is required by tobacco leaves for optimal photosynthetic performance in photorespiratory conditions and during transients.}, journal = {Plant physiology}, volume = {131}, number = {1}, pages = {264-275}, pmid = {12529534}, issn = {0032-0889}, mesh = {Amino Acid Oxidoreductases/metabolism ; Carbon Dioxide/pharmacology ; Cell Respiration/physiology ; Darkness ; Electron Transport/genetics/physiology ; Electron Transport Complex I ; Glycine/metabolism ; Glycine Dehydrogenase (Decarboxylating) ; Light ; Malate Dehydrogenase/metabolism ; Malate Dehydrogenase (NADP+) ; Mitochondria/*metabolism ; Mutation ; NADH, NADPH Oxidoreductases/*metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; Photosynthesis/drug effects/*physiology/radiation effects ; Photosynthetic Reaction Center Complex Proteins/genetics/metabolism ; Plant Leaves/genetics/*metabolism ; Ribulose-Bisphosphate Carboxylase/metabolism ; Nicotiana/genetics/*metabolism ; }, abstract = {The importance of the mitochondrial electron transport chain in photosynthesis was studied using the tobacco (Nicotiana sylvestris) mutant CMSII, which lacks functional complex I. Rubisco activities and oxygen evolution at saturating CO(2) showed that photosynthetic capacity in the mutant was at least as high as in wild-type (WT) leaves. Despite this, steady-state photosynthesis in the mutant was reduced by 20% to 30% at atmospheric CO(2) levels. The inhibition of photosynthesis was alleviated by high CO(2) or low O(2). The mutant showed a prolonged induction of photosynthesis, which was exacerbated in conditions favoring photorespiration and which was accompanied by increased extractable NADP-malate dehydrogenase activity. Feeding experiments with leaf discs demonstrated that CMSII had a lower capacity than the WT for glycine (Gly) oxidation in the dark. Analysis of the postillumination burst in CO(2) evolution showed that this was not because of insufficient Gly decarboxylase capacity. Despite the lower rate of Gly metabolism in CMSII leaves in the dark, the Gly to Ser ratio in the light displayed a similar dependence on photosynthesis to the WT. It is concluded that: (a) Mitochondrial complex I is required for optimal photosynthetic performance, despite the operation of alternative dehydrogenases in CMSII; and (b) complex I is necessary to avoid redox disruption of photosynthesis in conditions where leaf mitochondria must oxidize both respiratory and photorespiratory substrates simultaneously.}, }
@article {pmid12529529, year = {2003}, author = {Liepman, AH and Olsen, LJ}, title = {Alanine aminotransferase homologs catalyze the glutamate:glyoxylate aminotransferase reaction in peroxisomes of Arabidopsis.}, journal = {Plant physiology}, volume = {131}, number = {1}, pages = {215-227}, pmid = {12529529}, issn = {0032-0889}, support = {T32 GM008353/GM/NIGMS NIH HHS/United States ; T32 GM145304/GM/NIGMS NIH HHS/United States ; GM08353/GM/NIGMS NIH HHS/United States ; }, mesh = {Alanine Transaminase/genetics/*metabolism ; Amino Acid Sequence ; Arabidopsis/*enzymology/genetics ; Escherichia coli/genetics/metabolism ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Isoenzymes/genetics/metabolism ; Light ; Molecular Sequence Data ; Peroxisomes/*enzymology ; Phylogeny ; Sequence Homology, Amino Acid ; Substrate Specificity ; Transaminases/genetics/*metabolism ; gamma-Glutamyltransferase ; }, abstract = {Plant peroxisomal glyoxylate aminotransferases play central roles within the photorespiratory pathway. Genes encoding glyoxylate aminotransferases have been isolated from several animals and microbes, but only recently have plant homologs been identified. Three Arabidopsis homologs of alanine (Ala):glyoxylate aminotransferase 2 (AGT2) contain a putative type 1 peroxisomal targeting signal (PTS1), but the metabolic significance of these AGT2 homologs is unknown. GGT1 and GGT2 are Ala aminotransferase (AlaAT) homologs from Arabidopsis that represent another type of glyoxylate aminotransferase. These proteins are class I aminotransferases, each containing a putative PTS1. GGT1 and GGT2 are members of a small family of AlaATs in Arabidopsis. When expressed as recombinant proteins in Escherichia coli, GGT1 and GGT2 displayed biochemical characteristics very similar to one another, and to the Arabidopsis protein purified from leaves. Four aminotransferase activities were specifically associated with GGT1 and GGT2, using the substrate pairs glutamate (Glu):glyoxylate, Ala:glyoxylate, Glu:pyruvate, and Ala:2-oxoglutarate. GGT1 and GGT2 may have partially redundant functions; transcripts of both genes were detected in many of the same tissues. Although Glu:glyoxylate aminotransferase (GGT) activity has been observed in several locations in different plants and algae, including the cytoplasm and mitochondria, our subcellular fractionation data indicate that GGT activity was exclusively peroxisomal in Arabidopsis. Thus, glyoxylate aminotransferase reactions in plant peroxisomes appear to be catalyzed by at least two distinct types of aminotransferases: an AGT1 homolog with serine:glyoxylate aminotransferase activity (A.H. Liepman, L.J. Olsen [2001] Plant J 25: 487-498), and a pair of closely related, potentially redundant AlaAT homologs with GGT activity.}, }
@article {pmid12527366, year = {2003}, author = {Catoni, E and Schwab, R and Hilpert, M and Desimone, M and Schwacke, R and Flügge, UI and Schumacher, K and Frommer, WB}, title = {Identification of an Arabidopsis mitochondrial succinate-fumarate translocator.}, journal = {FEBS letters}, volume = {534}, number = {1-3}, pages = {87-92}, doi = {10.1016/s0014-5793(02)03782-1}, pmid = {12527366}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/*genetics/*metabolism ; Basic-Leucine Zipper Transcription Factors ; Carrier Proteins/*genetics/*metabolism ; Cloning, Molecular/methods ; DNA-Binding Proteins/genetics/metabolism ; Fumarates/metabolism ; Gene Expression Regulation, Plant ; Genetic Complementation Test ; Mitochondria/*metabolism ; Mitochondrial Proteins/*genetics/*metabolism ; Molecular Sequence Data ; Mutation ; Phylogeny ; Plant Leaves/genetics/metabolism ; Promoter Regions, Genetic ; Recombinant Fusion Proteins/genetics/metabolism ; Repressor Proteins/genetics/metabolism ; *Saccharomyces cerevisiae Proteins ; Seeds/genetics/metabolism ; Succinic Acid/metabolism ; Yeasts/genetics ; }, abstract = {Complementation of a yeast acr1 mutant carrying a deletion of the succinate/fumarate carrier gene enabled functional identification of a mitochondrial succinate translocator from Arabidopsis thaliana (AtmSFC1). Thus complementation of yeast mutants is applicable also for identification and characterization of organellar transporters. Reverse transcription polymerase chain reaction and promoter-GUS fusion showed expression of AtmSFC1 in 2 day old dark grown seedlings, which declined in cotyledons during further development, consistent with a role in export of fumarate for gluconeogenesis during lipid mobilization at early germination of Arabidopsis seeds. In mature plants, expression was found in developing and germinating pollen, suggesting a role in ethanolic fermentation.}, }
@article {pmid12525856, year = {2003}, author = {Nedergaard, J and Cannon, B}, title = {The 'novel' 'uncoupling' proteins UCP2 and UCP3: what do they really do? Pros and cons for suggested functions.}, journal = {Experimental physiology}, volume = {88}, number = {1}, pages = {65-84}, doi = {10.1113/eph8802502}, pmid = {12525856}, issn = {0958-0670}, mesh = {Animals ; Carrier Proteins/chemistry/genetics/metabolism/*physiology ; *Evolution, Molecular ; Fever/physiopathology ; Humans ; Intracellular Membranes/physiology ; Ion Channels ; Membrane Proteins/chemistry/genetics/metabolism/physiology ; *Membrane Transport Proteins ; Mice ; Mitochondria/physiology ; *Mitochondrial Proteins ; Obesity/physiopathology ; Proteins/chemistry/genetics/metabolism/*physiology ; Structure-Activity Relationship ; Thermogenesis/physiology ; Uncoupling Protein 1 ; Uncoupling Protein 2 ; Uncoupling Protein 3 ; }, abstract = {The scientifically novel, but evolutionarily ancient, so-called uncoupling proteins 2 and 3 (UCP2, UCP3) are structurally similar to the archetypical uncoupling protein UCP1. A series of suggestions have been forwarded for their physiological function. We discuss systematically here the pros and cons for these suggestions. We conclude that the novel UCPs do not seem to be physiologically relevant uncoupling proteins; the uncoupling property was apparently a late introduction into the subfamily through the evolution of UCP1. Physiological functions ascribed to UCP2 and UCP3 based on their purported uncoupling property may have to be revised (i.e. any type of thermogenesis, including protection against obesity, protection against the formation of reactive oxygen species and thermogenic involvement in the fever response). The presence of a mixed genetic background in most published studies of UCP2 or UCP3 gene-ablated mice also means that data concerning marked differences in diabetes propensity, infection sensitivity and production of reactive oxygen species may require confirmation in backcrossed mice. The increased expression of UCP2 and UCP3 under conditions of increased fatty acid metabolism implies an as yet undefined role in lipid metabolism. Thus, the novel UCPs should probably be considered as mitochondrial carriers, and the challenge now is to identify the transported molecule.}, }
@article {pmid12525853, year = {2003}, author = {Goffart, S and Wiesner, RJ}, title = {Regulation and co-ordination of nuclear gene expression during mitochondrial biogenesis.}, journal = {Experimental physiology}, volume = {88}, number = {1}, pages = {33-40}, doi = {10.1113/eph8802500}, pmid = {12525853}, issn = {0958-0670}, mesh = {Adaptation, Physiological/genetics ; Animals ; Biological Evolution ; Cell Nucleus/*genetics ; DNA, Mitochondrial/physiology ; Gene Expression Regulation/*genetics/physiology ; Genes, Regulator/*genetics/physiology ; Homeostasis/*genetics ; Hormones/physiology ; Humans ; Mitochondria/*genetics/physiology ; Origin of Life ; Transcription Factors/*genetics/physiology ; }, abstract = {Biogenesis of mitochondria is happening constantly due to the physiological and developmental situation of a cell. As mitochondrial biogenesis is a complex process producing about 20 % of cellular protein, the expression of the 1000 genes involved is expected to be coordinated and regulated tightly. The variety of physiological stimuli and differentiation states lead to the idea of a complex network connecting many different regulatory pathways. By analysing nuclear encoded mitochondrial genes some of the factors involved in the regulation and coordination of mitochondrial gene expression were identified. These factors include general transcription factors such as Sp1 or YY1, as well as transcription factors specific for mitochondrial genes like the nuclear respiratory factors NRF1 and 2. An important control function linked to the physiological situation of a cell is triggered by hormones such as steroid and thyroid hormones. Even cell type-specific regulatory proteins like the myogenin transcription factor family have a strong influence on some mitochondrial genes in the specific cellular background. The regulatory function of most of these proteins can be modulated and enhanced by the coactivators PGC-1a and b and PRC. Although regulatory pathways have been characterized in more detail in recent years, no regulation mechanism has been shown to work on all analysed mitochondrial genes, and the general concept of mitochondrial regulation still remains unclear.}, }
@article {pmid12524465, year = {2003}, author = {Moyes, CD and Hood, DA}, title = {Origins and consequences of mitochondrial variation in vertebrate muscle.}, journal = {Annual review of physiology}, volume = {65}, number = {}, pages = {177-201}, doi = {10.1146/annurev.physiol.65.092101.142705}, pmid = {12524465}, issn = {0066-4278}, mesh = {Animals ; Biological Evolution ; Energy Metabolism/*physiology ; Genetic Variation ; Humans ; Mitochondria/genetics/*metabolism ; Muscle, Skeletal/*metabolism ; Vertebrates ; }, abstract = {This review addresses the mechanisms by which mitochondrial structure and function are regulated, with a focus on vertebrate muscle. We consider the adaptive remodeling that arises during physiological transitions such as differentiation, development, and contractile activity. Parallels are drawn between such phenotypic changes and the pattern of change arising over evolutionary time, as suggested by interspecies comparisons. We address the physiological and evolutionary relationships between ATP production, thermogenesis, and superoxide generation in the context of mitochondrial function. Our discussion of mitochondrial structure focuses on the regulation of membrane composition and maintenance of the three-dimensional reticulum. Current studies of mitochondrial biogenesis strive to integrate muscle functional parameters with signal transduction and molecular genetics, providing insight into the origins of variation arising between physiological states, fiber types, and species.}, }
@article {pmid12523502, year = {2002}, author = {Rodríguez, M and Lucchesi, BR and Schaper, J}, title = {Apoptosis in myocardial infarction.}, journal = {Annals of medicine}, volume = {34}, number = {6}, pages = {470-479}, doi = {10.1080/078538902321012414}, pmid = {12523502}, issn = {0785-3890}, mesh = {Animals ; Apoptosis/*physiology ; Caspases/physiology ; DNA Fragmentation/physiology ; Humans ; In Situ Nick-End Labeling ; Mitochondria/physiology ; Myocardial Infarction/pathology/*physiopathology ; Myocardial Ischemia/physiopathology ; Myocardium/ultrastructure ; Myocytes, Cardiac/ultrastructure ; Tumor Suppressor Protein p53/physiology ; }, abstract = {Apoptosis, one of the major forms of cell death, has been implicated in different cardiovascular diseases. In this paper we review many of the different studies that have been performed to address the occurrence of apoptotic cell death associated with myocardial infarction. A definitive differentiation between apoptosis and other forms of cell death is still needed, mainly because of differences and limitations of the methods used for detection. In myocardial infarction apoptosis has been reported at acute stages of evolution in the ischemic area as well as in remote zones. In the ischemic area it might be a determinant of the final size of the infarct and it seems to depend on the presence of post-ischemic reperfusion. However, the incidence of apoptosis reported until now varies widely. In the myocardium remote from the ischemic area it might be associated with the progression towards heart failure. At present, the role and significance of apoptosis in myocardial infarction is rather inconclusive. Further studies are needed to solve methodological uncertainties and clarify the mechanisms involved in the process of cell death, which is particularly important as a basis for therapeutic interventions.}, }
@article {pmid16465265, year = {1997}, author = {Kroemer, G}, title = {Mitochondrial implication in apoptosis. Towards an endosymbiont hypothesis of apoptosis evolution.}, journal = {Cell death and differentiation}, volume = {4}, number = {6}, pages = {443-456}, doi = {10.1038/sj.cdd.4400266}, pmid = {16465265}, issn = {1350-9047}, abstract = {Recent evidence indicates that a profound alteration in mitochondrial function constitutes an obligatory early event of the apoptotic process. The molecular mechanism accounting for this alteration is mitochondrial permeability transition (PT). PT is both sufficient and necessary for apoptosis to occur. Experiments performed in cell-free systems of apoptosis demonstrate that mitochondria undergoing PT release protease activators that can trigger nuclear manifestations of apoptosis. Bcl-2 and its homologs are endogenous regulators of PT. It appears that some types of necrosis, those inhibited by Bcl-2, involve PT. If PT is a rate-limiting event of both apoptosis and necrosis, then downstream events including caspase activation and the bioenergetic consequences of PT must determine the choice between both modes of cell death. PT without caspase activation would cause necrosis. These findings have important implications for the comprehension of the apoptotic process, for the dichotomy between apoptosis and necrosis, and for the phylogeny of programmed cell death. Apoptosis may have evolved together with the endosymbiotic incorporation of aerobic bacteria (the precursors of mitochondria) into ancestral unicellular eukaryotes.}, }
@article {pmid16668993, year = {1992}, author = {Saradadevi, K and Raghavendra, AS}, title = {Dark Respiration Protects Photosynthesis Against Photoinhibition in Mesophyll Protoplasts of Pea (Pisum sativum).}, journal = {Plant physiology}, volume = {99}, number = {3}, pages = {1232-1237}, pmid = {16668993}, issn = {0032-0889}, abstract = {The optimal light intensity required for photosynthesis by mesophyll protoplasts of pea (Pisum sativum) is about 1250 microeinsteins per square meter per second. On exposure to supra-optimal light intensity (2500 microeinsteins per square meter per second) for 10 min, the protoplasts lost 30 to 40% of their photosynthetic capacity. Illumination with normal light intensity (1250 microeinsteins per square meter per second) for 10 min enhanced the rate of dark respiration in protoplasts. On the other hand, when protoplasts were exposed to photoinhibitory light, their dark respiration also was markedly reduced along with photosynthesis. The extent of photoinhibition was increased when protoplasts were incubated with even low concentrations of classic respiratory inhibitors: 1 micromolar antimycin A, 1 micromolar sodium azide, and 1 microgram per milliliter oligomycin. At these concentrations, the test inhibitors had very little or no effect directly on the process of photosynthetic oxygen evolution. The promotion of photoinhibition by inhibitors of oxidative electron transport (antimycin A, sodium azide) and phosphorylation (oligomycin) was much more pronounced than that by inhibitors of glycolysis and tricarboxylic acid cycle (sodium fluoride and sodium malonate, respectively). We suggest that the oxidative electron transport and phosphorylation in mitochondria play an important role in protecting the protoplasts against photoinhibition of photosynthesis. Our results also demonstrate that protoplasts offer an additional experimental system for studies on photoinhibition.}, }
@article {pmid15463602, year = {1992}, author = {Kita, K}, title = {Electron-transfer complexes of mitochondria in Ascaris suum.}, journal = {Parasitology today (Personal ed.)}, volume = {8}, number = {5}, pages = {155-159}, doi = {10.1016/0169-4758(92)90009-q}, pmid = {15463602}, issn = {0169-4758}, abstract = {During the past ten years, studies on the respiratory chain of mitochondria in parasites have progressed to provide new insight into the structural organization and physiological significance of the mitochondrial respiratory chain. In this review, Kiyoshi Kita focuses on studies on the respiratory chain of Ascaris mitochondria in which major advances have recently been made. These include the identification of the unique features of anaerobic respiration, the elucidation of the molecular structures of the components involved and an understanding of the evolution of the energy transducing system and of the developmental changes that occur during the life cycle of this nematode.}, }
@article {pmid16668785, year = {1992}, author = {Saiardi, A and Quagliariello, C}, title = {RNA Editing of Cytochrome Oxidase Subunit III in Sunflower Mitochondria.}, journal = {Plant physiology}, volume = {98}, number = {4}, pages = {1261-1263}, pmid = {16668785}, issn = {0032-0889}, abstract = {Direct sequencing of cytochrome oxidase subunit III (coxIII) mRNA with a specific primer confirms RNA editing in sunflower (Helianthus annus) mitochondria. Six instances of mRNA editing could be verified, one of these specific to this species. All the editing events involve C to U transitions in the coxIII mRNA causing codon changes that lead to amino acids better conserved in evolution than those encoded in the genomic DNA. This observation confirms RNA editing to be widespread in higher plant mitochondria.}, }
@article {pmid16667809, year = {1990}, author = {Tittle, FL and Goudey, JS and Spencer, MS}, title = {Effect of 2,4-Dichlorophenoxyacetic Acid on Endogenous Cyanide, beta-Cyanoalanine Synthase Activity, and Ethylene Evolution in Seedlings of Soybean and Barley.}, journal = {Plant physiology}, volume = {94}, number = {3}, pages = {1143-1148}, pmid = {16667809}, issn = {0032-0889}, abstract = {Treatment of etiolated seedlings of barley (Hordeum vulgare) and soybean (Glycine max) with 1 millimolar 2,4-dichlorophenoxyacetic acid (2,4-D) resulted in a 14-fold and greater than 100-fold increase in ethylene production, respectively. Simultaneous monitoring of endogenous cyanide and beta-cyanoalanine synthase (beta-CAS) (EC 4.4. 1.9) activity was also performed. Endogenous levels of cyanide did not change in barley. In soybean, endogenous cyanide increased within 3 hours, increased again 6 hours after exposure to 2,4-D, and continued to increase throughout the experimental period. The activity of beta-CAS increased in both barley and soybean 9 hours after herbicide treatment. The increase in cyanide preceded the increase in beta-CAS activity by 3 to 6 hours in soybean. The steady-state concentration of endogenous cyanide in soybean was 1 micromolar, based on rates of ethylene production and cyanide metabolism by beta-CAS. This agreed with the determination of endogenous cyanide by both distillation and isotope dilution. Given the apparent compartmentalization of beta-CAS in mitochondria and the localization of ethylene/HCN production at the plasmalemma and/or tonoplast, our results suggest that extra-mitochondrial accumulation of cyanide in the cytoplasm may occur. If so, the activity of cyanide-sensitive cytoplasmic enzymes could be adversely affected, thus possibly contributing to the toxicity of 2,4-D.}, }
@article {pmid16667214, year = {1989}, author = {Brown, RH and Hattersley, PW}, title = {Leaf anatomy of c(3)-c(4) species as related to evolution of c(4) photosynthesis.}, journal = {Plant physiology}, volume = {91}, number = {4}, pages = {1543-1550}, pmid = {16667214}, issn = {0032-0889}, abstract = {This study was undertaken to examine the degree of Kranz anatomy development in the species intermediate to C(3) and C(4) types (C(3)-C(4)) in Panicum, Neurachne, Flaveria, and Moricandia. In each genus, C(3) and/or C(4) species were used for comparison. Leaf transections from each species were examined by light and transmission electron microscopy. The percentages of leaf photosynthetic cell profiles partitioned to bundle sheaths were higher in C(4) than in C(3) species, while C(3)-C(4) species tended to be in between. However, percentages for C(3)-C(4) species in Moricandia and some C(3)-C(4)Flaveria species were not greater than C(3). When expressed on a cell profile area basis, C(3)-C(4) species partitioned more photosynthetic tissue to bundle sheaths than C(3) species in Moricandia, but not in Flaveria. Neurachne minor S. T. Blake (C(3)-C(4)) partitioned a very small portion of cell profile area to the inner bundle sheaths (5%) compared to Neurachne munroi F. Muell (C(4)) (21%). The percentage of organelles partitioned to bundle sheaths was much greater in C(3)-C(4) than in C(3) species. The average C(3) percentages for mitochondria plus peroxisomes were 19, 8, and 19.5% for Neurachne, Flaveria, and Moricandia, respectively, compared to 41, 29, and 46.5% for the C(3)-C(4) species. The CO(2) compensation concentration was negatively related to the partitioning of tissue to bundle sheaths and to the percentage of organelles in bundle sheaths. It is concluded that all of the C(3)-C(4) species examined have developed some degree of Kranz anatomy and that this altered anatomy is involved in their reduced apparent photorespiration.}, }
@article {pmid16665845, year = {1988}, author = {Nelson, N}, title = {Structure, Function, and Evolution of Proton-ATPases.}, journal = {Plant physiology}, volume = {86}, number = {1}, pages = {1-3}, pmid = {16665845}, issn = {0032-0889}, abstract = {Proton-ATPases are among the most important primary ion pumps in nature. There are three classes of these enzymes which are distinguished by their structure, function, mechanism of action, and evolution. They function in ATP formation at the expense of a protonmotive force generated by oxidative and photosynthetic electron transports, maintaining a constant pH in the cytoplasm, and forming acidic spaces in special compartments inside and outside the cell. The three classes of proton-ATPases evolved in a way that prevents functional assembly in the wrong compartment. This was achieved by a triple genetic system located in the nucleus, mitochondria and chloroplast, as well as delicate control of the proton pumping activity of the enzymes.}, }
@article {pmid16663088, year = {1983}, author = {Journet, EP and Douce, R}, title = {Mechanisms of citrate oxidation by percoll-purified mitochondria from potato tuber.}, journal = {Plant physiology}, volume = {72}, number = {3}, pages = {802-808}, pmid = {16663088}, issn = {0032-0889}, abstract = {The mechanisms and accurate control of citrate oxidation by Percoll-purified potato (Solanum tuberosum) tuber mitochondria were characterized in various metabolic conditions by recording time course evolution of the citric acid cycle related intermediates and O(2) consumption. Intact potato tuber mitochondria showed good rates of citrate oxidation, provided that nonlimiting amounts of NAD(+) and thiamine pyrophosphate were present in the matrix space. Addition of ATP increased initial oxidation rates, by activation of the energy-dependent net citrate uptake, and stimulated succinate and malate formation. When the intramitochondrial NADH to NAD(+) ratio was high, alpha-ketoglutarate only was excreted from the matrix space. After addition of ADP, aspartate, or oxaloacetate, which decreased the NADH to NAD(+) ratio, flux rates through the Krebs cycle dehydrogenases were strongly increased and alpha-ketoglutarate, succinate, and malate accumulated up to steady-state concentrations in the reaction medium. It was concluded that NADH to NAD(+) ratio could be the primary signal for coordination of fluxes through electron transport chain or malate dehydrogenase and NAD(+)-linked Krebs cycle dehydrogenases. In addition, these results clearly showed that the tricarboxylic acid cycle could serve as an important source of carbon skeletons for extra-mitochondrial synthetic processes, according to supply and demand of metabolites.}, }
@article {pmid16662419, year = {1982}, author = {Horn, ME and Mertz, D}, title = {Cyanide-Resistant Respiration in Suspension Cultured Cells of Nicotiana glutinosa L.}, journal = {Plant physiology}, volume = {69}, number = {6}, pages = {1439-1443}, pmid = {16662419}, issn = {0032-0889}, abstract = {The respiration of dark-grown Nicotiana glutinosa L. cells in liquid suspension culture was found to be highly cyanide resistant and salicylhydroxamic acid (SHAM) sensitive, indicative of an active alternative respiratory pathway. This was especially true during the lag and logarithmic phases of the 14-day growth cycle. Mitochondria isolated from logarithmically growing cells exhibited active oxidation of malate, succinate, and exogenous NADH. Oxidation of all three substrates had an optimum pH of 6.5 and all were highly resistant to inhibited by cyanide and sensitive to SHAM. Respiratory control was exhibited by all three substrates but only if SHAM was present to block the alternative pathway and divert electrons to the phosphorylating cytochrome pathway. The cyanide-resistant oxidation of exogenous NADH has previously only been associated with Arum spadix mitochondria. Coemergence during evolution of the alternative respiratory pathway and the exogenous NADH dehydrogenase in plant mitochondria as a possible mechanism for removal of cytoplasmic NADH is proposed. Evidence is presented which suggests that mitochondrial assays should be performed at pH 6.5.}, }
@article {pmid16660812, year = {1979}, author = {Woo, KC}, title = {Properties and intramitochondrial localization of serine hydroxymethyltransferase in leaves of higher plants.}, journal = {Plant physiology}, volume = {63}, number = {4}, pages = {783-787}, pmid = {16660812}, issn = {0032-0889}, abstract = {The activity of serine hydroxymethyltransferase in mitochondria isolated from spinach leaves was absolutely dependent on tetrahydrofolate; pyridoxal phosphate has no effect on the activity. The stability of this activity in the isolated mitochondria was dependent on the presence of sulfhydryl compounds. It was apparently more stable at pH 7.0 to 7.5 than at higher pH even though the pH optimum of serine hydroxymethyltransferase was 8.5 for both the mitochondrial and cytoplasmic fractions. Distribution studies have indicated that serine hydroxymethyltransferase was predominantly located in the mitochondria. The activity of serine hydroxymethyltransferase was observed to be co-compartmented with glycine decarboxylation and malate dehydrogenase behind the mitochondrial inner membrane. This activity could be solubilized by KCl from osmotically ruptured mitochondrial membrane fractions but substantial activity (35 to 40%) was still retained with the membrane fractions at 0.3 m KCl. This suggests that the glycine decarboxylation-serine hydroxymethyltransferase complex may be closely bound to the internal surface of the mitochondrial inner membrane.The relationship of this integrated enzyme complex to CO(2) evolution and serine synthesis during photorespiration and the physiological role of the dicarboxylate shuttle were discussed.}, }
@article {pmid16658075, year = {1972}, author = {Denius, HR and Homann, PH}, title = {The Relation between Photosynthesis, Respiration, and Crassulacean Acid Metabolism in Leaf Slices of Aloe arborescens Mill.}, journal = {Plant physiology}, volume = {49}, number = {6}, pages = {873-880}, pmid = {16658075}, issn = {0032-0889}, abstract = {Leaves and leaf slices from Aloe arborescens Mill. were used to study the interrelations between Crassulacean acid metabolism, photosynthesis, and respiration. Oxygen exchange of leaf slices was measured polarographically. It was found that the photosynthetic utilization of stored malic acid resulted in a net evolution of oxygen. This oxygen production, and the decrease in acid content of the leaf tissue, were completely inhibited by amytal, although the rate of respiratory oxygen uptake was hardly affected by the presence of this inhibitor of mitochondrial electron transport. Other poisons of respiration (cyanide) and of the tricarboxylic acid cycle (trifluoroacetate, 2-diethyl malonate) also were effective in preventing acid-dependent oxygen evolution. It is concluded that the mobilization of stored acids during light-dependent deacidification of the leaves depends on the operation of the tricarboxylic acid cycle and of the electron transport of the mitochondria.A comparison of enzyme activities in extracts from Aloe leaves and from other plants and studies of leaf anatomy and chloroplast morphology revealed typical characteristics of C(3)-, as well as C(4)-, plants in Aloe.}, }
@article {pmid16657879, year = {1971}, author = {Tillberg, JE and Kylin, A and Sundberg, I}, title = {Microcalorimetric Measurements of the Heat Evolution and Its Sensitivity to Dinitrophenol during Different Stages of Synchronous Cultures of Scenedesmus.}, journal = {Plant physiology}, volume = {48}, number = {6}, pages = {779-782}, pmid = {16657879}, issn = {0032-0889}, abstract = {The applicability of the LKB flow microcalorimeter in a microalgal system was tested. Respiration and its sensitivity to 2,4-dinitrophenol during different stages of a synchronous culture of Scenedesmus obtusiusculus were studied. In cells harvested during the first 8 hours of illumination, heat evolution was 10 to 15 microwatts per 10 million cells and then rose to a peak of about 80 microwatts per 10 million when the cells were harvested in the beginning of the dark period, just before the onset of the divisions. Calculated per milligram dry weight, the highest values were about 140 microwatts, also obtained early in the dark period, after which the values dropped. They were roughly 90 microwatts per milligram at the onset of light and a little below 70 microwatts per milligram after 8 hours of illumination. Thus, the synthesis of new cell material does not give rise to actively respiring mitochondria during the first half of the light period, after which the situation is reversed. Low concentrations of dinitrophenol increased heat evolution, and high concentrations were inhibitory. Cells from the early stages of development were more sensitive to dinitrophenol than older cells. Young cells gave a transient peak of heat evolution even when the steady state was inhibited. Coupled oxidative phosphorylation seems necessary for substrate mobilization and transport to the mitochondria of the young cells. Possibly, young cells use mainly fatty acids and old cells carbohydrates as their main substrate for respiration.}, }
@article {pmid16657076, year = {1969}, author = {Yamamoto, Y}, title = {Modification of metabolic pattern by variation of nicotinamide adenine dinucleotide phosphate level.}, journal = {Plant physiology}, volume = {44}, number = {3}, pages = {407-412}, pmid = {16657076}, issn = {0032-0889}, abstract = {The experiments were designed to get some information on the metabolism controlled by variation of the NADP level, which is known to change with the variation of environmental factors.The exogenous NADP added to the mitochondria prepared from Vigna sesquipedalis cotyledons was associated with and/or penetrated into the mitochondria. The combined NADP served in the operation of the mitochondrial NADP-isocitric acid dehydrogenase.The variation of NADP level by exogenous NADP was observed to modify the rates of metabolic processes. The increase of exogenous NADP in Vigna hypocotyl slices lowered malic- and citric-acid contents and raised the alpha-ketoglutaric acid content. The incorporation of (14)C from acetate-2-(14)C into lipid, organic acid, amino acid, was promoted with the exogenous NADP. The (14)C-incorporation into glycolic acid, malic acid and glutamic acid was accelerated.In the mannitol homogenate of Vigna cotyledon, (14)CO(2) evolution and (14)C-incorporation into lipid, sugar, and glycolic acid from acetate-2-(14)C were promoted with the exogenous NADP. Endogenous citric acid content was lowered by NADP, while malic acid content was increased.The activation of NADP-enzymes by NADP was discussed to be involved in these variations.}, }
@article {pmid16742506, year = {1967}, author = {Stewart, PR and Quayle, JR}, title = {The synergistic decarboxylation of glyoxylate and 2-oxoglutarate by an enzyme system from pig-liver mitochondria.}, journal = {The Biochemical journal}, volume = {102}, number = {3}, pages = {885-897}, pmid = {16742506}, issn = {0264-6021}, abstract = {1. An enzyme system that catalyses a synergistic decarboxylation of glyoxylate and 2-oxoglutarate has been purified from pig-liver mitochondria. 2. The purified system is specific for glyoxylate and 2-oxoglutarate as substrates, although in earlier stages of purification glycine and l-glutamate are also active. 3. The reaction is inhibited strongly by EDTA and N-ethylmaleimide. Substrate analogues, present at concentrations equimolar with respect to the substrates, are not effective as inhibitors. 4. The reaction proceeds in the absence of added cofactors. Magnesium chloride, mercaptoethanol and sucrose stimulate the reaction, and stabilize the activity of the enzyme. 5. The pH optimum of the reaction is 7.0. The K(m) values of glyoxylate and 2-oxoglutarate, at saturating concentration of the corresponding co-substrate, are 16mm and 3.6mm respectively. 6. Isotopic work with specifically labelled [(14)C]glyoxylate and 2-oxo[(14)C]-glutarate suggests that the enzyme system catalyses an initial condensation of glyoxylate and 2-oxoglutarate that results in, or leads to, release of C-1 of both substrates as carbon dioxide. C-2 of glyoxylate and C-5 of 2-oxoglutarate do not appear as carbon dioxide. 7. The stoicheiometry of the reaction is complex. During the initial stages of the reaction, more carbon dioxide is recovered from 2-oxoglutarate than from glyoxylate. Subsequently, there is a disproportionate increase with time of carbon dioxide evolution from the carboxyl group of glyoxylate. The excess of decarboxylation of glyoxylate over 2-oxogluturate is further increased by treatment of reaction products with acid.}, }
@article {pmid14424894, year = {1959}, author = {MUEHLETHALER, K and FREY-WYSSLING, A}, title = {[Development and structure of proplastids].}, journal = {The Journal of biophysical and biochemical cytology}, volume = {6}, number = {3}, pages = {507-512}, pmid = {14424894}, issn = {0095-9901}, mesh = {*Light ; Membranes ; *Phylogeny ; Plants/*anatomy &amp; histology ; *Plastids ; *Thylakoids ; }, abstract = {In this study the proplastid development in embryonic cells is described for the apical meristem of Elodea canadensis, embryo sacs from Lilies, and Begonia leaf buds. The formation of these cell organelles originates with submicroscopical particles which consist of a homogeneous stroma with a surrounding double membrane. When these proplastids reach an average size of 1 µ, the inner layer of the membrane begins to invaginate into the stroma. This process is comparable to tubuli formation in mitochondria. Under growth conditions with sufficient exposure to light, the development of the grana and stroma lamellae proceeds without interruption. If the plants are kept in the dark, small vesicles are formed which accumulate in the prolamellar body of the proplastids. After illumination these elementary vesicles merge to form membranes which evolve into grana and stroma lamellae. The structural similarity of the early proplastid stages with the mitochondria seems to indicate that there exists some phylogenetic relationship between the two cell organelles.}, }
@article {pmid13330232, year = {1956}, author = {GRASSE, PP and CARASSO, N and FAVARD, P}, title = {[Evolution of mitochondrial ultrastructure during the formation of the intermediary segment of spermatozoa of the snail Helix pomatia].}, journal = {Comptes rendus hebdomadaires des seances de l'Academie des sciences}, volume = {242}, number = {16}, pages = {1933-1935}, pmid = {13330232}, issn = {0001-4036}, mesh = {Animals ; *Biological Evolution ; *Helix, Snails ; Male ; *Mitochondria ; *Spermatozoa ; }, }
@article {pmid13163332, year = {1954}, author = {KRETCHMER, N and DICKERMAN, HW}, title = {Cellular mechanisms of protein metabolism in the nephron. IV. The partition of succinoxidase and cytochrome oxidase activities in the cells of the proximal convolution of the rat after intraperitoneal injection of egg white.}, journal = {The Journal of experimental medicine}, volume = {99}, number = {6}, pages = {629-635}, pmid = {13163332}, issn = {0022-1007}, mesh = {Animals ; *Egg White ; *Electron Transport Complex IV ; *Injections, Intraperitoneal ; Kidney/*metabolism ; *Mitochondria ; *Nephrons ; *Oxidoreductases ; Proteins/*metabolism ; Rats ; }, abstract = {1. Shifts of enzymatic activity have been followed during the formation and evolution of the droplets that form in the cells of the proximal convolution of the nephron of the rat after the injection of a 50 per cent solution of egg white in isotonic saline. 2. Twelve hours after injection there is a 35 to 40 per cent decrease in succinoxidase and cytochrome oxidase activities in the fraction containing the larger particles; i.e. mitochondria and droplets in equal concentration. Although after 30 hours the quantitative proportion of droplets and mitochondria is the same as previously, the activities of the fraction have returned to the normal observed originally in the uninjected rat in a corresponding fraction consisting of mitochondria only. 3. The microsome fraction shows an average increase of 35 per cent in oxidative enzyme activities during the early period following injection, and decreases to the original figure in the later period of droplet formation. 4. It is concluded from the shifting pattern of localization of oxidative enzyme activity within the cell particulates that the absorption droplets arise by the incorporation of the mitochondrial elements, which originally contain the highest enzyme activity, with absorbed protein through the intermediate stage of smaller (microsomal) particles.}, }
@article {pmid13163330, year = {1954}, author = {OLIVER, J and MOSES, MJ and MACDOWELL, MC and LEE, YC}, title = {Cellular mechanisms of protein metabolism in the nephron. II. The histochemical characteristics of protein absorption droplets.}, journal = {The Journal of experimental medicine}, volume = {99}, number = {6}, pages = {605-620}, pmid = {13163330}, issn = {0022-1007}, mesh = {*Cytoplasm ; Kidney/*metabolism ; *Mitochondria ; *Nephrons ; Proteins/*metabolism ; }, abstract = {Histochemical methods show not only the presence of absorbed protein in the cellular droplet, but also the general identity of its constituent substances with those of the mitochondrial rodlets. Both contain considerable amounts of phospholipid and probably some PNA. The reactivity of the cytoplasmic constituents in droplet and in rodlet are different, however, since in the droplet these substances stain more intensely. As judged by variations observed in this intensity during the evolution of the droplet, these constituents and the absorbed protein vary in their proportions and amount. The droplet would appear to be a highly active center of protein metabolism.}, }
@article {pmid13163329, year = {1954}, author = {OLIVER, J and MACDOWELL, M and LEE, YC}, title = {Cellular mechanisms of protein metabolism in the nephron. I. The structural aspects of proteinuria; tubular absorption, droplet formation, and the disposal of proteins.}, journal = {The Journal of experimental medicine}, volume = {99}, number = {6}, pages = {589-604}, pmid = {13163329}, issn = {0022-1007}, mesh = {Kidney/*metabolism ; *Kidney Diseases ; *Nephrons ; Proteins/*metabolism ; *Proteinuria ; }, abstract = {When proteins pass the glomerular filter they are in part directly absorbed by the epithelial cells of the proximal convolution of the nephron with no apparent alteration of the cytological pattern. If the capacity of the tubule cells to thus absorb protein from the tubule fluid is exceeded either by the amount or the nature of the protein the accessory mechanism of droplet formation occurs. This accessory mechanism is an intracellular process in which cytoplasmic elements, the mitochondria with their enzymes, and the absorbed protein combine to form droplets. As the droplets form and then disappear from the renal cells their evolution presents a constantly changing picture depending on the varying nature of their protein and cytoplasmic content. The droplet is therefore not a cytological structure of fixed characteristics (hyaline droplet) but a locus of metabolic activity and varied structural aspect.}, }
@article {pmid14954595, year = {1952}, author = {MEYER, J}, title = {[Cellular dedifferentiation and cleavage of mitochondria during the evolution of nursing cells of the galls in the bramble (Diastrophus Rubi Htg.)].}, journal = {Comptes rendus hebdomadaires des seances de l'Academie des sciences}, volume = {234}, number = {4}, pages = {463-464}, pmid = {14954595}, issn = {0001-4036}, mesh = {*Biological Evolution ; *Cell Physiological Phenomena ; *Cytokinesis ; Humans ; *Mitochondria ; *Neoplasms ; *Neoplasms, Experimental ; }, }
@article {pmid14944285, year = {1952}, author = {CHEVREMONT, M and FREDERIC, J}, title = {[The origin of the chondriosomes during somatic mitosis studied in living cells raised in vitro by phase contrast microscopy and microcinematography].}, journal = {Archives de biologie}, volume = {58}, number = {2}, pages = {259-277}, pmid = {14944285}, issn = {0003-9624}, mesh = {*Hepatocytes ; Humans ; In Vitro Techniques ; *Microscopy ; *Microscopy, Phase-Contrast ; *Mitochondria ; *Mitosis ; *Photography ; }, }
@article {pmid12520044, year = {2003}, author = {Rainaldi, G and Volpicella, M and Licciulli, F and Liuni, S and Gallerani, R and Ceci, LR}, title = {PLMItRNA, a database on the heterogeneous genetic origin of mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes.}, journal = {Nucleic acids research}, volume = {31}, number = {1}, pages = {436-438}, pmid = {12520044}, issn = {1362-4962}, mesh = {Chlorophyta/genetics ; *Databases, Nucleic Acid ; Eukaryota/*genetics ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; *Genes, Plant ; Genetic Variation ; Magnoliopsida/genetics ; Mitochondria/*genetics ; Photosynthesis ; Promoter Regions, Genetic ; RNA, Transfer/biosynthesis/*genetics ; Sequence Alignment ; Transcription, Genetic ; }, abstract = {The updated version of PLMItRNA reports information and multialignments on 609 genes and 34 tRNA molecules active in the mitochondria of Viridiplantae (27 Embryophyta and 10 Chlorophyta), and photosynthetic algae (one Cryptophyta, four Rhodophyta and two Stramenopiles). Colour-code based tables reporting the different genetic origin of identified genes allow hyper-textual link to single entries. Promoter sequences identified for tRNA genes in the mitochondrial genomes of Angiospermae are also reported. The PLMItRNA database is accessible at http://bighost.area.ba.cnr.it/PLMItRNA/.}, }
@article {pmid12519975, year = {2003}, author = {O'Brien, EA and Badidi, E and Barbasiewicz, A and deSousa, C and Lang, BF and Burger, G}, title = {GOBASE--a database of mitochondrial and chloroplast information.}, journal = {Nucleic acids research}, volume = {31}, number = {1}, pages = {176-178}, pmid = {12519975}, issn = {1362-4962}, mesh = {Animals ; Chloroplasts/*genetics ; *Databases, Genetic ; Evolution, Molecular ; Genome ; Mitochondria/*genetics ; Mitochondrial Proteins/chemistry ; Nucleic Acid Conformation ; Plant Proteins/chemistry ; RNA/chemistry ; RNA, Chloroplast/chemistry ; RNA, Mitochondrial ; User-Computer Interface ; }, abstract = {GOBASE is a relational database containing integrated sequence, RNA secondary structure and biochemical and taxonomic information about organelles. GOBASE release 6 (summer 2002) contains over 130 000 mitochondrial sequences, an increase of 37% over the previous release, and more than 30 000 chloroplast sequences in a new auxiliary database. To handle this flood of new data, we have designed and implemented GOpop, a Java system for population and verification of the database. We have also implemented a more powerful and flexible user interface using the PHP programming language. http://megasun.bch.umontreal.ca/gobase/gobase.html.}, }
@article {pmid12519917, year = {2003}, author = {Marx, S and Baumgärtner, M and Kannan, S and Braun, HP and Lang, BF and Burger, G}, title = {Structure of the bc1 complex from Seculamonas ecuadoriensis, a jakobid flagellate with an ancestral mitochondrial genome.}, journal = {Molecular biology and evolution}, volume = {20}, number = {1}, pages = {145-153}, doi = {10.1093/molbev/msg016}, pmid = {12519917}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Cells, Cultured ; Electron Transport Complex III/*chemistry/*genetics ; Eukaryota/*chemistry/genetics ; Evolution, Molecular ; Humans ; Mitochondria/*genetics/physiology ; Molecular Sequence Data ; *Protein Structure, Quaternary ; Protein Subunits/chemistry/genetics ; Sequence Alignment ; }, abstract = {In eubacteria, the respiratory bc(1) complex (complex III) consists of three or four different subunits, whereas that of mitochondria, which have descended from an alpha-proteobacterial endosymbiont, contains about seven additional subunits. To understand better how mitochondrial protein complexes evolved from their simpler bacterial predecessors, we purified complex III of Seculamonas ecuadoriensis, a member of the jakobid protists, which possess the most bacteria-like mitochondrial genomes known. The S. ecuadoriensis complex III has an apparent molecular mass of 460 kDa and exhibits antimycin-sensitive quinol:cytochrome c oxidoreductase activity. It is composed of at least eight subunits between 6 and 46 kDa in size, including two large "core" subunits and the three "respiratory" subunits. The molecular mass of the S. ecuadoriensis bc(1) complex is slightly lower than that reported for other eukaryotes, but about 2x as large as complex III in bacteria. This indicates that the departure from the small bacteria-like complex III took place at an early stage in mitochondrial evolution, prior to the divergence of jakobids. We posit that the recruitment of additional subunits in mitochondrial respiratory complexes is a consequence of the migration of originally alpha-proteobacterial genes to the nucleus.}, }
@article {pmid12517306, year = {2003}, author = {Catoni, E and Desimone, M and Hilpert, M and Wipf, D and Kunze, R and Schneider, A and Flügge, UI and Schumacher, K and Frommer, WB}, title = {Expression pattern of a nuclear encoded mitochondrial arginine-ornithine translocator gene from Arabidopsis.}, journal = {BMC plant biology}, volume = {3}, number = {}, pages = {1}, pmid = {12517306}, issn = {1471-2229}, mesh = {Arabidopsis/genetics/metabolism ; Arabidopsis Proteins/*genetics/metabolism ; Arginine/metabolism ; Cell Nucleus/genetics ; *Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genetic Complementation Test ; Glucuronidase/genetics/metabolism ; Membrane Transport Proteins/*genetics/metabolism ; Mitochondrial Proteins/*genetics/metabolism ; Mutation ; Ornithine/metabolism ; Phylogeny ; Plants, Genetically Modified ; Promoter Regions, Genetic/genetics ; Recombinant Fusion Proteins/genetics/metabolism ; Saccharomyces cerevisiae/genetics ; }, abstract = {BACKGROUND: Arginine and citrulline serve as nitrogen storage forms, but are also involved in biosynthetic and catabolic pathways. Metabolism of arginine, citrulline and ornithine is distributed between mitochondria and cytosol. For the shuttle of intermediates between cytosol and mitochondria transporters present on the inner mitochondrial membrane are required. Yeast contains a mitochondrial translocator for ornithine and arginine, Ort1p/Arg11p. Ort1p/Arg11p is a member of the mitochondrial carrier family (MCF) essential for ornithine export from mitochondria. The yeast arg11 mutant, which is deficient in Ort1p/Arg11p grows poorly on media lacking arginine.<br><br>RESULTS: High-level expression of a nuclear encoded Arabidopsis thaliana homolog (AtmBAC2) of Ort1p/Arg11p was able to suppress the growth deficiency of arg11. RT-PCR analysis demonstrated expression of AtmBAC2 in all tissues with highest levels in flowers. Promoter-GUS fusions showed preferential expression in flowers, i.e. pollen, in the vasculature of siliques and in aborted seeds. Variable expression was observed in leaf vasculature. Induction of the promoter was not observed during the first two weeks in seedlings grown on media containing NH4NO3, arginine or ornithine as sole nitrogen sources.<br><br>CONCLUSION: AtmBAC2 was isolated as a mitochondrial transporter for arginine in Arabidopsis. The absence of expression in developing seeds and in cotyledons of seedlings indicates that other transporters are responsible for storage and mobilization of arginine in seeds.}, }
@article {pmid12511651, year = {2003}, author = {Taylor, MS and Hellberg, ME}, title = {Genetic evidence for local retention of pelagic larvae in a Caribbean reef fish.}, journal = {Science (New York, N.Y.)}, volume = {299}, number = {5603}, pages = {107-109}, doi = {10.1126/science.1079365}, pmid = {12511651}, issn = {1095-9203}, mesh = {Animals ; Anthozoa ; Atlantic Ocean ; Bahamas ; Caribbean Region ; Color ; Cytochrome b Group/genetics ; *Ecosystem ; Genetic Drift ; Genetic Variation ; *Genetics, Population ; Geography ; Haplotypes ; Larva/growth &amp; development/physiology ; Mitochondria/genetics ; Otolithic Membrane/growth &amp; development ; Perciformes/classification/*genetics/growth &amp; development/*physiology ; Phylogeny ; Polymerase Chain Reaction ; Reproduction ; }, abstract = {The pelagic larvae of many marine organisms can potentially disperse across hundreds of kilometers, but whether oceanographic or behavioral mechanisms can constrain dispersal over periods sufficient for the evolution of genetic differentiation remains unclear. Here, we concurrently examine larval duration and genetic population differentiation in a cleaner goby, Elacatinus evelynae, a member of the most species-rich genus of Caribbean reef fishes. Despite evidence for extended pelagic duration (21 days), populations of E. evelynae show strong genetic differentiation: among color forms (1.36 to 3.04% divergent at mitochondrial cytochrome b) and among island populations within color forms (Phi(ST) up to 70%). These results suggest that marine populations can remain demographically closed for thousands of generations despite extended larval duration, and that recognition cues such as color may promote speciation when geographic barriers are transient or weak.}, }
@article {pmid12511632, year = {2003}, author = {Palumbi, SR and Warner, RR}, title = {Ecology. Why gobies are like Hobbits.}, journal = {Science (New York, N.Y.)}, volume = {299}, number = {5603}, pages = {51-52}, doi = {10.1126/science.1080775}, pmid = {12511632}, issn = {1095-9203}, mesh = {Animals ; Anthozoa ; Atlantic Ocean ; Bahamas ; Caribbean Region ; Color ; *Ecosystem ; Genetic Drift ; Genetic Variation ; *Genetics, Population ; Geography ; Haplotypes ; Larva/growth &amp; development/physiology ; Mitochondria/genetics ; Otolithic Membrane/growth &amp; development ; Perciformes/classification/*genetics/growth &amp; development/*physiology ; Phylogeny ; Polymerase Chain Reaction ; }, }
@article {pmid12509511, year = {2003}, author = {Mishmar, D and Ruiz-Pesini, E and Golik, P and Macaulay, V and Clark, AG and Hosseini, S and Brandon, M and Easley, K and Chen, E and Brown, MD and Sukernik, RI and Olckers, A and Wallace, DC}, title = {Natural selection shaped regional mtDNA variation in humans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {100}, number = {1}, pages = {171-176}, pmid = {12509511}, issn = {0027-8424}, support = {NS21328/NS/NINDS NIH HHS/United States ; R56 NS037167/NS/NINDS NIH HHS/United States ; TW01366/TW/FIC NIH HHS/United States ; TW01175/TW/FIC NIH HHS/United States ; R01 NS037167/NS/NINDS NIH HHS/United States ; R03 TW001366/TW/FIC NIH HHS/United States ; HL64017/HL/NHLBI NIH HHS/United States ; NS37167/NS/NINDS NIH HHS/United States ; R01 NS021328/NS/NINDS NIH HHS/United States ; R01 AG013154/AG/NIA NIH HHS/United States ; AG13154/AG/NIA NIH HHS/United States ; }, mesh = {Africa ; Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Genetic Variation ; Hominidae/*genetics ; Humans ; Mitochondria/genetics ; Molecular Sequence Data ; Oxidative Phosphorylation ; Phylogeny ; *Selection, Genetic ; }, abstract = {Human mtDNA shows striking regional variation, traditionally attributed to genetic drift. However, it is not easy to account for the fact that only two mtDNA lineages (M and N) left Africa to colonize Eurasia and that lineages A, C, D, and G show a 5-fold enrichment from central Asia to Siberia. As an alternative to drift, natural selection might have enriched for certain mtDNA lineages as people migrated north into colder climates. To test this hypothesis we analyzed 104 complete mtDNA sequences from all global regions and lineages. African mtDNA variation did not significantly deviate from the standard neutral model, but European, Asian, and Siberian plus Native American variations did. Analysis of amino acid substitution mutations (nonsynonymous, Ka) versus neutral mutations (synonymous, Ks) (kaks) for all 13 mtDNA protein-coding genes revealed that the ATP6 gene had the highest amino acid sequence variation of any human mtDNA gene, even though ATP6 is one of the more conserved mtDNA proteins. Comparison of the kaks ratios for each mtDNA gene from the tropical, temperate, and arctic zones revealed that ATP6 was highly variable in the mtDNAs from the arctic zone, cytochrome b was particularly variable in the temperate zone, and cytochrome oxidase I was notably more variable in the tropics. Moreover, multiple amino acid changes found in ATP6, cytochrome b, and cytochrome oxidase I appeared to be functionally significant. From these analyses we conclude that selection may have played a role in shaping human regional mtDNA variation and that one of the selective influences was climate.}, }
@article {pmid12505184, year = {2003}, author = {Yang, MY and Dong, HF and Jiang, MS}, title = {Ultrastructural observation of spermatozoa and fertilization in Schistosoma japonicum.}, journal = {Acta tropica}, volume = {85}, number = {1}, pages = {63-70}, doi = {10.1016/s0001-706x(02)00233-4}, pmid = {12505184}, issn = {0001-706X}, mesh = {Animals ; Female ; Fertilization/*physiology ; Male ; Microscopy, Electron ; Microtubules/ultrastructure ; Ovum/cytology/metabolism/ultrastructure ; Schistosoma japonicum/*embryology/ultrastructure ; Sperm Head/ultrastructure ; Sperm Tail/ultrastructure ; Sperm-Ovum Interactions ; Spermatozoa/cytology/*ultrastructure ; }, abstract = {The ultrastructure of the sperm and the process of fertilization are described in Schistosoma japonicum. The sperm of S. japonicum has an elongated head and a single tail. The head measures 6.2 x 1.4 microm in average size. No acrosome is present. A mass of mitochondria locates in front of the nucleus. A layer of about 100-120 peripheral microtubules is parallel with the long axis of the head under plasma membrane. The nucleus is dense with some electron-lucent patches. The tail is a single flagellum with unique axoneme, which originates from a centriole. The structure of axoneme includes two types: 9 x 2 + <<l>> in the main part of the flagellum, and 9 x 2 + 0 near the end of the flagellum. The sperm ultrastructure of S. japonicum is similar to that of other schistosomes, apart from the fact that two types of configuration coexisted in the same axoneme, and there is no striated root found in S. japonicum. The sperm differs distinctly from other Digenea. The aberrant ultrastructure of S. japonicum reflects that its evolution is far away from other genera in Digenea. Fertilization occurs at the posterior part of oviduct, in which region the oviduct wall lacks lamellae. Some cortical granules (CG) fuse with plasma membrane, and discharge their content on the surface of the fertilized ovum. The other CGs break down or degenerate in the cytoplasm. By the secondary mature division, the secondary oocyte finally divides to form a female pronucleus. During this period a male pronucleus also forms. The female and male pronucleus approach each other, come into contact in the central region and finally fuse to form a zygote. The function of CGs is discussed.}, }
@article {pmid12504895, year = {2003}, author = {Hanover, JA and Yu, S and Lubas, WB and Shin, SH and Ragano-Caracciola, M and Kochran, J and Love, DC}, title = {Mitochondrial and nucleocytoplasmic isoforms of O-linked GlcNAc transferase encoded by a single mammalian gene.}, journal = {Archives of biochemistry and biophysics}, volume = {409}, number = {2}, pages = {287-297}, doi = {10.1016/s0003-9861(02)00578-7}, pmid = {12504895}, issn = {0003-9861}, mesh = {Amino Acid Sequence ; Animals ; Cell Nucleus/*enzymology ; Chromosome Mapping ; Cytoplasm/*enzymology ; Gene Expression Regulation, Enzymologic ; HeLa Cells ; Humans ; Isoenzymes/*genetics ; Mice ; Mitochondria/*enzymology ; Molecular Sequence Data ; N-Acetylglucosaminyltransferases/chemistry/*genetics ; Rats ; Restriction Mapping ; }, abstract = {O-Linked N-acetylglucosamine (GlcNAc) transferase (OGT) mediates a novel hexosamine-dependent signal transduction pathway. Yet, little is known about the regulation of ogt gene expression in mammals. We report the sequence and characterization of the mouse ogt locus and provide a comparison with the human and rat ogt genes. The mammalian ogt genes are similar in structure and exhibit approximately 80% sequence identity. The mouse and human ogt genes contain two potential promoters producing four major transcripts. By analyzing 56 human cDNA clones and other existing expressed sequence tags, we found that at least three protein products differing at their amino terminus result from alternative splicing. We used OGT-specific antisera to demonstrate the presence of these isoforms in HeLa cells. The longest form is a nucleocytoplasmic OGT (ncOGT) with 12 tetratricopeptide repeats (TPRs); a shorter form of OGT encodes a mitochondrially sequestered enzyme with 9 TPRs and an N-terminal mitochondrion-targeting sequence (mOGT). An even shorter form of OGT (sOGT) contains only 2 TPRs. The genomic organization of OGT appears to be highly conserved throughout metazoan evolution. These results provide the basis for a more detailed analysis of the significance and regulation of the nucleocytoplasmic and mitochondrial isoforms of OGT in mammals.}, }
@article {pmid12493623, year = {2003}, author = {Rio, JP and Repérant, J and Vesselkin, NP and Kenigfest-Rio, NB and Miceli, D}, title = {Dual innervation of the lamprey retina by GABAergic and glutamatergic retinopetal fibers. A quantitative EM immunogold study.}, journal = {Brain research}, volume = {959}, number = {2}, pages = {336-342}, doi = {10.1016/s0006-8993(02)03803-9}, pmid = {12493623}, issn = {0006-8993}, mesh = {Animals ; Glutamine/*analysis ; Immunohistochemistry ; Lampreys/anatomy &amp; histology ; Microscopy, Immunoelectron/methods ; Nerve Fibers/chemistry/*ultrastructure ; Retina/*chemistry/*ultrastructure ; gamma-Aminobutyric Acid/*analysis ; }, abstract = {A quantitative electron microscopic analysis of glutamate and GABA immunocytochemistry, using the postembedding immunogold technique, was undertaken in the lamprey retina to determine the proportion of glutamate-immunoreactive (GLU-ir) centrifugal visual terminals which were identified by anterograde axonal transport after an iontophoretic deposit of HRP in the sectioned optic nerve. Single immunogold labeling carried out with two different GABA and GLU antibodies showed that about 45% of the retinopetal axon terminals were GABAergic, and that two types of GLU-ir terminals (GLU-ir/1 and GLU-ir/2) were observed in the inner plexiform layer. The former type showed a high density of gold particles (Neosystem: 19.38+/-0.74; Sigma: 106.26+/-5.70) which statistically differed from the GLU-ir/2 (Neosystem: 3.23+/-0.31; Sigma: 31.73+/-5.61). Subcellular estimates showed that gold particles were concentrated over the vesicular pool in the GLU-ir/1 terminals and over mitochondria in the second terminal type. Consecutive sections alternately processed for GABA and GLU revealed that the GABA-immunonegative terminals corresponded to the GLU-ir/1, whereas the GABA-ir terminals only contained few GLU-ir particles, mostly concentrated in mitochondria. The occurrence of GABAergic and glutamatergic retinopetal terminals in the adult lamprey retina is discussed in functional terms of their differential inhibitory and excitatory effects on ganglion cell activity and the possible role of the centrifugal visual system in visually-guided behavior.}, }
@article {pmid12483296, year = {2003}, author = {Niemi, AK and Hervonen, A and Hurme, M and Karhunen, PJ and Jylhä, M and Majamaa, K}, title = {Mitochondrial DNA polymorphisms associated with longevity in a Finnish population.}, journal = {Human genetics}, volume = {112}, number = {1}, pages = {29-33}, doi = {10.1007/s00439-002-0843-y}, pmid = {12483296}, issn = {0340-6717}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Aging/genetics ; DNA, Mitochondrial/*genetics ; Female ; Finland ; Gene Frequency ; Haplotypes ; Hospital Records ; Humans ; Infant ; Longevity/*genetics ; Male ; Middle Aged ; Phylogeny ; *Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; Residence Characteristics/statistics &amp; numerical data ; }, abstract = {Sequence variation in mitochondrial DNA (mtDNA) may cause slight differences both in the functioning of the respiratory chain and in free radical production, and an association between certain mtDNA haplogroups and longevity has been suggested. In order to determine further the role of mtDNA in longevity, we studied the frequencies of mtDNA haplogroups and haplogroup clusters among elderly subjects and controls in a Finnish population. Samples were obtained from 225 persons aged 90-91 years (Vitality 90+) and from 400 middle-aged controls and 257 infants. MtDNA haplogroups were determined by restriction fragment length polymorphism. The haplogroup frequencies of the Vitality 90+ group differed from both those of the middle-aged controls (P=0.01) and the infants (P=0.00005), haplogroup H being less frequent than among the middle-aged subjects (P=0.001) and infants (P=0.00001), whereas haplogroups U and J were more frequent. Haplogroup clusters also differed between Vitality 90+ and both the middle-aged subjects (P=0.002) and infants (P=0.00001), the frequency of haplogroup cluster HV being lower in the former and that of UK and WIX being higher. These data suggest an association between certain mtDNA haplogroups or haplogroup clusters and longevity. Furthermore, our data appear to favour the presence of advantageous polymorphisms and support a role for mitochondria and mtDNA in the degenerative processes involved in ageing.}, }
@article {pmid12482879, year = {2003}, author = {Fransson, A and Ruusala, A and Aspenström, P}, title = {Atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis.}, journal = {The Journal of biological chemistry}, volume = {278}, number = {8}, pages = {6495-6502}, doi = {10.1074/jbc.M208609200}, pmid = {12482879}, issn = {0021-9258}, mesh = {3T3 Cells ; Amino Acid Sequence ; Animals ; Apoptosis/*physiology ; COS Cells ; Chlorocebus aethiops ; Homeostasis ; Mammals ; Mice ; Mitochondria/*physiology/ultrastructure ; Mitochondrial Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Sequence Alignment ; Sequence Homology, Amino Acid ; Transfection ; rho GTP-Binding Proteins/chemistry/genetics/*metabolism ; }, abstract = {The human genomic sequencing effort has revealed the presence of a large number of Rho GTPases encoded by the human genome. Here we report the characterization of a new family of Rho GTPases with atypical features. These proteins, which were called Miro-1 and Miro-2 (for mitochondrial Rho), have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms from Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster to mammals, indicating that these genes evolved early during evolution. Immunolocalization experiments, in which transfected NIH3T3 and COS 7 cells were stained for ectopically expressed Miro as well as for the endogenous Miro-1 protein, showed that Miro was present in mitochondria. Interestingly, overexpression of a constitutively active mutant of Miro-1 (Miro-1/Val-13) induced an aggregation of the mitochondrial network and resulted in an increased apoptotic rate of the cells expressing activated Miro-1. These data indicate a novel role for Rho-like GTPases in mitochondrial homeostasis and apoptosis.}, }
@article {pmid12481049, year = {2002}, author = {Liu, F and Schnable, PS}, title = {Functional specialization of maize mitochondrial aldehyde dehydrogenases.}, journal = {Plant physiology}, volume = {130}, number = {4}, pages = {1657-1674}, pmid = {12481049}, issn = {0032-0889}, mesh = {Acetaldehyde/metabolism ; Aldehyde Dehydrogenase/chemistry/genetics/*metabolism ; Amino Acid Sequence ; Basic-Leucine Zipper Transcription Factors ; Flowers/genetics/physiology ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Indoleacetic Acids/metabolism ; Isoenzymes/chemistry/genetics/metabolism ; Kinetics ; Lipid Peroxidation ; Mitochondria/*enzymology ; Mitochondrial Proteins/chemistry/genetics/metabolism ; Molecular Sequence Data ; Nuclear Proteins/chemistry/genetics/metabolism ; Phylogeny ; Plant Proteins/chemistry/genetics/metabolism ; Protein Conformation ; RNA, Plant/genetics/metabolism ; Reactive Oxygen Species/metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Trans-Activators ; Zea mays/*enzymology/genetics/metabolism ; }, abstract = {The maize (Zea mays) rf2a and rf2b genes both encode homotetrameric aldehyde dehydrogenases (ALDHs). The RF2A protein was shown previously to accumulate in the mitochondria. In vitro import experiments and ALDH assays on mitochondrial extracts from rf2a mutant plants established that the RF2B protein also accumulates in the mitochondria. RNA gel-blot analyses and immunohistolocation experiments revealed that these two proteins have only partially redundant expression patterns in organs and cell types. For example, RF2A, but not RF2B, accumulates to high levels in the tapetal cells of anthers. Kinetic analyses established that RF2A and RF2B have quite different substrate specificities; although RF2A can oxidize a broad range of aldehydes, including aliphatic aldehydes and aromatic aldehydes, RF2B can oxidize only short-chain aliphatic aldehydes. These two enzymes also have different pH optima and responses to changes in substrate concentration. In addition, RF2A, but not RF2B or any other natural ALDHs, exhibits positive cooperativity. These functional specializations may explain why many species have two mitochondrial ALDHs. This study provides data that serve as a basis for identifying the physiological pathway by which the rf2a gene participates in normal anther development and the restoration of Texas cytoplasm-based male sterility. For example, the observations that Texas cytoplasm anthers do not accumulate elevated levels of reactive oxygen species or lipid peroxidation and the kinetic features of RF2A make it unlikely that rf2a restores fertility by preventing premature programmed cell death.}, }
@article {pmid12474263, year = {2003}, author = {Ziese, S and Dorn, A}, title = {Embryonic integument and "molts" in Manduca sexta (Insecta, Lepidoptera).}, journal = {Journal of morphology}, volume = {255}, number = {2}, pages = {146-161}, doi = {10.1002/jmor.10056}, pmid = {12474263}, issn = {0362-2525}, mesh = {Animals ; Digestive System/embryology ; Ectoderm/cytology/physiology ; Epidermis/embryology ; Larva/growth &amp; development ; Manduca/*embryology ; Phylogeny ; }, abstract = {In Manduca sexta the germ band is formed 12 h post-oviposition (p.o.) (=10% development completed) and is located above the yolk at the egg surface. The cells show a polar organization. They are engaged in the uptake and degradation of yolk globules, pinched off from the yolk cells. This process can be observed in the integumental cells during the first growth phase of the embryo that lasts until "katatrepsis," an embryonic movement that takes place at 40% development completed. At 37% development completed, the ectoderm deposits a thin membrane at its apical surface, the first embryonic membrane, which detaches immediately before katatrepsis. The second period of embryonic growth--from katatrepsis to 84 h p.o. (70% development completed)--starts with the deposition of a second embryonic membrane that is somewhat thicker than the first one and shows a trilaminar, cuticulin-like structure. Whereas the apical cell surface is largely smooth during the deposition of the first embryonic membrane, it forms microvilli during deposition of the second one. At the same time, uptake of formed yolk material ceases and the epidermal cells now contain clusters of mitochondria below the apical surface. Rough endoplasmic reticulum (RER) increases in the perinuclear region. The second embryonic membrane detaches about 63 h p.o. At 69 h p.o., a new generation of microvilli forms and islands of a typical cuticulin layer indicate the onset of the deposition of the larval cuticle. The third growth phase is characterized by a steady increase in the embryo length, the deposition of the larval procuticle, and by cuticular tanning at about 100 h p.o. Beginning at that stage, electron-lucent vesicles aggregate below the epidermal surface and are apparently released below the larval cuticle. Manduca sexta is the first holometabolous insect in which the deposition of embryonic membranes and cuticles has been examined by electron microscopy. In correspondence with hemimetabolous insects, the embryo of M. sexta secretes three covers at approximately the same developmental stage. A marked difference: the second embryonic cover, which in Hemimetabola clearly exhibits a cuticular organization, has instead a membranous, cuticulin-like structure. We see the difference as the result of an evolutionary reductional process promoted by the redundancy of embryonic covers in the egg shell. Embryonic "molts" also occur in noninsect arthropods; their phylogenetical aspects are discussed.}, }
@article {pmid12471441, year = {2002}, author = {Notsu, Y and Masood, S and Nishikawa, T and Kubo, N and Akiduki, G and Nakazono, M and Hirai, A and Kadowaki, K}, title = {The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants.}, journal = {Molecular genetics and genomics : MGG}, volume = {268}, number = {4}, pages = {434-445}, doi = {10.1007/s00438-002-0767-1}, pmid = {12471441}, issn = {1617-4615}, mesh = {Biological Evolution ; Cell Nucleus/genetics ; DNA Transposable Elements ; DNA, Mitochondrial/*genetics ; Flowering Tops/genetics ; Genes, Plant/*genetics ; Genome, Plant ; Mitochondria/*genetics ; Molecular Sequence Data ; Oryza/*genetics ; Plastids/genetics ; RNA Editing ; RNA, Transfer/genetics ; Recombination, Genetic ; Retroelements ; }, abstract = {The entire mitochondrial genome of rice (Oryza sativa L.), a monocot plant, has been sequenced. It was found to comprise 490,520 bp, with an average G+C content of 43.8%. Three rRNA genes, 17 tRNA genes and five pseudo tRNA sequences were identified. In addition, eleven ribosomal protein genes and two pseudo ribosomal protein genes were found, which are homologous to 13 of the 16 genes for ribosomal proteins in the mitochondrial genome of the liverwort (Marchantia polymorpha). A greater degree of variation in terms of presence/absence and integrity of genes was observed among the ribosomal protein genes and tRNA genes of rice, Arabidopsis and sugar beet. Transcription and post-transcriptional modification (RNA editing) in the rice mitochondrial sequence were also examined. In all, 491 Cs in the genomic DNA were converted to Ts in cDNA. The frequency of RNA editing differed markedly depending upon the ORF considered. Sequences derived from plastid and nuclear genomes make up 6.3% and 13.4% of the mitochondrial genome, respectively. The degree of conservation of plastid sequences in the mitochondrial genome ranged from 61% to 100%, suggesting that sequence migration has occurred very frequently. Three plastid DNA fragments that were incorporated into the mitochondrial genome were subsequently transferred to the nuclear genome. Nineteen fragments that were similar to transposon or retrotransposon sequences, but different from those found in the mitochondrial genomes of dicots, were identified. The results indicate frequent and independent DNA sequence flow to and from the mitochondrial genome during the evolution of flowering plants, and this may account for the range of genetic variation observed between the mitochondrial genomes of higher plants.}, }
@article {pmid12466530, year = {2002}, author = {Minczuk, M and Piwowarski, J and Papworth, MA and Awiszus, K and Schalinski, S and Dziembowski, A and Dmochowska, A and Bartnik, E and Tokatlidis, K and Stepien, PP and Borowski, P}, title = {Localisation of the human hSuv3p helicase in the mitochondrial matrix and its preferential unwinding of dsDNA.}, journal = {Nucleic acids research}, volume = {30}, number = {23}, pages = {5074-5086}, pmid = {12466530}, issn = {1362-4962}, support = {G0000153/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adenosine Triphosphatases/metabolism ; Amino Acid Sequence ; Animals ; COS Cells ; DEAD-box RNA Helicases ; DNA/metabolism ; DNA Helicases/*analysis/chemistry/*metabolism ; Escherichia coli/genetics ; HeLa Cells ; Humans ; Mitochondria/*enzymology ; Mutation ; Nucleic Acid Conformation ; Protein Transport ; RNA Helicases/*analysis/chemistry/*metabolism ; *Saccharomyces cerevisiae Proteins ; Substrate Specificity ; Yeasts/metabolism ; }, abstract = {We characterised the human hSuv3p protein belonging to the family of NTPases/helicases. In yeast mitochondria the hSUV3 orthologue is a component of the degradosome complex and participates in mtRNA turnover and processing, while in Caenorhabditis elegans the hSUV3 orthologue is necessary for viability of early embryos. Using immunofluorescence analysis, an in vitro mitochondrial uptake assay and sub-fractionation of human mitochondria we show hSuv3p to be a soluble protein localised in the mitochondrial matrix. We expressed and purified recombinant hSuv3p protein from a bacterial expression system. The purified enzyme was capable of hydrolysing ATP with a K(m) of 41.9 micro M and the activity was only modestly stimulated by polynucleotides. hSuv3p unwound partly hybridised dsRNA and dsDNA structures with a very strong preference for the latter. The presented analysis of the hSuv3p NTPase/helicase suggests that new functions of the protein have been acquired in the course of evolution.}, }
@article {pmid12460669, year = {2002}, author = {Mathiesen, C and Hägerhäll, C}, title = {Transmembrane topology of the NuoL, M and N subunits of NADH:quinone oxidoreductase and their homologues among membrane-bound hydrogenases and bona fide antiporters.}, journal = {Biochimica et biophysica acta}, volume = {1556}, number = {2-3}, pages = {121-132}, doi = {10.1016/s0005-2728(02)00343-2}, pmid = {12460669}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/*chemistry/classification/genetics/metabolism ; Cell Respiration/physiology ; Electron Transport ; Electron Transport Complex I ; Mitochondria/metabolism ; Molecular Sequence Data ; Multienzyme Complexes ; Multigene Family ; NADH, NADPH Oxidoreductases/*chemistry/classification/genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; Protein Structure, Secondary ; Protein Subunits/*chemistry/genetics/metabolism ; Recombinant Fusion Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; }, abstract = {Nicotinamide adenine dinucleotide-reduced form (NADH):quinone oxidoreductase (respiratory Complex I), F420H2 oxidoreductase and complex, membrane-bound NiFe-hydrogenase contain protein subunits homologous to a certain type of bona fide antiporters. In Complex I, these polypeptides (NuoL/ND5, NuoM/ND4, NuoN/ND2) are most likely core components of the proton pumping mechanism, and it is thus important to learn more about their structure and function. In this work, we have determined the transmembrane topology of one such polypeptide, and built a 2D structural model of the protein valid for all the homologous polypeptides. The experimentally determined transmembrane topology was different from that predicted by majority vote hydrophobicity analyses of members of the superfamily. A detailed phylogenetic analysis of a large set of primary sequences shed light on the functional relatedness of these polypeptides.}, }
@article {pmid12459260, year = {2002}, author = {Emelyanov, VV}, title = {Phylogenetic relationships of organellar Hsp90 homologs reveal fundamental differences to organellar Hsp70 and Hsp60 evolution.}, journal = {Gene}, volume = {299}, number = {1-2}, pages = {125-133}, doi = {10.1016/s0378-1119(02)01021-1}, pmid = {12459260}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Animals ; Chaperonin 60/genetics ; Chloroplasts/genetics ; *Evolution, Molecular ; HSP70 Heat-Shock Proteins/genetics ; HSP90 Heat-Shock Proteins/genetics ; Heat-Shock Proteins/*genetics ; Humans ; Mitochondria/genetics ; Models, Genetic ; Molecular Sequence Data ; Organelles/*genetics ; *Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; Symbiosis/genetics ; }, abstract = {In agreement with endosymbiont theory for the origin of organelles, mitochondria and chloroplasts (plastids) are universally accepted to have monophyletically arisen from within alpha-proteobacteria and cyanobacteria, respectively. Convincing particular evidence in support of this theory emerged from phylogenetic analysis of highly conserved, ubiquitous heat shock proteins (Hsps) chaperonin 60 and Hsp70. These apparently indispensable general chaperones have proven to be highly useful molecular tracers of organellar origin. Phylogenetic relationships of Hsp90--a less conserved and less widely distributed general chaperone--are reported here that are strikingly incongruent with canonical patterns of endosymbiotic ancestry. It appears that Hsp90 of chloroplasts derives from the endoplasmic reticulum-specific isoform while mitochondrial Hsp90 homologs affiliate with a eubacterial lineage other than alpha subdivision of proteobacteria. These data suggest that endosymbiont htpG genes, encoding Hsp90, have been either functionally displaced by pre-existing nuclear genes or completely lost during establishment of organelles and subsequently added to initial organellar complement.}, }
@article {pmid12456772, year = {2002}, author = {Stuart-Smith, K}, title = {Demystified. Nitric oxide.}, journal = {Molecular pathology : MP}, volume = {55}, number = {6}, pages = {360-366}, pmid = {12456772}, issn = {1366-8714}, mesh = {Animals ; Cell Respiration/physiology ; Endothelium, Vascular/physiology ; Evolution, Chemical ; Humans ; Mitochondria/metabolism ; Nitric Oxide/*physiology ; Oxidative Stress/physiology ; Sepsis/physiopathology ; }, abstract = {The discovery of nitric oxide (NO) demonstrated that cells could communicate via the manufacture and local diffusion of an unstable lipid soluble molecule. Since the original demonstration of the vascular relaxant properties of endothelium derived NO, this fascinating molecule has been shown to have multiple, complex roles within many biological systems. This review cannot hope to cover all of the recent advances in NO biology, but seeks to place the discovery of NO in its historical context, and show how far our understanding has come in the past 20 years. The role of NO in mitochondrial respiration, and consequently in oxidative stress, is described in detail because these processes probably underline the importance of NO in the development of disease.}, }
@article {pmid12455953, year = {2002}, author = {Nixon, JE and Wang, A and Field, J and Morrison, HG and McArthur, AG and Sogin, ML and Loftus, BJ and Samuelson, J}, title = {Evidence for lateral transfer of genes encoding ferredoxins, nitroreductases, NADH oxidase, and alcohol dehydrogenase 3 from anaerobic prokaryotes to Giardia lamblia and Entamoeba histolytica.}, journal = {Eukaryotic cell}, volume = {1}, number = {2}, pages = {181-190}, pmid = {12455953}, issn = {1535-9778}, support = {R01 AI046516/AI/NIAID NIH HHS/United States ; AI43273/AI/NIAID NIH HHS/United States ; R01 AI048082/AI/NIAID NIH HHS/United States ; AI46516/AI/NIAID NIH HHS/United States ; AI33492/AI/NIAID NIH HHS/United States ; }, mesh = {Alcohol Dehydrogenase/analysis/genetics ; Amino Acid Sequence ; Anaerobiosis ; Animals ; Bacteria/genetics ; Entamoeba histolytica/enzymology/*genetics ; Fermentation ; Ferredoxins/analysis/classification/*genetics ; *Gene Transfer, Horizontal ; Giardia lamblia/enzymology/*genetics ; Iron-Sulfur Proteins/genetics ; Mitochondria/genetics ; Models, Biological ; Molecular Sequence Data ; Multienzyme Complexes/analysis/genetics ; NADH, NADPH Oxidoreductases/analysis/genetics ; Nitroreductases/analysis/classification/genetics ; Oxidoreductases/*genetics ; Phylogeny ; Prokaryotic Cells/metabolism ; Sequence Alignment ; Sequence Analysis, Protein ; }, abstract = {Giardia lamblia and Entamoeba histolytica are amitochondriate, microaerophilic protists which use fermentation enzymes like those of bacteria to survive anaerobic conditions within the intestinal lumen. Genes encoding fermentation enzymes and related electron transport peptides (e.g., ferredoxins) in giardia organisms and amebae are hypothesized to be derived from either an ancient anaerobic eukaryote (amitochondriate fossil hypothesis), a mitochondrial endosymbiont (hydrogen hypothesis), or anaerobic bacteria (lateral transfer hypothesis). The goals here were to complete the molecular characterization of giardial and amebic fermentation enzymes and to determine the origins of the genes encoding them, when possible. A putative giardia [2Fe-2S]ferredoxin which had a hypothetical organelle-targeting sequence at its N terminus showed similarity to mitochondrial ferredoxins and the hydrogenosomal ferredoxin of Trichomonas vaginalis (another luminal protist). However, phylogenetic trees were star shaped, with weak bootstrap support, so we were unable to confirm or rule out the endosymbiotic origin of the giardia [2Fe-2S]ferredoxin gene. Putative giardial and amebic 6-kDa ferredoxins, ferredoxin-nitroreductase fusion proteins, and oxygen-insensitive nitroreductases each tentatively supported the lateral transfer hypothesis. Although there were not enough sequences to perform meaningful phylogenetic analyses, the unique common occurrence of these peptides and enzymes in giardia organisms, amebae, and the few anaerobic prokaryotes suggests the possibility of lateral transfer. In contrast, there was more robust phylogenetic evidence for the lateral transfer of G. lamblia genes encoding an NADH oxidase from a gram-positive coccus and a microbial group 3 alcohol dehydrogenase from thermoanaerobic prokaryotes. In further support of lateral transfer, the G. lamblia NADH oxidase and adh3 genes appeared to have an evolutionary history distinct from those of E. histolytica.}, }
@article {pmid12452432, year = {2002}, author = {Chen, M and Xie, K and Jiang, F and Yi, L and Dalbey, RE}, title = {YidC, a newly defined evolutionarily conserved protein, mediates membrane protein assembly in bacteria.}, journal = {Biological chemistry}, volume = {383}, number = {10}, pages = {1565-1572}, doi = {10.1515/BC.2002.176}, pmid = {12452432}, issn = {1431-6730}, support = {GM63862/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphatases/physiology ; Bacterial Proteins/chemistry/*genetics/*physiology ; Biological Transport ; *Conserved Sequence ; Escherichia coli Proteins/physiology ; Evolution, Molecular ; Intracellular Membranes/chemistry/metabolism ; Membrane Proteins/chemistry/*metabolism ; Membrane Transport Proteins/physiology ; Models, Biological ; SEC Translocation Channels ; SecA Proteins ; }, abstract = {Membranes contain proteins that catalyze a variety of reactions, which lead to the selective permeability of the membrane. For membrane proteins to function as receptors, transporters, channels, and ATPases, they must be targeted to their correct membrane and inserted into the lipid bilayer. Recently, a new membrane component called YidC was discovered that mediates the insertion of proteins into membranes in bacteria. YidC homologs also exist in mitochondria and chloroplasts. Depletion of YidC from the cell interferes with the insertion of membrane proteins that insert both dependent and independent of the SecYEG/SecDFYajC machinery. YidC directly interacts with membrane proteins during the membrane protein insertion process and assists in the folding of the hydrophobic regions into the membrane bilayer. The chloroplast and bacterial YidC homologs are truly functional homologs because the chloroplast homolog Alb3 functionally complements the bacterial YidC depletion strain. The role of YidC in the membrane insertion pathway will be reviewed.}, }
@article {pmid12449688, year = {2002}, author = {Howard, JM}, title = {"Mitochondrial Eve", "Y Chromosome Adam", testosterone, and human evolution.}, journal = {Rivista di biologia}, volume = {95}, number = {2}, pages = {319-325}, pmid = {12449688}, issn = {0035-6050}, mesh = {Animals ; *Evolution, Molecular ; Female ; *Hominidae ; Humans ; Male ; *Mitochondria ; *Testosterone ; *Y Chromosome ; }, abstract = {I suggest primate evolution began as a consequence of increased testosterone in males which increased aggression and sexuality, therefore, reproduction and success. With time, negative effects of excessive testosterone reduced spermatogenesis and started a decline of the group. Approximately 30-40 million years ago, the gene DAZ (Deleted in AZoospermia) appeared on the Y chromosome, increased spermatogenesis, and rescued the early primates from extinction. (Note: DAZ is considered by some to specifically, positively affect spermatogenesis; others suggest it has no effect on spermatogenesis.) Hominid evolution continued with increasing testosterone. The advent of increased testosterone in females of Homo erectus (or Homo ergaster) increased the female-to-male body size ratio, and eventually produced another era of excessive testosterone. Excessive testosterone caused a reduction in population size (bottleneck) that produced the "Mitochondrial Eve" (ME) mechanism. (Only certain females continued during the bottleneck to transmit their mitochondrial DNA.) That is, the ME mechanism culminated, again, in excessive testosterone and reduced spermatogenesis in the hominid line. Approximately 50,000 to 200,000 years ago, a "doubling" of the DAZ gene occurred on the Y chromosome in hominid males which rescued the hominid line with increased spermatogenesis in certain males. This produced the "Y Chromosome Adam" event. The doubling of DAZ allowed further increases in testosterone in hominids that resulted in the increased size and development of the brain. Modern humans periodically fluctuate between the positive and negative consequences of increased levels of testosterone, currently identifiable as the secular trend, increased infections, and reduced spermatogenesis.}, }
@article {pmid12446213, year = {2002}, author = {Castro, H and Sousa, C and Santos, M and Cordeiro-da-Silva, A and Flohé, L and Tomás, AM}, title = {Complementary antioxidant defense by cytoplasmic and mitochondrial peroxiredoxins in Leishmania infantum.}, journal = {Free radical biology &amp; medicine}, volume = {33}, number = {11}, pages = {1552-1562}, doi = {10.1016/s0891-5849(02)01089-4}, pmid = {12446213}, issn = {0891-5849}, mesh = {Amino Acid Sequence ; Animals ; Antioxidants/*pharmacology ; Blotting, Southern ; Blotting, Western ; Cosmids ; Cytoplasm/*metabolism ; DNA/metabolism ; DNA, Kinetoplast/metabolism ; Dose-Response Relationship, Drug ; Free Radicals ; Gene Library ; Genetic Vectors ; Hydrogen Peroxide/pharmacology ; Leishmania infantum/*metabolism ; Microscopy, Fluorescence ; Mitochondria/*metabolism ; Models, Biological ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidative Stress ; Peroxidases/*metabolism ; Peroxiredoxins ; Phenotype ; Phylogeny ; *Protozoan Proteins ; RNA/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sulfhydryl Compounds ; Transfection ; tert-Butylhydroperoxide/pharmacology ; }, abstract = {In Kinetoplastida 2-Cys peroxiredoxins are the ultimate members of unique enzymatic cascades for detoxification of peroxides, which are dependent on trypanothione, a small thiol specific to these organisms. Here we report on two distinct Leishmania infantum peroxiredoxins, LicTXNPx and LimTXNPx, that may be involved in such a pathway. LicTXNPx, found in the cytoplasm, is a typical 2-Cys peroxiredoxin encoded by LicTXNPx, a member of a multicopy gene family. LimTXNPx, encoded by a single copy gene, LimTXNPx, is confined to the mitochondrion and is unusual in possessing an Ile-Pro-Cys motif in the distal redox center, replacing the common peroxiredoxin Val-Cys-Pro sequence, apart from an N-terminal mitochondrial leader sequence. Based on sequence and subcellular localization, the peroxiredoxins of Kinetoplastida can be separated in two distinct subfamilies. As an approach to investigate the function of both peroxiredoxins in the cell, L. infantum promastigotes overexpressing LicTXNPx and LimTXNPx were assayed for their resistance to H(2)O(2) and tert-butyl hydroperoxide. The results show evidence that both enzymes are active as peroxidases in vivo and that they have complementary roles in parasite protection against oxidative stress.}, }
@article {pmid12443799, year = {2002}, author = {Testa, JM and Montoya-Lerma, J and Cadena, H and Oviedo, M and Ready, PD}, title = {Molecular identification of vectors of Leishmania in Colombia: mitochondrial introgression in the Lutzomyia townsendi series.}, journal = {Acta tropica}, volume = {84}, number = {3}, pages = {205-218}, doi = {10.1016/s0001-706x(02)00187-0}, pmid = {12443799}, issn = {0001-706X}, mesh = {ATP-Binding Cassette Transporters/analysis ; Animals ; Colombia ; Cytochrome b Group/analysis/genetics ; Insect Vectors/*genetics ; *Leishmania braziliensis ; Leishmaniasis/*transmission ; Mitochondria/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/methods ; Psychodidae/classification/*genetics ; *Schizosaccharomyces pombe Proteins ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The identity of the sandfly vectors of Leishmania braziliensis in Valle del Cauca Department, Colombia, was originally given as Lutzomyia townsendi, but then changed to L. youngi, another member of the L. townsendi series (Verrucarum group) with isomorphic females. To identify members of this series in Valle del Cauca, we analyzed the nuclear gene elongation factor-alpha (EF-alpha) and the mitochondrial gene cytochrome b (Cyt b). DNA sequences from the L. verrucarum series (L. columbiana, L. evansi and L. ovallesi) were used as outgroups. Flies from two locations on the western cordillera of the Andes were identified as L. townsendi s.s., according to male morphology and distinctive gene lineages. In the third location, on the central cordillera of the Andes, most specimens were identified as belonging to a geographical population of L. youngi, according to male morphology, an EF-alpha lineage shared with L. youngi from the Venezuelan-type locality, and a distinctive Cyt b sub-lineage. All other specimens were identified as L. youngi with the introgressed Cyt b sequences of L. townsendi. Such interspecific introgression implies that vectorial traits and ecological associations may no longer be viewed as fixed properties of different morphospecies.}, }
@article {pmid12442908, year = {2002}, author = {Park, JK and Lee, JS and Kim, W}, title = {A single mitochondrial lineage is shared by morphologically and allozymatically distinct freshwater Corbicula clones.}, journal = {Molecules and cells}, volume = {14}, number = {2}, pages = {318-322}, pmid = {12442908}, issn = {1016-8478}, mesh = {Animals ; Base Sequence ; Hybridization, Genetic ; Isoenzymes/genetics ; Korea ; Mitochondria/*genetics ; Molecular Sequence Data ; Mollusca/classification/enzymology/*genetics/*ultrastructure ; Phylogeny ; Sequence Alignment ; }, abstract = {Despite that the exotic invasion and rapid range expansion of Asian freshwater Corbicula into new environments have been of intensive research topic in freshwater ecology, the genetic structures of freshwater Corbicula in its native range remain poorly understood. In this study, the genetic structures of two Korean freshwater Corbicula clonal lineages were characterized by cross-referencing the nuclear genomic structures with mtDNA sequence analysis. In spite of substantial genetic differences (Nei's D = 0.363-0.372) and a pronounced level of fixed allelic distinctions (in six of 20 allozyme loci) between Corbicula lineages, no lineage-specific mtDNA differentiation was observed. The evident disjunction between mtDNA sequences and nuclear genomes is a compelling evidence for the existence of interspecific nuclear hybrid genome structures, comprising different combinations of paternal and maternal contributions. This unusual novel finding is the first case demonstrating that morphologically and allozymatically distinct, yet mitochondrially identical clonal lineages exist in the genus Corbicula. However, we could not find the ancestral species for these two clonal lineages in the present study, and the answer for this question must wait until the genetic structure of Asian Corbicula taxa is fully characterized.}, }
@article {pmid12442548, year = {2002}, author = {Litoshenko, AIa}, title = {[Evolution of mitochondria].}, journal = {TSitologiia i genetika}, volume = {36}, number = {5}, pages = {49-57}, pmid = {12442548}, issn = {0564-3783}, mesh = {DNA, Mitochondrial/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Mitochondria/*genetics ; Phylogeny ; Symbiosis ; }, abstract = {Until recently, the origin and evolution of mitochondria was explained by the serial endosymbiosis hypothesis. This hypothesis posits that contemporary mitochondria are the direct descendants of a bacterial endosymbiont, which was settled in a nucleus-containing amitochondriate host cell. Results of the mitochondrial gene sequences support a monophyletic origin of the mitochondria from a single eubacterial ancestor shared with a subdivision of the alpha-proteobacteria. In recent years, the complete sequences of the vast variety of mitochondrial and eubacterial genomes were determined. These data indicate that the mitochondrial genome evolved from a common ancestor of all extant eukaryotes and assume a possibility that the mitochondrial and nuclear constituents of the eukaryotic cell originated simultaneously.}, }
@article {pmid12436196, year = {2002}, author = {Sudoyo, H and Suryadi, H and Lertrit, P and Pramoonjago, P and Lyrawati, D and Marzuki, S}, title = {Asian-specific mtDNA backgrounds associated with the primary G11778A mutation of Leber's hereditary optic neuropathy.}, journal = {Journal of human genetics}, volume = {47}, number = {11}, pages = {594-604}, doi = {10.1007/s100380200091}, pmid = {12436196}, issn = {1434-5161}, mesh = {Asia, Southeastern/epidemiology ; DNA, Mitochondrial ; Female ; Haplotypes ; Humans ; Male ; Mitochondria/*genetics ; *Mutation ; Optic Atrophy, Hereditary, Leber/epidemiology/*genetics ; Phylogeny ; Polymorphism, Single Nucleotide ; }, abstract = {We studied 19 patients of Southeast Asian (SEA) ethnic ancestry with Leber's hereditary optic neuropathy (LHON) to investigate the mtDNA haplotypes associated with the primary mutation(s). Eighteen patients carried a mitochondrial DNA (mtDNA) G11778A mutation (Arg340His in the respiratory complex I ND4 subunit), while one had a T14484C mutation (Met64Val in the ND6 subunit). One patient had a class II LHON mtDNA mutation, G3316A. Sequencing data of the ND genes showed many single-nucleotide polymorphisms (62 SNPs in 17 individuals; 10 LHON patients and 7 normal controls) not previously reported in Europeans or Japanese. The SEA G11778A LHON mutation was associated mostly with two mtDNA haplogroups, M (47%) and a novel lineage, characterized by the gain of a 10394 DdeI site but absence of the 10397 AluI site, designated BM (37%). A significant association was observed between one SNP, A10398G, resulting in a Thr114Ala substitution in the ND3 subunit, and the primary LHON mutation. This SNP also characterizes haplogroup J, with which the European LHON 11778 and 14484 mutations show preferential association. The combination of A10398G and other SNPs, specific for the haplogroups J, M, or BM, might act synergistically to increase the penetrance of the LHON mutations, thus allowing their detection.}, }
@article {pmid12432061, year = {2002}, author = {Candé, C and Cecconi, F and Dessen, P and Kroemer, G}, title = {Apoptosis-inducing factor (AIF): key to the conserved caspase-independent pathways of cell death?.}, journal = {Journal of cell science}, volume = {115}, number = {Pt 24}, pages = {4727-4734}, doi = {10.1242/jcs.00210}, pmid = {12432061}, issn = {0021-9533}, support = {TCP99038/TI_/Telethon/Italy ; }, mesh = {Animals ; Apoptosis/*physiology ; Apoptosis Inducing Factor ; Caspases/*physiology ; Flavoproteins/chemistry/genetics/*physiology ; Humans ; Membrane Proteins/chemistry/genetics/*physiology ; Phylogeny ; }, abstract = {Numerous pro-apoptotic signal transducing molecules act on mitochondria and provoke the permeabilization of the outer mitochondrial membrane, thereby triggering the release of potentially toxic mitochondrial proteins. One of these proteins, apoptosis-inducing factor (AIF), is a phylogenetically old flavoprotein which, in healthy cells, is confined to the mitochondrial intermembrane space. Upon lethal signaling, AIF translocates, via the cytosol, to the nucleus where it binds to DNA and provokes caspase-independent chromatin condensation. The crystal structures of both human and mouse AIF have been determined, and the fine mechanisms accounting for its oxidoreductase activity and its electrostatic interaction with double-stranded DNA have been elucidated. Importantly, the apoptogenic and oxidoreductase functions of AIF can be dissociated. Thus, mutations that abolish the AIF-DNA interaction suppress AIF-induced chromatin condensation, yet have no effect on the NADH oxidase activity. Recent studies suggest AIF to be a major factor determining caspase-independent neuronal death, emphasizing the central role of mitochondria in the control of physiological and pathological cell demise.}, }
@article {pmid12430168, year = {2002}, author = {Sasagawa, I}, title = {Mineralization patterns in elasmobranch fish.}, journal = {Microscopy research and technique}, volume = {59}, number = {5}, pages = {396-407}, doi = {10.1002/jemt.10219}, pmid = {12430168}, issn = {1059-910X}, mesh = {Animals ; Biological Evolution ; Dental Enamel/*physiology ; Dentin/metabolism ; Dentinogenesis ; Elasmobranchii/*physiology ; Epithelial Cells/physiology ; Fluorides/analysis ; *Odontogenesis ; *Tooth Calcification ; }, abstract = {This article reviews current findings on the organic matrix and the mineralization patterns in elasmobranchs, including an analysis of the role of the dental epithelial cells and the odontoblasts during odontogenesis. Our electron micrographs demonstrated that tubular vesicles limited by a unit membrane occupied the bulk of the elasmobranch enameloid matrix during the stage of enameloid matrix formation. It is likely that the tubular vesicles originated from the odontoblast processes. Two types of electron-dense fibrils, with cross-striations at intervals of approximately either 17 nm or 55 nm, respectively, were detected in the enameloid matrix. These data suggest that odontoblasts were strongly involved in enameloid matrix formation and in initial enameloid mineralization. Two types of odontoblasts, dark and light cells, were recognized during the stage of dentinogenesis. The light cells contained numerous mitochondria, intermediate filaments, and microtubules that extended their processes into the dentin. The dark cells possessed a well-developed Golgi apparatus and many cisternae in the rough endoplasmic reticulum, which suggests that the dark cells are involved in the formation of dentin. The inner dental epithelial (IDE) cells exhibited a well-developed Golgi apparatus, many mitochondria, cisternae of smooth endoplasmic reticulum, vesicles, vacuoles, and granules during the mineralization and maturation stages. During the stages of mineralization and early maturation, ACPase-positive granules were visible in the IDE cells and ALPase and Ca-ATPase activities were found at the lateral and proximal cell membrane of the IDE cells, suggesting that the IDE cells are involved in the removal of enameloid organic matrix and in the process of mineralization during later stages of enameloid formation. Our data indicate that elasmobranch enameloid is distinct from teleost enameloid, based on its organic content, on the mechanisms of its mineralization, and on the role of IDE cells concerning enameloid formation.}, }
@article {pmid12430011, year = {2002}, author = {Rausch, C and Bucher, M}, title = {Molecular mechanisms of phosphate transport in plants.}, journal = {Planta}, volume = {216}, number = {1}, pages = {23-37}, doi = {10.1007/s00425-002-0921-3}, pmid = {12430011}, issn = {0032-0935}, mesh = {Arabidopsis/genetics/metabolism ; Biological Transport/genetics ; Chloroplasts/genetics/metabolism ; Gene Expression Regulation ; Mitochondria/genetics/metabolism ; Mycorrhizae/genetics/metabolism ; Phosphate Transport Proteins/genetics/physiology ; Phosphates/*metabolism ; Phylogeny ; Plants/genetics/*metabolism ; }, abstract = {Membrane-spanning transport proteins are responsible for the selective passage of most mineral nutrients and metabolites across cellular and intracellular membranes. This review's focus is on summarising the current state of research covering the molecular regulation and biochemical mechanisms involved in the transport of phosphorus, an often growth-limiting nutrient, in vascular plants. Physiological data illustrating the tight control of Pi homeostasis on the cellular as well as on the organism's level are discussed together with the recent results on molecular transport mechanisms.}, }
@article {pmid12429687, year = {2002}, author = {Posada, D and Crandall, KA and Holmes, EC}, title = {Recombination in evolutionary genomics.}, journal = {Annual review of genetics}, volume = {36}, number = {}, pages = {75-97}, doi = {10.1146/annurev.genet.36.040202.111115}, pmid = {12429687}, issn = {0066-4197}, mesh = {Base Sequence ; *Biological Evolution ; DNA ; Humans ; *Recombination, Genetic ; }, abstract = {Recombination can be a dominant force in shaping genomes and associated phenotypes. To better understand the impact of recombination on genomic evolution, we need to be able to identify recombination in aligned sequences. We review bioinformatic approaches for detecting recombination and measuring recombination rates. We also examine the impact of recombination on the reconstruction of evolutionary histories and the estimation of population genetic parameters. Finally, we review the role of recombination in the evolutionary history of bacteria, viruses, and human mitochondria. We conclude by highlighting a number of areas for future development of tools to help quantify the role of recombination in genomic evolution.}, }
@article {pmid12427752, year = {2003}, author = {Perraud, AL and Shen, B and Dunn, CA and Rippe, K and Smith, MK and Bessman, MJ and Stoddard, BL and Scharenberg, AM}, title = {NUDT9, a member of the Nudix hydrolase family, is an evolutionarily conserved mitochondrial ADP-ribose pyrophosphatase.}, journal = {The Journal of biological chemistry}, volume = {278}, number = {3}, pages = {1794-1801}, doi = {10.1074/jbc.M205601200}, pmid = {12427752}, issn = {0021-9258}, support = {GM18649/GM/NIGMS NIH HHS/United States ; GM64091/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Complementary ; *Evolution, Molecular ; Humans ; Mitochondria/*enzymology ; Molecular Sequence Data ; Pyrophosphatases/*genetics ; RNA Splicing ; RNA, Messenger/genetics ; Recombinant Proteins/genetics ; Sequence Homology, Amino Acid ; Subcellular Fractions/metabolism ; }, abstract = {We have recently characterized the protein product of the human NUDT9 gene as a highly specific ADP-ribose (ADPR) pyrophosphatase. We now report an analysis of the human NUDT9 gene and its potential alternative transcripts along with detailed studies of the enzymatic properties and cell biological behavior of human NUDT9 protein. Our analysis of the human NUDT9 gene and twenty-two distinct cloned NUDT9 transcripts indicates that the full-length NUDT9 alpha transcript is the dominant form, and suggests that an alternative NUDT9 beta transcript occurs as the result of a potentially aberrant splice from a cryptic donor site within the first exon to the splice acceptor site of exon 2. Computer analysis of the predicted protein of the NUDT9 alpha transcript identified an N-terminal signal peptide or subcellular targeting sequence. Using green fluorescence protein tagging, we demonstrate that the predicted human NUDT9 alpha protein is targeted highly specifically to mitochondria, whereas the predicted protein of the NUDT9 beta transcript, which is missing this sequence, exhibits no clear subcellular localization. Investigation of the physical and enzymatic properties of NUDT9 indicates that it is functional as a monomer, optimally active at near neutral pH, and that it requires divalent metal ions and an intact Nudix motif for enzymatic activity. Furthermore, partial proteolysis of NUDT9 suggests that NUDT9 enzymes consist of two distinct domains: a proteolytically resistant C-terminal domain retaining essentially full specific ADPR pyrophosphatase activity and a proteolytically labile N-terminal portion that functions to enhance the affinity of the C-terminal domain for ADPR.}, }
@article {pmid12422197, year = {2002}, author = {Abele, D}, title = {Toxic oxygen: the radical life-giver.}, journal = {Nature}, volume = {420}, number = {6911}, pages = {27}, doi = {10.1038/420027a}, pmid = {12422197}, issn = {0028-0836}, mesh = {Antioxidants/metabolism ; Biological Evolution ; Carbon Dioxide/metabolism ; Cell Respiration ; Mitochondria/*metabolism ; Oxygen/*metabolism ; Reactive Oxygen Species/*metabolism ; }, }
@article {pmid12421418, year = {2002}, author = {Schultheis, AS and Weigt, LA and Hendricks, AC}, title = {Arrangement and structural conservation of the mitochondrial control region of two species of Plecoptera: utility of tandem repeat-containing regions in studies of population genetics and evolutionary history.}, journal = {Insect molecular biology}, volume = {11}, number = {6}, pages = {605-610}, doi = {10.1046/j.1365-2583.2002.00371.x}, pmid = {12421418}, issn = {0962-1075}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Conserved Sequence ; DNA Primers ; DNA, Mitochondrial/chemistry/*genetics ; Genetics, Population ; Insecta/classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {Low levels of primary sequence similarity across insect taxa have led to the suggestion of conserved structural elements in the insect mitochondrial control region. Our aim was to determine whether previously described motifs and secondary structures exist in stoneflies (Plecoptera). Several motifs and structural elements previously described in Orthoptera and Diptera were found, including a conserved 'hairpin' structure that may play a role in the initiation of mtDNA replication. The repeat region had the highest percentage similarity, lowest A-T content and highest transition to transversion ratio, suggesting a unique evolutionary pattern for the repeats. Finally, we discuss the usefulness of the control region in population genetic and evolutionary studies.}, }
@article {pmid12417726, year = {2002}, author = {Li, X and Baumgart, E and Dong, GX and Morrell, JC and Jimenez-Sanchez, G and Valle, D and Smith, KD and Gould, SJ}, title = {PEX11alpha is required for peroxisome proliferation in response to 4-phenylbutyrate but is dispensable for peroxisome proliferator-activated receptor alpha-mediated peroxisome proliferation.}, journal = {Molecular and cellular biology}, volume = {22}, number = {23}, pages = {8226-8240}, pmid = {12417726}, issn = {0270-7306}, support = {P01 HD010981/HD/NICHD NIH HHS/United States ; R01 DK059479/DK/NIDDK NIH HHS/United States ; DK59479/DK/NIDDK NIH HHS/United States ; HD10981/HD/NICHD NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Antineoplastic Agents/pharmacology ; Diet ; Fatty Acids/chemistry/metabolism ; Fibroblasts/cytology/metabolism ; Gene Expression Regulation ; Gene Targeting ; Liver/cytology/metabolism ; Membrane Proteins/chemistry/classification/*genetics/metabolism ; Mice ; Mice, Inbred Strains ; Mice, Knockout ; Mitochondria/ultrastructure ; Molecular Sequence Data ; Oxidation-Reduction ; Peroxisome Proliferators/administration &amp; dosage/*pharmacology ; Peroxisomes/*drug effects/*metabolism/ultrastructure ; Phenotype ; Phenylbutyrates/*pharmacology ; Phylogeny ; Plasmalogens/metabolism ; Receptors, Cytoplasmic and Nuclear/*metabolism ; Sequence Alignment ; Tissue Distribution ; Transcription Factors/*metabolism ; }, abstract = {The PEX11 peroxisomal membrane proteins promote peroxisome division in multiple eukaryotes. As part of our effort to understand the molecular and physiological functions of PEX11 proteins, we disrupted the mouse PEX11alpha gene. Overexpression of PEX11alpha is sufficient to promote peroxisome division, and a class of chemicals known as peroxisome proliferating agents (PPAs) induce the expression of PEX11alpha and promote peroxisome division. These observations led to the hypothesis that PPAs induce peroxisome abundance by enhancing PEX11alpha expression. The phenotypes of PEX11alpha(-/-) mice indicate that this hypothesis remains valid for a novel class of PPAs that act independently of peroxisome proliferator-activated receptor alpha (PPARalpha) but is not valid for the classical PPAs that act as activators of PPARalpha. Furthermore, we find that PEX11alpha(-/-) mice have normal peroxisome abundance and that cells lacking both PEX11alpha and PEX11beta, a second mammalian PEX11 gene, have no greater defect in peroxisome abundance than do cells lacking only PEX11beta. Finally, we report the identification of a third mammalian PEX11 gene, PEX11gamma, and show that it too encodes a peroxisomal protein.}, }
@article {pmid12417132, year = {2002}, author = {Tielens, AG and Rotte, C and van Hellemond, JJ and Martin, W}, title = {Mitochondria as we don't know them.}, journal = {Trends in biochemical sciences}, volume = {27}, number = {11}, pages = {564-572}, doi = {10.1016/s0968-0004(02)02193-x}, pmid = {12417132}, issn = {0968-0004}, mesh = {Adenosine Triphosphate/*biosynthesis ; Animals ; Electron Transport/physiology ; Energy Metabolism ; Eukaryotic Cells/physiology ; Mitochondria/classification/*metabolism ; Oxygen/metabolism ; Phylogeny ; Proton Pumps/metabolism ; Succinate Dehydrogenase/genetics/metabolism ; }, abstract = {Biochemistry textbooks depict mitochondria as oxygen-dependent organelles, but many mitochondria can produce ATP without using any oxygen. In fact, several other types of mitochondria exist and they occur in highly diverse groups of eukaryotes - protists as well as metazoans - and possess an often overlooked diversity of pathways to deal with the electrons resulting from carbohydrate oxidation. These anaerobically functioning mitochondria produce ATP with the help of proton-pumping electron transport, but they do not need oxygen to do so. Recent advances in understanding of mitochondrial biochemistry provide many surprises and furthermore, give insights into the evolutionary history of ATP-producing organelles.}, }
@article {pmid12414316, year = {2002}, author = {Wilcox, TP and Zwickl, DJ and Heath, TA and Hillis, DM}, title = {Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support.}, journal = {Molecular phylogenetics and evolution}, volume = {25}, number = {2}, pages = {361-371}, doi = {10.1016/s1055-7903(02)00244-0}, pmid = {12414316}, issn = {1055-7903}, mesh = {Animals ; Bayes Theorem ; Boidae/*genetics ; Data Interpretation, Statistical ; Likelihood Functions ; Mitochondria/genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Four New World genera of dwarf boas (Exiliboa, Trachyboa, Tropidophis, and Ungaliophis) have been placed by many systematists in a single group (traditionally called Tropidophiidae). However, the monophyly of this group has been questioned in several studies. Moreover, the overall relationships among basal snake lineages, including the placement of the dwarf boas, are poorly understood. We obtained mtDNA sequence data for 12S, 16S, and intervening tRNA-val genes from 23 species of snakes representing most major snake lineages, including all four genera of New World dwarf boas. We then examined the phylogenetic position of these species by estimating the phylogeny of the basal snakes. Our phylogenetic analysis suggests that New World dwarf boas are not monophyletic. Instead, we find Exiliboa and Ungaliophis to be most closely related to sand boas (Erycinae), boas (Boinae), and advanced snakes (Caenophidea), whereas Tropidophis and Trachyboa form an independent clade that separated relatively early in snake radiation. Our estimate of snake phylogeny differs significantly in other ways from some previous estimates of snake phylogeny. For instance, pythons do not cluster with boas and sand boas, but instead show a strong relationship with Loxocemus and Xenopeltis. Additionally, uropeltids cluster strongly with Cylindrophis, and together are embedded in what has previously been considered the macrostomatan radiation. These relationships are supported by both bootstrapping (parametric and nonparametric approaches) and Bayesian analysis, although Bayesian support values are consistently higher than those obtained from nonparametric bootstrapping. Simulations show that Bayesian support values represent much better estimates of phylogenetic accuracy than do nonparametric bootstrap support values, at least under the conditions of our study.}, }
@article {pmid12414311, year = {2002}, author = {Sumida, M and Kondo, Y and Kanamori, Y and Nishioka, M}, title = {Inter- and intraspecific evolutionary relationships of the rice frog Rana limnocharis and the allied species R. cancrivora inferred from crossing experiments and mitochondrial DNA sequences of the 12S and 16S rRNA genes.}, journal = {Molecular phylogenetics and evolution}, volume = {25}, number = {2}, pages = {293-305}, doi = {10.1016/s1055-7903(02)00243-9}, pmid = {12414311}, issn = {1055-7903}, mesh = {Animals ; Body Constitution/genetics ; *Evolution, Molecular ; Fertility/genetics ; Haplotypes ; Hybridization, Genetic ; Mitochondria/genetics ; Phylogeny ; Point Mutation ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; Ranidae/*genetics ; }, abstract = {The rice frog Rana limnocharis is widely distributed in Southeast Asia and the rest of the Asian region extending from India to Japan. In Japan, the Sakishima-island populations of this species were regarded as a distinct species based on morphological and genetic divergences. The main purposes of this study were to confirm the presence of intraspecific reproductively isolating mechanisms in the Sakishima-island populations of R. limnocharis, and to clarify molecular inter- and intraspecific relationships of R. limnocharis and an allied species, Rana cancrivora. The hybridization experiments revealed that there were no reproductively isolating mechanisms between the Sakishima-island populations and other populations of R. limnocharis. The molecular evolutionary relationships were investigated by analyzing nucleotide sequences of the mitochondrial 12S and 16S rRNA genes using 12 populations of R. limnocharis from Japan and Taiwan, and two populations of R. cancrivora from Thailand and the Philippines. The phylogenetic trees constructed by the NJ method showed that the two populations of R. cancrivora were clearly separated from the 12 populations of R. limnocharis, and that the 12 populations of R. limnocharis were broadly divided into three clades; the first comprising eight populations from the main islands of Japan, the second comprising the Sakishima-island populations, and the third comprising the Okinawa-island and Taiwan populations. Interestingly, the Okinawa-island and Taiwan populations of R. limnocharis showed a close relationship that possibly reflected a secondary contact between the two populations. Based on the present crossing experiments and molecular data, it seems reasonable to regard the Sakishima-island populations as a single subspecies of R. limnocharis.}, }
@article {pmid12414306, year = {2002}, author = {Braband, A and Richter, S and Hiesel, R and Scholtz, G}, title = {Phylogenetic relationships within the Phyllopoda (Crustacea, Branchiopoda) based on mitochondrial and nuclear markers.}, journal = {Molecular phylogenetics and evolution}, volume = {25}, number = {2}, pages = {229-244}, doi = {10.1016/s1055-7903(02)00253-1}, pmid = {12414306}, issn = {1055-7903}, mesh = {Animals ; Cell Nucleus/*genetics ; Crustacea/*genetics ; DNA, Ribosomal ; Genetic Markers ; Likelihood Functions ; Mitochondria/*genetics ; Peptide Elongation Factor 1/genetics ; *Phylogeny ; }, abstract = {For several decades the relationships within the Branchiopoda (Anostraca + Phyllopoda) have been a matter of controversy. Interpretations of plesiomorphic or apomorphic character states are a difficult venture, in particular in the Phyllopoda. We explore the relationships within the Phyllopoda at the level of nucleotid comparisons of the two genes 12S rDNA (mitochondrial) and EF1alpha (nuclear), and at a higher molecular level based on introns found in the gene EF1alpha. Within the Phyllopoda our explorations show further evidence for a non-monophyletic Conchostraca (Spinicaudata + Cyclestherida + Laevicaudata). The monotypic Cyclestherida is more closely related to the Cladocera, both together forming the Cladoceromorpha. The Spinicaudata (Leptestheriidae, Limnadiidae, and Cyzicidae) is well supported. Spinicaudata and Cladoceromorpha form a monophylum. The position of the Laevicaudata remains unclear but we find neither support for a sister group relationship to the Spinicaudata nor for a close relationship of Laevicaudata and Cladocera. Within the Cladocera, we favour the Gymnomera concept with the monotypic Haplopoda being the sister group to the monophyletic Onychopoda. The Ctenopoda seems to be the sister group to the Gymnomera, which contradicts the common view of a more basal position of the Ctenopoda.}, }
@article {pmid12403467, year = {2002}, author = {Dai, L and Zimmerly, S}, title = {The dispersal of five group II introns among natural populations of Escherichia coli.}, journal = {RNA (New York, N.Y.)}, volume = {8}, number = {10}, pages = {1294-1307}, pmid = {12403467}, issn = {1355-8382}, mesh = {Base Sequence ; Blotting, Southern ; Cloning, Molecular ; DNA Transposable Elements ; Escherichia coli/*genetics ; Genetics, Population ; *Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Bacterial/chemistry ; Retroelements ; Sequence Analysis, DNA ; }, abstract = {Group II introns are self-splicing RNAs that also act as retroelements in bacteria, mitochondria, and chloroplasts. Group II introns were identified in Escherichia coli in 1994, but have not been characterized since, and, instead, other bacterial group II introns have been studied for splicing and mobility properties. Despite their apparent intractability, at least five distinct group II introns exist naturally in E. coli strains. To illuminate their function and learn how the introns have dispersed in their natural host, we have investigated their distribution in the ECOR reference collection. Two introns were cloned and sequenced to complete their partial sequences. Unexpectedly, southern blots showed all ECOR strains to contain fragments and/or full-length copies of group II introns, with some strains containing up to 15 intron copies. One intron, E.c.14, has two natural homing sites in IS629 and IS911 elements, and the intron can be present in one, both, or neither homing site in a given strain. Nearly all strains that contain full-length introns also contain unfilled homing sites, suggesting either that mobility is highly inefficient or that most full-length copies are nonfunctional. The data indicate independent mobility of the introns, as well as mobility via the host DNA elements, and overall, the pattern of intron distribution resembles that of IS elements.}, }
@article {pmid12399995, year = {2002}, author = {Klossa-Kilia, E and Prassa, M and Papasotiropoulos, V and Alahiotis, S and Kilias, G}, title = {Mitochondrial DNA diversity in Atherina boyeri populations as determined by RFLP analysis of three mtDNA segments.}, journal = {Heredity}, volume = {89}, number = {5}, pages = {363-370}, doi = {10.1038/sj.hdy.6800144}, pmid = {12399995}, issn = {0018-067X}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Fishes/*genetics ; *Genetic Variation ; Greece ; Haplotypes ; Mitochondria, Muscle/*genetics ; Phylogeny ; Polymerase Chain Reaction/methods ; Polymorphism, Restriction Fragment Length ; Restriction Mapping ; }, abstract = {The genetic differentiation and the phylogenetic relationships of eight Atherina boyeri Greek populations have been investigated at the mtDNA level. The populations studied are from two different lakes, a lagoon, the interface zone between the lagoon and the sea, and four marine sites. RFLP analysis of three mtDNA segments (12s rRNA, 16s rRNA and D-loop) amplified by PCR was used. Six, seven and eight restriction enzymes were found to have at least one recognition site at 12s rRNA, 16s rRNA and D-loop respectively. Twenty-one different haplotypes were detected among the populations studied. Several restriction patterns were revealed. These patterns can be used for the discrimination of the populations living in the sea ('marine' type populations) from the others inhabiting the lagoon and the lakes ('lagoon' type populations). The estimated net nucleotide sequence divergence between the populations examined ranged from 0 to 10.385%, while the Nst value of 0.92 indicates the existence of high interpopulation genetic differentiation. This high degree of differentiation detected between the 'lagoon' and 'marine' type populations makes the classification of these two types of populations as a single taxon questionable.}, }
@article {pmid12399993, year = {2002}, author = {Orth, A and Auffray, JC and Bonhomme, F}, title = {Two deeply divergent mitochondrial clades in the wild mouse Mus macedonicus reveal multiple glacial refuges south of Caucasus.}, journal = {Heredity}, volume = {89}, number = {5}, pages = {353-357}, doi = {10.1038/sj.hdy.6800147}, pmid = {12399993}, issn = {0018-067X}, mesh = {Animals ; Animals, Wild ; Base Sequence ; Chromosomes/chemistry/*genetics ; DNA, Mitochondrial/*analysis ; *Genetic Variation ; Haplotypes ; Mediterranean Region ; Mice/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {A survey of 77 individuals covering the range of Mus macedonicus from Georgia in the East to Greece and Bulgaria in the West and Israel in the South has shown the existence of two deeply divergent mitochondrial clades. The southern clade was until now undetected and characterises mice from Israel. Nuclear genes also show some amount of regional differentiation tending to separate the southern M. macedonicus from the northern ones. These results point towards the fact that the eastern Mediterranean short-tailed mouse, which was seen as a fairly homogeneous monotypic species, has in fact a more complex phylogeographic history than has been suspected, and that it warrants the existence of two subspecies. The reasons for this non-uniformity probably ought to be looked for in the history of faunal movements linked to glacial periods, underlining the possible existence of at least two refugia south of the Caucasus.}, }
@article {pmid12399392, year = {2002}, author = {Steinborn, R and Schinogl, P and Wells, DN and Bergthaler, A and Müller, M and Brem, G}, title = {Coexistence of Bos taurus and B. indicus mitochondrial DNAs in nuclear transfer-derived somatic cattle clones.}, journal = {Genetics}, volume = {162}, number = {2}, pages = {823-829}, pmid = {12399392}, issn = {0016-6731}, mesh = {Animals ; Cattle ; Cell Nucleus/*genetics ; *Cloning, Organism ; *DNA, Mitochondrial ; Gene Dosage ; Mitochondria/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; }, abstract = {We investigated the mitochondrial DNA (mtDNA) composition in one of the largest adult somatic mammalian clones (n = 20) reported so far. The healthy cloned cattle were derived from nuclear transfer of an identical nuclear genetic background (mural granulosa donor cells including surrounding cytoplasm) into enucleated oocytes with either Bos indicus or B. taurus mtDNA. Here we report the first cases of coexisting mtDNAs of two closely related subspecies following nuclear transfer. Heteroplasmy (0.6-2.8%) was found in 4 out of 11 cross-subspecies cloned cattle. Quantitation was performed using "amplification refractory mutation system (ARMS) allele-specific real-time PCR." We determined that the ratio of donor cell to recipient cytoplast mtDNA copy number was 0.9% before nuclear transfer. Therefore, we concluded that the percentage of donor cell mtDNA in the heteroplasmic intersubspecific cloned animals is in accordance with neutral transmission of donor mtDNA. We determined an amino acid sequence divergence of up to 1.3% for the two subspecies-specific mtDNA haplotypes. In addition, intrasubspecific B. indicus heteroplasmy of approximately 1% (but up to 7.3 and 12.7% in muscle and follicular cells of one animal) was detected in 7 out of the 9 B. indicus intrasubspecific cloned cattle.}, }
@article {pmid12393949, year = {2002}, author = {Anantharaju, A and Feller, A and Chedid, A}, title = {Aging Liver. A review.}, journal = {Gerontology}, volume = {48}, number = {6}, pages = {343-353}, doi = {10.1159/000065506}, pmid = {12393949}, issn = {0304-324X}, mesh = {Aging/*physiology ; Diet ; Free Radicals/metabolism ; Humans ; Liver/drug effects/pathology/*physiology ; Pharmaceutical Preparations/administration &amp; dosage ; Telomerase/metabolism ; }, abstract = {Aging is characterized by a progressive decline of cellular functions. The aging liver appears to preserve its function relatively well. Aging is associated in human liver with morphological changes such as decrease in size attributable to decreased hepatic blood flow. Ultrastructural analysis of the human liver has revealed that the integrity of mitochondria and enzymatic activity remain mostly unchanged with aging. Reactive oxygen species (ROS) are involved in the aging process and result mainly from nonenzymatic processes in the liver. Endogenous free radicals are generated within mitochondria and suspected to cause severe injury to mitochondrial DNA. This damaged DNA accumulates with aging. In addition, polyunsaturated fatty acids, highly sensitive to ROS, decrease in liver mitochondria from human centenarians, a feature acquired during evolution as a protective mechanism to favor longevity. Diet is considered the main environmental factor having effect on lifespan. It has a major impact on aging liver, the central metabolic organ of the body. The ubiquitin proteolytic pathway in the liver serves to destroy many proteins, among them p21 which is encoded by abundant mRNA in senescent cells, can inhibit cell proliferation and favors DNA repair. Drug therapy in the elderly may be complicated by several factors such as decline in body weight, renal function, liver mass and hepatic blood flow, making adverse drug reactions more frequent. Hepatic drug metabolism is mainly mediated by the cytochrome P(450)system and drug interactions in the elderly are likely related to the progressive decline of this system after the fifth decade of life and another decrease in individuals aged >70. Antihypertensive therapy in the elderly depends upon either hepatic or renal function and should be adjusted accordingly. Finally, telomerases are the biological clocks of replicative lifespan. Shortening of telomeric ends of chromosomes correlates with aging and decline in the replicative potential of the cell: replicative senescence. Telomere DNA of human somatic cells shortens during each cell division thus leading to a finite proliferation. Transfection of the telomerase reverse transcriptase gene results in elongation of telomeres and extension of lifespan. This also applies to humans. Replicative senescence in human cells evolved as a mechanism to protect them from continuous divisions leading to multiple mutations. Longer-lived species such as humans had to develop replicative senescence to ensure that they would have the increased protection that their longevity necessitates.}, }
@article {pmid12393015, year = {2002}, author = {Rutherford, S and Moore, I}, title = {The Arabidopsis Rab GTPase family: another enigma variation.}, journal = {Current opinion in plant biology}, volume = {5}, number = {6}, pages = {518-528}, doi = {10.1016/s1369-5266(02)00307-2}, pmid = {12393015}, issn = {1369-5266}, mesh = {Arabidopsis/*enzymology/genetics ; Chloroplasts/metabolism ; Chromosome Mapping ; Chromosomes, Plant/genetics ; Mitochondria/metabolism ; Multigene Family/*genetics/physiology ; Phylogeny ; rab GTP-Binding Proteins/*genetics/physiology ; }, abstract = {The Arabidopsis genome sequence reveals that gene families such as the Rab GTPase family, which encodes key determinants of vesicle-targeting specificity, are considerably more diverse in plants and mammals than in yeast. In mammals, this diversity appears to reflect the complexity of membrane trafficking. Phylogenetic analyses indicate that, despite its large size, the Arabidopsis Rab family lacks most of the Rab subclasses found in mammals. The Arabidopsis Rab family has, however, undergone a distinct 'adaptive radiation' that has given rise to proteins that may perform plant-specific functions.}, }
@article {pmid12392880, year = {2002}, author = {Opie, LH and Sack, MN}, title = {Metabolic plasticity and the promotion of cardiac protection in ischemia and ischemic preconditioning.}, journal = {Journal of molecular and cellular cardiology}, volume = {34}, number = {9}, pages = {1077-1089}, doi = {10.1006/jmcc.2002.2066}, pmid = {12392880}, issn = {0022-2828}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Energy Metabolism ; Glycolysis ; Humans ; *Ischemic Preconditioning, Myocardial ; Mitochondria, Heart/metabolism ; Models, Cardiovascular ; Myocardial Ischemia/*metabolism ; Myocardium/metabolism ; }, abstract = {The concept of metabolic protection of the ischemic myocardium is in constant evolution and has recently been supported by clinical studies. Historically, enhanced glucose metabolism and glycolysis were proposed as anti-ischemic cardioprotection. This hypothesis is supported by the sub-cellular linkage between key glycolytic enzymes and the activity of two survival-promoting membrane-bound pumps, namely the sodium-potassium ATPase, and the calcium uptake pump of the sarcoplasmic reticulum. Moreover, improved resistance against ischemia follows the administration of glucose-insulin-potassium in a variety of animal models and in patients following acute myocardial infarction. The metabolic plasticity paradigm has now been expanded to include (1) the benefit of improved coupling of glycolysis to glucose oxidation, which explains the action of anti-ischemic fatty acid inhibitors such as trimetazidine and ranolazine; (2) the role of malonyl CoA in the glucose-fatty acid interaction; and (3) the anti-apoptotic role of insulin. Furthermore, we argue for a protective role of increased glucose uptake in the preconditioning paradigm. Additionally, we postulate an adaptive role of mitochondrial respiration in the promotion of cardioprotection in the context of ischemic preconditioning. The mechanisms driving these mitochondrial perturbations are still unknown, but are hypothesized to involve an initial modest uncoupling of respiration from the production of mitochondrial ATP. These perturbations are in turn thought to prime the mitochondria to augment mitochondrial respiration during a subsequent ischemic insult to the heart. In this review we discuss studies that demonstrate how metabolic plasticity can promote cardioprotection against ischemia and reperfusion injury and highlight areas that require further characterization.}, }
@article {pmid12369098, year = {2002}, author = {Catanesi, CI and Vidal-Rioja, L and Crisci, JV and Zambelli, A}, title = {Phylogenetic relationships among Robertsonian karyomorphs of Graomys griseoflavus (Rodentia, Muridae) by mitochondrial cytochrome b DNA sequencing.}, journal = {Hereditas}, volume = {136}, number = {2}, pages = {130-136}, doi = {10.1034/j.1601-5223.2002.1360207.x}, pmid = {12369098}, issn = {0018-0661}, mesh = {Animals ; Argentina ; Cytochrome b Group/*genetics ; *DNA, Mitochondrial ; Karyotyping ; Mitochondria/*genetics ; Muridae/classification/*genetics ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; }, abstract = {Graomys griseoflavus (Waterhouse 1837) is a phyllotine murid rodent with a Robertsonian autosomal polymorphism, having been described 2n = 42, 41, 38, 37, 36, 35 and 34 karyomorphs, and proposed a chromosomal divergence pathway accounted by four sequential Robertsonian fusions. Sequences of a fragment (422 bp long) of the cytochrome b (cyt b) mitochondrial gene and its 5' flanking region (tRNA Glu) were obtained for 19 Graomys griseoflavus from different karyomorphs to infer phylogenetic relationships by using maximum parsimony. Outgroups considered for this analysis were the phyllotine rodents Phyllotis xanthopygus and Eligmodontia typus cyt b sequences. Three trees were produced showing the 2n = 38-34 karyomorphs grouped in a single clade while the 2n = 42-41 animals formed a different one. This is in agreement with a hypothesis of a single origin for 2n = 38-34 Robertsonian karyomorphs from the ancestral 2n = 42.}, }
@article {pmid12359132, year = {2002}, author = {Nguyen, TV and Andresen, BS and Corydon, TJ and Ghisla, S and Abd-El Razik, N and Mohsen, AW and Cederbaum, SD and Roe, DS and Roe, CR and Lench, NJ and Vockley, J}, title = {Identification of isobutyryl-CoA dehydrogenase and its deficiency in humans.}, journal = {Molecular genetics and metabolism}, volume = {77}, number = {1-2}, pages = {68-79}, doi = {10.1016/s1096-7192(02)00152-x}, pmid = {12359132}, issn = {1096-7192}, mesh = {Amino Acid Metabolism, Inborn Errors/enzymology/genetics ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Base Sequence ; DNA, Complementary/genetics ; Escherichia coli/genetics ; Exons ; Humans ; In Vitro Techniques ; Introns ; Kinetics ; Models, Molecular ; Oxidoreductases/*deficiency/*genetics/metabolism ; *Oxidoreductases Acting on CH-CH Group Donors ; Phylogeny ; Point Mutation ; Protein Conformation ; Recombinant Proteins/genetics/isolation &amp; purification/metabolism ; Sequence Homology, Amino Acid ; Substrate Specificity ; Valine/metabolism ; }, abstract = {The acyl-CoA dehydrogenases (ACDs) are a family of related enzymes that catalyze the alpha,beta-dehydrogenation of acyl-CoA esters. Two homologues active in branched chain amino acid metabolism have previously been identified. We have used expression in Escherichia coli to produce a previously uncharacterized ACD-like sequence (ACAD8) and define its substrate specificity. Purified recombinant enzyme had a k(cat)/K(m) of 0.8, 0.23, and 0.04 (microM(-1)s(-1)) with isobutyryl-CoA, (S) 2-methylbutyryl-CoA, and n-propionyl-CoA, respectively, as substrates. Thus, this enzyme is an isobutyryl-CoA dehydrogenase. A single patient has previously been described whose fibroblasts exhibit a specific deficit in the oxidation of valine. Amplified ACAD8 cDNA made from patient fibroblast mRNA was homozygous for a single nucleotide change (905G>A) in the ACAD8 coding region compared to the sequence from control cells. This encodes an Arg302Gln substitution in the full-length protein (position 280 in the mature protein), a position predicted by molecular modeling to be important in subunit interactions. The mutant enzyme was stable but inactive when expressed in E. coli. It was also stable and appropriately targeted to mitochondria, but inactive when expressed in mammalian cells. These data confirm further the presence of a separated ACD in humans specific to valine catabolism (isobutyryl-CoA dehydrogenase, IBDH), along with the first enzymatic and molecular confirmation of a deficiency of this enzyme in a patient.}, }
@article {pmid12355265, year = {2002}, author = {Misof, B and Anderson, CL and Buckley, TR and Erpenbeck, D and Rickert, A and Misof, K}, title = {An empirical analysis of mt 16S rRNA covarion-like evolution in insects: site-specific rate variation is clustered and frequently detected.}, journal = {Journal of molecular evolution}, volume = {55}, number = {4}, pages = {460-469}, doi = {10.1007/s00239-002-2341-1}, pmid = {12355265}, issn = {0022-2844}, mesh = {Animals ; Drosophila melanogaster/*genetics ; *Evolution, Molecular ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The structural and functional analysis of rRNA molecules has attracted considerable scientific interest. Empirical studies have demonstrated that sequence variation is not directly translated into modifications of rRNA secondary structure. Obviously, the maintenance of secondary structure and sequence variation are in part governed by different selection regimes. The nature of those selection regimes still remains quite elusive. The analysis of individual bacterial models cannot adequately explore this topic. Therefore, we used primary sequence data and secondary structures of a mitochondrial 16S rRNA fragment of 558 insect species from 15 monophyletic groups to study patterns of sequence variation, and variation of secondary structure. Using simulation studies to establish significance levels of change, we found that despite conservation of secondary structure, the location of sequence variation within the conserved rRNA structure changes significantly between groups of insects. Despite our conservative estimation procedure we found significant site-specific rate changes at 56 sites out of 184. Additionally, site-specific rate variation is somewhat clustered in certain helices. Both results confirm what has been predicted from an application of non-stationary maximum likelihood models to rRNA sequences. Clearly, constraints on sequence variation evolve and leave footprints in the form of evolutionary plasticity in rRNA sequences. Here, we show that a better understanding of the evolution of rRNA sequences can be obtained by integrating both phylogenetic and structural information.}, }
@article {pmid12354789, year = {2002}, author = {Duby, G and Foury, F and Ramazzotti, A and Herrmann, J and Lutz, T}, title = {A non-essential function for yeast frataxin in iron-sulfur cluster assembly.}, journal = {Human molecular genetics}, volume = {11}, number = {21}, pages = {2635-2643}, doi = {10.1093/hmg/11.21.2635}, pmid = {12354789}, issn = {0964-6906}, mesh = {Cysteine/metabolism ; In Vitro Techniques ; Iron-Binding Proteins/*metabolism ; Iron-Sulfur Proteins/*metabolism ; Mitochondria/*metabolism ; Protein Transport/physiology ; Saccharomyces cerevisiae/*metabolism ; Sulfur Radioisotopes/metabolism ; Frataxin ; }, abstract = {Friedreich's ataxia is caused by a deficit in frataxin, a small mitochondrial protein of unknown function that has been conserved during evolution. Previous studies have pointed out a role for frataxin in mitochondrial iron-sulfur (Fe-S) metabolism. Here, we have analyzed the incorporation of Fe-S clusters into yeast ferredoxin imported into isolated energized mitochondria from cells grown in the presence of glycerol, an obligatory respiratory carbon source. Similar amounts of apo-ferredoxin precursor were imported into mitochondria and processed in wild-type and yfh1-deleted (delta YF111) strains. However, the incorporation of Fe-S clusters into apo-ferredoxin was significantly reduced in delta YFH1 mitochondria. The newly assembled ferredoxin was stable, excluding the possibility that the decreased incorporation was a result of increased oxidative damage. When delta YFH1 cells were grown in raffinose medium, the formation of holo-ferredoxin was low, as a consequence of the decrease in ferredoxin precursor import into mitochondria. However, the decrease in the conversion rate of apo- into holo-ferredoxin was in the same range as for glycerol-grown cells, indicating that the extent of the defect in Fe-S protein assembly is similar under different physiological conditions. These data show that frataxin is not essential for Fe-S protein assembly, but improves the efficiency of the process. The large variations observed in the activity of Fe-S cluster proteins under different physiological conditions result from secondary defects in the physiology of delta YFH1 cells.}, }
@article {pmid12270904, year = {2002}, author = {Simpson, AG and Roger, AJ and Silberman, JD and Leipe, DD and Edgcomb, VP and Jermiin, LS and Patterson, DJ and Sogin, ML}, title = {Evolutionary history of "early-diverging" eukaryotes: the excavate taxon Carpediemonas is a close relative of Giardia.}, journal = {Molecular biology and evolution}, volume = {19}, number = {10}, pages = {1782-1791}, doi = {10.1093/oxfordjournals.molbev.a004000}, pmid = {12270904}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; Diplomonadida/*classification/*genetics ; *Evolution, Molecular ; Genes, Protozoan ; Giardia/*classification/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal/genetics ; Tubulin/genetics ; }, abstract = {Diplomonads, such as Giardia, and their close relatives retortamonads have been proposed as early-branching eukaryotes that diverged before the acquisition-retention of mitochondria, and they have become key organisms in attempts to understand the evolution of eukaryotic cells. In this phylogenetic study we focus on a series of eukaryotes suggested to be relatives of diplomonads on morphological grounds, the "excavate taxa". Phylogenies of small subunit ribosomal RNA (SSU rRNA) genes, alpha-tubulin, beta-tubulin, and combined alpha- + beta-tubulin all scatter the various excavate taxa across the diversity of eukaryotes. But all phylogenies place the excavate taxon Carpediemonas as the closest relative of diplomonads (and, where data are available, retortamonads). This novel relationship is recovered across phylogenetic methods and across various taxon-deletion experiments. Statistical support is strongest under maximum-likelihood (ML) (when among-site rate variation is modeled) and when the most divergent diplomonad sequences are excluded, suggesting a true relationship rather than an artifact of long-branch attraction. When all diplomonads are excluded, our ML SSU rRNA tree actually places retortamonads and Carpediemonas away from the base of the eukaryotes. The branches separating excavate taxa are mostly not well supported (especially in analyses of SSU rRNA data). Statistical tests of the SSU rRNA data, including an "expected likelihood weights" approach, do not reject trees where excavate taxa are constrained to be a clade (with or without parabasalids and Euglenozoa). Although diplomonads and retortamonads lack any mitochondria-like organelle, Carpediemonas contains double membrane-bounded structures physically resembling hydrogenosomes. The phylogenetic position of Carpediemonas suggests that it will be valuable in interpreting the evolutionary significance of many molecular and cellular peculiarities of diplomonads.}, }
@article {pmid12270262, year = {2002}, author = {Garda, AA and Colli, GR and Aguiar-Júnior, O and Recco-Pimentel, SM and Báo, SN}, title = {The ultrastructure of the spermatozoa of Epipedobates flavopictus (Amphibia, Anura, Dendrobatidae), with comments on its evolutionary significance.}, journal = {Tissue &amp; cell}, volume = {34}, number = {5}, pages = {356-364}, doi = {10.1016/s0040816602000368}, pmid = {12270262}, issn = {0040-8166}, mesh = {Acrosome/physiology/ultrastructure ; Animals ; Anura/*anatomy &amp; histology/*classification/physiology ; Cell Nucleus/physiology/ultrastructure ; Centrioles/physiology/ultrastructure ; Fertilization/*physiology ; Flagella/physiology/ultrastructure ; Intracellular Membranes/physiology/ultrastructure ; Male ; Microscopy, Electron ; Mitochondria/physiology/ultrastructure ; Phylogeny ; Spermatozoa/physiology/*ultrastructure ; Testis/physiology/*ultrastructure ; }, abstract = {We describe, for the first time, the spermatozoon ultrastructure of a dendrobatid frog, Epipedobates flavopictus. Mature spermatozoa of E. flavopictus are filiform, with a moderately curved head and a proportionally short tail. The acrosomal vesicle is a conical structure that covers the nucleus for a considerable distance. A homogeneous subacrosomal cone lies between the acrosome vesicle and the nucleus. The nucleus contains a nuclear space at its anterior end, and electron-lucent spaces and inclusions. No perforatorium is present. In the midpiece, the proximal centriole is housed inside a deep nuclear fossa. Mitochondria are scattered around the posterior end of the nucleus and inside the undulating membrane in the anterior portion of the tail. In transverse section the tail is formed by an U-shaped axial fiber connected to the axoneme through an axial sheath, which supports the undulating membrane. The juxta-axonemal fiber is absent. The spermatozoon of E. flavopictus has several characteristics not observed before in any anurans, such as a curved axial fiber, absence of a juxta-axonemal fiber, and presence of mitochondria in the typical undulating membrane. Our results endorse the view that, in anurans, the conical perforatorium and subacrosomal cone are homologous and that Dendrobatidae should be grouped within Bufonoidea rather than Ranoidea.}, }
@article {pmid12244696, year = {2002}, author = {Kuznetsova, MV and Kholodova, MV and Lushchekina, AA}, title = {[Phylogenetic analysis of sequences of the 12S and 16S rRNA mitochondrial genes in the family Bovidae: new evidence].}, journal = {Genetika}, volume = {38}, number = {8}, pages = {1115-1124}, pmid = {12244696}, issn = {0016-6758}, mesh = {Animals ; Mitochondria/genetics ; Models, Biological ; Molecular Sequence Data ; *Phylogeny ; *RNA, Ribosomal ; *RNA, Ribosomal, 16S ; Ruminants/classification/*genetics ; }, abstract = {The phylogeny of the family Bovidae has been inferred from our data on the 12S and 16S rRNA gene sequences and from the results of other authors. A considerable (2,460 bp) length of the analyzed fragments of these conserved genes and the use of different methods of cladogram construction allowed us to verify the systematic position of the genera Saiga, Pantholops, Procarpa, and Oreamnos. Saigas were shown to be phylogenetically far closer to gazelles than black-tailed gazelles and pygmy antelopes. In general, the genetic analysis data are in agreement with the results of morphological studies.}, }
@article {pmid12238891, year = {2002}, author = {Kita, K and Takamiya, S}, title = {Electron-transfer complexes in Ascaris mitochondria.}, journal = {Advances in parasitology}, volume = {51}, number = {}, pages = {95-131}, doi = {10.1016/s0065-308x(02)51004-6}, pmid = {12238891}, issn = {0065-308X}, mesh = {Anaerobiosis/physiology ; Animals ; Ascaris suum/growth &amp; development/*metabolism/physiology ; DNA, Mitochondrial/genetics/metabolism ; Electron Transport/genetics/physiology ; Evolution, Molecular ; Fatty Acid Desaturases/metabolism ; Life Cycle Stages/physiology ; Mitochondria/*metabolism ; Models, Biological ; Models, Molecular ; Oxidoreductases/metabolism ; *Oxidoreductases Acting on CH-CH Group Donors ; Phosphoenolpyruvate Carboxykinase (ATP)/metabolism ; Succinic Acid/metabolism ; Ubiquinone/*analogs &amp; derivatives/physiology ; }, abstract = {Parasites have developed a variety of physiological functions necessary for their survival within the specialized environment of the host. Using metabolic systems that are very different from those of the host, they can adapt to low oxygen tension present within the host animals. Most parasites do not use the oxygen available within the host to generate ATP, but rather employ anaerobic metabolic pathways. In addition, all parasites have a life cycle. In many cases, the parasite employs aerobic metabolism during its free-living stage outside the host. In such systems, parasite mitochondria play diverse roles. In particular, marked changes in the morphology and components of the mitochondria during the life cycle are very interesting elements of biological processes such as developmental control and environmental adaptation. Recent research on the respiratory chain of the parasitic helminth Ascaris suum has shown that the mitochondrial NADH-fumarate reductase system plays an important role in the anaerobic energy metabolism of adult parasites inhabiting hosts, as well as describing unique features of the developmental changes that occur during its life cycle.}, }
@article {pmid12207015, year = {2002}, author = {Roje, S and Janave, MT and Ziemak, MJ and Hanson, AD}, title = {Cloning and characterization of mitochondrial 5-formyltetrahydrofolate cycloligase from higher plants.}, journal = {The Journal of biological chemistry}, volume = {277}, number = {45}, pages = {42748-42754}, doi = {10.1074/jbc.M205632200}, pmid = {12207015}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Arabidopsis/*enzymology ; Base Sequence ; Carbon-Nitrogen Ligases/*genetics/metabolism ; Cloning, Molecular ; DNA Primers ; DNA, Complementary/genetics ; Escherichia coli/enzymology/genetics ; Humans ; Solanum lycopersicum/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Molecular Weight ; Phylogeny ; Recombinant Proteins/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Substrate Specificity ; }, abstract = {5-Formyltetrahydrofolate cycloligase (5-FCL) catalyzes the conversion of 5-formyltetrahydrofolate (5-CHO-H(4)PteGlu(n)) to 5,10-methenyltetrahydrofolate and is considered to be the main means whereby 5-CHO-H(4)PteGlu(n) is metabolized in mammals, yeast, and bacteria. 5-CHO-H(4)PteGlu(n) is known to occur in plants and to be highly abundant in leaf mitochondria. Genomics-based approaches identified Arabidopsis and tomato cDNAs encoding proteins homologous to 5-FCLs of other organisms but containing N-terminal extensions with the features of mitochondrial targeting peptides. These homologs were shown to have 5-FCL activity by characterizing recombinant enzymes produced in Escherichia coli and by functional complementation of a yeast fau1 mutation with the Arabidopsis 5-FCL cDNA. The recombinant Arabidopsis enzyme is active as a monomer, prefers the penta- to the monoglutamyl form of 5-CHO-H(4)PteGlu(n), and has kinetic properties broadly similar to those of 5-FCLs from other organisms. Enzyme assays and immunoblot analyses indicated that 5-FCL is located predominantly if not exclusively in plant mitochondria and that the mature, active enzyme lacks the putative targeting sequence. Serine hydroxymethyltransferase (SHMT) from plant mitochondria was shown to be inhibited by 5-CHO-H(4)PteGlu(n) as are SHMTs from other organisms. Since mitochondrial SHMT is crucial to photorespiration, 5-FCL may help prevent 5-CHO-H(4)PteGlu(n) from reaching levels that would inhibit this process. Consistent with this possibility, 5-FCL activity was far higher in leaf mitochondria than root mitochondria.}, }
@article {pmid12234672, year = {2002}, author = {Rampazzo, C and Kost-Alimova, M and Ruzzenente, B and Dumanski, JP and Bianchi, V}, title = {Mouse cytosolic and mitochondrial deoxyribonucleotidases: cDNA cloning of the mitochondrial enzyme, gene structures, chromosomal mapping and comparison with the human orthologs.}, journal = {Gene}, volume = {294}, number = {1-2}, pages = {109-117}, doi = {10.1016/s0378-1119(02)00651-0}, pmid = {12234672}, issn = {0378-1119}, support = {GP0140Y01/TI_/Telethon/Italy ; }, mesh = {5'-Nucleotidase/*genetics ; Amino Acid Sequence ; Animals ; Chromosome Mapping ; Cloning, Molecular ; Cytosol/*enzymology ; DNA, Complementary/chemistry/genetics ; Evolution, Molecular ; Genes/genetics ; Humans ; In Situ Hybridization, Fluorescence ; Isoenzymes/genetics ; Mice ; Mitochondria/*enzymology ; Molecular Sequence Data ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Synteny ; }, abstract = {Two of the five known mammalian 5'-nucleotidases show a preference for the dephosphorylation of deoxynucleoside-5'-phosphates. One is a cytoplasmic enzyme (dNT-1), the other occurs in mitochondria (dNT-2). The human mitochondrial enzyme, recently discovered and cloned by us, is encoded by a nuclear gene located on chromosome 17 p11.2 in the critical region deleted in the Smith-Magenis syndrome (SMS), a genetic disease of unknown etiology. Looking for a model system to study the possible involvement of dNT-2 in the disease, we have cloned the cDNA of the mouse ortholog. The deduced protein sequence is 84% identical to the human ortholog, has a very basic NH(2)-terminus, a very high calculated probability of being imported into mitochondria and contains the DXDXT/V motif conserved among nucleotidases. Expression in Escherichia coli of the predicted processed form of the protein produced an active deoxyribonucleotidase. We also identified in genomic sequences present in the data base the structures of the murine genes for the cytosolic and mitochondrial deoxyribonucleotidases (Nt5c and Nt5m). PAC clones for the two loci were isolated from a library and used for chromosomal localization by fluorescent in situ hybridization. Both genes map on chromosome 11: Nt5c at 11E and Nt5m at 11B, demonstrating the presence of the dNT-2 locus in the mouse shaker-2 critical region, the murine counterpart of the human SMS region. We performed pair-wise dot-plot and PIP (percent identity plot) analyses of mouse and human deoxyribonucleotidase genes, and found a strong conservation that extends also to some intronic sequences of possible regulatory significance.}, }
@article {pmid12233780, year = {2000}, author = {Olson, MS and McCauley, DE}, title = {Linkage disequilibrium and phylogenetic congruence between chloroplast and mitochondrial haplotypes in Silene vulgaris.}, journal = {Proceedings. Biological sciences}, volume = {267}, number = {1454}, pages = {1801-1808}, pmid = {12233780}, issn = {0962-8452}, mesh = {DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/genetics ; Genetic Variation ; Genetics, Population ; Haplotypes ; *Linkage Disequilibrium ; *Phylogeny ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; Silene/*genetics/physiology ; }, abstract = {Both the chloroplast and mitochondrial genomes are used extensively in studies of plant population genetics and systematics. In the majority of angiosperms, the chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) are each primarily transmitted maternally, but rare biparental transmission is possible. The extent to which the cpDNA and mtDNA are in linkage disequilibrium is argued to be dependent on the fidelity of co-transmission and the population structure. This study reports complete linkage disequilibrium between cpDNA and mtDNA haplotypes in 86 individuals from 17 populations of Silene vulgaris, a gynodioecious plant species. Phylogenetic analysis of cpDNA and mtDNA haplotypes within 14 individuals supports a hypothesis that the evolutionary histories of the chloroplasts and mitochondria are congruent within S. vulgaris, as might be expected if this association persists for long periods. This provides the first documentation of the evolutionary consequences of long-term associations between chloroplast and mitochondrial genomes within a species. Factors that contribute to the phylogenetic and linkage associations, as well as the potential for intergenomic hitchhiking resulting from selection on genes in one organellar genome are discussed.}, }
@article {pmid12233175, year = {2002}, author = {Gisi, U and Sierotzki, H and Cook, A and McCaffery, A}, title = {Mechanisms influencing the evolution of resistance to Qo inhibitor fungicides.}, journal = {Pest management science}, volume = {58}, number = {9}, pages = {859-867}, doi = {10.1002/ps.565}, pmid = {12233175}, issn = {1526-498X}, mesh = {*Biological Evolution ; Drug Resistance, Fungal/*genetics ; Electron Transport Complex III/genetics/metabolism ; Fungi/*drug effects/enzymology/genetics/*physiology ; Fungicides, Industrial/*pharmacology ; Plants/microbiology ; }, abstract = {Fungicides inhibiting the mitochondrial respiration of plant pathogens by binding to the cytochrome bc1 enzyme complex (complex III) at the Qo site (Qo inhibitors, QoIs) were first introduced to the market in 1996. After a short time period, isolates resistant to QoIs were detected in field populations of a range of important plant pathogens including Blumeria graminis Speer f sp tritici, Sphaerotheca fuliginea (Schlecht ex Fr) Poll, Plasmopara viticola (Berk &amp; MA Curtis ex de Bary) Berl &amp; de Toni, Pseudoperonospora cubensis (Berk &amp; MA Curtis) Rost, Mycosphaerella fijiensis Morelet and Venturia inaequalis (Cooke) Wint. In most cases, resistance was conferred by a point mutation in the mitochondrial cytochrome b (cyt b) gene leading to an amino-acid change from glycine to alanine at position 143 (G143A), although additional mutations and mechanisms have been claimed in a number of organisms. Transformation of sensitive protoplasts of M fijiensis with a DNA fragment of a resistant M fijiensis isolate containing the mutation yielded fully resistant transformants, demonstrating that the G143A substitution may be the most powerful transversion in the cyt b gene conferring resistance. The G143A substitution is claimed not to affect the activity of the enzyme, suggesting that resistant individuals may not suffer from a significant fitness penalty, as was demonstrated in B graminis f sp tritici. It is not known whether this observation applies also for other pathogen species expressing the G143A substitution. Since fungal cells contain a large number of mitochondria, early mitotic events in the evolution of resistance to QoIs have to be considered, such as mutation frequency (claimed to be higher in mitochondrial than nuclear DNA), intracellular proliferation of mitochondria in the heteroplasmatic cell stage, and cell to cell donation of mutated mitochondria. Since the cyt b gene is located in the mitochondrial genome, inheritance of resistance in filamentous fungi is expected to be non-Mendelian and, therefore, in most species uniparental. In the isogamous fungus B graminis f sp tritici, crosses of sensitive and resistant parents yielded cleistothecia containing either sensitive or resistant ascospores and the segregation pattern for resistance in the F1 progeny population was 1:1. In the anisogamous fungus V inaequalis, donation of resistance was maternal and the segregation ratio 1:0. In random mating populations, the sex ratio (mating type distribution) is generally assumed to be 1:1. Therefore, the overall proportion of sensitive and resistant individuals in unselected populations is expected to be 1:1. Evolution of resistance to QoIs will depend mainly on early mitotic events; the selection process for resistant mutants in populations exposed to QoI treatments may follow mechanisms similar to those described for resistance controlled by single nuclear genes in other fungicide classes. It will remain important to understand how the mitochondrial nature of QoI resistance and factors such as mutation, recombination, selection and migration might influence the evolution of QoI resistance in different plant pathogens.}, }
@article {pmid12230538, year = {2002}, author = {Martin, J and Guryev, V and Blinov, A}, title = {Population variability in Chironomus (Camptochironomus) species (Diptera, Nematocera) with a Holarctic distribution: evidence of mitochondrial gene flow.}, journal = {Insect molecular biology}, volume = {11}, number = {5}, pages = {387-397}, doi = {10.1046/j.1365-2583.2002.00348.x}, pmid = {12230538}, issn = {0962-1075}, mesh = {Animals ; Base Sequence ; Chironomidae/classification/enzymology/*genetics ; Cytochrome b Group/*genetics ; DNA, Complementary ; *DNA, Mitochondrial ; Electron Transport Complex IV/*genetics ; Globins/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Phylogenetic analysis of DNA sequences from mitochondrial (mt) genes (Cytochrome b and Cytochrome oxidase I) and one nuclear gene (globin 2b) was used for the investigation of Nearctic and Palearctic populations representing four Chironomus species of the subgenus Camptochironomus, namely C. biwaprimus, C. pallidivittatus, C. tentans sensu stricto and C. dilutus (the last two species constitute Holarctic C. tentans sensu lato). Phenograms constructed on the basis of mt sequences were not congruent with trees based on nuclear genes, or with morphological and cytological data. The mt tree divided the populations by continental region, rather than by the species groupings recognized by the other data sets. The incongruence is explained by mt gene flow resulting from hybridization between the sympatric species on each continent. Calculation of divergence times, based on the sequence data, suggest that C. tentans (s.l.) and C. pallidivittatus have both been in North America for about 2.5 My.}, }
@article {pmid12230260, year = {2002}, author = {Sobaniec-Lotowska, ME}, title = {Ultrastructure of synaptic junctions in the cerebellar cortex in experimental valproate encephalopathy and after terminating chronic application of the antiepileptic.}, journal = {Folia neuropathologica}, volume = {40}, number = {2}, pages = {87-96}, pmid = {12230260}, issn = {1641-4640}, mesh = {Animals ; Anticonvulsants/*adverse effects ; Cerebellar Cortex/drug effects/pathology/*ultrastructure ; Male ; Neurotoxicity Syndromes/*pathology ; Rats ; Rats, Wistar ; Synapses/drug effects/pathology/*ultrastructure ; Valproic Acid/*adverse effects ; }, abstract = {The aim of the study was to analyse in TEM the evolution of changes in structural elements of synaptic junctions of the cerebellar cortex in rats in valproate encephalopathy induced by chronic 12-month administration of sodium valproate - VPA (once daily intragastrically, in a dose of 200 mg/kg b.w.) and after withdrawal of this antiepileptic for 1 and 3 months. After 9 and 12 months of the experiment, synaptic endings of both the symmetrical and asymmetrical synapses in the neuropil of the cerebellar cortex, especially in the molecular layer, showed signs of severe damage (mainly swelling) and even disintegration. They were mostly observed in axodendritic endings and axospinal endings on the dendritic spines of Purkinje cells, being manifested in the presence of large vacuolar structures, electron lucent areas and swollen mitochondria within the cytoplasm. A reduced number of axonal synaptic vesicles (with more type F vesicles preserved) could be seen. One and 3 months after the end of chronic application of VPA, the synaptic junctions did not show morphological exponents of the repair processes. The alterations observed in the synapticjunctions of the cerebellar cortex may suggest disorders in neurotransmission processes, such as exhaustion and damage caused by ischaemia due to damage to the blood-brain barrier induced by VPA and/or its toxic metabolites.}, }
@article {pmid12228005, year = {2002}, author = {Savolainen, V and Chase, MW and Salamin, N and Soltis, DE and Soltis, PS and López, AJ and Fédrigo, O and Naylor, GJ}, title = {Phylogeny reconstruction and functional constraints in organellar genomes: plastid atpB and rbcL sequences versus animal mitochondrion.}, journal = {Systematic biology}, volume = {51}, number = {4}, pages = {638-647}, doi = {10.1080/10635150290102348}, pmid = {12228005}, issn = {1063-5157}, mesh = {Animals ; Codon ; *Genome ; Mitochondria/*genetics ; *Phylogeny ; Plants/genetics ; Plastids/*genetics ; Ribulose-Bisphosphate Carboxylase/*genetics ; }, }
@article {pmid12226508, year = {2002}, author = {Huertas, IE and Colman, B and Espie, GS}, title = {Mitochondrial-driven bicarbonate transport supports photosynthesis in a marine microalga.}, journal = {Plant physiology}, volume = {130}, number = {1}, pages = {284-291}, pmid = {12226508}, issn = {0032-0889}, mesh = {Azides/pharmacology ; Bicarbonates/*metabolism ; Biological Transport/drug effects ; Carbon Dioxide/metabolism ; Carbon Isotopes/metabolism ; Carbonic Anhydrases/metabolism ; Cell Respiration/radiation effects ; Darkness ; Diuron/pharmacology ; Electron Transport/drug effects ; Eukaryota/drug effects/*physiology/radiation effects ; Light ; Mitochondria/*metabolism ; Oxygen/metabolism ; Photosynthesis/*physiology/radiation effects ; Potassium Cyanide/pharmacology ; Rotenone/pharmacology ; }, abstract = {The CO(2)-concentrating mechanism (CCM) of the marine eustigmatophycean microalga Nannochloropsis gaditana consists of an active HCO(3)(-) transport system and an internal carbonic anhydrase to facilitate accumulation and conversion of HCO(3)(-) to CO(2) for photosynthetic fixation. Aqueous inlet mass spectrometry revealed that a portion of the CO(2) generated within the cells leaked to the medium, resulting in a significant rise in the extracellular CO(2) concentration to a level above its chemical equilibrium that was diagnostic for active HCO(3)(-) transport. The transient rise in extracellular CO(2) occurred in the light and the dark and was resolved from concurrent respiratory CO(2) efflux using H(13)CO(3)(-) stable isotope techniques. H(13)CO(3)(-) pump-(13)CO(2) leak activity of the CCM was unaffected by 10 microM 3(3,4-dichlorophenyl)-1,1-dimethylurea, an inhibitor of chloroplast linear electron transport, although photosynthetic O(2) evolution was reduced by 90%. However, low concentrations of cyanide, azide, and rotenone along with anoxia significantly reduced or abolished (13)CO(2) efflux in the dark and light. These results indicate that H(13)CO(3)(-) transport was supported by mitochondrial energy production in contrast to other algae and cyanobacteria in which it is supported by photosynthetic electron transport. This is the first report of a direct role for mitochondria in the energization and functioning of the CCM in a photosynthetic organism.}, }
@article {pmid12221298, year = {2002}, author = {Palenik, B}, title = {The genomics of symbiosis: hosts keep the baby and the bath water.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {19}, pages = {11996-11997}, pmid = {12221298}, issn = {0027-8424}, mesh = {Bacteria/genetics/metabolism ; Biological Evolution ; Cell Nucleus/genetics ; Chloroplasts/genetics/metabolism/microbiology ; Gene Transfer, Horizontal ; *Genomics ; Mitochondria/genetics/metabolism/microbiology ; Plants/genetics/microbiology ; Symbiosis/*genetics ; }, }
@article {pmid12206246, year = {2002}, author = {Clarke, KE and Rinderer, TE and Franck, P and Quezada-Euán, JG and Oldroyd, BP}, title = {The Africanization of honeybees (Apis mellifera L.) of the Yucatan: a study of a massive hybridization event across time.}, journal = {Evolution; international journal of organic evolution}, volume = {56}, number = {7}, pages = {1462-1474}, doi = {10.1111/j.0014-3820.2002.tb01458.x}, pmid = {12206246}, issn = {0014-3820}, mesh = {Africa ; Animals ; Bees/classification/*genetics/physiology ; *DNA, Mitochondrial ; *Genetics, Population ; *Hybridization, Genetic ; Microsatellite Repeats ; Phylogeny ; Time Factors ; }, abstract = {Until recently, African and European subspecies of the honeybee (Apis mellifera L.) had been geographically separated for around 10,000 years. However, human-assisted introductions have caused the mixing of large populations of African and European subspecies in South and Central America, permitting an unprecedented opportunity to study a large-scale hybridization event using molecular analyses. We obtained reference populations from Europe, Africa, and South America and used these to provide baseline information for a microsatellite and mitochondrial analysis of the process of Africanization of the bees of the Yucatan Peninsula, Mexico. The genetic structure of the Yucatecan population has changed dramatically over time. The pre-Africanized Yucatecan population (1985) comprised bees that were most similar to samples from southeastern Europe and northern and western Europe. Three years after the arrival of Africanized bees (1989), substantial paternal gene flow had occurred from feral Africanized drones into the resident European population, but maternal gene flow from the invading Africanized population into the local population was negligible. However by 1998, there was a radical shift with both African nuclear alleles (65%) and African-derived mitochondria (61%) dominating the genomes of domestic colonies. We suggest that although European mitochondria may eventually be driven to extinction in the feral population, stable introgression of European nuclear alleles has occurred.}, }
@article {pmid12216453, year = {2001}, author = {Puzyrev, VP and Golubenko, MV and Freĭdin, MB}, title = {[The realm of mitochondrial genetics competence].}, journal = {Vestnik Rossiiskoi akademii meditsinskikh nauk}, volume = {}, number = {10}, pages = {31-37}, pmid = {12216453}, issn = {0869-6047}, mesh = {Genetic Predisposition to Disease ; Genetics, Population/trends ; Genome ; Humans ; Mitochondria/*genetics ; *Mitochondrial Diseases/genetics/pathology ; Multifactorial Inheritance ; }, abstract = {The paper discusses the main applications of achievements of mitochondrial genetics: human pathology (mitochondrial diseases, complex disease susceptibility genes) and population genetics (evolution of mankind, demographic history, and migration ways of populations). Awareness of the physiological properties of the well-known nucleotide sequences of mitochondrial DNA is ascertained to be a strategy for studying the functional organization of nuclear genome whose structure is all but completely decoded.}, }
@article {pmid12208346, year = {2002}, author = {Cortopassi, GA}, title = {A neutral theory predicts multigenic aging and increased concentrations of deleterious mutations on the mitochondrial and Y chromosomes.}, journal = {Free radical biology &amp; medicine}, volume = {33}, number = {5}, pages = {605-610}, doi = {10.1016/s0891-5849(02)00966-8}, pmid = {12208346}, issn = {0891-5849}, mesh = {*Aging ; Alleles ; Animals ; Cell Nucleus/metabolism ; DNA, Mitochondrial/metabolism ; Female ; Free Radicals ; *Gene Deletion ; Genome ; Humans ; Male ; Mitochondria/*pathology ; Mutation ; Reactive Oxygen Species ; Recombination, Genetic ; Sex Factors ; *Y Chromosome ; }, abstract = {Population genetic forces have molded the constitution of the human genome over evolutionary time, and some of the most important parameters are the initial frequency of the allele, p, the effective population size, Ne, and the selection coefficient, s. There is considerable agreement among evolutionary gerontologists that the amplitude of -s is small for alleles that are Deleterious In Late Life (DILL), and thus DILL traits are effectively neutral and should be fixed in the human population in relationship to Ne and p. Even higher rates of fixation of deleterious mutations are predicted to occur in the two nonrecombinant genomes in humans, i.e., the Y chromosome and the mitochondrial genome, as a consequence of their lower Ne than autosomes, and the predicted higher rate of fixation of deleterious alleles on the Y may explain the reduced average life span of males vs. females. The high probability of fixation of neutral and mildly deleterious mutations in the mitochondrial genome explains in part its fast rate of evolution, the high observed frequency of mitochondrial disease in relationship to this genome's small size, and may be the underlying reason for the transfer of mitochondrial genes over evolutionary time to the nucleus. The predicted higher concentration of deleterious mutations on the mitochondrial genome could have some leverage to cause more dysfunction than that predicted by mitochondrial gene number alone, because of the essential role of mitochondrial gene function in multisubunit complexes, the coupling of mitochondrial functions, the observation that some mtDNA sequences facilitate somatic mutation, and the likelihood of deleterious mutations either increasing the production of or the sensitivity to mitochondrial ROS.}, }
@article {pmid12207654, year = {2002}, author = {Voznesenskaya, EV and Franceschi, VR and Kiirats, O and Artyusheva, EG and Freitag, H and Edwards, GE}, title = {Proof of C4 photosynthesis without Kranz anatomy in Bienertia cycloptera (Chenopodiaceae).}, journal = {The Plant journal : for cell and molecular biology}, volume = {31}, number = {5}, pages = {649-662}, doi = {10.1046/j.1365-313x.2002.01385.x}, pmid = {12207654}, issn = {0960-7412}, mesh = {Amino Acid Oxidoreductases/metabolism ; Blotting, Western ; Carbon/*metabolism ; Carbon Dioxide/pharmacology ; Carbon Isotopes ; Carbon Radioisotopes ; Cell Compartmentation/physiology ; Cell Respiration/physiology ; Chenopodiaceae/classification/cytology/*physiology ; Chloroplasts/ultrastructure ; Cytoplasm/ultrastructure ; Glycine Dehydrogenase (Decarboxylating) ; In Situ Hybridization ; Malate Dehydrogenase/metabolism ; Microscopy, Confocal ; Microscopy, Electron ; Phosphoenolpyruvate Carboxylase/metabolism ; Photosynthesis/drug effects/*physiology ; Pyruvate, Orthophosphate Dikinase/metabolism ; Ribulose-Bisphosphate Carboxylase/metabolism ; Vacuoles/ultrastructure ; }, abstract = {Kranz anatomy, with its separation of elements of the C4 pathway between two cells, has been an accepted criterion for function of C4 photosynthesis in terrestrial plants. However, Bienertia cycloptera (Chenopodiaceae), which grows in salty depressions of Central Asian semi-deserts, has unusual chlorenchyma, lacks Kranz anatomy, but has photosynthetic features of C4 plants. Its photosynthetic response to varying CO2 and O2 is typical of C4 plants having Kranz anatomy. Lack of night-time CO2 fixation indicates it is not acquiring carbon by Crassulacean acid metabolism. This species exhibits an independent, novel solution to function of the C4 mechanism through spatial compartmentation of dimorphic chloroplasts, other organelles and photosynthetic enzymes in distinct positions within a single chlorenchyma cell. The chlorenchyma cells have a large, spherical central cytoplasmic compartment interconnected by cytoplasmic channels through the vacuole to the peripheral cytoplasm. This compartment is filled with mitochondria and granal chloroplasts, while the peripheral cytoplasm apparently lacks mitochondria and has grana-deficient chloroplasts. Immunolocalization studies show enzymes compartmentalized selectively in the CC compartment, including Rubisco in chloroplasts, and NAD-malic enzyme and glycine decarboxylase in mitochondria, whereas pyruvate, Pi dikinase of the C4 cycle is localized selectively in peripheral chloroplasts. Phosphoenolpyruvate carboxylase, a cytosolic C4 cycle enzyme, is enriched in the peripheral cytoplasm. Our results show Bienertia utilizes strict compartmentation of organelles and enzymes within a single cell to effectively mimic the spatial separation of Kranz anatomy, allowing it to function as a C4 plant having suppressed photorespiration; this raises interesting questions about evolution of C4 mechanisms.}, }
@article {pmid12204220, year = {2002}, author = {Seeber, F}, title = {Biogenesis of iron-sulphur clusters in amitochondriate and apicomplexan protists.}, journal = {International journal for parasitology}, volume = {32}, number = {10}, pages = {1207-1217}, doi = {10.1016/s0020-7519(02)00022-x}, pmid = {12204220}, issn = {0020-7519}, mesh = {Animals ; Apicomplexa/cytology/genetics/*metabolism ; Bacterial Physiological Phenomena ; Eukaryota/cytology/*metabolism ; Eukaryotic Cells/physiology ; Iron-Sulfur Proteins/*biosynthesis/classification ; Mitochondria/metabolism ; Models, Biological ; Yeasts/physiology ; }, abstract = {During the last 4 years there has been an enormous interest in the question how iron-sulphur ([Fe-S]) clusters, which are essential building blocks for life, are synthesised and assembled into apo-proteins, both in prokaryotes and in eukaryotes. The emerging picture is that the basic mechanism of this pathway has been well conserved during evolution. In yeast and probably all other eukaryotes the mitochondrion is the place where [Fe-S] clusters are synthesised, even for extramitochondrial [Fe-S] cluster-containing proteins, and a number of proteins have been functionally characterised to a certain extent within this pathway. However, almost nothing is known about this aspect in parasitic protists, although recent studies of amitochondriate protists and on the plastid-like organelle of apicomplexan parasites, the apicoplast, have started to change this. In this article I will summarise the current view of [Fe-S] cluster biogenesis in eukaryotes and discuss its implications for amitochondriate protists and for the plastid-like organelle of apicomplexan parasites.}, }
@article {pmid12200480, year = {2002}, author = {Iwabe, N and Miyata, T}, title = {Kinesin-related genes from diplomonad, sponge, amphioxus, and cyclostomes: divergence pattern of kinesin family and evolution of giardial membrane-bounded organella.}, journal = {Molecular biology and evolution}, volume = {19}, number = {9}, pages = {1524-1533}, doi = {10.1093/oxfordjournals.molbev.a004215}, pmid = {12200480}, issn = {0737-4038}, mesh = {Animals ; Diplomonadida/genetics ; Eukaryotic Cells/*metabolism ; *Evolution, Molecular ; Giardia lamblia/*genetics ; Humans ; Kinesins/*genetics ; Molecular Sequence Data ; Phylogeny ; Porifera/genetics ; }, abstract = {To understand the question of whether divergence of eukaryotic genes by gene duplications and domain shufflings proceeded gradually or intermittently during evolution, we have cloned and sequenced Giardia lamblia cDNAs encoding kinesins and kinesin-related proteins and have obtained 13 kinesin-related cDNAs, some of which are likely homologs of vertebrate kinesins involved in vesicle transfer to ER, Golgi, and plasma membrane. A phylogenetic tree of the kinesin family revealed that most gene duplications that gave rise to different kinesin subfamilies with distinct functions have been completed before the earliest divergence of extant eukaryotes. This suggests that the complex endomembrane system has arisen very early in eukaryotic evolution, and the diminutive ER and Golgi apparatus recognized in the giardial cells, together with the absence of mitochondria, might be characters acquired secondarily during the evolution of parasitism. To understand the divergence pattern of the kinesin family in the lineage leading to vertebrates, seven more Unc104-related cDNAs have been cloned from sponge, amphioxus, hagfish, and lamprey. The divergence pattern of the animal Unc104/KIF1 subfamily is characterized by two active periods in gene duplication interrupted by a considerably long period of silence, instead of proceeding gradually: animals underwent extensive gene duplications before the parazoan-eumetazoan split. In the early evolution of vertebrates around the cyclostome-gnathostome split, further gene duplications occurred, by which a variety of genes with similar structures over the entire regions were generated. This pattern of divergence is similar to those of animal genes involved in cell-cell communication and developmental control.}, }
@article {pmid12200038, year = {2002}, author = {Rose, G and Passarino, G and Franceschi, C and De Benedictis, G}, title = {The variability of the mitochondrial genome in human aging: a key for life and death?.}, journal = {The international journal of biochemistry &amp; cell biology}, volume = {34}, number = {11}, pages = {1449-1460}, doi = {10.1016/s1357-2725(02)00042-0}, pmid = {12200038}, issn = {1357-2725}, mesh = {Aging/*physiology ; Apoptosis/physiology ; DNA, Mitochondrial/classification/*genetics ; Genetic Variation ; Humans ; Mitochondria/*genetics/metabolism ; Models, Biological ; Oxidative Phosphorylation ; Phylogeny ; }, abstract = {The impressive performance of the research in mitochondrial genetics and human aging in the last decade outlines a new scenery in which the inherited variation of the mitochondrial genome (mtDNA) may play a role in rate and quality of aging. This variation in humans was initially looked at as nearly neutral, and useful just for the reconstruction of human population history. However, recent data suggest that different mtDNA molecules are qualitatively different from each other. The aim of this paper is to discuss current ideas on the relationships among mitochondrial function, mtDNA inherited variation, and aging. The main processes where the mitochondrion is involved and the importance these processes have on aging and death of individuals will be described. A possible connection between programmed death phenomena (mitoptosis, apoptosis, phenoptosis) and rate and quality of aging will be discussed. Finally, the possible role played in these processes by the mtDNA germline variation will be explored.}, }
@article {pmid12192407, year = {2002}, author = {Williams, BA and Hirt, RP and Lucocq, JM and Embley, TM}, title = {A mitochondrial remnant in the microsporidian Trachipleistophora hominis.}, journal = {Nature}, volume = {418}, number = {6900}, pages = {865-869}, doi = {10.1038/nature00949}, pmid = {12192407}, issn = {0028-0836}, mesh = {Amino Acid Sequence ; Animals ; Blotting, Western ; Cell Line ; Cloning, Molecular ; Endocytosis ; Eukaryotic Cells/cytology/metabolism/ultrastructure ; Fluorescent Antibody Technique ; Fungi/cytology/genetics/metabolism/ultrastructure ; HSP70 Heat-Shock Proteins/*analysis/chemistry/genetics/immunology ; Humans ; Kidney/parasitology ; Microscopy, Electron ; Microscopy, Immunoelectron ; Microsporidia/*chemistry/*cytology/genetics/ultrastructure ; Mitochondria/*chemistry/genetics/ultrastructure ; Mitochondrial Proteins/analysis/chemistry/genetics/immunology ; Models, Biological ; Molecular Sequence Data ; *Phylogeny ; Rabbits ; Symbiosis ; }, abstract = {Microsporidia are obligate intracellular parasites of several eukaryotes. They have a highly complex and unique infection apparatus but otherwise appear structurally simple. Microsporidia are thought to lack typical eukaryotic organelles, such as mitochondria and peroxisomes. This has been interpreted as support for the hypothesis that these peculiar eukaryotes diverged before the mitochondrial endosymbiosis, which would make them one of the earliest offshoots in eukaryotic evolution. But microsporidial nuclear genes that encode orthologues of typical mitochondrial heatshock Hsp70 proteins have been detected, which provides evidence for secondary loss of the organelle or endosymbiont. In addition, gene trees and more sophisticated phylogenetic analyses have recovered microsporidia as the relatives of fungi, rather than as basal eukaryotes. Here we show that a highly specific antibody raised against a Trachipleistophora hominis Hsp70 protein detects the presence, under light and electron microscopy, of numerous tiny (approximately 50 x 90 nm) organelles with double membranes in this human microsporidial parasite. The finding of relictual mitochondria in microsporidia provides further evidence of the reluctance of eukaryotes to lose the mitochondrial organelle, even when its canonical function of aerobic respiration has been apparently lost.}, }
@article {pmid12192393, year = {2002}, author = {Roger, AJ and Silberman, JD}, title = {Cell evolution: mitochondria in hiding.}, journal = {Nature}, volume = {418}, number = {6900}, pages = {827-829}, doi = {10.1038/418827a}, pmid = {12192393}, issn = {0028-0836}, mesh = {Animals ; Endocytosis ; Eukaryotic Cells/cytology/metabolism ; Fungi/cytology/genetics/metabolism/ultrastructure ; HSP70 Heat-Shock Proteins/*analysis/genetics ; Humans ; Microscopy, Immunoelectron ; Microsporidia/*chemistry/*cytology/genetics/ultrastructure ; Mitochondria/*chemistry/genetics/ultrastructure ; Mitochondrial Proteins/analysis/genetics ; *Models, Biological ; *Phylogeny ; Symbiosis ; }, }
@article {pmid12192087, year = {2002}, author = {Städler, T and Delph, LF}, title = {Ancient mitochondrial haplotypes and evidence for intragenic recombination in a gynodioecious plant.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {18}, pages = {11730-11735}, pmid = {12192087}, issn = {0027-8424}, mesh = {Base Sequence ; Blotting, Southern ; DNA Primers ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Haplotypes ; Mitochondria/*genetics ; Molecular Sequence Data ; Plants/*genetics ; Polymerase Chain Reaction ; *Recombination, Genetic ; Sequence Homology, Nucleic Acid ; }, abstract = {Because of their extremely low nucleotide mutation rates, plant mitochondrial genes are generally not expected to show variation within species. Remarkably, we found nine distinct cytochrome b sequence haplotypes in the gynodioecious alpine plant Silene acaulis, with two or more haplotypes coexisting locally in each of three sampled regions. Moreover, there is evidence for intragenic recombination in the history of the haplotype sample, implying at least transient heteroplasmy of mitochondrial DNA (mtDNA). Heteroplasmy might be achieved by one of two potential mechanisms, either continuous coexistence of subgenomic fragments in low stoichiometry, or occasional paternal leakage of mtDNA. On the basis of levels of synonymous nucleotide substitutions, the average divergence time between haplotypes is estimated to be at least 15 million years. Ancient coalescence of extant haplotypes is further indicated by the paucity of fixed differences in haplotypes obtained from related species, a pattern expected under trans-specific evolution. Our data are consistent with models of frequency-dependent selection on linked cytoplasmic male-sterility factors, the putative molecular basis of females in gynodioecious populations. However, associations between marker loci and the inferred male-sterility genes can be maintained only with very low rates of recombination. Heteroplasmy and recombination between divergent haplotypes imply unexplored consequences for the evolutionary dynamics of gynodioecy, a widespread plant breeding system.}, }
@article {pmid12191771, year = {2002}, author = {Arnold, I and Langer, T}, title = {Membrane protein degradation by AAA proteases in mitochondria.}, journal = {Biochimica et biophysica acta}, volume = {1592}, number = {1}, pages = {89-96}, doi = {10.1016/s0167-4889(02)00267-7}, pmid = {12191771}, issn = {0006-3002}, mesh = {ATP-Dependent Proteases ; Endopeptidases/*metabolism ; Heat-Shock Proteins/chemistry/metabolism ; Intracellular Membranes/*enzymology ; Membrane Proteins/chemistry/*metabolism ; Mitochondria/*enzymology ; Prohibitins ; Protein Transport ; Proteins/metabolism ; *Repressor Proteins ; Saccharomyces cerevisiae ; Serine Endopeptidases/chemistry/metabolism ; }, abstract = {The inner membrane of mitochondria is one of the protein's richest cellular membranes. The biogenesis of the respiratory chain and ATP-synthase complexes present in this membrane is an intricate process requiring the coordinated function of various membrane-bound proteins including protein translocases and assembly factors. It is therefore not surprising that a distinct quality control system is present in this membrane that selectively removes nonassembled polypeptides and prevents their possibly deleterious accumulation in the membrane. The key components of this system are two AAA proteases, membrane-embedded ATP-dependent proteolytic complexes, which expose their catalytic sites at opposite membrane surfaces. Other components include the prohibitin complex with apparently chaperone-like properties and a regulatory function during proteolysis and a recently identified ATP-binding cassette (ABC) transporter that exports peptides derived from the degradation of membrane proteins from the matrix to the intermembrane space. All of these components are highly conserved during evolution and appear to be ubiquitously present in mitochondria of eukaryotic cells, indicating important cellular functions. This review will summarize our current understanding of this proteolytic system and, in particular, focus on the mechanisms guiding the degradation of membrane proteins by AAA proteases.}, }
@article {pmid12191770, year = {2002}, author = {Stuart, R}, title = {Insertion of proteins into the inner membrane of mitochondria: the role of the Oxa1 complex.}, journal = {Biochimica et biophysica acta}, volume = {1592}, number = {1}, pages = {79-87}, doi = {10.1016/s0167-4889(02)00266-5}, pmid = {12191770}, issn = {0006-3002}, mesh = {Binding Sites ; DNA, Mitochondrial/metabolism ; Electron Transport Complex IV/*metabolism ; Evolution, Molecular ; Intracellular Membranes/*metabolism ; Membrane Proteins/genetics/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins/metabolism ; Nuclear Proteins/genetics/*metabolism ; Protein Transport ; Saccharomyces cerevisiae ; }, abstract = {The inner mitochondrial membrane harbors a large number of proteins that display a wide range of topological arrangements. The majority of these proteins are encoded in the cell's nucleus, but a few polytopic proteins, all subunits of respiratory chain complexes are encoded by the mitochondrial genome. A number of distinct sorting mechanisms exist to direct these proteins into the mitochondrial inner membrane. One of these pathways involves the export of proteins from the matrix into the inner membrane and is used by both proteins synthesized within the mitochondria, as well as by a subset of nuclear encoded proteins. Prior to embarking on the export pathway, nuclear encoded proteins using this sorting route are initially imported into the mitochondrial matrix from the cytosol, their site of synthesis. Protein export from the matrix into the inner membrane bears similarities to Sec-independent protein export in bacteria and requires the function of the Oxa1 protein. Oxa1 is a component of a general protein insertion site in yeast mitochondrial inner membrane used by both nuclear and mitochondrial DNA encoded proteins. Oxa1 is a member of the conserved Oxa1/YidC/Alb3 protein family found throughout prokaryotes throughout eukaryotes (where it is found in mitochondria and chloroplasts). The evidence to demonstrate that the Oxa1/YidC/Alb3 protein family represents a novel evolutionarily conserved membrane insertion machinery is reviewed here.}, }
@article {pmid12191769, year = {2002}, author = {Gakh, O and Cavadini, P and Isaya, G}, title = {Mitochondrial processing peptidases.}, journal = {Biochimica et biophysica acta}, volume = {1592}, number = {1}, pages = {63-77}, doi = {10.1016/s0167-4889(02)00265-3}, pmid = {12191769}, issn = {0006-3002}, support = {AG15709/AG/NIA NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Escherichia coli ; Humans ; Intracellular Membranes/*enzymology ; Metalloendopeptidases/chemistry/genetics/*metabolism ; Mitochondria/*enzymology ; Mitochondrial Proteins/chemistry/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Precursors/*metabolism ; Saccharomyces cerevisiae ; Sequence Alignment ; Structure-Activity Relationship ; Substrate Specificity ; Mitochondrial Processing Peptidase ; }, abstract = {Three peptidases are responsible for the proteolytic processing of both nuclearly and mitochondrially encoded precursor polypeptides targeted to the various subcompartments of the mitochondria. Mitochondrial processing peptidase (MPP) cleaves the vast majority of mitochondrial proteins, while inner membrane peptidase (IMP) and mitochondrial intermediate peptidase (MIP) process specific subsets of precursor polypeptides. All three enzymes are structurally and functionally conserved across species, and their human homologues begin to be recognized as potential players in mitochondrial disease.}, }
@article {pmid12182806, year = {2002}, author = {Teixeira, RD and Scheltinga, DM and Trauth, SE and Colli, GR and Báo, SN}, title = {A comparative ultrastructural study of spermatozoa of the teiid lizards Cnemidophorus gularis gularis, Cnemidophorus ocellifer, and Kentropyx altamazonica (Reptilia, Squamata, Teiidae).}, journal = {Tissue &amp; cell}, volume = {34}, number = {3}, pages = {135-142}, doi = {10.1016/s0040-8166(02)00021-6}, pmid = {12182806}, issn = {0040-8166}, mesh = {Animals ; Cell Size ; Lizards/*anatomy &amp; histology/genetics ; Male ; Microscopy, Electron ; *Phylogeny ; Spermatozoa/*ultrastructure ; }, abstract = {The ultrastructure of the spermatozoa of Cnemidophorus gularis gularis, Cnemidophorus ocellifer, and Kentropyx altamazonica is described for the first time. Mature spermatozoa of Cnemidophorus spp. and K. altamazonica differ in the occurrence of a perforatorial base plate, the enlargement of axonemal fibers 3 and 8, and shape of mitochondria. The comparisons of the ultrastructure sperm of Cnemidophorus spp. and K. altamazonica with Ameiva ameiva [J. Morphol. (2002) in press] suggest that Ameiva and Cnemidophorus are more similar to each other than either is to Kentropyx. Statistical analyses reveal that sperm of all three species studied are significantly different in the following dimensions: head, acrosome, distal centriole length, and nuclear shoulders width. There was no variable statistically different between the Cnemidophorus spp. only. The length of the tail, midpiece, entire sperm, and nuclear rostrum are significantly different between K. altamazonica and Cnemidophorus spp. Our results indicate that sperm ultrastructure presents intra and intergeneric variability.}, }
@article {pmid12180017, year = {2002}, author = {Kuznetsov, AP and Lebkova, NP}, title = {[On bacterial origin of mitochondria in eukaryotes in the light of current ideas of evolution of the organic world].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {4}, pages = {501-507}, pmid = {12180017}, issn = {1026-3470}, mesh = {Aerobiosis ; Animals ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Eukaryotic Cells/*physiology ; Mitochondria/*physiology ; Mollusca/physiology ; Symbiosis ; }, abstract = {The hypothesis of bacterial origin of mitochondria, which existed until the end of the 20th century, has been confirmed on the basis of the current concepts of organic world evolution in the open sea hydrosphere and original data on the entry of bacteria (prokaryotes0 in the cells of eukaryotes and their transformation into the mitochondrial mechanism of aerobic energy metabolism. This hypothesis can now be considered as a factually substantiated theory. The process of endocytosis of bacteria in the tissues of eukaryotes, which began at the onset of transition of the anaerobic state of open sea hydrosphere and land atmosphere (Early Proterozoic), is considered as the beginning of symbiotic mode of life of organisms of the Proterozoic and Postproterozoic organic world.}, }
@article {pmid12176923, year = {2002}, author = {Brinkman, FS and Blanchard, JL and Cherkasov, A and Av-Gay, Y and Brunham, RC and Fernandez, RC and Finlay, BB and Otto, SP and Ouellette, BF and Keeling, PJ and Rose, AM and Hancock, RE and Jones, SJ and Greberg, H}, title = {Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast.}, journal = {Genome research}, volume = {12}, number = {8}, pages = {1159-1167}, pmid = {12176923}, issn = {1088-9051}, mesh = {Animals ; Bacterial Proteins/chemistry/genetics ; Base Composition/genetics ; Caenorhabditis elegans Proteins/chemistry/genetics ; Chlamydia/*genetics ; Chlamydiaceae/*genetics ; Chloroplasts/*genetics ; Computational Biology/methods ; Cyanobacteria/*genetics ; Databases, Genetic ; Databases, Protein ; Drosophila Proteins/chemistry/genetics ; *Evolution, Molecular ; Genes, Bacterial/*genetics ; Genes, Plant/*genetics ; Genome, Bacterial ; Humans ; Mitochondria/genetics ; Phylogeny ; Rickettsia/genetics ; Saccharomyces cerevisiae Proteins/chemistry/genetics ; Sequence Homology, Amino Acid ; }, abstract = {An unusually high proportion of proteins encoded in Chlamydia genomes are most similar to plant proteins, leading to proposals that a Chlamydia ancestor obtained genes from a plant or plant-like host organism by horizontal gene transfer. However, during an analysis of bacterial-eukaryotic protein similarities, we found that the vast majority of plant-like sequences in Chlamydia are most similar to plant proteins that are targeted to the chloroplast, an organelle derived from a cyanobacterium. We present further evidence suggesting that plant-like genes in Chlamydia, and other Chlamydiaceae, are likely a reflection of an unappreciated evolutionary relationship between the Chlamydiaceae and the cyanobacteria-chloroplast lineage. Further analyses of bacterial and eukaryotic genomes indicates the importance of evaluating organellar ancestry of eukaryotic proteins when identifying bacteria-eukaryote homologs or horizontal gene transfer and supports the proposal that Chlamydiaceae, which are obligate intracellular bacterial pathogens of animals, are not likely exchanging DNA with their hosts.}, }
@article {pmid12161560, year = {2002}, author = {Turmel, M and Otis, C and Lemieux, C}, title = {The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {17}, pages = {11275-11280}, pmid = {12161560}, issn = {0027-8424}, mesh = {*Biological Evolution ; Chlorophyta/classification/*genetics ; Chloroplasts/*genetics ; Chromosome Mapping ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; *Genome, Plant ; Introns ; Magnoliopsida/classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Organelles/genetics ; *Phylogeny ; }, abstract = {The land plants and their immediate green algal ancestors, the charophytes, form the Streptophyta. There is evidence that both the chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) underwent substantial changes in their architecture (intron insertions, gene losses, scrambling in gene order, and genome expansion in the case of mtDNA) during the evolution of streptophytes; however, because no charophyte organelle DNAs have been sequenced completely thus far, the suite of events that shaped streptophyte organelle genomes remains largely unknown. Here, we have determined the complete cpDNA (131,183 bp) and mtDNA (56,574 bp) sequences of the charophyte Chaetosphaeridium globosum (Coleochaetales). At the levels of gene content (124 genes), intron composition (18 introns), and gene order, Chaetosphaeridium cpDNA is remarkably similar to land-plant cpDNAs, implying that most of the features characteristic of land-plant lineages were gained during the evolution of charophytes. Although the gene content of Chaetosphaeridium mtDNA (67 genes) closely resembles that of the bryophyte Marchantia polymorpha (69 genes), this charophyte mtDNA differs substantially from its land-plant relatives at the levels of size, intron composition (11 introns), and gene order. Our finding that it shares only one intron with its land-plant counterparts supports the idea that the vast majority of mitochondrial introns in land plants appeared after the emergence of these organisms. Our results also suggest that the events accounting for the spacious intergenic spacers found in land-plant mtDNAs took place late during the evolution of charophytes or coincided with the transition from charophytes to land plants.}, }
@article {pmid12150917, year = {2002}, author = {Klingbeil, MM and Motyka, SA and Englund, PT}, title = {Multiple mitochondrial DNA polymerases in Trypanosoma brucei.}, journal = {Molecular cell}, volume = {10}, number = {1}, pages = {175-186}, doi = {10.1016/s1097-2765(02)00571-3}, pmid = {12150917}, issn = {1097-2765}, support = {5F32AI09789/AI/NIAID NIH HHS/United States ; GM27608/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; DNA, Kinetoplast ; DNA-Directed DNA Polymerase/chemistry/classification/genetics/*metabolism ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Protein Transport ; RNA, Double-Stranded/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Sequence Homology, Amino Acid ; Trypanosoma brucei brucei/*enzymology/genetics ; }, abstract = {Kinetoplast DNA (kDNA), the unusual mitochondrial DNA of Trypanosoma brucei, is a network containing thousands of catenated circles. Database searching for a kDNA replicative polymerase (pol) revealed no mitochondrial pol gamma homolog. Instead, we identified four proteins (TbPOLIA, IB, IC, and ID) related to bacterial pol I. Remarkably, all four localized to the mitochondrion. TbPOLIB and TbPOLIC localized beside the kDNA where replication occurs, and their knockdown by RNA interference caused kDNA network shrinkage. Furthermore, silencing of TbPOLIC caused loss of both minicircles and maxicircles and accumulation of minicircle replication intermediates, consistent with a role in replication. While typical mitochondria contain one DNA polymerase, pol gamma, trypanosome mitochondria contain five such enzymes, including the previously characterized pol beta.}, }
@article {pmid12145639, year = {2002}, author = {Ohtsuki, T and Sato, A and Watanabe, Y and Watanabe, K}, title = {A unique serine-specific elongation factor Tu found in nematode mitochondria.}, journal = {Nature structural biology}, volume = {9}, number = {9}, pages = {669-673}, doi = {10.1038/nsb826}, pmid = {12145639}, issn = {1072-8368}, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Caenorhabditis elegans/*metabolism ; DNA, Complementary ; Mitochondria/*metabolism ; Molecular Sequence Data ; Peptide Elongation Factor Tu/chemistry/genetics/*metabolism ; RNA, Transfer, Amino Acyl/metabolism ; Sequence Homology, Amino Acid ; Serine/*metabolism ; }, abstract = {The translation elongation factor Tu (EF-Tu) delivers aminoacyl-tRNAs to ribosomes by recognizing the tRNA acceptor and T stems. However, the unusual truncation observed in some animal mitochondrial tRNAs seems to prevent recognition by a canonical EF-Tu. For instance, nematode mitochondria contain tRNAs lacking a T or D arm. We recently found an atypical EF-Tu (EF-Tu1) specific for nematode mitochondrial tRNAs that lack the T arm. We have now discovered a second factor, EF-Tu2, which binds only to tRNAs that lack a D arm. EF-Tu2 seems unique in its amino acid specificity because it recognizes the aminoacyl moiety of seryl-tRNAs and the tRNA structure itself. Such EF-Tu evolution might explain tRNA structural divergence in animal mitochondria.}, }
@article {pmid12144780, year = {2002}, author = {Mears, JA and Cannone, JJ and Stagg, SM and Gutell, RR and Agrawal, RK and Harvey, SC}, title = {Modeling a minimal ribosome based on comparative sequence analysis.}, journal = {Journal of molecular biology}, volume = {321}, number = {2}, pages = {215-234}, doi = {10.1016/s0022-2836(02)00568-5}, pmid = {12144780}, issn = {0022-2836}, support = {R01 GM061576/GM/NIGMS NIH HHS/United States ; GM 61576/GM/NIGMS NIH HHS/United States ; GM-53827/GM/NIGMS NIH HHS/United States ; GM 48207/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Archaea/*cytology/genetics ; Bacteria/*cytology/genetics ; Base Sequence ; Binding Sites ; Caenorhabditis elegans/chemistry/*cytology/genetics ; Chloroplasts/chemistry/genetics ; Computer Simulation ; Conserved Sequence ; Eukaryotic Cells/cytology ; Evolution, Molecular ; Mitochondria/chemistry/genetics ; Models, Molecular ; Molecular Conformation ; Molecular Sequence Data ; Movement ; Phylogeny ; Protein Structure, Tertiary ; Protein Subunits ; RNA, Ribosomal/chemistry/genetics/metabolism ; RNA, Transfer/chemistry/genetics/metabolism ; Ribosomes/*chemistry/*genetics ; Sequence Alignment ; Sequence Deletion ; }, abstract = {We have determined the three-dimensional organization of ribosomal RNAs and proteins essential for minimal ribosome function. Comparative sequence analysis identifies regions of the ribosome that have been evolutionarily conserved, and the spatial organization of conserved domains is determined by mapping these onto structures of the 30S and 50S subunits determined by X-ray crystallography. Several functional domains of the ribosome are conserved in their three-dimensional organization in the Archaea, Bacteria, Eucaryotic nuclear, mitochondria and chloroplast ribosomes. In contrast, other regions from both subunits have shifted their position in three-dimensional space during evolution, including the L11 binding domain and the alpha-sarcin-ricin loop (SRL). We examined conserved bridge interactions between the two ribosomal subunits, giving an indication of which contacts are more significant. The tRNA contacts that are conserved were also determined, highlighting functional interactions as the tRNA moves through the ribosome during protein synthesis. To augment these studies of a large collection of comparative structural models sampled from all major branches on the phylogenetic tree, Caenorhabditis elegans mitochondrial rRNA is considered individually because it is among the smallest rRNA sequences known. The C.elegans model supports the large collection of comparative structure models while providing insight into the evolution of mitochondrial ribosomes.}, }
@article {pmid12144677, year = {2002}, author = {Castilla, JC and Collins, AG and Meyer, CP and Guiñez, R and Lindberg, DR}, title = {Recent introduction of the dominant tunicate, Pyura praeputialis (Urochordata, Pyuridae) to Antofagasta, Chile.}, journal = {Molecular ecology}, volume = {11}, number = {8}, pages = {1579-1584}, doi = {10.1046/j.1365-294x.2002.01524.x}, pmid = {12144677}, issn = {0962-1083}, mesh = {Animals ; Australia ; Chile ; Electron Transport Complex IV/genetics ; Mitochondria/enzymology ; Phylogeny ; South Africa ; Urochordata/classification/*genetics/*physiology ; }, abstract = {The large sessile tunicate Pyura stolonifera (Pleurogona: Stolibranchiata: Pyuridae), has been regarded as a complex taxon with disjointed distributions, including Australia (Pyura stolonifera praeputialis), South Africa (Pyura stolonifera stolonifera) and South America (Chile, Antofagasta: Pyura sp., the 'piure de Antofagasta'), and has been cited under at least five taxonomic combinations. The 'piure de Antofagasta' is a competitively dominant species in rocky intertidal habitats and shows a limited geographical range (60-70 km) exclusively inside the Bay of Antofagasta. Using cytochrome oxidase I (COI) mitochondrial sequence data from Pyura specimens of the three taxa we tested whether the Chilean taxon represents: (i) a Gondwana relict; (ii) a more recently divergent species; or (iii) a recently introduced species. The results suggest that the Chilean taxon is a recent introduction to Chile from Australian populations and that Pyura stolonifera praeputialis, from Australia, and the 'piure de Antofagasta' are geographical populations of a single species: Pyura praeputialis; whereas the South African taxon represents a second species: Pyura stolonifera.}, }
@article {pmid12140266, year = {2002}, author = {Espinoza, NR and Noor, MA}, title = {Population genetics of a polyploid: is there hybridization between lineages of Hyla versicolor?.}, journal = {The Journal of heredity}, volume = {93}, number = {2}, pages = {81-85}, doi = {10.1093/jhered/93.2.81}, pmid = {12140266}, issn = {0022-1503}, support = {GM58060/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Gene Frequency ; Genetic Markers ; *Genetics, Population ; Mitochondria/genetics ; Phylogeny ; Polymerase Chain Reaction ; *Polyploidy ; Ranidae/*genetics ; }, abstract = {Several studies have demonstrated that polyploid species can form recurrently from their progenitors, but few studies have evaluated gene flow between the resultant polyploid lineages. Here we examine the possibility of hybridization between lineages of the tetraploid common gray treefrog (Hyla versicolor). We utilize a polymerase chain reaction (PCR) cloning approach to estimate the genotypes of tetraploid individuals and measure genetic differentiation between (1) sympatric populations of two lineages and (2) allopatric populations of a single lineage. We find that allele frequencies in sympatric populations of two lineages do not differ, suggesting that frogs of these two lineages hybridize in areas where they co-occur.}, }
@article {pmid12140251, year = {2002}, author = {Yukuhiro, K and Sezutsu, H and Itoh, M and Shimizu, K and Banno, Y}, title = {Significant levels of sequence divergence and gene rearrangements have occurred between the mitochondrial genomes of the wild mulberry silkmoth, Bombyx mandarina, and its close relative, the domesticated silkmoth, Bombyx mori.}, journal = {Molecular biology and evolution}, volume = {19}, number = {8}, pages = {1385-1389}, doi = {10.1093/oxfordjournals.molbev.a004200}, pmid = {12140251}, issn = {0737-4038}, mesh = {Animals ; Bombyx/*genetics ; DNA, Mitochondrial/analysis/*genetics ; *Evolution, Molecular ; *Gene Rearrangement ; Genes, Insect ; *Genome ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Transfer/chemistry/genetics ; }, }
@article {pmid12140186, year = {2002}, author = {Chen, XJ}, title = {Induction of an unregulated channel by mutations in adenine nucleotide translocase suggests an explanation for human ophthalmoplegia.}, journal = {Human molecular genetics}, volume = {11}, number = {16}, pages = {1835-1843}, doi = {10.1093/hmg/11.16.1835}, pmid = {12140186}, issn = {0964-6906}, mesh = {Adenine Nucleotide Translocator 1/*genetics ; Alleles ; DNA, Mitochondrial/genetics ; Genes, Dominant ; Genes, Fungal ; Humans ; Membrane Potentials ; Mitochondria/metabolism ; Mitochondrial ADP, ATP Translocases/genetics ; Mitochondrial Swelling ; *Mutation, Missense ; Ophthalmoplegia, Chronic Progressive External/*enzymology/*genetics ; Saccharomyces cerevisiae/enzymology/genetics ; Saccharomyces cerevisiae Proteins/genetics ; }, abstract = {Adenine nucleotide translocase (Ant) is primarily involved in ATP/ADP exchange across the mitochondrial inner membrane. Recently, the A114P missense mutation in the human Ant1 protein was found to be associated with autosomal dominant progressive external ophthalmoplegia (adPEO). Ant1(A114P) was proposed to cause an imbalance of the mitochondrial deoxynucleotide pool that subsequently affects the accuracy of mtDNA replication, thereby leading to accumulation of mutant mtDNA. In the present study, it has been shown that the A128P mutation of the Saccharomyces cerevisiae Aac2 protein, equivalent to A114P in human Ant1p, does not always affect respiratory growth. However, expression of aac2(A128P) results in depolarization, structural swelling and disintegration of mitochondria, and ultimately an arrest of cell growth in a dominant-negative manner. The aac2(A128P) mutation likely induces an unregulated channel allowing free passage of solutes across the inner membrane. These data raise the possibility that the formation of an unregulated channel, rather than a defect in ATP/ADP exchange, is a direct pathogenic factor in human adPEO. The accumulation of mtDNA mutations might be a consequence of mitochondrial dysfunction.}, }
@article {pmid12138776, year = {2002}, author = {Odintsova, MS and Iurina, NP}, title = {[The mitochondrial genome of protists].}, journal = {Genetika}, volume = {38}, number = {6}, pages = {773-788}, pmid = {12138776}, issn = {0016-6758}, mesh = {Animals ; Biological Evolution ; Codon ; DNA, Mitochondrial ; Dictyostelium ; Eukaryota/*genetics ; *Genome ; Mitochondria/*genetics ; RNA, Ribosomal ; RNA, Transfer ; }, abstract = {The data on the structure and functions of the mitochondrial genomes of protists (Protozoa and unicellular red and green algae) are reviewed. It is emphasized that mitochondrial gene structure and composition, as well as organization of mitochondrial genomes in protists are more diverse than in multicellular eukaryotes. The gene content of mitochondrial genomes of protists are closer to those of plants than animals or fungi. In the protist mitochondrial DNA, both the universal (as in higher plants) and modified (as in animals and fungi) genetic codes are used. In the overwhelming majority of cases, protist mitochondrial genomes code for the major and minor rRNA components, some tRNAs, and about 30 proteins of the respiratory chain and ribosomes. Based on comparison of the mitochondrial genomes of various protists, the origin and evolution of mitochondria are briefly discussed.}, }
@article {pmid12138089, year = {2002}, author = {Besteiro, S and Biran, M and Biteau, N and Coustou, V and Baltz, T and Canioni, P and Bringaud, F}, title = {Succinate secreted by Trypanosoma brucei is produced by a novel and unique glycosomal enzyme, NADH-dependent fumarate reductase.}, journal = {The Journal of biological chemistry}, volume = {277}, number = {41}, pages = {38001-38012}, doi = {10.1074/jbc.M201759200}, pmid = {12138089}, issn = {0021-9258}, mesh = {Animals ; Biomarkers ; Cell Line ; Citric Acid Cycle ; Crithidia fasciculata/metabolism ; Digitonin/pharmacology ; Glucose/metabolism ; Leishmania/metabolism ; Magnetic Resonance Spectroscopy ; Microbodies/*enzymology ; Mitochondria/metabolism ; Molecular Sequence Data ; NADH Dehydrogenase/metabolism ; Oxidoreductases/classification/genetics/*metabolism ; *Oxidoreductases Acting on CH-CH Group Donors ; Phenotype ; Phylogeny ; Protozoan Proteins/classification/genetics/*metabolism ; Rats ; Succinic Acid/*metabolism ; Trypanosoma brucei brucei/cytology/drug effects/genetics/*metabolism ; }, abstract = {In all trypanosomatids, including Trypanosoma brucei, glycolysis takes place in peroxisome-like organelles called glycosomes. These are closed compartments wherein the energy and redox (NAD(+)/NADH) balances need to be maintained. We have characterized a T. brucei gene called FRDg encoding a protein 35% identical to Saccharomyces cerevisiae fumarate reductases. Microsequencing of FRDg purified from glycosome preparations, immunofluorescence, and Western blot analyses clearly identified this enzyme as a glycosomal protein that is only expressed in the procyclic form of T. brucei but is present in all the other trypanosomatids studied, i.e. Trypanosoma congolense, Crithidia fasciculata and Leishmania amazonensis. The specific inactivation of FRDg gene expression by RNA interference showed that FRDg is responsible for the NADH-dependent fumarate reductase activity detected in glycosomal fractions and that at least 60% of the succinate secreted by the T. brucei procyclic form (in the presence of d-glucose as the sole carbon source) is produced in the glycosome by FRDg. We conclude that FRDg plays a key role in the energy metabolism by participating in the maintenance of the glycosomal NAD(+)/NADH balance. We have also detected a significant pyruvate kinase activity in the cytosol of the T. brucei procyclic cells that was not observed previously. Consequently, we propose a revised model of glucose metabolism in procyclic trypanosomes that may also be valid for all other trypanosomatids except the T. brucei bloodstream form. Interestingly, H. Gest has hypothesized previously (Gest, H. (1980) FEMS Microbiol. Lett. 7, 73-77) that a soluble NADH-dependent fumarate reductase has been present in primitive organisms and evolved into the present day fumarate reductases, which are quinol-dependent. FRDg may have the characteristics of such an ancestral enzyme and is the only NADH-dependent fumarate reductase characterized to date.}, }
@article {pmid12125756, year = {2002}, author = {Moriya, M and Nakayama, T and Inouye, I}, title = {A new class of the stramenopiles, Placididea Classis nova: description of Placidia cafeteriopsis gen. et sp. nov.}, journal = {Protist}, volume = {153}, number = {2}, pages = {143-156}, doi = {10.1078/1434-4610-00093}, pmid = {12125756}, issn = {1434-4610}, mesh = {Animals ; DNA, Ribosomal/*genetics ; Eukaryota/*classification/cytology/*genetics/ultrastructure ; Eukaryotic Cells/*classification/cytology/*metabolism/ultrastructure ; Flagella/ultrastructure ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {A marine flagellate resembling Cafeteria roenbergensis (bicosoecids, stramenopiles) in cell shape and behavior of the cell while attached to substratum was collected from the coast of Japan. The flagellate was examined by light and electron microscopy, and the 18S rDNA was sequenced to elucidate its taxonomic and phylogenetic position. Ultrastructural features suggested that the flagellate is not a bicosoecid, but a relative of the recently described stramenopile, Wobblia lunata. 18S rDNA phylogenetic trees also revealed that the flagellate forms a monophyletic clade with W. lunata and that it is distantly related to Cafeteria and other bicosoecids. The flagellate differs from W. lunata due to its lack of wobbling motion as well as intracellular features such as the number of mitochondria, flagellar apparatus architecture, the presence of a paranuclear body and cytoplasmic microtubules. The similarity of 18S rDNA sequences was 81% between the flagellate and W. lunata. This new flagellate was described as Placidia cafeteriopsis gen. et sp. nov. Because the phylogenetic lineage comprised of W. lunata and P. cafeteriopsis was one of the major, deep-branching clades of the stramenopiles, the class Placididea (= Placidiophyceae) classis nova was proposed.}, }
@article {pmid12125065, year = {2002}, author = {Giugliano, LG and Teixeira, RD and Colli, GR and Báo, SN}, title = {Ultrastructure of spermatozoa of the lizard Ameiva ameiva, with considerations on polymorphism within the family Teiidae (Squamata).}, journal = {Journal of morphology}, volume = {253}, number = {3}, pages = {264-271}, doi = {10.1002/jmor.10002}, pmid = {12125065}, issn = {0362-2525}, mesh = {Acrosome/ultrastructure ; Animals ; Lizards/*anatomy &amp; histology/genetics ; Male ; Phylogeny ; *Polymorphism, Genetic ; Species Specificity ; Spermatozoa/*ultrastructure ; }, abstract = {A detailed description of sperm ultrastructure of the lizard Ameiva ameiva (Teiidae) is provided. Mature spermatozoa are characterized by: a depressed acrosome at the anterior portion; a unilateral ridge at the anterolateral portion; an acrosome vesicle divided into cortex and medulla; medulla divided into two regions with different electron-densities; paracrystalline subacrosomal material with radial organization in transverse section; a pointed prenuclear perforatorium; a stopper-like perforatorium base plate that appears embedded in the subacrosomal material; the presence of an epinuclear lucent zone surrounded by its own membrane; a large nuclear rostrum; round nuclear shoulders; a nuclear space at the nucleus tip; a bilateral stratified laminar structure; a central dense body within the proximal centriole; a short midpiece; an axonemal midpiece axial component; peripheral fibers 3 and 8 grossly enlarged at the anterior portion of axoneme; columnar mitochondria with linear cristae; solid dense bodies arranged as rings or spirals; a triangular-shaped annulus in transverse section; a fibrous sheath into the midpiece; a thin zone of cytoplasm at the anterior portion of the principal piece; and a slight decrease in diameter of the principal piece immediately after the annulus. Comparisons with Cnemidophorus sexlineatus and Micrablepharus maximiliani failed to identify unique sperm ultrastructure traits of Teiidae or Teiioidea (Teiidae + Gymnophthalmidae). High levels of polymorphism between Ameiva and Cnemidophorus, two closely related genera of the family Teiidae, were detected, suggesting that extensive sampling within squamate families is essential if sperm ultrastructure data are to be used in phylogenetic analyses at this taxonomic level.}, }
@article {pmid12122455, year = {2002}, author = {Hulbert, AJ and Else, PL and Manolis, SC and Brand, MD}, title = {Proton leak in hepatocytes and liver mitochondria from archosaurs (crocodiles) and allometric relationships for ectotherms.}, journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology}, volume = {172}, number = {5}, pages = {387-397}, doi = {10.1007/s00360-002-0264-1}, pmid = {12122455}, issn = {0174-1578}, mesh = {Alligators and Crocodiles/*metabolism ; Animals ; Biological Evolution ; Body Constitution ; Body Temperature Regulation/*physiology ; Cell Respiration/physiology ; Energy Metabolism/physiology ; Hepatocytes/*metabolism ; Mitochondria, Liver/chemistry/*metabolism ; Phospholipids/analysis ; Protons ; }, abstract = {It has previously been shown that mitochondrial proton conductance decreases with increasing body mass in mammals and is lower in a 250-g lizard than the laboratory rat. To examine whether mitochondrial proton conductance is extremely low in very large reptiles, hepatocytes and mitochondria were prepared from saltwater crocodiles (Crocodylus porosus) and freshwater crocodiles (Crocodylus johnstoni). Respiration rates of hepatocytes and liver mitochondria were measured at 37 degrees C and compared with values obtained for rat or previously measured for other species. Respiration rates of hepatocytes from either species of crocodile were similar to those reported for lizards and approximately one fifth of the rates measured using cells from mammals (rat and sheep). Ten-to-thirty percent of crocodile hepatocyte respiration was used to drive mitochondrial proton leak, similar to the proportion in other species. Respiration rates of crocodile liver mitochondria were similar to those of mammalian species. Proton leak rate in isolated liver mitochondria was measured as a function of membrane potential. Contrary to our prediction, the mitochondrial proton conductance of liver mitochondria from crocodiles was greater than that of liver mitochondria from lizards and was similar to that of rats. The acyl composition of liver mitochondrial phospholipids from the crocodiles was more similar to that in mitochondria from rats than in mitochondria from lizards. The relatively high mitochondrial proton conductance was associated with a relatively small liver, which seems to be characteristic of crocodilians. Comparison of data from a number of diverse ectothermic species suggested that hepatocyte respiration rate may decrease with body mass, with an allometric exponent of about -0.2, similar to the exponent in mammalian hepatocytes. However, unlike mammals, liver mitochondrial proton conductance in ectotherms showed no allometric relationship with body size.}, }
@article {pmid12120991, year = {2002}, author = {Zhu, G and Keithly, JS}, title = {Alpha-proteobacterial relationship of apicomplexan lactate and malate dehydrogenases.}, journal = {The Journal of eukaryotic microbiology}, volume = {49}, number = {3}, pages = {255-261}, doi = {10.1111/j.1550-7408.2002.tb00532.x}, pmid = {12120991}, issn = {1066-5234}, support = {AI40320/AI/NIAID NIH HHS/United States ; AI44594/AI/NIAID NIH HHS/United States ; }, mesh = {Alphaproteobacteria/enzymology/*genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Cryptosporidium parvum/*enzymology/genetics ; DNA, Mitochondrial/chemistry/genetics ; DNA, Protozoan/chemistry/genetics ; Gammaproteobacteria/genetics ; L-Lactate Dehydrogenase/chemistry/*genetics ; Malate Dehydrogenase/chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {We have cloned and sequenced a lactate dehydrogenase (LDH) gene from Cryptosporidium parvum (CpLDH1). With this addition, and that of four recently deposited alpha-proteobacterial malate dehydrogenase (MDH) genes, the phylogenetic relationships among apicomplexan LDH and bacterial MDH were re-examined. Consistent with previous studies, our maximum likelihood (ML) analysis using the quartet-puzzling method divided 105 LDH/MDH enzymes into five clades, and confirmed that mitochondrial MDH is a sister clade to those of y-proteobacteria, rather than to alpha-proteobacteria. In addition, a Cryptosporidium parvum MDH (CpMDH1) was identified from the ongoing Cryptosporidium genome project that appears to belong to a distinct clade (III) comprised of 22 sequences from one archaebacterium, numerous eubacteria, and several apicomplexans. Using the ML puzzling test and bootstrapping analysis with protein distance and parsimony methods, the resulting trees not only robustly confirmed the alpha-proteobacterial relationship of apicomplexan LDH/MDH, but also supported a monophyletic relationship of CpLDH1 with CpMDHI. These data suggest that, unlike most other eukaryotes, the Apicomplexa may be one of the few lineages retaining an alpha-proteobacterial-type MDH that could have been acquired from an ancestral alpha-proteobacterium through primary endosymbiosis giving rise to the mitochondria, or through an unknown lateral gene transfer (LGT) event.}, }
@article {pmid12119382, year = {2002}, author = {Adams, KL and Qiu, YL and Stoutemyer, M and Palmer, JD}, title = {Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {15}, pages = {9905-9912}, pmid = {12119382}, issn = {0027-8424}, support = {F32 GM017923/GM/NIGMS NIH HHS/United States ; R01 GM035087/GM/NIGMS NIH HHS/United States ; F32 GM-17923/GM/NIGMS NIH HHS/United States ; R01 GM-35087/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; *Evolution, Molecular ; Magnoliopsida/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {To study the tempo and pattern of mitochondrial gene loss in plants, DNAs from 280 genera of flowering plants were surveyed for the presence or absence of 40 mitochondrial protein genes by Southern blot hybridization. All 14 ribosomal protein genes and both sdh genes have been lost from the mitochondrial genome many times (6 to 42) during angiosperm evolution, whereas only two losses were detected among the other 24 genes. The gene losses have a very patchy phylogenetic distribution, with periods of stasis followed by bursts of loss in certain lineages. Most of the oldest groups of angiosperms are still mired in a prolonged stasis in mitochondrial gene content, containing nearly the same set of genes as their algal ancestors more than a billion years ago. In sharp contrast, other plants have rapidly lost many or all of their 16 mitochondrial ribosomal protein and sdh genes, thereby converging on a reduced gene content more like that of an animal or fungus than a typical plant. In these and many lineages with more modest numbers of losses, the rate of ribosomal protein and sdh gene loss exceeds, sometimes greatly, the rate of mitochondrial synonymous substitutions. Most of these mitochondrial gene losses are probably the consequence of gene transfer to the nucleus; thus, rates of functional gene transfer also may vary dramatically in angiosperms.}, }
@article {pmid12115897, year = {2002}, author = {Wilson, JM and Laurent, P}, title = {Fish gill morphology: inside out.}, journal = {The Journal of experimental zoology}, volume = {293}, number = {3}, pages = {192-213}, doi = {10.1002/jez.10124}, pmid = {12115897}, issn = {0022-104X}, mesh = {Adaptation, Physiological ; Animals ; Fishes/*anatomy &amp; histology ; Gills/*anatomy &amp; histology/blood supply/ultrastructure ; Mitochondria/physiology ; *Phylogeny ; Regional Blood Flow ; }, abstract = {In this short review of fish gill morphology we cover some basic gross anatomy as well as in some more detail the microscopic anatomy of the branchial epithelia from representatives of the major extant groups of fishes (Agnathans, Elasmobranchs, and Teleosts). The agnathan hagfishes have primitive gill pouches, while the lampreys have arch-like gills similar to the higher fishes. In the lampreys and elasmobranchs, the gill filaments are supported by a complete interbranchial septum and water exits via external branchial slits or pores. In contrast, the teleost interbranchial septum is much reduced, leaving the ends of the filaments unattached, and the multiple gill openings are replaced by the single caudal opening of the operculum. The basic functional unit of the gill is the filament, which supports rows of plate-like lamellae. The lamellae are designed for gas exchange with a large surface area and a thin epithelium surrounding a well-vascularized core of pillar cell capillaries. The lamellae are positioned for the blood flow to be counter-current to the water flow over the gills. Despite marked differences in the gross anatomy of the gill among the various groups, the cellular constituents of the epithelium are remarkably similar. The lamellar gas-exchange surface is covered by squamous pavement cells, while large, mitochondria-rich, ionocytes and mucocytes are found in greatest frequency in the filament epithelium. Demands for ionoregulation can often upset this balance. There has been much study of the structure and function of the branchial mitochondria-rich cells. These cells are generally characterized by a high mitochondrial density and an amplification of the basolateral membrane through folding or the presence of an intracellular tubular system. Morphological subtypes of MRCs as well as some methods of MRC detection are discussed.}, }
@article {pmid12114550, year = {2002}, author = {Considine, MJ and Holtzapffel, RC and Day, DA and Whelan, J and Millar, AH}, title = {Molecular distinction between alternative oxidase from monocots and dicots.}, journal = {Plant physiology}, volume = {129}, number = {3}, pages = {949-953}, doi = {10.1104/pp.004150}, pmid = {12114550}, issn = {0032-0889}, mesh = {Arabidopsis/enzymology/*genetics ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Isoenzymes/genetics ; Magnoliopsida/classification/enzymology/*genetics ; Mitochondria/enzymology/genetics ; Mitochondrial Proteins ; Multigene Family/genetics ; Oryza/enzymology/*genetics ; Oxidoreductases/*genetics ; Phylogeny ; Plant Proteins ; Review Literature as Topic ; }, }
@article {pmid12113307, year = {2002}, author = {Hine, PM and Wakefield, S and Diggles, BK and Webb, VL and Maas, EW}, title = {Ultrastructure of a haplosporidian containing Rickettsiae, associated with mortalities among cultured paua Haliotis iris.}, journal = {Diseases of aquatic organisms}, volume = {49}, number = {3}, pages = {207-219}, doi = {10.3354/dao049207}, pmid = {12113307}, issn = {0177-5103}, mesh = {Alphaproteobacteria/genetics/*isolation &amp; purification/ultrastructure ; Animals ; Apicomplexa/classification/genetics/microbiology/*ultrastructure ; Aquaculture ; DNA, Bacterial/chemistry ; DNA, Ribosomal/chemistry ; Gene Amplification ; Mollusca/microbiology/*parasitology ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Uninucleate and multinucleate stages of a protozoan parasite are described from cultured abalone Haliotis iris Martyn, 1784 in New Zealand. The parasite is identified as a haplosporidian by the occurrence of multinucleate plasmodia, mitochondria with tubular cristae, lipid droplets, anastomosing endoplasmic reticulum (aER), multivesicular bodies (MVBs), haplosporogenesis by the production of haplosporosome-like bodies from nuclear membrane-bound Golgi, and their maturation to haplosporosomes. Coated pits occurred in the plasma membrane and coated vesicles were scattered in the cytoplasm, particularly in association with the Golgi face away from the nucleus, and aER. It is concluded that the outward face of the Golgi may be the trans face, and that aER is the trans-Golgi network. Coated pits and bristle-coated vesicles are reported from a haplosporidian for the first time. The vesicles in the MVBs resembled the cores and inner membranes of haplosporosomes, without the outer layer. The possible inter-relationships of these features are discussed. The abalone parasite differs from previously described haplosporidians in the apparent absence of a persistent mitotic spindle, and the presence of intracytoplasmic coccoid to rod-shaped bacteria resembling Rickettsiales-like prokaryotes. Phylogenetic analysis of the 16S rRNA gene sequence of the Rickettsiales-like prokaryotes indicated that these organisms belong to the Rickettsia cluster. The prokaryotes have a high (7%) sequence divergence from known Rickettsieae, with Rickettsia sp. and R. massiliae being the closest relatives. The lack of non-molecular evidence prevents us from proposing a new rickettsial genus at this time.}, }
@article {pmid12110660, year = {2002}, author = {Bicudo, JE and Bianco, AC and Vianna, CR}, title = {Adaptive thermogenesis in hummingbirds.}, journal = {The Journal of experimental biology}, volume = {205}, number = {Pt 15}, pages = {2267-2273}, doi = {10.1242/jeb.205.15.2267}, pmid = {12110660}, issn = {0022-0949}, mesh = {*Acclimatization ; Animals ; Biological Evolution ; Calcium-Transporting ATPases/metabolism ; Carrier Proteins/genetics/metabolism ; Ion Channels ; Mammals ; Membrane Proteins/genetics/metabolism ; Mitochondria/physiology ; Mitochondrial Proteins ; Muscle, Skeletal/*physiology ; Sarcoplasmic Reticulum/physiology ; Songbirds/*physiology ; *Thermogenesis ; Uncoupling Protein 1 ; }, abstract = {The occurrence of non-shivering thermogenesis in birds has long been a controversial issue. Although birds are endothermic vertebrates, sharing with mammals (placental mammals and marsupials) a common ancestor, they do not possess brown adipose tissue or a similar type of tissue, unlike their mammalian counterparts. Some bird species are, however, able to withstand very low ambient temperatures (-70 degrees C) or undergo periods of heterothermia, and there is now good experimental evidence showing that non-shivering thermogenesis may indeed occur in birds under such conditions. The skeletal muscles of birds, particularly the flight muscles, occupy a significant fraction (approximately 30 %) of the total body mass, and recent results have shown that they are likely to be the main sites for non-shivering thermogenesis. The precise mechanisms involved in adaptive thermogenesis in birds are still not fully understood. The translocation of Ca(2+) between intracellular compartments and the cystosol mediated by the sarcoplasmic reticulum Ca(2+)-ATPase, uncoupled from ATP synthesis, is one mechanism whereby chemi-osmotic energy can be converted into heat, and it has been proposed as one of the possible mechanisms underlying non-shivering thermogenesis in birds on the basis of data obtained mainly from ducklings acclimatized to cold conditions. The recent characterization of an uncoupling protein homolog in avian skeletal muscle and the expression of its mRNA at different stages of the torpor/rewarming cycle of hummingbirds indicate that it has the potential to function as an uncoupling protein and could play a thermogenic role during rewarming in these birds.}, }
@article {pmid12102511, year = {2002}, author = {Haupt-Herting, S and Fock, HP}, title = {Oxygen exchange in relation to carbon assimilation in water-stressed leaves during photosynthesis.}, journal = {Annals of botany}, volume = {89 Spec No}, number = {7}, pages = {851-859}, pmid = {12102511}, issn = {0305-7364}, mesh = {Carbon/*metabolism ; Carbon Dioxide/metabolism ; Carbon Isotopes ; Electron Transport/physiology ; Light ; Solanum lycopersicum/drug effects/genetics/physiology ; Mass Spectrometry ; Mitochondria/metabolism ; Mutation ; Oxygen/*metabolism ; Oxygen Consumption/physiology ; Photosynthesis/*physiology ; Photosynthetic Reaction Center Complex Proteins/metabolism ; Plant Leaves/drug effects/*physiology ; Stress, Mechanical ; Water/pharmacology/*physiology ; }, abstract = {In a study on metabolic consumption of photosynthetic electrons and dissipation of excess light energy under water stress, O2 and CO2 gas exchange was measured by mass spectrometry in tomato plants using 18O2 and 13CO2. Under water stress, gross O2 evolution (E(O)), gross O2 uptake (U(O)), net CO2 uptake (PN), gross CO2 uptake (TPS), and gross CO2 evolution (Ec) declined. The ratio P(N)/E(O) fell during stress, while the ratios U(O)/E(O) and E(C)/TPS rose. Mitochondrial respiration in the light, which can be measured directly by 12CO2 evolution during 13CO2 uptake at 3000 microl l(-1) 13CO2, is small in relation to gross CO2 evolution and CO2 release from the glycolate pathway. It is concluded that PSII, the Calvin cycle and mitochondrial respiration are down-regulated under water stress. The percentages of photosynthetic electrons dissipated by CO2 assimilation, photorespiration and the Mehler reaction were calculated: in control leaves more than 50% of the electrons were consumed in CO2 assimilation, 23% in photorespiration and 13% in the Mehler reaction. Under severe stress the percentages of electrons dissipated by CO2 assimilation and the Mehler reaction declined while the percentage of electrons used in photorespiration doubled. The consumption of electrons in photorespiration may reduce the likelihood of damage during water deficit.}, }
@article {pmid12099802, year = {2002}, author = {Reed, DL and Carpenter, KE and deGravelle, MJ}, title = {Molecular systematics of the Jacks (Perciformes: Carangidae) based on mitochondrial cytochrome b sequences using parsimony, likelihood, and Bayesian approaches.}, journal = {Molecular phylogenetics and evolution}, volume = {23}, number = {3}, pages = {513-524}, doi = {10.1016/s1055-7903(02)00036-2}, pmid = {12099802}, issn = {1055-7903}, mesh = {Animals ; Bayes Theorem ; Cytochrome b Group/*genetics ; Likelihood Functions ; Mitochondria/*genetics ; *Models, Biological ; Perciformes/*classification/*genetics ; }, abstract = {The Carangidae represent a diverse family of marine fishes that include both ecologically and economically important species. Currently, there are four recognized tribes within the family, but phylogenetic relationships among them based on morphology are not resolved. In addition, the tribe Carangini contains species with a variety of body forms and no study has tried to interpret the evolution of this diversity. We used DNA sequences from the mitochondrial cytochrome b gene to reconstruct the phylogenetic history of 50 species from each of the four tribes of Carangidae and four carangoid outgroup taxa. We found support for the monophyly of three tribes within the Carangidae (Carangini, Naucratini, and Trachinotini); however, monophyly of the fourth tribe (Scomberoidini) remains questionable. A sister group relationship between the Carangini and the Naucratini is well supported. This clade is apparently sister to the Trachinotini plus Scomberoidini but there is uncertain support for this relationship. Additionally, we examined the evolution of body form within the tribe Carangini and determined that each of the predominant clades has a distinct evolutionary trend in body form. We tested three methods of phylogenetic inference, parsimony, maximum-likelihood, and Bayesian inference. Whereas the three analyses produced largely congruent hypotheses, they differed in several important relationships. Maximum-likelihood and Bayesian methods produced hypotheses with higher support values for deep branches. The Bayesian analysis was computationally much faster and yet produced phylogenetic hypotheses that were very similar to those of the maximum-likelihood analysis.}, }
@article {pmid12099801, year = {2002}, author = {Irestedt, M and Fjeldså, J and Johansson, US and Ericson, PG}, title = {Systematic relationships and biogeography of the tracheophone suboscines (Aves: Passeriformes).}, journal = {Molecular phylogenetics and evolution}, volume = {23}, number = {3}, pages = {499-512}, doi = {10.1016/s1055-7903(02)00034-9}, pmid = {12099801}, issn = {1055-7903}, mesh = {Animals ; Birds/*classification/*physiology ; Cytochrome b Group/genetics ; Genes, myc ; Homeodomain Proteins/genetics ; Introns ; Mitochondria/genetics ; Myoglobin/genetics ; Nuclear Proteins/genetics ; *Phylogeny ; }, abstract = {Based on their highly specialized "tracheophone" syrinx, the avian families Furnariidae (ovenbirds), Dendrocolaptidae (woodcreepers), Formicariidae (ground antbirds), Thamnophilidae (typical antbirds), Rhinocryptidae (tapaculos), and Conopophagidae (gnateaters) have long been recognized to constitute a monophyletic group of suboscine passerines. However, the monophyly of these families have been contested and their interrelationships are poorly understood, and this constrains the possibilities for interpreting adaptive tendencies in this very diverse group. In this study we present a higher-level phylogeny and classification for the tracheophone birds based on phylogenetic analyses of sequence data obtained from 32 ingroup taxa. Both mitochondrial (cytochrome b) and nuclear genes (c-myc, RAG-1, and myoglobin) have been sequenced, and more than 3000 bp were subjected to parsimony and maximum-likelihood analyses. The phylogenetic signals in the mitochondrial and nuclear genes were compared and found to be very similar. The results from the analysis of the combined dataset (all genes, but with transitions at third codon positions in the cytochrome b excluded) partly corroborate previous phylogenetic hypotheses, but several novel arrangements were also suggested. Especially interesting is the result that the genus Melanopareia represents a basal branch within the tracheophone group, positioned in the phylogenetic tree well away from the typical tapaculos with which it has been supposed to group. Other novel results include the observation that the ground antbirds are paraphyletic and that Sclerurus is the sister taxon to an ovenbird-woodcreeper clade. Patterns of generic richness within each clade suggest that the early differentiation of feeble-winged forest groups took place south of the Amazon Basin, while the more recent diversification was near the equator and (in tapaculos and ovenbirds) in the south of the continent.}, }
@article {pmid12099794, year = {2002}, author = {Wilkinson, M and A Sheps, J and Oommen, OV and Cohen, BL}, title = {Phylogenetic relationships of Indian caecilians (Amphibia: Gymnophiona) inferred from mitochondrial rRNA gene sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {23}, number = {3}, pages = {401-407}, doi = {10.1016/s1055-7903(02)00031-3}, pmid = {12099794}, issn = {1055-7903}, mesh = {Amphibians/*physiology ; Animals ; India ; Mitochondria/*genetics ; *Phylogeny ; Polymerase Chain Reaction ; *RNA, Ribosomal ; *RNA, Ribosomal, 16S ; }, abstract = {India has a diverse caecilian fauna, including representatives of three of the six currently recognized families, the Caeciliidae, Ichthyophiidae, the endemic Uraeotyphlidae, but previous molecular phylogenetic studies of caecilians have not included sequences for any Indian caecilians. Partial 12S and 16S mitochondrial gene sequences were obtained for a single representative of each of the caecilian families found in India and aligned against previously reported sequences for 13 caecilian species. The resulting alignment (16 taxa, 1200 sites, of which 288 cannot be aligned unambiguously) was analyzed using parsimony, maximum-likelihood, and distance methods. As judged by bootstrap proportions, decay indices, and leaf stabilities, well-supported relationships of the Indian caecilians are recovered from the alignment. The data (1) corroborate the hypothesis, based on morphology, that the Uraeotyphlidae and Ichthyophiidae are sister taxa, (2) recover a monophyletic Ichthyophiidae, including Indian and South East Asian representatives, and (3) place the Indian caeciliid Gegeneophis ramaswamii as the sister group of the caeciliid caecilians of the Seychelles. Rough estimates of divergence times suggest an origin of the Uraeotyphlidae and Ichthyophiidae while India was isolated from Laurasia and Africa and are most consistent with an Indian origin of these families and subsequent dispersal of ichthyophiids into South East Asia.}, }
@article {pmid12087190, year = {2002}, author = {Takumi, S and Tomioka, M and Eto, K and Naydenov, N and Nakamura, C}, title = {Characterization of two non-homoeologous nuclear genes encoding mitochondrial alternative oxidase in common wheat.}, journal = {Genes &amp; genetic systems}, volume = {77}, number = {2}, pages = {81-88}, doi = {10.1266/ggs.77.81}, pmid = {12087190}, issn = {1341-7568}, mesh = {Amino Acid Sequence ; Base Sequence ; Cell Nucleus/*genetics ; Chromosomes, Plant ; Cold Temperature ; DNA, Plant/genetics ; Enzyme Inhibitors/pharmacology ; Exons ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant/drug effects ; *Genes, Plant ; Genome, Plant ; Introns ; Mitochondria/*enzymology/genetics ; Mitochondrial Proteins ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Phylogeny ; Plant Proteins/genetics/metabolism ; Ploidies ; Potassium Cyanide/pharmacology ; Sequence Homology, Amino Acid ; Transcription, Genetic/drug effects/physiology ; Triticum/drug effects/*enzymology/genetics ; }, abstract = {Mitochondrial alternative oxidase (AOX) is the terminal oxidase responsible for cyanide-insensitive and salicylhydroxamic acid-sensitive respiration. We have isolated two non-homoeologous genes (Waox1a and Waox1c) encoding AOX proteins from common wheat (Triticum aestivum L.). These two genes were orthologous to rice AOX1a and AOX1c, and their exon/intron structure was conserved, as it is in most other plant AOX genes. Southern blot analysis indicated that both Waox1a and Waox1c were located in at least three homoeologous loci and that additional AOX genes with lower homology were present in the genome of common wheat. The Waox1a and Waox1c loci were respectively assigned to the homoeologous group 2 and 6 chromosomes. The steady-state level of Waox1a and Waox1c transcripts increased under cold stress, while only that of Waox1a was increased by cyanide treatment.}, }
@article {pmid12086685, year = {2002}, author = {Verlaet, M and Duyckaerts, C and Rahmouni, S and Denis, G and Humblet, C and Greimers, R and Sluse, FE and Boniver, J and Defresne, MP}, title = {Transient modifications of respiratory capacity in thymic cells during murine radioleukemogenesis.}, journal = {Free radical biology &amp; medicine}, volume = {33}, number = {1}, pages = {76-82}, doi = {10.1016/s0891-5849(02)00858-4}, pmid = {12086685}, issn = {0891-5849}, mesh = {8-Hydroxy-2'-Deoxyguanosine ; Animals ; Bone Marrow Transplantation ; Cell Respiration ; Cell Transformation, Neoplastic ; Deoxyguanosine/*analogs &amp; derivatives/metabolism ; Electron Transport Complex IV/genetics/metabolism ; Female ; Flow Cytometry ; In Situ Hybridization ; Leukemia, Radiation-Induced/*metabolism ; Lymphoma/*metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Microscopy, Fluorescence ; Oxidative Stress/physiology ; Oxygen Consumption ; Preleukemia/metabolism ; Thymus Gland/radiation effects ; Thymus Neoplasms/*metabolism ; Up-Regulation ; Whole-Body Irradiation ; }, abstract = {The evolution of mitochondrial oxidative phosphorylation was studied during cancer induction in a model of thymic radiolymphomagenesis in C57BL/Ka mice. During the preneoplastic period, thymuses displayed an increase of the cytochrome c oxidase activity and oxygen consumption together with oxidative DNA damage assessed by the presence of the 8-hydroxydeoxyguanine DNA base modification. These transient changes in mitochondrial functional activity were not observed in thymuses of mice rescued from lymphoma development by a bone marrow graft, suggesting an important role of mitochondria for neoplastic transformation in this model, which might therefore be of interest to test the utilization of antioxidants for the prevention of radiation-induced malignancies.}, }
@article {pmid12081462, year = {2002}, author = {Westermann, B and Prokisch, H}, title = {Mitochondrial dynamics in filamentous fungi.}, journal = {Fungal genetics and biology : FG &amp; B}, volume = {36}, number = {2}, pages = {91-97}, doi = {10.1016/S1087-1845(02)00019-1}, pmid = {12081462}, issn = {1087-1845}, mesh = {Actins/physiology ; Microscopy, Fluorescence ; Microtubules/*physiology/ultrastructure ; Mitochondria/*physiology/ultrastructure ; Molecular Motor Proteins/*physiology ; Neurospora crassa/*physiology/ultrastructure ; Protein Transport ; }, abstract = {Mitochondria are essential organelles of eukaryotic cells. They grow continuously throughout the cell cycle and are inherited by daughter cells upon cell division. Inheritance of mitochondria and maintenance of mitochondrial distribution and morphology require active transport of the organelles along the cytoskeleton and depend on membrane fission and fusion events. Many of the molecular components and cellular mechanisms mediating these complex processes have been conserved during evolution across the borders of the fungal and animal kingdoms. During the past few decades, several constituents of the cellular machinery mediating mitochondrial behavior have been identified and functionally characterized. Here, we review the contributions of fungi, with special emphasis on the filamentous fungus Neurospora crassa, to our current understanding of mitochondrial morphogenesis and inheritance.}, }
@article {pmid12079646, year = {2002}, author = {Shimodaira, H}, title = {An approximately unbiased test of phylogenetic tree selection.}, journal = {Systematic biology}, volume = {51}, number = {3}, pages = {492-508}, doi = {10.1080/10635150290069913}, pmid = {12079646}, issn = {1063-5157}, mesh = {Animals ; Mitochondria/metabolism ; Models, Statistical ; *Phylogeny ; }, abstract = {An approximately unbiased (AU) test that uses a newly devised multiscale bootstrap technique was developed for general hypothesis testing of regions in an attempt to reduce test bias. It was applied to maximum-likelihood tree selection for obtaining the confidence set of trees. The AU test is based on the theory of Efron et al. (Proc. Natl. Acad. Sci. USA 93:13429-13434; 1996), but the new method provides higher-order accuracy yet simpler implementation. The AU test, like the Shimodaira-Hasegawa (SH) test, adjusts the selection bias overlooked in the standard use of the bootstrap probability and Kishino-Hasegawa tests. The selection bias comes from comparing many trees at the same time and often leads to overconfidence in the wrong trees. The SH test, though safe to use, may exhibit another type of bias such that it appears conservative. Here I show that the AU test is less biased than other methods in typical cases of tree selection. These points are illustrated in a simulation study as well as in the analysis of mammalian mitochondrial protein sequences. The theoretical argument provides a simple formula that covers the bootstrap probability test, the Kishino-Hasegawa test, the AU test, and the Zharkikh-Li test. A practical suggestion is provided as to which test should be used under particular circumstances.}, }
@article {pmid12079285, year = {2002}, author = {Tourmen, Y and Baris, O and Dessen, P and Jacques, C and Malthièry, Y and Reynier, P}, title = {Structure and chromosomal distribution of human mitochondrial pseudogenes.}, journal = {Genomics}, volume = {80}, number = {1}, pages = {71-77}, doi = {10.1006/geno.2002.6798}, pmid = {12079285}, issn = {0888-7543}, mesh = {Chromosome Mapping ; Databases, Genetic ; Evolution, Molecular ; Genome, Human ; Humans ; Mitochondria/*genetics ; Phylogeny ; Polymerase Chain Reaction ; *Pseudogenes ; Sequence Analysis, DNA ; }, abstract = {Nuclear mitochondrial pseudogenes (Numts) have been found in the genome of many eukaryote species, including humans. Using a BLAST approach, we found 1105 DNA sequences homologous to mitochondrial DNA (mtDNA) in the August 2001 Goldenpath human genome database. We assembled these sequences manually into 286 pseudogenes on the basis of single insertion events and constructed a chromosomal map of these Numts. Some pseudogenes appeared highly modified, containing inversions, deletions, duplications, and displaced sequences. In the case of four randomly selected Numts, we used PCR tests on cells lacking mtDNA to ensure that our technique was free from genome-sequencing artifacts. Furthermore, phylogenetic investigation suggested that one Numt, apparently inserted into the nuclear genome 25-30 million years ago, had been duplicated at least 10 times in various chromosomes during the course of evolution. Thus, these pseudogenes should be very useful in the study of ancient mtDNA and nuclear genome evolution.}, }
@article {pmid12076630, year = {2002}, author = {Alvarez-Pellitero, P and Sitjà-Bobadilla, A}, title = {Cryptosporidium molnari n. sp. (Apicomplexa: Cryptosporidiidae) infecting two marine fish species, Sparus aurata L. and Dicentrarchus labrax L.}, journal = {International journal for parasitology}, volume = {32}, number = {8}, pages = {1007-1021}, doi = {10.1016/s0020-7519(02)00058-9}, pmid = {12076630}, issn = {0020-7519}, mesh = {Animals ; Bass/*parasitology ; Cryptosporidiidae/*classification/growth &amp; development/*isolation &amp; purification/ultrastructure ; Cryptosporidiosis/diagnosis/epidemiology/*parasitology/pathology ; Fish Diseases/diagnosis/epidemiology/parasitology/pathology ; Host-Parasite Interactions ; Oceans and Seas ; Phylogeny ; Prevalence ; Sea Bream/*parasitology ; Spain ; Stomach/parasitology ; }, abstract = {Cryptosporidium molnari n. sp. is described from two teleost fish, the gilthead sea bream (Sparus aurata L.) and the European sea bass (Dicentrarchus labrax L.). The parasite was found mainly in the stomach epithelium and seldom in the intestine. Oocysts were almost spherical, with four naked sporozoites and a prominent residuum, and measured 3.23-5.45 x 3.02-5.04 (mean 4.72 x 4.47) microm in the type host, gilthead sea bream (shape index 1-1.17, mean 1.05). Sporulation was endogenous, as fully sporulated oocysts were found within the fish, both in the stomach epithelium and lumen, and in faeces. Oocysts and other stages of C. molnari fit most of the diagnostic features of the genus Cryptosporidium, but differ from hitherto described species, including piscine ones. All stages were located within a host contributed parasitophorous vacuole lined by a double host microvillar membrane. Merogonial and gamogonial stages appeared in the typical extracytoplasmic position, whereas oogonial and sporogonial stages were located deeply within the epithelium. Ultrastructural features, including the characteristic contact zone of the parasite with the host epithelial surface, were mostly coincident with those of other Cryptosporidium spp. Mitochondria were found in dividing meronts, merozoites, microgamonts and sporozoites. Pathological effects were more evident in gilthead sea bream, which also exhibited a clearly higher prevalence (24.4 versus 4.64% in sea bass). External clinical signs, consisting of whitish faeces, abdominal swelling and ascites, were rarely observed, in contrast with important histopathological damage. The wide zones of epithelium invaded by oogonial and sporogonial stages appeared necrotic, with abundant cell debris, and sloughing of epithelial cells, which detached to the lumen. No inflammation reaction was observed and the cellular reaction was limited to the cells involved in the engulfing of intraepithelial stages and debris, probably macrophages.}, }
@article {pmid12067734, year = {2002}, author = {Aono, N and Shimizu, T and Inoue, T and Shiraishi, H}, title = {Palindromic repetitive elements in the mitochondrial genome of Volvox.}, journal = {FEBS letters}, volume = {521}, number = {1-3}, pages = {95-99}, doi = {10.1016/s0014-5793(02)02832-6}, pmid = {12067734}, issn = {0014-5793}, mesh = {Base Sequence ; Chlorophyta/*genetics ; Cloning, Molecular ; *DNA Transposable Elements ; *DNA, Mitochondrial ; Introns ; Mitochondria ; Molecular Sequence Data ; Multigene Family ; *Repetitive Sequences, Nucleic Acid ; }, abstract = {Group I introns were found in the cob and cox I genes of Volvox carteri. These introns contain tandem arrays of short palindromic sequences that are related to each other. Inspection of other regions in the mtDNA revealed that similar palindromic repetitive sequences are dispersed in the non-protein coding regions of the mitochondrial genome. Analysis of the group I intron in the cob gene of another member of Volvocaceae, Volvox aureus, has shown that its sequence is highly homologous to its counterpart in V. carteri with the exception of a cluster of palindromic sequences not found in V. carteri. This indicates that the palindromic clusters were inserted into the introns after divergence of the two species, presumably due to frequent insertions of the palindromic elements during evolution of the Volvocaceae. Possible involvement of the palindromic repetitive elements in the molecular evolution of functional RNAs is discussed.}, }
@article {pmid12067594, year = {2002}, author = {Barja, G}, title = {Endogenous oxidative stress: relationship to aging, longevity and caloric restriction.}, journal = {Ageing research reviews}, volume = {1}, number = {3}, pages = {397-411}, doi = {10.1016/s1568-1637(02)00008-9}, pmid = {12067594}, issn = {1568-1637}, mesh = {Aging/*metabolism/physiology ; Animals ; Diet, Reducing/methods ; Food Deprivation/*physiology ; Humans ; Longevity/physiology ; Oxidative Stress/*physiology ; }, abstract = {Available studies are consistent with the possibility that oxygen radicals endogenously produced by mitochondria are causally involved in the determination of the rate of aging in homeothermic vertebrates. Oxidative damage to tissue macromolecules seems to increase during aging. The rate of mitochondrial oxygen radical generation of post-mitotic tissues is negatively correlated with animal longevity. In agreement with this, long-lived animals show lower levels of oxidative damage in their mitochondrial DNA (mtDNA) than short-lived ones, whereas this does not occur in nuclear DNA (nDNA). Caloric restriction, which decreases the rate of aging, also decreases mitochondrial oxygen radical generation and oxidative damage to mitochondrial DNA. This decrease in free radical generation occurs in complex I and is due to a decrease in the degree of electronic reduction of the complex I free radical generator, similarly to what has been described in various cases in long-lived animals. These results suggest that similar mechanisms have been used to extend longevity through decreases in oxidative stress in caloric restriction and during the evolution of species with different longevities.}, }
@article {pmid12067335, year = {2002}, author = {Voncken, F and Boxma, B and Tjaden, J and Akhmanova, A and Huynen, M and Verbeek, F and Tielens, AG and Haferkamp, I and Neuhaus, HE and Vogels, G and Veenhuis, M and Hackstein, JH}, title = {Multiple origins of hydrogenosomes: functional and phylogenetic evidence from the ADP/ATP carrier of the anaerobic chytrid Neocallimastix sp.}, journal = {Molecular microbiology}, volume = {44}, number = {6}, pages = {1441-1454}, doi = {10.1046/j.1365-2958.2002.02959.x}, pmid = {12067335}, issn = {0950-382X}, mesh = {Adenosine Diphosphate/*metabolism ; Adenosine Triphosphate/*metabolism ; Amino Acid Sequence ; Animals ; Blotting, Western ; Escherichia coli/genetics ; Hydrogen/*metabolism ; Immunohistochemistry ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/chemistry/classification/genetics/*metabolism ; Molecular Sequence Data ; Neocallimastix/classification/*enzymology/genetics/metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; Trichomonas/genetics ; }, abstract = {A mitochondrial-type ADP/ATP carrier (AAC) has been identified in the hydrogenosomes of the anaerobic chytridiomycete fungus Neocallimastix sp. L2. Biochemical and immunocytochemical studies revealed that this ADP/ATP carrier is an integral component of hydrogenosomal membranes. Expression of the corresponding cDNA in Escherichia coli confers the ability on the bacterial host to incorporate ADP at significantly higher rates than ATP--similar to isolated mitochondria of yeast and animals. Phylogenetic analysis of this AAC gene (hdgaac) confirmed with high statistical support that the hydrogenosomal ADP/ATP carrier of Neocallimastix sp. L2 belongs to the family of veritable mitochondrial-type AACs. Hydrogenosome-bearing anaerobic ciliates possess clearly distinct mitochondrial-type AACs, whereas the potential hydrogenosomal carrier Hmp31 of the anaerobic flagellate Trichomonas vaginalis and its homologue from Trichomonas gallinae do not belong to this family of proteins. Also, phylogenetic analysis of genes encoding mitochondrial-type chaperonin 60 proteins (HSP 60) supports the conclusion that the hydrogenosomes of anaerobic chytrids and anaerobic ciliates had independent origins, although both of them arose from mitochondria.}, }
@article {pmid12066708, year = {1999}, author = {DeBry, RW}, title = {Maximum likelihood analysis of gene-based and structure-based process partitions, using mammalian mitochondrial genomes.}, journal = {Systematic biology}, volume = {48}, number = {2}, pages = {286-299}, doi = {10.1080/106351599260292}, pmid = {12066708}, issn = {1063-5157}, mesh = {Amino Acid Sequence ; Animals ; Biological Evolution ; Codon/genetics ; DNA, Mitochondrial/*genetics ; *Genome ; Humans ; Likelihood Functions ; Mammals/classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; Primates/classification/genetics ; Vertebrates/genetics ; }, abstract = {Aligned protein-coding genes from 19 completely sequenced mammalian mitochondrial genomes were examined by parsimony and maximum likelihood analyses. Particular attention is given to a comparison between gene-based and structure-based data partitions. Because actual structures are not known for most of the mitochondrially encoded proteins, three different surrogate partitioning schemes were examined, each based on the identity of the consensus amino acid at a specific homologous position. One of the amino-acid-based partitioning schemes gave the highest likelihood, but that scheme was based on concordance with a well-corroborated phylogeny from an earlier parsimony analysis. The gene-based partitioning scheme gave a significantly higher likelihood compared to the only structure-based scheme examined that could be generated without prior assumptions about the phylogeny. Two contrasting phylogenetic inferences were supported by the analyses. Both unpartitioned analyses and analyses in which all partitions were constrained to have identical patterns of branch lengths supported ((Artiodactyla, Cetacea) (Perissodactyla, Carnivora)), whereas all analyses with that constraint relaxed supported (((Artiodactyla, Cetacea) Carnivora) Perissodactyla).}, }
@article {pmid12064229, year = {1998}, author = {Davis, JI and Simmons, MP and Stevenson, DW and Wendel, JF}, title = {Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences.}, journal = {Systematic biology}, volume = {47}, number = {2}, pages = {282-310}, doi = {10.1080/106351598260923}, pmid = {12064229}, issn = {1063-5157}, mesh = {Adenosine Triphosphatases/chemistry/*genetics ; Base Sequence ; DNA Primers ; Magnoliopsida/classification/*genetics ; Mitochondria/*genetics ; *Phylogeny ; Reproducibility of Results ; Restriction Mapping ; }, abstract = {We examined three parallel data sets with respect to qualities relevant to phylogenetic analysis of 20 exemplar monocotyledons and related dicotyledons. The three data sets represent restriction-site variation in the inverted repeat region of the chloroplast genome, and nucleotide sequence variation in the chloroplast-encoded gene rbcL and in the mitochondrion-encoded gene atpA, the latter of which encodes the alpha-subunit of mitochondrial ATP synthase. The plant mitochondrial genome has been little used in plant systematics, in part because nucleotide sequence evolution in enzyme-encoding genes of this genome is relatively slow. The three data sets were examined in separate and combined analyses, with a focus on patterns of congruence, homoplasy, and data decisiveness. Data decisiveness (described by P. Goloboff) is a measure of robustness of support for most parsimonious trees by a data set in terms of the degree to which those trees are shorter than the average length of all possible trees. Because indecisive data sets require relatively fewer additional steps than decisive ones to be optimized on nonparsimonious trees, they will have a lesser tendency to be incongruent with other data sets. One consequence of this relationship between decisiveness and character incongruence is that if incongruence is used as a criterion of noncombinability, decisive data sets, which provide robust support for relationships, are more likely to be assessed as noncombinable with other data sets than are indecisive data sets, which provide weak support for relationships. For the sampling of taxa in this study, the atpA data set has about half as many cladistically informative nucleotides as the rbcL data set per site examined, and is less homoplastic and more decisive. The rbcL data set, which is the least decisive of the three, exhibits the lowest levels of character incongruence. Whatever the molecular evolutionary cause of this phenomenon, it seems likely that the poorer performance of rbcL than atpA, in terms of data decisiveness, is due to both its higher overall level of homoplasy and the fact that it is performing especially poorly at nonsynonymous sites.}, }
@article {pmid12062804, year = {2002}, author = {Richter, U and Kiessling, J and Hedtke, B and Decker, E and Reski, R and Börner, T and Weihe, A}, title = {Two RpoT genes of Physcomitrella patens encode phage-type RNA polymerases with dual targeting to mitochondria and plastids.}, journal = {Gene}, volume = {290}, number = {1-2}, pages = {95-105}, doi = {10.1016/s0378-1119(02)00583-8}, pmid = {12062804}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Bryopsida/enzymology/*genetics ; Cloning, Molecular ; DNA, Plant/chemistry/genetics/isolation &amp; purification ; DNA-Directed RNA Polymerases/*genetics/metabolism ; Exons ; Genes, Plant/drug effects ; Green Fluorescent Proteins ; Introns ; Isoenzymes/genetics ; Luminescent Proteins/genetics/metabolism ; Microscopy, Confocal ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics ; Plastids/*enzymology ; Protein Biosynthesis ; RNA, Messenger/genetics ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Angiosperms possess a small family of phage-type RNA polymerase genes that arose by gene duplication from an ancestral gene encoding the mitochondrial RNA polymerase. We have isolated and sequenced the genes and cDNAs encoding two phage-type RNA polymerases, PpRpoT1 and PpRpoT2, from the moss Physcomitrella patens. PpRpoT1 comprises 19 exons and 18 introns, PpRpoT2 contains two additional introns. The N-terminal transit peptides of both polymerases are shown to confer dual-targeting of green fluorescent protein fusions to mitochondria and plastids. In vitro translation of the cDNAs revealed initiation of translation at two in-frame AUG start codons. Translation from the first methionine gives rise to a plastid-targeted polymerase, whereas initiation from the second methionine results in exclusively mitochondrial-targeted protein. Thus, dual-targeting of Physcomitrella RpoT is caused by and might be regulated by multiple translational starts. In phylogenetic analyses, the Physcomitrella RpoT polymerases form a sister group to all other phage-type polymerases of land plants. The two genes result from a gene duplication event that occurred independently from the one which led to the organellar polymerases with mitochondrial or plastid targeting properties in angiosperms. Yet, according to their conserved exon-intron structures they are representatives of the molecular evolutionary line leading to the RpoT genes of higher land plants.}, }
@article {pmid12049666, year = {2002}, author = {Copley, SD and Dhillon, JK}, title = {Lateral gene transfer and parallel evolution in the history of glutathione biosynthesis genes.}, journal = {Genome biology}, volume = {3}, number = {5}, pages = {research0025}, pmid = {12049666}, issn = {1474-760X}, mesh = {Animals ; Bacterial Proteins/genetics ; Computational Biology/methods ; Databases, Protein ; *Evolution, Molecular ; Fungal Proteins/genetics ; Gene Deletion ; Gene Transfer, Horizontal/*genetics ; Genetic Variation ; Glutamate-Cysteine Ligase/*genetics ; Glutathione Synthase/*genetics ; Plant Proteins/genetics ; Protozoan Proteins/genetics ; }, abstract = {BACKGROUND: Glutathione is found primarily in eukaryotes and in Gram-negative bacteria. It has been proposed that eukaryotes acquired the genes for glutathione biosynthesis from the alpha-proteobacterial progenitor of mitochondria. To evaluate this, we have used bioinformatics to analyze sequences of the biosynthetic enzymes gamma-glutamylcysteine ligase and glutathione synthetase.<br><br>RESULTS: Gamma-glutamylcysteine ligase sequences fall into three groups: sequences primarily from gamma-proteobacteria; sequences from non-plant eukaryotes; and sequences primarily from alpha-proteobacteria and plants. Although pairwise sequence identities between groups are insignificant, conserved sequence motifs are found, suggesting that the proteins are distantly related. The data suggest numerous examples of lateral gene transfer, including a transfer from an alpha-proteobacterium to a plant. Glutathione synthetase sequences fall into two distinct groups: bacterial and eukaryotic. Proteins in both groups have a common structural fold, but the sequences are so divergent that it is uncertain whether these proteins are homologous or arose by convergent evolution.<br><br>CONCLUSIONS: The evolutionary history of the glutathione biosynthesis genes is more complex than anticipated. Our analysis suggests that the two genes in the pathway were acquired independently. The gene for gamma-glutamylcysteine ligase most probably arose in cyanobacteria and was transferred to other bacteria, eukaryotes and at least one archaeon, although other scenarios cannot be ruled out. Because of high divergence in the sequences, the data neither support nor refute the hypothesis that the eukaryotic gene comes from a mitochondrial progenitor. After acquiring gamma-glutamylcysteine ligase, eukaryotes and most bacteria apparently recruited a protein with the ATP-grasp superfamily structural fold to catalyze synthesis of glutathione from gamma-glutamylcysteine and glycine. The eukaryotic glutathione synthetase did not evolve directly from the bacterial glutathione synthetase.}, }
@article {pmid12045142, year = {2002}, author = {Woischnik, M and Moraes, CT}, title = {Pattern of organization of human mitochondrial pseudogenes in the nuclear genome.}, journal = {Genome research}, volume = {12}, number = {6}, pages = {885-893}, pmid = {12045142}, issn = {1088-9051}, support = {R01 GM055766/GM/NIGMS NIH HHS/United States ; GM 55766/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Transport/genetics ; Cell Nucleus/*genetics ; Chromosome Mapping/methods ; DNA, Mitochondrial/genetics/metabolism ; Databases, Genetic ; Gene Order ; *Genome, Human ; Humans ; Mitochondria/*genetics ; Phylogeny ; Pseudogenes/*genetics ; Recombination, Genetic/genetics ; }, abstract = {Mitochondrial pseudogenes in the human nuclear genome have been previously described, mostly as a source of artifacts during the analysis of the mitochondrial genome. With the availability of the complete human genome sequence, we performed a comprehensive analysis of mtDNA insertions into the nucleus. We found 612 independent integrations that are evenly distributed among all chromosomes as well as within each individual chromosome. The identified pseudogenes account for a content of at least 0.016% of the human nuclear DNA. Up to 30% of a chromosome's mtDNA pseudogene content is composed of fragments that encompass two or more adjacent mitochondrial genes, and we found no correlation between the abundance of mitochondrial transcripts and the multiplicity of integrations. These observations indicate that the migrations of mitochondrial DNA sequences to the nucleus were predominantly DNA mediated. Phylogenetic analysis of the mtDNA pseudogenes and mtDNA sequences of primates indicate a continuous transfer into the nucleus. Because of the limited window of opportunity for mtDNA transfer to the germline, sperm mtDNA, which is released from degenerating mitochondria after fertilization, could be an important source of nuclear mtDNA pseudogenes.}, }
@article {pmid12039439, year = {2002}, author = {Arking, R and Buck, S and Novoseltev, VN and Hwangbo, DS and Lane, M}, title = {Genomic plasticity, energy allocations, and the extended longevity phenotypes of Drosophila.}, journal = {Ageing research reviews}, volume = {1}, number = {2}, pages = {209-228}, doi = {10.1016/s1568-1637(01)00010-1}, pmid = {12039439}, issn = {1568-1637}, mesh = {Aging/*genetics ; Animals ; Drosophila ; Energy Metabolism/*genetics ; Genome ; Longevity/*genetics ; Phenotype ; }, abstract = {The antagonistic pleiotropy theory of the evolution of aging is shown to be too simple to fully apply to the situation in which Drosophila are selected directly for delayed female fecundity and indirectly for extended longevity. We re-evaluated our own previously reported selection experiments using previously unreported data, as well as new data from the literature. The facts that led to this re-evaluation were: (1) the recognition that there are at least three different extended longevity phenotypes; (2) the existence of metabolic and mitochondrial differences between normal- and long-lived organisms; and most importantly; (3) the observation that animals selected for extended longevity are both more fecund and longer-lived than their progenitor control animals. This latter observation appears to contradict the theory. A revised interpretation of the events underlying the selection process indicates that there is a two-step change in energy allocations leading to a complex phenotype. Initial selection first allows the up-regulation of the antioxidant defense system genes and a shift to the use of the pentose shunt. This is later followed by alterations in mitochondrial fatty acid composition and other changes necessary to reduce the leakage of H(2)O(2) from the mitochondria into the cytosol. The recaptured energy available from the latter step is diverted from somatic maintenance back into reproduction, resulting in animals that are both long-lived and fecund. Literature review suggests the involvement of mitochondrial and antioxidant changes are likely universal in the Type 1 extended longevity phenotype.}, }
@article {pmid12032073, year = {2002}, author = {Wang, HW and Sharp, TV and Koumi, A and Koentges, G and Boshoff, C}, title = {Characterization of an anti-apoptotic glycoprotein encoded by Kaposi's sarcoma-associated herpesvirus which resembles a spliced variant of human survivin.}, journal = {The EMBO journal}, volume = {21}, number = {11}, pages = {2602-2615}, pmid = {12032073}, issn = {0261-4189}, mesh = {*Alternative Splicing ; Amino Acid Sequence ; Apoptosis ; Blotting, Northern ; Caspase 3 ; Caspases/metabolism ; Cell Line ; Chromosomal Proteins, Non-Histone/*chemistry ; Cloning, Molecular ; DNA, Complementary/metabolism ; Endoplasmic Reticulum/metabolism ; Glutathione Transferase/metabolism ; Glycoproteins/*metabolism ; Herpesvirus 8, Human/*genetics/*metabolism ; Humans ; Inhibitor of Apoptosis Proteins ; Microscopy, Fluorescence ; *Microtubule-Associated Proteins ; Mitochondria/metabolism ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Neoplasm Proteins ; Oligonucleotide Array Sequence Analysis ; Open Reading Frames ; Phylogeny ; Protein Binding ; Protein Structure, Tertiary ; Proto-Oncogene Proteins c-bcl-2/metabolism ; Sequence Homology, Amino Acid ; Software ; Subcellular Fractions/metabolism ; Survivin ; Transfection ; }, abstract = {We have investigated the expression and function of a novel protein encoded by open reading frame (ORF) K7 of Kaposi's sarcoma-associated herpesvirus (KSHV). Computational analyses revealed that K7 is structurally related to survivin-DeltaEx3, a splice variant of human survivin that protects cells from apoptosis by an undefined mechanism. Both K7 and survivin-DeltaEx3 contain a mitochondrial-targeting sequence, an N-terminal region of a BIR (baculovirus IAP repeat) domain and a putative BH2 (Bcl-2 homology)-like domain. These suggested that K7 is a new viral anti-apoptotic protein and survivin-DeltaEx3 is its likely cellular homologue. We show that K7 is a glycoprotein, which can inhibit apoptosis and anchor to intracellular membranes where Bcl-2 resides. K7 does not associate with Bax, but does bind to Bcl-2 via its putative BH2 domain. In addition, K7 binds to active caspase-3 via its BIR domain and thus inhibits the activity of caspase-3. The BH2 domain of K7 is crucial for the inhibition of caspase-3 activity and is therefore essential for its anti-apoptotic function. Furthermore, K7 bridges Bcl-2 and activated caspase-3 into a protein complex. K7 therefore appears to be an adaptor protein and part of an anti-apoptotic complex that presents effector caspases to Bcl-2, enabling Bcl-2 to inhibit caspase activity. These data also suggest that survivin-DeltaEx3 might function by a similar mechanism to that of K7. We denote K7 as vIAP (viral inhibitor-of-apoptosis protein).}, }
@article {pmid12029389, year = {2002}, author = {Yen, MR and Tseng, YH and Nguyen, EH and Wu, LF and Saier, MH}, title = {Sequence and phylogenetic analyses of the twin-arginine targeting (Tat) protein export system.}, journal = {Archives of microbiology}, volume = {177}, number = {6}, pages = {441-450}, doi = {10.1007/s00203-002-0408-4}, pmid = {12029389}, issn = {0302-8933}, support = {GM55434/GM/NIGMS NIH HHS/United States ; GM64368/GM/NIGMS NIH HHS/United States ; }, mesh = {Arginine/chemistry ; Bacterial Proteins/genetics ; Biological Evolution ; Biological Transport ; Escherichia coli Proteins/*genetics ; Membrane Transport Proteins/*genetics ; Mitochondria/genetics/metabolism ; *Phylogeny ; Protein Isoforms/genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Twin-arginine targeting (Tat) protein secretion systems consist of two protein types, members of the TatA and TatC families. Homologues of these proteins are found in many archaea, bacteria, chloroplasts and mitochondria. Every prokaryotic organism with a fully sequenced genome exhibits either neither family member, or between one and three paralogues of these two family members. The Arabidopsis thaliana genome encodes three of each. Although many mitochondrially encoded TatC homologues have been identified, corresponding TatA homologues have not been found in this organelle. Phylogenetic analyses reveal that most prokaryotic Tat systems consist of one TatC homologue and two sequence-divergent TatA homologues (TatA and TatB). When only one TatA homologue is present, TatB is missing, and when three TatA homologues are present, the third one arose by duplication of TatA, not TatB. Further, homologues most resembling TatB are more sequence-divergent than those more closely resembling TatA. In contrast to the TatA family, the TatC family shows phylogenetic clustering in strict accordance with organismal type. These results are discussed in terms of their probable structural, functional and evolutionary significance.}, }
@article {pmid12022280, year = {2002}, author = {Vickerman, K and Le Ray, D and Hoef-Emden, K and De Jonckheere, J}, title = {The soil flagellate Proleptomonas faecicola: cell organisation and phylogeny suggest that the only described free-living trypanosomatid is not a kinetoplastid but has cercomonad affinities.}, journal = {Protist}, volume = {153}, number = {1}, pages = {9-24}, doi = {10.1078/1434-4610-00079}, pmid = {12022280}, issn = {1434-4610}, mesh = {Animals ; Eukaryota/*classification/ultrastructure ; Flagella/classification/*physiology/ultrastructure ; Kinetoplastida/classification ; Life Cycle Stages ; Microscopy, Electron ; Molecular Sequence Data ; Phylogeny ; Soil ; }, abstract = {The only putative free-living trypanosomatid is Proleptomonas faecicola described first by Woodcock in 1916 as a coprophilic flagellate with striking Leptomonas-like flagellar movement but lacking a kinetoplast. P faecicola was later identified by Sandon in 1927 as a widespread non-phagotrophic inhabitant of soils. No division stages were seen by either observer. An organism conforming to Woodcock's light microscope description has been isolated from tapwater and cultivated axenically in various serum-containing media. Division has been shown to occur in an aflagellate stage enclosed in a thin cyst wall. Electron microscopy of the flagellate stage reveals that, in addition to the long locomotory flagellum, a second non-motile flagellum is present attached to the body along its entire length. The flagellate's ultrastructure lacks all the major features of the Trypanosomatidae. The several mitochondria of Proleptomonas have tubular cristae and lie between intracytoplasmic microtubules originating as a loose cone associated with the flagellar basal bodies. This cytoskeleton is much reduced in the division cyst. A comparable Proleptomonas-like flagellate with similar division cysts has been observed in soil samples from farmland. Phylogenetic analysis based on SSU rRNA gene sequences suggests that the cultured organism identified here as Proleptomonas is unrelated to the Kinetoplastida and has affinities with the Phylum Cercozoa Cavalier-Smith, even though in morphology, life cycle and mode of feeding it bears little resemblance to any member of that diverse grouping.}, }
@article {pmid12022276, year = {2002}, author = {Brugerolle, G and Bricheux, G and Philippe, H and Coffea, G}, title = {Collodictyon triciliatum and Diphylleia rotans (=Aulacomonas submarina) form a new family of flagellates (Collodictyonidae) with tubular mitochondrial cristae that is phylogenetically distant from other flagellate groups.}, journal = {Protist}, volume = {153}, number = {1}, pages = {59-70}, doi = {10.1078/1434-4610-00083}, pmid = {12022276}, issn = {1434-4610}, mesh = {Animals ; Cell Division/physiology ; Cell Nucleus/metabolism/ultrastructure ; DNA, Ribosomal/analysis ; Eukaryota/*classification/genetics/physiology/ultrastructure ; Flagella/ultrastructure ; Golgi Apparatus/ultrastructure ; Microscopy, Electron ; Mitochondria/*ultrastructure ; Mitosis ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Comparative electron microscopic studies of Collodictyon triciliatum and Diphylleia rotans (=Aulacomonas submarina) showed that they share a distinctive flagellar transitional zone and a very similar flagellar apparatus. In both species, the basic couple of basal bodies and flagella #1 and #2 are connected to the dorsal and ventral roots, respectively. Collodictyon triciliatum has two additional basal bodies and flagella, #3 and #4, situated on each side of the basic couple, each of which also bears a dorsal root. The horseshoe-shaped arrangement of dictyosomes, mitochondria with tubular cristae and the deep ventral groove are very similar to those of Diphylleia rotans. These two genera have very specific features and are placed in a new family, Collodictyonidae, distinct from other eukaryotic groups. Electron microscopic observation of mitotic telophase in Diphylleia rotans revealed two chromosomal masses, surrounded by the nuclear envelope, within the dividing parental nucleus, as in the telophase stage of the heliozoan Actinophrys and the helioflagellate Dimorpha. Spindle microtubules arise from several MTOCs outside the nucleus, and several microtubules penetrate within the dividing nucleus, via pores at the poles. This semi-open type of orthomitosis is reminiscent of that of actinophryids. The SSU rDNA sequence of Diphylleia rotans was compared with that of all the eukaryotic groups that have a slow-evolving rDNA. Diphylleia did not strongly assemble with any group and emerged in a very poorly resolved part of the eukaryotic phylogenetic tree.}, }
@article {pmid12014002, year = {2002}, author = {Ohta, S}, title = {[The origin of mitochondria].}, journal = {Nihon rinsho. Japanese journal of clinical medicine}, volume = {60 Suppl 4}, number = {}, pages = {799-804}, pmid = {12014002}, issn = {0047-1852}, mesh = {Amino Acyl-tRNA Synthetases/genetics ; Animals ; Biological Evolution ; Cell Nucleus/genetics ; DNA, Mitochondrial ; Energy Metabolism ; Eukaryotic Cells/cytology ; Humans ; *Mitochondria/genetics/physiology ; Oxygen ; }, }
@article {pmid12013843, year = {2002}, author = {Yokobori, S and Oshima, T}, title = {[Evolution of genome structure and genetic code of metazoan mitochondria].}, journal = {Nihon rinsho. Japanese journal of clinical medicine}, volume = {60 Suppl 4}, number = {}, pages = {17-23}, pmid = {12013843}, issn = {0047-1852}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; *Genetic Code ; *Genome ; Humans ; Mitochondria/*genetics ; }, }
@article {pmid12013842, year = {2002}, author = {Okamoto, M and Katoh, Y}, title = {[Mitochondrial cytochrome P450].}, journal = {Nihon rinsho. Japanese journal of clinical medicine}, volume = {60 Suppl 4}, number = {}, pages = {164-167}, pmid = {12013842}, issn = {0047-1852}, mesh = {Animals ; Bile Acids and Salts/metabolism ; Cholecalciferol/metabolism ; Cholesterol/metabolism ; *Cytochrome P-450 Enzyme System/classification/physiology ; Evolution, Molecular ; Humans ; Mitochondria/*enzymology/metabolism ; }, }
@article {pmid12007814, year = {2002}, author = {Omelchenko, MV and Makarova, KS and Koonin, EV}, title = {Recurrent intragenomic recombination leading to sequence homogenization during the evolution of the lipoyl-binding domain.}, journal = {FEMS microbiology letters}, volume = {209}, number = {2}, pages = {255-260}, doi = {10.1111/j.1574-6968.2002.tb11140.x}, pmid = {12007814}, issn = {0378-1097}, mesh = {3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide) ; Bacteria/enzymology/*genetics ; Evolution, Molecular ; Gene Duplication ; Ketone Oxidoreductases/*chemistry/*genetics ; Multienzyme Complexes/*chemistry/*genetics ; Phylogeny ; Recombination, Genetic/*genetics ; }, abstract = {The lipoyl-binding domain is often present, in one or several copies, in the E2 subunit and, less often, in the E1 and E3 subunits of 2-oxo acid dehydrogenase complexes. Phylogenetic analysis shows evidence of multiple, independent intragenomic recombination events between different versions of the lipoyl-binding domain in various bacteria and eukaryotic mitochondria, leading to homogenization of the sequences of the lipoyl-binding domain within the same enzymatic complex in several bacterial lineages. This appears to be the first case of sequence homogenization at the level of an individual domain in prokaryotes.}, }
@article {pmid11999848, year = {2002}, author = {Skibbe, DS and Liu, F and Wen, TJ and Yandeau, MD and Cui, X and Cao, J and Simmons, CR and Schnable, PS}, title = {Characterization of the aldehyde dehydrogenase gene families of Zea mays and Arabidopsis.}, journal = {Plant molecular biology}, volume = {48}, number = {5-6}, pages = {751-764}, pmid = {11999848}, issn = {0167-4412}, mesh = {Aldehyde Dehydrogenase/*genetics/metabolism ; Arabidopsis/enzymology/*genetics ; Cloning, Molecular ; Escherichia coli/genetics ; Exons ; Genes/genetics ; Genetic Complementation Test ; Introns ; Isoenzymes/genetics/metabolism ; Mutation ; Phylogeny ; Species Specificity ; Zea mays/enzymology/*genetics ; }, abstract = {Cytoplasmic male sterility is a maternally transmitted inability to produce viable pollen. Male sterility occurs in Texas (T) cytoplasm maize as a consequence of the premature degeneration of the tapetal cell layer during microspore development. This sterility can be overcome by the combined action of two nuclear restorer genes, rf1 and rf2a. The rf2a gene encodes a mitochondrial aldehyde dehydrogenase (ALDH) that is capable of oxidizing a variety of aldehydes. Six additional ALDH genes were cloned from maize and Arabidopsis. In vivo complementation assays and in vitro enzyme analyses demonstrated that all six genes encode functional ALDHs. Some of these ALDHs are predicted to accumulate in the mitochondria, others in the cytosol. The intron/exon boundaries of these genes are highly conserved across maize and Arabidopsis and between mitochondrial and cytosolic ALDHs. Although animal, fungal, and plant genomes each encode both mitochondrial and cytosolic ALDHs, it appears that either the gene duplications that generated the mitochondrial and the cytosolic ALDHs occurred independently within each lineage or that homogenizing gene conversion-like events have occurred independently within each lineage. All studied plant genomes contain two confirmed or predicted mitochondrial ALDHs. It appears that these mitochondrial ALDH genes arose via independent duplications after the divergence of monocots and dicots or that independent gene conversion-like events have homogenized the mitochondrial ALDH genes in the monocot and dicot lineages. A computation approach was used to identify amino acid residues likely to be responsible for functional differences between mitochondrial and cytosolic ALDHs.}, }
@article {pmid11999303, year = {2001}, author = {Cummins, J}, title = {Mitochondrial DNA and the Y chromosome: parallels and paradoxes.}, journal = {Reproduction, fertility, and development}, volume = {13}, number = {7-8}, pages = {533-542}, doi = {10.1071/rd01064}, pmid = {11999303}, issn = {1031-3613}, mesh = {Animals ; Biological Evolution ; *DNA, Mitochondrial ; Female ; Fertility/genetics ; Genetic Markers ; Humans ; Infertility, Male/genetics ; Male ; Recombination, Genetic ; Selection, Genetic ; Spermatogenesis/genetics ; *Y Chromosome ; }, abstract = {Both mitochondrial DNA (mtDNA) and the Y chromosome have been used extensively by molecular paleoanthropologists in attempts to reconstruct human lineages. Both are inherited in a haploid manner: mtDNA through the female and the Y through the male. For mtDNA, maternal inheritance is ensured by a species-specific mechanism of proteolysis of the sperm midpiece in early embryogenesis, based on ubiquitination of the mitochondria during spermiogenesis. Both genomes are thought to lack recombination and are thus liable to high rates of neutral mutation. For the human Y chromosome, it is now clear that there has been selection on genes controlling spermatogenesis, resulting in differential long-term reproductive success. This is corroborated from studies of genealogies and hunting-gathering societies, although these lack the rigour provided by the modern molecular markers of inheritance. Selection is made more complicated by a concentration of genes controlling secondary sexual characteristics on the X chromosome. Likewise, mtDNA affects the bioenergetics of gametogenesis and embryo development, as well as longevity, disease and the aging process. Both Y chromosome and mitochondrial haplotypes show significant associations with patterns of male infertility that could distort their use for phylogenetic reconstruction. Moreover, the molecular analysis of mtDNA is complicated by the presence of numerous nuclear mitochondrial pseudogenes (Numts) that can be erroneously amplified by molecular techniques such as PCR. This review examines some of these complex interactions and suggests that some of the more contentious issues in understanding human evolution may be resolved by considering the biology of these genetic markers.}, }
@article {pmid11992819, year = {2002}, author = {Balmer, Y and Buchanan, BB}, title = {Yet another plant thioredoxin.}, journal = {Trends in plant science}, volume = {7}, number = {5}, pages = {191-193}, doi = {10.1016/s1360-1385(02)02263-x}, pmid = {11992819}, issn = {1360-1385}, mesh = {Animals ; Bacteria/genetics/metabolism ; Chloroplasts/genetics/metabolism ; Mitochondria/genetics/metabolism ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Plants/*genetics/metabolism ; Signal Transduction ; Thioredoxins/*genetics/metabolism ; Yeasts/genetics/metabolism ; }, abstract = {Thioredoxins are widely distributed proteins that function in a broad spectrum of cellular reactions. Plant cells have well characterized chloroplast and cytosolic thioredoxin systems, but, unlike animals and yeast, a mitochondrial counterpart has not been clearly defined. Recently, a complete thioredoxin system has been described in plant mitochondria, opening a new door for the study of thioredoxins as well as mitochondria.}, }
@article {pmid11983065, year = {2002}, author = {Martin, IV and MacNeill, SA}, title = {ATP-dependent DNA ligases.}, journal = {Genome biology}, volume = {3}, number = {4}, pages = {REVIEWS3005}, pmid = {11983065}, issn = {1474-760X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Cell Nucleus/enzymology ; DNA Ligases/chemistry/genetics/*physiology ; Evolution, Molecular ; Mitochondria/enzymology ; Models, Molecular ; Protein Structure, Tertiary ; }, abstract = {By catalyzing the joining of breaks in the phosphodiester backbone of duplex DNA, DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Three related classes of ATP-dependent DNA ligase are readily apparent in eukaryotic cells. Enzymes of each class comprise catalytic and non-catalytic domains together with additional domains of varying function. DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis, as well as for several DNA-repair pathways; these functions are mediated, at least in part, by interactions between DNA ligase I and the sliding-clamp protein PCNA. DNA ligase III, which is unique to vertebrates, functions both in the nucleus and in mitochondria. Two distinct isoforms of this enzyme, differing in their carboxy-terminal sequences, are produced by alternative splicing: DNA ligase IIIalpha has a carboxy-terminal BRCT domain that interacts with the mammalian DNA-repair factor XrccI, but both alpha and beta isoforms have an amino-terminal zinc-finger motif that appears to play a role in the recognition of DNA secondary structures that resemble intermediates in DNA metabolism. DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV forms a tight complex with Xrcc4 through an interaction motif located between a pair of carboxy-terminal BRCT domains in the ligase. Recent structural studies have shed light on the catalytic function of DNA ligases, as well as illuminating protein-protein interactions involving DNA ligases IIIalpha and IV.}, }
@article {pmid11978537, year = {2002}, author = {Shaw, JM and Nunnari, J}, title = {Mitochondrial dynamics and division in budding yeast.}, journal = {Trends in cell biology}, volume = {12}, number = {4}, pages = {178-184}, pmid = {11978537}, issn = {0962-8924}, support = {R01 GM053466/GM/NIGMS NIH HHS/United States ; }, mesh = {Cell Cycle ; GTP Phosphohydrolases/physiology ; Intracellular Membranes/physiology/ultrastructure ; Mitochondria/metabolism/*ultrastructure ; Mitochondrial Proteins/physiology ; Saccharomycetales/*cytology/ultrastructure ; }, abstract = {Mitochondria adopt a variety of different shapes in eukaryotic cells, ranging from multiple, small compartments to elaborate tubular networks. The establishment and maintenance of different mitochondrial morphologies depends, in part, on the equilibrium between opposing fission and fusion events. Recent studies in yeast, flies, worms and mammalian cells indicate that three high-molecular-weight GTPases control mitochondrial membrane dynamics. One of these is a dynamin-related GTPase that acts on the outer mitochondrial membrane to regulate fission. Recently, genetic approaches in budding yeast have identified additional components of the fission machinery. These and other new findings suggest a common mechanism for membrane fission events that has been conserved and adapted during eukaryotic evolution.}, }
@article {pmid11976966, year = {2002}, author = {Kudla, J and Albertazzi, FJ and Blazević, D and Hermann, M and Bock, R}, title = {Loss of the mitochondrial cox2 intron 1 in a family of monocotyledonous plants and utilization of mitochondrial intron sequences for the construction of a nuclear intron.}, journal = {Molecular genetics and genomics : MGG}, volume = {267}, number = {2}, pages = {223-230}, doi = {10.1007/s00438-002-0657-6}, pmid = {11976966}, issn = {1617-4615}, mesh = {Amino Acid Sequence ; Base Sequence ; Cell Nucleus/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; *Genes, Plant ; *Introns ; Magnoliopsida/enzymology/genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Plant Proteins/*genetics ; Plants/enzymology/*genetics ; RNA Editing ; RNA, Messenger/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {The intron content of plant organellar genes is a useful marker in molecular systematics and evolution. We have tested representatives of a wide range of monocotyledonous plant families for the presence of an intron (cox2 intron 1) in one of the most conservative mitochondrial genes, the cox2 locus. Almost all species analyzed were found to harbor a group II intron at a phylogenetically conserved position. The only exceptions were members of a single monocot family, the Ruscaceae: representatives of all genera in this family were found to lack cox2 intron 1, but instead harbor an intron in the 3' portion of the cox2 coding region (cox2 intron 2). The presence of cox2 intron 1 in families of monocotyledonous plants that are closely related to the Ruscaceae suggests that loss of the intron is specific to this family and may have accompanied the evolutionary appearance of the Ruscaceae. Interestingly, sequences that are highly homologous to cox2 intron 2 are found in a nuclear intron in a lineage of monocotyledonous plants, suggesting that the originally mitochondrial group II intron sequence was transferred to the nuclear genome and reused there to build a spliceosomal intron.}, }
@article {pmid11976221, year = {2002}, author = {Pamplona, R and Barja, G and Portero-Otín, M}, title = {Membrane fatty acid unsaturation, protection against oxidative stress, and maximum life span: a homeoviscous-longevity adaptation?.}, journal = {Annals of the New York Academy of Sciences}, volume = {959}, number = {}, pages = {475-490}, doi = {10.1111/j.1749-6632.2002.tb02118.x}, pmid = {11976221}, issn = {0077-8923}, mesh = {Aging/physiology ; Animals ; Dietary Fats ; Fatty Acids, Unsaturated/chemistry/*metabolism ; Humans ; Life Expectancy ; Lipid Peroxidation ; *Longevity ; Membrane Lipids/chemistry/*metabolism ; Mitochondria, Heart/metabolism ; Models, Biological ; *Oxidative Stress ; Reactive Oxygen Species/metabolism ; }, abstract = {Aging is a progressive and universal process originating endogenously that manifests during postmaturational life. Available comparative evidence supporting the mitochondrial free radical theory of aging consistently indicates that two basic molecular traits are associated with the rate of aging and thus with the maximum life span: the presence of low rates of mitochondrial oxygen radical production and low degrees of fatty acid unsaturation of cellular membranes in postmitotic tissues of long-lived homeothermic vertebrates in relation to those of short-lived ones. Recent research shows that steady-state levels of free radical-derived damage to mitochondrial DNA (mtDNA) and, in some cases, to proteins are lower in long- than in short-lived animals. Thus, nonenzymatic oxidative modification of tissue macromolecules is related to the rate of aging. The low degree of fatty acid unsaturation in biomembranes of long-lived animals may confer advantage by decreasing their sensitivity to lipid peroxidation. Furthermore, this may prevent lipoxidation-derived damage to other macromolecules. Taking into account the fatty acid distribution pattern, the origin of the low degree of membrane unsaturation in long-lived species seems to be the presence of species-specific desaturation pathways that determine membrane composition while an appropriate environment for membrane function is maintained. Mechanisms that prevent or decrease the generation of endogenous damage during the evolution of long-lived animals seem to be more important than trying to intercept those damaging agents or repairing the damage already inflicted. Here, the physiological meaning of these findings and the effects of experimental manipulations such as dietary stress, caloric restriction, and endocrine control in relation to aging and longevity are discussed.}, }
@article {pmid11973295, year = {2002}, author = {Zuo, XM and Clark-Walker, GD and Chen, XJ}, title = {The mitochondrial nucleoid protein, Mgm101p, of Saccharomyces cerevisiae is involved in the maintenance of rho(+) and ori/rep-devoid petite genomes but is not required for hypersuppressive rho(-) mtDNA.}, journal = {Genetics}, volume = {160}, number = {4}, pages = {1389-1400}, pmid = {11973295}, issn = {0016-6731}, mesh = {*DNA Replication ; DNA, Mitochondrial/*biosynthesis ; DNA-Binding Proteins ; Fungal Proteins/*physiology ; Hot Temperature ; Mitochondria/genetics ; Mitochondrial Proteins ; Mutation ; Nuclear Proteins/*physiology ; Replication Origin ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/*physiology ; }, abstract = {The Saccharomyces cerevisiae MGM101 gene encodes a DNA-binding protein targeted to mitochondrial nucleoids. MGM101 is essential for maintenance of a functional rho(+) genome because meiotic segregants, with a disrupted mgm101 allele, cannot undergo more than 10 divisions on glycerol medium. Quantitative analysis of mtDNA copy number in a rho(+) strain carrying a temperature-sensitive allele, mgm101-1, revealed that the amount of mtDNA is halved each cell division upon a shift to the restrictive temperature. These data suggest that mtDNA replication is rapidly blocked in cells lacking MGM101. However, a small proportion of meiotic segregants, disrupted in MGM101, have rho(-) genomes that are stably maintained. Interestingly, all surviving rho(-) mtDNAs contain an ori/rep sequence. Disruption of MGM101 in hypersuppressive (HS) strains does not have a significant effect on the propagation of HS rho(-) mtDNA. However, in petites lacking an ori/rep, disruption of MGM101 leads to either a complete loss or a dramatically decreased stability of mtDNA. This discriminatory effect of MGM101 suggests that replication of rho(+) and ori/rep-devoid rho(-) mtDNAs is carried out by the same process. By contrast, the persistence of ori/rep-containing mtDNA in HS petites lacking MGM101 identifies a distinct replication pathway. The alternative mtDNA replication mechanism provided by ori/rep is independent of mitochondrial RNA polymerase encoded by RPO41 as a HS rho(-) genome is stably maintained in a mgm101, rpo41 double mutant.}, }
@article {pmid11972043, year = {2002}, author = {Vermel, M and Guermann, B and Delage, L and Grienenberger, JM and Maréchal-Drouard, L and Gualberto, JM}, title = {A family of RRM-type RNA-binding proteins specific to plant mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {9}, pages = {5866-5871}, pmid = {11972043}, issn = {0027-8424}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Arabidopsis ; Blotting, Northern ; Cold Temperature ; DNA, Complementary/metabolism ; DNA, Single-Stranded ; Detergents/pharmacology ; Mitochondria/*metabolism ; Molecular Sequence Data ; Nucleic Acids/metabolism ; Octoxynol/pharmacology ; Phylogeny ; Plant Proteins/*metabolism ; Plants/metabolism ; Protein Binding ; Protein Structure, Tertiary ; RNA/*metabolism ; *RNA-Binding Proteins ; Reverse Transcriptase Polymerase Chain Reaction ; Ribonucleoside Diphosphate Reductase ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Solanum tuberosum/genetics ; Temperature ; Nicotiana/genetics ; Tumor Suppressor Proteins/metabolism ; }, abstract = {Expression of higher plant mitochondrial (mt) genes is regulated at the transcriptional, posttranscriptional, and translational levels, but the vast majority of the mtDNA and RNA-binding proteins involved remain to be identified. Plant mt single-stranded nucleic acid-binding proteins were purified by affinity chromatography, and corresponding genes have been identified. A majority of these proteins belong to a family of RNA-binding proteins characterized by the presence of an N-terminal RNA-recognition motif (RRM) sequence. They diverge in their C-terminal sequences, suggesting that they can be involved in different plant mt regulation processes. Mitochondrial localization of the proteins was confirmed both in vitro and in vivo and by immunolocalization. Binding experiments showed that several proteins have a preference for poly(U)-rich sequences. This mt protein family contains the ubiquitous RRM motif and has no known mt counterpart in non-plant species. Phylogenetic and functional analysis suggest a common ancestor with RNA-binding glycine-rich proteins (GRP), a family of developmentally regulated proteins of unknown function. As with several plant, cyanobacteria, and animal proteins that have similar structures, the expression of one of the Arabidopsis thaliana mt RNA-binding protein genes is induced by low temperatures.}, }
@article {pmid11971146, year = {2002}, author = {Adams, KL and Daley, DO and Whelan, J and Palmer, JD}, title = {Genes for two mitochondrial ribosomal proteins in flowering plants are derived from their chloroplast or cytosolic counterparts.}, journal = {The Plant cell}, volume = {14}, number = {4}, pages = {931-943}, pmid = {11971146}, issn = {1040-4651}, support = {R01 GM035087/GM/NIGMS NIH HHS/United States ; GM-35087/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Arabidopsis/genetics ; Cell Nucleus/genetics ; Chloroplasts/*genetics ; Cytosol/metabolism ; Fabaceae/genetics ; Gene Expression Profiling ; Gossypium/genetics ; Solanum lycopersicum/genetics ; Magnoliopsida/*genetics ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Ribosomal Proteins/*genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Often during flowering plant evolution, ribosomal protein genes have been lost from the mitochondrion and transferred to the nucleus. Here, we show that substitution by a duplicated, divergent gene originally encoding the chloroplast or cytosolic ribosomal protein counterpart accounts for two missing mitochondrial genes in diverse angiosperms. The rps13 gene is missing from the mitochondrial genome of many rosids, and a transferred copy of this gene is not evident in the nucleus of Arabidopsis, soybean, or cotton. Instead, these rosids contain a divergent nuclear copy of an rps13 gene of chloroplast origin. The product of this gene from all three rosids was shown to be imported into isolated mitochondria but not into chloroplasts. The rps8 gene is missing from the mitochondrion and nucleus of all angiosperms examined. A divergent copy of the gene encoding its cytosolic counterpart (rps15A) was identified in the nucleus of four angiosperms and one gymnosperm. The product of this gene from Arabidopsis and tomato was imported successfully into mitochondria. We infer that rps13 was lost from the mitochondrial genome and substituted by a duplicated nuclear gene of chloroplast origin early in rosid evolution, whereas rps8 loss and substitution by a gene of nuclear/cytosolic origin occurred much earlier, in a common ancestor of angiosperms and gymnosperms.}, }
@article {pmid11967744, year = {2002}, author = {Jürgens, KD and Gros, G}, title = {[Phylogeny of gas exchange systems].}, journal = {Anasthesiologie, Intensivmedizin, Notfallmedizin, Schmerztherapie : AINS}, volume = {37}, number = {4}, pages = {185-198}, doi = {10.1055/s-2002-25080}, pmid = {11967744}, issn = {0939-2661}, mesh = {Animals ; Capillaries/physiology ; Carbon Dioxide/*metabolism ; Gases/*metabolism ; Homeostasis ; Humans ; Lung/physiology ; Mitochondria/metabolism ; *Phylogeny ; *Respiratory Physiological Phenomena ; Trachea/physiology ; }, abstract = {Several systems of gas transport have developed during evolution, all of which are able to sufficiently supply oxygen to the tissues and eliminate the CO2 produced by the metabolism, in spite of great distances between the environment and the individual cells of the tissues. Almost all these systems utilize a combination of convection and diffusion steps. Convection achieves an efficient transport of gas over large distances, but requires energy and cannot occur across tissue barriers. Diffusion, on the other hand, achieves gas transport across barriers, but requires optimization of diffusion paths and diffusion areas. When two convectional gas flows are linked via a diffusional barrier (gas/fluid in the case of the avian lung, fluid/fluid in the case of gills), the directions in which the respective convectional movements pass each other are important determinants of gas exchange efficiency (concurrent, countercurrent and cross-current systems). The tracheal respiration found in insects has the advantage of circumventing the convective gas transport step in the blood, thereby avoiding the high energy expenditure of circulatory systems. This is made possible by a system of tracheae, ending in tracheoles, that reaches from the body surface to every cell within the body. The last step of gas transfer in these animals occurs by diffusion from the tracheoles ("air capillaries") to the mitochondria of cells. The disadvantage is that the tracheal system occupies a substantial fraction of body volume and that, due to limited mechanical stability of tracheal walls, this system would not be able to operate under conditions of high hydrostatic pressures, i. e. in large animals. Respiration in an "open" system, i. e. direct exposure of the diffusional barrier to the environmental air, eliminates the problem of bringing the oxygen to the barrier by convection, as is necessary in the avian and mammalian lung, in the insects' tracheal system and in the gills. An open system is found in the respiration via the skin, which is of significance in some amphibians, but is limited by the thickness of the skin that constitutes a substantial diffusion path for O2 and CO2. The thick skin, on the other hand, provides mechanical protection as well as flexibility for the animals' body and helps avoid massive water loss via the body surface. The gills of fishes, in contrast, exhibit rather short diffusion distances, are located in a mechanically protected space, and the problem of water loss does not exist. The flows of blood and water occur in opposite direction (countercurrent flow) and this situation makes an arterial PO2 approaching the environmental PO2 possible. A major disadvantage is constituted by the environmental medium since water contains little O2 compared to air and, to compensate this, much energy is expended to maintain a high flow rate of water through the gills. In the mammalian lung ("pool system"), the presence of a dead space and the rhythmic ventilation that replaces only a small fraction of the gas volume of the lung per breath, are responsible for an arterial PO2 (2/3 of the atmospheric PO2) that cannot reach the expiratory PO2. However, an advantage of this feature is the constantly high alveolar and arterial PCO2, which provides a highly effective H(+) buffer system in the entire body. The apparent disadvantage of the mammalian lung is avoided by the avian lung, which uses an extended system of airways to establish continuous equilibration of a part of the capillary blood with fresh air (cross current system), during inspiration as well as during expiration. In this system, arterial PO2 can significantly exceed expiratory PO2. A disadvantage here is the enormous amount of space taken up by the avian lung, in animals of 1 kg body weight three times as much as taken up by the mammalian lung. All respiratory exchange systems considered here exhibit high degrees of optimization - yet follow highly diverse construction principles. There is no such thing as an ideal gas exchange system. The system that has evolved in each species depends to an impressive extent on environmental conditions, on body build and size, on the animal's patterns of movement and on its energy consumption.}, }
@article {pmid11965492, year = {2002}, author = {Koonin, EV and Aravind, L}, title = {Origin and evolution of eukaryotic apoptosis: the bacterial connection.}, journal = {Cell death and differentiation}, volume = {9}, number = {4}, pages = {394-404}, doi = {10.1038/sj.cdd.4400991}, pmid = {11965492}, issn = {1350-9047}, mesh = {Animals ; Apoptosis/*genetics ; Apoptosis Inducing Factor ; Bacteria/*genetics/growth &amp; development ; Biological Evolution ; Caspases/genetics/physiology ; Eukaryotic Cells/cytology/*physiology ; Flavoproteins/physiology ; *Heat-Shock Proteins ; Membrane Proteins/physiology ; Mitochondria/genetics/physiology ; Models, Genetic ; *Periplasmic Proteins ; Phylogeny ; Sequence Homology ; Serine Endopeptidases/genetics ; Signal Transduction ; }, abstract = {The availability of numerous complete genome sequences of prokaryotes and several eukaryotic genome sequences provides for new insights into the origin of unique functional systems of the eukaryotes. Several key enzymes of the apoptotic machinery, including the paracaspase and metacaspase families of the caspase-like protease superfamily, apoptotic ATPases and NACHT family NTPases, and mitochondrial HtrA-like proteases, have diverse homologs in bacteria, but not in archaea. Phylogenetic analysis strongly suggests a mitochondrial origin for metacaspases and the HtrA-like proteases, whereas acquisition from Actinomycetes appears to be the most likely scenario for AP-ATPases. The homologs of apoptotic proteins are particularly abundant and diverse in bacteria that undergo complex development, such as Actinomycetes, Cyanobacteria and alpha-proteobacteria, the latter being progenitors of the mitochondria. In these bacteria, the apoptosis-related domains typically form multidomain proteins, which are known or inferred to participate in signal transduction and regulation of gene expression. Some of these bacterial multidomain proteins contain fusions between apoptosis-related domains, such as AP-ATPase fused with a metacaspase or a TIR domain. Thus, bacterial homologs of eukaryotic apoptotic machinery components might functionally and physically interact with each other as parts of signaling pathways that remain to be investigated. An emerging scenario of the origin of the eukaryotic apoptotic system involves acquisition of several central apoptotic effectors as a consequence of mitochondrial endosymbiosis and probably also as a result of subsequent, additional horizontal gene transfer events, which was followed by recruitment of newly emerging eukaryotic domains as adaptors.}, }
@article {pmid11965491, year = {2002}, author = {Ameisen, JC}, title = {On the origin, evolution, and nature of programmed cell death: a timeline of four billion years.}, journal = {Cell death and differentiation}, volume = {9}, number = {4}, pages = {367-393}, doi = {10.1038/sj.cdd.4400950}, pmid = {11965491}, issn = {1350-9047}, mesh = {Animals ; *Apoptosis ; *Biological Evolution ; Caenorhabditis elegans Proteins ; Caspases/physiology ; Eukaryota/cytology/physiology ; Eukaryotic Cells/physiology ; Homeodomain Proteins/physiology ; Humans ; Mitochondria/genetics/physiology ; Phylogeny ; Plant Physiological Phenomena ; Time ; }, abstract = {Programmed cell death is a genetically regulated process of cell suicide that is central to the development, homeostasis and integrity of multicellular organisms. Conversely, the dysregulation of mechanisms controlling cell suicide plays a role in the pathogenesis of a wide range of diseases. While great progress has been achieved in the unveiling of the molecular mechanisms of programmed cell death, a new level of complexity, with important therapeutic implications, has begun to emerge, suggesting (i) that several different self-destruction pathways may exist and operate in parallel in our cells, and (ii) that molecular effectors of cell suicide may also perform other functions unrelated to cell death induction and crucial to cell survival. In this review, I will argue that this new level of complexity, implying that there may be no such thing as a 'bona fide' genetic death program in our cells, might be better understood when considered in an evolutionary context. And a new view of the regulated cell suicide pathways emerges when one attempts to ask the question of when and how they may have become selected during evolution, at the level of ancestral single-celled organisms.}, }
@article {pmid11965489, year = {2002}, author = {Silke, J and Verhagen, AM}, title = {Jekyll and Hyde; changing places, changing faces.}, journal = {Cell death and differentiation}, volume = {9}, number = {4}, pages = {362-363}, doi = {10.1038/sj.cdd.4401004}, pmid = {11965489}, issn = {1350-9047}, mesh = {Amino Acid Sequence ; Animals ; *Apoptosis ; Biological Evolution ; *Heat-Shock Proteins ; High-Temperature Requirement A Serine Peptidase 2 ; Humans ; Mitochondria/*enzymology ; Mitochondrial Proteins ; Models, Genetic ; *Periplasmic Proteins ; Sequence Alignment ; Serine Endopeptidases/genetics/*physiology ; }, }
@article {pmid11965487, year = {2002}, author = {James, ER and Green, DR}, title = {Infection and the origins of apoptosis.}, journal = {Cell death and differentiation}, volume = {9}, number = {4}, pages = {355-357}, doi = {10.1038/sj.cdd.4400986}, pmid = {11965487}, issn = {1350-9047}, mesh = {Animals ; *Apoptosis ; *Biological Evolution ; Host-Parasite Interactions ; Humans ; Immunity ; *Infections/metabolism/pathology ; Mitochondria/physiology ; Models, Biological ; Signal Transduction ; }, }
@article {pmid11961110, year = {2002}, author = {Silberman, JD and Simpson, AG and Kulda, J and Cepicka, I and Hampl, V and Johnson, PJ and Roger, AJ}, title = {Retortamonad flagellates are closely related to diplomonads--implications for the history of mitochondrial function in eukaryote evolution.}, journal = {Molecular biology and evolution}, volume = {19}, number = {5}, pages = {777-786}, doi = {10.1093/oxfordjournals.molbev.a004135}, pmid = {11961110}, issn = {0737-4038}, support = {AI 28757/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Diplomonadida/classification/*genetics ; Eukaryota/classification/*genetics ; Evolution, Molecular ; Genes, Protozoan ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal/genetics ; }, abstract = {We present the first molecular phylogenetic examination of the evolutionary position of retortamonads, a group of mitochondrion-lacking flagellates usually found as commensals of the intestinal tracts of vertebrates. Our phylogenies include small subunit ribosomal gene sequences from six retortamonad isolates-four from mammals and two from amphibians. All six sequences were highly similar (95%-99%), with those from mammals being almost identical to each other. All phylogenetic methods utilized unequivocally placed retortamonads with another amitochondriate group, the diplomonads. Surprisingly, all methods weakly supported a position for retortamonads cladistically within diplomonads, as the sister group to Giardia. This position would conflict with a single origin and uniform retention of the doubled-cell organization displayed by most diplomonads, but not by retortamonads. Diplomonad monophyly was not rejected by Shimodaira-Hasegawa, Kishino-Hasegawa, and expected likelihood weights methods but was marginally rejected by parametric bootstrapping. Analyses with additional phylogenetic markers are needed to test this controversial branching order within the retortamonad + diplomonad clade. Nevertheless, the robust phylogenetic association between diplomonads and retortamonads suggests that they share an amitochondriate ancestor. Because strong evidence indicates that diplomonads have secondarily lost their mitochondria (rather than being ancestrally amitochondriate), our results imply that retortamonads are also secondarily amitochondriate. Of the various groups of eukaryotes originally suggested to be primitively amitochondriate under the archezoa hypothesis, all have now been found to have physical or genetic mitochondrial relics (or both) or form a robust clade with an organism with such a relic.}, }
@article {pmid11960028, year = {2002}, author = {Arimura, S and Tsutsumi, N}, title = {A dynamin-like protein (ADL2b), rather than FtsZ, is involved in Arabidopsis mitochondrial division.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {8}, pages = {5727-5731}, pmid = {11960028}, issn = {0027-8424}, mesh = {Amino Acid Motifs ; Amino Acid Sequence ; Arabidopsis/*metabolism ; Arabidopsis Proteins/*genetics/*physiology ; Chloroplasts/metabolism ; Cloning, Molecular ; DNA, Complementary/metabolism ; GTP Phosphohydrolases/*genetics/*physiology ; Genes, Dominant ; Genome, Plant ; Green Fluorescent Proteins ; Luminescent Proteins/metabolism ; Microscopy, Fluorescence ; Mitochondria/metabolism/*physiology ; Molecular Sequence Data ; Mutation ; Phylogeny ; Plant Proteins/*genetics/*physiology ; Plasmids/metabolism ; Sequence Analysis, DNA ; }, abstract = {Recently, the FtsZ protein, which is known as a key component in bacterial cell division, was reported to be involved in mitochondrial division in algae. In yeast and animals, however, mitochondrial fission depends on the dynamin-like proteins Dnm1p and Drp1, respectively, whereas in green plants, no potential mitochondrial division genes have been identified. BLAST searches of the nuclear and mitochondrial genome sequences of Arabidopsis thaliana did not find any obvious homologue of the alpha-proteobacterial-type ftsZ genes. To determine whether mitochondrial division of higher plants depends on a dynamin-like protein, we cloned a cDNA for ADL2b, an Arabidopsis homologue of Dnm1p, and tested its subcellular localization and its dominant-negative effect on mitochondrial division. The fusion protein of green fluorescent protein and ADL2b was observed as punctate structures localized at the tips and at the constriction sites of mitochondria in live plant cells. Cells expressing dominant-negative mutant ADL2b proteins (K56A and T77F) showed a significant fusion, aggregation, and/or tubulation of mitochondria. We propose that mitochondrial division in higher plants is conducted by dynamin-like proteins similar to ADL2b in Arabidopsis. The evolutional points of loss of mitochondrial FtsZ and the functional acquisition of dynamin-like proteins in mitochondrial division are discussed.}, }
@article {pmid11950885, year = {2002}, author = {Rojo, M and Legros, F and Chateau, D and Lombès, A}, title = {Membrane topology and mitochondrial targeting of mitofusins, ubiquitous mammalian homologs of the transmembrane GTPase Fzo.}, journal = {Journal of cell science}, volume = {115}, number = {Pt 8}, pages = {1663-1674}, doi = {10.1242/jcs.115.8.1663}, pmid = {11950885}, issn = {0021-9533}, mesh = {Actins/metabolism ; Animals ; Cell Fractionation ; Cytoskeleton/metabolism ; *Drosophila Proteins ; GTP Phosphohydrolases/*genetics ; HeLa Cells ; Humans ; Immunohistochemistry ; Membrane Proteins/chemistry/classification/*genetics/*metabolism ; Membrane Transport Proteins ; Microtubules/metabolism ; Mitochondria/*metabolism/ultrastructure ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Proteins/chemistry/classification/genetics/*metabolism ; Phylogeny ; *Protein Structure, Tertiary ; }, abstract = {Two human Fzo-homologs, mitofusins Mfn1 and Mfn2, are shown by RT-PCR and western blot to be ubiquitous mitochondrial proteins. Protease digestion experiments reveal that Mfn2 is an outer membrane protein with N-terminal and C-terminal domains exposed towards the cytosol. The transmembrane and C-terminal domains of Mfn2 (Mfn2-TMCT) are targeted to mitochondria and deletion of these domains leads to the cytosolic localization of truncated Mfn2 (Mfn2-NT). Mfn2 is targeted to the endoplasmic reticulum or to mitochondria when the C-terminal domain is replaced by short stretches of neutral/hydrophobic (Mfn2-IYFFT) or polar/basic (Mfn2-RRD) amino acids. The coiled-coil domains of Mfn2, upstream and downstream of the transmembrane domain, are also important for mitochondrial targeting: Mfn2-mutants deleted of any of its coiled-coil domains are only partially targeted to mitochondria and significant protein amounts remain cytosolic. We show that these coiled-coil domains interact with each other: mistargeted Mfn2-NT or Mfn2-IYFFT localize to mitochondria if co-expressed with Mfn2-TMCT. This relocalization is abolished when the coiled-coil domain is deleted in any of the co-transfected molecules. We also found that Mfn2 can cluster active mitochondria in the perinuclear region independently of the cytoskeleton, bring mitochondrial membranes into close contact and modify mitochondrial structure, without disturbing the integrity of the inner and outer membrane.}, }
@article {pmid11950614, year = {2002}, author = {Zerges, W}, title = {Does complexity constrain organelle evolution?.}, journal = {Trends in plant science}, volume = {7}, number = {4}, pages = {175-182}, doi = {10.1016/s1360-1385(02)02233-1}, pmid = {11950614}, issn = {1360-1385}, mesh = {*Biological Evolution ; Chloroplasts/genetics/physiology ; Light ; Mitochondria/genetics/physiology ; Organelles/genetics/*physiology ; Oxidation-Reduction ; Photosynthesis/genetics/*physiology ; Photosynthetic Reaction Center Complex Proteins/genetics/*metabolism ; *Selection, Genetic ; }, abstract = {The evolution of eukaryotes was punctuated by invasions of the bacteria that have evolved to mitochondria and plastids. These bacterial endosymbionts founded major eukaryotic lineages by enabling them to carry out aerobic respiration and oxygenic photosynthesis. Yet, having evolved as free-living organisms, they were at first poorly adapted organelles. Although mitochondria and plastids have integrated within the physiology of eukaryotic cells, this integration has probably been constrained by the high level of complexity of their bacterial ancestors and the inability of gradual evolutionary processes to drastically alter complex systems. Here, I review complex processes that directly involve translation of plastid mRNAs and how they could constrain transfer to the nucleus of the genes encoding them.}, }
@article {pmid11948211, year = {2001}, author = {Ingman, M and Gyllensten, U}, title = {Analysis of the complete human mtDNA genome: methodology and inferences for human evolution.}, journal = {The Journal of heredity}, volume = {92}, number = {6}, pages = {454-461}, doi = {10.1093/jhered/92.6.454}, pmid = {11948211}, issn = {0022-1503}, mesh = {Biological Evolution ; DNA, Mitochondrial/*genetics ; *Genome, Human ; Humans ; Mitochondria/*genetics ; Polymorphism, Restriction Fragment Length ; Selection, Genetic ; *Sequence Analysis, DNA ; }, abstract = {The analysis of mitochondrial DNA (mtDNA) sequences has been a potent tool in our understanding of human evolution. However, almost all studies of human evolution based on mtDNA sequencing have focused on the control region, which constitutes less than 7% of the mitochondrial genome. The rapid development of technology for automated DNA sequencing has made it possible to study the complete mtDNA genomes in large numbers of individuals, opening the field of mitochondrial population genomics. Here we describe a suitable methodology for determining the complete human mitochondrial sequence and the global mtDNA diversity in humans. Also, we discuss the implications of the results with respect to the different hypotheses for the evolution of modern humans.}, }
@article {pmid11943462, year = {2002}, author = {O'Brien, TW}, title = {Evolution of a protein-rich mitochondrial ribosome: implications for human genetic disease.}, journal = {Gene}, volume = {286}, number = {1}, pages = {73-79}, doi = {10.1016/s0378-1119(01)00808-3}, pmid = {11943462}, issn = {0378-1119}, mesh = {Animals ; Binding Sites ; *Evolution, Molecular ; GTP-Binding Proteins/genetics/metabolism ; Genetic Diseases, Inborn/genetics ; Guanosine Triphosphate/metabolism ; Humans ; Mitochondria/*genetics ; Ribosomal Proteins/*genetics/metabolism ; Ribosomes/*genetics ; }, abstract = {Mitochondrial ribosomes comprise the most diverse group of ribosomes known. The mammalian mitochondrial ribosomes (55S) differ unexpectedly from bacterial (70S) and cytoplasmic ribosomes (80S), as well as other kinds of mitochondrial ribosomes. The bovine mitochondrial ribosome has been developed as a model system for the study of human mitochondrial ribosomes to address several questions related to the structure, function, biosynthesis and evolution of these interesting ribosomes. Bovine mitochondrial ribosomal proteins (MRPs) from each subunit have been identified and characterized with respect to individuality and electrophoretic properties, amino acid sequence, topographic disposition, RNA binding properties, evolutionary relationships and reaction with affinity probes of ribosomal functional domains. Several distinctive properties of these ribosomes are being elucidated, including their antibiotic susceptibility and composition. Mammalian mitochondrial ribosomes lack several of the major RNA stem structures of bacterial ribosomes but they contain a correspondingly higher protein content (as many as 80 proteins), suggesting a model where proteins have replaced RNA structural elements during the evolution of these ribosomes. Despite their lower RNA content they are physically larger than bacterial ribosomes, because of the 'extra' proteins they contain. The extra proteins in mitochondrial ribosomes are 'new' in the sense that they are not homologous to proteins in bacterial or cytoplasmic ribosomes. Some of the new proteins appear to be bifunctional. All of the mammalian MRPs are encoded in nuclear genes (a separate set from those encoding cytoplasmic ribosomal proteins) which are evolving more rapidly than those encoding cytoplasmic ribosomal proteins. The MRPs are imported into mitochondria where they assemble coordinately with mitochondrially transcribed rRNAs into ribosomes that are responsible for translating the 13 mRNAs for essential proteins of the oxidative phosphorylation system. Interest is growing in the structure, organization, chromosomal location and expression of genes for human MRPs. Proteins which are essential for mitoribosome function are candidates for involvement in human genetic disease.}, }
@article {pmid11943453, year = {2002}, author = {}, title = {Mitochondria: evolution, genomics, homeostasis and pathology. Papers presented at an international meeting. May 12-20, 2001. Selva di Fasano (BR Italy).}, journal = {Gene}, volume = {286}, number = {1}, pages = {1-154}, pmid = {11943453}, issn = {0378-1119}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Homeostasis ; Humans ; Mitochondria/genetics/*physiology ; }, }
@article {pmid11940519, year = {2002}, author = {Brett, CL and Wei, Y and Donowitz, M and Rao, R}, title = {Human Na(+)/H(+) exchanger isoform 6 is found in recycling endosomes of cells, not in mitochondria.}, journal = {American journal of physiology. Cell physiology}, volume = {282}, number = {5}, pages = {C1031-41}, doi = {10.1152/ajpcell.00420.2001}, pmid = {11940519}, issn = {0363-6143}, support = {P01-DK-44484/DK/NIDDK NIH HHS/United States ; R01-DK-26523/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Biomarkers ; CHO Cells ; Cell Fractionation ; Cell Line ; Cell Membrane/*metabolism ; Cricetinae ; Endosomes/*metabolism ; Golgi Apparatus/metabolism ; Green Fluorescent Proteins ; Humans ; Luminescent Proteins/metabolism ; Membrane Proteins/*metabolism ; Microscopy, Fluorescence ; Mitochondria/*metabolism ; Opossums ; Phylogeny ; Protein Isoforms ; Receptors, Transferrin/metabolism ; Recombinant Fusion Proteins/metabolism ; Sodium-Hydrogen Exchangers/*metabolism ; }, abstract = {Since the discovery of the first intracellular Na(+)/H(+) exchanger in yeast, Nhx1, multiple homologs have been cloned and characterized in plants. Together, studies in these organisms demonstrate that Nhx1 is located in the prevacuolar/vacuolar compartment of cells where it sequesters Na(+) into the vacuole, regulates intravesicular pH, and contributes to vacuolar biogenesis. In contrast, the human homolog of Nhx1, Na(+)/H(+) exchanger isoform 6 (NHE6), has been reported to localize to mitochondria when transiently expressed as a fusion with green fluorescent protein. This result warrants reevaluation because it conflicts with predictions from phylogenetic analyses. Here we demonstrate that when epitope-tagged NHE6 is transiently expressed in cultured mammalian cells, it does not colocalize with mitochondrial markers. It also does not colocalize with markers of the lysosome, late endosome, trans-Golgi network, or Golgi cisternae. Rather, NHE6 is distributed in recycling compartments and transiently appears on the plasma membrane. These results suggest that, like its homologs in yeast and plants, NHE6 is an endosomal Na(+)/H(+) exchanger that may regulate intravesicular pH and volume and contribute to lysosomal biogenesis.}, }
@article {pmid11937687, year = {2002}, author = {Ikehara, K}, title = {Origins of gene, genetic code, protein and life: comprehensive view of life systems from a GNC-SNS primitive genetic code hypothesis.}, journal = {Journal of biosciences}, volume = {27}, number = {2}, pages = {165-186}, pmid = {11937687}, issn = {0250-5991}, mesh = {Amino Acids/metabolism ; Animals ; Biological Evolution ; Evolution, Molecular ; Exons/genetics ; *Genes ; *Genetic Code ; Mitochondria/genetics ; Models, Genetic ; *Origin of Life ; Protein Structure, Secondary ; Proteins/*chemistry/genetics ; RNA/genetics/metabolism ; }, abstract = {We have investigated the origin of genes, the genetic code, proteins and life using six indices (hydropathy, alpha-helix, beta-sheet and beta-turn formabilities, acidic amino acid content and basic amino acid content) necessary for appropriate three-dimensional structure formation of globular proteins. From the analysis of microbial genes, we have concluded that newly-born genes are products of nonstop frames (NSF) on antisense strands of microbial GC-rich genes [GC-NSF(a)] and from SNS repeating sequences [(SNS)n] similar to the GC-NSF(a) (S and N mean G or C and either of four bases, respectively). We have also proposed that the universal genetic code used by most organisms on the earth presently could be derived from a GNC-SNS primitive genetic code. We have further presented the [GADV]-protein world hypothesis of the origin of life as well as a hypothesis of protein production, suggesting that proteins were originally produced by random peptide formation of amino acids restricted in specific amino acid compositions termed as GNC-, SNS- and GC-NSF(a)-0th order structures of proteins. The [GADV]-protein world hypothesis is primarily derived from the GNC-primitive genetic code hypothesis. It is also expected that basic properties of extant genes and proteins could be revealed by considerations based on the scenario with four stages.}, }
@article {pmid11937507, year = {2002}, author = {Yadava, N and Potluri, P and Smith, EN and Bisevac, A and Scheffler, IE}, title = {Species-specific and mutant MWFE proteins. Their effect on the assembly of a functional mammalian mitochondrial complex I.}, journal = {The Journal of biological chemistry}, volume = {277}, number = {24}, pages = {21221-21230}, doi = {10.1074/jbc.M202016200}, pmid = {11937507}, issn = {0021-9258}, support = {GM59909/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Amino Acid Sequence ; Animals ; Blotting, Northern ; Blotting, Western ; CHO Cells ; Cricetinae ; DNA, Complementary/metabolism ; Electron Transport Complex I ; Electrophoresis, Polyacrylamide Gel ; Gene Deletion ; Genes, Dominant ; Genetic Complementation Test ; Humans ; Immunohistochemistry ; Membrane Proteins/*chemistry ; Mice ; Mitochondria/metabolism ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Mutation ; NADH Dehydrogenase ; Oxygen Consumption ; Peptides/chemistry ; Plasmids/metabolism ; RNA, Messenger/metabolism ; Species Specificity ; Time Factors ; }, abstract = {The MWFE protein (70 amino acids) is highly conserved in evolution, but the human protein (80% identical to hamster) does not complement a null mutation in Chinese hamster cells. We have identified a small protein segment where significant differences exist between rodents and primates, illustrating very specifically the need for compatibility of the nuclear and mitochondrial genomes in the assembly of complex I. The segment between amino acids 39 and 46 appears to be critical for species-specific compatibility. Amino acid substitutions in this region were tested that caused a reduction of activity of the hamster protein or converted the inactive human protein into a partially active one. Such mutations could be useful in making mice with partial complex I activity as models for mitochondrial diseases. Their potential as dominant negative mutants was explored. More deleterious mutations in the NDUFA1 gene were also characterized. A conservative substitution, R50K, or a short C-terminal deletion makes the protein completely inactive. In the absence of MWFE, no high molecular weight complex was detectable by Blue Native-gel electrophoresis. The MWFE protein itself is unstable in the absence of assembled mitochondrially encoded integral membrane proteins of complex I.}, }
@article {pmid11932440, year = {2002}, author = {Benito, B and Garciadeblás, B and Rodrı Guez-Navarro, A}, title = {Potassium- or sodium-efflux ATPase, a key enzyme in the evolution of fungi.}, journal = {Microbiology (Reading, England)}, volume = {148}, number = {Pt 4}, pages = {933-941}, doi = {10.1099/00221287-148-4-933}, pmid = {11932440}, issn = {1350-0872}, mesh = {Adenosine Triphosphatases/*genetics ; Cation Transport Proteins/*genetics ; *Evolution, Molecular ; Fungi/classification/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Potassium/metabolism ; Saccharomyces cerevisiae/enzymology/genetics ; Sodium/metabolism ; }, abstract = {Potassium is the most abundant cation in cells. Therefore, plant-associated fungi and intracellular parasites are permanently or circumstantially exposed to high K(+) and must avoid excessive K(+) accumulation activating K(+) efflux systems. Because high K(+) and high pH are compatible in natural environments, free-living organisms cannot keep a permanent transmembrane DeltapH and cannot rely only on K(+)/H(+) antiporters, as do mitochondria. This study shows that the Schizosaccharomyces pombe CTA3 is a K(+)-efflux ATPase, and that other fungi are furnished with Na(+)-efflux ATPases, which also pump Na(+). All these fungal ATPases, including those pumping only Na(+), form a phylogenetic group, IID or ENA, among P-type ATPases. By searching in databases and partial cloning of ENA genes in species of Zygomycetes and Basidiomycetes, the authors conclude that probably all fungi have these genes. This study indicates that fungal K(+)- or Na(+)-ATPases evolved from an ancestral K(+)-ATPase, through processes of gene duplication. In yeast hemiascomycetes these duplications have occurred recently and produced bifunctional ATPases, whereas in Neurospora, and probably in other euascomycetes, they occurred earlier in evolution and produced specialized ATPases. In Schizosaccharomyces, adaptation to Na(+) did not involve the duplication of the K(+)-ATPase and thus it retains an enzyme which is probably close to the original one. The parasites Leishmania and Trypanosoma have ATPases phylogenetically related to fungal K(+)-ATPases, which are probably functional homologues of the fungal enzymes.}, }
@article {pmid11931142, year = {2002}, author = {Cavalier-Smith, T}, title = {The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {52}, number = {Pt 2}, pages = {297-354}, doi = {10.1099/00207713-52-2-297}, pmid = {11931142}, issn = {1466-5026}, mesh = {Animals ; *Biological Evolution ; Eukaryota/*classification/physiology ; Eukaryotic Cells/classification/physiology ; Phagocytosis ; Phylogeny ; }, abstract = {Eukaryotes and archaebacteria form the clade neomura and are sisters, as shown decisively by genes fragmented only in archaebacteria and by many sequence trees. This sisterhood refutes all theories that eukaryotes originated by merging an archaebacterium and an alpha-proteobacterium, which also fail to account for numerous features shared specifically by eukaryotes and actinobacteria. I revise the phagotrophy theory of eukaryote origins by arguing that the essentially autogenous origins of most eukaryotic cell properties (phagotrophy, endomembrane system including peroxisomes, cytoskeleton, nucleus, mitosis and sex) partially overlapped and were synergistic with the symbiogenetic origin of mitochondria from an alpha-proteobacterium. These radical innovations occurred in a derivative of the neomuran common ancestor, which itself had evolved immediately prior to the divergence of eukaryotes and archaebacteria by drastic alterations to its eubacterial ancestor, an actinobacterial posibacterium able to make sterols, by replacing murein peptidoglycan by N-linked glycoproteins and a multitude of other shared neomuran novelties. The conversion of the rigid neomuran wall into a flexible surface coat and the associated origin of phagotrophy were instrumental in the evolution of the endomembrane system, cytoskeleton, nuclear organization and division and sexual life-cycles. Cilia evolved not by symbiogenesis but by autogenous specialization of the cytoskeleton. I argue that the ancestral eukaryote was uniciliate with a single centriole (unikont) and a simple centrosomal cone of microtubules, as in the aerobic amoebozoan zooflagellate Phalansterium. I infer the root of the eukaryote tree at the divergence between opisthokonts (animals, Choanozoa, fungi) with a single posterior cilium and all other eukaryotes, designated 'anterokonts' because of the ancestral presence of an anterior cilium. Anterokonts comprise the Amoebozoa, which may be ancestrally unikont, and a vast ancestrally biciliate clade, named 'bikonts'. The apparently conflicting rRNA and protein trees can be reconciled with each other and this ultrastructural interpretation if long-branch distortions, some mechanistically explicable, are allowed for. Bikonts comprise two groups: corticoflagellates, with a younger anterior cilium, no centrosomal cone and ancestrally a semi-rigid cell cortex with a microtubular band on either side of the posterior mature centriole; and Rhizaria [a new infrakingdom comprising Cercozoa (now including Ascetosporea classis nov.), Retaria phylum nov., Heliozoa and Apusozoa phylum nov.], having a centrosomal cone or radiating microtubules and two microtubular roots and a soft surface, frequently with reticulopodia. Corticoflagellates comprise photokaryotes (Plantae and chromalveolates, both ancestrally with cortical alveoli) and Excavata (a new protozoan infrakingdom comprising Loukozoa, Discicristata and Archezoa, ancestrally with three microtubular roots). All basal eukaryotic radiations were of mitochondrial aerobes; hydrogenosomes evolved polyphyletically from mitochondria long afterwards, the persistence of their double envelope long after their genomes disappeared being a striking instance of membrane heredity. I discuss the relationship between the 13 protozoan phyla recognized here and revise higher protozoan classification by updating as subkingdoms Lankester's 1878 division of Protozoa into Corticata (Excavata, Alveolata; with prominent cortical microtubules and ancestrally localized cytostome--the Parabasalia probably secondarily internalized the cytoskeleton) and Gymnomyxa [infrakingdoms Sarcomastigota (Choanozoa, Amoebozoa) and Rhizaria; both ancestrally with a non-cortical cytoskeleton of radiating singlet microtubules and a relatively soft cell surface with diffused feeding]. As the eukaryote root almost certainly lies within Gymnomyxa, probably among the Sarcomastigota, Corticata are derived. Following the single symbiogenetic origin of chloroplasts in a corticoflagellate host with cortical alveoli, this ancestral plant radiated rapidly into glaucophytes, green plants and red algae. Secondary symbiogeneses subsequently transferred plastids laterally into different hosts, making yet more complex cell chimaeras--probably only thrice: from a red alga to the corticoflagellate ancestor of chromalveolates (Chromista plus Alveolata), from green algae to a secondarily uniciliate cercozoan to form chlorarachneans and independently to a biciliate excavate to yield photosynthetic euglenoids. Tertiary symbiogenesis involving eukaryotic algal symbionts replaced peridinin-containing plastids in two or three dinoflagellate lineages, but yielded no major novel groups. The origin and well-resolved primary bifurcation of eukaryotes probably occurred in the Cryogenian Period, about 850 million years ago, much more recently than suggested by unwarranted backward extrapolations of molecular 'clocks' or dubious interpretations as 'eukaryotic' of earlier large microbial fossils or still more ancient steranes. The origin of chloroplasts and the symbiogenetic incorporation of a red alga into a corticoflagellate to create chromalveolates may both have occurred in a big bang after the Varangerian snowball Earth melted about 580 million years ago, thereby stimulating the ensuing Cambrian explosion of animals and protists in the form of simultaneous, poorly resolved opisthokont and anterokont radiations.}, }
@article {pmid11929988, year = {2002}, author = {Walden, WE}, title = {From bacteria to mitochondria: aconitase yields surprises.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {7}, pages = {4138-4140}, pmid = {11929988}, issn = {0027-8424}, mesh = {Aconitate Hydratase/genetics/*physiology ; Animals ; Bacteroides fragilis/*enzymology ; Biological Evolution ; *Citric Acid Cycle ; Humans ; Mitochondria/*enzymology ; }, }
@article {pmid11919680, year = {2002}, author = {Mollier, P and Hoffmann, B and Debast, C and Small, I}, title = {The gene encoding Arabidopsis thaliana mitochondrial ribosomal protein S13 is a recent duplication of the gene encoding plastid S13.}, journal = {Current genetics}, volume = {40}, number = {6}, pages = {405-409}, doi = {10.1007/s00294-002-0271-5}, pmid = {11919680}, issn = {0172-8083}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics ; Chloroplasts/*genetics ; Evolution, Molecular ; Exons/genetics ; *Gene Duplication ; Genes, Plant/genetics ; Green Fluorescent Proteins ; Introns/genetics ; Luminescent Proteins/genetics/metabolism ; Microscopy, Confocal ; Mitochondrial Proteins/chemistry/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/genetics/metabolism ; Protein Transport ; Ribosomal Proteins/chemistry/*genetics/metabolism ; Sequence Alignment ; Nicotiana/genetics ; }, abstract = {A gene encoding mitochondrial S13 is generally present in the mitochondrial genome of higher plants, but is lacking from the Arabidopsis thaliana mitochondrial genome. Previous research has failed to identify a nuclear gene capable of encoding a mitochondrial S13 protein or the protein itself. Doubts have even been raised as to whether a mitochondrial S13 exists in Arabidopsis. Here, we show that the nuclear gene encoding the plastid S13 has been partially duplicated in A. thaliana, such that the copy has lost the exon encoding the plastid transit peptide and acquired a sequence capable of encoding a mitochondrial targeting sequence. The two S13 sequences were fused to green fluorescent protein and shown to be targeted to plastids and mitochondria respectively.}, }
@article {pmid11919296, year = {2002}, author = {Schmitz, J and Ohme, M and Zischler, H}, title = {The complete mitochondrial sequence of Tarsius bancanus: evidence for an extensive nucleotide compositional plasticity of primate mitochondrial DNA.}, journal = {Molecular biology and evolution}, volume = {19}, number = {4}, pages = {544-553}, doi = {10.1093/oxfordjournals.molbev.a004110}, pmid = {11919296}, issn = {0737-4038}, mesh = {Animals ; Biological Evolution ; Codon/genetics ; DNA Primers/chemistry ; DNA, Mitochondrial/*genetics ; Mitochondria/*genetics ; Mutation/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Tarsiidae/*genetics ; }, abstract = {Inconsistencies between phylogenetic interpretations obtained from independent sources of molecular data occasionally hamper the recovery of the true evolutionary history of certain taxa. One prominent example concerns the primate infraordinal relationships. Phylogenetic analyses based on nuclear DNA sequences traditionally represent Tarsius as a sister group to anthropoids. In contrast, mitochondrial DNA (mtDNA) data only marginally support this affiliation or even exclude Tarsius from primates. Two possible scenarios might cause this conflict: a period of adaptive molecular evolution or a shift in the nucleotide composition of higher primate mtDNAs through directional mutation pressure. To test these options, the entire mt genome of Tarsius bancanus was sequenced and compared with mtDNA of representatives of all major primate groups and mammals. Phylogenetic reconstructions at both the amino acid (AA) and DNA level of the protein-coding genes led to faulty tree topologies depending on the algorithms used for reconstruction. We propose that these artifactual affiliations rather reflect the nucleotide compositional similarity than phylogenetic relatedness and favor the directional mutation pressure hypothesis because: (1) the overall nucleotide composition changes dramatically on the lineage leading to higher primates at both silent and nonsilent sites, and (2) a highly significant correlation exists between codon usage and the nucleotide composition at the third, silent codon position. Comparisons of mt genes with mt pseudogenes that presumably transferred to the nucleus before the directional mutation pressure took place indicate that the ancestral DNA composition is retained in the relatively fossilized mtDNA-like sequences, and that the directed acceleration of the substitution rate in higher primates is restricted to mtDNA.}, }
@article {pmid11919286, year = {2002}, author = {Dowling, TE and Martasian, DP and Jeffery, WR}, title = {Evidence for multiple genetic forms with similar eyeless phenotypes in the blind cavefish, Astyanax mexicanus.}, journal = {Molecular biology and evolution}, volume = {19}, number = {4}, pages = {446-455}, doi = {10.1093/oxfordjournals.molbev.a004100}, pmid = {11919286}, issn = {0737-4038}, mesh = {Animals ; Blindness/enzymology/*genetics ; DNA Primers/chemistry ; DNA, Mitochondrial/genetics ; Fishes/*genetics ; Gene Expression Regulation, Developmental/physiology ; Gene Expression Regulation, Enzymologic/*physiology ; Haplotypes ; Mitochondria/*enzymology ; NADH Dehydrogenase/*genetics/metabolism ; *Phenotype ; Polymerase Chain Reaction ; Polymorphism, Single-Stranded Conformational ; Thoracic Vertebrae ; }, abstract = {A diverse group of animals has adapted to caves and lost their eyes and pigmentation, but little is known about how these animals and their striking phenotypes have evolved. The teleost Astyanax mexicanus consists of an eyed epigean form (surface fish) and at least 29 different populations of eyeless hypogean forms (cavefish). Current alternative hypotheses suggest that adaptation to cave environments may have occurred either once or multiple times during the evolutionary history of this species. If the latter is true, the unique phenotypes of different cave-dwelling populations may result from convergence of form, and different genetic changes and developmental processes may have similar morphological consequences. Here we report an analysis of variation in the mitochondrial NADH dehydrogenase 2 (ND2) gene among different surface fish and cavefish populations. The results identify a minimum of two genetically distinctive cavefish lineages with similar eyeless phenotypes. The distinction between these divergent forms is supported by differences in the number of rib-bearing thoracic vertebrae in their axial skeletons. The geographic distribution of ND2 haplotypes is consistent with roles for multiple founder events and introgressive hybridization in the evolution of cave-related phenotypes. The existence of multiple genetic lineages makes A. mexicanus an excellent model to study convergence and the genes and developmental pathways involved in the evolution of the eye and pigment degeneration.}, }
@article {pmid11917078, year = {2002}, author = {Kabeya, Y and Hashimoto, K and Sato, N}, title = {Identification and characterization of two phage-type RNA polymerase cDNAs in the moss Physcomitrella patens: implication of recent evolution of nuclear-encoded RNA polymerase of plastids in plants.}, journal = {Plant &amp; cell physiology}, volume = {43}, number = {3}, pages = {245-255}, doi = {10.1093/pcp/pcf041}, pmid = {11917078}, issn = {0032-0781}, mesh = {Amino Acid Sequence ; Bryopsida/*enzymology/genetics ; Cell Nucleus/enzymology/genetics ; Cloning, Molecular ; DNA, Complementary/chemistry/genetics/isolation &amp; purification ; DNA-Directed RNA Polymerases/*genetics/metabolism ; Evolution, Molecular ; Gene Duplication ; Green Fluorescent Proteins ; Isoenzymes/genetics/metabolism ; Luminescent Proteins/genetics/metabolism ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Plants/*enzymology/genetics ; Plastids/*enzymology/genetics ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Sequence Homology, Amino Acid ; T-Phages/enzymology ; }, abstract = {We isolated two cDNAs for the genes PpRPOT1 and PpRPOT2 that encode phage-type RNA polymerases (RPOTs) from Physcomitrella patens. Transcriptional activity of the encoded proteins was demonstrated by an in vitro transcription assay. Transiently expressed RPOT green fluorescent protein fusion proteins were both targeted to mitochondria. These results suggest that both PpRPOT1 and PpRPOT2 proteins function as mitochondrial RNA polymerases. Detailed phylogenetic analysis using neighbor-joining and maximum-likelihood methods with both DNA and protein sequences indicated that the two genes of P. patens form a sister group to all flowering plant genes. This suggests that the gene duplication leading to the production of plastid-type isozymes occurred after the separation of vascular plant lineage from bryophyte lineage. We therefore suggest that the generation of nuclear-encoded RNA polymerase of chloroplast is a rather recent event during the evolution of land plants.}, }
@article {pmid11915939, year = {2002}, author = {Thomson, M}, title = {Evidence of undiscovered cell regulatory mechanisms: phosphoproteins and protein kinases in mitochondria.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {59}, number = {2}, pages = {213-219}, doi = {10.1007/s00018-002-8417-7}, pmid = {11915939}, issn = {1420-682X}, mesh = {Animals ; Apoptosis ; Biological Evolution ; Cell Respiration ; Cyclic AMP-Dependent Protein Kinases/metabolism ; Mitochondria/*enzymology/metabolism ; Mitochondrial Proteins/genetics/*metabolism ; Models, Biological ; Monomeric GTP-Binding Proteins/physiology ; Phosphoproteins/*metabolism ; Protein Kinases/metabolism ; Steroids/biosynthesis ; }, abstract = {The finding that mitochondria contain substrates for protein kinases lead to the discovery that protein kinases are located in the mitochondria of certain tissues and species. These include pyruvate dyhydrogenase kinase, branched-chain alpha-ketoacid dehydrogenase kinase, protein kinase A, protein kinase Cdelta, stress-activated kinase and A-Raf as well as unidentified kinases. Recent evidence suggests that mitochondrial protein kinases may be involved in physiological processes such as apoptosis and steroidogenesis. Additionally, the novel finding of low-molecular-weight GTP-binding proteins in mitochondria suggests the possibility that these may interact with mitochondrial protein kinases to regulate the activity of mitochondrial effector proteins. The fact that there are components of cellular regulatory systems in mitochondria indicates the exciting possibility of undiscovered systems regulating mitochondrial physiology.}, }
@article {pmid11914385, year = {2002}, author = {Egginton, S and Skilbeck, C and Hoofd, L and Calvo, J and Johnston, IA}, title = {Peripheral oxygen transport in skeletal muscle of Antarctic and sub-Antarctic notothenioid fish.}, journal = {The Journal of experimental biology}, volume = {205}, number = {Pt 6}, pages = {769-779}, doi = {10.1242/jeb.205.6.769}, pmid = {11914385}, issn = {0022-0949}, mesh = {Animals ; Antarctic Regions ; Capillaries ; Diffusion ; Mathematics ; Mediterranean Sea ; Microscopy, Electron ; Mitochondria, Muscle/metabolism ; Models, Biological ; Muscle, Skeletal/anatomy &amp; histology/blood supply/*metabolism ; Oxygen/analysis ; *Oxygen Consumption ; Perciformes/*metabolism ; Temperature ; }, abstract = {Transcellular oxygen flux was modelled mathematically in the aerobic skeletal muscles of perciform fish species living at widely different temperatures (Antarctica, sub-Antarctica and the Mediterranean Sea). Using structural data derived from stereological analysis of electron micrographs, mean fibre P(O(2)) was calculated on the basis of temperature-corrected rates of mitochondrial respiration and oxygen diffusion. The mean muscle fibre diameter (MFD) among Antarctic notothenioids was in the range 17-61 microm and mitochondrial volume density, Vv(mit,f), was 0.27-0.53, but capillary-to-fibre ratio varied only between 1.2 and 1.5. For a mean capillary P(O(2)) of 6 kPa, the model predicted a mean tissue P(O(2)) in the range 0.7-5.8 kPa at the estimated maximum aerobic capacity (M(O(2)max)). The lowest levels of tissue oxygenation were found in the pectoral muscle fibres of the icefish Chaenocephalus aceratus, which lacks the respiratory pigments haemoglobin and myoglobin. Red-blooded notothenioids found in the sub-Antarctic had a similar muscle fine structure to those caught south of the Antarctic Convergence, with an MFD of 20-41 microm and Vv(mit,f) of 0.27-0.33, resulting in an estimated mean P(O(2)) of 4-5 kPa at M(O(2)max). Mean tissue P(O(2)) in the sub-Antarctic icefish Champsocephalus esox, with greater MFD and Vv(mit,f), 56 microm and 0.51, respectively, was calculated to exceed 1 kPa at winter temperatures (4 degrees C), although oxidative metabolism was predicted to be impaired at the summer maximum of 10 degrees C. At the high end of the thermal range, related perciform species from the Mediterranean had a negligible drop in intracellular P(O(2)) across their small-diameter fibres, to a minimum of 5.4 kPa, comparable with that predicted for Trematomus newnesi from the Antarctic (5.6 kPa) with a similar MFD. These data suggest that, within a single phylogenetic group, integrative structural adaptations potentially enable a similar degree of tissue oxygenation over a 20 degrees C range of environmental temperature in the red-blooded notothenioids, and that this is compromised by the lack of respiratory pigments in the icefishes. The mean capillary radius was 1.5 times greater in the two icefish than in the other notothenioids, and the model simulations indicate that the evolution of wide-bore capillaries is essential to maintain tissue oxygenation in the absence of respiratory pigments.}, }
@article {pmid11912232, year = {2002}, author = {Suárez, MF and Avila, C and Gallardo, F and Cantón, FR and García-Gutiérrez, A and Claros, MG and Cánovas, FM}, title = {Molecular and enzymatic analysis of ammonium assimilation in woody plants.}, journal = {Journal of experimental botany}, volume = {53}, number = {370}, pages = {891-904}, doi = {10.1093/jexbot/53.370.891}, pmid = {11912232}, issn = {0022-0957}, mesh = {Amino Acid Oxidoreductases/genetics/metabolism ; Carbon/metabolism ; Cycadopsida/enzymology/genetics ; Enzymes/*genetics/metabolism ; Gene Expression Regulation, Plant ; Glutamate-Ammonia Ligase/genetics/metabolism ; Isocitrate Dehydrogenase/genetics/metabolism ; Magnoliopsida/enzymology/genetics ; Mitochondria/enzymology ; Nitrogen/*metabolism ; Phylogeny ; Plants, Genetically Modified ; Quaternary Ammonium Compounds/*metabolism ; Trees/enzymology/*genetics ; }, abstract = {Ammonium is assimilated into amino acids through the sequential action of glutamine synthetase (GS) and glutamate synthase (GOGAT) enzymes. This metabolic pathway is driven by energy, reducing power and requires the net supply of 2-oxoglutarate that can be provided by the reaction catalysed by isocitrate dehydrogenase (IDH). Most studies on the biochemistry and molecular biology of N-assimilating enzymes have been carried out on annual plant species and the available information on woody models is far more limited. This is in spite of their economic and ecological importance and the fact that nitrogen is a common limiting factor for tree growth. GS, GOGAT and IDH enzymes have been purified from several woody species and their kinetic and molecular properties determined. A number of cDNA clones have also been isolated and characterized. Although the enzymes are remarkably well conserved along the evolutionary scale, major differences have been found in their compartmentation within the cell between angiosperms and conifers, suggesting possible adaptations to specific functional roles. The analysis of the gene expression patterns in a variety of biological situations such as changes in N nutrition, development, biotic or abiotic stresses and senescence, suggest that cytosolic GS plays a central and pivotal role in ammonium assimilation and metabolism in woody plants. The modification of N assimilation efficiency has been recently approached in trees by overexpression of a cytosolic pine GS in poplar. The results obtained, suggest that an increase in cytosolic GS might lead to a global effect on the synthesis of nitrogenous compounds in the leaves, with enhanced vegetative growth of transgenic trees. All these data suggest that manipulation of cytosolic GS may have consequences for plant growth and biomass production.}, }
@article {pmid11912229, year = {2002}, author = {Weber, A and Flügge, UI}, title = {Interaction of cytosolic and plastidic nitrogen metabolism in plants.}, journal = {Journal of experimental botany}, volume = {53}, number = {370}, pages = {865-874}, doi = {10.1093/jexbot/53.370.865}, pmid = {11912229}, issn = {0022-0957}, mesh = {Amino Acid Oxidoreductases/metabolism ; Ammonia/*metabolism ; Biological Transport ; Cycadopsida/metabolism ; Cytosol/*metabolism ; Dicarboxylic Acid Transporters/genetics/metabolism ; Gene Expression Regulation, Plant ; Glucose-6-Phosphate/metabolism ; Glutamate-Ammonia Ligase/metabolism ; Glutamic Acid/metabolism ; Glutamine/metabolism ; Ketoglutaric Acids/metabolism ; Models, Biological ; Nitrogen/*metabolism ; Phylogeny ; Plants/classification/*metabolism ; Plastids/*metabolism ; }, abstract = {In angiosperms, the assimilation of ammonia resulting from nitrate reduction and from photorespiration depends on the operation of the plastidic GS/GOGAT cycle. The precursor for ammonia assimilation, 2-oxoglutarate, is synthesized in the mitochondria and in the cytosol. It is imported into the plastid by a 2-oxoglutarate/malate translocator (DiT1). In turn, the product of ammonia assimilation, glutamate, is exported from the plastids by a glutamate/malate translocator (DiT2). These transport processes link plastidic and cytosolic nitrogen metabolism and are essential for plant metabolism. DiT1 was purified to homogeneity from spinach chloroplast envelope membranes and identified as a protein with an apparent molecular mass of 45 kDa. Peptide sequences were obtained from the protein and the corresponding cDNA was cloned. The function of the DiT1 protein and its substrate specificity were confirmed by expression of the cDNA in yeast cells and functional reconstitution of the recombinant protein into liposomes. Recent advances in the molecular cloning of DiT2 and in the analysis of the in vivo function of DiT1 by antisense repression in transgenic tobacco plants will be discussed. In non-green tissues, the reducing equivalents required for glutamate formation by NADH-GOGAT are supplied by the oxidative pentose phosphate pathway. Glucose 6-phosphate, the immediate precursor of the oxidative pentose phosphate pathway is generated in the cytosol and imported into the plastids by the plastidic glucose 6-phosphate/phosphate translocator.}, }
@article {pmid11906012, year = {2001}, author = {Furuta, T and Kikuchi, T and Miyadera, H and Yoshikawa, Y}, title = {Pneumocystis carinii infection in red-bellied tamarins and cynomolgus monkeys, and the characterization of the mitochondrial large subunit ribosomal RNA gene of Pneumocystis carinii.}, journal = {The Journal of eukaryotic microbiology}, volume = {Suppl}, number = {}, pages = {107S-108S}, doi = {10.1111/j.1550-7408.2001.tb00472.x}, pmid = {11906012}, issn = {1066-5234}, mesh = {Animals ; Cats ; DNA, Fungal/analysis/isolation &amp; purification ; Dogs ; Genes, rRNA/*genetics ; Humans ; Lung/microbiology ; *Macaca fascicularis ; Mice ; Mitochondria/*genetics ; Monkey Diseases/epidemiology/*microbiology ; Phylogeny ; Pneumocystis/genetics/isolation &amp; purification ; Pneumonia, Pneumocystis/epidemiology/microbiology/*veterinary ; Polymerase Chain Reaction ; RNA, Ribosomal/*genetics ; Rats ; *Saguinus ; }, }
@article {pmid11903904, year = {2002}, author = {Goodacre, SL}, title = {Population structure, history and gene flow in a group of closely related land snails: genetic variation in Partula from the Society Islands of the Pacific.}, journal = {Molecular ecology}, volume = {11}, number = {1}, pages = {55-68}, doi = {10.1046/j.0962-1083.2001.01422.x}, pmid = {11903904}, issn = {0962-1083}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry/genetics ; Evolution, Molecular ; Genetic Variation ; *Genetics, Population ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Single-Stranded Conformational ; Polynesia ; RNA, Ribosomal, 16S/chemistry/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Snails/*genetics ; }, abstract = {Previous studies of Partula land snails from the Society Islands, French Polynesia, have shown that populations within species are highly differentiated in terms of their morphology, behaviour, ecology and molecular genetic variation. Despite this level of variability, differences between species are sometimes small, possibly reflecting the fact that reproductive isolation is not always complete and there exists the opportunity for genetic exchange between taxa through hybridization. The present study uses sequence data from a mitochondrial gene to further investigate genetic variation in Society Island Partula. Most populations are found in this study to be highly differentiated, but within individual species there seems to be no simple relationship either between genetic distance and geographical proximity, or between variation in mitochondria and that in allozymes or morphological characteristics. Among species there appears to be no simple correlation between degrees of reproductive isolation and genetic relatedness according to mitochondrial DNA. The results suggest that past events as well as ongoing drift and selection may have been important in affecting patterns of variation. Similarities among species at specific localities suggest that there must have been some genetic exchange in the past, although this may not necessarily reflect ongoing rates of hybridization. The discrepancy between results for different markers probably reflects the differential effects of drift and selection on mitochondrial and nuclear genes.}, }
@article {pmid11903896, year = {2001}, author = {Sota, T and Ishikawa, R and Ujiie, M and Kusumoto, F and Vogler, AP}, title = {Extensive trans-species mitochondrial polymorphisms in the carabid beetles Carabus subgenus Ohomopterus caused by repeated introgressive hybridization.}, journal = {Molecular ecology}, volume = {10}, number = {12}, pages = {2833-2847}, doi = {10.1046/j.1365-294x.2001.t01-1-01404.x}, pmid = {11903896}, issn = {0962-1083}, mesh = {Animals ; Base Sequence ; Coleoptera/anatomy &amp; histology/*genetics ; DNA, Mitochondrial/chemistry/*genetics ; Ecology ; Female ; Hybridization, Genetic/genetics ; Japan ; Male ; Molecular Sequence Data ; NADH Dehydrogenase/chemistry/genetics ; Phylogeny ; Polymerase Chain Reaction ; *Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; Sequence Homology, Nucleic Acid ; }, abstract = {To study the potential importance of introgressive hybridization to the evolutionary diversification of a carabid beetle lineage, we studied intraspecific and trans-species polymorphisms in the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene sequence (1083 bp) in four species of the subgenus Ohomopterus (genus Carabus) in central and eastern Honshu, Japan. Of the four species, C. insulicola is parapatric with the other three, and can hybridize naturally with at least two. This species possesses two haplotypes of remote lineages. We classified ND5 haplotypes using polymerase chain reaction-restriction fragment length polymorphism with TaqI endonuclease for 524 specimens, and sequenced 143 samples. Analysis revealed that each species was polyphyletic in its mitochondrial DNA phylogeny, representing a marked case of trans-species polymorphism. Recent one-way introgression of mitochondria from C. arrowianus nakamurai to C. insulicola, and from C. insulicola to C. esakii, was inferred from the frequency of identical sequences between these species and from direct evidence of hybridization in their contact zones. Other intraspecific polymorphisms in the four species may be due to undetected introgressive hybridization (e.g. C. insulicola to C. maiyasanus) or from stochastic lineage sorting of ancestral polymorphisms. This beetle group has a genital lock-and-key system, with species-specific or subspecies-specific genital morphology that may act as a barrier to hybridization. However, our results demonstrate that introgressive hybridization has occurred multiple times, at least for mitochondria, despite differences among, and stability within, morphological characters that distinguish local populations. Thus, hybridization and introgression could have been key processes in the evolutionary diversification of Ohomopterus.}, }
@article {pmid11903556, year = {2001}, author = {McVean, GA}, title = {What do patterns of genetic variability reveal about mitochondrial recombination?.}, journal = {Heredity}, volume = {87}, number = {Pt 6}, pages = {613-620}, doi = {10.1046/j.1365-2540.2001.00965.x}, pmid = {11903556}, issn = {0018-067X}, mesh = {Evolution, Molecular ; *Genetic Variation ; Linkage Disequilibrium/genetics ; Mitochondria/*genetics ; *Recombination, Genetic ; Statistics as Topic ; }, abstract = {Recent claims that patterns of genetic variability in human mitochondria show evidence for recombination, have provoked considerable argument and much correspondence concerning the quality of the data, the nature of the analyses, and the biological realism of mitochondrial recombination. While the majority of evidence now points towards a lack of effective recombination, at least in humans, the debate has highlighted how difficult the detection of recombination can be in genomes with unusual mutation processes and complex demographic histories. A major difficulty is the lack of consensus about how to measure linkage disequilibrium. I show that measures differ in the way they treat data that are uninformative about recombination, and that when just those pairwise comparisons that are informative about recombination are used, there is agreement between different statistics. In this light, the significant negative correlation between linkage disequilibrium and distance, in at least some of the data sets, is a real pattern that requires explanation. I discuss whether plausible mutational and selective processes can give rise to such a pattern.}, }
@article {pmid11901172, year = {2002}, author = {Zimmermann, KC and Ricci, JE and Droin, NM and Green, DR}, title = {The role of ARK in stress-induced apoptosis in Drosophila cells.}, journal = {The Journal of cell biology}, volume = {156}, number = {6}, pages = {1077-1087}, pmid = {11901172}, issn = {0021-9525}, support = {P01 CA069381/CA/NCI NIH HHS/United States ; R01 AI040646/AI/NIAID NIH HHS/United States ; AI40646/AI/NIAID NIH HHS/United States ; CA69381/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Apoptosis/*genetics ; Apoptotic Protease-Activating Factor 1 ; *Caenorhabditis elegans Proteins ; Calcium-Binding Proteins/genetics/*metabolism ; Caspase Inhibitors ; Caspases/genetics/metabolism ; Cytochrome c Group/drug effects/genetics/metabolism ; Down-Regulation/drug effects/physiology ; *Drosophila Proteins ; Drosophila melanogaster/cytology/genetics/*metabolism ; Enzyme Inhibitors/pharmacology ; Helminth Proteins/genetics/*metabolism ; Inhibitor of Apoptosis Proteins ; Insect Proteins/genetics/metabolism ; Membrane Potentials/drug effects/physiology ; Mitochondria/drug effects/metabolism ; Neuropeptides/genetics/metabolism ; Peptides/genetics/metabolism ; Proteins/genetics/*metabolism ; Proto-Oncogene Proteins c-bcl-2/antagonists &amp; inhibitors/metabolism ; RNA, Double-Stranded/genetics/pharmacology ; Stress, Physiological/genetics/*metabolism/physiopathology ; Ultraviolet Rays ; }, abstract = {The molecular mechanisms of apoptosis are highly conserved throughout evolution. The homologs of genes essential for apoptosis in Caenorhabditis elegans and Drosophila melanogaster have been shown to be important for apoptosis in mammalian systems. Although a homologue for CED-4/apoptotic protease-activating factor (Apaf)-1 has been described in Drosophila, its exact function and the role of the mitochondrial pathway in its activation remain unclear. Here, we used the technique of RNA interference to dissect apoptotic signaling pathways in Drosophila cells. Inhibition of the Drosophila CED-4/Apaf-1-related killer (ARK) homologue resulted in pronounced inhibition of stress-induced apoptosis, whereas loss of ARK did not protect the cells from Reaper- or Grim-induced cell death. Reduction of DIAP1 induced rapid apoptosis in these cells, whereas the inhibition of DIAP2 expression did not but resulted in increased sensitivity to stress-induced apoptosis; apoptosis in both cases was prevented by inhibition of ARK expression. Cells in which cytochrome c expression was decreased underwent apoptosis induced by stress stimuli, Reaper or Grim. These results demonstrate the central role of ARK in stress-induced apoptosis, which appears to act independently of cytochrome c. Apoptosis induced by Reaper or Grim can proceed via a distinct pathway, independent of ARK.}, }
@article {pmid11901123, year = {2002}, author = {v d Schulenburg, JH and Hurst, GD and Tetzlaff, D and Booth, GE and Zakharov, IA and Majerus, ME}, title = {History of infection with different male-killing bacteria in the two-spot ladybird beetle Adalia bipunctata revealed through mitochondrial DNA sequence analysis.}, journal = {Genetics}, volume = {160}, number = {3}, pages = {1075-1086}, pmid = {11901123}, issn = {0016-6731}, mesh = {Animals ; Biological Evolution ; Coleoptera/*genetics/*microbiology ; *DNA, Mitochondrial ; Electron Transport Complex IV/genetics ; Genotype ; Male ; Molecular Sequence Data ; NADH Dehydrogenase/genetics ; Phylogeny ; Rickettsia/*genetics ; Sequence Analysis, DNA ; Spiroplasma/*genetics ; *Symbiosis/genetics ; Wolbachia/*genetics ; }, abstract = {The two-spot ladybird beetle Adalia bipunctata (Coleoptera: Coccinellidae) is host to four different intracellular maternally inherited bacteria that kill male hosts during embryogenesis: one each of the genus Rickettsia (alpha-Proteobacteria) and Spiroplasma (Mollicutes) and two distinct strains of Wolbachia (alpha-Proteobacteria). The history of infection with these male-killers was explored using host mitochondrial DNA, which is linked with the bacteria due to joint maternal inheritance. Two variable regions, 610 bp of cytochrome oxidase subunit I and 563 bp of NADH dehydrogenase subunit 5, were isolated from 52 A. bipunctata with known infection status and different geographic origin from across Eurasia. Two outgroup taxa were also considered. DNA sequence analysis revealed that the distribution of mitochondrial haplotypes is not associated with geography. Rather, it correlates with infection status, confirming linkage disequilibrium between mitochondria and bacteria. The data strongly suggest that the Rickettsia male-killer invaded the host earlier than the other taxa. Further, the male-killing Spiroplasma is indicated to have undergone a recent and extensive spread through host populations. In general, male-killing in A. bipunctata seems to represent a highly dynamic system, which should prove useful in future studies on the evolutionary dynamics of this peculiar type of symbiont-host association.}, }
@article {pmid11894986, year = {2001}, author = {Otsuka, J and Kawai, Y and Sugaya, N}, title = {The influence of selection on the evolutionary distance estimated from the base changes observed between homologous nucleotide sequences.}, journal = {Journal of theoretical biology}, volume = {213}, number = {2}, pages = {129-144}, doi = {10.1006/jtbi.2001.2407}, pmid = {11894986}, issn = {0022-5193}, mesh = {Animals ; Base Sequence ; *Evolution, Molecular ; Fossils ; Mammals/*physiology ; Mitochondria/*physiology ; Molecular Sequence Data ; Mutation ; Phylogeny ; Proteins/*genetics ; Selection, Genetic ; *Sequence Homology ; }, abstract = {In most studies of molecular evolution, the nucleotide base at a site is assumed to change with the apparent rate under functional constraint, and the comparison of base changes between homologous genes is thought to yield the evolutionary distance corresponding to the site-average change rate multiplied by the divergence time. However, this view is not sufficiently successful in estimating the divergence time of species, but mostly results in the construction of tree topology without a time-scale. In the present paper, this problem is investigated theoretically by considering that observed base changes are the results of comparing the survivals through selection of mutated bases. In the case of weak selection, the time course of base changes due to mutation and selection can be obtained analytically, leading to a theoretical equation showing how the selection has influence on the evolutionary distance estimated from the enumeration of base changes. This result provides a new method for estimating the divergence time more accurately from the observed base changes by evaluating both the strength of selection and the mutation rate. The validity of this method is verified by analysing the base changes observed at the third codon positions of amino acid residues with four-fold codon degeneracy in the protein genes of mammalian mitochondria; i.e. the ratios of estimated divergence times are fairly well consistent with a series of fossil records of mammals. Throughout this analysis, it is also suggested that the mutation rates in mitochondrial genomes are almost the same in different lineages of mammals and that the lineage-specific base-change rates indicated previously are due to the selection probably arising from the preference of transfer RNAs to codons.}, }
@article {pmid11893511, year = {2002}, author = {Wipf, D and Ludewig, U and Tegeder, M and Rentsch, D and Koch, W and Frommer, WB}, title = {Conservation of amino acid transporters in fungi, plants and animals.}, journal = {Trends in biochemical sciences}, volume = {27}, number = {3}, pages = {139-147}, doi = {10.1016/s0968-0004(01)02054-0}, pmid = {11893511}, issn = {0968-0004}, mesh = {Amino Acid Transport Systems/genetics/*metabolism ; Amino Acids/*metabolism ; Animals ; Arabidopsis/genetics/metabolism ; Binding Sites ; Evolution, Molecular ; Fungal Proteins/metabolism ; Humans ; Mitochondria/metabolism ; Phylogeny ; Plant Proteins/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; }, abstract = {When comparing the transporters of three completely sequenced eukaryotic genomes--Saccharomyces cerevisiae, Arabidopsis thaliana and Homo sapiens--transporter types can be distinguished according to phylogeny, substrate spectrum, transport mechanism and cell specificity. The known amino acid transporters belong to five different superfamilies. Two preferentially Na(+)-coupled transporter superfamilies are not represented in the yeast and Arabidopsis genomes, whereas the other three groups, which often function as H(+)-coupled systems, have members in all investigated genomes. Additional superfamilies exist for organellar transport, including mitochondrial and plastidic carriers. When used in combination with phylogenetic analyses, functional comparison might aid our prediction of physiological functions for related but uncharacterized open reading frames.}, }
@article {pmid11891764, year = {2002}, author = {Gemmell, NJ and Sin, FY}, title = {Mitochondrial mutations may drive Y chromosome evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {24}, number = {3}, pages = {275-279}, doi = {10.1002/bies.10062}, pmid = {11891764}, issn = {0265-9247}, mesh = {Animals ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Humans ; Infertility, Male/genetics ; Male ; Mitochondria/*genetics ; Mutation/*physiology ; Y Chromosome/*genetics ; }, abstract = {The human Y chromosome contains very low levels of nucleotide variation. It has been variously hypothesized that this invariance reflects historic reductions in the human male population, a very recent common ancestry, a slow rate of molecular evolution, an inability to evolve adaptively, or frequent selective sweeps acting on genes borne on the Y chromosome. We propose an alternative theory in which human Y chromosome evolution is driven by mutations in the maternally inherited mitochondrial genome, which impair male fertility and ultimately lead to a reduction in the effective population size (N(e)) and consequently the variability of the Y chromosome.}, }
@article {pmid11891344, year = {2002}, author = {Taylor, DR and Zeyl, C and Cooke, E}, title = {Conflicting levels of selection in the accumulation of mitochondrial defects in Saccharomyces cerevisiae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {6}, pages = {3690-3694}, pmid = {11891344}, issn = {0027-8424}, mesh = {Cell Respiration/drug effects ; Chloramphenicol/pharmacology ; DNA, Mitochondrial/*genetics ; Drug Resistance, Fungal ; Evolution, Molecular ; Genome ; Mitochondria/drug effects/*genetics/metabolism/*pathology ; Models, Biological ; Mutation/genetics ; Saccharomyces cerevisiae/*cytology/drug effects/*genetics ; *Selection, Genetic ; }, abstract = {The somatic accumulation of defective mitochondria causes human degenerative syndromes, senescence in fungi, and male sterility in plants. These diverse phenomena may result from conflicts between natural selection at different levels of organization. Such conflicts are fundamental to the evolution of cooperating groups, from cells to populations. We present a model in which defective mitochondrial genomes accumulate because of a within-cell replication advantage when among-cell selection for efficient respiration is relaxed. We tested the model by using experimental populations of the yeast Saccharomyces cerevisiae. We constructed yeast strains that were heteroplasmic for mitochondrial mutations that destroy the ability to respire (the petite phenotype) and followed the accumulation of mitochondrial defects in cultures with different effective population sizes. As predicted by the model, the inability to respire evolved only in small populations of S. cerevisiae, where among-cell selection favoring cells that can respire was reduced relative to within-cell selection favoring parasitic mitochondria. In a control experiment, mitochondrial point mutations that confer resistance to chloramphenicol showed no tendency to change in frequency under any culture conditions. The accumulation of some mitochondrial defects is therefore an evolutionary process, involving multiple levels of selection. The relative intensities of within- and among-cell selection may also explain the tissue specificity of human mitochondrial defects.}, }
@article {pmid11884130, year = {2002}, author = {Schierling, K and Rösch, S and Rupprecht, R and Schiffer, S and Marchfelder, A}, title = {tRNA 3' end maturation in archaea has eukaryotic features: the RNase Z from Haloferax volcanii.}, journal = {Journal of molecular biology}, volume = {316}, number = {4}, pages = {895-902}, doi = {10.1006/jmbi.2001.5395}, pmid = {11884130}, issn = {0022-2836}, mesh = {Anticodon/genetics ; Base Sequence ; Cell Nucleus/enzymology ; Endoribonucleases/isolation &amp; purification/*metabolism ; Eukaryotic Cells/*enzymology ; Evolution, Molecular ; Haloferax volcanii/*enzymology/*genetics ; Hydrogen-Ion Concentration ; Introns/genetics ; Mitochondria/enzymology ; Mutation/genetics ; Nucleic Acid Conformation ; Osmolar Concentration ; Potassium Chloride/pharmacology ; *RNA 3' End Processing ; RNA, Archaeal/chemistry/genetics/*metabolism ; RNA, Transfer/chemistry/genetics/*metabolism ; RNA, Transfer, Tyr/chemistry/genetics/metabolism ; Substrate Specificity ; Temperature ; }, abstract = {Here, we report the first characterization and partial purification of an archaeal tRNA 3' processing activity, the RNase Z from Haloferax volcanii. The activity identified here is an endonuclease, which cleaves tRNA precursors 3' to the discriminator. Thus tRNA 3' processing in archaea resembles the eukaryotic 3' processing pathway. The archaeal RNase Z has a KCl optimum at 5mM, which is in contrast to the intracellular KCl concentration being as high as 4M KCl. The archaeal RNase Z does process 5' extended and intron-containing pretRNAs but with a much lower efficiency than 5' matured, intronless pretRNAs. At least in vitro there is thus no defined order for 5' and 3' processing and splicing. A heterologous precursor tRNA is cleaved efficiently by the archaeal RNase Z. Experiments with precursors containing mutated tRNAs revealed that removal of the anticodon arm reduces cleavage efficiency only slightly, while removal of D and T arm reduces processing effciency drastically, even down to complete inhibition. Comparison with its nuclear and mitochondrial homologs revealed that the substrate specificity of the archaeal RNase Z is narrower than that of the nuclear RNase Z but broader than that of the mitochondrial RNase Z.}, }
@article {pmid11880608, year = {2002}, author = {Baughn, AD and Malamy, MH}, title = {A mitochondrial-like aconitase in the bacterium Bacteroides fragilis: implications for the evolution of the mitochondrial Krebs cycle.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {7}, pages = {4662-4667}, pmid = {11880608}, issn = {0027-8424}, support = {R01 AI019497/AI/NIAID NIH HHS/United States ; R21 AI019497/AI/NIAID NIH HHS/United States ; AI-19497/AI/NIAID NIH HHS/United States ; }, mesh = {Aconitate Hydratase/chemistry/genetics/*physiology ; Amino Acid Sequence ; Bacteroides fragilis/*enzymology/genetics ; Biological Evolution ; *Citric Acid Cycle ; Genes, Bacterial/physiology ; Isocitrate Dehydrogenase/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; }, abstract = {Aconitase and isocitrate dehydrogenase (IDH) enzyme activities were detected in anaerobically prepared cell extracts of the obligate anaerobe Bacteroides fragilis. The aconitase gene was located upstream of the genes encoding the other two components of the oxidative branch of the Krebs cycle, IDH and citrate synthase. Mutational analysis indicates that these genes are cotranscribed. A nonpolar in-frame deletion of the acnA gene that encodes the aconitase prevented growth in glucose minimal medium unless heme or succinate was added to the medium. These results imply that B. fragilis has two pathways for alpha-ketoglutarate biosynthesis-one from isocitrate and the other from succinate. Homology searches indicated that the B. fragilis aconitase is most closely related to aconitases of two other Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria, Cytophaga hutchinsonii and Fibrobacter succinogenes. Phylogenetic analysis indicates that the CFB group aconitases are most closely related to mitochondrial aconitases. In addition, the IDH of C. hutchinsonii was found to be most closely related to the mitochondrial/cytosolic IDH-2 group of eukaryotic organisms. These data suggest a common origin for these Krebs cycle enzymes in mitochondria and CFB group bacteria.}, }
@article {pmid11880223, year = {2002}, author = {Arisue, N and Sánchez, LB and Weiss, LM and Müller, M and Hashimoto, T}, title = {Mitochondrial-type hsp70 genes of the amitochondriate protists, Giardia intestinalis, Entamoeba histolytica and two microsporidians.}, journal = {Parasitology international}, volume = {51}, number = {1}, pages = {9-16}, pmid = {11880223}, issn = {1383-5769}, support = {R01 AI011942/AI/NIAID NIH HHS/United States ; AI 31788/AI/NIAID NIH HHS/United States ; AI 11942/AI/NIAID NIH HHS/United States ; R01 AI031788/AI/NIAID NIH HHS/United States ; R01 AI031788-11/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Encephalitozoon/genetics ; Entamoeba histolytica/*genetics ; Giardia lamblia/*genetics ; HSP70 Heat-Shock Proteins/chemistry/*genetics ; Microsporidia/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/chemistry/genetics ; Sequence Analysis, DNA ; }, abstract = {Genes encoding putative mitochondrial-type heat shock protein 70 (mit-hsp70) were isolated and sequenced from amitochondriate protists, Giardia intestinalis, Entamoeba histolytica, and two microsporidians, Encephalitozoon hellem and Glugea plecoglossi. The deduced mit-hsp70 sequences were analyzed by sequence alignments and phylogenetic reconstructions. The mit-hsp70 sequence of these four amitochondriate protists were divergent from other mit-hsp70 sequences of mitochondriate eukaryotes. However, all of these sequences were clearly located within a eukaryotic mitochondrial clade in the tree including various type hsp70 sequences, supporting the emerging notion that none of these amitochondriate lineages are primitively amitochodrial, but lost their mitochondria secondarily in their evolutionary past.}, }
@article {pmid11867542, year = {2002}, author = {Pintard, L and Bujnicki, JM and Lapeyre, B and Bonnerot, C}, title = {MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase.}, journal = {The EMBO journal}, volume = {21}, number = {5}, pages = {1139-1147}, pmid = {11867542}, issn = {0261-4189}, mesh = {Amino Acid Sequence ; Cell Cycle Proteins/chemistry ; Consensus Sequence ; Culture Media/pharmacology ; DNA, Mitochondrial/metabolism ; Escherichia coli Proteins/chemistry ; Evolution, Molecular ; Gene Deletion ; Glycerol/pharmacology ; Hot Temperature ; Methylation ; Methyltransferases/chemistry ; Mitochondria/enzymology ; Mitochondrial Proteins/*genetics/physiology ; Molecular Sequence Data ; Oxidative Phosphorylation ; Protein Conformation ; *RNA Processing, Post-Transcriptional ; RNA, Fungal/*metabolism ; RNA, Ribosomal/*metabolism ; Saccharomyces cerevisiae/drug effects/enzymology/*genetics ; Saccharomyces cerevisiae Proteins/*genetics/physiology ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Mitochondria of the yeast Saccharomyces cerevisiae assemble their ribosomes from ribosomal proteins, encoded by the nuclear genome (with one exception), and rRNAs of 15S and 21S, encoded by the mitochondrial genome. Unlike cytoplasmic rRNA, which is highly modified, mitochondrial rRNA contains only three modified nucleotides: a pseudouridine (Psi(2918)) and two 2'-O-methylated riboses (Gm(2270) and Um(2791)) located at the peptidyl transferase centre of 21S rRNA. We demonstrate here that the yeast nuclear genome encodes a mitochondrial protein, named Mrm2, which is required for methylating U(2791) of 21S rRNA, both in vivo and in vitro. Deletion of the MRM2 gene causes thermosensitive respiration and leads to rapid loss of mitochondrial DNA. We propose that Mrm2p belongs to a new class of three eukaryotic RNA-modifying enzymes and is the orthologue of FtsJ/RrmJ, which methylates a nucleotide of the peptidyl transferase centre of Escherichia coli 23S rRNA that is homologous to U(2791) of 21S rRNA. Our data suggest that this universally conserved modified nucleotide plays an important function in vivo, possibly by inducing conformational rearrangement of the peptidyl transferase centre.}, }
@article {pmid11864821, year = {2002}, author = {Lloyd, D and Harris, JC}, title = {Giardia: highly evolved parasite or early branching eukaryote?.}, journal = {Trends in microbiology}, volume = {10}, number = {3}, pages = {122-127}, doi = {10.1016/s0966-842x(02)02306-5}, pmid = {11864821}, issn = {0966-842X}, mesh = {Animals ; *Biological Evolution ; Eukaryota/genetics ; Eukaryotic Cells/*physiology ; Giardia/*genetics ; Giardiasis/*parasitology ; Humans ; Phylogeny ; }, abstract = {The phylogeny of the commonest protozoal agent of intestinal disease, Giardia, is unclear. Although recent intensive research suggests this important human parasite is an early branching eukaryote that evolved before the endosymbiotic origin of mitochondria, there is also evidence to suggest that, as a highly evolved parasite, it has lost many of its ancestral characteristics. In this case, these organisms might have arisen much more recently from aerobic free-living flagellates.}, }
@article {pmid11861890, year = {2002}, author = {Forget, L and Ustinova, J and Wang, Z and Huss, VA and Lang, BF}, title = {Hyaloraphidium curvatum: a linear mitochondrial genome, tRNA editing, and an evolutionary link to lower fungi.}, journal = {Molecular biology and evolution}, volume = {19}, number = {3}, pages = {310-319}, doi = {10.1093/oxfordjournals.molbev.a004084}, pmid = {11861890}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; Cloning, Molecular ; Codon/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Fungi/*genetics ; Gene Order ; Genes, Fungal/genetics ; Molecular Sequence Data ; Phylogeny ; Physical Chromosome Mapping ; RNA/genetics ; RNA Editing/*genetics ; RNA, Fungal/genetics ; RNA, Mitochondrial ; RNA, Transfer/*genetics ; }, abstract = {We have sequenced the mitochondrial DNA (mtDNA) of Hyaloraphidium curvatum, an organism previously classified as a colorless green alga but now recognized as a lower fungus based on molecular data. The 29.97-kbp mitochondrial chromosome is maintained as a monomeric, linear molecule with identical, inverted repeats (1.43 kbp) at both ends, a rare genome architecture in mitochondria. The genome encodes only 14 known mitochondrial proteins, 7 tRNAs, the large subunit rRNA and small subunit rRNA (SSU rRNA), and 3 ORFs. The SSU rRNA is encoded in two gene pieces that are located 8 kbp apart on the mtDNA. Scrambled and fragmented mitochondrial rRNAs are well known from green algae and alveolate protists but are unprecedented in fungi. Protein genes code for apocytochrome b; cytochrome oxidase 1, 2, and 3, NADH dehydrogenase 1, 2, 3, 4, 4L, 5, and 6, and ATP synthase 6, 8, and 9 subunits, and several of these genes are organized in operon-like clusters. The set of seven mitochondrially encoded tRNAs is insufficient to recognize all codons that occur in the mitochondrial protein genes. When taking into account the pronounced codon bias, at least 16 nuclear-encoded tRNAs are assumed to be imported into the mitochondria. Three of the seven predicted mitochondria-encoded tRNA sequences carry mispairings in the first three positions of the acceptor stem. This strongly suggests that these tRNAs are edited by a mechanism similar to the one seen in the fungus Spizellomyces punctatus and the rhizopod amoeba Acanthamoeba castellanii. Our phylogenetic analysis confirms with overwhelming support that H. curvatum is a member of the chytridiomycete fungi, specifically related to the Monoblepharidales.}, }
@article {pmid11851985, year = {2001}, author = {Bandelt, HJ and Alves-Silva, J and Guimarães, PE and Santos, MS and Brehm, A and Pereira, L and Coppa, A and Larruga, JM and Rengo, C and Scozzari, R and Torroni, A and Prata, MJ and Amorim, A and Prado, VF and Pena, SD}, title = {Phylogeography of the human mitochondrial haplogroup L3e: a snapshot of African prehistory and Atlantic slave trade.}, journal = {Annals of human genetics}, volume = {65}, number = {Pt 6}, pages = {549-563}, doi = {10.1017/S0003480001008892}, pmid = {11851985}, issn = {0003-4800}, mesh = {Africa/ethnology ; Brazil ; Caribbean Region ; DNA, Mitochondrial/*genetics ; Databases, Genetic ; Emigration and Immigration/history ; *Haplotypes ; History, Ancient ; *Phylogeny ; Time ; }, abstract = {The mtDNA haplogroup L3e, which is identified by the restriction site +2349 MboI within the Afro-Eurasian superhaplogroup L3 (-3592 HpaI), is omnipresent in Africa but virtually absent in Eurasia (except for neighbouring areas with limited genetic exchange). L3e was hitherto poorly characterised in terms of HVS-I motifs, as the ancestral HVS-I type of L3e cannot be distinguished from the putative HVS-I ancestor of the entire L3 (differing from the CRS by a transition at np 16223). An MboI screening at np 2349 of a large number of Brazilian and Caribbean mtDNAs (encompassing numerous mtDNAs of African ancestry), now reveals that L3e is subdivided into four principal clades, each characterised by a single mutation in HVS-I, with additional support coming from HVS-II and partial RFLP analysis. The apparently oldest of these clades (transition at np 16327) occurs mainly in central Africa and was probably carried to southern Africa with the Bantu expansion(s). The most frequent clade (transition at np 16320) testifies to a pronounced expansion event in the mid-Holocene and seems to be prominent in many Bantu groups from all of Africa. In contrast, one clade (transition at np 16264) is essentially restricted to Atlantic western Africa (including Cabo Verde). We propose a tentative L3e phylogeny that is based on 197 HVS-I sequences. We conclude that haplogroup L3e originated in central or eastern Africa about 46,000 (+/-14,000) years ago, and was a hitchhiker of much later dispersal and local expansion events, with the rise of food production and iron smelting. Enforced migration of African slaves to the Americas translocated L3e mitochondria, the descendants of which in Brazil and the Caribbean still reflect their different regional African ancestries.}, }
@article {pmid11849133, year = {2002}, author = {Kim, KI and Lee, JH and Li, K and Zhang, YP and Lee, SS and Gongora, J and Moran, C}, title = {Phylogenetic relationships of Asian and European pig breeds determined by mitochondrial DNA D-loop sequence polymorphism.}, journal = {Animal genetics}, volume = {33}, number = {1}, pages = {19-25}, doi = {10.1046/j.1365-2052.2002.00784.x}, pmid = {11849133}, issn = {0268-9146}, mesh = {Animals ; Australia ; Base Sequence ; China ; Colombia ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Korea ; Likelihood Functions ; Molecular Sequence Data ; *Phylogeny ; *Polymorphism, Genetic ; Swine/*classification/genetics ; United Kingdom ; }, abstract = {Phylogenetic relationships among Asian and European pig breeds were assessed using 1036 bp of mitochondrial DNA (mtDNA) D-loop sequences. An unweighted pair-group method with arithmetic mean (UPGMA) tree was constructed on the basis of maximum likelihood distances using sequences determined for three Cheju (Korea), 11 Chinese, one Westran (Australian feral origin) and two European pigs (Berkshire and Welsh), and also published sequences for four Japanese (including two Wild Boars), one Yucatan miniature, five European (including Large White, Landrace, Duroc, Swedish and Wild Boar) and two Meishan pigs. The Colombian collared peccary (Tayassu tajacu) sequence was also determined and used as an outgroup. The maximum parsimony with heuristic search method was used to determine bootstrap support values. Asian-type pigs clustered together (bootstrap support 33%), but were separate from European-type pigs that also clustered together (93%). The Westran pig, derived from the feral descendants of pigs inhabiting Kangaroo Island of South Australia, clustered with Asian pigs, demonstrating Asian origin of their mitochondria. Berkshire and Large White clustered with Asian pigs, indicating that Asian pigs were involved in the development of these breeds. Our findings clearly demonstrate that pigs indigenous to China, Korea and Japan are only recently diverged from each other and distinctly different from European-type pigs. European pig breeds consist of pigs with mitochondria of Asian and non-Asian type, some of which were formed from closely related maternal ancestors, if not from a single ancestor.}, }
@article {pmid11847105, year = {2002}, author = {van der Giezen, M and Slotboom, DJ and Horner, DS and Dyal, PL and Harding, M and Xue, GP and Embley, TM and Kunji, ER}, title = {Conserved properties of hydrogenosomal and mitochondrial ADP/ATP carriers: a common origin for both organelles.}, journal = {The EMBO journal}, volume = {21}, number = {4}, pages = {572-579}, pmid = {11847105}, issn = {0261-4189}, support = {1U01 AI 48594-01/AI/NIAID NIH HHS/United States ; }, mesh = {Adenosine Diphosphate/*metabolism ; Adenosine Triphosphate/*metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA Primers ; Genetic Complementation Test ; Humans ; Hydrogen/*metabolism ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Sequence Homology, Amino Acid ; }, abstract = {Mitochondria are one of the hallmarks of eukaryotic cells, exporting ATP in exchange for cytosolic ADP using ADP/ATP carriers (AAC) located in the inner mitochondrial membrane. In contrast, several evolutionarily important anaerobic eukaryotes lack mitochondria but contain hydrogenosomes, peculiar organelles of controversial ancestry that also supply ATP but, like some fermentative bacteria, make molecular hydrogen in the process. We have now identified genes from two species of the hydrogenosome-containing fungus Neocallimastix that have three-fold sequence repeats and signature motifs that, along with phylogenetic analysis, identify them as AACs. When expressed in a mitochondrial AAC- deficient yeast strain, the hydrogenosomal protein was correctly targeted to the yeast mitochondria inner membrane and yielded mitochondria able to perform ADP/ATP exchange. Characteristic inhibitors of mitochondrial AACs blocked adenine nucleotide exchange by the Neocallimastix protein. Thus, our data demonstrate that fungal hydrogenosomes and yeast mitochondria use the same pathway for ADP/ATP exchange. These experiments provide some of the strongest evidence yet that yeast mitochondria and Neocallimastix hydrogenosomes are but two manifestations of the same fundamental organelle.}, }
@article {pmid11846802, year = {2002}, author = {Farge, G and Touraille, S and Le Goff, S and Petit, N and Renoux, M and Morel, F and Alziari, S}, title = {The nuclear genome is involved in heteroplasmy control in a mitochondrial mutant strain of Drosophila subobscura.}, journal = {European journal of biochemistry}, volume = {269}, number = {3}, pages = {998-1005}, doi = {10.1046/j.0014-2956.2001.02737.x}, pmid = {11846802}, issn = {0014-2956}, mesh = {Animals ; Biological Evolution ; Cell Nucleus/*genetics ; Citrate (si)-Synthase/genetics/metabolism ; Drosophila/*genetics ; Electron Transport Complex I ; Electron Transport Complex IV/genetics/metabolism ; Female ; *Genome ; Male ; Mitochondria/*genetics ; *Mutation ; NADH, NADPH Oxidoreductases/genetics/metabolism ; Transcription, Genetic ; }, abstract = {Most (78%) mitochondrial genomes in the studied mutant strain of Drosophila subobscura have undergone a large-scale deletion (5 kb) in the coding region. This mutation is stable, and is transmitted intact to the offspring. This animal model of major rearrangements of mitochondrial genomes can be used to analyse the involvement of the nuclear genome in the production and maintenance of these rearrangements. Successive backcrosses between mutant strain females and wild-type males yield a biphasic change in heteroplasmy level: (a) a 5% decrease in mutated genomes per generation (from 78 to 55%), until the nuclear genome is virtually replaced by the wild-type genome (seven to eight crosses); and (b) a continuous decrease of 0.5% per generation when the nuclear context is completely wild-type. In parallel with these changes, NADH dehydrogenase activity, which is halved in the mutant strain (five subunits of this complex are affected by the mutation), gradually increases and stabilizes near the wild-type activity. A return to a nuclear context is accompanied by the opposite phenomena: progressive increase in heteroplasmy level and stabilization at the value seen in the wild-type strain and a decrease in the activity of complex I. These results indicate that the nuclear genome plays an important role in the control of heteroplasmy level and probably in the production of rearranged genomes.}, }
@article {pmid11846788, year = {2002}, author = {Schnarrenberger, C and Martin, W}, title = {Evolution of the enzymes of the citric acid cycle and the glyoxylate cycle of higher plants. A case study of endosymbiotic gene transfer.}, journal = {European journal of biochemistry}, volume = {269}, number = {3}, pages = {868-883}, doi = {10.1046/j.0014-2956.2001.02722.x}, pmid = {11846788}, issn = {0014-2956}, mesh = {Aconitate Hydratase/physiology ; Citrate (si)-Synthase/physiology ; *Citric Acid Cycle ; Enzymes/*physiology ; *Evolution, Molecular ; Fumarate Hydratase/physiology ; Glyoxylates/*metabolism ; Isocitrate Dehydrogenase/physiology ; Isocitrate Lyase/physiology ; Ketone Oxidoreductases/physiology ; Malate Dehydrogenase/physiology ; Malate Synthase/physiology ; Phylogeny ; Plants/*metabolism ; Succinate Dehydrogenase/physiology ; }, abstract = {The citric acid or tricarboxylic acid cycle is a central element of higher-plant carbon metabolism which provides, among other things, electrons for oxidative phosphorylation in the inner mitochondrial membrane, intermediates for amino-acid biosynthesis, and oxaloacetate for gluconeogenesis from succinate derived from fatty acids via the glyoxylate cycle in glyoxysomes. The tricarboxylic acid cycle is a typical mitochondrial pathway and is widespread among alpha-proteobacteria, the group of eubacteria as defined under rRNA systematics from which mitochondria arose. Most of the enzymes of the tricarboxylic acid cycle are encoded in the nucleus in higher eukaryotes, and several have been previously shown to branch with their homologues from alpha-proteobacteria, indicating that the eukaryotic nuclear genes were acquired from the mitochondrial genome during the course of evolution. Here, we investigate the individual evolutionary histories of all of the enzymes of the tricarboxylic acid cycle and the glyoxylate cycle using protein maximum likelihood phylogenies, focusing on the evolutionary origin of the nuclear-encoded proteins in higher plants. The results indicate that about half of the proteins involved in this eukaryotic pathway are most similar to their alpha-proteobacterial homologues, whereas the remainder are most similar to eubacterial, but not specifically alpha-proteobacterial, homologues. A consideration of (a) the process of lateral gene transfer among free-living prokaryotes and (b) the mechanistics of endosymbiotic (symbiont-to-host) gene transfer reveals that it is unrealistic to expect all nuclear genes that were acquired from the alpha-proteobacterial ancestor of mitochondria to branch specifically with their homologues encoded in the genomes of contemporary alpha-proteobacteria. Rather, even if molecular phylogenetics were to work perfectly (which it does not), then some nuclear-encoded proteins that were acquired from the alpha-proteobacterial ancestor of mitochondria should, in phylogenetic trees, branch with homologues that are no longer found in most alpha-proteobacterial genomes, and some should reside on long branches that reveal affinity to eubacterial rather than archaebacterial homologues, but no particular affinity for any specific eubacterial donor.}, }
@article {pmid11846101, year = {2001}, author = {Lee, YH and Kim, KH}, title = {The ultrastructure of spermatozoa of the slender catfish Silurus microdorsalis (Teleostei, Siluriformes, Siluridae) with phylogenetic considerations.}, journal = {Journal of submicroscopic cytology and pathology}, volume = {33}, number = {3}, pages = {329-336}, pmid = {11846101}, issn = {1122-9497}, mesh = {Animals ; Catfishes/*physiology ; Male ; Organelles/ultrastructure ; *Phylogeny ; Species Specificity ; Spermatozoa/*ultrastructure ; }, abstract = {The spermatozoa of the slender catfish Silurus microdorsalis examined using transmission and scanning electron microscopy are characterized by a tubular structure and the absence of axonemal fins. Their characteristics can be considered to represent a valid symplesiomorphy uniting the Siluridae and taxon-specific for this family. The tubules of Silurus spermatozoon are not observed in the other siluroids. Unusual tubules occur in Citharinus spermatozoa of Characiformes. In addition, there is a considerable similarity in the absence of axonemal fins between Siluridae and Characiformes. Thus the two shared characteristics provide strong evidence that there exists a phylogenetic link between Characiformes and Siluriformes. Silurus appears to be plesiomorphic in having lost the axonemal fins while retaining the tubules in midpiece. The spermatozoa of S. microdorsalis are similar to those of other siluroids having a spherical head with a deep nuclear fossa, a short midpiece and an elongated tail. However, there are some differences between Silurus and other siluroids in the orientation of the centrioles, the number of the mitochondria and the axonemal fins, and minor differences between S. microdorsalis and S. asotus, in particular the orientation of the centriolar complex, and the arrangement of the tubules and the mitochondria in the midpiece. The deep nuclear fossa represents a synapomorphy uniting the Siluriformes, while the shallow nuclear fossa and the absence of axonemal fins are shared by two orders, Characiformes and Cypriniformes.}, }
@article {pmid11830664, year = {2002}, author = {Bapteste, E and Brinkmann, H and Lee, JA and Moore, DV and Sensen, CW and Gordon, P and Duruflé, L and Gaasterland, T and Lopez, P and Müller, M and Philippe, H}, title = {The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {99}, number = {3}, pages = {1414-1419}, pmid = {11830664}, issn = {0027-8424}, support = {R01 AI011942/AI/NIAID NIH HHS/United States ; AI11942/AI/NIAID NIH HHS/United States ; AI47087/AI/NIAID NIH HHS/United States ; }, mesh = {Amoeba/*classification/genetics ; Animals ; *Biological Evolution ; Dictyostelium/*classification/genetics ; Entamoeba/*classification/genetics ; *Genes ; Humans ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {The phylogenetic relationships of amoebae are poorly resolved. To address this difficult question, we have sequenced 1,280 expressed sequence tags from Mastigamoeba balamuthi and assembled a large data set containing 123 genes for representatives of three phenotypically highly divergent major amoeboid lineages: Pelobionta, Entamoebidae, and Mycetozoa. Phylogenetic reconstruction was performed on approximately 25,000 aa positions for 30 species by using maximum-likelihood approaches. All well-established eukaryotic groups were recovered with high statistical support, validating our approach. Interestingly, the three amoeboid lineages strongly clustered together in agreement with the Conosa hypothesis [as defined by T. Cavalier-Smith (1998) Biol. Rev. Cambridge Philos. Soc. 73, 203-266]. Two amitochondriate amoebae, the free-living Mastigamoeba and the human parasite Entamoeba, formed a significant sister group to the exclusion of the mycetozoan Dictyostelium. This result suggested that a part of the reductive process in the evolution of Entamoeba (e.g., loss of typical mitochondria) occurred in its free-living ancestors. Applying this inexpensive expressed sequence tag approach to many other lineages will surely improve our understanding of eukaryotic evolution.}, }
@article {pmid11828469, year = {2001}, author = {Ludwig, B and Bender, E and Arnold, S and Hüttemann, M and Lee, I and Kadenbach, B}, title = {Cytochrome C oxidase and the regulation of oxidative phosphorylation.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {2}, number = {6}, pages = {392-403}, doi = {10.1002/1439-7633(20010601)2:6&lt;392::AID-CBIC392&gt;3.0.CO;2-N}, pmid = {11828469}, issn = {1439-4227}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Bacterial Proteins/chemistry/*metabolism ; Diiodothyronines/metabolism ; Electron Transport Complex IV/chemistry/classification/*metabolism ; Heart/physiology ; Humans ; Membrane Potentials/physiology ; Mitochondria/enzymology/*metabolism ; Models, Molecular ; *Oxidative Phosphorylation ; Oxygen/metabolism ; Phylogeny ; Protein Structure, Tertiary ; Protein Subunits ; Reactive Oxygen Species/metabolism ; }, abstract = {Life of higher organisms is essentially dependent on the efficient synthesis of ATP by oxidative phosphorylation in mitochondria. An important and as yet unsolved question of energy metabolism is how are the variable rates of ATP synthesis at maximal work load during exercise or mental work and at rest or during sleep regulated. This article reviews our present knowledge on the structure of bacterial and eukaryotic cytochrome c oxidases and correlates it with recent results on the regulatory functions of nuclear-coded subunits of the eukaryotic enzyme, which are absent from the bacterial enzyme. A new molecular hypothesis on the physiological regulation of oxidative phosphorylation is proposed, assuming a hormonally controlled dynamic equilibrium in vivo between two states of energy metabolism, a relaxed state with low ROS (reactive oxygen species) formation, and an excited state with elevated formation of ROS, which are known to accelerate aging and to cause degenerative diseases and cancer. The hypothesis is based on the allosteric ATP inhibition of cytochrome c oxidase at high intramitochondrial ATP/ADP ratios ("second mechanism of respiratory control"), which is switched on by cAMP-dependent phosphorylation and switched off by calcium-induced dephosphorylation of the enzyme.}, }
@article {pmid11827457, year = {2002}, author = {Schwarz, QP and Cox, TC}, title = {Complementation of a yeast CYC3 deficiency identifies an X-linked mammalian activator of apocytochrome c.}, journal = {Genomics}, volume = {79}, number = {1}, pages = {51-57}, doi = {10.1006/geno.2001.6677}, pmid = {11827457}, issn = {0888-7543}, mesh = {3T3 Cells ; Amino Acid Sequence ; Animals ; Apoproteins/*metabolism ; COS Cells ; Cytochrome c Group/*metabolism ; Cytochromes c ; Enzyme Activators/metabolism ; Evolution, Molecular ; Female ; Genetic Linkage ; HeLa Cells ; Humans ; Lyases/*genetics/metabolism ; Male ; Mice ; Microphthalmos/*genetics ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Saccharomyces cerevisiae/*genetics ; Sequence Alignment ; Sequence Homology ; X Chromosome/genetics ; }, abstract = {We have shown by indirect immunofluorescence and enhanced green fluorescent protein fusions that a mammalian sequence exhibiting similar levels of homology to the two yeast heme lyases Cyc3p (holocytochrome c synthase; HCCS) and Cyt2p (holocytochrome c1 synthase; HCC1S) is also targeted to mitochondria. The human protein was able to complement the yeast Cyc3p (but not Cyt2p) deficiency, which indicates that it specifically activates apocytochrome c. Consistent with a respiratory role, expression of the mammalian gene was detected in all tissues, with the highest levels found in heart. Notably, the human gene HCCS is the only known gene located within the critical region for the deletion-defined disorder microphthalmia with linear skin defects (MLS). We believe the spectrum of clinical features seen in females with MLS and the paucity of male patients are consistent with significant involvement of HCCS. Toward clarification of a role for HCCS in disease, we have extensively characterized the X-linked mouse Hccs genomic locus, showing conservation in gene size and arrangement despite its location in a region that has undergone significant evolutionary rearrangement.}, }
@article {pmid11820431, year = {2001}, author = {Pérez-Castiñeira, JR and Gómez-García, R and López-Marqués, RL and Losada, M and Serrano, A}, title = {Enzymatic systems of inorganic pyrophosphate bioenergetics in photosynthetic and heterotrophic protists: remnants or metabolic cornerstones?.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {4}, number = {3}, pages = {135-142}, doi = {10.1007/s10123-001-0028-x}, pmid = {11820431}, issn = {1139-6709}, mesh = {Animals ; Biological Evolution ; Diphosphates/*metabolism ; Energy Metabolism ; Eukaryota/*enzymology/genetics/metabolism ; Intracellular Membranes/enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; Photosynthesis ; Phylogeny ; Plastids/enzymology ; Pyrophosphatases/chemistry/*physiology ; }, abstract = {An increasing body of biochemical and genetic evidence suggests that inorganic pyrophosphate (PPi) plays an important role in protist bioenergetics. In these organisms, two types of inorganic pyrophosphatases [EC 3.6.1.1, namely soluble PPases (sPPases) and proton-translocating PPases (H+-PPases)] that hydrolyse the PPi generated by cell anabolism, thereby replenishing the orthophosphate pool needed for phosphorylation reactions, are present in different cellular compartments. Photosynthetic and heterotrophic protists possess sPPases located in cellular organelles (plastids and mitochondria), where many anabolic and biosynthetic reactions take place, in addition to H+-PPases, which are integral membrane proteins of the vacuolysosomal membranes and use the chemical energy of PPi to generate an electrochemical proton gradient useful in cell bioenergetics. This last category of proton pumps was considered to be restricted to higher plants and some primitive photosynthetic bacteria, but it has been found recently in many protists (microalgae and protozoa) and bacteria, thus indicating that H+-PPases are much more widespread than previously thought. No cytosolic sPPase (in bacteria, fungi and animal cells) has been shown to occur in these lower eukaryotes. The widespread occurrence of these key enzymes of PPi metabolism among evolutionarily divergent protists strongly supports the ancestral character of the bioenergetics based on this simple energy-rich compound, which may play an important role in survival under different biotic and abiotic stress conditions.}, }
@article {pmid11818061, year = {2002}, author = {Andersson, JO and Roger, AJ}, title = {A cyanobacterial gene in nonphotosynthetic protists--an early chloroplast acquisition in eukaryotes?.}, journal = {Current biology : CB}, volume = {12}, number = {2}, pages = {115-119}, doi = {10.1016/s0960-9822(01)00649-2}, pmid = {11818061}, issn = {0960-9822}, mesh = {Arabidopsis/classification/genetics ; Chloroplasts/*metabolism ; Cyanobacteria/classification/*genetics ; *Genes, Bacterial ; Molecular Sequence Data ; Photosynthesis ; Phylogeny ; }, abstract = {Since the incorporation of mitochondria and chloroplasts (plastids) into the eukaryotic cell by endosymbiosis, genes have been transferred from the organellar genomes to the nucleus of the host, via an ongoing process known as endosymbiotic gene transfer. Accordingly, in photosynthetic eukaryotes, nuclear genes with cyanobacterial affinity are believed to have originated from endosymbiotic gene transfer from chloroplasts. Analysis of the Arabidopsis thaliana genome has shown that a significant fraction (2%-9%) of the nuclear genes have such an endosymbiotic origin. Recently, it was argued that 6-phosphogluconate dehydrogenase (gnd)-the second enzyme in the oxidative pentose phosphate pathway-was one such example. Here we show that gnd genes with cyanobacterial affinity also are present in several nonphotosynthetic protistan lineages, such as Heterolobosea, Apicomplexa, and parasitic Heterokonta. Current data cannot definitively resolve whether these groups acquired the gnd gene by primary and/or secondary endosymbiosis or via an independent lateral gene transfer event. Nevertheless, our data suggest that chloroplasts were introduced into eukaryotes much earlier than previously thought and that several major groups of heterotrophic eukaryotes have secondarily lost photosynthetic plastids.}, }
@article {pmid11811990, year = {2002}, author = {Fuku, N and Oshida, Y and Takeyasu, T and Guo, LJ and Kurata, M and Yamada, Y and Sato, Y and Tanaka, M}, title = {Mitochondrial ATPase subunit 6 and cytochrome B gene polymorphisms in young obese adults.}, journal = {Biochemical and biophysical research communications}, volume = {290}, number = {4}, pages = {1199-1205}, doi = {10.1006/bbrc.2002.6330}, pmid = {11811990}, issn = {0006-291X}, mesh = {Adenosine Triphosphatases/*genetics ; Adult ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/genetics ; Genetic Variation ; Humans ; Japan ; Mitochondria/enzymology ; Mitochondrial Proton-Translocating ATPases ; Models, Genetic ; Mutation ; Obesity/*genetics/metabolism ; Phylogeny ; *Polymorphism, Genetic ; }, abstract = {We hypothesized that the mutational strand asymmetry is more strongly exerted upon the mitochondrial cytochrome b (Cytb) gene, which is distant from the origin of the light-strand replication (Ori(L)), than upon the ATPase subunit 6 (ATP6) gene, which is close to the Ori(L). To test this hypothesis, we determined the sequences of these two genes in 96 Japanese young obese adults. The frequency of G-->A transitions was significantly higher than that of C-->T transitions in the Cytb gene, whereas the frequencies of G-->A and C-->T transitions were not significantly different in the ATP6 gene. The marked mutational strand asymmetry in the Cytb gene can be explained by the deamination of C to uracil in the long single-stranded state of the heavy strand during replication. The ratio of the nonsynonymous substitutions at the second codon positions to those at the first codon positions was significantly lower in the Cytb gene than in the ATP6 gene. The physicochemical differences between the standard and the replaced amino acid residues were significantly smaller in the Cytb gene than in ATP6 one. The present study indicates that amino acid sequences are less variable for Cytb than for ATP6 in spite of the strong mutational strand asymmetry for the Cytb gene.}, }
@article {pmid11810232, year = {2001}, author = {Pruchner, D and Nassal, B and Schindler, M and Knoop, V}, title = {Mosses share mitochondrial group II introns with flowering plants, not with liverworts.}, journal = {Molecular genetics and genomics : MGG}, volume = {266}, number = {4}, pages = {608-613}, doi = {10.1007/s004380100577}, pmid = {11810232}, issn = {1617-4615}, mesh = {Amino Acid Sequence ; Bryopsida/classification/genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Genes, Plant ; Introns/*genetics ; Magnoliopsida/classification/genetics ; Mitochondria/*genetics ; Mitochondrial Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics ; Plants/classification/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {Extant bryophytes are regarded as the closest living relatives of the first land plants, but relationships among the bryophyte classes (mosses, liverworts and hornworts) and between them and other embryophytes have remained unclear. We have recently found that plant mitochondrial genes with positionally stable introns are well suited for addressing questions of plant phylogeny at a deep level. To explore further data sets we have chosen to investigate the mitochondrial genes nad4 and nad7, which are particularly rich in intron sequences. Surprisingly, we find that in these genes mosses share three group II introns with flowering plants, but none with the liverwort Marchantia polymorpha or other liverworts investigated here. In mitochondria of Marchantia, nad7 is a pseudogene containing stop codons, but nad7 appears as a functional mitochondrial gene in mosses, including the isolated genus Takakia. We observe the necessity for strikingly frequent C-to-U RNA editing to reconstitute conserved codons in Takakia when compared to other mosses. The findings underline the great evolutionary distances among the bryophytes as the presumptive oldest division of land plants. A scenario involving differential intron gains from fungal sources in what are perhaps the two earliest diverging land plant lineages, liverworts and other embryophytes, is discussed. With their positionally stable introns, nad4 and nad7 represent novel marker genes that may permit a detailed phylogenetic resolution of early clades of land plants.}, }
@article {pmid11795501, year = {2001}, author = {Harman, D}, title = {Aging: overview.}, journal = {Annals of the New York Academy of Sciences}, volume = {928}, number = {}, pages = {1-21}, doi = {10.1111/j.1749-6632.2001.tb05631.x}, pmid = {11795501}, issn = {0077-8923}, mesh = {Adult ; Aged ; Aged, 80 and over ; *Aging/genetics/physiology ; Animals ; Antioxidants/administration &amp; dosage/pharmacology/therapeutic use ; Biological Evolution ; Cohort Studies ; Demography ; Environmental Exposure ; Female ; Forecasting ; Free Radicals ; Gerbillinae ; Humans ; Life Expectancy/trends ; Life Style ; Longevity/physiology ; Male ; Mice ; Mice, Inbred C57BL ; Middle Aged ; Mitochondria/physiology ; Models, Biological ; Mortality/trends ; Origin of Life ; Oxidation-Reduction ; Oxygen/adverse effects/physiology ; Rats ; Rats, Sprague-Dawley ; Species Specificity ; Superoxides/metabolism ; }, abstract = {Aging is a universal process that began with the origination of life about 3.5 billion years ago. Accumulation of the diverse deleterious changes produced by aging throughout the cells and tissues progressively impairs function and can eventually cause death. Aging changes can be attributed to development, genetic defects, the environment, disease, and an inborn process--the aging process. The chance of death at a given age serves as a measure of the average number of aging changes accumulated by persons of that age, that is, of physiologic age, and the rate of change of this measure as the rate of aging. Chances for death are decreased by improvements in general living conditions. As a result, during the past two millennia average life expectancy at birth (ALE-B), determined by the chances for death, of humans has risen from 30 years, in ancient Rome, to almost 80 years today in the developed countries. Chances for death in the developed countries are now near limiting values and ALE-Bs are approaching plateau values that are 6-9 years less than the potential maximum of about 85 years. Chances for death are now largely determined by the inherent aging process after age 28. Only 1.1% of female cohorts in Sweden die before this age; the remainder die off at an exponentially increasing rate with advancing age. The inherent aging process limits ALE-B to around 85 years, and the maximum life span (MLS) to about 122 years. Past efforts to increase ALE-B did not require an understanding of aging. Such knowledge will be necessary in the future to significantly increase ALE-B and MLS, and to satisfactorily ameliorate the medical, economic, and social problems associated with advancing age. The many theories advanced to account for aging should be used, to the extent it is feasible, to help with these important practical problems, including applications of the free radical theory of aging. Past measures evolved by societies to ensure adequate care for older individuals are rapidly becoming inadequate because of changes in life style, the growing percentage of older people, declining fertility rates, and the diminishing size of the work forces to provide for the elderly. Measures are being advanced to help with this problem. Prospects are bright for further increases in the span of functional life and improvements in the lives of the elderly.}, }
@article {pmid11803375, year = {2002}, author = {Arnoult, D and Akarid, K and Grodet, A and Petit, PX and Estaquier, J and Ameisen, JC}, title = {On the evolution of programmed cell death: apoptosis of the unicellular eukaryote Leishmania major involves cysteine proteinase activation and mitochondrion permeabilization.}, journal = {Cell death and differentiation}, volume = {9}, number = {1}, pages = {65-81}, doi = {10.1038/sj.cdd.4400951}, pmid = {11803375}, issn = {1350-9047}, mesh = {Animals ; Apoptosis/*physiology ; Apoptosis Regulatory Proteins ; Biological Evolution ; Carrier Proteins/pharmacology ; Cell Nucleus/drug effects/*physiology ; Chromatin/drug effects ; Cysteine Endopeptidases/drug effects/*metabolism ; Cysteine Proteinase Inhibitors/pharmacology ; Cytochrome c Group/metabolism ; DNA Fragmentation/drug effects/physiology ; Enzyme Activation ; Glycoproteins/pharmacology ; Humans ; *Intracellular Signaling Peptides and Proteins ; Jurkat Cells ; Leishmania major/drug effects/*physiology ; Mitochondria/physiology ; Permeability/drug effects ; Poly(ADP-ribose) Polymerases/drug effects/metabolism ; Proteins/metabolism ; Proto-Oncogene Proteins/pharmacology ; *Proto-Oncogene Proteins c-bcl-2 ; Staurosporine/*pharmacology ; bcl-2-Associated X Protein ; }, abstract = {Leishmania major is a protozoan parasite from one of the most ancient phylogenic branches of unicellular eukaryotes, and containing only one giant mitochondrion. Here we report that staurosporine, that induces apoptosis in all mammalian nucleated cells, also induces in L. major a death process with several cytoplasmic and nuclear features of apoptosis, including cell shrinkage, phosphatidyl serine exposure, maintenance of plasma membrane integrity, mitochondrial transmembrane potential (DeltaPsim) loss and cytochrome c release, nuclear chromatin condensation and fragmentation, and DNA degradation. Nuclear apoptosis-like features were prevented by cysteine proteinase inhibitors, and cell free assays using dying L. major cytoplasmic extracts indicated that the cysteine proteinases involved (i) also induced nuclear apoptosis-like features in isolated mammalian nuclei, and (ii) shared at least two nuclear substrates, but no cleavage site preference, with human effector caspases. Finally, isolated L. major mitochondria released cytochrome c and cysteine proteinases with nuclear pro-apoptotic activity when incubated with human recombinant Bax, even (although much less efficiently) when Bax was deleted of its transmembrane domain required for insertion in mitochondrial outermembranes, implying that L. major mitochondrion may express proteins able to interact with Bax. The recruitment of cysteine proteinases and mitochondria to the cell death machinery may be of very ancient evolutionary origin. Alternately, host/parasite interactions may have exerted selective pressures on the cell death phenotype of kinetoplastid parasites, resulting in the more recent emergence of an apoptotic machinery through a process of convergent evolution.}, }
@article {pmid11803022, year = {2002}, author = {Kita, K and Hirawake, H and Miyadera, H and Amino, H and Takeo, S}, title = {Role of complex II in anaerobic respiration of the parasite mitochondria from Ascaris suum and Plasmodium falciparum.}, journal = {Biochimica et biophysica acta}, volume = {1553}, number = {1-2}, pages = {123-139}, doi = {10.1016/s0005-2728(01)00237-7}, pmid = {11803022}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Anaerobiosis ; Animals ; Ascaris suum/*enzymology ; Electron Transport Complex II ; Energy Metabolism ; Fumarates/metabolism ; Life Cycle Stages ; Mitochondria/metabolism ; Models, Chemical ; Molecular Sequence Data ; Multienzyme Complexes/chemistry/*metabolism ; Oxidoreductases/chemistry/*metabolism ; *Oxidoreductases Acting on CH-CH Group Donors ; Phylogeny ; Plasmodium falciparum/*enzymology ; Sequence Alignment ; Succinate Dehydrogenase/chemistry/*metabolism ; Succinic Acid/metabolism ; }, abstract = {Parasites have developed a variety of physiological functions necessary for existence within the specialized environment of the host. Regarding energy metabolism, which is an essential factor for survival, parasites adapt to low oxygen tension in host mammals using metabolic systems that are very different from that of the host. The majority of parasites do not use the oxygen available within the host, but employ systems other than oxidative phosphorylation for ATP synthesis. In addition, all parasites have a life cycle. In many cases, the parasite employs aerobic metabolism during their free-living stage outside the host. In such systems, parasite mitochondria play diverse roles. In particular, marked changes in the morphology and components of the mitochondria during the life cycle are very interesting elements of biological processes such as developmental control and environmental adaptation. Recent research has shown that the mitochondrial complex II plays an important role in the anaerobic energy metabolism of parasites inhabiting hosts, by acting as quinol-fumarate reductase.}, }
@article {pmid11803017, year = {2002}, author = {Schäfer, G and Anemüller, S and Moll, R}, title = {Archaeal complex II: 'classical' and 'non-classical' succinate:quinone reductases with unusual features.}, journal = {Biochimica et biophysica acta}, volume = {1553}, number = {1-2}, pages = {57-73}, doi = {10.1016/s0005-2728(01)00232-8}, pmid = {11803017}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Archaea/classification/*enzymology ; Electron Transport Complex II ; Evolution, Molecular ; Fumarates/metabolism ; Iron-Sulfur Proteins/genetics ; Molecular Sequence Data ; Multienzyme Complexes/chemistry/*metabolism ; Operon ; Oxidation-Reduction ; Oxidoreductases/chemistry/*metabolism ; Phylogeny ; Sequence Alignment ; Succinate Dehydrogenase/chemistry/genetics/*metabolism ; Succinic Acid/metabolism ; }, abstract = {Reversible succinate dehydrogenase (SDH) activities have been ubiquitously detected in organisms from the three domains of life. They represent constituents either of respiratory complexes II in aerobes, or of fumarate dehydrogenase complexes in anaerobes. The present review gives a survey on archaeal succinate:quinone oxidoreductases (SQRs) analyzed so far. Though some of these could be studied in detail enzymologically and spectroscopically, the existence of others has been deduced only from published genome sequences. Interestingly, two groups of enzyme complexes can be distinguished in Archaea. One group resembles the properties of SDHs known from bacteria and mitochondria. The other represents a novel class with an unusual iron-sulfur cluster in subunit B and atypical sequence motifs in subunit C which may influence electron transport mechanisms and pathways. This novel class of SQRs is discussed in comparison to the so-called 'classical' complexes. A phylogenetic analysis is presented suggesting a co-evolution of the flavoprotein-binding subunit A and subunit B containing the three iron-sulfur clusters.}, }
@article {pmid11801744, year = {2002}, author = {Lavrov, DV and Boore, JL and Brown, WM}, title = {Complete mtDNA sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss.}, journal = {Molecular biology and evolution}, volume = {19}, number = {2}, pages = {163-169}, doi = {10.1093/oxfordjournals.molbev.a004068}, pmid = {11801744}, issn = {0737-4038}, mesh = {Animals ; Arthropods/classification/*genetics ; Base Sequence ; DNA Primers/chemistry ; DNA, Mitochondrial/*genetics ; *Gene Duplication ; Gene Order/genetics ; Gene Rearrangement/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Polymerase Chain Reaction ; Translocation, Genetic ; }, abstract = {We determined the complete mitochondrial DNA (mtDNA) sequences of the millipedes Narceus annularus and Thyropygus sp. (Arthropoda: Diplopoda) and identified, in both genomes, all 37 genes typical for metazoan mtDNA. The arrangement of these genes is identical in the two millipedes, but differs from others found in arthropod mtDNAs in the location of at least four genes or gene blocks. This novel gene arrangement is unusual for animal mtDNA in that genes with identical transcriptional polarities are clustered in the genome, and the two clusters are separated by two noncoding regions. The only exception to this pattern is the gene for cysteine tRNA, which is located in the part of the genome that otherwise contains all genes with the opposite transcriptional polarity. We suggest that a mechanism involving complete mtDNA duplication followed by the loss of genes, predetermined by their transcriptional polarity and location in the genome, could generate this gene arrangement from the one ancestral for arthropods. The proposed mechanism has important implications for phylogenetic inferences that are drawn on the basis of gene arrangement comparisons.}, }
@article {pmid11801237, year = {2002}, author = {Sluse, FE and Jarmuszkiewicz, W}, title = {Uncoupling proteins outside the animal and plant kingdoms: functional and evolutionary aspects.}, journal = {FEBS letters}, volume = {510}, number = {3}, pages = {117-120}, doi = {10.1016/s0014-5793(01)03229-x}, pmid = {11801237}, issn = {0014-5793}, mesh = {Acanthamoeba/*metabolism ; Animals ; Candida/*metabolism ; Carrier Proteins/*metabolism ; Dictyostelium/*metabolism ; Energy Metabolism/physiology ; *Evolution, Molecular ; Ion Channels ; Membrane Proteins/*metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins ; Oxidoreductases/metabolism ; Reactive Oxygen Species/metabolism ; Uncoupling Protein 1 ; }, abstract = {The appearance of intracellular oxidative phosphorylation at the time of acquisition of mitochondria in Eukarya was very soon accompanied by the emergence of uncoupling protein, a carrier specialized in free fatty acid-mediated H(+) recycling that can modulate the tightness of coupling between mitochondrial respiration and ATP synthesis, thereby maintaining a balance between energy supply and demand in the cell and defending cells against damaging reactive oxygen species production when electron carriers of the respiratory chain become over-reduced. The simultaneous occurrence of redox free energy-dissipating oxidase, which has the same final effect, could be related to the functional interactions between both dissipative systems.}, }
@article {pmid11797917, year = {2001}, author = {Hine, PM and Cochennec-Laureau, N and Berthe, FC}, title = {Bonamia exitiosus n. sp. (Haplosporidia) infecting flat oysters Ostrea chilensis in New Zealand.}, journal = {Diseases of aquatic organisms}, volume = {47}, number = {1}, pages = {63-72}, doi = {10.3354/dao047063}, pmid = {11797917}, issn = {0177-5103}, mesh = {Animals ; Base Sequence ; DNA, Ribosomal/*analysis/chemistry ; Eukaryota/*classification/genetics/*ultrastructure ; Host-Parasite Interactions ; Molecular Sequence Data ; New Zealand ; Ostreidae/*parasitology ; Phylogeny ; Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; Sequence Alignment/veterinary ; Sequence Analysis, DNA ; }, abstract = {Bonamia sp. is a pathogenic parasite that occurs in the haemocytes of dredge oysters Ostrea chilensis Philippi in New Zealand. Ultrastructurally it resembles other haplosporidians in the possession of haplosporosomes, haplosporogenesis, persistence of mitotic microtubules during interphase and of the nuclear envelope during mitosis, and occurrence of a diplokaryotic or multi-nucleate plasmodial stage. Another stage containing a large vacuole derived from enlargement of 1 or more mitochondria has not previously been described from other haplosporidians. It most closely resembles B. ostreae Pichot et al., 1979, which parasitises and is pathogenic in haemocytes of European flat oysters, O. edulis. However, B. ostreae is smaller and denser, and has fewer lipoid bodies and haplosporosomes. We have nearly completely sequenced the small ribosomal gene of the organism from O. chilensis. Initial comparisons of these sequences with those of other protozoans showed similarities to B. ostreae. Polymorphism within Bonamia sp. was confirmed by restriction fragment length polymorphism analysis. On the basis of ultrastructural and molecular considerations it is proposed that this organism be named Bonamia exitiosus sp. nov.}, }
@article {pmid11794786, year = {2001}, author = {Planes, S and Doherty, PJ and Bernardi, G}, title = {Strong genetic divergence among populations of a marine fish with limited dispersal, Acanthochromis polyacanthus, within the Great Barrier Reef and the Coral Sea.}, journal = {Evolution; international journal of organic evolution}, volume = {55}, number = {11}, pages = {2263-2273}, doi = {10.1111/j.0014-3820.2001.tb00741.x}, pmid = {11794786}, issn = {0014-3820}, mesh = {Animals ; Australia ; Cytochrome b Group/genetics ; *Genetic Variation ; Mitochondria/chemistry ; Perciformes/classification/*genetics/physiology ; Phylogeny ; }, abstract = {Acanthochromis polyacanthus is an unusual tropical marine damselfish that uniquely lacks pelagic larvae and has lost the capacity for broad-scale dispersal among coral reefs. On the modern Great Barrier Reef (GBR), three color morphs meet and hydridize at two zones of secondary contact. Allozyme electrophoreses revealed strong differences between morphs from the southern zone but few differences between morphs from the northern counterpart, thus suggesting different contact histories. We explore the phylogeography of Acanthochromis polyacanthus with mitochondrial cytochrome b region sequences (alignment of 565 positions) obtained from 126 individuals representing seven to 12 fish from 13 sites distributed over 12 reefs of the GBR and the Coral Sea. The samples revealed three major clades: (1) black fish collected from the southern GBR; (2) bicolored fish collected from the GBR and one reef (Osprey) from the northern Coral Sea; (3) black and white monomorphs collected from six reefs in the Coral Sea. All three clades were well supported (72-100%) by bootstrap analyses. Sequence divergences were very high between the major clades (mean = 7.6%) as well as within them (2.0-3.6%). Within clades, most reefs segregated as monophyletic assemblages. This was revealed both by phylogenetic analyses and AMOVAs that showed that 72-90% of the variance originated from differences among groups, whereas only 5-13% originated within populations. These patterns are discussed in relation to the known geological history of coral reefs of the GBR and the Coral Sea. Finally, we ask whether the monospecific status of Acanthochromis should be revisited because the sequence divergences found among our samples is substantially greater than those recorded among well-recognized species in other reef fishes.}, }
@article {pmid11780787, year = {2001}, author = {Fujita, K and Horie, T and Isono, K}, title = {Cross-genomic analysis of the translational systems of various organisms.}, journal = {Journal of industrial microbiology &amp; biotechnology}, volume = {27}, number = {3}, pages = {163-169}, doi = {10.1038/sj.jim.7000093}, pmid = {11780787}, issn = {1367-5435}, mesh = {Bacteria/*genetics ; Base Sequence ; Escherichia coli/genetics ; Genomics ; Mitochondria/*metabolism ; Phylogeny ; *Protein Biosynthesis ; Ribosomal Proteins/*genetics ; Saccharomyces cerevisiae/*genetics ; Saccharomyces cerevisiae Proteins/genetics ; }, abstract = {We have characterized the genes encoding ribosomal proteins (r-proteins) as well as other translation-related factors of 15 eubacteria and four archaebacteria, and the genes for the mitochondrial r-proteins of Saccharomyces cerevisiae by using the complete genomic nucleotide sequence data of these organisms. In eubacteria, including two species of Mycoplasma, the operon structure of the r-protein genes is well conserved, while their relative orientation and chromosomal location are quite divergent. The operon structure of the r-protein genes in archaebacteria, on the other hand, is quite different from eubacteria and also among themselves. In addition, many archaebacterial r-proteins show similarity to rat cytoplasmic r-proteins. Nonetheless, characteristic features of several genes encoding proteins of functional importance are well conserved throughout the bacterial species including archaebacteria, as well as in S. cerevisiae. We searched for the genes encoding mitochondrial r-proteins in yeast by combining informatics and genetic experiments. Furthermore, we characterized some of the r-proteins genes by exchanging portions between Escherichia coli and S. cerevisiae and performed functional analysis of some of the genes from different evolutionary points of view. Our work may be extended towards phylogenetic analysis of organisms producing secondary metabolites of various sorts.}, }
@article {pmid11779548, year = {2001}, author = {Castresana, J}, title = {Comparative genomics and bioenergetics.}, journal = {Biochimica et biophysica acta}, volume = {1506}, number = {3}, pages = {147-162}, doi = {10.1016/s0005-2728(01)00227-4}, pmid = {11779548}, issn = {0006-3002}, mesh = {Archaea/enzymology/*genetics ; Bacteria/enzymology/*genetics ; *Energy Metabolism ; Evolution, Molecular ; *Genomics ; Photosynthesis ; Phylogeny ; }, abstract = {Bacterial and archaeal complete genome sequences have been obtained from a wide range of evolutionary lines, which allows some general conclusions about the phylogenetic distribution and evolution of bioenergetic pathways to be drawn. In particular, I searched in the complete genomes for key enzymes involved in aerobic and anaerobic respiratory pathways and in photosynthesis, and mapped them into an rRNA tree of sequenced species. The phylogenetic distribution of these enzymes is very irregular, and clearly shows the diverse strategies of energy conservation used by prokaryotes. In addition, a thorough phylogenetic analysis of other bioenergetic protein families of wide distribution reveals a complex evolutionary history for the respective genes. A parsimonious explanation for these complex phylogenetic patterns and for the irregular distribution of metabolic pathways is that the last common ancestor of Bacteria and Archaea contained several members of every gene family as a consequence of previous gene or genome duplications, while different patterns of gene loss occurred during the evolution of every gene family. This would imply that the last universal ancestor was a bioenergetically sophisticated organism. Finally, important steps that occurred during the evolution of energetic machineries, such as the early evolution of aerobic respiration and the acquisition of eukaryotic mitochondria from a proteobacterium ancestor, are supported by the analysis of the complete genome sequences.}, }
@article {pmid11767942, year = {2001}, author = {Martin, W and Hoffmeister, M and Rotte, C and Henze, K}, title = {An overview of endosymbiotic models for the origins of eukaryotes, their ATP-producing organelles (mitochondria and hydrogenosomes), and their heterotrophic lifestyle.}, journal = {Biological chemistry}, volume = {382}, number = {11}, pages = {1521-1539}, doi = {10.1515/BC.2001.187}, pmid = {11767942}, issn = {1431-6730}, mesh = {Adenosine Triphosphate/*biosynthesis ; *Biological Evolution ; Mitochondria/*metabolism ; Models, Biological ; Organelles/*metabolism ; *Plant Physiological Phenomena ; Plants/*metabolism/ultrastructure ; }, abstract = {The evolutionary processes underlying the differentness of prokaryotic and eukaryotic cells and the origin of the latter's organelles are still poorly understood. For about 100 years, the principle of endosymbiosis has figured into thoughts as to how these processes might have occurred. A number of models that have been discussed in the literature and that are designed to explain this difference are summarized. The evolutionary histories of the enzymes of anaerobic energy metabolism (oxygen-independent ATP synthesis) in the three basic types of heterotrophic eukaryotes those that lack organelles of ATP synthesis, those that possess mitochondria and those that possess hydrogenosomes--play an important role in this issue. Traditional endosymbiotic models generally do not address the origin of the heterotrophic lifestyle and anaerobic energy metabolism in eukaryotes. Rather they take it as a given, a direct inheritance from the host that acquired mitochondria. Traditional models are contrasted to an alternative endosymbiotic model (the hydrogen hypothesis), which addresses the origin of heterotrophy and the origin of compartmentalized energy metabolism in eukaryotes.}, }
@article {pmid11766842, year = {2000}, author = {Pimentel-Smith, GE and Shi, L and Drummond, P and Tu, Z and Smith, EJ}, title = {Amplification of sequence tagged sites in five avian species using heterologous oligonucleotides.}, journal = {Genetica}, volume = {110}, number = {3}, pages = {219-226}, doi = {10.1023/a:1012772831699}, pmid = {11766842}, issn = {0016-6707}, mesh = {APOBEC-1 Deaminase ; Animals ; Chickens/genetics ; Collagen Type X/genetics ; Columbidae/genetics ; Coturnix/genetics ; Cytidine Deaminase/genetics ; DNA Primers/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Sequence Homology ; *Sequence Tagged Sites ; Species Specificity ; Turkeys/genetics ; }, abstract = {Short of a complete genomic DNA sequence, sequence tagged sites (STSs) have emerged as major genomic reagents for the genetic analysis of little-studied ecologically and agriculturally important organisms. Here, we report STS developed for the turkey (Meleagris gallopavo), guinea fowl (Numidea meleagris), Japanese quail (Coturnix coturnix) and pigeon using primers specific for reference DNA sequences of two chicken (Gallus gallus) genes, aggrecan (agc1) and type X collagen (col10). Additional STSs were also developed for turkey, quail and chicken using primers specific for the human apobec-1 gene. The total length of the STSs developed was 5990, 2522, 4127, 1539 and 6600 bp for the turkey, guinea fowl, Japanese quail, pigeon and chicken, respectively. Based on splice site consensus GT and AG sequences, four of the seven agc1-based chicken STS appear to contain introns. The human gene-based STSs showed no significant sequence identity with the reference GenBank sequences. Maximum likelihood, maximum parsimony and neighbour-joining analysis of an agc1-based STS that was common to all five species showed phylogenetic relationships consistent with those previously defined using mitochondria DNA sequences and nuclear gene restriction maps. Additionally, several putative single nucleotide polymorphisms (SNPs) were detected within the STSs, including eight in the turkey, two in the quail, and two in the chicken when multiple sequences were evaluated from each species. This report describes new STSs that are resources for genetic and physical mapping and genome analysis within and among avian species. These resources should further aid in our understanding of the biology of agriculturally important but little-studied guinea fowl and turkey.}, }
@article {pmid11764895, year = {2001}, author = {Wang, L and Yokoyama, K and Takahasi, H and Kase, N and Hanya, Y and Yashiro, K and Miyaji, M and Nishimura, K}, title = {Identification of species in Aspergillus section Flavi based on sequencing of the mitochondrial cytochrome b gene.}, journal = {International journal of food microbiology}, volume = {71}, number = {1}, pages = {75-86}, doi = {10.1016/s0168-1605(01)00597-9}, pmid = {11764895}, issn = {0168-1605}, mesh = {Amino Acid Sequence ; Aspergillus/*classification/*genetics/ultrastructure ; Base Sequence ; Cytochrome b Group/*genetics ; DNA, Fungal/genetics ; Microscopy, Electron, Scanning ; Mitochondria ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction/methods ; }, abstract = {The partial sequences of the mitochondrial (mt) cytochrome b gene (402 bp) were determined for species of Aspergillus section Flavi. On the basis of identities of DNA sequences, 77 strains were divided into seven DNA types, from D-1 to D-7. The type strains of A. sojae, A. parasiticus, A. flavus and A. oryzae together, A. tamarii, and A. nomius were placed in DNA types D-1. D-2, D-4, D-5 and D-7, respectively. These species could be differentiated from each other. Furthermore, two other DNA types, D-3 and D-6 were found. DNA type D-3 was closely related to A. parasiticus (D-2) and included one strain that deposited as A. flatus var. flavus and produced aflatoxins B and G. DNA types D-6 included one strain named A. flavus and closely related to A. tamarii. The observations of conidial wall texture by SEM (Scanning Electron Microscopy) supported the relationships derived from the cytochrome b gene. The production of aflatoxins was also examined. Using the DNA sequence of cytochrome b gene, several strains were reidentified. The derived amino acids sequences were all the same in the studied strains. The mt cytochrome b gene is useful and reliable in distinguishing and identifying the species in Aspergillus section Flavi.}, }
@article {pmid11754070, year = {2001}, author = {Brown, MD and Allen, JC and Van Stavern, GP and Newman, NJ and Wallace, DC}, title = {Clinical, genetic, and biochemical characterization of a Leber hereditary optic neuropathy family containing both the 11778 and 14484 primary mutations.}, journal = {American journal of medical genetics}, volume = {104}, number = {4}, pages = {331-338}, pmid = {11754070}, issn = {0148-7299}, support = {EY 11305/EY/NEI NIH HHS/United States ; NS 21328/NS/NINDS NIH HHS/United States ; P30 EY 06360/EY/NEI NIH HHS/United States ; }, mesh = {Cell Line ; Child ; DNA Mutational Analysis ; DNA, Mitochondrial/chemistry/*genetics ; Female ; Humans ; Mitochondria/genetics/metabolism ; Mutation ; Optic Atrophy, Hereditary, Leber/*genetics/pathology ; Oxidative Phosphorylation ; Polymorphism, Restriction Fragment Length ; }, abstract = {Four mitochondrial DNA (mtDNA) mutations at nps 3460, 11778, 14484, and 14459 account for roughly 90% of cases of Leber hereditary optic neuropathy (LHON) and are designated as "primary" LHON mutations since they act as major predisposition factors for LHON. Although each primary mutation can arise independently on different mtDNA backgrounds during human evolution, they characteristically do not co-occur in LHON patients. We report here a family with the simultaneous occurrence of the 11778A and 14484C mutations. Neuro-ophthalmological examination of the proband, a nine-year-old Caucasian female, revealed the bilateral optic atrophy, central scotomas, and reduced visual acuity typical of LHON. Her mother had normal appearing optic discs and is today visually asymptomatic. Analysis of the proband blood mtDNA revealed that she harbored both the 11778A (heteroplasmic, 94% mutant) and the 14484C (homoplasmic mutant) mutation. This genotype was maintained in proband lymphoblasts and transmitochondrial cybrids. The mother also had both mutations, with the 14484C mutation homoplasmic in all cell types examined. However, only 31% of her blood mtDNAs carried the 11778 mutation, which segregated to essentially 100% wild-type in lymphoblast and cybrid mtDNA. Complex I-linked respiration and specific enzyme activity were consistently lowest in proband lymphoblast and cybrid mitochondria compared to those from the mother, 11778A patients, 14484C patients, or controls, thus demonstrating both a deleterious synergistic interaction between the 11778A and 14484C mutations and the magnitude of 11778A-associated complex I dysfunction. Remarkably, spontaneous vision recovery occurred in the proband, highlighting the complexities encountered when associating mtDNA genotype and complex I function with LHON expression.}, }
@article {pmid11752472, year = {2001}, author = {Ravanel, S and Cherest, H and Jabrin, S and Grunwald, D and Surdin-Kerjan, Y and Douce, R and Rébeillé, F}, title = {Tetrahydrofolate biosynthesis in plants: molecular and functional characterization of dihydrofolate synthetase and three isoforms of folylpolyglutamate synthetase in Arabidopsis thaliana.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {26}, pages = {15360-15365}, pmid = {11752472}, issn = {0027-8424}, mesh = {Arabidopsis/enzymology/genetics/*metabolism ; DNA, Complementary ; Genetic Complementation Test ; Isoenzymes/*metabolism ; Molecular Sequence Data ; Peptide Synthases/genetics/*metabolism ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Subcellular Fractions/enzymology ; Tetrahydrofolates/*biosynthesis ; }, abstract = {Tetrahydrofolate coenzymes involved in one-carbon (C1) metabolism are polyglutamylated. In organisms that synthesize tetrahydrofolate de novo, dihydrofolate synthetase (DHFS) and folylpolyglutamate synthetase (FPGS) catalyze the attachment of glutamate residues to the folate molecule. In this study we isolated cDNAs coding a DHFS and three isoforms of FPGS from Arabidopsis thaliana. The function of each enzyme was demonstrated by complementation of yeast mutants deficient in DHFS or FPGS activity, and by measuring in vitro glutamate incorporation into dihydrofolate or tetrahydrofolate. DHFS is present exclusively in the mitochondria, making this compartment the sole site of synthesis of dihydrofolate in the plant cell. In contrast, FPGS is present as distinct isoforms in the mitochondria, the cytosol, and the chloroplast. Each isoform is encoded by a separate gene, a situation that is unique among eukaryotes. The compartmentation of FPGS isoforms is in agreement with the predominance of gamma-glutamyl-conjugated tetrahydrofolate derivatives and the presence of serine hydroxymethyltransferase and C1-tetrahydrofolate interconverting enzymes in the cytosol, the mitochondria, and the plastids. Thus, the combination of FPGS with these folate-mediated reactions can supply each compartment with the polyglutamylated folate coenzymes required for the reactions of C1 metabolism. Also, the multicompartmentation of FPGS in the plant cell suggests that the transported forms of folate are unconjugated.}, }
@article {pmid11752383, year = {2001}, author = {Skinner, DJ and Baker, SC and Meister, RJ and Broadhvest, J and Schneitz, K and Gasser, CS}, title = {The Arabidopsis HUELLENLOS gene, which is essential for normal ovule development, encodes a mitochondrial ribosomal protein.}, journal = {The Plant cell}, volume = {13}, number = {12}, pages = {2719-2730}, pmid = {11752383}, issn = {1040-4651}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/growth &amp; development ; Arabidopsis Proteins/classification/*genetics/metabolism ; Chromosome Mapping ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Plant ; Mitochondria/*metabolism ; *Mitochondrial Proteins ; Molecular Sequence Data ; Mutagenesis ; Phenotype ; Phylogeny ; Plant Stems/genetics/growth &amp; development ; Plant Structures/genetics/growth &amp; development ; *Recombinant Proteins ; Ribosomal Proteins/classification/*genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {The HUELLENLOS (HLL) gene participates in patterning and growth of the Arabidopsis ovule. We have isolated the HLL gene and shown that it encodes a protein homologous to the L14 proteins of eubacterial ribosomes. The Arabidopsis genome also includes a highly similar gene, HUELLENLOS PARALOG (HLP), and genes for both cytosolic (L23) and chloroplast ribosome L14 proteins. Phylogenetic analysis shows that HLL and HLP differ significantly from these other two classes of such proteins. HLL and HLP fusions to green fluorescent protein were localized to mitochondria. Ectopic expression of HLP complemented the hll mutant, indicating that HLP and HLL share redundant functions. We conclude that HLL and HLP encode L14 subunits of mitochondrial ribosomes. HLL mRNA was at significantly higher levels than HLP mRNA in pistils, with the opposite pattern in leaves. This differential expression can explain the confinement of effects of hll mutations to gynoecia and ovules. Our elucidation of the nature of HLL shows that metabolic defects can have specific effects on developmental patterning.}, }
@article {pmid11747308, year = {2002}, author = {Rokov-Plavec, J and Lesjak, S and Landeka, I and Mijakovic, I and Weygand-Durasevic, I}, title = {Maize seryl-tRNA synthetase: specificity of substrate recognition by the organellar enzyme.}, journal = {Archives of biochemistry and biophysics}, volume = {397}, number = {1}, pages = {40-50}, doi = {10.1006/abbi.2001.2600}, pmid = {11747308}, issn = {0003-9861}, mesh = {Amino Acid Sequence ; Base Sequence ; Chloroplasts/metabolism ; Cytosol/enzymology ; DNA, Complementary/metabolism ; Databases as Topic ; Electrophoresis, Polyacrylamide Gel ; Evolution, Molecular ; Expressed Sequence Tags ; Genetic Complementation Test ; Kinetics ; Mitochondria/metabolism ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Phenotype ; Phylogeny ; Protein Isoforms ; RNA, Transfer/chemistry ; Saccharomyces cerevisiae/metabolism ; Sequence Homology, Amino Acid ; Serine/metabolism ; Serine-tRNA Ligase/*chemistry ; Substrate Specificity ; Zea mays/*enzymology ; }, abstract = {In our study of seryl-tRNA formation in maize, we investigated the enzymes involved in serylation. Only two dissimilar seryl-tRNA synthetase (SerRS) cDNA clones were identified in the Zea mays EST (expressed sequence tag) databases. One encodes a seryl-tRNA synthetase, which presumably functions in the organelles (SerZMm), while the other synthetase product is more similar to eukaryotic cytosolic counterparts (SerZMc). The expression of SerZMm in Saccharomyces cerevisiae resulted in complementation of mutant respiratory phenotype, caused by a disruption of the nuclear gene, presumably encoding yeast mitochondrial seryl-tRNA synthetase (SerSCm). Purified mature SerZMm displays tRNA-assisted serine activation and aminoacylates maize mitochondrial and chloroplast tRNA(Ser) transcripts with similar efficiencies, raising the possibility that only two isoforms of seryl-tRNA synthetase may be sufficient to catalyze seryl-tRNA(Ser) formation in three cellular compartments of Zea mays. Phylogenetic analysis suggests that SerZMm is of mitochondrial origin.}, }
@article {pmid11743200, year = {2001}, author = {Murphy, WJ and Eizirik, E and O'Brien, SJ and Madsen, O and Scally, M and Douady, CJ and Teeling, E and Ryder, OA and Stanhope, MJ and de Jong, WW and Springer, MS}, title = {Resolution of the early placental mammal radiation using Bayesian phylogenetics.}, journal = {Science (New York, N.Y.)}, volume = {294}, number = {5550}, pages = {2348-2351}, doi = {10.1126/science.1067179}, pmid = {11743200}, issn = {0036-8075}, mesh = {Africa ; Animals ; Base Pairing ; *Bayes Theorem ; Biological Evolution ; Cell Nucleus/genetics ; Ecosystem ; Fossils ; Genes ; Genes, rRNA ; Likelihood Functions ; Mammals/*classification/*genetics ; Markov Chains ; Marsupialia/classification/genetics ; Mitochondria/genetics ; Monte Carlo Method ; *Phylogeny ; Placenta ; Probability ; Sequence Analysis, DNA ; South America ; }, abstract = {Molecular phylogenetic studies have resolved placental mammals into four major groups, but have not established the full hierarchy of interordinal relationships, including the position of the root. The latter is critical for understanding the early biogeographic history of placentals. We investigated placental phylogeny using Bayesian and maximum-likelihood methods and a 16.4-kilobase molecular data set. Interordinal relationships are almost entirely resolved. The basal split is between Afrotheria and other placentals, at about 103 million years, and may be accounted for by the separation of South America and Africa in the Cretaceous. Crown-group Eutheria may have their most recent common ancestry in the Southern Hemisphere (Gondwana).}, }
@article {pmid11742553, year = {2001}, author = {Pfenninger, M and Magnin, F}, title = {Phenotypic evolution and hidden speciation in Candidula unifasciata ssp. (Helicellinae, Gastropoda) inferred by 16S variation and quantitative shell traits.}, journal = {Molecular ecology}, volume = {10}, number = {10}, pages = {2541-2554}, doi = {10.1046/j.0962-1083.2001.01389.x}, pmid = {11742553}, issn = {0962-1083}, mesh = {Animals ; *Biological Evolution ; DNA, Ribosomal/*genetics ; Europe ; Genetic Variation ; Haplotypes ; Likelihood Functions ; Mitochondria/genetics ; Phenotype ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Snails/anatomy &amp; histology/classification/*genetics ; }, abstract = {In an effort to link quantitative morphometric information with molecular data on the population level, we have analysed 19 populations of the conchologically variable land snail Candidula unifasciata from across the species range for variation in quantitative shell traits and at the mitochondrial 16S ribosomal (r)DNA locus. In genetic analysis, including 21 additional populations, we observed two fundamental haplotype clades with an average pairwise sequence divergence of 0.209 +/- 0.009 between clades compared to 0.017 +/- 0.012 within clades, suggesting the presence of two different evolutionary lineages. Integrating additional shell material from the Senckenberg Malacological Collection, a highly significant discriminant analysis on the morphological shell traits with fundamental haplotype clades as grouping variable suggested that the less frequent haplotype corresponds to the described subspecies C. u. rugosiuscula, which we propose to regard as a distinct species. Both taxa were highly subdivided genetically (FST = 0.648 and 0.777 P < 0.001). This was contrasted by the partition of morphological variance, where only 29.6% and 21.9% of the variance were distributed among populations, respectively. In C. unifasciata, no significant association between population pairwise FST estimates and corresponding morphological fixation indices could be detected, indicating independent evolution of the two character sets. Partial least square analysis of environmental factors against shell trait variables in C. u. unifasciata revealed significant correlations between environmental factors and certain quantitative shell traits, whose potential adaptational values are discussed.}, }
@article {pmid11741306, year = {2001}, author = {Kobayashi, Y and Dokiya, Y and Sugita, M}, title = {Dual targeting of phage-type RNA polymerase to both mitochondria and plastids is due to alternative translation initiation in single transcripts.}, journal = {Biochemical and biophysical research communications}, volume = {289}, number = {5}, pages = {1106-1113}, doi = {10.1006/bbrc.2001.6130}, pmid = {11741306}, issn = {0006-291X}, mesh = {Alternative Splicing ; Amino Acid Sequence ; Bacteriophage T7/enzymology/genetics ; Base Sequence ; DNA, Complementary/genetics ; DNA, Plant/genetics ; DNA-Directed RNA Polymerases/*genetics/*metabolism ; Exons ; Genes, Plant ; Introns ; Mitochondria/*enzymology ; Molecular Sequence Data ; Peptide Chain Initiation, Translational ; Phylogeny ; *Plant Proteins ; Plastids/*enzymology ; RNA, Messenger/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Sequence Homology, Amino Acid ; Nicotiana/*enzymology/*genetics ; Viral Proteins ; }, abstract = {We isolated and sequenced a nuclear gene and cDNA encoding a bacteriophage T7-type RNA polymerase, NsRpoT-B, from Nicotiana sylvestris. The gene, NsRpoT-B, consists of 19 exons and 18 introns and encodes a polypeptide of 1020 amino acid residues. The predicted NsRpoT-B protein shows 71% amino acid identity with NsRpoT-A which is a mitochondrial protein. Quantitative RT-PCR revealed that steady-state NsRpoT-B mRNA accumulation is highest in the mature leaves and lowest in the cotyledons. Transient expression assays in protoplasts from N. sylvestris leaves demonstrated that the putative N-terminal transit peptide of NsRpoT-B encodes dual targeting signals directing the protein into mitochondria and plastids. This strongly suggests that NsRpoT-B functions as an RNA polymerase transcribing genes from two different plant organelle genomes. NsRpoT-B transcripts have two potential translation initiation codons. An in vitro translation assay indicated that a chimeric mRNA encoding the N-terminal NsRpoT-B fused to an sGFP produced two polypeptides translated from the first and second initiation codons. This implies that the dual targeting of NsRpoT-B protein is regulated, in part, at the level of translation. We have designated this protein NsRpoTpm.}, }
@article {pmid11738829, year = {2001}, author = {Iwabe, N and Miyata, T}, title = {Overlapping genes in parasitic protist Giardia lamblia.}, journal = {Gene}, volume = {280}, number = {1-2}, pages = {163-167}, doi = {10.1016/s0378-1119(01)00767-3}, pmid = {11738829}, issn = {0378-1119}, mesh = {Animals ; DNA, Complementary/chemistry/genetics ; Databases, Genetic ; Genes, Overlapping/*genetics ; Giardia lamblia/*genetics ; Kinesins/genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Phylogeny ; Protein Isoforms/genetics ; Sequence Analysis, DNA ; }, abstract = {The parasitic protist Giardia lamblia lacks mitochondria and peroxisomes, as well as many typical membrane-bound organella characteristics of higher eukaryotic cells, together with extremely economized usage of DNA sequence, as demonstrated by the lack of introns. We describe here the presence of overlapping genes in G. lamblia, in which a part of the protein coding sequence of one mRNA exists in a region corresponding to the 3'-noncoding region of another mRNA transcribed from a gene on the opposite strand. Recently we isolated 13 kinesin-related cDNAs from G. lamblia. Nine of these cDNAs contain long 3'-noncoding sequences in which long open reading frames (ORFs) exist (in the remaining four cDNAs, the lengths of the 3'-noncoding sequences are very short). The predicted amino acid sequences of these ORFs were subjected to a search for homologies with sequences in databases. The amino acid sequences of the six ORFs exhibited significant sequence similarities with known sequences. These lines of evidence suggest the frequent occurrence of gene overlap in Giardial genome.}, }
@article {pmid11736810, year = {2001}, author = {Nishibori, M and Hayashi, T and Tsudzuki, M and Yamamoto, Y and Yasue, H}, title = {Complete sequence of the Japanese quail (Coturnix japonica) mitochondrial genome and its genetic relationship with related species.}, journal = {Animal genetics}, volume = {32}, number = {6}, pages = {380-385}, doi = {10.1046/j.1365-2052.2001.00795.x}, pmid = {11736810}, issn = {0268-9146}, mesh = {Animals ; Base Sequence ; Coturnix/classification/*genetics ; DNA, Mitochondrial/genetics ; Genome ; Male ; Mitochondria/*genetics ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {The Japanese quail (Coturnix japonica; JQ) is one of the domesticated fowl species of Japan. To provide DNA sequence information for examination of its phylogenetic position in the order Galliformes, the complete sequence of the JQ mitochondria was determined. Sequence analysis revealed that the JQ mitochondrial genome is a circular DNA of 16 697 basepairs (bp), which is smaller than the chicken mitochondrial DNA of 16 775 bp, but the genomic structure of JQ mitochondria was the same as that of the chicken. The sequence homologies of all mitochondrial genes including those for 12S and 16S ribosomal RNA (rRNA), between Japanese quail and chicken ranged from 78.0 to 89.9%. Because the sequences of NADH dehydrogenase subunit 2 and cytochrome b genes had been reported in five species [Phasianus colchicus (ring-neck pheasant: RP), Gallus gallus domesticus (chicken: CH), Perdix perdix (grey partridge: GP), Bambusicola thoracia (Chinese bamboo partridge: CP), and Aythya americana (redhead: RH)], the concatenated nucleotide sequences (2184 bp) and amino acid sequences of these two genes were used in a phylogenetic analysis of JQ against these five species using a maximum likelihood (ML) method. Using the first and second bases of the codons, and the third base of the codons indicated a phylogenic tree of [RH, (RP, GP), (JQ, (CH, CP))]. A phylogenic tree of [RH, JQ, (RP, GP), (CH, CP)] was determined using amino acid sequences. Because the local bootstrap values for the JQ branch in these trees are not high, additional sequence is necessary for construction of a reliable tree.}, }
@article {pmid11735030, year = {2001}, author = {Hammarsund, M and Wilson, W and Corcoran, M and Merup, M and Einhorn, S and Grandér, D and Sangfelt, O}, title = {Identification and characterization of two novel human mitochondrial elongation factor genes, hEFG2 and hEFG1, phylogenetically conserved through evolution.}, journal = {Human genetics}, volume = {109}, number = {5}, pages = {542-550}, doi = {10.1007/s00439-001-0610-5}, pmid = {11735030}, issn = {0340-6717}, mesh = {Amino Acid Sequence ; Base Sequence ; Chromosomes, Artificial, Bacterial ; Cloning, Molecular ; DNA Primers ; DNA, Complementary ; *Evolution, Molecular ; Gene Expression ; Humans ; Mitochondria/*genetics ; *Mitochondrial Proteins ; Molecular Sequence Data ; Peptide Elongation Factor G/chemistry/*genetics ; *Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {Rapid progress in the sequencing of the genome of man and other species allows for the comparative analysis of their genetic structure and content. We have used a combined biochemical and computer-based approach to characterize a 146 kb human genomic bacterial artificial chromosome clone from chromosome 5q13 and discovered a novel human elongation-factor gene, hEFG2. The complete human EFG2 cDNA sequence is 3033 bp and contains 21 exons with conserved exon-intron splice junctions encompassing 45 kb of the genomic sequence with its 5'-end residing within a CpG island, characteristic of a housekeeping gene. The complete size of the hEFG2 cDNA was confirmed by Northern blot and reverse transcription/polymerase chain reaction analysis, which showed a single transcript of 3.2 kb ubiquitously expressed in various human tissues. The hEFG2 protein shows significant homology to several bacterial EF-G proteins, including that of Thermus thermophilus, and to the yeast Saccharomyces cerevisiae mitochondrial elongation factor-G (MEF2). Multiple alignments reveal a novel gene family of mitochondrial EF-G proteins that can by divided into two subgroups, EF-G1 and EF-G2, in several eukaryotic species including S. pombe, Caenorhabditis elegans and Drosophila melanogaster. Using the information contained in the public databases, we also identified and cloned the complete coding sequence of the human EFG1 gene on chromosome 3q25. The cloning and characterization of these human mitochondrial elongation factor genes should permit us to address their role in the regulation of normal mitochondrial function and in various disease states.}, }
@article {pmid11734904, year = {2002}, author = {Lin, JJ and Yang, TH and Wahlstrand, BD and Fields, PA and Somero, GN}, title = {Phylogenetic relationships and biochemical properties of the duplicated cytosolic and mitochondrial isoforms of malate dehydrogenase from a teleost fish, Sphyraena idiastes.}, journal = {Journal of molecular evolution}, volume = {54}, number = {1}, pages = {107-117}, doi = {10.1007/s00239-001-0023-z}, pmid = {11734904}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Cytosol/enzymology ; Fishes/classification/*genetics ; Isoenzymes/classification/genetics ; Kinetics ; Malate Dehydrogenase/classification/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; South America ; Temperature ; }, abstract = {Unlike birds and mammals, teleost fish express two paralogous isoforms (paralogues) of cytosolic malate dehydrogenase (cMDH; EC 1.1.1.37; NAD+: malate oxidoreductase) whose evolutionary relationships to the single cMDH of tetrapods are unknown. We sequenced complementary DNAs for both cMDHs and the mitochondrial isoform (mMDH) of the fish Sphyraena idiastes (south temperate barracuda) and compared the sequences, kinetic properties, and thermal stabilities of the three isoforms with those of mammalian orthologues. Both fish cMDHs comprise 333 residues and have subunit masses of approximately 36 kDa. One cytosolic isoform, cMDH-S, was significantly more heat-stable than either the other cMDH (cMDH-L) or mMDH. In contradiction to the generally accepted model of vertebrate cMDH evolution, our phylogenetic analysis indicates that the duplication of the fish cytosolic paralogues occurred after the divergence of the lineages leading to teleosts and tetrapods. cMDH-L and cMDH-S differed in optimal concentrations of substrates and cofactors and apparent Michaelis-Menten constants, suggesting that the two paralogues may play distinct physiological roles. Differences in intrinsic thermal stability among MDH paralogues may reflect different degrees of stabilization in vivo by extrinsic stabilizers, notably protein concentration in the case of mMDH. Thermal stabilities of porcine mMDH and cMDH-L, but not cMDH-S, were significantly increased when denaturation was measured at a high protein (bovine serum albumin; BSA) concentration, but the BSA-induced stabilization reduced the catalytic activity.}, }
@article {pmid11731127, year = {2001}, author = {Yen, MR and Harley, KT and Tseng, YH and Saier, MH}, title = {Phylogenetic and structural analyses of the oxa1 family of protein translocases.}, journal = {FEMS microbiology letters}, volume = {204}, number = {2}, pages = {223-231}, doi = {10.1111/j.1574-6968.2001.tb10889.x}, pmid = {11731127}, issn = {0378-1097}, support = {GM 64368-24/GM/NIGMS NIH HHS/United States ; GM55434-17/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bacteria/genetics/*metabolism ; Chloroplasts/metabolism ; Electron Transport Complex IV ; Evolution, Molecular ; Mitochondria/metabolism ; Mitochondrial Proteins ; Molecular Sequence Data ; Nuclear Proteins/*chemistry/*genetics/metabolism ; *Phylogeny ; Protein Transport ; }, abstract = {Mitochondrial Oxa1p homologs have been shown to function in protein export and membrane insertion in bacteria, mitochondria and chloroplasts, but their mode of action, organismal distribution and evolutionary origins are poorly understood. All sequenced homologs of Oxa1p were retrieved from the databases and multiply aligned. All organisms with a fully sequenced genome possess at least one Oxa1p homolog showing that the family is truly ubiquitous. Most prokaryotes possess just one Oxa1p homolog, but several Gram-positive bacteria and one archaeon possess two, and eukaryotes may have as many as six. Although these proteins vary in length over a 5-fold range, they exhibit a common hydrophobic core region of about 200 residues. Multiple sequence alignments reveal conserved residues and provide the basis for structural and phylogenetic analyses that serve to characterize the Oxa1 family.}, }
@article {pmid11729142, year = {2001}, author = {Clark-Walker, GD and Chen, XJ}, title = {Dual mutations reveal interactions between components of oxidative phosphorylation in Kluyveromyces lactis.}, journal = {Genetics}, volume = {159}, number = {3}, pages = {929-938}, pmid = {11729142}, issn = {0016-6731}, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Antimycin A/*analogs &amp; derivatives/pharmacology ; Cell Nucleus/metabolism ; Cytosol/metabolism ; DNA, Mitochondrial/metabolism ; Diploidy ; Electron Transport ; Genetic Complementation Test ; Heterozygote ; Hydrolysis ; Kinetics ; Kluyveromyces/*genetics/*metabolism ; Membrane Potentials ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/metabolism ; Models, Genetic ; *Mutation ; Oxygen/*metabolism ; Phenotype ; Phosphorylation ; Proton-Translocating ATPases/metabolism ; }, abstract = {Loss of mtDNA or mitochondrial protein synthesis cannot be tolerated by wild-type Kluyveromyces lactis. The mitochondrial function responsible for rho(0)-lethality has been identified by disruption of nuclear genes encoding electron transport and F(0)-ATP synthase components of oxidative phosphorylation. Sporulation of diploid strains heterozygous for disruptions in genes for the two components of oxidative phosphorylation results in the formation of nonviable spores inferred to contain both disruptions. Lethality of spores is thought to result from absence of a transmembrane potential, Delta Psi, across the mitochondrial inner membrane due to lack of proton pumping by the electron transport chain or reversal of F(1)F(0)-ATP synthase. Synergistic lethality, caused by disruption of nuclear genes, or rho(0)-lethality can be suppressed by the atp2.1 mutation in the beta-subunit of F(1)-ATPase. Suppression is viewed as occurring by an increased hydrolysis of ATP by mutant F(1), allowing sufficient electrogenic exchange by the translocase of ADP in the matrix for ATP in the cytosol to maintain Delta Psi. In addition, lethality of haploid strains with a disruption of AAC encoding the ADP/ATP translocase can be suppressed by atp2.1. In this case suppression is considered to occur by mutant F(1) acting in the forward direction to partially uncouple ATP production, thereby stimulating respiration and relieving detrimental hyperpolarization of the inner membrane. Participation of the ADP/ATP translocase in suppression of rho(0)-lethality is supported by the observation that disruption of AAC abolishes suppressor activity of atp2.1.}, }
@article {pmid11727998, year = {2001}, author = {Lutz, KA and Maliga, P}, title = {Lack of conservation of editing sites in mRNAs that encode subunits of the NAD(P)H dehydrogenase complex in plastids and mitochondria of Arabidopsis thaliana.}, journal = {Current genetics}, volume = {40}, number = {3}, pages = {214-219}, doi = {10.1007/s002940100242}, pmid = {11727998}, issn = {0172-8083}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics ; Arabidopsis Proteins/*genetics ; Evolution, Molecular ; Genes, Plant ; Mitochondria/*genetics ; Molecular Sequence Data ; NAD(P)H Dehydrogenase (Quinone)/*genetics ; Plastids/*genetics ; Protein Subunits ; *RNA Editing ; RNA, Messenger ; RNA, Plant/*metabolism ; Sequence Homology, Amino Acid ; }, abstract = {RNA editing in the plastids and mitochondria of higher plants involves C to U conversion of specific nucleotides in the mRNA. This leads to the synthesis of proteins that are different from those predicted by the DNA sequence. Editing appears to have arisen at about the same time in both plastids and mitochondria, suggesting a common evolutionary origin. The problem we address here is whether or not there has been co-evolution of the editing systems in the two organelles. Our test system was editing of the Arabidopsis thaliana mRNAs for ndhB and nad2, and for ndhD and nad4, which encode homologous subunits of the plastid and mitochondrial NAD(P)H dehydrogenases, respectively. The editing sites in the Arabidopsis nad2 and nad4 mRNAs have previously been determined and we report here 19 editing sites in eight mRNAs in Arabidopsis plastids. Out of these, eight sites are localized in the ndhB mRNA. In its mitochondrial counterpart, nad2, 31 editing sites are present, none of which are shared with the ndhB gene. The Arabidopsis ndhD mRNA is edited at four positions, only one of which is shared by its mitochondrial homologue, nad4, which contains 32 editing sites. These findings suggest that, although editing in the two organelles may have derived from a single system, there is no significant conservation of editing sites in cognate mRNAs in plastids and mitochondria.}, }
@article {pmid11727826, year = {2001}, author = {Reichert, AS and Thurlow, DL and Mörl, M}, title = {A eubacterial origin for the human tRNA nucleotidyltransferase?.}, journal = {Biological chemistry}, volume = {382}, number = {10}, pages = {1431-1438}, doi = {10.1515/BC.2001.176}, pmid = {11727826}, issn = {1431-6730}, support = {1R15GM57685-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bacteria/*enzymology ; Caenorhabditis elegans/enzymology ; Drosophila melanogaster/enzymology ; Evolution, Molecular ; HeLa Cells ; Humans ; Kinetics ; Mice ; Molecular Sequence Data ; Nucleotides/metabolism ; RNA Nucleotidyltransferases/*physiology ; Sequence Homology, Amino Acid ; }, abstract = {tRNA CCA-termini are generated and maintained by tRNA nucleotidyltransferases. Together with poly(A) polymerases and other enzymes they belong to the nucleotidyltransferase superfamily. However, sequence alignments within this family do not allow to distinguish between CCA-adding enzymes and poly(A) polymerases. Furthermore, due to the lack of sequence information about animal CCA-adding enzymes, identification of corresponding animal genes was not possible so far. Therefore, we looked for the human homolog using the baker's yeast tRNA nucleotidyltransferase as a query sequence in a BLAST search. This revealed that the human gene transcript CGI-47 (#AF151805) deposited in GenBank is likely to encode such an enzyme. To identify the nature of this protein, the cDNA of the transcript was cloned and the recombinant protein biochemically characterized, indicating that CGI-47 encodes a bona fide CCA-adding enzyme and not a poly(A) polymerase. This confirmed animal CCA-adding enzyme allowed us to identify putative homologs from other animals. Calculation of a neighbor-joining tree, using an alignment of several CCA-adding enzymes, revealed that the animal enzymes resemble more eubacterial ones than eukaryotic plant and fungal tRNA nucleotidyltransferases, suggesting that the animal nuclear cca genes might have been derived from the endosymbiotic progenitor of mitochondria and are therefore of eubacterial origin.}, }
@article {pmid11726496, year = {2001}, author = {Ceschini, S and Keeley, A and McAlister, MS and Oram, M and Phelan, J and Pearl, LH and Tsaneva, IR and Barrett, TE}, title = {Crystal structure of the fission yeast mitochondrial Holliday junction resolvase Ydc2.}, journal = {The EMBO journal}, volume = {20}, number = {23}, pages = {6601-6611}, pmid = {11726496}, issn = {0261-4189}, mesh = {Amino Acid Sequence ; Binding Sites ; Catalysis ; Catalytic Domain ; Cloning, Molecular ; *Crystallography, X-Ray ; Dimerization ; Endodeoxyribonucleases/*chemistry ; Evolution, Molecular ; Isomerism ; Mitochondria/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Open Reading Frames ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Schizosaccharomyces/*enzymology ; *Schizosaccharomyces pombe Proteins ; Sequence Homology, Amino Acid ; }, abstract = {Resolution of Holliday junctions into separate DNA duplexes requires enzymatic cleavage of an equivalent strand from each contributing duplex at or close to the point of strand exchange. Diverse Holliday junction-resolving enzymes have been identified in bacteria, bacteriophages, archaea and pox viruses, but the only eukaryotic examples identified so far are those from fungal mitochondria. We have now determined the crystal structure of Ydc2 (also known as SpCce1), a Holliday junction resolvase from the fission yeast Schizosaccharomyces pombe that is involved in the maintenance of mitochondrial DNA. This first structure of a eukaryotic Holliday junction resolvase confirms a distant evolutionary relationship to the bacterial RuvC family, but reveals structural features which are unique to the eukaryotic enzymes. Detailed analysis of the dimeric structure suggests mechanisms for junction isomerization and communication between the two active sites, and together with site-directed mutagenesis identifies residues involved in catalysis.}, }
@article {pmid11725869, year = {2001}, author = {Borecký, J and Maia, IG and Arruda, P}, title = {Mitochondrial uncoupling proteins in mammals and plants.}, journal = {Bioscience reports}, volume = {21}, number = {2}, pages = {201-212}, doi = {10.1023/a:1013604526175}, pmid = {11725869}, issn = {0144-8463}, mesh = {Amino Acid Sequence ; Animals ; Carrier Proteins/chemistry/classification/genetics/*metabolism ; Ion Channels ; Membrane Proteins/chemistry/classification/genetics/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins ; Molecular Sequence Data ; Phylogeny ; Plant Physiological Phenomena ; Plant Proteins/chemistry/classification/genetics/*metabolism ; Protein Structure, Tertiary ; Thermogenesis/physiology ; Uncoupling Protein 1 ; }, abstract = {Uncoupling proteins (UCPs) belong to a distinct cluster of the mitochondrial anion carrier family. Up to five different uncoupling protein types were found in mitochondria of mammals and plants, and recently in fishes, fungi and protozoa. They exhibit a significantly conserved structure with several motifs specific to either the whole cluster or protein type. Uncoupling proteins, as well as the whole mitochondrial anion carrier gene family, probably emerged in evolution before the separation of animal, fungi, and plant kingdoms and originate from an anion/nucleotide or anion/anion transporter ancestor. Mammalian UCP1, UCP2, UCP3, and plant uncoupling proteins pUCP1 and pUCP2 are similar and seem to form one subgroup, whereas UCP4 and BMCP1 belong to a different group. Molecular, biochemical, and phylogenic data suggest that UCP2 could be considered as an UCP-prototype. UCP1 plays its biological role mainly in the non-shivering thermogenesis while the role of the other types is unknown. However, hypotheses have suggested that they are involved in the general balance of basic energy expenditure, protection from reactive oxygen species, and, in plants, in fruit ripening and seed ontogeny.}, }
@article {pmid11724862, year = {2001}, author = {Wang, L and Yokoyama, K and Miyaji, M and Nishimura, K}, title = {Identification, classification, and phylogeny of the pathogenic species Exophiala jeanselmei and related species by mitochondrial cytochrome b gene analysis.}, journal = {Journal of clinical microbiology}, volume = {39}, number = {12}, pages = {4462-4467}, pmid = {11724862}, issn = {0095-1137}, mesh = {Cytochrome b Group/*genetics/metabolism ; DNA, Bacterial/analysis ; Exophiala/*classification/enzymology/genetics/pathogenicity ; Humans ; Mitochondria/*enzymology ; Molecular Sequence Data ; Mycoses/*microbiology ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {We analyzed a 402-bp sequence of the mitochondrial cytochrome b gene of 34 strains of Exophiala jeanselmei and 16 strains representing 12 related species. The strains of E. jeanselmei were classified into 20 DNA types and 17 amino acid types. The differences between these strains were found in 1 to 60 nucleotides and 1 to 17 amino acids. On the basis of the identities and similarities of nucleotide and amino acid sequences, some strains were reidentified: i.e., two strains of E. jeanselmei var. hetermorpha and one strain of E. castellanii as E. dermatitidis (including the type strain), three strains of E. jeanselmei as E. jeanselmei var. lecanii-corni (including the type strain), three strains of E. jeanselmei as E. bergeri (including the type strain), seven strains of E. jeanselmei as E. pisciphila (including the type strain), seven strains of E. jeanselmei as E. jeanselmei var. jeanselmei (including the type strain), one strain of E. jeanselmei as Fonsecaea pedrosoi (including the type strain), and one strain of E. jeanselmei as E. spinifera (including the type strain). Some E. jeanselmei strains showed distinct nucleotide and amino acid sequences. The amino-acid-based UPGMA (unweighted pair group method with the arithmetic mean) tree exhibited nearly the same topology as those of the DNA-based trees obtained by neighbor joining, maximum parsimony, and maximum likelihood methods.}, }
@article {pmid11724769, year = {2002}, author = {Lee, HJ and Shin, SY and Choi, C and Lee, YH and Lee, SJ}, title = {Formation and removal of alpha-synuclein aggregates in cells exposed to mitochondrial inhibitors.}, journal = {The Journal of biological chemistry}, volume = {277}, number = {7}, pages = {5411-5417}, doi = {10.1074/jbc.M105326200}, pmid = {11724769}, issn = {0021-9258}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Blotting, Western ; COS Cells ; Cysteine Endopeptidases/pharmacology ; Electron Transport ; Electrons ; Humans ; In Situ Nick-End Labeling ; Microscopy, Fluorescence ; Mitochondria/*metabolism ; Multienzyme Complexes/pharmacology ; Nerve Tissue Proteins/*chemistry/*metabolism ; Proteasome Endopeptidase Complex ; Protein Conformation ; Recombinant Proteins/metabolism ; Rotenone/pharmacology ; Synucleins ; Time Factors ; Tubulin/metabolism ; Ubiquitin/pharmacology ; Uncoupling Agents/pharmacology ; Vimentin/metabolism ; alpha-Synuclein ; }, abstract = {Mitochondrial dysfunction has been associated with Parkinson's disease. However, the role of mitochondrial defects in the formation of Lewy bodies, a pathological hallmark of Parkinson's disease has not been addressed directly. In this report, we investigated the effects of inhibitors of the mitochondrial electron-transport chain on the aggregation of alpha-synuclein, a major protein component of Lewy bodies. Treatment with rotenone, an inhibitor of complex I, resulted in an increase of detergent-resistant alpha-synuclein aggregates and a reduction in ATP level. Another inhibitor of the electron-transport chain, oligomycin, also showed temporal correlation between the formation of aggregates and ATP reduction. Microscopic analyses showed a progressive evolution of small aggregates of alpha-synuclein to a large perinuclear inclusion body. The inclusions were co-stained with ubiquitin, 20 S proteasome, gamma-tubulin, and vimentin. The perinuclear inclusion bodies, but not the small cytoplasmic aggregates, were thioflavin S-positive, suggesting the amyloid-like conformation. Interestingly, the aggregates disappeared when the cells were replenished with inhibitor-free medium. Disappearance of aggregates coincided with the recovery of mitochondrial metabolism and was partially inhibited by proteasome inhibitors. These results suggest that the formation of alpha-synuclein inclusions could be initiated by an impaired mitochondrial function and be reversed by restoring normal mitochondrial metabolism.}, }
@article {pmid11722843, year = {2001}, author = {Kobayashi, Y and Dokiya, Y and Sugiura, M and Niwa, Y and Sugita, M}, title = {Genomic organization and organ-specific expression of a nuclear gene encoding phage-type RNA polymerase in Nicotiana sylvestris.}, journal = {Gene}, volume = {279}, number = {1}, pages = {33-40}, doi = {10.1016/s0378-1119(01)00729-6}, pmid = {11722843}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Bacteriophage T7/enzymology ; Biological Transport ; Blotting, Northern ; Cell Nucleus/genetics ; DNA, Complementary/chemistry/genetics/isolation &amp; purification ; DNA, Plant/chemistry/genetics/isolation &amp; purification ; DNA-Directed RNA Polymerases/*genetics/metabolism ; Exons ; Gene Expression Regulation, Plant ; Genes, Plant/*genetics ; Green Fluorescent Proteins ; Introns ; Luminescent Proteins/genetics/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Messenger/genetics/metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Tissue Distribution ; Nicotiana/enzymology/*genetics ; }, abstract = {We have isolated and sequenced a nuclear gene and cDNA encoding bacteriophage T7-type single subunit RNA polymerase, NsRpoT-A, from Nicotiana sylvestris. NsRpoT-A consists of 19 exons and 18 introns; the first intron is 17 kb, the longest yet identified in a plant gene. Genomic Southern analysis indicated that N. sylvestris contains a small family of NsRpoT genes. Quantitative RT-PCR revealed that steady-state mRNA levels are highest in the leaves and lowest in the cotyledons. Phylogenetic analysis of NsRpoT-A and the RpoT proteins of other plant species suggested that NsRpoT-A is a mitochondrial protein. The TargetP program predicted localization of the NsRpoT-A gene product to the mitochondria. Using a transient expression assay and protoplasts from N. sylvestris mesophyll cells, we clearly demonstrated that the N-terminal sequence of NsRpoT-A targets the protein to the mitochondria. We therefore named this protein NsRpoTm.}, }
@article {pmid11719806, year = {2001}, author = {Katinka, MD and Duprat, S and Cornillot, E and Méténier, G and Thomarat, F and Prensier, G and Barbe, V and Peyretaillade, E and Brottier, P and Wincker, P and Delbac, F and El Alaoui, H and Peyret, P and Saurin, W and Gouy, M and Weissenbach, J and Vivarès, CP}, title = {Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi.}, journal = {Nature}, volume = {414}, number = {6862}, pages = {450-453}, doi = {10.1038/35106579}, pmid = {11719806}, issn = {0028-0836}, mesh = {Animals ; Biological Evolution ; Biological Transport ; DNA, Protozoan ; Encephalitozoon cuniculi/*genetics/metabolism/ultrastructure ; *Genome, Protozoan ; Mice ; Mitochondria/genetics ; Molecular Sequence Data ; Protozoan Proteins/genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Microsporidia are obligate intracellular parasites infesting many animal groups. Lacking mitochondria and peroxysomes, these unicellular eukaryotes were first considered a deeply branching protist lineage that diverged before the endosymbiotic event that led to mitochondria. The discovery of a gene for a mitochondrial-type chaperone combined with molecular phylogenetic data later implied that microsporidia are atypical fungi that lost mitochondria during evolution. Here we report the DNA sequences of the 11 chromosomes of the approximately 2.9-megabase (Mb) genome of Encephalitozoon cuniculi (1,997 potential protein-coding genes). Genome compaction is reflected by reduced intergenic spacers and by the shortness of most putative proteins relative to their eukaryote orthologues. The strong host dependence is illustrated by the lack of genes for some biosynthetic pathways and for the tricarboxylic acid cycle. Phylogenetic analysis lends substantial credit to the fungal affiliation of microsporidia. Because the E. cuniculi genome contains genes related to some mitochondrial functions (for example, Fe-S cluster assembly), we hypothesize that microsporidia have retained a mitochondrion-derived organelle.}, }
@article {pmid11719785, year = {2001}, author = {Keeling, PJ}, title = {Parasites go the full monty.}, journal = {Nature}, volume = {414}, number = {6862}, pages = {401-402}, doi = {10.1038/35106666}, pmid = {11719785}, issn = {0028-0836}, mesh = {Animals ; Encephalitozoon cuniculi/*genetics/physiology ; Evolution, Molecular ; Genome, Protozoan ; Humans ; Mitochondria ; Parasites/genetics/physiology ; }, }
@article {pmid11719578, year = {2001}, author = {Adams, KL and Ong, HC and Palmer, JD}, title = {Mitochondrial gene transfer in pieces: fission of the ribosomal protein gene rpl2 and partial or complete gene transfer to the nucleus.}, journal = {Molecular biology and evolution}, volume = {18}, number = {12}, pages = {2289-2297}, doi = {10.1093/oxfordjournals.molbev.a003775}, pmid = {11719578}, issn = {0737-4038}, support = {GM-35087/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Cell Nucleus/*genetics/metabolism ; Codon, Terminator ; DNA, Mitochondrial/*genetics ; *Genes, Plant ; Magnoliopsida/classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Ribosomal Proteins/classification/*genetics/metabolism ; Sequence Alignment ; }, abstract = {Mitochondrial genes are usually conserved in size in angiosperms. A notable exception is the rpl2 gene, which is considerably shorter in the eudicot Arabidopsis than in the monocot rice. Here, we show that a severely truncated mitochondrial rpl2 gene (termed 5' rpl2) was created by the formation of a premature stop codon early in eudicot evolution. This 5' rpl2 gene was subsequently lost many times from the mitochondrial DNAs of 179 core eudicots surveyed by Southern hybridization. The sequence corresponding to the 3' end of rice rpl2 (termed 3' rpl2) has been lost much more pervasively among the mitochondrial DNAs of core eudicots than has 5' rpl2. Furthermore, where still present in these mitochondrial genomes, 3' rpl2 always appears to be a pseudogene, and there is no evidence that 3' rpl2 was ever a functional mitochondrial gene. An intact and expressed 3' rpl2 gene was discovered in the nucleus of five diverse eudicots (tomato, cotton, Arabidopsis, soybean, and Medicago). In the first three of these species, 5' rpl2 is still present in the mitochondrion, unlike the two legumes, where both parts of rpl2 are present in the nucleus as separate genes. The full-length rpl2 gene has been transferred intact to the nucleus in maize. We propose that the 3' end of rpl2 was functionally transferred to the nucleus early in eudicot evolution, and that this event then permitted the nonsense mutation that gave rise to the mitochondrial 5' rpl2 gene. Once 5' rpl2 was established as a stand-alone mitochondrial gene, it was then lost, and was probably transferred to the nucleus many times. This complex history of gene fission and gene transfer has created four distinct types of rpl2 structures or compartmentalizations in angiosperms: (1) intact rpl2 gene in the mitochondrion, (2) intact gene in the nucleus, (3) split gene, 5' in the mitochondrion and 3' in the nucleus, and (4) split gene, both parts in the nucleus.}, }
@article {pmid11719183, year = {2001}, author = {Dacks, JB and Doolittle, WF}, title = {Reconstructing/deconstructing the earliest eukaryotes: how comparative genomics can help.}, journal = {Cell}, volume = {107}, number = {4}, pages = {419-425}, doi = {10.1016/s0092-8674(01)00584-0}, pmid = {11719183}, issn = {0092-8674}, mesh = {Animal Population Groups/genetics ; Animals ; Archaea/genetics ; Bacteria/genetics ; Bacterial Proteins/genetics ; Consensus Sequence ; *Escherichia coli Proteins ; Eukaryota/metabolism ; Eukaryotic Cells/*cytology ; Evolution, Molecular ; Expressed Sequence Tags ; Fungi/genetics ; *Genomics ; Golgi Apparatus/enzymology ; Introns/genetics ; Microsporidia/genetics ; Mitochondria ; Phylogeny ; Plants/genetics ; Species Specificity ; Spliceosomes ; Trichomonas/genetics ; }, abstract = {We could reconstruct the evolution of eukaryote-specific molecular and cellular machinery if some living eukaryotes retained primitive cellular structures and we knew which eukaryotes these were. It's not clear that either is the case, but the expanding protist genomic database could help us in several ways.}, }
@article {pmid11718729, year = {2001}, author = {Sweetlove, LJ and Mowday, B and Hebestreit, HF and Leaver, CJ and Millar, AH}, title = {Nucleoside diphosphate kinase III is localized to the inter-membrane space in plant mitochondria.}, journal = {FEBS letters}, volume = {508}, number = {2}, pages = {272-276}, doi = {10.1016/s0014-5793(01)03069-1}, pmid = {11718729}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Arabidopsis/cytology/*enzymology ; Electrophoresis, Gel, Two-Dimensional ; Mass Spectrometry ; Mitochondria/*enzymology ; Molecular Sequence Data ; Molecular Weight ; Nucleoside-Diphosphate Kinase/*analysis/chemistry/metabolism ; Peptide Mapping ; Phylogeny ; Sequence Homology, Amino Acid ; Solanum tuberosum/cytology/*enzymology ; }, abstract = {Three types of nucleoside diphosphate kinases (NDPKs) are found in plants but the intra-cellular compartmentation of these proteins is not certain, especially the location of the recently identified type III proteins. Through the fractionation of plant mitochondria from potato and Arabidopsis, display of protein profiles by 2D gel electrophoresis, and identification by mass spectrometry, we present the first direct evidence that type III proteins are localized in the inter-membrane space of plant mitochondria. The possible metabolic functions of NDPK III are discussed in light of its sub-cellular localization.}, }
@article {pmid11715050, year = {2001}, author = {Tilly, JL}, title = {Commuting the death sentence: how oocytes strive to survive.}, journal = {Nature reviews. Molecular cell biology}, volume = {2}, number = {11}, pages = {838-848}, doi = {10.1038/35099086}, pmid = {11715050}, issn = {1471-0072}, mesh = {Animals ; *Apoptosis ; Biological Evolution ; Cell Survival ; Female ; Fertility ; Humans ; Mice ; Mitochondria ; Models, Biological ; Oocytes/*cytology/*physiology ; Ovary/physiology ; Sphingomyelins/physiology ; }, abstract = {Programmed cell death claims up to 99.9% of the cells in the mammalian female germ line, which eventually drives irreversible infertility and ovarian failure - the menopause in humans. New insights into the mechanisms that underlie germ-cell apoptosis have been provided by the study of oocyte death in lower organisms and in genetically manipulated mice that lack apoptosis-regulatory proteins. With new therapeutic tools to control fertility, oocyte quality and ovarian lifespan on the horizon, understanding how and why the female body creates, only to delete, so many germ cells is imperative.}, }
@article {pmid11700280, year = {2001}, author = {Birky, CW}, title = {The inheritance of genes in mitochondria and chloroplasts: laws, mechanisms, and models.}, journal = {Annual review of genetics}, volume = {35}, number = {}, pages = {125-148}, doi = {10.1146/annurev.genet.35.102401.090231}, pmid = {11700280}, issn = {0066-4197}, mesh = {Animals ; Cell Nucleus/genetics ; Chloroplasts/*genetics ; Crosses, Genetic ; Eukaryota/genetics ; Eukaryotic Cells ; Evolution, Molecular ; Extrachromosomal Inheritance/*genetics ; Genomic Imprinting ; Mitochondria/*genetics ; Models, Genetic ; Plants/genetics ; Reproduction/genetics ; Saccharomyces cerevisiae/genetics ; Selection, Genetic ; }, abstract = {The inheritance of mitochondrial and chloroplast genes differs from that of nuclear genes in showing vegetative segregation, uniparental inheritance, intracellular selection, and reduced recombination. Vegetative segregation and some cases of uniparental inheritance are due to stochastic replication and partitioning of organelle genomes. The rate and pattern of vegetative segregation depend partly on the numbers of genomes and of organelles per cell, but more importantly on the extent to which genomes are shared between organelles, their distribution in the cell, the variance in number of replications per molecule, and the variance in numerical and genotypic partitioning of organelles and genomes. Most of these parameters are unknown for most organisms, but a simple binomial probability model using the effective number of genomes is a useful substitute. Studies using new cytological, molecular, and genetic methods are shedding some light on the processes involved in segregation, and also on the mechanisms of intracellular selection and uniparental inheritance in mammals. But significant issues remain unresolved, notably about the extent of paternal transmission and mitochondrial fusion in mammals.}, }
@article {pmid11696185, year = {2001}, author = {Papenbrock, J and Mishra, S and Mock, HP and Kruse, E and Schmidt, EK and Petersmann, A and Braun, HP and Grimm, B}, title = {Impaired expression of the plastidic ferrochelatase by antisense RNA synthesis leads to a necrotic phenotype of transformed tobacco plants.}, journal = {The Plant journal : for cell and molecular biology}, volume = {28}, number = {1}, pages = {41-50}, doi = {10.1046/j.1365-313x.2001.01126.x}, pmid = {11696185}, issn = {0960-7412}, mesh = {Cloning, Molecular ; Ferrochelatase/*biosynthesis/genetics/metabolism ; Gene Expression Regulation, Enzymologic ; *Gene Expression Regulation, Plant ; Heme/metabolism ; Isoenzymes/biosynthesis/genetics/metabolism ; Light ; Mitochondria/enzymology ; Necrosis ; Phenotype ; Phylogeny ; Plants, Genetically Modified ; Plastids/*enzymology/genetics/metabolism/radiation effects ; Protoporphyrins/metabolism ; RNA, Antisense/biosynthesis/genetics/*metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Nicotiana/*cytology/*enzymology/genetics/metabolism ; }, abstract = {Protoporphyrin IX is the last common intermediate of tetrapyrrole biosynthesis. The chelation of a Mg2+ ion by magnesium chelatase and of a ferrous ion by ferrochelatase directs protoporphyrin IX towards the formation of chlorophyll and heme, respectively. A full length cDNA clone encoding a ferrochelatase was identified from a Nicotiana tabacum cDNA library. The encoded protein consists of 497 amino acid residues with a molecular weight of 55.4 kDa. In vitro import of the protein into chloroplasts and its location in stroma and thylakoids confirm its close relationship to the previously described Arabidopsis thaliana plastid-located ferrochelatase (FeChII). A 1700-bp tobacco FeCh cDNA sequence was expressed in Nicotiana tabacum cv. Samsun NN under the control of the CaMV 35S promoter in antisense orientation allowing investigation into the consequences of selective reduction of the plastidic ferrochelatase activity for protoporphyrin IX channeling in chloroplasts and for interactions between plastidic and mitochondrial heme synthesis. Leaves of several transformants showed a reduced chlorophyll content and, during development, a light intensity-dependent formation of necrotic leaf lesions. In comparison with wild-type plants the total ferrochelatase activity was decreased in transgenic lines leading to an accumulation of photosensitizing protoporphyrin IX. Ferrochelatase activity was reduced only in plastids but not in mitochondria of transgenic plants. By means of the specifically diminished ferrochelatase activity consequences of the selective inhibition of protoheme formation for the intracellular supply of heme can be investigated in the future.}, }
@article {pmid11696011, year = {2001}, author = {Igamberdiev, AU and Kleczkowski, LA}, title = {Implications of adenylate kinase-governed equilibrium of adenylates on contents of free magnesium in plant cells and compartments.}, journal = {The Biochemical journal}, volume = {360}, number = {Pt 1}, pages = {225-231}, pmid = {11696011}, issn = {0264-6021}, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Monophosphate/metabolism ; Adenosine Triphosphate/metabolism ; Adenylate Kinase/*metabolism ; Animals ; Chloroplasts/metabolism ; Citric Acid Cycle ; Cytosol/metabolism ; Dose-Response Relationship, Drug ; Kinetics ; Magnesium/*metabolism ; Mitochondria/metabolism ; Models, Chemical ; Muscles/metabolism ; Oxygen Consumption ; Photosynthesis ; Plant Leaves/metabolism ; Rabbits ; Time Factors ; }, abstract = {On the basis of the equilibrium of adenylate kinase (AK; EC 2.7.4.3), which interconverts MgATP and free AMP with MgADP and free ADP, an approach has been worked out to calculate concentrations of free magnesium (Mg(2+)), based on concentrations of total ATP, ADP and AMP in plant tissues and in individual subcellular compartments. Based on reported total adenylate contents, [Mg(2+)] in plant tissues and organelles varies significantly depending on light and dark regimes, plant age and developmental stage. In steady-state conditions, [Mg(2+)] in chloroplasts is similar in light and darkness (in the millimolar range), whereas in the cytosol it is very low in the light and increases to about 0.4 mM in darkness. During the dark-to-light transition (photosynthetic induction), the [Mg(2+)] in chloroplasts falls to low values (0.2 mM or less), corresponding to a delay in photosynthetic oxygen evolution. This delay is considered to result from lower activities of Mg-dependent enzymes in the Calvin cycle. In mitochondria, the changes in [Mg(2+)] are similar but smoother. On the other hand, when the transition from light to darkness is considered, an initial increase in [Mg(2+)] occurs in both chloroplasts and mitochondria, which may be of importance for the control of key regulatory enzymes (e.g. mitochondrial malic enzyme and pyruvate dehydrogenase complex) and for processes connected with light-enhanced dark respiration. A rationale is presented for a possible role of [MgATP]/[MgADP] ratio (rather than [ATP(total)]/[ADP(total)]) as an important component of metabolic cellular control. It is postulated that assays of total adenylates may provide an accurate measure of [Mg(2+)] in plant tissues/cells and subcellular compartments, given that the adenylates are equilibrated by AK.}, }
@article {pmid11695831, year = {2001}, author = {Yano, T and Ohnishi, T}, title = {The origin of cluster N2 of the energy-transducing NADH-quinone oxidoreductase: comparisons of phylogenetically related enzymes.}, journal = {Journal of bioenergetics and biomembranes}, volume = {33}, number = {3}, pages = {213-222}, pmid = {11695831}, issn = {0145-479X}, support = {R01GM30736/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bacteria/enzymology ; Coenzymes ; Electron Transport ; Electron Transport Complex I ; Evolution, Molecular ; Mitochondria/enzymology ; Molecular Sequence Data ; NADH, NADPH Oxidoreductases/*chemistry/*genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; Sequence Homology, Amino Acid ; Ubiquinone/*analogs &amp; derivatives/metabolism ; }, abstract = {NADH-quinone (Q) oxidoreductase is a large and complex redox proton pump, which utilizes the free energy derived from oxidation of NADH with lipophilic electron/proton carrier Q to translocate protons across the membrane to generate an electrochemical proton gradient. Although its molecular mechanism is largely unknown, recent biochemical, biophysical, and molecular biological studies have revealed that particular subunits and cofactors play an essential role in the energy-coupling reaction. Based on these latest experimental data, we exhaustively analyzed the sequence information available from evolutionarily related enzymes such as [NiFe] hydrogenases. We found significant and conserved sequence differences in the PSST/Nqo6/NuoB, 49kDa/Nqo4/NuoD, and ND1/Nqo8/NuoH subunit homologs between complex I/NDH-1 and [NiFe] hydrogenases. The alterations, especially in the postulated ligand motif for cluster N2 in the PSST/Nqo6/NuoB subunits, appear to be evolutionarily important in determining the physiological function of complex I/NDH-1. These observations led us to propose a hypothetical evolutionary scheme: during the course of evolution, drastic changes have occurred in the putative cluster N2 binding site in the PSST/Nqo6/NuoB subunit and the progenitors of complex I/NDH-1 have concurrently become to utilize a lipophilic electron/proton carrier such as Q as its physiological substrate. This scheme provides new insights into the structure and function relationship of complex I/NDH-1 and may help us understand its energy-coupling mechanism.}, }
@article {pmid11695830, year = {2001}, author = {Schulte, U}, title = {Biogenesis of respiratory complex I.}, journal = {Journal of bioenergetics and biomembranes}, volume = {33}, number = {3}, pages = {205-212}, pmid = {11695830}, issn = {0145-479X}, mesh = {Acyl Carrier Protein/chemistry/genetics ; Electron Transport Complex I ; Genes, Fungal ; Mitochondria/enzymology ; Models, Molecular ; Mutation ; NADH, NADPH Oxidoreductases/*biosynthesis/chemistry/genetics ; Neurospora crassa/enzymology/genetics ; Oxidation-Reduction ; Phylogeny ; Protein Subunits ; }, abstract = {Proteins specifically involved in the biogenesis of respiratory complex I in eukaryotes have been characterized. The complex I intermediate associated proteins CIA30 and CIA84 are tightly bound to an assembly intermediate of the membrane arm. Like chaperones, they are involved in multiple rounds of membrane arm assembly without being part of the mature structure. Two biosynthetic subunits of eukaryotic complex I have been characterized. The acyl carrier subunit is needed for proper assembly of the peripheral arm as well as the membrane arm of complex I. It may interact with enzymes of a mitochondrial fatty acid synthetase. The 39/40-kDa subunit appears to be an isomerase with a tightly bound NADPH. It is related to a protein family of reductases/isomerases. Both subunits have been discussed to be involved in the synthesis of a postulated, novel, high-potential redox group.}, }
@article {pmid11694530, year = {2002}, author = {Holbrook, JD and Danpure, CJ}, title = {Molecular basis for the dual mitochondrial and cytosolic localization of alanine:glyoxylate aminotransferase in amphibian liver cells.}, journal = {The Journal of biological chemistry}, volume = {277}, number = {3}, pages = {2336-2344}, doi = {10.1074/jbc.M107047200}, pmid = {11694530}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Amphibians ; Animals ; Base Sequence ; COS Cells ; Cytosol/*enzymology ; DNA Primers ; DNA, Complementary ; Humans ; Liver/*enzymology/ultrastructure ; Mitochondria/*enzymology ; Molecular Sequence Data ; Open Reading Frames ; RNA, Messenger/genetics ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Subcellular Fractions/enzymology ; Transaminases/chemistry/genetics/*metabolism ; }, abstract = {To gain further insights into the molecular basis of the evolution of alanine:glyoxylate aminotransferase (AGT) intracellular targeting in vertebrates, we have studied the molecular basis of its dual mitochondrial and cytosolic distribution in amphibian liver cells. The AGT gene in Xenopus laevis encodes a polypeptide of 415 amino acids, which includes a 24-residue N-terminal mitochondrial targeting sequence (MTS), at either end of which are located two in-frame potential translation start sites. This MTS is necessary to target Xenopus AGT and sufficient to target a green fluorescent fusion protein to mitochondria in transfected COS cells. The C-terminal tripeptide (KKM), despite being similar to the nonconsensus type 1 peroxisomal targeting sequence in human AGT (KKL), was unable to target Xenopus AGT or human AGT to peroxisomes. The Xenopus AGT gene produces two types of transcript. The longer form encodes a polypeptide that contains the MTS and is targeted to mitochondria. The shorter form encodes a polypeptide that does not contain the MTS and remains in the cytosol. These results are discussed not only in terms of the molecular evolution of AGT targeting but also in terms of the ancillary requirements for the peroxisomal targeting of human AGT.}, }
@article {pmid11693658, year = {2001}, author = {Qian, Q and Keeling, PJ}, title = {Diplonemid glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and prokaryote-to-eukaryote lateral gene transfer.}, journal = {Protist}, volume = {152}, number = {3}, pages = {193-201}, doi = {10.1078/1434-4610-00059}, pmid = {11693658}, issn = {1434-4610}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA, Protozoan ; Eukaryota/classification/*enzymology/genetics ; Eukaryotic Cells ; Gene Transfer Techniques ; Genes, Protozoan ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics ; Molecular Sequence Data ; Phylogeny ; Prokaryotic Cells ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Lateral gene transfer refers to the movement of genetic information from one genome to another, and the integration of that foreign DNA into its new genetic environment. There are currently only a few well-supported cases of prokaryote-to-eukaryote transfer known that do not involve mitochondria or plastids, but it is not clear whether this reflects a lack of such transfer events, or poor sampling of diverse eukaryotes. One gene where this process is apparently active is glyceraldehyde-3-phosphate dehydrogenase (GAPDH), where lateral transfer has been implicated in the origin of euglenoid and kinetoplastid genes. We have characterised GAPDH genes from diplonemids, heterotrophic flagellates that are closely related to kinetoplastids and euglenoids. Two distinct classes of diplonemid GAPDH genes were found in diplonemids, however, neither class is closely related to any other euglenozoan GAPDH. One diplonemid GAPDH is related to the cytosolic gapC of eukaryotes, although not to either euglenoids or kinetoplastids, and the second is related to cyanobacterial and proteobacterial gap3. The bacterial gap3 gene in diplonemids provides one of the most well-supported examples of lateral gene transfer from a bacterium to a eukaryote characterised to date, and may indicate that diplonemids have acquired a novel biochemical capacity through lateral transfer.}, }
@article {pmid11689493, year = {2001}, author = {Huynen, MA and Snel, B and Bork, P and Gibson, TJ}, title = {The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly.}, journal = {Human molecular genetics}, volume = {10}, number = {21}, pages = {2463-2468}, doi = {10.1093/hmg/10.21.2463}, pmid = {11689493}, issn = {0964-6906}, mesh = {Animals ; Bacteria/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Buchnera/genetics/metabolism ; Eukaryotic Cells/metabolism ; Evolution, Molecular ; Genome ; HSP70 Heat-Shock Proteins ; Heat-Shock Proteins/genetics/metabolism ; Humans ; *Iron-Binding Proteins ; Iron-Sulfur Proteins/*metabolism ; Mitochondria/metabolism ; Mitochondrial Proteins ; Molecular Chaperones/genetics/metabolism ; Phosphotransferases (Alcohol Group Acceptor)/*genetics/metabolism/physiology ; *Phylogeny ; Protein Binding ; *Saccharomyces cerevisiae Proteins ; Frataxin ; }, abstract = {Much has been learned about the cellular pathology of Friedreich's ataxia, a recessive neurodegenerative disease resulting from insufficient expression of the mitochondrial protein frataxin. However, the biochemical function of frataxin has remained obscure, hampering attempts at therapeutic intervention. To predict functional interactions of frataxin with other proteins we investigated whether its gene specifically co-occurs with any other genes in sequenced genomes. In 56 available genomes we identified two genes with identical phylogenetic distributions to the frataxin/cyaY gene: hscA and hscB/JAC1. These genes have not only emerged in the same evolutionary lineage as the frataxin gene, they have also been lost at least twice with it, and they have been horizontally transferred with it in the evolution of the mitochondria. The proteins encoded by hscA and hscB, the chaperone HSP66 and the co-chaperone HSP20, have been shown to be required for the synthesis of 2Fe-2S clusters on ferredoxin in proteobacteria. JAC1, an ortholog of hscB, and SSQ1, a paralog of hscA, have been shown to be required for iron-sulfur cluster assembly in mitochondria of Saccharomyces cerevisiae. Combining data on the co-occurrence of genes in genomes with experimental and predicted cellular localization data of their proteins supports the hypothesis that frataxin is directly involved in iron-sulfur cluster protein assembly. They indicate that frataxin is specifically involved in the same sub-process as HSP20/Jac1p.}, }
@article {pmid11687891, year = {2001}, author = {Waterhouse, N and MacFarlane, M}, title = {A dead cool meeting in Keystone 2001.}, journal = {Cell death and differentiation}, volume = {8}, number = {11}, pages = {1125-1130}, doi = {10.1038/sj.cdd.4400939}, pmid = {11687891}, issn = {1350-9047}, mesh = {*Adaptor Proteins, Signal Transducing ; Animals ; Apoptosis/*physiology ; Biological Evolution ; Carrier Proteins/metabolism ; Caspases/metabolism ; Humans ; Mitochondria/physiology ; Phagocytosis/physiology ; Proto-Oncogene Proteins c-bcl-2/metabolism ; Signal Transduction/*physiology ; }, }
@article {pmid11687549, year = {2001}, author = {Politi, LE and Rotstein, NP and Carri, NG}, title = {Effect of GDNF on neuroblast proliferation and photoreceptor survival: additive protection with docosahexaenoic acid.}, journal = {Investigative ophthalmology &amp; visual science}, volume = {42}, number = {12}, pages = {3008-3015}, pmid = {11687549}, issn = {0146-0404}, mesh = {Animals ; Apoptosis/drug effects ; Cell Cycle/drug effects ; Cell Differentiation/drug effects ; Cell Division/drug effects ; Cell Survival/drug effects ; Cyclin G ; Cyclin G1 ; Cyclins/metabolism ; DNA/biosynthesis ; Docosahexaenoic Acids/*pharmacology ; Drug Combinations ; Drug Synergism ; Glial Cell Line-Derived Neurotrophic Factor ; Mitochondria/physiology ; *Nerve Growth Factors ; Nerve Tissue Proteins/*pharmacology ; Photoreceptor Cells, Vertebrate/*cytology/drug effects/metabolism ; Proliferating Cell Nuclear Antigen/metabolism ; Rats ; Rats, Wistar ; Rod Opsins/metabolism ; }, abstract = {PURPOSE: In a previous study, it was reported that docosahexaenoic acid (DHA) is essential to postpone apoptosis and to promote differentiation of rat retina photoreceptors in vitro. In the current study, the protective effects of GDNF on photoreceptor cells during development in vitro and its action when combined with DHA were investigated.<br><br>METHODS: Rat retina neuronal cultures were incubated in a chemically defined medium, either without photoreceptor survival factors or supplemented with GDNF, DHA, or GDNF plus DHA. Evolution of survival, apoptosis, opsin expression, mitochondrial functioning, and cell proliferation were investigated at different times of development in vitro.<br><br>RESULTS: Incubation with GDNF selectively increased the number of surviving photoreceptors, reduced their apoptosis, and augmented opsin expression. Proliferative cell nuclei antigen (PCNA) determination and addition of [(3)H]-thymidine or bromodeoxyuridine showed that GDNF promoted neuroblast proliferation during the first hours of development in vitro. The combined addition of GDNF and DHA enhanced opsin expression and photoreceptor survival in an additive manner. The advance of photoreceptor apoptosis in cultures without trophic factors correlated with an increased impairment in mitochondrial functionality. Addition of GDNF and DHA significantly diminished the loss of mitochondrial activity.<br><br>CONCLUSIONS: These results show that GDNF stimulated the cell cycle progression, leading to neuroblast proliferation at early stages of development, and delayed the onset of apoptosis later on, improving differentiation and acting as a trophic factor for photoreceptors. The combination of GDNF with DHA had an additive effect both on photoreceptor survival and on opsin expression. Preservation of mitochondrial function may be involved in the antiapoptotic effect of both factors.}, }
@article {pmid11682311, year = {2001}, author = {Ballard, JW and Dean, MD}, title = {The mitochondrial genome: mutation, selection and recombination.}, journal = {Current opinion in genetics &amp; development}, volume = {11}, number = {6}, pages = {667-672}, doi = {10.1016/s0959-437x(00)00251-3}, pmid = {11682311}, issn = {0959-437X}, mesh = {Animals ; Biological Evolution ; Cell Nucleus/metabolism ; Codon/genetics ; DNA, Mitochondrial/*genetics ; Genome ; Humans ; Models, Genetic ; *Mutation ; *Recombination, Genetic ; *Selection, Genetic ; }, abstract = {Within an individual, mitochondria must function in a range of tissue specific environments that are largely governed by expression of a particular suite of nuclear genes. Furthermore, mitochondrial proteins form large complexes with nuclear-encoded proteins to form the electron-transport system. These dynamics between mitochondrial and nuclear genomes have important implications in studies of within and among species genetic variation, and interpretation of disease phenotypes. Experimentally disrupting naturally occurring combinations of nuclear and mitochondrial genomes should provide insights into the coevolutionary dynamics among genomes.}, }
@article {pmid11675593, year = {2001}, author = {Watanabe, KI and Ohama, T}, title = {Regular spliceosomal introns are invasive in Chlamydomonas reinhardtii: 15 introns in the recently relocated mitochondrial cox2 and cox3 genes.}, journal = {Journal of molecular evolution}, volume = {53}, number = {4-5}, pages = {333-339}, doi = {10.1007/s002390010223}, pmid = {11675593}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Chlamydomonas reinhardtii/*genetics ; Chlorophyta/genetics ; Chromosomes, Artificial, Bacterial/genetics ; DNA, Protozoan/genetics ; Electron Transport Complex IV/chemistry/genetics ; Evolution, Molecular ; Genes, Protozoan ; *Introns ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Protein Subunits ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Spliceosomes/*genetics ; }, abstract = {In the unicellular green alga, Chlamydomonas reinhardtii, cytochrome oxidase subunit 2 (cox2) and 3 (cox3) genes are missing from the mitochondrial genome. We isolated and sequenced a BAC clone that carries the whole cox3 gene and its corresponding cDNA. Almost the entire cox2 gene and its cDNA were also determined. Comparison of the genomic and the corresponding cDNA sequences revealed that the cox3 gene contains as many as nine spliceosomal introns and that cox2 bears six introns. Putative mitochondria targeting signals were predicted at each N terminal of the cox genes. These spliceosomal introns were typical GT-AG-type introns, which are very common not only in Chlamydomonas nuclear genes but also in diverse eukaryotic taxa. We found no particular distinguishing features in the cox introns. Comparative analysis of these genes with the various mitochondrial genes showed that 8 of the 15 introns were interrupting the conserved mature protein coding segments, while the other 7 introns were located in the N-terminal target peptide regions. Phylogenetic analysis of the evolutionary position of C. reinhardtii in Chlorophyta was carried out and the existence of the cox2 and cox3 genes in the mitochondrial genome was superimposed in the tree. This analysis clearly shows that these cox genes were relocated during the evolution of Chlorophyceae. It is apparent that long before the estimated period of relocation of these mitochondrial genes, the cytosol had lost the splicing ability for group II introns. Therefore, at least eight introns located in the mature protein coding region cannot be the direct descendant of group II introns. Here, we conclude that the presence of these introns is due to the invasion of spliceosomal introns, which occurred during the evolution of Chlorophyceae. This finding provides concrete evidence supporting the "intron-late" model, which rests largely on the mobility of spliceosomal introns.}, }
@article {pmid11675591, year = {2001}, author = {Yokobori, S and Suzuki, T and Watanabe, K}, title = {Genetic code variations in mitochondria: tRNA as a major determinant of genetic code plasticity.}, journal = {Journal of molecular evolution}, volume = {53}, number = {4-5}, pages = {314-326}, doi = {10.1007/s002390010221}, pmid = {11675591}, issn = {0022-2844}, mesh = {Animals ; Anticodon/genetics ; Evolution, Molecular ; *Genetic Code ; Genetic Variation ; Humans ; Models, Genetic ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Transfer/*genetics ; }, abstract = {Characteristic features of tRNA such as the anticodon sequence and modified nucleotides in the anticodon loop are thought to be crucial effectors for promoting or restricting codon reassignment. Our recent findings on basepairing rules between anticodon and codon in various metazoan mitochondria suggest that the complete loss of a codon is not necessarily essential for codon reassignment to take place. We postulate that a possible competition between two tRNAs with cognate anticodon sequences towards the relevant codon to be varied has a potential role in codon reassignment. Our proposition can be viewed as an expanded version of the codon capture theory proposed by Osawa and Jukes (J Mol Evol 28: 271-278, 1989).}, }
@article {pmid11675590, year = {2001}, author = {Knight, RD and Landweber, LF and Yarus, M}, title = {How mitochondria redefine the code.}, journal = {Journal of molecular evolution}, volume = {53}, number = {4-5}, pages = {299-313}, doi = {10.1007/s002390010220}, pmid = {11675590}, issn = {0022-2844}, mesh = {Base Composition ; Codon/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Evolution, Molecular ; *Genetic Code ; Genome ; Models, Genetic ; Mutation ; RNA, Transfer/genetics ; }, abstract = {Annotated, complete DNA sequences are available for 213 mitochondrial genomes from 132 species. These provide an extensive sample of evolutionary adjustment of codon usage and meaning spanning the history of this organelle. Because most known coding changes are mitochondrial, such data bear on the general mechanism of codon reassignment. Coding changes have been attributed variously to loss of codons due to changes in directional mutation affecting the genome GC content (Osawa and Jukes 1988), to pressure to reduce the number of mitochondrial tRNAs to minimize the genome size (Anderson and Kurland 1991), and to the existence of transitional coding mechanisms in which translation is ambiguous (Schultz and Yarus 1994a). We find that a succession of such steps explains existing reassignments well. In particular, (1) Genomic variation in the prevalence of a codon's third-position nucleotide predicts relative mitochondrial codon usage well, though GC content does not. This is because A and T, and G and C, are uncorrelated in mitochondrial genomes. (2) Codons predicted to reach zero usage (disappear) do so more often than expected by chance, and codons that do disappear are disproportionately likely to be reassigned. However, codons predicted to disappear are not significantly more likely to be reassigned. Therefore, low codon frequencies can be related to codon reassignment, but appear to be neither necessary nor sufficient for reassignment. (3) Changes in the genetic code are not more likely to accompany smaller numbers of tRNA genes and are not more frequent in smaller genomes. Thus, mitochondrial codons are not reassigned during demonstrable selection for decreased genome size. Instead, the data suggest that both codon disappearance and codon reassignment depend on at least one other event. This mitochondrial event (leading to reassignment) occurs more frequently when a codon has disappeared, and produces only a small subset of possible reassignments. We suggest that coding ambiguity, the extension of a tRNA's decoding capacity beyond its original set of codons, is the second event. Ambiguity can act alone but often acts in concert with codon disappearance, which promotes codon reassignment.}, }
@article {pmid11665849, year = {2001}, author = {Hernandez-Pando, R and Schön, T and Orozco, EH and Serafin, J and Estrada-García, I}, title = {Expression of inducible nitric oxide synthase and nitrotyrosine during the evolution of experimental pulmonary tuberculosis.}, journal = {Experimental and toxicologic pathology : official journal of the Gesellschaft fur Toxikologische Pathologie}, volume = {53}, number = {4}, pages = {257-265}, doi = {10.1078/0940-2993-00182}, pmid = {11665849}, issn = {0940-2993}, mesh = {Animals ; Cell Count ; Disease Models, Animal ; Immunoenzyme Techniques ; Lung/chemistry/metabolism/pathology ; Macrophages, Alveolar/ultrastructure ; Male ; Mice ; Mice, Inbred BALB C ; Microscopy, Immunoelectron ; Nitric Oxide/analysis/metabolism ; Nitric Oxide Synthase/analysis/*biosynthesis/genetics ; Nitric Oxide Synthase Type II ; RNA, Messenger/analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Tuberculosis, Pulmonary/*enzymology/pathology ; Tyrosine/*analogs &amp; derivatives/analysis/*biosynthesis ; }, abstract = {Nitric oxide (NO) is a relevant antimycobacterial factor in mouse macrophages. NO is a product of inducible nitric oxide synthase (iNOS). NO toxicity is greatly enhanced by reacting with superoxide to form peroxynitrite that reacts with many biological molecules. Tyrosine is one of the molecules with which NO reacts and the product is nitrotyrosine (NT). The production of peroxynitrite and the nitrosylation of proteins might play a role in bacterial killing and also in mediating host injury. In this study, we used a well-characterized mouse model of pulmonary tuberculosis to examine the local kinetics of expression and cellular distribution of iNOS and NT at the cellular and subcellular level. The histopathological study showed two phases of the disease: early and late. The early phase was characterized by mononuclear inflammation and granuloma formation. During this phase, high percentages of activated macrophages were observed that were immunostained for iNOS and NT. Immuno-electronmicroscopy showed NT immunoreactivity in lysosomes and mycobacterial wall and cytoplasm. The concentration of iNOS mRNA and NO metabolites were also elevated. The late phase was characterized by progressive pneumonia with focal necrosis and a decrease of iNOS mRNA and NO metabolites. The strongest NT immunostained areas were the necrotic tissue. Macrophages became foamy cells with scarce iNOS immunostaining but strong NT immunoreactivity. At the ultrastructural level, these cells showed NT immunolabeling in cytoskeleton, mitochondria, lysosomes and cell membrane. NT was also located in bronchial epithelial cell mitochondria, in cell membranes and cytoplasm of endothelial cells and in actin bundles within smooth muscle cells. These results suggest an important role of NO in mycobacterial killing, particularly during the early phase of the infection. They also suggest an important participation by NO in tissue damage during the late phase of the disease.}, }
@article {pmid11642360, year = {2001}, author = {Hoffmann, M and Kuhn, J and Däschner, K and Binder, S}, title = {The RNA world of plant mitochondria.}, journal = {Progress in nucleic acid research and molecular biology}, volume = {70}, number = {}, pages = {119-154}, doi = {10.1016/s0079-6603(01)70015-3}, pmid = {11642360}, issn = {0079-6603}, mesh = {Base Sequence ; Genome, Plant ; Mitochondria/*genetics ; Plants/*genetics ; RNA Processing, Post-Transcriptional ; RNA, Plant/*genetics/metabolism ; Transcription, Genetic ; }, abstract = {Mitochondria are well known as the cellular power factory. Much less is known about these organelles as a genetic system. This is particularly true for mitochondria of plants, which subsist with respect to attention by the scientific community in the shadow of the chloroplasts. Nevertheless the mitochondrial genetic system is essential for the function of mitochondria and thus for the survival of the plant. In plant mitochondria the pathway from the genetic information encoded in the DNA to the functional protein leads through a very diverse RNA world. How the RNA is generated and what kinds of regulation and control mechanisms are operative in transcription are current topics in research. Furthermore, the modes of posttranscriptional alterations and their consequences for RNA stability and thus for gene expression in plant mitochondria are currently objects of intensive investigations. In this article current results obtained in the examination of plant mitochondrial transcription, RNA processing, and RNA stability are illustrated. Recent developments in the characterization of promoter structure and the respective transcription apparatus as well as new aspects of RNA processing steps including mRNA 3' processing and stability, mRNA polyadenylation, RNA editing, and tRNA maturation are presented. We also consider new suggestions concerning the endosymbiont hypothesis and evolution of mitochondria. These novel considerations may yield important clues for the further analysis of the plant mitochondrial genetic system. Conversely, an increasing knowledge about the mechanisms and components of the organellar genetic system might reveal new aspects of the evolutionary history of mitochondria.}, }
@article {pmid11606230, year = {2001}, author = {Fast, NM and Keeling, PJ}, title = {Alpha and beta subunits of pyruvate dehydrogenase E1 from the microsporidian Nosema locustae: mitochondrion-derived carbon metabolism in microsporidia.}, journal = {Molecular and biochemical parasitology}, volume = {117}, number = {2}, pages = {201-209}, doi = {10.1016/s0166-6851(01)00356-5}, pmid = {11606230}, issn = {0166-6851}, mesh = {Amino Acid Sequence ; Animals ; Carbon/*metabolism ; Cloning, Molecular ; *Evolution, Molecular ; Genome, Protozoan ; Grasshoppers/parasitology ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Nosema/*enzymology/genetics ; Phylogeny ; Pyruvate Dehydrogenase (Lipoamide)/*genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {Microsporidia are highly adapted eukaryotic intracellular parasites that infect a variety of animals. Microsporidia contain no recognisable mitochondrion, but recently have been shown to have evolved from fungi and to possess heat shock protein genes derived from mitochondria. These findings make it clear that microsporidian ancestors were mitochondrial, yet it remains unknown whether they still contain the organelle, and if so what its role in microsporidian metabolism might be. Here we have characterised genes encoding the alpha and beta subunits of pyruvate dehydrogenase complex E1 (PDH, EC 1.2.4.1) from the microsporidian Nosema locustae. All other amitochondriate eukaryotes studied to date have lost the PDH complex and replaced it with pyruvate:ferredoxin oxidoreductase (PFOR). Nevertheless, molecular phylogeny shows that these Nosema enzymes are most closely related to mitochondrial PDH from other eukaryotes, demonstrating that elements of mitochondrial metabolism have been retained in microsporidia, and that PDH has not been wholly lost. However, there is still no evidence for a mitochondrion in microsporidia, and neither PDH subunit is predicted to encode an amino terminal leader sequence that could function as a mitochondrion-targeting transit peptide, raising questions as to whether these proteins function in a relic organelle or in the cytosol. Moreover, it is also unclear whether these proteins remain part of the PDH complex, or whether they have been retained for another purpose. We propose that microsporidia may utilise a unique pyruvate decarboxylation pathway involving PDH, demonstrating once again the diversity of core metabolism in amitochondriate eukaryotes.}, }
@article {pmid11605957, year = {2001}, author = {Rubio, MC and Ramos, J and Webb, KJ and Minchin, FR and González, E and Arrese-Igor, C and Becana, M}, title = {Expression studies of superoxide dismutases in nodules and leaves of transgenic alfalfa reveal abundance of iron-containing isozymes, posttranslational regulation, and compensation of isozyme activities.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {14}, number = {10}, pages = {1178-1188}, doi = {10.1094/MPMI.2001.14.10.1178}, pmid = {11605957}, issn = {0894-0282}, mesh = {Amino Acid Sequence ; Antioxidants/metabolism ; Base Sequence ; Catalase/metabolism ; Chloroplasts/metabolism ; DNA, Complementary/chemistry/genetics ; Gene Expression Regulation, Enzymologic ; Isoenzymes ; Medicago sativa/*enzymology/genetics ; Mitochondria/metabolism ; Molecular Sequence Data ; Peroxidases/metabolism ; Phylogeny ; Plant Leaves/*enzymology/genetics ; Plant Roots/*enzymology/genetics/microbiology ; Plants, Genetically Modified ; Protein Processing, Post-Translational ; RNA, Messenger/genetics/metabolism ; Sequence Analysis, DNA ; Superoxide Dismutase/*genetics/metabolism ; Symbiosis ; Transcription, Genetic ; }, abstract = {The composition of antioxidant enzymes, especially superoxide dismutase (SOD), was studied in one nontransgenic and three transgenic lines of nodulated alfalfa plants. Transgenic lines overproduced MnSOD in the mitochondria of nodules and leaves (line 1-10), MnSOD in the chloroplasts (line 4-6), and FeSOD in the chloroplasts (line 10-7). In nodules of line 10-7, the absence of transgene-encoded FeSOD activity was due to a lack of mRNA, whereas in nodules of line 4-6 the absence of transgene-encoded MnSOD activity was due to enzyme inactivation or degradation. Transgenic alfalfa showed a novel compensatory effect in the activities of MnSOD (mitochondrial) and FeSOD (plastidic) in the leaves, which was not caused by changes in the mRNA levels. These findings imply that SOD activity in plant tissues and organelles is regulated, at least partially, at the posttranslational level. All four lines had low CuZnSOD activities and an abundant FeSOD isozyme, especially in nodules, indicating that FeSOD performs important antioxidant functions other than the scavenging of superoxide radicals generated in photosynthesis. This was confirmed by the detection of FeSOD cDNAs and proteins in nodules of other legumes such as cowpea, pea, and soybean. The cDNA encoding alfalfa nodule FeSOD was characterized and the deduced protein found to contain a plastid transit peptide. A comparison of sequences and other properties reveals that there are two types of FeSODs in nodules.}, }
@article {pmid11599560, year = {2001}, author = {Hill, JE and Hemmingsen, SM}, title = {Arabidopsis thaliana type I and II chaperonins.}, journal = {Cell stress &amp; chaperones}, volume = {6}, number = {3}, pages = {190-200}, pmid = {11599560}, issn = {1355-8145}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics/physiology ; Arabidopsis Proteins/chemistry/*genetics/metabolism ; Chaperonins/chemistry/classification/*genetics/metabolism ; Chloroplasts/genetics/metabolism ; Databases, Genetic ; Humans ; Mitochondria/genetics/metabolism ; Molecular Chaperones/chemistry/metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; }, abstract = {An examination of the Arabidopsis thaliana genome sequence led to the identification of 29 predicted genes with the potential to encode members of the chaperonin family of chaperones (CPN60 and CCT), their associated cochaperonins, and the cytoplasmic chaperonin cofactor prefoldin. These comprise the first complete set of plant chaperonin protein sequences and indicate that the CPN family is more diverse than previously described. In addition to surprising sequence diversity within CPN subclasses, the genomic data also suggest the existence of previously undescribed family members, including a 10-kDa chloroplast cochaperonin. Consideration of the sequence data described in this review prompts questions about the complexities of plant CPN systems and the evolutionary relationships and functions of the component proteins, most of which have not been studied experimentally.}, }
@article {pmid11598188, year = {2001}, author = {Arnoult, D and Tatischeff, I and Estaquier, J and Girard, M and Sureau, F and Tissier, JP and Grodet, A and Dellinger, M and Traincard, F and Kahn, A and Ameisen, JC and Petit, PX}, title = {On the evolutionary conservation of the cell death pathway: mitochondrial release of an apoptosis-inducing factor during Dictyostelium discoideum cell death.}, journal = {Molecular biology of the cell}, volume = {12}, number = {10}, pages = {3016-3030}, pmid = {11598188}, issn = {1059-1524}, mesh = {Amino Acid Sequence ; Animals ; Apoptosis/*physiology ; Apoptosis Inducing Factor ; Cell Nucleus/metabolism ; Cell-Free System ; Cytosol/metabolism ; DNA Fragmentation/physiology ; Dictyostelium/*physiology/ultrastructure ; *Evolution, Molecular ; Flavoproteins/chemistry/*genetics/*metabolism ; Humans ; Jurkat Cells ; Mammals/physiology ; Membrane Potentials/physiology ; Membrane Proteins/chemistry/*genetics/*metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Phagocytosis/physiology ; Phosphatidylserines/metabolism ; Protoporphyrins/chemistry/*metabolism ; Sequence Homology ; }, abstract = {Mitochondria play a pivotal role in apoptosis in multicellular organisms by releasing apoptogenic factors such as cytochrome c that activate the caspases effector pathway, and apoptosis-inducing factor (AIF) that is involved in a caspase-independent cell death pathway. Here we report that cell death in the single-celled organism Dictyostelium discoideum involves early disruption of mitochondrial transmembrane potential (DeltaPsim) that precedes the induction of several apoptosis-like features, including exposure of the phosphatidyl residues at the external surface of the plasma membrane, an intense vacuolization, a fragmentation of DNA into large fragments, an autophagy, and the release of apoptotic corpses that are engulfed by neighboring cells. We have cloned a Dictyostelium homolog of mammalian AIF that is localized into mitochondria and is translocated from the mitochondria to the cytoplasm and the nucleus after the onset of cell death. Cytoplasmic extracts from dying Dictyostelium cells trigger the breakdown of isolated mammalian and Dictyostelium nuclei in a cell-free system, and this process is inhibited by a polyclonal antibody specific for Dictyostelium discoideum apoptosis-inducing factor (DdAIF), suggesting that DdAIF is involved in DNA degradation during Dictyostelium cell death. Our findings indicate that the cell death pathway in Dictyostelium involves mitochondria and an AIF homolog, suggesting the evolutionary conservation of at least part of the cell death pathway in unicellular and multicellular organisms.}, }
@article {pmid11598119, year = {2001}, author = {Perez-Jannotti, RM and Klein, SM and Bogenhagen, DF}, title = {Two forms of mitochondrial DNA ligase III are produced in Xenopus laevis oocytes.}, journal = {The Journal of biological chemistry}, volume = {276}, number = {52}, pages = {48978-48987}, doi = {10.1074/jbc.M107177200}, pmid = {11598119}, issn = {0021-9258}, support = {R01GM29681/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Cell Fractionation ; Cloning, Molecular ; Cross-Linking Reagents/chemistry ; DNA Ligase ATP ; DNA Ligases/chemistry/classification/*genetics/metabolism ; Female ; Genes, Reporter ; HeLa Cells ; Humans ; Isoenzymes/chemistry/genetics/metabolism ; Male ; Mitochondria/*enzymology/physiology ; Molecular Sequence Data ; Molecular Weight ; Oocytes/chemistry/*enzymology ; Ovary/enzymology ; Phylogeny ; Poly-ADP-Ribose Binding Proteins ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Sequence Alignment ; Testis/enzymology ; Tissue Distribution ; Xenopus Proteins ; Xenopus laevis/genetics/*metabolism ; }, abstract = {Full-length cDNAs for DNA ligase IV and the alpha and beta isoforms of DNA ligase III were cloned from Xenopus laevis to permit study of the genes encoding mitochondrial DNA ligase. DNA ligase III alpha and III beta share a common NH(2) terminus that encodes a mitochondrial localization signal capable of targeting green fluorescent protein to mitochondria while the NH(2) terminus of DNA ligase IV does not. Reverse transcriptase-polymerase chain reaction analyses with adult frog tissues demonstrate that while DNA ligase III alpha and DNA ligase IV are ubiquitously expressed, DNA ligase III beta expression is restricted to testis and ovary. Mitochondrial lysates from X. laevis oocytes contain both DNA ligase III alpha and III beta but no detectable DNA ligase IV. Gel filtration, sedimentation, native gel electrophoresis, and in vitro cross-linking experiments demonstrate that mtDNA ligase III alpha exists as a high molecular weight complex. We discuss the possibility that DNA ligase III alpha exists in mitochondria in association with novel mitochondrial protein partners or as a homodimer.}, }
@article {pmid11594626, year = {2001}, author = {James, SA and Collins, MD and Roberts, IN}, title = {Phylogenetic analysis of the psychrophobic yeast Arxiozyma telluris and the reinstatement of Candida pintolopesii (van Uden) Meyer et Yarrow and Candida slooffii van Uden et do Carmo Sousa.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {51}, number = {Pt 5}, pages = {1917-1925}, doi = {10.1099/00207713-51-5-1917}, pmid = {11594626}, issn = {1466-5026}, mesh = {Candida/*classification/*genetics ; DNA, Ribosomal/analysis ; Electron Transport Complex IV/genetics ; Genes, rRNA ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 18S/genetics ; Saccharomycetales/*classification/*genetics ; Sequence Analysis, DNA ; }, abstract = {A phylogenetic analysis was conducted upon ten strains of the psychrophobic yeast species Arxiozyma telluris using nuclear rDNA (18S and 26S) and mitochondrial cytochrome-c oxidase subunit II (COX2) gene sequences. Strains examined included those described originally as Candida slooffii, Torulopsis bovina (= Candida bovina) and Torulopsis pintolopesii (= Candida pintolopesii), which are all currently accepted as synonyms of Arxiozyma telluris. Comparative 18S rDNA sequence analysis showed that these strains formed a genealogically highly related group, which was phylogenetically distinct from any other ascomycetous species studied. The results showed that A. telluris, as currently described, appears to be composed of a complex of closely related but nevertheless separate taxa. rDNA and COX2 gene sequence data revealed that CBS 1787T, the type strain of C. pintolopesii, the currently recognized asexual form (anamorph) of A. telluris, along with strains CBS 2676 and CBS 2985 formed a distinct taxon that is phylogenetically separate from A. telluris. Similarly, the sequence data also showed that C. slooffii is a distinct taxon and support the reinstatement of this species. However, with regard to the relationship between the type strains of A. telluris (CBS 2685T) and C bovina (CBS 2760T), discrepancies were observed between the rDNA and COX2 sequence datasets, and these results are discussed in more detail.}, }
@article {pmid11592478, year = {2001}, author = {García, G and Lalanne, AI and Aguirre, G and Cappetta, M}, title = {Chromosome evolution in the annual killifish genus Cynolebias and mitochondrial phylogenetic analysis.}, journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology}, volume = {9}, number = {6}, pages = {437-448}, pmid = {11592478}, issn = {0967-3849}, mesh = {Animals ; Chromosome Banding ; Chromosomes/*genetics ; Cytochrome b Group/genetics ; DNA, Mitochondrial/analysis ; Evolution, Molecular ; Karyotyping ; Killifishes/classification/*genetics ; Mitochondria/*genetics ; Phylogeny ; RNA, Ribosomal/genetics ; }, abstract = {Extensive chromosome variation involving Robertsonian and non-Robertsonian changes were proposed to explain chromosomal evolution within killifishes of the aplocheiloid group belonging to the order Cyprinodontiforms. In the present work we describe the karyotypes of four Cynolebias species and analyze chromosome changes by means of mitochondrial phylogenetic studies, including 10 taxa of this genus. Diploid numbers varied from 48 to 44 and the number of chromosome arms from 50 to 54. Molecular phylogenetic analyses allow us to corroborate previous hypothesis about chromosome evolution in aplocheiloid fishes. The tree topology based on a combined dataset of mitochondrial cytochrome b and 12S genes shows that recent cladogenetic events within the genus Cynolebias could have occurred by allopatric or 'in-situ' differentiation involving chromosomal rearrangements. Our analyses of approximately 10% of mitochondrial genome can be helpful in determining these recent cladogenetic events but it showed limited phylogenetic resolution at intermediate levels of divergence. This can be explained in part by the high levels of DNA sequence divergence (ranging from 0.015 to 0.245) detected at intrageneric level. Different methodological approaches suggest that chromosomal changes in Cynolebias have occurred during their differentiation, supporting the hypothesis that the unresolved basal polytomy could be the result of rapid speciation events, like a true 'star polytomy'.}, }
@article {pmid11592395, year = {2001}, author = {Schürer, H and Schiffer, S and Marchfelder, A and Mörl, M}, title = {This is the end: processing, editing and repair at the tRNA 3'-terminus.}, journal = {Biological chemistry}, volume = {382}, number = {8}, pages = {1147-1156}, doi = {10.1515/BC.2001.144}, pmid = {11592395}, issn = {1431-6730}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Biological Evolution ; Eukaryotic Cells/physiology ; Exonucleases/metabolism ; Models, Genetic ; Nucleotidyltransferases/metabolism ; Organelles/physiology ; RNA Editing ; *RNA Processing, Post-Transcriptional ; RNA, Transfer/*metabolism ; }, abstract = {The generation of a mature tRNA 3'-end is an important step in the processing pathways leading to functional tRNA molecules. While 5'-end processing by RNase P is similar in all organisms, generation of the mature 3'-terminus seems to be more variable and complex. The first step in this reaction is the removal of 3'-trailer sequences. In bacteria, this is a multistep process performed by endo- and exonucleases. In contrast, the majority of eukaryotes generate the mature tRNA 3'-end in a single step reaction, which consists of an endonucleolytic cut at the tRNA terminus. After removal of the 3'-trailer, a terminal CCA triplet has to be added to allow charging of the tRNA with its cognate amino acid. The enzyme catalyzing this reaction is tRNA nucleotidyltransferase, homologs of which have been found in representatives of all three kingdoms. Furthermore, in metazoan mitochondria, some genes encode 3'-terminally truncated tRNAs, which are restored in an editing reaction in order to yield functional tRNAs. Interestingly, this reaction is not restricted to distinct tRNAs, but seems to act on a variety of tRNA molecules and represents therefore a more general tRNA repair mechanism than a specialized editing reaction. In this review, the current knowledge about these crucial reactions is summarized.}, }
@article {pmid11585646, year = {2001}, author = {Schneider, A}, title = {Does the evolutionary history of aminoacyl-tRNA synthetases explain the loss of mitochondrial tRNA genes?.}, journal = {Trends in genetics : TIG}, volume = {17}, number = {10}, pages = {557-559}, doi = {10.1016/s0168-9525(01)02439-8}, pmid = {11585646}, issn = {0168-9525}, mesh = {Amino Acyl-tRNA Synthetases/*genetics/metabolism ; Animals ; *Evolution, Molecular ; Models, Genetic ; RNA/*genetics/metabolism ; RNA, Mitochondrial ; RNA, Transfer/*genetics/metabolism ; }, abstract = {The importation of cytosolic tRNAs is required for protein synthesis in the mitochondria of the wide variety of eukaryotes that lack a complete set of mitochondrial tRNA genes. The evolutionary history of the process, however, is still enigmatic. The analysis presented here suggests that the loss of distinct mitochondrial tRNA genes was not random and that it might be explained by the differential capabilities of mitochondrial aminoacyl-tRNA synthetases to charge imported eukaryotic-type tRNAs with amino acid.}, }
@article {pmid11580860, year = {2001}, author = {Hedges, SB and Chen, H and Kumar, S and Wang, DY and Thompson, AS and Watanabe, H}, title = {A genomic timescale for the origin of eukaryotes.}, journal = {BMC evolutionary biology}, volume = {1}, number = {}, pages = {4}, pmid = {11580860}, issn = {1471-2148}, mesh = {Animals ; Archaea/genetics ; Eubacterium/genetics ; *Eukaryotic Cells ; *Evolution, Molecular ; Genetic Variation/genetics ; *Genome ; Genome, Archaeal ; Genome, Bacterial ; Genome, Protozoan ; Giardia/genetics ; Models, Genetic ; Phylogeny ; }, abstract = {BACKGROUND: Genomic sequence analyses have shown that horizontal gene transfer occurred during the origin of eukaryotes as a consequence of symbiosis. However, details of the timing and number of symbiotic events are unclear. A timescale for the early evolution of eukaryotes would help to better understand the relationship between these biological events and changes in Earth's environment, such as the rise in oxygen. We used refined methods of sequence alignment, site selection, and time estimation to address these questions with protein sequences from complete genomes of prokaryotes and eukaryotes.<br><br>RESULTS: Eukaryotes were found to evolve faster than prokaryotes, with those eukaryotes derived from eubacteria evolving faster than those derived from archaebacteria. We found an early time of divergence (approximately 4 billion years ago, Ga) for archaebacteria and the archaebacterial genes in eukaryotes. Our analyses support at least two horizontal gene transfer events in the origin of eukaryotes, at 2.7 Ga and 1.8 Ga. Time estimates for the origin of cyanobacteria (2.6 Ga) and the divergence of an early-branching eukaryote that lacks mitochondria (Giardia) (2.2 Ga) fall between those two events.<br><br>CONCLUSIONS: We find support for two symbiotic events in the origin of eukaryotes: one premitochondrial and a later mitochondrial event. The appearance of cyanobacteria immediately prior to the earliest undisputed evidence for the presence of oxygen (2.4-2.2 Ga) suggests that the innovation of oxygenic photosynthesis had a relatively rapid impact on the environment as it set the stage for further evolution of the eukaryotic cell.}, }
@article {pmid11577165, year = {2001}, author = {Sakamoto, J and Shibata, T and Mine, T and Miyahara, R and Torigoe, T and Noguchi, S and Matsushita, K and Sone, N}, title = {Cytochrome c oxidase contains an extra charged amino acid cluster in a new type of respiratory chain in the amino-acid-producing Gram-positive bacterium Corynebacterium glutamicum.}, journal = {Microbiology (Reading, England)}, volume = {147}, number = {Pt 10}, pages = {2865-2871}, doi = {10.1099/00221287-147-10-2865}, pmid = {11577165}, issn = {1350-0872}, mesh = {Amino Acid Sequence ; *Cloning, Molecular ; Corynebacterium/*enzymology/genetics/physiology ; Electron Transport Complex IV/*chemistry/genetics/*metabolism ; *Genes, Bacterial ; Glutamates/metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The membranes from Corynebacterium glutamicum cells contain a hydrophobic di-haem C protein as the cytochrome c subunit of the new type of cytochrome bc complex (complex III in the respiratory chain) encoded by the qcrCAB operon [Sone, N., Nagata, K., Kojima, H., Tajima, J., Kodera, Y., Kanamaru, T., Noguchi, S. &amp; Sakamoto, J. (2001). Biochim Biophys Acta 1503, 279-290]. To characterize complex IV, cytochrome c oxidase and its structural genes were isolated. The oxidase is of the cytochrome aa(3) type, but mass spectrometry indicated that the haem is haem As, which contains a geranylgeranyl side-chain instead of a farnesyl group. The enzyme is a SoxM-type haem-copper oxidase composed of three subunits. Edman degradation and mass spectrometry suggested that the N-terminal signal sequence of subunit II is cleaved and that the new N-terminal cysteine residue is diacylglycerated, while neither subunit I nor subunit III is significantly modified. The genes for subunits II (ctaC) and III (ctaE) are located upstream of the qcrCAB operon, while that for subunit I (ctaD) is located separately. The oxidase showed low enzyme activity with extrinsic substrates such as cytochromes c from horse heart or yeast, and has the Cu(A)-binding motif in its subunit II. A prominent structural feature is the insertion of an extra charged amino acid cluster between the beta2 and beta4 strands in the substrate-binding domain of subunit II. The beta2-beta4 loop of this oxidase is about 30 residues longer than that of major cytochrome c oxidases from mitochondria and proteobacteria, and is rich in both acidic and basic residues. These findings suggest that the extra charged cluster may play a role in the interaction of the oxidase with the cytochrome c subunit of the new type of bc complex.}, }
@article {pmid11560369, year = {2001}, author = {Heininger, K}, title = {The deprivation syndrome is the driving force of phylogeny, ontogeny and oncogeny.}, journal = {Reviews in the neurosciences}, volume = {12}, number = {3}, pages = {217-287}, doi = {10.1515/revneuro.2001.12.3.217}, pmid = {11560369}, issn = {0334-1763}, mesh = {Aging/physiology ; Animals ; Apoptosis/physiology ; Cell Communication/physiology ; Cell Differentiation/physiology ; Energy Metabolism/*physiology ; General Adaptation Syndrome/*physiopathology ; Homeostasis ; Mitochondria/metabolism ; Mutagenesis ; Neoplasms/*physiopathology ; *Phylogeny ; Prokaryotic Cells/*physiology ; Sex ; Signal Transduction/physiology ; *Stress, Physiological ; }, abstract = {Energy is the motor of life. Energy ensures the organism's survival and competitive advantage for reproductive success. For almost 3 billion years, unicellular organisms were the only life form on earth. Competition for limited energy resources and raw materials exerted an incessant selective pressure on organisms. In the adverse environment and due to their 'feast and famine' life style, hardiness to a variety of stressors, particularly to nutrient deprivation, was the selection principle. Both resistance and mutagenic adaptation to stressors were established as survival strategies by means of context-specific processes creating stability or variability of DNA sequence. The conservation of transduction pathways and functional homology of effector molecules clearly bear witness that the principles of life established during prokaryotic and eukaryotic unicellular evolution, although later diversified, have been unshakably cast to persist during metazoan phylogenesis. A wealth of evidence suggests that unicellular organisms evolved the phenomena of differentiation and apoptosis, sexual reproduction, and even aging, as responses to environmental challenges. These evolutionary accomplishments were elaborated from the dichotomous resistance/mutagenesis response and sophisticated the capacity of cells to tune their genetic information to changing environmental conditions. Notably, the social deprivation responses, differentiation and apoptosis, evolved as intercellularly coordinated events: a multitude of differentiation processes were elaborated from sporulation, the prototypic stress resistance response, while apoptosis, contrary to current concepts, is no altruistic cell suicide but was programmed as a mutagenic survival response; this response, however, is socially thwarted leading into mutagenic error catastrophe. In the hybrid differentiation-apoptosis process, cytocide and cannibalism of apoptotic cells thus serve the purpose of fueling the survival of the selfish genes in the differentiating cells. However, successful mutagenesis, although repressed, persisted in the asocial stress response of carcinogenesis as a regression to primitive unicellular behavior following failure of intercellular communication. While somatic mutagenesis was largely prevented, Metazoa elaborated germ cell mutagenesis as an evolutionary vehicle. Genetic competence, a primitive, stress-induced mating behavior, evolved into sexual reproduction which harnessed mutagenesis by subjecting highly mutable germ cells to a rigid viability selection. These processes were programmatically fixed as life- and cell-cycle events but retained their deprivation response phenotypes. Thus, the differentiation-apoptosis tandem evolved as the 'clay' to mold the specialized structures and functions of a multicellular organism while sexual reproduction elaborated the principle of quality-checked mutagenesis to create the immense diversity of Metazoa following the Cambrian explosion. Throughout these events, reactive oxygen and nitrogen species, which are regulated by energy homeostasis, shape the genetic information in a regulated but random, uncoded process providing the fitness-related feedback of phenotype to genotype. The interplay of genes and environment establishes a dynamic stimulus-response feedback cycle which, in animate nature, may be the organizing principle to contrive the reciprocal duality of energy and matter.}, }
@article {pmid11557978, year = {2001}, author = {Hwang, UW and Friedrich, M and Tautz, D and Park, CJ and Kim, W}, title = {Mitochondrial protein phylogeny joins myriapods with chelicerates.}, journal = {Nature}, volume = {413}, number = {6852}, pages = {154-157}, doi = {10.1038/35093090}, pmid = {11557978}, issn = {0028-0836}, mesh = {Animals ; Arthropods/*classification/genetics ; Biological Evolution ; DNA ; Insecta/classification/genetics ; Mitochondria/*genetics ; Models, Biological ; Phylogeny ; Proteins/*genetics ; Sequence Analysis, Protein ; }, abstract = {The animal phylum Arthropoda is very useful for the study of body plan evolution given its abundance of morphologically diverse species and our profound understanding of Drosophila development. However, there is a lack of consistently resolved phylogenetic relationships between the four extant arthropod subphyla, Hexapoda, Myriapoda, Chelicerata and Crustacea. Recent molecular studies have strongly supported a sister group relationship between Hexapoda and Crustacea, but have not resolved the phylogenetic position of Chelicerata and Myriapoda. Here we sequence the mitochondrial genome of the centipede species Lithobius forficatus and investigate its phylogenetic information content. Molecular phylogenetic analysis of conserved regions from the arthropod mitochondrial proteome yields highly resolved and congruent trees. We also find that a sister group relationship between Myriapoda and Chelicerata is strongly supported. We propose a model to explain the apparently parallel evolution of similar head morphologies in insects and myriapods.}, }
@article {pmid11557802, year = {2001}, author = {Horner, DS and Embley, TM}, title = {Chaperonin 60 phylogeny provides further evidence for secondary loss of mitochondria among putative early-branching eukaryotes.}, journal = {Molecular biology and evolution}, volume = {18}, number = {10}, pages = {1970-1975}, doi = {10.1093/oxfordjournals.molbev.a003737}, pmid = {11557802}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Chaperonin 60/*genetics ; Diplomonadida/classification/genetics ; Eukaryotic Cells/classification/*metabolism ; Humans ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Homology, Amino Acid ; }, }
@article {pmid11557797, year = {2001}, author = {Tachezy, J and Sánchez, LB and Müller, M}, title = {Mitochondrial type iron-sulfur cluster assembly in the amitochondriate eukaryotes Trichomonas vaginalis and Giardia intestinalis, as indicated by the phylogeny of IscS.}, journal = {Molecular biology and evolution}, volume = {18}, number = {10}, pages = {1919-1928}, doi = {10.1093/oxfordjournals.molbev.a003732}, pmid = {11557797}, issn = {0737-4038}, support = {AI11942/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/genetics ; Carbon-Sulfur Lyases/*genetics/metabolism ; DNA, Protozoan/chemistry/genetics ; Giardia lamblia/enzymology/*genetics ; Iron-Sulfur Proteins/*biosynthesis ; Mitochondria/*metabolism ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/enzymology/*genetics ; }, abstract = {Pyridoxal-5'-phosphate-dependent cysteine desulfurase (IscS) is an essential enzyme in the assembly of FeS clusters in bacteria as well as in the mitochondria of eukaryotes. Although FeS proteins are particularly important for the energy metabolism of amitochondrial anaerobic eukaryotes, there is no information about FeS cluster formation in these organisms. We identified and sequenced two IscS homologs of Trichomonas vaginalis (TviscS-1 and TviscS-2) and one of Giardia intestinalis (GiiscS). TviscS-1, TviscS-2, and GiiscS possess the typical conserved regions implicated in cysteine desulfurase activity. N-termini of TviscS-1 and TviscS-2 possess eight amino acid extensions, which resemble the N-terminal presequences that target proteins to hydrogenosomes in trichomonads. No presequence was evident in GiiscS from Giardia, an organism that apparently lacks hydrogenosmes or mitochondria. Phylogenetic analysis showed a close relationship among all eukaryotic IscS genes including those of amitochondriates. IscS of proteobacteria formed a sister group to the eukaryotic clade, suggesting that isc-related genes were present in the proteobacterial endosymbiotic ancestor of mitochondria and hydrogenosomes. NifS genes of nitrogen-fixing bacteria, which are IscS homologs required for specific formation of FeS clusters in nitrogenase, formed a more distant group. The phylogeny indicates the presence of a common mechanism for FeS cluster formation in mitochondriates as well as in amitochondriate eukaryotes. Furthermore, the analyses support a common origin of Trichomonas hydrogenosomes and mitochondria, as well as secondary loss of mitochondrion/hydrogenosome-like organelles in Giardia.}, }
@article {pmid11554311, year = {2001}, author = {Krokan, HE and Otterlei, M and Nilsen, H and Kavli, B and Skorpen, F and Andersen, S and Skjelbred, C and Akbari, M and Aas, PA and Slupphaug, G}, title = {Properties and functions of human uracil-DNA glycosylase from the UNG gene.}, journal = {Progress in nucleic acid research and molecular biology}, volume = {68}, number = {}, pages = {365-386}, doi = {10.1016/s0079-6603(01)68112-1}, pmid = {11554311}, issn = {0079-6603}, mesh = {Animals ; Apurinic Acid/metabolism ; Bacterial Proteins/genetics/physiology ; Binding Sites ; Catalytic Domain ; Cell Cycle ; Chromosome Mapping ; Chromosomes, Human, Pair 12/genetics ; *DNA Glycosylases ; DNA Repair ; DNA, Mitochondrial/genetics/metabolism ; Deoxyribonuclease (Pyrimidine Dimer) ; Deoxyuracil Nucleotides/metabolism ; Endodeoxyribonucleases/metabolism ; Escherichia coli/enzymology/genetics ; Gene Expression Regulation, Enzymologic ; Genes ; Humans ; Mice ; Mice, Knockout ; Mitochondria/enzymology ; Multigene Family ; N-Glycosyl Hydrolases/chemistry/genetics/*physiology ; Phosphorylation ; Promoter Regions, Genetic ; Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Pyrimidines/metabolism ; Thymine/*analogs &amp; derivatives/metabolism ; Uracil-DNA Glycosidase ; }, abstract = {The human UNG-gene at position 12q24.1 encodes nuclear (UNG2) and mitochondrial (UNG1) forms of uracil-DNA glycosylase using differentially regulated promoters, PA and PB, and alternative splicing to produce two proteins with unique N-terminal sorting sequences. PCNA and RPA co-localize with UNG2 in replication foci and interact with N-terminal sequences in UNG2. Mitochondrial UNG1 is processed to shorter forms by mitochondrial processing peptidase (MPP) and an unidentified mitochondrial protease. The common core catalytic domain in UNG1 and UNG2 contains a conserved DNA binding groove and a tight-fitting uracil-binding pocket that binds uracil only when the uracil-containing nucleotide is flipped out. Certain single amino acid substitutions in the active site of the enzyme generate DNA glycosylases that remove either thymine or cytosine. These enzymes induce cytotoxic and mutagenic abasic (AP) sites in the E. coli chromosome and were used to examine biological consequences of AP sites. It has been assumed that a major role of the UNG gene product(s) is to repair mutagenic U:G mispairs caused by cytosine deamination. However, one major role of UNG2 is to remove misincorporated dUMP residues. Thus, knockout mice deficient in Ung activity (Ung-/- mice) have only small increases in GC-->AT transition mutations, but Ung-/- cells are deficient in removal of misincorporated dUMP and accumulate approximately 2000 uracil residues per cell. We propose that BER is important both in the prevention of cancer and for preserving the integrity of germ cell DNA during evolution.}, }
@article {pmid11553611, year = {2001}, author = {Abadjieva, A and Pauwels, K and Hilven, P and Crabeel, M}, title = {A new yeast metabolon involving at least the two first enzymes of arginine biosynthesis: acetylglutamate synthase activity requires complex formation with acetylglutamate kinase.}, journal = {The Journal of biological chemistry}, volume = {276}, number = {46}, pages = {42869-42880}, doi = {10.1074/jbc.M103732200}, pmid = {11553611}, issn = {0021-9258}, mesh = {Acetyltransferases/genetics/*metabolism ; Alleles ; Amino Acid Sequence ; Amino Acids/chemistry ; Amino-Acid N-Acetyltransferase ; Arginine/*biosynthesis/*metabolism ; Blotting, Western ; Catalysis ; Cloning, Molecular ; DNA/metabolism ; DNA Primers/metabolism ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/metabolism ; Evolution, Molecular ; *Growth Substances ; Models, Biological ; Molecular Sequence Data ; Mutation ; Open Reading Frames ; Phosphotransferases (Carboxyl Group Acceptor)/*metabolism ; Plant Proteins/*genetics/*metabolism ; Plasmids/metabolism ; Precipitin Tests ; Protein Binding ; Protein Structure, Tertiary ; Saccharomyces cerevisiae/*metabolism ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; }, abstract = {Open reading frame YJL071W of Saccharomyces cerevisiae was shown to be ARG2 and identified as the structural gene for acetylglutamate synthase, first step in arginine biosynthesis. The three Ascomycete acetylglutamate synthases characterized to date appear homologous, but unlike the other enzymes of the yeast arginine biosynthesis pathway, they showed no significant similarity to their prokaryotic equivalents. The measured synthase activity did not increase with the number of ARG2 gene copies unless the number of ARG5,6 gene copies was increased similarly. ARG5,6 encodes a precursor that is maturated in the mitochondria into acetylglutamate kinase and acetylglutamyl-phosphate reductase, catalyzing the second and third steps in the pathway. The results imply that the synthase must interact stoichiometrically in vivo with the kinase, the reductase, or both to be active. Results obtained with synthetic ARG5 and ARG6 genes suggested that both the kinase and the reductase could be needed. This situation, which has completely escaped notice in yeast until now, is reminiscent of the observation in Neurospora crassa that nonsense arg-6 kinase/reductase mutants lack synthase activity (Hinde, R. W., Jacobson, J. A., Weiss, R. L., and Davis, R. H. (1986) J. Biol. Chem. 261, 5848-5852). In immunoprecipitation experiments, hemagglutinin-tagged synthase coprecipitated with a protein proven by microsequencing to be the kinase. Western blot analyses showed that the synthase has reduced stability in the absence of the kinase/reductase. Our data demonstrate the existence of a new yeast arginine metabolon involving at least the first two, and possibly the first three, enzymes of the pathway. Hypotheses regarding the biological significance of this interaction are discussed.}, }
@article {pmid11551911, year = {2001}, author = {Entelis, NS and Kolesnikova, OA and Dogan, S and Martin, RP and Tarassov, IA}, title = {5 S rRNA and tRNA import into human mitochondria. Comparison of in vitro requirements.}, journal = {The Journal of biological chemistry}, volume = {276}, number = {49}, pages = {45642-45653}, doi = {10.1074/jbc.M103906200}, pmid = {11551911}, issn = {0021-9258}, support = {RG0349/1999-M/RG/CSR NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Biological Transport ; DNA Primers ; Humans ; In Vitro Techniques ; Mitochondria/*metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Ribosomal, 5S/chemistry/*metabolism ; RNA, Transfer, Lys/chemistry/*metabolism ; Saccharomyces cerevisiae/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {In vivo, human mitochondria import 5 S rRNA and do not import tRNAs from the cytoplasm. We demonstrated previously that isolated human mitochondria are able to internalize a yeast tRNA(Lys) in the presence of yeast soluble factors. Here, we describe an assay for specific uptake of 5 S rRNA by isolated human mitochondria and compare its requirements with the artificial tRNA import. The efficiency of 5 S rRNA uptake by isolated mitochondria was comparable with that found in vivo. The import was shown to depend on ATP and the transmembrane electrochemical potential and was directed by soluble proteins. Blocking the pre-protein import channel inhibited internalization of both 5 S rRNA and tRNA, which suggests this apparatus be involved in RNA uptake by the mitochondria. We show that human mitochondria can also selectively internalize several in vitro synthesized versions of yeast tRNA(Lys) as well as a transcript of the human mitochondrial tRNA(Lys). Either yeast or human soluble proteins can direct this import, suggesting that human cells possess all factors needed for such an artificial translocation. On the other hand, the efficiency of import directed by yeast or human protein factors varies significantly, depending on the tRNA version. Similarly to the yeast system, tRNA(Lys) import into human mitochondria depended on aminoacylation and on the precursor of the mitochondrial lysyl-tRNA synthetase. 5 S rRNA import was also dependent upon soluble protein(s), which were distinct from the factors providing tRNA internalization.}, }
@article {pmid11543278, year = {2000}, author = {Sidell, BD}, title = {Life at body temperatures below 0 degrees C: the physiology and biochemistry of Antarctic fishes.}, journal = {Gravitational and space biology bulletin : publication of the American Society for Gravitational and Space Biology}, volume = {13}, number = {2}, pages = {25-34}, pmid = {11543278}, issn = {1089-988X}, mesh = {Adaptation, Biological ; *Adaptation, Physiological ; Animals ; Antarctic Regions ; Antifreeze Proteins ; Biological Evolution ; Cardiac Output/physiology ; Cold Climate ; *Cold Temperature ; Fishes/genetics/metabolism/*physiology ; Gene Expression ; Glycoproteins/metabolism ; Heart/physiology ; L-Lactate Dehydrogenase/metabolism ; Mitochondria ; Myoglobin/*genetics ; }, abstract = {Fishes of the Southern Ocean surrounding Antarctica are dominated by species of the suborder Notothenoidei. For approximately 14MY, these highly successful fishes have evolved under stable thermal conditions that result in a body temperature of ca. 0 degrees C throughout their life histories. Evolution in this chronically cold environment has led to unusual physiological and biochemical characteristics. In some cases, these characteristics are essential to survival and normal biological function at cold body temperature (e.g., development of antifreeze glycoproteins, structural modification of enzymes, cold-stable microtubules, and cardiovascular adaptations). In other instances, mutations that probably would have been lethal in warmer, less oxygen-rich environments than the Southern Ocean have been retained in Antarctic fishes (e.g., loss of hemoglobin production and variable expression of myoglobin in one notothenioid family, the Channichthyidae). These unique animals offer opportunities for insight into evolutionary processes leading to physiological and biochemical characteristics that either arise from strong selective pressure or persist through relaxation of selective pressure. After briefly describing the Antarctic marine environment, I discuss several unique aspects of the physiology and biochemistry of Antarctic fishes, specifically emphasizing our laboratory's recent studies of an unusual pattern of myoglobin expression in the Channichthyid icefishes.}, }
@article {pmid11536915, year = {1999}, author = {Patterson, DJ and Simpson, AG and Weerakoon, N}, title = {Free-living flagellates from anoxic habitats and the assembly of the eukaryotic cell.}, journal = {The Biological bulletin}, volume = {196}, number = {3}, pages = {381-3; discussion 383-4}, doi = {10.2307/1542975}, pmid = {11536915}, issn = {0006-3185}, mesh = {Anaerobiosis ; Animals ; *Biological Evolution ; Eukaryota/*classification/physiology/*ultrastructure ; Eukaryotic Cells/physiology/*ultrastructure ; Mitochondria/physiology/*ultrastructure ; Phylogeny ; Protozoan Proteins ; Symbiosis ; Water Microbiology ; }, }
@article {pmid11530796, year = {2001}, author = {Roy, SW and Lewis, BP and Fedorov, A and Gilbert, W}, title = {Footprints of primordial introns on the eukaryotic genome.}, journal = {Trends in genetics : TIG}, volume = {17}, number = {9}, pages = {496-501}, doi = {10.1016/s0168-9525(01)02375-7}, pmid = {11530796}, issn = {0168-9525}, mesh = {Animals ; Caenorhabditis elegans/*genetics ; Codon ; Databases, Factual ; *Eukaryotic Cells/cytology ; Evolution, Molecular ; Exons ; Genes, Archaeal ; Genes, rRNA ; *Genome ; *Introns ; Mitochondria/*genetics ; Mutagenesis, Insertional ; Nematoda ; Open Reading Frames ; Phylogeny ; Predictive Value of Tests ; Selection, Genetic ; Statistics as Topic ; }, }
@article {pmid11526065, year = {2001}, author = {Halanych, KM and Feldman, RA and Vrijenhoek, RC}, title = {Molecular evidence that Sclerolinum brattstromi is closely related to vestimentiferans, not to frenulate pogonophorans (Siboglinidae, Annelida).}, journal = {The Biological bulletin}, volume = {201}, number = {1}, pages = {65-75}, doi = {10.2307/1543527}, pmid = {11526065}, issn = {0006-3185}, mesh = {Animals ; Annelida/*classification/*genetics ; Cell Nucleus/chemistry ; DNA, Ribosomal/analysis ; Mitochondria/chemistry ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Sequence Alignment ; }, abstract = {Siboglinids, previously referred to as pogonophorans, have typically been divided into two groups, frenulates and vestimentiferans. Adults of these marine protostome worms lack a functional gut and harbor endosymbiotic bacteria. Frenulates usually live in deep, sedimented reducing environments, and vestimentiferans inhabit hydrothermal vents and sulfide-rich hydrocarbon seeps. Taxonomic literature has often treated frenulates and vestimentiferans as sister taxa. Sclerolinum has traditionally been thought to be a basal siboglinid that was originally regarded as a frenulate and later as a third lineage of siboglinids, Monilifera. Evidence from the 18S nuclear rDNA gene and the 16S mitochondrial rDNA gene presented here shows that Sclerolinum is the sister clade to vestimentiferans although it lacks the characteristic morphology (i.e., a vestimentum). The rDNA data confirm the contention that Sclerolinum is different from frenulates, and further supports the idea that siboglinid evolution has been driven by a trend toward increased habitat specialization. The evidence now available indicates that vestimentiferans lack the molecular diversity expected of a group that has been argued to have Silurian or possibly Cambrian origins.}, }
@article {pmid11525463, year = {2001}, author = {Buckley, TR and Simon, C and Chambers, GK}, title = {Phylogeography of the New Zealand cicada Maoricicada campbelli based on mitochondrial DNA sequences: ancient clades associated with cenozoic environmental change.}, journal = {Evolution; international journal of organic evolution}, volume = {55}, number = {7}, pages = {1395-1407}, doi = {10.1111/j.0014-3820.2001.tb00661.x}, pmid = {11525463}, issn = {0014-3820}, mesh = {Adenosine Triphosphatases/genetics ; Animals ; Base Sequence ; Bayes Theorem ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Environment ; *Evolution, Molecular ; Genes, Insect/genetics ; Genetic Variation ; Geography ; Haplotypes ; Hemiptera/*classification/*genetics ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; New Zealand ; *Phylogeny ; RNA, Transfer/genetics ; }, abstract = {New Zealand's isolation, its well-studied rapidly changing landscape, and its many examples of rampant speciation make it an excellent location for studying the process of genetic differentiation. Using 1520 base pairs of mitochondrial DNA from the cytochrome oxidase subunit I, ATPase subunits 6 and 8 and tRNA(Asp) genes, we detected two well-differentiated, parapatrically distributed clades within the widespread New Zealand cicada species Maoricicada campbelli that may prove to represent two species. The situation that we uncovered is unusual in that an ancient lineage with low genetic diversity is surrounded on three sides by two recently diverged lineages. Using a relaxed molecular clock model coupled with Bayesian statistics, we dated the earliest divergence within M. campbelli at 2.3 +/- 0.55 million years. Our data suggest that geological and climatological events of the late Pliocene divided a once-widespread species into northern and southern components and that near the middle of the Pleistocene the northern lineage began moving south eventually reaching the southern clade. The southern clade seems to have moved northward to only a limited extent. We discovered five potential zones of secondary contact through mountain passes that will be examined in future work. We predict that, as in North American periodical cicadas, contact between these highly differentiated lineages will exist but will not involve gene flow.}, }
@article {pmid11520353, year = {2001}, author = {Clark, TL and Meinke, LJ and Foster, JE}, title = {Molecular phylogeny of Diabrotica beetles (Coleoptera: Chrysomelidae) inferred from analysis of combined mitochondrial and nuclear DNA sequences.}, journal = {Insect molecular biology}, volume = {10}, number = {4}, pages = {303-314}, doi = {10.1046/j.0962-1075.2001.00269.x}, pmid = {11520353}, issn = {0962-1075}, mesh = {Animals ; Base Sequence ; Cell Nucleus ; Coleoptera/classification/*genetics ; DNA/*analysis ; DNA Transposable Elements ; DNA, Complementary ; DNA, Mitochondrial/*analysis ; Genetic Variation ; Mitochondria ; Molecular Sequence Data ; Phylogeny ; }, abstract = {The phylogenetic relationships of thirteen Diabrotica (representing virgifera and fucata species groups) and two outgroup Acalymma beetle species (Coleoptera: Chrysomelidae) were inferred from the phylogenetic analysis of a combined data set of 1323 bp of mitochondrial DNA (mtDNA) cytochrome oxidase subunit 1 (COI) and the entire second internal transcribed spacer region (ITS-2) of nuclear ribosomal DNA of 362 characters. Species investigated were D. adelpha, D. balteata, D. barberi, D. cristata, D. lemniscata, D. longicornis, D. porracea, D. speciosa, D. undecimpunctata howardi, D. u. undecimpunctata, D. virgifera virgifera, D. v. zeae, D. viridula, and outgroup A. blandulum and A. vittatum. Maximum parsimony (MP), minimum evolution (ME), and maximum likelihood (ML) analyses of combined COI and ITS-2 sequences clearly place species into their traditional morphological species groups with MP and ME analyses resulting in identical topologies. Results generally confer with a prior work based on allozyme data, but within the virgifera species group, D. barberi and D. longicornis strongly resolve as sister taxa as well as monophyletic with the neotropical species, D. viridula, D. cristata and D. lemniscata also resolve as sister taxa. Both relationships are not in congruence with the prior allozyme-based hypothesis. Within the fucata species group, D. speciosa and D. balteata resolve as sister taxa. Results also strongly supported the D. virgifera and D. undecimpunctata subspecies complexes. Our proposed phylogeny provides some insight into current hypotheses regarding distribution status and evolution of various life history traits for Diabrotica.}, }
@article {pmid11517311, year = {2001}, author = {Löytynoja, A and Milinkovitch, MC}, title = {Molecular phylogenetic analyses of the mitochondrial ADP-ATP carriers: the Plantae/Fungi/Metazoa trichotomy revisited.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {98}, number = {18}, pages = {10202-10207}, pmid = {11517311}, issn = {0027-8424}, mesh = {Animals ; Eukaryotic Cells ; Evolution, Molecular ; Fungi/genetics/metabolism ; Mitochondria/*genetics ; Mitochondrial ADP, ATP Translocases/*genetics ; *Phylogeny ; Plants/genetics/metabolism ; }, abstract = {We investigated the basal phylogeny of eukaryotes through analyses of sequences from the ADP-ATP mitochondrial carrier, a transmembrane protein that is stable in function across eukaryote kingdoms. The ADP-ATP data strongly suggest the grouping of Plantae and Fungi to the exclusion of Metazoa. We implemented several procedures to avoid pervasive analytical artifacts such as erroneous alignment, random rooting, long branch attraction, and misidentification of noisy characters. The quest of an eukaryote tree that would be largely consistent across multiple loci might be essentially illusory because of differential lineage sorting, horizontal gene transfer, and the chimeric nature of early eukaryotes. Better understanding of these evolutionary parameters, requiring separate phylogenetic analyses of multiple independent loci, is fundamental for resolution of the modes of emergence and evolution of the major eukaryote lineages.}, }
@article {pmid11508688, year = {2001}, author = {Emelyanov, VV}, title = {Rickettsiaceae, rickettsia-like endosymbionts, and the origin of mitochondria.}, journal = {Bioscience reports}, volume = {21}, number = {1}, pages = {1-17}, doi = {10.1023/a:1010409415723}, pmid = {11508688}, issn = {0144-8463}, mesh = {Animals ; Bacteria/cytology/genetics/metabolism ; Chaperonin 60/genetics/metabolism ; Energy Metabolism/genetics ; Eukaryotic Cells/*cytology/metabolism ; Humans ; Mitochondria/genetics/metabolism/*ultrastructure ; *Phylogeny ; Rickettsiaceae/*cytology/genetics/metabolism ; Symbiosis/*genetics ; }, abstract = {Accumulating evolutionary data point to a monophyletic origin of mitochondria from the order Rickettsiales. This large group of obligate intracellular alpha-Proteobacteria includes the family Rickettsiaceae and several rickettsia-like endosymbionts (RLEs). Detailed phylogenetic analysis of small subunit (SSU) rRNA and chaperonin 60 (Cpn60) sequences testify to polyphyly of the Rickettsiales, and consistently indicate a sisterhood of Rickettsiaceae and mitochondria that excludes RLEs. Thus RLEs are considered as the nearest extant relatives of an extinct last common ancestor of mitochondria and rickettsiae. Phylogenetic inferences prompt the following assumptions. (1) Mitochondrial origin has been predisposed by the long-term endosymbiotic relationship between rickettsia-like bacteria and proto-eukaryotes, in which many endosymbiont genes have been lost while some indispensable genes have been transferred to the host genome. (2) The obligate dependence of rickettsiae upon a eukaryotic host rests on the import of proteins encoded by these transferred genes. The nature of a proto-eukaryotic cell still remains elusive. The divergence of Rickettsiaceae and mitochondria based on Cpn60, and the evolutionary history of two aminoacyl-tRNA synthetases favor the hypothesis that it was a chimera created by fusion of an archaebacterium and a eubacterium not long before an endosymbiotic event. These and other, mostly biochemical data suggest that all the mitochondrion-related organelles, i.e., both aerobically and anaerobically respiring mitochondria and hydrogenosomes, have originated from the same RLE, while hydrogenosomal energy metabolism may have a separate origin resulting from a eubacterial fusion partner.}, }
@article {pmid11500935, year = {2001}, author = {Triana, O and Galanti, N and Olea, N and Hellman, U and Wernstedt, C and Lujan, H and Medina, C and Toro, GC}, title = {Chromatin and histones from Giardia lamblia: a new puzzle in primitive eukaryotes.}, journal = {Journal of cellular biochemistry}, volume = {82}, number = {4}, pages = {573-582}, doi = {10.1002/jcb.1159}, pmid = {11500935}, issn = {0730-2312}, mesh = {Amino Acid Sequence ; Animals ; Cattle ; Cells, Cultured ; Chromatin/*ultrastructure ; DNA/analysis ; DNA, Protozoan/*genetics ; Electrophoresis, Polyacrylamide Gel ; Evolution, Molecular ; Giardia lamblia/chemistry/*genetics ; Histones/*chemistry ; Micrococcal Nuclease/chemistry ; *Phylogeny ; Protozoan Proteins/*chemistry ; }, abstract = {The three deepest eukaryote lineages in small subunit ribosomal RNA phylogenies are the amitochondriate Microsporidia, Metamonada, and Parabasalia. They are followed by either the Euglenozoa (e.g., Euglena and Trypanosoma) or the Percolozoa as the first mitochondria-containing eukaryotes. Considering the great divergence of histone proteins in protozoa we have extended our studies of histones from Trypanosomes (Trypanosoma cruzi, Crithidia fasciculata and Leishmania mexicana) to the Metamonada Giardia lamblia, since Giardia is thought to be one of the most primitive eukaryotes. In the present work, the structure of G. lamblia chromatin and the histone content of the soluble chromatin were investigated and compared with that of higher eukaryotes, represented by calf thymus. The chromatin is present as nucleosome filaments which resemble the calf thymus array in that they show a more regular arrangement than those described for Trypanosoma. SDS-polyacrylamide gel electrophoresis and protein characterization revealed that the four core histones described in Giardia are in the same range of divergence with the histones from other lower eukaryotes. In addition, G. lamblia presented an H1 histone with electrophoretic mobility resembling the H1 of higher eukaryotes, in spite of the fact that H1 has a different molecular mass in calf thymus. Giardia also presents a basic protein which was identified as an HU-like DNA-binding protein usually present in eubacteria, indicating a chimaeric composition for the DNA-binding protein set in this species. Finally, the phylogenetic analysis of selected core histone protein sequences place Giardia divergence before Trypanosoma, despite the fact that Trypanosoma branch shows an acceleration in the evolutionary rate pointing to an unusual evolutionary behavior in this lineage.}, }
@article {pmid11489939, year = {2001}, author = {Clayton, PT and Eaton, S and Aynsley-Green, A and Edginton, M and Hussain, K and Krywawych, S and Datta, V and Malingre, HE and Berger, R and van den Berg, IE}, title = {Hyperinsulinism in short-chain L-3-hydroxyacyl-CoA dehydrogenase deficiency reveals the importance of beta-oxidation in insulin secretion.}, journal = {The Journal of clinical investigation}, volume = {108}, number = {3}, pages = {457-465}, pmid = {11489939}, issn = {0021-9738}, mesh = {3-Hydroxyacyl CoA Dehydrogenases/*deficiency/*genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Carnitine/*analogs &amp; derivatives/blood/chemistry ; DNA Primers/genetics ; Evolution, Molecular ; Fatty Acids/metabolism ; Female ; Gene Expression ; Homozygote ; Humans ; Hyperinsulinism/enzymology/*genetics/*physiopathology ; Hypoglycemia/enzymology/etiology/physiopathology ; In Vitro Techniques ; Infant ; Insulin/*metabolism ; Insulin Secretion ; Models, Biological ; Molecular Sequence Data ; Oxidation-Reduction ; *Point Mutation ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {A female infant of nonconsanguineous Indian parents presented at 4 months with a hypoglycemic convulsion. Further episodes of hypoketotic hypoglycemia were associated with inappropriately elevated plasma insulin concentrations. However, unlike other children with hyperinsulinism, this patient had a persistently elevated blood spot hydroxybutyrylcarnitine concentration when fed, as well as when fasted. Measurement of the activity of L-3-hydroxyacyl-CoA dehydrogenase in cultured skin fibroblasts with acetoacetyl-CoA substrate showed reduced activity. In fibroblast mitochondria, the activity was less than 5% that of controls. Sequencing of the short-chain L-3-hydroxyacyl-CoA dehydrogenase (SCHAD) genomic DNA from the fibroblasts showed a homozygous mutation (C773T) changing proline to leucine at amino acid 258. Analysis of blood from the parents showed they were heterozygous for this mutation. Western blot studies showed undetectable levels of immunoreactive SCHAD protein in the child's fibroblasts. Expression studies showed that the P258L enzyme had no catalytic activity. We conclude that C773T is a disease-causing SCHAD mutation. This is the first defect in fatty acid beta-oxidation that has been associated with hyperinsulinism and raises interesting questions about the ways in which changes in fatty acid and ketone body metabolism modulate insulin secretion by the beta cell. The patient's hyperinsulinism was easily controlled with diazoxide and chlorothiazide.}, }
@article {pmid11485800, year = {2001}, author = {Wolf, YI and Koonin, EV}, title = {Origin of an animal mitochondrial DNA polymerase subunit via lineage-specific acquisition of a glycyl-tRNA synthetase from bacteria of the Thermus-Deinococcus group.}, journal = {Trends in genetics : TIG}, volume = {17}, number = {8}, pages = {431-433}, doi = {10.1016/s0168-9525(01)02370-8}, pmid = {11485800}, issn = {0168-9525}, mesh = {Animals ; DNA-Directed DNA Polymerase/*chemistry/*genetics ; Drosophila melanogaster ; Evolution, Molecular ; Glycine-tRNA Ligase/*genetics ; Mitochondria/*enzymology ; Models, Genetic ; Phylogeny ; Protein Structure, Tertiary ; Xenopus laevis ; }, abstract = {Phylogenetic tree analysis shows that the accessory subunit animal mitochondrial DNA polymerase emerges as a result of horizontal transfer of the gene encoding glycyl-tRNA synthetase from a bacterium of the Thermus-Deinococcus group into the animal nuclear genome. This acquisition by a distinct eukaryotic lineage of a gene encoding a mitochondrial protein from a nonmitochondrial bacterial source underscores the contribution of different types of horizontal transfer event to the evolution of eukaryotes.}, }
@article {pmid11483992, year = {2001}, author = {Leist, M and Jäättelä, M}, title = {Four deaths and a funeral: from caspases to alternative mechanisms.}, journal = {Nature reviews. Molecular cell biology}, volume = {2}, number = {8}, pages = {589-598}, doi = {10.1038/35085008}, pmid = {11483992}, issn = {1471-0072}, mesh = {Animals ; Apoptosis/drug effects/*physiology ; Caenorhabditis elegans/physiology ; Caspases/*physiology ; Chromatin/ultrastructure ; Cysteine Proteinase Inhibitors/pharmacology ; Enzyme Activation ; Eukaryotic Cells/cytology/enzymology ; Evolution, Molecular ; Fungal Proteins/physiology ; Helminth Proteins/physiology ; Humans ; Mitochondria/physiology ; Necrosis ; Neoplasms/pathology/therapy ; Nervous System/cytology/embryology/growth &amp; development ; Receptors, Tumor Necrosis Factor/physiology ; Saccharomyces cerevisiae/physiology ; Signal Transduction ; fas Receptor/physiology ; }, abstract = {A single family of proteases, the caspases, has long been considered the pivotal executioner of all programmed cell death. However, recent findings of evolutionarily conserved, caspase-independent controlled death mechanisms have opened new perspectives on the biology of cell demise, with particular implications for neurobiology, cancer research and immunological processes.}, }
@article {pmid11483969, year = {2001}, author = {Rotte, C and Martin, W}, title = {Does endo-symbiosis explain the origin of the nucleus?.}, journal = {Nature cell biology}, volume = {3}, number = {8}, pages = {E173-4}, doi = {10.1038/35087104}, pmid = {11483969}, issn = {1465-7392}, mesh = {Animals ; Archaea/*genetics ; *Biological Evolution ; Cell Compartmentation/genetics ; Cell Nucleus/*genetics/metabolism/ultrastructure ; Genes/physiology ; Humans ; Mitochondria/genetics/metabolism/ultrastructure ; Symbiosis/*genetics ; }, }
@article {pmid11470849, year = {2001}, author = {Gerbod, D and Edgcomb, VP and Noël, C and Vanácová, S and Wintjens, R and Tachezy, J and Sogin, ML and Viscogliosi, E}, title = {Phylogenetic relationships of class II fumarase genes from trichomonad species.}, journal = {Molecular biology and evolution}, volume = {18}, number = {8}, pages = {1574-1584}, doi = {10.1093/oxfordjournals.molbev.a003944}, pmid = {11470849}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; DNA, Protozoan/chemistry/genetics ; Evolution, Molecular ; Fumarate Hydratase/*genetics ; Gene Expression Regulation, Enzymologic ; Molecular Sequence Data ; *Phylogeny ; RNA, Protozoan/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Trichomonadida/classification/enzymology/*genetics ; }, abstract = {Class II fumarase sequences were obtained by polymerase chain reaction from five trichomonad species. All residues known to be highly conserved in this enzyme were present. Nuclear run-on assays showed that one of the two genes identified in Tritrichomonas foetus was expressed, whereas no fumarase transcripts were detected in the related species Trichomonas vaginalis. These findings corroborate previous biochemical data. Fumarase genes were also expressed in Monocercomonas sp. and Tetratrichomonas gallinarum but not in Pentatrichomonas hominis, Trichomonas gallinae, Trichomonas tenax, and Trichomitus batrachorum under the culture conditions used. Molecular trees inferred by likelihood methods reveal that trichomonad sequences have no affinity to described class II fumarase genes from other eukaryotes. The absence of functional mitochondria in protists such as trichomonads suggests that they diverged from other eukaryotes prior to the alpha-proteobacterial symbiosis that led to mitochondria. Furthermore, they are basal to other eukaryotes in rRNA analyses. However, support for the early-branching status of trichomonads and other amitochondriate protists based on phylogenetic analyses of multiple data sets has been equivocal. Although the presence of hydrogenosomes suggests that trichomonads once had mitochondria, their class II iron-independent fumarase sequences differ markedly from those of other mitochondriate eukaryotes. All of the class II fumarase genes described from other eukaryotes are of apparent alpha-proteobacterial origin and hence a marker of mitochondrial evolution. In contrast, the class II fumarase from trichomonads emerges among other eubacterial homologs. This is intriguing evidence for an independent acquisition of these genes in trichomonads apart from the mitochondrial endosymbiosis event that gave rise to the form present in other eukaryotes. The ancestral trichomonad class II fumarase may represent a prokaryotic form that was replaced in other eukaryotes after the divergence of trichomonads with the movement of endosymbiont genes into the nucleus. Alternatively, it may have been acquired via a separate endosymbiotic event or lateral gene transfer.}, }
@article {pmid11470839, year = {2001}, author = {Williams, ST and Knowlton, N}, title = {Mitochondrial pseudogenes are pervasive and often insidious in the snapping shrimp genus Alpheus.}, journal = {Molecular biology and evolution}, volume = {18}, number = {8}, pages = {1484-1493}, doi = {10.1093/oxfordjournals.molbev.a003934}, pmid = {11470839}, issn = {0737-4038}, mesh = {Animals ; Cell Nucleus/genetics ; DNA/chemistry/genetics ; DNA, Mitochondrial/chemistry/genetics ; Decapoda/classification/*genetics ; Electron Transport Complex IV/genetics ; Gene Dosage ; Mitochondria/*genetics ; Molecular Sequence Data ; Mutation ; Phylogeny ; Pseudogenes/*genetics ; Sequence Analysis, DNA ; }, abstract = {Here we show that multiple DNA sequences, similar to the mitochondrial cytochrome oxidase I (COI) gene, occur within single individuals in at least 10 species of the snapping shrimp genus Alpheus. Cloning of amplified products revealed the presence of copies that differed in length and (more frequently) in base substitutions. Although multiple copies were amplified in individual shrimp from total genomic DNA (gDNA), only one sequence was amplified from cDNA. These results are best explained by the presence of nonfunctional duplications of a portion of the mtDNA, probably located in the nuclear genome, since transfer into the nuclear gene would render the COI gene nonfunctional due to differences in the nuclear and mitochondrial genetic codes. Analysis of codon variation suggests that there have been 21 independent transfer events in the 10 species examined. Within a single animal, differences between the sequences of these pseudogenes ranged from 0.2% to 20.6%, and those between the real mtDNA and pseudogene sequences ranged from 0.2% to 18.8% (uncorrected). The large number of integration events and the large range of divergences between pseudogenes and mtDNA sequences suggest that genetic material has been repeatedly transferred from the mtDNA to the nuclear genome of snapping shrimp. Unrecognized pseudogenes in phylogenetic or population studies may result in spurious results, although previous estimates of rates of molecular evolution based on Alpheus sister taxa separated by the Isthmus of Panama appear to remain valid. Especially worrisome for researchers are those pseudogenes that are not obviously recognizable as such. An effective solution may be to amplify transcribed copies of protein-coding mitochondrial genes from cDNA rather than using genomic DNA.}, }
@article {pmid11470833, year = {2001}, author = {Worobey, M}, title = {A novel approach to detecting and measuring recombination: new insights into evolution in viruses, bacteria, and mitochondria.}, journal = {Molecular biology and evolution}, volume = {18}, number = {8}, pages = {1425-1434}, doi = {10.1093/oxfordjournals.molbev.a003928}, pmid = {11470833}, issn = {0737-4038}, mesh = {Bacteria/genetics ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Models, Genetic ; *Phylogeny ; Recombination, Genetic/*genetics ; Viruses/genetics ; }, abstract = {An accurate estimate of the extent of recombination is important whenever phylogenetic methods are applied to potentially recombining nucleotide sequences. Here, data sets from viruses, bacteria, and mitochondria were examined for deviations from clonality using a new approach for detecting and measuring recombination. The apparent rate heterogeneity (ARH) among sites in a sequence alignment can be inflated as an artifact of recombination. However, the composition of polymorphic sites will differ in a data set with recombination-generated ARH versus a clonal data set that exhibits the equivalent degree of rate heterogeneity. This is because recombinant data sets, encompassing regions of conflicting phylogenetic history, tend to yield "starlike" trees that are superficially similar to those inferred from clonal data sets with weak phylogenetic signal throughout. Specifically, a recombinant data set will be unexpectedly rich in conflicting phylogenetic information compared with clonally generated data sets supporting the same tree shape. Its value of q-defined as the proportion of two-state parsimony-informative sites to all polymorphic sites-will be greater than that expected for nonrecombinant data. The method proposed here, the informative-sites test, compares the value of q against a null distribution of values found using Monte Carlo-simulated data evolved under the null hypothesis of clonality. A significant excess of q indicates that the assumption of clonality is not valid and hence that the ARH in the data is at least partly an artifact of recombination. Investigations of the procedure using simulated sequences indicated that it can successfully detect and measure recombination and that it is unlikely to produce "false positives." Simulations also showed that for recombinant data, naïve use of maximum-likelihood models incorporating rate heterogeneity can lead to overestimation of the time to the most recent common ancestor. Application of the test to real data revealed for the first time that populations of viruses, like those of bacteria, can be brought close to complete linkage equilibrium by pervasive recombination. On the other hand, the test did not reject the hypothesis of clonality when applied to a data set from the coding region of human mitochondrial DNA, despite its high level of ARH and homoplasy.}, }
@article {pmid11470518, year = {2001}, author = {Milyutina, IA and Aleshin, VV and Mikrjukov, KA and Kedrova, OS and Petrov, NB}, title = {The unusually long small subunit ribosomal RNA gene found in amitochondriate amoeboflagellate Pelomyxa palustris: its rRNA predicted secondary structure and phylogenetic implication.}, journal = {Gene}, volume = {272}, number = {1-2}, pages = {131-139}, doi = {10.1016/s0378-1119(01)00556-x}, pmid = {11470518}, issn = {0378-1119}, mesh = {Amoeba/*genetics ; Animals ; Base Sequence ; DNA, Protozoan/chemistry/genetics ; Evolution, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal/chemistry/*genetics ; Sequence Analysis, DNA ; }, abstract = {In order to ascertain a phylogenetic position of the freshwater amitochondriate amoeboflagellate Pelomyxa palustris its small subunit (SSU) rRNA gene was amplified and sequenced. It was shown to be 3502 bp long. The predicted secondary structure of its rRNA includes at least 16 separate expansion zones located in all the variable regions (V1-V9), as well as in some conservative gene regions. Most insertions are represented by sequences of low complexity that have presumably arisen by a slippage mechanism. Relatively conservative, uniformly positioned motifs contained in regions V4 and V7, as well as in some others, made it possible to perform folding. In maximum likelihood, maximum parsimony, and neighbor-joining trees, P. palustris tends to cluster with amitochondriate and secondary lost mitochondria amoebae and amoeboflagellates Entamoeba, Endolimax nana, and Phreatamoeba balamuthi, comprising together with them and aerobic lobose amoebae Vannella, Acanthamoeba, Balamuthia, and Hartmannella a monophyletic cluster. Another pelobiont, Mastigamoeba invertens, does not belong to this cluster. No specific similarity was discovered between the SSU rRNA of P. palustris and amitochondriate taxa of 'Archezoa': Diplomonada, Parabasalia, Microsporidia. Pelomyxa palustris SSU rRNA does not occupy a basal position in the phylogenetic trees and could be ascribed to the so-called eukaryotic 'crown' group if the composition of the latter were not so sensitive to the methods of tree building. Thus, molecular and morphological data suggest that P. palustris represents a secondarily modified eukaryotic lineage.}, }
@article {pmid11464628, year = {2001}, author = {Siordia-Reyes, AG and Ferman-Cano, F and García, GR and Rodríguez-Velasco, A}, title = {[Wilson disease. Report of a case of autopsy with copper tissue quantification and electronic microscopy].}, journal = {Revista de gastroenterologia de Mexico}, volume = {66}, number = {1}, pages = {38-41}, pmid = {11464628}, issn = {0375-0906}, mesh = {Adolescent ; Copper/analysis ; Fatal Outcome ; Female ; Hepatolenticular Degeneration/metabolism/*pathology ; Humans ; Microscopy, Electron ; }, abstract = {UNLABELLED: Wilson's disease is a rare autosomal recessive disorder of copper metabolism. Kinnear Wilson described the entity in 1912 and considered it to be a degenerative disorder of the central nervous system associated with asymptomatic cirrhosis. Gene linkage analysis has localized the genetic defect on chromosome 13.<br><br>CLINICAL CASE: Woman of 15 years of age. She began with amenorrhea at 8 months of evolution, and acholia and hepatomegaly 1 month before her death. The viral serology panel was negative. She evolved with severe hepatic insufficiency and died. The quantitation of copper dose postmortem in hepatic tissue by atomic absorption spectrophotometry resulted in 250.57 micrograms/g. Electronic microscopy showed dense bodies in the mitochondria. Young adolescents frequently develop hepatic insufficiency as a first manifestation of Wilson's disease. Histologically, some morphology data such as the glucogenized naked nuclei, microvesticular fatty change, Mallory bodies, and hepatic regeneration, but the definitive diagnosis was decreased serum ceruloplasmin level, quantitation of copper in tissue, electron microscopy, and more recently, the molecular biology or genetic alterations.}, }
@article {pmid11459176, year = {2001}, author = {Handa, H and Kobayashi-Uehara, A and Murayama, S}, title = {Characterization of a wheat cDNA encoding mitochondrial ribosomal protein L11: qualitative and quantitative tissue-specific differences in its expression.}, journal = {Molecular genetics and genomics : MGG}, volume = {265}, number = {4}, pages = {569-575}, doi = {10.1007/s004380100457}, pmid = {11459176}, issn = {1617-4615}, mesh = {Amino Acid Sequence ; Cold Temperature ; DNA, Complementary/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Genes, Reporter ; Green Fluorescent Proteins ; Luminescent Proteins/analysis ; Mitochondria/chemistry ; Molecular Sequence Data ; Organ Specificity ; Plant Leaves/metabolism/ultrastructure ; Plant Proteins/analysis/biosynthesis/*genetics ; Plant Roots/metabolism/ultrastructure ; Plant Shoots/metabolism/ultrastructure ; RNA, Messenger/biosynthesis ; RNA, Plant/biosynthesis ; Recombinant Fusion Proteins/analysis ; Ribosomal Proteins/analysis/biosynthesis/*genetics ; Seeds/metabolism/ultrastructure ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Subcellular Fractions/chemistry ; Triticum/*genetics ; }, abstract = {We have cloned a cDNA for a ribosomal protein of wheat that is similar to the bacterial ribosomal protein L11 (RPL11). To determine the subcellular localization of the gene product, we fused the whole cDNA sequence to the coding sequence for Green Fluorescent Protein, and expressed the fusion product transiently in epidermal cells of pea hypocotyls or dayflower leaves. Localized fluorescence was detectable in mitochondria, indicating that this nuclear cDNA encodes a mitochondrial ribosomal protein L11 (MRPL11). In lower protists, mitochondrial RPL11 is encoded by the mitochondrial genome, but higher organisms, including animals, fungi and plants, do not have genes for RPL11 in their mitochondrial genomes, suggesting that transfer of the genetic information for RPL11 from the mitochondrial genome to the nucleus was a very early event in evolution. Transcripts of this wheat gene (TaMRPL11) for mitochondrial RPL11 were found in all tissues examined, although qualitative and quantitative differences in expression were noted. The transcript sizes were different in different plant tissues: 1.0 kb in flowers and roots, and 1.5 kb in shoots. Cold stress transiently increased the steady-state level of TaMRPL11 mRNA in shoots, but the transcription of TaMRPL11 was completely inhibited by cold treatment for longer periods. However, the transcript level in flowers decreased gradually on exposure to low temperature. On the other hand, the accumulation of TaMRPL11 transcripts in roots was not affected by low temperature. These results suggest that the expression of MRPL11 in wheat is regulated precisely, in a tissue-specific manner.}, }
@article {pmid11457448, year = {2001}, author = {Emelyanov, VV}, title = {Evolutionary relationship of Rickettsiae and mitochondria.}, journal = {FEBS letters}, volume = {501}, number = {1}, pages = {11-18}, doi = {10.1016/s0014-5793(01)02618-7}, pmid = {11457448}, issn = {0014-5793}, mesh = {Energy Metabolism ; Genome ; Mitochondria/genetics/metabolism/*physiology ; *Models, Biological ; *Phylogeny ; Rickettsia/classification/genetics/*physiology ; Symbiosis ; }, abstract = {Phylogenetic data support an origin of mitochondria from the alpha-proteobacterial order Rickettsiales. This high-rank taxon comprises exceptionally obligate intracellular endosymbionts of eukaryotic cells, and includes family Rickettsiaceae and a group of microorganisms termed Rickettsia-like endosymbionts (RLEs). Most detailed phylogenetic analyses of small subunit rRNA and chaperonin 60 sequences consistently show the RLEs to have emerged before Rickettsiaceae and mitochondria sister clades. These data suggest that the origin of mitochondria and Rickettsiae has been preceded by the long-term mutualistic relationship of an intracellular bacterium with a pro-eukaryote, in which an invader has lost many dispensable genes, yet evolved carrier proteins to exchange respiration-derived ATP for host metabolites as envisaged in classic endosymbiont theory.}, }
@article {pmid11456326, year = {2001}, author = {Simpson, AG and Patterson, DJ}, title = {On core jakobids and excavate taxa: the ultrastructure of Jakoba incarcerata.}, journal = {The Journal of eukaryotic microbiology}, volume = {48}, number = {4}, pages = {480-492}, doi = {10.1111/j.1550-7408.2001.tb00183.x}, pmid = {11456326}, issn = {1066-5234}, mesh = {Animals ; Eukaryota/classification/genetics/*ultrastructure ; Evolution, Molecular ; Microscopy, Electron ; }, abstract = {The cellular organisation of the 'excavate' flagellate Jakoba incarcerata Bernard, Simpson and Patterson 2000 is described. Cells have one nucleus and dictyosome. The putative mitochondria lack cristae. Two flagella (anterior and posterior) insert anterior to the feeding groove. The posterior flagellum bears a dorsal vane. An 'anterior' microtubular root arises against the anterior basal body. Two main microtubular roots, left and right, and a singlet 'root' arise around the posterior basal body and support the groove. Non-microtubular fibres termed 'A', 'B', 'I', and 'composite' associate with the right root. A multilaminar 'C' fibre associates with the left root. The cytoskeleton of J. incarcerata indicates a common ancestry with other excavate taxa (i.e. diplomonads, retortamonads, heteroloboseids, 'core jakobids', Malawimonas, Carpediemonas, and Trimastix). Overall, J. incarcerata is most similar to (other) core jakobids, namely Jakoba libera, Reclinomonas, and Histiona. We regard J. incarcerata as a core jakobid and identify the group by the synapomorphy 'vanes restricted to dorsal side of the posterior flagellum'. The anterior root and position of the B fibre (and presence of dense inclusions in the cartwheels and a conscpicuous singlet root-associated fibre) in J. incarcerata are novel for core jakobids and argue for close relationships with Trimastix and/or Heterolobosea. The C fibre is similar in substructure to the costal fibre of parabasalids and it is possible that the structures are homologous.}, }
@article {pmid11454775, year = {2001}, author = {Adams, KL and Rosenblueth, M and Qiu, YL and Palmer, JD}, title = {Multiple losses and transfers to the nucleus of two mitochondrial succinate dehydrogenase genes during angiosperm evolution.}, journal = {Genetics}, volume = {158}, number = {3}, pages = {1289-1300}, pmid = {11454775}, issn = {0016-6731}, support = {GM-35087/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Cell Nucleus/*enzymology ; DNA, Complementary ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Isoenzymes/chemistry/*genetics ; Magnoliopsida/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Succinate Dehydrogenase/chemistry/*genetics ; }, abstract = {Unlike in animals, the functional transfer of mitochondrial genes to the nucleus is an ongoing process in plants. All but one of the previously reported transfers in angiosperms involve ribosomal protein genes. Here we report frequent transfer of two respiratory genes, sdh3 and sdh4 (encoding subunits 3 and 4 of succinate dehydrogenase), and we also show that these genes are present and expressed in the mitochondria of diverse angiosperms. Southern hybridization surveys reveal that sdh3 and sdh4 have been lost from the mitochondrion about 40 and 19 times, respectively, among the 280 angiosperm genera examined. Transferred, functional copies of sdh3 and sdh4 were characterized from the nucleus in four and three angiosperm families, respectively. The mitochondrial targeting presequences of two sdh3 genes are derived from preexisting genes for anciently transferred mitochondrial proteins. On the basis of the unique presequences of the nuclear genes and the recent mitochondrial gene losses, we infer that each of the seven nuclear sdh3 and sdh4 genes was derived from a separate transfer to the nucleus. These results strengthen the hypothesis that angiosperms are experiencing a recent evolutionary surge of mitochondrial gene transfer to the nucleus and reveal that this surge includes certain respiratory genes in addition to ribosomal protein genes.}, }
@article {pmid11454615, year = {2001}, author = {Renzaglia, KS and Johnson, TH and Gates, HD and Whittier, DP}, title = {Architecture of the sperm cell of Psilotum.}, journal = {American journal of botany}, volume = {88}, number = {7}, pages = {1151-1163}, pmid = {11454615}, issn = {0002-9122}, abstract = {In this correlated SEM (scanning electron microscope) and TEM (transmission electron microscope) investigation, we describe architectural details of the multiflagellated sperm cell of Psilotum nudum. Comparisons with other pteridophytes are made to (1) assess the placement of Psilotum among pteridophyte taxa and (2) evaluate structural modifications of sperm cells during land plant evolution. The released spermatozoid of Psilotum coils 2.0 revolutions and is outlined by a parallel band of up to 190 microtubules. The elongated nucleus is highly compacted and parallels the cellular coils with numerous mitochondria and starch-laden plastids distributed along its length. Along the anterior coil is an elaborate locomotory apparatus that includes ∼36 flagella that are inserted into the cell by basal bodies. Subtending the basal bodies is the multilayered structure, which consists of a long narrow lamellar strip and an overlying band of microtubules. An elongated anterior mitochondrion underlies the multilayered structure. Additional amyloplasts and mitochondria are aggregated along the anterior coil in association with the locomotory apparatus, while a fibrous band encircles the leading edge of the cell. Salient features of this cell, including details of the locomotory apparatus, structure and position of organelles, and arrangement of the spline, are shared by spermatozoids of Equisetum and ferns (including eusporangiate and leptosporangiate taxa). Thus, this study provides morphological support for the hypothesis that Psilotum nudum is a member of an assemblage that includes ferns and Equisetum. However, the less streamlined architecture of Psilotum gametes and the lack of architectural features shared with any specific taxon examined to date suggest that Psilotum is an early divergent fern, with relatively remote affinities to Ophioglossaceae and Equisetaceae.}, }
@article {pmid11454299, year = {2001}, author = {Phillips, MJ and Lin, YH and Harrison, GL and Penny, D}, title = {Mitochondrial genomes of a bandicoot and a brushtail possum confirm the monophyly of australidelphian marsupials.}, journal = {Proceedings. Biological sciences}, volume = {268}, number = {1475}, pages = {1533-1538}, doi = {10.1098/rspb.2001.1677}, pmid = {11454299}, issn = {0962-8452}, mesh = {Animals ; Cytosine Nucleotides/analysis ; Genetic Heterogeneity ; Marsupialia/classification/*genetics ; Mitochondria, Liver/*genetics ; Phylogeny ; Pyrimidines/analysis ; RNA/analysis ; Thymine Nucleotides/analysis ; }, abstract = {Recent molecular analyses suggest that the position of bandicoots is the major difficulty in determining the root of the tree of extant marsupials. To resolve this, we analyse mitochondrial genome sequences of a bandicoot (Isoodon macrourus) and a brushtail possum (Trichosurus vulpecula) together with the previously available marsupial mitochondrial genomes, the Virginia opossum (Didelphis virginiana) and the wallaroo (Macropus robustus). Analyses of mitochondrial protein-coding and RNA genes strongly support the bandicoot as sister to the wallaroo and the brushtail possum. This result, combined with other recent molecular analyses, confirms the monophyly of Australidelphia (Australasian marsupials plus Dromiciops from South America). Further, RY coding was found to nullify AGCT coding nucleotide composition bias.}, }
@article {pmid11454296, year = {2001}, author = {Piertney, SB and Summers, R and Marquiss, M}, title = {Microsatellite and mitochondrial DNA homogeneity among phenotypically diverse crossbill taxa in the UK.}, journal = {Proceedings. Biological sciences}, volume = {268}, number = {1475}, pages = {1511-1517}, doi = {10.1098/rspb.2001.1015}, pmid = {11454296}, issn = {0962-8452}, mesh = {Alleles ; Animals ; Base Sequence ; *DNA, Mitochondrial ; Gene Frequency ; Genetic Variation ; Microsatellite Repeats/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Songbirds/classification/*genetics ; Species Specificity ; United Kingdom ; }, abstract = {Genetic differentiation within and between the three morphologically divergent crossbill species extant in the UK was assessed by comparison of allele frequencies at five unlinked microsatellite loci and DNA sequence variation across the mitochondrial control region. No significant differences in microsatellite allele frequency were found either between different populations of the same species or between the crossbill species themselves. A similar lack of genetic divergence was apparent from the mitochondrial sequence data. We resolved 33 different haplotypes, separated by low levels of sequence divergence (0-0.15%). Levels of divergence within and between species were not significantly different. Haplotypes formed a polyphyletic phylogeny, indicating that the crossbill species do not form genetically separate clades. Discordance between neutral DNA polymorphisms and adaptive morphological variation is discussed in relation to defining the systematic relationship between crossbill forms. If adaptive differences have arisen without a concomitant divergence in neutral DNA then attempting to define crossbill types from microsatellite and mitochondrial DNA without recourse to ecology and behaviour may be misleading.}, }
@article {pmid11437920, year = {2001}, author = {Malloch, G and Fenton, B and Goodrich, MA}, title = {Phylogeny of raspberry beetles and other Byturidae (Coleoptera).}, journal = {Insect molecular biology}, volume = {10}, number = {3}, pages = {281-291}, doi = {10.1046/j.1365-2583.2001.00266.x}, pmid = {11437920}, issn = {0962-1075}, mesh = {Animals ; Base Sequence ; Coleoptera/classification/enzymology/*genetics ; DNA ; Electron Transport Complex IV/*genetics ; Fruit ; Genetic Variation ; Mitochondria ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Point Mutation ; Polymerase Chain Reaction/methods ; Repetitive Sequences, Nucleic Acid ; Ribosomes ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Nuclear ribosomal ITS2 and mitochondrial cytochrome oxidase DNA sequences were analysed from the Byturidae (Coleoptera), which includes the raspberry beetles. The secondary structure of ITS2 was plotted and interspecific changes analysed. Evidence for selection on simple sequence repeats within the ITS2 was found. Phylogenetic trees based on the mitochondrial and ribosomal sequences were compared. They were in parity, indicating they reflect the true evolutionary histories of these insects. There was no evidence for hybridization in the populations surveyed, but there was evidence that the American raspberry beetle, Byturus unicolor, is divided into at least three distinct groupings. Despite sharing a related host, the raspberry pests from America were not the most related to the European raspberry beetle. Instead, links between Byturus affinis from Japan and the American raspberry beetle suggest that this lineage originated in Asia and colonized the Western USA.}, }
@article {pmid11427190, year = {2001}, author = {Agarraberes, FA and Dice, JF}, title = {Protein translocation across membranes.}, journal = {Biochimica et biophysica acta}, volume = {1513}, number = {1}, pages = {1-24}, doi = {10.1016/s0304-4157(01)00005-3}, pmid = {11427190}, issn = {0006-3002}, support = {AG06116/AG/NIA NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Bacteria ; Biological Transport ; Cell Membrane/*metabolism ; Chloroplasts ; Cytoplasm/metabolism ; Eukaryotic Cells ; Guanosine Triphosphate/metabolism ; Humans ; Intracellular Membranes/*metabolism ; Models, Chemical ; Molecular Chaperones/metabolism ; Organelles/metabolism ; Proteins/*metabolism ; }, abstract = {Cellular membranes act as semipermeable barriers to ions and macromolecules. Specialized mechanisms of transport of proteins across membranes have been developed during evolution. There are common mechanistic themes among protein translocation systems in bacteria and in eukaryotic cells. Here we review current understanding of mechanisms of protein transport across the bacterial plasma membrane as well as across several organelle membranes of yeast and mammalian cells. We consider a variety of organelles including the endoplasmic reticulum, outer and inner membranes of mitochondria, outer, inner, and thylakoid membranes of chloroplasts, peroxisomes, and lysosomes. Several common principles are evident: (a) multiple pathways of protein translocation across membranes exist, (b) molecular chaperones are required in the cytosol, inside the organelle, and often within the organelle membrane, (c) ATP and/or GTP hydrolysis is required, (d) a proton-motive force across the membrane is often required, and (e) protein translocation occurs through gated, aqueous channels. There are exceptions to each of these common principles indicating that our knowledge of how proteins translocate across membranes is not yet complete.}, }
@article {pmid11425482, year = {2001}, author = {Yokoyama, K and Wang, L and Miyaji, M and Nishimura, K}, title = {Identification, classification and phylogeny of the Aspergillus section Nigri inferred from mitochondrial cytochrome b gene.}, journal = {FEMS microbiology letters}, volume = {200}, number = {2}, pages = {241-246}, doi = {10.1111/j.1574-6968.2001.tb10722.x}, pmid = {11425482}, issn = {0378-1097}, mesh = {Aspergillus/*classification/genetics ; Base Sequence ; Cytochrome b Group/*genetics ; DNA, Fungal/analysis ; Mitochondria/enzymology/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, Protein ; Sequence Homology, Nucleic Acid ; }, abstract = {The partial mitochondrial cytochrome b gene from 32 strains of 12 species belonging to Aspergillus section Nigri was amplified by the polymerase chain reaction and sequenced directly. Using 402 nucleotide characters, nucleotide-based and amino acid-based phylogenetic trees were inferred and the genetic divergence among the species was evaluated. Based on analyses of the 402-bp nucleotide and 133-amino acid sequences, strains were divided into 11 DNA types and five amino acid types. Aspergillus niger and Aspergillus awamori showed different amino acid sequences. A. niger clade included A. niger var. niger and Aspergillus ficuum. A. awamori clade included A. awamori, Aspergillus phoenicis, Aspergillus pulverulentus, Aspergillus tubingensis, Aspergillus foetidus, and two varieties of A. niger, var. nanus and var. intermedius. Two varieties of A. niger will be reclassified. One strain of A. phoenicis and one strain of Aspergillus carbonarius were reidentified.}, }
@article {pmid11423013, year = {2001}, author = {Gray, MW and Burger, G and Lang, BF}, title = {The origin and early evolution of mitochondria.}, journal = {Genome biology}, volume = {2}, number = {6}, pages = {REVIEWS1018}, pmid = {11423013}, issn = {1474-760X}, mesh = {Alphaproteobacteria/genetics ; Cell Nucleus/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genome ; Genome, Bacterial ; Mitochondria/*genetics ; Rickettsia prowazekii/genetics ; Saccharomyces cerevisiae/genetics ; }, abstract = {Complete sequences of numerous mitochondrial, many prokaryotic, and several nuclear genomes are now available. These data confirm that the mitochondrial genome originated from a eubacterial (specifically alpha-proteobacterial) ancestor but raise questions about the evolutionary antecedents of the mitochondrial proteome.}, }
@article {pmid11420358, year = {2001}, author = {Ladoukakis, ED and Zouros, E}, title = {Direct evidence for homologous recombination in mussel (Mytilus galloprovincialis) mitochondrial DNA.}, journal = {Molecular biology and evolution}, volume = {18}, number = {7}, pages = {1168-1175}, doi = {10.1093/oxfordjournals.molbev.a003904}, pmid = {11420358}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; Bivalvia/*genetics ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Female ; Male ; Molecular Sequence Data ; Polymerase Chain Reaction ; *Recombination, Genetic ; Time Factors ; }, abstract = {The assumption that animal mitochondrial DNA (mtDNA) does not undergo homologous recombination is based on indirect evidence, yet it has had an important influence on our understanding of mtDNA repair and mutation accumulation (and thus mitochondrial disease and aging) and on biohistorical inferences made from population data. Recently, several studies have suggested recombination in primate mtDNA on the basis of patterns of frequency distribution and linkage associations of mtDNA mutations in human populations, but others have failed to produce similar evidence. Here, we provide direct evidence for homologous mtDNA recombination in mussels, where heteroplasmy is the rule in males. Our results indicate a high rate of mtDNA recombination. Coupled with the observation that mammalian mitochondria contain the enzymes needed for the catalysis of homologous recombination, these findings suggest that animal mtDNA molecules may recombine regularly and that the extent to which this generates new haplotypes may depend only on the frequency of biparental inheritance of the mitochondrial genome. This generalization must, however, await evidence from animal species with typical maternal mtDNA inheritance.}, }
@article {pmid11418217, year = {2001}, author = {Henze, K and Martin, W}, title = {How do mitochondrial genes get into the nucleus?.}, journal = {Trends in genetics : TIG}, volume = {17}, number = {7}, pages = {383-387}, doi = {10.1016/s0168-9525(01)02312-5}, pmid = {11418217}, issn = {0168-9525}, mesh = {Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genes, Plant/genetics ; Introns/genetics ; Models, Genetic ; Plant Cells ; Plants/genetics ; RNA Editing/genetics ; Recombination, Genetic/genetics ; }, abstract = {It is well known that genes from chloroplasts and mitochondria were transferred to the nucleus many times during plant evolution. But in what form do the transferred genes physically make that intracellular journey--as RNA, as cDNA, as pieces of organelle DNA, or as whole organelle chromosomes? Current views focus upon cDNA as the vehicle, based upon some examples from plants. But other mechanisms, involving direct transfer of DNA from organelle chromosomes, could also account for the available data. Direct DNA transfer, rather than cDNA-mediated transfer, does occur today, and it probably prevailed during the early phases of organelle evolution.}, }
@article {pmid11413367, year = {2001}, author = {Hayajneh, WA and Contopoulos-Ioannidis, DG and Lesperance, MM and Venegas, AM and Colberg-Poley, AM}, title = {The carboxyl terminus of the human cytomegalovirus UL37 immediate-early glycoprotein is conserved in primary strains and is important for transactivation.}, journal = {The Journal of general virology}, volume = {82}, number = {Pt 7}, pages = {1569-1579}, doi = {10.1099/0022-1317-82-7-1569}, pmid = {11413367}, issn = {0022-1317}, mesh = {Amino Acid Sequence ; Cell Line ; Chloramphenicol O-Acetyltransferase ; Cytomegalovirus/*genetics/metabolism ; Endoplasmic Reticulum/metabolism ; Genetic Variation ; Glycoproteins/genetics/metabolism ; HSP70 Heat-Shock Proteins/genetics ; Humans ; Immediate-Early Proteins/*genetics/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Mutation ; Open Reading Frames ; Phylogeny ; Promoter Regions, Genetic ; *Transcriptional Activation ; Transfection ; Viral Proteins/*genetics/metabolism ; }, abstract = {The human cytomegalovirus (HCMV) UL37 exon 3 (UL37x3) open reading frame (ORF) encodes the carboxyl termini of two immediate-early glycoproteins (gpUL37 and gpUL37(M)). UL37x3 homologous sequences are not required for mouse cytomegalovirus (MCMV) growth in vitro; yet, they are important for MCMV growth and pathogenesis in vivo. Similarly, UL37x3 sequences are dispensable for HCMV growth in culture, but their requirement for HCMV growth in vivo is not known. To determine this requirement, we directly sequenced the complete UL37x3 gene in multiple HCMV primary strains. A total of 63 of the 310 amino acids in the UL37x3 ORF differ non-conservatively in one or more HCMV primary strains. The HCMV UL37x3 genetic diversity is non-random: the N-glycosylation (46/186 aa) and basic (9/15 aa) domains have the highest proportion of non-conservative variant amino acids. Nonetheless, most (15/17 signals) of the N-glycosylation signals are retained in all HCMV primary strains. Moreover, new N-glycosylation signals are encoded by 5/20 primary strains. In sharp contrast, the UL37x3 transmembrane (TM) ORF completely lacks diversity in all 20 HCMV sequenced primary strains, and only 1 of 28 cytosolic tail residues differs non-conservatively. To test the functional significance of the conserved carboxyl terminus, gpUL37 mutants lacking the TM and/or cytosolic tail were tested for transactivating activity. The gpUL37 carboxyl-terminal mutants are partially defective in hsp70 promoter transactivation even though they trafficked similarly to the wild-type protein into the endoplasmic reticulum and to mitochondria. From these results, we conclude that N-glycosylated gpUL37, particularly its TM and cytosolic domains, is important for HCMV growth in humans.}, }
@article {pmid11411938, year = {2001}, author = {Sopott-Ehlers, B and Kearn, GC and Ehlers, U}, title = {Evidence for the mitochondrial origin of the eye lenses in embryos of Entobdella soleae (Plathelminthes, Monogenea).}, journal = {Parasitology research}, volume = {87}, number = {6}, pages = {421-427}, doi = {10.1007/s004360000331}, pmid = {11411938}, issn = {0932-0113}, mesh = {Animals ; Anterior Eye Segment/embryology/ultrastructure ; Embryo, Nonmammalian/*ultrastructure ; Lens, Crystalline/*embryology/ultrastructure ; Mitochondria/*ultrastructure ; Platyhelminths/*embryology ; }, abstract = {The lens associated with each of the four pigmented eyes of the oncomiracidium of Entobdella soleae (Plathelminthes, Monogenea, Capsalidae) develops in a special region of the pigment cup cell of the eye. It is confirmed that the inner of the two membranes enclosing each lens bears short, inwardly projecting, membranous profiles identical to mitochondrial cristae. Studies of embryos incubated for 19 days at 12 degrees C (hatching begins at 28 days at this temperature) revealed that the matrix of the developing lens of each anterior eye contains many mitochondrial membrane compartments, some having the configuration of separate, small mitochondria. The implication is that the lens is derived from many fused mitochondria, rather than from a single large one. The anterior eyes of 19-day-old embryos are less well developed than the posterior eyes. Pigment granules in the anterior eyes appear to be at the premelanosome stage and contain dispersed dense particles lacking an obvious orderly arrangement. The posterior eyes mostly contain mature melanosomes. Membranous compartments in the matrix of the posterior eye lenses are rare. Apart from longer peripheral cristae, lenses of 22-day-old embryos are identical with those of oncomiracidia. The evolution of mitochondrial lenses in Plathelminthes is considered.}, }
@article {pmid11407527, year = {2001}, author = {Altavilla, G and Chiarelli, S and Fassina, A}, title = {Duodenal periampullary gangliocytic paraganglioma: report of two cases with immunohistochemical and ultrastructural study.}, journal = {Ultrastructural pathology}, volume = {25}, number = {2}, pages = {137-145}, doi = {10.1080/019131201750222220}, pmid = {11407527}, issn = {0191-3123}, mesh = {Adult ; Chromogranin A ; Chromogranins/analysis ; Cytoplasmic Granules/ultrastructure ; *Duodenum ; Endoplasmic Reticulum/ultrastructure ; Female ; Humans ; *Immunohistochemistry ; Intestinal Mucosa/pathology ; Intestinal Neoplasms/chemistry/*diagnosis/ultrastructure ; Lysosomes/ultrastructure ; Male ; *Microscopy, Electron ; Middle Aged ; Mitochondria/ultrastructure ; Neurofibrils/ultrastructure ; Paraganglioma/chemistry/*diagnosis/ultrastructure ; S100 Proteins/analysis ; Synaptophysin/analysis ; }, abstract = {We report two cases of Gangliocytic Paraganglioma (GP) of the ampulla of Vater occurring in a 63-year-old and a 34-year-old individual. The patients were both admitted for a long history of intermittent gastrointestinal bleeding and abdominal discomfort, with no other symptoms. At endoscopy, the GP appeared as a polypoid, ulcerated mass in the ampullar region, measuring 2.5x1.8 and 2 cm, respectively. Microscopically, the tumors showed similar features and were composed of epithelial cells (more than 50%), spindle cells, and ganglion-like cells. The epithelial cells showed clear cytoplasm and formed nests (zellballen or paraganglioma-like groups), and less frequently, cords (carcinoid-like), extending to mucosa and submucosa. Ganglion cells were sparse, constantly associated with the spindle cells. Both epithelial and ganglion cells were synaptophysin, chromogranin A, and anti-neurofilament immunoreactive. The spindle cells were all S-100 positive. Ultrastructural studies revealed dark and light cells, rare elongated cellular processes, secretory granules, and fine fibrils resembling neurofilaments. The histogenesis of GP is still a matter of debate, however its neoplastic nature is supported by the occasionally reported malignant evolution.}, }
@article {pmid11403851, year = {2001}, author = {Appel, D and Lutz-Wahl, S and Fischer, P and Schwaneberg, U and Schmid, RD}, title = {A P450 BM-3 mutant hydroxylates alkanes, cycloalkanes, arenes and heteroarenes.}, journal = {Journal of biotechnology}, volume = {88}, number = {2}, pages = {167-171}, doi = {10.1016/s0168-1656(01)00249-8}, pmid = {11403851}, issn = {0168-1656}, mesh = {Alkanes/*metabolism ; *Bacterial Proteins ; Cytochrome P-450 Enzyme System/*genetics/*metabolism ; Mixed Function Oxygenases/*genetics/*metabolism ; *Mutation ; NADPH-Ferrihemoprotein Reductase ; Naphthalenes/*metabolism ; *Norisoprenoids ; Octanes/metabolism ; Quinolines/*metabolism ; Substrate Specificity ; Terpenes/metabolism ; }, abstract = {P450 monooxygenases from microorganisms, similar to those of eukaryotic mitochondria, display a rather narrow substrate specificity. For native P450 BM-3, no other substrates than fatty acids or an indolyl-fatty acid derivative have been reported (Li, Q.S., Schwaneberg, U., Fischer, P., Schmid, R.D., 2000. Directed evolution of the fatty-acid hydroxylase P450BM-3 into an indole-hydroxylating catalyst. Chem. Eur. J. 6 (9), 1531-1536). Engineering the substrate specificity of Bacillus megaterium cytochrome P-450 BM3: hydroxylation of alkyl trimethylammonium compounds. Biochem. J. 327, 537-544). We thus were quite surprised to observe, in the course of our investigations on the rational evolution of this enzyme towards mutants, capable of hydroxylating shorter-chain fatty acids, that a triple mutant P450 BM-3 (Phe87Val, Leu188-Gln, Ala74Gly, BM-3 mutant) could efficiently hydroxylate indole, leading to the formation of indigo and indirubin (Li, Q.S., Schwaneberg, U., Fischer, P., Schmid, R.D., 2000. Directed evolution of the fatty-acid hydroxylase P450BM-3 into an indole-hydroxylating catalyst. Chem. Eur. J. 6 (9), 1531-1536). Indole is not oxidized by the wild-type enzyme; it lacks the carboxylate group by which the proper fatty acid substrates are supposed to be bound at the active site of the native enzyme, via hydrogen bonds to the charged amino acid residues Arg47 and Tyr51. Our attempts to predict the putative binding mode of indole to P450 BM-3 or the triple mutant by molecular dynamics simulations did not provide any useful clue. Encouraged by the unexpected activity of the triple mutant towards indole, we investigated in a preliminary, but systematic manner several alkanes, alicyclic, aromatic, and heterocyclic compounds, all of which are unaffected by the native enzyme, for their potential as substrates. We here report that this triple mutant indeed is capable to hydroxylate a respectable range of other substrates, all of which bear little or no resemblance to the fatty acid substrates of the native enzyme.}, }
@article {pmid11402041, year = {2001}, author = {Suzuki, T and Terasaki, M and Takemoto-Hori, C and Hanada, T and Ueda, T and Wada, A and Watanabe, K}, title = {Proteomic analysis of the mammalian mitochondrial ribosome. Identification of protein components in the 28 S small subunit.}, journal = {The Journal of biological chemistry}, volume = {276}, number = {35}, pages = {33181-33195}, doi = {10.1074/jbc.M103236200}, pmid = {11402041}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/genetics ; Caenorhabditis elegans/genetics ; Cattle ; Chromatography, Liquid ; DNA, Complementary ; Drosophila melanogaster/genetics ; Humans ; Mammals ; Mass Spectrometry ; Mice ; Mitochondria, Liver/*chemistry/genetics ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Peptide Fragments/chemistry ; *Phylogeny ; Protein Structure, Secondary ; Proteome/*chemistry ; Recombinant Proteins/chemistry ; Ribosomal Proteins/*chemistry/genetics/isolation &amp; purification ; Ribosomes/*chemistry/genetics ; Saccharomyces cerevisiae/genetics ; }, abstract = {The mammalian mitochondrial ribosome (mitoribosome) has a highly protein-rich composition with a small sedimentation coefficient of 55 S, consisting of 39 S large and 28 S small subunits. In the previous study, we analyzed 39 S large subunit proteins from bovine mitoribosome (Suzuki, T., Terasaki, M., Takemoto-Hori, C., Hanada, T., Ueda, T., Wada, A., and Watanabe, K. (2001) J. Biol. Chem. 276, 21724-21736). The results suggested structural compensation for the rRNA deficit through proteins of increased molecular mass in the mitoribosome. We report here the identification of 28 S small subunit proteins. Each protein was separated by radical-free high-reducing two-dimensional polyacrylamide gel electrophoresis and analyzed by liquid chromatography/mass spectrometry/mass spectrometry using electrospray ionization/ion trap mass spectrometer to identify cDNA sequence by expressed sequence tag data base searches in silico. Twenty one proteins from the small subunit were identified, including 11 new proteins along with their complete cDNA sequences from human and mouse. In addition to these proteins, three new proteins were also identified in the 55 S mitoribosome. We have clearly identified a mitochondrial homologue of S12, which is a key regulatory protein of translation fidelity and a candidate for the autosomal dominant deafness gene, DFNA4. The apoptosis-related protein DAP3 was found to be a component of the small subunit, indicating a new function for the mitoribosome in programmed cell death. In summary, we have mapped a total of 55 proteins from the 55 S mitoribosome on the two-dimensional polyacrylamide gels.}, }
@article {pmid11398974, year = {2001}, author = {Green-Marroquin, BL and Kupfer, H and Virkki, N and Wise, DA}, title = {Orientation of nonrandomly segregating sex chromosomes in spermatocytes of the flea beetle, Alagoasa bicolor L.}, journal = {Chromosoma}, volume = {110}, number = {1}, pages = {32-38}, doi = {10.1007/s004120100129}, pmid = {11398974}, issn = {0009-5915}, support = {P41 01219//PHS HHS/United States ; R01 40198//PHS HHS/United States ; R15 GM46133/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Coleoptera/*genetics/*ultrastructure ; Image Processing, Computer-Assisted ; Kinetochores/ultrastructure ; Male ; Meiosis ; Microscopy, Confocal ; Microscopy, Electron ; Microtubules/ultrastructure ; Spermatocytes/*ultrastructure ; X Chromosome/*ultrastructure ; Y Chromosome/*ultrastructure ; }, abstract = {In males of the flea beetle, Alagoasa bicolor L., spermatocytes have two achiasmate sex chromosomes, X and Y, each of which is approximately five times larger than the ten pairs of chiasmate autosomes. At metaphase I, these univalent sex chromosomes are located on a spindle domain separated from the autosomal spindle domain by a sheath of mitochondria. A single centriole pair is located at each pole of the spindle. In prometaphase I, each sex chromosome appears to maintain an attachment to both spindle poles via kinetochore microtubules (i.e., amphitelic orientation). Before anaphase I, this orientation changes to the syntelic orientation (both sister kinetochores connected to the same pole), perhaps by the release of microtubule attachments from the more distant pole by each of the chromosomes. The syntelic orientation just prior to anaphase I leaves each sex chromosome attached to the nearest pole via kinetochore microtubules, ensuring nonrandom segregation. As the sex chromosomes reorient, the autosomes follow in a sequential manner, starting with the bivalent closest to the sex spindle domain. We report here data that shed new light on the mechanism of this exceptional meiotic chromosome behavior.}, }
@article {pmid11389758, year = {2001}, author = {Ducos, E and Touzet, P and Boutry, M}, title = {The male sterile G cytoplasm of wild beet displays modified mitochondrial respiratory complexes.}, journal = {The Plant journal : for cell and molecular biology}, volume = {26}, number = {2}, pages = {171-180}, doi = {10.1046/j.1365-313x.2001.01017.x}, pmid = {11389758}, issn = {0960-7412}, mesh = {Amino Acid Sequence ; Base Sequence ; Blotting, Northern ; Blotting, Southern ; Blotting, Western ; Chenopodiaceae/genetics/*metabolism ; Cyclooxygenase 2 ; Cytoplasm/classification/genetics ; Electron Transport/genetics/physiology ; Electron Transport Complex I ; Electron Transport Complex IV/biosynthesis/genetics/metabolism ; Fertility ; Gene Expression Regulation, Plant ; Genome, Plant ; Isoenzymes/biosynthesis/genetics/*metabolism ; Mitochondria/enzymology/*genetics ; Mitochondrial Proteins ; Molecular Sequence Data ; Molecular Weight ; Mutation ; NADH, NADPH Oxidoreductases/biosynthesis/genetics/metabolism ; Oxidoreductases/biosynthesis ; Plant Proteins ; Pollen/genetics ; Prostaglandin-Endoperoxide Synthases/biosynthesis/genetics/*metabolism ; Sequence Analysis ; }, abstract = {Cytoplasmic male sterility (CMS) in higher plants has been mainly studied in cultivated species. In most cases, pollen abortion is linked to the presence of an additional mitochondrial polypeptide leading to organelle dysfunction in reproductive tissues. In wild beet, both CMS and hermaphrodite plants coexist in natural populations. The G cytoplasm is widely distributed along the Western European coast, and previous genetic studies have demonstrated that this cytoplasm confers male sterility in beet. In the present study, we have identified two mutations of G mitochondrial genes, each of which results in the production of a respiratory chain complex subunit with an altered molecular weight; the NAD9 subunit has a C-terminal extension while the COX2 subunit has a truncated C-terminus. NADH dehydrogenase activity was unchanged in leaves, but cytochrome c oxidase activity was reduced by 50%. Moreover, Western blot analyses revealed that alternative oxidase was more abundant in male sterile G plants than in a fertile control (Nv), suggesting that this alternative pathway might compensate for the cytochrome c oxidase deficiency. Implications of respiratory chain changes and a putative link with CMS are discussed.}, }
@article {pmid11387759, year = {2001}, author = {Uspenskaia, AV and Raĭkova, EV}, title = {[Cytological aspects of similarity and difference of Myxozoa and Cnidaria].}, journal = {Tsitologiia}, volume = {43}, number = {3}, pages = {284-309}, pmid = {11387759}, issn = {0041-3771}, mesh = {Animals ; Cnidaria/*anatomy &amp; histology ; Eukaryota/*cytology ; Phylogeny ; }, abstract = {A comparative cytomorphological analysis of Myxozoa and parasitic Cnidaria Polypodium hydriforme has been carried out in view of the Weill (1938) hypothesis, which regards Myxozoa as a reduced Cnidaria. The question on the relation of Myxozoa and Cnidaria was arising several times with the application of some new methods during the Myxozoa studies. At present the idea on their phylogenetic relationships has appeared again in connection with an absolutely new understanding of the myxozoan life cycle (Wolf, Markiw, 1984), as well as with the application of molecular-biological methods for their phylogenetic studies. The latter, however, provided some diverse results. So far no comparative cytomorphological analysis of Myxozoa and Polypodium has been carried out. The present paper is to fill the gap on the basis of accumulated facts. According to Weill (1938), the features of similarity of parasitic Cnidaria and Myxozoa are the following: 1) the presence in both of extrusomes (nematocysts and polar capsules) whose structure and development are surprizingly similar; 2) the nuclear dimorphism and somato-generative segregation; 3) the presence of a somatic nutritional cell, surrounding the multiplying generative cells; at present it is known that polyploidy of somatic nuclei and the absence of parasitophorous vacuole are characteristic of trophamnion of Polypodium and trophozoite of Myxozoa; 4) the presence of radial symmetry in both groups; 5) the construction of a diblastic organism made of a cluster of endodermal cells and a few ectodermal cells; 6) the similarity of their cell contacts (Grassé, 1970). At present it is possible to add to Weill's (1938) list of features common for parasitic Cnidaria and Myxozoa the number of important similarities between Polypodium and Myxozoa, some of which being not characteristic of Cnidaria: 1) the "cell in cell" organization of all Polypodium parasitic stages and all Myxozoa life cycle stages; 2) the presence of gametophore supplied with extrusomes; 3) both organisms have haplophase in their life cycles preceded by two-step meiosis; 4) there are mitochondria with tubular cristae in both organisms; 5) the absence of spermatozoa and eggs in both organisms; 6) the similarity of Polypodium cnidocile structure and the cone-like formation situated at the anterior end of polar capsule of actinospore (Lom. Dykova, 1997); 7) the participation of MTOC in the formation of extrusomes in both animals. In spite of the obvious similarity between Myxozoa and parasitic Cnidaria (including Polypodium) it is, however, necessary to take into account differences between them, the main being as follows: the absence in Myxozoa of flagellated stages, centrioles, tissues and organs, true blastophylla, planula-like larvae, gastrulation; the presence of low cell integrations in Myxozoa; Cnidaria and Myxozoa have different types of mitosis, their life cycles and the discharge mechanism of their stinging apparatus being also different. We consider as quite valid a suggestion by Siddall et al. (1995) that parasitic Cnidaria could present an early separated branch of the cnidarian evolution. Further studies of Myxozoa life cycle may show their more definite relation to parasitic Cnidaria. The problem has not yet been solved completely since the available molecular-biological data are rather contradictory and moreover there is no distinct idea as to the Eumetazoa ancestor so far. A further thorough investigation is badly needed in the feelds of developmental cycle, cytomorphology and molecular biology of the variety of narcomedusae and representatives of Myxozoa. This may help to find some transitional forms and stages of the animals and to understand whether we deal with a regressive evolution of parasitic Cnidaria or with a parallel evolution of taxa originated from the common ancestor.}, }
@article {pmid11377800, year = {2001}, author = {Scheffler, IE}, title = {Mitochondria make a come back.}, journal = {Advanced drug delivery reviews}, volume = {49}, number = {1-2}, pages = {3-26}, doi = {10.1016/s0169-409x(01)00123-5}, pmid = {11377800}, issn = {0169-409X}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/drug effects/*physiology/ultrastructure ; Electron Transport/drug effects/physiology ; Energy Metabolism ; Enzyme Inhibitors/pharmacology ; Eukaryotic Cells/drug effects/*physiology/ultrastructure ; Humans ; Mitochondria/drug effects/*physiology/ultrastructure ; Molecular Biology ; Oxidative Phosphorylation/drug effects ; }, abstract = {This review attempts to summarize our present state of knowledge of mitochondria in relation to a number of areas of biology, and to indicate where future research might be directed. In the evolution of eukaryotic cells mitochondria have for a long time played a prominent role. Nowadays their integration into many activities of a cell, and their dynamic behavior as subcellular organelles within a cell and during cell division are a major focus of attention. The crystal structures of the major complexes of the electron transport chain (except complex I) have been established, permitting increasingly detailed analyses of the important mechanism of proton pumping coupled to electron transport. The mitochondrial genome and its replication and expression are beginning to be understood in considerable detail, but more questions remain with regard to mutations and their repair, and the segregation of the mtDNA in oogenesis and development. Much emphasis and a large effort have recently been devoted to understand the role of mitochondria in programmed cell death (apoptosis). The understanding of their central role in mitochondrial diseases is a major achievement of the past decade. Finally, various drugs have traditionally played a part in understanding biochemical mechanisms within mitochondria; the repertoire of drugs with novel and interesting targets is expanding.}, }
@article {pmid11374907, year = {2001}, author = {Gao, J and Yu, L and Zhang, P and Jiang, J and Chen, J and Peng, J and Wei, Y and Zhao, S}, title = {Cloning and characterization of human and mouse mitochondrial elongation factor G, GFM and Gfm, and mapping of GFM to human chromosome 3q25.1-q26.2.}, journal = {Genomics}, volume = {74}, number = {1}, pages = {109-114}, doi = {10.1006/geno.2001.6536}, pmid = {11374907}, issn = {0888-7543}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Northern ; Chromosome Mapping ; Chromosomes, Human, Pair 3/*genetics ; Cloning, Molecular ; DNA, Complementary/chemistry/genetics ; Exons ; Female ; Genes/genetics ; Humans ; Introns ; Male ; Mice ; Mitochondria/*metabolism ; Molecular Sequence Data ; Peptide Elongation Factor G/*genetics ; Phylogeny ; RNA, Messenger/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Tissue Distribution ; }, abstract = {Similar to the translational system in the cell cytoplasm, the initiation, elongation, and termination of protein synthesis in the mitochondria of eukaryotes are catalyzed by several protein factors. These factors, from the viewpoint of evolution, are more closely related to the corresponding prokaryotic factors than to those in the eukaryotic cytoplasm. In this paper, we isolated two cDNAs coding for human and mouse mitochondrial elongation factor G (GFM and Gfm, respectively). The GFM cDNA, which is 3481 bp in length, predicts a protein of 751 amino acids sharing 84 and 42% identity and 88 and 62% similarity to rat EF-G(mt) and Escherichia coli EF-G, respectively, and 24% identity and 39% similarity to human EF-2, the equivalent of EF-G in the cytoplasm. The mouse Gfm cDNA is 2564 bp and contains an intact open reading frame that encodes 751 amino acids showing 89% sequence identity and 94% similarity to human GFM. Northern blot analysis of human GFM revealed three transcripts of 3.8, 3.4, and 2.9 kb. The first two were expressed at high levels in heart, skeletal muscle, and testis, at moderate levels in liver and kidney, and at low levels in other tissues including brain, placenta, and lung, while the last transcript was expressed only in testis. The relative abundance of GFM was consistent with the observations for human EF-Tu(mt) and EF-Ts(mt), the other two mitochondrial elongation factors, indicating that the three factors were expressed at corresponding levels. The expression pattern of mouse Gfm was also determined, which showed that Gfm was expressed as a 3.0-kb transcript, abundantly in heart, skeletal muscle, kidney, and testis. In addition, GFM was assigned to human chromosome 3q25.1-q26.2 by the radiation hybrid mapping method. The genomic organization of GFM was also analyzed by comparing this cDNA with a genomic DNA sequence (Accession No. AC010936), which showed that GFM contained 18 exons and spanned at least 40 kb.}, }
@article {pmid11371592, year = {2001}, author = {Dacks, JB and Silberman, JD and Simpson, AG and Moriya, S and Kudo, T and Ohkuma, M and Redfield, RJ}, title = {Oxymonads are closely related to the excavate taxon Trimastix.}, journal = {Molecular biology and evolution}, volume = {18}, number = {6}, pages = {1034-1044}, doi = {10.1093/oxfordjournals.molbev.a003875}, pmid = {11371592}, issn = {0737-4038}, support = {GM32964/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/genetics ; Eukaryota/classification/*genetics ; Evolution, Molecular ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Despite intensive study in recent years, large-scale eukaryote phylogeny remains poorly resolved. This is particularly problematic among the groups considered to be potential early branches. In many recent systematic schemes for early eukaryotic evolution, the amitochondriate protists oxymonads and Trimastix have figured prominently, having been suggested as members of many of the putative deep-branching higher taxa. However, they have never before been proposed as close relatives of each other. We amplified, cloned, and sequenced small-subunit ribosomal RNA genes from the oxymonad Pyrsonympha and from several Trimastix isolates. Rigorous phylogenetic analyses indicate that these two protist groups are sister taxa and are not clearly related to any currently established eukaryotic lineages. This surprising result has important implications for our understanding of cellular evolution and high-level eukaryotic phylogeny. Given that Trimastix contains small, electron-dense bodies strongly suspected to be derived mitochondria, this study constitutes the best evidence to date that oxymonads are not primitively amitochondriate. Instead, Trimastix and oxymonads may be useful organisms for investigations into the evolution of the secondary amitochondriate condition. All higher taxa involving either oxymonads or Trimastix may require modification or abandonment. Affected groups include four contemporary taxa given the rank of phylum (Metamonada, Loukozoa, Trichozoa, Percolozoa), and the informal excavate taxa. A new "phylum-level" taxon may be warranted for oxymonads and Trimastix.}, }
@article {pmid11370791, year = {2001}, author = {Carafoli, E and Santella, L and Branca, D and Brini, M}, title = {Generation, control, and processing of cellular calcium signals.}, journal = {Critical reviews in biochemistry and molecular biology}, volume = {36}, number = {2}, pages = {107-260}, doi = {10.1080/20014091074183}, pmid = {11370791}, issn = {1040-9238}, mesh = {Animals ; Calcium Signaling/*physiology ; Calcium-Binding Proteins/physiology ; Cell Membrane/metabolism ; Humans ; Intracellular Membranes/metabolism ; Ion Transport ; }, abstract = {In the course of evolution, Ca2+ has emerged as the most versatile intracellular messenger. Its concentration within cells is controlled by reversible binding to specific classes of proteins that act as Ca2+ sensors to decode its information before passing it on to targets. The decoding operation is based on specific conformational changes in the sensor proteins. Other proteins intrinsic to membranes simply control Ca2+ concentration without processing its message, by transporting it across membrane boundaries. They are located in the plasma membrane and in the membranes of the organelles (the endo(sarco)plasmic reticulum, the mitochondria, the nuclear envelope), which play distinctive roles in the cellular homeostasis of Ca2+. Ca2+ is an ambivalent signaling agent. It carries information to virtually all processes important to cell life (e.g., it couples excitation to contraction, secretion, gene transcription, and controls enzyme activity through protein phosphorylation-dephosphorylation), but also transmits signals that promote the programmed demise of cells. When escaping control, Ca2+ also precipitates toxic cell death.}, }
@article {pmid11358998, year = {2001}, author = {Andersson, JO and Doolittle, WF and Nesbø, CL}, title = {Genomics. Are there bugs in our genome?.}, journal = {Science (New York, N.Y.)}, volume = {292}, number = {5523}, pages = {1848-1850}, doi = {10.1126/science.1062241}, pmid = {11358998}, issn = {0036-8075}, mesh = {Animals ; *Biological Evolution ; Chloroplasts/genetics ; Computational Biology ; *Gene Transfer, Horizontal ; *Genes, Bacterial ; Genome ; *Genome, Human ; Humans ; Mitochondria/genetics ; Oxo-Acid-Lyases/genetics ; Phylogeny ; Sequence Analysis, DNA ; Symbiosis ; Vertebrates/genetics ; }, }
@article {pmid11357388, year = {2001}, author = {Kuznetsov, AP and Lebkova, NP}, title = {[Significance of the energy of symbiotic bacteria in metabolism of hydrothermal and other chemotrophic biota of the ocean].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {2}, pages = {220-226}, pmid = {11357388}, issn = {1026-3470}, mesh = {Aerobiosis ; Animals ; Bacteria/*metabolism ; Biological Evolution ; Ecosystem ; *Energy Metabolism ; Microscopy, Electron ; Mitochondria/*metabolism ; Mollusca/*metabolism/microbiology/ultrastructure ; Oceans and Seas ; Symbiosis ; }, abstract = {The bacterial origin of eukaryotic mitochondria, specifically in Metazoa, as a mechanism of their basic (aerobic) respiration and the role of symbiotic bacteria during the supply of energy to the metazoan host is proved for the first time from the viewpoint of the monophyletic development of the organic world and the origin of eukaryotes as descendants of prokaryotes Representatives of the hydrothermal bacteriochemosymbiotrophic bottom fauna of the open sea were used as examples.}, }
@article {pmid11356517, year = {2001}, author = {Rathore, D and Wahl, AM and Sullivan, M and McCutchan, TF}, title = {A phylogenetic comparison of gene trees constructed from plastid, mitochondrial and genomic DNA of Plasmodium species.}, journal = {Molecular and biochemical parasitology}, volume = {114}, number = {1}, pages = {89-94}, doi = {10.1016/s0166-6851(01)00241-9}, pmid = {11356517}, issn = {0166-6851}, mesh = {Adenosine Triphosphatases/chemistry ; Amino Acid Sequence ; Animals ; Birds ; Cell Nucleus/genetics ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/chemistry/*genetics ; DNA, Protozoan/chemistry/*genetics ; DNA, Ribosomal/genetics ; *Evolution, Molecular ; Genes, Protozoan ; Haplorhini ; Humans ; Mitochondria/genetics ; Molecular Sequence Data ; Peptide Hydrolases/chemistry/genetics ; *Phylogeny ; Plasmodium/*classification/*genetics ; Plastids/genetics ; Rodentia ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Gene trees of Plasmodium species have been reported for the nuclear encoded genes (e.g. the Small Subunit rRNA) and a mitochondrial encoded gene, cytochrome b. Here, we have analyzed a plastid gene coding for caseinolytic protease ClpC, whose structure, function and evolutionary history have been studied in various organisms. This protein possesses a 220-250 amino acid long AAA domain (ATPases associated with a variety of cellular activities) that belongs to the Walker super family of ATPases and GTPases. We have sequenced the AAA motif of this gene, encoding the protein from nine different species of Plasmodium infecting rodents, birds, monkeys, and humans. The codon usage and GC content of each gene were nearly identical in contrast to the widely varying nucleotide composition of genomic DNAs. Phylogenetic trees derived from both DNA and inferred protein sequences have consistent topologies. We have used the ClpC sequence to analyze the phylogenetic relationship among Plasmodium species and compared it with those derived from mitochondrial and genomic sequences. The results corroborate well with the trees constructed using the mitochondrially encoded cytochrome b. However, an important element distinguishes the trees: the placement of Plasmodium elongatum near the base of the plastid tree, indicating an ancient lineage of parasites in birds that branches from the tree prior to other lineages of avian malaria and the human parasite, P. falciparum.}, }
@article {pmid11352464, year = {2001}, author = {Halperin, T and Zheng, B and Itzhaki, H and Clarke, AK and Adam, Z}, title = {Plant mitochondria contain proteolytic and regulatory subunits of the ATP-dependent Clp protease.}, journal = {Plant molecular biology}, volume = {45}, number = {4}, pages = {461-468}, pmid = {11352464}, issn = {0167-4412}, mesh = {ATPases Associated with Diverse Cellular Activities ; Adenosine Triphosphatases/*genetics/metabolism ; Amino Acid Sequence ; Arabidopsis/enzymology/*genetics ; *Bacterial Proteins ; Caseins/metabolism ; DNA, Complementary/chemistry/genetics ; Endopeptidase Clp ; Escherichia coli Proteins ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Mitochondria/*enzymology/metabolism ; Molecular Chaperones ; Molecular Sequence Data ; Phylogeny ; Protein Subunits ; RNA, Messenger/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Serine Endopeptidases/metabolism ; Tissue Distribution ; }, abstract = {The proteolytic machinery of plant organelles is largely unknown, although indications so far point to several proteases of bacterial origin. In this study an Arabidopsis thaliana cDNA was isolated that encodes a homologue of bacterial ClpX, a molecular chaperone and regulatory subunit of the ATP-dependent, serine-type Clp protease. Computer analysis of the predicted plant ClpX revealed a putative mitochondrial transit peptide at the N-terminus, as well as overall sequence similarity to other eukaryotic ClpX homologues. Specific polyclonal antibodies were made to the Arabidopsis ClpX protein and used to confirm its localization in plant mitochondria. In addition to ClpX, a ClpP protein located in mitochondria was also identified from the numerous ClpP isomers in Arabidopsis. Localization of this nuclear-encoded protein, termed ClpP2, was determined first by its close sequence similarity to mitochondrial ClpP human, and later experimentally using ClpP2-specific antibodies with isolated plant organellar fractions. In Arabidopsis, transcripts for both clpX and clpP2 genes were detected in various tissues and under different growth conditions, with no significant variation in mRNA level (i.e. 2-fold) for each gene between samples. Using beta-casein as a substrate, plant mitochondria were found to possess an ATP-stimulated, serine-type proteolytic activity that could be strongly inhibited by antibodies specific for ClpX or ClpP2, suggesting an active ClpXP protease. The recent discovery of homologous mitochondrial ClpX and ClpP proteins in mammals suggests that this type of protease may be common to multicellular eukaryotes.}, }
@article {pmid11351269, year = {2001}, author = {Palau, F}, title = {Friedreich's ataxia and frataxin: molecular genetics, evolution and pathogenesis (Review).}, journal = {International journal of molecular medicine}, volume = {7}, number = {6}, pages = {581-589}, doi = {10.3892/ijmm.7.6.581}, pmid = {11351269}, issn = {1107-3756}, mesh = {Alleles ; Amino Acid Sequence ; Animals ; Chromosomes, Human, Pair 9 ; *Evolution, Molecular ; Fibroblasts/metabolism ; Friedreich Ataxia/*diagnosis/*genetics/therapy ; Heterozygote ; Humans ; Introns ; *Iron-Binding Proteins ; Mice ; Mitochondria/metabolism ; Models, Genetic ; Molecular Sequence Data ; Mutation ; Oxidative Stress ; Phenotype ; Phosphotransferases (Alcohol Group Acceptor)/*genetics/*metabolism ; Point Mutation ; Sequence Homology, Amino Acid ; Trinucleotide Repeat Expansion ; Frataxin ; }, abstract = {Friedreich's ataxia is an autosomal recessive neuro-degenerative disorder involving both central and peripheral nervous system. Patients also show a systemic clinical picture presenting heart disease and diabetes mellitus or glucose intolerance. The disease is caused by mutations in the FRDA gene mapped on chromosome 9q13. The product of the gene is frataxin, an 18 kDa soluble mitochondrial protein with 210 amino acids. Crystal structure suggests a new, not previously reported, protein fold. The most frequent mutation is the expansion of a GAA trinucleotide repeat located within the first intron of the gene, and represents 98% of the mutations. Point mutations are described in compound heterozygous subjects with one expanded allele. A two-step model of GAA normal alleles towards premutation alleles, which might generate further full expanded mutations in the population with Indo-European ancestry, has been postulated. Clinical phenotype is variable and an inverse correlation with the GAA expansion size has been observed. Analysis of the GAA triplet is a strong molecular tool for clinical diagnosis, genetic counselling and prenatal diagnosis. Friedreich's ataxia patho-genesis is not solved yet. Substantial data from organism models, such the S. cerevisae yeast and more recently conditioned knock-outs in mouse, and studies in heart biopsies and fibroblast cultures from patients suggest an important role of mitochondrial iron in the development of the disease. Iron is accumulated in the mitochondrial matrix of both the yeast frataxin deficient mutant and the patient fibroblasts. It has been postulated that iron-induced oxygen radical affects the oxidative phosphorylation in frataxin deficiency states favouring the disease pathology. A second hypothesis postulates a direct role of frataxin in the mitochondrial energy activation and oxidative phosphorylation. Iron chelator drugs and antioxidant drugs have been postulated for Friedreich's treatment. No results from clinical trials are available yet, but idebenone, a short-chain quinone, seems to reduce the size of hypertrophic cardiomyopathy and levels of oxidative stress molecules in patients.}, }
@article {pmid11351101, year = {2001}, author = {Haupt-Herting, S and Klug, K and Fock, HP}, title = {A new approach to measure gross CO2 fluxes in leaves. Gross CO2 assimilation, photorespiration, and mitochondrial respiration in the light in tomato under drought stress.}, journal = {Plant physiology}, volume = {126}, number = {1}, pages = {388-396}, pmid = {11351101}, issn = {0032-0889}, mesh = {Carbon Dioxide/*metabolism ; *Light ; Solanum lycopersicum/*physiology ; Mitochondria/*physiology ; Plant Leaves/*metabolism ; *Water ; }, abstract = {We developed a new method using 13CO2 and mass spectrometry to elucidate the role of photorespiration as an alternative electron dissipating pathway under drought stress. This was achieved by experimentally distinguishing between the CO2 fluxes into and out of the leaf. The method allows us to determine the rates of gross CO2 assimilation and gross CO2 evolution in addition to net CO2 uptake by attached leaves during steady-state photosynthesis. Furthermore, a comparison between measurements under photorespiratory and non-photorespiratory conditions may give information about the contribution of photorespiration and mitochondrial respiration to the rate of gross CO2 evolution at photosynthetic steady state. In tomato (Lycopersicon esculentum Mill. cv Moneymaker) leaves, drought stress decreases the rates of net and gross CO2 uptake as well as CO2 release from photorespiration and mitochondrial respiration in the light. However, the ratio of photorespiratory CO2 evolution to gross CO2 assimilation rises with water deficit. Also the contribution of re-assimilation of (photo) respiratory CO2 to gross CO2 assimilation increases under drought.}, }
@article {pmid11350928, year = {2001}, author = {Anandatheerthavarada, HK and Amuthan, G and Biswas, G and Robin, MA and Murali, R and Waterman, MR and Avadhani, NG}, title = {Evolutionarily divergent electron donor proteins interact with P450MT2 through the same helical domain but different contact points.}, journal = {The EMBO journal}, volume = {20}, number = {10}, pages = {2394-2403}, pmid = {11350928}, issn = {0261-4189}, mesh = {Adrenodoxin/*metabolism ; Animals ; Binding Sites ; Cattle ; Chromosome Mapping ; Cross-Linking Reagents ; Cytochrome P-450 CYP1A1/chemistry/genetics/*metabolism ; *Evolution, Molecular ; Flavodoxin/*metabolism ; Mammals ; Mitochondria, Liver/*metabolism ; Models, Molecular ; Mutagenesis ; NADPH-Ferrihemoprotein Reductase/genetics/*metabolism ; Protein Structure, Secondary ; Rats ; Two-Hybrid System Techniques ; }, abstract = {We have investigated the sites of N-terminally truncated cytochrome P4501A1 targeted to mitochondria (P450MT2) which interact with adrenodoxin (Adx), cytochrome P450 reductase (CPR) and bacterial flavodoxin (Fln). The binding site was mapped by a combination of in vitro mutagenesis, in vivo screening with a mammalian two-hybrid system, spectral analysis, reconstitution of enzyme activity and homology-based structural modeling. Our results show that part of an aqueous accessible helix (putative helix G, residues 264-279) interacts with all three electron donor proteins. Mutational studies revealed that Lys267 and Lys271 are crucial for binding to Adx, while Lys268 and Arg275 are important for binding to CPR and FLN: Additive effects of different electron donor proteins on enzyme activity and models on protein docking show that Adx and CPR bind in a non-overlapping manner to the same helical domain in P450MT2 at different angular orientations, while CPR and Fln compete for the same binding site. We demonstrate that evolutionarily divergent electron donor proteins interact with the same domain but subtly different contact points of P450MT2.}, }
@article {pmid11348583, year = {2000}, author = {Takagi, H and Kaneko, K and Yomo, T}, title = {Evolution of genetic codes through isologous diversification of cellular states.}, journal = {Artificial life}, volume = {6}, number = {4}, pages = {283-305}, doi = {10.1162/106454600300103647}, pmid = {11348583}, issn = {1064-5462}, mesh = {Biological Clocks ; Cell Differentiation ; Cell Division ; *Cell Physiological Phenomena ; Enzymes/*genetics/metabolism ; *Evolution, Molecular ; Genetic Code/*genetics ; Genotype ; Mitochondria/genetics ; *Models, Genetic ; Mutation ; Nucleic Acids/*genetics/metabolism ; Phenotype ; }, abstract = {Evolution of genetic codes is studied as change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states of a cell allows for a choice of enzymes, and this choice is later fixed genetically through evolution. To demonstrate this theory, a dynamical systems model consisting of the concentrations of metabolites, enzymes, amino acyl tRNA synthetase, and tRNA - amino acid complexes in a cell is introduced and studied numerically. It is shown that the biochemical states of cells are differentiated by cell-cell interactions, and each differentiated type starts to use a different synthetase. Through the mutation of genes, this difference in the genetic code is amplified and stabilized. The relevance of this theory to the evolution of non-universal genetic code in mitochondria is suggested. The present theory is based on our recent theory of isologous symbiotic speciation, which is briefly reviewed. According to the theory, phenotypes of organisms are first differentiated into distinct types through the interaction and developmental dynamics, even though they have identical genotypes; later, with mutation in the genotype, the genotype also differentiates into discrete types, while maintaining the "symbiotic" relationship between the types. Relevance of the theory to natural as well as artificial evolution is discussed.}, }
@article {pmid11347902, year = {2001}, author = {Legen, J and Miséra, S and Herrmann, RG and Meurer, J}, title = {Map positions of 69 Arabidopsis thaliana genes of all known nuclear encoded constituent polypeptides and various regulatory factors of the photosynthetic membrane: a case study.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {8}, number = {2}, pages = {53-60}, doi = {10.1093/dnares/8.2.53}, pmid = {11347902}, issn = {1340-2838}, mesh = {Arabidopsis/*genetics ; *Chromosome Mapping ; Chromosomes, Artificial, Bacterial/genetics ; Crosses, Genetic ; Gene Duplication ; *Genome, Plant ; Membrane Proteins/biosynthesis/genetics/*physiology ; Nuclear Proteins/biosynthesis/genetics/*physiology ; Photosynthetic Reaction Center Complex Proteins/genetics ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Thylakoids/chemistry/genetics/*physiology ; }, abstract = {Landsberg erecta x Columbia F8 recombinant inbred lines of Arabidopsis thaliana, arrayed BAC clones covering most of the genome, and databank sequence information were used to map the positions of 69 genes in the genome of A. thaliana. These genes encode all known constituents of the photosynthetic thylakoid membrane, some regulatory factors involved in its biogenesis, and the RNA polymerases of nuclear origin that operate in chloroplasts and mitochondria. Designations of novel genes are proposed. The data of these three approaches are generally consistent, although ambiguities have been noted for some genome segments and with gene duplications. For thylakoid multi-subunit structures, no positional clustering of genes has been found, not even for genes encoding different subunits of the same membrane complex. The genes of the lhc superfamily encoding antenna apoproteins and their relatives are a particularly intriguing example. The lack of positional clustering is consistent with phylogenetically independent gene translocations from the plastid (endosymbiont) to the nucleus. This raises the basic question of how independently translocated genes which acquired different promoter sequences and transit peptides were functionally integrated into common signal transduction chains.}, }
@article {pmid11345318, year = {2000}, author = {Toda, S and Osakabe, M and Komazaki, S}, title = {Interspecific diversity of mitochondrial COI sequences in Japanese Panonychus species (Acari: Tetranychidae).}, journal = {Experimental &amp; applied acarology}, volume = {24}, number = {10-11}, pages = {821-829}, pmid = {11345318}, issn = {0168-8162}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/*genetics ; Female ; Genetic Variation/*genetics ; Japan ; Mites/classification/enzymology/*genetics ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {Sequences of a part of the mitochondrial cytochrome oxidase subunit I (COI) gene were analyzed in four Japanese Panonychus species to determine their phylogenetic relationships. Neighbor-Joining and maximum likelihood analysis resulted in a high bootstrap support of the relationships within the genus Panonychus. In contrast with a previous study based on ribosomal DNA data, the COI phylogeny suggested that P. mori was more distantly related to P. citri than to P. ulmi. This study shows for the first time that P. osmanthi is closely related to P. citri. Intraspecific variation analysis shows that the genetic distance between two local populations of P. mori is higher than between P. citri and P. osmanthi.}, }
@article {pmid11342215, year = {2001}, author = {Lorain, S and Lécluse, Y and Scamps, C and Mattéi, MG and Lipinski, M}, title = {Identification of human and mouse HIRA-interacting protein-5 (HIRIP5), two mammalian representatives in a family of phylogenetically conserved proteins with a role in the biogenesis of Fe/S proteins.}, journal = {Biochimica et biophysica acta}, volume = {1517}, number = {3}, pages = {376-383}, doi = {10.1016/s0167-4781(00)00300-6}, pmid = {11342215}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Carrier Proteins/*genetics/*metabolism ; *Cell Cycle Proteins ; Chromosome Mapping ; Conserved Sequence ; DNA, Complementary/genetics ; HeLa Cells ; Histone Chaperones ; Humans ; In Situ Hybridization ; In Vitro Techniques ; Iron-Sulfur Proteins/*biosynthesis ; Mice ; Molecular Sequence Data ; Nuclear Proteins/genetics/*metabolism ; Phylogeny ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Transcription Factors/genetics/*metabolism ; Two-Hybrid System Techniques ; }, abstract = {The human HIRA protein is encoded from a region of chromosome 22q that is critical for the DiGeorge syndrome and the velocardiofacial syndrome. We have previously reported that it directly interacts with core histones, with a novel histone-binding protein, HIRIP3, and during mouse embryogenesis, with the developmentally regulated homeodomain protein Pax3, suggesting a promoter-targeted function at the chromatin level. We here report on HIRA-interacting protein 5 (HIRIP5), a small acidic protein that interacted with HIRA in a double-hybrid screen performed in yeast and in in vitro protein interaction experiments. HIRIP5 has highly conserved homologs in both prokaryotes and eukaryotes, including the NFU1 gene product which has been implicated in iron metabolism in mitochondria of the yeast Saccharomyces cerevisiae. By radioactive in situ hybridization, the HIRIP5 gene was mapped to the 2p13-p15 chromosomal region, separate from any region previously associated with DiGeorge syndrome.}, }
@article {pmid11330038, year = {2000}, author = {Hayashi, S and Fujiwara, S and Noguchi, T}, title = {Evolution of urate-degrading enzymes in animal peroxisomes.}, journal = {Cell biochemistry and biophysics}, volume = {32 Spring}, number = {}, pages = {123-129}, doi = {10.1385/cbb:32:1-3:123}, pmid = {11330038}, issn = {1085-9195}, mesh = {Amidohydrolases/genetics/*metabolism ; Animals ; Evolution, Molecular ; Peroxisomes/*metabolism ; Purines/*metabolism ; Species Specificity ; Urate Oxidase/genetics/*metabolism ; Ureohydrolases/genetics/*metabolism ; }, abstract = {The end product of purine metabolism varies from species to species. The degradation of purines to urate is common to all animal species, but the degradation of urate is much less complete in higher animals. The comparison of subcellular distribution, intraperoxisomal localization forms, molecular structures, and some other properties of urate-degrading enzymes (urate oxidase, allantoinase, and allantoicase) among animals is described. Liver urate oxidase (uricase) is located in the peroxisomes in all animals with urate oxidase. On the basis of the comparison of intraperoxisomal localization forms, mol wt, and solubility of liver urate oxidase among animals, it is suggested that amphibian urate oxidase is a transition form in the evolution of aquatic animals to land animals. Allantoinase and allantoicase are different proteins in fish liver, but the two enzymes form a complex in amphibian liver. The subcellular localization of allantoinase and allantoicase varies among fishes. Hepatic allantoinase is located both in the peroxisomes and in the cytosol in saltwater fishes, and only in the cytosol in freshwater fishes. Hepatic allantoicase is located on the outer surface of the peroxisomal membrane in the mackerel group and in the peroxisomal matrix in the sardine group. Amphibian hepatic allantoinase-allantoicase complex is probably located in the mitochondria. On the basis of previous data, changes of allantoinase and allantoicase in molecular structure and intracellular localization during animal evolution may be as follows: Fish liver allantoinase is a single peptide with a mol wt of 54,000, and is located both in the peroxisomes and in the cytosol, or only in the cytosol. Fish liver allantoicase consists of two identical subunits with a mol wt of 48,000, and is located in the peroxisomal matrix or on the outer surface of the peroxisomal membrane. The evolution of fishes to amphibia resulted in the dissociation of allantoicase into subunits, and in the association of allantoinase with the subunit of allantoicase. This amphibian enzyme was lost by further evolution.}, }
@article {pmid11328648, year = {2000}, author = {Kato, A and Fujita, S and Komeda, Y}, title = {Identification and characterization of the gene encoding the mitochondrial elongation factor G in rice.}, journal = {DNA sequence : the journal of DNA sequencing and mapping}, volume = {11}, number = {5}, pages = {395-404}, doi = {10.3109/10425170009033990}, pmid = {11328648}, issn = {1042-5179}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics ; Base Sequence ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Exons ; Genome, Plant ; Introns ; Mitochondria/genetics ; Molecular Sequence Data ; Oryza/*genetics ; Peptide Elongation Factor G/*genetics ; Plant Proteins/*genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {A plant nuclear gene coding for a mitochondrial elongation factor G (mEF-G) was cloned from a cDNA library and genomic library of rice (Oryza sativa L.). This DNA sequence predicts a 757-amino-acid protein exhibiting 79%, 55% and 49% homology to Arabidopsis thaliana, Saccharomyces cerevisiae and rat mEF-G respectively, 53% homology to the elongation factor G in Escherichia coli and 43% homology to soybean chloroplast elongation factor G. The deduced amino acid sequence contains the characteristic motifs shared by all GTP binding proteins. Comparison of the sequence of the genomic clone to that of the cDNA clone revealed that this gene is split nineteen times by introns, although the gene of Arabidopsis is split seventeen times by introns. Some of the introns found in the rice genome are relatively long and they result in a long gene with a size of approximately 15 kb.}, }
@article {pmid11328608, year = {2001}, author = {Takabatake, R and Siddique, AB and Kouchi, H and Izui, K and Hata, S}, title = {Characterization of a Saccharomyces cerevisiae gene that encodes a mitochondrial phosphate transporter-like protein.}, journal = {Journal of biochemistry}, volume = {129}, number = {5}, pages = {827-833}, doi = {10.1093/oxfordjournals.jbchem.a002926}, pmid = {11328608}, issn = {0021-924X}, mesh = {Amino Acid Sequence/genetics ; Animals ; Carrier Proteins/*genetics/*metabolism ; Cell Division/genetics/physiology ; Escherichia coli/genetics ; Evolution, Molecular ; Gene Expression/*genetics ; Humans ; Mitochondria/*metabolism/ultrastructure ; *Mitochondrial Proteins ; Molecular Sequence Data ; Mutation/genetics/physiology ; Oxidative Phosphorylation ; *Phosphate Transport Proteins ; Phosphate-Binding Proteins ; Phylogeny ; Plants/genetics ; Promoter Regions, Genetic/genetics ; Proteolipids/metabolism ; Saccharomyces cerevisiae/*genetics ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Species Specificity ; Vacuoles/*metabolism/ultrastructure ; }, abstract = {The mitochondrial phosphate transporter of Saccharomyces cerevisiae, encoded by MIR1 (YJR077C) gene, shows divergence among the transporters in various eukaryotes. We have characterized another gene, YER053C, that appeared to encode an orthologous mitochondrial phosphate transporter of yeast. The predicted amino acid sequence of the YER053C protein is much more similar to that of mitochondrial phosphate transporters of other species than that of MIR1. RNA gel blot analysis indicated that, like the MIR1 promoter, the YER053C promoter is functional and that its activity varies according to aeration. An MIR1 gene null mutant did not grow on glycerol medium, whereas a YER053C null mutant grew well on the medium, suggesting that the YER053C gene is not essential for the mitochondrial function. YER053C also did not support the growth of the MIR1 null mutant on glycerol. The MIR1 and YER053C proteins were expressed in Escherichia coli and then reconstituted into liposomes. Unlike the proteoliposomes of MIR1, those of YER053C did not exhibit significant phosphate transport activity. Unexpectedly, it was shown that YER053C is localized in vacuoles, not mitochondria, by immunological electron microscopy. These results suggest that, during evolution, yeast lost the function and/or mitochondrial targeting of YER053C and then recruited an atypical MIR1 as the only transporter.}, }
@article {pmid11320888, year = {2001}, author = {Gietl, C and Schmid, M}, title = {Ricinosomes: an organelle for developmentally regulated programmed cell death in senescing plant tissues.}, journal = {Die Naturwissenschaften}, volume = {88}, number = {2}, pages = {49-58}, doi = {10.1007/s001140000203}, pmid = {11320888}, issn = {0028-1042}, mesh = {Apoptosis/*physiology ; Cysteine Endopeptidases/genetics/metabolism ; Organelles/*physiology ; Phylogeny ; *Plant Cells ; *Plant Development ; Plants, Toxic ; Ricinus/cytology/growth &amp; development/ultrastructure ; Signal Transduction ; }, abstract = {This review describes aspects of programmed cell death (PCD). Present research maps the enzymes involved and explores the signal transduction pathways involved in their synthesis. A special organelle (the ricinosome) has been discovered in the senescing endosperm of germinating castor beans (Ricinus communis) that develops at the beginning of PCD and delivers large amounts of a papain-type cysteine endopeptidase (CysEP) in the final stages of cellular disintegration. Castor beans store oil and proteins in a living endosperm surrounding the cotyledons. These stores are mobilized during germination and transferred into the cotyledons. PCD is initiated after this transfer is complete. The CysEP is synthesized in the lumen of the endoplasmic reticulum (ER) where it is retained by its C-terminal KDEL peptide as a rather inactive pro-enzyme. Large number of ricinosomes bud from the ER at the same time as the nuclear DNA is characteristically fragmented during PCD. The mitochondria, glyoxysomes and ribosomes are degraded in autophagic vacuoles, while the endopeptidase is activated by removal of the propeptide and the KDEL tail and enters the cytosol. The endosperm dries and detaches from the cotyledons. A homologous KDEL-tailed cysteine endopeptidase has been found in several senescing tissues; it has been localized in ricinosomes of withering day-lily petals and dying seed coats. Three genes for a KDEL-tailed cysteine endopeptidase have been identified in Arabidopsis. One is expressed in senescing ovules, the second in the vascular vessels and the third in maturing siliques. These genes open the way to exploring PCD in plants.}, }
@article {pmid11319256, year = {2001}, author = {von Nickisch-Rosenegk, M and Brown, WM and Boore, JL}, title = {Complete sequence of the mitochondrial genome of the tapeworm Hymenolepis diminuta: gene arrangements indicate that Platyhelminths are Eutrochozoans.}, journal = {Molecular biology and evolution}, volume = {18}, number = {5}, pages = {721-730}, doi = {10.1093/oxfordjournals.molbev.a003854}, pmid = {11319256}, issn = {0737-4038}, mesh = {Animals ; Cestoda ; Codon, Nonsense/genetics ; DNA, Mitochondrial/*genetics ; Gene Order/genetics ; Genetic Linkage ; Hymenolepis/classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Platyhelminths/classification/genetics ; Polymerase Chain Reaction ; RNA, Transfer/genetics ; }, abstract = {Using "long-PCR," we amplified in overlapping fragments the complete mitochondrial genome of the tapeworm Hymenolepis diminuta (Platyhelminthes: Cestoda) and determined its 13,900-nt sequence. The gene content is the same as that typically found for animal mitochondrial DNA (mtDNA) except that atp8 appears to be lacking, a condition found previously for several other animals. Despite the small size of this mtDNA, there are two large noncoding regions, one of which contains 13 repeats of a 31-nt sequence and a potential stem-loop structure of 25 bp with an 11-member loop. Large potential secondary structures were identified also for the noncoding regions of two other cestode mtDNAS: Comparison of the mitochondrial gene arrangement of H. diminuta with those previously published supports a phylogenetic position of flatworms as members of the Eutrochozoa, rather than placing them basal to either a clade of protostomes or a clade of coelomates.}, }
@article {pmid11319255, year = {2001}, author = {Rotte, C and Stejskal, F and Zhu, G and Keithly, JS and Martin, W}, title = {Pyruvate : NADP+ oxidoreductase from the mitochondrion of Euglena gracilis and from the apicomplexan Cryptosporidium parvum: a biochemical relic linking pyruvate metabolism in mitochondriate and amitochondriate protists.}, journal = {Molecular biology and evolution}, volume = {18}, number = {5}, pages = {710-720}, doi = {10.1093/oxfordjournals.molbev.a003853}, pmid = {11319255}, issn = {0737-4038}, support = {AI 40320/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Anaerobiosis ; Animals ; Apicomplexa/*parasitology ; Blotting, Northern ; Blotting, Southern ; Cryptosporidium parvum/*enzymology/genetics/metabolism ; Euglena gracilis/*enzymology/metabolism ; Ketone Oxidoreductases/*genetics/*metabolism ; Kinetics ; Mitochondria/drug effects/*genetics/*metabolism ; Molecular Sequence Data ; NAD/metabolism ; NADP/metabolism ; Oxygen/*pharmacology ; Phylogeny ; Protozoan Infections/parasitology ; Pyruvate Dehydrogenase Complex/*genetics/*metabolism ; Pyruvate Synthase ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Most eukaryotes perform the oxidative decarboxylation of pyruvate in mitochondria using pyruvate dehydrogenase (PDH). Eukaryotes that lack mitochondria also lack PDH, using instead the O(2)-sensitive enzyme pyruvate : ferredoxin oxidoreductase (PFO), which is localized either in the cytosol or in hydrogenosomes. The facultatively anaerobic mitochondria of the photosynthetic protist Euglena gracilis constitute a hitherto unique exception in that these mitochondria oxidize pyruvate with the O(2)-sensitive enzyme pyruvate : NADP oxidoreductase (PNO). Cloning and analysis of Euglena PNO revealed that the cDNA encodes a mitochondrial transit peptide followed by an N-terminal PFO domain that is fused to a C-terminal NADPH-cytochrome P450 reductase (CPR) domain. Two independent 5.8-kb full-size cDNAs for Euglena mitochondrial PNO were isolated; the gene was expressed in cultures supplied with 2% CO(2) in air and with 2% CO(2) in N(2). The apicomplexan Cryptosporidium parvum was also shown to encode and express the same PFO-CPR fusion, except that, unlike E. gracilis, no mitochondrial transit peptide for C. parvum PNO was found. Recombination-derived remnants of PNO are conserved in the genomes of Saccharomyces cerevisiae and Schizosaccharomyces pombe as proteins involved in sulfite reduction. Notably, Trypanosoma brucei was found to encode homologs of both PFO and all four PDH subunits. Gene organization and phylogeny revealed that eukaryotic nuclear genes for mitochondrial, hydrogenosomal, and cytosolic PFO trace to a single eubacterial acquisition. These findings suggest a common ancestry of PFO in amitochondriate protists with Euglena mitochondrial PNO and Cryptosporidium PNO. They are also consistent with the view that eukaryotic PFO domains are biochemical relics inherited from a facultatively anaerobic, eubacterial ancestor of mitochondria and hydrogenosomes.}, }
@article {pmid11311562, year = {2001}, author = {Choglay, AA and Chapple, JP and Blatch, GL and Cheetham, ME}, title = {Identification and characterization of a human mitochondrial homologue of the bacterial co-chaperone GrpE.}, journal = {Gene}, volume = {267}, number = {1}, pages = {125-134}, doi = {10.1016/s0378-1119(01)00396-1}, pmid = {11311562}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/metabolism ; Base Sequence ; DNA, Complementary/chemistry/genetics ; HSP40 Heat-Shock Proteins ; HSP70 Heat-Shock Proteins/metabolism ; Heat-Shock Proteins/chemistry/*genetics/metabolism ; Humans ; Mitochondria/*metabolism ; Models, Molecular ; Molecular Chaperones/metabolism ; Molecular Sequence Data ; Protein Binding ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Tumor Cells, Cultured ; }, abstract = {We have identified a novel human cDNA with a predicted protein sequence that has 28% amino acid identity with the E. coli Hsp70 co-chaperone GrpE and designated it HMGE. Even with this low level of amino acid identity the human sequence could be efficiently modelled on the X-ray structure of the E. coli protein, suggesting that there may be significant functional conservation. Indeed, HMGE expressed in E. coli as a GST fusion protein co-purified with the E. coli Hsp70 protein DnaK in the absence of ATP. DnaK could be released from the GST-HMGE with a Mg-ATP wash. Subcellular fractionation and immunocytochemistry studies using antisera raized against HMGE show that it is a mitochondrial protein. In contrast to studies of rat GrpE, however, HMGE also appears to bind the constitutive cytosolic Hsp70, Hsc70, in addition to mitochondrial Hsp70, Mt-Hsp70. We have previously shown that Hsc70 nucleotide-exchange is rate limiting in the presence of the DnaJ-protein, HSJ1b. However, HMGE was found to inhibit the HSJ1b-enhanced Hsc70 ATPase activity and may mediate this inhibition by binding the DnaJ-protein, HSJ1b. This is the first description of a direct interaction between a DnaJ protein and GrpE-like protein. These studies suggest that the structure of GrpE has been conserved throughout evolution and that the conserved structure can interact with several forms of Hsp70, but that HMGE cannot form part of the reaction cycle for cytosolic Hsc70.}, }
@article {pmid11308016, year = {2001}, author = {Tomáska, L and Nosek, J and Kucejová, B}, title = {Mitochondrial single-stranded DNA-binding proteins: in search for new functions.}, journal = {Biological chemistry}, volume = {382}, number = {2}, pages = {179-186}, doi = {10.1515/BC.2001.025}, pmid = {11308016}, issn = {1431-6730}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/metabolism ; Candida/genetics/metabolism ; DNA, Single-Stranded/*metabolism ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; *Evolution, Molecular ; Humans ; Mitochondria/*metabolism ; Molecular Sequence Data ; Protein Conformation ; Sequence Homology, Amino Acid ; }, abstract = {During the evolution of the eukaryotic cell, genes encoding proteins involved in the metabolism of mitochondrial DNA (mtDNA) have been transferred from the endosymbiont into the host genome. Mitochondrial single-stranded DNA-binding (mtSSB) proteins serve as an excellent argument supporting this aspect of the endosymbiotic theory. The crystal structure of the human mtSSB, together with an abundance of biochemical and genetic data, revealed several exciting features of mtSSB proteins and enabled a detailed comparison with their prokaryotic counterparts. Moreover, identification of a novel member of the mtSSB family, mitochondrial telomere-binding protein of the yeast Candida parapsilosis, has raised interesting questions regarding mtDNA metabolism and evolution.}, }
@article {pmid11297180, year = {2001}, author = {Janke, A and Erpenbeck, D and Nilsson, M and Arnason, U}, title = {The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): implications for amniote phylogeny.}, journal = {Proceedings. Biological sciences}, volume = {268}, number = {1467}, pages = {623-631}, doi = {10.1098/rspb.2000.1402}, pmid = {11297180}, issn = {0962-8452}, mesh = {Alligators and Crocodiles/*genetics ; Animals ; Base Sequence ; Birds/genetics ; Codon/genetics ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; *Evolution, Molecular ; Fishes/genetics ; Genome ; Humans ; Iguanas/*genetics ; Mitochondria, Heart/chemistry ; Mitochondria, Liver/chemistry ; *Phylogeny ; RNA/genetics ; RNA, Mitochondrial ; Species Specificity ; Turtles/genetics ; Xenopus/genetics ; }, abstract = {The complete mitochondrial genomes of two reptiles, the common iguana (Iguana iguana) and the caiman (Caiman crocodylus), were sequenced in order to investigate phylogenetic questions of tetrapod evolution. The addition of the two species allows analysis of reptilian relationships using data sets other than those including only fast-evolving species. The crocodilian mitochondrial genomes seem to have evolved generally at a higher rate than those of other vertebrates. Phylogenetic analyses of 2889 amino-acid sites from 35 mitochondrial genomes supported the bird-crocodile relationship, lending no support to the Haematotherma hypothesis (with birds and mammals representing sister groups). The analyses corroborated the view that turtles are at the base of the bird-crocodile branch. This position of the turtles makes Diapsida paraphyletic. The origin of the squamates was estimated at 294 million years (Myr) ago and that of the turtles at 278 Myr ago. Phylogenetic analysis of mammalian relationships using the additional outgroups corroborated the Marsupionta hypothesis, which joins the monotremes and the marsupials to the exclusion of the eutherians.}, }
@article {pmid11285367, year = {2001}, author = {Vianna, CR and Hagen, T and Zhang, CY and Bachman, E and Boss, O and Gereben, B and Moriscot, AS and Lowell, BB and Bicudo, JE and Bianco, AC}, title = {Cloning and functional characterization of an uncoupling protein homolog in hummingbirds.}, journal = {Physiological genomics}, volume = {5}, number = {3}, pages = {137-145}, doi = {10.1152/physiolgenomics.2001.5.3.137}, pmid = {11285367}, issn = {1531-2267}, support = {R37 DK053477/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Birds/*genetics/physiology ; Carrier Proteins/*genetics ; Cloning, Molecular ; Ion Channels ; Membrane Potentials ; Membrane Proteins/*genetics ; *Membrane Transport Proteins ; Mitochondria/physiology ; *Mitochondrial Proteins ; Molecular Sequence Data ; Phylogeny ; Proteins/*genetics ; RNA, Messenger/biosynthesis ; Saccharomyces cerevisiae/physiology ; Sequence Homology, Amino Acid ; Thermogenesis ; Tissue Distribution ; Uncoupling Protein 1 ; Uncoupling Protein 2 ; Uncoupling Protein 3 ; }, abstract = {The cDNA of an uncoupling protein (UCP) homolog has been cloned from the swallow-tailed hummingbird, Eupetomena macroura. The hummingbird uncoupling protein (HmUCP) cDNA was amplified from pectoral muscle (flight muscle) using RT-PCR and primers for conserved domains of various known UCP homologs. The rapid amplification of cDNA ends (RACE) method was used to complete the cloning of the 5' and 3' ends of the open reading frame. The HmUCP coding region contains 915 nucleotides, and the deduced protein sequence consists of 304 amino acids, being approximately 72, 70, and 55% identical to human UCP3, UCP2, and UCP1, respectively. The uncoupling activity of this novel protein was characterized in yeast. In this expression system, the 12CA5-tagged HmUCP fusion protein was detected by Western blot in the enriched mitochondrial fraction. Similarly to rat UCP1, HmUCP decreased the mitochondrial membrane potential as measured in whole yeast by uptake of the fluorescent potential-sensitive dye 3',3-dihexyloxacarbocyanine iodide. The HmUCP mRNA is primarily expressed in skeletal muscle, but high levels can also be detected in heart and liver, as assessed by Northern blot analysis. Lowering the room's temperature to 12-14 degrees C triggered the cycle torpor/rewarming, typical of hummingbirds. Both in the pectoral muscle and heart, HmUCP mRNA levels were 1.5- to 3.4-fold higher during torpor. In conclusion, this is the first report of an UCP homolog in birds. The data indicate that HmUCP has the potential to function as an UCP and could play a thermogenic role during rewarming.}, }
@article {pmid11284664, year = {2001}, author = {Cummins, JM}, title = {Mitochondria: potential roles in embryogenesis and nucleocytoplasmic transfer.}, journal = {Human reproduction update}, volume = {7}, number = {2}, pages = {217-228}, doi = {10.1093/humupd/7.2.217}, pmid = {11284664}, issn = {1355-4786}, mesh = {Aging/physiology ; Animals ; Apoptosis/physiology ; Cell Nucleus/genetics ; Cloning, Organism/methods ; DNA, Mitochondrial/genetics/physiology ; Female ; Humans ; Infertility, Male/therapy ; Male ; Mitochondria/genetics/*physiology ; Oogenesis/physiology ; *Reproductive Techniques ; }, abstract = {This review examines current understanding of mammalian mitochondria and mitochondrial DNA in the light of new reproductive technologies. Mitochondria are central to ageing, apoptosis, metabolism and many diseases. They are controlled by a dual genome system, with cooperation between endogenous mitochondrial genes and mitochondrial genes translocated to the nucleus over the course of evolution. This translocation has been accompanied by extreme compression of the mitochondrial genome, with little tolerance for mutations or heteroplasmy (multiple genomes). The highly compact mitochondrial genome appears to be maintained by a stringent numerical bottleneck in embryogenesis and oogenesis, followed by clonal expansion from a highly selected subset of precursor molecules. The dual nature of control between nucleus and cytoplasm sets up potential conflicts, which are normally resolved by natural selection. Such potentially opposing interests and mechanisms are probably partly to blame for the poor rates of success in cloning animals by nuclear transfer. The ability to construct cell systems and animal embryos with novel combinations and permutations of nuclear and cytoplasmic genes will provide powerful tools for examining these fundamental biological questions. Clinically, attempts to 'rescue' abnormal human oocytes or embryos by cytoplasmic transfer risk complex and unpredictable outcomes emerging from disharmonious nuclear-cytoplasmic interactions.}, }
@article {pmid11282628, year = {2001}, author = {Barroso, G and Bois, F and Labarère, J}, title = {Duplication of a truncated paralog of the family B DNA polymerase gene Aa-polB in the Agrocybe aegerita mitochondrial genome.}, journal = {Applied and environmental microbiology}, volume = {67}, number = {4}, pages = {1739-1743}, pmid = {11282628}, issn = {0099-2240}, mesh = {Agaricales/*genetics/growth &amp; development ; Amino Acid Sequence ; DNA, Fungal/genetics ; DNA, Mitochondrial/*genetics ; DNA-Directed DNA Polymerase/chemistry/*genetics/metabolism ; Evolution, Molecular ; *Fungal Proteins ; *Gene Duplication ; *Genome, Fungal ; Molecular Sequence Data ; Polymorphism, Genetic/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The Agrocybe aegerita mitochondrial genome contains a truncated family B DNA polymerase gene (Aa-polB P1) whose nucleotide sequence is 86% identical to the previously described and potentially functional Aa-polB gene. A tRNA(Met) gene occurs at the 3' end of the Aa-polB P1 gene. The Aa-polB P1 gene could result from reverse transcription of an Aa-polB mRNA primed by a tRNA(Met) followed by the integration of the cDNA after recombination at the mitochondrial tRNA locus. Two naturally occurring alleles of Aa-polB P1 carry one or two copies of the disrupted sequence. In strains with two copies of Aa-polB P1, these copies are inverted relative to one another and separated by a short sequence carrying the tRNA(Met) gene. Both A. aegerita mitochondrial family B DNA polymerases were found to be related to other family B DNA polymerases (36 to 53% amino acid similarity), including the three enzymes of the archaebacterium Sulfolobus solfataricus. If mitochondria originated from a fusion between a Clostridium-like eubacterium and a Sulfolobus-like archaebacterium, then the A. aegerita family B DNA polymerase genes could be remnants of the archaebacterial genes.}, }
@article {pmid11280008, year = {2000}, author = {Kim, CG and Tominaga, O and Su, ZH and Osawa, S}, title = {Differentiation within the genus Leptocarabus (excl. L. kurilensis) in the Japanese Islands as deduced from mitochondrial ND5 gene sequences (Coleoptera, Carabidae).}, journal = {Genes &amp; genetic systems}, volume = {75}, number = {6}, pages = {335-342}, doi = {10.1266/ggs.75.335}, pmid = {11280008}, issn = {1341-7568}, mesh = {Animals ; *Coleoptera/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; Databases, Factual ; Electron Transport Complex IV/*genetics ; Environment ; Evolution, Molecular ; *Geography ; Japan ; Mitochondria/*enzymology/genetics ; NADH Dehydrogenase/*genetics ; Phenotype ; *Phylogeny ; RNA, Ribosomal, 28S/genetics ; Trehalase/genetics ; }, abstract = {The phylogenetic trees have been constructed for the mitochondrial ND5 gene sequences from the Japanese Leptocarabus ground beetles, which contain 101 specimens collected from nearly the complete distribution ranges of them consisting of five morphological species, i.e., Leptocarabus procerulus, L. kumagaii, L. hiurai, L. kyushuensis and L. arboreus. On the trees, there are recognized two major lineages, each of which is further divided into two or more sublineages. The phylogenetic lines are geographically linked. Two or more species occur in a single lineage, and the same species appear in different lines. We suggest that transformation from one type of morphology to another took place in parallel in various periods of evolution of the Japanese Leptocarabus. From the phylogenetic tree and the dating from the nucleotide substitution rate and the geohistorical data it is inferred that the ancestry of all the Japanese Leptocarabus species was derived from a protoform of L. kyushuensis inhabited the ancient Japan area, followed by separation into two lineages after split of the Japanese Islands from the Eurasian Continent. They then propagated distribution to occupy their own habitat ranges, during which the morphological transformation took place in some lineages.}, }
@article {pmid11280005, year = {2000}, author = {Zouros, E}, title = {The exceptional mitochondrial DNA system of the mussel family Mytilidae.}, journal = {Genes &amp; genetic systems}, volume = {75}, number = {6}, pages = {313-318}, doi = {10.1266/ggs.75.313}, pmid = {11280005}, issn = {1341-7568}, mesh = {Animals ; Bivalvia ; *DNA, Mitochondrial/classification/*genetics ; Extrachromosomal Inheritance/*genetics ; Female ; Male ; Mitochondria/genetics ; Pedigree ; Phylogeny ; Sex Determination Analysis ; Sex Determination Processes ; Sex Ratio ; }, abstract = {Species of the families Mytilidae (sea mussels) and Unionidae (fresh water mussels) contain two types of mitochondrial DNA (mtDNA), the F that behaves as the standard animal mtDNA and the M that is transmitted through the sperm and establishes itself only in the male gonad. The two molecules have, therefore, separate transmission routes, one through the female and the other through the male lineage. The system has been named doubly uniparental inheritance (DUI). Another important feature of sea mussels is that the sex ratio among offspring of a pair mating is determined by the female parent only. The mechanism of DUI remains unknown. One hypothesis that is consistent with all observations is that the standard maternal inheritance was modified in mussels via the evolution of a suppressor gene that is expressed during oogenesis and has two alleles, the inactive and the active allele. In the presence of the active allele in the mother's genotype the egg is supplied with a substance that interferes and the normal mechanism of elimination of sperm mitochondria. This will explain why half of mussels have the father's mtDNA and half do not, but would not explain why presence/absence of paternal mtDNA is linked with the male and female gender, respectively. To provide an explanation for this linkage, one would have to assume that there is a causal relationship between retention of paternal mtDNA and sex determination.}, }
@article {pmid11279363, year = {2000}, author = {Röll, B}, title = {Gecko vision-visual cells, evolution, and ecological constraints.}, journal = {Journal of neurocytology}, volume = {29}, number = {7}, pages = {471-484}, doi = {10.1023/a:1007293511912}, pmid = {11279363}, issn = {0300-4864}, mesh = {Animals ; *Biological Evolution ; Cell Size ; Cilia/ultrastructure ; Dark Adaptation ; Darkness ; Ecology ; Light ; *Lizards/physiology ; Microscopy, Electron ; Microvilli/ultrastructure ; Mitochondria/ultrastructure ; Presynaptic Terminals/ultrastructure ; Retinal Cone Photoreceptor Cells/cytology/*ultrastructure ; Rod Cell Outer Segment/cytology/*ultrastructure ; }, abstract = {Geckos comprise both nocturnal and diurnal genera, and between these categories there are several transitions. As all geckos depend on their visual sense for prey capture, they are promising subjects for comparison of morphological modifications of visual cells adapted to very different photic environments. Retinae of 22 species belonging to 15 genera with different activity periods are examined electron microscopically. Scotopic and photopic vision in geckos is not divided between "classical" rods and cones, respectively; both are performed by one basic visual cell type. Independent of the activity periods of the individual species, the visual cells of geckos exhibit characteristics of cones at all levels of their ultrastructure. Thus, gecko retinae have to be classified as cone retinae. Only the large size and the shape of the photoreceptor outer segments in nocturnal geckos are reminiscent of rods; the outer segments are up to 60 microm in length and up to 10 microm in diameter. The visual cells of diurnal geckos have considerably smaller outer segments with lengths ranging from 6 to 12 microm and diameters ranging from 1.3 to 2.1 microm. Nocturnal and diurnal species differ in the structure of their ellipsoids. One type of visual cell in nocturnal geckos has modified mitochondria with either rudimentary cristae or no cristae at all, and one type of visual cell in diurnal geckos possesses an oil droplet. The visual cells of Phelsuma guentheri and Rhoptropus barnardi are intermediate between those of nocturnal and diurnal species.}, }
@article {pmid11277633, year = {2001}, author = {Goto, SG and Kimura, MT}, title = {Phylogenetic utility of mitochondrial COI and nuclear Gpdh genes in Drosophila.}, journal = {Molecular phylogenetics and evolution}, volume = {18}, number = {3}, pages = {404-422}, doi = {10.1006/mpev.2000.0893}, pmid = {11277633}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Cell Nucleus/enzymology ; DNA Primers ; DNA, Mitochondrial/*genetics ; Drosophila/*classification/enzymology/*genetics ; Drosophila melanogaster/classification/enzymology/genetics ; Electron Transport Complex IV/chemistry/*genetics ; *Evolution, Molecular ; *Genetic Variation ; Glycerolphosphate Dehydrogenase/chemistry/*genetics ; Mitochondria/enzymology ; *Phylogeny ; }, abstract = {Phylogenetic utility of the mitochondrial COI (cytochrome oxidase subunit I) and nuclear Gpdh (glycerol-3-phosphate dehydrogenase) genes was studied in the Drosophila melanogaster species group. The rate of substitution was higher in the COI gene than in the Gpdh gene. In addition, multiple substitutions, not only for transitional but also for transversional substitutions, occurred faster in the COI gene. None of the trees obtained using the COI gene supported the well-established monophyly of the ananassae subgroup. In addition, the incongruence length difference test, Templeton test, and partitioned Bremer support revealed that the trees based on the COI data are considerably different from those based on the Gpdh and the combined data set. Thus, the COI gene did not show good phylogenetic performance in the melanogaster group. The present analyses based on the Gpdh gene and the combined data set revealed that the ananassae subgroup branched off first in the melanogaster group followed by the montium subgroup and further by the melanogaster subgroup in contrast to the most recent phylogenetic hypothesis based on Amy multigenes.}, }
@article {pmid11277632, year = {2001}, author = {Hedin, MC and Maddison, WP}, title = {A combined molecular approach to phylogeny of the jumping spider subfamily dendryphantinae (araneae: salticidae).}, journal = {Molecular phylogenetics and evolution}, volume = {18}, number = {3}, pages = {386-403}, doi = {10.1006/mpev.2000.0883}, pmid = {11277632}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; DNA, Ribosomal/genetics ; Drosophila/genetics ; Electron Transport Complex IV/chemistry/genetics ; *Evolution, Molecular ; *Genetic Variation ; Likelihood Functions ; Models, Molecular ; Molecular Sequence Data ; NADH Dehydrogenase/genetics ; Nucleic Acid Conformation ; *Phylogeny ; Protein Structure, Secondary ; RNA, Ribosomal, 16S/chemistry/genetics ; RNA, Ribosomal, 28S/chemistry/genetics ; RNA, Transfer, Leu/chemistry/genetics ; Spiders/*classification/*genetics ; }, abstract = {Four gene regions were sequenced for 30 species of jumping spiders, most from the subfamily Dendryphantinae, to investigate their molecular phylogeny and evolution. These are three regions from the mitochondria (ca. 560 bp of 16S plus adjacent tRNA, 1047 bp of cytochrome oxidase 1 (CO1), and 414 bp of NADH1 (ND1) and one region from the nuclear genome (ca. 750 bp of 28S). Parsimony and likelihood analyses of these gene regions separately and together support the monophyly of the dendryphantines as delimited previously by morphological characters. A group of elongate-bodied genera are placed as basal among the dendryphantines, and previously proposed relationships of Poultonella, Paraphidippus, and Sassacus vitis are confirmed. Comparison of overall rates of molecular evolution indicates striking differences across the gene regions, with highest divergence in ND1, CO1, 16S, and 28S in decreasing order. All four regions are characterized by both within- and among-site rate variation. Phylogenetic results from CO1 conflict conspicuously with phylogenetic results from the other genes and morphological data. Attempts to account for potential sources of this conflict (e.g., accommodating biased base composition, high homoplasy, within- and among-site rate variation, etc.) are largely unsuccessful.}, }
@article {pmid11272466, year = {2000}, author = {Gottlieb, RA}, title = {Role of mitochondria in apoptosis.}, journal = {Critical reviews in eukaryotic gene expression}, volume = {10}, number = {3-4}, pages = {231-239}, doi = {10.1615/critreveukargeneexpr.v10.i3-4.20}, pmid = {11272466}, issn = {1045-4403}, support = {AG13501/AG/NIA NIH HHS/United States ; HL61518/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Apoptosis/*physiology ; Caenorhabditis elegans/cytology/enzymology ; Caspases/metabolism ; Cytochrome c Group/metabolism ; Enzyme Activation ; Mitochondria/enzymology/*physiology/ultrastructure ; Proto-Oncogene Proteins c-bcl-2/metabolism ; Receptor Cross-Talk ; }, abstract = {Apoptosis is characterized by biochemical processes that are largely conserved throughout evolution. The basic elements of the system comprise caspases, their activators and inhibitors, and regulators of mitochondrial integrity. New evidence reveals the role of mitochondria as the central coordinators of apoptosis. Accordingly, some caspases are sequestered within the mitochondria, and mitochondria contain additional proapoptotic factors. Bcl-2 and Bax homologs regulate the integrity of the mitochondrial outer membrane, which may also serve as a scaffold for the apoptotic machinery.}, }
@article {pmid11269666, year = {2001}, author = {Lopez, JM and Hegardt, FG and Haro, D}, title = {Differential expression of cytosolic and mitochondrial 3-hydroxy-3-methylglutaryl CoA synthases during adipocyte differentiation.}, journal = {Molecular and cellular biochemistry}, volume = {217}, number = {1-2}, pages = {57-66}, pmid = {11269666}, issn = {0300-8177}, mesh = {Adipocytes/*cytology/*enzymology ; Animals ; Blotting, Northern ; CCAAT-Enhancer-Binding Proteins/metabolism ; Cell Differentiation ; Cell Line ; Cytosol/enzymology ; Gene Expression Profiling ; *Gene Expression Regulation, Enzymologic ; Humans ; Hydroxymethylglutaryl-CoA Synthase/biosynthesis/*genetics ; Mitochondria/*enzymology ; Promoter Regions, Genetic ; RNA, Messenger/genetics/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic ; Tumor Cells, Cultured ; }, abstract = {Mitochondrial and cytosolic 3-hydroxy-3-methylglutaryl CoA synthase (m-HMS and c-HMS) genes show high identity at the nucleotide and amino acid level, but no homology has been found in the promoter area. The main regulator for c-HMS is SREBP. The best known transcription factor that regulates m-HMS is PPAR alpha. Three types of PPAR, alpha, gamma and delta have been described in vertebrates. Here we found that they display distinct ligand response profiles in the m-HMS promoter. In some conditions PPAR gamma is a significant activator of m-HMS. Thus, the m-HMS gene is transiently expressed during the clonal expansion phase of 3T3-L1 differentiation. We found that C/EBP delta and PPAR gamma activate the m-HMS promoter in 3T3-L1 cells synergistically. This synergistic effect was only observed in the whole promoter (-1148 to +28). A small construct (-116 to +28) which contains the PPRE did not respond to C/EBP delta and/or PPAR gamma. This suggests that a putative C/EBP site lie somewhere between -1148 and -116 bp. We also show that C/EBP delta was more efficient that C/EBP alpha and C/EBP beta to activate the m-HMS promoter. The time course of c-HMS mRNA expression during 3T3-L1 differentiation was different, with a significant increase at terminal adipogenesis. We found that the transcription factor C/EBP alpha did not activate the c-HMS promoter. The differential pattern of expression shown by these two genes, which have a common ancestor, exemplifies refinements of transcriptional control during evolution.}, }
@article {pmid11264402, year = {2001}, author = {Edgcomb, VP and Roger, AJ and Simpson, AG and Kysela, DT and Sogin, ML}, title = {Evolutionary relationships among "jakobid" flagellates as indicated by alpha- and beta-tubulin phylogenies.}, journal = {Molecular biology and evolution}, volume = {18}, number = {4}, pages = {514-522}, doi = {10.1093/oxfordjournals.molbev.a003830}, pmid = {11264402}, issn = {0737-4038}, mesh = {Animals ; Codon/genetics ; DNA, Protozoan ; Eukaryota/classification/*genetics ; *Evolution, Molecular ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Sequence Analysis, DNA ; Tubulin/*genetics ; }, abstract = {Jakobids are free-living, heterotrophic flagellates that might represent early-diverging mitochondrial protists. They share ultrastructural similarities with eukaryotes that occupy basal positions in molecular phylogenies, and their mitochondrial genome architecture is eubacterial-like, suggesting a close affinity with the ancestral alpha-proteobacterial symbiont that gave rise to mitochondria and hydrogenosomes. To elucidate relationships among jakobids and other early-diverging eukaryotic lineages, we characterized alpha- and beta-tubulin genes from four jakobids: Jakoba libera, Jakoba incarcerata, Reclinomonas americana (the "core jakobids"), and Malawimonas jakobiformis. These are the first reports of nuclear genes from these organisms. Phylogenies based on alpha-, beta-, and combined alpha- plus beta-tubulin protein data sets do not support the monophyly of the jakobids. While beta-tubulin and combined alpha- plus beta-tubulin phylogenies showed a sister group relationship between J. libera and R. americana, the two other jakobids, M. jakobiformis and J. incarcerata, had unclear affinities. In all three analyses, J. libera, R. americana, and M. jakobiformis emerged from within a well-supported large "plant-protist" clade that included plants, green algae, cryptophytes, stramenopiles, alveolates, Euglenozoa, Heterolobosea, and several other protist groups, but not animals, fungi, microsporidia, parabasalids, or diplomonads. A preferred branching order within the plant-protist clade was not identified, but there was a tendency for the J. libera-R. americana lineage to group with a clade made up of the heteroloboseid amoeboflagellates and euglenozoan protists. Jakoba incarcerata branched within the plant-protist clade in the beta- and the combined alpha- plus beta-tubulin phylogenies. In alpha- tubulin trees, J. incarcerata occupied an unresolved position, weakly grouping with the animal/fungal/microsporidian group or with amitochondriate parabasalid and diplomonad lineages, depending on the phylogenetic method employed. Tubulin gene phylogenies were in general agreement with mitochondrial gene phylogenies and ultrastructural data in indicating that the "jakobids" may be polyphyletic. Relationships with the putatively deep-branching amitochondriate diplomonads remain uncertain.}, }
@article {pmid11262399, year = {2001}, author = {Ohtsuki, T and Watanabe Yi,  and Takemoto, C and Kawai, G and Ueda, T and Kita, K and Kojima, S and Kaziro, Y and Nyborg, J and Watanabe, K}, title = {An "elongated" translation elongation factor Tu for truncated tRNAs in nematode mitochondria.}, journal = {The Journal of biological chemistry}, volume = {276}, number = {24}, pages = {21571-21577}, doi = {10.1074/jbc.M011118200}, pmid = {11262399}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/genetics ; Base Sequence ; Caenorhabditis elegans/*genetics/metabolism ; Cattle ; Cloning, Molecular ; DNA Primers ; DNA, Helminth/genetics ; DNA, Mitochondrial/genetics ; Escherichia coli/genetics ; Helminth Proteins/chemistry/genetics/metabolism ; Humans ; Kinetics ; Mitochondria/genetics/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Peptide Elongation Factor Tu/chemistry/*genetics/*metabolism ; Protein Conformation ; RNA/chemistry/*genetics ; RNA, Mitochondrial ; RNA, Transfer/chemistry/*genetics ; Recombinant Proteins/chemistry/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {We have found the gene for a translation elongation factor Tu (EF-Tu) homologue in the genome of the nematode Caenorhabditis elegans. Because the corresponding protein was detected immunologically in a nematode mitochondrial (mt) extract, it could be regarded as a nematode mt EF-Tu. The protein possesses an extension of about 57 amino acids (we call this domain 3') at the C terminus, which is not found in any other known EF-Tu. Because most nematode mt tRNAs lack a T stem, domain 3' may be related to this feature. The nematode EF-Tu bound to nematode T stem-lacking tRNA, but bacterial EF-Tu was unable to do so. A series of domain exchange experiments strongly suggested that domains 3 and 3' are essential for binding to T stem-lacking tRNAs. This finding may constitute a novel example of the co-evolution of a structurally simplified RNA and the cognate RNA-binding protein, the latter having apparently acquired an additional domain to compensate for the lack of a binding site(s) on the RNA.}, }
@article {pmid11255014, year = {2001}, author = {Pineda, AO and Ellington, WR}, title = {Organization of the gene for an invertebrate mitochondrial creatine kinase: comparisons with genes of higher forms and correlation of exon boundaries with functional domains.}, journal = {Gene}, volume = {265}, number = {1-2}, pages = {115-121}, doi = {10.1016/s0378-1119(01)00352-3}, pmid = {11255014}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Creatine Kinase/*genetics ; DNA/chemistry/genetics ; Exons ; Genes/*genetics ; Introns ; Mitochondria/*enzymology ; Molecular Sequence Data ; Polychaeta/enzymology/*genetics ; Sequence Analysis, DNA ; }, abstract = {Two major gene duplication events are thought to have taken place in the evolution of creatine kinases (CK) in the vertebrates - (1) the formation of distinct mitochondrial (MiCK) and cytoplasmic forms from the primordial gene and (2) subsequent formation of the sarcomeric (sar-) and ubiquitous (ubi-) isoforms of octameric MiCK and muscle (M) and brain (B) isoforms of dimeric, cytoplasmic CK. The genes of these two CK clades reflect a distant divergence as sar- and ubiMiCK genes consistently have nine protein-coding exons while M- and B-CK genes have seven protein-coding exons; these genes share only one common exon. CKs are also widely distributed in the invertebrates and it has recently been shown that MiCKs evolved well before the divergence of the major metazoan groups. In the present communication, we report the structure and topology of the gene for MiCK from the protostome marine worm Chaetopterus variopedatus. The protein-coding region of the gene for this primitive MiCK spans over 10 kb and consists of eight exons, the last five (E4-E8) have identical boundaries to the corresponding exons of sar- and ubiMiCK genes. Exon-3 of the C. variopedatus MiCK gene consists of the corresponding E3 and E4 of the vertebrate MiCKs with no intervening intron. E1 is longer and E2 is shorter in the polychaete MiCK gene than the counterpart sarcomeric and ubiquitous genes. The insertion of the intron in C. variopedatus E3 creating the two exons as well as the rearrangement of the intron between E1 and E2 must have occurred prior to or coincident with the duplication event creating the two vertebrate mitochondrial isoforms. Sarcomeric and ubiMiCKs display substantial differences from their invertebrate MiCK counterparts in properties relating to octamer stability and membrane binding. The evolutionary changes in gene topology may be a component of this functional progression.}, }
@article {pmid11255012, year = {2001}, author = {Karan, D and David, JR and Capy, P}, title = {Molecular evolution of the AMP-forming Acetyl-CoA synthetase.}, journal = {Gene}, volume = {265}, number = {1-2}, pages = {95-101}, doi = {10.1016/s0378-1119(01)00358-4}, pmid = {11255012}, issn = {0378-1119}, mesh = {Acetate-CoA Ligase/*genetics/metabolism ; Adenosine Monophosphate/metabolism ; Amino Acid Sequence ; Animals ; Conserved Sequence ; Databases, Factual ; *Evolution, Molecular ; Humans ; Introns ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Acetyl-CoA-Synthetase (ACS) is involved in the production of acetate, a major metabolite in numerous organisms. There are two forms of this enzyme: ADP-forming ACS and ATP-forming ACS. We focus mainly on the AMP-forming ACS gene, which is relatively well conserved in eubacteria, archeaebacteria, and eukaryotes. BLAST searches in databases showed 30 protein sequences significantly related to the ACS. Most of these sequences were identified as ACS but three of them, belonging to the mammalian species, were annotated as another gene named: the SA gene, which is involved in the essential hypertension. The ACS and SA genes probably derived from a duplication of an ancestral gene but have acquired different functions. Six conserved regions of the ACS protein were defined across the three domains of life. While the precise function of the conserved regions remains unknown, they are probably involved in the enzymatic activity. Among eukaryotes, we found a high variability with respect to the number and the position of introns. However, some positions are conserved between fungi and a nematode. A maximum likelihood tree based upon the conserved regions showed that all sequences except the one from B. subtilis, belong to two basic groups: one the SA-like group including sequences from Archaeoglobus fulgidus and Streptomyces coelicolor, and second, the ACS group. The later can be further divided in two parts: a prokaryotic one including eubacteria and an archaebacterium, and a eukaryotic group within which two proteobacterial sequences branch including ACS from the alpha-proteobacterium Rhodobacter capsulatus. Within the eukaryotic group, bootstrap support is very low, but overall the data are consistent with the view that eukaryotes acquired their ACS gene from the ancestors of mitochondria. The localization of this enzyme in eukaryotic mitochondria is the additional evidence in favor of this interpretation.}, }
@article {pmid11251792, year = {2001}, author = {Hurwood, DA and Hughes, JM}, title = {Nested clade analysis of the freshwater shrimp, Caridina zebra (Decapoda: Atyidae), from north-eastern Australia.}, journal = {Molecular ecology}, volume = {10}, number = {1}, pages = {113-125}, doi = {10.1046/j.1365-294x.2001.01175.x}, pmid = {11251792}, issn = {0962-1083}, mesh = {Animals ; Australia ; Base Sequence ; DNA, Mitochondrial/analysis/*genetics ; Decapoda/*genetics ; Electron Transport Complex IV/*genetics ; Gene Frequency ; *Genetic Variation ; Haplotypes/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {The freshwater shrimp, Caridina zebra, is endemic to montane rainforest streams of the Atherton Tableland, north-eastern Australia. As the confluences of many of the headwater streams are in unsuitable habitat, dispersal is expected to be highly restricted. Results from a previous allozyme survey for this species suggested that historical dispersal between separate river drainages had occurred due to rearrangements of the drainage lines at some stage in the recent past. The aim of this study was to use temporal information from the mitochondrial cytochrome oxidase subunit I (CO-I) gene to determine whether the observed genetic structure was a result of historical processes, or alternatively, due to low levels of terrestrial dispersal. The mitochondrial DNA (mtDNA) data were analysed using nested clade analysis, which can differentiate between historical fragmentation and range expansion vs. contemporary restricted gene flow. The results displayed three divergent clades that were likely to have arisen in allopatry. One widespread clade, with individuals in more than one river drainage, reflected a pattern of restricted gene flow. This suggests that this species is capable of terrestrial dispersal.}, }
@article {pmid11250078, year = {2001}, author = {Ohtsu, K and Nakazono, M and Tsutsumi, N and Hirai, A}, title = {Characterization and expression of the genes for cytochrome c oxidase subunit VIb (COX6b) from rice and Arabidopsis thaliana.}, journal = {Gene}, volume = {264}, number = {2}, pages = {233-239}, doi = {10.1016/s0378-1119(01)00334-1}, pmid = {11250078}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Arabidopsis/enzymology/*genetics ; Blotting, Northern ; Blotting, Southern ; DNA, Complementary/chemistry/genetics ; DNA, Plant/chemistry/genetics ; Electron Transport Complex IV/*genetics ; Exons ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Genes, Plant/genetics ; Introns ; Isoenzymes/genetics ; Molecular Sequence Data ; Oryza/enzymology/*genetics ; Phylogeny ; RNA, Messenger/genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Tissue Distribution ; }, abstract = {Many of the subunits of cytochrome c oxidase (COX) in the mitochondria of higher plants are encoded by nuclear genes. These genes are less characterized compared to mitochondrial-encoded genes. We previously isolated a cDNA encoding COX6b (designated OsCOX6b1 in this study) from the rice nuclear genome and analyzed its expression. The deduced protein had an extended N-terminus compared with human and yeast COX6b proteins. In this study, we identified another COX6b gene (OsCOX6b2) in rice and revealed that it was actually expressed. The deduced protein of this gene did not have an extended N-terminus and had about the same size as the human and yeast proteins. Genomic Southern hybridization analysis revealed that there was at least one OsCOX6b-homologus sequences in the rice genome other than OsCOX6b1 and OsCOX6b2. Furthermore, we identified three COX6b genes in a dicotyledonous plant, Arabidopsis thaliana. One of these genes (AtCOX6b1) was relatively long, with a length similar to that of OsCOX6b1, and the other two (AtCOX6b2 and AtCOX6b3) were shorter, with lengths similar to the length of OsCOX6b2. Genomic Southern hybridization analysis indicated there were no additional COX6b genes in the Arabidopsis genome. The coding regions of OsCOX6b1 and AtCOX6b1 were separated by four introns and those of OsCOX6b2, AtCOX6b2 and AtCOX6b3 were separated by three introns. A Northern hybridization analysis showed that OsCOX6b1, AtCOX6b1 and AtCOX6b3 were expressed in all organs examined, although with some differences in the amount of expression among the organs. OsCOX6b2 and AtCOX6b2 were strongly expressed in roots but most of the transcripts of AtCOX6b2 were degraded. The evolution of COX6b genes from rice and Arabidopsis is discussed.}, }
@article {pmid11245219, year = {2000}, author = {Hosoda, T and Suzuki, H and Harada, M and Tsuchiya, K and Han, SH and Zhang, Y and Kryukov, AP and Lin, LK}, title = {Evolutionary trends of the mitochondrial lineage differentiation in species of genera Martes and Mustela.}, journal = {Genes &amp; genetic systems}, volume = {75}, number = {5}, pages = {259-267}, doi = {10.1266/ggs.75.259}, pmid = {11245219}, issn = {1341-7568}, mesh = {Animals ; Carnivora/*genetics ; Cytochrome b Group/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; }, abstract = {We compared partial sequences (402 bp) of the mitochondrial cytochrome b gene in 68 individuals of martens (Martes), weasels (Mustela) and their relatives from the Northern Hemisphere to identify the modes of geographic differentiation in each species. We then compared complete sequences (1140 bp) of the gene in 17 species of the family Mustelidae to know the spatial and temporal modes of speciation, constructing linearized trees with transversional substitutions for deeper lineage divergences and with transversions and transitions for younger lineages. Our data suggested that these lineages of Martes and Mustela differentiated in a stepwise fashion with five radiation stages from the generic divergences (stage I) to the intraspecific divergences (stage V), during the last 10 or 20 million years as the fossil evidence suggests. In the lineage of Martes, the first offshoots are of Martes flavigula, M. pennanti, and Gulo gulo (stage II), the second is M. foina (stage III), and the third are M. americana, M. martes, M. melampus, and M. zibellina (stage IV). The divergence of the lineages of Mustela is likely to have taken place concurrently with the radiations of the Martes. These divergence processes are attributable in part to the geographic allocation along the two continents, North America and Eurasia, as well as among peripheral insular domains, such as Taiwan and the Japanese Islands. In addition, the Eurasian continent itself was shown to have been involved in the species diversification in the martens and weasels.}, }
@article {pmid11236273, year = {2000}, author = {Conte, VP}, title = {[Chronic viral hepatitis C. Part 1. General considerations].}, journal = {Arquivos de gastroenterologia}, volume = {37}, number = {3}, pages = {187-194}, doi = {10.1590/s0004-28032000000300010}, pmid = {11236273}, issn = {0004-2803}, mesh = {Hepacivirus/isolation &amp; purification/pathogenicity ; Hepatitis C, Chronic/*virology ; Humans ; }, abstract = {Hepatitis C virus was identified in 1989 as the main causative agent of non-A, non-B and was followed by the recognition of a high prevalence of hepatitis C virus infection after transfusion of infected blood or blood products and in association with intravenous drug abuse. The availability of sensitive and reliable techniques to screen blood for hepatitis C virus has reduced the incidence of post-transfusion hepatitis. True healthy carriers of hepatitis C virus did not exist. Approximately 95% of hepatitis C virus infected individuals can be identified by third generation anti-hepatitis C virus testing. Retrospective studies of iatrogenic hepatitis C virus infection are the main source of the natural history of the disease. The distribution of different hepatitis C virus genotypes varies according to the geographic region. In South America, Europe, The United States and Japan hepatitis C virus genotypes 1, 2 and 3 account for the majority of the infections, being (sub)type 1b the most prevalent. Epidemiological parameters (age, risk factors and duration of infection) may be associated with hepatitis C virus genotypes (intravenous drug abuse with types 1-a and 3-a and 1-b with post-transfusion hepatitic C). Subtype 1-b, lead to a more severe course of viral infection, with ultrastructural alterations of the mitochondria, and greater impairment of the process of oxidative phosphorylation. No increased production of free radicals may influence the evolution of the liver disease by an enhancement of the cytopathic effect of hepatitis C virus. The clinical significance of intrahepatic hepatitis C virus level in patients with chronic hepatitis C virus infection is not determined by host factors (age of patient, mode or duration of infection) or by virus factors (hepatitis C virus genotypes) and, repeatedly negative RT-PCR for hepatitis C virus RNA in serum does not indicate absence of hepatitis C virus from the liver. The association between autoimmunity and hepatitis C virus is questioned. Markers of its does occur with high frequency in these patients. Modulation of immune responses to hepatitis C virus envelope E2 protein following injection of plasmid DNA, has been used for induction of specific response to hepatitis C virus. The spectrum of such responses could likely be broadened by combining plasmids, delivery routes, and other forms of encoded immunogens (peptide vaccines). These may be important to the development of a vaccine against the high mutable hepatitis C virus. The pathogenic role of novel DNA virus (TTV) is under spotlight. As with hepatitis G, however, the association of TTV with disease is far from clear.}, }
@article {pmid11231339, year = {2001}, author = {Tzen, CY and Tsai, JD and Wu, TY and Chen, BF and Chen, ML and Lin, SP and Chen, SC}, title = {Tubulointerstitial nephritis associated with a novel mitochondrial point mutation.}, journal = {Kidney international}, volume = {59}, number = {3}, pages = {846-854}, doi = {10.1046/j.1523-1755.2001.059003846.x}, pmid = {11231339}, issn = {0085-2538}, mesh = {Animals ; Base Sequence/genetics ; Biological Evolution ; Child, Preschool ; Conserved Sequence/genetics ; DNA, Mitochondrial/metabolism ; Humans ; Kidney/metabolism/pathology ; Male ; Microscopy, Electron ; Mitochondria/*genetics ; Molecular Sequence Data ; Nephritis, Interstitial/*genetics/pathology ; *Point Mutation ; RNA, Transfer, Phe/genetics ; Reference Values ; }, abstract = {BACKGROUND: Nephropathy caused by mitochondrial disorders is a relatively newly recognized disease. Only a few cases have been reported in the literature, and most of them are proximal tubulopathy-presenting Fanconi syndrome. Here we report on a novel mutation in two familial cases of tubulointerstitial nephropathy associated with concentrating defect.<br><br>METHODS: Renal biopsy specimens were examined by light microscopy and electron microscopy. Mitochondrial genomic DNA isolated from renal biopsy specimens was amplified by polymerase chain reaction (PCR) and sequenced in its entirety. The DNA sequences were analyzed by (1) comparing with the Anderson et al's mitochondrial sequences; (2) comparing with DNA sequences obtained from 97 human controls, including both healthy individuals and patients with renal diseases; and (3) comparing with the counterparts in 90 different species.<br><br>RESULTS: Dismorphic mitochondria with occasional intramitochondrial inclusions were found in the renal tubular epithelial cells. A novel mitochondrial point mutation was identified at the position 608, that is, the distal end of the anticodon stem of the tRNA(Phe) molecule. The A to G substitution at this position was not observed in 97 human controls and was found to be highly conserved in evolution.<br><br>CONCLUSIONS: We have identified an A608G mutation of mitochondrial genome in two cases whose presentation include tubulointerstitial nephritis and stroke.}, }
@article {pmid11231122, year = {2001}, author = {Lozupone, CA and Knight, RD and Landweber, LF}, title = {The molecular basis of nuclear genetic code change in ciliates.}, journal = {Current biology : CB}, volume = {11}, number = {2}, pages = {65-74}, doi = {10.1016/s0960-9822(01)00028-8}, pmid = {11231122}, issn = {0960-9822}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Ciliophora/*genetics ; Codon, Terminator ; DNA Primers ; *Genetic Code ; Molecular Sequence Data ; Peptide Termination Factors/*genetics ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {BACKGROUND: The nuclear genetic code has changed in several lineages of ciliates. These changes, UAR to glutamine and UGA to cysteine, imply that eukaryotic release factor 1 (eRF1), the protein that recognizes stop codons and terminates translation, changes specificity. Here we test whether changes in eRF1 drive genetic code evolution.<br><br>RESULTS: Database sequence analysis reveals numerous genetic code alterations in ciliates, including UGA --> tryptophan in Blepharisma americanum and the distantly related Colpoda. We sequenced eRF1 from four ciliates: B. americanum, a heterotrich that independently derived the same eRF1 specificity as Euplotes, and three spirotrichs, Stylonychia lemnae, S. mytilus, and Oxytricha trifallax, that independently derived the same genetic code as Tetrahymena (UAR --> glutamine). Distantly related ciliates with similar codes show characteristic changes in eRF1. We used a sliding window analysis to test associations between changes in specific eRF1 residues and changes in the genetic code. The regions of eRF1 that display convergent substitutions are identical to those identified in a recently reported nonsense suppression mutant screen in yeast.<br><br>CONCLUSIONS: Genetic code change by stop codon reassignment is surprisingly frequent in ciliates, with UGA --> tryptophan occurring twice independently. This is the first description of this code, previously found only in bacteria and mitochondria, in a eukaryotic nuclear genome. eRF1 has evolved strikingly convergently in lineages with variant genetic codes. The strong concordance with biochemical data indicates that our methodology may be generally useful for detecting molecular determinants of biochemical changes in evolution.}, }
@article {pmid11226586, year = {2001}, author = {Rujan, T and Martin, W}, title = {How many genes in Arabidopsis come from cyanobacteria? An estimate from 386 protein phylogenies.}, journal = {Trends in genetics : TIG}, volume = {17}, number = {3}, pages = {113-120}, doi = {10.1016/s0168-9525(00)02209-5}, pmid = {11226586}, issn = {0168-9525}, mesh = {Arabidopsis/*genetics ; Cyanobacteria/*genetics ; *Genes, Bacterial ; *Genes, Plant ; *Phylogeny ; }, abstract = {It is well known that chloroplasts and mitochondria donated many genes to nuclear chromosomes during evolution - but how many is "many"? A sample of 3961 Arabidopsis nuclear protein-coding genes was compared with the complete set of proteins from yeast and 17 reference prokaryotic genomes, including one cyanobacterium (the lineage from which plastids arose). The analysis of 386 phylogenetic trees distilled from these data suggests that between approximately 400 (1.6%) and approximately 2200 (9.2%) of Arabidopsis nuclear genes stem from cyanobacteria. The degree of conservation preserved in protein sequences in addition to lateral gene transfer between free-living prokaryotes pose substantial challenges to genome phylogenetics.}, }
@article {pmid11212890, year = {2000}, author = {Beech, PL and Landweber, LF and Gilson, PR}, title = {Meeting report: XIIIth meeting of the International Society for Evolutionary Protistology, Ceské Budejovice, Czech Republic, July 31-August 4, 2000.}, journal = {Protist}, volume = {151}, number = {4}, pages = {299-305}, doi = {10.1078/S1434-4610(04)70028-0}, pmid = {11212890}, issn = {1434-4610}, support = {GM59708/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Chloroplasts/physiology ; Ciliophora/physiology ; *Energy Metabolism ; Euglenida/physiology ; Eukaryota/*physiology ; Eukaryotic Cells/*physiology ; Microsporidia/physiology ; Mitochondria/metabolism ; Organelles/metabolism ; Trypanosoma/physiology ; }, }
@article {pmid11203236, year = {2000}, author = {Moreira, D and Rodríguez-Valera, F}, title = {A mitochondrial origin for eukaryotic C2H2 zinc finger regulators?.}, journal = {Trends in microbiology}, volume = {8}, number = {10}, pages = {448-450}, doi = {10.1016/s0966-842x(00)01850-3}, pmid = {11203236}, issn = {0966-842X}, mesh = {Bacteria/*genetics ; *Eukaryotic Cells ; Gene Expression Regulation ; *Gene Transfer, Horizontal ; Mitochondria/*genetics ; Phylogeny ; Proteins/chemistry/*genetics ; *Zinc Fingers ; }, }
@article {pmid11199398, year = {2000}, author = {Lam, E and del Pozo, O}, title = {Caspase-like protease involvement in the control of plant cell death.}, journal = {Plant molecular biology}, volume = {44}, number = {3}, pages = {417-428}, pmid = {11199398}, issn = {0167-4412}, mesh = {*Apoptosis ; Caspases/*physiology ; Plant Cells ; Plants/*enzymology ; Signal Transduction ; }, abstract = {Cell death as a highly regulated process has now been recognized to be an important, if not essential, pathway that is ubiquitous in all multicellular eukaryotes. In addition to playing key roles in the morphogenesis and sculpting of the organs to give rise to highly specialized forms and shapes, cell death also participates in the programmed creation of specialized cell types for essential functions such as the selection of B cells in the immune system of mammals and the formation of tracheids in the xylem of vascular plants. Studies of apoptosis, the most well-characterized form of animal programmed cell death, have culminated in the identification of a central tripartite death switch the enzymatic component of which is a conserved family of cysteine proteases called caspases. Studies in invertebrates and other animal models suggest that caspases are conserved regulators of apoptotic cell death in all metazoans. In plant systems, the identities of the main executioners that orchestrate cell death remain elusive. Recent evidence from inhibitor studies and biochemical approaches suggests that caspase-like proteases may also be involved in cell death control in higher plants. Furthermore, the mitochondrion and reactive oxygen species may well constitute a common pathway for cell death activation in both animal and plant cells. Cloning of plant caspase-like proteases and elucidation of the mechanisms through which mitochondria may regulate cell death in both systems should shed light on the evolution of cell death control in eukaryotes and may help to identify essential components that are highly conserved in eukaryotes.}, }
@article {pmid11198014, year = {2000}, author = {van der Kuyl, AC and van Gennep, DR and Dekker, JT and Goudsmit, J}, title = {Routine DNA analysis based on 12S rRNA gene sequencing as a tool in the management of captive primates.}, journal = {Journal of medical primatology}, volume = {29}, number = {5}, pages = {309-317}, pmid = {11198014}, issn = {0047-2565}, mesh = {Animal Husbandry ; Animals ; Animals, Zoo ; Cercopithecidae/*genetics ; *Classification ; Mitochondria/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal ; Sequence Analysis, DNA ; }, abstract = {Automated DNA sequencing of a fragment of the relatively slowly evolving mitochondrial 12S rRNA gene was used to distinguish primate species, and the method was compared with species determination based upon classical taxonomy. DNA from blood from 53 monkeys housed at the Stichting AAP Shelter for Exotic Animals, all Old World monkeys, was amplified by polymerase chain reaction (PCR) with a primer set spanning approximately 390 nucleotides of the mitochondrial 12S rRNA gene. The products were directly sequenced and compared with our database of primate 12S sequences. Many individuals were found to harbor a 12S sequence identical to one of the reference sequences. For others, phylogenetic methods were used for species estimation, which was especially informative in Cercopithecus species.}, }
@article {pmid11195343, year = {2000}, author = {Chiang, TY}, title = {Lineage sorting accounting for the disassociation between chloroplast and mitochondrial lineages in oaks of southern France.}, journal = {Genome}, volume = {43}, number = {6}, pages = {1090-1094}, pmid = {11195343}, issn = {0831-2796}, mesh = {Chloroplasts/*genetics ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; France ; Haplotypes ; Mitochondria/*genetics ; Models, Genetic ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Recombination, Genetic ; Rosales/*genetics ; }, abstract = {Dumolin-Lapégue et al. (Mol. Biol. Evol. 15: 1321-1331. 1998) suggested that recurrent inversions of a 4-bp sequence of the mtDNA nad4-1/2 locus due to intramolecular recombination were responsible for the disassociation of chloroplast and mitochondrial genomes of French oaks. Based on their PCR-RFLP (PCR-restriction fragment length polymorphism) data obtained from three noncoding spacers, a minimum spanning network representing the phylogeny of the cpDNA was reconstructed. The mapping of alleles b and c of the mtDNA nad4-1/2 locus on the cpDNA network revealed a nonrandom distribution, which contradicted the expected patterns when repeated, and ongoing inversions had been occurring. The fact that polymorphisms (a mixed c + d type) were mostly restricted to the interior nodes of the network, which represented ancient haplotypes and geographically coincided with probable glacial refugia in southern Europe, agreed with a migrant-pool model. Evidence of a widespread pattern of polymorphism distribution indicated that mtDNA haplotypes were likely to be more ancient than the cpDNA haplotypes. Lineage sorting, due to relative age of cpDNA vs. mtDNA, plus the specific migratory mode, which recruited colonists from a random sample of resource populations during glacial expansion (thereby extending the lineage sorting period, LSP), may have resulted in the disassociation of chloroplast and mitochondrial genomes in oaks.}, }
@article {pmid11194567, year = {1999}, author = {von Heijne, G}, title = {Recent advances in the understanding of membrane protein assembly and structure.}, journal = {Quarterly reviews of biophysics}, volume = {32}, number = {4}, pages = {285-307}, doi = {10.1017/s0033583500003541}, pmid = {11194567}, issn = {0033-5835}, mesh = {Animals ; Bacterial Proteins/metabolism ; Biological Evolution ; Biophysical Phenomena ; Biophysics ; Endoplasmic Reticulum/metabolism ; Escherichia coli/metabolism ; Genome ; Membrane Proteins/*chemistry/genetics/*metabolism ; Mitochondria/metabolism ; Protein Structure, Secondary ; }, }
@article {pmid11175788, year = {2001}, author = {Johnson, KR and Zheng, QY and Bykhovskaya, Y and Spirina, O and Fischel-Ghodsian, N}, title = {A nuclear-mitochondrial DNA interaction affecting hearing impairment in mice.}, journal = {Nature genetics}, volume = {27}, number = {2}, pages = {191-194}, pmid = {11175788}, issn = {1061-4036}, support = {R01 DC004301-01/DC/NIDCD NIH HHS/United States ; R01 DC005827/DC/NIDCD NIH HHS/United States ; R01 DC001402/DC/NIDCD NIH HHS/United States ; R01 DC005827-01/DC/NIDCD NIH HHS/United States ; R03 DC004376-01A1/DC/NIDCD NIH HHS/United States ; R01 DC004092-01/DC/NIDCD NIH HHS/United States ; R01 DC001402-07/DC/NIDCD NIH HHS/United States ; R01 DC004301/DC/NIDCD NIH HHS/United States ; }, mesh = {Age Factors ; Animals ; Base Sequence ; Cell Nucleus/*genetics ; Crosses, Genetic ; DNA, Mitochondrial/*genetics ; Deafness/*genetics ; Evoked Potentials, Auditory/genetics ; Evolution, Molecular ; Mice ; Mice, Inbred Strains ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Point Mutation ; RNA, Transfer, Arg/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {The pathophysiologic pathways and clinical expression of mitochondrial DNA (mtDNA) mutations are not well understood. This is mainly the result of the heteroplasmic nature of most pathogenic mtDNA mutations and of the absence of clinically relevant animal models with mtDNA mutations. mtDNA mutations predisposing to hearing impairment in humans are generally homoplasmic, yet some individuals with these mutations have severe hearing loss, whereas their maternal relatives with the identical mtDNA mutation have normal hearing. Epidemiologic, biochemical and genetic data indicate that nuclear genes are often the main determinants of these differences in phenotype. To identify a mouse model for maternally inherited hearing loss, we screened reciprocal backcrosses of three inbred mouse strains, A/J, NOD/LtJ and SKH2/J, with age-related hearing loss (AHL). In the (A/J x CAST/Ei) x A/J backcross, mtDNA derived from the A/J strain exerted a significant detrimental effect on hearing when compared with mtDNA from the CAST/Ei strain. This effect was not seen in the (NOD/LtJ x CAST/Ei) x NOD/LtJ and (SKH2/J x CAST/Ei) x SKH2/J backcrosses. Genotyping revealed that this effect was seen only in mice homozygous for the A/J allele at the Ahl locus on mouse chromosome 10. Sequencing of the mitochondrial genome in the three inbred strains revealed a single nucleotide insertion in the tRNA-Arg gene (mt-Tr) as the probable mediator of the mitochondrial effect. This is the first mouse model with a naturally occurring mtDNA mutation affecting a clinical phenotype, and it provides an experimental model to dissect the pathophysiologic processes connecting mtDNA mutations to hearing loss.}, }
@article {pmid11175755, year = {2001}, author = {Horiike, T and Hamada, K and Kanaya, S and Shinozawa, T}, title = {Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis.}, journal = {Nature cell biology}, volume = {3}, number = {2}, pages = {210-214}, doi = {10.1038/35055129}, pmid = {11175755}, issn = {1465-7392}, mesh = {Archaea/*genetics/physiology ; Bacteria/*genetics ; Bacterial Physiological Phenomena ; Cell Nucleus/*genetics/physiology ; DNA/genetics ; Databases, Factual ; *Evolution, Molecular ; Models, Biological ; Open Reading Frames/*genetics ; Sequence Homology ; *Symbiosis ; Yeasts/*genetics/physiology ; }, abstract = {The origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria was proposed on the basis of the phylogenetic topologies of genes. However, it was not possible to conclude whether or not the genes involved were authentic representative genes. Furthermore, using the BLAST and FASTA programs, the similarity of open reading frame (ORF) groups between three domains (Eukarya, Archaea and Bacteria) was estimated at one threshold. Therefore, their similarities at other thresholds could not be clarified. Here we use our newly developed 'homology-hit analysis' method, which uses multiple thresholds, to determine the origin of the nucleus. We removed mitochondria-related ORFs from yeast ORFs, and determined the number of yeast orthologous ORFs in each functional category to the ORFs in six Archaea and nine Bacteria at several thresholds (E-values) using the BLAST. Our results indicate that yeast ORFs related to the nucleus may share their origins with archaeal ORFs, whereas ORFs that are related to the cytoplasm may share their origins with bacterial ORFs. Our results thus strongly support the idea of nucleus symbiosis.}, }
@article {pmid11169765, year = {2001}, author = {Liu, L and Zhou, J and Pesacreta, TC}, title = {Maize myosins: diversity, localization, and function.}, journal = {Cell motility and the cytoskeleton}, volume = {48}, number = {2}, pages = {130-148}, doi = {10.1002/1097-0169(200102)48:2&lt;130::AID-CM1004&gt;3.0.CO;2-Y}, pmid = {11169765}, issn = {0886-1544}, mesh = {Amino Acid Sequence ; Blotting, Northern ; Blotting, Southern ; Cell Membrane/chemistry/physiology ; Cloning, Molecular ; Cytoskeleton/*chemistry/metabolism ; DNA Probes ; DNA, Plant/analysis ; DNA-Binding Proteins/genetics ; Gene Expression Regulation, Plant ; Gene Library ; Genetic Testing ; Genetic Variation ; Immunohistochemistry ; MADS Domain Proteins ; Molecular Sequence Data ; Myosins/*analysis/*genetics/metabolism ; Phylogeny ; Plant Proteins ; Plant Roots/chemistry/physiology ; Polymerase Chain Reaction ; RNA, Messenger/analysis ; RNA, Plant/analysis ; Transcription Factors/genetics ; Zea mays/*genetics ; }, abstract = {This first analysis of monocotyledon myosin genes showed that at least five genes, one of which was probably spliced to yield two isoforms, were expressed in maize (Zea mays L.). The complete coding sequence of ZMM1 was determined, as were most of the sequences of two other myosin cDNAs (ZMM2 and ZMM3). ZMM1 and ZMM2 belonged to myosin class XI while ZMM3 was in class VIII. ZMM1 was abundantly expressed in leaves, roots, coleoptiles, and stems. ZMM3 showed a similar distribution but was expressed poorly in pollen. ZMM2 was predominantly expressed in seeds and may be part of a suite of cytoskeletal proteins in reproductive tissues. Phylogenetic analysis suggested that the origin of myosin classes VIII and XI predated that of angiosperms. Immunofluorescence studies using M11L1, a myosin XI antibody specific for the exposed loop 1 head region of myosin, indicated that myosin XI occurred in the cytoplasm of all root tip cells. The highest concentration of myosin XI was in the differentiating epidermal cells. In dividing cells, myosin XI was present near the cytokinetic apparatus at approximately the same concentration seen in other portions of the cytoplasm. Western blot analysis of subcellular fractions indicated that myosin XI was concentrated in mitochondria and low-density membranes.}, }
@article {pmid11165515, year = {2001}, author = {Gabriel, K and Buchanan, SK and Lithgow, T}, title = {The alpha and the beta: protein translocation across mitochondrial and plastid outer membranes.}, journal = {Trends in biochemical sciences}, volume = {26}, number = {1}, pages = {36-40}, doi = {10.1016/s0968-0004(00)01684-4}, pmid = {11165515}, issn = {0968-0004}, mesh = {Bacterial Proteins/chemistry/metabolism ; *Escherichia coli Proteins ; Intracellular Membranes/metabolism ; Membrane Proteins/*chemistry/*metabolism ; *Membrane Transport Proteins ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins ; *Plant Proteins ; Plastids/*metabolism ; Porins/metabolism ; Protein Conformation ; Protein Precursors/metabolism ; Protein Transport ; SEC Translocation Channels ; *Saccharomyces cerevisiae Proteins ; Voltage-Dependent Anion Channels ; }, abstract = {In the evolution of mitochondria and plastids from endosymbiotic bacteria, most of the proteins that make up these organelles have become encoded by nuclear genes and must therefore be transported across the organellar membranes, following synthesis in the cytosol. The core component of the protein translocation machines in both the mitochondrial and plastid outer membranes appears to be a beta-barrel protein, perhaps a relic from their bacterial ancestry, distinguishing these translocases from the alpha-helical-based protein translocation pores found in all other eukaryotic membranes.}, }
@article {pmid11164276, year = {2001}, author = {Wegiel, J and Wang, KC and Imaki, H and Rubenstein, R and Wronska, A and Osuchowski, M and Lipinski, WJ and Walker, LC and LeVine, H}, title = {The role of microglial cells and astrocytes in fibrillar plaque evolution in transgenic APP(SW) mice.}, journal = {Neurobiology of aging}, volume = {22}, number = {1}, pages = {49-61}, doi = {10.1016/s0197-4580(00)00181-0}, pmid = {11164276}, issn = {0197-4580}, mesh = {Alzheimer Disease/metabolism/pathology ; Amyloid beta-Peptides/*metabolism ; Amyloid beta-Protein Precursor/genetics/*metabolism ; Amyloidosis/metabolism/*pathology ; Animals ; Astrocytes/metabolism/*pathology ; Humans ; Hypertrophy/metabolism/pathology ; Mice ; Mice, Transgenic ; Microglia/metabolism/*pathology ; Microscopy, Electron ; Peptide Fragments/*metabolism ; Plaque, Amyloid/metabolism/*pathology ; Synapses/metabolism/*pathology ; }, abstract = {Ultrastructural reconstruction of 27 fibrillar plaques in different stages of formation and maturation was undertaken to characterize the development of fibrillar plaques in the brains of human APP(SW) transgenic mice (Tg2576). The study suggests that microglial cells are not engaged in Abeta removal and plaque degradation, but in contrast, are a driving force in plaque formation and development. Fibrillar Abeta deposition at the amyloid pole of microglial cells appears to initiate three types of neuropil response: degeneration of neurons, protective activation of astrocytes, and attraction and activation of microglial cells sustaining plaque growth. Enlargement of neuronal processes and synapses with accumulation of degenerated mitochondria, dense bodies, and Hirano-type bodies is the marker of toxic injury of neurons by fibrillar Abeta. Separation of amyloid cores from neurons and degradation of amyloid cores by cytoplasmic processes of hypertrophic astrocytes suggest the protective and defensive character of astrocytic response to fibrillar Abeta. The growth of cored plaque from a small plaque with one microglial cell with an amyloid star and a few dystrophic neurites to a large plaque formed by several dozen microglial cells seen in old mice is the effect of attraction and activation of microglial cells residing outside of the plaque perimeter. This mechanism of growth of plaques appears to be characteristic of cored plaques in transgenic mice. Other features in mouse microglial cells that are absent in human brain are clusters of vacuoles, probably of lysosomal origin. They evolve into circular cisternae and finally into large vacuoles filled with osmiophilic, amorphous material and bundles of fibrils that are poorly labeled with antibody to Abeta. Microglial cells appear to release large amounts of fibrillar Abeta and accumulate traces of fibrillar Abeta in a lysosomal pathway.}, }
@article {pmid11164046, year = {2000}, author = {Saccone, C and Gissi, C and Lanave, C and Larizza, A and Pesole, G and Reyes, A}, title = {Evolution of the mitochondrial genetic system: an overview.}, journal = {Gene}, volume = {261}, number = {1}, pages = {153-159}, doi = {10.1016/s0378-1119(00)00484-4}, pmid = {11164046}, issn = {0378-1119}, mesh = {Animals ; Codon/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genetic Variation ; Humans ; Mammals/genetics ; }, abstract = {Mitochondria, semi-autonomous organelles possessing their own genetic system, are commonly accepted to descend from free-living eubacteria, namely hydrogen-producing alpha-proteobacteria. The progressive loss of genes from the primitive eubacterium to the nucleus of the eukaryotic cell is strongly justified by the Muller rachet principle, which postulates that asexual genomes, like mitochondrial ones, accumulate deleterious and sublethal mutations faster than sexual genomes, like the nucleus. According to this principle, the mitochondrial genome would be doomed to death; instead, we observe that the mitochondrial genome has a variable size and structure in the different organisms, though it contains more or less the same set of genes. This is an example of genetic conservation versus structural diversity. From an evolutionary point of view the genetic system of organelles is clearly under strong selective pressure and for its survival it needs to utilize strategies to slow down or halt the ratchet. Anyway, the mitochondrial genome changes with time, and the rate of evolution is different for both diverse regions of the mtDNA and between lineages, as demonstrated in the case of mammalian mt genomes. We report here our data on the evolution of the mitochondrial DNA in mammals which demonstrate the suitability of mtDNA as a molecular tool for evolutionary analyses.}, }
@article {pmid11161756, year = {2001}, author = {Maus, C and Peschke, K and Dobler, S}, title = {Phylogeny of the genus Aleochara inferred from mitochondrial cytochrome oxidase sequences (Coleoptera: Staphylinidae).}, journal = {Molecular phylogenetics and evolution}, volume = {18}, number = {2}, pages = {202-216}, doi = {10.1006/mpev.2000.0874}, pmid = {11161756}, issn = {1055-7903}, mesh = {Animals ; Coleoptera/*classification/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Likelihood Functions ; Mitochondria/*enzymology ; Models, Genetic ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {The phylogeny of the genus Aleochara was previously poorly understood due to difficulties with phylogenetic reconstruction by morphological characters. We present here a phylogeny based on the sequences of a 2022-bp fragment of the COI/II genes; 50 Aleochara and 10 outgroup species were included in the analysis. We used parsimony, minimum-evolution, and maximum-likelihood analyses to infer the phylogeny of the group. Our data do not support the commonly assumed sister group relationship between Aleocharini and Hoplandriini. Aleochara is resolved as a monophylum, although A. clavicornis might not belong to the genus. Within Aleochara, there are two large monophyletic clades. Many of the existing subgenera are shown to be para- or polyphyletic; others are likely to be monophyletic. Tinotus morion, previously assigned to the Hoplandriini, is strongly supported as belonging to Aleochara. According to our data, the mesosternal carina that has been used as an important character for classification has arisen and been reduced independently in several clades within Aleochara.}, }
@article {pmid11161748, year = {2001}, author = {Beckert, S and Muhle, H and Pruchner, D and Knoop, V}, title = {The mitochondrial nad2 gene as a novel marker locus for phylogenetic analysis of early land plants: a comparative analysis in mosses.}, journal = {Molecular phylogenetics and evolution}, volume = {18}, number = {1}, pages = {117-126}, doi = {10.1006/mpev.2000.0868}, pmid = {11161748}, issn = {1055-7903}, mesh = {Bryopsida/*classification/*genetics ; Evolution, Molecular ; Introns ; Mitochondria/*enzymology ; *Mitochondrial Proteins ; Models, Genetic ; NADH Dehydrogenase/*genetics/metabolism ; Phylogeny ; Plant Proteins/genetics ; RNA Editing ; Sequence Analysis, DNA ; }, abstract = {The mitochondrial nad2 gene is established as a novel marker locus for phylogenetic analyses among early land plants. The potential of this gene for phylogenetic resolution was checked with a broad taxon sampling of 42 mosses (Bryopsida, including the enigmatic genus Takakia) to allow both a comparative analysis with the recently explored nad5 gene and the fusion of independent data sets. The mitochondrial gene sequences provide valuable phylogenetic information on the relationships of classically defined orders and their respective monophylies. The more rapidly diverging sequences of a group I intron in nad5 and of a group II intron in nad2 add information for fine resolution. Although both genes provide phylogenetic information in the same taxonomic range (above family level), the combined sequence alignment results in an approximate doubling in the number of nodes with significant bootstrap support (>90). According to our data, Buxbaumiales are a paraphyletic taxon in a key position between the earliest branching taxa (Sphagnales, Takakiales, Andreaeales, Polytrichales, and Tetraphidales) and all other orders, possibly to be placed in the subclass Bryidae. A dichotomy in the latter recalls two previously suggested superorders Hypnanae and Dicrananae. Both genes independently question the monophyly of the orders Dicranales and Neckerales and reject the inclusion of the genera Schistostega, Timmia, and Encalypta among Eubryales.}, }
@article {pmid11161741, year = {2001}, author = {Söller, R and Wohltmann, A and Witte, H and Blohm, D}, title = {Phylogenetic relationships within terrestrial mites (Acari: Prostigmata, Parasitengona) inferred from comparative DNA sequence analysis of the mitochondrial cytochrome oxidase subunit I gene.}, journal = {Molecular phylogenetics and evolution}, volume = {18}, number = {1}, pages = {47-53}, doi = {10.1006/mpev.2000.0855}, pmid = {11161741}, issn = {1055-7903}, mesh = {Animals ; Codon ; Electron Transport Complex IV/*genetics ; Likelihood Functions ; Mites/*classification/*genetics ; Mitochondria/*enzymology ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Partial DNA and amino acid sequences translated from the mitochondrial cytochrome subunit I gene (408 bp) of 17 mite species have been used for analyzing the phylogenetic relationships within the terrestrial Parasitengona (Trombidia). Due to mutational saturation of the third codon position, only first and second codon positions and amino acid sequences were analyzed, applying neighbor-joining, maximum-parsimony, and maximum-likelihood tree-building methods. The reconstructed trees revealed similar topologies of taxa; however, the phylogenetic relationships could be convincingly resolved only within several trombidioid taxa. The proposed basic relationships within the Parasitengona, in particular those of Calyptostomatoidea, Smarididae, and Erythraeidae, were poorly supported in bootstrap tests. A comparison of the presented gene tree with a phylogenetic tree based upon traditional characters revealed only few contradictions in nodes only weakly supported by morphological data. The most astonishing result is the proposed early derivative position of Microtrombidiidae within the terrestrial Parasitengona.}, }
@article {pmid11158381, year = {2001}, author = {Buckley, TR and Simon, C and Shimodaira, H and Chambers, GK}, title = {Evaluating hypotheses on the origin and evolution of the New Zealand alpine cicadas (Maoricicada) using multiple-comparison tests of tree topology.}, journal = {Molecular biology and evolution}, volume = {18}, number = {2}, pages = {223-234}, doi = {10.1093/oxfordjournals.molbev.a003796}, pmid = {11158381}, issn = {0737-4038}, mesh = {Animals ; DNA Primers/chemistry ; Electron Transport Complex IV/*genetics ; *Evolution, Molecular ; Genetic Variation/*genetics ; Hemiptera/classification/enzymology/*genetics ; Invertebrates/*classification/enzymology/genetics ; Mitochondria/*enzymology ; New Zealand ; Phylogeny ; Polymerase Chain Reaction ; Sequence Alignment ; Species Specificity ; }, abstract = {The statistical testing of alternative phylogenetic trees is central to evaluating competing evolutionary hypotheses. Fleming proposed that the New Zealand cicada species Maoricicada iolanthe is the sister species to the major radiation of both low-altitude and montane Maoricicada species. However, using 1,520 bp of mitochondrial DNA sequence data from the cytochrome oxidase subunit I, tRNA aspartic acid, and the ATPase subunit 6 and 8 genes, we inferred that both M. iolanthe and another low-altitude species, Maoricicada campbelli, are nested within the montane Maoricicada radiation. Therefore, we examined the stability of the inferred phylogenetic placement of these two species using the newly developed Shimodaira-Hasegawa test (SH test) implemented in a maximum-likelihood framework. The SH test has two advantages over the more commonly used Kishino-Hasegawa (KH) and Templeton tests. First, the SH test simultaneously compares multiple topologies and corrects the corresponding P: values to accommodate the multiplicity of testing. Second, the SH test is correct when applied to a posteriori hypotheses, unlike the KH test, because it readjusts the expectation of the null hypothesis (that two trees are not different) accordingly. The comparison of P: values estimated under the assumptions of both the KH test and the SH test clearly demonstrate that the KH test has the potential to be misleading when the issue of comparing of a posteriori hypotheses is ignored and when multiple comparisons are not taken into account. The SH test, in combination with a variety of character-weighting schemes applied to our data, reveals a surprising amount of ambiguity in the phylogenetic placement of M. iolanthe and M. campbelli.}, }
@article {pmid11156972, year = {2001}, author = {Funk, DJ and Wernegreen, JJ and Moran, NA}, title = {Intraspecific variation in symbiont genomes: bottlenecks and the aphid-buchnera association.}, journal = {Genetics}, volume = {157}, number = {2}, pages = {477-489}, pmid = {11156972}, issn = {0016-6731}, mesh = {Alleles ; Animals ; Aphids/*genetics ; Buchnera/*genetics ; Chromosomes ; DNA/genetics ; Evolution, Molecular ; *Genetic Variation ; *Genome ; Haplotypes ; Mitochondria/metabolism ; Models, Genetic ; Mutation ; Phylogeny ; Polymorphism, Genetic ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Buchnera are maternally transmitted bacterial endosymbionts that synthesize amino acids that are limiting in the diet of their aphid hosts. Previous studies demonstrated accelerated sequence evolution in Buchnera compared to free-living bacteria, especially for nonsynonymous substitutions. Two mechanisms may explain this acceleration: relaxed purifying selection and increased fixation of slightly deleterious alleles under drift. Here, we test the divergent predictions of these hypotheses for intraspecific polymorphism using Buchnera associated with natural populations of the ragweed aphid, Uroleucon ambrosiae. Contrary to expectations under relaxed selection, U. ambrosiae from across the United States yielded strikingly low sequence diversity at three Buchnera loci (dnaN, trpBC, trpEG), revealing polymorphism three orders of magnitude lower than in enteric bacteria. An excess of nonsynonymous polymorphism and of rare alleles was also observed. Local sampling of additional dnaN sequences revealed similar patterns of polymorphism and no evidence of food plant-associated genetic structure. Aphid mitochondrial sequences further suggested that host bottlenecks and large-scale dispersal may contribute to genetic homogenization of aphids and symbionts. Together, our results support reduced N(e) as a primary cause of accelerated sequence evolution in Buchnera. However, our study cannot rule out the possibility that mechanisms other than bottlenecks also contribute to reduced N(e) at aphid and endosymbiont loci.}, }
@article {pmid11139291, year = {2001}, author = {Marín, I and Fares, MA and González-Candelas, F and Barrio, E and Moya, A}, title = {Detecting changes in the functional constraints of paralogous genes.}, journal = {Journal of molecular evolution}, volume = {52}, number = {1}, pages = {17-28}, doi = {10.1007/s002390010130}, pmid = {11139291}, issn = {0022-2844}, mesh = {Adenosine Triphosphatases/chemistry/*genetics ; Amino Acid Sequence ; Archaeal Proteins/chemistry/*genetics ; Bacterial Proteins/chemistry/*genetics ; *Evolution, Molecular ; Mitochondria/physiology ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Tertiary ; *Protein Subunits ; Proton-Translocating ATPases/chemistry/genetics ; Sequence Alignment ; Sequence Analysis, DNA/*methods ; *Vacuolar Proton-Translocating ATPases ; }, abstract = {We describe a new procedure to determine whether regional alterations in the evolutionary constraints imposed on paralogous proteins have occurred. We used as models the A and B (alternatively called alpha and beta) subunits of V/F/A-ATPases, originated by a gene duplication more than 3 billion years ago. Changes associated to three major splits (eubacteria versus Archaea-eukaryotes; Archaea versus eukaryotes; and among free-living bacteria and symbiotic mitochondria) were studied. Only in the first case, when we compared eubacterial or mitochondrial F-ATPases versus eukaryotic vacuolar V-ATPases or archaeal A-ATPases, constraint changes were observed. Modifications in the degree of regional constraining were not detected for the other two types of comparisons (V-ATPases versus A-ATPases and within F-ATPases, respectively). When the rates of evolution of the two subunits were compared, it was found that F-ATPases regulatory subunits evolved faster than catalytic subunits, but the opposite was true for A- and V-ATPases. Our results suggest that, even for universal and essential proteins, selective constraints may be occasionally altered. On the other hand, in some cases no changes were detected after periods of more than 2.2 billion years.}, }
@article {pmid11155936, year = {2000}, author = {McDonnell, A and Love, S and Tait, A and Lichtenfels, JR and Matthews, JB}, title = {Phylogenetic analysis of partial mitochondrial cytochrome oxidase c subunit I and large ribosomal RNA sequences and nuclear internal transcribed spacer I sequences from species of Cyathostominae and Strongylinae (Nematoda, Order Strongylida), parasites of the horse.}, journal = {Parasitology}, volume = {121 Pt 6}, number = {}, pages = {649-659}, doi = {10.1017/s003118200000696x}, pmid = {11155936}, issn = {0031-1820}, mesh = {Animals ; DNA, Helminth/*chemistry ; DNA, Ribosomal Spacer/*chemistry ; Electron Transport Complex IV/*genetics ; Horse Diseases/*parasitology ; Horses ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/*chemistry ; Strongylida/*classification/genetics ; Strongylida Infections/parasitology/*veterinary ; }, abstract = {Three nucleotide data sets, one nuclear (ITS-2) and two mitochondrial (COI and l-rRNA), have been investigated in order to determine relationships among species of Strongylinae and Cyathostominae, intestinal parasites of the horse. The data exhibited a strong mutational bias towards A and T and in the COI gene, silent sites appeared to saturate rapidly partly due to this substitution bias. Thus, the COI gene was found to be less phylogenetically informative than the l-rRNA and ITS-2 genes. Combined analysis of the l-rRNA and ITS-2 genes supported a monophyletic clade of the cyathostomes with Tridentoinfundibulum gobi, which had previously been classified as a nematode of' uncertain origin'. The Strongylinae grouped consistently outside the clade containing the cyathostomes and T. gobi. Molecular analysis failed to provide strong evidence for the separation of cyathostomes into classical genera, as previously defined by morphological classification.}, }
@article {pmid11147969, year = {2000}, author = {Gianguzza, F and Ragusa, MA and Roccheri, MC and Di Liegro, I and Rinaldi, AM}, title = {Isolation and characterization of a Paracentrotus lividus cDNA encoding a stress-inducible chaperonin.}, journal = {Cell stress &amp; chaperones}, volume = {5}, number = {2}, pages = {87-89}, pmid = {11147969}, issn = {1355-8145}, mesh = {Amino Acid Sequence ; Animals ; Chaperonin 60/*genetics/metabolism ; DNA, Complementary/genetics ; Embryo, Nonmammalian/metabolism ; Heat-Shock Response ; Mitochondria/genetics ; Molecular Sequence Data ; RNA, Messenger/metabolism ; Sea Urchins/*genetics/metabolism ; }, abstract = {Chaperonins are ubiquitous proteins that facilitate protein folding in an adenosine triphosphate-dependent manner. Here we report the isolation of a sea urchin cDNA (Plhsp60) coding for mitochondrial chaperonin (Cpn60), whose basal expression is further enhanced by heat shock. The described cDNA corresponds to a full-length mRNA encoding a protein of 582 amino acids, the first 32 of which constitute a putative mitochondrial targeting leader sequence. Comparative analysis has demonstrated that this protein is highly conserved in evolution.}, }
@article {pmid11141193, year = {2001}, author = {Scouras, A and Smith, MJ}, title = {A novel mitochondrial gene order in the crinoid echinoderm Florometra serratissima.}, journal = {Molecular biology and evolution}, volume = {18}, number = {1}, pages = {61-73}, doi = {10.1093/oxfordjournals.molbev.a003720}, pmid = {11141193}, issn = {0737-4038}, mesh = {Animals ; Base Composition ; DNA, Mitochondrial/*genetics ; Echinodermata/*genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Gene Rearrangement ; Genetic Code ; Likelihood Functions ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Species Specificity ; }, abstract = {The complete nucleotide sequence of the mitochondrial genome of the crinoid Florometra serratissima has been determined. It is a circular DNA molecule, 16,005 bp in length, containing the genes for 13 proteins, small and large ribosomal RNAs, and 22 transfer RNAs (tRNAs). Three regions of unassigned sequence (UAS) greater than 73 bp have been located. The largest, UAS I, is 432 bp long and exhibits sequence similarity to the putative mitochondrial control regions seen in other animals. UAS II (77 bp) and UAS III (73 bp) are located between the 5' ends of coding sequences and may play roles as bidirectional promoters. Analyses of nucleotide composition revealed that the major peptide-encoding strand is high in T and low in C. This bias is reflected in a specific pattern of codon usage. Molecular phylogenetic analyses based on cytochrome c oxidase (COI, COII, and COIII) amino acid and nucleotide sequences did not resolve all the relationships between echinoderm classes. The overall animal mitochondrial gene content has been maintained in the crinoid, but there is extensive rearrangement with respect to both the echinoid and the asteroid mtDNA gene maps. Florometra serratissima has a novel genome organization in a segment containing most of the tRNA genes, large and small rRNA genes, and the NADH dehydrogenase subunit 1 and 2 genes. Potential pathways and mechanisms for gene rearrangements between mitochondrial gene maps of echinoderm classes and vertebrates are discussed as indicators of early deuterostome phylogeny.}, }
@article {pmid11141190, year = {2001}, author = {Misof, B and Rickert, AM and Buckley, TR and Fleck, G and Sauer, KP}, title = {Phylogenetic signal and its decay in mitochondrial SSU and LSU rRNA gene fragments of Anisoptera.}, journal = {Molecular biology and evolution}, volume = {18}, number = {1}, pages = {27-37}, doi = {10.1093/oxfordjournals.molbev.a003717}, pmid = {11141190}, issn = {0737-4038}, mesh = {Animals ; Base Composition ; *Genes, Insect ; Insecta/classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; }, abstract = {The phylogeny of Anisoptera, dragonflies in the strict sense, has proven to be notoriously difficult to resolve. Based on morphological characters, several recent publications dealing with the phylogeny of dragonflies proposed contradicting inter- and intrafamily relationships. We explored phylogenetic information content of mitochondrial large-subunit (LSU) and small-subunit (SSU) ribosomal gene fragments for these systematic problems. Starting at published universal primers, we developed primer sets suitable for amplifying large parts of the LSU and SSU rRNA genes within dragonflies. These fragments turned out to harbor sufficient phylogenetic information to satisfyingly resolve intrafamily relationships, but they contain insufficient phylogenetic structure to permit reliable conclusions about several interfamily relationships. We demonstrate that decay of phylogenetic signal progresses from intrafamily to interfamily to outgroup relationships and is correlated with an increase of genetic distances. As expected, signal decay is most pronounced in fast-changing sites. Additionally, base composition among fast-changing sites significantly deviates from the expected homogeneity. Homogeneity of base composition among all included taxa was restored only after removing fast-changing sites from the data set. The molecular data tentatively support interfamily relationships proposed by the most recent publication based on morphological characters of fossil and extant dragonflies.}, }
@article {pmid11137175, year = {2000}, author = {Brown, JK}, title = {Molecular markers for the identification and global tracking of whitefly vector-Begomovirus complexes.}, journal = {Virus research}, volume = {71}, number = {1-2}, pages = {233-260}, doi = {10.1016/s0168-1702(00)00221-5}, pmid = {11137175}, issn = {0168-1702}, mesh = {Amino Acid Sequence ; Animals ; Capsid/genetics ; Geminiviridae/classification/*genetics ; Genes, Insect ; Genes, Viral ; Genetic Markers ; Genetic Variation ; Geography ; Hemiptera/*genetics/virology ; Insect Vectors/genetics ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Plant Diseases/*virology ; Sequence Alignment ; Species Specificity ; Virus Replication/genetics ; }, abstract = {Recent unprecedented upsurges in populations of the whitefly Bemisia tabaci (Genn.) have drawn much attention to its worldwide importance as an insect pest and as the vector of emergent begomoviruses (Family: Geminiviridae; Genus: Begomovirus). Several begomoviruses that are considered 'new' and others previously regarded as minor pathogens have been linked to recent epidemics. Recent studies have revealed much variation in begomoviruses, despite the view that DNA-containing viruses do not rapidly accumulate mutations. Also, certain B. tabaci 'variants' are known that more effectively or selectively transmit certain begomoviruses and exhibit biotic differences that may influence their spread. Patterns of distribution and dissemination of begomoviruses transmitted by B. tabaci are poorly understood because standardized molecular-based tracking methods have not been available. Understanding virus/whitefly vector/host plant interrelationships in the context of emerging problems can be achieved only by linking predicted evolutionary histories with epidemiology using molecular phylogenetic approaches. Identification and validation of informative molecular sequences are essential initial steps in this process. Genus-wide degenerate polymerase chain reaction (PCR) primers have been developed to amplify and sequence the 'core' region of the coat protein open reading frame (ORF) (V1), permitting 'universal' detection and provisional virus identification by comparisons with described viral genotypes. In subsequent studies reported here, several potentially informative viral ORFs and a non-coding region are explored. Of particular use for expanding diversity studies are group- or virus-specific sequences that can be targeted by utilizing newly available core CP sequences, or additional conserved regions around which broad spectrum primers can be designed to target variable sequences in key ORFs or non-coding regions. Prospective markers under exploration were selected with a basis in the most highly conserved viral ORFs, CP (V1) and a portion of replication-associated protein (REP) (L1/C1), and a key non-coding sequence that contain sufficient variability and/or virus-specific sequences, and are consequently of potential epidemiological relevance. Because B. tabaci occurs as a cryptic species, or species complex, that exhibits biotic polymorphism, yet morphological invariance, traditional morphologically based identification is impossible. An overriding complication to establishing molecular markers for identifying whitefly vector variants is that whitefly sequences in general, have not been available. However, recent work has shown that a partial mitochondria cytochrome oxidase I (mt COI) sequence separates vector variants with a basis in geographical origin, suggesting it is useful for further exploring variability and the phylogenetic history of whiteflies on a large scale. Here, the utility of whitefly mt COI nucleotides (nt) sequences is illustrated for inferring relationships between B. tabaci collected from major world regions. Used collectively, these approaches permit investigations of the patterns of distribution and dissemination of begomovirus-whitefly vector complexes for the first time. Ultimately, more immediate recognition of exotic viruses and whitefly vectors and early detection of upsurges in vector populations and of emerging viruses will be possible.}, }
@article {pmid11133195, year = {2000}, author = {Leys, R and Cooper, SJ and Schwarz, MP}, title = {Molecular phylogeny of the large carpenter bees, genus Xylocopa (Hymenoptera: apidae), based on mitochondrial DNA sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {17}, number = {3}, pages = {407-418}, doi = {10.1006/mpev.2000.0851}, pmid = {11133195}, issn = {1055-7903}, mesh = {Animals ; Base Composition ; Bees/*classification/enzymology/*genetics ; Calibration ; Classification ; Codon/genetics ; Cytochrome b Group/genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Genetic Variation/genetics ; Geography ; Likelihood Functions ; Mitochondria/enzymology/genetics ; Models, Biological ; Mutation/genetics ; *Phylogeny ; }, abstract = {Carpenter bees, genus Xylocopa Latreille, a group of bees found on all continents, are of particular interest to behavioral ecologists because of their utility for studies of the evolution of mating strategies and sociality. This paper presents phylogenetic analyses based on sequences of two mitochondrial genes cytochrome oxidase 1 and cytochrome b for 22 subgenera of Xylocopa. Maximum-parsimony and maximum-likelihood methods were used to infer phylogenetic relationships. The analyses resulted in three resolved clades of subgenera: a South American group (including the subgenera Stenoxylocopa, Megaxylocopa, and Neoxylocopa), a group including the subgenera Xylocopa s.s. and Ctenoxylocopa, and an Ethiopean group (including the subgenera Afroxylocopa, Mesotrichia, Alloxylocopa, Platynopoda, Hoploxylocopa, and Koptortosoma). The relationships between the 11 other subgenera and the resolved clades are unclear. Within the Ethiopian group we found a clear separation of the African and the Oriental taxa and apparent polyphyly of the subgenus Koptortosoma. Using an evolutionary rate for ants, we investigated whether Gondwana vicariance or more recent dispersal events could best explain the present-day distribution of subgenera. Although some taxa show divergences that approach Gondwanan breakup times, most divergences between geographic groups are too recent to support a vicariance hypothesis.}, }
@article {pmid11130711, year = {2000}, author = {, }, title = {Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.}, journal = {Nature}, volume = {408}, number = {6814}, pages = {796-815}, doi = {10.1038/35048692}, pmid = {11130711}, issn = {0028-0836}, mesh = {Animals ; Arabidopsis/cytology/*genetics/growth &amp; development/physiology ; Biological Transport ; Cell Membrane/metabolism ; Cell Nucleus/genetics ; Centromere ; Chloroplasts/genetics ; Chromosome Mapping ; DNA Repair ; DNA Transposable Elements ; DNA, Plant ; DNA, Ribosomal ; Gene Duplication ; Gene Expression Regulation, Plant ; *Genome, Plant ; Humans ; Light ; Mitochondria/genetics ; Photosynthesis ; Plant Diseases ; Proteome ; Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; Sequence Analysis, DNA ; Signal Transduction ; Species Specificity ; Telomere ; }, abstract = {The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.}, }
@article {pmid11130070, year = {2000}, author = {Ingman, M and Kaessmann, H and Pääbo, S and Gyllensten, U}, title = {Mitochondrial genome variation and the origin of modern humans.}, journal = {Nature}, volume = {408}, number = {6813}, pages = {708-713}, doi = {10.1038/35047064}, pmid = {11130070}, issn = {0028-0836}, mesh = {Africa ; Animals ; *DNA, Mitochondrial ; *Evolution, Molecular ; *Genetic Variation ; Genome ; Humans ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; X Chromosome ; }, abstract = {The analysis of mitochondrial DNA (mtDNA) has been a potent tool in our understanding of human evolution, owing to characteristics such as high copy number, apparent lack of recombination, high substitution rate and maternal mode of inheritance. However, almost all studies of human evolution based on mtDNA sequencing have been confined to the control region, which constitutes less than 7% of the mitochondrial genome. These studies are complicated by the extreme variation in substitution rate between sites, and the consequence of parallel mutations causing difficulties in the estimation of genetic distance and making phylogenetic inferences questionable. Most comprehensive studies of the human mitochondrial molecule have been carried out through restriction-fragment length polymorphism analysis, providing data that are ill suited to estimations of mutation rate and therefore the timing of evolutionary events. Here, to improve the information obtained from the mitochondrial molecule for studies of human evolution, we describe the global mtDNA diversity in humans based on analyses of the complete mtDNA sequence of 53 humans of diverse origins. Our mtDNA data, in comparison with those of a parallel study of the Xq13.3 region in the same individuals, provide a concurrent view on human evolution with respect to the age of modern humans.}, }
@article {pmid11129049, year = {2000}, author = {Takahara, M and Takahashi, H and Matsunaga, S and Miyagishima, S and Takano, H and Sakai, A and Kawano, S and Kuroiwa, T}, title = {A putative mitochondrial ftsZ gene is present in the unicellular primitive red alga Cyanidioschyzon merolae.}, journal = {Molecular &amp; general genetics : MGG}, volume = {264}, number = {4}, pages = {452-460}, doi = {10.1007/s004380000307}, pmid = {11129049}, issn = {0026-8925}, mesh = {Amino Acid Sequence ; Animals ; Antibodies/isolation &amp; purification ; Arabidopsis Proteins ; Base Sequence ; Chromosome Mapping ; Cloning, Molecular ; DNA Primers/genetics ; Gene Expression ; *Genes, Plant ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics/metabolism ; Plasmids/genetics ; Rhodophyta/*genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Two ftsZ homologues were isolated from the unicellular primitive red alga Cyanidioschyzon merolae (CmftsZ1 and CmftsZ2). Phylogenetic analysis revealed that CmftsZ1 is most closely related to the ftsZ genes of alpha-Proteobacteria, suggesting that it is a mitochondrial-type ftsZ gene, whereas CmftsZ2 is most closely related to the ftsZ genes of cyanobacteria, suggesting that it is a plastid-type ftsZ gene. Southern analysis indicates that CmftsZ1 and CmftsZ2 are both single-copy genes located on chromosome XIV in the C. merolae genome. Northern analysis revealed that both CmftsZ1 and CmftsZ2 are transcribed, and accumulate specifically before cell and organelle division. The results of Western analysis suggest that CmFtsZ1 is localized in mitochondria.}, }
@article {pmid11127902, year = {2000}, author = {Eyre-Walker, A}, title = {Do mitochondria recombine in humans?.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {355}, number = {1403}, pages = {1573-1580}, pmid = {11127902}, issn = {0962-8436}, mesh = {Animals ; *DNA, Mitochondrial ; Humans ; Linkage Disequilibrium ; Mitochondria ; *Recombination, Genetic ; }, abstract = {Until very recently, mitochondria were thought to be clonally inherited through the maternal line in most higher animals. However, three papers published in 2000 claimed population-genetic evidence of recombination in human mitochondrial DNA. Here I review the current state of the debate. I review the evidence for the two main pathways by which recombination might occur: through paternal leakage and via a mitochondrial DNA sequence in the nuclear genome. There is no strong evidence for either pathway, although paternal leakage seems a definite possibility. However, the population-genetic evidence, although not conclusive, is strongly suggestive of recombination in mitochondrial DNA. The implications of non-clonality for our understanding of human and mitochondrial evolution are discussed.}, }
@article {pmid11125891, year = {2000}, author = {Gérard, Y and Maulin, L and Yazdanpanah, Y and De La Tribonnière, X and Amiel, C and Maurage, CA and Robin, S and Sablonnière, B and Dhennain, C and Mouton, Y}, title = {Symptomatic hyperlactataemia: an emerging complication of antiretroviral therapy.}, journal = {AIDS (London, England)}, volume = {14}, number = {17}, pages = {2723-2730}, doi = {10.1097/00002030-200012010-00012}, pmid = {11125891}, issn = {0269-9370}, mesh = {Acidosis, Lactic/blood/*chemically induced/complications/physiopathology ; Adult ; Aged ; Anti-HIV Agents/*adverse effects/pharmacology/*therapeutic use ; Antiretroviral Therapy, Highly Active ; CD4 Lymphocyte Count ; Cell Respiration/drug effects ; Female ; HIV Infections/blood/complications/*drug therapy/virology ; Humans ; Lactic Acid/blood/metabolism ; Liver/drug effects/metabolism/pathology ; Male ; Middle Aged ; Mitochondria, Muscle/drug effects/metabolism/pathology/ultrastructure ; Muscles/drug effects/metabolism/pathology/ultrastructure ; Viral Load ; }, abstract = {BACKGROUND: Fatal lactic acidosis is a serious complication of therapy with nucleoside analogues.<br><br>OBJECTIVE: To examine symptomatic hyperlactataemia in HIV-infected adults treated with antiretroviral drugs.<br><br>METHODS: In this prospective study, arterial blood lactate levels were measured in patients presenting with unexplained clinical symptoms. When these levels were high, functional respiratory tests (FRT) were carried out. Liver or muscle biopsies were further proposed. Incidences were calculated by comparison with the entire cohort of patients treated in the department.<br><br>RESULTS: Fourteen HIV-infected adults treated with antiretroviral drugs were identified with symptomatic hyperlactataemia during a 2-year period follow-up study. The incidence of hyperlactataemia was 0.8% per year but reached 1.2% if only patients treated with a regimen including stavudine were considered. Clinical symptoms included abnormal fatigue, tachycardia, abdominal pain, weight loss, peripheral neuropathy, and more specifically exercise-induced dyspnoea occurring despite effective antiretroviral treatment. FRT showed a metabolic deviation towards anaerobiosis with a high lactate/pyruvate ratio. Ultrastructural mitochondrial abnormalities were seen in all four patients for whom this was examined. There was a marked decrease in complex IV activity in muscle biopsies from four of five patients, consistent with a mitochondrial dysfunction. Evolution was favourable in 13 patients, probably because of an early diagnosis.<br><br>CONCLUSIONS: Potentially fatal adverse events occurring during antiretroviral treatment may be avoided by close monitoring of clinical signs and blood lactate levels. If other studies confirm that the cumulative long-term toxicity of antiretroviral drugs results from mitochondrial dysfunction, the incidence of hyperlactataemia and its clinical consequences may become more important.}, }
@article {pmid11122242, year = {2000}, author = {Moretti, S and Marcellini, S and Boschini, A and Famularo, G and Santini, G and Alesse, E and Steinberg, SM and Cifone, MG and Kroemer, G and De Simone, C}, title = {Apoptosis and apoptosis-associated perturbations of peripheral blood lymphocytes during HIV infection: comparison between AIDS patients and asymptomatic long-term non-progressors.}, journal = {Clinical and experimental immunology}, volume = {122}, number = {3}, pages = {364-373}, pmid = {11122242}, issn = {0009-9104}, mesh = {Acquired Immunodeficiency Syndrome/blood/*immunology/physiopathology/virology ; Adult ; Apoptosis/*immunology ; CD4-Positive T-Lymphocytes/cytology/*immunology ; CD8-Positive T-Lymphocytes/cytology/*immunology ; Cells, Cultured ; Fas Ligand Protein ; Female ; *HIV Long-Term Survivors ; Humans ; Leukocytes, Mononuclear/cytology/immunology ; Male ; Membrane Glycoproteins/*biosynthesis ; Membrane Potentials ; Mitochondria/physiology ; Reactive Oxygen Species/metabolism ; fas Receptor/*biosynthesis ; }, abstract = {This study was designed to compare the degree of lymphocyte apoptosis and Fas-Fas ligand (FasL) expression in AIDS patients and long-term non-progressors (LTNPs) and correlate these parameters with apoptosis-associated perturbations in lymphocyte function. LTNPs had a lower frequency of apoptotic CD4+ and CD8+ T cells compared with subjects with AIDS. This correlated with a lower frequency of cells expressing Fas and FasL. The frequency of selected lymphocyte populations exhibiting a disrupted mitochondrial transmembrane potential (DeltaPsim) and increased superoxide generation was lower in LTNPs than in patients with AIDS; these abnormalities were associated with lower levels of caspase-1 activation in LTNPs. The results indicate a significantly reduced level of apoptosis and apoptosis-associated parameters in LTNPs than in patients developing AIDS. Based on these findings, a crucial role for mitochondria can be predicted in the process of lymphocyte apoptosis during the evolution of AIDS.}, }
@article {pmid11121736, year = {2000}, author = {Schneider, A and Maréchal-Drouard, L}, title = {Mitochondrial tRNA import: are there distinct mechanisms?.}, journal = {Trends in cell biology}, volume = {10}, number = {12}, pages = {509-513}, doi = {10.1016/s0962-8924(00)01854-7}, pmid = {11121736}, issn = {0962-8924}, mesh = {Animals ; Biological Transport ; Cell Nucleus/genetics/metabolism ; Humans ; Mitochondria/*genetics/metabolism ; Models, Biological ; Nucleic Acid Conformation ; Phylogeny ; RNA/genetics/*metabolism ; RNA, Mitochondrial ; RNA, Transfer/genetics/*metabolism ; }, abstract = {Sequence information from an increasing number of complete mitochondrial genomes indicates that a large number of evolutionary distinct organisms import nucleus-encoded tRNAs. In the past five years, much research has been initiated on the features of imported tRNAs, the mechanism and the energetics of the process as well as on the components of the import machinery. In summary, these studies show that the import systems of different species exhibit some unique features, suggesting that more than one mechanism might exist to import tRNAs.}, }
@article {pmid11115380, year = {2001}, author = {Elson, JL and Andrews, RM and Chinnery, PF and Lightowlers, RN and Turnbull, DM and Howell, N}, title = {Analysis of European mtDNAs for recombination.}, journal = {American journal of human genetics}, volume = {68}, number = {1}, pages = {145-153}, pmid = {11115380}, issn = {0002-9297}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Africa ; DNA, Mitochondrial/*genetics ; Databases as Topic ; Europe ; *Evolution, Molecular ; Haplotypes/genetics ; Humans ; Linkage Disequilibrium/genetics ; Mitochondria/*genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Recombination, Genetic/*genetics ; Reproducibility of Results ; Sensitivity and Specificity ; }, abstract = {The standard paradigm postulates that the human mitochondrial genome (mtDNA) is strictly maternally inherited and that, consequently, mtDNA lineages are clonal. As a result of mtDNA clonality, phylogenetic and population genetic analyses should therefore be free of the complexities imposed by biparental recombination. The use of mtDNA in analyses of human molecular evolution is contingent, in fact, on clonality, which is also a condition that is critical both for forensic studies and for understanding the transmission of pathogenic mtDNA mutations within families. This paradigm, however, has been challenged recently by Eyre-Walker and colleagues. Using two different tests, they have concluded that recombination has contributed to the distribution of mtDNA polymorphisms within the human population. We have assembled a database that comprises the complete sequences of 64 European and 2 African mtDNAs. When this set of sequences was analyzed using any of three measures of linkage disequilibrium, one of the tests of Eyre-Walker and colleagues, there was no evidence for mtDNA recombination. When their test for excess homoplasies was applied to our set of sequences, only a slight excess of homoplasies was observed. We discuss possible reasons that our results differ from those of Eyre-Walker and colleagues. When we take the various results together, our conclusion is that mtDNA recombination has not been sufficiently frequent during human evolution to overturn the standard paradigm.}, }
@article {pmid11114722, year = {2000}, author = {Cizeau, J and Ray, R and Chen, G and Gietz, RD and Greenberg, AH}, title = {The C. elegans orthologue ceBNIP3 interacts with CED-9 and CED-3 but kills through a BH3- and caspase-independent mechanism.}, journal = {Oncogene}, volume = {19}, number = {48}, pages = {5453-5463}, doi = {10.1038/sj.onc.1203929}, pmid = {11114722}, issn = {0950-9232}, mesh = {Amino Acid Chloromethyl Ketones/chemistry ; Amino Acid Sequence ; Animals ; Apoptosis/drug effects/*physiology ; Apoptosis Regulatory Proteins ; *Caenorhabditis elegans Proteins ; Carrier Proteins/genetics/metabolism/*physiology ; Caspase Inhibitors ; Caspases/*physiology ; Cell Line ; Conserved Sequence ; Cysteine Endopeptidases/metabolism/*physiology ; Cysteine Proteinase Inhibitors/pharmacology ; Dimerization ; Gene Expression Regulation ; Helminth Proteins/metabolism/*physiology ; Humans ; Membrane Proteins/genetics/metabolism/physiology ; Mice ; Molecular Sequence Data ; Multienzyme Complexes/physiology ; Protein Structure, Tertiary ; Proto-Oncogene Proteins/metabolism/*physiology ; Proto-Oncogene Proteins c-bcl-2/metabolism/*physiology ; Sequence Homology, Amino Acid ; Subcellular Fractions/metabolism ; *Tumor Suppressor Proteins ; bcl-X Protein ; }, abstract = {We have studied ceBNIP3, the orthologue of BNIP3 in C. elegans. Sequence analysis reveals that the different domains of BNIP3 have been conserved throughout evolution. ceBNIP3 contains a C-terminal transmembrane (TM) domain, a conserved domain (CD) of 19 amino acids, a BCL-2 homology-3 (BH3)-like domain and a PEST sequence. ceBNIP3 is expressed primarily as a 25 kDa monomer and a 50 kDa homodimer. After transfection, ceBNIP3 protein is rapidly degraded through a ubiquitin-dependent pathway by the proteasome. Like BNIP3, the TM domain of ceBNIP3 mediates the localization of the protein to mitochondria and is also necessary for homodimerization and cell death in mammalian cells. Neither the putative BH3 domain nor conserved domain is necessary for killing. ceBNIP3 protein interacts with CED-9 and BCL-XL, but unlike other pro-apoptotic BCL-2 family members, the BH3-like domain does not participate in dimerization. The ceBNIP3 TM domain mediates interaction with both CED-9 and BCL-XL. ceBNIP3 interacts with CED-3 but co-expression of CED-3 and ceBNIP3 does not significantly enhance induction of cell death in the presence or absence of CED-4. ceBNIP3 kills mammalian cells by a caspase-independent mechanism. In conclusion, we find that although ceBNIP3 interacts with CED-9 and CED-3 it kills by a BH3- and caspase-independent mechanism.}, }
@article {pmid11104819, year = {2000}, author = {Kurland, CG and Andersson, SG}, title = {Origin and evolution of the mitochondrial proteome.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {64}, number = {4}, pages = {786-820}, pmid = {11104819}, issn = {1092-2172}, mesh = {Alphaproteobacteria/genetics ; *Biological Evolution ; Energy Metabolism ; Eukaryotic Cells ; *Mitochondria/genetics ; Models, Biological ; *Proteome ; Saccharomyces cerevisiae/physiology ; Symbiosis ; }, abstract = {The endosymbiotic theory for the origin of mitochondria requires substantial modification. The three identifiable ancestral sources to the proteome of mitochondria are proteins descended from the ancestral alpha-proteobacteria symbiont, proteins with no homology to bacterial orthologs, and diverse proteins with bacterial affinities not derived from alpha-proteobacteria. Random mutations in the form of deletions large and small seem to have eliminated nonessential genes from the endosymbiont-mitochondrial genome lineages. This process, together with the transfer of genes from the endosymbiont-mitochondrial genome to nuclei, has led to a marked reduction in the size of mitochondrial genomes. All proteins of bacterial descent that are encoded by nuclear genes were probably transferred by the same mechanism, involving the disintegration of mitochondria or bacteria by the intracellular membranous vacuoles of cells to release nucleic acid fragments that transform the nuclear genome. This ongoing process has intermittently introduced bacterial genes to nuclear genomes. The genomes of the last common ancestor of all organisms, in particular of mitochondria, encoded cytochrome oxidase homologues. There are no phylogenetic indications either in the mitochondrial proteome or in the nuclear genomes that the initial or subsequent function of the ancestor to the mitochondria was anaerobic. In contrast, there are indications that relatively advanced eukaryotes adapted to anaerobiosis by dismantling their mitochondria and refitting them as hydrogenosomes. Accordingly, a continuous history of aerobic respiration seems to have been the fate of most mitochondrial lineages. The initial phases of this history may have involved aerobic respiration by the symbiont functioning as a scavenger of toxic oxygen. The transition to mitochondria capable of active ATP export to the host cell seems to have required recruitment of eukaryotic ATP transport proteins from the nucleus. The identity of the ancestral host of the alpha-proteobacterial endosymbiont is unclear, but there is no indication that it was an autotroph. There are no indications of a specific alpha-proteobacterial origin to genes for glycolysis. In the absence of data to the contrary, it is assumed that the ancestral host cell was a heterotroph.}, }
@article {pmid11101587, year = {2000}, author = {Yokoyama, K and Biswas, SK and Miyaji, M and Nishimura, K}, title = {Identification and phylogenetic relationship of the most common pathogenic Candida species inferred from mitochondrial cytochrome b gene sequences.}, journal = {Journal of clinical microbiology}, volume = {38}, number = {12}, pages = {4503-4510}, pmid = {11101587}, issn = {0095-1137}, mesh = {Amino Acid Sequence ; Base Sequence ; Candida/*classification/enzymology/genetics ; Cytochrome b Group/*genetics ; DNA, Fungal/*chemistry ; Humans ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; }, abstract = {We sequenced a 396-bp region of the mitochondrial cytochrome b gene of the most common clinically important Candida species: Candida albicans, C. glabrata, C. parapsilosis, C. tropicalis, C. krusei, and C. lusitaniae. The recently described species of Candida, C. dubliniensis, associated with mucosal candidiasis in human immunodeficiency virus-infected individuals, was also included. Two to five strains of each species were examined. Some species represented intraspecies variation, which was not more than 1.8% (DNA). However, interspecies variations were more than 10 and 7%, respectively, for DNA and amino acid sequences. Multiple alignments of nucleotide and deduced amino acid sequences revealed species-specific nucleotides and amino acids. Nucleotide- and amino acid-based phylogenetic trees were constructed and are discussed. Using the database, it is possible to identify presumptive Candida species within a working day.}, }
@article {pmid11099041, year = {2000}, author = {Adams, KL and Daley, DO and Qiu, YL and Whelan, J and Palmer, JD}, title = {Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants.}, journal = {Nature}, volume = {408}, number = {6810}, pages = {354-357}, doi = {10.1038/35042567}, pmid = {11099041}, issn = {0028-0836}, mesh = {Amino Acid Sequence ; Cell Nucleus/*genetics ; DNA, Mitochondrial ; DNA, Plant ; *Evolution, Molecular ; *Genes, Plant ; Magnoliopsida/classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics ; Polymerase Chain Reaction ; *Recombination, Genetic ; Ribosomal Proteins/genetics ; Sequence Homology, Amino Acid ; }, abstract = {A central component of the endosymbiotic theory for the bacterial origin of the mitochondrion is that many of its genes were transferred to the nucleus. Most of this transfer occurred early in mitochondrial evolution; functional transfer of mitochondrial genes has ceased in animals. Although mitochondrial gene transfer continues to occur in plants, no comprehensive study of the frequency and timing of transfers during plant evolution has been conducted. Here we report frequent loss (26 times) and transfer to the nucleus of the mitochondrial gene rps10 among 277 diverse angiosperms. Characterization of nuclear rps10 genes from 16 out of 26 loss lineages implies that many independent, RNA-mediated rps10 transfers occurred during recent angiosperm evolution; each of the genes may represent a separate functional gene transfer. Thus, rps10 has been transferred to the nucleus at a surprisingly high rate during angiosperm evolution. The structures of several nuclear rps10 genes reveal diverse mechanisms by which transferred genes become activated, including parasitism of pre-existing nuclear genes for mitochondrial or cytoplasmic proteins, and activation without gain of a mitochondrial targeting sequence.}, }
@article {pmid11099026, year = {2000}, author = {Gray, MW}, title = {Mitochondrial genes on the move.}, journal = {Nature}, volume = {408}, number = {6810}, pages = {302-3, 305}, doi = {10.1038/35042663}, pmid = {11099026}, issn = {0028-0836}, mesh = {Animals ; Cell Nucleus/genetics ; DNA, Mitochondrial ; Eukaryotic Cells ; *Evolution, Molecular ; Genes, Plant ; Genome, Bacterial ; Magnoliopsida/*genetics ; Mitochondria/*genetics ; Recombination, Genetic ; Ribosomal Proteins/genetics ; }, }
@article {pmid11095730, year = {2000}, author = {Lavrov, DV and Brown, WM and Boore, JL}, title = {A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {25}, pages = {13738-13742}, pmid = {11095730}, issn = {0027-8424}, mesh = {Animals ; Arthropods/*genetics ; Base Sequence ; Cloning, Molecular ; DNA Primers ; Evolution, Molecular ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Polymerase Chain Reaction ; *RNA Editing ; RNA, Transfer/chemistry/*genetics ; }, abstract = {We determined the complete mtDNA sequence of the centipede Lithobius forficatus and found that only one of the 22 inferred tRNA genes encodes a fully paired aminoacyl acceptor stem. The other 21 genes encode tRNAs with up to five mismatches in these stems, and some of these overlap extensively with the downstream genes. Because a well-paired acceptor stem is required for proper tRNA functioning, RNA editing in the products of these genes was suspected. We investigated this hypothesis by studying cDNA sequences from eight tRNAs and found the editing of up to 5 nt at their 3' ends. This editing appears to occur by a novel mechanism with the 5' end of the acceptor stem being used as a template for the de novo synthesis of the 3' end, presumably by an RNA-dependent RNA polymerase. In addition, unusual secondary structures for several tRNAs were found, including those lacking a TPsiC (T) or a dihydrouridine (D) arm, and having an unusual number of base pairs in the acceptor or anticodon stems.}, }
@article {pmid11094747, year = {2000}, author = {Filipenko, ML and Timofeeva, OA and Gusachenko, AM and Sergeev, MG and Vysotskaia, LV}, title = {[Reconstruction of phylogeny of locusts from the family Acrididae (Orthoptera) based on analysis of nucleotide sequences of 16S ribosome RNA gene in mitochondria].}, journal = {Genetika}, volume = {36}, number = {10}, pages = {1355-1361}, pmid = {11094747}, issn = {0016-6758}, mesh = {Animals ; Base Sequence ; Grasshoppers/classification/*genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {The sequences of two mitochondrial 16S RNA gene fragments (137- and 174-bp in size) were determined in nine grasshopper species belonging to three Acrididae subfamilies. Phylogenetic reconstruction was performed using the sequences of twelve grasshopper species and the cricket Acheta domesticus sequence as an outgroup (some data were purchased from the GeneBank Data Library (NCBI). In the phylogenetic tree, the Acridinae and Locustinae formed compact groups. Annexpected position of Celes scalozubovi (Locustinae) within the subfamily Acridinae indicated its vague phylogeny. The Catantopinae species lied close to the base of the Acridinae. Almost all branches of phylogenetic trees were strongly (55-100%) supported by bootstrap analysis.}, }
@article {pmid11091905, year = {2000}, author = {Wu, CH and Li, HP and Wang, YX and Zhang, YP}, title = {Low genetic variation of the Yunnan hare (Lepus comus G. Allen 1927) as revealed by mitochondrial cytochrome b gene sequences.}, journal = {Biochemical genetics}, volume = {38}, number = {5-6}, pages = {149-155}, pmid = {11091905}, issn = {0006-2928}, mesh = {Animals ; Body Constitution ; China ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Fossils ; Genetic Variation/*genetics ; Geography ; Haplotypes ; Lagomorpha/*genetics ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, }
@article {pmid11088007, year = {2000}, author = {Philippe, H and Germot, A and Moreira, D}, title = {The new phylogeny of eukaryotes.}, journal = {Current opinion in genetics &amp; development}, volume = {10}, number = {6}, pages = {596-601}, doi = {10.1016/s0959-437x(00)00137-4}, pmid = {11088007}, issn = {0959-437X}, mesh = {Animals ; Biomarkers ; *Evolution, Molecular ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; RNA, Ribosomal ; }, abstract = {Molecular phylogeny has been regarded as the ultimate tool for the reconstruction of relationships among eukaryotes-especially the different protist groups-given the difficulty in interpreting morphological data from an evolutionary point of view. In fact, the use of ribosomal RNA as a marker has provided the first well resolved eukaryotic phylogenies, leading to several important evolutionary hypotheses. The most significant is that several early-emerging, amitochondriate lineages, are living relics from the early times of eukaryotic evolution. The use of alternative protein markers and the recognition of several molecular phylogeny reconstruction artefacts, however, have strongly challenged these ideas. The putative early emerging lineages have been demonstrated as late-emerging ones, artefactually misplaced to the base of the tree. The present state of eukaryotic evolution is best described by a multifurcation, in agreement with the 'big bang' hypothesis that assumes a rapid diversification of the major eukaryotic phyla. For further resolution, the analysis of genomic data through improved phylogenetic methods will be required.}, }
@article {pmid11087829, year = {2000}, author = {Houman, F and Rho, SB and Zhang, J and Shen, X and Wang, CC and Schimmel, P and Martinis, SA}, title = {A prokaryote and human tRNA synthetase provide an essential RNA splicing function in yeast mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {25}, pages = {13743-13748}, pmid = {11087829}, issn = {0027-8424}, support = {R01 GM023562/GM/NIGMS NIH HHS/United States ; 1R431I36615//PHS HHS/United States ; GM23562/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Cloning, Molecular ; Genetic Complementation Test ; Humans ; Introns ; Leucine-tRNA Ligase/chemistry/genetics/*physiology ; Molecular Sequence Data ; Mycobacterium tuberculosis/enzymology/genetics ; RNA Splicing/*physiology ; Reverse Transcriptase Polymerase Chain Reaction ; Saccharomyces cerevisiae/enzymology/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {Mitochondrial leucyl-tRNA synthetase (LeuRS) in the yeast Saccharomyces cerevisiae provides two essential functions. In addition to aminoacylation, LeuRS functions in RNA splicing. The details of how it came to act in splicing are not known. Here we show that Mycobacterium tuberculosis and human mitochondrial LeuRSs can substitute in splicing for the S. cerevisiae mitochondrial LeuRS. Mutations of yeast mitochondrial LeuRS that had previously been shown to abolish splicing activity also eliminate splicing by the M. tuberculosis enzyme. These results suggest the role of LeuRS in splicing in yeast mitochondria results from features of the enzyme that are broadly conserved in evolution. These features are not likely to be designed for splicing per se, but instead have been adopted in yeast for that purpose.}, }
@article {pmid11080589, year = {2000}, author = {Choi, KR and Roh, K and Kim, J and Sim, W}, title = {Genomic cloning and characterization of mitochondrial elongation factor Tu (EF-Tu) gene (tufM) from maize (Zea mays L.).}, journal = {Gene}, volume = {257}, number = {2}, pages = {233-242}, doi = {10.1016/s0378-1119(00)00404-2}, pmid = {11080589}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Base Sequence ; Blotting, Southern ; Cloning, Molecular ; DNA, Plant/chemistry/*genetics/isolation &amp; purification ; Genes, Plant/*genetics ; Mitochondria/*chemistry ; Molecular Sequence Data ; Peptide Elongation Factor Tu/*genetics ; Phylogeny ; Promoter Regions, Genetic ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Transcription, Genetic ; Zea mays/*genetics ; }, abstract = {We have cloned and characterized a mitochondrial elongation factor Tu (EF-Tu) gene (tufM) in maize (Zea mays L.). This maize tufM gene encoded a polypeptide of 452 amino acid residues, consisting of a putative transit peptide of 55 residues and a mature EF-Tu of 397 residues. The coding region was composed of 12 exons and 11 introns that ranged from 76 to 1673bp in length. The deduced amino acid sequence showed 85.9% and 61.2% identity with Arabidopsis mitochondrial EF-Tu and Arabidopsis chloroplast EF-Tu sequence respectively. The transcription initiation site was determined to be 165bp upstream of the AUG initiation codon by primer extension analysis. Southern blot analysis revealed that the cloned EF-Tu gene was encoded by the members of small gene family in maize. Although this gene does not resemble the Arabidopsis nuclear tufA gene, which encodes the plastid EF-Tu, and does not contain sequence elements found in all cyanobacterial and plastid tufA genes, the predicted amino acid sequence includes an N-terminal extension that resembles a mitochondrial targeting sequence, and shares three unique sequence elements with mitochondrial EF-Tu's from Arabidopsis thaliana, Saccharomyces cerevisiae, and Homo sapiens. Therefore, we concluded that this gene encodes the maize mitochondrial EF-Tu.}, }
@article {pmid11080313, year = {2000}, author = {Moran, JF and Iturbe-Ormaetxe, I and Matamoros, MA and Rubio, MC and Clemente, MR and Brewin, NJ and Becana, M}, title = {Glutathione and homoglutathione synthetases of legume nodules. Cloning, expression, and subcellular localization.}, journal = {Plant physiology}, volume = {124}, number = {3}, pages = {1381-1392}, pmid = {11080313}, issn = {0032-0889}, mesh = {Amino Acid Sequence ; Bacteroides/enzymology ; Blotting, Northern ; Cell Compartmentation ; Cloning, Molecular ; Cytosol/enzymology ; DNA, Complementary/isolation &amp; purification ; Fabaceae/enzymology/*genetics/microbiology ; Glutathione Synthase/*genetics/metabolism ; Molecular Sequence Data ; *Nitrogen Fixation ; Peptide Synthases/*genetics/metabolism ; Phylogeny ; Plant Roots/enzymology/ultrastructure ; *Plants, Medicinal ; Plastids/enzymology ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Subcellular Fractions/*enzymology ; Symbiosis ; }, abstract = {The thiol tripeptides glutathione (GSH) and homoglutathione (hGSH) are very abundant in legume root nodules and their synthesis is catalyzed by the enzymes gamma-glutamylcysteine synthetase (gammaECS), GSH synthetase (GSHS), and hGSH synthetase (hGSHS). As an essential step to elucidate the role of thiols in N(2) fixation we have isolated cDNAs encoding the three enzymes and have quantified the transcripts in nodules. Assay of enzyme activities in highly purified nodule organelles revealed that gammaECS is localized in the plastids, hGSHS in the cytosol, and GSHS in the cytosol and mitochondria. These results are consistent with sequence analyses. Subcellular fractionation of nodules also showed that bacteroids contain high thiol concentrations and high specific gammaECS and GSHS activities. Results emphasize the role of nodule plastids in antioxidant protection and in control of thiol synthesis, and suggest that plastids may be important in the stress response of nodules. Overall, our results provide further evidence that thiol synthesis is critical for nodule functioning.}, }
@article {pmid11069584, year = {2000}, author = {Szilágyi, N and Kovács, R and Kardos, J}, title = {Coupled intra- and extracellular Ca2+ dynamics in recurrent seizure-like events.}, journal = {The European journal of neuroscience}, volume = {12}, number = {11}, pages = {3893-3899}, doi = {10.1046/j.1460-9568.2000.00284.x}, pmid = {11069584}, issn = {0953-816X}, mesh = {Animals ; Calcium/*physiology ; Cells, Cultured ; Cytosol/metabolism ; Hippocampus/*physiology ; In Vitro Techniques ; Kinetics ; Magnesium/pharmacology/physiology ; Mathematics ; Mitochondria/metabolism ; Models, Neurological ; Neurons/drug effects/*physiology ; Oscillometry ; Rats ; Recurrence ; Seizures/*physiopathology ; Time Factors ; }, abstract = {We considered the evolution of Ca2+ oscillation dynamics in recurrent seizure-like events. Dynamic system behaviour was characterized in the state space reconstructed from intra- and extracellular [Ca2+] fluctuations simultaneously measured in cultured rat hippocampal slices under low-[Mg2+] conditions. When associated in the seizure-like event, these fluctuations occurred on a restricted set, the attractor, embedded in the full state space with less than five degrees of freedom. Instantaneous relative phase differences indicated field potential-driven phase jumps locked onto seizure-like events. To account for recurrent dynamics, calculations were performed on different extensions of a model for Ca2+ oscillation. These identified bidirectional, asymmetrical coupling of extracellular with intracellular (cytosolic, Ca2+ store, mitochondrial) Ca2+ dynamics as critical in its development.}, }
@article {pmid11063052, year = {2000}, author = {Fiskum, G}, title = {Mitochondrial participation in ischemic and traumatic neural cell death.}, journal = {Journal of neurotrauma}, volume = {17}, number = {10}, pages = {843-855}, doi = {10.1089/neu.2000.17.843}, pmid = {11063052}, issn = {0897-7151}, support = {NS34152/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Apoptosis/*physiology ; Astrocytes/metabolism ; Brain Injuries/*metabolism/pathology/physiopathology ; Brain Ischemia/*metabolism/pathology/physiopathology ; Calcium/metabolism ; Cytochrome c Group/metabolism ; Energy Metabolism/physiology ; Humans ; Mitochondria/*metabolism/pathology ; Nerve Degeneration/*metabolism/pathology/physiopathology ; Neurons/metabolism ; Neurotoxins/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {Mitochondria play critical roles in cerebral energy metabolism and in the regulation of cellular Ca2+ homeostasis. They are also the primary intracellular source of reactive oxygen species, due to the tremendous number of oxidation-reduction reactions and the massive utilization of O2 that occur there. Metabolic trafficking among cells is also highly dependent upon normal, well-controlled mitochondrial activities. Alterations of any of these functions can cause cell death directly or precipitate death indirectly by compromising the ability of cells to withstand stressful stimuli. Abnormal accumulation of Ca2+ by mitochondria in response to exposure of neurons to excitotoxic levels of excitatory neurotransmitters, for example, glutamate, is a primary mediator of mitochondrial dysfunction and delayed cell death. Excitoxicity, along with inflammatory reactions, mechanical stress, and altered trophic signal transduction, all likely contribute to mitochondrial damage observed during the evolution of traumatic brain injury. The release of apoptogenic proteins from mitochondria into the cytosol serves as a primary mechanism responsible for inducing apoptosis, a form of cell death that contributes significantly to neurologic impairment following neurotrauma. Although several signals for the release of mitochondrial cell death proteins have been identified, the mechanisms by which these signals increase the permeability of the mitochondrial outer membrane to apoptogenic proteins is controversial. Elucidation of the precise biochemical mechanisms responsible for mitochondrial dysfunction during neurotrauma and the roles that mitochondria play in both necrotic and apoptotic cell death should provide new molecular targets for neuroprotective interventions.}, }
@article {pmid11056213, year = {2000}, author = {Lutziger, I and Oliver, DJ}, title = {Molecular evidence of a unique lipoamide dehydrogenase in plastids: analysis of plastidic lipoamide dehydrogenase from Arabidopsis thaliana.}, journal = {FEBS letters}, volume = {484}, number = {1}, pages = {12-16}, doi = {10.1016/s0014-5793(00)02116-5}, pmid = {11056213}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Arabidopsis/cytology/*enzymology/genetics/metabolism ; Cell Nucleus/genetics ; Chloroplasts/enzymology/genetics/metabolism ; Cloning, Molecular ; Cyanobacteria/enzymology ; Dihydrolipoamide Dehydrogenase/chemistry/genetics/*metabolism ; Genes, Plant/genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Pisum sativum/cytology/metabolism ; Phylogeny ; Plastids/*enzymology/genetics/metabolism ; RNA, Messenger/analysis/genetics ; RNA, Plant/analysis/genetics ; Sequence Alignment ; }, abstract = {Lipoamide dehydrogenase is a subunit of the alpha-ketoacid dehydrogenases and the glycine decarboxylase complex in mitochondria, and the pyruvate dehydrogenase complex in plastids. We report here the unexpected finding of two plastidic isoforms of lipoamide dehydrogenase from Arabidopsis thaliana that are different from the mitochondrial form of the enzyme. The cDNA clones were confirmed by sequence alignment analysis and their location verified by chloroplast import assay. They are single copy genes that appear to be expressed in parallel in different tissues with highest level in developing siliques. Phylogenetic analysis gives further exemplary evidence for the plastidic evolution derived from cyanobacteria.}, }
@article {pmid11053672, year = {2000}, author = {Brand, MD}, title = {Uncoupling to survive? The role of mitochondrial inefficiency in ageing.}, journal = {Experimental gerontology}, volume = {35}, number = {6-7}, pages = {811-820}, doi = {10.1016/s0531-5565(00)00135-2}, pmid = {11053672}, issn = {0531-5565}, mesh = {*Aging ; Animals ; Biological Evolution ; Humans ; Mitochondria/*physiology ; Oxidative Phosphorylation ; Proton-Motive Force ; Rats ; Reactive Oxygen Species/metabolism ; }, abstract = {Mitochondria are incompletely coupled, and during oxidative phosphorylation some of the redox energy in substrates is lost as heat. Incomplete coupling is mostly due to a natural leak of protons across the mitochondrial inner membrane. In rat hepatocytes the futile cycle of proton pumping and proton leak is responsible for 20-25% of respiration; in perfused rat muscle the value is 35-50%. Mitochondrial proton cycling is estimated to cause 20-25% of basal metabolic rate in rats. Proton cycling is equally prominent in hepatocytes from several different mammalian and ectotherm species, so it may be a general pathway of ecologically significant energy loss in all aerobes. Because it occurs in ectotherms, thermogenesis cannot be its primary function. Instead, an attractive candidate for the function of the universal and expensive energy-dissipating proton cycle is to decrease the production of superoxide and other reactive oxygen species (ROS). This could be important in helping to minimise oxidative damage to DNA and in slowing ageing. Mitochondria are the major source of cellular ROS, and increased mitochondrial proton conductance leads to oxidation of ubiquinone and decreased ROS production in isolated mitochondria. However, to date there is no direct evidence in cells or organisms that mitochondrial proton cycling lowers ROS production or oxidative damage or that it increases lifespan.}, }
@article {pmid11050446, year = {2000}, author = {Rotte, C and Henze, K and Müller, M and Martin, W}, title = {Origins of hydrogenosomes and mitochondria.}, journal = {Current opinion in microbiology}, volume = {3}, number = {5}, pages = {481-486}, doi = {10.1016/s1369-5274(00)00126-0}, pmid = {11050446}, issn = {1369-5274}, mesh = {Aerobiosis ; Alphaproteobacteria ; Anaerobiosis ; Animals ; *Biological Evolution ; *Electron Transport ; Eukaryota ; Mitochondria/*physiology ; Organelles/*physiology ; }, abstract = {Complete genome sequences for many oxygen-respiring mitochondria, as well as for some bacteria, leave no doubt that mitochondria are descendants of alpha-proteobacteria, a finding for which the endosymbiont hypothesis can easily account. Yet a wealth of data indicate that mitochondria and hydrogenosomes - the ATP-producing organelles of many anaerobic protists - share a common ancestry, a finding that traditional formulations of the endosymbiont hypothesis less readily accommodates. Available evidence suggests that a more in-depth understanding of the origins of eukaryotes and their organelles will hinge upon data from the genomes of protists that synthesize ATP without the need for oxygen.}, }
@article {pmid11048747, year = {2000}, author = {Mahadevan, A and Santosh, V and Gayatri, N and Ratnavalli, E and NandaGopal, R and Vasanth, A and Roy, AK and Shankar, SK}, title = {Infantile neuroaxonal dystrophy and giant axonal neuropathy--overlap diseases of neuronal cytoskeletal elements in childhood?.}, journal = {Clinical neuropathology}, volume = {19}, number = {5}, pages = {221-229}, pmid = {11048747}, issn = {0722-5091}, mesh = {Biopsy ; Brain/pathology ; Child ; Child, Preschool ; Female ; Humans ; Intermediate Filaments/*pathology ; Magnetic Resonance Imaging ; Male ; Microscopy, Electron ; Nerve Fibers, Myelinated/pathology/ultrastructure ; Neuroaxonal Dystrophies/classification/*pathology ; Neurodegenerative Diseases/classification/*pathology ; Organelles/pathology ; Sural Nerve/pathology/ultrastructure ; }, abstract = {Giant axonal neuropathy (GAN) and infantile neuroaxonal dystrophy (INAD) are two progressive neurodegenerative disorders of childhood that have considerable clinical as well as histological overlap but are believed to be ultrastructurally distinct. The clinicopathological and ultrastructural features of three cases of INAD, two of whom are siblings and one case of GAN are described. The sural nerve biopsies in all four cases were essentially similar on light microscopy revealing giant axons. On electron microscopy, the findings in the case of GAN were typical with dense accumulation of neurofilaments within the giant axons. In the three cases of INAD, too, in addition to accumulation of mitochondria and organelles with vesiculotubular profiles, a similar increase in neurofilaments was evident. We, therefore, believe that these two disorders may represent a spectrum in evolution of intermediate filament pathology with various organelles participating in the temporal evolution of the disease process.}, }
@article {pmid11041518, year = {2000}, author = {Hoekstra, RF}, title = {Evolutionary origin and consequences of uniparental mitochondrial inheritance.}, journal = {Human reproduction (Oxford, England)}, volume = {15 Suppl 2}, number = {}, pages = {102-111}, doi = {10.1093/humrep/15.suppl_2.102}, pmid = {11041518}, issn = {0268-1161}, mesh = {DNA Repair/genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Extrachromosomal Inheritance/*genetics ; Fertility/genetics ; Humans ; Mitochondria/*genetics ; Mutation/genetics ; Reproduction, Asexual/genetics ; }, abstract = {In the great majority of sexual organisms, cytoplasmic genomes such as the mitochondrial genome are inherited (almost) exclusively through only one, usually the maternal, parent. This rule probably evolved to minimize the potential spread of selfish cytoplasmic genomic mutations through a species. Maternal inheritance creates an asymmetry between the sexes from which several evolutionary consequences follow. Because natural selection on mitochondria operates only in females, mitochondrial mutations may have more deleterious effects in males than in females. Strictly uniparental inheritance creates asexual mitochondrial lineages that are vulnerable to mutation accumulation (Muller's ratchet). There is evidence that over evolutionary time mitochondrial genomes have indeed accumulated slightly deleterious mutations. Mutation accumulation in animal mitochondrial genomes is probably slowed down mainly by two processes: a severe reduction in germline mitochondrial genome copy number at some point in the life cycle, enabling more effective elimination of mutations by natural selection, and occasional recombination between maternal and paternal mitochondrial genomes following paternal leakage.}, }
@article {pmid11041508, year = {2000}, author = {Jansen, RP}, title = {Origin and persistence of the mitochondrial genome.}, journal = {Human reproduction (Oxford, England)}, volume = {15 Suppl 2}, number = {}, pages = {1-10}, doi = {10.1093/humrep/15.suppl_2.1}, pmid = {11041508}, issn = {0268-1161}, mesh = {Animals ; DNA, Mitochondrial/chemistry/*genetics/metabolism ; Evolution, Molecular ; Extrachromosomal Inheritance ; *Genome ; Humans ; Mitochondria/*genetics ; Mutation ; }, abstract = {The mitochondrial genome comprises a circular, histone-free 'chromosome' of 16.6 kb of DNA, present in one or more copies in every mitochondrion. This chromosome has been tightly conserved for more than half a billion years, coding in every multicellular animal so far investigated, both vertebrate and invertebrate: (i) the same 13 protein subunits required for oxidative phosphorylation; (ii) a component of each of the two mitochondrial ribosome subunits; and (iii) the 22 transport RNAs present within the mitochondrion. Exons on the circle are tightly packed, with no spacing introns. Mitochondrial DNA is histone-free, has limited repair ability, and has a relatively high mutation-fixation rate. Inheritance is cytoplasmic and maternal, with epidemiological evidence (namely the familial distribution of polymorphisms) indicating that recombination with mtDNA of paternal origin is exceedingly rare. Thus the maintenance and evolution of mtDNA (its remarkably successful symbiotic persistence with the nuclear genome) has been essentially asexual. The machinery for homologous recombination is present in mitochondria of at least some species, however, and it might be surprising if it did not occur between circles in some circumstances. By bringing together the fields of mitochondrial biochemistry, evolutionary genetics, reproductive physiology, and neuromuscular medicine in focusing on the inheritance of normal and abnormal human mtDNA, we can hope to better understand the forces behind this genome's inheritance and what might be required of ovarian function to satisfy its accurate persistence over millions of years. Clinically we can hope also for a better understanding of ooplasmic factors in human fertility and in the wide manifestations of mitochondrial genomic disease.}, }
@article {pmid11040285, year = {2000}, author = {van Herwerden, L and Blair, D and Agatsuma, T}, title = {Multiple lineages of the mitochondrial gene NADH dehydrogenase subunit 1 (ND1) in parasitic helminths: implications for molecular evolutionary studies of facultatively anaerobic eukaryotes.}, journal = {Journal of molecular evolution}, volume = {51}, number = {4}, pages = {339-352}, doi = {10.1007/s002390010096}, pmid = {11040285}, issn = {0022-2844}, mesh = {Animals ; DNA, Mitochondrial ; *Evolution, Molecular ; *Genetic Variation ; Insect Proteins/*genetics ; *NADH Dehydrogenase ; Paragonimus/*genetics ; Phylogeny ; Polymorphism, Single-Stranded Conformational ; Pseudogenes ; Trematoda/genetics ; }, abstract = {The task of using partial ND1 sequences to infer a phylogeny for species of the genus Paragonimus (Trematoda: Digenea) was complicated by the discovery of at least two ND1 lineages within individual worms. The divergence of the ND1 lineages is shown by phylogenetic analysis not only to predate the divergence of the three Paragonimus species or species groups investigated but also the divergence of some trematode families. Some sequences are clearly pseudogenes as they contain single base deletions and/or premature termination codons. The presence of both pseudogenes and/or mitochondrial heteroplasmy are invoked to explain the presence of multiple and divergent ND1 lineages in these trematodes, which have two distinct cytochemical types of mitochondria. The implications for phylogenetic studies generally and of parasitic helminths specifically, using ND1 sequence data, are discussed. The ability of these organisms to adapt their metabolic processes to the variable availability of oxygen as an electron acceptor are proposed to explain some of the molecular diversity observed in parasitic helminths and possibly also in other anaerobically adapted eukaryotes.}, }
@article {pmid11038324, year = {2000}, author = {Shin, WS and Tanaka, M and Suzuki, J and Hemmi, C and Toyo-oka, T}, title = {A novel homoplasmic mutation in mtDNA with a single evolutionary origin as a risk factor for cardiomyopathy.}, journal = {American journal of human genetics}, volume = {67}, number = {6}, pages = {1617-1620}, pmid = {11038324}, issn = {0002-9297}, mesh = {Cardiomyopathies/*genetics/pathology ; Cytoplasm/*genetics ; DNA Mutational Analysis ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Female ; Genetic Predisposition to Disease/*genetics ; Genetic Testing ; Genetic Variation/genetics ; Humans ; Male ; Middle Aged ; Mitochondria/genetics/pathology/ultrastructure ; Phylogeny ; Point Mutation/*genetics ; Polymorphism, Single-Stranded Conformational ; }, abstract = {To clarify the relationship between variation in mtDNA and the development of cardiomyopathy (CM), the complete sequences of mtDNAs of two brothers with dilated CM were compared with those of 181 patients who had CM and with those of 168 control subjects. Five patients with CM shared a novel homoplasmic point mutation (G12192A tRNA(His)), and all of them demonstrated the evolutionarily related D-loop sequence. The results suggest that this novel mutation originated from the same ancestor and that its presence strongly predisposes carriers to CM.}, }
@article {pmid11038192, year = {2000}, author = {van der Bliek, AM}, title = {A mitochondrial division apparatus takes shape.}, journal = {The Journal of cell biology}, volume = {151}, number = {2}, pages = {F1-4}, pmid = {11038192}, issn = {0021-9525}, support = {GM58166/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Evolution ; Fungal Proteins/metabolism ; *GTP-Binding Proteins ; Intracellular Membranes ; Mitochondria/*physiology ; *Mitochondrial Proteins ; Models, Biological ; *Saccharomyces cerevisiae Proteins ; }, }
@article {pmid11035803, year = {2000}, author = {Marcotte, EM and Xenarios, I and van Der Bliek, AM and Eisenberg, D}, title = {Localizing proteins in the cell from their phylogenetic profiles.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {22}, pages = {12115-12120}, pmid = {11035803}, issn = {0027-8424}, mesh = {Algorithms ; Animals ; Caenorhabditis elegans/genetics/metabolism ; Membrane Proteins/*metabolism ; *Phylogeny ; Protein Sorting Signals/*physiology ; Saccharomyces cerevisiae/genetics/metabolism ; Subcellular Fractions/*metabolism ; }, abstract = {We introduce a computational method for identifying subcellular locations of proteins from the phylogenetic distribution of the homologs of organellar proteins. This method is based on the observation that proteins localized to a given organelle by experiments tend to share a characteristic phylogenetic distribution of their homologs-a phylogenetic profile. Therefore any other protein can be localized by its phylogenetic profile. Application of this method to mitochondrial proteins reveals that nucleus-encoded proteins previously known to be destined for mitochondria fall into three groups: prokaryote-derived, eukaryote-derived, and organism-specific (i.e., found only in the organism under study). Prokaryote-derived mitochondrial proteins can be identified effectively by their phylogenetic profiles. In the yeast Saccharomyces cerevisiae, 361 nucleus-encoded mitochondrial proteins can be identified at 50% accuracy with 58% coverage. From these values and the proportion of conserved mitochondrial genes, it can be inferred that approximately 630 genes, or 10% of the nuclear genome, is devoted to mitochondrial function. In the worm Caenorhabditis elegans, we estimate that there are approximately 660 nucleus-encoded mitochondrial genes, or 4% of its genome, with approximately 400 of these genes contributed from the prokaryotic mitochondrial ancestor. The large fraction of organism-specific and eukaryote-derived genes suggests that mitochondria perform specialized roles absent from prokaryotic mitochondrial ancestors. We observe measurably distinct phylogenetic profiles among proteins from different subcellular compartments, allowing the general use of prokaryotic genomes in learning features of eukaryotic proteins.}, }
@article {pmid11035802, year = {2000}, author = {Chihade, JW and Brown, JR and Schimmel, PR and Ribas De Pouplana, L}, title = {Origin of mitochondria in relation to evolutionary history of eukaryotic alanyl-tRNA synthetase.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {22}, pages = {12153-12157}, pmid = {11035802}, issn = {0027-8424}, support = {R01 GM023562/GM/NIGMS NIH HHS/United States ; GM23562/GM/NIGMS NIH HHS/United States ; }, mesh = {Alanine-tRNA Ligase/chemistry/*genetics ; Amino Acid Sequence ; Animals ; *Evolution, Molecular ; Humans ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {The origin of the eukaryotic cell remains an unsolved question. Numerous experimental and phylogenetic observations support the symbiotic origin of the modern eukaryotic cell, with its nucleus and (typically) mitochondria. Incorporation of mitochondria has been proposed to precede development of the nucleus, but it is still unclear whether mitochondria were initially part of basal eukaryotes. Data on alanyl-tRNA synthetase from an early eukaryote and other sources are presented and analyzed here. These data are consistent with the notion that mitochondrial genesis did not significantly precede nucleus formation. Moreover, the data raise the possibility that diplomonads are primary amitochondriates that radiated from the eukaryotic lineage before mitochondria became fully integrated as a cellular organelle.}, }
@article {pmid11034499, year = {2000}, author = {Sauer, C and Stackebrandt, E and Gadau, J and Hölldobler, B and Gross, R}, title = {Systematic relationships and cospeciation of bacterial endosymbionts and their carpenter ant host species: proposal of the new taxon Candidatus Blochmannia gen. nov.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {50 Pt 5}, number = {}, pages = {1877-1886}, doi = {10.1099/00207713-50-5-1877}, pmid = {11034499}, issn = {1466-5026}, mesh = {Animals ; Ants/classification/enzymology/*microbiology ; Base Composition ; Base Sequence ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Digestive System/microbiology ; Electron Transport Complex IV/genetics ; Gammaproteobacteria/*classification/genetics/isolation &amp; purification ; Genes, rRNA ; In Situ Hybridization ; Introns ; Mitochondria/enzymology ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; rRNA Operon ; }, abstract = {The systematic relationships of intracellular bacteria of 13 Camponotus species (carpenter ants) from America and Europe were compared to those of their hosts. Phylogenetic trees of the bacteria and the ants were based on 16S rDNA (rrs) gene sequences and mitochondrial cytochrome oxidase subunit I (COI) gene sequences, respectively. The bacterial endosymbionts of Camponotus spp. form a distinct lineage in the y-subclass of the Proteobacteria. The taxa most closely related to these bacteria are endosymbionts of aphids and the tsetse fly. The bacterial and host phylogenies deduced from the sequence data show a high degree of congruence, providing significant evidence for cospeciation of the bacteria and the ants and a maternal transmission route of the symbionts. The cloned rrs genes of the endosymbionts contain putative intervening sequences (IVSs) with a much lower G+C content than the mean of the respective rrs genes. By in situ hybridization specific 16S rDNA oligonucleotide probes verified the presence of the bacteria within tissues of three of the eukaryotic hosts. It is proposed that the endosymbionts of these three carpenter ants be assigned to a new taxon 'Candidatus Blochmannia gen. nov.' with the symbionts of the individual ants being species named according to their host, 'Candidatus Blochmannia floridanus sp. nov.', 'Candidatus Blochmannia herculeanus sp. nov.' and 'Candidatus Blochmannia rufipes sp. nov.'.}, }
@article {pmid11029671, year = {2000}, author = {Lessinger, AC and Martins Junqueira, AC and Lemos, TA and Kemper, EL and da Silva, FR and Vettore, AL and Arruda, P and Azeredo-Espin, AM}, title = {The mitochondrial genome of the primary screwworm fly Cochliomyia hominivorax (Diptera: Calliphoridae).}, journal = {Insect molecular biology}, volume = {9}, number = {5}, pages = {521-529}, doi = {10.1046/j.1365-2583.2000.00215.x}, pmid = {11029671}, issn = {0962-1075}, mesh = {Animals ; Base Composition ; Codon ; DNA, Mitochondrial/chemistry/*genetics ; Diptera/classification/*genetics ; *Genes, Insect ; *Genome ; Insect Proteins/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymorphism, Restriction Fragment Length ; Sequence Analysis, DNA ; }, abstract = {The complete sequence of the mitochondrial genome of the screwworm Cochliomyia hominivorax was determined. This genome is 16,022 bp in size and corresponds to a typical Brachycera mtDNA. A Serine start codon for COI and incomplete termination codons for COII, NADH 5 and NADH 4 genes were described. The nucleotide composition of C. hominivorax mtDNA is 77% AT-rich, reflected in the predominance of AT-rich codons in protein-coding genes. Non-optimal codon usage was commonly observed in C. hominivorax mitochondrial genes. Phylogenetic analysis distributed the Acalypterate species as a monophyletic group and assembled the C. hominivorax (Calyptratae) and the Acalyptratae in a typical Brachycera cluster. The identification of diagnostic restriction sites on the sequenced mitochondrial genome and the correlation with previous RFLP analysis are discussed.}, }
@article {pmid11027690, year = {2001}, author = {Glover, KE and Spencer, DF and Gray, MW}, title = {Identification and structural characterization of nucleus-encoded transfer RNAs imported into wheat mitochondria.}, journal = {The Journal of biological chemistry}, volume = {276}, number = {1}, pages = {639-648}, doi = {10.1074/jbc.M007708200}, pmid = {11027690}, issn = {0021-9258}, mesh = {Base Sequence ; Biological Transport ; Cell Nucleus/*genetics ; Codon/genetics ; Cytoplasm/genetics ; DNA, Mitochondrial/genetics ; Electrophoresis, Gel, Two-Dimensional ; Evolution, Molecular ; Mitochondria/*genetics/*metabolism ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Nucleic Acid Hybridization ; RNA/chemistry/genetics/metabolism ; RNA Probes ; RNA, Mitochondrial ; RNA, Plant/chemistry/genetics/metabolism ; RNA, Transfer/*chemistry/genetics/*metabolism ; RNA, Transfer, Asp/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, RNA ; *Triticum/cytology/genetics/metabolism ; }, abstract = {Despite its large size (200-2400 kilobase pairs), the mitochondrial genome of angiosperms does not encode the minimal set of tRNAs required to support mitochondrial protein synthesis. Here we report the identification of cytosolic-like tRNAs in wheat mitochondria using a method involving quantitative hybridization to distinguish among three tRNA classes: (i) those encoded by mitochondrial DNA (mtDNA) and localized in mitochondria, (ii) those encoded by nuclear DNA and located in the cytosol, and (iii) those encoded by nuclear DNA and found in both the cytosol and mitochondria. The latter class comprises tRNA species that are considered to be imported into mitochondria to compensate for the deficiency of mtDNA-encoded tRNAs. In a comprehensive survey of the wheat mitochondrial tRNA population, we identified 14 such imported tRNAs, the structural characterization of which is presented here. These imported tRNAs complement 16 mtDNA-encoded tRNAs, for a total of at least 30 distinct tRNA species in wheat mitochondria. Considering differences in the set of mtDNA-encoded and imported tRNAs in the mitochondria of various land plants, the import system must be able to adapt relatively rapidly over evolutionary time with regard to the particular cytosolic-like tRNAs that are brought into mitochondria.}, }
@article {pmid11027335, year = {2000}, author = {Telford, MJ and Herniou, EA and Russell, RB and Littlewood, DT}, title = {Changes in mitochondrial genetic codes as phylogenetic characters: two examples from the flatworms.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {21}, pages = {11359-11364}, pmid = {11027335}, issn = {0027-8424}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Codon ; DNA Primers ; *Genetic Code ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; Platyhelminths/*genetics ; Species Specificity ; }, abstract = {Shared molecular genetic characteristics other than DNA and protein sequences can provide excellent sources of phylogenetic information, particularly if they are complex and rare and are consequently unlikely to have arisen by chance convergence. We have used two such characters, arising from changes in mitochondrial genetic code, to define a clade within the Platyhelminthes (flatworms), the Rhabditophora. We have sampled 10 distinct classes within the Rhabditophora and find that all have the codon AAA coding for the amino acid Asn rather than the usual Lys and AUA for Ile rather than the usual Met. We find no evidence to support claims that the codon UAA codes for Tyr in the Platyhelminthes rather than the standard stop codon. The Rhabditophora are a very diverse group comprising the majority of the free-living turbellarian taxa and the parasitic Neodermata. In contrast, three other classes of turbellarian flatworm, the Acoela, Nemertodermatida, and Catenulida, have the standard invertebrate assignments for these codons and so are convincingly excluded from the rhabditophoran clade. We have developed a rapid computerized method for analyzing genetic codes and demonstrate the wide phylogenetic distribution of the standard invertebrate code as well as confirming already known metazoan deviations from it (ascidian, vertebrate, echinoderm/hemichordate).}, }
@article {pmid11027334, year = {2000}, author = {Karlin, S and Brocchieri, L}, title = {Heat shock protein 60 sequence comparisons: duplications, lateral transfer, and mitochondrial evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {21}, pages = {11348-11353}, pmid = {11027334}, issn = {0027-8424}, support = {R01 GM010452/GM/NIGMS NIH HHS/United States ; 5R01GM10452-36/GM/NIGMS NIH HHS/United States ; 5R01HG00335-12/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Chaperonin 60/*genetics ; *Evolution, Molecular ; Fungi/genetics ; *Gene Duplication ; *Gene Transfer Techniques ; Mitochondria/*genetics ; Plants/genetics ; *Sequence Homology, Nucleic Acid ; }, abstract = {Heat shock proteins 60 (GroEL) are highly expressed essential proteins in eubacterial genomes and in eukaryotic organelles. These chaperone proteins have been advanced as propitious marker sequences for tracing the evolution of mitochondrial (Mt) genomes. Similarities among HSP60 sequences based on significant segment pair alignment calculations are used to deduce associations of sequences taking into account GroEL functional/structural domain differences and to relate HSP60 duplications pervasive in alpha-proteobacterial lineages to the dynamics of lateral transfer and plasmid integration. Multiple alignments with consensuses are determined for 10 natural groups. The group consensuses sharpen the similarity contrasts among individual sequences. In particular, the Mt group matches best with the classical alpha-proteobacteria and closely with Rickettsia but significantly worse with the rickettsial groups Ehrlichia and Orientia. However, across broad protein sequence comparisons, there appears to be no consistent prokaryote whose protein sequences align best with animal Mt genomes. There are plausible scenarios indicating that the nuclear-encoded HSP60 (and HSP70) sequences functioning in Mt are results of lateral transfer and are probably derived from an alpha-proteobacterium. This hypothesis relates to the plethora of duplicated HSP60 sequences among the classical alpha-proteobacteria contrasted with no duplications of HSP60 among other clades of proteobacterial genomes. Evolutionary relations are confounded by differential selection pressures, convergence, variable mutational rates, site variability, and lateral gene transfer.}, }
@article {pmid11025528, year = {2000}, author = {Karlberg, O and Canbäck, B and Kurland, CG and Andersson, SG}, title = {The dual origin of the yeast mitochondrial proteome.}, journal = {Yeast (Chichester, England)}, volume = {17}, number = {3}, pages = {170-187}, pmid = {11025528}, issn = {0749-503X}, mesh = {Alphaproteobacteria/chemistry/genetics ; Databases, Factual ; *Evolution, Molecular ; Fungal Proteins/chemistry/*genetics ; Humans ; Mitochondria/chemistry/*genetics ; Phylogeny ; Proteome/*genetics ; Rickettsia prowazekii/chemistry/genetics ; Saccharomyces cerevisiae/chemistry/*genetics ; }, abstract = {We propose a scheme for the origin of mitochondria based on phylogenetic reconstructions with more than 400 yeast nuclear genes that encode mitochondrial proteins. Half of the yeast mitochondrial proteins have no discernable bacterial homologues, while one-tenth are unequivocally of alpha-proteobacterial origin. These data suggest that the majority of genes encoding yeast mitochondrial proteins are descendants of two different genomic lineages that have evolved in different modes. First, the ancestral free-living alpha-proteobacterium evolved into an endosymbiont of an anaerobic host. Most of the ancestral bacterial genes were lost, but a small fraction of genes supporting bioenergetic and translational processes were retained and eventually transferred to what became the host nuclear genome. In a second, parallel mode, a larger number of novel mitochondrial genes were recruited from the nuclear genome to complement the remaining genes from the bacterial ancestor. These eukaryotic genes, which are primarily involved in transport and regulatory functions, transformed the endosymbiont into an ATP-exporting organelle.}, }
@article {pmid11018162, year = {2000}, author = {Lovette, IJ and Bermingham, E}, title = {c-mos variation in songbirds: molecular evolution, phylogenetic implications, and comparisons with mitochondrial differentiation.}, journal = {Molecular biology and evolution}, volume = {17}, number = {10}, pages = {1569-1577}, doi = {10.1093/oxfordjournals.molbev.a026255}, pmid = {11018162}, issn = {0737-4038}, mesh = {Animals ; Base Composition ; Cell Nucleus/genetics ; *Evolution, Molecular ; Genetic Variation ; Mitochondria/*genetics ; Phylogeny ; Proto-Oncogene Proteins c-mos/*genetics ; Songbirds/*classification/*genetics ; }, abstract = {Nucleotide sequences from the c-mos proto-oncogene have previously been used to reconstruct the phylogenetic relationships between distantly related vertebrate taxa. To explore c-mos variation at shallower levels of avian divergence, we compared c-mos sequences from representative passerine taxa that span a range of evolutionary differentiation, from basal passerine lineages to closely allied genera. Phylogenetic reconstructions based on these c-mos sequences recovered topologies congruent with previous DNA-DNA hybridization-based reconstructions, with many nodes receiving high support, as indicated by bootstrap and reliability values. One exception was the relationship of Acanthisitta to the remaining passerines, where the c-mos-based searches indicated a three-way polytomy involving the Acanthisitta lineage and the suboscine and oscine passerine clades. We also compared levels of c-mos and mitochondrial differentiation across eight oscine passerine taxa and found that c-mos nucleotide substitutions accumulate at a rate similar to that of transversion substitutions in mitochondrial protein-coding genes. These comparisons suggest that nuclear-encoded loci such as c-mos provide a temporal window of phylogenetic resolution that overlaps the temporal range where mitochondrial protein-coding sequences have their greatest utility and that c-mos substitutions and mtDNA transversions can serve as complementary, informative, and independent phylogenetic markers for the study of avian relationships.}, }
@article {pmid11018157, year = {2000}, author = {Barrientos, A and Müller, S and Dey, R and Wienberg, J and Moraes, CT}, title = {Cytochrome c oxidase assembly in primates is sensitive to small evolutionary variations in amino acid sequence.}, journal = {Molecular biology and evolution}, volume = {17}, number = {10}, pages = {1508-1519}, doi = {10.1093/oxfordjournals.molbev.a026250}, pmid = {11018157}, issn = {0737-4038}, support = {GM55766/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Fusion ; Cell Nucleus/*genetics ; Chick Embryo ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Gorilla gorilla/genetics ; Haplorhini/*genetics ; Hominidae/genetics ; Humans ; Hybrid Cells ; In Situ Hybridization, Fluorescence ; Karyotyping ; Mitochondria/*enzymology/*genetics ; Oxidative Phosphorylation ; Pongo pygmaeus/genetics ; Species Specificity ; }, abstract = {Respiring mitochondria require many interactions between nuclear and mitochondrial genomes. Although mitochondrial DNA (mtDNA) from the gorilla and the chimpanzee are able to restore oxidative phosphorylation in a human cell, mtDNAs from more distant primate species are functionally incompatible with human nuclear genes. Using microcell-mediated chromosome and mitochondria transfer, we introduced and maintained a functional orangutan mtDNA in a human nuclear background. However, partial oxidative phosphorylation function was restored only in the presence of most orangutan chromosomes, suggesting that human oxidative phosphorylation-related nuclear-coded genes are not able to replace many orangutan ones. The respiratory capacity of these hybrids was decreased by 65%-80%, and cytochrome c oxidase (COX) activity was decreased by 85%-95%. The function of other respiratory complexes was not significantly altered. The translation of mtDNA-coded COX subunits was normal, but their steady-state levels were approximately 10% of normal ones. Nuclear-coded COX subunits were loosely associated with mitochondrial membranes, a characteristic of COX assembly-defective mutants. Our results suggest that many human nuclear-coded genes not only cannot replace the orangutan counterparts, but also exert a specific interference at the level of COX assembly. This cellular model underscores the precision of COX assembly in mammals and sheds light on the nature of nuclear-mtDNA coevolutionary constraints.}, }
@article {pmid11013889, year = {2000}, author = {Fishelson, L and Delarea, Y and Galil, BS}, title = {Pathological alterations typical of human Tay-Sachs disease, in the retina of a deep-sea fish.}, journal = {Die Naturwissenschaften}, volume = {87}, number = {8}, pages = {363-365}, doi = {10.1007/s001140050741}, pmid = {11013889}, issn = {0028-1042}, mesh = {Animals ; Biological Evolution ; *Fishes/genetics ; Humans ; Intracellular Membranes/pathology/ultrastructure ; Mitochondria/pathology/ultrastructure ; Retina/*pathology/*ultrastructure ; Retinal Rod Photoreceptor Cells/pathology/ultrastructure ; Seawater ; Tay-Sachs Disease/genetics/*pathology ; }, abstract = {Micrographs of retinas from the deep-sea fish Cataetyx laticeps revealed visual cells containing membranous whorls in the ellipsoids of the inner segments resulting from stretching and modifications of the mitochondria membranes and their cristae. These pathological structures seem to be homologous to the whorls observed in retinas of human carriers of Tay-Sachs disease. This disease, a genetic disorder, is found in humans and some mammals. Our findings in fish suggest that the gene responsible can be found throughout the vertebrate evolutionary tree, possibly dormant in most taxa.}, }
@article {pmid11013755, year = {2001}, author = {Dunn, AM and Terry, RS and Smith, JE}, title = {Transovarial transmission in the microsporidia.}, journal = {Advances in parasitology}, volume = {48}, number = {}, pages = {57-100}, doi = {10.1016/s0065-308x(01)48005-5}, pmid = {11013755}, issn = {0065-308X}, mesh = {Animals ; Arthropods/growth &amp; development/*parasitology ; Biological Evolution ; Female ; Host-Parasite Interactions ; Male ; Microsporidia/genetics/growth &amp; development/pathogenicity/*physiology ; Microsporidiosis/parasitology/transmission ; Ovary/parasitology ; Sex Ratio ; Virulence ; }, abstract = {The microsporidia are an ancient and diverse group of protists which have many unusual characteristics. These include prokaryotic-like 70s ribosomes, enclosed nuclear division, a lack of mitochondria and complex life cycles which frequently involve vertical transmission. This use of vertical transmission is unparalleled by other protists and is seen only among bacterial endosymbionts and sex ratio distorters and in host cell organelles. Transovarially transmitted microsporidia can have unusual and profound effects on host population sex ratios. We here consider the mechanisms of transovarial transmission and its implications for parasite evolution. We review parasite/host relationships and the evolution of virulence under transovarial transmission and consider the implications of these parasites for host ecology and evolution.}, }
@article {pmid11009418, year = {2000}, author = {Denver, DR and Morris, K and Lynch, M and Vassilieva, LL and Thomas, WK}, title = {High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans.}, journal = {Science (New York, N.Y.)}, volume = {289}, number = {5488}, pages = {2342-2344}, doi = {10.1126/science.289.5488.2342}, pmid = {11009418}, issn = {0036-8075}, support = {R01-GM36827/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Substitution ; Animals ; Base Composition ; Base Pairing ; Caenorhabditis elegans/*genetics ; DNA, Helminth/chemistry/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Evolution, Molecular ; Frameshift Mutation ; *Genome ; Mitochondria/*genetics ; Mutagenesis, Insertional ; *Mutation ; NADH Dehydrogenase/genetics ; Phylogeny ; Point Mutation ; RNA, Transfer, Amino Acid-Specific/genetics ; Repetitive Sequences, Nucleic Acid ; Selection, Genetic ; Sequence Deletion ; }, abstract = {Mutations in the mitochondrial genome have been implicated in numerous human genetic disorders and offer important data for phylogenetic, forensic, and population genetic studies. Using a long-term series of Caenorhabditis elegans mutation accumulation lines, we performed a wide-scale screen for mutations in the mitochondrial genome that revealed a mutation rate that is two orders of magnitude higher than previous indirect estimates, a highly biased mutational spectrum, multiple mutations affecting coding function, as well as mutational hotspots at homopolymeric nucleotide stretches.}, }
@article {pmid11007602, year = {2000}, author = {Houle-Leroy, P and Garland, T and Swallow, JG and Guderley, H}, title = {Effects of voluntary activity and genetic selection on muscle metabolic capacities in house mice Mus domesticus.}, journal = {Journal of applied physiology (Bethesda, Md. : 1985)}, volume = {89}, number = {4}, pages = {1608-1616}, doi = {10.1152/jappl.2000.89.4.1608}, pmid = {11007602}, issn = {8750-7587}, mesh = {Animals ; Carnitine O-Palmitoyltransferase/metabolism ; Citrate (si)-Synthase/metabolism ; Electron Transport Complex IV/metabolism ; Female ; Glycolysis ; Heterozygote ; Hexokinase/metabolism ; L-Lactate Dehydrogenase/metabolism ; Male ; Mice ; Mice, Inbred ICR ; Mitochondria, Muscle/*enzymology ; Motor Activity/*physiology ; Muscle, Skeletal/*physiology ; Phosphofructokinase-1/metabolism ; Pyruvate Dehydrogenase Complex/metabolism ; Running ; *Selection, Genetic ; }, abstract = {Selective breeding is an important tool in behavioral genetics and evolutionary physiology, but it has rarely been applied to the study of exercise physiology. We are using artificial selection for increased wheel-running behavior to study the correlated evolution of locomotor activity and physiological determinants of exercise capacity in house mice. We studied enzyme activities and their response to voluntary wheel running in mixed hindlimb muscles of mice from generation 14, at which time individuals from selected lines ran more than twice as many revolutions per day as those from control (unselected) lines. Beginning at weaning and for 8 wk, we housed mice from each of four replicate selected lines and four replicate control lines with access to wheels that were free to rotate (wheel-access group) or locked (sedentary group). Among sedentary animals, mice from selected lines did not exhibit a general increase in aerobic capacities: no mitochondrial [except pyruvate dehydrogenase (PDH)] or glycolytic enzyme activity was significantly (P < 0.05) higher than in control mice. Sedentary mice from the selected lines exhibited a trend for higher muscle aerobic capacities, as indicated by higher levels of mitochondrial (cytochrome-c oxidase, carnitine palmitoyltransferase, citrate synthase, and PDH) and glycolytic (hexokinase and phosphofructokinase) enzymes, with concomitant lower anaerobic capacities, as indicated by lactate dehydrogenase (especially in male mice). Consistent with previous studies of endurance training in rats via voluntary wheel running or forced treadmill exercise, cytochrome-c oxidase, citrate synthase, and carnitine palmitoyltransferase activity increased in the wheel-access groups for both genders; hexokinase also increased in both genders. Some enzymes showed gender-specific responses: PDH and lactate dehydrogenase increased in wheel-access male but not female mice, and glycogen phosphorylase decreased in female but not in male mice. Two-way analysis of covariance revealed significant interactions between line type and activity group; for several enzymes, activities showed greater changes in mice from selected lines, presumably because such mice ran more revolutions per day and at greater velocities. Thus genetic selection for increased voluntary wheel running did not reduce the capability of muscle aerobic capacity to respond to training.}, }
@article {pmid11004453, year = {2000}, author = {Mühlenhoff, U and Lill, R}, title = {Biogenesis of iron-sulfur proteins in eukaryotes: a novel task of mitochondria that is inherited from bacteria.}, journal = {Biochimica et biophysica acta}, volume = {1459}, number = {2-3}, pages = {370-382}, doi = {10.1016/s0005-2728(00)00174-2}, pmid = {11004453}, issn = {0006-3002}, mesh = {Animals ; Bacteria/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Carbon-Sulfur Lyases/chemistry/metabolism ; *Escherichia coli Proteins ; Eukaryotic Cells/*metabolism ; Evolution, Molecular ; Ferredoxins/genetics/metabolism ; Genes, Bacterial ; Humans ; Iron-Sulfur Proteins/*biosynthesis/genetics/metabolism ; Mitochondria/genetics/*metabolism ; Models, Chemical ; Nitrogen Fixation/genetics ; }, abstract = {Fe/S clusters are co-factors of numerous proteins with important functions in metabolism, electron transport and regulation of gene expression. Presumably, Fe/S proteins have occurred early in evolution and are present in cells of virtually all species. Biosynthesis of these proteins is a complex process involving numerous components. In mitochondria, this process is accomplished by the so-called ISC (iron-sulfur cluster assembly) machinery which is derived from the bacterial ancestor of the organelles and is conserved from lower to higher eukaryotes. The mitochondrial ISC machinery is responsible for biogenesis iron-sulfur proteins both within and outside the organelle. Maturation of the latter proteins involves the ABC transporter Atm1p which presumably exports iron-sulfur clusters from the organelle. This review summarizes recent developments in our understanding of the biogenesis of iron-sulfur proteins both within bacteria and eukaryotes.}, }
@article {pmid11004440, year = {2000}, author = {Kerscher, SJ}, title = {Diversity and origin of alternative NADH:ubiquinone oxidoreductases.}, journal = {Biochimica et biophysica acta}, volume = {1459}, number = {2-3}, pages = {274-283}, doi = {10.1016/s0005-2728(00)00162-6}, pmid = {11004440}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Bacteria ; Cell Membrane/enzymology ; Conserved Sequence ; Electron Transport Complex I ; Eukaryotic Cells/enzymology ; Evolution, Molecular ; Fungi ; Intracellular Membranes/enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; NADH, NADPH Oxidoreductases/antagonists &amp; inhibitors/chemistry/*genetics ; Plants ; Prokaryotic Cells/enzymology ; Sequence Alignment ; Substrate Specificity ; }, abstract = {Mitochondria from various organisms, especially plants, fungi and many bacteria contain so-called alternative NADH:ubiquinone oxidoreductases that catalyse the same redox reaction as respiratory chain complex I, but do not contribute to the generation of transmembrane proton gradients. In eucaryotes, these enzymes are associated with the mitochondrial inner membrane, with their NADH reaction site facing either the mitochondrial matrix (internal alternative NADH:ubiquinone oxidoreductases) or the cytoplasm (external alternative NADH:ubiquinone oxidoreductases). Some of these enzymes also accept NADPH as substrate, some require calcium for activity. In the past few years, the characterisation of several alternative NADH:ubiquinone oxidoreductases on the DNA and on the protein level, of substrate specificities, mitochondrial import and targeting to the mitochondrial inner membrane has greatly improved our understanding of these enzymes. The present review will, with an emphasis on yeast model systems, illuminate various aspects of the biochemistry of alternative NADH:ubiquinone oxidoreductases, address recent developments and discuss some of the questions still open in the field.}, }
@article {pmid11003903, year = {2000}, author = {Rebage Moisés, V and Rite Gracia, S and López-Pisón, J and Muñoz Albillos, M and Aisa Pardo, E and Giménez Más, JA and Arenas Barbero, J and Montoya Vilarroya, J and Marco Telloa, A and Salazar García-Blanco, MI and Baldellou Vázquez, A}, title = {[Oxidative phosphorylation defects with neonatal presentation: review of our caseload].}, journal = {Anales espanoles de pediatria}, volume = {52}, number = {3}, pages = {251-257}, pmid = {11003903}, issn = {0302-4342}, mesh = {Female ; Humans ; Incidence ; Infant, Newborn ; Male ; *Metabolism, Inborn Errors/diagnosis/epidemiology/etiology/metabolism ; *Oxidative Phosphorylation ; Phenotype ; }, abstract = {OBJECTIVES: To define the oxidative phosporilation deficit syndrome in the neonatal in terms of incidence and clinical, biochemical and genetic features.<br><br>MATERIAL AND METHODS: We report 9 newborns diagnosed as oxidatic phosporilation deficit during the last 8 years in our hospital by means of clinical, metabolic, pathological and molecular studies, among other evaluations. The diagnosis was established based on ensymatic deficit of the respiratory chain, associated with alterations in the mtDNA in one case, and with mitochondrial ultrastructural anomalies in 5 cases.<br><br>RESULTS: There was an incidence of 1/3.555 newborns and 1/832 newborns admitted in our Neonatal Unit. In four of them there were familial antecedents and polihidramnios in two. Most of them, 8 out of 9, were born at term after a normal pregnancy and delivery, with normal Apgar score and auxological examination. Symptomatology started immediately at the neonatal period as acute neurological damage in most of them. There was a severe evolution as 5 children died and 4 survived with severe damage. All of them had the classical phenotype of early severe encefalopathy, associated with dismorphic features, hypotom&#xed;a, neurosensorial defects, brain dysgenesis and atrophy, anomalies in the EEG and in 5 of them there were also systemic anomalies, mainly cardiopathy. The most frequent biochemical alteration was a significative increment of the quotient lactate/piruvate. Five patients presented ultrastructural alterations of the mitochondria in thr muscle biopsy but Cox stain was not positive in any case. Three cases has a deficit of the complex IV, e of the complex I-IV, 2 of the complex I and one the complex I-III-IV. Only one patient had multiple deletions in the mtDNA.<br><br>CONCLUSIONS: Oxidatic phosporilation deficit are frequent and severe diseases of prenatal onset with limited fetal effects, homogeneous clinical phenotype with frequent damage of the central nervous system and variable extraneurological alteration and inconsistent biochemical pattern. Enzymatic studies ar need for making the diagnosis in all suspected cases,}, }
@article {pmid11003673, year = {2000}, author = {Oxelmark, E and Marchini, A and Malanchi, I and Magherini, F and Jaquet, L and Hajibagheri, MA and Blight, KJ and Jauniaux, JC and Tommasino, M}, title = {Mmf1p, a novel yeast mitochondrial protein conserved throughout evolution and involved in maintenance of the mitochondrial genome.}, journal = {Molecular and cellular biology}, volume = {20}, number = {20}, pages = {7784-7797}, pmid = {11003673}, issn = {0270-7306}, mesh = {Amino Acid Sequence ; Animals ; Antibodies/immunology ; Bacterial Proteins/chemistry/genetics ; Cloning, Molecular ; *Conserved Sequence ; DNA Replication ; DNA, Mitochondrial/biosynthesis/*genetics ; Evolution, Molecular ; Fungal Proteins/chemistry/genetics/immunology/*metabolism ; Gene Deletion ; Genome ; Humans ; Intracellular Membranes/chemistry/metabolism ; Microscopy, Electron ; Mitochondria/chemistry/genetics/*metabolism/ultrastructure ; *Mitochondrial Proteins ; Molecular Sequence Data ; Phenotype ; Protein Transport ; Proteins/chemistry/genetics/immunology/*metabolism ; Rats ; Saccharomyces cerevisiae/cytology/*genetics/metabolism/ultrastructure ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Solubility ; }, abstract = {A novel protein family (p14.5, or YERO57c/YJGFc) highly conserved throughout evolution has recently been identified. The biological role of these proteins is not yet well characterized. Two members of the p14.5 family are present in the yeast Saccharomyces cerevisiae. In this study, we have characterized some of the biological functions of the two yeast proteins. Mmf1p is a mitochondrial matrix factor, and homologous Mmf1p factor (Hmf1p) copurifies with the soluble cytoplasmic fraction. Deltammf1 cells lose mitochondrial DNA (mtDNA) and have a decreased growth rate, while Deltahmf1 cells do not display any visible phenotype. Furthermore, we demonstrate by genetic analysis that Mmf1p does not play a direct role in replication and segregation of the mtDNA. rho(+) Deltammf1 haploid cells can be obtained when tetrads are directly dissected on medium containing a nonfermentable carbon source. Our data also indicate that Mmf1p and Hmf1p have similar biological functions in different subcellular compartments. Hmf1p, when fused with the Mmf1p leader peptide, is transported into mitochondria and is able to functionally replace Mmf1p. Moreover, we show that homologous mammalian proteins are functionally related to Mmf1p. Human p14.5 localizes in yeast mitochondria and rescues the Deltammf1-associated phenotypes. In addition, fractionation of rat liver mitochondria showed that rat p14.5, like Mmf1p, is a soluble protein of the matrix. Our study identifies a biological function for Mmf1p and furthermore indicates that this function is conserved between members of the p14.5 family.}, }
@article {pmid11001143, year = {2000}, author = {Canning, EU and Curry, A and Feist, SW and Longshaw, M and Okamura, B}, title = {A new class and order of myxozoans to accommodate parasites of bryozoans with ultrastructural observations on Tetracapsula bryosalmonae (PKX organism).}, journal = {The Journal of eukaryotic microbiology}, volume = {47}, number = {5}, pages = {456-468}, doi = {10.1111/j.1550-7408.2000.tb00075.x}, pmid = {11001143}, issn = {1066-5234}, mesh = {Animals ; Bryozoa/*parasitology/ultrastructure ; Cell Nucleus/ultrastructure ; Eukaryota/*classification/growth &amp; development/ultrastructure ; Mitochondria/genetics ; Protozoan Infections, Animal/*parasitology ; }, abstract = {Tetracapsula bryosalmonae, formerly PKX organism, is a myxozoan parasite that causes proliferative kidney disease in salmonid fish. Its primary hosts, in which it undergoes a sexual phase, are phylactolaemate bryozoans. It develops in the bryozoan coelomic cavity as freely floating sacs which contain two types of cells, stellate cells and sporoplasmogenic cells, which become organised as spores. Eight stellate cells differentiate as four capsulogenic cells and four valve cells which surround a single sporoplasmogenic cell. The sporoplasmogenic cell undergoes meiosis and cytoplasmic fission to produce two sporoplasms with haploid nuclei. Sporoplasms contain secondary cells. The unusual development supports previously obtained data from 18S rDNA sequences, indicating that species of Tetracapsula form a clade. It diverged early in the evolution of the Myxozoa, before the radiation that gave rise to the better known genera belonging to the two orders in the single class Myxosporea. The genus Tetracapsula as seen in bryozoans shares some of the characters unique to the myxosporean phase and others typical of the actinosporean phase of genera belonging to the class Myxosporea. However, it exhibits other features which are not found in either phase. A new class Malacosporea and order Malacovalvulida are proposed to accommodate the family Saccosporidae and genus Tetracapsula. Special features of the new class are the sac-like proliferative body, valve cells not covering the exit point of the polar filament, lack of a stopper-like structure sealing the exit, maintenance of valve cell integrity even at spore maturity, absence of hardened spore walls and unique structure of sporoplasmosomes in the sporoplasms.}, }
@article {pmid10996508, year = {2000}, author = {Kannan, K and Jain, SK}, title = {Oxidative stress and apoptosis.}, journal = {Pathophysiology : the official journal of the International Society for Pathophysiology}, volume = {7}, number = {3}, pages = {153-163}, doi = {10.1016/s0928-4680(00)00053-5}, pmid = {10996508}, issn = {0928-4680}, abstract = {Apoptosis or programmed cell death, is essential for the normal functioning and survival of most multi-cellular organisms. The morphological and biochemical characteristics of apoptosis, however, are highly conserved during the evolution. It is currently believed that apoptosis can be divided into at least three functionally distinct phases, i.e. induction, effector and execution phase. Recent studies have demonstrated that reactive oxygen species (ROS) and the resulting oxidative stress play a pivotal role in apoptosis. Antioxidants and thiol reductants, such as N-acetylcysteine, and overexpression of manganese superoxide (MnSOD) can block or delay apoptosis. Bcl-2, an endogenously produced protein, has been shown to prevent cells from dying of apoptosis apparently by an antioxidative mechanism. Taken together ROS, and the resulting cellular redox change, can be part of signal transduction pathway during apoptosis. It is now established that mitochondria play a prominent role in apoptosis. During mitochondrial dysfunction, several essential players of apoptosis, including pro-caspases, cytochrome C, apoptosis-inducing factor (AIF), and apoptotic protease-activating factor-1 (APAF-1) are released into the cytosol. The multimeric complex formation of cytochrome C, APAF-1 and caspase 9 activates downstream caspases leading to apoptotic cell death. All the three functional phases of apoptosis are under the influence of regulatory controls. Thus, increasing evidences provide support that oxidative stress and apoptosis are closely linked physiological phenomena and are implicated in pathophysiology of some of the chronic diseases including AIDS, autoimmunity, cancer, diabetes mellitus, Alzheimer's and Parkinson's and ischemia of heart and brain.}, }
@article {pmid10996302, year = {2000}, author = {Juhola, MK and Shah, ZH and Grivell, LA and Jacobs, HT}, title = {The mitochondrial inner membrane AAA metalloprotease family in metazoans.}, journal = {FEBS letters}, volume = {481}, number = {2}, pages = {91-95}, doi = {10.1016/s0014-5793(00)01989-x}, pmid = {10996302}, issn = {0014-5793}, mesh = {Animals ; Humans ; Intracellular Membranes/*enzymology ; Invertebrates ; Metalloendopeptidases/*genetics/*metabolism ; Mitochondria/*enzymology ; Multigene Family ; Phylogeny ; }, abstract = {Three metalloproteases belonging to the AAA superfamily (Yme1p, Afg3p and Rca1p) are involved in protein turnover and respiratory chain complex assembly in the yeast inner mitochondrial membrane. Analysis of the completed genome sequences of Caenorhabditis elegans and Drosophila melanogaster indicates that this gene family typically comprises 3-4 members in metazoans. Phylogenetic analysis reveals three main branches represented, respectively, by Saccharomyces cerevisiae YME1, human SPG7 (paraplegin) and S. cerevisiae AFG3 and RCA1. mt-AAA metalloproteases are weak candidates for several previously studied Drosophila mutants. A full elucidation of the cellular and physiological roles of mt-AAA metalloproteases in metazoans will require the creation of targeted mutations.}, }
@article {pmid10989156, year = {2000}, author = {Bakatselou, C and Kidgell, C and Graham Clark, C}, title = {A mitochondrial-type hsp70 gene of Entamoeba histolytica.}, journal = {Molecular and biochemical parasitology}, volume = {110}, number = {1}, pages = {177-182}, doi = {10.1016/s0166-6851(00)00264-4}, pmid = {10989156}, issn = {0166-6851}, mesh = {Amino Acid Sequence ; Animals ; Blotting, Northern ; Entamoeba histolytica/*genetics/growth &amp; development/metabolism ; HSP70 Heat-Shock Proteins/chemistry/*genetics/*metabolism ; Mitochondria/*genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; }, }
@article {pmid10981697, year = {2000}, author = {Nakai, R and Sen, K and Kurosawa, S and Shibai, H}, title = {Basidiomycetous fungus Flammulina velutipes harbors two linear mitochondrial plasmids encoding DNA and RNA polymerases.}, journal = {FEMS microbiology letters}, volume = {190}, number = {1}, pages = {99-102}, doi = {10.1111/j.1574-6968.2000.tb09269.x}, pmid = {10981697}, issn = {0378-1097}, mesh = {Agaricales/*enzymology/genetics/ultrastructure ; Amino Acid Sequence ; Cloning, Molecular ; DNA, Fungal/analysis/genetics ; DNA-Directed DNA Polymerase/chemistry/*genetics ; DNA-Directed RNA Polymerases/chemistry/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Plasmids/*genetics ; Sequence Analysis, DNA ; }, abstract = {Basidiomycetous fungus Flammulina velutipes R15 strain had two linear plasmids in its mitochondria designated pFV1 and pFV2. They were double-stranded DNAs, whose sizes were 8.3 and 8.9 kb, respectively. Sequencing analysis of 7364 bases of the pFV1 and 6861 bases of the pFV2 revealed that the both plasmids had one set of two open reading frames (ORFs) each of that encoded putative DNA and RNA polymerases similar to those of mitochondrial plasmids in other filamentous fungi. In phylogenetic analysis of deduced amino acid sequences of the ORFs and counterparts of other filamentous fungi, the pFV2 was expectedly clustered with plasmids of basidiomycetous fungi. whereas the pFV1 with kalilo plasmid of ascomycetous fungus Neurospora intermedia.}, }
@article {pmid10978543, year = {2000}, author = {Gupta, RS}, title = {The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes.}, journal = {FEMS microbiology reviews}, volume = {24}, number = {4}, pages = {367-402}, doi = {10.1111/j.1574-6976.2000.tb00547.x}, pmid = {10978543}, issn = {0168-6445}, mesh = {ATP-Dependent Proteases ; Adenosine Triphosphatases/genetics ; Alanine-tRNA Ligase/genetics ; Amino Acid Sequence ; Bacterial Proteins/*classification/genetics ; Carrier Proteins/genetics ; Chaperonin 60/genetics ; DNA Topoisomerases, Type II/genetics ; *Escherichia coli Proteins ; Eukaryotic Cells ; Gene Deletion ; HSP70 Heat-Shock Proteins/genetics ; Heat-Shock Proteins/genetics ; Ligases/genetics/metabolism ; *Membrane Transport Proteins ; Mitochondria ; Molecular Sequence Data ; Phosphoribosyl Pyrophosphate/metabolism ; Phylogeny ; Proteobacteria/chemistry/*classification/genetics ; Pyrophosphatases/genetics ; Ribosomal Proteins/genetics ; SEC Translocation Channels ; SecA Proteins ; Sequence Alignment ; Serine Endopeptidases/genetics ; Succinate-CoA Ligases/genetics ; Sulfurtransferases/genetics ; Terminology as Topic ; UDPglucose 4-Epimerase/genetics ; Valine-tRNA Ligase/genetics ; }, abstract = {The evolutionary relationships of proteobacteria, which comprise the largest and phenotypically most diverse division among prokaryotes, are examined based on the analyses of available molecular sequence data. Sequence alignments of different proteins have led to the identification of numerous conserved inserts and deletions (referred to as signature sequences), which either are unique characteristics of various proteobacterial species or are shared by only members from certain subdivisions of proteobacteria. These signature sequences provide molecular means to define the proteobacterial phyla and their various subdivisions and to understand their evolutionary relationships to the other groups of eubacteria as well as the eukaryotes. Based on signature sequences that are present in different proteins it is now possible to infer that the various eubacterial phyla evolved from a common ancestor in the following order: low-G+C Gram-positive-->high-G+C Gram-positive-->Deinococcus-Thermus (green nonsulfur bacteria)-->cyanobacteria-->Spirochetes-->Chlamydia-Cytophaga-Aquifex -green sulfur bacteria-->Proteobacteria-1 (epsilon and delta)-->Proteobacteria-2 (alpha)-->Proteobacteria-3 (beta)-->Proteobacteria-4 (gamma). An unexpected but important aspect of the relationship deduced here is that the main eubacterial phyla are related to each other linearly rather than in a tree-like manner, suggesting that the major evolutionary changes within Bacteria have taken place in a directional manner. The identified signatures permit placement of prokaryotes into different groups/divisions and could be used for determinative purposes. These signatures generally support the origin of mitochondria from an alpha-proteobacterium and provide evidence that the nuclear cytosolic homologs of many genes are also derived from proteobacteria.}, }
@article {pmid10974565, year = {2000}, author = {Tomaska, L}, title = {Mitochondrial protein phosphorylation: lessons from yeasts.}, journal = {Gene}, volume = {255}, number = {1}, pages = {59-64}, doi = {10.1016/s0378-1119(00)00315-2}, pmid = {10974565}, issn = {0378-1119}, mesh = {Databases, Factual ; Evolution, Molecular ; Fungal Proteins/genetics/*metabolism ; Mitochondria/*metabolism ; Phosphoric Monoester Hydrolases/genetics ; Phosphorylation ; Protein Kinases/genetics ; Saccharomyces cerevisiae/enzymology/genetics/metabolism ; }, abstract = {The genome of Saccharomyces cerevisiae contains as many as 136 protein kinase encoding genes. However, only a limited number of mitochondrial protein kinases have been characterized. A computer-aided analysis revealed that only seven members of this large protein family are potentially localized in mitochondria. The low abundance of mitochondrially targeted protein kinases in yeast reflects the reductive evolution of mitochondrial signaling components and/or the apparent lack of selection pressure for acquiring mitochondrially localized protein kinases encoded by the host genome. This suggests that mitochondria, like obligatory intracellular bacterial parasites, are no longer dependent on signalling mechanisms mediated by protein kinases residing within the mitochondria. Instead, the nucleo-mitochondrial communication system requiring protein phosphorylation may be predominantly regulated by protein kinases, which are cytosolic and/or anchored to the outer mitochondrial membrane.}, }
@article {pmid10973051, year = {2000}, author = {Malik, HS and Henikoff, S}, title = {Dual recognition-incision enzymes might be involved in mismatch repair and meiosis.}, journal = {Trends in biochemical sciences}, volume = {25}, number = {9}, pages = {414-418}, doi = {10.1016/s0968-0004(00)01623-6}, pmid = {10973051}, issn = {0968-0004}, support = {GM-29009/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adenosine Triphosphatases ; Amino Acid Sequence ; Animals ; Bacterial Proteins/*genetics/metabolism/physiology ; *Base Pair Mismatch ; Cnidaria/genetics/metabolism ; DNA/biosynthesis ; *DNA Repair ; *DNA-Binding Proteins ; *Escherichia coli Proteins ; Mitochondria/metabolism ; Models, Genetic ; Molecular Sequence Data ; MutL Proteins ; MutS DNA Mismatch-Binding Protein ; Phylogeny ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; }, abstract = {Mismatch repair in many organisms depends on three proteins: the mismatch-recognition protein MutS, a nicking endonuclease MutH, and MutL, which acts as a scaffold between these. However, many genomes lack MutL but possess MutS. In one of these cases, in a coral mitochondrial genome, a gene is present that encodes a MutS protein fused to an HNH nicking endonuclease, potentially eliminating the requirement for MutL. Likewise, many prokaryotes could operate similarly, independently of MutL by encoding a fused MutS-Smr (MutS2) protein. Smr, which is proposed to be a nicking endonuclease, can also be found separately in many eukaryotes, where it might play a role in mismatch repair or meiotic chromosome crossing-over.}, }
@article {pmid10972502, year = {2000}, author = {Dyall, SD and Johnson, PJ}, title = {Origins of hydrogenosomes and mitochondria: evolution and organelle biogenesis.}, journal = {Current opinion in microbiology}, volume = {3}, number = {4}, pages = {404-411}, doi = {10.1016/s1369-5274(00)00112-0}, pmid = {10972502}, issn = {1369-5274}, support = {AI27857/AI/NIAID NIH HHS/United States ; }, mesh = {*Biological Evolution ; Hydrogen/*metabolism ; *Mitochondria/genetics/metabolism ; *Organelles/genetics/metabolism ; Symbiosis ; }, abstract = {It is becoming increasingly evident that all eukaryotes characterized to date bear some mitochondrial trait, whether it be a 'real' mitochondrion, a hydrogenosome, a mitosome or a few genes left behind from secondary losses of organelles. The implication is that the evolutionary history of the mitochondrion may reveal the history of the eukaryotic cell itself.}, }
@article {pmid10964222, year = {2000}, author = {Johnson, JB and Jordan, S}, title = {Phylogenetic divergence in leatherside chub (Gila copei) inferred from mitochondrial cytochrome b sequences.}, journal = {Molecular ecology}, volume = {9}, number = {8}, pages = {1029-1035}, doi = {10.1046/j.1365-294x.2000.00960.x}, pmid = {10964222}, issn = {0962-1083}, mesh = {Animals ; Conservation of Natural Resources ; Cyprinidae/*classification/genetics ; Cytochrome b Group/*genetics ; Ecology ; Evolution, Molecular ; Genetic Variation ; Haplotypes ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Utah ; }, abstract = {We examined intra-specific phylogenetic relationships in leatherside chub, Gila copei. The complete mitochondrial (mt) cytochrome b gene (1140 bp) was sequenced for 30 individuals from 10 populations that span the geographical distribution of this species. Traditional phylogenetic analyses revealed two deeply divergent and evolutionarily distinct mtDNA clades that are geographically separated in northern and southern drainage basins. Interpopulation sequence variation between clades ranged from 7.7 to 8.1%. The northern clade was genetically more similar and phylogenetically more closely related to the selected out-group Lepidomeda m. mollispinus than to the southern clade, suggesting that the taxonomy of this species may require revision. Sequence variation among populations within clades ranged from 0 to 0.3% in the north and from 0 to 0.7% in the south. Statistical parsimony was used to construct phylogenetic networks of haplotypes within clades. Nested clade analysis revealed that geographical fragmentation has played an important role in genetic structuring within northern and southern clades.}, }
@article {pmid10958850, year = {2000}, author = {Schmitz, J and Ohme, M and Zischler, H}, title = {The complete mitochondrial genome of Tupaia belangeri and the phylogenetic affiliation of scandentia to other eutherian orders.}, journal = {Molecular biology and evolution}, volume = {17}, number = {9}, pages = {1334-1343}, doi = {10.1093/oxfordjournals.molbev.a026417}, pmid = {10958850}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry/*genetics ; Mitochondria/genetics/metabolism ; Molecular Sequence Data ; *Phylogeny ; Proteins/genetics ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Transfer/genetics ; Scandentia/classification/*genetics ; Sequence Analysis, DNA ; Tupaia/*genetics ; }, abstract = {The complete mitochondrial genome of Tupaia belangeri, a representative of the eutherian order Scandentia, was determined and compared with full-length mitochondrial sequences of other eutherian orders described to date. The complete mitochondrial genome is 16, 754 nt in length, with no obvious deviation from the general organization of the mammalian mitochondrial genome. Thus, features such as start codon usage, incomplete stop codons, and overlapping coding regions, as well as the presence of tandem repeats in the control region, are within the range of mammalian mitochondrial (mt) DNA variation. To address the question of a possible close phylogenetic relationship between primates and Tupaia, the evolutionary affinities among primates, Tupaia and bats as representatives of the Archonta superorder, ferungulates, guinea pigs, armadillos, rats, mice, and hedgehogs were examined on the basis of the complete mitochondrial DNA sequences. The opossum sequence was used as an outgroup. The trees, estimated from 12 concatenated genes encoded on the mitochondrial H-strand, add further molecular evidence against an Archonta monophyly. With the new data described in this paper, most of both the mitochondrial and the nuclear data point away from Scandentia as the closest extant relatives to primates. Instead, the complete mitochondrial data support a clustering of Scandentia with Lagomorpha connecting to the branch leading to ferungulates. This closer phylogenetic relationship of Tupaia to rabbits than to primates first received support from several analyses of nuclear and partial mitochondrial DNA data sets. Given that short sequences are of limited use in determining deep mammalian relationships, the partial mitochondrial data available to date support this hypothesis only tentatively. Our complete mitochondrial genome data therefore add considerably more evidence in support of this hypothesis.}, }
@article {pmid10958796, year = {2000}, author = {Esterbauer, H and Oberkofler, H and Krempler, F and Strosberg, AD and Patsch, W}, title = {The uncoupling protein-3 gene is transcribed from tissue-specific promoters in humans but not in rodents.}, journal = {The Journal of biological chemistry}, volume = {275}, number = {46}, pages = {36394-36399}, doi = {10.1074/jbc.M005713200}, pmid = {10958796}, issn = {0021-9258}, mesh = {Adipose Tissue, Brown/metabolism ; Animals ; Carrier Proteins/*genetics ; Cells, Cultured ; *Gene Expression Regulation ; Humans ; Ion Channels ; Mice ; Mitochondria/metabolism ; Mitochondrial Proteins ; Molecular Sequence Data ; Muscle, Skeletal/metabolism ; Nuclease Protection Assays ; Organ Specificity ; Phylogeny ; Promoter Regions, Genetic/*genetics ; Protein Isoforms/genetics ; RNA, Messenger/analysis/genetics/metabolism ; Rats ; Sequence Alignment ; Uncoupling Protein 3 ; }, abstract = {Uncoupling protein-3 (UCP3), a mitochondrial membrane transporter, is a candidate effector of thermogenesis. Even though mice with targeted disruption of the UCP3 gene are not obese, indirect evidence suggests that this protein contributes to the control of energy expenditure in humans. We therefore characterized the human UCP3 gene and compared it with its rodent homologues with respect to tissue-specific expression and regulatory regions. Like rodent UCP3, human UCP3 was expressed in skeletal muscle and brown adipose tissue (BAT). The short mRNA isoform, UCP3(S), which is absent in rodents, was relatively more abundant in human skeletal muscle in comparison to human BAT. Two tissue-specific transcription start sites for each skeletal muscle and BAT were delineated for human UCP3. Tissue-specific transcript initiation was maintained in both tissues and cultured cells over a wide range of expression levels. In contrast, rodent transcripts were initiated at the same site in BAT and muscle tissue. Comparison of human and rodent promoters indicated a rapid phylogenetic evolution suggesting functional diversification. The transcription from tissue-specific promoters in humans is a novel finding that may provide the basis for therapeutic interventions aimed at regulating energy expenditure in a tissue-specific fashion.}, }
@article {pmid10950302, year = {2000}, author = {Ribas de Pouplana, L and Schimmel, P}, title = {A view into the origin of life: aminoacyl-tRNA synthetases.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {57}, number = {6}, pages = {865-870}, doi = {10.1007/pl00000729}, pmid = {10950302}, issn = {1420-682X}, mesh = {Amino Acyl-tRNA Synthetases/chemistry/genetics/*metabolism ; Cytoplasm/enzymology ; DNA/genetics/metabolism ; *Evolution, Molecular ; Genetic Code ; Mitochondria/enzymology/genetics ; *Origin of Life ; Protein Biosynthesis ; RNA/genetics/metabolism ; }, }
@article {pmid10944470, year = {2000}, author = {Jones, JM and Gould, SJ}, title = {Identification of PTE2, a human peroxisomal long-chain acyl-CoA thioesterase.}, journal = {Biochemical and biophysical research communications}, volume = {275}, number = {1}, pages = {233-240}, doi = {10.1006/bbrc.2000.3285}, pmid = {10944470}, issn = {0006-291X}, support = {DK45787/DK/NIDDK NIH HHS/United States ; HD10981/HD/NICHD NIH HHS/United States ; }, mesh = {Acyl Coenzyme A/*metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Cell Line ; Databases, Factual ; Fluorescent Antibody Technique ; Humans ; Hydrogen-Ion Concentration ; Mitochondria/enzymology ; Molecular Sequence Data ; Multigene Family ; Peroxisomes/*enzymology/metabolism ; Phylogeny ; Protein Sorting Signals ; Recombinant Proteins/metabolism ; Sequence Alignment ; Substrate Specificity ; Thiolester Hydrolases/chemistry/*genetics/*metabolism ; Transfection ; }, abstract = {Computer-based approaches identified PTE2 as a candidate human peroxisomal acyl-CoA thioesterase gene. The PTE2 gene product is highly similar to the rat cytosolic and mitochondrial thioesterases, CTE1 and MTE1, respectively, and terminates in a tripeptide sequence, serine-lysine-valine(COOH), that resembles the consensus sequence for type-1 peroxisomal targeting signals. PTE2 was targeted to peroxisomes and recombinant PTE2 showed intrinsic acyl-CoA thioesterase activity with a pH optimum of 8.5. A comparison of PTE2 and PTE1 thioesterase activities across multiple acyl-CoA substrates indicated that while PTE1 was most active on medium-chain acyl-CoAs, with little activity on long-chain acyl-CoAs, PTE2 displayed high activity on medium- and long-chain acyl-CoAs. The identification of PTE2 therefore offers an explanation for the observed long-chain acyl-CoA thioesterase activity of mammalian peroxisomes.}, }
@article {pmid10942615, year = {2000}, author = {Pruess, KP and Adams, BJ and Parsons, TJ and Zhu, X and Powers, TO}, title = {Utility of the mitochondrial cytochrome oxidase II gene for resolving relationships among black flies (Diptera: simuliidae).}, journal = {Molecular phylogenetics and evolution}, volume = {16}, number = {2}, pages = {286-295}, doi = {10.1006/mpev.2000.0807}, pmid = {10942615}, issn = {1055-7903}, support = {AI29456/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Classification ; Diptera/*classification/*genetics ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {The complete mitochondrial cytochrome oxidase II gene was sequenced from 17 black flies, representing 13 putative species, and used to infer phylogenetic relationships. A midge (Paratanytarsus sp.) and three mosquitoes (Aedes aegypti, Anopheles quadrimaculatus, and Culex quinquefasciatus) were used as outgroup taxa. All outgroup taxa were highly divergent from black flies. Phylogenetic trees based on weighted parsimony (a priori and a posteriori), maximum likelihood, and neighbor-joining (log-determinant distances) differed topologically, with deeper nodes being the least well-supported. All analyses supported current classification into species groups but relationships among those groups were poorly resolved. The majority of phylogenetic signal came from closely related sister taxa. The CO-II gene may be useful for exploring relationships at or below the subgeneric level, but is of questionable value at higher taxonomic levels. The weighting method employed gave phylogenetic results similar to those reported by other authors for other insect CO-II data sets. A best estimate of phylogenetic relationships based on the CO-II gene is presented and discussed in relation to current black fly classification.}, }
@article {pmid10940569, year = {2000}, author = {Williams, EJ and Pal, C and Hurst, LD}, title = {The molecular evolution of signal peptides.}, journal = {Gene}, volume = {253}, number = {2}, pages = {313-322}, doi = {10.1016/s0378-1119(00)00233-x}, pmid = {10940569}, issn = {0378-1119}, mesh = {Amino Acid Substitution ; Animals ; Databases, Factual ; *Evolution, Molecular ; Gene Frequency ; Immunity/genetics ; Mice ; Mitochondria/metabolism ; Mutation ; Protein Sorting Signals/*genetics ; Proteins/genetics ; Rats ; Receptor, IGF Type 2/genetics ; Selection, Genetic ; }, abstract = {Signal peptides direct mature peptides to their appropriate cellular location, after which they are cleaved off. Very many random alternatives can serve the same function. Of all coding sequences, therefore, signal peptides might come closest to being neutrally evolving. Here we consider this issue by examining the molecular evolution of 76 mouse-rat orthologues, each with defined signal peptides. Although they do evolve rapidly, they evolve about half as fast as neutral sequences. This indicates that a substantial proportion of mutations must be under stabilizing selection. A few putative signal sequences lack a hydrophobic core and these tend to be more slowly evolving than others, indicating even stronger stabilizing selection. However, closer scrutiny suggests that some of these represent mis-annotations in GenBank. It is also likely that some of the substitutions are not neutral. We find, for example, that the rate of protein evolution correlates with that of the mature peptide. This may be a result of compensatory evolution. We also find that signal peptides of immune genes tend to be faster evolving than the average, which suggests an association with antagonistic co-evolution. Previous reports also indicated that the signal peptide of the imprinted gene, Igf2r, is also unusually fast evolving. This, it was hypothesized, might also be indicative of antagonistic co-evolution. Comparison of Igf2r's signal peptide evolution shows that, although it is not an outlier, its rate of evolution is comparable to that of many of the faster evolving immune system signal sequences and 5/6 of the amino acid changes do not conserve hydrophobicity. This is at least suggestive that there is something unusual about Igf2r's signal sequence.}, }
@article {pmid10940562, year = {2000}, author = {Jost, R and Berkowitz, O and Wirtz, M and Hopkins, L and Hawkesford, MJ and Hell, R}, title = {Genomic and functional characterization of the oas gene family encoding O-acetylserine (thiol) lyases, enzymes catalyzing the final step in cysteine biosynthesis in Arabidopsis thaliana.}, journal = {Gene}, volume = {253}, number = {2}, pages = {237-247}, doi = {10.1016/s0378-1119(00)00261-4}, pmid = {10940562}, issn = {0378-1119}, mesh = {Arabidopsis/enzymology/*genetics ; Cell Compartmentation ; Cysteine/*biosynthesis ; Cysteine Synthase/*genetics/metabolism ; DNA, Plant/chemistry/genetics ; Evolution, Molecular ; Exons ; Gene Expression Regulation, Enzymologic ; Genes, Plant/*genetics ; Introns ; Isoenzymes/genetics ; Kinetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Promoter Regions, Genetic ; Protein Binding ; Recombinant Fusion Proteins/genetics/metabolism ; Sequence Analysis, DNA ; Serine/*analogs &amp; derivatives/metabolism ; Substrate Specificity ; }, abstract = {The final step of cysteine biosynthesis in plants is catalyzed by O-acetylserine (thiol) lyase (OAS-TL), which occurs as several isoforms found in the cytosol, the plastids and the mitochondria. Genomic DNA blot hybridization and isolation of genomic clones indicate single copy genes (oasA1, oasA2, oasB and oasC) that encode the activities of OAS-TL A, B and C found in separate subcellular compartments in the model plant Arabidopsis thaliana. Sequence analysis reveals that the newly discovered oasA2 gene represents a pseudogene that is still transcribed, but is not functionally translated. The comparison of gene structures suggests that oasA1/oasA2 and oasB/oasC are closely related and may be derived from a common ancestor by subsequent duplications. OAS-TL A, B and C were overexpressed in an Escherichia coli mutant lacking cysteine synthesis and exhibited bifunctional OAS-TL and beta-cyanoalanine synthase (CAS) activities. However, all three proteins represent true OAS-TLs according to kinetic analysis and are unlikely to function in cyanide detoxification or secondary metabolism. In addition, it was demonstrated that the mitochondrial OAS-TL C exhibits in vivo protein-protein interaction capabilities with respect to cysteine synthase complex formation similar to cytosolic OAS-TL A and plastid OAS-TL B. Multiple database accessions for each of the A. thaliana OAS-TL isoforms can thus be attributed to a specified number of oas genes to which functionally defined gene products are assigned, and which are responsible for compartment-specific cysteine synthesis.}, }
@article {pmid10940377, year = {2000}, author = {Friedrich, T and Scheide, D}, title = {The respiratory complex I of bacteria, archaea and eukarya and its module common with membrane-bound multisubunit hydrogenases.}, journal = {FEBS letters}, volume = {479}, number = {1-2}, pages = {1-5}, doi = {10.1016/s0014-5793(00)01867-6}, pmid = {10940377}, issn = {0014-5793}, mesh = {Archaea/enzymology/genetics ; Bacteria/enzymology/genetics ; Chloroplasts/enzymology ; Electron Transport ; Electron Transport Complex I ; Eukaryotic Cells ; Evolution, Molecular ; Mitochondria/enzymology ; NADH, NADPH Oxidoreductases/*chemistry/genetics/*metabolism ; Protein Structure, Quaternary ; Protons ; }, abstract = {The proton-pumping NADH:ubiquinone oxidoreductase, also called complex I, is the first of the respiratory complexes providing the proton motive force which is essential for energy consuming processes like the synthesis of ATP. Homologues of this complex exist in bacteria, archaea, in mitochondria of eukaryotes and in chloroplasts of plants. The bacterial and mitochondrial complexes function as NADH dehydrogenase, while the archaeal complex works as F420H2 dehydrogenase. The electron donor of the cyanobacterial and plastidal complex is not yet known. Despite the different electron input sites, 11 polypeptides constitute the structural framework for proton translocation and quinone binding in the complex of all three domains of life. Six of them are also present in a family of membrane-bound multisubunit [NiFe] hydrogenases. It is discussed that they build a module for electron transfer coupled to proton translocation.}, }
@article {pmid10939242, year = {2000}, author = {Wu, LF and Ize, B and Chanal, A and Quentin, Y and Fichant, G}, title = {Bacterial twin-arginine signal peptide-dependent protein translocation pathway: evolution and mechanism.}, journal = {Journal of molecular microbiology and biotechnology}, volume = {2}, number = {2}, pages = {179-189}, pmid = {10939242}, issn = {1464-1801}, mesh = {Arginine/metabolism ; Bacteria/*genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/*metabolism ; Biological Evolution ; Biological Transport, Active ; Carrier Proteins/chemistry/genetics/metabolism ; *Escherichia coli Proteins ; Gene Products, tat/chemistry/genetics/*metabolism ; Genes, Bacterial ; Genes, tat ; *Membrane Transport Proteins ; Models, Molecular ; Operon ; Protein Sorting Signals/chemistry/genetics/metabolism ; }, abstract = {The recently identified bacterial Tat pathway is capable of exporting proteins with a peculiar twin-arginine signal peptide in folded conformation independently of the Sec machinery. It is structurally and mechanistically similar to the delta pH-dependent pathway used for importing chloroplast proteins into the thylakoid. The tat genes are not ubiquitously present and are absent from half of the completely sequenced bacterial genomes. The presence of the tat genes seems to correlate with genome size and with the presence of important enzymes with a twin-arginine signal peptide. A minimal Tat system requires a copy of tatA and a copy of tatC. The composition and gene order of a tat locus are generally conserved within the same taxonomy group but vary considerably to other groups, which would exclude an acquisition of the Tat system by recent horizontal gene transfer. The tat genes are also found in the genomes of chloroplasts and plant mitochondria but are absent from animal mitochondrial genomes. The topology of evolution trees suggests a bacterial origin of the Tat system. In general, the twin-arginine signal peptide is capable of targeting any passenger protein to the Tat pathway. However, a structural signal carried by the mature part of a passenger protein can override targeting information in a signal peptide under certain circumstances. Tat systems show a substrate-Tat component specificity and a species specificity. The pore size of the Tat channel is estimated as being between 5 and 9 nm. Operational models of the Tat system are proposed.}, }
@article {pmid10938340, year = {2000}, author = {Osteryoung, KW}, title = {Organelle fission. Crossing the evolutionary divide.}, journal = {Plant physiology}, volume = {123}, number = {4}, pages = {1213-1216}, doi = {10.1104/pp.123.4.1213}, pmid = {10938340}, issn = {0032-0889}, mesh = {Arabidopsis Proteins ; Bacterial Proteins/genetics ; Cell Division/genetics/physiology ; Chloroplasts/genetics/physiology ; *Cytoskeletal Proteins ; *Evolution, Molecular ; Mitochondria/genetics/physiology ; Organelles/genetics/*physiology ; Plant Proteins/genetics ; }, }
@article {pmid10937248, year = {2000}, author = {Krakauer, DC}, title = {Stability and evolution of overlapping genes.}, journal = {Evolution; international journal of organic evolution}, volume = {54}, number = {3}, pages = {731-739}, doi = {10.1111/j.0014-3820.2000.tb00075.x}, pmid = {10937248}, issn = {0014-3820}, mesh = {*Evolution, Molecular ; Gene Expression Regulation ; Genes, Overlapping/*genetics ; *Models, Genetic ; *Models, Theoretical ; Selection, Genetic ; Transcriptional Activation ; }, abstract = {When the same sequence of nucleotides codes for regions of more than one functional polypeptide, this sequence contains overlapping genes. Overlap is most common in rapidly evolving genomes with high mutation rates such as viruses, bacteria, and mitochondria. Overlap is thought to be important as: (1) a means of compressing a maximum amount of information into short sequences of structural genes; and (2) as a mechanism for regulating gene expression through translational coupling of functionally related polypeptides. The stability of overlapping codes is examined in relation to the information cost of overlap and the mutation rate of the genome. The degree of overlap in a given population will tend to become monomorphic. Evolution toward partial overlap of genes is shown to depend on a convex cost function of overlap. Overlap does not evolve when expression of overlapping genes is mutually exclusive and produced by rare mutations to the wild-type genome. Assuming overlap increases coupling between functionally related genes, the conditions favoring overlap are explored in relation to the kinetics of gene activation and decay. Coupling is most effective for genes in which the gene overlapping at its 5' end (leading gene) decays rapidly, while the gene overlapping at the 3' end (induced gene) decays slowly. If gene expression can feedback on itself (autocatalysis), then high rates of activation favor overlap.}, }
@article {pmid10937239, year = {2000}, author = {Allendorf, FW and Seeb, LW}, title = {Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers.}, journal = {Evolution; international journal of organic evolution}, volume = {54}, number = {2}, pages = {640-651}, doi = {10.1111/j.0014-3820.2000.tb00065.x}, pmid = {10937239}, issn = {0014-3820}, mesh = {Animals ; Base Sequence ; Cell Nucleus/*genetics ; DNA/*genetics ; DNA Primers ; Enzymes/*genetics ; Gene Duplication ; *Genetic Markers ; Mitochondria/*genetics ; Salmon/*genetics ; }, abstract = {We examined genetic variation at 21 polymorphic allozyme loci, 15 nuclear DNA loci, and mitochondrial DNA in four spawning populations of sockeye salmon (Oncorhynchus nerka) from Cook Inlet, Alaska, to test for differences in the patterns of divergence among different types of markers. We were specifically interested in testing the suggestion that natural selection at allozyme loci compromises the effectiveness of these markers for describing the amount and patterns of gene flow among populations. We found concordance among markers in the amount of genetic variation within and among populations, with the striking exception of one allozyme locus (sAH), which exhibited more than three times the amount of among-population differentiation as other loci. A consideration of reports of discordance between allozymes and other loci indicates that these differences usually result from one or two exceptional loci. We conclude that it is important to examine many loci when estimating genetic differentiation to infer historical amounts of gene flow and patterns of genetic exchange among populations. It is less important whether those loci are allozymes or nuclear DNA markers.}, }
@article {pmid10930580, year = {2000}, author = {Shah, ZH and Hakkaart, GA and Arku, B and de Jong, L and van der Spek, H and Grivell, LA and Jacobs, HT}, title = {The human homologue of the yeast mitochondrial AAA metalloprotease Yme1p complements a yeast yme1 disruptant.}, journal = {FEBS letters}, volume = {478}, number = {3}, pages = {267-270}, doi = {10.1016/s0014-5793(00)01859-7}, pmid = {10930580}, issn = {0014-5793}, mesh = {ATP-Dependent Proteases ; ATPases Associated with Diverse Cellular Activities ; Adenosine Triphosphatases/chemistry/genetics/*metabolism ; Cell Line ; Chromosomes, Human, Pair 10/genetics ; Cloning, Molecular ; *Gene Deletion ; *Genetic Complementation Test ; Glycerol/metabolism ; Humans ; Metalloendopeptidases/chemistry/genetics/*metabolism ; Mitochondria/*enzymology/metabolism ; Mitochondrial Proteins ; Phylogeny ; Recombinant Fusion Proteins/chemistry/genetics/metabolism ; Saccharomyces cerevisiae/enzymology/*genetics/growth &amp; development/metabolism ; *Saccharomyces cerevisiae Proteins ; }, abstract = {In yeast, three AAA superfamily metalloproteases (Yme1p, Afg3p and Rca1p) are localized to the mitochondrial inner membrane where they perform roles in the assembly and turnover of the respiratory chain complexes. We have investigated the function of the proposed human orthologue of yeast Yme1p, encoded by the YME1L gene on chromosome 10p. Transfection of both HEK-293EBNA and yeast cells with a green fluorescent protein-tagged YME1L cDNA confirmed mitochondrial targeting. When expressed in a yme1 disruptant yeast strain, YME1L restored growth on glycerol at 37 degrees C. We propose that YME1L plays a phylogenetically conserved role in mitochondrial protein metabolism and could be involved in mitochondrial pathologies.}, }
@article {pmid10928858, year = {2000}, author = {Barrett, TG and Scott-Brown, M and Seller, A and Bednarz, A and Poulton, K and Poulton, J}, title = {The mitochondrial genome in Wolfram syndrome.}, journal = {Journal of medical genetics}, volume = {37}, number = {6}, pages = {463-466}, doi = {10.1136/jmg.37.6.463}, pmid = {10928858}, issn = {1468-6244}, mesh = {Adult ; Cohort Studies ; DNA, Mitochondrial/*genetics ; Female ; Genome ; Haplotypes/genetics ; Humans ; Male ; Membrane Proteins/genetics ; Mitochondria/enzymology/*genetics ; Mutation/genetics ; Phylogeny ; United Kingdom ; Wolfram Syndrome/diagnosis/enzymology/*genetics ; }, }
@article {pmid10922475, year = {2000}, author = {Zhang, F and Hogue, DL and Liu, L and Fisher, CL and Hui, D and Childs, S and Ling, V}, title = {M-ABC2, a new human mitochondrial ATP-binding cassette membrane protein.}, journal = {FEBS letters}, volume = {478}, number = {1-2}, pages = {89-94}, doi = {10.1016/s0014-5793(00)01823-8}, pmid = {10922475}, issn = {0014-5793}, mesh = {ATP-Binding Cassette Transporters/chemistry/*genetics/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Bone Marrow/metabolism ; Cell Line ; Chromosomes, Human, Pair 1/genetics ; Chromosomes, Human, Pair 15/genetics ; Cloning, Molecular ; Gene Expression Profiling ; Humans ; In Situ Hybridization, Fluorescence ; Intracellular Membranes/chemistry ; Mitochondria/*chemistry ; Molecular Sequence Data ; Phylogeny ; Physical Chromosome Mapping ; Protein Sorting Signals/genetics ; Pseudogenes/genetics ; RNA, Messenger/analysis/genetics ; Sequence Alignment ; Transfection ; }, abstract = {We have isolated a human cDNA encoding a novel ATP-binding cassette (ABC) protein whose gene was previously localized to chromosome 1q42 [Allikmets et al. (1995) Mamm. Genome 6, 111-117]. The gene transcript is expressed in all human tissues examined, with the highest levels in bone marrow. A non-expressed pseudogene also exists at chromosome 15q13-14. The new protein, which is most similar to the mitochondrial (M)-ABC1 protein, was also localized to mitochondria and therefore designated 'M-ABC2'. The N-terminus of M-ABC2 was shown to contain a mitochondrial-targeting signal sequence.}, }
@article {pmid10916154, year = {2000}, author = {Bullerwell, CE and Burger, G and Lang, BF}, title = {A novel motif for identifying rps3 homologs in fungal mitochondrial genomes.}, journal = {Trends in biochemical sciences}, volume = {25}, number = {8}, pages = {363-365}, doi = {10.1016/s0968-0004(00)01612-1}, pmid = {10916154}, issn = {0968-0004}, mesh = {*Amino Acid Motifs ; Amino Acid Sequence ; Fungal Proteins/genetics ; *Membrane Proteins ; Mitochondria/*genetics ; Mitochondrial Proteins ; Molecular Sequence Data ; Mortierella/*genetics ; Phylogeny ; Ribosomal Proteins/chemistry/*genetics ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Sequence Analysis, Protein ; *Sequence Homology, Amino Acid ; }, }
@article {pmid10916152, year = {2000}, author = {Lill, R and Kispal, G}, title = {Maturation of cellular Fe-S proteins: an essential function of mitochondria.}, journal = {Trends in biochemical sciences}, volume = {25}, number = {8}, pages = {352-356}, doi = {10.1016/s0968-0004(00)01589-9}, pmid = {10916152}, issn = {0968-0004}, mesh = {Biological Transport ; Evolution, Molecular ; Humans ; Iron-Sulfur Proteins/*biosynthesis/metabolism ; Mitochondria/genetics/*metabolism ; Models, Biological ; Saccharomyces cerevisiae/metabolism ; }, abstract = {Iron-sulfur (Fe-S) cluster-containing proteins perform important tasks in catalysis, electron transfer and regulation of gene expression. In eukaryotes, mitochondria are the primary site of cluster formation of most Fe-S proteins. Assembly of the Fe-S clusters is mediated by the iron-sulphate cluster assembly (ISC) machinery consisting of some ten proteins.}, }
@article {pmid10908563, year = {2000}, author = {McKenzie, M and Trounce, I}, title = {Expression of Rattus norvegicus mtDNA in Mus musculus cells results in multiple respiratory chain defects.}, journal = {The Journal of biological chemistry}, volume = {275}, number = {40}, pages = {31514-31519}, doi = {10.1074/jbc.M004070200}, pmid = {10908563}, issn = {0021-9258}, mesh = {Animals ; Blotting, Southern ; Cell Line ; Cell Nucleus/metabolism ; DNA, Mitochondrial/*metabolism ; Electron Transport/*genetics/*physiology ; Genotype ; Humans ; Hybrid Cells ; Lactic Acid/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Inbred CBA ; Oxidative Phosphorylation ; Phylogeny ; Protein Biosynthesis ; Rats ; Sequence Analysis, DNA ; Species Specificity ; Time Factors ; }, abstract = {The production of in vitro and in vivo models of mitochondrial DNA (mtDNA) defects is currently limited by a lack of characterized mouse cell mtDNA mutants that may be expected to model human mitochondrial diseases. Here we describe the creation of transmitochondrial mouse (Mus musculus) cells repopulated with mtDNA from different murid species (xenomitochondrial cybrids). The closely related Mus spretus mtDNA is readily maintained when introduced into M. musculus mtDNA-less (rho(0)) cells, and the resulting cybrids have normal oxidative phosphorylation (OXPHOS). When the more distantly related Rattus norvegicus mtDNA is transferred to the mouse nuclear background the mtDNA is replicated, transcribed, and translated efficiently. However, function of several OXPHOS complexes that depend on the coordinated assembly of nuclear and mtDNA-encoded proteins is impaired. Complex I activity in the Rattus xenocybrid was 46% of the control mean; complex III was 37%, and complex IV was 78%. These defects combined to restrict maximal respiration to 12-31% of the control and M. spretus xenocybrids, as measured polarographically using isolated cybrid mitochondria. These defects are distinct to those previously reported for human/primate xenocybrids. It should be possible to produce other mouse xenocybrid constructs with less severe OXPHOS phenotypes, to model human mtDNA diseases.}, }
@article {pmid10908562, year = {2000}, author = {Dey, R and Barrientos, A and Moraes, CT}, title = {Functional constraints of nuclear-mitochondrial DNA interactions in xenomitochondrial rodent cell lines.}, journal = {The Journal of biological chemistry}, volume = {275}, number = {40}, pages = {31520-31527}, doi = {10.1074/jbc.M004053200}, pmid = {10908562}, issn = {0021-9258}, support = {GM55766/GM/NIGMS NIH HHS/United States ; }, mesh = {3T3 Cells ; Animals ; Cell Division ; Cell Line ; Cell Nucleus/*metabolism ; Cell Survival ; DNA/*metabolism ; DNA, Mitochondrial/*metabolism ; Evolution, Molecular ; Galactose/metabolism ; Gene Transfer Techniques ; Hybrid Cells ; Immunoblotting ; Mice ; Mitochondria/*metabolism ; Oxygen/metabolism ; Phenotype ; Phosphorylation ; Polymorphism, Restriction Fragment Length ; Rats ; Respiration ; Time Factors ; }, abstract = {The co-evolution of nuclear and mitochondrial genomes in vertebrates led to more than 100 specific interactions that are crucial for an optimized ATP generation. These interactions have been examined by introducing rat mtDNA into mouse cells devoid of mitochondrial DNA (mtDNA). When mtDNA-less cells derived from the common mouse (Mus musculus domesticus) were fused to cytoplasts prepared from Mus musculus, Mus spretus, or rat (Rattus norvegicus), a comparable number of respiring clones could be obtained. Mouse xenomitochondrial cybrids harboring rat mtDNA had a slower growth rate in medium containing galactose as the carbon source, suggesting a defect in oxidative phosphorylation. These clones respired approximately 50% less than the parental mouse cells or xenomitochondrial cybrids harboring Mus spretus mtDNA. The activities of respiratory complexes I and IV were approximately 50% lower, but mitochondrial protein synthesis was unaffected. The defects in complexes I and IV were associated with decreased steady-state levels of respective subunits suggesting problems in assembly. We also showed that the presence of 10% mouse mtDNA co-existing with rat mtDNA was sufficient to restore respiration to normal levels. Our results suggest that evolutionary distance alone is not a precise predictor of nuclear-mitochondrial interactions as previously suggested for primates.}, }
@article {pmid10906275, year = {2000}, author = {Käser, M and Langer, T}, title = {Protein degradation in mitochondria.}, journal = {Seminars in cell &amp; developmental biology}, volume = {11}, number = {3}, pages = {181-190}, doi = {10.1006/scdb.2000.0166}, pmid = {10906275}, issn = {1084-9521}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Fungal Proteins/metabolism ; HSP70 Heat-Shock Proteins/metabolism ; Humans ; Intracellular Membranes/metabolism ; Mitochondria/enzymology/*metabolism ; Peptide Hydrolases/*metabolism ; Protein Processing, Post-Translational ; Proteins/*metabolism ; Saccharomyces cerevisiae/metabolism ; }, abstract = {The biogenesis of mitochondria and the maintenance of mitochondrial functions depends on an autonomous proteolytic system in the organelle which is highly conserved throughout evolution. Components of this system include processing peptidases and ATP-dependent proteases, as well as molecular chaperone proteins and protein complexes with apparently regulatory functions. While processing peptidases mediate maturation of nuclear-encoded mitochondrial preproteins, quality control within various subcompartments of mitochondria is ensured by ATP-dependent proteases which selectively remove non-assembled or misfolded polypeptides. Moreover; these proteases appear to control the activity- or steady-state levels of specific regulatory proteins and thereby ensure mitochondrial genome integrity, gene expression and protein assembly.}, }
@article {pmid10903947, year = {2000}, author = {Musco, G and Stier, G and Kolmerer, B and Adinolfi, S and Martin, S and Frenkiel, T and Gibson, T and Pastore, A}, title = {Towards a structural understanding of Friedreich's ataxia: the solution structure of frataxin.}, journal = {Structure (London, England : 1993)}, volume = {8}, number = {7}, pages = {695-707}, doi = {10.1016/s0969-2126(00)00158-1}, pmid = {10903947}, issn = {0969-2126}, support = {MC_U117584256/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry ; Carrier Proteins/chemistry ; Circular Dichroism ; Evolution, Molecular ; Friedreich Ataxia/genetics/*metabolism ; Fungal Proteins/chemistry ; Helminth Proteins/chemistry ; Heterozygote ; Humans ; Iron/metabolism ; Iron-Binding Proteins ; Ligands ; Mice ; Mitochondria/metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxidative Stress ; Phosphotransferases (Alcohol Group Acceptor)/*chemistry/deficiency/genetics/physiology ; Plant Proteins/chemistry ; Point Mutation ; Protein Conformation ; Protein Structure, Secondary ; Recombinant Fusion Proteins/chemistry ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Structure-Activity Relationship ; Transferrin-Binding Proteins ; Frataxin ; }, abstract = {BACKGROUND: Lesions in the gene for frataxin, a nuclear-encoded mitochondrial protein, cause the recessively inherited condition Friedreich's ataxia. It is thought that the condition arises from disregulation of mitochondrial iron homeostasis, with concomitant oxidative damage leading to neuronal death. Very little is, as yet, known about the biochemical function of frataxin.<br><br>RESULTS: Here, we show that the mature form of recombinant frataxin behaves in solution as a monodisperse species that is composed of a 15-residue-long unstructured N terminus and an evolutionarily conserved C-terminal region that is able to fold independently. The structure of the C-terminal domain consists of a stable seven-stranded antiparallel beta sheet packing against a pair of parallel helices. The structure is compact with neither grooves nor cavities, features that are typical of iron-binding modules. Exposed evolutionarily conserved residues cover a broad area and all cluster on the beta-sheet face of the structure, suggesting that this is a functionally important surface. The effect of two clinically occurring mutations on the fold was checked experimentally. When the mature protein was titrated with iron, no tendency to iron-binding or to aggregation was observed.<br><br>CONCLUSIONS: Knowledge of the frataxin structure provides important guidelines as to the nature of the frataxin binding partner. The absence of all the features expected for an iron-binding activity, the large conserved area on its surface and lack of evidence for iron-binding activity strongly support an indirect involvement of frataxin in iron metabolism. The effects of point mutations associated with Friedreich's ataxia can be rationalised by knowledge of the structure and suggest possible models for the occurrence of the disease in compound heterozygous patients.}, }
@article {pmid10886416, year = {2000}, author = {Lefai, E and Fernández-Moreno, MA and Kaguni, LS and Garesse, R}, title = {The highly compact structure of the mitochondrial DNA polymerase genomic region of Drosophila melanogaster: functional and evolutionary implications.}, journal = {Insect molecular biology}, volume = {9}, number = {3}, pages = {315-322}, doi = {10.1046/j.1365-2583.2000.00191.x}, pmid = {10886416}, issn = {0962-1075}, support = {GM45295/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Conserved Sequence ; DNA Polymerase gamma ; DNA-Directed DNA Polymerase/*genetics ; Drosophila melanogaster/*enzymology/genetics ; *Evolution, Molecular ; *Genes, Insect ; Mitochondria/*enzymology ; Multigene Family ; }, abstract = {The structure of a Drosophila melanogaster genomic region containing five tightly clustered genes has been determined and evaluated with regard to its functional and evolutionary relationships. In addition to the genes encoding the two subunits (alpha and beta) of the DNA polymerase gamma holoenzyme, the key enzyme for mitochondrial DNA replication, other genes contained in the cluster may be also involved in the cellular distribution of mitochondria and in the coordination of mitochondrial and nuclear DNA replication. The gene cluster is extremely compact, with very little intergenic space. It contains two bidirectional promoter regions, and particularly notable is the 5' end overlap detected in two of its genes, an exceptional situation in both prokaryotic and eukaryotic genome organization.}, }
@article {pmid10886388, year = {2000}, author = {Carmona, JA and Domínguez, J and Doadrio, I}, title = {Congruence between allozyme and cytochrome b gene sequence data in assessing genetic differentiation within the Iberian endemic Chondrostoma lemmingii (Pisces: cyprinidae).}, journal = {Heredity}, volume = {84 (Pt 6)}, number = {}, pages = {721-732}, doi = {10.1046/j.1365-2540.2000.00720.x}, pmid = {10886388}, issn = {0018-067X}, mesh = {Animals ; Cyprinidae/*genetics ; Cytochrome b Group/*genetics ; Genetic Variation ; Mitochondria/enzymology ; Phylogeny ; }, abstract = {To understand further the fragmentation of the hydrographical basins and the processes of divergence and speciation of freshwater fishes of the Iberian Peninsula, 10 populations of the Iberian endemic cyprinid Chondrostoma lemmingii were studied using 26 loci encoding 19 enzymes and the complete nucleotide sequence of the mitochondrial cytochrome b gene. Nuclear and mitochondrial DNA markers showed complete congruence in assessing the genetic differentiation among the samples analysed. This congruence was supported by a Mantel test in which a significant correlation (r=0.89) between Nei's genetic distances and sequence divergence (uncorrected p distances) was obtained. Diagnostic loci, Nei's genetic distances, and FST values, as well as the percentage of sequence divergence indicate that the Duero basin population accumulates the highest level of genetic differentiation. A moderate divergence was also observed among populations of the rest of the basins. Phenetic and phylogenetic relationships support the hypothesis that the differentiation process was not only due to hydrographical basin isolation but also due to an ancient endorrheism event, previous to hydrographical configuration, that could explain the marked differentiation of the Duero basin population.}, }
@article {pmid10899162, year = {2000}, author = {Pérez-Martínez, X and Vazquez-Acevedo, M and Tolkunova, E and Funes, S and Claros, MG and Davidson, E and King, MP and González-Halphen, D}, title = {Unusual location of a mitochondrial gene. Subunit III of cytochrome C oxidase is encoded in the nucleus of Chlamydomonad algae.}, journal = {The Journal of biological chemistry}, volume = {275}, number = {39}, pages = {30144-30152}, doi = {10.1074/jbc.M003940200}, pmid = {10899162}, issn = {0021-9258}, support = {TW01176-01/TW/FIC NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Cell Nucleus/*genetics ; Chlorophyta/enzymology/*genetics ; Electron Transport Complex IV/classification/*genetics/isolation &amp; purification ; Eukaryota/enzymology/genetics ; Magnoliopsida/enzymology/genetics ; Membrane Proteins/classification/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Protein Sorting Signals ; Protein Structure, Quaternary ; Saccharomyces cerevisiae Proteins ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {The algae of the family Chlamydomonadaceae lack the gene cox3 that encodes subunit III of cytochrome c oxidase in their mitochondrial genomes. This observation has raised the question of whether this subunit is present in cytochrome c oxidase or whether the corresponding gene is located in the nucleus. Cytochrome c oxidase was isolated from the colorless chlamydomonad Polytomella spp., and the existence of subunit III was established by immunoblotting analysis with an antibody directed against Saccharomyces cerevisiae subunit III. Based partly upon the N-terminal sequence of this subunit, oligodeoxynucleotides were designed and used for polymerase chain reaction amplification, and the resulting product was used to screen a cDNA library of Chlamydomonas reinhardtii. The complete sequences of the cox3 cDNAs from Polytomella spp. and C. reinhardtii are reported. Evidence is provided that the genes for cox3 are encoded by nuclear DNA, and the predicted polypeptides exhibit diminished physical constraints for import as compared with mitochondrial-DNA encoded homologs. This indicates that transfer of this gene to the nucleus occurred before Polytomella diverged from the photosynthetic Chlamydomonas lineage and that this transfer may have occurred in all chlamydomonad algae.}, }
@article {pmid10898984, year = {2000}, author = {Lo, N and Tokuda, G and Watanabe, H and Rose, H and Slaytor, M and Maekawa, K and Bandi, C and Noda, H}, title = {Evidence from multiple gene sequences indicates that termites evolved from wood-feeding cockroaches.}, journal = {Current biology : CB}, volume = {10}, number = {13}, pages = {801-804}, doi = {10.1016/s0960-9822(00)00561-3}, pmid = {10898984}, issn = {0960-9822}, mesh = {Animals ; Cellulase/genetics ; Cockroaches/*genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Isoptera/*genetics ; Mitochondria/enzymology ; Models, Genetic ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Despite more than half a century of research, the evolutionary origin of termites remains unresolved [1] [2] [3]. A clear picture of termite ancestry is crucial for understanding how these insects evolved eusociality, particularly because they lack the haplodiploid genetic system associated with eusocial evolution in bees, ants, wasps and thrips [4] [5]. Termites, together with cockroaches and praying mantids, constitute the order Dictyoptera, which has been the focus of numerous conflicting phylogenetic studies in recent decades [6] [7] [8] [9] [10] [11] [12]. With the aim of settling the debate over the sister-group of termites, we have determined the sequences of genes encoding 18S ribosomal RNA, mitochondrial cytochrome oxidase subunit II (COII) and endogenous endo-beta-1, 4-glucanase (EG) from a diverse range of dictyopterans. Maximum parsimony and likelihood analyses of these sequences revealed strong support for a clade consisting of termites and subsocial, wood-feeding cockroaches of the genus Cryptocercus. This clade is nested within a larger cockroach clade, implicating wood-feeding cockroaches as an evolutionary intermediate between primitive non-social taxa and eusocial termites.}, }
@article {pmid10889265, year = {2000}, author = {Hatzfeld, Y and Maruyama, A and Schmidt, A and Noji, M and Ishizawa, K and Saito, K}, title = {beta-Cyanoalanine synthase is a mitochondrial cysteine synthase-like protein in spinach and Arabidopsis.}, journal = {Plant physiology}, volume = {123}, number = {3}, pages = {1163-1171}, pmid = {10889265}, issn = {0032-0889}, mesh = {Arabidopsis/*enzymology/genetics ; Cysteine Synthase/genetics/*metabolism ; Escherichia coli/genetics/metabolism ; Evolution, Molecular ; Immunoblotting ; Isoenzymes/genetics/metabolism ; Lyases/genetics/*metabolism ; Mitochondria/*enzymology/genetics ; Phylogeny ; Recombinant Proteins/genetics/metabolism ; Spinacia oleracea/*enzymology/genetics ; Substrate Specificity ; }, abstract = {beta-Cyano-alanine synthase (CAS; EC 4.4.1.9) plays an important role in cyanide metabolism in plants. Although the enzymatic activity of beta-cyano-Ala synthase has been detected in a variety of plants, no cDNA or gene has been identified so far. We hypothesized that the mitochondrial cysteine synthase (CS; EC 4.2.99. 8) isoform, Bsas3, could actually be identical to CAS in spinach (Spinacia oleracea) and Arabidopsis. An Arabidopsis expressed sequence tag database was searched for putative Bsas3 homologs and four new CS-like isoforms, ARAth;Bsas1;1, ARAth;Bsas3;1, ARAth;Bsas4;1, and ARAth;Bsas4;2, were identified in the process. ARAth;Bsas3;1 protein was homologous to the mitochondrial SPIol;Bsas3;1 isoform from spinach, whereas ARAth;Bsas4;1 and ARAth;Bsas4;2 proteins defined a new class within the CS-like proteins family. In contrast to spinach SPIol;Bsas1;1 and SPIol;Bsas2;1 recombinant proteins, spinach SPIol;Bsas3;1 and Arabidopsis ARAth;Bsas3;1 recombinant proteins exhibited preferred substrate specificities for the CAS reaction rather than for the CS reaction, which identified these Bsas3 isoforms as CAS. Immunoblot studies supported this conclusion. This is the first report of the identification of CAS synthase-encoding cDNAs in a living organism. A new nomenclature for CS-like proteins in plants is also proposed.}, }
@article {pmid10889223, year = {2000}, author = {Prychitko, TM and Moore, WS}, title = {Comparative evolution of the mitochondrial cytochrome b gene and nuclear beta-fibrinogen intron 7 in woodpeckers.}, journal = {Molecular biology and evolution}, volume = {17}, number = {7}, pages = {1101-1111}, doi = {10.1093/oxfordjournals.molbev.a026391}, pmid = {10889223}, issn = {0737-4038}, mesh = {Animals ; Birds/*genetics ; Cell Nucleus/metabolism ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/genetics ; *Evolution, Molecular ; Fibrinogen/*genetics ; *Introns ; Mitochondria/*enzymology ; Phylogeny ; Species Specificity ; }, abstract = {Most molecular phylogenetic studies of vertebrates have been based on DNA sequences of mitochondrial-encoded genes. MtDNA evolves rapidly and is thus particularly useful for resolving relationships among recently evolved groups. However, it has the disadvantage that all of the mitochondrial genes are inherited as a single linkage group so that only one independent gene tree can be inferred regardless of the number of genes sequenced. Introns of nuclear genes are attractive candidates for independent sources of rapidly evolving DNA: they are pervasive, most of their nucleotides appear to be unconstrained by selection, and PCR primers can be designed for sequences in adjacent exons where nucleotide sequences are conserved. We sequenced intron 7 of the beta-fibrinogen gene (beta-fibint7) for a diversity of woodpeckers and compared the phylogenetic signal and nucleotide substitution properties of this DNA sequence with that of mitochondrial-encoded cytochrome b (cyt b) from a previous study. A few indels (insertions and deletions) were found in the beta-fibint7 sequences, but alignment was not difficult, and the indels were phylogentically informative. The beta-fibint7 and cyt b gene trees were nearly identical to each other but differed in significant ways from the traditional woodpecker classification. Cyt b evolves 2.8 times as fast as beta-fibint7 (14. 0 times as fast at third codon positions). Despite its relatively slow substitution rate, the phylogenetic signal in beta-fibint7 is comparable to that in cyt b for woodpeckers, because beta-fibint7 has less base composition bias and more uniform nucleotide substitution probabilities. As a consequence, compared with cyt b, beta-fibint7 nucleotide sites are expected to enter more distinct character states over the course of evolution and have fewer multiple substitutions and lower levels of homoplasy. Moreover, in contrast to cyt b, in which nearly two thirds of nucleotide sites rarely vary among closely related taxa, virtually all beta-fibint7 nucleotide sites appear free of selective constraints, which increases informative sites per unit sequenced. However, the estimated gamma distribution used to model rate variation among sites suggests constraints on some beta-fibint7 sites. This study suggests that introns will be useful for phylogenetic studies of recently evolved groups.}, }
@article {pmid10889220, year = {2000}, author = {Mundy, NI and Pissinatti, A and Woodruff, DS}, title = {Multiple nuclear insertions of mitochondrial cytochrome b sequences in callitrichine primates.}, journal = {Molecular biology and evolution}, volume = {17}, number = {7}, pages = {1075-1080}, doi = {10.1093/oxfordjournals.molbev.a026388}, pmid = {10889220}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; Callitrichinae/*genetics ; Cell Nucleus/*enzymology ; Cytochrome b Group/*genetics ; DNA Primers ; DNA Transposable Elements ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; }, abstract = {We report the presence of four nuclear paralogs of a 380-bp segment of cytochrome b in callitrichine primates (marmosets and tamarins). The mitochondrial cytochrome b sequence and each nuclear paralog were obtained from several species, allowing multiple comparisons of rates and patterns of substitution both between mitochondrial and nuclear sequences and among nuclear sequences. The mitochondrial DNA had high overall rates of molecular evolution and a strong bias toward substitutions at third codon positions. Rates of molecular evolution among the nuclear sequences were low and constant, and there were small differences in substitution patterns among the nuclear clades which were probably attributable to the small number of sites involved. A novel method of phylogenetic reconstruction based on the large difference in rates of evolution at different codon positions among mitochondrial and nuclear clades was used to determine whether different nuclear paralogs represent independent transposition events or duplications following a single insertion. This method is generally applicable in cases where differences in pattern of molecular evolution are known, and it showed that at least three of the four nuclear clades represent independent transposition events. The insertion events giving rise to two of the nuclear clades predate the divergence of the callitrichines, whereas those leading to the other two nuclear clades may have occurred in the common ancestor of marmosets.}, }
@article {pmid10880490, year = {2000}, author = {Taylor, JS and Breden, F}, title = {Slipped-strand mispairing at noncontiguous repeats in Poecilia reticulata: a model for minisatellite birth.}, journal = {Genetics}, volume = {155}, number = {3}, pages = {1313-1320}, pmid = {10880490}, issn = {0016-6731}, mesh = {Animals ; Base Pair Mismatch/*genetics ; Base Sequence ; DNA, Mitochondrial/analysis/genetics ; Genetics, Population ; Minisatellite Repeats/*genetics ; Mitochondria/*genetics ; *Models, Genetic ; Molecular Sequence Data ; Mutation ; Phylogeny ; Poecilia/*genetics ; Sequence Analysis, DNA ; Trinidad and Tobago ; }, abstract = {The standard slipped-strand mispairing (SSM) model for the formation of variable number tandem repeats (VNTRs) proposes that a few tandem repeats, produced by chance mutations, provide the "raw material" for VNTR expansion. However, this model is unlikely to explain the formation of VNTRs with long motifs (e.g., minisatellites), because the likelihood of a tandem repeat forming by chance decreases rapidly as the length of the repeat motif increases. Phylogenetic reconstruction of the birth of a mitochondrial (mt) DNA minisatellite in guppies suggests that VNTRs with long motifs can form as a consequence of SSM at noncontiguous repeats. VNTRs formed in this manner have motifs longer than the noncontiguous repeat originally formed by chance and are flanked by one unit of the original, noncontiguous repeat. SSM at noncontiguous repeats can therefore explain the birth of VNTRs with long motifs and the "imperfect" or "short direct" repeats frequently observed adjacent to both mtDNA and nuclear VNTRs.}, }
@article {pmid10874035, year = {2000}, author = {Turner, RJ and Lovato, M and Schimmel, P}, title = {One of two genes encoding glycyl-tRNA synthetase in Saccharomyces cerevisiae provides mitochondrial and cytoplasmic functions.}, journal = {The Journal of biological chemistry}, volume = {275}, number = {36}, pages = {27681-27688}, doi = {10.1074/jbc.M003416200}, pmid = {10874035}, issn = {0021-9258}, support = {GM23562/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Chromosomes, Fungal/genetics ; Cytoplasm/enzymology ; Evolution, Molecular ; Gene Deletion ; *Genes, Fungal ; Glycine-tRNA Ligase/chemistry/*genetics/metabolism ; Isoenzymes/chemistry/genetics/metabolism ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Saccharomyces cerevisiae/*enzymology/*genetics/growth &amp; development ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {In the yeast Saccharomyces cerevisiae, two genes (GRS1 and GRS2) encode glycyl-tRNA synthetase (GlyRS1 and GlyRS2, respectively). 59% of the sequence of GlyRS2 is identical to that of GlyRS1. Others have proposed that GRS1 and GRS2 encode the cytoplasmic and mitochondrial enzymes, respectively. In this work, we show that GRS1 encodes both functions, whereas GRS2 is dispensable. In addition, both cytoplasmic and mitochondrial phenotypes of the knockout allele of GRS1 in S. cerevisiae are complemented by the expression of the only known gene for glycyl-tRNA synthetase in Schizosaccharomyces pombe. Thus, a single gene for glycyl-tRNA synthetase likely encodes both cytoplasmic and mitochondrial activities in most or all yeast. Phylogenetic analysis shows that GlyRS2 is a predecessor of all yeast GlyRS homologues. Thus, GRS1 appears to be the result of a duplication of GRS2, which itself is pseudogene-like.}, }
@article {pmid10873789, year = {2000}, author = {Tully, LA and Parsons, TJ and Steighner, RJ and Holland, MM and Marino, MA and Prenger, VL}, title = {A sensitive denaturing gradient-Gel electrophoresis assay reveals a high frequency of heteroplasmy in hypervariable region 1 of the human mtDNA control region.}, journal = {American journal of human genetics}, volume = {67}, number = {2}, pages = {432-443}, pmid = {10873789}, issn = {0002-9297}, mesh = {Base Sequence ; Cytoplasm/*genetics ; DNA Mutational Analysis/methods ; DNA, Mitochondrial/*genetics ; Electrophoresis, Agar Gel ; Ethnicity/genetics ; Evolution, Molecular ; Genetic Variation/*genetics ; Humans ; Least-Squares Analysis ; Mitochondria/genetics ; Mutation/genetics ; Nucleic Acid Denaturation/genetics ; Nucleic Acid Heteroduplexes/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Regulatory Sequences, Nucleic Acid/*genetics ; Sensitivity and Specificity ; }, abstract = {A population study of heteroplasmy in the hypervariable region 1 (HV1) portion of the human mtDNA control region was performed. Blood samples from 253 randomly chosen individuals were examined using a sensitive denaturing gradient-gel electrophoresis (DGGE) system. This method is capable of detecting heteroplasmic proportions as low as 1% and virtually all heteroplasmy where the minor component is > or = 5%. Heteroplasmy was observed in 35 individuals (13.8%; 95% confidence interval [CI] 9.6-18.0). Of these individuals, 33 were heteroplasmic at one nucleotide position, whereas 2 were heteroplasmic at two different positions (a condition known as "triplasmy"). Although heteroplasmy occurred at a total of 16 different positions throughout HV1, it was most frequently observed at positions 16093 (n=13) and 16129 (n=6). In addition, the majority of heteroplasmic variants occurred at low proportions and could not be detected by direct sequencing of PCR products. This study indicates that low-level heteroplasmy in HV1 is relatively common and that it occurs at a broad spectrum of sites. Our results corroborate those of other recent reports indicating that heteroplasmy in the control region is more common than was previously believed-a finding that is of potential importance to evolutionary studies and forensic applications that are based on mtDNA variation.}, }
@article {pmid10871400, year = {2000}, author = {Chesnick, JM and Goff, M and Graham, J and Ocampo, C and Lang, BF and Seif, E and Burger, G}, title = {The mitochondrial genome of the stramenopile alga Chrysodidymus synuroideus. Complete sequence, gene content and genome organization.}, journal = {Nucleic acids research}, volume = {28}, number = {13}, pages = {2512-2518}, pmid = {10871400}, issn = {1362-4962}, mesh = {Algal Proteins/chemistry/genetics ; Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics ; Codon/genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; Eukaryota/*cytology/*genetics ; Evolution, Molecular ; *Genes ; Genetic Code/genetics ; Genetic Variation/genetics ; *Genome ; Mitochondria/*genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Physical Chromosome Mapping ; RNA, Transfer/genetics ; Sequence Alignment ; }, abstract = {This is the first report of a complete mitochondrial genome sequence from a photosynthetic member of the stramenopiles, the chrysophyte alga Chrysodidymus synuroideus. The circular-mapping mitochondrial DNA (mtDNA) of 34 119 bp contains 58 densely packed genes (all without introns) and five unique open reading frames (ORFs). Protein genes code for components of respiratory chain complexes, ATP synthase and the mitoribosome, as well as one product of unknown function, encoded in many other protist mtDNAs (YMF16). In addition to small and large subunit ribosomal RNAs, 23 tRNAs are mtDNA-encoded, permitting translation of all codons present in protein-coding genes except ACN (Thr) and CGN (Arg). The missing tRNAs are assumed to be imported from the cytosol. Comparison of the C.SYNUROIDEUS: mtDNA with that of other stramenopiles allowed us to draw conclusions about mitochondrial genome organization, expression and evolution. First, we provide evidence that mitochondrial ORFs code for highly derived, unrecognizable versions of ribosomal or respiratory genes otherwise 'missing' in a particular mtDNA. Secondly, the observed constraints in mitochondrial genome rearrangements suggest operon-based, co-ordinated expression of genes functioning in common biological processes. Finally, stramenopile mtDNAs reveal an unexpectedly low variability in genome size and gene complement, testifying to substantial differences in the tempo of mtDNA evolution between major eukaryotic lineages.}, }
@article {pmid10867997, year = {2000}, author = {Schipke, JD and Birkenkamp-Demtröder, K and Schwanke, U}, title = {[Myocardial hibernation: another view].}, journal = {Zeitschrift fur Kardiologie}, volume = {89}, number = {4}, pages = {259-263}, doi = {10.1007/s003920050482}, pmid = {10867997}, issn = {0300-5860}, mesh = {Animals ; Biological Evolution ; Coronary Circulation/*physiology ; Energy Metabolism/*physiology ; Humans ; Myocardial Stunning/*physiopathology ; Opioid Peptides/physiology ; Oxygen Consumption/*physiology ; }, abstract = {In the following, three newer concepts are brought together: myocardial hibernation, heterogeneity in myocardial blood flow and oxidative metabolism, and effects of hibernating animal serum on non-hibernators. Myocardial hibernation is viewed as a protective mechanism that helps to maintain myocardial integrity and viability by down-regulating contractile function as an adaptation to reduced blood flow. Myocardial flow is considerably heterogeneous. Consequently, oxygen supply to the myocardium is also heterogeneous. Many lines of evidence show a close correlation between regional flow and regional metabolism. In low-flow/low-metabolism areas, myocardial function must be reduced, since the myocardium would otherwise undergo necrosis. Thus, others and we hypothesize that function must be down-regulated to induce hibernation in low-flow areas. Because no regional histologic differences exist (the mitochondria are uniformly distributed within the myocardium), the pattern of heterogeneity seems to shift over time. Hence, we hypothesize that such very regional hibernation presents an evolutionary, protective mechanism, permitting subsequent myocardial areas to rest within the ceaselessly working heart. We also hypothesize that this mechanism ensures the down-regulation of function following myocardial ischemia in order to induce myocardial hibernation on a broader level. Surprisingly, a substance (opioid in nature) contained in hibernator serum both induced hibernation-like state in non-hibernators and suppressed myocardial oxygen consumption. Thus, we lastly hypothesize that myocardial hibernation is a remnant of the early stages of evolution and is closer to physiologic hibernation than traditionally viewed.}, }
@article {pmid10865960, year = {2000}, author = {Andersson, JO and Andersson, SG}, title = {A century of typhus, lice and Rickettsia.}, journal = {Research in microbiology}, volume = {151}, number = {2}, pages = {143-150}, doi = {10.1016/s0923-2508(00)00116-9}, pmid = {10865960}, issn = {0923-2508}, mesh = {Animals ; France ; *Genome, Bacterial ; History, 20th Century ; Humans ; Mitochondria/genetics ; Phthiraptera/*microbiology ; Phylogeny ; Rickettsia prowazekii/*genetics ; Sequence Analysis, DNA ; Typhus, Epidemic Louse-Borne/epidemiology/*history/microbiology ; }, abstract = {At the beginning of the 20th century, it was discovered at the Pasteur Institute in Tunis that epidemic typhus is transmitted by the human body louse. The complete genome sequence of its causative agent, Rickettsia prowazekii, was determined at Uppsala University in Sweden at the end of the century. In this mini-review, we discuss insights gained from the genome sequence of this fascinating and deadly organism.}, }
@article {pmid10862357, year = {2000}, author = {Serizawa, K and Suzuki, H and Tsuchiya, K}, title = {A phylogenetic view on species radiation in Apodemus inferred from variation of nuclear and mitochondrial genes.}, journal = {Biochemical genetics}, volume = {38}, number = {1-2}, pages = {27-40}, doi = {10.1023/a:1001828203201}, pmid = {10862357}, issn = {0006-2928}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/*genetics ; Cytochrome b Group/genetics ; Evolution, Molecular ; *Eye Proteins ; Genetic Markers ; Geography ; Mitochondria/*genetics ; Molecular Sequence Data ; Muridae/*classification/*genetics ; Phylogeny ; Rats ; Retinol-Binding Proteins/genetics ; Sequence Analysis, DNA ; }, abstract = {Species of field mice (genus Apodemus) are the most common rodents inhabiting woodlands and forests of the Palaearctic region. We examined the cytochrome b (cyt b) gene in mitochondrial DNA (1140 bp) and the interphotoreceptor retinoid binding protein (IRBP) gene in nuclear DNA (1152 bp) in nine species of Apodemus. Based on the genetic variation, the nine species were grouped into four lineages: (1) Agrarius group (A. agrarius, A. peninsulae, A. semotus, and A. speciosus), (2) Argenteus group (A. argenteus), (3) Gurkha group (A. gurkha), and (4) Sylvaticus group (A. alpicola, A. flavicollis, and A. sylvaticus). It was shown that these four lineages diverged within a short period of evolutionary time, suggestive of a radiation event. Soon after the radiation, the Agrarius group was likely to have differentiated again into the species lineages simultaneously. In contrast, the European clade, the Sylvaticus group, radiated rather recently. The relative ratio of the extent of sequence divergence among the four main lineages to that among the members of the subfamily Murinae (including Mus and Rattus) was calculated to be 72.4% in the cyt b gene with transversional substitutions, and 58.5% in the IRBP gene with all substitutions, using the Kimura two-parameter method. The value for the three European lineages was 27.6% in the cyt b gene and 12.3% in the IRBP gene. These results may have a correlation with the notion that deciduous broadleaf forests remained in Central East Asia through the late Tertiary to the present, while those in Europe to a large extent had disappeared by the Pliocene.}, }
@article {pmid10860961, year = {2000}, author = {Simpson, L and Thiemann, OH and Savill, NJ and Alfonzo, JD and Maslov, DA}, title = {Evolution of RNA editing in trypanosome mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {13}, pages = {6986-6993}, pmid = {10860961}, issn = {0027-8424}, mesh = {Animals ; *Biological Evolution ; RNA/*genetics ; *RNA Editing ; RNA, Mitochondrial ; RNA, Protozoan/*genetics ; Trypanosoma/*genetics ; }, abstract = {Two different RNA editing systems have been described in the kinetoplast-mitochondrion of trypanosomatid protists. The first involves the precise insertion and deletion of U residues mostly within the coding regions of maxicircle-encoded mRNAs to produce open reading frames. This editing is mediated by short overlapping complementary guide RNAs encoded in both the maxicircle and the minicircle molecules and involves a series of enzymatic cleavage-ligation steps. The second editing system is a C(34) to U(34) modification in the anticodon of the imported tRNA(Trp), thereby permitting the decoding of the UGA stop codon as tryptophan. U-insertion editing probably originated in an ancestor of the kinetoplastid lineage and appears to have evolved in some cases by the replacement of the original pan-edited cryptogene with a partially edited cDNA. The driving force for the evolutionary fixation of these retroposition events was postulated to be the stochastic loss of entire minicircle sequence classes and their encoded guide RNAs upon segregation of the single kinetoplast DNA network into daughter cells at cell division. A large plasticity in the relative abundance of minicircle sequence classes has been observed during cell culture in the laboratory. Computer simulations provide theoretical evidence for this plasticity if a random distribution and segregation model of minicircles is assumed. The possible evolutionary relationship of the C to U and U-insertion editing systems is discussed.}, }
@article {pmid10860956, year = {2000}, author = {Margulis, L and Dolan, MF and Guerrero, R}, title = {The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {13}, pages = {6954-6959}, pmid = {10860956}, issn = {0027-8424}, mesh = {Animals ; *Biological Evolution ; *Cell Nucleus ; *Eukaryotic Cells ; Hybrid Cells ; Mitochondria ; Models, Biological ; }, abstract = {We present a testable model for the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. A chimeric cell evolved via symbiogenesis by syntrophic merger between an archaebacterium and a eubacterium. The archaebacterium, a thermoacidophil resembling extant Thermoplasma, generated hydrogen sulfide to protect the eubacterium, a heterotrophic swimmer comparable to Spirochaeta or Hollandina that oxidized sulfide to sulfur. Selection pressure for speed swimming and oxygen avoidance led to an ancient analogue of the extant cosmopolitan bacterial consortium "Thiodendron latens." By eubacterial-archaebacterial genetic integration, the chimera, an amitochondriate heterotroph, evolved. This "earliest branching protist" that formed by permanent DNA recombination generated the nucleus as a component of the karyomastigont, an intracellular complex that assured genetic continuity of the former symbionts. The karyomastigont organellar system, common in extant amitochondriate protists as well as in presumed mitochondriate ancestors, minimally consists of a single nucleus, a single kinetosome and their protein connector. As predecessor of standard mitosis, the karyomastigont preceded free (unattached) nuclei. The nucleus evolved in karyomastigont ancestors by detachment at least five times (archamoebae, calonymphids, chlorophyte green algae, ciliates, foraminifera). This specific model of syntrophic chimeric fusion can be proved by sequence comparison of functional domains of motility proteins isolated from candidate taxa.}, }
@article {pmid10854413, year = {2000}, author = {Nedelcu, AM and Lee, RW and Lemieux, C and Gray, MW and Burger, G}, title = {The complete mitochondrial DNA sequence of Scenedesmus obliquus reflects an intermediate stage in the evolution of the green algal mitochondrial genome.}, journal = {Genome research}, volume = {10}, number = {6}, pages = {819-831}, pmid = {10854413}, issn = {1088-9051}, mesh = {Chlorophyta/*genetics ; Cloning, Molecular ; Codon/chemistry/genetics ; DNA, Mitochondrial/chemistry/*genetics/*isolation &amp; purification ; Genes ; Genetic Code ; Genome ; Mitochondria/*chemistry/*genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Two distinct mitochondrial genome types have been described among the green algal lineages investigated to date: a reduced-derived, Chlamydomonas-like type and an ancestral, Prototheca-like type. To determine if this unexpected dichotomy is real or is due to insufficient or biased sampling and to define trends in the evolution of the green algal mitochondrial genome, we sequenced and analyzed the mitochondrial DNA (mtDNA) of Scenedesmus obliquus. This genome is 42,919 bp in size and encodes 42 conserved genes (i.e., large and small subunit rRNA genes, 27 tRNA and 13 respiratory protein-coding genes), four additional free-standing open reading frames with no known homologs, and an intronic reading frame with endonuclease/maturase similarity. No 5S rRNA or ribosomal protein-coding genes have been identified in Scenedesmus mtDNA. The standard protein-coding genes feature a deviant genetic code characterized by the use of UAG (normally a stop codon) to specify leucine, and the unprecedented use of UCA (normally a serine codon) as a signal for termination of translation. The mitochondrial genome of Scenedesmus combines features of both green algal mitochondrial genome types: the presence of a more complex set of protein-coding and tRNA genes is shared with the ancestral type, whereas the lack of 5S rRNA and ribosomal protein-coding genes as well as the presence of fragmented and scrambled rRNA genes are shared with the reduced-derived type of mitochondrial genome organization. Furthermore, the gene content and the fragmentation pattern of the rRNA genes suggest that this genome represents an intermediate stage in the evolutionary process of mitochondrial genome streamlining in green algae.}, }
@article {pmid10852618, year = {2000}, author = {Blusch, JH and Roos, C and Nitschko, H}, title = {A polymerase chain reaction-based protocol for the detection of transmission of pig endogenous retroviruses in pig to human xenotransplantation.}, journal = {Transplantation}, volume = {69}, number = {10}, pages = {2167-2172}, doi = {10.1097/00007890-200005270-00036}, pmid = {10852618}, issn = {0041-1337}, mesh = {Actins/genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Cell Line ; Cytochrome b Group/chemistry/*genetics ; DNA Primers ; Endogenous Retroviruses/*isolation &amp; purification ; Humans ; Mitochondria/genetics ; Molecular Sequence Data ; Papio ; Phylogeny ; Polymerase Chain Reaction/*methods ; Primates ; Sequence Alignment ; Sequence Homology, Amino Acid ; Swine/*virology ; *Terminal Repeat Sequences ; Transplantation Chimera ; *Transplantation, Heterologous ; }, abstract = {BACKGROUND: Xenotransplantation of pig organs and tissues to humans bears the risk of infection of immunosuppressed recipients by porcine endogenous retrovirus (PERV) released from the transplanted tissue. However, when diagnosing potential PERV transmission, it is essential to exclude microchimerism, i.e., persisting pig cells in analyzed bioptic material of xenotransplanted patients, which give rise to false positive PERV signals. Polymerase chain reaction (PCR) is so far the only suitable method to diagnose a cross-species transfer of PERV, but the exclusion of microchimerism might be a serious problem because most of the presently employed primer pairs detect PERV sequences with higher sensitivity than primers used for the detection of contaminating pig sequences.<br><br>METHODS: We designed and evaluated a novel and improved primer set for detection of pig sequences as well as complementing positive control primers on the basis of mitochondrial cytochrome B, an approved marker for phylogenetic studies. We further established primer pairs derived from the long terminal repeat/leader region of PERV isolated from a Duroc German Landrace cross-bred pig and tested their sensitivity in comparison with known PERV- and pig-specific PCR markers.<br><br>RESULTS: In standard PCR assays, the new cytochrome B-derived primers are at least 10 times more sensitive than the presently used PERV retroviral polymerase gene and mammalian beta-actin primers. When tested in a tissue culture infection model, PERV transmission to human 293 cells can be unambiguously demonstrated, even in the presence of up to 10% pig cells. One of the primer combinations derived from the PERV DuxDL3791 long terminal repeat/leader region amplifies with even lower sensitivity than primers detecting porcine beta-globin, thus permitting the exclusion of microchimerism also via chromosomal loci.<br><br>CONCLUSIONS: The availability of the new PCR markers allows the proposal of a rigorous setup for the routine detection of PERV transmission after xenotransplantation.}, }
@article {pmid10849078, year = {2000}, author = {Mirol, PM and Mascheretti, S and Searle, JB}, title = {Multiple nuclear pseudogenes of mitochondrial cytochrome b in Ctenomys (Caviomorpha, rodentia) with either great similarity to or high divergence from the true mitochondrial sequence.}, journal = {Heredity}, volume = {84 (Pt 5)}, number = {}, pages = {538-547}, doi = {10.1046/j.1365-2540.2000.00689.x}, pmid = {10849078}, issn = {0018-067X}, mesh = {Animals ; Cytochrome b Group/*genetics ; DNA Primers/chemistry ; DNA, Mitochondrial/*genetics ; Genetic Markers ; Genetic Variation ; Mitochondria/*enzymology/genetics ; Mutation ; Phylogeny ; Polymerase Chain Reaction ; Pseudogenes/*genetics ; Rodentia/*genetics ; Sequence Analysis, DNA ; }, abstract = {A fragment of the mitochondrial cytochrome b gene was studied in 13 species of the South American fossorial rodent Ctenomys using PCR with 'universal' primers and DNA sequencing after cloning. Five different groups of sequences were found, one of which corresponds to the functional mitochondrial gene (mt). The other four groups (A, B, C and D) were believed to be nuclear pseudogenes. Sequences A-C were highly divergent from the mt sequences and included substitutions, deletions and insertions such that they could not possibly have coded a functional protein. They all shared a common insertion between positions 15055 and 15056 suggestive of a common origin, although the A, B and C sequences otherwise differed greatly from each other. The D sequences also could not have been functional on the basis of nucleotide sequence, but the differences with the mt sequences were far more subtle and in a more limited study the D sequences could easily have been classified as a true mtDNA sequence. It is suggested that there were two transfers of the cytochrome b gene from the mitochondrion to the nucleus; the first leading to sequences A-C and the second to the D sequence. Subsequent to transfer, a sequence of duplications within the nucleus appears to have generated the full range of pseudogenes that are observed. This study adds to other recent observations suggesting the frequent transfer of mtDNA sequences to the nucleus and reinforces the necessity of great care in interpreting PCR-generated sequences, particularly those produced with universal primers. There are now data from several species of mammals and birds relating to PCR-generated nuclear copies of cytochrome b, which we review.}, }
@article {pmid10844700, year = {2000}, author = {Draculic, T and Dawes, IW and Grant, CM}, title = {A single glutaredoxin or thioredoxin gene is essential for viability in the yeast Saccharomyces cerevisiae.}, journal = {Molecular microbiology}, volume = {36}, number = {5}, pages = {1167-1174}, doi = {10.1046/j.1365-2958.2000.01948.x}, pmid = {10844700}, issn = {0950-382X}, mesh = {Culture Media ; Gene Dosage ; *Genes, Fungal ; Glutaredoxins ; Membrane Proteins/*genetics ; Mutagenesis ; Oxidoreductases/*genetics ; Peroxiredoxins ; Phenotype ; Proteins/*genetics ; Saccharomyces cerevisiae/*enzymology/genetics/*growth &amp; development ; *Saccharomyces cerevisiae Proteins ; Sulfates/metabolism ; Thioredoxins/*genetics ; }, abstract = {Glutaredoxins and thioredoxins are small heat-stable oxidoreductases that have been conserved throughout evolution. The yeast Saccharomyces cerevisiae contains two gene pairs encoding cytoplasmic glutaredoxins (GRX1, GRX2) and thioredoxins (TRX1, TRX2). We report here that the quadruple trx1 trx2 grx1 grx2 mutant is inviable and that either a single glutaredoxin or a single thioredoxin (i.e. grx1 grx2 trx1, grx1 grx2 trx2, grx1 trx1 trx2, grx2 trx1 trx2) is essential for viability. Loss of both thioredoxins has been reported previously to lead to methionine auxotrophy consistent with thioredoxins being the sole reductants for 3'-phosphoadenosine 5'-phosphosulphate reductase (PAPS) in yeast. However, we present evidence for the existence of a novel yeast hydrogen donor for PAPS reductase, as strains lacking both thioredoxins assimilated sulphate under conditions that minimized the generation of reactive oxygen species (low aeration and absence of functional mitochondria). In addition, the assimilation of [35S]-sulphate was approximately 60-fold higher in the trx1 trx2 grx1 and trx1 trx2 grx2 mutants compared with the trx1 trx2 mutant. Furthermore, in contrast to the trx1 trx2 mutant, the trx1 trx2 grx2 mutant grew on minimal agar plates, and the trx1 trx2 grx1 mutant grew on minimal agar plates under anaerobic conditions. We propose a model in which the novel reductase activity normally functions in the repair of oxidant-mediated protein damage but, under conditions that minimize the generation of reactive oxygen species, it can serve as a hydrogen donor for PAPS reductase.}, }
@article {pmid10842310, year = {2000}, author = {Jacobs, HT and Lehtinen, SK and Spelbrink, JN}, title = {No sex please, we're mitochondria: a hypothesis on the somatic unit of inheritance of mammalian mtDNA.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {22}, number = {6}, pages = {564-572}, doi = {10.1002/(SICI)1521-1878(200006)22:6&lt;564::AID-BIES9&gt;3.0.CO;2-4}, pmid = {10842310}, issn = {0265-9247}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Mammals/genetics ; *Models, Genetic ; }, abstract = {In this article we develop a model for the organization and maintenance of mitochondrial DNA (mtDNA) in mammalian somatic cells, based on the idea that the unit of genetic function comprises a group of mtDNA molecules that are semi-permanently associated as a mitochondrial nucleoid. Different mtDNA molecules within a nucleoid need not be genetically identical. We propose that nucleoids replicate faithfully via a kind of mitochondrial mitosis, generating daughter nucleoids that are identical copies of each other, but which can themselves segregate freely. This model can account for the very slow rates of mitotic segregation observed in cultured, heteroplasmic cell-lines, and also for the apparently poor complementation observed between different mutant mtDNAs co-introduced into rho(0) cells (cells that lack endogenous mtDNA). It also provides a potential system for maintaining the mitochondrial genetic fitness of stem cells in the face of a presumed high somatic mutation rate of mtDNA and many rounds of cell division in the absence of phenotypic selection. BioEssays 22:564-572, 2000.}, }
@article {pmid10838480, year = {2000}, author = {Hansen, A and Finger, TE}, title = {Phyletic distribution of crypt-type olfactory receptor neurons in fishes.}, journal = {Brain, behavior and evolution}, volume = {55}, number = {2}, pages = {100-110}, doi = {10.1159/000006645}, pmid = {10838480}, issn = {0006-8977}, support = {P01DC00244/DC/NIDCD NIH HHS/United States ; R01DC03792/DC/NIDCD NIH HHS/United States ; }, mesh = {Animals ; Fishes/*anatomy &amp; histology ; Microscopy, Electron ; Microscopy, Electron, Scanning ; Mitochondria/ultrastructure ; Olfactory Mucosa/*ultrastructure ; Olfactory Receptor Neurons/*ultrastructure ; Phylogeny ; }, abstract = {The olfactory epithelium of teleost fishes contains ciliated and microvillous olfactory receptor neurons intermingled with supporting cells. Recently the crypt cell, a third type of olfactory receptor neuron (ORN), was described for two ostariophysans. This type of ORN bears apical microvilli as well as occult cilia extending into a crypt at the apex of the cell. The present study used scanning and transmission electron-microscopic methods to examine how widespread this cell type is in other groups of fish. We investigated the olfactory epithelia of 18 species, freshwater and marine, including various actinopterygian fish as well as 2 species of lungfishes belonging to the sarcopterygians. Crypt cells were detected in 13 species of actinopterygian fish, but in none of the sarcopterygian lungfishes. Crypt cells are present in basic as well as in highly derived actinopterygians. We conclude that crypt cells are a common feature of actinopterygian fish.}, }
@article {pmid10837153, year = {2000}, author = {Ståhls, G and Nyblom, K}, title = {Phylogenetic analysis of the genus Cheilosia (Diptera, Syrphidae) using mitochondrial COI sequence data.}, journal = {Molecular phylogenetics and evolution}, volume = {15}, number = {2}, pages = {235-241}, doi = {10.1006/mpev.1999.0748}, pmid = {10837153}, issn = {1055-7903}, mesh = {Animals ; Diptera/*classification/genetics ; Electron Transport Complex IV/genetics ; Mitochondria/enzymology/*genetics ; *Phylogeny ; }, abstract = {The genus Cheilosia is one of the most diverse and speciose genera of Syrphidae (Diptera). The phylogenetic relationships of the hoverfly genus Cheilosia was investigated for the first time using molecular data. The mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) was chosen for sequencing; 1341 characters were obtained for 24 ingroup taxa and these were analyzed with parsimony. The monophyly of the genus Cheilosia was well supported. Current taxonomic division of Cheilosia into two subgenera (sg. Nigrocheilosia and sg. Neocheilosia) and most nonformalized species groups based on morphology were supported by the monophyletic groups identified in the molecular analysis. The phylogenetic informativeness of COI in resolving the subtribal relationships within the tribe Cheilosiini remains ambiguous.}, }
@article {pmid10837149, year = {2000}, author = {Held, C}, title = {Phylogeny and biogeography of serolid isopods (Crustacea, Isopoda, Serolidae) and the use of ribosomal expansion segments in molecular systematics.}, journal = {Molecular phylogenetics and evolution}, volume = {15}, number = {2}, pages = {165-178}, doi = {10.1006/mpev.1999.0739}, pmid = {10837149}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Cell Nucleus/genetics ; Crustacea/*classification/genetics ; DNA Primers ; Geography ; Mitochondria/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Ribosomes ; }, abstract = {In this study, a molecular phylogenetic hypothesis for 16 species of serolid isopods (Crustacea, Isopoda, Serolidae) from Antarctic waters, the deep sea, South America, and Australia is presented. The genes used are a 500-bp fragment of the mitochondrial LSU rRNA gene and a 700-bp fragment located in the variable region V4 of the nuclear SSU rRNA gene. The species composition and monophyly of morphologically defined genera of which several members were available are confirmed by the molecular data (Ceratoserolis, Spinoserolis, and Cuspidoserolis). The molecular data also support the redefinition of Frontoserolis s.l. and Serolella and the erection of the new genera Septemserolis and Paraserolis, as proposed by W]agele. The relationship among several genera is resolved differently in the molecular hypothesis than in the two existing morphological hypotheses, however. The molecular phylogeny may have important consequences for understanding the biogeography of the Serolidae, indicating that all Antarctic species in this study form a monophyletic group which has probably derived from species with closest extant relatives in South America. All 3 species included in this study living today in deep waters (>2000 m) of the Southern Ocean are most closely related to species living on the Antarctic shelf, so that parallel colonization of the deep sea by way of polar submergence can be reconstructed. In this study, a V4 expansion segment is reported which exceeds the longest crustacean sequences known until now by more than 270 bp. Although the V4 expansion segment has proven useful for phylogenetic purposes in this study, there is circumstantial evidence that its mechanism of evolution may depend not only on inheritance of single-site substitutions, making its routine use in phylogenetic studies potentially dangerous.}, }
@article {pmid10837088, year = {2000}, author = {Gerard, CJ and Andrejka, LM and Macina, RA}, title = {Mitochondrial ATP synthase 6 as an endogenous control in the quantitative RT-PCR analysis of clinical cancer samples.}, journal = {Molecular diagnosis : a journal devoted to the understanding of human disease through the clinical application of molecular biology}, volume = {5}, number = {1}, pages = {39-46}, pmid = {10837088}, issn = {1084-8592}, mesh = {Deoxyribonucleases/metabolism ; Gene Expression Profiling ; Humans ; Mitochondria/*enzymology/genetics ; *Mitochondrial Proton-Translocating ATPases ; Neoplasms/genetics/*metabolism ; Proton-Translocating ATPases/*analysis/genetics ; Quality Control ; Reference Standards ; Reverse Transcriptase Polymerase Chain Reaction/*methods ; Tissue Distribution ; }, abstract = {BACKGROUND: Real-time polymerase chain reaction (PCR) is a powerful new technique in the evolution of quantitative reverse transcription-PCR assays. With the increased sensitivity and resolution of real-time techniques, the requirements for constitutive expression of endogenous controls have become increasingly stringent.<br><br>METHODS AND RESULTS: We compare the expression of the mitochondrial gene, adenosine triphosphate synthase 6 (ATPsy6), to the expression of other routinely used endogenous control genes (e.g., beta-actin, glyceraldehyde-3-phosphate dehydrogenase [GAPDH], ribosomal RNA 18S [18S rRNA], and cyclophilin). In a diverse assortment of tissues and across a wide range of disease stages, ATPsy6 shows a relative steady state of expression compared with other endogenous controls. ATPsy6 gene expression has been used as an endogenous control in a quantitative real-time PCR assay designed to evaluate the expression of potential cancer diagnostic leads across a diverse tissue panel.<br><br>CONCLUSION: Mitochondrial ATPsy6 serves as a good endogenous control to measure target gene expression independent of the tissue- or disease-specific variation inherent with many housekeeping genes.}, }
@article {pmid10833527, year = {2000}, author = {Saier, MH}, title = {Families of proteins forming transmembrane channels.}, journal = {The Journal of membrane biology}, volume = {175}, number = {3}, pages = {165-180}, doi = {10.1007/s00232001065}, pmid = {10833527}, issn = {0022-2631}, support = {9RO1 GM55434/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacterial Proteins ; Biological Warfare ; Carrier Proteins/*classification/physiology ; Evolution, Molecular ; Humans ; Ion Channels/*classification/physiology ; *N-Acetylmuramoyl-L-alanine Amidase ; Porins/classification/physiology ; Toxins, Biological/classification ; }, abstract = {Channel-forming proteins/peptides fall into over 100 currently recognized families, most of which are restricted to prokaryotes or eukaryotes, but a few of which are ubiquitous. These proteins fall into three major currently recognized classes: (i) alpha-helix-type channels present in bacterial, archaeal and eukaryotic cytoplasmic and organellar membranes, (ii) beta-barrel-type porins present in the outer membranes of Gram-negative bacterial cells, mitochondria and chloroplasts, and (iii) protein/peptide toxins targeted to the cytoplasmic membranes of cells other than those that synthesize the toxins. High-resolution 3-dimensional structural data are available for representative proteins/peptides of all three of these channel-forming types. Each type exhibits distinctive features that distinguish them from the other channel protein types and from carriers. Structural, functional, and evolutionary aspects of transmembrane channel-formers are discussed.}, }
@article {pmid10833333, year = {2000}, author = {Decker, WK and Craigen, WJ}, title = {The tissue-specific, alternatively spliced single ATG exon of the type 3 voltage-dependent anion channel gene does not create a truncated protein isoform in vivo.}, journal = {Molecular genetics and metabolism}, volume = {70}, number = {1}, pages = {69-74}, doi = {10.1006/mgme.2000.2987}, pmid = {10833333}, issn = {1096-7192}, support = {R01 GM055713-02/GM/NIGMS NIH HHS/United States ; }, mesh = {*Alternative Splicing ; Animals ; Antibody Specificity/immunology ; Base Sequence ; Brain/metabolism ; Conserved Sequence ; DNA/chemistry/genetics ; Exons/*genetics ; Gene Expression Regulation ; Humans ; Male ; Mice ; Mitochondria, Muscle/*metabolism ; Mitochondrial Membrane Transport Proteins ; Molecular Sequence Data ; Muscle, Skeletal/metabolism ; Porins/*genetics/immunology ; Protein Isoforms/genetics ; RNA, Messenger/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Voltage-Dependent Anion Channels ; }, abstract = {Voltage-dependent anion channels (VDACs) are small, integral membrane proteins that traverse the outer mitochondrial membrane and conduct ATP and other small metabolites. They are known to bind several kinases of intermediary metabolism in a tissue-specific fashion, have been found in close association with the adenine nucleotide translocator of the inner mitochondrial membrane, and are hypothesized to form part of the mitochondrial permeability transition pore, which results in the release of cytochrome c at the onset of apoptotic cell death. VDACs are found throughout all strata of eukaryotic evolution and exhibit biophysical characteristics that are well conserved from yeast to mammals. The mammalian VDAC gene family consists of three isoforms, each of which shares approximately 70% sequence identity with the other two family members. Recently, we reported that a single codon (ATG) exon is alternatively spliced into the transcript of the type 3 voltage-dependent anion channel (VDAC3) in a tissue-specific fashion. This unusual splicing event was shown to be conserved between mouse and human, and we theorized that the spliced exon could lead to the creation of an alternative translational initiation site. Here we report that a highly specific polyclonal VDAC3 antibody was unable to detect the truncated protein isoform indicative of this putative downstream start site. From these in vivo studies, we conclude that the alternatively spliced exon results in the insertion of a single methionine residue at amino acid position 39 of the mature VDAC3 protein. Additionally, we have used a cross-species genomic sequence comparison to identify conserved regions that may be involved in the regulation of small exon splicing.}, }
@article {pmid10833205, year = {2000}, author = {Reyes, A and Gissi, C and Pesole, G and Catzeflis, FM and Saccone, C}, title = {Where do rodents fit? Evidence from the complete mitochondrial genome of Sciurus vulgaris.}, journal = {Molecular biology and evolution}, volume = {17}, number = {6}, pages = {979-983}, doi = {10.1093/oxfordjournals.molbev.a026379}, pmid = {10833205}, issn = {0737-4038}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Genome ; Humans ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; Rodentia/*classification/*genetics ; Sciuridae/classification/*genetics ; }, }
@article {pmid10833203, year = {2000}, author = {Walton, C and Handley, JM and Tun-Lin, W and Collins, FH and Harbach, RE and Baimai, V and Butlin, RK}, title = {Population structure and population history of Anopheles dirus mosquitoes in Southeast Asia.}, journal = {Molecular biology and evolution}, volume = {17}, number = {6}, pages = {962-974}, doi = {10.1093/oxfordjournals.molbev.a026377}, pmid = {10833203}, issn = {0737-4038}, mesh = {Animals ; Anopheles/*classification/*genetics ; Asia, Southeastern ; Bangladesh ; Base Sequence ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; *Evolution, Molecular ; Genetic Variation ; Geography ; Haplotypes ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Myanmar ; *Phylogeny ; Population Dynamics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Thailand ; }, abstract = {Separating the confounding effects of long-term population history from gene flow can be difficult. Here, we address the question of what inferences about gene flow can be made from mitochondrial sequence data in three closely related species of mosquitoes, Anopheles dirus species A, C, and D, from southeast Asia. A total of 84 sequences of 923 bp of the mitochondrial cytochrome oxidase I gene were obtained from 14 populations in Thailand, Myanmar, and Bangladesh. The genealogy of sequences obtained from two populations of AN: dirus C indicates no contemporary gene flow between them. The F(ST) value of 0.421 therefore probably represents a recent common history, perhaps involving colonization events. Anopheles dirus A and D are parapatric, yet no differentiation was seen either within or between species. The starlike genealogy of their haplotypes, smooth unimodal mismatch distributions, and excess of low frequency mutations indicate population expansion in An. dirus A and D. This, rather than widespread gene flow, explains their low within-species F(ST) values (0.018 and 0.022). The greater genetic diversity of An. dirus D suggests that expansion occurred first in species D and subsequently in species A. The current geographical separation and low hybrid fitness of these species also argue against ongoing interspecific gene flow. They suggest instead either historical introgression of mtDNA from An. dirus D into species A followed by independent range expansions, or a selective sweep of mtDNA that originated in An. dirus D. While not excluding contemporary gene flow, historical population processes are sufficient to explain the data in An. dirus A and D. The genealogical relationships between haplotypes could not be used to make inferences of gene flow because of extensive homoplasy due to hypervariable sites and possibly also recombination. However, it is concluded that this approach, rather than the use of fixation indices, is required in the future to understand contemporary gene flow in these mosquitoes. The implications of these results for understanding gene flow in another important and comparable group of malaria vector mosquitoes in Africa, the An. gambiae complex, are also discussed.}, }
@article {pmid10833202, year = {2000}, author = {Berg, OG and Kurland, CG}, title = {Why mitochondrial genes are most often found in nuclei.}, journal = {Molecular biology and evolution}, volume = {17}, number = {6}, pages = {951-961}, doi = {10.1093/oxfordjournals.molbev.a026376}, pmid = {10833202}, issn = {0737-4038}, mesh = {Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Gene Transfer Techniques ; Haploidy ; Mitochondria/*genetics ; *Models, Genetic ; Models, Statistical ; Mutation ; Population Density ; Selection, Genetic ; }, abstract = {A very small fraction of the proteins required for the propagation and function of mitochondria are coded by their genomes, while nuclear genes code the vast majority. We studied the migration of genes between the two genomes when transfer mechanisms mediate this exchange. We could calculate the influence of differential mutation rates, as well as that of biased transfer rates, on the partitioning of genes between the two genomes. We observe no significant difference in partitioning for haploid and diploid cell populations, but the effective size of cell populations is important. For infinitely large effective populations, higher mutation rates in mitochondria than in nuclear genomes are required to drive mitochondrial genes to the nuclear genome. In the more realistic case of finite populations, gene transfer favoring the nucleus and/or higher mutation rates in the mitochondrion will drive mitochondrial genes to the nucleus. We summarize experimental data that identify a gene transfer process mediated by vacuoles that favors the accumulation of mitochondrial genes in the nuclei of modern cells. Finally, we compare the behavior of mitochondrial genes for which transfer to the nucleus is neutral or influenced by purifying selection.}, }
@article {pmid10832628, year = {2000}, author = {Martin, W}, title = {Primitive anaerobic protozoa: the wrong host for mitochondria and hydrogenosomes?.}, journal = {Microbiology (Reading, England)}, volume = {146 (Pt 5)}, number = {}, pages = {1021-1022}, doi = {10.1099/00221287-146-5-1021}, pmid = {10832628}, issn = {1350-0872}, mesh = {Anaerobiosis ; Animals ; Biological Evolution ; Eukaryota/*physiology ; Eukaryotic Cells ; Hydrogen/metabolism ; Mitochondria/metabolism ; Organelles/metabolism ; Symbiosis ; }, }
@article {pmid10832627, year = {2000}, author = {Biagini, GA and Bernard, C}, title = {Primitive anaerobic protozoa: a false concept?.}, journal = {Microbiology (Reading, England)}, volume = {146 (Pt 5)}, number = {}, pages = {1019-1020}, doi = {10.1099/00221287-146-5-1019}, pmid = {10832627}, issn = {1350-0872}, mesh = {Anaerobiosis ; Animals ; Biological Evolution ; Eukaryota/cytology/metabolism/*physiology ; Mitochondria/physiology ; Oxygen/metabolism ; Symbiosis ; }, }
@article {pmid10826829, year = {2000}, author = {Belloch, C and Querol, A and García, MD and Barrio, E}, title = {Phylogeny of the genus Kluyveromyces inferred from the mitochondrial cytochrome-c oxidase II gene.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {50 Pt 1}, number = {}, pages = {405-416}, doi = {10.1099/00207713-50-1-405}, pmid = {10826829}, issn = {1466-5026}, mesh = {Electron Transport Complex IV/*genetics ; Genes, Fungal ; Kluyveromyces/*classification/enzymology/genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {A phylogenetic analysis of 17 species belonging to the genus Kluyveromyces and 12 reference and outgroup species was performed using mitochondrial cytochrome-c oxidase II gene sequences. The genus Kluyveromyces appears as a polyphyletic taxon formed by species included within the following four main groups. The Kluyveromyces phaffii group encompasses the species Kluyveromyces blattae, K. phaffii and Kluyveromyces yarrowii. The Kluyveromyces marxianus group is a monophyletic group consisting of the species Kluyveromyces aestuarii, Kluyveromyces dobzhanskii, Kluyveromyces lactis, K. marxianus and Kluyveromyces wickerhamii. The monophyletic Kluyveromyces thermotolerans group is formed by K. thermotolerans, Kluyveromyces waltii and Saccharomyces kluyveri (which appears in the mitochondrial tree as the sister clade of the K. marxianus group). Finally, the Saccharomyces cerevisiae group contains the remaining Kluyveromyces species, as well as the reference Saccharomyces species (sensu lato and sensu stricto) and Candida glabrata (the phylogenetic relationships within this group are unclear according to the bootstrap test). The phylogenetic relationships obtained for this mitochondrial gene are, for the most part, congruent with previous trees based on nuclear rRNA sequences, except for the position of K. yarrowii and the close relationship between the K. marxianus and K. thermotolerans groups. These differences, as well as the existence of these groups, are discussed in the context of previous studies based on phenotypic, genetic and molecular data. Although additional studies are required to decipher the phylogenetic relationships between the genus Kluyveromyces and the closely related genera Saccharomyces, Torulaspora and Zygosaccharomyces, future changes to their taxonomic status should take account of the existence of these four groups of Kluyveromyces species.}, }
@article {pmid10824085, year = {2000}, author = {Peeters, NM and Chapron, A and Giritch, A and Grandjean, O and Lancelin, D and Lhomme, T and Vivrel, A and Small, I}, title = {Duplication and quadruplication of Arabidopsis thaliana cysteinyl- and asparaginyl-tRNA synthetase genes of organellar origin.}, journal = {Journal of molecular evolution}, volume = {50}, number = {5}, pages = {413-423}, doi = {10.1007/s002390010044}, pmid = {10824085}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/chemistry/*genetics ; Animals ; Arabidopsis/enzymology/*genetics ; *Aspartate-tRNA Ligase ; Base Sequence ; DNA Primers ; DNA, Complementary ; *Gene Duplication ; Humans ; Molecular Sequence Data ; Organelles/enzymology ; Phylogeny ; *RNA, Transfer, Amino Acyl ; Sequence Homology, Amino Acid ; }, abstract = {Two cysteinyl-tRNA synthetases (CysRS) and four asparaginyl-tRNA synthetases (AsnRS) from Arabidopsis thaliana were characterized from genome sequence data, EST sequences, and RACE sequences. For one CysRS and one AsnRS, sequence alignments and prediction programs suggested the presence of an N-terminal organellar targeting peptide. Transient expression of these putative targeting sequences joined to jellyfish green fluorescent protein (GFP) demonstrated that both presequences can efficiently dual-target GFP to mitochondria and plastids. The other CysRS and AsnRSs lack targeting sequences and presumably aminoacylate cytosolic tRNAs. Phylogenetic analysis suggests that the four AsnRSs evolved by repeated duplication of a gene transferred from an ancestral plastid and that the CysRSs also arose by duplication of a transferred organelle gene (possibly mitochondrial). These case histories are the best examples to date of capture of organellar aminoacyl-tRNA synthetases by the cytosolic protein synthesis machinery.}, }
@article {pmid10811653, year = {2000}, author = {Zhang, H and Huang, Q and Ke, N and Matsuyama, S and Hammock, B and Godzik, A and Reed, JC}, title = {Drosophila pro-apoptotic Bcl-2/Bax homologue reveals evolutionary conservation of cell death mechanisms.}, journal = {The Journal of biological chemistry}, volume = {275}, number = {35}, pages = {27303-27306}, doi = {10.1074/jbc.M002846200}, pmid = {10811653}, issn = {0021-9258}, support = {GM 60554/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Apoptosis/*genetics ; Base Sequence ; Carrier Proteins/*genetics ; DNA Primers ; Drosophila/*genetics ; *Evolution, Molecular ; *Genes, bcl-2 ; Humans ; Membrane Proteins/*genetics ; Molecular Sequence Data ; Proto-Oncogene Proteins/*genetics ; *Proto-Oncogene Proteins c-bcl-2 ; Sequence Homology, Amino Acid ; bcl-2-Associated X Protein ; }, abstract = {Genetic analysis of programmed cell death in Drosophila reveals many similarities with mammals. Heretofore, a missing link in the fly has been the absence of any Bcl-2/Bax family members, proteins that function in mammals as regulators of mitochondrial cytochrome c release. A Drosophila homologue of the human killer protein Bok (DBok) was identified. The predicted structure of DBok is similar to pore-forming Bcl-2/Bax family members. DBok induces apoptosis in insect and human cells, which is suppressible by anti-apoptotic human Bcl-2 family proteins. A caspase inhibitor suppressed DBok-induced apoptosis but did not prevent DBok-induced cell death. Moreover, DBok targets mitochondria and triggers cytochrome c release through a caspase-independent mechanism. These characteristics of DBok reveal evolutionary conservation of cell death mechanisms in flies and humans.}, }
@article {pmid10811205, year = {2000}, author = {Palmer, JD}, title = {A single birth of all plastids?.}, journal = {Nature}, volume = {405}, number = {6782}, pages = {32-33}, doi = {10.1038/35011184}, pmid = {10811205}, issn = {0028-0836}, mesh = {Chlorophyta/genetics ; Cyanobacteria/physiology ; DNA-Directed RNA Polymerases/genetics ; Eukaryota/*genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Mitochondria/genetics ; Peptide Elongation Factor 2/genetics ; *Plastids ; RNA, Ribosomal/genetics ; Rhodophyta/genetics ; *Symbiosis ; }, }
@article {pmid10806421, year = {2000}, author = {Kayingo, G and Potier, S and Hohmann, S and Prior, BA}, title = {Isolation and characterization of the TIM10 homologue from the yeast Pichia sorbitophila: a putative component of the mitochondrial protein import system.}, journal = {Yeast (Chichester, England)}, volume = {16}, number = {7}, pages = {589-596}, doi = {10.1002/(SICI)1097-0061(200005)16:7&lt;589::AID-YEA555&gt;3.0.CO;2-G}, pmid = {10806421}, issn = {0749-503X}, mesh = {Amino Acid Sequence ; Base Sequence ; Blotting, Western ; Cross Reactions ; Fungal Proteins/genetics/immunology/*isolation &amp; purification/*metabolism ; Genes, Fungal ; Genetic Complementation Test ; Membrane Proteins/genetics/metabolism ; Mitochondria/*metabolism ; Mitochondrial Precursor Protein Import Complex Proteins ; Molecular Sequence Data ; Phylogeny ; Pichia/genetics/growth &amp; development/*metabolism ; Saccharomyces cerevisiae/genetics/growth &amp; development/metabolism ; *Saccharomyces cerevisiae Proteins ; Sequence Analysis, DNA ; }, abstract = {The Saccharomyces cerevisiae TIM10 gene encodes one of the few essential mitochondrial proteins that are required for the import of nuclear-encoded precursor proteins from the cytosol and their subsequent sorting into the different mitochondrial compartments. We have isolated and characterized a putative homologue of TIM10 from the halotolerant yeast Pichia sorbitophila. The Pichia TIM10 gene encodes a protein of 90 amino acids with 66% identity to S. cerevisiae Tim10p. It was capable of suppressing the temperature sensitivity of tim10-1 mutant in S. cerevisiae, suggesting that Pichia TIM10 is both a functional and structural homologue of S. cerevisiae TIM10. The putative Pichia TIM10 gene product contains all the four conserved cysteine residues and the two CX(3)C motifs typical of the Tim family proteins in the mitochondrial intermembrane space. Using anti-Tim10p serum, Western blots detected a protein of about 10 kDa, suggesting that the Pichia Tim10p is a mitochondrial protein. The results suggest that mitochondrial import and sorting systems might be also strongly conserved in other fungi. The coding sequence of the P. sorbitophila TIM10 has been deposited in the EMBL Nucleotide Sequence Database under Accession No. AJ243940.}, }
@article {pmid10791428, year = {2000}, author = {Kuroiwa, T}, title = {The discovery of the division apparatus of plastids and mitochondria.}, journal = {Journal of electron microscopy}, volume = {49}, number = {1}, pages = {123-134}, doi = {10.1093/oxfordjournals.jmicro.a023776}, pmid = {10791428}, issn = {0022-0744}, mesh = {Animals ; Bacterial Proteins/chemistry/genetics/physiology ; Cell Division ; Chloroplasts/physiology/*ultrastructure ; *Cytoskeletal Proteins ; Evolution, Molecular ; Microscopy, Electron ; Mitochondria/physiology/*ultrastructure ; Plastids/physiology/*ultrastructure ; Rhodophyta/physiology/*ultrastructure ; }, abstract = {Mitochondria and plastids contain distinct genomes and multiply by binary division of existing organelles. Mitochondrial and plastid division can be clearly separated into two main events: division of the organelle nuclei (nucleoids), and subsequent division of the rest of the organelles, the process of organellokinesis. Organellokinesis makes use of organelle dividing apparatuses such as plastid-dividing ring (PD ring) and mitochondrion-dividing ring (MD ring). The plastid-dividing apparatus (PD apparatus) is composed of three electron-dense rings (the outer, middle and inner), while the mitochondrion-dividing apparatus (MD apparatus) is a pair of electron-dense rings in cytoplasm and inner ring in the mitochondrial matrix. The behaviour of both the PD and MD apparatuses throughout organelle division in Cyanidioschyzon merolae has been studied in detail by electron microscopy. When cells enter mitosis, the inner PD ring forms first, followed by the outer and middle rings and finally the MD rings. The PD rings begin to contract before the MD rings. However, the MD rings start to contract at about 4 times the speed of the PD rings and catch up to the PD rings. The cross-sectional areas of both the outer PD and MD rings increase as contraction in the plane of division progress. This suggests that the outer rings of organelle dividing apparatuses (OD apparatus) provide the motive force for contraction. FtsZ protein is located on the bacterial contractile ring at the equator of dividing bacteria, and controls bacterial division. Since FtsZ contains a tubulin motif, and host eukaryotic organisms and chloroplasts evolved from bacteria, there is debate whether that tubulins found in the cytoskeleton and the inner or outer PD ring evolved from FtsZ protein during eukaryogenesis.}, }
@article {pmid10790415, year = {2000}, author = {Yang, Z and Nielsen, R and Goldman, N and Pedersen, AM}, title = {Codon-substitution models for heterogeneous selection pressure at amino acid sites.}, journal = {Genetics}, volume = {155}, number = {1}, pages = {431-449}, pmid = {10790415}, issn = {0016-6731}, mesh = {Amino Acid Substitution ; *Amino Acids ; Animals ; *Codon ; Drosophila/genetics ; Gene Products, vif/genetics ; Genes, pol ; Globins/genetics ; HIV Envelope Protein gp120/genetics ; Hemagglutinin Glycoproteins, Influenza Virus/genetics ; Humans ; Membrane Glycoproteins/genetics ; Mitochondria ; *Models, Genetic ; Peptide Fragments/genetics ; *Selection, Genetic ; Vertebrates/genetics ; Viral Envelope Proteins/genetics ; Viral Nonstructural Proteins/genetics ; }, abstract = {Comparison of relative fixation rates of synonymous (silent) and nonsynonymous (amino acid-altering) mutations provides a means for understanding the mechanisms of molecular sequence evolution. The nonsynonymous/synonymous rate ratio (omega = d(N)d(S)) is an important indicator of selective pressure at the protein level, with omega = 1 meaning neutral mutations, omega < 1 purifying selection, and omega > 1 diversifying positive selection. Amino acid sites in a protein are expected to be under different selective pressures and have different underlying omega ratios. We develop models that account for heterogeneous omega ratios among amino acid sites and apply them to phylogenetic analyses of protein-coding DNA sequences. These models are useful for testing for adaptive molecular evolution and identifying amino acid sites under diversifying selection. Ten data sets of genes from nuclear, mitochondrial, and viral genomes are analyzed to estimate the distributions of omega among sites. In all data sets analyzed, the selective pressure indicated by the omega ratio is found to be highly heterogeneous among sites. Previously unsuspected Darwinian selection is detected in several genes in which the average omega ratio across sites is <1, but in which some sites are clearly under diversifying selection with omega > 1. Genes undergoing positive selection include the beta-globin gene from vertebrates, mitochondrial protein-coding genes from hominoids, the hemagglutinin (HA) gene from human influenza virus A, and HIV-1 env, vif, and pol genes. Tests for the presence of positively selected sites and their subsequent identification appear quite robust to the specific distributional form assumed for omega and can be achieved using any of several models we implement. However, we encountered difficulties in estimating the precise distribution of omega among sites from real data sets.}, }
@article {pmid10790399, year = {2000}, author = {Noguchi, Y and Endo, K and Tajima, F and Ueshima, R}, title = {The mitochondrial genome of the brachiopod Laqueus rubellus.}, journal = {Genetics}, volume = {155}, number = {1}, pages = {245-259}, pmid = {10790399}, issn = {0016-6731}, mesh = {Animals ; Base Sequence ; *DNA, Mitochondrial ; Invertebrates/*genetics ; Mathematical Computing ; Mitochondria ; Molecular Sequence Data ; Nucleic Acid Conformation ; *RNA ; RNA, Mitochondrial ; *RNA, Ribosomal ; *RNA, Transfer ; }, abstract = {The complete nucleotide sequence of the 14,017-bp mitochondrial (mt) genome of the articulate brachiopod Laqueus rubellus is presented. Being one of the smallest of known mt genomes, it has an extremely compact gene organization. While the same 13 polypeptides, two rRNAs, and 22 tRNAs are encoded as in most other animal mtDNAs, lengthy noncoding regions are absent, with the longest apparent intergenic sequence being 54 bp in length. Gene-end sequence overlaps are prevalent, and several stop codons are abbreviated. The genes are generally shorter, and three of the protein-coding genes are the shortest among known homologues. All of the tRNA genes indicate size reduction in either or both of the putative TPsiC and DHU arms compared with standard tRNAs. Possession of a TV (TPsiC arm-variable loop) replacement loop is inferred for tRNA(R) and tRNA(L-tag). The DHU arm appears to be unpaired not only in tRNA(S-tct) and tRNA(S-tga), but also in tRNA(C), tRNA(I), and tRNA(T), a novel condition. All the genes are encoded in the same DNA strand, which has a base composition rich in thymine and guanine. The genome has an overall gene arrangement drastically different from that of any other organisms so far reported, but contains several short segments, composed of 2-3 genes, which are found in other mt genomes. Combined cooccurrence of such gene assortments indicates that the Laqueus mt genome is similar to the annelid Lumbricus, the mollusc Katharina, and the octocoral Sarcophyton mt genomes, each with statistical significance. Widely accepted schemes of metazoan phylogeny suggest that the similarity with the octocoral could have arisen through a process of convergent evolution, while it appears likely that the similarities with the annelid and the mollusc reflect phylogenetic relationships.}, }
@article {pmid10786838, year = {2000}, author = {Fey, J and Tomita, K and Bergdoll, M and Maréchal-Drouard, L}, title = {Evolutionary and functional aspects of C-to-U editing at position 28 of tRNA(Cys)(GCA) in plant mitochondria.}, journal = {RNA (New York, N.Y.)}, volume = {6}, number = {4}, pages = {470-474}, doi = {10.1017/s1355838200992380}, pmid = {10786838}, issn = {1355-8382}, mesh = {Anticodon/chemistry/genetics ; Base Pairing/genetics ; Base Sequence ; *Evolution, Molecular ; Isomerism ; Models, Genetic ; RNA/chemistry/*genetics ; RNA Editing/*genetics/physiology ; RNA Precursors/chemistry/genetics ; RNA Stability ; RNA, Mitochondrial ; RNA, Plant/chemistry/*genetics ; RNA, Transfer, Cys/chemistry/*genetics ; Sequence Alignment ; Solanum tuberosum/cytology/*genetics ; }, }
@article {pmid10779593, year = {2000}, author = {Wu, Y and Egerton, G and Ball, A and Tanguay, RM and Bianco, AE}, title = {Characterization of the heat-shock protein 60 chaperonin from Onchocerca volvulus.}, journal = {Molecular and biochemical parasitology}, volume = {107}, number = {2}, pages = {155-168}, doi = {10.1016/s0166-6851(99)00227-3}, pmid = {10779593}, issn = {0166-6851}, mesh = {Amino Acid Sequence ; Animals ; Antibodies, Helminth/blood ; Chaperonin 60/*chemistry/genetics/*immunology/metabolism ; Cloning, Molecular ; Cross Reactions ; DNA, Helminth/genetics ; Enzyme-Linked Immunosorbent Assay ; Humans ; Immunohistochemistry ; Mitochondria/metabolism ; Molecular Sequence Data ; Onchocerca volvulus/*chemistry/genetics/immunology/metabolism ; Onchocerciasis/immunology/parasitology ; Phylogeny ; Rabbits ; Recombinant Proteins/immunology ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {Chaperonin 60 (cpn60) belongs to the group of ubiquitous molecular chaperones that comprise the heat shock proteins, nucleoplasmins and chaperonins. Antibodies to recombinant CPN60 from humans was used to screen a cDNA library of Onchocerca volvulus and antigen-positive clones were selected. Sequencing of the DNA inserts confirmed their identity as cpn60 transcripts. These are distinct from a cpn60 sequence recorded previously from O. volvulus (GenBank accession number Y09416) that appears to be of endobacterial origin, rather than derived from the parasite itself. The full-length sequence of the cDNA (designated Ov-cpn60) codes for a protein of 64.3kDa (598 amino acid residues) and shares significant identity with homologous gene products from Caenorhabditis elegans (72%), humans (69%), yeast (53%) and Escherichia coli (50%). The endobacterial and parasite sequences are 41% conserved. Ov-CPN60 migrates with an apparent molecular mass of 65kDa on SDS-PAGE and is present in all life-cycle stages, as determined by immunoblotting with rabbit antibodies raised against the recombinant protein. Immunogold electron microscopy identified the protein within mitochondria, as expected, but also in extra-mitochondrial sites, including inclusion bodies of the glandular oesophagus (in infective larvae), the uterine wall, cytosol of developing spermatids, and the hypodermis and cuticle. Endobacteria were also labelled, indicating cross-reactivity between CPN60 from the parasite and its intracellular symbiont. In human infections, serum antibodies to Ov-CPN60 were present in only 11% of cases from Ecuador, but in 81-89% of subjects in three separate foci from West Africa. There was no relationship between antibody levels and age, sex, or infection intensity, and no consistent association between the serological response and immune status. An evaluation of antibody specificities in individual sera revealed a mixture of parasite-specific and host crossreactive anti-CPN60 antibodies, the ratio of which varied amongst geographic areas. It is concluded that antibody responses to Ov-CPN60 are unlikely to contribute either to host protection or pathology in onchocerciasis.}, }
@article {pmid10779538, year = {2000}, author = {Wang, XQ and Tank, DC and Sang, T}, title = {Phylogeny and divergence times in Pinaceae: evidence from three genomes.}, journal = {Molecular biology and evolution}, volume = {17}, number = {5}, pages = {773-781}, doi = {10.1093/oxfordjournals.molbev.a026356}, pmid = {10779538}, issn = {0737-4038}, mesh = {Cell Nucleus/genetics ; Chloroplasts/genetics ; *Evolution, Molecular ; *Genetic Variation ; *Genome, Plant ; Mitochondria/genetics ; *Phylogeny ; Trees/*classification/*genetics ; }, abstract = {In Pinaceae, the chloroplast, mitochondrial, and nuclear genomes are paternally, maternally, and biparentally inherited, respectively. Examining congruence and incongruence of gene phylogenies among the three genomes should provide insights into phylogenetic relationships within the family. Here we studied intergeneric relationships of Pinaceae using sequences of the chloroplast matK gene, the mitochondrial nad5 gene, and the low-copy nuclear gene 4CL. The 4CL gene may exist as a single copy in some species of Pinaceae, but it constitutes a small gene family with two or three members in others. Duplication and deletion of the 4CL gene occurred at a tempo such that paralogous loci are maintained within but not between genera. Exons of the 4CL gene have diverged approximately twice as fast as the matK gene and five times more rapidly than the nad5 gene. The partition-homogeneity test indicates that the three data sets are homogeneous. A combined analysis of the three gene sequences generated a well-resolved and strongly supported phylogeny. The combined phylogeny, which is topologically congruent with the three individual gene trees based on the Templeton test, is likely to represent the organismal phylogeny of Pinaceae. This phylogeny agrees to a certain extent with previous phylogenetic hypotheses based on morphological, anatomical, and immunological data. Disagreement between the previous hypotheses and the three-genome phylogeny suggests that morphology of both vegetative and reproductive organs has undergone convergent evolution within the pine family. The strongly supported monophyly of Nothotsuga longibracteata, Tsuga mertensiana, and Tsuga canadensis on all three gene phylogenies provides evidence against previous hypotheses of intergeneric hybrid origins of N. longibracteata and T. mertensiana. Divergence times of the genera were estimated based on sequence divergence of the matK gene, and they correspond well with the fossil record.}, }
@article {pmid10767311, year = {2000}, author = {Puccio, H and Koenig, M}, title = {Recent advances in the molecular pathogenesis of Friedreich ataxia.}, journal = {Human molecular genetics}, volume = {9}, number = {6}, pages = {887-892}, doi = {10.1093/hmg/9.6.887}, pmid = {10767311}, issn = {0964-6906}, mesh = {Friedreich Ataxia/*genetics/therapy ; Humans ; Iron/metabolism ; *Iron-Binding Proteins ; Iron-Sulfur Proteins/deficiency ; Mitochondria/metabolism ; Mutation ; Phosphotransferases (Alcohol Group Acceptor)/genetics ; Frataxin ; }, abstract = {Friedreich ataxia, the most frequent cause of recessive ataxia, is due in most cases to a homozygous intronic expansion resulting in the loss of function of frataxin. Frataxin is a mitochondrial protein conserved through evolution. Yeast knock-out models and histological data from patient heart autopsies have shown that frataxin defect causes mitochondrial iron accumulation. Biochemical data from patient heart biopsies or autopsies have revealed a specific deficiency in the activities of aconitases and of mitochondrial iron-sulfur proteins. These results suggest that frataxin may play a role either in mitochondrial iron transport or in iron-sulfur cluster assembly or transport. Iron abnormalities suggest a pathogenic mechanism involving free radical production and oxidative stress, a process that might be sensitive to antioxidant therapies.}, }
@article {pmid10766564, year = {1999}, author = {Karaki, H}, title = {[Evolution in programmed cell death].}, journal = {Nihon yakurigaku zasshi. Folia pharmacologica Japonica}, volume = {114}, number = {6}, pages = {384-385}, pmid = {10766564}, issn = {0015-5691}, mesh = {Animals ; Apoptosis/*physiology ; *Biological Evolution ; Humans ; Mitochondria/physiology ; }, }
@article {pmid10765727, year = {2000}, author = {Emel'ianov, VV}, title = {[Evolutionary relationship of Rickettsia and eukaryotic mitochondria].}, journal = {Vestnik Rossiiskoi akademii meditsinskikh nauk}, volume = {}, number = {3}, pages = {3-7}, pmid = {10765727}, issn = {0869-6047}, mesh = {Animals ; Archaea/genetics ; Eukaryota/genetics ; Heat-Shock Proteins/genetics ; Mitochondria/*genetics ; Paramecium/genetics ; *Phylogeny ; Rickettsia/*genetics ; Rickettsia prowazekii/genetics ; }, abstract = {To clarify the evolutionary relationship of rickettsiae and mitochondria, the conserved flat heat-shock protein Hsp60 was phylogenetically studied in detail by using PHYLIP and PROTML packages. The ample data set (50 species) included as many as possible representatives from the Rickettsiaceae family, mitochondrial-type homologs from Archezoa and mitochondrial homologs from Protozoa. Rickettsia prowazekii (that is the genus Rickettsia) was shown to be the least diverging member within Rickettsia--a sister group to the monophyletic clade of mitochondria. These findings were also evidenced by the phylogenetic analysis of 16S rRNA. Rickettsia-like endosymbionts (the parasites Paramecium caudatum and the etiological agent of hepatopancreatitis in shrimps) included within the order Rickettsiales appear to have diverged prior to the Rickettsiaceae/mitochondria cluster. Thus, the Rickettsiales does not seem to be a monophyletic group. An idea concerning the nature of obligate intracellular parasitism of rickettsiae is proposed in the paper from the suggested profound similarity of Rickettsiae genus bacteria and mitochondria which could have a common evolutionary history.}, }
@article {pmid10764533, year = {2000}, author = {Vences, M and Kosuch, J and Lötters, S and Widmer, A and Jungfer, KH and Köhler, J and Veith, M}, title = {Phylogeny and classification of poison frogs (Amphibia: dendrobatidae), based on mitochondrial 16S and 12S ribosomal RNA gene sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {15}, number = {1}, pages = {34-40}, doi = {10.1006/mpev.1999.0738}, pmid = {10764533}, issn = {1055-7903}, mesh = {Amphibians/classification/*genetics ; Animals ; DNA/chemistry/genetics ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {An analysis of partial sequences of the 16S ribosomal rRNA gene (582 bp) of 20 poison frog species (Dendrobatidae) confirmed their phylogenetic relationships to bufonid and leptodactylid frogs. Representatives of the ranoid families and subfamilies Raninae, Mantellinae, Petropedetinae, Cacosterninae, Arthroleptidae, Astylosternidae, and Microhylidae did not cluster as sister group of the Dendrobatidae. Similar results were obtained in an analysis using a partial sequence of the 12S gene (350 bp) in a reduced set of taxa and in a combined analysis. Within the Dendrobatidae, our data supported monophyly of the genus Phyllobates but indicated paraphyly of Epipedobates and Colostethus. Minyobates clustered within Dendrobates, contradicting its previously assumed phylogenetic position. Phobobates species clustered as a monophyletic unit within Epipedobates. Allobates was positioned in a group containing two Colostethus species, indicating that lack of amplexus, presence of skin alkaloids, and aposematic coloration evolved independently in Allobates and the remaining aposematic dendrobatids.}, }
@article {pmid10764531, year = {2000}, author = {Suzuki, H and Tsuchiya, K and Takezaki, N}, title = {A molecular phylogenetic framework for the Ryukyu endemic rodents Tokudaia osimensis and Diplothrix legata.}, journal = {Molecular phylogenetics and evolution}, volume = {15}, number = {1}, pages = {15-24}, doi = {10.1006/mpev.1999.0732}, pmid = {10764531}, issn = {1055-7903}, mesh = {Animals ; Cytochrome b Group/genetics ; DNA/chemistry/genetics ; Evolution, Molecular ; *Eye Proteins ; Genetic Variation ; Japan ; Mitochondria/genetics ; Molecular Sequence Data ; Muridae/classification/*genetics ; *Phylogeny ; Rats ; Retinol-Binding Proteins/genetics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Diplothrix legata and Tokudaia osimensis are rodent species endemic to the Ryukyu Islands (Okinawa area) of the southern part of Japan. To place them within a phylogenetic framework of Asian rodent species, we examined the molecular relationships among these species and Apodemus, Micromys, Mus, and Rattus, using an analysis of mitochondrial cytochrome b gene (1140 bp) and nuclear IRBP gene (782 bp) sequences. The results indicate that the four main murine genera and Tokudaia diverged at similar evolutionary times, namely at the time of the radiation of Murinae, 14 to 40 million years ago, depending on different concepts for the divergence times of Rattus and Mus. In contrast, Diplothrix separated from the Rattus group more recently. Our results indicate that D. legata and the Rattus group diverged at 20-30% of the divergence time of Rattus and Mus under the assumption of the molecular clock, suggesting that D. legata established its lineage at least by the beginning of the Pleistocene era. It is thus evident that the Okinawa area preserves rare indigenous species with various levels of genetic endemicity.}, }
@article {pmid10764530, year = {2000}, author = {Misof, B and Anderson, CL and Hadrys, H}, title = {A phylogeny of the damselfly genus calopteryx (Odonata) using mitochondrial 16S rDNA markers.}, journal = {Molecular phylogenetics and evolution}, volume = {15}, number = {1}, pages = {5-14}, doi = {10.1006/mpev.1999.0724}, pmid = {10764530}, issn = {1055-7903}, mesh = {Animals ; DNA, Ribosomal/chemistry/genetics ; Genetic Markers ; Geography ; Insecta/classification/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {We seek to reconstruct the phylogenetic relationships of the damselfly genus Calopteryx, for which extensive behavioral and morphological knowledge already exists. To date, analyses of the evolutionary pathways of different life history traits have been hampered by the absence of a robust phylogeny based on morphological data. In this study, we concentrate on establishing phylogenetic information from parts of the 16S rDNA gene, which we sequenced for nine Calopteryx species and five outgroup species. The mt 16S rDNA data set did not show signs of saturated variation for ingroup taxa, and phylogenetic reconstructions were insensitive to variation of outgroup taxa. Parsimony, neighbor-joining, and maximum-likelihood reconstructions agreed on parts of the tree. A consensus tree summarizes the significant results and indicates problematic nodes. The 16S rDNA sequences support monophyly of the genera Mnais, Matrona, and Calopteryx. However, the genus Calopteryx may not be monophyletic, since Matrona basilaris and Calopteryx atrata are sister taxa under every parameter setting. The North American and European taxa each appear as monophyletic clades, while the Asian Calopteryx atrata and Calopteryx cornelia are not monophyletic. Our data implies a different paleobiogeographic history of the Eurasian and North American species, with extant Eurasian species complexes shaped by glacial periods, in contrast to extant North American species groups.}, }
@article {pmid10760462, year = {2000}, author = {Hiltunen, JK and Qin, Y}, title = {beta-oxidation - strategies for the metabolism of a wide variety of acyl-CoA esters.}, journal = {Biochimica et biophysica acta}, volume = {1484}, number = {2-3}, pages = {117-128}, doi = {10.1016/s1388-1981(00)00013-5}, pmid = {10760462}, issn = {0006-3002}, mesh = {3-Hydroxyacyl CoA Dehydrogenases/metabolism ; Acetyl-CoA C-Acyltransferase/metabolism ; Acyl-CoA Dehydrogenase ; Acyl-CoA Oxidase ; Animals ; Carbon-Carbon Double Bond Isomerases/metabolism ; Enoyl-CoA Hydratase/metabolism ; Fatty Acid Desaturases/metabolism ; Fatty Acids/*metabolism ; Fatty Acids, Unsaturated/metabolism ; Humans ; Mitochondria/enzymology ; Mitochondrial Trifunctional Protein ; Multienzyme Complexes/*metabolism ; Oxidoreductases/metabolism ; Racemases and Epimerases/metabolism ; }, abstract = {Living organisms are exposed to a number of different fatty acids and their various derivatives arising either via endogenous synthesis or from exogenous sources. These hydrophobic compounds can play specific metabolic, structural or endocrinic functions in the organisms before their elimination, which can be metabolism to CO(2) or to more polar lipid metabolites allowing their excretion. Quantitatively, one of the major pathways metabolizing fatty acids is beta-oxidation, which consists of a set of four reactions operating at the carbons 2 or 3 of acyl-CoA esters and shortening of the acyl-chain. To allow the beta-oxidation of acyl groups with various steric variants to proceed, different strategies have been developed. These strategies include evolution of beta-oxidation enzymes as paralogues showing specificity with respect to either chain-length or modified acyl-chain, metabolic compartmentalization in eukaryotic cells, controlling of substrate transport across membranes, development of auxiliary enzyme systems, acquisition of enzymes with adaptive active sites and recruiting and optimizing enzymes from non-homologous sources allowing them to catalyze a parallel set of reactions with different substrate specificities.}, }
@article {pmid10750846, year = {2000}, author = {Morin, L}, title = {Long branch attraction effects and the status of "basal eukaryotes": phylogeny and structural analysis of the ribosomal RNA gene cluster of the free-living diplomonad Trepomonas agilis.}, journal = {The Journal of eukaryotic microbiology}, volume = {47}, number = {2}, pages = {167-177}, doi = {10.1111/j.1550-7408.2000.tb00028.x}, pmid = {10750846}, issn = {1066-5234}, mesh = {Animals ; Base Sequence ; DNA, Protozoan/genetics ; DNA, Ribosomal/*genetics ; Eukaryota/*classification/*genetics ; Humans ; Molecular Sequence Data ; *Multigene Family ; Nucleic Acid Conformation ; *Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal/*genetics ; }, abstract = {The three taxa emerging at the base of the eukaryotic ribosomal RNA phylogenetic tree (Diplomonadida, Microspora, and Parabasalia) include a wide array of parasitic species. and some free-living organisms that appear to be derived from a parasitic ancestry. The basal position of these taxa, which lack mitochondria, has recently been questioned. I sequenced most of the ribosomal RNA gene cluster of the free-living diplomonad Trepomonas agilis and a secondary structure model was reconstructed for the SSU rRNA. I conducted a RASA matrix analysis to identify, independently from tree reconstruction, putative long branch attraction effects in the data matrix. The results show that each of the basal clades and the euglenozoan clade act, indeed, as long branches and may have been engaged in a process of accelerated rate of evolution. A nucleotide signature analysis was conducted in the conserved regions for positions defining the three great domains of life (Eubacteria, Archea, and Eukaryota). For the three basal taxa, this analysis showed the presence of a significant number of different non-eukaryotic nucleotides. A precise study of the nature and location of these nucleotides led to conclusions supporting the results of the RASA analysis. Altogether, these findings suggest that the basal placement of these taxa in the SSU ribosomal RNA phylogenetic tree is artifactual, and flawed by long branch attraction effects.}, }
@article {pmid10748252, year = {2000}, author = {Howitt, SM and Udvardi, MK}, title = {Structure, function and regulation of ammonium transporters in plants.}, journal = {Biochimica et biophysica acta}, volume = {1465}, number = {1-2}, pages = {152-170}, doi = {10.1016/s0005-2736(00)00136-x}, pmid = {10748252}, issn = {0006-3002}, mesh = {Acyltransferases/metabolism ; Amino Acid Sequence ; Biological Transport ; Carrier Proteins/chemistry/genetics/*metabolism ; *Cation Transport Proteins ; Cell Membrane/chemistry/metabolism ; Gene Expression Regulation, Plant ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/*metabolism ; Proton-Motive Force ; Proton-Translocating ATPases/metabolism ; Quaternary Ammonium Compounds/metabolism ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; }, abstract = {Ammonium is an important source of nitrogen for plants. It is taken up by plant cells via ammonium transporters in the plasma membrane and distributed to intracellular compartments such as chloroplasts, mitochondria and vacuoles probably via different transporters in each case. Ammonium is generally not used for long-distance transport of nitrogen within the plant. Instead, most of the ammonium transported into plant cells is assimilated locally via glutamine synthetases in the cytoplasm and plastids. Ammonium is also produced by plant cells during normal metabolism, and ammonium transporters enable it to be moved from intracellular sites of production to sites of consumption. Ammonium can be generated de novo from molecular nitrogen (N(2)) by nitrogen-fixing bacteria in some plant cells, such as rhizobia in legume root nodule cells, and at least one ammonium transporter is implicated in the transfer of ammonium from the bacteria to the plant cytoplasm. Plant physiologists have described many of these ammonium transport processes over the last few decades. However, the genes and proteins that underlie these processes have been isolated and studied only recently. In this review, we consider in detail the molecular structure, function and regulation of plant ammonium transporters. We also attempt to reconcile recent discoveries at the molecular level with our knowledge of ammonium transport at the whole plant level.}, }
@article {pmid10748222, year = {2000}, author = {Takano, R and Hisahara, S and Namikawa, K and Kiyama, H and Okano, H and Miura, M}, title = {Nerve growth factor protects oligodendrocytes from tumor necrosis factor-alpha-induced injury through Akt-mediated signaling mechanisms.}, journal = {The Journal of biological chemistry}, volume = {275}, number = {21}, pages = {16360-16365}, doi = {10.1074/jbc.M910419199}, pmid = {10748222}, issn = {0021-9258}, mesh = {Androstadienes/pharmacology ; Animals ; Brain/metabolism ; Cell Death/drug effects ; Cell Survival/drug effects ; Cells, Cultured ; Chromones/pharmacology ; Culture Media, Conditioned/pharmacology ; Humans ; Immunohistochemistry ; Membrane Potentials/drug effects ; Mitochondria/metabolism ; Morpholines/pharmacology ; Nerve Growth Factor/*pharmacology ; Oligodendroglia/*metabolism ; Protein Serine-Threonine Kinases/genetics/*metabolism ; *Proto-Oncogene Proteins ; Proto-Oncogene Proteins c-akt ; Rats ; *Signal Transduction ; Tumor Necrosis Factor-alpha/*pharmacology ; Wortmannin ; }, abstract = {Tumor necrosis factor-alpha is thought to be one of the most important inflammatory cytokines associated with the demyelinating disease multiple sclerosis. We determined whether neurotrophins could protect oligodendrocytes from tumor necrosis factor-alpha-mediated cytotoxicity. Among the neurotrophins tested, nerve growth factor was most effective at preventing cell death. Nerve growth factor also prevented the tumor necrosis factor-induced loss of mitochondrial membrane potential. Overexpression of constitutively active Akt, a downstream target of phosphatidylinositol 3-kinase, but not of constitutively active MEK, protected oligodendrocytes from tumor necrosis factor-induced injury. Moreover, overexpression of dominant-negative Akt negated the protective effects of nerve growth factor on tumor necrosis factor-mediated oligodendrocyte cytotoxicity. These findings indicate that the Akt pathway is crucial in nerve growth factor-mediated oligodendrocyte protection.}, }
@article {pmid10747106, year = {2000}, author = {Wang, L and Yokoyama, K and Miyaji, M and Nishimura, K}, title = {Mitochondrial cytochrome b gene analysis of Aspergillus fumigatus and related species.}, journal = {Journal of clinical microbiology}, volume = {38}, number = {4}, pages = {1352-1358}, pmid = {10747106}, issn = {0095-1137}, mesh = {Amino Acid Sequence ; Aspergillosis/microbiology ; Aspergillus/*classification/enzymology/*genetics ; Aspergillus fumigatus/*classification/enzymology/genetics ; Base Sequence ; Cytochrome b Group/*genetics ; DNA, Fungal/genetics ; Genes, Fungal ; Humans ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Nucleotide sequences of 426 bp from the mitochondrial (mt) cytochrome b genes of six anamorph species and two species of Neosartorya teleomophs of Aspergillus section Fumigati were determined. These sequences were used to build nucleotide- and amino acid-based trees for phylogenetic analysis. Thirteen strains of A. fumigatus including 10 clinical isolates of A. fumigatus, 1 type culture of A. fumigatus var. fumigatus, 1 type culture of A. fumigatus var. ellipticus, and 1 strain of A. fumigatus var. albus, had the same nucleotide sequences. One strain of A. fumisynnematus, two strains labeled A. neoellipticus, two strains of A. viridinutans, and one strain of A. duricaulis had distinct nucleotide and amino acid sequences. Two strains of A. brevipes were divided into two types. One produced a 1,500-bp fragment that included an intron. The nucleotide sequences of its two exons were similar to those of the A. fumigatus, and the derived amino acid sequence was the same as that for A. fumigatus. The other produced a 426-bp fragment and had the same nucleotide and amino acid sequences as A. unilateralis. Neosartorya fischeri var. fischeri and N. stramenia had nucleotide sequences that differed from that of A. fumigatus. These species possessed their own characteristic nucleotide sequences that differed from each other. In comparisons of homologous sequences from four other pathogenic species of Aspergillus, regions specific to section Fumigati were found. The mt cytochrome b gene analysis was valuable for the identification, classification, and phylogenetic analysis of isolates of section Fumigati.}, }
@article {pmid10743607, year = {2000}, author = {Plümper, E and Bradley, PJ and Johnson, PJ}, title = {Competition and protease sensitivity assays provide evidence for the existence of a hydrogenosomal protein import machinery in Trichomonas vaginalis.}, journal = {Molecular and biochemical parasitology}, volume = {106}, number = {1}, pages = {11-20}, doi = {10.1016/s0166-6851(99)00196-6}, pmid = {10743607}, issn = {0166-6851}, support = {AI07323/AI/NIAID NIH HHS/United States ; AI27857/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Biological Transport, Active/drug effects ; Dose-Response Relationship, Drug ; Electrophoresis, Polyacrylamide Gel ; Ferredoxins/metabolism ; Genes, Protozoan ; Membrane Proteins/metabolism ; Mitochondria/drug effects/metabolism ; Organelles/drug effects/metabolism ; Protein Precursors/metabolism ; Protozoan Proteins/*metabolism ; Temperature ; Time Factors ; Trichomonas vaginalis/*metabolism ; Trypsin/pharmacology ; }, abstract = {Hydrogenosomes are double membrane bounded redox organelles found in a number of amitochondriate protists and fungi. They are involved in carbohydrate metabolism and ATP synthesis and thus resemble mitochondria. Molecular analysis of the hydrogenosomal heat shock proteins Hsp70, Hsp60 and Hsp10 in Trichomonas vaginalis, one of the deepest-branching eukaryotes known to date, has revealed that these group exclusively with mitochondrial heat shock proteins. This finding indicates strongly that a progenitor organelle which gave rise to contemporary mitochondria and hydrogenosomes existed early in eukaryotic life. This hypothesis is further supported by similarities of hydrogenosomal and mitochondrial biogenesis. It was shown that T. vaginalis hydrogenosomal proteins are synthesized on free ribosomes in the cytosol with an N-terminal presequence that carries targeting information and is cleaved upon import into the organelle. Furthermore, as in mitochondrial import, hydrogenosomal protein import requires ATP, an electrochemical transmembrane potential and cytosolic protein factor(s). Here we demonstrate that inhibition of hydrogenosomal protein import occurs (i) in the presence of a synthetic presequence peptide and (ii) after pretreatment of hydrogenosomes with the protease trypsin. Trypsin pretreatment affects two hydrogenosomal membrane proteins of 31 and 70 kDa, respectively. Thus, we present evidence that import is saturable and that proteinaceous hydrogenosomal import receptor(s) exist. These results are a first step towards a characterization of the hydrogenosomal import machinery which should provide further insights into the relationship of hydrogenosomes and mitochondria and the evolution of protein targeting into organelles of endosymbiotic origin.}, }
@article {pmid10737788, year = {2000}, author = {Shimizu, S and Konishi, A and Kodama, T and Tsujimoto, Y}, title = {BH4 domain of antiapoptotic Bcl-2 family members closes voltage-dependent anion channel and inhibits apoptotic mitochondrial changes and cell death.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {7}, pages = {3100-3105}, pmid = {10737788}, issn = {0027-8424}, mesh = {Apoptosis/*physiology ; Base Sequence ; DNA Primers ; Humans ; Ion Channel Gating/*physiology ; Mitochondria/*physiology ; Porins/*physiology ; Proto-Oncogene Proteins c-bcl-2/chemistry/*physiology ; Voltage-Dependent Anion Channels ; }, abstract = {A change of mitochondrial membrane permeability is essential for apoptosis, leading to translocation of apoptogenic cytochrome c and apoptosis-inducing factor into the cytoplasm. We recently showed that the Bcl-2 family of proteins regulate cytochrome c release and the mitochondrial membrane potential (Deltapsi) by directly modulating the activity of the voltage-dependent anion channel (VDAC) through binding. Here we investigated the biochemical role of the conserved N-terminal homology domain (BH4) of Bcl-x(L), which has been shown to be essential for inhibition of apoptosis, with respect to the regulation of mitochondrial membrane permeability and found that BH4 was required for Bcl-x(L) to prevent cytochrome c release and Deltapsi loss. A study using VDAC liposomes revealed that Bcl-x(L), but not Bcl-x(L) lacking the BH4 domain, inhibited VDAC activity. Furthermore, BH4 oligopeptides of Bcl-2 and Bcl-x(L), but not mutant peptides, were able to inhibit both VDAC activity on liposomes even in the presence of Bax and apoptotic Deltapsi loss in isolated mitochondria. It was also shown that the BH4 domain, fused to the protein transduction domain of HIV TAT protein (TAT-BH4), efficiently prevented apoptotic cell death. These results indicate that the BH4 of Bcl-2/Bcl-x(L) is essential and sufficient for inhibiting VDAC activity, which in turn prevents apoptotic mitochondrial changes, and for preventing apoptotic cell death. Finally, the data suggest that the TAT-BH4 peptide is potentially useful as a therapeutic agent for diseases caused by accelerated apoptosis.}, }
@article {pmid10734603, year = {1999}, author = {Cao, Y and Kim, KS and Ha, JH and Hasegawa, M}, title = {Model dependence of the phylogenetic inference: relationship among carnivores, Perissodactyls and cetartiodactyls as inferred from mitochondrial genome sequences.}, journal = {Genes &amp; genetic systems}, volume = {74}, number = {5}, pages = {211-217}, doi = {10.1266/ggs.74.211}, pmid = {10734603}, issn = {1341-7568}, mesh = {Animals ; Artiodactyla/*classification/genetics ; Carnivora/*classification/genetics ; Cetacea/*classification/genetics ; Genetic Heterogeneity ; Genome ; Mitochondria/*genetics ; Models, Genetic ; Perissodactyla/*classification/genetics ; *Phylogeny ; Proteins/genetics ; }, abstract = {Some previous analysis of mitochondrial proteins strongly support the Carnivora/Perissodactyla grouping excluding Cetartiodactyla (Artiodactyla + Cetacea) as an outgroup, but the support of the hypothesis remains equivocal from the analysis of several nuclear-encoded proteins. In order to evaluate the strength of the support by mitochondrial proteins, phylogenetic relationship among Carnivora, Perissodactyla, and Cetartiodactyla was estimated with the ML method by using the updated data set of the 12 mitochondrial proteins with several alternative models. The analyses demonstrate that the phylogenetic inference depends on the model used in the ML analysis; i.e., whether the site-heterogeneity is taken into account and whether the rate parameters are estimated for each individual proteins or for the concatenated sequences. Although the analysis of concatenated sequences strongly supports the Carnivora/Perissodactyla grouping, the total evaluation of the separate analyses of individual proteins, which approximates the data better than the concatenated analysis, gives only ambiguous results, and therefore it is concluded that more data are needed to resolve this trichotomy.}, }
@article {pmid10723739, year = {2000}, author = {Holbrook, JD and Birdsey, GM and Yang, Z and Bruford, MW and Danpure, CJ}, title = {Molecular adaptation of alanine:glyoxylate aminotransferase targeting in primates.}, journal = {Molecular biology and evolution}, volume = {17}, number = {3}, pages = {387-400}, doi = {10.1093/oxfordjournals.molbev.a026318}, pmid = {10723739}, issn = {0737-4038}, mesh = {5' Untranslated Regions ; Adaptation, Biological/*genetics ; Animals ; Base Sequence ; Cloning, Molecular ; Evolution, Molecular ; Haplorhini/*genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Protein Biosynthesis ; Selection, Genetic ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Transaminases/*genetics ; }, abstract = {The intermediary metabolic enzyme alanine:glyoxylate aminotransferase (AGT) is targeted to different organelles (mitochondria and/or peroxisomes) in different species. Possibly under the influence of dietary selection pressure, the subcellular distribution of AGT has changed on at least eight occasions during the evolution of mammals. AGT targeting is dependent on the variable use of two alternative transcription and translation initiation sites which determine whether or not the region encoding the N-terminal mitochondrial targeting sequence is contained within the open reading frame. In the present study, we sequenced the 5' region of the AGT gene, including both ancestral translation start sites, for 11 anthropoid primates and compared the results with data already available for two others. We show that while the more 3' of the two translation start sites is maintained in all species, the more 5' site has been lost in six species (five of seven catarrhines and one of six platyrrhines). In addition, the remaining two catarrhines, which have maintained the 5' translation start site, are predicted to have lost mitochondrial targeting by a different mechanism, possibly loss of the more 5' transcription start site. Analysis of the relative frequencies of nonsynonymous and synonymous mutations in the region encoding the extant or ancestral mitochondrial targeting sequences led us to suggest that there has been recent strong positive selection pressure to lose, or decrease the efficiency of, mitochondrial AGT targeting in several anthropoid lineages, and that the loss of mitochondrial targeting in this group of mammals is likely to have occurred on at least four, and possibly five, separate occasions.}, }
@article {pmid10719376, year = {2000}, author = {Sluse, FE and Jarmuszkiewicz, W}, title = {Activity and functional interaction of alternative oxidase and uncoupling protein in mitochondria from tomato fruit.}, journal = {Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas}, volume = {33}, number = {3}, pages = {259-268}, doi = {10.1590/s0100-879x2000000300002}, pmid = {10719376}, issn = {0100-879X}, mesh = {Adenosine Triphosphate/biosynthesis ; Carrier Proteins/*metabolism/physiology ; Cell Respiration/physiology ; Ion Channels ; Solanum lycopersicum/*enzymology ; Membrane Proteins/*metabolism/physiology ; Mitochondria/enzymology/*metabolism ; Mitochondrial Proteins ; Oxidoreductases/*metabolism/physiology ; Uncoupling Agents/*metabolism ; Uncoupling Protein 1 ; }, abstract = {Cyanide-resistant alternative oxidase (AOX) is not limited to plant mitochondria and is widespread among several types of protists. The uncoupling protein (UCP) is much more widespread than previously believed, not only in tissues of higher animals but also in plants and in an amoeboid protozoan. The redox energy-dissipating pathway (AOX) and the proton electrochemical gradient energy-dissipating pathway (UCP) lead to the same final effect, i.e., a decrease in ATP synthesis and an increase in heat production. Studies with green tomato fruit mitochondria show that both proteins are present simultaneously in the membrane. This raises the question of a specific physiological role for each energy-dissipating system and of a possible functional connection between them (shared regulation). Linoleic acid, an abundant free fatty acid in plants which activates UCP, strongly inhibits cyanide-resistant respiration mediated by AOX. Moreover, studies of the evolution of AOX and UCP protein expression and of their activities during post-harvest ripening of tomato fruit show that AOX and plant UCP work sequentially: AOX activity decreases in early post-growing stages and UCP activity is decreased in late ripening stages. Electron partitioning between the alternative oxidase and the cytochrome pathway as well as H+ gradient partitioning between ATP synthase and UCP can be evaluated by the ADP/O method. This method facilitates description of the kinetics of energy-dissipating pathways and of ATP synthase when state 3 respiration is decreased by limitation of oxidizable substrate.}, }
@article {pmid10719181, year = {2000}, author = {Clark-Walker, GD and Hansbro, PM and Gibson, F and Chen, XJ}, title = {Mutant residues suppressing rho(0)-lethality in Kluyveromyces lactis occur at contact sites between subunits of F(1)-ATPase.}, journal = {Biochimica et biophysica acta}, volume = {1478}, number = {1}, pages = {125-137}, doi = {10.1016/s0167-4838(00)00003-0}, pmid = {10719181}, issn = {0006-3002}, mesh = {Alleles ; Crystallography ; Genes, Lethal ; Genes, Suppressor ; Genotype ; Kluyveromyces/enzymology/*genetics/growth &amp; development ; Mitochondria/enzymology ; Models, Molecular ; Mutation ; Proton-Translocating ATPases/chemistry/*genetics ; }, abstract = {Characterisation of 35 Kluyveromyces lactis strains lacking mitochondrial DNA has shown that mutations suppressing rho(0)-lethality are limited to the ATP1, 2 and 3 genes coding for the alpha-, beta- and gamma- subunits of mitochondrial F(1)-ATPase. All atp mutations reduce growth on glucose and three alleles, atp1-2, 1-3 and atp3-1, produce a respiratory deficient phenotype that indicates a drop in efficiency of the F(1)F(0)-ATP synthase complex. ATPase activity is needed for suppression as a double mutant containing an atp allele, together with a mutation abolishing catalytic activity, does not suppress rho(0)-lethality. Positioning of the seven amino acids subject to mutation on the bovine F(1)-ATPase structure shows that two residues are found in a membrane proximal region while five amino acids occur at a region suggested to be a molecular bearing. The intriguing juxtaposition of mutable amino acids to other residues subject to change suggests that mutations affect subunit interactions and alter the properties of F(1) in a manner yet to be determined. An explanation for suppressor activity of atp mutations is discussed in the context of a possible role for F(1)-ATPase in the maintenance of mitochondrial inner membrane potential.}, }
@article {pmid10717481, year = {2000}, author = {Young, ET and Sloan, J and Miller, B and Li, N and van Riper, K and Dombek, KM}, title = {Evolution of a glucose-regulated ADH gene in the genus Saccharomyces.}, journal = {Gene}, volume = {245}, number = {2}, pages = {299-309}, doi = {10.1016/s0378-1119(00)00035-4}, pmid = {10717481}, issn = {0378-1119}, support = {GM 26079/GM/NIGMS NIH HHS/United States ; }, mesh = {Alcohol Dehydrogenase/*genetics/metabolism ; Base Sequence ; DNA, Fungal/chemistry/genetics/isolation &amp; purification ; DNA-Binding Proteins/genetics/physiology ; *Evolution, Molecular ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Fungal ; Glucose/*physiology ; Isoenzymes/genetics/metabolism ; Lac Operon/genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Mutagenesis ; Phylogeny ; Promoter Regions, Genetic/genetics ; Recombinant Fusion Proteins/genetics ; Regulatory Sequences, Nucleic Acid ; Saccharomyces/enzymology/*genetics ; Saccharomyces cerevisiae/genetics ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Transcription Factors/genetics/physiology ; }, abstract = {To determine when a glucose-repressed alcohol dehydrogenase isozyme and its regulatory gene, ADR1, arose during evolution, we surveyed species of the genus Saccharomyces for glucose-repressed ADH isozymes and for ADR1 homologues. Glucose-repressed ADH isozymes were present in all species of Saccharomyces sensu strictu and also in Saccharomyces kluyveri, the most distant member of the Saccharomyces clade. We cloned and characterized ADH promoters from S. bayanus, S. douglasii, and S. kluyveri. The ADH promoters from S. bayanus and S. douglasii had conserved sequences, including upstream regulatory elements, and an extended polydA tract. The expression of a reporter gene driven by the S. bayanus promoter was glucose-repressed and dependent on the major activator of transcription, ADR1, when it was introduced into S. cerevisiae. One S. kluyveri promoter was also glucose-repressed and ADR1-dependent in S. cerevisiae. The other S. kluyveri ADH promoter was expressed constitutively and was ADR1-independent. Although showing little sequence conservation with the S. cerevisiae ADH2 promoter, the glucose-repressed S. kluyveri promoter contains numerous potential binding sites for Adr1. The glucose-repressed ADH from S. kluyveri is a mitochondrial isozyme most closely related to S. cerevisiae ADHIII. ADR1 homologues from S. douglasii and S. paradoxus contain a trinucleotide repeat encoding polyAsn that is lacking in S. cerevisiae and S. bayanus. No ADR1 homologue could be detected in S. kluyveri, suggesting that the potential for Adr1 regulation may have arisen first, before ADR1 evolved.}, }
@article {pmid10715697, year = {1999}, author = {Rivarola, HW and Fernández, AR and Enders, JE and Fretes, R and Gea, S and Suligoy, M and Palma, JA and Paglini-Oliva, P}, title = {Thioridazine treatment modifies the evolution of Trypanosoma cruzi infection in mice.}, journal = {Annals of tropical medicine and parasitology}, volume = {93}, number = {7}, pages = {695-702}, pmid = {10715697}, issn = {0003-4983}, mesh = {Animals ; Chagas Disease/*drug therapy/enzymology ; Drug Evaluation, Preclinical ; Mice ; Thioridazine/administration &amp; dosage/*therapeutic use ; Trypanocidal Agents/administration &amp; dosage/*therapeutic use ; Trypanosoma cruzi/*drug effects/enzymology ; }, abstract = {Thioridazine, a tricyclic drug, is known to have a direct effect on Trypanosoma cruzi, disrupting the parasites' mitochondria and kinetoplasts. In the present study, the drug was used orally, at 80 mg/kg.day for 3 days, to treat mice inoculated with low numbers of T. cruzi. The drug caused no apparent toxicity in the host. It cleared trypomastigotes from the bloodstream, prevented the histological and functional alterations of the heart normally observed in the chronic phase of the experimental disease, and greatly reduced the mortality rate compared with that in untreated, infected controls. When checked 135 days post-infection, the density of cardiac beta receptors and the cardiac histology of the treated mice were indistinguishable from those of uninfected, untreated controls. The drug is already used to treat humans, as a neuroleptic drug. It appears to be able to prevent acute infection with T. cruzi evolving into chronic disease, at least in mice, and may be a useful base from which to design new agents for the treatment of Chagas disease.}, }
@article {pmid10715202, year = {2000}, author = {Hiller, R and Hetzer, M and Schweyen, RJ and Mueller, MW}, title = {Transposition and exon shuffling by group II intron RNA molecules in pieces.}, journal = {Journal of molecular biology}, volume = {297}, number = {2}, pages = {301-308}, doi = {10.1006/jmbi.2000.3582}, pmid = {10715202}, issn = {0022-2836}, mesh = {Base Sequence ; Binding Sites ; Catalysis ; Evolution, Molecular ; Exons/*genetics ; Genetic Complementation Test ; Introns/*genetics ; Kinetics ; Models, Genetic ; Molecular Weight ; Nucleic Acid Conformation ; RNA/chemistry/genetics/metabolism ; RNA Splicing/*genetics ; RNA, Catalytic/chemistry/*genetics/*metabolism ; RNA, Mitochondrial ; Recombination, Genetic/*genetics ; Sequence Deletion/genetics ; Sequence Homology, Nucleic Acid ; Yeasts/enzymology/genetics ; }, abstract = {In the realms of RNA, transposable elements created by self-inserting introns recombine novel combinations of exon sequences in the background of replicating molecules. Although intermolecular RNA recombination is a wide-spread phenomenon reported for a variety of RNA-containing viruses, direct evidence to support the theory that modern splicing systems, together with the exon-intron structure, have evolved from the ability of RNA to recombine, is lacking. Here, we used an in vitro deletion-complementation assay to demonstrate trans-activation of forward and reverse self-splicing of a fragmented derivative of the group II intron bI1 from yeast mitochondria. We provide direct evidence for the functional interchangeability of analogous but non-identical domain 1 RNA molecules of group II introns that result in trans-activation of intron transposition and RNA-based exon shuffling. The data extend theories on intron evolution and raise the intriguing possibility that naturally fragmented group III and spliceosomal introns themselves can create transposons, permitting rapid evolution of protein-coding sequences by splicing reactions.}, }
@article {pmid10713448, year = {2000}, author = {Kirby, RR}, title = {Cloning and primary structure of putative cytosolic and mitochondrial malate dehydrogenase from the mollusc Nucella lapillus (L.).}, journal = {Gene}, volume = {245}, number = {1}, pages = {81-88}, doi = {10.1016/s0378-1119(00)00036-6}, pmid = {10713448}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Cytosol/enzymology ; DNA, Complementary/chemistry/genetics ; Malate Dehydrogenase/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Snails/enzymology/*genetics ; }, abstract = {The evolutionary history of the malate dehydrogenase (MDH) gene family [NAD-dependent MDH; EC 1.1.1.37 and NAD(P)-dependent MDH; EC 1.1.1.82] has received much attention. MDHs have also featured extensively as electrophoretic markers in population genetics and evolutionary ecology, and in many cases, intraspecific variation in MDH has been correlated with environmental variables. However, while the amino acid residues essential for MDH function are known, no studies have examined intraspecific nucleotide variation despite evidence indicating that natural selection may be operating on this locus. This study presents two sets of degenerate oligonucleotide PCR primers to facilitate the cloning of cytosolic MDH (cMDH) and mitochondrial MDH (mMDH) from a broad range of animals (cMDH) and animals and plants (mMDH). These primers were used to obtain putative cMDH and mMDH cDNAs from the mollusc Nucella lapillus. The N. lapillus cMDH cDNA was found to encode a putative cMDH protein of 334aa and 36kDa, while the mMDH cDNA encoded a putative mature mMDH protein of 315aa and 33kDa. The putative amino acid sequences of the two compartmentalised N. lapillus MDHs are presented and compared to other known MDH sequences.}, }
@article {pmid10713172, year = {2000}, author = {Dyall, SD and Koehler, CM and Delgadillo-Correa, MG and Bradley, PJ and Plümper, E and Leuenberger, D and Turck, CW and Johnson, PJ}, title = {Presence of a member of the mitochondrial carrier family in hydrogenosomes: conservation of membrane-targeting pathways between hydrogenosomes and mitochondria.}, journal = {Molecular and cellular biology}, volume = {20}, number = {7}, pages = {2488-2497}, pmid = {10713172}, issn = {0270-7306}, support = {T32 AI007323/AI/NIAID NIH HHS/United States ; R01 AI027857/AI/NIAID NIH HHS/United States ; AI07323/AI/NIAID NIH HHS/United States ; AI27857/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R37 AI027857/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Carrier Proteins/chemistry/*genetics/metabolism ; Cloning, Molecular ; Energy Metabolism ; Evolution, Molecular ; Fungal Proteins/chemistry ; Membrane Proteins/chemistry/genetics/metabolism ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/chemistry/genetics/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Sorting Signals/chemistry/metabolism ; Protozoan Proteins/chemistry/*genetics/metabolism ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Trichomonas vaginalis/*chemistry/cytology ; }, abstract = {A number of microaerophilic eukaryotes lack mitochondria but possess another organelle involved in energy metabolism, the hydrogenosome. Limited phylogenetic analyses of nuclear genes support a common origin for these two organelles. We have identified a protein of the mitochondrial carrier family in the hydrogenosome of Trichomonas vaginalis and have shown that this protein, Hmp31, is phylogenetically related to the mitochondrial ADP-ATP carrier (AAC). We demonstrate that the hydrogenosomal AAC can be targeted to the inner membrane of mitochondria isolated from Saccharomyces cerevisiae through the Tim9-Tim10 import pathway used for the assembly of mitochondrial carrier proteins. Conversely, yeast mitochondrial AAC can be targeted into the membranes of hydrogenosomes. The hydrogenosomal AAC contains a cleavable, N-terminal presequence; however, this sequence is not necessary for targeting the protein to the organelle. These data indicate that the membrane-targeting signal(s) for hydrogenosomal AAC is internal, similar to that found for mitochondrial carrier proteins. Our findings indicate that the membrane carriers and membrane protein-targeting machinery of hydrogenosomes and mitochondria have a common evolutionary origin. Together, they provide strong evidence that a single endosymbiont evolved into a progenitor organelle in early eukaryotic cells that ultimately give rise to these two distinct organelles and support the hydrogen hypothesis for the origin of the eukaryotic cell.}, }
@article {pmid10712839, year = {2000}, author = {Koulianos, S and Schmid-Hempel, P}, title = {Phylogenetic relationships among bumble bees (Bombus, latreille) inferred from mitochondrial cytochrome b and cytochrome oxidase I sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {14}, number = {3}, pages = {335-341}, doi = {10.1006/mpev.1999.0621}, pmid = {10712839}, issn = {1055-7903}, mesh = {Animals ; Bees/classification/*enzymology/*genetics ; Cytochrome b Group/*genetics ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology ; Phylogeny ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {We conducted a molecular study intending to derive an estimate of the relationships within the genus Bombus (bumble bees) by comparing the mitochondrial cytochrome b and cytochrome oxidase I (COI) genes from 19 species, spanning 10 of approximately 16 European subgenera and 3 subgenera from North and South America. Our trees differ from the most recent classifications of bumble bees. Although bootstrap values for deep branches are low, our sequences show significant data structure and low homoplasy, and all trees share some groups and patterns. In all cases, the subgenus Bombus s. str. clusters among the most derived bumble bees, contrary to other molecular studies. In all trees, B. funebris is the sister taxon of B. robustus, and in five of the six trees, B. wurflenii is the sister taxon to this clade. B. nevadensis is basal to the other species in the analysis of the cytochrome b gene, but appears to be among the most derived according to the analysis of the COI region. The species representing the subgenera Thoracobombus and Fervidobombus are consistently among the earliest diverged. Species that appear in very different positions in different trees are B. nevadensis, B. mesomelas, B. balteatus, and B. hyperboreus. All subgenera with two representatives in our analysis are apparently monophyletic except Fervidobombus, Melanobombus, and Pyrobombus. The groups formed by pocket makers and non-pocket makers within Bombus also appear to be paraphyletic, and therefore some subgenera may not accurately reflect phylogeny.}, }
@article {pmid10712157, year = {2000}, author = {Martin, W}, title = {Perspectives: evolutionary biology. A powerhouse divided.}, journal = {Science (New York, N.Y.)}, volume = {287}, number = {5456}, pages = {1219}, doi = {10.1126/science.287.5456.1219}, pmid = {10712157}, issn = {0036-8075}, mesh = {Actins/chemistry/metabolism ; Alphaproteobacteria/chemistry/genetics ; Arabidopsis Proteins ; Bacterial Proteins/chemistry/genetics/metabolism ; *Biological Evolution ; Chloroplasts/chemistry/metabolism ; *Cytoskeletal Proteins ; Cytoskeleton/chemistry ; Dynamins ; Eukaryota/*chemistry/metabolism/physiology/ultrastructure ; Evolution, Molecular ; GTP Phosphohydrolases/chemistry/metabolism ; GTP-Binding Proteins/*chemistry/genetics/*metabolism ; Mitochondria/*chemistry/metabolism ; Plant Proteins/*chemistry/genetics/*metabolism ; Symbiosis ; Tubulin/chemistry/metabolism ; Yeasts/chemistry/metabolism ; }, }
@article {pmid10710706, year = {1999}, author = {Cavalier-Smith, T and Beaton, MJ}, title = {The skeletal function of non-genic nuclear DNA: new evidence from ancient cell chimaeras.}, journal = {Genetica}, volume = {106}, number = {1-2}, pages = {3-13}, doi = {10.1023/a:1003701925110}, pmid = {10710706}, issn = {0016-6707}, mesh = {Cell Nucleus/*genetics ; DNA/*genetics ; DNA, Bacterial/genetics ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; DNA, Viral/genetics ; Eukaryota/*genetics ; *Eukaryotic Cells ; *Evolution, Molecular ; *Genome ; Symbiosis ; }, abstract = {DNA can be divided functionally into three categories: (1) genes--which code for proteins or specify non-messenger RNAs; (2) semons--short specific sequences involved in the replication, segregation, recombination or specific attachments of chromosomes, or chromosome regions (e.g. loops or domains) or selfish genetic elements; (3) secondary DNA--which does not function by means of specific sequences. Probably more than 90% of DNA in the biosphere is secondary DNA present in the nuclei of plants and phytoplankton. The amount of genic DNA is related to the complexity of the organism, whereas the amount of secondary DNA increases proportionally with cell volume, and not with complexity. This correlation is most simply explained by the skeletal DNA hypothesis, according to which nuclear DNA functions as the basic framework for the assembly of the nucleus and the total genomic DNA content functions (together with relatively invariant folding rules) in determining nuclear volumes. Balanced growth during the cell cycle requires the cytonuclear ratio to be basically constant, irrespective of cell volume; thus nuclear volumes, and therefore the overall genome size, have to be evolutionarily adjusted to changing cell volumes for optimal function. Bacteria, mitochondria, chloroplasts and viruses have no nuclear envelope; and the skeletal DNA hypothesis simply explains why secondary DNA is essentially absent from them but present in large cell nuclei. Hitherto it has been difficult to refute the alternative hypothesis that nuclear secondary DNA (whether 'junk' or selfish DNA) accumulates merely by mutation pressure, and that selection for economy is not strong enough to eliminate it, whereas accumulation in mitochondria and plastids is prevented by intracellular replicative competition between their multiple genomes. New data that discriminate clearly between these explanations for secondary DNA come from cryptomonads and chlorarachneans, two groups of algae that originated independently by secondary symbiogenesis (i.e., the merger of two radically different eukaryote cells) several hundred million years ago. In both groups the nucleus and plasma membrane of the former algal symbiont persist as the nucleomorphs and periplastid membrane, respectively. The fact that nucleomorphs have undergone a 200- to 1000-fold reduction in genome size and have virtually no secondary DNA shows that selection against non-functional nuclear DNA is strong enough to eliminate it very efficiently; therefore, the large amounts of secondary DNA in the former host nuclei of these chimaeras, and in nuclei generally, must be being maintained by positive selection. The divergent selection for secondary DNA in the nucleus and against it in nucleomorphs is readily explicable by the skeletal DNA hypothesis, given the different spectrum of gene functions that it encodes.}, }
@article {pmid10677847, year = {2000}, author = {van Hoek, AH and van Alen, TA and Sprakel, VS and Leunissen, JA and Brigge, T and Vogels, GD and Hackstein, JH}, title = {Multiple acquisition of methanogenic archaeal symbionts by anaerobic ciliates.}, journal = {Molecular biology and evolution}, volume = {17}, number = {2}, pages = {251-258}, doi = {10.1093/oxfordjournals.molbev.a026304}, pmid = {10677847}, issn = {0737-4038}, mesh = {Anaerobiosis ; Animals ; Ciliophora/genetics/*physiology ; Cockroaches ; DNA, Archaeal/genetics ; DNA, Ribosomal/genetics ; Euryarchaeota/genetics/*physiology ; *Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/*genetics ; Rana ridibunda ; *Symbiosis ; }, abstract = {Anaerobic heterotrichous ciliates (Armophoridae and Clevelandellidae) possess hydrogenosomes that generate molecular hydrogen and ATP. This intracellular source of hydrogen provides the basis for a stable endosymbiotic association with methanogenic archaea. We analyzed the SSU rRNA genes of 18 heterotrichous anaerobic ciliates and their methanogenic endosymbionts in order to unravel the evolution of this mutualistic association. Here, we show that the anaerobic heterotrichous ciliates constitute at least three evolutionary lines. One group consists predominantly of gut-dwelling ciliates, and two to three, potentially four, additional clades comprise ciliates that thrive in freshwater sediments. Their methanogenic endosymbionts belong to only two different taxa that are closely related to free-living methanogenic archaea from the particular ecological niches. The close phylogenetic relationships between the endosymbionts and free-living methanogenic archaea argue for multiple acquisitions from environmental sources, notwithstanding the strictly vertical transmission of the endosymbionts. Since phylogenetic analysis of the small-subunit (SSU) rRNA genes of the hydrogenosomes of these ciliates indicates a descent from the mitochondria of aerobic ciliates, it is likely that anaerobic heterotrichous ciliates hosted endosymbiotic methanogens prior to their radiation. Therefore, our data strongly suggest multiple acquisitions and replacements of endosymbiotic methanogenic archaea during their host's adaptation to the various ecological niches.}, }
@article {pmid10677845, year = {2000}, author = {Corneli, PS and Ward, RH}, title = {Mitochondrial genes and mammalian phylogenies: increasing the reliability of branch length estimation.}, journal = {Molecular biology and evolution}, volume = {17}, number = {2}, pages = {224-234}, doi = {10.1093/oxfordjournals.molbev.a026302}, pmid = {10677845}, issn = {0737-4038}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Enzymes/genetics ; *Evolution, Molecular ; Humans ; Mammals/classification/*genetics ; Mitochondria/*genetics ; *Phylogeny ; Proteins/genetics ; }, abstract = {Since branch lengths provide important information about the timing and the extent of evolutionary divergence among taxa, accurate resolution of evolutionary history depends as much on branch length estimates as on recovery of the correct topology. However, the empirical relationship between the choice of genes to sequence and the quality of branch length estimation remains ill defined. To address this issue, we evaluated the accuracy of branch lengths estimated from subsets of the mitochondrial genome for a mammalian phylogeny with known subordinal relationships. Using maximum-likelihood methods, we estimated branch lengths from an 11-kb sequence of all 13 protein-coding genes and compared them with estimates from single genes (0.2-1.8 kb) and from 7 different combinations of genes (2-3.5 kb). For each sequence, we separated the component of the log-likelihood deviation due to branch length differences associated with alternative topologies from that due to those that are independent of the topology. Even among the sequences that recovered the same tree topology, some produced significantly better branch length estimates than others did. The combination of correct topology and significantly better branch length estimation suggests that these gene combinations may prove useful in estimating phylogenetic relationships for mammalian divergences below the ordinal level. Thus, the proper choice of genes to sequence is a critical factor for reliable estimation of evolutionary history from molecular data.}, }
@article {pmid10677844, year = {2000}, author = {Liaud, MF and Lichtlé, C and Apt, K and Martin, W and Cerff, R}, title = {Compartment-specific isoforms of TPI and GAPDH are imported into diatom mitochondria as a fusion protein: evidence in favor of a mitochondrial origin of the eukaryotic glycolytic pathway.}, journal = {Molecular biology and evolution}, volume = {17}, number = {2}, pages = {213-223}, doi = {10.1093/oxfordjournals.molbev.a026301}, pmid = {10677844}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/enzymology/genetics ; Chloroplasts/enzymology ; Diatoms/*enzymology/genetics ; Evolution, Molecular ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics/metabolism ; *Glycolysis ; Humans ; Isoenzymes/chemistry/genetics/*metabolism ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; Plants/enzymology/genetics ; Plastids/enzymology ; Recombinant Fusion Proteins/metabolism ; Triose-Phosphate Isomerase/chemistry/*genetics/*metabolism ; }, abstract = {Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and triosephosphate isomerase (TPI) are essential to glycolysis, the major route of carbohydrate breakdown in eukaryotes. In animals and other heterotrophic eukaryotes, both enzymes are localized in the cytosol; in photosynthetic eukaryotes, GAPDH and TPI exist as isoenzymes that function in the glycolytic pathway of the cytosol and in the Calvin cycle of chloroplasts. Here, we show that diatoms--photosynthetic protists that acquired their plastids through secondary symbiotic engulfment of a eukaryotic rhodophyte--possess an additional isoenzyme each of both GAPDH and TPI. Surprisingly, these new forms are expressed as an TPI-GAPDH fusion protein which is imported into mitochondria prior to its assembly into a tetrameric bifunctional enzyme complex. Homologs of this translational fusion are shown to be conserved and expressed also in nonphotosynthetic, heterokont-flagellated oomycetes. Phylogenetic analyses show that mitochondrial GAPDH and its N-terminal TPI fusion branch deeply within their respective eukaryotic protein phylogenies, suggesting that diatom mitochondria may have retained an ancestral state of glycolytic compartmentation that existed at the onset of mitochondrial symbiosis. These findings strongly support the view that nuclear genes for enzymes of glycolysis in eukaryotes were acquired from mitochondrial genomes and provide new insights into the evolutionary history (host-symbiont relationships) of diatoms and other heterokont-flagellated protists.}, }
@article {pmid10677517, year = {2000}, author = {Shah, GN and Hewett-Emmett, D and Grubb, JH and Migas, MC and Fleming, RE and Waheed, A and Sly, WS}, title = {Mitochondrial carbonic anhydrase CA VB: differences in tissue distribution and pattern of evolution from those of CA VA suggest distinct physiological roles.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {4}, pages = {1677-1682}, pmid = {10677517}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Animals ; COS Cells ; Carbonic Anhydrases/genetics/*metabolism ; Cloning, Molecular ; Cytosol/enzymology ; Evolution, Molecular ; Humans ; Isoenzymes/genetics/metabolism ; Mice ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; RNA, Messenger/metabolism ; Sequence Homology, Amino Acid ; Transfection ; }, abstract = {A cDNA for a second mouse mitochondrial carbonic anhydrase (CA) called CA VB was identified by homology to the previously characterized murine CA V, now called CA VA. The full-length cDNA encodes a 317-aa precursor that contains a 33-aa classical mitochondrial leader sequence. Comparison of products expressed from cDNAs for murine CA VB and CA VA in COS cells revealed that both expressed active CAs that localized in mitochondria, and showed comparable activities in crude extracts and in mitochondria isolated from transfected COS cells. Northern blot analyses of total RNAs from mouse tissues and Western blot analyses of mouse tissue homogenates showed differences in tissue-specific expression between CA VB and CA VA. CA VB was readily detected in most tissues, while CA VA expression was limited to liver, skeletal muscle, and kidney. The human orthologue of murine CA VB was recently reported also. Comparison of the CA domain sequence of human CA VB with that reported here shows that the CA domains of CA VB are much more highly conserved between mouse and human (95% identity) than the CA domains of mouse and human CA VAs (78% identity). Analysis of phylogenetic relationships between these and other available human and mouse CA isozyme sequences revealed that mammalian CA VB evolved much more slowly than CA VA, accepting amino acid substitutions at least 4.5 times more slowly since each evolved from its respective human-mouse ancestral gene around 90 million years ago. Both the differences in tissue distribution and the much greater evolutionary constraints on CA VB sequences suggest that CA VB and CA VA have evolved to assume different physiological roles.}, }
@article {pmid10677478, year = {2000}, author = {Huang, Q and Deveraux, QL and Maeda, S and Salvesen, GS and Stennicke, HR and Hammock, BD and Reed, JC}, title = {Evolutionary conservation of apoptosis mechanisms: lepidopteran and baculoviral inhibitor of apoptosis proteins are inhibitors of mammalian caspase-9.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {97}, number = {4}, pages = {1427-1432}, pmid = {10677478}, issn = {0027-8424}, support = {F32 ES005707/ES/NIEHS NIH HHS/United States ; ES02710/ES/NIEHS NIH HHS/United States ; R01 ES002710/ES/NIEHS NIH HHS/United States ; P30 ES005707/ES/NIEHS NIH HHS/United States ; P30 CA030199/CA/NCI NIH HHS/United States ; P42 ES004699/ES/NIEHS NIH HHS/United States ; R01 AG015402/AG/NIA NIH HHS/United States ; ES04699/ES/NIEHS NIH HHS/United States ; AG15402/AG/NIA NIH HHS/United States ; R37 ES002710/ES/NIEHS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Apoptosis/*drug effects/genetics ; Bacterial Proteins/chemistry/*genetics ; Baculoviridae/chemistry ; Caspase 9 ; *Caspase Inhibitors ; Cell Line ; Cells, Cultured ; Cloning, Molecular ; *Drosophila Proteins ; Enzyme Inhibitors/*chemistry ; Evolution, Molecular ; Humans ; Inhibitor of Apoptosis Proteins ; Insect Proteins/*chemistry ; Molecular Sequence Data ; Neuropeptides/chemistry ; Peptide Fragments/pharmacology ; *Proteins ; Sequence Alignment ; Spodoptera/*chemistry ; Viral Proteins/chemistry/pharmacology ; }, abstract = {We cloned a new inhibitor of apoptosis protein (IAP) homolog, SfIAP, from Spodoptera frugiperda Sf-21 cells, a host of insect baculoviruses. SfIAP contains two baculovirus IAP repeat domains followed by a RING domain. SfIAP has striking amino acid sequence similarity with baculoviral IAPs, CpIAP and OpIAP, suggesting that baculoviral IAPs may be host-derived genes. SfIAP and baculoviral CpIAP inhibit Bax but not Fas-induced apoptosis in human cells. Their apoptosis-suppressing activity in mammalian cells requires both baculovirus IAP repeat and RING domains. Further biochemical data suggest that SfIAP and CpIAP are specific inhibitors of mammalian caspase-9, the pinnacle caspase in the mitochondria/cytochrome c pathway for apoptosis, but are not inhibitors of downstream caspase-3 and caspase-7. Thus the mechanisms by which insect and baculoviral IAPs suppress apoptosis may involve inhibition of an insect caspase-9 homologue. Peptides representing the IAP-binding domain of the Drosophila cell death protein Grim abrogated human caspase suppression by SfIAP and CpIAP, implying evolutionary conservation of the functions of IAPs and their inhibitors.}, }
@article {pmid10690412, year = {1999}, author = {Lang, BF and Gray, MW and Burger, G}, title = {Mitochondrial genome evolution and the origin of eukaryotes.}, journal = {Annual review of genetics}, volume = {33}, number = {}, pages = {351-397}, doi = {10.1146/annurev.genet.33.1.351}, pmid = {10690412}, issn = {0066-4197}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Fungi/genetics ; Mitochondria/*genetics ; Phylogeny ; }, abstract = {Recent results from ancestral (minimally derived) protists testify to the tremendous diversity of the mitochondrial genome in various eukaryotic lineages, but also reinforce the view that mitochondria, descendants of an endosymbiotic alpha-Proteobacterium, arose only once in evolution. The serial endosymbiosis theory, currently the most popular hypothesis to explain the origin of mitochondria, postulates the capture of an alpha-proteobacterial endosymbiont by a nucleus-containing eukaryotic host resembling extant amitochondriate protists. New sequence data have challenged this scenario, instead raising the possibility that the origin of the mitochondrion was coincident with, and contributed substantially to, the origin of the nuclear genome of the eukaryotic cell. Defining more precisely the alpha-proteobacterial ancestry of the mitochondrial genome, and the contribution of the endosymbiotic event to the nuclear genome, will be essential for a full understanding of the origin and evolution of the eukaryotic cell as a whole.}, }
@article {pmid10678836, year = {2000}, author = {Beech, PL and Nheu, T and Schultz, T and Herbert, S and Lithgow, T and Gilson, PR and McFadden, GI}, title = {Mitochondrial FtsZ in a chromophyte alga.}, journal = {Science (New York, N.Y.)}, volume = {287}, number = {5456}, pages = {1276-1279}, doi = {10.1126/science.287.5456.1276}, pmid = {10678836}, issn = {0036-8075}, mesh = {Alphaproteobacteria/chemistry ; Arabidopsis Proteins ; Biological Evolution ; Chloroplasts/chemistry/physiology ; Eukaryota/*chemistry/genetics/physiology/ultrastructure ; Fungal Proteins/analysis ; GTP Phosphohydrolases/analysis ; GTP-Binding Proteins/*chemistry/genetics/*metabolism ; Gene Library ; Microscopy, Confocal ; Microscopy, Fluorescence ; Mitochondria/*chemistry/metabolism/physiology/ultrastructure ; Mitochondrial Proteins ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*chemistry/genetics/*metabolism ; Recombinant Fusion Proteins/analysis ; Saccharomyces cerevisiae/chemistry ; *Saccharomyces cerevisiae Proteins ; }, abstract = {A homolog of the bacterial cell division gene ftsZ was isolated from the alga Mallomonas splendens. The nuclear-encoded protein (MsFtsZ-mt) was closely related to FtsZs of the alpha-proteobacteria, possessed a mitochondrial targeting signal, and localized in a pattern consistent with a role in mitochondrial division. Although FtsZs are known to act in the division of chloroplasts, MsFtsZ-mt appears to be a mitochondrial FtsZ and may represent a mitochondrial division protein.}, }
@article {pmid10684970, year = {2000}, author = {Bullard, JM and Cai, YC and Spremulli, LL}, title = {Expression and characterization of the human mitochondrial leucyl-tRNA synthetase.}, journal = {Biochimica et biophysica acta}, volume = {1490}, number = {3}, pages = {245-258}, doi = {10.1016/s0167-4781(99)00240-7}, pmid = {10684970}, issn = {0006-3002}, support = {GM19117/GM/NIGMS NIH HHS/United States ; GM32734/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/chemistry ; Amino Acid Sequence ; Biological Evolution ; Chromatography, Gel ; Cloning, Molecular ; DNA, Complementary/chemistry/genetics ; Enzyme Activation ; Escherichia coli/genetics/metabolism ; Humans ; Kinetics ; Leucine-tRNA Ligase/chemistry/classification/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Molecular Weight ; RNA, Messenger/chemistry/genetics ; RNA, Transfer/chemistry ; Sequence Alignment ; Sequence Homology ; Species Specificity ; }, abstract = {A cDNA clone encoding the human mitochondrial leucyl-tRNA synthetase (mtLeuRS) has been identified from the EST databases. Analysis of the protein encoded by this cDNA indicates that the protein is 903 amino acids in length and contains a mitochondrial signal sequence that is predicted to encompass the first 21 amino acids. Sequence analysis shows that this protein contains the characteristic motifs of class I aminoacyl-tRNA synthetases and regions of high homology to other mitochondrial and bacterial LeuRS proteins. The mature form of this protein has been cloned and expressed in Escherichia coli. Gel filtration indicates that human mtLeuRS is active in a monomeric state, with an apparent molecular mass of 101 kDa. The human mtLeuRS is capable of aminoacylating E. coli tRNA(Leu). Its activity is inhibited at high levels of either monovalent or divalent cations. K(M) and k(cat) values for ATP:PP(i) exchange and for the aminoacylation reaction have been determined.}, }
@article {pmid10684923, year = {2000}, author = {Saguez, C and Lecellier, G and Koll, F}, title = {Intronic GIY-YIG endonuclease gene in the mitochondrial genome of Podospora curvicolla: evidence for mobility.}, journal = {Nucleic acids research}, volume = {28}, number = {6}, pages = {1299-1306}, pmid = {10684923}, issn = {1362-4962}, mesh = {Alleles ; Amino Acid Motifs ; Amino Acid Sequence ; Base Sequence ; Cell Fusion ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/*genetics ; Endonucleases/chemistry/*genetics/metabolism ; Evolution, Molecular ; Fungal Proteins/chemistry/genetics/metabolism ; Genes, Fungal/genetics ; Interspersed Repetitive Sequences/*genetics ; Introns/*genetics ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Mutagenesis, Insertional/genetics ; Open Reading Frames/genetics ; Protein Biosynthesis/genetics ; Recombinant Fusion Proteins/chemistry/genetics/metabolism ; Recombination, Genetic/genetics ; Sordariales/cytology/enzymology/*genetics/growth &amp; development ; }, abstract = {Endonuclease genes encoded in invasive introns are themselves supposed to be mobile elements which, during evolution, have colonized pre-existing introns converting them into invasive elements. This hypothesis is supported by numerous data concerning the LAGLI-DADG subclass of intronic endonucleases. Less is known about the GIY-YIG ORFs which constitute another family of endonucleases. In this paper we describe the presence of one optional GIY-YIG ORF in the second intron of the mitochondrial cytochrome b gene in the fungus Podospora curvicolla. We show that this GIY-YIG ORF is efficiently transferred from an ORF-containing intron to an ORF-less allele. We also show that the products of both the GIY-YIG ORF and the non-canonical LAGLI-DADG-GIY-YIG ORF, which is generated by its integration, have endonuclease activities which recognize and cut the insertion site of the optional sequence. This constitutes the first direct evidence for potential mobility of an intronic GIY-YIG endonuclease. We discuss the role that such a mobile sequence could have played during evolution.}, }
@article {pmid10684348, year = {2000}, author = {Peek, AS and Gaut, BS and Feldman, RA and Barry, JP and Kochevar, RE and Lutz, RA and Vrijenhoek, RC}, title = {Neutral and nonneutral mitochondrial genetic variation in deep-sea clams from the family vesicomyidae.}, journal = {Journal of molecular evolution}, volume = {50}, number = {2}, pages = {141-153}, doi = {10.1007/s002399910016}, pmid = {10684348}, issn = {0022-2844}, support = {TW00735-01/TW/FIC NIH HHS/United States ; }, mesh = {Animals ; Bivalvia/*genetics ; Costa Rica ; DNA, Ribosomal/genetics ; Electron Transport Complex IV/genetics ; *Genetic Variation ; Mexico ; Mitochondria/*genetics ; *Phylogeny ; }, abstract = {Nucleotide sequences at two mitochondrial genes from 57 individuals representing eight species of deep-sea clams (Vesicomyidae) were examined for variation consistent with the neutral model of molecular evolution. One gene, cytochrome oxidase subunit I (COI), deviated from the expectations of neutrality by containing an excess of intraspecific nonsynonymous polymorphism. Additionally, one species, Calyptogena kilmeri, showed a significant excess of rare polymorphism specifically at the COI locus. In contrast, a second mitochondrial gene, the large-subunit 16S ribosomal RNA gene (16S), showed little deviation from neutrality either between or within species. Together, COI and 16S show no deviation from neutral expectations by the HKA test, produce congruent phylogenetic relationships between species, and show correlated numbers of fixed differences between species and polymorphism within species. These patterns of both neutral and nonneutral evolution within the mitochondrial genome are most consistent with a model where intraspecific nonsynonymous polymorphism at COI is near neutrality. In addition to examining the forces of molecular evolution, we extend hypotheses about interspecific relationships within this family for geographical locations previously unexamined by molecular methods including habitats near the Middle Atlantic, the Aleutian Trench, and Costa Rica.}, }
@article {pmid10676949, year = {2000}, author = {Perez, GI and Trbovich, AM and Gosden, RG and Tilly, JL}, title = {Mitochondria and the death of oocytes.}, journal = {Nature}, volume = {403}, number = {6769}, pages = {500-501}, doi = {10.1038/35000651}, pmid = {10676949}, issn = {0028-0836}, mesh = {Animals ; Apoptosis/*physiology ; Biological Evolution ; Cells, Cultured ; DNA, Mitochondrial ; Female ; Follicular Atresia ; Humans ; Mice ; Microinjections ; Mitochondria/*physiology ; Oocytes/*physiology ; Polymerase Chain Reaction ; Sequence Deletion ; }, }
@article {pmid10672158, year = {2000}, author = {Desplanque, B and Viard, F and Bernard, J and Forcioli, D and Saumitou-Laprade, P and Cuguen, J and Van Dijk, H}, title = {The linkage disequilibrium between chloroplast DNA and mitochondrial DNA haplotypes in Beta vulgaris ssp. maritima (L.): the usefulness of both genomes for population genetic studies.}, journal = {Molecular ecology}, volume = {9}, number = {2}, pages = {141-154}, doi = {10.1046/j.1365-294x.2000.00843.x}, pmid = {10672158}, issn = {0962-1083}, mesh = {Chenopodiaceae/*genetics ; Chloroplasts/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; France ; *Genetic Variation ; *Genetics, Population ; Genome, Plant ; Geography ; Haplotypes ; *Linkage Disequilibrium ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Spain ; }, abstract = {The structure and evolution of the plant mitochondrial genome may allow recurrent appearance of the same mitochondrial variants in different populations. Whether the same mitochondrial variant is distributed by migration or appears recurrently by mutation (creating homoplasy) in different populations is an important question with regard to the use of these markers for population genetic analyses. The genetic association observed between chloroplasts and mitochondria (i.e. two maternally inherited cytoplasmic genomes) may indicate whether or not homoplasy occurs in the mitochondrial genome. Four-hundred and fourteen individuals sampled in wild populations of beets from France and Spain were screened for their mitochondrial and chloroplast polymorphisms. Mitochondrial DNA (mtDNA) polymorphism was investigated with restriction fragment length polymorphism (RFLP) and chloroplast DNA (cpDNA) polymorphism was investigated with polymerase chain reaction PCR-RFLP, using universal primers for the amplification. Twenty and 13 variants for mtDNA and cpDNA were observed, respectively. Most exhibited a widespread geographical distribution. As a very strong linkage disequilibrium was estimated between mtDNA and cpDNA haplotypes, a high rate of recurrent mutation was excluded for the mitochondrial genome of beets. Identical mitochondrial variants found in populations of different regions probably occurred as a result of migration. We concluded from this study that mtDNA is a tool as valuable as cpDNA when a maternal marker is needed for population genetics analyses in beet on a large regional scale.}, }
@article {pmid10667973, year = {2000}, author = {Suarez, RK and Staples, JF and Lighton, JR and Mathieu-Costello, O}, title = {Mitochondrial function in flying honeybees (Apis mellifera): respiratory chain enzymes and electron flow from complex III to oxygen.}, journal = {The Journal of experimental biology}, volume = {203}, number = {Pt 5}, pages = {905-911}, doi = {10.1242/jeb.203.5.905}, pmid = {10667973}, issn = {0022-0949}, support = {5PO1 HL17731/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Bees/metabolism/*ultrastructure ; *Electron Transport ; Electron Transport Complex III/*metabolism ; Electron Transport Complex IV/metabolism ; Enzymes/*metabolism ; Microscopy, Electron ; Mitochondria/*physiology ; Muscles/ultrastructure ; *Oxygen Consumption ; }, abstract = {The biochemical bases for the high mass-specific metabolic rates of flying insects remain poorly understood. To gain insights into mitochondrial function during flight, metabolic rates of individual flying honeybees were measured using respirometry, and their thoracic muscles were fixed for electron microscopy. Mitochondrial volume densities and cristae surface densities, combined with biochemical data concerning cytochrome content per unit mass, were used to estimate respiratory chain enzyme densities per unit cristae surface area. Despite the high content of respiratory enzymes per unit muscle mass, these are accommodated by abundant mitochondria and high cristae surface densities such that enzyme densities per unit cristae surface area are similar to those found in mammalian muscle and liver. These results support the idea that a unit area of mitochondrial inner membrane constitutes an invariant structural unit. Rates of O(2) consumption per unit cristae surface area are much higher than those estimated in mammals as a consequence of higher enzyme turnover rates (electron transfer rates per enzyme molecule) during flight. Cytochrome c oxidase, in particular, operates close to its maximum catalytic capacity (k(cat)). Thus, high flux rates are achieved via (i) high respiratory enzyme content per unit muscle mass and (ii) the operation of these enzymes at high fractional velocities.}, }
@article {pmid10666720, year = {2000}, author = {van Hoek, AH and Akhmanova, AS and Huynen, MA and Hackstein, JH}, title = {A mitochondrial ancestry of the hydrogenosomes of Nyctotherus ovalis.}, journal = {Molecular biology and evolution}, volume = {17}, number = {1}, pages = {202-206}, doi = {10.1093/oxfordjournals.molbev.a026234}, pmid = {10666720}, issn = {0737-4038}, mesh = {Base Sequence ; Cytoplasmic Granules/*genetics/ultrastructure ; *DNA, Mitochondrial ; *Evolution, Molecular ; Fungi/*genetics/ultrastructure ; Mitochondria/*genetics/ultrastructure ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA ; }, }
@article {pmid10664124, year = {2000}, author = {Nakazono, M and Imamura, T and Tsutsumi, N and Sasaki, T and Hirai, A}, title = {Characterization of two cDNA clones encoding isozymes of the F(1)F(0)-ATPase inhibitor protein of rice mitochondria.}, journal = {Planta}, volume = {210}, number = {2}, pages = {188-194}, doi = {10.1007/pl00008125}, pmid = {10664124}, issn = {0032-0935}, mesh = {Amino Acid Sequence ; Base Sequence ; Blotting, Northern ; DNA, Complementary/chemistry/*genetics ; Gene Expression Regulation, Plant ; Green Fluorescent Proteins ; Isoenzymes/antagonists &amp; inhibitors ; Luminescent Proteins/genetics ; Microscopy, Confocal ; Mitochondria/*genetics ; Molecular Sequence Data ; Oryza/*genetics ; Phylogeny ; Protein Isoforms/genetics ; Proteins/*genetics ; Proton-Translocating ATPases/antagonists &amp; inhibitors ; RNA, Plant/genetics/metabolism ; Recombinant Fusion Proteins/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Tissue Distribution ; ATPase Inhibitory Protein ; }, abstract = {Two cDNA clones encoding F(1)F(0)-ATPase inhibitor proteins, which are loosely associated with the F(1) part of the mitochondrial F(1)F(0)-ATPase, were characterized from rice (Oryza sativa L. cv. Nipponbare). A Northern hybridization showed that the two genes (designated as IF(1)-1 and IF(1)-2) are transcribed in all the organs examined. However, the steady-state mRNA levels varied among organs. A comparison of the deduced amino acid sequences of the two IF(1) genes and the amino acid sequence of the mature IF(1) protein from potato revealed that IF(1)-1 and IF(1)-2 have N-terminal extensions with features that are characteristic of a mitochondrial targeting signal. To determine the subcellular localization of the gene products, the IF(1)-1 or IF(1)-2 proteins were fused in frame to the green fluorescent protein (GFP) or the fused GFP-beta-glucuronidase, and expressed transiently in onion or dayflower epidermal cells. Localized fluorescence was detected in mitochondria, confirming that the two IF(1) proteins are targeted to mitochondria.}, }
@article {pmid10664070, year = {2000}, author = {Cancio, I and Völkl, A and Beier, K and Fahimi, HD and Cajaraville, MP}, title = {Peroxisomes in molluscs, characterization by subcellular fractionation combined with western blotting, immunohistochemistry, and immunocytochemistry.}, journal = {Histochemistry and cell biology}, volume = {113}, number = {1}, pages = {51-60}, doi = {10.1007/s004180050007}, pmid = {10664070}, issn = {0948-6143}, mesh = {Acetyl-CoA C-Acyltransferase/analysis ; Amino Acid Oxidoreductases/analysis ; Animals ; Bivalvia/*enzymology/ultrastructure ; Blotting, Western ; Catalase/analysis/ultrastructure ; Cell Fractionation ; Digestive System/enzymology/ultrastructure ; Guinea Pigs ; Immunohistochemistry ; Microscopy, Immunoelectron ; Multienzyme Complexes/analysis/ultrastructure ; Oxidoreductases/analysis ; Peroxisomes/*enzymology/ultrastructure ; Rabbits ; }, abstract = {Peroxisomes of the digestive glands of mussels, Mytilus galloprovincialis Lmk, were investigated by immunoblotting and immunohistochemistry using rabbit antibodies against several mammalian hepatic peroxisomal proteins. Western blot analysis of main subcellular fractions revealed immunoreactive polypeptides with molecular weights comparable to those of the corresponding mammalian hepatic proteins. They could be localized to the peroxisomal matrix in the case of catalase, multifunctional enzyme (PH), and palmitoyl-CoA oxidase (AOX), and to the peroxisomal membrane in respect to PMP 70. The purification of peroxisomes by metrizamide density gradient centrifugation revealed the existence of two subpopulations with densities of 1.16 and 1.20 g cm(-3) exhibiting different protein compositions. In paraffin sections, positive immunolabeling for catalase was distributed along the apical cytoplasm of the epithelia of digestive ducts and stomach and throughout the cytoplasm of digestive tubule cells. The peroxisomal beta-oxidation enzymes, AOX and PH, also appeared predominantly in the ducts and the stomach epithelia with a weaker immunolabeling in the tubules. At the electron microscopic level a clear labeling with gold particles was observed in the peroxisomal matrix with the anti-guinea pig catalase antibody. In addition to peroxisomes, the anti-PH antibody also labeled the mitochondria. The similarity in the protein composition of molluscan and mammalian peroxisomes as revealed by the present study indicates that those proteins have been well conserved in evolution suggesting that functionally peroxisomes in molluscs could also be involved in the metabolism of lipids and in detoxification of xenobiotics. Thus, the antibodies tested could provide useful tools for detection of peroxisomal induction in molluscan biomonitoring programs for the assessment of aquatic environmental pollution.}, }
@article {pmid10661858, year = {1999}, author = {Dessanti, A and Massarelli, G and Bosincu, L and Canu, L and Noya, G and Dettori, G}, title = {Aggressive congenital fibromatosis of the small intestine in the newborn. Report of a case and review of the literature.}, journal = {European journal of pediatric surgery : official journal of Austrian Association of Pediatric Surgery ... [et al] = Zeitschrift fur Kinderchirurgie}, volume = {9}, number = {6}, pages = {422-425}, doi = {10.1055/s-2008-1072298}, pmid = {10661858}, issn = {0939-7248}, mesh = {Female ; Fibromatosis, Aggressive/congenital/metabolism/*pathology/surgery ; Humans ; Immunohistochemistry ; Infant, Newborn ; Intestinal Neoplasms/congenital/metabolism/*pathology/surgery ; Neoplasm Invasiveness ; }, abstract = {A case of so-called congenital fibro(leio)myosarcoma of the small intestine in a 18-day-old female baby, treated only with surgical resection, was studied by immunohistochemistry and electron microscopy in order to investigate the proliferating cell type. The tumour cells showed positivity only for vimentin and CD 34 and were negative for smooth muscle actin, desmin, alpha-sarcomeric actin, factor VIIIR: Ag and S-100 protein. Ultrastructural findings showed oval nuclei with prominent nucleoli, rare intracytoplasmic mitochondria and well developed rough endoplasmic reticulum. According to histoimmunological and electron microscopy findings the proliferating cells were likely to be of fibroblastic origin. A 7-year follow-up showed a favourable clinical evolution thus confirming that surgical resection can be a sufficient therapeutic approach. The morphological findings and clinical behaviour suggest that more appropriate terminology for this tumour would be "aggressive congenital fibromatosis" which better highlights its local progressive invasion without metastases.}, }
@article {pmid10658200, year = {2000}, author = {Liquori, GE and Ferri, D and Scillitani, G}, title = {Fine structure of the oxynticopeptic cells in the gastric glands of the ruin lizard, Podarcis sicula campestris De Betta, 1857.}, journal = {Journal of morphology}, volume = {243}, number = {2}, pages = {167-171}, doi = {10.1002/(SICI)1097-4687(200002)243:2&lt;167::AID-JMOR5&gt;3.0.CO;2-G}, pmid = {10658200}, issn = {0362-2525}, mesh = {Animals ; Female ; Gastric Fundus/cytology/ultrastructure ; Gastric Mucosa/*cytology/metabolism/ultrastructure ; Lizards/*anatomy &amp; histology ; Male ; Microscopy, Electron ; Parietal Cells, Gastric/*ultrastructure ; }, abstract = {The results of an ultrastructural investigation of the gastric glands of the ruin lizard are reported. In this reptile the stomach can be divided into a larger fundus and a smaller pars pilorica. Fundic glands are characterized by three main kinds of cells: mucous, endocrine, and oxynticopeptic; the latter were not observed in the pyloric glands. The morphological features of the oxynticopeptic cells change from the proximal to the distal region of the fundic mucosa. In the proximal region, numerous electron-dense secretory granules, a well-developed granular endoplasmic reticulum, an evident Golgi complex, and a reduced system of smooth-surfaced vesicles and tubules in the apical cytoplasm characterize these cells. In the distal fundic region, oxynticopeptic cells possessed numerous mitochondria and a well-developed smooth-surfaced endoplasmic reticulum, but secretory granules were rare. These data suggest the existence of a gradient in the production of proteolytic enzymes, and perhaps also of hydrochloric acid, along the oral-aboral axis of the stomach. The results are discussed with regard to the evolution of the gastric glands and of the digestive mechanism in vertebrates.}, }
@article {pmid10656989, year = {2000}, author = {Strasser, A and Vaux, DL}, title = {Death in the snow: report on Keystone Conference on 'Apoptosis and Programmed Cell Death' at Breckenridge, CO, April 6-11th 1999.}, journal = {Biochimica et biophysica acta}, volume = {1470}, number = {1}, pages = {R1-R11}, doi = {10.1016/s0304-419x(99)00029-3}, pmid = {10656989}, issn = {0006-3002}, mesh = {Animals ; *Apoptosis ; Apoptosis Inducing Factor ; Apoptosis Regulatory Proteins ; BH3 Interacting Domain Death Agonist Protein ; Bcl-2-Like Protein 11 ; Biological Evolution ; Caenorhabditis elegans ; *Caenorhabditis elegans Proteins ; Carrier Proteins/metabolism ; Caspase Inhibitors ; Caspases/*metabolism ; *Cell Death ; Cell Line ; Drosophila ; Enzyme Activation ; Enzyme Precursors/metabolism ; Flavoproteins/metabolism ; Genes, bcl-2 ; Humans ; JNK Mitogen-Activated Protein Kinases ; Membrane Proteins/metabolism ; Mitochondria/*metabolism ; Mitogen-Activated Protein Kinases/metabolism ; Mutation ; Nuclear Envelope/metabolism ; Proteins/metabolism ; *Proto-Oncogene Proteins ; Proto-Oncogene Proteins c-bcl-2/metabolism ; Repressor Proteins/metabolism ; bcl-Associated Death Protein ; }, }
@article {pmid10654089, year = {1999}, author = {Ogihara, Y and Kurihara, Y and Futami, K and Tsuji, K and Murai, K}, title = {Photoperiod-sensitive cytoplasmic male sterility in wheat: nuclear-mitochondrial incompatibility results in differential processing of the mitochondrial orf25 gene.}, journal = {Current genetics}, volume = {36}, number = {6}, pages = {354-362}, doi = {10.1007/s002940050510}, pmid = {10654089}, issn = {0172-8083}, mesh = {Amino Acid Sequence ; Base Sequence ; Cell Nucleus/genetics ; Cytoplasm/*genetics ; Evolution, Molecular ; Gene Expression Regulation, Plant ; Mitochondria/genetics ; *Mitochondrial Proteins ; Molecular Sequence Data ; *Photoperiod ; Plant Proteins/*genetics/metabolism ; RNA Editing ; RNA Processing, Post-Transcriptional ; Reproduction ; Ribonucleases/genetics/metabolism ; Sequence Analysis ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; Triticum/*physiology ; }, abstract = {An alloplasmic wheat line with the cytoplasm of Aegilops crassa expresses photoperiod-sensitive cytoplasmic male sterility (PCMS). Southern- and Northern-hybridization analyses showed that this line contains alterations in both the gene structure and transcription patterns of the mitochondrial gene orf25. In this study, the nucleotide sequence around the orf25 gene of Ae. crassa (CR-orf25) and common wheat (AE-orf25) was determined, and we found that the upstream region of CR-orf25 had been replaced by that of rps7 of common wheat (AE-rps7) through recombination. A novel open reading frame (orf48) is present upstream of CR-orf25. In these three genes, transcription was initiated from the consensus promoter motif of plant mitochondrial genes located in the upstream regions. Processing enzymes in Ae. crassa and common wheat cleave the respective precursor mRNAs, namely CR-orf25 and AE-rps7, at sites similar to that of the premature mitochondrial 26S rRNA. In contrast, the precursor mRNA is not effectively processed at the target sequence of CR-orf25 in the alloplasmic wheat line. Because major transcripts of the euplasmic CR-orf25 and AE-rps7 genes would result in a truncated orf48 product, one possibility is that the orf48 protein might disturb mitochondrial function at a specific stage and hence affect the expression of the PCMS trait.}, }
@article {pmid10646602, year = {2000}, author = {Teeling, EC and Scally, M and Kao, DJ and Romagnoli, ML and Springer, MS and Stanhope, MJ}, title = {Molecular evidence regarding the origin of echolocation and flight in bats.}, journal = {Nature}, volume = {403}, number = {6766}, pages = {188-192}, doi = {10.1038/35003188}, pmid = {10646602}, issn = {0028-0836}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/genetics ; Chiroptera/classification/genetics/*physiology ; Echolocation/*physiology ; Flight, Animal/*physiology ; Humans ; Mitochondria/genetics ; Phylogeny ; }, abstract = {Bats (order Chiroptera) are one of the few orders of mammals that echolocate and the only group with the capacity for powered flight. The order is subdivided into Microchiroptera and Megachiroptera, with an array of characteristics defining each group, including complex laryngeal echolocation systems in microbats and enhanced visual acuity in megabats. The respective monophylies of the two suborders have been tacitly assumed, although microbat monophyly is uncorroborated by molecular data. Here we present a phylogenetic analysis of bat relationships using DNA sequence data from four nuclear genes and three mitochondrial genes (total of 8,230 base pairs), indicating that microbat families in the superfamily Rhinolophoidea are more closely related to megabats than they are to other microbats. This implies that echolocation systems either evolved independently in rhinolophoids and other microbats or were lost in the evolution of megabats. Our data also reject flying lemur (order Dermoptera) as the bat sister group, indicating that presumed shared derived characters for flying lemurs and bats are convergent features that evolved in association with gliding and flight, respectively.}, }
@article {pmid10645945, year = {2000}, author = {Leipe, DD and Aravind, L and Grishin, NV and Koonin, EV}, title = {The bacterial replicative helicase DnaB evolved from a RecA duplication.}, journal = {Genome research}, volume = {10}, number = {1}, pages = {5-16}, pmid = {10645945}, issn = {1088-9051}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/metabolism ; Computational Biology ; Conserved Sequence ; DNA Helicases/*genetics/metabolism ; DNA Replication/*genetics ; DNA, Bacterial/*metabolism ; DnaB Helicases ; Evolution, Molecular ; *Gene Duplication ; Humans ; Molecular Sequence Data ; Protein Folding ; Rec A Recombinases/*genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {The RecA/Rad51/DCM1 family of ATP-dependent recombinases plays a crucial role in genetic recombination and double-stranded DNA break repair in Archaea, Bacteria, and Eukaryota. DnaB is the replication fork helicase in all Bacteria. We show here that DnaB shares significant sequence similarity with RecA and Rad51/DMC1 and two other related families of ATPases, Sms and KaiC. The conserved region spans the entire ATP- and DNA-binding domain that consists of about 250 amino acid residues and includes 7 distinct motifs. Comparison with the three-dimensional structure of Escherichia coli RecA and phage T7 DnaB (gp4) reveals that the area of sequence conservation includes the central parallel beta-sheet and most of the connecting helices and loops as well as a smaller domain that consists of a amino-terminal helix and a carboxy-terminal beta-meander. Additionally, we show that animals, plants, and the malarial Plasmodium but not Saccharomyces cerevisiae encode a previously undetected DnaB homolog that might function in the mitochondria. The DnaB homolog from Arabidopsis also contains a DnaG-primase domain and the DnaB homolog from the nematode seems to contain an inactivated version of the primase. This domain organization is reminiscent of bacteriophage primases-helicases and suggests that DnaB might have been horizontally introduced into the nuclear eukaryotic genome via a phage vector. We hypothesize that DnaB originated from a duplication of a RecA-like ancestor after the divergence of the bacteria from Archaea and eukaryotes, which indicates that the replication fork helicases in Bacteria and Archaea/Eukaryota have evolved independently.}, }
@article {pmid10644738, year = {2000}, author = {Saas, J and Ziegelbauer, K and von Haeseler, A and Fast, B and Boshart, M}, title = {A developmentally regulated aconitase related to iron-regulatory protein-1 is localized in the cytoplasm and in the mitochondrion of Trypanosoma brucei.}, journal = {The Journal of biological chemistry}, volume = {275}, number = {4}, pages = {2745-2755}, doi = {10.1074/jbc.275.4.2745}, pmid = {10644738}, issn = {0021-9258}, mesh = {Aconitate Hydratase/*genetics/metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; Cytoplasm/*enzymology ; DNA, Complementary ; *Gene Expression Regulation, Enzymologic ; Iron Regulatory Protein 1 ; Iron-Regulatory Proteins ; Iron-Sulfur Proteins/*genetics ; Kinetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; RNA-Binding Proteins/*genetics ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Trypanosoma brucei brucei/*enzymology ; }, abstract = {Mitochondrial energy metabolism and Krebs cycle activities are developmentally regulated in the life cycle of the protozoan parasite Trypanosoma brucei. Here we report cloning of a T. brucei aconitase gene that is closely related to mammalian iron-regulatory protein 1 (IRP-1) and plant aconitases. Kinetic analysis of purified recombinant TbACO expressed in Escherichia coli resulted in a K(m) (isocitrate) of 3 +/- 0.4 mM, similar to aconitases of other organisms. This was unexpected since an arginine conserved in the aconitase protein family and crucial for substrate positioning in the catalytic center and for activity of pig mitochondrial aconitase (Zheng, L., Kennedy, M. C., Beinert, H., and Zalkin, H. (1992) J. Biol. Chem. 267, 7895-7903) is substituted by leucine in the TbACO sequence. Expression of the 98-kDa TbACO was shown to be lowest in the slender bloodstream stage of the parasite, 8-fold elevated in the stumpy stage, and increased a further 4-fold in the procyclic stage. The differential expression of TbACO protein contrasted with only minor changes in TbACO mRNA, indicating translational or post-translational mechanisms of regulation. Whereas animal cells express two distinct compartmentalized aconitases, mitochondrial aconitase and cytoplasmic aconitase/IRP-1, TbACO accounts for total aconitase activity in trypanosomes. By cell fractionation and immunofluorescence microscopy, we show that native as well as a transfected epitope-tagged TbACO localizes in both the mitochondrion (30%) and in the cytoplasm (70%). Together with phylogenetic reconstructions of the aconitase family, this suggests that animal IRPs have evolved from a multicompartmentalized ancestral aconitase. The possible functions of a cytoplasmic aconitase in trypanosomes are discussed.}, }
@article {pmid10635118, year = {1999}, author = {Watanabe, A and Nakazono, M and Tsutsumi, N and Hirai, A}, title = {AtUCP2: a novel isoform of the mitochondrial uncoupling protein of Arabidopsis thaliana.}, journal = {Plant &amp; cell physiology}, volume = {40}, number = {11}, pages = {1160-1166}, doi = {10.1093/oxfordjournals.pcp.a029501}, pmid = {10635118}, issn = {0032-0781}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; Base Sequence ; Cloning, Molecular ; Cold Temperature ; DNA, Complementary ; Ion Channels ; *Membrane Transport Proteins ; *Mitochondrial Proteins ; Molecular Sequence Data ; Phylogeny ; Protein Isoforms/chemistry/genetics/*metabolism ; Proteins/chemistry/genetics/*metabolism ; Sequence Homology, Amino Acid ; Uncoupling Protein 2 ; }, abstract = {Mitochondrial uncoupling proteins (UCPs) play a central role in adaptive thermogenesis in mammals. The UCPs dissipate the proton gradient formed through respiration without ATP synthesis, and the freed energy is readily converted to heat, helping the animals to maintain their body temperature in cold environments. Recently, it was found that UCPs also function in plant mitochondria. Subsequently, a cDNA clone encoding a UCP in potato was isolated. Whereas the UCP gene constitutes a multigene family in mammals, only a single cDNA sequence has been reported so far for the potato UCP. Moreover, it has been recently suggested that Arabidopsis has only a single nuclear gene for UCP. Here we report the existence of another UCP gene in the Arabidopsis genome, showing for the first time the occurrence of a multigene family for the protein in higher plants. A cDNA analysis of this gene showed that the novel isoform possesses all typical features reported for known UCPs. However, the new gene, unlike the other gene in Arabidopsis and the gene in potato, did not appear to respond to low temperature.}, }
@article {pmid10632780, year = {1999}, author = {Andreeva, L and Heads, R and Green, CJ}, title = {Cyclophilins and their possible role in the stress response.}, journal = {International journal of experimental pathology}, volume = {80}, number = {6}, pages = {305-315}, pmid = {10632780}, issn = {0959-9673}, mesh = {Cell Death/physiology ; Heat-Shock Proteins/physiology ; Heat-Shock Response/*physiology ; Humans ; Mitochondria/metabolism ; Oxidative Stress/*physiology ; Peptidylprolyl Isomerase/*physiology ; }, abstract = {Cyclophilins are proteins which are remarkably conserved through evolution; moreover they have been found in every possible existing organism, which indicates their fundamental importance. Due to their enzymatic properties, multiplicity, cellular localization and role in protein folding they belong to the group of proteins termed molecular chaperones. All the proteins of the cyclophilin family possess enzymatic peptidyl-prolyl isomerase activity (PPI-ase), which is essential to protein folding in vivo. Recently PPI-ase activity was suggested as playing a role in regulation of transcription and differentiation. However, not all cyclophilin functions are explained by PPI-ase activity. For instance, one of the cyclophilins plays a regulatory role in the heat shock response and the mitochondrial cyclophilin (Cyclophilin D) is an integral part of the mitochondrial permeability transition complex, which is regarded as having a crucial role in mechanisms of cell death. In support of a role in the stress response, the expression of certain cyclophilins has recently been shown to be up-regulated under various stressful conditions. Current evidence of functional involvement of cyclophilins in various intracellular pathways is reviewed along with the indications that cyclophilin D (Cyp D) represents a crucial part of the mitochondrial permeability transition pore, which is detrimental in apoptotic and necrotic cell death. This review does not attempt to cover all the existing information related to cyclophilin family of proteins, but focus on the existing evidence of the involvement of these proteins in the intracellular stress response.}, }
@article {pmid10629653, year = {1999}, author = {Rocchi, E and Vigo, J and Viallet, P and Bonnard, I and Banaigs, B and Salmon, JM}, title = {Multiwavelength videomicrofluorometric study of cytotoxic properties of a marine peptide, didemnin B, using adriamycin as reference compound.}, journal = {Anticancer research}, volume = {19}, number = {4C}, pages = {3559-3568}, pmid = {10629653}, issn = {0250-7005}, mesh = {Apoptosis ; Benzimidazoles/metabolism ; Cell Cycle/drug effects ; Cell Nucleus/drug effects ; *Depsipeptides ; Dose-Response Relationship, Drug ; Doxorubicin/*chemistry/pharmacokinetics/pharmacology ; Fluorescent Dyes/metabolism ; Fluorometry ; Humans ; Inhibitory Concentration 50 ; Microscopy, Video ; Mitochondria/drug effects ; Oxazines/metabolism ; Peptides, Cyclic/*chemistry/*pharmacokinetics/pharmacology ; Rhodamine 123/metabolism ; Time Factors ; Tumor Cells, Cultured ; }, abstract = {Didemnin B (DB), a marine natural product, has very encouraging biological activity in vitro (Antineoplastic, immunosuppressive, antiviral). To learn more about its intracellular effects and targets, videomicrofluorometry on single living cells and a protocol of multiple labeling: Hoechst 342 for nuclear DNA, Rhodamine 123 for mitochondria and Nile Red for plasma membrane, have been used. DB behaves differently from Adriamycin, inducing at its IC50 dose of (20 nM) an accumulation of the CEM-WT lymphoblasts in the S phase of the cell cycle while we observed a 50% decrease of the mitochondrial labeling by R123, showing a decrease of the mitochondrial energetic state. Cytostatic dose of DB (250 nM) confirms these observations. However the treatment with a dose reported as apoptotic (1000 nM) induces a much faster effect (corresponding to that of 72 hours at the IC50 dose), 24 hours incubation induced a drastic decrease of nuclear DNA content as well as of the mitochondria energetic state. The evolution of NAD(P)H cellular content exhibited an increase that seems to indicate that the decrease of mitochondrial energetic state was dependent on inhibition of the mitochondrial activity due to an effect of DB at the mitochondrial level, either direct or mediated. Furthermore, the decrease of mitochondrial labeling appears as a very early event in the mechanisms leading to apoptosis.}, }
@article {pmid11125115, year = {2001}, author = {Szymanski, M and Deniziak, MA and Barciszewski, J}, title = {Aminoacyl-tRNA synthetases database.}, journal = {Nucleic acids research}, volume = {29}, number = {1}, pages = {288-290}, pmid = {11125115}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/*genetics ; *Databases, Factual ; Information Services ; Internet ; Molecular Sequence Data ; }, abstract = {Aminoacyl-tRNA synthetases (AARSs) are at the center of the question of the origin of life. They constitute a family of enzymes integrating the two levels of cellular organization: nucleic acids and proteins. AARSs arose early in evolution and are believed to be a group of ancient proteins. They are responsible for attaching amino acid residues to their cognate tRNA molecules, which is the first step in the protein synthesis. The role they play in a living cell is essential for the precise deciphering of the genetic code. The analysis of AARSs evolutionary history was not possible for a long time due to a lack of a sufficiently large number of their amino acid sequences. The emerging picture of synthetases' evolution is a result of recent achievements in genomics [Woese,C., Olsen,G.J., Ibba,M. and Söll,D. (2000) Microbiol. Mol. Biol. Rev., 64, 202-236]. In this paper we present a short introduction to the AARSs database. The updated database contains 1047 AARS primary structures from archaebacteria, eubacteria, mitochondria, chloroplasts and eukaryotic cells. It is the compilation of amino acid sequences of all AARSs known to date, which are available as separate entries via the WWW at http://biobases.ibch.poznan.pl/aars/.}, }
@article {pmid11125084, year = {2001}, author = {García-Martínez, J and Bescós, I and Rodríguez-Sala, JJ and Rodríguez-Valera, F}, title = {RISSC: a novel database for ribosomal 16S-23S RNA genes spacer regions.}, journal = {Nucleic acids research}, volume = {29}, number = {1}, pages = {178-180}, pmid = {11125084}, issn = {1362-4962}, mesh = {DNA, Ribosomal Spacer/*genetics ; *Databases, Factual ; Internet ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/*genetics ; Sequence Alignment ; }, abstract = {A novel database, under the acronym RISSC (Ribosomal Intergenic Spacer Sequence Collection), has been created. It compiles more than 1600 entries of edited DNA sequence data from the 16S-23S ribosomal spacers present in most prokaryotes and organelles (e.g. mitochondria and chloroplasts) and is accessible through the Internet (http://ulises.umh.es/RISSC), where systematic searches for specific words can be conducted, as well as BLAST-type sequence searches. Additionally, a characteristic feature of this region, the presence/absence and nature of tRNA genes within the spacer, is included in all the entries, even when not previously indicated in the original database. All these combined features could provide a useful documentation tool for studies on evolution, identification, typing and strain characterization, among others.}, }
@article {pmid10626001, year = {1999}, author = {Carvalho, TM and Ferreira, AG and Coimbra, ES and Rosestolato, CT and De Souza, W}, title = {Distribution of cytoskeletal structures and organelles of the host cell during evolution of the intracellular parasitism by Trypanosoma cruzi.}, journal = {Journal of submicroscopic cytology and pathology}, volume = {31}, number = {3}, pages = {325-333}, pmid = {10626001}, issn = {1122-9497}, mesh = {Actin Cytoskeleton/metabolism ; Actins/metabolism ; Animals ; Chlorocebus aethiops ; Cytoskeleton/*metabolism/*ultrastructure ; Intracellular Fluid/metabolism ; Mice ; Microscopy, Confocal ; Microtubules/metabolism ; Organelles/*metabolism/ultrastructure ; Trypanosoma cruzi/*pathogenicity ; Vero Cells ; }, abstract = {The distribution of microtubules, microfilaments, mitochondria, Golgi complex and endosomes/lysosomes was analyzed in Vero cells allowed to interact for different periods of time with the pathogenic protozoan Trypanosoma cruzi and observed by confocal laser scanning microscopy. Microtubules were revealed using a mouse monoclonal anti-alpha-tubulin antibody. Actin filaments were revealed using phalloidin-rhodamine. To identify mitochondria, endosomes/lysosomes and the Golgi complex the cells were labelled with Rhodamine 123, Lucifer yellow and C6-NBD-ceramide, respectively. During cell invasion actin filaments concentrate at the site of parasite penetration in some, but not in all cells, probably depending upon the mechanism used by the trypomastigote form to penetrate into the host cells. Following internalization the trypomastigote form gradually changes into the amastigote form, disruption of the parasitophorous vacuole membrane takes place and the amastigote form enters in direct contact with host cell structures and organelles, and starts to divide. The presence of the parasite in the cytoplasm of the host cell did not induce significant changes in the distribution of actin filaments, microtubules, the Golgi complex, mitochondria and endosomes/lysosomes during the first 48 h of infection. Amastigote forms were seen close to the microtubules. After 72 h of interaction, the number of microtubules and microfilaments around the parasites was reduced and lysosomes and mitochondria were seen in between the parasites.}, }
@article {pmid10620491, year = {2000}, author = {Ricquier, D and Bouillaud, F}, title = {The uncoupling protein homologues: UCP1, UCP2, UCP3, StUCP and AtUCP.}, journal = {The Biochemical journal}, volume = {345 Pt 2}, number = {Pt 2}, pages = {161-179}, pmid = {10620491}, issn = {0264-6021}, mesh = {Adipose Tissue, Brown/metabolism ; Amino Acid Sequence ; Animals ; Carrier Proteins/classification/genetics/*metabolism ; Energy Metabolism/*physiology ; Evolution, Molecular ; Hot Temperature ; Humans ; Mice ; Mitochondria/*metabolism ; Molecular Sequence Data ; Oxygen Consumption ; Plant Proteins/classification/genetics/metabolism ; Uncoupling Agents/*metabolism ; }, abstract = {Animal and plant uncoupling protein (UCP) homologues form a subfamily of mitochondrial carriers that are evolutionarily related and possibly derived from a proton/anion transporter ancestor. The brown adipose tissue (BAT) UCP1 has a marked and strongly regulated uncoupling activity, essential to the maintenance of body temperature in small mammals. UCP homologues identified in plants are induced in a cold environment and may be involved in resistance to chilling. The biochemical activities and biological functions of the recently identified mammalian UCP2 and UCP3 are not well known. However, recent data support a role for these UCPs in State 4 respiration, respiration uncoupling and proton leaks in mitochondria. Moreover, genetic studies suggest that UCP2 and UCP3 play a part in energy expenditure in humans. The UCPs may also be involved in adaptation of cellular metabolism to an excessive supply of substrates in order to regulate the ATP level, the NAD(+)/NADH ratio and various metabolic pathways, and to contain superoxide production. A major goal will be the analysis of mice that either lack the UCP2 or UCP3 gene or overexpress these genes. Other aims will be to investigate the possible roles of UCP2 and UCP3 in response to oxidative stress, lipid peroxidation, inflammatory processes, fever and regulation of temperature in certain specific parts of the body.}, }
@article {pmid10620406, year = {1999}, author = {Kretzer, AM and Bruns, TD}, title = {Use of atp6 in fungal phylogenetics: an example from the boletales.}, journal = {Molecular phylogenetics and evolution}, volume = {13}, number = {3}, pages = {483-492}, doi = {10.1006/mpev.1999.0680}, pmid = {10620406}, issn = {1055-7903}, mesh = {Adenosine Triphosphatases/*genetics ; Basidiomycota/classification/*physiology ; Biological Evolution ; Classification ; Codon/genetics ; DNA Primers/genetics ; Electron Transport Complex IV/genetics ; Fungal Proteins/genetics ; Fungi/classification/physiology ; Membrane Proteins/genetics ; Mitochondria/genetics ; Mitochondrial Proton-Translocating ATPases ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction/methods ; Saccharomyces cerevisiae Proteins ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Complete nucleotide sequences have been determined for atp6 from Suillus luteus and cox3 from Suillus sinuspaulianus (Boletales, Hymenomycetes, Basidiomycota), which code for ATPase subunit 6 and cytochrome oxidase subunit 3, respectively. These sequences were used to design PCR primers for the amplification of partial atp6 and cox3 sequences from other members of the Boletales and outgroup taxa. In atp6 and cox3 from Russula rosacea, one of the outgroup taxa, we observed a number of in-frame TGA(trp) codons, which imply a Neurospora crassa-type mitochondrial code in R. rosacea and possibly in basidiomycetes in general. Interestingly, however, most basidiomycetes other than R. rosacea appear to strongly prefer the TGG(trp) codon, which is unusual, given the strong A + T bias in fungal mitochondrial genomes. Pairwise comparisons were performed between atp6 sequences from increasingly divergent fungal lineages, and results show that all three codon positions become saturated in substitutions after an estimated divergence time of approx 300 Ma. This means that atp6 is likely to provide phylogenetic resolution within fungal classes but not at higher taxonomic levels. Also, because of the strong A + T bias in fungal mitochondrial genomes, A/T transversions were found to be more common than any other type of substitution, resulting in transversions being about two to three times more common in most pairwise sequence comparisons. Finally, atp6 sequences were used to infer phylogenetic relationships between 27 taxa from the Boletales and 4 outgroup taxa. Analyses were performed (i) on nucleotide sequence data using parsimony (successive approximation) as well as maximum likelihood methods and (ii) on deduced amino acid sequences using distance methods based on empirical substitution probabilities. Results from the various analyses are largely concordant with each other as well as with prior analyses of partial mitochondrial large-subunit rDNA (mtLSU rDNA). Analysis of the combined atp6 and mtLSU rDNA sequences results in increased bootstrap support for several key branches. Relationships that have been resolved for the first time in the current analysis are discussed.}, }
@article {pmid10620198, year = {2000}, author = {Coimbra, TM and Janssen, U and Gröne, HJ and Ostendorf, T and Kunter, U and Schmidt, H and Brabant, G and Floege, J}, title = {Early events leading to renal injury in obese Zucker (fatty) rats with type II diabetes.}, journal = {Kidney international}, volume = {57}, number = {1}, pages = {167-182}, doi = {10.1046/j.1523-1755.2000.00836.x}, pmid = {10620198}, issn = {0085-2538}, mesh = {Aging/pathology ; Animals ; Cell Death ; Cell Division ; Collagen/metabolism ; Cytoskeletal Proteins/metabolism ; Diabetes Mellitus, Type 2/*pathology ; Diabetic Nephropathies/complications/metabolism/*pathology ; Fibronectins/metabolism ; Immunohistochemistry ; In Situ Nick-End Labeling ; Intercellular Adhesion Molecule-1/metabolism ; Kidney Glomerulus/metabolism/pathology/ultrastructure ; Leukocytes/pathology ; Microscopy, Electron ; Obesity/complications/*pathology ; Rats ; Rats, Zucker ; }, abstract = {UNLABELLED: Early events leading to renal injury in obese Zucker (fatty) rats with type II diabetes.<br><br>BACKGROUND: More than half of the new patients admitted to dialysis therapy in some centers are diagnosed with type IIb diabetes, that is, diabetes associated with obesity. This study searched for a common final pathway of renal damage in this progressive renal disease.<br><br>METHODS: The evolution of biochemical and morphological renal changes was examined in 6- to 60-week-old Zucker rats (fa/fa-rats), a model of obesity associated with type II diabetes.<br><br>RESULTS: fa/fa-rats exhibited pronounced hyperinsulinemia and hyperlipidemia at 6 weeks and became diabetic after 14 weeks of age. Significant focal segmental glomerulosclerosis was first noted in 18-week-old fa/fa-rats and tubulointerstitial damage and proteinuria in 40-week-old fa/fa-rats. A comparison of kidneys of six-week-old fa/fa-and lean control (Fa/?) rats by immunohistology revealed a 1.8-fold increase in glomerular monocyte/macrophage counts in fa/fa-rats and a significant increase in de novo desmin expression in podocytes. Electron microscopy demonstrated an increase in the number of podocyte mitochondria and intracytoplasmic protein and fat droplets. Podocyte desmin scores markedly increased until week 18 in fa/fa-rats, whereas glomerular monocyte/macrophage counts peaked at 3.2-fold at week 14. Podocyte desmin expression, but not glomerular macrophage infiltration, correlated with damage in adjacent tubular cells, as evidenced by their de novo expression of vimentin. Progressive glomerular hypertrophy was detected in fa/fa-rats after 10 weeks. GBM width was significantly increased in 14-week-old fa/fa-rats as compared with lean controls. Mesangial cell activation (de novo expression of alpha-smooth muscle actin) and proliferation was low to absent throughout the observation period in fa/fa-rats. Renal cell death counts (TUNEL) remained unchanged in 6- to 40-week-old fa/fa-rats. Tubulointerstitial myofibroblast formation and matrix accumulation occurred late during the study duration in fa/fa-rats.<br><br>CONCLUSION: These data suggest that early progressive podocyte damage and macrophage infiltration is associated with hyperlipidemia and type IIb diabetes mellitus, and antedates both the development of glomerulosclerosis and tubulointerstitial damage.}, }
@article {pmid10618642, year = {1999}, author = {Tsuiki, H and Nitta, M and Furuya, A and Hanai, N and Fujiwara, T and Inagaki, M and Kochi, M and Ushio, Y and Saya, H and Nakamura, H}, title = {A novel human nucleoside diphosphate (NDP) kinase, Nm23-H6, localizes in mitochondria and affects cytokinesis.}, journal = {Journal of cellular biochemistry}, volume = {76}, number = {2}, pages = {254-269}, doi = {10.1002/(sici)1097-4644(20000201)76:2&lt;254::aid-jcb9&gt;3.0.co;2-g}, pmid = {10618642}, issn = {0730-2312}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cell Cycle/physiology ; Cell Division/*physiology ; Cell Line ; Chromosome Mapping ; Cloning, Molecular ; DNA Primers/genetics ; Female ; Gene Expression ; Humans ; Mitochondria/*enzymology ; Molecular Sequence Data ; Monomeric GTP-Binding Proteins/*metabolism ; NM23 Nucleoside Diphosphate Kinases ; Nucleoside-Diphosphate Kinase/*metabolism ; Pregnancy ; RNA, Messenger/genetics/metabolism ; Sequence Homology, Amino Acid ; Subcellular Fractions/enzymology ; Transcription Factors/*metabolism ; }, abstract = {Nucleoside diphosphate kinases (NDP kinases) are enzymes known to be conserved throughout evolution and have been shown to be involved in various biological events, in addition to the "housekeeping" phosphotransferase activity. We present the molecular cloning of a novel human NDP kinase gene, termed Nm23-H6. Nm23-H6 gene has been mapped at chromosome 3p21.3 and is highly expressed in heart, placenta, skeletal muscle, and some of the cancer cell lines. Recombinant Nm23-H6 protein has been identified to exhibit functional NDP kinase activity. Immunolocalization studies showed that both endogenous and inducibly expressed Nm23-H6 proteins were present as short, filament-like, perinuclear radical arrays and that they colocalized with mitochondria. Cell fractionation study also demonstrated the presence of Nm23-H6 protein in a mitochondria-rich fraction. Moreover, induction of overexpression of Nm23-H6 in SAOS2 cells, using the Cre-loxP gene activation system, resulted in growth suppression and generation of multinucleated cells. Flow cytometric analysis also demonstrated that the proportion of cells with more than 4N DNA content increased to 28.1% after induction of Nm23-H6, coinciding with the appearance of multinucleated cells. These observations suggest that Nm23-H6, a new member of the NDP kinase family, resides in mitochondria and plays a role in regulation of cell growth and cell cycle progression.}, }
@article {pmid10618092, year = {2000}, author = {Sanson, GF and Briones, MR}, title = {Typing of Candida glabrata in clinical isolates by comparative sequence analysis of the cytochrome c oxidase subunit 2 gene distinguishes two clusters of strains associated with geographical sequence polymorphisms.}, journal = {Journal of clinical microbiology}, volume = {38}, number = {1}, pages = {227-235}, pmid = {10618092}, issn = {0095-1137}, mesh = {*Bacterial Proteins ; Bacteriocins ; Base Sequence ; Brazil ; Candida/*classification/enzymology/genetics ; Candidiasis/epidemiology/*microbiology ; Cluster Analysis ; Cytotoxins/*genetics ; DNA Primers ; Electron Transport Complex IV/*genetics ; *Genes, Bacterial ; Geography ; Mitochondria/enzymology/genetics ; Molecular Epidemiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; *Polymorphism, Genetic ; Sequence Homology, Nucleic Acid ; Species Specificity ; United States ; }, abstract = {We tested whether comparative sequence analysis of the mitochondrion-encoded cytochrome c oxidase subunit 2 gene (COX2) could be used to distinguish intraspecific variants of Candida glabrata. Mitochondrial genes are suitable for investigation of close phylogenetic relationships because they evolve much faster than nuclear genes, which in general exhibit very limited intraspecific variation. For this survey we used 11 clinical isolates of C. glabrata from three different geographical locations in Brazil, 10 isolates from one location in the United States, 1 American Type Culture Collection strain as an internal control, and the published sequence of strain CBS 138. The complete coding region of COX2 was amplified from total cellular DNA, and both strands were sequenced twice for each strain. These sequences were aligned with published sequences from other fungi, and the numbers of substitutions and phylogenetic relationships were determined. Typing of these strains was done by using 17 substitutions, with 8 being nonsynonymous and 9 being synonymous. Also, cDNAs made from purified mitochondrial polyadenylated RNA were sequenced to confirm that our sequences correspond to the expressed copies and not nuclear pseudogenes and that a frameshift mutation exists in the 3' end of the coding region (position 673) relative to the Saccharomyces cerevisiae sequence and the previously published C. glabrata sequence. We estimated the average evolutionary rate of COX2 to be 11.4% sequence divergence/10(8) years and that phylogenetic relationships of yeasts based on these sequences are consistent with rRNA sequence data. Our analysis of COX2 sequences enables typing of C. glabrata strains based on 13 haplotypes and suggests that positions 51 and 519 indicate a geographical polymorphism that discriminates strains isolated in the United States and strains isolated in Brazil. This provides for the first time a means of typing of Candida strains that cause infections by use of direct sequence comparisons and the associated divergence estimates.}, }
@article {pmid10617197, year = {1999}, author = {Lin, X and Kaul, S and Rounsley, S and Shea, TP and Benito, MI and Town, CD and Fujii, CY and Mason, T and Bowman, CL and Barnstead, M and Feldblyum, TV and Buell, CR and Ketchum, KA and Lee, J and Ronning, CM and Koo, HL and Moffat, KS and Cronin, LA and Shen, M and Pai, G and Van Aken, S and Umayam, L and Tallon, LJ and Gill, JE and Adams, MD and Carrera, AJ and Creasy, TH and Goodman, HM and Somerville, CR and Copenhaver, GP and Preuss, D and Nierman, WC and White, O and Eisen, JA and Salzberg, SL and Fraser, CM and Venter, JC}, title = {Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.}, journal = {Nature}, volume = {402}, number = {6763}, pages = {761-768}, doi = {10.1038/45471}, pmid = {10617197}, issn = {0028-0836}, mesh = {Arabidopsis/*genetics ; Cell Nucleus/genetics ; Centromere ; *Chromosome Mapping ; *DNA, Plant ; Evolution, Molecular ; Gene Duplication ; *Genes, Plant/physiology ; Mitochondria/genetics ; Molecular Sequence Data ; Plant Proteins/genetics/physiology ; Sequence Analysis, DNA ; }, abstract = {Arabidopsis thaliana (Arabidopsis) is unique among plant model organisms in having a small genome (130-140 Mb), excellent physical and genetic maps, and little repetitive DNA. Here we report the sequence of chromosome 2 from the Columbia ecotype in two gap-free assemblies (contigs) of 3.6 and 16 megabases (Mb). The latter represents the longest published stretch of uninterrupted DNA sequence assembled from any organism to date. Chromosome 2 represents 15% of the genome and encodes 4,037 genes, 49% of which have no predicted function. Roughly 250 tandem gene duplications were found in addition to large-scale duplications of about 0.5 and 4.5 Mb between chromosomes 2 and 1 and between chromosomes 2 and 4, respectively. Sequencing of nearly 2 Mb within the genetically defined centromere revealed a low density of recognizable genes, and a high density and diverse range of vestigial and presumably inactive mobile elements. More unexpected is what appears to be a recent insertion of a continuous stretch of 75% of the mitochondrial genome into chromosome 2.}, }
@article {pmid10611480, year = {1999}, author = {Bauer, MF and Rothbauer, U and Mühlenbein, N and Smith, RJ and Gerbitz, K and Neupert, W and Brunner, M and Hofmann, S}, title = {The mitochondrial TIM22 preprotein translocase is highly conserved throughout the eukaryotic kingdom.}, journal = {FEBS letters}, volume = {464}, number = {1-2}, pages = {41-47}, doi = {10.1016/s0014-5793(99)01665-8}, pmid = {10611480}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Blotting, Northern ; Carrier Proteins/*chemistry/genetics/metabolism ; Conserved Sequence ; DNA, Complementary/metabolism ; DNA-Binding Proteins/chemistry/metabolism ; *Escherichia coli Proteins ; Evolution, Molecular ; Fungal Proteins/chemistry/metabolism ; Humans ; Membrane Proteins/*chemistry/genetics/metabolism ; *Membrane Transport Proteins ; Mitochondria/*enzymology ; *Mitochondrial Membrane Transport Proteins ; Mitochondrial Precursor Protein Import Complex Proteins ; *Mitochondrial Proteins ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Physical Chromosome Mapping ; Protein Precursors/*chemistry/genetics/metabolism ; Saccharomyces cerevisiae/enzymology ; *Saccharomyces cerevisiae Proteins ; Sequence Homology, Amino Acid ; Tissue Distribution ; }, abstract = {The Mohr-Tranebjaerg syndrome (MTS), a neurodegenerative syndrome characterized by progressive sensorineural hearing loss, dystonia, mental retardation and blindness, is a mitochondrial disease caused by mutations in the deafness/dystonia peptide 1 (DDP1) gene. DDP1 shows similarity to the yeast proteins Tim9, Tim10 and Tim12, components of the mitochondrial import machinery for carrier proteins. Here, we show that DDP1 belongs to a large family of evolutionarily conserved proteins. We report the identification, chromosomal localization and expressional analysis of six human family members which represent further candidate genes for neurodegenerative diseases.}, }
@article {pmid10609758, year = {1999}, author = {Hwang, JS and Lee, JS and Goo, TW and Yun, EY and Sohn, HR and Kim, HR and Kwon, OY}, title = {Molecular genetic relationships between Bombycidae and Saturniidae based on the mitochondria DNA encoding of large and small rRNA.}, journal = {Genetic analysis : biomolecular engineering}, volume = {15}, number = {6}, pages = {223-228}, doi = {10.1016/s1050-3862(99)00008-x}, pmid = {10609758}, mesh = {Animals ; Base Sequence ; Bombyx/*classification/genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/*genetics ; Molecular Sequence Data ; Moths/*classification/genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; }, abstract = {The phylogenetic relationships between Bombycidae (Bombyx mori and Bombyx mandarina) and Saturniidae (Antheraea yamamai and Antheraea pernyi) were investigated based on large and small mitochondiral rRNA genes. About 430 bp of four kinds of PCR-amplified fragments were sequenced and aligned. For the 16S rRNA gene, B. mori shared a 98, 87 and 86% sequence homology with B. mandarina, A. yamamai and A. pernyi, and for the 12S rRNA gene, B. mori shared a 99, 89 and 88% sequence homology with B. mandarina, A. yamamai and A. pernyi, respectively. DNA sequence data were also used for a phylogenetic analysis. All of the trees showed monophyly for both Bombycidae and Saturniidae. The monophyly confidence limits of these trees were estimated using bootstrapping tests and measured more than 99% for all trees for both Bombycidae and Saturniidae.}, }
@article {pmid10607615, year = {1999}, author = {Gray, MW}, title = {Evolution of organellar genomes.}, journal = {Current opinion in genetics &amp; development}, volume = {9}, number = {6}, pages = {678-687}, doi = {10.1016/s0959-437x(99)00030-1}, pmid = {10607615}, issn = {0959-437X}, mesh = {Animals ; Chloroplasts/genetics ; DNA, Chloroplast/*genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genes, Bacterial/genetics ; Genes, Plant/genetics ; *Genome ; Mitochondria/genetics ; Models, Genetic ; Organelles/*genetics ; Phylogeny ; }, abstract = {Accumulating molecular data, particularly complete organellar genome sequences, continue to advance our understanding of the evolution of mitochondrial and chloroplast DNAs. Although the notion of a single primary origin for each organelle has been reinforced, new models have been proposed that tie the acquisition of mitochondria more closely to the origin of the eukaryotic cell per se than is implied by classic endosymbiont theory. The form and content of the ancestral proto-mitochondrial and proto-chloroplast genomes are becoming clearer but unusual patterns of organellar genome structure and organization continue to be discovered. The 'single-gene circle' arrangement recently reported for dinoflagellate chloroplast genomes is a notable example of a highly derived organellar genome.}, }
@article {pmid10607403, year = {1999}, author = {Escobar Galvis, ML and Håkansson, G and Alexciev, K and Knorpp, C}, title = {Cloning and characterisation of a pea mitochondrial NDPK.}, journal = {Biochimie}, volume = {81}, number = {12}, pages = {1089-1096}, doi = {10.1016/s0300-9084(99)00353-3}, pmid = {10607403}, issn = {0300-9084}, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; DNA Primers/genetics ; DNA, Complementary/genetics/isolation &amp; purification ; DNA, Plant/genetics/isolation &amp; purification ; Gene Expression ; Mitochondria/*enzymology ; Molecular Sequence Data ; Nucleoside-Diphosphate Kinase/*genetics ; Pisum sativum/*enzymology/*genetics ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {Here we report the cloning of a cDNA encoding the first nucleoside diphosphate kinase (NDPK) isolated from plant mitochondria. Amplification of a 317 nt product was performed by PCR, using oligonucleotide primers based on partial amino acid sequences of the pea mitochondria NDPK and other NDPK isoforms. By screening of a pea cDNA library with this PCR product, a full length clone was obtained. Northern analysis revealed the presence of a 1.1 kb single transcript, with high expression in young leaves and reproductive tissues. The clone encodes a precursor protein of 232 amino acids (26 kDa), including an N-terminal extension of 80 amino acids (9 kDa). Analysis of the deduced amino acid sequence confirmed its identity with the sequences obtained from the purified mature pea mitochondrial NDPK. In vitro import experiments carried out in isolated pea mitochondria showed targeting and processing of the 27 kDa precursor into a 16.5 kDa mature form. Phylogenetic analysis of some vertebrate and plant isoforms of NDPK showed that the pea mtNDPK groups together with the NDPK3 isoform from A. thaliana and the chloroplastic NDPK III from spinach. We suggest that it is possible to design a novel classification of the different NDPK isoforms according to their subcellular localisation and origin.}, }
@article {pmid10605115, year = {1999}, author = {Silberman, JD and Clark, CG and Diamond, LS and Sogin, ML}, title = {Phylogeny of the genera Entamoeba and Endolimax as deduced from small-subunit ribosomal RNA sequences.}, journal = {Molecular biology and evolution}, volume = {16}, number = {12}, pages = {1740-1751}, doi = {10.1093/oxfordjournals.molbev.a026086}, pmid = {10605115}, issn = {0737-4038}, support = {GM32964/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; DNA, Ribosomal/genetics ; Endolimax/*genetics ; Entamoeba/*genetics ; Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/*genetics ; Sequence Analysis, DNA ; }, abstract = {We sequenced small-subunit ribosomal RNA genes (16S-like rDNAs) of 10 species belonging to the genera Entamoeba and Endolimax. This study was undertaken to (1) resolve the relationships among the major lineages of Entamoeba previously identified by riboprinting; (2) examine the validity of grouping the genera Entamoeba and Endolimax in the same family, the Entamoebidae; and (3) examine how different models of nucleotide evolution influence the position of Entamoeba in eukaryotic phylogenetic reconstructions. The results obtained with distance, parsimony, and maximum-likelihood analyses support monophyly of the genus Entamoeba and are largely in accord with riboprinting results. Species of Entamoeba producing cysts with the same number of nuclei from monophyletic groups. The most basal Entamoeba species are those that produce cysts with eight nuclei, while the group producing four-nucleated cysts is most derived. Most phylogenetic reconstructions support monophyly of the Entamoebidae. In maximum-likelihood and parsimony analyses, Endolimax is a sister taxon to Entamoeba, while in some distance analyses, it represents a separate lineage. The secondary loss of mitochondria and other organelles from these genera is confirmed by their relatively late divergence in eukaryotic 16S-like rDNA phylogenies. Finally, we show that the positions of some (fast-evolving) eukaryotic lineages are uncertain in trees constructed with models that make corrections for among-site rate variation.}, }
@article {pmid10605113, year = {1999}, author = {Vavre, F and Fleury, F and Lepetit, D and Fouillet, P and Boulétreau, M}, title = {Phylogenetic evidence for horizontal transmission of Wolbachia in host-parasitoid associations.}, journal = {Molecular biology and evolution}, volume = {16}, number = {12}, pages = {1711-1723}, doi = {10.1093/oxfordjournals.molbev.a026084}, pmid = {10605113}, issn = {0737-4038}, mesh = {Animals ; Bacterial Outer Membrane Proteins/*genetics ; Base Sequence ; Data Interpretation, Statistical ; Drosophila/*microbiology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Wolbachia/*genetics ; }, abstract = {Endosymbiotic Wolbachia infect a number of arthropod species in which they can affect the reproductive system. While maternally transmitted, unlike mitochondria their molecular phylogeny does not parallel that of their hosts. This strongly suggests horizontal transmission among species, the mechanisms of which remain unknown. Such transfers require intimate between-species relationships, and thus host-parasite associations are outstandingly appropriate for study. Here, we demonstrate that hymenopteran parasitoids of frugivorous Drosophila species are especially susceptible to Wolbachia infection. Of the five common European species, four proved to be infected; furthermore, multiple infections are common, with one species being doubly infected and two triply infected (first report). Phylogenetic statuses of the Wolbachia infecting the different species of the community have been studied using the gene wsp, a highly variable gene recently described. This study reveals exciting similarities between the Wolbachia variants found in parasitoids and their hosts. These arguments strongly support the hypothesis of frequent natural Wolbachia transfers into other species and open a new field for genetic exchanges among species, especially in host-parasitoid associations.}, }
@article {pmid10603267, year = {1999}, author = {Kennedy, M and Paterson, AM and Morales, JC and Parsons, S and Winnington, AP and Spencer, HG}, title = {The long and short of it: branch lengths and the problem of placing the New Zealand short-tailed bat, Mystacina.}, journal = {Molecular phylogenetics and evolution}, volume = {13}, number = {2}, pages = {405-416}, doi = {10.1006/mpev.1999.0660}, pmid = {10603267}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Chiroptera/*classification/*genetics ; Cytochrome b Group/*genetics ; DNA/chemistry/genetics ; Evolution, Molecular ; Mitochondria/genetics ; Molecular Sequence Data ; New Zealand ; *Phylogeny ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Time Factors ; }, abstract = {The taxonomic position of the endemic New Zealand bat genus Mystacina has vexed systematists ever since its erection in 1843. Over the years the genus has been linked with many microchiropteran families and superfamilies. Most recent classifications place it in the Vespertilionoidea, although some immunological evidence links it with the Noctilionoidea (=Phyllostomoidea). We have sequenced 402 bp of the mitochondrial cytochrome b gene for M. tuberculata (Gray in Dieffenbach, 1843), and using both our own and published DNA sequences for taxa in both superfamilies, we applied different tree reconstruction methods to find the appropriate phylogeny and different methods of estimating confidence in the parts of the tree. All methods strongly support the classification of Mystacina in the Noctilionoidea. Spectral analysis suggests that parsimony analysis may be misleading for Mystacina's precise placement within the Noctilionoidea because of its long terminal branch. Analyses not susceptible to long-branch attraction suggest that the Mystacinidae is a sister family to the Phyllostomidae. Dating the divergence times between the different taxa suggests that the extant chiropteran families radiated around and shortly after the Cretaceous-Tertiary boundary. We discuss the biogeographical implications of classifying Mystacina within the Noctilionoidea and contrast our result with those classifications placing Mystacina in the Vespertilionoidea, concluding that evidence for the latter is weak.}, }
@article {pmid10603254, year = {1999}, author = {Shank, TM and Black, MB and Halanych, KM and Lutz, RA and Vrijenhoek, RC}, title = {Miocene radiation of deep-sea hydrothermal vent shrimp (Caridea: Bresiliidae): evidence from mitochondrial cytochrome oxidase subunit I.}, journal = {Molecular phylogenetics and evolution}, volume = {13}, number = {2}, pages = {244-254}, doi = {10.1006/mpev.1999.0642}, pmid = {10603254}, issn = {1055-7903}, mesh = {Animals ; DNA/chemistry/genetics ; Decapoda/*genetics ; Electron Transport Complex IV/*genetics ; *Evolution, Molecular ; Mitochondria/enzymology ; Phylogeny ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {The evolutionary history of deep-sea shrimp (Caridea: Bresiliidae) inhabiting deep-sea hydrothermal vent and hydrocarbon seep environments was assessed using the mitochondrial Cytochrome c Oxidase subunit I (COI) gene (600 bp). Phylogenetic analyses (parsimony, likelihood, and neighbor-joining) recovered three distinct clades (A, Rimicaris/Chorocaris/Opaepele; B, Alvinocaris; and C, Mirocaris) consistent with higher level taxonomy based on morphology. However, robust phylogenetic results suggested that Chorocaris is paraphyletic and that Mirocaris fortunata and M. keldyshi may not be genetically distinct. A Kishino-Hasegawa likelihood approach was used to test alternative phylogenetic hypotheses based on biogeography and morphology. Evolutionary relationships of vent-endemic shrimp species did not appear to be correlated either with their extant biogeographic distribution or with the history of sea floor spreading. Additionally, COI data suggested that these vent-endemic organisms are not remnants of a Mesozoic vent assemblage; instead, they radiated in the Miocene.}, }
@article {pmid10603253, year = {1999}, author = {Hassanin, A and Douzery, EJ}, title = {The tribal radiation of the family Bovidae (Artiodactyla) and the evolution of the mitochondrial cytochrome b gene.}, journal = {Molecular phylogenetics and evolution}, volume = {13}, number = {2}, pages = {227-243}, doi = {10.1006/mpev.1999.0619}, pmid = {10603253}, issn = {1055-7903}, mesh = {Animals ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/chemistry/genetics ; *Evolution, Molecular ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Point Mutation ; Polymorphism, Genetic ; Ruminants/classification/*genetics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {The nucleotide sequence of the complete mitochondrial cytochrome b gene has been determined and compared for 51 species of the family Bovidae and 10 potential pecoran and tragulid outgroups. A detailed saturation analysis at each codon position relative to the maximum parsimony procedure indicates that all transitions on third codon positions do not accumulate in a similar fashion: C-T are more saturated than A-G substitutions. The same trend is observed for second positions but not for first positions where A-G and C-T transitions exhibit roughly the same levels of saturation. Maximum parsimony reconstructions were weighted according to these observations. Maximum parsimony, maximum likelihood, and distance phylogenetic reconstructions all depict a major split within Bovidae. The subfamily Bovinae includes four multifurcating tribes and subtribes: Boselaphini, Tragelaphini, cattle-Bovini (Bos and Bison), and buffalo-Bovini (Bubalus and Syncerus). Its sister group is the subfamily Antilopinae, i.e., all non-Bovinae taxa, represented by seven lineages: Antilopini (including Saiga), Caprini sensu lato (i. e., Caprinae including Pantholops), Hippotragini, Alcelaphini, Reduncini (including Pelea), Aepyceros possibly linked to Neotragus, and Cephalophini possibly linked to Oreotragus (the suni and the klipspringer being members of a polyphyletic Neotragini). These various tribes and major lineages were produced by two noteworthy explosive radiations, which occurred simultaneously between 12.0 and 15.3 MY (Middle Miocene) in the subfamilies Bovinae and Antilopinae.}, }
@article {pmid10601861, year = {2000}, author = {Papenbrock, J and Schmidt, A}, title = {Characterization of a sulfurtransferase from Arabidopsis thaliana.}, journal = {European journal of biochemistry}, volume = {267}, number = {1}, pages = {145-154}, doi = {10.1046/j.1432-1327.2000.00980.x}, pmid = {10601861}, issn = {0014-2956}, mesh = {Amino Acid Sequence ; Arabidopsis/cytology/*enzymology ; Blotting, Southern ; Chloroplasts/enzymology ; Cloning, Molecular ; Cyanides/metabolism ; Cysteine/*analogs &amp; derivatives/metabolism ; Expressed Sequence Tags ; Genes, Plant/genetics ; Hydrogen-Ion Concentration ; Isoenzymes/chemistry/genetics/isolation &amp; purification/metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Molecular Weight ; Phylogeny ; Protein Sorting Signals/chemistry/genetics/metabolism ; Recombinant Fusion Proteins/chemistry/genetics/isolation &amp; purification/metabolism ; Sequence Alignment ; Sequence Deletion/genetics ; Substrate Specificity ; Sulfurtransferases/chemistry/genetics/isolation &amp; purification/*metabolism ; Thiosulfate Sulfurtransferase/chemistry/genetics ; Thiosulfates/*metabolism ; }, abstract = {A database search for similarities between sequenced parts of the Arabidopsis thaliana genome with known sulfurtransferase sequences from Escherichia coli and mammals was undertaken to obtain information about plant sulfurtransferase-like proteins. One gene and several homologous EST clones were identified. One of the EST clones was used for screening an Arabidopsis cDNA library. The isolated full-length clone consists of 1134 bp and encodes a 42.6 kDa protein that includes a putative transit peptide sequence of about 7.1 kDa. Sequence comparisons with known sulfurtransferases from different organisms confirmed high homology between them and the existence of several highly conserved regions. Results of a Southern blot performed with genomic Arabidopsis DNA showed the occurrence of at least two sulfurtransferase-like isozymes in Arabidopsis. Recombinant proteins with and without the putative transit peptide were expressed in E. coli with an N-terminal His6-tag, purified by affinity chromatography and tested for enzyme activity using different sulfur donors and acceptors. Both recombinant proteins catalyzed the formation of SCN- from thiosulfate and cyanide as a rhodanese per definition; however, both recombinant proteins preferred 3-mercaptopyruvate to thiosulfate. A monospecific antibody produced by using the mature recombinant protein as an antigen recognized a single protein band in total extracts of Arabidopsis plants equating to the full-length protein size. A single band equating to the size of the mature protein was detected from purified Arabidopsis mitochondria, but there was no antigenic reaction with any protein from chloroplasts. The function of the protein is still speculative. Now tools are available to elucidate the roles and substrates of this sulfurtransferase in higher plants.}, }
@article {pmid10601657, year = {1999}, author = {Balk, J and Leaver, CJ and McCabe, PF}, title = {Translocation of cytochrome c from the mitochondria to the cytosol occurs during heat-induced programmed cell death in cucumber plants.}, journal = {FEBS letters}, volume = {463}, number = {1-2}, pages = {151-154}, doi = {10.1016/s0014-5793(99)01611-7}, pmid = {10601657}, issn = {0014-5793}, mesh = {*Apoptosis ; Blotting, Southern ; Blotting, Western ; Cell Membrane/metabolism ; Cucumis sativus/cytology/genetics/*metabolism ; Cytochrome c Group/*metabolism ; Cytosol/*metabolism ; DNA Fragmentation ; Mitochondria/*metabolism ; Oxygen Consumption ; Temperature ; Time Factors ; }, abstract = {In mammals mitochondria play a critical role in the activation of programmed cell death (PCD). One mechanism by which mitochondria can commit a cell to death is by translocating cytochrome c into the cytosol where it activates cell death caspases. However, release of cytochrome c does not appear to be a feature of caspase activation in nematodes or insects, similarly, there is no evidence for cytochrome c release during the caspase-independent PCD that can occur in Dictyostelium cells. In an attempt to understand the underlying regulation of PCD in plants we investigated if mitochondrial components were released into the cytosol when plant cells are induced to undergo PCD. PCD was triggered in cucumber cotyledons by subjecting them to a short 55 degrees C heat treatment. This heat treatment has previously been shown to trigger PCD in other plant species and cell death was confirmed in cucumber using morphological (cellular condensation) and molecular (DNA 'laddering') markers of PCD. We present evidence that, unlike Dictyostelium and invertebrate PCDs, cytochrome c release is an early event in plant PCD. The mitochondrial release of cytochrome c following a PCD-inducing stimulus in both plants and mammals suggests the pathways have been conserved during evolution, having been derived from ancestral unicellular death programmes.}, }
@article {pmid10554032, year = {1999}, author = {Nomura, M and Shimizu, S and Ito, T and Narita, M and Matsuda, H and Tsujimoto, Y}, title = {Apoptotic cytosol facilitates Bax translocation to mitochondria that involves cytosolic factor regulated by Bcl-2.}, journal = {Cancer research}, volume = {59}, number = {21}, pages = {5542-5548}, pmid = {10554032}, issn = {0008-5472}, mesh = {*Apoptosis ; Biological Transport ; Caspase 3 ; Caspases/metabolism ; Cytochrome c Group/metabolism ; Cytosol/*metabolism ; Etoposide/pharmacology ; Gene Expression Regulation, Neoplastic ; HeLa Cells ; Humans ; Mitochondria/*metabolism ; Proto-Oncogene Proteins/*metabolism ; Proto-Oncogene Proteins c-bcl-2/*metabolism ; Time Factors ; Transfection ; bcl-2-Associated X Protein ; }, abstract = {Proapoptotic members of the Bcl-2 family, including Bax, Bak, and Bid, directly trigger the mitochondrial release of apoptogenic cytochrome c and apoptosis-inducing factor into the cytoplasm. One of the crucial steps before Bax can exert its proapoptotic activity is translocation from the cytoplasm to the mitochondria, but the molecular mechanism of this translocation is not understood. To investigate the mechanism of apoptosis-associated Bax translocation, we used an in vitro system comprising isolated mitochondria and cytosol. We found that both endogenous and exogenous added recombinant Bax translocated to the mitochondria more efficiently in the presence of cytosol from cells with VP16-induced apoptosis than with cytoplasm from normal cells. This apoptosis-dependent promotion of Bax translocation was not seen with cytosol that was prepared from VP16-treated cells expressing Bcl-2. Cytosol from cells with VP16-induced apoptosis, but not that from normal cells or Bcl-2-expressing cells, induced cytochrome c release from isolated mitochondria, which, as assessed by immunodepletion experiments, was mainly mediated by Bax. These results suggest that Bcl-2 exerts its antiapoptotic activity partly by inhibiting the translocation of Bax through the modification of cytosolic factors that are involved in such translocation during apoptosis.}, }
@article {pmid10591532, year = {1999}, author = {Glaser, E and Dessi, P}, title = {Integration of the mitochondrial-processing peptidase into the cytochrome bc1 complex in plants.}, journal = {Journal of bioenergetics and biomembranes}, volume = {31}, number = {3}, pages = {259-274}, doi = {10.1023/a:1005475930477}, pmid = {10591532}, issn = {0145-479X}, mesh = {Animals ; *Electron Transport ; Electron Transport Complex III/*chemistry/metabolism ; Evolution, Molecular ; Fungal Proteins/chemistry ; Iron-Sulfur Proteins/*chemistry ; Mammals/metabolism ; Metalloendopeptidases/*chemistry/metabolism ; Mitochondria/*enzymology ; Oxidation-Reduction ; Plant Proteins/*chemistry/*metabolism ; Protein Precursors/metabolism ; Species Specificity ; Substrate Specificity ; Mitochondrial Processing Peptidase ; }, abstract = {The plant mitochondrial cytochrome bc1 complex, like nonplant mitochondrial complexes, consists of cytochromes b and c1, the Rieske iron-sulfur protein, two Core proteins, and five low-molecular mass subunits. However, in contrast to nonplant sources, the two Core proteins are identical to subunits of the general mitochondrial processing peptidase (MPP). The MPP is a fascinating enzyme that catalyzes the specific cleavage of the diverse presequence peptides from hundreds of the nuclear-encoded mitochondrial precursor proteins that are synthesized in the cytosol and imported into the mitochondrion. Integration of the MPP into the bc1 complex renders the bc1 complex in plants bifunctional, being involved both in electron transport and in protein processing. Despite the integration of MPP into the bc1 complex, electron transfer as well as translocation of the precursor through the import channel are independent of the protein-processing activity. Recognition of the processing site by MPP occurs via the recognition of higher-order structural elements in combination with charge and cleavage-site properties. Elucidation of the three-dimensional (3-D) structure of the mammalian cytochrome bc1 complex is highly useful for understanding of the mechanism of action of MPP.}, }
@article {pmid10586879, year = {1999}, author = {Qiu, YL and Lee, J and Bernasconi-Quadroni, F and Soltis, DE and Soltis, PS and Zanis, M and Zimmer, EA and Chen, Z and Savolainen, V and Chase, MW}, title = {The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes.}, journal = {Nature}, volume = {402}, number = {6760}, pages = {404-407}, doi = {10.1038/46536}, pmid = {10586879}, issn = {0028-0836}, mesh = {Biological Evolution ; Cell Nucleus/classification/genetics ; DNA, Plant ; Genes, Plant ; *Genome, Plant ; Magnoliopsida/*classification/genetics ; Mitochondria/classification/genetics ; Molecular Sequence Data ; *Phylogeny ; Plastids/classification/genetics ; Sequence Alignment ; }, abstract = {Angiosperms have dominated the Earth's vegetation since the mid-Cretaceous (90 million years ago), providing much of our food, fibre, medicine and timber, yet their origin and early evolution have remained enigmatic for over a century. One part of the enigma lies in the difficulty of identifying the earliest angiosperms; the other involves the uncertainty regarding the sister group of angiosperms among extant and fossil gymnosperms. Here we report a phylogenetic analysis of DNA sequences of five mitochondrial, plastid and nuclear genes (total aligned length 8,733 base pairs), from all basal angiosperm and gymnosperm lineages (105 species, 103 genera and 63 families). Our study demonstrates that Amborella, Nymphaeales and Illiciales-Trimeniaceae-Austrobaileya represent the first stage of angiosperm evolution, with Amborella being sister to all other angiosperms. We also show that Gnetales are related to the conifers and are not sister to the angiosperms, thus refuting the Anthophyte Hypothesis. These results have far-reaching implications for our understanding of diversification, adaptation, genome evolution and development of the angiosperms.}, }
@article {pmid10585886, year = {1999}, author = {Fiermonte, G and Dolce, V and Arrigoni, R and Runswick, MJ and Walker, JE and Palmieri, F}, title = {Organization and sequence of the gene for the human mitochondrial dicarboxylate carrier: evolution of the carrier family.}, journal = {The Biochemical journal}, volume = {344 Pt 3}, number = {Pt 3}, pages = {953-960}, pmid = {10585886}, issn = {0264-6021}, mesh = {Alu Elements ; Amino Acid Sequence ; Animals ; Base Sequence ; Biological Transport/genetics ; Carrier Proteins/*genetics ; Cloning, Molecular ; Dicarboxylic Acid Transporters ; Evolution, Molecular ; Exons ; Humans ; Introns ; Kidney/metabolism ; Liver/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; RNA, Messenger/metabolism ; Rats ; Sequence Alignment ; Sequence Analysis ; }, abstract = {The dicarboxylate carrier (DIC) is a nuclear-encoded protein located in the mitochondrial inner membrane. It catalyses the transport of dicarboxylates such as malate and succinate across the mitochondrial membrane in exchange for phosphate, sulphate and thiosulphate. We have determined the sequences of the human cDNA and gene for the DIC. The gene sequence was established from overlapping genomic clones generated by PCRs by use of primers and probes based upon the human cDNA sequence. It is spread over 8.6 kb of human DNA and is divided into 11 exons. Five short interspersed repetitive Alu sequences are found in intron I. The protein encoded by the gene is 287 amino acids long. In common with the rat protein, it does not have a processed presequence to help to target it into mitochondria. It has been demonstrated by Northern- and Western-blot analyses that the DIC is present in high amounts in liver and kidney, and at lower levels in all the other tissues analysed. The positions of introns contribute towards an understanding of the processes involved in the evolution of human genes for carrier proteins.}, }
@article {pmid10581290, year = {1999}, author = {Yokobori, Si and Ueda, T and Feldmaier-Fuchs, G and Pääbo, S and Ueshima, R and Kondow, A and Nishikawa, K and Watanabe, K}, title = {Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata).}, journal = {Genetics}, volume = {153}, number = {4}, pages = {1851-1862}, pmid = {10581290}, issn = {0016-6731}, mesh = {Animals ; Base Sequence ; Cloning, Molecular ; Codon ; DNA, Mitochondrial/*genetics ; *Genome ; Humans ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Transfer, Gly/chemistry/genetics ; Urochordata/*genetics ; }, abstract = {The complete nucleotide sequence of the 14,771-bp-long mitochondrial (mt) DNA of a urochordate (Chordata)-the ascidian Halocynthia roretzi-was determined. All the Halocynthia mt-genes were found to be located on a single strand, which is rich in T and G rather than in A and C. Like nematode and Mytilus edulis mtDNAs, that of Halocynthia encodes no ATP synthetase subunit 8 gene. However, it does encode an additional tRNA gene for glycine (anticodon TCT) that enables Halocynthia mitochondria to use AGA and AGG codons for glycine. The mtDNA carries an unusual tRNA(Met) gene with a TAT anticodon instead of the usual tRNA(Met)(CAT) gene. As in other metazoan mtDNAs, there is not any long noncoding region. The gene order of Halocynthia mtDNA is completely different from that of vertebrate mtDNAs except for tRNA(His)-tRNA(Ser)(GCU), suggesting that evolutionary change in the mt-gene structure is much accelerated in the urochordate line compared with that in vertebrates. The amino acid sequences of Halocynthia mt-proteins deduced from their gene sequences are quite different from those in other metazoans, indicating that the substitution rate in Halocynthia mt-protein genes is also accelerated.}, }
@article {pmid10576736, year = {1999}, author = {Sambongi, Y and Iko, Y and Tanabe, M and Omote, H and Iwamoto-Kihara, A and Ueda, I and Yanagida, T and Wada, Y and Futai, M}, title = {Mechanical rotation of the c subunit oligomer in ATP synthase (F0F1): direct observation.}, journal = {Science (New York, N.Y.)}, volume = {286}, number = {5445}, pages = {1722-1724}, doi = {10.1126/science.286.5445.1722}, pmid = {10576736}, issn = {0036-8075}, mesh = {Actins/chemistry/metabolism ; Adenosine Triphosphate/*metabolism ; Binding Sites ; Biotinylation ; Energy Transfer ; Enzymes, Immobilized ; Escherichia coli/enzymology ; Hydrolysis ; Molecular Motor Proteins/*chemistry/*metabolism ; Proton-Motive Force ; Proton-Translocating ATPases/*chemistry/*metabolism ; Uncoupling Agents/metabolism/pharmacology ; Venturicidins/pharmacology ; Video Recording ; }, abstract = {F0F1, found in mitochondria or bacterial membranes, synthesizes adenosine 5'-triphosphate (ATP) coupling with an electrochemical proton gradient and also reversibly hydrolyzes ATP to form the gradient. An actin filament connected to a c subunit oligomer of F0 was able to rotate by using the energy of ATP hydrolysis. The rotary torque produced by the c subunit oligomer reached about 40 piconewton-nanometers, which is similar to that generated by the gamma subunit in the F1 motor. These results suggest that the gamma and c subunits rotate together during ATP hydrolysis and synthesis. Thus, coupled rotation may be essential for energy coupling between proton transport through F0 and ATP hydrolysis or synthesis in F1.}, }
@article {pmid10571867, year = {1999}, author = {Rasmusson, AG and Svensson, AS and Knoop, V and Grohmann, L and Brennicke, A}, title = {Homologues of yeast and bacterial rotenone-insensitive NADH dehydrogenases in higher eukaryotes: two enzymes are present in potato mitochondria.}, journal = {The Plant journal : for cell and molecular biology}, volume = {20}, number = {1}, pages = {79-87}, doi = {10.1046/j.1365-313x.1999.00576.x}, pmid = {10571867}, issn = {0960-7412}, mesh = {Amino Acid Motifs/genetics ; Amino Acid Sequence ; Bacteria/enzymology/genetics ; Base Sequence ; Cloning, Molecular ; DNA Primers/genetics ; DNA, Complementary/genetics/isolation &amp; purification ; DNA, Plant/genetics/isolation &amp; purification ; Enzyme Inhibitors/pharmacology ; Escherichia coli/genetics ; Evolution, Molecular ; Gene Duplication ; Gene Expression ; Genes, Plant ; Mitochondria/enzymology ; Molecular Sequence Data ; NADH Dehydrogenase/antagonists &amp; inhibitors/*genetics ; Phylogeny ; Rotenone/pharmacology ; Sequence Homology, Amino Acid ; Solanum tuberosum/*enzymology/*genetics ; Yeasts/enzymology/genetics ; }, abstract = {Two different cDNAs, homologous to genes for rotenone-insensitive NADH dehydrogenases of bacteria and yeast, were isolated from potato. The encoded proteins, called NDA and NDB, have calculated molecular masses of 55 and 65 kDa, respectively. The N-terminal parts show similarity to mitochondrial targeting peptides and the polypeptides are in vitro imported into potato mitochondria. Import processing to a smaller polypeptide is seen for the NDA but not the NDB protein. After import, NDA is intramitochondrially sorted to the matrix side of the inner membrane, whereas NDB becomes exposed to the intermembrane space. Imported proteins are associated to membranes upon digitonin permeabilization. On expression in Escherichia coli, NDB is released from the bacterial membrane in the absence of divalent cations whereas detergents are necessary for solubilization of NDA. Both deduced amino-acid sequences contain the dual motifs for nucleotide binding with the characteristics of the core criteria, similar to the bacterial homologues. Unique among NADH dehydro- genases, the NDB amino-acid sequence contains a non-conserved insert, which is similar to EF-hand motifs for calcium binding. Phylogenetic analyses group the rotenone-insensitive NADH dehydrogenases largely by species, but suggest ancient gene duplications.}, }
@article {pmid10570164, year = {1999}, author = {Adams, KL and Song, K and Roessler, PG and Nugent, JM and Doyle, JL and Doyle, JJ and Palmer, JD}, title = {Intracellular gene transfer in action: dual transcription and multiple silencings of nuclear and mitochondrial cox2 genes in legumes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {96}, number = {24}, pages = {13863-13868}, pmid = {10570164}, issn = {0027-8424}, support = {R01 GM035087/GM/NIGMS NIH HHS/United States ; R01 GM-35087/GM/NIGMS NIH HHS/United States ; }, mesh = {Cell Nucleus ; Electron Transport Complex IV/*genetics ; Fabaceae/enzymology/*genetics ; Genes, Plant ; Mitochondria/*genetics ; Molecular Sequence Data ; Plant Proteins/*genetics ; *Plants, Medicinal ; *Recombination, Genetic ; *Transcription, Genetic ; }, abstract = {The respiratory gene cox2, normally present in the mitochondrion, was previously shown to have been functionally transferred to the nucleus during flowering plant evolution, possibly during the diversification of legumes. To search for novel intermediate stages in the process of intracellular gene transfer and to assess the evolutionary timing and frequency of cox2 transfer, activation, and inactivation, we examined nuclear and mitochondrial (mt) cox2 presence and expression in over 25 legume genera and mt cox2 presence in 392 genera. Transfer and activation of cox2 appear to have occurred during recent legume evolution, more recently than previously inferred. Many intermediate stages of the gene transfer process are represented by cox2 genes in the studied legumes. Nine legumes contain intact copies of both nuclear and mt cox2, although transcripts could not be detected for some of these genes. Both cox2 genes are transcribed in seven legumes that are phylogenetically interspersed with species displaying only nuclear or mt cox2 expression. Inactivation of cox2 in each genome has taken place multiple times and in a variety of ways, including loss of detectable transcripts or transcript editing and partial to complete gene loss. Phylogenetic evidence shows about the same number (3-5) of separate inactivations of nuclear and mt cox2, suggesting that there is no selective advantage for a mt vs. nuclear location of cox2 in plants. The current distribution of cox2 presence and expression between the nucleus and mitochondrion in the studied legumes is probably the result of chance mutations silencing either cox2 gene.}, }
@article {pmid10569190, year = {1999}, author = {Salto, R and Girón, MD and del Mar Sola, M and Vargas, AM}, title = {Evolution of pyruvate carboxylase and other biotin containing enzymes in developing rat liver and kidney.}, journal = {Molecular and cellular biochemistry}, volume = {200}, number = {1-2}, pages = {111-117}, pmid = {10569190}, issn = {0300-8177}, mesh = {Animals ; Animals, Newborn ; Base Sequence ; Biotin/metabolism ; DNA Primers/genetics ; Female ; Fetus/metabolism ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Enzymologic ; Kidney/embryology/*enzymology/*growth &amp; development ; Liver/embryology/*enzymology/*growth &amp; development ; Male ; Mitochondria/enzymology ; Mitochondria, Liver/enzymology ; Pregnancy ; Pyruvate Carboxylase/genetics/*metabolism ; RNA, Messenger/genetics/metabolism ; Rats ; Rats, Wistar ; }, abstract = {The evolution of pyruvate carboxylase has been studied in rat liver and kidney during perinatal development. The pyruvate carboxylase activity, amount of enzyme and mRNA levels have been assayed from 2 days before delivery to weaning. In liver, there is a peak of activity and amount of enzyme 24 h before delivery and 2 peaks, at 12 h and 6 days, after parturition. The transcription of the enzyme gene followed a similar pattern, with mRNA peaks preceding those of activity and amount of enzyme. However, in kidney, pyruvate carboxylase activity, amount and mRNA remain low until weaning. These results confirm the limited role of renal gluconeogenesis during the perinatal development. Since all carboxylases contain biotin as prosthetic group, the biotinylation of pyruvate carboxylase during the perinatal period was investigated by western-blot using streptavidin-biotin peroxidase. In the mitochondrial samples from liver and kidney, all the pyruvate carboxylase detected was fully biotinylated, indicating an early development of the holocarboxylase synthetase activity in the perinatal period. This Western-blot technique also allowed us the detection of other biotin-enzymes based on their molecular weight. In liver, during the perinatal development propionyl-coA and 3-methyl-crotonyl-coA carboxylases followed a pattern of induction similar to pyruvate carboxylase. In kidney, the expression of mitochondrial carboxylases was lower compared to liver and propionyl-coA carboxylase was not detected during the studied period.}, }
@article {pmid10552927, year = {1999}, author = {Jin, H and Kendall, E and Freeman, TC and Roberts, RG and Vetrie, DL}, title = {The human family of Deafness/Dystonia peptide (DDP) related mitochondrial import proteins.}, journal = {Genomics}, volume = {61}, number = {3}, pages = {259-267}, doi = {10.1006/geno.1999.5966}, pmid = {10552927}, issn = {0888-7543}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Blotting, Northern ; Carrier Proteins/*genetics/metabolism ; Chromosome Mapping ; Chromosomes, Artificial, Yeast ; Deafness/*genetics ; Dystonia/*genetics ; Humans ; In Situ Hybridization, Fluorescence ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Proteins/*genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Alignment ; Sequence Analysis, DNA ; Yeasts/genetics/metabolism ; }, abstract = {The gene responsible for the human genetic neurodegenerative disorder DFN-1/MTS encodes a small protein known as deafness/dystonia peptide (DDP). It bears a strong resemblance to a recently characterized set of zinc-binding yeast proteins (Tim8p, Tim9p, Tim10p, Tim12p, and Tim13p) that are implicated in the import of a class of transmembrane carrier proteins from the cytoplasm to the mitochondrial inner membrane. We describe here the human complement of DDP/Tim-like proteins and establish the likely orthologous relationships between sequences from human, yeast, and other organisms. We also describe the expression patterns and chromosomal locations of their genes, which are candidate loci for autosomal recessive neurodegenerative disorders.}, }
@article {pmid10564443, year = {1999}, author = {Ross, TK}, title = {Phylogeography and conservation genetics of the Iowa pleistocene snail.}, journal = {Molecular ecology}, volume = {8}, number = {9}, pages = {1363-1373}, doi = {10.1046/j.1365-294x.1999.00696.x}, pmid = {10564443}, issn = {0962-1083}, mesh = {Animals ; Conservation of Natural Resources ; DNA, Mitochondrial/genetics ; Genes, rRNA ; Genetic Variation ; Genetics, Population ; Geography ; Iowa ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Snails/*genetics/physiology ; }, abstract = {The Iowa Pleistocene snail, Discus macclintocki, is an endangered species that survives only in relictual populations on algific (cold-air) talus slopes in northeast Iowa and northwest Illinois in the central region of the USA. These populations are believed to have been isolated since the temperatures began to warm at the end of the last glacial period around 16 500 years ago. DNA sequencing of the 16s rRNA gene of the mitochondria was used to determine the genetic relationship among 10 populations and the genetic diversity within these populations. Genetic diversity is extremely high within this species with 40 haplotypes spread across the 10 populations sampled within a 4000 km2 region. Phylogenetic analyses showed that haplotypes formed monophyletic groups by the watershed on which they were found, suggesting that watersheds were important historical avenues of gene flow. Genetic distances were strongly related to the geographical distance among all populations, but this relationship was dependent on the scale being considered.}, }
@article {pmid10548718, year = {1999}, author = {Voos, W and Martin, H and Krimmer, T and Pfanner, N}, title = {Mechanisms of protein translocation into mitochondria.}, journal = {Biochimica et biophysica acta}, volume = {1422}, number = {3}, pages = {235-254}, doi = {10.1016/s0304-4157(99)00007-6}, pmid = {10548718}, issn = {0006-3002}, mesh = {Animals ; Biological Transport ; Caenorhabditis elegans ; Carrier Proteins/metabolism ; Cytosol/metabolism ; Evolution, Molecular ; Fungal Proteins/metabolism ; HSP70 Heat-Shock Proteins/metabolism ; Intracellular Membranes/*metabolism ; Membrane Potentials ; Membrane Proteins/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Precursor Protein Import Complex Proteins ; Saccharomyces cerevisiae ; *Saccharomyces cerevisiae Proteins ; }, abstract = {Mitochondrial biogenesis utilizes a complex proteinaceous machinery for the import of cytosolically synthesized preproteins. At least three large multisubunit protein complexes, one in the outer membrane and two in the inner membrane, have been identified. These translocase complexes cooperate with soluble proteins from the cytosol, the intermembrane space and the matrix. The translocation of presequence-containing preproteins through the outer membrane channel includes successive electrostatic interactions of the charged mitochondrial targeting sequence with a chain of import components. Translocation across the inner mitochondrial membrane utilizes the energy of the proton motive force of the inner membrane and the hydrolysis of ATP. The matrix chaperone system of the mitochondrial heat shock protein 70 forms an ATP-dependent import motor by interaction with the polypeptide chain in transit and components of the inner membrane translocase. The precursors of integral inner membrane proteins of the metabolite carrier family interact with newly identified import components of the intermembrane space and are inserted into the inner membrane by a second translocase complex. A comparison of the full set of import components between the yeast Sacccharomyces cerevisiae and the nematode Caenorhabditis elegans demonstrates an evolutionary conservation of most components of the mitochondrial import machinery with a possible greater divergence for the import pathway of the inner membrane carrier proteins.}, }
@article {pmid10546224, year = {1999}, author = {Emel'ianov, VV}, title = {[Hypothetic molecular basis of obligate parasitism of Rickettsiae].}, journal = {Molekuliarnaia biologiia}, volume = {33}, number = {4}, pages = {684-687}, pmid = {10546224}, issn = {0026-8984}, mesh = {DNA, Bacterial/*genetics ; DNA, Mitochondrial/*genetics ; Mitochondria/genetics ; *Phylogeny ; Rickettsiaceae/*genetics ; }, }
@article {pmid10542417, year = {1999}, author = {Boore, JL and Fuerstenberg, SI}, title = {Entamoeba histolytica: a derived, mitochondriate eukaryote?.}, journal = {Trends in microbiology}, volume = {7}, number = {11}, pages = {426-428}, doi = {10.1016/s0966-842x(99)01606-6}, pmid = {10542417}, issn = {0966-842X}, mesh = {Animals ; Cell Nucleus/genetics ; Entamoeba histolytica/*classification/*genetics/metabolism/ultrastructure ; *Eukaryotic Cells ; Mitochondria/*genetics ; Organelles/physiology ; Phylogeny ; }, }
@article {pmid10532800, year = {1999}, author = {}, title = {Proceedings of a joint symposium of the Phycological Society of America, International Society for Evolutionary Protistology and the Society of Protozoologists. Evolution of Mitochondria and Chloroplasts. Flagstaff, Arizona, USA. 1-8 August 1998.}, journal = {The Journal of eukaryotic microbiology}, volume = {46}, number = {4}, pages = {319-449}, pmid = {10532800}, issn = {1066-5234}, mesh = {*Chloroplasts ; *Eukaryotic Cells ; *Mitochondria ; Symbiosis ; }, }
@article {pmid10529522, year = {1999}, author = {Collin, SP and Potter, IC and Braekevelt, CR}, title = {The ocular morphology of the southern hemisphere lamprey geotria australis gray, with special reference to optical specialisations and the characterisation and phylogeny of photoreceptor types.}, journal = {Brain, behavior and evolution}, volume = {54}, number = {2}, pages = {96-118}, doi = {10.1159/000006616}, pmid = {10529522}, issn = {0006-8977}, mesh = {Animals ; Axons/physiology/ultrastructure ; Cornea/physiology/ultrastructure ; Eye/*anatomy &amp; histology/ultrastructure ; Lampreys/*anatomy &amp; histology ; Microscopy, Electron ; *Ocular Physiological Phenomena ; Photoreceptor Cells, Vertebrate/*physiology/ultrastructure ; Phylogeny ; Retina/physiology/ultrastructure ; Retinal Cone Photoreceptor Cells/physiology/ultrastructure ; }, abstract = {This paper describes the ocular morphology of young adults of the southern hemisphere lamprey Geotria australis, the sole representative of the Geotriidae, and makes comparisons with those of holarctic lampreys (Petromyzontidae). As previously reported for the holarctic lamprey Ichthyomyzon unicuspis [Collin and Fritzsch, 1993], the lens of G. australis is non-spherical and possesses a cone-shaped posterior that may be capable of mediating variable focus. The avascular retina of G. australis is well differentiated, containing three retinal ganglion cell populations, three layers of horizontal cells and three photoreceptor types. In contrast to petromyzontids that contain only two photoreceptor types (short and long), G. australis possesses one rod-like (R1) and two cone-like (C1 and C2) photoreceptors. Although the rod-like receptor in G. australis may be homologous with the short receptors of holarctic lampreys, the two cone-like receptors have morphological characteristics that differ markedly from those of the long receptors of their holarctic counterparts. The features which distinguish the two cone-like receptors from those of the long receptor type in holarctic lampreys are the characteristics of the mitochondria and the presence of large amounts of two different types of stored secretory material in the endoplasmic reticulum of the myoid (refractile bodies). The endoplasmic reticulum of each receptor type has a different shape and staining profile and is polymorphic, each showing a continuum of distension. It is proposed that the presence of two cone-like photoreceptors with different characteristics would increase the spectral range of G. australis and thus be of value during the parasitic phase, when this lamprey lives in the surface marine waters. The irideal flap, present in G. australis but not petromyzontids, would assist in reducing intraocular flare during life in surface waters. The results of this study, which are discussed in the context of the proposed evolution of lampreys, emphasise that it is important to take into account the characteristics of the eyes of southern hemisphere lampreys when making generalizations about the eyes of lampreys as a whole.}, }
@article {pmid10527924, year = {1999}, author = {Roger, AJ}, title = {Reconstructing Early Events in Eukaryotic Evolution.}, journal = {The American naturalist}, volume = {154}, number = {S4}, pages = {S146-S163}, doi = {10.1086/303290}, pmid = {10527924}, issn = {1537-5323}, abstract = {Resolving the order of events that occurred during the transition from prokaryotic to eukaryotic cells remains one of the greatest problems in cell evolution. One view, the Archezoa hypothesis, proposes that the endosymbiotic origin of mitochondria occurred relatively late in eukaryotic evolution and that several mitochondrion-lacking protist groups diverged before the establishment of the organelle. Phylogenies based on small subunit ribosomal RNA and several protein-coding genes supported this proposal, placing amitochondriate protists such as diplomonads, parabasalids, and Microsporidia as the earliest diverging eukaryotic lineages. However, trees of other molecules, such as tubulins, heat shock protein 70, TATA box-binding protein, and the largest subunit of RNA polymerase II, indicate that Microsporidia are not deeply branching eukaryotes but instead are close relatives of the Fungi. Furthermore, recent discoveries of mitochondrion-derived genes in the nuclear genomes of entamoebae, Microsporidia, parabasalids, and diplomonads suggest that these organisms likely descend from mitochondrion-bearing ancestors. Although several protist lineages formally remain as candidates for Archezoa, most evidence suggests that the mitochondrial endosymbiosis took place prior to the divergence of all extant eukaryotes. In addition, discoveries of proteobacterial-like nuclear genes coding for cytoplasmic proteins indicate that the mitochondrial symbiont may have contributed more to the eukaryotic lineage than previously thought. As genome sequence data from parabasalids and diplomonads accumulate, it is becoming clear that the last common ancestor of these protist taxa and other extant eukaryotic groups already possessed many of the complex features found in most eukaryotes but lacking in prokaryotes. However, our confidence in the deeply branching position of diplomonads and parabasalids among eukaryotes is weakened by conflicting phylogenies and potential sources of artifact. Our current picture of early eukaryotic evolution is in a state of flux.}, }
@article {pmid10520935, year = {1999}, author = {Pandolfo, M}, title = {Molecular pathogenesis of Friedreich ataxia.}, journal = {Archives of neurology}, volume = {56}, number = {10}, pages = {1201-1208}, doi = {10.1001/archneur.56.10.1201}, pmid = {10520935}, issn = {0003-9942}, mesh = {Friedreich Ataxia/*etiology/*genetics/metabolism ; Humans ; *Iron-Binding Proteins ; Phosphotransferases (Alcohol Group Acceptor)/*genetics ; Frataxin ; }, abstract = {Friedreich ataxia, the most common type of inherited ataxia, is itself caused in most cases by a large expansion of an intronic GAA repeat, resulting in decreased expression of the target frataxin gene. The autosomal recessive inheritance of the disease gives this triplet repeat mutation some unique features of natural history and evolution. Frataxin is a mitochondrial protein that has homologues in yeast and even in gram-negative bacteria. Yeast organisms deficient in the frataxin homologue accumulate iron in mitochondria and show increased sensitivity to oxidative stress. This suggests that Friedreich ataxia is caused by mitochondrial dysfunction and free radical toxicity.}, }
@article {pmid10519246, year = {1999}, author = {Riordan, CE and Langreth, SG and Sanchez, LB and Kayser, O and Keithly, JS}, title = {Preliminary evidence for a mitochondrion in Cryptosporidium parvum: phylogenetic and therapeutic implications.}, journal = {The Journal of eukaryotic microbiology}, volume = {46}, number = {5}, pages = {52S-55S}, pmid = {10519246}, issn = {1066-5234}, support = {AI 43020/AI/NIAID NIH HHS/United States ; }, mesh = {Adenylate Kinase/genetics ; Amino Acid Sequence ; Animals ; Chaperonins/genetics ; Cryptosporidium parvum/drug effects/*genetics/metabolism/*ultrastructure ; DNA, Protozoan/genetics ; Mitochondria/drug effects/*genetics/*metabolism ; Molecular Sequence Data ; Naphthoquinones/pharmacology ; Phylogeny ; Sequence Analysis, DNA ; Valine-tRNA Ligase/genetics ; }, }
@article {pmid10515941, year = {1999}, author = {Marinoni, G and Manuel, M and Petersen, RF and Hvidtfeldt, J and Sulo, P and Piskur, J}, title = {Horizontal transfer of genetic material among Saccharomyces yeasts.}, journal = {Journal of bacteriology}, volume = {181}, number = {20}, pages = {6488-6496}, pmid = {10515941}, issn = {0021-9193}, mesh = {Cell Nucleus ; Chimera/*genetics ; Chromosomes, Fungal ; Crosses, Genetic ; DNA, Fungal ; Ethyl Methanesulfonate ; *Evolution, Molecular ; *Gene Transfer, Horizontal ; Haploidy ; Mitochondria/genetics ; Models, Genetic ; Mutagenesis ; Mutagens ; Pheromones ; Saccharomyces/classification/*genetics ; Saccharomyces cerevisiae/classification/genetics ; Zygote ; }, abstract = {The genus Saccharomyces consists of several species divided into the sensu stricto and the sensu lato groups. The genomes of these species differ in the number and organization of nuclear chromosomes and in the size and organization of mitochondrial DNA (mtDNA). In the present experiments we examined whether these yeasts can exchange DNA and thereby create novel combinations of genetic material. Several putative haploid, heterothallic yeast strains were isolated from different Saccharomyces species. All of these strains secreted an a- or alpha-like pheromone recognized by S. cerevisiae tester strains. When interspecific crosses were performed by mass mating between these strains, hybrid zygotes were often detected. In general, the less related the two parental species were, the fewer hybrids they gave. For some crosses, viable hybrids could be obtained by selection on minimal medium and their nuclear chromosomes and mtDNA were examined. Often the frequency of viable hybrids was very low. Sometimes putative hybrids could not be propagated at all. In the case of sensu stricto yeasts, stable viable hybrids were obtained. These contained both parental sets of chromosomes but mtDNA from only one parent. In the case of sensu lato hybrids, during genetic stabilization one set of the parental chromosomes was partially or completely lost and the stable mtDNA originated from the same parent as the majority of the nuclear chromosomes. Apparently, the interspecific hybrid genome was genetically more or less stable when the genetic material originated from phylogenetically relatively closely related parents; both sets of nuclear genetic material could be transmitted and preserved in the progeny. In the case of more distantly related parents, only one parental set, and perhaps some fragments of the other one, could be found in genetically stabilized hybrid lines. The results obtained indicate that Saccharomyces yeasts have a potential to exchange genetic material. If Saccharomyces isolates could mate freely in nature, horizontal transfer of genetic material could have occurred during the evolution of modern yeast species.}, }
@article {pmid10508728, year = {1999}, author = {Andersson, SG and Kurland, CG}, title = {Origins of mitochondria and hydrogenosomes.}, journal = {Current opinion in microbiology}, volume = {2}, number = {5}, pages = {535-541}, doi = {10.1016/s1369-5274(99)00013-2}, pmid = {10508728}, issn = {1369-5274}, mesh = {*Evolution, Molecular ; Genome, Bacterial ; Hydrogen/*metabolism ; Mitochondria/*genetics ; Organelles/*genetics ; }, abstract = {Complete genome sequences for many mitochondria, as well as for some bacteria, together with the nuclear genome sequence of yeast have provided a coherent view of the origin of mitochondria. In particular, conventional phylogenetic reconstructions with genes coding for proteins active in energy metabolism and translation have confirmed the simplest version of the endosymbiosis hypothesis. In contrast, the hydrogen and the syntrophy hypotheses for the origin of mitochondria do not receive support from the available data. It remains to be seen how the evolution of hydrogenosomes is related to that of mitochondria.}, }
@article {pmid10505415, year = {1999}, author = {O'Kelly, CJ and Farmer, MA and Nerad, TA}, title = {Ultrastructure of Trimastix pyriformis (Klebs) Bernard et al.: similarities of Trimastix species with retortamonad and jakobid flagellates.}, journal = {Protist}, volume = {150}, number = {2}, pages = {149-162}, doi = {10.1016/S1434-4610(99)70018-0}, pmid = {10505415}, issn = {1434-4610}, mesh = {Animals ; Biological Evolution ; Cell Division ; Eukaryota/*classification/*ultrastructure ; Fresh Water/parasitology ; Interphase ; Microscopy, Electron ; Phylogeny ; Species Specificity ; }, abstract = {Trimastix pyriformis (Klebs 1893) Bernard et al. 1999, is a quadriflagellate, free-living, bacterivorous heterotrophic nanoflagellate from anoxic freshwaters that lacks mitochondria. Monoprotist cultures of this species contained naked trophic cells with anterior flagellar insertion and a conspicuous ventral groove. Bacteria were ingested at the posterior end of the ventral groove, but there was no persistent cytopharyngeal complex. The posterior flagellum resided in this groove, and bore two prominent vanes. A Golgi body (dictyosome) was present adjacent to the flagellar insertion. The kinetid consisted of four basal bodies, four microtubular roots, and associated fibers and bands. Duplicated kinetids, each with four basal bodies and microtubular root templates, appeared at the poles of the open mitotic spindle. Trimastix pyriformis is distinguishable from other Trimastix species on the basis of external morphology, kinetid architecture and the distribution of endomembranes. Trimastix species are most similar to jakobid flagellates, especially Malawimonas jakobiformis, and to species of the retortamonad genus Chilomastix. Retortamonads may have evolved from a Trimastix-like ancestor through loss of "canonical" (easily seen with electron microscopy) endomembrane systems and elaboration of cytoskeletal elements associated with the cytostome/cytopharynx complex.}, }
@article {pmid10505262, year = {1999}, author = {Emel'ianov, VV and Sinitsyn, BV}, title = {[Phylogenetic analysis based on groE shows the closest evolutionary relationship between mitochondria and Rickettsia].}, journal = {Genetika}, volume = {35}, number = {6}, pages = {733-743}, pmid = {10505262}, issn = {0016-6758}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/*genetics ; Chaperonins ; DNA, Mitochondrial/*genetics ; Escherichia coli Proteins ; *Evolution, Molecular ; Heat-Shock Proteins/chemistry/*genetics ; Mitochondria/*metabolism ; Molecular Sequence Data ; Operon ; *Phylogeny ; Rickettsia prowazekii/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {The nucleotide sequence of the groE operon of Rickettsia prowazekii, the obligate intracellular parasite of eukaryotes, was determined. The alignment of DNA-inferred amino acid sequences of the Hsp10 and Hsp60 heat-shock proteins with bacterial and mitochondrial homologues revealed the presence within Hsp60 of signatures shared by mitochondria and rickettsiae. Phylogenetic analysis demonstrated that heat-shock proteins of R. prowazekii are the earliest and the least diverging homologues within the family Rickettsiaceae--a sister group to the monophyletic clade of mitochondria. These results are in good agreement with the data obtained when using other molecular chronometers and show the closest relationship between mitochondria and Rickettsia. The possible nature of obligate intracellular parasitism of rickettsiae has been considered on the basis of the assumption that they and mitochondria could have a common evolutionary origin.}, }
@article {pmid10503531, year = {1999}, author = {Funke, RP and Kovar, JL and Logsdon, JM and Corrette-Bennett, JC and Straus, DR and Weeks, DP}, title = {Nucleus-encoded, plastid-targeted acetolactate synthase genes in two closely related chlorophytes, Chlamydomonas reihardtii and Volvox carteri: phylogenetic origins and recent insertion of introns.}, journal = {Molecular &amp; general genetics : MGG}, volume = {262}, number = {1}, pages = {12-21}, doi = {10.1007/s004380051054}, pmid = {10503531}, issn = {0026-8925}, mesh = {Acetolactate Synthase/classification/*genetics/metabolism ; Amino Acids/biosynthesis ; Animals ; Cell Nucleus/*genetics ; Chlamydomonas reinhardtii/classification/genetics ; Chlorophyta/classification/*genetics ; Chloroplasts/*enzymology ; *Evolution, Molecular ; Exons ; Genes, Bacterial ; Introns ; Mutagenesis, Insertional ; RNA Splicing ; }, abstract = {Acetolactate synthase (ALS) catalyzes the first committed step in the synthesis of branched-chain amino acids. In green plants and fungi, ALS is encoded by a nuclear gene whose product is targeted to plastids (in plants) or to mitochondria (in fungi). In red algae, the gene is plastid-encoded. We have determined the complete sequence of nucleus-encoded ALS genes from the green algae Chlamydomonas reinhardtii and Volvox carteri. Phylogenetic analyses of the ALS gene family indicate that the ALS genes of green algae and plants are closely related, sharing a recent common ancestor. Furthermore, although these genes are clearly of eubacterial origin, a relationship to the ALS genes of red algae and cyanobacteria (endosymbiotic precursors of plastids) is only weakly indicated. The algal ALS genes are distinguished from their homologs in higher plants by the fact that they are interrupted by numerous spliceosomal introns; plant ALS genes completely lack introns. The restricted phylogenetic distribution of these introns suggests that they were inserted recently, after the divergence of these green algae from plants. Two introns in the Volvox ALS gene, not found in the Chlamydomonas gene, are positioned precisely at sites which resemble "proto-splice" sequences in the Chlamydomonas gene.}, }
@article {pmid10501981, year = {1999}, author = {Decker, WK and Bowles, KR and Schatte, EC and Towbin, JA and Craigen, WJ}, title = {Revised fine mapping of the human voltage-dependent anion channel loci by radiation hybrid analysis.}, journal = {Mammalian genome : official journal of the International Mammalian Genome Society}, volume = {10}, number = {10}, pages = {1041-1042}, doi = {10.1007/s003359901158}, pmid = {10501981}, issn = {0938-8990}, support = {1P30-HD27823/HD/NICHD NIH HHS/United States ; R01 GM055713-02/GM/NIGMS NIH HHS/United States ; R01 HL53392/HL/NHLBI NIH HHS/United States ; }, mesh = {Chromosome Mapping ; Chromosomes, Human, Pair 10 ; Chromosomes, Human, Pair 5 ; Chromosomes, Human, Pair 8 ; Evolution, Molecular ; Genetic Linkage ; Genetic Markers/genetics ; Humans ; Ion Channels/*genetics ; Lod Score ; Mitochondria/metabolism ; Molecular Sequence Data ; Porins/*genetics ; Protein Isoforms/genetics ; Voltage-Dependent Anion Channels ; }, }
@article {pmid10497022, year = {1999}, author = {Schulte, U and Haupt, V and Abelmann, A and Fecke, W and Brors, B and Rasmussen, T and Friedrich, T and Weiss, H}, title = {A reductase/isomerase subunit of mitochondrial NADH:ubiquinone oxidoreductase (complex I) carries an NADPH and is involved in the biogenesis of the complex.}, journal = {Journal of molecular biology}, volume = {292}, number = {3}, pages = {569-580}, doi = {10.1006/jmbi.1999.3096}, pmid = {10497022}, issn = {0022-2836}, mesh = {Electron Spin Resonance Spectroscopy ; Electron Transport ; Electron Transport Complex I ; Electrophoresis, Polyacrylamide Gel ; Gene Deletion ; Kinetics ; Mitochondria/*enzymology ; NAD/chemistry ; NAD(P)H Dehydrogenase (Quinone)/*biosynthesis ; NADH, NADPH Oxidoreductases/*chemistry/genetics ; NADP/*chemistry ; Neurospora crassa/*enzymology/genetics ; Oxidation-Reduction ; Phylogeny ; Protein Binding ; Spectrophotometry ; }, abstract = {Respiratory chains of bacteria and mitochondria contain closely related forms of the proton-pumping NADH:ubiquinone oxidoreductase, or complex I. The bacterial complex I consists of 14 subunits, whereas the mitochondrial complex contains some 25 extra subunits in addition to the homologues of the bacterial subunits. One of these extra subunits with a molecular mass of 40 kDa belongs to a heterogeneous family of reductases/isomerases with a conserved nucleotide binding site. We deleted this subunit in Neurospora crassa by gene disruption. In the mutant nuo 40, a complex I lacking the 40 kDa subunit is assembled. The mutant complex I does not contain tightly bound NADPH present in wild-type complex I. This NADPH cofactor is not connected to the respiratory electron pathway of complex I. The mutant complex has normal NADH dehydrogenase activity and contains the redox groups known for wild-type complex I, one flavin mononucleotide and four iron-sulfur clusters detectable by electron paramagnetic resonance spectroscopy. In the mutant complex these groups are all readily reduced by NADH. However, the mutant complex is not capable of reducing ubiquinone. A recently described redox group identified in wild-type complex I by UV-visible spectroscopy is not detectable in the mutant complex. We propose that the reductase/isomerase subunit with its NADPH cofactor takes part in the biosynthesis of this new redox group.}, }
@article {pmid10494626, year = {2000}, author = {Soltys, BJ and Gupta, RS}, title = {Mitochondrial proteins at unexpected cellular locations: export of proteins from mitochondria from an evolutionary perspective.}, journal = {International review of cytology}, volume = {194}, number = {}, pages = {133-196}, doi = {10.1016/s0074-7696(08)62396-7}, pmid = {10494626}, issn = {0074-7696}, mesh = {Animals ; Apoptosis ; Bacteria/metabolism ; Biological Evolution ; Biological Transport, Active ; Endoplasmic Reticulum/metabolism ; Humans ; Membrane Fusion ; Microscopy, Immunoelectron ; Mitochondria/genetics/*metabolism ; Molecular Chaperones/metabolism ; Proteins/*metabolism ; Signal Transduction ; Symbiosis ; }, abstract = {Researchers in a wide variety of unrelated areas studying functions of different proteins are unexpectedly finding that their proteins of interest are actually mitochondrial proteins, although functions would appear to be extramitochondrial. We review the leading current examples of mitochondrial macromolecules indicated to be also present outside of mitochondria that apparently exit from mitochondria to arrive at their destinations. Mitochondrial chaperones, which have been implicated in growth and development, autoimmune diseases, cell mortality, antigen presentation, apoptosis, and resistance to antimitotic drugs, provide some of the best studied examples pointing to roles for mitochondria and mitochondrial proteins in diverse cellular phenomena. To explain the observations, we propose that specific export mechanisms exist by which certain proteins exit mitochondria, allowing these proteins to have additional functions at specific extramitochondrial sites. Several possible mechanisms by which mitochondrial proteins could be exported are discussed. Gram-negative proteobacteria, from which mitochondria evolved, contain a number of different mechanisms for protein export. It is likely that mitochondria either retained or evolved export mechanisms for certain specific proteins.}, }
@article {pmid10494622, year = {1999}, author = {Coleman, AW and Nerozzi, AM}, title = {Temporal and spatial coordination of cells with their plastid component.}, journal = {International review of cytology}, volume = {193}, number = {}, pages = {125-164}, doi = {10.1016/s0074-7696(08)61780-5}, pmid = {10494622}, issn = {0074-7696}, abstract = {Careful coordination of cell multiplication with plastid multiplication and partition at cytokinesis is required to maintain the universal presence of plastids in the major photosynthetic lines of evolution. However, no cell cycle control points are known that might underlie this coordination. We review common properties, and their variants, of plastids and plastid DNA in germline, multiplying, and mature cells of phyla capable of photosynthesis. These suggest a basic level of control dictated perhaps by the same mechanisms that coordinate cell size with the nuclear ploidy level. No protein synthesis within the plastid appears to be necessary for this system to operate successfully at the level that maintains the presence of plastids in cells. A second, and superimposed, level of controls dictates expansion of the plastid in both size and number in response to signals associated with differentiation and with the environment. We also compare the germane properties of plastids with those of mitochondria. With the advent of genomics and new cell and molecular techniques, the players in these control mechanisms should now be identifiable.}, }
@article {pmid10491312, year = {1999}, author = {Gudayol, M and Vidal-Taboada, JM and Usac, EF and Costa, A and Cristòbal, P and dell'Anna, C and Oliva, R and Gomis, R}, title = {Detection of a new variant of the mitochondrial glycerol-3-phosphate dehydrogenase gene in Spanish type 2 DM patients.}, journal = {Biochemical and biophysical research communications}, volume = {263}, number = {2}, pages = {439-445}, doi = {10.1006/bbrc.1999.1394}, pmid = {10491312}, issn = {0006-291X}, mesh = {Base Sequence ; Binding Sites/genetics ; Diabetes Mellitus, Type 2/enzymology/etiology/*genetics ; Exons ; Female ; Flavin-Adenine Dinucleotide/metabolism ; Flavoproteins/*genetics ; Genetic Testing ; *Genetic Variation ; Glycerolphosphate Dehydrogenase/*genetics ; Humans ; Introns ; Male ; Meiosis ; Mitochondria/enzymology/*genetics ; Molecular Sequence Data ; Pedigree ; Polymorphism, Single-Stranded Conformational ; Pseudogenes ; Reverse Transcriptase Polymerase Chain Reaction ; Spain ; Untranslated Regions ; White People/genetics ; }, abstract = {To evaluate if potential defects in the FAD-binding domain of the mitochondrial glycerol-3-phosphate dehydrogenase (mGPDH) gene could contribute to susceptibility to type 2 diabetes mellitus, we have screened 151 type 2 DM patients for mutations using PCR single-strand conformational polymorphism. Both a single substitution (T to A) at position 18 and a 6-base-pair deletion (TTTTAA) at position 26 of intron 3 have been detected in five type 2 DM patients and in one control subject. The evolution time of diabetes was longer in patients with these mutations than in patients without (24.2 +/- 11.1 vs 12.6 +/- 8.7 years, p < 0.02). These mutations generate a cryptic site that may have functional significance in the correct mechanism of the FAD-binding domain. In the process of PCR amplification of the mGPDH gene we also unexpectedly amplified the mGPDH retropseudogene. Subsequently, we decided to further characterize and completely sequence 2213 bp of this mGPDH retropseudogene. Our results suggest that two previously reported mGPDH pseudogene partial sequences may be identical copies of the mGPDH gene inserted in two different genomic locations and provide information about the alternative 5'- and 3'-untranslated regions. The data obtained are also important in order to avoid artifactual amplification of the mGPDH pseudogene in the process of screening for mGPDH mutations in diabetic patients.}, }
@article {pmid10488338, year = {1999}, author = {Walther, TC and Kennell, JC}, title = {Linear mitochondrial plasmids of F. oxysporum are novel, telomere-like retroelements.}, journal = {Molecular cell}, volume = {4}, number = {2}, pages = {229-238}, doi = {10.1016/s1097-2765(00)80370-6}, pmid = {10488338}, issn = {1097-2765}, mesh = {Base Sequence ; Cloning, Molecular ; DNA, Complementary ; DNA, Fungal/chemistry/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Fusarium/*genetics ; Genome, Fungal ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Plants/microbiology ; Plasmids/*genetics ; RNA/chemistry/*genetics ; RNA, Fungal/chemistry/genetics ; RNA, Mitochondrial ; Restriction Mapping ; Reverse Transcriptase Polymerase Chain Reaction ; Telomere/*genetics ; }, abstract = {Diverse types of linear RNA and DNA autonomously replicating genetic elements exist in prokaryotic and eukaryotic hosts, yet linear elements that replicate by reverse transcription have not been identified. Here, we report the sequence and organization of two linear mitochondrial plasmids of the fungal plant pathogen F. oxysporum and the characterization of a plasmid-associated reverse transcriptase activity. Plasmids pFOXC2 and pFOXC3 are 1.9 kb in length and have a "clothespin" genomic structure, which includes a terminal hairpin and a telomere-like iteration of a 5 bp sequence at the other terminus. The retroplasmid replication cycle involves novel strategies for copying terminal sequences, which may provide clues concerning the origin of telomerase as well as the evolution of linear DNAs.}, }
@article {pmid10488229, year = {1999}, author = {Smith, HB}, title = {Interorganellar communication and the onus of being eukaryotic.}, journal = {The Plant cell}, volume = {11}, number = {9}, pages = {1605-1608}, pmid = {10488229}, issn = {1040-4651}, mesh = {*Biological Evolution ; Cell Nucleus/physiology ; Eukaryotic Cells/*cytology/ultrastructure ; Mitochondria/genetics/physiology ; Plastids/genetics/physiology ; Signal Transduction/*genetics ; Symbiosis ; }, }
@article {pmid10486982, year = {1999}, author = {Horner, DS and Hirt, RP and Embley, TM}, title = {A single eubacterial origin of eukaryotic pyruvate: ferredoxin oxidoreductase genes: implications for the evolution of anaerobic eukaryotes.}, journal = {Molecular biology and evolution}, volume = {16}, number = {9}, pages = {1280-1291}, doi = {10.1093/oxfordjournals.molbev.a026218}, pmid = {10486982}, issn = {0737-4038}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Anaerobiosis ; Animals ; Base Sequence ; Clostridium/enzymology/genetics ; DNA Primers/genetics ; Diplomonadida/enzymology/genetics ; Eukaryotic Cells ; *Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Genes, Bacterial ; Genes, Protozoan ; Giardia lamblia/enzymology/genetics ; Ketone Oxidoreductases/*genetics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Pyruvate Synthase ; }, abstract = {The iron sulfur protein pyruvate: ferredoxin oxidoreductase (PFO) is central to energy metabolism in amitochondriate eukaryotes, including those with hydrogenosomes. Thus, revealing the evolutionary history of PFO is critical to understanding the origin(s) of eukaryote anaerobic energy metabolism. We determined a complete PFO sequence for Spironucleus barkhanus, a large fragment of a PFO sequence from Clostridium pasteurianum, and a fragment of a new PFO from Giardia lamblia. Phylogenetic analyses of eubacterial and eukaryotic PFO genes suggest a complex history for PFO, including possible gene duplications and horizontal transfers among eubacteria. Our analyses favor a common origin for eukaryotic cytosolic and hydrogenosomal PFOs from a single eubacterial source, rather than from separate horizontal transfers as previously suggested. However, with the present sampling of genes and species, we were unable to infer a specific eubacterial sister group for eukaryotic PFO. Thus, we find no direct support for the published hypothesis that the donor of eukaryote PFO was the common alpha-proteobacterial ancestor of mitochondria and hydrogenosomes. We also report that several fungi and protists encode proteins with PFO domains that are likely monophyletic with PFOs from anaerobic protists. In Saccharomyces cerevisiae, PFO domains combine with fragments of other redox proteins to form fusion proteins which participate in methionine biosynthesis. Our results are consistent with the view that PFO, an enzyme previously considered to be specific to energy metabolism in amitochondriate protists, was present in the common ancestor of contemporary eukaryotes and was retained, wholly or in part, during the evolution of oxygen-dependent and mitochondrion-bearing lineages.}, }
@article {pmid10480381, year = {1999}, author = {Ikeda, TM and Gray, MW}, title = {Identification and characterization of T3/T7 bacteriophage-like RNA polymerase sequences in wheat.}, journal = {Plant molecular biology}, volume = {40}, number = {4}, pages = {567-578}, pmid = {10480381}, issn = {0167-4412}, mesh = {Amino Acid Sequence ; Bacteriophage T3/*enzymology ; Bacteriophage T7/*enzymology ; Base Sequence ; Cloning, Molecular ; DNA-Directed RNA Polymerases/*genetics ; Genes, Plant/genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/isolation &amp; purification ; Sequence Alignment ; Sequence Analysis ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Triticum/chemistry/enzymology/*genetics ; }, abstract = {Using PCR-based methods, we assembled two wheat cDNA sequences, wheat-G and wheat-C, that encode T3/T7 bacteriophage-like RNA polymerases (RNAPs) sharing 45% amino acid identity. In phylogenetic analyses using maximum likelihood, parsimony and distance methods, the predicted protein sequence of wheat-G (1005 amino acids, 113 kDa) clusters with sequences of previously assigned mitochondrial RNAPs from dicotyledonous plants (Arabidopsis thaliana, Chenopodium album); likewise, in such analyses, the wheat-C sequence (949 amino acids, 107 kDa) affiliates specifically with the Arabidopsis sequence that encodes a phage-like RNAP thought to function in chloroplasts. To confirm biochemically the assignment of the gene encoding the putative wheat mitochondrial RNAP, we isolated a ca. 100 kDa wheat mitochondrial protein that is enriched in fractions displaying specific in vitro transcription activity and that reacts with an antibody raised against a recombinant maize phage-type RNAP. Internal peptide sequence information obtained from the 100-kDa polypeptide revealed that it corresponds to the predicted wheat-G cDNA sequence, providing direct evidence that the wheat-G gene (which we propose to call RpoTm) encodes the wheat mitochondrial RNAP.}, }
@article {pmid10468587, year = {1999}, author = {Schilke, B and Voisine, C and Beinert, H and Craig, E}, title = {Evidence for a conserved system for iron metabolism in the mitochondria of Saccharomyces cerevisiae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {96}, number = {18}, pages = {10206-10211}, pmid = {10468587}, issn = {0027-8424}, support = {R01 GM027870/GM/NIGMS NIH HHS/United States ; GM27870/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics ; Cell Fractionation ; Fungal Proteins/chemistry/*genetics ; *Genes, Fungal ; Genes, Lethal ; HSP70 Heat-Shock Proteins/genetics ; Iron/*metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins ; Molecular Chaperones/*genetics ; Molecular Sequence Data ; Saccharomyces cerevisiae/genetics/*physiology/ultrastructure ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {nifU of nitrogen-fixing bacteria is involved in the synthesis of the Fe-S cluster of nitrogenase. In a synthetic lethal screen with the mitochondrial heat shock protein (HSP)70, SSQ1, we identified a gene of Saccharomyces cerevisiae, NFU1, which encodes a protein with sequence identity to the C-terminal domain of NifU. Two other yeast genes were found to encode proteins related to the N-terminal domain of bacterial NifU. They have been designated ISU1 and ISU2. Isu1, Isu2, and Nfu1 are located in the mitochondrial matrix. ISU genes of yeast carry out an essential function, because a Deltaisu1Deltaisu2 strain is inviable. Growth of Deltanfu1Delta isu1 cells is significantly compromised, allowing assessment of the physiological roles of Nfu and Isu proteins. Mitochondria from Deltanfu1Deltaisu1 cells have decreased activity of several respiratory enzymes that contain Fe-S clusters. As a result, Deltanfu1Deltaisu1 cells grow poorly on carbon sources requiring respiration. Deltanfu1Deltaisu1 cells also accumulate abnormally high levels of iron in their mitochondria, similar to Deltassq1 cells, indicating a role for these proteins in iron metabolism. We suggest that NFU1 and ISU1 gene products play a role in iron homeostasis, perhaps in assembly, insertion, and/or repair of mitochondrial Fe-S clusters. The conservation of these protein domains in many organisms suggests that this role has been conserved throughout evolution.}, }
@article {pmid10467746, year = {1999}, author = {Vellai, T and Vida, G}, title = {The origin of eukaryotes: the difference between prokaryotic and eukaryotic cells.}, journal = {Proceedings. Biological sciences}, volume = {266}, number = {1428}, pages = {1571-1577}, pmid = {10467746}, issn = {0962-8452}, mesh = {Animals ; *Biological Evolution ; DNA/genetics ; Eukaryotic Cells/*classification ; Genome ; Models, Genetic ; Phylogeny ; Prokaryotic Cells/*classification ; }, abstract = {Eukaryotes have long been thought to have arisen by evolving a nucleus, endomembrane, and cytoskeleton. In contrast, it was recently proposed that the first complex cells, which were actually proto-eukaryotes, arose simultaneously with the acquisition of mitochondria. This so-called symbiotic association hypothesis states that eukaryotes emerged when some ancient anaerobic archaebacteria (hosts) engulfed respiring alpha-proteobacteria (symbionts), which evolved into the first energy-producing organelles. Therefore, the intracellular compartmentalization of the energy-converting metabolism that was bound originally to the plasma membrane appears to be the key innovation towards eukaryotic genome and cellular organization. The novel energy metabolism made it possible for the nucleotide synthetic apparatus of cells to be no longer limited by subsaturation with substrates and catalytic components. As a consequence, a considerable increase has occurred in the size and complexity of eukaryotic genomes, providing the genetic basis for most of the further evolutionary changes in cellular complexity. On the other hand, the active uptake of exogenous DNA, which is general in bacteria, was no longer essential in the genome organization of eukaryotes. The mitochondrion-driven scenario for the first eukaryotes explains the chimera-like composition of eukaryotic genomes as well as the metabolic and cellular organization of eukaryotes.}, }
@article {pmid10461383, year = {1999}, author = {Blanchard, JL and Hicks, JS}, title = {The non-photosynthetic plastid in malarial parasites and other apicomplexans is derived from outside the green plastid lineage.}, journal = {The Journal of eukaryotic microbiology}, volume = {46}, number = {4}, pages = {367-375}, doi = {10.1111/j.1550-7408.1999.tb04615.x}, pmid = {10461383}, issn = {1066-5234}, support = {R01-GM36827/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Apicomplexa/genetics ; Base Sequence ; Chromosome Mapping ; *Evolution, Molecular ; Genetic Code ; Molecular Sequence Data ; Photosynthesis ; Phylogeny ; Plasmodium falciparum/*genetics/ultrastructure ; Plastids/*genetics ; RNA, Transfer, Ile/genetics ; RNA, Transfer, Met/genetics ; Ribosomal Proteins/genetics ; }, abstract = {The discovery of a non-photosynthetic plastid genome in Plasmodium falciparum and other apicomplexans has provided a new drug target, but the evolutionary origin of the plastid has been muddled by the lack of characters, that typically define major plastid lineages. To clarify the ancestry of the plastid, we undertook a comprehensive analysis of all genomic characters shared by completely sequenced plastid genomes. Cladistic analysis of the pattern of plastid gene loss and gene rearrangements suggests that the apicomplexan plastid is derived from an ancestor outside of the green plastid lineage. Phylogenetic analysis of primary sequence data (DNA and amino acid characters) produces results that are generally independent of the analytical method, but similar genes (i.e., rpoB and rpoC) give similar topologies. The conflicting phylogenies in primary sequence data sets make it difficult to determine the the exact origin of the apicomplexan plastid and the apparent artifactual association of apicomplexan and euglenoid sequences suggests that DNA sequence data may be an inappropriate set of characters to address this phylogenetic question. At present we cannot reject our null hypothesis that the apicomplexan plastid is derived from a shared common ancestor between apicomplexans and dinoflagellates. During the analysis, we noticed that the Plasmodium tRNA-Met is probably tRNA-fMet and the tRNA-fMet is probably tRNA-Ile. We suggest that P. falciparum has lost the elongator type tRNA-Met and that similar to metazoan mitochondria there is only one species of methionine tRNA. In P. falciparum, this has been accomplished by recruiting the fMet-type tRNA to dually function in initiation and elongation. The tRNA-Ile has an unusual stem-loop in the variable region. The insertion in this region appears to have occurred after the primary origin of the plastid and further supports the monophyletic ancestory of plastids.}, }
@article {pmid10461380, year = {1999}, author = {Lang, BF and Seif, E and Gray, MW and O'Kelly, CJ and Burger, G}, title = {A comparative genomics approach to the evolution of eukaryotes and their mitochondria.}, journal = {The Journal of eukaryotic microbiology}, volume = {46}, number = {4}, pages = {320-326}, doi = {10.1111/j.1550-7408.1999.tb04611.x}, pmid = {10461380}, issn = {1066-5234}, mesh = {Animals ; Base Sequence ; Chromosome Mapping ; Conserved Sequence ; DNA, Mitochondrial/*genetics ; Databases, Factual ; Endoribonucleases/chemistry/genetics ; Eukaryotic Cells/*physiology ; *Evolution, Molecular ; *Genome ; Genome, Fungal ; Mitochondria/*genetics ; Molecular Sequence Data ; Organelles/genetics ; Phylogeny ; RNA, Catalytic/chemistry/genetics ; Ribonuclease P ; Ribosomal Proteins/genetics ; Sequence Analysis, DNA ; }, abstract = {The Organelle Genome Megasequencing Program (OGMP) investigates mitochondrial genome diversity and evolution by systematically determining the complete mitochondrial DNA (mtDNA) sequences of a phylogenetically broad selection of protists. The mtDNAs of lower fungi and choanoflagellates are being analyzed by the Fungal Mitochondrial Genome Project (FMGP), a sister project to the OGMP. Some of the most interesting protists include the jakobid flagellates Reclinomonas americana, Malawimonas jakobiformis, and Jakoba libera, which share ultrastructural similarities with amitochondriate retortamonads, and harbor mitochondrial genes not seen before in mtDNAs of other organisms. In R. americana and J. libera, gene clusters are found that resemble, to an unprecedented degree, the contiguous ribosomal protein operons str, S10, spc, and alpha of eubacteria. In addition, their mtDNAs code for an RNase P RNA that displays all the elements of a bacterial minimum consensus structure. This structure has been instrumental in detecting the rnpB gene in additional protists. Gene repertoire and gene order comparisons as well as multiple-gene phylogenies support the view of a single endosymbiotic origin of mitochondria, whose closest extant relatives are Rickettsia-type alpha-Proteobacteria.}, }
@article {pmid10461205, year = {1999}, author = {Race, HL and Herrmann, RG and Martin, W}, title = {Why have organelles retained genomes?.}, journal = {Trends in genetics : TIG}, volume = {15}, number = {9}, pages = {364-370}, doi = {10.1016/s0168-9525(99)01766-7}, pmid = {10461205}, issn = {0168-9525}, mesh = {*Biological Evolution ; Genome ; Models, Biological ; Organelles/*genetics/metabolism ; Oxidation-Reduction ; Plastids/genetics/metabolism ; Plastoquinone/metabolism ; Signal Transduction ; }, abstract = {The observation that chloroplasts and mitochondria have retained relics of eubacterial genomes and a protein-synthesizing machinery has long puzzled biologists. If most genes have been transferred from organelles to the nucleus during evolution, why not all? What selective pressure maintains genomes in organelles? Electron transport through the photosynthetic and respiratory membranes is a powerful - but dangerous - source of energy. Recent evidence suggests that organelle genomes have persisted because structural proteins that maintain redox balance within bioenergetic membranes must be synthesized when and where they are needed, to counteract the potentially deadly side effects of ATP-generating electron transport.}, }
@article {pmid10458912, year = {1999}, author = {Herrnstadt, C and Clevenger, W and Ghosh, SS and Anderson, C and Fahy, E and Miller, S and Howell, N and Davis, RE}, title = {A novel mitochondrial DNA-like sequence in the human nuclear genome.}, journal = {Genomics}, volume = {60}, number = {1}, pages = {67-77}, doi = {10.1006/geno.1999.5907}, pmid = {10458912}, issn = {0888-7543}, mesh = {Cell Nucleus/metabolism ; Chromosome Mapping ; Chromosomes, Bacterial/genetics ; Chromosomes, Human, Pair 1/genetics ; DNA/chemistry/*genetics ; DNA, Mitochondrial/chemistry/*genetics ; Evolution, Molecular ; Gene Dosage ; Gene Expression ; Genetic Variation ; Genome, Human ; Genomic Library ; Humans ; Hybrid Cells ; Mitochondria/genetics ; Molecular Sequence Data ; Sequence Analysis, DNA ; Tumor Cells, Cultured ; }, abstract = {We describe here a nuclear mitochondrial DNA-like sequence (numtDNA) that is nearly identical in sequence to a continuous 5842 bp segment of human mitochondrial DNA (mtDNA) that spans nucleotide positions 3914 to 9755. On the basis of evolutionary divergence among modern primates, this numtDNA molecule appears to represent mtDNA from a hominid ancestor that has been translocated to the nuclear genome during the recent evolution of humans. This numtDNA sequence harbors synonymous and nonsynonymous nucleotide substitutions relative to the authentic human mtDNA sequence, including an array of substitutions that was previously found in the cytochrome c oxidase subunit 1 and 2 genes. These substitutions were previously reported to occur in human mtDNA, but subsequently contended to be present in a nuclear pseudogene sequence. We now demonstrate their exclusive association with this 5842-bp numtDNA, which we have characterized in its entirety. This numtDNA does not appear to be expressed as a mtDNA-encoded mRNA. It is present in nuclear DNA from human blood donors, in human SH-SY5Y and A431 cell lines, and in rho(0) SH-SY5Y and rho(0) A431 cell lines that were depleted of mtDNA. The existence of human numtDNA sequences with great similarities to human mtDNA renders the amplification of pure mtDNA from cellular DNA very difficult, thereby creating the potential for confounding studies of mitochondrial diseases and population genetics.}, }
@article {pmid10455226, year = {1999}, author = {Shi, NQ and Davis, B and Sherman, F and Cruz, J and Jeffries, TW}, title = {Disruption of the cytochrome c gene in xylose-utilizing yeast Pichia stipitis leads to higher ethanol production.}, journal = {Yeast (Chichester, England)}, volume = {15}, number = {11}, pages = {1021-1030}, doi = {10.1002/(SICI)1097-0061(199908)15:11&lt;1021::AID-YEA429&gt;3.0.CO;2-V}, pmid = {10455226}, issn = {0749-503X}, support = {R01 GM12702/GM/NIGMS NIH HHS/United States ; }, mesh = {Antifungal Agents/chemistry/metabolism ; Base Sequence ; Blotting, Southern ; Cytochrome c Group/chemistry/*genetics ; DNA Primers ; DNA, Fungal/chemistry ; Electron Transport/genetics ; Ethanol/*metabolism ; Fermentation ; Molecular Sequence Data ; Mutation/genetics ; Phylogeny ; Pichia/genetics/growth &amp; development/*metabolism ; Polymerase Chain Reaction ; Salicylamides/chemistry/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Xylose/*metabolism ; }, abstract = {The xylose-utilizing yeast, Pichia stipitis, has a complex respiratory system that contains cytochrome and non-cytochrome alternative electron transport chains in its mitochondria. To gain primary insights into the alternative respiratory pathway, a cytochrome c gene (PsCYC1, Accession No. AF030426) was cloned from wild-type P. stipitis CBS 6054 by cross-hybridization to CYC1 from Saccharomyces cerevisiae. The 333 bp open reading frame of PsCYC1 showed 74% and 69% identity to ScCYC1 and ScCYC7, respectively, at the DNA level. Disruption of PsCYC1 resulted in a mutant that uses the salicylhydroxamic acid (SHAM)-sensitive respiratory pathway for aerobic energy production. Cytochrome spectra revealed that cytochromes c and a.a(3) both disappeared in the cyc1-Delta mutant, so no electron flow through the cytochrome c oxidase was possible. The cyc1-Delta mutant showed 50% lower growth rates than the parent when grown on fermentable sugars. The cyc1-Delta mutant was also found to be unable to grow on glycerol. Interestingly, the mutant produced 0.46 g/g ethanol from 8% xylose, which was 21% higher in yield than the parental strain (0.38 g/g). These results suggested that the alternative pathway might play an important role in supporting xylose conversion to ethanol under oxygen-limiting conditions.}, }
@article {pmid10449446, year = {1999}, author = {Herr, RA and Ajello, L and Taylor, JW and Arseculeratne, SN and Mendoza, L}, title = {Phylogenetic analysis of Rhinosporidium seeberi's 18S small-subunit ribosomal DNA groups this pathogen among members of the protoctistan Mesomycetozoa clade.}, journal = {Journal of clinical microbiology}, volume = {37}, number = {9}, pages = {2750-2754}, pmid = {10449446}, issn = {0095-1137}, mesh = {DNA, Ribosomal/*chemistry ; Microscopy, Electron ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Rhinosporidium/*classification/genetics/ultrastructure ; }, abstract = {For the past 100 years the phylogenetic affinities of Rhinosporidium seeberi have been controversial. Based on its morphological features, it has been classified as a protozoan or as a member of the kingdom Fungi. We have amplified and sequenced nearly a full-length 18S small-subunit (SSU) ribosomal DNA (rDNA) sequence from R. seeberi. Using phylogenetic analysis, by parsimony and distance methods, of R. seeberi's 18S SSU rDNA and that of other eukaryotes, we found that this enigmatic pathogen of humans and animals clusters with a novel group of fish parasites referred to as the DRIP clade (Dermocystidium, rossete agent, Ichthyophonus, and Psorospermium), near the animal-fungal divergence. Our phylogenetic analyses also indicate that R. seeberi is the sister taxon of the two Dermocystidium species used in this study. This molecular affinity is remarkable since members of the genus Dermocystidium form spherical structures in infected hosts, produce endospores, have not been cultured, and possess mitochondria with flat cristae. With the addition of R. seeberi to this clade, the acronym DRIP is no longer appropriate. We propose to name this monophyletic clade Mesomycetozoa to reflect the group's phylogenetic association within the Eucarya.}, }
@article {pmid10447674, year = {1999}, author = {Pineda, AO and Ellington, WR}, title = {Structural and functional implications of the amino acid sequences of dimeric, cytoplasmic and octameric mitochondrial creatine kinases from a protostome invertebrate.}, journal = {European journal of biochemistry}, volume = {264}, number = {1}, pages = {67-73}, doi = {10.1046/j.1432-1327.1999.00577.x}, pmid = {10447674}, issn = {0014-2956}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Creatine Kinase/*chemistry ; Cytoplasm/*enzymology ; DNA Primers ; DNA, Complementary ; Dimerization ; Mitochondria/*enzymology ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Polychaeta/*enzymology ; Sequence Homology, Amino Acid ; }, abstract = {The cDNA and deduced amino-acid sequences for dimeric and octameric isoforms of creatine kinase (CK) from a protostome, the polychaete Chaetopterus variopedatus, were elucidated and then analysed in the context of available vertebrate CK sequences and the recently determined crystal structure of chicken sarcomeric mitochondrial CK (MiCK). As protostomes last shared a common ancestor with vertebrates roughly 700 million years ago, observed conserved residues may serve to confirm or reject contemporary hypotheses about the roles of particular amino acids in functional/structural processes such as dimer/octamer formation and membrane binding. The isolated cDNA from the dimeric CK consisted of 1463 nucleotides with an open reading frame of 1116 nucleotides encoding a 372-amino-acid protein having a calculated molecular mass of 41.85 kDa. The percentage identity of C. variopedatus dimeric CK to vertebrate CK is as high as 69%. The octameric MiCK cDNA is composed of 1703 nucleotides with an open reading frame of 1227 nucleotides. The first 102 nucleotides of the open reading frame encode a 34-amino-acid leader peptide whereas the mature protein is composed of 375 amino acids with a calculated molecular mass of 42.17 kDa. The percentage identity of C. variopedatus MiCK to vertebrate CK is as high as 71%. This similarity is also evident in residues purported to be important in the structure and function of dimeric and octameric CK: (a) presence of seven basic amino acids in the C-terminal end thought to be important in binding of MiCK to membranes; (b) presence of a lysine residue (Lys110 in chicken MiCK) also thought to be involved in membrane binding; and (c) presence of a conserved tryptophan thought to be important in dimer stabilization which is present in all dimeric and octameric guanidino kinases. However, C. variopedatus MiCK lacks the N-terminal heptapeptide present in chicken MiCK, which is thought to mediate octamer stabilization. In contrast with vertebrate MiCK, polychaete octamers are very stable indicating that dimer binding into octamers may be mediated by additional and/or other residues. Phylogenetic analyses showed that both octamer and dimer evolved very early in the CK lineage, well before the divergence of deuterostomes and protostomes. These results indicate that the octamer is a primitive feature of CK rather than being a derived and advanced character.}, }
@article {pmid10447593, year = {1999}, author = {Jan, PS and Stein, T and Hehl, S and Lisowsky, T}, title = {Expression studies and promoter analysis of the nuclear gene for mitochondrial transcription factor 1 (MTF1) in yeast.}, journal = {Current genetics}, volume = {36}, number = {1-2}, pages = {37-48}, doi = {10.1007/s002940050470}, pmid = {10447593}, issn = {0172-8083}, mesh = {5' Untranslated Regions/genetics ; Antibodies ; Base Sequence ; Cell Nucleus/*genetics ; Conserved Sequence/genetics ; Evolution, Molecular ; *Gene Expression Regulation, Fungal ; Genes, Fungal/*genetics ; Genetic Complementation Test ; Kluyveromyces/genetics ; Mitochondria/genetics ; Mitochondrial Proteins ; Molecular Sequence Data ; Mutagenesis, Insertional ; Promoter Regions, Genetic/*genetics ; RNA, Messenger/genetics/metabolism ; Saccharomyces/genetics ; Saccharomyces cerevisiae/cytology/*genetics/growth &amp; development/metabolism ; *Saccharomyces cerevisiae Proteins ; Sequence Deletion ; Species Specificity ; Transcription Factors/*genetics/metabolism ; }, abstract = {The basal mitochondrial transcription apparatus of Saccharomyces cerevisiae consists of the core enzyme for mitochondrial RNA polymerase and the specificity factor. The core enzyme is homologous to those of bacteriophages T3, T7 and SP6 whereas the specificity factor shows similarities with bacterial sigma factors. Recently it was shown that the bacteriophage-type core enzyme is widespread among the eukaryotic lineage and a common picture for the mitochondrial transcription apparatus in eukaryotic cells is now emerging. In contrast to the situation for the core enzyme, the gene for the specificity factor has only been identified from S. cerevisiae and more recently from two other yeast species. As the specificity factor is the key component for initiation of transcription at the mitochondrial promoter we wanted to study in more detail gene expression, regulation, and the function of the promoter of the nuclear MTF1 gene. For this purpose the messenger RNA level for scMTF1 was investigated under a large number of different growth conditions and thereby exhibited a very low, but regulated and carbon source-dependent, expression. Deletion experiments identify the minimal promoter for functional complementation in yeast. To evaluate the functional conservation of the promoter elements the homologous MTF1 gene from the closely related yeast Saccharomyces douglasii was isolated and tested in heterologous complementation experiments. In spite of a highly conserved protein sequence these studies demonstrate that at low-copy number sdMTF1 is not able to substitute for scMTF1 in S. cerevisiae. Promoter exchange experiments with MTF1 from S. cerevisiae and S. douglasii demonstrate that differences in gene expression are responsible for the failure in heterologous complementation. This finding prompted us to compare the promoter regions of MTF1 from four different yeast species. For this purpose the sequences of the 5' regions from S. douglasii, S. kluyveri and Kluyveromyces lactis were determined. A comparison of these sequences identifies significant differences and rapid changes in the intergenic regions, even between closely related yeast species.}, }
@article {pmid10445550, year = {1999}, author = {Barbaro, G and Di Lorenzo, G and Asti, A and Ribersani, M and Belloni, G and Grisorio, B and Filice, G and Barbarini, G}, title = {Hepatocellular mitochondrial alterations in patients with chronic hepatitis C: ultrastructural and biochemical findings.}, journal = {The American journal of gastroenterology}, volume = {94}, number = {8}, pages = {2198-2205}, doi = {10.1111/j.1572-0241.1999.01294.x}, pmid = {10445550}, issn = {0002-9270}, mesh = {Adult ; Biopsy ; DNA, Mitochondrial/ultrastructure ; Female ; Genotype ; Glutathione/blood ; Hepacivirus/genetics ; Hepatitis C, Chronic/*pathology ; Humans ; Lipid Peroxidation/*physiology ; Liver/pathology ; Liver Function Tests ; Male ; Malondialdehyde/blood ; Microscopy, Electron ; Middle Aged ; Mitochondria, Liver/*ultrastructure ; Oxidation-Reduction ; }, abstract = {OBJECTIVE: Hepatitis C virus (HCV) infection is associated with increased lipoperoxidation, which may lead to interference with mitochondrial function with possible depletion of mitochondrial DNA (mtDNA). We correlated the ultrastructural findings of liver biopsy specimens with the lipoperoxidation markers and contents of mtDNA in chronic hepatitis C (CHC) patients with a different HCV genotype.<br><br>METHODS: Liver biopsy samples obtained from 75 CHC patients were processed for histological and electron microscopic examination. Twenty-two subjects without known liver disease served as controls. Hepatic glutathione in its reduced (H-GSH) and oxidized (H-GSSG) forms were determined from biopsy specimens by high-performance liquid chromatography. Plasmatic and lymphocytic GSH and erythrocytic malonyldialdehyde (MDA) were also determined, along with the ratio between mtDNA and nuclear DNA (nDNA).<br><br>RESULTS: Ultrastructural alterations of the mitochondria were documented in 23 patients with genotype 1b, compared with 15 patients with genotype 2a/2c (p = 0.020) and seven patients with genotype 3a (p < 0.001). A significant depletion of H-GSH and lymphocytic GSH, an increase of H-GSSG and MDA, and a reduction of the mtDNA/nDNA ratio were documented in patients with genotype 1b, compared with patients with genotype 2a/2c and 3a and with controls.<br><br>CONCLUSIONS: In patients with genotype 1b frequent ultrastructural alterations of the mitochondria may be observed, and the depletion of mtDNA in these patients may represent the expression of a greater impairment of the process of oxidative phosphorylation. An increased production of free radicals in patients with genotype 1b may influence the evolution of the liver disease by enhancement of the cytopathic effect of HCV.}, }
@article {pmid10441671, year = {1999}, author = {Blanchette, M and Kunisawa, T and Sankoff, D}, title = {Gene order breakpoint evidence in animal mitochondrial phylogeny.}, journal = {Journal of molecular evolution}, volume = {49}, number = {2}, pages = {193-203}, doi = {10.1007/pl00006542}, pmid = {10441671}, issn = {0022-2844}, mesh = {Animals ; Chromosome Inversion ; *Chromosome Mapping ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; *Gene Rearrangement ; *Genome ; Humans ; Mitochondria/*genetics ; *Phylogeny ; }, abstract = {Multiple genome rearrangement methodology facilitates the inference of animal phylogeny from gene orders on the mitochondrial genome. The breakpoint distance is preferable to other, highly correlated but computationally more difficult, genomic distances when applied to these data. A number of theories of metazoan evolution are compared to phylogenies reconstructed by ancestral genome optimization, using a minimal total breakpoints criterion. The notion of unambiguously reconstructed segments is introduced as a way of extracting the invariant aspects of multiple solutions for a given ancestral genome; this enables a detailed reconstruction of the evolution of non-tRNA mitochondrial gene order.}, }
@article {pmid10441670, year = {1999}, author = {Tomita, M and Wada, M and Kawashima, Y}, title = {ApA dinucleotide periodicity in prokaryote, eukaryote, and organelle genomes.}, journal = {Journal of molecular evolution}, volume = {49}, number = {2}, pages = {182-192}, doi = {10.1007/pl00006541}, pmid = {10441670}, issn = {0022-2844}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; *Base Sequence ; Chloroplasts/genetics ; *Evolution, Molecular ; *Genome ; Humans ; Mitochondria/genetics ; Oligonucleotides/*analysis ; Organelles/*genetics ; Plants/genetics ; Saccharomyces cerevisiae/genetics ; }, abstract = {Computer analyses of various genome sequences revealed the existence of certain periodical patterns of adenine-adenine dinucleotides (ApA). For each genome sequence of 13 eubacteria, 3 archaebacteria, 10 eukaryotes, 60 mitochondria, and 9 chloroplasts, we counted frequencies of ApA dinucleotides at each downstream position within 50 bp from every ApA. We found that the complete genomes of all three archaebacteria have clear ApA periodicities of about 10 bps. On the other hand, all of the 13 eubacteria we analyzed were found to have an ApA periodicity of about 11 bp. Similar periodicities exist in the 10 eukaryotes, although higher organisms such as primates tend to have weaker periodic patterns. None of the mitochondria and chloroplasts we analyzed showed an evident periodic pattern.}, }
@article {pmid10438738, year = {1999}, author = {Everett, KD and Kahane, S and Bush, RM and Friedman, MG}, title = {An unspliced group I intron in 23S rRNA links Chlamydiales, chloroplasts, and mitochondria.}, journal = {Journal of bacteriology}, volume = {181}, number = {16}, pages = {4734-4740}, pmid = {10438738}, issn = {0021-9193}, mesh = {Acanthamoeba/genetics ; Animals ; *Bacterial Proteins ; Base Sequence ; Chlamydiales/*genetics ; Chloroplasts/enzymology/*genetics ; Consensus Sequence ; DNA Primers ; Endodeoxyribonucleases/genetics ; Eukaryota/genetics ; Evolution, Molecular ; Introns ; *Membrane Proteins ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames/genetics ; Phylogeny ; RNA/analysis ; *RNA Splicing ; RNA, Bacterial/analysis/chemistry ; RNA, Mitochondrial ; RNA, Ribosomal, 23S/*analysis/chemistry ; Reverse Transcriptase Polymerase Chain Reaction ; Ribosomes/genetics ; Sequence Homology, Amino Acid ; }, abstract = {Chlamydia was the only genus in the order Chlamydiales until the recent characterization of Simkania negevensis Z(T) and Parachlamydia acanthamoebae strains. The present study of Chlamydiales 23S ribosomal DNA (rDNA) focuses on a naturally occurring group I intron in the I-CpaI target site of 23S rDNA from S. negevensis. The intron, SnLSU. 1, belonged to the IB4 structural subgroup and was most closely related to large ribosomal subunit introns that express single-motif, LAGLIDADG endonucleases in chloroplasts of algae and in mitochondria of amoebae. RT-PCR and electrophoresis of in vivo rRNA indicated that the intron was not spliced out of the 23S rRNA. The unspliced 658-nt intron is the first group I intron to be found in bacterial rDNA or rRNA, and it may delay the S. negevensis developmental replication cycle by affecting ribosomal function.}, }
@article {pmid10437831, year = {1999}, author = {Takabatake, R and Hata, S and Taniguchi, M and Kouchi, H and Sugiyama, T and Izui, K}, title = {Isolation and characterization of cDNAs encoding mitochondrial phosphate transporters in soybean, maize, rice, and Arabidopis.}, journal = {Plant molecular biology}, volume = {40}, number = {3}, pages = {479-486}, pmid = {10437831}, issn = {0167-4412}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics/metabolism ; Carrier Proteins/*genetics/metabolism ; Cloning, Molecular ; DNA, Complementary/*genetics/*isolation &amp; purification ; DNA, Plant/*genetics/*isolation &amp; purification ; Escherichia coli/genetics ; Gene Expression ; Mitochondria/metabolism ; Molecular Sequence Data ; Oryza/genetics/metabolism ; Phosphate-Binding Proteins ; Phosphates/*metabolism ; Phylogeny ; Plants/*genetics/*metabolism ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; Glycine max/genetics/metabolism ; Zea mays/genetics/metabolism ; }, abstract = {cDNA clones encoding mitochondrial phosphate transporters were isolated from four herbaceous plants. The cDNAs for the soybean, maize and rice transporters contained entire coding regions, whereas the Arabidopsis cDNA lacked the 5' portion. The hydropathy profiles of the deduced amino acid sequences predicted the existence of six membrane-spanning domains which are highly conserved in the mitochondrial transporter family. In soybeans, the mRNA level for the transporter was high in tissues containing dividing cells. It was suggested that there are multiple copies of transporter genes in both dicots and monocots. The soybean transporter was expressed as inclusion bodies in Escherichia coli, solubilized with detergents, and then reconstituted into liposomes. The resulting proteoliposomes exhibited high phosphate transport activity. The activity was inhibited by N-ethylmaleimide, like those of mammalian phosphate transporters.}, }
@article {pmid10430918, year = {1999}, author = {Karlin, S and Brocchieri, L and Mrázek, J and Campbell, AM and Spormann, AM}, title = {A chimeric prokaryotic ancestry of mitochondria and primitive eukaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {96}, number = {16}, pages = {9190-9195}, pmid = {10430918}, issn = {0027-8424}, support = {R01 GM010452/GM/NIGMS NIH HHS/United States ; 5R01GM10452-34/GM/NIGMS NIH HHS/United States ; 5R01HG00335-11/HG/NHGRI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Archaea/*genetics ; Bacteria/*genetics ; *Biological Evolution ; *Chimera ; Clostridium/genetics ; DNA, Mitochondrial/*genetics ; Energy Metabolism/genetics ; Eukaryotic Cells ; Heat-Shock Proteins/genetics ; Humans ; Mitochondria/*genetics ; *Models, Genetic ; Proteins/chemistry/genetics ; Sulfolobus/genetics ; Vertebrates ; }, abstract = {We provide data and analysis to support the hypothesis that the ancestor of animal mitochondria (Mt) and many primitive amitochondrial (a-Mt) eukaryotes was a fusion microbe composed of a Clostridium-like eubacterium and a Sulfolobus-like archaebacterium. The analysis is based on several observations: (i) The genome signatures (dinucleotide relative abundance values) of Clostridium and Sulfolobus are compatible (sufficiently similar) and each has significantly more similarity in genome signatures with animal Mt sequences than do all other available prokaryotes. That stable fusions may require compatibility in genome signatures is suggested by the compatibility of plasmids and hosts. (ii) The expanded energy metabolism of the fusion organism was strongly selective for cementing such a fusion. (iii) The molecular apparatus of endospore formation in Clostridium serves as raw material for the development of the nucleus and cytoplasm of the eukaryotic cell.}, }
@article {pmid10430591, year = {1999}, author = {Rigaud, T and Bouchon, D and Souty-Grosset, C and Raimond, R}, title = {Mitochondrial DNA polymorphism, sex ratio distorters and population genetics in the isopod Armadillidium vulgare.}, journal = {Genetics}, volume = {152}, number = {4}, pages = {1669-1677}, pmid = {10430591}, issn = {0016-6731}, mesh = {Animals ; Crustacea/*genetics/microbiology/physiology ; DNA, Mitochondrial/*genetics ; Female ; France ; Genetics, Population ; Male ; Plasmids/*genetics ; Rickettsiaceae/*genetics ; *Sex Ratio ; }, abstract = {Two maternally inherited sex ratio distorters (SRD) impose female-biased sex ratios on the wood louse Armadillidium vulgare by feminizing putative males. These SRD are (i) an intracytoplasmic bacterium of the genus Wolbachia, and (ii) another non-Mendelian element of unknown nature: the f element. Mitochondrial DNA variation was investigated in A. vulgare field populations to trace the evolution of host-SRD relationships and to investigate the effect of SRD on host cytoplasmic polymorphism. The Wolbachia endosymbionts showed no polymorphism in their ITS2 sequence and were associated with two closely related mitochondrial types. This situation probably reflects a single infection event followed by a slight differentiation of mitochondria. There was no association between the f element and a given mitochondrial type, which may confirm the fact that this element can be partially paternally transmitted. The spreading of a maternally inherited SRD in a population should reduce the mitochondrial diversity by a hitchhiking process. In A. vulgare, however, a within-population mtDNA polymorphism was often found, because of the deficient spread of Wolbachia and the partial paternal inheritance of the f element. The analysis of molecular variance indicated that A. vulgare populations are genetically structured, but without isolation by distance.}, }
@article {pmid10419971, year = {1999}, author = {Westenberg, DJ and Guerinot, ML}, title = {Succinate dehydrogenase (Sdh) from Bradyrhizobium japonicum is closely related to mitochondrial Sdh.}, journal = {Journal of bacteriology}, volume = {181}, number = {15}, pages = {4676-4679}, pmid = {10419971}, issn = {0021-9193}, mesh = {Animals ; Base Sequence ; Bradyrhizobium/classification/*enzymology/genetics ; Cloning, Molecular ; Consensus Sequence ; Genetic Complementation Test ; Humans ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Operon ; *Phylogeny ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Glycine max/microbiology ; Succinate Dehydrogenase/chemistry/*genetics/metabolism ; Symbiosis ; }, abstract = {The sdhCDAB operon, encoding succinate dehydrogenase, was cloned from the soybean symbiont Bradyrhizobium japonicum. Sdh from B. japonicum is phylogenetically related to Sdh from mitochondria. This is the first example of a mitochondrion-like Sdh functionally expressed in Escherichia coli.}, }
@article {pmid10415483, year = {1999}, author = {Simpson, L and Maslov, DA}, title = {Evolution of the U-insertion/deletion RNA editing in mitochondria of kinetoplastid protozoa.}, journal = {Annals of the New York Academy of Sciences}, volume = {870}, number = {}, pages = {190-205}, doi = {10.1111/j.1749-6632.1999.tb08879.x}, pmid = {10415483}, issn = {0077-8923}, mesh = {Animals ; Base Sequence ; *DNA, Kinetoplast ; Eukaryota/genetics ; *Evolution, Molecular ; Models, Genetic ; Molecular Sequence Data ; *Mutagenesis ; *RNA ; *RNA Editing ; RNA, Mitochondrial ; *RNA, Protozoan ; Trypanosoma/genetics ; }, }
@article {pmid10400536, year = {1999}, author = {Hederstedt, L}, title = {Respiration without O2.}, journal = {Science (New York, N.Y.)}, volume = {284}, number = {5422}, pages = {1941-1942}, doi = {10.1126/science.284.5422.1941}, pmid = {10400536}, issn = {0036-8075}, mesh = {Anaerobiosis ; Bacillus subtilis/enzymology ; Binding Sites ; Cell Membrane/enzymology ; Crystallography, X-Ray ; Dimerization ; Electron Transport ; *Energy Metabolism ; Escherichia coli/*enzymology ; Evolution, Molecular ; Fumarates/metabolism ; Mitochondria/enzymology ; Oxidation-Reduction ; Oxygen Consumption ; Protein Conformation ; Protein Structure, Secondary ; Succinate Dehydrogenase/*chemistry/*metabolism ; Succinic Acid/metabolism ; }, }
@article {pmid10394948, year = {1999}, author = {Zhuo, D and Nguyen-Lowe, HT and Subramanian, S and Bonen, L}, title = {The S7 ribosomal protein gene is truncated and overlaps a cytochrome c biogenesis gene in pea mitochondria.}, journal = {Plant molecular biology}, volume = {40}, number = {1}, pages = {91-97}, pmid = {10394948}, issn = {0167-4412}, mesh = {ATP-Binding Cassette Transporters/genetics ; Amino Acid Sequence ; *Bacterial Proteins ; Base Sequence ; Cell Nucleus/genetics ; Cytochrome c Group/*genetics ; Evolution, Molecular ; Gene Dosage ; *Genes, Plant ; Mitochondria/*genetics ; Molecular Sequence Data ; Pisum sativum/*genetics ; RNA Editing ; RNA, Messenger/genetics ; RNA, Plant/genetics ; Recombination, Genetic ; Ribosomal Proteins/*genetics ; Sequence Deletion ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Glycine max/genetics ; }, abstract = {The pea mitochondrial genome contains a truncated rps7 gene lacking ca. 40 codons at its 5' terminus. This single-copy sequence is immediately downstream of and slightly overlapping an actively transcribed and edited reading frame of 744 bp (designated ccb248) homologous to the bacterial helC gene which encodes a subunit of the ABC-type heme transporter involved in cytochrome c biogenesis. This region of mitochondrial DNA appears recombinogenic, and the carboxy-termini of helC-type proteins are predicted to vary in sequence and length among plants. Sequences corresponding to the 5' coding region of rps7 were not detected elsewhere in the pea mitochondrial genome using wheat rps7 probes, and only a very short internal rps7 segment was observed in soybean mitochondrial DNA. The presence of rps7-homologous sequences in the nuclear genomes of pea and soybean is consistent with the recent transfer of a functional mitochondrial rps7 gene to the nucleus in certain plant lineages.}, }
@article {pmid10381654, year = {1999}, author = {Lorenzo, HK and Susin, SA and Penninger, J and Kroemer, G}, title = {Apoptosis inducing factor (AIF): a phylogenetically old, caspase-independent effector of cell death.}, journal = {Cell death and differentiation}, volume = {6}, number = {6}, pages = {516-524}, doi = {10.1038/sj.cdd.4400527}, pmid = {10381654}, issn = {1350-9047}, mesh = {Amino Acid Sequence ; Animals ; *Apoptosis ; Apoptosis Inducing Factor ; Apoptosis Regulatory Proteins ; Caenorhabditis elegans ; *Caenorhabditis elegans Proteins ; *Caspases ; Cell Death ; Cysteine Endopeptidases ; Evolution, Molecular ; *Flavoproteins/classification ; Helminth Proteins ; Humans ; Mammals ; *Membrane Proteins/classification ; Mice ; Molecular Sequence Data ; Phylogeny ; Proto-Oncogene Proteins ; Proto-Oncogene Proteins c-bcl-2 ; Sequence Analysis ; }, abstract = {Although much emphasis has been laid on the role of caspase in cell death, recent data indicate that, in many instances, mammalian cell death is caspase-independent. Thus, in many examples of mammalian cell death the 'decision' between death and life is upstream or independent of caspase activation. Similarly, it is unclear whether PCD of plants and fungi involves the activation of caspase-like enzymes, and no caspase-like gene has thus far been cloned in these phyla. Apoptosis inducing factor (AIF) is a new mammalian, caspase-independent death effector which, upon apoptosis induction, translocates from its normal localization, the mitochondrial intermembrane space, to the nucleus. Once in the nucleus, AIF causes chromatin condensation and large scale DNA fragmentation to fragments of approximately 50 kbp. The AIF cDNA from mouse and man codes for a protein which possesses three domains (i) an amino-terminal presequence which is removed upon import into the intermembrane space of mitochondria; (ii) a spacer sequence of approximately 27 amino acids; and (iii) a carboxyterminal 484 amino acid oxidoreductase domain with strong homology to oxidoreductases from other vertebrates (X. laevis), non-vertebrate animals (C. elegans, D. melanogaster), plants, fungi, eubacteria, and archaebacteria. Functionally important amino acids involved in the interaction with the prosthetic groups flavin adenine nucleotide and nicotinamide adenine nucleotide are strongly conserved between AIF and bacterial oxidoreductase. Several eukaryotes possess a similar domain organisation in their AIF homologs, making them candidates to be mitochondrial oxidoreductases as well as caspase-independent death effectors. The phylogenetic implications of these findings are discussed.}, }
@article {pmid10381390, year = {1999}, author = {Kerscher, SJ and Okun, JG and Brandt, U}, title = {A single external enzyme confers alternative NADH:ubiquinone oxidoreductase activity in Yarrowia lipolytica.}, journal = {Journal of cell science}, volume = {112 (Pt 14)}, number = {}, pages = {2347-2354}, doi = {10.1242/jcs.112.14.2347}, pmid = {10381390}, issn = {0021-9533}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA Primers/genetics ; Electron Transport Complex I ; Gene Deletion ; Genes, Fungal ; Molecular Sequence Data ; NADH, NADPH Oxidoreductases/chemistry/genetics/*metabolism ; Phylogeny ; Protein Folding ; Saccharomycetales/*enzymology/genetics ; Sequence Homology, Amino Acid ; }, abstract = {NADH:ubiquinone oxidoreductases catalyse the first step within the diverse pathways of mitochondrial NADH oxidation. In addition to the energy-conserving form commonly called complex I, fungi and plants contain much simpler alternative NADH:ubiquinone oxido-reductases that catalyze the same reaction but do not translocate protons across the inner mitochondrial membrane. Little is known about the distribution and function of these enzymes. We have identified YLNDH2 as the only gene encoding an alternative NADH:ubiquinone oxidoreductase (NDH2) in the obligate aerobic yeast Yarrowia lipolytica. Cells carrying a deletion of YLNDH2 were fully viable; full inhibition by piericidin A indicated that complex I activity was the sole NADH:ubiquinone oxidoreductase activity left in the deletion strains. Studies with intact mitochondria revealed that NDH2 in Y. lipolytica is oriented towards the external face of the mitochondrial inner membrane. This is in contrast to the situation seen in Saccharomyces cerevisiae, Neurospora crassa and in green plants, where internal alternative NADH:ubiquinone oxidoreductases have been reported. Phylogenetic analysis of known NADH:ubiquinone oxidoreductases suggests that during evolution conversion of an ancestral external alternative NADH:ubiquinone oxidoreductase to an internal enzyme may have paved the way for the loss of complex I in fermenting yeasts like S. cerevisiae.}, }
@article {pmid10380813, year = {1999}, author = {Däschner, K and Thalheim, C and Guha, C and Brennicke, A and Binder, S}, title = {In plants a putative isovaleryl-CoA-dehydrogenase is located in mitochondria.}, journal = {Plant molecular biology}, volume = {39}, number = {6}, pages = {1275-1282}, pmid = {10380813}, issn = {0167-4412}, mesh = {Amino Acid Sequence ; Animals ; Arabidopsis/*enzymology/genetics ; Blotting, Western ; Cell Fractionation ; Cloning, Molecular ; Conserved Sequence/genetics ; Evolution, Molecular ; Expressed Sequence Tags ; Genes, Plant/genetics ; Isovaleryl-CoA Dehydrogenase ; Mitochondria/*enzymology ; Molecular Sequence Data ; Oxidoreductases/*analysis/chemistry/genetics ; *Oxidoreductases Acting on CH-CH Group Donors ; Pisum sativum/enzymology ; Seeds/enzymology ; Sequence Analysis ; Sequence Homology, Amino Acid ; }, abstract = {In plants the degradation pathways of branched-chain amino acids have remained somewhat unclear with respect to both their biochemistry and their intracellular location. While biochemical evidence has localized some of the catabolic enzymes in peroxisomes/glyoxysomes, others cofractionate with mitochondria. We have now identified a candidate protein and corresponding cDNA for an enzyme of the leucine catabolic pathway, the isovaleryl-CoA-dehydrogenase (IVD). This polypeptide is a member of the acyl-CoA-dehydrogenase (ACDH) family and is encoded in the nuclear genome of Arabidopsis thaliana. Expression of the putative IVD gene in pea seedlings is documented by western blot analyses with an antibody against the mammalian IVD. Subcellular fractionation identifies the putative IVD enzyme in the mitochondrion. This localization suggests that in plants mitochondria contain at least part of the branched-chain amino acid degradation pathway(s).}, }
@article {pmid10380679, year = {1999}, author = {Hassanin, A and Douzery, EJ}, title = {Evolutionary affinities of the enigmatic saola (Pseudoryx nghetinhensis) in the context of the molecular phylogeny of Bovidae.}, journal = {Proceedings. Biological sciences}, volume = {266}, number = {1422}, pages = {893-900}, pmid = {10380679}, issn = {0962-8452}, mesh = {Animals ; Base Composition ; Biomarkers ; Cattle ; Cell Nucleus ; Cytochrome P-450 Enzyme System/*genetics ; Cytochrome b Group/*genetics ; *Evolution, Molecular ; Lactoferrin/*genetics ; Mitochondria ; Phylogeny ; *RNA, Ribosomal ; Ruminants/*classification/*genetics ; }, abstract = {To elucidate the systematic status of the enigmatic saola (Pseudoryx nghetinhensis), a new bovid genus recently discovered in Vietnam, and to investigate phylogenetic relationships within the family Bovidae, four distinct DNA markers were sequenced. Complete mitochondrial cytochrome b (1143 bp) and 12S rRNA (956 bp) genes and non-coding regions from the nuclear genes for aromatase cytochrome P-450 (199 bp) and lactoferrin (338 bp) have been compared for 25 bovid species and three Cervidae and Antilocapridae outgroups. Independent and/or combined analyses of the four nucleotide matrices through maximum parsimony and maximum-likelihood methods indicated that Bovidae consists of two major lineages, i.e. Bovinac which contains the tribes Bovini, Boselaphini and Tragelaphini, and Antilopinae which encompasses all other bovids. Within Bovinae, the tribe Bovini is divided into buffalo Bovini (Bubalus and Syncerus) and cattle Bovini (Bos and Bison) and Tragelaphini are possibly related to Boselaphini. Pseudoryx is shown to be (i) robustly nested within Bovinae; (ii) strongly associated with Bovini; and (iii) tentatively sharing a sister-group relationship with cattle Bovini. Within Antilopinae, three robust clades are in evidence: (i) Hippotragus and Damaliscus are linked to Ovis; (ii) Aepyceros joins Neotragus; and (iii) Cephalophus clusters with Oreotragus.}, }
@article {pmid10376009, year = {1999}, author = {Müller, M and Martin, W}, title = {The genome of Rickettsia prowazekii and some thoughts on the origin of mitochondria and hydrogenosomes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {21}, number = {5}, pages = {377-381}, doi = {10.1002/(SICI)1521-1878(199905)21:5&lt;377::AID-BIES4&gt;3.0.CO;2-W}, pmid = {10376009}, issn = {0265-9247}, support = {AI11942/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; *Genome, Bacterial ; Humans ; Mitochondria/*genetics ; Organelles/*genetics ; Phylogeny ; Rickettsia prowazekii/*genetics/ultrastructure ; }, abstract = {The sequence of an alpha-proteobacterial genome, that of Rickettsia prowazekii, is a substantial advance in microbial and evolutionary biology. The genome of this obligately aerobic intracellular parasite is small and is apparently still undergoing reduction, reflecting gene losses attributable to its intracellular parasitic lifestyle. Evolutionary analyses of proteins encoded in the genome contain the strongest phylogenetic evidence to date for the view that mitochondria descend from alpha-proteobacteria. Although both Rickettsia and mitochondrial genomes are highly reduced, it appears that genome reduction in these lineages has occurred independently. Rickettsia's genome encodes an ATP-generating machinery that is strikingly similar to that of aerobic mitochondria. But it does not encode homologues for the ATP-producing pathways of anaerobic mitochondria or hydrogenosomes, leaving an important issue regarding the origin and nature of the ancestral mitochondrial symbiont unresolved.}, }
@article {pmid10371040, year = {1999}, author = {Schön, A}, title = {Ribonuclease P: the diversity of a ubiquitous RNA processing enzyme.}, journal = {FEMS microbiology reviews}, volume = {23}, number = {3}, pages = {391-406}, doi = {10.1111/j.1574-6976.1999.tb00406.x}, pmid = {10371040}, issn = {0168-6445}, mesh = {Animals ; Base Sequence ; Endoribonucleases/chemistry/genetics/*metabolism ; Humans ; Mitochondria/enzymology ; Models, Molecular ; Molecular Sequence Data ; Plastids/enzymology ; Protein Conformation ; RNA, Archaeal/metabolism ; RNA, Bacterial/metabolism ; RNA, Catalytic/chemistry/genetics/*metabolism ; RNA, Transfer/metabolism ; Ribonuclease P ; }, abstract = {Ribonuclease P is the endonuclease required for generating the mature tRNA 5'-end. The ribonucleoprotein character of this enzyme has now been proven in most organisms and organelles. Exceptions, however, are still the chloroplasts, plant nuclei and animal mitochondria where no associated RNAs have been detected to date. In contrast to the known RNA subunits, which are fairly well-conserved in size and structure among diverse phylogenetic groups, the protein contribution to the holoenzyme is highly variable in size and number of the individual components. The structure of the bacterial protein component has recently been solved. In contrast, the spatial arrangement of the multiple subunits in eukaryotic enzymes is still enigmatic. Substrate requirements of the enzymes or their catalytic RNA subunits are equally diverse, ranging from simple single domain mimics to an almost intact three-dimensional structure of the pre-tRNA substrate. As an example for an intermediate in the enzyme evolution, ribonuclease P from the Cyanophora paradoxa cyanelle will be discussed in more detail. This enzyme is unique, as it combines cyanobacterial and eukaryotic features in its function, subunit composition and holoenzyme topology.}, }
@article {pmid10371035, year = {1999}, author = {Brennicke, A and Marchfelder, A and Binder, S}, title = {RNA editing.}, journal = {FEMS microbiology reviews}, volume = {23}, number = {3}, pages = {297-316}, doi = {10.1111/j.1574-6976.1999.tb00401.x}, pmid = {10371035}, issn = {0168-6445}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Cell Nucleus/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Plants/metabolism ; Plastids/metabolism ; RNA Editing/genetics/*physiology ; RNA, Messenger/chemistry/metabolism ; }, abstract = {The term RNA editing describes those molecular processes in which the information content is altered in an RNA molecule. To date such changes have been observed in tRNA. rRNA and mRNA molecules of eukaryotes, but not prokaryotes. The demonstration of RNA editing in prokaryotes may only be a matter of time, considering the range of species in which the various RNA editing processes have been found. RNA editing occurs in the nucleus, as well as in mitochondria and plastids, which are thought to have evolved from prokaryotic-like endosymbionts. Most of the RNA editing processes, however, appear to be evolutionarily recent acquisitions that arose independently. The diversity of RNA editing mechanisms includes nucleoside modifications such as C to U and A to I deaminations, as well as non-templated nucleotide additions and insertions. RNA editing in mRNAs effectively alters the amino acid sequence of the encoded protein so that it differs from that predicted by the genomic DNA sequence.}, }
@article {pmid10367178, year = {1999}, author = {Michel, PP and Lambeng, N and Ruberg, M}, title = {Neuropharmacologic aspects of apoptosis: significance for neurodegenerative diseases.}, journal = {Clinical neuropharmacology}, volume = {22}, number = {3}, pages = {137-150}, pmid = {10367178}, issn = {0362-5664}, mesh = {Animals ; Apoptosis/*physiology ; Astrocytes/physiology ; Calcium/physiology ; Caspases/physiology ; Ceramides/physiology ; Humans ; Mitochondria/physiology ; Neurodegenerative Diseases/*physiopathology ; Neurons/physiology ; Nitric Oxide/physiology ; Oncogene Proteins/physiology ; Signal Transduction/*physiology ; }, abstract = {The cause of neuronal death in Parkinson's, Alzheimer's, and other neurodegenerative diseases is not known, except in some hereditary forms of these disorders in which a mutated gene has been identified. Even in these cases, the molecular mechanisms that underlie the loss of specific populations of neurons have not been determined, although it is highly probable that apoptosis is involved. Some of the biochemical events that occur during apoptosis have been elucidated. We focus in this review on the role played by the proapoptotic caspases, the antiapoptotic proteins of the Bcl-2 family, and the apoptosis associated signal transducers such as ceramide, calcium, and reactive nitrogen or oxygen species. The role of the mitochondria and the possible implication of cell cycle regulators will also be addressed. Of particular interest are the endogenous inhibitory mechanisms and the pharmacologic agents that can be used to block apoptosis signaling cascades, because they offer models for the development of therapeutic strategies designed to prevent the evolution of pathologic neurodegeneration.}, }
@article {pmid10366854, year = {1999}, author = {Knight, RD and Freeland, SJ and Landweber, LF}, title = {Selection, history and chemistry: the three faces of the genetic code.}, journal = {Trends in biochemical sciences}, volume = {24}, number = {6}, pages = {241-247}, doi = {10.1016/s0968-0004(99)01392-4}, pmid = {10366854}, issn = {0968-0004}, mesh = {Biological Evolution ; Cell Nucleus/genetics ; Escherichia coli/genetics ; *Evolution, Molecular ; *Genetic Code ; Mitochondria/genetics ; Models, Biological ; RNA/physiology ; }, abstract = {The genetic code might be a historical accident that was fixed in the last common ancestor of modern organisms. 'Adaptive', 'historical' and 'chemical' arguments, however, challenge such a 'frozen accident' model. These arguments propose that the current code is somehow optimal, reflects the expansion of a more primitive code to include more amino acids, or is a consequence of direct chemical interactions between RNA and amino acids, respectively. Such models are not mutually exclusive, however. They can be reconciled by an evolutionary model whereby stereochemical interactions shaped the initial code, which subsequently expanded through biosynthetic modification of encoded amino acids and, finally, was optimized through codon reassignment. Alternatively, all three forces might have acted in concert to assign the 20 'natural' amino acids to their present positions in the genetic code.}, }
@article {pmid10366551, year = {1999}, author = {Campbell, RB}, title = {The coalescent time in the presence of background fertility selection.}, journal = {Theoretical population biology}, volume = {55}, number = {3}, pages = {260-269}, doi = {10.1006/tpbi.1998.1402}, pmid = {10366551}, issn = {0040-5809}, mesh = {Female ; *Fertility ; Gene Frequency/*genetics ; Genetic Linkage/genetics ; Genetic Variation/*genetics ; Haploidy ; Humans ; Male ; Markov Chains ; Mitochondria/genetics ; *Models, Genetic ; Pedigree ; Phylogeny ; Poisson Distribution ; Reproducibility of Results ; *Selection, Genetic ; Sex Characteristics ; Time Factors ; Y Chromosome/genetics ; }, abstract = {Selection ultimately entails differential reproductive success over several generations. This can be measured as a correlation of the number of progeny an individual has with the number of progeny its parent had. This correlation could have a genetic or a cultural basis. The effect of such a correlation is to multiply the single generation sampling variance (Vdeltap) in the diffusion approximation for fixation time by (1-b)+bx(1+r)/(1-r), where bxrn is the correlation between the number of progeny of an individual and its ancestor n generations ago (e.g., b is the heritability and br is the resultant parent-offspring progeny number correlation if the progeny number is genetically determined). This results in a reduction of the fixation or coalescent time by division by this factor. Sex differences in this correlation have been observed, and this provides an explanation for the difference of coalescent times of y-chromosomes and mitochondria.}, }
@article {pmid10361733, year = {1999}, author = {Germot, A and Philippe, H}, title = {Critical analysis of eukaryotic phylogeny: a case study based on the HSP70 family.}, journal = {The Journal of eukaryotic microbiology}, volume = {46}, number = {2}, pages = {116-124}, doi = {10.1111/j.1550-7408.1999.tb04594.x}, pmid = {10361733}, issn = {1066-5234}, mesh = {Animals ; Cloning, Molecular ; Cytosol/metabolism ; Endoplasmic Reticulum/metabolism ; Eukaryotic Cells/*classification ; Evolution, Molecular ; Genes, Protozoan/genetics ; HSP70 Heat-Shock Proteins/*genetics/*metabolism ; Mitochondria/metabolism ; *Phylogeny ; Protozoan Proteins/metabolism ; Sequence Analysis, DNA ; Trichomonas vaginalis/classification/*genetics/metabolism ; }, abstract = {Trichomonads, together with diplomonads and microsporidia, emerge at the base of the eukaryotic tree, on the basis of the small subunit rRNA phylogeny. However, phylogenies based on protein sequences such as tubulin are markedly different with these protists emerging much later. We have investigated 70 kDa heat-shock protein (HSP70), which could be a reliable phylogenetic marker. In eukaryotes, HSP70s are found in cytosol, endoplasmic reticulum, and organelles (mitochondria and chloroplasts). In Trichomonas vaginalis we identified nine different HSP70-encoding genes and sequenced three nearly complete cDNAs corresponding to cytosolic, endoplasmic reticulum, and mitochondrial-type HSP70. Phylogenies of eukaryotes were reconstructed using the classical methods while varying the number of species and characters considered. Almost all the undoubtedly monophyletic groups, defined by ultrastructural characters, were recovered. However, due to the long branch attraction phenomenon, the evolutionary rates were the main factor determining the position of species, even with the use of a close outgroup, which is an important advantage of HSP70 with respect to many other markers. Numerous variable sites are peculiar to Trichomonas and probably generated the artefactual placement of this species at the base of the eukaryotes or as the sister group of fast-evolving species. The inter-phyla relationships were not well supported and were sensitive to the reconstruction method, the number of species; and the quantity of information used. This lack of resolution could be explained by the very rapid diversification of eukaryotes, likely after the mitochondrial endosymbiosis.}, }
@article {pmid10361311, year = {1999}, author = {Akhmanova, A and Voncken, FG and Hosea, KM and Harhangi, H and Keltjens, JT and op den Camp, HJ and Vogels, GD and Hackstein, JH}, title = {A hydrogenosome with pyruvate formate-lyase: anaerobic chytrid fungi use an alternative route for pyruvate catabolism.}, journal = {Molecular microbiology}, volume = {32}, number = {5}, pages = {1103-1114}, doi = {10.1046/j.1365-2958.1999.01434.x}, pmid = {10361311}, issn = {0950-382X}, mesh = {Acetyltransferases/chemistry/genetics/*metabolism ; Amino Acid Sequence ; Anaerobiosis ; Base Sequence ; Blotting, Northern ; Blotting, Western ; DNA, Complementary ; DNA, Fungal ; Endopeptidase K/metabolism ; Gene Library ; Genes, Fungal ; Hydrogen/*metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Multigene Family ; Organelles/*enzymology ; Phylogeny ; Piromyces/*enzymology/genetics ; Pyruvic Acid/*metabolism ; Sequence Alignment ; }, abstract = {The chytrid fungi Piromyces sp. E2 and Neocallimastix sp. L2 are obligatory amitochondriate anaerobes that possess hydrogenosomes. Hydrogenosomes are highly specialized organelles engaged in anaerobic carbon metabolism; they generate molecular hydrogen and ATP. Here, we show for the first time that chytrid hydrogenosomes use pyruvate formate-lyase (PFL) and not pyruvate:ferredoxin oxidoreductase (PFO) for pyruvate catabolism, unlike all other hydrogenosomes studied to date. Chytrid PFLs are encoded by a multigene family and are abundantly expressed in Piromyces sp. E2 and Neocallimastix sp. L2. Western blotting after cellular fractionation, proteinase K protection assays and determinations of enzyme activities reveal that PFL is present in the hydrogenosomes of Piromyces sp. E2. The main route of the hydrogenosomal carbon metabolism involves PFL; the formation of equimolar amounts of formate and acetate by isolated hydrogenosomes excludes a significant contribution by PFO. Our data support the assumption that chytrid hydrogenosomes are unique and argue for a polyphyletic origin of these organelles.}, }
@article {pmid10359795, year = {1999}, author = {Heddi, A and Grenier, AM and Khatchadourian, C and Charles, H and Nardon, P}, title = {Four intracellular genomes direct weevil biology: nuclear, mitochondrial, principal endosymbiont, and Wolbachia.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {96}, number = {12}, pages = {6814-6819}, pmid = {10359795}, issn = {0027-8424}, mesh = {Biological Evolution ; DNA, Mitochondrial ; Gene Expression Regulation ; Genome, Bacterial ; *Genome, Plant ; Molecular Sequence Data ; Oryza/*genetics ; Symbiosis/*genetics ; }, abstract = {Cell physiology in the weevil Sitophilus oryzae is coordinated by three integrated genomes: nuclear, mitochondrial, and the "S. oryzae principal endosymbiont" (SOPE). SOPE, a cytoplasmic bacterium (2 x 10(3) bacteria per specialized bacteriocyte cell and 3 x 10(6) bacteria per weevil) that belongs to the proteobacteria gamma3-subgroup, is present in all weevils studied. We discovered a fourth prokaryotic genome in somatic and germ tissues of 57% of weevil strains of three species, S. oryzae, Sitophilus zeamais, and Sitophilus granarius, distributed worldwide. We assigned this Gram-negative prokaryote to the Wolbachia group (alpha-proteobacteria), on the basis of 16S rDNA sequence and fluorescence in situ DNA-RNA hybridization (FISH). Both bacteria, SOPE and Wolbachia, were selectively eliminated by combined heat and antibiotic treatments. Study of bacteria involvement in this insect's genetics and physiology revealed that SOPE, which induces the specific differentiation of the bacteriocytes, increases mitochondrial oxidative phosphorylation through the supply of pantothenic acid and riboflavin. Elimination of this gamma3-proteobacterium impairs many physiological traits. By contrast, neither the presence nor the absence of Wolbachia significantly affects the weevil's physiology. Wolbachia, disseminated throughout the body cells, is in particularly high density in the germ cells, where it causes nucleocytoplasmic incompatibility. The coexistence of two distinct types of intracellular proteobacteria at different levels of symbiont integration in insects illustrates the genetic complexity of animal tissue. Furthermore, evolutionary timing can be inferred: first nucleocytoplasm, then mitochondria, then SOPE, and finally Wolbachia. Symbiogenesis, the genetic integration of long-term associated members of different species, in the weevil appears to be a mechanism of speciation (with Wolbachia) and provides a means for animals to acquire new genes that permit better adaptation to the environment (with SOPE).}, }
@article {pmid10359519, year = {1999}, author = {Andreuccetti, P and Iodice, M and Prisco, M and Gualtieri, R}, title = {Intercellular bridges between granulosa cells and the oocyte in the elasmobranch Raya asterias.}, journal = {The Anatomical record}, volume = {255}, number = {2}, pages = {180-187}, doi = {10.1002/(SICI)1097-0185(19990601)255:2&lt;180::AID-AR8&gt;3.0.CO;2-S}, pmid = {10359519}, issn = {0003-276X}, mesh = {Animals ; Biological Evolution ; Elasmobranchii/*anatomy &amp; histology ; Female ; Granulosa Cells/*ultrastructure ; Intercellular Junctions/*ultrastructure ; Oocytes/*ultrastructure ; Oogenesis/physiology ; }, abstract = {In the present ultrastructural study intercellular bridges, connecting somatic granulosa cells to oocyte, have been detected for the first time and their modifications have been followed during Raja oogenesis. Intercellular bridges make their first appearance in small previtellogenic follicles as connecting devices between small cells and the oocyte. Later on, when the follicular epithelium becomes polymorphic and multilayered, for the presence of small, large, and pyriform-like cells, intercellular bridges link the oocyte and the different granulosa cells. Intercellular bridges contain ribosomes, whorl of membranes, mitochondria and vacuoles. Such cytoplasmic components are present also in the cell apex of large and pyriform-like cells thus suggesting, in agreement with other species (Motta et al. J. Exp. Zool., 1996;276:223-241) they may flow toward the oocyte. In this regard the presence of intercellular bridges during the oogenesis of cartilagineous fish may represent a crucial event of the active cooperation between granulosa cells and the oocyte.}, }
@article {pmid10355120, year = {1999}, author = {Brennicke, A and Zabaleta, E and Dombrowski, S and Hoffmann, M and Binder, S}, title = {Transcription signals of mitochondrial and nuclear genes for mitochondrial proteins in dicot plants.}, journal = {The Journal of heredity}, volume = {90}, number = {3}, pages = {345-350}, doi = {10.1093/jhered/90.3.345}, pmid = {10355120}, issn = {0022-1503}, mesh = {Arabidopsis/*genetics ; Biological Evolution ; Cell Nucleus/*metabolism ; Mitochondria/*metabolism ; Plant Proteins/*genetics/metabolism ; Promoter Regions, Genetic ; *Transcription, Genetic ; }, abstract = {Mitochondria contain several large multisubunit enzyme complexes that are composed of proteins encoded in the nuclear and mitochondrial genomes. Particularly for correct assembly of these enzyme complexes, expression of the respective mitochondrial and nuclear genes has to be coordinated to ensure correct stoichiometries of the protein subunits. Part of this control and the response to specific demands is exercised at the level of transcription. To determine the respective transcription signals we have analyzed the mitochondrial promoters in dicot plants and the promoter structure for nuclear-encoded genes of the respiratory chain complex I. We summarize the results of these investigations and extend the mitochondrial promoter survey to the mitochondrial genome in Arabidopsis thaliana.}, }
@article {pmid10342099, year = {1999}, author = {Corsaro, D and Venditti, D and Padula, M and Valassina, M}, title = {Intracellular life.}, journal = {Critical reviews in microbiology}, volume = {25}, number = {1}, pages = {39-79}, doi = {10.1080/10408419991299167}, pmid = {10342099}, issn = {1040-841X}, mesh = {Animals ; Biological Evolution ; Host-Parasite Interactions/physiology ; Models, Biological ; Organelles/physiology ; Parasites/*pathogenicity/*physiology ; Symbiosis/*physiology ; Virulence ; }, abstract = {Intracellular parasites and endosymbionts are present in almost all forms of life, including bacteria. Some eukaryotic organelles are believed to be derived from ancestral endosymbionts. Parasites and symbionts show several adaptations to intracellular life. A comparative analysis of their biology suggests some general considerations involved in adapting to intracellular life and reveals a number of independently achieved strategies for the exploitation of an intracellular habitat. Symbioses mainly based on a form of syntrophy may have led to the establishment of unique physiological systems. Generally, a symbiont can be considered to be an attenuated pathogen. The combination of morphological studies, molecular phylogenetic analyses, and palaeobiological data has led to considerable improvement in the understanding of intracellular life evolution. Comparing host and symbiont phylogenies could lead to an explanation of the evolutionary history of symbiosis. These studies also provide strong evidences for the endosymbiogenesis of the eukaryotic cell. Indeed, an eubacterial origin for mitochondria and plastids is well accepted and is suggested for other organelles. The expansion of intracellular living associations is presented, with a particular emphasis on peculiar aspects and/or recent data, providing a global evaluation.}, }
@article {pmid10335652, year = {1999}, author = {Takezaki, N and Gojobori, T}, title = {Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences.}, journal = {Molecular biology and evolution}, volume = {16}, number = {5}, pages = {590-601}, doi = {10.1093/oxfordjournals.molbev.a026141}, pmid = {10335652}, issn = {0737-4038}, mesh = {Amino Acids/genetics ; Animals ; DNA, Mitochondrial/*genetics ; Humans ; *Models, Biological ; Molecular Sequence Data ; *Phylogeny ; Vertebrates/*physiology ; }, abstract = {Concatenated sequences of all protein-coding genes in mitochondria recovered a known phylogeny of 11 vertebrate species correctly with statistical significance. However, when it was rooted by lampreys or sea urchins, the root of the vertebrate tree was placed between the mammal cluster and the chicken-frog-fish cluster or between the mammal-chicken cluster and the frog-fish cluster, depending on the tree-making method used. Although the frog-fish or chicken-frog-fish cluster was biologically incorrect, it was again supported with a significantly high bootstrap value. In this study, we investigated the reasons why this happened. It has been suggested that an incorrect phylogeny may be constructed due to a change of amino acid composition in different lineages or due to homoplasies at sites with hydrophobic amino acids. However, our results indicated that these were not the causes of the incorrect rooting of the vertebrate tree. Rather, it was important to take into account an extensive rate variation across sites and different probabilities of substitution among different amino acids. The substitution rates for mitochondrial sequences vary considerably for different vertebrate lineages. In such a case, it is known to be important to use the model that reflects the actual substitution probability to obtain a correct tree topology. The correct rooting of the vertebrate tree was recovered when rate variation across sites was properly accounted for.}, }
@article {pmid10331270, year = {1999}, author = {Figge, RM and Schubert, M and Brinkmann, H and Cerff, R}, title = {Glyceraldehyde-3-phosphate dehydrogenase gene diversity in eubacteria and eukaryotes: evidence for intra- and inter-kingdom gene transfer.}, journal = {Molecular biology and evolution}, volume = {16}, number = {4}, pages = {429-440}, doi = {10.1093/oxfordjournals.molbev.a026125}, pmid = {10331270}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/*enzymology/*genetics ; Base Sequence ; Cloning, Molecular ; DNA Primers/genetics ; Euglena/enzymology/genetics ; Eukaryotic Cells ; Evolution, Molecular ; Gene Transfer Techniques ; Genes, Bacterial ; Genetic Variation ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Species Specificity ; Treponema/enzymology/genetics ; }, abstract = {Cyanobacteria contain up to three highly divergent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes: gap1, gap2, and gap3. Genes gap1 and gap2 are closely related at the sequence level to the nuclear genes encoding cytosolic and chloroplast GAPDH of higher plants and have recently been shown to play distinct key roles in catabolic and anabolic carbon flow, respectively, of the unicellular cyanobacterium Synechocystis sp. PCC6803. In the present study, sequences of 10 GAPDH genes distributed across the cyanobacteria Prochloron didemni, Gloeobacter violaceus PCC7421, and Synechococcus PCC7942 and the alpha-proteobacterium Paracoccus denitrificans and the beta-proteobacterium Ralstonia solanacearum were determined. Prochloron didemni possesses homologs to the gap2 and gap3 genes from Anabaena, Gloeobacter harbors gap1 and gap2 homologs, and Synechococcus possesses gap1, gap2, and gap3. Paracoccus harbors two highly divergent gap genes that are related to gap3, and Ralstonia possesses a homolog of the gap1 gene. Phylogenetic analyses of these sequences in the context of other eubacterial and eukaryotic GAPDH genes reveal that divergence across eubacterial gap1, and gap2, and gap3 genes is greater than that between eubacterial gap1 and eukaroytic glycolytic GapC or between eubacterial gap2 and eukaryotic Calvin cycle GapAB. These data strongly support previous analyses which suggested that eukaryotes acquired their nuclear genes for GapC and GapAB via endosymbiotic gene transfer from the antecedents of mitochondria and chloroplasts, and extend the known range of sequence diversity of the antecedent eubacterial genes. Analyses of available GAPDH sequences from other eubacterial sources indicate that the glycosomal gap gene from trypanosomes (cytosolic in Euglena) and the gap gene from the spirochete Treponema pallidum are each other's closest relatives. This specific relationship can therefore not reflect organismal evolution but must be the result of an interkingdom gene transfer, the direction of which cannot be determined with certainty at present. Contrary to this, the origin of the cytosolic Gap gene from trypanosomes can now be clearly defined as gamma-proteobacterial, since the newly established Ralstonia sequence (beta-proteobacteria) branches basally to the gamma-proteobacterial/trypanosomal assemblage.}, }
@article {pmid10331264, year = {1999}, author = {Duncan, R and Faggart, MA and Roger, AJ and Cornell, NW}, title = {Phylogenetic analysis of the 5-aminolevulinate synthase gene.}, journal = {Molecular biology and evolution}, volume = {16}, number = {3}, pages = {383-396}, doi = {10.1093/oxfordjournals.molbev.a026119}, pmid = {10331264}, issn = {0737-4038}, support = {GM32964/GM/NIGMS NIH HHS/United States ; }, mesh = {5-Aminolevulinate Synthetase/*genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; DNA Primers/genetics ; Evolution, Molecular ; Gene Expression Regulation, Enzymologic ; Invertebrates/genetics ; Molecular Sequence Data ; *Phylogeny ; Vertebrates/genetics ; }, abstract = {The evolution of 5-aminolevulinate synthase (ALS) was studied by acquiring sequence data and generating phylogenetic trees. Gene sequences were already available for a variety of vertebrates (which have both a housekeeping and an erythroid form of the gene), fungi, alpha-proteobacteria, and one protist and one protostome. In order to generate representative trees, ALS sequence data were acquired from various deuterostomes and protostomes. The species and tissues selected for study were beluga whale liver, hagfish blood, sea urchin gonadal tissue, cuttlefish hepatopancreas, horseshoe crab hepatopancreas, and bloodworm blood. The new sequences and those previously published were examined for the presence of heme-regulatory motifs (HRMs) and iron-responsive elements (IREs). The HRMs are present in almost all eukaryotic species, which suggests their fundamental role in the regulation of ALS. The IREs are present in all vertebrate erythroid forms of ALS, which indicates that in those animals, expression of the erythroid form of the enzyme and, hence, hemoglobin production can be influenced by the intracellular content of iron. The new sequences were aligned with previously reported ALS sequences, and phylogenetic analyses were performed. The resulting trees provided evidence regarding the timing of the gene duplication event that led to the two forms of the ALS gene in vertebrates. It appears that the housekeeping and erythroid forms of ALS probably arose before the divergence of hagfish from the deuterostome line leading to the vertebrates. The data also add to the evidence indicating that alpha-proteobacteria are the nearest contemporary relatives of mitochondria.}, }
@article {pmid10329574, year = {1999}, author = {Hong, Y and Dover, SL and Cole, TE and Brasier, CM and Buck, KW}, title = {Multiple mitochondrial viruses in an isolate of the Dutch Elm disease fungus Ophiostoma novo-ulmi.}, journal = {Virology}, volume = {258}, number = {1}, pages = {118-127}, doi = {10.1006/viro.1999.9691}, pmid = {10329574}, issn = {0042-6822}, mesh = {3' Untranslated Regions ; 5' Untranslated Regions ; Amino Acid Sequence ; Ascomycota/*virology ; Biological Evolution ; Helper Viruses ; Mitochondria/*virology ; Molecular Sequence Data ; Nucleic Acid Conformation ; Plant Diseases/microbiology ; RNA Viruses/*genetics ; *RNA, Viral ; RNA-Dependent RNA Polymerase/genetics ; Sequence Analysis, RNA ; Sequence Homology, Amino Acid ; Trees/microbiology ; }, abstract = {The nucleotide sequences of three mitochondrial virus double-stranded (ds) RNAs, RNA-4 (2599 nucleotides), RNA-5 (2474 nucleotides), and RNA-6 (2343 nucleotides), in a diseased isolate Log1/3-8d2 (Ld) of the Dutch elm disease fungus Ophiostoma novo-ulmi have been determined. All these RNAs are A-U-rich (71-73% A + U residues). Using the fungal mitochondrial genetic code in which UGA codes for tryptophan, the positive-strand of each of RNAs 4, 5, and 6 contains a single open reading frame (ORF) with the potential to encode a protein of 783, 729, and 695 amino acids, respectively, all of which contain conserved motifs characteristic of RNA-dependent RNA polymerases (RdRps). Sequence comparisons showed that these RNAs are related to each other and to a previously characterized RNA, RNA-3a, from the same O. novo-ulmi isolate, especially within the RdRp-like motifs. However, the overall RNA nucleotide and RdRp amino acid sequence identities were relatively low (43-55% and 20-32%, respectively). The 5'- and 3'-terminal sequences of these RNAs are different, but they can all be folded into potentially stable stem-loop structures. Those of RNA-4 and RNA-6 have inverted complementarity, potentially forming panhandle structures. Their molecular and biological properties indicate that RNAs 3a, 4, 5, and 6 are the genomes of four different viruses, which replicate independently in the same cell. These four viruses are also related to a mitochondrial RNA virus from another fungus, Cryphonectria parasitica, recently designated the type species of the Mitovirus genus of the Narnaviridae family, and to a virus from the fungus Rhizoctonia solani. It is proposed that the four O. novo-ulmi mitochondrial viruses are assigned to the Mitovirus genus and designated O. novo-ulmi mitovirus (OnuMV) 3a-Ld, 4-Ld, 5-Ld, and 6-Ld, respectively. Northern blot analysis indicated that O. novo-ulmi Ld nucleic acid extracts contain more single-stranded (ss, positive-stranded) RNA than dsRNA for all three newly described mitoviruses. O. novo-ulmi RNA-7, previously believed to be a satellite-like RNA, is shown to be a defective RNA, derived from OnuMV4-Ld RNA by multiple internal deletions. OnuMV4-Ld is therefore the helper virus for the replication of both RNA-7 and another defective RNA, RNA-10. Sequence comparisons indicate that RNA-10 could be derived from RNA-7, as previously suggested, or derived directly from RNA-4.}, }
@article {pmid10319184, year = {1999}, author = {Hesse, H and Lipke, J and Altmann, T and Höfgen, R}, title = {Molecular cloning and expression analyses of mitochondrial and plastidic isoforms of cysteine synthase (O-acetylserine(thiol)lyase) from Arabidopsis thaliana.}, journal = {Amino acids}, volume = {16}, number = {2}, pages = {113-131}, doi = {10.1007/BF01321531}, pmid = {10319184}, issn = {0939-4451}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics ; Cloning, Molecular ; Cysteine Synthase/*genetics/*metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Plastids/*metabolism ; *Protein Isoforms ; Recombinant Fusion Proteins ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Time Factors ; Tissue Distribution ; }, abstract = {Cysteine synthase, the key enzyme for fixation of inorganic sulfide, catalyses the formation of cysteine from O-acetylserine and inorganic sulfide. Here we report the cloning of cDNAs encoding cysteine synthase isoforms from Arabidopsis thaliana. The isolated cDNA clones encode for a mitochondrial and a plastidic isoform of cysteine synthase (O-acetylserine (thiol)-lyase, EC 4.2.99.8), designated cysteine synthase C (AtCS-C, CSase C) and B (AtCS-B; CSase B), respectively. AtCS-C and AtCS-B, having lengths of 1569-bp and 1421-bp, respectively, encode polypeptides of 430 amino acids (approximately 45.8 kD) and of 392 amino acids (approximately 41.8 kD), respectively. The deduced amino acid sequences of the mitochondrial and plastidic isoforms exhibit high homology even with respect to the presequences. The predicted presequence of AtCS-C has a N-terminal extension of 33 amino acids when compared to the plastidic isoform. Northern blot analysis showed that AtCS-C is higher expressed in roots than in leaves whereas the expression of AtCS-B is stronger in leaves. Furthermore, gene expression of both genes was enhanced by sulfur limitation which in turn led to an increase in enzyme activity in crude extracts of plants. Expression of the AtCS-B gene is regulated by light. The mitochondrial, plastidic and cytosolic (Hesse and Altmann, 1995) isoforms of cysteine synthase of Arabidopsis are able to complement a cysteine synthase-deficient mutant of Escherichia coli unable to grow on minimal medium without cysteine, indicating synthesis of functional plant proteins in the bacterium. Two lines of evidence proved that AtCS-C encodes a mitochondrial form of cysteine synthase; first, import of in vitro translation products derived from AtCS-C in isolated intact mitochondria and second, Western blot analysis of mitochondria isolated from transgenic tobacco plants expressing AtCS-C cDNA/c-myc DNA fusion protein.}, }
@article {pmid10229579, year = {1999}, author = {Roger, AJ and Morrison, HG and Sogin, ML}, title = {Primary structure and phylogenetic relationships of a malate dehydrogenase gene from Giardia lamblia.}, journal = {Journal of molecular evolution}, volume = {48}, number = {6}, pages = {750-755}, doi = {10.1007/pl00006519}, pmid = {10229579}, issn = {0022-2844}, support = {GM32964/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Cytosol/enzymology ; Giardia lamblia/*genetics ; Malate Dehydrogenase/*genetics ; Molecular Sequence Data ; *Phylogeny ; Protozoan Proteins/genetics ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/genetics ; }, abstract = {The lactate and malate dehydrogenases comprise a complex protein superfamily with multiple enzyme homologues found in eubacteria, archaebacteria, and eukaryotes. In this study we describe the sequence and phylogenetic relationships of a malate dehydrogenase (MDH) gene from the amitochondriate diplomonad protist, Giardia lamblia. Parsimony, distance, and maximum-likelihood analyses of the MDH protein family solidly position G. lamblia MDH within a eukaryote cytosolic MDH clade, to the exclusion of chloroplast, mitochondrial, and peroxisomal homologues. Furthermore, G. lamblia MDH is specifically related to a homologue from Trichomonas vaginalis. This MDH topology, together with published phylogenetic analyses of beta-tubulin, chaperonin 60, valyl-tRNA synthetase, and EF-1alpha, suggests a sister-group relationship between diplomonads and parabasalids. Since these amitochondriate lineages contain genes encoding proteins which are characteristic of mitochondria and alpha-proteobacteria, their shared ancestry suggests that mitochondrial properties were lost in the common ancestor of both groups.}, }
@article {pmid10228558, year = {1999}, author = {Baker, ME and Grundy, WN and Elkan, CP}, title = {A common ancestor for a subunit in the mitochondrial proton-translocating NADH:ubiquinone oxidoreductase (complex I) and short-chain dehydrogenases/reductases.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {55}, number = {3}, pages = {450-455}, doi = {10.1007/s000180050301}, pmid = {10228558}, issn = {1420-682X}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry/genetics ; Cattle ; Evolution, Molecular ; Fungal Proteins/chemistry/genetics ; Gram-Negative Aerobic Rods and Cocci/enzymology/genetics ; Humans ; Hydroxysteroid Dehydrogenases/chemistry/genetics ; Markov Chains ; Molecular Sequence Data ; Multigene Family ; NAD(P)H Dehydrogenase (Quinone)/chemistry/*genetics ; Neurospora crassa/enzymology/genetics ; Oxidoreductases/chemistry/*genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Software ; }, abstract = {The proton-translocating NADH:ubiquinone oxidoreductase or complex I is located in the inner membranes of mitochondria, where it catalyzes the transfer of electrons from NADH to ubiquinone. Here we report that one of the subunits in complex I is homologous to short-chain dehydrogenases and reductases, a family of enzymes with diverse activities that include metabolizing steroids, prostaglandins and nucleotide sugars. We discovered that a subunit of complex I in human, cow, Neurospora crassa and Aquifex aeolius is homologous to nucleotide-sugar epimerases and hydroxysteroid dehydrogenases while seeking distant homologs of these enzymes with a hidden Markov model-based search of Genpept. This homology allows us to use information from the solved three-dimensional structures of nucleotide-sugar epimerases and hydroxysteroid dehydrogenases and our motif analysis of these enzymes to predict functional domains on their homologs in complex I.}, }
@article {pmid10222647, year = {1999}, author = {Kotliarova, SE and Toda, T and Takenaka, O and Matsushita, I and Hida, A and Shinka, T and Goto, J and Tokunaga, K and Nakagome, Y and Nakahori, Y}, title = {Novel (CA)n marker DXYS241 on the nonrecombinant part of the human Y chromosome.}, journal = {Human biology}, volume = {71}, number = {2}, pages = {261-275}, pmid = {10222647}, issn = {0018-7143}, mesh = {Alleles ; Animals ; Asian People/genetics ; *Biological Evolution ; Black People/genetics ; Female ; Genetic Markers/*genetics ; Humans ; Japan ; Male ; Pan troglodytes/genetics ; Pedigree ; Polymorphism, Genetic/*genetics ; Pongo pygmaeus/genetics ; Sequence Homology ; Translocation, Genetic/*genetics ; White People/genetics ; Y Chromosome/*genetics ; }, abstract = {The origin of modern humans can be traced by comparing polymorphic sites in either mitochondria or genomic sequences between humans and other primates. The human Y chromosome has both a non-recombining region and X-Y homologous pseudo-autosomal regions. In the nonrecombining region events during evolution can be directly detected. At least a part of homology between Xq21 and Yp11 is a result of rather recent translocations from the X chromosome to the Y chromosome. DNA markers residing in the nonrecombining region of the human Y chromosome are potentially useful in tracing male-specific gene flow in human evolution. However, the number of available markers in the region is limited. Here, we report a novel X-Y homologous (CA)n repeat locus in the nonrecombining region of the Y chromosome. This marker, DXYS241, has several interesting features. Y- and X-chromosome alleles are distinguishable because the Y-chromosome alleles are shorter than the X-chromosome alleles most of the time. We developed 2 primer sets for specific examination of Y- and X-chromosome alleles. The marker should be useful in establishing relationships between populations based on patrilineal gene flow. Sequences homologous to DXYS241 are also found on the X chromosome of primates. Four events during primate evolution that led to the modern human Y chromosome were identified.}, }
@article {pmid10222164, year = {1999}, author = {Murrell, A and Campbell, NJ and Barker, SC}, title = {Mitochondrial 12S rDNA indicates that the Rhipicephalinae (Acari: Ixodida) is paraphyletic.}, journal = {Molecular phylogenetics and evolution}, volume = {12}, number = {1}, pages = {83-86}, doi = {10.1006/mpev.1998.0595}, pmid = {10222164}, issn = {1055-7903}, mesh = {Animals ; Ixodes/*classification/*genetics ; Mitochondria/*genetics ; *Phylogeny ; RNA, Ribosomal/*genetics ; Sequence Analysis, RNA ; }, }
@article {pmid10203753, year = {1999}, author = {López-Garćia, P and Moreira, D}, title = {Metabolic symbiosis at the origin of eukaryotes.}, journal = {Trends in biochemical sciences}, volume = {24}, number = {3}, pages = {88-93}, doi = {10.1016/s0968-0004(98)01342-5}, pmid = {10203753}, issn = {0968-0004}, mesh = {Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; Biological Evolution ; Eukaryotic Cells ; Hydrogen/metabolism ; Mitochondria/metabolism ; *Models, Biological ; Symbiosis/*physiology ; }, abstract = {Thirty years after Margulis revived the endosymbiosis theory for the origin of mitochondria and chloroplasts, two novel symbiosis hypotheses for the origin of eukaryotes have been put forward. Both propose that eukaryotes arose through metabolic symbiosis (syntrophy) between eubacteria and methanogenic Archaea. They also propose that this was mediated by interspecies hydrogen transfer and that, initially, mitochondria were anaerobic. These hypotheses explain the mosaic character of eukaryotes (i.e. an archaeal-like genetic machinery and a eubacterial-like metabolism), as well as distinct eukaryotic characteristics (which are proposed to be products of symbiosis). Combined data from comparative genomics, microbial ecology and the fossil record should help to test their validity.}, }
@article {pmid10214932, year = {1999}, author = {Kadenbach, B and Arnold, S}, title = {A second mechanism of respiratory control.}, journal = {FEBS letters}, volume = {447}, number = {2-3}, pages = {131-134}, doi = {10.1016/s0014-5793(99)00229-x}, pmid = {10214932}, issn = {0014-5793}, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Biological Evolution ; Electron Transport Complex IV/metabolism ; Eukaryotic Cells ; Humans ; Mitochondria/metabolism ; *Models, Biological ; Osmosis ; Oxygen Consumption/*physiology ; }, abstract = {According to the chemosmotic hypothesis, ATP is synthesized in mitochondria, bacteria and chloroplasts via the proton motive force delta p, the energy-rich intermediate of electron transport and photosynthetic phosphorylation. The general applicability of the chemosmotic hypothesis, however, was disputed until present. In particular the relationship between the rate of respiration and delta p in mitochondria was found variable, depending on the experimental conditions. Recently, a new mechanism of respiratory control was found, based on binding of ATP or ADP to subunit IV of cytochrome c oxidase, which is independent of delta p and could explain many previous results contradicting the chemosmotic hypothesis.}, }
@article {pmid10200968, year = {1999}, author = {Corral-Debrinski, M and Belgareh, N and Blugeon, C and Claros, MG and Doye, V and Jacq, C}, title = {Overexpression of yeast karyopherin Pse1p/Kap121p stimulates the mitochondrial import of hydrophobic proteins in vivo.}, journal = {Molecular microbiology}, volume = {31}, number = {5}, pages = {1499-1511}, doi = {10.1046/j.1365-2958.1999.01295.x}, pmid = {10200968}, issn = {0950-382X}, mesh = {ATP-Binding Cassette Transporters/metabolism ; Apoproteins/metabolism ; Blotting, Northern ; Carrier Proteins/metabolism ; Cytochrome b Group/metabolism ; Cytochromes b ; DNA Primers ; Endopeptidase K/metabolism ; Glucose/metabolism ; Glycerol/metabolism ; Green Fluorescent Proteins ; Luminescent Proteins/metabolism ; *Membrane Transport Proteins ; Mitochondria/*metabolism ; Models, Biological ; Multigene Family/genetics ; Mutagenesis ; Nuclear Envelope/metabolism ; Nuclear Proteins/metabolism ; Oxygen Consumption ; Phenotype ; Protein Biosynthesis ; Receptors, Cytoplasmic and Nuclear/*genetics ; Ribosomes/metabolism ; Saccharomyces cerevisiae/*genetics ; *Saccharomyces cerevisiae Proteins ; Translocation, Genetic ; beta Karyopherins ; }, abstract = {During evolution, cellular processes leading to the transfer of genetic information failed to send all the mitochondrial genes into the nuclear genome. Two mitochondrial genes are still exclusively located in the mitochondrial genome of all living organisms. They code for two highly hydrophobic proteins: the apocytochrome b and the subunit I of cytochrome oxidase. Assuming that the translocation machinery could not efficiently transport long hydrophobic fragments, we searched for multicopy suppressors of this physical blockage. We demonstrated that overexpression of Pse1p/Kap121p or Kap123p, which belong to the superfamily of karyopherin beta proteins, facilitates the translocation of chimeric proteins containing several stretches of apocytochrome b fused to a reporter mitochondrial gene. The effect of PSE1/KAP121 overexpression (in which PSE1 is protein secretion enhancer 1) on mitochondrial import of the chimera is correlated with an enrichment of the corresponding transcript in cytoplasmic ribosomes associated with mitochondria. PSE1/KAP121 overexpression also improves the import of the hydrophobic protein Atm1p, an ABC transporter of the mitochondrial inner membrane. These results suggest that in vivo PSE1/KAP121 overexpression facilitates, either directly or indirectly, the co-translational import of hydrophobic proteins into mitochondria.}, }
@article {pmid10191388, year = {1998}, author = {Urry, DW and Peng, SQ and Hayes, LC and McPherson, D and Xu, J and Woods, TC and Gowda, DC and Pattanaik, A}, title = {Engineering protein-based machines to emulate key steps of metabolism (biological energy conversion).}, journal = {Biotechnology and bioengineering}, volume = {58}, number = {2-3}, pages = {175-190}, doi = {10.1002/(sici)1097-0290(19980420)58:2/3&lt;175::aid-bit10&gt;3.0.co;2-c}, pmid = {10191388}, issn = {1097-0290}, abstract = {Metabolism is the conversion of available energy sources to those energy forms required for sustaining and propagating living organisms; this is simply biological energy conversion. Proteins are the machines of metabolism; they are the engines of motility and the other machines that interconvert energy forms not involving motion. Accordingly, metabolic engineering becomes the use of natural protein-based machines for the good of society. In addition, metabolic engineering can utilize the principles, whereby proteins function, to design new protein-based machines to fulfill roles for society that proteins have never been called upon throughout evolution to fulfill. This article presents arguments for a universal mechanism whereby proteins perform their diverse energy conversions; it begins with background information, and then asserts a set of five axioms for protein folding, assembly, and function and for protein engineering. The key process is the hydrophobic folding and assembly transition exhibited by properly balanced amphiphilic protein sequences. The fundamental molecular process is the competition for hydration between hydrophobic and polar, e.g., charged, residues. This competition determines Tt, the onset temperature for the hydrophobic folding and assembly transition, Nhh, the numbers of waters of hydrophobic hydration, and the pKa of ionizable functions. Reported acid-base titrations and pH dependence of microwave dielectric relaxation data simultaneously demonstrate the interdependence of Tt, Nhh and the pKa using a series of microbially prepared protein-based poly(30mers) with one glutamic acid residue per 30mer and with an increasing number of more hydrophobic phenylalanine residues replacing valine residues. Also, reduction of nicotinamides and flavins is shown to lower Tt, i.e., to increase hydrophobicity. Furthermore, the argument is presented, and related to an extended Henderson-Hasselbalch equation, wherein reduction of nicotinamides represents an increase in hydrophobicity and resulting hydrophobic-induced pKa shifts become the basis for understanding a primary energy conversion (proton transport) process of mitochondria. Copyright 1998 John Wiley &amp; Sons, Inc.}, }
@article {pmid10189711, year = {1999}, author = {Eyre-Walker, A and Smith, NH and Smith, JM}, title = {How clonal are human mitochondria?.}, journal = {Proceedings. Biological sciences}, volume = {266}, number = {1418}, pages = {477-483}, pmid = {10189711}, issn = {0962-8452}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Base Sequence ; Clone Cells ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Haplorhini/*genetics ; Hominidae/genetics ; Humans ; Hylobates/genetics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Proteins/*genetics ; }, abstract = {Phylogenetic trees constructed using human mitochondrial sequences contain a large number of homoplasies. These are due either to repeated mutation or to recombination between mitochondrial lineages. We show that a tree constructed using synonymous variation in the protein coding sequences of 29 largely complete human mitochondrial molecules contains 22 homoplasies at 32 phylogenetically informative sites. This level of homoplasy is very unlikely if inheritance is clonal, even if we take into account base composition bias. There must either be 'hypervariable' sites or recombination between mitochondria. We present evidence which suggests that hypervariable sites do not exist in our data. It therefore seems likely that recombination has occurred between mitochondrial lineages in humans.}, }
@article {pmid10101183, year = {1999}, author = {Boore, JL}, title = {Animal mitochondrial genomes.}, journal = {Nucleic acids research}, volume = {27}, number = {8}, pages = {1767-1780}, doi = {10.1093/nar/27.8.1767}, pmid = {10101183}, issn = {0305-1048}, mesh = {Animals ; Arthropods/genetics ; Chordata, Nonvertebrate/genetics ; *DNA, Mitochondrial ; Echinodermata/genetics ; Humans ; Mitochondria/genetics ; }, abstract = {Animal mitochondrial DNA is a small, extrachromosomal genome, typically approximately 16 kb in size. With few exceptions, all animal mitochondrial genomes contain the same 37 genes: two for rRNAs, 13 for proteins and 22 for tRNAs. The products of these genes, along with RNAs and proteins imported from the cytoplasm, endow mitochondria with their own systems for DNA replication, transcription, mRNA processing and translation of proteins. The study of these genomes as they function in mitochondrial systems-'mitochondrial genomics'-serves as a model for genome evolution. Furthermore, the comparison of animal mitochondrial gene arrangements has become a very powerful means for inferring ancient evolutionary relationships, since rearrangements appear to be unique, generally rare events that are unlikely to arise independently in separate evolutionary lineages. Complete mitochondrial gene arrangements have been published for 58 chordate species and 29 non-chordate species, and partial arrangements for hundreds of other taxa. This review compares and summarizes these gene arrangements and points out some of the questions that may be addressed by comparing mitochondrial systems.}, }
@article {pmid10093228, year = {1999}, author = {DeWoody, JA and Chesser, RK and Baker, RJ}, title = {A translocated mitochondrial cytochrome b pseudogene in voles (Rodentia: Microtus).}, journal = {Journal of molecular evolution}, volume = {48}, number = {3}, pages = {380-382}, doi = {10.1007/pl00013154}, pmid = {10093228}, issn = {0022-2844}, mesh = {Animals ; Arvicolinae/classification/*genetics ; Base Sequence ; Cytochrome b Group/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; *Pseudogenes ; Sequence Homology, Nucleic Acid ; *Translocation, Genetic ; }, abstract = {A full-length cytochrome b pseudogene was found in rodents; it has apparently been translocated from a mitochondrion to the nuclear genome in the subfamily Arvicolinae. The pseudogene (psi cytb) differed from its mitochondrial counterpart at 201 of 1143 sites (17.6%) and by four indels. Cumulative evidence suggests that the pseudogene has been translocated to the nucleus. Phylogenetic reconstruction indicates that the pseudogene arose before the diversification of M. arvalis/M. rossiaemeridionalis from M. oeconomus, but after the divergence of the peromyscine/sigmodontine/ arvicoline clades some approximately 10 MYA. Published rates of divergence between mitochondrial genes and their nuclear pseudogenes suggest that the translocation of this mitochondrial gene to the nuclear genome occurred some 6 MYA, in agreement with the phylogenetic evidence.}, }
@article {pmid10093219, year = {1999}, author = {Steinhauser, S and Beckert, S and Capesius, I and Malek, O and Knoop, V}, title = {Plant mitochondrial RNA editing.}, journal = {Journal of molecular evolution}, volume = {48}, number = {3}, pages = {303-312}, doi = {10.1007/pl00006473}, pmid = {10093219}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Base Sequence ; Chloroplasts/metabolism ; DNA Primers ; *Mitochondrial Proteins ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/chemistry/genetics ; Plants/classification/*genetics ; Polymerase Chain Reaction ; RNA/*genetics ; *RNA Editing ; RNA, Mitochondrial ; Sequence Homology, Amino Acid ; }, abstract = {RNA editing affects messenger RNAs and transfer RNAs in plant mitochondria by site-specific exchange of cytidine and uridine bases in both seed and nonseed plants. Distribution of the phenomenon among bryophytes has been unclear since RNA editing has been detected in some but not all liverworts and mosses. A more detailed understanding of RNA editing in plants required extended data sets for taxa and sequences investigated. Toward this aim an internal region of the mitochondrial nad5 gene (1104 nt) was analyzed in a large collection of bryophytes and green algae (Charles). The genomic nad5 sequences predict editing in 30 mosses, 2 hornworts, and 7 simple thalloid and leafy liverworts (Jungermanniidae). No editing is, however, required in seven species of the complex thalloid liverworts (Marchantiidae) and the algae. RNA editing among the Jungermanniidae, on the other hand, reaches frequencies of up to 6% of codons being modified. Predictability of RNA editing from the genomic sequences was confirmed by cDNA analysis in the mosses Schistostega pennata and Rhodobryum roseum, the hornworts Anthoceros husnotii and A. punctatus, and the liverworts Metzgeria conjugata and Moerckia flotoviana. All C-to-U nucleotide exchanges predicted to reestablish conserved codons were confirmed. Editing in the hornworts includes the removal of genomic stop codons by frequent reverse U-to-C edits. Expectedly, no RNA editing events were identified by cDNA analysis in the marchantiid liverworts Ricciocarpos natans, Corsinia coriandra, and Lunularia cruciata. The findings are discussed in relation to models on the phylogeny of land plants.}, }
@article {pmid10093063, year = {1998}, author = {Campos, Y and Martín, MA and García-Silva, T and del Hoyo, P and Rubio, JC and Castro-Gago, M and García-Peñas, J and Casas, J and Cabello, A and Ricoy, JR and Arenas, J}, title = {Clinical heterogeneity associated with mitochondrial DNA depletion in muscle.}, journal = {Neuromuscular disorders : NMD}, volume = {8}, number = {8}, pages = {568-573}, doi = {10.1016/s0960-8966(98)00080-7}, pmid = {10093063}, issn = {0960-8966}, mesh = {Age Factors ; Blotting, Southern ; Child ; Child, Preschool ; Cytochrome-c Oxidase Deficiency ; DNA, Mitochondrial/*genetics/*metabolism ; DNA, Ribosomal/metabolism ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Mitochondria/enzymology/metabolism ; Mitochondrial Myopathies/*diagnosis/enzymology/*genetics ; Muscle, Skeletal/enzymology/*metabolism ; }, abstract = {We studied 10 patients with a variable degree of mtDNA depletion in muscle. Seven patients showed a clear-cut myopathic pattern, while the three remaining had brain involvement. There was no relationship between age at onset and relative mtDNA copy number in muscle, but we found an apparent correlation between clinical severity and degree of muscle mtDNA depletion. Muscle morphology showed that mtDNA depletion was associated with mitochondrial proliferation and cytochrome c oxidase negative fibers. Biochemical studies revealed single or combined defects of mtDNA-dependent respiratory chain complexes. Our data indicate that patients with mtDNA depletion may have a more variable age at onset and clinical evolution and wider phenotype than previously thought. The diagnosis of this condition, so far regarded as rare, may have been overlooked to some extent.}, }
@article {pmid10092866, year = {1999}, author = {Bof, M and Brandolin, G and Satre, M and Klein, G}, title = {The mitochondrial adenine nucleotide translocator from Dictyostelium discoideum. Functional characterization and DNA sequencing.}, journal = {European journal of biochemistry}, volume = {259}, number = {3}, pages = {795-800}, doi = {10.1046/j.1432-1327.1999.00088.x}, pmid = {10092866}, issn = {0014-2956}, mesh = {Animals ; Atractyloside/analogs &amp; derivatives/pharmacology ; Cell Differentiation/genetics ; Cell Division/drug effects ; Cloning, Molecular ; Dictyostelium/*genetics ; Enzyme Inhibitors/pharmacology ; Gene Expression Regulation, Developmental/genetics ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/chemistry/*genetics ; Phylogeny ; Protozoan Proteins/chemistry/*genetics ; RNA, Messenger/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The mitochondrial adenine nucleotide translocator (ANT) catalyses the exchange of ATP and ADP between the mitochondria and the cytosol. We have cloned and sequenced the gene encoding the Dictyostelium discoideum ANT (DdANT) and analysed its transcriptional regulation. The single copy D. discoideum ant gene encodes a protein of 309 amino acid residues with a predicted molecular mass of 33,469 Da and a pI of 9.85. These values are comparable to those of ANTs from mammals, insects and fungi. The long N-terminal extension characteristic of plant ANT is absent in DdANT. The protein coding region of the D. discoideum ant gene is interrupted by three introns. Polyclonal antibodies directed against the beef heart mitochondrial ANT or its C-terminal peptide recognized the D. discoideum protein. Northern blot analysis revealed that the expression of the D. discoideum ant gene decreased rapidly during the first hours of multicellular development but the amount of protein remained stable throughout differentiation.}, }
@article {pmid10085128, year = {1999}, author = {Nosek, J and Tomáska, L and Pagácová, B and Fukuhara, H}, title = {Mitochondrial telomere-binding protein from Candida parapsilosis suggests an evolutionary adaptation of a nonspecific single-stranded DNA-binding protein.}, journal = {The Journal of biological chemistry}, volume = {274}, number = {13}, pages = {8850-8857}, doi = {10.1074/jbc.274.13.8850}, pmid = {10085128}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Base Sequence ; Candida/*metabolism ; Cloning, Molecular ; Cross-Linking Reagents ; DNA, Mitochondrial/*genetics ; DNA, Single-Stranded/*genetics ; DNA-Binding Proteins/chemistry/*genetics ; Evolution, Molecular ; Fungal Proteins/genetics ; Glutaral/metabolism ; Molecular Sequence Data ; RNA, Messenger/metabolism ; Recombinant Proteins/genetics ; Repressor Proteins ; Saccharomyces cerevisiae/genetics ; *Saccharomyces cerevisiae Proteins ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Telomere/*genetics ; }, abstract = {The mitochondrial genome in a number of organisms is represented by linear DNA molecules with defined terminal structures. The telomeres of linear mitochondrial DNA (mtDNA) of yeast Candida parapsilosis consist of tandem arrays of large repetitive units possessing single-stranded 5' extension of about 110 nucleotides. Recently we identified the first mitochondrial telomere-binding protein (mtTBP) that specifically binds a sequence derived from the extreme end of C. parapsilosis linear mtDNA and protects it from attack by various DNA-modifying enzymes (Tomáska, L'., Nosek, J., and Fukuhara, H. (1997) J. Biol. Chem. 272, 3049-3059). Here we report the isolation of MTP1, the gene encoding mtTBP of C. parapsilosis. Sequence analysis revealed that mtTBP shares homology with several bacterial and mitochondrial single-stranded DNA-binding proteins that nonspecifically bind to single-stranded DNA with high affinity. Recombinant mtTBP displays a preference for the telomeric 5' overhang of C. parapsilosis mtDNA. The heterologous expression of a mtTBP-GFP fusion protein resulted in its localization to the mitochondria but was unable to functionally substitute for the loss of the S. cerevisiae homologue Rimlp. Analysis of the MTP1 gene and its translation product mtTBP may provide an insight into the evolutionary origin of linear mitochondrial genomes and the role it plays in their replication and maintenance.}, }
@article {pmid10082617, year = {1999}, author = {Koufopanou, V and Reid, DG and Ridgway, SA and Thomas, RH}, title = {A molecular phylogeny of the patellid limpets (Gastropoda: Patellidae) and its implications for the origins of their antitropical distribution.}, journal = {Molecular phylogenetics and evolution}, volume = {11}, number = {1}, pages = {138-156}, doi = {10.1006/mpev.1998.0557}, pmid = {10082617}, issn = {1055-7903}, mesh = {Animals ; DNA, Mitochondrial/chemistry/genetics ; *Evolution, Molecular ; Mitochondria/genetics ; Molecular Sequence Data ; Mollusca/classification/*genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Statistics as Topic ; Tropical Climate ; }, abstract = {The geographical distribution of the limpet family Patellidae is essentially antitropical, with 18 species in southern Africa, 10 in the northeastern Atlantic, and only 11 species elsewhere (although 4 of these do occur in the tropics). One possible explanation for this distribution is the suggestion of a recent, perhaps Early Pliocene, migration from southern Africa northward. We tested this hypothesis by constructing a molecular phylogeny, derived from partial sequences of the 12S and 16S mitochondrial genes, obtained from 34 of the 38 patellid species. Five species of Nacellidae and 3 of Lottiidae were included as potential outgroups. Analysis revealed that two patellid clades are represented in the northeastern Atlantic. The typical European patellids (Patella sensu stricto) form a single clade within which there is little molecular divergence, but are distant from all other patellids, thus refuting the idea of recent southern ancestry. From the limited fossil record and estimated rates of molecular divergence, we suggest that Patella s.s. may have originated at least as early as the Upper Cretaceous and that its northern distribution may have been achieved at the same time. The second patellid clade present in the northeastern Atlantic is the genus Cymbula, of which the single species Cymbula safiana extends from West Africa to the Mediterranean. In contrast to Patella s.s., C. safiana is indeed a member of an otherwise southern African clade and may have attained its present distribution more recently, during the Miocene. The geographical origin of the family remains unclear, but a Mesozoic radiation in southern Gondwana is possible. By optimizing morphological characters on our molecular tree, we consider the evolution of shell mineralogy and sperm ultrastructure. We also discuss the phylogenetic classification of the patellids and present some evidence that the family may not be monophyletic.}, }
@article {pmid10082616, year = {1999}, author = {Caterino, MS and Sperling, FA}, title = {Papilio phylogeny based on mitochondrial cytochrome oxidase I and II genes.}, journal = {Molecular phylogenetics and evolution}, volume = {11}, number = {1}, pages = {122-137}, doi = {10.1006/mpev.1998.0549}, pmid = {10082616}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Butterflies/classification/*genetics ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Mitochondria/enzymology/*genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Transfer, Leu/genetics ; RNA, Transfer, Tyr/genetics ; Statistics as Topic ; }, abstract = {Butterflies of the genus Papilio have served as the basis for numerous studies in insect physiology, genetics, and ecology. However, phylogenetic work on relationships among major lineages in the genus has been limited and inconclusive. We have sequenced 2.3 kb of DNA from the mitochondrial cytochrome oxidase I and II genes (COI and COII) for 23 Papilio taxa and two outgroups, Pachliopta neptunus and Eurytides marcellus, in order to assess the potential of these genes for use in Papilio phylogenetics and to examine patterns of gene evolution across a broad taxonomic range. Nucleotide and amino acid variation is distributed heterogeneously, both within and between genes. Structural features of the proteins are not always reliable predictors of variation. In a combined analysis, these sequences support a nearly fully resolved topology within subgenera and species groups, though higher level relationships among species groups require additional study. The most noteworthy findings are that neither Papilio alexanor nor P. xuthus belongs in the machaon group and that the subgenus Pterourus is paraphyletic with respect to the subgenus Pyrrhosticta. We leave relationships among members of the phorcas species group as a trichotomy. These two protein coding genes, particularly COI, show excellent performance in resolving relationships at the level of species and species groups among Papilionidae. We strongly endorse a similar approach for future studies aimed at these levels.}, }
@article {pmid10082615, year = {1999}, author = {Chippindale, PT and Davé, VK and Whitmore, DH and Robinson, JV}, title = {Phylogenetic relationships of North American damselflies of the genus Ischnura (Odonata: Zygoptera: Coenagrionidae) based on sequences of three mitochondrial genes.}, journal = {Molecular phylogenetics and evolution}, volume = {11}, number = {1}, pages = {110-121}, doi = {10.1006/mpev.1998.0559}, pmid = {10082615}, issn = {1055-7903}, mesh = {Animals ; Cytochrome b Group/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Electron Transport Complex IV/genetics ; Genetic Variation ; Insecta/classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/genetics ; Species Specificity ; Statistics as Topic ; }, abstract = {Relationships of North American damselflies of the genus Ischnura (Odonata: Zygoptera: Coenagrionidae) were investigated using a total of 1205 bp from portions of three mitochondrial genes: cytochrome b, cytochrome oxidase II, and 12S ribosomal DNA. Parsimony and neighbor joining analyses reveal a monophyletic group consisting of I. damula, I. demorsa, I. perparva, I. posita posita, I. posita atezca, I. verticalis, and probably I. denticollis, likely reflecting a recent radiation in North America. Ischnura kellicotti, I. barberi, I. prognata, I. hastata, I. ramburii, and I. capreola appear to represent much earlier divergences in the group. Many previous hypotheses of relationships among North American species of Ischnura are not supported by the molecular-based analyses. However, there is agreement in many respects between the results of the molecular phylogenetic analyses and the morphologically based conclusions of Kennedy (1919, "The Phylogeny of the Zygoptera," Ph.D. Dissertation, Cornell University, Ithaca). Although results of single-gene phylogenetic analyses often differ, there are very few cases in which there is strong support for conflicting relationships using different partitions of the data. Combined analysis of all three genes yields trees with stronger support overall than the single-gene analyses, and the combined data trees that result from diverse data treatments are congruent with one another in most respects.}, }
@article {pmid10082613, year = {1999}, author = {Voelker, G}, title = {Molecular evolutionary relationships in the avian genus Anthus (Pipits: Motacillidae).}, journal = {Molecular phylogenetics and evolution}, volume = {11}, number = {1}, pages = {84-94}, doi = {10.1006/mpev.1998.0555}, pmid = {10082613}, issn = {1055-7903}, mesh = {Animals ; Birds/classification/*genetics ; Cytochrome b Group/genetics ; DNA, Mitochondrial/chemistry/genetics ; *Evolution, Molecular ; Mitochondria/genetics ; Phylogeny ; Statistics as Topic ; }, abstract = {Nucleotide sequences for 1035 bp of the mitochondrial cytochrome b gene were used to determine the molecular evolutionary relationships of species in the cosmopolitan avian genus Anthus. Phylogenetic analysis of these mtDNA sequences supported four major clades within the genus: (1) the small-bodied African pipits, (2) a largely Palearctic clade, (3) a largely South American clade, and (4) an African-Eurasian-Australian clade. Anthus hellmayri, A. correndera, and A. rubescens are shown to be paraphyletic. The possibility of paraphyly within A. similis is instead inferred to be the discovery of a new species and supported by reference to the museum voucher specimen. Sequence divergence suggests a Pliocene/Miocene origin for the genus. Although Anthus cytochrome b is found not to be behaving in a clocklike fashion across all taxa, speciation during the Pleistocene epoch can be reasonably inferred for the 66% of sister pairs that are diverging in a clocklike manner. Base compositions at each codon position are similar to those found across a growing number of avian lineages. The resulting phylogenetic hypothesis is compared to previous hypotheses of Anthus relationships, all of which deal with relationships of a particular species or a particular species complex; roughly half of these previous hypotheses are supported.}, }
@article {pmid10082609, year = {1999}, author = {Kimball, RT and Braun, EL and Zwartjes, PW and Crowe, TM and Ligon, JD}, title = {A molecular phylogeny of the pheasants and partridges suggests that these lineages are not monophyletic.}, journal = {Molecular phylogenetics and evolution}, volume = {11}, number = {1}, pages = {38-54}, doi = {10.1006/mpev.1998.0562}, pmid = {10082609}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Birds/*genetics ; Cytochrome b Group/genetics ; DNA, Mitochondrial/chemistry/genetics ; *Evolution, Molecular ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {Cytochrome b and D-loop nucleotide sequences were used to study patterns of molecular evolution and phylogenetic relationships between the pheasants and the partridges, which are thought to form two closely related monophyletic galliform lineages. Our analyses used 34 complete cytochrome b and 22 partial D-loop sequences from the hypervariable domain I of the D-loop, representing 20 pheasant species (15 genera) and 12 partridge species (5 genera). We performed parsimony, maximum likelihood, and distance analyses to resolve these phylogenetic relationships. In this data set, transversion analyses gave results similar to those of global analyses. All of our molecular phylogenetic analyses indicated that the pheasants and partridges arose through a rapid radiation, making it difficult to establish higher level relationships. However, we were able to establish six major lineages containing pheasant and partridge taxa, including one lineage containing both pheasants and partridges (Gallus, Bambusicola and Francolinus). This result, supported by maximum likelihood tests, indicated that the pheasants and partridges do not form independent monophyletic lineages.}, }
@article {pmid10079281, year = {1999}, author = {Pesole, G and Gissi, C and De Chirico, A and Saccone, C}, title = {Nucleotide substitution rate of mammalian mitochondrial genomes.}, journal = {Journal of molecular evolution}, volume = {48}, number = {4}, pages = {427-434}, doi = {10.1007/pl00006487}, pmid = {10079281}, issn = {0022-2844}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; *Genome ; Humans ; Mammals/*genetics ; *Mutation ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {We present here for the first time a comprehensive study based on the analysis of closely related organisms to provide an accurate determination of the nucleotide substitution rate in mammalian mitochondrial genomes. This study examines the evolutionary pattern of the different functional mtDNA regions as accurately as possible on the grounds of available data, revealing some important "genomic laws." The main conclusions can be summarized as follows. (1) High intragenomic variability in the evolutionary dynamic of mtDNA was found. The substitution rate is strongly dependent on the region considered, and slow- and fast-evolving regions can be identified. Nonsynonymous sites, the D-loop central domain, and tRNA and rRNA genes evolve much more slowly than synonymous sites and the two peripheral D-loop region domains. The synonymous rate is fairly uniform over the genome, whereas the rate of nonsynonymous sites depends on functional constraints and therefore differs considerably between genes. (2) The commonly accepted statement that mtDNA evolves more rapidly than nuclear DNA is valid only for some regions, thus it should be referred to specific mitochondrial components. In particular, nonsynonymous sites show comparable rates in mitochondrial and nuclear genes; synonymous sites and small rRNA evolve about 20 times more rapidly and tRNAs about 100 times more rapidly in mitochondria than in their nuclear counterpart. (3) A species-specific evolution is particularly evident in the D-loop region. As the divergence times of the organism pairs under consideration are known with sufficient accuracy, absolute nucleotide substitution rates are also provided.}, }
@article {pmid10079198, year = {1999}, author = {Fey, J and Maréchal-Drouard, L}, title = {Compilation and analysis of plant mitochondrial promoter sequences: An illustration of a divergent evolution between monocot and dicot mitochondria.}, journal = {Biochemical and biophysical research communications}, volume = {256}, number = {2}, pages = {409-414}, doi = {10.1006/bbrc.1999.0349}, pmid = {10079198}, issn = {0006-291X}, mesh = {Base Sequence ; Consensus Sequence/genetics ; Conserved Sequence/genetics ; DNA, Mitochondrial/classification/*genetics ; DNA, Plant/classification/*genetics ; Deoxyribonucleotides/analysis/genetics ; *Evolution, Molecular ; Plants/classification/*genetics ; Promoter Regions, Genetic/*genetics ; RNA, Messenger/analysis ; RNA, Plant/analysis ; Response Elements/genetics ; Sequence Alignment ; Transcription, Genetic/genetics ; }, abstract = {We have analyzed 67 sequences surrounding transcription initiation sites identified in higher plant mitochondria. The sequences were classified, independently for monocots and dicots, according to the presence of the CRTA core element found upstream of the first transcribed nucleotide and previously reported as an essential element of plant mitochondrial consensus promoters. This compilation provides new elements concerning the structure of consensus promoters and the relative importance of non-conserved promoters in plant mitochondria. It can be emphasized that promoter regions exhibit several differences between monocot and dicot mitochondria, presumably reflecting a divergent evolution: The sequences classified among consensus promoters as well as the distance between the first transcribed nucleotide and the core element are highly conserved in dicots while more plasticity is observed in monocots. It also appears that the proportion of promoters with neither the conserved promoter sequence nor any conserved motif is far greater in dicots than in monocots.}, }
@article {pmid10070258, year = {1999}, author = {Blackstone, NW and Green, DR}, title = {The evolution of a mechanism of cell suicide.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {21}, number = {1}, pages = {84-88}, doi = {10.1002/(SICI)1521-1878(199901)21:1&lt;84::AID-BIES11&gt;3.0.CO;2-0}, pmid = {10070258}, issn = {0265-9247}, support = {AI40646/AI/NIAID NIH HHS/United States ; CA69831/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Apoptosis ; *Biological Evolution ; Cytochrome c Group/*physiology ; Humans ; Mitochondria/*physiology ; }, abstract = {In the vertebrates, programmed cell death or apoptosis frequently involves the relocalization of mitochondrial cytochrome c to the cytoplasm. This prominent role in the regulation of apoptosis is in addition to the primary function of cytochrome c in the mitochondrial electron transport chain. These seemingly divergent roles become plausible when considering the symbiotic origin of the mitochondrion. Symbiosis involves conflicts between levels of selection, in this case between the primitive host cell and the protomitochondria. In an aerobic environment, selection on the protomitochondria may have favored routine manipulations of the host cell's phenotype using products and by-products of oxidative phosphorylation, in particular reactive oxygen species (ROS). Blocking the mitochondrial electron transport chain by removing cytochrome c enhances the production of ROS; thus cytochrome c release by protomitochondria may have altered the host cell's phenotype via enhanced ROS production. Subsequently, this signaling pathway may have been refined by selection so that cytochrome c itself became the trigger for changes in the host's phenotype. A mechanism of apoptosis in metazoans may thus be a vestige of evolutionary conflicts within the eukaryotic cell.}, }
@article {pmid10066161, year = {1999}, author = {Gray, MW and Burger, G and Lang, BF}, title = {Mitochondrial evolution.}, journal = {Science (New York, N.Y.)}, volume = {283}, number = {5407}, pages = {1476-1481}, doi = {10.1126/science.283.5407.1476}, pmid = {10066161}, issn = {0036-8075}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; *Biological Evolution ; DNA, Mitochondrial/chemistry/*genetics ; *Eukaryotic Cells/physiology/ultrastructure ; Evolution, Molecular ; Genes ; Mitochondria/*genetics ; Models, Biological ; Phylogeny ; Symbiosis ; }, abstract = {The serial endosymbiosis theory is a favored model for explaining the origin of mitochondria, a defining event in the evolution of eukaryotic cells. As usually described, this theory posits that mitochondria are the direct descendants of a bacterial endosymbiont that became established at an early stage in a nucleus-containing (but amitochondriate) host cell. Gene sequence data strongly support a monophyletic origin of the mitochondrion from a eubacterial ancestor shared with a subgroup of the alpha-Proteobacteria. However, recent studies of unicellular eukaryotes (protists), some of them little known, have provided insights that challenge the traditional serial endosymbiosis-based view of how the eukaryotic cell and its mitochondrion came to be. These data indicate that the mitochondrion arose in a common ancestor of all extant eukaryotes and raise the possibility that this organelle originated at essentially the same time as the nuclear component of the eukaryotic cell rather than in a separate, subsequent event.}, }
@article {pmid10050274, year = {1999}, author = {Andreassen, J and Bennet-Jenkins, EM and Bryant, C}, title = {Immunology and biochemistry of Hymenolepis diminuta.}, journal = {Advances in parasitology}, volume = {42}, number = {}, pages = {223-275}, doi = {10.1016/s0065-308x(08)60150-5}, pmid = {10050274}, issn = {0065-308X}, mesh = {Animals ; Biological Evolution ; Host-Parasite Interactions ; Hymenolepiasis/immunology/*veterinary ; Hymenolepis/*immunology/*metabolism ; Larva/metabolism ; Mitochondria/metabolism ; Ovum/metabolism ; Rats ; Rodent Diseases/*immunology ; }, abstract = {This review is an account of modern research into the immunology and biochemistry of the rat tapeworm, Hymenolepis diminuta. The first half of the review is devoted to the immunological responses of the host to the parasite. It describes the specific responses that occur when the host is exposed to a primary infection, and the changes that occur when further infections are superimposed on the primary one. The aquisition of immunity to the tapeworm and its persistence in the absence of the infection are also discussed, as well as the non-specific responses of the host to the parasite. The second half of the review is concerned with biochemistry, summarizing the early biochemical work that has been carried out on the tapeworm and describing the metabolic pathways now thought to be characteristic of the parasite. What little information that exists on intermediary metabolism in eggs and larvae is summarized here. Much of this section is concerned with the role of mitochondria in H. diminuta, especially the control of the critical branchpoint (PK/PEPCK), which partitions carbon into either the cytosol or the mitochondrion. The role of 5-hydroxytryptamine in controlling both worm behaviour and metabolism is discussed, followed by a brief look at some other effectors that may prove in the future to have great significance in regulating the parasite. Finally, there is a detailed consideration of strain variation within H. diminuta and of the impact on the tapeworm of components of the immune system, formerly described as the 'crowding effect'. The review concludes with a brief discussion of evolutionary aspects of the rat-tapeworm relationship and a comprehensive bibliography.}, }
@article {pmid10048710, year = {1999}, author = {Calore, EE and Sesso, A and Puga, FR and Cavaliere, MJ and Calore, NM and Weg, R}, title = {Sarcoplasmic lipase and non-specific esterase inhibition in myofibers of rats intoxicated with the organophosphate isofenphos.}, journal = {Experimental and toxicologic pathology : official journal of the Gesellschaft fur Toxikologische Pathologie}, volume = {51}, number = {1}, pages = {27-33}, doi = {10.1016/S0940-2993(99)80054-2}, pmid = {10048710}, issn = {0940-2993}, mesh = {Animals ; Carboxylesterase ; Carboxylic Ester Hydrolases/*antagonists &amp; inhibitors/metabolism ; Cholinesterases/blood ; Diaphragm ; Histocytochemistry ; Insecticides/*toxicity ; Lipase/*antagonists &amp; inhibitors/metabolism ; Lipid Metabolism ; Male ; Necrosis ; Organothiophosphorus Compounds/*toxicity ; Rats ; Rats, Wistar ; Sarcoplasmic Reticulum/*enzymology/ultrastructure ; }, abstract = {The expression of sarcoplasmic esterases, lipases as well as the lipid content in the myofibers of the diaphragm of rats intoxicated with the organophosphate isofenphos was studied. Lipid accumulation was documented at light, electron microsopic and by morphometric studies. The distribution of these lipid droplets was irregular and abundant in myofibers with numerous mitochondria (predominantly oxidative fibers). Histochemical inhibition of sarcoplasmic esterases and lipases was observed in the intoxicated animals. This sarcoplasmic inhibition of esterases occurs roughly in parallel to the inhibition of plasma cholinesterase activity. The inhibition of sarcoplasmic lipases may explain, at least partially, the accumulation of lipids. This inhibition probably makes difficult the use of lipids as fuel, especially in the oxidative fibers. In contrast to the small amount of muscle necrosis, (1.30+/-0.745), metabolic muscle impairment was intense and extensive, i.e., decreased activities of esterases and lipases in the sarcoplasm, that should contribute to muscle weakness. Therefore, because segmental necrosis was most prominent in oxidative fibers (and these fibers use lipids as the principal fuel and contain the greater amount of lipases in the sarcoplasm), it is possible that inhibition of activity of lipases is responsible for the segmental necrosis. Although the exact role of these metabolic changes is not known, it is possible that they contribute not only to the induction and evolution of muscle cell necrosis but also to the muscle weakness and clinical impairment of animals and humans in the acute intoxication by these compounds.}, }
@article {pmid10028295, year = {1999}, author = {Dowton, M and Austin, AD}, title = {Evolutionary dynamics of a mitochondrial rearrangement "hot spot" in the Hymenoptera.}, journal = {Molecular biology and evolution}, volume = {16}, number = {2}, pages = {298-309}, doi = {10.1093/oxfordjournals.molbev.a026111}, pmid = {10028295}, issn = {0737-4038}, mesh = {Adenosine Triphosphatases/genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Codon ; DNA, Mitochondrial ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Gene Rearrangement/*physiology ; *Genes, Insect ; Hymenoptera/*genetics ; Molecular Sequence Data ; Mutation ; RNA ; RNA, Mitochondrial ; RNA, Transfer/*genetics ; }, abstract = {The arrangement of tRNA genes at the junction of the cytochrome oxidase II and ATPase 8 genes was examined across a broad range of Hymenoptera. Seven distinct arrangements of tRNA genes were identified among a group of wasps that have diverged over the last 180 Myr (suborder Apocrita); many of the rearrangements represent evolutionarily independent events. Approximately equal proportions of local rearrangements, inversions, and translocations were observed, in contrast to vertebrate mitochondria, in which local rearrangements predominate. Surprisingly, homoplasy was evident among certain types of rearrangement; a reversal of the plesiomorphic gene order has arisen on three separate occasions in the Insecta, while the tRNA(H) gene has been translocated to this locus on two separate occasions. Phylogenetic analysis indicates that this gene translocation is real and is not an artifactual translocation resulting from the duplication of a resident tRNA gene followed by mutation of the anticodon. The nature of the intergenic sequences surrounding this region does not indicate that it should be especially prone to rearrangement; it does not generally have the tandem or inverted repeats that might facilitate this plasticity. Intriguingly, these findings are consistent with the view that during the evolution of the Hymenoptera, rearrangements increased at the same time that the rate of point mutations and compositional bias also increased. This association may direct investigations into mitochondrial genome plasticity in other invertebrate lineages.}, }
@article {pmid10027191, year = {1998}, author = {Ragan, MA and Gaasterland, T}, title = {Microbial genescapes: a prokaryotic view of the yeast genome.}, journal = {Microbial &amp; comparative genomics}, volume = {3}, number = {4}, pages = {219-235}, doi = {10.1089/omi.1.1998.3.219}, pmid = {10027191}, issn = {1090-6592}, mesh = {Archaea/genetics ; Bacteria/genetics ; Computational Biology ; DNA, Fungal/genetics/metabolism ; DNA, Mitochondrial/genetics/metabolism ; Genes, Fungal ; *Genome, Fungal ; Open Reading Frames ; Phylogeny ; Saccharomyces cerevisiae/*genetics/metabolism ; }, abstract = {We examine the translated open reading frames (ORFs) of the yeast Saccharomyces cerevisiae, focusing on those that have FASTA matches in phyletically defined sets of completely sequenced genomes. On this basis, we identify archaeal yeast, bacterial yeast, universal yeast, and yeast ORFs that do not have a match in any of nine prokaryote genomes. Similarly, we examine the yeast mitochondrial genome and the subset of the yeast nuclear ORFs identified as being involved in mitochondrial biogenesis. For the yeast ORFs that match one or more ORFs in these prokaryote genomes, we examine the phyletic and functional distributions of these matches as a function of match strength. These results provide genome level insights into the origin of the eukaryotic cell and the origin of mitochondria. More generally, they exemplify how the growing database of prokaryote genome sequences can help us understand eukaryote genomes.}, }
@article {pmid10025161, year = {1998}, author = {Ito, A}, title = {[Processing of mitochondrial protein precursors].}, journal = {Seikagaku. The Journal of Japanese Biochemical Society}, volume = {70}, number = {12}, pages = {1401-1412}, pmid = {10025161}, issn = {0037-1017}, mesh = {Amino Acid Sequence ; Animals ; Evolution, Molecular ; Metalloendopeptidases/chemistry/physiology ; Mitochondria/*metabolism ; Protein Precursors/*metabolism ; Mitochondrial Processing Peptidase ; }, }
@article {pmid9972448, year = {1998}, author = {Nelson, DR}, title = {Metazoan cytochrome P450 evolution.}, journal = {Comparative biochemistry and physiology. Part C, Pharmacology, toxicology &amp; endocrinology}, volume = {121}, number = {1-3}, pages = {15-22}, doi = {10.1016/s0742-8413(98)10027-0}, pmid = {9972448}, issn = {1367-8280}, mesh = {Animals ; *Biological Evolution ; Cytochrome P-450 Enzyme System/*genetics ; Invertebrates/*enzymology ; Microsomes/enzymology ; Mitochondria/enzymology ; Phylogeny ; }, abstract = {There are 37 cytochrome P450 families currently identified in animals. The concept of higher order groupings of P450 families called P450 CLANS is introduced. The mammalian CYP3 and CYP5 families belong to the same clan as insect CYP6 and CYP9. All mitochondrial P450s seem to belong to the same clan. Lack of mitochondrial P450s in C. elegans suggests that mitochondrial P450s probably arose from the mistargeting of a microsomal P450 after the coelomates diverged from acoelomates and pseudocoelomates. Different taxonomic groups appear to have recruited different ancestral P450s for expansion as they evolved, since each major taxon seems to have one large cluster of P450s. In insects, this cluster derives from the ancestor to the CYP4 family. Vertebrates and C. elegans may have used the same ancestor independently to generate the CYP1, 2, 17, and 21 families in vertebrates and a large distinctive clan with 45 genes in C. elegans.}, }
@article {pmid9952460, year = {1999}, author = {Thelen, JJ and Miernyk, JA and Randall, DD}, title = {Molecular cloning and expression analysis of the mitochondrial pyruvate dehydrogenase from maize.}, journal = {Plant physiology}, volume = {119}, number = {2}, pages = {635-644}, pmid = {9952460}, issn = {0032-0889}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA, Complementary/genetics ; DNA, Plant/genetics ; Gene Expression Regulation, Enzymologic ; Gene Expression Regulation, Plant ; Genes, Plant ; Humans ; Mitochondria/enzymology ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Protein Conformation ; Pyruvate Dehydrogenase Complex/chemistry/*genetics ; Sequence Homology, Amino Acid ; Zea mays/*enzymology/*genetics ; }, abstract = {Four cDNAs, one encoding an alpha-subunit and three encoding beta-subunits of the mitochondrial pyruvate dehydrogenase, were isolated from maize (Zea mays L.) libraries. The deduced amino acid sequences of both alpha- and beta-subunits are approximately 80% identical with Arabidopsis and pea (Pisum sativum L.) homologs. The mature N terminus was determined for the beta-subunit by microsequencing the protein purified from etiolated maize shoot mitochondria and was resolved by two-dimensional gel electrophoresis. This single isoelectric species comprised multiple isoforms. Both alpha- and beta-subunits are encoded by multigene families in maize, as determined by Southern-blot analyses. RNA transcripts for both alpha- and beta-subunits were more abundant in roots than in young leaves or etiolated shoots. Pyruvate dehydrogenase activity was also higher in roots (5-fold) compared with etiolated shoots and leaves. Both subunits were present at similar levels in all tissues examined, indicating coordinated gene regulation. The protein levels were highest in heterotrophic organs and in pollen, which contained about 2-fold more protein than any other organ examined. The relative abundance of these proteins in nonphotosynthetic tissues may reflect a high cellular content of mitochondria, a high level of respiratory activity, or an extra plastidial requirement for acetate.}, }
@article {pmid9952445, year = {1999}, author = {Krath, BN and Hove-Jensen, B}, title = {Organellar and cytosolic localization of four phosphoribosyl diphosphate synthase isozymes in spinach.}, journal = {Plant physiology}, volume = {119}, number = {2}, pages = {497-506}, pmid = {9952445}, issn = {0032-0889}, mesh = {Amino Acid Sequence ; Base Sequence ; Chloroplasts/enzymology ; Cloning, Molecular ; Cytosol/enzymology ; DNA, Complementary/genetics/isolation &amp; purification ; DNA, Plant/genetics/isolation &amp; purification ; Escherichia coli/genetics ; Genetic Complementation Test ; Isoenzymes/genetics/*metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Organelles/enzymology ; Pisum sativum/enzymology ; Phylogeny ; RNA, Messenger/genetics ; RNA, Plant/genetics ; Ribose-Phosphate Pyrophosphokinase/genetics/*metabolism ; Sequence Homology, Amino Acid ; Spinacia oleracea/*enzymology/genetics ; }, abstract = {Four cDNAs encoding phosphoribosyl diphosphate (PRPP) synthase were isolated from a spinach (Spinacia oleracea) cDNA library by complementation of an Escherichia coli Deltaprs mutation. The four gene products produced PRPP in vitro from ATP and ribose-5-phosphate. Two of the enzymes (isozymes 1 and 2) required inorganic phosphate for activity, whereas the others were phosphate independent. PRPP synthase isozymes 2 and 3 contained 76 and 87 amino acid extensions, respectively, at their N-terminal ends in comparison with other PRPP synthases. Isozyme 2 was synthesized in vitro and shown to be imported and processed by pea (Pisum sativum) chloroplasts. Amino acid sequence analysis indicated that isozyme 3 may be transported to mitochondria and that isozyme 4 may be located in the cytosol. The deduced amino acid sequences of isozymes 1 and 2 and isozymes 3 and 4 were 88% and 75% identical, respectively. In contrast, the amino acid identities of PRPP synthase isozyme 1 or 2 with 3 or 4 was modest (22%-25%), but the sequence motifs for binding of PRPP and divalent cation-nucleotide were identified in all four sequences. The results indicate that PRPP synthase isozymes 3 and 4 belong to a new class of PRPP synthases that may be specific to plants.}, }
@article {pmid9949831, year = {1998}, author = {Green, DR and Amarante-Mendes, GP}, title = {The point of no return: mitochondria, caspases, and the commitment to cell death.}, journal = {Results and problems in cell differentiation}, volume = {24}, number = {}, pages = {45-61}, doi = {10.1007/978-3-540-69185-3_3}, pmid = {9949831}, issn = {0080-1844}, mesh = {Animals ; *Apoptosis/genetics ; *Caspases ; Humans ; *Mitochondria ; Models, Biological ; Oncogenes ; }, abstract = {Apoptosis is a specialized mode of cell death finely regulated at the molecular level and conserved throughout evolution. In many instances during normal development or in order to maintain the homeostasis of a multicellular organism, a strategic intracellular program is initiated ensuring the fate of unwanted cells. Interference with this program has been implicated in many pathologies, particularly in cancer and autoimmune diseases. What is most important, from the organism's point of view, is that the dismissal of the outcast cells is accomplished serenely, i.e., the dying cells resign their existence without causing an inflammatory reaction. Therefore, the ability to manipulate the cell death machinery is an obvious goal of medical research. Here, we debate the idea of the point-of-no-return and propose models for the role of "initiator" and "executioner" caspases in the death program. We argue that, in many circumstances, the cells are committed to die before the execution phase of apoptosis starts. This commitment event is coordinated by the mitochondria and can be blocked by anti-apoptotic oncogenes.}, }
@article {pmid9931253, year = {1999}, author = {Rassow, J and Dekker, PJ and van Wilpe, S and Meijer, M and Soll, J}, title = {The preprotein translocase of the mitochondrial inner membrane: function and evolution.}, journal = {Journal of molecular biology}, volume = {286}, number = {1}, pages = {105-120}, doi = {10.1006/jmbi.1998.2455}, pmid = {9931253}, issn = {0022-2836}, mesh = {Adenosine Triphosphatases/*physiology ; Amino Acid Sequence ; Animals ; Bacterial Proteins/*physiology ; Carrier Proteins/metabolism ; *Escherichia coli Proteins ; HSP70 Heat-Shock Proteins/metabolism ; Intracellular Membranes/enzymology ; Membrane Proteins/chemistry/metabolism ; *Membrane Transport Proteins ; Mitochondria/*enzymology/metabolism ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Precursor Protein Import Complex Proteins ; Molecular Sequence Data ; Plants ; *Repressor Proteins ; SEC Translocation Channels ; *Saccharomyces cerevisiae Proteins ; SecA Proteins ; Sequence Homology, Amino Acid ; }, abstract = {Growing mitochondria acquire most of their proteins by the uptake of mitochondrial preproteins from the cytosol. To mediate this protein import, both mitochondrial membranes contain independent protein transport systems: the Tom machinery in the outer membrane and the Tim machinery in the inner membrane. Transport of proteins across the inner membrane and sorting to the different inner mitochondrial compartments is mediated by several protein complexes which have been identified in the past years. A complex containing the integral membrane proteins Tim17 and Tim23 constitutes the import channel for preproteins containing amino-terminal hydrophilic presequences. This complex is associated with Tim44 which serves as an adaptor protein for the binding of mtHsp70 to the membrane. mtHsp70, a 70 kDa heat shock protein of the mitochondrial matrix, drives the ATP-dependent import reaction of the processed preprotein after cleavage of the presequence. Preproteins containing internal targeting information are imported by a separate import machinery, which consists of the intermembrane-space proteins Tim9, Tim10, and Tim12, and the inner membrane proteins Tim22 and Tim54. The proteins Tim17, Tim22, and Tim23 have in common a similar topology in the membrane and a homologous amino acid sequence. Moreover, they show a sequence similarity to OEP16, a channel-forming amino acid transporter in the outer envelope of chloroplasts, and to LivH, a component of a prokaryotic amino acid permease, defining a new PRAT-family of preprotein and amino acid transporters.}, }
@article {pmid9928538, year = {1998}, author = {Ohno, S}, title = {The notion of the Cambrian pananimalia genome and a genomic difference that separated vertebrates from invertebrates.}, journal = {Progress in molecular and subcellular biology}, volume = {21}, number = {}, pages = {97-117}, doi = {10.1007/978-3-642-72236-3_5}, pmid = {9928538}, issn = {0079-6484}, mesh = {Animals ; *Biological Evolution ; Cyanobacteria ; Evolution, Molecular ; Fossils ; *Genome ; Invertebrates/classification/*genetics ; Mitochondria ; Vertebrates/classification/*genetics ; }, }
@article {pmid9921284, year = {1998}, author = {de-Souza, W and de-Carvalho, TU and de-Melo, ET and Soares, CP and Coimbra, ES and Rosestolato, CT and Ferreira, SR and Vieira, M}, title = {The use of confocal laser scanning microscopy to analyze the process of parasitic protozoon-host cell interaction.}, journal = {Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas}, volume = {31}, number = {11}, pages = {1459-1470}, doi = {10.1590/s0100-879x1998001100015}, pmid = {9921284}, issn = {0100-879X}, mesh = {Animals ; Chlorocebus aethiops ; *Host-Parasite Interactions ; Macrophages, Peritoneal ; Mice/*parasitology ; Microscopy, Confocal ; Toxoplasma/*physiology ; Trypanosoma cruzi/*physiology ; Vero Cells ; }, abstract = {In this communication we review the results obtained with the confocal laser scanning microscope to characterize the interaction of epimastigote and trypomastigote forms of Trypanosoma cruzi and tachyzoites of Toxoplasma gondii with host cells. Early events of the interaction process were studied by the simultaneous localization of sites of protein phosphorylation, revealed by immunocytochemistry, and sites of actin assembly, revealed by the use of labeled phaloidin. The results obtained show that proteins localized in the interaction sites are phosphorylated. The process of formation of the parasitophorous vacuole was monitored by labeling the host cell surface with fluorescent probes for lipids (PKH26), proteins (DTAF) and sialic acid (FITC-thiosemicarbazide) before interaction with the parasites. Evidence was obtained indicating transfer of components of the host cell surface to the parasite surface in the beginning of the interaction process. We also analyzed the distribution of cytoskeletal structures (microtubules and microfilaments visualized with specific antibodies), mitochondria (visualized with rhodamine 123), the Golgi complex (visualized with C6-NBD-ceramide) and the endoplasmic reticulum (visualized with anti-reticulin antibodies and DIOC6) during the evolution of intracellular parasitism. The results obtained show that some, but not all, structures change their position during evolution of the intracellular parasitism.}, }
@article {pmid9914833, year = {1998}, author = {Azzone, GF}, title = {From bioenergetics to philosophy of science: a brief report of an exciting cultural journey.}, journal = {BioFactors (Oxford, England)}, volume = {8}, number = {3-4}, pages = {305-316}, doi = {10.1002/biof.5520080319}, pmid = {9914833}, issn = {0951-6433}, mesh = {Animals ; Biological Evolution ; *Energy Metabolism ; History, 20th Century ; Humans ; Italy ; Membrane Potentials ; Mitochondria/*physiology ; Physiology/history ; Proton Pumps ; }, }
@article {pmid9890461, year = {1999}, author = {Sokol, RJ and Treem, WR}, title = {Mitochondria and childhood liver diseases.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {28}, number = {1}, pages = {4-16}, doi = {10.1097/00005176-199901000-00005}, pmid = {9890461}, issn = {0277-2116}, support = {5 MO1 RR00069/RR/NCRR NIH HHS/United States ; R01DK38446/DK/NIDDK NIH HHS/United States ; }, mesh = {Child ; DNA, Mitochondrial/genetics/*physiology ; Humans ; Liver Diseases/*etiology/physiopathology/therapy ; Metabolism, Inborn Errors/genetics/physiopathology ; Mitochondria/genetics/*physiology ; Mitochondria, Liver/physiology ; }, abstract = {The newly recognized mitochondrial hepatopathies should be considered in the differential diagnosis of acute and chronic liver disease in childhood. It may appear as neonatal liver failure, delayed onset liver failure in early childhood or as a multisystemic process. Comparison of features of several of the known primary mitochondrial hepatopathies is provided in Table 5. Secondary mitochondrial hepatopathies are examples of the critical importance of mitochondrial function in the pathogenesis of liver injury. Our improved understanding of the role of the mitochondria in cellular necrosis and apoptosis opens the way for development of new therapeutic approaches to several hepatic disorders. Primary mitochondrial hepatopathies (especially the respiratory chain defects) should be considered in any child with liver disease and neuromuscular involvement, multisystemic disease, lactic acidosis or rapidly progressive disease, and when hepatic steatosis is the dominant histologic finding on examination of a liver specimen. Current therapies are inadequate; improved therapeutic strategies are needed for these disorders. Some patients with respiratory chain defects limited to the liver have had successful liver transplantation. This field is in evolution and will undoubtedly provide new and important developments as the next millennium begins.}, }
@article {pmid9889265, year = {1999}, author = {Lenhard, B and Orellana, O and Ibba, M and Weygand-Durasević, I}, title = {tRNA recognition and evolution of determinants in seryl-tRNA synthesis.}, journal = {Nucleic acids research}, volume = {27}, number = {3}, pages = {721-729}, doi = {10.1093/nar/27.3.721}, pmid = {9889265}, issn = {0305-1048}, mesh = {Acylation ; Animals ; Escherichia coli ; *Evolution, Molecular ; Phylogeny ; Protein Biosynthesis ; RNA, Transfer, Amino Acid-Specific/metabolism ; RNA, Transfer, Amino Acyl/*biosynthesis ; Serine-tRNA Ligase/*metabolism ; }, abstract = {We have analyzed the evolution of recognition of tRNAsSerby seryl-tRNA synthetases, and compared it to other type 2 tRNAs, which contain a long extra arm. In Eubacteria and chloroplasts this type of tRNA is restricted to three families: tRNALeu, tRNASer and tRNATyr. tRNALeuand tRNASer also carry a long extra arm in Archaea, Eukarya and all organelles with the exception of animal mitochondria. In contrast, the long extra arm of tRNATyr is far less conserved: it was drastically shortened after the separation of Archaea and Eukarya from Eubacteria, and it is also truncated in animal mitochondria. The high degree of phylo-genetic divergence in the length of tRNA variable arms, which are recognized by both class I and class II aminoacyl-tRNA synthetases, makes type 2 tRNA recognition an ideal system with which to study how tRNA discrimination may have evolved in tandem with the evolution of other components of the translation machinery.}, }
@article {pmid9882656, year = {1999}, author = {Gribaldo, S and Lumia, V and Creti, R and Conway de Macario, E and Sanangelantoni, A and Cammarano, P}, title = {Discontinuous occurrence of the hsp70 (dnaK) gene among Archaea and sequence features of HSP70 suggest a novel outlook on phylogenies inferred from this protein.}, journal = {Journal of bacteriology}, volume = {181}, number = {2}, pages = {434-443}, pmid = {9882656}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Animals ; Archaea/*classification/*genetics ; Bacteria/classification/*genetics ; *Escherichia coli Proteins ; *Evolution, Molecular ; Gram-Positive Bacteria/classification/genetics ; HSP70 Heat-Shock Proteins/*chemistry/*genetics ; Likelihood Functions ; Molecular Chaperones/genetics ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Occurrence of the hsp70 (dnaK) gene was investigated in various members of the domain Archaea comprising both euryarchaeotes and crenarchaeotes and in the hyperthermophilic bacteria Aquifex pyrophilus and Thermotoga maritima representing the deepest offshoots in phylogenetic trees of bacterial 16S rRNA sequences. The gene was not detected in 8 of 10 archaea examined but was found in A. pyrophilus and T. maritima, from which it was cloned and sequenced. Comparative analyses of the HSP70 amino acid sequences encoded in these genes, and others in the databases, showed that (i) in accordance with the vicinities seen in rRNA-based trees, the proteins from A. pyrophilus and T. maritima form a thermophilic cluster with that from the green nonsulfur bacterium Thermomicrobium roseum and are unrelated to their counterparts from gram-positive bacteria, proteobacteria/mitochondria, chlamydiae/spirochetes, deinococci, and cyanobacteria/chloroplasts; (ii) the T. maritima HSP70 clusters with the homologues from the archaea Methanobacterium thermoautotrophicum and Thermoplasma acidophilum, in contrast to the postulated unique kinship between archaea and gram-positive bacteria; and (iii) there are exceptions to the reported association between an insert in HSP70 and gram negativity, or vice versa, absence of insert and gram positivity. Notably, the HSP70 from T. maritima lacks the insert, although T. maritima is phylogenetically unrelated to the gram-positive bacteria. These results, along with the absence of hsp70 (dnaK) in various archaea and its presence in others, suggest that (i) different taxa retained either one or the other of two hsp70 (dnaK) versions (with or without insert), regardless of phylogenetic position; and (ii) archaea are aboriginally devoid of hsp70 (dnaK), and those that have it must have received it from phylogenetically diverse bacteria via lateral gene transfer events that did not involve replacement of an endogenous hsp70 (dnaK) gene.}, }
@article {pmid9878631, year = {1999}, author = {Wu, D and Wright, DA and Wetzel, C and Voytas, DF and Rodermel, S}, title = {The IMMUTANS variegation locus of Arabidopsis defines a mitochondrial alternative oxidase homolog that functions during early chloroplast biogenesis.}, journal = {The Plant cell}, volume = {11}, number = {1}, pages = {43-55}, pmid = {9878631}, issn = {1040-4651}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics ; *Arabidopsis Proteins ; Base Sequence ; Chloroplasts/*genetics ; Cloning, Molecular ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Mutation ; Nuclear Proteins/*genetics/metabolism ; Oxidoreductases/*genetics ; Phylogeny ; Pigmentation/*genetics ; Plant Leaves/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Nuclear gene-induced variegation mutants provide a powerful system to dissect interactions between the genetic systems of the nucleus-cytoplasm, the chloroplast, and the mitochondrion. The immutans (im) variegation mutation of Arabidopsis is nuclear and recessive and results in the production of green- and white-sectored leaves. The green sectors contain cells with normal chloroplasts, whereas the white sectors are heteroplastidic and contain cells with abnormal, pigment-deficient plastids as well as some normal chloroplasts. White sector formation can be promoted by enhanced light intensities, but sectoring becomes irreversible early in leaf development. The white sectors accumulate the carotenoid precursor phytoene. We have positionally cloned IM and found that the gene encodes a 40.5-kD protein with sequence motifs characteristic of alternative oxidase, a mitochondrial protein that functions as a terminal oxidase in the respiratory chains of all plants. However, phylogenetic analyses revealed that the IM protein is only distantly related to these other alternative oxidases, suggesting that IM is a novel member of this protein class. We sequenced three alleles of im, and all are predicted to be null. Our data suggest a model of variegation in which the IM protein functions early in chloroplast biogenesis as a component of a redox chain responsible for phytoene desaturation but that a redundant electron transfer function is capable of compensating for IM activity in some plastids and cells.}, }
@article {pmid9878551, year = {1998}, author = {Loeffen, JL and Triepels, RH and van den Heuvel, LP and Schuelke, M and Buskens, CA and Smeets, RJ and Trijbels, JM and Smeitink, JA}, title = {cDNA of eight nuclear encoded subunits of NADH:ubiquinone oxidoreductase: human complex I cDNA characterization completed.}, journal = {Biochemical and biophysical research communications}, volume = {253}, number = {2}, pages = {415-422}, doi = {10.1006/bbrc.1998.9786}, pmid = {9878551}, issn = {0006-291X}, mesh = {Adult ; Aged ; Amino Acid Sequence ; Animals ; Base Sequence ; Cattle ; Cell Nucleus/*enzymology/*genetics ; DNA, Complementary/*isolation &amp; purification ; Escherichia coli/enzymology/genetics ; Evolution, Molecular ; Female ; Humans ; Male ; Middle Aged ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; NAD(P)H Dehydrogenase (Quinone)/*chemistry/*genetics/isolation &amp; purification ; Neurospora crassa/enzymology/genetics ; }, abstract = {NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits of which 34 are encoded by nDNA. Here we report the cDNA sequences of the hitherto uncharacterized 8 nuclear encoded subunits, all located within the hydrophobic protein (HP) fraction of complex I. Now all currently known 41 proteins of human NADH:ubiquinone oxidoreductase have been characterized and reported in literature, which enables more complete mutational analysis studies of isolated complex I-deficient patients.}, }
@article {pmid9878234, year = {1998}, author = {Gleeson, DM and Rowell, DM and Tait, NN and Briscoe, DA and Higgins, AV}, title = {Phylogenetic relationships among onychophora from Australasia inferred from the mitochondrial cytochrome oxidase subunit I gene.}, journal = {Molecular phylogenetics and evolution}, volume = {10}, number = {2}, pages = {237-248}, doi = {10.1006/mpev.1998.0512}, pmid = {9878234}, issn = {1055-7903}, mesh = {Animals ; Asia ; Australia ; Base Sequence ; Electron Transport Complex IV/*genetics ; Invertebrates/*classification/enzymology/genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {Nucleotide sequence variation in a region of the mitochondrial cytochrome oxidase subunit I (COI) gene (456 bp) was examined for 26 onychophorans representing 15 genera of the family Peripatopsidae from Australasia. Sequence analysis revealed high intergeneric COI sequence divergence (up to 20.6% corrected) but low amino acid substitution rates, with high levels of transitional saturation evident. Among unambiguously alignable sequences, parsimony and distance analyses revealed a broadly congruent tree topology, robust to various algorithms and statistical analysis. There are two major groupings. One, largely unresolved, consists entirely of Australian mainland taxa. The other, for which there is convincing support, includes all of the New Zealand and Tasmanian taxa together with one mainland Australian species. In respect of the two major groupings, this topology is consistent with previous morphologically based phylogenies and provides further evidence for an ancient radiation within the mainland Australian Onychophora. The biogeographic implications of the close affinities revealed between the Tasmanian and New Zealand taxa are discussed.}, }
@article {pmid9873084, year = {1999}, author = {Rasmussen, AS and Arnason, U}, title = {Phylogenetic studies of complete mitochondrial DNA molecules place cartilaginous fishes within the tree of bony fishes.}, journal = {Journal of molecular evolution}, volume = {48}, number = {1}, pages = {118-123}, doi = {10.1007/pl00006439}, pmid = {9873084}, issn = {0022-2844}, mesh = {Animals ; DNA, Mitochondrial/*chemistry/*genetics ; Dogfish/genetics ; Fishes/*classification/*genetics ; Genome ; Likelihood Functions ; Mitochondria, Liver/chemistry ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {It is commonly acknowledged that cartilaginous fishes, Chondrichthyes, have a basal position among the Gnathostomata (jawed vertebrates). In order to explore this relationship we have sequenced the complete mitochondrial genome of the spiny dogfish, Squalus acanthias, and included it in a phylogenetic analysis together with a number of bony fishes and amniotes. The phylogenetic reconstructions placed the dogfish among the bony fishes. Thus, and contrary to the common view, the analyses have shown that the position of the sharks is not basal among the gnathostomes. The presently recognized phylogenetic position of the dogfish was identified irrespective of the outgroup used, echinoderms or agnathan fishes. The lungfish was the most basal gnathostome fish, while the teleosteans had an apical position in the piscine tree. A basal position of the dogfish among the gnathostomes was statistically rejected, but the phylogenetic relationship among the coelacanth, spiny dogfish, and teleosts was not conclusively resolved. The findings challenge the current theory that sharks and other chondrichthyans, if monophyletic, are the sister group to all other extant gnathostomes. The results open to question the status of several morphological characters commonly used in piscine phylogenetic reconstruction, most notably the presence versus absence of endochondral bone in the endoskeleton, the macromeric versus micromeric structure of the exoskeleton, and the presence/absence of swimbladder and/or lung. The study also confirmed recent findings demonstrating that the origin of the amniotes is deeper than the diversification of extant bony fishes.}, }
@article {pmid9867626, year = {1998}, author = {Pennisi, E}, title = {Genome links typhus bug to mitochondrion.}, journal = {Science (New York, N.Y.)}, volume = {282}, number = {5392}, pages = {1243}, doi = {10.1126/science.282.5392.1243}, pmid = {9867626}, issn = {0036-8075}, mesh = {Biological Evolution ; DNA, Bacterial/genetics ; DNA, Mitochondrial/*genetics ; Gene Expression ; Genes, Bacterial ; *Genome, Bacterial ; Mitochondria/*genetics ; Rickettsia prowazekii/*genetics/metabolism ; }, }
@article {pmid9866199, year = {1998}, author = {Cao, Y and Waddell, PJ and Okada, N and Hasegawa, M}, title = {The complete mitochondrial DNA sequence of the shark Mustelus manazo: evaluating rooting contradictions to living bony vertebrates.}, journal = {Molecular biology and evolution}, volume = {15}, number = {12}, pages = {1637-1646}, doi = {10.1093/oxfordjournals.molbev.a025891}, pmid = {9866199}, issn = {0737-4038}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Lampreys/genetics ; Likelihood Functions ; Mammals/genetics ; *Models, Genetic ; *Phylogeny ; Proteins/genetics ; Sharks/*genetics ; Vertebrates/*genetics ; }, abstract = {A remarkable example of a misleading mitochondrial protein tree is presented, involving ray-finned fishes, coelacanths, lungfishes, and tetrapods, with sea lampreys as an outgroup. In previous molecular phylogenetic studies on the origin of tetrapods, ray-finned fishes have been assumed as an outgroup to the tetrapod/lungfish/coelacanth clade, an assumption supported by morphological evidence. Standard methods of molecular phylogenetics applied to the protein-encoding genes of mitochondria, however, give a bizarre tree in which lamprey groups with lungfish and, therefore, ray-finned fishes are not the outgroup to a tetrapod/lungfish/coelacanth clade. All of the dozens of published phylogenetic methods, including every possible modification to maximum likelihood known to us (such as inclusion of site heterogeneity and exclusion of potentially misleading hydrophobic amino acids), fail to place the ray-finned fishes in a biologically acceptable position. A likely cause of this failure may be the use of an inappropriate outgroup. Accordingly, we have determined the complete mitochondrial DNA sequence from the shark, Mustelus manazo, which we have used as an alternative and more proximal outgroup than the lamprey. Using sharks as the outgroup, lungfish appear to be the closest living relative of tetrapods, although the possibility of a lungfish/coelacanth clade being the sister group of tetrapods cannot be excluded.}, }
@article {pmid9866196, year = {1998}, author = {Yang, Z and Nielsen, R and Hasegawa, M}, title = {Models of amino acid substitution and applications to mitochondrial protein evolution.}, journal = {Molecular biology and evolution}, volume = {15}, number = {12}, pages = {1600-1611}, doi = {10.1093/oxfordjournals.molbev.a025888}, pmid = {9866196}, issn = {0737-4038}, support = {GM40282/GM/NIGMS NIH HHS/United States ; }, mesh = {*Amino Acid Substitution ; Animals ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Humans ; Likelihood Functions ; Mammals/*genetics ; Mitochondria/*metabolism ; *Models, Genetic ; Models, Statistical ; *Phylogeny ; Proteins/*genetics ; }, abstract = {Models of amino acid substitution were developed and compared using maximum likelihood. Two kinds of models are considered. "Empirical" models do not explicitly consider factors that shape protein evolution, but attempt to summarize the substitution pattern from large quantities of real data. "Mechanistic" models are formulated at the codon level and separate mutational biases at the nucleotide level from selective constraints at the amino acid level. They account for features of sequence evolution, such as transition-transversion bias and base or codon frequency biases, and make use of physicochemical distances between amino acids to specify nonsynonymous substitution rates. A general approach is presented that transforms a Markov model of codon substitution into a model of amino acid replacement. Protein sequences from the entire mitochondrial genomes of 20 mammalian species were analyzed using different models. The mechanistic models were found to fit the data better than empirical models derived from large databases. Both the mutational distance between amino acids (determined by the genetic code and mutational biases such as the transition-transversion bias) and the physicochemical distance are found to have strong effects on amino acid substitution rates. A significant proportion of amino acid substitutions appeared to have involved more than one codon position, indicating that nucleotide substitutions at neighboring sites may be correlated. Rates of amino acid substitution were found to be highly variable among sites.}, }
@article {pmid9859986, year = {1998}, author = {Akhmanova, A and Voncken, F and van Alen, T and van Hoek, A and Boxma, B and Vogels, G and Veenhuis, M and Hackstein, JH}, title = {A hydrogenosome with a genome.}, journal = {Nature}, volume = {396}, number = {6711}, pages = {527-528}, doi = {10.1038/25023}, pmid = {9859986}, issn = {0028-0836}, mesh = {Anaerobiosis ; Animals ; Ciliophora/genetics/*metabolism/ultrastructure ; Cloning, Molecular ; Cockroaches/parasitology ; DNA, Complementary ; DNA, Mitochondrial/genetics/isolation &amp; purification ; DNA, Protozoan/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics/isolation &amp; purification ; *Evolution, Molecular ; *Genome, Protozoan ; Hydrogen/*metabolism ; Hydrogenase/genetics ; Mitochondria/genetics/*metabolism/ultrastructure ; Organelles/genetics/*metabolism/ultrastructure ; Polymerase Chain Reaction ; }, }
@article {pmid9859981, year = {1998}, author = {Embley, TM and Martin, W}, title = {A hydrogen-producing mitochondrion.}, journal = {Nature}, volume = {396}, number = {6711}, pages = {517-519}, doi = {10.1038/24994}, pmid = {9859981}, issn = {0028-0836}, mesh = {Adenosine Triphosphate/biosynthesis ; Anaerobiosis ; Animals ; Biological Evolution ; Ciliophora/genetics/*metabolism/ultrastructure ; Cockroaches/parasitology ; DNA, Mitochondrial ; DNA, Protozoan ; Energy Metabolism ; Hydrogen/*metabolism ; Mitochondria/genetics/*metabolism ; Organelles/metabolism ; }, }
@article {pmid9857177, year = {1998}, author = {Clavería, C and Albar, JP and Serrano, A and Buesa, JM and Barbero, JL and Martínez-A, C and Torres, M}, title = {Drosophila grim induces apoptosis in mammalian cells.}, journal = {The EMBO journal}, volume = {17}, number = {24}, pages = {7199-7208}, pmid = {9857177}, issn = {0261-4189}, mesh = {3T3 Cells/cytology ; Amino Acid Sequence ; Animals ; *Apoptosis ; Caspases/metabolism ; Cell Compartmentation ; Conserved Sequence ; Drosophila ; *Drosophila Proteins ; Fluorescent Antibody Technique ; In Situ Nick-End Labeling ; Insect Proteins/genetics/*metabolism ; Mice ; Microscopy, Video ; Mitochondria/*metabolism ; Neuropeptides/genetics/*metabolism ; Proto-Oncogene Proteins c-bcl-2/metabolism ; Recombinant Proteins ; Signal Transduction ; Species Specificity ; Transfection ; Tumor Suppressor Protein p53/metabolism ; fas Receptor/metabolism ; }, abstract = {Genetic studies have shown that grim is a central genetic switch of programmed cell death in Drosophila; however, homologous genes have not been described in other species, nor has its mechanism of action been defined. We show here that grim expression induces apoptosis in mouse fibroblasts. Cell death induced by grim in mammalian cells involves membrane blebbing, cytoplasmic loss and nuclear DNA fragmentation. Grim-induced apoptosis is blocked by both natural and synthetic caspase inhibitors. We found that grim itself shows caspase-dependent proteolytic processing of its C-terminus in vitro. Grim-induced death is antagonized by bcl-2 in a dose-dependent manner, and neither Fas signalling nor p53 are required for grim pro-apoptotic activity. Grim protein localizes both in the cytosol and in the mitochondria of mouse fibroblasts, the latter location becoming predominant as apoptosis progresses. These results show that Drosophila grim induces death in mammalian cells by specifically acting on mitochondrial apoptotic pathways executed by endogenous caspases. These findings advance our knowledge of the mechanism by which grim induces apoptosis and show the conservation through evolution of this crucial programmed cell death pathway.}, }
@article {pmid9850675, year = {1998}, author = {Andersson, SG and Kurland, CG}, title = {Ancient and recent horizontal transfer events: the origins of mitochondria.}, journal = {APMIS. Supplementum}, volume = {84}, number = {}, pages = {5-14}, doi = {10.1111/j.1600-0463.1998.tb05641.x}, pmid = {9850675}, issn = {0903-465X}, mesh = {*Evolution, Molecular ; Genome, Bacterial ; Mitochondria/*genetics ; Recombination, Genetic ; Rickettsia prowazekii/*genetics ; Transformation, Genetic ; }, }
@article {pmid9837879, year = {1998}, author = {Artigues, A and Crawford, DL and Iriarte, A and Martinez-Carrion, M}, title = {Divergent Hsc70 binding properties of mitochondrial and cytosolic aspartate aminotransferase. Implications for their segregation to different cellular compartments.}, journal = {The Journal of biological chemistry}, volume = {273}, number = {50}, pages = {33130-33134}, doi = {10.1074/jbc.273.50.33130}, pmid = {9837879}, issn = {0021-9258}, support = {GM-38341/GM/NIGMS NIH HHS/United States ; HL-38412/HL/NHLBI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Aspartate Aminotransferases/chemistry/classification/*metabolism ; Binding Sites ; Carrier Proteins/*metabolism ; Cattle ; Cell Compartmentation ; Cytosol/*enzymology ; HSC70 Heat-Shock Proteins ; *HSP70 Heat-Shock Proteins ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Protein Binding ; }, abstract = {Cytosolic Hsc70 discriminates between the homologous mitochondrial and cytosolic isozymes of aspartate aminotransferase, binding exclusively the mitochondrial form. By screening a library of synthetic peptides spanning the sequence of the mitochondrial enzyme, we have identified binding sites in this polypeptide that interact with Hsc70. These potential binding sites are scattered over the entire sequence and map to secondary structure elements, particularly the alpha-helix, that are partly exposed on the surface of the native protein. Several peptides corresponding to analogous positions in the cytosolic enzyme sequence do not bind to Hsc70. Phylogenetic analyses suggest that Hsc70 binding sequences have diverged as a consequence of biochemical specialization ensuring differential interaction of each isozyme with the cellular machinery in charge of protein folding and translocation.}, }
@article {pmid9828149, year = {1998}, author = {Paglini-Oliva, P and Fernández, AR and Fretes, R and Peslman, A}, title = {Structural, ultrastructural studies and evolution of Trypanosoma cruzi-infected mice treated with thioridazine.}, journal = {Experimental and molecular pathology}, volume = {65}, number = {2}, pages = {78-86}, doi = {10.1006/exmp.1998.2227}, pmid = {9828149}, issn = {0014-4800}, mesh = {Animals ; Antipsychotic Agents/*therapeutic use ; Chagas Cardiomyopathy/*drug therapy/*pathology ; Dose-Response Relationship, Drug ; Heart/drug effects/parasitology ; Male ; Mice ; Mitochondria/drug effects/ultrastructure ; Myocarditis/drug therapy/parasitology/pathology ; Myocardium/pathology ; Parasitemia/*drug therapy/pathology ; Thioridazine/*therapeutic use ; Trypanosoma cruzi/drug effects/*ultrastructure ; }, abstract = {Thioridazine (THI) is a tricyclic drug that belongs to the phenothiazine series. THI had a lethal effect upon epimastigotes in culture medium in a concentration of 0.5 microM. Trypanocidal effect upon trypomastigotes of Trypanosoma cruzi was observed above 0.5 mM of THI. Ultrastructural studies showed intracellular vacuoles in both parasite forms and mitochondrion reorganization. To analyze the use of THI as a therapy, male mice were inoculated with 7.10(4) trypomastigotes of T. cruzi, Tulahuen strain, and treated with THI for 3 days, with 80 mg/kg/day. Survival and parasitemia of mice treated with lower doses were similar to those observed in the control group (14 days postinfection). THI treatment modified parasitemia levels. They were negative by day 20 p.i. Hearts from control untreated mice presented typical chagasic myocarditis. Hearts from THI-treated mice sacrificed by day 30 p.i. showed inflammatory infiltrates without amastigote nests. Three months postinfection a mild infiltrate located in the interventricular septum was observed. Survival of this group was 9 months. Present results show that THI had a direct effect upon parasitemia, improved survival of treated mice, and modified the evolution of experimental Chagas disease.}, }
@article {pmid9826685, year = {1998}, author = {Cho, Y and Qiu, YL and Kuhlman, P and Palmer, JD}, title = {Explosive invasion of plant mitochondria by a group I intron.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {95}, number = {24}, pages = {14244-14249}, pmid = {9826685}, issn = {0027-8424}, support = {GM-17923/GM/NIGMS NIH HHS/United States ; GM-35087/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Cell Nucleus/genetics/metabolism ; Electron Transport Complex IV/*genetics ; *Evolution, Molecular ; *Introns ; Magnoliopsida/classification/enzymology/*genetics ; Mitochondria/*enzymology/genetics ; *Models, Genetic ; Molecular Sequence Data ; *Phylogeny ; Plants/enzymology/*genetics ; RNA, Ribosomal/genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {Group I introns are mobile, self-splicing genetic elements found principally in organellar genomes and nuclear rRNA genes. The only group I intron known from mitochondrial genomes of vascular plants is located in the cox1 gene of Peperomia, where it is thought to have been recently acquired by lateral transfer from a fungal donor. Southern-blot surveys of 335 diverse genera of land plants now show that this intron is in fact widespread among angiosperm cox1 genes, but with an exceptionally patchy phylogenetic distribution. Four lines of evidence-the intron's highly disjunct distribution, many incongruencies between intron and organismal phylogenies, and two sources of evidence from exonic coconversion tracts-lead us to conclude that the 48 angiosperm genera found to contain this cox1 intron acquired it by 32 separate horizontal transfer events. Extrapolating to the over 13,500 genera of angiosperms, we estimate that this intron has invaded cox1 genes by cross-species horizontal transfer over 1,000 times during angiosperm evolution. This massive wave of lateral transfers is of entirely recent occurrence, perhaps triggered by some key shift in the intron's invasiveness within angiosperms.}, }
@article {pmid9823893, year = {1998}, author = {Andersson, SG and Zomorodipour, A and Andersson, JO and Sicheritz-Pontén, T and Alsmark, UC and Podowski, RM and Näslund, AK and Eriksson, AS and Winkler, HH and Kurland, CG}, title = {The genome sequence of Rickettsia prowazekii and the origin of mitochondria.}, journal = {Nature}, volume = {396}, number = {6707}, pages = {133-140}, doi = {10.1038/24094}, pmid = {9823893}, issn = {0028-0836}, mesh = {DNA Replication ; DNA, Bacterial ; DNA, Mitochondrial ; *Evolution, Molecular ; *Genome, Bacterial ; Membrane Proteins/genetics ; Mitochondria/*genetics ; Protein Biosynthesis ; Recombination, Genetic ; Regulatory Sequences, Nucleic Acid ; Repetitive Sequences, Nucleic Acid ; Replication Origin ; Rickettsia prowazekii/*genetics/pathogenicity ; Transcription, Genetic ; Virulence/genetics ; }, abstract = {We describe here the complete genome sequence (1,111,523 base pairs) of the obligate intracellular parasite Rickettsia prowazekii, the causative agent of epidemic typhus. This genome contains 834 protein-coding genes. The functional profiles of these genes show similarities to those of mitochondrial genes: no genes required for anaerobic glycolysis are found in either R. prowazekii or mitochondrial genomes, but a complete set of genes encoding components of the tricarboxylic acid cycle and the respiratory-chain complex is found in R. prowazekii. In effect, ATP production in Rickettsia is the same as that in mitochondria. Many genes involved in the biosynthesis and regulation of biosynthesis of amino acids and nucleosides in free-living bacteria are absent from R. prowazekii and mitochondria. Such genes seem to have been replaced by homologues in the nuclear (host) genome. The R. prowazekii genome contains the highest proportion of non-coding DNA (24%) detected so far in a microbial genome. Such non-coding sequences may be degraded remnants of 'neutralized' genes that await elimination from the genome. Phylogenetic analyses indicate that R. prowazekii is more closely related to mitochondria than is any other microbe studied so far.}, }
@article {pmid9823885, year = {1998}, author = {Gray, MW}, title = {Rickettsia, typhus and the mitochondrial connection.}, journal = {Nature}, volume = {396}, number = {6707}, pages = {109-110}, doi = {10.1038/24030}, pmid = {9823885}, issn = {0028-0836}, mesh = {DNA, Mitochondrial ; Disease Outbreaks ; *Evolution, Molecular ; *Genome, Bacterial ; Humans ; Mitochondria/*genetics ; Rickettsia prowazekii/*genetics ; Typhus, Epidemic Louse-Borne/epidemiology/microbiology ; }, }
@article {pmid9821489, year = {1998}, author = {McNiff, BE and Allard, MW}, title = {A test of Archonta monophyly and the phylogenetic utility of the mitochondrial gene 12S rRNA.}, journal = {American journal of physical anthropology}, volume = {107}, number = {3}, pages = {225-241}, doi = {10.1002/(SICI)1096-8644(199811)107:3&lt;225::AID-AJPA1&gt;3.0.CO;2-N}, pmid = {9821489}, issn = {0002-9483}, mesh = {Animals ; Genetic Markers ; Mammals/classification/genetics ; Mitochondria/*genetics ; Molecular Biology ; *Phylogeny ; Primates/*classification/genetics ; RNA, Ribosomal/classification/*genetics ; Sequence Analysis, RNA ; }, abstract = {The relationships within the superorder Archonta, which contains the orders Dermoptera (flying lemurs), Scandentia (tree shrews), Chiroptera (bats), and Primates, were examined through the analysis of five newly derived and complete mitochondrial 12S rRNA sequences. The new data is combined with 83 additional known mammalian sequences to provide a full phylogenetic sampling. Phylogenetic hypotheses are generated using PAUP 3.1.1 (Swofford [1993] Illinois Natural History Survey, Champaign, IL) through analyses of all characters equally weighted, transversions only, and the effect of alignment gaps on phylogeny. The Parsimony Jackknifer (Farris et al. [1996] Cladistics 12:99-124) was used to assess the level of ambiguity present in the sequence data, and therefore the strength of the tree topologies. The conclusions of Springer and Douzery (1996, J. Mol. Evol. 43:357-373) which states that 12S rRNA is reliable to a time depth of 100 mya is unsupported by these analyses. The usefulness of 12S rRNA to aid in solving Archonta relationships and others of similar time depth is found to be suspect.}, }
@article {pmid9819051, year = {1998}, author = {Albertazzi, FJ and Kudla, J and Bock, R}, title = {The cox2 locus of the primitive angiosperm plant Acorus calamus: molecular structure, transcript processing and RNA editing.}, journal = {Molecular &amp; general genetics : MGG}, volume = {259}, number = {6}, pages = {591-600}, doi = {10.1007/s004380050852}, pmid = {9819051}, issn = {0026-8925}, mesh = {Base Sequence ; Cloning, Molecular ; DNA, Plant/chemistry/genetics ; Electron Transport Complex IV/biosynthesis/*genetics ; Evolution, Molecular ; Genes, Plant ; Introns ; Magnoliopsida/enzymology/*genetics ; Mitochondria/genetics ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Plant Leaves ; Plant Proteins/biosynthesis/*genetics ; Plant Roots ; Pollen ; *RNA Editing ; RNA, Plant/*genetics ; *Transcription, Genetic ; }, abstract = {Acorus calamus, or sweet flag, is a semiaquatic plant of uncertain taxonomic position. Molecular phylogenetic analysis using plastid rbcL sequences have suggested that Acorus calamus might be the most ancient surviving representative of the ancestral monocotyledonous plants. In order to provide molecular and phylogenetic data for the mitochondrial genetic system of Acorus, we have determined the structure of a mitochondrial locus, the cytochrome oxidase subunit II gene cox2. The Acorus cox2 gene harbors an unusually small group II intron, the smallest plant mitochondrial intron known to date. The transcript undergoes C-to-U RNA editing at eight sites. One of these sites is likely to play a dual functional role in both intron splicing and protein function. The 3' end of the mature transcript folds into a characteristic stem-loop structure that is presumably required for mitochondrial mRNA stability. Phylogenetic analysis of the cox2 sequence data, as well as the unusual intron structure, all support an evolutionarily isolated position for Acorus calamus.}, }
@article {pmid9818877, year = {1998}, author = {Andreu, AL and Bruno, C and Shanske, S and Shtilbans, A and Hirano, M and Krishna, S and Hayward, L and Systrom, DS and Brown, RH and DiMauro, S}, title = {Missense mutation in the mtDNA cytochrome b gene in a patient with myopathy.}, journal = {Neurology}, volume = {51}, number = {5}, pages = {1444-1447}, doi = {10.1212/wnl.51.5.1444}, pmid = {9818877}, issn = {0028-3878}, support = {1P01AG12992/AG/NIA NIH HHS/United States ; NS11766/NS/NINDS NIH HHS/United States ; P01HD32062/HD/NICHD NIH HHS/United States ; }, mesh = {Adult ; Amino Acid Sequence ; Animals ; Base Sequence ; Coenzymes ; Conserved Sequence ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex III/deficiency ; Evolution, Molecular ; Exercise/physiology ; Female ; Folic Acid/therapeutic use ; Humans ; Magnetic Resonance Spectroscopy ; Mitochondria, Muscle/metabolism ; Mitochondrial Myopathies/drug therapy/*genetics/metabolism ; Molecular Sequence Data ; Muscle, Skeletal/metabolism ; *Mutation, Missense ; Phosphates/metabolism ; Phosphocreatine/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; Ubiquinone/analogs &amp; derivatives/therapeutic use ; }, abstract = {A patient with progressive exercise intolerance, proximal weakness, and complex III deficiency in skeletal muscle had a missense mutation in the cytochrome b gene of mitochondrial DNA (G15762A). The mutation, which leads to the substitution of a highly conserved amino acid (G339E), was heteroplasmic (85%) in the patient's muscle and was not present in 100 individuals of different ethnic backgrounds. These data strongly suggest that this molecular defect is the primary cause of the myopathy.}, }
@article {pmid9810587, year = {1998}, author = {Enríquez, JA and Martínez-Azorín, F and Garesse, R and López-Pérez, MJ and Pérez-Martos, A and Bornstein, B and Montoya, J}, title = {[Human mitochondrial genetic system].}, journal = {Revista de neurologia}, volume = {26 Suppl 1}, number = {}, pages = {S21-6}, pmid = {9810587}, issn = {0210-0010}, mesh = {DNA, Mitochondrial/*genetics ; Female ; Gene Expression ; Humans ; Male ; Phenotype ; RNA/genetics ; }, abstract = {The mitochondria are subcellular organelles devoted to energy production in form of ATP that contain their own genetic system. Mitochondrial DNA codify a small, but extremely important, number of polypeptides of the respiratory chain. The other mitochondrial proteins are encoded in the nucleus. Therefore, mitochondrial biogenesis require the coordinated expression of nuclear and mitochondrial genetic systems. The gene arrangement in mitochondrial DNA is extremely compact with the tRNA genes interspersed with the rRNA and protein-coding genes. This organization has its precise counterpart in the mode of expression and distinctive structural features of the RNAs. Both mitochondrial DNA strands are transcribed as a whole in the form of three polycistronic molecules that are later cut by specific enzymes that recognize the 5' and 3' end of the tRNA sequences, to produced the mature rRNA, mRNA and tRNA. The mitochondrial coded mRNAs are translated into proteins by a mitochondrial specific protein-synthesizing machinery. The genetics of the mitochondrial DNA differs from that of the nuclear DNA in several features. In particular, the mitochondrial genome is inherited from the mother that transmit their mitochondrial DNA to all her offsprings. Another characteristic of this genome is its tendency to mutate more frequently than the nuclear DNA. This provides a powerful tool for studying the evolution of man.}, }
@article {pmid9807225, year = {1998}, author = {Feng, QL and Ladd, TR and Retnakaran, A and Davey, KG and Palli, SR}, title = {Identification and developmental expression of the mitochondrial phosphate transport protein gene from the spruce budworm, Choristoneura fumiferana.}, journal = {Insect biochemistry and molecular biology}, volume = {28}, number = {10}, pages = {791-799}, doi = {10.1016/s0965-1748(98)00055-1}, pmid = {9807225}, issn = {0965-1748}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biological Transport ; Carrier Proteins/biosynthesis/*genetics ; Cloning, Molecular ; DNA, Complementary/genetics ; Evolution, Molecular ; Gene Expression ; Genes, Insect ; Larva/metabolism ; Membrane Proteins/biosynthesis/*genetics ; *Mitochondria ; Moths/*genetics/growth &amp; development/metabolism ; Phosphate-Binding Proteins ; Phosphates/metabolism ; Phylogeny ; Pupa/metabolism ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {Phosphate transport protein (PTP) is a mitochondrial inner membrane protein responsible for the translocation of inorganic phosphate into the mitochondrial matrix. A full length cDNA clone encoding the PTP was isolated from the spruce budworm, Choristoneura fumiferana. The deduced amino acid sequence of the longest ORF of CfPTP cDNA showed high similarity with the amino acid sequences of PTPs cloned from several species. Phylogenetic tree analysis indicated that CfPTP occupied an intermediate position between vertebrates on the one side and yeast and nematodes on the other side. Studies on the developmental expression of CfPTP mRNA showed that higher levels of mRNA were present during the feeding and growing stages than during molting periods.}, }
@article {pmid9804424, year = {1998}, author = {Garry, DJ and Ordway, GA and Lorenz, JN and Radford, NB and Chin, ER and Grange, RW and Bassel-Duby, R and Williams, RS}, title = {Mice without myoglobin.}, journal = {Nature}, volume = {395}, number = {6705}, pages = {905-908}, doi = {10.1038/27681}, pmid = {9804424}, issn = {0028-0836}, mesh = {Animals ; Biological Evolution ; Female ; Fertility/physiology ; Heart/physiology ; Mice ; Mice, Knockout ; Muscle, Skeletal/physiology ; Muscles/*physiology ; Myoglobin/deficiency/genetics/*physiology ; Oxygen/metabolism ; Physical Exertion/physiology ; Pregnancy ; }, abstract = {Myoglobin, an intracellular haemoprotein expressed in the heart and oxidative skeletal myofibres of vertebrates, binds molecular oxygen and may facilitate oxygen transport from erythrocytes to mitochondria, thereby maintaining cellular respiration during periods of high physiological demand. Here we show, however, that mice without myoglobin, generated by gene-knockout technology, are fertile and exhibit normal exercise capacity and a normal ventilatory response to low oxygen levels (hypoxia). Heart and soleus muscles from these animals are depigmented, but function normally in standard assays of muscle performance in vitro across a range of work conditions and oxygen availability. These data show that myoglobin is not required to meet the metabolic requirements of pregnancy or exercise in a terrestrial mammal, and raise new questions about oxygen transport and metabolic regulation in working muscles.}, }
@article {pmid9801318, year = {1998}, author = {Ohta, N and Sato, N and Kuroiwa, T}, title = {Structure and organization of the mitochondrial genome of the unicellular red alga Cyanidioschyzon merolae deduced from the complete nucleotide sequence.}, journal = {Nucleic acids research}, volume = {26}, number = {22}, pages = {5190-5198}, doi = {10.1093/nar/26.22.5190}, pmid = {9801318}, issn = {0305-1048}, mesh = {Base Sequence ; Codon/genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; Evolution, Molecular ; Genes, Plant ; *Genome, Plant ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Physical Chromosome Mapping ; Plant Proteins/genetics ; RNA, Plant/genetics ; RNA, Transfer/genetics ; Rhodophyta/*genetics ; Ribosomal Proteins/genetics ; Species Specificity ; }, abstract = {The complete nucleotide sequence of the mitochondrial genome of a very primitive unicellular red alga, Cyanidioschyzon merolae , has been determined. The mitochondrial genome of C.merolae contains 34 genes for proteins including unidentified open reading frames (ORFs) (three subunits of cytochrome c oxidase, apocytochrome b protein, three subunits of F1F0-ATPase, seven subunits of NADH ubiquinone oxidoreductase, three subunits of succinate dehydrogenase, four proteins implicated in c-type cytochrome biogenesis, 11 ribosomal subunits and two unidentified open reading frames), three genes for rRNAs and 25 genes for tRNAs. The G+C content of this mitochondrial genome is 27.2%. The genes are encoded on both strands. The genome size is comparatively small for a plant mitochondrial genome (32 211 bp). The mitochondrial genome resembles those of plants in its gene content because it contains several ribosomal protein genes and ORFs shared by other plant mitochondrial genomes. In contrast, it resembles those of animals in the genome organization, because it has very short intergenic regions and no introns. The gene set in this mitochondrial genome is a subset of that of Reclinomonas americana , an amoeboid protozoan. The results suggest that plant mitochondria originate from the same ancestor as other mitochondria and that most genes were lost from the mitochondrial genome at a fairly early stage of the evolution of the plants.}, }
@article {pmid9799364, year = {1998}, author = {Kato, S and Kanazawa, A and Mikami, T and Shimamoto, Y}, title = {Evolutionary changes in the structures of the cox2 and atp6 loci in the mitochondrial genome of soybean involving recombination across small interspersed sequences.}, journal = {Current genetics}, volume = {34}, number = {4}, pages = {303-312}, doi = {10.1007/s002940050400}, pmid = {9799364}, issn = {0172-8083}, mesh = {Base Sequence ; Cloning, Molecular ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; *Evolution, Molecular ; Genes, Plant/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Plant Proteins/*genetics ; Proton-Translocating ATPases ; Recombination, Genetic/*genetics ; Repetitive Sequences, Nucleic Acid ; Restriction Mapping ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Glycine max/*enzymology/genetics ; }, abstract = {Mitochondrial DNA (mtDNA) fragments that contained cox2 or atp6 loci were cloned from three accessions of wild soybean (Glycine soja) in order to understand the evolutionary changes of mitochondrial genomes in the genus Glycine subgenus Soja. Cox2 was cloned as a single configuration, while atp6 was cloned as either one or two configurations from each accession. Structural variations were detected in the 5' upstream region of cox2 and in both the 5' upstream and 3' downstream regions of atp6. These variations appeared to be the results of recombination events. A comparison of the mtDNA fragments previously cloned from a cultivated soybean (G. max) and a wild soybean revealed various sites of recombination, as well as various combinations of the 5' and 3' regions, at the cox2 and atp6 loci. Some of the cloned fragments were found to contain a set of repeated sequences, namely 299-bp and 23-bp repeats in the 5' region of cox2 or atp6, which were interspersed in the mitochondrial genome in the subgenus Soja. Recombination events involving the 299-bp or 23-bp repeated sequences were shown to account for the generation of structural variations in the 5' regions of these loci.}, }
@article {pmid9799263, year = {1998}, author = {Castresana, J and Feldmaier-Fuchs, G and Yokobori, S and Satoh, N and Pääbo, S}, title = {The mitochondrial genome of the hemichordate Balanoglossus carnosus and the evolution of deuterostome mitochondria.}, journal = {Genetics}, volume = {150}, number = {3}, pages = {1115-1123}, pmid = {9799263}, issn = {0016-6731}, mesh = {Animals ; Annelida/*genetics/ultrastructure ; Base Sequence ; *DNA, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {The complete nucleotide sequence of the mitochondrial genome of the hemichordate Balanoglossus carnosus (acorn worm) was determined. The arrangement of the genes encoding 13 protein, 22 tRNA, and 2 rRNA genes is essentially the same as in vertebrates, indicating that the vertebrate and hemichordate mitochondrial gene arrangement is close to that of their common ancestor, and, thus, that it has been conserved for more than 600 million years, whereas that of echinoderms has been rearranged extensively. The genetic code of hemichordate mitochondria is similar to that of echinoderms in that ATA encodes isoleucine and AGA serine, whereas the codons AAA and AGG, whose amino acid assignments also differ between echinoderms and vertebrates, are absent from the B. carnosus mitochondrial genome. There are three noncoding regions of length 277, 41, and 32 bp: the larger one is likely to be equivalent to the control region of other deuterostomes, while the two others may contain transcriptional promoters for genes encoded on the minor coding strand. Phylogenetic trees estimated from the inferred protein sequences indicate that hemichordates are a sister group of echinoderms.}, }
@article {pmid9797407, year = {1998}, author = {Karlin, S and Brocchieri, L}, title = {Heat shock protein 70 family: multiple sequence comparisons, function, and evolution.}, journal = {Journal of molecular evolution}, volume = {47}, number = {5}, pages = {565-577}, doi = {10.1007/pl00006413}, pmid = {9797407}, issn = {0022-2844}, support = {2RO1HG00335-09/HG/NHGRI NIH HHS/United States ; 5RO1GM10452-33/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Consensus Sequence ; Conserved Sequence ; *Evolution, Molecular ; HSP70 Heat-Shock Proteins/*genetics/physiology ; Molecular Sequence Data ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {The heat shock protein 70 kDa sequences (HSP70) are of great importance as molecular chaperones in protein folding and transport. They are abundant under conditions of cellular stress. They are highly conserved in all domains of life: Archaea, eubacteria, eukaryotes, and organelles (mitochondria, chloroplasts). A multiple alignment of a large collection of these sequences was obtained employing our symmetric-iterative ITERALIGN program (Brocchieri and Karlin 1998). Assessments of conservation are interpreted in evolutionary terms and with respect to functional implications. Many archaeal sequences (methanogens and halophiles) tend to align best with the Gram-positive sequences. These two groups also miss a signature segment [about 25 amino acids (aa) long] present in all other HSP70 species (Gupta and Golding 1993). We observed a second signature sequence of about 4 aa absent from all eukaryotic homologues, significantly aligned in all prokaryotic sequences. Consensus sequences were developed for eight groups [Archaea, Gram-positive, proteobacterial Gram-negative, singular bacteria, mitochondria, plastids, eukaryotic endoplasmic reticulum (ER) isoforms, eukaryotic cytoplasmic isoforms]. All group consensus comparisons tend to summarize better the alignments than do the individual sequence comparisons. The global individual consensus "matches" 87% with the consensus of consensuses sequence. A functional analysis of the global consensus identifies a (new) highly significant mixed charge cluster proximal to the carboxyl terminus of the sequence highlighting the hypercharge run EEDKKRRER (one-letter aa code used). The individual Archaea and Gram-positive sequences contain a corresponding significant mixed charge cluster in the location of the charge cluster of the consensus sequence. In contrast, the four Gram-negative proteobacterial sequences of the alignment do not have a charge cluster (even at the 5% significance level). All eukaryotic HSP70 sequences have the analogous charge cluster. Strikingly, several of the eukaryotic isoforms show multiple mixed charged clusters. These clusters were interpreted with supporting data related to HSP70 activity in facilitating chaperone, transport, and secretion function. We observed that the consensus contains only a single tryptophan residue and a single conserved cysteine. This is interpreted with respect to the target rule for disaggregating misfolded proteins. The mitochondrial HSP70 connections to bacterial HSP70 are analyzed, suggesting a polyphyletic split of Trypanosoma and Leishmania protist mitochondrial (Mt) homologues separated from Mt-animal/fungal/plant homologues. Moreover, the HSP70 sequences from the amitochondrial Entamoeba histolytica and Trichomonas vaginalis species were analyzed. The E. histolytica HSP70 is most similar to the higher eukaryotic cytoplasmic sequences, with significantly weaker alignments to ER sequences and much diminished matching to all eubacterial, mitochondrial, and chloroplast sequences. This appears to be at variance with the hypothesis that E. histolytica rather recently lost its mitochondrial organelle. T. vaginalis contains two HSP70 sequences, one Mt-like and the second similar to eukaryotic cytoplasmic sequences suggesting two diverse origins.}, }
@article {pmid9788245, year = {1998}, author = {Pamplona, R and Portero-Otín, M and Riba, D and Ruiz, C and Prat, J and Bellmunt, MJ and Barja, G}, title = {Mitochondrial membrane peroxidizability index is inversely related to maximum life span in mammals.}, journal = {Journal of lipid research}, volume = {39}, number = {10}, pages = {1989-1994}, pmid = {9788245}, issn = {0022-2275}, mesh = {Aging ; Animals ; Cattle ; Dogs ; Fatty Acids/analysis ; Fatty Acids, Unsaturated/analysis ; Guinea Pigs ; Horses ; Intracellular Membranes/*metabolism ; *Lipid Peroxidation ; *Longevity ; Membrane Lipids/analysis/*metabolism ; Mice ; Mitochondria/*ultrastructure ; Oxidative Stress ; Rats ; Sheep ; Species Specificity ; Swine ; }, abstract = {The oxidative stress theory of aging predicts a low degree of fatty acid unsaturation in tissues of longevous animals, because membrane lipids increase their sensitivity to oxidative damage as a function of their unsaturation. Accordingly, the fatty acids analyses of liver mitochondria from eight mammals, ranging in maximum life span from 3.5 to 46 years, show that the total number of double bonds and the peroxidizability index are negatively correlated with maximum life span (r = -0. 88, P < 0.003; r = -0.87, P < 0.004, respectively). This is not due to a low content of unsaturated fatty acids in longevous animals, but mainly to a redistribution between kinds of the polyunsaturated n-3 fatty acids series, shifting from the highly unsaturated docosahexaenoic acid (r = -0.89, P < 0.003) to the less unsaturated linolenic acid (r = 0.97, P < 0.0001). This redistribution pattern strongly suggests the presence of a constitutively low delta6-desaturase activity in longevous animals (r = -0.96, P < 0.0001). Thus, it may be proposed that, during evolution, a low degree of fatty acid unsaturation in liver mitochondria may have been selected in longevous mammals in order to protect the tissues against oxidative damage, while maintaining an appropriate environment for membrane function.}, }
@article {pmid9784365, year = {1998}, author = {Richard, O and Bonnard, G and Grienenberger, JM and Kloareg, B and Boyen, C}, title = {Transcription initiation and RNA processing in the mitochondria of the red alga Chondrus crispus: convergence in the evolution of transcription mechanisms in mitochondria.}, journal = {Journal of molecular biology}, volume = {283}, number = {3}, pages = {549-557}, doi = {10.1006/jmbi.1998.2112}, pmid = {9784365}, issn = {0022-2836}, mesh = {Animals ; Base Sequence ; DNA ; DNA, Mitochondrial/genetics ; Evolution, Molecular ; Mitochondria/*genetics ; Molecular Sequence Data ; *RNA Processing, Post-Transcriptional ; Restriction Mapping ; Rhodophyta/*genetics ; Sequence Homology, Nucleic Acid ; *Transcription, Genetic ; }, abstract = {The mitochondrial DNA (mt DNA) of the red alga Chondrus crispus is shown to be transcribed into two large RNA molecules. These primary transcripts are cleaved once, at the level of a tRNA, then the resulting products are processed via multiple maturation events into either mono- or poly-cistronic RNAs. Transcripts were detected for all genes and open reading frames, except for rps11 and orf172. For both transcription units the initiation of transcription was mapped by in vitro RNA capping and primer extension experiments within inverse repeated sequences at the north pole of the molecule. Consistent with primer extension mapping, putative promoter motifs sharing significant similarities with both chicken and Xenopus mitochondrial promoters were found in the C. crispus mitochondrial genome. Altogether C. crispus mitochondrial DNA appears to be transcribed as animal mtDNA is, suggesting that transcription mechanisms in mitochondria are dependent on the overall organization of the mitochondrial genome irrespective of the eukaryotic phylogeny.}, }
@article {pmid9778725, year = {1998}, author = {Margulis, L and Chapman, MJ}, title = {Endosymbioses: cyclical and permanent in evolution.}, journal = {Trends in microbiology}, volume = {6}, number = {9}, pages = {342-5; discussion 345-6}, doi = {10.1016/s0966-842x(98)01325-0}, pmid = {9778725}, issn = {0966-842X}, mesh = {Animals ; *Biological Evolution ; Chloroplasts/physiology ; Host-Parasite Interactions ; Humans ; Mitochondria/physiology ; Plants/microbiology/parasitology ; Plastids/physiology ; Symbiosis/*physiology ; }, }
@article {pmid9767689, year = {1998}, author = {Hiendleder, S and Lewalski, H and Wassmuth, R and Janke, A}, title = {The complete mitochondrial DNA sequence of the domestic sheep (Ovis aries) and comparison with the other major ovine haplotype.}, journal = {Journal of molecular evolution}, volume = {47}, number = {4}, pages = {441-448}, doi = {10.1007/pl00006401}, pmid = {9767689}, issn = {0022-2844}, mesh = {Animals ; Animals, Domestic ; Base Sequence ; Cattle/genetics ; DNA, Mitochondrial/chemistry/*genetics ; *Evolution, Molecular ; Female ; Haplotypes ; Male ; Mammals/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Pedigree ; *Phylogeny ; RNA, Transfer/genetics ; Ruminants/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Sheep/*genetics ; }, abstract = {The complete mitochondrial DNA (mtDNA) molecule of the domestic sheep, Ovis aries, was sequenced, together with part of the mtDNA of a specimen representing the other major O. aries haplotype group. The length of the complete ovine mtDNA presented is 16,616 nucleotides (nt). This length is not absolute, however, due to heteroplasmy caused by the occurrence of different numbers of a 75-nt-long tandem repeat in the control region. The sequence data were included in analyses of intraspecific ovine molecular differences, molecular comparisons with bovine mtDNAs, and phylogenetic analyses based on complete mtDNAs. The comparisons with bovine mtDNAs were based on the central domains of the ovine control regions, representing both major ovine haplotype groups, and the corresponding domains of Bos taurus and B. indicus. The comparisons showed that the difference between the bovids was 1.4 times greater than the intraspecific ovine difference. These findings suggest that the strains of wild sheep from which domestic sheep originated were more closely related than were the B. primigenius subspecies which gave rise to B. indicus and B. taurus cattle. Datings based on complete mtDNAs suggest that the bovine and ovine lineages diverged about 30 million years before present. This dating is considerably earlier than that proposed previously.}, }
@article {pmid9767687, year = {1998}, author = {Hepperle, D and Nozaki, H and Hohenberger, S and Huss, VA and Morita, E and Krienitz, L}, title = {Phylogenetic position of the Phacotaceae within the Chlamydophyceaeas revealed by analysis of 18S rDNA and rbcL sequences.}, journal = {Journal of molecular evolution}, volume = {47}, number = {4}, pages = {420-430}, doi = {10.1007/pl00006399}, pmid = {9767687}, issn = {0022-2844}, mesh = {Chlorophyta/*classification/*genetics/ultrastructure ; DNA, Plant/chemistry/genetics ; DNA, Ribosomal/chemistry/*genetics ; *Evolution, Molecular ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Plant/chemistry/genetics ; RNA, Ribosomal, 18S/chemistry/*genetics ; }, abstract = {Four genera of the Phacotaceae (Phacotus, Pteromonas, Wislouchiella, Dysmorphococcus), a family of loricated green algal flagellates within the Volvocales, were investigated by means of transmission electron microscopy and analysis of the nuclear encoded small-subunit ribosomal RNA (18S rRNA) genes and the plastid-encoded rbcL genes. Additionally, the 18S rDNA of Haematococcus pluvialis and the rbcL sequences of Chlorogonium elongatum, C. euchlorum, Dunaliella parva, Chloromonas serbinowii, Chlamydomonas radiata, and C. tetragama were determined. Analysis of ultrastructural data justified the separation of the Phacotaceae into two groups. Phacotus, Pteromonas, and Wislouchiella generally shared the following characters: egg-shaped protoplasts, a single pyrenoid with planar thylakoid double-lamellae, three-layered lorica, flagellar channels as part of the central lorica layer, mitochondria located in the central cytoplasm, lorica development that occurs in mucilaginous zoosporangia that are to be lysed, and no acid-resistant cell walls. Dysmorphococcus was clearly different in each of the characters mentioned. Direct comparison of sequences of Phacotus lenticularis, Pteromonas sp., Pteromonas protracta, and Wislouchiella planctonica revealed DNA sequence homologies of >/=98. 0% within the 18S gene and 93.9% within the rbcL gene. D. globosus was quite different from these species, with a maximum of 92.9% homology in the 18S rRNA and </=86.6% in the rbcL gene. It showed major similarities to the 18S rDNA of Dunaliella salina, with 95.3%, and to the rbcL sequence of Chlamydomonas tetragama, with 90.3% sequence homology. Additionally, the Phacotaceae sensu stricto exclusively shared 10 (rbcL: 4) characters which were present neither in other Chlamydomonadales nor in Dysmorphococcus globosus. Different phylogenetic analysis methods confirmed the hypothesis that the Phacotaceae are polyphyletic. The Phacotaceae sensu stricto form a stable cluster with affinities to the Dunaliellaes and possibly Haematococcus pluvialis. Dysmorphococcus globosus represented an independent lineage that is possibly related to Chlamydomonas moewusii and C. tetragama.}, }
@article {pmid9767683, year = {1998}, author = {Inagaki, Y and Ehara, M and Watanabe, KI and Hayashi-Ishimaru, Y and Ohama, T}, title = {Directionally evolving genetic code: the UGA codon from stop to tryptophan in mitochondria.}, journal = {Journal of molecular evolution}, volume = {47}, number = {4}, pages = {378-384}, doi = {10.1007/pl00006395}, pmid = {9767683}, issn = {0022-2844}, mesh = {Amoeba/enzymology/*genetics ; Animals ; Base Sequence ; Codon/*genetics ; Codon, Terminator/*genetics ; DNA Primers ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Eukaryota/enzymology/*genetics ; *Evolution, Molecular ; *Genetic Code ; Macromolecular Substances ; Mitochondria/enzymology ; *Phylogeny ; Polymerase Chain Reaction/methods ; *Tryptophan ; }, abstract = {For the comprehensive analyses of deviant codes in protistan mitochondria (mt), we sequenced about a 1.1-kb region of a mitochondrial (mt) gene, the cytochrome c oxidase subunit I (coxI) in two chlorarachniophytes, the filose amoeba Euglypha rotunda, the cryptomonad Cryptomonas ovata, the prymnesiophyte (haptophyte) Diacronema vlkianum (Pavlovales), and the diatom Melosira ambigua. As a result of this analysis, we noticed that the UGA codon is assigned to tryptophan (Trp) instead of being a signal for translational termination in two chlorarachniophytes and in E. rotunda. The same type of deviant code was reported previously in animals, fungi, ciliates, kinetoplastids, Chondrus crispus (a red alga), Acanthamoeba castellanii (an amoeboid protozoon), and three of the four prymnesiophyte orders with the exception of the Pavlovales. A phylogenetic analysis based on the COXI sequences of 56 eukaryotes indicated that the organisms bearing the modified code, UGA for Trp, are not monophyletic. Based on these studies, we propose that the ancestral mitochondrion was bearing the universal genetic code and subsequently reassigned the codon to Trp independently, at least in the lineage of ciliates, kinetoplastids, rhodophytes, prymnesiophytes, and fungi. We also discuss how this codon was directionally captured by Trp tRNA.}, }
@article {pmid9763293, year = {1998}, author = {Keddie, EM and Higazi, T and Unnasch, TR}, title = {The mitochondrial genome of Onchocerca volvulus: sequence, structure and phylogenetic analysis.}, journal = {Molecular and biochemical parasitology}, volume = {95}, number = {1}, pages = {111-127}, doi = {10.1016/s0166-6851(98)00102-9}, pmid = {9763293}, issn = {0166-6851}, support = {P01-AI28780/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Ascaris suum/genetics ; Base Sequence ; Caenorhabditis elegans/genetics ; Chromosome Mapping ; Codon ; DNA, Helminth/analysis/genetics ; DNA, Mitochondrial/*analysis/genetics ; Genes, rRNA/genetics ; *Genome ; Helminth Proteins/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Onchocerca volvulus/*genetics ; *Phylogeny ; Protein Biosynthesis ; RNA, Transfer/chemistry/genetics ; Sequence Analysis, DNA ; }, abstract = {The complete DNA sequence of the mitochondrial genome of Onchocerca volvulus is described. The O. volvulus mitochondrial genome is 13747 bp, slightly smaller than the mitochondrial genomes of the nematodes Ascaris suum and Caenorhabditis elegans, and the smallest metazoan mitochondrial DNA molecule reported to date. The O. volvulus mitochondrial genome contains genes for two ribosomal RNAs, 22 transfer RNAs and 12 proteins. Consistent with the small size of the genome, four gene pairs overlap and eight contain no intergenic regions. Only 17 intergenic regions are found, ranging in size from 1 to 46 bp. As in C. elegans and A. suum, the O. volvulus mitochondrial genome lacks an open reading frame encoding ATPase subunit 8, and all genes are apparently transcribed in the same direction. However, the mitochondrial gene order of O. volvulus differs from that of A. suum, C. elegans and other metazoan mitochondrial genomes. A total of 20 of the 22 transfer RNAs encoded in the O. volvulus mitochondrial genome have the potential to fold into secondary structures lacking the TpsiC arm, as has been reported in other nematodes. The genome exhibits a striking codon bias, with 15/20 amino acids having a single codon preference of > 70%.}, }
@article {pmid9751924, year = {1998}, author = {Sturmbauer, C and Berger, B and Dallinger, R and Föger, M}, title = {Mitochondrial phylogeny of the genus Regulus and implications on the evolution of breeding behavior in sylvioid songbirds.}, journal = {Molecular phylogenetics and evolution}, volume = {10}, number = {1}, pages = {144-149}, doi = {10.1006/mpev.1997.0486}, pmid = {9751924}, issn = {1055-7903}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; Reproduction ; Songbirds/*classification/genetics ; }, abstract = {We tested four hypotheses about the relationships of the kinglets (genus Regulus)to seven closely related genera of the songbird superfamily Sylvioidea using mitochondrial DNA sequences. The kinglets were suggested to be closely related to the tits (Parus) or to the Old World Warblers (Phylloscopus) and were also suggested to constitute the, or at least one of the, most ancestral splits among the sylvioids. Our phylogenetic analysis grouped the kinglets as the sister group of a clade comprising Parus and Phylloscopus and including the genera Sylvia, Aegithalos, and Leptopoecile. Two of the taxa were placed more ancestral to the kinglets: Sitta and Certhia. We also identified the endemic kinglet species from the Canary Islands s the sister group of R. regulus. The superimposition of breeding behavior on the phylogeny suggests that hole nesting is ancestral and various other patterns of nest construction have evolved from it. The placement of Parus implies that hole nesting in the Paridae is likely to have originated secondarily. Further, Leptopoecile and Aegithalos, two genera for which a helper system of elder offspring in breeding was described, were resolved as a clade.}, }
@article {pmid9751923, year = {1998}, author = {Gilles, A and Lecointre, G and Faure, E and Chappaz, R and Brun, G}, title = {Mitochondrial phylogeny of the European cyprinids: implications for their systematics, reticulate evolution, and colonization time.}, journal = {Molecular phylogenetics and evolution}, volume = {10}, number = {1}, pages = {132-143}, doi = {10.1006/mpev.1997.0480}, pmid = {9751923}, issn = {1055-7903}, mesh = {Animals ; Biological Evolution ; Cyprinidae/*classification/genetics ; Cytochrome b Group/genetics ; Europe ; Mitochondria/*genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Two different mitochondrial genes, the cytochrome b and the 16S rDNA, support the same European cyprinid molecular phylogeny: the most basal subfamily is the paraphyletic Rasborinae, the Cyprininae are monophyletic, the Tincinae and Gobioninae are close to the Cyprininae or more basal lineages but not close to Leuciscinae or Alburninae, and the Leuciscinae are paraphyletic but can become monophyletic if we include the biphyletic alburninae and exclude the Phoxinini. The relationship of the Acheilognathinae remains obscure. Natural intergeneric and interspecific hybridizations are clearly demonstrated within the Leuciscinae, both from high bootstrap proportions and intermediate morphological features: Chondrostoma toxostoma and Rutilus rutilus, Scardinius erythrophthalmus and R. rutilus, and Leuciscus multicellus and Leuciscus soufia. Finally, the use of the nonsaturated and clockwise 16S mtDNA sequences have been used to infer from nonintrogressive taxa the time of the first European cyprinid cladogeneses. The estimation confirms the hypothesis of Almaça and Banarescu that European cyprinid subfamilies started to diversify 35 mya and confirms the hypothesis of Bianco on the diversification of European leuciscines in the Mediterranean area during the late Messinian (6.5 to 5.3 mya).}, }
@article {pmid9751919, year = {1998}, author = {Johnson, KP and Sorenson, MD}, title = {Comparing molecular evolution in two mitochondrial protein coding genes (cytochrome b and ND2) in the dabbling ducks (Tribe: Anatini).}, journal = {Molecular phylogenetics and evolution}, volume = {10}, number = {1}, pages = {82-94}, doi = {10.1006/mpev.1997.0481}, pmid = {9751919}, issn = {1055-7903}, mesh = {Amino Acid Substitution ; Animals ; Codon ; Cytochrome b Group/*genetics ; Ducks/classification/*genetics ; *Evolution, Molecular ; Genetic Heterogeneity ; Genetic Variation ; Mitochondria/*genetics ; Molecular Sequence Data ; NADH Dehydrogenase/*genetics ; Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Rates of sequence evolution were estimated for the cytochrome b (cyt b) and NADH dehydrogenase sub-unit 2 (ND2) genes using a phylogeny of the dabbling ducks (Tribe: Anatini) and outgroups. This speciose group was densely sampled, reducing the impact of undetected homoplasy on rate comparisons. Phylogenies based on sequences of the two gene regions and various weighting schemes differed, but most of the differences involved weakly supported nodes. In addition, partition homogeneity tests show that these differences were not due to statistically significant conflict between the data sets. Cyt b and ND2 also showed similar rates and types of both nucleotide and amino acid substitutions. For both genes, substitutions between isoleucine and valine and between alanine and threonine were most common; both of these substitution types are the result of A-G transitions at first positions of codons. Rates of sequence evolution varied substantially and significantly among nucleotide positions, and even within a given codon position (first, second, or third), rates were significantly heterogeneous among sites. Within Anatini, cyt b and ND2 show similar levels of variation and homoplasy, and are equally useful for reconstructing the species level phylogeny of this group.}, }
@article {pmid9751916, year = {1998}, author = {Harris, DJ and Arnold, EN and Thomas, RH}, title = {Rapid speciation, morphological evolution, and adaptation to extreme environments in South African sand lizards (Meroles) as revealed by mitochondrial gene sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {10}, number = {1}, pages = {37-48}, doi = {10.1006/mpev.1997.0463}, pmid = {9751916}, issn = {1055-7903}, mesh = {Adaptation, Physiological ; Animals ; Base Sequence ; *Biological Evolution ; Evolution, Molecular ; Lizards/*classification/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; South America ; }, abstract = {Data derived from the morphology of the seven species of South African sand lizards, Meroles (Reptilia, Lacertidae), and their outgroups produce a robust estimate of phylogeny when a maximum parsimony approach is applied. The estimate is fully resolved with little character conflict and internal branches are relatively long. This analysis indicates that Meroles is a true clade that includes the aberrant lacertid long separated as Aporosaura anchietae. The tree is pectinate, its successive external branches representing species with increasing adaptation to desert conditions, especially aeolian sand habitats. This pattern, and the robustness of the tree, support a model of invasion of severe habitats in which successive rounds of speciation, displacement, and adaptation result in spread into extreme ecological situations. To test the robust morphological phylogeny and, indirectly, the model as well, DNA from mitochondrial 12S and 16S ribosomal genes was sequenced and analyzed by both maximum parsimony and maximum likelihood approaches. Trees produced were largely congruent with that derived from morphology, although different from ones resulting from protein electrophoresis. However, in contrast to the internal branches of the morphological tree, those of the DNA maximum likelihood tree are quite short. The DNA data provide some corroboration for the relationships within Meroles based on morphology and consequently for the model as well. The disparity in internal branch lengths between the maximum parsimony morphological and maximum likelihood DNA trees may well indicate that the multiple adaptations to desert conditions arising on the main lineage of Meroles evolved quite rapidly. In this study DNA thus not only corroborates the phylogeny but also provides evidence about another aspect of evolutionary history.}, }
@article {pmid9751740, year = {1998}, author = {Stiller, JW and Duffield, EC and Hall, BD}, title = {Amitochondriate amoebae and the evolution of DNA-dependent RNA polymerase II.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {95}, number = {20}, pages = {11769-11774}, pmid = {9751740}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Amoeba/*enzymology/*genetics ; Animals ; Base Sequence ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; *Evolution, Molecular ; Fossils ; Genes, Protozoan ; Introns ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; RNA Polymerase II/*genetics ; Repetitive Sequences, Nucleic Acid ; Time Factors ; }, abstract = {Unlike parasitic protist groups that are defined by the absence of mitochondria, the Pelobiontida is composed mostly of free-living species. Because of the presence of ultrastructural and cellular features that set them apart from all other eukaryotic organisms, it has been suggested that pelobionts are primitively amitochondriate and may represent the earliest-evolved lineage of extant protists. Analyses of rRNA genes, however, have suggested that the group arose well after the diversification of the earliest-evolved protists. Here we report the sequence of the gene encoding the largest subunit of DNA-dependent RNA polymerase II (RPB1) from the pelobiont Mastigamoeba invertens. Sequences within RPB1 encompass several of the conserved catalytic domains that are common to eubacterial, archaeal, and eukaryotic nuclear-encoded RNA polymerases. In RNA polymerase II, these domains catalyze the transcription of all nuclear pre-mRNAs, as well as the majority of small nuclear RNAs. In contrast with rDNA-based trees, phylogenetic analyses of RPB1 sequences indicate that Mastigamoeba represents an early branch of eukaryotic evolution. Unlike sequences from parasitic amitochondriate protists that were included in our study, there is no indication that Mastigamoeba RPB1 is attracted to the base of the eukaryotic tree artifactually. In addition, the presence of introns and a heptapeptide C-terminal repeat in the Mastigamoeba RPB1 sequence, features that are typically associated with more recently derived eukaryotic groups, raise provocative questions regarding models of protist evolution that depend almost exclusively on rDNA sequence analyses.}, }
@article {pmid9746332, year = {1998}, author = {Di Lisa, F and Bernardi, P}, title = {Mitochondrial function as a determinant of recovery or death in cell response to injury.}, journal = {Molecular and cellular biochemistry}, volume = {184}, number = {1-2}, pages = {379-391}, pmid = {9746332}, issn = {0300-8177}, support = {847/TI_/Telethon/Italy ; }, mesh = {Adenine Nucleotides/metabolism ; Adenosine Triphosphate/metabolism ; Calcium/physiology ; Cell Membrane Permeability/physiology ; Cells, Cultured ; Cyclosporine/pharmacology ; Heart/*physiopathology ; Ion Channels/physiology ; Ischemia/*physiopathology ; Mitochondria/*pathology ; Myocardium/pathology ; Oxidative Phosphorylation ; Reperfusion Injury/physiopathology ; }, abstract = {Many pathological conditions can be the cause or the consequence of mitochondrial dysfunction. For instance anoxia, which is initiated by a critical reduction of oxygen availability for mitochondrial oxidations, is followed by a wide variety of mitochondrial alterations. A crucial role in the evolution of cell injury is to be attributed to the direction of operation of the F0F1 ATPase, which may turn mitochondria into the major consumers of cellular ATP in the futile attempt to restore the proton electrochemical gradient. On the other hand, functional mitochondria can paradoxically accelerate or exacerbate cell damage. This concept is particularly relevant for the ischemic myocardium. Indeed, inhibition of the respiratory chain or addition of uncouplers of oxidative phosphorylation can both limit the extent of enzyme release in the intact heart and prevent the onset of irreversible morphological changes in isolated myocytes. From studies on different tissues in a variety of pathological conditions a general consensus emerges on the role of intracellular Ca2+ overload as a pivotal link between cellular alterations and mitochondrial dysfunction. Oxidative phosphorylation is reduced by a massive mitochondrial uptake of Ca2+, resulting in a vicious cycle whereby the reduced ATP availability is followed by a failure of the mechanisms which extrude Ca2+ from the sarcoplasm. In addition, the rise in [Ca2+]i could promote opening of the cyclosporin-sensitive mitochondrial permeability transition pore, leading to a sudden deltapsi(m) dissipation. Here, we review the changes in intracellular and intramitochondrial ionic homeostasis occurring during ischemia and reperfusion. In particular, we evaluate the potential contribution of the permeability transition pore to cellular damage and discuss the mechanisms which can determine the cellular fate from a mitochondrial point of view.}, }
@article {pmid9746319, year = {1998}, author = {Qin, W and Khuchua, Z and Cheng, J and Boero, J and Payne, RM and Strauss, AW}, title = {Molecular characterization of the creatine kinases and some historical perspectives.}, journal = {Molecular and cellular biochemistry}, volume = {184}, number = {1-2}, pages = {153-167}, pmid = {9746319}, issn = {0300-8177}, mesh = {Amino Acid Sequence ; Cloning, Molecular ; Creatine Kinase/*genetics ; Evolution, Molecular ; Gene Expression Regulation, Enzymologic/genetics ; Humans ; Isoenzymes ; Mitochondria/*genetics ; Molecular Sequence Data ; Muscles/*metabolism ; RNA, Messenger/genetics ; Sequence Alignment ; }, abstract = {Over the last 15 years, molecular characterization of the creatine kinase (CK) gene family has paralleled the molecular revolution of understanding gene structure, function, and regulation. In this review, we present a summary of advances in molecular analysis of the CK gene family with a few vignettes of historical interest. We describe how the muscle CK gene provided an essential model system to examine myogenic regulatory mechanisms, leading to the discovery of the binding site for the MyoD family of basic helix-loop-helix transcription factors essential in skeletal myogenesis and the characterization of the MEF2 family of factors with an A/T rich consensus binding site essential in skeletal myogenesis and cardiogenesis. Cloning and characterization of the four mRNAs and nuclear genes encoding the cytosolic CKs, muscle and brain CKs, and the mitochondrial (Mt) CKs, sarcomeric MtCK and ubiquitous MtCK, has allowed intriguing study of tissue-specific and cell-specific expression of the different CKs and analysis of structural, functional, regulatory, and evolutionary relationships among both the four CK proteins and genes. Current and future studies focus on understanding both cellular energetics facilitated by the CK enzymes, especially energy channelling from the site of production, the mitochondrial matrix and inner membrane, to various cytosolic foci of utilization, and regulation of MtCK gene expression at the cell and tissue-specific level as models of regulation of energy producing genes.}, }
@article {pmid9745025, year = {1998}, author = {Miyata, S and Nakazono, M and Hirai, A}, title = {Transcription of plastid-derived tRNA genes in rice mitochondria.}, journal = {Current genetics}, volume = {34}, number = {3}, pages = {216-220}, doi = {10.1007/s002940050389}, pmid = {9745025}, issn = {0172-8083}, mesh = {DNA Probes/genetics ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Gene Expression Regulation, Plant/genetics ; Genes, Plant/genetics ; Mitochondria/*genetics ; Oryza/*genetics ; Plastids/*genetics ; RNA/genetics ; RNA, Messenger/metabolism ; RNA, Mitochondrial ; RNA, Transfer/*genetics ; RNA, Transfer, Arg/genetics ; Transcription, Genetic/*genetics ; }, abstract = {Previous investigations located nine of the genes for rice tRNAs on plastid (pt)-derived sequences in mitochondrial DNA. In the present study, we examined whether these genes were also transcribed in rice mitochondria. Northern-blot hybridization revealed that seven of these genes (trnC, trnF, trnH, trnM, trnN, trnS and trnW) are transcribed and are precisely processed to mature tRNAs. One of the other two genes (trnP) is transcribed but cannot be processed efficiently, while the other (trnR), which has 100% identity to the original plastid tRNAArg gene, is not transcribed in rice mitochondria. These results suggest that seven of the nine pt-derived tRNAs may be utilized for the biosynthesis of protein in plant mitochondria.}, }
@article {pmid9732451, year = {1998}, author = {Andrews, TD and Jermiin, LS and Easteal, S}, title = {Accelerated evolution of cytochrome b in simian primates: adaptive evolution in concert with other mitochondrial proteins?.}, journal = {Journal of molecular evolution}, volume = {47}, number = {3}, pages = {249-257}, doi = {10.1007/pl00006382}, pmid = {9732451}, issn = {0022-2844}, mesh = {Adaptation, Physiological ; Amino Acid Sequence ; Animals ; Base Composition ; Base Sequence ; Cats ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/analysis ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; Hominidae/genetics ; Humans ; Mammals/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Primates/*genetics ; Rats ; }, abstract = {We have sequenced the cytochrome b gene of Horsfield's tarsier, Tarsius bancanus, to complete a data set of sequences for this gene from representatives of each primate infraorder. These primate cytochrome b sequences were combined with those from representatives of three other mammalian orders (cat, whale, and rat) in an analysis of relative evolutionary rates. The nonsynonymous nucleotide substitution rate of the cytochrome b gene has increased approximately twofold along lineages leading to simian primates compared to that of the tarsier and other primate and nonprimate mammalian species. However, the rate of transversional substitutions at fourfold degenerate sites has remained uniform among all lineages. This increase in the evolutionary rate of cytochrome b is similar in character and magnitude to that described previously for the cytochrome c oxidase subunit II gene. We propose that the evolutionary rate increase observed for cytochrome b and cytochrome c oxidase subunit II may underlie an episode of coadaptive evolution of these two proteins in the mitochondria of simian primates.}, }
@article {pmid9724766, year = {1998}, author = {Mindell, DP and Sorenson, MD and Dimcheff, DE}, title = {Multiple independent origins of mitochondrial gene order in birds.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {95}, number = {18}, pages = {10693-10697}, pmid = {9724766}, issn = {0027-8424}, abstract = {Mitochondrial genomes of all vertebrate animals analyzed to date have the same 37 genes, whose arrangement in the circular DNA molecule varies only in the relative position of a few genes. This relative conservation suggests that mitochondrial gene order characters have potential utility as phylogenetic markers for higher-level vertebrate taxa. We report discovery of a mitochondrial gene order that has had multiple independent originations within birds, based on sampling of 137 species representing 13 traditionally recognized orders. This provides evidence of parallel evolution in mitochondrial gene order for animals. Our results indicate operation of physical constraints on mitochondrial gene order changes and support models for gene order change based on replication error. Bird mitochondria have a displaced OL (origin of light-strand replication site) as do various other Reptilia taxa prone to gene order changes. Our findings point to the need for broad taxonomic sampling in using mitochondrial gene order for phylogenetic analyses. We found, however, that the alternative mitochondrial gene orders distinguish the two primary groups of songbirds (order Passeriformes), oscines and suboscines, in agreement with other molecular as well as morphological data sets. Thus, although mitochondrial gene order characters appear susceptible to some parallel evolution because of mechanistic constraints, they do hold promise for phylogenetic studies.}, }
@article {pmid9720859, year = {1998}, author = {Kranz, R and Lill, R and Goldman, B and Bonnard, G and Merchant, S}, title = {Molecular mechanisms of cytochrome c biogenesis: three distinct systems.}, journal = {Molecular microbiology}, volume = {29}, number = {2}, pages = {383-396}, doi = {10.1046/j.1365-2958.1998.00869.x}, pmid = {9720859}, issn = {0950-382X}, support = {GM 47909/GM/NIGMS NIH HHS/United States ; GM 48350/GM/NIGMS NIH HHS/United States ; }, mesh = {Apoproteins/metabolism ; Biological Transport ; Cell Membrane/metabolism ; Chloroplasts/*metabolism ; Cytochrome c Group/*genetics/*metabolism ; Cytochromes c ; Eukaryotic Cells/*metabolism ; Evolution, Molecular ; Heme/metabolism ; Mitochondria/metabolism ; Oxidation-Reduction ; Prokaryotic Cells/*metabolism ; }, abstract = {The past 10 years have heralded remarkable progress in the understanding of the biogenesis of c-type cytochromes. The hallmark of c-type cytochrome synthesis is the covalent ligation of haem vinyl groups to two cysteinyl residues of the apocytochrome (at a Cys-Xxx-Yyy-Cys-His signature motif). From genetic, genomic and biochemical studies, it is clear that three distinct systems have evolved in nature to assemble this ancient protein. In this review, common principles of assembly for all systems and the molecular mechanisms predicted for each system are summarized. Prokaryotes, plant mitochondria and chloroplasts use either system I or II, which are each predicted to use dedicated mechanisms for haem delivery, apocytochrome ushering and thioreduction. Accessory proteins of systems I and II co-ordinate the positioning of these two substrates at the membrane surface for covalent ligation. The third system has evolved specifically in mitochondria of fungi, invertebrates and vertebrates. For system III, a pivotal role is played by an enzyme called cytochrome c haem lyase (CCHL) in the mitochondrial intermembrane space.}, }
@article {pmid9718722, year = {1998}, author = {Budin, K and Philippe, H}, title = {New insights into the phylogeny of eukaryotes based on ciliate Hsp70 sequences.}, journal = {Molecular biology and evolution}, volume = {15}, number = {8}, pages = {943-956}, doi = {10.1093/oxfordjournals.molbev.a026010}, pmid = {9718722}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Ciliophora/*genetics ; Cloning, Molecular ; Cytosol/metabolism ; DNA Primers/genetics ; Endoplasmic Reticulum/metabolism ; Eukaryotic Cells ; Euplotes/genetics ; Genes, Protozoan ; Genetic Markers ; HSP70 Heat-Shock Proteins/*genetics ; Mitochondria/metabolism ; Molecular Sequence Data ; Multigene Family ; Paramecium tetraurelia/genetics ; *Phylogeny ; Protozoan Proteins/*genetics ; }, abstract = {The current framework of the eukaryotic phylogeny is based on the analysis of a comprehensive set of sequences of the small subunit ribosomal RNA. However, phylogenies based on protein-encoding genes are not completely congruent with this picture. Since congruence between different markers is the best tool to determine evolutionary history, we focused on Hsp70 (heat-shock protein of 70 kDa), a chaperone protein which is highly conserved and is a potentially reliable phylogenetic marker. We used a PCR-based approach to sequence Hsp70s in two distinct classes of Ciliates. Seven Hsp70s were identified from Paramecium tetraurelia (Oligohymenophora) and six Hsp70s from Euplotes aediculatus (Hypotricha), encompassing orthologous genes for all major Hsp70 classes of Eukaryotes, i.e., those localized in cytosol, in endoplasmic reticulum, and in mitochondria. Three independent phylogenies of eukaryotes, based on each set of orthologous genes, have been constructed using different tree reconstruction methods. A significant advantage of Hsp70s is the existence of outgroups close to Eukaryotes for these major classes, reducing the long-branch attraction artifact due to the outgroup. The monophyly of Ciliates is supported by good bootstrap proportions in the phylogenetic reconstructions, and this phylum is generally a sister-group of Sporozoa, forming the expected Alveolates clade. The Hsp70 seems to be a suitable phylogenetic marker since it recovers all the monophyletic groups, undoubtedly defined by morphological criteria. The Hsp70 trees are, however, notably different from the rRNA ones and do not show two aspects of the classical topology, i.e., the successive emergence of deeply branching groups and the vast assembly of the major eukaryotic groups, emerging at the tip of the tree, i.e., the "terminal crown". More precisely, the Hsp70 trees do not resolve the relationships between the major groups of Eukaryotes with confidence, in keeping with the hypothesis that all these groups emerged in a great radiation that occurred at the origin of all the extant Eukaryotes.}, }
@article {pmid9716129, year = {1998}, author = {Qiu, YL and Cho, Y and Cox, JC and Palmer, JD}, title = {The gain of three mitochondrial introns identifies liverworts as the earliest land plants.}, journal = {Nature}, volume = {394}, number = {6694}, pages = {671-674}, doi = {10.1038/29286}, pmid = {9716129}, issn = {0028-0836}, mesh = {Base Sequence ; DNA, Plant ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; *Introns ; Mitochondria/*genetics ; *Mitochondrial Proteins ; Molecular Sequence Data ; Plant Proteins/genetics ; Plants/*genetics ; Sequence Alignment ; }, abstract = {The first evidence for the emergence of land plants (embryophytes) consists of mid-Ordovician spore tetrads (approximately 476 Myr old). The identity of the early plants that produced these spores is unclear; they are sometimes claimed to be liverworts, but there are no associated megafossils, and similar spores can be produced by a diversity of plants. Indeed, the earliest unequivocal megafossils of land plants consist of early vascular plants and various plants of uncertain affinity. Different phylogenetic analyses have identified liverworts, hornworts and bryophytes as each being the first lineage of land plants; the consensus of these conflicting topologies yields an unresolved polychotomy at the base of land plants. Here we survey 352 diverse land plants and find that three mitochondrial group II introns are present, with occasional losses, in mosses, hornworts and all major lineages of vascular plants, but are entirely absent from liverworts, green algae and all other eukaryotes. These results indicate that liverworts are the earliest land plants, with the three introns having been acquired in a common ancestor of all other land plants, and have important implications concerning the early stages of plant evolution.}, }
@article {pmid9714744, year = {1998}, author = {Di Lisa, F and Menabò, R and Canton, M and Petronilli, V}, title = {The role of mitochondria in the salvage and the injury of the ischemic myocardium.}, journal = {Biochimica et biophysica acta}, volume = {1366}, number = {1-2}, pages = {69-78}, doi = {10.1016/s0005-2728(98)00121-2}, pmid = {9714744}, issn = {0006-3002}, mesh = {Adenosine Triphosphate/metabolism ; Calcium/metabolism ; Cell Death/*physiology ; Cytochrome c Group/metabolism ; Energy Metabolism ; Humans ; Membrane Potentials ; Mitochondria, Heart/*physiology ; Mitochondrial ADP, ATP Translocases/metabolism ; Myocardial Ischemia/physiopathology ; Myocardial Reperfusion Injury/physiopathology ; Oxygen Consumption ; Proton-Translocating ATPases/metabolism ; }, abstract = {The relationships between mitochondrial derangements and cell necrosis are exemplified by the changes in the function and metabolism of mitochondria that occur in the ischemic heart. From a mitochondrial point of view, the evolution of ischemic damage can be divided into three phases. The first is associated with the onset of ischemia, and changes mitochondria from ATP producers into powerful ATP utilizers. During this phase, the inverse operation of F0F1 ATPase maintains the mitochondrial membrane potential by using the ATP made available by glycolysis. The second phase can be identified from the functional and structural alterations of mitochondria caused by prolongation of ischemia, such as decreased utilization of NAD-linked substrates, release of cytochrome c and involvement of mitochondrial channels. These events indicate that the relationship between ischemic damage and mitochondria is not limited to the failure in ATP production. Finally, the third phase links mitochondria to the destiny of the myocytes upon post-ischemic reperfusion. Indeed, depending on the duration and the severity of ischemia, not only is mitochondrial function necessary for cell recovery, but it can also exacerbate cell injury.}, }
@article {pmid9713860, year = {1998}, author = {Pandolfo, M}, title = {Molecular genetics and pathogenesis of Friedreich ataxia.}, journal = {Neuromuscular disorders : NMD}, volume = {8}, number = {6}, pages = {409-415}, doi = {10.1016/s0960-8966(98)00039-x}, pmid = {9713860}, issn = {0960-8966}, mesh = {Friedreich Ataxia/*genetics/*physiopathology ; Genotype ; Humans ; *Iron-Binding Proteins ; Phenotype ; Phosphotransferases (Alcohol Group Acceptor)/physiology ; Point Mutation/genetics ; Repetitive Sequences, Nucleic Acid ; Frataxin ; }, abstract = {Friedreich ataxia, the most frequent cause of inherited ataxia, is due in most cases to a large expansion of an intronic GAA repeat, resulting in decreased expression of the target frataxin gene. The autosomal recessive inheritance of the disease gives this triplet repeat mutation some unique features of natural history and evolution. Frataxin is a mitochondrial protein that has homologues in yeast and even in gram negative bacteria. Yeast deficient in the frataxin homologue accumulate iron in mitochondria and show increased sensitivity to oxidative stress. This suggests that Friedreich ataxia is caused by mitochondrial dysfunction and free radical toxicity.}, }
@article {pmid9711305, year = {1998}, author = {Sicheritz-Pontén, T and Kurland, CG and Andersson, SG}, title = {A phylogenetic analysis of the cytochrome b and cytochrome c oxidase I genes supports an origin of mitochondria from within the Rickettsiaceae.}, journal = {Biochimica et biophysica acta}, volume = {1365}, number = {3}, pages = {545-551}, doi = {10.1016/s0005-2728(98)00099-1}, pmid = {9711305}, issn = {0006-3002}, mesh = {Amino Acids ; Base Composition ; Cloning, Molecular ; Cytochrome b Group/*genetics ; DNA, Bacterial/chemistry/genetics ; Electron Transport Complex IV/*genetics ; Genes, Bacterial/genetics ; Mitochondria/enzymology/*genetics ; Molecular Sequence Data ; *Phylogeny ; Rickettsia prowazekii/enzymology/genetics ; Rickettsiaceae/enzymology/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {We have cloned and sequenced the genes encoding cytochrome b (cob) and cytochrome c oxidase subunit I (cox1) from Rickettsia prowazekii, a member of the alpha-proteobacteria. The phylogenetic analysis supports the hypothesis that mitochondria are derived from the alpha-proteobacteria and more specifically from within the Rickettsiaceae. We have estimated that the common ancestor of mitochondria and Rickettsiaceae dates back to more than 1500 million years ago.}, }
@article {pmid9693743, year = {1998}, author = {Xie, Z and Merchant, S}, title = {A novel pathway for cytochromes c biogenesis in chloroplasts.}, journal = {Biochimica et biophysica acta}, volume = {1365}, number = {1-2}, pages = {309-318}, doi = {10.1016/s0005-2728(98)00085-1}, pmid = {9693743}, issn = {0006-3002}, support = {GM 48350/GM/NIGMS NIH HHS/United States ; GM08375/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Chloroplasts/*enzymology ; Cytochrome c Group/chemistry/*metabolism ; Evolution, Molecular ; Humans ; Mitochondria/*enzymology ; Molecular Sequence Data ; Plants/enzymology ; }, abstract = {The cytochromes c are a useful model for the study of the pathways and mechanisms of assembly of the cofactor-containing components of energy transducing membranes. Genetic analyses have identified proteins that are required for the assembly of c-type cytochromes in mitochondria, bacteria and chloroplasts. The components of the pathway operating in fungal and animal mitochondria, i.e. the cytochrome (cyt) c and c1 heme lyases in the intermembrane space, were identified over a decade ago through the study of cytochrome deficiencies in Neurospora crassa and Saccharomyces cerevisiae. More recently, a large number of membrane or membrane-associated components were identified in various alpha- and gamma-proteobacteria as c-type cytochrome assembly factors; they comprise an assembly pathway that is evolutionarily and mechanistically distinct from that in fungal and animal mitochondria. The components function not only in the lyase reaction but also in the delivery and maintenance of the substrates in a state that is suitable for reaction in the bacterial periplasm. Yet a third pathway is required for cytochrome maturation in chloroplasts. Genetic analyses of Chlamydomonas reinhardtii ccs mutants, which are pleiotropically deficient in both the membrane-anchored cytochrome f and the soluble cytochrome c6, revealed a minimum of six loci, plastid ccsA and nuclear CCS1 through CCS5, that are required for the conversion of the chloroplast apocytochromes to their respective holo forms. Sequence analysis of the cloned ccsA and Ccs1 genes indicates that the predicted protein products are integral membrane proteins with homologues in cyanobacteria, some gram-positive bacteria (Bacillus subtilis, Mycobacterium spp.), beta-proteobacteria (Neisseria spp.) and an epsilon-proteobacterium (Helicobacter pylori). CcsA and Ccs1 require each other for accumulation in vivo and are therefore proposed to function in a complex, possibly with the products of some of the other CCS loci. A tryptophan-rich motif, which has been proposed to represent a heme binding site in bacterial cytochrome biogenesis proteins (CcmC and CcmF), is functionally important in plastid CcsA. As is the case for CcmC and CcmF, the tryptophan-rich sequence is predicted to occur in a loop on the p-side of the membrane, where the heme attachment reaction occurs. Conserved histidine residues in the CcsA and Ccs1 may serve as ligands to the heme iron. A multiple alignment of the tryptophan-rich regions of the CcsA-, CcmC- and CcmF-like sequences in the genome databases indicates that they represent three different families.}, }
@article {pmid9693729, year = {1998}, author = {Andersson, SG}, title = {Bioenergetics of the obligate intracellular parasite Rickettsia prowazekii.}, journal = {Biochimica et biophysica acta}, volume = {1365}, number = {1-2}, pages = {105-111}, doi = {10.1016/s0005-2728(98)00050-4}, pmid = {9693729}, issn = {0006-3002}, mesh = {Citric Acid/metabolism ; Electron Transport ; Energy Metabolism/genetics/*physiology ; Genome, Bacterial ; Mitochondria/physiology ; Mitochondrial ADP, ATP Translocases/genetics ; Operon ; Oxidation-Reduction ; Proton-Translocating ATPases/genetics ; Rickettsia prowazekii/genetics/*physiology ; }, abstract = {Mitochondria are thought to be derived from an ancestor of the alpha-proteobacteria and more specifically from the Rickettsiaceae. The bioenergetic repertoire of the obligate intracellular parasite Rickettsia prowazekii is consistent with its postulated role as the ancestor of the mitochondria. For example, the R. prowazekii genome contains genes encoding components of the tricarboxylic acid cycle as well as of the electron transport system, but lacks genes to support glycolysis. In addition, the R. prowazekii genome contains multiple genes coding for adenine nucleotide translocators which enables this intracellular parasite to exploit the cytoplasmic ATP of its host cell as a source of energy. The aim of this review is to describe the different aspects of the bioenergetic system in R. prowazekii and to discuss the results of phylogenetic reconstructions based on a variety of bioenergetic molecules which shed light on the origin and evolution of the mitochondrial genomes.}, }
@article {pmid9691064, year = {1998}, author = {Bergstrom, CT and Pritchard, J}, title = {Germline bottlenecks and the evolutionary maintenance of mitochondrial genomes.}, journal = {Genetics}, volume = {149}, number = {4}, pages = {2135-2146}, pmid = {9691064}, issn = {0016-6731}, support = {GM 28016/GM/NIGMS NIH HHS/United States ; }, mesh = {Antibody Diversity ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Genetic Variation ; Genome ; Mitochondria/*genetics ; *Models, Genetic ; Mutation ; }, abstract = {Several features of the biology of mitochondria suggest that mitochondria might be susceptible to Muller's ratchet and other forms of evolutionary degradation: Mitochondria have predominantly uniparental inheritance, appear to be nonrecombining, and have high mutation rates producing significant deleterious variation. We demonstrate that the persistence of mitochondria may be explained by recent data that point to a severe "bottleneck" in the number of mitochondria passing through the germline in humans and other mammals. We present a population-genetic model in which deleterious mutations arise within individual mitochondria, while selection operates on assemblages of mitochondria at the level of their eukaryotic hosts. We show that a bottleneck increases the efficacy of selection against deleterious mutations by increasing the variance in fitness among eukaryotic hosts. We investigate both the equilibrium distribution of deleterious variation in large populations and the dynamics of Muller's ratchet in small populations. We find that in the absence of the ratchet, a bottleneck leads to improved mitochondrial performance and that, over a longer time scale, a bottleneck acts to slow the progression of the ratchet.}, }
@article {pmid9684018, year = {1997}, author = {Debouverie, M and Wagner, M and Ducrocq, X and Grignon, Y and Mousson, B and Weber, M}, title = {[MNGIE syndrome in 2 siblings].}, journal = {Revue neurologique}, volume = {153}, number = {10}, pages = {547-553}, pmid = {9684018}, issn = {0035-3787}, mesh = {Adult ; Female ; Humans ; Intestinal Pseudo-Obstruction/*genetics ; Male ; Mitochondrial Encephalomyopathies/*genetics ; Pedigree ; Peripheral Nervous System Diseases/*genetics ; Syndrome ; }, abstract = {Two siblings (one man, one woman), presenting with diarrhea, severe weight loss peripheral neuropathy, ophthalmoparesis, asymptomatic leukoencephalopathy were diagnosed as a new cases of Mitochondrial Neuro Gastro Intestinal Encephalomyopathy syndrome (MNGIE). Hirano (1994) defined four criteria for the diagnostic: peripheral neuropathy, ophthalmoparesis, gastro intestinal dysmotility, muscle biopsy with histologic features of mitochondrial myopathy (ragged-red fibers, muscle fibers with increased succinate deshydrogenase stain or ultra structurally abnormal mitochondria). In a review of the literature, we found 31 cases with MNGIE. With our two cases, we study this group of 33 patients. First symptoms begin about 13.5 years with a median of 10 years and extremes for 1 to 32 years. The first signs are gastro intestinal symptoms (recurrent nausea, vomiting or diarrhea with intestinal dysmotility) in 22 cases, an ophthalmoparesia in 4 cases, intestinal and ocular signs in 1 case, gait ataxia or peripheral neuropathy in 3 cases, hearing loss in 1 case, gait ataxia or peripheral neuropathy in 3 cases, hearing loss in 1 case. During the evolution, besides the cardinal signs, the following features have been observed with a variable frequency: hearing loss, short stature, facial palsy, dysphonia, dysarthria, sweating, orthostatic hypotension, bladder dysfunction, hepatomegalia, The laboratory features are: abnormal Nerve Condition Studies/EMG compatible with a sensory motor neuropathy, lactic acidosis, mitochondrial respiratory chain defect (essentially complex IV deficiency, complex I deficiency or multiple complex defect), MRI leukodystrophy, elevated CSF protein, heart block, ragged-red fibers or increased SDH stain. The prognosis is poor, due to a severe weight loss bordering on cachexia 13 patients died with a mean age of 28.5 years (median 24 years, extreme 3 years to 51 years). The prognosis seems to be worsened by a young age of onset. The 33 patients belong to 19 families with 7 cases of consanguinity. 25 patients had a brother, a sister or a cousin affected. The study of these families is compatible with an autosomic recessive transmission, suggesting a pathology of the nuclear genomi, probably impliying the control of the mitochondrial DNA replication. In fact, in 13 cases, a study of the mt DNA was realized: multiple deletions were founded in 6 cases, multiples mutations in one case, unique mutation in 1 case. In 5 cases ther was no evidence of abnormality. These precise etiology and pathophysiologic significance of the mt DNA deletions, and the heterogeneity of the modifications of the mt DNA remain unknown. However, the possibility of various phenotypes for a same genotype or inversely is known in mitochondriopathies.}, }
@article {pmid9675873, year = {1998}, author = {Navajas, M and Lagnel, J and Gutierrez, J and Boursot, P}, title = {Species-wide homogeneity of nuclear ribosomal ITS2 sequences in the spider mite Tetranychus urticae contrasts with extensive mitochondrial COI polymorphism.}, journal = {Heredity}, volume = {80 (Pt 6)}, number = {}, pages = {742-752}, doi = {10.1046/j.1365-2540.1998.00349.x}, pmid = {9675873}, issn = {0018-067X}, mesh = {Animals ; Base Sequence ; Cell Nucleus/metabolism ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/*genetics ; Electron Transport Complex IV/biosynthesis/*genetics ; Evolution, Molecular ; Genetic Variation ; Mites/enzymology/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; *Polymorphism, Genetic ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; Transcription, Genetic ; }, abstract = {We compared patterns of intraspecific polymorphism of two markers with contrasted modes of evolution, nuclear ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA), in the phytophagous mite Tetranychus urticae Koch. The second internal transcribed spacer (ITS2) of rDNA and a fragment in the mtDNA gene coding for Cytochrome Oxidase I (COI), were PCR-amplified and sequenced in samples of various geographical origins distributed worldwide. The 15 COI haplotypes found fell into two major phylogenetic lineages differing by an average of 5% nucleotide divergence. Samples from the Mediterranean basin were represented in both lineages, and showed no phylogeographical structure. The other samples, from temperate regions of the northern hemisphere, were clustered in one of the lineages and displayed little variation, indicating a recent colonization of this region. In contrast, no variation at all was found at the ITS2 in this species. We sequenced both COI and ITS2 in four other species of the genus Tetranychus and found that, despite the absence of intraspecific polymorphism, ITS appears to evolve 2.5 times faster than COI. We argue that rDNA homogeneity over the species range of T. urticae results from the high colonization potential of this species, preventing long-term differentiation. Preliminary data on two other mite species (Amphitetranychus viennensis Zacher and Mononychellus progresivus Doreste) with stricter ecological requirements and more restricted colonization potential revealed substantial and concordant geographical differentiation for both ITS2 and COI.}, }
@article {pmid9671812, year = {1998}, author = {Peyretaillade, E and Biderre, C and Peyret, P and Duffieux, F and Méténier, G and Gouy, M and Michot, B and Vivarès, CP}, title = {Microsporidian Encephalitozoon cuniculi, a unicellular eukaryote with an unusual chromosomal dispersion of ribosomal genes and a LSU rRNA reduced to the universal core.}, journal = {Nucleic acids research}, volume = {26}, number = {15}, pages = {3513-3520}, pmid = {9671812}, issn = {0305-1048}, mesh = {Animals ; Base Sequence ; Chromosome Mapping ; DNA, Ribosomal ; Encephalitozoon cuniculi/*genetics ; Eukaryotic Cells ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Phylogeny ; *RNA, Protozoan/chemistry ; *RNA, Ribosomal/chemistry ; *RNA, Ribosomal, 5S/chemistry ; Ribosomes ; }, abstract = {Microsporidia are eukaryotic parasites lacking mitochondria, the ribosomes of which present prokaryote-like features. In order to better understand the structural evolution of rRNA molecules in microsporidia, the 5S and rDNA genes were investigated in Encephalitozoon cuniculi . The genes are not in close proximity. Non-tandemly arranged rDNA units are on every one of the 11 chromosomes. Such a dispersion is also shown in two other Encephalitozoon species. Sequencing of the 5S rRNA coding region reveals a 120 nt long RNA which folds according to the eukaryotic consensus structural shape. In contrast, the LSU rRNA molecule is greatly reduced in length (2487 nt). This dramatic shortening is essentially due to truncation of divergent domains, most of them being removed. Most variable stems of the conserved core are also deleted, reducing the LSU rRNA to only those structural features preserved in all living cells. This suggests that the E.cuniculi LSU rRNA performs only the basic mechanisms of translation. LSU rRNA phylogenetic analysis with the BASEML program favours a relatively recent origin of the fast evolving microsporidian lineage. Therefore, the prokaryote-like ribosomal features, such as the absence of ITS2, may be derived rather than primitive characters.}, }
@article {pmid9667982, year = {1998}, author = {Milinkovitch, MC and Lyons-Weiler, J}, title = {Finding optimal ingroup topologies and convexities when the choice of outgroups is not obvious.}, journal = {Molecular phylogenetics and evolution}, volume = {9}, number = {3}, pages = {348-357}, doi = {10.1006/mpev.1998.0503}, pmid = {9667982}, issn = {1055-7903}, mesh = {Animals ; Cytochrome b Group/chemistry/*genetics ; *Evolution, Molecular ; Mammals ; Mitochondria/metabolism ; *Models, Genetic ; *Phylogeny ; Sequence Analysis ; *Sequence Homology, Amino Acid ; }, abstract = {Considerable confusion remains among theoreticians and practicioners of phylogenetic science on the use of outgroup taxa. Here, we show that, despite claims to the contrary, details of the optimal ingroup topology can be changed by switching outgroup taxa. This has serious implications for phylogenetic accuracy. We delineate between the process of outgroup selection and the various possible processes involved in using an outgroup taxon after one has been selected. Criteria are needed for the determination that particular outgroup taxa do not reduce the accuracy of evolutionary tree topologies and inferred character state transformations. We compare previous results from a sensitivity bootstrap analysis of the mitochondrial cytochrome b phylogenetic relationships among whales to the results of a Bremer support sensitivity analysis and of a recently developed application of RASA theory to the question of putative outgroup taxon plesiomorphy content.}, }
@article {pmid9657003, year = {1998}, author = {Hong, Y and Cole, TE and Brasier, CM and Buck, KW}, title = {Evolutionary relationships among putative RNA-dependent RNA polymerases encoded by a mitochondrial virus-like RNA in the Dutch elm disease fungus, Ophiostoma novo-ulmi, by other viruses and virus-like RNAs and by the Arabidopsis mitochondrial genome.}, journal = {Virology}, volume = {246}, number = {1}, pages = {158-169}, doi = {10.1006/viro.1998.9178}, pmid = {9657003}, issn = {0042-6822}, mesh = {Amino Acid Sequence ; Arabidopsis/genetics ; Ascomycota/enzymology/*genetics/virology ; Basidiomycota/enzymology/genetics ; DNA, Fungal/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; *Evolution, Molecular ; Molecular Sequence Data ; Open Reading Frames/genetics ; *Phylogeny ; RNA/*genetics ; RNA, Double-Stranded/genetics ; RNA, Fungal/genetics ; RNA, Mitochondrial ; RNA, Viral/*genetics ; RNA-Dependent RNA Polymerase/*genetics ; Sequence Homology, Amino Acid ; Trees/microbiology ; Tryptophan/genetics ; }, abstract = {The nucleotide sequence (2617 nucleotides) of virus-like double-stranded (ds) RNA 3a in a diseased isolate, Log1/3-8d2 (Ld), of the ascomycete fungus Ophiostoma novo-ulmi has been determined. One strand of the dsRNA contains an open reading frame (ORF) with the potential to encode a protein of 718 amino acids, and the complementary strand contains two smaller ORFs with the potential to encode proteins of 178 and 182 amino acids, respectively. The large ORF contains 12 UGA codons which code for tryptophan in ascomycete mitochondria and has a codon bias typical of mitochondrial genes, consistent with the localization of Ld dsRNAs within the mitochondria. The amino acid sequence contains motifs characteristic of RNA-dependent RNA polymerases (RdRps). This putative RdRp was shown to be related to putative RdRps of mitochondrial dsRNAs of another ascomycete and a basidiomycete fungus and also to a putative RdRp encoded by the mitochondrial genome of Arabidopsis thaliana. In multiple sequence alignments, the fungal mitochondrial dsRNA-encoded RdRp-like proteins formed a cluster, ancestrally related to the RdRps of the yeast 20S and 23S RNA replicons and of the positive-stranded RNA bacteriophages of the Leviviridae family, but distinct from RdRps of other families and genera of fungal RNA viruses and related plant and animal RNA viruses. Northern blot analysis with RNA 3a strand-specific probes indicated that nucleic acid extracts of Ld contain more single-stranded (positive-stranded) RNA than dsRNA, consistent with an evolutionary relationship between RNA 3a and positive-stranded RNA phages.}, }
@article {pmid9655342, year = {1998}, author = {Jeffery, CJ and Barry, T and Doonan, S and Petsko, GA and Ringe, D}, title = {Crystal structure of Saccharomyces cerevisiae cytosolic aspartate aminotransferase.}, journal = {Protein science : a publication of the Protein Society}, volume = {7}, number = {6}, pages = {1380-1387}, pmid = {9655342}, issn = {0961-8368}, mesh = {Animals ; Aspartate Aminotransferases/*chemistry/genetics/metabolism ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Cytosol/enzymology ; DNA, Fungal/chemistry ; Dimerization ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Molecular Structure ; Protein Conformation ; Pyridoxal Phosphate/metabolism ; Saccharomyces cerevisiae/*enzymology ; Sequence Homology ; }, abstract = {The crystal structure of Saccharomyces cerevisiae cytoplasmic aspartate aminotransferase (EC 2.6.1.1) has been determined to 2.05 A resolution in the presence of the cofactor pyridoxal-5'-phosphate and the competitive inhibitor maleate. The structure was solved by the method of molecular replacement. The final value of the crystallographic R-factor after refinement was 23.1% with good geometry of the final model. The yeast cytoplasmic enzyme is a homodimer with two identical active sites containing residues from each subunit. It is found in the "closed" conformation with a bound maleate inhibitor in each active site. It shares the same three-dimensional fold and active site residues as the aspartate aminotransferases from Escherichia coli, chicken cytoplasm, and chicken mitochondria, although it shares less than 50% sequence identity with any of them. The availability of four similar enzyme structures from distant regions of the evolutionary tree provides a measure of tolerated changes that can arise during millions of years of evolution.}, }
@article {pmid9651529, year = {1998}, author = {Nowitzki, U and Flechner, A and Kellermann, J and Hasegawa, M and Schnarrenberger, C and Martin, W}, title = {Eubacterial origin of nuclear genes for chloroplast and cytosolic glucose-6-phosphate isomerase from spinach: sampling eubacterial gene diversity in eukaryotic chromosomes through symbiosis.}, journal = {Gene}, volume = {214}, number = {1-2}, pages = {205-213}, doi = {10.1016/s0378-1119(98)00229-7}, pmid = {9651529}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Bacteria/classification/enzymology/genetics ; Base Sequence ; Chloroplasts/enzymology/genetics ; Cloning, Molecular ; Cyanobacteria/classification/enzymology/genetics ; Cytosol/enzymology ; DNA Primers/genetics ; Escherichia coli/enzymology/genetics ; *Genes, Bacterial ; *Genes, Plant ; Genetic Variation ; Glucose-6-Phosphate Isomerase/*genetics ; Haemophilus/enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Spinacia oleracea/*enzymology/*genetics/microbiology ; Symbiosis/genetics ; }, abstract = {Higher plants possess two distinct nuclear-encoded glucose-6-phosphate isomerase (GPI) isoenzymes, a cytosolic enzmye of the Embden-Meyerhof pathway and a chloroplast enzyme essential to storage and mobilization of carbohydrate fixed by the Calvin cycle. We have purified spinach chloroplast GPI to homogeneity, determined amino acid sequences from the active enzyme, and cloned cDNAs for chloroplast and cytosolic GPI isoenzymes from spinach. Sequence comparisons reveal three distantly related families of GPI genes that are non-uniformly distributed among contemporary eubacteria and archaebacteria, suggesting that ancient gene diversity existed for this glycolytic enzyme. Spinach chloroplast GPI is much more similar to its homologue from the cyanobacterium Synechocystis PCC6803 than it is to the enzyme from any other source, providing strong evidence that the gene for chloroplast GPI was acquired by the nucleus via endosymbiotic gene transfer from the cyanobacterial antecedants of chloroplasts. Eukaryotic nuclear genes for cytosolic GPI are more similar to eubacterial than to archaebacterial homologues, suggesting that these too were acquired by eukaryotes from eubacteria, probably during the course of the endosymbiotic origin of mitochondria. Chloroplast and cytosolic GPI provide evidence for a eubacterial origin of yet another component of the eukaryotic glycolytic pathway.}, }
@article {pmid9650294, year = {1998}, author = {Jian, JH and Lakshman, DK and Tavantzis, SM}, title = {A virulence-associated, 6.4-kb, double-stranded RNA from Rhizoctonia solani is phylogenetically related to plant bromoviruses and electron transport enzymes.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {11}, number = {7}, pages = {601-609}, doi = {10.1094/MPMI.1998.11.7.601}, pmid = {9650294}, issn = {0894-0282}, mesh = {Amino Acid Sequence ; Base Sequence ; Bromovirus/*genetics ; Conserved Sequence ; Cytosol/metabolism ; DNA, Complementary/chemistry ; Electron Transport ; Electron Transport Complex IV/chemistry ; Fabaceae/virology ; Mitochondria/metabolism ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Plants, Medicinal ; RNA, Bacterial/chemistry/genetics ; RNA, Double-Stranded/chemistry/*genetics ; Rhizoctonia/*genetics/*pathogenicity ; Sequence Alignment ; Sequence Homology, Amino Acid ; Viral Proteins/biosynthesis/chemistry ; Virulence ; }, abstract = {We have recently shown that acquisition of a 6.4-kb, double-stranded (ds) RNA (M1) by hyphal anastomosis is associated with enhanced vigor and virulence, whereas its removal by hyphal tipping correlates with diminished virulence in the plant-pathogenic basidiomycete Rhizoctonia solani. The M1 dsRNA is not encapsidated by a typical nucleocapsid, has a circular and/or concatemeric form, and is associated with the mitochondrial and cytosolic fractions. M1 possesses six open reading frames (ORFs) the longest of which (ORF 2) is located on the (+) strand, and encodes a putative polypeptide consisting of 1,747 amino acids or 199.4 kDa. This polypeptide has a significant amino acid sequence similarity, including six conserved helicase domains and an ATP/GTP binding motif, with the 1A protein of broad bean mottle virus (BBMV) and other bromoviruses. ORF 5, which is located on the (-) strand of M1 and is complementary to a region of ORF 2, codes for a putative polypeptide that has a significant amino acid sequence similarity with the cytochrome c oxidase assembly factor. This complementarity provides direct evidence suggesting that the long-standing hypothesis of viruses evolving from cellular genes may be valid.}, }
@article {pmid9650281, year = {1998}, author = {Lunt, DH and Ibrahim, KM and Hewitt, GM}, title = {mtDNA phylogeography and postglacial patterns of subdivision in the meadow grasshopper Chorthippus parallelus.}, journal = {Heredity}, volume = {80 (Pt 5)}, number = {}, pages = {633-641}, doi = {10.1046/j.1365-2540.1998.00311.x}, pmid = {9650281}, issn = {0018-067X}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Europe ; *Evolution, Molecular ; *Genetic Variation ; Geography ; Grasshoppers/classification/enzymology/*genetics ; Mitochondria/enzymology ; *Phylogeny ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {A 300 bp portion of the mitochondrial cytochrome oxidase subunit I (COI) gene was used to investigate the intraspecific genetic structure of the European meadow grasshopper Chorthippus parallelus. Levels of genetic subdivision between geographical regions in Europe were assessed using the KST statistic and revealed patterns indicative of the postglacial history of this organism. Northern European populations are shown to share a very recent common ancestor with, and hence originate from, a Balkan expansion. Genetic distances between these areas and both southern Italy and central Spain are shown to be approximately equal, even though only the Spanish form is recognized as a distinct subspecies. Distance estimates indicate that the common ancestor of the two subspecies lived more than one glacial cycle ago, and the refugial populations have probably been diverging in isolation for five or six glacial cycles (approximately equal to 550,000 years). Comparisons are made to the analysis of a similar data set using an anonymous nuclear DNA marker (Cooper et al., 1995). Although the structure revealed is generally very similar, differences in the location of transition zones between different genetic forms of C. parallelus may reflect the different historical assortment of these molecules.}, }
@article {pmid9600846, year = {1998}, author = {Ptitsyn, OB}, title = {Protein folding and protein evolution: common folding nucleus in different subfamilies of c-type cytochromes?.}, journal = {Journal of molecular biology}, volume = {278}, number = {3}, pages = {655-666}, doi = {10.1006/jmbi.1997.1620}, pmid = {9600846}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/metabolism ; Binding Sites ; Chloroplasts/metabolism ; Conserved Sequence ; Cytochrome c Group/*chemistry/*genetics/metabolism ; *Evolution, Molecular ; Heme/metabolism ; Horses ; Kinetics ; Mitochondria/metabolism ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; *Protein Folding ; Saccharomyces cerevisiae/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Amino acid sequences of seven subfamilies of cytochromes c (mitochondrial cytochromes c, c1; chloroplast cytochromes c6, cf; bacterial cytochromes c2, c550, c551; in total 164 sequences) have been compared. Despite extensive homology within eukaryotic subfamilies, homology between different subfamilies is very weak. Other than the three heme-binding residues (Cys13, Cys14, His18, in numeration of horse cytochrome c) there are only four positions which are conserved in all subfamilies: Gly/Ala6, Phe/Tyr10, Leu/Val/Phe94 and Tyr/Trp/Phe97. In all 17 cytochromes c with known 3D-structures, these residues form a network of conserved contacts (6-94, 6-97, 10-94, 10-97 and 94-97). Especially strong is the contact between aromatic groups in positions 10 and 97, which corresponds to 13 interatomic contacts. As residues 6, 10 and residues 94, 97 are in (i, i+4) and (i, i+3) positions in the N and C-terminal helices, respectively, the above mentioned system of conserved contacts consists mainly of contacts between one turn of N-terminal helix and one turn of C-terminal helix. The importance of the contacts between interfaces of these helices has been confirmed by the existence of these contacts in both equilibrium and kinetic molten globule-like folding intermediates, as well as by mutational evidence that these contacts are involved in tight packing between the N and C-helices. Since these four residues are not involved in heme binding and have no other apparent functional role, their conservation in highly diverged cytochromes c suggests that they are of a critical importance for protein folding. The author assumes that they are involved in a common folding nucleus of all subfamilies of c-type cytochromes.}, }
@article {pmid9547276, year = {1998}, author = {Akashi, K and Takenaka, M and Yamaoka, S and Suyama, Y and Fukuzawa, H and Ohyama, K}, title = {Coexistence of nuclear DNA-encoded tRNAVal(AAC) and mitochondrial DNA-encoded tRNAVal(UAC) in mitochondria of a liverwort Marchantia polymorpha.}, journal = {Nucleic acids research}, volume = {26}, number = {9}, pages = {2168-2172}, pmid = {9547276}, issn = {0305-1048}, mesh = {Biological Transport ; Cell Compartmentation ; Cell Nucleus/*genetics/metabolism ; DNA, Mitochondrial/*genetics/metabolism ; DNA, Plant/*genetics/metabolism ; Genes, Plant ; RNA, Transfer, Val/*genetics/metabolism ; Sequence Analysis, DNA ; }, abstract = {The liverwort Marchantia polymorpha mitochondrial DNA encodes almost all tRNAs required for mitochondrial translation except for the isoleucine (AUU, AUC) and threonine (ACA, ACG) codons, while the missing tRNAs are supplied in part by the nucleus and imported in mitochondria. In this paper, we report a finding of two radically different nuclear tRNAVal(AAC) genes and import of the corresponding tRNA isoacceptors in M.polymorpha mitochondria. This finding is surprising since the mtDNA encodes the gene for tRNAVal(UAC), which alone was considered sufficient for translating all four valine codons GUN by the U/N wobble mechanism. The present results suggest for the first time that the import of ncDNA-encoded tRNAs may result in decoding overlaps in plant mitochondria. The coexistence of nuclear DNA-encoded tRNAVal(AAC) and mitochondrial DNA-encoded tRNAVal(UAC) in liverwort mitochondria and the significance for the decoding mechanism as well as evolution of tRNA import are discussed.}, }
@article {pmid9618503, year = {1998}, author = {Hashimoto, T and Sánchez, LB and Shirakura, T and Müller, M and Hasegawa, M}, title = {Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogeny.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {95}, number = {12}, pages = {6860-6865}, pmid = {9618503}, issn = {0027-8424}, support = {AI11942/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Giardia lamblia/*genetics/*ultrastructure ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Trichomonas vaginalis/*genetics/*ultrastructure ; Valine-tRNA Ligase/*genetics ; }, abstract = {Nuclear-coded valyl-tRNA synthetase (ValRS) of eukaryotes is regarded of mitochondrial origin. Complete ValRS sequences obtained by us from two amitochondriate protists, the diplomonad, Giardia lamblia and the parabasalid, Trichomonas vaginalis were of the eukaryotic type, strongly suggesting an identical history of ValRS in all eukaryotes studied so far. The findings indicate that diplomonads are secondarily amitochondriate and give further evidence for such conclusion reached recently concerning parabasalids. Together with similar findings on other amitochondriate groups (microsporidia and entamoebids), this work provides critical support for the emerging notion that no representatives of the premitochondrial stage of eukaryotic phylogenesis exist among the species living today.}, }
@article {pmid9603924, year = {1998}, author = {Barrientos, A and Kenyon, L and Moraes, CT}, title = {Human xenomitochondrial cybrids. Cellular models of mitochondrial complex I deficiency.}, journal = {The Journal of biological chemistry}, volume = {273}, number = {23}, pages = {14210-14217}, doi = {10.1074/jbc.273.23.14210}, pmid = {9603924}, issn = {0021-9258}, support = {GM55766/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cell Respiration/drug effects/physiology ; Cells, Cultured ; Clone Cells/metabolism ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Hominidae ; Humans ; Hybrid Cells/metabolism ; Kinetics ; Mitochondria/*metabolism ; NAD/metabolism ; NAD(P)H Dehydrogenase (Quinone)/chemistry/deficiency ; *Oxidative Phosphorylation ; Oxygen Consumption/physiology ; Rotenone/pharmacology ; }, abstract = {The subunits forming the mitochondrial oxidative phosphorylation system are coded by both nuclear and mitochondrial genes. Recently, we attempted to introduce mtDNA from non-human apes into a human cell line lacking mtDNA (rho degrees), and succeeded in producing human-common chimpanzee, human-pigmy chimpanzee, and human-gorilla xenomitochondrial cybrids (HXC). Here, we present a comprehensive characterization of oxidative phosphorylation function in these cells. Mitochondrial complexes II, III, IV, and V had activities indistinguishable from parental human or non-human primate cells. In contrast, a complex I deficiency was observed in all HXC. Kinetic studies of complex I using decylubiquinone or NADH as limiting substrates showed that the Vmax was decreased in HXC by approximately 40%, and the Km for the NADH was significantly increased (3-fold, p < 0.001). Rotenone inhibition studies of intact cell respiration and pyruvate-malate oxidation in permeabilized cells showed that 3 nM rotenone produced a mild effect in control cells (0-10% inhibition) but produced a marked inhibition of HXC respiration (50-75%). Immunoblotting analyses of three subunits of complex I (ND1, 75 and 49 kDa) showed that their relative amounts were not significantly altered in HXC cells. These results establish HXC as cellular models of complex I deficiency in humans and underscore the importance of nuclear and mitochondrial genomes co-evolution in optimizing oxidative phosphorylation function.}, }
@article {pmid9615625, year = {1998}, author = {Kobayashi, N and Tamura, K and Aotsuka, T and Katakura, H}, title = {Molecular phylogeny of twelve Asian species of epilachnine ladybird beetles (Coleoptera, Coccinellidae) with notes on the direction of host shifts.}, journal = {Zoological science}, volume = {15}, number = {1}, pages = {147-151}, doi = {10.2108/zsj.15.147}, pmid = {9615625}, issn = {0289-0003}, mesh = {Amino Acid Sequence ; Animals ; Coleoptera/*genetics ; Electron Transport Complex IV/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {We determined the nucleotide sequences of a part of the mitochondrial cytochrome c oxidase I gene (1,000 bp) for twelve species of Asian phytophagous ladybird beetles belonging to the genus Epilachna, and constructed molecular phylogenetic trees for ten "Henosepilachna" species, using two "Epilachna" species as outgroups. Based on the suggested phylogenetic trees, we discussed taxonomic issues and the direction of host shift in these epilachnines.}, }
@article {pmid9615624, year = {1998}, author = {Onuma, M and Kusakabe, T and Kusakabe, S}, title = {Phylogenetic positions of insectivora in eutheria inferred from mitochondrial cytochrome c oxidase subunit II gene.}, journal = {Zoological science}, volume = {15}, number = {1}, pages = {139-145}, doi = {10.2108/zsj.15.139}, pmid = {9615624}, issn = {0289-0003}, mesh = {Animals ; Base Sequence ; Electron Transport Complex IV/*genetics ; Eulipotyphla/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {For the elucidation of the phylogenetic position of insectivora in eutheria, we have sequenced the cytochrome c oxidase subunit II (COII) gene of mitochondria for three insectivoran species [musk screw (Suncus murinus), shrew mole (Urotrichus talpoides), Japanese mole (Mogera wogura)] and analyzed these amino acid sequences with neighbor-joining (NJ) method and maximum likelihood (ML) method. NJ analysis shows polyphyly of Insectivora and Chiroptera. Assuming that each of Primates, Ferungulata, Chiroptera, Insectivora and Rodentia is a monophyletic group, ML analysis suggests that Chiroptera is a sister group of Insectivora and that Ferungulata is the closest outgroup to the (Insectivora and Chiroptera) clade.}, }
@article {pmid9615449, year = {1998}, author = {Peyretaillade, E and Broussolle, V and Peyret, P and Méténier, G and Gouy, M and Vivarès, CP}, title = {Microsporidia, amitochondrial protists, possess a 70-kDa heat shock protein gene of mitochondrial evolutionary origin.}, journal = {Molecular biology and evolution}, volume = {15}, number = {6}, pages = {683-689}, doi = {10.1093/oxfordjournals.molbev.a025971}, pmid = {9615449}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/genetics ; Base Sequence ; Blotting, Southern ; Cloning, Molecular ; Cyanobacteria/genetics ; DNA, Mitochondrial/*genetics ; Encephalitozoon/*genetics/ultrastructure ; *Evolution, Molecular ; *Genes, Protozoan ; HSP70 Heat-Shock Proteins/*genetics ; Microsporida/classification/genetics ; Molecular Sequence Data ; *Phylogeny ; Plants/genetics ; Polymerase Chain Reaction ; Protozoan Proteins/*genetics ; Rats ; Saccharomyces/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Trichomonas/genetics ; Trypanosoma/genetics ; Xenopus/genetics ; }, abstract = {An intronless gene encoding a protein of 592 amino acid residues with similarity to 70-kDa heat shock proteins (HSP70s) has been cloned and sequenced from the amitochondrial protist Encephalitozoon cuniculi (phylum Microsporidia). Southern blot analyses show the presence of a single gene copy located on chromosome XI. The encoded protein exhibits an N-terminal hydrophobic leader sequence and two motifs shared by proteobacterial and mitochondrially expressed HSP70 homologs. Phylogenetic analysis using maximum likelihood and evolutionary distances place the E. cuniculi sequence in the cluster of mitochondrially expressed HSP70s, with a higher evolutionary rate than those of homologous sequences. Similar results were obtained after cloning a fragment of the homologous gene in the closely related species E. hellem. The presence of a nuclear targeting signal-like sequence supports a role of the Encephalitozoon HSP70 as a molecular chaperone of nuclear proteins. No evidence for cytosolic or endoplasmic reticulum forms of HSP70 was obtained through PCR amplification. These data suggest that Encephalitozoon species have evolved from an ancestor bearing mitochondria, which is in disagreement with the postulated presymbiotic origin of Microsporidia. The specific role and intracellular localization of the mitochondrial HSP70-like protein remain to be elucidated.}, }
@article {pmid9545462, year = {1998}, author = {Musser, SM and Chan, SI}, title = {Evolution of the cytochrome c oxidase proton pump.}, journal = {Journal of molecular evolution}, volume = {46}, number = {5}, pages = {508-520}, doi = {10.1007/pl00006332}, pmid = {9545462}, issn = {0022-2844}, support = {GM22432/GM/NIGMS NIH HHS/United States ; }, mesh = {Electron Transport Complex IV/*physiology ; *Evolution, Molecular ; Mitochondria/metabolism ; *Models, Biological ; Phylogeny ; Proteins ; Proton Pumps/*physiology ; RNA, Ribosomal ; }, abstract = {The superfamily of quinol and cytochrome c terminal oxidase complexes is related by a homologous subunit containing six positionally conserved histidines that ligate a low-spin heme and a heme-copper dioxygen activating and reduction center. On the basis of the structural similarities of these enzymes, it has been postulated that all members of this superfamily catalyze proton translocation by similar mechanisms and that the CuA center found in most cytochrome c oxidase complexes serves merely as an electron conduit shuttling electrons from ferrocytochrome c into the hydrophobic core of the enzyme. The recent characterization of cytochrome c oxidase complexes and structurally similar cytochrome c:nitric oxide oxidoreductase complexes without CuA centers has strengthened this view. However, recent experimental evidence has shown that there are two ubiquinone(ol) binding sites on the Escherichia coli cytochrome bo3 complex in dynamic equilibrium with the ubiquinone(ol) pool, thereby strengthening the argument for a Q(H2)-loop mechanism of proton translocation [Musser SM et al. (1997) Biochemistry 36:894-902]. In addition, a number of reports suggest that a Q(H2)-loop or another alternate proton translocation mechanism distinct from the mitochondrial aa3-type proton pump functions in Sulfolobus acidocaldarius terminal oxidase complexes. The possibility that a primitive quinol oxidase complex evolved to yield two separate complexes, the cytochrome bc1 and cytochrome c oxidase complexes, is explored here. This idea is the basis for an evolutionary tree constructed using the notion that respiratory complexity and efficiency progressively increased throughout the evolutionary process. The analysis suggests that oxygenic respiration is quite an old process and, in fact, predates nitrogenic respiration as well as reaction-center photosynthesis.}, }
@article {pmid9545461, year = {1998}, author = {Vellai, T and Takács, K and Vida, G}, title = {A new aspect to the origin and evolution of eukaryotes.}, journal = {Journal of molecular evolution}, volume = {46}, number = {5}, pages = {499-507}, doi = {10.1007/pl00006331}, pmid = {9545461}, issn = {0022-2844}, mesh = {*Biological Evolution ; DNA Replication ; Energy Metabolism ; Escherichia coli/genetics/growth &amp; development ; Eukaryotic Cells/*physiology ; Genetic Vectors ; *Genome, Bacterial ; *Models, Biological ; Organelles/metabolism ; Prokaryotic Cells/*physiology ; }, abstract = {One of the most important omissions in recent evolutionary theory concerns how eukaryotes could emerge and evolve. According to the currently accepted views, the first eukaryotic cell possessed a nucleus, an endomembrane system, and a cytoskeleton but had an inefficient prokaryotic-like metabolism. In contrast, one of the most ancient eukaryotes, the metamonada Giardia lamblia, was found to have formerly possessed mitochondria. In sharp contrast with the traditional views, this paper suggests, based on the energetic aspect of genome organization, that the emergence of eukaryotes was promoted by the establishment of an efficient energy-converting organelle, such as the mitochondrion. Mitochondria were acquired by the endosymbiosis of ancient alpha-purple photosynthetic Gram-negative eubacteria that reorganized the prokaryotic metabolism of the archaebacterial-like ancestral host cells. The presence of an ATP pool in the cytoplasm provided by this cell organelle allowed a major increase in genome size. This evolutionary change, the remarkable increase both in genome size and complexity, explains the origin of the eukaryotic cell itself. The loss of cell wall and the appearance of multicellularity can also be explained by the acquisition of mitochondria. All bacteria use chemiosmotic mechanisms to harness energy; therefore the periplasm bounded by the cell wall is an essential part of prokaryotic cells. Following the establishment of mitochondria, the original plasma membrane-bound metabolism of prokaryotes, as well as the funcion of the periplasm providing a compartment for the formation of different ion gradients, has been transferred into the inner mitochondrial membrane and intermembrane space. After the loss of the essential function of periplasm, the bacterial cell wall could also be lost, which enabled the naked cells to establish direct connections among themselves. The relatively late emergence of mitochondria may be the reason why multicellularity evolved so slowly.}, }
@article {pmid9600982, year = {1998}, author = {Lakshman, DK and Jian, J and Tavantzis, SM}, title = {A double-stranded RNA element from a hypovirulent strain of Rhizoctonia solani occurs in DNA form and is genetically related to the pentafunctional AROM protein of the shikimate pathway.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {95}, number = {11}, pages = {6425-6429}, pmid = {9600982}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Complementary/analysis/genetics ; DNA, Fungal/*genetics ; Fungal Proteins/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Fungal/*genetics ; Rhizoctonia/*genetics/pathogenicity ; Sequence Analysis ; Virulence ; }, abstract = {M2 is a double-stranded RNA (dsRNA) element occurring in the hypovirulent isolate Rhs 1A1 of the plant pathogenic basidiomycete Rhizoctonia solani. Rhs 1A1 originated as a sector of the virulent field isolate Rhs 1AP, which contains no detectable amount of the M2 dsRNA. The complete sequence (3,570 bp) of the M2 dsRNA has been determined. A 6.9-kbp segment of total DNA from either Rhs 1A1 or Rhs 1AP hybridizes with an M2-specific cDNA probe. The sequences of M2 dsRNA and of PCR products generated from Rhs 1A1 total DNA were found to be identical. Thus this report describes a fungal host containing full-length DNA copies of a dsRNA element. A major portion of the M2 dsRNA is located in the cytoplasm, whereas a smaller amount is found in mitochondria. Based on either the universal or the mitochondrial genetic code of filamentous fungi, one strand of M2 encodes a putative protein of 754 amino acids. The resulting polypeptide has all four motifs of a dsRNA viral RNA-dependent RNA polymerase (RDRP) and is phylogenetically related to the RDRP of a mitochondrial dsRNA associated with hypovirulence in strain NB631 of Cryphonectria parasitica, incitant of chestnut blight. This polypeptide also has significant sequence similarity with two domains of a pentafunctional polypeptide, which catalyzes the five central steps of the shikimate pathway in yeast and filamentous fungi.}, }
@article {pmid9512533, year = {1998}, author = {Helm, M and Brulé, H and Degoul, F and Cepanec, C and Leroux, JP and Giegé, R and Florentz, C}, title = {The presence of modified nucleotides is required for cloverleaf folding of a human mitochondrial tRNA.}, journal = {Nucleic acids research}, volume = {26}, number = {7}, pages = {1636-1643}, pmid = {9512533}, issn = {0305-1048}, mesh = {Cloning, Organism ; Female ; Genetic Variation ; Humans ; Methylation ; Mitochondria/*metabolism ; Models, Molecular ; Mutagenesis, Site-Directed ; *Nucleic Acid Conformation ; Phylogeny ; Placenta/metabolism ; Polymerase Chain Reaction ; Pregnancy ; RNA/biosynthesis/*chemistry ; RNA Editing ; RNA, Mitochondrial ; RNA, Transfer, Lys/biosynthesis/*chemistry ; *Transcription, Genetic ; }, abstract = {Direct sequencing of human mitochondrial tRNALysshows the absence of editing and the occurrence of six modified nucleotides (m1A9, m2G10, Psi27, Psi28 and hypermodified nucleotides at positions U34 and A37). This tRNA folds into the expected cloverleaf, as confirmed by structural probing with nucleases. The solution structure of the corresponding in vitro transcript unexpectedly does not fold into a cloverleaf but into an extended bulged hairpin. This non-canonical fold, established according to the reactivity to a large set of chemical and enzymatic probes, includes a 10 bp aminoacyl acceptor stem (the canonical 7 bp and 3 new pairs between residues 8-10 and 65-63), a 13 nt large loop and an anticodon-like domain. It is concluded that modified nucleotides have a predominant role in canonical folding of human mitochondrial tRNALys. Phylogenetic comparisons as well as structural probing of selected in vitro transcribed variants argue in favor of a major contribution of m1A9 in this process.}, }
@article {pmid9582354, year = {1998}, author = {Brumme, S and Kruft, V and Schmitz, UK and Braun, HP}, title = {New insights into the co-evolution of cytochrome c reductase and the mitochondrial processing peptidase.}, journal = {The Journal of biological chemistry}, volume = {273}, number = {21}, pages = {13143-13149}, doi = {10.1074/jbc.273.21.13143}, pmid = {9582354}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Electrophoresis, Gel, Two-Dimensional ; *Evolution, Molecular ; Humans ; Metalloendopeptidases/chemistry/*genetics/metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; NADH Dehydrogenase/chemistry/*genetics/metabolism ; Plants/ultrastructure ; Protein Processing, Post-Translational ; Sequence Homology, Amino Acid ; Mitochondrial Processing Peptidase ; }, abstract = {The mitochondrial processing peptidase (MPP) is a heterodimeric enzyme that forms part of the cytochrome c reductase complex from higher plants. Mitochondria from mammals and yeast contain two homologous enzymes: (i) an active MPP within the mitochondrial matrix and (ii) an inactive MPP within the cytochrome c reductase complex. To elucidate the evolution of MPP, the cytochrome c reductase complexes from lower plants were isolated and tested for processing activity. Mitochondria were prepared from the staghorn fern Platycerium bifurcatum, from the horsetail Equisetum arvense, and from the colorless algae Polytomella, and cytochrome c reductase complexes were purified by a micro-isolation procedure based on Blue-native polyacrylamide gel electrophoresis and electroelution. This is the first report on the subunit composition of a respiratory enzyme complex from a fern or a horsetail. The cytochrome c reductase complexes from P. bifurcatum and E. arvense are shown to efficiently process mitochondrial precursor proteins, whereas the enzyme complex from Polytomella lacks proteolytic activity. An evolutionary model is suggested that assumes a correlation between the presence of an active MPP within the cytochrome c reductase complex and the occurrence of chloroplasts.}, }
@article {pmid9594577, year = {1998}, author = {Scheffler, IE}, title = {Molecular genetics of succinate:quinone oxidoreductase in eukaryotes.}, journal = {Progress in nucleic acid research and molecular biology}, volume = {60}, number = {}, pages = {267-315}, doi = {10.1016/s0079-6603(08)60895-8}, pmid = {9594577}, issn = {0079-6603}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; DNA/genetics ; Electron Transport ; Electron Transport Complex II ; Evolution, Molecular ; Gene Expression Regulation, Enzymologic ; Humans ; Molecular Biology ; Molecular Sequence Data ; Multienzyme Complexes/chemistry/*genetics/metabolism ; Mutation ; Oxidoreductases/chemistry/*genetics/metabolism ; Sequence Homology, Amino Acid ; Succinate Dehydrogenase/chemistry/*genetics/metabolism ; }, abstract = {Succinate:quinone oxidoreductase is a membrane-associated complex in mitochondria, often referred to as complex II, based on the fractionation scheme developed by Y. Hatefi and colleagues. It consists of four peptides, two of which are integral membrane proteins (15 and 12-13 kDa, respectively) and two others that are peripheral membrane proteins, i.e., a flavoprotein (Fp, 70 kDa) and an iron-protein (Ip, 27 kDa). The mature, functional complex contains a cytochrome in association with the membrane proteins, a flavin linked covalently to the largest peptide, and three iron-sulfur clusters in the 27-kDa subunit. The present review touches only briefly on the biochemical and biophysical properties of this complex. Instead, the focus is on the molecular-genetic studies that have become possible since the first genes from eukaryotes were cloned in 1989. The evolutionary conservation of the amino acid sequence of both the Fp and the Ip peptides has facilitated the cloning of these genes from a large variety of eukaryotic organisms by PCR-based methods. The review addresses questions related to the regulation of the expression of these genes, with an emphasis on mammals and yeast, for which most of the information is available. Four different genes have to be co-ordinately regulated. Transcriptional as well as posttranscriptional regulatory mechanisms have been observed in diverse organisms. Intriguing observations have been made in studies of this enzyme during the life cycle of organisms existing alternately under aerobic and anaerobic conditions. Naturally occurring or induced mutations in these genes have shed light on several questions related to the assembly of this complex, and on the relationship between structure and function. Four different peptides are imported into the mitochondria. They have to be modified, folded, and assembled. The stage is set for the exploration of highly specific changes introduced by site-directed mutagenesis. Until recently the genes were believed to be exclusively nuclear in all eukaryotes, but exceptions have since been found. This finding has relevance in the discussion of the evolution of mitochondria from prokaryotes. A highly conserved set of genes is found in prokaryotes, and some informative comparisons on gene organization and expression in prokaryotes and eukaryotes have been included.}, }
@article {pmid9571021, year = {1998}, author = {Rousvoal, S and Oudot, M and Fontaine, J and Kloareg, B and Goër, SL}, title = {Witnessing the evolution of transcription in mitochondria: the mitochondrial genome of the primitive brown alga Pylaiella littoralis (L.) Kjellm. Encodes a T7-like RNA polymerase.}, journal = {Journal of molecular biology}, volume = {277}, number = {5}, pages = {1047-1057}, doi = {10.1006/jmbi.1998.1679}, pmid = {9571021}, issn = {0022-2836}, mesh = {Chromosome Mapping ; Cloning, Molecular ; DNA, Mitochondrial/genetics ; DNA-Directed RNA Polymerases/*chemistry ; Eukaryota/*enzymology ; Evolution, Molecular ; Mitochondria/*genetics ; Models, Genetic ; Phylogeny ; Plasmids/genetics ; Promoter Regions, Genetic/genetics ; RNA, Messenger/analysis ; Sequence Alignment ; Sequence Analysis, DNA ; Transcription, Genetic/genetics ; }, abstract = {A region of the mitochondrial genome of the primitive brown alga Pylaiella littoralis containing a plasmid-like insert which contains a transcribed T7-phage-type RNA polymerase gene is described. This is a first report of a phage-type RNA polymerase gene integrated in a mitochondrial genome. As the mitochondrial genome of this alga also contains sigma-70 proteobacterial promoter regions, i.e. traces of the ancestral alpha2betabeta'sigma-70 proteobacterial RNA polymerase, this genome witnesses two types of RNA polymerases. As such the mitochondrial genome of P. littoralis represents a unique stage in the evolution of transcription in mitochondria, which contrasts with that of the primitive protist Reclinomonas americana, which still retains the ancestral alpha2betabeta'sigma-70 proteobacterial RNA polymerase genes, and with animals, land plants and fungi, which use phage-type polymerases.}, }
@article {pmid9591361, year = {1998}, author = {Perez-Campo, R and López-Torres, M and Cadenas, S and Rojas, C and Barja, G}, title = {The rate of free radical production as a determinant of the rate of aging: evidence from the comparative approach.}, journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology}, volume = {168}, number = {3}, pages = {149-158}, doi = {10.1007/s003600050131}, pmid = {9591361}, issn = {0174-1578}, mesh = {Aging/*metabolism ; Animals ; Antioxidants/metabolism ; Biological Evolution ; DNA Damage ; Free Radicals/*metabolism ; Humans ; Hydrogen Peroxide/metabolism ; Longevity/physiology ; Mammals/metabolism ; Mitochondria/metabolism ; Models, Biological ; Oxidative Stress ; Vertebrates/metabolism ; }, abstract = {The relationship of oxidative stress with maximum life span (MLSP) in different vertebrate species is reviewed. In all animal groups the endogenous levels of enzymatic and non-enzymatic antioxidants in tissues negatively correlate with MLSP and the most longevous animals studied in each group, pigeon or man, show the minimum levels of antioxidants. A possible evolutionary reason for this is that longevous animals produce oxygen radicals at a low rate. This has been analysed at the place where more than 90% of oxygen is consumed in the cell, the mitochondria. All available work agrees that, across species, the longer the life span, the lower the rate of mitochondrial oxygen radical production. This is true even in animal groups that do not conform to the rate of living theory of aging, such as birds. Birds have low rates of mitochondrial oxygen radical production, frequently due to a low free radical leak in their respiratory chain. Possibly the low rate of mitochondrial oxygen radical production of longevous species can decrease oxidative damage at targets important for aging (like mitochondrial DNA) that are situated near the places of free radical generation. A low rate of free radical production can contribute to a low aging rate both in animals that conform to the rate of living (metabolic) theory of aging and in animals with exceptional longevities, like birds and primates. Available research indicates there are at least two main characteristics of longevous species: a high rate of DNA repair together with a low rate of free radical production near DNA. Simultaneous consideration of these two characteristics can explain part of the quantitative differences in longevity between animal species.}, }
@article {pmid9585178, year = {1998}, author = {Kurzik-Dumke, U and Debes, A and Kaymer, M and Dienes, P}, title = {Mitochondrial localization and temporal expression of the Drosophila melanogaster DnaJ homologous tumor suppressor Tid50.}, journal = {Cell stress &amp; chaperones}, volume = {3}, number = {1}, pages = {12-27}, doi = {10.1379/1466-1268(1998)003&lt;0012:mlateo&gt;2.3.co;2}, pmid = {9585178}, issn = {1355-8145}, mesh = {Animals ; Cell Fractionation ; Cell Line ; *Drosophila Proteins ; Drosophila melanogaster/embryology/*genetics ; Embryo, Nonmammalian/chemistry ; Gene Expression Regulation, Developmental/*physiology ; Gene Expression Regulation, Neoplastic ; Genes, Insect/genetics ; Genes, Tumor Suppressor/genetics ; HSP40 Heat-Shock Proteins ; Heat-Shock Proteins/*analysis/*genetics ; Larva/chemistry ; Mitochondria/*chemistry ; Mitochondrial Proteins ; Neoplasms, Experimental/chemistry ; Organ Specificity ; Pupa/chemistry ; RNA, Messenger/analysis ; Rabbits ; Sequence Analysis, DNA ; }, abstract = {The Drosophila melanogaster tumor suppressor gene lethal(2)tumorous imaginal discs (tid) was identified as a homolog of all dnaJ-like genes known to date which have been well preserved in evolution. Homozygous D. melanogaster l(2)tid mutants l(2)tid1, l(2)tid2 and l(2)tid3 are characterized by neoplastic transformation of the adult integumental primordia, the imaginal discs, and the death at the time of puparium formation. The first part of this study is concerned with the identification and subcellular localization of the l(2)tid-encoded protein, Tid50. The second part examines its tissue specific expression during wild-type development and in tumorous imaginal discs. To specify the function(s) of the Tid50 protein polyclonal rabbit antibodies directed against various domains of it were generated and used for staining of Western blots and whole-mounts and paraffin sections of various tissues isolated from wild-type and mutant tumor-developing animals. To identify the mutational events leading in homozygous l(2)tid mutants to abnormal expression level of l(2)tid-encoded RNA and protein, the mutant gene was isolated from homozygous l(2)tid1 and l(2)tid2 animals and sequenced.}, }
@article {pmid9512461, year = {1998}, author = {Birdsey, GM and Danpure, CJ}, title = {Evolution of alanine:glyoxylate aminotransferase intracellular targeting: structural and functional analysis of the guinea pig gene.}, journal = {The Biochemical journal}, volume = {331 (Pt 1)}, number = {Pt 1}, pages = {49-60}, pmid = {9512461}, issn = {0264-6021}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cell Compartmentation ; Cell Line ; Cloning, Molecular ; *Evolution, Molecular ; Fibroblasts/enzymology ; Fluorescent Antibody Technique ; Guinea Pigs ; Humans ; Liver/*enzymology/ultrastructure ; Molecular Sequence Data ; Sequence Alignment ; Transaminases/*genetics/metabolism ; Transfection ; }, abstract = {The distribution of alanine:glyoxylate aminotransferase 1 (AGT) within liver cells has changed many times during mammalian evolution. Depending on the particular species, AGT can be found in mitochondria or peroxisomes, or mitochondria and peroxisomes. In some cases significant cytosolic AGT is also present. In the livers of most rodents, AGT has what is thought to be the more 'ancestral' distribution (i.e. mitochondrial and peroxisomal). However, AGT is distributed very differently in the guinea pig, being peroxisomal and cytosolic. In this study, we have attempted to determine the molecular basis for the loss of mitochondrial AGT targeting and the apparent inefficiency of peroxisomal targeting of AGT in the guinea pig. Our results show that the former is owing to the evolutionary loss of the more 5' of two potential transcription and translation initiation sites, resulting in the loss of the ancestral N-terminal mitochondrial targeting sequence from the open reading frame. Guinea pig AGT is targeted to peroxisomes via the peroxisomal targeting sequence type 1 (PTS1) peroxisomal import machinery, even though its C-terminal tripeptide, HRL, deviates from the standard consensus PTS1 motif. Although HRL appears to target AGT to peroxisomes less efficiently than the classical PTS1 SKL, the main reason for the low efficiency of AGT peroxisomal targeting in guinea pig cells (compared with cells from other species) lies not with guinea pig AGT but with some other, as yet undefined, part of the guinea pig peroxisomal import machinery.}, }
@article {pmid9580216, year = {1997}, author = {Chagoya de Sánchez, V and Hernández-Muñoz, R and López-Barrera, F and Yañez, L and Vidrio, S and Suárez, J and Cota-Garza, MD and Aranda-Fraustro, A and Cruz, D}, title = {Sequential changes of energy metabolism and mitochondrial function in myocardial infarction induced by isoproterenol in rats: a long-term and integrative study.}, journal = {Canadian journal of physiology and pharmacology}, volume = {75}, number = {12}, pages = {1300-1311}, pmid = {9580216}, issn = {0008-4212}, mesh = {Animals ; Blood Pressure/drug effects ; *Cardiotonic Agents ; Edema/complications/pathology ; Electrophysiology ; Energy Metabolism/*drug effects ; Heart/*drug effects/physiology ; Heart Rate/drug effects ; *Isoproterenol ; Male ; Microscopy, Electron ; Mitochondria, Heart/*drug effects/metabolism/pathology/ultrastructure ; Myocardial Infarction/*chemically induced/enzymology/pathology/physiopathology ; Rats ; Rats, Wistar ; }, abstract = {Acute myocardial infarction is the second cause of mortality in most countries, therefore, it is important to know the evolution and sequence of the physiological and biochemical changes involved in this pathology. This study attempts to integrate these changes and to correlate them in a long-term model (96 h) of isoproterenol-induced myocardial cell damage in the rat. We achieved an infarct-like damage in the apex region of the left ventricle, occurring 12-24 h after isoproterenol administration. The lesion was defined by histological criteria, continuous telemetric ECG recordings, and the increase in serum marker enzymes, specific for myocardial damage. A distinction is made among preinfarction, infarction, and postinfarction. Three minutes after drug administration, there was a 60% increase in heart rate and a lowering of blood pressure, resulting possibly in a functional ischemia. Ultrastructural changes and mitochondrial swelling were evident from the first hour of treatment, but functional alterations in isolated mitochondria, such as decreases in oxygen consumption, respiratory quotient, ATP synthesis, and membrane potential, were noticed only 6 h after drug administration and lasted until 72 h later. Mitochondrial proteins decreased after 3 h of treatment, reaching almost a 50% diminution, which was maintained during the whole study. An energy imbalance, reflected by a decrease in energy charge and in the creatine phosphate/creatine ratio, was observed after 30 min of treatment; however, ATP and total adenine nucleotides diminished clearly only after 3 h of treatment. All these alterations reached a maximum at the onset of infarction and were accompanied by damage to the myocardial function, drastically decreasing left ventricular pressure and shortening the atrioventricular interval. During postinfarction, a partial recovery of energy charge, creatine phosphate/creatine ratio, membrane potential, and myocardial function occurred, but not of mitochondrial oxygen consumption, rate of ATP synthesis, total adenine nucleotides, or mitochondrial proteins. Interesting correlations of the sequential changes in heart and mitochondrial functions with energy metabolism were obtained at different stages of the isoproterenol-induced cardiotoxicity. These correlations could be useful to study and understand the cellular events involved in this pathology.}, }
@article {pmid9573371, year = {1998}, author = {Moriya, S and Ohkuma, M and Kudo, T}, title = {Phylogenetic position of symbiotic protist Dinenympha [correction of Dinemympha] exilis in the hindgut of the termite Reticulitermes speratus inferred from the protein phylogeny of elongation factor 1 alpha.}, journal = {Gene}, volume = {210}, number = {2}, pages = {221-227}, doi = {10.1016/s0378-1119(98)00078-x}, pmid = {9573371}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Digestive System ; *Diplomonadida ; In Situ Hybridization ; *Insecta ; Molecular Sequence Data ; Peptide Elongation Factor 1 ; Peptide Elongation Factors/*genetics ; Phylogeny ; Sequence Homology, Amino Acid ; *Symbiosis ; }, abstract = {The phylogenetic position of the symbiotic oxymonad Dinenympha exilis, found in the hindgut of the lower termite Reticulitermes speratus, was determined by analysis of translation elongation factor 1 alpha (EF-1 alpha). cDNA corresponding to a major part of the amino acid coding region of EF-1 alpha mRNA was amplified by the reverse transcription polymerase chain reaction (RT-PCR) method from total mRNA of termite hindgut microorganisms without cultivation. The product was cloned into a plasmid vector, pGEM-T, and the clones were isolated and sequenced. One of the EF-1 alpha clones isolated was assigned to the protist D. exilis by whole-cell in-situ hybridization using a specific oligonucleotide probe with enzymatic signal amplification. The deduced amino acid sequence was aligned with those of other eukaryotic and archaeabacterial EF-1 alpha s, and the phylogenetic relationships among early branching eukaryotes were inferred by using the distance matrix method and the maximum parsimony method. The phylogenetic analysis indicated that the D. exilis offshoot occurred before mitochondria-containing organisms and D. exilis branched out after the diplomonads clade. These results indicate that the oxymonad D. exilis is one of the early branching organisms and suggest that the oxymonads form a lineage independent of other early branching organisms.}, }
@article {pmid9520430, year = {1998}, author = {Castresana, J and Feldmaier-Fuchs, G and Pääbo, S}, title = {Codon reassignment and amino acid composition in hemichordate mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {95}, number = {7}, pages = {3703-3707}, pmid = {9520430}, issn = {0027-8424}, mesh = {Amino Acids/genetics ; Animals ; Chordata, Nonvertebrate/*genetics ; Codon/genetics ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Molecular Sequence Data ; Phylogeny ; Proteins/genetics ; Sequence Analysis ; }, abstract = {In the mitochondrial genome of the hemichordate Balanoglossus carnosus, the codon AAA, which is assigned to lysine in most metazoans but to asparagine in echinoderms, is absent. Furthermore, the lysine tRNA gene carries an anticodon substitution that renders its gene product unable to decode AAA codons, whereas the asparagine tRNA gene has not changed to encode a tRNA with the ability to recognize AAA codons. Thus, the hemichordate mitochondrial genome can be regarded as an intermediate in the process of reassignment of mitochondrial AAA codons, where most metazoans represent the ancestral situation and the echinoderms the derived situation. This lends support to the codon capture hypothesis. We also show that the reassignment of the AAA codon is associated with a reduction in the relative abundance of lysine residues in mitochondrial proteins.}, }
@article {pmid9549409, year = {1998}, author = {Yokobori, S}, title = {[RNA editing in transfer RNAs of metazoan mitochondria].}, journal = {Seikagaku. The Journal of Japanese Biochemical Society}, volume = {70}, number = {2}, pages = {100-104}, pmid = {9549409}, issn = {0037-1017}, mesh = {Animals ; DNA, Mitochondrial ; Evolution, Molecular ; Invertebrates ; Mitochondria/genetics/*metabolism ; RNA, Transfer/genetics/*metabolism ; Vertebrates ; }, }
@article {pmid9541559, year = {1998}, author = {Boison, G and Schmitz, O and Schmitz, B and Bothe, H}, title = {Unusual gene arrangement of the bidirectional hydrogenase and functional analysis of its diaphorase subunit HoxU in respiration of the unicellular cyanobacterium anacystis nidulans.}, journal = {Current microbiology}, volume = {36}, number = {5}, pages = {253-258}, doi = {10.1007/s002849900305}, pmid = {9541559}, issn = {1432-0991}, abstract = {The bidirectional, NAD+-dependent hydrogenase from cyanobacteria is encoded by the structural genes hoxFUYH, which have been found to be clustered, though interspersed with different open reading frames (ORFs), in the heterocystous, N2-fixing Anabaena variabilis and in the unicellular Synechocystis PCC 6803. In another unicellular, non N2-fixing cyanobacterium, Anacystis nidulans, hoxF has now been identified as being separated by at least 16 kb from the residual structural genes hoxUYH. An ORF (termed hoxE gene) is located immediately upstream of hoxF in A. nidulans and in Synechocystis. Its deduced amino acid sequence shows similarities to the NuoE subunit of NADH dehydrogenase I of E. coli, to the homologous subunit of respiratory complex I in mitochondria, and also to the first 104 amino acids of HoxF in A. nidulans and Synechocystis. The diversity in the arrangement of hydrogenase genes in cyanobacteria is puzzling. The subunits HoxE, HoxF, and HoxU of the diaphorase part of the bidirectional hydrogenase have been discussed to be shared both by respiratory complex I and bidirectional hydrogenase in cyanobacteria. Different hoxU mutants were obtained by inserting a lacZKmR cassette into the gene both in A. nidulans and Anacystis PCC 7942. Such mutants showed reduced H2-evolution activities catalyzed by the bidirectional hydrogenase, but had nonimpaired respiratory O2-uptake. A common link between respiratory complex I and the diaphorase part of the bidirectional hydrogenase in cyanobacteria may still exist, but this hypothesis could not be verified in the present study by analyzing defined mutants impaired in one of the diaphorase genes.}, }
@article {pmid9541536, year = {1998}, author = {Pont-Kingdon, G and Okada, NA and Macfarlane, JL and Beagley, CT and Watkins-Sims, CD and Cavalier-Smith, T and Clark-Walker, GD and Wolstenholme, DR}, title = {Mitochondrial DNA of the coral Sarcophyton glaucum contains a gene for a homologue of bacterial MutS: a possible case of gene transfer from the nucleus to the mitochondrion.}, journal = {Journal of molecular evolution}, volume = {46}, number = {4}, pages = {419-431}, pmid = {9541536}, issn = {0022-2844}, support = {GM 18375/GM/NIGMS NIH HHS/United States ; RR 07092/RR/NCRR NIH HHS/United States ; }, mesh = {*Adenosine Triphosphatases ; Amino Acid Sequence ; Animals ; Bacterial Proteins/*genetics ; Base Sequence ; Cell Nucleus/genetics ; Cnidaria/*genetics ; Codon/genetics ; DNA, Mitochondrial/chemistry/*genetics ; *DNA-Binding Proteins ; *Escherichia coli Proteins ; Evolution, Molecular ; Gene Transfer Techniques ; *Genes, Bacterial ; Genetic Code ; Humans ; Molecular Sequence Data ; MutS DNA Mismatch-Binding Protein ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer, Met/genetics ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {The nucleotide sequences of two segments of 6,737 ntp and 258 nto of the 18.4-kb circular mitochondrial (mt) DNA molecule of the soft coral Sarcophyton glaucum (phylum Cnidaria, class Anthozoa, subclass Octocorallia, order Alcyonacea) have been determined. The larger segment contains the 3' 191 ntp of the gene for subunit 1 of the respiratory chain NADH dehydrogenase (ND1), complete genes for cytochrome b (Cyt b), ND6, ND3, ND4L, and a bacterial MutS homologue (MSH), and the 5' terminal 1,124 ntp of the gene for the large subunit rRNA (1-rRNA). These genes are arranged in the order given and all are transcribed from the same strand of the molecule. The smaller segment contains the 3' terminal 134 ntp of the ND4 gene and a complete tRNA(f-Met) gene, and these genes are transcribed in opposite directions. As in the hexacorallian anthozoan, Metridium senile, the mt-genetic code of S. glaucum is near standard: that is, in contrast to the situation in mt-genetic codes of other invertebrate phyla, AGA and AGG specify arginine, and ATA specifies isoleucine. However, as appears to be universal for metazoan mt-genetic codes, TGA specifies tryptophan rather than termination. Also, as in M. senile the mt-tRNA(f-Met) gene has primary and secondary structural features resembling those of Escherichia coli initiator tRNA, including standard dihydrouridine and T psi C loop sequences, and a mismatched nucleotide pair at the top of the amino-acyl stem. The presence of a mutS gene homologue, which has not been reported to occur in any other known mtDNA, suggests that there is mismatch repair activity in S. glaucum mitochondria. In support of this, phylogenetic analysis of MutS family protein sequences indicates that the S. glaucum mtMSH protein is more closely related to the nuclear DNA-encoded mitochondrial mismatch repair protein (MSH1) of the yeast Saccharomyces cerevisiae than to eukaryotic homologues involved in nuclear function, or to bacterial homologues. Regarding the possible origin of the S. glaucum mtMSH gene, the phylogenetic analysis results, together with comparative base composition considerations, and the absence of an MSH gene in any other known mtDNA best support the hypothesis that S. glaucum mtDNA acquired the mtMSH gene from nuclear DNA early in the evolution of octocorals. The presence of mismatch repair activity in S. glaucum mitochondria might be expected to influence the rate of evolution of this organism's mtDNA.}, }
@article {pmid9541010, year = {1998}, author = {Ellington, WR and Roux, K and Pineda, AO}, title = {Origin of octameric creatine kinases.}, journal = {FEBS letters}, volume = {425}, number = {1}, pages = {75-78}, doi = {10.1016/s0014-5793(98)00204-x}, pmid = {9541010}, issn = {0014-5793}, mesh = {Animals ; *Biological Evolution ; Biopolymers ; Chromatography, Gel ; Chromatography, Ion Exchange ; Creatine Kinase/*genetics/isolation &amp; purification ; Electrophoresis, Polyacrylamide Gel ; Microscopy, Electron ; Polychaeta/enzymology ; }, abstract = {Mitochondrial creatine kinase (MiCK) occurs primarily as an octameric form localized in the mitochondrial intermembrane compartment in vertebrate tissues and echinoderm spermatozoa (both deuterostome groups). The octameric quaternary structure is thought to play important functional and enzyme targeting roles. We have found that the spermatozoa of the protostome polychaete Chaetopterus variopedatus contain three distinct isoenzymes of creatine kinase (CK) termed CK1, CK2 and CK3. CK3 appears to be present only in the sperm head/midpiece complex where mitochondria are restricted and has a subunit relative molecular mass (Mr) of 43.4 kDa. Gel permeation chromatography using Superdex 200HR showed that CK3 has a native Mr of 344.9 kDa indicating that this enzyme exists as an octamer. Electron micrographs of negatively stained CK3 preparations show structures which are virtually identical to those that have been seen for octameric vertebrate MiCK. The above observations show that CK3 from C. variopedatus displays great similarities to MiCKs from vertebrates and echinoderms. Octamerization of CK is not an advanced feature. The evolution of octameric subunit association is ancient and occurred prior to the divergence of protostomes and deuterostomes.}, }
@article {pmid9526504, year = {1998}, author = {Koga, R and Fukuhara, T and Nitta, T}, title = {Molecular characterization of a single mitochondria-associated double-stranded RNA in the green alga Bryopsis.}, journal = {Plant molecular biology}, volume = {36}, number = {5}, pages = {717-724}, pmid = {9526504}, issn = {0167-4412}, mesh = {Amino Acid Sequence ; Base Sequence ; Chlorophyta/*genetics ; Cloning, Molecular ; Codon/genetics ; DNA, Complementary/genetics ; Evolution, Molecular ; Frameshift Mutation ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames ; RNA/chemistry/*genetics/isolation &amp; purification ; RNA, Double-Stranded/chemistry/*genetics/isolation &amp; purification ; RNA, Mitochondrial ; Sequence Homology, Amino Acid ; }, abstract = {Mitochondria from the green alga Bryopsis sp. very often contained a 4.5 kb double-stranded RNA (dsRNA) at a defined level. Complementary DNA probes derived from the mitochondrial dsRNA hybridized with none of the algal chloroplast dsRNAs of 1.7 to 2.2 kb, but did hybridize with a similar-sized dsRNA among several dsRNAs from the mitochondria of B. maxima. Sequence analysis of the mitochondrial dsRNA from Bryopsis sp. revealed only two large, overlapping, open reading frames (ORFs) on one strand if UGA was taken as a non-termination codon, suggesting the independent phylogenetic evolution of the mitochondrial dsRNA. Consensus sequence for RNA-dependent RNA polymerase was found within the longer ORF (2472 bp) of the dsRNA. The overlapping 52 bp of the ORFs in different reading frames is suggestive of the occurrence of a -1 ribosomal frameshift in the mitochondrial translation system. The observed simple genetic structures suggest that the algal mitochondrial dsRNA might be deficient in a gene for movement from cell to cell in host plants and, hence, has a plasmid-like nature that is distinct from that of infectious plant viruses. The nature and origin of the endogenous dsRNAs of various sizes and their relationships are discussed.}, }
@article {pmid9523706, year = {1998}, author = {Mignotte, B and Vayssiere, JL}, title = {Mitochondria and apoptosis.}, journal = {European journal of biochemistry}, volume = {252}, number = {1}, pages = {1-15}, doi = {10.1046/j.1432-1327.1998.2520001.x}, pmid = {9523706}, issn = {0014-2956}, mesh = {Animals ; Apoptosis/genetics/*physiology ; Apoptotic Protease-Activating Factor 1 ; Caenorhabditis elegans/physiology ; Cysteine Endopeptidases/physiology ; Cytochrome c Group/physiology ; Evolution, Molecular ; Genes, bcl-2/genetics ; Intracellular Membranes/physiology ; Mammals ; Membrane Potentials/physiology ; Mitochondria/*physiology ; Permeability ; Proteins/physiology ; Reactive Oxygen Species/metabolism ; }, abstract = {Programmed cell death serves as a major mechanism for the precise regulation of cell numbers and as a defense mechanism to remove unwanted and potentially dangerous cells. Despite the striking heterogeneity of cell death induction pathways, the execution of the death program is often associated with characteristic morphological and biochemical changes, and this form of programmed cell death has been termed apoptosis. Genetic studies in Caenorhabditis elegans had led to the identification of cell death genes (ced). The genes ced-3 and ced-4 are essential for cell death; ced-9 antagonizes the activities of ced-3 and ced-4, and thereby protects cells that should survive from any accidental activation of the death program. Caspases (cysteine aspartases) are the mammalian homologues of CED-3. CED-9 protein is homologous to a family of many members termed the Bcl-2 family (Bcl-2s) in reference to the first discovered mammalian cell death regulator. In both worm and mammalian cells, the antiapoptotic members of the Bcl-2 family act upstream of the execution caspases somehow preventing their proteolytic processing into active killers. Two main mechanisms of action have been proposed to connect Bcl-2s to caspases. In the first one, antiapoptotic Bcl-2s would maintain cell survival by dragging caspases to intracellular membranes (probably the mitochondrial membrane) and by preventing their activation. The recently described mammalian protein Apaf-1 (apoptosis protease-activating factor 1) could be the mammalian equivalent of CED-4 and could be the physical link between Bcl-2s and caspases. In the second one, Bcl-2 would act by regulating the release from mitochondria of some caspases activators: cytochrome c and/or AIF (apoptosis-inducing factor). This crucial position of mitochondria in programmed cell death control is reinforced by the observation that mitochondria contribute to apoptosis signaling via the production of reactive oxygen species. Although for a long time the absence of mitochondrial changes was considered as a hallmark of apoptosis, mitochondria appear today as the central executioner of programmed cell death. In this review, we examine the data concerning the mitochondrial features of apoptosis. Furthermore, we discuss the possibility that the mechanism originally involved in the maintenance of the symbiosis between the bacterial ancestor of the mitochondria and the host cell precursor of eukaryotes, provided the basis for the actual mechanism controlling cell survival.}, }
@article {pmid9518375, year = {1998}, author = {Vogel, G}, title = {Did the first complex cell eat hydrogen?.}, journal = {Science (New York, N.Y.)}, volume = {279}, number = {5357}, pages = {1633-1634}, doi = {10.1126/science.279.5357.1633}, pmid = {9518375}, issn = {0036-8075}, mesh = {Animals ; *Bacteria/metabolism ; *Biological Evolution ; Carbon Dioxide/metabolism ; *Eukaryotic Cells/metabolism/microbiology/ultrastructure ; *Euryarchaeota/metabolism ; Hydrogen/*metabolism ; Mitochondria/metabolism ; Organelles/metabolism ; Trichostomatida/microbiology/ultrastructure ; }, }
@article {pmid9461620, year = {1998}, author = {Souri, M and Aoyama, T and Cox, GF and Hashimoto, T}, title = {Catalytic and FAD-binding residues of mitochondrial very long chain acyl-coenzyme A dehydrogenase.}, journal = {The Journal of biological chemistry}, volume = {273}, number = {7}, pages = {4227-4231}, doi = {10.1074/jbc.273.7.4227}, pmid = {9461620}, issn = {0021-9258}, mesh = {Acyl-CoA Dehydrogenase, Long-Chain/*chemistry/genetics ; Amino Acid Sequence ; Binding Sites ; Flavin-Adenine Dinucleotide/*metabolism ; Humans ; Kinetics ; Mitochondria, Liver/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed/genetics ; Palmitoyl Coenzyme A/metabolism ; Phylogeny ; Protein Binding ; Protein Folding ; Recombinant Proteins/genetics ; Sequence Alignment ; Trypsin/metabolism ; }, abstract = {Very long-chain acyl-CoA dehydrogenase (VLCAD) is one of four flavoproteins which catalyze the initial step of the mitochondrial beta-oxidation spiral. By sequence comparison with other acyl-CoA dehydrogenases, Glu-422 of VLCAD has been presumed to be the catalytic residue that abstracts the alpha-proton in the alphabeta-dehydrogenation reaction. Replacing Glu-422 with glutamine (E422Q) caused a loss of enzyme activity by preventing the formation of a charge transfer complex between VLCAD and palmitoyl-CoA. This result provides further evidence for Glu-422 being part of the active site of VLCAD. F418L is a disease-causing mutation in human VLCAD deficiency. Unlike wild-type VLCAD, F418L and F418V contained no bound FAD when expressed at extremely high levels in the baculovirus expression system. Although F418T and F418Y bound FAD at a level similar to that of wild-type VLCAD, both showed reduced Vmax values toward palmitoyl-CoA, most likely due to a decrease in the rate of enzyme-bound FAD reduction. These data suggest that Phe-418 is involved in the binding and subsequent reduction of FAD. FAD-deficient VLCADs (F418L, F418V, and apo-VLCAD) showed increased sensitivity to trypsinization. Loss of FAD may change the folding of VLCAD subunit.}, }
@article {pmid9514725, year = {1998}, author = {Guénebaut, V and Schlitt, A and Weiss, H and Leonard, K and Friedrich, T}, title = {Consistent structure between bacterial and mitochondrial NADH:ubiquinone oxidoreductase (complex I).}, journal = {Journal of molecular biology}, volume = {276}, number = {1}, pages = {105-112}, doi = {10.1006/jmbi.1997.1518}, pmid = {9514725}, issn = {0022-2836}, mesh = {Bacterial Proteins/*chemistry/ultrastructure ; Escherichia coli/enzymology ; Evolution, Molecular ; Fungal Proteins/*chemistry/ultrastructure ; Macromolecular Substances ; Mitochondria/*chemistry ; Models, Molecular ; Molecular Weight ; NAD(P)H Dehydrogenase (Quinone)/*chemistry/ultrastructure ; Negative Staining ; Neurospora crassa/enzymology ; Structure-Activity Relationship ; }, abstract = {Respiratory chains of bacteria and mitochondria contain closely related forms of the proton-pumping NADH:ubiquinone oxidoreductase (complex I). In bacteria the complex has a molecular mass of approximately 530 kDa and consists of 14 different subunits. The homologues of these 14 subunits together with some 27 additional subunits make up the mitochondrial complex, adding up to a molecular mass of approximately 1 MDa. We calculated three-dimensional models at medium resolution of isolated and negatively stained complex I particles from Eschericha coli and Neurospora crassa by electron microscopy using the random conical tilt reconstruction technique. Both the bacterial and the mitochondrial complexes are L-shaped molecules with an intrinsic membrane arm extending into the lipid bilayer and a peripheral arm protruding from the membrane. It is discussed whether the consistent length of the arms of both complexes has an implication for their function. The additional protein mass of the mitochondrial complex is distributed along both arms, but especially around the junction between the two arms and around the membrane arm. It appears that the structural framework of procaryotic complex I is stabilized in eucaryotes by this additional mass. A discrete location of additional protein in the peripheral arm of the mitochondrial complex is interpreted as being the possible position of two subunits with a specialized role in the biosynthesis of a yet unknown cofactor of complex I.}, }
@article {pmid9510239, year = {1998}, author = {Doolittle, WF}, title = {A paradigm gets shifty.}, journal = {Nature}, volume = {392}, number = {6671}, pages = {15-16}, doi = {10.1038/32033}, pmid = {9510239}, issn = {0028-0836}, mesh = {*Archaea/metabolism ; *Bacteria/metabolism ; Biological Evolution ; *Eukaryotic Cells/metabolism ; Hydrogen/*metabolism ; Mitochondria ; Models, Biological ; *Symbiosis ; }, }
@article {pmid9504342, year = {1998}, author = {Brown, DM and Upcroft, JA and Edwards, MR and Upcroft, P}, title = {Anaerobic bacterial metabolism in the ancient eukaryote Giardia duodenalis.}, journal = {International journal for parasitology}, volume = {28}, number = {1}, pages = {149-164}, doi = {10.1016/s0020-7519(97)00172-0}, pmid = {9504342}, issn = {0020-7519}, mesh = {Amino Acids/metabolism ; Animals ; Bacteria, Anaerobic/*metabolism ; Biological Evolution ; Electron Transport ; Energy Metabolism ; Fermentation ; Giardia/genetics/*metabolism ; Models, Biological ; Oxidation-Reduction ; Oxidative Stress ; Oxygen Consumption ; }, abstract = {The protozoan parasite, Giardia duodenalis, shares many metabolic and genetic attributes of the bacteria, including fermentative energy metabolism which relies heavily on pyrophosphate rather than adenosine triphosphate and as a result contains two typically bacterial glycolytic enzymes which are pyrophosphate dependent. Pyruvate decarboxylation and subsequent electron transport to as yet unidentified anaerobic electron acceptors relies on a eubacterial-like pyruvate:ferredoxin oxidoreductase and an archaebacterial/eubacterial-like ferredoxin. The presence of another 2-ketoacid oxidoreductase (with a preference for alpha-ketobutyrate) and multiple ferredoxins in Giardia is also a trait shared with the anaerobic bacteria. Giardia pyruvate:ferredoxin oxidoreductase is distinct from the pyruvate dehydrogenase multienzyme complex invariably found in mitochondria. This is consistent with a lack of mitochondria, citric acid cycle, oxidative phosphorylation and glutathione in Giardia. Giardia duodenalis actively consumes oxygen and yet lacks the conventional mechanisms of oxidative stress management, including superoxide dismutase, catalase, peroxidase, and glutathione cycling, which are present in most eukaryotes. In their place Giardia contains a prokaryotic H2O-producing NADH oxidase, a membrane-associated NADH peroxidase, a broad-range prokaryotic thioredoxin reductase-like disulphide reductase and the low molecular weight thiols, cysteine, thioglycolate, sulphite and coenzyme A. NADH oxidase is a major component of the electron transport pathway of Giardia which, in conjunction with disulphide reductase, protects oxygen-labile proteins such as ferredoxin and pyruvate:ferredoxin oxidoreductase against oxidative stress by maintaining a reduced intracellular environment. As the terminal oxidase, NADH oxidase provides a means of removing excess H+, thereby enabling continued pyruvate decarboxylation and the resultant production of acetate and adenosine triphosphate. A further example of the bacterial-like metabolism of Giardia is the utilisation of the amino acid arginine as an energy source. Giardia contain the arginine dihydrolase pathway, which occurs in a number of anaerobic prokaryotes, but not in other eukaryotes apart from trichomonads and Chlamydomonas reinhardtii. The pathway includes substrate level phosphorylation and is sufficiently active to make a major contribution to adenosine triphosphate production. Two enzymes of the pathway, arginine deiminase and carbamate kinase, are rare in eukaryotes and do not occur in higher animals. Arginine is transported into the trophozoite via a bacterial-like arginine:ornithine antiport. Together these metabolic pathways in Giardia provide a wide range of potential drug targets for future consideration.}, }
@article {pmid9504331, year = {1998}, author = {Sogin, ML and Silberman, JD}, title = {Evolution of the protists and protistan parasites from the perspective of molecular systematics.}, journal = {International journal for parasitology}, volume = {28}, number = {1}, pages = {11-20}, doi = {10.1016/s0020-7519(97)00181-1}, pmid = {9504331}, issn = {0020-7519}, support = {GM32964/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Archaea/classification/genetics ; Bacteria/classification/genetics ; *Biological Evolution ; Eukaryota/*classification/*genetics ; Evolution, Molecular ; Fungi/classification/genetics ; Phylogeny ; Plants/classification/genetics ; RNA, Ribosomal, 16S ; }, abstract = {Unlike prokaryotes, the Protista are rich in morphological and ultrastructure information. Their amazing phenotypic diversity permits assignment of many protists to cohesive phyletic assemblages but sometimes blurs relationships between major lineages. With the advent of molecular techniques, it became possible to test evolutionary hypotheses that were originally formulated according to shared phenotypic traits. More than any other gene family, studies of rRNAs changed our understanding of protist evolution. Stramenopiles (oomycetes, chrysophytes, phaeophytes, synurophytes, diatoms, xanthophytes, bicosoecids, slime nets) and alveolates (dinoflagellates, apicomplexans, ciliates) are two novel, complex evolutionary assemblages which diverged nearly simultaneously with animals, fungi, plants, rhodophytes, haptophytes and a myriad of independent amoeboid lineages. Their separation may have occurred one billion years ago and collectively these lineages make up the "crown" of the eukaryotic tree. Deeper branches in the eukaryotic tree show 16S-like rRNA sequence variation that is much greater than that observed within the Archaea and the Bacteria. A progression of independent protist branches, some as ancient as the divergence between the two prokaryotic domains, preceded the sudden radiation of "crown" groups. Trichomonads, diplomonads and Microsporidia are basal to all other eukaryotes included in rRNA studies. Together with pelobionts, oxymonads, retortamonads and hypermastigids, these amitochondriate taxa comprise the Archaezoa. This skeletal phylogeny suggested that early branching eukaryotes lacked mitochondria, peroxisomes and typical stacked Golgi dictyosomes. However, recent studies of heat shock proteins indicate that the first eukaryotes may have had mitochondria. When evaluated in terms of evolution of ultrastructure, lifestyles and other phenotypic traits, the rRNA phylogenies provide the most consistent of molecular trees. They permit identification of the phylogenetic affinity of many parasitic groups as well as a means to integrate molecular and cell biological information from diverse eukaryotes. We must place greater emphasis upon improved phylogenetic inference techniques and investigations of genomic diversity in protists.}, }
@article {pmid9503641, year = {1998}, author = {Moyes, CD and Battersby, BJ and Leary, SC}, title = {Regulation of muscle mitochondrial design.}, journal = {The Journal of experimental biology}, volume = {201}, number = {Pt 3}, pages = {299-307}, pmid = {9503641}, issn = {0022-0949}, mesh = {Animals ; Base Sequence ; Biological Evolution ; DNA, Mitochondrial/genetics ; DNA-Binding Proteins/genetics/metabolism ; Electron Transport Complex IV/genetics/metabolism ; Energy Metabolism ; Gene Expression Regulation ; Humans ; Mitochondria, Muscle/genetics/*metabolism ; Nuclear Respiratory Factors ; Oxidative Phosphorylation ; Trans-Activators/genetics/metabolism ; }, abstract = {Mitochondria are responsible for the generation of ATP to fuel muscle contraction. Hypermetabolic stresses imposed upon muscles can lead to mitochondrial proliferation, but the resulting mitochondria greatly resemble their progenitors. During the mitochondrial biogenesis that accompanies phenotypic adaptation, the stoichiometric relationships between functional elements are preserved through shared sensitivities of respiratory genes to specific transcription factors. Although the properties of muscle mitochondria are generally thought to be highly conserved across species, there are many examples of mitochondrial differences between muscle types, species and developmental states and even within single cells. In this review, we discuss (1) the nature and regulation of gene families that allow coordinated expression of genes for mitochondrial products and (2) the regulatory mechanisms by which mitochondrial differences can arise over physiological and evolutionary time.}, }
@article {pmid9506761, year = {1998}, author = {Hirai, M and Suzuki, S and Onoda, M and Hinokio, Y and Hirai, A and Ohtomo, M and Chiba, M and Kasuga, S and Hirai, S and Satoh, Y and Akai, H and Miyabayashi, S and Toyota, T}, title = {Mitochondrial deoxyribonucleic acid 3256C-T mutation in a Japanese family with noninsulin-dependent diabetes mellitus.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {83}, number = {3}, pages = {992-994}, doi = {10.1210/jcem.83.3.4643}, pmid = {9506761}, issn = {0021-972X}, mesh = {Adolescent ; Adult ; Base Sequence ; Blood Cells/metabolism ; Cheek/pathology/physiology ; DNA, Mitochondrial/blood/*genetics/metabolism ; Densitometry ; Diabetes Mellitus, Type 2/*genetics/metabolism/pathology ; Female ; Hair/metabolism ; Humans ; Japan/ethnology ; Male ; Middle Aged ; Mitochondria, Muscle/metabolism ; Mutation/*genetics ; Pedigree ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; }, abstract = {Accumulating reports indicate a relationship between mitochondrial DNA mutation and impaired glucose-induced insulin secretion leading to a subtype of noninsulin-dependent diabetes mellitus. DNA from a 45-yr-old Japanese woman with noninsulin-dependent diabetes mellitus and muscle atrophy was isolated and studied for mitochondrial DNA mutations. We identified a mitochondrial DNA C-T heteroplasmic mutation at nucleotide position 3256. The mutation was located in the transfer ribonucleic acidLeu in a region conserved in evolution. Eight other members of her family were examined for the mutation. Six of them had the same mutation together with noninsulin-dependent diabetes mellitus, and one teenage boy had the mutation and impaired glucose tolerance. The other family member who did not have this mutation had normal glucose tolerance. The enzyme activity of the mitochondrial oxidative phosphorylation pathway in the muscle of the proband was measured. The enzyme activity was decreased in the proband, especially in complex I. This mutation might be responsible for the abnormal glucose metabolism.}, }
@article {pmid9495347, year = {1998}, author = {Podar, M and Chu, VT and Pyle, AM and Perlman, PS}, title = {Group II intron splicing in vivo by first-step hydrolysis.}, journal = {Nature}, volume = {391}, number = {6670}, pages = {915-918}, doi = {10.1038/36142}, pmid = {9495347}, issn = {0028-0836}, mesh = {Esterification ; Genes, Fungal ; Hydrolysis ; *Introns ; Mitochondria/metabolism ; Mutagenesis, Site-Directed ; *RNA Splicing ; RNA, Fungal/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; }, abstract = {Group I, group II and spliceosomal introns splice by two sequential transesterification reactions. For both spliceosomal and group II introns, the first-step reaction occurs by nucleophilic attack on the 5' splice junction by the 2' hydroxyl of an internal adenosine, forming a 2'-5' phosphodiester branch in the intron. The second reaction joins the two exons with a 3'-5' phosphodiester bond and releases intron lariat. In vitro, group II introns can self-splice by an efficient alternative pathway in which the first-step reaction occurs by hydrolysis. The resulting linear splicing intermediate participates in normal second-step reactions, forming spliced exon and linear intron RNAs. Here we show that the group II intron first-step hydrolysis reaction occurs in vivo in place of transesterification in the mitochondria of yeast strains containing branch-site mutations. As expected, the mutations block branching, but surprisingly still allow accurate splicing. This hydrolysis pathway may have been a step in the evolution of splicing mechanisms.}, }
@article {pmid9491070, year = {1998}, author = {Pi, M and Morio, T and Urushihara, H and Tanaka, Y}, title = {Characterization of a novel small RNA encoded by Dictyostelium discoideum mitochondrial DNA.}, journal = {Molecular &amp; general genetics : MGG}, volume = {257}, number = {2}, pages = {124-131}, doi = {10.1007/s004380050631}, pmid = {9491070}, issn = {0026-8925}, mesh = {Animals ; Base Sequence ; DNA, Fungal/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Protozoan/*genetics ; Dictyostelium/*genetics ; Evolution, Molecular ; Mitochondria/chemistry ; Molecular Sequence Data ; Nuclear Proteins/*genetics ; Nucleic Acid Conformation ; Phylogeny ; Plants/genetics ; *Protozoan Proteins ; RNA, Fungal/*genetics ; RNA, Protozoan/*genetics ; RNA, Ribosomal, 5S/genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Transcription Factors/*genetics ; }, abstract = {In this study, we analyzed a mitochondrial small (ms) RNA in Dictyostelium discoideum, which is 129 nucleotides long and has a GC content of only 22.5%. In the mitochondrial DNA, a single-copy gene (msr) for the ms RNA was located downstream of the gene for large-subunit rRNA. The location of msr was similar to that of the 5S rRNA gene in prokaryotes and chloroplasts, but clearly different from that in mitochondria of plants, liverwort and the chlorophycean alga Prototheca wikerhamii, in which small-subunit rRNA and 5S rRNA genes are closely linked. THe primary sequence of ms rRNA showed low homology with mitochondrial 5S rRNA from plants, liverwort and the chlorophycean alga, but the proposed secondary structure of ms RNA was similar to that of cytoplasmic 5S rRNA. In addition, ms RNA showed a highly conserved GAAC sequence in the same loop as in common 5S rRNA. However, ms RNA was detected mainly in the mitochondrial 25,000 x g supernatant fraction which was devoid of ribosomes. It is possible that ms RNA is an evolutionary derivative of mitochondrial 5S rRNA.}, }
@article {pmid9452517, year = {1998}, author = {Albert, B and Godelle, B and Gouyon, P}, title = {Evolution of the plant mitochondrial genome: dynamics of duplication and deletion of sequences.}, journal = {Journal of molecular evolution}, volume = {46}, number = {2}, pages = {155-158}, doi = {10.1007/pl00006290}, pmid = {9452517}, issn = {0022-2844}, mesh = {*DNA, Mitochondrial ; *Evolution, Molecular ; Genome, Plant ; Models, Genetic ; *Multigene Family ; Plants/*genetics ; *Sequence Deletion ; }, abstract = {Several descriptive models have been proposed to explain the occurrence of deletion-duplication events in the plant mitochondrial genome. In order to investigate the dynamics of these events, we have simulated them using a computer model. The simulation shows that whatever the recombination rates between repeats, if a mitochondrial sequence becomes unnecessary for the proper function of mitochondria, this sequence can be deleted and another sequence can be duplicated in consequence. Furthermore, the model shows that the organization of the sequences with respect to the origin of replication has a great influence over the dynamics of the deletion-duplication events.}, }
@article {pmid9445368, year = {1998}, author = {Graack, HR and Wittmann-Liebold, B}, title = {Mitochondrial ribosomal proteins (MRPs) of yeast.}, journal = {The Biochemical journal}, volume = {329 (Pt 3)}, number = {Pt 3}, pages = {433-448}, pmid = {9445368}, issn = {0264-6021}, mesh = {Amino Acid Sequence ; Evolution, Molecular ; Fungal Proteins/*chemistry/genetics/physiology ; Genes, Fungal ; Mitochondria/*chemistry/genetics/physiology ; Molecular Sequence Data ; Ribosomal Proteins/*chemistry/genetics/physiology ; Saccharomyces cerevisiae/*chemistry/genetics/physiology ; }, abstract = {Mitochondrial ribosomal proteins (MRPs) are the counterparts in that organelle of the cytoplasmic ribosomal proteins in the host. Although the MRPs fulfil similar functions in protein biosynthesis, they are distinct in number, features and primary structures from the latter. Most progress in the eludication of the properties of individual MRPs, and in the characterization of the corresponding genes, has been made in baker's yeast (Saccharomyces cerevisiae). To date, 50 different MRPs have been determined, although biochemical data and mutational analysis propose a total number which is substantially higher. Surprisingly, only a minority of the MRPs that have been characterized show significant sequence similarities to known ribosomal proteins from other sources, thus limiting the deduction of their functions by simple comparison of amino acid sequences. Further, individual MRPs have been characterized functionally by mutational studies, and the regulation of expression of MRP genes has been described. The interaction of the mitochondrial ribosomes with transcription factors specific for individual mitochondrial mRNAs, and the communication between mitochondria and the nucleus for the co-ordinated expression of ribosomal constituents, are other aspects of current MRP research. Although the mitochondrial translational system is still far from being described completely, the yeast MRP system serves as a model for other organisms, including that of humans.}, }
@article {pmid9484435, year = {1998}, author = {Williams, MA and Kutcher, BM and Mulligan, RM}, title = {Editing site recognition in plant mitochondria: the importance of 5'-flanking sequences.}, journal = {Plant molecular biology}, volume = {36}, number = {2}, pages = {229-237}, pmid = {9484435}, issn = {0167-4412}, support = {5T32GM07311/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Cytidine ; DNA, Mitochondrial/chemistry/*genetics ; DNA, Plant/chemistry/*genetics ; Exons ; Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Plant Proteins/biosynthesis/genetics ; Plants/*genetics ; Polymerase Chain Reaction ; *RNA Editing ; RNA, Plant/*biosynthesis/chemistry ; Recombinant Fusion Proteins/biosynthesis ; Regulatory Sequences, Nucleic Acid ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; Uridine ; Zea mays/*genetics ; }, abstract = {Cytidine to uridine (C-to-U) editing occurs in plant mitochondria with very high specificity such that only specific cytidines are converted to uridines. The mechanisms for editing site selection in plant mitochondria are unknown. In order to examine the determinants of editing site recognition, repeated mitochondrial DNA sequences that include edited nucleotides have been evaluated as editing substrates. During evolution the maize mitochondrial ribosomal protein subunit 12 (rps12) gene recombined with intron 1 of the ribosomal protein subunit 3 (rps3) gene and a region of the S1-like sequence of the 2.3 kb plasmid. These recombinations created a second copy of an internal portion of the rps12 gene, known as rps12b, which includes the first four editing sites of rps12 transcripts. The duplicated sequence extends seven nucleotides upstream of editing site 1 and six nucleotides downstream from editing site 4. The sequences of rps12 and rps12b are identical between these sites except for a single change at -5 from editing site 1. These modifications did not effect C-to-U conversion at editing sites 2, 3, or 4 in rps12b; however, no editing was detected at editing site 1 in rps12b cDNAs. Thus, the 5' recombination abolished editing at site I, while the 3' recombination modified the downstream RNA sequence, but did not effect editing at site IV. Secondary structure prediction suggests that changes in editing site recognition do not correlate with differences in secondary structures, and that primary RNA sequence may be responsible for editing site specification.}, }
@article {pmid9481814, year = {1998}, author = {Gray, MW and Lang, BF}, title = {Transcription in chloroplasts and mitochondria: a tale of two polymerases.}, journal = {Trends in microbiology}, volume = {6}, number = {1}, pages = {1-3}, doi = {10.1016/S0966-842X(97)01182-7}, pmid = {9481814}, issn = {0966-842X}, mesh = {Arabidopsis/genetics ; Bacterial Proteins/genetics ; Chloroplasts/*genetics ; *DNA-Binding Proteins ; DNA-Directed RNA Polymerases/*genetics ; Gene Expression ; Mitochondria/*genetics ; Organelles ; *Phylogeny ; Plants/genetics ; Sigma Factor/genetics ; T-Phages/genetics ; *Transcription, Genetic ; }, }
@article {pmid9479704, year = {1998}, author = {Siddall, ME and Burreson, EM}, title = {Phylogeny of leeches (Hirudinea) based on mitochondrial cytochrome c oxidase subunit I.}, journal = {Molecular phylogenetics and evolution}, volume = {9}, number = {1}, pages = {156-162}, doi = {10.1006/mpev.1997.0455}, pmid = {9479704}, issn = {1055-7903}, mesh = {Animals ; DNA, Mitochondrial/analysis/isolation &amp; purification ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Leeches/classification/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {The phylogenetic relationships of leeches were investigated for the first time using molecular data. Twenty-one species were examined representing 7 of the 10 conventionally recognized euhirudinean families. In addition, Acanthobdella peledina, a branchiobdellid, four oligochaetes, and two polychaetes were included. Cladistic analysis of the mitochondrial cytochrome c oxidase subunit I gene yielded one most-parsimonious tree. Contemporary taxonomic groupings of leeches into higher categories were found to be largely consistent with monophyletic groups identified in the analysis. Unusual relationships for which there is some precedent include a sister-group relationship between the piscicolids and Arhynchobdellida, as well as the grouping of the haemopids within Hirudinidae.}, }
@article {pmid9419358, year = {1998}, author = {Roger, AJ and Svärd, SG and Tovar, J and Clark, CG and Smith, MW and Gillin, FD and Sogin, ML}, title = {A mitochondrial-like chaperonin 60 gene in Giardia lamblia: evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {95}, number = {1}, pages = {229-234}, pmid = {9419358}, issn = {0027-8424}, support = {GM53835/GM/NIGMS NIH HHS/United States ; AI24285/AI/NIAID NIH HHS/United States ; DK35108/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Chaperonin 60/*genetics ; Cloning, Molecular ; Evolution, Molecular ; Giardia lamblia/*genetics ; Mitochondria ; Molecular Sequence Data ; Phylogeny ; Symbiosis ; }, abstract = {Diplomonads, parabasalids, as represented by trichomonads, and microsporidia are three protist lineages lacking mitochondria that branch earlier than all other eukaryotes in small subunit rRNA and elongation factor phylogenies. The absence of mitochondria and plastids in these organisms suggested that they diverged before the origin of these organelles. However, recent discoveries of mitochondrial-like heat shock protein 70 and/or chaperonin 60 (cpn60) genes in trichomonads and microsporidia imply that the ancestors of these two groups once harbored mitochondria or their endosymbiotic progenitors. In this report, we describe a mitochondrial-like cpn60 homolog from the diplomonad parasite Giardia lamblia. Northern and Western blots reveal that the expression of cpn60 is independent of cellular stress and, except during excystation, occurs throughout the G. lamblia life cycle. Phylogenetic analyses position the G. lamblia cpn60 in a clade that includes mitochondrial and hydrogenosomal cpn60 proteins. The most parsimonious interpretation of these data is that the cpn60 gene was transferred from the endosymbiotic ancestors of mitochondria to the nucleus early in eukaryotic evolution, before the divergence of the diplomonads and trichomonads from other extant eukaryotic lineages. A more complicated explanation requires that these genes originated from distinct alpha-proteobacterial endosymbioses that formed transiently within these protist lineages.}, }
@article {pmid9419244, year = {1997}, author = {Cermakian, N and Ikeda, TM and Miramontes, P and Lang, BF and Gray, MW and Cedergren, R}, title = {On the evolution of the single-subunit RNA polymerases.}, journal = {Journal of molecular evolution}, volume = {45}, number = {6}, pages = {671-681}, doi = {10.1007/pl00006271}, pmid = {9419244}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; DNA-Directed RNA Polymerases/chemistry/*genetics ; *Evolution, Molecular ; Fungal Proteins/chemistry/*genetics ; Mitochondria/enzymology/physiology ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Plant Proteins/chemistry/genetics ; Sequence Alignment ; Viral Proteins/chemistry/genetics ; }, abstract = {Many eukaryotic nuclear genomes as well as mitochondrial plasmids contain genes displaying evident sequence similarity to those encoding the single-subunit RNA polymerase (ssRNAP) of bacteriophage T7 and its relatives. We have collected and aligned these ssRNAP sequences and have constructed unrooted phylogenetic trees that demonstrate the separation of ssRNAPs into three well-defined and nonoverlapping clusters (phage-encoded, nucleus-encoded, and plasmid-encoded). Our analyses indicate that these three subfamiles of T7-like RNAPs shared a common ancestor; however, the order in which the groups diverged cannot be inferred from available data. On the basis of structural similarities and mutational data, we suggest that the ancestral ssRNAP gene may have arisen via duplication and divergence of a DNA polymerase or reverse transcriptase gene. Considering the current phylogenetic distribution of ssRNAP sequences, we further suggest that the origin of the ancestral ssRNAP gene closely paralleled in time the introduction of mitochondria into eukaryotic cells through a eubacterial endosymbiosis.}, }
@article {pmid9382838, year = {1997}, author = {Hirt, RP and Healy, B and Vossbrinck, CR and Canning, EU and Embley, TM}, title = {A mitochondrial Hsp70 orthologue in Vairimorpha necatrix: molecular evidence that microsporidia once contained mitochondria.}, journal = {Current biology : CB}, volume = {7}, number = {12}, pages = {995-998}, doi = {10.1016/s0960-9822(06)00420-9}, pmid = {9382838}, issn = {0960-9822}, mesh = {Animals ; Base Sequence ; Biological Evolution ; DNA, Protozoan ; HSP70 Heat-Shock Proteins/chemistry/classification/*genetics ; Microsporida/*genetics/ultrastructure ; *Mitochondria ; Molecular Sequence Data ; Phylogeny ; Symbiosis ; }, abstract = {Microsporidia are small (1-20 micron) obligate intracellular parasites of a variety of eukaryotes, and they are serious opportunistic pathogens of immunocompromised patients [1]. Microsporidia are often assigned to the first branch in gene trees of eukaryotes [2,3], and are reported to lack mitochondria [2,4]. Like diplomonads and trichomonads, microsporidia are hypothesised to have diverged from the main eukaryotic stock prior to the event that led to the mitochondrion endosymbiosis [2,4]. They have thus assumed importance as putative relics of premitochondrion eukaryote evolution. Recent data have now revealed that diplomonads and trichomonads contain genes that probably originated from the mitochondrion endosymbiont [5-9], leaving microsporidia as chief candidates for an extant primitively amitochondriate eukaryote group. We have now identified a gene in the microsporidium Vairimorpha necatrix that appears to be orthologous to the eukaryotic (symbiont-derived) Hsp70 gene, the protein product of which normally functions in mitochondria. The simplest interpretation of our data is that microporidia have lost mitochondria while retaining genetic evidence of their past presence. This strongly suggests that microsporidia are not primitively amitochondriate and makes feasible an evolutionary scenario whereby all extant eukaryotes share a common ancestor which contained mitochondria.}, }
@article {pmid9468789, year = {1997}, author = {Sogin, Ml}, title = {History assignment: when was the mitochondrion founded?.}, journal = {Current opinion in genetics &amp; development}, volume = {7}, number = {6}, pages = {792-799}, doi = {10.1016/s0959-437x(97)80042-1}, pmid = {9468789}, issn = {0959-437X}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/genetics ; Eukaryotic Cells ; Genome ; Heat-Shock Proteins/genetics ; *Mitochondria/genetics ; Phylogeny ; Symbiosis ; }, abstract = {The near simultaneous radiation of the major eukaryotic evolutionary assemblages-plants, animals, fungi, and at least three other complex protist assemblages worthy of 'kingdom level' status-was preceded by the divergence of many independent protist lineages. The earliest branches are represented by organisms that do not contain mitochondria or plastids, suggesting that the primitive eukaryotic state did not include these organelles. New information about nuclear-coded proteins that localize in the mitochondrion, however, suggests that the ancestral symbionts for mitochondria were present in the first eukaryotes. Phylogenetic support for this hypothesis is persuasive but it is not possible to account for the relative times of divergence for mitochondria and their ancestral symbionts relative to eukaryotic branching patterns inferred from nuclear genes.}, }
@article {pmid9467721, year = {1998}, author = {Miquel, J}, title = {An update on the oxygen stress-mitochondrial mutation theory of aging: genetic and evolutionary implications.}, journal = {Experimental gerontology}, volume = {33}, number = {1-2}, pages = {113-126}, doi = {10.1016/s0531-5565(97)00060-0}, pmid = {9467721}, issn = {0531-5565}, mesh = {Aging/*genetics ; Animals ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; Drosophila/genetics ; Energy Metabolism/physiology ; Humans ; Mutation ; Oxidative Stress/drug effects/*physiology ; Stochastic Processes ; }, abstract = {The acceleration of fixed-postmitotic cell aging by a high metabolic rate and the age related loss of mitochondria found in that cell type led us to propose an oxygen stress-mitochondrial mutation theory of aging, according to which senescence may be linked to mutations of the mitochondrial genome (mtDNA) of the irreversibly differentiated cells. This extranuclear somatic gene mutation concept of aging is supported by the fact that mtDNA synthesis takes place at the inner mitochondrial membrane near the sites of formation of highly reactive oxygen species. Mitochondrial DNA may be unable to prevent the intrinsic mutagenesis caused by those byproducts of respiration because, in contrast to the nuclear genome, it lacks excision and recombination repair. The resulting mitochondrial impairment and concomitant cell bioenergetic decline may cause the senescent loss of physiological performance and may play a key role in the pathogenesis of many age-related degenerative diseases. These concepts are integrated with classic and contemporary hypotheses in a unitary theory that reconciles programmed and stochastic concepts of aging. Thus, it is suggested that cells are programmed to differentiate, and then they accumulate mitochondrial-genetic damage because of their high levels of oxyradical stress and the loss of the organelle rejuvenating power of mitosis.}, }
@article {pmid9464882, year = {1998}, author = {Mannen, H and Kojima, T and Oyama, K and Mukai, F and Ishida, T and Tsuji, S}, title = {Effect of mitochondrial DNA variation on carcass traits of Japanese Black cattle.}, journal = {Journal of animal science}, volume = {76}, number = {1}, pages = {36-41}, doi = {10.2527/1998.76136x}, pmid = {9464882}, issn = {0021-8812}, mesh = {Animals ; Base Sequence ; Body Composition/*genetics ; Breeding ; Cattle/anatomy &amp; histology/classification/*genetics ; DNA, Mitochondrial/analysis/chemistry/*genetics ; *Genetic Variation ; Haplotypes ; Male ; Meat/*standards ; Molecular Sequence Data ; Mutation ; Phylogeny ; }, abstract = {Japanese Black fattening steers were used to examine relationships between carcass traits and mitochondria displacement loop (D-loop) variations. The D-loop region of Japanese Black cattle was sequenced and revealed 26 mitochondrial haplotypes defined by 25 polymorphic sites. The haplotypes were classified into five mitochondrial types (type 1 to 5) using the unweighted pair-group method with arithmetic means. Carcass weight, longissimus muscle area (LMA), rib thickness, subcutaneous fat thickness, yield estimate, and beef marbling score (BMS) were compared among five mitochondrial types with BLUP procedures. Significant differences between mitochondria types were detected for LMA and BMS. Difference (P < . 05) was observed between mitochondrial types 2 and 4 for LMA. There was a highly significant difference (P < .01) in BMS between types 2 and 4. Difference (P < .05) was also found between types 1 and 4 on BMS. These results suggest that cytoplasmic genetic effects are important sources of variation for carcass traits in Japanese Black cattle.}, }
@article {pmid9432010, year = {1997}, author = {Kawachi, H and Shimizu, K and Atomi, H and Sanuki, S and Ueda, M and Tanaka, A}, title = {Gene analysis of an NADP-linked isocitrate dehydrogenase localized in peroxisomes of the n-alkane-assimilating yeast Candida tropicalis.}, journal = {European journal of biochemistry}, volume = {250}, number = {1}, pages = {205-211}, doi = {10.1111/j.1432-1033.1997.00205.x}, pmid = {9432010}, issn = {0014-2956}, mesh = {Alkanes/*metabolism ; Amino Acid Sequence ; Base Sequence ; Candida/*enzymology/genetics ; Cloning, Molecular ; Electrophoresis, Polyacrylamide Gel ; Evolution, Molecular ; Gene Expression ; Genes, Fungal/genetics ; Isocitrate Dehydrogenase/*chemistry/*genetics/metabolism ; Microbodies/*enzymology/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Fungal/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Restriction Mapping ; Saccharomyces cerevisiae/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {In n-alkane-utilizing yeast, Candida tropicalis, two NADP-linked isocitrate dehydrogenase (NADP-IDH) isozymes are present, one in mitochondria (Mt-NADP-IDH) and the other in peroxisomes (Ps-NADP-IDH). Here we report the isolation, sequencing, and expression of the gene encoding Ps-NADP-IDH (CtIDP2), distinct from the Mt-NADP-IDH gene (CtIDP1). Based on the N-terminal amino acid sequence of purified Ps-NADP-IDH, a cDNA fragment specific for Ps-NADP-IDH was obtained by the 5'-RACE method. Using this fragment as a probe, the genomic CtIDP2 gene was isolated. Nucleotide sequence analysis of CtIDP2 disclosed that the region encoding CtIdp2p had a length of 1233 bp, corresponding to 411 amino acid residues. The deduced N-terminal amino acid sequence matched the results obtained from the purified protein. When this CtIDP2 was expressed in Saccharomyces cerevisiae using the C. tropicalis isocitrate lyase gene promoter (UPR-ICL), high intracellular NADP-IDH activity was observed. Comparison of amino acid sequences and phylogenetic tree analysis with NADP-IDH enzymes from all reported eukaryotic sources revealed that mammalian mitochondrial NADP-IDHs formed a cluster, as did plant NADP-IDHs. CtIdp2p and other yeast NADP-IDHs were not included in these clusters and seemed to diverge at an early stage from all other enzymes of higher eukaryotes. Ps-NADP-IDH had no typical C-terminal peroxisomal targeting signal and no processing was demonstrated at the N-terminus. However, we could find a region near the N-terminus of the protein with high similarity to both the putative N-terminal peroxisomal targeting signal sequence of Fox3p of S. cerevisiae and an internal region of Pox4p of C. tropicalis. The results of northern blot analysis indicated that the biosynthesis of CtIdp2p was induced in a medium containing alkanes as a carbon source, where profuse proliferation of peroxisomes is observed.}, }
@article {pmid9371887, year = {1997}, author = {Fey, J and Dietrich, A and Cosset, A and Desprez, T and Maréchal-Drouard, L}, title = {Evolutionary aspects of "chloroplast-like" trnN and trnH expression in higher-plant mitochondria.}, journal = {Current genetics}, volume = {32}, number = {5}, pages = {358-360}, doi = {10.1007/s002940050288}, pmid = {9371887}, issn = {0172-8083}, mesh = {Base Sequence ; Chloroplasts/genetics ; Chromosome Mapping ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; Evolution, Molecular ; *Genes, Plant ; Multigene Family ; Polymerase Chain Reaction ; RNA, Plant/genetics ; RNA, Transfer, Asn/genetics ; Solanum tuberosum/*genetics ; }, abstract = {Two identical "chloroplast-like" tRNAAsn genes, trnN1 and trnN2, have been identified in the potato (Solanum tuberosum) mitochondrial genome. The flanking sequences of trnN1 are unrelated to the corresponding authentic potato chloroplast regions, whilst those of trnN2 are very similar to the chloroplast sequences. The trnN1 copy is present in the mitochondrial genome of various plants whereas the second copy, trnN2, is absent from all the other plant genomes studied so far. Interestingly, both trnN copies are expressed in potato mitochondria. Sequences flanking the chloroplast-like tRNAHis gene (trnH), present as a single copy in the potato mitochondrial DNA, are unrelated to the corresponding chloroplast sequences, whereas chloroplast-derived sequences have been maintained in the vicinity of the maize chloroplast-like mitochondrial trnH gene. However, both the potato and the maize trnH are expressed in mitochondria.}, }
@article {pmid9446909, year = {1997}, author = {Yu, JR and Chung, JS and Huh, S and Lee, SH and Chai, JY}, title = {PCR-RFLP pattern of three kinds of Metagonimus in Korea.}, journal = {The Korean journal of parasitology}, volume = {35}, number = {4}, pages = {271-276}, doi = {10.3347/kjp.1997.35.4.271}, pmid = {9446909}, issn = {0023-4001}, mesh = {Animals ; Electron Transport Complex IV/genetics ; Evolution, Molecular ; Fishes ; Genetic Variation ; Heterophyidae/*classification/*genetics ; Korea ; Mitochondria/enzymology ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Helminth/genetics ; RNA, Ribosomal/genetics ; Rats ; Rats, Sprague-Dawley ; }, abstract = {We tried to compare the three kinds of Metagonimus species, M. yokogawai, Metagonimus Miyata type, and M. takahashii, which were known to be distributed in Korea with polymerase chain reaction based-restriction fragment length polymorphism (PCR-RFLP) patterns. We amplified the internal transcribed spacer 1 (ITS1) site of ribosomal RNA and mitochondrial cytochrome c oxidase I (mCOI) gene. The restriction patterns of ITS1 gene with Rsa I, Alu I and Msp I showed multiple fragmented bands of different sizes between three kinds of Metagonimus. In case of mCOI gene, Rsa I and Alu I enzymes produced differentially fragmented band patterns. According to the parsimony analysis of PCR-RFLP patterns, the estimated genetic divergence between M. yokogawai and Metagonimus Miyata type was 0.034880, between Metagonimus Miyata type and M. takahashii was 0.028098, between M. yokogawai and M. takahashii was 0.018179. It is suggested that Metagonimus Miyata type may be separate species and evolutionize at the older time than the other two species.}, }
@article {pmid9388297, year = {1997}, author = {Kanno, A and Nakazono, M and Hirai, A and Kameya, T}, title = {Maintenance of chloroplast-derived sequences in the mitochondrial DNA of Gramineae.}, journal = {Current genetics}, volume = {32}, number = {6}, pages = {413-419}, doi = {10.1007/s002940050296}, pmid = {9388297}, issn = {0172-8083}, mesh = {Base Sequence ; Chloroplasts/*genetics ; Conserved Sequence/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; Gene Expression Regulation, Plant/genetics ; Genetic Variation/genetics ; Molecular Sequence Data ; Poaceae/*genetics ; Promoter Regions, Genetic/genetics ; RNA, Transfer/genetics ; Restriction Mapping ; Sequence Alignment ; }, abstract = {Evidence for the transfer of DNA from the chloroplast to the mitochondrion has been reported in many higher plants and, in most cases, the transferred chloroplast genes do not have the ability to encode functional products as a consequence of base substitutions and/or multiple rearrangements. We reported previously that the sequence of one end of a chloroplast-derived (ct-derived) fragment of DNA that contained the rps19 and trnH genes has been maintained in most gramineous plants and that its presence seems to be correlated with gene expression in this region. In the present study, we have investigated whether or not the ct-derived sequences in mitochondrial DNA (mtDNA) from some gramineous plants and species of Oryza are conserved, and whether or not such conservation is related to gene expression in these regions. We identified two junctions between ct-derived and mitochondrial sequences that were conserved among some gramineous plants. Around these regions, we found a ct-derived gene for tRNA and the promoter of a mitochondrial gene on the ct-derived sequences, respectively, and these regions were transcribed through the junctions. This result indicates that the junctions and/or regions that are transcribed and functional in mitochondria have been strongly conserved and maintained during their evolution. In Oryza, some junctions between ct-derived and mitochondrial sequences were conserved and other junctions were not. These variations seem to have been caused by deletions and/or rearrangements, and appear to be specific to the type of genome. In the case of Oryza, the timing of deletions and/or rearrangements of ct-derived sequences is likely to have coincided with the divergence of the various genome types.}, }
@article {pmid9434900, year = {1997}, author = {Kabsch, W and Fritz-Wolf, K}, title = {Mitochondrial creatine kinase--a square protein.}, journal = {Current opinion in structural biology}, volume = {7}, number = {6}, pages = {811-818}, doi = {10.1016/s0959-440x(97)80151-0}, pmid = {9434900}, issn = {0959-440X}, mesh = {Adenosine Triphosphate/chemistry/metabolism ; Binding Sites ; Creatine Kinase/*chemistry/metabolism ; Crystallography, X-Ray ; Evolution, Molecular ; Glutamate-Ammonia Ligase/chemistry ; Mitochondria/*enzymology ; Models, Molecular ; Protein Binding ; *Protein Conformation ; Protein Structure, Secondary ; }, abstract = {The recently determined structure of octameric mitochondrial creatine kinase has provided new insights into the functioning of this enzyme and its role in channelling energy from the mitochondria to the cytoplasm. Creatine kinase, a member of the family of guanidino kinases, is structurally similar to glutamine synthetase, suggesting a possible evolutionary link between both protein families.}, }
@article {pmid9418268, year = {1997}, author = {De Stordeur, E}, title = {Nonrandom partition of mitochondria in heteroplasmic Drosophila.}, journal = {Heredity}, volume = {79 (Pt 6)}, number = {}, pages = {615-623}, doi = {10.1038/hdy.1997.207}, pmid = {9418268}, issn = {0018-067X}, mesh = {Animals ; DNA, Mitochondrial/genetics ; Drosophila/*genetics ; Female ; Microinjections ; Mitochondria/*genetics ; Selection, Genetic ; Temperature ; }, abstract = {In order to understand the status of heteroplasmy and its evolution within the Drosophila melanogaster subgroup, cytoplasm microinjections between eggs were performed involving three lineages of Drosophila simulans, carrying the siI, siII or siIII mtDNA type, respectively, and two strains of Drosophila mauritiana carrying the maI or maII mtDNA type. Progeny of eggs from all combinations of injection were analysed. The maII or siI molecules, when provided by the donor, were never detected in the offspring of the hosts, whatever the host's mitochondrial type. Heteroplasmic flies were detected when siII, siIII or maI mitochondria were injected into any of the other cytoplasms. In the majority of cases the percentage of foreign mtDNA increased over generations, leading to a complete replacement of the endogenous mtDNA. In most cases, siII was prevalent. The stochastic processes involved in the evolution of heteroplasmic states are strongly affected by selective values of the different mtDNA types, with a clear hierarchy among them: siII has the most advantage, then siIII and maI, and finally siI and maII. In the siII/maII heteroplasmy case, the loss of maII was more rapid at a high temperature.}, }
@article {pmid9409151, year = {1997}, author = {Zumft, WG}, title = {Cell biology and molecular basis of denitrification.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {61}, number = {4}, pages = {533-616}, pmid = {9409151}, issn = {1092-2172}, mesh = {Amino Acid Sequence ; Bacteria/genetics/*metabolism ; Fungi/genetics/*metabolism ; Gene Expression ; Genes, Bacterial ; Genes, Fungal ; Heme/metabolism ; Molecular Sequence Data ; Multigene Family ; Nitric Oxide/metabolism ; Nitrites/metabolism ; Nitrogen/*metabolism ; Nitrous Oxide/metabolism ; Phylogeny ; }, abstract = {Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.}, }
@article {pmid9374771, year = {1997}, author = {Consolini, AE and Márquez, MT and Ponce-Hornos, JE}, title = {Energetics of heart muscle contraction under high K perfusion: verapamil and Ca effects.}, journal = {The American journal of physiology}, volume = {273}, number = {5}, pages = {H2343-50}, doi = {10.1152/ajpheart.1997.273.5.H2343}, pmid = {9374771}, issn = {0002-9513}, mesh = {Animals ; Calcium/*pharmacology ; Calorimetry ; Electric Stimulation ; Energy Metabolism/drug effects ; Female ; Heart/*physiology ; Heart Ventricles ; In Vitro Techniques ; Kinetics ; Male ; Mitochondria, Heart/drug effects/*metabolism ; Myocardial Contraction/drug effects/*physiology ; Perfusion ; Potassium/*pharmacology ; Rats ; Rats, Wistar ; Verapamil/*pharmacology ; }, abstract = {Tension-dependent (TDH) and tension-independent heat (TIH) release were measured during single isovolumetric contractions in the arterially perfused rat ventricle. Under perfusion with 7 mM K-0.5 mM Ca, TDH showed only one component (H3), whereas TIH could be divided into two components (H1 and H2) of short evolution (similar to the classically identified activation heat) and one component (H4) of long duration (dependent on mitochondrial respiration). Under 25 mM K, TIH components (i.e., H1, H2, and H4) increased with the increase in extracellular Ca concentration ([Ca]o) from 0.5 to 4 mM, and H3 correlated with pressure at all [Ca]o, with regression parameters similar to those observed under 7 mM K. Under 25 mM K-2 mM Ca, peak pressure development (P), H1, H2, and H3, plotted against the number of beats under 0.4 microM verapamil, exponentially decreased, but H4 decreased to 5.5 +/- 2.9% in the first contraction and remained constant thereafter. Under hypoxia, P, H1, H2, and H3 progressively decreased for about six contractions, but H4 was not detectable from the second contraction. The results suggest that increasing extracellular K concentration decreases contractile economy mainly by increasing energy expenditure related to a Ca-dependent (verapamil-sensitive) mitochondrial activity that is not related to force generation.}, }
@article {pmid9353914, year = {1997}, author = {Choudhary, M and Mackenzie, C and Nereng, K and Sodergren, E and Weinstock, GM and Kaplan, S}, title = {Low-resolution sequencing of Rhodobacter sphaeroides 2.4.1T: chromosome II is a true chromosome.}, journal = {Microbiology (Reading, England)}, volume = {143 (Pt 10)}, number = {}, pages = {3085-3099}, doi = {10.1099/00221287-143-10-3085}, pmid = {9353914}, issn = {1350-0872}, mesh = {Base Sequence ; Chromosome Mapping ; Chromosomes, Bacterial/*genetics ; Codon/genetics ; DNA Primers/genetics ; DNA, Bacterial/genetics ; Databases, Factual ; Evolution, Molecular ; Genes, Bacterial ; Genome, Bacterial ; Mitochondria/genetics ; Molecular Sequence Data ; Multigene Family ; Rhodobacter sphaeroides/*genetics/physiology ; Sequence Analysis, DNA ; }, abstract = {The photosynthetic bacterium Rhodobacter sphaeroides 2.4.1T has two chromosomes, CI (approximately 3.0 Mb) and CII (approximately 0.9 Mb). In this study a low-redundancy sequencing strategy was adopted to analyse 23 out of 47 cosmids from an ordered CII library. The sum of the lengths of these 23 cosmid inserts was approximately 495 kb, which comprised approximately 417 kb of unique DNA. A total of 1145 sequencing runs was carried out, with each run generating 559 +/- 268 bases of sequence to give approximately 640 kb of total sequence. After editing, approximately 2.8% bases per run were estimated to be ambiguous. After the removal of vector and Escherichia coli sequences, the remaining approximately 565 kb of R. sphaeroides sequences were assembled, generating approximately 291 kb of unique sequences. BLASTX analysis of these unique sequences suggested that approximately 131 kb (45% of the unique sequence) had matches to either known genes, or database ORFs of hypothetical or unknown function (dORFs). A total of 144 strong matches to the database was found; 101 of these matches represented genes encoding a wide variety of functions, e.g. amino acid biosynthesis, photosynthesis, nutrient transport, and various regulatory functions. Two rRNA operons (rrnB and rrnC) and five tRNAs were also identified. The remaining 160 kb of DNA sequence which did not yield database matches was then analysed using CODONPREFERENCE from the GCG package. This analysis suggested that 122 kb (42% of the total unique DNA sequence) could encode putative ORFs (pORFs), with the remaining 38 kb (13%) possibly representing non-coding intergenic DNA. From the data so far obtained, CII does not appear to be specialized for encoding any particular metabolic function, physiological state or growth condition. These data suggest that CII contains genes which are functionally as diverse as those found on any other bacterial chromosome and also contains sequences (pORFs), which may prove to be unique to this organism.}, }
@article {pmid9351194, year = {1997}, author = {Biagini, GA and Finlay, BJ and Lloyd, D}, title = {Evolution of the hydrogenosome.}, journal = {FEMS microbiology letters}, volume = {155}, number = {2}, pages = {133-140}, doi = {10.1016/s0378-1097(97)00333-9}, pmid = {9351194}, issn = {0378-1097}, mesh = {Animals ; Hydrogen/metabolism ; Mitochondria/metabolism ; Phylogeny ; Trichomonas vaginalis/*classification/metabolism ; }, abstract = {Since its discovery almost 25 years ago the enigmatic hydrogenosome, a redox organelle of anaerobic unicellular eukaryotes, has puzzled evolutionists as to its origin and function. Synthesis of recent molecular, physiological and morphological studies now favours the hypothesis that hydrogenosomes derived from a modification of pre-existing mitochondria, and argues against the previously held view that the hydrogenosome had a polyphyletic origin. These data provide evidence for a more ancient origin of mitochondria than hitherto thought.}, }
@article {pmid9344756, year = {1997}, author = {Liedtke, AJ}, title = {The changing metabolic role of fatty acids in increasingly complex organisms: an evolutionary perspective.}, journal = {Journal of molecular and cellular cardiology}, volume = {29}, number = {10}, pages = {2611-2619}, doi = {10.1006/jmcc.1997.0510}, pmid = {9344756}, issn = {0022-2828}, mesh = {Animals ; Archaea/metabolism ; *Biological Evolution ; Citric Acid Cycle ; Fatty Acids/*metabolism ; Mitochondria/metabolism ; Oxygen/metabolism ; Symbiosis ; }, }
@article {pmid9312854, year = {1997}, author = {Vogel, G}, title = {Searching for living relics of the cell's early days.}, journal = {Science (New York, N.Y.)}, volume = {277}, number = {5332}, pages = {1604}, doi = {10.1126/science.277.5332.1604}, pmid = {9312854}, issn = {0036-8075}, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; Eukaryota/genetics/ultrastructure ; *Eukaryotic Cells/physiology/ultrastructure ; *Genes, Bacterial ; Giardia lamblia/physiology/ultrastructure ; Microsporida/physiology/ultrastructure ; *Mitochondria/genetics ; }, }
@article {pmid9304815, year = {1997}, author = {Weekers, PH and Kleyn, J and Vogels, GD}, title = {Phylogenetic position of Psalteriomonas lanterna deduced from the SSU rDNA sequence.}, journal = {The Journal of eukaryotic microbiology}, volume = {44}, number = {5}, pages = {467-470}, doi = {10.1111/j.1550-7408.1997.tb05725.x}, pmid = {9304815}, issn = {1066-5234}, mesh = {Animals ; Base Composition ; Cloning, Molecular ; DNA, Protozoan/analysis/chemistry ; DNA, Ribosomal/analysis/chemistry ; Eukaryota/*genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Protozoan/*genetics ; RNA, Ribosomal/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The small subunit ribosomal DNA sequence (SSU rDNA) of the microaerophilic free-living amoeboflagellate Psalteriomonas lanterna has been sequenced and analyzed. The gene is 1,945 bp long and has a G + C content of 33.4%. Based upon ultrastructural studies, P. lanterna has been placed in the class Lyromonadea within the phylum Percolozoa Cavalier-Smith, 1991. However, based upon cytological characteristics, this microaerophilic free-living amoeboflagellate appears to be very primitive. It shares certain characteristics in common with some archezoans, i.e. it lacks mitochondria and dictyosomes but contains hydrogenosomes. Despite sharing these characteristics with the amitochondriate taxa, P. lanterna is not related to any of these taxa but instead to the Vahlkampfiidae. Therefore, we used primary sequence data and the secondary structure of the SSU rDNA gene to determine the placement P. lanterna in the phylogenetic tree. Our analyses showed that P. lanterna groups as a sister taxon to the Vahlkampfiidae but probably diverged from them quite early.}, }
@article {pmid9302324, year = {1997}, author = {Inagaki, Y and Hayashi-Ishimaru, Y and Ehara, M and Igarashi, I and Ohama, T}, title = {Algae or protozoa: phylogenetic position of euglenophytes and dinoflagellates as inferred from mitochondrial sequences.}, journal = {Journal of molecular evolution}, volume = {45}, number = {3}, pages = {295-300}, doi = {10.1007/pl00006233}, pmid = {9302324}, issn = {0022-2844}, mesh = {Animals ; Codon ; DNA, Mitochondrial/*genetics ; Dinoflagellida/*genetics ; Electron Transport Complex IV/genetics ; Eukaryota/*genetics ; *Phylogeny ; Polymerase Chain Reaction ; Tryptophan/genetics ; }, abstract = {The chloroplasts of euglenophytes and dinoflagellates have been suggested to be the vestiges of endosymbiotic algae acquired during the process of evolution. However, the evolutionary positions of these organisms are still inconclusive, and they have been tentatively classified as both algae and protozoa. A representative gene of the mitochondrial genome, cytochrome oxidase subunit I (coxI), was chosen and sequenced to clarify the phylogenetic positions of four dinoflagellates, two euglenophytes and one apicomplexan protist. This is the first report of mitochondrial DNA sequences for dinoflagellates and euglenophytes. Our COXI tree shows clearly that dinoflagellates are closely linked to apicomplexan parasites but not with algae. Euglenophytes and algae appear to be only remotely related, with euglenophytes sharing a possible evolutionary link with kinetoplastids. The COXI tree is in general agreement with the tree based on the nuclear encoded small subunit of ribosomal RNA (SSU rRNA) genes, but conflicts with that based on plastid genes. These results support the interpretation that chloroplasts present in euglenophytes and dinoflagellates were captured from algae through endosymbioses, while their mitochondria were inherited from the host cell. We suggest that dinoflagellates and euglenophytes were originally heterotrophic protists and that their chloroplasts are remnants of endosymbiotic algae.}, }
@article {pmid9302321, year = {1997}, author = {Guimarães, RC and Trifonov, EN and Lagunez-Otero, J}, title = {Taxonomy of 5 S ribosomal RNA by the linguistic technique: probing with mitochondrial and mammalian sequences.}, journal = {Journal of molecular evolution}, volume = {45}, number = {3}, pages = {271-277}, doi = {10.1007/pl00006230}, pmid = {9302321}, issn = {0022-2844}, mesh = {Animals ; Bacteria/genetics ; DNA, Mitochondrial/*genetics ; Eukaryotic Cells ; Fungi/genetics ; Mammals/*genetics ; *Models, Genetic ; Phylogeny ; Plants/genetics ; RNA, Ribosomal, 5S/*classification ; Sensitivity and Specificity ; Glycine max/genetics ; }, abstract = {Linguistic similarities and dissimilarities between 5 S rRNA sequences allowed taxonomical separation of species and classes. Comparisons with the molecule from mammals distinguished fungi and plants from protists and animals. Similarities to mammalians progressively increased from protists to invertebrates and to somatic-type molecules of the vertebrates lineage. In this, deviations were detected in avian, oocyte type, and pseudogene sequences. Among bacteria, actinobacteria were most similar to the mammalians, which could be related to the high frequency of associations among members of these groups. Some archaebacterial species most similar to the mammalians belonged to the Thermoproteales and Halobacteria groups. Comparisons with the soybean mitochondrial molecule revealed high internal homogeneity among plant mitochondria. The eubacterial groups most similar to it were Thermus and Rhodobacteria gamma-1 and alpha-2. Other procedures have already indicated similarities of Rhodobacteria alpha to mitochondria but the linguistic similarities were on the average higher with the first two groups.}, }
@article {pmid9379714, year = {1997}, author = {Herrero, A and Barja, G}, title = {Sites and mechanisms responsible for the low rate of free radical production of heart mitochondria in the long-lived pigeon.}, journal = {Mechanisms of ageing and development}, volume = {98}, number = {2}, pages = {95-111}, doi = {10.1016/s0047-6374(97)00076-6}, pmid = {9379714}, issn = {0047-6374}, mesh = {Aging/*metabolism ; Animals ; Biological Evolution ; Columbidae/*metabolism ; Electron Transport/*drug effects ; Free Radicals ; Hydrogen Peroxide/metabolism ; Longevity/*physiology ; Male ; Mitochondria, Heart/*metabolism ; Mitosis ; Oxygen Consumption/physiology ; Rats ; Rats, Wistar/*metabolism ; Reactive Oxygen Species/*metabolism ; Species Specificity ; }, abstract = {Basal (substrate alone) and maximum rates of H2O2 production, oxygen consumption and free radical leak in the respiratory chain were higher in heart mitochondria of the short-lived rat (4 years) than in the long-lived pigeon (35 years). This suggests that the low free radical production of pigeon heart mitochondria is due in part to both a low electron flow and a low percent leak of electrons out of sequence in the respiratory chain. Thenoyltrifluoroacetone did not increase H2O2 production with succinate either in rats or pigeons. Mitochondrial H2O2 production was higher with pyruvate/malate than with succinate in both animal species. Rotenone and antimycin A increased H2O2 production with pyruvate/malate to the maximum levels observed in each species. Addition of myxothiazol to antimycin A-treated mitochondria supplemented with pyruvate/malate decreased H2O2 production in both species. All the combinations of inhibitors added with pyruvate/malate resulted in higher rates of H2O2 production in rats than in pigeons. When succinate instead of pyruvate/malate was used as substrate, rotenone and thenoyltrifluoroacetone decreased mitochondrial H2O2 production in the rat and did not change it in the pigeon. The results indicate that Complexes I and III are the main H2O2 generators of heart mitochondria in rats and pigeons and that both Complexes are responsible for the low H2O2 production of the bird. p-Chloromercuribenzoate and ethoxyformic anhydride strongly inhibited the H2O2 production induced by rotenone with pyruvate/malate in both species. This suggests that the free radical generator of Complex I is located after the ferricyanide reduction site, between the ethoxyformic and the rotenone-sensitive sites.}, }
@article {pmid9297974, year = {1997}, author = {Frade, JM and Michaelidis, TM}, title = {Origin of eukaryotic programmed cell death: a consequence of aerobic metabolism?.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {19}, number = {9}, pages = {827-832}, doi = {10.1002/bies.950190913}, pmid = {9297974}, issn = {0265-9247}, mesh = {Aerobiosis ; *Apoptosis ; Eukaryotic Cells/*pathology ; }, abstract = {A marked feature of eukaryotic programmed cell death is an early drop in mitochondrial transmembrane potential. This results from the opening of permeability transition pores, which are composed of adenine nucleotide translocators and mitochondrial porins. The latter share striking similarities with bacterial porins, including down-regulation of their pore size by purine nucleotides), suggesting a common origin. The porins of some invasive bacteria play a crucial role during their accommodation inside the host cell and this coexistence resembles the endosymbiotic origin of mitochondria. The above observations suggest that early in eukaryotic evolution, former invaders may have used porin-type channels to enter their host and to induce its death when the levels of its cytoplasmic purine nucleotides were dropped. The appearance of adenosine nucleotide translocators in the primitive eukaryotes, which permitted usage of the oxidative metabolism of the invaders, provided the basis for the permeability transition phenomena, now linked to the apoptotic process. Bcl-2-type molecules, being able to modulate the permeability transition pores by interaction with adenosine nucleotide translocators, may have played an essential role in conferring a means of controlling apoptosis.}, }
@article {pmid9287424, year = {1997}, author = {Lynch, M}, title = {Mutation accumulation in nuclear, organelle, and prokaryotic transfer RNA genes.}, journal = {Molecular biology and evolution}, volume = {14}, number = {9}, pages = {914-925}, doi = {10.1093/oxfordjournals.molbev.a025834}, pmid = {9287424}, issn = {0737-4038}, support = {GM36827/GM/NIGMS NIH HHS/United States ; }, mesh = {Animal Population Groups/genetics ; Animals ; Bacteria/genetics ; Base Composition ; Cell Nucleus/genetics ; Evolution, Molecular ; Gene Frequency ; Genes/genetics ; Mitochondria/genetics ; *Mutagenesis ; Nucleic Acid Conformation ; Plants/genetics ; RNA, Bacterial/genetics ; RNA, Transfer/chemistry/*genetics ; }, abstract = {A comparative analysis of the transfer RNA genes in the genomes of the major kingdoms of eukaryotes and prokaryotes leads to the general conclusion that the rate of evolution of organelle tRNA genes is typically equal to of greater than that of their nuclear counterparts. Situations where this is not the case, most notably in vascular plants, are attributable to an elevated mutation rate in the nuclear genome. Through a comparison of rates of mutation with rates of nucleotide substitution, it is shown that there is a reduction in the efficiency of selection on new mutations in organelle genes. Numerous lines of evidence, including observed reductions in stem duplex stability and changes in loop sizes, suggest that the excess changes observed in the organelle genes are mildly deleterious. Uniparental inheritance of organelles causes a reduction in the efficiency of selection through the joint effects of an increase in linkage disequilibrium and a decrease in effective population size. These results provide molecular support for the idea that asexually propagating genomes are subject to long-term, gradual fitness loss and raise questions about the role of organelle mutations in the long-term survival of major phylogenetic lineages.}, }
@article {pmid9299297, year = {1997}, author = {Friedrich, T and Weiss, H}, title = {Modular evolution of the respiratory NADH:ubiquinone oxidoreductase and the origin of its modules.}, journal = {Journal of theoretical biology}, volume = {187}, number = {4}, pages = {529-540}, doi = {10.1006/jtbi.1996.0387}, pmid = {9299297}, issn = {0022-5193}, mesh = {Adenosine Triphosphate/biosynthesis ; Animals ; Bacteria/metabolism ; *Biological Evolution ; Mitochondria/metabolism ; Models, Biological ; Molecular Sequence Data ; NAD/*metabolism ; NAD(P)H Dehydrogenase (Quinone)/*metabolism ; *Oxygen Consumption ; *Proton Pumps ; }, abstract = {The proton-pumping NADH:ubiquinone oxidoreductase is the foremost of the respiratory chain complexes providing the proton motive force required for the synthesis of ATP. The complex is found in purple bacteria and in the mitochondria of most eukaryotes. The bacterial complex consists of 14 different subunits while the mitochondrial complex contains at least 28 accessory proteins which do not directly participate in the electron and proton transport function. A homologous complex which has 11 subunits in common with the respiratory complex I exists in cyanobacteria and chloroplasts. This complex might probably work as a NADPH:plastoquinone oxidoreductase being possibly involved in a cyclic photosynthetic electron transport. Homologues of the functional modules of the complex are also found in other bacterial electron transfer and ion transport proteins. The modular evolution of the complex and the possible origin of its modules are discussed in this paper.}, }
@article {pmid9268729, year = {1997}, author = {Chen, HC and Viry-Moussaïd, M and Dietrich, A and Wintz, H}, title = {Evolution of a mitochondrial tRNA PHE gene in A. thaliana: import of cytosolic tRNA PHE into mitochondria.}, journal = {Biochemical and biophysical research communications}, volume = {237}, number = {2}, pages = {432-437}, doi = {10.1006/bbrc.1997.7138}, pmid = {9268729}, issn = {0006-291X}, mesh = {Arabidopsis/*genetics ; Base Sequence ; Biological Transport ; Cytosol/*metabolism ; DNA, Mitochondrial ; *Evolution, Molecular ; Mitochondria/*metabolism ; Molecular Sequence Data ; RNA, Messenger/genetics/metabolism ; RNA, Transfer, Phe/*genetics/metabolism ; Sequence Homology, Nucleic Acid ; }, abstract = {Previously we have described a putative tRNATyr in Arabidopsis thaliana mitochondria, the sequence of which is different from that of other plant mitochondrial tRNATyr genes. We show here that this tRNATyr gene sequence is present in several copies in the mitochondrial genome of A. thaliana. One copy of these tRNATyr gene sequences, termed here tRNATyr-1, could encode a functional tRNA. Expression analysis has shown that the tRNATyr-1 gene is cotranscribed with the downstream tRNAGlu gene, and that the corresponding mature-sized tRNA is present in mitochondria. We also show that the native tRNATyr gene, similar to the mitochondrial tRNATyr genes found in plants, is present in the A. thaliana mitochondrial genome and expressed. The tRNATyr-1 gene has been previously suggested to be derived from a tRNAPhe gene sequence. We show here that, as a consequence, there is no tRNAPhe gene in the mitochondrial genome of A. thaliana and that a cytosolic tRNAPhe is imported in A. thaliana mitochondria.}, }
@article {pmid9242608, year = {1997}, author = {Hedtke, B and Börner, T and Weihe, A}, title = {Mitochondrial and chloroplast phage-type RNA polymerases in Arabidopsis.}, journal = {Science (New York, N.Y.)}, volume = {277}, number = {5327}, pages = {809-811}, doi = {10.1126/science.277.5327.809}, pmid = {9242608}, issn = {0036-8075}, mesh = {Amino Acid Sequence ; Arabidopsis/*enzymology/genetics ; Cell Nucleus/genetics ; Chloroplasts/*enzymology ; Cloning, Molecular ; DNA-Directed RNA Polymerases/chemistry/*genetics ; Exons ; *Genes, Plant ; Introns ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Recombinant Fusion Proteins/metabolism ; Sequence Alignment ; T-Phages/enzymology ; }, abstract = {In addition to the RNA polymerases (RNAPs) transcribing the nuclear genes, eukaryotic cells also require RNAPs to transcribe the genes of the mitochondrial genome and, in plants, of the chloroplast genome. The plant Arabidopsis thaliana was found to contain two nuclear genes similar to genes encoding the mitochondrial RNAP from yeast and RNAPs of bacteriophages T7, T3, and SP6. The putative transit peptides of the two polymerases were capable of targeting fusion proteins to mitochondria and chloroplasts, respectively, in vitro. The results indicate that the mitochondrial RNAP in plants is a bacteriophage-type enzyme. A gene duplication event may have generated the second RNAP, which along with the plastid-encoded eubacteria-like RNAP could transcribe the chloroplast genome.}, }
@article {pmid9252184, year = {1997}, author = {Naylor, GJ and Brown, WM}, title = {Structural biology and phylogenetic estimation.}, journal = {Nature}, volume = {388}, number = {6642}, pages = {527-528}, doi = {10.1038/41460}, pmid = {9252184}, issn = {0028-0836}, mesh = {Animals ; Mitochondria/*genetics ; *Phylogeny ; }, }
@article {pmid9387093, year = {1997}, author = {Golshani-Hebroni, SG and Bessman, SP}, title = {Hexokinase binding to mitochondria: a basis for proliferative energy metabolism.}, journal = {Journal of bioenergetics and biomembranes}, volume = {29}, number = {4}, pages = {331-338}, pmid = {9387093}, issn = {0145-479X}, mesh = {Adenosine Triphosphate/biosynthesis ; Animals ; *Energy Metabolism ; Glycolysis ; Hexokinase/*metabolism ; Insulin/metabolism ; Mitochondria/*metabolism ; NAD/metabolism ; NADP/metabolism ; Protein Biosynthesis ; Tumor Cells, Cultured ; }, abstract = {Current thought is that proliferating cells undergo a shift from oxidative to glycolytic metabolism, where the energy requirements of the rapidly dividing cell are provided by ATP from glycolysis. Drawing on the hexokinase-mitochondrial acceptor theory of insulin action, this article presents evidence suggesting that the increased binding of hexokinase to porin on mitochondria of cancer cells not only accelerates glycolysis by providing hexokinase with better access to ATP, but also stimulates the TCA cycle by providing the mitochondrion with ADP that acts as an acceptor for phosphoryl groups. Furthermore, this acceleration of the TCA cycle stimulates protein synthesis via two mechanisms: first, by increasing ATP production, and second, by provision of certain amino acids required for protein synthesis, since the amino acids glutamate, alanine, and aspartate are either reduction products or partially oxidized products of the intermediates of glycolysis and the TCA cycle. The utilization of oxygen in the course of the TCA cycle turnover is relatively diminished even though TCA cycle intermediates are being consumed. With partial oxidation of TCA cycle intermediates into amino acids, there is necessarily a reduction in formation of CO2 from pyruvate, seen as a relative diminution in utilization of oxygen in relation to carbon utilization. This has been assumed to be an inhibition of oxygen uptake and therefore a diminution of TCA cycle activity. Therefore a switch from oxidative metabolism to glycolytic metabolism has been assumed (the Crabtree effect). By stimulating both ATP production and protein synthesis for the rapidly dividing cell, the binding of hexokinase to mitochondrial porin lies at the core of proliferative energy metabolism. This article further reviews literature on the binding of the isozymes of hexokinase to porin, and on the evolution of insulin, proposing that intracellular insulin-like proteins directly bind hexokinase to mitochondrial porin.}, }
@article {pmid9260887, year = {1997}, author = {Singh, B and Soltys, BJ and Wu, ZC and Patel, HV and Freeman, KB and Gupta, RS}, title = {Cloning and some novel characteristics of mitochondrial Hsp70 from Chinese hamster cells.}, journal = {Experimental cell research}, volume = {234}, number = {2}, pages = {205-216}, doi = {10.1006/excr.1997.3609}, pmid = {9260887}, issn = {0014-4827}, mesh = {Amino Acid Sequence ; Animals ; Antibody Specificity ; Base Sequence ; Biological Transport ; *CHO Cells ; Cloning, Molecular ; Cricetinae ; DNA, Complementary/genetics ; Escherichia coli ; HSP70 Heat-Shock Proteins/*analysis/*genetics/metabolism ; Mitochondria/*chemistry ; Mitochondria, Heart/metabolism ; Molecular Sequence Data ; Phylogeny ; Protein Processing, Post-Translational ; Rats ; Recombinant Fusion Proteins ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {The cDNA for Chinese hamster mitochondrial Hsp70 (mHsp70) was cloned and sequenced using a polymerase chain reaction probe based on conserved regions in the Hsp70 family of proteins. The encoded protein consists of 679 amino acids which includes a N-terminal mitochondrial targeting sequence of 46 amino acids. The mHsp70 protein contains several sequence signatures that are characteristics of prokaryotic and eukaryotic organellar Hsp70 homologs. In a phylogenetic tree based on Hsp70 sequences, it branches with the gram-negative proteobacteria, supporting the endosymbiotic origin of mitochondria from this group of prokaryotes. The mHsp70 cDNA was transcribed and translated in vitro and its import into isolated rat heart mitochondria was examined. The precursor mHsp70 was converted into a mature form of lower molecular mass (approximately 71 kDa) which became resistant to trypsin digestion. The import of mHsp70 into mitochondria was not observed in the presence of an uncoupler of energy metabolism or when the N-terminal presequence was lacking. The cDNA for mHsp70 was expressed in Escherichia coli and a polyclonal antibody to the purified recombinant protein was raised. The antibody shows no cross-reactivity to recombinant cytosolic Hsp70 protein and in 2-D gel blots it reacted specifically with the mHsp70 protein only. In immunofluorescence experiments, the antibody predominantly labeled mitochondria, and the observed labeling pattern was identical to that seen with a monoclonal antibody to the mitochondrial Hsp60 chaperonin. The affinity-purified antibody to mHsp70 was also employed to examine the subcellular distribution of the protein by cryoelectron microscopy and the immunogold-labeling technique. In these experiments, in addition to mitochondria, labeling with mitochondrial Hsp70 antibody was also observed on the plasma membrane and in unidentified cytoplasmic vesicles and granules. These studies raise the possibility that similar to the Hsp60 chaperonin and a number of other mitochondrial proteins, mHsp70 may have an extramitochondrial role.}, }
@article {pmid9249985, year = {1997}, author = {Oh-hama, T}, title = {Evolutionary consideration on 5-aminolevulinate synthase in nature.}, journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life}, volume = {27}, number = {4}, pages = {405-412}, doi = {10.1023/a:1006583601341}, pmid = {9249985}, issn = {0169-6149}, mesh = {5-Aminolevulinate Synthetase/*genetics/*metabolism ; Acetyltransferases/genetics ; Acyltransferases/genetics ; Animals ; Bacteria/enzymology/genetics ; *Biological Evolution ; Birds ; Energy Metabolism ; Eukaryota/enzymology/genetics ; Eukaryotic Cells ; Gene Expression ; Humans ; Mammals ; Phylogeny ; Plants/enzymology/genetics ; Prokaryotic Cells ; Saccharomyces cerevisiae/enzymology/genetics ; }, abstract = {5-Aminolevulinic acid (ALA), a universal precursor of tetrapyrrole compounds can be synthesized by two pathways: the C5 (glutamate) pathway and ALA synthase. From the phylogenetic distribution it is shown that distribution of ALA synthase is restricted to the alpha subclass of purple bacteria in prokaryotes, and further distributed to mitochondria of eukaryotes. The monophyletic origin of bacterial and eukaryotic ALA synthase is shown by sequence analysis of the enzyme. Evolution of ALA synthase in the alpha subclass of purple bacteria is discussed in relation to the energy-generating and biosynthetic devices in subclasses of this bacteria.}, }
@article {pmid9247927, year = {1997}, author = {Germot, A and Philippe, H and Le Guyader, H}, title = {Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae.}, journal = {Molecular and biochemical parasitology}, volume = {87}, number = {2}, pages = {159-168}, doi = {10.1016/s0166-6851(97)00064-9}, pmid = {9247927}, issn = {0166-6851}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA Primers/genetics ; Eukaryotic Cells ; Genes, Protozoan ; HSP70 Heat-Shock Proteins/*genetics ; Microsporida/*genetics/ultrastructure ; Mitochondria/*genetics ; Molecular Sequence Data ; Nosema/*genetics/ultrastructure ; Open Reading Frames ; Phylogeny ; Polymerase Chain Reaction ; Protozoan Proteins/genetics ; Sequence Homology, Amino Acid ; }, abstract = {In molecular phylogenies based on ribosomal RNA, three amitochondriate protist lineages, Microsporidia, Metamonada (including diplomonads) and Parabasala (including trichomonads), are the earliest offshoots of the eukaryotic tree. As an explantation for the lack of mitochondria in these organisms, the hypothesis that they have diverged before the mitochondrial endosymbiosis is preferred to the less parsimonious hypothesis of several independent losses of the organelle. Nevertheless, if they had descended from mitochondrion-containing ancestors, it may be possible to find in their nuclear DNA genes that derive from the endosymbiont which gave rise to mitochondria. Based on similar evidence, secondary losses of mitochondria have recently been suggested for Entamoeba histolytica and for Trichomonas vaginalis. In this study, we have isolated a gene encoding a chaperone protein (HSP70, 70 kDa heat shock protein) from the microspordian Nosema locustae. In phylogenetic trees, this HSP70 was located within a group of sequences that in other lineages is targetted to the mitochondrial compartment, itself included in the proteobacterial clade. In addition, the N. locustae protein contained the GDAW(V) motif shared by mitochondrial and proteobacterial sequences, with only one conservative substitution. Moreover, microsporidia, a phylum which was assumed to emerge close to the base of the eukaryotic tree, appears as the sister-group of fungi in the HSP70 phylogeny, in agreement with some ultrastructural characters and phylogenies based on alpha- and beta-tubulins. Loss of mitochondria, now demonstrated for several amitochondriate groups, indicates that the common ancestor of all the extant eukaryotic species could have been a mitochondriate eukaryote.}, }
@article {pmid9236270, year = {1997}, author = {Ehara, M and Hayashi-Ishimaru, Y and Inagaki, Y and Ohama, T}, title = {Use of a deviant mitochondrial genetic code in yellow-green algae as a landmark for segregating members within the phylum.}, journal = {Journal of molecular evolution}, volume = {45}, number = {2}, pages = {119-124}, pmid = {9236270}, issn = {0022-2844}, mesh = {DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Eukaryota/classification/*genetics ; *Genetic Code ; Isoleucine/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {Several algae that were previously classified in the phylum Xanthophyta (yellow-green algae) were assigned in 1971 to a new phylum, Eustigmatophyta. It was anticipated that the number of algae reclassified to Eustigmatophyta would increase. However, due to the fact that the morphological characteristics that segregate eustigmatophytes from other closely related algae can be only obtained through laborious electron microscopic techniques, the number of members in this phylum have increased rather slowly. We attempted, therefore, to segregate two closely related groups of algae, eustigmatophytes and yellow-green algae, on the basis of a molecular phylogenetic tree as a means of providing an alternative method of distinguishing these phyla. We analyzed the mitochondrial cytochrome oxidase subunit I (COXI) gene sequences of eight algae classified as xanthophyceans and found that six manifested the expected deviant genetic code where AUA codes for methionine (AUA/Met), but not for isoleucine (AUA/Ile) as in the universal genetic code. The other two, Monodus sp. (CCMP 505) and Ophiocytium majus (CCAP 855/1), which were presumed to be yellow-green algae, and all the examined eustigmatophytes utilized AUA for Ile. In addition, the phylogenetic tree of COXI gene sequences showed that the six yellow-green algae bearing the AUA/Met deviant code composed a tight clade with a bootstrap value of 100%. The phylogenetic tree of the corresponding sequences from Monodus sp. and Ophiocytium majus and the eustigmatophytes also composed a tight cluster, but with a bootstrap value of 92%. These results strongly suggest that two previously classified members of yellow-green algae belong to the phylum Eustigmatophyta. Therefore, examination of the mitochondrial genetic code in algae appears to be a potentially very useful genetic marker for classifying these organisms, especially when it is considered with the results obtained through a molecular phylogenetic tree.}, }
@article {pmid9228078, year = {1997}, author = {Sampson, MJ and Lovell, RS and Craigen, WJ}, title = {The murine voltage-dependent anion channel gene family. Conserved structure and function.}, journal = {The Journal of biological chemistry}, volume = {272}, number = {30}, pages = {18966-18973}, doi = {10.1074/jbc.272.30.18966}, pmid = {9228078}, issn = {0021-9258}, support = {1P30-HD27823/HD/NICHD NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; Conserved Sequence ; Evolution, Molecular ; Humans ; Ion Channels/*genetics ; Membrane Proteins/*genetics ; Mice ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins ; Models, Molecular ; Molecular Sequence Data ; Multigene Family ; Nerve Tissue Proteins/*genetics ; Plasmids/metabolism ; Poly A/metabolism ; *Porins ; Promoter Regions, Genetic ; Protein Structure, Secondary ; Sequence Analysis, DNA ; Structure-Activity Relationship ; Transcription, Genetic ; Voltage-Dependent Anion Channel 1 ; Voltage-Dependent Anion Channel 2 ; Voltage-Dependent Anion Channels ; }, abstract = {Voltage-dependent anion channels (VDACs) are pore-forming proteins found in the outer mitochondrial membrane of all eucaryotes. VDACs are the binding sites for several cytosolic enzymes, including the isoforms of hexokinase and glycerol kinase. VDACs have recently been shown to conduct ATP when in the open state, allowing bound kinases preferential access to mitochondrial ATP and providing a possible mechanism for the regulation of adenine nucleotide flux. Two human VDAC cDNAs have been described previously, and we recently reported the isolation of mouse VDAC1 and VDAC2 cDNAs, as well as a third novel VDAC cDNA, designated VDAC3. In this report we describe the structural organization of each mouse VDAC gene and demonstrate that, based on conserved exon/intron boundaries, the three VDAC isoforms belong to a single gene family. The 5'-flanking region of each VDAC gene was shown to have transcription promoter activity by transient expression in cultured cells. The promoter region of each VDAC isoform lacks a canonical TATA box, but all are G+C-rich, a characteristic of housekeeping gene promoters. To examine the conservation of VDAC function, each mouse VDAC was expressed in yeast lacking the endogenous VDAC gene. Both VDAC1 and VDAC2 are able to complement the phenotypic defect associated with the mutant yeast strain. VDAC3, however, is only able to partially complement the mutant phenotype, suggesting an alternative physiologic function for the VDAC3 protein.}, }
@article {pmid9214502, year = {1997}, author = {Springer, MS and Cleven, GC and Madsen, O and de Jong, WW and Waddell, VG and Amrine, HM and Stanhope, MJ}, title = {Endemic African mammals shake the phylogenetic tree.}, journal = {Nature}, volume = {388}, number = {6637}, pages = {61-64}, doi = {10.1038/40386}, pmid = {9214502}, issn = {0028-0836}, mesh = {Africa ; Animals ; Biological Evolution ; Cell Nucleus/genetics ; Eulipotyphla/*classification ; Humans ; Mammals/*classification ; Mitochondria/genetics ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; }, abstract = {The order Insectivora, including living taxa (lipotyphlans) and archaic fossil forms, is central to the question of higher-level relationships among placental mammals. Beginning with Huxley, it has been argued that insectivores retain many primitive features and are closer to the ancestral stock of mammals than are other living groups. Nevertheless, cladistic analysis suggests that living insectivores, at least, are united by derived anatomical features. Here we analyse DNA sequences from three mitochondrial genes and two nuclear genes to examine relationships of insectivores to other mammals. The representative insectivores are not monophyletic in any of our analyses. Rather, golden moles are included in a clade that contains hyraxes, manatees, elephants, elephant shrews and aardvarks. Members of this group are of presumed African origin. This implies that there was an extensive African radiation from a single common ancestor that gave rise to ecologically divergent adaptive types. 12S ribosomal RNA transversions suggest that the base of this radiation occurred during Africa's window of isolation in the Cretaceous period before land connections were developed with Europe in the early Cenozoic era.}, }
@article {pmid9437876, year = {1997}, author = {Sahnoun, Z and Jamoussi, K and Zeghal, KM}, title = {[Free radicals and antioxidants: human physiology, pathology and therapeutic aspects].}, journal = {Therapie}, volume = {52}, number = {4}, pages = {251-270}, pmid = {9437876}, issn = {0040-5957}, mesh = {Antioxidants/*metabolism ; Free Radicals/adverse effects/*metabolism ; Humans ; Oxidative Stress ; Oxygen/metabolism ; }, abstract = {Oxygen has invaded progressively, and through the ages, an initially anaerobic world. Living organisms had to invent, in the course of evolution, diverse and ingenious defence systems, to survive the toxicity of this element, which was new for them. Strengthened by this experience over billions of years, the present superior organisms, and particularly human species, are thoroughly adapted to 21 per cent of atmospheric oxygen. Nevertheless, the equilibrium is fragile and the menace of oxygen hovers continually. This deleterious potential of oxygen is attributed to the formation, in vivo, of free radicals, a free radical being, by definition, any chemical species possessing one or several mismatched electrons. These free radicals are, in general, very active. They trigger chain reactions able to damage the different constituents of the living organism. Basic oxygen, must be pre-activated to manifest its toxicity. Such an activation can be achieved in two ways: it can be photodynamic, ending mainly in singlet oxygen, it can be reducing, followed by the formation of the anion hydrogen peroxide and of radical hydroxyl; the latter is the most reactive chemical species in the biological world. The reductive process is accelerated in the presence of transition metals, such as iron and copper, and/or specific enzymes (monoxygenase and certain oxydases). This activation takes place in different cellular compartments: mitochondria, microsomes, peroxysomes, cytoplasmic membrane. To this potential toxicity of oxygen the organism opposes different anti-oxidant defence systems. A first group works up the radical chain, inhibiting activation mechanisms. Such a group, as a consequence, warns of the initiation of radical reactions. The second group neutralizes the free radicals already formed and thus stops the chain of propagation. In this group can be found detoxifying enzymes, notably superoxide dismutase and catalase, producing jointly peroxidases, particularly peroxidase glutathions. Such enzymes for the most part have trace elements as cofactors. In this second group can also be found various molecules which act like 'substrate suicide', or as an anti-oxidant shield. Among these molecules, some can act in the lipidic phase, such as tocopherols, carotenoïds and ubiquinones. Other molecules which are lipophobic, mainly ascorbic acid and uric acid, are active in a hydrated environment. In the case of a weakening of such an antioxidant defence or excess production of radicals, a state of oxidative stress occurs. Uncontrolled, these radicals will damage different biological targets: lipids, DNA, proteins. Disturbances of cellular metabolism will occur, unless corrective defences intervene. The identification of these radical phenomena is an obligatory stage. But because of the very short life span of free radicals, identification poses a real analytical problem. However, three approaches are possible: identification of free radicals, either directly by means of paramagnetic electron resonance, or indirectly by identifying some more stable intermediates. evaluation of the traces of radical attack on biological molecules, for example by high performance liquid chromatography, gas-liquid chromatography, colorimetric tests, estimation of the antioxidant status, for example by colorimetric tests, immunoenzymatic methods, high performance liquid chromatography.}, }
@article {pmid9377224, year = {1997}, author = {Wang, Y and Toury, R and Hauchecorne, M and Balmain, N}, title = {Expression of Bcl-2 protein in the epiphyseal plate cartilage and trabecular bone of growing rats.}, journal = {Histochemistry and cell biology}, volume = {108}, number = {1}, pages = {45-55}, doi = {10.1007/s004180050145}, pmid = {9377224}, issn = {0948-6143}, mesh = {Animals ; Apoptosis/physiology ; Chondrocytes/*metabolism ; Growth Plate/cytology/growth &amp; development/*metabolism ; Immunohistochemistry ; Proto-Oncogene Proteins c-bcl-2/*biosynthesis ; Rats ; Rats, Sprague-Dawley ; Tibia/growth &amp; development/*metabolism ; }, abstract = {The protooncogene protein, Bcl-2, protects cells from apoptosis and ensures their survival in vitro by inhibiting the action of the apoptosis-inducer, Bax. Its expression in proliferative and long-lived cells in vivo also indicates that it protects against cell death. The chondrocytes of the epiphyseal plate cartilage undergo a series of maturation steps and deposit mineral in the cartilage matrix before dying. The possibility that Bcl-2 helps protect chondrocytes until mineral deposition is completed was investigated by determining the distribution of Bcl-2 immunoreactivity in the epiphyseal plate cartilage of growing rats and its subcellular localization, using a specific antibody. The involvement of Bax in the triggering of chondrocyte death was checked by immunocytochemistry. Bcl-2 expression in the osteoblasts and the final result of their evolution, the osteocytes, was also examined in trabecular bone. Bcl-2 immunoreactivity was non-uniformly distributed throughout the epiphyseal cartilage. It was maximal in proliferative chondrocytes, decreased in mature chondrocytes, and low in hypertrophic chondrocytes, whereas there was Bax immunoreactivity in all chondrocytes examined. Immunolabeling was intense in osteoblasts but considerably lower in fully differentiated osteocytes. Bcl-2 immunoreactivity was mainly in the cytoplasm of chondrocytes, osteoblasts, and early osteocytes; the nuclei appeared clear. The subcellular distribution of Bcl-2 immunolabeling in chondrocytes, revealed by gold particles in the electron microscope, showed that gold particles were frequently concentrated in the mitochondria in all the cartilage zones and lay mainly within the organelles, not at their periphery. The endoplasmic reticulum contained moderate immunoreactivity and there were few gold particles in the cytoplasm and nuclei. The number of gold particles decreased in all the subcellular compartments from proliferative to hypertrophic chondrocytes. In contrast, Bax immunoreactivity changed little during chondrocyte terminal evolution, and its subcellular distribution mirrored that of Bcl-2. These immunocytochemical data indicate that Bcl-2 helps maintain chondrocytes and osteoblasts until their terminal maturation.}, }
@article {pmid9315444, year = {1997}, author = {Kirkwood, TB and Kowald, A}, title = {Network theory of aging.}, journal = {Experimental gerontology}, volume = {32}, number = {4-5}, pages = {395-399}, doi = {10.1016/s0531-5565(96)00171-4}, pmid = {9315444}, issn = {0531-5565}, mesh = {Aging/*physiology ; Animals ; Antioxidants/metabolism ; *Biological Evolution ; Computer Simulation ; Free Radical Scavengers/metabolism ; Free Radicals/metabolism ; Humans ; Mitochondria/physiology ; *Models, Biological ; Proteins/physiology ; }, abstract = {Evolution theory indicates that investment in mechanisms of somatic maintenance and repair is likely to be limited, suggesting that aging may result from the accumulation of unrepaired somatic defects. An important corollary of this hypothesis is that multiple mechanisms of aging operate in parallel. We describe a recently developed "network theory of aging" that integrates the contributions of defective mitochondria, aberrant proteins, and free radicals in the aging process and that includes the protective effects of antioxidant enzymes and proteolytic scavengers. Possibilities for further extension of the theory and its role in prediction and simulation of experimental results are discussed.}, }
@article {pmid9243185, year = {1997}, author = {Häusler, T and Stierhof, YD and Blattner, J and Clayton, C}, title = {Conservation of mitochondrial targeting sequence function in mitochondrial and hydrogenosomal proteins from the early-branching eukaryotes Crithidia, Trypanosoma and Trichomonas.}, journal = {European journal of cell biology}, volume = {73}, number = {3}, pages = {240-251}, pmid = {9243185}, issn = {0171-9335}, mesh = {Amino Acid Sequence ; Animals ; Biological Transport/genetics ; *Conserved Sequence ; Crithidia/*genetics/ultrastructure ; DNA, Fungal/analysis ; DNA, Protozoan/analysis ; Microscopy, Electron ; Mitochondria/metabolism/ultrastructure ; Molecular Sequence Data ; Mutagenesis/physiology ; Protein Sorting Signals/*genetics/metabolism ; Trichomonas vaginalis/*genetics/ultrastructure ; Trypanosoma/*genetics/ultrastructure ; Yeasts/genetics ; }, abstract = {Kinetoplastid protozoa are the earliest-branching eukaryotes to possess a true mitochondrion. This organelle is host to a variety of intriguing and unique features, including RNA editing. We examined the characteristics of protein import into mitochondria of Trypanosoma brucei. Dihydrofolate reductase (DHFR) carrying a yeast mitochondrial targeting signal was correctly translocated into trypanosome mitochondria in vivo, as were DHFR fusion proteins bearing two unusually short (7-9 amino acids) presequences from trypanosomatids. The short trypanosomal targeting signals were functional in Saccharomyces cerevisiae as well, but their targeting efficiency was lower and processing was absent. Trichomonads branched even earlier than kinetoplastids in eukaryotic evolution and contain energy-generating organelles called hydrogenosomes. The origin of hydrogenosomes has been controversial, but most evidence suggests that they are related to mitochondria. Putative hydrogenosomal targeting signals from Trichomonas vaginalis are short (5-12 amino acids). Three such sequences were capable of targeting a passenger protein to mitochondria both in yeast and in trypanosomes, and one of the hydrogenosomal presequences was efficiently processed in both organisms. These findings suggest a resemblance between the import machineries of mitochondria and hydrogenosomes.}, }
@article {pmid9241672, year = {1997}, author = {Suter, L and Bobadilla, M and Koch, E and Bechter, R}, title = {Flow cytometric evaluation of the effects of doxorubicin on rat spermatogenesis.}, journal = {Reproductive toxicology (Elmsford, N.Y.)}, volume = {11}, number = {4}, pages = {521-531}, doi = {10.1016/s0890-6238(97)00019-1}, pmid = {9241672}, issn = {0890-6238}, mesh = {Animals ; Antibiotics, Antineoplastic/*toxicity ; Body Weight/drug effects ; Doxorubicin/*toxicity ; Flow Cytometry ; Male ; Organ Size/drug effects ; Rats ; Rats, Wistar ; Sperm Count/drug effects ; Spermatogenesis/*drug effects ; Testis/drug effects ; }, abstract = {Histopathologic examination of testicular tissue allows testicular impairment to be investigated. As an alternative to histopathology, flow cytometry (FCM) using a triple staining technique that combines DNA-ploidy with mitochondria stainability and vimentin immunostaining has also been utilized to evaluate testicular damage. In this article we evaluate the effects on spermatogenesis after acute exposure of rats to doxorubicin. Testicular cell suspensions of treated and control animals were analyzed by FCM. This allows several cell types to be identified and quantified, giving a control pattern. Deviations from this control pattern are considered as an indication of testicular damage. Doxorubicin produced a depletion of spermatogonia as early as 3 d after treatment. This effect could be followed through the temporal evolution of spermatogenesis. Comparable results were obtained by histopathology. The presented results show that FCM is a suitable and sensitive method for the detection of testicular damage. The advantages of FCM over other techniques include its rapidity and objectivity.}, }
@article {pmid9214748, year = {1997}, author = {Härlid, A and Janke, A and Arnason, U}, title = {The mtDNA sequence of the ostrich and the divergence between paleognathous and neognathous birds.}, journal = {Molecular biology and evolution}, volume = {14}, number = {7}, pages = {754-761}, doi = {10.1093/oxfordjournals.molbev.a025815}, pmid = {9214748}, issn = {0737-4038}, mesh = {Animals ; Base Composition ; Base Sequence ; Birds/*genetics ; Chickens/*genetics ; DNA, Mitochondrial/*genetics ; Genes ; Mitochondria, Heart ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer/chemistry/genetics ; Regulatory Sequences, Nucleic Acid ; }, abstract = {The complete mitochondrial DNA (mtDNA) molecule of the ostrich, Struthio camelus, was sequenced. The size of the molecule is 16,591 nucleotides. Since the ostrich represents the paleognathous birds, comparison with the mtDNA of the neognathous chicken, the only avian species reported so far in databases, made it possible to identify common and, probably, general avian mtDNA characteristics. Relative to other vertebrates, the avian NADH6 and tRNA-Glu genes are positioned upstream of the control region rather than the cytochrome b gene. The NADH3 gene of the ostrich is terminated by a stop codon at position 207. Thus, the gene is about 140 nucleotides shorter than in other vertebrates. The sequence for L-strand origin of replication is missing in both birds, and four transfer RNA genes of the two avian mtDNAs deviate from common characteristics of tRNAs of vertebrate mtDNAs by having an adenine (and not a thymidine) at position 8. Due to the absence of suitable fossils, most paleontological datings of avian divergences are conjectural. Molecular dating of the divergence between the ostrich and the chicken indicates that these two avian lineages separated 80-90 MYA. Phylogenetic analysis of complete cytochrome b genes of six avian orders showed that Passeriformes represent the earliest divergence among recent birds, contradicting the commonly accepted notion of a basal position of the Palaeognathae among recent birds.}, }
@article {pmid9171096, year = {1997}, author = {Gelfand, MS and Koonin, EV}, title = {Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes.}, journal = {Nucleic acids research}, volume = {25}, number = {12}, pages = {2430-2439}, doi = {10.1093/nar/25.12.2430}, pmid = {9171096}, issn = {0305-1048}, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Base Sequence ; Chloroplasts/metabolism ; Cyanobacteria/genetics ; *Genome, Bacterial ; Haemophilus influenzae/genetics ; Mathematics ; Methanococcus/genetics ; Mitochondria/metabolism ; *Models, Genetic ; Mycoplasma/genetics ; Organelles ; }, abstract = {Short palindromic sequences (4, 5 and 6 bp palindromes) are avoided at a statistically significant level in the genomes of several bacteria, including the completely sequenced Haemophilus influenzae and Synechocystis sp. genomes and in the complete genome of the archaeon Methanococcus jannaschii. In contrast, there is only moderate avoidance of palindromes in the small genome of the bacterium Mycoplasma genitalium and no detectable avoidance in the genomes of chloroplasts and mitochondria. The sites for type II restriction-modification enzymes detected in the given species tend to be among the most avoided palindromes in a particular genome, indicating a direct connection between the avoidance of short oligonucleotide words and restriction-modification systems with the respective specificity. Palindromes corresponding to sites for restriction enzymes from other species are also avoided, albeit less significantly, suggesting that in the course of evolution bacterial DNA has been exposed to a wide spectrum of restriction enzymes, probably as the result of lateral transfer mediated by mobile genetic elements, such as plasmids and prophages. Palindromic words appear to accumulate in DNA once it becomes isolated from restriction-modification systems, as demonstrated by the case of organellar genomes. By combining these observations with protein sequence analysis, we show that the most avoided 4-palindrome and the most avoided 6-palindrome in the archaeon M.jannaschii are likely to be recognition sites for two novel restriction-modification systems.}, }
@article {pmid9171081, year = {1997}, author = {Weihe, A and Hedtke, B and Börner, T}, title = {Cloning and characterization of a cDNA encoding a bacteriophage-type RNA polymerase from the higher plant Chenopodium album.}, journal = {Nucleic acids research}, volume = {25}, number = {12}, pages = {2319-2325}, pmid = {9171081}, issn = {0305-1048}, mesh = {Amino Acid Sequence ; Bacteriophages/*enzymology ; Base Sequence ; Cells, Cultured ; Cloning, Molecular ; Conserved Sequence ; DNA Primers ; DNA, Complementary ; DNA-Directed RNA Polymerases/*biosynthesis/*chemistry ; Evolution, Molecular ; Mitochondria/enzymology ; Molecular Sequence Data ; Molecular Weight ; Neurospora crassa/enzymology ; Phylogeny ; Plants/*enzymology ; Polymerase Chain Reaction ; RNA/biosynthesis ; RNA, Mitochondrial ; Recombinant Proteins/biosynthesis/chemistry ; Saccharomyces cerevisiae/enzymology ; Sequence Alignment ; Sequence Homology, Amino Acid ; Transcription, Genetic ; }, abstract = {We have cloned a full-length cDNA from the higher plant Chenopodium album coding for a single subunit bacteriophage-type RNA polymerase. The cDNA isolated from an actively growing cell suspension culture recognized a 3.8 kb transcript on Northern blots. The open reading frame comprises 987 amino acids with a predicted molecular mass of 112 kDa. A comparison of the protein sequence with those of the two known fungal mitochondrial RNA polymerases, from Saccharomyces cerevisiae and Neurospora crassa , reveals extensive homology between the three enzymes. with complete conservation of all catalytically essential amino acids. The putative mitochondrial RNA polymerase from C.album , as well as homologous sequences from rice and barley, which have been partially cloned, lack two catalytically non-essential regions of up to 176 amino acids near the C-terminus present in the two fungal mitochondrial RNA polymerases. The extreme N-terminus of the cloned C.album RNA polymerase displays features of a potential mitochondrial transit sequence. In phylogenetic trees constructed to compare the evolutionary relationships between the different single subunit RNA polymerases the C.album sequence forms a subgroup together with the S.cerevisiae and the N.crassa mitochondrial RNA polymerases, well separating from both bacteriophage enzymes and plasmid-encoded RNA polymerases found in mitochondria of many fungi and some higher plants.}, }
@article {pmid9202414, year = {1997}, author = {Hill, KA and Singh, SM}, title = {The evolution of species-type specificity in the global DNA sequence organization of mitochondrial genomes.}, journal = {Genome}, volume = {40}, number = {3}, pages = {342-356}, doi = {10.1139/g97-047}, pmid = {9202414}, issn = {0831-2796}, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; Eukaryota/genetics ; Genome ; Humans ; Invertebrates/*genetics ; *Models, Biological ; Molecular Sequence Data ; Phylogeny ; Plants/genetics ; Species Specificity ; Vertebrates/*genetics ; Yeasts/genetics ; }, abstract = {Prokaryote genomes and nuclear genomes of eukaryotes have a global DNA sequence organization that is species type specific, determined primarily by nearest-neighbor nucleotide associations, and independent of gene function and sequence length. The determinants of such a global structure have remained largely uncharacterized. The monophyletic and endosymbiotic origin of mitochondria permit examination of the influence of evolutionary time and host species type. Different global structures were seen among (i) protozoan and plant (ii) fungal, (iii) algal (iv) nematode, (v) echinoderm, (vi) insect, and (vii) vertebrate species followed examination of 28 complete mitochondrial genomes using chaos representation and measure of short-sequence representation. The mitochondrial genomes have biases in single-nucleotide and dinucleotide representation, specifically, an overrepresentation of A and T nucleotides and CC/GG and AG/CT dinucleotides and a deficiency of CG dinucleotides, in all but one genome. Dinucleotide representation is similar among (i) mitochondrial genomes of more closely related species; (ii) mitochondrial genomes and the Mycoplasma capricolum genome, a proposed progenitor of mitochondrial genomes; and (iii) mitochondrial genomes of diverse species, more so than between the mitochondrial and the nuclear genome of the same or a closely related species. It is hypothesized that sufficient evolutionary time has permitted host-specific constraints to affect nuclear and mitochondrial genomes and that different species type specific constraints influence nuclear and mitochondrial genome global structure.}, }
@article {pmid9199249, year = {1997}, author = {Grossman, LI and Lomax, MI}, title = {Nuclear genes for cytochrome c oxidase.}, journal = {Biochimica et biophysica acta}, volume = {1352}, number = {2}, pages = {174-192}, doi = {10.1016/s0167-4781(97)00025-0}, pmid = {9199249}, issn = {0006-3002}, support = {GM48517/GM/NIGMS NIH HHS/United States ; GM48800/GM/NIGMS NIH HHS/United States ; }, mesh = {Aging ; Animals ; Cell Nucleus/*enzymology ; Electron Transport Complex IV/chemistry/*genetics/metabolism ; Evolution, Molecular ; Gene Expression Regulation ; Humans ; Mitochondria/enzymology ; Oxidative Phosphorylation ; Protein Biosynthesis ; Species Specificity ; Transcription, Genetic ; }, }
@article {pmid9192996, year = {1997}, author = {Nair, S and Ribas de Pouplana, L and Houman, F and Avruch, A and Shen, X and Schimmel, P}, title = {Species-specific tRNA recognition in relation to tRNA synthetase contact residues.}, journal = {Journal of molecular biology}, volume = {269}, number = {1}, pages = {1-9}, doi = {10.1006/jmbi.1997.1025}, pmid = {9192996}, issn = {0022-2836}, support = {GM23562/GM/NIGMS NIH HHS/United States ; }, mesh = {Acylation ; Amino Acid Sequence ; Binding Sites ; Escherichia coli/enzymology ; Geobacillus stearothermophilus/enzymology ; Mitochondria/metabolism ; Molecular Sequence Data ; Multigene Family ; Mycobacterium tuberculosis/*enzymology ; Neurospora crassa/enzymology ; RNA, Transfer/*metabolism ; RNA, Transfer, Tyr/metabolism ; Recombinant Proteins/chemistry/genetics/metabolism ; Saccharomyces cerevisiae/*enzymology/growth &amp; development ; Sequence Alignment ; Sequence Analysis ; Sequence Homology, Amino Acid ; Species Specificity ; Tyrosine-tRNA Ligase/chemistry/*genetics/*metabolism ; }, abstract = {In spite of variations in the sequences of tRNAs, the genetic code (anticodon trinucleotides) is conserved in evolution. However, non-anticodon nucleotides which are species specific are known to prevent a given tRNA from functioning in all organisms. Conversely, species-specific tRNA contact residues in synthetases should also prevent cross-species acylation in a predictable way. To address this question, we investigated the relatively small tyrosine tRNA synthetase where contacts of Escherichia coli tRNA(Tyr) with the alpha2 dimeric protein have been localized by others to four specific sequence clusters on the three-dimensional structure of the Bacillus stearothermophilus enzyme. We used specific functional tests with a previously not-sequenced and not-characterized Mycobacterium tuberculosis enzyme and showed that it demonstrates species-specific aminoacylation in vivo and in vitro. The specificity observed fits exactly with the presence of the clusters characteristic of those established as important for recognition of E. coli tRNA. Conversely, we noted that a recent analysis of the tyrosine enzyme from the eukaryote pathogen Pneumocystis carinii showed just the opposite species specificity of tRNA recognition. According to our alignments, the sequences of the clusters diverge substantially from those seen with the M. tuberculosis, B. stearothermophilus and other enzymes. Thus, the presence or absence of species-specific residues in tRNA synthetases correlates in both directions with cross-species aminoacylation phenotypes, without reference to the associated tRNA sequences. We suggest that this kind of analysis can identify those synthetase-tRNA covariations which are needed to preserve the genetic code. These co-variations might be exploited to develop novel antibiotics against pathogens such as M. tuberculosis and P. carinii.}, }
@article {pmid9168110, year = {1997}, author = {Lang, BF and Burger, G and O'Kelly, CJ and Cedergren, R and Golding, GB and Lemieux, C and Sankoff, D and Turmel, M and Gray, MW}, title = {An ancestral mitochondrial DNA resembling a eubacterial genome in miniature.}, journal = {Nature}, volume = {387}, number = {6632}, pages = {493-497}, doi = {10.1038/387493a0}, pmid = {9168110}, issn = {0028-0836}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*genetics ; DNA, Protozoan/*genetics ; Eukaryota/*genetics ; Evolution, Molecular ; Genome, Bacterial ; Gram-Negative Bacteria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protozoan Proteins/genetics ; RNA, Protozoan ; RNA, Transfer/genetics ; }, abstract = {Mitochondria, organelles specialized in energy conservation reactions in eukaryotic cells, have evolved from eubacteria-like endosymbionts whose closest known relatives are the rickettsial group of alpha-proteobacteria. Because characterized mitochondrial genomes vary markedly in structure, it has been impossible to infer from them the initial form of the proto-mitochondrial genome. This would require the identification of minimally derived mitochondrial DNAs that better reflect the ancestral state. Here we describe such a primitive mitochondrial genome, in the freshwater protozoon Reclinomonas americana. This protist displays ultrastructural characteristics that ally it with the retortamonads, a protozoan group that lacks mitochondria. R. americana mtDNA (69,034 base pairs) contains the largest collection of genes (97) so far identified in any mtDNA, including genes for 5S ribosomal RNA, the RNA component of RNase P, and at least 18 proteins not previously known to be encoded in mitochondria. Most surprising are four genes specifying a multisubunit, eubacterial-type RNA polymerase. Features of gene content together with eubacterial characteristics of genome organization and expression not found before in mitochondrial genomes indicate that R. americana mtDNA more closely resembles the ancestral proto-mitochondrial genome than any other mtDNA investigated to date.}, }
@article {pmid9159140, year = {1997}, author = {Laroche, J and Li, P and Maggia, L and Bousquet, J}, title = {Molecular evolution of angiosperm mitochondrial introns and exons.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {94}, number = {11}, pages = {5722-5727}, pmid = {9159140}, issn = {0027-8424}, mesh = {DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; *Evolution, Molecular ; *Exons ; Genes, Plant ; *Introns ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; Plants/classification/*genetics ; }, abstract = {Numbers of substitutions per site for 15 protein-coding genes and six introns of the plant mitochondria were estimated to compare modes and tempos of evolution between exons and introns, and numbers of insertions-deletions per site also were investigated in introns. Intra-gene homogeneity of numbers of substitutions per site was assessed further among different taxa and between mitochondrial and nuclear paralogs translocated from the mitochondrial genome. Gene-to-gene differences in numbers of substitutions per site were found to be higher for nonsynonymous than synonymous sites, and this could be due to differential selection if mutation rate is assumed constant for the genome. Some mitochondrial genes have evolved as fast as chloroplast genes, thus faster than previously thought. For coxI, relative rate tests showed that woody taxa evolved slower than annuals at synonymous sites. Generation time, population size, and speciation rate are likely factors involved in this rate heterogeneity. Introns were less constrained than their adjacent exons for both overall numbers of substitutions per site and indels, but, on average, overall numbers of substitutions per site for introns were similar to numbers of synonymous substitutions per site for exons. Correlations were generally high between numbers of substitutions and numbers of indels per site for the same intron. Mitochondrial genes transferred to the nucleus had an accelerated rate of substitution per site, which was most significant at synonymous sites. These differences between paralogs in two different genomes are likely the result of different mutation rates.}, }
@article {pmid9187356, year = {1997}, author = {van der Giezen, M and Sjollema, KA and Artz, RR and Alkema, W and Prins, RA}, title = {Hydrogenosomes in the anaerobic fungus Neocallimastix frontalis have a double membrane but lack an associated organelle genome.}, journal = {FEBS letters}, volume = {408}, number = {2}, pages = {147-150}, doi = {10.1016/s0014-5793(97)00409-2}, pmid = {9187356}, issn = {0014-5793}, mesh = {Biological Evolution ; DNA, Fungal/analysis ; Fungi/metabolism/*ultrastructure ; Hydrogen/*metabolism ; Intracellular Membranes/ultrastructure ; Lipid Bilayers ; Microscopy, Electron ; Microscopy, Immunoelectron ; Mitochondria/genetics/ultrastructure ; Organelles/genetics/metabolism/*ultrastructure ; Saccharomyces cerevisiae/ultrastructure ; }, abstract = {The presence of hydrogenosomes in phylogenetically distinct anaerobic eukaryotes implies that they have been acquired independently, and previously reported differences in ultrastructure among taxa have suggested that some hydrogenosomes have different origins. Of particular interest are reports that Neocallimastix frontalis hydrogenosomes resemble microbodies in possessing a single membrane, in contrast to those in ciliates and trichomonads which have two and thus resemble mitochondria. In this investigation we have clearly demonstrated that N. frontalis hydrogenosomes possess two, rather than one, closely apposed membranes and in some preparations cristae-like structures were observed. These observations have led us to reject the microbody hypothesis and provide some indirect support for a possible mitochondrion origin as proposed for other hydrogenosomes. N. frontalis hydrogenosomes were shown to lack an associated genome as previously demonstrated for trichomonad hydrogenosomes. This might be explained by assuming that a mitochondrial genome encoding proteins for aerobic function is no longer necessary for either organelle.}, }
@article {pmid9144197, year = {1997}, author = {Yeliseev, AA and Krueger, KE and Kaplan, S}, title = {A mammalian mitochondrial drug receptor functions as a bacterial "oxygen" sensor.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {94}, number = {10}, pages = {5101-5106}, pmid = {9144197}, issn = {0027-8424}, support = {GM15590/GM/NIGMS NIH HHS/United States ; MH44284/MH/NIMH NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/*chemistry/*physiology ; Biological Evolution ; Cell Membrane/physiology ; Conserved Sequence ; Intracellular Membranes/*metabolism ; Isoquinolines/metabolism/pharmacology ; Kinetics ; Ligands ; Mammals ; Membrane Proteins/*chemistry/*physiology ; Mitochondria/*metabolism ; Molecular Sequence Data ; Oxygen/*metabolism ; Rats ; Receptors, GABA-A/biosynthesis/*chemistry/*physiology ; Recombinant Proteins/biosynthesis/metabolism ; Rhodobacter sphaeroides/*physiology ; Sequence Homology, Amino Acid ; Transcription, Genetic/drug effects ; beta-Galactosidase/biosynthesis ; }, abstract = {The rat mitochondrial outer membrane-localized benzodiazepine receptor (MBR) was expressed in wild-type and TspO- (tryptophan-rich sensory protein) strains of the facultative photoheterotroph, Rhodobacter sphaeroides 2.4.1, and was shown to retain its structure within the bacterial outer membrane as assayed by its binding properties with a variety of MBR ligands. Functionally, it was able to substitute for TspO by negatively regulating the expression of photosynthesis genes in response to oxygen. This effect was reversed pharmacologically with the MBR ligand PK11195. These results suggest a close evolutionary and functional relationship between the bacterial TspO and the MBR. This relationship provides further support for the origin of the mammalian mitochondrion from a "photosynthetic" precursor. Finally, these findings provide novel insights into the physiological role that has been obscure for the MBR in situ.}, }
@article {pmid9175861, year = {1997}, author = {Schneider, R and Brors, B and Massow, M and Weiss, H}, title = {Mitochondrial fatty acid synthesis: a relic of endosymbiontic origin and a specialized means for respiration.}, journal = {FEBS letters}, volume = {407}, number = {3}, pages = {249-252}, doi = {10.1016/s0014-5793(97)00360-8}, pmid = {9175861}, issn = {0014-5793}, mesh = {3-Oxoacyl-(Acyl-Carrier-Protein) Synthase/genetics/metabolism ; Acyl Carrier Protein/genetics/metabolism ; Animals ; Electron Transport Complex I ; Fatty Acids/*biosynthesis ; Humans ; Mitochondria/genetics/*metabolism ; Molecular Sequence Data ; NADH Dehydrogenase/metabolism ; NADH, NADPH Oxidoreductases/metabolism ; Oxygen Consumption ; Phospholipids/metabolism ; Phylogeny ; Symbiosis ; }, abstract = {Genes that encode mitochondrial homologues to the bacterial enzymes of fatty acid synthesis were found in various eukaryotic species. Inactivation of these genes leads to a disturbed mitochondrial respiration and an increase in mitochondrial lysophospholipids. We postulate that there is a mitochondrial biosynthetic system providing fatty acids for phospholipid repair. The mitochondrial acyl carrier protein may also play another role, supporting the formation of the respiratory NADH:ubiquinone oxidoreductase.}, }
@article {pmid9178508, year = {1997}, author = {el Moualij, B and Duyckaerts, C and Lamotte-Brasseur, J and Sluse, FE}, title = {Phylogenetic classification of the mitochondrial carrier family of Saccharomyces cerevisiae.}, journal = {Yeast (Chichester, England)}, volume = {13}, number = {6}, pages = {573-581}, doi = {10.1002/(SICI)1097-0061(199705)13:6&lt;573::AID-YEA107&gt;3.0.CO;2-I}, pmid = {9178508}, issn = {0749-503X}, mesh = {Amino Acid Sequence ; Base Sequence ; Carrier Proteins/chemistry/*classification/genetics ; DNA, Fungal ; Fungal Proteins/chemistry/*classification/genetics ; Mitochondria/chemistry ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Protein Structure, Secondary ; Saccharomyces cerevisiae/*chemistry ; }, abstract = {The screening of the open reading frames identified in the whole yeast genome has allowed us to discover 34 proteins belonging to the mitochondrial carrier family. By phylogenetic study, they can be divided into 27 subfamilies including ADP/ATP, phosphate and citrate carriers, putative oxoglutarate and GDC carriers and 22 new subfamilies. Topology predictions using the 'positive inside rule' approach have shown that the yeast carriers are similarly oriented with both extremities exposed to the cytosol. In each subfamily, a strict conservation of the charged residues in the six transmembrane alpha-helices is observed, suggesting a functional role for these residues and the existence of 27 functionally distinct carriers.}, }
@article {pmid9162109, year = {1997}, author = {Paquin, B and Laforest, MJ and Forget, L and Roewer, I and Wang, Z and Longcore, J and Lang, BF}, title = {The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression.}, journal = {Current genetics}, volume = {31}, number = {5}, pages = {380-395}, doi = {10.1007/s002940050220}, pmid = {9162109}, issn = {0172-8083}, mesh = {Base Sequence ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Gene Expression Regulation, Fungal/*physiology ; Genetic Code ; *Genome, Fungal ; Introns ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA Editing ; Ribosomal Proteins/genetics ; }, abstract = {The goal of the fungal mitochondrial genome project (FMGP) is to sequence complete mitochondrial genomes for a representative sample of the major fungal lineages; to analyze the genome structure, gene content, and conserved sequence elements of these sequences; and to study the evolution of gene expression in fungal mitochondria. By using our new sequence data for evolutionary studies, we were able to construct phylogenetic trees that provide further solid evidence that animals and fungi share a common ancestor to the exclusion of chlorophytes and protists. With a database comprising multiple mitochondrial gene sequences, the level of support for our mitochondrial phylogenies is unprecedented, in comparison to trees inferred with nuclear ribosomal RNA sequences. We also found several new molecular features in the mitochondrial genomes of lower fungi, including: (1) tRNA editing, which is the same type as that found in the mitochondria of the amoeboid protozoan Acanthamoeba castellanii; (2) two novel types of putative mobile DNA elements, one encoding a site-specific endonuclease that confers mobility on the element, and the other constituting a class of highly compact, structured elements; and (3) a large number of introns, which provide insights into intron origins and evolution. Here, we present an overview of these results, and discuss examples of the diversity of structures found in the fungal mitochondrial genome.}, }
@article {pmid9159928, year = {1997}, author = {Nedelcu, AM}, title = {Fragmented and scrambled mitochondrial ribosomal RNA coding regions among green algae: a model for their origin and evolution.}, journal = {Molecular biology and evolution}, volume = {14}, number = {5}, pages = {506-517}, doi = {10.1093/oxfordjournals.molbev.a025787}, pmid = {9159928}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; Chlamydomonas/genetics ; Chlorophyta/classification/*genetics ; *Evolution, Molecular ; Genes, Protozoan ; Mitochondria/*genetics ; *Models, Genetic ; Molecular Sequence Data ; Oligonucleotide Probes/genetics ; Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal/*genetics ; Recombination, Genetic ; Species Specificity ; }, abstract = {Mitochondrial ribosomal RNA coding regions in the only three green algal taxa investigated to date are fundamentally different in that they are continuous in Prototheca wickerhamii, but highly fragmented and scrambled in Chlamydomonas reinhardtii and Chlamydomonas eugametos. To gain more insight into the mode of evolution of fragmented and scrambled mitochondrial ribosomal RNA (rRNA) genes within the green algal group, this work (1) provides additional information on fragmentation patterns of mitochondrial small- and large-subunit (SSU and LSU) rRNAs that strongly supports the concept of a gradual increase in the extent of discontinuity of mitochondrial rRNAs among chlorophycean green algae and (2) reports the first example of fragmented and scrambled mitochondrial LSU rRNA coding regions in a green algal taxon outside the Chlamydomonas group. The present study (1) suggests that the scrambling of the mitochondrial rRNA coding regions may have occurred early in the evolution of fragmented and scrambled mitochondrial rRNA genes within the chlorophycean green algal group, most likely in parallel with the fragmentation events, (2) proposes recombination as a possible mechanism involved in the evolution of these mitochondrial rRNA genes, and (3) presents a hypothetical pathway for converting continuous mitochondrial rRNA genes into the highly fragmented and scrambled rRNA coding regions of Chlamydomonas through a series of recombinatorial events between short repeated sequences.}, }
@article {pmid9156326, year = {1997}, author = {Giannattasio, S and Jurgelevicius, V and Lattanzio, P and Cimbalistienè, L and Marra, E and Kucinskas, V}, title = {Phenylketonuria mutations and linked haplotypes in the Lithuanian population: origin of the most common R408W mutation.}, journal = {Human heredity}, volume = {47}, number = {3}, pages = {155-160}, doi = {10.1159/000154403}, pmid = {9156326}, issn = {0001-5652}, mesh = {Evolution, Molecular ; Founder Effect ; *Haplotypes ; Humans ; Lithuania ; Minisatellite Repeats/genetics ; Mutation/*genetics ; Phenylalanine Hydroxylase/genetics ; Phenylketonurias/ethnology/*genetics ; Repetitive Sequences, Nucleic Acid/genetics ; }, abstract = {A genealogical study was performed in Lithuanian phenylketonuria (PKU) families with the aim of tracing the origins of the R408W/haplotype 2/VNTR3 allele. The relative frequency of six phenylalanine hydroxylase (PAH) mutations (R408W, R158Q, R261Q, G272X, IVS10nt-11g --> a, and IVS12nt1g --> a) common in Eastern European populations and their association with variable number of tandem repeat (VNTR) and short tandem repeat (STR) sites in the PAH gene were examined in 130 PKU Lithuanian chromosomes, including 95 of Baltic, 28 of Slavonic and 7 of unknown origin. R408W was found to be the most frequent (70%) mutation in both Balts or Slavonians with a uniform frequency distribution. No statistically significant differences in the frequency distribution of the other mutations analysed were found. In Balts and Slavonians, the R408W mutation is strongly associated with the three-copy VNTR and the 240-bp STR allele. The frequency of this association is 68% in both ethnic groups. The genealogical data provided in this paper indicate that the most common R408W/VNTR3/STR240 allele arose in ancient times possibly among pre-Indo-Europeans and suggest that the high frequency of the R408W mutation and associated minihaplotype in Balts of Lithuania is due to a founder effect.}, }
@article {pmid9115381, year = {1997}, author = {Sogin, ML}, title = {Organelle origins: energy-producing symbionts in early eukaryotes?.}, journal = {Current biology : CB}, volume = {7}, number = {5}, pages = {R315-7}, doi = {10.1016/s0960-9822(06)00147-3}, pmid = {9115381}, issn = {0960-9822}, mesh = {Animals ; *Biological Evolution ; *Energy Metabolism ; Eukaryotic Cells ; Genes, Protozoan ; Mitochondria/physiology ; Organelles/*physiology ; Symbiosis ; Trichomonas vaginalis/genetics/*physiology/ultrastructure ; }, abstract = {The discovery that Trichomonas vaginalis, an early diverging protist that lacks mitochondria but has energy-producing hydrogenosomes, makes bacterial-like heat shock proteins suggests that symbionts ancestral to mitochondria and hydrogenosomes were present at early stages of eukaryote evolution.}, }
@article {pmid9099578, year = {1997}, author = {Zhang, DX and Hewitt, GM}, title = {Assessment of the universality and utility of a set of conserved mitochondrial COI primers in insects.}, journal = {Insect molecular biology}, volume = {6}, number = {2}, pages = {143-150}, doi = {10.1111/j.1365-2583.1997.tb00082.x}, pmid = {9099578}, issn = {0962-1075}, mesh = {*Conserved Sequence ; DNA Primers ; *DNA, Mitochondrial ; Electron Transport Complex IV/*genetics ; Insect Proteins/*genetics ; Mitochondria/*enzymology ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {A set of mitochondrial COI primers has been studied by genomic PCR and many primer combinations shown to work universally well across Insecta. They are able to amplify various amplicons with different variability which enables the selection of a particular amplicon as a suitable DNA marker for a project. The potential usefulness of different amplicons is examined, with analysis on published study cases employing these regions. With respect to their variability, amplicons UEA5/UEA6, UEA7/UEA8 and UEA5/UEA8 could be useful for low- to mid-level phylogenetic analysis, i.e. from species, genus to perhaps family level depending on taxa involved. UEA5/UEA6 will be too conserved for intraspecific studies. Amplicons UEA3/UEA4 and UEA9/UEA10 would be better suited to low-level phylogenetic investigations, such a analysis of relationships among closely related species and population genetic studies. However, these guidelines should not be over-generalized for the reasons given. Amplification conditions of various primer combinations, and general problems in the use of conserved PCR primers are discussed.}, }
@article {pmid9143492, year = {1997}, author = {Crnogorac-Jurcevic, T and Brown, JR and Lehrach, H and Schalkwyk, LC}, title = {Tetraodon fluviatilis, a new puffer fish model for genome studies.}, journal = {Genomics}, volume = {41}, number = {2}, pages = {177-184}, doi = {10.1006/geno.1997.4646}, pmid = {9143492}, issn = {0888-7543}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cytochrome b Group/classification/*genetics ; DNA, Complementary ; Fishes, Poisonous/classification/*genetics ; Genome ; Mitochondria ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {The puffer fish Fugu rubripes rubripes was recently introduced by S. Brenner et al. (1993, Nature 366: 265-268) as a new model for genomic studies. Due to difficulties in obtaining material from this Japanese marine puffer, we have started work on Tetraodon fluviatilis, a small, freshwater puffer fish that can be kept and bred in an aquarium. It was originally described by E. Hinegardner (1968, Am. Nat. 102(928) 517-523) as the teleost with the smallest amount of DNA per cell (0.4 pg, 380 Mb). To estimate the extent of divergence between T. fluviatilis and F. r. rubripes, part of the mitochondrial cytochrome b (cyt b) gene from both fishes was cloned and sequenced. A comparison of these two sequences indicated that F.r. rubripes and T. fluviatilis diverged approximately 18-30 million years ago, and phylogenetic analysis placed both fishes at the base of the Perciformes lineage. To facilitate and extend further the use of the puffer fish as a model for genome studies, we have constructed and characterized a T. fluviatilis cDNA library.}, }
@article {pmid9176870, year = {1997}, author = {Margaritis, I and Tessier, F and Prou, E and Marconnet, P and Marini, JF}, title = {Effects of endurance training on skeletal muscle oxidative capacities with and without selenium supplementation.}, journal = {Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS)}, volume = {11}, number = {1}, pages = {37-43}, doi = {10.1016/S0946-672X(97)80008-9}, pmid = {9176870}, issn = {0946-672X}, mesh = {Adult ; Analysis of Variance ; Creatine Kinase/metabolism ; Double-Blind Method ; Electron Transport Complex IV/metabolism ; Fluorescent Antibody Technique, Direct ; Glutathione Peroxidase/metabolism ; Humans ; Male ; Mitochondria, Muscle/enzymology ; Muscle Fibers, Skeletal/metabolism ; Muscle, Skeletal/drug effects/metabolism/*physiology ; Myosin Heavy Chains/biosynthesis ; Oxygen Consumption/*drug effects ; Physical Endurance/*physiology ; *Physical Fitness ; Placebos ; Selenium/administration &amp; dosage/*pharmacology ; Succinate Dehydrogenase/metabolism ; Vitamin E/blood ; }, abstract = {The purpose of this study was to examine the changes induced by endurance training, with or without selenium (Se) supplementation on: 1) mitochondrial activity of succinate dehydrogenase (SDH) and cytochrome c oxidase (Cyt Ox),2) the myosin heavy chain (MHC) expression in muscle fibers and 3) their association with aerobic performance. Twenty-four male students volunteered to participate in this double blind study: selenium (Sel, N = 12) vs placebo (Pla, N = 12). During a 10-wk endurance training program, the Sel group received a daily Se supplementation containing 180 micrograms of organic selenium (selenomethionine), while the Pla group received a placebo. Before (Pre) and after (Post) the program (3 sessions wk-1) an endurance exercise (Capmax) was performed in order to determine the aerobic endurance capacity assessed by the total oxygen uptake during the running test (VO2tot). All parameters of aerobic performance were increased in both groups, concomitantly to a rise in mitochondrial Cyt Ox activity. Two positive relationships were found: 1) between type I MHC and VO2tot increments (r = 0.65, P < 0.05), 2) between training volumes and VO2tot increments (r = 0.53, P < 0.05; N = 23). The training program produced an 8.2% significant increase in type I MHC (P < 0.05) while type II MHC decrease was not significant (-4.4%). Although they were almost non-existent before the program, muscle fibers which co-expressed type I and II MHC displayed a marked increase afterwards (4.9 +/- 5.7 vs 1.1 +/- 2.1%, P < 0.05). Muscle GSH-Px activity, at rest, did not respond to endurance training or Se supplementation. The results suggest that the neuromuscular system is still in an evolutive state after 10 weeks of endurance training, and that selenium supplementation has no effect on endurance training-induced adaptations.}, }
@article {pmid9136629, year = {1997}, author = {Danpure, CJ}, title = {Variable peroxisomal and mitochondrial targeting of alanine: glyoxylate aminotransferase in mammalian evolution and disease.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {19}, number = {4}, pages = {317-326}, doi = {10.1002/bies.950190409}, pmid = {9136629}, issn = {0265-9247}, mesh = {Alanine Transaminase/*metabolism ; Animals ; Biological Transport ; Catalysis ; Cytosol/enzymology ; Diet ; Dimerization ; Energy Metabolism ; Enzyme Induction ; Evolution, Molecular ; Glucose/metabolism ; Glyoxylates/metabolism ; Humans ; Hyperoxaluria/*enzymology/genetics ; Mammals/*metabolism ; Microbodies/*enzymology ; Mitochondria/*enzymology ; Polymorphism, Genetic ; Protein Sorting Signals/physiology ; Selection, Genetic ; Species Specificity ; *Transaminases ; }, abstract = {Under the putative influence of dietary selection pressure, the subcellular distribution of alanine:glyoxylate aminotransferase 1 (AGT) has changed on many occasions during the evolution of mammals. Depending on the particular species, AGT can be found either in peroxisomes or mitochondria, or in both peroxisomes and mitochondria. This variable localization depends on the differential expression of N-terminal mitochondrial and C-terminal peroxisomal targeting sequences by the use of alternative transcription and translation initiation sites. AGT is peroxisomal in most humans, but it is mistargeted to the mitochondria in a subset of patients suffering from the rare hereditary disease primary hyperoxaluria type 1. Mistargeting is due to the unlikely combination of a normally occurring polymorphism that generates a functionally weak mitochondrial targeting sequence and a disease-specific mutation which, in combination with the polymorphism, inhibits AGT dimerization. The mechanisms by which AGT can be targeted differentially to peroxisomes and/or mitochondria highlight the different molecular requirements for protein import into these two organelles.}, }
@article {pmid9108143, year = {1997}, author = {Topczewski, J and Sienko, M and Paszewski, A}, title = {Cloning and characterization of the Aspergillus nidulans cysB gene encoding cysteine synthase.}, journal = {Current genetics}, volume = {31}, number = {4}, pages = {348-356}, doi = {10.1007/s002940050215}, pmid = {9108143}, issn = {0172-8083}, mesh = {Amino Acid Sequence ; Amino Acids, Sulfur/genetics/metabolism ; Aspergillus nidulans/*genetics/*metabolism ; Base Sequence ; Cloning, Molecular ; Cysteine Synthase/*genetics/*metabolism ; DNA, Complementary/genetics ; Mitochondria/chemistry/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Messenger/genetics ; Restriction Mapping ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; }, abstract = {The cysB gene of A. nidulans was cloned by complementation of a cysB mutation. This is the first cloned eukaryotic genomic sequence coding for cysteine synthase. The gene contains one 71-bp intron and codes for a protein of 370 amino acids. Its N-terminal region has characteristic features of transit peptides, suggesting mitochondrial localisation of the enzyme. The protein shows homology with bacterial and plant cysteine synthases among which it occupies a remote phylogenetic position and apparently represents a distinct subfamily. Transcription of the cysB gene is not appreciably regulated by the concentration of methionine in the growth medium.}, }
@article {pmid9099850, year = {1997}, author = {Milon, L and Rousseau-Merck, MF and Munier, A and Erent, M and Lascu, I and Capeau, J and Lacombe, ML}, title = {nm23-H4, a new member of the family of human nm23/nucleoside diphosphate kinase genes localised on chromosome 16p13.}, journal = {Human genetics}, volume = {99}, number = {4}, pages = {550-557}, doi = {10.1007/s004390050405}, pmid = {9099850}, issn = {0340-6717}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Chromosome Mapping ; *Chromosomes, Human, Pair 16 ; DNA, Complementary ; Humans ; Molecular Sequence Data ; *Monomeric GTP-Binding Proteins ; Multigene Family ; NM23 Nucleoside Diphosphate Kinases ; Nucleoside Diphosphate Kinase D ; Nucleoside-Diphosphate Kinase/*genetics ; Phylogeny ; Sequence Homology, Amino Acid ; Transcription Factors/*genetics ; }, abstract = {A novel human nm23/nucleoside diphosphate (NDP) kinase gene, called nm23-H4, was identified by screening a human stomach cDNA library with a probe generated by amplification by reverse transcription-polymerase chain reaction. The primers were designed from publicly available database cDNA sequences selected according to their homology to the human nn23-H1 putative metastasis suppressor gene. The full-length cDNA sequence predicts a 187 amino acid protein possessing the region homologous to NDP kinases with all residues crucial for nucleotide binding and catalysis, strongly suggesting that Nm23-H4 possesses NDP kinase activity. It shares 56, 55 and 60% identity with Nm23-H1, Nm23-H2 and DR-Nm23, respectively, the other human Nm23 proteins isolated so far. Compared with these proteins, Nm23-H4 contains an additional NH2-terminal region that is rich in positively charged residues and could indicate routing to mitochondria. The nm23-H4 gene has been localised to human chromosomal band 16p13.3. The corresponding 1.2 kb mRNA is widely distributed and expressed in a tissue-dependent manner, being found at very high levels in prostate, heart, liver, small intestine and skeletal muscle tissues and in low amounts in the brain and in blood leucocytes. Nm23-H4 naturally possesses the Pro-Ser substitution equivalent to the K-pn mutation (P97S) of Drosophila.}, }
@article {pmid9098019, year = {1997}, author = {Kurose, I and Higuchi, H and Kato, S and Miura, S and Watanabe, N and Kamegaya, Y and Tomita, K and Takaishi, M and Horie, Y and Fukuda, M and Mizukami, K and Ishii, H}, title = {Oxidative stress on mitochondria and cell membrane of cultured rat hepatocytes and perfused liver exposed to ethanol.}, journal = {Gastroenterology}, volume = {112}, number = {4}, pages = {1331-1343}, doi = {10.1016/s0016-5085(97)70147-1}, pmid = {9098019}, issn = {0016-5085}, mesh = {Alcohol Dehydrogenase/antagonists &amp; inhibitors ; Animals ; Cell Membrane/metabolism ; Cells, Cultured ; Ethanol/*pharmacology ; Fomepizole ; Free Radical Scavengers ; In Vitro Techniques ; Liver/cytology/*drug effects/*metabolism ; Male ; Membrane Potentials/drug effects ; Microscopy, Confocal ; Microscopy, Fluorescence ; Mitochondria/*metabolism/physiology ; *Oxidative Stress ; Perfusion ; Permeability ; Pyrazoles/pharmacology ; Rats ; Rats, Wistar ; Thiourea/analogs &amp; derivatives/pharmacology ; }, abstract = {BACKGROUND &amp; AIMS: The precise pathogenic significance of oxidative injury in the evolution of alcohol-induced liver disease is still obscure. The present report was designed to investigate whether ethanol alters the production of active oxidants and biological activities of hepatocytes.<br><br>METHODS: The following parameters in rat hepatocytes were investigated by using fluorescence probes in vitro and ex vivo: (1) mitochondrial membrane potential and membrane permeability transition, (2) oxygen radicals generation, (3) membrane barrier function, and (4) glutathione level.<br><br>RESULTS: Ethanol (50 mmol/L) increased oxidative stress in hepatocytes and subsequently induced an increased mitochondrial permeability transition and a decreased membrane potential. These ethanol-induced alterations were attenuated by an inhibitor of alcohol dehydrogenase and an intracellular oxidant scavenger, whereas they were enhanced by diethyl maleic acid, a glutathione depletor. Ethanol plus diethyl maleic acid but not ethanol alone increased the number of hepatocytes with membrane barrier dysfunction. A continuous infusion of ethanol (50 mmol/L) increased oxidative stress and decreased mitochondrial membrane potential in the pericentral area of isolated perfused rat liver.<br><br>CONCLUSIONS: Active oxidants generated during ethanol metabolism increase mitochondrial permeability transition and modulate mitochondrial energy synthesis in hepatocytes. Reduction of glutathione level enhances mitochondrial dysfunction and impairs membrane barrier function of hepatocytes.}, }
@article {pmid9381856, year = {1997}, author = {Malikov, NG and Grachev, MA and Mertvetsov, NP}, title = {[An estimation of the time of divergence of the seals Phoca vitulina, Phoca largha and Phoca sibirica from a common ancestral species].}, journal = {Zhurnal evoliutsionnoi biokhimii i fiziologii}, volume = {33}, number = {2}, pages = {252-254}, pmid = {9381856}, issn = {0044-4529}, mesh = {Animals ; Base Sequence ; Cytochrome b Group/genetics ; DNA, Mitochondrial/genetics ; Mitochondria, Liver/genetics ; Molecular Sequence Data ; Phylogeny ; Seals, Earless/*classification/genetics ; Time Factors ; }, }
@article {pmid9190222, year = {1997}, author = {Kogan, AKh and Grachev, SV and Eliseeva, SV and Bolevich, S}, title = {[Carbon dioxide--a universal inhibitor of the generation of active oxygen forms by cells (deciphering one enigma of evolution)].}, journal = {Izvestiia Akademii nauk. Seriia biologicheskaia}, volume = {}, number = {2}, pages = {204-217}, pmid = {9190222}, issn = {1026-3470}, mesh = {Aerobiosis/drug effects ; Anaerobiosis/drug effects ; Animals ; *Biological Evolution ; Carbon Dioxide/*pharmacology ; Humans ; Leukocytes/drug effects/metabolism ; Luminescent Measurements ; Macrophages, Alveolar/drug effects/metabolism ; Male ; Mice ; Mitochondria, Liver/drug effects/metabolism ; NADPH Oxidases/antagonists &amp; inhibitors/drug effects ; Neutrophils/drug effects/metabolism ; Phagocytes/drug effects/metabolism ; Reactive Oxygen Species/*metabolism ; }, abstract = {Studies were carried out on blood phagocytes and alveolar macrophages of 96 humans, on the cells of the viscera and tissue phagocytes (liver, brain, myocardium, lungs, kidneys, stomach, and skeletal muscle), and liver mitochondria of 186 random bred white mice. Generation of the active oxygen forms was determined using different methods after direct effect of CO2 on the cells and biopsies and indirect effect of CO2 on the integral organism. The results obtained suggest that CO2 at a tension close to that observed in the blood (37.0 mm Hg) and high tensions (60 or 146 mm Hg) is a potent inhibitor of generation of the active oxygen forms by the cells and mitochondria of the human and tissues. The mechanism of CO2 effect appears to be realized, partially, through inhibition of the NADPH-oxidase activity. The results are important for deciphering of a paradox of evolution, life preservation upon appearance of oxygen in the atmosphere and succession of anaerobiosis by aerobiosis, and elucidation of some other problems of biology and medicine, as well as analysis of the global bioecological problem, such as ever increasing CO2 content in the atmosphere.}, }
@article {pmid9157643, year = {1997}, author = {Maliarchuk, BA}, title = {[MtDNA-like sequences and the coordination of the functioning of mammalian nuclear and mitochondrial genomes].}, journal = {TSitologiia i genetika}, volume = {31}, number = {2}, pages = {53-61}, pmid = {9157643}, issn = {0564-3783}, mesh = {Animals ; Biological Evolution ; Cell Nucleus/*genetics/physiology ; DNA, Mitochondrial/*genetics/physiology ; *Genome ; Mammals/*genetics ; Mitochondria/*genetics/physiology ; Repetitive Sequences, Nucleic Acid/genetics ; *Sequence Analysis, DNA ; }, abstract = {Mitochondrial DNA-like sequences in the nuclear genome of mammals are classified in two types: ontogenetic and evolutionary. Mechanisms of the transfer of DNA from mitochondria into nucleus and transformation of the ontogenetic mtDNA-like sequences to evolutionary ones are discussed. The origin of short sequences of DNA common to nuclear and mitochondrial genome and the role of these sequences in the coordination of gene expression have received much attention.}, }
@article {pmid9085155, year = {1997}, author = {Kint, A and Baran, R and Geerts, ML}, title = {The onychomatricoma: an electron microscopic study.}, journal = {Journal of cutaneous pathology}, volume = {24}, number = {3}, pages = {183-188}, doi = {10.1111/j.1600-0560.1997.tb01574.x}, pmid = {9085155}, issn = {0303-6987}, mesh = {Female ; Humans ; Male ; Middle Aged ; Nail Diseases/*pathology ; Nails/*pathology/*ultrastructure ; Neoplasms/pathology/ultrastructure ; Stromal Cells/pathology/ultrastructure ; }, abstract = {The electron microscopic findings in the onychomatricoma are described. In the proximal zone of the onychomatricoma, basal cells have various aspects, some being lacunar while others have only a limited cytoplasmic rim containing mitochondria and tonofilaments. In the parakeratotic cell columns the cells elongate and homogenized tonofilaments appear. Around the lacunae the cells are poorly differentiated and their cytoplasm is granular. It can be concluded that in an onychomatricoma the basal cells have a decreased amount of tonofilaments and desmosomes and that their evolution is not uniform. The tumour can be considered as being the result of a disturbed differentiation of nail matrix cells.}, }
@article {pmid9066800, year = {1997}, author = {Shields, DC and Wolfe, KH}, title = {Accelerated evolution of sites undergoing mRNA editing in plant mitochondria and chloroplasts.}, journal = {Molecular biology and evolution}, volume = {14}, number = {3}, pages = {344-349}, doi = {10.1093/oxfordjournals.molbev.a025768}, pmid = {9066800}, issn = {0737-4038}, mesh = {Base Sequence ; *Biological Evolution ; Chloroplasts/genetics ; Codon ; Conserved Sequence ; Genes, Plant ; Mitochondria/genetics ; Models, Genetic ; Molecular Sequence Data ; Mutagenesis ; Organelles/*genetics ; Plants/genetics ; RNA Editing/*genetics ; RNA, Messenger/*genetics ; RNA, Plant/*genetics ; Selection, Genetic ; Time Factors ; Transcription, Genetic ; }, abstract = {The selective constraints influencing mRNA editing in plant organelles are largely unknown. To investigate these, we compared patterns of editing between monocot and dicot mitochondrial mRNA. On average, 24% of sites that are edited form C to U in one species have been substituted during evolution by a genomic T in the other: this is four times the rate of evolution seen at nonedited synonymously variable C residues. A similar, but weaker trend (not statistically significant) is seen at sites edited in chloroplast mRNA. The elevated substitution rate does not appear to be a consequence of a higher mutability of the trinucleotide motif (T-C-purine) associated with editing. nor to be a result of reverse transcription from mature mRNA. Selection to replace the genomic C with a T may account for the accelerated evolution, either due to elimination of inefficient transcripts and protein products or as a consequence of the prior loss of components outside the edit site which are necessary for editing; the latter hypothesis is supported by the frequent loss of editing without genomic mutation at third codon positions. Whatever the cause, the rapid rate of evolution indicates that editing confers little selective advantage at most sites.}, }
@article {pmid9066793, year = {1997}, author = {Ruvolo, M}, title = {Molecular phylogeny of the hominoids: inferences from multiple independent DNA sequence data sets.}, journal = {Molecular biology and evolution}, volume = {14}, number = {3}, pages = {248-265}, doi = {10.1093/oxfordjournals.molbev.a025761}, pmid = {9066793}, issn = {0737-4038}, mesh = {Animals ; Chromosome Mapping ; Chromosomes, Human ; *Evolution, Molecular ; Hominidae/*genetics ; Humans ; Mitochondria/genetics ; Models, Genetic ; *Phylogeny ; Sequence Analysis, DNA ; }, abstract = {Consensus on the evolutionary relationships of humans, chimpanzees, and gorillas has not been reached, despite the existence of a number of DNA sequence data sets relating to the phylogeny, partly because not all gene trees from these data sets agree. However, given the well-known phenomenon of gene tree-species tree mismatch, agreement among gene trees is not expected. A majority of gene trees from available DNA sequence data support one hypothesis, but is this evidence sufficient for statistical confidence in the majority hypothesis? All available DNA sequence data sets showing phylogenetic resolution among the hominoids are grouped according to genetic linkage of their corresponding genes to form independent data sets. Of the 14 independent data sets defined in this way, 11 support a human-chimpanzee clade, 2 support a chimpanzee-gorilla clade, and one supports a human-gorilla clade. The hypothesis of a trichotomous speciation event leading to Homo; Pan, and Gorilla can be firmly rejected on the basis of this data set distribution. The multiple-locus test (Wu 1991), which evaluates hypotheses using gene tree-species tree mismatch probabilities in a likelihood ratio test, favors the phylogeny with a Homo-Pan clade and rejects the other alternatives with a P value of 0.002. When the probabilities are modified to reflect effective population size differences among different types of genetic loci, the observed data set distribution is even more likely under the Homo-Pan clade hypothesis. Maximum-likelihood estimates for the time between successive hominoid divergences are in the range of 300,000-2,800,000 years, based on a reasonable range of estimates for long-term hominoid effective population size and for generation time. The implication of the multiple-locus test is that existing DNA sequence data sets provide overwhelming and sufficient support for a human-chimpanzee clade: no additional DNA data sets need to be generated for the purpose of estimating hominoid phylogeny. Because DNA hybridization evidence (Caccone and Powell 1989) also supports a Homo-Pan clade, the problem of hominoid phylogeny can be confidently considered solved.}, }
@article {pmid9065382, year = {1997}, author = {Leblanc, C and Richard, O and Kloareg, B and Viehmann, S and Zetsche, K and Boyen, C}, title = {Origin and evolution of mitochondria: what have we learnt from red algae?.}, journal = {Current genetics}, volume = {31}, number = {3}, pages = {193-207}, doi = {10.1007/s002940050196}, pmid = {9065382}, issn = {0172-8083}, mesh = {DNA, Circular/genetics ; DNA, Mitochondrial/genetics ; DNA, Plant/genetics ; DNA, Protozoan/genetics ; Eukaryotic Cells ; Genetic Code ; Genome ; *Mitochondria ; *Phylogeny ; Plant Proteins/genetics ; Protein Biosynthesis ; RNA, Plant/genetics ; RNA, Ribosomal/genetics ; Rhodophyta/*cytology/physiology ; Sequence Homology ; }, abstract = {The purpose of this review is to present an account of our current understanding of the structure, organization and evolution of mitochondrial genomes, and to discuss the origin and evolution of mitochondria from the perspective recently provided by the extensive sequencing of various mitochondrial genomes. Mitochondrial-en-coded protein phylogenies are congruent with nuclear phylogenies and strongly support a monophyletic origin of mitochondria. The newly available data from red-algal mitochondrial genomes, in particular, show that the structural and functional diversity of mitochondrial genomes can be accounted for by paralogous evolution. We also discuss the influence of other constraints, such as uniparental inheritance, on the evolution of genome organization in mitochondria.}, }
@article {pmid9060401, year = {1997}, author = {Yasuhira, S and Simpson, L}, title = {Phylogenetic affinity of mitochondria of Euglena gracilis and kinetoplastids using cytochrome oxidase I and hsp60.}, journal = {Journal of molecular evolution}, volume = {44}, number = {3}, pages = {341-347}, doi = {10.1007/pl00006152}, pmid = {9060401}, issn = {0022-2844}, mesh = {Animals ; Chaperonin 60/*genetics ; Cloning, Molecular ; DNA, Mitochondrial ; Electron Transport Complex IV/*genetics ; Euglena gracilis/*genetics ; Kinetoplastida/*genetics ; Mitochondria/enzymology/*metabolism ; Molecular Sequence Data ; *Phylogeny ; }, abstract = {The mitochondrial DNA-encoded cytochrome oxidase subunit I (COI) gene and the nuclear DNA-encoded hsp60 gene from the euglenoid protozoan Euglena gracilis were cloned and sequenced. The COI sequence represents the first example of a mitochondrial genome-encoded gene from this organism. This gene contains seven TGG tryptophan codons and no TGA tryptophan codons, suggesting the use of the universal genetic code. This differs from the situation in the mitochondrion of the related kinetoplastid protozoa, in which TGA codes for tryptophan. In addition, a complete absence of CGN triplets may imply the lack of the corresponding tRNA species. COI cDNAs from E. gracilis possess short 5' and 3' untranslated transcribed sequences and lack a 3' poly[A] tail. The COI gene does not require uridine insertion/ deletion RNA editing, as occurs in kinetoplastid mitochondria, to be functional, and no short guide RNA-like molecules could be visualized by labeling total mitochondrial RNA with [alpha-32P]GTP and guanylyl transferase. In spite of the differences in codon usage and the 3' end structures of mRNAs, phylogenetic analysis using the COI and hsp60 protein sequences suggests a monophyletic relationship between the mitochondrial genomes of E. gracilis and of the kinetoplastids, which is consistent with the phylogenetic relationship of these groups previously obtained using nuclear ribosomal RNA sequences.}, }
@article {pmid9060394, year = {1997}, author = {Foster, PG and Jermiin, LS and Hickey, DA}, title = {Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria.}, journal = {Journal of molecular evolution}, volume = {44}, number = {3}, pages = {282-288}, doi = {10.1007/pl00006145}, pmid = {9060394}, issn = {0022-2844}, mesh = {Amino Acids/*analysis ; Animals ; Bees ; Chickens ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/*chemistry ; Electron Transport Complex IV/*genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {We show that in animal mitochondria homologous genes that differ in guanine plus cytosine (G + C) content code for proteins differing in amino acid content in a manner that relates to the G + C content of the codons. DNA sequences were analyzed using square plots, a new method that combines graphical visualization and statistical analysis of compositional differences in both DNA and protein. Square plots divide codons into four groups based on first and second position A + T (adenine plus thymine) and G + C content and indicate differences in amino acid content when comparing sequences that differ in G + C content. When sequences are compared using these plots, the amino acid content is shown to correlate with the nucleotide bias of the genes. This amino acid effect is shown in all protein-coding genes in the mitochondrial genome, including cox I, cox II, and cyt b, mitochondrial genes which are commonly used for phylogenetic studies. Furthermore, nucleotide content differences are shown to affect the content of all amino acids with A + T- and G + C-rich codons. We speculate that phylogenetic analysis of genes so affected may tend erroneously to indicate relatedness (or lack thereof) based only on amino acid content.}, }
@article {pmid9179498, year = {1997}, author = {Takano, H and Kawano, S and Kuroiwa, T}, title = {No editing of mitochondrial plasmid transcripts in mitochondria of Physarum that have an RNA-editing system.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {4}, number = {1}, pages = {67-71}, doi = {10.1093/dnares/4.1.67}, pmid = {9179498}, issn = {1340-2838}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Physarum/*genetics ; Physarum polycephalum/genetics ; Plasmids/*genetics ; Polymerase Chain Reaction ; *RNA Editing ; Sequence Analysis, DNA ; *Transcription, Genetic ; }, abstract = {Two types of RNA editing have been reported in the mitochondria of Physarum; extensive insertions of nucleotides and single-base substitutions. In the Ng strain of P. polycephalum and its derivatives, mitochondria have a specific plasmid (mF) that promotes fusion of mitochondria. We examined the editing of transcripts derived from the mF plasmid. For analysis, we selected three regions of the plasmid, including a DNA fragment that corresponded to missing conserved domains of the RNA polymerase. In contrast to the mitochondrial DNA (mtDNA), no RNA editing of the transcripts of the mF plasmid was detected. Our results suggest that the mechanism of transcription of the mitochondrial plasmid is independent of that of mtDNA, indicating that the plasmid has a different evolutionary origin from the mtDNA.}, }
@article {pmid9027308, year = {1997}, author = {Cooper, A and Penny, D}, title = {Mass survival of birds across the Cretaceous-Tertiary boundary: molecular evidence.}, journal = {Science (New York, N.Y.)}, volume = {275}, number = {5303}, pages = {1109-1113}, doi = {10.1126/science.275.5303.1109}, pmid = {9027308}, issn = {0036-8075}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; *Birds/genetics ; Evolution, Molecular ; *Fossils ; *Genes ; Genes, mos ; Mammals/genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/genetics ; }, abstract = {The extent of terrestrial vertebrate extinctions at the end of the Cretaceous is poorly understood, and estimates have ranged from a mass extinction to limited extinctions of specific groups. Molecular and paleontological data demonstrate that modern bird orders started diverging in the Early Cretaceous; at least 22 avian lineages of modern birds cross the Cretaceous-Tertiary boundary. Data for several other terrestrial vertebrate groups indicate a similar pattern of survival and, taken together, favor incremental changes during a Cretaceous diversification of birds and mammals rather than an explosive radiation in the Early Tertiary.}, }
@article {pmid9037043, year = {1997}, author = {Janke, A and Xu, X and Arnason, U}, title = {The complete mitochondrial genome of the wallaroo (Macropus robustus) and the phylogenetic relationship among Monotremata, Marsupialia, and Eutheria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {94}, number = {4}, pages = {1276-1281}, pmid = {9037043}, issn = {0027-8424}, mesh = {Animals ; Anticodon/genetics ; Cloning, Molecular ; DNA, Mitochondrial/*genetics ; Gene Rearrangement ; Genome ; Likelihood Functions ; Mammals/classification/*genetics ; Marsupialia/classification/*genetics ; Mitochondria/*genetics ; Models, Biological ; Molecular Sequence Data ; Monotremata/classification/genetics ; *Phylogeny ; RNA Editing ; RNA, Transfer, Asp/genetics ; RNA, Transfer, Lys/genetics ; RNA, Transfer, Ser/genetics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {The complete mitochondrial DNA (mtDNA) (16,896 nt) of the wallaroo (Macropus robustus) was sequenced. The concatenated amino acid sequences of 12 mitochondrial protein-coding genes of the wallaroo plus those of a number of other mammals were included in a phylogenetic study of early mammalian divergences. The analysis joined monotremes and marsupials (the Marsupionta hypothesis) to the exclusion of eutherians. The analysis rejected significantly the commonly acknowledged Theria hypothesis, according to which Marsupialia and Eutheria are grouped together to the exclusion of Monotremata. The region harboring the gene for lysine tRNA (tRNA-Lys) in the mtDNA of other vertebrates is in the wallaroo occupied by a sequence (tRNA-Lys) that lacks both an anticodon loop as well as the anticodon for the amino acid lysine. An alternative tRNA-Lys gene was not identified in any other region of the mtDNA of the wallaroo, suggesting that a tRNA-Lys of nuclear origin is imported into marsupial mitochondria. Previously described RNA editing of tRNA-Asp and rearrangement of some tRNA genes were reconfirmed in the mtDNA of the wallaroo. The divergence between Monotremata/Marsupialia and Eutheria was timed to approximately 130 million years before present (MYBP). The same calculations suggested that Monotremata and Marsupialia diverged approximately 115 MYBP and that Australian and American marsupials separated approximately 75 MYBP. The findings also show that many, probably most, extant eutherian orders had their origin in middle to late Cretaceous times, 115-65 MYBP.}, }
@article {pmid9036544, year = {1997}, author = {Palmer, JD}, title = {Organelle genomes: going, going, gone!.}, journal = {Science (New York, N.Y.)}, volume = {275}, number = {5301}, pages = {790-791}, doi = {10.1126/science.275.5301.790}, pmid = {9036544}, issn = {0036-8075}, mesh = {Animals ; Biological Evolution ; Eukaryota/genetics/ultrastructure ; Fungi/genetics/ultrastructure ; *Genome ; Heat-Shock Proteins/analysis ; Mitochondria/genetics/physiology ; Organelles/chemistry/*genetics/physiology ; Phylogeny ; Trichomonas vaginalis/genetics/ultrastructure ; }, }
@article {pmid9069175, year = {1997}, author = {Frati, F and Simon, C and Sullivan, J and Swofford, DL}, title = {Evolution of the mitochondrial cytochrome oxidase II gene in collembola.}, journal = {Journal of molecular evolution}, volume = {44}, number = {2}, pages = {145-158}, doi = {10.1007/pl00006131}, pmid = {9069175}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Base Composition ; Codon/genetics ; Electron Transport Complex IV/*genetics ; *Evolution, Molecular ; Genes ; Insecta/enzymology/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Sequence Alignment ; }, abstract = {The sequence of the mitochondrial COII gene has been widely used to estimate phylogenetic relationships at different taxomonic levels across insects. We investigated the molecular evolution of the COII gene and its usefulness for reconstructing phylogenetic relationships within and among four collembolan families. The collembolan COII gene showed the lowest A + T content of all insects so far examined, confirming that the well-known A + T bias in insect mitochondrial genes tends to increase from the basal to apical orders. Fifty-seven percent of all nucleotide positions were variable and most of the third codon positions appeared free to vary. Values of genetic distance between congeneric species and between families were remarkably high; in some cases the latter were higher than divergence values between other orders of insects. The remarkably high divergence levels observed here provide evidence that collembolan taxa are quite old; divergence levels among collembolan families equaled or exceeded divergences among pterygote insect orders. Once the saturated third-codon positions (which violated stationarity of base frequencies) were removed, the COII sequences contained phylogenetic information, but the extent of that information was overestimated by parsimony methods relative to likelihood methods. In the phylogenetic analysis, consistent statistical support was obtained for the monophyly of all four genera examined, but relationships among genera/families were not well supported. Within the genus Orchesella, relationships were well resolved and agreed with allozyme data. Within the genus Isotomurus, although three pairs of populations were consistently identified, these appeared to have arisen in a burst of evolution from an earlier ancestor. Isotomurus italicus always appeared as basal and I. palustris appeared to harbor a cryptic species, corroborating allozyme data.}, }
@article {pmid9067807, year = {1997}, author = {Wilson, JE}, title = {Homologous and heterologous interactions between hexokinase and mitochondrial porin: evolutionary implications.}, journal = {Journal of bioenergetics and biomembranes}, volume = {29}, number = {1}, pages = {97-102}, pmid = {9067807}, issn = {0145-479X}, support = {NS 09910/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Binding Sites ; Evolution, Molecular ; Hexokinase/*metabolism ; Mammals ; Mitochondria/*metabolism ; Plants/metabolism ; Yeasts ; }, abstract = {Binding of the Type I isozyme of mammalian hexokinase to mitochondria is mediated by the porin present in the outer mitochondrial membrane. Type I hexokinase from rat brain is avidly bound by rat liver mitochondria while, under the same conditions, there is no significant binding to mitochondria from S. cerevisiae. Previously published work demonstrates the lack of significant interaction of yeast hexokinase with mitochondria from either liver or yeast. Thus, structural features required for the interaction of porin and hexokinase must have emerged during evolution of the mammalian forms of these proteins. If these structural features serve no functional role other than facilitating this interaction of hexokinase with mitochondria, it seems likely that they evolved in synchrony since operation of selective pressures on the hexokinase-mitochondrial interaction would require the simultaneous presence of hexokinase and porin capable of at least minimal interaction, and be responsive to changes in either partner that affected this interaction. Recent studies have indicated that a second type of binding site, which may or may not involve porin, is present on mammalian mitochondria. There are also reports of hexokinase binding to mitochondria in plant tissues, but the nature of the binding site remains undefined.}, }
@article {pmid9066123, year = {1997}, author = {Tu, Z and Hagedorn, HH}, title = {Biochemical, molecular, and phylogenetic analysis of pyruvate carboxylase in the yellow fever mosquito, Aedes aegypti.}, journal = {Insect biochemistry and molecular biology}, volume = {27}, number = {2}, pages = {133-147}, doi = {10.1016/s0965-1748(96)00078-1}, pmid = {9066123}, issn = {0965-1748}, mesh = {Aedes/*enzymology ; Animals ; Base Sequence ; Cell Line ; DNA, Complementary ; Gene Dosage ; Insect Proteins/*chemistry/classification/genetics/metabolism ; Molecular Sequence Data ; Peptides/metabolism ; Phylogeny ; Pyruvate Carboxylase/*chemistry/classification/genetics/metabolism ; Tissue Distribution ; }, abstract = {Pyruvate carboxylase (PC, pyruvate: carbon dioxide ligase [ADP-forming], EC 6.4.1.1) was purified from the yellow fever mosquito, Aedes aegypti. The purified PC showed two polypeptides of similar M(r) (133 and 128 k). The N-terminal sequences of both polypeptides were shown to be very similar, if not identical. A polyclonal antiserum against the 133 kDa polypeptide cross-reacted strongly with the 128 kDa polypeptide. PC was found in all tissues examined. Using a semi-quantitative Western blot assay, PC was shown to be concentrated in the indirect flight muscles and fat body preparations. The ratios of the 133 to 128 kDa polypeptides were shown to differ in various tissues and an Aedes albopictus cell line. The indirect flight muscle was the only tissue in which the 128 kDa polypeptide was more abundant, while both the midgut and the cell line showed almost exclusively the 133 kDa polypeptide. Both peptides were present in varying amounts in brain, malpighian tubule, ovary and fat body preparation. The two isoforms of PC could play different roles in the flight muscle and other tissues. Clones covering a complete cDNA of PC of A. aegypti were obtained using a directional approach. The 3952 bp nucleotide sequence, including a 3585 bp coding region, was determined from these cDNA clones. The deduced 1195 amino acid sequence has a calculated M(r) of 132,200. A putative mitochondrial targeting sequence was determined by comparing the deduced amino acid sequence to the N-terminal sequences of the mature protein. The presence of a mitochondrial targeting sequence indicates that the mosquito PC encoded by the cloned cDNA may be localized in the mitochondria. After the targeting sequence, three functional domains were identified in the following order; biotin carboxylase (BC), carboxyltransferase (CT) and biotin carboxyl carrier protein (BCCP). The mosquito PC showed very high similarity to PCs from other sources (55.1-75.2% identity). Genomic Southern analysis indicated that there could be two similar PC genes or a single PC gene with allelic polymorphism in the A. aegypti genome. The evolutionary relationship of PCs among different organisms was consistent with the accepted evolutionary relationship of their host organisms. The evolution of the domain structures of the biotin-dependent carboxylases including PC was also investigated. This analysis indicates that biotin-dependent carboxylases evolved from a common origin. The analysis also provides evidence for early gene duplication events that shaped the family of biotin-dependent carboxylases. Clear evidence for the coevolution of BC and BCCP domains is presented, although they are associated with very different CT domains and the relative position of the three functional domains varies between members of the biotin-dependent carboxylases.}, }
@article {pmid9061940, year = {1997}, author = {Bessho, Y and Tamura, S and Hori, H and Tanaka, H and Ohama, T and Osawa, S}, title = {Planarian mitochondria sequence heterogeneity: relationships between the type of cytochrome c oxidase subunit I gene sequence, karyotype and genital organ.}, journal = {Molecular ecology}, volume = {6}, number = {2}, pages = {129-136}, doi = {10.1046/j.1365-294x.1997.00162.x}, pmid = {9061940}, issn = {0962-1083}, mesh = {Animals ; DNA, Helminth/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Genes, Helminth/genetics ; Genetic Variation/*genetics ; Genitalia ; Japan ; Karyotyping ; Molecular Sequence Data ; Phylogeny ; Planarians/*genetics/physiology ; Sequence Analysis, DNA ; Taiwan ; }, abstract = {Freshwater planarians Dugesia japonica from three localities were examined for cytochrome c oxidase subunit I (COI) gene sequence, karyotype and the presence of genital organ. The planarians from Mt Fujiwara in Japan were composed of two different groups; one revealed inter- and intraindividual COI gene heterogeneity, while another revealed no sequence heterogeneity. The sequence in planarians from Mt Alishan in Taiwan was homogeneous, while that from the Kenting National Park in Taiwan revealed a considerable heterogeneity. All the planarians having the homogeneous gene sequences carry the 2X karyotype and many of them had genital organs. These are assumed to belong to the sexual lineage. In contrast, almost all planarians having heterogeneous sequences carry the karyotype of either 3X plus 2X (mixoploid) or 3X, and all of them lack genital organs. These lineages are assumed to be asexual. The heterogeneity of COI gene sequences in the presumed asexual lineages would have resulted from an accumulation of mutations by repeated asexual reproduction.}, }
@article {pmid9056852, year = {1997}, author = {Wilson, JE}, title = {An introduction to the isoenzymes of mammalian hexokinase types I-III.}, journal = {Biochemical Society transactions}, volume = {25}, number = {1}, pages = {103-107}, doi = {10.1042/bst0250103}, pmid = {9056852}, issn = {0300-5127}, mesh = {Animals ; Biological Evolution ; Hexokinase/genetics/*metabolism ; Isoenzymes/genetics/*metabolism ; Kinetics ; Mammals ; Mitochondria/enzymology ; Saccharomyces cerevisiae/enzymology ; Subcellular Fractions/enzymology ; Substrate Specificity ; }, }
@article {pmid9021137, year = {1997}, author = {Perrotta, G and Cavallotti, A and Quagliariello, C}, title = {Reduced requirement for RNA editing in the mitochondrial cox3 transcript of Olea europaea L.}, journal = {Current genetics}, volume = {31}, number = {2}, pages = {185-189}, doi = {10.1007/s002940050194}, pmid = {9021137}, issn = {0172-8083}, mesh = {Amino Acid Sequence ; Base Composition ; Base Sequence ; Cloning, Molecular ; DNA, Complementary/analysis ; DNA, Plant/genetics ; DNA-Binding Proteins/*genetics ; Genome, Plant ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Plants/*genetics ; Polymerase Chain Reaction ; *RNA Processing, Post-Transcriptional ; RNA, Plant/*genetics ; Sequence Analysis, DNA ; *Transcription, Genetic ; Viral Proteins/*genetics ; }, abstract = {Transcripts from the mitochondrial cox3 locus in Olea europaea L. are edited in ten nucleotide positions. Nine of these C-to-U transitions affect 3.4% of the genomically encoded amino-acid identity to specify a COXIII polypeptide better conserved in evolution. RNA editing of cox3 in olive tree mitochondria is, thus, less extensive than in the other higher plants so far investigated. This low RNA editing frequency might correlate with both the GC content observed in the cox3 gene and the phylogenetic position of Olea.}, }
@article {pmid9034326, year = {1997}, author = {Lecrenier, N and Van Der Bruggen, P and Foury, F}, title = {Mitochondrial DNA polymerases from yeast to man: a new family of polymerases.}, journal = {Gene}, volume = {185}, number = {1}, pages = {147-152}, doi = {10.1016/s0378-1119(96)00663-4}, pmid = {9034326}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Animals ; Chromosome Mapping ; Cloning, Molecular ; DNA, Complementary/genetics ; DNA-Directed DNA Polymerase/classification/*genetics ; Drosophila melanogaster ; Exonucleases/genetics ; Gene Library ; Humans ; Melanoma/*genetics ; Mice ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; Pichia ; Repetitive Sequences, Nucleic Acid ; Saccharomyces cerevisiae ; Schizosaccharomyces ; Sequence Alignment ; Sequence Homology, Amino Acid ; Xenopus laevis ; }, abstract = {We report the sequence of a 4.5-kb cDNA clone isolated from a human melanoma library which bears high amino acid sequence identity to the yeast mitochondrial (mt) DNA polymerase (Mip1p). This cDNA contains a 3720-bp open reading frame encoding a predicted 140-kDa polypeptide that is 43% identical to Mip1p. The N-terminal part of the sequence contains a 13 glutamine stretch encoded by a CAG trinucleotide repeat which is not found in the other DNA polymerases gamma (Pol gamma). Multiple amino acid sequence alignments with Pol gamma from Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pichia pastoris, Drosophila melanogaster, Xenopus laevis and Mus musculus show that these DNA polymerases form a family strongly conserved from yeast to man and are only loosely related to the Family A DNA polymerases.}, }
@article {pmid9012822, year = {1997}, author = {Malek, O and Brennicke, A and Knoop, V}, title = {Evolution of trans-splicing plant mitochondrial introns in pre-Permian times.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {94}, number = {2}, pages = {553-558}, pmid = {9012822}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Base Sequence ; Biological Evolution ; DNA, Complementary/genetics ; Genes, Plant ; Hydrogen Bonding ; *Introns ; Molecular Sequence Data ; NADH Dehydrogenase/genetics ; Nucleic Acid Conformation ; Plants/*genetics ; RNA/*genetics ; *RNA Splicing ; RNA, Mitochondrial ; RNA, Plant/*genetics ; }, abstract = {Trans-splicing in angiosperm plant mitochondria connects exons from independent RNA molecules by means of group II intron fragments. Homologues of trans-splicing introns in the angiosperm mitochondrial nad2 and nad5 genes are now identified as uninterrupted group II introns in the ferns Asplenium nidus and Marsilea drummondii. These fern introns are correctly spliced from the pre-mRNA at the sites predicted from their well-conserved secondary structures. The flanking exon sequences of the nad2 and nad5 genes in the ferns require RNA editing, including the removal of in-frame stop codons by U-to-C changes for correct expression of the genetic information. We conclude that cis-splicing introns like the ones now identified in ferns are the ancestors of trans-splicing introns in angiosperm mitochondria. Intron disruption is apparently due to a size increase of the structurally variable group II intron domain IV followed by DNA recombination in the plant mitochondrial genome.}, }
@article {pmid9020972, year = {1997}, author = {Yokobori, S and Pääbo, S}, title = {Polyadenylation creates the discriminator nucleotide of chicken mitochondrial tRNA(Tyr).}, journal = {Journal of molecular biology}, volume = {265}, number = {2}, pages = {95-99}, doi = {10.1006/jmbi.1996.0728}, pmid = {9020972}, issn = {0022-2836}, mesh = {Animals ; Base Sequence ; Chickens ; Cloning, Molecular ; DNA, Complementary/genetics ; Evolution, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Poly A/*metabolism ; RNA/*genetics/metabolism ; *RNA Editing ; RNA, Mitochondrial ; RNA, Transfer, Amino Acyl/*genetics/metabolism ; }, abstract = {In the chicken mitochondrial genome, the gene for tRNA(Tyr) overlaps by one nucleotide with the downstream tRNA(Cys) gene, which is located on the same strand. The overlapping nucleotide, a guanosine residue, thus encodes both the discriminator base of the tRNA(Tyr) and the 5'base of the tRNA(Cys). When cDNA clones of circularized forms of the tRNA(Tyr) are analyzed, the discriminator nucleotide is an adenosine residue rather than the genomically encoded guanosine. Thus, the tRNA(Tyr) is subjected to an RNA editing activity similar to that shown to exist in the mitochondria of two other animal species. Interestingly, some cDNA clones have several adenosine residues at their 3'-ends instead of the expected CCA-sequence. Furthermore, a review of sequence data from animal mitochondrial genomes suggests that only tRNAs whose discriminator bases are adenosines tend to have genes that overlap with downstream genes. Thus, polyadenylation seems to be a major component of the RNA editing machinery that affects overlapping genes in animal mitochondria.}, }
@article {pmid9016954, year = {1997}, author = {Champagne, AM and Dufresne, C and Viney, L and Guéride, M}, title = {Cloning, sequencing and expression of the two genes encoding the mitochondrial single-stranded DNA-binding protein in Xenopus laevis.}, journal = {Gene}, volume = {184}, number = {1}, pages = {65-71}, doi = {10.1016/s0378-1119(96)00574-4}, pmid = {9016954}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Northern ; Cloning, Molecular ; DNA, Mitochondrial/*chemistry ; DNA, Single-Stranded/*metabolism ; DNA-Binding Proteins/*metabolism ; Gene Expression Regulation, Developmental/genetics ; Gene Library ; Introns/genetics ; Molecular Sequence Data ; Oocytes/metabolism ; Sequence Alignment ; Sequence Analysis ; Xenopus laevis/*metabolism ; }, abstract = {In Xenopus laevis the single-stranded DNA binding protein imported into the mitochondria consists of two highly related polypeptides. The establishment of the genomic nucleotide sequences reveals that they are encoded by two different genes, XLSSB1 and XLSSB2. The deduced amino acid sequence is identical to the direct amino acid sequence determined by Edman degradation of the mitochondrial polypeptides [Ghrir. R., Lecaer, J.P., Dufresne, C. and Gueride, M. (1991) Primary structure of the two variants of Xenopus laevis mtSSB, a mitochondrial DNA binding protein. Arch. Biochem. Biophys. 291, 395-400]. Both genes are organized in seven exons and six introns, the sequence of the peptide leader is interrupted by an intervening sequence (intron 2). The exon/intron junctions are in exactly conserved positions, splitting the same codon. A high level of identity is observed between corresponding introns of the two genes over part or most of their lengths. Structural features of intronic sequences reveal multiple rearrangements and exchanges during the evolution of X. laevis species. A CCAAT box and the potential regulatory elements NRF-2 and Sp 1 are observed in the 5'-flanking region of both genes. During oogenesis, XLSSB gene expression is correlated with the replicative activity of the mitochondrial DNA.}, }
@article {pmid11543276, year = {1997}, author = {Margulis, L and Dolan, MF}, title = {Swimming against the current.}, journal = {The Sciences}, volume = {37}, number = {1}, pages = {20-25}, doi = {10.1002/j.2326-1951.1997.tb03281.x}, pmid = {11543276}, issn = {0036-861X}, mesh = {Animals ; Bacteria ; *Biological Evolution ; Cell Nucleus/genetics/ultrastructure ; Centrioles/*genetics/ultrastructure ; Chlamydomonas/genetics ; *DNA, Bacterial ; *DNA, Protozoan ; History, 20th Century ; Isoptera ; Microbiology/*history ; Mitochondria ; Mitosis ; Symbiosis/*genetics ; }, }
@article {pmid9505342, year = {1997}, author = {Kudriavtsev, BN and Anatskaia, OV and Nilova, VK and Komarov, SA}, title = {[Interconnection of parameters of the mitochondrial and myofibrillar apparatus of cardiomyocytes and ploidy and hypertrophy in certain mammalian species, differing in body mass].}, journal = {Tsitologiia}, volume = {39}, number = {10}, pages = {946-964}, pmid = {9505342}, issn = {0041-3771}, mesh = {Animals ; Body Weight ; Cardiomegaly/genetics/*pathology ; Microscopy, Electron ; Mitochondria, Heart/*ultrastructure ; Myocardium/pathology/*ultrastructure ; Myofibrils/*ultrastructure ; *Ploidies ; Species Specificity ; }, abstract = {Using cytophotometry and interferometry, ploidy levels and dry weights were determined in cardiac atrium and ventricle myocytes in various mammalian species. Besides, in the same species, using electron microscopy and image analysis, myofibril volume density (MFVD) and mitochondrial volume density (MTVD), as well as the total length of internal mitochondrial membranes (IMM) per cell area unit were measured. The total of 14 mammalian species were studied, with approximately 100,000-fold interspecies differences in the body weight. The dry weights of the left ventricle myocytes in different mammalian species have been shown to vary from 3660 +/- 127 to 8890 +/- 160 pg. Somewhat smaller were the right ventricle myocytes; their dry weight varied from 3598 +/- 134 to 8189 +/- 160 pg. The atrium myocytes were significantly smaller than the ventricle myocytes in all the mammalian species studied. The lowest dry weight of the left atrium myocytes was revealed in the mouse (2415 +/- 96 pg), while the largest weights of the left atrium myocytes were found in the pig (5530 +/- 138 pg). Myocytes of the right atrium, with their mean dry weights in different species varying from 2379 +/- 93 (in the mouse) to 5123 +/- 124 pg (in the pig), were the smallest among all cardiac chamber myocytes. The data obtained indicate that differences in size between the ventricles and atria in mammals are owing predominantly to differences in the number of cardiomyocytes in different parts of the heart rather than to the size of these cells. The dry weight ratio between the right and left ventricle myocytes in various mammalian species was, on average, 0.937 +/- 0.02, and between the right and left atrium myocytes 0.938 +/- 0.04. This ratio between the left atrium and left ventricle myocytes was 0.717 +/- 0.03 and that between the right atrium and right ventricle was 0.722 +/- 0.02. The data obtained indicate that the ratios of cardiomyocyte sizes in different heart parts are rather stable parameters in the mammalian evolution. The mean ploidy levels in myocytes in different parts of the heart corresponded to the mean sizes of the cells. In all the species studied in this work, the ploidy of myocytes of the right ventricle was lower, on average, by 7% compared to myocytes of the left ventricle. The atrial cardiomyocytes had a markedly lower ploidy than the ventricular cardiomyocytes, the myocyte ploidy levels in the left atrium being in all the species higher than in the right atrium. In spite of a higher ploidy level in the ventricular than in the atrial myocytes, this difference in ploidy was less pronounced than the corresponding difference in the myocyte sizes in the same heart parts. In the majority of mammalian species studied, myocyte polyploidization in different parts of the heart combined two ways promoting the increase in the number of genomes in the cells: (1) acytokinetic mitoses in binuclear and multinuclear cells, i. e. mitotic divisions of diploid nuclei without cytoplasm division; in this case no increase in the tissue cell number occurred, (2) alternation of acytokinetic mitoses in mononuclear cells and of bimitoses in binuclear cells; in this case tissue cells increased in number. The ratio of these two ways of polyploid cell formation differed in various species. The former way appeared to be the only in the nutria and horse, whereas the latter way was found in the shrew and arctic fox. In pigs, whose polyploid cardiomyocytes are also formed mainly through the increase in number of diploid cell nuclei, the multinuclear cardiomyocytes contained, apart from diploid nuclei, a small amount of polyploid 4c and 8c nuclei. The formation of such cells is due presumably to the two mechanisms: the asynchronous DNA synthesis in one of the nuclei in a multinuclear cell, and the subsequent incomplete polyploidizing mitosis. (ABSTRACT TRUNCATED)}, }
@article {pmid9493969, year = {1997}, author = {Dion, M and Chamberland, H and St-Michel, C and Plante, M and Darveau, A and Lafontaine, JG and Brisson, LF}, title = {Detection of a homologue of bcl-2 in plant cells.}, journal = {Biochemistry and cell biology = Biochimie et biologie cellulaire}, volume = {75}, number = {4}, pages = {457-461}, doi = {10.1139/o97-056}, pmid = {9493969}, issn = {0829-8211}, mesh = {Animals ; Antibodies/metabolism ; Antibody Specificity ; Brassica ; Cell Line ; Cell Nucleus/chemistry/ultrastructure ; Chlamydomonas reinhardtii ; Genes, bcl-2/*genetics ; Lymphocytes ; Mice ; Mitochondria/chemistry/ultrastructure ; Plant Proteins/*genetics/immunology ; Plants, Toxic ; Rats ; *Sequence Homology, Nucleic Acid ; Nicotiana ; Zea mays ; }, abstract = {An emerging family of bcl-2-like genes has been identified from nematode to humans. These genes play a role in the maintenance of homeostasis. Its members have highly conserved domains that are important for their dimerization. Since nothing is known about the importance of these genes in plant cells, we have investigated their presence in an alga as well as in three higher plants both by Western analysis and by immunocytochemistry. Immunoblots revealed the presence of a protein immunoreacting with the anti-bcl-2 polyclonal antibody in leaves of tobacco plants. Furthermore, immunocytochemical localization has shown that this protein is mainly associated with mitochondria, plastids, and nuclei of plant cells. Taken together, our results suggest that bcl-2 is a protein highly conserved throughout evolution.}, }
@article {pmid9412116, year = {1997}, author = {Kulaev, IS and Kulakovskaia, TV and Andreeva, NA and Lichko, LP}, title = {[The evolution of the functions of inorganic polyphosphates at different stages in the phylogenetic development of living creatures].}, journal = {Zhurnal evoliutsionnoi biokhimii i fiziologii}, volume = {33}, number = {1}, pages = {74-82}, pmid = {9412116}, issn = {0044-4529}, mesh = {Animals ; Bacteria/metabolism ; Eukaryotic Cells/metabolism ; *Evolution, Molecular ; Mitochondria/metabolism ; *Phylogeny ; Polyphosphates/*metabolism ; }, }
@article {pmid9404460, year = {1997}, author = {Lestienne, P}, title = {[Do mitochondria play a role in aging?].}, journal = {Comptes rendus des seances de la Societe de biologie et de ses filiales}, volume = {191}, number = {4}, pages = {579-592}, pmid = {9404460}, issn = {0037-9026}, mesh = {Aging/*physiology ; Alzheimer Disease/genetics/metabolism ; Animals ; DNA, Mitochondrial/genetics/metabolism ; Forecasting ; Free Radicals/metabolism ; Humans ; Mitochondria/*metabolism/physiology ; Parkinson Disease/genetics/metabolism ; }, abstract = {Ageing is an unavoidable and complex phenomenon which may be a price to pay to evolution. Thus genetics appear to play a predominant role besides environmental factors. Energetic metabolism slowly declines with ageing supporting a possible active role of mitochondria, the power supply of the cells, to this process. Mitochondrial DNA alterations appear during the mid-life and in degenerative diseases such as in Parkinson's and Alzheimer's; they include large scale deletions and point mutations. Since the respiratory chain plays a major role in the generation of superoxide anions which are converted into hydroxyl radicals that may impair lipids, proteins and DNA function in mitochondria, this vicious cycle may result from both an altered control of mitochondrial biogenesis dependent from the nucleus, and/or from a lack of repair and accumulation of somatic mitochondrial DNA mutations.}, }
@article {pmid9322030, year = {1997}, author = {Hunter, L and Zeeberg, B}, title = {Identifying chimerism in proteins using hidden Markov models of codon usage.}, journal = {Proceedings. International Conference on Intelligent Systems for Molecular Biology}, volume = {5}, number = {}, pages = {153-156}, pmid = {9322030}, issn = {1553-0833}, mesh = {Amino Acyl-tRNA Synthetases/genetics ; Base Sequence ; Cell Nucleus/enzymology ; Codon/*genetics ; DNA, Fungal/genetics ; Databases, Factual ; Evolution, Molecular ; *Markov Chains ; Mitochondria/enzymology ; *Models, Genetic ; Recombinant Fusion Proteins/*genetics ; Saccharomyces cerevisiae/enzymology/genetics ; Sequence Analysis, DNA ; }, abstract = {Protein chimerism is a phenomenon involving the combination of multiple ancestral sequences into a single, multi-domain protein through evolution. We propose a novel method for detecting chimeric proteins by analyzing their nucleotide sequence. The method tests for differences in the distributions of synonymous (isoaccepting) codons in different regions of the protein. The test involves the comparison of the ability of varying size hidden Markov models (HMMs) of codon usage to fit the natural sequence, relative to a set of randomized controls. We demonstrate the method on the families of yeast nuclear and mitochondrial amino-acyl tRNA synthetases. The method is potentially useful for the automated screening of entire genomes or large databases.}, }
@article {pmid9117996, year = {1997}, author = {Müller, EC and Wittmann-Liebold, B}, title = {Phylogenetic relationship of organisms obtained by ribosomal protein comparison.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {53}, number = {1}, pages = {34-50}, doi = {10.1007/pl00000578}, pmid = {9117996}, issn = {1420-682X}, mesh = {Amino Acid Sequence ; Animals ; Archaea/classification ; Bacteria/classification ; Conserved Sequence ; Fungi/classification ; Humans ; Mitochondria/chemistry ; Molecular Sequence Data ; *Phylogeny ; Plants/classification ; Protein Conformation ; Ribosomal Proteins/chemistry/*classification ; Sequence Homology, Amino Acid ; }, abstract = {The evolutionary relationships of ribosomal proteins from eubacteria, archaea, eukaryotes, chloroplasts and mitochondria were examined by their degree of conservation, their structural and functional properties and by the occurrence of conserved structural elements. The structural domains formed by the different protein families were studied. The occurrence of monophyletic groups was investigated for each protein family within the archaea. Phylogenetic trees were constructed between these organisms and together with the homologous sequences of the other phylogenetic domains. All organisms belonging to the archaea clearly formed a monophyletic group. The conserved sequence motifs were checked for the potential to form similar secondary structural elements.}, }
@article {pmid9050228, year = {1997}, author = {Harvey, WR and Wieczorek, H}, title = {Animal plasma membrane energization by chemiosmotic H+ V-ATPases.}, journal = {The Journal of experimental biology}, volume = {200}, number = {Pt 2}, pages = {203-216}, doi = {10.1242/jeb.200.2.203}, pmid = {9050228}, issn = {0022-0949}, support = {AI 30464/AI/NIAID NIH HHS/United States ; AI-22444/AI/NIAID NIH HHS/United States ; }, mesh = {Adenosine Triphosphatases/chemistry/classification ; Adenosine Triphosphate/metabolism ; Animals ; Binding Sites ; Carrier Proteins/metabolism ; Cell Membrane/*metabolism ; Evolution, Molecular ; Membrane Potentials ; Neoplasm Proteins/metabolism ; Neoplasms/metabolism ; Oxidation-Reduction ; Proton Pumps/*metabolism ; *Proton-Motive Force ; Proton-Translocating ATPases/chemistry/*metabolism ; Sodium/metabolism ; Sulfhydryl Compounds/metabolism ; *Vacuolar Proton-Translocating ATPases ; }, abstract = {Proton-motive forces are thought to be less important than sodium-motive forces in energizing animal membranes. On the supply side, proton-motive forces across mitochondrial inner membranes are well-known energizers of ATP synthesis, catalyzed by F-type ATP synthases. However, on the demand side, proton-motive forces, generated from ATP by V-ATPases, are not widely accepted as energizers of animal membranes; instead, sodium-motive forces, generated by P-ATPases, are thought to predominate. During the 1980s, Anraku, Nelson, Forgac and others showed that proton-motive forces from H+ V-ATPases energize endomembranes of all eukaryotic cells; in most cases, chloride ions accompany the protons and the output compartment is acidified. Unexpectedly, numerous examples of animal plasma membrane energization by proton-motive forces are now appearing. In many insect epithelia, H+ V-ATPases generate transmembrane voltages which secondarily drive sensory signalling, fluid secretion and even alkalization, rather than acidification. Plasma membranes of phagocytes and osteoclasts as well as polarized membranes of epithelia in vertebrate kidney, bladder and epididymis, even apical membranes of frog skin epithelial cells, are now known to be energized by proton-motive forces. The list of proton-energized animal plasma membranes grows daily and includes cancer cells. The localization of H+ V-ATPases either on endomembranes or on plasma membranes may reflect a key event in their evolution. Proton-motive ATPases, like the H+ A-ATPases in present-day archaebacteria, appear to be ancestors of both H+ F-ATP synthases and H+ V-ATPases. On the basis of a greater than 25% overall sequence identity and much higher identity in the nucleotide-binding and regulatory sites, Nelson and others have argued that the A and B subunits of V-ATPases, like the corresponding beta and alpha subunits of F-ATP synthases, derive from common 'A-ATPase-like' ancestral subunits. They postulate that oxygen, introduced into the earth's atmosphere by cyanobacteria, was a selective agent as these key subunits diverged during evolution. Forgac has focused the issue more sharply by showing that the catalytic 'A' subunit of H+ V-ATPases has tow key sulfhydryl residues that are proximal to each other in the tertiary structure; these residues form a disulfide bond under oxidizing conditions, thereby inactivating the enzyme. The corresponding beta subunit of H+ F-ATPases lacks such sulfhydryl residues. Perhaps because their plasma membranes are the site of oxygen-dependent ATP synthesis, which would select against their sulfhydryl-containing regulatory sites, eubacterial cells lack H+ V-ATPases. This retention of the regulatory cysteine residue in the active sites during evolution may explain why H+ V-ATPases. are commonly found in the reducing atmosphere of the cytoplasm, where they would be active, rather than in the putatively oxidizing atmosphere of many plasma membranes, where they would be inactive. It may also explain why animal plasma membrane H+ V-ATPases are commonly found in 'mitochondria-rich' cells. We suggest that the high oxygen affinity of cytochrome oxidase leads to localized reducing conditions near mitochondria which would allow H+ V-ATPases to remain active in plasma membranes of such cells. Moreover, this 'redox modulation mechanism' may obviate the need to evoke two types of enzyme to explain selective targeting of H+ V-ATPases to plasma membranes or endomembranes: membrane that contains a single form of H+ V-ATPase may cycle between the membranes of the cytoplasmic organelles and the cell surface, the enzyme being active only when reducing conditions remove the disulfide bonding restraint.}, }
@article {pmid9032545, year = {1997}, author = {Di Tonno, F and Fabris, C and Mazzon, E and Lavelli, D and Milanesi, C}, title = {Ultrastructural mucosal appearance in the ileal neobladder.}, journal = {European urology}, volume = {31}, number = {1}, pages = {108-111}, doi = {10.1159/000474428}, pmid = {9032545}, issn = {0302-2838}, mesh = {Aged ; Biopsy ; Follow-Up Studies ; Humans ; Ileum/surgery/*ultrastructure ; Intestinal Mucosa/ultrastructure ; Male ; Microscopy, Electron ; Middle Aged ; Time Factors ; Urinary Diversion/methods ; *Urinary Reservoirs, Continent ; }, abstract = {METHODS: 15 patients with ileal neobladder underwent endoscopic biopsy at different postoperative intervals. The specimens were analyzed by electron microscopy in order to evaluate the evolution of the mucosal changes ultrastructurally.<br><br>RESULTS: No significant change was observed 3 months after the operation. After 6 months, the number and height of the microvilli were reduced, the cell borders crooked and the terminal web upset. After 12 months disappearance of the glycocalyx, increased lysosomal features, increased activity of the muciparous cells, rounded mitochondria and loss of the polarized disposition of the cytoplasmic organelles were detected in the enterocytes. We observed no other substantial change after 24 months and more.<br><br>CONCLUSIONS: Progressive modifications occur in the cytoplasmic structures involved in the absorptive process. They do not seem to begin before 3 months and are almost totally completed after 1 year.}, }
@article {pmid9010141, year = {1997}, author = {Yamamoto, A and Hashimoto, T and Asaga, E and Hasegawa, M and Goto, N}, title = {Phylogenetic position of the mitochondrion-lacking protozoan Trichomonas tenax, based on amino acid sequences of elongation factors 1alpha and 2.}, journal = {Journal of molecular evolution}, volume = {44}, number = {1}, pages = {98-105}, pmid = {9010141}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Base Composition ; Biological Evolution ; Cloning, Molecular ; Gene Dosage ; Genes, Protozoan/genetics ; Mitochondria ; Molecular Sequence Data ; Peptide Elongation Factor 1 ; Peptide Elongation Factor 2 ; Peptide Elongation Factors/*genetics ; *Phylogeny ; Restriction Mapping ; Sequence Alignment ; Sequence Analysis, DNA ; Trichomonas/*genetics ; }, abstract = {Major parts of amino-acid-coding regions of elongation factor (EF)-1alpha and EF-2 in Trichomonas tenax were amplified by PCR from total genomic DNA and the products were cloned into a plasmid vector, pGEM-T. The three clones from each of the products of the EF-1alpha and EF-2 were isolated and sequenced. The insert DNAs of the clones containing EF-1alpha coding regions were each 1,185 bp long with the same nucleotide sequence and contained 53.1% of G + C nucleotides. Those of the clones containing EF-2 coding regions had two different sequences; one was 2,283 bp long and the other was 2,286 bp long, and their G + C contents were 52.5 and 52.9%, respectively. The copy numbers of the EF-1alpha and EF-2 gene per chromosome were estimated as four and two, respectively. The deduced amino acid sequences obtained by the conceptual translation were 395 residues from EF-1alpha and 761 and 762 residues from the EF-2s. The sequences were aligned with the other eukaryotic and archaebacterial EF-1alphas and EF-2s, respectively. The phylogenetic position of T. tenax was inferred by the maximum likelihood (ML) method using the EF-1alpha and EF-2 data sets. The EF-1alpha analysis suggested that three mitochondrion-lacking protozoa, Glugea plecoglossi, Giardia lamblia, and T. tenax, respectively, diverge in this order in the very early phase of eukaryotic evolution. The EF-2 analysis also supported the divergence of T. tenax to be immediately next to G. lamblia.}, }
@article {pmid9004216, year = {1997}, author = {van der Giezen, M and Rechinger, KB and Svendsen, I and Durand, R and Hirt, RP and Fèvre, M and Embley, TM and Prins, RA}, title = {A mitochondrial-like targeting signal on the hydrogenosomal malic enzyme from the anaerobic fungus Neocallimastix frontalis: support for the hypothesis that hydrogenosomes are modified mitochondria.}, journal = {Molecular microbiology}, volume = {23}, number = {1}, pages = {11-21}, doi = {10.1046/j.1365-2958.1997.1891553.x}, pmid = {9004216}, issn = {0950-382X}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Anaerobiosis ; Animals ; Base Sequence ; DNA, Complementary ; DNA, Fungal ; Fungi/*enzymology/genetics ; Gene Library ; Humans ; Malate Dehydrogenase/classification/*genetics ; Mitochondria ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Signal Transduction ; }, abstract = {The hydrogenosomal malic enzyme (ME) was purified from the anaerobic fungus Neocallimastix frontalis. Using reverse genetics, the corresponding cDNA was isolated and characterized. The deduced amino acid sequence of the ME showed high similarity to ME from metazoa, plants and protists. Putative functional domains for malate and NAD+/NADP+ binding were identified. Phylogenetic analysis of the deduced amino acid sequence of the new ME suggests that it is homologous to reference bacterial and eukaryotic ME. Most interestingly, the cDNA codes for a protein which contains a 27-amino-acid N-terminus which is not present on the purified mature protein. This presequence shares features with known mitochondrial targeting signals, including an enrichment in Ala, Leu, Ser, and Arg, and the presence of an Arg at position-2 relative to amino acid 1 of the mature protein. This is the first report of a mitochondrial-like targeting signal on a hydrogenosomal enzyme from an anaerobic fungus and provides support for the hypothesis that hydrogenosomes in Neocallimastix frontalis might be modified mitochondria.}, }
@article {pmid9000384, year = {1997}, author = {Ogawa, S and Matsuo, K and Angata, K and Yanagisawa, K and Tanaka, Y}, title = {Group-I introns in the cytochrome c oxidase genes of Dictyostelium discoideum: two related ORFs in one loop of a group-I intron, a cox1/2 hybrid gene and an unusually large cox3 gene.}, journal = {Current genetics}, volume = {31}, number = {1}, pages = {80-88}, doi = {10.1007/s002940050179}, pmid = {9000384}, issn = {0172-8083}, mesh = {Amino Acid Sequence ; Animals ; Chromosome Mapping ; Cloning, Molecular ; DNA, Mitochondrial/genetics ; DNA-Binding Proteins/*genetics ; Dictyostelium/*genetics ; Electron Transport Complex IV/*genetics ; Endonucleases/genetics ; Endoribonucleases/genetics ; *Introns ; Membrane Proteins/*genetics ; Molecular Sequence Data ; Molecular Structure ; Nucleotidyltransferases/genetics ; *Open Reading Frames ; Phylogeny ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Viral Proteins/*genetics ; }, abstract = {The DNA sequences of cytochrome oxidase (subunits 1, 2 and 3) genes of the cellular slime mold Dictyostelium discoideum mitochondria were determined. The genes for subunits 1 and 2 have a single continuous ORF (COX1/2) which contains four group-I introns. The insertion sites of the two group-I introns (DdOX1/2.2 and DdOX1/2.3) coincide with those of fungal and algal group-I introns, as well as a liverwort group-I intron, in the cytochrome oxidase subunit 1. Interestingly, intron DdOX1/2.2 has two free-standing ORFs in a loop (L8) which have similar amino-acid sequences and are homologous to ai4 DNA endonuclease (I-Sce II) and bi4 RNA maturase found in group-I introns of Saccharomyces cerevisiae mitochondrial DNA. Two group-I introns (DdOX1/2.3 and DdOX1/2.4) also have a free-standing ORF in loop 1 and loop 2, respectively. These results show that these group-I introns and the intronic ORFs have evolved from the same ancestral origin, but that these ORFs have been propagated independently.}, }
@article {pmid8962102, year = {1996}, author = {Roger, AJ and Clark, CG and Doolittle, WF}, title = {A possible mitochondrial gene in the early-branching amitochondriate protist Trichomonas vaginalis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {93}, number = {25}, pages = {14618-14622}, pmid = {8962102}, issn = {0027-8424}, mesh = {Animals ; Chaperonin 60/*genetics ; DNA, Mitochondrial/*genetics ; Molecular Sequence Data ; Phylogeny ; Trichomonas vaginalis/*genetics ; }, abstract = {Trichomonads are anaerobic flagellated protists that, based on analyses of ribosomal RNA sequences, represent one of the earliest branching lineages among the eukaryotes. The absence of mitochondria in these organisms coupled with their deep phylogenetic position has prompted several authors to suggest that trichomonads, along with other deeply-branching amitochondriate protist groups, diverged from the main eukaryotic lineage prior to the endosymbiotic origin of mitochondria. In this report we describe the presence of a gene in Trichomonas vaginalis specifically related to mitochondrial chaperonin 60 (cpn60). A recent study indicates that a protein immunologically related to cpn60 is located in trichomonad hydrogenosomes. Together, these data provide evidence that ancestors of trichomonads perhaps harbored the endosymbiotic progenitors of mitochondria, but that these evolved into hydrogenosomes early in trichomonad evolution.}, }
@article {pmid8962101, year = {1996}, author = {Germot, A and Philippe, H and Le Guyader, H}, title = {Presence of a mitochondrial-type 70-kDa heat shock protein in Trichomonas vaginalis suggests a very early mitochondrial endosymbiosis in eukaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {93}, number = {25}, pages = {14614-14617}, pmid = {8962101}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Animals ; DNA, Mitochondrial/*genetics ; HSP70 Heat-Shock Proteins/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment ; Symbiosis ; Trichomonas vaginalis/*genetics ; }, abstract = {Molecular phylogenetic analyses, based mainly on ribosomal RNA, show that three amitochondriate protist lineages, diplomonads, microsporidia, and trichomonads, emerge consistently at the base of the eukaryotic tree before groups having mitochondria. This suggests that these groups could have diverged before the mitochondrial endosymbiosis. Nevertheless, since all these organisms live in anaerobic environments, the absence of mitochondria might be due to secondary loss, as demonstrated for the later emerging eukaryote Entamoeba histolytica. We have now isolated from Trichomonas vaginalis a gene encoding a chaperone protein (HSP70) that in other lineages is addressed to the mitochondrial compartment. The phylogenetic reconstruction unambiguously located this HSP70 within a large set of mitochondrial sequences, itself a sister-group of alpha-purple bacteria. In addition, the T. vaginalis protein exhibits the GDAWV sequence signature, so far exclusively found in mitochondrial HSP70 and in proteobacterial dnaK. Thus mitochondrial endosymbiosis could have occurred earlier than previously assumed. The trichomonad double membrane-bounded organelles, the hydrogenosomes, could have evolved from mitochondria.}, }
@article {pmid8978691, year = {1996}, author = {Kadowaki, K and Kubo, N and Ozawa, K and Hirai, A}, title = {Targeting presequence acquisition after mitochondrial gene transfer to the nucleus occurs by duplication of existing targeting signals.}, journal = {The EMBO journal}, volume = {15}, number = {23}, pages = {6652-6661}, pmid = {8978691}, issn = {0261-4189}, mesh = {Adenosine Triphosphatases/chemistry/*genetics ; Amino Acid Sequence ; Base Sequence ; Biological Evolution ; Cell Nucleus/*metabolism ; Conserved Sequence ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/chemistry/*genetics ; Enzyme Precursors/chemistry/*genetics ; Gene Library ; Mitochondria/*metabolism ; Molecular Sequence Data ; Oryza/metabolism ; Plants/genetics/*metabolism ; Restriction Mapping ; Ribosomal Proteins/*genetics/*metabolism ; Sequence Homology, Amino Acid ; }, abstract = {We have cloned a gene for mitochondrial ribosomal protein S11 (RPS11), which is encoded in lower plants by the mitochondrial genome, in higher plants by the nuclear genome, demonstrating genetic information transfer from the mitochondrial genome to the nucleus during flowering plant evolution. The sequence s11-1 encodes an N-terminal extension as well as an organelle-derived RPS11 region. Surprisingly, the N-terminal region has high amino acid sequence similarity with the presequence of the beta-subunit of ATP synthase from plant mitochondria, suggesting a common lineage of the presequences. The deduced N-terminal region of s11-2, a second nuclear-encoded homolog of rps11, shows high sequence similarity with the putative presequence of cytochrome oxidase subunit Vb. The sharing of the N-terminal region together with its 5' flanking untranslated nucleotide sequence in different proteins strongly suggests an involvement of duplication/recombination for targeting signal acquisition after gene migration. A remnant of ancestral rps11 sequence, transcribed and subjected to RNA editing, is found in the mitochondrial genome, indicating that inactivation of mitochondrial rps11 gene expression was initiated at the translational level prior to termination of transcription.}, }
@article {pmid8975691, year = {1996}, author = {Masuda, R and Lopez, JV and Slattery, JP and Yuhki, N and O'Brien, SJ}, title = {Molecular phylogeny of mitochondrial cytochrome b and 12S rRNA sequences in the Felidae: ocelot and domestic cat lineages.}, journal = {Molecular phylogenetics and evolution}, volume = {6}, number = {3}, pages = {351-365}, doi = {10.1006/mpev.1996.0085}, pmid = {8975691}, issn = {1055-7903}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Carnivora/*classification/genetics ; Cats/*classification/genetics ; Cytochrome b Group/classification/*genetics ; DNA ; Evolution, Molecular ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; RNA/genetics ; RNA, Mitochondrial ; RNA, Ribosomal/classification/*genetics ; }, abstract = {Molecular phylogeny of the cat family Felidae is derived using two mitochondrial genes, cytochrome b and 12S rRNA. Phylogenetic methods of weighted maximum parsimony and minimum evolution estimated by neighbor-joining are employed to reconstruct topologies among 20 extant felid species. Sequence analyses of 363 bp of cytochrome b and 376 bp of the 12S rRNA genes yielded average pair-wise similarity values between felids ranging from 94 to 99% and from 85 to 99%, respectively. Phylogenetic reconstruction supports more recent, intralineage associations but fails to completely resolve interlineage relationships. Both genes produce a monophyletic group of Felis species but vary in the placement of the pallas cat. The ocelot lineage represents an early divergence within the Felidae, with strong associations between ocelot and margay, Geoffroy's cat and kodkod, and pampas cat and tigrina. Implications of the relative recency of felid evolution, presence of ancestral polymorphisms, and influence of outgroups in placement of the topological root are discussed.}, }
@article {pmid8943026, year = {1996}, author = {Ankel-Simons, F and Cummins, JM}, title = {Misconceptions about mitochondria and mammalian fertilization: implications for theories on human evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {93}, number = {24}, pages = {13859-13863}, pmid = {8943026}, issn = {0027-8424}, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; Female ; *Fertilization ; Genomic Imprinting ; Humans ; Male ; Mammals ; Mitochondria/*physiology ; Models, Genetic ; Oocytes/physiology ; Organelles/physiology ; *Sperm-Ovum Interactions ; Spermatozoa/physiology ; }, abstract = {In vertebrates, inheritance of mitochondria is thought to be predominantly maternal, and mitochondrial DNA analysis has become a standard taxonomic tool. In accordance with the prevailing view of strict maternal inheritance, many sources assert that during fertilization, the sperm tail, with its mitochondria, gets excluded from the embryo. This is incorrect. In the majority of mammals-including humans-the midpiece mitochondria can be identified in the embryo even though their ultimate fate is unknown. The "missing mitochondria" story seems to have survived--and proliferated-unchallenged in a time of contention between hypotheses of human origins, because it supports the "African Eve" model of recent radiation of Homo sapiens out of Africa. We will discuss the infiltration of this mistake into concepts of mitochondrial inheritance and human evolution.}, }
@article {pmid8946381, year = {1996}, author = {Sánchez, LB and Hashimoto, T and Müller, M}, title = {Sequence of a malic enzyme gene of Giardia lamblia.}, journal = {Molecular and biochemical parasitology}, volume = {82}, number = {2}, pages = {145-151}, doi = {10.1016/0166-6851(96)02728-4}, pmid = {8946381}, issn = {0166-6851}, support = {AI 11942/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Evolution, Molecular ; *Genes, Protozoan ; Giardia lamblia/enzymology/*genetics ; Likelihood Functions ; Malate Dehydrogenase/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis ; Sequence Homology, Amino Acid ; }, abstract = {The nucleotide sequence and predicted amino acid sequence of malate dehydrogenase (decarboxylating) or malic enzyme (EC 1.1.1.40) of the amitochondriate protist Giardia lamblia were determined. The overall amino acid identity with malic enzyme sequences from other eukaryotes was between 34 and 39%. Functional domains previously defined in other malic enzymes, the malate-, the ADP- and the NAD(P)-binding domains, were present also in the G. lamblia sequence. In phylogenetic reconstructions, the G. lamblia sequence is part of the eukaryotic clade, but its relative position versus the other early branches of the eukaryotic tree (Trichomonas vaginalis hydrogenosome and plant mitochondria) cannot be firmly established. The results indicate, however, a long, independent evolutionary past of this enzyme.}, }
@article {pmid9131018, year = {1996}, author = {Wissmann, PB and Goodman, BK and Vockley, JG and Kern, RM and Cederbaum, SD and Grody, WW}, title = {Delivery of cytosolic liver arginase into the mitochondrial matrix space: a possible novel site for gene replacement therapy.}, journal = {Somatic cell and molecular genetics}, volume = {22}, number = {6}, pages = {489-498}, doi = {10.1007/BF02369440}, pmid = {9131018}, issn = {0740-7750}, support = {HD-04612/HD/NICHD NIH HHS/United States ; HD-06576/HD/NICHD NIH HHS/United States ; HD-08243/HD/NICHD NIH HHS/United States ; }, mesh = {Arginase/*genetics ; Cell Line ; Drug Delivery Systems ; *Gene Transfer Techniques ; *Genetic Therapy ; Humans ; Mitochondria, Liver/enzymology/*genetics ; }, abstract = {As a toxic metabolic byproduct in mammals, excess ammonia is converted into urea by a series of five enzymatic reactions in the liver that constitute the urea cycle. A portion of this cycle takes place in the mitochondria, while the remainder is cytosolic. Liver arginase (L-arginine ureahydrolase, A1) is the fifth enzyme of the cycle, catalyzing the hydrolysis of arginine to ornithine and urea within the cytosol. Patients deficient in this enzyme exhibit hyperargininemia with episodic hyperammonemia and long-term effects of mental retardation and spasticity. However, the hyperammonemic effects are not so catastrophic in arginase deficiency as compared to other urea cycle defects. Earlier studies have suggested that this is due to the mitigating effect of a second isozyme of arginase (AII) expressed predominantly in the kidney and localized within the mitochondria. In order to explore the curious dual evolution of these two isozymes, and the ways in which the intriguing, aspects of AII physiology might be exploited for gene replacement therapy of AI deficiency, the cloned cDNA for human AI was inserted into an expression vector downstream from the mitochondrial targeting leader sequence for the mitochondrial enzyme ornithine transcarbamylase and transfected into a variety of recipient cell types. AI expression in the target cells was confirmed by northern blot analysis, and competition and immunoprecipitation studies showed successful translocation of the exogenous AI enzyme into the transfected cell mitochondria. Stability studies demonstrated that the translocated enzyme had a longer half-life than either native cytosolic AI or mitochondrial AII. Incubation of the transfected cells with increasing amounts of arginine produced enhanced levels of mitochondrial AI activity, a substrate-induced effect that we have previously seen with native AII but never AI. Along with exploring the basic biological questions of regulation and subcellular localization in this unique dual-enzyme system, these results suggest that the mitochondrial matrix space may be a preferred site for delivery of enzymes in gene replacement therapy.}, }
@article {pmid9022265, year = {1996}, author = {Salomone, N and Frati, F and Bernini, F}, title = {Investigation on the taxonomic status of Steganacarus magnus and Steganacarus anomalus (Acari:Oribatida) using mitochondrial DNA sequences.}, journal = {Experimental &amp; applied acarology}, volume = {20}, number = {11}, pages = {607-615}, pmid = {9022265}, issn = {0168-8162}, mesh = {Amino Acid Sequence ; Animals ; Base Composition ; Base Sequence ; DNA, Complementary ; *DNA, Mitochondrial ; Electron Transport Complex IV/classification/*genetics ; Mites/classification/*enzymology/genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; }, abstract = {To test the previously suggested synonymization of S. anomalus with the older S. magnus, a fragment of the mitochondrial COI gene was amplified via the polymerase chain reaction and sequenced. The sequence variation was examined in a total of 327 base pairs for four steganacarid mite populations, two of which belong to S. anomalus, one to S. magnus and one to S. hirsutus. The sequence variation suggests that S. magnus and S. anomalus are not distinct species and that the population from Fioreta (Siena) is more similar to that from Apulia than to the nearer population from the Apuan Alps. The results show the usefulness of this molecular approach as a tool for determining taxonomic status and for suggesting faunistic movements in the past millions of years.}, }
@article {pmid8923800, year = {1996}, author = {Baker, A and Kaplan, CP and Pool, MR}, title = {Protein targeting and translocation; a comparative survey.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {71}, number = {4}, pages = {637-702}, doi = {10.1111/j.1469-185x.1996.tb01286.x}, pmid = {8923800}, issn = {1464-7931}, mesh = {Bacteria/genetics/metabolism ; Fungi/genetics/metabolism ; *Gene Targeting ; Protein Folding ; Protein Sorting Signals/genetics ; Proteins/chemistry/*genetics/*metabolism ; }, abstract = {The last few years has seen enormous progress in understanding of protein targeting and translocation across biological membranes. Many of the key molecules involved have been identified, isolated, and the corresponding genes cloned, opening up the way for detailed analysis of the structure and function of these molecular machines. It has become clear that the protein translocation machinery of the endoplasmic reticulum is very closely related to that of bacteria, and probably represents an ancient solution to the problem of how to get a protein across a membrane. One of the thylakoid translocation systems looks as if it will also be very similar, and probably represents a pathway inherited from the ancestral endosymbiont. It is interesting that, so far, there is a perfect correlation between thylakoid proteins which are present in photosynthetic prokaryotes and those which use the sec pathway in chloroplasts; conversely, OE16 and 23 which use the delta pH pathway are not found in cyanobacteria. To date, no Sec-related proteins have been found in mitochondria, although these organelles also arose as a result of endosymbiotic events. However, virtually nothing is known about the insertion of mitochondrially encoded proteins into the inner membrane. Is the inner membrane machinery which translocates cytoplasmically synthesized proteins capable of operating in reverse to export proteins from the matrix, or is there a separate system? Alternatively, do membrane proteins encoded by mitochondrial DNA insert independently of accessory proteins? Unlike nuclear-encoded proteins, proteins encoded by mtDNA are not faced with a choice of membrane and, in principle, could simply partition into the inner membrane. The ancestors of mitochondria almost certainly had a Sec system; has this been lost along with many of the proteins once encoded in the endosymbiont genome, or is there still such a system waiting to be discovered? The answer to this question may also shed light on the controversy concerning the sorting of the inter-membrane space proteins cytochrome c1 and cytochrome b2, as the conservative-sorting hypothesis would predict re-export of matrix intermediates via an ancestral (possibly Sec-type) pathway. Whereas the ER and bacterial systems clearly share homologous proteins, the protein import machineries of mitochondria and chloroplasts appear to be analogous rather than homologous. In both cases, import occurs through contact sites and there are separate translocation complexes in each membrane, however, with the exception of some of the chaperone molecules, the individual protein components do not appear to be related. Their similarities may be a case of convergent rather than divergent evolution, and may reflect what appear to be common requirements for translocation, namely unfolding, a receptor, a pore complex and refolding. There are also important differences. Translocation across the mitochondrial inner membrane is absolutely dependent upon delta psi, but no GTP requirement has been identified. In chloroplasts the reverse is the case. The roles of delta psi and GTP, respectively, remain uncertain, but it is tempting to speculate that they may play a role in regulating the import process, perhaps by controlling the assembly of a functional translocation complex. In the case of peroxisomes, much still remains to be learned. Many genes involved in peroxisome biogenesis have been identified but, in most cases, the biochemical function remains to be elucidated. In this respect, understanding of peroxisome biogenesis is at a similar stage to that of the ER 10 years ago. The coming together of genetic and biochemical approaches, as with the other organelles, should provide many of the answers.}, }
@article {pmid8923013, year = {1996}, author = {Fu, K and Hartlen, R and Johns, T and Genge, A and Karpati, G and Shoubridge, EA}, title = {A novel heteroplasmic tRNAleu(CUN) mtDNA point mutation in a sporadic patient with mitochondrial encephalomyopathy segregates rapidly in skeletal muscle and suggests an approach to therapy.}, journal = {Human molecular genetics}, volume = {5}, number = {11}, pages = {1835-1840}, doi = {10.1093/hmg/5.11.1835}, pmid = {8923013}, issn = {0964-6906}, mesh = {Base Sequence ; Blepharoptosis/genetics ; Cells, Cultured ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/metabolism ; Hearing Loss, Sensorineural/genetics ; Humans ; Male ; Middle Aged ; Mitosis ; Molecular Sequence Data ; Muscle Fibers, Skeletal/enzymology ; *Muscle, Skeletal ; Ophthalmoplegia, Chronic Progressive External/*genetics ; Point Mutation/*genetics ; RNA, Transfer, Leu/*genetics ; Retinitis Pigmentosa/genetics ; }, abstract = {A novel mtDNA point mutation was detected in the tRNAleu(CUN) gene (G to A at position 12315) in a sporadic patient with chronic progressive external ophthalmoplegia, ptosis, limb weakness, sensorineural hearing loss and a pigmentary retinopathy. The mutation disrupts base pairing in the T psi C stem at a site which has been conserved throughout evolution. Although the other mtDNA tRNAleu gene (UUR) is a hotspot for mutation, this is the first pathogenic mutation to be reported in the gene coding for tRNAleu(CUN). MtDNAs carrying the mutation constituted 94% of total mtDNAs in two separate muscle biopsies. Single fibre analysis showed that skeletal muscle fibres without detectable cytochrome c oxidase activity (COX-ve fibres) contained predominantly mutant mtDNAs (93-98%) while fibres with apparently normal COX activity had up to 90% mutant mtDNAs, demonstrating that the G12315A mutation is functionally recessive. Immunofluorescence studies with specific antibodies to mtDNA- or nuclear-encoded subunits of COX were consistent with a defect in mitochondrial protein translation. The mutation was not present in blood cells or cultured fibroblasts and surprisingly, it could not be detected in satellite cells cultured from the patient's muscle. This pattern, which may by typical of patients who have inherited new germline pathogenic mtDNA mutations, possibly reflects loss of the mutation by random genetic drift in mitotic tissues and proliferation of mitochondria containing the mutant mtDNA in post-mitotic cells. The absence of mtDNA carrying the mutation in satellite cells suggests that regeneration of skeletal muscle fibres from satellite cells could restore a wild-type mtDNA genotype and normal muscle function.}, }
@article {pmid8913766, year = {1996}, author = {Templeton, AR}, title = {Contingency tests of neutrality using intra/interspecific gene trees: the rejection of neutrality for the evolution of the mitochondrial cytochrome oxidase II gene in the hominoid primates.}, journal = {Genetics}, volume = {144}, number = {3}, pages = {1263-1270}, pmid = {8913766}, issn = {0016-6731}, support = {1 RO1 HL-39107/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; DNA/*analysis ; Electron Transport Complex IV/classification/*genetics ; *Evolution, Molecular ; Genes ; Gorilla gorilla ; Humans ; Mitochondria/*enzymology ; Pan troglodytes ; Pongo pygmaeus ; }, abstract = {Contingency tests of neutrality are performed using mitochondrial cytochrome oxidase II (COII) DNA sequences from hominoid primates, including humans. An intra-/interspecific haplotype tree is estimated, including a statistical assessment of ambiguities in tree topology and branch lengths. Four functional mutational categories are considered: silent and replacement substitutions in the transmembrane portion of the COII molecule, and silent and replacement substitutions in the cytosolic portion. Three tree topological mutational categories are used: intraspecific tips, intraspecific interiors, and interspecific fixed mutations. A full contingency analysis is performed, followed by nested contingency analyses. The analyses indicate that replacement mutations in the cytosolic portion are deleterious, and replacement mutations in the transmembrane portion and silent mutations throughout tend to be neutral. These conclusions are robust to ambiguities in tree topology and branch lengths. These inferences would have been impossible with an analysis that only contrasts silent and replacement vs. polymorphic and fixed. Also, intraspecific interior mutations have similar evolutionary dynamics to fixed mutations, so pooling tip and interior mutations into a single "polymorphic" class reduces power. Finally, the detected deleterious selection causes lowered inbreeding effective sizes, so arguments for small effective sizes in recent human evolutionary history based upon mitochondrial DNA may be invalid.}, }
@article {pmid8896379, year = {1996}, author = {Jenkins, TM and Basten, CJ and Anderson, WW}, title = {Mitochondrial gene divergence of Colombian Drosophila pseudoobscura.}, journal = {Molecular biology and evolution}, volume = {13}, number = {9}, pages = {1266-1275}, doi = {10.1093/oxfordjournals.molbev.a025692}, pmid = {8896379}, issn = {0737-4038}, mesh = {Animals ; Colombia ; *DNA, Mitochondrial ; Drosophila/*genetics ; Genes, Insect ; *Genetic Variation ; Genetics, Population ; Mexico ; Models, Biological ; Models, Genetic ; Molecular Sequence Data ; North America ; Phylogeny ; RNA, Ribosomal ; Sequence Homology, Nucleic Acid ; }, abstract = {Isolated populations of drosophila pseudoobscura, separated from North American populations by about 2,400 km, were found in Colombia in 1960. We compared for sequences of the small ribosomal RNA (srRNA) gene on the mitochondria between North American and Colombian D. pseudoobscura in order to clarify the age of the Colombian isolates. The North American populations were not genetically different from each other but were genetically different from the Colombian populations. The Mexican strains represent the area from which the Colombian founders might have come. The estimated net nucleotide divergence between Mexican and Colombian D. pseudoobscura indicates that the Colombian population is not an ancient lineage. Phylogenies using both distance and parsimony methodologies reinforced this conclusion. The Colombian samples group together with both methods but, according to the bootstrap analysis, not significantly. It appears that the populations have not been separated long enough for their DNA sequences to show much divergence.}, }
@article {pmid8875858, year = {1996}, author = {Pesole, G and Ceci, LR and Gissi, C and Saccone, C and Quagliariello, C}, title = {Evolution of the nad3-rps12 gene cluster in angiosperm mitochondria: comparison of edited and unedited sequences.}, journal = {Journal of molecular evolution}, volume = {43}, number = {5}, pages = {447-452}, pmid = {8875858}, issn = {0022-2844}, mesh = {DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; Genes, Plant/genetics ; Molecular Sequence Data ; Multigene Family/*genetics ; NADH Dehydrogenase/*genetics ; Phylogeny ; *RNA Editing ; RNA, Messenger/genetics ; RNA, Plant/genetics ; }, abstract = {We have analyzed the nad3-rps12 locus for eight angiosperms in order to compare the utility of mitochondrial DNA and edited mRNA sequences in phylogenetic reconstruction. The two coding regions, containing from 25 to 35 editing sites in the various plants, have been concatenated in order to increase the significance of the analysis. Differing from the corresponding chloroplast sequences, unedited mitochondrial DNA sequences seem to evolve under a quasi-neutral substitution process which undifferentiates the nucleotide substitution rates for the three codon positions. By using complete gene sequences (all codon positions) we found that genomic sequences provide a classical angiosperm phylogenetic tree with a clear-cut grouping of monocotyledons and dicotyledons with Magnoliidae at the basal branch of the tree. Conversely, owing to their low nucleotide substitution rates, edited mRNA sequences were found not to be suitable for studying phylogenetic relationships among angiosperms.}, }
@article {pmid9039497, year = {1996}, author = {Marienfeld, J and Unseld, M and Brandt, P and Brennicke, A}, title = {Genomic recombination of the mitochondrial atp6 gene in Arabidopsis thaliana at the protein processing site creates two different presequences.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {3}, number = {5}, pages = {287-290}, doi = {10.1093/dnares/3.5.287}, pmid = {9039497}, issn = {1340-2838}, mesh = {Amino Acid Sequence ; Arabidopsis/enzymology/*genetics ; DNA, Mitochondrial/*genetics ; *Genes, Plant ; Mitochondria/*enzymology ; Molecular Sequence Data ; Proton-Translocating ATPases/*genetics ; *Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; }, abstract = {In the mitochondrial genome of the flowering plant Arabidopsis thaliana the atp6 open reading frame is located on the border of one of the repeats resulting in two copies with different presequence extensions. The two presequences of 135 and 97 amino acids respectively show no similarity to each other, while the mature protein sequences are identical. Both preproteins are most likely synthesized in Arabidopsis mitochondria from promoter elements upstream of each copy. The presence of two arrangements in the mitochondrial genome of fertile Arabidopsis plants suggests this recombination to be unrelated to a cytoplasmic male sterile phenotype. This recombination precisely at the mature protein terminus is reminiscent of the domain shuffling model in protein evolution.}, }
@article {pmid8917433, year = {1996}, author = {Oatey, PB and Lumb, MJ and Danpure, CJ}, title = {Molecular basis of the variable mitochondrial and peroxisomal localisation of alanine-glyoxylate aminotransferase.}, journal = {European journal of biochemistry}, volume = {241}, number = {2}, pages = {374-385}, doi = {10.1111/j.1432-1033.1996.00374.x}, pmid = {8917433}, issn = {0014-2956}, mesh = {Alanine Transaminase/genetics/*metabolism ; Animals ; Base Sequence ; Callithrix ; Cats ; Cell Line ; DNA Primers/genetics ; DNA, Complementary/administration &amp; dosage/genetics ; Fibroblasts ; Humans ; Microbodies/*enzymology ; Microinjections ; Microscopy, Fluorescence ; Mitochondria/*enzymology ; Plasmids/genetics ; Protein Biosynthesis ; RNA/genetics ; Rabbits ; Recombinant Proteins/genetics/metabolism ; Species Specificity ; Subcellular Fractions/enzymology ; *Transaminases ; Transcription, Genetic ; }, abstract = {The molecular basis of the variable species-specific peroxisomal and/or mitochondrial targeting of the enzyme alanine-glyoxylate aminotransferase 1 (AGT) has been studied in human fibroblasts by confocal immunofluorescence microscopy after intranuclear microinjection of various human, rabbit, marmoset, and feline AGT cDNA constructs. The expression of full-length human and rabbit AGT cDNA led to an exclusively peroxisomal distribution of AGT. However, the distribution of feline and marmoset AGT depended on the cDNA construct injected. In both species, injection of the short cDNAs (from transcripts that occur naturally in marmoset liver but not in feline liver) led to an exclusively peroxisomal distribution. However, injection of the long cDNAs (from transcripts that occur naturally in both species) led to most of the AGT being targeted to the mitochondria and only a small, yet significant, fraction to the peroxisomes. Reintroduction of the 'ancestral' first potential translation initiation site into human AGT cDNA led to an 'ancestral' distribution of AGT (i.e. both mitochondrial and peroxisomal). Deletion of the second potential translation start site from the long feline cDNA led to a distribution that was almost entirely mitochondrial, which suggests that most peroxisomal AGT encoded by the long cDNA results from internal translation initiation from this site with the consequent loss of the N-terminal mitochondrial targeting sequence. Expression of rabbit cDNA and the short marmoset and feline cDNAs in cells selectively deficient in the import of peroxisomal matrix proteins showed that peroxisomal AGT in all these species is imported via the peroxisomal targeting sequence type 1 (PTS1) import pathway. The almost complete functional dominance of the N-terminal mitochondrial targeting sequence over the C-terminal PTS. which was not due to any direct interference of the former with peroxisomal import, was maintained even when the unusual PTS1 of AGT (KKL in human) was replaced by the prototypical PTS1 SKL. The results demonstrate that the major determinant of alanine-glyoxylate aminotransferase subcellular distribution in mammals is the presence or absence of the mitochondrial targeting sequence rather than the peroxisomal targeting sequence. Various strategies have arisen during the evolution of mammals to enable the exclusion of the mitochondrial targeting sequence from the newly synthesised polypeptide, all of which involve the use of alternative transcription and/or translation initiation sites.}, }
@article {pmid8876257, year = {1996}, author = {Eriksson, M and Karlsson, J and Ramazanov, Z and Gardeström, P and Samuelsson, G}, title = {Discovery of an algal mitochondrial carbonic anhydrase: molecular cloning and characterization of a low-CO2-induced polypeptide in Chlamydomonas reinhardtii.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {93}, number = {21}, pages = {12031-12034}, pmid = {8876257}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Carbon Dioxide ; Carbonic Anhydrases/*biosynthesis/*chemistry ; Chlamydomonas reinhardtii/classification/*enzymology ; Cyanobacteria/classification/enzymology ; Enzyme Induction ; Escherichia coli/classification/enzymology ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; Plants/classification/*enzymology ; Sequence Homology, Amino Acid ; }, abstract = {In green unicellular algae, several polypeptides are induced upon exposure to limiting CO2. We report here on the localization and characterization of one of these, a 22-kDa polypeptide in Chlamydomonas reinhardtii. This nuclear-encoded polypeptide is induced in the mitochondria by a lowering of the partial pressure of CO2 in the growth medium from 5% to air CO2 levels. Sequencing of two different cDNA clones coding for the polypeptide identified it as a 20.7-kDa beta-type carbonic anhydrase (CA; carbonate dehydratase, carbonate hydro-lyase, EC 4.2.1.1). The two clones differ in their nucleotide sequences but code for identical proteins, showing that this CA is encoded by at least two genes. Northern blot hybridization reveals that mRNA transcripts are only present in cells transferred to air CO2 levels. A comparison of the deduced amino acid sequence with those of other beta-CAs shows the largest degree of similarity with CA from the cyanobacterium Synechocystis (50% identity and 66% similarity). To our knowledge, this is the first identification and characterization of a mitochondrial CA from a photosynthetic organism.}, }
@article {pmid8876236, year = {1996}, author = {Ragan, MA and Goggin, CL and Cawthorn, RJ and Cerenius, L and Jamieson, AV and Plourde, SM and Rand, TG and Söderhäll, K and Gutell, RR}, title = {A novel clade of protistan parasites near the animal-fungal divergence.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {93}, number = {21}, pages = {11907-11912}, pmid = {8876236}, issn = {0027-8424}, support = {GM 48207/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Conserved Sequence ; Crustacea/parasitology ; Eukaryota/*classification/genetics/isolation &amp; purification ; Fungi/*classification/genetics ; *Genes, Protozoan ; Gills/parasitology ; Microscopy, Electron ; Mitochondria/ultrastructure ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; RNA, Ribosomal/chemistry/genetics ; Salmon/parasitology ; Trout/parasitology ; }, abstract = {Sequences of nuclear-encoded small-subunit rRNA genes have been determined for representatives of the enigmatic genera Dermocystidium, Ichthyophonus, and Psorospermium, protistan parasites of fish and crustaceans. The small-subunit rRNA genes from these parasites and from the "rosette agent" (also a parasite of fish) together form a novel, statistically supported clade. Phylogenetic analyses demonstrate this clade to diverge near the animal-fungal dichotomy, although more precise resolution is problematic. In the most parsimonious and maximally likely phylogenetic frameworks inferred from the most stably aligned sequence regions, the clade constitutes the most basal branch of the metazoa; but within a limited range of model parameters, and in some analyses that incorporate less well-aligned sequence regions, an alternative topology in which it diverges immediately before the animal-fungal dichotomy was recovered. Mitochondrial cristae of Dermocystidium spp. are flat, whereas those of Ichthyophonus hoferi appear tubulovesiculate. These results extend our understanding of the types of organisms from which metazoa and fungi may have evolved.}, }
@article {pmid8893850, year = {1996}, author = {Bömer, U and Rassow, J and Zufall, N and Pfanner, N and Meijer, M and Maarse, AC}, title = {The preprotein translocase of the inner mitochondrial membrane: evolutionary conservation of targeting and assembly of Tim17.}, journal = {Journal of molecular biology}, volume = {262}, number = {4}, pages = {389-395}, doi = {10.1006/jmbi.1996.0522}, pmid = {8893850}, issn = {0022-2836}, mesh = {Adenosine Triphosphatases/chemistry/*genetics ; Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry/*genetics ; Base Sequence ; Biological Transport ; Carrier Proteins/biosynthesis/*genetics ; *Conserved Sequence ; Drosophila melanogaster ; *Escherichia coli Proteins ; Humans ; Intracellular Membranes/enzymology ; Membrane Proteins/biosynthesis/*genetics ; *Membrane Transport Proteins ; Mitochondria/*enzymology ; Mitochondrial Membrane Transport Proteins ; Mitochondrial Precursor Protein Import Complex Proteins ; Molecular Sequence Data ; Protein Conformation ; Rats ; *Repressor Proteins ; SEC Translocation Channels ; Saccharomyces cerevisiae ; *Saccharomyces cerevisiae Proteins ; SecA Proteins ; }, abstract = {The preprotein translocase of the inner mitochondrial membrane has only been described in Saccharomyces cerevisiae to date. We report that the essential subunit Tim17 is highly conserved in evolution. The targeting and assembly of yeast Tim17 as well as that of human and Drosophila melanogaster Tim17 were characterized with isolated yeast mitochondria. Targeting signals in the mature protein direct the Tim17 precursors to the receptor Tom70 on the mitochondrial surface. In a membrane potential-dependent step the precursors insert into the inner membrane, adopt a characteristic topology and assemble with Tim23. The mechanisms of targeting and assembly were indistinguishable between the Tim17s from distinct organisms, indicating a high evolutionary conservation.}, }
@article {pmid8979399, year = {1996}, author = {La Cognata, U and Landschütze, V and Willmitzer, L and Müller-Röber, B}, title = {Structure and expression of mitochondrial citrate synthases from higher plants.}, journal = {Plant &amp; cell physiology}, volume = {37}, number = {7}, pages = {1022-1029}, doi = {10.1093/oxfordjournals.pcp.a029033}, pmid = {8979399}, issn = {0032-0781}, mesh = {Amino Acid Sequence ; Citrate (si)-Synthase/chemistry/*genetics ; Cloning, Molecular ; Crystallography, X-Ray ; DNA, Complementary ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Plants/classification/*enzymology ; Protein Conformation ; Sequence Homology, Amino Acid ; }, abstract = {Mitochondrial citrate synthase (EC 4.1.3.7) represents the first enzyme of the tricarboxylic acid cycle, catalyzing the condensation of acetyl-CoA and oxaloacetate, finally yielding citrate and CoA. We report here the isolation of cDNA clones encoding citrate synthase from Nicotiana tabacum, Beta vulgaris and Populus. Nucleotide and deduced amino acid sequences were compared with previously published sequences of mitochondrial citrate synthases from Arabidopsis thaliana and potato, as well as with the sequence of glyoxysomal citrate synthase from pumpkin. Homologies between the various plant mitochondrial enzymes were in the range from 77.2% (potato vs. Arabidopsis) to 94.2% (potato vs. tobacco) on the nucleotide level (coding regions only), and in the range from 70.1% to 90.4% (potato vs. Arabidopsis, and potato vs. tobacco, respectively) on the amino acid level. Identities of the mitochondrial isozymes to the pumpkin glyoxysomal enzyme were below 30% on the nucleotide and amino acid level. In Northern blot experiments citrate synthase mRNA was detected in all tissues analyzed. However, levels of expression showed tissue dependency despite the fact that citrate synthase is usually considered a house-keeping enzyme. Whether these different levels of expression reflect tissue-specific variations with respect to basic metabolism awaits further analysis.}, }
@article {pmid8899726, year = {1996}, author = {Lavergne, A and Douzery, E and Stichler, T and Catzeflis, FM and Springer, MS}, title = {Interordinal mammalian relationships: evidence for paenungulate monophyly is provided by complete mitochondrial 12S rRNA sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {6}, number = {2}, pages = {245-258}, doi = {10.1006/mpev.1996.0074}, pmid = {8899726}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Evolution, Molecular ; Mammals/*classification/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; *Phylogeny ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/*genetics ; Sequence Alignment ; }, abstract = {The complete mitochondrial 12S rRNA sequences of 5 placental mammals belonging to the 3 orders Sirenia, Proboscidea, and Hyracoidea are reported together with phylogenetic analyses (distance and parsimony) of a total of 51 mammalian orthologues. This 12S rRNA database now includes the 2 extant proboscideans (the African and Asiatic elephants Loxodonta africana and Elephas maximus), 2 of the 3 extant sirenian genera (the sea cow Dugong dugon and the West Indian manatee Trichechus manatus), and 2 of the 3 extant hyracoid genera (the rock and tree hyraxes Procavia capensis and Dendrohyrax dorsalis). The monophyly of the 3 orders Sirenia, Proboscidea, and Hyracoidea is supported by all kinds of analysis. There are 23 and 3 diagnostic subsitutions shared by the 2 proboscideans and the 2 hyracoids, respectively, but none by the 2 sirenians. The 2 proboscideans exhibit the fastest rates of 12S rRNA evolution among the 11 placental orders studied. Based on various taxonomic sampling methods among eutherian orders and marsupial outgroups, the most strongly supported clade in our comparisons clusters together the 3 orders Sirenia, Proboscidea, and Hyracoidea in the superorder Paenungulata. Within paenungulates, the grouping of sirenians and proboscideans within the mirorder Tethytheria is observed. This branching pattern is supported by all analyses by high bootstrap percentages (BPs) and decay indices. When only one species is selected per order or suborder, the taxonomic sampling leads to a relative variation in bootstrap support of 53% for Tethytheria (BPs ranging from 44 to 93%) and 7% for Paernungulata (92-99%). When each order or suborder is represented by two species, this relative variation decreased to 10% for Tethytheria (78-87%) and 3% for Paenungulata (96-99%). Two nearly exclusive synapomorphies for paenungulates are identified in the form of one transitional compensatory change, but none were detected for tethytherians. Such a robust and reliable resolution of the paenungulate node implies a long history of the common ancestors, allowing time for synapomorphies to accumulate. This observation suggests a Late Cretaceous/Early Paleocene origin for the Paenungulata.}, }
@article {pmid8894701, year = {1996}, author = {Lanterman, MM and Dickinson, JR and Danner, DJ}, title = {Functional analysis in Saccharomyces cerevisiae of naturally occurring amino acid substitutions in human dihydrolipoamide dehydrogenase.}, journal = {Human molecular genetics}, volume = {5}, number = {10}, pages = {1643-1648}, doi = {10.1093/hmg/5.10.1643}, pmid = {8894701}, issn = {0964-6906}, support = {DK38320/DK/NIDDK NIH HHS/United States ; GM08367/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acids/genetics ; Dihydrolipoamide Dehydrogenase/*genetics ; Enzyme Activation/genetics ; Humans ; Mutagenesis, Site-Directed ; Saccharomyces cerevisiae/*genetics ; }, abstract = {Dihydrolipoamide dehydrogenase is a common component of mammalian multienzyme complexes that decarboxylate alpha-ketoacids and catabolize glycine. The common function is to reoxidize a reduced lipoate component of each complex, thereby preparing that lipoate for another round of catalysis. Regions within dihydrolipoamide dehydrogenase involved in association with other proteins of the complexes are poorly defined, and despite high amino acid sequence conservation through evolution, it is unknown if dihydrolipoamide dehydrogenases are functionally equivalent across species. To address this issue, we asked whether the human enzyme could restore function to the alpha-ketoacid dehydrogenase complexes in a yeast strain deficient in endogenous dihydrolipoamide dehydrogenase. This dihydrolipoamide dehydrogenase null mutant will not grow on non-fermentable carbon sources. The human enzyme expressed from a CEN plasmid complemented the growth phenotype and restored full activity to the pyruvate and alpha-ketoglutarate dehydrogenase complexes. Human dihydrolipoamide dehydrogenases with selected amino acid substitutions were then tested in the null strain for their ability to restore function. Substitutions tested represented naturally occurring candidate mutations identified in an individual with inactive dihydrolipoamide dehydrogenase. A K37E change had full function while a P453L change resulted in reduced dihydrolipoamide dehydrogenase abundance in the mitochondria and no detectable catalytic activity.}, }
@article {pmid8879241, year = {1996}, author = {Kumar, R and Maréchal-Drouard, L and Akama, K and Small, I}, title = {Striking differences in mitochondrial tRNA import between different plant species.}, journal = {Molecular &amp; general genetics : MGG}, volume = {252}, number = {4}, pages = {404-411}, pmid = {8879241}, issn = {0026-8925}, mesh = {Base Sequence ; Biological Transport ; Blotting, Northern ; Blotting, Southern ; Cloning, Molecular ; DNA Probes ; DNA, Mitochondrial/chemistry/genetics ; Evolution, Molecular ; Genes, Plant ; Mitochondria/metabolism ; Molecular Sequence Data ; Plants/*genetics ; RNA/genetics/isolation &amp; purification/*metabolism ; RNA, Mitochondrial ; RNA, Plant/genetics/*metabolism ; RNA, Transfer/genetics/*metabolism ; Solanum tuberosum/genetics/metabolism ; Trees/genetics/metabolism ; Triticum/genetics/metabolism ; Zea mays/genetics/metabolism ; }, abstract = {A systematic comparison of the tRNAs imported into the mitochondria of larch, maize and potato reveals considerable differences among the three species. Larch mitochondria import at least eleven different tRNAs (more than half of those tested) corresponding to ten different amino acids. For five of these tRNAs [tRNA(Phe(GAA)), tRNA(Lys(CUU)), tRNA(Pro(UGG)), tRNA(Ser(GCU)) and tRNA(Ser(UGA))] this is the first report of import into mitochondria in any plant species. There are also differences in import between relatively closely related plants; wheat mitochondria, unlike maize mitochondria import tRNA(His), and sunflower mitochondria, unlike mitochondria from other angiosperms tested, import tRNA(Ser(GCU)) and tRNA(Ser(UGA)). These results suggest that the ability to import each tRNA has been acquired independently at different times during the evolution of higher plants, and that there are few apparent restrictions on which tRNAs can or cannot be imported. The implications for the mechanisms of mitochondrial tRNA import in plants are discussed.}, }
@article {pmid8879237, year = {1996}, author = {Nakazono, M and Nishiwaki, S and Tsutsumi, N and Hirai, A}, title = {A chloroplast-derived sequence is utilized as a source of promoter sequences for the gene for subunit 9 of NADH dehydrogenase (nad9) in rice mitochondria.}, journal = {Molecular &amp; general genetics : MGG}, volume = {252}, number = {4}, pages = {371-378}, pmid = {8879237}, issn = {0026-8925}, mesh = {Base Sequence ; Blotting, Northern ; Chloroplasts/*genetics ; DNA Primers ; DNA, Mitochondrial/*genetics ; DNA, Plant/genetics ; Gene Expression Regulation, Plant ; Genes, Plant ; In Situ Hybridization ; *Mitochondrial Proteins ; NADH Dehydrogenase/genetics ; Oryza/*genetics ; Plant Proteins/*genetics ; *Promoter Regions, Genetic ; RNA, Transfer, Phe/genetics ; RNA, Transfer, Pro/genetics ; RNA, Transfer, Ser/genetics ; Transcription, Genetic ; }, abstract = {The chloroplast-derived sequence trnS-rps4/ 3'trnL-trnF-ndhJ-ndhK (4066 bases in length) is present in a region that starts 355 bases upstream of the gene for subunit 9 of NADH dehydrogenase (nad9) in the mitochondrial genome of rice. Northern blot hybridization revealed that three large transcripts of 3.05, 1.62 and 1.05 kb hybridized to strand-specific probes for both the nad9 gene and the chloroplast-derived sequence, indicating that the nad9 gene was transcribed together with the chloroplast-derived sequence. From the results of in vitro capping and ribonuclease protection experiments, as well as primer extension analysis, we identified at least seven sites for the initiation of transcription of nad9 in the chloroplast-derived sequence. All of the initiation sites for transcription of the nad9 gene were located in sequences homologous to chloroplast DNA. Two of seven initiation sites were flanked by a sequence homologous to the consensus promoter motif that includes the CRTA motif (where R is A or G) of the rice mitochondrion. However, the sequences surrounding the other five sites showed only limited similarity to the conserved sequence. It is suggested that all the promoters of the rice nad9 gene exist in a sequence that was transferred from the chloroplast during evolution. Thus, the chloroplast-derived sequence has a novel, significant function in the mitochondrial genome of this higher plant.}, }
@article {pmid8800209, year = {1996}, author = {Lang, BF and Goff, LJ and Gray, MW}, title = {A 5 S rRNA gene is present in the mitochondrial genome of the protist Reclinomonas americana but is absent from red algal mitochondrial DNA.}, journal = {Journal of molecular biology}, volume = {261}, number = {5}, pages = {407-413}, doi = {10.1006/jmbi.1996.0486}, pmid = {8800209}, issn = {0022-2836}, mesh = {Animals ; Base Sequence ; Conserved Sequence ; DNA, Bacterial ; DNA, Mitochondrial/*genetics ; DNA, Plant ; DNA, Protozoan ; Electron Transport Complex IV/genetics ; Eukaryota/*genetics ; Evolution, Molecular ; Molecular Sequence Data ; Multigene Family ; Nucleic Acid Conformation ; RNA, Ribosomal, 5S/chemistry/*genetics ; Rhodobacter/genetics ; Rhodophyta/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Triticum/genetics ; }, abstract = {Except in the case of land plants, mitochondrial ribosomes apparently lack a 5 S rRNA species, even though this small RNA is a component of all prokaryotic, chloroplast and eukaryotic cytosol ribosomes. In plants, the mitochondrial 5 S rRNA is encoded by mtDNA and differs in sequence from the 5 S rRNA specified by plant nuclear and chloroplast genomes. A distinctive 5 S rRNA component has not been found in the mitochondrial ribosomes of non-plant eukaryotes and, with the notable exception of the chlorophycean alga, Prototheca wickerhamii, a 5 S rRNA gene has not been identified in those non-plant mtDNAs characterized to date. Here, we report the presence of a 5 S rRNA gene in the mtDNA of the heterotrophic flagellate Reclinomonas americana. This unicellular eukaryote is a member of the jakobid flagellates, an early-diverging group of protists that share ultrastructural characteristics with the retortamonads, primitive protists that lack mitochondria. We report sequence data from the mtDNAs of the red algae Porphyra purpurea and Gracilariopsis lemaneiformis, which we use to evaluate a recent claim that a 5 S rRNA gene exists in the mtDNA of a third rhodophyte alga, Chondrus crispus. Our results lead us to the opposite conclusion: that a 5 S rRNA gene is not encoded by red algal mtDNA. In view of the accumulating evidence favoring a monophyletic origin of the mitochondrial genome, it is likely that a 5 S rRNA gene was present in an ancestral proto-mitochondrial genome, and that contemporary mtDNA-encoded 5 S rRNA genes have all descended from this ancestral gene. Considering the highly restricted phylogenetic distribution of identified mtDNA-encoded 5 S rRNA genes, it follows that the mitochondrial 5 S rRNA gene must have been lost multiple times during evolutionary diversification of the eukaryotic lineage.}, }
@article {pmid8790385, year = {1996}, author = {Bui, ET and Bradley, PJ and Johnson, PJ}, title = {A common evolutionary origin for mitochondria and hydrogenosomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {93}, number = {18}, pages = {9651-9656}, pmid = {8790385}, issn = {0027-8424}, support = {AI07323/AI/NIAID NIH HHS/United States ; AI27857/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Chaperonin 10/analysis ; Chaperonin 60/analysis ; Conserved Sequence ; HSP70 Heat-Shock Proteins/analysis ; Hydrogen ; *Mitochondria/chemistry ; Molecular Sequence Data ; *Organelles/chemistry ; Sequence Homology, Amino Acid ; *Trichomonas/chemistry ; }, abstract = {Trichomonads are among the earliest eukaryotes to diverge from the main line of eukaryotic descent. Keeping with their ancient nature, these facultative anaerobic protists lack two "hallmark" organelles found in most eukaryotes: mitochondria and peroxisomes. Trichomonads do, however, contain an unusual organelle involved in carbohydrate metabolism called the hydrogenosome. Like mitochondria, hydrogenosomes are double-membrane bounded organelles that produce ATP using pyruvate as the primary substrate. Hydrogenosomes are, however, markedly different from mitochondria as they lack DNA, cytochromes and the citric acid cycle. Instead, they contain enzymes typically found in anaerobic bacteria and are capable of producing molecular hydrogen. We show here that hydrogenosomes contain heat shock proteins, Hsp70, Hsp60, and Hsp10, with signature sequences that are conserved only in mitochondrial and alpha-Gram-negative purple bacterial Hsps. Biochemical analysis of hydrogenosomal Hsp60 shows that the mature protein isolated from the organelle lacks a short, N-terminal sequence, similar to that observed for most nuclear-encoded mitochondrial matrix proteins. Moreover, phylogenetic analyses of hydrogenosomal Hsp70, Hsp60, and Hsp10 show that these proteins branch within a monophyletic group composed exclusively of mitochondrial homologues. These data establish that mitochondria and hydrogenosomes have a common eubacterial ancestor and imply that the earliest-branching eukaryotes contained the endosymbiont that gave rise to mitochondria in higher eukaryotes.}, }
@article {pmid8878700, year = {1996}, author = {Albert, B and Godelle, B and Atlan, A and De Paepe, R and Gouyon, PH}, title = {Dynamics of plant mitochondrial genome: model of a three-level selection process.}, journal = {Genetics}, volume = {144}, number = {1}, pages = {369-382}, pmid = {8878700}, issn = {0016-6731}, mesh = {*Genome, Plant ; *Mitochondria ; *Models, Genetic ; Plants/*genetics ; *Selection, Genetic ; }, abstract = {The plant mitochondrial genome is composed of a set of molecules of various sizes that generate each other through recombination between repeated sequences. Molecular observations indicate that these different molecules are present in an equilibrium state. Different compositions of molecules have been observed within species. Recombination could produce deleted molecules with a high replication rate but bearing little useful information for the cell (such as "petite" mutants in yeast). In this paper we use a multilevel model to examine selection among rapidly replicating incomplete molecules and relatively slowly replicating complete molecules. Our model simulates the evolution of mitochondrial information through a three-level selection process including intermolecular, intermitochondrial, and intercellular selection. The model demonstrates that maintenance of the mitochondrial genome can result from multilevel selection, but maintenance is difficult to explain without the existence of selection at the intermitochondrial level. This study shows that compartmentation into mitochondria is useful for maintenance of the mitochondrial information. Our examination of evolutionary equilibria shows that different equilibria (with different combinations of molecules) can be obtained when recombination rates are lower than a threshold value. This may be interpreted as a drift-mutation balance.}, }
@article {pmid8752002, year = {1996}, author = {Zardoya, R and Meyer, A}, title = {Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates.}, journal = {Molecular biology and evolution}, volume = {13}, number = {7}, pages = {933-942}, doi = {10.1093/oxfordjournals.molbev.a025661}, pmid = {8752002}, issn = {0737-4038}, mesh = {Adenosine Triphosphatases/genetics ; Animals ; DNA, Mitochondrial/*genetics ; Evolution, Molecular ; Fishes/genetics ; Humans ; Least-Squares Analysis ; Mammals/genetics ; Mitochondria/*chemistry ; Models, Genetic ; Models, Statistical ; *Phylogeny ; Proteins/classification/*genetics ; Time Factors ; Vertebrates/classification/*genetics ; }, abstract = {A large number of studies in evolutionary biology utilize phylogenetic information obtained from mitochondrial DNA. Researchers place trust in this molecule and expect it generally to be a reliable marker for addressing questions ranging from population genetics to phylogenies among distantly related lineages. Yet, regardless of the phylogenetic method and weighting treatment, individual mitochondrial genes might potentially produce misleading evolutionary inferences and hence might not constitute an adequate representation neither of the entire mitochondrial genome nor of the evolutionary history of the organisms from which they are derived. We investigated the performance of all mitochondrial protein-coding genes to recover two expected phylogenies of tetrapods and mammals. According to these tests, mitochondrial protein-coding genes can be roughly classified into three groups of good (ND4, ND5, ND2, cytb, and COI), medium (COII, COIII, ND1, and ND6), and poor (ATPase 6, ND3, ATPase 8, and ND4L) phylogenetic performers in recovering these expected trees among phylogenetically distant relatives. How general our findings are is unclear. Simple length differences and rate differences between these genes cannot account for their different phylogenetic performance. The phylogenetic performance of these mitochondrial genes might depend on various factors that play a role in determining the probability of discovering the correct phylogeny such as the density of lineage creation events in time, the phylogenetic "depth" of the question, lineage-specific rate heterogeneity, and the completeness of taxa representation.}, }
@article {pmid8703097, year = {1996}, author = {Rannala, B and Yang, Z}, title = {Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference.}, journal = {Journal of molecular evolution}, volume = {43}, number = {3}, pages = {304-311}, pmid = {8703097}, issn = {0022-2844}, support = {GM40282/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bayes Theorem ; Death ; *Evolution, Molecular ; Female ; Globins/genetics ; Gorilla gorilla ; Humans ; Labor, Obstetric ; Markov Chains ; Mitochondria/metabolism ; *Models, Genetic ; Models, Statistical ; Pan troglodytes ; *Phylogeny ; Pongo pygmaeus ; Pregnancy ; Probability ; Pseudogenes ; RNA/genetics ; RNA, Mitochondrial ; }, abstract = {A new method is presented for inferring evolutionary trees using nucleotide sequence data. The birth-death process is used as a model of speciation and extinction to specify the prior distribution of phylogenies and branching times. Nucleotide substitution is modeled by a continuous-time Markov process. Parameters of the branching model and the substitution model are estimated by maximum likelihood. The posterior probabilities of different phylogenies are calculated and the phylogeny with the highest posterior probability is chosen as the best estimate of the evolutionary relationship among species. We refer to this as the maximum posterior probability (MAP) tree. The posterior probability provides a natural measure of the reliability of the estimated phylogeny. Two example data sets are analyzed to infer the phylogenetic relationship of human, chimpanzee, gorilla, and orangutan. The best trees estimated by the new method are the same as those from the maximum likelihood analysis of separate topologies, but the posterior probabilities are quite different from the bootstrap proportions. The results of the method are found to be insensitive to changes in the rate parameter of the branching process.}, }
@article {pmid8702755, year = {1996}, author = {Eden, A and Simchen, G and Benvenisty, N}, title = {Two yeast homologs of ECA39, a target for c-Myc regulation, code for cytosolic and mitochondrial branched-chain amino acid aminotransferases.}, journal = {The Journal of biological chemistry}, volume = {271}, number = {34}, pages = {20242-20245}, doi = {10.1074/jbc.271.34.20242}, pmid = {8702755}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Cytoplasm/enzymology ; Fungal Proteins ; Gene Expression ; Genes, Fungal ; Humans ; Mice ; Mitochondria/enzymology ; Mitochondrial Proteins ; Molecular Sequence Data ; Phylogeny ; Proteins/*genetics ; Proto-Oncogene Proteins c-myc/*physiology ; RNA, Messenger/genetics ; Saccharomyces cerevisiae/*genetics ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Sequence Homology, Amino Acid ; Signal Transduction ; Transaminases/*genetics ; }, abstract = {ECA39 was isolated as a target gene for c-Myc regulation in mice. We identified two homologs for the murine ECA39 in the yeast Saccharomyces cerevisiae, ECA39 and ECA40, as well as two human homologs. These genes show a significant homology to prokaryotic branched-chain amino acid aminotransferase (BCAT) (EC). To understand the function of eukaryotic ECA39 and ECA40, we deleted either gene from the yeast genome. Activity of branched-chain amino acid aminotransferase was measured in the wild-type and mutants with either leucine, isoleucine, or valine as substrates. The results demonstrate that in S. cerevisiae ECA39 and ECA40 code for mitochondrial and cytosolic branched-chain amino acid aminotransferases, respectively. ECA39 is highly expressed during log phase and is down-regulated during the stationary phase of growth, while ECA40 shows an inverse pattern of gene expression. In agreement with these results, while we previously showed that deletion of ECA39 affected the cell cycle in proliferating cells, we do not observe a growth phenotype in eca40Delta cells. We suggest that BCAT is a target for c-Myc activity and discuss the evolutionary conservation of prokaryotic and eukaryotic BCATs and their possible involvement in regulation of cell proliferation.}, }
@article {pmid8805838, year = {1996}, author = {Horner, DS and Hirt, RP and Kilvington, S and Lloyd, D and Embley, TM}, title = {Molecular data suggest an early acquisition of the mitochondrion endosymbiont.}, journal = {Proceedings. Biological sciences}, volume = {263}, number = {1373}, pages = {1053-1059}, doi = {10.1098/rspb.1996.0155}, pmid = {8805838}, issn = {0962-8452}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Evolution, Molecular ; *Mitochondria ; Phylogeny ; Symbiosis ; Trichomonas vaginalis/*physiology/ultrastructure ; }, abstract = {The three deepest branching eucaryotic lineages in small subunit ribosomal RNA phylogenies are the amitochondriate Microspora, Metamonada and Parabasala. They are followed by either the Euglenozoa (e.g. Euglena and Trypanosoma) or the Percolozoa as the first mitochondria-containing eucaryotes. To investigate the hypothesis of an even earlier timing of the mitochondrion endosymbiosis we have amplified a partial cpn-60 coding region from the parabasalid Trichomonas vaginalis and the first such sequence from a percolozoan, Naegleria fowleri. Analysis of predicted protein sequences reveals a high degree of sequence similarity (> or = 40%) with a selection of published bacterial and mitochondrial cpn-60s for both taxa. Both sequences were recovered within a strongly supported monophyletic group, otherwise defined by mitochondrial sequences, which systematically clustered with alpha-proteobacteria. These results provide compelling evidence that the ancestor of T. vaginalis once contained the endosymbiont which gave rise to mitochondria, and suggest that this symbiosis probably occurred before the Trichomonas lineage diverged from the main eukaryote trunk. It also makes feasible the published hypothesis that the Trichomonas hydrogenosome might represent a biochemically modified mitochondrion. Analysis of the N. fowleri cpn-60 did not support the hypothesis that the mitochondrion-containing Percolozoa represent an earlier branch in the cpn-60 tree than Trichomonas or Trypanosoma.}, }
@article {pmid8812436, year = {1996}, author = {Sampson, MJ and Lovell, RS and Davison, DB and Craigen, WJ}, title = {A novel mouse mitochondrial voltage-dependent anion channel gene localizes to chromosome 8.}, journal = {Genomics}, volume = {36}, number = {1}, pages = {192-196}, doi = {10.1006/geno.1996.0445}, pmid = {8812436}, issn = {0888-7543}, support = {1P30-HD27823/HD/NICHD NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Chromosome Mapping/*methods ; Cloning, Molecular ; Crosses, Genetic ; DNA, Complementary/genetics ; Ion Channels/*genetics ; Membrane Proteins/*genetics ; Mice ; Mice, Inbred C57BL ; *Mitochondria ; Molecular Sequence Data ; Muridae ; Organ Specificity ; Phylogeny ; *Porins ; RNA, Messenger/analysis ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Transcription, Genetic/genetics ; Voltage-Dependent Anion Channels ; }, abstract = {Voltage-dependent anion channels (VDACs) are small pore-forming channels found in the outer membrane of mitochondria. VDACs translocate adenine nucleotides and are the binding sites for several cytosolic kinases important in intermediary metabolism. Recently two human VDAC cDNAs (HVDAC1 and HVDAC2) were isolated, and possible orthologues of these genes have been isolated from mouse, bovine, and rat tissues. We report the isolation of a novel third VDAC cDNA from the mouse, designated MVDAC3. The deduced MVDAC3 protein is approximately 70% identical to the previously isolated MVDAC1 and MVDAC2 proteins. The MVDAC3 gene was mapped by an interspecies backcross panel to mouse chromosome 8. A database search using the mouse VDACs identified a second yeast VDAC-like gene that retains about 20% amino acid sequence identity with the mouse VDAC genes and 50% identity with the previously isolated yeast VDAC gene. The phylogenetic relationship of the eukaryotic VDAC genes is presented.}, }
@article {pmid8774905, year = {1996}, author = {Maréchal-Drouard, L and Kumar, R and Remacle, C and Small, I}, title = {RNA editing of larch mitochondrial tRNA(His) precursors is a prerequisite for processing.}, journal = {Nucleic acids research}, volume = {24}, number = {16}, pages = {3229-3234}, pmid = {8774905}, issn = {0305-1048}, mesh = {Base Sequence ; Biological Evolution ; Cloning, Molecular ; DNA, Complementary/genetics ; Genes, Plant ; Mitochondria/*genetics ; Molecular Sequence Data ; *RNA Editing ; RNA Precursors/*metabolism ; RNA, Transfer, His/*genetics ; Sequence Analysis, DNA ; Trees/*genetics ; }, abstract = {Larch mitochondria contain a'native'tRNAHis which is absent from angiosperms. Sequence comparisons of genomic DNA and cDNA obtained from unprocessed primary transcripts of the larch mitochondrial gene trnH encoding this tRNA revealed three nucleotide discrepancies. These three nucleotide alterations, in the acceptor stem, D stem and anticodon stem respectively, are conversions of genomic cytidines to thymidines in the cDNA (uridines in the tRNA) and thus resemble the RNA editing events observed in nearly all plant mitochondrial mRNAs. Two cases of editing affecting mitochondrial tRNAs from angiosperms have already been described, but we present here the first example of such events in a gymnosperm mitochondrial tRNA. All three editing events correct mismatched C x A base pairs which appear when folding the gene sequence into the standard cloverleaf structure, thereby improving the secondary structure of the tRNA. When incubated with a heterologous potato mitochondrial processing extract, only the edited form of the larch mitochondrial tRNAHis precursor was efficiently processed in vitro. These data strongly suggest that editing of larch mitochondrial tRNAHis is a prerequisite for its processing.}, }
@article {pmid8765228, year = {1996}, author = {Pawelek, PD and MacKenzie, RE}, title = {Methylenetetrahydrofolate dehydrogenase-cyclohydrolase from Photobacterium phosphoreum shares properties with a mammalian mitochondrial homologue.}, journal = {Biochimica et biophysica acta}, volume = {1296}, number = {1}, pages = {47-54}, doi = {10.1016/0167-4838(96)00052-0}, pmid = {8765228}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Enzyme Activation/drug effects ; Genetic Complementation Test ; Humans ; Kinetics ; Methylenetetrahydrofolate Dehydrogenase (NADP)/chemistry/*genetics/*metabolism ; Mitochondria/*enzymology ; Molecular Sequence Data ; Nucleotides/metabolism ; Phosphates/metabolism/pharmacology ; Photobacterium/*enzymology ; Phylogeny ; Recombinant Proteins/chemistry/genetics/metabolism ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {The marine bioluminescent bacterium Photobacterium phosphoreum expresses a bifunctional methylenetetrahydrofolate dehydrogenase-cyclohydrolase with dual cofactor specificity. An investigation of the kinetic parameters of the P. phosphoreum enzyme indicate that its utilization of dinucleotide cofactors shares similarities with the human mitochondrial dehydrogenase-cyclohydrolase. Both enzymes exhibit dual cofactor specificity and the NAD(+)-dependent dehydrogenase activities from both enzymes can be activated by inorganic phosphate. Furthermore, an analysis of multiply aligned dehydrogenase-cyclohydrolase sequences from 11 species revealed that bacterial and mitochondrial enzymes are more closely related to each other than to the dehydrogenase-cyclohydrolase domains from eukaryotic trifunctional enzymes, and that the bacterial and mitochondrial enzymes share a common point of divergence. Since the NADP+ cofactor is kinetically favoured by a factor of 18 over NAD+, and is therefore likely to be the preferred in vivo cofactor, we propose that the P. phosphoreum enzyme and the human mitochondrial enzyme evolved from a common ancestral dehydrogenase-cyclohydrolase with dual cofactor specificity, but that cofactor preference in these two enzymes diverged in response to different metabolic requirements.}, }
@article {pmid8940916, year = {1996}, author = {Suzuki, T and Yuasa, H and Machida, Y}, title = {Phylogenetic position of the Japanese river otter Lutra nippon inferred from the nucleotide sequence of 224 bp of the mitochondrial cytochrome b gene.}, journal = {Zoological science}, volume = {13}, number = {4}, pages = {621-626}, doi = {10.2108/zsj.13.621}, pmid = {8940916}, issn = {0289-0003}, mesh = {Animals ; Base Sequence ; Cytochrome b Group/*genetics ; DNA ; Fossils ; Mitochondria/*enzymology ; Molecular Sequence Data ; Otters/*classification/genetics ; *Phylogeny ; Polymerase Chain Reaction ; }, abstract = {A 224 bp fragment of the mitochondrial cytochrome b gene has been amplified from a 30-year-old mummy-like specimen of the Japanese river otter Lutra nippon by polymerase chain reaction (PCR). The amplified products were subcloned in the Smal site of pUC 18 and sequenced. The sequence was different from those of the congeneric Eurasian otters Lutra lutra (Latvia) and Lutra lutra (China) in 7-9 nucleotides, all of which were located at the third position of a codon and identified as transitional differences A<-->G or C<-->T. The phylogenetic analysis using the 224 bp sequences of Lutra nippon, Lutra lutra (Lativa), Lutra lutra (China), Aonyx cinerea (Asian small-clawed otter), Mustela sibirica and Mustela itatsi (weasels) supports the recent morphological study that the Japanese river otter is not a subspecies of Lutra lutra, but a distinct species, Lutra nippon. We found that Lutra nippon and Lutra lutra contain the cytochrome b-like sequences, that appear to be a pseudo-form of cytochrome b gene. The sequences are characterized by the presence of deletion and termination codons by the presence of several types of sequences with minor variations, and by the faster evolutionary rate compared with that of the mitochondrial cytochrome b gene. The genes would present in the nuclear DNA rather than in the mitochondrial DNA, as in the case of the nonfunctional cytochrome b-like sequences previously reported in a rodent.}, }
@article {pmid8874090, year = {1996}, author = {Tandler, B and Phillips, CJ and Nagato, T}, title = {Histological convergent evolution of the accessory submandibular glands in four species of frog-eating bats.}, journal = {European journal of morphology}, volume = {34}, number = {3}, pages = {163-168}, doi = {10.1076/ejom.34.3.163.13028}, pmid = {8874090}, issn = {0924-3860}, mesh = {Animals ; *Biological Evolution ; Chiroptera/*physiology ; Cytoplasm/ultrastructure ; Gap Junctions/ultrastructure ; Inclusion Bodies/ultrastructure ; Microscopy, Electron ; Species Specificity ; Submandibular Gland/*cytology/ultrastructure ; }, abstract = {The accessory submandibular glands in four species of bats were examined by electron microscopy. These four species represent two independently evolved lineages. The fringe-lipped bat, Trachops cirrhosis, is a Neotropical phyllostomid species, whereas the false vampire bats of southeast Asia, Megaderma lyra and M. spasma, and the heart-nosed bat, Cardioderma cor, of East Africa are megadermatid species. These glands show extreme deviation from typical salivary gland histology: their secretory endpieces are in the form of follicles and their ducts lack the cytological details that permit identification of diverse duct segments. Despite their unusual histology, the secretory endpieces in M. lyra, M. spasma, and C. cor consist of secretory cells that conform to typical secretory cell morphology. In contrast, secretion by follicular cells in T. cirrhosis involves unusual cytoplasmic bodies, and their mitochondria frequently have intracristal crystalloids. Ducts in all four species consist of simple cuboidal to columnar epithelium without basal striations. Follicles and ducts in all four bats are surrounded by numerous myoepithelial cells and are heavily innervated by hypolemmal nerve terminals. Despite their widely separated geographical ranges, all four bat species consume frogs and other vertebrates. Frogs and toads often possess toxic cutaneous glands that provide a chemical defense against predation. It is postulated that the unusual accessory glands in the four frog-eating species secrete toxin-neutralizing salivary factors. The follicular form of the endpieces permits storage of preformed saliva and their coterie of myoepithelial cells and hypolemmal nerve terminals facilitates the sudden and rapid expulsion of saliva into the oral cavity during the consumption of noxious amphibians.}, }
@article {pmid8776869, year = {1996}, author = {Parker, A and Kornfield, I}, title = {An improved amplification and sequencing strategy for phylogenetic studies using the mitochondrial large subunit rRNA gene.}, journal = {Genome}, volume = {39}, number = {4}, pages = {793-797}, doi = {10.1139/g96-099}, pmid = {8776869}, issn = {0831-2796}, mesh = {Animals ; Base Sequence ; Birds/genetics ; Conserved Sequence ; DNA Primers/*chemistry ; DNA, Mitochondrial/genetics ; Drosophila melanogaster/genetics ; Fishes/genetics ; Genetic Variation ; Mitochondria/*genetics ; Models, Genetic ; Molecular Sequence Data ; Nephropidae/genetics ; *Phylogeny ; Polymerase Chain Reaction/*methods ; RNA, Ribosomal, 16S/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Numerous molecular systematic studies have employed variation in the mitochondrial large subunit (16s) rRNA gene to infer patterns of relationship among species and higher taxa. The primers most commonly employed in 16s rRNA amplification and sequencing bracket an approximately 600 bp portion of this gene. However, most of the informative variation occurs within a 200 bp subset of this segment. We describe a novel primer pair designed to amplify this variable region in a wide range of taxa, allowing broader application and considerable streamlining of data acquisition for studies using this gene.}, }
@article {pmid8755543, year = {1996}, author = {Long, M and de Souza, SJ and Rosenberg, C and Gilbert, W}, title = {Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome c1 precursor.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {93}, number = {15}, pages = {7727-7731}, pmid = {8755543}, issn = {0027-8424}, support = {GM37997/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Cell Nucleus/metabolism ; Conserved Sequence ; Cytochromes c1/chemistry/*genetics ; *Exons ; *Genes, Plant ; Glyceraldehyde-3-Phosphate Dehydrogenases/genetics ; Humans ; Introns ; Mitochondria/*metabolism ; Molecular Sequence Data ; Pisum sativum/genetics ; *Phylogeny ; Plants/genetics/*metabolism ; Protein Precursors/chemistry/*genetics ; Sequence Homology, Amino Acid ; Solanum tuberosum/genetics ; Vertebrates ; }, abstract = {Since most of the examples of "exon shuffling" are between vertebrate genes, the view is often expressed that exon shuffling is limited to the evolutionarily recent lineage of vertebrates. Although exon shuffling in plants has been inferred from the analysis of intron phases of plant genes [Long, M., Rosenberg, C. &amp; Gilbert, W. (1995) Proc. Natl. Acad. Sci. USA 92, 12495-12499] and from the comparison of two functionally unknown sunflower genes [Domon, C. &amp; Steinmetz, A. (1994) Mol. Gen. Genet. 244, 312-317], clear cases of exon shuffling in plant genes remain to be uncovered. Here, we report an example of exon shuffling in two important nucleus-encoded plant genes: cytosolic glyceraldehyde-3-phosphate dehydrogenase (cytosolic GAPDH or GapC) and cytochrome c1 precursor. The intron-exon structures of the shuffled region indicate that the shuffling event took place at the DNA sequence level. In this case, we can establish a donor-recipient relationship for the exon shuffling. Three amino terminal exons of GapC have been donated to cytochrome c1, where, in a new protein environment, they serve as a source of the mitochondrial targeting function. This finding throws light upon an old important but unsolved question in gene evolution: the origin of presequences or transit peptides that generally exist in nucleus-encoded organelle genes.}, }
@article {pmid8670880, year = {1996}, author = {Szczepanek, T and Lazowska, J}, title = {Replacement of two non-adjacent amino acids in the S.cerevisiae bi2 intron-encoded RNA maturase is sufficient to gain a homing-endonuclease activity.}, journal = {The EMBO journal}, volume = {15}, number = {14}, pages = {3758-3767}, pmid = {8670880}, issn = {0261-4189}, mesh = {Amino Acid Sequence ; Base Sequence ; Conserved Sequence ; Cytochrome b Group/*genetics ; DNA/metabolism ; DNA, Fungal ; Deoxyribonuclease I/chemistry/genetics/*metabolism ; Endoribonucleases/chemistry/genetics/*metabolism ; *Introns ; Molecular Sequence Data ; Mutagenesis ; Nucleotidyltransferases/chemistry/genetics/*metabolism ; Saccharomyces/*enzymology/genetics ; Saccharomyces cerevisiae/*enzymology/genetics ; Structure-Activity Relationship ; }, abstract = {Two homologous group I introns, the second intron of the cyt b gene, from related Saccharomyces species differ in their mobility. The S.capensis intron is mobile and encodes the I-ScaI endonuclease promoting intron homing, whilst the homologous S.cerevisiae intron is not mobile, but functions as an RNA maturase promoting splicing. These two intron-encoded proteins differ by only four amino acid substitutions. Taking advantage of the remarkable similarity of the two intron open reading frames and using biolistic transformation of mitochondria, we show that the replacement of only two non-adjacent residues in the S.cerevisiae maturase carboxy-terminal sequence is sufficient to induce a homing-endonuclease activity without losing the splicing function. Also, we demonstrate that these two activities reside in the S.capensis bi2-encoded protein which functions in both splicing and intron mobility in the wild-type cells. These results provide new insight into our understanding of the activity and the evolution of group I intron-encoded proteins.}, }
@article {pmid8663075, year = {1996}, author = {Kobayashi, M and Matsuo, Y and Takimoto, A and Suzuki, S and Maruo, F and Shoun, H}, title = {Denitrification, a novel type of respiratory metabolism in fungal mitochondrion.}, journal = {The Journal of biological chemistry}, volume = {271}, number = {27}, pages = {16263-16267}, doi = {10.1074/jbc.271.27.16263}, pmid = {8663075}, issn = {0021-9258}, mesh = {*Adaptor Proteins, Signal Transducing ; *Adaptor Proteins, Vesicular Transport ; Adenosine Triphosphate/metabolism ; Antimycin A/pharmacology ; Cytochromes/metabolism ; Energy Metabolism ; Fusarium/*metabolism ; Guanine Nucleotide Exchange Factors ; Kinetics ; Microscopy, Fluorescence ; Mitochondria/drug effects/*metabolism ; Mitosporic Fungi/*metabolism ; Nitrate Reductases/antagonists &amp; inhibitors/*metabolism ; Nitrite Reductases/antagonists &amp; inhibitors/*metabolism ; *Oxygen Consumption/drug effects ; Proteins/isolation &amp; purification/*metabolism ; Rotenone/pharmacology ; Shc Signaling Adaptor Proteins ; Spectrophotometry ; Thenoyltrifluoroacetone/pharmacology ; }, abstract = {Subcellular localization and coupling to ATP synthesis were investigated with respect to the denitrifying systems of two fungi, Fusarium oxysporum and Cylindrocarpon tonkinense. Dissimilatory nitrate reductase of F. oxysporum or nitrite reductase of C. tonkinense could be detected in the mitochondrial fraction prepared from denitrifying cells of each fungus. Fluorescence immunolocalization, cofractionation with mitochondrial marker enzymes, and cytochromes provided evidence that the denitrifying enzymes are co-purified with mitochondria. Respiratory substrates such as malate plus pyruvate, succinate, and formate were effective donors of electrons to these activities in the mitochondrial fractions. Moreover, nitrite and nitrate reduction were shown to be coupled to the synthesis of ATP with energy yields (P:NO3- or P:2e ratios) of 0.88 to 1.4, depending upon whether malate/pyruvate or succinate were provided as substrates. Nitrate or nitrite reductase activity was inhibited by inhibitors such as rotenone, antimycin A, and thenoyltrifluoroacetone. Thus, fungal denitrification activities are localized to mitochondria and are coupled to the synthesis of ATP. The existence of these novel respiration systems are discussed with regard to the origin and evolution of mitochondria.}, }
@article {pmid8660429, year = {1996}, author = {Sbisà, E and Pesole, G and Tullo, A and Saccone, C}, title = {The evolution of the RNase P- and RNase MRP-associated RNAs: phylogenetic analysis and nucleotide substitution rate.}, journal = {Journal of molecular evolution}, volume = {43}, number = {1}, pages = {46-57}, pmid = {8660429}, issn = {0022-2844}, mesh = {Animals ; Arabidopsis/genetics ; Base Sequence ; *Biological Evolution ; Cell Nucleus/metabolism ; Endoribonucleases/*genetics ; Humans ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA/chemistry/*genetics ; RNA, Catalytic/*genetics ; RNA, Mitochondrial ; Ribonuclease P ; Ribonucleoproteins/genetics ; Saccharomyces/genetics ; Schizosaccharomyces/genetics ; Sequence Homology, Nucleic Acid ; Vertebrates/genetics ; }, abstract = {We report a detailed evolutionary study of the RNase P- and RNase MRP- associated RNAs. The analyses were performed on all the available complete sequences of RNase MRP (vertebrates, yeast, plant), nuclear RNase P (vertebrates, yeast), and mitochondrial RNase P (yeast) RNAs. For the first time the phylogenetic distance between these sequences and the nucleotide substitution rates have been quantitatively measured.The analyses were performed by considering the optimal multiple alignments obtained mostly by maximizing similarity between primary sequences. RNase P RNA and MRP RNA display evolutionary dynamics following the molecular clock. Both have similar rates and evolve about one order of magnitude faster than the corresponding small rRNA sequences which have been, so far, the most common gene markers used for phylogeny. However, small rRNAs evolve too slowly to solve close phylogenetic relationships such as those between mammals. The quicker rate of RNase P and MRP RNA allowed us to assess phylogenetic relationships between mammals and other vertebrate species and yeast strains. The phylogenetic data obtained with yeasts perfectly agree with those obtained by functional assays, thus demonstrating the potential offered by this approach for laboratory experiments.}, }
@article {pmid8660427, year = {1996}, author = {Xia, X and Hafner, MS and Sudman, PD}, title = {On transition bias in mitochondrial genes of pocket gophers.}, journal = {Journal of molecular evolution}, volume = {43}, number = {1}, pages = {32-40}, pmid = {8660427}, issn = {0022-2844}, mesh = {Analysis of Variance ; Animals ; Base Sequence ; Consensus Sequence ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Mathematics ; Mitochondria/metabolism ; *Models, Genetic ; Mutation ; *Phylogeny ; Probability ; Rodentia/*genetics ; }, abstract = {The relative contribution of mutation and purifying selection to transition bias has not been quantitatively assessed in mitochondrial protein genes. The observed transition/transversion (s/v) ratio is (micros Ps)/(microv Pv), where micros and microv denote mutation rate of transitions and transversions, respectively, and Ps and Pv denote fixation probabilities of transitions and transversions, respectively. Because selection against synonymous transitions can be assumed to be roughly equal to that against synonymous transversions, Ps/Pv approximately 1 at fourfold degenerate sites, so that the s/v ratio at fourfold degenerate sites is approximately micros/microv, which is a measure of mutational contribution to transition bias. Similarly, the s/v ratio at nondegenerate sites is also an estimate of micros/microv if we assume that selection against nonsynonymous transitions is roughly equal to that against nonsynonymous transversions. In two mitochondrial genes, cytochrome oxidase subunit I (COI) and cytochrome b (cyt-b) in pocket gophers, the s/v ratio is about two at nondegenerate and fourfold degenerate sites for both the COI and the cyt-b genes. This implies that mutation contribution to transition bias is relatively small. In contrast, the s/v ratio is much greater at twofold degenerate sites, being 48 for COI and 40 for cyt-b. Given that the micros/microv ratio is about 2, the Ps/Pv ratio at twofold degenerate sites must be on the order of 20 or greater. This suggests a great effect of purifying selection on transition bias in mitochondrial protein genes because transitions are synonymous and transversions are nonsynonymous at twofold degenerate sites in mammalian mitochondrial genes. We also found that nonsynonymous mutations at twofold degenerate sites are more neutral than nonsynonymous mutations at nondegenerate sites, and that the COI gene is subject to stronger purifying selection than is the cyt-b gene. A model is presented to integrate the effect of purifying selection, codon bias, DNA repair and GC content on s/v ratio of protein-coding genes.}, }
@article {pmid8662929, year = {1996}, author = {Gagnon, Y and Lacoste, L and Champagne, N and Lapointe, J}, title = {Widespread use of the glu-tRNAGln transamidation pathway among bacteria. A member of the alpha purple bacteria lacks glutaminyl-trna synthetase.}, journal = {The Journal of biological chemistry}, volume = {271}, number = {25}, pages = {14856-14863}, doi = {10.1074/jbc.271.25.14856}, pmid = {8662929}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/biosynthesis/*chemistry/*metabolism ; Chromatography, High Pressure Liquid ; Cloning, Molecular ; Confidence Intervals ; Enzyme Induction ; Escherichia coli/*metabolism ; Genes, Bacterial ; Glutamate-tRNA Ligase/*chemistry ; Isopropyl Thiogalactoside/pharmacology ; Molecular Sequence Data ; Phylogeny ; Promoter Regions, Genetic ; RNA, Transfer, Amino Acyl/isolation &amp; purification/*metabolism ; RNA, Transfer, Gln/*metabolism ; Recombinant Proteins/biosynthesis/metabolism ; Sequence Homology, Amino Acid ; Sinorhizobium meliloti/*enzymology/genetics ; Transferases/*metabolism ; }, abstract = {The expression of the Rhizobium meliloti glutamyl-tRNA synthetase gene in Escherichia coli under the control of a trc promoter results in a toxic effect upon isopropyl-beta-D-thiogalactopyranoside induction, which is probably caused by a misacylation activity. To further investigate this unexpected result, we looked at the pathway of Gln-tRNAGln formation in R. meliloti. No glutaminyl-tRNA synthetase activity has been found in R. meliloti crude extract, but we detected a specific aminotransferase activity that changes Glu-tRNAGln to Gln-tRNAGln. Our results show that R. meliloti, a member of the alpha-subdivision of the purple bacteria, is the first Gram-negative bacteria reported to use a transamidation pathway for Gln-tRNAGln synthesis. A phylogenetic analysis of the contemporary glutamyl-tRNA synthetase and glutaminyl-tRNA synthetase amino acid sequences reveals that a close evolutionary relationship exists between R. meliloti and yeast mitochondrial glutamyl-tRNA synthetases, which is consistent with an origin of mitochondria in the alpha-subdivision of Gram-negative purple bacteria. A 256-amino acid open reading frame closely related to bacterial glutamyl-tRNA synthetases, which probably originates from a glutamyl-tRNA synthetase gene duplication, was found in the 4-min region of the E. coli chromosome. We suggest that this open reading frame is a relic of an ancient transamidation pathway that occurred in an E. coli ancestor before the horizontal transfer of a eukaryotic glutaminyl-tRNA synthetase (Lamour, V., Quevillon, S., Diriong, S., N'Guyen, V. C., Lipinski, M., and Mirande, M.(1994) Proc. Natl. Acad. Sci. U. S. A. 91, 8670-8674) and that it favored its stable acquisition. From these observations, a revisited model for the evolution of the contemporary glutamyl-tRNA synthetases and glutaminyl-tRNA synthetases that differs from the generally accepted model for the evolution of aminoacyl-tRNA synthetases is proposed.}, }
@article {pmid8672552, year = {1996}, author = {Bouzidi, MF and Enjolras, N and Carrier, H and Vial, C and Lopez-Mediavilla, C and Burt-Pichat, B and Couthon, F and Godinot, C}, title = {Variations of muscle mitochondrial creatine kinase activity in mitochondrial diseases.}, journal = {Biochimica et biophysica acta}, volume = {1316}, number = {2}, pages = {61-70}, doi = {10.1016/0925-4439(95)00126-3}, pmid = {8672552}, issn = {0006-3002}, mesh = {Adolescent ; Adult ; Aged ; Blotting, Western ; Child ; Child, Preschool ; Citrate (si)-Synthase/metabolism ; Creatine Kinase/*metabolism ; Female ; HeLa Cells ; Humans ; Male ; Middle Aged ; Mitochondria, Muscle/*enzymology ; Mitochondrial Myopathies/*enzymology ; Oxidative Phosphorylation ; }, abstract = {Mitochondrial creatine kinase (mtCK) activity has been measured in the mitochondria isolated from the muscle of 69 patients suspected of mitochondrial diseases. The isolated mitochondria did not contain significant amounts of the muscle isoform of creatine kinase, as checked by an immunoassay performed after electrophoretic separation of the various isoforms. Hence, the enzyme assay reliably represented the mtCK activity. Therefore, a simple measurement of CK activity in isolated mitochondria permitted the measurement of mtCK activity. An absence of mtCK activity in muscle was never observed. The lowest activities were not associated to defined mitochondrial diseases linked to defects of respiratory chain complexes or to defects of citric cycle enzymes. On the contrary, mtCK activity was significantly increased in the muscle of patients exhibiting ragged red fibers. This increase was generally associated to an increase of citrate synthase activity. Since ragged-red fibers and elevated mtCK activities were generally not found in children younger than 3 years, even in cases of characteristic oxidative phosphorylation deficiency, it is suggested that the increase in mtCK activity as well as the appearance of ragged-red fibers are not the first events which occur during the evolution of mitochondrial diseases but would rather be long-term secondary processes which slowly develop in deficient mitochondria.}, }
@article {pmid8652667, year = {1996}, author = {Arts, GJ and Benne, R}, title = {Mechanism and evolution of RNA editing in kinetoplastida.}, journal = {Biochimica et biophysica acta}, volume = {1307}, number = {1}, pages = {39-54}, doi = {10.1016/0167-4781(96)00021-8}, pmid = {8652667}, issn = {0006-3002}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Gene Expression ; Kinetoplastida/*genetics ; Mitochondria/genetics ; Models, Genetic ; Molecular Sequence Data ; Proteins/genetics ; *RNA Editing ; }, }
@article {pmid8881281, year = {1996}, author = {Garcia-Machado, E and Dennebouy, N and Suarez, MO and Mounolou, JC and Monnerot, M}, title = {Partial sequence of the shrimp Penaeus notialis mitochondrial genome.}, journal = {Comptes rendus de l'Academie des sciences. Serie III, Sciences de la vie}, volume = {319}, number = {6}, pages = {473-486}, pmid = {8881281}, issn = {0764-4469}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/*chemistry ; Drosophila/genetics ; Genetic Code ; *Genome ; Mitochondria/genetics ; Molecular Sequence Data ; Penaeidae/*genetics ; Phylogeny ; RNA, Transfer/chemistry/ultrastructure ; *Sequence Homology, Nucleic Acid ; }, abstract = {About half of the mitochondrial DNA of the shrimp Penaeus notialis (Crustacea: Decapoda) has been cloned (in 2 overlapping fragments of 7.9 kb and 1 kb) and partially sequenced. The gene content and arrangement are identical to that of the homologous domain in Drosophila yakuba. Intergenic nucleotides are scarce and a 982 bp non-coding sequence exhibit features similar to that of mtDNA control regions. The gene organization and the tRNA structures differentiate the Penaeus notialis mitochondrial genome from that of Artemia franciscana. Paraphyletism of crustacean mtDNA with respect to Insecta is discussed. A secondary structure of s-rRNA is proposed.}, }
@article {pmid8744769, year = {1996}, author = {Talbot, SL and Shields, GF}, title = {A phylogeny of the bears (Ursidae) inferred from complete sequences of three mitochondrial genes.}, journal = {Molecular phylogenetics and evolution}, volume = {5}, number = {3}, pages = {567-575}, doi = {10.1006/mpev.1996.0051}, pmid = {8744769}, issn = {1055-7903}, mesh = {Animals ; Asia ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/*chemistry/genetics ; *Evolution, Molecular ; Mammals ; Molecular Sequence Data ; North America ; Paleontology ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Transfer, Pro/*genetics ; RNA, Transfer, Thr/*genetics ; Software ; Time ; Ursidae/*classification/*genetics ; }, abstract = {Complete sequences of DNA are described for the cytochrome b tRNA(Thr) and tRNA(Pro) genes of mitochondria of four extant species of ursids and compared to sequences of four other species of ursids previously studied by us. Phylogenetic analyses indicate that the giant panda and the spectacled bear are the basal taxa of the ursid radiation. The ursines, a group which includes the sun bear, sloth bear, American black bear, Asiatic black bear, brown bear, and polar bear, experienced a rapid radiation during the mid Pliocene to early Pleistocene. The Asiatic black bear and American black bear are sister taxa. The brown bear and polar bear are the most recently derived of the ursines, with the polar bear originating from within a clade of brown bears during the Pleistocene. This paraphyletic association suggests that the rate of morphological evolution may be accelerated relative to that of molecular evolution when a new ecological niche is occupied. Calibration of the corrected average number of nucleotide differences per site with the fossil record indicates that transitions at third positions of codons in the ursid cytochrome b gene occur at a rate of approximately 6% per million years, which is considerably slower than comparable values reported for other species of mammal.}, }
@article {pmid8744351, year = {1996}, author = {Cedergren, R and Miramontes, P}, title = {The puzzling origin of the genetic code.}, journal = {Trends in biochemical sciences}, volume = {21}, number = {6}, pages = {199-200}, pmid = {8744351}, issn = {0968-0004}, mesh = {Amino Acids/metabolism ; Amino Acyl-tRNA Synthetases/genetics/metabolism ; Codon/genetics ; *Evolution, Molecular ; Genetic Code/*genetics ; Oligoribonucleotides/metabolism ; Phylogeny ; RNA/metabolism ; RNA, Transfer/metabolism ; }, abstract = {Recent results add to the mystery of the origin of the genetic code. In spite of early doubts, RNA can discriminate between hydrophobic amino acids under certain contexts. Moreover, codon reassignment, which has taken place in several organisms and mitochondria, is not a random process. Finally, phylogenies of some aminoacyl-tRNA synthetases suggest that the entire code was not completely assigned at the time of the divergence of bacteria from nucleated cells.}, }
@article {pmid8662206, year = {1996}, author = {Hayashi-Ishimaru, Y and Ohama, T and Kawatsu, Y and Nakamura, K and Osawa, S}, title = {UAG is a sense codon in several chlorophycean mitochondria.}, journal = {Current genetics}, volume = {30}, number = {1}, pages = {29-33}, doi = {10.1007/s002940050096}, pmid = {8662206}, issn = {0172-8083}, mesh = {Alanine/genetics ; Amino Acid Sequence ; Base Sequence ; Chlorophyta/classification/enzymology/*genetics ; Codon/*genetics ; DNA Primers/genetics ; Electron Transport Complex IV/chemistry/genetics ; Leucine/genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Protein Conformation ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {The mitochondrial genetic code of those land plants and green algae that have been examined does not deviate from the universal one. A red alga, Chondrus crispus, is the sole reported example throughout the algae that uses a deviant (non-universal) mitochondrial genetic code (UGA=Trp). We have analyzed 366-bp DNA sequences of the gene for mitochondrial cytochrome oxidase subunit I (COXI) from ten chlorophyceaen algae, and detected 3-8 in-frame UAG codons in the sequences of five species. Comparisons of these sequences with those of other algae and land plants have shown that most of the UAG sites in Hydrodictyon reticulatum, Pediastrum boryanum and Tetraedron bitridens correspond to alanine, and those of Coelastrum microporum and Scenedesmus quadricauda to leucine. The three species in which UAG probably codes for alanine are characterized by zoospore formation in asexual reproduction and form a clade in the COXI phylogenetic tree. The two species in which UAG codes for leucine are known to form daughter coenobia and pair in the tree. This is the first report on a deviant mitochondrial genetic code in green algae. Mutational change(s) in the release factor corresponding to UAG would be involved in these code changes. No genetic code deviation has been found in five other species examined.}, }
@article {pmid8675018, year = {1996}, author = {Couzin, N and Trézéguet, V and Le Saux, A and Lauquin, GJ}, title = {Cloning of the gene encoding the mitochondrial adenine nucleotide carrier of Schizosaccharomyces pombe by functional complementation in Saccharomyces cerevisiae.}, journal = {Gene}, volume = {171}, number = {1}, pages = {113-117}, doi = {10.1016/0378-1119(96)00095-9}, pmid = {8675018}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Base Sequence ; Chromosome Mapping ; Chromosomes, Fungal/genetics ; Cloning, Molecular/methods ; DNA, Complementary/genetics ; DNA, Fungal/analysis ; Fungal Proteins/*genetics ; Gene Dosage ; Genes, Fungal/*genetics ; Genetic Complementation Test ; Mitochondria ; *Mitochondrial ADP, ATP Translocases ; Molecular Sequence Data ; Nuclear Proteins/*genetics ; Phylogeny ; Restriction Mapping ; Saccharomyces cerevisiae/*genetics ; *Saccharomyces cerevisiae Proteins ; Schizosaccharomyces/*genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; *Transcription Factor TFIID ; }, abstract = {We describe the isolation and sequencing of both cDNA and genomic clones encoding the mitochondrial ADP/ATP carrier (Anc) of Schizosaccharomyces pombe (Sp). The cDNA clone was isolated from a cDNA library of this fission yeast by complementation of a Saccharomyces cerevisiae (Sc) strain defective in adenine nucleotide carrier. The predicted amino acid (aa) sequence (322 aa) shared similarity with the known Anc sequences. It is more closely related to Neurospora crassa (Nc) Anc than to ScAnc1, 2, or 3 or Kluyveromyces lactis (Kl) Anc. Hybridization experiments with ordered libraries of Sp genomic DNA led to the physical mapping (chromosome II, NotI-B region) and the isolation of the Sp ANC1 gene. We also conclude that a single-copy gene encodes the Sp Anc.}, }
@article {pmid8638151, year = {1996}, author = {Pennisi, E}, title = {Seeking life's bare (genetic) necessities.}, journal = {Science (New York, N.Y.)}, volume = {272}, number = {5265}, pages = {1098-1099}, doi = {10.1126/science.272.5265.1098}, pmid = {8638151}, issn = {0036-8075}, mesh = {Animals ; Biological Evolution ; *Genes ; Genes, Bacterial ; *Genome ; *Genome, Bacterial ; Mitochondria/genetics ; *Software ; }, }
@article {pmid8692273, year = {1996}, author = {Yang, J and Zimmerly, S and Perlman, PS and Lambowitz, AM}, title = {Efficient integration of an intron RNA into double-stranded DNA by reverse splicing.}, journal = {Nature}, volume = {381}, number = {6580}, pages = {332-335}, doi = {10.1038/381332a0}, pmid = {8692273}, issn = {0028-0836}, mesh = {Base Sequence ; DNA/*genetics ; DNA, Fungal/genetics ; *Introns ; Molecular Sequence Data ; *RNA Splicing ; RNA, Fungal/*genetics ; RNA-Directed DNA Polymerase/*genetics ; *Recombination, Genetic ; Ribonucleoproteins/metabolism ; Saccharomyces cerevisiae/genetics ; }, abstract = {Some group II introns are mobile elements as well as catalytic RNAs. Introns aI1 and aI2 found in the gene COX1 in yeast mitochondria encode reverse transcriptases which promote site-specific insertion of the intron into intronless alleles ('homing'). For aI2 this predominantly occurs by reverse transcription of unspliced precursor RNA at a break in double-strand DNA made by an endonuclease encoded by the intron. The aI2 endonuclease involves both the excised intron RNA, which cleaves the DNA's sense strand by partial reverse splicing; and the intron-encoded reverse transcriptase which cleaves the anti-sense strand. Here we show that aI1 encodes an analogous endonuclease specific for a different target site compatible with the different exon-binding sequences of the intron RNA. Over half of aI1 undergoes complete reverse splicing in vitro, thus integrating linear intron RNA directly into the DNA. This unprecedented reaction has implications for both intron mobility and evolution, and potential genetic engineering applications.}, }
@article {pmid8763364, year = {1996}, author = {Allen, JF}, title = {Separate sexes and the mitochondrial theory of ageing.}, journal = {Journal of theoretical biology}, volume = {180}, number = {2}, pages = {135-140}, doi = {10.1006/jtbi.1996.0089}, pmid = {8763364}, issn = {0022-5193}, mesh = {Aging/*physiology ; Animals ; Chloroplasts ; Death ; Female ; Humans ; Male ; Mitochondria/*physiology ; *Models, Genetic ; Mutation/*physiology ; Ovum/ultrastructure ; Plants ; *Sex ; Sperm Motility ; Spermatozoa/ultrastructure ; }, abstract = {An hypothesis is presented by which gamete specialization resolves a conflict between the function and replication of mitochondria. The function of mitochondria is to synthesize ATP by oxidative phosphorylation, which is coupled to respiratory electron transport. This requires a mitochondrial genetic system. However, "incorrect" electron transfers produce free radicals that cause mutation, and the frequency of these events is increased by mutation. Mitochondrial function is therefore detrimental to the fidelity of mitochondrial replication. Damage to somatic mitochondrial DNA may accumulate within, and indeed determine, the life span of individual organisms. Motility of one gamete is required for fertilization, and requires ATP. It is proposed that male gametes maximize energy production for motility by sacrificing mitochondrial DNA to electron transfer and its mutagenic by-products, while female gametes, which are non-motile, repress mitochondrial oxidative phosphorylation, thus protecting mitochondrial DNA for faithful transmission between generations. Male gametes then make no contribution to the mitochondrial genome of the zygote: mitochondria are maternally inherited. This testable hypothesis may help to explain the evolution of separate sexes and a number of their characteristics. Maternal inheritance of chloroplasts may be explained in a similar way, and contribute to the maintenance of separate sexes in plants.}, }
@article {pmid8622763, year = {1996}, author = {Hedges, SB and Parker, PH and Sibley, CG and Kumar, S}, title = {Continental breakup and the ordinal diversification of birds and mammals.}, journal = {Nature}, volume = {381}, number = {6579}, pages = {226-229}, doi = {10.1038/381226a0}, pmid = {8622763}, issn = {0028-0836}, mesh = {Animals ; *Biological Evolution ; Birds/classification/*genetics ; Cell Nucleus/genetics ; Evolution, Molecular ; Fossils ; Genes ; Geography ; Humans ; Mammals/classification/*genetics ; Mitochondria/genetics ; }, abstract = {The classical hypothesis for the diversification of birds and mammals proposes that most of the orders diverged rapidly in adaptive radiations after the Cretaceous/Tertiary (K/T) extinction event 65 million years ago. Evidence is provided by the near-absence of fossils representing modern orders before the K/T boundary. However, fossil-based estimates of divergence time are known to be conservative because of sampling biases, and some molecular/time estimates point to earlier divergences among orders. In an attempt to resolve this controversy, we have estimated times of divergence among avian and mammalian orders with a comprehensive set of genes that exhibit a constant rate of substitution. Here we report molecular estimates of divergence times that average about 50-90% earlier than those predicted by the classical hypothesis, and show that the timing of these divergences coincides with the Mesozoic fragmentation of emergent land areas. This suggests that continental breakup may have been an important mechanism in the ordinal diversification of birds and mammals.}, }
@article {pmid8626705, year = {1996}, author = {Marty, L and Fort, P}, title = {A delayed-early response nuclear gene encoding MRPL12, the mitochondrial homologue to the bacterial translational regulator L7/L12 protein.}, journal = {The Journal of biological chemistry}, volume = {271}, number = {19}, pages = {11468-11476}, doi = {10.1074/jbc.271.19.11468}, pmid = {8626705}, issn = {0021-9258}, mesh = {3T3 Cells ; Amino Acid Sequence ; Animals ; Bacterial Proteins/metabolism ; Base Sequence ; *Cell Cycle Proteins ; Cell Division ; Cell Line ; Cell Nucleus ; Chlorocebus aethiops ; Chloroplasts/metabolism ; Cloning, Molecular ; Cricetinae ; DNA, Complementary ; Escherichia coli/metabolism ; Gene Expression ; Geobacillus stearothermophilus/metabolism ; Glutathione Transferase/biosynthesis ; HeLa Cells ; Humans ; Mice ; Mitochondria/*metabolism ; Molecular Sequence Data ; Nuclear Proteins/*biosynthesis/*genetics/metabolism ; Oligodeoxyribonucleotides ; Phylogeny ; Protein Biosynthesis ; Recombinant Fusion Proteins/biosynthesis/metabolism ; Ribosomal Proteins/*biosynthesis/*genetics/*metabolism ; Ribosomes ; Sequence Homology, Amino Acid ; Spinacia oleracea ; }, abstract = {We have characterized a new delayed-early response mRNA encoding a 21-kDa product (MRPL12) that accumulates during the G1 phase of growth-stimulated cells. MRPL12 is the mammalian homologue to chloroplastic and bacterial L12 ribosomal proteins. Immunofluorescence microscopy and cell fractionation indicate a predominant mitochondrial localization in various mammalian cell lines. The NH2-terminal 49 amino acids are necessary and sufficient to target the protein within the mitochondria and are probably cleaved off during import. MRPL12 proteins associated in vitro and cofractionate with ribosomal structures, as is the case for prokaryotic L12 proteins. Expression of a dominant inhibitory truncated protein leads to a severe reduction in cell growth by inhibiting mitochondrial ATP production. MRPL12 is the first mammalian mitochondrial ribosomal protein to be characterized.}, }
@article {pmid8859949, year = {1996}, author = {Manderscheid, EJ and Rogers, AR}, title = {Genetic admixture in the late pleistocene.}, journal = {American journal of physical anthropology}, volume = {100}, number = {1}, pages = {1-5}, doi = {10.1002/(SICI)1096-8644(199605)100:1&lt;1::AID-AJPA1&gt;3.0.CO;2-3}, pmid = {8859949}, issn = {0002-9483}, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/analysis/genetics ; Female ; Fossils ; Hominidae/*genetics ; Humans ; Male ; *Models, Genetic ; }, abstract = {The replacement hypothesis of modern human origins holds that the original population of modern humans expanded throughout the world, replacing existing archaic populations as it went. If this expanding population interbred with the peoples it replaced, then some archaic mitochondria might have been introduced into the early modern gene pool. Such mitochondria would be recognizable today because they should differ from other modern mitochondria at several times the number of sites that we are used to seeing in pairwise comparisons. In this paper we ask what can be inferred from the absence of these "divergent" mitochondria from modern samples. We show that if the effective number of females in our species has been large for the past 40,000 years, then the level of admixture must have been low. For example, if this effective number exceeded 1.6 million, then we can reject the hypothesis that more more than 2/1,000 of the mitochondria in the early modern population derived from admixture with archaic peoples. We argue elsewhere that regional continuity would be detectable in the fossil record only if the rate of admixture exceeded 76%. Here, we show that this level of admixture would require the effective female size of the human population to have been less than 1,777 for the past 40,000 years.}, }
@article {pmid8813670, year = {1996}, author = {Nakamura, Y and Hashimoto, T and Yoshikawa, H and Kamaishi, T and Nakamura, F and Okamoto, K and Hasegawa, M}, title = {Phylogenetic position of Blastocystis hominis that contains cytochrome-free mitochondria, inferred from the protein phylogeny of elongation factor 1 alpha.}, journal = {Molecular and biochemical parasitology}, volume = {77}, number = {2}, pages = {241-245}, doi = {10.1016/0166-6851(96)02600-x}, pmid = {8813670}, issn = {0166-6851}, mesh = {Animals ; Base Composition ; Blastocystis hominis/*classification/*genetics ; Cytochromes ; Mitochondria ; Molecular Sequence Data ; Peptide Elongation Factor 1 ; Peptide Elongation Factors/*genetics ; *Phylogeny ; Protozoan Proteins/*genetics ; RNA, Messenger/genetics ; RNA, Protozoan/genetics ; }, }
@article {pmid8722802, year = {1996}, author = {Kumar, S}, title = {Patterns of nucleotide substitution in mitochondrial protein coding genes of vertebrates.}, journal = {Genetics}, volume = {143}, number = {1}, pages = {537-548}, pmid = {8722802}, issn = {0016-6731}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Chickens ; Codon ; Cytochrome b Group/genetics ; DNA, Mitochondrial/chemistry/*genetics/metabolism ; Electron Transport Complex IV/genetics ; Mammals/genetics ; Mathematics ; Mitochondria/*metabolism ; *Models, Genetic ; Molecular Sequence Data ; NADH Dehydrogenase/genetics ; Probability ; Proton-Translocating ATPases/genetics ; Vertebrates/*genetics ; }, abstract = {Maximum likelihood methods were used to study the differences in substitution rates among the four nucleotides and among different nucleotide sites in mitochondrial protein-coding genes of vertebrates. In the 1st + 2nd codon position data, the frequency of nucleotide G is negatively correlated with evolutionary rates of genes, substitution rates vary substantially among sites, and the transition/transversion rate bias (R) is two to five times larger than that expected at random. Generally, largest transition biases and greatest differences in substitution rates among sites are found in the highly conserved genes. The 3rd positions in placental mammal genes exhibit strong nucleotide composition biases and the transitional rates exceed transversional rates by one to two orders of magnitude. Tamura-Nei and Hasegawa-Kishino-Yano models with gamma distributed variable rates among sites (gamma parameter, alpha) adequately describe the nucleotide substitution process in 1st+2nd position data. In these data, ignoring differences in substitution rates among sites leads to largest biases while estimating substitution rates. Kimura's two-parameter model with variable-rates among sites performs satisfactorily in likelihood estimation of R, alpha, and overall amount of evolution for 1st+2nd position data. It can also be used to estimate pairwise distances with appropriate values of alpha for a majority of genes.}, }
@article {pmid8722794, year = {1996}, author = {Prager, EM and Tichy, H and Sage, RD}, title = {Mitochondrial DNA sequence variation in the eastern house mouse, Mus musculus: comparison with other house mice and report of a 75-bp tandem repeat.}, journal = {Genetics}, volume = {143}, number = {1}, pages = {427-446}, pmid = {8722794}, issn = {0016-6731}, support = {R01 AI-29800/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Asia ; Base Sequence ; *Biological Evolution ; DNA Primers ; DNA, Mitochondrial/chemistry/*genetics ; Europe ; *Genetic Variation ; Geography ; Mice/*genetics ; Mitochondria, Liver ; Molecular Sequence Data ; Muridae/*genetics ; Nucleic Acid Conformation ; Phylogeny ; Polymerase Chain Reaction ; *Repetitive Sequences, Nucleic Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {The control region and flanking tRNAs were sequenced from 139 Mus musculus mitochondrial DNAs (mtDNAs) from mice collected at 44 localities extending from Germany to Japan. Among the 36 types of M. musculus mtDNA resolved, five have an added 75-bp direct repeat; the two copies within an individual differ by two to four base substitutions. Among 90 M. domesticus mtDNAs sequenced, 12 new types were found; 96 M. domesticus types have now been identified by sequencing this segment. Representative mtDNAs from M. castaneus, M. macedonicus, M. spicilegus and M. spretus were also sequenced. A parsimony tree for the M. musculus mtDNAs is about half as deep as the tree for the M. domesticus mtDNAs, which is consistent with the idea that M. musculus is genetically less diverse and younger than M. domesticus. The patterns of variation as a function of position are similar but not identical in M. musculus and M. domesticus mtDNAs. M. castaneus and M. musculus mtDNAs are allied, at a tree depth about three times as great as the start of intra-M. musculus divergence. The coalescence of the M. musculus and M. castaneus mtDNAs is about half as deep as their coalescence with the M. domesticus mtDNA lineages. The mtDNAs of the aboriginal M. macedonicus and M. spicilegus are each other's closest relatives, at a tree depth greater than the deepest intracommensal node. The mtDNA results support the view that the aboriginal M. spretus is the sister group of the other five species.}, }
@article {pmid8662000, year = {1996}, author = {Allen, JF and Raven, JA}, title = {Free-radical-induced mutation vs redox regulation: costs and benefits of genes in organelles.}, journal = {Journal of molecular evolution}, volume = {42}, number = {5}, pages = {482-492}, pmid = {8662000}, issn = {0022-2844}, mesh = {Aging/genetics ; Cell Nucleus/genetics ; Chloroplasts/genetics ; DNA Repair/genetics ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/genetics ; Electron Transport/genetics ; Energy Metabolism/genetics ; Eukaryotic Cells/metabolism/ultrastructure ; Evolution, Molecular ; Free Radicals ; Mitochondria/genetics ; *Mutation ; Nitrogen Fixation/genetics ; Organelles/*genetics ; Oxidation-Reduction ; Oxidative Stress/*genetics ; Prokaryotic Cells/metabolism/ultrastructure ; Reactive Oxygen Species/metabolism ; Recombination, Genetic ; Symbiosis ; }, }
@article {pmid8649456, year = {1996}, author = {Kowald, A and Kirkwood, TB}, title = {A network theory of ageing: the interactions of defective mitochondria, aberrant proteins, free radicals and scavengers in the ageing process.}, journal = {Mutation research}, volume = {316}, number = {5-6}, pages = {209-236}, doi = {10.1016/s0921-8734(96)90005-3}, pmid = {8649456}, issn = {0027-5107}, mesh = {Aging/*metabolism ; Computer Simulation ; Free Radical Scavengers/*metabolism ; Free Radicals/metabolism ; Mitochondria/*metabolism ; Models, Theoretical ; }, abstract = {Evolution theory indicates that ageing is caused by progressive accumulation of defects, since the evolutionary optimal level of maintenance is always below the minimum required for indefinite survival. Evolutionary theories also suggest that multiple processes are operating in parallel, but unfortunately they make no predictions about specific mechanisms. To understand and evaluate the many different mechanistic theories of ageing which have been proposed, it is therefore important to understand and study the network of maintenance processes which control cellular homeostasis. In this paper we describe a Network Theory of Ageing which integrates the contributions of defective mitochondria, aberrant proteins, and free radicals to the ageing process, and which includes the protective effects of antioxidant enzymes and proteolytic scavengers. The model simulations not only confirm and explain many experimental, age related findings like an increase in the fraction of inactive proteins, a significant rise in protein half-life, an increase in the amount of damaged mitochondria, and a drop in the energy generation per mitochondrion, but they also show interactions between the different theories which could not have been observed without the network approach. In some simulations, for example, the mechanism of the final breakdown seems to be a consequence of the cooperation of mitochondrial and cytoplasmic reactions, the mitochondria being responsible for a long term, gradual change which eventually triggers a short lived cytoplasmic error loop.}, }
@article {pmid8626323, year = {1996}, author = {Imlay, KR and Imlay, JA}, title = {Cloning and analysis of sodC, encoding the copper-zinc superoxide dismutase of Escherichia coli.}, journal = {Journal of bacteriology}, volume = {178}, number = {9}, pages = {2564-2571}, pmid = {8626323}, issn = {0021-9193}, support = {GM49640/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Escherichia coli/*enzymology/genetics ; Genes, Bacterial/*genetics ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Secondary ; RNA, Bacterial/biosynthesis ; RNA, Messenger/biosynthesis ; Restriction Mapping ; Sequence Alignment ; Sequence Analysis ; Sequence Analysis, DNA ; Superoxide Dismutase/chemistry/*genetics/metabolism ; }, abstract = {Benov and Fridovich recently reported the existence of a copper- and zinc-containing superoxide dismutase (CuZnSOD) in Escherichia coli (L. T. Benov and I. Fridovich, J. Biol. Chem. 269:25310-25314,1994). We have used the N-terminal protein sequence to isolate the gene encoding this enzyme. The gene, denoted sodC, is located at 37.1 min on the chromosome, adjacent to lhr and sodB. A monocistronic transcript of sodC accumulates only in stationary phase. The presence of a conventional leader sequence is consistent with physical data indicating that the E. coli enzyme, like other bacterial CuZnSODs, is secreted into the periplasm. Because superoxide cannot cross membranes, this localization indicates that the enzyme has evolved to defend periplasmic biomolecules against an extracytoplasmic superoxide source. Neither the source nor the target of the superoxide is known. Although once considered an exclusively eukaryotic enzyme, CuZnSOD has now been found in species that span three subdivisions of the purple bacteria. The bacterial CuZnSODs are more homologous to one another than to the eukaryotic enzymes, but active-site residues and structural motifs are clearly shared by both families of enzymes. The use of copper and an invariant disulfide bond suggest that the ancestral gene of present-day CuZnSODs evolved in an aerobic environment, long after the evolutionary split between the eukaryotes and the eubacteria. If so, a CuZnSOD gene must have been transferred laterally between members of these domains. The eukaryotic SODs most closely resemble that of Caulobacter crescentus, a relatively close descendant of the mitochondrial ancestor, suggesting that sodC may have entered the eukaryotes during the establishment of mitochondria.}, }
@article {pmid8660972, year = {1996}, author = {Lopez, JV and Cevario, S and O'Brien, SJ}, title = {Complete nucleotide sequences of the domestic cat (Felis catus) mitochondrial genome and a transposed mtDNA tandem repeat (Numt) in the nuclear genome.}, journal = {Genomics}, volume = {33}, number = {2}, pages = {229-246}, doi = {10.1006/geno.1996.0188}, pmid = {8660972}, issn = {0888-7543}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cats/*genetics ; Cell Nucleus ; DNA Transposable Elements ; *DNA, Mitochondrial ; Genome ; Humans ; Mitochondria ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Repetitive Sequences, Nucleic Acid ; }, abstract = {The complete 17,009-bp mitochondrial genome of the domestic cat, Felis catus, has been sequenced and conforms largely to the typical organization of previously characterized mammalian mtDNAs. Codon usage and base composition also followed canonical vertebrate patterns, except for an unusual ATC (non-AUG) codon initiating the NADH dehydrogenase subunit 2 (ND2) gene. Two distinct repetitive motifs at opposite ends of the control region contribute to the relatively large size (1559 bp) of this carnivore mtDNA. Alignment of the feline mtDNA genome to a homologous 7946-bp nuclear mtDNA tandem repeat DNA sequence in the cat, Numt, indicates simple repeat motifs associated with insertion/deletion mutations. Overall DNA sequence divergence between Numt and cytoplasmic mtDNA sequence was only 5.1%. Substitutions predominate at the third codon position of homologous feline protein genes. Phylogenetic analysis of mitochondrial gene sequences confirms the recent transfer of the cytoplasmic mtDNA sequences to the domestic cat nucleus and recapitulates evolutionary relationships between mammal species.}, }
@article {pmid8907651, year = {1996}, author = {de Duve, C}, title = {The birth of complex cells.}, journal = {Scientific American}, volume = {274}, number = {4}, pages = {50-57}, doi = {10.1038/scientificamerican0496-50}, pmid = {8907651}, issn = {0036-8733}, mesh = {Animals ; Bacteria/*ultrastructure ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Cell Nucleus/physiology ; Cell Size ; Cell Wall ; Eukaryotic Cells/*physiology/*ultrastructure ; Humans ; Microbodies/physiology ; Mitochondria/physiology ; Oxygen/metabolism ; Phagocytosis ; Plants/ultrastructure ; Plastids/physiology ; }, }
@article {pmid8801189, year = {1996}, author = {Coenen, A and Croft, JH and Slakhorst, M and Debets, F and Hoekstra, R}, title = {Mitochondrial inheritance in Aspergillus nidulans.}, journal = {Genetical research}, volume = {67}, number = {2}, pages = {93-100}, doi = {10.1017/s0016672300033553}, pmid = {8801189}, mesh = {Aspergillus nidulans/drug effects/*genetics/growth &amp; development ; Biological Evolution ; Chloramphenicol Resistance/genetics ; Crosses, Genetic ; DNA, Fungal/genetics ; DNA, Mitochondrial/*genetics ; Drug Resistance, Microbial/genetics ; *Extrachromosomal Inheritance ; Genetic Markers ; Mitochondria/*genetics ; Oligomycins/pharmacology ; Polymorphism, Restriction Fragment Length ; }, abstract = {Mitochondrial chloramphenicol and oligomycin resistance mutations were used to investigate mitochondrial inheritance in A. nidulans. Mitochondrial RFLPs could not be used to distinguish between paternal and maternal mitochondria because none were detected in the 54 isolates investigated. Several thousand ascospores from each of 111 hybrid cleistothecia from 21 different crosses between 7 heterokaryon incompatible isolates were tested for biparental inheritance. All mitochondrial inheritance was strictly uniparental. Not one instance of paternal inheritance of mitochondria was observed. The implications of our results for the theory that uniparental inheritance evolved to avoid cytoplasmic conflict are discussed. Possible explanations for the maintenance of strict uniparental inheritance of mitochondria in an inbreeding homothallic organism are suggested. The chloramphenicol resistance marker was inherited preferentially to the oligomycin resistance marker probably due to the inhibited energy production of mitochondria with the oligomycin resistance mutation. The maternal parent was determined for 93 hybrid cleistothecia from 17 crosses between 7 different strains. Contrary to previous reports A. nidulans strains functioned as both maternal and paternal parent in most crosses.}, }
@article {pmid8752867, year = {1996}, author = {Okamoto, K and Sekito, T and Yoshida, K}, title = {The secondary structure and phylogenetic relationship deduced from complete nucleotide sequence of mitochondrial small subunit rRNA in yeast Hansenula wingei.}, journal = {Genes &amp; genetic systems}, volume = {71}, number = {2}, pages = {69-74}, doi = {10.1266/ggs.71.69}, pmid = {8752867}, issn = {1341-7568}, mesh = {Ascomycota/genetics ; Aspergillus nidulans/genetics ; Base Sequence ; Conserved Sequence ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; Pichia/*genetics ; RNA/chemistry/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/chemistry/*genetics ; Saccharomyces cerevisiae/genetics ; Schizosaccharomyces/genetics ; }, abstract = {We have accomplished the nucleotide sequence of the 1537 bp mitochondrial gene coding for small subunit (SSU) rRNA of yeast Hansenula wingei, and also determined the 5'- and 3'-termini by S1 nuclease mapping. Eight universally conserved (U) elements of the SSU rRNA were identified. Comparison of U regions among five fungal mitochondrial SSU rRNA shows the striking similarity between H. wingei and Saccharomyces cerevisiae. The construction of the secondary structure revealed a core structure similar to the counterpart of Escherichia coli 16S rRNA. The secondary structure also enabled us the specify seven variable (V) regions differing from those of other mitochondrial SSU rRNAs in size, sequence and possible secondary structure. Molecular phylogenetic evaluation based on U regions of five fungi indicates that mitochondria of H. wingei and S. cerevisiae diverged from the same lineage. This suggests that the evolution of mitochondria-encoded genes does not directly correlate with the alteration of mitochondrial genetic system: genome size, gene organization and codon usage.}, }
@article {pmid8728396, year = {1996}, author = {Ritchie, PA and Bargelloni, L and Meyer, A and Taylor, JA and Macdonald, JA and Lambert, DM}, title = {Mitochondrial phylogeny of trematomid fishes (Nototheniidae, Perciformes) and the evolution of Antarctic fish.}, journal = {Molecular phylogenetics and evolution}, volume = {5}, number = {2}, pages = {383-390}, doi = {10.1006/mpev.1996.0033}, pmid = {8728396}, issn = {1055-7903}, mesh = {Animals ; Antarctic Regions ; Base Sequence ; *Biological Evolution ; DNA Primers ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/genetics ; Genetic Variation ; Mitochondria, Liver/metabolism ; Mitochondria, Muscle/metabolism ; Molecular Sequence Data ; Muscle, Skeletal/metabolism ; Perciformes/classification/*genetics ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; Regression Analysis ; Sequence Homology, Nucleic Acid ; }, abstract = {The subfamily of fishes Trematominae is endemic to the subzero waters of antarctica and is part of the longer notothenioid radiation. Partial mitochondrial sequences from the 12S and 16S ribosomal RNA (rRNA) genes and a phylogeny for 10 trematomid species are presented. As has been previously suggested, two taxa, Trematomus scotti and T. newnesi, do not appear to be part of the main trematomid radiation. The genus Pagothenia is nested within the genus Trematomus and has evolved a unique cyropelagic existence, an association with pack ice. Using a mitochondrial rRNA molecular clock rate of 0.14% transversion changes per million years, the average age of the trematomids is estimated at 3.4 million years (MY). If the age of the trematomids is approximately 3.4 MY, this group could have speciated during the period of deglaciation in Antarctica 2.5-4.8 million years ago. This era was marked by significant changes on the Antarctic shores, such as the opening of fjords, which might have provided a stimulus for specification.}, }
@article {pmid8728394, year = {1996}, author = {Edlind, TD and Li, J and Visvesvara, GS and Vodkin, MH and McLaughlin, GL and Katiyar, SK}, title = {Phylogenetic analysis of beta-tubulin sequences from amitochondrial protozoa.}, journal = {Molecular phylogenetics and evolution}, volume = {5}, number = {2}, pages = {359-367}, doi = {10.1006/mpev.1996.0031}, pmid = {8728394}, issn = {1055-7903}, support = {AI32433/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Entamoeba histolytica/genetics ; Eukaryota/*genetics ; Fungi/genetics ; *Genes, Protozoan ; Giardia lamblia/genetics ; Humans ; Molecular Sequence Data ; *Phylogeny ; Protozoan Proteins/chemistry/*genetics ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/genetics ; Tubulin/chemistry/*genetics ; }, abstract = {It has been proposed that certain extant anaerobic protozoa are descended from organisms that diverged early in eukaryotic evolution prior to the acquisition of mitochondria. Among these are the extracellular parasites Giardia lamblia, Trichomonas vaginalis, and Entamoeba histolytica, and the obligately intracellular microsporidia. Phylogenetic analysis of rRNA sequences from these amitochondrial organisms suggests that G. lamblia, T. vaginalis, and microsporidia are near the base of the eukaryotic tree, while E. histolytica clusters with mitochondria-containing species. However, since eukaryotes likely evolved by symbiotic associations, it is important to analyze other sequences which may have independent origins. Unlike ribosomes, microtubules appear to be unique to eukaryotes. Complete gene sequences for the beta-tubulin subunit of microtubules from T. vaginalis, E. histolytica, and the microsporidian Encephalitozoon hellem have recently been determined. Phylogenetic relationships among these, G. lamblia, and 20 additional beta-tubulins were analyzed by distance matrix and parsimony methods, using alpha- and gamma-tubulin outgroups. All analyses placed the E. histolytica sequence at the base of the beta-tubulin evolutionary tree. Similar results were obtained for E. histolytica alpha-tubulin using a less representative set of sequences. In contrast, the E. hellem sequence branched considerably higher, within the lineage containing animal and fungal beta-tubulins. Possible explanations are considered for these unexpected differences between the beta-tubulin and rRNA trees.}, }
@article {pmid8728390, year = {1996}, author = {De Giorgi, C and Martiradonna, A and Lanave, C and Saccone, C}, title = {Complete sequence of the mitochondrial DNA in the sea urchin Arbacia lixula: conserved features of the echinoid mitochondrial genome.}, journal = {Molecular phylogenetics and evolution}, volume = {5}, number = {2}, pages = {323-332}, doi = {10.1006/mpev.1996.0027}, pmid = {8728390}, issn = {1055-7903}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Codon ; Conserved Sequence ; DNA, Mitochondrial/chemistry/*genetics ; Fishes ; Mammals ; Mitochondria ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; Promoter Regions, Genetic ; Sea Urchins/classification/*genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {The complete nucleotide sequence (15,719 nucleotides) of the mitochondrial DNA (mtDNA) from the sea urchin Arbacia lixula is presented. The comparison of gene arrangement between different echinoderm orders of the same class provides evidence that the gene organization is conserved within the same echinoderm class. The peculiarities of sea urchin mtDNA features, already described, are confirmed by the A. lixula mtDNA sequence. The comparison of the entire sequences of mtDNA among A. lixula, Paracentrotus lividus, and Strongylocentrotus purpuratus allowed us to detect peculiar features, common to the three sea urchin species, that can represent the molecular signature of the mt genome in the sea urchin group. Analysis of the nucleotide composition indicates that A. lixula mtDNA, in contrast with the mtDNA of other sea urchins, shows a bias in the use of T and tends to avoid the use of C, most evident in the neutral part of the molecule, such as the third codon positions. This observation indicates that the three sea urchin mtDNAs evolve under different mutation pressure. Analysis of the sequence evolution allowed us to confirm the phylogenetic tree. However, the absolute divergence time, calculated on the basis of paleontological estimates, largely diverged from the expected one.}, }
@article {pmid8728387, year = {1996}, author = {Pedersen, BV}, title = {A phylogenetic analysis of cuckoo bumblebees (Psithyrus, Lepeletier) and bumblebees (Bombus, Latreille) inferred from sequences of the mitochondrial gene cytochrome oxidase I.}, journal = {Molecular phylogenetics and evolution}, volume = {5}, number = {2}, pages = {289-297}, doi = {10.1006/mpev.1996.0024}, pmid = {8728387}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Bees/classification/enzymology/*genetics ; DNA Primers ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Mitochondria, Muscle/*enzymology ; Molecular Sequence Data ; *Phylogeny ; Point Mutation ; Polymerase Chain Reaction ; Probability ; Sequence Homology, Nucleic Acid ; }, abstract = {PCR amplification and direct sequencing of a 532-bp region of the mt CO-1 (cytochrome oxidase I) gene from five true bumblebee species and six cuckoo bumblebee species were performed. The sequences were then aligned to the corresponding sequence in the honey bee. Phylogenetic analyses based on parsimony and maximum likelihood indicate that the cuckoo bumblebees form a monophyletic group within the true bumblebees. The Bombus lucorum group (subgenus Bombus) falls out as the sister group to a clade comprising the cuckoo bumblebees and the remaining true bumblebees. A strong A + T bias (A + T = 75%) was recorded. Comparisons of all the sequences show a high-transversion bias (A<-->T) even among closely related species. The bias is most pronounced in third positions.}, }
@article {pmid8642610, year = {1996}, author = {Rouhbakhsh, D and Lai, CY and von Dohlen, CD and Clark, MA and Baumann, L and Baumann, P and Moran, NA and Voegtlin, DJ}, title = {The tryptophan biosynthetic pathway of aphid endosymbionts (Buchnera): genetics and evolution of plasmid-associated anthranilate synthase (trpEG) within the aphididae.}, journal = {Journal of molecular evolution}, volume = {42}, number = {4}, pages = {414-421}, pmid = {8642610}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Anthranilate Synthase/*genetics ; Aphids/*microbiology ; Bacteria/*genetics/metabolism ; Base Sequence ; Biological Evolution ; Conserved Sequence ; Escherichia coli/genetics ; Molecular Sequence Data ; Mutagenesis ; Phylogeny ; Plasmids/genetics ; Replication Origin ; Sequence Homology, Amino Acid ; Symbiosis/*genetics ; Tryptophan/*biosynthesis ; Tryptophan Synthase/genetics ; }, abstract = {The bacterial endosymbionts (Buchnera) from the aphids Rhopalosiphum padi, R. maidis, Schizaphis graminum, and Acyrthosiphon pisum contain the genes for anthranilate synthase (trpEG) on plasmids made up of one or more 3.6-kb units. Anthranilate synthase is the first as well as the rate-limiting enzyme in the tryptophan biosynthetic pathway. The amplification of trpEG on plasmids may result in an increase of enzyme protein and overproduction of this essential amino acid, which is required by the aphid host. The nucleotide sequence of trpEG from endosymbionts of different species of aphids is highly conserved, as is an approximately 500-bp upstream DNA segment which has the characteristics of an origin of replication. Phylogenetic analyses were performed using trpE and trpG from the endosymbionts of these four aphids as well as from the endosymbiont of Schlechtendalia chinensis, in which trpEG occurs on the chromosome. The resulting phylogeny was congruent with trees derived from sequences of two chromosome-located bacterial genes (part of trpB and 16S ribosomal DNA). In turn, trees obtained from plasmid-borne and bacterial chromosome-borne sequences were congruent with the tree resulting from phylogenetic analysis of three aphid mitochondrial regions (portions of the small and large ribosomal DNA subunits, as well as cytochrome oxidase II). Congruence of trees based on genes from host mitochondria and from bacteria adds to previous support for exclusively vertical transmission of the endosymbionts within aphid lineages. Congruence with trees based on plasmid-borne genes supports the origin of the plasmid-borne trpEG from the chromosomal genes of the same lineage and the absence of subsequent plasmid exchange among endosymbionts of different species of aphids.}, }
@article {pmid8625418, year = {1996}, author = {Nakazono, M and Ito, Y and Tsutsumi, N and Hirai, A}, title = {The gene for a subunit of an ABC-type heme transporter is transcribed together with the gene for subunit 6 of NADH dehydrogenase in rice mitochondria.}, journal = {Current genetics}, volume = {29}, number = {5}, pages = {412-416}, pmid = {8625418}, issn = {0172-8083}, mesh = {ATP-Binding Cassette Transporters/*genetics ; Amino Acid Sequence ; Base Sequence ; *Genes, Plant ; Mitochondria/enzymology/*genetics ; Molecular Probe Techniques ; Molecular Sequence Data ; NADH Dehydrogenase/*biosynthesis/genetics ; Oryza/enzymology/*genetics ; *Plant Proteins ; RNA Editing ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; *Transcription, Genetic ; }, abstract = {We previously identified a chloroplast-derived (ct-derived) sequence of 32 base pairs (bp) in rice mitochondrial DNA that includes a part (30 bp; psitrnI) of a gene for isoleucine tRNA (CAU) of the chloroplast. Analyzing the ct-derived psitrnI, we found that an open reading frame (orf240), which was homologous to the gene for a subunit of an ATP-binding cassette-type (ABC-type) heme transporter, namely helC, of Rhodobacter capsulatus, and a gene for subunit 6 of NADH dehydrogenase (nad6) were located upstream of and downstream from the ct-derived psitrnI, respectively. Northern-blot hybridization and analysis by reverse transcription-polymerase chain reaction (RT-PCR) revealed that both orf240 and nad6 were co-transcribed in rice mitochondria. An analysis of PCR-amplified fragments of the region of orf240/nad6 from the DNA of some Gramineae suggests that the arrangement of orf240/nad6 was generated in the mitochondrial genome of the genus Oryza during evolution after its divergence from the other Gramineae. Most of the transcripts of orf240 are edited, with a change from cytidine to uridine, at 35 positions. Editing of the RNA changes 33 amino-acid residues among the 240 encoded amino-acid residues, suggesting that the orf240 gene is functional in rice mitochondria.}, }
@article {pmid8616156, year = {1996}, author = {Antaramian, A and Coria, R and Ramírez, J and González-Halphen, D}, title = {The deduced primary structure of subunit I from cytochrome c oxidase suggests that the genus Polytomella shares a common mitochondrial origin with Chlamydomonas.}, journal = {Biochimica et biophysica acta}, volume = {1273}, number = {3}, pages = {198-202}, doi = {10.1016/0005-2728(95)00158-1}, pmid = {8616156}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Chlamydomonas/classification/*enzymology/genetics ; Chlorophyta/classification/*enzymology/genetics ; Codon ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*chemistry/genetics ; Macromolecular Substances ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {We cloned and sequenced the mitochondrial gene encoding subunit I of cytochrome c oxidase (coxI) of Polytomella spp., a colorless alga related to Chlamydomonas. The purpose was to explore whether homology between the two species also exists at the level of a mitochondrial enzyme. The gene is 1512 bp long and contains no introns. The translated protein sequence exhibits 73.8% identity with its Chlamydomonas reinhardtii counterpart. The data obtained support the hypothesis that the separation of the colorless alga from the Chlamydomonas lineage was a late event in evolution, that occurred after the endosymbiotic process that gave rise to mitochondria.}, }
@article {pmid8920257, year = {1996}, author = {Thomaz, D and Guiller, A and Clarke, B}, title = {Extreme divergence of mitochondrial DNA within species of pulmonate land snails.}, journal = {Proceedings. Biological sciences}, volume = {263}, number = {1368}, pages = {363-368}, doi = {10.1098/rspb.1996.0056}, pmid = {8920257}, issn = {0962-8452}, mesh = {Animals ; Base Sequence ; DNA Primers/genetics ; DNA, Mitochondrial/*genetics ; Europe ; Female ; Genetic Variation ; Haplotypes ; Male ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Snails/classification/*genetics ; Species Specificity ; }, abstract = {Mitochondrial DNA, inherited predominantly through the female line, has been exceptionally useful for reconstructing phylogenies (Avise, in Molecular markers, natural history and evolution. New York: Chapman and Hall (1994)). However, at the lowest taxonomic level, if there are polymorphisms within species the lineages of mitochondria need not correspond to the lineages of the species (Avise, in Phil. Trans. R. Soc. Lond. B 312, 325-342 (1986)). We find that a classic organism in ecological genetics, Cepaea nemoralis, has the most extreme intraspecific variation and polymorphism so far recorded, and that at least one other pulmonate land mollusc also has very high levels of mitochondrial diversity. Making the simplest assumptions, the data suggest times of divergence as long ago as 20 million years between haplotypes now coexisting within a single population. There are four overlapping explanations of the diversity: (i) that mitochondrial evolution in pulmonates is exceptionally fast; (ii) that the morphs have differentiated in isolated 'refuges' and then come together; (iii) that natural selection has acted to preserve the variation; and (iv) that the population structure of pulmonates favours the persistence of ancient haplotypes. We argue for the importance of the last explanation.}, }
@article {pmid8637872, year = {1996}, author = {Burger, G and Lang, BF and Reith, M and Gray, MW}, title = {Genes encoding the same three subunits of respiratory complex II are present in the mitochondrial DNA of two phylogenetically distant eukaryotes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {93}, number = {6}, pages = {2328-2332}, pmid = {8637872}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/chemistry ; *DNA, Mitochondrial ; Electron Transport Complex II ; Eukaryota/*genetics ; Fungal Proteins/chemistry ; Genes ; Molecular Sequence Data ; Multienzyme Complexes/*genetics ; Oxidoreductases/*genetics ; Phylogeny ; Rhodophyta/*genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Succinate Dehydrogenase/*genetics ; }, abstract = {Although mitochondrial DNA is known to encode a limited number (<20) of the polypeptide components of respiratory complexes I, III, IV, and V, genes for components of complex II [succinate dehydrogenase (ubiquinone); succinate:ubiquinone oxidoreductase, EC 1.3.5.1] are conspicuously lacking in mitochondrial genomes so far characterized. Here we show that the same three subunits of complex II are encoded in the mitochondrial DNA of two phylogenetically distant eukaryotes, Porphyra purpurea (a photosynthetic red alga) and Reclinomonas americana (a heterotrophic zooflagellate). These complex II genes, sdh2, sdh3, and sdh4, are homologs, respectively, of Escherichia coli sdhB, sdhC, and sdhD. In E. coli, sdhB encodes the iron-sulfur subunit of succinate dehydrogenase (SDH), whereas sdhC and sdhD specify, respectively, apocytochrome b558 and a hydrophobic 13-kDa polypeptide, which together anchor SDH to the inner mitochondrial membrane. Amino acid sequence similarities indicate that sdh2, sdh3, and sdh4 were originally encoded in the protomitochondrial genome and have subsequently been transferred to the nuclear genome in most eukaryotes. The data presented here are consistent with the view that mitochondria constitute a monophyletic lineage.}, }
@article {pmid8635473, year = {1996}, author = {Malek, O and Lättig, K and Hiesel, R and Brennicke, A and Knoop, V}, title = {RNA editing in bryophytes and a molecular phylogeny of land plants.}, journal = {The EMBO journal}, volume = {15}, number = {6}, pages = {1403-1411}, pmid = {8635473}, issn = {0261-4189}, mesh = {Base Sequence ; *Biological Evolution ; Bryopsida/classification/genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Genetic Markers ; Membrane Proteins/*genetics ; Mitochondria/*genetics ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Plants/*classification/*genetics ; RNA, Messenger/genetics ; Saccharomyces cerevisiae Proteins ; Sequence Homology, Nucleic Acid ; }, abstract = {RNA editing has been observed to date in all groups of vascular plants, but not in bryophytes. Its occurrence was therefore assumed to correlate with the evolution of tracheophytes. To gain more insight into both the phylogeny of early land plants and the evolution of mitochondrial RNA editing we have investigated a number of vascular and non-vascular plant species. Contrary to the belief that editing is absent from bryophytes, here we report mitochondrial RNA editing in cox3 mRNA of the liverwort Pellia epiphylla, the mosses Tetraphis pellucida and Ceratodon purpureus and the hornwort Anthroceros crispulus. RNA editing in plants consequently predates the evolution of tracheophytes. Editing is also found in the eusporangiate ferns Ophioglossum petiolatum and Angiopteris palmiformis, the whisk fern Tmesipteris elongata and the gnetopsid Ephedra gerardiana, but was not detected in Gnetum gnemon.cox3 mRNA of the lycopsid Isoetes lacustris shows the highest frequency of RNA editing ever observed in a plant, with 39% of all cytidine residues converted to uridines. The frequency of RNA editing correlates with the genomic GC content rather than with the phylogenetic position of a species. Phylogenetic trees derived from the slowly evolving mitochondrial sequences find external support from the assessments of classical systematics.}, }
@article {pmid8612730, year = {1996}, author = {Altamura, N and Capitanio, N and Bonnefoy, N and Papa, S and Dujardin, G}, title = {The Saccharomyces cerevisiae OXA1 gene is required for the correct assembly of cytochrome c oxidase and oligomycin-sensitive ATP synthase.}, journal = {FEBS letters}, volume = {382}, number = {1-2}, pages = {111-115}, doi = {10.1016/0014-5793(96)00165-2}, pmid = {8612730}, issn = {0014-5793}, mesh = {Adenosine Triphosphatases/*biosynthesis/metabolism ; *Carrier Proteins ; Electron Transport Complex IV/*biosynthesis/metabolism ; Fungal Proteins/genetics/*physiology ; Genes, Fungal/physiology ; Heme/analogs &amp; derivatives/analysis ; Membrane Proteins/*biosynthesis/metabolism ; Mitochondria/enzymology ; Mitochondrial Proteins ; Mitochondrial Proton-Translocating ATPases ; Nuclear Proteins/genetics/*physiology ; Oligomycins ; Open Reading Frames/genetics ; Saccharomyces cerevisiae/*enzymology/genetics ; Sequence Deletion ; Succinate Cytochrome c Oxidoreductase/metabolism ; }, abstract = {The nuclear gene OXA1 was first isolated in Saccharomyces cerevisiae and found to be required at a post-translational step in cytochrome c oxidase biogenesis, probably at the level of assembly. Mutations in OXA1 lead to a complete respiratory deficiency. The protein Oxa1p is conserved through evolution and a human homolog has been isolated by functional complementation of a yeast oxa1- mutant. In order to further our understanding of the role of Oxa1p, we have constructed two yeast strains in which the OXA1 open reading frame was almost totally deleted. Cytochrome spectra and enzymatic activity measurements show the absence of heme aa3 and of a cytochrome c oxido-reductase activity and dramatic decrease of the oligomycin sensitive ATPase activity. Analysis of the respiratory complexes in non-denaturing gels reveals that Oxa1p is necessary for the correct assembly of the cytochrome c oxidase and the ATP synthase complex.}, }
@article {pmid9019132, year = {1996}, author = {Margulis, L and Olendzenski, L and Dolan, M and MacIntyre, F}, title = {Diversity of eukaryotic microorganisms: computer-based resources, "The Handbook of Protoctista" and its "Glossary".}, journal = {Microbiologia (Madrid, Spain)}, volume = {12}, number = {1}, pages = {29-42}, pmid = {9019132}, issn = {0213-4101}, mesh = {Animals ; Archaea/classification ; *CD-ROM ; *Classification ; Dictionaries as Topic ; Eukaryota/classification/ultrastructure ; *Eukaryotic Cells/ultrastructure ; *Phylogeny ; *Reference Books ; }, abstract = {The kingdom Protoctista comprises some 30 phyla, including the eukaryotic anaerobes that permanently lack mitochondria, the Phylum Archaeprotista, with its three classes: (i) Archamoebae, e.g., Pelomyxa, Mastigina, (ii) Metamonada, e.g., Giardia, Pyrsonympha, and (iii) Parabasalia, e.g., Trichomonas, Calonympha, and the Phylum Microspora (Microsporidia), e.g., Vairimorpha. These and all algae, protozoa, labyrinthulids, "water molds" (oomycota, plasmodiophorans, hyphochytrids, chytrids, etc.) and other eukaryotes excluded from plants, animals and fungi are detailed in the Handbook of Protoctista. The Illustrated Glossary of Protoctista contains descriptions of the morphology and taxonomy of these microorganisms, including the many equivalent and homologous structures with different names. The Glossary has also been made into a Macintosh-compatible CD-ROM disk.}, }
@article {pmid8742640, year = {1996}, author = {Sunnucks, P and Hales, DF}, title = {Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae).}, journal = {Molecular biology and evolution}, volume = {13}, number = {3}, pages = {510-524}, doi = {10.1093/oxfordjournals.molbev.a025612}, pmid = {8742640}, issn = {0737-4038}, mesh = {Animals ; Aphids/*enzymology/*genetics ; Base Sequence ; *Biological Evolution ; Blotting, Southern ; Cloning, Molecular ; DNA Primers ; DNA, Mitochondrial/*chemistry/genetics ; Electron Transport Complex IV/*genetics ; Haplotypes ; Macromolecular Substances ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; Species Specificity ; Time ; }, abstract = {Polymerase chain reaction (PCR) products corresponding to 803 bp of the cytochrome oxidase subunits I and II region of mitochondrial DNA (mtDNA COI-II) were deduced to consist of multiple haplotypes in three Sitobion species. We investigated the molecular basis of these observations. PCR products were cloned, and six clones from one individual per species were sequenced. In each individual, one sequence was found commonly, but also two or three divergent sequences were seen. The divergent sequences were shown to be nonmitochondrial by sequencing from purified mtDNA and Southern blotting experiments. All seven nonmitochondrial clones sequenced to completion were unique. Nonmitochondrial sequences have a high proportion of unique sites, and very few characters are shared between nonmitochondrial clones to the exclusion of mtDNA. From these data, we infer that fragments of mtDNA have been transposed separately (probably into aphid chromosomes), at a frequency only known to be equalled in humans. The transposition phenomenon appears to occur infrequently or not at all in closely related genera and other aphids investigated. Patterns of nucleotide substitution in mtDNA inferred over a parsimony tree are very different from those in transposed sequences. Compared with mtDNA, nonmitochondrial sequences have less codon position bias, more even exchanges between A, G, C and T, and a higher proportion of nonsynonymous replacements. Although these data are consistent with the transposed sequences being under less constraint than mtDNA, changes in the nonmitochondrial sequences are not random: there remains significant position bias, and probable excesses of synonymous replacements and of conservative inferred amino acid replacements. We conclude that a proportion of the inferred change in the nonmitochondrial sequences occurred before transposition. We believe that Sitobion aphids (and other species exhibiting mtDNA transposition) may be important for studying the molecular evolution of mtDNA and pseudogenes. However, our data highlight the need to establish the true evolutionary relationships between sequences in comparative investigations.}, }
@article {pmid8742633, year = {1996}, author = {Pawlowski, J and Bolivar, I and Fahrni, JF and Cavalier-Smith, T and Gouy, M}, title = {Early origin of foraminifera suggested by SSU rRNA gene sequences.}, journal = {Molecular biology and evolution}, volume = {13}, number = {3}, pages = {445-450}, doi = {10.1093/oxfordjournals.molbev.a025605}, pmid = {8742633}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; DNA Primers ; DNA, Protozoan/genetics ; DNA, Ribosomal/*genetics ; Eukaryota/classification/*genetics ; Fossils ; Macromolecular Substances ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Protozoan/genetics ; RNA, Ribosomal/*genetics ; }, abstract = {Foraminifera are one of the largest groups of unicellular eukaryotes with probably the best known fossil record. However, the origin of foraminifera and their phylogenetic relationships with other eukaryotes are not well established. In particular, two recent reports, based on ribosomal RNA gene sequences, have reached strikingly different conclusions about foraminifera's evolutionary position within eukaryotes. Here, we present the complete small subunit (SSU) rRNA gene sequences of three species of foraminifera. Phylogenetic analysis of these sequences indicates that they branch very deeply in the eukaryotic evolutionary tree: later than those of the amitochondrial Archezoa, but earlier than those of the Euglenozoa and other mitochondria-bearing phyla. Foraminifera are clearly among the earliest eukaryotes with mitochondria, but because of the peculiar nature of their SSU genes we cannot be certain that they diverged first, as our data suggest.}, }
@article {pmid8622771, year = {1996}, author = {Maier, UG and Hofmann, CJ and Sitte, P}, title = {[Evolution of cells].}, journal = {Die Naturwissenschaften}, volume = {83}, number = {3}, pages = {103-112}, pmid = {8622771}, issn = {0028-1042}, mesh = {Animals ; Archaea ; Bacteria ; *Biological Evolution ; Biomarkers ; Enzymes/analysis ; Eukaryotic Cells/*cytology/physiology ; Models, Biological ; Prokaryotic Cells/*cytology/physiology ; Symbiosis ; }, abstract = {Life has existed on earth for some 4 x 10(9) years. During most of this time, evolution took place at the level of cell evolution. The cells of presently existing organisms belong to two fundamentally different cell types, protocytes (of bacteria and archaea) and eucytes (of eukarya). Thanks to molecular phylogenetics, the path of evolution can now be traced back to its very beginnings, although the picture may be blurred by repeated horizontal gene transfer. A symbiogenetic origin of plastids and mitochondria is now very well documented, and it is being discussed also for some other constituents of eucytes, including even the cells nucleus. It could be demonstrated that not only did bacterial cells become incorporated into protoeucytes and transformed into organelles of their respective hosts, but also that endocytic eucytes have apparently been transformed to complex organelles by coevolution with host cells.}, }
@article {pmid8657188, year = {1996}, author = {Wachsman, JT}, title = {The beneficial effects of dietary restriction: reduced oxidative damage and enhanced apoptosis.}, journal = {Mutation research}, volume = {350}, number = {1}, pages = {25-34}, doi = {10.1016/0027-5107(95)00087-9}, pmid = {8657188}, issn = {0027-5107}, mesh = {Aging ; Animals ; *Apoptosis ; *Energy Intake ; Hormones/metabolism ; Humans ; Mitochondria/metabolism ; Neoplasms/prevention &amp; control ; *Oxidative Stress ; Poly(ADP-ribose) Polymerases/genetics/metabolism ; Reactive Oxygen Species/metabolism ; }, abstract = {There is compelling evidence for the central role of oxidative damage in the aging process and for the participation of reactive oxygen species in tumor initiation and promotion. Caloric restriction (CR) or energy restriction retards age-associated increases in mitochondrial free-radical production and reduces the accumulation of oxidatively damaged cell components. CR has also been shown to slow down age-related declines in various repair capabilities, including some types of DNA repair. It is proposed that inhibitors of mitochondrial electron transport and/or uncouplers of oxidative phosphorylation (rotenone, amytal, amiodarone, valinomycin, etc.), when used at extremely low doses, could mimic the effects of CR in model systems. The objective is to lower mitochondrial free-radical production by decreasing the fraction of electron carriers in the reduced state. In addition to a variety of other effects, CR has been shown to increase the rate of apoptosis, particularly in preneoplastic cells, and in general, to promote elevated levels of free glucocorticoids (GCs). GCs are known to induce tissue-specific apoptosis and to upregulate gap-junction-mediated intercellular communication (GJIC). Tumor promoters like phorbol esters have the opposite effect, in that they inhibit both the process of apoptosis and GJIC. The enzyme poly (ADP-ribose) polymerase (PARP) is thought to play a central role in apoptosis, in a manner that has been highly conserved in evolution. There is good evidence that the apoptosis-associated Ca/Mg-dependent DNA endonuclease is maintained in a latent form by being poly (ADP-ribosylated). Apoptosis would require the removal of this polymer from the endonuclease, and, most likely, its removal from topoisomerase II and histone H1 as well. The role of poly (ADP-ribose) in apoptosis, carcinogenesis, and aging could be studied by the use of modulators of PARP activity (3-aminobenzamide, 3-nitrosobenzamide, 1% ethanol, etc.), inhibitors of poly ADP-ribose) glycohydrolase activity (ethacridine, 43 degrees C, etc.), and inhibitors of the PARP-specific protease (interleukin-1 beta converting enzyme (ICE)-like protease). Also, it would be of interest to determine if CR can decrease the half-life of poly (ADP-ribose), upregulate GJIC, and modulate the activities of PARP, the glycohydrolase, and the PARP-specific protease, factors potentially important in these processes.}, }
@article {pmid8636971, year = {1996}, author = {Paquin, B and Lang, BF}, title = {The mitochondrial DNA of Allomyces macrogynus: the complete genomic sequence from an ancestral fungus.}, journal = {Journal of molecular biology}, volume = {255}, number = {5}, pages = {688-701}, doi = {10.1006/jmbi.1996.0056}, pmid = {8636971}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Base Sequence ; *Biological Evolution ; Chytridiomycota/*genetics ; DNA, Fungal/*chemistry/genetics ; DNA, Mitochondrial/*chemistry/genetics ; Escherichia coli/genetics ; Genes, Fungal ; *Genome, Fungal ; Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames ; RNA, Fungal/chemistry ; RNA, Ribosomal/chemistry ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; }, abstract = {We have determined the complete nucleotide sequence of the circular mitochondrial DNA (mtDNA) of the chytridiomycete fungus, Allomyces macrogynus (57,473 bp; A + T content 60.5%). The identified genes that are typical for most fungal mitochondria include those for the large (rnl) and small subunit (rns) ribosomal RNAs, a complete set of 25 tRNAs, three ATPase subunits (atp6, atp8 and atp9), apocytochrome b(cob), three subunits of the cytochrome oxidase complex (cox1, cox2 and cox3), and seven subunits of the NADH dehydrogenase complex (nad1, nad2, nad3, nad4, nad4L, nad5 and nad6). A total of 28 introns of both groups are found, some of which contain open reading frames (ORFs) coding for potential endonucleases (group I) or reverse-transcriptases (group II). All mitochondrial genes are transcribed from the same DNA strand, as is the case in many other eufungi. Particular features of the A. macrogynus mtDNA include: (1) the first documented case of a fungal mitochondrial ribosomal protein gene (rps3) that is clearly identified by similarity with bacterial homologues; (2) four unique ORFs; (3) the presence of an insert in the atp6 gene that may have been acquired by interspecific transfer; (4) more than 67 short, highly structured and conserved DNA elements inserted in intergenic spacers, introns, and variable regions of the rnl and rns genes: these elements are unusually G + C rich; (5) rRNA structures that resemble more closely those of eubacteria than their counterparts in other fungal mitochondria. The high degree of conservation of the A. macrogynus mitochondrial rRNA secondary structures, the existence of a mitochondrial rps3 gene (common to protist but unique in fungal mtDNAs), and phylogenetic relationships inferred from highly conserved protein genes, demonstrate consistently the ancestral character of this fungal mitochondrial genome.}, }
@article {pmid8920004, year = {1996}, author = {Kohl, L and Drmota, T and Thi, CD and Callens, M and Van Beeumen, J and Opperdoes, FR and Michels, PA}, title = {Cloning and characterization of the NAD-linked glycerol-3-phosphate dehydrogenases of Trypanosoma brucei brucei and Leishmania mexicana mexicana and expression of the trypanosome enzyme in Escherichia coli.}, journal = {Molecular and biochemical parasitology}, volume = {76}, number = {1-2}, pages = {159-173}, doi = {10.1016/0166-6851(95)02556-1}, pmid = {8920004}, issn = {0166-6851}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Chromosome Mapping ; Cloning, Molecular ; Gene Expression ; Glycerol-3-Phosphate Dehydrogenase (NAD+) ; Glycerolphosphate Dehydrogenase/*chemistry/genetics ; Leishmania mexicana/*enzymology/genetics ; Molecular Sequence Data ; NAD/metabolism ; Phylogeny ; Sequence Homology ; Trypanosoma brucei brucei/*enzymology/genetics ; }, abstract = {A polyclonal antiserum raised against the purified glycosomal glycerol-3-phosphate dehydrogenase of Trypanosoma brucei brucei has been used to identify the corresponding cDNA clone in a T.b. brucei expression library. This cDNA was subsequently used to obtain genomic clones containing glycerol-3-phosphate dehydrogenase genes. Two tandemly arranged genes were detected in these clones. Characterization of one of the genes showed that it codes for a polypeptide of 353 amino acids, with a molecular mass of 37,651 Da and a calculated net charge of +8. Using the T.b. brucei gene as a probe, a corresponding glycerol-3-phosphate dehydrogenase gene was also identified in a genomic library of Leishmania mexicana mexicana. The L.m. mexicana gene codes for a polypeptide of 365 amino acids, with a molecular mass of 39,140 Da and a calculated net charge of +8. The amino-acid sequences of both polypeptides are 63% identical and carry a type-1 peroxisomal targeting signal (PTS1) SKM and -SKL at their respective C-termini. Moreover, the L.m. mexicana polypeptide also carries a short N-terminal extension reminiscent of a mitochondrial transit sequence. Subcellular localisation analysis showed that in L.m. mexicana the glycerol-3-phosphate dehydrogenase activity co-fractionated both with mitochondria and with glycosomes. This is not the case in T. brucei, where the enzyme is predominantly glycosomal. The two trypanosomatid sequences resemble their prokaryotic homologues (32-36%) more than their eukaryotic counterparts (25-31%) and carry typical prokaryotic signatures. The possible reason for this prokaryotic nature of a trypanosomatid glycerol-3-phosphate dehydrogenase is discussed.}, }
@article {pmid8907726, year = {1996}, author = {Rey, RA and Nagle, CA and Chemes, H}, title = {Morphometric study of the testicular interstitial tissue of the monkey Cebus apella during postnatal development.}, journal = {Tissue &amp; cell}, volume = {28}, number = {1}, pages = {31-42}, doi = {10.1016/s0040-8166(96)80042-5}, pmid = {8907726}, issn = {0040-8166}, mesh = {Animals ; Cebus/*anatomy &amp; histology/growth &amp; development ; Cell Count ; Histocytochemistry ; Immunohistochemistry ; Leydig Cells/*ultrastructure ; Male ; Microscopy, Electron ; Stem Cells/ultrastructure ; Testis/*growth &amp; development/ultrastructure ; }, abstract = {The purpose of this study was to evaluate the developmental changes of the Leydig cells and their precursors during postnatal development in the monkey Cebus apella. Four groups of monkeys were studied: neonatal, infantile, early pubertal and late pubertal. Light microscopy, immunocytochemistry, electron microscopy and stereological studies were performed to determine cytologic and cytochemical characteristics, volume density, absolute volume and cell counts of Leydig cells. In the interstitial tissue two components were recognized: specific interstitium comprising mature and immature Leydig cells and differentiating Leydig cell precursors, and non-specific interstitium including connective tissue and blood vessels. Mature Leydig cells were polygonal with a round, euchromatic nucleus and abundant cytoplasm. Immature Leydig cells were more elongated and the nucleus showed more heterochromatin. Mature and immature Leydig cells showed either a pale- or a dark-stained cytoplasm. Pale Leydig cells showed abundant smooth endoplasmic reticulum (SER), mitochondria with tubular cristae and glycogen granules. The SER of dark Leydig cells consisted of abundant flat cisternae, only few glycogen inclusions and abundant lipid droplets. All Leydig cells were intensely reactive for 3beta-hydrohysteroid dehydrogenase (3beta-HSD). Some peritubular cells acquired nuclear and cytoplasmic characteristics that indicated that they were differentiating to Leydig cells, as evidenced by the strong 3beta-HSD positivity found in scattered elongated cells of the peritubular tissue. Absolute interstitial volume increased from birth to the end of puberty due to an increment in Leydig cells numbers and size. The mature and immature Leydig cell populations showed a different evolution during postnatal development. While immature Leydig cells increased 7-fold from the neonatal to the early pubertal period and increased at a lower rate during puberty, mature Leydig cells remained stable until early puberty and increased significantly during late pubertal development.}, }
@article {pmid8852854, year = {1996}, author = {Wright, DA and Ke, N and Smalle, J and Hauge, BM and Goodman, HM and Voytas, DF}, title = {Multiple non-LTR retrotransposons in the genome of Arabidopsis thaliana.}, journal = {Genetics}, volume = {142}, number = {2}, pages = {569-578}, pmid = {8852854}, issn = {0016-6731}, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics ; *Arabidopsis Proteins ; Base Sequence ; *DNA, Plant ; *Genome, Plant ; Mitochondria ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/*genetics ; Repetitive Sequences, Nucleic Acid ; *Retroelements ; Sequence Homology, Amino Acid ; Transcription Factors ; }, abstract = {DNA sequence analysis near the Arabidopsis thaliana ABI3 gene revealed the presence of a non-LTR retrotransposon insertion that we have designated Ta11-1. This insertion is 6.2 kb in length and encodes two overlapping reading frames with similarity to non-LTR retrotransposon proteins, including reverse transcriptase. A polymerase chain reaction assay was developed based on conserved amino acid sequences shared between the Ta11-1 reverse transcriptase and those of non-LTR retrotransposons from other species. Seventeen additional A. thaliana reverse transcriptases were identified that range in nucleotide similarity from 48-88% (Ta12-Ta28). Phylogenetic analyses indicated that the A. thaliana sequences are more closely related to each other than to elements from other organisms, consistent with the vertical evolution of these sequences over most of their evolutionary history. One sequence, Ta17, is located in the mitochondrial genome. The remaining are nuclear and of low copy number among 17 diverse A. thaliana ecotypes tested, suggesting that they are not highly active in transposition. The paucity of retrotransposons and the small genome size of A. thaliana support the hypothesis that most repetitive sequences have been lost from the genome and that mechanisms may exist to prevent amplification of extant element families.}, }
@article {pmid8838675, year = {1996}, author = {Hauser, R and Pypaert, M and Häusler, T and Horn, EK and Schneider, A}, title = {In vitro import of proteins into mitochondria of Trypanosoma brucei and Leishmania tarentolae.}, journal = {Journal of cell science}, volume = {109 (Pt 2)}, number = {}, pages = {517-523}, doi = {10.1242/jcs.109.2.517}, pmid = {8838675}, issn = {0021-9533}, mesh = {Aldehyde Oxidoreductases/*metabolism ; Animals ; Chemical Fractionation ; Dihydrolipoamide Dehydrogenase/*metabolism ; Fungal Proteins/metabolism ; Leishmania/*metabolism ; Mice ; Mitochondria/*metabolism ; Protozoan Proteins/metabolism ; Tetrahydrofolate Dehydrogenase/*metabolism ; Trypanosoma brucei brucei/*metabolism ; }, abstract = {In eukaryotic evolution, the earliest branch of organisms to have mitochondria are the trypanosomatids. Their mitochondrial biogenesis not only includes import of most proteins, but also, unlike in other organisms, import of the whole set of tRNAs. In order to investigate these processes, we devised novel procedures for the isolation of mitochondria from two trypanosomatid species: Trypanosoma brucei and Leishmania tarentolae. Isotonic cell lysis followed by equilibrium density centrifugation in Nycodenz gradients yielded mitochondrial fractions exhibiting a membrane potential. Furthermore, we have used these fractions to reconstitute import of mitochondrial matrix proteins in vitro. Energy-dependent uptake of an artificial precursor protein, containing a trypanosomal presequence attached to mouse dihydrofolate reductase and of yeast mitochondrial alcohol dehydrogenase could be demonstrated. The presequences of both proteins were processed in T. brucei whereas only the trypanosomal one was cleaved in L. tarentolae. Trypsin pretreatment abolished the ability of the mitochondria to import proteins, indicating the involvement of proteinaceous components at the surface of mitochondria.}, }
@article {pmid9689214, year = {1996}, author = {Andersson, SG and Eriksson, AS and Näslund, AK and Andersen, MS and Kurland, CG}, title = {The Rickettsia prowazekii genome: a random sequence analysis.}, journal = {Microbial &amp; comparative genomics}, volume = {1}, number = {4}, pages = {293-315}, pmid = {9689214}, issn = {1090-6592}, mesh = {Base Sequence ; Citric Acid Cycle/genetics ; DNA, Mitochondrial/genetics ; Electron Transport/genetics ; Genes, Bacterial/genetics ; *Genome, Bacterial ; Mitochondrial ADP, ATP Translocases/genetics ; Molecular Sequence Data ; Phylogeny ; Rickettsia prowazekii/*genetics ; Sequence Analysis ; }, abstract = {We describe here the first general survey of the genomic content and the coding capacity of the 1.1 Mb genome of Rickettsia prowazekii based on an analysis of a total of 200 kb of unique sequence data collected in a random manner. Based on nucleotide distribution profiles, we estimate that the R. prowazekii genome may have a coding density of 60%-70% and that it may contain a total of circa 800 genes. Here, we have tentatively identified and classified 173 of these genes. Our analysis suggests that the R. prowazekii genome is a highly derived, reduced genome that has lost many genes involved in amino acid biosynthetic pathways and regulatory functions. Furthermore, the R. prowazekii genome seems to lack glycolytic genes, but it does contain genes encoding components of the tricarboxylic acid cycle as well as of the electron transport system. We have also encountered a family of homologous genes coding for ATP/ADP translocases, as observed in several mitochondrial genomes. We relate these findings to previous phylogenetic studies that suggest that Rickettsia and mitochondria share a common ancestor.}, }
@article {pmid9196077, year = {1996}, author = {Carrodeguas, JA and Yun, S and Shadel, GS and Clayton, DA and Bogenhagen, DF}, title = {Functional conservation of yeast mtTFB despite extensive sequence divergence.}, journal = {Gene expression}, volume = {6}, number = {4}, pages = {219-230}, pmid = {9196077}, issn = {1052-2166}, support = {R01 GM029681/GM/NIGMS NIH HHS/United States ; GM29681/GM/NIGMS NIH HHS/United States ; GM33088/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Conserved Sequence ; DNA, Fungal/chemistry/*metabolism ; DNA, Mitochondrial/chemistry/*metabolism ; Evolution, Molecular ; Fungal Proteins/genetics/*metabolism ; Kluyveromyces/genetics/metabolism ; Mitochondria/*metabolism ; Mitochondrial Proteins ; Molecular Sequence Data ; Polymerase Chain Reaction ; Recombinant Proteins/metabolism ; Saccharomyces/genetics/metabolism ; Saccharomyces cerevisiae/genetics/metabolism ; *Saccharomyces cerevisiae Proteins ; Sequence Alignment ; Transcription Factors/genetics/*metabolism ; Transcription, Genetic ; }, abstract = {Transcription of mtDNA in the yeast S. cerevisiae depends on recognition of a consensus nonanucleotide promoter sequence by mtRNA polymerase acting with a 40-kDa dissociable factor known as mtTFB or Mtflp. mtTFB has been cloned and characterized in S. cerevisiae, but has not been studied in similar detail in any other organism. Although it is known that mitochondrial transcription in the dairy yeast, Kluyveromyces lactis, initiates within the same consensus promoter sequence used in S. cerevisiae, no previous studies have focused on the proteins involved in transcription initiation in K. lactis. In this article, we report the cloning of mtTFB from K. lactis and from a yeast more closely related to S. cerevisiae, S. kluyveri. Both novel mtTFB genes were able to substitute for the MTF1 gene in S. cerevisiae. Both proteins purified following expression in E. coli were able to support specific transcription initiation in vitro with the S. cerevisiae mtRNA polymerase. The S. kluyveri and K. lactis mtTFB proteins share only 56% and 40% identity with S. cerevisiae mtTFB, respectively. Alignments of the three mtTFB sequences did not reveal any regions larger than 30 amino acids with greater than 60% amino acid identity. In particular, regions proposed to show sequence similarity to bacterial sigma factors were not more highly conserved than other regions of the mtTFB proteins. All three yeast mtTFB genes lack conventional amino-terminal mitochondrial targeting sequences, suggesting that all three proteins may be imported into mitochondria by the same unusual mechanism reported for S. cerevisiae mtTFB.}, }
@article {pmid8915541, year = {1996}, author = {Dietrich, A and Small, I and Cosset, A and Weil, JH and Maréchal-Drouard, L}, title = {Editing and import: strategies for providing plant mitochondria with a complete set of functional transfer RNAs.}, journal = {Biochimie}, volume = {78}, number = {6}, pages = {518-529}, doi = {10.1016/0300-9084(96)84758-4}, pmid = {8915541}, issn = {0300-9084}, mesh = {Biological Transport/genetics ; Blotting, Western ; Evolution, Molecular ; Fabaceae/metabolism ; Gene Expression Regulation, Plant/genetics ; Genes, Plant/genetics ; Mitochondria/chemistry/genetics/*metabolism ; Plants, Genetically Modified ; Plants, Medicinal ; RNA Editing/*genetics ; RNA Processing, Post-Transcriptional/genetics ; RNA, Transfer/*metabolism ; Solanum tuberosum/metabolism ; Transcription, Genetic/genetics ; }, abstract = {The recombinations and mutations that plant mitochondrial DNA has undergone during evolution have led to the inactivation or complete loss of a number of the 'native' transfer RNA genes deriving from the genome of the ancestral endosymbiont. Following sequence divergence in their genes, some native mitochondrial tRNAs are 'rescued' by editing, a post-transcriptional process which changes the RNA primary sequence. According to in vitro studies with the native mitochondrial tRNA(Phe) from potato and tRNA(His) from larch, editing is required for efficient processing. Some of the native tRNA genes which have been inactivated or lost have been replaced by tRNA genes present in plastid DNA sequences acquired by the mitochondrial genome during evolution, which raises the problem of the transcriptional regulation of tRNA genes in plant mitochondria. Finally, tRNAs for which no gene is present in the mitochondrial genome are imported from the cytosol. This process is highly specific for certain tRNAs, and it has been suggested that the cognate aminoacyl-tRNA synthetases may be responsible for this specificity. Indeed, a mutation which blocks recognition of the cytosolic Arabidopsis thaliana tRNA(Ala) by the corresponding alanyl-tRNA synthetase also prevents mitochondrial import of this tRNA in transgenic plants. Conversely, no significant mitochondrial co-import of the normally cytosol-specific tRNA(Asp) was detected in transgenic plants expressing the yeast cytosolic aspartyl-tRNA synthetase fused to a mitochondrial targeting sequence, suggesting that, although necessary, recognition by a cognate aminoacyl-tRNA synthetase might not be sufficient to allow tRNA import into plant mitochondria.}, }
@article {pmid8915540, year = {1996}, author = {Blanc, V and Jordana, X and Litvak, S and Araya, A}, title = {Control of gene expression by base deamination: the case of RNA editing in wheat mitochondria.}, journal = {Biochimie}, volume = {78}, number = {6}, pages = {511-517}, doi = {10.1016/0300-9084(96)84757-2}, pmid = {8915540}, issn = {0300-9084}, mesh = {Cytosine Deaminase ; Deamination ; Evolution, Molecular ; Fertility/genetics ; Gene Expression Regulation, Plant/*genetics ; Gene Transfer Techniques ; Mitochondria/*metabolism ; Nucleoside Deaminases/metabolism ; Plants, Genetically Modified/genetics ; RNA Editing/*genetics ; RNA-Binding Proteins/genetics/metabolism ; Triticum/enzymology/metabolism ; }, abstract = {The term 'RNA editing' was used for the first time in 1986 to describe the process of uridylate insertion into trypanosomal mitochondrial transcripts. Since then, the term has been used more generally to describe a large variety of processes involving base insertions, deletions and conversions that generate RNAs with a primary sequence different to those encoded by the gene. RNA editing has been observed in the mitochondrial fraction of trypanosomes, plants and other organisms, in the animal nuclear fraction in the case of the apolipoprotein B and glutamate brain receptors mRNAs as well as in viruses like paramyxovirus, hepatitis delta and probably HIV. The role of cytidine and adenine deamination leading to C to U and A to I transitions has became pivotal to explain this process by base conversion. In this review we will focus mainly on the work performed in our group on plant mitochondria and more specifically on the mechanism and the functional significance of RNA editing in wheat organelles. The original contributions of our laboratory in this field are: i) showing that RNA editing is reflected at the protein level; ii) settling three in vitro systems to assay C to U conversion using a wheat mitochondrial lysate as source of enzymes and factors, and unedited mRNA from the same source, as substrate; iii) determination by double labelling of the unedited substrate that RNA editing in wheat mitochondria occurs via a deamination step; and iv) that introducing unedited proteins in the mitochondria of transgenic plants leads to the emergence of cytoplasmic male sterility supporting the idea that the role of this process is to produce functional proteins. Using the antisense approach in transgenic plants we were able to obtain a significant male fertility restoration.}, }
@article {pmid8900960, year = {1996}, author = {Thorsness, PE and Weber, ER}, title = {Escape and migration of nucleic acids between chloroplasts, mitochondria, and the nucleus.}, journal = {International review of cytology}, volume = {165}, number = {}, pages = {207-234}, doi = {10.1016/s0074-7696(08)62223-8}, pmid = {8900960}, issn = {0074-7696}, support = {GM47390/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Cell Nucleus/*metabolism ; Chloroplasts/*metabolism ; Humans ; Mitochondria/*metabolism ; Nucleic Acids/*metabolism ; Saccharomyces cerevisiae ; }, abstract = {The escape and migration of genetic information between mitochondria, chloroplasts, and nuclei have been an integral part of evolution and has a continuing impact on the biology of cells. The evolutionary transfer of functional genes and fragments of genes from chloroplasts to mitochondria, from chloroplasts to nuclei, and from mitochondria to nuclei has been documented for numerous organisms. Most documented instances of genetic material transfer have involved the transfer of information from mitochondria and chloroplasts to the nucleus. The pathways for the escape of DNA from organelles may include transient breaches in organellar membranes during fusion and/or budding processes, terminal degradation of organelles by autophagy coupled with the subsequent release of nucleic acids to the cytoplasm, illicit use of nucleic acid or protein import machinery, or fusion between heterotypic membranes. Some or all of these pathways may lead to the escape of DNA or RNA from organellar compartments with subsequent uptake of nucleic acids from the cytoplasm into the nucleus. Investigations into the escape of DNA from mitochondria in yeast have shown the rate of escape for gene-sized fragments of DNA from mitochondria and its subsequent migration to the nucleus to be roughly equivalent to the rate of spontaneous mutation of nuclear genes. Smaller fragments of mitochondrial DNA may appear in the nucleus even more frequently. Mutations of nuclear genes that define gene products important in controlling the rate of DNA escape from mitochondria in yeast also have been described. The escape of genetic material from mitochondria and chloroplasts has clearly had an impact on nuclear genetic organization throughout evolution and may also affect cellular metabolic processes.}, }
@article {pmid8870075, year = {1996}, author = {Ullmann, SL and Butcher, L}, title = {Mammalian oocyte organelles with special reference to pleomorphic mitochondria and vacuole formation in marsupials.}, journal = {Reproduction, fertility, and development}, volume = {8}, number = {4}, pages = {491-508}, doi = {10.1071/rd9960491}, pmid = {8870075}, issn = {1031-3613}, mesh = {Animals ; Female ; Marsupialia/*anatomy &amp; histology ; Microscopy, Electron ; Mitochondria/*ultrastructure ; Oocytes/*ultrastructure ; Opossums/anatomy &amp; histology ; Organelles/*ultrastructure ; Vacuoles/*ultrastructure ; }, abstract = {Marsupial oocytes are larger and have a thinner zona than eutherian oocytes; and the ooplasm becomes almost completely filled with empty-looking vacuoles the contents of which have, so far, defied histochemical analysis. In the opossum, Monodelphis domestica, apart from orthodox mitochondria, a 'hooded' form is found occasionally in young primary oocytes, and a novel 'spiked' form-which is very elongate and has longitudinally-running filaments attached to the outer membrane--is found in mature oocytes. On the genesis of the ooplasmic vacuoles in mammals, information is available only for two marsupials. In Monodelphis, the vacuoles originate from endoplasmic, endocytotic and Golgi vesicles which generate multivesicular bodies; these give rise to the vacuoles. For the bandicoot, Isoodon macrourus, evidence is presented for the formation of the vacuoles from enlarged, transformed mitochondria which undergo a complex evolution during development. Primordial oocytes of Isoodon contain three ooplasmic localizations--a paranuclear complex, a vesicle microtubule complex and an aggregate of tubular cistenae-which have not been described for other mammalian oocytes. The origin, fate and function of these organelle localizations is unknown. In this paper, problems with respect to the definition of 'yolk' are described and the extent of our ignorance concerning oocyte organelles is discussed.}, }
@article {pmid8829635, year = {1996}, author = {Manfredi, G and Schon, EA and Bonilla, E and Moraes, CT and Shanske, S and DiMauro, S}, title = {Identification of a mutation in the mitochondrial tRNA(Cys) gene associated with mitochondrial encephalopathy.}, journal = {Human mutation}, volume = {7}, number = {2}, pages = {158-163}, doi = {10.1002/(SICI)1098-1004(1996)7:2&lt;158::AID-HUMU12&gt;3.0.CO;2-1}, pmid = {8829635}, issn = {1059-7794}, mesh = {Base Sequence ; Child, Preschool ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/metabolism ; Evolution, Molecular ; Female ; Humans ; Mitochondria, Muscle/ultrastructure ; Mitochondrial Encephalomyopathies/enzymology/*genetics/pathology ; Molecular Sequence Data ; Muscle Fibers, Skeletal/enzymology/pathology ; *Mutation ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Polymorphism, Single-Stranded Conformational ; RNA, Transfer, Cys/chemistry/*genetics ; Succinate Dehydrogenase/metabolism ; }, }
@article {pmid8845346, year = {1995}, author = {Leehey, MA and Squassoni, CA and Friederich, MW and Mills, JB and Hagerman, PJ}, title = {A noncanonical tertiary conformation of a human mitochondrial transfer RNA.}, journal = {Biochemistry}, volume = {34}, number = {50}, pages = {16235-16239}, doi = {10.1021/bi00050a001}, pmid = {8845346}, issn = {0006-2960}, support = {AG00621/AG/NIA NIH HHS/United States ; GM35305/GM/NIGMS NIH HHS/United States ; }, mesh = {Anticodon/chemistry ; Base Sequence ; Birefringence ; Electrophoresis, Polyacrylamide Gel ; Humans ; Mitochondria/*chemistry ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Nucleic Acid Heteroduplexes/chemistry ; RNA ; RNA, Transfer, Lys/*chemistry/genetics ; Time Factors ; }, abstract = {Transfer RNAs possess highly conserved secondary structures, and crystallographic studies suggest a common, L-shaped tertiary conformation in which the anticodon and acceptor stems are disposed at approximately right angles to one another. However, many animal mitochondrial tRNAs possess unusual secondary structures, and little is known regarding their tertiary conformations, in particular, the relative orientations of their acceptor and anticodon stems. To address this issue, we have constructed heteroduplex RNA molecules corresponding to human mitochondrial and cytoplasmic lysyl tRNAs in which the acceptor and anticodon stems of each tRNA have been extended by approximately 70 base pairs. The rotational decay times of the two "extended" tRNA(Lys) species were compared to the decay times of a linear RNA control and to an extended yeast cytoplasmic tRNA(Phe) species whose interstem angle had been reported previously. Whereas the apparent interstem angle of the human cytoplasmic tRNA(Lys) species is essentially identical to that of the yeast tRNA(Phe) heteroduplex, with both conforming to the canonical L-shape, the angle for the mitochondrial tRNA(Lys) construct is much larger (approximately 140 degrees). Thus, the universal L-shape may not be applicable to noncanonical mitochondrial tRNAs, a finding of significance for both tRNA evolution and mitochondrial disease.}, }
@article {pmid8790446, year = {1995}, author = {Miyata, S and Kanazawa, A and Tsutsumi, N and Sano, Y and Hirai, A}, title = {Mitochondrial plasmid-like DNAs of the B1 family in the genus Oryza: sequence heterogeneity and evolution.}, journal = {Idengaku zasshi}, volume = {70}, number = {6}, pages = {675-685}, doi = {10.1266/jjg.70.675}, pmid = {8790446}, issn = {0021-504X}, mesh = {Base Sequence ; Cloning, Molecular ; DNA, Mitochondrial/*genetics ; *Evolution, Molecular ; Genome, Plant ; Molecular Sequence Data ; Oryza/*genetics/physiology ; Plasmids/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Four kinds of circular plasmid-like DNA, designated B1, B2, B3 and B4, have been found in the mitochondria of Oryza sativa L. with an AA genome. Three novel B1-homologous mitochondrial plasmid-like DNAs, designated, M1, M2 and M3, were isolated in the present study from strains with CC and CCDD genomes in the genus Oryza. We cloned and sequenced these DNAs and found that the sequences of these molecules have wide regions of homology. B1, M2 and M3 each lack about 300 bp of a region that is present in M1 and small repeats were found at the sites of deleted sequences. Therefore, we propose the hypothesis that the B1 family differentiated from a common ancient molecule that was similar to M1 via, probably, slipped mispairing during DNA replication at several stages in the evolution in the genus Oryza.}, }
@article {pmid8747299, year = {1995}, author = {Emerson, BC and Wallis, GP}, title = {Phylogenetic relationships of the Prodontria (Coleoptera; Scarabaeidae; subfamily Melolonthinae), derived from sequence variation in the mitochondrial cytochrome oxidase II gene.}, journal = {Molecular phylogenetics and evolution}, volume = {4}, number = {4}, pages = {433-447}, doi = {10.1006/mpev.1995.1040}, pmid = {8747299}, issn = {1055-7903}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Coleoptera/classification/enzymology/*genetics ; DNA/genetics ; DNA Primers/genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {The beetle genus Prodontria is of importance to New Zealand conservation programs. All Prodontria species are brachypterous (having reduced wings), and the genus presents some interesting evolutionary and biogeographic questions that are testable using phylogenetic reconstruction. A phylogeny was produced for 14 flightless Prodontria species, 2 macropterous (fully winged) Odontria species, and single representatives of 2 outgroup genera using sequence data from the mitochondrial COII gene. The data support probable conspecificity of the morphologically similar P. modesta and P. bicolorata but do not support their hypothesized sister-species relationship with the geographically proximate P. lewisi. The alpine P. capito is found to be a paraphyletic group, with the most eastern population diverging after the western populations made their appearance. Many interesting biogeographic disjunctions are here proposed to be anomalous and the result of morphological convergence. The data do not support the idea of a common flightless ancester for Prodontria, but suggest that brachyptery has evolved numerous times. In some instances, this appears to have led to contemporaneous speciation resulting in little resolution of phylogenetic relationships in some parts of the tree. These data allow for a new interpretation of the origin and diversification of the southern New Zealand flightless melolonthine fauna. Multiple speciation events involving wing reduction are suggested to involve at least one widespread flighted ancestor that has given rise to brachypterous forms.}, }
@article {pmid8721994, year = {1995}, author = {Andersson, SG and Kurland, CG}, title = {Genomic evolution drives the evolution of the translation system.}, journal = {Biochemistry and cell biology = Biochimie et biologie cellulaire}, volume = {73}, number = {11-12}, pages = {775-787}, doi = {10.1139/o95-086}, pmid = {8721994}, issn = {0829-8211}, mesh = {Animals ; *Biological Evolution ; Genetic Code ; *Genome ; Mitochondria/*genetics ; Prokaryotic Cells ; *Protein Biosynthesis ; RNA, Bacterial/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {Our thesis is that the characteristics of the translational machinery and its organization are selected in part by evolutionary pressure on genomic traits have nothing to do with translation per se. These genomic traits include size, composition, and architecture. To illustrate this point, we draw parallels between the structure of different genomes that have adapted to intracellular niches independently of each other. Our starting point is the general observation that the evolutionary history of organellar and parasitic bacteria have favored bantam genomes. Furthermore, we suggest that the constraints of the reductive mode of genomic evolution account for the divergence of the genetic code in mitochondria and the genetic organization of the translational system observed in parasitic bacteria. In particular, we associate codon reassignments in animal mitochondria with greatly simplified tRNA populations. Likewise, we relate the organization of translational genes in the obligate intracellular parasite Rickettsia prowazekii to the processes supporting the reductive mode of genomic evolution. Such findings provide strong support for the hypothesis that genomes of organelles and of parasitic bacteria have arisen from the much larger genomes of ancestral bacteria that have been reduced by intrachromosomal recombination and deletion events. A consequence of the reductive mode of genomic evolution is that the resulting translation systems may deviate markedly from conventional systems.}, }
@article {pmid8682229, year = {1995}, author = {Trevi, G and Sheiban, I and Gorni, R}, title = {[Myocardial hypertrophy and arterial hypertension].}, journal = {Giornale italiano di cardiologia}, volume = {25}, number = {10}, pages = {1331-1338}, pmid = {8682229}, issn = {0046-5968}, mesh = {Cardiomegaly/*complications/pathology/physiopathology ; Humans ; Hypertension/*complications/pathology/physiopathology ; }, abstract = {Myocardial hypertrophy in different cardiac diseases is considered to be an adaptive mechanism to the increase of hemodynamic load which might restore to normal radius/wall thickness ratio and consequently to normalize wall stress. However, it has been widely demonstrated that beside the hemodynamic load, other factors contribute to the development of myocardial hypertrophy. It has been shown that in hypertensive patients, functional abnormalities (increased contribution of atrial systole to total diastolic filling, increased isovolumic relaxation period, prolonged diastolic duration, slowed ventricular filling and altered diastolic distensibility) precede the development of myocardial hypertrophy. Thus, in hypertensive patients, sign and symptoms of heart failure could be manifested in absence of myocardial hypertrophy, and might be exclusively due to diastolic dysfunction (with normal systolic function). Systolic function might be involved and compromised late when focal myocardial cell death and fibrosis occur and consequently ¿adequate¿ hypertrophy is shifted to ¿inadequate¿. This evolution is accompanied by morphological and functional changes of the myocardium similar to those encountered in dilated cardiomyopathy. Impairment of systolic function in ¿inadequate¿ hypertrophy is also due to structural changes; altered ratio between sarcomers and mitochondria, increased intercapillary distance, sarcoplasmatic reticulum dysfunction, increase of collagene component with a consequent increment of wall rigidity, hypertrophy of arterial tunica media, which alters coronary flow and coronary reserve. The progression of these morpho-functional abnormalities is a very slow process, in which adaptive mechanism mediated by several enzymes and contractile protein, contribute to maintain myocardial viability. However, over the long course, disseminated focal myocardial cell necrosis and fibrosis, which is an evolving process, is considered to be the main responsible factor for the irreversible myocardial damage and systolic dysfunction in advanced myocardial inadequate hypertrophy.}, }
@article {pmid8748016, year = {1995}, author = {Nee, S and Holmes, EC and Rambaut, A and Harvey, PH}, title = {Inferring population history from molecular phylogenies.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {349}, number = {1327}, pages = {25-31}, doi = {10.1098/rstb.1995.0087}, pmid = {8748016}, issn = {0962-8436}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {*Genetics, Population ; Genome, Viral ; Humans ; Mathematics ; Mitochondria/genetics ; Molecular Biology ; *Phylogeny ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {Variable molecular sequences sampled from a population can be used to infer its dynamic history. Graphical methods are developed and applied to real data, illustrating ways of navigating through hypothesis space with two landmarks for reference: constant population size and exponentially growing population size.}, }
@article {pmid8901493, year = {1995}, author = {Reilly, TH and Schmitt, ME}, title = {The yeast, Saccharomyces cerevisiae, RNase P/MRP ribonucleoprotein endoribonuclease family.}, journal = {Molecular biology reports}, volume = {22}, number = {2-3}, pages = {87-93}, pmid = {8901493}, issn = {0301-4851}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Conserved Sequence ; DNA Replication ; DNA, Fungal/biosynthesis ; DNA, Mitochondrial/biosynthesis ; Endoribonucleases/*chemistry/*metabolism ; Evolution, Molecular ; Mammals ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Structure, Secondary ; RNA, Catalytic/*chemistry/*metabolism ; Ribonuclease P ; Ribonucleoproteins/chemistry/metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Ribonuclease P (RNase P) is a ribonucleoprotein responsible for the endonucleolytic cleavage of the 5'-termini of tRNAs. Ribonuclease MRP (RNase MRP) is a ribonucleoprotein that has the ability to cleave both mitochondrial RNA primers presumed to be involved in mitochondrial DNA replication and rRNA precursors for the production of mature rRNAs. Several lines of evidence suggest that these two ribonucleoproteins are related to each other, both functionally and evolutionarily. Both of these enzymes have activity in the nucleus and mitochondria. Each cleave their RNA substrates in a divalent cation dependent manner to generate 5'-phosphate and 3'-OH termini. In addition, the RNA subunits of both complexes can be folded into a similar secondary structure. Each can be immunoprecipitated from mammalian cells with Th antibodies. In yeast, both have been found to share at least one common protein. This review will discuss some of the recent advances in our understanding of the structure, function and evolutionary relationship of these two enzymes in the yeast, Saccharomyces cerevisiae.}, }
@article {pmid8868450, year = {1995}, author = {Frolov, AO and Karpov, SA}, title = {Comparative morphology of kinetoplastids.}, journal = {Tsitologiia}, volume = {37}, number = {11}, pages = {1072-1096}, pmid = {8868450}, issn = {0041-3771}, mesh = {Animals ; Cell Nucleus/ultrastructure ; DNA, Kinetoplast/analysis ; Flagella/ultrastructure ; Kinetoplastida/*cytology/ultrastructure ; Mitochondria/chemistry/ultrastructure ; }, abstract = {The common structural plan of bodonids, cryptobiids and trypanosomatids permits placing them in one phylum Kinetoplastidae. Analysis of evolutionary changes in the initial "bodonid" structural plan in separate groups within the Kinetoplastidae, illustrated by an evolutionary series of homologous characters, enables us to conclude that the cryptobiids occupy an intermediate position in kinetoplastid evolution between the free-living bodonids and Trypanosoma spp from lower vertebrates and can be considered to be potential ancestors of the latter.}, }
@article {pmid8868447, year = {1995}, author = {Sleigh, MA}, title = {Progress in understanding the phylogeny of flagellates.}, journal = {Tsitologiia}, volume = {37}, number = {11}, pages = {985-1009}, pmid = {8868447}, issn = {0041-3771}, mesh = {Animals ; Eukaryota/*classification/genetics/ultrastructure ; *Phylogeny ; RNA, Protozoan/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Heterotrophic free-living flagellates appear to provide the ancestry for all other eukaryote groups. Not only are the oldest surviving anaerobic eukaryotes flagellated protists, but also there appear to be survivors of a lineage of flagellate forms which could have been close to the sources of the main branches of eukaryote evolution. These 'stem' forms of flagellates developed more complex flagellation with anchoring fibres which became the main components of the cytoskeleton and supported the cytostome; by their phagotrophic activities these flagellates established symbiotic relationships, first with aerobic bacteria to form mitochondria, and later with various forms of prokaryotic and eukaryotic algal cells to form chloroplasts of a variety of types having different pigments, different structure and different food storage patterns. The specific patterns of flagellation, cytoskeleton, cytostome, secreted surface structures and cell aggregation into colonies enable groups of organisms to be recognised, whose most primitive survivors in almost all cases are heterotrophic flagellates. The current view of the phylogeny of eukaryotes suggests that heterotrophic flagellates have provided the origins of all major eukaryote groups, and that the phylogeny of these flagellates is the key to understanding the evolution of all eukaryotes. We anticipate that further rRNA analyses, supported by ultrastructural data, will confirm the central role played by these flagellates in eukaryote evolution.}, }
@article {pmid8824418, year = {1995}, author = {Craig, E and Ziegelhoffer, T and Nelson, J and Laloraya, S and Halladay, J}, title = {Complex multigene family of functionally distinct Hsp70s of yeast.}, journal = {Cold Spring Harbor symposia on quantitative biology}, volume = {60}, number = {}, pages = {441-449}, doi = {10.1101/sqb.1995.060.01.049}, pmid = {8824418}, issn = {0091-7451}, support = {2 RO1 GM-278760/GM/NIGMS NIH HHS/United States ; 5 RO1 GM-31107/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Transport, Active ; *Calcium-Transporting ATPases ; Carrier Proteins/metabolism ; Fungal Proteins/metabolism ; *Genes, Fungal ; HSP70 Heat-Shock Proteins/*genetics/*metabolism ; *Heat-Shock Proteins ; *Membrane Transport Proteins ; Mitochondria/metabolism ; Mitochondrial Membrane Transport Proteins ; Molecular Chaperones/metabolism ; *Multigene Family ; Phylogeny ; Saccharomyces cerevisiae/*genetics/*metabolism ; *Saccharomyces cerevisiae Proteins ; }, }
@article {pmid8643412, year = {1995}, author = {Thomas, BC and Gao, L and Stomp, D and Li, X and Gegenheimer, PA}, title = {Spinach chloroplast RNase P: a putative protein enzyme.}, journal = {Nucleic acids symposium series}, volume = {}, number = {33}, pages = {95-98}, pmid = {8643412}, issn = {0261-3166}, mesh = {Biological Evolution ; Chloroplasts/*enzymology ; Chromatography, Gel ; Cross Reactions ; Endoribonucleases/immunology/isolation &amp; purification/*metabolism ; Epitopes ; Humans ; Molecular Weight ; Plant Proteins/immunology/isolation &amp; purification ; RNA, Catalytic/immunology/isolation &amp; purification/*metabolism ; Ribonuclease P ; Spinacia oleracea/*enzymology ; }, abstract = {Ribonuclease P (RNase P) is the enzyme responsible for endonucleolytically separating the 5'-leader sequence from precursor tRNA molecules. In bacteria, and in the nuclei and mitochondria of all eukaryotes studied so far, RNase P contains an RNA subunit which is necessary for activity in vitro and in vivo. In contrast, we showed earlier that partially-purified RNase P from spinach chloroplasts had physical properties inconsistent with the presence of any RNA. We now report that the properties of the chloroplast enzyme, after 500 to 1500-fold purification, are consistent with enzymatic activity residing in a approximately 70 kDa polypeptide. Gel filtration chromatography on Sephacryl S-200 and S-300 provides a mass for chloroplast RNase P of approximately 70 +/- 5 kDa. A single polypeptide of approximately 70-80 kDa can be crosslinked to iodoUMP-substituted pre-tRNA. The labeling intensity of this polypeptide corresponds closely to the peak of RNase P activity on Sephacryl S-200 chromatography. Unlike the bacterial ribozyme-type RNase P, chloroplast RNase P is not a metalloenzyme. We showed previously that phosphodiester bond cleavage by the E. coli RNA enzyme absolutely requires Mg2+ or Mn2+ coordinated to the pro-Rp oxygen of the scissile phosphodiester phosphate. In contrast, we now find that chloroplast RNase P has no such requirement, and can accurately and efficiently cleave pre-tRNA containing an Rp-thio-substitution at the scissile bond. These data are entirely consistent with the hypothesis that RNase P in plant chloroplasts is not a ribozyme, but a conventional protein enzyme.}, }
@article {pmid11542508, year = {1994}, author = {Day, S}, title = {Hot bacteria &amp; other ancestors.}, journal = {New scientist (1971)}, volume = {142}, number = {1920}, pages = {21-25}, pmid = {11542508}, issn = {0262-4079}, mesh = {Amino Acid Sequence ; Animals ; Archaea/*classification/genetics ; *Biological Evolution ; Cell Nucleus ; Diplomonadida ; Environmental Microbiology ; Eukaryotic Cells/*classification/physiology/ultrastructure ; Giardia/*classification/*genetics/ultrastructure ; *Hot Temperature ; Mitochondria ; Peptide Elongation Factor Tu/chemistry/genetics ; Phylogeny ; RNA, Protozoan ; RNA, Ribosomal ; }, }
@article {pmid8790455, year = {1994}, author = {Ferretti, V and Lang, BF and Sankoff, D}, title = {Skewed base compositions, asymmetric transition matrices, and phylogenetic invariants.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {1}, number = {1}, pages = {77-92}, doi = {10.1089/cmb.1994.1.77}, pmid = {8790455}, issn = {1066-5277}, mesh = {Algorithms ; Aspergillus ; *Base Composition ; Computer Simulation ; Models, Biological ; *Phylogeny ; Rhizobium ; Rickettsia ; Saccharomyces cerevisiae ; Schizosaccharomyces ; }, abstract = {Evolutionary inference methods that assume equal DNA base compositions and symmetric nucleotide substitution matrices, where these assumptions do not hold, are likely to group species on the basis of similar base compositions rather than true phylogenetic relationships. We propose an invariants-based method for dealing with this problem. An invariant QT of a tree T under a k-state Markov model, where a generalized time parameter is identified with the E edges of T, allows us to recognize whether data on N observed species can be associated with the N terminal vertices of T in the sense of having been generated on T rather than on any other tree with N terminals. The form of the generalized time parameter is a positive determinant matrix in some semigroup S of stochastic matrices. The invariance is with respect to the choice of the set of E matrices in S, one associated with each of the E edges of T. We apply a general "empirical" method of finding invariants of a parametrized functional form. It involves calculating the probability f of all KN data possibilities for each of m sets of E matrices in S to associate with the edges of T, then solving for the parameters using the m equations of form Q(f) = 0. We discuss the problems of finding asymmetric models satisfying the property of semigroup closure, of finding asymmetric models that admit invariants at all, and of the computational complexity of the method. We propose a class of semigroups Sc containing matrices of form [formula: see text] to account for A+T versus G+C asymmetries in DNA base composition. Quadratic invariants are obtained for rooted trees with three and with four terminals. In the latter case the smallest set of algebraically independent invariants is sought. These invariants are applied to data pertaining the fungal evolution and to the origin of mitochondria as bacterial endosymbionts.}, }
@article {pmid11541390, year = {1993}, author = {Sagan, L}, title = {On the origin of mitosing cells. 1967.}, journal = {The Journal of NIH research : life sciences research and news about the National Institutes of Health and the Alcohol, Drug Abuse, and Mental Health Administration}, volume = {5}, number = {3}, pages = {65-72}, pmid = {11541390}, issn = {1043-609X}, mesh = {Animals ; *Biological Evolution ; Cell Physiological Phenomena ; Cyanobacteria ; Eukaryota ; Eukaryotic Cells/cytology/*physiology/*ultrastructure ; Extrachromosomal Inheritance/genetics/physiology ; Flagella ; History, 20th Century ; Mitochondria ; *Mitosis ; Oxidation-Reduction ; Photosynthesis ; Plastids ; Prokaryotic Cells/cytology/physiology/ultrastructure ; *Symbiosis ; }, abstract = {A theory of the origin of eukaryotic cells ("higher" cells which divide by classical mitosis) is presented. By hypothesis, three fundamental organelles: the mitochondria, the photosynthetic plastids and the (9+2) [9(2)+2] basal bodies [kinetosomes] of flagella [undulipodia] were themselves once free-living (prokaryotic) cells. The evolution of photosynthesis under the anaerobic [anoxic] conditions of the early atmosphere to form anaerobic bacteria, photosynthetic bacteria and eventually blue-green algae (and protoplastids) is described. The subsequent evolution of aerobic metabolism in prokayotes to form aerobic bacteria (protoflagella [undulipodia] and protomitochondria) presumably occurred during the transition to the oxidizing atmosphere. Classical mitosis evolved in protozoan-type cells millions of years after the evolution of photosynthesis. A plausible scheme for the origin of classical mitosis in primitive amoeboflagellates [amoebomastigotes] is presented. During the course of the evolution of mitosis, photosynthetic plastids (themselves derived from prokaryotes) were symbolically acquired by some of these protozoans to form the ["eukaryotic" deleted] algae and the green plants. The cytological, biochemical and paleontological evidence for this theory is presented, along with suggestions for further possible experimental verification. The implications of this scheme for the systematics of the lower [smaller] organisms is discussed.}, }
@article {pmid11542099, year = {1987}, author = {Margulis, L and Sagan, D}, title = {Microcosmos: the universe within us reveals evolution's secrets.}, journal = {Bostonia (Boston, Mass. : 1986)}, volume = {61}, number = {}, pages = {55-58}, pmid = {11542099}, issn = {1067-2834}, mesh = {Bacteria/*genetics ; Bacterial Physiological Phenomena ; *Biological Evolution ; DNA ; Environmental Microbiology ; Genetics, Microbial ; Microtubules ; Mitochondria/genetics ; Prokaryotic Cells ; Symbiosis/genetics/*physiology ; }, }
@article {pmid11542100, year = {1987}, author = {Sagan, D and Margulis, L}, title = {Bacterial bedfellows: a microscopic menage a trois may be responsible for a major step in evolution.}, journal = {Natural history}, volume = {96}, number = {3}, pages = {26-33}, pmid = {11542100}, issn = {0028-0712}, mesh = {Amoeba/cytology/genetics ; Animals ; Archaea ; Bacteria/genetics ; *Biological Evolution ; DNA ; Eukaryotic Cells/cytology/physiology ; Mitochondria/physiology ; Plastids/physiology ; Spirochaetales/cytology ; *Symbiosis ; Thermoplasma/cytology ; }, }
@article {pmid11542098, year = {1987}, author = {Bermudes, D and Margulis, L}, title = {Symbiont acquisition as neoseme: origin of species and higher taxa.}, journal = {Symbiosis (Philadelphia, Pa.)}, volume = {4}, number = {}, pages = {185-198}, pmid = {11542098}, issn = {0334-5114}, mesh = {Bacteria ; *Biological Evolution ; Eukaryotic Cells/classification ; Fungi ; Mitochondria ; *Phylogeny ; Plastids ; Prokaryotic Cells/classification ; *Symbiosis ; }, abstract = {We examine the hypothesis that, in the origin of species and higher taxa of eukaryotes, symbiont acquisition followed by partner integration has been equivalent to neoseme appearance leading to speciation. The formation of stable symbiotic associations involves partner-surface recognition, behavioral and metabolic interaction, and, in some cases, gene product (RNA, protein) and genic (RNA, DNA) integration. This analysis is applied here to examples of neosemes that define specific taxa and to neosemes in plants, fungi, and animals that involve the appearance of new types of tissue. If this hypothesis is correct--if the origin of major genetic variation leading to speciation and even higher taxa may occur through symbiont acquisition and integration--then the analysis of "origins of species and higher taxa" becomes analogous to the study of microbial community ecology.}, }
@article {pmid11536580, year = {1987}, author = {Delihas, N and Fox, GE}, title = {Origins of the plant chloroplasts and mitochondria based on comparisons of 5S ribosomal RNAs.}, journal = {Annals of the New York Academy of Sciences}, volume = {503}, number = {}, pages = {92-102}, doi = {10.1111/j.1749-6632.1987.tb40601.x}, pmid = {11536580}, issn = {0077-8923}, support = {DMB 85-02213/MB/BHP HRSA HHS/United States ; NSG-7440/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Bacteria ; *Biological Evolution ; Cyanobacteria ; Euglena gracilis ; Mitochondria/*genetics/physiology ; Plants/*genetics/ultrastructure ; *RNA, Bacterial ; *RNA, Chloroplast ; RNA, Plant ; RNA, Protozoan ; RNA, Ribosomal, 5S/classification/*genetics/physiology ; Sequence Analysis, RNA ; Sequence Homology, Nucleic Acid ; Symbiosis ; Triticum ; }, abstract = {In this paper, we provide macromolecular comparisons utilizing the 5S ribosomal RNA structure to suggest extant bacteria that are the likely descendants of chloroplast and mitochondria endosymbionts. The genetic stability and near universality of the 5S ribosomal gene allows for a useful means to study ancient evolutionary changes by macromolecular comparisons. The value in current and future ribosomal RNA comparisons is in fine tuning the assignment of ancestors to the organelles and in establishing extant species likely to be descendants of bacteria involved in presumed multiple endosymbiotic events.}, }
@article {pmid11537244, year = {1986}, author = {Tabushi, I}, title = {Minimum requirements for single cell activity.}, journal = {Advances in space research : the official journal of the Committee on Space Research (COSPAR)}, volume = {6}, number = {11}, pages = {45-52}, doi = {10.1016/0273-1177(86)90274-7}, pmid = {11537244}, issn = {0273-1177}, mesh = {Adenosine Triphosphate/chemical synthesis ; Cell Membrane ; Cell Respiration ; Cells/*chemistry ; Cytochrome c Group/chemistry ; Dithionite ; Electron Transport ; *Evolution, Chemical ; Kinetics ; Liposomes ; *Membranes, Artificial ; Mitochondria ; Oxidation-Reduction ; }, }
@article {pmid11543608, year = {1985}, author = {Margulis, L and Bermudes, D}, title = {Symbiosis as a mechanism of evolution: status of cell symbiosis theory.}, journal = {Symbiosis (Philadelphia, Pa.)}, volume = {1}, number = {}, pages = {101-124}, pmid = {11543608}, issn = {0334-5114}, mesh = {*Biological Evolution ; Eukaryotic Cells/classification/*physiology ; Microtubules ; Mitochondria ; Nuclear Envelope ; Organelles ; Phylogeny ; Plastids ; Prokaryotic Cells/classification/*physiology ; *Symbiosis ; }, abstract = {Several theories for the origin of eukaryotic (nucleated) cells from prokaryotic (bacterial) ancestors have been published: the progenote, the direct filiation and the serial endosymbiotic theory (SET). Compelling evidence for two aspects of the SET is now available suggesting that both mitochondria and plastids originated by symbioses with a third type of microbe, probably a Thermoplasma-like archaebacterium ancestral to the nucleocytoplasm. We conclude that not enough information is available to negate or substantiate another SET hypothesis: that the undulipodia (cilia, eukaryotic flagella) evolved from spirochetes. Recognizing the power of symbiosis to recombine in single individual semes from widely differing partners, we develop the idea that symbiosis has been important in the origin of species and higher taxa. The abrupt origin of novel life forms through the formation of stable symbioses is consistent with certain patterns of evolution (e.g punctuated equilibria) described by some paleontologists.}, }
@article {pmid11542018, year = {1985}, author = {Villanueva, E and Luehrsen, KR and Gibson, J and Delihas, N and Fox, GE}, title = {Phylogenetic origins of the plant mitochondrion based on a comparative analysis of 5S ribosomal RNA sequences.}, journal = {Journal of molecular evolution}, volume = {22}, number = {}, pages = {46-52}, pmid = {11542018}, issn = {0022-2844}, support = {NSG-7440/NS/NINDS NIH HHS/United States ; PCM 83-02127/PC/NCI NIH HHS/United States ; }, mesh = {Base Sequence ; Burkholderia cepacia/*genetics ; Mitochondria/*genetics ; Nucleic Acid Conformation ; Paracoccus denitrificans/*genetics ; Phylogeny ; RNA, Bacterial/analysis/genetics ; RNA, Plant/*analysis/genetics ; RNA, Ribosomal, 5S/*analysis/genetics ; Rhodobacter sphaeroides/genetics ; Rhodospirillaceae/*genetics ; Sequence Homology, Nucleic Acid ; Symbiosis/genetics ; Triticum/genetics ; }, abstract = {The complete nucleotide sequences of 5S ribosomal RNAs from Rhodocyclus gelatinosa, Rhodobacter sphaeroides, and Pseudomonas cepacia were determined. Comparisons of these 5S RNA sequences show that rather than being phylogenetically related to one another, the two photosynthetic bacterial 5S RNA sequences show that rather than being phylogenetically related to one another, the two photosynthetic bacterial 5S RNAs share more sequence and signature homology with the RNAs of two nonphotosynthetic strains. Rhodobacter sphaeroides is specifically related to Paracoccus denitrificans and Rc. gelatinosa is related to Ps. cepacia. These results support earlier 16S ribosomal RNA studies and add two important groups to the 5S RNA data base. Unique 5S RNA structural features previously found in P. denitrificans are present also in the 5S RNA of Rb. sphaeroides; these provide the basis for subdivisional signatures. The immediate consequence of our obtaining these new sequences is that we are able to clarify the phylogenetic origins of the plant mitochondrion. In particular, we find a close phylogenetic relationship between the plant mitochondria and members of the alpha subdivision of the purple photosynthetic bacteria, namely, Rb. sphaeroides, P. denitrificans, and Rhodospirillum rubrum.}, }
@article {pmid11541973, year = {1984}, author = {Hartman, H}, title = {The origin of the eukaryotic cell.}, journal = {Speculations in science and technology}, volume = {7}, number = {2}, pages = {77-81}, pmid = {11541973}, issn = {0155-7785}, mesh = {*Biological Evolution ; Cell Nucleus/*physiology ; Chromosomes/physiology ; DNA/physiology ; Eukaryotic Cells/*physiology ; RNA/*physiology ; Symbiosis ; }, abstract = {The endosymbiotic hypothesis for the origin of the eukaryotic cell has been applied to the origin of the mitochondria and chloroplasts. However as has been pointed out by Mereschowsky in 1905, it should also be applied to the nucleus as well. If the nucleus, mitochondria and chloroplasts are endosymbionts, then it is likely that the organism that did the engulfing was not a DNA-based organism. In fact, it is useful to postulate that this organism was a primitive RNA-based organism. This hypothesis would explain the preponderance of RNA viruses found in eukaryotic cells. The centriole and basal body do not have a double membrane or DNA. Like all MTOCs (microtubule organising centres), they have a structural or morphic RNA implicated in their formation. This would argue for their origin in the early RNA-based organism rather than in an endosymbiotic event involving bacteria. Finally, the eukaryotic cell uses RNA in ways quite unlike bacteria, thus pointing to a greater emphasis of RNA in both control and structure in the cell. The origin of the eukaryotic cell may tell us why it rather than its prokaryotic relative evolved into the metazoans who are reading this paper.}, }
@article {pmid11537790, year = {1984}, author = {Ross, MD}, title = {The influence of gravity on structure and function of animals.}, journal = {Advances in space research : the official journal of the Committee on Space Research (COSPAR)}, volume = {4}, number = {12}, pages = {305-314}, doi = {10.1016/0273-1177(84)90575-1}, pmid = {11537790}, issn = {0273-1177}, support = {NSG-9047/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Calcification, Physiologic/physiology ; Calcium/*metabolism ; Cardiovascular System ; Cell Movement/physiology ; Cell Physiological Phenomena ; Cytoskeleton/physiology ; Eukaryotic Cells/physiology ; *Gravitation ; Gravity Sensing/*physiology ; Mitochondria/physiology ; Musculoskeletal System ; Nervous System ; Prokaryotic Cells/physiology ; }, abstract = {Gravity is the only environmental parameter that has remained constant during the period of evolution of living matter on Earth. Thus, it must have been a major force in shaping living things. The influence of gravitational loading in evolution of the vertebrate skeleton is well recognized, and scale effects have been studied. This paper, however, considers in addition four pivotal events in early evolution that would seem to have been significant for the later success and diversification of animal life. These are evolution of the cytoskeleton, cell motility (flagellae and cilia), gravity detecting devices (accelerometers), and biomineralization. All are functionally calcium dependent in eukaryotes and all occurred or were foreshadowed in prokaryotes. A major question is why calcium was selected as an ion of great importance to the structure and function of living matter; another is whether gravity played a role in its selection.}, }
@article {pmid11537775, year = {1984}, author = {Margulis, L and Stolz, JF}, title = {Cell symbiosis [correction of symbioisis] theory: status and implications for the fossil record.}, journal = {Advances in space research : the official journal of the Committee on Space Research (COSPAR)}, volume = {4}, number = {12}, pages = {195-201}, doi = {10.1016/0273-1177(84)90562-3}, pmid = {11537775}, issn = {0273-1177}, mesh = {Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; *Biological Evolution ; Cilia/physiology ; Eukaryotic Cells/*physiology ; *Fossils ; Genome ; Mitochondria/physiology ; Nuclear Envelope/physiology ; Organelles/*physiology ; Plastids/physiology ; Ribosomes/physiology ; *Symbiosis ; }, abstract = {Recent geological treatises have presented three alternative models of the origins of eukaryotes as if they merited equal treatment. However, modern biological techniques, especially nucleic acid and protein sequencing, have clearly established the validity of the symbiotic theory of the origin of eukaryotic organelles. The serial endosymbiotic theory in its most extreme form states that three classes of eukaryotic cell organelles (mitochondria, plastids and undulipodia) originated as free-living bacteria (aerobic respirers, phototrophic bacteria and spirochetes respectively) in association with hosts that become the nucleocytoplasm (Thermoplasma-like archaebacterial hosts). Molecular biological information, primarily derived from ribosomal RNA nucleotide sequencing studies leads to the conclusion that the symbiotic origin theory for both mitochondria and plastids has been proven. The probability of an ancestral archaebacterial-Thermoplasma-like host for the nucleocytoplasm has been rendered more likely by discoveries by Dennis Searcy and his colleagues and Carl Woese and his colleagues. The most equivocal postulate of the symbiotic theory, the origin of undulipodia (cilia and other organelles of motility that develop from kinetosomes is under investigation now. The status of these postulates, as well as their implications for the fossil record, is briefly summarized here.}, }
@article {pmid11537772, year = {1984}, author = {Jukes, TH}, title = {Evolution of anticodons.}, journal = {Advances in space research : the official journal of the Committee on Space Research (COSPAR)}, volume = {4}, number = {12}, pages = {177-182}, doi = {10.1016/0273-1177(84)90560-x}, pmid = {11537772}, issn = {0273-1177}, mesh = {Amino Acids/*biosynthesis/chemistry ; *Anticodon ; *Codon ; *Evolution, Molecular ; *Genetic Code ; Mitochondria/genetics ; Molecular Sequence Data ; Origin of Life ; *RNA, Transfer ; }, abstract = {Anticodons are trinucleotides in transfer RNA (tRNA) molecules. The latter carry amino acids for insertion into the polypeptide sequences of proteins during the translation of messenger RNA (mRNA) molecules. Messenger RNA molecules are transcribed from genes. Evolution of tRNA molecules has resulted in a set of anticodons for the 20 amino acids that are used in protein synthesis. This set of anticodons is slightly different in mitochondrial codes from the set that used in the nuclear "universal" code. Theories for the evolution of the code include frozen accident, doublet expansion, repeating triplets and coevolutionary distribution. The number of codons has always been fixed at 64 by mathematical rules, but because an anticodon may pair with more than one codon, the number of anticodons is only 54 in the universal code, is smaller in mitochondrial codes, and was probably even smaller in archetypal primitive codes. Evidence of anticodon evolution can be seen by comparing mitochondrial codes with the universal code. Codes used by very primitive organisms that are now extinct might have specified fewer amino acids than are now used.}, }
@article {pmid11542440, year = {1983}, author = {Jukes, TH}, title = {Changes in the amino acid code.}, journal = {Advances in space research : the official journal of the Committee on Space Research (COSPAR)}, volume = {3}, number = {9}, pages = {107-111}, doi = {10.1016/0273-1177(83)90047-9}, pmid = {11542440}, issn = {0273-1177}, mesh = {Amino Acids/genetics ; Animals ; *Anticodon ; *Biological Evolution ; *Codon ; DNA ; DNA, Mitochondrial ; *Genetic Code ; Humans ; Mitochondria/*genetics ; Yeasts ; }, abstract = {The genetic code is characterized by a pattern arising from "wobble-pairing" between codons and anticodons, so that one nucleotide in the first anticodon position can pair with more than one nucleotide in the third position of a codon. Earlier codes may have existed in which there were fewer anticodons than at present, so that these earlier codes contained fewer amino acids. The universal code was formerly thought to be the only currently existing code used by terrestrial species. It is now known that differences exist from the universal code in mitochondrial coding systems, and also that mitochondrial systems differ from each other. These findings lend support to the proposal that archetypal codes preceded the present universal code. Such archetypal codes may have had some resemblances to mitochondrial codes.}, }
@article {pmid11541392, year = {1967}, author = {Sagan, L}, title = {On the origin of mitosing cells.}, journal = {Journal of theoretical biology}, volume = {14}, number = {3}, pages = {255-274}, doi = {10.1016/0022-5193(67)90079-3}, pmid = {11541392}, issn = {0022-5193}, mesh = {Animals ; *Biological Evolution ; Cell Physiological Phenomena ; Cyanobacteria ; DNA ; Eukaryotic Cells/cytology/*physiology/*ultrastructure ; Extrachromosomal Inheritance/genetics/physiology ; Flagella ; Mitochondria ; *Mitosis ; Oxidation-Reduction ; Photosynthesis ; Phylogeny ; Plastids ; Prokaryotic Cells/cytology/physiology/*ultrastructure ; *Symbiosis ; }, abstract = {A theory of the origin of eukaryotic cells ("higher" cells which divide by classical mitosis) is presented. By hypothesis, three fundamental organelles: the mitochondria, the photosynthetic plastids and the (9+2) basal bodies of flagella were themselves once free-living (prokaryotic) cells. The evolution of photosynthesis under the anaerobic conditions of the early atmosphere to form anaerobic bacteria, photosynthetic bacteria and eventually blue-green algae (and protoplastids) is described. The subsequent evolution of aerobic metabolism in prokaryotes to form aerobic bacteria (protoflagella and protomitochondria) presumably occurred during the transition to the oxidizing atmosphere. Classical mitosis evolved in protozoan-type cells millions of years after the evolution of photosynthesis. A plausible scheme for the origin of classical mitosis in primitive amoeboflagellates is presented. During the course of the evolution of mitosis, photosynthetic plastids (themselves derived from prokaryotes) were symbiotically acquired by some of these protozoans to form the eukaryotic algae and the green plants. The cytological, biochemical and paleontological evidence for this theory is presented, along with suggestions for further possible experimental verification. The implications of this scheme for the systematics of the lower organisms is discussed.}, }
@article {pmid8602146, year = {1996}, author = {Li, GY and Tian, GL and Slonimski, PP and Herbert, CJ}, title = {The CBP2 gene from Saccharomyces douglasii is a functional homologue of the Saccharomyces cerevisiae gene and is essential for respiratory growth in the presence of a wild-type (intron-containing) mitochondrial genome.}, journal = {Molecular &amp; general genetics : MGG}, volume = {250}, number = {3}, pages = {316-322}, pmid = {8602146}, issn = {0026-8925}, mesh = {Amino Acid Sequence ; Blotting, Southern ; Cell Division/genetics ; Cloning, Molecular ; Cytochrome b Group/genetics ; Evolution, Molecular ; Fungal Proteins/chemistry/*genetics ; Genes, Fungal/*genetics ; Genotype ; Introns ; Mitochondria/chemistry/genetics ; Molecular Sequence Data ; *Ribonucleoproteins ; Saccharomyces/chemistry/*genetics/growth &amp; development/metabolism ; Saccharomyces cerevisiae/chemistry/*genetics ; *Saccharomyces cerevisiae Proteins ; Sequence Analysis ; Sequence Homology, Amino Acid ; Transformation, Genetic/genetics ; }, abstract = {In Saccharomyces cerevisiae the only known role of the CBP2 gene is the excision of the fifth intron of the mitochondrial cyt b gene (bI5). We have cloned the CBP2 gene from Saccharomyces douglasii (a close relative of S. cerevisiae). A comparison of the S. douglasii and S. cerevisiae sequences shows that there are 14% nucleotide substitutions in the coding region, with transitions being three times more frequent than transversions. At the protein level sequence identity is 87%. We have demonstrated that the S. douglasii CBP2 gene is essential for respiratory growth in the presence of a wild-type S. douglasii mitochondrial genome, but not in the presence of an intronless S. cerevisiae mitochondrial genome. Also the S. douglasii and S. cerevisiae CBP2 genes are completely interchangeable, even though the intron bI5 is absent from the S. douglasii mitochondrial genome.}, }
@article {pmid8604305, year = {1996}, author = {Cermakian, N and Ikeda, TM and Cedergren, R and Gray, MW}, title = {Sequences homologous to yeast mitochondrial and bacteriophage T3 and T7 RNA polymerases are widespread throughout the eukaryotic lineage.}, journal = {Nucleic acids research}, volume = {24}, number = {4}, pages = {648-654}, pmid = {8604305}, issn = {0305-1048}, mesh = {Amino Acid Sequence ; Animals ; Bacteriophage T3/*enzymology ; Bacteriophage T7/*enzymology ; Base Sequence ; DNA-Directed RNA Polymerases/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Saccharomyces cerevisiae/*enzymology ; Sequence Homology, Amino Acid ; }, abstract = {Although mitochondria and chloroplasts are considered to be descendants of eubacteria-like endo- symbionts, the mitochondrial RNA polymerase of yeast is a nucleus-encoded, single-subunit enzyme homologous to bacteriophage T3 and T7 RNA polymerases, rather than a multi-component, eubacterial-type alpha 2 beta beta' enzyme, as encoded in chloroplast DNA. To broaden our knowledge of the mitochondrial transcriptional apparatus, we have used a polymerase chain reaction (PCR) approach designed to amplify an internal portion of phage T3/T7-like RNA polymerase genes. Using this strategy, we have recovered sequences homologous to yeast mitochondrial and phage T3/T7 RNA polymerases from a phylogenetically broad range of multicellular and unicellular eukaryotes. These organisms display diverse patterns of mitochondrial genome organization and expression, and include species that separated from the main eukaryotic line early in the evolution of this lineage. In certain cases, we can deduce that PCR-amplified sequences, some of which contain small introns, are localized in nuclear DNA. We infer that the T3/T7-like RNA polymerase sequences reported here are likely derived from genes encoding the mitochondrial RNA polymerase in the organisms in which they occur, suggesting a phage T3/T7-like RNA polymerase was recruited to act in transcription in the mitochondrion at an early stage in the evolution of this organelle.}, }
@article {pmid8595866, year = {1996}, author = {Markos, A and Morris, A and Rozario, C and Müller, M}, title = {Primary structure of a cytosolic malate dehydrogenase of the amitochondriate eukaryote, Trichomonas vaginalis.}, journal = {FEMS microbiology letters}, volume = {135}, number = {2-3}, pages = {259-264}, doi = {10.1111/j.1574-6968.1996.tb07998.x}, pmid = {8595866}, issn = {0378-1097}, support = {AI 11942/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cytosol/*enzymology ; Genes, Protozoan/genetics ; Malate Dehydrogenase/*chemistry/genetics/isolation &amp; purification ; Molecular Sequence Data ; Peptide Fragments/chemistry ; Phylogeny ; Sequence Analysis ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Trichomonas vaginalis/classification/*enzymology/genetics ; }, abstract = {The nucleotide sequence of a gene coding for a 37 kDa subunit of a cytosolic malate dehydrogenase of Trichomonas vaginalis was established. The sequence of a gDNA clone and a cDNA clone, which lacked seven amino-terminal codons, were identical, indicating an absence of introns from the gene. Cell fractionation combined with sequencing of peptide fragments of the purified enzyme showed that the gene codes for an expressed cytosolic enzyme. The derived amino acid sequence was closely related to cytosolic malate dehydrogenases from animals and plants and from the eubacteria Thermus aquaticus and Mycobacterium leprae and was more distant from the enzyme of mitochondria and from Escherichia coli and certain other eubacteria. In phylogenetic reconstructions this enzyme shared a most recent common ancestor with other cytosolic enzymes.}, }
@article {pmid8555164, year = {1996}, author = {Aphasizhev, R and Senger, B and Rengers, JU and Sprinzl, M and Walter, P and Nussbaum, G and Fasiolo, F}, title = {Conservation in evolution for a small monomeric phenylalanyl-tRNA synthetase of the tRNA(Phe) recognition nucleotides and initial aminoacylation site.}, journal = {Biochemistry}, volume = {35}, number = {1}, pages = {117-123}, doi = {10.1021/bi9517998}, pmid = {8555164}, issn = {0006-2960}, mesh = {Amino Acid Sequence ; Base Sequence ; Binding Sites ; *Biological Evolution ; Conserved Sequence ; Escherichia coli/genetics ; Genetic Variation ; Humans ; Kinetics ; Macromolecular Substances ; Mitochondria/enzymology ; Molecular Sequence Data ; Molecular Weight ; *Nucleic Acid Conformation ; Phenylalanine-tRNA Ligase/*chemistry/genetics/*metabolism ; RNA, Transfer, Phe/*chemistry/*metabolism ; Saccharomyces cerevisiae/enzymology/genetics ; Sequence Homology, Nucleic Acid ; Substrate Specificity ; }, abstract = {We previously showed that yeast mitochondrial phenylalanyl-tRNA synthetase (MSF protein) is evolutionarily distant to the cytoplasmic counterpart based on a high degree of divergence in protein sequence, molecular mass, and quaternary structure. Using yeast cytoplasmic tRNA(Phe) which is efficiently aminoacylated by MSF protein, we report here the tRNA(Phe) primary site of aminoacylation and the identity determinants for MSF protein. As for the cytoplasmic phenylalanyl-tRNA synthetase (Sampson, J. R., Di Renzo, A. B., Behlen, L. S., &amp; Uhlenbeck, O. C. (1989) Science 243, 1363-1366), MSF protein recognizes nucleotides from the anticodon and the acceptor end including base A73 and, as shown here, adjacent G1-C72 base pair or at least C72 base. This indicates that the way of tRNA(Phe) binding for the two phenylalanine enzymes is conserved in evolution. However, tRNA(Phe) tertiary structure seems more critical for the interaction with the cytoplasmic enzyme than with MSF protein, and unlike cytoplasmic phenylalanyl-tRNA synthetase, the small size of the monomeric MSF protein probably does not allow contacts with residue 20 at the top corner of the L molecule. We also show that MSF protein preferentially aminoacylates the terminal 2'-OH group of tRNA(Phe) but with a catalytic efficiency for tRNA(Phe)-CC-3'-deoxyadenosine reduced 100-fold from that of native tRNA(Phe), suggesting a role of the terminal 3'-OH in catalysis. The loss is only 1.5-fold when tRNA(Phe)-CC-3'-deoxyadenosine is aminoacylated by yeast cytoplasmic PheRS (Sprinzl, M., &amp; Cramer, F. (1973) Nature 245, 3-5), indicating mechanistic differences between the two PheRS's active sites for the amino acid transfer step.}, }
@article {pmid8583894, year = {1996}, author = {Krajewski, C and King, DG}, title = {Molecular divergence and phylogeny: rates and patterns of cytochrome b evolution in cranes.}, journal = {Molecular biology and evolution}, volume = {13}, number = {1}, pages = {21-30}, doi = {10.1093/oxfordjournals.molbev.a025558}, pmid = {8583894}, issn = {0737-4038}, mesh = {Animals ; Birds/*genetics ; Cytochrome b Group/*genetics ; *Evolution, Molecular ; Mitochondria/metabolism ; Sequence Analysis ; }, abstract = {Analyses of complete cytochrome b sequences from all species of cranes (Aves: Gruidae) reveal aspects of sequence evolution in the early stages of divergence. These DNA sequences are > or = 89% identical, but expected departures from random substitution are evident. Silent, third-position pyrimidine transitions are the dominant substitution type, with transversion comprising only a small fraction of sequence differences. Substitution patterns are not clearly manifested until divergence has reached a moderate level (> 3%), as expected for a stochastic process. Variation in the frequency of mismatch types among lineages decreases at larger divergences, but the level of bias does not decay. Divergence varies up to fivefold among gene regions but is not correlated with structural domain. All protein structural domains except extramembrane 4 display < 20% variable residues. Regions corresponding to putative functional domains show the excepted conservation of amino acids, although the C-terminal portion of the Q0 reaction center displays several nonconservative replacements. Phylogenetic analyses incorporating substitution asymmetries produced mixed results. Distances estimated with multiple parameters (transition, codon-position, composition, and pyrimidine-transition biases) yielded identical additive tree topologies with comparable bootstrap values, all consistent with uncontroversial species relationships. Maximum likelihood analysis incorporating these biases, as well as equally weighted parsimony analysis, produced similar results. Static, differential weighting for parsimony did not improve the phylogenetic signal but produced unusual trees with low bootstraps. The overall rate of nucleotide substitution varies slightly but significantly among cranes, and calibration of distances against fossil dates suggests divergence rates of 0.7%-1.7% per million years.}, }
@article {pmid8581162, year = {1996}, author = {Blair, A and Ngo, L and Park, J and Paulsen, IT and Saier, MH}, title = {Phylogenetic analyses of the homologous transmembrane channel-forming proteins of the F0F1-ATPases of bacteria, chloroplasts and mitochondria.}, journal = {Microbiology (Reading, England)}, volume = {142 (Pt 1)}, number = {}, pages = {17-32}, doi = {10.1099/13500872-142-1-17}, pmid = {8581162}, issn = {1350-0872}, support = {2RO1 AI 14176/AI/NIAID NIH HHS/United States ; 5RO1 AI 21702/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacteria/classification/enzymology/*genetics ; Chloroplasts/classification/enzymology/*genetics ; Macromolecular Substances ; Mitochondria/classification/enzymology/*genetics ; Molecular Sequence Data ; *Phylogeny ; Protein Conformation ; Proton-Translocating ATPases/classification/*genetics ; Sequence Alignment/methods ; Sequence Homology, Amino Acid ; }, abstract = {Sequences of the three integral membrane subunits (subunits a, b and c) of the F0 sector of the proton-translocating F-type (F0F1-) ATPases of bacteria, chloroplasts and mitochondria have been analysed. All homologous-sequenced proteins of these subunits, comprising three distinct families, have been identified by database searches, and the homologous protein sequences have been aligned and analysed for phylogenetic relatedness. The results serve to define the relationships of the members of each of these three families of proteins, to identify regions of relative conservation, and to define relative rates of evolutionary divergence. Of these three subunits, c-subunits exhibited the slowest rate of evolutionary divergence, b-subunits exhibited the most rapid rate of evolutionary divergence, and a-subunits exhibited an intermediate rate of evolutionary divergence. The results allow definition of the relative times of occurrence of specific events during evolutionary history, such as the intragenic duplication event that gave rise to large c-subunits in eukaryotic vacuolar-type ATPases after eukaryotes diverged from archaea, and the extragenic duplication of F-type ATPase b-subunits that occurred in blue-green bacteria before the advent of chloroplasts. The results generally show that the three F0 subunits evolved as a unit from a primordial set of genes without appreciable horizontal transmission of the encoding genetic information although a few possible exceptions were noted.}, }
@article {pmid8524824, year = {1995}, author = {Hedges, SB and Simmons, MD and van Dijk, MA and Caspers, GJ and de Jong, WW and Sibley, CG}, title = {Phylogenetic relationships of the hoatzin, an enigmatic South American bird.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {92}, number = {25}, pages = {11662-11665}, pmid = {8524824}, issn = {0027-8424}, mesh = {Animals ; Base Sequence ; Birds/*classification/genetics ; Crystallins/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/*genetics ; South America ; }, abstract = {The hoatzin (Opisthocomus hoazin) lives in the humid lowlands of northern and central South America, often in riparian habitats. It is a slender bird approximately 65 cm in length, brownish with lighter streaks and buffy tips to the long tail feathers. The small head has a ragged, bristly crest of reddish-brown feathers, and the bare skin of the face is bright blue. It resembles a chachalaca (Ortalis, Cracidae) in size and shape, but its plumage and markings are similar to those of the smaller guira cuckoo (Guira guira). The hoatzin (pronounced Watson) has been a taxonomic puzzle since it was described in 1776. It usually has been viewed as related to the gallinaceous birds, but alliances to other groups have been suggested, including the cuckoos. We present DNA sequence evidence from the 12S and 16S rRNA mitochondrial genes, and from the nuclear gene that codes for the eye lens protein, alpha A-crystallin. The results indicate that the hoatzin is most closely related to the typical cuckoos and that the divergence occurred at or near the base of the cuculiform phylogenetic tree.}, }
@article {pmid8524780, year = {1995}, author = {Birky, CW}, title = {Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {92}, number = {25}, pages = {11331-11338}, pmid = {8524780}, issn = {0027-8424}, mesh = {Animals ; *Biological Evolution ; Chloroplasts/*genetics ; Eukaryota/genetics ; Eukaryotic Cells ; *Extrachromosomal Inheritance ; Fungi/genetics ; Mitochondria/*genetics ; Models, Genetic ; Plants/genetics ; }, abstract = {In nearly all eukaryotes, at least some individuals inherit mitochondrial and chloroplast genes from only one parent. There is no single mechanism of uniparental inheritance: organelle gene inheritance is blocked by a variety of mechanisms and at different stages of reproduction in different species. Frequent changes in the pattern of organelle gene inheritance during evolution suggest that it is subject to varying selective pressures. Organelle genes often fail to recombine even when inherited biparentally; consequently, their inheritance is asexual. Sexual reproduction is apparently less important for genes in organelles than for nuclear genes, probably because there are fewer of them. As a result organelle sex can be lost because of selection for special reproductive features such as oogamy or because uniparental inheritance reduces the spread of cytoplasmic parasites and selfish organelle DNA.}, }
@article {pmid8595656, year = {1995}, author = {Arganoza, MT and Akins, RA}, title = {Recombinant mitochondrial plasmids in Neurospora composed of Varkud and a new multimeric mitochondrial plasmid.}, journal = {Current genetics}, volume = {29}, number = {1}, pages = {34-43}, pmid = {8595656}, issn = {0172-8083}, mesh = {Base Sequence ; Chromosome Mapping ; DNA Transposable Elements ; DNA, Mitochondrial/*genetics ; Deoxyribonuclease EcoRI/genetics ; Genes, Fungal ; Molecular Sequence Data ; Neurospora/*genetics ; Plasmids/*genetics ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; }, abstract = {A mitochondrial plasmid, V5124, in Neurospora intermedia isolate 5124 has a deletion in its sequence relative to the highly similar Mauriceville and Varkud plasmids. These insertions in the latter plasmids are 28 bp in length and are positioned at sites that correspond to their major transcript 5' termini. The 28-bp sequence is nearly identical to a putative processing site upstream of the ND4L gene on the mitochondrial genome. The absence of this 28-bp sequence in V5124 apparently results in transcripts whose 5' termini correspond to an upstream consensus promoter sequence. Two variant forms of V5124 coexist with V5124 and have either of two similar 0.3-kb inserts positioned exactly as is the 28-bp insert in Varkud. These long inserts are chimeric, partly deriving from a newly discovered multimeric plasmid, MP. MP has significant similarity to a short region of the mitochondrial satellite plasmid VS. Another part of the 0.3-kb inserts in V5124 variants derives from the mitochondrial genome, within restriction fragment EcoRI-8. Neurospora mitochondria in many isolates can have several types of mitochondrial plasmids belonging to different homology groups. We propose that a common ancestral plasmid acquired insertions from either the mitochondrial genome or from other plasmids. The V5124 variants are the first instance of a chimeric mitochondrial plasmid in which distinct plasmids have recombined. This recombination proves that different plasmids coexist currently, or else did so at some point in their evolution, within a single mitochondrion.}, }
@article {pmid8587120, year = {1995}, author = {Spicer, GS}, title = {Phylogenetic utility of the mitochondrial cytochrome oxidase gene: molecular evolution of the Drosophila buzzatii species complex.}, journal = {Journal of molecular evolution}, volume = {41}, number = {6}, pages = {749-759}, pmid = {8587120}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; Drosophila/enzymology/*genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis ; }, abstract = {Phylogenetic relationships among eight species of the Drosophila buzzatii species complex (D. mulleri subgroup; D. repleta species group) and D. hamatofila were determined by sequencing the mitochondrial cytochrome oxidase subunit I, II, and III genes. The species examined included members of the martensis cluster (D. martensis, D. starmeri, D. venezolana), the buzzatii cluster (D. buzzatii, D. serido, D. borborema), and the stalkeri cluster (D. stalkeri, D. richardsoni). The molecular phylogeny was found to be congruent with the chromosomal inversion phylogeny. Analyzing the cytochrome oxidase subunits separately revealed that not all the subunits seem to have the same phylogenetic information content. Parameters are discussed that might explain these differences.}, }
@article {pmid8555450, year = {1995}, author = {Kessler, U and Zetsche, K}, title = {Physical map and gene organization of the mitochondrial genome from the unicellular green alga Platymonas (Tetraselmis) subcordiformis (Prasinophyceae).}, journal = {Plant molecular biology}, volume = {29}, number = {5}, pages = {1081-1086}, pmid = {8555450}, issn = {0167-4412}, mesh = {Chlorophyta/*genetics ; Cloning, Molecular ; *DNA, Mitochondrial ; Genome, Plant ; Molecular Sequence Data ; Phylogeny ; Restriction Mapping ; }, abstract = {The entire mitochondrial genome (mt genome) of the unicellular green alga Platymonas subcordiformis (synonym Tetraselmis subcordiformis; Prasinophyceae) was cloned and a physical map for the four restriction enzymes Hind III, Eco RI, Bg/II and Xba I was constructed. The mt genome of P. subcordiformis is a 42.8 kb circular molecule, coding for at least 23 genes. Hybridization and sequence analysis revealed the presence of a ca. 1.5 kb inverted repeat on the mt genome of P. subcordiformis. Phylogenetic analyses based on sequences of several coxI genes were carried out. Our data indicate that mitochondria from P. subcordiformis and from land plants form a natural, monophyletic group.}, }
@article {pmid8555448, year = {1995}, author = {Kuhlman, P and Palmer, JD}, title = {Isolation, expression, and evolution of the gene encoding mitochondrial elongation factor Tu in Arabidopsis thaliana.}, journal = {Plant molecular biology}, volume = {29}, number = {5}, pages = {1057-1070}, pmid = {8555448}, issn = {0167-4412}, support = {GM-35087/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Arabidopsis/*genetics ; DNA, Complementary ; Humans ; Mitochondria/*metabolism ; Molecular Sequence Data ; Peptide Elongation Factor Tu/*genetics ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {We have characterized a second nuclear gene (tufM) in Arabidopsis thaliana that encodes a eubacterial-like protein synthesis elongation factor Tu (EF-Tu). This gene does not closely resemble the previously described Arabidopsis nuclear tufA gene, which encodes the plastid EF-Tu, and does not contain sequence elements found in all cyanobacterial and plastid tufA genes. However, the predicted amino acid sequence includes an N-terminal extension which resembles an organellar targeting sequence and shares three unique sequence elements with mitochondrial EF-Tu's, from Saccharomyces cerevisiae and Homo sapiens, suggesting that this gene encodes the Arabidopsis mitochondrial EF-Tu. Consistent with this interpretation, the gene is expressed at a higher level in flowers than in leaves. Phylogenetic analysis confirms the mitochondrial character of the sequence and indicates that the human, yeast, and Arabidopsis tufM genes have undergone considerably more sequence divergence than their cytoplasmic counterparts, perhaps reflecting a cross-compartmental acceleration of gene evolution for components of the mitochondrial translation apparatus. As previously observed for tufA, the tufM gene is present in one copy in Arabidopsis but in several copies in other species of crucifers.}, }
@article {pmid8531891, year = {1995}, author = {Griffiths, AJ}, title = {Natural plasmids of filamentous fungi.}, journal = {Microbiological reviews}, volume = {59}, number = {4}, pages = {673-685}, pmid = {8531891}, issn = {0146-0749}, mesh = {Ascomycota/*genetics ; Biological Evolution ; DNA Replication ; DNA, Fungal/*genetics/physiology ; Gene Rearrangement ; Mitochondria/genetics ; Mutagenesis ; Phenotype ; Plasmids/*genetics/physiology/ultrastructure ; }, abstract = {Among eukaryotes, plasmids have been found in fungi and plants but not in animals. Most plasmids are mitochondrial. In filamentous fungi, plasmids are commonly encountered in isolates from natural populations. Individual populations may show a predominance of one type, but some plasmids have a global distribution, often crossing species boundaries. Surveys have shown that strains can contain more than one type of plasmid and that different types appear to be distributed independently. In crosses, plasmids are generally inherited maternally. Horizontal transmission is by cell contact. Circular plasmids are common only in Neurospora spp., but linear plasmids have been found in many fungi. Circular plasmids have one open reading frame (ORF) coding for a DNA polymerase or a reverse transcriptase. Linear plasmids generally have two ORFs, coding for presumptive DNA and RNA polymerases with amino acid motifs showing homology to viral polymerases. Plasmids often attain a high copy number, in excess of that of mitochondrial DNA. Linear plasmids have a protein attached to their 5' end, and this is presumed to act as a replication primer. Most plasmids are neutral passengers, but several linear plasmids integrate into mitochondrial DNA, causing death of the host culture. Inferred amino acid sequences of linear plasmid ORFs have been used to plot phylogenetic trees, which show a fair concordance with conventional trees. The circular Neurospora plasmids have replication systems that seem to be evolutionary intermediates between the RNA and the DNA worlds.}, }
@article {pmid7499431, year = {1995}, author = {Gudi, R and Bowker-Kinley, MM and Kedishvili, NY and Zhao, Y and Popov, KM}, title = {Diversity of the pyruvate dehydrogenase kinase gene family in humans.}, journal = {The Journal of biological chemistry}, volume = {270}, number = {48}, pages = {28989-28994}, doi = {10.1074/jbc.270.48.28989}, pmid = {7499431}, issn = {0021-9258}, support = {DK 47844/DK/NIDDK NIH HHS/United States ; GM 51262/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Catalysis ; Cloning, Molecular ; DNA Primers/chemistry ; DNA, Complementary ; Escherichia coli/genetics ; *Genetic Variation ; Humans ; Isoenzymes/chemistry/*genetics/metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Protein Kinases/chemistry/*genetics/metabolism ; Protein Serine-Threonine Kinases ; Pyruvate Dehydrogenase Acetyl-Transferring Kinase ; Rats ; Recombinant Proteins/genetics/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Recent evidence from this laboratory indicates that at least two isoenzymic forms of pyruvate dehydrogenase kinase (PDK1 and PDK2) may be involved in the regulation of enzymatic activity of mammalian pyruvate dehydrogenase complex by phosphorylation (Popov, K.M., Kedishvili, N.Y., Zhao, Y., Gudi, R., and Harris, R.A. (1994) J. Biol. Chem. 269, 29720-29724). The present study was undertaken to further explore the diversity of the pyruvate dehydrogenase kinase gene family. Here we report the deduced amino acid sequences of three isoenzymic forms of PDK found in humans. In terms of their primary structures, two isoenzymes identified in humans correspond to rat PDK1 and PDK2, whereas a third gene (PDK3) encodes for a new isoenzyme that shares 68% and 67% of amino acid identities with PDK1 and PDK2, respectively. PDK3 cDNA expressed in Eschierichia coli directs the synthesis of a polypeptide with a molecular mass of approximately 45,000 Da that possesses catalytic activity toward kinase-depleted pyruvate dehydrogenase. PDK3 appears to have the highest specific activity among the three isoenzymes tested as recombinant proteins. Tissue distribution of all three isoenzymes of human PDK was characterized by Northern blot analysis. The highest amount of PDK2 mRNA was found in heart and skeletal muscle, the lowest amount in placenta and lung. Brain, kidney, pancreas, and liver expressed an intermediate amount of PDK2 (brain > kidney = pancreas > liver). The tissue distribution of PDK1 mRNA differs markedly from PDK2. The message for PDK1 was expressed predominantly in heart with only modest levels of expression in other tissues (skeletal muscle > liver > pancreas > brain > placenta = lung > kidney). In contrast to PDk1 and PDK2, which are expressed in all tissues tested, the message for PDK3 was found almost exclusively in heart and skeletal muscle, indicating that PDK3 may serve specialized functions characteristic of muscle tissues. In all tissues tested thus far, the level of expression of PDK2 mRNA was essentially higher than that of PDK1 and PDK3, consistent with the idea that PDK2 is a major isoenzyme responsible for regulation of pyruvate dehydrogenase in human tissues.}, }
@article {pmid7492331, year = {1995}, author = {Fujiwara, S and Noguchi, T}, title = {Degradation of purines: only ureidoglycollate lyase out of four allantoin-degrading enzymes is present in mammals.}, journal = {The Biochemical journal}, volume = {312 (Pt 1)}, number = {Pt 1}, pages = {315-318}, pmid = {7492331}, issn = {0264-6021}, mesh = {Allantoin/*metabolism ; *Amidine-Lyases ; Amidohydrolases/metabolism ; Animals ; Biological Evolution ; Cell Fractionation ; Electrophoresis, Polyacrylamide Gel ; Glyoxylates/metabolism ; Immunoblotting ; Lyases/chemistry/isolation &amp; purification/*metabolism ; Male ; Mammals/*metabolism ; Mitochondria, Liver/*enzymology ; Purines/*metabolism ; Rats ; Rats, Sprague-Dawley ; Tissue Distribution ; Urea/metabolism ; Urease/metabolism ; Ureohydrolases/metabolism ; }, abstract = {It is generally accepted that all of the allantoin-degrading enzymes (allantoinase, allantoicase, ureidoglycollate lyase and urease), used in purine degradation, were lost during mammalian evolution. However, surprisingly, ureidoglycollate lyase has been found in a mammalian tissue. Ureidoglycollate lyase was purified to homogeneity and characterized from rat-liver mitochondria. The apparent Km (17 mM) of the rat enzyme for ureidoglycollate was much higher than that (0.33 mM) of fish-liver ureidoglycollate lyase. The rat-liver enzyme differed from the fish-liver enzyme in enzymic, physical and immunological properties.}, }
@article {pmid8561830, year = {1995}, author = {Wink, M}, title = {Phylogeny of Old and New World vultures (Aves: Accipitridae and Cathartidae) inferred from nucleotide sequences of the mitochondrial cytochrome b gene.}, journal = {Zeitschrift fur Naturforschung. C, Journal of biosciences}, volume = {50}, number = {11-12}, pages = {868-882}, doi = {10.1515/znc-1995-11-1220}, pmid = {8561830}, issn = {0939-5075}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Birds/classification/*genetics ; Chickens ; Cytochrome b Group/*genetics ; DNA/blood/*chemistry/isolation &amp; purification ; DNA Primers ; Europe ; Geography ; Mitochondria/metabolism ; Molecular Sequence Data ; North America ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; South America ; Species Specificity ; }, abstract = {The molecular phylogeny of 11 Old World and 5 New World vultures was inferred from nucleotide sequences of the mitochondrial cytochrome b (cyt b) gene. According to this analysis carrion-feeding has evolved independently at least three times during evolution: 1.) In the New World vultures, which are clearly separated from vultures of the family Accipitridae; 2.) in the Neophron-Gypaetus clade which is positioned at the base of the Accipitrid tree and 3.) in the Gyps-Aegypius-complex which encloses the largest group of Old World vultures. Thus the genetic data clearly show that the carrion-feeding lifestyles and associated morphologies shared by New and Old World vultures are rather based on convergence than on close genetic relatedness. Employing the cyt b sequences of 12 other members of the Falconiformes and 10 members of the Ciconiiformes (sensu Sibley and Monroe, 1990) the phylogenetic relationship between the three clades of vultures and these other taxa was assessed. New World Vultures appear to share distant ancestry with storks but a close relationship is unlikely.}, }
@article {pmid8520584, year = {1995}, author = {Gilson, P and Waller, R and McFadden, G}, title = {Preliminary characterisation of chlorarachniophyte mitochondrial DNA.}, journal = {The Journal of eukaryotic microbiology}, volume = {42}, number = {6}, pages = {696-701}, doi = {10.1111/j.1550-7408.1995.tb01618.x}, pmid = {8520584}, issn = {1066-5234}, mesh = {Animals ; Bacteria/classification/genetics ; Chloroplasts/metabolism ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; DNA, Protozoan/*genetics/isolation &amp; purification ; Eukaryota/classification/*genetics ; Fungi/classification/genetics ; Humans ; In Situ Hybridization ; Karyotyping ; Mitochondria/metabolism ; *Phylogeny ; Plants/classification/genetics ; Transcription, Genetic ; }, abstract = {The division Chlorarachniophyte comprises amoeboflagellate protists with complex chloroplasts derived from the endosymbiosis of a eukaryotic alga. Analysis of chlorarachniophyte chromosomal DNAs by pulsed-field gel electrophoresis revealed an apparently linear 36-kb chromosome that could not be ascribed to either the host or endosymbiont nuclei. A single eubacterial-like small subunit ribosomal RNA gene is encoded on this chromosome and phylogenetic analyses places this gene within a clade of mitochondrial genes from other eukaryotes. High resolution in situ hybridization demonstrates that transcripts of the small subunit ribosomal RNA gene encoded by the 36-kb chromosome are exclusively located in the mitochondria. The 36-kb chromosome thus likely represents a linear mitochondrial genome. Small amounts of an apparently dimeric (72 kb) form are also detectable in pulsed-field gel electrophoresis.}, }
@article {pmid7490780, year = {1995}, author = {Paquin, B and Forget, L and Roewer, I and Lang, BF}, title = {Molecular phylogeny of Allomyces macrogynus: congruency between nuclear ribosomal RNA- and mitochondrial protein-based trees.}, journal = {Journal of molecular evolution}, volume = {41}, number = {5}, pages = {657-665}, pmid = {7490780}, issn = {0022-2844}, mesh = {Ascomycota/classification ; Cell Nucleus/*genetics ; Chytridiomycota/*classification/genetics ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Fungi/classification ; Genes, Fungal ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/*genetics ; }, abstract = {We have sequenced the nuclear and mitochondrial small subunit rRNA genes (rns) and the mitochondrial genes coding for subunits 1 and 3 of the cytochrome oxidase (cox1 and cox3, respectively) of the chytridiomycete Allomyces macrogynus. Phylogenetic trees inferred from the derived COX1 and COX3 proteins and the nuclear rns sequences show with good bootstrap support that A. macrogynus is an early diverging fungus. The trees inferred from mitochondrial rns sequences do not yield a topology that is supported by bootstrap analysis. The similarity and the relative robustness of the nuclear rns and the mitochondrial protein-derived phylogenetic trees suggest that protein sequences are of higher value than rRNA sequences for reconstructing mitochondrial evolution. In addition, our trees support a monophyletic origin of mitochondria for the range of analyzed eukaryotes.}, }
@article {pmid7490777, year = {1995}, author = {Douzery, E and Catzeflis, FM}, title = {Molecular evolution of the mitochondrial 12S rRNA in Ungulata (mammalia).}, journal = {Journal of molecular evolution}, volume = {41}, number = {5}, pages = {622-636}, pmid = {7490777}, issn = {0022-2844}, mesh = {Animals ; Artiodactyla/genetics ; Base Sequence ; *Evolution, Molecular ; Gene Rearrangement ; Hyraxes/genetics ; Mammals/classification/*genetics ; Marsupialia/genetics ; Mitochondria/*genetics ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; Perissodactyla/genetics ; Phylogeny ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/*genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {The complete 12S rRNA gene has been sequenced in 4 Ungulata (hoofed eutherians) and 1 marsupial and compared to 38 available mammalian sequences in order to investigate the molecular evolution of the mitochondrial small-subunit ribosomal RNA molecule. Ungulata were represented by one artiodactyl (the collared peccary, Tayassu tajacu, suborder Suiformes), two perissodactyls (the Grevy's zebra, Equus grevyi, suborder Hippomorpha; the white rhinoceros, Ceratotherium simum, suborder Ceratomorpha), and one hyracoid (the tree hyrax, Dendrohyrax dorsalis). The fifth species was a marsupial, the eastern gray kangaroo (Macropus giganteus). Several transition/transversion biases characterized the pattern of changes between mammalian 12S rRNA molecules. A bias toward transitions was found among 12S rRNA sequences of Ungulata, illustrating the general bias exhibited by ribosomal and protein-encoding genes of the mitochondrial genome. The derivation of a mammalian 12S rRNA secondary structure model from the comparison of 43 eutherian and marsupial sequences evidenced a pronounced bias against transversions in stems. Moreover, transversional compensatory changes were rare events within double-stranded regions of the ribosomal RNA. Evolutionary characteristics of the 12S rRNA were compared with those of the nuclear 18S and 28S rRNAs. From a phylogenetic point of view, transitions, transversions and indels in stems as well as transversional and indels events in loops gave congruent results for comparisons within orders. Some compensatory changes in double-stranded regions and some indels in single-stranded regions also constituted diagnostic events. The 12S rRNA molecule confirmed the monophyly of infraorder Pecora and order Cetacea and demonstrated the monophyly of the suborder Ruminantia was not supported and the branching pattern between Cetacea and the artiodacytyl suborders Ruminantia and Suiformes was not established. The monophyly of the order Perissodactyla was evidenced, but the relationships between Artiodactyla, Cetacea, and Perissodactyla remained unresolved. Nevertheless, we found no support for a Perissodactyla + Hyracoidea clade, neither with distance approach, nor with parsimony reconstruction. The 12S rRNA was useful to solve intraordinal relationships among Ungulata, but it seemed to harbor too few informative positions to decipher the bushlike radiation of some Ungulata orders, an event which has most probably occurred in a short span of time between 55 and 70 MYA.}, }
@article {pmid7490770, year = {1995}, author = {Vaughn, JC and Mason, MT and Sper-Whitis, GL and Kuhlman, P and Palmer, JD}, title = {Fungal origin by horizontal transfer of a plant mitochondrial group I intron in the chimeric CoxI gene of Peperomia.}, journal = {Journal of molecular evolution}, volume = {41}, number = {5}, pages = {563-572}, pmid = {7490770}, issn = {0022-2844}, support = {GM-35087/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Electron Transport Complex IV/*genetics ; Evolution, Molecular ; Fungi/genetics ; *Gene Transfer, Horizontal ; Genes, Plant ; *Introns ; Mitochondria/enzymology/*genetics ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; Plants/enzymology/*genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {We present phylogenetic evidence that a group I intron in an angiosperm mitochondrial gene arose recently by horizontal transfer from a fungal donor species. A 1,716-bp fragment of the mitochondrial coxI gene from the angiosperm Peperomia polybotrya was amplified via the polymerase chain reaction and sequenced. Comparison to other coxI genes revealed a 966-bp group I intron, which, based on homology with the related yeast coxI intron aI4, potentially encodes a 279-amino-acid site-specific DNA endonuclease. This intron, which is believed to function as a ribozyme during its own splicing, is not present in any of 19 coxI genes examined from other diverse vascular plant species. Phylogenetic analysis of intron origin was carried out using three different tree-generating algorithms, and on a variety of nucleotide and amino acid data sets from the intron and its flanking exon sequences. These analyses show that the Peperomia coxI gene intron and exon sequences are of fundamentally different evolutionary origin. The Peperomia intron is more closely related to several fungal mitochondrial introns, two of which are located at identical positions in coxI, than to identically located coxI introns from the land plant Marchantia and the green alga Prototheca. Conversely, the exon sequence of this gene is, as expected, most closely related to other angiosperm coxI genes. These results, together with evidence suggestive of co-conversion of exonic markers immediately flanking the intron insertion site, lead us to conclude that the Peperomia coxI intron probably arose by horizontal transfer from a fungal donor, using the double-strand-break repair pathway. The donor species may have been one of the symbiotic mycorrhizal fungi that live in close obligate association with most plants.}, }
@article {pmid7479994, year = {1995}, author = {Embley, TM and Finlay, BJ and Dyal, PL and Hirt, RP and Wilkinson, M and Williams, AG}, title = {Multiple origins of anaerobic ciliates with hydrogenosomes within the radiation of aerobic ciliates.}, journal = {Proceedings. Biological sciences}, volume = {262}, number = {1363}, pages = {87-93}, doi = {10.1098/rspb.1995.0180}, pmid = {7479994}, issn = {0962-8452}, mesh = {Aerobiosis ; Anaerobiosis ; Animals ; DNA/analysis ; Eukaryota/*genetics/metabolism ; *Evolution, Molecular ; Molecular Sequence Data ; Phylogeny ; Radiation ; Sequence Analysis ; }, abstract = {Some ciliates live anaerobically and lack mitochondria, but possess hydrogenosomes: organelles that contain hydrogenase and produce hydrogen. The origin of hydrogenosomes has been explained by two competing hypotheses: (i) they are biochemically modified mitochondria; or (ii) they are derived from endosymbiotic association(s) of ciliates and anaerobic eubacteria that possessed the hydrogenosome biochemistry. Phylogenetic analyses of representative aerobic, and anaerobic hydrogenosomal ciliates using host nuclear SSU rDNA sequences indicate a minimum of three, but more likely four, separate origins of hydrogenosomes. Whereas this does not refute either hypothesis, the implausibility of multiple convergent endosymbioses gives further support to the view that hydrogenosomes in ciliates derive from an existing organelle, which ultrastructural evidence suggests is the mitochondrion. Our results indicate a considerable potential for physiological-biochemical plasticity among a group of predominantly aerobic eucaryotes, and provide a phylogenetic framework to further refine and test hypotheses of the origins of the hydrogenosomal enzymes.}, }
@article {pmid7585872, year = {1995}, author = {Chaloupka, J}, title = {[Proteolytic enzymes in cell physiology and pathophysiology].}, journal = {Casopis lekaru ceskych}, volume = {134}, number = {19}, pages = {611-614}, pmid = {7585872}, issn = {0008-7335}, mesh = {Animals ; Cells/enzymology ; *Endopeptidases/chemistry/physiology ; Evolution, Molecular ; Humans ; }, abstract = {Extracellular proteases (proteinases, endopeptidases) are usually synthesized as larger precursors containing a signal sequence in the N-terminal part of their molecule. The signal sequence contains a sequence composed of hydrophobic amino acids which facilitate the transport of the polypeptide through membranes of the secretory apparatus. Extracellular proteinases play an important role in reproduction and spreading of tumor cells and in tissue remodelling in addition to their function in digestion food proteins. Intracellular proteinases are mostly localized in the cytoplasm and in specialized organelles (lysosomes) but are present also in nuclei and in mitochondria. They degrade or modify cell proteins and are thus involved in protein turnover which is necessary for cell viability. Intracellular proteinases are important components of the cell defense system which protects the cell against the effect of different stress factors by removing damaged and nonfunctional proteins. They modify different proteins and are thus involved in virus reproduction because some proteins are synthesized as nonfunctional virus precursors. Intracellular proteinases also play a role in the cell cycle control and in cytodifferentiation. Rather complex proteolytic enzymes were found even in very primitive organisms (archebacteria).}, }
@article {pmid8575014, year = {1995}, author = {Karpinska, B and Karpinski, S and Hällgren, JE}, title = {The genes encoding subunit 3 of NADH dehydrogenase and ribosomal protein S12 are co-transcribed and edited in Pinus sylvestris (L.) mitochondria.}, journal = {Current genetics}, volume = {28}, number = {5}, pages = {423-428}, pmid = {8575014}, issn = {0172-8083}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Complementary ; DNA, Mitochondrial ; Mitochondria/enzymology/*metabolism ; Molecular Sequence Data ; NADH Dehydrogenase/chemistry/*genetics ; Pinus sylvestris ; *RNA Editing ; Ribosomal Proteins/*genetics ; *Transcription, Genetic ; }, abstract = {The nucleotide sequence of the region encoding NADH dehydrogenase subunit 3 and ribosomal protein S12 from Pinus sylvestris (L.) mitochondrial DNA (mtDNA) has been determined. A sequence comparison of this region with six individual cDNA clones prepared by RT-PCR revealed 35 C-to-T differences, showing the occurrence of RNA editing. All but one of these alterations in mRNA sequence change codon identities to specify amino acid better conserved in evolution. Most of these modifications take place within the nad3 gene changing 20% of the amino-acid sequence, which is much more than in angiosperms. Of six cDNA clones investigated, four clones of nad3 were differentially edited, but the editing of the rps12 sequences was identical. As in angiosperms, the two genes are separated by a short sequence of 52 bp, which is not edited. Two transcripts of about 0.9 kb and 1.2 kb, each encoding both proteins, have been detected by Northern hybridisation. The hybridisation of nad3 and rps12 probes with pine mtDNA digested with different restriction enzymes indicates that both genes are present in a single copy in pine mtDNA. The analysis of PCR amplification products with gene-specific primers shows a conserved order of these genes in a wide range of gymnosperms.}, }
@article {pmid8557473, year = {1995}, author = {Tang, J and Toé, L and Back, C and Unnasch, TR}, title = {Mitochondrial alleles of Simulium damnosum sensu lato infected with Onchocerca volvulus.}, journal = {International journal for parasitology}, volume = {25}, number = {10}, pages = {1251-1254}, doi = {10.1016/0020-7519(95)00047-6}, pmid = {8557473}, issn = {0020-7519}, support = {AI 33008/AI/NIAID NIH HHS/United States ; }, mesh = {*Alleles ; Animals ; Base Sequence ; DNA, Mitochondrial ; Mitochondria/*genetics ; Molecular Sequence Data ; *Onchocerca volvulus/isolation &amp; purification ; Phylogeny ; Polymerase Chain Reaction ; Simuliidae/*genetics/parasitology ; }, abstract = {Onchocerca volvulus infected Simulium damnosum s.l. were analysed by directed heteroduplex analysis. Of 73 infected flies, 68 produced heteroduplex products identical to those previously identified. All 6 major sibling species, except S. leonense, were present in this group. In the 5 remaining flies, 2 new heteroduplex patterns were noted. Molecular phylogenetic analysis of these samples suggested that they belonged to the S. squamosum/S. yahense subcomplex. The ability to reliably genotype adult flies will permit studies of the vectorial capacity of the sibling species of S. damnosum s.l. for the blinding and non-blinding strains of O. volvulus.}, }
@article {pmid7579176, year = {1995}, author = {Moeykens, CA and Mackenzie, SA and Shoemaker, RC}, title = {Mitochondrial genome diversity in soybean: repeats and rearrangements.}, journal = {Plant molecular biology}, volume = {29}, number = {2}, pages = {245-254}, pmid = {7579176}, issn = {0167-4412}, mesh = {Base Sequence ; Blotting, Southern ; Cloning, Molecular ; DNA, Mitochondrial/*genetics ; DNA, Plant/*genetics ; Gene Rearrangement ; Genome ; Mitochondria/*genetics ; Models, Genetic ; Molecular Sequence Data ; Polymorphism, Genetic ; *Recombination, Genetic ; Repetitive Sequences, Nucleic Acid ; Restriction Mapping ; Sequence Analysis, DNA ; Glycine max/*genetics ; }, abstract = {Mitochondrial (mt) genome organization in soybean was examined at the molecular level. This study builds upon previous reports that four soybean cytoplasmic groups, Bedford, Arksoy, Lincoln, and soja-forage, are differentiated by polymorphisms detected with a 2.3 kb Hind III mtDNA probe [12]. The variation detected results from DNA alterations in a region within and around a 4.8 kb repeat. The Bedford-type cytoplasm is the only cytoplasm that contains copies of a 4.8 kb repeat in four different genomic environments, evidence that it is recombinationally active. The Lincoln- and Arksoy-type cytoplasms each contain two copies of the repeat, as well as unique fragments that appear to result from rare recombination events outside, but near, the repeat. The soja-forage-type cytoplasm contains no complete copies of the repeat, but does contain a unique truncated version of the repeat. Sequence analysis indicates that the truncation is a result of recombination across a 9 bp repeated sequence, CCCCTCCCC. The structural rearrangements that have occurred in the region surrounding the 4.8 kb repeat may provide a means to dissect species relationships and evolution within the subgenus soja.}, }
@article {pmid7579156, year = {1995}, author = {Elkeles, A and Devos, KM and Graur, D and Zizi, M and Breiman, A}, title = {Multiple cDNAs of wheat voltage-dependent anion channels (VDAC): isolation, differential expression, mapping and evolution.}, journal = {Plant molecular biology}, volume = {29}, number = {1}, pages = {109-124}, pmid = {7579156}, issn = {0167-4412}, mesh = {Amino Acid Sequence ; Base Sequence ; *Chromosome Mapping ; DNA, Complementary ; *Evolution, Molecular ; *Gene Expression Regulation, Plant ; Ion Channels/*genetics/metabolism ; Membrane Proteins/*genetics/metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Multigene Family ; *Porins ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; Triticum/*genetics ; Voltage-Dependent Anion Channels ; }, abstract = {The mitochondrial outer membrane of eukaryotic cells contains voltage-dependent anion channels (VDAC) also termed porins. Three cDNAs from wheat (Triticum aestivum) were isolated and sequenced (Tavdac 1-3). They share 65% similarity of their amino acid sequences, and therefore they probably represent isoforms. The deduced amino acid sequence of one of the cDNAs was found to be identical to the purified VDAC protein from wheat mitochondria [8]. Secondary structure analysis of the deduced amino acid sequences of the three vdac cDNAs revealed a characteristic alpha helix at their N-terminal and beta-barrel cylinders characteristic of VDAC channels. The Tavdac cDNAs are differentially expressed in meristematic tissues. The transcript levels of Tavdac 1 in all wheat tissues is at least 2.5-fold higher than Tavdac 2 and Tavdac 3. Tavdac 2 has a low level of expression in all floral tissues whereas Tavdac 3 is highly expressed in anthers. This is the first report on differential expression of vdac genes in plants. The Tavdac genes have been mapped on the wheat genome. Tavdac 1 is located on the long arm of chromosome 5, Tavdac 2 on the long arm of chromosome 1 and Tavdac 3 on the long arm of chromosome 3. A phylogenetic reconstruction indicates that vdac genes underwent numerous duplication events throughout their evolution. All duplications occurred after the separation of plants from animals and fungi, and no orthologous genes are shared among phyla. Within plants, some of the vdac gene duplications probably occurred before the monocotydelon-dicotydelon split.}, }
@article {pmid7568085, year = {1995}, author = {Henze, K and Badr, A and Wettern, M and Cerff, R and Martin, W}, title = {A nuclear gene of eubacterial origin in Euglena gracilis reflects cryptic endosymbioses during protist evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {92}, number = {20}, pages = {9122-9126}, pmid = {7568085}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Animals ; Base Composition ; Base Sequence ; *Biological Evolution ; Cell Nucleus/*metabolism ; Consensus Sequence ; Eubacterium/*classification/*genetics ; Euglena gracilis/*genetics ; Eukaryota/*classification/*genetics ; Fungi/classification/genetics ; *Genes, Bacterial ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics ; Introns ; Molecular Sequence Data ; *Multigene Family ; Nucleic Acid Conformation ; RNA, Bacterial/chemistry/genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Symbiosis ; }, abstract = {Genes for glycolytic and Calvin-cycle glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of higher eukaryotes derive from ancient gene duplications which occurred in eubacterial genomes; both were transferred to the nucleus during the course of endosymbiosis. We have cloned cDNAs encoding chloroplast and cytosolic GAPDH from the early-branching photosynthetic protist Euglena gracilis and have determined the structure of its nuclear gene for cytosolic GAPDH. The gene contains four introns which possess unusual secondary structures, do not obey the GT-AG rule, and are flanked by 2- to 3-bp direct repeats. A gene phylogeny for these sequences in the context of eubacterial homologues indicates that euglenozoa, like higher eukaryotes, have obtained their GAPDH genes from eubacteria via endosymbiotic (organelle-to-nucleus) gene transfer. The data further suggest that the early-branching protists Giardia lamblia and Entamoeba histolytica--which lack mitochondria--and portions of the trypanosome lineage have acquired GAPDH genes from eubacterial donors which did not ultimately give rise to contemporary membrane-bound organelles. Evidence that "cryptic" (possibly ephemeral) endosymbioses during evolution may have entailed successful gene transfer is preserved in protist nuclear gene sequences.}, }
@article {pmid7673215, year = {1995}, author = {Bruel, C and di Rago, JP and Slonimski, PP and Lemesle-Meunier, D}, title = {Role of the evolutionarily conserved cytochrome b tryptophan 142 in the ubiquinol oxidation catalyzed by the bc1 complex in the yeast Saccharomyces cerevisiae.}, journal = {The Journal of biological chemistry}, volume = {270}, number = {38}, pages = {22321-22328}, doi = {10.1074/jbc.270.38.22321}, pmid = {7673215}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Binding Sites ; Biological Evolution ; Electron Transport ; Electron Transport Complex III/chemistry/*metabolism ; Mitochondria/metabolism ; Molecular Sequence Data ; Point Mutation ; Protein Structure, Secondary ; Saccharomyces cerevisiae/*enzymology ; Spectrum Analysis ; Structure-Activity Relationship ; Tryptophan ; Ubiquinone/*analogs &amp; derivatives/metabolism ; }, abstract = {Trp-142 is a highly conserved residue of the cytochrome b subunit in the bc1 complexes. To study the importance of this residue in the quinol oxidation catalyzed by the bc1 complex, we characterized four yeast mutants with arginine, lysine, threonine, and serine at position 142. The mutant W142R was isolated previously as a respiration-deficient mutant unable to grow on non-fermentable carbon sources (Lemesle-Meunier, D., Brivet-Chevillotte, P., di Rago, J.-P, Slonimski, P.P., Bruel, C., Tron, T., and Forget, N. (1993) J. Biol. Chem. 268, 15626-15632). The mutants W142K, W142T, and W142S were obtained here as respiration-sufficient revertants from mutant W142R. Mutant W142R exhibited a decreased complex II turnover both in the presence and absence of antimycin A; this suggests that the structural effect of W142R in the bc1 complex probably interferes with the correct assembly of the succinate-ubiquinone reductase complex. The mutations resulted in a parallel decrease in turnover number and apparent Km, with the result that there was no significant change in the second-order rate constant for ubiquinol oxidation. Mutants W142K and W142T exhibited some resistance toward myxothiazol, whereas mutant W142R showed increased sensitivity. The cytochrome cc1 reduction kinetics were found to be severely affected in mutants W142R, W142K, and W142T. The respiratory activities and the amounts of reduced cytochrome b measured during steady state suggest that the W142S mutation also modified the quinol-cytochrome c1 electron transfer pathway. The cytochrome b reduction kinetics through center P were affected when Trp-142 was replaced with arginine or lysine, but not when it was replaced with threonine or serine. Of the four amino acids tested at position 142, only arginine resulted in a decrease in cytochrome b reduction through center N. These findings are discussed in terms of the structure and function of the quinol oxidation site and seem to indicate that Trp-142 is not critical to the kinetic interaction of ubiquinol with the reductase, but plays an important role in the electron transfer reactions that intervene between ubiquinol oxidation and cytochrome c1 reduction.}, }
@article {pmid8590480, year = {1995}, author = {Kumar, R and Drouaud, J and Raynal, M and Small, I}, title = {Characterization of the nuclear gene encoding chloroplast ribosomal protein S13 from Arabidopsis thaliana.}, journal = {Current genetics}, volume = {28}, number = {4}, pages = {346-352}, pmid = {8590480}, issn = {0172-8083}, mesh = {Amino Acid Sequence ; Arabidopsis/chemistry/*genetics ; Base Sequence ; Blotting, Northern ; Blotting, Southern ; Blotting, Western ; Cell Nucleus/chemistry/genetics ; Chloroplasts/*chemistry ; Chromosome Mapping ; Cloning, Molecular ; DNA, Complementary ; Evolution, Molecular ; *Genes, Plant ; Mitochondria/chemistry/genetics ; Molecular Sequence Data ; Molecular Weight ; Phylogeny ; Ribosomal Proteins/analysis/*chemistry ; Sequence Alignment ; Sequence Analysis ; }, abstract = {We have characterised a cDNA clone and a nuclear gene encoding the chloroplast 30 s ribosomal protein S13 from Arabidopsis thaliana. The identification is based on the high similarity of the predicted amino-acid sequence with eubacterial S13 protein sequences, and immunodetection of a 14.5-kDa chloroplast ribosomal polypeptide using antibodies raised against the polypeptide produced from part of the cDNA expressed in bacteria. The predicted amino-acid sequence contains an N-terminal extension which has several features characteristic of chloroplast transit peptides. Experiments suggest there is a single copy of this gene in A. thaliana and multiple copies in Brassica species. The origin of the mitochondrial S13 polypeptide in crucifers is also discussed.}, }
@article {pmid7565409, year = {1995}, author = {Clayton, C and Häusler, T and Blattner, J}, title = {Protein trafficking in kinetoplastid protozoa.}, journal = {Microbiological reviews}, volume = {59}, number = {3}, pages = {325-344}, pmid = {7565409}, issn = {0146-0749}, mesh = {Animals ; Biological Transport ; Endocytosis ; Kinetoplastida/growth &amp; development/*physiology/ultrastructure ; Leishmania/growth &amp; development/ultrastructure ; Membrane Proteins/biosynthesis ; Microbodies/physiology/ultrastructure ; Mitochondria/chemistry/physiology/ultrastructure ; Monosaccharide Transport Proteins/physiology ; Protozoan Proteins/*metabolism ; Trypanosoma/growth &amp; development/ultrastructure ; }, abstract = {The kinetoplastid protozoa infect hosts ranging from invertebrates to plants and mammals, causing diseases of medical and economic importance. They are the earliest-branching organisms in eucaryotic evolution to have either mitochondria or peroxisome-like microbodies. Investigation of their protein trafficking enables us to identify characteristics that have been conserved throughout eucaryotic evolution and also reveals how far variations, or alternative mechanisms, are possible. Protein trafficking in kinetoplastids is in many respects similar to that in higher eucaryotes, including mammals and yeasts. Differences in signal sequence specificities exist, however, for all subcellular locations so far examined in detail--microbodies, mitochondria, and endoplasmic reticulum--with signals being more degenerate, or shorter, than those of their higher eucaryotic counterparts. Some components of the normal array of trafficking mechanisms may be missing in most (if not all) kinetoplastids: examples are clathrin-coated vesicles, recycling receptors, and mannose 6-phosphate-mediated lysosomal targeting. Other aspects and structures are unique to the kinetoplastids or are as yet unexplained. Some of these peculiarities may eventually prove to be weak points that can be used as targets for chemotherapy; others may turn out to be much more widespread than currently suspected.}, }
@article {pmid7563123, year = {1995}, author = {De Rijk, P and Van de Peer, Y and Van den Broeck, I and De Wachter, R}, title = {Evolution according to large ribosomal subunit RNA.}, journal = {Journal of molecular evolution}, volume = {41}, number = {3}, pages = {366-375}, pmid = {7563123}, issn = {0022-2844}, mesh = {Animal Population Groups/genetics ; Animals ; Bacteria/genetics ; Base Sequence ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/*genetics ; Fungi/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; Plants/genetics ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; Time Factors ; }, abstract = {Evolutionary trees were constructed, by distance methods, from an alignment of 225 complete large subunit (LSU) rRNA sequences, representing Eucarya, Archaea, Bacteria, plastids, and mitochondria. A comparison was made with trees based on sets of small subunit (SSU) rRNA sequences. Trees constructed on the set of 172 species and organelles for which the sequences of both molecules are known had a very similar topology, at least with respect to the divergence order of large taxa such as the eukaryotic kingdoms and the bacterial divisions. However, since there are more than ten times as many SSU as LSU rRNA sequences, it is possible to select many SSU rRNA sequence sets of equivalent size but different species composition. The topologies of these trees showed considerable differences according to the particular species set selected. The effect of the dataset and of different distance correction methods on tree topology was tested for both LSU and SSU rRNA by repetitive random sampling of a single species from each large taxon. The impact of the species set on the topology of the resulting consensus trees is much lower using LSU than using SSU rRNA. This might imply that LSU rRNA is a better molecule for studying wide-range relationships. The mitochondria behave clearly as a monophyletic group, clustering with the Proteobacteria. Gram-positive bacteria appear as two distinct groups, which are found clustered together in very few cases. Archaea behave as if monophyletic in most cases, but with a low confidence.}, }
@article {pmid7476125, year = {1995}, author = {Hashimoto, T and Nakamura, Y and Kamaishi, T and Nakamura, F and Adachi, J and Okamoto, K and Hasegawa, M}, title = {Phylogenetic place of mitochondrion-lacking protozoan, Giardia lamblia, inferred from amino acid sequences of elongation factor 2.}, journal = {Molecular biology and evolution}, volume = {12}, number = {5}, pages = {782-793}, doi = {10.1093/oxfordjournals.molbev.a040256}, pmid = {7476125}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Archaea/classification/genetics ; Base Sequence ; Blotting, Southern ; Cloning, Molecular ; DNA Primers ; DNA, Protozoan/chemistry/isolation &amp; purification ; Escherichia coli ; Giardia lamblia/classification/*genetics ; Humans ; Mitochondria ; Molecular Sequence Data ; Peptide Elongation Factor 2 ; Peptide Elongation Factors/biosynthesis/chemistry/*genetics ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Messenger/analysis/biosynthesis ; Sequence Homology, Amino Acid ; }, abstract = {Partial regions of the mRNA encoding a major part of translation elongation factor 2 (EF-2) from a mitochondrion-lacking protozoan, Giardia lamblia, were amplified by polymerase chain reaction, and their primary structures were analyzed. The deduced amino acid sequence was aligned with other eukaryotic and archaebacterial EF-2's, and the phylogenetic relationships among eukaryotes were inferred by the maximum likelihood (ML) and the maximum parsimony (MP) methods. The ML analyses using six different models of amino acid substitutions and the MP analysis consistently suggest that among eukaryotic species being analyzed, G. lamblia is likely to have diverged from other higher eukaryotes on the early phase of eukaryotic evolution.}, }
@article {pmid8589847, year = {1995}, author = {Howland, DE and Hewitt, GM}, title = {Phylogeny of the Coleoptera based on mitochondrial cytochrome oxidase I sequence data.}, journal = {Insect molecular biology}, volume = {4}, number = {3}, pages = {203-215}, doi = {10.1111/j.1365-2583.1995.tb00026.x}, pmid = {8589847}, issn = {0962-1075}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Coleoptera/*classification/enzymology/genetics ; DNA, Mitochondrial ; Electron Transport Complex IV/classification/*genetics ; Genes, Insect ; Genetic Variation ; Mitochondria/*enzymology/genetics ; Molecular Sequence Data ; Phylogeny ; }, abstract = {A 400 base pair region of the mitochondrial cytochrome oxidase I gene (COI) was sequenced for thirty-seven species of beetle, representing fifteen families. The sequence was found to be highly variable, with 12-18% divergence within families, and up to 27% divergence between families. Phylogenetic analysis using the neighbour-joining method shows the Carabidae (Adephaga) as a distinct clade, but also shows that all other beetles (Polyphaga) diverged soon after the Adephaga/Polyphaga split. Whilst some species are grouped within their respective families, others are too diverged for easy resolution. The main disagreement with trees constructed using comparative morphology and the fossil record is the position of the Coccinellidae. Whilst COI may be an informative gene for molecular systematics at lower taxonomic levels, or in other insects, improved resolution of this particular phylogeny will require a more highly conserved sequence.}, }
@article {pmid8550293, year = {1995}, author = {Gozar, MM and Bagnara, AS}, title = {An organelle-like small subunit ribosomal RNA gene from Babesia bovis: nucleotide sequence, secondary structure of the transcript and preliminary phylogenetic analysis.}, journal = {International journal for parasitology}, volume = {25}, number = {8}, pages = {929-938}, doi = {10.1016/0020-7519(95)00022-t}, pmid = {8550293}, issn = {0020-7519}, mesh = {Animals ; Babesia ; Babesia bovis/*genetics ; Bacteria/genetics ; Base Sequence ; Cyanobacteria/genetics ; DNA Primers ; DNA, Mitochondrial/genetics ; *Genes, Protozoan ; Genome ; Mitochondria/physiology ; Molecular Sequence Data ; Nucleic Acid Conformation ; Organelles/physiology ; *Phylogeny ; Piroplasmida ; Plasmodium falciparum/genetics ; Plastids/physiology ; Polymerase Chain Reaction ; RNA, Protozoan/chemistry/*genetics ; RNA, Ribosomal/chemistry/*genetics ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; }, abstract = {Investigations aimed at identifying the mitochondrial genome of Babesia bovis using the polymerase chain reaction (PCR) have established the existence of an organelle-like small subunit ribosomal RNA (SSU rRNA) gene in the parasite. The sequence, compiled from three main PCR products, was 1448 bp in length (including the primer regions), had a 73% A+T content and showed significant similarity (68% sequence identity) to the "organellar" SSU rRNA gene from Plasmodium falciparum. The proposed secondary structure of the transcript showed several features which were consistent with a eubacterial origin for the organelle-like gene. The presence of putative binding sites for streptomycin and tetracycline also supported an "organellar" location for the gene and suggested that the SSU rRNA transcript is functional in protein synthesis because tetracycline has anti-babesial activity. Phylogenetic analyses based on the conserved regions of the SSU-like rRNA genes from a wide variety of organisms showed only a weak association of the babesial sequence with its mitochondrial homologues and an even weaker association with the corresponding genes of plastid origin. The origin of this organelle-like gene in B. bovis therefore remains unresolved, as is the case for its homologue from P. falciparum.}, }
@article {pmid7666449, year = {1995}, author = {Leblanc, C and Kloareg, B and Loiseaux-deGoër, S and Boyen, C}, title = {DNA sequence, structure, and phylogenetic relationship of the mitochondrial small-subunit rRNA from the red alga Chondrus crispus (Gigartinales rhodophytes).}, journal = {Journal of molecular evolution}, volume = {41}, number = {2}, pages = {196-202}, pmid = {7666449}, issn = {0022-2844}, mesh = {Base Sequence ; Cloning, Molecular ; DNA, Mitochondrial/*genetics ; Molecular Sequence Data ; *Nucleic Acid Conformation ; *Phylogeny ; RNA, Ribosomal/*chemistry/genetics ; Restriction Mapping ; Rhodophyta/*genetics ; Sequence Alignment ; Sequence Analysis, DNA ; }, abstract = {The entire nucleotide sequence containing the small-subunit ribosomal RNA gene (SSU rRNA) from the mitochondrial genome of Chondrus crispus was determined. To our knowledge, this is the first sequence of a mitochondrial 16S-like rRNA from a red alga. The length of this gene is 1,376 nucleotides. Its secondary structure was constructed and compared with other known secondary structures from eubacteria and from mitochondria of land plants, green and brown algae, and fungi. Phylogenetic trees were built upon SSU rRNA sequence alignment from mitochondria and eubacteria. The results show that rhodophytes and chromophytes provide additional links in the evolution of mitochondria between the green plant lineage and the "nonplant" lineages.}, }
@article {pmid7648620, year = {1995}, author = {Wrobel, KH and Bickel, D and Kujat, R and Schimmel, M}, title = {Evolution and ultrastructure of the bovine spermatogonia precursor cell line.}, journal = {Cell and tissue research}, volume = {281}, number = {2}, pages = {249-259}, pmid = {7648620}, issn = {0302-766X}, mesh = {Animals ; Cattle ; Cytoplasm/ultrastructure ; Male ; Organelles/ultrastructure ; Seminiferous Epithelium/ultrastructure ; Seminiferous Tubules/ultrastructure ; Spermatogenesis ; Spermatogonia/*cytology/ultrastructure ; Stem Cells/*ultrastructure ; Testis/cytology ; }, abstract = {The spermatogonial stem cell line in prepubertal and adult bovine testis was studied by electron microscopy and protein gene product 9.5 immunohistochemistry. Three successive spermatogonia precursor cell configurations were observed. Small basal stem cells were found to possess a spherical shape and nuclei with two to three nucleoli. They were observed in prepubertal testes (25 and 30 weeks) and in low numbers during all the stages of the seminiferous epithelial cycle in the adult. Aggregated spermatogonia precursor cells are the dominating germ cell type in the 25-week-old and 30-week-old calf. In the adult seminiferous epithelium, they cause expansion of the basal tubular compartment as they form dense groups containing up to 15 cells. These groups are observed concomitantly with cycling A-spermatogonia and preleptotenes at the beginning of spermatocytogenesis. At the end of A-spermatogonia propagation, the aggregated spermatogonia precursor cells separate and intermingle with cycling A-spermatogonia. The spermatogonia precursor cells can later be found together with I-spermatogonia as members of an interconnected cellular network of medium-sized cells. When the I-spermatogonia divide to form the smaller B-spermatogonia, the precursor cells, which stay connected with the cycling spermatogonial population, pass through a growth phase. They can now be considered as committed spermatogonia precursor cells and are continuously being transformed into A1-spermatogonia to start a new round of spermatocytogenesis. Ultrastructurally, all members of the precursor cell line are similar. However, a number of features have been found to show a quantitative increase (endoplasmic reticulum, mitochondria) or to exhibit a rising degree of complexity (nucleolus) during the progression from basal stem cells to committed spermatogonia precursor cells.}, }
@article {pmid7616569, year = {1995}, author = {Leblanc, C and Boyen, C and Richard, O and Bonnard, G and Grienenberger, JM and Kloareg, B}, title = {Complete sequence of the mitochondrial DNA of the rhodophyte Chondrus crispus (Gigartinales). Gene content and genome organization.}, journal = {Journal of molecular biology}, volume = {250}, number = {4}, pages = {484-495}, doi = {10.1006/jmbi.1995.0392}, pmid = {7616569}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Base Sequence ; Biological Evolution ; *Chromosome Mapping ; DNA, Circular/chemistry/genetics ; DNA, Mitochondrial/chemistry/*genetics ; *Genome ; Introns/genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames/genetics ; RNA, Ribosomal/genetics ; RNA, Transfer/chemistry/genetics ; Rhodophyta/*genetics ; Sequence Alignment ; *Sequence Analysis, DNA ; Transcription, Genetic/genetics ; }, abstract = {The complete nucleotide sequence of the circular mitochondrial (mt) DNA from the red alga Chondrus crispus was determined (25,836 nucleotides, A+T content 72.1%). Fifty one genes were identified. They include genes encoding three subunits of the cytochrome oxidase (cox1 to 3), apocytochrome b (cob), seven subunits of the NADH dehydrogenase complex (nad1 to 6, nad4L), two ATPase subunits (atp6 and atp9), three ribosomal RNAs (rrn5, srn and lrn), 23 tRNAs and four ribosomal proteins (rps3, rps11, rps12 and rpl16). Two subunits of the succinate dehydrogenase complex (sdhB and sdhC), usually found on nuclear genomes, are also located on the mtDNA of C. crispus. One group IIb intron is inserted in the tRNAIle gene. Six potentially functional open reading frames were identified, four of them having counterparts among green plant mtDNAs. The use of a modified genetic code and the absence of RNA editing, previously reported for the cox3 gene, appears as a general characteristic of this molecule. Mitochondrial genes are encoded on both DNA strands, in two opposite major transcriptional directions, suggesting the existence of two main transcriptional units. Two long and stable stem-loops were identified in intergenic regions, which are believed to be involved with transcription and replication. The main structural features of this genome are compared with the overall organization of mtDNAs and are discussed in view of the evolution of mitochondria.}, }
@article {pmid7624338, year = {1995}, author = {Hutchin, T and Cortopassi, G}, title = {A mitochondrial DNA clone is associated with increased risk for Alzheimer disease.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {92}, number = {15}, pages = {6892-6895}, pmid = {7624338}, issn = {0027-8424}, support = {AG10283/AG/NIA NIH HHS/United States ; AG11967/AG/NIA NIH HHS/United States ; MH/NS 31862/MH/NIMH NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Alzheimer Disease/etiology/*genetics ; Autopsy ; Case-Control Studies ; DNA, Mitochondrial/*genetics ; Humans ; Mitochondria/*genetics ; Models, Genetic ; *Mutation ; Phylogeny ; Polymerase Chain Reaction ; RNA, Transfer, Gly/*genetics ; Risk Factors ; White People/genetics ; }, abstract = {Severe mitochondrial genetic mutations lead to early degeneration of specific human tissues; milder mitochondrial mutations may cause degeneration at a later point in life. A mutation at position 4336 was reported to occur at increased frequency in individuals with Alzheimer disease (AD) and Parkinson disease [Shoffner, J. M., Brown, M. D., Torroni, A., Lott, M. T., Cabell, M. F., Mirra, S. S., Beal, M. F., Yang, C.-C., Gearing, M., Salvo, R., Watts, R. L., Juncos, J. L., Hansen, L. A., Crain, B. J., Fayad, M., Reckord, C. L. &amp; Wallace, D. C. (1993) Genomics 17, 171-184]. We have investigated the notion that this mutation leads to excess risk of AD by using a case-control study design of 72 AD autopsies and 296 race- and age-matched controls. The 4336G mutation occurred at higher frequency in AD autopsies than age-matched controls, a statistically significant difference. Evolutionary analysis of mtDNAs bearing the 4336G mutation indicated they were more closely related to each other than to other mtDNAs, consistent with the model of a single origin for this mutation. The tight evolutionary relatedness and homoplasmy of mtDNAs that confer elevated risk for a late-onset disease contrast strikingly with the distant relatedness and heteroplasmy of mitochondrial genomes that cause early-onset disease. The dichotomy can be explained by a lack of selection against mutations that confer a phenotype at advanced age during most of the evolution of humans. We estimate that approximately 1.5 million Caucasians in the United States bear the 4336G mutation and are at significantly increased risk of developing mitochondrial AD in their lifetime. A mechanism for 4336G-mediated cell death is proposed.}, }
@article {pmid7608189, year = {1995}, author = {Nagahara, N and Okazaki, T and Nishino, T}, title = {Cytosolic mercaptopyruvate sulfurtransferase is evolutionarily related to mitochondrial rhodanese. Striking similarity in active site amino acid sequence and the increase in the mercaptopyruvate sulfurtransferase activity of rhodanese by site-directed mutagenesis.}, journal = {The Journal of biological chemistry}, volume = {270}, number = {27}, pages = {16230-16235}, doi = {10.1074/jbc.270.27.16230}, pmid = {7608189}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites/genetics ; Biological Evolution ; Blotting, Western ; Cysteine/analogs &amp; derivatives/metabolism ; Cytosol/*enzymology ; Liver/*enzymology ; Male ; Mitochondria/*enzymology ; Molecular Sequence Data ; Mutagenesis ; Rats ; Rats, Wistar ; Recombinant Proteins/metabolism ; Sequence Analysis ; Sequence Homology, Amino Acid ; Species Specificity ; Structure-Activity Relationship ; Sulfurtransferases/chemistry/*genetics/isolation &amp; purification/metabolism ; Thiosulfate Sulfurtransferase/*genetics ; }, abstract = {Rat liver mercaptopyruvate sulfurtransferase (MST) was purified to homogeneity. MST is very similar to rhodanese in physicochemical properties. Further, rhodanese cross-reacts with anti-MST antibody. Both purified authentic MST and expressed rhodanese possess MST and rhodanese activities, although the ratio of rhodanese to MST activity is low in MST and high in rhodanese. In order to compare the active site regions of MST and rhodanese, the primary structure of a possible active site region of MST was determined. The sequence showed 66% homology with that of rat liver rhodanese. An active site cysteine residue (Cys246; site of formation of persulfide in catalysis) and an arginine residue (Arg185; substrate binding site) in rhodanese were also conserved in MST. On the other hand, two other active site residues (Arg247 and Lys248) were replaced by Gly and Ser, respectively. Conversion of rhodanese to MST was tried by site-directed mutagenesis. After cloning of rat liver rhodanese, recombinant wild type and three mutants (Arg247-->Gly and/or Lys248-->Ser) were constructed. The enzymes were expressed in Escherichia coli strain BL21 (DE3) with a T7 promoter system. The mutation of these residues decreases rhodanese activity and increases MST activity.}, }
@article {pmid7622059, year = {1995}, author = {Au, HC and Ream-Robinson, D and Bellew, LA and Broomfield, PL and Saghbini, M and Scheffler, IE}, title = {Structural organization of the gene encoding the human iron-sulfur subunit of succinate dehydrogenase.}, journal = {Gene}, volume = {159}, number = {2}, pages = {249-253}, doi = {10.1016/0378-1119(95)00162-y}, pmid = {7622059}, issn = {0378-1119}, support = {2 T32 GM07240/GM/NIGMS NIH HHS/United States ; GM33752/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; DNA, Complementary/genetics ; Exons/genetics ; Genomic Library ; Humans ; Introns/genetics ; Iron-Sulfur Proteins/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Promoter Regions, Genetic/genetics ; Protein Conformation ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Succinate Dehydrogenase/*genetics ; }, abstract = {The iron-sulfur protein (Ip) subunit of succinate dehydrogenase (SDH and complex II) of the respiratory chain is highly conserved in evolution [Gould et al., Proc. Natl. Acad. Sci. USA 86 (1989) 1934-1938]. We have cloned the entire human Ip cDNA, as well as the Ip-encoding gene (SDH-B) from two genomic human libraries. The cDNA contains a coding sequence of 840 nt, flanked by a 5'-UTR of 133 nt and a 3'-UTR of 123 nt. The entire transcript is encoded by eight exons within approx. 40 kb. The seven introns range in size from 0.75 kb to > 11 kb, and they appear to be of the 'late' intron class. Approx. 5 kb of upstream sequence was also cloned, and approx. 2.4 kb of the promoter region were sequenced and analyzed for consensus elements binding potential transcription factors and transcriptional activators.}, }
@article {pmid7604025, year = {1995}, author = {Clark, CG and Roger, AJ}, title = {Direct evidence for secondary loss of mitochondria in Entamoeba histolytica.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {92}, number = {14}, pages = {6518-6521}, pmid = {7604025}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Animals ; Cattle ; Consensus Sequence ; Eimeria tenella/genetics ; Entamoeba histolytica/*classification/*genetics/metabolism ; Escherichia coli/genetics ; Humans ; Mitochondria/*metabolism ; Molecular Sequence Data ; NADP Transhydrogenases/chemistry/*genetics ; *Phylogeny ; RNA, Ribosomal/genetics ; Rhodospirillum rubrum/enzymology ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {Archezoan protists are though to represent lineages that diverged from other eukaryotes before acquisition of the mitochondrion and other organelles. The parasite Entamoeba histolytica was originally included in this group. Ribosomal RNA based phylogenies, however, place E. histolytica on a comparatively recent branch of the eukaryotic tree, implying that its ancestors had these structures. In this study, direct evidence for secondary loss of mitochondrial function was obtained by isolating two E. histolytica genes encoding proteins that in other eukaryotes are localized in the mitochondrion: the enzyme pyridine nucleotide transhydrogenase and the chaperonin cpn60. Phylogenetic analysis of the E. histolytica homolog of cpn60 confirmed that it is specifically related to the mitochondrial lineage. The data suggest that a mitochondrial relic may persist in this organism. Similar studies are needed in archezoan protists to ascertain which, if any, eukaryotic lineages primitively lack mitochondria.}, }
@article {pmid7603983, year = {1995}, author = {Rich, SM and Caporale, DA and Telford, SR and Kocher, TD and Hartl, DL and Spielman, A}, title = {Distribution of the Ixodes ricinus-like ticks of eastern North America.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {92}, number = {14}, pages = {6284-6288}, pmid = {7603983}, issn = {0027-8424}, support = {AI 19693/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; DNA Primers ; DNA, Mitochondrial/genetics ; DNA, Ribosomal/*genetics ; Demography ; Geography ; Mitochondria/metabolism ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Population ; RNA, Ribosomal, 16S/*genetics ; Ticks/classification/*genetics ; United States ; }, abstract = {We analyzed the geographic distribution of the Ixodes ricinus-like ticks in eastern North America by comparing the mitochondrial 16S rDNA sequences of specimens sampled directly from the field during the 1990s. Two distinct lineages are evident. The southern clade includes ticks from the southeastern and middle-eastern regions of the United States. The range of the northern clade, which appears to have been restricted to the northeastern region until the mid-1900s, now extends throughout the northeastern and middle-eastern regions. These phyletic units correspond to northern and southern taxa that have previously been assigned specific status as Ixodes dammini and Ixodes scapularis, respectively. The expanding range of I. dammini appears to drive the present outbreaks of zoonotic disease in eastern North America that include Lyme disease and human babesiosis.}, }
@article {pmid7659010, year = {1995}, author = {Turmel, M and Côté, V and Otis, C and Mercier, JP and Gray, MW and Lonergan, KM and Lemieux, C}, title = {Evolutionary transfer of ORF-containing group I introns between different subcellular compartments (chloroplast and mitochondrion).}, journal = {Molecular biology and evolution}, volume = {12}, number = {4}, pages = {533-545}, doi = {10.1093/oxfordjournals.molbev.a040234}, pmid = {7659010}, issn = {0737-4038}, mesh = {Acanthamoeba/genetics ; Animals ; Base Sequence ; *Biological Evolution ; Chlamydomonas/genetics ; Chloroplasts/*genetics ; DNA/metabolism ; Deoxyribonucleases, Type I Site-Specific/genetics/metabolism ; Introns/*genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Open Reading Frames/*genetics ; RNA, Protozoan/chemistry/genetics ; RNA, Ribosomal/chemistry/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {We describe here a case of homologous introns containing homologous open reading frames (ORFs) that are inserted at the same site in the large subunit (LSU) rRNA gene of different organelles in distantly related organisms. We show that the chloroplast LSU rRNA gene of the green alga Chlamydomonas pallidostigmatica contains a group I intron (CpLSU.2) encoding a site-specific endonuclease (I-CpaI). This intron is inserted at the identical site (corresponding to position 1931-1932 of the Escherichia coli 23S rRNA sequence) as a group I intron (AcLSU.m1) in the mitochondrial LSU rRNA gene of the amoeboid protozoon Acanthamoeba castellanii. The CpLSU.2 intron displays a remarkable degree of nucleotide similarity in both primary sequence and secondary structure to the AcLSU.m1 intron; moreover, the Acanthamoeba intron contains an ORF in the same location within its secondary structure as the CpLSU.2 ORF and shares with it a strikingly high level of amino acid similarity (65%; 42% identity). A comprehensive survey of intron distribution at site 1931 of the chloroplast LSU rRNA gene reveals a rather restricted occurrence within the polyphyletic genus Chlamydomonas, with no evidence of this intron among a number of non-Chlamydomonad green algae surveyed, nor in land plants. A parallel survey of homologues of a previously described and similar intron/ORF pair (C. reinhardtii chloroplast CrLSU/A. castellanii mitochondrial AcLSU.m3) also shows a restricted occurrence of this intron (site 2593) among chloroplasts, although the intron distribution is somewhat broader than that observed at site 1931, with site-2593 introns appearing in several green algal branches outside of the Chlamydomonas lineage. The available data, while not definitive, are most consistent with a relatively recent horizontal transfer of both site-1931 and site-2593 introns (and their contained ORFs) between the chloroplast of a Chlamydomonas-type organism and the mitochondrion of an Acanthamoeba-like organism, probably in the direction chloroplast to mitochondrion. The data also suggest that both introns could have been acquired in a single event.}, }
@article {pmid7647296, year = {1995}, author = {Zhou, YH and Ragan, MA}, title = {Characterization of the nuclear gene encoding mitochondrial aconitase in the marine red alga Gracilaria verrucosa.}, journal = {Plant molecular biology}, volume = {28}, number = {4}, pages = {635-646}, pmid = {7647296}, issn = {0167-4412}, mesh = {Aconitate Hydratase/*genetics ; Amino Acid Sequence ; Base Sequence ; Cell Compartmentation/*genetics ; Cell Nucleus/*genetics ; Gene Dosage ; Genomic Library ; Introns/genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Polymerase Chain Reaction ; Protein Sorting Signals/genetics ; Protein Structure, Secondary ; RNA Splicing ; Regulatory Sequences, Nucleic Acid/genetics ; Restriction Mapping ; Rhodophyta/*genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Species Specificity ; Transcription, Genetic ; }, abstract = {We have cloned a nuclear gene from the marine red alga Gracilaria verrucosa that encodes the complete 779 amino-acid mitochondrial aconitase (m-ACN), the first characterized from a photosynthetic organism. The N-terminal 28 deduced amino acids are predicted to constitute the mitochondrial transit peptide, the first described from a red alga. Putative transcriptional cis-acting elements were identified in the upstream untranslated region. The G. verrucosa m-ACN gene (m-ACN) is present in a single copy and is located ca. 1.5 kb upstream from the single-copy polyubiquitin gene. The single spliceosomal intron is located near the 5' end of the region encoding the mature m-ACN in precisely the same location and phase as intron 2 in Caenorhabditis elegans m-ACN; sequences at its 3' and 5' splice junctions and at the predicted lariat branch point conform well to the eukaryote consensus sequences. Multiple protein-sequence alignment of m-ACN, bacterial aconitase (b-ACN) and iron-responsive element-binding protein (IRE-BP), and phylogenetic analyses, revealed that m-ACN does not share a recent common ancestry with either b-ACN or IRE-BP.}, }
@article {pmid7638255, year = {1995}, author = {Gaullier, JM and Gèze, M and Santus, R and Sa e Melo, T and Mazière, JC and Bazin, M and Morlière, P and Dubertret, L}, title = {Subcellular localization of and photosensitization by protoporphyrin IXhuman keratinocytes and fibroblasts cultivated with 5-aminolevulinic acid.}, journal = {Photochemistry and photobiology}, volume = {62}, number = {1}, pages = {114-122}, doi = {10.1111/j.1751-1097.1995.tb05247.x}, pmid = {7638255}, issn = {0031-8655}, mesh = {Aminolevulinic Acid/*pharmacology ; Cells, Cultured ; Fibrinogen/drug effects/metabolism ; Fibroblasts/*drug effects/metabolism ; Humans ; Keratinocytes/*drug effects/metabolism ; Photochemistry ; Photosensitizing Agents/*pharmacology ; Porphyrins/biosynthesis ; Protoporphyrins/metabolism/*pharmacology ; Spectrometry, Fluorescence ; Subcellular Fractions/metabolism ; }, abstract = {The subcellular localization of protoporphyrin (PP) has been studied by microspectrofluorometric techniques in NCTC 2544 keratinocytes incubated with 5-aminolevulinic acid (ALA) for times up to 42 h. Whereas the plasma membrane shows strong staining, fluorescent spots are observed within the cytoplasm especially in the perinuclear region. Although the topographic pattern of the PP distribution does not change much with the incubation time with ALA, the fluorescence spectra suggest that the PP microenvironments are quite different at short and long incubation times. Addition of 18 microM desferrioxamine almost doubles the ALA-induced PP concentration. Colocalization experiments with rhodamine 123, a mitochondrial probe, and lucifer yellow (LY) or neutral red (NR), two lysosome probes, demonstrate that at least some of these spots are of lysosomal origin. Study of the time evolution of the NR fluorescence under irradiation with visible light in the presence and absence of ALA demonstrates that lysosomes are damaged cells that have synthesized PP. No PP fluorescence can be detected in mitochondria after incubation with ALA. However, photosensitization of mitochondria occurs under irradiation with visible light. Very little formation of lipofuscins by photosensitization with exogenous PP or ALA-induced PP is observed with the NCTC 2544 keratinocytes, as compared to normal human fibroblasts.}, }
@article {pmid7603435, year = {1995}, author = {Takemura, M and Nozato, N and Oda, K and Kobayashi, Y and Fukuzawa, H and Ohyama, K}, title = {Active transcription of the pseudogene for subunit 7 of the NADH dehydrogenase in Marchantia polymorpha mitochondria.}, journal = {Molecular &amp; general genetics : MGG}, volume = {247}, number = {5}, pages = {565-570}, pmid = {7603435}, issn = {0026-8925}, mesh = {Amino Acid Sequence ; Base Sequence ; Introns ; Mitochondria/enzymology ; Molecular Sequence Data ; NADH Dehydrogenase/*genetics ; Plants/enzymology/*genetics ; Pseudogenes/*genetics ; RNA Splicing ; Sequence Alignment ; Transcription, Genetic ; }, abstract = {A pseudogene, psi nad7, which has significant sequence similarity (66.7% amino acid identity) with the bovine nuclear gene for a 49 kDa subunit of the NADH dehydrogenase (NADH:ubiquinone oxidoreductase, EC 1.6.99.3), has been identified on the mitochondrial genome of the liverwort Marchantia polymorpha. The predicted coding region, which includes six termination codons, is actively transcribed into RNA molecules of 16 and 9.6 kb in length, but RNA splicing products were not detected in the liverwort mitochondria. Genomic DNA blot analysis and RNA blot analysis using poly(A)+ RNA suggest that a structurally related nuclear gene encodes the mitochondrial ND7 polypeptide. These results imply that this psi nad7 is a relic of a gene transfer event from the mitochondrial genome into the nuclear genome during mitochondrial evolution in M. polymorpha.}, }
@article {pmid8525056, year = {1995}, author = {Tsai, MH and Saier, MH}, title = {Phylogenetic characterization of the ubiquitous electron transfer flavoprotein families ETF-alpha and ETF-beta.}, journal = {Research in microbiology}, volume = {146}, number = {5}, pages = {397-404}, doi = {10.1016/0923-2508(96)80285-3}, pmid = {8525056}, issn = {0923-2508}, support = {2RO1AI14176/AI/NIAID NIH HHS/United States ; 5RO1AI21702/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Biological Evolution ; DNA/*chemistry/genetics ; DNA, Bacterial/*chemistry/genetics ; Electron-Transferring Flavoproteins ; Flavoproteins/*classification/genetics ; Humans ; In Vitro Techniques ; Molecular Sequence Data ; Rats ; }, abstract = {Electron transfer flavoproteins (ETF) are alpha beta-heterodimers found in eukaryotic mitochondria and bacteria. We have identified currently sequenced protein members of the ETF-alpha and ETF-beta families. Members of these two families include (a) the ETF subunits of mammals and bacteria, (b) homologous pairs of proteins (FixB/FixA) that are essential for nitrogen fixation in some bacteria, and (c) a pair of carnitine-inducible proteins encoded by two open reading frames in Escherichia coli (YaaQ and YaaR). These three groups of proteins comprise three clusters on both the ETF-alpha and ETF-beta phylogenetic trees, separated from each other by comparable phylogenetic distances. This fact suggests that these two protein families evolved with similar overall rates of evolutionary divergence. Relative regions of sequence conservation are evaluated, and signature sequences for both families are derived.}, }
@article {pmid7762568, year = {1995}, author = {Heyer, E}, title = {Mitochondrial and nuclear genetic contribution of female founders to a contemporary population in northeast Quebec.}, journal = {American journal of human genetics}, volume = {56}, number = {6}, pages = {1450-1455}, pmid = {7762568}, issn = {0002-9297}, mesh = {Biological Evolution ; Cell Nucleus/*genetics ; DNA, Mitochondrial/*genetics ; Databases, Factual ; Emigration and Immigration ; Europe/ethnology ; Female ; *Founder Effect ; Humans ; Mitochondria/*genetics ; Models, Genetic ; Pedigree ; Quebec ; Time Factors ; White People/genetics ; }, abstract = {A common challenge in population genetics is to reconstruct the evolutionary history of populations on the basis of current allele frequencies. Through pedigree analysis, we have the opportunity to study the genetic contribution of founders to the contemporary population. This contribution over many generations accounts for the probable introduction, survival, and extinction of genes in the population. I use this method to follow nuclear and mitochondrial genes in the Saguenay population of northeast Quebec by tracing back ascending genealogies of 160,315 individuals born between 1950 and 1971 by using the BALSAC database. This study leads us to conclude that even in a growing population, the loss rate of mtDNA is high. The survival of mtDNA in the population is independent of the time of introduction in the population. The number of copies of a particular mtDNA gene in the contemporary population is higher for genes introduced earlier, but the correlation between these two variables is low (the relation is not linear). Compared to nuclear contribution, mitochondrial contribution is higher, but the loss rate of nuclear DNA is lower. The differential contribution (the fact that few founders contribute a lot) is the same proportion for nuclear and mtDNA, but only 592 female founders contribute 50% of the mtDNA gene pool of the contemporary cohort, compared to 994 for nuclear DNA. Since we have no molecular data on founders' haplotypes, these results cannot give us the diversity level in the population. However, this study enables us to compare the evolutionary fates of nuclear and mitochondrial genes in this expanding population.}, }
@article {pmid7643412, year = {1995}, author = {Cole, RA and Slade, MB and Williams, KL}, title = {Dictyostelium discoideum mitochondrial DNA encodes a NADH:ubiquinone oxidoreductase subunit which is nuclear encoded in other eukaryotes.}, journal = {Journal of molecular evolution}, volume = {40}, number = {6}, pages = {616-621}, pmid = {7643412}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Dictyostelium/enzymology/*genetics ; Electron Transport Complex I ; Molecular Sequence Data ; NADH, NADPH Oxidoreductases/*genetics ; Paracoccus denitrificans/enzymology/genetics ; Phylogeny ; Sequence Alignment ; }, abstract = {Complex I, a key component of the mitochondrial electron transport system, is thought to have evolved from at least two separate enzyme systems prior to the evolution of mitochondria from a bacterial endosymbiont, but the genes for one of the enzyme systems are thought to have subsequently been transferred to the nuclear DNA. We demonstrated that the cellular slime mold Dictyostelium discoideum retains the ancestral characteristic of having mitochondria encoding at least one gene (80-kDa subunit) that is nuclear encoded in other eukaryotes. This is consistent with the cellular slime molds of the family Dictyosteliaceae having diverged from other eukaryotes at an early stage prior to the loss of the mitochondrial gene in the lineage giving rise to plants and animals. The D. discoideum mitochondrially encoded 80-kDa subunit of complex I exhibits a twofold-higher mutation rate compared with the homologous chromosomal gene in other eukaryotes, making it the most divergent eukaryotic form of this protein.}, }
@article {pmid7640891, year = {1995}, author = {Hayashi, M and De Bellis, L and Alpi, A and Nishimura, M}, title = {Cytosolic aconitase participates in the glyoxylate cycle in etiolated pumpkin cotyledons.}, journal = {Plant &amp; cell physiology}, volume = {36}, number = {4}, pages = {669-680}, pmid = {7640891}, issn = {0032-0781}, mesh = {Aconitate Hydratase/genetics/immunology/*metabolism ; Amino Acid Sequence ; Animals ; Antibodies/immunology ; Antibody Specificity ; Base Sequence ; Cotyledon/enzymology ; Cytosol/enzymology ; DNA, Plant ; Escherichia coli ; Fruit/*enzymology ; Germination ; Glyoxylates/metabolism ; Iron-Regulatory Proteins ; Molecular Sequence Data ; Phylogeny ; RNA-Binding Proteins/metabolism ; Recombinant Fusion Proteins/genetics/immunology/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {Two different aconitases are known to be expressed after the germination of oil-seed plants. One is a mitochondrial aconitase that is involved in the tricarboxylic acid cycle. The other participates in the glyoxylate cycle, playing a role in gluconeogenesis from stored oil. We isolated and characterized a cDNA for an aconitase from etiolated pumpkin cotyledons. The cDNA was 3,145 bp long and capable of encoding a protein of 98 kDa. N-terminal and C-terminal amino acid sequences deduced from the cDNA did not contain mitochondrial or glyoxysomal targeting signals. A search of protein databases suggested that the cDNA encoded a cytosolic aconitase. Immunoblotting analysis with a specific antibody against the aconitase expressed in Escherichia coli revealed that developmental changes in the amount of the aconitase were correlated with changes in levels of other enzymes of the glyoxylate cycle during growth of seedlings. Further analysis by subcellular fractionation and immunofluorescence microscopy revealed that aconitase was present only the cytosol and mitochondria. No glyoxysomal aconitase was found in etiolated cotyledons even though all the other enzymes of the glyoxylate cycle are known to be localized in glyoxysomes. Taken together, the data suggest that the cytosolic aconitase participates in the glyoxylate cycle with four glyoxysomal enzymes.}, }
@article {pmid7632440, year = {1995}, author = {Yamagata, T and Ohishi, K and Faruque, MO and Masangkay, JS and Ba-Loc, C and Vu-Binh, D and Mansjoer, SS and Ikeda, H and Namikawa, T}, title = {Genetic variation and geographic distribution on the mitochondrial DNA in local populations of the musk shrew, Suncus murinus.}, journal = {Idengaku zasshi}, volume = {70}, number = {3}, pages = {321-337}, doi = {10.1266/jjg.70.321}, pmid = {7632440}, issn = {0021-504X}, mesh = {Animals ; Animals, Wild/genetics ; Asia ; DNA, Mitochondrial/*genetics ; Demography ; *Genetic Variation ; Haplotypes ; Kidney ; Mitochondria, Liver/genetics ; Phylogeny ; Polymorphism, Genetic ; Shrews/*genetics ; }, abstract = {The musk shrew (Suncus Murinus) is widely distributed throughout Asia and East Africa. The mitochondrial DNA (mtDNA) of this species was analyzed in individuals from 31 local populations in nine Asian countries and Mauritius, using 17 restriction endonucleases. Although fourteen and nine mtDNA haplotypes were detected from Bangladesh and Nepal, respectively, one to four haplotypes were found in each Southeast Asian country, and one common haplotype existed in Japan, Philippines, Vietnam, Thailand and Indonesia. Clustering analysis of mtDNA haplotypes classified shrew populations to three groups--continental group (Bangladesh and Nepal), islands' group (insular countries and Vietnam) and Malay group. The average nucleotide diversity among these three groups was calculated to be about 3.5%. These results indicate that the origin of feral populations in this species might be old and their population sizes are extremely large in the continent, and suggest a rapid spread of this animal throughout the islands. Although we have not shown yet an evidence of close relationships between islands' and continental mtDNA haplotypes, it is likely that the musk shrew had migrated from the continent in South Asia to the islands in Southeast Asia recently.}, }
@article {pmid7554586, year = {1995}, author = {Mitchell, GA and Kassovska-Bratinova, S and Boukaftane, Y and Robert, MF and Wang, SP and Ashmarina, L and Lambert, M and Lapierre, P and Potier, E}, title = {Medical aspects of ketone body metabolism.}, journal = {Clinical and investigative medicine. Medecine clinique et experimentale}, volume = {18}, number = {3}, pages = {193-216}, pmid = {7554586}, issn = {0147-958X}, mesh = {3-Hydroxybutyric Acid ; Acetoacetates/metabolism ; Acetone/metabolism ; Biological Evolution ; Brain/metabolism ; Humans ; Hydroxybutyrates/metabolism ; Hypoglycemia/*diagnosis/metabolism ; Ketone Bodies/biosynthesis/*metabolism ; Ketosis/*diagnosis/metabolism/therapy ; Menotropins/metabolism ; Metabolism, Inborn Errors/*diagnosis/metabolism/therapy ; Mitochondria, Liver/enzymology/metabolism ; }, abstract = {Ketone bodies are produced in the liver, mainly from the oxidation of fatty acids, and are exported to peripheral tissues for use as an energy source. They are particularly important for the brain, which has no other substantial non-glucose-derived energy source. The 2 main ketone bodies are 3-hydroxybutyrate (3HB) and acetoacetate (AcAc). Biochemically, abnormalities of ketone body metabolism can present in 3 fashions: ketosis, hypoketotic hypoglycemia, and abnormalities of the 3HB/AcAc ratio. Normally, the presence of ketosis implies 2 things: that lipid energy metabolism has been activated and that the entire pathway of lipid degradation is intact. In rare patients, ketosis reflects an inability to utilize ketone bodies. Ketosis is normal during fasting, after prolonged exercise, and when a high-fat diet is consumed. During the neonatal period, infancy and pregnancy, times at which lipid energy metabolism is particularly active, ketosis develops readily. Pathologic causes of ketosis include diabetes, ketotic hypoglycemia of childhood, corticosteroid or growth hormone deficiency, intoxication with alcohol or salicylates, and several inborn errors of metabolism. The absence of ketosis in a patient with hypoglycemia is abnormal and suggests the diagnosis of either hyperinsulinism or an inborn error of fat energy metabolism. An abnormal elevation of the 3HB/AcAc ratio usually implies a non-oxidized state of the hepatocyte mitochondrial matrix resulting from hypoxia-ischemia or other causes. We summarize the differential diagnosis of abnormalities of ketone body metabolism, as well as pertinent recent advances in research.}, }
@article {pmid7543951, year = {1995}, author = {van der Kuyl, AC and Kuiken, CL and Dekker, JT and Perizonius, WR and Goudsmit, J}, title = {Nuclear counterparts of the cytoplasmic mitochondrial 12S rRNA gene: a problem of ancient DNA and molecular phylogenies.}, journal = {Journal of molecular evolution}, volume = {40}, number = {6}, pages = {652-657}, pmid = {7543951}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; Cercocebus ; DNA/*genetics ; DNA Primers ; Humans ; Molecular Sequence Data ; Mummies ; Papio/genetics ; *Phylogeny ; Polymerase Chain Reaction ; Primates/genetics ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/*genetics ; Sequence Alignment ; }, abstract = {Monkey mummy bones and teeth originating from the North Saqqara Baboon Galleries (Egypt), soft tissue from a mummified baboon in a museum collection, and nineteenth/twentieth-century skin fragments from mangabeys were used for DNA extraction and PCR amplification of part of the mitochondrial 12S rRNA gene. Sequences aligning with the 12S rRNA gene were recovered but were only distantly related to contemporary monkey mitochondrial 12S rRNA sequences. However, many of these sequences were identical or closely related to human nuclear DNA sequences resembling mitochondrial 12S rRNA (isolated from a cell line depleted in mitochondria) and therefore have to be considered contamination. Subsequently in a separate study we were able to recover genuine mitochondrial 12S rRNA sequences from many extant species of nonhuman Old World primates and sequences closely resembling the human nuclear integrations. Analysis of all sequences by the neighbor-joining (NJ) method indicated that mitochondrial DNA sequences and their nuclear counterparts can be divided into two distinct clusters. One cluster contained all temporary cytoplasmic mitochondrial DNA sequences and approximately half of the monkey nuclear mitochondriallike sequences. A second cluster contained most human nuclear sequences and the other half of monkey nuclear sequences with a separate branch leading to human and gorilla mitochondrial and nuclear sequences. Sequences recovered from ancient materials were equally divided between the two clusters. These results constitute a warning for when working with ancient DNA or performing phylogenetic analysis using mitochondrial DNA as a target sequence: Nuclear counterparts of mitochondrial genes may lead to faulty interpretation of results.}, }
@article {pmid7599200, year = {1995}, author = {Wallace, DC and Shoffner, JM and Trounce, I and Brown, MD and Ballinger, SW and Corral-Debrinski, M and Horton, T and Jun, AS and Lott, MT}, title = {Mitochondrial DNA mutations in human degenerative diseases and aging.}, journal = {Biochimica et biophysica acta}, volume = {1271}, number = {1}, pages = {141-151}, doi = {10.1016/0925-4439(95)00021-u}, pmid = {7599200}, issn = {0006-3002}, support = {HL45572/HL/NHLBI NIH HHS/United States ; NS21328/NS/NINDS NIH HHS/United States ; NS30164/NS/NINDS NIH HHS/United States ; }, mesh = {Adult ; Aged ; Aging/*genetics ; Amino Acid Sequence ; Animals ; *Biological Evolution ; Child ; Conserved Sequence ; DNA, Mitochondrial/*genetics ; Energy Metabolism ; Female ; Humans ; Male ; Middle Aged ; Mitochondria/*metabolism ; Mitochondrial Myopathies/*genetics/metabolism ; Molecular Sequence Data ; *Mutation ; Nervous System Diseases/genetics/metabolism ; Optic Atrophies, Hereditary/*genetics/metabolism ; Oxidative Phosphorylation ; Pedigree ; *Point Mutation ; Sequence Homology, Amino Acid ; }, abstract = {A wide variety of mitochondrial DNA (mtDNA) mutations have recently been identified in degenerative diseases of the brain, heart, skeletal muscle, kidney and endocrine system. Generally, individuals inheriting these mitochondrial diseases are relatively normal in early life, develop symptoms during childhood, mid-life, or old age depending on the severity of the maternally-inherited mtDNA mutation; and then undergo a progressive decline. These novel features of mtDNA disease are proposed to be the product of the high dependence of the target organs on mitochondrial bioenergetics, and the cumulative oxidative phosphorylation (OXPHOS) defect caused by the inherited mtDNA mutation together with the age-related accumulation mtDNA mutations in post-mitotic tissues.}, }
@article {pmid7599195, year = {1995}, author = {Luft, R}, title = {The development of mitochondrial medicine.}, journal = {Biochimica et biophysica acta}, volume = {1271}, number = {1}, pages = {1-6}, doi = {10.1016/0925-4439(95)00002-l}, pmid = {7599195}, issn = {0006-3002}, mesh = {Aging/metabolism ; Animals ; Antioxidants/pharmacology ; Central Nervous System/metabolism ; DNA, Mitochondrial/genetics/metabolism ; Diabetes Mellitus, Type 2/metabolism ; Free Radicals/metabolism ; Humans ; Mitochondria/*metabolism ; Mitochondrial Encephalomyopathies/genetics ; Mitochondrial Myopathies/genetics/*metabolism ; Organ Specificity ; }, abstract = {I consider mitochondrial medicine a tentative designation for an area within clinical medicine still to be delineated. Its development extends over a period of 35 years, from its discovery in 1959 [1]. Progress had been gradual until recent years when it has become explosive in nature with extensions in many different directions. My presentation is an effort to illustrate this evolution with emphasis on especially important observations which by leaps advanced the area. We are fortunate to have here several of the distinguished investigators, who have contributed so much to those advances. They will share with us their deep knowledge in different aspects of mitochondrial medicine, what is known, what remains to be elucidated, and what the problems are to be encountered in that elucidation.}, }
@article {pmid7753839, year = {1995}, author = {Kaneda, H and Hayashi, J and Takahama, S and Taya, C and Lindahl, KF and Yonekawa, H}, title = {Elimination of paternal mitochondrial DNA in intraspecific crosses during early mouse embryogenesis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {92}, number = {10}, pages = {4542-4546}, pmid = {7753839}, issn = {0027-8424}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; *Crosses, Genetic ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Embryo, Mammalian/physiology ; *Embryonic and Fetal Development ; Female ; Haplotypes ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Inbred DBA ; Mitochondria/metabolism ; Molecular Sequence Data ; Muridae/*genetics ; Oocytes/physiology ; Polymerase Chain Reaction ; Spermatozoa/physiology ; }, abstract = {To examine whether mtDNA is uni- or biparentally transmitted in mice, we developed an assay that can detect sperm mtDNA in a single mouse embryo. In intraspecific hybrids of Mus musculus, paternal mtDNA was detected only through the early pronucleus stage, and its disappearance co-incided with loss of membrane potential in sperm-derived mitochondria. By contrast, in interspecific hybrids between M. musculus and Mus spretus, paternal mtDNA was detected throughout development from pronucleus stage to neonates. We propose that oocyte cytoplasm has a species-specific mechanism that recognizes and eliminates sperm mitochondria and mtDNA. This mechanism must recognize nuclearly encoded proteins in the sperm midpiece, and not the mtDNA or the proteins it encodes, because sperm mitochondria from the congenic strain B6.mtspr, which carries M. spretus mtDNA on background of M. musculus (B6) nuclear genes, were eliminated early by B6 oocytes as in intraspecific crosses. We conclude that cytoplasmic genomes are transmitted uniparentally in intraspecific crosses in mammals as in Chlamydomonas and that leakage of parental mtDNA is limited to interspecific crosses, which rarely occur in nature.}, }
@article {pmid7751302, year = {1995}, author = {Margolin, W and Bramhill, D and Long, SR}, title = {The dnaA gene of Rhizobium meliloti lies within an unusual gene arrangement.}, journal = {Journal of bacteriology}, volume = {177}, number = {10}, pages = {2892-2900}, pmid = {7751302}, issn = {0021-9193}, support = {2R01-GM30962/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacteria/genetics ; Bacterial Proteins/*genetics ; Base Sequence ; Biological Evolution ; Caulobacter/genetics ; Conserved Sequence ; DNA-Binding Proteins/*genetics ; Enoyl-CoA Hydratase/genetics ; Genes, Bacterial/*genetics ; Genomic Library ; Mitochondria/enzymology/genetics ; Molecular Sequence Data ; Open Reading Frames/genetics ; Restriction Mapping ; Ribosomal Proteins/genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Sinorhizobium meliloti/*genetics ; }, abstract = {Rhizobium meliloti exists either as a free-living soil organism or as a differentiated endosymbiont bacteroid form within the nodules of its host plant, alfalfa (Medicago sativa), where it fixes atmospheric N2. Differentiation is accompanied by major changes in DNA replication and cell division. In addition, R. meliloti harbors three unique large circular chromosome-like elements whose replication coordination may be complex. As part of a study of DNA replication control in R. meliloti, we isolated a dnaA homolog. The deduced open reading frame predicts a protein of 57 kDa that is 36% identical to the DnaA protein of Escherichia coli, and the predicted protein was confirmed by immunoblot analysis. In a comparison with the other known DnaA proteins, this protein showed the highest similarity to that of Caulobacter crescentus and was divergent in some domains that are highly conserved in other unrelated species. The dnaA genes of a diverse group of bacteria are adjacent to a common set of genes. Surprisingly, analysis of the DNA sequence flanking dnaA revealed none of these genes, except for an rpsT homolog, also found upstream of dnaA in C. crescentus. Instead, upstream of rpsT lie homologs of fpg, encoding a DNA glycosylase, and fadB1, encoding an enoyl-coenzyme A hydratase with a strikingly high (53 to 55%) level of predicted amino acid identity to two mammalian mitochondrial homologs. Downstream of dnaA, there are two open reading frames that are probably expressed but are not highly similar to any genes in the databases. These results show that R. meliloti dnaA is located within a novel gene arrangement.}, }
@article {pmid7641080, year = {1995}, author = {Palmisano, A and Aurilia, V and Ferrara, L and Cubellis, MV and Sannia, G and Marino, G}, title = {Nucleotide sequence of a cDNA coding for bovine mitochondrial aspartate aminotransferase.}, journal = {The international journal of biochemistry &amp; cell biology}, volume = {27}, number = {5}, pages = {507-511}, doi = {10.1016/1357-2725(95)00013-f}, pmid = {7641080}, issn = {1357-2725}, mesh = {Amino Acid Sequence ; Animals ; Aspartate Aminotransferases/*genetics ; Base Sequence ; Cattle ; Cloning, Molecular ; DNA, Complementary ; Mitochondria, Heart/*enzymology ; Molecular Sequence Data ; }, abstract = {Aspartate aminotransferase is a pyridoxal-phosphate dependent enzyme which plays a key role in cell metabolism. We describe the cloning and sequence analysis of the cDNA encoding bovine mitochondrial aspartate aminotransferase and compare the sequence with those of isoenzymes from other mammalian species. An adult bovine heart cDNA library constructed in lambda lambda gt11 was screened using two 32P-end labeled synthetic oligonucleotides. From the screening of the cDNA library two positive clones were isolated. A subclone in pEMBL18, 6B2, generated from the longest recombinant phage was further analyzed. This clone contains an insert of 2500 bp with an Open Reading Frame of 1287 bp that encodes a protein of 430 amino acids. The deduced amino acid sequence confirms previous results obtained by mass spectrometric sequencing. We calculated the percentage of amino acid identity for each protein pair and for each comparison the average number of amino acid substitution per site (Kaa); the lowest Kaa values were obtained from the comparison between the bovine and pig enzymes. This study shows that the rate of evolution of mammalian mitochondrial AspAT is lower and more constant than the equivalent cytosolic enzyme and adds to the growing body of knowledge on the evolution of the aspartate aminotransferase.}, }
@article {pmid7553941, year = {1995}, author = {Kempken, F and Höfken, G and Pring, DR}, title = {Analysis of silent RNA editing sites in atp6 transcripts of Sorghum bicolor.}, journal = {Current genetics}, volume = {27}, number = {6}, pages = {555-558}, pmid = {7553941}, issn = {0172-8083}, mesh = {Base Sequence ; Binding Sites ; Biological Evolution ; DNA, Complementary/genetics ; DNA, Plant/genetics ; Edible Grain/*genetics/*metabolism ; Genes, Plant ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA Editing/*genetics ; RNA, Messenger/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Transcription, Genetic ; }, abstract = {We have observed numerous examples of silent or rare non-silent editing sites in the amino-extension and part of the conserved core of mitochondrial atp6 transcripts of Sorghum. In this region of the 1.4-kb atp6-2 mRNA (position 300 to 550) two editing sites, which alter the amino-acid sequence and occur in all cDNAs analysed, were already known, while nine others were found which are silent or occur in a few mRNAs only. Many aspects of RNA editing in the mitochondria of higher plants are still unknown. This includes the influence of genomic background or silent RNA editing. We were interested in the influence of nuclear and mitochondrial backgrounds on RNA editing. Previous preliminary results indicated the possibility of line-specific editing at silent sites. However, a more comprehensive approach gave no consistent evidence for such editing. These results are discussed with respect to their potential impact on the evolution of mitochondrial genes.}, }
@article {pmid7731996, year = {1995}, author = {Authier, F and Bergeron, JJ and Ou, WJ and Rachubinski, RA and Posner, BI and Walton, PA}, title = {Degradation of the cleaved leader peptide of thiolase by a peroxisomal proteinase.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {92}, number = {9}, pages = {3859-3863}, pmid = {7731996}, issn = {0027-8424}, mesh = {Acetyl-CoA C-Acetyltransferase/biosynthesis/*metabolism ; Amino Acid Sequence ; Animals ; Antibodies ; CHO Cells ; Cell Line ; Cricetinae ; Endopeptidases/biosynthesis/genetics/*metabolism ; Liver/enzymology ; Microbodies/*enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; Peptides/chemical synthesis/immunology ; Phylogeny ; Protein Processing, Post-Translational ; Protein Sorting Signals/*metabolism ; Rats ; Recombinant Proteins/biosynthesis/metabolism ; Transfection ; }, abstract = {A peroxisomal location for insulin-degrading enzyme (IDE) has been defined by confocal immunofluorescence microscopy of stably transfected CHO cells overexpressing IDE and digitonin-permeabilization studies in normal nontransfected fibroblasts. The functional significance of IDE in degrading cleaved leader peptides of peroxisomal proteins targeted by the type II motif was evaluated with a synthetic peptide corresponding to the type II leader peptide of prethiolase. The peptide effectively competed for degradation and cross-linking of the high-affinity substrate 125I-labeled insulin to IDE. Direct proteolysis of the leader peptide of prethiolase was confirmed by HPLC; degradation was inhibited by immunodepletion with an antibody to IDE. Phylogenetic analysis of proteinases related to IDE revealed sequence similarity to mitochondrial processing peptidases.}, }
@article {pmid7769621, year = {1995}, author = {Winefield, CS and Farnden, KJ and Reynolds, PH and Marshall, CJ}, title = {Evolutionary analysis of aspartate aminotransferases.}, journal = {Journal of molecular evolution}, volume = {40}, number = {4}, pages = {455-463}, pmid = {7769621}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Aspartate Aminotransferases/classification/*genetics ; Bacterial Proteins/genetics ; *Biological Evolution ; Cell Nucleus ; Cytosol/enzymology ; Eukaryotic Cells/enzymology ; Fungal Proteins/genetics ; Genes ; Isoenzymes/*genetics ; Mitochondria/enzymology ; Models, Molecular ; Molecular Sequence Data ; Phylogeny ; Plant Proteins/genetics ; Prokaryotic Cells/enzymology ; Protein Conformation ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {Aspartate aminotransferase isoenzymes are located in both the cytosol and organelles of eukaryotes, but all are encoded in the nuclear genome. In the work described here, a phylogenetic analysis was made of aspartate aminotransferases from plants, animals, yeast, and a number of bacteria. This analysis suggested that five distinct branches are present in the aspartate aminotransferase tree. Mitochondrial forms of the enzyme form one distinct group, bacterial aspartate aminotransferase formed another, and the plant and vertebrate cytosolic isoenzymes each formed a distinct group. Plant cytosolic isozymes formed a further group of which the plastid sequences were a member. The yeast mitochondrial and cytosolic aspartate aminotransferases formed groups separate from other members of the family.}, }
@article {pmid7769615, year = {1995}, author = {Zhang, DX and Szymura, JM and Hewitt, GM}, title = {Evolution and structural conservation of the control region of insect mitochondrial DNA.}, journal = {Journal of molecular evolution}, volume = {40}, number = {4}, pages = {382-391}, pmid = {7769615}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; Bees/genetics ; *Biological Evolution ; Consensus Sequence ; Crossing Over, Genetic ; DNA, Mitochondrial/*genetics ; Drosophila/genetics ; Grasshoppers/genetics ; Gryllidae/genetics ; Insecta/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Recombination, Genetic ; *Regulatory Sequences, Nucleic Acid ; Repetitive Sequences, Nucleic Acid ; Replication Origin ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Species Specificity ; Vertebrates/genetics ; }, abstract = {The control regions of mitochondrial DNA of two insects, Schistocerca gregaria and Chorthippus parallelus, have been isolated and sequenced. Their sizes are 752 bp and 1,512 bp, respectively, with the presence of a tandem repeat in C. parallelus. (The sequences of the two repeats are highly conserved, having a homology of 97.5%.) Comparison of their nucleotide sequences revealed the presence of several conserved sequence blocks dispersed through the whole control region, showing a different evolutionary pattern of this region in these insects as compared to that in Drosophila. A highly conserved secondary structure, located in the 3' region near the small rRNA gene, has been identified. Sequences immediately flanking this hairpin structure rather than the sequences of this structure themselves are conserved between S. gregaria/C. parallelus and Drosophila, having a sequence consensus of "TATA" at 5' and "GAA(A)T" at 3'. The motif "G(A)nT" is also present in the 3' flanking sequences of mammalian, amphibian, and fish mitochondrial L-strand replication origins and a potential plant mitochondrial second-strand-replication origin, indicating its universal conservation and functional importance related to replication origins. The stem-and-loop structure in S. gregaria/C. parallelus appears to be closely related to that found in Drosophila despite occupying a different position, and may be potentially associated with a second-strand-replication origin. This in turn suggests that such a secondary structure might be widely conserved across invertebrates while their location in the control region may be variable. We have looked for such a conserved structure in the control regions of two other insects, G. firmus and A. mellifera, whose DNA sequences have been published, and their possible presence is discussed. Mitochondrial control regions characterized to date in five different insect taxa (Drosophila, G. firmus, A. mellifera, S. gregaria, and C. parallelus) may be classed into two distinct groups having different evolutionary patterns. It is observed that tandem repetition of regions containing a probable replication origin occurred in some species from disjunct lineages in both groups, which would be the result of convergent evolution. We also discuss the possibility of a mechanism of "parahomologous recombination by unequal crossing-over" in mitochondria, which can explain the generation of such tandemly repeated sequences (especially the first critical repetition) in the control region of mtDNA, and also their convergent evolution in disjunct biological lineages during evolution.}, }
@article {pmid7604961, year = {1995}, author = {Jamieson, BG and Koehler, L and Todd, BJ}, title = {Spermatozoal ultrastructure in three species of parrots (aves, Psittaciformes) and its phylogenetic implications.}, journal = {The Anatomical record}, volume = {241}, number = {4}, pages = {461-468}, doi = {10.1002/ar.1092410404}, pmid = {7604961}, issn = {0003-276X}, mesh = {Animals ; Cell Nucleus/ultrastructure ; Centrioles/ultrastructure ; In Vitro Techniques ; Male ; Microscopy, Electron ; *Parrots ; Phylogeny ; Spermatozoa/*ultrastructure ; }, abstract = {BACKGROUND: DNA-DNA hybridization studies suggest that Psittaciformes are highly, but not the most, derived nonpasserines. Multilocus protein electrophoresis indicates that cockatoos (Cacatuinae) form a monophyletic lineage distant from the other Australo-Papuan psittacids (Psittacinae).<br><br>METHODS: Transmission electron microscope procedures are applied to the spermatozoa of three parrots, in the Cacatuninae and Psittacinae, to investigate these relationships.<br><br>RESULTS: Psittaciform sperm have the following characteristics: (1) conical acrosome vesicle; rodlike perforatorium; cylindrical, highly condensed nucleus; proximal and distal centriole embedded in dense material; elongate periaxonemal mitochondrial midpiece, (2) nine dense peripheral axonemal fibers (coarse fibers), (3) no fibrous sheath around the axoneme, (4) mitochondria with linear cristae, lacking intra- (or inter-) mitochondrial dense bodies, (5) restriction of the endonuclear perforatorial canal to the anterior region of the nucleus, (6) a short distal centriole, and (7) nucleus abutting on but not penetrating the acrosome.<br><br>CONCLUSIONS: (1) These features are tetrapod symplesiomorphies, (2) is an amniote synapomorphy; the fibers differ from those of reptiles in being uniform in size, (3) loss of the fibrous sheath is an apomorphy known elsewhere only in columbiforms, (4) are apomorphies relative to basal aminiotes (Chelonia, Sphenodon, and Crocodilia), (5) is an apomorphic condition shared with other nonpasserines (galliforms and the white-naped crane) and crocodilians, (6) the latter taxa differ from parrots in a plesiomorphic elongation of the distal centriole, and (7) is a unique apomorphy of parrot sperm relative to other nonpasserines and reptiles. The short midpiece of N. hollandicus distinguishes this cacatuine from the two psittacines.}, }
@article {pmid7706307, year = {1995}, author = {Sidhu, SS and Kalmar, GB and Willis, LG and Borgford, TJ}, title = {Protease evolution in Streptomyces griseus. Discovery of a novel dimeric enzymes.}, journal = {The Journal of biological chemistry}, volume = {270}, number = {13}, pages = {7594-7600}, doi = {10.1074/jbc.270.13.7594}, pmid = {7706307}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Bacillus subtilis/enzymology ; *Bacterial Proteins ; *Biological Evolution ; Cloning, Molecular ; Escherichia coli ; Gene Expression ; Genes, Bacterial ; Humans ; Macromolecular Substances ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Promoter Regions, Genetic ; Recombinant Proteins/biosynthesis/chemistry ; Ribosomes/metabolism ; Sequence Homology, Amino Acid ; Serine Endopeptidases/biosynthesis/chemistry/*genetics ; Streptomyces griseus/*enzymology/genetics ; Substrate Specificity ; }, abstract = {This report describes the cloning and sequencing of a novel protease gene derived from Streptomyces griseus. Also described is the heterologous expression of the gene in Bacillus subtilis and characterization of the gene product. The sprD gene encodes a prepro mature protease of 392 amino acids tentatively named S. griseus protease D (SGPD). A significant component of the enzyme preregion was found to be homologous with the mitochondrial import signal of hsp60. The sprD gene was subcloned into an Escherichia coli/B. subtilis shuttle vector system such that the pro mature portion of SGPD was fused in frame with the promoter, ribosome binding site, and signal sequences of subtilisin. The gene fusion was subsequently expressed in B. subtilis DB104, and active protease was purified. SGPD has a high degree of sequence homology to previously described S. griseus proteases A, B, C, and E and the alpha-lytic protease of Lysobacter enzymogenes, but unlike all previously characterized members of the chymotrypsin superfamily, the recombinant SGPD forms a stable alpha 2 dimer. The amino acid sequence of the protein in the region of the specificity pocket is similar to that of S. griseus proteases A, B, and C. The purified enzyme was found to have a primary specificity for large aliphatic or aromatic amino acids. Nucleotide sequence data were used to construct a phylogenetic tree using a method of maximum parsimony which reflects the relationships and potentially the lineage of the chymotrypsin-like proteases of S. griseus.}, }
@article {pmid7737175, year = {1995}, author = {Claros, MG and Perea, J and Shu, Y and Samatey, FA and Popot, JL and Jacq, C}, title = {Limitations to in vivo import of hydrophobic proteins into yeast mitochondria. The case of a cytoplasmically synthesized apocytochrome b.}, journal = {European journal of biochemistry}, volume = {228}, number = {3}, pages = {762-771}, pmid = {7737175}, issn = {0014-2956}, mesh = {Amino Acid Sequence ; Apoproteins/biosynthesis/genetics/*metabolism ; Base Sequence ; Biological Transport ; Cell Membrane/metabolism ; Cell Nucleus/enzymology ; Cytochrome b Group/biosynthesis/genetics/*metabolism ; Cytochromes b ; Cytoplasm/*enzymology ; DNA, Fungal ; Fungal Proteins/*metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Protein Biosynthesis ; Recombinant Fusion Proteins/genetics/metabolism ; Saccharomyces cerevisiae/*metabolism ; }, abstract = {The apocytochrome b gene, exclusively encoded by the mitochondrial genome, was engineered so that it could be expressed in the yeast cytoplasm. Different combinations of the apocytochrome b transmembrane domains were produced in the form of hybrid proteins fused to both the N-terminal mitochondrial targeting sequence of the ATPase subunit 9 from Neurospora crassa and to a cytoplasmic version of the bI4 RNA maturase, localised on the N-terminal and C-terminal sides, respectively, of the hydrophobic stretches. The bI4 RNA maturase, which can complement mitochondrial mutations, was used as an in vivo reporter to assess the mitochondrial import of the different groups of transmembrane helices. This new, reliable and sensitive reporter activity allowed us to experimentally determine the limitations to the mitochondrial import of hydrophobic proteins. All eight transmembrane helices of apocytochrome b could be imported into mitochondria, either alone or in combination, but no more than three to four transmembrane helices could be imported together at one time. This limit is close to that observed in the population of nuclear-encoded mitochondrial proteins. The hydrophobic characteristics of engineered and natural proteins targeted to the mitochondrial inner membrane revealed two factors important in the import process. These were (a) the local hydrophobicity of a transmembrane segment, and (b) the average regional hydrophobicity of the protein over an extended length of 60-80 residues. Such features may have played a major role in the evolution of mitochondrial genomes.}, }
@article {pmid7737148, year = {1995}, author = {Jaussi, R}, title = {Homologous nuclear-encoded mitochondrial and cytosolic isoproteins. A review of structure, biosynthesis and genes.}, journal = {European journal of biochemistry}, volume = {228}, number = {3}, pages = {551-561}, doi = {10.1111/j.1432-1033.1995.tb20294.x}, pmid = {7737148}, issn = {0014-2956}, mesh = {Animals ; Cell Nucleus/*metabolism ; Cytosol/*metabolism ; Gene Expression Regulation ; Humans ; Mitochondria/*metabolism ; Protein Biosynthesis ; Protein Conformation ; *Proteins/chemistry/genetics ; RNA, Messenger/genetics ; }, abstract = {Mitochondrial and cytosolic proteins may be expected to differ in specific traits due to their different intracellular location. However, the identification of these differences between mitochondrial and cytosolic proteins is complicated by the heterogeneity of the two protein groups. These difficulties have been overcome by comparing traits of homologous genes, which are derived from a common ancestor gene, and their gene products. An earlier report [Hartmann, C., Christen, P. &amp; Jaussi, R. (1991) Nature 352, 762-763] describing a positive net charge difference between the mature parts of nuclear-encoded mitochondrial proteins and their homologous cytosolic isoproteins, could be corroborated by extending the data collection. New data were gathered from computer databases and published studies. The average isoelectric points of the mitochondrial and cytosolic isoproteins are 7.5 and 6.5, respectively. Depending on the type of protein, the observed difference results from differences in the number of basic and/or acidic amino acid residues in the isoproteins. Probably both the conditions required for mitochondrial protein import and the local conditions within the organelle furthered the evolution of basic protein structures. The contribution of the mitochondrial targeting peptide to the positive charge of precursors of nuclear-encoded mitochondrial proteins is largest when the value of the isoelectric point of the mature protein is small. This mutual dependence of the charge of the targeting peptide and the mature protein part supports the notion that positive charge is essential for mitochondrial protein import. Several traits other than electric charge, i.e. codon usage, chromosome location, structural organization or regulation of the genes, do not show specific differences between the sets of the heterotopic isoproteins. There is no preference of gene location for any of the gene sets; only rarely are the genes for a mitochondrial and a cytosolic isoprotein located on the same chromosome. A variant of the 3' splice-site consensus exists in genes of nuclear-encoded mitochondrial proteins. This is most likely a consequence of the evolution of the genes in separate lineages before endosymbiosis led to the formation of mitochondria. Some of the original mRNA group II intron self-splicing functions of the endosymbiont seem to persist in part of the cytosolic splicing machinery and apparently require a specific consensus sequence [Juretic, N., Jaussi, R., Mattes, U. &amp; Christen, P. (1987) Nucleic Acids Res.15, 10083-10086].}, }
@article {pmid7883039, year = {1995}, author = {Murgia, I and Maciver, SK and Morandini, P}, title = {An actin-related protein from Dictyostelium discoideum is developmentally regulated and associated with mitochondria.}, journal = {FEBS letters}, volume = {360}, number = {3}, pages = {235-241}, doi = {10.1016/0014-5793(95)00111-l}, pmid = {7883039}, issn = {0014-5793}, mesh = {Actins/*genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Cell Compartmentation ; Cloning, Molecular ; DNA Primers/chemistry ; DNA, Complementary/genetics ; Dictyostelium/*genetics ; Gene Expression Regulation, Developmental ; *Genes, Fungal ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; }, abstract = {An actin-related protein (ACLA) has been identified in the cellular slime mould Dictyostelium discoideum. The complete cDNA sequence indicates that within the actin superfamily it belongs to the ARP3 family of actin-related proteins together with Arp66B from Drosophila melanogaster, Actin2 from Bos taurus, act2 from Schizosaccharomyces pombe and possibly act2 from Caenorhabditis elegans. The ACLA mRNA is regulated during development, showing a maximum between 2 and 4 h after starvation. The protein has been expressed in E. coli and antibodies raised against it. Immunofluorescence microscopy shows that ACLA protein co-localises with mitochondria; the protein copurifies with Dictyostelium mitochondria.}, }
@article {pmid8591812, year = {1995}, author = {McClung, JK and Jupe, ER and Liu, XT and Dell'Orco, RT}, title = {Prohibitin: potential role in senescence, development, and tumor suppression.}, journal = {Experimental gerontology}, volume = {30}, number = {2}, pages = {99-124}, doi = {10.1016/0531-5565(94)00069-7}, pmid = {8591812}, issn = {0531-5565}, mesh = {Aging/genetics/*physiology ; Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Conserved Sequence ; Embryonic and Fetal Development/genetics ; *Genes, Tumor Suppressor ; Humans ; Molecular Sequence Data ; Prohibitins ; Proteins/genetics/*physiology ; *Repressor Proteins ; }, abstract = {Prohibitin is an evolutionarily conserved gene with homologues found in organisms ranging from yeast to man. In man the gene is located on chromosome 17 at q21. The deduced amino acid sequences of the protein products from mouse and rat are identical; and these differ from the human protein sequence by a single conserved amino acid. Prohibitin has antiproliferative activity and available data suggest a role in such diverse processes as normal cell cycle regulation, replicative senescence, cellular immortalization, and the development of sporadic breast tumors. Although its functional activity is presently unknown, the 30,000-Da protein has been located in the inner membrane of mitochondria, where it is postsynthetically modified, as well as on the plasma membrane of B cells, where it is associated with the IgM receptor. Prohibitin's evolutionary conservation and ubiquitous expression indicate that it is a fundamentally important gene; and current data suggest a functional role in such dissimilar processes as development, senescence, and tumor suppression.}, }
@article {pmid7766872, year = {1995}, author = {Thompson, MD and Paavola, CD and Lenvik, TR and Gantt, JS}, title = {Chlamydomonas transcripts encoding three divergent plastid chaperonins are heat-inducible.}, journal = {Plant molecular biology}, volume = {27}, number = {5}, pages = {1031-1035}, pmid = {7766872}, issn = {0167-4412}, support = {GM38769/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Chaperonins/*biosynthesis/genetics ; Chlamydomonas/*genetics/*metabolism ; *Gene Expression Regulation, Plant ; Hot Temperature ; Kinetics ; Mitochondria/metabolism ; Molecular Sequence Data ; *Phylogeny ; Plants/metabolism ; Plastids/*metabolism ; RNA, Plant/biosynthesis ; *Transcription, Genetic ; }, abstract = {Three cDNAs encoding plastid cpn60 chaperonin subunits have been isolated from the unicellular green alga Chlamydomonas reinhardtii. Based on comparisons of the predicted amino acid sequences, we conclude that Chlamydomonas, like higher plants, contains divergent plastid cpn60-alpha and cpn60-beta subunits. The predicted amino acid sequences of the two Chlamydomonas cpn60-beta subunits differ significantly (24% divergent), indicating that the two cpn60-beta subunits have been selectively maintained for a considerable period of time. Unlike plastid chaperonin transcripts in higher plants, heat shock conditions (42 degrees C) lead to a rapid increase (10- to 30-fold) in the level of each of the three plastid transcripts.}, }
@article {pmid7766262, year = {1995}, author = {Heidrich, P and König, C and Wink, M}, title = {Molecular phylogeny of South American screech owls of the Otus atricapillus complex (Aves: Strigidae) inferred from nucleotide sequences of the mitochondrial cytochrome b gene.}, journal = {Zeitschrift fur Naturforschung. C, Journal of biosciences}, volume = {50}, number = {3-4}, pages = {294-302}, doi = {10.1515/znc-1995-3-420}, pmid = {7766262}, issn = {0939-5075}, mesh = {Animals ; Base Sequence ; Birds/*classification/*genetics ; Chickens/genetics ; Cytochrome b Group/*genetics ; DNA Primers ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Geography ; Mitochondria/metabolism ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; South America ; }, abstract = {The cytochrome b gene of 6 South American screech owls of the genus Otus (O. choliba, O. atricapillus, O. usta, O. sanctaecatarinae, O. guatemalae, and O. hoyi) and two Old World species (Otus scops and Otus leucotis) was amplified by polymerase chain reaction (PCR) and partially sequenced (300 nucleotides). Otus atricapillus, O. guatemalae, O. hoyi and O. sanctaecatarinae which are morphologically very similar, have been treated as belonging to a single species. A. atricapillus (Sibley and Monroe, 1990). Nucleotide sequences differ substantially between these taxa (6.3 to 8.8% nucleotide substitutions) indicating that they represent well established and distinct species which had been implicated already from ecological and bioacoustical analyses (König, 1991, 1994). The importance of vocal and ecological characters for the taxonomy of nocturnal birds is thus confirmed by our molecular analysis. Phylogenetic relationships were reconstructed between Old and New World owls using character state ("maximum parsimony"; PAUP 3.1.1) and distance matrix methods (neighbour-joining; MEGA).}, }
@article {pmid7700157, year = {1995}, author = {Graven, L and Passarino, G and Semino, O and Boursot, P and Santachiara-Benerecetti, S and Langaney, A and Excoffier, L}, title = {Evolutionary correlation between control region sequence and restriction polymorphisms in the mitochondrial genome of a large Senegalese Mandenka sample.}, journal = {Molecular biology and evolution}, volume = {12}, number = {2}, pages = {334-345}, doi = {10.1093/oxfordjournals.molbev.a040206}, pmid = {7700157}, issn = {0737-4038}, mesh = {Base Sequence ; Biological Evolution ; Black People/*genetics ; DNA, Mitochondrial/classification/*genetics ; Haplotypes ; Humans ; Mitochondria/*genetics ; Molecular Sequence Data ; *Polymorphism, Restriction Fragment Length ; Regulatory Sequences, Nucleic Acid/*genetics ; Senegal ; Sequence Homology, Nucleic Acid ; }, abstract = {We present here the first comparative analysis at the population level between Restriction Fragment Length Polymorphism (RFLP) and control region sequence polymorphism in a large and homogeneous Senegalese Mandenka sample. Eleven RFLP haplotypes and 60 different sequences are found in 119 individuals, revealing that a very high level of mtDNA diversity can be maintained in a small population. A sequence neighbor-joining tree and an analysis of molecular variance show that sequences associated with a given restriction haplotype are evolutionarily highly correlated: sequencing generally leads to the subtyping of RFLP haplotypes. Evolutionary relationships among RFLP haplotypes inferred from restriction site differences are in good agreement with those inferred from sequence data. A single difference is observed and is likely due to a single restriction homoplasy having occurred in the control region. Selective neutrality tests on both RFLP and sequence data accept the hypotheses of mtDNA neutrality and population equilibrium. The deep coalescence times (exceeding 50,000 yr) of sequences associated with the two most frequent restriction haplotypes confirm that the Niokolo Mandenka population has not passed through a recent bottleneck and that gene flow is maintained among West African populations despite ethnic differences.}, }
@article {pmid7620632, year = {1995}, author = {Ohland, DP and Harley, EH and Best, PB}, title = {Systematics of cetaceans using restriction site mapping of mitochondrial DNA.}, journal = {Molecular phylogenetics and evolution}, volume = {4}, number = {1}, pages = {10-19}, doi = {10.1006/mpev.1995.1002}, pmid = {7620632}, issn = {1055-7903}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Mitochondria, Heart/chemistry ; *Phylogeny ; *Restriction Mapping ; Software ; Species Specificity ; Whales/*classification/genetics ; }, abstract = {Phylogenetic analysis of 14 cetacean species, including members from two baleen whale families and three toothed whale families, was undertaken using restriction site mapping of mitochondrial DNA and using cladistic and distance measures to infer phylogenies. The amount of between-taxa sequence divergence inferred from the data was lower than expected from the standard interpretation of the fossil record, but more consistent with some recent estimates of sequence divergence in cetacean mitochondrial DNA or nuclear DNA. This implies either that the rate of molecular evolution of cetacean DNA is much lower than that of other mammalian orders or that the fossil record of cetaceans requires reinterpretation. The incompleteness of the cetacean fossil record precludes resolution of the paradox at the present time. However, this discrepancy could in part be attributed to the sampling error inherent in the restriction site mapping technique, as comparative studies using the complete mtDNA genome and restriction site data of the blue and fin whales (genus Balaenoptera) indicate that the restriction site maps underestimate sequence divergence by about 40%. In contrast to a recent study suggesting that toothed whales were paraphyletic, with the sperm whales being more closely related to the rorquals than to the other toothed whales, the restriction data tend to support the monophyly of the baleen and the toothed whales, a finding which is consistent with a recent molecular-based study and with morphological and paleontological data. Topologies of the subfamily and generic levels are generally consistent with morphologically based schemes.}, }
@article {pmid7857961, year = {1995}, author = {Lefai, E and Terrier-Cayre, A and Vincent, A and Boespflug-Tanguy, O and Tanguy, A and Alziari, S}, title = {Enzymatic activities of mitochondrial respiratory complexes from children muscular biopsies. Age-related evolutions.}, journal = {Biochimica et biophysica acta}, volume = {1228}, number = {1}, pages = {43-50}, doi = {10.1016/0005-2728(94)00157-z}, pmid = {7857961}, issn = {0006-3002}, mesh = {Adolescent ; Aging ; Child ; Citrate (si)-Synthase/analysis ; Electron Transport Complex III/*analysis ; Electron Transport Complex IV/*analysis ; Humans ; Mitochondria, Muscle/*enzymology ; NAD(P)H Dehydrogenase (Quinone)/*analysis ; Reference Values ; }, abstract = {Measurements were performed to determine maximum enzymatic activities of citrate synthetase and respiratory complexes I, III, and IV of mitochondria obtained from muscular biopsies in control children. The significant number of determinations carried out (43 different biopsies in controls aged 3.8 to 19.1 years) permits the formulation of a table of statistically validated reference values for these activities. These values are independent of sex of the controls, and of the studied muscles. Citrate synthetase activity, which remains stable in this age range, thus constitutes a good internal indicator of mitochondrial activity. Complexes I and III manifest activity which does not vary with age. On the other hand, cytochrome oxidase activity shows a highly significant decrease in this age group. This decrease may be correlated with qualitative changes (subunits VIa and VIIa) in composition of this complex.}, }
@article {pmid7736615, year = {1995}, author = {Kubo, T and Yanai, Y and Kinoshita, T and Mikami, T}, title = {The chloroplast trnP-trnW-petG gene cluster in the mitochondrial genomes of Beta vulgaris, B. trigyna and B. webbiana: evolutionary aspects.}, journal = {Current genetics}, volume = {27}, number = {3}, pages = {285-289}, pmid = {7736615}, issn = {0172-8083}, mesh = {Base Sequence ; Biological Evolution ; Blotting, Northern ; Blotting, Southern ; DNA Transposable Elements ; DNA, Chloroplast/genetics ; DNA, Mitochondrial/*genetics ; Genes, Plant/genetics ; Molecular Sequence Data ; Multigene Family ; Plants, Edible/*genetics ; Protozoan Proteins/*genetics ; RNA, Transfer, Pro/*genetics ; RNA, Transfer, Trp/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {The chloroplast trnP-trnW-petG gene cluster has been identified in the mitochondrial DNA (mtDNA) of sugar beet (Beta vulgaris). The chloroplast-derived trnW gene is transcribed in the mitochondria; the other two genes, however, do not seem to be transcribed. This gene cluster is also present in the mitochondrial genomes of two wild Beta species, B. trigyna and B. webbiana. Sugar beet and the two wild relatives share 100% sequence identity in the coding regions of both the mitochondrial trnP and trnW genes. On the other hand, the petG genes from the wild Beta mtDNAs were found to be disrupted either by a 5-bp duplication (B. trigyna) or by a deletion of the 5' region (B. webbiana). A data-base search revealed that a conserved sequence of 60 bp is present in the trnP-trnW intergenic region of the mitochondrial genomes of the three Beta species as well as in other higher plants, including wheat and maize, and that the conserved sequence is absent from the chloroplast counterpart. Our results thus favour the hypothesis of a monophyletic origin of the trnP-trnW-petG cluster found in the plant mitochondrial genomes examined.}, }
@article {pmid7696497, year = {1995}, author = {Schneider, G and Schuchhardt, J and Wrede, P}, title = {Peptide design in machina: development of artificial mitochondrial protein precursor cleavage sites by simulated molecular evolution.}, journal = {Biophysical journal}, volume = {68}, number = {2}, pages = {434-447}, pmid = {7696497}, issn = {0006-3495}, mesh = {Amino Acid Sequence ; Biological Evolution ; Fungal Proteins/chemistry/metabolism ; Metalloendopeptidases/chemistry ; Mitochondria/*metabolism ; Molecular Sequence Data ; Neural Networks, Computer ; Neurospora crassa ; Protein Precursors/*chemistry/metabolism ; Protein Processing, Post-Translational ; Structure-Activity Relationship ; }, abstract = {Artificial neural networks were used for extraction of characteristic physiochemical features from mitochondrial matrix metalloprotease target sequences. The amino acid properties hydrophobicity and volume were used for sequence encoding. A window of 12 residues was employed, encompassing positions -7 to +5 of precursors with cleavage sites. Two sets of noncleavage site examples were selected for network training which was performed by an evolution strategy. The weight vectors of the optimized networks were visualized and interpreted by Hinton diagrams. A neural filter system consisting of 13 perceptron-type networks accurately classified the data. It served as the fitness function in a simulated molecular evolution procedure for sequence-oriented de novo design of idealized cleavage sites. A detailed description of the strategy is given. Several putative high-quality cleavage sites were obtained revealing the critical nature of the residues in the positions -2 and -5. Charged residues seem to have a major influence on cleavage site function.}, }
@article {pmid7532606, year = {1995}, author = {Kennell, JC and Saville, BJ and Mohr, S and Kuiper, MT and Sabourin, JR and Collins, RA and Lambowitz, AM}, title = {The VS catalytic RNA replicates by reverse transcription as a satellite of a retroplasmid.}, journal = {Genes &amp; development}, volume = {9}, number = {3}, pages = {294-303}, doi = {10.1101/gad.9.3.294}, pmid = {7532606}, issn = {0890-9369}, support = {GM37949/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Blotting, Northern ; DNA, Complementary ; DNA, Mitochondrial/*genetics ; Molecular Sequence Data ; Neurospora/enzymology/*genetics ; Plasmids/genetics ; RNA/*genetics ; RNA, Satellite ; RNA-Directed DNA Polymerase/*genetics ; Transcription, Genetic/genetics ; Vesicular stomatitis Indiana virus/*genetics ; }, abstract = {The mitochondria of certain natural isolates of Neurospora contain both the Varkud plasmid, which encodes a reverse transcriptase, and a small unrelated RNA (VS RNA) that performs RNA-mediated self-cleavage and ligation reactions. Here, we show that VS RNA is transcribed from a VS plasmid DNA template by the Neurospora mitochondrial RNA polymerase using a promoter located immediately upstream of the RNA self-cleavage site that generates monomeric transcripts. VS RNA is then reverse transcribed by the Varkud plasmid reverse transcriptase to yield a full-length (-) strand cDNA, a predicted replication intermediate. Combined with previous genetic evidence, our results indicate that the VS plasmid replicates by reverse transcription as a satellite of the Varkud plasmid. This mode of replication, unprecedented for a satellite RNA, likely reflects the promiscuity of the Varkud plasmid reverse transcriptase, which does not require a specific primer to initiate cDNA synthesis. Our findings indicate how primitive reverse transcriptases with similar relaxed specificity could have facilitated the evolution of new retroelements.}, }
@article {pmid7706553, year = {1995}, author = {Wales, B and Ferrero, EA}, title = {Multiterminal proprioceptors in Squilla mantis (Stomatopoda, Crustacea).}, journal = {The Journal of comparative neurology}, volume = {351}, number = {3}, pages = {465-475}, doi = {10.1002/cne.903510312}, pmid = {7706553}, issn = {0021-9967}, mesh = {Animals ; Cell Size ; Crustacea/*physiology ; Dendrites/physiology/ultrastructure ; Glycogen/metabolism ; Mechanoreceptors/*physiology/ultrastructure ; Microscopy, Electron ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Nerve Endings/ultrastructure ; Proprioception/*physiology ; }, abstract = {A series of morphologically simple multiterminal proprioceptors is described in the thoracopods of the hoplocaridian crustacean, Squilla mantis, which is a primitive offshoot of the main malacostracan evolutionary line. The description given here is primarily for the largest and most complex receptor that occurs in the second thoracopod, the raptorial limb. These stretch receptors, which lie distally in the coxopodite, consist of single multiterminal sensory neurons with widely branching dendrites innervating broad connective tissue strands. The single primary dendrite divides dichotomously or, occasionally, trichotomously to produce a large number of terminal dendrites. The terminal dendrites, which exhibit a beaded structure, run parallel to the connective tissue strands' longitudinal axis. Dendrites possess an elaborate connective tissue sheath consisting of a single inner glial layer and a multiple outer connective tissue layer. The presence of the beaded structure has been confirmed by transmission electron microscopy (EM), and, because microtubule density does not vary with dendrite diameter, the beads are not fixation artifacts. Beads have high numbers of mitochondria and glycogen deposits, which suggests that they have a high metabolic activity. Dendritic tips are not associated with beads, arise from the terminals of smaller dendrites, and are embedded in the extracellular ground matrix of the connective tissue strand, where they lie parallel to and surround bundles of elastic fibrils. The different degree of development within the receptor series allows comparison between functionally different limbs, and comparison is made with other segmental receptor series. The evolution of multiterminal proprioceptors is discussed.}, }
@article {pmid7752884, year = {1995}, author = {Gupta, RS}, title = {Evolution of the chaperonin families (Hsp60, Hsp10 and Tcp-1) of proteins and the origin of eukaryotic cells.}, journal = {Molecular microbiology}, volume = {15}, number = {1}, pages = {1-11}, doi = {10.1111/j.1365-2958.1995.tb02216.x}, pmid = {7752884}, issn = {0950-382X}, mesh = {Amino Acid Sequence ; Bacteria/chemistry/*genetics ; *Biological Evolution ; Cell Nucleus ; Chaperonin 10/chemistry/genetics ; Chaperonin 60/chemistry/genetics ; *Chaperonins/chemistry/genetics ; Chloroplasts/genetics ; *Eukaryotic Cells ; *Intracellular Signaling Peptides and Proteins ; *Microtubule-Associated Proteins ; Mitochondria/genetics ; Molecular Sequence Data ; Nuclear Proteins/chemistry/genetics ; Phylogeny ; Sequence Alignment ; Ubiquitin-Protein Ligases ; t-Complex Genome Region ; }, abstract = {The members of the 10 kDa and 60 kDa heat-shock chaperonin proteins (Hsp10 and Hsp60 or Cpn10 and Cpn60), which form an operon in bacteria, are present in all eubacteria and eukaryotic cell organelles such as mitochondria and chloroplasts. In archaebacteria and eukaryotic cell cytosol, no close homologues of Hsp10 or Hsp60 have been identified. However, these species (or cell compartments) contain the Tcp-1 family of proteins (distant homologues of Hsp60). Phylogenetic analysis based on global alignments of Hsp60 and Hsp10 sequences presented here provide some evidence regarding the evolution of mitochondria from a member of the alpha-subdivision of Gram-negative bacteria and chloroplasts from cyanobacterial species, respectively. This interference is strengthened by the presence of sequence signatures that are uniquely shared between Hsp60 homologues from alpha-purple bacteria and mitochondria on one hand, and the chloroplasts and cyanobacterial hsp60s on the other. Within the alpha-purple subdivision, species such as Rickettsia and Ehrlichia, which live intracellularly within eukaryotic cells, are indicated to be the closest relatives of mitochondrial homologues. In the Hsp60 evolutionary tree, rooted using the Tcp-1 homologue, the order of branching of the major groups was as follows: Gram-positive bacteria--cyanobacteria and chloroplasts--chlamydiae and spirochaetes--beta- and gamma-Gram-negative purple bacteria--alpha-purple bacteria--mitochondria. A similar branching order was observed independently in the Hsp10 tree. Multiple Hsp60 homologues, when present in a group of species, were found to be clustered together in the trees, indicating that they evolved by independent gene-duplication events. This review also considers in detail the evolutionary relationship between Hsp60 and Tcp-1 families of proteins based on two different models (viz. archaebacterial and chimeric) for the origin of eukaryotic cell nucleus. Some predictions of the chimeric model are also discussed.}, }
@article {pmid7735141, year = {1995}, author = {el Kebbaj, MH and Cherkaoui Malki, M and Latruffe, N}, title = {Effect of peroxisomes proliferators and hypolipemic agents on mitochondrial inner membrane linked D-3-hydroxybutyrate dehydrogenase (BDH).}, journal = {Biochemistry and molecular biology international}, volume = {35}, number = {1}, pages = {65-77}, pmid = {7735141}, issn = {1039-9712}, mesh = {2,4-Dichlorophenoxyacetic Acid/pharmacology ; Animals ; Binding, Competitive ; Clofibrate/analogs &amp; derivatives/pharmacology ; Clofibric Acid/analogs &amp; derivatives/pharmacology ; Fenofibrate/pharmacology ; Fibric Acids ; Hydroxybutyrate Dehydrogenase/*drug effects/metabolism ; Hypolipidemic Agents/*pharmacology ; In Vitro Techniques ; Intracellular Membranes/*enzymology ; Male ; Microbodies/*physiology ; Mitochondria/*enzymology/ultrastructure ; Mitochondria, Liver/enzymology/ultrastructure ; Phospholipids/pharmacology ; Rats ; Rats, Wistar ; Tetrahymena pyriformis/enzymology ; }, abstract = {1. D-3-hydroxybutyrate dehydrogenase EC 1.1.1.30 (BDH) activity was measured in mitochondria of rats submitted to an intermittent feeding treatment with ciprofibrate or fenofibrate, i.e. fibrate analogues with hypolipemic activity and peroxisome proliferation properties. Our data shows an inhibition of rat liver mitochondrial BDH activity. This inhibitory effect is abolished when the treatment is stopped and reappears after a second treatment. 2. Incubation of hypolipemic agents (ciprofibrate, clofibrate, clobuzarit, fenofibrate or 2,4 dichlorophenoxyacetic acid) with submitochondrial linked BDH leads to an inhibition in a concentration dependent manner. 3. The protection by NAD(H) (coenzymes) and by methyl-malonate (a substrate analogue and competitive inhibitor) indicates that the inhibition occurs in the active site. On the other hand, there is a strong protection by phospholipid vesicles. This trapping effect may be attributed to lipophilic properties of hypolipemic agents. 4. Comparative effect of hypolipemic agents on mitochondrial BDH activity from rat liver and from Tetrahymena pyriformis indicates the same inhibition and same protection effects. This supports conservation of the enzymatic properties according to the evolution.}, }
@article {pmid7714914, year = {1995}, author = {Arnason, U and Bodin, K and Gullberg, A and Ledje, C and Mouchaty, S}, title = {A molecular view of pinniped relationships with particular emphasis on the true seals.}, journal = {Journal of molecular evolution}, volume = {40}, number = {1}, pages = {78-85}, pmid = {7714914}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; Cytochrome b Group/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Seals, Earless/*genetics ; Sequence Analysis ; }, abstract = {Phylogenetic analysis of conservative nucleotide substitutions in 18 complete sequences of the mitochondrial cytochrome b gene of Phocidae (true seals), Odobenidae (walruses), and Otariidae (sea lions and fur seals), plus three ursid and three felid sequences, identified the pinnipeds as monophyletic with Otariidae and Odobenidae on a common evolutionary branch. Analysis of total nucleotide differences separated the evolutionary lineages of northern and southern phocids. Both lineages are distinct from the most ancestral phocid genus, Monachus (monk seals), represented by the Hawaiian monk seal. The inclusion of the Hawaiian monk seal in the subfamily Monachinae makes the subfamily paraphyletic. Among the northern phocids, the hooded seal (genus Cystophora, chromosome number 2n = 34) is sister taxon to the Phoca complex. The Phoca complex, which is characterized by the chromosome number 2n = 32, includes genus Phoca and the monotypic genus Halichoerus (grey seal). The comparison does not support a generic distinction of Halichoerus within the Phoca complex. The present data suggest that Cystophora and Phoca separated > or = 6 million years ago. Among the southern phocids the close molecular relationship of the Weddell and leopard seals relative to their morphological distinction exemplifies rapid adaptation to different ecological niches. This result stands in contrast to the limited morphological differentiation relative to the pronounced molecular distinctions that may occur within the Phoca complex.}, }
@article {pmid7703887, year = {1995}, author = {Kogan, AKh and Grachev, SV and Eliseeva, SV}, title = {[Carbon dioxide gas and generation of active forms of oxygen by cells from various tissues and mitochondria. (To decipher one of the mysteries of evolution)].}, journal = {Doklady Akademii nauk}, volume = {340}, number = {1}, pages = {132-134}, pmid = {7703887}, issn = {0869-5652}, mesh = {Animals ; Brain/cytology/drug effects/metabolism ; Carbon Dioxide/*pharmacology ; Cells, Cultured ; Heart/drug effects ; Mice ; Mitochondria, Liver/*drug effects/metabolism ; Muscle, Skeletal/cytology/drug effects/metabolism ; Myocardium/cytology/metabolism ; Pyloric Antrum/cytology/drug effects/metabolism ; Superoxides/*metabolism ; }, }
@article {pmid7599280, year = {1995}, author = {Yu, W and Fester, T and Bock, H and Schuster, W}, title = {RNA editing in higher plant mitochondria: analysis of biochemistry and specificity.}, journal = {Biochimie}, volume = {77}, number = {1-2}, pages = {79-86}, doi = {10.1016/0300-9084(96)88108-9}, pmid = {7599280}, issn = {0300-9084}, mesh = {Biological Evolution ; Cytidine/metabolism ; Mitochondria/*genetics/metabolism ; Plants/*genetics/metabolism ; RNA Editing/*genetics ; RNA, Messenger/metabolism ; RNA, Plant/genetics/*metabolism ; Transcription, Genetic/genetics ; }, abstract = {RNA editing alters genomically encoded cytidines to uridines posttranscriptionally in higher plant mitochondria. Most of these editing events occur in translated regions and consequently alter the amino acid sequence. In Oenothera berteriana more than 500 editing sites have been detected and the total number of editing sites exceeds 1000 sites in this mitochondrial genome. To identify the components involved in this process we investigated the factors determining the specificity of RNA editing and the apparent conversion of cytidine to uridine residues. The possible biochemical reactions responsible for RNA editing in plant mitochondria are de- or transamination, base substitution and nucleotide replacement. In order to discriminate between these different biochemical mechanisms we followed the fate of the sugar-phosphate backbone by analysing radiolabeled nucleotides after incorporation into high molecular mass RNA. Plant mitochondria were supplied with [alpha-32P]CTP to radiolabel CMP residues in newly synthesized transcripts. Radiolabeled mtRNA was extracted and digested with nuclease P1 to hydrolyse the RNA to monophosphates. The resulting monophosphates were analysed on one- and two-dimensional TLC systems to separate pC from pU. Radiolabeled pU was detected in increasing quantities during the course of incubation. These results suggest that RNA editing in plant mitochondria involves either a deamination or a transglycosylation reaction. The editing product was identified as uridine and not as a hypermodified nucleotide which is recognized as uridine. Similar results have been obtained by incubating in vitro transcribed mRNAs with mitochondrial lysates indicating that RNA editing and transcription is not directly linked in plant mitochondria.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid7529407, year = {1994}, author = {Watanabe, Y and Kawai, G and Yokogawa, T and Hayashi, N and Kumazawa, Y and Ueda, T and Nishikawa, K and Hirao, I and Miura, K and Watanabe, K}, title = {Higher-order structure of bovine mitochondrial tRNA(SerUGA): chemical modification and computer modeling.}, journal = {Nucleic acids research}, volume = {22}, number = {24}, pages = {5378-5384}, pmid = {7529407}, issn = {0305-1048}, mesh = {Alkylating Agents ; Animals ; Anticodon/chemistry ; Base Sequence ; Cattle ; *Computer Simulation ; Diethyl Pyrocarbonate ; Mitochondria/*chemistry ; Models, Molecular ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Phylogeny ; RNA/*chemistry ; RNA, Mitochondrial ; RNA, Transfer, Ser/*chemistry/genetics ; Sequence Alignment ; Sulfuric Acid Esters ; }, abstract = {On the basis of enzymatic probing and phylogenetic comparison, we have previously proposed that mammalian mitochondrial tRNA(sSer) (anticodon UGA) possess a slightly altered cloverleaf structure in which only one nucleotide exists between the acceptor stem and D stem (usually two nucleotides) and the anticodon stem consists of six base pairs (usually five base pairs) [Yokogawa et al. (1991) Nucleic Acids Res. 19, 6101-6105]. To ascertain whether such tRNA(sSer) can be folded into a normal L-shaped tertiary structure, the higher-order structure of bovine mitochondrial tRNA(SerUGA) was examined by chemical probing using dimethylsulfate and diethylpyrocarbonate, and on the basis of the results a tertiary structure model was obtained by computer modeling. It was found that a one-base-pair elongation in the anticodon stem was compensated for by multiple-base deletions in the D and extra loop regions of the tRNA(SerUGA), which resulted in preservation of an L-shaped tertiary structure similar to that of conventional tRNAs. By summarizing the findings, the general structural requirements of mitochondrial tRNAs necessary for their functioning in the mitochondrial translation system are considered.}, }
@article {pmid7881821, year = {1994}, author = {Yang, SY}, title = {The large subunit of the pig heart mitochondrial membrane-bound beta-oxidation complex is a long-chain enoyl-CoA hydratase: 3-hydroxyacyl-CoA dehydrogenase bifunctional enzyme.}, journal = {Comparative biochemistry and physiology. Part B, Biochemistry &amp; molecular biology}, volume = {109}, number = {4}, pages = {557-566}, doi = {10.1016/0305-0491(94)90117-1}, pmid = {7881821}, issn = {1096-4959}, support = {DK 47392/DK/NIDDK NIH HHS/United States ; }, mesh = {3-Hydroxyacyl CoA Dehydrogenases/*isolation &amp; purification/metabolism ; Amino Acid Sequence ; Animals ; Cell Membrane ; Enoyl-CoA Hydratase/*isolation &amp; purification/metabolism ; Mitochondria, Heart/*enzymology ; Molecular Sequence Data ; Multienzyme Complexes/*chemistry/metabolism ; Phylogeny ; Sequence Alignment ; Swine ; }, abstract = {The subunit locations of the component enzymes of the pig heart trifunctional mitochondrial beta-oxidation complex are suggested by analyzing the primary structure of the large subunit of this membrane-bound multienzyme complex [Yang S.-Y. et al. (1994) Biochem. biophys. Res. Commun. 198, 431-437] with those of the subunits of the E. coli fatty acid oxidation complex and the corresponding mitochondrial matrix beta-oxidation enzymes. Long-chain enoyl-CoA hydratase and long-chain 3-hydroxyacyl-CoA dehydrogenase are located in the amino-terminal and the central regions of the 79 kDa polypeptide, respectively, whereas the long-chain 3-ketoacyl-CoA thiolase is associated with the 46 kDa subunit of this complex. The pig heart mitochondrial bifunctional beta-oxidation enzyme is more homologous to the large subunit of the prokaryotic fatty acid oxidation complex than to the peroxisomal trifunctional beta-oxidation enzyme. The evolutionary trees of 3-hydroxyacyl-CoA dehydrogenases and enoyl-CoA hydratases suggest that the mitochondrial inner membrane-bound bifunctional beta-oxidation enzyme and the corresponding matrix monofunctional beta-oxidation enzymes are more remotely related to each other than to their corresponding prokaryotic enzymes, and that the genes of E. coli multifunctional fatty acid oxidation protein and pig heart mitochondrial bifunctional beta-oxidation enzyme diverged after the appearance of eukaryotic cells.}, }
@article {pmid7721722, year = {1994}, author = {Papa, S and Lorusso, M and Capitanio, N}, title = {Mechanistic and phenomenological features of proton pumps in the respiratory chain of mitochondria.}, journal = {Journal of bioenergetics and biomembranes}, volume = {26}, number = {6}, pages = {609-618}, pmid = {7721722}, issn = {0145-479X}, mesh = {Animals ; Electron Transport Complex IV/metabolism ; Kinetics ; Mitochondria/*metabolism ; Models, Biological ; NADH Dehydrogenase/metabolism ; *Oxygen Consumption ; Proton Pumps/*metabolism ; Thermodynamics ; }, abstract = {Various direct, indirect (kinetic and thermodynamic), and combined mechanisms have been proposed to explain the conversion of redox energy into a transmembrane protonmotive force (delta p) by enzymatic complexes of respiratory chains. The conceptual evolution of these models is examined. The characteristics of thermodynamic coupling between redox transitions of electron carriers and scalar proton transfer in cytochrome c oxidase and its possible involvement in proton pumping is discussed. Other aspects dealt with in this paper are: (i) variability of <--H+/e- stoichiometries, in cytochrome c oxidase and cytochrome c reductase and its mechanistic implications; (ii) possible models by which the reduction of dioxygen to water at the binuclear heme-copper center of protonmotive oxidases can be directly involved in proton pumping. Finally a unifying concept for proton pumping by the redox complexes of respiratory chain is presented.}, }
@article {pmid7704116, year = {1994}, author = {Van Syoc, RJ}, title = {Genetic divergence between subpopulations of the eastern Pacific goose barnacle Pollicipes elegans: mitochondrial cytochrome c subunit 1 nucleotide sequences.}, journal = {Molecular marine biology and biotechnology}, volume = {3}, number = {6}, pages = {338-346}, pmid = {7704116}, issn = {1053-6426}, mesh = {Animals ; Base Sequence ; Cytochrome c Group/chemistry/*genetics ; DNA, Mitochondrial ; *Genetic Variation ; Mitochondria/*enzymology ; Molecular Sequence Data ; Phylogeny ; Thoracica/*genetics ; }, abstract = {Nucleotide sequence data derived from polymerase chain reaction products from the cytochrome oxidase subunit 1 gene of mitochondrial DNA provide evidence for interrupted gene flow and subsequent genetic divergence between geographically separate subpopulations of the edible goose barnacle, Pollicipes elegans, with a 4400-km latitudinal distribution in the eastern Pacific Ocean. The amphitropical subpopulations of Pollicipes elegans have a net nucleotide sequence divergence of about 1.2%. A range of mutation rates are applied to calculate estimates for the timing of this divergence. The earliest estimated time of divergence agrees with a Pliocene time of general warming in the eastern Pacific. The latest estimated times coincide with the Pleistocene epoch and periods of cooling and warming that could have allowed for a series of expansions and contractions of P. elegans populations in the eastern tropical Pacific. These expansions and contractions may, therefore, represent alternating periods of genetic exchange and isolation of the two populations.}, }
@article {pmid7528811, year = {1994}, author = {Okimoto, R and Macfarlane, JL and Wolstenholme, DR}, title = {The mitochondrial ribosomal RNA genes of the nematodes Caenorhabditis elegans and Ascaris suum: consensus secondary-structure models and conserved nucleotide sets for phylogenetic analysis.}, journal = {Journal of molecular evolution}, volume = {39}, number = {6}, pages = {598-613}, pmid = {7528811}, issn = {0022-2844}, support = {GM-18375/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Ascaris suum/*genetics ; Base Composition ; Base Sequence ; Caenorhabditis elegans/*genetics ; *Consensus Sequence ; *Conserved Sequence ; Mitochondria/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/*genetics ; Sequence Alignment ; }, abstract = {The small- and large-subunit mitochondrial ribosomal RNA genes (mt-s-rRNA and mt-l-rRNA) of the nematode worms Caenorhabditis elegans and Ascaris suum encode the smallest rRNAs so far reported for metazoa. These size reductions correlate with the previously described, smaller, structurally anomalous mt-tRNAs of C. elegans and A. suum. Using primer extension analysis, the 5' end nucleotides of the mt-s-rRNA and mt-l-rRNA genes were determined to be adjacent to the 3' end nucleotides of the tRNA(Glu) and tRNA(His) genes, respectively. Detailed, consensus secondary-structure models were constructed for the mt-s-rRNA genes and the 3' 64% of mt-l-rRNA genes of the two nematodes. The mt-s-rRNA secondary-structure model bears a remarkable resemblance to the previously defined universal core structure of E. coli 16S rRNA: most of the nucleotides that have been classified as variable or semiconserved in the E. coli model appear to have been eliminated from the C. elegans and A. suum sequences. Also, the secondary structure model constructed for the 3' 64% of the mt-l-rRNA is similar to the corresponding portion of the previously defined E. coli 23S rRNA core secondary structure. The proposed C. elegans/A. suum mt-s-rRNA and mt-l-rRNA models include all of the secondary-structure element-forming sequences that in E. coli rRNAs contain nucleotides important for A-site and P-site (but not E-site) interactions with tRNAs. Sets of apparently homologous sequences within the mt-s-rRNA and mt-l-rRNA core structures, derived by alignment of the C. elegans and A. suum mt-rRNAs to the corresponding mt-rRNAs of other eukaryotes, and E. coli rRNAs were used in maximum-likelihood analyses. The patterns of divergence of metazoan phyla obtained show considerable agreement with the most prevalent metazoan divergence patterns derived from more classical, morphological, and developmental data.}, }
@article {pmid7528198, year = {1994}, author = {Falah, M and Gupta, RS}, title = {Cloning of the hsp70 (dnaK) genes from Rhizobium meliloti and Pseudomonas cepacia: phylogenetic analyses of mitochondrial origin based on a highly conserved protein sequence.}, journal = {Journal of bacteriology}, volume = {176}, number = {24}, pages = {7748-7753}, pmid = {7528198}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Burkholderia cepacia/classification/*genetics ; Chloroplasts/genetics ; Cloning, Molecular ; Conserved Sequence ; Cyanobacteria/genetics ; *Escherichia coli Proteins ; Genes, Bacterial/*genetics ; Gram-Negative Bacteria/classification/genetics ; HSP70 Heat-Shock Proteins/*genetics ; Mitochondria/genetics ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Sinorhizobium meliloti/classification/*genetics ; }, abstract = {The genes for hsp70 (or dnaK) have been cloned and sequenced from Rhizobium meliloti and Pseudomonas cepacia, two bacterial species belonging to the alpha- and beta-subdivisions of gram-negative proteobacteria, respectively. On the basis of global alignment of HSP70 proteins, several sequence signatures have been identified that are distinctive of mitochondrial homologs and gram-negative proteobacteria on the one hand and the chloroplasts and cyanobacteria on the other. Detailed phylogenetic analyses of HSP70 sequences from various eubacteria and eukaryotic organellar and cytosolic homologs support the inference regarding the origin of mitochondria from a member of the alpha-proteobacteria and of chloroplasts from cyanobacteria. The analysis presented here also suggests a monophyletic origin of the mitochondrial homologs.}, }
@article {pmid7961755, year = {1994}, author = {Saito, K and Tatsuguchi, K and Takagi, Y and Murakoshi, I}, title = {Isolation and characterization of cDNA that encodes a putative mitochondrion-localizing isoform of cysteine synthase (O-acetylserine(thiol)-lyase) from Spinacia oleracea.}, journal = {The Journal of biological chemistry}, volume = {269}, number = {45}, pages = {28187-28192}, pmid = {7961755}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Cysteine Synthase/*biosynthesis/genetics ; DNA Primers ; DNA, Complementary/isolation &amp; purification/metabolism ; Escherichia coli/enzymology ; Genetic Complementation Test ; Isoenzymes/*biosynthesis ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Recombinant Proteins/biosynthesis/genetics ; Sequence Homology, Amino Acid ; Spinacia oleracea/*enzymology ; }, abstract = {The cDNA clones that encode a putative mitochondrion-localizing isoform of cysteine synthase (O-acetyl-L-serine(thiol)-lyase, O-acetyl-L-serine acetate-lyase (adding hydrogen sulfide), EC 4.2.99.8), which is denoted as cysteine synthase C, were isolated from spinach (Spinacia oleracea L.). The cDNA encodes a polypeptide of 368 amino acids containing a putative transit peptide of 30-40 amino acids at the N terminus. This leader peptide sequence exhibited several structural features common to other mitochondrion-targeting transit peptides. Homology was also detected between the putative transit peptide sequence of cysteine synthase C and other mitochondrion-targeting leader sequences. A deduced amino acid sequence of cysteine synthase C exhibited a homology of 61% with cytoplasmic isoform A and 63% with chloroplastic isoform B. A bacterial expression vector of the cDNA clone could genetically complement an Escherichia coli auxotroph lacking cysteine synthase loci and could produce the functionally active and immunoreactive cysteine synthase in E. coli. DNA blot hybridization analysis showed the presence of one or two copies of cysC gene in the genome of spinach. RNA blot hybridization analysis indicated that the expression level of cysC gene was lower than those of cysA and cysB and that the mode of cysC expression was constitutive in green and etiolated seedlings of spinach. The molecular evolutionary study of cysteine synthase proteins from plants and bacteria suggested that a common ancestor cysteine synthase gene has evolved into five cysteine synthase gene families, plant isoform A family, plant isoform B family, plant isoform C family, bacterial cysK family, and bacterial cysM family.}, }
@article {pmid7971961, year = {1994}, author = {Shigenaga, MK and Hagen, TM and Ames, BN}, title = {Oxidative damage and mitochondrial decay in aging.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {91}, number = {23}, pages = {10771-10778}, pmid = {7971961}, issn = {0027-8424}, support = {CA39910/CA/NCI NIH HHS/United States ; ESO1896/ES/NIEHS NIH HHS/United States ; }, mesh = {*Aging ; Animals ; DNA, Mitochondrial/chemistry ; Electron Transport ; Energy Metabolism ; Humans ; Hydrogen Peroxide/metabolism ; Immune System/metabolism ; Intracellular Membranes/chemistry ; Lipids/chemistry ; Longevity ; Mitochondria/*physiology ; Mutation ; Neurons/metabolism ; Oxidation-Reduction ; Phylogeny ; Proteins/chemistry ; Superoxides/metabolism ; }, abstract = {We argue for the critical role of oxidative damage in causing the mitochondrial dysfunction of aging. Oxidants generated by mitochondria appear to be the major source of the oxidative lesions that accumulate with age. Several mitochondrial functions decline with age. The contributing factors include the intrinsic rate of proton leakage across the inner mitochondrial membrane (a correlate of oxidant formation), decreased membrane fluidity, and decreased levels and function of cardiolipin, which supports the function of many of the proteins of the inner mitochondrial membrane. Acetyl-L-carnitine, a high-energy mitochondrial substrate, appears to reverse many age-associated deficits in cellular function, in part by increasing cellular ATP production. Such evidence supports the suggestion that age-associated accumulation of mitochondrial deficits due to oxidative damage is likely to be a major contributor to cellular, tissue, and organismal aging.}, }
@article {pmid7883436, year = {1994}, author = {Watson, NA and Rohde, K}, title = {Ultrastructure of sperm and spermiogenesis in the monocotylid monogeneans Monocotyle helicophallus and Calicotyle australiensis (Platyhelminthes).}, journal = {International journal for parasitology}, volume = {24}, number = {7}, pages = {1019-1030}, doi = {10.1016/0020-7519(94)90168-6}, pmid = {7883436}, issn = {0020-7519}, mesh = {Animals ; Cell Nucleus/ultrastructure ; Male ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Models, Structural ; Phylogeny ; Platyhelminths/*classification/*ultrastructure ; Sperm Tail/ultrastructure ; Spermatids/ultrastructure ; *Spermatogenesis ; Spermatozoa/*ultrastructure ; }, abstract = {Spermiogenesis in Monocotyle helicophallus involves formation of free flagella which rotate to lie parallel before fusing. There is no median cytoplasmic process. A small number of microtubules (usually 2-4) is associated with the axonemes in the zone of differentiation. Nucleus and a fused mitochondrion migrate alongside the axonemes and one basal body moves distally. A coil of nucleus, originally in the cytophore, also moves out along the shaft. The mature spermatozoan has only a single axoneme for a short distance at each end, with two associated microtubules at the proximal end, as well as one axoneme, nucleus and mitochondrion throughout most of its length (the nucleus being enlarged and roughly coiled in one region), and a short region of two overlapping axonemes. We interpret our findings as two axonemes arranged almost end to end, one extending from the proximal end to some point in the mid-region, where the second axoneme begins and continues to the distal end of the sperm. Spermatozoa of Calicotyle australiensis develop from a zone of differentiation which has two basal bodies and a complete ring of cortical microtubules. Two initially free axonemes fuse with each other and there is no median cytoplasmic process. Spermatids form within parallel canals in the cytophore, by backward movement of the zone of differentiation. Prior to detachment, an electron-dense spiral end-piece forms around and proximal to the basal body region. Sixty-four spermatids are present in each isogenic group. With the study of spermiogenesis in more species of Monogenea Monopisthocotylea, it is apparent that the previously designated sperm patterns 2 and 3 are not distinct and should be combined and re-defined. Species previously designated as having sperm patterns 2 and 3 can all be accommodated by the description "two normal axonemes or one normal and one shortened, altered or displaced axoneme, and none, one or a few cortical microtubules remaining in a region of the sperm derived from the zone of differentiation in which a few or a complete ring of microtubules was present".}, }
@article {pmid7874746, year = {1994}, author = {Watanabe, N and Nakazono, M and Kanno, A and Tsutsumi, N and Hirai, A}, title = {Evolutionary variations in DNA sequences transferred from chloroplast genomes to mitochondrial genomes in the Gramineae.}, journal = {Current genetics}, volume = {26}, number = {5-6}, pages = {512-518}, pmid = {7874746}, issn = {0172-8083}, mesh = {Base Sequence ; *Biological Evolution ; Chloroplasts/*metabolism ; DNA Primers ; DNA, Mitochondrial/genetics/metabolism ; DNA, Plant/genetics/*metabolism ; *Genetic Variation ; Genomic Library ; Mitochondria/*metabolism ; Molecular Sequence Data ; Open Reading Frames ; Oryza/genetics ; Plants/*genetics/metabolism ; Poaceae/genetics ; Polymerase Chain Reaction ; Recombination, Genetic ; Secale/genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; Zea mays/genetics ; }, abstract = {The transfer of fragments of DNA from chloroplast genomes to mitochondrial genomes is considered to be a general phenomenon in higher plants. In the present study, Southern hybridization, together with amplification by PCR and DNA sequencing techniques, was used to examine the regions homologous to chloroplast rps19 in the mitochondrial genomes of several gramineous plants. In all the mitochondrial DNAs from the gramineous plants examined, except for that from wheat, the transferred fragments of chloroplast DNA were found to be maintained and the same junctions of mitochondrion-specific and chloroplast-like sequences were found at one terminus. This finding indicates that the transfer of the chloroplast sequence occurred in the distant past during the evolution of gramineous plants. Subsequent analysis revealed that the fragments had been variously rearranged among species with respect to the other terminus. Considering the current diversity of this one particular transferred fragment of chloroplast DNA, we propose that chloroplast-derived DNA sequences that have lost their original functions tend to be rearranged during evolution in mitochondrial genomes.}, }
@article {pmid7855299, year = {1994}, author = {Hasegawa, M and Cao, Y and Adachi, J}, title = {[Phylogenetic evolution of eutheria as viewed from molecules].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {39}, number = {15}, pages = {2751-2758}, pmid = {7855299}, issn = {0039-9450}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Cytochrome b Group/chemistry/genetics ; DNA, Mitochondrial ; *Mammals ; Mitochondria ; *Phylogeny ; }, }
@article {pmid7855291, year = {1994}, author = {Ishikawa, H}, title = {[The symbiosis theory and evolution of eukaryotic cells].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {39}, number = {15}, pages = {2671-2681}, pmid = {7855291}, issn = {0039-9450}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; *Eukaryotic Cells ; Genome ; Humans ; Mitochondria ; Phylogeny ; RNA, Ribosomal ; *Symbiosis ; }, }
@article {pmid7815925, year = {1994}, author = {Bargelloni, L and Ritchie, PA and Patarnello, T and Battaglia, B and Lambert, DM and Meyer, A}, title = {Molecular evolution at subzero temperatures: mitochondrial and nuclear phylogenies of fishes from Antarctica (suborder Notothenioidei), and the evolution of antifreeze glycopeptides.}, journal = {Molecular biology and evolution}, volume = {11}, number = {6}, pages = {854-863}, doi = {10.1093/oxfordjournals.molbev.a040168}, pmid = {7815925}, issn = {0737-4038}, mesh = {Animals ; Antarctic Regions ; Antifreeze Proteins ; *Biological Evolution ; Cell Nucleus/metabolism ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/*genetics ; Fishes/*genetics ; Freezing ; Glycoproteins/*genetics ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Software ; }, abstract = {Most fishes of the perciform suborder Notothenioidei are endemic to the subzero marine waters of Antarctica. A number of remarkable physiological attributes allow them to inhabit this extreme environment; for example, the blood of almost all notothenioid species contains antifreeze glycopeptides. To establish a molecular phylogenetic hypothesis for these fishes, DNA sequences from two mitochondrial genes, portions of the 12S and 16S ribosomal genes (928 base pairs [bp]), were determined for 18 species. These belong to 15 genera in five families of the suborder. The DNA data suggest that two of these families are unnatural groups and consequently that the classification and phylogeny of this suborder is in need of revision. In terms of DNA variation, the Bovichtidae are a distantly related sister group to the other families of the suborder that includes the icefishes, the only vertebrates without hemoglobin. The fishes of the suborder (except the Bovichtidae) seem to have speciated rapidly, forming an adaptive radiation in the Antarctic waters. A phylogenetic analysis of published hemoglobin amino acid sequences for other notothenioid fishes supports these results from mtDNA. On the basis of molecular phylogeny, the evolution of antifreeze glycopeptides was studied. The age of the radiation of notothenioid fishes had been estimated to be at least 38 Mya. However, the level of mtDNA variation detected in notothenioid fishes appears to be too low to agree with this date of origin and might instead suggest a younger age (10-15 Mya). Alternatively, the low level of detected mtDNA variation would agree with the traditional old-age estimate if an extremely slow rate of mtDNA evolution is postulated for this group. This slow-rate hypothesis, if true, could be explained by decreased metabolic rates slowing down the tempo of molecular evolution.}, }
@article {pmid7807540, year = {1994}, author = {Cao, Y and Adachi, J and Janke, A and Pääbo, S and Hasegawa, M}, title = {Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: instability of a tree based on a single gene.}, journal = {Journal of molecular evolution}, volume = {39}, number = {5}, pages = {519-527}, pmid = {7807540}, issn = {0022-2844}, mesh = {Animals ; Artiodactyla/classification/genetics ; Carnivora/classification/genetics ; Genes/genetics ; Humans ; Likelihood Functions ; Mammals/*classification/*genetics ; Mitochondria/*genetics ; *Models, Genetic ; Opossums/classification/genetics ; Phylogeny ; Proteins/genetics ; Rodentia/classification/genetics ; Sequence Analysis/*methods ; }, abstract = {The phylogenetic relationships among Primates (human), Artiodactyla (cow), Cetacea (whale), Carnivora (seal), and Rodentia (mouse and rat) were estimated from the inferred amino acid sequences of the mitochondrial genomes using Marsupialia (opossum), Aves (chicken), and Amphibia (Xenopus) as an outgroup. The overall evidence of the maximum likelihood analysis suggests that Rodentia is an outgroup to the other four eutherian orders and that Cetacea and Artiodactyla form a clade with Carnivora as a sister taxon irrespective of the assumed model for amino acid substitutions. Although there remains an uncertainty concerning the relation among Artiodactyla, Cetacea, and Carnivora, the existence of a clade formed by these three orders and the outgroup status of Rodentia to the other eutherian orders seems to be firmly established. However, analyses of individual genes do not necessarily conform to this conclusion, and some of the genes reject the putatively correct tree with nearly 5% significance. Although this discrepancy can be due to convergent or parallel evolution in the specific genes, it was pointed out that, even without a particular reason, such a discrepancy can occur in 5% of the cases if the branching among the orders in question occurred within a short period. Due to uncertainty about the assumed model underlying the phylogenetic inference, this can occur even more frequently. This demonstrates the importance of analyzing enough sequences to avoid the danger of concluding an erroneous tree.}, }
@article {pmid7755710, year = {1994}, author = {Milinkovitch, MC and Meyer, A and Powell, JR}, title = {Phylogeny of all major groups of cetaceans based on DNA sequences from three mitochondrial genes.}, journal = {Molecular biology and evolution}, volume = {11}, number = {6}, pages = {939-948}, doi = {10.1093/oxfordjournals.molbev.a040164}, pmid = {7755710}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Cetacea/classification/*genetics ; DNA Primers ; DNA, Mitochondrial/*genetics ; Mitochondria/metabolism ; Mitochondria, Liver/metabolism ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Skin/metabolism ; Spleen/metabolism ; }, abstract = {Traditionally, living cetaceans (order Cetacea) are classified into two highly distinct suborders: the echolocating toothed whales, Odontoceti, and the filter-feeding baleen whales, Mysticeti. A molecular phylogeny based on 1,352 base pairs of two mitochondrial ribosomal gene segments and the mitochondrial cytochrome b gene for all major groups of cetaceans contradicts this long-accepted taxonomic subdivision. One group of toothed whales, the sperm whales, is more closely related to the morphologically highly divergent baleen whales than to other odontocetes. This finding suggests that the suborder Odontoceti constitutes an unnatural grouping and challenges the conventional scenario of a long, independent evolutionary history of odontocetes and mysticetes. The superfamily Delphinoidea (dolphins, porpoises, and white whales) appears to be monophyletic; the Amazon River dolphin, Inia geoffrensis, is its sister species. This river dolphin is genetically more divergent from the morphologically similar marine dolphins than the sperm whales are from the morphologically dissimilar baleen whales. The phylogenetic relationships among the three families of Delphinoidea remain uncertain, and we suggest that the two cladogenetic events that generated these three clades occurred within a very short period of time. Among the baleen whales, the bowhead is basal, and the gray whale is the sister species to the rorquals (family Balaenopteridae). The phylogenetic position of beaked whales (Ziphioidea) remains weakly supported by molecular data. Based on molecular clock assumptions, the mitochondrial-DNA data suggest a more recent origin of baleen whales (approximately 25 mya) than has been previously assumed (> 40 mya). This revised phylogeny has important implications for the rate and mode of evolution of morphological and physiological innovations in cetaceans.}, }
@article {pmid7531858, year = {1994}, author = {Ueda, T and Yokobori, S and Watanabe, K}, title = {[Origin and evolution of genetic code: an idea on the mechanism of emergence of unusual genetic codes].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {39}, number = {15}, pages = {2427-2437}, pmid = {7531858}, issn = {0039-9450}, mesh = {Animals ; Anticodon ; Base Sequence ; *Biological Evolution ; DNA, Mitochondrial/genetics ; *Genetic Code ; *Genome ; Humans ; Mitochondria ; Molecular Sequence Data ; RNA/genetics ; RNA, Mitochondrial ; }, }
@article {pmid7525275, year = {1994}, author = {Lukes, J and Arts, GJ and van den Burg, J and de Haan, A and Opperdoes, F and Sloof, P and Benne, R}, title = {Novel pattern of editing regions in mitochondrial transcripts of the cryptobiid Trypanoplasma borreli.}, journal = {The EMBO journal}, volume = {13}, number = {21}, pages = {5086-5098}, pmid = {7525275}, issn = {0261-4189}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Consensus Sequence ; Cytochrome b Group/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; Genes, Protozoan/genetics ; Kinetoplastida/classification/genetics ; Mitochondria/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA/*genetics ; *RNA Editing ; RNA, Messenger/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Trypanosoma/classification/*genetics ; }, abstract = {In mitochondria of Kinetoplastida belonging to the suborder Trypanosomatina, the nucleotide sequence of transcripts is post-transcriptionally edited via insertion and deletion of uridylate residues. In order to shed more light on the evolutionary history of this process we have searched for editing in mitochondrial RNAs of Trypanoplasma borreli, an organism belonging to the suborder Bodonina. We have cloned and sequenced a 5.3 kb fragment derived from a 37 kb mitochondrial DNA molecule which does not appear to be a part of a network structure and have found genes encoding cytochrome c oxidase (cox) subunit 1, cox 2 and apocytochrome (cyt) b, and genes encoding the small and large subunit mitoribosomal RNAs. The order in which these genes occur is completely different from that of trypanosomatid maxicircle genes. The 5' and 3' termini of both the cytb and cox1 gene are cryptic, the protein coding sequences being created by extensive insertion/deletion of Us in the corresponding mRNA sections. Phylogenetic analyses of the protein and ribosomal RNA sequences demonstrated that the separation between T.borreli and Trypanosomatina was an early event, implying that U-insertion/deletion processes are ancient. Different patterns of editing have persisted in different lineages, however, since editing of cox1 RNA and of relatively small 3'-terminal RNA sections is not found in trypanosomatids. In contrast, cox2 RNA which is edited in trypanosomatids by the insertion of four Us, is unedited in T.borreli.}, }
@article {pmid7953605, year = {1994}, author = {Edwards, JP and Lee, CC and Duchen, LW}, title = {The evolution of an experimental distal motor axonopathy. Physiological studies of changes in neuromuscular transmission caused by cycloleucine, an inhibitor of methionine adenosyltransferase.}, journal = {Brain : a journal of neurology}, volume = {117 (Pt 5)}, number = {}, pages = {959-974}, doi = {10.1093/brain/117.5.959}, pmid = {7953605}, issn = {0006-8950}, mesh = {Animals ; *Axons ; Cycloleucine/*pharmacology ; Electric Conductivity ; Female ; Male ; Membrane Potentials ; Methionine Adenosyltransferase/*antagonists &amp; inhibitors ; Mice ; Mice, Inbred BALB C ; Motor Endplate/*drug effects/*physiopathology/ultrastructure ; Muscle Spindles/physiopathology ; Muscle, Skeletal/drug effects/physiopathology ; Muscles/drug effects/physiopathology ; Neuromuscular Junction/*drug effects/*physiopathology/ultrastructure ; Peripheral Nervous System Diseases/metabolism/pathology/*physiopathology ; Synaptic Transmission/*drug effects ; }, abstract = {Cycloleucine (CL), a synthetic amino acid is known to cause degeneration of motor nerve terminals. This paper describes the changes in neuromuscular transmission, the morphology of motor end-plates and the responses of muscle spindles after a single dose of CL was administered to weanling and adult mice. Animals were allowed to survive for between 12 h and 7 days. Twitch and tetanic responses of muscles stimulated through their nerves fell dramatically within 24 h in both young and adult mice and intracellular recordings revealed that a large proportion of end-plates in calf muscles became denervated, whilst at other end-plates intermittent failure of transmission and end-plate potentials (EPPs) with prolonged latency were demonstrated. End-plates with an abnormally high frequency of miniature end-plate potentials (mEPPs) were found in young mice at 12 h, and in the adult mice at 24 h. Morphological abnormalities in intramuscular nerves and nerve terminals included areas of electron lucent axoplasm, swollen degenerative mitochondria and loss of synaptic vesicles. Over the next 2-3 days further reductions occurred in the number of end-plates at which mEPPs or EPPs could be demonstrated. At 7 days a limited recovery of function occurred in distal muscles but proximal muscles, hitherto unaffected, now began to show abnormalities of transmission. Muscle spindles were found to be both functionally and structurally intact. It is suggested that this acute distal motor axonopathy is due to abnormalities in phospholipid composition of the axolemma of motor nerve terminals resulting from the failure of methyl-transfer pathways. These abnormalities in phospholipid composition might cause an increase in microviscosity of the axolemma and hence a decrease in efficiency of ion channels and pumps responsible for maintaining electrochemical gradients, essential for the structural and functional integrity of the neuromuscular junction.}, }
@article {pmid7948926, year = {1994}, author = {Taniguchi, M and Mori, J and Sugiyama, T}, title = {Structure of genes that encode isozymes of aspartate aminotransferase in Panicum miliaceum L., a C4 plant.}, journal = {Plant molecular biology}, volume = {26}, number = {2}, pages = {723-734}, pmid = {7948926}, issn = {0167-4412}, mesh = {Animals ; Aspartate Aminotransferases/*biosynthesis/genetics ; Bacteria/enzymology/genetics ; Base Sequence ; Blotting, Southern ; Cytosol/enzymology ; DNA Primers ; DNA, Plant/isolation &amp; purification/metabolism ; Exons ; *Genes, Plant ; Genomic Library ; Humans ; Introns ; Isoenzymes/*biosynthesis/genetics ; Mice ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; Plants/enzymology/*genetics ; Regulatory Sequences, Nucleic Acid ; Restriction Mapping ; }, abstract = {The cytosolic and mitochondrial isozymes of aspartate aminotransferase (AspAT) function in the C4 photosynthetic cycle in NAD-malic enzyme-type C4 plants and are expressed at high levels in mesophyll cells and bundle sheath cells, respectively. We constructed a genomic library from Panicum miliaceum, a NAD-malic enzyme-type C4 plant, and cloned the genes for these isozymes. The sequence of the cloned gene for cytosolic AspAT spans 7800 bp and consists of 12 exons. The sequence of the cloned gene for mitochondrial AspAT spans 9000 bp and consists of 10 exons. The results of primer-extension analysis suggest that transcription may be initiated from multiple adjacent sites. Both genes have significant GC-rich regions around the site of initiation of transcription, and these regions showed no CpG suppression. The 5'- flanking regions of both genes include several short sequences similar to the regulatory elements found in other genes for components of the photosynthetic machinery. In particular, the cytosolic AspAT gene contains sequences similar to nuclear protein-binding sites in other mesophyll-expressed C4 photosynthetic genes and the mitochondrial AspAT gene contains elements for light-sensitive and constitutive expression of a bundle sheath-expressed gene. The results of Southern analysis indicated that there are at least two genes that encode each isozyme in the genome of P. miliaceum. A comparison of intron-insertion positions between AspAT genes of plants and animals revealed that several introns are located at identical positions. On the basis of a phylogenetic tree among AspATs and tyrosine aminotransferase, we have shown that the introns of aminotransferase genes antedate the divergence of eubacteria, archaebacteria, and eukaryotes.}, }
@article {pmid7851882, year = {1994}, author = {Boukaftane, Y and Duncan, A and Wang, S and Labuda, D and Robert, MF and Sarrazin, J and Schappert, K and Mitchell, GA}, title = {Human mitochondrial HMG CoA synthase: liver cDNA and partial genomic cloning, chromosome mapping to 1p12-p13, and possible role in vertebrate evolution.}, journal = {Genomics}, volume = {23}, number = {3}, pages = {552-559}, doi = {10.1006/geno.1994.1542}, pmid = {7851882}, issn = {0888-7543}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Chromosome Mapping ; *Chromosomes, Human, Pair 1 ; Cloning, Molecular ; DNA Primers ; DNA, Complementary ; Gene Amplification ; Genetic Variation ; Genomic Library ; Hominidae/*genetics ; Humans ; Hydroxymethylglutaryl-CoA Synthase/*genetics ; Liver/metabolism ; Mice ; Mitochondria, Liver/*enzymology ; Molecular Sequence Data ; Phylogeny ; RNA Splicing ; Rats ; Sequence Homology, Amino Acid ; Vertebrates/*genetics ; }, abstract = {Mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase (mHS) is the first enzyme of ketogenesis, whereas the cytoplasmic HS isozyme (cHS) mediates an early step in cholesterol synthesis. We here report the sequence of human and mouse liver mHS cDNAs, the sequence of a HS-like cDNA from Caenorhabditis elegans, the structure of a partial human mHS genomic clone, and the mapping of the human mHS gene to chromosome 1p12-p13. The nucleotide sequence of the human mHS cDNA encodes a mature mHS peptide of 471 residues, with a mean amino acid identity of 66.5% with cHS from mammals and chicken. Comparative analysis of all known mHS and cHS protein and DNA sequences shows a high degree of conservation near the N-terminus that decreases progressively toward the C-terminus and suggests that the two isozymes arose from a common ancestor gene 400-900 million years ago. Comparison of the gene structure of mHS and cHS is also consistent with a recent duplication event. We hypothesize that the physiologic result of the HS gene duplication was the appearance of HS within the mitochondria around the time of emergence of early vertebrates, which linked preexisting pathways of beta oxidation and leucine catabolism and created the HMG CoA pathway of ketogenesis, thus providing a lipid-derived energy source for the vertebrate brain.}, }
@article {pmid7828828, year = {1994}, author = {Casane, D and Dennebouy, N and de Rochambeau, H and Mounolou, JC and Monnerot, M}, title = {Genetic analysis of systematic mitochondrial heteroplasmy in rabbits.}, journal = {Genetics}, volume = {138}, number = {2}, pages = {471-480}, pmid = {7828828}, issn = {0016-6731}, mesh = {Animals ; DNA, Mitochondrial/*genetics ; Female ; Gene Frequency ; Kidney/metabolism ; Mitochondria/metabolism ; Mitochondria, Liver/metabolism ; Models, Genetic ; Organ Specificity ; Ovary/metabolism ; Pedigree ; Rabbits/*genetics ; *Repetitive Sequences, Nucleic Acid ; Replication Origin ; Restriction Mapping ; Sequence Deletion ; Spleen/metabolism ; }, abstract = {One unusual property of rabbit mitochondrial DNA (mtDNA) is the existence of repeated 153-bp motifs in the vicinity of the replication origin of its H strand. Furthermore, every individual is heteroplasmic: it carries mtDNA molecules with a variable number of repeats. A systematic study of 8 females and their progeny has been devised to analyze mtDNA transmission through generations. The results suggest that three mechanisms are acting simultaneously. (1) Genetic drift in the germ line is revealed by the evolution of heteroplasmy when two major molecular forms are present in a female. (2) A high mutation rate (around 10(-2) per animal generation) generating molecular diversity, by deletion and addition of repeated units, is required to explain the observation of heteroplasmy in every individual. Moreover, the rates of mutation from the most frequent type to the other types are unequal. The deletion of one unit is more frequent than a deletion of two units, which is in turn more frequent than a deletion of three. (3) Selection for shorter molecules in somatic cells is probable. The frequency distribution of mtDNA types depends on the organ analyzed (kidney-spleen and liver vs. gonads).}, }
@article {pmid7926799, year = {1994}, author = {Hu, G and Thilly, WG}, title = {Evolutionary trail of the mitochondrial genome as based on human 16S rDNA pseudogenes.}, journal = {Gene}, volume = {147}, number = {2}, pages = {197-204}, doi = {10.1016/0378-1119(94)90065-5}, pmid = {7926799}, issn = {0378-1119}, support = {NIEHS P01 ESO 3926/EH/NCEH CDC HHS/United States ; NIEHS P01 ESO 5622/EH/NCEH CDC HHS/United States ; }, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal/*genetics ; Humans ; Mitochondria/genetics ; Molecular Sequence Data ; Mutation ; *Pseudogenes ; RNA, Ribosomal, 16S/*genetics ; Sequence Homology, Nucleic Acid ; T-Lymphocytes/metabolism ; }, abstract = {In the course of studies on mutations in human mitochondrial (mt) DNA, we have uncovered and sequenced four new nuclear pseudogenes corresponding to bp 2457-2657 of the mt 16S rDNA. The four genes and their homologies with human mtDNA are E2 (62.4%), K10 (74.4%), E1 (84.6%) and LE6 (93.2%). When these five pseudogene sequences and another previously reported pseudogene sequence are compared with each other, they display what appears to be an ordered series of steps from a hypothetical common ancestor. The sequence of the hypothetical ancestor closely resembles that found in a wide variety of present-day mammalian mt genomes. The pseudogene sequences suggest an evolutionary trail of mt mutation dominated by base pair transitions punctuated by integration into the nuclear genome. Once integrated into the nuclear genome, the pseudogenes appear to follow the distinctive nuclear mutational pathway in which GC to AT transitions predominate and CpG sequences are preferentially eliminated.}, }
@article {pmid7937116, year = {1994}, author = {Thanaraj, TA}, title = {Phylogenetically preserved inter-rRNA base pairs: involvement in ribosomal subunit association.}, journal = {Nucleic acids research}, volume = {22}, number = {19}, pages = {3936-3942}, pmid = {7937116}, issn = {0305-1048}, mesh = {Animals ; Bacteria/genetics ; *Base Composition ; Base Sequence ; Binding Sites ; Eukaryotic Cells/chemistry ; Humans ; Mitochondria/chemistry ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/*chemistry ; RNA, Ribosomal, 16S/chemistry/metabolism ; RNA, Ribosomal, 23S/chemistry/metabolism ; }, abstract = {Intermolecular complementary base pairs, that can be formed between the bases from single-stranded and weak stem regions on 16S rRNA and those on 23S rRNA, were located and checked for preservation in a variety of species covering the complete phylogenetic spectrum. Putative base pairs that exhibited two 'compensatory base pair changes' (a requisite as dictated by the approach of 'comparative sequence data analysis') were picked up. Potential base pairs were selected by assessing the frequency and taxonomy specificity of the occurrence of compensatory base pair changes against those of other types of base pair changes. The selected base pairs were classified as universal, non-mitochondrial, and prokaryote-specific. The positions of the proposed base pairs occur near the structurally and functionally important regions on rRNAs.}, }
@article {pmid8090716, year = {1994}, author = {Wallace, DC}, title = {Mitochondrial DNA sequence variation in human evolution and disease.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {91}, number = {19}, pages = {8739-8746}, pmid = {8090716}, issn = {0027-8424}, support = {HL45572/HL/NHLBI NIH HHS/United States ; NS21328/NS/NINDS NIH HHS/United States ; NS30164/NS/NINDS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Biological Evolution ; Chromosome Mapping ; Consensus Sequence ; DNA, Mitochondrial/*genetics ; Genes ; Humans ; Mitochondria/physiology ; Mitochondrial Myopathies/*genetics ; Molecular Sequence Data ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Germ-line and somatic mtDNA mutations are hypothesized to act together to shape our history and our health. Germ-line mtDNA mutations, both ancient and recent, have been associated with a variety of degenerative diseases. Mildly to moderately deleterious germ-line mutations, like neutral polymorphisms, have become established in the distant past through genetic drift but now may predispose certain individuals to late-onset degenerative diseases. As an example, a homoplasmic, Caucasian, tRNA(Gln) mutation at nucleotide pair (np) 4336 has been observed in 5% of Alzheimer disease and Parkinson disease patients and may contribute to the multifactorial etiology of these diseases. Moderately to severely deleterious germ-line mutations, on the other hand, appear repeatedly but are eliminated by selection. Hence, all extant mutations of this class are recent and associated with more devastating diseases of young adults and children. Representative of these mutations is a heteroplasmic mutation in MTND6 at np 14459 whose clinical presentations range from adult-onset blindness to pediatric dystonia and basal ganglial degeneration. To the inherited mutations are added somatic mtDNA mutations which accumulate in random arrays within stable tissues. These mutations provide a molecular clock that measures our age and may cause a progressive decline in tissue energy output that could precipitate the onset of degenerative diseases in individuals harboring inherited deleterious mutations.}, }
@article {pmid7949744, year = {1994}, author = {Arques, DG and Michel, CJ}, title = {Analytical expression of the purine/pyrimidine autocorrelation function after and before random mutations.}, journal = {Mathematical biosciences}, volume = {123}, number = {1}, pages = {103-125}, doi = {10.1016/0025-5564(94)90020-5}, pmid = {7949744}, issn = {0025-5564}, mesh = {Base Sequence ; Biological Evolution ; DNA/genetics ; Mathematics ; Models, Genetic ; *Mutation ; Probability ; Proteins/genetics ; Purines ; Pyrimidines ; }, abstract = {The mutation process is a classical evolutionary genetic process. The type of mutations studied here is the random substitutions of a purine base R (adenine or guanine) by a pyrimidine base Y (cytosine or thymine) and reciprocally (transversions). The analytical expressions derived allow us to analyze in genes the occurrence probabilities of motifs and d-motifs (two motifs separated by any d bases) on the R/Y alphabet under transversions. These motif probabilities can be obtained after transversions (in the evolutionary sense; from the past to the present) and, unexpectedly, also before transversions (after back transversions, in the inverse evolutionary sense, from the present to the past). This theoretical part in Section 2 is a first generalization of a particular formula recently derived. The application in Section 3 is based on the analytical expression giving the autocorrelation function (the d-motif probabilities) before transversions. It allows us to study primitive genes from actual genes. This approach solves a biological problem. The protein coding genes of chloroplasts and mitochondria have a preferential occurrence of the 6-motif YRY(N)6YRY (maximum of the autocorrelation function for d = 6, N = R or Y) with a periodicity modulo 3. The YRY(N)6YRY preferential occurrence without the periodicity modulo 3 is also observed in the RNA coding genes (ribosomal, transfer, and small nuclear RNA genes) and in the noncoding genes (introns and 5' regions of eukaryotic nuclei). However, there are two exceptions to this YRY(N)6YRY rule: the protein coding genes of eukaryotic nuclei, and prokaryotes, where YRY(N)6YRY has the second highest value after YRY(N)0YRY (YRYYRY) with a periodicity modulo 3. When we go backward in time with the analytical expression, the protein coding genes of both eukaryotic nuclei and prokaryotes retrieve the YRY(N)6YRY preferential occurrence with a periodicity modulo 3 after 0.2 back transversions per base. In other words, the actual protein coding genes of chloroplasts and mitochondria are similar to the primitive protein coding genes of eukaryotic nuclei and prokaryotes. On the other hand, this application represents the first result concerning the mutation process in the model of DNA sequence evolution we recently proposed. According to this model, the actual genes on the R/Y alphabet derive from two successive evolutionary genetic processes: an independent mixing of a few nonrandom types of oligonucleotides leading to genes called primitive followed by a mutation process in these primitive genes.(ABSTRACT TRUNCATED AT 400 WORDS)}, }
@article {pmid7829107, year = {1994}, author = {Corti, O and Finocchiaro, G and Rossi, E and Zuffardi, O and DiDonato, S}, title = {Molecular cloning of cDNAs encoding human carnitine acetyltransferase and mapping of the corresponding gene to chromosome 9q34.1.}, journal = {Genomics}, volume = {23}, number = {1}, pages = {94-99}, doi = {10.1006/geno.1994.1463}, pmid = {7829107}, issn = {0888-7543}, support = {315/TI_/Telethon/Italy ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Blotting, Northern ; Carnitine O-Acetyltransferase/*genetics ; Chromosome Mapping ; *Chromosomes, Human, Pair 9 ; Cloning, Molecular ; DNA, Complementary/genetics ; Genes ; Humans ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {Using a combination of PCR screening of cDNA libraries and reverse transcription PCR, we have cloned three overlapping DNA fragments that encode human carnitine acetyltransferase (CAT), a key enzyme for metabolic pathways involved with the control of the acyl-CoA/CoA ratio in mitochondria, peroxisomes, and endoplasmic reticulum. The resulting cDNA (2436 bp) hybridizes to a mRNA species of approximately 2.9 kb that is particularly abundant in skeletal muscle and encodes a 68-kDa protein containing a peroxisomal targeting signal. The sequence matches those of several tryptic peptides obtained from purified human liver CAT and shows striking similarities with other members of the carnitine/choline acetyltransferase family very distant throughout evolution. CAT cDNA has also been used for fluorescence in situ hybridization on metaphase spreads of human chromosomes, and the corresponding gene, CAT1, has been mapped to chromosome 9q34.1.}, }
@article {pmid7521869, year = {1994}, author = {Nosek, J and Fukuhara, H}, title = {NADH dehydrogenase subunit genes in the mitochondrial DNA of yeasts.}, journal = {Journal of bacteriology}, volume = {176}, number = {18}, pages = {5622-5630}, pmid = {7521869}, issn = {0021-9193}, mesh = {Amino Acid Sequence ; Base Sequence ; Candida/enzymology/*genetics ; DNA, Fungal/analysis/genetics ; DNA, Mitochondrial/*genetics ; Genes, Fungal/genetics ; Mitochondria/chemistry ; Molecular Sequence Data ; NADH Dehydrogenase/*genetics ; Nucleic Acid Hybridization ; Phylogeny ; RNA/analysis ; RNA, Fungal/analysis ; RNA, Mitochondrial ; Sequence Alignment ; Sequence Analysis, DNA ; Transcription, Genetic ; Yeasts/enzymology/*genetics ; }, abstract = {The genes encoding the NADH dehydrogenase subunits of respiratory complex I have not been identified so far in the mitochondrial DNA (mtDNA) of yeasts. In the linear mtDNA of Candida parapsilosis, we found six new open reading frames whose sequences were unambiguously homologous to those of the genes known to code for NADH dehydrogenase subunit proteins of different organisms, i.e., ND1, ND2, ND3, ND4L, ND5, and ND6. The gene for ND4 also appears to be present, as judged from hybridization experiments with a Podospora gene probe. Specific transcripts from these open reading frames (ND genes) could be detected in the mitochondria. Hybridization experiments using C. parapsilosis genes as probes suggested that ND genes are present in the mtDNAs of a wide range of yeast species including Candida catenulata, Pichia guilliermondii, Clavispora lusitaniae, Debaryomyces hansenii, Hansenula polymorpha, and others.}, }
@article {pmid7521532, year = {1994}, author = {Polashock, JJ and Hillman, BI}, title = {A small mitochondrial double-stranded (ds) RNA element associated with a hypovirulent strain of the chestnut blight fungus and ancestrally related to yeast cytoplasmic T and W dsRNAs.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {91}, number = {18}, pages = {8680-8684}, pmid = {7521532}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Ascomycota/*genetics/pathogenicity ; Base Sequence ; *Genes, Viral ; Molecular Sequence Data ; Phylogeny ; Plant Diseases/microbiology ; Plant Viruses/*genetics ; RNA/genetics ; RNA, Double-Stranded/*genetics ; RNA, Fungal/*genetics ; RNA, Mitochondrial ; RNA, Viral/*genetics ; RNA-Dependent RNA Polymerase/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Trees ; Viral Structural Proteins/*genetics ; }, abstract = {A small double-stranded (ds) RNA element was isolated from a moderately hypovirulent strain of the chestnut blight fungus Cryphonectria parasitica (Murr.) Barr. from eastern New Jersey. Virulence was somewhat lower in the dsRNA-containing strain than in a virulent dsRNA-free control strain, but colony morphology and sporulation levels were comparable. A library of cDNA clones was constructed, and overlapping clones representing the entire genome were sequenced. The 2728-bp dsRNA was considerably smaller than previously characterized C. parasitica dsRNAs, which are 12-13 kb and ancestrally related to the Potyviridae family of plant viruses. Sequence analysis revealed one large open reading frame, but only if mitochondrial codon usage (UGA = Trp) was invoked. Nuclease assays of purified mitochondria confirmed that the dsRNA was localized within mitochondria. Assuming mitochondrial translation, the deduced amino acid sequence had landmarks typical of RNA-dependent RNA polymerases. Alignments of the conserved regions indicate that this dsRNA is more closely related to yeast T and W dsRNAs and single-stranded RNA bacteriophages such as Q beta than to other hypovirulence-associated dsRNAs.}, }
@article {pmid8066445, year = {1994}, author = {Hafner, MS and Sudman, PD and Villablanca, FX and Spradling, TA and Demastes, JW and Nadler, SA}, title = {Disparate rates of molecular evolution in cospeciating hosts and parasites.}, journal = {Science (New York, N.Y.)}, volume = {265}, number = {5175}, pages = {1087-1090}, doi = {10.1126/science.8066445}, pmid = {8066445}, issn = {0036-8075}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Electron Transport Complex IV/*genetics ; Host-Parasite Interactions ; Likelihood Functions ; Mitochondria/enzymology ; Molecular Sequence Data ; Mutation ; Phthiraptera/classification/enzymology/*genetics/physiology ; Phylogeny ; Rodentia/classification/*genetics/metabolism/*parasitology ; }, abstract = {DNA sequences for the gene encoding mitochondrial cytochrome oxidase I in a group of rodents (pocket gophers) and their ectoparasites (chewing lice) provide evidence for cospeciation and reveal different rates of molecular evolution in the hosts and their parasites. The overall rate of nucleotide substitution (both silent and replacement changes) is approximately three times higher in lice, and the rate of synonymous substitution (based on analysis of fourfold degenerate sites) is approximately an order of magnitude greater in lice. The difference in synonymous substitution rate between lice and gophers correlates with a difference of similar magnitude in generation times.}, }
@article {pmid7520083, year = {1994}, author = {Denovan-Wright, EM and Lee, RW}, title = {Comparative structure and genomic organization of the discontinuous mitochondrial ribosomal RNA genes of Chlamydomonas eugametos and Chlamydomonas reinhardtii.}, journal = {Journal of molecular biology}, volume = {241}, number = {2}, pages = {298-311}, doi = {10.1006/jmbi.1994.1505}, pmid = {7520083}, issn = {0022-2836}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Blotting, Northern ; Chlamydomonas/*genetics ; Chlamydomonas reinhardtii/*genetics ; Genes ; Introns ; Mitochondria/*chemistry ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA/chemistry/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/chemistry/*genetics ; Transcription, Genetic ; }, abstract = {We report that the mitochondrial ribosomal RNAs (rRNAs) of Chlamydomonas eugametos are discontinuously encoded in separate gene pieces that are scrambled in order and interspersed with protein coding genes. Individual transcripts of these mitochondrial rRNA gene pieces have the potential to form standard rRNA secondary structures through intermolecular base-pairing and they all have termini that are confined to previously defined variable rRNA domains. The C. eugametos and the previously described Chlamydomonas reinhardtii mitochondrial DNAs, therefore, share the unusual feature of highly fragmented and extensively rearranged rRNA coding regions, which contrasts with the conventional mitochondrial rRNA gene structure of land plants and other green algae. Although many of the sites of mitochondrial rRNA discontinuity are in corresponding variable regions in the two Chlamydomonas species, several variable rRNA regions are interrupted in one species but not the other and the 5' to 3' order of the C. eugametos and C. reinhardtii gene pieces is very different. Based on these results, we conclude that the last common ancestor of C. eugametos and C. reinhardtii had discontinuous mitochondrial rRNA genes and that processes responsible for the further division and scrambling of these coding regions have continued since the divergence of C. eugametos and C. reinhardtii. The presence of four group I introns within the C. eugametos mitochondrial rRNA gene pieces leads us to favour recombination rather than reverse-transcription as the mechanism giving rise to the scrambled arrangement of rRNA genes in Chlamydomonas mitochondria.}, }
@article {pmid7967620, year = {1994}, author = {Barrai, I and Scapoli, C and Nesti, C}, title = {Possible identity of transcription and translation signals in early vital systems.}, journal = {Journal of theoretical biology}, volume = {169}, number = {3}, pages = {289-294}, doi = {10.1006/jtbi.1994.1149}, pmid = {7967620}, issn = {0022-5193}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Codon/*genetics ; DNA/genetics ; Eukaryotic Cells/*chemistry ; Fibrinogen/genetics ; Histones/genetics ; Markov Chains ; *Protein Biosynthesis ; Proteins/*genetics ; *Transcription, Genetic ; Tubulin/genetics ; }, abstract = {The distribution of codons was analysed in three classes of eukaryote proteins having widely different evolutionary rates: 78 histones, 40 tubulins, and seven fibrinogens. In this set of genes, (i) it was confirmed that codons which are components of known transcription signals, like ATA, are used infrequently when a synonym is available, particularly in the more constrained proteins, and (ii) it was observed that the three codons which have an iso-accepting transfer with anticodon UAA, UAG or UGA are also suppressed. Then, the distribution of UAA, UAG and UGA trimers was studied in 498 tDNAs and 198 rDNAs. It was found that these trimers are weakly but significantly suppressed in tDNAs and to a lesser extent in rDNAs. It was advanced that the present suppression of ATA, which codes for Methionine in several mitochondria, and of the TAA, TAG and TGA trimers in tDNAs, might be an indication that at the very early stages of the evolution of translation and transcription the signals for initiation and termination were shared by the two processes.}, }
@article {pmid7932783, year = {1994}, author = {Gemmell, NJ and Janke, A and Western, PS and Watson, JM and Pääbo, S and Graves, JA}, title = {Cloning and characterization of the platypus mitochondrial genome.}, journal = {Journal of molecular evolution}, volume = {39}, number = {2}, pages = {200-205}, pmid = {7932783}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Blotting, Southern ; DNA, Complementary ; DNA, Mitochondrial/*genetics ; Mitochondria, Heart/genetics ; Mitochondria, Liver/genetics ; Molecular Sequence Data ; Platypus/*genetics ; Polymerase Chain Reaction ; Sequence Alignment ; }, abstract = {The vertebrate mitochondrial genome is highly conserved in size and gene content. Among the chordates there appears to be one basic gene arrangement, but rearrangements in the mitochondrial gene order of the avian lineages have indicated that the mitochondrial genome may be more variable than once thought. Different gene orders in marsupials and eutherian mammals leave the ancestral mammalian order in some doubt. We have investigated the mitochondrial gene order in the platypus (Ornithorhynchus anatinus), a representative of the third major group of mammals, to determine which mitochondrial gene arrangement is ancestral in mammals. We have found that the platypus mtDNA conforms to the basic chordate gene arrangement, common to fish, amphibians, and eutherian mammals, indicating that this arrangement was the original mammalian arrangement, and that the unusual rearrangements observed in the avians and marsupials are probably lineage-specific.}, }
@article {pmid7813517, year = {1994}, author = {Danpure, CJ and Fryer, P and Jennings, PR and Allsop, J and Griffiths, S and Cunningham, A}, title = {Evolution of alanine:glyoxylate aminotransferase 1 peroxisomal and mitochondrial targeting. A survey of its subcellular distribution in the livers of various representatives of the classes Mammalia, Aves and Amphibia.}, journal = {European journal of cell biology}, volume = {64}, number = {2}, pages = {295-313}, pmid = {7813517}, issn = {0171-9335}, mesh = {Alanine Transaminase/*analysis ; Amphibians/*metabolism ; Animals ; *Biological Evolution ; Birds/*metabolism ; Catalysis ; Cell Compartmentation/physiology ; Cross Reactions ; Immunoblotting ; Liver/*enzymology/ultrastructure ; Mammals/*metabolism ; Microbodies/enzymology ; Microscopy, Immunoelectron ; Mitochondria, Liver/enzymology ; Subcellular Fractions/enzymology ; *Transaminases ; }, abstract = {As part of a wider study on the molecular evolution of alanine:glyoxylate aminotransferase 1 (AGT1) intracellular compartmentalization, we have determined the subcellular distribution of immunoreactive AGT1, using postembedding protein A-gold immunoelectron microscopy, in the livers of various members of the classes Mammalia, Aves, and Amphibia. As far as organellar distribution is concerned, three categories could be distinguished. In members of the first category (type I), all, or nearly all, of the immunoreactive AGT1 was concentrated within the peroxisomes. In the second category (type II), AGT1 was found more evenly distributed in both peroxisomes and mitochondria. In the third category (type III), AGT1 was localized mainly within the mitochondria with much lower, but widely variable, amounts in the peroxisomes. Type I animals include the human, two great apes (gorilla, orangutan), two Old World monkeys (anubis baboon, Japanese macaque), a New World monkey (white-faced Saki monkey), a lago, morph (European rabbit), a bat (Seba's short-tailed fruit bat), two caviomorph rodents (guinea pig, orange-rumped agouti), and two Australian marsupials (koala, Bennett's wallaby). Type II animals include two New World monkeys (common marmoset, cotton-top tamarin), three prosimians (brown lemur, fat-tailed dwarf lemur, pygmy slow loris), five rodents (a hybrid crested porcupine, Colombian ground squirrel, laboratory rat, laboratory mouse, golden hamster), an American marsupial (grey short-tailed opossum), and a bird (raven). Type III animals include the large tree shrew, three insectivores (common Eurasian mole, European hedgehog, house shrew), four carnivores (domestic cat, ocelot, domestic dog, polecat ferret), and an amphibian (common frog). In addition to these categories, some animals (e.g. guinea pig, common frog) possessed significant amounts of cytosolic AGT1. Whereas the subcellular distribution of AGT1 in some orders (e.g. Insectivora and Carnivora) did not appear to vary markedly between the different members, in other orders (e.g. Primates, Rodentia and Marsupialia) it fluctuated widely between the different species. Phylogenetic analysis indicates that the subcellular distribution of AGT1 has changed radically on numerous occasions during the evolution of mammals. The new observations presented in this paper are compatible with our previous demonstration of a relationship between AGT1 subcellular distribution and either present or putative ancestral dietary habit, and our previous suggestion that the molecular evolution of the AGT gene has been markedly influenced by dietary selection pressure.}, }
@article {pmid7525879, year = {1994}, author = {Hattori, Y and Goto, Y and Sakuta, R and Nonaka, I and Mizuno, Y and Horai, S}, title = {Point mutations in mitochondrial tRNA genes: sequence analysis of chronic progressive external ophthalmoplegia (CPEO).}, journal = {Journal of the neurological sciences}, volume = {125}, number = {1}, pages = {50-55}, doi = {10.1016/0022-510x(94)90241-0}, pmid = {7525879}, issn = {0022-510X}, mesh = {Adult ; Aged ; Animals ; Base Sequence ; Chronic Disease ; Female ; *Genes ; Humans ; Male ; Middle Aged ; Mitochondria/*physiology ; Molecular Probes/genetics ; Ophthalmoplegia, Chronic Progressive External/*genetics ; *Point Mutation ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Transfer/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {We have sequenced all mitochondrial tRNA genes from 9 Japanese patients with chronic progressive external ophthalmoplegia (CPEO) who had no detectable large mtDNA deletions nor mutations previously reported, and identified 6 different base substitutions in 6 patients. Since 5 of the 6 substitutions were homoplasmic in distribution and recognizable in some normal controls, they were thought to be polymorphisms in normal individuals. One mutation at nucleotide (nt) 12311 in the tRNA(Leu(CUN)) gene was not present in 90 normal controls nor in 103 patients with other mitochondrial myopathies. This mutation was in a heteroplasmic state, and the mutated site was conserved among other species during evolution, suggesting a disease-related mutation. However, the significance of this mutation has to be studied further. In Japanese CPEO patients without large deletions, a point mutation in the mitochondrial tRNA gene is not likely to be a frequent cause.}, }
@article {pmid7845368, year = {1994}, author = {Demarquoy, J and Fairand, A and Gautier, C and Vaillant, R}, title = {Demonstration of argininosuccinate synthetase activity associated with mitochondrial membrane: characterization and hormonal regulation.}, journal = {Molecular and cellular biochemistry}, volume = {136}, number = {2}, pages = {145-155}, pmid = {7845368}, issn = {0300-8177}, mesh = {Adrenal Cortex Hormones/*physiology ; Animals ; Animals, Newborn ; Argininosuccinate Synthase/*metabolism ; Chemical Fractionation ; Cytosol/metabolism ; Embryonic and Fetal Development/physiology ; Enzyme Stability ; Female ; Intracellular Membranes/*enzymology ; Kinetics ; Male ; Mitochondria, Liver/*enzymology/ultrastructure ; Pancreatic Hormones/*physiology ; Rats ; Rats, Wistar ; Solubility ; }, abstract = {Argininosuccinate synthetase (AS) is the third enzyme in ureogenesis, it catalyses the reaction of condensation of citrulline and aspartate into argininosuccinate. In the present report, we described the first characterization of AS within the outer membrane of rat liver mitochondria. Mitochondria-associated AS displayed the same kinetic characteristics as the cytoplasmic enzyme, but was found to be thermostable while cytoplasmic AS was not. The evolution of the co-location of AS was analyzed during ontogenesis. Total AS activity increased throughout rat fetal development. Simultaneously, the subcellular distribution of the enzyme has changed. AS activity was mainly mitochondrial in fetal and new-born liver liver and cytoplasmic in adult rat liver. The variation in subcellular distribution of AS may be due to the dramatic changes in hormonal levels that occur during this period. The role of corticosteroid and pancreatic hormones was studied. During fetal period, corticosteroid hormones induced an increase in mitochondria-associated AS activity. This was prevented by insulin. Glucagon did not modify total AS activity but reduced mitochondrial AS activity, meanwhile, a comparable increase in cytoplasmic AS activity was observed. One may hypothesize that glucagon may participate in the transfer of mitochondrial enzyme into the cytosol.}, }
@article {pmid8022788, year = {1994}, author = {Nachman, MW and Boyer, SN and Aquadro, CF}, title = {Nonneutral evolution at the mitochondrial NADH dehydrogenase subunit 3 gene in mice.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {91}, number = {14}, pages = {6364-6368}, pmid = {8022788}, issn = {0027-8424}, support = {R01 GM036431/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Conserved Sequence ; DNA Primers ; DNA, Mitochondrial/*genetics ; Macromolecular Substances ; Mice/*genetics ; Mitochondria/*metabolism ; Molecular Sequence Data ; Muridae/*genetics ; NADH Dehydrogenase/*genetics ; *Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Sequence Homology, Amino Acid ; }, abstract = {The neutral theory of molecular evolution asserts that while many mutations are deleterious and rapidly eliminated from populations, those that we observe as polymorphisms within populations are functionally equivalent to each other and thus neutral with respect to fitness. Mitochondrial DNA (mtDNA) is widely used as a genetic marker in evolutionary studies and is generally assumed to evolve according to a strictly neutral model of molecular evolution. One prediction of the neutral theory is that the ratio of replacement (nonsynonymous) to silent (synonymous) nucleotide substitutions will be the same within and between species. We tested this prediction by measuring DNA sequence variation at the mitochondrially encoded NADH dehydrogenase subunit 3 (ND3) gene among 56 individual house mice, Mus domesticus. We also compared ND3 sequence from M. domesticus to ND3 sequence from Mus musculus and Mus spretus. A significantly greater number of replacement polymorphisms were observed within M. domesticus than expected based on comparisons to either M. musculus or M. spretus. This result challenges the conventional view that mtDNA evolves according to a strictly neutral model. However, this result is consistent with a nearly neutral model of molecular evolution and suggests that most amino acid polymorphisms at this gene may be slightly deleterious.}, }
@article {pmid7914934, year = {1994}, author = {Laud, PR and Campbell, JW}, title = {Genetic basis for tissue isozymes of glutamine synthetase in elasmobranchs.}, journal = {Journal of molecular evolution}, volume = {39}, number = {1}, pages = {93-100}, pmid = {7914934}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Brain/enzymology ; Chickens/genetics ; Cytosol/enzymology ; Dogfish/*genetics ; Drosophila/genetics ; Glutamate-Ammonia Ligase/*genetics/metabolism ; Humans ; Isoenzymes/*genetics/metabolism ; Kidney/enzymology ; Liver/enzymology ; Mammals/genetics ; Mitochondria/enzymology ; Mitochondria, Liver/enzymology ; Molecular Sequence Data ; Organ Specificity ; *Phylogeny ; Polymerase Chain Reaction ; RNA, Messenger/analysis/biosynthesis ; Sequence Homology, Amino Acid ; Spleen/enzymology ; }, abstract = {Tissue-specific isozymes of glutamine synthetase are present in elasmobranchs. A larger isozyme occurs in tissues in which the enzyme is localized in mitochondria (liver, kidney) whereas a smaller form occurs in tissues in which it is cytosolic (brain, spleen, etc.). The nucleotide sequence of spiny dogfish shark (Squalus acanthias) liver glutamine synthetase mRNA, derived from its cDNA, shows there are two in-frame initiation codons (AUG) at the N-terminus which will account for the size differences between the two isozymes. Initiation at the up-stream and down-stream sites would yield peptides of 45,406 and 41,869 mol. wts. representing the precursor of the mitochondrial isozyme and the cytosolic isozyme, respectively. The additional N-terminal 29 amino acids present in the mitochondrial isozyme precursor contains two putative cleavage sites based on the Arg-X-(Phe,Ile,Leu) motif. The predicted two-step processing would remove 14 of the 29 N-terminal amino acids. These 14 amino acids can be predicted to form a very strong amphipathic mitochondrial targeting signal. Their removal would yield a mature peptide of 43,680 mol. wt. The calculated mol. wts. based on the derived amino acid sequence are therefore in good agreement with previous estimates of an approximately 1.5-2-kDa difference between the M(r)s of the mitochondrial and cytosolic isozymes. A model for the evolution of the mitochondrial targeting of glutamine synthetase in vertebrates is proposed.}, }
@article {pmid7798168, year = {1994}, author = {Lee, IS and Takio, K and Kido, R and Titani, K}, title = {Purification and amino- and carboxyl-terminal amino acid sequences of alanine-glyoxylate transaminase 1 from human liver.}, journal = {Journal of biochemistry}, volume = {116}, number = {1}, pages = {12-17}, doi = {10.1093/oxfordjournals.jbchem.a124483}, pmid = {7798168}, issn = {0021-924X}, mesh = {Alanine Transaminase/*chemistry/isolation &amp; purification ; Amino Acid Sequence ; Amino Acids/*chemistry ; Animals ; Humans ; Liver/*enzymology ; Mitochondria, Liver/enzymology ; Molecular Sequence Data ; Protein Processing, Post-Translational ; Rats ; Sequence Homology, Amino Acid ; Transaminases/chemistry ; }, abstract = {In order to confirm the amino acid sequence predicted from the nucleotide sequence of cDNA and also to elucidate the intracellular localization and molecular evolution, human liver alanine-glyoxylate transaminase 1 (AGT1) was purified and subjected to partial amino acid sequence determination, with special attention to posttranslational modification. The enzyme was purified to homogeneity from the 10,000 x g supernatant of human liver homogenate. The purified enzyme showed only a single protein band at about 43 kDa on SDS-PAGE, indicating that it is a homodimer of two identical subunits, because the native enzyme has a molecular mass of about 80 kDa. Both the amino- and carboxyl-terminal peptides of the enzyme were isolated from a cyanogen bromide digest of the S-carboxyl-methylated protein and subjected to amino acid sequence determination. The alpha-amino group of the amino-terminal peptide was shown to be blocked by an acetyl group. The carboxyl-terminal sequence contained a putative N-glycosylation sequence (-Asn-Ala-Thr-), the only one present in the whole molecule, but this sequence was normally determined, indicating that the enzyme is not N-glycosylated. Purdue et al. [J. Cell Biol. 111, 2341-2351 (1990)] have reported that Pro-11, Gly-170, and Ile-340 in normal human AGT1 were replaced by Leu, Arg, and Met, respectively, in a patient with primary hyperoxaluria type 1. We confirmed that residue-11 was Pro. Both the amino- and carboxyl-terminal sequences of the enzyme showed extensive similarity with those of rat liver mitochondrial serine-pyruvate aminotransferase and the small chain of hydrogenase from a thermophilic unicellular cyanobacterium, Synechococcus PCC 6716.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid7545947, year = {1994}, author = {Rensing, SA and Maier, UG}, title = {Phylogenetic analysis of the stress-70 protein family.}, journal = {Journal of molecular evolution}, volume = {39}, number = {1}, pages = {80-86}, pmid = {7545947}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Consensus Sequence ; Databases, Factual ; Heat-Shock Proteins/*genetics ; Humans ; Molecular Sequence Data ; *Multigene Family ; *Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {The eukaryotic cyto-/nucleoplasmatic 70-kDa heat-shock protein (HSP70) has homologues in the endoplasmic reticulum as well as in bacteria, mitochondria, and plastids. We selected a representative subset from the large number of sequenced stress-70 family members which covers all known branches of the protein family and calculated and manually improved an alignment. Here we present the consensus sequence of the aligned proteins and putative nuclear localization signals (NLS) in the eukaryotic HSP70 homologues. The phylogenetic relationships of the stress-70 group family members were estimated by use of different computation methods. We present a phylogenetic tree containing all known stress-70 subfamilies and demonstrate the usefulness of stress-70 protein sequences for the estimation of intertaxonic phylogeny.}, }
@article {pmid8018725, year = {1994}, author = {Johansen, S and Johansen, T}, title = {Sequence analysis of 12 structural genes and a novel non-coding region from mitochondrial DNA of Atlantic cod, Gadus morhua.}, journal = {Biochimica et biophysica acta}, volume = {1218}, number = {2}, pages = {213-217}, doi = {10.1016/0167-4781(94)90015-9}, pmid = {8018725}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; DNA/*genetics ; Enzymes/chemistry/genetics ; Fishes/*genetics/metabolism ; *Genes ; Mitochondria/metabolism ; Molecular Sequence Data ; Phylogeny ; RNA, Transfer/genetics ; Sequence Alignment ; }, abstract = {We have determined the nucleotide sequences of 12 structural genes from the mitochondrial DNA of Atlantic cod, Gadus morhua. These genes encode the proteins NADH dehydrogenase subunit 2, cytochrome c oxidase subunit I, cytochrome c oxidase subunit II, and apocytochrome b, as well as the transfer RNAs tRNA(Ile), tRNA(Gln), tRNA(Met), tRNA(Ser) (UCN), tRNA(Asp), tRNA(Glu), tRNA(Thr) and tRNA(Pro). The apocytochrome b sequences were used to construct a phylogenetic tree revealing the evolutionary divergence between modern bony fishes, sturgeon and sharks. We found that bony fishes display the same slow amino acid substitution rates in the mitochondrial encoded proteins as cartilaginous fishes (sharks). A novel non-coding region of 74 base pairs not found in other fishes where sequence data are available is located between the genes encoding tRNA(Thr) and tRNA(Pro). This region contains both direct and inverted repeat motifs that may function in termination of the H-strand transcript.}, }
@article {pmid8006963, year = {1994}, author = {Lonergan, KM and Gray, MW}, title = {The ribosomal RNA gene region in Acanthamoeba castellanii mitochondrial DNA. A case of evolutionary transfer of introns between mitochondria and plastids?.}, journal = {Journal of molecular biology}, volume = {239}, number = {4}, pages = {476-499}, doi = {10.1006/jmbi.1994.1390}, pmid = {8006963}, issn = {0022-2836}, mesh = {Acanthamoeba/*genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Chromosome Mapping ; DNA, Mitochondrial/*genetics ; DNA, Protozoan/genetics ; Genes, Protozoan/genetics ; *Introns ; Mitochondria ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames/genetics ; Plastids ; RNA, Protozoan/genetics ; RNA, Ribosomal/*genetics/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Acanthamoeba castellanii, an amoeboid protozoan, occupies an intriguing position in phylogenetic trees based on nuclear rRNA sequences, branching together with or near (as an outgroup to) green algae and land plants. To gain insight into the organization, expression and evolutionary affiliations of the mtDNA of this non-photosynthetic protist, we determined the sequence of a 7778 base-pair region containing the single-copy large subunit (LSU) and small subunit (SSU) rRNA genes (rnl and rns, respectively) of the approximately 40 kilobase-pair A. castellanii mitochondrial genome. We also sequenced the 5'- and 3'-terminal portions of the corresponding LSU and SSU rRNAs. In A. castellanii mtDNA, rnl is flanked both upstream and downstream by a cluster of five tRNA genes, with rns and then cox1 (the cytochrome oxidase subunit 1 gene) following immediately further downstream. These genes are all in the same transcriptional orientation and are separated by only short non-coding spacers. Although rnl and rns are organized in a novel way in A. castellanii mtDNA, their SSU and LSU rRNA products are strikingly similar to their eubacterial homologs in primary sequence, secondary structure and post-transcriptional modification. In these characteristics, the A. castellanii mitochondrial rRNAs much more closely resemble their counterparts in land plants than do the corresponding mitochondrial rRNAs in the green alga, Chlamydomonas reinhardtii. Although no intervening sequences have so far been found in the mitochondrial rnl of angiosperms (flowering plants), A. castellanii mitochondrial rnl contains three group I introns, all located within highly conserved regions in the 3'-half of the gene and each possessing a free-standing open reading frame (ORF). The insertion site of one of these introns is identical to that of the single group I intron in the chloroplast rnl of C. reinhardtii, and sequence comparison reveals that these two introns (one mitochondrial, the other chloroplast) are structurally homologous both within the core region and within the ORFs they encode. These observations are indicative of intron movement between mitochondria and chloroplasts, either intracellularly in a photosynthetic, remote common ancestor of A. castellanii and C. reinhardtii or, more recently, as a result of an intercellular exchange of genetic information.}, }
@article {pmid7515499, year = {1994}, author = {Valverde, JR and Marco, R and Garesse, R}, title = {A conserved heptamer motif for ribosomal RNA transcription termination in animal mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {91}, number = {12}, pages = {5368-5371}, pmid = {7515499}, issn = {0027-8424}, mesh = {Animals ; Base Sequence ; Consensus Sequence ; Hydrogen Bonding ; Mitochondria/*metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA/chemistry/*genetics ; RNA, Bacterial/chemistry/genetics ; RNA, Mitochondrial ; RNA, Ribosomal/chemistry/*genetics ; Regulatory Sequences, Nucleic Acid ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; *Terminator Regions, Genetic ; Transcription, Genetic ; }, abstract = {A search of sequence data bases for a tridecamer transcription termination signal, previously described in human mtDNA as being responsible for the accumulation of mitochondrial ribosomal RNAs (rRNAs) in excess over the rest of mitochondrial genes, has revealed that this termination signal occurs in equivalent positions in a wide variety of organisms from protozoa to mammals. Due to the compact organization of the mtDNA, the tridecamer motif usually appears as part of the 3' adjacent gene sequence. Because in phylogenetically widely separated organisms the mitochondrial genome has experienced many rearrangements, it is interesting that its occurrence near the 3' end of the large rRNA is independent of the adjacent gene. The tridecamer sequence has diverged in phylogenetically widely separated organisms. Nevertheless, a well-conserved heptamer--TGGCAGA, the mitochondrial rRNA termination box--can be defined. Although extending the experimental evidence of its role as a transcription termination signal in humans will be of great interest, its evolutionary conservation strongly suggests that mitochondrial rRNA transcription termination could be a widely conserved mechanism in animals. Furthermore, the conservation of a homologous tridecamer motif in one of the last 3' secondary loops of nonmitochondrial 23S-like rRNAs suggests that the role of the sequence has changed during mitochondrial evolution.}, }
@article {pmid7522918, year = {1994}, author = {Weiner, AM and Maizels, N}, title = {Molecular evolution. Unlocking the secrets of retroviral evolution.}, journal = {Current biology : CB}, volume = {4}, number = {6}, pages = {560-563}, doi = {10.1016/s0960-9822(00)00126-3}, pmid = {7522918}, issn = {0960-9822}, mesh = {Base Sequence ; *Biological Evolution ; DNA, Fungal/genetics ; DNA, Mitochondrial/genetics ; Models, Genetic ; Molecular Sequence Data ; Neurospora crassa/genetics/metabolism ; RNA Viruses/genetics ; RNA-Directed DNA Polymerase/metabolism ; Retroviridae/*genetics ; }, abstract = {Studies of a small circular plasmid found in the mitochondria of the fungus Neurospora crassa shed unexpected light on the evolution of RNA viruses into retroviruses.}, }
@article {pmid7910968, year = {1994}, author = {Burton, RS and Lee, BN}, title = {Nuclear and mitochondrial gene genealogies and allozyme polymorphism across a major phylogeographic break in the copepod Tigriopus californicus.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {91}, number = {11}, pages = {5197-5201}, pmid = {7910968}, issn = {0027-8424}, mesh = {Animals ; Base Sequence ; Cell Nucleus ; Crustacea/*classification/enzymology/genetics ; DNA ; Electron Transport Complex IV/*genetics ; Female ; Isoenzymes/*genetics ; Mitochondria ; Molecular Sequence Data ; *Phylogeny ; *Polymorphism, Restriction Fragment Length ; }, abstract = {The genetic structure of natural populations is frequently inferred from geographic distributions of alleles at multiple gene loci. Surveys of allozyme polymorphisms in the tidepool copepod Tigriopus californicus have revealed sharp genetic differentiation of populations, indicating that gene flow among populations is highly restricted. Analysis of population structure in this species has now been extended to include nuclear and mitochondrial gene genealogies. DNA sequences of the mtDNA-encoded cytochrome-c oxidase subunit I gene from 21 isofemale lines derived from seven populations reveal a phylogeographic break between populations north and south of Point Conception, California, with sequence divergence across the break exceeding 18%, the highest level of mtDNA divergence yet reported among conspecific populations. Divergence between populations based on 22 sequences of the nuclear histone H1 gene is geographically concordant with the mitochondrial sequences. In contrast with previously studied nuclear genes in other sexually reproducing metazoans, the H1 gene genealogy from T. californicus shows no evidence of recombination. The apparent absence of intragenic recombinants probably results from the persistent lack of gene flow among geographically separated populations, a conclusion strongly supported by allozyme data and the mitochondrial gene genealogy. Despite strong population differentiation at allozyme loci, the phylogeographic break identified by the DNA sequences was not evident in the allozyme data.}, }
@article {pmid7909811, year = {1994}, author = {Alconada, A and Flores, AI and Blanco, L and Cuezva, JM}, title = {Antibodies against F1-ATPase alpha-subunit recognize mitochondrial chaperones. Evidence for an evolutionary relationship between chaperonin and ATPase protein families.}, journal = {The Journal of biological chemistry}, volume = {269}, number = {18}, pages = {13670-13679}, pmid = {7909811}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Antibodies/immunology ; Bacterial Proteins/immunology ; *Biological Evolution ; Cells, Cultured ; Chaperonin 60 ; Chaperonins ; Cross Reactions ; Drosophila melanogaster ; Heat-Shock Proteins/genetics/immunology ; Mitochondria, Liver/enzymology ; Molecular Sequence Data ; Peptide Fragments/immunology ; Proteins/genetics/*immunology ; Proton-Translocating ATPases/chemistry/genetics/*immunology ; Rats ; Rats, Wistar ; Sequence Homology, Amino Acid ; }, abstract = {Antibodies raised against two synthetic peptides from rat liver F1-ATPase alpha-subunit sequence recognized two main heat-shock proteins from Drosophila (p71 and p56) and rat liver (p74 and p54) cells. One of the antisera showed a 20-fold higher reactivity toward Escherichia coli GroEL chaperonin than toward the alpha-subunit purified from Drosophila. Indirect immunofluorescence microscopy and subcellular fractionation experiments located both mammalian heat-shock proteins in the mitochondria. The recent findings of functional homology between chaperonins and alpha-subunits, together with the unsuspected immunological reactivity of two mitochondrial molecular chaperones toward antisera derived from two different sequence motifs of the alpha-subunit, strongly argue in favor of the existence of an evolutionary relationship between chaperonins and alpha-subunits. The complete sequence alignment of F-type ATPase alpha-subunits and chaperonins revealed the existence of eleven most conserved regions (approximately 30% of each protein sequence) with an overall amino acid identity of 20 +/- 2% and similarity of 39 +/- 4%. A search of protein data bases with three different consensus sequences derived from this alignment identified a significant proportion of proteins belonging only to these two protein families. Since the alpha-subunit protein family is evolutionary related to the other catalytic (A and beta) and regulatory (B) subunits of V- and F-type ATPases, the homology reported herein allowed us to analyze, in the chaperonin sequences, the conservation of critical residues involved in nucleotide binding. These data support the hypothesis that chaperonins and the major subunits of V- and F-type ATPases are evolutionary related.}, }
@article {pmid8056314, year = {1994}, author = {Janke, A and Feldmaier-Fuchs, G and Thomas, WK and von Haeseler, A and Pääbo, S}, title = {The marsupial mitochondrial genome and the evolution of placental mammals.}, journal = {Genetics}, volume = {137}, number = {1}, pages = {243-256}, pmid = {8056314}, issn = {0016-6731}, mesh = {Amino Acid Sequence ; Animals ; Anticodon ; Base Composition ; Base Sequence ; *Biological Evolution ; DNA ; DNA Replication ; Gene Rearrangement ; Genetic Variation ; Humans ; Mammals/*genetics ; *Mitochondria ; Molecular Sequence Data ; Opossums/*genetics ; Phylogeny ; Placenta ; RNA Editing ; RNA Processing, Post-Transcriptional ; RNA, Ribosomal/genetics ; RNA, Transfer, Asp/genetics ; }, abstract = {The entire nucleotide sequence of the mitochondrial genome of the American opossum, Didelphis virginiana, was determined. Two major features distinguish this genome from those of other mammals. First, five tRNA genes around the origin of light strand replication are rearranged. Second, the anticodon of tRNA(Asp) is posttranscriptionally changed by an RNA editing process such that its coding capacity is altered. When the complete protein-coding region of the mitochondrial genome is used as an outgroup for placental mammals it can be shown that rodents represent an earlier branch among placental mammals than primates and artiodactyls and that artiodactyls share a common ancestor with carnivores. The overall rates of evolution of most of the mitochondrial genome of placentals are clock-like. Furthermore, the data indicate that the lineages leading to the mouse and rat may have diverged from each other as much as 35 million years ago.}, }
@article {pmid8170990, year = {1994}, author = {Cardon, LR and Burge, C and Clayton, DA and Karlin, S}, title = {Pervasive CpG suppression in animal mitochondrial genomes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {91}, number = {9}, pages = {3799-3803}, pmid = {8170990}, issn = {0027-8424}, mesh = {Base Composition ; Base Sequence ; Biological Evolution ; Cell Nucleus/chemistry ; DNA, Fungal/genetics ; DNA, Mitochondrial/chemistry/*genetics ; Genes ; Methylation ; Molecular Sequence Data ; }, abstract = {All available complete mitochondrial genomes (21 species) are evaluated for dinucleotide over- and under-representation. The CpG dinucleotide is pervasively under-represented in all animal mitochondria, but it is of variable relative abundance in fungal, protist, and plant mitochondrial genomes. Interpretations and hypotheses are considered relative to mitochondrial genome organization, methylation, structural specificities, directed mutation, and evolutionary events. In particular, our results support Mycoplasma capricolum or a close relative as the most likely bacterial ancestor of the mitochondria.}, }
@article {pmid8190631, year = {1994}, author = {Boyen, C and Leblanc, C and Bonnard, G and Grienenberger, JM and Kloareg, B}, title = {Nucleotide sequence of the cox3 gene from Chondrus crispus: evidence that UGA encodes tryptophan and evolutionary implications.}, journal = {Nucleic acids research}, volume = {22}, number = {8}, pages = {1400-1403}, pmid = {8190631}, issn = {0305-1048}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; *Codon ; DNA, Mitochondrial ; Electron Transport Complex IV/*genetics ; Humans ; Mitochondria/enzymology ; Molecular Sequence Data ; Rhodophyta/enzymology/*genetics ; Sequence Homology, Amino Acid ; Tryptophan/*genetics ; }, abstract = {We present the nucleotide sequence of the gene encoding subunit 3 of cytochrome c oxidase in Chondrus crispus, the first report on a mitochondrial gene from a red alga. Amino acid alignment with homologous proteins shows that tryptophan is specified by UGA, as in the mitochondrial code of most organisms other than green plants. However, phylogenetic analyses of cox3 amino acid and nucleotide sequences indicate that C. crispus COX3 is related to the green-plant mitochondrial lineage. No RNA editing was detected on the corresponding transcript. As the only known photosynthetic eukaryotes that both share an immediate mitochondrial ancestor with green plants and exhibit features characteristic of non-plant mitochondria, ie, a small-sized mitochondrial genome and a modified genetic code, rhodophytes may be thought of as an intermediate evolutionary link at the root of the green-plant mitochondrial lineage.}, }
@article {pmid8163532, year = {1994}, author = {Hayashi, S and Jain, S and Chu, R and Alvares, K and Xu, B and Erfurth, F and Usuda, N and Rao, MS and Reddy, SK and Noguchi, T}, title = {Amphibian allantoinase. Molecular cloning, tissue distribution, and functional expression.}, journal = {The Journal of biological chemistry}, volume = {269}, number = {16}, pages = {12269-12276}, pmid = {8163532}, issn = {0021-9258}, support = {R37 GM23750/GM/NIGMS NIH HHS/United States ; }, mesh = {Amidohydrolases/analysis/*biosynthesis/genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Blotting, Northern ; Cloning, Molecular ; DNA, Complementary/analysis/metabolism ; *Gene Expression Regulation, Enzymologic ; Immunohistochemistry ; Kidney/*enzymology ; Kinetics ; Liver/*enzymology ; Microbodies/enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; Open Reading Frames ; Organ Specificity ; RNA, Messenger/analysis/biosynthesis ; Rana catesbeiana ; Restriction Mapping ; Saccharomyces cerevisiae/enzymology ; Sequence Homology, Amino Acid ; }, abstract = {The chain of enzymes necessary to convert uric acid to its metabolic products urea and glyoxylic acid in vertebrates is truncated through the successive loss of allantoicase, allantoinase, and urate oxidase during phylogenetic evolution. Previous studies have assigned the localization of both urate oxidase and allantinase to the peroxisome in the amphibian liver. This study reports the cloning of a cDNA encoding bullfrog (Rana catesbeiana) allantoinase, an enzyme that converts allantoin to allantoic acid. The cDNA is 2112 base pairs in length containing a 1449-base pair open reading frame which corresponds to a 483-residue protein (53,296 Da). Structural analysis of the deduced protein suggested two potential transmembrane segments and the presence of a putative mitochondrial localization sequence in the amino terminus. Immunocytochemical analysis revealed that allantoinase is localized to mitochondria and not to peroxisomes. On Northern blotting, a single mRNA species was detected in the liver and kidney of frog but not in other tissues; this distribution was confirmed by immunoblotting. The hepatic- and renal-specific expression of allantoinase coincides with the distribution of urate oxidase in these tissues in the frog. The allantoinase expressed in Saccharomyces cerevisiae and in Spodoptera frugiperda (Sf9) insect cells exhibits catalytic activity and is antigenically identical to the native frog enzyme.}, }
@article {pmid8168541, year = {1994}, author = {Lumb, MJ and Purdue, PE and Danpure, CJ}, title = {Molecular evolution of alanine/glyoxylate aminotransferase 1 intracellular targeting. Analysis of the feline gene.}, journal = {European journal of biochemistry}, volume = {221}, number = {1}, pages = {53-62}, doi = {10.1111/j.1432-1033.1994.tb18714.x}, pmid = {8168541}, issn = {0014-2956}, mesh = {Alanine Transaminase/chemistry/*genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Blotting, Northern ; Blotting, Southern ; Callithrix ; Cats/*genetics ; Cloning, Molecular ; DNA, Complementary/chemistry/genetics ; Humans ; Liver/enzymology ; Microbodies/enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; Protein Biosynthesis ; Rabbits ; Rats ; Sequence Homology ; Species Specificity ; Subcellular Fractions/*enzymology ; *Transaminases ; Transcription, Genetic ; }, abstract = {The subcellular distribution of hepatic alanine:glyoxylate aminotransferase 1 (AGT) has changed, under the influence of dietary selection pressure, on several o occasions during the evolution of mammals. In some species (e.g. human and rabbit) AGT is entirely peroxisomal; in other species (e.g. marmoset and rat) this enzyme is found in similar amounts in peroxisomes and mitochondria; in yet other species (e.g. cat) it is mainly mitochondrial. The molecular basis of the species-specific dual intracellular targeting of AGT has been partially elucidated in the human and rabbit (as examples of the first group), and in the rat and marmoset (as examples of the second group). As part of a wider study on the molecular evolution of AGT intracellular targeting, we report in the present paper the results of an investigation into the molecular basis of the subcellular distribution of AGT in the cat (as an example of the third group). Cat liver AGT cDNA has been cloned and sequenced, and shown to have a high degree of similarity to AGT from human, rabbit, marmoset and rat. Southern-blotting analysis showed that AGT in the cat is probably encoded by a single gene, as it is in other species. Transcript analysis by RNase protection indicated that almost all of the AGT mRNA would possess an open reading frame encoding a polypeptide of 414 amino acids and a molecular mass of 45,508 Da. The N-terminal 22 amino acids comprised the putative mitochondrial-targeting sequence (by analogy with the equivalent sequence in marmoset and rat pre-mitochondrial AGT). The very low level of peroxisomal AGT in cat liver is compatible with the absence of any RNase-protected transcripts initiating downstream of the first putative translation initiation codon (i.e. absence of any transcripts in which the mitochondrial-targeting sequence is excluded from the open reading frame). In vitro studies showed that the 45 kDa polypeptide was imported into rat liver mitochondria and processed to a mature protein of approximately 43 kDa, compatible with the cleavage of the N-terminal 22 amino acids, as is also the case in rat and marmoset. A polypeptide in which the N-terminal 22 amino acids was absent could not be imported into mitochondria in vitro.}, }
@article {pmid8074887, year = {1994}, author = {Shirakura, T and Hashimoto, T and Nakamura, Y and Kamaishi, T and Cao, Y and Adachi, J and Hasegawa, M and Yamamoto, A and Goto, N}, title = {Phylogenetic place of a mitochondria-lacking protozoan, Entamoeba histolytica, inferred from amino acid sequences of elongation factor 2'.}, journal = {Idengaku zasshi}, volume = {69}, number = {2}, pages = {119-135}, doi = {10.1266/jjg.69.119}, pmid = {8074887}, issn = {0021-504X}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; DNA Primers ; Entamoeba histolytica/*classification/genetics ; Humans ; Mitochondria ; Molecular Sequence Data ; Peptide Elongation Factor 2 ; Peptide Elongation Factors/*genetics ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {Partial DNA regions encoding a major part of translation elongation factor 2 (EF-2) from a mitochondria-lacking protozoan, Entamoeba histolytica, were amplified by polymerase chain reaction and their primary structures were analyzed. The deduced amino acid sequence was aligned with other eukaryotic and archaebacterial EF-2's, and the phylogenetic relationships among eukaryotes were inferred by the maximum likelihood (ML) method. The ML analyses using four different stochastic models of amino acid substitutions consistently suggest that among eukaryotic species being analyzed, E. histolytica is likely to have diverged from other higher eukaryotes on the early phase of eukaryotic evolution.}, }
@article {pmid8032211, year = {1994}, author = {Adler, BK and Hajduk, SL}, title = {Mechanisms and origins of RNA editing.}, journal = {Current opinion in genetics &amp; development}, volume = {4}, number = {2}, pages = {316-322}, doi = {10.1016/s0959-437x(05)80060-7}, pmid = {8032211}, issn = {0959-437X}, support = {AI21401/AI/NIAID NIH HHS/United States ; CA60151/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Biological Evolution ; Humans ; Molecular Sequence Data ; *RNA Editing/genetics ; RNA, Guide, Kinetoplastida ; RNA, Messenger ; }, abstract = {RNA editing is an essential post-transcriptional process that has been identified in an increasing number of eukaryotic organisms. In the past year, progress has been made in the development of in vitro systems to study the mechanism of RNA editing. Analysis of nucleotide insertion/deletion editing in trypanosome mitochondria has revealed the existence of putative editing intermediates in vivo and in vitro. The development of an in vitro editing system for mammalian apolipoprotein B mRNA has allowed the elucidation of both the sequence requirements and the biochemical mechanism of this form of RNA editing. In addition, recent work has underscored the diversity of RNAs whose structure and function are altered by post-translational editing reactions.}, }
@article {pmid8007000, year = {1994}, author = {Liaud, MF and Valentin, C and Martin, W and Bouget, FY and Kloareg, B and Cerff, R}, title = {The evolutionary origin of red algae as deduced from the nuclear genes encoding cytosolic and chloroplast glyceraldehyde-3-phosphate dehydrogenases from Chondrus crispus.}, journal = {Journal of molecular evolution}, volume = {38}, number = {4}, pages = {319-327}, pmid = {8007000}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; *Biological Evolution ; Cell Compartmentation ; Chloroplasts/physiology ; Cytosol/physiology ; DNA, Complementary/genetics ; Gene Library ; Glyceraldehyde-3-Phosphate Dehydrogenases/classification/*genetics ; Molecular Sequence Data ; Protein Sorting Signals/genetics ; Rhodophyta/*genetics ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Homology, Amino Acid ; }, abstract = {Algae are a heterogeneous group of photosynthetic eukaryotes traditionally separated into three major subdivisions: rhodophytes, chlorophytes, and chromophytes. The evolutionary origin of rhodophytes or red algae and their links to other photosynthetic and nonphotosynthetic eukaryotes have been a matter of much controversy and speculation. Here we present the first cDNAs of nuclear protein genes from red algae: Those encoding cytosolic and chloroplast glyceraldehyde-3-phosphate dehydrogenases (GAPDH) from Chondrus crispus. A phylogenetic analysis including GAPDH gene sequences from a number of eukaryotic taxa, cyanobacteria, and purple bacteria suggests that chloroplasts and rhodoplasts together form a monophyletic group of cyanobacterial descent and that rhodophytes separated from chlorophytes at about the same time as animals and fungi. The composite GAPDH tree further demonstrates that chloroplast and cytosolic GAPDH genes are closely related to their homologs in cyanobacteria and purple bacteria, respectively, the presumptive ancestors of chloroplasts and mitochondria, thereby firmly establishing the endosymbiotic origin of these nuclear genes and their fixation in eukaryotic cells before the rhodophyte/chlorophyte separation. The present data are in conflict with phylogenetic inferences based on plastid-encoded rbcL sequences supporting a polyphyletic origin of rhodoplasts and chloroplasts. Comparison of rbcL to GAPDH phylogenies suggests that rbcL trees may be misleading because they are composed of branches representing ancient duplicated (paralogous) genes.}, }
@article {pmid7912616, year = {1994}, author = {Giuffra, E and Bernatchez, L and Guyomard, R}, title = {Mitochondrial control region and protein coding genes sequence variation among phenotypic forms of brown trout Salmo trutta from northern Italy.}, journal = {Molecular ecology}, volume = {3}, number = {2}, pages = {161-171}, doi = {10.1111/j.1365-294x.1994.tb00117.x}, pmid = {7912616}, issn = {0962-1083}, mesh = {Animals ; Base Sequence ; DNA, Mitochondrial/chemistry/*genetics ; *Genetic Variation ; Genotype ; Italy ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Sequence Homology, Nucleic Acid ; Trout/*genetics ; }, abstract = {The Pô River basin of northern Italy is the home of distinctive and endemic morphological forms of brown trout Salmo trutta. We used PCR-direct sequencing and RFLP techniques to study variation in the mitochondrial control region of 225 trout in order to assess genetic relatedness among 18 populations from that region. The distribution analysis of these genotypes among north Italian populations confirmed the phylogenetic differentiation of marbled trout Salmo trutta marmoratus populations and the postglacial origin of S. t. carpio. Extensive genetic heterogeneity was observed among morphologically identical S. t. fario populations. Introgression with domestic strains of Atlantic basin origin was detected in all forms. In order to assess the phylogenetic congruence detected in coding and noncoding regions of the mitochondrial genome, we also analysed sequence variation in segments of the cytochrome b and ATPase subunit VI genes among representatives of all variants detected in the analysis of the control region. Variation in protein coding genes was only slightly less than that observed in the control region of the same individuals, both in terms of number of variants detected and of pairwise sequence divergence estimates among variants. Phylogenetic analysis based on protein coding genes sequences identified the same phylogenetic groupings defined by the control region analysis and also allowed a partial resolution of their phyletic relationships that was previously unresolved. However, coding and noncoding segments differed substantially in the transition-transversion ratio (17:0 in coding segments vs. 17:6 in control region segments).}, }
@article {pmid7514712, year = {1994}, author = {Lippok, B and Brennicke, A and Wissinger, B}, title = {Differential RNA editing in closely related introns in Oenothera mitochondria.}, journal = {Molecular &amp; general genetics : MGG}, volume = {243}, number = {1}, pages = {39-46}, pmid = {7514712}, issn = {0026-8925}, mesh = {Amino Acid Sequence ; Base Sequence ; Biological Evolution ; Conserved Sequence ; Exons ; *Introns ; Mitochondria/*metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Plant Proteins/genetics ; Plants/*genetics ; RNA/*metabolism ; *RNA Editing ; RNA, Mitochondrial ; Restriction Mapping ; }, abstract = {Introns a/b of the nad2 gene and b/c of the nad1 gene in Oenothera mitochondria were found to be closely related. Within a scaffold of conserved sequence regions, a 48 bp sequence element covering intron domain V and flanking nucleotides is identical in both group II introns. The third nucleotide of this element is edited in the nad2, but not in the nad1 intervening sequence. The C to U editing event compensates an nad2-specific nucleotide mismatch in the stem domain IV and thus improves secondary structure stability. This differential editing event indicates that the identical upstream 2 and downstream 45 nucleotides are not sufficient to specify this editing site. Comparison of adjacent exon editing patterns in spliced and unspliced transcripts shows a higher degree of editing in processed sequences, confirming that RNA editing is a posttranscriptional process in plant mitochondria.}, }
@article {pmid8127370, year = {1994}, author = {Maslov, DA and Avila, HA and Lake, JA and Simpson, L}, title = {Evolution of RNA editing in kinetoplastid protozoa.}, journal = {Nature}, volume = {368}, number = {6469}, pages = {345-348}, doi = {10.1038/368345a0}, pmid = {8127370}, issn = {0028-0836}, mesh = {Adenosine Triphosphatases/genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Electron Transport Complex IV/genetics ; Genes, Protozoan ; Kinetoplastida/classification/*genetics ; *Mitochondrial Proton-Translocating ATPases ; Molecular Sequence Data ; NADH Dehydrogenase/genetics ; *Oxidative Phosphorylation Coupling Factors ; Phylogeny ; Protozoan Proteins/genetics ; *RNA Editing ; RNA, Messenger/genetics ; RNA, Protozoan/*genetics ; }, abstract = {The editing of RNA in trypanosomatid mitochondria involves the insertion and occasional deletion of uridine residues within coding regions of maxicircle messenger RNA transcripts. The extent to which the transcripts of homologous genes undergo editing differs in different species. In some, entire genes are edited (pan-editing), whereas in others, editing is limited to the 5' termini of editing domains (5' editing). Here we investigate which type of editing is ancestral and which is derived, by analysing RNA editing in the different lineages, using a kinetoplastid phylogeny reconstructed from nuclear small subunit ribosomal RNA sequences. We conclude that the ancestral cryptogenes were pan-edited, and we hypothesize that the 5'-edited homologues were generated by several independent events from partially edited RNAs, in which case editing may be a more primitive mechanism than previously thought.}, }
@article {pmid7907991, year = {1994}, author = {Viale, AM and Arakaki, AK}, title = {The chaperone connection to the origins of the eukaryotic organelles.}, journal = {FEBS letters}, volume = {341}, number = {2-3}, pages = {146-151}, doi = {10.1016/0014-5793(94)80446-x}, pmid = {7907991}, issn = {0014-5793}, mesh = {Animals ; Bacteria ; *Biological Evolution ; Chaperonin 60 ; Chaperonins ; Heat-Shock Proteins/physiology ; Humans ; Organelles/classification/*physiology ; Plastids ; Proteins/*physiology ; }, abstract = {The heat-shock 60 proteins (Hsp60) constitute a subset of molecular chaperones essential for the survival of the cell, present in eubacteria as well as in eukaryotic organelles. Here, we have employed these highly conserved proteins for the inferences of the origins of the organelles. Hsp60s present in mitochondria from different eukaryotic lineages formed a clade, which showed the closest relationship to that of the Ehrlichia/Rickettsia cluster among the alpha-Proteobacteria. This, in addition to phenotypic characteristics, suggests that these obligate intracellular parasites and the lineage that generated the mitochondrion shared last common ancestry. In turn, Hsp60s present in chloroplasts from plants and a red alga, respectively, clustered specifically with those of the cyanobacteria, suggesting that all plastids derive exclusively from this eubacterial lineage.}, }
@article {pmid7907589, year = {1994}, author = {Gessert, SF and Kim, JH and Nargang, FE and Weiss, RL}, title = {A polyprotein precursor of two mitochondrial enzymes in Neurospora crassa. Gene structure and precursor processing.}, journal = {The Journal of biological chemistry}, volume = {269}, number = {11}, pages = {8189-8203}, pmid = {7907589}, issn = {0021-9258}, support = {GM36552/GM/NIGMS NIH HHS/United States ; }, mesh = {Aldehyde Oxidoreductases/*biosynthesis/genetics ; Amino Acid Sequence ; Base Sequence ; Biological Evolution ; Chromosome Mapping ; Chromosomes, Fungal ; Cloning, Molecular ; Conserved Sequence ; Cosmids ; Enzyme Precursors/genetics/*metabolism ; Escherichia coli/enzymology/genetics ; *Genes, Fungal ; Mitochondria/*enzymology ; Molecular Sequence Data ; Neurospora crassa/*enzymology/*genetics ; Phosphotransferases (Carboxyl Group Acceptor)/*biosynthesis/genetics ; Plasmids ; Polymorphism, Restriction Fragment Length ; Protein Biosynthesis ; *Protein Processing, Post-Translational ; Restriction Mapping ; Sequence Homology, Amino Acid ; Transcription, Genetic ; Transformation, Genetic ; }, abstract = {N-Acetylglutamate kinase (AGK) and N-acetyl-gamma-glutamyl-phosphate reductase (AGPR) function as two separate mitochondrial enzymes, but are encoded by a single nuclear gene in several fungi. The Neurospora crassa arg-6 gene encoding these enzymes has been cloned and sequenced, and the enzymes responsible for processing the polyprotein precursor have been identified. The 871-amino acid precursor contains a normal N-terminal mitochondrial targeting sequence, an internal connecting region (approximately 200 amino acids) upstream of the distal reductase domain, and coding regions with N-terminal amino acid sequences identical with those of purified N-acetylglutamate kinase and N-acetyl-gamma-glutamyl-phosphate reductase. Sequence comparisons of the coding regions indicate high levels of conservation between prokaryotic and fungal proteins. Regions suggesting ancestral relationships to N-acetylglutamate synthase and aspartate beta-semialdehyde dehydrogenase have been identified. Both the N-terminal targeting sequence and the connecting region contain consensus sites for cleavage by the mitochondrial processing peptidase and processing enhancing protein. In vitro processing assays with intact mitochondria, solubilized mitochondria, and purified enzymes have shown that the mitochondrial processing peptidase and processing enhancing protein cleave not only the N-terminal mitochondrial targeting sequence but also process the polyprotein precursor into the two mature enzymes.}, }
@article {pmid8135845, year = {1994}, author = {Tassani, V and Cattapan, F and Magnanimi, L and Peschechera, A}, title = {Anaplerotic effect of propionyl carnitine in rat heart mitochondria.}, journal = {Biochemical and biophysical research communications}, volume = {199}, number = {2}, pages = {949-953}, doi = {10.1006/bbrc.1994.1321}, pmid = {8135845}, issn = {0006-291X}, mesh = {Acetylcarnitine/metabolism ; Animals ; Carbon Dioxide/analysis ; Cardiotonic Agents/*pharmacology ; Carnitine/*analogs &amp; derivatives/pharmacology ; Male ; Malonates/pharmacology ; Mitochondria, Heart/drug effects/*metabolism ; Mitochondria, Liver/drug effects/*metabolism ; Oxygen Consumption/*drug effects ; Pyruvates/*metabolism ; Rats ; Rats, Wistar ; }, abstract = {Carnitine and propionyl carnitine both increase production of 14CO2 from [1-14C]pyruvate but only the latter, in a process inhibited by malonate, increases oxygen uptake and 14CO2 evolution from [2-14C]pyruvate. Carnitine increases the rate of formation of acetyl carnitine from pyruvate to a greater extent than propionyl carnitine. These effects of carnitine and propionyl carnitine are not detectable in mitochondria (e.g., rat liver) deficient in carnitine acetyl transferase activity.}, }
@article {pmid8114942, year = {1994}, author = {Kersanach, R and Brinkmann, H and Liaud, MF and Zhang, DX and Martin, W and Cerff, R}, title = {Five identical intron positions in ancient duplicated genes of eubacterial origin.}, journal = {Nature}, volume = {367}, number = {6461}, pages = {387-389}, doi = {10.1038/367387a0}, pmid = {8114942}, issn = {0028-0836}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Chlamydomonas reinhardtii/enzymology/genetics ; Chloroplasts/enzymology ; Cytosol/enzymology ; Exons ; Fabaceae/enzymology/genetics ; *Genes, Bacterial ; *Genes, Plant ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics ; *Introns ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Plants, Medicinal ; Sequence Alignment ; Zea mays/enzymology/genetics ; }, abstract = {In 1985 Cornish-Bowden wrote "although there is now much to suggest that introns are an ancient relic of primordial genes, convincing proof must await the discovery of clearly corresponding intron arrangements in genes that arose by duplication before the separation of prokaryotes and eukaryotes". Genes for chloroplast and cytosolic glyceraldehyde-3-phosphate dehydrogenases of eukaryotes are descendants of an ancient gene family that existed in the common ancestor of extant eubacteria. During eukaryotic evolution, both genes were transferred to the nucleus from the antecedents of present-day chloroplasts and mitochondria, respectively. Here we report the discovery of five spliceosomal introns at positions that are precisely conserved between nuclear genes for this chloroplast/cytosol enzyme pair. These data provide strong evidence in favour of the 'introns early' hypothesis, which proposes that introns were present in the earliest cells, consistent with the idea that introns facilitated the assembly of primordial genes by accelerating the rate of exon shuffling.}, }
@article {pmid8290575, year = {1994}, author = {Hiesel, R and Combettes, B and Brennicke, A}, title = {Evidence for RNA editing in mitochondria of all major groups of land plants except the Bryophyta.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {91}, number = {2}, pages = {629-633}, pmid = {8290575}, issn = {0027-8424}, mesh = {Base Sequence ; Biological Evolution ; Chlorophyta/genetics/metabolism ; DNA Primers/genetics ; DNA, Complementary/genetics ; Mitochondria/metabolism ; Molecular Sequence Data ; Plants/classification/genetics/*metabolism ; *RNA Editing ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {RNA editing has been documented in mitochondria of higher plants, notably dicots and monocots. To determine the distribution of mitochondrial RNA editing in the plant kingdom, we have now undertaken a survey of evolutionarily distant plants. RNA editing occurs in all major groups of land plants except the Bryophyta, suggesting that this process is an ancient trait that was established before the radiation of kormophyte plants. No editing is observed in representatives of the green algae, suggesting that editing arose in early land plants after the split of the Bryophyta or has been lost selectively in both algae and mosses. In ferns several U-->C changes are observed, one of which eliminates a genomically encoded UAA termination codon and creates a functional open reading frame.}, }
@article {pmid7507251, year = {1994}, author = {Hiesel, R and von Haeseler, A and Brennicke, A}, title = {Plant mitochondrial nucleic acid sequences as a tool for phylogenetic analysis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {91}, number = {2}, pages = {634-638}, pmid = {7507251}, issn = {0027-8424}, mesh = {Base Sequence ; DNA, Complementary/genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; Genes, Plant ; Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; Plants/classification/*genetics/metabolism ; RNA/chemistry/genetics ; RNA Editing ; RNA, Mitochondrial ; Species Specificity ; }, abstract = {To evaluate the potential of mitochondrial nucleic acid sequences as a phylogenetic tool, we have analyzed cytochrome oxidase subunit III (coxIII) coding sequences in representatives of the major groups of land plants. The phylogenetic tree derived from these mitochondrial sequences confirms the monophyletic origin of land plant mitochondria with the general order and descent of land plants deduced by other molecular, physiological, and morphological traits. The mitochondrial sequences strongly suggest a close phylogenetic relationship between Bryophyta and Lycopodiatae, whereas Psilophytatae cluster with the other vascular plants. In addition to the high sequence similarity, both Hepaticophytina and Lycopodiatae contain a related intron in the coxIII gene that, to our knowledge, is not found in any other plant species. The slowly evolving mitochondrial sequences of plants are shown to provide a useful phylogenetic tool to evaluate distant evolutionary relationships within this kingdom.}, }
@article {pmid8276120, year = {1994}, author = {Roise, D and Maduke, M}, title = {Import of a mitochondrial presequence into P. denitrificans. Insight into the evolution of protein transport.}, journal = {FEBS letters}, volume = {337}, number = {1}, pages = {9-13}, doi = {10.1016/0014-5793(94)80619-5}, pmid = {8276120}, issn = {0014-5793}, support = {T32-GM08326/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Biological Evolution ; Biological Transport ; Electron Transport Complex IV/chemistry/*metabolism ; Mitochondria/*enzymology ; Molecular Sequence Data ; Paracoccus denitrificans/*metabolism ; Peptide Fragments/chemistry/metabolism ; Protein Precursors/*metabolism ; Saccharomyces cerevisiae/enzymology/ultrastructure ; }, abstract = {According to the endosymbiont hypothesis, mitochondria are descended from ancient aerobic bacteria that were engulfed by protoeukaryotic cells. Experiments described here show that a synthetic peptide corresponding to a yeast mitochondrial targeting sequence can be imported into Paracoccus denitrificans, a soil bacterium thought to be closely related to the protomitochondrion. The import is very similar to that observed with isolated yeast mitochondria. The results suggest that the protomitochondrion may have been inherently able to translocate mitochondrial presequences. This ability may partly explain the development of the protein import process during the evolution of the mitochondrion.}, }
@article {pmid8151709, year = {1994}, author = {Boorstein, WR and Ziegelhoffer, T and Craig, EA}, title = {Molecular evolution of the HSP70 multigene family.}, journal = {Journal of molecular evolution}, volume = {38}, number = {1}, pages = {1-17}, pmid = {8151709}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; DNA, Fungal ; Genes, Fungal ; Heat-Shock Proteins/*genetics ; Humans ; Molecular Sequence Data ; *Multigene Family ; Phylogeny ; Saccharomyces cerevisiae/classification/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, abstract = {Eukaryotic genomes encode multiple 70-kDa heat-shock proteins (HSP70s). The Saccharomyces cerevisiae HSP70 family is comprised of eight members. Here we present the nucleotide sequence of the SSA3 and SSB2 genes, completing the nucleotide sequence data for the yeast HSP70 family. We have analyzed these yeast sequences as well as 29 HSP70s from 24 additional eukaryotic and prokaryotic species. Comparison of the sequences demonstrates the extreme conservation of HSP70s; proteins from the most distantly related species share at least 45% identity and more than one-sixth of the amino acids are identical in the aligned region (567 amino acids) among all proteins analyzed. Phylogenetic trees constructed by two independent methods indicate that ancient molecular and cellular events have given rise to at least four monophyletic groups of eukaryotic HSP70 proteins. Each group of evolutionarily similar HSP70s shares a common intracellular localization and is presumed to be comprised of functional homologues; these include heat-shock proteins of the cytoplasm, endoplasmic reticulum, mitochondria, and chloroplasts. HSP70s localized in mitochondria and plastids are most similar to the DnaK HSP70 homologues in purple bacteria and cyanobacteria, respectively, which is consistent with the proposed prokaryotic origin of these organelles. The analyses indicate that the major eukaryotic HSP70 groups arose prior to the divergence of the earliest eukaryotes, roughly 2 billion years ago. In some cases, as exemplified by the SSA genes encoding the cytoplasmic HSP70s of S. cerevisiae, more recent duplication events have given rise to subfamilies within the major groups. The S. cerevisiae SSB proteins comprise a unique subfamily not identified in other species to date. This subfamily appears to have resulted from an ancient gene duplication that occurred at approximately the same time as the origin of the major eukaryotic HSP70 groups.}, }
@article {pmid8151072, year = {1994}, author = {Rosenberg, RN}, title = {Mitochondria in evolution and disease.}, journal = {Journal of child neurology}, volume = {9}, number = {1}, pages = {1-3}, doi = {10.1177/088307389400900101}, pmid = {8151072}, issn = {0883-0738}, mesh = {*Biological Evolution ; Black People/genetics ; DNA Mutational Analysis ; DNA, Mitochondrial/*genetics ; Humans ; MELAS Syndrome/*genetics ; Polymorphism, Genetic/genetics ; }, }
@article {pmid8121287, year = {1994}, author = {Hashimoto, T and Nakamura, Y and Nakamura, F and Shirakura, T and Adachi, J and Goto, N and Okamoto, K and Hasegawa, M}, title = {Protein phylogeny gives a robust estimation for early divergences of eukaryotes: phylogenetic place of a mitochondria-lacking protozoan, Giardia lamblia.}, journal = {Molecular biology and evolution}, volume = {11}, number = {1}, pages = {65-71}, doi = {10.1093/oxfordjournals.molbev.a040093}, pmid = {8121287}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Base Composition ; Base Sequence ; Biological Evolution ; DNA Primers/genetics ; DNA, Protozoan/genetics ; Entamoeba histolytica/genetics ; Euglena gracilis/genetics ; Giardia lamblia/*genetics ; Molecular Sequence Data ; Peptide Elongation Factor 1 ; Peptide Elongation Factors/genetics ; *Phylogeny ; Plasmodium falciparum/genetics ; Protozoan Proteins/*genetics ; }, abstract = {A partial nucleotide sequence of the mRNA encoding a major part of elongation factor 1 alpha (EF1 alpha) from a mitochondria-lacking protozoan, Giardia lamblia, was reported, and the phylogenetic relationship among lower eukaryotes was inferred by the maximum-likelihood and maximum-parsimony methods of protein phylogeny. Both the methods consistently demonstrated that, G. lamblia among the four protozoan species being analyzed, is the earliest offshoot of the eukaryotic tree. Although the Giardia EF1 alpha gene showed an extremely high G+C content as compared with those of other protozoa, it was concentrated only at the third codon positions, resulting in no remarkable differences of amino acid frequencies vis-à-vis those of other species. This clearly suggests (a) that the amino acid frequencies of conservative proteins are free from the drastic bias of genome G+C content, which is a serious problem in the widely used tree of ribosomal RNA, and (b) that protein phylogeny gives a robust estimation for the early divergences in the evolution of eukaryotes.}, }
@article {pmid8121281, year = {1994}, author = {Brown, JM and Pellmyr, O and Thompson, JN and Harrison, RG}, title = {Phylogeny of Greya (Lepidoptera: Prodoxidae), based on nucleotide sequence variation in mitochondrial cytochrome oxidase I and II: congruence with morphological data.}, journal = {Molecular biology and evolution}, volume = {11}, number = {1}, pages = {128-141}, doi = {10.1093/oxfordjournals.molbev.a040087}, pmid = {8121281}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Genes, Insect ; Genetic Variation ; Lepidoptera/anatomy &amp; histology/*enzymology/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; Species Specificity ; }, abstract = {The phylogeny of Greya Busck (Lepidoptera: Prodoxidae) was inferred from nucleotide sequence variation across a 765-bp region in the cytochrome oxidase I and II genes of the mitochondrial genome. Most parsimonious relationships of 25 haplotypes from 16 Greya species and two outgroup genera (Tetragma and Prodoxus) showed substantial congruence with the species relationships indicated by morphological variation. Differences between mitochondrial and morphological trees were found primarily in the positions of two species, G. variabilis and G. pectinifera, and in the branching order of the three major species groups in the genus. Conflicts between the data sets were examined by comparing levels of homoplasy in characters supporting alternative hypotheses. The phylogeny of Greya species suggests that host-plant association at the family level and larval feeding mode are conservative characters. Transition/transversion ratios estimated by reconstruction of nucleotide substitutions on the phylogeny had a range of 2.0-9.3, when different subsets of the phylogeny were used. The decline of this ratio with the increase in maximum sequence divergence among taxa indicates that transitions are masked by transversions along deeper internodes or long branches of the phylogeny. Among transitions, substitutions of A-->G and T-->C outnumbered their reciprocal substitutions by 2-6 times, presumably because of the approximately 4:1 (77%) A+T-bias in nucleotide base composition. Of all transversions, 73%-80% were A<-->T substitutions, 85% of which occurred at third positions of codons; these estimates did not decrease with an increase in maximum sequence divergence of taxa included in the analysis. The high frequency of A<-->T substitutions is either a reflection or an explanation of the 92% A+T bias at third codon positions.}, }
@article {pmid7748934, year = {1994}, author = {Megraw, TL and Kao, LR and Chae, CB}, title = {The mitochondrial histone HM: an evolutionary link between bacterial HU and nuclear HMG1 proteins.}, journal = {Biochimie}, volume = {76}, number = {10-11}, pages = {909-916}, doi = {10.1016/0300-9084(94)90015-9}, pmid = {7748934}, issn = {0300-9084}, mesh = {Bacterial Proteins/*genetics ; Biological Evolution ; Carrier Proteins/*genetics ; DNA-Binding Proteins/*genetics ; Fungal Proteins/*genetics ; HMGB1 Protein ; High Mobility Group Proteins/*genetics ; Histones/*genetics ; Mitochondria/*genetics ; Nuclear Proteins/*genetics ; }, abstract = {The mitochondrial histone HM is a very abundant protein in yeast mitochondria that wraps DNA and activates transcription in vitro and is required within the cell for proper maintenance of the mitochondrial chromosome. HM and the bacterial histone-like protein HU have similar activities in vitro and can substitute for each other in E coli cells and in yeast mitochondria. HM also appears to be functionally homologous to nuclear HMG1 proteins, with which it shares a high degree of sequence homology. We report here the isolation of extragenic suppressors of the yeast HM mutant temperature-sensitive phenotype. We also examined the effects of the lack of HM protein and of respiration deficiency on yeast cells mutant for the NHP6 proteins, the putative yeast nuclear HMG1 homologues.}, }
@article {pmid7511376, year = {1994}, author = {Saier, MH}, title = {Convergence and divergence in the evolution of transport proteins.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {16}, number = {1}, pages = {23-29}, doi = {10.1002/bies.950160104}, pmid = {7511376}, issn = {0265-9247}, support = {2 RO1AI14176/AI/NIAID NIH HHS/United States ; 5RO1AI21702/AI/NIAID NIH HHS/United States ; }, mesh = {Adenosine Triphosphatases/metabolism ; Animals ; *Biological Evolution ; Carrier Proteins/classification/*genetics/metabolism ; Ion Channels/genetics/physiology ; Mitochondria/metabolism ; Models, Biological ; }, abstract = {Different families of transport proteins catalyze transmembrane solute translocation, employing different mechanisms and energy sources. Several of these functionally dissimilar proteins nevertheless exhibit similar structural units, consisting of six tightly packed alpha-helices which may comprise all or part of a transmembrane channel. It is now recognized that some of these families arose independently of each other by convergence, while others arose from common precursors by divergence. The former families apparently arose at different times in evolutionary history, in different groups of organisms, employing different routes.}, }
@article {pmid8132860, year = {1993}, author = {Koyama, H and Kusunoki, T}, title = {Organization of the cerebral ganglion of the colonial ascidian Polyandrocarpa misakiensis.}, journal = {The Journal of comparative neurology}, volume = {338}, number = {4}, pages = {549-559}, doi = {10.1002/cne.903380405}, pmid = {8132860}, issn = {0021-9967}, mesh = {Animals ; Central Nervous System/*anatomy &amp; histology ; Ganglia, Invertebrate/*ultrastructure ; Microscopy, Electron ; Phylogeny ; Urochordata/*anatomy &amp; histology ; Vertebrates/anatomy &amp; histology ; }, abstract = {The cerebral ganglion of a budding styelid ascidian, Polyandrocarpa misakiensis, whose phylogenetic location is midway between vertebrates and invertebrates, was studied by light and electron microscopy to obtain some insight into the evolution of the central nervous system. The lateral and ventral sides of the ganglion are surrounded by blood sinuses. The ganglion is covered with a thin fibrous sheath through which many nerve fibers run. The ganglion is composed of a cellular cortex and a fibrous medulla. The cortex consists of three to six layers of large and small neurons. Some neurons are also scattered within the medulla. Many neurons are monopolar, and some are bi- or multipolar. The cytoplasm of the large neurons is dense with extensive rough endoplasmic reticulum, free ribosomes, mitochondria, one or more Golgi complexes, large dense bodies, and many clear or dense vesicular structures. Some neurons send their processes directly into the lumen of the sinuses. The medulla is composed of loosely arranged nerve fibers without cellular wrappings. The medullary fibers contain vesicles and granules of various sizes, and microtubules. At the anterior and posterior ends of the ganglion, the medullary fibers are assembled into thick peripheral nerve fiber bundles. The peripheral nerve fibers are enveloped and subdivided by fibrous structures. Synapses are found in the medulla, in the cortex, and between the peripheral nerve fibers. The presence of neurons and axodendritic or axoaxonic synapses in the peripheral nerve fibers is consistent with a diffuse organization of the central nervous system of the ascidians. The morphology of the central nervous system synapses is comparable to that of other invertebrates, but the locations of the synapses are similar to those of vertebrates.}, }
@article {pmid8253773, year = {1993}, author = {Kamijo, T and Aoyama, T and Miyazaki, J and Hashimoto, T}, title = {Molecular cloning of the cDNAs for the subunits of rat mitochondrial fatty acid beta-oxidation multienzyme complex. Structural and functional relationships to other mitochondrial and peroxisomal beta-oxidation enzymes.}, journal = {The Journal of biological chemistry}, volume = {268}, number = {35}, pages = {26452-26460}, pmid = {8253773}, issn = {0021-9258}, mesh = {3-Hydroxyacyl CoA Dehydrogenases/*genetics/metabolism ; Acetyl-CoA C-Acyltransferase/*genetics/metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; *Carbon-Carbon Double Bond Isomerases ; Cells, Cultured ; Cloning, Molecular ; DNA, Complementary ; Enoyl-CoA Hydratase/*genetics/metabolism ; Fatty Acids/*metabolism ; Isomerases/*genetics/metabolism ; Microbodies/*enzymology ; Mitochondria, Liver/*enzymology ; Mitochondrial Trifunctional Protein ; Molecular Sequence Data ; Multienzyme Complexes/*genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; Protein Conformation ; RNA, Messenger/metabolism ; Racemases and Epimerases/*genetics/metabolism ; Rats ; Sequence Homology, Amino Acid ; }, abstract = {Rat liver mitochondrial fatty acid oxidation multienzyme complex consists of 4 mol of the alpha-subunit and 4 mol of the beta-subunit, and has three enzyme activities of long chain enoyl-CoA hydratase, long chain 3-hydroxyacyl-CoA dehydrogenase, and long chain 3-ketoacyl-CoA thiolase. The following cDNA clones for the rat enzyme complex were isolated, sequenced, and expressed: 1) the 2,789-base pair (bp) cDNA clone had a 2,289-bp open reading frame encoding a 82,511-Da precursor and a 78,637-Da mature subunit. The deduced amino acid sequence of this subunit revealed that this cDNA encodes the alpha-subunit and had regions similar to the structure of rat mitochondrial enoyl-CoA hydratase and rat mitochondrial enoyl-CoA isomerase on the amino-terminal side, and a part similar to that of pig mitochondrial 3-hydroxyacyl-CoA dehydrogenase on the carboxyl-terminal side. Expression of this cDNA in COS-1 cells yielded a protein with long chain enoyl-CoA hydratase and long chain 3-hydroxyacyl-CoA dehydrogenase activities. 2) The 1,943-bp cDNA clone had a 1,425-bp open reading frame encoding a 51,413-Da precursor and a 47,583-Da mature subunit. A high similarity of the structure to 3-ketoacyl-CoA thiolases and acetoacetyl-CoA thiolases from various sources suggests that this clone encodes the beta-subunits. Expression of this cDNA in COS-1 cells yielded a protein with long chain 3-ketoacyl-CoA thiolase activity. By phylogenetic analysis of the deduced amino acid sequences of the alpha- and beta-subunits with those of other beta-oxidation enzymes, it was suggested that the alpha-subunit is a descendant of short chain enoyl-CoA hydratase and short chain 3-hydroxyacyl-CoA dehydrogenase while the beta-subunit first diverged from a common ancestor gene of the thiolase family.}, }
@article {pmid8274505, year = {1993}, author = {Cartwright, P and Timms, M and Lithgow, T and Høj, P and Hoogenraad, N}, title = {An Escherichia coli gene showing a potential ancestral relationship to the genes for the mitochondrial import site proteins ISP42 and MOM38.}, journal = {Biochimica et biophysica acta}, volume = {1153}, number = {2}, pages = {345-347}, doi = {10.1016/0005-2736(93)90425-y}, pmid = {8274505}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Bacterial Proteins/*genetics ; Base Sequence ; *Biological Evolution ; Escherichia coli/*genetics ; *Escherichia coli Proteins ; Fungal Proteins/*genetics ; *Genes, Bacterial ; Membrane Proteins/*genetics ; *Membrane Transport Proteins ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins ; Molecular Sequence Data ; Neurospora crassa/genetics/metabolism ; Open Reading Frames ; Saccharomyces cerevisiae/genetics/metabolism ; *Saccharomyces cerevisiae Proteins ; Sequence Homology, Amino Acid ; }, abstract = {An ORF (OrfT) of 1911 base pairs, upstream of the hip operon in Escherichia coli at map position 33.82 has been identified. The protein encoded by this sequence is predicted to have a molecular mass of 68,249 Da and the carboxyterminal 276 residues shows 26.8% and 25.4% identity with the import site proteins ISP42 and MOM38 from the mitochondrial outer membrane of Saccharomyces cerevisiae and Neurospora crassa, respectively. These mitochondrial membrane proteins have been shown to be essential components of the protein translocation apparatus in yeast. These similarities raise the possibility that OrfT might represent the bacterial gene from which these eukaryotic genes evolved.}, }
@article {pmid8244981, year = {1993}, author = {Troll, H and Winckler, T and Lascu, I and Müller, N and Saurin, W and Véron, M and Mutzel, R}, title = {Separate nuclear genes encode cytosolic and mitochondrial nucleoside diphosphate kinase in Dictyostelium discoideum.}, journal = {The Journal of biological chemistry}, volume = {268}, number = {34}, pages = {25469-25475}, pmid = {8244981}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Antibodies/pharmacology ; Base Sequence ; Cell Nucleus/*metabolism ; Cytosol/enzymology ; DNA, Fungal/isolation &amp; purification/*metabolism ; Dictyostelium/*enzymology/*genetics ; Exons ; *Genes, Fungal ; Genomic Library ; Humans ; Introns ; Isoenzymes/biosynthesis/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Nucleoside-Diphosphate Kinase/biosynthesis/*genetics ; Oligodeoxyribonucleotides ; *Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {We have previously isolated cDNA clones for the gip17 gene encoding the cytosolic nucleoside diphosphate (NDP) kinase from Dictyostelium discoideum, and partial cDNAs for guk, a second member of the NDP kinase gene family (Wallet, V., Mutzel, R., Troll, H., Barzu, O., Wurster, B., Véron, M., and Lacombe, M. L. (1990) J. Natl. Cancer Inst. 80, 1199-1202). We now characterize genomic DNA clones for both NDP kinase genes, and we show that guk defines a nuclear-encoded mitochondrial NDP kinase. Isolated D. discoideum mitochondria contain 3% of the total cellular NDP kinase activity. Antibodies which specifically recognize and inhibit the activity of either cytosolic or mitochondrial NDP kinase unambiguously distinguish between these activities. The nascent mitochondrial NDP kinase contains a presequence of 57 amino acids that is removed during import into the organelle as shown by determination of the NH2 terminus of the mature protein from mitochondria. The genes for mitochondrial and cytosolic NDP kinases contain four and two introns, respectively. The positions of the of the introns in the gene for the cytosolic enzyme match exactly the positions of the second and fourth introns in the coding region of its mitochondrial homologue. From these results we conclude that the isozymes diverged from a common ancestor, and we discuss possible phylogenetic pathways for the evolution of cytosolic and organelle NDP kinases.}, }
@article {pmid8278609, year = {1993}, author = {Ueda, T and Watanabe, K}, title = {[Non-universal genetic codes and their evolutionary processes].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {38}, number = {16}, pages = {2677-2691}, pmid = {8278609}, issn = {0039-9450}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Candida/genetics ; Codon ; DNA ; *Genetic Code ; Genome ; Mitochondria ; Molecular Sequence Data ; RNA, Transfer ; }, }
@article {pmid8209098, year = {1993}, author = {dePaula, M and Darder, M and Torres, M and Martínez-Honduvilla, CJ}, title = {[Evaluation of the malate dehydrogenase activity in deteriorated sunflower seeds].}, journal = {Revista espanola de fisiologia}, volume = {49}, number = {4}, pages = {225-229}, pmid = {8209098}, issn = {0034-9402}, mesh = {Cell Membrane/physiology ; Cell Survival ; Desiccation ; Malate Dehydrogenase/*analysis ; Mitochondria/enzymology ; Plant Proteins/*analysis ; Plants, Edible ; *Preservation, Biological ; Seeds/*enzymology/physiology ; Temperature ; }, abstract = {Malate dehydrogenase (MDH) activity in sunflower (Helianthus annus L. cv. Peredovik) seeds stored at 65 degrees C and 90 degrees C for 1, 3, 5, 7, and 14 days was evaluated. This study was design to discern the usefulness of this viability test for deteriorated seeds. Differences in the resistance to the heat storage were detected between treatments as reflected by changes in the evolution of MDH activity. A decrease of MDH activity in both soluble and mitochondrial fractions was observed, which was more evident in seeds stored at high temperature. These differences are poorly correlated to viability as determined by tetrazolium staining, and should be related to integrity of cellular membranes as evidenced by differential MDH activity in soluble and mitochondrial fractions.}, }
@article {pmid8118213, year = {1993}, author = {Gray, MW}, title = {Origin and evolution of organelle genomes.}, journal = {Current opinion in genetics &amp; development}, volume = {3}, number = {6}, pages = {884-890}, doi = {10.1016/0959-437x(93)90009-e}, pmid = {8118213}, issn = {0959-437X}, mesh = {*Biological Evolution ; Eukaryotic Cells ; *Genome ; Mitochondria ; *Organelles ; Plastids ; RNA Editing ; Symbiosis ; }, abstract = {Molecular data (particularly sequence analyses) have established that two eukaryotic organelles, the mitochondrion and the plastid, are the descendants of endosymbiotic (eu)bacteria whose closest living relatives are the alpha-Proteobacteria (mitochondrion) and Cyanobacteria (plastid). This review describes recent data that favor the view that each organelle arose via this primary endosymbiotic pathway only once (monophyletic origin), such as the discovery of group I introns that appear to be structurally homologous and have identical insertion sites in metaphyte, chlorophyte and fungal mitochondrial genomes. However, it is also evident that the plastids in certain algal groups were acquired secondarily through a eukaryotic rather than a prokaryotic endosymbiont.}, }
@article {pmid8115164, year = {1993}, author = {Ueda, T and Watanabe, K}, title = {The evolutionary change of the genetic code as restricted by the anticodon and identity of transfer RNA.}, journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life}, volume = {23}, number = {5-6}, pages = {345-364}, pmid = {8115164}, issn = {0169-6149}, mesh = {Animals ; Anticodon/*genetics ; Base Sequence ; *Biological Evolution ; DNA, Mitochondrial/genetics ; *Genetic Code ; Models, Genetic ; Molecular Sequence Data ; Nucleic Acid Conformation ; Origin of Life ; RNA, Transfer/chemistry/*genetics ; }, abstract = {The discovery of non-universal genetic codes in several mitochondria and nuclear systems during the part ten years has necessitated a reconsideration of the concept that the genetic code is universal and frozen, as was once believed. Here, the flexibility of the relationship between codons and amino acids is discussed on the basis of the distribution of non-universal genetic codes in various organisms insofar as has been observed to date. Judging from the result of recent investigations into tRNA identity, it would appear that the non-participation of the anticodon in recognition by aminoacyl-tRNA synthetase has significantly influenced the variability of codons.}, }
@article {pmid8307368, year = {1993}, author = {Sitnikova, TL and Zharkikh, AA}, title = {[Sequences resembling fragments of mitochondrial DNA in the human genome: features of evolution].}, journal = {Genetika}, volume = {29}, number = {11}, pages = {1793-1805}, pmid = {8307368}, issn = {0016-6758}, mesh = {Base Composition ; *Biological Evolution ; Cytosine/analysis ; DNA, Mitochondrial/*genetics ; *Genome, Human ; Guanine/analysis ; Humans ; RNA, Transfer ; Sequence Homology, Nucleic Acid ; }, abstract = {Mitochondrial-like sequences and their homologues from primate mitochondria are investigated to define direction and rate of evolution, time of integration into nuclear genome. The analysis showed that mito-like sequences differ from mitochondrial homologues by high level of symmetria of two chains of DNA. Besides that, difference between mito-like and Homo sapiens sequences in their GC-contents is found. Apparently there is GC-pressure of nuclear genome region, being the place of integration of mito-like sequence, that brings about equalization of GC-contents in nuclear region and mito-like sequences. Properties of descent mitochondrial sequence play important role in the difference of mito-like and Homo sapiens sequences also.}, }
@article {pmid8281749, year = {1993}, author = {Jukes, TH and Osawa, S}, title = {Evolutionary changes in the genetic code.}, journal = {Comparative biochemistry and physiology. B, Comparative biochemistry}, volume = {106}, number = {3}, pages = {489-494}, doi = {10.1016/0305-0491(93)90122-l}, pmid = {8281749}, issn = {0305-0491}, support = {R01 HG00312/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Anticodon ; *Biological Evolution ; Codon ; *Genetic Code ; Mitochondria/physiology ; Mycoplasma/genetics ; Plants/genetics ; }, abstract = {1. The genetic code was thought to be identical ("universal") in all biological systems until 1981, when it was discovered that the coding system in mammalian mitochondria differed from the universal code in the use of codons AUA, UGA, AGA and AGG. 2. Many other differences have since been discovered, some in mitochondria of various phyla, others in bacteria, ciliated protozoa, algae and yeasts. 3. The original thesis that the code was universal and "frozen" depended on the precept that any mutational change in the code would be lethal, because it would produce widespread alterations in the amino acid sequences of proteins. Such changes would destroy protein function, and hence would be intolerable. 4. The objection was "by-passed" by nature. It is possible for a codon to disappear from mRNA molecules, often as a result of directional mutation pressure in DNA: thus all UGA stop codons can be replaced by UAA. 5. The missing UGA codon can then reappear when some UGG tryptophan codons mutate to UGA. The new UGA codons will be translated as tryptophan, as is the case in non-plant mitochondria and Mycoplasma. Therefore, no changes have taken place in the amino acid sequences of proteins. 6. Variations of this procedure have occurred, affecting various codons, and discoveries are still being made. The findings illustrate the evolutionary interplay between tRNA, release factors and codon-anticodon pairing.}, }
@article {pmid8277854, year = {1993}, author = {Taylor, MF and McKechnie, SW and Pierce, N and Kreitman, M}, title = {The lepidopteran mitochondrial control region: structure and evolution.}, journal = {Molecular biology and evolution}, volume = {10}, number = {6}, pages = {1259-1272}, doi = {10.1093/oxfordjournals.molbev.a040075}, pmid = {8277854}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Caenorhabditis elegans/genetics ; Conserved Sequence ; DNA Primers ; DNA, Mitochondrial/*genetics ; Drosophila/genetics ; Genome ; Larva ; Lepidoptera/*genetics ; Mammals/genetics ; Mitochondria/metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Polymerase Chain Reaction ; Pupa ; RNA, Ribosomal/*genetics ; RNA, Transfer, Met/genetics ; Saccharomyces cerevisiae/genetics ; Sequence Homology, Nucleic Acid ; Species Specificity ; Tetrahymena thermophila/genetics ; }, abstract = {For several species of lepidoptera, most of the approximately 350-bp mitochondrial control-region sequences were determined. Six of these species are in one genus, Jalmenus; are closely related; and are believed to have undergone recent rapid speciation. Recent speciation was supported by the observation of low interspecific sequence divergence. Thus, no useful phylogeny could be constructed for the genus. Despite a surprising conservation of control-region length, there was little conservation of primary sequences either among the three lepidopteran genera or between lepidoptera and Drosophila. Analysis of secondary structure indicated only one possible feature in common--inferred stem loops with higher-than-random folding energies--although the positions of the structures in different species were unrelated to regions of primary sequence similarity. We suggest that the conserved, short length of control regions is related to the observed lack of heteroplasmy in lepidopteran mitochondrial genomes. In addition, determination of flanking sequences for one Jalmenus species indicated (i) only weak support for the available model of insect 12S rRNA structure and (ii) that tRNA translocation is a frequent event in the evolution of insect mitochondrial genomes.}, }
@article {pmid8123196, year = {1993}, author = {Tsukamoto, H and French, SW}, title = {Evolution of intragastric ethanol infusion model.}, journal = {Alcohol (Fayetteville, N.Y.)}, volume = {10}, number = {6}, pages = {437-441}, doi = {10.1016/0741-8329(93)90060-2}, pmid = {8123196}, issn = {0741-8329}, mesh = {Animals ; Cytochrome P-450 CYP2E1 ; Cytochrome P-450 Enzyme System/physiology ; Dietary Fats/pharmacology ; Dose-Response Relationship, Drug ; Drug Tolerance ; Ethanol/*administration &amp; dosage/*adverse effects/blood ; Intubation, Gastrointestinal ; Liver Diseases, Alcoholic/etiology ; Mitochondria, Liver/physiology ; Oxidoreductases, N-Demethylating/physiology ; Rats ; }, }
@article {pmid8132485, year = {1993}, author = {Klingenberg, M}, title = {Dialectics in carrier research: the ADP/ATP carrier and the uncoupling protein.}, journal = {Journal of bioenergetics and biomembranes}, volume = {25}, number = {5}, pages = {447-457}, pmid = {8132485}, issn = {0145-479X}, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Adipose Tissue, Brown/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Biological Transport ; Carrier Proteins/chemistry/*physiology ; *Energy Metabolism ; Intracellular Membranes/*metabolism ; Ion Channels ; Mammals/metabolism ; Membrane Proteins/chemistry/*physiology ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/chemistry/*physiology ; Mitochondrial Proteins ; Molecular Sequence Data ; Phylogeny ; Protein Structure, Tertiary ; Protons ; Structure-Activity Relationship ; Uncoupling Protein 1 ; }, abstract = {A concise review is given of the research in our laboratory on the ADP/ATP carrier (AAC) and the uncoupling protein (UCP). Although homologous proteins, their widely different functions and contrasts are stressed. The pioneer role of research on the AAC, not only for the mitochondrial but also for other carriers, and the present state of their structure-function relationship is reviewed. The function of UCP as a highly regulated H+ carrier is described in contrast to the largely unregulated ADP/ATP exchange in AAC. General principles of carrier catalysis as derived from studies on the AAC and UCP are elucidated.}, }
@article {pmid7916674, year = {1993}, author = {Brandt, P and Unseld, M and Eckert-Ossenkopp, U and Brennicke, A}, title = {An rps14 pseudogene is transcribed and edited in Arabidopsis mitochondria.}, journal = {Current genetics}, volume = {24}, number = {4}, pages = {330-336}, pmid = {7916674}, issn = {0172-8083}, mesh = {Amino Acid Sequence ; Apoproteins/genetics ; Arabidopsis/*genetics/ultrastructure ; Base Sequence ; Biological Evolution ; Cytochrome b Group/genetics ; Cytochromes b ; DNA ; Molecular Sequence Data ; Open Reading Frames ; *Pseudogenes ; *RNA Editing ; Restriction Mapping ; Ribosomal Proteins/*genetics ; *Transcription, Genetic ; }, abstract = {Sequence analysis of the region upstream of the apocytochrome b (cob) gene in the Arabidopsis mitochondrial genome identifies an open reading frame with homology to ribosomal protein L5, (rpl5), and a pseudogene with similarity to ribosomal protein S14 (rps14) genes. Both cob and rpl5 genes have intact reading frames, but the rps14 homology is disrupted by a stop codon and a deleted nucleotide. The rpl5 gene, the rps14 pseudogene, and the cob gene are separated by one nucleotide and a 1604-nucleotide-long spacer respectively. A plastid-like tRNA(Ser) is encoded downstream from the cob gene. The entire region is transcribed into a 5-kb transcript, containing the rps14 pseudogene and the cob gene. Cob and rpl5 mRNAs are edited in several positions with different frequencies. The rps14 pseudogene is transcribed and edited in one position in common with other plants. Since no intact rps14 gene is found in the mitochondrial genome of Arabidopsis, the functional gene is presumably encoded in the nucleus.}, }
@article {pmid7508516, year = {1993}, author = {Kumazawa, Y and Nishida, M}, title = {Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics.}, journal = {Journal of molecular evolution}, volume = {37}, number = {4}, pages = {380-398}, pmid = {7508516}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA ; Humans ; Mitochondria/*metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Transfer/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Mitochondrial DNA sequences are often used to construct molecular phylogenetic trees among closely related animals. In order to examine the usefulness of mtDNA sequences for deep-branch phylogenetics, genes in previously reported mtDNA sequences were analyzed among several animals that diverged 20-600 million years ago. Unambiguous alignment was achieved for stem-forming regions of mitochondrial tRNA genes by virtue of their conservative secondary structures. Sequences derived from stem parts of the mitochondrial tRNA genes appeared to accumulate much variation linearly for a long period of time: nearly 100 Myr for transition differences and more than 350 Myr for transversion differences. This characteristic could be attributed, in part, to the structural variability of mitochondrial tRNAs, which have fewer restrictions on their tertiary structure than do nonmitochondrial tRNAs. The tRNA sequence data served to reconstruct a well-established phylogeny of the animals with 100% bootstrap probabilities by both maximum parsimony and neighbor-joining methods. By contrast, mitochondrial protein genes coding for cytochrome b and cytochrome oxidase subunit I did not reconstruct the established phylogeny or did so only weakly, although a variety of fractions of the protein gene sequences were subjected to tree-building. This discouraging phylogenetic performance of mitochondrial protein genes, especially with respect to branches originating over 300 Myr ago, was not simply due to high randomness in the data. It may have been due to the relative susceptibility of the protein genes to natural selection as compared with the stem parts of mitochondrial tRNA genes. On the basis of these results, it is proposed that mitochondrial tRNA genes may be useful in resolving deep branches in animal phylogenies with divergences that occurred some hundreds of Myr ago. For this purpose, we designed a set of primers with which mtDNA fragments encompassing clustered tRNA genes were successfully amplified from various vertebrates by the polymerase chain reaction.}, }
@article {pmid8396421, year = {1993}, author = {Lawson, JE and Niu, XD and Browning, KS and Trong, HL and Yan, J and Reed, LJ}, title = {Molecular cloning and expression of the catalytic subunit of bovine pyruvate dehydrogenase phosphatase and sequence similarity with protein phosphatase 2C.}, journal = {Biochemistry}, volume = {32}, number = {35}, pages = {8987-8993}, doi = {10.1021/bi00086a002}, pmid = {8396421}, issn = {0006-2960}, support = {GM06590/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites/genetics ; Biological Evolution ; Cattle ; Cloning, Molecular ; Escherichia coli/genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Peptide Fragments/genetics ; Phosphoprotein Phosphatases/biosynthesis/*genetics ; Pyruvate Dehydrogenase (Lipoamide)-Phosphatase/biosynthesis/*genetics ; RNA, Messenger/genetics ; Recombinant Proteins/biosynthesis ; Sequence Analysis ; Sequence Homology, Amino Acid ; }, abstract = {After many unsuccessful attempts to detect cDNA encoding the catalytic subunit of bovine pyruvate dehydrogenase phosphatase (PDPc) in bovine cDNA libraries, an approach based on the polymerase chain reaction (PCR) was undertaken. Overlapping DNA fragments were generated by PCR from bovine genomic DNA and from cDNA synthesized from total RNA with synthetic oligonucleotide primers on the basis of experimentally determined amino acid sequences. The DNA fragments were subcloned and sequenced. The complete cDNA is 1900 base pairs in length and contains an open reading frame of 1614 nucleotides encoding a putative presequence of 71 amino acid residues and a mature protein of 467 residues with a calculated M(r) of 52,625. Hybridization analysis showed a single mRNA transcript of about 2.0 kilobases. Comparison of the deduced amino acid sequences of the mitochondrial PDPc and the rat cytosolic protein phosphatase 2C indicates that these protein serine/threonine phosphatases evolved from a common ancestor. The mature form of PDPc was coexpressed in Escherichia coli with the chaperonin proteins groEL and groES. The recombinant protein (rPDPc) was purified to near homogeneity. Its activity toward the bovine 32P-labeled pyruvate dehydrogenase complex was Mg(2+)-dependent and Ca(2+)-stimulated and comparable to that of native bovine PDP. An active, truncated form of rPDPc, with M(r) approximately 45,000, was produced in variable amounts during growth of cells and/or during the purification procedure.}, }
@article {pmid8370534, year = {1993}, author = {Vodkin, MH and Gordon, VR and McLaughlin, GL}, title = {A ribosomal protein in Acanthamoeba polyphaga is conserved in eukaryotic nuclei, organelles and bacteria.}, journal = {Gene}, volume = {131}, number = {1}, pages = {141-144}, doi = {10.1016/0378-1119(93)90683-t}, pmid = {8370534}, issn = {0378-1119}, support = {R01 EYO8205/EY/NEI NIH HHS/United States ; }, mesh = {Acanthamoeba/chemistry/*genetics ; Amino Acid Sequence ; Animals ; Archaea/chemistry/genetics ; Bacteria/chemistry/genetics ; Base Sequence ; Chloroplasts/chemistry ; Cloning, Molecular ; Conserved Sequence ; DNA, Mitochondrial/analysis/*genetics ; Eukaryotic Cells/chemistry ; Molecular Sequence Data ; Open Reading Frames ; *Phylogeny ; Ribosomal Proteins/chemistry/*genetics ; Sequence Alignment ; }, abstract = {An EcoRI fragment from the mitochondrial DNA of Acanthamoeba polyphaga was cloned and partly sequenced, and the conceptual translation product of the open reading frame (partial sequence) was found to have similarities with rp114, a ribosomal protein. Phylogenetic analysis based on the amino acid (aa) sequences of this conserved protein resolved four branches that consisted of: (1) eubacteria and the chloroplasts of algae and higher plants, (2) ciliate mitochondria, (3) Acanthamoeba, and (4) archaebacteria and the nuclei of eukaryotes. The groupings based on the rp114 aa sequences were consistent with the phylogenies derived by rRNA analysis of these organisms.}, }
@article {pmid7690854, year = {1993}, author = {Weidner, U and Geier, S and Ptock, A and Friedrich, T and Leif, H and Weiss, H}, title = {The gene locus of the proton-translocating NADH: ubiquinone oxidoreductase in Escherichia coli. Organization of the 14 genes and relationship between the derived proteins and subunits of mitochondrial complex I.}, journal = {Journal of molecular biology}, volume = {233}, number = {1}, pages = {109-122}, doi = {10.1006/jmbi.1993.1488}, pmid = {7690854}, issn = {0022-2836}, mesh = {Alcaligenes/genetics ; Amino Acid Sequence ; Base Sequence ; Chromosome Mapping ; DNA, Recombinant ; Escherichia coli/enzymology/*genetics ; Formate Dehydrogenases/genetics ; Gene Library ; Genes, Bacterial/*genetics ; Hydrogenase/genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Multienzyme Complexes/genetics ; NAD(P)H Dehydrogenase (Quinone)/*genetics ; Polymerase Chain Reaction ; Pseudomonas/enzymology ; RNA/genetics ; Regulatory Sequences, Nucleic Acid/genetics ; Sequence Analysis, DNA ; Sequence Homology, Amino Acid ; Transcription, Genetic ; }, abstract = {The gene locus nuo of the proton-translocating NADH: ubiquinone oxidoreductase in Escherichia coli was identified by means of a DNA probe made by the polymerase chain reaction. The primers used for the reaction were derived from consensus sequences of the NAD(H)-binding subunit of mitochondrial NADH: ubiquinone oxidoreductase and the NAD(+)-reducing hydrogenase of Alcaligenes eutrophus. The nuo locus lies between minutes 49.2 and 49.6 on the E. coli chromosome and contains a cluster of 14 genes. They are bordered upstream by a sequence resembling sigma 70-dependent promoters and downstream by a sequence resembling rho-independent terminators. All 14 proteins derived from the nuo-genes are related to subunits of mitochondrial NADH: ubiquinone oxidoreductase, among which all subunits presumed to bind the substrates and to harbour the redox groups are found, as well as all seven mitochondrially encoded subunits. The E. coli enzyme seems to represent the minimal form of a proton-translocating NADH: ubiquinone oxidoreductase. The gene order in the nuo locus is conserved in comparison with other bacterial genomes and the chloroplast genome of higher plants. To some extent, the gene order correlates with the topological arrangement of the encoded subunits. The conception of modular evolution of NADH: ubiquinone oxidoreductase is further supported by the arrangement of the nuo-genes.}, }
@article {pmid8300282, year = {1993}, author = {Rohde, K and Watson, NA}, title = {Spermatogenesis in Udonella (Platyhelminthes, Udonellidea) and the phylogenetic position of the genus.}, journal = {International journal for parasitology}, volume = {23}, number = {6}, pages = {725-735}, doi = {10.1016/0020-7519(93)90068-a}, pmid = {8300282}, issn = {0020-7519}, mesh = {Animals ; Male ; Microscopy, Electron ; Phylogeny ; Platyhelminths/*classification/physiology ; Spermatids/ultrastructure ; Spermatogenesis/*physiology ; Testis/ultrastructure ; Trematoda/*classification/physiology ; }, abstract = {Spermatids are joined (cytophores). Two centrioles lateral and/or proximal to the nucleus form axonemes, arranged parallel with each other, that extend into a short distal cytoplasmic process. The nucleus elongates, and mitochondria fuse to form a single elongate mitochondrion. The part of the spermatid containing the axonemes, nucleus and mitochondrion elongates to a thread-like spermatozoon, surrounded at its base (at the level near the basal bodies) by an arching membrane where the sperm detaches from the residual cytoplasm. At no stage are there free flagella (except for short free flagellar tips), an intercentriolar body or a median cytoplasmic process. A few peripheral microtubules and a compact dense body, not membrane bound and closely associated with the mitochondrion, were seen in spermatids. Spermiogenesis in Udonella is interpreted as derived from proximo-distal fusion by a shifting of the basal bodies deeper into the cytoplasm and a consequent loss of the median cytoplasmic process. Both the ultrastructure of the protonephridia and spermiogenesis indicate that Udonella does not represent the sister group of all other neodermatans, but is a secondarily modified "advanced" neodermatan. Lack of convincing synapomorphies indicates that the taxon Cercomeridea as a defined by Brooks (1989a, b) is invalid.}, }
@article {pmid8221935, year = {1993}, author = {Wegener, S and Schmitz, UK}, title = {The presequence of cytochrome c1 from potato mitochondria is encoded on four exons.}, journal = {Current genetics}, volume = {24}, number = {3}, pages = {256-259}, pmid = {8221935}, issn = {0172-8083}, mesh = {Amino Acid Sequence ; Base Sequence ; Cytochromes c1/*genetics ; DNA, Mitochondrial/genetics ; *Exons ; *Genes, Plant ; Introns ; Mitochondria/*enzymology ; Molecular Sequence Data ; Restriction Mapping ; Solanum tuberosum/enzymology/*genetics ; }, abstract = {The structural organization of a nuclear gene encoding cytochrome c1 from potato was determined. The gene spans 5.1 kb and contains eight introns. All intron/exon junctions follow the GT/AG rule. Functional domains of the mature cytochrome c1 protein are located on separate exons. The presequence, which targets the cytochrome c1 precursor to the mitochondrion and to the correct intra-mitochondrial location, is encoded on the first four exons. The largest intron (2.8 kb) separates the information for mitochondrial targeting from the "intra-mitochondrial sorting domain" of the cytochrome c1 protein. In contrast to other organellar precursor proteins, there is no intron between the DNA sequence encoding the presequence and the mature protein. This may indicate that during evolution the genetic information for the prokaryotic cytochrome c1 was transferred to the nucleus together with the bacterial secretion signal which is structurally and functionally related to "intramitochondrial sorting domains".}, }
@article {pmid8136925, year = {1993}, author = {Graybeal, A}, title = {The phylogenetic utility of cytochrome b: lessons from bufonid frogs.}, journal = {Molecular phylogenetics and evolution}, volume = {2}, number = {3}, pages = {256-269}, doi = {10.1006/mpev.1993.1024}, pmid = {8136925}, issn = {1055-7903}, mesh = {Amino Acid Sequence ; Animals ; Bufonidae/*classification/*genetics ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/*genetics ; Geography ; Mitochondria/metabolism ; Molecular Sequence Data ; North America ; *Phylogeny ; Sequence Homology, Amino Acid ; Species Specificity ; Xenopus laevis/classification/genetics ; }, abstract = {The mitochondrial cytochrome b gene is widely used in systematic studies to resolve divergences of many different ages. To investigate phylogenetic relationships among frogs of the large family Bufonidae, and to explore the utility of cytochrome b for this purpose, approximately one-third of the gene was sequenced from representatives of this group. Samples were chosen to represent a range of divergence levels within Bufonidae: (1) deep (= old), among species from around the world; (2) middle, among North American species; and (3) shallow (= young), within a single species group (the Bufo boreas group). The inferred amino acid sequences of cytochrome b are highly similar in these frogs although most pairwise comparisons of the nucleotide sequences are 15-20% different. Consequently insufficient information is available to generate robust phylogenetic hypotheses for the older divergences; silent differences are saturated and yet almost no informative replacement differences exist. Among the younger divergences, silent differences are not saturated and some resolution is possible. These results show that (1) the amino acid sequence of cytochrome b evolves differently in Bufonidae than expected based on other vertebrates (2) it consequently provides surprisingly little information about old divergences in Bufonidae, and (3) phylogenetic studies applying particular genes to new groups should begin with preliminary surveys of exemplar taxa representing the range of divergence times within the group to estimate the likely phylogenetic utility of that gene in that group.}, }
@article {pmid8136924, year = {1993}, author = {da Silva, MN and Patton, JL}, title = {Amazonian phylogeography: mtDNA sequence variation in arboreal echimyid rodents (Caviomorpha).}, journal = {Molecular phylogenetics and evolution}, volume = {2}, number = {3}, pages = {243-255}, doi = {10.1006/mpev.1993.1023}, pmid = {8136924}, issn = {1055-7903}, mesh = {Animals ; Base Sequence ; Brazil ; Cytochrome b Group/*genetics ; DNA Primers ; DNA, Mitochondrial/chemistry/*genetics ; *Genetic Variation ; Geography ; Mitochondria, Liver/metabolism ; Molecular Sequence Data ; *Phylogeny ; Rodentia/classification/*genetics ; Species Specificity ; }, abstract = {Patterns of evolutionary relationships among haplotype clades of sequences of the mitochondrial cytochrome b DNA gene are examined for five genera of arboreal rodents of the Caviomorph family Echimyidae from the Amazon Basin. Data are available for 798 bp of sequence from a total of 24 separate localities in Peru, Venezuela, Bolivia, and Brazil for Mesomys, Isothrix, Makalata, Dactylomys, and Echimys. Sequence divergence, corrected for multiple hits, is extensive, ranging from less than 1% for comparisons within populations of over 20% among geographic units within genera. Both the degree of differentiation and the geographic patterning of the variation suggest that more than one species composes the Amazonian distribution of the currently recognized Mesomys hispidus, Isothrix bistriata, Makalata didelphoides, and Dactylomys dactylinus. There is general concordance in the geographic range of haplotype clades for each of these taxa, and the overall level of differentiation within them is largely equivalent. These observations suggest that a common vicariant history underlies the respective diversification of each genus. However, estimated times of divergence based on the rate of third position transversion substitutions for the major clades within each genus typically range above 1 million years. Thus, allopatric isolation precipitating divergence must have been considerably earlier than the late Pleistocene forest fragmentation events commonly invoked for Amazonian biota.}, }
@article {pmid8136921, year = {1993}, author = {DeWalt, TS and Sudman, PD and Hafner, MS and Davis, SK}, title = {Phylogenetic relationships of pocket gophers (Cratogeomys and Pappogeomys) based on mitochondrial DNA cytochrome b sequences.}, journal = {Molecular phylogenetics and evolution}, volume = {2}, number = {3}, pages = {193-204}, doi = {10.1006/mpev.1993.1020}, pmid = {8136921}, issn = {1055-7903}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cytochrome b Group/*genetics ; DNA Primers ; DNA, Mitochondrial/chemistry/*genetics ; Genetic Variation ; Kidney/metabolism ; Mitochondria/*metabolism ; Mitochondria, Liver/metabolism ; Molecular Sequence Data ; *Phylogeny ; Polymerase Chain Reaction ; Rodentia/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Phylogenetic relationships among 7 of the 10 species of pocket gophers in the genera Pappogeomys and Cratogeomys were addressed using nucleotide sequence data from the entire cytochrome b gene of the mitochondrial genome (1140 base pairs). Results of parsimony analysis were concordant with the results of morphological analysis (R. J. Russell, Univ. Kans. Pub. Mus. Nat. Hist. 16: 581-776, 1968), but differed somewhat from the conclusions drawn from an allozymic study of these species (R. L. Honeycutt and S. L. Williams, J. Mammal. 63: 208-217, 1982). Phylogenetic analysis indicated that Cratogeomys is monophyletic, as are the two species groups within this genus. Estimates of levels of nucleotide sequence divergence between species of these genera indicated that the cytochrome b gene of pocket gophers may have evolved at a dramatically higher rate than in organisms examined previously (D. M. Irwin, T. D. Kocher, and A. C. Wilson, J. Mol. Evol. 32: 128-144, 1991).}, }
@article {pmid8226714, year = {1993}, author = {Friedrich, T and Weidner, U and Nehls, U and Fecke, W and Schneider, R and Weiss, H}, title = {Attempts to define distinct parts of NADH:ubiquinone oxidoreductase (complex I).}, journal = {Journal of bioenergetics and biomembranes}, volume = {25}, number = {4}, pages = {331-337}, pmid = {8226714}, issn = {0145-479X}, mesh = {Animals ; Bacterial Proteins/chemistry/genetics ; Biological Evolution ; Cattle ; Electron Transport ; Escherichia coli/enzymology/genetics ; Fungal Proteins/chemistry/isolation &amp; purification/ultrastructure ; Genes, Bacterial ; Microscopy, Electron ; Mitochondria, Heart/enzymology ; NAD(P)H Dehydrogenase (Quinone)/*chemistry/genetics/isolation &amp; purification/ultrastructure ; Paracoccus denitrificans/enzymology/genetics ; *Protein Conformation ; Protein Folding ; }, abstract = {The NADH:ubiquinone oxidoreductase (complex I) is made up of a peripheral part and a membrane part. The two parts are arranged perpendicular to each other and give the complex an unusual L-shaped structure. The peripheral part protrudes into the matrix space and constitutes the proximal segment of the electron pathway with the NADH-binding site, the FMN and at least three iron-sulfur clusters. The membrane part constitutes the distal segment of the electron pathway with at least one iron-sulfur cluster and the ubiquinone-binding site. Both parts are assembled separately and relationships of the major structural modules of the two parts with different bacterial enzymes suggest, that both parts also emerged independently in evolution. This assumption is further supported by the conserved order of bacterial complex I genes, which correlates with the topological arrangement of the corresponding subunits in the two parts of complex I.}, }
@article {pmid7905491, year = {1993}, author = {Lohse, AW and Dienes, HP and Herkel, J and Hermann, E and van Eden, W and Meyer zum Büschenfelde, KH}, title = {Expression of the 60 kDa heat shock protein in normal and inflamed liver.}, journal = {Journal of hepatology}, volume = {19}, number = {1}, pages = {159-166}, doi = {10.1016/s0168-8278(05)80189-8}, pmid = {7905491}, issn = {0168-8278}, mesh = {Chaperonin 60 ; Chronic Disease ; Heat-Shock Proteins/*analysis ; Hepatitis/*metabolism ; Humans ; Liver/*chemistry ; Reference Values ; }, abstract = {The 60 kDa heat shock proteins (HSP 60) have been well conserved throughout evolution and are highly immunogenic. Cross-reactivity between bacterial and mammalian HSP 60 is considered a likely mechanism in the pathogenesis of autoimmune diseases. T cell and B cell reactivity to HSP 60 is found in patients with rheumatoid or juvenile arthritis, and the expression of HSP 60 in the inflamed joint is found to be increased. In this study the presence of HSP 60 was demonstrated in normal and inflamed lives. HSP 60 was found to be predominantly expressed in hepatocytes and Kupffer cells, and mainly localized in mitochondria. Heat stress in the form of a 1 h incubation at 42 degrees C increased HSP 60 expression. The expression of HSP 60 in chronic active hepatitis was found to be markedly increased, with predominant expression in areas of inflammatory infiltrates. This increased expression in the inflamed liver was found both in viral and autoimmune hepatitis. High expression of HSP 60 in chronic active hepatitis was entirely due to self (i.e. human) HSP 60; no additional bacterial HSP 60 could be detected. Increased expression of HSP 60 in chronic active hepatitis suggests that immune reactions to HSP 60 may play a role in the immunopathogenesis and perpetuation of chronic inflammatory liver disease.}, }
@article {pmid8343174, year = {1993}, author = {Schneider, G and Röhlk, S and Wrede, P}, title = {Analysis of cleavage-site patterns in protein precursor sequences with a perceptron-type neural network.}, journal = {Biochemical and biophysical research communications}, volume = {194}, number = {2}, pages = {951-959}, doi = {10.1006/bbrc.1993.1913}, pmid = {8343174}, issn = {0006-291X}, mesh = {Algorithms ; *Amino Acid Sequence ; Bacterial Proteins/metabolism ; Biological Evolution ; Chloroplasts/metabolism ; Databases, Factual ; Escherichia coli/metabolism ; Humans ; Mitochondria/metabolism ; *Neural Networks, Computer ; Plant Proteins/metabolism ; Plants/metabolism ; Protein Precursors/*chemistry/metabolism ; Protein Processing, Post-Translational ; Protein Sorting Signals/*chemistry/metabolism ; }, abstract = {A method for feature extraction from protein sequences has been developed which is based on an artificial neural filter system. Amino acid sequences are analyzed with regard to physicochemical residue properties. This alternative representation of a sequence allows an interpretation of the networks' weight values in a comprehensive and biochemically meaningful way by displaying the optimized network weights in Hinton diagrams. Signal peptidase cleavage sites of E.coli periplasmic proteins, human mitochondrial precursors and chloroplast precursors from spinach have been investigated. The network for E.coli periplasmic protein precursors classified both training and test data with 100% accuracy. The interpretation of its network weights clearly confirms the "-3,-1 rule" and the existence of a hydrophobic core region starting at position -6. Further striking features and dominant positions can be found for all three types of cleavage sites.}, }
@article {pmid8329437, year = {1993}, author = {Esposti, MD and De Vries, S and Crimi, M and Ghelli, A and Patarnello, T and Meyer, A}, title = {Mitochondrial cytochrome b: evolution and structure of the protein.}, journal = {Biochimica et biophysica acta}, volume = {1143}, number = {3}, pages = {243-271}, doi = {10.1016/0005-2728(93)90197-n}, pmid = {8329437}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites ; Biological Evolution ; Cytochrome b Group/antagonists &amp; inhibitors/chemistry/*isolation &amp; purification ; Humans ; Mitochondria/*enzymology ; Molecular Sequence Data ; Sequence Alignment ; Terminology as Topic ; }, abstract = {Cytochrome b is the central redox catalytic subunit of the quinol: cytochrome c or plastocyanin oxidoreductases. It is involved in the binding of the quinone substrate and it is responsible for the transmembrane electron transfer by which redox energy is converted into a protonmotive force. Cytochrome b also contains the sites to which various inhibitors and quinone antagonists bind and, consequently, inhibit the oxidoreductase. Ten partial primary sequences of cytochrome b are presented here and they are compared with sequence data from over 800 species for a detailed analysis of the natural variation in the protein. This sequence information has been used to predict some aspects of the structure of the protein, in particular the folding of the transmembrane helices and the location of the quinone- and heme-binding pockets. We have observed that inhibitor sensitivity varies greatly among species. The comparison of inhibition titrations in combination with the analysis of the primary structures has enabled us to identify amino acid residues in cytochrome b that may be involved in the binding of the inhibitors and, by extrapolation, quinone/quinol. The information on the quinone-binding sites obtained in this way is expected to be both complementary and supplementary to that which will be obtained in the future by mutagenesis and X-ray crystallography.}, }
@article {pmid8345516, year = {1993}, author = {Guo, HC and De Abreu, DM and Tillier, ER and Saville, BJ and Olive, JE and Collins, RA}, title = {Nucleotide sequence requirements for self-cleavage of Neurospora VS RNA.}, journal = {Journal of molecular biology}, volume = {232}, number = {2}, pages = {351-361}, doi = {10.1006/jmbi.1993.1395}, pmid = {8345516}, issn = {0022-2836}, mesh = {Base Sequence ; Consensus Sequence ; DNA Mutational Analysis ; Genetic Variation ; Mitochondria/metabolism ; Molecular Sequence Data ; Mutagenesis, Insertional ; Neurospora/genetics/*metabolism ; Phylogeny ; Plasmids/genetics ; *RNA Processing, Post-Transcriptional ; RNA, Catalytic/genetics/*metabolism ; RNA, Fungal/genetics/*metabolism ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Structure-Activity Relationship ; }, abstract = {We have used several complementary approaches to investigate the minimal contiguous sequence required for the in vitro self cleavage reaction performed by Neurospora VS RNA. Deletion analysis and site-directed mutagenesis revealed that only a single nucleotide is required upstream of the self-cleavage site, and that the identity of this nucleotide is not critical. This distinguishes VS RNA from all currently known ribozymes except hepatitis delta virus RNA. The shortest contiguous sequence capable of cleavage contains 153 nt downstream of the cleavage site. Linker insertion mutagenesis suggests that much of this downstream sequence is important for self-cleavage. Comparative sequence analysis of the VS plasmid from six natural isolates supports the importance in vivo of the minimal region determined by in vitro methods. Also, phylogenetic analysis raises the possibility of a recent horizontal transfer of the VS plasmid from Neurospora intermedia to Neurospora sitophila.}, }
@article {pmid8332461, year = {1993}, author = {Barker, C and Makris, A and Patriotis, C and Bear, SE and Tsichlis, PN}, title = {Identification of the gene encoding the mitochondrial elongation factor G in mammals.}, journal = {Nucleic acids research}, volume = {21}, number = {11}, pages = {2641-2647}, pmid = {8332461}, issn = {0305-1048}, support = {CA-06927/CA/NCI NIH HHS/United States ; CA-38047/CA/NCI NIH HHS/United States ; RR-05539/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Chromosome Mapping ; Cloning, Molecular ; Conserved Sequence ; DNA, Mitochondrial/genetics ; Escherichia coli/genetics ; Humans ; Mammals/genetics ; Mitochondria/*metabolism ; Molecular Sequence Data ; Oligodeoxyribonucleotides ; Organ Specificity ; Peptide Elongation Factor G ; Peptide Elongation Factors/*genetics ; Pseudomonas aeruginosa/genetics ; Rats/*genetics ; Receptors, Somatotropin/*genetics ; Ribosomes/metabolism ; Saccharomyces cerevisiae/genetics ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Thermus thermophilus/genetics ; }, abstract = {Protein synthesis in cytosolic and rough endoplasmic reticulum associated ribosomes is directed by factors, many of which have been well characterized. Although these factors have been the subject of intense study, most of the corresponding factors regulating protein synthesis in the mitochondrial ribosomes remain unknown. In this report we present the cloning and initial characterization of the gene encoding the rat mitochondrial elongation factor-G (rEF-Gmt). The rat gene encoding EF-Gmt (rMef-g) maps to rat chromosome 2 and it is expressed in all tissues with highest levels in liver, thymus and brain. Its DNA sequence predicts a 752 amino acid protein exhibiting 72% homology to the yeast Saccharomyces cerevisiae mitochondrial elongation factor-G (YMEF-G), 62% and 61% homology to the Thermus thermophilus and E. coli elongation factor-G (EF-G) respectively and 52% homology to the rat elongation factor-2 (EF-2). The deduced amino acid sequence of EF-G contains characteristic motifs shared by all GTP binding proteins. Therefore, similarly to other elongation factors, the enzymatic function of EF-Gmt is predicted to depend on GTP binding and hydrolysis. EF-Gmt differs from its cytoplasmic homolog, EF-2, in that it contains an aspartic acid residue at amino acid position 621 which corresponds to the EF-2 histidine residue at position 715. Since this histidine residue, following posttranslational modification into diphthamide, appears to be the sole cellular target of diphtheria toxin and Pseudomonas aeruginosa endotoxin A, we conclude that EF-Gmt will not be inactivated by these toxins. The severe effects of these toxins on protein elongation in tissues expressing EF-Gmt suggest that EF-Gmt and EF-2 exhibit nonoverlapping functions. The cloning and characterization of the mammalian mitochondrial elongation factor G will permit us to address its role in the regulation of normal mitochondrial function and in disease states attributed to mitochondrial dysfunction.}, }
@article {pmid8394320, year = {1993}, author = {Graham, LA and Brandt, U and Sargent, JS and Trumpower, BL}, title = {Mutational analysis of assembly and function of the iron-sulfur protein of the cytochrome bc1 complex in Saccharomyces cerevisiae.}, journal = {Journal of bioenergetics and biomembranes}, volume = {25}, number = {3}, pages = {245-257}, pmid = {8394320}, issn = {0145-479X}, mesh = {Amino Acid Sequence ; Bacterial Proteins/chemistry ; Catalysis ; Electron Transport ; Electron Transport Complex III/genetics/*physiology ; Fungal Proteins/genetics/*metabolism ; Iron-Sulfur Proteins/genetics/*physiology ; Mitochondria/enzymology ; Models, Molecular ; Molecular Sequence Data ; *Mutagenesis ; Oxidation-Reduction ; Phylogeny ; Plant Proteins/chemistry ; Protein Conformation ; Protein Processing, Post-Translational ; Saccharomyces cerevisiae/*enzymology/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Ubiquinone/analogs &amp; derivatives/metabolism ; }, abstract = {The iron-sulfur protein of the cytochrome bc1 complex oxidizes ubiquinol at center P in the protonmotive Q cycle mechanism, transferring one electron to cytochrome c1 and generating a low-potential ubisemiquinone anion which reduces the low-potential cytochrome b-566 heme group. In order to catalyze this divergent transfer of two reducing equivalents from ubiquinol, the iron-sulfur protein must be structurally integrated into the cytochrome bc1 complex in a manner which facilitates electron transfer from the iron-sulfur cluster to cytochrome c1 and generates a strongly reducing ubisemiquinone anion radical which is proximal to the b-566 heme group. This radical must also be sequestered from spurious reactivities with oxygen and other high-potential oxidants. Experimental approaches are described which are aimed at understanding how the iron-sulfur protein is inserted into center P, and how the iron-sulfur cluster is inserted into the apoprotein.}, }
@article {pmid8365657, year = {1993}, author = {Kaneko, M and Satta, Y and Matsuura, ET and Chigusa, SI}, title = {Evolution of the mitochondrial ATPase 6 gene in Drosophila: unusually high level of polymorphism in D. melanogaster.}, journal = {Genetical research}, volume = {61}, number = {3}, pages = {195-204}, doi = {10.1017/s0016672300031360}, pmid = {8365657}, mesh = {Adenosine Triphosphatases/*genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; DNA, Mitochondrial/*chemistry ; Drosophila/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Mutation ; *Polymorphism, Genetic ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {We have determined 1990 bp mitochondrial DNA sequence which extends from 3' end of the cytochrome oxidase subunit I (COI) gene to 5' end of the COIII gene from two sibling species of Drosophila, D. simulans and D. mauritiana. Analyses of the sequences and part of the NADH dehydrogenase subunit 2 gene and the COI gene together with those from D. melanogaster and D. yakuba revealed that amino-acid substitution rate of the ATPase 6 gene seems to be higher in some strains of D. melanogaster than in the other species. High level of amino-acid polymorphism in this gene was observed in D. melanogaster. Synonymous substitution rate is relatively constant in all the genes examined, suggesting that mutation rate is not higher in the ATPase 6 gene of D. melanogaster. The amino-acid substitutions found specifically in D. melanogaster are at the sites which are not conserved among mammals, yeast and E. coli. These sites of the ATPase 6 gene might lose the selective constraint in D. melanogaster, and the amino-acid substitutions can be explained by neutral mutations and random genetic drift.}, }
@article {pmid8387160, year = {1993}, author = {Landweber, LF and Gilbert, W}, title = {RNA editing as a source of genetic variation.}, journal = {Nature}, volume = {363}, number = {6425}, pages = {179-182}, doi = {10.1038/363179a0}, pmid = {8387160}, issn = {0028-0836}, mesh = {Animals ; Base Sequence ; Biological Evolution ; DNA, Protozoan/genetics ; Electron Transport Complex IV/genetics ; Frameshift Mutation ; Genetic Variation/*genetics ; Mitochondria ; *RNA Editing ; RNA, Messenger/genetics ; RNA, Protozoan/genetics ; Sequence Alignment ; Trypanosomatina/*genetics ; }, abstract = {Kinetoplastid RNA editing alters mitochondrial RNA transcripts by addition and deletion of uridine residues, producing open reading frames that may be twice as long as the original RNA. Although the COIII gene encoding cytochrome c oxidase subunit III in Trypanosoma brucei is edited along its entire length, the presumably homologous genes in two related trypanosomes, Leishmania tarentolae and Crithidia fasciculata, are only modestly edited at their 5' ends. We used a comparative approach to investigate the evolution of an edited gene and to determine how well editing creates conserved protein sequences. As RNA editing probably involves the pairing of several guide RNA molecules with the messenger RNA, we expected the edited proteins to be resistant to evolutionary change. Here we report that RNA editing is extensive in the mitochondria of four species of the insect parasite Herpetomonas, which is possibly an evolutionary precursor of T. brucei and L. tarentolae, and the discovery that RNA editing is a novel source of frameshift mutations over evolutionary time. The edited proteins accumulate mutations nearly twice as rapidly as the unedited versions.}, }
@article {pmid8481382, year = {1993}, author = {Hoesche, JA and Berzborn, RJ}, title = {Primary structure, deduced from cDNA, secondary structure analysis and conclusions concerning interaction surfaces of the delta subunit of the photosynthetic ATP-synthase (E.C. 3.6.1.34) from millet (Sorghum bicolor) and maize (Zea mays).}, journal = {Biochimica et biophysica acta}, volume = {1142}, number = {3}, pages = {293-305}, doi = {10.1016/0005-2728(93)90157-b}, pmid = {8481382}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; Base Sequence ; Biological Evolution ; Chloroplasts/enzymology ; Cloning, Molecular ; Conserved Sequence ; DNA ; Molecular Sequence Data ; Panicum/*enzymology ; Polymerase Chain Reaction ; *Protein Structure, Secondary ; Proton-Translocating ATPases/*chemistry/genetics/metabolism ; Sequence Homology, Amino Acid ; Zea mays/*enzymology ; }, abstract = {Lambda gt11 cDNA clones for the nuclear-encoded subunit delta of the chloroplast ATP-synthase from Zea mays and Sorghum bicolor were sequenced. The processing site for S. bicolor delta was established, and the sequence of the mature subunit delta from Z. mays was completed by N-terminal sequencing of the proteins isolated from chloroplasts. Only five amino acids are identical and not more than 16% conservatively exchanged in all sequences of delta subunits from higher plants and the corresponding proteins from alga, bacteria and mitochondria (OSCP) available. In binary comparison the comparatively high conservation of hydrophilic residues indicates the importance of the surface of delta. The degree in identities of surface residues correlates with the capacity in hybrid reconstitution of photophosphorylation. A hypothetical secondary structure model for a typical delta subunit can be deduced from prediction algorithms. Three putative amphipathic alpha helices and an antiparallel amphipathic beta sheet seem to be conserved. These common secondary structure features should be significant for the function of the delta subunit of F0F1 ATPases.}, }
@article {pmid8393127, year = {1993}, author = {Beckenbach, AT and Wei, YW and Liu, H}, title = {Relationships in the Drosophila obscura species group, inferred from mitochondrial cytochrome oxidase II sequences.}, journal = {Molecular biology and evolution}, volume = {10}, number = {3}, pages = {619-634}, doi = {10.1093/oxfordjournals.molbev.a040034}, pmid = {8393127}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Codon ; Conserved Sequence ; DNA/isolation &amp; purification ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Drosophila/classification/enzymology/*genetics ; Drosophila melanogaster/enzymology/genetics ; Electron Transport Complex IV/*genetics ; Genetic Variation ; Mitochondria/*enzymology ; Molecular Sequence Data ; Oligodeoxyribonucleotides ; *Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {We compare the sequences for the mitochondrial cytochrome oxidase II gene of 13 species of the Drosophila obscura group. The survey includes six members of the D. affinis subgroup, four of the D. pseudoobscura subgroup, and three of the D. obscura subgroup. In all species, the gene is 688 nucleotides in length, encoding a protein of 229 amino acids plus the first position T of the stop codon. The sequences show the typical high-transition bias for closely related species, but that bias is essentially eliminated for species pairs of > 5% sequence divergence. The phylogenetic relationships in the species group are inferred using both neighbor-joining and maximum parsimony. The two procedures give comparable results, showing that the D. affinis and D. pseudoobscura subgroups are monophyletic groupings that appear to have closer affinities to one another than either has to the D. obscura subgroup. We use transversion distances to estimate times of divergence, on the basis of three different estimates of the time of separation of the D. obscura species group from the D. melanogaster group. If that event occurred 35 Mya, then we can estimate the origin of the nearctic forms at approximately 22 Mya and the separation of the D. affinis and D. pseudoobscura subgroups at approximately 17 Mya.}, }
@article {pmid8342426, year = {1993}, author = {Angulo, JC and López, JI and Flores, N}, title = {[Conceptual review of oncocytic lesions].}, journal = {Actas urologicas espanolas}, volume = {17}, number = {5}, pages = {295-298}, pmid = {8342426}, issn = {0210-4806}, mesh = {Adenoma/*pathology ; Cell Division ; Humans ; Hyperplasia/*pathology ; Mitochondria/pathology ; }, abstract = {Updating of a series of entities which significance is not always pathological, or it is poorly known, and which are related to oxyphilic transformation of epithelial cells. Review of concepts such as "oncocytosis", "oncocytic hyperplasia" and "oncocytoma", establishing a hypothetical continuum of damage which could actually be contemplated within the evolution spectrum of hyperplasia-adenoma-carcinoma. Also, both the changes occurring at subcellular level and the hypothesis considered to explain them are commented.}, }
@article {pmid8337383, year = {1993}, author = {Sato, S and Kawaguchi, A}, title = {[Control system of metabolism: oxidative degradation of fatty acid].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {38}, number = {7}, pages = {1109-1116}, pmid = {8337383}, issn = {0039-9450}, mesh = {3-Hydroxyacyl CoA Dehydrogenases/genetics/physiology ; Acyl-CoA Oxidase ; Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Enoyl-CoA Hydratase/genetics/physiology ; Fatty Acid Desaturases/genetics/physiology ; Fatty Acids/*metabolism ; Macromolecular Substances ; Microbodies/enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; Oxidoreductases/genetics/physiology ; Pseudomonas/metabolism ; }, }
@article {pmid8326863, year = {1993}, author = {Riley, DE and Campbell, LA and Puolakkainen, M and Krieger, JN}, title = {Trichomonas vaginalis and early evolving DNA and protein sequences of the CDC2/28 protein kinase family.}, journal = {Molecular microbiology}, volume = {8}, number = {3}, pages = {517-519}, doi = {10.1111/j.1365-2958.1993.tb01595.x}, pmid = {8326863}, issn = {0950-382X}, support = {R01 DK38955/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; CDC2 Protein Kinase/*genetics ; CDC28 Protein Kinase, S cerevisiae/*genetics ; DNA, Protozoan/*genetics ; *Genes ; Molecular Sequence Data ; Phylogeny ; Protozoan Proteins/*genetics ; RNA, Protozoan/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Trichomonas vaginalis/enzymology/*genetics ; }, abstract = {The human sexually transmitted parasite Trichomonas vaginalis is a representative of one of the three earliest evolving eukaryotic lineages. We investigated whether T. vaginalis has DNA sequences and peptides related to cell division control molecules universal among yeasts and higher eukaryotes. A T. vaginalis cell division control (CDC2/28) homologue was amplified by the polymerase chain reaction and sequenced. The absolute similarity with other CDC2/28 genes was 47%, with conservative replacement similarity of 67%. Western blots demonstrated a single T. vaginalis peptide reactive with antiserum to the PSTAIRE peptide, an expressed component of CDC2/28 genes in higher eukaryotes. Although eukaryotic, T. vaginalis has properties similar to those of bacteria and is the earliest evolving eukaryote reported to possess CDC2/28 DNA and peptide homologues. These observations suggest that the molecular origins of cell division control in eukaryotes preceded mitochondria, 28S ribosomes and regulated glycolysis.}, }
@article {pmid8482537, year = {1993}, author = {Tiranti, V and Rocchi, M and DiDonato, S and Zeviani, M}, title = {Cloning of human and rat cDNAs encoding the mitochondrial single-stranded DNA-binding protein (SSB).}, journal = {Gene}, volume = {126}, number = {2}, pages = {219-225}, doi = {10.1016/0378-1119(93)90370-i}, pmid = {8482537}, issn = {0378-1119}, support = {116/TI_/Telethon/Italy ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Blotting, Northern ; Blotting, Southern ; Chromosome Mapping ; Chromosomes, Human, Pair 7 ; Cloning, Molecular ; DNA, Mitochondrial ; DNA, Single-Stranded/*metabolism ; DNA-Binding Proteins/*genetics/metabolism ; Humans ; Mitochondria/*metabolism ; Molecular Sequence Data ; Rats ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {We have retro-transcribed and amplified by PCR the full-length cDNAs specifying the rat and human precursors of the single-stranded mitochondrial DNA (mtDNA)-binding protein (mtSSB). Each deduced sequence is composed of a 16-amino-acid (aa) N-terminal basic pre-sequence and a mature protein (132 aa in humans and 135 aa in the rat). The mature proteins are highly conserved among themselves and with the mtSSB from Xenopus laevis (Xl). Moreover, three regions of the protein are similar to corresponding domains of the SSB of Escherichia coli and to the E. coli F-sex factor SSB, indicating the existence of a broad class of DNA-binding proteins with structural and functional similarities both in prokaryotes and in prokaryote-derived organelles of higher organisms.}, }
@article {pmid8469974, year = {1993}, author = {Block, BA and Finnerty, JR and Stewart, AF and Kidd, J}, title = {Evolution of endothermy in fish: mapping physiological traits on a molecular phylogeny.}, journal = {Science (New York, N.Y.)}, volume = {260}, number = {5105}, pages = {210-214}, doi = {10.1126/science.8469974}, pmid = {8469974}, issn = {0036-8075}, support = {AR40246/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; *Biological Evolution ; *Body Temperature Regulation ; Brain/physiology ; Cytochrome b Group/genetics ; Fishes/classification/genetics/*physiology ; Mitochondria/enzymology ; Molecular Sequence Data ; Muscles/physiology ; Phylogeny ; Retina/physiology ; Tuna/classification/genetics/*physiology ; }, abstract = {Mackerels, tunas, and billfishes (suborder Scombroidei and Teleostei) provide an ideal taxonomic context in which to examine the evolution of endothermy. Multiple origins and diverse strategies for endothermy exist among these fish. Here a molecular phylogeny of the Scombroidei has been determined by direct sequencing of a portion of the mitochondrial cytochrome b gene. The distribution of endothermic species within this proposed genealogy indicates that the ability to warm the brain and retina arose independently in three lineages, each time in association with a movement into colder water. This suggests that the evolution of cranial endothermy in fish was selected in order to permit thermal niche expansion and not selected for increased aerobic capacity.}, }
@article {pmid8315658, year = {1993}, author = {Hasegawa, M and Hashimoto, T and Adachi, J and Iwabe, N and Miyata, T}, title = {Early branchings in the evolution of eukaryotes: ancient divergence of entamoeba that lacks mitochondria revealed by protein sequence data.}, journal = {Journal of molecular evolution}, volume = {36}, number = {4}, pages = {380-388}, pmid = {8315658}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animal Population Groups/classification/genetics ; Animals ; Archaea/classification/genetics ; DNA, Ribosomal/genetics ; Entamoeba/*genetics ; *Eukaryotic Cells ; Fungi/classification/genetics ; Likelihood Functions ; Mitochondria ; Peptide Elongation Factor 1 ; Peptide Elongation Factors/*genetics ; *Phylogeny ; Plants/classification/genetics ; Protozoan Proteins/*genetics ; Species Specificity ; }, abstract = {Phylogenetic analyses of ribosomal RNA sequences have played an important role in the study of early evolution of life. However, Loomis and Smith suggested that the ribosomal RNA tree is sometimes misleading--especially when G+C content differs widely among lineages--and that a protein tree from amino acid sequences may be more reliable. In this study, we analyzed amino acid sequence data of elongation factor-1 alpha by a maximum likelihood method to clarify branching orders in the early evolution of eukaryotes. Contrary to Sogin et al.'s tree of small-subunit ribosomal RNA, a protozoan species, Entamoeba histolytica, that lacks mitochondria was shown to have diverged from the line leading to eukaryotes with mitochondria before the latter separated into several kingdoms. This indicates that Entamoeba is a living relic of the earliest phase of eukaryotic evolution before the symbiosis of protomitochondria occurred. Furthermore, this suggests that, among eukaryotic kingdoms with mitochondria, Fungi is the closest relative of Animalia, and that a cellular slime mold, Dictyostelium discoideum, had not diverged from the line leading to Plantae-Fungi-Animalia before these three kingdoms separated.}, }
@article {pmid8462546, year = {1993}, author = {Miyata, A and Yoshida, T and Yamaguchi, K and Yokoyama, C and Tanabe, T and Toh, H and Mitsunaga, T and Izumi, Y}, title = {Molecular cloning and expression of the gene for serine hydroxymethyltransferase from an obligate methylotroph Hyphomicrobium methylovorum GM2.}, journal = {European journal of biochemistry}, volume = {212}, number = {3}, pages = {745-750}, doi = {10.1111/j.1432-1033.1993.tb17713.x}, pmid = {8462546}, issn = {0014-2956}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/*enzymology/genetics ; Base Sequence ; Blotting, Southern ; Cloning, Molecular/methods ; DNA, Bacterial/genetics/isolation &amp; purification ; Escherichia coli/genetics ; *Genes, Bacterial ; Glycine Hydroxymethyltransferase/*genetics/isolation &amp; purification/*metabolism ; Mitochondria, Liver/enzymology ; Molecular Sequence Data ; Oligodeoxyribonucleotides ; Phylogeny ; Rabbits ; Recombinant Proteins/isolation &amp; purification/metabolism ; Restriction Mapping ; Sequence Homology, Amino Acid ; }, abstract = {The gene encoding serine hydroxymethyltransferase (SHMT), one of the key enzymes of the one-carbon-compound assimilation of a methylotroph, Hyphomicrobium methylovorum GM2, and its flanking regions were isolated using a DNA fragment encoding Escherichia coli SHMT as a probe. Nucleotide sequencing of the recombinant plasmids revealed the SHMT gene codes for the 434-amino-acid protein with a calculated molecular mass of 46,068 Da. The amino-acid sequence of the enzyme showed identity to the sequences of the enzymes from E. coli (55%) and rabbit liver (44%). The recombinant plasmid, which was constructed by ligation of the cloned gene and an expression vector pKK223-3, was introduced to an SHMT-deficient E. coli mutant ME5427 (glyA-). The transformed E. coli cells expressed SHMT, which was immunologically and enzymologically indistinguishable from the enzyme isolated from H. methylovorum GM2.}, }
@article {pmid8459836, year = {1993}, author = {Peterson, GC and Souza, AE and Parsons, M}, title = {Characterization of a Trypanosoma brucei nuclear gene encoding a protein homologous to a subunit of bovine NADH:ubiquinone oxidoreductase (complex I).}, journal = {Molecular and biochemical parasitology}, volume = {58}, number = {1}, pages = {63-70}, doi = {10.1016/0166-6851(93)90091-b}, pmid = {8459836}, issn = {0166-6851}, support = {AI-22635/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Biological Transport ; Cattle/genetics ; Cell Compartmentation ; Cell Nucleus ; Conserved Sequence ; Genes, Protozoan/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; NAD(P)H Dehydrogenase (Quinone)/*genetics ; Protein Sorting Signals/genetics ; Protozoan Proteins/*genetics ; Sequence Homology, Amino Acid ; Trypanosoma brucei brucei/enzymology/*genetics ; }, abstract = {A Trypanosoma brucei gene has been identified that encodes a protein predicted to be a component of the trypanosome homologue of mitochondrial NADH:ubiquinone oxidoreductase (complex I). High homology was found to a 20-kDa component of the iron-sulfur protein fraction of bovine mitochondrial NADH:ubiquinone oxidoreductase and the products of the ndhK locus of Paramecium tetraurelia mitochondria and the NQO6 locus of Paracoccus denitrificans. The homology extends to several other proteins predicted to function as part of electron transport systems, including the psbG/ndhK gene products of chloroplast and cyanobacterial genomes which are thought to be subunits of a NADH:plastoquinone oxidoreductase involved in chlororespiration. The T. brucei ndhK counterpart is nuclearly encoded. An extended amino terminus of the T. brucei ndhK with structural similarity to mitochondrial presequences indicates that its transfer into mitochondria is likely. Stumpy and slender bloodforms and procyclic forms all possess similar levels of ndhK transcripts despite previous reports of stage-regulated expression of complex I-like activity.}, }
@article {pmid8383070, year = {1993}, author = {Tian, GL and Michel, F and Macadre, C and Lazowska, J}, title = {Sequence of the mitochondrial gene encoding subunit I of cytochrome oxidase in Saccharomyces douglasii.}, journal = {Gene}, volume = {124}, number = {2}, pages = {153-163}, doi = {10.1016/0378-1119(93)90389-k}, pmid = {8383070}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Base Sequence ; Biological Evolution ; DNA, Fungal ; DNA, Mitochondrial ; Electron Transport Complex IV/*genetics/metabolism ; Exons ; Genetic Variation ; Introns ; Mitochondria/*enzymology ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Fungal/chemistry/genetics ; Restriction Mapping ; Saccharomyces/enzymology/*genetics ; Sequence Homology, Amino Acid ; }, abstract = {We have determined the complete sequence of the mitochondrial (mt) gene (COXI) coding for cytochrome oxidase subunit I of Saccharomyces douglasii. This gene is 7238 bp long and includes four introns. The salient feature of the S. douglasii COXI gene is the presence of two introns, Sd.ai1 and Sd.ai2, which have not been observed in S. cerevisiae genes. Both are group-I introns and are located at novel positions compared with the S. cerevisiae COXI. Interestingly, one of these introns (the second one) is inserted at the same position as intron 2 of COXI of Kluyveromyces lactis and also as intron 8 of the same gene in Podospora anserina. The ORFs contained in these three introns display a high degree of similarity. Comparisons of exonic and intronic sequences of the COXI of two Saccharomyces species reinforces our previous conclusions: the evolution of mt genes in yeast obeys different rules to those found in vertebrates.}, }
@article {pmid7680126, year = {1993}, author = {Wolff, G and Burger, G and Lang, BF and Kück, U}, title = {Mitochondrial genes in the colourless alga Prototheca wickerhamii resemble plant genes in their exons but fungal genes in their introns.}, journal = {Nucleic acids research}, volume = {21}, number = {3}, pages = {719-726}, pmid = {7680126}, issn = {0305-1048}, mesh = {Amino Acid Sequence ; Animals ; Ascomycota/genetics ; Base Sequence ; Conserved Sequence ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Exons ; *Genes, Fungal ; *Genes, Plant ; Humans ; *Introns ; Mitochondria/*metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Open Reading Frames ; Phylogeny ; Prototheca/*genetics ; RNA/genetics ; RNA, Mitochondrial ; RNA, Ribosomal/genetics ; Sequence Homology, Amino Acid ; }, abstract = {The mitochondrial DNA from the colourless alga Prototheca wickerhamii contains two mosaic genes as was revealed from complete sequencing of the circular extranuclear genome. The genes for the large subunit of the ribosomal RNA (LSUrRNA) as well as for subunit I of the cytochrome oxidase (coxI) carry two and three intronic sequences respectively. On the basis of their canonical nucleotide sequences they can be classified as group I introns. Phylogenetic comparisons of the coxI protein sequences allow us to conclude that the P.wickerhamii mtDNA is much closer related to higher plant mtDNAs than to those of the chlorophyte alga C.reinhardtii. The comparison of the intron sequences revealed several unusual features: (1) The P.wickerhamii introns are structurally related to mitochondrial introns from various ascomycetous fungi. (2) Phylogenetic analyses indicate a close relationship between fungal and algal intronic sequences. (3) The P. wickerhamii introns are located at positions within the structural genes which can be considered as preferred intron insertion sites in homologous mitochondrial genes from fungi or liverwort. In all cases, the sequences adjacent to the insertion sites are very well conserved over large evolutionary distances. Our finding of highly similar introns in fungi and algae is consistent with the idea that introns have already been present in the bacterial ancestors of present day mitochondria and evolved concomitantly with the organelles.}, }
@article {pmid8455552, year = {1993}, author = {Sharpe, JA and Day, A}, title = {Structure, evolution and expression of the mitochondrial ADP/ATP translocator gene from Chlamydomonas reinhardtii.}, journal = {Molecular &amp; general genetics : MGG}, volume = {237}, number = {1-2}, pages = {134-144}, pmid = {8455552}, issn = {0026-8925}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Blotting, Southern ; Cell Nucleus ; Chlamydomonas reinhardtii/classification/enzymology/*genetics ; Codon ; Consensus Sequence ; Mitochondria/*enzymology ; Mitochondrial ADP, ATP Translocases/biosynthesis/*genetics ; Molecular Sequence Data ; RNA, Messenger/biosynthesis/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Transcription, Genetic ; }, abstract = {The first AUG in the Chlamydomonas reinhardtii ADP/ATP translocator (CRANT) mRNA initiates an open reading frame (ORF) which is very similar (51-79% amino acid identity) to other ANT proteins. In contrast to higher plants, no evidence for a long amino-terminal extension was obtained. The 5' non-transcribed region of the single-copy CRANT gene contains sequence motifs present in other C. reinhardtii nuclear genes. Four introns, whose positions are not conserved in other ANT genes, interrupt the protein coding region. A short heat shock specifically reduces CRANT mRNA levels. CRANT mRNA levels were unaffected by a mutation in photosynthesis. In a dark/light regime CRANT mRNA levels are high in the dark phase and low in the early light phase. Data on translation initiation sites, splice junctions and the codon preferences of C. reinhardtii nuclear genes were compiled. With the exception of two rare codons, ACA and GGA, the CRANT gene exhibits the biased codon usage of C. reinhardtii nuclear genes that are highly expressed during normal vegetative growth.}, }
@article {pmid8431869, year = {1993}, author = {Diengdoh, JV and Shaw, MD}, title = {Oncocytic variant of choroid plexus papilloma. Evolution from benign to malignant "oncocytoma".}, journal = {Cancer}, volume = {71}, number = {3}, pages = {855-858}, doi = {10.1002/1097-0142(19930201)71:3&lt;855::aid-cncr2820710332&gt;3.0.co;2-7}, pmid = {8431869}, issn = {0008-543X}, mesh = {Adenoma/*pathology ; Child ; Choroid Plexus Neoplasms/*pathology/surgery ; Ependymoma/*pathology/surgery ; Female ; Humans ; Microscopy, Electron ; }, abstract = {BACKGROUND: The case of a left temporoparietal choroid plexus papilloma in a 12-year-old girl, which recurred 12 months after subtotal resection and apparent full recovery, is described.<br><br>METHODS: The two consecutive surgical specimens were studied by light and electron microscopy.<br><br>RESULTS: The first surgical specimen showed a tumor composed of cells with distended cytoplasm packed with numerous mitochondria characteristic of "oncocytic" change. Thus, tumor was the rare benign oncocytic variant of choroid plexus papilloma. A repeat histologic study of the recurrent tumor 12 months later showed evidence of malignant evolution in the form of multinucleated cells with frequent, often bizarre, mitotic figures.<br><br>CONCLUSION: A rarely described oncocytic variant of choroid plexus papilloma that showed evidence of evolution from benign to malignant "oncocytoma" is discussed.}, }
@article {pmid8429559, year = {1993}, author = {Gerstein, M and Schulz, G and Chothia, C}, title = {Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers.}, journal = {Journal of molecular biology}, volume = {229}, number = {2}, pages = {494-501}, doi = {10.1006/jmbi.1993.1048}, pmid = {8429559}, issn = {0022-2836}, mesh = {Adenylate Kinase/*chemistry/metabolism ; Animals ; Cattle ; Computer Simulation ; Escherichia coli/enzymology ; Mitochondria, Heart/enzymology ; Models, Molecular ; Protein Conformation ; }, abstract = {In large variants of adenylate kinase the AMP and ATP substrates are buried by a domain rotating by 90 degrees. Here conformational changes responsible for this domain closure are determined by an analysis of the open state of beef heart mitochondrial adenylate kinase and the closed state of Escherichia coli adenylate kinase. Although these two proteins have sequence differences, the principal structural changes responsible for the domain movements are large, and can clearly be distinguished from the effects of evolution. The mobile domain is linked to the rest of the protein by two helices packed together in an antiparallel fashion. During the closure, deformations take place in four localized regions, called joints, near the N and C termini of these helices. Three of these joints have simple motions that can be well approximated by rotations of three torsion angles, but the joint that makes contact with the ligand involves motion throughout an extended loop: i.e. two torsions on either side of a reverse turn change significantly. The main chain atoms of the joints have few packing constraints. The first pair of joints is responsible for approximately 30 degrees of the total rotation and the second pair for the remaining approximately 60 degrees. These movements carries along the regions between the joints, the two helices and the rest of the mobile domain, to a first approximation, as rigid bodies. This jointed domain closure mechanism is contrasted with the shear mechanisms found in other enzymes.}, }
@article {pmid8507692, year = {1993}, author = {Danpure, CJ}, title = {Primary hyperoxaluria type 1 and peroxisome-to-mitochondrion mistargeting of alanine:glyoxylate aminotransferase.}, journal = {Biochimie}, volume = {75}, number = {3-4}, pages = {309-315}, doi = {10.1016/0300-9084(93)90091-6}, pmid = {8507692}, issn = {0300-9084}, mesh = {Alanine Transaminase/*deficiency ; Amino Acid Sequence ; Animals ; Biological Evolution ; Humans ; Hyperoxaluria, Primary/*enzymology ; Microbodies/*enzymology ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Transaminases ; }, abstract = {Under the influence of dietary selection pressure, the intracellular compartmentalization of alanine:glyoxylate aminotransferase (AGT) has changed on many occasions during the evolution of mammals. In some mammals, AGT is peroxisomal in others it is mainly mitochondrial while in yet others it is more-or-less equally divided between both organelles. Although in normal human liver AGT is usually found exclusively within the peroxisomes, in some individuals a small proportion (approximately 5%) is found also in the mitochondria. This apparently trivial intracellular redistribution of AGT is caused by the presence of a Pro11Leu polymorphism which allows the N-terminus of AGT to fold into a conformation (ie a positively-charged amphiphilic alpha-helix) which functions as a mitochondrial targeting sequence. In one third of patients with the autosomal recessive disease primary hyperoxaluria type 1, there is a further redistribution of AGT so that the great majority (approximately 90%) is located in the mitochondria and only a small minority (10%) in the peroxisomes. AGT cannot fulfil its proper metabolic role in human liver (ie glyoxylate detoxification) when located in the mitochondria. The erroneous compartmentalization is due to the presence of a Gly170Arg mutation superimposed upon the Pro11Leu polymorphism. The Gly170Arg mutation appears to have no direct effect on mitochondrial targeting and is predicted to enhance mitochondrial import of AGT by interfering with its peroxisomal targeting and/or import. The mitochondrial targeting sequence generated by the Pro11Leu polymorphism is not homologous to that found in the AGT of other mammals which localise AGT within the mitochondria normally. The identity of the peroxisomal targeting sequence in AGT is unknown, but the Gly170Arg mutation is found in a highly conserved region of the protein which might be involved in some aspects of the peroxisomal import pathway for AGT.}, }
@article {pmid8467535, year = {1993}, author = {Creasey, AM and Ranford-Cartwright, LC and Moore, DJ and Williamson, DH and Wilson, RJ and Walliker, D and Carter, R}, title = {Uniparental inheritance of the mitochondrial gene cytochrome b in Plasmodium falciparum.}, journal = {Current genetics}, volume = {23}, number = {4}, pages = {360-364}, pmid = {8467535}, issn = {0172-8083}, support = {MC_U117532072/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Base Sequence ; Cytochrome b Group/*genetics ; DNA, Single-Stranded ; Genes, Protozoan ; Genetic Variation ; Mitochondria/*enzymology ; Molecular Sequence Data ; Plasmodium falciparum/enzymology/*genetics ; }, abstract = {The inheritance of an extrachromosomal 6-kb element has been examined in the human malaria parasite Plasmodium falciparum. A single base pair difference in the cytochrome b gene from the 6-kb element of two different cloned lines of the parasite was identified, and used as a marker in a cross in the mosquito stage of the life cycle. Analysis of 59 individual hybrid oocysts resulting from this cross clearly demonstrated that inheritance of the cytochrome b gene was uniparental. This observation makes it possible to investigate the inheritance and evolution of cytoplasmic traits, including certain forms of drug resistance, in natural populations of this parasite.}, }
@article {pmid8383274, year = {1993}, author = {Wieseler, B and Müller, M}, title = {Translocation of precytochrome c2 into intracytoplasmic membrane vesicles of Rhodobacter capsulatus requires a peripheral membrane protein.}, journal = {Molecular microbiology}, volume = {7}, number = {2}, pages = {167-176}, doi = {10.1111/j.1365-2958.1993.tb01108.x}, pmid = {8383274}, issn = {0950-382X}, mesh = {Bacterial Proteins/*metabolism ; Biological Transport, Active ; Cell-Free System ; Cytochrome c Group/*metabolism ; Electrochemistry ; Intracellular Membranes/*metabolism ; Membrane Proteins/*metabolism ; Osmolar Concentration ; Protein Precursors/*metabolism ; Proton-Translocating ATPases/antagonists &amp; inhibitors/metabolism ; Protons ; Recombinant Fusion Proteins/metabolism ; Rhodobacter capsulatus/*metabolism ; }, abstract = {Rhodobacter capsulatus is a member of the group of alpha-purple bacteria which are closely related to the ancestral endosymbiont that gave rise to mitochondria. It has therefore been hypothesized that the molecular mechanisms governing protein export in alpha-purple bacteria have been conserved during the evolution of mitochondria. To enable analysis of protein export in alpha-purple bacteria we describe here the development of a homologous cell-free synthesis/export system consisting entirely of components of R. capsulatus. Translocation of precytochrome c2 into intracytoplasmic membrane vesicles of this organism was found to require the proton-motive force and proceed at a significantly higher efficiency when membranes were present during protein synthesis. Furthermore, we show that, in this cell-free system, translocation depends on a preparation of peripheral membrane proteins which do not possess detectable SecA- and SecB-like activities.}, }
@article {pmid8374071, year = {1993}, author = {Sitnikova, TL and Zharkikh, AA}, title = {Statistical analysis of L-tuple frequencies in eubacteria and organelles.}, journal = {Bio Systems}, volume = {30}, number = {1-3}, pages = {113-135}, doi = {10.1016/0303-2647(93)90066-l}, pmid = {8374071}, issn = {0303-2647}, mesh = {Analysis of Variance ; Bacteria/*genetics ; Base Sequence ; Biological Evolution ; Biometry ; Codon/genetics ; DNA/*genetics ; Genetic Vectors ; Mathematics ; Organelles/*chemistry ; }, abstract = {This work is an attempt to study the structural features and evolutionary patterns of nucleotide sequences by analyzing their 1- through 4-plet frequencies and statistical relations between them. We present mathematical apparatus for this analysis. In particular, we introduce criteria to estimate the degree of homogeneity of L-plet composition in a given set of sequences and the dependence of the L-plet frequencies on the composition of lower orders. We apply these criteria to the study of eubacteria, mitochondria and chloroplasts. We demonstrate that L-plet frequencies are quite useful for revealing evolutionary relationship between DNA sequences and that the non-random distribution is more typical for doublets than to triplets. Non-randomness of triplet composition is more characteristic to coding than to non-coding regions, while no significant differences in dinucleotide composition can be observed. The obtained results can be used for revealing possible mechanisms of the codon usage phenomena.}, }
@article {pmid8353724, year = {1993}, author = {Collin, SP and Collin, HB}, title = {The visual system of the Florida garfish, Lepisosteus platyrhincus (Ginglymodi). II. Cornea and lens.}, journal = {Brain, behavior and evolution}, volume = {42}, number = {2}, pages = {98-115}, doi = {10.1159/000114143}, pmid = {8353724}, issn = {0006-8977}, support = {NS 24669/NS/NINDS NIH HHS/United States ; NS 24869/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Collagen/ultrastructure ; Cornea/*anatomy &amp; histology ; Endothelium, Corneal/ultrastructure ; Epithelium/ultrastructure ; Fishes/*anatomy &amp; histology ; Florida ; Lens, Crystalline/*anatomy &amp; histology ; Microscopy, Electron, Scanning ; *Phylogeny ; }, abstract = {The cornea of the Florida gar, Lepisosteus platyrhincus (Ginglymodi) was examined at the scanning and transmission electron microscopic levels. In addition, the schematic eye of the garfish was revealed by frozen sectioning of the whole orbit in the horizontal and transverse planes. The lens is spherical, obeys Matthiessen's ratio, and is supported by a dorsal suspensory ligament and a ventral retractor lentis muscle. The cornea, devoid of a spectacle, is comprised anteriorly of an epithelium (eight to ten cells thick) and covered by a layer of flattened cells up to 26 microns in diameter. On the scanning electron microscope, these cells appear to be covered in microplicae and microvilli. Beneath the epithelium lies a granular basement membrane abutting a true Bowman's layer, composed of a random arrangement of collagen fibrils with no keratocytes. The corneal stroma constitutes 54% of the total thickness and contains 55-65 collagen fibril lamellae, oriented perpendicular to neighbouring lamellae. Scattered keratocytes, containing large amounts of mitochondria, lipid droplets and glycogen granules lie in between the perpendicularly oriented lamellae. Posterior to the stroma is a thin and partially broken basement membrane (no true Descemet's membrane exists), adjacent to a monolayered endothelium covered in microvilli. In the periphery, an autochthonous layer is found between the stroma and the endothelium. Stromal pigment granules, enveloped in large nucleated cells, act as a non-occlusible yellow filter in the dorsal cornea. Functional correlations are made and the presence and/or thickness of corneal structures discussed in relation to the evolution of the vertebrate cornea.}, }
@article {pmid8347727, year = {1993}, author = {Sankoff, D}, title = {Analytical approaches to genomic evolution.}, journal = {Biochimie}, volume = {75}, number = {5}, pages = {409-413}, doi = {10.1016/0300-9084(93)90174-q}, pmid = {8347727}, issn = {0300-9084}, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/genetics ; *Genome ; Humans ; Mice ; Mitochondria ; Models, Genetic ; Mutation ; Phylogeny ; *Sequence Analysis, DNA ; Translocation, Genetic ; }, abstract = {We model the non-local mechanisms of genomic evolution and propose methods for studying the evolutionary divergence of species based on these models. Mechanisms include the movement of segments of genomes within a single chromosome (transpositions), the reciprocal translocation of segments between two chromosomes, and the inversion of segments. Each of these is studied in the context of a different type of genomic data. We introduce the theory of phylogenetic invariants for evolutionary inference based on very long macromolecular sequences.}, }
@article {pmid8328023, year = {1993}, author = {Seravin, LN}, title = {[The basic types and forms of the fine structure of mitochondrial cristae: the degree of their evolutionary stability (capacity for morphological transformations)].}, journal = {Tsitologiia}, volume = {35}, number = {4}, pages = {3-34}, pmid = {8328023}, issn = {0041-3771}, mesh = {Animals ; *Biological Evolution ; Classification ; Eukaryota/ultrastructure ; Mitochondria/*ultrastructure ; Plants/ultrastructure ; }, abstract = {The organellological analysis being made of the fine structure of mitochondria in different species of the kingdom Protista, and in different cells of representatives of the kingdoms Plantae and Animalia (Metazoa). On the base of this analysis the following classification of types and forms of the fine structure of mitochondrial cristae is proposed. The Ist type, with lamellar (flat) cristae includes four morphological forms: ribbon, sheet, bundle-like and rounded ones (discoidal and plate-like). The 2nd type, with vesicular cristae, includes bubble, ampule, and sac-like ones. The 3rd type with tubular cristae. Among the representatives of each kingdom (Protista, Plantae and Metazoa) all the three types of mitochondrial cristae have been observed. The majority of cells of higher plants and higher animals have lamellar mitochondrial cristae, but sometimes (in some tissues) there are cells with tubular or vesicular mitochondrial cristae. On the base of the above classification some other conclusions have been made. Among the eukaryotes the vesicular cristae are spread as widely as tubular and lamellar ones. Only in a few macrotaxa (superphyla and phyla) of Protista all the investigated organisms have mitochondria of similar cristal organization. For example, Ciliophora have only tubular, and Cryptophyta only lamellar mitochondrial cristae. In the majority of protistan macrotaxa a certain mitochondrial type of cristae may dominate, but there is the number of species with some different mitochondrial patterns (Euglenophyta, Chlorophyta, Chrysophyta, Mycetozoa, etc.). In some macrotaxa (Chrysophyta, Mycetozoa, etc.) such mitochondrial patterns as mentioned above, are characteristic of the lower organisms. Finally, in some macrotaxa of Protista mitochondrial cristae of two or three types may appear in different species, sometimes even within the same genus; for example--Sporozoa, Myxospora and Ascetospora. In the course of ontogenesis of the vertebrates and insects, cell mitochondria in some of their tissues can change their morphological type from lamellar to tubular or vesicular. Similar transformations of mitochondrial cristae were observed in the life cycles of some trypanosomes (Kinetoplastida) and in the flagellate Polytoma (Chlorophyta) due to modifications in the culture conditions. It is undoubtedly that the principle of morphological concervatism in the organization of mitochondrial cristae may be used for purposes of systematics and phylogeny, however only after a thorough comparative organellological analysis of the fine structure in numerous species of the examined taxon.}, }
@article {pmid8325039, year = {1993}, author = {Kuan, J and Saier, MH}, title = {The mitochondrial carrier family of transport proteins: structural, functional, and evolutionary relationships.}, journal = {Critical reviews in biochemistry and molecular biology}, volume = {28}, number = {3}, pages = {209-233}, doi = {10.3109/10409239309086795}, pmid = {8325039}, issn = {1040-9238}, support = {2RO1 AI14176/AI/NIAID NIH HHS/United States ; 5RO1 AI21702/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Biological Evolution ; Carrier Proteins/*genetics ; Mitochondria/*metabolism ; Mitochondrial ADP, ATP Translocases/*genetics ; Molecular Sequence Data ; Multigene Family/genetics ; Phylogeny ; Sequence Homology, Amino Acid ; }, abstract = {Energy transduction in mitochondria requires the transport of many specific metabolites across the inner membrane of this eukaryotic organelle. We have screened the protein sequence database for proteins homologous to the mitochondrial ATP/ADP exchange carrier, and the homologous proteins found were similarly screened to ensure that all currently sequenced members of the mitochondrial carrier family (MCF) had been identified. Thirty-seven proteins were identified, 28 of which were less than 90% identical to any other sequenced member of the MCF, and the latter proteins fell into 10 clusters or subfamilies as follows: (1) ATP/ADP exchangers of mammals, plants, algae, yeast, and fungi (11 members); (2) a bovine oxoglutarate/malate exchanger (one member); (3) mammalian uncoupling carriers (five members); (4) yeast and mammalian phosphate carriers (three members); (5) MRS proteins that suppress mitochondrial splicing defects in Saccharomyces cerevisiae (two members); (6) a putative peroxysomal carrier of Candida boidinii; (7) a putative solute carrier from the protozoan, Oxytricha fallax; (8) a putative solute carrier from S. cerevisiae; (9) a putative solute carrier from Zea mays, and (10) two putative solute carriers from the mammalian thyroid gland. The specificities of proteins in clusters 5 to 10 are not known. A multiple alignment and an evolutionary tree of the 28 selected members of the MCF were constructed, thus defining the conserved residues and the phylogenetic relationships of the proteins. Hydropathy plots of the homologous regions were determined and averaged, and the average hydropathy plots were evaluated for sequence similarity. These analyses revealed that the six transmembrane spanners exhibited varying degrees of sequence conservation and hydrophilicity. These spanners, and immediately adjacent hydrophilic loop regions, were more highly conserved than other regions of these proteins. All members of the MCF appear to consist of a tripartite structure with each of the three repeated segments being about 100 residues in length. Each repeat contains two transmembrane spanners, the first being more hydrophobic with conserved glycyl and prolyl residues, the second, preceded by a highly conserved glycyl residue, being more hydrophilic with largely conserved hydrophilic residues in certain positions. Five of the six spanners are followed by the largely conserved sequence (D/E)-Hy (K/R)[- = any residue; Hy = a hydrophobic residue]. Based on both intracluster and intercluster statistical comparisons, repeats 1, 2, and 3 are homologous, but repeats 1 are more similar to each other than they are to repeats 2 or 3 or repeats 2 or 3 are to each other.(ABSTRACT TRUNCATED AT 400 WORDS)}, }
@article {pmid8247638, year = {1993}, author = {Gorczyca, W and Melamed, MR and Darzynkiewicz, Z}, title = {[Programmed death of cells (apoptosis)].}, journal = {Patologia polska}, volume = {44}, number = {3}, pages = {113-119}, pmid = {8247638}, issn = {0031-3114}, mesh = {Apoptosis/*physiology ; Cell Membrane/ultrastructure ; Cytoplasm/ultrastructure ; DNA/analysis ; Humans ; Leukemia/pathology ; Mitochondria/ultrastructure ; Necrosis/pathology ; }, abstract = {Apoptosis is a mode of cell death defined by characteristic morphological, biochemical and molecular changes. It was first described as a "shrinkage necrosis", and then this term was replaced by apoptosis to emphasize its role opposite mitosis in tissue kinetics. During apoptosis the cell decrease in size, loose contact with neighboring cells, and loose specialized surface elements such as microvilli and cell-cell junctions. A shift of fluid out of the cells causes cytoplasm condensation, which is followed by convolution of the nuclear and cellular outlines. In later stages of apoptosis the entire cell becomes fragmented, forming a number of plasma membrane-bounded apoptotic bodies which contain nuclear and or cytoplasmic elements. The ultrastructural appearance of necrosis is quite different, the main features being mitochondrial swelling, plasma membrane breakdown and cellular disintegration. Apoptosis occurs in many physiological and pathological processes. It plays an important role during embryonal development as programmed cell death and accompanies a variety of normal involutional processes in which it serves as a mechanism to remove "unwanted" cells. Apoptosis is associated with prostate atrophy after castration or atrophy of the adrenal cortex and thymus after administration of glucocorticoids. Apoptosis is involved in elimination of CD4 T lymphocytes in the course of HIV infection. The interest in apoptosis in oncology stems from the fact that it occurs in tumors, spontaneously as well as triggered by different antitumor drugs, radiation or after withdraw of growth factors. Spontaneous apoptosis may play a role in evolution of tumor malignancy.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid8155851, year = {1993}, author = {Wallin, IE}, title = {Symbionticism in the light of recent cytological investigations--Ivan E. Wallin, 1969.}, journal = {Bio Systems}, volume = {31}, number = {2-3}, pages = {181-183}, doi = {10.1016/0303-2647(93)90047-g}, pmid = {8155851}, issn = {0303-2647}, mesh = {Bacteria ; Biological Evolution ; Fabaceae/microbiology ; History, 20th Century ; Mitochondria ; Plants, Medicinal ; *Symbiosis ; }, }
@article {pmid8055001, year = {1993}, author = {Jukes, TH}, title = {The genetic code-function and evolution.}, journal = {Cellular &amp; molecular biology research}, volume = {39}, number = {7}, pages = {685-688}, pmid = {8055001}, issn = {0968-8773}, mesh = {Amino Acids/metabolism ; Animals ; Base Sequence ; *Biological Evolution ; Codon/genetics ; *Genetic Code ; Mitochondria/metabolism ; Plants/metabolism ; Protein Biosynthesis ; RNA, Transfer/metabolism ; Ribosomes/metabolism ; }, abstract = {The genetic code is reviewed from the standpoints of its function and evolution. The code has probably always consisted of 64 units (codons), each containing three bases. Each codon pairs with a three-base anticodon that is part of an adaptor molecule. The adaptors are transfer RNA molecules that are each joined to a specific amino acid. Many departures from the universal code have recently been discovered. These are discussed.}, }
@article {pmid7903408, year = {1993}, author = {DeSalle, R and Williams, AK and George, M}, title = {Isolation and characterization of animal mitochondrial DNA.}, journal = {Methods in enzymology}, volume = {224}, number = {}, pages = {176-204}, doi = {10.1016/0076-6879(93)24015-m}, pmid = {7903408}, issn = {0076-6879}, mesh = {Animal Population Groups/*classification/genetics ; Animals ; Base Sequence ; Biological Evolution ; Chromosome Mapping ; Cloning, Molecular/methods ; DNA/isolation &amp; purification ; DNA Primers ; DNA, Mitochondrial/genetics/*isolation &amp; purification ; Drosophila/chemistry/genetics ; Female ; Genetic Variation ; Hair/chemistry ; Humans ; Mitochondria/ultrastructure ; Molecular Sequence Data ; Polymerase Chain Reaction/methods ; *Polymorphism, Genetic ; Polymorphism, Restriction Fragment Length ; Specimen Handling/methods ; Ultracentrifugation/methods ; }, }
@article {pmid7678563, year = {1993}, author = {Schmitt, ME and Bennett, JL and Dairaghi, DJ and Clayton, DA}, title = {Secondary structure of RNase MRP RNA as predicted by phylogenetic comparison.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {7}, number = {1}, pages = {208-213}, doi = {10.1096/fasebj.7.1.7678563}, pmid = {7678563}, issn = {0892-6638}, support = {GM07365-15/GM/NIGMS NIH HHS/United States ; GM08294-04/GM/NIGMS NIH HHS/United States ; GM33088-22/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Binding Sites ; Endoribonucleases/*chemistry/genetics ; Humans ; Mitochondria/*chemistry ; Molecular Sequence Data ; *Nucleic Acid Conformation ; Phylogeny ; RNA, Bacterial/chemistry ; RNA, Catalytic/chemistry ; Ribonuclease P ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; }, abstract = {RNase MRP is a ribonucleoprotein endoribonuclease that has been shown to cleave mitochondrial primer RNA sequences from a variety of sources. The bulk of RNase MRP activity is found in the nucleus where its function remains unknown. Two different approaches have resulted in predictions of distinct secondary structures for RNase MRP RNA. In order to analyze more definitively the higher-order structure of RNase MRP RNA, we have conducted a phylogenetic comparison of the available RNase MRP RNA sequences from human, mouse, rat, cow, toad, and yeast. The resulting secondary structure shares features in common with previously described structures for prokaryotic and eukaryotic RNase P RNAs (1) and RNase MRP RNAs (2, 3). In addition, the phylogenetic structure is consistent with available chemical modification data on RNase MRP RNA and with the detailed analysis of the To antigen binding domain located near the 5' end of the RNase MRP RNA. The structure is not limited to RNase MRP RNAs, but can be expanded to cover both eukaryotic RNase P RNAs and RNase P/MRP RNAs from plants.}, }
@article {pmid1469708, year = {1992}, author = {Mandrup, S and Hummel, R and Ravn, S and Jensen, G and Andreasen, PH and Gregersen, N and Knudsen, J and Kristiansen, K}, title = {Acyl-CoA-binding protein/diazepam-binding inhibitor gene and pseudogenes. A typical housekeeping gene family.}, journal = {Journal of molecular biology}, volume = {228}, number = {3}, pages = {1011-1022}, doi = {10.1016/0022-2836(92)90888-q}, pmid = {1469708}, issn = {0022-2836}, mesh = {Animals ; Base Sequence ; Carrier Proteins/*genetics ; Cloning, Molecular ; Diazepam Binding Inhibitor ; Exons ; Introns ; Models, Genetic ; Molecular Sequence Data ; Multigene Family/*genetics ; Phylogeny ; Pseudogenes/*genetics ; RNA Precursors/metabolism ; RNA Splicing ; RNA, Antisense ; Rats ; Restriction Mapping ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; }, abstract = {Acyl-CoA-binding protein (ACBP) is a 10 kDa protein isolated from bovine liver by virtue of its ability to bind and induce the synthesis of medium-chain acyl-CoA esters. Surprisingly, it turned out to be identical to a protein named diazepam-binding Inhibitor (DBI) claimed to be an endogenous modulator of the GABAA receptor in brain membranes. ACBP/DBI, or proteolytically derived polypeptides of ACBP/DBI, have also been implicated in the control of steroidogenesis in mitochondria and glucose-stimulated insulin secretion. Thus, it appears that ACBP/DBI is a remarkable, versatile protein. Now we have molecularly cloned and characterized the ACBP/DBI gene family in rat. The rat ACBP/DBI gene family comprises one expressed gene and four processed pseudogenes of which one was shown to exist in two allelic forms. The expressed gene is organized into four exons and three introns. There is a remarkable correspondence between the structural modules of ACBP/DBI as determined by 1H nuclear magnetic resonance spectroscopy and the exon-intron architecture of the ACBP/DBI gene. Detailed analyses of transcription of the ACBP/DBI gene in brain and liver were performed to map transcription initiation sites and to examine if transcripts from the ACBP/DBI gene were subject to alternative processing. In both brain and liver, transcription is initiated from two major and multiple minor initiation sites. No evidence for alternative splicing was obtained. The promoter region of the ACBP/DBI gene is located in a CpG island and lacks a canonical TATA box. Thus, the ACDB/DBI gene exhibits all the hallmarks of a typical housekeeping gene.}, }
@article {pmid1473724, year = {1992}, author = {Moum, T and Johansen, S}, title = {The mitochondrial NADH dehydrogenase subunit 6 (ND6) gene in Murres: relevance to phylogenetic and population studies among birds.}, journal = {Genome}, volume = {35}, number = {6}, pages = {903-906}, doi = {10.1139/g92-139}, pmid = {1473724}, issn = {0831-2796}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Birds/*genetics/metabolism ; DNA, Mitochondrial ; *Genetics, Population ; Mitochondria/*enzymology ; Molecular Sequence Data ; NADH Dehydrogenase/*genetics ; *Phylogeny ; Sequence Homology, Nucleic Acid ; }, abstract = {The nucleotide sequences of the mitochondrial ND6 and tRNA(Glu) genes and part of the displacement loop region in two closely related seabird species are presented. A chicken type gene organization in which the tRNA(Glu), ND6, and displacement loop are localized next to each other was found in these species and suggests that this is a conserved feature of avian mitochondrial DNA. The nucleotide and amino acid divergences of ND6 at different taxonomic levels are assessed, and its relevance to phylogenetic studies in birds is discussed.}, }
@article {pmid1452043, year = {1992}, author = {de Zamaroczy, M and Bernardi, G}, title = {The mosaic organization of the mitochondrial introns of Saccharomyces cerevisiae: features and evolutionary origins.}, journal = {Gene}, volume = {122}, number = {1}, pages = {91-99}, doi = {10.1016/0378-1119(92)90036-o}, pmid = {1452043}, issn = {0378-1119}, mesh = {Base Composition ; *Biological Evolution ; Genes, Fungal ; *Introns ; Mitochondria/*metabolism ; Molecular Sequence Data ; *Mosaicism ; Open Reading Frames ; Saccharomyces cerevisiae/*genetics ; }, abstract = {The introns of three genes (oxi3, cob and 21S) from the mitochondrial (mt) genome of Saccharomyces cerevisiae contain closed reading frames (CRFs). In the present work, we have analyzed these sequences in their oligodeoxyribonucleotide (oligo; isostich) patterns. We have shown that the relative amounts of di- to hexanucleotides, when compared to random sequences having the same sizes and compositions, exhibit the same deviations as the intergenic noncoding sequences of the mt genome (except for the CRFs from 21S intron). In contrast, intronic open reading frames (ORFs) showed oligo patterns which were generally quite distinct from those of CRFs, although some similarities could be detected in some cases (especially for aI5 alpha). The mt introns of yeast, therefore, are endowed with a mosaic structure, in which CRFs derive from mt intergenic sequences, whereas ORFs have a different origin (indicated as exogenous by other evidences) yet show, in some cases, the effects of 'sequence assimilation' with CRFs.}, }
@article {pmid1446896, year = {1992}, author = {Hirano, T and Kaplowitz, N and Tsukamoto, H and Kamimura, S and Fernandez-Checa, JC}, title = {Hepatic mitochondrial glutathione depletion and progression of experimental alcoholic liver disease in rats.}, journal = {Hepatology (Baltimore, Md.)}, volume = {16}, number = {6}, pages = {1423-1427}, doi = {10.1002/hep.1840160619}, pmid = {1446896}, issn = {0270-9139}, support = {AA06603/AA/NIAAA NIH HHS/United States ; }, mesh = {Alanine Transaminase/blood ; Animals ; Cytosol/metabolism ; Glutathione/*metabolism ; Kidney/*metabolism ; Liver/*metabolism ; Liver Cirrhosis, Alcoholic/*metabolism/*physiopathology ; Male ; Malondialdehyde/metabolism ; Mitochondria/*metabolism ; Mitochondria, Liver/*metabolism ; Organ Size ; Rats ; Rats, Wistar ; Reference Values ; }, abstract = {Long-term ethanol feeding has been shown to selectively reduce hepatic mitochondrial glutathione content by impairing mitochondrial uptake of this thiol. In this study, we assessed the role of this defect in evolution of alcoholic liver disease by examining the mitochondrial glutathione pool and lipid peroxidation during progression of experimental alcoholic liver disease to centrilobular liver necrosis and fibrosis. Male Wistar rats were intragastrically infused with a high-fat diet plus ethanol for 3, 6 or 16 wk (the duration that resulted in induction of liver steatosis, necrosis and fibrosis, respectively). During this feeding period, the cytosolic pool of glutathione remained unchanged in the ethanol-fed animals compared with that in pair-fed controls. In contrast, the mitochondrial pool of glutathione selectively and progressively decreased in rats infused with ethanol for 3, 6 or 16 wk, by 39%, 61% and 85%, respectively. Renal mitochondrial glutathione level remained unaffected throughout the experiment. Serum ALT levels increased significantly in the ethanol-fed rats at 6 wk and remained elevated at 16 wk. In the mitochondria with severely depleted glutathione levels at 16 wk, enhanced lipid peroxidation was evidenced by increased malondialdehyde levels. Thus a progressive and selective depletion of mitochondrial glutathione is demonstrated in the liver in this experimental model of alcoholic liver disease and associated with mitochondrial lipid peroxidation and progression of liver damage.}, }
@article {pmid1281057, year = {1992}, author = {Lang, P and Klein, R and Becker, EW and Berg, PA}, title = {Distribution of the PBC-specific- (M2) and the naturally-occurring mitochondrial antigen- (NOMAg) systems in plants.}, journal = {Clinical and experimental immunology}, volume = {90}, number = {3}, pages = {509-516}, pmid = {1281057}, issn = {0009-9104}, mesh = {Antigens/*analysis/immunology/isolation &amp; purification ; Autoantigens/analysis ; Blotting, Western ; Enzyme-Linked Immunosorbent Assay ; Epitopes/immunology ; Humans ; Liver Cirrhosis, Biliary/*immunology ; Mitochondria/*immunology ; Plants/*ultrastructure ; }, abstract = {In previous studies it was demonstrated that antibodies in sera from patients with primary biliary cirrhosis (PBC) and their relatives can recognize two different antigen systems in the ATPase fraction prepared from beef heart mitochondria, namely the PBC-related M2- and the naturally occurring mitochondrial antigen (NOMAg)-related epitopes. Since separation of these two antigen systems could not be achieved using mammalian mitochondria, mitochondria from a wide spectrum of plants were analysed with respect to the presence of mitochondrial antigens. Mitochondria from 29 species of plants were prepared and tested by ELISA and Western blot using marker sera from patients with PBC reacting in the Western blot with M2a,b,c,d (alpha-ketoacid-dehydrogenase complex) and NOMAg-specific sera recognizing the three major epitopes epsilon, zeta, and eta at 65, 61 and 58 kD. Naturally occurring mitochondrial antibody (NOMA)-positive marker sera reacted in the ELISA with mitochondria from all plants, and the zeta/eta positive sera gave also a positive reaction at 61/58 kD in the Western blot while the epsilon epitope could not be visualized by this method. In contrast, the M2 antigen was detected preferentially in lower plants such as algae, fungi, and ferns. Analysing these data with respect to the evolution of proteins one would have to assume that the M2 antigen was lost in most higher plants or underwent some structural alterations. Furthermore, considering the fact that the M2- and the NOMAg-related epitopes could be only partially separated, i.e. there were no plant mitochondria showing only M2 but no NOMAg, one could speculate that anti-M2 antibodies are derived from the pool of naturally occurring antibodies.}, }
@article {pmid1446820, year = {1992}, author = {Lee, YH and Huang, XY and Hirsh, D and Fox, GE and Hecht, RM}, title = {Conservation of gene organization and trans-splicing in the glyceraldehyde-3-phosphate dehydrogenase-encoding genes of Caenorhabditis briggsae.}, journal = {Gene}, volume = {121}, number = {2}, pages = {227-235}, doi = {10.1016/0378-1119(92)90126-a}, pmid = {1446820}, issn = {0378-1119}, support = {2-S07-RR07147-15/RR/NCRR NIH HHS/United States ; GM36318/GM/NIGMS NIH HHS/United States ; GM37823/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Caenorhabditis/*genetics ; Caenorhabditis elegans/genetics ; *Genes, Helminth ; Glyceraldehyde-3-Phosphate Dehydrogenases/*genetics ; Introns ; Molecular Sequence Data ; *RNA Splicing ; RNA, Messenger/genetics ; Regulatory Sequences, Nucleic Acid ; Sequence Alignment ; Species Specificity ; }, abstract = {The genes encoding body-wall-specific glyceraldehyde-3-phosphate dehydrogenase from Caenorhabditis briggsae were sequenced and compared to the homologous genes from Caenorhabditis elegans. The direct tandem organization of these genes, gpd-2 and gpd-3, and the size and location of the two introns in each gene are the same in C. elegans and C. briggsae. Primer-extension studies demonstrated that the two genes in C. briggsae are trans-splice differentially with the same splice leader (SL) RNAs as are observed in C. elegans. The gdp-2 gene is trans-spliced with SL1 while gdp-3 is trans-spliced with SL2. Significant sequence conservation was observed within the promoter regions of each species and may indicate those regions responsible for body-wall-muscle-specific gene expression and/or differential trans-splicing. Comparisons of the sequences suggest that the tandem repeat of the genes has been subjected to concerted evolution and that C. briggsae and C. elegans diverged much earlier than would be anticipated based on morphological similarities alone. Finally, an open reading frame found several hundred nucleotides upstream from gpd-2, in both species, appears to be homologous to the ATP synthase subunit, ATPase inhibitor protein, from bovine mitochondria.}, }
@article {pmid1421143, year = {1992}, author = {Haouazine, N and Pereira de Souza, A and Jubier, MF and Lancelin, D and Delcher, E and Lejeune, B}, title = {The wheat mitochondrial genome contains an ORF showing sequence homology to the gene encoding the subunit 6 of the NADH-ubiquinone oxidoreductase.}, journal = {Plant molecular biology}, volume = {20}, number = {3}, pages = {395-404}, pmid = {1421143}, issn = {0167-4412}, mesh = {Amino Acid Sequence ; Base Sequence ; Genes, Plant/*genetics ; Genome ; Mitochondria/*physiology ; Molecular Sequence Data ; NAD(P)H Dehydrogenase (Quinone)/*genetics ; RNA, Messenger/*genetics ; Sequence Homology, Amino Acid ; Transcription, Genetic ; Triticum/enzymology/*genetics ; }, abstract = {A region of the mitochondrial (mt) DNA of wheat was studied because of its homology with other plant mtDNAs. Sequence analysis revealed an open reading frame encoding a polypeptide of 247 amino acids. Comparison of the sequence of the putative polypeptide with the protein sequence data of the Swiss-Prot library reveals homology with subunit 6 of the NADH-ubiquinone complex of mitochondria from Marchantia polymorpha, Podospora anserina, Chlamydomonas reinhardtii and of chloroplasts from M. polymorpha and Oryza sativa. No similarity was detected when compared with the subunit 6 of animal mitochondria, probably due to the rapid evolution of the sequence. A single 1.2 kb transcript appears in northern RNA blots. We found 15 edited sites of which only 13 give amino acid changes. This is the first report of a mt nad6 gene in higher plants.}, }
@article {pmid1369804, year = {1992}, author = {Wolf, HK and Garcia, JA and Bossen, EH}, title = {Oncocytic differentiation in intrahepatic biliary cystadenocarcinoma.}, journal = {Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc}, volume = {5}, number = {6}, pages = {665-668}, pmid = {1369804}, issn = {0893-3952}, mesh = {Bile Duct Neoplasms/*pathology ; *Bile Ducts, Intrahepatic ; Cell Differentiation ; Cholangiocarcinoma/diagnostic imaging/*pathology ; Cystadenocarcinoma/diagnostic imaging/*pathology ; Humans ; Male ; Middle Aged ; Tomography, X-Ray Computed ; }, abstract = {An intrahepatic biliary cystadenocarcinoma in a 56-yr-old white man was characterized by pronounced oncocytic differentiation. Grossly the tumor was a well-demarcated cyst filled with numerous branching papillary fronds. Most tumor cells had abundant granular, intensely eosinophilic cytoplasm on light microscopic examination and large numbers of densely packed mitochondria by electron microscopy. Mucin-secreting cells were also present. The patient returned 20 mo after resection of the primary tumor with recurrent tumor in the liver and widely disseminated disease throughout the abdominal cavity, and he died 5 mo later. Although less differentiated, the recurrent tumor again contained greatly increased numbers of mitochondria. The partial loss of oncocytic differentiation in the evolution of the present case and the benign nature of purely oncocytic tumors suggest that in the presence of mixed histologic features the potential for tumor progression is primarily determined by the lesser differentiated or nononcocytic component. To the best of our knowledge, oncocytic differentiation has not been previously described in biliary neoplasia.}, }
@article {pmid1426143, year = {1992}, author = {Roten, CA and Karamata, D}, title = {Endogenous synthesis of peptidoglycan in eukaryotic cells; a novel concept involving its essential role in cell division, tumor formation and the biological clock.}, journal = {Experientia}, volume = {48}, number = {10}, pages = {921-931}, pmid = {1426143}, issn = {0014-4754}, mesh = {Animals ; Bacteria/metabolism ; Carbohydrate Sequence ; Humans ; Molecular Sequence Data ; Peptidoglycan/*biosynthesis/chemistry/metabolism ; Periodicity ; Phylogeny ; Plants/metabolism ; }, abstract = {Degradation products of peptidoglycan, the universal bacterial cell wall constituent, were previously found in animal tissues and urine. Reassessment and quantitative analysis of available data lead to an original concept, i.e. that eukaryotic cells synthesize peptidoglycan. We present a model in which this endogenously synthesized peptidoglycan is essential for the processes of eukaryotic cell division and sleep induction in animals. Genes for peptidoglycan metabolism, like those for lysine biosynthesis in plants, are probably inherited from endosymbiotic bacteria, the ancestors of mitochondria and chloroplasts. Corollaries of this concept, i.e. roles for peptidoglycan metabolism in tumor formation and in the biological clock, are supported by abundant evidence. We propose that many interactions between bacteria and eukaryotes are conditioned by their common genetic heritage.}, }
@article {pmid1515599, year = {1992}, author = {Ambrosini, M and Ceci, LR and Fiorella, S and Gallerani, R}, title = {Comparison of regions coding for tRNA(His) genes of mitochondrial and chloroplast DNA in sunflower: a proposal concerning the classification of 'CP-like' tRNA genes.}, journal = {Plant molecular biology}, volume = {20}, number = {1}, pages = {1-4}, pmid = {1515599}, issn = {0167-4412}, mesh = {Base Sequence ; Biological Evolution ; Chloroplasts/*physiology ; DNA/classification/*genetics ; DNA, Mitochondrial/*genetics ; *Genes, Plant ; Mitochondria/*physiology ; Molecular Sequence Data ; Plants/*genetics ; RNA, Transfer/*genetics ; RNA, Transfer, His/*genetics ; Sequence Homology, Nucleic Acid ; }, }
@article {pmid1473161, year = {1992}, author = {de Melo, EJ and de Carvalho, TU and de Souza, W}, title = {Penetration of Toxoplasma gondii into host cells induces changes in the distribution of the mitochondria and the endoplasmic reticulum.}, journal = {Cell structure and function}, volume = {17}, number = {5}, pages = {311-317}, doi = {10.1247/csf.17.311}, pmid = {1473161}, issn = {0386-7196}, mesh = {4-Chloro-7-nitrobenzofurazan/analogs &amp; derivatives ; Animals ; Carbocyanines ; Ceramides ; Endoplasmic Reticulum/*ultrastructure ; Fluorescent Dyes ; Microscopy, Electron ; Microscopy, Fluorescence ; Mitochondria/*ultrastructure ; Rhodamine 123 ; Rhodamines ; Toxoplasma/*physiology ; Vero Cells ; }, abstract = {Fluorescence microscopy, using dyes which specifically label mitochondria, endoplasmic reticulum and the Golgi complex, and transmission electron microscopy, were used to analyze the changes which occur in the organization of these structures during interaction of Toxoplasma gondii with host cells. In uninfected cells the mitochondria are long filamentous structures which radiate from the nuclear region toward the cell periphery. After parasite penetration they become shorter and tend to concentrate around the parasite-containing vacuole (parasitophorous vacuole) located in the cytoplasm of the host cell. The mitochondria of extracellular parasites, but not of those located within the parasitophorous vacuole, were also stained by rhodamine 123. Labeling with DiOC6, which binds to elements of the endoplasmic reticulum, in association with transmission electron microscopy, revealed a concentration of this structure around the parasitophorous vacuole. The membrane lining this vacuole was also stained, suggesting that components of the endoplasmic reticulum are also incorporated into this membrane. The Golgi complex, as revealed by staining with NBD-ceramide and electron microscopy, maintains its perinuclear position throughout the evolution of the intracellular parasitism.}, }
@article {pmid1409592, year = {1992}, author = {Nagy, M and Lacroute, F and Thomas, D}, title = {Divergent evolution of pyrimidine biosynthesis between anaerobic and aerobic yeasts.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {89}, number = {19}, pages = {8966-8970}, pmid = {1409592}, issn = {0027-8424}, mesh = {Aerobiosis ; Amino Acid Sequence ; Anaerobiosis ; Animals ; Base Sequence ; *Biological Evolution ; DNA, Fungal/genetics/isolation &amp; purification ; Dihydroorotate Dehydrogenase ; Drosophila melanogaster/enzymology/genetics ; Escherichia coli/enzymology/genetics ; Gene Deletion ; *Genes, Fungal ; Kinetics ; Molecular Sequence Data ; Oxidoreductases/*genetics/metabolism ; *Oxidoreductases Acting on CH-CH Group Donors ; Pyrimidines/*biosynthesis ; Saccharomyces cerevisiae/enzymology/*genetics/metabolism ; Schizosaccharomyces/enzymology/*genetics/metabolism ; Sequence Homology, Amino Acid ; Subcellular Fractions/enzymology ; }, abstract = {A cDNA encoding the dihydroorotate dehydrogenase (DHOdehase; EC 1.3.3.1) of the yeast Schizosaccharomyces pombe was isolated by functional complementation in Saccharomyces cerevisiae. A divergent subcellular compartmentation of the DHOdehase of each yeast was shown. The DHOdehase from Sch. pombe was localized in the mitochondria whereas its homolog from S. cerevisiae was found to be cytosolic. The heterologous expression of the Sch. pombe enzyme in S. cerevisiae allowed us to demonstrate that the Sch. pombe DHOdehase activity requires the integrity of the mitochondrial electron transport chain. Indeed, the presence of a mutation inactivating cytochrome b abolished the complementation of a S. cerevisiae ura1 mutant by the corresponding Sch. pombe gene. By contrast, in vitro studies have revealed that the DHOdehase of S. cerevisiae uses fumarate as terminal electron acceptor. These results are discussed in relation to the anaerobic growth competence of the two yeasts and to the fermentative processes they use.}, }
@article {pmid1365884, year = {1992}, author = {Kurland, CG}, title = {Evolution of mitochondrial genomes and the genetic code.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {14}, number = {10}, pages = {709-714}, doi = {10.1002/bies.950141013}, pmid = {1365884}, issn = {0265-9247}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/metabolism ; Codon/genetics ; DNA, Mitochondrial/*genetics ; *Genetic Code ; *Genome ; Models, Genetic ; Mutation ; Protein Biosynthesis ; RNA, Transfer/genetics ; Recombination, Genetic ; Selection, Genetic ; Sequence Deletion ; Symbiosis ; }, abstract = {Mitochondrial genomes are clearly marked by a strong tendency towards reductive evolution. This tendency has been facilitated by the transfer of most of the essential genes for mitochondrial propogation and function to the nuclear genome. The most extreme examples of genomic simplification are seen in animal mitochondria, where there also are the greatest tendencies to codon reassignment. The reassignment of codons to amino acids different from those designated in the so called universal code is seen in part as an expression of the reduction of the number of genes used by these genomes to code for tRNA species. The driving force for the reductive evolution of mitochondrial genomes is identified with two population genetic effects which may also be operating on populations of parasites.}, }
@article {pmid1302540, year = {1992}, author = {Ren, HY and Niu, LD}, title = {[Histopathology of spleen deficiency syndrome of chronic atrophic gastritis and its ultrastructural changes].}, journal = {Zhongguo Zhong xi yi jie he za zhi Zhongguo Zhongxiyi jiehe zazhi = Chinese journal of integrated traditional and Western medicine}, volume = {12}, number = {10}, pages = {593-7, 579-80}, pmid = {1302540}, issn = {1003-5370}, mesh = {Gastric Mucosa/*ultrastructure ; Gastritis, Atrophic/*pathology ; Humans ; Medicine, Chinese Traditional ; Microscopy, Electron ; Microscopy, Electron, Scanning ; Mitochondria/ultrastructure ; Splenic Diseases/*pathology ; Yang Deficiency/pathology ; Yin Deficiency/pathology ; }, abstract = {Pathologic change of gastric mucosa in 247 CAG patients of Spleen Qi (Yang) Deficiency (QYD) and Spleen-Stomach Yin Deficiency(YD) Syndrome were observed. The surface of gastric antrum mucosa of 26 patients with scanning electron microscope as well as the gastric mucosa of 34 patients with transmission electron microscope was observed for their intracellular structure. It was found that the CSAG and CAG I of Spleen QYD amounted to 165 cases (66.8%), and CAG II and III of Spleen-Stomach YD amounted to 34 cases (64.2%). It denoted that the Spleen QYD belonged to mild case, while the Spleen-Stomach YD belonged to severe case. The mitochondria of all kinds of gastric antrum mucosa cells showed retrograded degeneration, the pathologic basis of Spleen Deficiency of CAG, those of Spleen-Stomach QD had sparse broken and swollen mitochondria (82.3%), while the 53.3% of Spleen-Stomach YD displayed vacuolation as its predominant change. The different severity of retrograde degeneration and damage of mitochondria yielded various stage in atrophy of gastric mucosa which was the basis of Syndromes evolution from Defi. to QYD and then YD. Inflammatory change of the gastric mucosa was predominant in Spleen-Stomach YD (45.3%), and far less in QYD (27.1%), P < 0.01.}, }
@article {pmid1390679, year = {1992}, author = {Lewandowski, ED}, title = {Metabolic heterogeneity of carbon substrate utilization in mammalian heart: NMR determinations of mitochondrial versus cytosolic compartmentation.}, journal = {Biochemistry}, volume = {31}, number = {37}, pages = {8916-8923}, doi = {10.1021/bi00152a031}, pmid = {1390679}, issn = {0006-2960}, mesh = {Alanine/metabolism ; Animals ; Carbon/*metabolism ; Cell Compartmentation ; Cytosol/metabolism ; Energy Metabolism ; Glutamates/metabolism ; Lactates/metabolism ; Magnetic Resonance Spectroscopy ; Mitochondria, Heart/*metabolism ; Myocardial Contraction ; Myocardium/*metabolism ; Pyruvates/metabolism ; Rabbits ; }, abstract = {Carbon-13 (13C) nuclear magnetic resonance (NMR) spectroscopy can be used to target specific pathways of intermediary metabolism within intact tissues and was employed in this study to evaluate the compartmentation of pyruvate metabolism between the cytosol and mitochondrial matrix. The distribution of 13C into the tissue alanine, lactate, and glutamate pools was evaluated during metabolism of [3-13C]-pyruvate in intact, isolated perfused rabbit hearts with and without activation of pyruvate dehydrogenase activity by dichloroacetate (5 mM). Equilibrium between the intracellular alanine and pyruvate pools was in evidence from the rapid evolution of the steady-state 13C signal arising from the 3-carbon of alanine in intact hearts perfused with 2.5 mM 99.4% [3-13C]pyruvate. Augmented pyruvate oxidation, in response to perfusion with dichloroacetate, was evident within 13C NMR spectra of intact hearts as a relative increase in signal intensity of 53-62% (p less than 0.05) from the 4-carbon resonance of 13C-enriched glutamate when compared to the unaffected alanine signal. The increased bulk flow of [3-13C]pyruvate into the tricarboxylic acid cycle in response to dichloroacetate resulted in elevated fractional enrichment of glutamate from 68% in controls to 83% in the treated group (p less than 0.04), via interconversion with alpha-ketoglutarate, without changes in the actual tissue content of glutamate. Evidence of metabolic heterogeneity of cytosolic and mitochondrial pyruvate pools was also obtained from analysis of tissue extracts with in vitro NMR spectroscopy.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid1390628, year = {1992}, author = {Schmidt, DM and Saghbini, M and Scheffler, IE}, title = {The C-terminus of the succinate dehydrogenase IP peptide of Saccharomyces cerevisiae is significant for assembly of complex II.}, journal = {Biochemistry}, volume = {31}, number = {36}, pages = {8442-8448}, doi = {10.1021/bi00151a008}, pmid = {1390628}, issn = {0006-2960}, support = {GM33752/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Biological Transport ; DNA Mutational Analysis ; Enzyme Stability ; Iron/metabolism ; Metalloproteins/*metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Conformation ; Recombinant Proteins/biosynthesis ; Saccharomyces cerevisiae/*enzymology/genetics ; Structure-Activity Relationship ; Succinate Dehydrogenase/genetics/*metabolism ; }, abstract = {Site-directed mutagenesis was used to introduce mutations into the gene for the iron protein (IP) of succinate dehydrogenase (SDH) of Saccharomyces cerevisiae. Specifically, three mutations were examined which caused the synthesis of truncated IP peptides missing four, seven, or 17 amino acids from the C-terminus, respectively. The deletion of seven or more amino acids includes the loss of two lysine residues, which appear to have been highly conserved in evolution. While the deletion of four amino acids had no effect on the assembly of complex II and on its activity, the deletion including the two lysines abolished SDS activity completely and led to the failure of the imported IP peptide to be incorporated into a stable complex II or SDH complex. Replacement of one of the lysines by threonine had no effect, but replacement of both by threonine affected the specific activity of complex II but not its assembly and stability.}, }
@article {pmid1356223, year = {1992}, author = {Campbell, JW and Smith, DD}, title = {Metabolic compartmentation of vertebrate glutamine synthetase: putative mitochondrial targeting signal in avian liver glutamine synthetase.}, journal = {Molecular biology and evolution}, volume = {9}, number = {5}, pages = {787-805}, doi = {10.1093/oxfordjournals.molbev.a040759}, pmid = {1356223}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Amino Acids/physiology ; Animals ; Base Sequence ; Biological Evolution ; Blotting, Northern ; Blotting, Southern ; *Cell Compartmentation ; Chickens/genetics/metabolism ; Cloning, Molecular ; DNA ; Escherichia coli ; Glutamate-Ammonia Ligase/genetics/*metabolism ; Mammals/genetics/metabolism ; Mitochondria, Liver/*enzymology ; Molecular Sequence Data ; Organ Specificity/genetics ; Protein Biosynthesis ; Protein Conformation ; Protein Sorting Signals/*metabolism ; Recombinant Proteins/genetics/metabolism ; Restriction Mapping ; Sequence Homology, Nucleic Acid ; }, abstract = {The evolution of uricoteley as a mechanism for hepatic ammonia detoxication in vertebrates required targeting of glutamine synthetase (GS) to liver mitochondria in the sauropsid line of descent leading to the squamate reptiles and archosaurs. Previous studies have shown that in birds and crocodilians, sole survivors of the archosaurian line, hepatic GS is translated without a transient, N-terminal targeting signal common to other mitochondrial matrix proteins. To identify a putative internal targeting sequence in the avian enzyme, the amino acid sequence of chicken liver GS was derived by a combination of sequencing of cloned cDNA, direct sequencing of mRNA, and sequencing of polymerase chain reaction (PCR) products amplified from reverse-transcribed mRNA. Analysis of the first 20 or so N-terminal amino acids of the derived sequence for the chicken enzyme shows that they are devoid of acidic amino acids, contain several hydroxy amino acids, and can be predicted to form a positively charged, amphipathic helix, all of which are characteristic properties of mitochondrial targeting signals. A comparison of the N-terminus of chicken GS with the N-termini of cytosolic mammalian GSs indicates that at least three amino acid replacements may have been responsible for converting the N-terminus of the cytosolic mammalian enzyme into a mitochondrial targeting signal. Two of these, His15 and Lys19, result in additional positive charges, as well as in changes in hydrophilicity. Both could have resulted from third-base-codon substitutions. A third replacement, Ala12, may contribute to the helicity of the N-terminus of the chicken enzyme. The N-terminus of the cytosolic chicken brain GS (positions 1-36) was found to be identical to that of the liver enzyme. The complete sequence of chicken retinal GS is also identical to that of the liver enzyme. GS is coded by a single gene in birds, so these sequence data suggest that, unlike the situation in other tissue-specific compartmental isozymes, differential targeting of avian GS to the mitochondrial or cytosolic compartments is not dependent on the sequence of the primary translation product of its mRNA but may involve some other tissue-specific factor(s).}, }
@article {pmid1381286, year = {1992}, author = {Mörl, M and Niemer, I and Schmelzer, C}, title = {New reactions catalyzed by a group II intron ribozyme with RNA and DNA substrates.}, journal = {Cell}, volume = {70}, number = {5}, pages = {803-810}, doi = {10.1016/0092-8674(92)90313-2}, pmid = {1381286}, issn = {0092-8674}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; DNA/*metabolism ; Introns ; Molecular Sequence Data ; RNA/*metabolism ; *RNA Splicing ; RNA, Catalytic/chemistry/*metabolism ; Substrate Specificity ; }, abstract = {Here we describe three novel reactions of the self-splicing group II intron bI1 (the first intron of the COB gene of yeast mitochondria) demonstrating its catalytic versatility: reversal of the first step of the self-splicing reaction catalyzed by a linear form of the intron utilizing the energy of a phosphoanhydride bond for transesterification, ligation of a single-stranded DNA to an RNA, and cleavage of a single-stranded DNA substrate. These results have the following evolutionary implications: use of the alpha-beta bond of a terminal triphosphate for transesterification suggests that an RNA RNA replicase could use mononucleotide triphosphates as precursors, and cleavage of single-stranded DNA and DNA-RNA ligation suggests that excised group II introns might integrate directly into DNA without prior reverse transcription.}, }
@article {pmid1462374, year = {1992}, author = {Makhmudov, ES and Alimukhamedov, AA and Akhmerov, RI and Babaeva, RN and Baratova, GKh}, title = {[Effect of hyperglycemia and hyperthermia on liver mitochondrial respiration and blood glucose content of rats during postnatal ontogenesis].}, journal = {Ukrainskii biokhimicheskii zhurnal (1978)}, volume = {64}, number = {5}, pages = {77-82}, pmid = {1462374}, issn = {0201-8470}, mesh = {Animals ; Animals, Newborn/growth &amp; development/*metabolism ; Blood Glucose/*metabolism ; Body Temperature/*physiology ; Caprylates/metabolism ; Hyperglycemia/blood/*metabolism ; Malates/metabolism ; Mitochondria, Liver/*metabolism ; Oxygen Consumption/*physiology ; Pyruvates/metabolism ; Pyruvic Acid ; Rats ; Rats, Wistar ; Succinates/metabolism ; Succinic Acid ; }, abstract = {Correlation between glucose level in blood and liver mitochondrial energetics of 1, 10, 20-days rats under hyperglycemia and high environmental temperature (38 degrees C) has been studied. Glucose feeding led to a significant increase of glucose content in blood, this increase being less at hyperthermia. Glucose feeding strengthened the oxidation of such intermediates as succinate (Krebs cycle), pyruvate and malate (hydrocarbonates) and caprylate (lipid). High environmental temperature with hyperglycemia suppresses the liver mitochondria breathing, hydrocarbon and lipid intermediates being used; the suppression is less in the presence of succinate. It is found that liver mitochondria of growing rats at different experimental conditions oxidize different intermediates with various rates. These data can be explained in the light of ontogenetic evolution of the energetic apparatus. It is supposed that exogenic glucose is the factor which activates growing processes of animals and to certain extent diminishes the negative influence of hyperthermia on the organism.}, }
@article {pmid1383762, year = {1992}, author = {Miquel, J}, title = {An update on the mitochondrial-DNA mutation hypothesis of cell aging.}, journal = {Mutation research}, volume = {275}, number = {3-6}, pages = {209-216}, doi = {10.1016/0921-8734(92)90024-j}, pmid = {1383762}, issn = {0027-5107}, mesh = {Animals ; Biological Evolution ; Cellular Senescence/*genetics ; *DNA Damage ; DNA, Mitochondrial/*genetics ; Genome ; Humans ; Insecta ; Mammals ; Mitochondria/*physiology ; Models, Biological ; *Mutation ; }, abstract = {Our electron microscopic study of aging insects and mammals suggests that metazoan senescence is linked to a gradual process of mitochondrial breakdown (and lipofuscin accumulation) in fixed postmitotic cells. This led us to propose in the early 1980s an oxyradical-mitochondrial DNA damage hypothesis, according to which metazoan aging may be caused by mutation, inactivation or loss of the mitochondrial genome (mtDNA) in irreversibly differentiated cells. This extranuclear somatic gene mutation concept of aging is in agreement with the fact that mtDNA synthesis takes place at the inner mitochondrial membrane near the sites of formation of highly reactive oxygen species and their products. Mitochondrial DNA may be unable to counteract the damage inflicted by those by-products of respiration because, in contrast to the nuclear genome, it lacks excision and recombination repair. Since mtDNA contains the structural genes for 13 hydrophobic proteins of the respiratory chain and ATP synthase as well as mitochondrial rRNAs and tRNAs, damage to this organellar genome will decrease or prevent the 'rejuvenation' of the mitochondria through the process of macromolecular turnover and organelle fission. Thus deprived of the ability to regenerate their mitochondria, the fixed postmitotic cells will sustain a decrease in the number of functional organelles, with resulting decline in ATP production. At higher levels of biological organization, this will lead to a loss in the bioenergetic capacity of cells, with concomitant decreases in ATP dependent protein synthesis and specialized physiological function, thus paving the way for age related degenerative diseases. The above concept is supported by a wealth of recent observations confirming the genomic instability of mitochondria and suggesting that animal and human aging is accompanied by mtDNA deletions and other types of injury to the mitochondrial genome. Our hypothesis of mtDNA damage is integrated with the classic concepts of Weissman and Minot in order to provide a preliminary explanation of the evolutionary roots of aging and reconcile the programed and stochastic views of metazoan senescence.}, }
@article {pmid1379562, year = {1992}, author = {Guo, Q and Lambowitz, AM}, title = {A tyrosyl-tRNA synthetase binds specifically to the group I intron catalytic core.}, journal = {Genes &amp; development}, volume = {6}, number = {8}, pages = {1357-1372}, doi = {10.1101/gad.6.8.1357}, pmid = {1379562}, issn = {0890-9369}, support = {GM37951/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Binding Sites/genetics ; Biological Evolution ; Introns/*genetics ; Mitochondria/*metabolism ; Molecular Sequence Data ; Neurospora/genetics/metabolism ; Nucleic Acid Conformation ; Plasmids/genetics ; RNA/genetics/*metabolism ; RNA Splicing/genetics ; RNA, Mitochondrial ; RNA, Ribosomal/genetics/*metabolism ; Sequence Homology, Nucleic Acid ; Tyrosine-tRNA Ligase/genetics/*metabolism ; }, abstract = {The Neurospora CYT-18 protein, the mitochondrial tyrosyl-tRNA synthetase, functions in splicing group I introns in mitochondria. Here, we show that CYT-18 binds strongly to diverse group I introns that have minimal sequence homology and recognizes highly conserved structural features of the catalytic core of these introns. Inhibition experiments indicate that the intron RNA and tRNA(Tyr) compete for the same or overlapping binding sites in the CYT-18 protein. Considered together with functional analysis, our results indicate that the CYT-18 protein promotes splicing by binding to the intron core and stabilizing it in a conformation required for catalytic activity. Furthermore, the specific binding of the synthetase suggests that the group I intron catalytic core has structural similarities to tRNAs, which could reflect either convergent evolution or an evolutionary relationship between group I introns and tRNAs.}, }
@article {pmid1339289, year = {1992}, author = {Elhag, GA and Bourque, DP}, title = {Nuclear-encoded chloroplast ribosomal protein L27 of Nicotiana tabacum: cDNA sequence and analysis of mRNA and genes.}, journal = {Biochemistry}, volume = {31}, number = {29}, pages = {6856-6864}, doi = {10.1021/bi00144a028}, pmid = {1339289}, issn = {0006-2960}, support = {GM26937/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; Biological Evolution ; Cell Nucleus/*physiology ; Chloroplasts/*physiology ; DNA/*genetics/isolation &amp; purification ; Gene Library ; *Genes ; Genetic Vectors ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Plants, Toxic ; RNA, Messenger/*genetics/isolation &amp; purification ; Ribosomal Proteins/*genetics ; Sequence Homology, Nucleic Acid ; Nicotiana/*genetics/physiology ; }, abstract = {A tobacco (Nicotiana tabacum cv. Petite Havana) leaf cDNA library was constructed in the expression vector lambda gt11. Immunological and nucleic acid hybridization screening yielded several cDNAs encoding an M(r) 19,641 precursor to an M(r) 14,420 mature protein which is homologous to Escherichia coli ribosomal protein L27. One cDNA (L27-1; 882 nucleotides long) contains 104 bp of 5'-noncoding sequence, 51 codons for a transit peptide, 128 codons for the predicted mature L27 polypeptide, and 241 bp of 3'-noncoding sequence, including the poly(A)29 tail. A beta-galactosidase-L27 fusion protein was bound to nitrocellulose filters, expressed, and used as an affinity matrix to purify monospecific antibody to L27 protein from an antiserum of rabbits immunized with 50S chloroplast ribosomal proteins. Using this monospecific antibody, protein L27 was identified among HPLC-purified tobacco chloroplast ribosome 50S subunit proteins. The predicted amino terminus of the mature L27 protein was confirmed by partial sequencing of the HPLC-purified L27 protein. The mature L27 protein has 66%, 61%, 56%, and 48% amino acid sequence identity with the L27-type ribosomal proteins of Bacillus subtilis, E. coli, Bacillus stearo-thermophilus, and yeast mitochondria (MRP7), respectively, in the homologous overlapping regions. The transit peptide of tobacco chloroplast ribosomal protein L27 has 41% amino acid sequence similarity with the MRP7 mitochondrial targeting sequence. Tobacco chloroplast L27 protein also has a 40 amino acid long carboxyl-terminal extension (compared to its bacterial counterparts) which is similar to the corresponding portion of yeast MRP7.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid1339350, year = {1992}, author = {Purdue, PE and Lumb, MJ and Danpure, CJ}, title = {Molecular evolution of alanine/glyoxylate aminotransferase 1 intracellular targeting. Analysis of the marmoset and rabbit genes.}, journal = {European journal of biochemistry}, volume = {207}, number = {2}, pages = {757-766}, doi = {10.1111/j.1432-1033.1992.tb17106.x}, pmid = {1339350}, issn = {0014-2956}, mesh = {Alanine Transaminase/*genetics/metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Biological Transport ; Blotting, Southern ; Callithrix/*genetics ; Cell Compartmentation ; Cloning, Molecular ; DNA/genetics ; Gene Expression ; Genes ; Humans ; Microbodies/enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; Oligodeoxyribonucleotides/chemistry ; RNA, Messenger/genetics ; Rabbits/*genetics ; Rats ; Sequence Alignment ; *Transaminases ; }, abstract = {In mammals, the subcellular distribution of alanine:glyoxylate aminotransferase 1 (AGT) is species dependent, with the proportion of AGT targeted to mitochondria varying between 0% and greater than 90%, the remainder being located in the peroxisome. In order to extend our studies on the molecular evolution of intracellular targeting of AGT, we have investigated the organization and expression of the AGT genes of rabbit, which has all of its AGT located in the peroxisome, and marmoset, which has approximately 50% of its AGT located in the peroxisome and 50% in the mitochondrion. Southern-blot analysis indicates that, in both of these species, AGT is encoded by a single-copy gene, as has previously been shown for human (all AGT in the peroxisome) and rat (50% AGT in the peroxisome and 50% in the mitochondrion). Comparison of the cDNA sequences encoding marmoset, rabbit, human and rat AGT, combined with transcript mapping and in vitro mitochondrial protein-import analysis, has provided a molecular explanation for the differential targeting of AGT in these species. As in the rat, marmoset AGT is synthesized in two forms, via the use of alternative transcription and translation-initiation sites. These two forms of AGT differ only in the presence or absence of a 22-amino-acid amino-terminal peptide, which acts as a cleavable mitochondrial-targeting sequence, directing the longer form of AGT to mitochondria. The shorter form of AGT, lacking the mitochondrial-targeting sequence, is presumed to be localized in the peroxisomes. In humans and rabbits, similar but distinct evolutionary mutational events within the AGT gene have resulted in exclusion of the region encoding the mitochondrial-targeting sequence from the open reading frame, explaining the exclusive peroxisomal localization of AGT in these species. We discuss the impact of these results on our understanding of both the evolution of species dependence of AGT subcellular distribution and the recent identification of amino acid changes in human AGT which result in mistargeting of this protein to mitochondria.}, }
@article {pmid1611670, year = {1992}, author = {Li, GY and Herbert, CJ and Labouesse, M and Slonimski, PP}, title = {In vitro mutagenesis of the mitochondrial leucyl-tRNA synthetase of S. cerevisiae reveals residues critical for its in vivo activities.}, journal = {Current genetics}, volume = {22}, number = {1}, pages = {69-74}, pmid = {1611670}, issn = {0172-8083}, mesh = {Base Sequence ; Blotting, Northern ; Electrophoresis, Polyacrylamide Gel ; Introns ; Leucine-tRNA Ligase/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Mutagenesis ; RNA Splicing ; RNA, Messenger/genetics ; Saccharomyces cerevisiae/*enzymology ; }, abstract = {The mitochondrial leucyl-tRNA synthetase (mLRS) of Saccharomyces cerevisiae is involved in both mitochondrial protein synthesis and pre-mRNA splicing. We have created mutations in the regions HIGH, GWD and KMSKS, which are involved in ATP-, amino acid- and tRNA-binding respectively, and which have been conserved in the evolution of group I tRNA synthetases. The mutants GRD and NMSKS have no discernible phenotype. The mutants AWD and ARD act as null alleles and lead to the production of 100% cytoplasmic petites. The mutants HIGN, NIGH and KMSNS are unable to grow on glycerol even in the presence of an intronless mitochondrial genome and accumulate petites to a greater extent than the wild-type but less than 40%. Experiments with an imported bI4 maturase indicate that the lesion in these mutations primarily affects the synthetase and not the splicing functions.}, }
@article {pmid1378523, year = {1992}, author = {Kraus, F and Jarecki, L and Miyamoto, MM and Tanhauser, SM and Laipis, PJ}, title = {Mispairing and compensational changes during the evolution of mitochondrial ribosomal RNA.}, journal = {Molecular biology and evolution}, volume = {9}, number = {4}, pages = {770-774}, doi = {10.1093/oxfordjournals.molbev.a040745}, pmid = {1378523}, issn = {0737-4038}, mesh = {Animals ; Base Composition ; *Biological Evolution ; Mitochondria/*metabolism ; Phylogeny ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/*genetics ; }, }
@article {pmid1323891, year = {1992}, author = {Cooperman, BS and Baykov, AA and Lahti, R}, title = {Evolutionary conservation of the active site of soluble inorganic pyrophosphatase.}, journal = {Trends in biochemical sciences}, volume = {17}, number = {7}, pages = {262-266}, doi = {10.1016/0968-0004(92)90406-y}, pmid = {1323891}, issn = {0968-0004}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/enzymology ; Binding Sites/*genetics ; Biological Evolution ; Inorganic Pyrophosphatase ; Kinetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Mutagenesis, Site-Directed/genetics ; Pyrophosphatases/*genetics ; Retina/enzymology ; Saccharomyces cerevisiae/enzymology ; Sequence Homology, Nucleic Acid ; Structure-Activity Relationship ; }, abstract = {Soluble inorganic pyrophosphatases (PPases) are essential enzymes that are important for controlling the cellular levels of inorganic pyrophosphate (PPi). Although prokaryotic and eukaryotic PPases differ substantially in amino acid sequence, recent evidence now demonstrates clearly that PPases throughout evolution show a remarkable level of conservation of both an extended active site structure, which has the character of a mini-mineral, and a catalytic mechanism. PPases require several (three or four) Mg2+ ions at the active site for activity and many of the 15-17 fully conserved active site residues are directly involved in the binding of metal ions. Each of the eight microscopic rate constants that has been evaluated for the PPases from both Escherichia coli and Saccharomyces cerevisiae is quite similar in magnitude for the two enzymes, supporting the notion of a conserved mechanism.}, }
@article {pmid1593640, year = {1992}, author = {Möller, W and Janssen, GM}, title = {Statistical evidence for remnants of the primordial code in the acceptor stem of prokaryotic transfer RNA.}, journal = {Journal of molecular evolution}, volume = {34}, number = {6}, pages = {471-477}, pmid = {1593640}, issn = {0022-2844}, mesh = {Amino Acyl-tRNA Synthetases/genetics ; Biological Evolution ; Codon ; Eukaryotic Cells ; *Genetic Code ; Models, Statistical ; Nucleic Acid Conformation ; Prokaryotic Cells ; RNA, Transfer/*genetics ; }, abstract = {The specificity of interaction of amino acids with triplets in the acceptor helix stem of tRNA was investigated by means of a statistical analysis of 1400 tRNA sequences. The imprint of a prototypic genetic code at position 3-5 of the acceptor helix was detected, but only for those major amino acids, glycine, alanine, aspartic acid, and valine, that are formed by spark discharges of simple gases in the laboratory. Although remnants of the code at position 3-5 are typical for tRNAs of archaebacteria, eubacteria, and chloroplasts, eukaryotes do not seem to contain this code, and mitochondria take up an intermediary position. A duplication mechanism for the transposition of the original 3-5 code toward its present position in the anticodon stem of tRNA is proposed. From this viewpoint, the mode of evolution of mRNA and functional ribosomes becomes more understandable.}, }
@article {pmid1511870, year = {1992}, author = {Hastings, IM}, title = {Population genetic aspects of deleterious cytoplasmic genomes and their effect on the evolution of sexual reproduction.}, journal = {Genetical research}, volume = {59}, number = {3}, pages = {215-225}, doi = {10.1017/s0016672300030500}, pmid = {1511870}, mesh = {Animals ; *Biological Evolution ; Cytoplasm/*physiology ; *Genetics, Population ; Reproduction/*genetics ; }, abstract = {A conflict of interest may arise between intra-cellular genomes and their host cell. The example explicitly investigated is that of a 'selfish' mitochondrion which increases its own rate of replication at the cost of reduced metabolic activity which is deleterious to the host cell. The results apply to deleterious cytoplasmic agents in general, such as intracellular parasites. Numerical simulation suggests that selfish mitochondria are able to invade an isogamous sexual population and are capable of reducing its fitness to below 5% of that prior to their invasion. Their spread is enhanced by decreasing the number of mitotic divisions between meioses, and this may constitute a significant constraint on the evolution of lifecycles. The presence of such deleterious cytoplasmic agents favours a nuclear mutation whose expression prevents cytoplasm from the other gamete entering the zygote at fertilization, resulting in uniparental inheritance of cytoplasm. Such a mutation appears physiologically plausible and can increase in frequency despite its deleterious effect in halving the amount of cytoplasm in the zygote. It is suggested that these were the conditions under which anisogamy evolved. These results have implications for the evolution of sexual reproduction. Standard theory suggests there is no immediate cost of sex, a twofold cost being incurred later as anisogamy evolves. The analysis described here predicts a large, rapid reduction in fitness associated with isogamous sexual reproduction, due to the spread of deleterious cytoplasmic agents with fitness only subsequently rising to a maximum twofold cost as uniparental inheritance of cytoplasm and anisogamy evolve.}, }
@article {pmid1535221, year = {1992}, author = {Nelson, N}, title = {Evolution of organellar proton-ATPases.}, journal = {Biochimica et biophysica acta}, volume = {1100}, number = {2}, pages = {109-124}, doi = {10.1016/0005-2728(92)90072-a}, pmid = {1535221}, issn = {0006-3002}, mesh = {Amino Acid Sequence ; *Biological Evolution ; Chloroplasts/enzymology ; Mitochondria/enzymology ; Molecular Sequence Data ; Operon ; Organelles/*enzymology ; Protein Conformation ; *Proton-Translocating ATPases/genetics/metabolism ; }, abstract = {Proton ATPases function in biological energy conversion in every known living cell. Their ubiquity and antiquity make them a prime source for evolutionary studies. There are two related families of H(+)-ATPases; while the family of F-ATPases function in eubacteria chloroplasts and mitochondria, the family of V-ATPases are present in archaebacteria and the vacuolar system of eukaryotic cells. Sequence analysis of several subunits of V- and F-ATPases revealed several of the important steps in their evolution. Moreover, these studies shed light on the evolution of the various organelles of eukaryotes and suggested some events in the evolution of the three kingdoms of eubacteria, archaebacteria and eukaryotes.}, }
@article {pmid1585174, year = {1992}, author = {Knoll, AH}, title = {The early evolution of eukaryotes: a geological perspective.}, journal = {Science (New York, N.Y.)}, volume = {256}, number = {5057}, pages = {622-627}, doi = {10.1126/science.1585174}, pmid = {1585174}, issn = {0036-8075}, mesh = {*Biological Evolution ; Cyanobacteria ; Eukaryota ; *Eukaryotic Cells ; Fossils ; Geological Phenomena ; *Geology ; Mitochondria ; Phylogeny ; }, abstract = {Molecular phylogenies of eukaryotic organisms imply patterns of biological and environmental history that can be tested against the geological record. As predicted by sequence comparisons, Precambrian rocks show evidence of episodic increases in biological diversity and atmospheric oxygen concentrations. Nonetheless, complete integration of the two records remains elusive and may require that the earliest macroscopic organisms be recognized as extinct experiments in eukaryotic multicellularity.}, }
@article {pmid1584013, year = {1992}, author = {Gatesy, J and Yelon, D and DeSalle, R and Vrba, ES}, title = {Phylogeny of the Bovidae (Artiodactyla, Mammalia), based on mitochondrial ribosomal DNA sequences.}, journal = {Molecular biology and evolution}, volume = {9}, number = {3}, pages = {433-446}, doi = {10.1093/oxfordjournals.molbev.a040734}, pmid = {1584013}, issn = {0737-4038}, mesh = {Animals ; Artiodactyla/*classification/genetics ; Base Sequence ; DNA ; DNA, Ribosomal/*genetics ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Nucleic Acid ; }, abstract = {Portions of the 12S and 16S mitochondrial ribosomal genes for 16 species representing nine tribes in the mammal family Bovidae were compared with six previously published orthologous sequences. Phylogenetic analysis of variable nucleotide positions under different constraints and weighting schemes revealed no robust groupings among tribes. Consensus trees support previous hypotheses of monophyly for four clades, including the traditional subfamily Bovinae. However, the basal diversification of bovid tribes, which was largely unresolved by morphological, immunodiffusion, allozyme, and protein sequence data, remains unresolved with the addition of DNA sequence data. The intractability of this systematic problem is consistent with a rapid radiation of the major bovid groups. Several analyses of our data show that monophyly of the Bovidae, which was weakly supported by previous morphological and molecular work, is questionable.}, }
@article {pmid1534855, year = {1992}, author = {Morioka, S and Honda, M and Ishikawa, S and Ishinaga, Y and Yano, S and Tanaka, K and Moriyama, K}, title = {Changes in contractile and non-contractile proteins, intracellular Ca2+ and ultrastructures during the development of right ventricular hypertrophy and failure in rats.}, journal = {Japanese circulation journal}, volume = {56}, number = {5}, pages = {469-474}, doi = {10.1253/jcj.56.469}, pmid = {1534855}, issn = {0047-1828}, mesh = {Animals ; Calcium/*metabolism ; Cardiomegaly/etiology/*metabolism/pathology ; Collagen/*metabolism ; Heart Failure/etiology/*metabolism/pathology ; Hypertension, Pulmonary/chemically induced/complications ; Male ; Microscopy, Electron, Scanning ; Mitochondria, Heart/ultrastructure ; Monocrotaline ; *Myocardial Contraction ; Myocardium/*metabolism/ultrastructure ; Myosins/*metabolism ; Rats ; Rats, Inbred Strains ; Sarcoplasmic Reticulum/ultrastructure ; }, abstract = {Whether cardiac hypertrophy is a compensatory response or a cause of decompensation has been an interesting and important controversy in cardiology. The purpose of this study is to assess qualitative and quantitative changes in biological factors involved in the evolution and the development of right ventricular hypertrophy (RVH) and right ventricular failure in response to pressure overload in rats with pulmonary hypertension induced by monocrotaline injection, and to clarify the process from compensation to deterioration in cardiac hypertrophy biochemically and morphologically. Significant RVH was produced in rats at 2 weeks after single subcutaneous injection of monocrotaline, and signs of right ventricular failure became obvious at 4 weeks as RVH became more severe. In the right ventricle of these rats, we found that: 1) myosin isoenzymes shifted from V1 to V3 both at 2 and 4 weeks; 2) total collagen content increased, and type III and type V collagens increased with a relative decrease in type I collagen at both 2 and 4 weeks; 3) intracellular Ca2+ transient recorded from isolated myocytes showed a lower peak and slower descent slope compared to those of control rats; 4) ultrastructural changes observed by scanning electron microscopy at 1 and 2 weeks disappeared gradually as heart failure developed, and degeneration or destruction of mitochondria or sarcoplasmic reticulum became remarkable at 3 and 4 weeks. These findings suggest that cardiac hypertrophy might be an ominous sign of cardiac failure rather than a benign adaptive process, at least in this model.}, }
@article {pmid1515149, year = {1992}, author = {Thiaw, OT and Mattei, X}, title = {Natural degenerating mitochondria in ovarian follicles of a cyprinodontidae fish, Epiplatys spilargyreus (teleost).}, journal = {Molecular reproduction and development}, volume = {32}, number = {1}, pages = {67-72}, doi = {10.1002/mrd.1080320111}, pmid = {1515149}, issn = {1040-452X}, mesh = {Animals ; Female ; Fishes/*anatomy &amp; histology ; Mitochondria/*ultrastructure ; Oogenesis ; Ovarian Follicle/*ultrastructure ; Vacuoles/ultrastructure ; }, abstract = {This study examines the evolution of mitochondria in the follicular cells during the development of the ovarian follicle in the teleostean fish Epiplatys spilargyreus. The mitochondria are few in number until the end of previtellogenesis; their matrix is dense, and their cristae are well developed. They proliferate during vitellogenesis and then are modified by deterioration of their matrix. Multilamellar structures are organized in the vacuolized mitochondria. During postvitellogenesis, these modifications become more advanced. The mitochondria degenerate, leaving vacuoles that contain heterogeneous structures, which will be released into the intercellular spaces. At the end of these mitochondrial transformations, the follicular cells degenerate. They release the elements which will participate in forming the secondary envelope.}, }
@article {pmid1441793, year = {1992}, author = {Ivashchenko, AT and Karpeniuk, TA and Ponomarenko, SV and Uteulin, KR and Goncharova, AV and Gabdulkhaeva, BB and Zakarina, AE}, title = {[The evolutionary changes in the amino acid sequences and properties of the ATP-synthase in chloroplasts, mitochondria and bacteria].}, journal = {Zhurnal evoliutsionnoi biokhimii i fiziologii}, volume = {28}, number = {3}, pages = {287-297}, pmid = {1441793}, issn = {0044-4529}, mesh = {Adenosine Triphosphatases/chemistry/*genetics ; Amino Acid Sequence ; Animals ; Bacteria/*enzymology ; *Biological Evolution ; Chemical Phenomena ; Chemistry, Physical ; Chloroplasts/*enzymology ; Humans ; Mitochondria/*enzymology ; Molecular Sequence Data ; Proton-Translocating ATPases/chemistry/*genetics ; Recombination, Genetic ; Sequence Homology, Amino Acid ; Species Specificity ; }, abstract = {Studies have been made on ATPase from chloroplasts, cyanobacteria and mitochondria of higher plants and animals. No intraspecies and interspecies variability of chloroplast and mitochondrial ATPase was found with respect to pH optimum of the activity, to specificity to cations as substrate components, to sensitivity to stimulating and inhibiting anions and ethanol, to optimal stimulating ethanol concentration. Intergenus variation of these properties of ATPase from chloroplasts, plant mitochondria, and cyanobacteria was revealed. Analysis of homology of the amino acid sequence in ATP-synthase subunits showed that ATP-synthase genes in chloroplast DNA originate from cyanobacterial genome, whereas ATP-synthase genes in plant and animal mitochondria-from genome of Rhodospirillum rubrum or closely related species. It was established that no recombination between the genetic material of chloroplasts and mitochondria took place during evolution.}, }
@article {pmid1565639, year = {1992}, author = {Rogers, MJ and Adachi, T and Inokuchi, H and Söll, D}, title = {Switching tRNA(Gln) identity from glutamine to tryptophan.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {89}, number = {8}, pages = {3463-3467}, pmid = {1565639}, issn = {0027-8424}, mesh = {Amino Acyl-tRNA Synthetases/*metabolism ; Anticodon/genetics ; Base Sequence ; Cloning, Molecular ; Escherichia coli/enzymology/*genetics ; *Genes, Bacterial ; *Genes, Suppressor ; Genes, Synthetic ; Glutamine/*metabolism ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Nucleic Acid Conformation ; RNA, Transfer, Gln/genetics/*metabolism ; Suppression, Genetic ; Tetrahydrofolate Dehydrogenase/biosynthesis/genetics/isolation &amp; purification ; Tryptophan/*metabolism ; beta-Galactosidase/genetics/metabolism ; }, abstract = {The middle base (U35) of the anticodon of tRNA(Gln) is a major element ensuring the accuracy of aminoacylation by Escherichia coli glutaminyl-tRNA synthetase (GlnRS). An opal suppressor of tRNA(Gln) (su+2UGA) containing C35 (anticodon UCA) was isolated by genetic selection and mutagenesis. Suppression of a UGA mutation in the E. coli fol gene followed by N-terminal sequence analysis of purified dihydrofolate reductase showed that this tRNA was an efficient suppressor that inserted predominantly tryptophan. Mutations of the 3-70 base pair (U70 and A3U70) were made. These mutants of su+2UGA are less efficient suppressors and inserted predominantly tryptophan in vivo; alanine insertion was not observed. Mutations of the discriminator nucleotide (A73, U73, C73) result in very weak opal suppressors. Aminoacylation in vitro by E. coli TrpRS of tRNA(Gln) transcripts mutated in the anticodon demonstrate that TrpRS recognizes all three nucleotides of the anticodon. The results show the interchangeability of the glutamine and tryptophan identities by base substitutions in their respective tRNAs. The amber suppressor (anticodon CUA) tRNA(Trp) was known previously to insert predominantly glutamine. We show that the opal suppressor (anticodon UCA) tRNA(Gln) inserts mainly tryptophan. Discrimination by these synthetases for tRNA includes position 35, with recognition of C35 by TrpRS and U35 by GlnRS. As the use of the UGA codon as tryptophan in mycoplasma and in yeast mitochondria is conserved, recognition of the UCA anticodon by TrpRS may also be maintained in evolution.}, }
@article {pmid1588917, year = {1992}, author = {Shain, DH and Salvadore, C and Denis, CL}, title = {Evolution of the alcohol dehydrogenase (ADH) genes in yeast: characterization of a fourth ADH in Kluyveromyces lactis.}, journal = {Molecular &amp; general genetics : MGG}, volume = {232}, number = {3}, pages = {479-488}, pmid = {1588917}, issn = {0026-8925}, mesh = {Alcohol Dehydrogenase/*genetics/isolation &amp; purification/metabolism ; Amino Acid Sequence ; Base Sequence ; *Biological Evolution ; Cloning, Molecular/methods ; DNA, Bacterial/genetics ; Isoenzymes/*genetics ; Kinetics ; Kluyveromyces/enzymology/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Multigene Family ; Plasmids ; Recombinant Proteins/isolation &amp; purification/metabolism ; Restriction Mapping ; Saccharomyces cerevisiae/enzymology/*genetics ; Sequence Homology, Nucleic Acid ; Substrate Specificity ; }, abstract = {Three alcohol dehydrogenase (ADH) genes have recently been characterized in the yeast Kluyveromyces lactis. We report on a fourth ADH in K. lactis (KADH II: KADH2* gene) which is highly similar to other ADHs in K. lactis and Saccharomyces cerevisiae. KADH II appears to be a cytoplasmic enzyme, and after expression of KADH2 in S. cerevisiae enzyme activity comigrated with a K. lactis ADH present in cells grown in glucose or in ethanol. KADH I was also expressed in S. cerevisiae and it comigrated with a major ADH species expressed under glucose growth conditions in K. lactis. The substrate specificities for KADH I and KADH II were shown to be more similar to that of SADH II than to SADH I. SADH I cannot efficiently utilize long chain alcohols, in contrast to other cytoplasmic yeast ADHs, presumably because of the presence of a methionine (residue 271) in its substrate binding cleft. A comparison of the DNA sequences of ADHs among K. lactis, S. cerevisiae and Schizosaccharomyces pombe suggests that the ancestral yeast species contained one cytoplasmic ADH. After divergence from S. pombe, the ADH in the ancestor to K. lactis and S. cerevisiae was duplicated, and one ADH became localized to the mitochondrion, presumably for the oxidative use of ethanol. Following the speciation of S. cerevisiae and K. lactis, the gene encoding the cytoplasmic ADH in S. cerevisiae duplicated, which resulted in the development of the SADH II protein as the primary oxidative enzyme in place of SADH III. In contrast, the K. lactis mitochondrial ADH duplicated to give rise to the highly expressed KADH3 and KADH4 genes, both of which may still play primary roles in oxidative metabolism. These data suggest that K. lactis and S. cerevisiae use different compartments for their metabolism of ethanol. Our results also indicate that the complex regulatory circuits controlling the glucose-repressible SADH2 in S. cerevisiae are a recent acquisition from regulatory networks used for the control of genes other than SADH2.}, }
@article {pmid1533253, year = {1992}, author = {Recipon, H and Perasso, R and Adoutte, A and Quetier, F}, title = {ATP synthase subunit c/III/9 gene sequences as a tool for interkingdom and metaphytes molecular phylogenies.}, journal = {Journal of molecular evolution}, volume = {34}, number = {4}, pages = {292-303}, pmid = {1533253}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Eukaryotic Cells/enzymology ; Genome ; Humans ; Molecular Sequence Data ; Organelles/*enzymology ; *Phylogeny ; Prokaryotic Cells/enzymology ; Proton-Translocating ATPases/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {The 38 sequences of the ATPase c/III/9 gene determined in bacteria, fungi, mammals, and higher plants have been used to construct phylogenetic trees by distance matrix and parsimony methods (checked by bootstrapping); alignments have been performed on the deduced amino-acid sequences and then transferred back to the nucleotide sequences. Three lineages stand out: (1) eubacteria (except cyanobacteria and alpha purple bacteria), (2) chloroplasts, together with cyanobacteria, and (3) mitochondria together with nuclei and alpha purple bacteria. The clear monophyly of the mitochondrial/nuclear lineage, taken all together, strongly suggests that the nuclear copies of the gene now residing in the eukaryotic nucleus originate from a mitochondrial transfer. Within this lineage, metaphytes emerge late and as a cohesive group, after fungi (as a dispersed group) and metazoa, yielding an order that markedly differs from that obtained through typical RNA nuclear molecules. The possible biphyletic origin of mitochondria based on mitochondrial rRNA sequences is not evidenced by these sequences. Internal branches within both the chloroplastic and the mitochondrial lineages are consistent with botanical evolutionary schemes based on morphological characters. In spite of its relatively small size, the ATPase c/III/9 gene therefore displays remarkable properties as a phylogenetic index and adds a new tool for molecular evolutionary reconstructions, especially within the metaphytes.}, }
@article {pmid1588598, year = {1992}, author = {Karlovsky, P and Fartmann, B}, title = {Genetic code and phylogenetic origin of oomycetous mitochondria.}, journal = {Journal of molecular evolution}, volume = {34}, number = {3}, pages = {254-258}, pmid = {1588598}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Base Sequence ; Codon ; DNA, Fungal ; DNA, Mitochondrial ; *Mitochondria ; Molecular Sequence Data ; *Phylogeny ; Phytophthora/classification/*genetics ; Sequence Alignment ; }, abstract = {We sequenced the 3'-terminal part of the COX3 gene encoding cytochrome c oxidase subunit 3 from mitochondria of Phytophthora parasitica (phylum Oomycota, kingdom Protoctista). Comparison of the sequence with known COX3 genes revealed that UGG is used as a tryptophan codon in contrast to UGA in the mitochondrial codes of most organisms other than green plants. A very high AT mutation pressure operates on the mitochondrial genome of Phytophthora, as revealed by codon usage and by A+T content of noncoding regions, which seems paradoxical because AT pressure causes tryptophan codon reassignment from UGG to UGA in mitochondria of most species. The genetic code and other data suggest that mitochondria of Oomycota share a direct common ancestor with mitochondria of plants and that mitochondria of the ancestor of Planta and Oomycota were acquired in a second endosymbiotic event, which occurred later than the acquisition of mitochondria by other eukaryotes.}, }
@article {pmid1579111, year = {1992}, author = {Osawa, S and Jukes, TH and Watanabe, K and Muto, A}, title = {Recent evidence for evolution of the genetic code.}, journal = {Microbiological reviews}, volume = {56}, number = {1}, pages = {229-264}, pmid = {1579111}, issn = {0146-0749}, support = {R01 HG00312/HG/NHGRI NIH HHS/United States ; }, mesh = {Base Sequence ; *Biological Evolution ; Cell Nucleus/chemistry ; Codon/*classification ; *Genetic Code ; Mitochondria/chemistry ; Molecular Sequence Data ; Nucleic Acid Conformation ; }, abstract = {The genetic code, formerly thought to be frozen, is now known to be in a state of evolution. This was first shown in 1979 by Barrell et al. (G. Barrell, A. T. Bankier, and J. Drouin, Nature [London] 282:189-194, 1979), who found that the universal codons AUA (isoleucine) and UGA (stop) coded for methionine and tryptophan, respectively, in human mitochondria. Subsequent studies have shown that UGA codes for tryptophan in Mycoplasma spp. and in all nonplant mitochondria that have been examined. Universal stop codons UAA and UAG code for glutamine in ciliated protozoa (except Euplotes octacarinatus) and in a green alga, Acetabularia. E. octacarinatus uses UAA for stop and UGA for cysteine. Candida species, which are yeasts, use CUG (leucine) for serine. Other departures from the universal code, all in nonplant mitochondria, are CUN (leucine) for threonine (in yeasts), AAA (lysine) for asparagine (in platyhelminths and echinoderms), UAA (stop) for tyrosine (in planaria), and AGR (arginine) for serine (in several animal orders) and for stop (in vertebrates). We propose that the changes are typically preceded by loss of a codon from all coding sequences in an organism or organelle, often as a result of directional mutation pressure, accompanied by loss of the tRNA that translates the codon. The codon reappears later by conversion of another codon and emergence of a tRNA that translates the reappeared codon with a different assignment. Changes in release factors also contribute to these revised assignments. We also discuss the use of UGA (stop) as a selenocysteine codon and the early history of the code.}, }
@article {pmid1560764, year = {1992}, author = {Bowman, BH and Taylor, JW and Brownlee, AG and Lee, J and Lu, SD and White, TJ}, title = {Molecular evolution of the fungi: relationship of the Basidiomycetes, Ascomycetes, and Chytridiomycetes.}, journal = {Molecular biology and evolution}, volume = {9}, number = {2}, pages = {285-296}, doi = {10.1093/oxfordjournals.molbev.a040720}, pmid = {1560764}, issn = {0737-4038}, support = {AI28545-02/AI/NIAID NIH HHS/United States ; }, mesh = {Ascomycota/classification/genetics ; Base Sequence ; Basidiomycota/classification/genetics ; *Biological Evolution ; Chytridiomycota/classification/genetics ; DNA, Fungal ; Fungi/classification/*genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Establishing the phylogeny of fungi and protists often has proved difficult owing to the simple morphologies and convergent characters in these organisms. We used DNA sequences of nuclear small-subunit ribosomal RNA genes to determine phylogenetic relationships among three major classes of organisms considered to be fungi--Basidiomycetes, Ascomycetes and Chytridiomycetes--and to assess the taxonomic position of Neocallimastix, an economically important anaerobic rumen microorganism whose classification is controversial. The Basidiomycetes and Ascomycetes, two classes of nonflagellated fungi, are the most closely related taxa. Chytridiomycetes, though bearing flagella, group with these higher fungi rather than with the protists. Neocallimastix, a eukaryote lacking mitochondria and variously classified as a protist or as a fungus, shows closest molecular affinities with the Chytridiomycete fungi in the order Spizellomycetales.}, }
@article {pmid1537093, year = {1992}, author = {Lewandowski, ED}, title = {Nuclear magnetic resonance evaluation of metabolic and respiratory support of work load in intact rabbit hearts.}, journal = {Circulation research}, volume = {70}, number = {3}, pages = {576-582}, doi = {10.1161/01.res.70.3.576}, pmid = {1537093}, issn = {0009-7330}, support = {HL-42267/HL/NHLBI NIH HHS/United States ; }, mesh = {Acetates/*metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Carbon Radioisotopes ; Citric Acid Cycle/*physiology ; Glutamates/*metabolism ; In Vitro Techniques ; Isoproterenol/pharmacology ; Magnetic Resonance Spectroscopy ; Mitochondria, Heart/drug effects/*metabolism ; Models, Cardiovascular ; Perfusion ; Phosphocreatine/metabolism ; Phosphorus Radioisotopes ; Potassium Chloride/pharmacology ; Rabbits ; }, abstract = {Pre-steady-state 13C nuclear magnetic resonance (NMR) spectra can provide a nondestructive probe of metabolic events associated with the physiology of intact organs. Therefore, the relation between phosphorylation state and intermediary metabolism in rabbit hearts, oxidizing [2-13C]acetate, was examined with a combination of 31P and 13C NMR. Multiple enrichment of the tissue glutamate pool with 13C as an index of metabolic turnover within the tricarboxylic acid cycle was readily observed as a function of work load. Dynamic changes in pre-steady-state 13C spectra evolved according to work load and correlated closely to respiratory rate in rabbit hearts perfused 1) under normal conditions (n = 7), 2) at basal metabolic rates (20 mM KCl arrest, n = 5), 3) and at heightened contractile state (10(-7) M isoproterenol, n = 7). The ratio of signal intensity arising from the secondary labeling sites within glutamate (C-2 and C-3) to that of the initial labeling site (C-4) reached steady state within 8.5 minutes in isoproterenol-treated hearts versus 18.5 minutes in control hearts. Work load did not affect glutamate concentration or fractional enrichment at the C-4 position, although an unlabeled fraction of glutamate persisted. Arrested hearts displayed slowed evolution of steady-state 13C enrichment with increased contributions from anaplerotic sources for tricarboxylic acid intermediate formation (32%) as compared with control (9%). Thus, the response of mitochondrial dehydrogenase activity to the demands of cardiac performance is likely to influence the recruitment of anabolic sources supplying the tricarboxylic acid cycle.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid1413112, year = {1992}, author = {Korobov, VN and Nazarenko, VI and Radomskiĭ, NF and Starodub, NF}, title = {[Comparative analysis of the spatial organization of myoglobins. I. Hydrophobicity profiles].}, journal = {Ukrainskii biokhimicheskii zhurnal (1978)}, volume = {64}, number = {2}, pages = {22-26}, pmid = {1413112}, issn = {0201-8470}, mesh = {Alligators and Crocodiles ; Animals ; Humans ; Mitochondria/*metabolism ; Mollusca ; Myoglobin/*chemistry ; Oxygen/*metabolism ; *Phylogeny ; Protein Conformation ; Rodentia ; Water ; Whales ; }, abstract = {Hydrophobicity profiles of myoglobins in the animal species far remote in the evolutionary series are considerably similar. A complete coincidence as to the arrangement of hydrophobic zones along the polypeptide chain in myoglobins of the compared species (from a man to mollusc) is revealed at the beginning of alpha-helix of B-segment and in the area corresponding to a cluster which embodies a heme- bound water molecule, distal histidine E7 being directed to this cluster. The mollusc myoglobin with two absent (as compared to myoglobins of other species) hydrophobic sites differs in the profile of hydrophobicity most of all. It is supposed that hydrophobic nuclei forming the heme circumference create a globule "skeleton" thus pre-setting general spatial structure of the myoglobin molecule, which is very significant for its functional activity.}, }
@article {pmid1342923, year = {1992}, author = {Liu, H and Beckenbach, AT}, title = {Evolution of the mitochondrial cytochrome oxidase II gene among 10 orders of insects.}, journal = {Molecular phylogenetics and evolution}, volume = {1}, number = {1}, pages = {41-52}, doi = {10.1016/1055-7903(92)90034-e}, pmid = {1342923}, issn = {1055-7903}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Codon/genetics ; DNA Primers/genetics ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; *Genes, Insect ; Insecta/classification/enzymology/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Phylogeny ; Sequence Homology, Amino Acid ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {We examine the complete nucleotide sequences of the mitochondrial cytochrome oxidase II gene of 13 species of insects, representing 10 orders. The genes range from 673 to 690 bp in length, encoding 226 to 229 amino acids. Several insertion or deletion events, each involving one or two codons, can be observed. The 3' end of the gene is extremely variable in both length and sequence, making alignment of the ends unreliable. Using the first 639 nucleotide positions, for which unambiguous alignments could be obtained, we examine the neighbor-joining trees based on nucleotide divergences and based on conserved subsets of that data, including transversion and amino acid and second codon position divergences. Each of these subsets produces different trees, none of which can be easily reconciled with trees constructed using morphology and the fossil record. Bootstrap analysis using second codon positions strongly supports affinities between the order Blatteria (cockroaches) and the order Isoptera (termites) and between a wasp and the published honeybee sequence (Order Hymenoptera). The divergence of insect orders is very ancient and may have occurred too rapidly for easy resolution using mitochondrial protein sequences. Unambiguous resolution of insect orders will probably require analysis of many additional taxa, using the COII gene and other conserved sequences.}, }
@article {pmid1310149, year = {1992}, author = {Goguel, V and Delahodde, A and Jacq, C}, title = {Connections between RNA splicing and DNA intron mobility in yeast mitochondria: RNA maturase and DNA endonuclease switching experiments.}, journal = {Molecular and cellular biology}, volume = {12}, number = {2}, pages = {696-705}, pmid = {1310149}, issn = {0270-7306}, mesh = {Amino Acid Sequence ; Base Sequence ; Blotting, Northern ; Cytochrome b Group/genetics ; Deoxyribonuclease I/genetics/*metabolism ; Electron Transport Complex IV/genetics ; Endoribonucleases/genetics/*metabolism ; Introns/genetics/physiology ; Mitochondria/*enzymology ; Molecular Sequence Data ; Nucleotidyltransferases/genetics/*metabolism ; RNA Splicing/physiology ; Recombinant Fusion Proteins/genetics/metabolism ; Recombination, Genetic/genetics ; Saccharomyces cerevisiae/enzymology/genetics/*metabolism ; Sequence Homology, Nucleic Acid ; }, abstract = {The intron-encoded proteins bI4 RNA maturase and aI4 DNA endonuclease can be faithfully expressed in yeast cytoplasm from engineered forms of their mitochondrial coding sequences. In this work we studied the relationships between these two activities associated with two homologous intron-encoded proteins: the bI4 RNA maturase encoded in the fourth intron of the cytochrome b gene and the aI4 DNA endonuclease (I-SceII) encoded in the fourth intron of the gene coding for the subunit I of cytochrome oxidase. Taking advantage of both the high recombinogenic properties of yeast and the similarities between the two genes, we constructed in vivo a family of hybrid genes carrying parts of both RNA maturase and DNA endonuclease coding sequences. The presence of a sequence coding for a mitochondrial targeting peptide upstream from these hybrid genes allowed us to study the properties of their translation products within the mitochondria in vivo. We thus could analyze the ability of the recombinant proteins to complement RNA maturase deficiencies in different strains. Many combinations of the two parental intronic sequences were found in the recombinants. Their structural and functional analysis revealed the following features. (i) The N-terminal half of the bI4 RNA maturase could be replaced in total by its equivalent from the aI4 DNA endonuclease without affecting the RNA maturase activity. In contrast, replacing the C-terminal half of the bI4 RNA maturase with its equivalent from the aI4 DNA endonuclease led to a very weak RNA maturase activity, indicating that this region is more differentiated and linked to the maturase activity. (ii) None of the hybrid proteins carrying an RNA maturase activity kept the DNA endonuclease activity, suggesting that the latter requires the integrity of the aI4 protein. These observations are interesting because the aI4 DNA endonuclease is known to promote the propagation, at the DNA level, of the aI4 intron, whereas the bI4 RNA maturase, which is required for the splicing of its coding intron, also controls the splicing process of the aI4 intron. We propose a scenario for the evolution of these intronic proteins that relies on a switch from DNA endonuclease to RNA maturase activity.}, }
@article {pmid1476798, year = {1992}, author = {Dietrich, A and Weil, JH and Maréchal-Drouard, L}, title = {Nuclear-encoded transfer RNAs in plant mitochondria.}, journal = {Annual review of cell biology}, volume = {8}, number = {}, pages = {115-131}, doi = {10.1146/annurev.cb.08.110192.000555}, pmid = {1476798}, issn = {0743-4634}, mesh = {Amino Acids ; Anticodon ; Biological Evolution ; Biological Transport ; *Cell Nucleus ; Codon ; *Genes ; *Genes, Plant ; Mitochondria/*metabolism ; Plants/*genetics/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Transfer/*genetics/metabolism ; Substrate Specificity ; }, }
@article {pmid1455549, year = {1992}, author = {Seravin, LN}, title = {[Eukaryotes devoid of the most important cellular organelles (flagella, Golgi apparatus, mitochondria) and the main task of organellology].}, journal = {Tsitologiia}, volume = {34}, number = {5}, pages = {3-33}, pmid = {1455549}, issn = {0041-3771}, mesh = {Animal Population Groups/anatomy &amp; histology ; Animals ; Biological Evolution ; Eukaryota/ultrastructure ; Eukaryotic Cells/*ultrastructure ; Flagella/ultrastructure ; Fungi/ultrastructure ; Golgi Apparatus/ultrastructure ; Mitochondria/ultrastructure ; Organelles/*ultrastructure ; Plants/ultrastructure ; }, abstract = {Comparative evidence on the lack of three important organelles (flagella, Golgi-complex, mitochondria) in cells and organisms at the cellular level of organization has been summarized for all the four eukaryotic kingdoms--Protista, Fungi, Plantae and Animalia (Metazoa). It is established that in the course of evolution these organelles may undergo the total reduction. There is no cellular organelle to be regarded as universal, indispensable. There are only three main obligatory cell components--the plasmalemma, nucleus and cytoplasm (with applied cytoskeleton, cytomembranes and ribosomes). The reduction of flagella (cilia) is occurring in different taxa independent of the transition of protists from the flagellate type of locomotion to the amoeboid, gliding of metabolizing ones, and in the number of metazoan cells. The members of Protista and Fungi, which line in microaerobic or anaerobic conditions, nearly inevitably lose their mitochondria. The tendency to lose Golgi-complex is demonstrated in protists with parasitic mode of life, especially in combination with anaerobiosis. There is so far no satisfied morphological criterium that could say with certainty whether the lacking of flagella, Golgi complex or mitochondria in the low eukaryotes may be primary or secondary (as the result of reduction). Data on the composition, structure and RNA nucleotide sequences cannot be either the straight evidence. A comparative analysis of these data shows that the ribosomes of the primary eukaryotes were, presumably, of a prokaryotic type. Their eukaryotization was carried out for a long time during the evolution of the low eukaryotes (Protista and Fungi), probably, independently in different phylogenetic lines. It is unknown at what steps and in what main phylogenetic lines the three above mentioned organelles may have appeared. It is proposed to single out a special division of cytology--organellology (organoidology)--as an individual science whose main purpose may be investigation of the origination, evolution and disappearance of organelles.}, }
@article {pmid1452433, year = {1992}, author = {Gray, MW}, title = {The endosymbiont hypothesis revisited.}, journal = {International review of cytology}, volume = {141}, number = {}, pages = {233-357}, doi = {10.1016/s0074-7696(08)62068-9}, pmid = {1452433}, issn = {0074-7696}, mesh = {Animals ; Bacteria/genetics ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Eukaryotic Cells ; *Mitochondria ; *Models, Biological ; *Organelles ; Phylogeny ; Plants/genetics ; RNA, Ribosomal/genetics ; *Symbiosis ; }, }
@article {pmid1438405, year = {1992}, author = {Tanaka, K and Indo, Y}, title = {Evolution of the acyl-CoA dehydrogenase/oxidase superfamily.}, journal = {Progress in clinical and biological research}, volume = {375}, number = {}, pages = {95-110}, pmid = {1438405}, issn = {0361-7742}, mesh = {Acyl-CoA Dehydrogenases/*genetics ; Acyl-CoA Oxidase ; Amino Acid Sequence ; *Biological Evolution ; Microbodies/enzymology/metabolism ; Mitochondria/enzymology/metabolism ; Molecular Sequence Data ; Oxidoreductases/*genetics ; Sequence Alignment ; Sequence Homology, Amino Acid ; }, }
@article {pmid1399706, year = {1992}, author = {Birt, TP and Friesen, VL and Green, JM and Montevecchi, WA and Davidson, WS}, title = {Cytochrome-b sequence variation among parrots.}, journal = {Hereditas}, volume = {117}, number = {1}, pages = {67-72}, doi = {10.1111/j.1601-5223.1992.tb00009.x}, pmid = {1399706}, issn = {0018-0661}, mesh = {Animals ; Base Sequence ; Cytochrome b Group/*genetics ; Mitochondria/physiology ; Molecular Sequence Data ; Parrots/*genetics ; Phylogeny ; Polymerase Chain Reaction ; }, abstract = {The nucleotide sequence of a 307 bp fragment of the mitochondrial cytochrome-b gene was determined for 12 species of parrot, using the polymerase chain reaction and direct sequencing. Sequence divergence ranged from 26-54 differences in pairwise comparisons, with the majority of base substitutions occurring at third positions of codons. The transition:transversion ratio was determined to be higher (approximately 24.3:1) in recently divergent parrot lineages than has generally been observed in other groups. Strongly biased base composition, particularly at the third position of codons, is evident among the sequences. Phylogenetic relationships among more divergent taxa were estimated, using only transversion substitutions, while all the substitutions were useful for closely related taxa. The African genera Psittacus and Poicephalus are closely related, in contrast to the Australian genera Nymphicus, Purpureicephalus and Melopsittacus, which represent more divergent lineages. The cockatoos appear to represent an ancient lineage within the parrots.}, }
@article {pmid1378037, year = {1992}, author = {Ruttkay, H and Solignac, M and Sperlich, D}, title = {Nuclear and mitochondrial ribosomal RNA variability in the obscura group of Drosophila.}, journal = {Genetica}, volume = {85}, number = {2}, pages = {131-138}, pmid = {1378037}, issn = {0016-6707}, mesh = {Animals ; Base Sequence ; Cell Nucleus/*metabolism ; Drosophila/*genetics ; *Genetic Variation ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phylogeny ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 28S/*genetics ; Sequence Alignment ; Species Specificity ; }, abstract = {Parts of 28S (nuclear) and 12S (mitochondrial) ribosomal RNA of Palearctic, Nearctic and African species of the obscura group have been sequenced by the direct method of sequencing. Rates of nucleotide substitutions in both molecules were compared. The nucleotide divergence is higher in the mitochondrial rRNA. Average distances of species taken in pairwise were compared to results obtained with the melanogaster subgroup: the divergence of nuclear rRNA appears lower, that of the mtDNA higher whereas genetic distances (allozymes) and sncDNA distances are similar. Noticeable variability of evolutionary rates can be observed even in low taxonomical levels. Phylogenetic trees for the obscura group are in general agreement with those obtained with other characters.}, }
@article {pmid1292670, year = {1992}, author = {Cavalier-Smith, T}, title = {The number of symbiotic origins of organelles.}, journal = {Bio Systems}, volume = {28}, number = {1-3}, pages = {91-106; discussion 107-8}, doi = {10.1016/0303-2647(92)90011-m}, pmid = {1292670}, issn = {0303-2647}, mesh = {*Biological Evolution ; Chloroplasts/ultrastructure ; Eukaryotic Cells/ultrastructure ; Mitochondria/ultrastructure ; Models, Biological ; *Organelles/ultrastructure ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; }, abstract = {Mitochondria and chloroplasts both originated from bacterial endosymbionts. The available evidence strongly supports a single origin for mitochondria and only somewhat less strongly a single, slightly later, origin for chloroplasts. The arguments and evidence that have sometimes been presented in favor of the alternative theories of the multiple or polyphyletic origins of these two organelles are evaluated and the kinds of data that are needed to test more rigorously the monophyletic theory are discussed. Although chloroplasts probably originated only once, eukaryotic algae are polyphyletic because chloroplasts have been secondarily transferred to new lineages by the permanent incorporation of a photosynthetic eukaryotic algal cell into a phagotrophic protozoan host. How often this has happened is much less clear. It is particularly unclear whether or not the chloroplasts of typical dinoflagellates and euglenoids originated in this way from a eukaryotic symbiont: their direct divergence from the ancestral chloroplast cannot be ruled out and indeed has several arguments in its favor. The evidence for and against the view that the chloroplast of the kingdom Chromista was acquired in a single endosymbiotic event is discussed. The possibility that even the chloroplast of Chlorarachnion might have been acquired during the same symbiosis that created the cryptomonad cell, if the symbiont was a primitive alga that had chlorophyll a, b and c as well as phycobilins, is also considered. An alga with such a combination of pigments might have been ancestral to all eukaryote algae.}, }
@article {pmid1292668, year = {1992}, author = {Maier, UG}, title = {The four genomes of the alga Pyrenomonas salina (Cryptophyta).}, journal = {Bio Systems}, volume = {28}, number = {1-3}, pages = {69-73}, doi = {10.1016/0303-2647(92)90009-n}, pmid = {1292668}, issn = {0303-2647}, mesh = {Biological Evolution ; Cell Nucleus/ultrastructure ; DNA, Mitochondrial/genetics/ultrastructure ; Eukaryota/*genetics/ultrastructure ; Genome ; Organelles/ultrastructure ; RNA, Ribosomal/genetics ; Symbiosis ; }, abstract = {Cryptomonads are a group of unicellular eukaryotic algae with unusual features. First, their plastids are surrounded by four membranes and second, between the two pairs of membranes there is a plasmatic compartment. This supernumerary eukaryotic compartment of the cryptomonad cell is devoid of mitochondria but contains starch grains, 80S ribosomes and a small vestigial eukaryotic nucleus called the nucleomorph. Isolation and characterization of the four genomes (from mitochondrion, plastid, nucleus and nucleomorph) of one cryptomonad, Pyrenomonas salina, demonstrates that the cryptomonads have originated from an unicellular organism related to green algae which endosymbiotically took up a eukaryotic protist related to the red algae.}, }
@article {pmid1292665, year = {1992}, author = {Müller, M}, title = {Energy metabolism of ancestral eukaryotes: a hypothesis based on the biochemistry of amitochondriate parasitic protists.}, journal = {Bio Systems}, volume = {28}, number = {1-3}, pages = {33-40}, doi = {10.1016/0303-2647(92)90005-j}, pmid = {1292665}, issn = {0303-2647}, support = {AI 11942/AI/NIAID NIH HHS/United States ; RR 07065/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; Energy Metabolism ; Entamoeba histolytica/metabolism ; Eukaryotic Cells/*metabolism ; Giardia lamblia/metabolism ; Mitochondria/metabolism ; Models, Biological ; Trichomonas vaginalis/metabolism ; }, abstract = {Parasitic amitochondriate protists, representatives of early branches of eukaryote evolution, differ considerably in their central, energy metabolism from mitochondrion-bearing cells. These differences are: significant metabolic functions of inorganic pyrophosphate, major role of iron-sulfur proteins in key metabolic steps and in hydrogenosome-bearing organisms the disposal of electrons by H2 formation. Cytochrome-mediated electron transport and electron transport-linked phosphorylation are absent. All proteins which have been sequenced so far were found to be homologous to isofunctional proteins from other organisms. A few reactions, however, are catabolized by proteins which are not homologous to enzymes performing similar reactions in other eukaryotes. Two significantly different types of metabolism of amitochondriate protists can be distinguished: (a) without compartmentation and (b) with cytosol/hydrogenosome compartmentation. It is likely that these metabolic types have conserved certain traits present in ancestral eukaryotes before mitochondria became established.}, }
@article {pmid1756976, year = {1991}, author = {Hegedus, DD and Pfeifer, TA and MacPherson, JM and Khachatourians, GG}, title = {Cloning and analysis of five mitochondrial tRNA-encoding genes from the fungus Beauveria bassiana.}, journal = {Gene}, volume = {109}, number = {1}, pages = {149-154}, doi = {10.1016/0378-1119(91)90601-7}, pmid = {1756976}, issn = {0378-1119}, mesh = {Base Sequence ; Cloning, Molecular ; Genetic Code ; Mitochondria/*chemistry ; Mitosporic Fungi/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer/*genetics ; RNA, Transfer, Ile/genetics ; RNA, Transfer, Pro/genetics ; RNA, Transfer, Ser/genetics ; RNA, Transfer, Trp/genetics ; RNA, Transfer, Val/genetics ; Sequence Homology, Nucleic Acid ; Transcription, Genetic ; }, abstract = {Five mitochondrial (mt) tRNA genes from the filamentous fungus, Beauveria bassiana, were cloned and sequenced. The genes encoding the Val-, Ile-, Ser-, Trp- and Pro-accepting tRNAs were found clustered in the region 5' to the lrRNA-encoding gene. The genes were 64-77% homologous with the equivalent genes from other filamentous fungi, 49-58% to yeasts with the exception of the Val-accepting tRNA-encoding gene which was 76%, and only slightly homologous with Escherichia coli. The B. bassiana mt genetic code was found to be similar to that of other fungal mitochondria in that the UGA codon is used as a signal for Trp rather than as a stop codon. Transcript analysis has revealed that the genes present in tRNA cluster are transcribed and processed into tRNA-size products. Secondary structure models proposed for the gene products show that conservation of tRNA secondary structure also exists. The presence of a GGC sequence rather than a GGU sequence in the D-loop of the tRNA(Trp)-encoding gene is a feature unique to the B. bassiana mt tRNA. An unconventional G-A base pair present in the D-stem of the tRNA(Ser)-encoding gene is a feature conserved in the mt tRNA of other filamentous fungi. Comparison of the B. bassiana tRNA-encoding genes with those of two other filamentous fungi and two yeasts revealed that the differences between closely related species favoured transition-type mutations.}, }
@article {pmid1661610, year = {1991}, author = {Rizzuto, R and Sandonà, D and Brini, M and Capaldi, RA and Bisson, R}, title = {The most conserved nuclear-encoded polypeptide of cytochrome c oxidase is the putative zinc-binding subunit: primary structure of subunit V from the slime mold Dictyostelium discoideum.}, journal = {Biochimica et biophysica acta}, volume = {1129}, number = {1}, pages = {100-104}, doi = {10.1016/0167-4781(91)90220-g}, pmid = {1661610}, issn = {0006-3002}, support = {HL22050/HL/NHLBI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Binding Sites/genetics ; Biological Evolution ; Dictyostelium/*enzymology/genetics ; Electron Transport Complex IV/chemistry/*genetics/metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; Protein Conformation ; Sequence Alignment ; Sequence Homology, Nucleic Acid ; Zinc/metabolism ; }, abstract = {A full-length 515 base pairs cDNA for cytochrome c oxidase subunit V of D. discoideum was isolated from a lambda gt11 expression library. The encoded polypeptide, whose identity was confirmed by partial protein sequencing, is 119 amino acids long (Mr = 13,352) and does not contain a cleavable presequence. The protein, which is homologous to human subunit Vb and yeast subunit IV, exhibits the highest degree of sequence conservation found among nuclear-encoded subunits of cytochrome c oxidase from distantly related organisms. All the invariant residues are clustered in two regions of the C-terminus which include the putative amino acids involved in the coordination of the Zn ion tightly associated to eukaryotic oxidase.}, }
@article {pmid1823597, year = {1991}, author = {Henderson, PJ}, title = {Studies of translocation catalysis.}, journal = {Bioscience reports}, volume = {11}, number = {6}, pages = {477-53; discussion 534-8}, doi = {10.1007/BF01130216}, pmid = {1823597}, issn = {0144-8463}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Amino Acid Sequence ; Biological Transport, Active ; *Catalysis ; Energy Metabolism ; Molecular Sequence Data ; Osmosis ; Sequence Homology, Nucleic Acid ; }, abstract = {There is a symbiotic relationship between the evolution of fundamental theory and the winning of experimentally-based knowledge. The impact of the General Chemiosmotic Theory on our understanding of the nature of membrane transport processes is described and discussed. The history of experimental studies on transport catalysed by ionophore antibiotics and the membrane proteins of mitochondria and bacteria are used to illustrate the evolution of knowledge and theory. Recent experimental approaches to understanding the lactose-H+ symport protein of Escherichia coli and other sugar porters are described to show that the lack of experimental knowledge of the three-dimensional structures of the proteins currently limits the development of theories about their molecular mechanism of translocation catalysis.}, }
@article {pmid1822283, year = {1991}, author = {Bonen, L}, title = {The mitochondrial genome: so simple yet so complex.}, journal = {Current opinion in genetics &amp; development}, volume = {1}, number = {4}, pages = {515-522}, doi = {10.1016/s0959-437x(05)80201-1}, pmid = {1822283}, issn = {0959-437X}, mesh = {Animal Population Groups/genetics ; Animals ; *Biological Evolution ; Cell Nucleus ; DNA, Mitochondrial/*genetics ; Eukaryotic Cells ; Fungi/genetics ; Genes ; Genetic Variation ; Plants/genetics ; Protein Biosynthesis ; RNA Processing, Post-Transcriptional ; RNA, Messenger/genetics ; Transcription, Genetic ; }, abstract = {Mitochondria possess a small set of genes that are essential for respiratory function. This review highlights recent advances in our understanding of mitochondrial gene organization and expression. These studies illustrate a remarkable diversity among eukaryotic lineages and an impressive complexity of events needed to achieve nuclear-mitochondrial harmony.}, }
@article {pmid1779435, year = {1991}, author = {Pesole, G and Sbisá, E and Mignotte, F and Saccone, C}, title = {The branching order of mammals: phylogenetic trees inferred from nuclear and mitochondrial molecular data.}, journal = {Journal of molecular evolution}, volume = {33}, number = {6}, pages = {537-542}, pmid = {1779435}, issn = {0022-2844}, mesh = {Animals ; Databases, Factual ; Genetic Variation ; Humans ; Mammals/*genetics ; Markov Chains ; Mitochondria/*metabolism ; *Phylogeny ; }, abstract = {In order to clarify some controversial phylogenies such as those regarding the triplet of human, rodent, and cow and the evolutionary position of Lagomorpha with respect to other mammals, we have analyzed both nuclear and mitochondrial genes using the stationary Markov model developed in our laboratory. We found that the two sets of genes give different results. In particular the mitochondrial tree showed rabbit linked first to rodents and the rabbit-rodents branch linked to artiodactyls with human as the outgroup. The most favorite nuclear tree showed human linked first to artiodactyls and the human-artiodactyls branch linked to rabbit with rodents as the outgroup. The obvious questions, (1) which tree is the correct one, or (2) both trees can be incorrect, and (3) how can we explain such an evolutionary pattern, are discussed on the basis of our limited knowledge of factors that influence the clocklike behavior of biological macromolecules.}, }
@article {pmid1773659, year = {1991}, author = {Carmo-Fonseca, M and Hurt, EC}, title = {Across the nuclear pores with the help of nucleoporins.}, journal = {Chromosoma}, volume = {101}, number = {4}, pages = {199-205}, pmid = {1773659}, issn = {0009-5915}, mesh = {Animals ; Biological Evolution ; Biological Transport ; Humans ; Nuclear Envelope/*metabolism/ultrastructure ; Nucleoproteins/*physiology ; }, abstract = {Proteins targeted to specific intracellular organelles such as mitochondria or the endoplasmic reticulum are able to cross membranes. Yet, to enter or exit the nucleus, proteins and RNA must pass through nonmembranous "gates" of the nuclear envelope, the nuclear pore complexes. Recently, the primary amino acid sequence of a few nuclear pore proteins (the nucleoporins) became available. Nucleoporins from mammals, amphibians and yeast are structurally homologous indicating that nuclear pore structures are evolutionarily conserved in the eukaryotic cell. The role of nucleoporins in nucleocytoplasmic transport is still unclear: are nucleoporins involved in decoding nuclear targeting signals or are they mere transporters? Although definite answers are not yet available, data are rapidly accumulating from several laboratories using a variety of approaches.}, }
@article {pmid1660306, year = {1991}, author = {Collins, S and Rudduck, C and Marzuki, S and Dennett, X and Byrne, E}, title = {Mitochondrial genome distribution in histochemically cytochrome c oxidase-negative muscle fibres in patients with a mixture of deleted and wild type mitochondrial DNA.}, journal = {Biochimica et biophysica acta}, volume = {1097}, number = {4}, pages = {309-317}, doi = {10.1016/0925-4439(91)90086-o}, pmid = {1660306}, issn = {0006-3002}, mesh = {Base Sequence ; Biopsy ; Chromosome Mapping ; DNA Probes ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; DNA, Single-Stranded ; Electron Transport Complex IV/*genetics/isolation &amp; purification ; Histocytochemistry ; Humans ; Microtomy ; Mitochondria, Muscle/*metabolism/ultrastructure ; Molecular Sequence Data ; *Mutation ; Nucleic Acid Hybridization ; Ophthalmoplegia/*genetics ; }, abstract = {In situ hybridization studies were performed on a series of chronic progressive external ophthalmoplegia patients harbouring large mitochondrial DNA deletions, using intra- and extra-deletional probes. Clear differences in the distribution of wild type and deleted mitochondrial genomes were seen in both ragged-red and non-ragged red, cytochrome c oxidase-negative fibres, with an accumulation of deleted genomes in the subsarcolemmal zone. Wild type genome content was normal or decreased in the cytochrome c oxidase-negative regions of one case, but in two patients, wild type mtDNA content in cytochrome c oxidase-negative regions was either normal (most fibres) or increased (occasional fibres). The latter observation suggests there may be a stage in the natural history of ragged-red fibre evolution where wild type genomes are transiently increased. The significance of this finding is discussed.}, }
@article {pmid1823914, year = {1991}, author = {Razanoelina, M and Freund, N and Bismuth, J and Geloso, JP and Delaval, E}, title = {Effect of lipid diet on mitochondrial palmitoyl-l-carnitine oxidation in kidney at postnatal development.}, journal = {Journal of developmental physiology}, volume = {16}, number = {5}, pages = {283-286}, pmid = {1823914}, issn = {0141-9846}, mesh = {3-Hydroxyacyl CoA Dehydrogenases/*analysis ; Age Factors ; Animals ; Dietary Fats/*pharmacology ; Kidney/growth &amp; development/*metabolism ; Mitochondria/*metabolism ; Oxygen Consumption ; Palmitoylcarnitine/*metabolism ; Rats ; Rats, Inbred Strains ; }, abstract = {Oxygen consumption (VO2) and beta-hydroxyacyl-CoA dehydrogenase (beta OAC) activity were measured in isolated mitochondria of developing rat kidney from late fetal to adult age. In the presence of palmitoyl-L-carnitine, VO2 consumption was higher in suckling than in adult rats while beta OAC activity rose during the postnatal period and declined after weaning. During postnatal development, the high level of mitochondrial fatty acid oxidation was linked to the high level of fatty acid supply and any change in lipid diet altered mitochondrial fatty acid oxidation. By contrast at adult age, a high fat diet did not change either mitochondrial fatty acid oxidation or beta OAC activity measured in two nephron structures (PCT and mTAL). Dietary lipids seem to play an important role in the evolution of mitochondrial fatty acid oxidation in developing rat kidney.}, }
@article {pmid1807832, year = {1991}, author = {Louis, EJ and Haber, JE}, title = {Evolutionarily recent transfer of a group I mitochondrial intron to telomere regions in Saccharomyces cerevisiae.}, journal = {Current genetics}, volume = {20}, number = {5}, pages = {411-415}, pmid = {1807832}, issn = {0172-8083}, support = {RR04671/RR/NCRR NIH HHS/United States ; }, mesh = {Base Sequence ; *Biological Evolution ; DNA, Fungal ; *Introns ; *Mitochondria ; Molecular Sequence Data ; *Recombination, Genetic ; Saccharomyces cerevisiae/*genetics/ultrastructure ; *Telomere ; }, abstract = {The junctions between X and Y' subtelomeric repeats in Saccharomyces cerevisiae usually contain a stretch of telomere sequences, (G1-3T)n. Two of three cloned X-Y' junctions from strain YP1 have a replacement of about 200 bp of X, the internal telomere sequence, and 49 bp of Y' by a 292 bp sequence. The first 227 bp of this insertion sequence are 100% identical to the fourth intron of cytochrome b. The rest of the insertion has homology to an unknown dispersed nuclear sequence. Recombination among subtelomeric regions can explain the nuclear distribution of this sequence and why telomeres can trap and maintain sequences that would otherwise be lost.}, }
@article {pmid1794596, year = {1991}, author = {Bolgiano, B and Davies, HC and Poole, RK}, title = {Using the bacterium, Paracoccus denitrificans and other 'runaway mitochondria' as classroom models for respiratory electron transport studies.}, journal = {Biochemical Society transactions}, volume = {19}, number = {4}, pages = {976-981}, doi = {10.1042/bst0190976a}, pmid = {1794596}, issn = {0300-5127}, mesh = {Biological Evolution ; Biology/*education ; *Electron Transport ; Energy Metabolism ; Escherichia coli/metabolism ; Mitochondria/metabolism ; Paracoccus denitrificans/*metabolism ; }, abstract = {Our suggestions for experiments demonstrating electron-transport-chain composition and reactions all exploit bacteria which can be prepared quickly, easily and cheaply from cells grown in Erlenmeyer flasks. While they have been designed from a cytochrome oxidase point of view using organisms of our own prejudice, strains containing mutations in other sites could be just as educational. Most bacteria that can grow aerobically have features in common with the mitochondrial respiratory chain. Because of the vital importance of oxygen utilization throughout most of evolution, and consequent conservation of electron-transport complexes and carriers, the teaching of bioenergetics, whether in the laboratory or lecture room, could benefit from the inclusion of micro-organisms in the curriculum.}, }
@article {pmid1775064, year = {1991}, author = {Hedges, SB and Bezy, RL and Maxson, LR}, title = {Phylogenetic relationships and biogeography of xantusiid lizards, inferred from mitochondrial DNA sequences.}, journal = {Molecular biology and evolution}, volume = {8}, number = {6}, pages = {767-780}, doi = {10.1093/oxfordjournals.molbev.a040689}, pmid = {1775064}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; Cytochrome b Group/genetics ; DNA ; DNA, Mitochondrial/*genetics ; Genetic Variation ; Lizards/*classification/genetics ; Mitochondria/enzymology/metabolism ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Portions of two mitochondrial genes (12S ribosomal RNA and cytochrome b) were sequenced in seven species to examine phylogenetic relationships within the lizard family Xantusiidae. Phylogenies derived from these sequences (709 total bp) are concordant and indicate that the Cuban species Cricosaura typica is the sister group to all other xantusiids. The Middle American genus Lepidophyma is the closest relative of Xantusia, and X. riversiana (California Islands) the closest relative of X. vigilis (mainland). These findings are not in agreement either with the results of a recent morphological analysis that united Cricosaura and Lepidophyma as closest relatives or with past studies that have recognized X. riversiana as a separate genus. Levels of sequence divergence, as well as the age and affinities of some mainland fossil taxa, suggest that the origin of Cricosaura was associated with the tectonic evolution of the Greater Antilles in the late Cretaceous. These results further demonstrate that significant resolution of phylogenies can be obtained with relatively short DNA sequences and that these mitochondrial genes are concordant in their estimation of phylogeny.}, }
@article {pmid1720859, year = {1991}, author = {Maier, UG and Hofmann, CJ and Eschbach, S and Wolters, J and Igloi, GL}, title = {Demonstration of nucleomorph-encoded eukaryotic small subunit ribosomal RNA in cryptomonads.}, journal = {Molecular &amp; general genetics : MGG}, volume = {230}, number = {1-2}, pages = {155-160}, pmid = {1720859}, issn = {0026-8925}, mesh = {Animals ; Base Sequence ; Electrophoresis ; Eukaryota/*chemistry/genetics/ultrastructure ; Eukaryotic Cells/*chemistry ; Molecular Sequence Data ; Nucleic Acid Conformation ; Organelles/chemistry ; Phylogeny ; RNA ; RNA, Ribosomal/*analysis ; Symbiosis ; }, abstract = {In cryptomonads, unicellular phototrophic flagellates, the plastid(s) is (are) located in a special narrow compartment which is bordered by two membranes; it harbours neither mitochondria nor Golgi dictyosomes but comprises eukaryotic ribosomes and starch grains together with a small organelle called the nucleomorph. The nucleomorph contains DNA and is surrounded by a double membrane with pores. It is thought to be the vestigial nucleus of a phototrophic eukaryotic endosymbiont. Cryptomonads are therefore supposed to represent an intermediate state in the evolution of complex plastids from endosymbionts. We have succeeded in isolating pure nucleomorph fractions, and can thus provide, using pulsed field gel electrophoresis, polymerase chain reaction and sequence analysis, definitive proof for the eukaryotic nature of the symbiont and its phylogenetic origin.}, }
@article {pmid1663570, year = {1991}, author = {McClure, MA}, title = {Evolution of retroposons by acquisition or deletion of retrovirus-like genes.}, journal = {Molecular biology and evolution}, volume = {8}, number = {6}, pages = {835-856}, doi = {10.1093/oxfordjournals.molbev.a040686}, pmid = {1663570}, issn = {0737-4038}, support = {AI 28309/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; Capsid/genetics ; Chromosome Deletion ; *DNA Transposable Elements ; Endopeptidases/genetics ; *Genes, Viral ; Molecular Sequence Data ; Phylogeny ; Retroviridae/*genetics ; Ribonuclease H/genetics ; Sequence Alignment ; }, abstract = {The retroid family consists of all genetic elements that encode a potential reverse transcriptase (RT). Members of this family include a diversity of eukaryotic genetic elements (viruses, transposable elements, organelle introns, and plasmids) and the retrons of prokaryotes. Some retroid elements have, in addition to the RT gene, other genes in common with the retroviruses. On the basis of RT sequence similarity, the retroposon group is defined as the eukaryotic long interspersed nuclear elements, the transposable elements of (1) Drosophila melanogaster (I and F factors), (2) Trypanosoma brucei (ingi element), (3) Zea mays (Cin4), (4) Bombyx mori (R2Bm), and members of the group II introns and plasmids of yeast mitochondria. The data presented here elucidate the extent of the relationships between the retroposons and other retroid-family members. Protein-sequence alignment data demonstrate that subsets of the retroposons contain different assortments of retroviral-like genes. Sequence similarities can be detected between the capsid, protease, ribonuclease H, and integrase proteins of retroviruses and several retroposon sequences. The relationships among the retroposon capsid-like sequences are congruent with the RT sequence phylogeny. In contrast, the similarity between ribonuclease H sequences varies in different subbranches of the retroposon lineage. These data suggest that xenologous recombination (i.e., the replacement of a homologous resident gene by a homologous foreign gene) and/or independent gene assortment have played a role in the evolution of the retroposons.}, }
@article {pmid1663569, year = {1991}, author = {Normark, BB and McCune, AR and Harrison, RG}, title = {Phylogenetic relationships of neopterygian fishes, inferred from mitochondrial DNA sequences.}, journal = {Molecular biology and evolution}, volume = {8}, number = {6}, pages = {819-834}, doi = {10.1093/oxfordjournals.molbev.a040685}, pmid = {1663569}, issn = {0737-4038}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Cytochrome b Group/chemistry/genetics ; DNA ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/chemistry/genetics ; Fishes/classification/*genetics ; Humans ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment ; }, abstract = {To investigate the relationships among the three main groups of extant neopterygian fishes--Amiidae, Lepisosteidae, and Teleostei--we sequenced fragments of three mitochondrial genes from 12 different actinopterygian fishes and translated the nucleotide sequences into amino acid sequences. When all three regions are considered together, Amiidae clusters with Lepisosteidae in the most parsimonious cladograms, but other clades, such as Neopterygii and Teleostei, that are well supported by morphological evidence fail to emerge as monophyletic. When the cytochrome b sequences are analyzed together with previously published sequences for other taxa, the majority-rule consensus tree is consistent with the monophyly of Teleostei and Neopterygii and marginally supports the Amiidae + Lepisosteidae clade. In either analysis, when Neopterygii and Teleostei are constrained to monophyly, all the most-parsimonious cladograms support the Amiidae + Lepisosteidae topology. Where molecules and morphology disagree, provisional morphology-based constraints on the analysis of molecular data offer a practical means of integrating the two types of data.}, }
@article {pmid1924298, year = {1991}, author = {Sanni, A and Walter, P and Boulanger, Y and Ebel, JP and Fasiolo, F}, title = {Evolution of aminoacyl-tRNA synthetase quaternary structure and activity: Saccharomyces cerevisiae mitochondrial phenylalanyl-tRNA synthetase.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {88}, number = {19}, pages = {8387-8391}, pmid = {1924298}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Base Sequence ; Biological Evolution ; DNA Mutational Analysis ; Escherichia coli/genetics ; Fungal Proteins/genetics/metabolism/ultrastructure ; Genes, Fungal ; Kinetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Oligonucleotides/chemistry ; Phenylalanine-tRNA Ligase/*genetics/metabolism/ultrastructure ; Protein Conformation ; Recombinant Fusion Proteins/metabolism ; Restriction Mapping ; Saccharomyces cerevisiae/*enzymology ; Sequence Alignment ; Structure-Activity Relationship ; Substrate Specificity ; }, abstract = {Phenylalanyl-tRNA synthetases [L-phenylalanine:tRNAPhe ligase (AMP-forming), EC 6.1.1.20] from Escherichia coli, yeast cytoplasm, and mammalian cytoplasm have an unusual conserved alpha 2 beta 2 quaternary structure that is shared by only one other aminoacyl-tRNA synthetase. Both subunits are required for activity. We show here that a single mitochondrial polypeptide from Saccharomyces cerevisiae is an active phenylalanyl-tRNA synthetase. This protein (the MSF1 gene product) is active as a monomer. It has all three characteristic sequence motifs of the class II aminoacyl-tRNA synthetases, and its activity may result from the recruitment of additional sequences into an alpha-subunit-like structure.}, }
@article {pmid1653062, year = {1991}, author = {Mann, V and Ekstein, I and Nissen, H and Hiser, C and McIntosh, L and Hirschberg, J}, title = {The cytochrome oxidase II gene in mitochondria of the sugar-beet Beta vulgaris L.}, journal = {Plant molecular biology}, volume = {17}, number = {3}, pages = {559-566}, pmid = {1653062}, issn = {0167-4412}, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; *DNA, Mitochondrial/isolation &amp; purification ; Electron Transport Complex IV/*genetics ; Exons ; Molecular Sequence Data ; Plants/genetics ; Pseudogenes ; RNA, Messenger ; Sequence Homology, Nucleic Acid ; }, abstract = {We have cloned and analyzed the sugar-beet mitochondrial gene for cytochrome oxidase subunit II (coxII). The sugar-beet and its deduced amino acid sequence were compared to its homologous coxII gene sequences from both monocot and dicot plants. It was found to be highly conserved (89-95%) compared to homologue in other plant species. The 780 bp coding sequence of the sugar beet coxII gene is interrupted at position 383 by a 1463 bp intron. This intron contains an additional 107 bp sequence that is not found in any of the plant coxII genes studied thus far. The structure of the intron suggests that a large intron existed in an ancestral coxII gene before monocots and dicots diverged in evolution. Three CGG codons in the sugar-beet coxII coding sequence align with conserved tryptophan residues in the homologous gene of other species, suggesting that RNA editing takes place also in sugar-beet mitochondria. In 13 out of 24 codons of coxII mRNA that were found to be edited in four other plants, the sugar-beet gene already utilizes the edited codons. This phenomenon may indicate that the mitochondrial genome in sugar-beet is phylogenetically more archaic relative to these plants. An additional sequence of 279 bp that is identical to the first exon of coxII was identified in the mtDNA of the sugar-beet. This 'pseudo-gene' is transcribed and its existence in the mitochondrial genome is unexplained.}, }
@article {pmid1920454, year = {1991}, author = {Reizer, A and Pao, GM and Saier, MH}, title = {Evolutionary relationships among the permease proteins of the bacterial phosphoenolpyruvate: sugar phosphotransferase system. Construction of phylogenetic trees and possible relatedness to proteins of eukaryotic mitochondria.}, journal = {Journal of molecular evolution}, volume = {33}, number = {2}, pages = {179-193}, pmid = {1920454}, issn = {0022-2844}, support = {2 RO1 AI 14176/AI/NIAID NIH HHS/United States ; 5 RO1 AI 21702/AI/NIAID NIH HHS/United States ; }, mesh = {Acetylglucosamine/metabolism ; Amino Acid Sequence ; Bacteria/enzymology ; *Biological Evolution ; Biological Transport ; Fructose/metabolism ; Glucose/metabolism ; Glucosides/metabolism ; Lactose/metabolism ; Mannitol/metabolism ; Membrane Transport Proteins/*metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Phosphoenolpyruvate Sugar Phosphotransferase System/*metabolism ; *Phylogeny ; Sequence Alignment ; Sucrose/metabolism ; }, abstract = {The amino acid sequences of 15 sugar permeases of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (PTS) were divided into four homologous segments, and these segments were analyzed to give phylogenetic trees. The permease segments fell into four clusters: the lactose-cellobiose cluster, the fructose-mannitol cluster, the glucose-N-acetylglucosamine cluster, and the sucrose-beta-glucoside cluster. Sequences of the glucitol and mannose permeases (clusters 5 and 6, respectively) were too dissimilar to establish homology with the other permeases, but short regions of statistically significant sequence similarities were noted. The functional and structural relationships of these permease segments are discussed. Some of the homologous PTS permeases were found to exhibit sufficient sequence similarity to subunits 4 and 5 of the eukaryotic mitochondrial NADH dehydrogenase complex to suggest homology. Moreover, subunits 4 and 5 of this complex appeared to be homologous to each other, suggesting that these PTS and mitochondrial proteins comprise a superfamily. The integral membrane subunits of the evolutionarily divergent mannose PTS permease, the P and M subunits, exhibited limited sequence similarity to subunit 6 of the mitochondrial F1F0-ATPase and subunit 5b of cytochrome oxidase, respectively. These results suggest that PTS sugar permeases and mitochondrial proton-translocating proteins may be related, although the possibility of convergent evolution cannot be ruled out.}, }
@article {pmid1679525, year = {1991}, author = {Perl, A and Aviv, D and Galun, E}, title = {Nuclear-organelle interaction in Solanum: interspecific cybridizations and their correlation with a plastome dendrogram.}, journal = {Molecular &amp; general genetics : MGG}, volume = {228}, number = {1-2}, pages = {193-200}, pmid = {1679525}, issn = {0026-8925}, mesh = {Blotting, Southern ; Cell Nucleus/chemistry ; Chloroplasts ; Cloning, Molecular ; DNA/*analysis/isolation &amp; purification ; DNA, Mitochondrial ; Extrachromosomal Inheritance ; Hybridization, Genetic ; *Phylogeny ; *Plants, Edible ; Polymorphism, Restriction Fragment Length ; Protoplasts ; }, abstract = {Alloplasmic compatibility, namely the functional interaction between the nuclear genome of a given species with plastomes and chondriomes of alien species, is of considerable relevance in plant biology. The genus Solanum encompasses a wide spectrum of species and is therefore suitable for a study of this compatibility. We thus chose the nuclear genome of Solanum tuberosum (potato) and organelles (chloroplast and mitochondria) from 14 other Solanum species to initiate an investigation of intrageneric nucleus/organelle interactions. An assessment of the diversity of the chloroplast DNAs from these 15 species resulted in the construction of a plastome dendrogram (phylogenetic tree). In parallel we extended a previous study and performed ten additional fusion combinations by the "donor-recipient protoplast fusion" procedure, using potato protoplasts as recipients and protoplasts from any of ten other Solanum species as donors. We found that two fusion combinations did not yield cybrids and that the chloroplasts of S. polyadenium and the mitochondria (or mitochondrial components) from S. tarijense could not be transferred to cybrids bearing potato nuclei. In general, there is a correlation, albeit not perfect, between the cybridization data and the plastome dendrogram. These results furnish valuable information toward future transfer of plasmone-encoded breeding traits from wild Solanum species into potato. This information should also be useful for the planning of asymmetric protoplast fusion between potato and wild accessions for the improvement of pathogen and stress resistance of potato cultivars.}, }
@article {pmid1648084, year = {1991}, author = {Lundin, M and Baltscheffsky, H and Ronne, H}, title = {Yeast PPA2 gene encodes a mitochondrial inorganic pyrophosphatase that is essential for mitochondrial function.}, journal = {The Journal of biological chemistry}, volume = {266}, number = {19}, pages = {12168-12172}, pmid = {1648084}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Base Sequence ; Catalysis ; Chromosomes, Fungal ; *Genes, Fungal ; Mitochondria/*enzymology/physiology ; Molecular Sequence Data ; Phylogeny ; Plasmids ; Pyrophosphatases/*genetics ; Restriction Mapping ; Saccharomyces cerevisiae/*genetics ; Sequence Alignment ; }, abstract = {We have cloned a gene encoding a mitochondrial inorganic pyrophosphatase (PPase) in the yeast Saccharomyces cerevisiae by low stringency hybridization to PPA1, the yeast gene for cytoplasmic PPase. The new gene, PPA2, is located on chromosome 13 and encodes a protein whose sequence is 49% identical to the cytoplasmic enzyme. The protein differs from cytoplasmic PPase in that it has a leader sequence enriched in basic and hydroxylated residues, which is typically found in mitochondrial proteins. Yeast cells overproducing PPA2 had a 47-fold increase in mitochondrial PPase activity. This activity was further stimulated 3-fold by the uncoupler carbonyl cyanide p-trifluoromethoxyphenylhydrazone, which suggests that PPA2 is part of an energy-linked enzyme. Using gene disruptions, we found that PPA1 is required for cell growth. In contrast, cells disrupted for PPA2 are viable, but unable to grow on respiratory carbon sources. Fluorescence microscopy revealed that these cells have lost their mitochondrial DNA. We conclude that the mitochondrial PPase encoded by PPA2 is essential for mitochondrial function and maintenance of the mitochondrial genome.}, }
@article {pmid1921708, year = {1991}, author = {Andersson, GE and Kurland, CG}, title = {An extreme codon preference strategy: codon reassignment.}, journal = {Molecular biology and evolution}, volume = {8}, number = {4}, pages = {530-544}, doi = {10.1093/oxfordjournals.molbev.a040666}, pmid = {1921708}, issn = {0737-4038}, mesh = {Base Composition ; Biological Evolution ; Codon/genetics ; DNA, Mitochondrial/chemistry/classification/*genetics ; *Genetic Code ; RNA, Messenger/chemistry ; RNA, Transfer/genetics ; }, abstract = {We argue that in animal mitochondria codon reassignments, such as those for AGA and AGG from arginine to serine or of AUA from isoleucine to methionine, are the result of an interplay between biased mutational forces and selective ones. In particular, there is a marked tendency for animal mitochondria to have very small genomes and to minimize their investment in components required for gene expression. These tendencies are expressed as a reduction in the diversity of tRNA isoacceptor species. In our view, the pressure to simplify tRNA populations, together with mutational bias against certain codons, will account for the codon reassignments observed in animal mitochondria. A parallel to the major codon bias in microorganisms, which likewise tends to reduce the diversity of the tRNA isoacceptor populations under fast growth conditions, may be drawn. Therefore, we suggest that codon reassignments are usefully viewed as an extreme form of codon bias.}, }
@article {pmid1917282, year = {1991}, author = {Rohde, K and Watson, NA and Cribb, T}, title = {Ultrastructure of sperm and spermatogenesis of Lobatostoma manteri (Trematoda, Aspidogastrea).}, journal = {International journal for parasitology}, volume = {21}, number = {4}, pages = {409-419}, doi = {10.1016/0020-7519(91)90098-r}, pmid = {1917282}, issn = {0020-7519}, mesh = {Animals ; Male ; Microscopy, Electron ; Phylogeny ; Spermatogenesis ; Spermatozoa/*ultrastructure ; Trematoda/physiology/*ultrastructure ; }, abstract = {Mature sperm has two axonemes of the 9 + '1' pattern incorporated in the sperm body, a row of peripheral microtubules interrupted along part of the sperm by the axonemes, some microtubules in the interior of the sperm and a long lateral extension (lobe) of the sperm body, an elongate nucleus and mitochondrion, and many dense rod-like structures. A supporting rod extends underneath a specialized region consisting of alternating thin and thick transverse rows of irregular dense patches, and with surface ridges around (all or) most of the surface of the sperm. Primary spermatocytes in the prophase of the first meiotic division have synaptonemal complex(es), and are rich in mitochondria. In early spermiogenesis, mitochondria are arranged around the surface of the nucleus, a dense layer appears at one pole of the nucleus, close to an apposed dense layer at the cell membrane in which a row of microtubules develops. The intercentriolar (= central) body develops close to the nucleus. The fully developed intercentriolar body has a regular striation and is located perpendicular and close to the surface of the nucleus. Two flagella extend into the space surrounding the outgoing median process, their basal bodies are located perpendicular to the intercentriolar body and their cross-striated rootlets extend along the surface of the rounded nucleus. At a later stage, rootlets and flagella become more parallel with the intercentriolar body, the nucleus and the fused mitochondria migrate into the median process, and the flagella become incorporated into the median process (= sperm body). The outgrowing spermatozoa are connected to the cytoplasm of the cytophore by dense arching membranes. Finally, rootlets of flagella are resorbed and the spermatozoa are pinched off close to the basal bodies. Two species (Lobatostoma and Multicotyle) of the same family differ strongly in the type of spermiogenesis, although their mature sperm is of the same basic type, i.e. spermiogenesis is not necessarily more useful for phylogenetic considerations than sperm structure.}, }
@article {pmid1676260, year = {1991}, author = {Ledley, FD and Crane, AM and Klish, KT and May, GS}, title = {Is there methylmalonyl CoA mutase in Aspergillus nidulans?.}, journal = {Biochemical and biophysical research communications}, volume = {177}, number = {3}, pages = {1076-1081}, doi = {10.1016/0006-291x(91)90648-q}, pmid = {1676260}, issn = {0006-291X}, support = {HD-24064/HD/NICHD NIH HHS/United States ; HD-24186/HD/NICHD NIH HHS/United States ; }, mesh = {Aspergillus nidulans/*enzymology/growth &amp; development ; Gas Chromatography-Mass Spectrometry ; Kinetics ; Malonates/metabolism ; Methylmalonyl-CoA Mutase/*analysis/metabolism ; Saccharomyces cerevisiae/physiology ; }, abstract = {In most animal species and many prokaryotes, methylmalonyl CoA mutase catalyzes isomerization between methylmalonyl CoA and succinyl CoA using adenosylcobalamin as a cofactor. We describe the absence of this enzyme in Aspergillus nidulans based on the absence of enzyme activity in vitro and the failure to metabolize methylmalonate or grow in media containing this organic acid as the sole carbon source. These data contrast previous assumptions that propionate may be metabolized through propionyl CoA and methylmalonyl CoA to the TCA cycle in this organism. This is consistent with the separate evolution of these pathways in animals and lower eukaryotes due to the distinct endosymbiotic origin of their mitochondria.}, }
@article {pmid1764527, year = {1991}, author = {Pietromonaco, SF and Denslow, ND and O'Brien, TW}, title = {Proteins of mammalian mitochondrial ribosomes.}, journal = {Biochimie}, volume = {73}, number = {6}, pages = {827-835}, doi = {10.1016/0300-9084(91)90062-6}, pmid = {1764527}, issn = {0300-9084}, support = {GM-15438/GM/NIGMS NIH HHS/United States ; GM-23322/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Antibody Specificity ; Biological Evolution ; Cattle ; Cross Reactions ; Cytoplasm/*chemistry ; Electrophoresis, Gel, Two-Dimensional ; Mitochondria, Liver/*chemistry ; Models, Biological ; Ribosomal Proteins/*chemistry/immunology/isolation &amp; purification ; Ribosomes/*chemistry ; }, abstract = {The bovine mitochondrial system is being developed as a model system for studies on mammalian mitochondrial ribosomes. Information is emerging on the structural organization and RNA binding properties of proteins in these mitochondrial ribosomes. Unexpectedly, these ribosomes appear to interact directly with GTP, via a high affinity binding site on the small subunit. Despite major differences in their RNA content and physical properties, mammalian mitochondrial and cytoplasmic ribosomes contain about the same number of proteins. The proteins in each kind of ribosome have a similar size distribution, and both sets are entirely coded by nuclear genes, raising the possibility that these different ribosomes may contain the same set of proteins. Comparison of bovine mitochondrial and cytoplasmic r-proteins by co-electrophoresis in two-dimensional gels reveals that most of the cytoplasmic ribosomal proteins are more basic than the mitochondrial ribosomal proteins, and that none are co-migratory with mitochondrial ribosomal proteins, suggesting that the proteins in the two ribosomes are different. To exclude the possibility that the electrophoretic differences result only from post-translational modification of otherwise identical proteins, antibodies against several proteins from the large subunit of bovine mitochondrial ribosomes were tested against cytoplasmic ribosomes by solid phase radioimmunoassay and against cytoplasmic ribosomal proteins on Western blots. The lack of cross-reaction of these antibodies with cytoplasmic r-proteins suggests that mitochondrial ribosomal proteins have different primary structures and thus are most likely encoded by a separate set of nuclear genes.}, }
@article {pmid1649066, year = {1991}, author = {Thomas, WK and Wilson, AC}, title = {Mode and tempo of molecular evolution in the nematode caenorhabditis: cytochrome oxidase II and calmodulin sequences.}, journal = {Genetics}, volume = {128}, number = {2}, pages = {269-279}, pmid = {1649066}, issn = {0016-6731}, mesh = {Amino Acid Sequence ; Amino Acids/analysis ; Animals ; Base Composition ; Base Sequence ; *Biological Evolution ; Caenorhabditis/enzymology/*genetics ; Calmodulin/*genetics/metabolism ; Codon ; DNA ; Electron Transport Complex IV/*genetics/metabolism ; Genetic Variation ; Genome, Human ; Humans ; Mitochondria/enzymology/metabolism ; Molecular Sequence Data ; Nematoda/genetics ; Sequence Alignment ; }, abstract = {Through direct sequencing methods, the mitochondrial gene for cytochrome oxidase subunit two (CO II) and the single-copy nuclear gene for calmodulin were compared among strains of Caenorhabidits elegans and two other Caenorhabditis species (C. remanei and C. briggsae). In addition the CO II sequence was determined from a distantly related nematode, Steinernema intermedii. Among the 11 strains of C. elegans tested, there are four types of CO II gene, arising from two major lineages. Levels of intraspecific difference in the CO II gene are low (less than 2.0%) compared to the extraordinary divergence between congeneric species, which is about 50% when corrected for multiple hits. Concordant with the increase in divergence between taxa is a change in the pattern of substitution from a strong transition bias (24 transitions compared to two transversions) within species to a substitution pattern that appears to reflect the base composition of the mitochondrial genome when more divergent nematodes are compared. The base composition of the Caenorhabditis CO II gene is strongly biased toward A + T at all three positions of codons and appears to constrain the amino acid composition of the protein. Both the CO II and calmodulin genes show extreme conservation of amino acid sequences. When the accumulation of changes at silent sites in the two genes is compared among strains, it becomes evident that the mitochondrial gene is changing faster than the nuclear gene.}, }
@article {pmid2068786, year = {1991}, author = {Cavalier-Smith, T}, title = {Intron phylogeny: a new hypothesis.}, journal = {Trends in genetics : TIG}, volume = {7}, number = {5}, pages = {145-148}, pmid = {2068786}, issn = {0168-9525}, mesh = {Animals ; *Introns ; *Phylogeny ; RNA Splicing ; RNA, Transfer/genetics/metabolism ; }, abstract = {The three major classes of intron are clearly of unequal antiquity. Structured (often self-splicing and sometimes mobile) introns are the most ancient, probably dating (at least for group I) from the ancestral (eubacterial) cell 3500 million years ago, and were originally restricted to tRNA. Protein-spliced introns (usually in tRNA) probably evolved from them by a radical change in splicing mechanism in the common ancestor of eukaryotes and archaebacteria, perhaps only about 1700 million years ago. Spliceosomal introns probably evolved from group-II-like self-splicing introns after the origin of the nucleus between 1700 and 1000 million years ago, and were probably mostly inserted into previously unsplit protein-coding genes after the origin of mitochondria 1000 million years ago.}, }
@article {pmid2025303, year = {1991}, author = {Ozawa, T and Tanaka, M and Ino, H and Ohno, K and Sano, T and Wada, Y and Yoneda, M and Tanno, Y and Miyatake, T and Tanaka, T}, title = {Distinct clustering of point mutations in mitochondrial DNA among patients with mitochondrial encephalomyopathies and with Parkinson's disease.}, journal = {Biochemical and biophysical research communications}, volume = {176}, number = {2}, pages = {938-946}, doi = {10.1016/s0006-291x(05)80276-1}, pmid = {2025303}, issn = {0006-291X}, mesh = {Adolescent ; Adult ; DNA, Mitochondrial/*chemistry ; Female ; Humans ; Male ; Middle Aged ; Mitochondria, Muscle/*pathology ; *Multigene Family ; *Mutation ; Parkinson Disease/*genetics ; Phylogeny ; }, abstract = {The total sequence data for mitochondrial DNA (mtDNA) revealed distinct clustering of point mutations (pms) in mtDNA among one patient with myoclonus epilepsy with ragged-red fibers (MERRF), two patients with Parkinson's disease (PD), two patients with mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes (MELAS), and one patient with fatal infantile cardiomyopathy (FICM). Among 33 to 62 pms found in each patients, sequentially diverged five clusters of pms were detected and designated as C-1 to C-5. C-1, consisted of fourteen pms, existed in the MERRF patient, C-1 and C-2 (nine pms) in one PD patient, C-1 to C-3 (seven pms) in another PD patient, C-1 to C-4 (one pm) in one MELAS patient and C-1 to C-5 (three pms) in another MELAS patient and the FICM patient. From these clustering of pms, a phylogenetic tree of mitochondrial encephalomyopathies (ME) was constructed. This tree clearly indicated that the ME and PD patients are members of the same gene family, and the MELAS and FICM patients are each others' closest relative. Each patient's unique pms (14 to 28 pms) were detected and, from their characteristic features, the types of the mutations specific for the disease were classified as mit- + syn- for MERRF, mit- + p- for PD, and syn- + mit- for MELAS. An inverse relation was found between the total number of pms and life span of the MELAS and FICM patients.}, }
@article {pmid2016746, year = {1991}, author = {Gatti, DL and Tzagoloff, A}, title = {Structure and evolution of a group of related aminoacyl-tRNA synthetases.}, journal = {Journal of molecular biology}, volume = {218}, number = {3}, pages = {557-568}, doi = {10.1016/0022-2836(91)90701-7}, pmid = {2016746}, issn = {0022-2836}, support = {GM 13026/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Aspartate-tRNA Ligase/genetics/metabolism ; *Biological Evolution ; Blotting, Southern ; Blotting, Western ; Cloning, Molecular ; Escherichia coli/enzymology/genetics ; *Genes, Fungal ; Genotype ; Lysine-tRNA Ligase/*genetics/metabolism ; Molecular Sequence Data ; Mutation ; Restriction Mapping ; Saccharomyces cerevisiae/enzymology/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {A yeast nuclear gene, designated MSK1, has been selected from a yeast genomic library by transformation of a respiratory deficient mutant impaired in acylation of mitochondrial lysine tRNA. This gene confers a respiratory competent phenotype and restores the mutant's ability to acylate the mitochondrial lysine tRNA. The amino acid sequence of the protein encoded by MSK1 is homologous to yeast cytoplasmic lysyl-tRNA synthetase and to the product of the herC gene, which has recently been suggested to code for the Escherichia coli enzyme. These observations indicate that MSK1 codes for the lysyl-tRNA synthetase of yeast mitochondria. Several regions of high primary sequence conservation have been identified in the bacterial and yeast lysyl-tRNA synthetases. These domains are also present in the aspartyl- and asparaginyl-tRNA synthetases, further confirming the notion that all three present-day enzymes originated from a common ancestral gene. The most conserved domain, located near the carboxyl terminal ends of this group of synthetases is characterized by a cluster of glycines and is also highly homologous to the carboxyl-terminal region of the E. coli ammonia-dependent asparagine synthetase. A catalytic function of the carboxyl terminal domain is indicated by in vitro mutagenesis of the yeast mitochondrial lysyl-tRNA synthetase. Replacement of any one of three glycine residues by alanine and in one case by aspartic acid completely suppresses the activity of the enzymes, as evidenced by the inability of the mutant genes to complement an msk1 mutant, even when present in high copy. Other mutations result in partial loss of activity. Only one glycine replacement affects the stability of the protein in vivo. The observed presence of a homologous domain in asparagine synthetase, which, like the aminoacyl-tRNA synthetases, catalyzes the formation of an aminoacyladenylate, suggests that the glycine-rich sequence is part of a catalytic site involved in binding of ATP and of the aminoacyladenylate intermediate.}, }
@article {pmid1933479, year = {1991}, author = {Serratrice, G}, title = {[The history of mitochondrial encephalomyopathies].}, journal = {Bulletin de l'Academie nationale de medecine}, volume = {175}, number = {4}, pages = {631-9; discussion 640-1}, pmid = {1933479}, issn = {0001-4079}, mesh = {Brain Diseases/classification/genetics/*history ; DNA, Mitochondrial/*genetics ; History, 19th Century ; History, 20th Century ; Muscular Diseases/classification/genetics/*history ; Terminology as Topic ; }, abstract = {At the end of the XIXth century, the first cases of primary progressive ophthalmoplegia reported were related to a primary degeneration of the oculomotor nuclei; and this concept was accepted until there were considered of purely muscular origin in the 1950's. From this time and during twenty years these cases were reported as ocular myopathies. However the coexistence of neurological abnormalities and above all, the presence of mitochondrial abnormalities in the muscles, the brain and the tissues rich in energy, gave ground to the concept of mitochondrial encephalomyopathies. Then the nature of the dysfunctioning was assessed through biochemical studies, mainly the enzyme deficits of the respiratory chain mitochondria. But correlations between clinical and biochemical data were still difficult as these cases corresponded either to muscular damage (myalgia, exercise intolerance), either to various neurological alterations (epilepsy, cerebellar syndrome) or to multisystemic manifestations. Molecular biology technics introduced the notion of mitochondrial inheritance which contributed to underline the identity of certain varieties, mainly the Kearns and Sayre Syndrome. The increasing number of cases with mitochondrial abnormalities leads to the inverse approach: in central or peripheral damage of the nervous system or in very variable muscular alterations, the investigation of a mitochondrial dysfunctioning is justified and shows the way to possible therapies. This evolution of concept is remarkable in the history of medicine. An abnormality which, at first, was considered as an esthetic alteration, became the subject of the study which, through the advances of the clinical data, of the pathological anatomy, biochemistry and genetics, explained the mechanism of several alterations of the muscles and of the nervous system.}, }
@article {pmid1879437, year = {1991}, author = {Koechlin, N and Pisam, M and Poujeol, P and Tauc, M and Rambourg, A}, title = {Conversion of a rabbit proximal convoluted tubule (PCT) into a cell monolayer: ultrastructural study of cell dedifferentiation and redifferentiation.}, journal = {European journal of cell biology}, volume = {54}, number = {2}, pages = {224-236}, pmid = {1879437}, issn = {0171-9335}, mesh = {Animals ; *Cell Differentiation ; Cell Division ; Cell Survival ; Cells, Cultured ; Colchicine/pharmacology ; Endoplasmic Reticulum/ultrastructure ; Glycogen/analysis ; Golgi Apparatus/ultrastructure ; Kidney Tubules, Proximal/chemistry/*cytology/ultrastructure ; Leucyl Aminopeptidase/metabolism ; Microscopy, Electron ; Microscopy, Electron, Scanning ; Microvilli/*ultrastructure ; Mitochondria/ultrastructure ; Organelles/ultrastructure ; Rabbits ; Vacuoles/ultrastructure ; }, abstract = {The evolution of a primary culture of kidney proximal convoluted tubule (PCT) cells was followed step by step from the plating time of an isolated tubule to the 39th day of culture. During the first 48 h, the structural remodeling of PCT, leading to the formation of a cell monolayer without cell division, is accompanied by intracytoplasmic changes indicating cell dedifferentiation. Numerous autophagic vacuoles are observed inside the cells, and the ultrastructural features characteristic of in situ PCT cells are progressively lost. Despite these drastic modifications, cell polarity, as observed by immunocytochemical detection of the leucine aminopeptidase, remains unaltered. Starting at 48 h, the peripheral cells divide, and the culture proliferates in a centrifugal direction while newly formed cells differentiate. From 6 days onwards, glycogen granules, never encountered in in situ PCT cells, appear in cultured cells and progressively accumulate. At the optimal stage of the culture (12-17 days old), cells somewhat resemble PCT cells, but their apical brush borders remain rudimentary, and basal cytoplasmic interdigitations surrounding densely packed mitochondria are poorly developed. Subsequently, the cells become overloaded with glycogen and lipid inclusions and resemble degenerating cells.}, }
@article {pmid1850242, year = {1991}, author = {Brand, MD and Couture, P and Else, PL and Withers, KW and Hulbert, AJ}, title = {Evolution of energy metabolism. Proton permeability of the inner membrane of liver mitochondria is greater in a mammal than in a reptile.}, journal = {The Biochemical journal}, volume = {275 (Pt 1)}, number = {Pt 1}, pages = {81-86}, pmid = {1850242}, issn = {0264-6021}, mesh = {Adenosine Triphosphate/biosynthesis ; Animals ; *Biological Evolution ; *Energy Metabolism ; Fatty Acids/analysis ; Intracellular Membranes/chemistry/metabolism ; Kinetics ; Lizards/*metabolism ; Membrane Lipids/analysis ; Membrane Potentials ; Mitochondria, Liver/*metabolism/ultrastructure ; Permeability ; *Protons ; Rats ; }, abstract = {Standard metabolic rate is 7-fold greater in the rat (a typical mammal) than in the bearded dragon, Amphibolurus vitticeps (a reptile with the same body mass and temperature). Rat hepatocytes respire 4-fold faster than do hepatocytes from the lizard. The inner membrane of isolated rat liver mitochondrial has a proton permeability that is 4-5-fold greater than the proton permeability of the lizard liver mitochondrial membrane per mg of mitochondrial protein. The greater permeability of rat mitochondria is not caused by differences in the surface area of the mitochondrial inner membrane, but differences in the fatty acid composition of the mitochondrial phospholipids may be involved in the permeability differences. Greater proton permeability of the mitochondrial inner membrane may contribute to the greater standard metabolic rate of mammals.}, }
@article {pmid1830906, year = {1991}, author = {Jacobs, HT}, title = {Structural similarities between a mitochondrially encoded polypeptide and a family of prokaryotic respiratory toxins involved in plasmid maintenance suggest a novel mechanism for the evolutionary maintenance of mitochondrial DNA.}, journal = {Journal of molecular evolution}, volume = {32}, number = {4}, pages = {333-339}, pmid = {1830906}, issn = {0022-2844}, mesh = {*Biological Evolution ; DNA, Mitochondrial/*genetics ; Molecular Structure ; Peptides/chemistry/genetics ; Plasmids ; Prokaryotic Cells ; Proton-Translocating ATPases/genetics ; Sequence Homology, Nucleic Acid ; Toxins, Biological/chemistry/genetics ; }, abstract = {Subunit 8 of mitochondrial ATP synthase (A8), a mitochondrially encoded polypeptide, has no known homologue in any prokaryotic or plastid ATP synthase, suggesting that it has been recruited to its present role in the enzyme from an extraneous source. The polypeptide is poorly conserved at the primary sequence level, but shows a well-conserved hydropathy profile. The hydropathy profiles of A8 from diverse taxa were compared with those of the hok family of prokaryotic respiratory toxins, some of whose members are involved in plasmid maintenance, through postsegregational killing of cells that lose the plasmid at cell division. Such comparisons revealed a highly significant degree of similarity, suggesting a functional relationship. Based on these findings, it is proposed that A8 evolved from a hok-like protein, whose original role was the maintenance of an extrachromosomal replicon in the endosymbiont ancestor of mitochondria. An aggressive mechanism for the evolutionary maintenance of mitochondrial DNA overcomes many of the failings of traditional explanations for its retention as a separate genome.}, }
@article {pmid1646800, year = {1991}, author = {Kadenbach, B and Stroh, A and Hüther, FJ and Reimann, A and Steverding, D}, title = {Evolutionary aspects of cytochrome c oxidase.}, journal = {Journal of bioenergetics and biomembranes}, volume = {23}, number = {2}, pages = {321-334}, pmid = {1646800}, issn = {0145-479X}, mesh = {Animals ; *Biological Evolution ; Cell Nucleus/metabolism ; *Electron Transport Complex IV/genetics/metabolism ; Mitochondria/metabolism ; Paracoccus denitrificans/enzymology/genetics ; Valinomycin/metabolism ; }, abstract = {The presence of additional subunits in cytochrome oxidase distinguish the multicellular eukaryotic enzyme from that of a simple unicellular bacterial enzyme. The number of these additional subunits increases with increasing evolutionary stage of the organism. Subunits I-III of the eukaryotic enzyme are related to the three bacterial subunits, and they are encoded on mitochondrial DNA. The additional subunits are nuclear encoded. Experimental evidences are presented here to indicate that the lower enzymatic activity of the mammalian enzyme is due to the presence of nuclear-coded subunits. Dissociation of some of the nuclear-coded subunits (e.g. VIa) by laurylmaltoside and anions increased the activity of the rat liver enzyme to a value similar to that of the bacterial enzyme. Further, it is shown that the intraliposomal nucleotides influence the kinetics of ferrocytochrome c oxidation by the reconstituted enzyme from bovine heart but not from P. denitrificans. The regulatory function attributed to the nuclear-coded subunits of mammalian cytochrome c oxidase is also demonstrated by the tissue-specific response of the reconstituted enzyme from bovine heart but not from bovine liver to intraliposomal ADP. These enzymes from bovine heart and liver differ in the amino acid sequences of subunits VIa, VIIa, and VIII. The results presented here are taken to indicate a regulation of cytochrome c oxidase activity by nuclear-coded subunits which act like receptors for allosteric effectors and influence the catalytic activity of the core enzyme via conformational changes.}, }
@article {pmid1880129, year = {1991}, author = {Kumazawa, Y and Himeno, H and Miura, K and Watanabe, K}, title = {Unilateral aminoacylation specificity between bovine mitochondria and eubacteria.}, journal = {Journal of biochemistry}, volume = {109}, number = {3}, pages = {421-427}, doi = {10.1093/oxfordjournals.jbchem.a123397}, pmid = {1880129}, issn = {0021-924X}, mesh = {Amino Acyl-tRNA Synthetases/*metabolism ; Animals ; Base Sequence ; *Biological Evolution ; Cattle ; Escherichia coli/enzymology/*genetics ; Mitochondria/*enzymology ; Nucleic Acid Conformation ; RNA, Transfer/*chemistry ; Species Specificity ; Substrate Specificity ; Thermus/enzymology/*genetics ; }, abstract = {The present study shows unilateral aminoacylation specificity between bovine mitochondria and eubacteria (Escherichia coli and Thermus thermophilus) in five amino acid-specific aminoacylation systems. Mitochondrial synthetases were capable of charging eubacterial tRNA as well as mitochondrial tRNA, whereas eubacterial synthetases did not efficiently charge mitochondrial tRNA. Mitochondrial phenylalanyl-, threonyl-, arginyl-, and lysyl-tRNA synthetases were shown to charge and discriminate cognate E. coli tRNA species from noncognate ones strictly, as did the corresponding E. coli synthetases. By contrast, mitochondrial seryl-tRNA synthetase not only charged cognate E. coli serine tRNA species but also extensively misacylated noncognate E. coli tRNA species. These results suggest a certain conservation of tRNA recognition mechanisms between the mitochondrial and E. coli aminoacyl-tRNA synthetases in that anticodon sequences are most likely to be recognized by the former four synthetases, but not sufficiently by the seryl-tRNA synthetase. The unilaterality in aminoacylation may imply that tRNA recognition mechanisms of the mitochondrial synthetases have evolved to be, to some extent, simpler than their eubacterial counterparts in response to simplifications in the species-number and the structural elements of animal mitochondrial tRNAs.}, }
@article {pmid1878939, year = {1991}, author = {Ruiz, S and Anadón, R}, title = {The fine structure of lamellate cells in the brain of amphioxus (Branchiostoma lanceolatum, Cephalochordata).}, journal = {Cell and tissue research}, volume = {263}, number = {3}, pages = {597-600}, pmid = {1878939}, issn = {0302-766X}, mesh = {Animals ; Biological Evolution ; Brain/*cytology/physiology/ultrastructure ; Cell Nucleus/ultrastructure ; Chordata, Nonvertebrate/*anatomy &amp; histology/physiology ; Cilia/ultrastructure ; Cytoplasm/ultrastructure ; Microscopy, Electron ; Microtubules/ultrastructure ; Photoreceptor Cells/cytology/physiology/ultrastructure ; }, abstract = {The lamellate cells of amphioxus have round nuclei, and cytoplasm with many mitochondria and a large amount of glycogen. Each of these cells projects a highly modified, branched cilium into the central canal, where it characteristically forms lamellar structures. Primary branches and secondary lamellae often contain accessory microtubules that are not derived from the axonema. The functional and evolutionary significance of this cell type is discussed in relation to the ciliary photoreceptors found in other chordates.}, }
@article {pmid1705012, year = {1991}, author = {Schulte, U and Lambowitz, AM}, title = {The LaBelle mitochondrial plasmid of Neurospora intermedia encodes a novel DNA polymerase that may be derived from a reverse transcriptase.}, journal = {Molecular and cellular biology}, volume = {11}, number = {3}, pages = {1696-1706}, pmid = {1705012}, issn = {0270-7306}, support = {GM37949/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Blotting, Southern ; DNA, Fungal/biosynthesis ; DNA-Directed DNA Polymerase/*genetics/isolation &amp; purification ; Genes, Fungal ; Mitochondria/enzymology/*physiology ; Molecular Sequence Data ; Neurospora/*genetics ; Nucleoproteins/chemistry ; *Plasmids ; RNA-Directed DNA Polymerase/genetics ; Restriction Mapping ; }, abstract = {The LaBelle-1b strain of Neurospora intermedia contains a 4.1-kb closed-circular mitochondrial plasmid DNA, which encodes a single long open reading frame of 1,151 amino acids reported to have sequence similarity to reverse transcriptases. Here, we show that the LaBelle strain contains a novel DNA polymerase activity that is highly specific for the endogenous LaBelle plasmid DNA in nucleoprotein particles and can be distinguished from the mitochondrial DNA polymerase by several characteristics. Photolabeling experiments indicate that the LaBelle-specific DNA polymerase activity is associated with a polypeptide of 120 kDa, which is in good agreement with the size predicted for the protein encoded by the LaBelle plasmid open reading frame (132 kDa). This 120-kDa polypeptide is found only in the LaBelle strain that contains the mitochondrial plasmid, and it cosegregates with mitochondria in sexual crosses, suggesting that it is encoded by the plasmid. The LaBelle-specific DNA polymerase efficiently uses the artificial DNA substrates, poly(dA)-oligo(dT) and poly(dC)-oligo(dG), but despite its reported sequence similarity to reverse transcriptases, it has very low activity with analogous RNA substrates, poly(rA)-oligo(dT), poly(rC)-oligo(dG), or poly(rCm)-oligo(dG). Considered together with the previous sequence comparisons, our results suggest that the LaBelle plasmid encodes a novel DNA polymerase, which was derived from a protein that was at one time a reverse transcriptase but lost its ability to use RNA templates. This DNA polymerase now presumably functions in replication of the plasmid. Our results constitute the first biochemical evidence for a DNA polymerase activity associated with a mitochondrial plasmid. Further, they may provide insight into the evolution of DNA polymerases from reverse transcriptases, as presumably occurred in the course of evolution following the transition from the so-called RNA world to the present DNA world.}, }
@article {pmid1877981, year = {1991}, author = {Adami, P and Berrez, JM and Latruffe, N}, title = {Mitochondrial pyruvate dehydrogenase complex subunits as autoantigens in human primary biliary cirrhosis.}, journal = {Biochemistry international}, volume = {23}, number = {3}, pages = {429-437}, pmid = {1877981}, issn = {0158-5231}, mesh = {Autoantigens/*immunology ; Autoimmune Diseases/*immunology ; Humans ; Immunoblotting ; Liver Cirrhosis, Biliary/*enzymology/immunology ; Mitochondria, Liver/*enzymology/immunology ; Pyruvate Dehydrogenase Complex/*immunology ; }, abstract = {Primary biliary cirrhosis is an evolutive and chronic human liver disease characterized by presence of antimitochondrial autoantibodies in the serum. We present the biochemical definition of these autoantigens and show that purified pyruvate dehydrogenase complex contains three of the major mitochondrial antigens of M2 type i.e. the E2 subunit (dihydrolipoamide acetyl transferase), the X subunit and the E1 alpha subunit (pyruvate dehydrogenase), by immunoblotting experiments and inhibition of enzyme activity with several types of serums.}, }
@article {pmid1706782, year = {1991}, author = {Desjardins, P and Morais, R}, title = {Nucleotide sequence and evolution of coding and noncoding regions of a quail mitochondrial genome.}, journal = {Journal of molecular evolution}, volume = {32}, number = {2}, pages = {153-161}, pmid = {1706782}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Base Composition ; Base Sequence ; *Biological Evolution ; Chickens ; Chromosome Mapping ; Cloning, Molecular ; Codon ; Coturnix/*genetics ; DNA Replication ; Genes ; *Introns ; Mitochondria/*metabolism ; Molecular Sequence Data ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/genetics ; RNA, Transfer ; Regulatory Sequences, Nucleic Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {Segments of the Japanese quail mitochondrial genome encompassing many tRNA and protein genes, the small and part of the large rRNA genes, and the control region have been cloned and sequenced. Analysis of the relative position of these genes confirmed that the tRNA(Glu) and ND6 genes in galliform mitochondrial DNA are located immediately adjacent to the control region of the molecule instead of between the cytochrome b and ND5 genes as in other vertebrates. Japanese quail and chicken display another distinctive characteristic, that is, they both lack an equivalent to the light-strand replication origin found between the tRNA(Cys) and tRNA(Asn) genes in all vertebrate mitochondrial genomes sequenced thus far. Comparison of the protein-encoding genes revealed that a great proportion of the substitutions are silent and involve mainly transitions. This bias toward transitions also occurs in the tRNA and rRNA genes but is not observed in the control region where transversions account for many of the substitutions. Sequence alignment indicated that the two avian control regions evolve mainly through base substitutions but are also characterized by the occurrence of a 57-bp deletion/addition event at their 5' end. The overall sequence divergence between the two gallinaceous birds suggests that avian mitochondrial genomes evolve at a similar rate to other vertebrate mitochondrial DNAs.}, }
@article {pmid2058346, year = {1991}, author = {De Groote, J}, title = {[Mitochondrial antigens and their antibodies].}, journal = {Acta gastro-enterologica Belgica}, volume = {54}, number = {1}, pages = {19-26}, pmid = {2058346}, issn = {1784-3227}, mesh = {Autoantibodies/*immunology ; Autoantigens/*immunology ; Autoimmune Diseases/immunology ; Collagen Diseases/immunology ; Humans ; Infections/immunology ; Liver Cirrhosis, Biliary/immunology ; Mitochondria/*immunology ; Prognosis ; }, abstract = {In the mitochondria nine antigens and their corresponding antibodies are already known. They can be subdivided in three groups. The first one (M2-M4-M6-M8) appears during the evolution of primary biliary cirrhosis. The antibody against M2 is practically pathognomic for this disease. The M9-antibody is found in PBC with a slow and favourable evolution. The antibodies against M4-M8 are signs of a worse prognosis and a more rapid evolution into terminal cirrhosis. The second group is connected with infections and collagen diseases. The M1-antibody is directed against cardiolipin and diagnostic for syphilis. The M5-antibody appears in definite collagenoses. The M7-antibody is found in certain forms of acute and chronic cardiomyopathy. The third group of antibodies is induced by drugs: the anti-M3 by Venocuran containing a.o. phenopyrazone and the anti-M6 by Iproniazid. The role of the antigens and their antibodies concerning the aetiology and pathogenesis of the relevant diseases, especially primary biliary cirrhosis, is not known.}, }
@article {pmid2036622, year = {1991}, author = {Thiele, J and Schmidt, J and Sander, C and Fischer, R}, title = {Ultrastructure of bone marrow tissue in so-called primary (idiopathic) myelofibrosis-osteomyelosclerosis (agnogenic myeloid metaplasia). II. The myeloid stroma (hematopoietic microenvironment).}, journal = {Journal of submicroscopic cytology and pathology}, volume = {23}, number = {1}, pages = {109-121}, pmid = {2036622}, issn = {1122-9497}, mesh = {Bone Marrow/pathology/*ultrastructure ; Extracellular Matrix/pathology/*ultrastructure ; Hematopoietic System/*pathology ; Humans ; Metaplasia/pathology ; Osteosclerosis/*pathology ; Primary Myelofibrosis/*pathology ; }, abstract = {An ultrastructural study was performed on bone marrow tissue in 8 patients revealing early and late stages of so-called primary (idiopathic) myelofibrosis - osteomyelosclerosis (agnogenic myeloid metaplasia) to evaluate the constituents of the hematopoietic microenvironment (myeloid stroma). A survey of the stroma cells disclosed an overall increase, particularly in so-called undifferentiated (primitive - pluripotent), but also in transitional (fibroblastic) reticular cells and myofibroblasts. The most primitive reticular cells were characterized by their stellate aspect with elongated slender cytoplasmic processes traversing the interstitial space, and by the scarcity of organelles. The transition into a fibroblast was preceded by the appearance of branching cisternal structures of the rough endoplasmic reticulum, extensively developed Golgi fields and an abundance in mitochondria. Frequently, so-called myofibroblasts were encountered displaying bundles of filaments along the subplasmalemmal region. Extracellularly fibrillar material with an irregular cross-banding as well as microfibrils could be observed. The many vascular structures (sinusoids and capillaries) exhibited a multilayered basement membrane-like material including many fibrils and adventitial cells (pericytes, smooth muscle and transitional reticular cells) with numerous cytoplasmic processes. Undifferentiated and transitional reticular cells as well as myofibroblasts seem to form an integral part of the hematopoietic microenvironment in OMF and are assumed to play an important role for the evolution of the disease-specific myelofibrosis in this disorder.}, }
@article {pmid2002767, year = {1991}, author = {Smith, MF and Patton, JL}, title = {Variation in mitochondrial cytochrome b sequence in natural populations of South American akodontine rodents (Muridae: Sigmodontinae).}, journal = {Molecular biology and evolution}, volume = {8}, number = {1}, pages = {85-103}, doi = {10.1093/oxfordjournals.molbev.a040638}, pmid = {2002767}, issn = {0737-4038}, mesh = {Animals ; Base Sequence ; Cytochrome b Group/*genetics/metabolism ; DNA, Mitochondrial/genetics ; Electrophoresis, Polyacrylamide Gel ; Genes ; *Genetic Variation ; Mice ; Mitochondria/*enzymology ; Molecular Sequence Data ; Muridae/*genetics ; Phylogeny ; Polymerase Chain Reaction ; Sequence Homology, Nucleic Acid ; South America ; }, abstract = {A 401-bp fragment of the mitochondrial cytochrome b gene was sequenced from polymerase chain reaction-amplified products for 20 natural populations representing 12 species of South American akodontine rodents (Muridae). Variation among these taxa increased with their hierarchical position, from comparisons within local populations to those among different genera. Two individuals from the same local population differed by less than 1% sequence divergence. Sequence divergence among geographic samples within a species was 0.25%-8%, while that among species was 3%-21%. Comparisons of the akodontine sequences with that for the house mouse show 21%-25% sequence difference. A parsimony-based phylogenetic analysis of the data supports the placement of the taxon Microxus within Akodon (sensu stricto), of Bolomys just outside the Akodon cluster, and of Chroeomys as a separate genus quite distinct from the other members of this group. This phylogenetic hypothesis is identical to that determined from electrophoretic data but is quite divergent from the present taxonomy of the group.}, }
@article {pmid1962055, year = {1991}, author = {Roger, J and Bureau, M and Dravet, C and Genton, P and Tassinari, CA and Michelucci, R}, title = {[The role of mitochondrial encephalopathies in progressive myoclonus epilepsy].}, journal = {Revue neurologique}, volume = {147}, number = {6-7}, pages = {480-490}, pmid = {1962055}, issn = {0035-3787}, mesh = {Biopsy ; Electroencephalography ; Epilepsies, Myoclonic/*pathology/physiopathology ; Humans ; Mitochondria/*pathology ; Mitochondria, Muscle/*pathology ; Muscular Diseases/*pathology ; }, abstract = {The authors compare the clinical, neurophysiological and evolutive features of progressive myoclonus epilepsy (PME) associated with mitochondrial encephalomyopathy with ragged-red fibers (MERRF), based on 49 cases from the literature, and the two well-described types of degenerative PME: Baltic myoclonus (BM), of which over 100 cases have been reported from Finland, and Mediterranean myoclonus (MM), based on a personal series of 43 patients. Degenerative PMEs are age-dependent, recessively inherited conditions with homogeneous clinical signs and course; there are no major clinical symptoms beside the cardinal symptoms: generalized epileptic seizures, predominantly action myoclonus and cerebellar dysfunction; mental deterioration when present, is slight and progresses very slowly; associated neurological symptoms are uncommon and limited to mild spino-cerebellar involvement. In MERRF, the transmission is maternal, the age of onset is variable, the evolution is not stereotyped and associated symptoms are many (deafness, muscle weakness, optic atrophy, short stature, sensory disturbances, spasticity, clinical or neurophysiological signs of peripheral neuropathy, absence of motor reflexes); muscle biopsy generally shows ragged-red fibers. The differential diagnosis between these conditions is usually easy, although pathological examination (i.e. muscle biopsy) should be performed.}, }
@article {pmid1962046, year = {1991}, author = {Serratrice, G and Baumann, N}, title = {[From muscle to central nervous system: birth and future of the mitochondrial encephalomyopathy concept].}, journal = {Revue neurologique}, volume = {147}, number = {6-7}, pages = {413-416}, pmid = {1962046}, issn = {0035-3787}, mesh = {Central Nervous System Diseases/history/*pathology ; History, 19th Century ; History, 20th Century ; Humans ; Kearns-Sayre Syndrome/history ; Mitochondria/*pathology ; Mitochondria, Muscle/*pathology ; Ophthalmoplegia/history/*pathology ; Syndrome ; }, abstract = {The various types of ophthalmoplegia described in the second half of the 19th century were attributed to degeneration of the oculomotor nuclei. In the middle of the 20th century, a reversal of opinions ascribed these disorders to a primary muscle lesion, and this was accepted as a dogma for 20 years. However, the finding of mitochondrial abnormalities, not only in muscles but also in the nervous system and in a variety of viscera, gradually led to the concept of a multiple system syndrome. Advances in biochemistry then revealed multiple alterations of the mitochondrial function, especially in the respiratory chain, and ultimately the concept of mitochondrial heredity was developed by molecular biology. At present, two approaches are possible. Those who opt for the first one consider that a large number of muscular, nervous, endocrine, cardiac, hepatic or renal abnormalities have as common substrate a disease of mitochondria producing unclassifiable biochemical abnormalities. Partisans of the second approach individualize, for clinical and genetic reasons, several autonomous syndromes, the best known of which is Kearns-Sayre syndrome. In any case, this evolution of concepts illustrates an advance in medicine: the starting point was a localized muscle lesion, while the end-point is a complex, multiple system dysfunction which, analyzed with increasingly greater precision, gives a glimpse of future therapeutic applications.}, }
@article {pmid1912948, year = {1991}, author = {Cordeau-Lossouarn, L and Vayssière, JL and Larcher, JC and Gros, F and Croizat, B}, title = {Mitochondrial maturation during neuronal differentiation in vivo and in vitro.}, journal = {Biology of the cell}, volume = {71}, number = {1-2}, pages = {57-65}, doi = {10.1016/0248-4900(91)90051-n}, pmid = {1912948}, issn = {0248-4900}, mesh = {Animals ; Blotting, Western ; Cell Differentiation ; Cells, Cultured ; Cerebral Cortex/cytology/*growth &amp; development ; Electrophoresis, Gel, Two-Dimensional ; Fluorescent Antibody Technique ; Microscopy, Electron ; Mitochondria/*metabolism ; Neurons/*cytology/ultrastructure ; Rats ; }, abstract = {The evolution of the mitochondrion has been followed within differentiating neuronal cells, both in primary cultures of neurons from fetal rat cortex and during rat brain cortex maturation. Changes in total mitochondrial proteins (mt-proteins) were evaluated, and qualitative changes in the mt-proteins pattern were analyzed using the Western blot technique. The evolution of mt-protein contents in cultured neurons resembles what is observed during rat brain maturation. The mitochondrion exhibits pronounced changes in the course of neurogenesis, in particular, bursts of mitochondrial masses accompanying the successive steps of neurogenesis are observed. There are indications that protein equipment of mitochondria during neuronal development undergoes variations. Although more work is required to establish the significance of these correlations, the present data might suggest an important role of the mitochondrion in neurogenesis.}, }
@article {pmid1898982, year = {1991}, author = {Hoke, GD and McCabe, FL and Faucette, LF and Bartus, JO and Sung, CM and Jensen, BD and Heys, JR and Rush, GF and Alberts, DW and Johnson, RK}, title = {In vivo development and in vitro characterization of a subclone of murine P388 leukemia resistant to bis(diphenylphosphine)ethane.}, journal = {Molecular pharmacology}, volume = {39}, number = {1}, pages = {90-97}, pmid = {1898982}, issn = {0026-895X}, mesh = {Adenosine Triphosphate/metabolism ; Animals ; Antineoplastic Agents/*pharmacology ; Carbon Dioxide/metabolism ; Cell Line/drug effects ; Drug Resistance/*genetics ; Flow Cytometry ; Gold/pharmacology ; Leukemia P388/*genetics ; Mice ; Mitochondria/*drug effects/physiology ; Organogold Compounds ; Organometallic Compounds/*pharmacology ; Organophosphorus Compounds/*pharmacology ; Phenotype ; Rhodamine 123 ; Rhodamines/metabolism ; }, abstract = {Bis(diphenylphosphine)ethane (DPPE) and its gold coordination complexes have demonstrated antitumor activity in transplantable tumor models. This report describes the development of a P388 cell line (P388/DPPEc) that is resistant to DPPE and its analogues and the in vitro characterization of the cross-resistance of this subline to various antitumor and cytotoxic agents. The P388/DPPE tumor cell line was developed by serial transplantation in DPPE-treated mice. Resistance to DPPE was phenotypically stable. The P388/DPPE subline was cross-resistant to DPPE analogues and metal coordination complexes of DPPE. In addition, P388/DPPE cells were resistant to several mitochondrial uncouplers, including rhodamine-123, tetraphenylphosphonium, and carbonylcyanide-p-trifluro-methoxyphenyl hydrazone. P388/DPPE cells were less capable of sequestering and retaining 123Rh than were sensitive (P388/S) cells. Exposure to Au(DPPE)2+, a gold complex of DPPE with increased antitumor activity, resulted in a depletion of cellular ATP; the depletion was more rapid in the sensitive than the resistant cells. The rate of mitochondrial respiration, as measured by 14CO2 evolution from [6-14C]glucose, was greater in P388/S than in P388/DPPE. As with that evidenced for 123Rh, the cellular uptake of radiolabeled DPPE was decreased in P388/DPPEc cells. The results suggest that the basis for the resistance of this cell line may be an alteration in mitochondrial membrane potential. These data and the striking cross-resistance of P388/DPPE to mitochondrial uncouplers support the hypothesis that mitochondria may be one target involved in the cytotoxic or antitumor activities of these compounds. Mitochondria may also be causally related to the cytotoxic or antitumor activities, in that DPPE may be concentrated in cells via the presence of the inner mitochondrial membrane potential. Thus, P388/DPPE cells can serve as a tool to screen for and evaluate drugs that rely on affecting mitochondrial function, either mechanistically or causally, for their antitumor efficacy.}, }
@article {pmid1854912, year = {1991}, author = {Cavalier-Smith, T}, title = {Archamoebae: the ancestral eukaryotes?.}, journal = {Bio Systems}, volume = {25}, number = {1-2}, pages = {25-38}, doi = {10.1016/0303-2647(91)90010-i}, pmid = {1854912}, issn = {0303-2647}, mesh = {Amoeba ; Animals ; *Eukaryota ; *Eukaryotic Cells ; Organelles ; *Phylogeny ; }, abstract = {The archezoan phylum Archamoebae Cavalier-Smith, 1983 is here modified by adding a new order Phreatamoebida (presently containing only Phreatamoeba) and removing the family Entamoebidae. Entamoebidae are instead tentatively placed as a class Entamoebea together with the classes Heterolobosea, Percolomonadea and Pseudociliatea in the new protozoan phylum Percolozoa Cavalier-Smith, 1991. Thus emended the phylum Archamoebae is more homogeneous; it is more distinguished from the other two phyla of the primitively amitochondrial kingdom and superkingdom Archezoa (i.e. Metamonada and Microsporidia) by having kinetids with only a single flagellum and basal body and a flagellar root consisting of a cone of evenly spaced microtubules. This unikont character of the archamoebae suggests that they may be ancestral to the tetrakont Metamonada, from which the non-flagellate Microsporidia possibly evolved. Higher eukaryotes (superkingdom Metakaryota) probably evolved from a tetrakont metamonad by the symbiotic origin of mitochondria and peroxisomes. If so, the Archamoebae are the most primitive extant phylum of eukaryotes; if molecular phylogenetic studies confirm this idea, Archamoebae will deserve intensive study, which could reveal much about the origin of the eukaryote condition and also establish what is truly universal among eukaryotes. Archamoebae, like other Archezoa, lack mitochondria and peroxisomes and have no obvious Golgi dictyosomes. Their evolutionary significance is discussed and a detailed classification is presented in which the two earlier classes are merged into a single one: Pelobiontea Page, 1976 stat. nov., containing two orders Mastigamoebida Frenzel, 1892 (Syn. Rhizo-Flagellata Kent, 1880 non Rhizomastigida auct.) (including Mastigamoeba, Mastigina, Mastigella, Pelomyxa and probably a few other genera, which have one or more flagella or cilia (motile or immotile, 9 + 2 or otherwise) in the amoeboid trophic phase), and Phreatamoebida ord. nov. (including only Phreatamoeba in the new family Phreatamoebidae, which has alternating phases of non-flagellate amoebae and uniflagellate cells). Mastigamoebida are divided into three families: Mastigamoebidae Goldschmidt, 1907; Mastigellidae fam. nov.; Pelomyxidae Schulze, 1877. Archamoebae may be uni- or multi-nucleate and either gut parasites or (more usually) free-living in soil, freshwater, or marine habitats. Some can form cysts that would probably fossilize; the earliest (1450 My old) smooth-walled fossil cells large enough to be probable eukaryotes might therefore be archamoebal cysts.}, }
@article {pmid1854909, year = {1991}, author = {Spiegel, FW}, title = {A proposed phylogeny of the flagellated protostelids.}, journal = {Bio Systems}, volume = {25}, number = {1-2}, pages = {113-120}, doi = {10.1016/0303-2647(91)90017-f}, pmid = {1854909}, issn = {0303-2647}, mesh = {Animals ; Eukaryota/*classification ; Flagella ; Mitochondria ; *Phylogeny ; Terminology as Topic ; }, abstract = {The flagellated members of the group of mycetozoans known as protostelids have been recognized for some time to be members of a monophyletic group which also includes the myxomycetes. This inference was based primarily upon comparisons of the flagellar apparatus of the amoeboflagellate state. However, more detailed comparisons based on the whole life history and comparisons with an outgroup were necessary to have information sufficient to determine the interrelationships within the group. Recent studies of the other states of the life history of protostelids have provided a wealth of additional morphological and developmental characters such that an in depth phylogenetic analysis is possible. The results show that the group can be resolved into two major clades, one of which contains the myxomycetes and the myxomycete-like protostelid genera, Protosporangium, Clastostelium, and Ceratiomyxa, and another which contains the protostelid genera Planoprotostelium, Cavostelium, and Ceratiomyxella. As the myxomycetes appear to be part of the ingroup, and not a sister group to the protostelids, L.S. Olive's subclass Protostelia must be considered paraphyletic.}, }
@article {pmid1831167, year = {1991}, author = {Upcroft, P}, title = {DNA fingerprinting of the human intestinal parasite Giardia intestinalis with hypervariable minisatellite sequences.}, journal = {EXS}, volume = {58}, number = {}, pages = {70-84}, doi = {10.1007/978-3-0348-7312-3_5}, pmid = {1831167}, issn = {1023-294X}, mesh = {Animals ; Base Sequence ; *DNA Fingerprinting ; *DNA, Protozoan ; *DNA, Satellite ; Electrophoresis, Agar Gel ; Giardia/enzymology/*genetics ; Humans ; Intestines/parasitology ; Isoenzymes/genetics ; Karyotyping/methods ; Molecular Sequence Data ; }, abstract = {Individual isolates of the Giardia duodenalis group of protozoan intestinal parasites were identified by DNA fingerprinting with hypervariable minisatellite sequences. A morphologically identical parasite is found in some forty different animal species. Although the species name intestinalis is reserved for the human isolates, electrophoretic karyotyping suggests that most duodenalis isolates fall into the same species grouping. Distinction based upon morphology, restriction endonuclease cleavage of genomic DNA or isoenzyme analysis has not been adequate to identify individual strains. The successful use of hypervariable sequences in the identification of individual human genomes encouraged us to examine the use of these same sequences for the possible identification of parasite isolates. We initially use as a fingerprinting probe the genome of the bacteriophage M13, which has repeated sequences recognising homologous hypervariable sequences in the human genome. The M13 probe recognises a weakly homologous set of hypervariable sequences in Giardia. The number of informative bands is comparable to those seen in mammals, since the lower molecular weight bands are also useful. There is considerable divergence in the sequences of individual Giardia minisatellites. Some cloned Giardia hypervariable sequences are more homologous to M13 than they are to each other. Similar results were observed with the hypervariable repeat sequences 3' to the human alpha-globin gene when they were used as a probe to distinguish Giardia isolates. The poly(dA-dC).poly(dG-dT) probe which recognises frequent TG tracts in a number of organisms also detects a few variable bands amidst a hybridisation background in the Giardia genome. Thus Giardia isolates which could not be distinguished by restriction endonuclease cleavage, antibody typing or isoenzyme analysis have been identified by DNA fingerprinting procedures. Detailed analysis of strain movement, resurgence, variation, host range and drug resistance is now possible. Similar families of sequences may be widespread in lower eukaryotes and useful for generating individual specific fingerprints. A procedure for detecting individual parasites is also presented. Since Giardia is regarded as the most ancient eukaryote before the occurrence of symbiosis with purple non-sulphur bacteria to generate mitochondria, the identification of hypervariable sequences in the Giardia genome should also aid in understanding the mechanism of generation and evolution of these sequences.}, }
@article {pmid1727028, year = {1991}, author = {Silva González, E and Mosqueira Pérez Salazar, FG}, title = {[Functional and evolutionary aspects of the aminoacyl-tRNA synthetases].}, journal = {Revista latinoamericana de microbiologia}, volume = {33}, number = {1}, pages = {87-101}, pmid = {1727028}, issn = {0187-4640}, mesh = {Amino Acid Sequence ; Amino Acids/metabolism ; Amino Acyl-tRNA Synthetases/chemistry/*physiology ; Animals ; Bacterial Proteins/chemistry ; Biological Evolution ; Eukaryotic Cells/enzymology ; Genetic Code ; Molecular Sequence Data ; Protein Biosynthesis ; Protein Conformation ; RNA, Bacterial/metabolism ; RNA, Transfer/metabolism ; Sequence Homology, Amino Acid ; }, abstract = {A main event in protein bioshynthesis is the esterification of the correct aminoacid to cognate tRNA catalized by the aminoacyl-tRNA synthetases. The central role of this family of enzymes in metabolism is an evidence of their ancient origin. As it is the case in many others molecules involved in protein synthesis, the emergence of the aminoacyl-tRNA synthetases appears to be a problem that is not yet solved in order to understand the origin of the genetic translation. To obtain a comprehensive view of the evolution of the relationship between each one of the twenty aminoacyl-tRNA synthetases from one organism as well as from different sources (eubacteria, archaebacteria and eukaryotes) we review the information collected from the structural and catalytic properties of these enzyme. The results allow us to establish the following relationship between aminoacyl-tRNA synthetases. On one side there is a monofiletic origin for glutamyl, glutamynil and argynil-tRNA synthetases from Escherichia coli and for valyl, leucyl, metionyl, isoleucyl and phenylalanil-tRNA synthetases from eubacterias, archaebacterias and eukaryotes. On the other side there is an evolutionary relationship between aminoacyl-tRNA synthetases of eubacteria and organelles (plastids and mitochondria) and among eukaryotes and archaebacteria.}, }
@article {pmid2125748, year = {1990}, author = {Kuhsel, MG and Strickland, R and Palmer, JD}, title = {An ancient group I intron shared by eubacteria and chloroplasts.}, journal = {Science (New York, N.Y.)}, volume = {250}, number = {4987}, pages = {1570-1573}, doi = {10.1126/science.2125748}, pmid = {2125748}, issn = {0036-8075}, support = {35087//PHS HHS/United States ; }, mesh = {Anticodon/genetics ; Base Sequence ; Biological Evolution ; Chloroplasts/*metabolism ; Cloning, Molecular ; Cyanobacteria/genetics ; Eubacterium/*genetics ; Eukaryota/genetics ; Introns/*genetics ; Molecular Sequence Data ; Nucleic Acid Conformation ; Plants/genetics ; Polymerase Chain Reaction ; RNA, Transfer, Leu/*genetics ; }, abstract = {Introns have been found in the genomes of all major groups of organisms except eubacteria. The presence of introns in chloroplasts and mitochondria, both of which are of eubacterial origin, has been interpreted as evidence either for the recent acquisition of introns by organelles or for the loss of introns from their eubacterial progenitors. The gene for the leucine transfer RNA with a UAA anticodon [tRNALeu (UAA)] from five diverse cyanobacteria and several major groups of chloroplasts contains a single group I intron. The intron is conserved in secondary structure and primary sequence, and occupies the same position, within the UAA anticodon. The homology of the intron across chloroplasts and cyanobacteria implies that it was present in their common ancestor and that it has been maintained in their genomes for at least 1 billion years.}, }
@article {pmid2253709, year = {1990}, author = {Jukes, TH and Osawa, S}, title = {The genetic code in mitochondria and chloroplasts.}, journal = {Experientia}, volume = {46}, number = {11-12}, pages = {1117-1126}, pmid = {2253709}, issn = {0014-4754}, support = {GM 40903 01/GM/NIGMS NIH HHS/United States ; }, mesh = {Animal Population Groups/genetics ; Animals ; Biological Evolution ; Chloroplasts/*physiology ; Codon ; DNA, Mitochondrial/*genetics ; *Genetic Code ; Mitochondria/*physiology ; Peptide Chain Initiation, Translational ; Peptide Chain Termination, Translational ; Plants/genetics ; }, abstract = {The universal genetic code is used without changes in chloroplasts and in mitochondria of green plants. Non-plant mitochondria use codes that include changes from the universal code. Chloroplasts use 31 anticodons in translating the code; a number smaller than that used by bacteria, because chloroplasts have eliminated 10 CNN anticodons that are found in bacteria. Green plant mitochondria (mt) obtain some tRNAs from the cytosol, and genes for some other tRNAs have been acquired from chloroplast DNA. The code in non-plant mt differs from the universal code in the following usages found in various organisms: UGA for Trp, AUA for Met, AGR for Ser and stop, AAA for Asn, CUN for Thr, and possibly UAA for Tyr. CGN codons are not used by Torulopsis yeast mt. Non-plant mt, e.g. in vertebrates, may use a minimum of 22 anticodons for complete translation of mRNA sequences. The following possible causes are regarded as contributing to changes in the non-plant mt: directional mutation pressure, genomic economization, changes in charging specificity of tRNAs, loss of release factor RF2, changes in RF1, changes in anticodons, loss of lysidine-forming enzyme system, and disappearance of codons from coding sequences.}, }
@article {pmid2147658, year = {1990}, author = {Jukes, TH}, title = {Genetic code 1990. Outlook.}, journal = {Experientia}, volume = {46}, number = {11-12}, pages = {1149-1157}, pmid = {2147658}, issn = {0014-4754}, support = {GM 40903 01/GM/NIGMS NIH HHS/United States ; }, mesh = {Anaerobiosis ; Anticodon ; Base Sequence ; Biological Evolution ; Codon ; Cysteine/analogs &amp; derivatives/metabolism ; DNA, Mitochondrial/genetics ; Formate Dehydrogenases/genetics ; *Genetic Code ; Molecular Sequence Data ; Mutation ; Peptide Chain Termination, Translational ; Protein Biosynthesis ; RNA Processing, Post-Transcriptional ; RNA, Messenger/genetics ; RNA, Transfer/genetics ; Selenium/metabolism ; Selenocysteine ; }, abstract = {The genetic code is evolving as shown by 9 departures from the universal code: 6 of them are in mitochondria and 3 are in nuclear codes. We propose that these changes are preceded by disappearance of a codon from coding sequences in mRNA of an organism or organelle. The function of the codon that disappears is taken by other, synonymous codons, so that there is no change in amino acid sequences of proteins. The deleted codon then reappears with a new function. Wobble pairing between anticodons and codons has evolved, starting with a single UNN anticodon pairing with 4 codons. Directional mutation pressure affects codon usage and may produce codon reassignments, especially of stop codons. Selenocysteine is coded by UGA, which is also a stop codon, and this anomaly is discussed. The outlook for discovery of more changes in the code is favorable, and open reading frames should be compared with actual sequential analyses of protein molecules in this search.}, }
@article {pmid2127597, year = {1990}, author = {Danpure, CJ and Guttridge, KM and Fryer, P and Jennings, PR and Allsop, J and Purdue, PE}, title = {Subcellular distribution of hepatic alanine:glyoxylate aminotransferase in various mammalian species.}, journal = {Journal of cell science}, volume = {97 (Pt 4)}, number = {}, pages = {669-678}, doi = {10.1242/jcs.97.4.669}, pmid = {2127597}, issn = {0021-9533}, mesh = {Alanine Transaminase/*metabolism ; Animals ; Biological Evolution ; Biological Transport ; Callitrichinae ; Cats ; Centrifugation, Density Gradient ; Humans ; Immunoblotting ; Liver/*enzymology/ultrastructure ; Mammals ; Microbodies/enzymology ; Microscopy, Immunoelectron ; Mitochondria, Liver/enzymology ; *Transaminases ; }, abstract = {The subcellular distribution of alanine:glyoxylate aminotransferase 1 (AGT1) enzyme activity and immunoreactive protein has been determined in the livers of a variety of mammalian species (marmoset, baboon, cat, rabbit, pig, sheep) using the techniques of post-embedding protein A-gold immunoelectron microscopy and isopycnic density gradient centrifugation. In baboon and rabbit livers, AGT1 was exclusively peroxisomal. Morphometric analysis of the distribution of immunoreactive AGT1 protein in cat liver showed that 91-92% was located in the mitochondria with 8-9% in the peroxisomes. In marmoset liver, 59% of AGT1 was found in the mitochondrial matrix and 41% in the peroxisomal matrix. The results from pig and sheep were ambiguous, because of the low levels of expression of AGT1. The implications of these data in terms of the metabolic roles of AGT1 (gluconeogenesis and glyoxylate detoxification) and in terms of the evolutionary acquisition and loss of functional mitochondrial and peroxisomal targeting sequences are discussed.}, }
@article {pmid1967076, year = {1990}, author = {Huang, J and Hack, E and Thornburg, RW and Myers, AM}, title = {A yeast mitochondrial leader peptide functions in vivo as a dual targeting signal for both chloroplasts and mitochondria.}, journal = {The Plant cell}, volume = {2}, number = {12}, pages = {1249-1260}, pmid = {1967076}, issn = {1040-4651}, mesh = {Amino Acid Sequence ; Base Sequence ; Biological Evolution ; Biological Transport ; Cell Compartmentation/*physiology ; Chloramphenicol O-Acetyltransferase/biosynthesis/genetics ; Chloroplasts/*metabolism ; Cytosol/metabolism ; Electron Transport Complex IV/genetics/metabolism ; Mitochondria/*metabolism ; Molecular Sequence Data ; Protein Processing, Post-Translational ; Protein Sorting Signals/*metabolism ; Recombinant Fusion Proteins/biosynthesis/genetics ; Saccharomyces cerevisiae/*genetics ; }, abstract = {A fusion protein was expressed in transgenic tobacco and yeast cells to examine the functional conservation of mechanisms for importing precursor proteins from the cytosol into mitochondria and chloroplasts. The test protein consisted of the mitochondrial leader peptide from the yeast precursor to cytochrome oxidase subunit Va (prC5) fused to the reporter protein chloramphenicol acetyltransferase. This protein, denoted prC5/CAT, was transported into the mitochondrial interior in yeast and tobacco cells. In both organisms, the mitochondrial form of prC5/CAT was smaller than the primary translation product, suggesting that proteolytic processing occurred during the transport process. prC5/CAT also was translocated into chloroplasts in vivo, accumulating to approximately the same levels as in plant mitochondria. However, accumulation of prC5/CAT in chloroplasts relative to mitochondria varied with the conditions under which plants were grown. The chloroplast form of prC5/CAT also appeared to have been proteolytically processed, yielding a mature protein of the same apparent size as that seen in mitochondria of either tobacco or yeast. Chloramphenicol acetyltransferase lacking a mitochondrial targeting peptide did not associate with either chloroplasts or mitochondria. The results demonstrated that in plant cells a single leader peptide can interact functionally with the protein translocation systems of both chloroplasts and mitochondria, and raised the possibility that certain native proteins might be shared between these two organelles.}, }
@article {pmid1965436, year = {1990}, author = {Gonzales, DH and Neupert, W}, title = {Biogenesis of mitochondrial c-type cytochromes.}, journal = {Journal of bioenergetics and biomembranes}, volume = {22}, number = {6}, pages = {753-768}, pmid = {1965436}, issn = {0145-479X}, mesh = {Animals ; Biological Evolution ; Biological Transport ; Cytochrome c Group/biosynthesis/*metabolism ; Mitochondria/*metabolism ; Models, Biological ; }, abstract = {Cytochromes c and c1 are essential components of the mitochondrial respiratory chain. In both cytochromes the heme group is covalently linked to the polypeptide chain via thioether bridges. The location of the two cytochromes is in the intermembrane space; cytochrome c is loosely attached to the surface of the inner mitochondrial membrane, whereas cytochrome c1 is firmly anchored to the inner membrane. Both cytochrome c and c1 are encoded by nuclear genes, translated on cytoplasmic ribosomes, and are transported into the mitochondria where they become covalently modified and assembled. Despite the many similarities, the import pathways of cytochrome c and c1 are drastically different. Cytochrome c1 is made as a precursor with a complex bipartite presequence. In a first step the precursor is directed across outer and inner membranes to the matrix compartment of the mitochondria where cleavage of the first part of the presequence takes place. In a following step the intermediate-size form is redirected across the inner membrane; heme addition then occurs on the surface of the inner membrane followed by the second processing reaction. The import pathway of cytochrome c is exceptional in practically all aspects, in comparison with the general import pathway into mitochondria. Cytochrome c is synthesized as apocytochrome c without any additional sequence. It is translocated selectively across the outer membrane. Addition of the heme group, catalyzed by cytochrome c heme lyase, is a requirement for transport. In summary, cytochrome c1 import appears to follow a "conservative pathway" reflecting features of cytochrome c1 sorting in prokaryotic cells. In contrast, cytochrome c has "invented" a rather unique pathway which is essentially "non-conservative."}, }
@article {pmid2249682, year = {1990}, author = {Pietrobon, D and Di Virgilio, F and Pozzan, T}, title = {Structural and functional aspects of calcium homeostasis in eukaryotic cells.}, journal = {European journal of biochemistry}, volume = {193}, number = {3}, pages = {599-622}, doi = {10.1111/j.1432-1033.1990.tb19378.x}, pmid = {2249682}, issn = {0014-2956}, mesh = {Animals ; Calcium/*metabolism ; Cell Membrane/metabolism ; Cytoplasm/metabolism ; Eukaryotic Cells/metabolism ; Homeostasis ; Mitochondria/metabolism ; }, abstract = {The maintenance of a low cytosolic free-Ca2+ concentration, ([Ca2+]i) is a common feature of all eukaryotic cells. For this purpose a variety of mechanisms have developed during evolution to ensure the buffering of Ca2+ in the cytoplasm, its extrusion from the cell and/or its accumulation within organelles. Opening of plasma membrane channels or release of Ca2+ from intracellular pools leads to elevation of [Ca2+]i; as a result, Ca2+ binds to cytosolic proteins which translate the changes in [Ca2+]i into activation of a number of key cellular functions. The purpose of this review is to provide a comprehensive description of the structural and functional characteristics of the various components of [Ca2+]i homeostasis in eukaryotes.}, }
@article {pmid2279712, year = {1990}, author = {Fujisawa, S and Tachikawa, N and Murakami, E and Masuda, M and Mizutani, S and Mizutani, M and Hirose, Y and Yamada, H and Fujita, K and Hasebe, T}, title = {[Limitation of experimental infarct size by levo-carnitine chloride (LC-80), a new mitochondrial function-reactivating agent].}, journal = {Nihon yakurigaku zasshi. Folia pharmacologica Japonica}, volume = {96}, number = {5}, pages = {227-242}, doi = {10.1254/fpj.96.5_227}, pmid = {2279712}, issn = {0015-5691}, mesh = {Animals ; Carnitine/metabolism ; Disease Models, Animal ; Dogs ; Hemodynamics/drug effects ; Male ; Microscopy, Electron ; Mitochondria, Heart/drug effects ; Myocardial Infarction/*drug therapy/pathology ; Myocardium/metabolism/pathology/ultrastructure ; }, abstract = {The effect of LC-80 on infarct size induced by 6 hr coronary occlusion was studied in anesthetized dogs. LC-80 at a dose of 100 mg/kg, i.v. was injected 5 min after coronary occlusion and then infused at a rate of 50 mg/kg, i.v./hr until the heart was excised. The two risk areas were determined both by injecting a fluorescent dye (Thioflavin S) into the left atrium (in vivo) and by perfusing the non-occluded coronary bed with Monastral Blue (in vitro). The infarct size was determined by topographically tracing the area of myocardium unstained by triphenyltetrazolium chloride. Four zones such as Zone 1 (normal tissue), Zone 2 (tissue characterized by collateral blood flow), Zone 3a (tissue developing necrosis), Zone 3b (necrotic tissue) were delimited . As a result, (1) LC-80 significantly diminished the incidence of ventricular arrhythmias. (2) LC-80 significantly inhibited the decrease in myocardial free carnitine level in Zone 2 and Zone 3b. (3) LC-80 significantly reduced the infarct size expressed as a percentage of the risk area and increased the size of Zone 2. (4) In the electron microscopic findings, LC-80 showed lesser morphological changes such as swollen mitochondria and intracellular and extracellular edema, especially in Zone 2. (5) LC-80 may be useful for inhibiting the evolution of myocardial ischemic cell death both by the protection of ischemic myocardium and presumably by the increase in the collateral blood flow.}, }
@article {pmid1702156, year = {1990}, author = {Thackeray, JR and Kyriacou, CP}, title = {Molecular evolution in the Drosophila yakuba period locus.}, journal = {Journal of molecular evolution}, volume = {31}, number = {5}, pages = {389-401}, pmid = {1702156}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Cell Nucleus/chemistry ; Cloning, Molecular ; DNA/*chemistry ; Drosophila/*genetics ; Mitochondria/chemistry ; Molecular Sequence Data ; Mutation ; RNA/chemistry ; Restriction Mapping ; Selection, Genetic ; }, abstract = {Two nuclear genes from Drosophila yakuba were cloned, the orthologue of the Drosophila melanogaster period (per) clock gene and the orthologue of an unnamed D. melanogaster gene adjacent to per, which encodes a 0.9-kb RNA transcript. The DNA and presumed protein sequences of both genes are presented and compared with their orthologues in D. melanogaster. Consistent with the per orthologues described in other Drosophila species, some parts of the per gene have accumulated nonsynonymous substitutions at a much higher rate than others. This contrasts markedly with the evenly distributed amino acid replacements observed in the protein encoded by the adjacent gene. The level of synonymous and nonsynonymous substitutions between D. yakuba and D. melanogaster per were compared in small subsections across the gene. The results suggest that the divergence observed in the less well-conserved regions of the per protein is principally due to reduced selective constraint, although the limitations of the method used prevent positive selection acting upon a small proportion of sites being ruled out. The level of silent substitution observed in both of these nuclear genes is very similar to the level of silent substitution previously reported between D. melanogaster and D. yakuba mitochondrial genes, confirming several indirect studies, which have suggested that, in contrast to the case in mammals, silent sites are evolving at similar rates in mitochondrial and nuclear genes of Drosophila.}, }
@article {pmid2226844, year = {1990}, author = {James, P and Wyss, M and Lutsenko, S and Wallimann, T and Carafoli, E}, title = {ATP binding site of mitochondrial creatine kinase. Affinity labelling of Asp-335 with C1RATP.}, journal = {FEBS letters}, volume = {273}, number = {1-2}, pages = {139-143}, doi = {10.1016/0014-5793(90)81069-z}, pmid = {2226844}, issn = {0014-5793}, mesh = {Adenosine Triphosphate/*analogs &amp; derivatives/*metabolism/pharmacology ; Affinity Labels/*pharmacology ; Amino Acid Sequence ; Animals ; *Aspartic Acid ; Binding Sites ; Chickens ; Creatine Kinase/*metabolism ; Isoenzymes ; Mitochondria, Heart/*metabolism ; Molecular Sequence Data ; Pepsin A ; Peptide Fragments/isolation &amp; purification ; Sequence Homology, Nucleic Acid ; }, abstract = {The ATP binding site of mitochondrial creatine kinase from chicken heart has been studied by modifying the purified enzyme with a 14C-labelled ATP analogue, C1RATP, in which the reactive label was covalently bound to the gamma-phosphate group of ATP. The modified enzyme was digested by pepsin, and a single radioactive nonapeptide was isolated by HPLC. Amino acid analysis and direct sequence determination revealed that the isolated peptide corresponds to amino acids 335-343 within the C-terminal region of Mi-CK, this peptide being highly preserved throughout evolution. Asp-335 is very likely the site of modification by C1RATP. The specificity of the ATP analogue for the active site of creatine kinase was demonstrated by the inhibition of the enzymatic activity of Mi-CK by C1RATP and by the prevention of this inhibition bij ADP.}, }
@article {pmid2150080, year = {1990}, author = {Kobayashi, H}, title = {[Regulatory mechanism of the cytoplasmic pH by H(+)-adenosinetriphosphatase].}, journal = {Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan}, volume = {110}, number = {10}, pages = {703-710}, doi = {10.1248/yakushi1947.110.10_703}, pmid = {2150080}, issn = {0031-6903}, mesh = {Adenosine Triphosphate/biosynthesis ; Cytoplasm/*metabolism ; Enterococcus faecalis/*metabolism ; Hydrogen-Ion Concentration ; Mitochondria/metabolism ; Proton-Translocating ATPases/metabolism/*physiology ; }, abstract = {Nature prefers simplicity. Streptococcal cytoplasmic pH is regulated in a simple biological manner: change in the amount of the adenosinetriphosphatase (H(+)-ATPase). This enzyme is identical to the F0F1-complex of oxidative phosphorylation, which synthesizes adenosinetriphosphate in mitochondria and most of bacteria, whereas it is used as a regulator of the cytoplasmic pH in streptococci which have no respiratory chain. Eukaryotes use the another type of H(+)-ATPase to regulate the internal pH. Thus, the evolutional process of H(+)-ATPase is quite interesting.}, }
@article {pmid2145157, year = {1990}, author = {Mahlke, K and Pfanner, N and Martin, J and Horwich, AL and Hartl, FU and Neupert, W}, title = {Sorting pathways of mitochondrial inner membrane proteins.}, journal = {European journal of biochemistry}, volume = {192}, number = {2}, pages = {551-555}, doi = {10.1111/j.1432-1033.1990.tb19260.x}, pmid = {2145157}, issn = {0014-2956}, mesh = {Base Sequence ; Biological Evolution ; DNA, Fungal/genetics/isolation &amp; purification ; Heat-Shock Proteins/metabolism ; Intracellular Membranes/*enzymology ; Mitochondrial ADP, ATP Translocases/genetics/metabolism ; Molecular Sequence Data ; Neurospora crassa/enzymology/*genetics ; Oligonucleotide Probes ; *Protein Processing, Post-Translational ; Proton-Translocating ATPases/*genetics/metabolism ; Recombinant Fusion Proteins/metabolism ; Submitochondrial Particles/*enzymology ; }, abstract = {Two distinct pathways of sorting and assembly of nuclear-encoded mitochondrial inner membrane proteins are described. In the first pathway, precursor proteins that carry amino-terminal targeting signals are initially translocated via contact sites between both mitochondrial membranes into the mitochondrial matrix. They become proteolytically processed, interact with the 60-kDa heat-shock protein hsp60 in the matrix and are retranslocated to the inner membrane. The sorting of subunit 9 of Neurospora crassa F0-ATPase has been studied as an example. F0 subunit 9 belongs to that class of nuclear-encoded mitochondrial proteins which are evolutionarily derived from a prokaryotic ancestor according to the endosymbiont hypothesis. We suggest that after import into mitochondria, these proteins follow the ancestral sorting and assembly pathways established in prokaryotes (conservative sorting). On the other hand, ADP/ATP carrier was found not to require interaction with hsp60 for import and assembly. This agrees with previous findings that the ADP/ATP carrier possesses non-amino-terminal targeting signals and uses a different import receptor to other mitochondrial precursor proteins. It is proposed that the ADP/ATP carrier represents a class of mitochondrial inner membrane proteins which do not have a prokaryotic equivalent and thus appear to follow a non-conservative sorting pathway.}, }
@article {pmid1698277, year = {1990}, author = {Muto, A and Andachi, Y and Yuzawa, H and Yamao, F and Osawa, S}, title = {The organization and evolution of transfer RNA genes in Mycoplasma capricolum.}, journal = {Nucleic acids research}, volume = {18}, number = {17}, pages = {5037-5043}, pmid = {1698277}, issn = {0305-1048}, mesh = {Base Sequence ; *Biological Evolution ; Cloning, Molecular ; Genes, Bacterial ; Molecular Sequence Data ; *Multigene Family ; Mycoplasma/*genetics ; RNA, Bacterial/genetics ; RNA, Transfer/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {The genes for presumably all the tRNA species in Mycoplasma capricolum, a derivative of Gram-positive eubacteria, have been cloned and sequenced. There are 30 genes encoding 29 tRNA species. This number is the smallest in all the known genetic systems except for mitochondria. The sequences of 9 tRNA genes of them have been previously reported (1-3). Twenty-two genes are organized in 5 clusters consisting of nine, five, four and two genes (2 sets), respectively. The other eight genes exist as a single transcription unit. All the tRNAs are encoded each by a single gene, except for the occurrence of two tRNA(Lys)(TTT) genes. The arrangement of tRNA genes in the 9-gene cluster, the 5-gene cluster, the 4-gene cluster and one of the 2-gene clusters reveals extensive similarity with a part of the 21-tRNA gene cluster and/or the 16-tRNA gene cluster in Bacillus subtilis, respectively. The results suggest that the present M. capricolum tRNA genes have evolved from large tRNA gene clusters in the ancestral Gram-positive bacterial genome common to M. capricolum and B. subtilis, by discarding genes for redundant as well as non-obligate tRNAs, so that all the codons may be translated by as small a number of tRNAs as possible.}, }
@article {pmid2120456, year = {1990}, author = {Iwabe, N and Kuma, K and Kishino, H and Hasegawa, M and Miyata, T}, title = {Compartmentalized isozyme genes and the origin of introns.}, journal = {Journal of molecular evolution}, volume = {31}, number = {3}, pages = {205-210}, pmid = {2120456}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Biological Evolution ; Cytosol/enzymology ; Genes ; *Introns ; Isoenzymes/*genetics ; Malate Dehydrogenase/*genetics ; Mice ; Mitochondria/enzymology ; Molecular Sequence Data ; *Phylogeny ; Sequence Homology, Nucleic Acid ; }, abstract = {Both the mouse cytosolic malate dehydrogenase gene and its mitochondrial counterpart contain eight introns, of which two are present at identical positions between the isozyme genes. The probability that the two intron positions coincide by chance between the two genes has been shown to be significantly small (= 1.3 x 10(-3), suggesting that the conservation of the intron positions has a biological significance. On the basis of a rooted phylogenetic tree inferred from a comparison of these isozymes and lactate dehydrogenases, we have shown that the origins of the conserved introns are very old, possibly going back to a date before the divergence of eubacteria, archaebacteria, and eukaryotes. In the aspartate aminotransferase isozyme genes, five of the introns are at identical places. The origins of the five conserved introns, however, are not obvious at present. It remains possible that some or all of the conserved introns have evolved after the divergence of eubacteria and eukaryotes.}, }
@article {pmid2401287, year = {1990}, author = {Juretić, N and Mattes, U and Ziak, M and Christen, P and Jaussi, R}, title = {Structure of the genes of two homologous intracellularly heterotopic isoenzymes. Cytosolic and mitochondrial aspartate aminotransferase of chicken.}, journal = {European journal of biochemistry}, volume = {192}, number = {1}, pages = {119-126}, doi = {10.1111/j.1432-1033.1990.tb19204.x}, pmid = {2401287}, issn = {0014-2956}, mesh = {Amino Acid Sequence ; Animals ; Aspartate Aminotransferases/*genetics ; Base Sequence ; Biological Evolution ; Body Fluids/*enzymology ; Chickens ; Chromosome Mapping ; Cloning, Molecular ; Cytosol/enzymology ; Exons ; Intracellular Fluid/*enzymology ; Introns ; Mitochondria/enzymology ; Molecular Sequence Data ; Protein Conformation ; Restriction Mapping ; Sequence Homology, Nucleic Acid ; }, abstract = {The genes of mitochondrial and cytosolic aspartate aminotransferase of chicken were cloned and sequenced. In both genes nine exons encode the mature enzyme. The additional exon for the N-terminal presequence that directs mitochondrial aspartate aminotransferase into the mitochondria is separated by the largest intron from the rest of the gene. A comparison of the two genes of chicken with the aspartate aminotransferase genes of mouse [Tsuzuki, T., Obaru, K., Setoyama, C. &amp; Shimada, K. (1987) J. Mol. Biol. 198, 21-31; Obaru, K., Tsuzuki, T., Setoyama, C. &amp; Shimada, K. (1988) J. Mol. Biol. 200, 13-22] reveals closely similar structures: in the gene of both the mitochondrial and the cytosolic isoenzyme all but one intron positions are conserved in the two species and five introns out of nine are placed at the same positions in all four genes indicating that the introns were in place before the genes of the two isoenzymes diverged. The variant consensus sequence (T/C)11 T(C/T)AG at the 3' splice site of the introns of the genes for nuclear-encoded mitochondrial proteins, which had been deduced from a total of 34 introns [Juretić, N., Jaussi, R., Mattes, U. &amp; Christen, P. (1987) Nucleic Acids Res. 15, 10,083-10,086], was confirmed by including an additional 22 introns into the comparison. The position -4 at the 3' splice site is occupied by base T in 43% of the total 56 introns and appears to be subject to a special evolutionary constraint in this particular group of genes. The following course of evolution of the aspartate aminotransferase genes is proposed. Originating from a common ancestor, the genes of the two isoenzymes intermediarily evolved in separate lineages, i.e. the ancestor eukaryotic and ancestor endosymbiontic cells. When endosymbiosis was established, part of the endosymbiontic genome, including the aspartate aminotransferase gene, was transferred to the nucleus. This process probably led to the conservation of certain splicing factors specific for nuclear-encoded mitochondrial proteins. The presequence for the mitochondrial isoenzyme was acquired by DNA rearrangement. In the eukaryotic lineage, the mitochondrial isoenzyme evolved more slowly than its cytosolic counterpart.}, }
@article {pmid2246894, year = {1990}, author = {Freeman, S}, title = {The evolution of the scrotum: a new hypothesis.}, journal = {Journal of theoretical biology}, volume = {145}, number = {4}, pages = {429-445}, doi = {10.1016/s0022-5193(05)80479-5}, pmid = {2246894}, issn = {0022-5193}, mesh = {Animals ; *Biological Evolution ; Humans ; Male ; Mammals/*physiology ; Models, Biological ; Scrotum/*physiology ; Spermatozoa/physiology ; Temperature ; Testis/physiology ; }, abstract = {The adaptive significance of the scrotum is unresolved after more than 60 years of debate and experimentation. The "training hypothesis" introduced here suggests that testicular descent is a mechanism for improving sperm quality. The hypothesis proposes that: (1) testicular descent decreases blood supply to maturing sperm cells, (2) sperm mitochondria respond to the resulting oxygen stress by enhancing their enzymatic machinery for oxidative metabolism, as do oxygen-stressed muscle cell mitochondria, and (3) the resulting increase in aerobic fitness of sperm cells is advantageous in inter-ejaculate competition. The hypothesis suggests that there is a quantity-quality trade-off in sperm production, where taxa with internal testes produce large volumes of low-quality sperm while taxa with scrotal testes produce smaller volumes of higher-quality sperm.}, }
@article {pmid2178164, year = {1990}, author = {Jenkins, JR and Pocklington, MJ and Orr, E}, title = {The F1 ATP synthetase beta-subunit: a major yeast novobiocin binding protein.}, journal = {Journal of cell science}, volume = {96 (Pt 4)}, number = {}, pages = {675-682}, doi = {10.1242/jcs.96.4.675}, pmid = {2178164}, issn = {0021-9533}, mesh = {Amino Acid Sequence ; Animals ; Antibodies, Fungal/biosynthesis ; Blotting, Western ; Carrier Proteins/*metabolism ; Cattle ; Chickens ; Chromatography, Affinity ; DNA Topoisomerases, Type II/metabolism ; Escherichia coli/enzymology/metabolism ; Fluorescent Antibody Technique ; Humans ; Mammals ; Mitochondria/drug effects/*enzymology ; Molecular Sequence Data ; Novobiocin/*metabolism ; Proton-Translocating ATPases/immunology/isolation &amp; purification/*metabolism ; Saccharomyces cerevisiae/drug effects/*enzymology ; Species Specificity ; Tumor Cells, Cultured ; }, abstract = {Novobiocin affects DNA metabolism in both prokaryotes and eukaryotes, resulting in cell death. In prokaryotes, the drug is a specific inhibitor of DNA gyrase, a type II topoisomerase that can be purified on a novobiocin-Sepharose column. The yeast type II topoisomerase is neither the biochemical, nor the genetic target of the antibiotic. We have purified the major yeast novobiocin binding proteins and identified one of them as the beta-subunit of the yeast mitochondrial F1 ATP synthetase, a protein highly conserved throughout evolution. The inactivation of this protein might explain the toxic effects of novobiocin on higher eukaryotic cells.}, }
@article {pmid2165219, year = {1990}, author = {Thorsness, PE and Fox, TD}, title = {Escape of DNA from mitochondria to the nucleus in Saccharomyces cerevisiae.}, journal = {Nature}, volume = {346}, number = {6282}, pages = {376-379}, doi = {10.1038/346376a0}, pmid = {2165219}, issn = {0028-0836}, mesh = {Cell Nucleus/*metabolism ; DNA, Fungal/genetics/*metabolism ; DNA, Mitochondrial/genetics/*metabolism ; Electron Transport Complex IV/genetics ; Genes, Fungal ; Genotype ; Mitochondria/*metabolism ; Plasmids ; Saccharomyces cerevisiae/*genetics/growth &amp; development/metabolism ; Temperature ; }, abstract = {The migration of genetic information from ancestral prokaryotic endosymbionts into eukaryotic nuclei is thought to have had an important role in the evolution of mitochondria and chloroplasts. Here we describe an assay for the detection of movement of DNA between mitochondria and the nucleus in yeast. Because recombinant plasmid DNA replicates after transformation into mitochondria of yeast strains lacking endogenous mitochondrial DNA we were able to propagate the nuclear genetic marker URA3 in mitochondria. As expected, the wild-type URA3 gene in mitochondria failed to complement the uracil auxotrophy (Ura-) caused by a nuclear ura3 mutation. But selection of Ura+ prototrophs from a Ura- strain carrying URA3 on a plasmid in its mitochondria enabled us to detect plasmid movement to the nucleus. Conversely, as the plasmid used also contained the mitochondrial gene COX2 required for respiratory growth, we were able to set up corresponding selections to detect migration of DNA from the nucleus to the mitochondria. Our results show that, in yeast, DNA escapes from mitochondria and appears in the nucleus at a surprisingly high frequency (approximately 2 x 10(-5) per cell per generation). But the rate at which DNA makes the journey in the opposite direction--nucleus to mitochondria--is apparently at least 100,000 times less.}, }
@article {pmid1978331, year = {1990}, author = {Osawa, S and Muto, A and Jukes, TH and Ohama, T}, title = {Evolutionary changes in the genetic code.}, journal = {Proceedings. Biological sciences}, volume = {241}, number = {1300}, pages = {19-28}, doi = {10.1098/rspb.1990.0060}, pmid = {1978331}, issn = {0962-8452}, mesh = {Base Sequence ; *Biological Evolution ; Codon ; *Genetic Code ; Mitochondria/chemistry ; *Mutation ; Nucleic Acid Conformation ; }, abstract = {The genetic code has been influenced by directional mutation pressure affecting the base composition of DNA, sometimes in the direction of increased GC content and at other times, in the direction of AT. Such pressure led to changes in species-specific usages of codons and tRNA anticodons, and also in amino acid assignments of codons in mitochondria and in several intact organisms. These code changes are probably recent evolutionary events. The genetic code is not 'frozen', but instead it is still evolving.}, }
@article {pmid2395164, year = {1990}, author = {Clarke, A}, title = {Mitochondrial genome: defects, disease, and evolution.}, journal = {Journal of medical genetics}, volume = {27}, number = {7}, pages = {451-456}, pmid = {2395164}, issn = {0022-2593}, mesh = {*Biological Evolution ; Cell Nucleus/analysis ; *Chromosome Aberrations ; DNA, Mitochondrial/*analysis ; Humans ; Mitochondria/*ultrastructure ; Models, Genetic ; Mutation ; Selection, Genetic ; }, abstract = {Defects of mitochondrial function are often caused by defects of the mitochondrial genome. The hypothesis that defective organelles may spread through syncytial tissues as a result of a process of subcellular Darwinian selection is proposed. Tissues are likely to be involved in mitochondrial disease if they are syncytial, are derived from a few embryonic cells only, have little redundancy of function, and are subject to repeated metabolic stress. These effects, together with the random distribution of genetically heterogeneous mitochondria within the fertilised zygote, may account for the varied clinical pictures of mitochondrial disease. Evolution will have favoured the shift of mitochondrial DNA sequences to the nucleus, once the differentiation of tissues had created body compartments in which defective mitochondria could flourish to the detriment of the organism. This model of mitochondrial disease allows the generation of several predictions, testable using currently available laboratory techniques. Avenues of potential therapeutic value are indicated, including the avoidance of hypoglycaemia and the use of selective mitochondrial toxins.}, }
@article {pmid2382074, year = {1990}, author = {Bonard, EC}, title = {[Eve and the mitochondria].}, journal = {Revue medicale de la Suisse romande}, volume = {110}, number = {7}, pages = {639-640}, pmid = {2382074}, issn = {0035-3655}, mesh = {*Biological Evolution ; DNA, Mitochondrial/analysis/*genetics ; Female ; Humans ; Mitochondria/*analysis ; }, }
@article {pmid2354773, year = {1990}, author = {de Jong-Brink, M and Nagle, GT and Dictus, WJ and Painter, SD and Broers-Vendrig, T and Blankenship, JE}, title = {A calfluxin-related peptide is present in the bag cells and atrial gland of Aplysia.}, journal = {General and comparative endocrinology}, volume = {79}, number = {1}, pages = {114-122}, doi = {10.1016/0016-6480(90)90094-3}, pmid = {2354773}, issn = {0016-6480}, support = {NS 22079/NS/NINDS NIH HHS/United States ; NS 23169/NS/NINDS NIH HHS/United States ; RR 97925/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Aplysia/*metabolism ; Calcium/metabolism ; Exocrine Glands/drug effects/metabolism/ultrastructure ; Invertebrate Hormones/*metabolism ; Lymnaea/metabolism ; Microscopy, Electron ; Mitochondria/metabolism ; Neuropeptides/*metabolism/pharmacology ; Neurosecretory Systems/*metabolism/ultrastructure ; }, abstract = {The caudodorsal cells of Lymnaea and the bag cells of Aplysia are neuroendocrine cells whose peptide products have homologous functions, i.e., regulation of egg deposition. One of the Lymnaea products, calfluxin, increases cytosolic and hence mitochondrial calcium concentrations in secretory cells of the albumen gland, an exocrine organ that secretes perivitellin fluid around the egg cells during packaging; the changes can be visualized at the ultrastructural level for quantification with the pyroantimonate precipitation technique and are correlated with changes in the secretory and biosynthetic activity in the gland. Comparable studies have now been carried out with Aplysia and indicate that the bag cells of A. californica and A. brasiliana also contain a factor with calfluxin-related activity, and that the factor is not the egg-laying hormone (ELH). The bag cell factor does not affect mitochondrial calcium levels in the Lymnaea albumen gland, and synthetic calfluxin does not affect the Aplysia gland. Thus, although the bag cell and caudodorsal cell peptides have the same activity in their respective genera, the sequences have diverged sufficiently during the course of evolution to preclude cross-reactivity. Calfluxin-related activity was also detected in the atrial gland of A. californica and the atrial gland-like epithelium of A. brasiliana, two exocrine organs in the oviduct that express genes structurally related to the bag cell ELH gene. It is postulated that the active atrial gland factors may be peptides A and B.}, }
@article {pmid1367465, year = {1990}, author = {Schopf, B and Howaldt, MW and Bailey, JE}, title = {DNA distribution and respiratory activity of Spodoptera frugiperda populations infected with wild-type and recombinant Autographa californica nuclear polyhedrosis virus.}, journal = {Journal of biotechnology}, volume = {15}, number = {1-2}, pages = {169-185}, doi = {10.1016/0168-1656(90)90059-k}, pmid = {1367465}, issn = {0168-1656}, mesh = {Animals ; Baculoviridae/*genetics ; Cell Division ; Cell Line ; Cell Nucleus/metabolism ; Cell Survival ; DNA/*metabolism ; Flow Cytometry ; Fluorescent Dyes ; Lepidoptera/*genetics/metabolism/ultrastructure ; Mitochondria/metabolism ; Oxygen Consumption ; Rhodamine 123 ; Rhodamines/metabolism ; *Transfection ; beta-Galactosidase/biosynthesis/genetics ; }, abstract = {Spodoptera frugiperda cells were infected with a wild-type Autographa californica nuclear polyhedrosis virus and with a recombinant Autographa californica nuclear polyhedrosis virus. The recombinant virus was derived from the wild-type virus and produced beta-galactosidase instead of polyhedrin. The changes in cell size, cell growth, viability, DNA distribution, and respiratory activity were followed through the time course of the infection. The DNA content as measured by flow cytometry of infected cells increased to approximately 1.8 times the value of uninfected cells and the distributions of single-cell DNA content of the infected cells were strongly deformed. Early in the infection the respiratory activity passed through a maximum. The mitochondrial activity based on Rhodamine 123 labelling of cells infected with the recombinant virus, as determined by flow cytometry, also passed through a maximum at 24 h post infection while the mitochondrial activity of cells infected with the wild-type virus continued to increase. Evolution of single-cell mitochondrial activity was different in uninfected populations and in populations infected with wild-type and with recombinant virus. In all experiments performed, the recombinant virus influenced cell behavior and the measured parameters earlier than the wild-type virus. The influence of the multiplicity of infection was stronger for the wild-type virus than for the recombinant virus.}, }
@article {pmid2141652, year = {1990}, author = {Tuschen, G and Sackmann, U and Nehls, U and Haiker, H and Buse, G and Weiss, H}, title = {Assembly of NADH: ubiquinone reductase (complex I) in Neurospora mitochondria. Independent pathways of nuclear-encoded and mitochondrially encoded subunits.}, journal = {Journal of molecular biology}, volume = {213}, number = {4}, pages = {845-857}, doi = {10.1016/S0022-2836(05)80268-2}, pmid = {2141652}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Base Sequence ; Cell Nucleus/*enzymology ; Centrifugation, Density Gradient ; Chromatography, High Pressure Liquid ; DNA, Fungal/genetics ; DNA, Mitochondrial/genetics ; Genes, Fungal ; Kinetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Multienzyme Complexes/genetics/*metabolism ; NAD/*metabolism ; NAD(P)H Dehydrogenase (Quinone) ; Neurospora/*enzymology ; Neurospora crassa/*enzymology ; Precipitin Tests ; Protein Biosynthesis ; Quinone Reductases/genetics/*metabolism ; }, abstract = {NADH:ubiquinone reductase, the respiratory chain complex I of mitochondria, consists of some 25 nuclear-encoded and seven mitochondrially encoded subunits, and contains as redox groups one FMN, probably one internal ubiquinone and at least four iron-sulphur clusters. We are studying the assembly of the enzyme in Neurospora crassa. The flux of radioactivity in cells that were pulse-labelled with [35S]methionine was followed through immunoprecipitable assembly intermediates into the holoenzyme. Labelled polypeptides were observed to accumulate transiently in a Mr 350,000 intermediate complex. This complex contains all mitochondrially encoded subunits of the enzyme as well as subunits encoded in the nucleus that have no homologous counterparts in a small, merely nuclear-encoded form of the NADH:ubiquinone reductase made by Neurospora crassa cells poisoned with chloramphenicol. With regard to their subunit compositions, the assembly intermediate and small NADH:ubiquinone reductase complement each other almost perfectly to give the subunit composition of the large complex I. These results suggest that two pathways exist in the assembly of complex I that independently lead to the preassembly of two major parts, which subsequently join to form the complex. One preassembled part is related to the small form of NADH:ubiquinone reductase and contributes most of the nuclear-encoded subunits, FMN, three iron-sulphur clusters and the site for the internal ubiquinone. The other part is the assembly intermediate and contributes all mitochondrially encoded subunits, one iron-sulphur cluster and the catalytic site for the substrate ubiquinone. We discuss the results with regard to the evolution of the electron pathway through complex I.}, }
@article {pmid2363689, year = {1990}, author = {Takada, Y and Kaneko, N and Esumi, H and Purdue, PE and Danpure, CJ}, title = {Human peroxisomal L-alanine: glyoxylate aminotransferase. Evolutionary loss of a mitochondrial targeting signal by point mutation of the initiation codon.}, journal = {The Biochemical journal}, volume = {268}, number = {2}, pages = {517-520}, pmid = {2363689}, issn = {0264-6021}, mesh = {Alanine Transaminase/*genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; *Codon ; DNA, Mitochondrial/analysis ; DNA, Recombinant/analysis ; Humans ; Hyperoxaluria/enzymology/genetics ; Microbodies/*enzymology ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Mutation ; *RNA, Messenger ; Rats ; *Transaminases ; }, abstract = {The amino acid sequence of human hepatic peroxisomal L-alanine: glyoxylate aminotransferase 1 (AGTI) deduced from cDNA shows 78% sequence identity with that of rat mitochondrial AGTI, but lacks the N-terminal 22 amino acids (the putative mitochondrial targeting signal). In humans this signal appears to have been deleted during evolution by a point mutation of the initiation codon ATG to ATA. These data suggest that the targeting defect in primary hyperoxaluria type 1, in which AGT1 is diverted from the peroxisomes to the mitochondria, could be due to a point mutation that reintroduces all or part of the mitochondrial signal sequence.}, }
@article {pmid2258575, year = {1990}, author = {Costante, G and Crupi, D and Catalfamo, R and Trimarchi, F}, title = {Effects of active immunization against L-triiodothyronine on serum thyrotropin levels and liver mitochondrial alpha-glycerophosphate dehydrogenase activity in rats: evidence for reduced hormone disposal to cells.}, journal = {Journal of endocrinological investigation}, volume = {13}, number = {6}, pages = {469-474}, pmid = {2258575}, issn = {0391-4097}, mesh = {Animals ; Autoantibodies/*physiology ; Glycerolphosphate Dehydrogenase/*chemistry ; Male ; Mitochondria/metabolism ; Radioimmunoassay ; Rats ; Rats, Inbred Strains ; Thyrotropin/*blood ; Triiodothyronine/*immunology/metabolism ; Vaccination ; }, abstract = {Thyroid hormone binding autoantibodies have been observed in serum from patients affected by either thyroid disorders or autoimmune nonthyroid diseases. In most instances, no major involvement of thyroid status of these patients has been reported. However, some authors have attributed the occurrence of hypothyroidism to high capacity thyroid hormone binding autoantibodies. In order to verify such a hypothesis, the effect of these autoantibodies on serum TSH and liver mitochondrial alpha-glycerophosphate dehydrogenase has been investigated in rats, wherein circulating T3-binding antibodies (max cap 10(-12) 10(-8) to mol/l) were induced by active immunization. Starting from the 3rd week after antigen injection, the binding of 125I-T3 to serum immunoglobulins was progressively increased, with a peak at the 5th week. In immunized animals considered as a whole group, serum TSH levels were significantly higher and liver mitochondrial alpha-glycerophosphate dehydrogenase activity was significantly lower than in normal rats (m +/- SE: 145 +/- 15 vs 34 +/- 2 ng/dl and 0.0450 +/- 008 vs 0.0980 +/- 005 delta A. mg/prot/.min, respectively; p less than 0.001). The pattern of both TSH increase and alpha-glycerophosphate dehydrogenase decrease were similar to the evolution of 125-I-T3 binding to serum immunoglobulins, the maximal TSH values and lowest enzyme levels being observed at the 5th week after the beginning of the experiments.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid1695396, year = {1990}, author = {Benne, R}, title = {RNA editing in trypanosomes: is there a message?.}, journal = {Trends in genetics : TIG}, volume = {6}, number = {6}, pages = {177-181}, doi = {10.1016/0168-9525(90)90173-4}, pmid = {1695396}, issn = {0168-9525}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Mitochondria/metabolism ; Models, Genetic ; Molecular Sequence Data ; RNA/*genetics/metabolism ; RNA, Mitochondrial ; Transcription, Genetic ; Trypanosomatina/*genetics ; Uridine/genetics ; }, abstract = {The uridine sequence of mitochondrial transcripts of trypanosomes sometimes differs from the one predicted by the genome. The question is whether the RNA editing processes that generate these deviating U sequences operate within the principles of the 'central dogma' of molecular genetics. The answer is probably yes.}, }
@article {pmid1970818, year = {1990}, author = {Luis, AM and Alconada, A and Cuezva, JM}, title = {The alpha regulatory subunit of the mitochondrial F1-ATPase complex is a heat-shock protein. Identification of two highly conserved amino acid sequences among the alpha-subunits and molecular chaperones.}, journal = {The Journal of biological chemistry}, volume = {265}, number = {14}, pages = {7713-7716}, pmid = {1970818}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Biological Evolution ; Blotting, Western ; Chaperonins ; Drosophila/enzymology ; *Heat-Shock Proteins/biosynthesis ; Hot Temperature ; Larva/enzymology ; Macromolecular Substances ; Mitochondria/*enzymology ; Molecular Sequence Data ; *Proteins ; *Proton-Translocating ATPases/biosynthesis ; *Regulatory Sequences, Nucleic Acid ; Sequence Homology, Nucleic Acid ; }, abstract = {The recent identification of the alpha-subunit of mitochondrial F1-ATPase complex in rat liver peroxisomes suggests another functional role for this protein in both organelles in addition to its involvement in mitochondrial oxidative phosphorylation. We report here that a very rapid response (15 min) in the induction of the alpha-regulatory subunit of the mitochondrial F1-ATPase complex is observed in 37 degrees C heat-shocked larvae of Drosophila hydei. Under the same heat-shock treatment, a similar-fold induction for the heat-shock protein hsp-70 was less rapid (45 min). Although the amino acid sequence identities between the "chaperonine" and the alpha-subunit protein families are very low (less than 20%), two amino acid sequences, of 12 and 13 residues each, are found in the alpha-subunits of the F1-ATPase complex from various eukaryotes which show a highly conserved identity (over 50%) with amino acid sequences found in molecular chaperones. We suggest that the nuclear coded alpha-subunit belongs to the family of stress proteins hsp-60 and thus, that it could perform similar functional role(s) to those recently described for mitochondrial hsp-60 (Cheng, M. Y., Hartl, F. U., Martin, J., Pollock, R. A., Kalousek, F., Neupert, W., Hallberg, E. M., Hallberg, R. L., and Horwich, A. L. (1989) Nature 337, 620-625 and Ostermann, J., Horwich, A. L., Neupert, W., and Ultrich-Hartl, F. (1989) Nature 341, 125-130) in both the mitochondria and the peroxisomes. Furthermore, we suggest that the two conserved elements among the chaperonines and the alpha-subunits could putatively be involved in the chaperonine function of these proteins.}, }
@article {pmid2325659, year = {1990}, author = {Schuster, W and Hiesel, R and Wissinger, B and Brennicke, A}, title = {RNA editing in the cytochrome b locus of the higher plant Oenothera berteriana includes a U-to-C transition.}, journal = {Molecular and cellular biology}, volume = {10}, number = {5}, pages = {2428-2431}, pmid = {2325659}, issn = {0270-7306}, mesh = {Amino Acid Sequence ; Base Sequence ; Biological Evolution ; Cytochrome b Group/*genetics ; DNA/genetics ; DNA, Mitochondrial/*genetics ; Molecular Sequence Data ; Plants ; *RNA Processing, Post-Transcriptional ; }, abstract = {RNA editing in the cytochrome b locus of Oenothera berteriana mitochondria modified a number of cytidine nucleotides to uridines, mostly altering codon identities. One nucleotide alteration involved a reverse modification changing a genomic thymidine to a cytidine in the cDNA sequence. The enzymatic editing activity in higher-plant mitochondria thus appears to be able to catalyze the interconversion of pyrimidines in both directions at specific nucleotides in the mRNA template.}, }
@article {pmid2111858, year = {1990}, author = {Van de Peer, Y and Neefs, JM and De Wachter, R}, title = {Small ribosomal subunit RNA sequences, evolutionary relationships among different life forms, and mitochondrial origins.}, journal = {Journal of molecular evolution}, volume = {30}, number = {5}, pages = {463-476}, pmid = {2111858}, issn = {0022-2844}, mesh = {Algorithms ; Animals ; Bacteria/*genetics ; *Biological Evolution ; Brucella abortus/genetics ; Mitochondria/*analysis ; Mutation ; Nucleic Acid Conformation ; *RNA, Ribosomal/analysis ; Rana catesbeiana/*genetics ; Thermoplasma/genetics ; }, abstract = {A tree was constructed from a structurally conserved area in an alignment of 83 small ribosomal subunit sequences of eukaryotic, archaebacterial, eubacterial, plastidial, and mitochondrial origin. The algorithm involved computation and optimization of a dissimilarity matrix. According to the tree, only plant mitochondria belong to the eubacterial primary kingdom, whereas animal, fungal, algal, and ciliate mitochondria branch off from an internal node situated between the tree primary kingdoms. This result is at variance with a parsimony tree of similar size published by Cedergren et al. (J Mol Evol 28:98-112, 1988), which postulates the mitochondria to be monophyletic and to belong to the eubacterial primary kingdom. The discrepancy does not follow from the use of conflicting sequence alignments, hence it must be due to the use of different treeing algorithms. We tested our algorithm on a set of sequences resulting from a simulated evolution and found it capable of faithfully reconstructing a branching topology that involved very unequal evolutionary rates. The use of more limited or more extended areas of the complete sequence alignment, comprising only very conserved or also more variable portions of the small ribosomal subunit structure, does have some influence on the tree topology. In all cases, however, the nonplant mitochondria seem to branch off before the emergence of eubacteria, and the differences are limited to the branching pattern among different types of mitochondria.}, }
@article {pmid1691179, year = {1990}, author = {Kuiper, MT and Sabourin, JR and Lambowitz, AM}, title = {Identification of the reverse transcriptase encoded by the Mauriceville and Varkud mitochondrial plasmids of Neurospora.}, journal = {The Journal of biological chemistry}, volume = {265}, number = {12}, pages = {6936-6943}, pmid = {1691179}, issn = {0021-9258}, support = {CA24710/CA/NCI NIH HHS/United States ; GM37949/GM/NIGMS NIH HHS/United States ; }, mesh = {Cloning, Molecular ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Escherichia coli/genetics ; Mitochondria/*metabolism ; Molecular Weight ; Neurospora/enzymology/*genetics ; Neurospora crassa/enzymology/*genetics ; *Plasmids ; RNA-Directed DNA Polymerase/*genetics/isolation &amp; purification/metabolism ; Restriction Mapping ; Ribonucleoproteins/genetics/isolation &amp; purification ; Species Specificity ; }, abstract = {The Mauriceville and Varkud mitochondrial plasmids of Neurospora are closely related, closed-circular DNAs (3.6 and 3.7 kilobases, respectively) that have characteristics of mtDNA introns and retroid elements. The plasmids contain a single long open reading frame (710 amino acids), whose amino-terminal half has structural similarity to reverse transcriptases. Using antibodies against synthetic peptides and trpE fusion proteins, we detected an 81-kDa protein encoded by this open reading frame in mitochondrial preparations from the plasmid-containing strains. This 81-kDa protein cosegregates with reverse transcriptase activity in sexual crosses and comigrates with reverse transcriptase activity in sodium dodecyl sulfate-polyacrylamide gels, where it can be assayed after renaturation of the protein. In glycerol gradients under nondenaturing conditions, the reverse transcriptase activity sediments at approximately 145 kDa, close to the value expected for a dimer of the 81-kDa protein. The 81-kDa protein represents most of the 710-amino acid open reading frame, but may be missing some amino acids at the amino terminus. The regions upstream and downstream of the putative reverse transcriptase domain lack sequences characteristic of gag, protease, RNase H, or integrase domains found in other retroid elements. The plasmid-encoded 81-kDa protein seems to be a novel type of reverse transcriptase that may provide insight into the evolution of these enzymes.}, }
@article {pmid2199255, year = {1990}, author = {Doonan, S}, title = {Aspartate aminotransferases and malate dehydrogenases: patterns of evolution.}, journal = {Biochemical Society transactions}, volume = {18}, number = {2}, pages = {167-169}, doi = {10.1042/bst0180167}, pmid = {2199255}, issn = {0300-5127}, mesh = {Amino Acid Sequence ; Animals ; Aspartate Aminotransferases/*genetics ; *Biological Evolution ; Cytosol/enzymology ; Humans ; Isoenzymes/*genetics ; Malate Dehydrogenase/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Sequence Homology, Nucleic Acid ; }, }
@article {pmid2194239, year = {1990}, author = {Ishida, MR}, title = {[Evolutionary origin of the intracellular oligogenic system].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {35}, number = {5}, pages = {805-813}, pmid = {2194239}, issn = {0039-9450}, mesh = {Animals ; *Biological Evolution ; *Chloroplasts ; *DNA ; DNA, Mitochondrial ; Genomic Library ; *Mitochondria ; }, }
@article {pmid2166594, year = {1990}, author = {Kostetsky, P and Vladimirova, R}, title = {Identification of significant conservative and variable regions in homologous protein sequences.}, journal = {Biochimie}, volume = {72}, number = {4}, pages = {295-297}, doi = {10.1016/0300-9084(90)90087-w}, pmid = {2166594}, issn = {0300-9084}, mesh = {Amino Acid Sequence ; Animals ; Aspartate Aminotransferases/genetics ; *Genetic Variation ; Humans ; Mitochondria/analysis ; Phospholipases A/genetics ; *Phylogeny ; Proteins/*genetics ; Rats ; Sequence Homology, Nucleic Acid ; Snake Venoms/genetics ; Sodium-Potassium-Exchanging ATPase/genetics ; Swine ; }, abstract = {A set of aligned homologous protein sequences is divided into 2 groups consisting of m and n sequences. Each group contains sequences from the most related species. Value of the position variability of homologous proteins sequences is defined as a number of failures to coincide in comparison of all possible m.n pairs of amino acid residues (each from a different group) in that position divided by m.n. The variability value plotted vs the sequence position number with a window of 10 positions gives the intergroup variability profile (VP). Area of the figure included between the VP and its mean value line characterizes the overall irregularity of amino acid substitutions along the protein sequences. If the area value S is greater than the average area Sr for 1000 random VPs by more than 2 standard deviation units (sigma), the real VP extrema containing the surplus of area S-(Sr + 2 sigma) are cut off. The cut-off stretches are likely to be significant variable and conservative regions. Intergroup comparisons of protein sequences reveal high overall irregularity of amino acid substitutions and identify variable and conservative regions for all considered families of proteins: phospholipases A2, aspartate aminotransferases, alpha-subunits of Na+,K(+)-ATPase, L- and M-subunits of photosynthetic bacteria photoreaction centre, and human rhodopsins.}, }
@article {pmid2111847, year = {1990}, author = {Ohama, T and Osawa, S and Watanabe, K and Jukes, TH}, title = {Evolution of the mitochondrial genetic code. IV. AAA as an asparagine codon in some animal mitochondria.}, journal = {Journal of molecular evolution}, volume = {30}, number = {4}, pages = {329-332}, pmid = {2111847}, issn = {0022-2844}, mesh = {Animals ; Asparagine/*genetics ; Bacteria/genetics ; Base Sequence ; *Biological Evolution ; Codon/*genetics ; Echinodermata/genetics ; Fasciola hepatica/*genetics ; Genetic Code ; Humans ; Insecta/genetics ; Mammals/genetics ; *Mitochondria ; Molecular Sequence Data ; RNA, Messenger/*genetics ; RNA, Transfer, Lys/genetics ; }, abstract = {Differences in assignments from those in the universal genetic code occur in codes of mitochondria. In this report, the published sequences of the mitochondrial genes for COI and ND1 in a platyhelminth (Fasciola hepatica) are examined and it is concluded that AAA may be a codon for asparagine instead of lysine, whereas AAG is the sole codon for lysine in this species.}, }
@article {pmid2111846, year = {1990}, author = {Osawa, S and Collins, D and Ohama, T and Jukes, TH and Watanabe, K}, title = {Evolution of the mitochondrial genetic code. III. Reassignment of CUN codons from leucine to threonine during evolution of yeast mitochondria.}, journal = {Journal of molecular evolution}, volume = {30}, number = {4}, pages = {322-328}, pmid = {2111846}, issn = {0022-2844}, mesh = {Adenine/metabolism ; Base Composition ; Base Sequence ; *Biological Evolution ; Codon/*genetics ; Genetic Code ; Leucine/*genetics ; *Mitochondria ; Molecular Sequence Data ; RNA, Fungal/genetics ; RNA, Messenger/*genetics ; RNA, Transfer, Thr/genetics ; Threonine/*genetics ; Thymine/metabolism ; Yeasts/*genetics ; }, abstract = {Yeast mitochondria use UUR as the sole leucine codons. CUN, universal leucine codons, are read as threonine by aberrant threonine tRNA with anticodon sequence (UAG). The reassignment of CUN codons to threonine during yeast mitochondrial evolution could have proceeded by the disappearance of CUN codons from the reading frames of messenger RNA, through mutation mainly to UUR leucine codons as a result of AT pressure. We suggest that this was accompanied by a loss of leucine-accepting ability of tRNA Leu(UAG). This tRNA could have then acquired threonine-accepting activity through the appearance of an additional threonyl-tRNA synthetase. CUN codons that subsequently appeared from mutations of various other codons would have been translated as threonine. This change in the yeast mitochondrial genetic code is likely to have evolved through a series of nondisruptive nucleotide substitutions that produced no widespread replacement of leucine by threonine in proteins as a consequence.}, }
@article {pmid1692773, year = {1990}, author = {Wolff, G and Kück, U}, title = {The structural analysis of the mitochondrial SSUrRNA implies a close phylogenetic relationship between mitochondria from plants and from the heterotrophic alga Prototheca wickerhamii.}, journal = {Current genetics}, volume = {17}, number = {4}, pages = {347-351}, pmid = {1692773}, issn = {0172-8083}, mesh = {Base Sequence ; Chlamydomonas/genetics ; Genes ; Mitochondria/*analysis ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; Plants/genetics/ultrastructure ; Prototheca/*genetics/ultrastructure ; RNA/*genetics ; RNA, Mitochondrial ; RNA, Ribosomal/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {The gene for the mitochondrial small subunit rRNA (SSUrRNA) from the heterotrophic alga Prototheca wickerhamii has been isolated from a gene library of extranuclear DNA. Sequence and structural analyses allow the determination of a secondary structure model for this rRNA. In addition, several sequence motifs are present which are typically found in SSUrRNAs of various mitochondrial origins. Unexpectedly, the Prototheca RNA sequence has more features in common with mitochondrial SSUrRNAs from plants than with that from the green alga Chlamydomonas reinhardtii. The phylogenetic relationship between mitochondria from plants and algae is discussed.}, }
@article {pmid2314461, year = {1990}, author = {Baldauf, SL and Palmer, JD}, title = {Evolutionary transfer of the chloroplast tufA gene to the nucleus.}, journal = {Nature}, volume = {344}, number = {6263}, pages = {262-265}, doi = {10.1038/344262a0}, pmid = {2314461}, issn = {0028-0836}, mesh = {Amino Acid Sequence ; Base Sequence ; *Biological Evolution ; Cell Nucleus/*metabolism ; Chlorophyta/genetics ; Chloroplasts/*metabolism ; DNA/*genetics ; Molecular Sequence Data ; Neurospora/genetics ; Nucleic Acid Hybridization ; Peptide Elongation Factor Tu/*genetics ; Plants/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Evolutionary gene transfer is a basic corollary of the now widely accepted endosymbiotic theory, which proposes that mitochondria and chloroplasts originated from once free-living eubacteria. The small organellar chromosomes are remnants of larger bacterial genomes, with most endosymbiont genes having been either transferred to the nucleus soon after endosymbiosis or lost entirely, with some being functionally replaced by pre-existing nuclear genes. Several lines of evidence indicate that relocation of some organelle genes could have been more recent. These include the abundance of non-functional organelle sequences of recent origin in nuclear DNA, successful artificial transfer of functional organelle genes to the nucleus, and several examples of recently lost organelle genes, although none of these is known to have been replaced by a nuclear homologue that is clearly of organellar ancestry. We present gene sequence and molecular phylogenetic evidence for the transfer of the chloroplast tufA gene to the nucleus in the green algal ancestor of land plants.}, }
@article {pmid2158156, year = {1990}, author = {Klingenberg, M}, title = {Mechanism and evolution of the uncoupling protein of brown adipose tissue.}, journal = {Trends in biochemical sciences}, volume = {15}, number = {3}, pages = {108-112}, doi = {10.1016/0968-0004(90)90194-g}, pmid = {2158156}, issn = {0968-0004}, mesh = {Adipose Tissue, Brown/*metabolism ; Amino Acid Sequence ; Animals ; *Biological Evolution ; Carrier Proteins/classification/genetics/metabolism ; Hydroxides ; Ion Channels ; Membrane Proteins/classification/*genetics/metabolism ; Mitochondrial Proteins ; Molecular Sequence Data ; Protein Conformation ; Protons ; Uncoupling Protein 1 ; }, abstract = {The uncoupling protein found in mitochondria from thermogenic brown adipose tissue is structurally very similar to two other mitochondrial carrier proteins transporting ADP/ATP and phosphate, respectively. Similarities are also seen with the mechanism of these carriers, which are part of a family of H+/OH(-)-substrate anion co-transporters, further strengthening the evidence that the uncoupling protein has evolved from this family of mitochondrial carrier proteins.}, }
@article {pmid2406905, year = {1990}, author = {Hartl, FU and Neupert, W}, title = {Protein sorting to mitochondria: evolutionary conservations of folding and assembly.}, journal = {Science (New York, N.Y.)}, volume = {247}, number = {4945}, pages = {930-938}, doi = {10.1126/science.2406905}, pmid = {2406905}, issn = {0036-8075}, mesh = {Amino Acid Sequence ; *Biological Evolution ; Biological Transport, Active ; Cytosol/metabolism ; Heat-Shock Proteins/metabolism ; Intracellular Membranes/metabolism ; Mitochondria/*metabolism ; Models, Biological ; Molecular Sequence Data ; Peptide Hydrolases/metabolism ; Protein Conformation ; Protein Precursors/metabolism ; Proteins/*metabolism ; }, abstract = {According to the endosymbiont hypothesis, mitochondria have lost the autonomy of their prokaryotic ancestors. They have to import most of their proteins from the cytosol because the mitochondrial genome codes for only a small percentage of the polypeptides that reside in the organelle. Recent findings show that the sorting of proteins into the mitochondrial subcompartments and their folding and assembly follow principles already developed in prokaryotes. The components involved may have structural and functional equivalents in bacteria.}, }
@article {pmid2306101, year = {1990}, author = {Furbank, RT and Agostino, A and Hatch, MD}, title = {C4 acid decarboxylation and photosynthesis in bundle sheath cells of NAD-malic enzyme-type C4 plants: mechanism and the role of malate and orthophosphate.}, journal = {Archives of biochemistry and biophysics}, volume = {276}, number = {2}, pages = {374-381}, doi = {10.1016/0003-9861(90)90735-h}, pmid = {2306101}, issn = {0003-9861}, mesh = {Carboxylic Acids/*metabolism ; Cytosol/metabolism ; Kinetics ; Malate Dehydrogenase/*metabolism ; Malates/*metabolism/pharmacology ; Mitochondria/metabolism ; Models, Biological ; NAD/metabolism ; Phosphates/*metabolism ; *Photosynthesis ; Plant Cells ; Plants/enzymology/*metabolism ; Pyruvates/metabolism ; }, abstract = {The mechanism and possible regulation of C4 acid decarboxylation in NAD-malic enzyme-type C4 plants was studied using isolated bundle sheath cells and mitochondria from Panicum miliaceum. Rates of C4 acid-dependent photosynthetic O2 evolution equalled those observed with saturating NaHCO3; the rates ranged from 3 to 5 mumol min-1 (mg chlorophyll)-1. C4 acid-dependent O2 evolution required the addition of aspartate and 2-oxoglutarate (as a source of oxaloacetate) and also malate and orthophosphate. C4 acid decarboxylation by both isolated cells and mitochondria, measured as pyruvate production, also required all four of these components. The scheme previously proposed to account for aspartate decarboxylation in NAD-malic enzyme-type C4 plants does not envisage a role for externally derived malate. However, the mandatory requirement for malate (with orthophosphate), together with the observation that C4 acid decarboxylation is blocked by an inhibitor of the mitochondrial dicarboxylate transporter, suggests that a net flux of malate from outside the mitochondria is required to sustain this process. Arsenate was found to substitute for orthophosphate favoring a role for orthophosphate in malate transport rather than a metabolic one. The results are discussed in terms of likely mitochondrial metabolite transport mechanisms and regulation of the C4 acid decarboxylation process.}, }
@article {pmid2165819, year = {1990}, author = {Stuart, RA and Neupert, W}, title = {Apocytochrome c: an exceptional mitochondrial precursor protein using an exceptional import pathway.}, journal = {Biochimie}, volume = {72}, number = {2-3}, pages = {115-121}, doi = {10.1016/0300-9084(90)90136-5}, pmid = {2165819}, issn = {0300-9084}, mesh = {Apoproteins/*metabolism ; Cytochrome c Group/*metabolism ; Cytochromes c ; Cytochromes c1/metabolism ; Intracellular Membranes/metabolism ; Lyases/metabolism ; Mitochondria/*metabolism ; Protein Conformation ; Protein Precursors/*metabolism ; *Protein Processing, Post-Translational ; }, abstract = {The cytochrome c import pathway differs markedly from the general route taken by the majority of other imported proteins, which is characterized by the import involvement of namely, surface receptors, the general insertion protein (GIP), contact sites and by the requirement of a membrane potential (delta psi). Unique features of both the cytochrome c precursor (apocytochrome c) and of the mechanism that transports it into mitochondria, have contributed to the evolution of a distinct import pathway that is not shared by any other mitochondrial protein analysed thus far. The cytochrome c pathway is particularly unique because i) apocytochrome c appears to have spontaneous membrane insertion-activity; ii) cytochrome c heme lyase seems to act as a specific binding site in lieu of a surface receptor and; iii) covalent heme addition and the associated refolding of the polypeptide appears to provide the free energy for the translocation of the cytochrome c polypeptide across the outer mitochondrial membrane.}, }
@article {pmid2326162, year = {1990}, author = {Schuster, W and Unseld, M and Wissinger, B and Brennicke, A}, title = {Ribosomal protein S14 transcripts are edited in Oenothera mitochondria.}, journal = {Nucleic acids research}, volume = {18}, number = {2}, pages = {229-233}, pmid = {2326162}, issn = {0305-1048}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Mitochondrial/*genetics ; Genes, Plant ; Mitochondria/*metabolism ; Molecular Sequence Data ; Plants/*genetics ; Restriction Mapping ; Ribosomal Proteins/*genetics ; Sequence Homology, Nucleic Acid ; *Transcription, Genetic ; }, abstract = {The gene encoding ribosomal protein S14 (rps14) in Oenothera mitochondria is located upstream of the cytochrome b gene (cob). Sequence analysis of independently derived cDNA clones covering the entire rps14 coding region shows two nucleotides edited from the genomic DNA to the mRNA derived sequences by C to U modifications. A third editing event occurs four nucleotides upstream of the AUG initiation codon and improves a potential ribosome binding site. A CGG codon specifying arginine in a position conserved in evolution between chloroplasts and E. coli as a UGG tryptophan codon is not edited in any of the cDNAs analysed. An inverted repeat 3' of an unidentified open reading frame is located upstream of the rps14 gene. The inverted repeat sequence is highly conserved at analogous regions in other Oenothera mitochondrial loci.}, }
@article {pmid2335842, year = {1990}, author = {Melacini, P and Angelini, C and Buja, G and Micaglio, G and Valente, ML}, title = {Evolution of cardiac involvement in progressive ophthalmoplegia with deleted mitochondrial DNA.}, journal = {Japanese heart journal}, volume = {31}, number = {1}, pages = {115-120}, doi = {10.1536/ihj.31.115}, pmid = {2335842}, issn = {0021-4868}, support = {C.10/TI_/Telethon/Italy ; }, mesh = {Adult ; Blepharoptosis/complications ; Cardiomyopathy, Dilated/*metabolism/pathology ; DNA/*analysis ; Electrocardiography ; Female ; Heart Block/*metabolism/pathology/physiopathology ; Histocytochemistry ; Humans ; Mitochondria, Heart/*analysis ; Mitochondria, Muscle/analysis ; Myocardium/*pathology ; Ophthalmoplegia/*metabolism ; }, abstract = {A 43-year-old woman with progressive external ophthalmoplegia developed a bifascicular block and dilatation of the right ventricle during 4 years of follow-up. Histochemical and electron microscopy studies detected mitochondrial abnormalities in ocular, skeletal muscle and cardiac biopsies. This case registers disease progression from the external ocular to the skeletal and cardiac muscles. Mitochondrial DNA was deleted in relation to the morphological abnormality.}, }
@article {pmid2332418, year = {1990}, author = {Arakawa, H and Amaya, Y and Mori, M}, title = {The NH2-terminal 14-16 amino acids of mitochondrial and bacterial thiolases can direct mature ornithine carbamoyltransferase into mitochondria.}, journal = {Journal of biochemistry}, volume = {107}, number = {1}, pages = {160-164}, doi = {10.1093/oxfordjournals.jbchem.a123001}, pmid = {2332418}, issn = {0021-924X}, mesh = {Acetyl-CoA C-Acyltransferase/*metabolism ; Acyltransferases/*metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; Biological Transport/physiology ; Cells, Cultured ; DNA/genetics ; Microbodies/enzymology ; Mitochondria/*enzymology ; Ornithine Carbamoyltransferase/*metabolism ; Plasmids ; Rats ; Recombinant Fusion Proteins/metabolism ; Transfection ; Zoogloea/*enzymology/genetics ; }, abstract = {Unlike most mitochondrial matrix proteins, the mitochondrial 3-oxoacyl-CoA thiolase [EC 2.3.1.16] is synthesized with no cleavable presequence and possesses information for mitochondrial targeting and import in the mature protein. This mitochondrial thiolase is homologous with the mature portion of peroxisomal 3-oxoacyl-CoA thiolase and acetoacetyl-CoA thiolase [EC 2.3.1.9] of Zoogloea ramigera along the entire sequence. A hybrid gene encoding the NH2-terminal 16 residues (MALLRGVFIVAAKRTP) of the mitochondrial thiolase fused to the mature portion of rat ornithine carbamoyltransferase [EC 2.1.3.3] (lacking its own presequence) was transfected into COS cells, and subcellular localization of the fusion protein was analyzed. Cell fractionation and immunocytochemical analyses showed that the fusion protein was localized in the mitochondria. These results indicate that the NH2-terminal 16 residues of the mitochondrial thiolase function as a noncleavable signal for mitochondrial targeting and import of this enzyme protein. The fusion protein containing the NH2-terminal 14 residues (MSTPSIVIASARTA) of the bacterial thiolase was also localized in the mitochondria. On the other hand, the fusion protein containing the corresponding portion (MQASASDVVVVHGQRTP) of the peroxisomal thiolase appeared not to be localized to the mitochondria. These results show that the import signal of mitochondrial 3-oxoacyl-CoA thiolase originated from the NH2-terminal portion of the ancestral thiolase. The ancestral enzyme might have already possessed a mitochondrial import activity when mitochondria appeared first, or that it might have acquired the import activity during evolution by accumulation of point mutations in the NH2-terminal portion of the enzyme.}, }
@article {pmid2279193, year = {1990}, author = {Arquès, DG and Michel, CJ}, title = {A model of DNA sequence evolution.}, journal = {Bulletin of mathematical biology}, volume = {52}, number = {6}, pages = {741-772}, pmid = {2279193}, issn = {0092-8240}, mesh = {Base Sequence ; Biological Evolution ; DNA/*genetics ; Genetics, Population ; *Models, Genetic ; }, abstract = {Statistical studies of gene populations on the purine/pyrimidine alphabet have shown that the mean occurrence probability of the i-motif YRY(N)iYRY (R = purine, Y = pyrimidine, N = R or Y) is not uniform by varying i in the range, but presents a maximum at i = 6 in the following populations: protein coding genes of eukaryotes, prokaryotes, chloroplasts and mitochondria, and also viral introns, ribosomal RNA genes and transfer RNA genes (Arquès and Michel, 1987b, J. theor. Biol. 128, 457-461). From the "universality" of this observation, we suggested that the oligonucleotide YRY(N)6 is a primitive one and that it has a central function in DNA sequence evolution (Arquès and Michel, 1987b, J. theor. Biol. 128, 457-461). Following this idea, we introduce a concept of a model of DNA sequence evolution which will be validated according to a schema presented in three parts. In the first part, using the last version of the gene database, the YRY(N)6YRY preferential occurrence (maximum at i = 6) is confirmed for the populations mentioned above and is extended to some newly analysed populations: chloroplast introns, chloroplast 5' regions, mitochondrial 5' regions and small nuclear RNA genes. On the other hand, the YRY(N)6YRY preferential occurrence and periodicities are used in order to classify 18 gene populations. In the second part, we will demonstrate that several statistical features characterizing different gene populations (in particular the YRY(N)6YRY preferential occurrence and the periodicities) can be retrieved from a simple Markov model based on the mixing of the two oligonucleotides YRY(N)6 and YRY(N)3 and based on the percentages of RYR and YRY in the unspecified trinucleotides (N)3 of YRY(N)6 and YRY(N)3. Several properties are identified and prove in particular that the oligonucleotide mixing is an independent process and that several different features are functions of a unique parameter. In the third part, the return of the model to the reality shows a strong correlation between reality and simulation concerning the presence of a large alternating purine/pyrimidine stretches and of periodicities. It also contributes to a greater understanding of biological reality, e.g. the presence or the absence of large alternating purine/pyrimidine stretches can be explained as being a simple consequence of the mixing of two particular oligonucleotides. Finally, we believe that such an approach is the first step toward a unified model of DNA sequence evolution allowing the molecular understanding of both the origin of life and the actual biological reality.}, }
@article {pmid2266771, year = {1990}, author = {Grace, SC}, title = {Phylogenetic distribution of superoxide dismutase supports an endosymbiotic origin for chloroplasts and mitochondria.}, journal = {Life sciences}, volume = {47}, number = {21}, pages = {1875-1886}, doi = {10.1016/0024-3205(90)90399-c}, pmid = {2266771}, issn = {0024-3205}, mesh = {Animals ; Chloroplasts/*enzymology ; Isoenzymes/genetics/*physiology ; Mitochondria/*enzymology ; *Phylogeny ; Plants/enzymology ; Species Specificity ; Superoxide Dismutase/genetics/*physiology ; Symbiosis/genetics ; }, abstract = {Three isozymes of superoxide dismutase (SOD) have been identified and characterized. The iron and manganese isozymes (Fe-SOD and Mn-SOD, respectively) show extensive primary sequence and structural homology, suggesting a common evolutionary ancestor. In contrast, the copper/zinc isozyme (CuZn-SOD) shows no homology with Fe-SOD or Mn-SOD, suggesting an independent origin for this enzyme. The three isozymes are unequally distributed throughout the biological kingdoms and are located in different subcellular compartments. Obligate anaerobes and aerobic diazotrophs contain Fe-SOD exclusively. Facultative aerobes contain either Fe-SOD or Mn-SOD or both. Fe-SOD is found in the cytosol of cyanobacteria while the thylakoid membranes of these organisms contain a tightly bound Mn-SOD. Similarly, most eukaryotic algae contain Fe-SOD in the chloroplast stroma and Mn-SOD bound to the thylakoids. Most higher plants contain a cytosol-specific and a chloroplast-specific CuZn-SOD, and possibly a thylakoid-bound Mn-SOD as well. Plants also contain Mn-SOD in their mitochondria. Likewise, animals and fungi contain a cytosolic CuZn-SOD and a mitochondrial Mn-SOD. The Mn-SOD found in the mitochondria of eukaryotes shows strong homology to the prokaryotic form of the enzyme. Taken together, the phylogenetic distribution and subcellular localization of the SOD isozymes provide strong support for the hypothesis that the chloroplasts and mitochondria of eukaryotic cells arose from prokaryotic endosymbionts.}, }
@article {pmid2246114, year = {1990}, author = {Bereiter-Hahn, J}, title = {Behavior of mitochondria in the living cell.}, journal = {International review of cytology}, volume = {122}, number = {}, pages = {1-63}, doi = {10.1016/s0074-7696(08)61205-x}, pmid = {2246114}, issn = {0074-7696}, mesh = {Animals ; Cell Cycle ; Cell Nucleus/physiology ; Cytoskeleton/physiology ; Endoplasmic Reticulum/physiology ; Mitochondria/metabolism/*physiology/ultrastructure ; Phylogeny ; }, }
@article {pmid2238007, year = {1990}, author = {Billheimer, JT and Reinhart, MP}, title = {Intracellular trafficking of sterols.}, journal = {Sub-cellular biochemistry}, volume = {16}, number = {}, pages = {301-331}, doi = {10.1007/978-1-4899-1621-1_10}, pmid = {2238007}, issn = {0306-0225}, mesh = {Animals ; Biological Transport ; Carrier Proteins/metabolism ; Humans ; Organelles/metabolism ; Sterols/*metabolism ; Subcellular Fractions/*metabolism ; }, abstract = {Cavalier-Smith (1981) has identified 22 characters that are universally present in eukaryotes but absent in prokaryotes. Of these, he argues that one, exocytosis, might have been the driving force behind the evolution of modern eukaryotic cells. Bloom and Mouritsen (1988) further argue that sterols may have removed an evolutionary bottleneck to cytosis. Therefore, the advent of sterols in membranes might have been the single feature that led to eukaryote evolution. The evolutionary advantage conferred by cholesterol is associated primarily with plasma membrane function, since the majority of cellular free cholesterol resides in that membrane. However, sterol synthesis occurs in the ER; therefore, the cell must have a mechanism for transporting sterol to the plasma membrane and its regulation. As has been pointed out in this review, much remains to be elucidated in the study of intracellular sterol trafficking. To date, neither diffusion nor vesicle-mediated transport can be fully confirmed or ruled out. Microtubule and microfilament involvement appears important in some routes (e.g., mitochondria) but not in others. In addition, trafficking roles of cytoplasmic lipoproteinlike particles have not been addressed. Finally, although some "sterol carrier proteins" demonstrate the ability to mediate intervesicular transfer of cholesterol in vitro, the true physiological role of these proteins remains obscure. Future research in this field awaits the refinement of available techniques. Particularly valuable would be cytochemical methods for detection of sterol at the ultrastructural level. Possibly, direct microscopic visualization of radiolabeled components in cells represents the necessary approach. Purification of elements carrying newly synthesized sterols would allow the proteins mediating transport to be identified. Continued analysis of mutants defective in transport, such as in type C Niemann-Pick disease, will shed light on this complex problem. The importance of extracellular trafficking of cholesterol owing to its involvement in the progression of atherosclerosis, has been emphasized in recent years. Little emphasis has been placed on intracellular trafficking of sterol; however, it can be argued that such transport also plays a major role in atherosclerosis, possibly by fueling retrotransport of cholesterol to the liver and secretion in the bile. Therefore, we hope this review will serve to stimulate research interest in this area.}, }
@article {pmid2216410, year = {1990}, author = {Soto, MA and Toha, J}, title = {Phylogenetic tree of tRNAs using a simple algorithm.}, journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life}, volume = {20}, number = {2}, pages = {161-166}, pmid = {2216410}, issn = {0169-6149}, mesh = {*Algorithms ; Amino Acid Sequence ; Animals ; Base Sequence ; Chloroplasts ; Codon ; Escherichia coli/genetics ; Genetic Code ; Humans ; Mitochondria ; Molecular Sequence Data ; Phenylalanine/genetics ; Phylogeny ; Plants/genetics ; RNA, Transfer/*classification ; }, abstract = {A simple method for phylogenetic tree construction is described. In this method each node is calculated considering the distance between the elements and the difference between these elements and an average element, allowing the selection of the most probable node. Two examples of tRNA phylogenies (E. coli set and Phe family) are analyzed, giving both reliable trees. Data from these dendrograms give support to the idea of an early cloverleaf arising.}, }
@article {pmid2192617, year = {1990}, author = {Christen, P and Jaussi, R and Juretić, N and Mehta, PK and Hale, TI and Ziak, M}, title = {Evolutionary and biosynthetic aspects of aspartate aminotransferase isoenzymes and other aminotransferases.}, journal = {Annals of the New York Academy of Sciences}, volume = {585}, number = {}, pages = {331-338}, doi = {10.1111/j.1749-6632.1990.tb28065.x}, pmid = {2192617}, issn = {0077-8923}, mesh = {Animals ; Aspartate Aminotransferases/*biosynthesis/genetics ; *Biological Evolution ; Cytosol/enzymology ; Isoenzymes/*biosynthesis/genetics ; Mitochondria/enzymology ; Pyridoxine/pharmacology ; Transaminases/*biosynthesis ; }, abstract = {The mitochondrial and cytosolic isoenzymes of aspartate aminotransferase are homologous proteins. Both are encoded by nuclear DNA and synthesized on free polysomes. The organization of their genes is very similar, five out of a total of eight introns are located at the same nucleotide position. A variant consensus sequence was observed at the 3' splice site of introns of genes of imported mitochondrial proteins which may reflect the existence of splicing factors specific for the genes of this particular group of nuclear-encoded proteins. To date the amino acid sequences of 22 aminotransferases are known. A rigorous analysis yielded clear evidence that aspartate, tyrosine, and histidinol-phosphate aminotransferases are homologous proteins despite their low degree of sequence identity. The evolutionary relationship among the vitamin B6-dependent enzymes in general appears less clear. Conceivably, their common structural and mechanistic features are dictated by the chemical properties of pyridoxal 5'-phosphate rather than being due to a common ancestor of their protein moieties. In agreement with this notion, the ubiquitous active-site lysine residue that forms a Schiff base with the coenzyme can be replaced in the case of aspartate aminotransferase by a histidine residue without complete loss of catalytic competence.}, }
@article {pmid2156131, year = {1990}, author = {Saccone, C and Lanave, C and Pesole, G and Preparata, G}, title = {Influence of base composition on quantitative estimates of gene evolution.}, journal = {Methods in enzymology}, volume = {183}, number = {}, pages = {570-583}, doi = {10.1016/0076-6879(90)83037-a}, pmid = {2156131}, issn = {0076-6879}, mesh = {Animals ; *Base Composition ; *Biological Evolution ; Electron Transport Complex IV/genetics ; *Genes ; Humans ; Mitochondria/enzymology ; *Models, Genetic ; Models, Statistical ; Mutation ; Phylogeny ; Primates/genetics ; Pseudogenes ; Stochastic Processes ; }, }
@article {pmid2155710, year = {1990}, author = {Gualberto, JM and Domon, C and Weil, JH and Grienenberger, JM}, title = {Structure and transcription of the gene coding for subunit 3 of cytochrome oxidase in wheat mitochondria.}, journal = {Current genetics}, volume = {17}, number = {1}, pages = {41-47}, pmid = {2155710}, issn = {0172-8083}, mesh = {Amino Acid Sequence ; Base Sequence ; Biological Evolution ; Blotting, Northern ; Codon ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; Gene Rearrangement ; *Genes, Plant ; Molecular Sequence Data ; Sequence Homology, Nucleic Acid ; *Transcription, Genetic ; Triticum/enzymology/*genetics ; }, abstract = {The wheat mitochondrial (mt) cox3 has been localized and sequenced. The gene exists as a single copy in the wheat mt master chromosome and is transcribed into a single 1.2 kb RNA, whose extremities have been mapped. Comparison of the wheat and Oenothera cox3 sequences gives ambiguous indications concerning the amino acid coded by the codon CGG. Upstream and downstream of the wheat cox3 gene, two short sequences of 43 bp and 69 bp respectively are present, which are almost identical to sequences present in the flanking regions of other plant mitochondrial genes. These common sequences seem to have played a role in the rearrangements which caused sequence divergence of the plant mt genomes during evolution. Furthermore, mapping of wheat and maize cox3 and cob transcripts suggests that some of these common sequences can play a role in the regulation of transcription or processing.}, }
@article {pmid2085956, year = {1990}, author = {Eisenstein, RS and Miller, RH and Hoganson, G and Harper, AE}, title = {Phylogenetic comparisons of the branched-chain alpha-ketoacid dehydrogenase complex.}, journal = {Comparative biochemistry and physiology. B, Comparative biochemistry}, volume = {97}, number = {4}, pages = {719-726}, doi = {10.1016/0305-0491(90)90113-8}, pmid = {2085956}, issn = {0305-0491}, support = {AM-10748/AM/NIADDK NIH HHS/United States ; }, mesh = {3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide) ; Animals ; Antibodies/pharmacology ; Cattle ; Chickens ; Immunoblotting ; Ketone Oxidoreductases/antagonists &amp; inhibitors/immunology/*metabolism ; Kidney/enzymology ; Mitochondria/enzymology ; Mitochondria, Liver/enzymology ; Multienzyme Complexes/antagonists &amp; inhibitors/immunology/*metabolism ; Peptide Fragments/metabolism ; *Phylogeny ; Rats ; Rats, Inbred Strains ; Serine Endopeptidases/metabolism ; Sheep ; Species Specificity ; Trout ; }, abstract = {1. Antibodies against the E1b and E2b components of bovine branched-chain alpha-ketoacid (BCKA) dehydrogenase (BCKAD) complex completely inhibited BCKA oxidation in mammalian and avian mitochondria. BCKA oxidation by salmonid mitochondria was less affected and the enzyme from Pseudomonas putida was unaffected. 2. In rodents, anti-E1b E2b IgG inhibited oxidation of all three BCKA in a similar dose-dependent manner: oxidation of alpha-ketobutyrate and alpha-keto-y-methiolbutyrate was also partially inhibited. 3. Except for the salmonid BCKAD, a similar Mr for the E2b and E1b alpha proteins was observed in these species. 4. After digestion with V-8 protease similar immunoreactive peptides were observed for the human and rodent complex.}, }
@article {pmid1963305, year = {1990}, author = {García-Horsman, JA and Escamilla, E}, title = {Review article: structural and functional properties of cytochrome aa3 from bacteria.}, journal = {Boletin de estudios medicos y biologicos}, volume = {38}, number = {1-2}, pages = {29-40}, pmid = {1963305}, issn = {0067-9666}, mesh = {Bacteria/*enzymology ; *Bacterial Proteins/chemistry ; Biological Evolution ; Copper ; Electron Transport ; Electron Transport Complex IV/chemistry/*physiology ; Mitochondria/enzymology ; Molecular Structure ; Paracoccus denitrificans/enzymology ; Protons ; Structure-Activity Relationship ; }, abstract = {The aa3 oxidases from bacteria form a group of related enzymes that resemble the far more complex mitochondrial cytochrome c oxidase, both functionally and structurally. These enzymes catalyze electron transfer from ferrocytochrome c to oxygen to produce water. This transfer is coupled to proton translocation. Several oxidases of this type have been purified from cytoplasmic membranes of bacteria. This review summarizes the present knowledge on purified bacterial aa3 oxidases and correlates these findings with data available for the eukaryotic cytochrome c-oxidases.}, }
@article {pmid1688800, year = {1990}, author = {Leprat, P and Ratinaud, MH and Maftah, A and Petit, JM and Julien, R}, title = {Use of nonyl acridine orange and rhodamine 123 to follow biosynthesis and functional assembly of mitochondrial membrane during L1210 cell cycle.}, journal = {Experimental cell research}, volume = {186}, number = {1}, pages = {130-137}, doi = {10.1016/0014-4827(90)90219-z}, pmid = {1688800}, issn = {0014-4827}, mesh = {Acridine Orange/metabolism/pharmacokinetics ; Animals ; Carbonyl Cyanide m-Chlorophenyl Hydrazone/pharmacology ; Cell Cycle ; Cell Line ; DNA/metabolism ; Dinitrophenols/pharmacology ; Gramicidin/pharmacology ; Intracellular Membranes/*metabolism/physiology/ultrastructure ; Leukemia L1210/metabolism/*pathology/physiopathology ; Mice ; Mitochondria, Liver/metabolism/physiology/*ultrastructure ; Rhodamine 123 ; *Rhodamines/metabolism/pharmacokinetics ; *Xanthenes ; }, abstract = {Specific mitochondrial incorporation of 10 N-nonyl acridine orange (NAO) is demonstrated by subcellular fractionation of rat hepatocytes. Moreover, comparative studies with NAO and rhodamine 123 (Rh 123) prove that acridine orange-derivative uptake is independent of transmembrane mitochondrial potential, a property allowing its utilization for the assessment of mitochondrial membrane mass modifications under various physiological states. Using NAO and Rh 123, we have respectively followed the biosynthesis of mitochondrial membrane and its assembly under a functional state during the L1210 cell cycle. Their evolution occurs in two stages according to a well-defined sequential order. Mitochondrial biogenesis, as revealed by NAO incorporation, occurs essentially in the G1 phase (probably mitochondrion enlargement) but also starts in late S phase (probably mitochondrion division). The increased amount of functional mitochondrial membrane, monitored by Rh 123 uptake, is emphasized in late G1 (prerequisite to DNA synthesis) and during G2M phases (prerequisite to mitosis). This alternative succession of phases displays the existence of a time-lag between the biosynthesis of mitochondrial membrane and its functional organization. Such an analysis confirms the potential of the NAO probe to evaluate mitochondrial membrane mass changes in various biological fields.}, }
@article {pmid1688531, year = {1990}, author = {Schuster, W and Wissinger, B and Unseld, M and Brennicke, A}, title = {Transcripts of the NADH-dehydrogenase subunit 3 gene are differentially edited in Oenothera mitochondria.}, journal = {The EMBO journal}, volume = {9}, number = {1}, pages = {263-269}, pmid = {1688531}, issn = {0261-4189}, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; Cytochrome Reductases/*genetics ; DNA/genetics ; DNA, Mitochondrial/*genetics ; *Gene Expression Regulation ; Mitochondria/metabolism ; Molecular Sequence Data ; NADH Dehydrogenase/*genetics ; Plants/*genetics/ultrastructure ; RNA/*genetics ; RNA, Messenger/genetics ; Transcription, Genetic/*genetics ; Uridine ; }, abstract = {A number of cytosines are altered to be recognized as uridines in transcripts of the nad3 locus in mitochondria of the higher plant Oenothera. Such nucleotide modifications can be found at 16 different sites within the nad3 coding region. Most of these alterations in the mRNA sequence change codon identities to specify amino acids better conserved in evolution. Individual cDNA clones differ in their degree of editing at five nucleotide positions, three of which are silent, while two lead to codon alterations specifying different amino acids. None of the cDNA clones analysed is maximally edited at all possible sites, suggesting slow processing or lowered stringency of editing at these nucleotides. Differentially edited transcripts could be editing intermediates or could code for differing polypeptides. Two edited nucleotides in an open reading frame located upstream of nad3 change two amino acids in the deduced polypeptide. Part of the well-conserved ribosomal protein gene rps12 also encoded downstream of nad3 in other plants, is lost in Oenothera mitochondria by recombination events. The functional rps12 protein must be imported from the cytoplasm since the deleted sequences of this gene are not found in the Oenothera mitochondrial genome. The pseudogene sequence is not edited at any nucleotide position.}, }
@article {pmid2480644, year = {1989}, author = {Hiesel, R and Wissinger, B and Schuster, W and Brennicke, A}, title = {RNA editing in plant mitochondria.}, journal = {Science (New York, N.Y.)}, volume = {246}, number = {4937}, pages = {1632-1634}, doi = {10.1126/science.2480644}, pmid = {2480644}, issn = {0036-8075}, mesh = {Amino Acid Sequence ; Base Sequence ; Cloning, Molecular ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/*genetics ; *Genes, Plant ; Humans ; Mitochondria/*enzymology ; Molecular Sequence Data ; Plants/enzymology/*genetics ; RNA/*genetics ; RNA Processing, Post-Transcriptional ; RNA, Messenger/genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Comparative sequence analysis of genomic and complementary DNA clones from several mitochondrial genes in the higher plant Oenothera revealed nucleotide sequence divergences between the genomic and the messenger RNA-derived sequences. These sequence alterations could be most easily explained by specific post-transcriptional nucleotide modifications. Most of the nucleotide exchanges in coding regions lead to altered codons in the mRNA that specify amino acids better conserved in evolution than those encoded by the genomic DNA. Several instances show that the genomic arginine codon CGG is edited in the mRNA to the tryptophan codon TGG in amino acid positions that are highly conserved as tryptophan in the homologous proteins of other species. This editing suggests that the standard genetic code is used in plant mitochondria and resolves the frequent coincidence of CGG codons and tryptophan in different plant species. The apparently frequent and non-species-specific equivalency of CGG and TGG codons in particular suggests that RNA editing is a common feature of all higher plant mitochondria.}, }
@article {pmid2685000, year = {1989}, author = {Janser, JC and Pusel, J and Rodier, JF and Navarrete, E and Rodier, D}, title = {[Hürthle cell tumor of the thyroid gland. Analysis of a series of 33 cases].}, journal = {Journal de chirurgie}, volume = {126}, number = {11}, pages = {619-624}, pmid = {2685000}, issn = {0021-7697}, mesh = {Adenoma/mortality/*pathology/surgery ; Adolescent ; Adult ; Aged ; Female ; Follow-Up Studies ; Humans ; Lymph Node Excision ; Male ; Middle Aged ; Neoplasm Recurrence, Local ; Neoplasm Staging ; Survival Rate ; Thyroid Neoplasms/mortality/*pathology/surgery ; Thyroidectomy ; }, abstract = {Hurthle cell or oxyphil cell tumours of the thyroid, which consist of large cells with eosinophilic granular cytoplasm, rich in mitochondria, have given rise to much controversy in recent years. Difficulty in histological diagnosis (benign or malignant), unexpected evolution, and the possibility of very late recurrence and metastasis occurring in cases which were previously labelled benign, characterise these ambiguous tumours. Their malignant forms are most often classified with vesicular cancers of the thyroid. They differ from the latter by the frequent presence of lymphatic metastases, the lack of effect of I 131 on distant metastases and their poorer prognosis. The experience of the authors is based upon a series of 33 cases of Hurthle cell tumours of the thyroid treated surgically (27 benign, 6 malignant), with a mean age of 44 years for benign lesions and 50 years for cancers (range 17 to 69 years) showing a clear female predominance (66% of cases). They most often presented clinically as a cold thyroid nodule which tended to be larger in the case of cancers (5 out of 6 cases had a diameter of more than 5 cm). The limits of resection were most often dictated by the results of per-operative frozen section: total lobectomy + isthmectomy for benign tumours and total thyroidectomy if macroscopic or histological signs of malignancy were present (spread beyond the capsule, vascular invasion, lymphatic metastases), with cervical node clearance if N+. The 27 cases who underwent surgery for benign tumours have survived (1 single local recurrence after 7 years, without any malignant progression and a median survival of 7 years). No deaths have occurred among the 6 cases of malignant tumours (follow-up ranging from 1 to 9 years, median 5.4 years) but a present metastases. A study of the series published in the literature confirms the difficulty with diagnosis in terms of the benign or malignant nature of the tumours. It also stresses the justification for relatively aggressive surgery on the thyroid parenchyma and the need for a very long period of locoregional and general surveillance in order to assess the results of treatment. Survival rates for malignant forms range from 60 to 65% at 10 years and from 25 to 47% at 15 years.}, }
@article {pmid2806264, year = {1989}, author = {Minami-Ishii, N and Taketani, S and Osumi, T and Hashimoto, T}, title = {Molecular cloning and sequence analysis of the cDNA for rat mitochondrial enoyl-CoA hydratase. Structural and evolutionary relationships linked to the bifunctional enzyme of the peroxisomal beta-oxidation system.}, journal = {European journal of biochemistry}, volume = {185}, number = {1}, pages = {73-78}, doi = {10.1111/j.1432-1033.1989.tb15083.x}, pmid = {2806264}, issn = {0014-2956}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; *Cloning, Molecular ; DNA/*analysis ; Enoyl-CoA Hydratase/analysis/*genetics ; Hydro-Lyases/*genetics ; Microbodies/*enzymology ; Mitochondria/*enzymology ; Molecular Sequence Data ; Oxidation-Reduction ; Rats ; }, abstract = {To elucidate structural relationships between the mitochondrial and peroxisomal isozymes of beta-oxidation systems, cDNA of the mitochondrial enoyl-CoA hydratase was cloned and sequenced. The 1454-bp cDNA sequence contained a 870 bp of open reading frame, encoding a polypeptide of 290 amino acid residues. When compared with the amino-terminal sequence of the mature enzyme, the predicted sequence contained a 29-residue presequence at the amino terminus. This presequence had characteristics typical of a mitochondrial signal peptide. The primary structure of this enzyme showed significant similarity with the amino-terminal portion of sequence of the peroxisomal enoyl-CoA hydratase: 3-hydroxyacyl-CoA dehydrogenase bifunctional enzyme. The carboxy-terminal part of the latter enzyme has sequence similarity with mitochondrial 3-hydroxyacyl-CoA dehydrogenase [Ishii, N., Hijikata, M., Osumi, T. &amp; Hashimoto, T. (1987) J. Biol. Chem. 262, 8144-8150]. These findings suggest that the peroxisomal bifunctional enzyme has the hydratase and dehydrogenase functions on the amino- and carboxy-terminal sides, respectively. The mitochondrial beta-oxidation enzymes and the peroxisomal bifunctional enzyme may have common evolutionary origins.}, }
@article {pmid2684776, year = {1989}, author = {Michel, F and Umesono, K and Ozeki, H}, title = {Comparative and functional anatomy of group II catalytic introns--a review.}, journal = {Gene}, volume = {82}, number = {1}, pages = {5-30}, doi = {10.1016/0378-1119(89)90026-7}, pmid = {2684776}, issn = {0378-1119}, mesh = {Animals ; Base Sequence ; Chloroplasts/analysis ; DNA, Mitochondrial/genetics ; *Introns ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; Plants/*genetics ; RNA Precursors/genetics ; *RNA Splicing ; RNA, Catalytic ; RNA, Fungal/*genetics ; RNA, Ribosomal/*genetics ; }, abstract = {The 70 published sequences of group II introns from fungal and plant mitochondria and plant chloroplasts are analyzed for conservation of primary sequence, secondary structure and three-dimensional base pairings. Emphasis is put on structural elements with known or suspected functional significance with respect to self-splicing: the exon-binding and intron-binding sites, the bulging A residue involved in lariat formation, structural domain V and two isolated base pairs, one of them involving the last intron nucleotide and the other one, the first nt of the 3' exon. Separate sections are devoted to the 29 group II-like introns from Euglena chloroplasts and to the possible relationship of catalytic group II introns to nuclear premessenger introns. Alignments of all available sequences of group II introns are provided in the APPENDIX.}, }
@article {pmid2701260, year = {1989}, author = {Puzzolo, D}, title = {[Morphological adaptations of the eyes of vertebrates: retinal trophism and the response to environmental stimuli].}, journal = {Archivio italiano di anatomia e di embriologia. Italian journal of anatomy and embryology}, volume = {94}, number = {4}, pages = {317-378}, pmid = {2701260}, issn = {0004-0223}, mesh = {*Adaptation, Biological/radiation effects ; Animals ; Biological Evolution ; Environmental Exposure ; *Photic Stimulation ; Photoreceptor Cells/radiation effects/ultrastructure ; Retina/growth &amp; development/*ultrastructure ; Retinal Vessels/*anatomy &amp; histology/growth &amp; development ; Vertebrates/*anatomy &amp; histology/growth &amp; development ; }, abstract = {The results of many investigations on the morphology of the eyes of Vertebrates are proposed, comparing our personal data with the literature available on this argument. It is firstly taken into account the retinal nourishment: it takes place according to direct and indirect mechanisms (Scheme 1). The former (Scheme 2) consist of intraretinal blood vessels and are particularly rare among the Vertebrates; the latter are more numerous and can be classified as constant (choriocapillaris) (Schemes 3A, B), if they are present in all the species up today investigated, or unconstant [Müller cells increased in their number and size (Scheme 5A), papillary cone (Schemes 5B, 8B), membrana vascularis retinae (Schemes 6A, C), falciform process (Schemes 6B, 7A, B, 8B), pecten oculi (Schemes 8A, B)], if they can be demonstrated only in some species, even if belonging to different classes. Their structural and ultrastructural organization, likewise their embryological processes, are examined in detail. The effects of the cyclic changes of light and darkness during a 24 hrs period on the eyeball are then examined; quantitative and qualitative modifications of the mitochondria (Schemes 9A, B) and of the synaptic ribbons (Schemes 10A, B) in the outer plexiform layer, of the photosensitive disks of rods and cones, and of the secretory cells and of the excretory ducts of the Meibomian tarsal glands (Schemes 11A, B, 12A, B) are described. If the animals are exposed to prolonged darkness, no structural changes can be demonstrated; nevertheless, a dark environment can induce the differentiation of peculiar structural specializations, such as the retinal or choroidal tapetum lucidum (Schemes 13, 14, 15). On the contrary, the light, if prolonged or of high intensity, is able to induce irreversible lesions on the photoreceptors and on the pigment epithelium, according to similar mechanisms in all the animals up to now investigated (Scheme 16). In conclusion, it is confirmed the peculiar structural complexity of the eyeball in all the classes of Vertebrates, due to adaptation to the various environmental requests and developed either during the evolutionary processes or during the different steps of the life of a single animal.}, }
@article {pmid2693936, year = {1989}, author = {Matsushita, Y and Kitakawa, M and Isono, K}, title = {Cloning and analysis of the nuclear genes for two mitochondrial ribosomal proteins in yeast.}, journal = {Molecular &amp; general genetics : MGG}, volume = {219}, number = {1-2}, pages = {119-124}, pmid = {2693936}, issn = {0026-8925}, mesh = {Amino Acid Sequence ; Base Sequence ; Biological Evolution ; Blotting, Southern ; Cloning, Molecular ; Electrophoresis, Gel, Two-Dimensional ; Fungal Proteins/*genetics ; *Genes, Fungal ; Mitochondria ; Mitochondrial Proteins ; Molecular Sequence Data ; Restriction Mapping ; Ribosomal Proteins/*genetics ; Saccharomyces cerevisiae/*genetics ; *Saccharomyces cerevisiae Proteins ; }, abstract = {Two mitochondrial ribosomal proteins of yeast (Saccharomyces cerevisiae) were purified and their N-terminal amino acid sequences determined. The sequence data were used for the synthesis of oligonucleotide probes to clone the corresponding genes. Thus, the genes for two proteins, termed YMR-31 and YMR-44, were cloned and their nucleotide sequences determined. From the nucleotide sequence data, the coding region of the gene for protein YMR-31 was found to be composed of 369 nucleotide pairs. Comparison of the amino acid sequence of protein YMR-31 and the one deduced from the nucleotide sequence of its gene suggests that it contains an octapeptide leader sequence. The calculated molecular weight of protein YMR-31 without the leader sequence is 12,792 dalton. The gene for protein YMR-44 was found to contain a 147 bp intron which contains two sequences conserved among yeast introns. The length of the two exons flanking the intron totals 294 nucleotide pairs which can encode a protein with a calculated molecular weight of 11,476 dalton. The gene for protein YMR-31 is located on chromosome VI, while the gene for protein YMR-44 is located on either chromosome XIII or XVI.}, }
@article {pmid2571331, year = {1989}, author = {Gupta, RS and Picketts, DJ and Ahmad, S}, title = {A novel ubiquitous protein 'chaperonin' supports the endosymbiotic origin of mitochondrion and plant chloroplast.}, journal = {Biochemical and biophysical research communications}, volume = {163}, number = {2}, pages = {780-787}, doi = {10.1016/0006-291x(89)92290-0}, pmid = {2571331}, issn = {0006-291X}, mesh = {Amino Acid Sequence ; Animals ; Biological Evolution ; Cells, Cultured ; Chaperonins ; *Chloroplasts ; Coxiella ; Cricetinae ; Cricetulus ; Cyanobacteria ; Escherichia coli ; Humans ; *Mitochondria ; Molecular Sequence Data ; Mycobacterium ; *Plants ; *Proteins ; Saccharomyces cerevisiae ; }, abstract = {The deduced amino acid sequences for a major mitochondrial protein (designated P1, related to the 'chaperonin' family of proteins) from human and Chinese hamster cells show extensive similarity (greater than 60% identity observed over the entire length) with a related protein present in evolutionarily as divergent organisms as Escherichia coli, Coxiella burnetii, Mycobacterium species, cyanobacteria as well as in yeast mitochondria and higher plant chloroplasts. Of the different groups of bacteria for which sequence data is available, maximum similarity of the mammalian/yeast P1 protein is observed with the corresponding protein from purple bacteria (especially C. burnetii) while the protein from plant chloroplasts exhibited highest similarity with the corresponding protein from cyanobacteria. The sequence data for this protein thus support the contention that the endosymbiont that gave rise to mitochondrion was a member of purple bacteria, while plant chloroplast originated from a member of the cyanobacterial lineage.}, }
@article {pmid2686121, year = {1989}, author = {Gray, MW}, title = {The evolutionary origins of organelles.}, journal = {Trends in genetics : TIG}, volume = {5}, number = {9}, pages = {294-299}, doi = {10.1016/0168-9525(89)90111-x}, pmid = {2686121}, issn = {0168-9525}, mesh = {*Biological Evolution ; Chloroplasts ; DNA, Mitochondrial ; Mitochondria ; *Organelles ; RNA, Ribosomal/analysis ; Sequence Homology, Nucleic Acid ; }, abstract = {Analysis of organellar genomes strongly supports the idea that chloroplasts and mitochondria originated in evolution as eubacteria-like endosymbionts, whose closest contemporaries are cyanobacteria and purple photosynthetic bacteria, respectively. However, there is still much debate about whether a single endosymbiotic event or multiple ones gave rise to each organelle in different eukaryotes, and considerable uncertainty about what has happened to the genomes of chloroplasts and mitochondria since their appearance in the eukaryotic cell.}, }
@article {pmid2554073, year = {1989}, author = {Villa, RF and Gorini, A and Geroldi, D and Lo Faro, A and Dell'Orbo, C}, title = {Enzyme activities in perikaryal and synaptic mitochondrial fractions from rat hippocampus during development.}, journal = {Mechanisms of ageing and development}, volume = {49}, number = {3}, pages = {211-225}, doi = {10.1016/0047-6374(89)90072-9}, pmid = {2554073}, issn = {0047-6374}, mesh = {Age Factors ; Animals ; Citrate (si)-Synthase/metabolism ; Electron Transport Complex IV/metabolism ; Energy Metabolism ; Female ; Glutamate Dehydrogenase/metabolism ; Hippocampus/*enzymology/growth &amp; development ; In Vitro Techniques ; Malate Dehydrogenase/metabolism ; Mitochondria/*enzymology ; NADH Dehydrogenase/metabolism ; Rats ; Rats, Inbred Strains ; Synapses/enzymology ; }, abstract = {When pharmacological or basic neurochemical systematic characterization of mitochondrial enzymatic systems correlated to energy transduction processes is attempted, studies must be based on subcellular fractions with a high degree of purity from specific brain areas and from individual animals. Distinct populations of mitochondria heterogenous with respect to biochemical enzyme characteristics from rat brain hippocampus are described. Two mitochondrial populations were derived from synaptosomes by lysis and a third consists of free non-synaptic mitochondria. The maximum rate of some cerebral enzyme activities which are part of energy transduction (citrate synthase, malate dehydrogenase; total NADH-cytochrome c reductase, cytochrome oxidase) and amino acid metabolism (glutamate dehydrogenase) were tested on these mitochondrial populations of 8- and 16-week-old rats. A comprehensive analysis of the data suggests that extensive but highly diversified catalytic expressions of the enzymes studied occur in the hippocampus. This is true even when a short period of the rat life span is studied. Hence the varying pattern of evolution of the differing cerebral mitochondria, probably a consequence of different metabolic functions, should be taken into account in any pharmacological study on these systems.}, }
@article {pmid2506356, year = {1989}, author = {Osawa, S and Ohama, T and Jukes, TH and Watanabe, K}, title = {Evolution of the mitochondrial genetic code. I. Origin of AGR serine and stop codons in metazoan mitochondria.}, journal = {Journal of molecular evolution}, volume = {29}, number = {3}, pages = {202-207}, pmid = {2506356}, issn = {0022-2844}, mesh = {Animals ; Anticodon/genetics ; Arginine ; Base Sequence ; *Biological Evolution ; Codon/*genetics ; *Genetic Code ; Humans ; Invertebrates ; Mitochondria/*metabolism ; Molecular Sequence Data ; RNA, Messenger/*genetics ; RNA, Transfer/genetics ; *Serine ; Species Specificity ; Vertebrates ; }, abstract = {AGA and AGG (AGR) are arginine codons in the universal genetic code. These codons are read as serine or are used as stop codons in metazoan mitochondria. The arginine residues coded by AGR in yeast or Trypanosoma are coded by arginine CGN throughout metazoan mitochondria. AGR serine sites in metazoan mitochondria are occupied mainly in corresponding sites in yeast or Trypanosoma mitochondria by UCN serine, AGY serine, or codons for amino acids other than serine or arginine. Based on these observations, we propose the following evolutionary events. AGR codons became unassigned because of deletion of tRNA Arg (UCU) and elimination of AGR codons by conversion to CGN arginine codons. Upon acquisition by serine tRNA of pairing ability with AGR codons, some codons for amino acids other than arginine mutated to AGR, and were captured by anticodon GCU in serine tRNA. During vertebrate mitochondrial evolution, AGR stop codons presumably were created from UAG stop by deletion of the first nucleotide U and by use of R as the third nucleotide that had existed next to the ancestral UAG stop.}, }
@article {pmid2508761, year = {1989}, author = {}, title = {Bioenergetic systems, structure control and evolution. Autumn congress. (Sept. 28-30, 1988, Bombannes, France). Proceedings.}, journal = {Biochimie}, volume = {71}, number = {8}, pages = {877-979}, pmid = {2508761}, issn = {0300-9084}, mesh = {Animals ; Biological Transport ; *Energy Metabolism ; Mitochondria/*metabolism ; Yeasts/*metabolism ; }, }
@article {pmid2762145, year = {1989}, author = {Joyce, PB and Gray, MW}, title = {Chloroplast-like transfer RNA genes expressed in wheat mitochondria.}, journal = {Nucleic acids research}, volume = {17}, number = {14}, pages = {5461-5476}, pmid = {2762145}, issn = {0305-1048}, mesh = {Base Sequence ; Chloroplasts/metabolism ; Cloning, Molecular ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; *Genes ; Mitochondria/*metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Plants/*genetics/metabolism ; Plasmids ; RNA, Transfer/*genetics ; Triticum/genetics/metabolism ; }, abstract = {In the course of a systematic survey of wheat mitochondrial tRNA genes, we have sequenced chloroplast-like serine (trnS-GGA), phenylalanine (trnF-GAA) and cysteine (trnC-GCA) tRNA genes and their flanking regions. These genes are remnants of 'promiscuous' chloroplast DNA that has been incorporated into wheat mtDNA in the course of its evolution. Each gene differs by one or a few nucleotides from the authentic chloroplast homolog previously characterized in wheat or other plants, and each could potentially encode a functional tRNA whose secondary structure shows no deviations from the generalized model. To determine whether these chloroplast-like tRNA genes are actually expressed, wheat mitochondrial tRNAs were resolved by a series of polyacrylamide gel electrophoreses, after being specifically end-labeled in vitro by 3'-CCA addition mediated by wheat tRNA nucleotidyltransferase. Subsequent direct RNA sequence analysis identified prominent tRNA species corresponding to the mitochondrial and not the chloroplast trnS, trnF and trnC genes. This analysis also revealed chloroplast-like elongator methionine, asparagine and tryptophan tRNAs. Our results suggest that at least some chloroplast-like tRNA genes in wheat mtDNA are transcribed, with transcripts undergoing processing, post-transcriptional modification and 3'-CCA addition, to produce mature tRNAs that may participate in mitochondrial protein synthesis.}, }
@article {pmid2745441, year = {1989}, author = {May, BP and Dennis, PP}, title = {Evolution and regulation of the gene encoding superoxide dismutase from the archaebacterium Halobacterium cutirubrum.}, journal = {The Journal of biological chemistry}, volume = {264}, number = {21}, pages = {12253-12258}, pmid = {2745441}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Base Sequence ; *Biological Evolution ; Blotting, Southern ; DNA, Bacterial/genetics ; Enzyme Induction ; *Gene Expression Regulation ; *Genes ; *Genes, Bacterial ; *Genes, Regulator ; Halobacterium/enzymology/*genetics ; Molecular Sequence Data ; Paraquat/pharmacology ; RNA, Messenger/biosynthesis/drug effects ; Superoxide Dismutase/biosynthesis/*genetics ; Transcription, Genetic/drug effects ; }, abstract = {The gene encoding the manganese-containing superoxide dismutase (SOD) of Halobacterium cutirubrum was isolated and characterized. The gene and 5'- and 3'-untranslated regions were located on a genomic DNA fragment of 1127 nucleotides. The deduced amino acid sequence is 200 residues long and has 39-42% identity with manganese-containing SODs of eubacteria and mitochondria. This homology may be due to either lateral transfer of the gene between eubacteria and archaebacteria or to high amino acid sequence conservation in the enzyme during the separate evolution of eubacteria and archaebacteria. Transcription of the gene initiates only about three nucleotides upstream of the translation initiation codon. The 5' end of the transcript does not contain a purine-rich Shine-Dalgarno sequence, and the promoter region does not contain consensus sequences found in other archaebacterial promoters. Termination of transcription occurs at 5 consecutive thymine residues that are preceded by a GC-rich region. The gene is basally expressed in anaerobically grown cells but is also inducible by paraquat, a generator of oxygen radicals. The same transcription initiation site is used in both types of expression, suggesting that one promoter is responsible for both basal and regulated expression. In addition to the single copy of the authentic SOD gene, the genome of H. cutirubrum contains a sequence that is very closely related to but does not code for the previously purified SOD of this organism.}, }
@article {pmid2570428, year = {1989}, author = {Healy, JM}, title = {Spermatozoa of the deep-sea cephalopod Vampyroteuthis infernalis Chun: ultrastructure and possible phylogenetic significance.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {323}, number = {1219}, pages = {589-600}, doi = {10.1098/rstb.1989.0038}, pmid = {2570428}, issn = {0962-8436}, mesh = {Animals ; Male ; Microscopy, Electron ; Mollusca/*physiology ; Octopodiformes/physiology ; *Phylogeny ; Species Specificity ; Spermatogenesis ; Spermatozoa/*ultrastructure ; }, abstract = {Sperm ultrastructure in the rare deep-sea cephalopod Vampyroteuthis infernalis is described, based on formalin-fixed material held in the Australian Museum (Sydney). The species is the sole member of the coleoidean order Vampyromorpha, which represents a level of organization intermediate between that of the Sepioidea-Teuthoidea and the Octopoda. Spermatozoa of Vampyroteuthis, the simplest observed in any cephalopod, exhibit the following features: (1) a spheroidal acrosome lacking any complex substructure; (2) a short (8.5 microns) fusiform nucleus with a deep (2.2-2.5 microns) basal invagination (containing an extensive plug of dense material); (3) two triplet centrioles arranged parallel to the sperm longitudinal axis; (4) a short (1 micron) midpiece composed of a triangular cluster of mitochondria surrounding the centrioles; and (5) a tail (length 130-135 microns) that is continuous with one of the centrioles (here considered as a 'distal' centriole). An annulus and membranous skirt are absent, though the coarse fibres do fuse into a ring at the tail-midpiece junction). These cells show some resemblance to sperm or spermatids of sepioids and teuthoids (spheroidal acrosome, short nucleus) but are also remarkably similar to mid-spermatids of Octopus (with the exception of the uncondensed nucleus in Octopus spermatids). Sperm morphology supports the current assignment of Vampyroteuthis to a separate coleoidean order--Vampyromorpha--and also suggests that a close link exists between the Vampyromorpha and Octopoda.}, }
@article {pmid2549417, year = {1989}, author = {Vaidya, AB and Akella, R and Suplick, K}, title = {Sequences similar to genes for two mitochondrial proteins and portions of ribosomal RNA in tandemly arrayed 6-kilobase-pair DNA of a malarial parasite.}, journal = {Molecular and biochemical parasitology}, volume = {35}, number = {2}, pages = {97-107}, doi = {10.1016/0166-6851(89)90112-6}, pmid = {2549417}, issn = {0166-6851}, support = {R01 AI028398/AI/NIAID NIH HHS/United States ; RR07241-01/RR/NCRR NIH HHS/United States ; }, mesh = {Acyltransferases/*genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Cloning, Molecular ; Cytochrome b Group/*genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; Molecular Sequence Data ; Molecular Weight ; Nucleic Acid Conformation ; Peptidyl Transferases/*genetics ; Plasmodium yoelii/*genetics ; RNA, Ribosomal/*genetics ; *Repetitive Sequences, Nucleic Acid ; Restriction Mapping ; Sequence Homology, Nucleic Acid ; }, abstract = {Erythrocytic stages of mammalian malarial parasites contain acristate mitochondria whose functions are not well understood. Moreover, little is known about the genome of these organelles. We have previously reported that all species of malarial parasites examined contain highly conserved, tandemly arrayed DNA with a unit length of about 6.0 kb that is transcribed into discrete RNA molecules in erythrocytic stages. We now report the complete DNA sequence of the 5984-bp repeating unit of Plasmodium yoelii, a rodent parasite. Two slightly overlapping regions transcribed into large RNA molecules were found to have significant DNA and protein sequence similarity with mitochondrion-coded proteins, cytochrome c oxidase subunit I and cytochrome b. Significant sequence similarity with other mitochondrial protein genes could not be detected. Ribosomal RNA (rRNA)-like genes were not detected in this sequence either. However, two regions, 82 and 50 nucleotides long, specified by different strands, were found to have extensive similarity with the highly conserved central loop of the peptidyl transferase domain of the large rRNA of Escherichia coli, mitochondria, and chloroplasts. Compensatory nucleotide substitutions were present in these regions, so that the predicted secondary structure was not affected. Functional utilization of these regions, if it exists, could argue for a trans-associative origin of rRNA. In organization, size and sequence, the tandem arrays of 6.0 kb malarial DNA appear to be a very unusual form of mitochondrial DNA.}, }
@article {pmid2504926, year = {1989}, author = {Gadaleta, G and Pepe, G and De Candia, G and Quagliariello, C and Sbisà, E and Saccone, C}, title = {The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: cryptic signals revealed by comparative analysis between vertebrates.}, journal = {Journal of molecular evolution}, volume = {28}, number = {6}, pages = {497-516}, pmid = {2504926}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Codon ; DNA, Mitochondrial/*genetics ; Genes ; Genetic Code ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; Rats/*genetics ; Sequence Homology, Nucleic Acid ; Vertebrates/genetics ; }, abstract = {This paper reports the nucleotide sequence of rat mitochondrial DNA, only the fourth mammalian mitochondrial genome to be completely sequenced. Extensive comparative studies performed with similar genomes from other organisms revealed a number of interesting features. 1) Messenger RNA genes: the codon strategy is mainly dictated by the base compositional constraints of the corresponding codogenic DNA strand. The usage of the initiation and termination codons follows well-established rules. In general the canonical initiator, ATG, and terminators, TAA and TAG (in rat, only TAA), are always present when there is gene overlapping or when the mRNAs possess untranslated nucleotides at the 5' or 3' ends. 2) Transfer RNA genes: a number of features suggest the peculiar evolutionary behavior of this class of genes and confirm their role in the duplication and rearrangement processes that took place in the evolution of the animal mitochondrial genome. 3) Ribosomal RNA genes: accurate sequence analysis revealed a number of significant examples of complementarity between ribosomal and messenger RNAs. This suggests that they might play an important role in the regulation of mitochondrial translation and transcription mechanisms. The properties revealed by our work shed new light on the organization and evolution of the vertebrate mitochondrial genome and more importantly open up the way to clearly aimed experimental studies of the regulatory mechanisms in mitochondria.}, }
@article {pmid2543413, year = {1989}, author = {Suzuki, H and Hosokawa, Y and Toda, H and Nishikimi, M and Ozawa, T}, title = {Isolation of a single nuclear gene encoding human ubiquinone-binding protein in complex III of mitochondrial respiratory chain.}, journal = {Biochemical and biophysical research communications}, volume = {161}, number = {1}, pages = {371-378}, doi = {10.1016/0006-291x(89)91607-0}, pmid = {2543413}, issn = {0006-291X}, mesh = {Amino Acid Sequence ; Base Sequence ; Blotting, Southern ; Carrier Proteins/*genetics/isolation &amp; purification ; Cloning, Molecular ; Electron Transport Complex III/*metabolism ; *Genes ; Humans ; Mitochondria/*enzymology ; Molecular Sequence Data ; Nucleic Acid Hybridization ; Oxidative Phosphorylation ; Ubiquinone/*metabolism ; }, abstract = {We have isolated five genomic DNA clones which contain nucleotide sequences hybridizable to a cDNA for human ubiquinone-binding protein in Complex III (QP). Nucleotide sequence analysis revealed that two of them contained different types of pseudogenes suggesting molecular evolution of the gene, and that the other three clones contained the overlapping fragments from the same QP gene. The gene spans 4.5 to 5 kb in length. The sequences of exons in the gene were determined and found to be identical to the corresponding parts of the human QP cDNA. The exon-intron boundaries follow the GT/AG rule. Two CAAT boxes were found in the promoter region. It is concluded from these results that the isolated human QP gene is functional. Genomic Southern blot analysis showed that the gene is present in a single copy in the human genome.}, }
@article {pmid2670676, year = {1989}, author = {Pritchard, AE and Venuti, SE and Ghalambor, MA and Sable, CL and Cummings, DJ}, title = {An unusual region of Paramecium mitochondrial DNA containing chloroplast-like genes.}, journal = {Gene}, volume = {78}, number = {1}, pages = {121-134}, doi = {10.1016/0378-1119(89)90320-x}, pmid = {2670676}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Chlorophyll/genetics ; *Chloroplasts ; DNA, Mitochondrial/*genetics ; Light-Harvesting Protein Complexes ; Molecular Sequence Data ; Paramecium/*genetics ; Photosynthetic Reaction Center Complex Proteins ; Photosystem II Protein Complex ; Plant Proteins/genetics ; Restriction Mapping ; Ribosomal Proteins/genetics ; }, abstract = {Based on DNA and amino acid comparisons with known genes and their products, a region of the Paramecium aurelia mitochondrial (mt) genome has been found to encode the following gene products: (1) photosystem II protein G (psbG); (2) a large open reading frame (ORF400) which is also found encoded in the chloroplast (cp) DNA of tobacco (as ORF393) and liverwort (as ORF392), and in the kinetoplast maxicircle DNA of Leishmania tarentolae (as ORFs 3 and 4); (3) ribosomal protein L2 (rpl2); (4) ribosomal protein S12 (rps12); (5) ribosomal protein S14 (rps14); and (6) NADH dehydrogenase subunit 2 (ndh2). All of these genes have been found in cp DNA, but the psbG gene has never been identified in a mt genome, and ribosomal protein genes have never been located in an animal or protozoan mitochondrion. The ndh2 gene has been found in both mitochondria and plastids. The Paramecium genes are among the most divergent of those sequenced to date. Two of the genes are encoded on the strand of DNA complementary to that encoding all other known Paramecium mt genes. No gene contains an identifiable intron. The rps12 and psbG genes are probably overlapping. It is not yet known whether these genes are transcribed or have functional gene products. The presence of these genes in the mt genome raises interesting questions concerning their evolutionary origin.}, }
@article {pmid2675996, year = {1989}, author = {Jamieson, BG and Rouse, GW}, title = {The spermatozoa of the polychaeta (Annelida): an ultrastructural review.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {64}, number = {2}, pages = {93-157}, doi = {10.1111/j.1469-185x.1989.tb00673.x}, pmid = {2675996}, issn = {1464-7931}, mesh = {Acrosome/ultrastructure ; Animals ; Cell Nucleus/ultrastructure ; Fertilization ; Male ; Mitochondria/ultrastructure ; Polychaeta/*anatomy &amp; histology/physiology ; Spermatozoa/*ultrastructure ; }, abstract = {1. Polychaete sperm are divisible into ect-aquasperm, ent-aquasperm, and introsperm. 2. Ect-aquasperm are the commonest type of polychaete sperm and are considered plesiomorphic for the Polychaeta. Re-evolution of ect-aquasperm (as neo-aquasperm) is, nevertheless, tentatively hypothesized for some Sabellida. 3. In terms of ultrastructural studies of sperm in the investigated polychaete families, only ect-aquasperm have been demonstrated for 16 families; only ent-aquasperm for 3 families; ect- and ent-aquasperm for 3; ect- and intro-sperm for 2; ect-, ent- and intro-sperm for 1 family; and only introsperm for 11 families but investigations can only be regarded as preliminary. To date no family is known to have ent- and intro-sperm only. Sperm ultrastructure has yet to be examined in the orders Magelonida, Psammodrilida, Cossurida, Spintherida, Sternapsida, Flabelligerida and Fauvelopsida. 4. Much variation occurs in gross morphology, ultrastructure and configuration of the several components of ect-aquasperm: acrosome, nucleus, mitochondria, and centrioles and associated anchoring apparatus. A 9 + 2 axoneme is constant. 5. Group-specific sperm structure has been demonstrated for the Nereidae (chiefly ect-aquasperm), and for introsperm of the families Histriobdellidae, Questidae; Capitellidae, Spionidae and Protodrilidae. Species-specificity of all classes of spermatozoa is well established. 6. The very small size of ect-aquasperm is correlated with production of large numbers of sperm as an adaptation to broadcast spawning. Simplicity of structure may relate more to conservation of materials than to hydrodynamics. 7. Fertilization by ent-aquasperm requires fewer eggs than in external fertilization and is accompanied by a tendency to lecithotrophy. Elongation of the nucleus and development of asymmetry are seen in several of the few known examples of ent-aquasperm. Whether modifications are related to transfer or to other features, such as lecithotrophy, is uncertain. 8. Evident multiple origins of polychaete introsperm contraindicate their value in establishing relationship between families, in contrast with their utility in groups such as decapod crustacea. 9. At the intrafamilial level polychaete introsperm have taxonomic and phylogenetic value, as seen in the Spionidae, Capitellidae, and Histriobdellidae, and are distinctive of each of these and other families. 10. At higher taxonomic levels, the ultrastructure of the sperm of the oligochaetoid Questidae distinguishes this family from euclitellates, each class of which has its own distinctive subtype of the euclitellate introsperm. 11.(ABSTRACT TRUNCATED AT 400 WORDS)}, }
@article {pmid2667219, year = {1989}, author = {Schinkel, AH and Tabak, HF}, title = {Mitochondrial RNA polymerase: dual role in transcription and replication.}, journal = {Trends in genetics : TIG}, volume = {5}, number = {5}, pages = {149-154}, doi = {10.1016/0168-9525(89)90056-5}, pmid = {2667219}, issn = {0168-9525}, mesh = {Animals ; Biological Evolution ; *DNA Replication ; DNA, Mitochondrial/*biosynthesis/genetics ; DNA-Directed RNA Polymerases/*metabolism ; Humans ; Mitochondria/*enzymology ; Promoter Regions, Genetic ; *Transcription, Genetic ; }, abstract = {Mitochondrial RNA polymerases from humans, Xenopus laevis and Saccharomyces cerevisiae are very similar in protein composition and function. They consist of a nonspecific core RNA polymerase and a protein factor that confers promoter selectivity on the core component, and they participate in transcription as well as in DNA replication. Amino acid sequence comparisons indicate that the yeast mitochondrial core component is related to bacteriophage T3 and T7 RNA polymerases; mitochondrial and phage polymerases may therefore belong to a family of related polymerases.}, }
@article {pmid2499683, year = {1989}, author = {Osawa, S and Jukes, TH}, title = {Codon reassignment (codon capture) in evolution.}, journal = {Journal of molecular evolution}, volume = {28}, number = {4}, pages = {271-278}, pmid = {2499683}, issn = {0022-2844}, mesh = {Animals ; *Biological Evolution ; Codon/*genetics ; DNA, Mitochondrial/genetics ; Eukaryota/genetics ; Genetic Code ; Mutation ; Mycoplasma/genetics ; RNA, Messenger/*genetics ; }, abstract = {The genetic code, once thought to be "frozen," shows variations from the universal code. Variations are found in mitochondria, Mycoplasma, and ciliated protozoa. The variations result from reassignment of codons, especially stop codons. The reassignments take place by disappearance of a codon from coding sequences, followed by its reappearance in a new role. Simultaneously, a changed anticodon must appear. We discuss the role of directional mutation pressure in the events, and we also describe the possibility that such events have taken place during early evolution of the genetic code and can occur during its present evolution.}, }
@article {pmid2541251, year = {1989}, author = {Cozens, AL and Runswick, MJ and Walker, JE}, title = {DNA sequences of two expressed nuclear genes for human mitochondrial ADP/ATP translocase.}, journal = {Journal of molecular biology}, volume = {206}, number = {2}, pages = {261-280}, doi = {10.1016/0022-2836(89)90477-4}, pmid = {2541251}, issn = {0022-2836}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Cattle ; Cloning, Molecular ; DNA/*genetics ; Exons ; Gene Expression Regulation ; *Genes ; Humans ; Mitochondria/*enzymology ; Mitochondrial ADP, ATP Translocases/*genetics ; Molecular Sequence Data ; Nucleotidyltransferases/*genetics ; Repetitive Sequences, Nucleic Acid ; }, abstract = {Mitochondrial ADP/ATP translocase is an abundant component of the inner membrane. It carries ATP from the matrix into the intermembrane space and transports ADP back. Clones coding for two different but related forms of the protein have been characterized from bovine cDNA libraries. The corresponding genes are referred to as T1 and T2 and they are expressed at different levels in bovine tissues. The bovine cDNAs have been used to isolate clones from a human genomic library that contain the human T1 and T2 genes. Two nucleotide sequences of 9756 and 8625 base-pairs have been determined and they contain the transcribed regions of the human T1 and T2 genes which cover 4.2 and 5.9 kb of the human genome, respectively (1 kb = 10(3) base-pairs). Both genes are split into four exons. The introns in each gene are at exactly equivalent locations and interrupt sequences coding for segments of the protein that are thought to be extramembranous loops linking transmembrane segments. The proteins encoded in the genes differ in 32 amino acids out of 297, and in common with other ADP/ATP translocases, neither has a processed mitochondrial import sequence. The human T1 and T2 genes are members of a larger gene family that includes a third expressed gene T3 and also at least two spliced pseudogenes. Other studies have shown that T3 is expressed in liver and HeLa cells, and different levels of transcripts of T1 have been found in various tissues. A notable feature of the T1 and T2 genes, that may influence their expression, is that "CpG-rich islands" are associated with their 5' ends. That of the T2 gene contains numerous potential sites for binding the mammalian transcription factor SP1, but no TATA or CCAAT sequences are evident near to its 5' end, although these latter features are associated with the human T1 gene. The two DNA sequence also contain many short interspersed repetitive sequences including 11 Alu repeats, and a novel element about 236 base-pairs in length, which is repeated in a six-fold tandem array in intron B of the T2 gene.}, }
@article {pmid2469098, year = {1989}, author = {Doolittle, RF and Feng, DF and Johnson, MS and McClure, MA}, title = {Origins and evolutionary relationships of retroviruses.}, journal = {The Quarterly review of biology}, volume = {64}, number = {1}, pages = {1-30}, doi = {10.1086/416128}, pmid = {2469098}, issn = {0033-5770}, support = {GM-34434/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Deltaretrovirus/genetics ; HIV/genetics ; Humans ; Molecular Sequence Data ; Peptide Hydrolases/genetics ; Phylogeny ; RNA-Directed DNA Polymerase/genetics ; Retroviridae/*genetics ; }, abstract = {As is the case for some other RNA viruses, the amino acid sequences of retroviral proteins change at an astonishing rate. For example, the proteases of the human immunodeficiency virus (HIV) and the visna lentivirus with which it is often compared are as different as the proteases of fungi and mammals, and those of the human type I leukemia virus are as different from HIV or visna as are the proteins of humans and bacteria. That the sequences of retrovirus proteins can be recognized as sharing common ancestry with non-retroviral proteins implies that the vastly accelerated change has begun only recently or occurs very sporadically. Only a scheme whereby exogenous retroviruses exist as short-lived bursts upon a backdrop of germline-encoded endogenous viruses is consistent with the sequence data. Retroviruses are related to many other reverse transcriptase-bearing entities present in the genomes of eukaryotes. They also have proteins that are homologous with those of some plant and animal DNA viruses, and their reverse transcriptase is recognizably similar to sequences found in the introns of some fungal mitochondria. Computer alignment of all these sequences allows an overall phylogeny to be constructed that chronicles the history of events leading to infectious retroviruses.}, }
@article {pmid2465776, year = {1989}, author = {Benne, R}, title = {RNA-editing in trypanosome mitochondria.}, journal = {Biochimica et biophysica acta}, volume = {1007}, number = {2}, pages = {131-139}, doi = {10.1016/0167-4781(89)90031-6}, pmid = {2465776}, issn = {0006-3002}, mesh = {Animals ; Biological Evolution ; DNA, Mitochondrial/*physiology ; Mitochondria/*physiology ; Protein Biosynthesis ; RNA/*physiology ; *RNA Processing, Post-Transcriptional ; *Transcription, Genetic ; Trypanosoma/*genetics ; }, }
@article {pmid2536736, year = {1989}, author = {Kimura, T and Nakamura, K and Kajiura, H and Hattori, H and Nelson, N and Asahi, T}, title = {Correspondence of minor subunits of plant mitochondrial F1ATPase to F1F0ATPase subunits of other organisms.}, journal = {The Journal of biological chemistry}, volume = {264}, number = {6}, pages = {3183-3186}, pmid = {2536736}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/enzymology ; Chloroplasts/enzymology ; Chromatography, Gel ; Chromatography, High Pressure Liquid ; Electrophoresis, Polyacrylamide Gel ; Mitochondria/enzymology ; Molecular Sequence Data ; Molecular Weight ; Oligomycins/pharmacology ; Plants/*enzymology/ultrastructure ; *Proton-Translocating ATPases/isolation &amp; purification ; Sequence Homology, Nucleic Acid ; Vegetables ; Zea mays ; }, abstract = {In addition to two major alpha- and beta-subunits, the soluble oligomycin-insensitive F1ATPase purified from sweet potato root mitochondria contains four different minor subunits of gamma (Mr = 35,500), delta (Mr = 27,000), delta' (Mr = 23,000), and epsilon (Mr = 12,000) (Iwasaki, Y., and Asashi, T. (1983) Arch. Biochem. Biophys. 227, 164-173). Among these minor subunits, the delta-subunit specifically cross-reacted with an antibody against the delta-subunit of maize mitochondrial F1 which contains only three minor gamma-, delta- and epsilon-subunits like F1ATPases from other organisms, indicating that the delta'-subunit is an extra subunit of sweet potato F1 which is absent in the maize F1. All of the four minor subunits of sweet potato F1 were purified and their N-terminal amino acid sequences of 30-36 residues were determined. The N-terminal sequence of gamma-subunit was homologous to those of the gamma-subunits of bacterial F1 and mammalian mitochondrial F1. The N-terminal sequence of the delta-subunit was homologous to those of the delta-subunits of bacterial F1, chloroplast CF1, and oligomycin sensitivity conferring protein of bovine mitochondrial F1F0. A sequence homology was also observed between the sweet potato epsilon-subunit and the epsilon-subunit of bovine mitochondrial F1. The N-terminal sequence of the delta'-subunit did not show any significant sequence homology to known protein sequences. These subunit correspondences place plant mitochondrial F1 at an unique position in the evolution of F1ATPase.}, }
@article {pmid2742125, year = {1989}, author = {Thomas, SM and Jessup, W and Gebicki, JM and Dean, RT}, title = {A continuous-flow automated assay for iodometric estimation of hydroperoxides.}, journal = {Analytical biochemistry}, volume = {176}, number = {2}, pages = {353-359}, doi = {10.1016/0003-2697(89)90322-9}, pmid = {2742125}, issn = {0003-2697}, mesh = {Animals ; Humans ; Hydrogen Peroxide/*analysis ; Iodine/*analysis ; Kinetics ; Lipid Peroxides/analysis ; Lipoproteins, LDL/isolation &amp; purification ; Liposomes/isolation &amp; purification ; Mitochondria/analysis ; Oxidation-Reduction ; Phosphatidylcholines/isolation &amp; purification ; Rats ; Rats, Inbred Strains ; Solutions ; }, abstract = {An iodometric method for the analysis of hydroperoxides has been automated to allow analysis of aqueous biological samples (containing less than 20 mg/ml protein) and lipid hydroperoxide extracts. The evolution of triiodide ions is measured spectrophotometrically at 360 nm. Dependent on the type of sample, 30-60 samples can be analyzed per hour and the system allows detection of less than 100 pmol of peroxide. The assay is linear over a range of 100 pmol to 25 nmol. The sample volume used routinely was 80 microliters.}, }
@article {pmid2710162, year = {1989}, author = {Campbell, T and Rubin, N and Komuniecki, R}, title = {Succinate-dependent energy generation in Ascaris suum mitochondria.}, journal = {Molecular and biochemical parasitology}, volume = {33}, number = {1}, pages = {1-12}, doi = {10.1016/0166-6851(89)90036-4}, pmid = {2710162}, issn = {0166-6851}, support = {AI18427/AI/NIAID NIH HHS/United States ; }, mesh = {Adenine Nucleotides/metabolism ; Animals ; Ascaris/*metabolism ; *Energy Metabolism ; Ferricyanides/pharmacology ; Hydrogen Peroxide/pharmacology ; Malates/metabolism ; Mitochondria/*metabolism ; Models, Biological ; Phosphorylation ; Succinates/*metabolism ; Succinic Acid ; }, abstract = {Phosphorylation in isolated Ascaris suum mitochondria was much greater in the presence of malate than succinate, but, in the absence of added adenine nucleotides, incubations in succinate resulted in substantial elevations in intramitochondrial ATP levels. Succinate-dependent phosphorylation was stimulated aerobically and this stimulation was due almost entirely to a site I, rotenone-sensitive, phosphorylation. Increased substrate level phosphorylation, coupled to propionate formation, or additional sites of electron-transport associated ATP synthesis were not significant. Under aerobic conditions, 14CO2 evolution from 1,4-[14C]succinate was stimulated and NADH/NAD+ ratios were elevated, but the formation of [14C]propionate was unchanged. It appears that succinate was metabolized to pyruvate and acetate, and NADH, generated from the decarboxylations of malate and pyruvate, was the primary source of reducing power fueling electron-transport. The terminal oxidase and final electron-acceptor are still not clearly defined. However, ferricyanide, H2O2, and 100% oxygen all stimulated succinate-dependent phosphorylation. A possible role for cytochrome c peroxidase in A. suum mitochondrial metabolism is discussed.}, }
@article {pmid2707959, year = {1989}, author = {Casado, N and Rodriguez-Caabeiro, F}, title = {Ultrastructural study of in vitro larval development of Echinococcus granulosus protoscoleces.}, journal = {International journal for parasitology}, volume = {19}, number = {1}, pages = {21-28}, doi = {10.1016/0020-7519(89)90017-9}, pmid = {2707959}, issn = {0020-7519}, mesh = {Animals ; Echinococcus/*growth &amp; development/ultrastructure ; Larva/growth &amp; development/ultrastructure ; Microscopy, Electron ; }, abstract = {Through ultrastructural study of the morphological forms developed in vitro during protoscolex culture, we describe larval E. granulosus histogenesis. The transformation of the spined microtriches in the protoscolex into truncated microtriches that develop within the hydatid cyst is discussed. The paper also describes the mitochondria location change that occurs during the evolution; the mitochondria pass from the most internal area of the distal cytoplasm along the cytoplasmic extensions into the cytoplasm of tegumental cells. The ultrastructures of both the vesiculated protoscolex and the posterior bladder demonstrate that each state corresponds to the initial step on one of the two paths of in vitro vesicular development.}, }
@article {pmid2521486, year = {1989}, author = {Nelson, H and Mandiyan, S and Nelson, N}, title = {A conserved gene encoding the 57-kDa subunit of the yeast vacuolar H+-ATPase.}, journal = {The Journal of biological chemistry}, volume = {264}, number = {3}, pages = {1775-1778}, pmid = {2521486}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Fungal/analysis ; Molecular Sequence Data ; Proton-Translocating ATPases/*genetics ; Saccharomyces cerevisiae/*enzymology/genetics ; }, abstract = {The peripheral (catalytic) sector of vacuolar H+-ATPases contains five different polypeptides denoted as subunits A-E in order of decreasing molecular masses from 72 to 33 kDa. The gene encoding subunit B (57 kDa) of yeast vacuolar H+-ATPase was cloned on a 5-kilobase pair genomic DNA fragment and sequenced. Four open reading frames were identified in the sequenced DNA. One of them encodes a protein of 504 amino acids with a calculated Mr of 56,557. Hydropathy plot revealed no apparent transmembrane segments. Southern analysis demonstrated that a single gene encodes this polypeptide in the yeast genome. The amino acid sequence exhibits extensive identity with the homologous protein from the plant Arabidopsis (77%). This polypeptide also contains regions of homology with the alpha subunits of H+-ATPases from mitochondria, chloroplasts, and bacteria. However, less similarity was detected when it was compared with the beta subunits of those enzymes. The implication of these phenomena on the evolution of proton pumps is discussed.}, }
@article {pmid2538624, year = {1989}, author = {Lazowska, J and Claisse, M and Gargouri, A and Kotylak, Z and Spyridakis, A and Slonimski, PP}, title = {Protein encoded by the third intron of cytochrome b gene in Saccharomyces cerevisiae is an mRNA maturase. Analysis of mitochondrial mutants, RNA transcripts proteins and evolutionary relationships.}, journal = {Journal of molecular biology}, volume = {205}, number = {2}, pages = {275-289}, doi = {10.1016/0022-2836(89)90341-0}, pmid = {2538624}, issn = {0022-2836}, mesh = {Aspergillus nidulans ; Base Sequence ; Biological Evolution ; Cytochrome b Group/*genetics ; Endoribonucleases/*genetics ; Fungal Proteins/*genetics ; *Genes, Fungal ; *Introns ; Mitochondria ; Molecular Sequence Data ; Mutation ; Nucleotidyltransferases/*genetics ; Protein Biosynthesis ; RNA Splicing ; RNA, Fungal/*genetics ; Saccharomyces cerevisiae/genetics ; }, abstract = {We have established the nucleotide sequence of the wild-type and that of a trans-acting mutant located in the third (bi3) intron of the Saccharomyces cerevisiae mitochondrial cytochrome b gene. The intron, 1691 base-pairs long, has an open reading frame 1045 base-pairs long, in phase with the preceding exon and the mutation replaces the evolutionarily conserved Gly codon of the second consensus motif by an Asp codon and blocks the formation of mature cytochrome b mRNA. Splicing intermediates of 5300 and 3900 bases with unexcised bi3 intron and a characteristic novel polypeptide (p50), the size of which corresponds to the chimeric protein encoded by upstream exons and the bi3 intronic open reading frame (ORF), accumulate in this and other bi3 splicing-deficient mutants. We conclude that the protein encoded by the bi3 ORF is a specific mRNA maturase involved in the splicing of the cytochrome b mRNA. The open reading frame of the third intron is remarkably similar to that of the unique intron of the cytochrome b gene (cob A) of Aspergillus nidulans. Both are located in exactly the same position and possibly derive from a recent common ancestor by a horizontal transfer. We have established the nucleotide sequence of an exonic mutant located in the B3 exon. This missense mutation changes the Phe codon 151 into a Cys codon and leads to the absence of functional cytochrome b but does not affect splicing. Finally, we have studied the splicing pathway leading to the synthesis of cytochrome b mRNA by analysing, in a comprehensive manner, the 22 splicing intermediates of several mutants located in bi3.}, }
@article {pmid2536249, year = {1989}, author = {Hulbert, AJ and Else, PL}, title = {Evolution of mammalian endothermic metabolism: mitochondrial activity and cell composition.}, journal = {The American journal of physiology}, volume = {256}, number = {1 Pt 2}, pages = {R63-9}, doi = {10.1152/ajpregu.1989.256.1.R63}, pmid = {2536249}, issn = {0002-9513}, mesh = {Animals ; *Body Composition ; Electron Transport Complex IV/metabolism ; Fatty Acids/analysis ; Liver/analysis ; Lizards/*physiology ; Mitochondria/enzymology ; Oxygen Consumption ; Phospholipids/analysis ; Proteins/analysis ; Rats/*physiology ; }, abstract = {Body composition was measured and compared in Amphibolurus vitticeps and Rattus norvegicus (a reptile and a mammal with the same weight and body temperature). Homogenates were prepared from liver, kidney, brain, heart, lung, and skeletal (gastrocnemius) muscle, and mitochondria were isolated. Cytochrome oxidase activities of both tissue homogenates and isolated mitochondria were measured (at 37 degrees C) as was protein content. Phospholipids were extracted from liver and kidney, and the fatty acid composition was determined. The brain, liver, kidney, heart, and skeletal muscle were significantly larger in the mammal, whereas the skin, reproductive organs, lung, and digestive tract showed no significant difference in size. All mammalian tissues examined contained approximately 50% more protein and phospholipid than the respective reptilian tissue. Although the mammalian phospholipids contained significantly less total unsaturated fatty acids, these unsaturated fatty acids were significantly more polyunsaturated than in the reptilian tissues. Tissue cytochrome oxidase activity was significantly greater in mammals when expressed on a wet weight basis but not when expressed on a tissue protein basis. Mitochondrial cytochrome oxidase activity (on a protein basis) was the same in both species in liver, kidney, and brain, but in heart, lung, and skeletal muscle mammalian mitochondria were twice as active as reptilian mitochondria. The implications of these differences in tissue composition were discussed relative to the evolution of mammalian endothermy.}, }
@article {pmid2486157, year = {1989}, author = {Harman, D}, title = {Lipofuscin and ceroid formation: the cellular recycling system.}, journal = {Advances in experimental medicine and biology}, volume = {266}, number = {}, pages = {3-15}, doi = {10.1007/978-1-4899-5339-1_1}, pmid = {2486157}, issn = {0065-2598}, mesh = {Animals ; Cell Survival/physiology ; Ceroid/*biosynthesis ; Fluorescence ; Free Radicals ; Humans ; Lipofuscin/*biosynthesis ; Microscopy, Electron ; Oxidation-Reduction ; Proteins/metabolism ; }, abstract = {Lipofuscin, age pigment, is a dark pigment with a strong autofluorescence seen with increasing frequency with advancing age in the cytoplasm of postmitotic cells. By bright-field light microscopy lipofuscin appears as irregular yellow to brown granules ranging in size from 1-2 nm in diameter. The fluorescent spectra of lipofuscin in situ generally show excitation maxima at about 360 nm and a yellowish emission maxima at 540-650 nm. Ultrastructurally the granules, localized in residual body-type lysosomes, are extremely heterogeneous and vary from one cell type to another, and frequently within a single cell. The pigment granules usually contain numerous liquid droplets embedded in an electron-dense matrix. The granules stain positively for neutral lipids but are not soluble in polar or non-polar lipid solvents. Lipofuscin contains about 50 percent by weight of proteinaceous substances, a lesser fraction of lipid-like material, and probably less than one percent by weight fluorophore(s); it is enriched in metals such as Al, Cu, and Fe, and in dolichols. Free radical reactions and the proteolytic system are implicated in lipopigment formation. Thus the rate of lipopigment formation is increased by vitamin E deficiency and by increased intake of polyunsaturated fatty acids as well as by protease inhibitors such as leupeptin. Free radical reactions and proteolysis are involved in the continual turnover of cellular components. Cellular damage from free radical reactions, and others such as hydrolysis, has been present since the beginning of life. The evolution of more complex cells necessitated development of defenses - DNA repair processes, antioxidants, etc. - against damaging reactions as well as the removal and replacement of altered parts, and of those no longer needed by the cells. Proteins "marked" for disposal by oxidation damage, or other means such as conjugation with ubiquitin, are apparently rendered more hydrophobic so that they are "recognized" for degradation by the lysosomes and the proteinases and peptidases of the cytosol and mitochondria. Oxidatively altered lipids are removed by enzymes such as phospholipase A2. The products of the degradation processes are reused by the cells. Normally the recycling of damaged components works extremely well. There may be some slow slippage with advancing age as the rate of free radical damage increases while protease activity decreases. As a result a gradually increasing fraction of lysosomal "food" may be converted to non-digestible forms, lipofuscin, before it can be broken down to reusable components. Ceroid is apparently formed when the disposal system is "overloaded" or impaired.(ABSTRACT TRUNCATED AT 400 WORDS)}, }
@article {pmid2477069, year = {1989}, author = {Krasil'nikov, OV}, title = {[Proteins--channel formers. II. Porins and proteins of the external mitochondrial membranes].}, journal = {Nauchnye doklady vysshei shkoly. Biologicheskie nauki}, volume = {}, number = {7}, pages = {13-24}, pmid = {2477069}, issn = {0470-4606}, mesh = {Bacterial Outer Membrane Proteins/*metabolism ; Hydrogen-Ion Concentration ; Ion Channels/*metabolism ; Lipid Bilayers/metabolism ; Membrane Potentials ; Membrane Proteins/*metabolism ; Mitochondria/*metabolism ; Porins ; Protein Conformation ; }, abstract = {The physical and chemical properties in protein external membranes of gram-negative bacteria and mitochondria are considered. A possible evolutional affinity between these proteins is discussed. The data on peculiarities of their polypeptide chain structure depending on environmental parameters and chemical modification of ionogeneous groups of protein-channel formers as well on a possible structure of water pore in ion channels are presented.}, }
@article {pmid2907499, year = {1988}, author = {Bonen, L and Bird, S}, title = {Sequence analysis of the wheat mitochondrial atp6 gene reveals a fused upstream reading frame and markedly divergent N termini among plant ATP6 proteins.}, journal = {Gene}, volume = {73}, number = {1}, pages = {47-56}, doi = {10.1016/0378-1119(88)90311-3}, pmid = {2907499}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Base Sequence ; *Biological Evolution ; Blotting, Northern ; Blotting, Southern ; DNA, Mitochondrial/*genetics ; *Genes ; Macromolecular Substances ; Mitochondria/*enzymology ; Molecular Sequence Data ; Plants/enzymology/*genetics ; Proton-Translocating ATPases/*genetics ; Restriction Mapping ; Triticum/enzymology/genetics ; }, abstract = {The nucleotide sequence of the wheat mitochondrial gene for subunit 6 (atp6) of the F1F0 ATPase complex has been determined. Unlike bacterial, chloroplast or animal/fungal mitochondrial atp6 counterparts, which encode proteins of about 230-270 amino acids, the wheat mitochondrial atp6 homologue comprises the latter part of an open reading frame (ORF) of 386 codons. The ATP6 protein may therefore by synthesized with a long N-terminal presequence. This is supported by the finding that the ORF is preceded by a conserved sequence block closely related to ones preceding several other actively transcribed wheat mitochondrial protein-coding genes. The fused upstream ORF is similar in length, but unrelated in sequence, to those preceding the maize and tobacco mitochondrial atp6 genes. In wheat, the atp6 gene is located on a recombinationally active repeated DNA element, whose length of 1.4 kb corresponds approximately to that of the atp6 mRNA. A comparison of the wheat and maize ATP6 sequences reveals unexpectedly high divergence in the region corresponding to the mature N-terminal domain and may reflect mitochondrial DNA rearrangements during atp6 gene evolution in monocotyledonous plants.}, }
@article {pmid3242866, year = {1988}, author = {Boer, PH and Gray, MW}, title = {Transfer RNA genes and the genetic code in Chlamydomonas reinhardtii mitochondria.}, journal = {Current genetics}, volume = {14}, number = {6}, pages = {583-590}, pmid = {3242866}, issn = {0172-8083}, mesh = {Base Sequence ; Chlamydomonas/*genetics ; Codon/genetics ; DNA, Mitochondrial/genetics ; Genes ; *Genetic Code ; *Mitochondria ; Molecular Sequence Data ; Nucleic Acid Conformation ; Phylogeny ; RNA, Transfer/*genetics ; Restriction Mapping ; Transcription, Genetic ; }, abstract = {Only three tRNA genes are present within a sequenced 12.35 kbp region of the 15.8 kbp mtDNA of Chlamydomonas reinhardtii, a unicellular green alga. The corresponding tRNAs, whose anticodons are specific for TGG (Trp), CAA/G (Gln) and ATG (Met) codons, all display conventional secondary structures. The tRNA(Met) gene encodes an elongator rather than initiator species. The standard genetic code is used in C. reinhardtii mitochondria, but codon distribution is highly biased: in a collection of six identified protein coding genes, nine codons (including TGA) are not used at all, while four other sense codons occur very infrequently. In spite of the absence of certain codons, a minimum of 23 tRNAs (assuming separate initiator and elongator tRNAs(Met) are used) is needed to translate the C. reinhardtii mitochondrial genetic code. It appears unlikely that this minimal tRNA set is encoded by C. reinhardtii mtDNA.}, }
@article {pmid3238378, year = {1988}, author = {Kogaya, Y and Furuhashi, K}, title = {Comparison of the calcium distribution pattern among several kinds of hard tissue forming cells of some living vertebrates.}, journal = {Scanning microscopy}, volume = {2}, number = {4}, pages = {2029-2043}, pmid = {3238378}, issn = {0891-7035}, mesh = {Ameloblasts/*analysis/ultrastructure ; Amphibians ; Animals ; Antimony ; Calcium/*analysis ; Cartilage/analysis/*cytology/ultrastructure ; Fishes ; Microscopy, Electron/instrumentation/methods ; Odontoblasts/*analysis/ultrastructure ; Osteoblasts/*analysis/ultrastructure ; Phylogeny ; Rats ; Reptiles ; Spectrum Analysis/methods ; }, abstract = {We investigated the ultrastructural distribution of calcium in several kinds of hard tissue forming cells (secretory and maturation ameloblasts, odontoblasts osteoblasts, chondrocytes, and osteodentine forming cells) of mammals, amphibians, and fish by use of the potassium pyroantimonate technique. The calcium distribution pattern is compared among these cells, and its biological significance is discussed. Except for mammalian odontoblasts, all types of the hard tissue forming cells exhibited fundamentally the same distribution pattern of calcium; the antimonate reaction product was mainly localized on the inner face of the plasmalemma and inside mitochondria. On the other hand, in mammalian odontoblasts, the reaction product was found within secretory granules and in the intercellular spaces. Thus, the calcium distribution pattern in odontoblasts of lower vertebrates differed from that of mammalian odontoblasts and was similar to that of the osteoblasts or chondrocytes of the vertebrates examined. The differences in calcium distribution pattern among these hard tissue forming cells were not related to their origin, ectodermal or mesodermal (ectomesenchymal). We suggest on the basis of previous studies cited in this paper and of the present data that they are closely associated with the phylogeny and physiological system of Ca-ATPase.}, }
@article {pmid3148747, year = {1988}, author = {Cedergren, R and Gray, MW and Abel, Y and Sankoff, D}, title = {The evolutionary relationships among known life forms.}, journal = {Journal of molecular evolution}, volume = {28}, number = {1-2}, pages = {98-112}, pmid = {3148747}, issn = {0022-2844}, mesh = {Base Sequence ; *Biological Evolution ; DNA, Ribosomal/*genetics ; Information Systems ; Models, Genetic ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {Sequences of small subunit (SSU) and large subunit (LSU) ribosomal RNA genes from archaebacteria, eubacteria, and the nucleus, chloroplasts, and mitochondria of eukaryotes have been compared in order to identify the most conservative positions. Aligned sets of these positions for both SSU and LSU rRNA have been used to generate tree diagrams relating the source organisms/organelles. Branching patterns were evaluated using the statistical bootstrapping technique. The resulting SSU and LSU trees are remarkably congruent and show a high degree of similarity with those based on alternative data sets and/or generated by different techniques. In addition to providing insights into the evolution of prokaryotic and eukaryotic (nuclear) lineages, the analysis reported here provides, for the first time, an extensive phylogeny of the mitochondrial lineage.}, }
@article {pmid3060359, year = {1988}, author = {Schwob, E and Sanni, A and Fasiolo, F and Martin, RP}, title = {Purification of the yeast mitochondrial methionyl-tRNA synthetase. Common and distinctive features of the cytoplasmic and mitochondrial isoenzymes.}, journal = {European journal of biochemistry}, volume = {178}, number = {1}, pages = {235-242}, doi = {10.1111/j.1432-1033.1988.tb14448.x}, pmid = {3060359}, issn = {0014-2956}, mesh = {Acylation ; Amino Acyl-tRNA Synthetases/*isolation &amp; purification ; Antibodies/pharmacology ; Antibody Formation ; Binding Sites/drug effects ; Chromatography, Affinity ; Cytosol/*enzymology ; Electrophoresis, Polyacrylamide Gel ; Heparin ; Isoenzymes/isolation &amp; purification ; Kinetics ; Methionine-tRNA Ligase/antagonists &amp; inhibitors/immunology/*isolation &amp; purification ; Mitochondria/*enzymology ; Saccharomyces cerevisiae/*enzymology ; }, abstract = {Yeast-mitochondrial methionyl-tRNA synthetase was purified 1060-fold from mitochondrial matrix proteins of Saccharomyces cerevisiae using a four-step procedure based on affinity chromatography (heparin-Ultrogel, tRNA(Met)-Sepharose, Agarose-hexyl-AMP) to yield to a single polypeptide of high specific activity (1800 U/mg). Like the cytoplasmic methionyl-tRNA synthetase (Mr 85,000), the mitochondrial isoenzyme is a monomer, but of significantly smaller polypeptide size (Mr 65,000). In contrast, the corresponding enzyme of Escherichia coli is a dimer (Mr 152,000) made up of identical subunits. The measured affinity constants of the purified mitochondrial enzyme for methionine and tRNA(Met) are similar to those of the cytoplasmic isoenzyme. However, the two yeast enzymes exhibit clearly different patterns of aminoacylation of heterologous yeast and E. coli tRNA(Met). Furthermore, polyclonal antibodies raised against the two proteins did not show any cross-reactivity by inhibition of enzymatic activity and by the highly sensitive immunoblotting technique, indicating that the two enzymes share little, if any, common antigenic determinants. Taken together, our results further support the belief that the yeast mitochondrial and cytoplasmic methionyl-tRNA synthetases are different proteins coded for by two distinct nuclear genes. Like the yeast cytoplasmic aminoacyl-tRNA synthetases, the mitochondrial enzymes displayed affinity for immobilized heparin. This distinguishes them from the corresponding enzymes of E. coli. Such an unexpected property of the mitochondrial enzymes suggests that they have acquired during evolution a domain for binding to negatively charged cellular components.}, }
@article {pmid3210228, year = {1988}, author = {Howell, N and Gilbert, K}, title = {Mutational analysis of the mouse mitochondrial cytochrome b gene.}, journal = {Journal of molecular biology}, volume = {203}, number = {3}, pages = {607-618}, doi = {10.1016/0022-2836(88)90195-7}, pmid = {3210228}, issn = {0022-2836}, support = {GM33683/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Antimycin A/metabolism ; Base Sequence ; Binding Sites ; Biological Evolution ; Cell Line ; Cytochrome b Group/antagonists &amp; inhibitors/*genetics/metabolism ; *Genes ; Mice ; Mitochondria/*metabolism ; Models, Genetic ; Mutation ; Protein Conformation ; }, abstract = {The protonmotive cytochrome b protein of the mitochondrial bc1 respiratory chain complex contains two reactions centers, designated Qo and Qi, which can be distinguished by the effects of different inhibitors. The nucleotide sequences have been determined of the mitochondrial cytochrome b genes from a series of mouse cell mutants selected for increased inhibitor resistance. Each mutant contains a single nucleotide change which results in an amino acid substitution. When the proximity of the altered amino acid residues to the histidines involved in heme ligation is considered, the results support a model for cytochrome b folding in which there are eight transmembrane domains rather than the nine of the Widger-Saraste model. Replacement of the Gly38 residue by valine results in resistance to the Qi inhibitors antimycin A and funiculosin but not 2-n-heptyl-hydroxyquinoline-N-oxide. Based upon sequence comparisons of mitochondrial and bacterial cytochrome b and chloroplast b6 proteins, the region of the molecule involved in antimycin binding is as highly conserved as those domains involved in heme ligation. It is suggested that the antimycin binding domain of cytochrome b is involved in forming the Qi reaction center. Alterations of the Gly142 and Thr147 residues result in resistance to myxothiazol and stimatellin, respectively. While both inhibitors block the Qo reaction center, the two mutations do not confer cross-resistance to each other. This region of cytochrome b is the most highly conserved during evolution and these inhibitor binding sites probably occur within the protein domain constituting the Qo reaction center. In addition, there is a less conserved region of the protein, defined by the Leu294 residue, which may function in binding the hydrophobic portions of Qo inhibitors.}, }
@article {pmid3177634, year = {1988}, author = {Miller, RH and Harper, AE}, title = {Regulation of valine and alpha-ketoisocaproate metabolism in rat kidney mitochondria.}, journal = {The American journal of physiology}, volume = {255}, number = {4 Pt 1}, pages = {E475-81}, doi = {10.1152/ajpendo.1988.255.4.E475}, pmid = {3177634}, issn = {0002-9513}, support = {AM-10748/AM/NIADDK NIH HHS/United States ; }, mesh = {Animals ; Calcium/pharmacology ; Caproates/*metabolism ; Detergents/pharmacology ; Keto Acids/*metabolism ; Kidney/*metabolism ; Kinetics ; Male ; Mitochondria/drug effects/*metabolism ; Octoxynol ; Oxidation-Reduction ; Polyethylene Glycols/pharmacology ; Rats ; Valine/*metabolism ; }, abstract = {Activities of branched-chain amino acid (BCAA) aminotransferase (BCAT) and alpha-keto acid dehydrogenase (BCKD) were assayed in mitochondria isolated from kidneys of rats. Rates of transamination of valine and oxidation of keto acids alpha-ketoisocaproate (KIC) or alpha-ketoisovalerate (KIV) were estimated using radioactive tracers of the appropriate substrate from amounts of 14C-labeled products formed (14CO2 or [1-14C]-keto acid). Because of the high mitochondrial BCAT activity, an amino acceptor for BCAT, alpha-ketoglutarate (alpha-KG) or KIC, was added to the assay medium when valine was the substrate. Rates of valine transamination and subsequent oxidation of the KIV formed were determined with 0.5 mM alpha-KG as the amino acceptor; these rates were 5- to 50-fold those without added alpha-KG. Rates of CO2 evolution from valine also increased when KIC (0.01-0.10 mM) was present; however, with KIC concentrations above 0.2 mM, rates of CO2 evolution from valine declined although rates of transamination continued to rise. When 0.05 mM KIC was added to the assay medium, oxidation of KIC was suppressed by inclusion of valine or glutamate in the medium. When valine was present KIC was not oxidized preferentially, presumably because it was also serving as an amino acceptor for BCAT. These results indicate that as the supply of amino acceptor, alpha-KG or KIC, is increased in mitochondria not only is the rate of valine transamination stimulated but also the rate of oxidation of the KIV formed from valine.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid3049806, year = {1988}, author = {Van de Water, J and Fregeau, D and Davis, P and Ansari, A and Danner, D and Leung, P and Coppel, R and Gershwin, ME}, title = {Autoantibodies of primary biliary cirrhosis recognize dihydrolipoamide acetyltransferase and inhibit enzyme function.}, journal = {Journal of immunology (Baltimore, Md. : 1950)}, volume = {141}, number = {7}, pages = {2321-2324}, pmid = {3049806}, issn = {0022-1767}, support = {DK 39588/DK/NIDDK NIH HHS/United States ; }, mesh = {Autoantibodies/*immunology/physiology ; Autoantigens/immunology ; Autoimmune Diseases/blood/*enzymology/immunology ; Dihydrolipoamide Dehydrogenase/*antagonists &amp; inhibitors/immunology/isolation &amp; purification ; Humans ; Immunoblotting ; Immunosorbent Techniques ; Liver Cirrhosis, Biliary/blood/*enzymology/immunology ; }, abstract = {Autoantibodies against mitochondria occur in the sera of patients with primary biliary cirrhosis (PBC) with characteristic reactivity to an inner membrane protein of approximately 74 kDa. To precisely define these autoantigens, we recently cloned and sequenced a rat liver cDNA (pRMIT) that encodes for all of the epitopes recognized by Ig to the 74-kDa autoantigen. In the present study we have used this recombinant probe as a tool, in addition to purified enzymes, to demonstrate by immunoblotting that the 74-kDa mitochondrial autoantigen is dihydrolipoamide acetyltransferase (EC 2.3.1.12), the core protein of the pyruvate dehydrogenase complex. Furthermore, and of particular interest, inhibition of pyruvate dehydrogenase enzyme activity was demonstrated after incubation with sera from patients with PBC but not from normal volunteers or patients with chronic active hepatitis. Such inhibition was abrogated by absorption of the PBC sera with an expressing subclone of pRMIT, designated pRMIT-603. Identification of dihydrolipoamide acetyltransferase as the target of autoimmunity in PBC provides a reagent that can be used to determine mechanisms by which this molecule is recognized. It will allow study of whether autoimmune reactivity, at the humoral or T cell level, is the basis for the pathogenesis of PBC. Additionally, such data present evidence of functional inhibition of a critical metabolic enzyme. Dihydrolipoamide acetyltransferase is well-known to mitochondrial biochemistry and, similar to identified autoantigens in other autoimmune diseases, is highly conserved in evolution.}, }
@article {pmid2978296, year = {1988}, author = {Amann, R and Ludwig, W and Schleifer, KH}, title = {Beta-subunit of ATP-synthase: a useful marker for studying the phylogenetic relationship of eubacteria.}, journal = {Journal of general microbiology}, volume = {134}, number = {10}, pages = {2815-2821}, doi = {10.1099/00221287-134-10-2815}, pmid = {2978296}, issn = {0022-1287}, mesh = {Adenosine Triphosphatases/*genetics ; Amino Acid Sequence ; Bacteroides fragilis/*genetics ; Base Sequence ; Cytophaga/*genetics ; Flavobacterium/*genetics ; *Genes, Bacterial ; Molecular Sequence Data ; Phylogeny ; }, abstract = {The genes encoding the beta-subunits of ATP-synthases (ATPases) from Bacteroides fragilis DSM 2151, Cytophaga lytica DSM 2039 and 'Taxeobacter ocellatus' were cloned. The nucleotide sequences were determined completely for the genes of the first two organisms and to a major part for that of 'T. ocellatus'. The predicted amino acid sequences were compared with previously published amino acid sequences of beta-subunits. Two characteristic insertions were found in genes from organisms belonging to the so-called bacteroides-cytophaga-flavo-bacterium group. The remaining structure shows a high degree of sequence similarity within this group. These data support the conclusions drawn from comparative 16S rRNA sequence analyses that organisms in this phenotypically heterogeneous group are phylogenetically related. A phylogenetic tree was constructed based on a distance matrix of optimally aligned amino acid sequences of beta-subunits of ATPases of various eubacteria, chloroplasts and mitochondria. It is in good agreement with a tree derived from 16S rRNA sequence analyses.}, }
@article {pmid2843508, year = {1988}, author = {Bibus, CR and Lemire, BD and Suda, K and Schatz, G}, title = {Mutations restoring import of a yeast mitochondrial protein with a nonfunctional presequence.}, journal = {The Journal of biological chemistry}, volume = {263}, number = {26}, pages = {13097-13102}, pmid = {2843508}, issn = {0021-9258}, support = {CBY-1 1 R01 GM37803-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; DNA, Fungal/analysis ; Electron Transport Complex IV/metabolism ; Fungal Proteins/*genetics ; Mitochondria/*analysis ; Molecular Sequence Data ; Mutation ; Plasmids ; Saccharomyces cerevisiae/*ultrastructure ; }, abstract = {An internal deletion in the presequence of the precursor to yeast cytochrome oxidase subunit IV blocks import of the protein into mitochondria. We have identified two mechanisms by which yeast cells can suppress the defect of the plasmid-borne defective gene. One mechanism creates a new functional presequence by point mutations, or local DNA rearrangements, within the open reading frame or its 5'-untranslated region. The second mechanism compensates for the defective presequence by recessive mutations in single nuclear genes. The plasmid-linked mutations may mimic the mechanism(s) by which mitochondrial presequences arose during evolution whereas the chromosomal mutations may help to identify components of the mitochondrial import machinery.}, }
@article {pmid2976939, year = {1988}, author = {Mullenbach, GT and Tabrizi, A and Irvine, BD and Bell, GI and Tainer, JA and Hallewell, RA}, title = {Selenocysteine's mechanism of incorporation and evolution revealed in cDNAs of three glutathione peroxidases.}, journal = {Protein engineering}, volume = {2}, number = {3}, pages = {239-246}, doi = {10.1093/protein/2.3.239}, pmid = {2976939}, issn = {0269-2139}, mesh = {Animals ; Base Sequence ; Cattle ; Cysteine/*analogs &amp; derivatives/metabolism ; DNA/*metabolism ; Glutathione Peroxidase/*metabolism ; Humans ; Mice ; Molecular Sequence Data ; Molecular Structure ; Selenium/*metabolism ; Selenocysteine ; }, abstract = {The nonsense codon, UGA, has for the first time recently been shown to encode selenocysteine in two proteins, mouse glutathione peroxidase (GSH-Px) (EC 1.11.1.9) and bacterial formate dehydrogenase. A co-translational rather than post-translational selenium-incorporation mechanism has been implicated. Furthermore, high expression levels of GSH-Px have suggested that suppression of termination is efficient and specific. We have isolated and characterized pituitary, kidney and placenta cDNAs for bovine, human and mouse GSH-Px respectively. It is demonstrated that this novel suppression event occurs in diverse tissues, in at least three mammalian species and at the translational step. Surprisingly, GSH-Px is shown to be extramitochondrially encoded, indicating a cytosolic suppression event rather than one utilizing the mitochondria's well-documented extended codon-reading ability. Sequence analysis reveals that a simple proximal contextual pattern responsible for readthrough does not exist. Analysis of predicted secondary structures of mRNAs, however, has revealed a conformation which may be unique to selenocysteine proteins and may prove useful as a tool for artificial incorporation of selenocysteines. A human intron for GSH-Px from an unspliced mRNA has been isolated whose position indicates an ancient, divergent evolutionary relationship with thioredoxin-S2, rather than an independent convergent one.}, }
@article {pmid3225475, year = {1988}, author = {Hrudka, F}, title = {Nodulous corpuscles and mitochondrial inclusions in Sertoli cells of deer hybrids.}, journal = {Journal of ultrastructure and molecular structure research}, volume = {100}, number = {2}, pages = {107-117}, doi = {10.1016/0889-1605(88)90018-3}, pmid = {3225475}, issn = {0889-1605}, mesh = {Animals ; Cytoplasmic Granules/*ultrastructure ; Deer/*anatomy &amp; histology ; Endoplasmic Reticulum/*ultrastructure ; Male ; Microscopy, Electron ; Mitochondria/*ultrastructure ; Sertoli Cells/*ultrastructure ; }, abstract = {Unusual transformations of endoplasmic reticulum and mitochondria were identified in the Sertoli cells of deer hybrids. A portion of the mitochondrial population was converted from the common, flexible mitochondrial form into stiff rods, with an increased volume of the matrix and relative paucity of cristae. The matrix displayed arrays of tubuloid elements or percursors at various stages of assembly. The second and more conspicuous adaptation concerned the agranular endoplasmic reticulum, which frequently transformed into oval or elongate, often interconnected bodies. These bodies consisted of a dozen or more concentrically arranged fenestrated cisternae and a variable amount of glycogen in between. An integral and distinctive feature of the cisternous bodies was nodes, together constituting the so-called nodulous corpuscles (NC). The nodes appeared as a dense meshwork or lattice, which has the potential to generate a new set of cisternae and NC that interconnect into a chain or tridimensional complex. The course of NC evolution from precursors to mature complexes is proposed. Both organelle adaptations occurred independently and in only Sertoli cells. They are believed to be a product of hybridization in deer.}, }
@article {pmid3054483, year = {1988}, author = {Herbert, CJ and Dujardin, G and Labouesse, M and Slonimski, PP}, title = {Divergence of the mitochondrial leucyl tRNA synthetase genes in two closely related yeasts Saccharomyces cerevisiae and Saccharomyces douglasii: a paradigm of incipient evolution.}, journal = {Molecular &amp; general genetics : MGG}, volume = {213}, number = {2-3}, pages = {297-309}, pmid = {3054483}, issn = {0026-8925}, mesh = {Alleles ; Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/*genetics ; Base Sequence ; Biological Evolution ; *Genes, Fungal ; Introns ; Leucine-tRNA Ligase/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Saccharomyces/enzymology/*genetics ; Saccharomyces cerevisiae/enzymology/genetics ; Suppression, Genetic ; Transcription, Genetic ; }, abstract = {We studied the NAM2 genes of Saccharomyces douglasii and Saccharomyces cerevisiae, and showed that they are interchangeable for all the known functions of these genes, both mitochondrial protein synthesis and mitochondrial mRNA splicing. This confirms the prediction that the S. douglasii NAM2D gene encodes the mitochondrial leucyl tRNA synthetase (EC 6.1.1.4.). The observation that these enzymes are interchangeable for their mRNA splicing functions, even though there are significant differences in the intron/exon structure of their mitochondrial genome, suggests that they may have a general role in yeast mitochondrial RNA splicing. A short open reading frame (ORF) precedes the synthetase-encoding ORF, and we showed that at least in S. cerevisiae this is not essential for the expression of the gene; however, it may be involved in a more subtle type of regulation. Sequence comparisons of S. douglasii and S. cerevisiae revealed a particularly interesting situation from the evolutionary point of view. It appears that the two yeasts have diverged relatively recently: there is remarkable nucleotide sequence conservation, with no deletions or insertions, but numerous (albeit non-saturating) silent substitutions resulting from transitions. This applies not only to the NAM2 coding regions, but also to two other ORFs flanking the NAM2 ORF. The regions between the ORFs (believed to be intergenic regions) are much less conserved, with several deletions and insertions. Thus S. douglasii and S. cerevisiae provide an ideal system for the study of molecular evolution, being two yeasts "caught in the act" of speciation.}, }
@article {pmid2456571, year = {1988}, author = {Mandel, M and Moriyama, Y and Hulmes, JD and Pan, YC and Nelson, H and Nelson, N}, title = {cDNA sequence encoding the 16-kDa proteolipid of chromaffin granules implies gene duplication in the evolution of H+-ATPases.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {85}, number = {15}, pages = {5521-5524}, pmid = {2456571}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Carrier Proteins/*genetics ; Chloroplasts/enzymology ; Chromaffin Granules/*enzymology/ultrastructure ; Chromaffin System/*enzymology ; Cloning, Molecular ; DNA/genetics ; Escherichia coli/enzymology ; Intracellular Membranes/enzymology ; Ion Channels/metabolism ; Mitochondria/enzymology ; Molecular Sequence Data ; *Multigene Family ; Proteolipids/*genetics ; Proton-Translocating ATPases/*genetics ; Protons ; Sequence Homology, Nucleic Acid ; Vacuoles/enzymology ; }, abstract = {Vacuolar H+-ATPases function in generating protonmotive force across the membranes of organelles connected with the vacuolar system of eukaryotic cells. This family of H+-ATPases is distinct from the two other families of H+-ATPases, the plasma membrane-type and the eubacterial-type. One of the subunits of the vacuolar H+-ATPase binds N,N'-dicyclohexylcarbodiimide (DCCD) and has been implicated in the proton-conducting activity of these enzymes. We have cloned and sequenced the gene encoding the DCCD-binding protein (proteolipid) of the H+-ATPase of bovine chromaffin granules. The gene encodes a highly hydrophobic protein of 15,849 Da. Hydropathy plots revealed four transmembrane segments, one of which contains a glutamic residue that is the likely candidate for the DCCD binding site. Sequence homology with the vacuolar proteolipid and with the proteolipids of eubacterial-type H+-ATPases was detected. The proteolipids from Escherichia coli, spinach chloroplasts, and yeast mitochondria matched better to the NH2-terminal part of the vacuolar protein. The proteolipids of bovine mitochondria and Neurospora mitochondria matched better to the COOH-terminal end of the vacuolar proteolipid. These findings suggest that the proteolipids of the vacuolar H+-ATPases were evolved in parallel with the eubacterial proteolipid, from a common ancestral gene that underwent gene duplication.}, }
@article {pmid3399407, year = {1988}, author = {Low, RL and Buzan, JM and Couper, CL}, title = {The preference of the mitochondrial endonuclease for a conserved sequence block in mitochondrial DNA is highly conserved during mammalian evolution.}, journal = {Nucleic acids research}, volume = {16}, number = {14A}, pages = {6427-6445}, pmid = {3399407}, issn = {0305-1048}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Chromatography, Affinity ; Chromatography, Gel ; DNA, Mitochondrial/*metabolism ; DNA, Single-Stranded/metabolism ; Endodeoxyribonucleases/*metabolism ; Genes ; Humans ; Mitochondria, Heart/*enzymology ; Rats ; Structure-Activity Relationship ; Substrate Specificity ; }, abstract = {Endonuclease activity identified in crude preparations of rat and human heart mitochondria has each been partially purified and characterized. Both the rat and human activities purify as a single enzyme that closely resembles the endonuclease of bovine-heart mitochondria (Cummings, O.W. et. al. (1987) J. Biol. Chem. 262:2005-2015). All three enzymes, for example elute similarly during gel filtration and DNA-cellulose chromatography, and exhibit similar enzymatic properties. Although the nucleotide sequences of the mtDNAs indicate that there has occurred an unusual degree of divergence in the displacement-loop region during mammalian evolution, the nucleotide specificities of the mt endonucleases appear highly conserved and show a striking preference for an evolutionarily-conserved sequence tract that is located upstream from the heavy (H)-strand origin of DNA replication (OriH).}, }
@article {pmid3070867, year = {1988}, author = {Osawa, S and Jukes, TH}, title = {Evolution of the genetic code as affected by anticodon content.}, journal = {Trends in genetics : TIG}, volume = {4}, number = {7}, pages = {191-198}, doi = {10.1016/0168-9525(88)90075-3}, pmid = {3070867}, issn = {0168-9525}, mesh = {Anticodon/*genetics ; Base Composition ; *Biological Evolution ; Chloroplasts/ultrastructure ; DNA/ultrastructure ; Eukaryotic Cells/ultrastructure ; *Genetic Code ; Mitochondria/ultrastructure ; Prokaryotic Cells/ultrastructure ; RNA, Transfer/*genetics ; }, }
@article {pmid2846487, year = {1988}, author = {Tang, XM and Clermont, Y and Hermo, L}, title = {Origin and fate of autophagosomes in Leydig cells of normal adult rats.}, journal = {Journal of andrology}, volume = {9}, number = {4}, pages = {284-293}, doi = {10.1002/j.1939-4640.1988.tb01053.x}, pmid = {2846487}, issn = {0196-3635}, mesh = {Animals ; Glucose-6-Phosphatase/metabolism ; Leydig Cells/*cytology ; Male ; Microscopy, Electron ; Nucleotidases/metabolism ; Phagocytes/*cytology ; Rats ; }, abstract = {Autophagosomes were observed frequently in electron microscope photographs of Leydig cells from normal adult rat testis. Their formation, evolution and fate were analyzed morphologically in preparations treated to show cytidine monophosphatase (CMPase) and glucose-6-phosphatase (G-6-Pase) activities and in animals sacrificed at various time intervals ranging from 5 min to 6 hrs after a single intratesticular injection of cationic ferritin. Analysis of the morphologic data led to the following interpretation and model. Preautophagosomal structures appeared as flattened, elongated membranous profiles. These expanded, took on a C-shape and fused at their edges to demarcate a small cytoplasmic territory containing normal-looking smooth endoplasmic reticulum (ER) and mitochondria. Such early autophagosomes were thus delimited by two membranes separated by a narrow lumen. Following fusion of these elements with secondary lysosomes, the space between the two membranes increased in size, the inner membrane disintegrated and the enclosed organelles no longer could be identified. The late autophagosomes then reached the cell surface and appeared to exocytose their residual content. In contrast to secondary lysosomes and trans-Golgi elements, which were CMPase-positive, the preautophagosomal flattened membranous elements and early autophagosomes were CMPase-negative. The late autophagosomes on the contrary were CMPase-positive. While ER cisternae were G-6-Pase-positive, the pre-, early and late autophagosomal structures were unreactive for this enzyme. Cationic ferritin tracer experiments showed that only late autophagosomes became labeled with cationic ferritin following their fusion with secondary lysosomes into which the tracer had accumulated following its endocytosis from the cell surface.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid2837198, year = {1988}, author = {Hruszkewycz, AM}, title = {Evidence for mitochondrial DNA damage by lipid peroxidation.}, journal = {Biochemical and biophysical research communications}, volume = {153}, number = {1}, pages = {191-197}, doi = {10.1016/s0006-291x(88)81207-5}, pmid = {2837198}, issn = {0006-291X}, support = {CA 07955/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *DNA Damage ; DNA, Mitochondrial/*metabolism ; Electrophoresis, Agar Gel ; Ferrous Compounds/metabolism ; Hydrogen Peroxide/metabolism ; Hydroxides ; Hydroxyl Radical ; Lipid Peroxides/*metabolism ; Male ; Malondialdehyde/metabolism ; Mitochondria, Liver/metabolism ; NADP/metabolism ; Rats ; Rats, Inbred Strains ; Vitamin E/pharmacology ; }, abstract = {When mitochondria of rat liver were incubated in an in vitro system containing NADPH and ferrous chloride, marked lipid peroxidation occurred, as evidenced by the evolution of malonic dialdehyde. DNA isolated from these peroxidized mitochondrial preparations had completely different electrophoretic mobility than DNA isolated from mitochondria protected from peroxidation. Scavengers of superoxide anion, hydrogen peroxide and hydroxyl radicals offered no protection against either lipid peroxidation or DNA damage. However, alpha-tocopherol protected against both lipid peroxidation and damage to the mitochondrial genome. These results support the hypothesis that lipid peroxidation can mediate DNA damage.}, }
@article {pmid2458607, year = {1988}, author = {Grivell, LA and Van der Veen, R and Kwakman, JH and Oudshoorn, P and Meijer, M}, title = {Mitochondrial biogenesis: recent developments and insights.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {319}, number = {1193}, pages = {85-95}, doi = {10.1098/rstb.1988.0033}, pmid = {2458607}, issn = {0962-8436}, mesh = {DNA, Mitochondrial/*genetics ; *Genes, Fungal ; Mitochondria/*metabolism ; Mutation ; Proteins/genetics ; RNA/genetics ; RNA, Mitochondrial ; Saccharomyces cerevisiae/genetics ; }, abstract = {Biosynthesis of a functional mitochondrion requires the coordinate expression of genes in both mitochondrial and nuclear DNAs. In yeast, three mitochondrial genes are split and RNA splicing plays a pivotal role in their expression. The recent finding that some introns are capable of self-splicing activity in vitro has permitted analysis of the mechanisms involved in RNA catalysis and may eventually shed light on the evolution of splicing mechanisms in general. Most mitochondrial proteins are encoded by nuclear genes, synthesized in the cytoplasm and imported by the organelle. The availability of cloned genes coding for several constituent subunits of the ubiquinol-cytochrome c reductase, which are imported by mitochondria, has allowed study of selected steps in the addressing of proteins to mitochondria and their intercompartmental sorting within the organelle. Recent developments are discussed.}, }
@article {pmid3076279, year = {1988}, author = {McAlister-Henn, L}, title = {Evolutionary relationships among the malate dehydrogenases.}, journal = {Trends in biochemical sciences}, volume = {13}, number = {5}, pages = {178-181}, doi = {10.1016/0968-0004(88)90146-6}, pmid = {3076279}, issn = {0968-0004}, mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; Escherichia coli/enzymology ; Malate Dehydrogenase/*genetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Saccharomyces cerevisiae/enzymology ; Swine ; }, }
@article {pmid3044395, year = {1988}, author = {Gray, MW}, title = {Organelle origins and ribosomal RNA.}, journal = {Biochemistry and cell biology = Biochimie et biologie cellulaire}, volume = {66}, number = {5}, pages = {325-348}, doi = {10.1139/o88-042}, pmid = {3044395}, issn = {0829-8211}, mesh = {*Biological Evolution ; Mitochondria/metabolism ; RNA, Ribosomal/*genetics ; Subcellular Fractions/*metabolism ; }, abstract = {As the detailed molecular biology of organelle genomes has unfolded, there has been a general acceptance of the view that plastids and mitochondria are of endosymbiotic, eubacterial origin. Plastid genes are strikingly similar to their eubacterial (particularly cyanobacterial) counterparts in sequence, organization, and mode of expression, and such features strongly support the hypothesis that the plastid and its genome were derived in evolution from a blue-green alga-like endosymbiont. Mitochondria, on the other hand, are problematic: mitochondrial genes are organized and expressed in remarkably diverse ways in the different major groups of eukaryotes, and in no case are these features particularly characteristic of either bacterial or nuclear genomes. There is, however, clear evidence derived from gene sequence supporting the eubacterial ancestry of mitochondria, and some of the most compelling data have come from analyses of mitochondrial ribosomal RNA (rRNA). Plant mitochondrial rRNA genes diverge in sequence at a particularly slow rate, and these genes have proven to be especially supportive of the endosymbiont hypothesis, pointing to an origin of mitochondria from within the alpha subdivision of the purple bacteria. Ribosomal RNA sequences provide a basis for the construction of global phylogenetic trees that probe the evolutionary history of organelles, and that address the question of whether mitochondria and plastids are monophyletic or polyphyletic in origin. Such studies raise the possibility that the rRNA genes of plant mitochondria originated separately from the mitochondrial rRNA genes of other eukaryotes.}, }
@article {pmid3282178, year = {1988}, author = {Deshaies, RJ and Koch, BD and Werner-Washburne, M and Craig, EA and Schekman, R}, title = {A subfamily of stress proteins facilitates translocation of secretory and mitochondrial precursor polypeptides.}, journal = {Nature}, volume = {332}, number = {6167}, pages = {800-805}, doi = {10.1038/332800a0}, pmid = {3282178}, issn = {0028-0836}, support = {GM26755/GM/NIGMS NIH HHS/United States ; GM36881/GM/NIGMS NIH HHS/United States ; }, mesh = {Biological Evolution ; Biological Transport, Active ; Endoplasmic Reticulum/metabolism ; Heat-Shock Proteins/genetics/*physiology ; Mating Factor ; Mitochondria/*metabolism ; Models, Biological ; Nucleic Acid Hybridization ; Peptides/genetics/metabolism ; Protein Precursors/*metabolism ; Protein Processing, Post-Translational ; Proteins/*metabolism ; Saccharomyces cerevisiae/genetics/metabolism/ultrastructure ; }, abstract = {Depletion of a subset of 70K stress proteins in yeast mutants shows that they are involved in the post-translational import of precursor polypeptides into both mitochondria and the lumen of the endoplasmic reticulum. The identification of such a basic function may explain the remarkable evolutionary conservation of the gene family encoding these proteins.}, }
@article {pmid2837172, year = {1988}, author = {Munneke, LR and Collier, GE}, title = {Cytoplasmic and mitochondrial arginine kinases in Drosophila: evidence for a single gene.}, journal = {Biochemical genetics}, volume = {26}, number = {1-2}, pages = {131-141}, pmid = {2837172}, issn = {0006-2928}, mesh = {Animals ; Arginine Kinase/*genetics/metabolism ; Crosses, Genetic ; Drosophila melanogaster/enzymology/*genetics ; Female ; *Genes ; Homozygote ; Male ; Mitochondria/*enzymology ; Phenotype ; Phosphotransferases/*genetics ; }, abstract = {Mitochondrial and cytoplasmic isozymes of arginine kinase have been identified in Drosophila melanogaster. On the basis of their immunological similarity, parallel dosage responses, and cosegregation of electrophoretic mobility differences, it is concluded that both isozymes are the product of a single gene. The consequences of this in relation to the regulation and evolution of this unusual gene-enzyme system are discussed. It is inferred that the origin of the phosphagen shuttle must predate the divergence of invertebrates and vertebrates.}, }
@article {pmid2834264, year = {1988}, author = {May, G and Taylor, JW}, title = {Patterns of mating and mitochondrial DNA inheritance in the agaric Basidiomycete Coprinus cinereus.}, journal = {Genetics}, volume = {118}, number = {2}, pages = {213-220}, pmid = {2834264}, issn = {0016-6731}, mesh = {Agaricales/*genetics ; Coprinus/*genetics ; Crosses, Genetic ; DNA Restriction Enzymes ; DNA, Mitochondrial/*genetics ; Nucleic Acid Hybridization ; }, abstract = {Patterns of mating and mitochondrial DNA (mtDNA) inheritance were investigated for the Basidiomycete, Coprinus cinereus in order to better understand the relationship of reproductive biology and mtDNA evolution in fungi. Results showed that the unique mating system of basidiomycetes can lead to the formation of mitochondrial mosaics (i.e., colonies composed of sectors differing in mtDNA). Mitochondria do not migrate along with nuclei during mating. Intracellular mixed or recombinant mtDNA molecules were not observed. Interestingly, it was found that mating asymmetry, caused by nonreciprocal nuclear migration, may be an important part of the reproductive biology of C. cinereus.}, }
@article {pmid2831186, year = {1988}, author = {Gabellini, N}, title = {Organization and structure of the genes for the cytochrome b/c1 complex in purple photosynthetic bacteria. A phylogenetic study describing the homology of the b/c1 subunits between prokaryotes, mitochondria, and chloroplasts.}, journal = {Journal of bioenergetics and biomembranes}, volume = {20}, number = {1}, pages = {59-83}, pmid = {2831186}, issn = {0145-479X}, mesh = {Chloroplasts/enzymology ; Electron Transport Complex III/*genetics ; *Genes ; *Genes, Bacterial ; Mitochondria/enzymology ; Phylogeny ; Rhodospirillaceae/enzymology/*genetics ; Sequence Homology, Nucleic Acid ; }, abstract = {The cytochrome b/c1 complex is an ubiquitous energy transducing enzyme, part of the electron transport chain of prokaryotes, mitochondria, and chloroplasts (b6/f). In the ancient purple photosynthetic bacteria, the b/c1 complex occupies a central metabolic role, being part of their photosynthetic and respiratory electron transport chain. In Rhodobacter the three subunits of the b/c1 complex are FeS protein, cytochrome b, and cytochrome c1, and they are encoded by a constitutively expressed operon named fbc. The organization of the genes for the cytochrome b/c1 complex, the modality of transcription, and the biogenesis of the encoded polypeptides will be described. The Rhodobacter species used to isolate the fbc genes, previously reported as R. sphaeroides was identified as R. capsulatus. Further biochemical characterization of the prokaryotic b/c1 complex indicated that the three polypeptides encoded by the fbc operon comprise the entire catalytic structure: ubiquinol-cytochrome-c reductase. The amino acid sequences of the three b/c1 subunits from the photosynthetic bacterium Rhodobacter capsulatus were compared with the corresponding sequences from yeast mitochondria and spinach chloroplasts. The high homology found between the sequences of all three redox polypeptides from R. capsulatus and yeast mitochondria (cytochrome b 41%, FeS protein 46%, cytochrome c1 31%) provided further evidence that mitochondria arose from the phylogenetic line of purple bacteria. The structure of cytochrome b also exhibited considerable homology to chloroplast cytochrome b6 plus subunit IV (26%). The amino acid sequence of the Rieske FeS protein from R. capsulatus and chloroplasts were found to be conserved only in the C-terminal part (14% total identity), whereas the homology between cytochrome c1 and cytochrome f is very weak (12%), despite similar topology of the two polypeptides. Analysis of the homology suggested that the catalytic sites quinol oxidase (Q0) and quinone reductase (Qi) arose monophonetically, whereas cytochrome c and plastocyanin reductase sites are not homologous and could derive from diverse ancestral genes by convergent evolution.}, }
@article {pmid3340166, year = {1988}, author = {Schön, A and Kannangara, CG and Gough, S and Söll, D}, title = {Protein biosynthesis in organelles requires misaminoacylation of tRNA.}, journal = {Nature}, volume = {331}, number = {6152}, pages = {187-190}, doi = {10.1038/331187a0}, pmid = {3340166}, issn = {0028-0836}, mesh = {Acylation ; Base Sequence ; Chloroplasts/metabolism ; Hordeum/genetics ; Organoids/*metabolism ; Plant Proteins/*biosynthesis ; RNA, Transfer, Amino Acid-Specific/*metabolism ; RNA, Transfer, Gln/metabolism ; RNA, Transfer, Glu/genetics/*metabolism ; }, abstract = {In the course of our studies on transfer RNA involvement in chlorophyll biosynthesis, we have determined the structure of chloroplast glutamate tRNA species. Barley chloroplasts contain in addition to a tRNA(Glu) species at least two other glutamate-accepting tRNAs. We now show that the sequences of these tRNAs differ significantly: they are differentially modified forms of tRNA(Gln) (as judged by their UUG anticodon). These mischarged Glu-tRNA(Gln) species can be converted in crude chloroplast extracts to Gln-tRNA(Gln). This reaction requires a specific amidotransferase and glutamine or asparagine as amide donors. Aminoacylation studies show that chloroplasts, plant and animal mitochondria, as well as cyanobacteria, lack any detectable glutaminyl-tRNA synthetase activity. Therefore, the requirement for glutamine in protein synthesis in these cells and organelles is provided by the conversion of glutamate attached to an 'incorrectly' charged tRNA. A similar situation has been described for several species of Gram-positive bacteria. Thus, it appears that the occurrence of this pathway of Gln-tRNA(Gln) formation is widespread among organisms and is a function conserved during evolution. These findings raise questions about the origin of organelles and about the evolution of the mechanisms maintaining accuracy in protein biosynthesis.}, }
@article {pmid3406522, year = {1988}, author = {Wolff, RL and Combe, NA and Entressangles, B}, title = {[Time-course changes in the alkenyl and acyl chain composition of plasmalogens from the heart and kidneys of rats ingesting trielaidin].}, journal = {Reproduction, nutrition, developpement}, volume = {28}, number = {3A}, pages = {603-615}, pmid = {3406522}, issn = {0181-1916}, mesh = {Animals ; Chromatography, Gas ; Fatty Acids/analysis ; Kidney/*metabolism ; Male ; Mitochondria/*metabolism ; Mitochondria, Heart/*metabolism ; *Oleic Acid ; Oleic Acids/*metabolism ; Plasmalogens/analysis/*metabolism ; Rats ; Rats, Inbred Strains ; Stereoisomerism ; Time Factors ; }, abstract = {Weaned rats were fed for 7 or 32 days a semi-purified diet containing 10% of fat supplement in which elaidic acid accounted for 64.5% of total fatty acids. Alkenyl groups from plasmalogens of kidney and heart mitochondria were analysed as their alkyl-substituted dioxane derivatives by gas liquid chromatography (GLC). Acyl chains of total and individual phospholipids (phosphatidylcholine: PC; phosphatidylethanolamine: PE, diacyl and alkenyl-acyl forms; phosphatidylinositol: PI; cardiolipin: CL) were also analysed by GLC. Maximum level of elaidic acid incorporation was attained after only one week on the experimental diet in either total or individual phospholipids. Heart mitochondria phospholipids contained about 40% more trans-monounsaturated acids (20.9%) than kidney mitochondria phospholipids (12.5%) after one month. trans-Monounsaturated acids (t-18: 1 plus t-16: 1 acids) were incorporated in individual phospholipids from both organs in decreasing order: PI greater than PE (total) greater than PC much greater than CL. The order of incorporation of elaidic acid seemed to be related to the content of stearic acid in these phospholipids when the diet was devoid of elaidic acid (PI greater than PE greater than PC much greater than CL). The content of elaidic acid in alkenyl-acyl-glycerophosphoethanolamine (alkenyl-acyl-GPE) was the same (6% of total fatty acids) in both organs. The time-course incorporation of trans-monounsaturated alkenyl chains was different. After one week on the elaidic acid-enriched diet, they represented only 65% (kidney) or 43% (heart) of the values reached after one month. At the end of the feeding period, the trans-monounsaturated alkenyl chains were also about 40% less in total plasmalogens from kidney mitochondria (27.8%) than from heart mitochondria (46%). trans-Monounsaturated acyl chains were incorporated at a higher rate in the 2-position of alkenyl-acyl-GPE than trans-monounsaturated alkenyl chains in their 1-position. Our results confirm the unique observation of Kramer et al. (1985) who noticed that the fatty acid composition of phospholipids was much more rapidly equilibrated than the alkenyl chain composition of plasmalogens (1 week vs 2-3 weeks) from heart of rats fed diets supplemented with different oils.}, }
@article {pmid3400413, year = {1988}, author = {de Paz Cabello, P and Fernandez, M and Chamorro, CA and Fernandez, JG and Villar, JM}, title = {Stereological study of the early ultrastructural differentiation of chick embryo neuroepithelial cells during neurulation.}, journal = {Acta anatomica}, volume = {132}, number = {1}, pages = {12-16}, doi = {10.1159/000146545}, pmid = {3400413}, issn = {0001-5180}, mesh = {Animals ; Chick Embryo ; Cytoplasm/ultrastructure ; Epithelial Cells ; Epithelium/embryology/ultrastructure ; Microscopy, Electron/methods ; Morphogenesis ; Nervous System/*cytology/embryology ; }, abstract = {The neuroectodermal cells of chick embryos have been analyzed during neurulation by stereological and morphometrical ultrastructural methods in an attempt to describe their cytometric evolution. A profound change of cellular form coefficient was observed which is related to the typical process of columnarization of these cells. At stages 7 and 8, the nucleus appeared round in shape, probably due to a loss of pressure of the vitelline inclusions. In this sense, the volume density of these inclusions falls during this period. There was also a significant increase of the nuclear surface density, the significance of which is discussed on the basis of the nucleo-cytoplasmic interchanges and the differentiation process. At the same time, an increase in the number of mitochondria was observed, which is related to the neural folding process. Simultaneously, the amount of rough endoplasmic reticulum increases, presumably related to the remarkable changes of the embryonic extracellular matrix.}, }
@article {pmid3395680, year = {1988}, author = {Wolters, J and Erdmann, VA}, title = {Cladistic analysis of ribosomal RNAs--the phylogeny of eukaryotes with respect to the endosymbiotic theory.}, journal = {Bio Systems}, volume = {21}, number = {3-4}, pages = {209-214}, doi = {10.1016/0303-2647(88)90015-9}, pmid = {3395680}, issn = {0303-2647}, mesh = {Base Sequence ; Eukaryota/*genetics ; Information Systems ; Models, Biological ; Molecular Sequence Data ; Nucleic Acid Conformation ; *Phylogeny ; Plants/*genetics ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 5S/genetics ; Symbiosis ; }, abstract = {A strict cladistic analysis of 5S and 16S rRNA secondary and primary structure confirms particular hypotheses concerning the phylogeny of eukaryotes: plastids of Euglena, green algae and land plants, and the cyanelle of Cyanophora share a specific character and are closely related to cyanobacteria of the Synechococcus-type. Angiosperm mitochondria share specific signatures with the alpha subdivision of rhodobacteria. Cyanophora is a member of the Euglenozoa, the Oomycetes are derived from a group of heterokont algae.}, }
@article {pmid3341736, year = {1988}, author = {Gans, P and Rebeille, F}, title = {Light inhibition of mitochondrial respiration in a mutant of Chlamydomonas reinhardtii devoid of ribulose-1,5-bisphosphate carboxylase/oxygenase activity.}, journal = {Archives of biochemistry and biophysics}, volume = {260}, number = {1}, pages = {109-117}, doi = {10.1016/0003-9861(88)90430-4}, pmid = {3341736}, issn = {0003-9861}, mesh = {Chlamydomonas/enzymology/genetics/*metabolism ; Citric Acid Cycle ; *Light ; Mitochondria/*metabolism ; Mutation ; Nucleotides/metabolism ; *Oxygen Consumption ; Ribulose-Bisphosphate Carboxylase/*metabolism ; }, abstract = {The effect of light on mitochondrial respiration has been investigated in Chlamydomonas reinhardtii rcl-u-1-10-6C, a mutant devoid of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) activity. No CO2 uptake was observed in the light, confirming that there was no Rubisco activity, but the CO2 evolution rate was diminished by 65 to 80%. This inhibition was ascribable to a decrease in the tricarboxylic acid cycle (Krebs cycle) activity. At the same time, O2 evolution associated with stimulation of the O2 uptake appears. Darkness or addition of DCMU fully reversed the effect of light, indicating that the inhibitory process is linked to photosystem activities. Levels of pyridine nucleotides (NAD(H) and NADP(H)) and adenine nucleotides (ATP and ADP), the most probable mediators of the interaction between photosynthesis and respiration, were measured in dark and in light. During a dark to light transition the level of NADPH increased significantly whereas the NAD(H) pool remained almost fully oxidized. The level of ADP was always extremely low. These results suggest that the inhibition of Krebs cycle activity is due to a competition for cytosolic ADP between chloroplastic photophosphorylations and oxidative phosphorylations.}, }
@article {pmid3338968, year = {1988}, author = {Langille, RM and Hall, BK}, title = {The organ culture and grafting of lamprey cartilage and teeth.}, journal = {In vitro cellular &amp; developmental biology : journal of the Tissue Culture Association}, volume = {24}, number = {1}, pages = {1-8}, pmid = {3338968}, issn = {0883-8364}, mesh = {Allantois ; Animals ; Cartilage/cytology/*growth &amp; development/transplantation ; Chick Embryo ; Chorion ; Culture Media ; Culture Techniques ; Fishes/*anatomy &amp; histology ; Lampreys/*anatomy &amp; histology ; *Organ Culture Techniques ; Temperature ; Tooth/cytology/*growth &amp; development/transplantation ; }, abstract = {Cartilage from larval (ammocoetes) and adult (prespawning upstream migrant) lamprey was successfully maintained both when cultured in vitro or grafted in vivo (on the chorioallantoic membrane (CAM) of host chick embryos). In addition teeth from adult lamprey were successfully cultured in vitro. Cartilages were cultured in supplemented Lebovitz's l15 medium at 15 and 20 degrees C for periods of up to 56 d and in supplemented BGJb medium at 37 degrees C for periods of up to 14 d. Cartilages were also grafted onto the CAM for up to 16 d. Both the cultured and grafted cartilages retained their structural and cellular integrity as verified histologically. The viability of the cartilage, even after extended culture periods, was demonstrated ultrastructurally by the presence of chondrocytes displaying abundant rough endoplasmic reticulum, mitochondria, and Golgi apparatii with associated vesicles. In addition the cartilages were shown to be metabolically active in vitro by the incorporation of radioactive sulfur into the matrix. Some cell outgrowth from other tissues, such as connective tissue, muscle, and gill when left adjacent to the cartilage, occurred over time in cultures. No cell outgrowth was observed in CAM-grafted tissue nor was there any invasion of the agnathan tissue by chorioallantoic blood vessels. Teeth cultured in L15-supplemented media for up to 14 d at either 15 or 20 degrees C retained their structural and cellular integrity as observed histologically, with no apparent cell outgrowth. With the successful culture of these tissues, their development, biochemistry, and physiology, potentially of great importance in understanding early vertebrate evolution, can be better understood.}, }
@article {pmid3275942, year = {1988}, author = {Storey, KB and Storey, JM}, title = {Freeze tolerance in animals.}, journal = {Physiological reviews}, volume = {68}, number = {1}, pages = {27-84}, doi = {10.1152/physrev.1988.68.1.27}, pmid = {3275942}, issn = {0031-9333}, mesh = {*Adaptation, Physiological ; Animals ; Anura/metabolism ; Avoidance Learning ; Cryoprotective Agents/metabolism ; *Freezing ; Ice ; Insecta/metabolism ; Membrane Proteins/physiology ; Mitochondria/physiology ; Phylogeny ; Proteins/physiology ; Water ; }, }
@article {pmid3268426, year = {1988}, author = {Lemaire, M and Lange, C and Bazire, M and Cassier, P and Clément, JL and Escoubas, P and Basselier, JJ}, title = {Alkaloid venom of European ants in the genus Monomorium. Site of synthesis, identification and quantification.}, journal = {Experimental biology}, volume = {48}, number = {1}, pages = {27-40}, pmid = {3268426}, issn = {0176-8638}, mesh = {Animals ; Ant Venoms/analysis/*biosynthesis ; Ants/*metabolism/ultrastructure ; Arthropod Venoms/*biosynthesis ; Exocrine Glands/metabolism/ultrastructure ; Gas Chromatography-Mass Spectrometry ; Mass Spectrometry ; Microscopy, Electron, Scanning ; Molecular Structure ; Pyrroles/analysis ; Pyrrolidines/analysis ; }, abstract = {The venom of the European Ant Monomorium is composed of five alkaloids: three 2.5 transdialkylpyrrolidines and two 2.5 transdialkylpyrrolines. The venom is synthesized by a glandular complex composed of a biramous external filamentous gland, and a single internal gland invaginated into the reservoir. External glands and the proximal two-thirds of the internal gland are composed of glandular units, with one glandular cell and one associated duct cell. Glandular cells contain numerous giant mitochondria, a well-developed smooth endoplasmic reticulum and enigmatic rod-shaped structures. The secretory product is electron-lucent. The distal third of the internal gland is composed of 38-48 large secretory cells issuing directly into the reservoir. Their secretory product presents the same characteristics as the venom accumulated in the reservoir (opacity, affinity to stains and osmium).}, }
@article {pmid3198044, year = {1988}, author = {Leung, LK}, title = {Ultrastructure of the spermatozoon of Lepidogalaxias salamandroides and its phylogenetic significance.}, journal = {Gamete research}, volume = {19}, number = {1}, pages = {41-49}, doi = {10.1002/mrd.1120190105}, pmid = {3198044}, issn = {0148-7280}, mesh = {Acrosome/ultrastructure ; Animals ; Cell Nucleus/ultrastructure ; Centrioles/ultrastructure ; Fishes/*anatomy &amp; histology ; Male ; Microscopy, Electron ; Mitochondria/ultrastructure ; *Phylogeny ; Sperm Tail/ultrastructure ; Spermatozoa/*ultrastructure ; }, abstract = {The spermatozoon of Lepidogalaxias salamandroides possesses an acrosome (putative), one or two perforatoria (putative) but no nine-triplet centrioles. Two elongated mitochondria (12 micron long) are situated in parallel between the nucleus (20 micron long) and the axoneme (53 micron long). The above features are unique among other teleosts with internal fertilization. The presence of an "acrosome" in this primitive teleost supports the hypothesis that this structure has been secondarily lost in teleosts during evolution. The uncertainty of phylogenetic placement of this fish is reflected by its unique sperm ultrastructure.}, }
@article {pmid3134965, year = {1988}, author = {Canning, EU}, title = {Nuclear division and chromosome cycle in microsporidia.}, journal = {Bio Systems}, volume = {21}, number = {3-4}, pages = {333-340}, doi = {10.1016/0303-2647(88)90030-5}, pmid = {3134965}, issn = {0303-2647}, mesh = {Animals ; Apicomplexa/*cytology/ultrastructure ; *Cell Cycle ; *Cell Division ; Cell Nucleus/*ultrastructure ; Chromosomes/*ultrastructure ; Microscopy, Electron ; Phylogeny ; }, abstract = {Nuclear division and chromosome cycle of microsporidia are reviewed in the light of recent speculation that the group diverged as an early branch in the eukaryotic line of descent. Microsporidia are primitive eukaryotes with simple cytoplasmic organisation, lacking mitochondria, peroxisomes and a classical Golgi apparatus. The ribosomes resemble prokaryotic ribosomes in size and in having sequences complementary to the eukaryotic 5.8S rRNA contained within their large (23S) ribosomal subunit, rather than a separate 5.8S molecule. Nuclei may be isolated or closely appressed as a diplokaryotic pair which divide synchronously. Mitosis is intranuclear: there are no centrioles but spindle termini are electron dense plaques in pores in the nuclear envelope. Some genera have isolated nuclei throughout the life cycle, while others have diplokaryotic nuclei throughout: meiosis is not known in either of these categories of genera. In contrast, certain polymorphic species, which are transmitted horizontally between copepods and mosquitoes and vertically between generations of mosquitoes, alternate between stages with isolated nuclei and stages with diplokaryotic nuclei. Haploid spores in copepods are infective to mosquito larvae, in which gametogenesis and plasmogamy occur to give diplokaryotic (diploid) stages. Stages remain diplokaryotic through transovarial transmission to the next generation, when an unusual form of meiosis is initiated in both nuclei of the diplokaryon (as indicated by synaptonemal complexes), and mingling of chromosomes occurs when the two nuclei fuse during pachytene.}, }
@article {pmid3124745, year = {1988}, author = {Burnell, JN and Hatch, MD}, title = {Photosynthesis in phosphoenolpyruvate carboxykinase-type C4 plants: photosynthetic activities of isolated bundle sheath cells from Urochloa panicoides.}, journal = {Archives of biochemistry and biophysics}, volume = {260}, number = {1}, pages = {177-186}, doi = {10.1016/0003-9861(88)90439-0}, pmid = {3124745}, issn = {0003-9861}, mesh = {Carbon Dioxide/metabolism ; Cell Separation ; Chloroplasts/*enzymology ; Decarboxylation ; Oxygen Consumption ; Phosphoenolpyruvate Carboxykinase (GTP)/*metabolism ; *Photosynthesis ; Poaceae/cytology/enzymology/*metabolism ; }, abstract = {A method has been developed for rapidly preparing bundle sheath cell strands from Urochloa panicoides, a phosphoenolpyruvate (PEP) carboxykinase-type C4 plant. These cells catalyzed both HCO3(-)- and oxaloacetate-dependent oxygen evolution; oxaloacetate-dependent oxygen evolution was stimulated by ATP. For this activity oxaloacetate could be replaced by aspartate plus 2-oxoglutarate. Both oxaloacetate- and aspartate plus 2-oxoglutarate-dependent oxygen evolution were accompanied by PEP production and both were inhibited by 3-mercaptopicolinic acid, an inhibitor of PEP carboxykinase. The ATP requirement for oxaloacetate- and aspartate plus 2-oxoglutarate-dependent oxygen evolution could be replaced by ADP plus malate. The increased oxygen evolution observed when malate plus ADP was added with oxaloacetate was accompanied by pyruvate production. These results are consistent with oxaloacetate being decarboxylated via PEP carboxykinase. We suggest that the ATP required for oxaloacetate decarboxylation via PEP carboxykinase may be derived by phosphorylation coupled to malate oxidation in mitochondria. These bundle sheath cells apparently contain diffusion paths for the rapid transfer of compounds as large as adenine nucleotides.}, }
@article {pmid3059999, year = {1988}, author = {Müller, M}, title = {Energy metabolism of protozoa without mitochondria.}, journal = {Annual review of microbiology}, volume = {42}, number = {}, pages = {465-488}, doi = {10.1146/annurev.mi.42.100188.002341}, pmid = {3059999}, issn = {0066-4227}, mesh = {Anaerobiosis ; Animals ; Biological Evolution ; Decarboxylation ; Electron Transport ; *Energy Metabolism ; Eukaryota/*metabolism ; Glycolysis ; Mitochondria/metabolism ; Pyruvates/metabolism ; }, }
@article {pmid3047833, year = {1988}, author = {Reynaud, P and Loiseau, H and Coquet, M and Vital, C and Loiseau, P}, title = {[An adult case of Leigh's subacute necrotizing encephalomyelopathy].}, journal = {Revue neurologique}, volume = {144}, number = {4}, pages = {259-265}, pmid = {3047833}, issn = {0035-3787}, mesh = {Adult ; Brain/pathology ; Brain Diseases, Metabolic/*physiopathology ; Humans ; Leigh Disease/pathology/*physiopathology ; Male ; Muscles/pathology ; }, abstract = {Leigh's encephalomyelopathy has been mainly observed in infancy and childhood. A later onset, during adolescence or adulthood has been rarely reported. Our patient was a 35 year-old man who died after 10 months of evolution of a subacute neurological syndrome, beginning with behavioural changes then a confusional state, epileptic fits, ataxia, autonomic disorders, abnormal alimentary behaviour and dementia. Diagnosis was only obtained by neuropathology, as in most of the published reports. However this diagnosis is suggested when exists an acute or subacute neurological pattern, beginning with visual defects and alimentary and social impairment, followed by a brain-stem syndrome. CT and M.R.I. will make it more easy. An earlier diagnosis could perhaps allow to discover the suspected enzymopathy responsible for Leigh's encephalomyelopathy and make clearer the relationship between Leigh's disease and encephalopathies with abnormal mitochondria.}, }
@article {pmid2842512, year = {1988}, author = {Granero-Porati, MI and Porati, A}, title = {Informational parameters and randomness of mitochondrial DNA.}, journal = {Journal of molecular evolution}, volume = {27}, number = {2}, pages = {109-113}, pmid = {2842512}, issn = {0022-2844}, mesh = {Adenosine Triphosphatases/genetics ; Animals ; *Biological Evolution ; Cytochrome b Group/genetics ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; *Genes ; Humans ; *Models, Genetic ; Thermodynamics ; }, abstract = {The informational content of genomes of nuclear and mitochondrial origin is examined. By using the parameters of Shannon's information theory the language of mitochondrial DNA is shown to be more similar to the language of bacterial DNA than to that of nuclear DNA in more evolutionarily advanced animals. Moreover, using the parameters of Kolmogorov's theory on randomness, genes of different organisms (Neurospora crassa and Saccharomyces cerevisiae) coding for the same protein (subunit 9 of ATPase) are shown to have, if both of mitochondrial origin, a similar degree of randomness, whereas genes coding for the same protein, both belonging to the same organisms, exhibit a quite different degree of randomness when one is of mitochondrial origin and the other of nuclear origin. These results are in favor of the symbiotic origin of mitochondria.}, }
@article {pmid2841681, year = {1988}, author = {Smith, L and Bolgiano, B and Davies, HC}, title = {Kinetics of the interaction of cytochrome c oxidase of Paracoccus denitrificans with Paracoccus and mitochondrial cytochrome c.}, journal = {Progress in clinical and biological research}, volume = {274}, number = {}, pages = {619-635}, pmid = {2841681}, issn = {0361-7742}, support = {HL28272/HL/NHLBI NIH HHS/United States ; RR-0703/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Cattle ; Cell Membrane/enzymology ; Cytochrome c Group/genetics/*metabolism ; Electron Transport Complex IV/*metabolism ; Kinetics ; Mitochondria/*metabolism ; Mutation ; Oxygen Consumption ; Paracoccus denitrificans/*enzymology/genetics ; Protein Binding ; }, abstract = {We have studied the reactions of the oxidase of Paracoccus dentrificans with its membrane-bound cytochrome c and with soluble cytochrome c550 of Paracoccus and of bovine heart. The turnover rate of Paracoccus oxidase with membrane-bound cytochrome c is high, approaching 1000/sec. at 25 degrees. When soluble cytochrome c is added to the electron transport chain oxidizing NADH or succinate, no increase in 02 uptake is observed. When the oxidase is reacting with the membrane-bound cytochrome c, the reaction site is not exposed for reaction with soluble cytochrome c. We have purified the Paracoccus oxidase, following relatively simple methodology. It has three major subunits similar in molecular weight to those of the larger subunits of the bovine oxidase. When reconstituted in the presence of asolectin, it is just as active as the intact membrane-bound oxidase in reaction with soluble cytochrome c. The soluble cytochrome c reacts directly with the cytochrome aa3. We found direct evidence that the oxidase is stimulated in the presence of low concentrations of cytochrome c. The stimulatory effect could be the explanation for the so-called "high affinity" site for reaction with cytochrome c. The reaction of bovine cytochrome c with Paracoccus oxidase resembles that with the bovine oxidase in every way tested. The Paracoccus oxidase must have a cytochrome c binding site equivalent to that of the bovine enzyme. The reaction of the Paracoccus oxidase with its own soluble cytochrome c550, which has a highly negative hemisphere on the side of the molecule away from the heme crevice, has different properties from those seen in its reaction with bovine cytochrome c. However the properties all change to be like those with bovine cytochrome c on addition of poly-L-lysine. These data emphasize the importance of all of the charged groups on the cytochrome c in influencing binding or electron transfer reactions. The respiratory chain on the membranes of a cytochrome c-deficient mutant can reduce cytochrome aa3 using NADH as substrate in a manner similar to that of the wild type, although at somewhat lower rate, suggesting diffusional encounter of the large complexes within the membrane. Our data permit speculations about the possible evolution from the bacterial to the mitochondrial electron transport system.}, }
@article {pmid3443105, year = {1987}, author = {Libert, F and Ruel, J and Ludgate, M and Swillens, S and Alexander, N and Vassart, G and Dinsart, C}, title = {Thyroperoxidase, an auto-antigen with a mosaic structure made of nuclear and mitochondrial gene modules.}, journal = {The EMBO journal}, volume = {6}, number = {13}, pages = {4193-4196}, pmid = {3443105}, issn = {0261-4189}, mesh = {Amino Acid Sequence ; Autoantigens/*genetics ; Cell Nucleus/*metabolism ; Cloning, Molecular ; DNA/genetics/isolation &amp; purification ; DNA, Mitochondrial/*genetics ; *Genes ; Humans ; Iodide Peroxidase/*genetics ; Mitochondria/*enzymology ; Molecular Sequence Data ; Sequence Homology, Nucleic Acid ; Thyroid Gland/*enzymology ; }, abstract = {A lambda gt11 cDNA library was constructed from a normal human thyroid and screened with a rabbit anti-porcine thyroperoxidase antibody. A series of thyroperoxidase (TPO) clones were obtained which allowed determination of the complete primary structure of the protein. The library was also screened with serum from a patient with Hashimoto's thyroiditis, an autoimmune disease characterized by the presence in the serum of high titers of autoantibodies directed against the 'microsomal antigen' (McAg). Comparison of the cDNA sequences from TPO clones and McAg clones provides definite proof that the McAg is TPO. A short segment of TPO was characterized as bearing a major epitope involved in autoimmunity. The primary structure of TPO was 42% homologous to myeloperoxidase (MPO). It contains, in addition, a C-terminal extension with a membrane anchor region contiguous to two domains encoded by modules belonging to the EGF and C4b gene families. The existence in TPO of still another domain presenting a significant homology with a putative heme-binding region of cytochrome C oxidase polypeptide I raises the possibility that a mitochondrial gene module has contributed a piece to the evolution of a typical nuclear mosaic gene.}, }
@article {pmid3127204, year = {1987}, author = {Bernad, A and Zaballos, A and Salas, M and Blanco, L}, title = {Structural and functional relationships between prokaryotic and eukaryotic DNA polymerases.}, journal = {The EMBO journal}, volume = {6}, number = {13}, pages = {4219-4225}, pmid = {3127204}, issn = {0261-4189}, support = {2 RO1 GM27242-08/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Aphidicolin ; Bacillus subtilis/*enzymology ; Bacteriophages/*enzymology ; Biological Evolution ; DNA Replication ; DNA-Directed DNA Polymerase/genetics/*metabolism ; Diterpenes/pharmacology ; Escherichia coli/*enzymology ; Kinetics ; Mitochondria/enzymology ; Molecular Sequence Data ; Plants/enzymology ; Species Specificity ; T-Phages/*enzymology ; Viruses/enzymology ; }, abstract = {The Bacillus subtilis phage luminal diameter 29 DNA polymerase, involved in protein-primed viral DNA replication, was inhibited by phosphonoacetic acid (PAA), a known inhibitor of alpha-like DNA polymerases, by decreasing the rate of elongation. Three highly conserved regions of amino acid homology, found in several viral alpha-like DNA polymerases and in the luminal diameter 29 DNA polymerase, one of them proposed to be the PAA binding site, were also found in the T4 DNA polymerase. This prokaryotic enzyme was highly sensitive to the drugs aphidicolin and the nucleotide analogues butylanilino dATP (BuAdATP) and butylphenyl dGTP (BuPdGTP), known to be specific inhibitors of eukaryotic alpha-like DNA polymerases. Two potential DNA polymerases from the linear plasmid pGKL1 from yeast and the S1 mitochondrial DNA from maize have been identified, based on the fact that they contain the three conserved regions of amino acid homology. Comparison of DNA polymerases from prokaryotic and eukaryotic origin showed extensive amino acid homology in addition to highly conserved domains. These findings reflect evolutionary relationships between hypothetically unrelated DNA polymerases.}, }
@article {pmid2824505, year = {1987}, author = {Wallace, CJ}, title = {Functional consequences of the excision of an omega loop, residues 40-55, from mitochondrial cytochrome c.}, journal = {The Journal of biological chemistry}, volume = {262}, number = {35}, pages = {16767-16770}, pmid = {2824505}, issn = {0021-9258}, mesh = {Animals ; Bacteria/enzymology ; Binding Sites ; Cytochrome c Group/analogs &amp; derivatives/*analysis ; Mitochondria, Heart/*enzymology ; Oxidation-Reduction ; Protein Conformation ; Structure-Activity Relationship ; }, abstract = {A novel technique for protein semisynthesis, enzymic activation, has been used to create a mitochondrial cytochrome c analogue in which the conventional bottom loop has been deleted. The resulting structure resembles that of cytochrome c555 from a primitive photosynthetic sulfur bacteria. Comparisons of this analogue with natural cytochromes show which of the functional differences between cytochromes c and c555 may be related directly to the incorporation of the loop. The structure is an example of an omega loop, recently defined as a discrete category of protein secondary structure. The analogue maintains the overall structure of the parent protein, but a significant change in redox potential has been engineered. It provides support for the prediction that omega loops act as independent modules in folding, function, and evolution. The rapidity of the synthesis and the high yield of product show that this technique for protein engineering is both competitive with, and complementary to, genetic methods.}, }
@article {pmid2446871, year = {1987}, author = {Lang, BF and Cedergren, R and Gray, MW}, title = {The mitochondrial genome of the fission yeast, Schizosaccharomyces pombe. Sequence of the large-subunit ribosomal RNA gene, comparison of potential secondary structure in fungal mitochondrial large-subunit rRNAs and evolutionary considerations.}, journal = {European journal of biochemistry}, volume = {169}, number = {3}, pages = {527-537}, doi = {10.1111/j.1432-1033.1987.tb13641.x}, pmid = {2446871}, issn = {0014-2956}, mesh = {Base Sequence ; Biological Evolution ; Escherichia coli/genetics ; Molecular Sequence Data ; *Nucleic Acid Conformation ; RNA, Bacterial/analysis ; RNA, Fungal/*analysis ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 23S/analysis ; Saccharomycetales/*genetics ; Schizosaccharomyces/*genetics ; }, abstract = {The DNA sequence of the mitochondrial large subunit (LSU) rRNA gene of Schizosaccharomyces pombe has been determined. In the direction of transcription, this gene is located between the gene coding for subunit II of cytochrome oxidase and a cluster of three tRNA genes. Both the 5' and 3' ends of the LSU rRNA have been mapped precisely: whereas the 5' end can be assigned unambiguously to a single nucleotide position, multiple 3' ends occur within a run of eight U residues. Based on these results, the S. pombe LSU rRNA is between 2818 and 2826 nucleotides long. A sequence motif immediately upstream of the 5' end of the gene resembles that of the mitochondrial promoter motif of Saccharomyces cerevisiae; however, the sequence at the 3' end of the gene is not similar to any of the motifs implicated as processing signals in other mitochondrial systems. Unlike its counterparts in S. cerevisiae and Aspergillus nidulans, the mitochondrial LSU rRNA gene of S. pombe does not contain an intron. Comparison of potential secondary structure among the three fungal mitochondrial and Escherichia coli LSU rRNAs has defined a common secondary structure core, held together by long-range hydrogen-bonding interactions. A 5.8S-like structure is present within the 5'-terminal region of all three fungal mitochondrial LSU rRNAs; in contrast, no 4.5S-like structure is evident at the 3' end of these molecules. An evolutionary evaluation of highly conserved regions of a small set of LSU rRNA sequences suggests that S. pombe mitochondria diverged from a mitochondrial proto-fungal branch earlier than either A. nidulans or S. cerevisiae mitochondria. This result, considered in conjunction with the patterns of genome organization and codon usage in fungal mitochondria, points to a slower evolutionary clock speed in the mitochondrial genome of S. pombe.}, }
@article {pmid2828632, year = {1987}, author = {Tsuzuki, T and Obaru, K and Setoyama, C and Shimada, K}, title = {Structural organization of the mouse mitochondrial aspartate aminotransferase gene.}, journal = {Journal of molecular biology}, volume = {198}, number = {1}, pages = {21-31}, doi = {10.1016/0022-2836(87)90454-2}, pmid = {2828632}, issn = {0022-2836}, mesh = {Animals ; Aspartate Aminotransferases/*genetics ; Base Sequence ; DNA Restriction Enzymes ; *DNA, Mitochondrial ; Exons ; *Genes ; Introns ; Mice ; Molecular Sequence Data ; Promoter Regions, Genetic ; Transcription, Genetic ; }, abstract = {Structural organization of the entire mouse mitochondrial aspartate aminotransferase (EC 2.6.1.1) gene was determined by analyzing the overlapping genomic clones obtained from a Charon 4A DNA library. The gene is 25 X 10(3) base-pairs long and contains ten exons interrupted by nine introns of various sizes. The 5' and 3'-flanking regions, the exact sizes and boundaries of the exon blocks including the transcription-initiation sites were determined. The 5' end of the gene lacks the prototypical 5' transcriptional regulatory sequence elements, such as TATA and CAAT boxes, but contains G + C-rich sequences, two putative binding sites for a cellular transcription factor, Sp1, and multiple transcription-initiation sites. Moreover, the sequences around the transcription-initiation sites are compatible with the formation of a number of potentially stable stem-loop structures. The leader sequence, which is essential for the transport of the protein into the mitochondria, is coded by the first exon and is separated from the mature protein by the first intron. The pyridoxal 5'-phosphate-binding domain, consisting of seven alternating beta-sheets and alpha-helical polypeptide strands, is separated by four introns present at the ends of alpha-helices. These genomic DNA structures suggest that the introns were not inserted into a previously uninterrupted coding sequence, but rather are products of evolution of the ancestral gene. However, a further correlation between the positions of introns relative to the well-defined structural domains of the mature protein was not obvious.}, }
@article {pmid3484338, year = {1987}, author = {Nelson, DR and Strobel, HW}, title = {Evolution of cytochrome P-450 proteins.}, journal = {Molecular biology and evolution}, volume = {4}, number = {6}, pages = {572-593}, doi = {10.1093/oxfordjournals.molbev.a040471}, pmid = {3484338}, issn = {0737-4038}, support = {CA37148/CA/NCI NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins/genetics ; *Biological Evolution ; Cytochrome P-450 Enzyme System/*genetics ; Humans ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Time Factors ; }, abstract = {Thirty-four cytochrome P-450 sequences from one bacterial and six vertebrate species have been aligned with the aid of a computer alignment algorithm. Phylogenetic trees were constructed using the unweighted-pair-group and neighbor-joining methods. The two trees differed at only a single branch point near the base of the tree. The cytochrome P-450 superfamily of proteins clustered into eight families and contained 16 gene-duplication events. The first gene duplication occurred approximately 1,360 Myr before the present (Mybp) and gave rise to cytochrome P-450s found in two different cellular organelles, the mitochondria and the endoplasmic reticulum. Both groups utilize cholesterol or its metabolites as substrates, implying that cholesterol existed greater than 1,360 Mybp. The fourth gene duplication (approximately 900 Mybp) gave rise to the drug-metabolizing P-450s. These proteins aid in the detoxification of foreign chemicals, as opposed to the metabolism of endogenous compounds. The importance of the capacity to metabolize drugs is reflected in 11 further gene duplications occurring in this lineage. The first occurred approximately 800 Mybp and gave rise to the two major P-450 families, the phenobarbital and 3-methylcholanthrene families. An apparent increase in the rate of cytochrome P-450 evolution is noted between the bird-mammal divergence (300 Mybp) and the mammalian radiation (75 Mybp).}, }
@article {pmid3446957, year = {1987}, author = {Arquès, DG and Michel, CJ}, title = {A purine-pyrimidine motif verifying an identical presence in almost all gene taxonomic groups.}, journal = {Journal of theoretical biology}, volume = {128}, number = {4}, pages = {457-461}, doi = {10.1016/s0022-5193(87)80190-x}, pmid = {3446957}, issn = {0022-5193}, mesh = {Base Sequence ; DNA/classification ; *Genes ; Phylogeny ; Probability ; *Purines ; *Pyrimidines ; }, abstract = {A statistical parameter identifies, with a high degree of significance, a motif which is present in protein-coding sequences of eukaryotes, prokaryotes, chloroplasts, mitochondria, viral introns, ribosomal RNA genes, and transfer RNA genes. The random probability of occurrence of such a situation is 10(-12). This motif has the following properties: (i) its significant presence in almost all present-day genes explains why it can be considered as primitive oligonucleotide, (ii) its nucleotide order is: YRY (N)6YRY, R being a purine base, Y a pyrimidine one and N any base, (iii) its length and its terminal trinucleotides YRY suggest a primordial function related to the spatial structure of the DNA sequences. This motif is found in some viral protein-coding genes, but not in eukaryotic introns.}, }
@article {pmid3670390, year = {1987}, author = {Cantatore, P and Gadaleta, MN and Roberti, M and Saccone, C and Wilson, AC}, title = {Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes.}, journal = {Nature}, volume = {329}, number = {6142}, pages = {853-855}, doi = {10.1038/329853a0}, pmid = {3670390}, issn = {0028-0836}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Codon ; DNA, Mitochondrial/*genetics ; *Genes ; Mitochondria/*metabolism ; RNA, Transfer/*genetics ; Sea Urchins/genetics ; }, abstract = {During the evolution of sea urchins, a transfer RNA gene lost its tRNA function and became part of a protein-coding gene. This functional loss of a tRNA with specificity for one group of leucine codons (CUN, where N is any base) was accompanied by the gain of a new tRNA with that specificity. The new tRNA gene for CUN codons appears to have evolved by duplication and divergence from a tRNA gene specific for another group of leucine codons (UUR, where R is a purine). These proposals account for (1) the strong sequence resemblance between the modern tRNA genes for CUN and UUR codons in Paracentrotus, (2) the altered location of the CUN gene in mitochondrial DNA of this urchin, and (3) the persistence of a 72-base pair sequence containing a trace of the old CUN gene at its original location. The old CUN gene now codes for an extra 24 amino acids at the amino end of subunit 5 in NADH dehydrogenase. Besides giving clues about the mechanisms by which tRNA genes move during mitochondrial DNA evolution, this finding leads us to propose a pathway relating the arrangements of other genes in mitochondrial DNAs from four animal phyla.}, }
@article {pmid2890702, year = {1987}, author = {Campbell, JW and Vorhaben, JE and Smith, DD}, title = {Uricoteley:its nature and origin during the evolution of tetrapod vertebrates.}, journal = {The Journal of experimental zoology}, volume = {243}, number = {3}, pages = {349-363}, doi = {10.1002/jez.1402430302}, pmid = {2890702}, issn = {0022-104X}, mesh = {Ammonia/*metabolism ; Animals ; *Biological Evolution ; Gluconeogenesis ; Glutamate-Ammonia Ligase/metabolism ; Liver/*metabolism ; Urea/metabolism ; Uric Acid/metabolism ; Vertebrates/*metabolism ; }, abstract = {The hepatic mechanism for detoxication of ammonia formed during amino acid gluconeogenesis in uricotelic vertebrates requires the intramitochondrial synthesis of glutamine by glutamine synthetase. This glutamine then serves as a precursor of uric acid in the cytosol. The evolutionary development of uricoteley thus required the localization of glutamine synthetase in liver mitochondria. The mechanism for the mitochondrial import of glutamine synthetase in uricotelic vertebrate liver is not yet known. Tortoises, extant relatives of the stem reptiles, possess both the ureotelic and uricotelic hepatic systems. It therefore seems likely that the genetic events allowing the mitochondrial localization of glutamine synthetase in liver occurred in the amniote amphibian ancestors of the stem reptiles. The selection of ureoteley by the theropsids and of uricoteley by the sauropsids were major events in the divergence and subsequent evolution of these two lines. Once established in the sauropsid line, uricoteley has persisted through to the higher reptiles, crocodilians, and birds. Uricoteley was in part responsible for the radiation of the archosaurs during the Triassic as a water-conserving mechanism in the adult, thereby allowing them to invade the arid environments of that period. Contrary to dogma, uricoteley was probably of minor significance in the development of the cleidoic egg. Neither mammalian nor avian embryonic liver tissues catabolize amino acids to any great extent, so it is inappropriate to attribute to them a kind of "waste" nitrogen metabolism.}, }
@article {pmid3628017, year = {1987}, author = {Kuzmin, EV and Levchenko, IV}, title = {S1 plasmid from cms-S-maize mitochondria encodes a viral type DNA-polymerase.}, journal = {Nucleic acids research}, volume = {15}, number = {16}, pages = {6758}, pmid = {3628017}, issn = {0305-1048}, mesh = {Amino Acid Sequence ; Biological Evolution ; DNA-Directed DNA Polymerase/*genetics/isolation &amp; purification ; Mitochondria/analysis ; Mosaic Viruses/genetics ; Plant Proteins/*genetics/isolation &amp; purification ; *Plasmids ; Sequence Homology, Nucleic Acid ; Viral Proteins/genetics ; Zea mays/*genetics ; }, }
@article {pmid3607872, year = {1987}, author = {Akins, RA and Lambowitz, AM}, title = {A protein required for splicing group I introns in Neurospora mitochondria is mitochondrial tyrosyl-tRNA synthetase or a derivative thereof.}, journal = {Cell}, volume = {50}, number = {3}, pages = {331-345}, doi = {10.1016/0092-8674(87)90488-0}, pmid = {3607872}, issn = {0092-8674}, mesh = {Amino Acid Sequence ; Amino Acyl-tRNA Synthetases/*metabolism ; Base Sequence ; Chromatography ; Cloning, Molecular ; DNA, Mitochondrial ; Genes, Fungal ; Introns ; Mitochondria/*enzymology ; Mutation ; Neurospora/enzymology/*genetics ; *RNA Splicing ; Sequence Homology, Nucleic Acid ; Tyrosine-tRNA Ligase/*metabolism ; }, abstract = {The nuclear cyt-18 mutants of Neurospora crassa are defective in splicing a number of group I introns in mitochondria. Here, cloning and sequencing of the cyt-18 gene show that it contains an open reading frame having significant homology to bacterial tyrosyl-tRNA synthetases. Biochemical and genetic experiments lead to the conclusions that the cyt-18 gene encodes mitochondrial tyrosyl-tRNA synthetase, that mutations in this gene inhibit splicing directly, and that mitochondrial tyrosyl-tRNA synthetase or a derivative of this protein is related to the soluble activity that functions in splicing the mitochondrial large rRNA intron and possibly other group I introns. Analysis of partial revertants provides direct evidence that the cyt-18 gene encodes a protein or proteins with two activities, splicing and aminoacylation, that can be partially separated by mutation. Our findings may be relevant to the evolution of introns and splicing mechanisms in eukaryotes.}, }
@article {pmid3673378, year = {1987}, author = {Korinteli, VI and Dzhidzheishvili, LSh and Meĭpariani, AN and Chanishvili, TG and Sharmazanashvili, TI}, title = {[Changes in the functional activity of the liver cells in rabbits during a bacterial infection].}, journal = {Zhurnal mikrobiologii, epidemiologii i immunobiologii}, volume = {}, number = {7}, pages = {74-77}, pmid = {3673378}, issn = {0372-9311}, mesh = {Animals ; Histocytochemistry ; Liver/*enzymology/ultrastructure ; Microscopy, Electron ; Rabbits ; Staphylococcal Infections/*enzymology/pathology ; Time Factors ; }, abstract = {In the process of the development of bacterial infections, the activity of marker enzymes in the membrane structure of liver cells has been studied in rabbits by biochemical and electron-histochemical methods. The results of these studies have shown that, simultaneously with the progressing course of cell pathology and inhibition of the function of mitochondria, microsomes and peroxisomes, the lysosomes activate for the realization of the protective function formed in the course of evolution. At the same time the excessive labilization of lysosomal membranes facilitates the development of cell pathology, which is confirmed by the accumulation of residual bodies in the cytoplasm.}, }
@article {pmid3313520, year = {1987}, author = {Nakamura, H}, title = {[Origin of mitochondria and chloroplast in the eukaryotic cell].}, journal = {Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme}, volume = {32}, number = {8}, pages = {1019-1030}, pmid = {3313520}, issn = {0039-9450}, mesh = {Biological Evolution ; *Cells/metabolism ; *Chloroplasts/metabolism ; DNA/genetics ; DNA, Mitochondrial/genetics ; Eukaryota/genetics ; *Eukaryotic Cells/metabolism ; Macromolecular Substances ; *Mitochondria/metabolism ; Photochemistry ; Symbiosis ; }, }
@article {pmid3302679, year = {1987}, author = {Zhu, H and Macreadie, IG and Butow, RA}, title = {RNA processing and expression of an intron-encoded protein in yeast mitochondria: role of a conserved dodecamer sequence.}, journal = {Molecular and cellular biology}, volume = {7}, number = {7}, pages = {2530-2537}, pmid = {3302679}, issn = {0270-7306}, support = {GM22525/GM/NIGMS NIH HHS/United States ; GM35510/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; Biological Evolution ; Exons ; Fungal Proteins/biosynthesis/*genetics ; Genes, Fungal ; Introns ; Mitochondria/*metabolism ; Mutation ; RNA Processing, Post-Transcriptional ; RNA, Fungal/*genetics/metabolism ; RNA, Messenger/genetics/metabolism ; RNA, Ribosomal/genetics/metabolism ; Saccharomyces cerevisiae/*genetics/metabolism ; Transcription, Genetic ; }, abstract = {The 3' ends of most Saccharomyces cerevisiae mitochondrial mRNAs terminate at a conserved dodecamer sequence, 5'-AAUAAUAUUCUU-3', of unknown function. We have studied the consequences of mutations within a dodecamer found in an 1,143-base-pair optional intron of the mitochondrial large (21S) rRNA gene on RNA processing. The dodecamer is situated at the 3' end of an expressed open reading frame (ORF) within that intron, and the mutations are two adjacent transversions that extend the intron ORF by 51 nucleotides. The strain harboring these mutations, L5-10-1, is defective in biased intron transmission in crosses to strains that lack the intron, as are other mutants which contain nucleotide changes within the ORF (I. G. Macreadie, R. M. Scott, A. R. Zinn, and R. A. Butow, Cell 41:395-402, 1985). However, unlike these other mutants, wild-type strains, or petites which retain the intron allele, L5-10-1 is defective in processing at the intron dodecamer. In addition, L5-10-1 lacks a prominent 2.7-kilobase RNA containing both intron and exon sequences and at least two of four RNAs that correspond to various forms of the excised intron. We propose that these RNAs, missing in L5-10-1 but present in all other strains examined, arise in part by processing at the intron dodecamer. In addition, in all strains examined, we have detected a novel processing activity in which precursor 21S rRNA transcripts are cleaved in the upstream exon, about 1,500 nucleotides from the 5' end of the RNA. This activity, together with 3' intron dodecamer cleavage, probably accounts for the 2.7-kilobase RNA species, a candidate for the mRNA for the intron-encoded protein.}, }
@article {pmid3295876, year = {1987}, author = {Cheng, MY and Pollock, RA and Hendrick, JP and Horwich, AL}, title = {Import and processing of human ornithine transcarbamoylase precursor by mitochondria from Saccharomyces cerevisiae.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {84}, number = {12}, pages = {4063-4067}, pmid = {3295876}, issn = {0027-8424}, support = {GM34433/GM/NIGMS NIH HHS/United States ; }, mesh = {Enzyme Precursors/*genetics ; Galactose/pharmacology ; Genotype ; Humans ; Macromolecular Substances ; Mitochondria/*enzymology ; Mutation ; Operon ; Ornithine Carbamoyltransferase/*genetics ; Plasmids ; Promoter Regions, Genetic ; Protein Processing, Post-Translational ; Saccharomyces cerevisiae/enzymology/*genetics ; Subcellular Fractions/enzymology ; }, abstract = {Expression of the subunit precursor of the human mitochondrial matrix enzyme ornithine transcarbamoylase (OTCase; EC 2.1.3.3) was programmed in Saccharomyces cerevisiae from a 2-micron plasmid by using an inducible galactose operon promoter. In the presence of the inducing sugar (galactose), two polypeptides were specifically precipitable with anti-OTCase antiserum: the human OTCase precursor (40 kDa); and the mature OTCase subunit (36 kDa). When yeast cells containing these species were lysed and fractionated, the OTCase precursor was found to be associated with mitochondrial membranes, while the mature subunit was found partly with mitochondrial membranes and partly in the soluble mitochondrial matrix-containing fraction. When OTCase enzymatic activity was assayed in fractions similarly derived from an S. cerevisiae strain devoid of yeast OTCase activity (an arg3 mutant) but expressing human OTCase, activity was detected specifically in the mitochondrial matrix fraction. A mutant human OTCase precursor containing an artificial mutation in the NH2-terminal leader peptide (arginine-23 to glycine) was similarly examined. As was previously observed with mammalian mitochondria, this precursor failed both to reach the matrix compartment and to be proteolytically processed; it also failed to exhibit OTCase enzymatic activity. Presence of OTCase enzymatic activity in an arg3 strain expressing wild-type precursor was utilized to obtain selective growth in a medium devoid of arginine but supplemented with the OTCase substrate ornithine. We conclude that, during evolution, the pathway of mitochondrial import utilized by the human OTCase precursor is conserved between yeast and humans, and that, by using selective growth conditions, it may be possible to examine genetically this pathway in S. cerevisiae.}, }
@article {pmid3032252, year = {1987}, author = {Ljungdahl, PO and Pennoyer, JD and Robertson, DE and Trumpower, BL}, title = {Purification of highly active cytochrome bc1 complexes from phylogenetically diverse species by a single chromatographic procedure.}, journal = {Biochimica et biophysica acta}, volume = {891}, number = {3}, pages = {227-241}, doi = {10.1016/0005-2728(87)90218-0}, pmid = {3032252}, issn = {0006-3002}, support = {GM 20379/GM/NIGMS NIH HHS/United States ; GM 27309/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cattle ; Chromatography, Gel ; Chromatography, Ion Exchange ; Electron Transport Complex III/genetics/*isolation &amp; purification ; Electrophoresis, Polyacrylamide Gel ; Mitochondria/*enzymology ; Mitochondria, Heart/*enzymology ; *Phylogeny ; Rhodobacter sphaeroides/*enzymology ; Rhodopseudomonas/*enzymology ; Saccharomyces cerevisiae/*enzymology ; Species Specificity ; }, abstract = {A method has been developed for purification of highly active ubiquinol-cytochrome c oxidoreductase (cytochrome bc1) complexes from wild-type Rhodobacter sphaeroides, Rhodobacter capsulatus MT1131, bovine heart and yeast mitochondria. This is the first report of the isolation of cytochrome bc1 complex from a wild-type strain of Rb. sphaeroides and from any strain of Rb. capsulatus. The purification involves extraction of membranes with dodecyl maltoside and two successive DEAE column chromatography steps. All of the resulting bc1 complexes are free of succinate dehydrogenase and cytochrome c oxidase activities. The purified bc1 complexes from both photosynthetic bacteria contain four polypeptide subunits, although the molecular weights of some of their subunits differ. They are also free of reaction center and light-harvesting pigments and polypeptides. The turnover number of the Rb. sphaeroides complex is 128 s-1, and that of the Rb. capsulatus complex is 64 s-1. The bc1 complex from bovine heart contains eight polypeptides and has a turnover number of 1152 s-1, while the yeast complex contains nine polypeptides and has a turnover number of 219 s-1. The activities of these complexes are equal to or better than those commonly obtained by previously reported methods. This method of purification is relatively simple, reproducible, and yields cytochrome bc1 complexes which largely retain the turnover number of the starting material and are pure on the basis of optical spectra, enzymatic activities and polypeptide composition. The purification of cytochrome bc1 complexes from energy-transducing membranes which differ markedly in their lipid and protein composition makes it likely that with minor modifications this method could be applied to species other than those described here.}, }
@article {pmid3038520, year = {1987}, author = {Arakawa, H and Takiguchi, M and Amaya, Y and Nagata, S and Hayashi, H and Mori, M}, title = {cDNA-derived amino acid sequence of rat mitochondrial 3-oxoacyl-CoA thiolase with no transient presequence: structural relationship with peroxisomal isozyme.}, journal = {The EMBO journal}, volume = {6}, number = {5}, pages = {1361-1366}, pmid = {3038520}, issn = {0261-4189}, mesh = {Acetyl-CoA C-Acyltransferase/*genetics ; Acyltransferases/*genetics ; Amino Acid Sequence ; Animals ; Base Sequence ; Cloning, Molecular ; DNA/*metabolism ; DNA Restriction Enzymes ; Liver/*enzymology ; Microbodies/*enzymology ; Mitochondria, Liver/*enzymology ; Rats ; Sequence Homology, Nucleic Acid ; }, abstract = {The sorting of homologous proteins between two separate intracellular organelles is a major unsolved problem. 3-Oxoacyl-CoA thiolase is localized in mitochondria and peroxisomes, and provides a good system for the study on the problem. Unlike most mitochondrial matrix proteins, mitochondrial 3-oxoacyl-CoA thiolase in rats is synthesized with no transient presequence and possess information for mitochondrial targeting and import in the mature protein. Two overlapping cDNA clones contained an open reading frame encoding a polypeptide of 397 amino acid residues (predicted Mr = 41,868), a 5' untranslated sequence of 164 bp, a 3' untranslated sequence of 264 bp and a poly(A) tract. The amino acid sequence of the mitochondrial thiolase is 37% identical with that of the mature portion of rat peroxisomal 3-oxoacyl-CoA thiolase precursor. These results suggest that the two thiolases have a common origin and obtained information for targeting to respective organelles during evolution. Two portions in the mitochondrial thiolase that may serve as a mitochondrial targeting signal are presented.}, }
@article {pmid3033634, year = {1987}, author = {Baker, A and Schatz, G}, title = {Sequences from a prokaryotic genome or the mouse dihydrofolate reductase gene can restore the import of a truncated precursor protein into yeast mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {84}, number = {10}, pages = {3117-3121}, pmid = {3033634}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Animals ; Cloning, Molecular ; Electron Transport Complex IV/*genetics ; *Genes ; *Genes, Fungal ; Macromolecular Substances ; Mice ; Mitochondria/*enzymology ; Saccharomyces cerevisiae/enzymology/*genetics ; Tetrahydrofolate Dehydrogenase/*genetics ; }, abstract = {Sequences that are capable of restoring mitochondrial targeting to a truncated yeast cytochrome c oxidase subunit IV presequence are encoded within the genome of Escherichia coli and within the gene for a higher eukaryotic cytosolic protein, mouse dihydrofolate reductase. These sequences, which resemble authentic presequences in their overall amino acid composition and degree of hydrophobicity, are rather frequent; greater than 2.7% of clones generated from E. coli DNA and greater than 5% of clones from the dihydrofolate reductase gene were functional in our screening system. These results suggest that, during evolution, mitochondrial precursor proteins could arise as a result of DNA rearrangements that place potential mitochondrial presequences at the amino terminus of existing open reading frames. Primitive eukaryotic cells may have used this mechanism to target proteins to their endosymbiotic protomitochondria.}, }
@article {pmid3038859, year = {1987}, author = {Okamura, K and Miyata, T and Iwanaga, S and Takamiya, K and Nishimura, M}, title = {Complete amino acid sequence of cytochrome c551 from Erythrobacter species strain OCh 114.}, journal = {Journal of biochemistry}, volume = {101}, number = {4}, pages = {957-966}, doi = {10.1093/oxfordjournals.jbchem.a121965}, pmid = {3038859}, issn = {0021-924X}, mesh = {Amino Acid Sequence ; Amino Acids/analysis ; Bacteria, Aerobic/classification/*enzymology ; *Bacterial Proteins ; *Cytochrome c Group ; Mitochondria/enzymology ; Oxidation-Reduction ; Peptide Fragments/analysis ; Photosynthesis ; Phylogeny ; }, abstract = {The complete amino acid sequence of cytochrome c551 isolated from an aerobic photosynthetic bacterium, Erythrobacter sp. strain OCh 114, was determined. The cytochrome molecule was composed of a total of 119 amino acid residues and its molecular weight including heme was calculated to be 13,235. The sequence was (Sequence: see text). Its molecular weight indicates that this cytochrome is of the L-type. Sequence alignment with other bacterial cytochromes c shows that this cytochrome is similar to cytochromes c of Rhodobacter capsulatus, Rhodobacter sphaeroides, and Paracoccus denitrificans, which were grouped into the alpha-3 subcluster from the 16S rRNA sequence analysis.}, }
@article {pmid3590993, year = {1987}, author = {Omel'ianchuk, LV and Kolchanov, NA}, title = {[Evolutionary study of genomes based on an analysis of primary tRNA structures].}, journal = {Zhurnal obshchei biologii}, volume = {48}, number = {2}, pages = {156-166}, pmid = {3590993}, issn = {0044-4596}, mesh = {Animals ; Bacteria/genetics ; *Biological Evolution ; Chloroplasts/ultrastructure ; Eukaryotic Cells/ultrastructure ; *Genes ; Mitochondria/ultrastructure ; Mutation ; Phylogeny ; RNA, Transfer/*genetics ; }, }
@article {pmid3561476, year = {1987}, author = {Cavalier-Smith, T}, title = {Eukaryotes with no mitochondria.}, journal = {Nature}, volume = {326}, number = {6111}, pages = {332-333}, doi = {10.1038/326332a0}, pmid = {3561476}, issn = {0028-0836}, mesh = {Animals ; Base Sequence ; Cells/*ultrastructure ; Chloroplasts ; Eukaryota/genetics/*ultrastructure ; Eukaryotic Cells/*ultrastructure ; *Mitochondria ; Phylogeny ; RNA, Ribosomal/genetics ; }, }
@article {pmid3550472, year = {1987}, author = {Vossbrinck, CR and Maddox, JV and Friedman, S and Debrunner-Vossbrinck, BA and Woese, CR}, title = {Ribosomal RNA sequence suggests microsporidia are extremely ancient eukaryotes.}, journal = {Nature}, volume = {326}, number = {6111}, pages = {411-414}, doi = {10.1038/326411a0}, pmid = {3550472}, issn = {0028-0836}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Escherichia coli/genetics ; Eukaryota/*genetics ; Eukaryotic Cells ; Mitochondria ; Phylogeny ; RNA, Ribosomal/*genetics ; Saccharomyces cerevisiae/genetics ; }, abstract = {The microsporidia are a group of unusual, obligately parasitic protists that infect a great variety of other eukaryotes, including vertebrates, arthropods, molluscs, annelids, nematodes, cnidaria and even various ciliates, myxosporidia and gregarines. They possess a number of unusual cytological and molecular characteristics. Their nuclear division is considered to be primitive, they have no mitochondria, their ribosomes and ribosomal RNAs are reported to be of prokaryotic size and their large ribosomal subunit contains no 5.8S rRNA. The uniqueness of the microsporidia may reflect their phylogenetic position, because comparative sequence analysis shows that the small subunit rRNA of the microsporidium Vairimorpha necatrix is more unlike those of other eukaryotes than any known eukaryote 18S rRNA sequence. We conclude that the lineage leading to microsporidia branched very early from that leading to other eukaryotes.}, }
@article {pmid3026849, year = {1987}, author = {Aquila, H and Link, TA and Klingenberg, M}, title = {Solute carriers involved in energy transfer of mitochondria form a homologous protein family.}, journal = {FEBS letters}, volume = {212}, number = {1}, pages = {1-9}, doi = {10.1016/0014-5793(87)81546-6}, pmid = {3026849}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; *Carrier Proteins ; Ion Channels ; *Membrane Proteins ; Mitochondria/*metabolism ; *Mitochondrial ADP, ATP Translocases ; Mitochondrial Proteins ; Models, Molecular ; *Nucleotidyltransferases ; Phosphate-Binding Proteins ; Phosphates/*metabolism ; Protein Conformation ; Uncoupling Protein 1 ; }, abstract = {The sequences of three mitochondrial carriers involved in energy transfer, the ADP/ATP carrier, phosphate carrier and uncoupling carrier, are analyzed. Similarly to what has been previously reported for the ADP/ATP carrier and the uncoupling protein, now also the phosphate carrier is found to have a tripartite structure comprising three similar repeats of approx. 100 residues each. The three sequences show a fair overall homology with each other. More significant homologies are found by comparing the repeats within and between the carriers in a scheme where the sequences are spliced into repeats, which are arranged for maximum homology by allowing possible insertions or deletions. A striking conservation of critical residues, glycine, proline, of charged and of aromatic residues is found throughout all nine repeats. This is indicative of a similar structural principle in the repeats. Hydropathy profiles of the three proteins and a search for amphipathic alpha-spans reveal six membrane-spanning segments for each carrier, providing further support for the basic structural identity of the repeats. The proposed folding pattern of the carriers in the membrane is exemplified with the phosphate carrier. A possible tertiary arrangement of the repeats and the membrane-spanning helices is shown. The emergence of a mitochondrial carrier family by triplication and by divergent evolution from a common gene of about 100 residues is discussed.}, }
@article {pmid3678836, year = {1987}, author = {Himeno, H and Masaki, H and Kawai, T and Ohta, T and Kumagai, I and Miura, K and Watanabe, K}, title = {Unusual genetic codes and a novel gene structure for tRNA(AGYSer) in starfish mitochondrial DNA.}, journal = {Gene}, volume = {56}, number = {2-3}, pages = {219-230}, doi = {10.1016/0378-1119(87)90139-9}, pmid = {3678836}, issn = {0378-1119}, mesh = {Animals ; Base Sequence ; Chromosome Mapping ; Codon/genetics ; DNA, Mitochondrial/*genetics ; *Genetic Code ; Humans ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Transfer, Amino Acid-Specific/*genetics ; RNA, Transfer, Ser/*genetics ; Species Specificity ; Starfish/*genetics ; }, abstract = {The nucleotide sequence of a 3849-bp fragment of starfish mitochondrial genome was determined. The genes for NADH dehydrogenase subunits 3, 4, 5, and COIII, and three kinds of (tRNA(UCNSer), tRNA(His), and tRNA(AGYSer) were identified by comparing with the genes of other animal mitochondria so far elucidated. The gene arrangement of starfish mitochondrial genome was different from those of vertebrate and insect mitochondrial genomes. Comparison of the protein-encoding nucleotide sequences of starfish mitochondria with those of other animal mitochondria suggested a unique genetic code in starfish mitochondrial genome; both AGA and AGG (arginine in the universal code) code for serine, AUA (isoleucine in the universal code but methionine in most mitochondrial systems) for isoleucine, and AAA (lysine) for asparagine. It was also inferred that these AGA and AGG codons are decoded by serine tRNA(AGYSer) originally corresponding to AGC and AGU codons. This situation is similar to the case of Drosophila mitochondrial genome. Variations in the use of AGA and AGG codons were discussed on the basis of the evolution of animals and decoding capacity of various tRNA(AGYSer) species possessing different sizes of the dihydrouridine (D) arm.}, }
@article {pmid3577898, year = {1987}, author = {Di Trapani, G and David, P and La Cara, A and Tonali, P and Laurienzo, P}, title = {Light and ultrastructural studies in sural biopsies of the pseudopolyneuropathic form of ALS.}, journal = {Advances in experimental medicine and biology}, volume = {209}, number = {}, pages = {111-119}, doi = {10.1007/978-1-4684-5302-7_18}, pmid = {3577898}, issn = {0065-2598}, mesh = {Amyotrophic Lateral Sclerosis/diagnosis/*pathology/physiopathology ; Biopsy ; Diagnosis, Differential ; Electromyography ; Humans ; Polyneuropathies/diagnosis ; Spinal Nerves/*ultrastructure ; Sural Nerve/*ultrastructure ; }, abstract = {The aim of this work was to study the neuropathological picture of the sural nerve in the pseudopolineuropathic form of A.L.S. Five patients were considered: in all cases the clinical and electromyographic follow-up excluded other diseases. EMG-studies were repeatedly performed: they showed the progressive evolution of the spinal anterior horn cell pathology from lower spinal to cervical levels. The sural nerve was processed according to the procedure used in our laboratory for light and ultrastructural examination. Quantitative analysis of myelinated fiber density was carried out on photographic enlargement and reported on histograms. The light and ultrastructural examination showed a severe loss of myelinated fibers; the decrease affected all types of fibers, but predominated in the largest ones. In the axons there was an increase of mitochondria, dilation of the small vesicles and increase in the number of neurofilaments. It is our opinion that all histopathologic data obtained in the sural nerve biopsy in this form of A.L.S. reveal a clear involvement of the sensory neurons of the spinal ganglia and the results can be useful for the study of precocius lesions in the A.L.S.}, }
@article {pmid3315862, year = {1987}, author = {Cox, JL and Cox, BJ and Fidanza, V and Calhoun, DH}, title = {The complete nucleotide sequence of the ilvGMEDA cluster of Escherichia coli K-12.}, journal = {Gene}, volume = {56}, number = {2-3}, pages = {185-198}, doi = {10.1016/0378-1119(87)90136-3}, pmid = {3315862}, issn = {0378-1119}, support = {GM23182/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Bacterial Proteins/genetics ; Base Sequence ; Biological Evolution ; Codon/genetics ; Escherichia coli/*genetics ; *Genes, Bacterial ; Information Systems ; Molecular Sequence Data ; *Multigene Family ; }, abstract = {The ilvGMEDA gene cluster of Escherichia coli K-12 has been the focus of intensive genetic and biochemical analysis for the past 30 years. Genetic regulation of the ilvGMEDA cluster involves attenuation, internal promoters, internal Rho-dependent termination sites, a site of polarity in the ilvG pseudogene of the wild-type organism, and autoregulation by the ilvA gene product, the biosynthetic L-threonine deaminase. We have now completed the nucleotide sequence of the 6600-bp cluster and have analyzed it, along with the ilvYC, ilvBN, and ilvIH genes, for codon frequencies and possible evolutionary relationships. The isoleucine content of each of the gene products of the ilvGMEDA cluster is quite similar (less than a two-fold variation), thus excluding one possible interpretation of the isoleucine-specific downstream amplification phenomenon. There is no evidence for retrograde evolution in the cluster since no significant homologies are detectable among genes that catalyze sequential reactions of the pathway. A highly significant homology does exist, however, between the threonine deaminases of yeast mitochondria and E. coli. The sequence at the boundary of the ilvA and ilvD genes is TAATAATG, so that the second TAA stop codon of ilvD overlaps the ATG initiation codon of ilvA.}, }
@article {pmid3304084, year = {1987}, author = {Cavalier-Smith, T}, title = {The simultaneous symbiotic origin of mitochondria, chloroplasts, and microbodies.}, journal = {Annals of the New York Academy of Sciences}, volume = {503}, number = {}, pages = {55-71}, doi = {10.1111/j.1749-6632.1987.tb40597.x}, pmid = {3304084}, issn = {0077-8923}, mesh = {Animals ; *Biological Evolution ; *Chloroplasts ; Genes ; *Microbodies ; *Mitochondria ; *Symbiosis ; }, }
@article {pmid3304083, year = {1987}, author = {Kippert, F}, title = {Endocytobiotic coordination, intracellular calcium signaling, and the origin of endogenous rhythms.}, journal = {Annals of the New York Academy of Sciences}, volume = {503}, number = {}, pages = {476-495}, doi = {10.1111/j.1749-6632.1987.tb40631.x}, pmid = {3304083}, issn = {0077-8923}, mesh = {*Biological Clocks ; Biological Evolution ; Calcium/*physiology ; *Cell Physiological Phenomena ; Cytoskeleton/physiology ; Eukaryotic Cells/*physiology ; Mitochondria/physiology ; Prokaryotic Cells/*physiology ; }, }
@article {pmid3304075, year = {1987}, author = {Bermudes, D and Margulis, L and Tzertzinis, G}, title = {Prokaryotic origin of undulipodia. Application of the panda principle to the centriole enigma.}, journal = {Annals of the New York Academy of Sciences}, volume = {503}, number = {}, pages = {187-197}, doi = {10.1111/j.1749-6632.1987.tb40608.x}, pmid = {3304075}, issn = {0077-8923}, mesh = {Bacteria/ultrastructure ; *Biological Evolution ; Cells/*ultrastructure ; *Centrioles/ultrastructure ; *Cilia/ultrastructure ; Eukaryotic Cells/*ultrastructure ; *Flagella/ultrastructure ; Mitochondria ; Models, Biological ; Prokaryotic Cells/*ultrastructure ; Symbiosis ; }, }
@article {pmid3300813, year = {1987}, author = {Szathmáry, E}, title = {Early evolution of microtubules and undulipodia.}, journal = {Bio Systems}, volume = {20}, number = {2}, pages = {115-131}, doi = {10.1016/0303-2647(87)90039-6}, pmid = {3300813}, issn = {0303-2647}, mesh = {*Biological Evolution ; *Cell Movement ; Cilia/*physiology ; Flagella/*physiology ; Microtubules/*physiology ; Models, Biological ; Spirochaeta/physiology ; }, abstract = {A critique of both autogeneous and symbiotic hypotheses for the origin of microtubules and cilia and eukaryotic flagella (undulipodia) is presented. It is proposed that spirochetes provided the ancient eukaryotic cell with microtubules twice; cytoplasmic microtubules originated from phagocytosed spirochetes whereas axopodial tubules of undulipodia were transformed from ectosymbiotic spirochetes. A role in transport for microtubules in spirochetes together with a detailed scenario by which free-living spirochetes attached as ectosymbionts and subsequently differentiated into undulipodia is outlined. A mechanism for the continuity of motility in the form of "training" of the novel microtubular axoneme by the ancient spirochete motility apparatus is proposed. Transitional states (missing links) are unlikely to have survived. Constraints regarding the nature of the host cell are discussed. A corresponding flowchart of the early evolution of eukaryotes is presented in which plastids and mitochondria are polyphyletic in their origins.}, }
@article {pmid3129569, year = {1987}, author = {Manske, CL and Chapman, DJ}, title = {Nonuniformity of nucleotide substitution rates in molecular evolution: computer simulation and analysis of 5S ribosomal RNA sequences.}, journal = {Journal of molecular evolution}, volume = {26}, number = {3}, pages = {226-251}, pmid = {3129569}, issn = {0022-2844}, mesh = {Animals ; Bacteria/genetics ; Base Sequence ; *Biological Evolution ; Computer Simulation ; *Genetic Variation ; Humans ; *Models, Genetic ; Phylogeny ; RNA, Ribosomal/*genetics ; RNA, Ribosomal, 5S/*genetics ; }, abstract = {The effects of temporal (among different branches of a phylogeny) and spatial (among different nucleotide sites within a gene) nonuniformities of nucleotide substitution rates on the construction of phylogenetic trees from nucleotide sequences are addressed. Spatial nonuniformity may be estimated by using Shannon's (1948) entropy formula to measure the Relative Nucleotide Variability (RNV) at each nucleotide site in an aligned set of sequences; this is demonstrated by a comparative analysis of 5S rRNAs. New methods of constructing phylogenetic trees are proposed that augment the Unweighted Pair-Group Using Arithmetic Averages (UPGMA) algorithm by estimating and compensating for both spatial and temporal nonuniformity in substitution rates. These methods are evaluated by computer simulations of 5S rRNA evolution that include both kinds of nonuniformities. It was found that the proposed Reference Ratio Method improved both the ability to reconstruct the correct topology of a tree and also the estimation of branch lengths as compared to UPGMA. A previous method (Farris et al. 1970; Klotz et al. 1979; Li 1981) was found to be less successful in reconstructing topologies when there is high probability of multiple mutations at some sites. Phylogenetic analyses of 5S rRNA sequences support the endosymbiotic origins of both chloroplasts and mitochondria, even though the latter exhibit an accelerated rate of nucleotide substitution. Phylogenetic trees also reveal an adaptive radiation within the eubacteria and another within the eukaryotes for the origins of most major phyla within each group during the Precambrian era.}, }
@article {pmid3125340, year = {1987}, author = {Ochman, H and Wilson, AC}, title = {Evolution in bacteria: evidence for a universal substitution rate in cellular genomes.}, journal = {Journal of molecular evolution}, volume = {26}, number = {1-2}, pages = {74-86}, pmid = {3125340}, issn = {0022-2844}, support = {GM-10158/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/*genetics ; *Biological Evolution ; Fossils ; *Genes, Bacterial ; Genetic Variation ; *Models, Genetic ; Phylogeny ; RNA, Ribosomal/genetics ; }, abstract = {This paper constructs a temporal scale for bacterial evolution by tying ecological events that took place at known times in the geological past to specific branch points in the genealogical tree relating the 16S ribosomal RNAs of eubacteria, mitochondria, and chloroplasts. One thus obtains a relationship between time and bacterial RNA divergence which can be used to estimate times of divergence between other branches in the bacterial tree. According to this approach, Salmonella typhimurium and Escherichia coli diverged between 120 and 160 million years (Myr) ago, a date which fits with evidence that the chief habitats occupied now by these two enteric species became available that long ago. The median extent of divergence between S. typhimurium and E. coli at synonymous sites for 21 kilobases of protein-coding DNA is 100%. This implies a silent substitution rate of 0.7-0.8%/Myr--a rate remarkably similar to that observed in the nuclear genes of mammals, invertebrates, and flowering plants. Similarities in the substitution rates of eucaryotes and procaryotes are not limited to silent substitutions in protein-coding regions. The average substitution rate for 16S rRNA in eubacteria is about 1%/50 Myr, similar to the average rate for 18S rRNA in vertebrates and flowering plants. Likewise, we estimate a mean rate of roughly 1%/25 Myr for 5S rRNA in both eubacteria and eucaryotes. For a few protein-coding genes of these enteric bacteria, the extent of silent substitution since the divergence of S. typhimurium and E. coli is much lower than 100%, owing to extreme bias in the usage of synonymous codons. Furthermore, in these bacteria, rates of amino acid replacement were about 20 times lower, on average, than the silent rate. By contrast, for the mammalian genes studied to date, the average replacement rate is only four to five times lower than the rate of silent substitution.}, }
@article {pmid3125338, year = {1987}, author = {Lake, JA}, title = {Determining evolutionary distances from highly diverged nucleic acid sequences: operator metrics.}, journal = {Journal of molecular evolution}, volume = {26}, number = {1-2}, pages = {59-73}, pmid = {3125338}, issn = {0022-2844}, support = {GM24034/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; *Biological Evolution ; Genetic Vectors ; *Models, Genetic ; Nucleic Acids/*genetics ; Species Specificity ; }, abstract = {Operator metrics are explicitly designed to measure evolutionary distances from nucleic acid sequences when substitution rates differ greatly among the organisms being compared, or when substitutions have been extensive. Unlike lengths calculated by the distance matrix and parsimony methods, in which substitutions in one branch of a tree can alter the measured length of another branch, lengths determined by operator metrics are not affected by substitutions outside the branch. In the method, lengths (operator metrics) corresponding to each of the branches of an unrooted tree are calculated. The metric length of a branch reconstructs the number of (transversion) differences between sequences at a tip and a node (or between nodes) of a tree. The theory is general and is fundamentally independent of differences in substitution rates among the organisms being compared. Mathematically, the independence has been obtained because the metrics are eigenvectors of fundamental equations which describe the evolution of all unrooted trees. Even under conditions when both the distance matrix method or a simple parismony length method are shown to indicate lengths that are an order of magnitude too large or too small, the operator metrics are accurate. Examples, using data calculated with evolutionary rates and branchings designed to confuse the measurement of branch lengths and to camouflage the topology of the true tree, demonstrate the validity of operator metrics. The method is robust. Operator metric distances are easy to calculate, can be extended to any number of taxa, and provide a statistical estimate of their variances. The utility of the method is demonstrated by using it to analyze the origins and evolution of chloroplasts, mitochondria, and eubacteria.}, }
@article {pmid3116275, year = {1987}, author = {Mikelsaar, R}, title = {A view of early cellular evolution.}, journal = {Journal of molecular evolution}, volume = {25}, number = {2}, pages = {168-183}, pmid = {3116275}, issn = {0022-2844}, mesh = {Animals ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Genetic Code ; *Models, Genetic ; Phylogeny ; Species Specificity ; }, abstract = {Some recent puzzling data on mitochondria put in question their place on the phylogenetic tree. A hypothesis, the archigenetic hypothesis, is presented, which generally agrees with Woese-Fox's concept of the common origin of eubacteria, archaebacteria, and eukaryotic hosts. However, for the first time, a case is made for the evolution of mitochondria from the ancient predecessors of pro- and eukaryotes (protobionts), not from eubacteria. Animal, fungal, and plant mitochondria are considered to be endosymbionts derived from independent free-living cells (mitobionts), which, having arisen at different developmental stages of protobionts, retained some of their ancient primitive features of the genetic code and the transcription-translation systems. The molecular-biological, bioenergetic, and paleontological aspects of this new concept of cellular evolution are discussed.}, }
@article {pmid3037091, year = {1987}, author = {Kunisawa, T and Horimoto, K and Otsuka, J}, title = {Accumulation pattern of amino acid substitutions in protein evolution.}, journal = {Journal of molecular evolution}, volume = {24}, number = {4}, pages = {357-365}, pmid = {3037091}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; *Amino Acids ; Animals ; *Biological Evolution ; Cytochrome c Group/genetics ; Hemoglobins/genetics ; Humans ; Mitochondria/metabolism ; Proteins/*genetics ; Species Specificity ; }, abstract = {A simple method for the evolutionary analysis of amino acid sequence data is presented and used to examine whether the number of variable sites (NVS) of a protein is constant during its evolution. The NVSs for hemoglobin and for mitochondrial cytochrome c are each found to be almost constant, and the ratio between the NVSs is close to the ratio between the unit evolutionary periods. This indicates that the substitution rate per variable site is almost uniform for these proteins, as the neutral theory claims. An advantage of the present analysis is that it can be done without knowledge of paleontological divergence times and can be extended to bacterial proteins such as bacterial c-type cytochromes. It is suggested that the NVS of cytochrome c has been almost constant even over the long period (ca. 3.0 billion years) of bacterial evolution but that at least two different substitution rates are necessary to describe the accumulated changes in the sequence. This "two clock" interpretation is consistent with fossil evidence for the appearance times of photosynthetic bacteria and eukaryotes.}, }
@article {pmid2896550, year = {1987}, author = {Wallace, DC and Ye, JH and Neckelmann, SN and Singh, G and Webster, KA and Greenberg, BD}, title = {Sequence analysis of cDNAs for the human and bovine ATP synthase beta subunit: mitochondrial DNA genes sustain seventeen times more mutations.}, journal = {Current genetics}, volume = {12}, number = {2}, pages = {81-90}, pmid = {2896550}, issn = {0172-8083}, support = {GM33022/GM/NIGMS NIH HHS/United States ; NS21328/NS/NINDS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Cattle ; Cloning, Molecular ; DNA/*genetics ; DNA Restriction Enzymes ; DNA, Mitochondrial/*genetics ; *Genes ; Humans ; Macromolecular Substances ; Mitochondria, Liver/enzymology ; Molecular Sequence Data ; *Mutation ; Proton-Translocating ATPases/*genetics ; Species Specificity ; }, abstract = {We have cloned and sequenced human and bovine cDNAs for the beta subunit of the ATP synthase (ATP-syn beta), a nuclear DNA (nDNA) encoded oxidative phosphorylation (OXPHOS) gene. The two cDNAs were found to share 99% amino acid homology and 94% nucleotide homology. The evolutionary rate of ATPsyn beta was then compared with that of two mitochondrial DNA (mtDNA) ATP synthase genes (ATPase 6 and 8), seven other mtDNA OXPHOS genes, and a number of nuclear genes. The synonymous substitution rate for ATPsyn beta proved to be 1.9 x 10(-9) substitutions per site per year (substitutions x site-1 x year-1) (SSY). This is less than 1/2 that of the average nDNA gene, 1/12 the rate of ATPase 6 and 8, and 1/17 the rate of the average mtDNA gene. The synonymous and replacement substitution rates were used to calculate a new parameter, the "selective constraint ratio". This revealed that even the most variable mtDNA protein was more constrained than the average nDNA protein. Thus, the high substitution mutation rate and strong selective constraints of mammalian mtDNA proteins suggest that mtDNA mutations may result in a disproportionately large number of human hereditary diseases of OXPHOS.}, }
@article {pmid2884075, year = {1987}, author = {Smith, DD and Campbell, JW}, title = {Glutamine synthetase in liver of the American alligator, Alligator mississippiensis.}, journal = {Comparative biochemistry and physiology. B, Comparative biochemistry}, volume = {86}, number = {4}, pages = {755-762}, doi = {10.1016/0305-0491(87)90223-9}, pmid = {2884075}, issn = {0305-0491}, mesh = {Alligators and Crocodiles/*metabolism ; Animals ; Glutamate-Ammonia Ligase/genetics/*metabolism ; Liver/*enzymology ; Macromolecular Substances ; Mitochondria, Liver/*enzymology/ultrastructure ; Molecular Weight ; Protein Biosynthesis ; RNA, Messenger/genetics ; Reptiles/*metabolism ; }, abstract = {Glutamine synthetase was shown to be localized in liver mitochondria of the American alligator, Alligator mississippiensis, by immunofluorescent staining of frozen liver sections and by the detection of enzymatic activity and immunoreactive protein in the mitochondrial fraction following subcellular fractionation of liver tissue by differential centrifugation. The primary translation product of alligator liver glutamine synthetase mRNA was shown to have an Mr = 45,000 which is similar if not identical in size to that of the mature subunit. This mRNA was found to be heterogeneous in size with a major form corresponding to 2.8-3.0 kb and a lesser form corresponding to around 2 kb. Both are in excess of the size required to code for the glutamine synthetase subunit. The synthesis and presumably the mitochondrial import of glutamine synthetase in alligator liver are thus very similar to the same processes in avian liver. Despite the excretion of a high percentage of nitrogen as ammonia, the demonstration of a mitochondrial glutamine synthetase indicates the alligator has the typical avian-type uricotelic ammonia-detoxification system in liver. This suggests that the transition to uricotelism occurred in the sauropsid line of evolution and has persisted through both the lepidosaurian (snakes, lizards) and archosaurian (dinosaurs, crocodilians, birds) lines.}, }
@article {pmid2825587, year = {1987}, author = {Simpson, L}, title = {The mitochondrial genome of kinetoplastid protozoa: genomic organization, transcription, replication, and evolution.}, journal = {Annual review of microbiology}, volume = {41}, number = {}, pages = {363-382}, doi = {10.1146/annurev.mi.41.100187.002051}, pmid = {2825587}, issn = {0066-4227}, support = {AI 09102/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; DNA Replication ; DNA, Circular/genetics ; DNA, Kinetoplast ; DNA, Mitochondrial/*genetics ; Eukaryota/*genetics/ultrastructure ; *Genes ; Mitochondria/metabolism ; *Transcription, Genetic ; }, }
@article {pmid2822348, year = {1987}, author = {Montecucco, C and Schiavo, G and Bacci, B and Bisson, R}, title = {Isolation and characterization of cytochrome c oxidase from bird and fish heart mitochondria.}, journal = {Comparative biochemistry and physiology. B, Comparative biochemistry}, volume = {87}, number = {4}, pages = {851-856}, doi = {10.1016/0305-0491(87)90401-9}, pmid = {2822348}, issn = {0305-0491}, mesh = {Animals ; Birds/*metabolism ; Electron Transport Complex IV/*isolation &amp; purification/metabolism ; Fishes/*metabolism ; Kinetics ; Mitochondria, Heart/*enzymology ; Species Specificity ; }, abstract = {1. Several bird and fish heart mitochondrial cytochrome c oxidases have been isolated with a rapid and simple method involving hydrophobic and affinity chromatography. 2. Their spectrophotometric and kinetic properties are very similar to those of the mammalian enzymes. 3. These oxidases show a polypeptide composition simpler than the mammalian enzymes being composed of 9-10, instead of 13, different polypeptides. 4. These data suggest that the complexity of the mitochondrial heart oxidase increases with the stage of evolution.}, }
@article {pmid2446672, year = {1987}, author = {Benne, R and Sloof, P}, title = {Evolution of the mitochondrial protein synthetic machinery.}, journal = {Bio Systems}, volume = {21}, number = {1}, pages = {51-68}, doi = {10.1016/0303-2647(87)90006-2}, pmid = {2446672}, issn = {0303-2647}, mesh = {Animals ; *Biological Evolution ; Eukaryota/genetics/metabolism ; Mitochondria/*metabolism ; *Protein Biosynthesis ; RNA/genetics/metabolism ; RNA, Mitochondrial ; Ribosomal Proteins/genetics/metabolism ; Ribosomes/metabolism ; }, abstract = {Comparative analysis of the components of the mitochondrial translational apparatus reveals a remarkable variability. For example the mitochondrial ribosomal rRNAs, display a three-fold difference in size in different organisms as a result of insertions or deletions, which affect specific areas of the rRNA molecule. This suggests that such areas are either not essential for mitoribosome function or that they can be replaced by proteins. Also mitochondrial tRNAs and mitoribosomal proteins are much less conserved than their cytoplasmic counterparts. Not only do the mitochondrial translational molecules vary in properties, also the location of the genes from which they are derived is not the same in all cases: mitochondrial tRNA genes which usually are found in the mtDNA, may have a nuclear location in protozoa and, conversely, only in fungi one finds a mitoribosomal protein gene in the organellar genome. The high rate of change of the components of the mitochondrial protein synthesizing machinery is accompanied by a number of unique features of the translation process: (i) the mitochondrial genetic code differs substantially from the standard code in a species-specific manner; (ii) special codon-anticodon recognition rules are followed; (iii) unusual mechanisms of translational initiation may exist. These observations suggest that the evolutionary pressures that have shaped the present day mitochondrial translational apparatus have been different in different organisms and also distinct from those acting on the cytoplasmic machinery. In spite of the interspecies variability, however, many features of the mitochondrial and bacterial protein synthetic apparatus show a clear resemblance, providing support for the hypothesis of a prokaryotic endosymbiont ancestry of mitochondria.}, }
@article {pmid3022944, year = {1986}, author = {Hartl, FU and Schmidt, B and Wachter, E and Weiss, H and Neupert, W}, title = {Transport into mitochondria and intramitochondrial sorting of the Fe/S protein of ubiquinol-cytochrome c reductase.}, journal = {Cell}, volume = {47}, number = {6}, pages = {939-951}, doi = {10.1016/0092-8674(86)90809-3}, pmid = {3022944}, issn = {0092-8674}, mesh = {Amino Acid Sequence ; Biological Transport ; Electron Transport Complex III/*metabolism ; Intracellular Membranes/metabolism ; Iron-Sulfur Proteins/*metabolism ; Metalloproteins/*metabolism ; Mitochondria/*metabolism ; Models, Biological ; Neurospora crassa ; Peptide Hydrolases/metabolism ; Protein Conformation ; Protein Precursors/metabolism ; Protein Processing, Post-Translational ; }, abstract = {The Fe/S protein of complex III is encoded by a nuclear gene, synthesized in the cytoplasm as a precursor with a 32 residue amino-terminal extension, and transported to the outer surface of the inner mitochondrial membrane. Our data suggest the following transport pathway. First, the precursor is translocated via translocation contact sites into the matrix. There, cleavage to an intermediate containing an eight residue extension occurs. The intermediate is then redirected across the inner membrane, processed to the mature subunit, and assembled into complex III. We suggest that the folding and membrane-translocation pathway in the endosymbiotic ancestor of mitochondria has been conserved during evolution of eukaryotic cells; transfer of the gene for Fe/S protein to the nucleus has led to addition of the presequence, which routes the precursor back to its "ancestral" assembly pathway.}, }
@article {pmid2881782, year = {1986}, author = {Gearing, DP and Nagley, P}, title = {Yeast mitochondrial ATPase subunit 8, normally a mitochondrial gene product, expressed in vitro and imported back into the organelle.}, journal = {The EMBO journal}, volume = {5}, number = {13}, pages = {3651-3655}, pmid = {2881782}, issn = {0261-4189}, mesh = {Biological Evolution ; Electron Transport Complex IV/genetics ; *Genes ; *Genes, Fungal ; Macromolecular Substances ; Mitochondria/*enzymology ; Protein Biosynthesis ; *Protein Processing, Post-Translational ; Proteolipids/*genetics ; Proton-Translocating ATPases/*genetics ; Saccharomyces cerevisiae/enzymology/*genetics ; Transcription, Genetic ; }, abstract = {Subunit 8 of yeast mitochondrial F1F0-ATPase is a proteolipid made on mitochondrial ribosomes and inserted directly into the inner membrane for assembly with the other F0 membrane-sector components. We have investigated the possibility of expressing this extremely hydrophobic, mitochondrially encoded protein outside the organelle and directing its import back into mitochondria using a suitable N-terminal targeting presequence. This report describes the successful import in vitro of ATPase subunit 8 proteolipid into yeast mitochondria when fused to the targeting sequence derived from the precursor of Neurospora crassa ATPase subunit 9. The predicted cleavage site of matrix protease was correctly recognized in the fusion protein. A targeting sequence from the precursor of yeast cytochrome oxidase subunit VI was unable to direct the subunit 8 proteolipid into mitochondria. The proteolipid subunit 8 exhibited a strong tendency to embed itself in mitochondrial membranes, which interfered with its ability to be properly imported when part of a synthetic precursor.}, }
@article {pmid3097641, year = {1986}, author = {Powell, JR and Caccone, A and Amato, GD and Yoon, C}, title = {Rates of nucleotide substitution in Drosophila mitochondrial DNA and nuclear DNA are similar.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {83}, number = {23}, pages = {9090-9093}, pmid = {3097641}, issn = {0027-8424}, mesh = {Animals ; Biological Evolution ; Cell Nucleus ; DNA/*genetics ; DNA, Mitochondrial/*genetics ; Drosophila/*genetics ; Drosophila melanogaster/genetics ; Nucleic Acid Denaturation ; Tetraethylammonium ; Tetraethylammonium Compounds ; }, abstract = {While the majority of DNA in eukaryotes is in the nucleus, a small but functionally significant amount is found in organelles such as chloroplasts and mitochondria. A recent, rather remarkable, finding has been that in vertebrates the DNA in the mitochondria (mtDNA) is evolving 5-10 times faster than the DNA in the nucleus. No similar studies have been done with invertebrates. Using the technique of DNA X DNA hybridization, we have measured the degree of nucleotide substitution between Drosophila melanogaster and Drosophila yakuba for both single-copy nuclear DNA (scnDNA) and mtDNA. The change in melting temperature is the same in both types of DNA hybrids. Thus we conclude that mtDNA and scnDNA are evolving at similar rates in these Drosophila. Considerable DNA sequence data are available for the mtDNAs studied, allowing us to estimate that a 1 degree C change in melting temperature corresponds to a 1.5-2% base-pair mismatch.}, }
@article {pmid3022735, year = {1986}, author = {Woolley, KJ and Athalye, M}, title = {A use for principal coordinate analysis in the comparison of protein sequences.}, journal = {Biochemical and biophysical research communications}, volume = {140}, number = {3}, pages = {808-813}, doi = {10.1016/0006-291x(86)90705-9}, pmid = {3022735}, issn = {0006-291X}, mesh = {*Amino Acid Sequence ; Animals ; Biological Evolution ; Cytochrome c Group/genetics ; Humans ; Mathematics ; Mitochondria/enzymology ; Proteins/*genetics ; Species Specificity ; }, abstract = {Principal Coordinate analysis (PCO) was applied to the comparison of protein sequences. A similarity matrix was derived from a dataset containing 21 c-type cytochrome sequences and this was analysed using PCO to produce a plot of the first three principal axes. The relationships indicated from this plot are considered in conjunction with those derived by cluster analysis using the UPGMA method, and the advantages offered by a nonhierarchical method of sequence comparison discussed.}, }
@article {pmid3800286, year = {1986}, author = {Fabiani, JN and Camilleri, JP}, title = {[Membrane modifications in myocardial infarction following emergency reperfusion].}, journal = {Annales de cardiologie et d'angeiologie}, volume = {35}, number = {7 Pt 2}, pages = {439-446}, pmid = {3800286}, issn = {0003-3928}, mesh = {Allopurinol/pharmacology ; Animals ; Calcium/metabolism ; *Cell Membrane Permeability ; Free Radicals ; Mitochondria, Heart/metabolism ; Myocardial Infarction/*metabolism/pathology/therapy ; *Myocardial Revascularization ; Peroxides/*metabolism ; Sarcolemma/ultrastructure ; Succinate Dehydrogenase/metabolism ; Time Factors ; }, abstract = {The effects of revascularization on the morphological aspects of myocardial infarction have been studied in 87 animals. After permanent ligation of a coronary artery, the aspects are stereotyped and the histo-enzymatic and ultrastructural evolution is quite well known. On the contrary, early revascularization of this infarction at different times causes specific alterations: alteration of the membrane permeability with an intense edema of myocardial cells, restriction of the negative succinate dehydrogenase zone, cleavage of the sarcolemma membrane, intra-mitochondrial calcium deposits and destruction of endothelial membranes. These lesions are responsible for the non-revascularization phenomenon which limits considerably the metabolic recovery of the ischemic area. These spectacular membrane destructions of the revascularization could be linked to the release of free radicals. Besides, the use of Mannitol and Allopurinol, with their known protective effect on the free radicals, enables to greatly reduce the size of the resulting infarction (60 animals). 12 patients, after failure of a coronary dilatation, were treated in the first six hours with a cardioplegic perfusion with allopurinol followed by a by-pass. The long term results show the retrogression of the Q waves in 11 out of 12 cases and the functional recovery of the akinetic area on the echocardiogram.}, }
@article {pmid3541331, year = {1986}, author = {Seravin, LN}, title = {[The origin of the eukaryotic cell. IV. The general hypothesis of the autogenous origin of eukaryotes].}, journal = {Tsitologiia}, volume = {28}, number = {9}, pages = {899-910}, pmid = {3541331}, issn = {0041-3771}, mesh = {Aerobiosis ; Animals ; Biological Evolution ; Cell Membrane/ultrastructure ; Cells/*cytology ; Chloroplasts/ultrastructure ; DNA/genetics ; DNA, Bacterial/genetics ; Eukaryotic Cells/*cytology/metabolism ; Mitochondria/ultrastructure ; Mitosis ; Photosynthesis ; Prokaryotic Cells/cytology/metabolism ; }, abstract = {The general hypothesis of autogenous (non-symbiotic) origin of the eukaryotic cell summarises some hypotheses explaining possible ways of the origin of main components and organelles of such a cell (the primary unicellular protist). Six hypothesises are suggested. Arising of the eukaryotic surface membrane of protist (cell) as a result of modification of its lipidoacidic composition, when most of synblocks and ensembles of eukaryotic enzymes sink into the cytoplasm (due to membrane vesiculation). Establishment of eukaryotic cytoplasm on the basis of successive formation of two locomotory-supporting apparates: the primary one (microtrabecular system), and the second one (cytoskeleton). Arising of the nucleus from a polyheteronomous nucleoid of proeukaryotes. A combinatorical hypothesis of mitosis formation. Polyheteronucleoid hypothesis of the origin of the mitochondria and chloroplasts. Arising of the flagellum from the contractile tentacle-like organelle, whose axoneme is made of single microtubules. A close interrelation and interaction in the process of evolution is noted between surface membranes, the cytoplasm and the nucleus. In accord a principles of block-construction and heterochrony (see: Seravin, 1986r), the author explains the preservation of prokaryotic signs of organization in some components (and organelles) of eukaryotic cell (and protists).}, }
@article {pmid3744027, year = {1986}, author = {Gillespie, JH}, title = {Variability of evolutionary rates of DNA.}, journal = {Genetics}, volume = {113}, number = {4}, pages = {1077-1091}, pmid = {3744027}, issn = {0016-6731}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Codon ; DNA/*genetics ; Genes ; *Genetic Variation ; Humans ; Mitochondria/metabolism ; *Models, Genetic ; Phylogeny ; Species Specificity ; Statistics as Topic ; }, abstract = {A statistical analysis of DNA sequences from four nuclear loci and five mitochondrial loci from different orders of mammals is described. A major aim of the study is to describe the variation in the rate of molecular evolution of proteins and DNA. A measure of rate variability is the statistic R, the ratio of the variance in the number of substitutions to the mean number. For proteins, R is found to be in the range 0.16 less than R less than 35.55, thus extending in both directions the values seen in previous studies. An analysis of codons shows that there is a highly significant excess of double substitutions in the first and second positions, but not in the second and third or first and third positions. The analysis of the dynamics of nucleotide evolution showed that the ergodic Markov chain models that are the basis of most published formulas for correcting for multiple substitutions are incompatible with the data. A bootstrap procedure was used to show that the evolution of the individual nucleotides, even the third positions, show the same variation in rates as seen in the proteins. It is argued that protein and silent DNA evolution are uncoupled, with the evolution at both levels showing patterns that are better explained by the action of natural selection than by neutrality. This conclusion is based primarily on a comparison of the nuclear and mitochondrial results.}, }
@article {pmid3535181, year = {1986}, author = {Seravin, LN}, title = {[The origin of the eukaryotic cell. III. Principles of the morphofunctional organization of the eukaryotic cell].}, journal = {Tsitologiia}, volume = {28}, number = {8}, pages = {779-789}, pmid = {3535181}, issn = {0041-3771}, mesh = {Animals ; Biological Evolution ; Cell Compartmentation ; Cells/*ultrastructure ; Eukaryota/physiology/ultrastructure ; Eukaryotic Cells/physiology/*ultrastructure ; Intracellular Membranes/physiology/ultrastructure ; Organoids/physiology/ultrastructure ; }, abstract = {The eukaryotic plasmalemma, eukaryotic cytoplasm with its usual cytomembranes, and eukaryotic nucleus are obligatory components of the eukaryotic cell. All other structural elements (organelles) are only derivates of the aforesaid cell components and they may be absent sometimes. There are protozoans having simultaneously no flagelles, mitochondria and chloroplasts (all the representatives of phylum Microspora, amoeba Pelomyxa palustris, and others). The following five general principles play the main role in the morphofunctional organization of the cell. The principle of hierarchy of block organization of living systems. Complex morphofunctional blocks (organelles) specific for the eukaryotic cell are formed. The compartmentalization principle. The main cell organelles (nuclei, flagellae, mitochondria, chloroplasts, etc.) undergo a relative morphological isolation from each other and other cell organelles by means of the total or partial surrounding by membranes; this may ensure the originality of their evolution and function. The principle of poly- and oligomerization of morphofunctional blocks. It permits the cell to enlarge its sizes and to raise the level of integration. The principle of heterochrony, including three subprinciples: conservatism of useful signs; a strong acceleration of evolutionary development of the separate blocks; simplification of the structure, reduction or total disappearance of some blocks. It explains a preservation of prokaryotic signs in the eukaryotic cell or in its organelles. The principle of independent origin of similar morphofunctional blocks in the process of evolution of living systems. The parallelism of the signs in unrelated groups of cells (or protists) arises due to this principle.}, }
@article {pmid3641921, year = {1986}, author = {Bishop, MJ and Thompson, EA}, title = {Maximum likelihood alignment of DNA sequences.}, journal = {Journal of molecular biology}, volume = {190}, number = {2}, pages = {159-165}, doi = {10.1016/0022-2836(86)90289-5}, pmid = {3641921}, issn = {0022-2836}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Cattle ; DNA/*genetics ; Genes ; Humans ; Mice ; Mitochondria/analysis ; Models, Genetic ; Probability ; RNA, Transfer, Amino Acyl/genetics ; }, abstract = {The optimal alignment problem for pairs of molecular sequences under a probabilistic model of evolutionary change is equivalent to the problem of estimating the maximum likelihood time required to transform one sequence to the other. When this time has been estimated, various alignments of high posterior probability may be written down. A simple model with two parameters is presented and a method is described by which the likelihood may be computed. Maximum likelihood estimates for some pairs of tRNA genes illustrate the method and allow us to obtain the best alignments under the model.}, }
@article {pmid3532640, year = {1986}, author = {Kharchenko, EP}, title = {[The invariance of the genetic code and its possible evolutionary path].}, journal = {Zhurnal evoliutsionnoi biokhimii i fiziologii}, volume = {22}, number = {4}, pages = {351-356}, pmid = {3532640}, issn = {0044-4529}, mesh = {Animals ; Base Composition ; Base Sequence ; *Biological Evolution ; Exons ; Genes ; *Genetic Code ; *Genetic Variation ; Introns ; Mitochondria/ultrastructure ; Protein Biosynthesis ; }, }
@article {pmid3095864, year = {1986}, author = {Portelli, C and Ursu, C and Portelli, AP}, title = {The distribution of codons by classes of triplets in the sequence of genes.}, journal = {Physiologie (Bucarest)}, volume = {23}, number = {3}, pages = {209-212}, pmid = {3095864}, issn = {1011-6206}, mesh = {Base Sequence ; Codon/*classification ; Genes, Viral ; Genetic Code ; Humans ; Mitochondria/analysis ; RNA, Messenger/*classification ; }, abstract = {According to a criterion of symmetry-asymmetry, the triplets of the genetic code can be divided into four classes. In the genes of viruses and human mitochondria, the frequency by which a codon is followed by a codon of the same class is higher than that theoretically estimated. This is the consequence of the fact that in an initial stage of evolution many codons were duplicated.}, }
@article {pmid3094213, year = {1986}, author = {Seravin, LN}, title = {[The origin of the eukaryotic cell. II. A critical analysis of the symbiotic (exogenous) concept].}, journal = {Tsitologiia}, volume = {28}, number = {7}, pages = {659-669}, pmid = {3094213}, issn = {0041-3771}, mesh = {Animals ; Bacteria/ultrastructure ; Cells/*ultrastructure ; Chloroplasts/ultrastructure ; Cyanobacteria/ultrastructure ; DNA/ultrastructure ; Eukaryotic Cells/*ultrastructure ; Fungi/ultrastructure ; Mitochondria/ultrastructure ; *Symbiosis ; }, abstract = {The exogenous (symbiotic) conception of the eukaryotic cell origin is unable to explain satisfactory the structure of mitochondria and chloroplasts. Either of these organelles possess its genome that can be compared with the viral one rather than with the bacterial one, judging by the dimensions and quantity of coding genes. The mitochondria resemble a little prokaryotes in the number of their proteins, chemical composition of their inner membrane and peculiarities of the protein-synthesizing apparatus. The primitive structure of mt DNA, the lesser quantity and greater unspecifity of the mitochondrial tRNA prove, additionally, the non-bacterial origin of this organelles. The deflexion of the genetic code from the universal one in the mitochondrial nucleoids also testify in favour of this point of view. The results of micropaleontological and paleobiochemical investigations evidence towards initial ability of the primary eukaryotes (primary protists) to photosynthesis. In this case, they did not need to acquire plastids from outside by symbiotic way. The autogenous origin of the flagellum of the primary protists was reported earlier (Seravin, 1985). The accumulated data permit us to consider that the cell organelles formed endogenously in the process of evolution of the cell.}, }
@article {pmid3516224, year = {1986}, author = {Borst, P}, title = {How proteins get into microbodies (peroxisomes, glyoxysomes, glycosomes).}, journal = {Biochimica et biophysica acta}, volume = {866}, number = {4}, pages = {179-203}, doi = {10.1016/0167-4781(86)90044-8}, pmid = {3516224}, issn = {0006-3002}, mesh = {Acetyl-CoA C-Acyltransferase/physiology ; Acyl-CoA Oxidase ; Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Carnitine O-Acetyltransferase/physiology ; Catalase/physiology ; Endoplasmic Reticulum/metabolism ; Facial Bones/abnormalities ; Glycolysis ; Humans ; In Vitro Techniques ; Isoelectric Point ; Kidney Diseases, Cystic/metabolism ; Liver Diseases/congenital ; Malate Dehydrogenase/physiology ; Microbodies/*metabolism ; Mitochondria/metabolism ; Oxidoreductases/physiology ; Phosphoglycerate Kinase/genetics ; Proteins/*metabolism ; Protoplasts/metabolism ; Skull/abnormalities ; Triose-Phosphate Isomerase/analysis ; Trypanosoma/metabolism ; }, abstract = {All microbody proteins studies, including one microbody membrane protein, are made on free polysomes and imported post-translationally. This holds for animal tissues, plants, and fungi. The majority of microbody protein sub-units are synthesized in a form not detectably different from mature sub-units. In five cases a larger precursor protein has been found. The position of the extra piece in this precursor is not known. In two of the five cases, processing of the precursor is not coupled to import; in the other three this remains to be determined. It is not even known whether information in the prepiece contributes to topogenesis, or serves other purposes. Microbody preparations from Neurospora, plant tissue and rat liver can take up some newly synthesized microbody proteins in vitro. In most cases uptake is inefficient. No special requirements for uptake have been established and whether a receptor is involved is not yet known. Several examples have been reported of peroxisomal enzymes with a counterpart in another cell compartment. With the exception of catalase, no direct evidence is available in any of these cases for two isoenzymes specified by the same gene. In the Zellweger syndrome, a lethal hereditary disease of man, characterized by a lack of peroxisomes, the levels of several enzymes of lipid metabolism are strongly decreased. In contrast, D-amino-acid oxidase, L-alpha-hydroxyacid oxidase and catalase levels are normal. The catalase resides in the cytosol. Since there is no separate gene for cytosolic catalase, the normal catalase levels in Zellweger cells show that some peroxisomal enzymes can mature and survive stably in the cytosol. It is possible that maturation of the peroxisomal enzyme in the cytoplasm can account for the finding of cytosolic catalase in some normal mammalian cells. The glycosomes of trypanosomes are microbodies that contain a glycolytic system. Comparison of the glycosomal phosphoglycerate kinase with its cytosolic counterpart has shown that these isoenzymes are 93% homologous in amino-acid sequence, but less than 50% homologous to the corresponding enzymes of yeast and mammals. This implies that few alterations are required to direct a protein into microbodies. This interpretation is supported by the evidence for homology between some microbody and mitochondrial isoenzymes in other organisms mentioned under point 4. The major changes of the glycosomal phosphoglycerate kinase relative to the cytosolic enzyme are a large increase in positive charge and a C-terminal extension of 20 amino acids.(ABSTRACT TRUNCATED AT 400 WORDS)}, }
@article {pmid3720069, year = {1986}, author = {di Trapani, G and David, P and La Cara, A and Servidei, S and Tonali, P}, title = {Morphological studies of sural nerve biopsies in the pseudopolyneuropathic form of amyotrophic lateral sclerosis.}, journal = {Clinical neuropathology}, volume = {5}, number = {3}, pages = {134-138}, pmid = {3720069}, issn = {0722-5091}, mesh = {Adult ; Aged ; Amyotrophic Lateral Sclerosis/diagnosis/etiology/*pathology ; Biopsy ; Electromyography ; Female ; Humans ; Male ; Microscopy, Electron ; Middle Aged ; Neural Conduction ; Spinal Nerves/*pathology ; Sural Nerve/*pathology ; }, abstract = {The aim of this work was to study the neuropathological picture of the sural nerve in the pseudopolyneuropathic form of amyotrophic lateral sclerosis (ALS). Five patients were considered: in all cases the clinical and electromyographic follow-up excluded other diseases. EMG-studies were repeatedly performed: they showed the progressive evolution of the spinal anterior horn cell pathology from lower spinal to cervical levels. The sural nerve was removed and immediately fixed in phosphate-buffered 2.5% glutaraldehyde and processed according to the procedure used in our laboratory for light and ultrastructural microscopy. Quantitative analysis of myelinated fiber density was carried out on photographic enlargements of 1 micron semithin sections and recorded on histograms. The light and ultrastructural findings revealed a severe loss of myelinated fibers, the decrease affecting all types of fibers, but predominantly the largest ones. In the teased fibers, Wallerian-like degeneration was observed. In the axons there was an increase of mitochondria, dilatation of the small vesicles, and an increase in the number of neurofilaments. It can be assumed from the histopathologic data that the neuropathologic pattern in the pseudopolyneuropathic form of ALS shows an axonal degeneration. It is our opinion that the histopathologic data obtained in the sural nerve biopsy in this form of ALS reveals a clear involvement of the sensory neurons of the spinal ganglia, and the results can be useful for the study of precocious lesions in ALS.}, }
@article {pmid3083871, year = {1986}, author = {Parlo, RA and Coleman, PS}, title = {Continuous pyruvate carbon flux to newly synthesized cholesterol and the suppressed evolution of pyruvate-generated CO2 in tumors: further evidence for a persistent truncated Krebs cycle in hepatomas.}, journal = {Biochimica et biophysica acta}, volume = {886}, number = {2}, pages = {169-176}, doi = {10.1016/0167-4889(86)90134-5}, pmid = {3083871}, issn = {0006-3002}, support = {CA 28677/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Benzene Derivatives/pharmacology ; Carbon/*metabolism ; Carbon Dioxide/*metabolism ; Carbon Radioisotopes ; Cholesterol/*metabolism ; Citrates/metabolism ; Citric Acid ; *Citric Acid Cycle ; In Vitro Techniques ; Liver Neoplasms, Experimental/*metabolism ; Male ; Mitochondria, Liver/metabolism ; Pyruvates/*metabolism ; Pyruvic Acid ; Rats ; Rats, Inbred ACI ; Tricarboxylic Acids/pharmacology ; }, abstract = {Viable tissue slices from rat liver and Morris hepatoma 3924A were compared as to their ability to incorporate carbons from [U-14 C]pyruvate into newly synthesized cholesterol versus CO2. By 4 h, the tumor slice incubation had incorporated over 6-fold more pyruvate carbons into the sterol than into CO2, relative to the normal liver slice incubation, per g tissue protein. However, the presence of the mitochondrial citrate exchange carrier inhibitor 1,2,3-benzenetricarboxylate in the incubation inhibited the formation of [14C]cholesterol, while simultaneously leading to an increase in the rate of 14CO2 production in the tumor. In the normal liver system by contrast, benzenetricarboxylate also inhibited [14C]cholesterol formation, but had hardly any effect on the already high rate of 14CO2 production. The ability of benzenetricarboxylate to inhibit the rapid carbon flux from pyruvate to cholesterol, and to steer the metabolic flow of carbons toward oxidative decarboxylation via the Krebs cycle in whole, viable tumor tissue, indirectly emphasizes the importance of the mitochondrial citrate exchange carrier in supporting the decontrol of cholesterogenesis de novo in tumors by accelerating the supply of lipogenic precursor carbons to the tumor cytosol. These studies may be therefore interpreted as extensions, to the level of whole-cell metabolism, of the concept of a persistent 'truncated' Krebs cycle in the mitochondria of metastatic cancer tissue. This concept states, in part, that a rapid efflux of mitochondrially generated citrate would operate preferentially in tumors, and thus provide carbons continuously to the cytoplasmic compartment where the well-established deregulated pathway of cholesterogenesis occurs (Parlo, R.A. and Coleman, P.S. (1984) J. Biol. Chem. 259, 9997-10003; Coleman, P.S. and Lavietes, B.B. (1981) CRC Crit. Rev. Biochem. 11, 341-393).}, }
@article {pmid3515968, year = {1986}, author = {Humes, HD}, title = {Role of calcium in pathogenesis of acute renal failure.}, journal = {The American journal of physiology}, volume = {250}, number = {4 Pt 2}, pages = {F579-89}, doi = {10.1152/ajprenal.1986.250.4.F579}, pmid = {3515968}, issn = {0002-9513}, mesh = {Acute Kidney Injury/*physiopathology ; Aminoglycosides/toxicity ; Animals ; Calcium/*physiology ; Cell Compartmentation ; Cell Membrane/physiology ; Cell Membrane Permeability ; Intracellular Membranes/physiology ; Ischemia/physiopathology ; Kidney/blood supply/drug effects/metabolism ; Mitochondria/physiology ; }, abstract = {The potential for calcium to play a key role in cell injury has been long suspected. Major sites of calcium action to promote cell injury include the plasma membrane, mitochondria, endoplasmic reticulum, and the cytoskeleton. Major mechanisms of calcium action to promote cell injury include activation of phospholipases, direct and indirect effects on permeability pathways, and effects on contractile and cytoskeletal structure and function. The activation of phospholipases and deterioration of mitochondrial structure and function by calcium appear to be most important in the evolution of cell injury. Tissue calcium levels invariably increase when lethal cell injury develops in a tissue and is due predominantly to mitochondrial accumulation and sequestration. The simultaneous occurrence of cell calcium overload and lethal cell injury, however, only establishes an association between these two events but does not prove causality. Over the past several years, a large amount of data has established that calcium plays a critical modifying role in the pathogenesis of both ischemic and toxic cell injury, but evidence for the thesis that calcium is the "final common pathway" for lethal cell injury is not conclusive. Many studies have emphasized the role of calcium influx from extracellular to intracellular spaces with resulting cellular calcium overload in cell injury. A critical role for intracellular redistribution of calcium pools rather than cellular calcium influx during the important early stages of cell injury may be more important. Modifying alterations in cell calcium redistribution or cellular calcium influx with a variety of agents has been beneficial in ameliorating the degree of cell injury in a number of experimental settings. It is still unclear whether these beneficial effects are due mainly to alterations of calcium-mediated processes that determine the reversibility of injury or are due to alterations in other critical metabolic processes not importantly influenced by calcium.}, }
@article {pmid2980114, year = {1986}, author = {de Paz, P and Zapata, A and Renau-Piqueras, J and Miragall, F}, title = {Morphological differentiation of mitochondria in the early chick embryo: a stereological analysis.}, journal = {Histology and histopathology}, volume = {1}, number = {2}, pages = {197-201}, pmid = {2980114}, issn = {0213-3911}, mesh = {Animals ; Brain/*embryology/ultrastructure ; Cell Differentiation ; Chick Embryo ; Mesoderm/*ultrastructure ; Mitochondria/*ultrastructure ; }, abstract = {The morphological evolution of mitochondria in three cell types of chick embryo in neurulation was analyzed by stereological methods. Mitochondria, showing a random distribution, were characterized by moderate electron-dense matrices and normal cristae. The numerical density of mitochondria significantly increased in the neuroectoderm and epiblastic cells while their volume density remained unchanged. The mitochondria in mesoderm cells were ellipsoidal (axial ratio 2:1) at stages 5 and 8 although they underwent an elongation in neuroectoderm and epiblastic cells (axial ratio from 2:1 to 1.6:1). The individual size of "average mitochondria" in the mesoderm cells was smaller than in other cell types. The total V/S (volume/surface) ratio of mitochondria decreased during neurulation. These morphological changes have been discussed emphasizing the possible metabolical role of mitochondria during morphogenesis.}, }
@article {pmid3514271, year = {1986}, author = {von Heijne, G}, title = {Why mitochondria need a genome.}, journal = {FEBS letters}, volume = {198}, number = {1}, pages = {1-4}, doi = {10.1016/0014-5793(86)81172-3}, pmid = {3514271}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Animals ; Biological Evolution ; *Genes ; Humans ; Membrane Proteins/biosynthesis ; Mitochondria/*analysis ; Proteins/*analysis ; Xenopus ; Yeasts/genetics ; }, abstract = {The evolution of the mitochondrial genome towards the compact organization found in the higher eukaryotes is discussed. It is suggested that the machinery for co-translational protein export across the endoplasmic reticulum membrane sets strict limits on the kinds of protein-coding genes that can be successfully transferred from the mitochondrial to the nuclear genome. This hypothesis is in perfect agreement with the pattern of mitochondrially vs nuclearly encoded mitochondrial proteins found in species such as man, mouse, and Xenopus.}, }
@article {pmid3959009, year = {1986}, author = {Zierdt, CH}, title = {Cytochrome-free mitochondria of an anaerobic protozoan--Blastocystis hominis.}, journal = {The Journal of protozoology}, volume = {33}, number = {1}, pages = {67-69}, doi = {10.1111/j.1550-7408.1986.tb05559.x}, pmid = {3959009}, issn = {0022-3921}, mesh = {Aerobiosis ; Anaerobiosis ; Animals ; Catalase/analysis ; Cell Fractionation/methods ; Cytochromes/*analysis ; Eukaryota/*ultrastructure ; Microscopy, Electron ; Mitochondria/*ultrastructure ; }, abstract = {Isolated mitochondria of the anaerobic protozoan Blastocystis hominis were subjected to spectral analysis, color, catalase, and peroxidase tests and found to be completely negative for cytochrome enzymes, catalase, and peroxide. Based on the absence of cytochrome enzymes, the possible evolution of B. hominis mitochondria from anaerobic bacteria is postulated.}, }
@article {pmid3959152, year = {1986}, author = {Rouse, GW and Robson, SK}, title = {An ultrastructural study of megachiropteran (Mammalia: Chiroptera) spermatozoa: implications for chiropteran phylogeny.}, journal = {Journal of submicroscopic cytology}, volume = {18}, number = {1}, pages = {137-152}, pmid = {3959152}, issn = {0022-4782}, mesh = {Acrosome/ultrastructure ; Animals ; Cell Nucleus/ultrastructure ; Chiroptera/*classification/physiology ; Eulipotyphla/classification ; Male ; Microscopy, Electron ; Phylogeny ; Primates/classification ; Sperm Head/ultrastructure ; Spermatozoa/*ultrastructure ; }, abstract = {The fine structure of epididymal or electro-ejaculated spermatozoa of Pteropus poliocephalus, P. scapulatus, P. conspiculatus, P. alecto and Syconycteris australis is described. The sperm of all species were found to be very similar. The head is extremely flattened and spatulate; the nucleus is capped by a long acrosome that comprises the proximal half of the head and covers two-thirds of the nucleus area, and a prominent sub-acrosomal space possesses a unique 'anvil'-like shape. Redundant nuclear envelope forms a 'scroll' in a restricted region of the neck, next to the base of the proximal centriole and the most proximal of the mitochondria. The axoneme is atypical for mammals, the central singlets arising distal to the outer doublets. Coarse fibres 1, 5, 6 and 9 are larger than the remainder, a feature shared with the Microchiroptera, most insectivores and the Primates. The large sub-acrosomal space of the megachiropteran sperm is significantly is different from that of the Microchiroptera. We consider that the difference in sperm ultrastructure between the chiropteran sub-orders is not inconsistent with theories of a di-phyletic origin for this group. The use of sperm ultrastructure as a phylogenetic tool is discussed and comparisons with the spermatozoa of other closely related Eutheria are made.}, }
@article {pmid3779045, year = {1986}, author = {Rauhut, R and Gabius, HJ and Cramer, F}, title = {Phenylalanyl-tRNA synthetases as an example for comparative and evolutionary aspects of aminoacyl-tRNA synthetases.}, journal = {Bio Systems}, volume = {19}, number = {3}, pages = {173-183}, doi = {10.1016/0303-2647(86)90038-9}, pmid = {3779045}, issn = {0303-2647}, mesh = {*Amino Acyl-tRNA Synthetases ; Bacteria/enzymology/genetics ; Biological Evolution ; Chloroplasts/physiology ; Eukaryotic Cells/physiology ; Mitochondria/physiology ; Models, Biological ; *Phenylalanine-tRNA Ligase ; Protein Biosynthesis ; Structure-Activity Relationship ; Substrate Specificity ; }, abstract = {Aminoacyl-tRNA synthetases are indispensable components of protein synthesis in all three lines of evolutionary descent, eubacteria, archaebacteria and eukaryotes. Furthermore they are also present in the translational apparatus of the semi-autonomous organelles, mitochondria and chloroplasts, of the eukaryotic cell. Therefore aminoacyl-tRNA synthetases are appropriate objects for comparative molecular biology in order to obtain a comprehensive picture of the evolution of the translational process. The analysis of the phenylalanyl-tRNA synthetase in a large variety of organisms and organelles in this respect is the most advanced. In addition to comparison of quaternary structure, analysis includes functional aspects of accuracy mechanisms (proofreading) and comparison of structural features by means of substrate analogs. Evolutionary relationships are furthermore elucidated using the immunological approach and heterologous aminoacylation.}, }
@article {pmid3751487, year = {1986}, author = {de Paz, P and Fernandez, JG and Chamorro, CA and Fernandez, M and Villar, JM}, title = {Stereological analysis of ultrastructural changes of surrounding tissues to neuroectoderm during chick embryo neurulation.}, journal = {Acta anatomica}, volume = {126}, number = {3}, pages = {177-182}, doi = {10.1159/000146211}, pmid = {3751487}, issn = {0001-5180}, mesh = {Animals ; Chick Embryo ; Ectoderm/*physiology/ultrastructure ; Embryo, Mammalian/cytology/*ultrastructure ; *Embryo, Nonmammalian ; Mesencephalon/embryology ; Mesoderm/cytology/ultrastructure ; Nervous System/*embryology ; }, abstract = {The cytometric evolution of different subcellular components in the epiblast and the mesoderm of chick embryo during neurulation has been studied with stereological methods. The coefficient of cellular form (CFc) has specific values for each type, the epiblast having a mean CFc of 0.474, while the mesoderm, which has ellipsoidal cells, has a mean CFc of 0.643. The nucleus does not show any change of its coefficient of form although its surface density increases significantly. The proportion of mitochondria, present in the cells of each embryonic layer, remains constant during the 4 stages, being higher in the mesoderm cells (epiblast 3.6%; mesoderm 4.3%). The epiblast cells show a stable vitelline reserve, though the relative proportions of lipid bodies and yolk droplets vary: the volume density of yolk droplets increases from stage 5 (3.1%) to stage 8 (7.7%), while the lipid bodies diminish from 7 to 3.6% during this period. The mesoderm cells undergo a remarkable loss of vitelline volume during the same period. The rough endoplasmic reticulum of each cellular type has a remarkable length density increase, the significance of which is discussed in relation to production of extracellular matrix.}, }
@article {pmid3555260, year = {1986}, author = {Coleman, PS}, title = {Membrane cholesterol and tumor bioenergetics.}, journal = {Annals of the New York Academy of Sciences}, volume = {488}, number = {}, pages = {451-467}, doi = {10.1111/j.1749-6632.1986.tb46578.x}, pmid = {3555260}, issn = {0077-8923}, support = {CA28677/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Cholesterol/*metabolism ; Citrates/metabolism ; Citric Acid ; Citric Acid Cycle ; *Energy Metabolism ; Liver Neoplasms, Experimental/*metabolism ; Membrane Lipids/*metabolism ; Mitochondria, Liver/metabolism ; Rats ; }, abstract = {We have established that a preferential export of pyruvate-generated citrate occurs from cholesterol-rich tumor mitochondria, with both isolated mitochondrial systems as well as with viable tumor tissue slices (i.e., with whole tumors cells). Furthermore, we have demonstrated that the more rapid citrate efflux kinetics (catalyzed by the tricarboxylate exchange carrier) of isolated tumor mitochondria is completely inhibited upon addition of 1,2,3-benzenetricarboxylate (BTC) and have shown that this inhibition is apparently also obtained in viable tumor tissue when the inhibitor is added to the tissue incubation. Upon BTC inhibition of tumor mitochondrial citrate export in viable tumor tissue incubations, the incorporation of [14C]pyruvate into newly synthesized cholesterol is severely inhibited as well. Among the most interesting conclusions drawn from our results, we catalog the following. The preferential export of citrate from isolated tumor mitochondria appears to be coupled, functionally, to a high linear rate of incorporation of 14C from pyruvate to cholesterol in viable tumor tissue slices, simultaneously supporting the postulate of a truncated Krebs cycle and corroborating the well-established deregulated and continuous cholesterogenesis pathway in tumors, especially hepatomas. The extent of [14C]pyruvate flux to newly generated cholesterol in either tumor or normal liver tissue is inversely related to the extent of 14CO2 production. Despite the evolution of some CO2 during cholesterogenesis, the predominant portion presumably arises via metabolic processing of pyruvate-generated citrate during Krebs cycle-linked respiration. Isolated tumor mitochondrial systems, as well as viable tumor tissue incubations, can manifest a reversal in the pattern of enhanced mitochondrial citrate efflux coupled to increased cholesterogenesis, when BTC is added to the system. This implies that BTC, a hydrophobic but negatively charged moiety at pH 7, can indeed penetrate the plasma membrane of cells. Upon entry into the cell, BTC apparently blocks the tricarboxylate carrier of tumor tissue mitochondria, thus forcing the mitochondrial citrate into Krebs cycle-linked respiration rather than permitting it to serve as the predominant provider of an increased supply of cytosolic acetyl CoA precursor required for deregulated cholesterogenesis during the development of the tumor.}, }
@article {pmid3104617, year = {1986}, author = {Jukes, TH and Bhushan, V}, title = {Silent nucleotide substitutions and G + C content of some mitochondrial and bacterial genes.}, journal = {Journal of molecular evolution}, volume = {24}, number = {1-2}, pages = {39-44}, pmid = {3104617}, issn = {0022-2844}, mesh = {Amino Acids ; Animals ; Bacteria/genetics ; Base Composition ; Codon ; *Cytosine ; DNA, Mitochondrial/*genetics ; *Genes ; *Genes, Bacterial ; *Guanine ; Humans ; Species Specificity ; }, abstract = {The G + C content of DNA varies widely in different organisms, especially microorganisms. This variation is accompanied by changes in the nucleotide composition of silent positions in codons. (Silent positions are defined and explained in the text). These changes are mostly neutral or near neutral, and appear to result from mutation pressure in the direction of increasing either A + T (AT pressure) or G + C (GC pressure) content. Variations in G + C content are also accompanied by substitutions at replacement positions in codons. These substitutions produce changes in the amino acid content of homologous proteins. The examples studied were genes for 13 mitochondrial proteins in five species, and A and B genes for bacterial tryptophan synthase in four species. In microorganisms, varying AT and GC mutational pressures, presumably resulting from shifts in the DNA polymerase system, exert strong effects on molecular evolution by changing the G + C content of DNA. These effects may be greater than those of random drift. The effects of GC pressure on silent substitutions in the systems examined are several times as great as the effects on replacement substitutions. GC pressure is exerted on noncoding as well as coding regions in mitochondrial DNA. This is shown by the close correlation (correlation coefficient, 0.99) of the G + C content of the noncoding D loop of mitochondria with the G + C content of silent positions in the corresponding mitochondrial genes.}, }
@article {pmid3104609, year = {1986}, author = {Pietromonaco, SF and Hessler, RA and O'Brien, TW}, title = {Evolution of proteins in mammalian cytoplasmic and mitochondrial ribosomes.}, journal = {Journal of molecular evolution}, volume = {24}, number = {1-2}, pages = {110-117}, pmid = {3104609}, issn = {0022-2844}, support = {GM-15438/GM/NIGMS NIH HHS/United States ; GM-23322/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Cattle ; Chickens ; Cytoplasm/metabolism ; Humans ; Mitochondria/metabolism ; Rabbits ; Rats ; Ribosomal Proteins/*genetics/isolation &amp; purification ; Ribosomes/metabolism ; Species Specificity ; }, abstract = {The proteins of cytoplasmic and mitochondrial ribosomes from the cow and the rat were analyzed by co-electrophoresis in two dimensional polyacrylamide gels to determine their relative evolutionary rates. In a pairwise comparison of individual ribosomal proteins (r-proteins) from the cow and the rat, over 85% of the cytoplasmic r-proteins have conserved electrophoretic properties in this system, while only 15% of the proteins of mitochondrial ribosomes from these animals fell into this category. These values predict that mammalian mitochondrial r-proteins are evolving about 13 times more rapidly than cytoplasmic r-proteins. Based on actual evolutionary rates for representative cytoplasmic r-proteins, this mitochondrial r-protein evolutionary rate corresponds to an amino acid substitution rate of 40 X 10(-10) per site per year, placing mitochondrial r-proteins in the category of rapidly evolving proteins. The mitochondrial r-proteins are apparently evolving at a rate comparable to that of the mitochondrial rRNA, suggesting that functional constraints act more or less equally on both kinds of molecules in the ribosome. It is significant that mammalian mitochondrial r-proteins are evolving more rapidly than cytoplasmic r-proteins in the same cell, since both sets of r-proteins are encoded by nuclear genes. Such a difference in evolutionary rates implies that the functional constraints operating on ribosomes are somewhat relaxed for mitochondrial ribosomes.}, }
@article {pmid3104605, year = {1986}, author = {Doonan, S and Martini, F and Angelaccio, S and Pascarella, S and Barra, D and Bossa, F}, title = {The complete amino acid sequences of cytosolic and mitochondrial aspartate aminotransferases from horse heart, and inferences on evolution of the isoenzymes.}, journal = {Journal of molecular evolution}, volume = {23}, number = {4}, pages = {328-335}, pmid = {3104605}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Aspartate Aminotransferases/*genetics ; *Biological Evolution ; Chickens ; Cytosol/enzymology ; Horses ; Humans ; Isoenzymes/*genetics ; Mitochondria, Heart/*enzymology ; Myocardium/*enzymology ; Species Specificity ; Swine ; }, abstract = {We report here the complete amino acid sequences of the cytosolic and mitochondrial aspartate aminotransferases from horse heart. The two sequences can be aligned so that 48.1% of the amino acid residues are identical. The sequences have been compared with those of the cytosolic isoenzymes from pig and chicken, the mitochondrial isoenzymes from pig, chicken, rat, and human, and the enzyme from Escherichia coli. The results suggest that the mammalian cytosolic and mitochondrial isoenzymes have evolved at equal and constant rates whereas the isoenzymes from chicken may have evolved somewhat more slowly. Based on the rate of evolution of the mammalian isoenzymes, the gene-duplication event that gave rise to cytosolic and mitochondrial aspartate aminotransferases is estimated to have occurred at least 10(9) years ago. The cytosolic and mitochondrial isoenzymes are equally related to the enzyme from E. coli; the prokaryotic and eukaryotic enzymes diverged from one another at least 1.3 X 10(9) years ago.}, }
@article {pmid3026914, year = {1986}, author = {Trinkl, H and Wolf, K}, title = {The mosaic cox1 gene in the mitochondrial genome of Schizosaccharomyces pombe: minimal structural requirements and evolution of group I introns.}, journal = {Gene}, volume = {45}, number = {3}, pages = {289-297}, doi = {10.1016/0378-1119(86)90027-2}, pmid = {3026914}, issn = {0378-1119}, mesh = {Amino Acid Sequence ; Base Sequence ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/*genetics ; *Genes ; *Genes, Fungal ; Introns ; Mitochondria/enzymology ; Nucleic Acid Conformation ; Saccharomycetales/*genetics ; Schizosaccharomyces/enzymology/*genetics ; }, abstract = {The gene encoding subunit 1 of cytochrome oxidase (cox1) in the fission yeast Schizosaccharomyces pombe is polymorphic. In strain 50 it contains two group I introns with open reading frames (ORFs) in phase with the upstream exons (Lang, 1984). In strain EF1 two additional very short group I introns which do not possess ORFs were detected by DNA sequencing. These two introns (AI2a and AI3) share distinct characteristics concerning their nucleotide sequence and secondary structure and are located at identical positions as the introns AI4 and AI5 beta, respectively, in the cox1 gene of Saccharomyces cerevisiae. The sequence homology of the cob and cox1 genes around the splice points of introns AI2a, AI4, and BI4 (cob intron 4) might reflect horizontal gene transfer between the distantly related species S. pombe and S. cerevisiae.}, }
@article {pmid3001728, year = {1986}, author = {Meyer, TE and Cusanovich, MA and Kamen, MD}, title = {Evidence against use of bacterial amino acid sequence data for construction of all-inclusive phylogenetic trees.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {83}, number = {2}, pages = {217-220}, pmid = {3001728}, issn = {0027-8424}, support = {GM21277/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Bacterial Proteins ; *Cytochrome c Group/genetics ; Mitochondria ; *Phylogeny ; RNA, Ribosomal/genetics ; }, abstract = {It has been proposed that phylogenetic trees, intended to show divergence of eukaryotic protein and nucleic acid sequences, be extended to include those from bacteria. However, we have compared the amino acid sequences of 18 of the most divergent mitochondrial cytochromes c with those of 18 bacterial cytochromes c2 and have found that the average percentage difference between these mitochondrial cytochromes c and cytochromes c2 was not significantly greater than that among the cytochromes c2 alone. The large discontinuities in physical-chemical properties recognized between the prokaryote and eukaryote cytochromes render it highly improbable that members of the two classes should be no more different from one another than members of either class alone, assuming that sequence differences can accurately reveal evolutionary divergence. Instead, we propose that divergent amino acid sequences approach a limit of change considerably less than for comparison of random sequences. This limit of change presumably is determined by the structure/function relationship. When two homologous protein sequences have reached such a limit, convergence or back-mutations and parallel mutations become as frequent as divergent mutations. As two diverging proteins approach this steady-state condition, sequence differences no longer reflect the numbers of mutations resulting in amino acid substitution and therefore species cannot be positioned on a phylogenetic tree. Insertions and deletions are less reversible than are amino acid substitutions and, provided they are well-documented, might be more reliable indicators of bacterial relationships. Nevertheless, we suggest that data available on bacterial protein sequences do not permit construction of all-inclusive phylogenetic trees. Comparisons of protein and rRNA trees suggest that similar restrictions apply to use of rRNA sequence data.}, }
@article {pmid2856125, year = {1986}, author = {Ljungdahl, PO and Pennoyer, JD and Trumpower, BL}, title = {Purification of cytochrome bc1 complexes from phylogenically diverse species by a single method.}, journal = {Methods in enzymology}, volume = {126}, number = {}, pages = {181-191}, doi = {10.1016/s0076-6879(86)26020-6}, pmid = {2856125}, issn = {0076-6879}, mesh = {Animals ; Cattle ; Cell Membrane/enzymology ; Chromatography, DEAE-Cellulose/methods ; Chromatography, Ion Exchange/methods ; Electron Transport Complex III/*isolation &amp; purification/metabolism ; Indicators and Reagents ; Kinetics ; Mitochondria, Heart/*enzymology ; Phylogeny ; Rhodobacter sphaeroides/*enzymology ; Saccharomyces cerevisiae/*enzymology ; Species Specificity ; Submitochondrial Particles/enzymology ; }, }
@article {pmid2483246, year = {1986}, author = {Godinot, C and Moradi-Ameli, M and Gautheron, DC}, title = {Monoclonal antibodies to F1-ATPase subunits as probes of structure, conformation, and functions of isolated or membrane-bound F1.}, journal = {Methods in enzymology}, volume = {126}, number = {}, pages = {761-769}, doi = {10.1016/s0076-6879(86)26075-9}, pmid = {2483246}, issn = {0076-6879}, mesh = {Animals ; *Antibodies, Monoclonal ; Antigen-Antibody Complex ; Epitopes/analysis ; Kinetics ; Macromolecular Substances ; Mitochondria, Heart/enzymology ; Phylogeny ; Protein Conformation ; Proton-Translocating ATPases/immunology/isolation &amp; purification/*metabolism ; Swine ; }, }
@article {pmid2420451, year = {1985}, author = {Attimonelli, M and Lanave, C and Sbisá, E and Preparata, G and Saccone, C}, title = {Multisequence comparisons in protein coding genes. Search for functional constraints.}, journal = {Cell biophysics}, volume = {7}, number = {4}, pages = {239-250}, pmid = {2420451}, issn = {0163-4992}, mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Biological Evolution ; Cattle ; Codon ; DNA, Mitochondrial/genetics ; Electron Transport Complex IV/genetics ; *Genes ; Humans ; Mice ; Mitochondria/*physiology ; Proteins/*genetics ; Proton-Translocating ATPases/genetics ; RNA, Ribosomal/genetics ; Rats ; Sequence Homology, Nucleic Acid ; }, abstract = {A very powerful method for detecting functional constraints operative in biological macromolecules is presented. This method entails performing a base permanence analysis of protein coding genes at each codon position simultaneously in different species. It calculates the degree of permanence of subregions of the gene by dividing it into segments, c codons long, counting how many sites remain unchanged in each segment among all species compared. By comparing the base permanence among several sequences with the expectations based on a stochastic evolutionary process, gene regions showing different degrees of conservation can be selected. This means that wherever the permanence deviates significantly from the expected value generated by the simulation, the corresponding regions are considered "constrained" or "hypervariable". The constrained regions are of two types: alpha and beta. The alpha regions result from constraints at the amino acid level, whereas the beta regions are those probably involved in "control" processing. The method has been applied to mitochondrial genes coding for subunit 6 of the ATPase and subunit 1 of the cytochrome oxidase in four mammalian species: human, rat, mouse, and cow. In the two mitochondrial genes a few regions that are highly conserved in all codon positions have been identified. Among these regions a sequence, common to both genes, that is complementary to a strongly conserved region of 12S rRNA has been found. This method can also be of great help in studying molecular evolution mechanisms.}, }
@article {pmid2932445, year = {1985}, author = {Ness, SA and Weiss, RL}, title = {Carbamoyl-phosphate synthetases from Neurospora crassa. Immunological relatedness of the enzymes from Neurospora, bacteria, yeast, and mammals.}, journal = {The Journal of biological chemistry}, volume = {260}, number = {26}, pages = {14355-14362}, pmid = {2932445}, issn = {0021-9258}, support = {GM07185/GM/NIGMS NIH HHS/United States ; GM28864/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Antibody Specificity ; Biological Evolution ; Carbamoyl-Phosphate Synthase (Ammonia)/analysis/*immunology/isolation &amp; purification ; Cell Nucleus/enzymology ; Enzyme Precursors/analysis ; Escherichia coli/enzymology ; Immune Sera/immunology ; Immunosorbent Techniques ; Kidney/enzymology ; Ligases/*immunology ; Liver/enzymology ; Mitochondria/*enzymology ; Molecular Weight ; Mutation ; Neurospora/*enzymology ; Neurospora crassa/*enzymology ; Rats ; Saccharomyces cerevisiae/enzymology ; }, abstract = {Neurospora crassa contains two carbamoyl-phosphate synthetases: a mitochondrial enzyme (CPS-A) which supplies carbamoyl phosphate for arginine biosynthesis, and a nuclear enzyme whose product is used for the synthesis of pyrimidines. We have prepared antiserum against a highly purified preparation of the large subunit of CPS-A and have used the antiserum to demonstrate that the large subunit is, like most mitochondrially localized proteins, initially synthesized as a higher molecular weight precursor. The CPS-A antiserum cross-reacts with the nuclear enzyme, allowing us to identify the product of the complex N. crassa pyr-3 genetic locus as a protein with a subunit molecular weight of 180,000. Finally, we have found that the CPS-A antiserum also cross-reacts with carbamoyl-phosphate synthetases from bacteria, yeast, and mammals. The immunological relatedness of carbamoyl-phosphate synthetases from such diverse species suggests that the protein sequences required for carbamoyl phosphate production have been highly conserved during the course of evolution.}, }
@article {pmid4090739, year = {1985}, author = {Ratner, VA and Omel'ianchuk, LV and Zharkikh, AA and Kolchanov, NA}, title = {[Theoretical analysis of the structural characteristics and evolution of transfer RNAs].}, journal = {Zhurnal obshchei biologii}, volume = {46}, number = {6}, pages = {732-742}, pmid = {4090739}, issn = {0044-4596}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Cell Nucleus/metabolism ; Humans ; Mitochondria/metabolism ; Mutation ; *Nucleic Acid Conformation ; Phylogeny ; Plants ; RNA, Transfer/*genetics ; }, }
@article {pmid4092310, year = {1985}, author = {Marini, F and Radin, S and Tenchini, P and Manganelli, G}, title = {[The other face of oxygen (2)].}, journal = {Chirurgia italiana}, volume = {37}, number = {5}, pages = {517-524}, pmid = {4092310}, issn = {0009-4773}, mesh = {Animals ; Ascorbic Acid/metabolism ; Catalase/metabolism ; Cell Survival ; Ceruloplasmin/metabolism ; Energy Transfer ; Free Radicals ; Glutathione Peroxidase/metabolism ; Humans ; Hydrogen Peroxide/metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; Superoxide Dismutase/metabolism ; Vitamin E/metabolism ; Wounds, Gunshot/metabolism ; }, abstract = {The authors, in this second part of "The other face of Oxygen", pay attention no more to O2, the "untrustworthy" protagonist of oxidation, but to the opposite side, namely the "physiologic" antioxidative protections. Such antioxidative protections, which were being prepared and improved in cell, in interstices and in organic liquids, during millions of pears, perhaps represent the "most true" witness of the always "traumatic" cohabitation between organisms, although eukaryote, and oxygen. This, after all, in spite of the evolutive push, remained an element "foreign" to life, although, paradoxically, first protagonist of it. Similarly, "singularly foreign" appear mitochondria, namely the forges specifically entrusted with the respiratory metabolism.}, }
@article {pmid3895229, year = {1985}, author = {Nazarea, AD and Bloch, DP and Semrau, AC}, title = {Detection of a fundamental modular format common to transfer and ribosomal RNAs: second-order spectral analysis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {82}, number = {16}, pages = {5337-5341}, pmid = {3895229}, issn = {0027-8424}, support = {GM-23331/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Cattle ; Escherichia coli/genetics ; Halobacterium/genetics ; Mitochondria/metabolism ; Nucleic Acid Conformation ; RNA, Ribosomal/*genetics ; RNA, Transfer/*genetics ; Saccharomyces cerevisiae/genetics ; Species Specificity ; Spectrophotometry ; }, abstract = {Second-order spectral analysis is used to detect rigorously and to characterize the principal periodicities in the positions of conserved sequences common to tRNAs and rRNAs. It is shown that the shared periodicity having the largest spectral amplitude is 9, followed by 8 and 10, thus forming a closed triad of significant multiplets centered at 9 bases. This conclusion is proposed to reflect a closed triadic set of fundamental tandem repeat lengths in a class of ancestral macromolecules possessing a restricted sequence symmetry. The terms "remanent" and "archeomodular" are used to describe a relic modular format, traces of which are shown here to persist despite the changes that have occurred in the primary structures of ribonucleic acids during the course of their evolution.}, }
@article {pmid4052383, year = {1985}, author = {Rauhut, R and Gabius, HJ and Cramer, F}, title = {Evolutionary aspects of accuracy of phenylalanyl-tRNA synthetase. Accuracy of the cytoplasmic and chloroplastic enzymes of a higher plant (Phaseolus vulgaris).}, journal = {Biochemistry}, volume = {24}, number = {15}, pages = {4052-4057}, doi = {10.1021/bi00336a038}, pmid = {4052383}, issn = {0006-2960}, mesh = {Amino Acyl-tRNA Synthetases/*genetics ; Animals ; *Biological Evolution ; Chloroplasts/*enzymology ; Cytoplasm/enzymology ; Kinetics ; Phenylalanine-tRNA Ligase/*genetics/metabolism ; Plants/*enzymology ; Species Specificity ; Substrate Specificity ; }, abstract = {The phenylalanyl-tRNA synthetases from cytoplasm and chloroplasts of bean (Phaseolus vulgaris) leaves employ different strategies with respect to accuracy. The chloroplastic enzyme that is coded for by the nuclear genome follows the pathway of posttransfer proofreading, also characteristic for enzymes from eubacteria and cytoplasm and mitochondria of lower eukaryotic organisms. In contrast, the cytoplasmic enzyme uses pretransfer proofreading in the case of noncognate natural amino acids, characteristic for higher eukaryotic organisms and archaebacteria. Dependent on the nature of the noncognate amino acid, pretransfer proofreading in this case occurs without tRNA stimulation or with tRNA stimulated with no or little effect of the nonaccepting 3'-OH group of the terminal adenosine. The fundamental mechanistic difference in proofreading between the heterotopic intracellular isoenzymes of the plant cell supports the idea of the origin of the chloroplastic gene by gene transfer from a eubacterial endosymbiont to the nucleus. Origin by duplication of the nuclear gene, as indicated for mitochondrial phenylalanyl-tRNA synthetases [Gabius, H.-J., Engelhardt, R., Schroeder, F.R., &amp; Cramer, F. (1983) Biochemistry 22, 5306-5315], appears unlikely. Further analyses of the ATP/PPi pyrophosphate exchange and aminoacylation of tRNAPhe-C-C-A(3'NH2), using 11 phenylalanine analogues, reveal intraspecies and interspecies variability of the architecture of the amino acid binding part within the active site.}, }
@article {pmid3892535, year = {1985}, author = {Yang, D and Oyaizu, Y and Oyaizu, H and Olsen, GJ and Woese, CR}, title = {Mitochondrial origins.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {82}, number = {13}, pages = {4443-4447}, pmid = {3892535}, issn = {0027-8424}, support = {AM-34527/AM/NIADDK NIH HHS/United States ; }, mesh = {Base Sequence ; Escherichia coli/genetics ; *Mitochondria ; Phylogeny ; Pseudomonas/*ultrastructure ; RNA, Ribosomal/analysis ; Rhizobium/*ultrastructure ; }, abstract = {The 16S ribosomal RNA sequences from Agrobacterium tumefaciens and Pseudomonas testosteroni have been determined to further delimit the origin of the endosymbiont that gave rise to the mitochondrion. These two prokaryotes represent the alpha and beta subdivisions, respectively, of the so-called purple bacteria. The endosymbiont that gave rise to the mitochondrion belonged to the alpha subdivision, a group that also contains the rhizobacteria, the agrobacteria, and the rickettsias--all prokaryotes that have developed intracellular or other close relationships with eukaryotic cells.}, }
@article {pmid3889225, year = {1985}, author = {Strong, AJ and Miller, SA and West, IC}, title = {Protection of respiration of a crude mitochondrial preparation in cerebral ischaemia by control of blood glucose.}, journal = {Journal of neurology, neurosurgery, and psychiatry}, volume = {48}, number = {5}, pages = {450-454}, pmid = {3889225}, issn = {0022-3050}, mesh = {Animals ; Blood Glucose/*analysis ; Blood Pressure ; Brain/*metabolism ; Brain Ischemia/blood/metabolism/*therapy ; Female ; Insulin/*therapeutic use ; Male ; Mitochondria/metabolism ; Oxygen Consumption ; Rats ; Rats, Inbred Strains ; }, abstract = {There is evidence that systemic hyperglycaemia influences the evolution of cerebral ischaemia adversely, through enhancement of brain lactic acidosis. A potential protective regimen based on induction of mild hypoglycaemia with insulin was therefore studied. Respiratory control in brain mitochondria prepared from the ischaemic hemisphere of rats subjected to unilateral common carotid artery occlusion for one hour was abolished, but was partially preserved in insulin-treated rats (p = 0.01).}, }
@article {pmid3006116, year = {1985}, author = {Senn, H and Wüthrich, K}, title = {Amino acid sequence, haem-iron co-ordination geometry and functional properties of mitochondrial and bacterial c-type cytochromes.}, journal = {Quarterly reviews of biophysics}, volume = {18}, number = {2}, pages = {111-134}, doi = {10.1017/s0033583500005151}, pmid = {3006116}, issn = {0033-5835}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/*metabolism ; *Cytochrome c Group/metabolism ; Heme/analysis ; Histidine ; Iron/analysis ; Ligands ; Methionine ; Mitochondria/*metabolism ; Phylogeny ; Protein Binding ; Protein Conformation ; }, }
@article {pmid3929283, year = {1985}, author = {Portelli, C and Portelli, AP}, title = {The symmetries of the genetic code of mammalian mitochondria.}, journal = {Physiologie (Bucarest)}, volume = {22}, number = {2}, pages = {117-120}, pmid = {3929283}, issn = {1011-6206}, mesh = {Amino Acids/genetics ; Animals ; Base Composition ; Codon/genetics ; *Genetic Code ; Mammals/*genetics ; Mitochondria/classification/*ultrastructure ; }, abstract = {The genetic code of mammalian mitochondria presents some symmetric in the sequences of certain codons and in the relationships existing between the codons and aminoacids. These symmetries suggest the classification of codons in four classes and indicate that the evolution of the genetic code developed in four stages.}, }
@article {pmid3921961, year = {1985}, author = {Eigen, M and Lindemann, B and Winkler-Oswatitsch, R and Clarke, CH}, title = {Pattern analysis of 5S rRNA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {82}, number = {8}, pages = {2437-2441}, pmid = {3921961}, issn = {0027-8424}, mesh = {Archaea/metabolism ; Base Composition ; Base Sequence ; *Biological Evolution ; Chloroplasts/metabolism ; Codon/genetics ; Eubacterium/metabolism ; Eukaryotic Cells/metabolism ; Mitochondria/metabolism ; RNA, Ribosomal/*genetics ; }, abstract = {Some 200 different 5S rRNA sequences from eubacteria, chloroplasts, mitochondria, archaebacteria, and eukaryotes were analyzed for evolutionary kinship relationships and associated sequential features. Group-specific occupation schemes for the 149 positions of an overall alignment were established. Eubacterial, archaebacterial, and intermediate occupation schemes all yield a strongly biased base triplet pattern in one of the three possible reading frames strongest for eubacterial, chloroplastic, and archaebacterial, but still detectable for mitochondrial and eukaryotic cytoplasmic sequences. The frequency of triplets decays in the order RNY greater than RNR greater than YNY greater than YNR; R being a purine (guanine or adenine), Y is a pyrimidine (cytosine or uracil), and N is any base. A strong preference for guanine or cytosine was found in all triplet positions. The effects show no exceptions and are clearly above the level of statistical fluctuations.}, }
@article {pmid3887399, year = {1985}, author = {Yamao, F and Muto, A and Kawauchi, Y and Iwami, M and Iwagami, S and Azumi, Y and Osawa, S}, title = {UGA is read as tryptophan in Mycoplasma capricolum.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {82}, number = {8}, pages = {2306-2309}, pmid = {3887399}, issn = {0027-8424}, mesh = {Biological Evolution ; Codon/*genetics ; DNA, Mitochondrial/genetics ; Escherichia coli/genetics ; Genes, Bacterial ; Mitochondria/metabolism ; Mycoplasma/*genetics ; RNA, Messenger/*genetics ; RNA, Transfer, Amino Acyl/genetics ; Species Specificity ; Tryptophan/*genetics ; }, abstract = {UGA is a nonsense or termination (opal) codon throughout prokaryotes and eukaryotes. However, mitochondria use not only UGG but also UGA as a tryptophan codon. Here, we show that UGA also codes for tryptophan in Mycoplasma capricolum, a wall-less bacterium having a genome only 20-25% the size of the Escherichia coli genome. This conclusion is based on the following evidence. First, the nucleotide sequence of the S3 and L16 ribosomal protein genes from M. capricolum includes UGA codons in the reading frames; they appear at positions corresponding to tryptophan in E. coli S3 and L16. Second, a tRNATrp gene and its product tRNA found in M. capricolum have the anticodon sequence 5' U-C-A 3', which can form a complementary base-pairing interaction with UGA.}, }
@article {pmid2992672, year = {1985}, author = {Opperdoes, FR}, title = {Biochemical peculiarities of trypanosomes, African and South American.}, journal = {British medical bulletin}, volume = {41}, number = {2}, pages = {130-136}, doi = {10.1093/oxfordjournals.bmb.a072039}, pmid = {2992672}, issn = {0007-1420}, mesh = {Animals ; Cyclic AMP/metabolism ; DNA, Mitochondrial ; Glutathione Reductase/metabolism ; Glycolysis ; Microbodies/metabolism ; Mitochondria/metabolism ; Phylogeny ; Protein Biosynthesis ; Purines/metabolism ; Pyrimidines/biosynthesis ; Trypanosoma/genetics ; Trypanosoma brucei brucei/*metabolism ; Trypanosoma cruzi/*metabolism ; }, }
@article {pmid2861815, year = {1985}, author = {Crabb, JW and Hanstein, WG}, title = {Bovine heart mitochondrial F6: HPLC purification, NH2-terminal sequence and the possible structural relatedness to other components of ATPase complexes.}, journal = {Biochemistry international}, volume = {10}, number = {3}, pages = {385-393}, pmid = {2861815}, issn = {0158-5231}, mesh = {Adenosine Triphosphatases/genetics/*isolation &amp; purification ; Amino Acid Sequence ; Amino Acids/analysis ; Animals ; Biological Evolution ; *Carrier Proteins ; Cattle ; Chromatography, High Pressure Liquid ; Membrane Proteins/genetics ; Mitochondria, Heart/*enzymology ; *Mitochondrial Proton-Translocating ATPases ; Molecular Weight ; *Oxidative Phosphorylation Coupling Factors ; Proton-Translocating ATPases/genetics ; }, abstract = {The mitochondrial factor F6 has been purified by reverse-phase HPLC and the molecular weight (8500), amino acid composition and about 25% of the amino acid sequence determined. In the NH2-terminal sequence of the first 18 amino acids (NKELDPVQKLFVDKIREY), six identities with the NH2-terminal sequence of the oligomycin-sensitivity conferring protein (OSCP) are apparent, as well as less striking similarities with the OSCP related subunit delta of E. coli F1. The possibility that F6, OSCP and subunit delta of E. coli F1 could have evolved from a common ancestral gene is supported by apparent gene duplication within the OSCP and subunit delta sequences.}, }
@article {pmid3970966, year = {1985}, author = {Mbemba, F and Houbion, A and Raes, M and Remacle, J}, title = {Subcellular localization and modification with ageing of glutathione, glutathione peroxidase and glutathione reductase activities in human fibroblasts.}, journal = {Biochimica et biophysica acta}, volume = {838}, number = {2}, pages = {211-220}, doi = {10.1016/0304-4165(85)90081-9}, pmid = {3970966}, issn = {0006-3002}, mesh = {Cell Line ; Cell Survival ; Centrifugation, Density Gradient ; Fibroblasts/*ultrastructure ; Glutathione/*analysis ; Glutathione Peroxidase/*analysis ; Glutathione Reductase/*analysis ; Humans ; Hydrogen-Ion Concentration ; Subcellular Fractions/analysis ; Time Factors ; }, abstract = {Differential centrifugation and isopycnic equilibration in density gradients were used to localize glutathione (GSH), glutathione peroxidase and glutathione reductase in the subcellular organelles of WI-38 fibroblasts. GSH was present in all the subcellular fractions, whereas the glutathione peroxidase and reductase activities were restrained to the cytoplasm and the mitochondrial fractions. After equilibration in density gradients, the results showed the presence of GSH, glutathione peroxidase and glutathione reductase in both the cytoplasm and mitochondria. GSH was also located in plasma membranes and probably in peroxisomes, endoplasmic reticulum and lysosomal membranes. Evolution of GSH in ageing fibroblasts showed a sudden increase of its concentration just before cell death. The glutathione peroxidase activity already decreases in the early passages, while the decrease of the glutathione reductase activity was constant and reached a drastic low level at the end of the culture. In conclusion, GSH is probably involved in the cell degeneration associated with ageing but because of its multiple functions and its ubiquitous localization, it is difficult to assert to which extent this metabolite is implicated in the ageing process.}, }
@article {pmid4024870, year = {1985}, author = {Kalimo, H and Auer, RN and Siesjö, BK}, title = {The temporal evolution of hypoglycemic brain damage. III. Light and electron microscopic findings in the rat caudoputamen.}, journal = {Acta neuropathologica}, volume = {67}, number = {1-2}, pages = {37-50}, pmid = {4024870}, issn = {0001-6322}, support = {5 RO1 NS07838/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Brain Damage, Chronic/*etiology/pathology ; Caudate Nucleus/*pathology/ultrastructure ; Cell Survival ; Hypoglycemia/*complications/pathology ; Male ; Microscopy, Electron ; Neurons/ultrastructure ; Putamen/*pathology/ultrastructure ; Rats ; Rats, Inbred Strains ; }, abstract = {The caudate nucleus and putamen belong to the selectively vulnerable brain regions which incur neuronal damage in clinical and experimental settings of both hypoglycemia and ischemia. We have previously documented the density and distribution of the hypoglycemic damage in rat caudoputamen, but the evolution of the injury, i.e., the sequence of structural changes, has not been assessed. Therefore, in the present study we analyze the light and electron microscopic alterations in the caudoputamen of rats exposed to standardized, pure insults of severe hypoglycemia with isoelectric EEG for 10-60 min, or in rats which, following insults of 30 or 60 min, were allowed to recover for periods from 5 min to 6 months. The hypoglycemic insult produced severe nerve cell injury in the dorsolateral caudoputamen. Immediately after the insult abnormal light neurons with clearing of the peripheral cytoplasm were present. These cells disappeared early in the recovery period, as they do in the cerebral cortex. Dark neurons were also present, but unlike those in the cerebral cortex they did not appear until recovery was instituted. Their number increased for a couple of hours and they became acidophilic within 4-6 h. At this stage, electron microscopy revealed severe clumping of the nuclear chromatin and cytoplasm as well as incipient fragmentation of cell membranes, all these changes indicating an irreversible injury. Within 24 h flocculent densities appeared in the mitochondria and by day 2-3 of recovery the great majority of the medium-sized neurons had undergone karyorrhexis and cytorrhexis, their remnants being subsequently removed by macrophages. After some weeks only large and a few medium-sized neurons remained amidst reactive astrocytes and numerous macrophages. The delay in the appearance of dark, lethally injured medium-sized neurons until the recovery was instituted suggests an effect that does not become apparent until the substrate supply and energy production are restored. Furthermore, it points out again the selectivity of the hypoglycemic nerve cell injury with respect to the type (metabolic characteristics?) and topographic location of the neurons.}, }
@article {pmid4024866, year = {1985}, author = {Auer, RN and Kalimo, H and Olsson, Y and Siesjö, BK}, title = {The temporal evolution of hypoglycemic brain damage. I. Light- and electron-microscopic findings in the rat cerebral cortex.}, journal = {Acta neuropathologica}, volume = {67}, number = {1-2}, pages = {13-24}, pmid = {4024866}, issn = {0001-6322}, support = {5 R01 NS07838/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Brain Damage, Chronic/*etiology/pathology ; Cerebral Cortex/*pathology/ultrastructure ; Hypoglycemia/*complications/pathology ; Male ; Microscopy, Electron ; Neurons/pathology/ultrastructure ; Rats ; Rats, Inbred Strains ; Time Factors ; }, abstract = {In the course of a study on the pathogenesis of neuronal necrosis in severe hypoglycemia, the morphological characteristics reflecting reversible and irreversible neuronal lesions were examined as a function of time following normalization of blood glucose. To that end, closely spaced time intervals were studied in the rat cerebral cortex before, during, and up to 1 year after standardized pure hypoglycemic insults of 30 and 60 min of cerebral isoelectricity. Both the superficial and deep layers of the cerebral cortex showed dark and light neurons during and several hours after the insult. By electron microscopy (EM) the dark neurons were characterized by marked condensation of both karyoplasm and cytoplasm, with discernible, tightly packed cytoplasmic organelles. The light neurons displayed clustering of normal organelles around the nucleus with clearing of the peripheral cytoplasm. Some cells, both dark neurons and neurons of normal electron density, contained swollen mitochondria with fractured cristae. Light neurons disappeared from the cerebral cortex by 4 h of recovery. Some dark neurons in the superficial cortex and almost all in the deep cortex evolved through transitional forms into normal neurons by 6 h recovery. Another portion of the dark neurons in the superficial cortex became acidophilic between 4 and 12 h, and by EM they demonstrated karyorrhexis with stippled electron-dense chromatin. The plasma membrane was disrupted, the cytoplasm was composed of amorphous granular debris, and the mitochondria contained flocculent densities. These definitive indices of irreversible neuronal damage were seen as early as 4-8 h recovery. Subsequently, the acidophilic neurons were removed from the tissue, and gliosis ensued. Thus, even markedly hyperchromatic "dark" neurons are compatible with survival of the cell, as are neurons with conspicuous mitochondrial swelling. Definite nerve cell death is verified as the appearance of acidophilic neurons at which stage extensive damage to mitochondria is already seen in the form of flocculent densities, and cell membranes are ruptured. Our previous results have shown that hypoglycemic neocortical damage affects the superficial laminae, chiefly layer 2. The present results demonstrate that, following the primary insult, this damage evolves relatively rapidly within the first 4-12 h. We have obtained no evidence that additional necrotic neurons are recruited after longer recovery periods.}, }
@article {pmid3992000, year = {1985}, author = {Decaux, JF and Ferré, P and Robin, P and Robin, D and Girard, JR}, title = {[Development of hepatic fatty acid metabolism in the rat during weaning].}, journal = {Reproduction, nutrition, developpement}, volume = {25}, number = {1B}, pages = {329-330}, pmid = {3992000}, issn = {0181-1916}, mesh = {Animals ; Dietary Carbohydrates/administration &amp; dosage ; Dietary Fats/administration &amp; dosage ; Fatty Acids/*metabolism ; Gluconeogenesis ; Lipids/biosynthesis ; Liver/growth &amp; development/*metabolism ; Malonyl Coenzyme A/metabolism ; Mitochondria, Liver/metabolism ; Rats ; *Weaning ; }, }
@article {pmid3935805, year = {1985}, author = {Obar, R and Green, J}, title = {Molecular archaeology of the mitochondrial genome.}, journal = {Journal of molecular evolution}, volume = {22}, number = {3}, pages = {243-251}, pmid = {3935805}, issn = {0022-2844}, mesh = {Base Sequence ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; *Genes ; Mitochondria/*metabolism ; Models, Genetic ; RNA Splicing ; RNA, Messenger/genetics ; RNA, Small Nuclear/genetics ; Species Specificity ; }, abstract = {We develop a stepwise model for the net transfer of nucleic acid sequences between non-homologous genomes. This model is then used to explain the two major patterns in the evolutionary history of mitochondrial genomes: the gross reduction of the number of genes, and the subsequent acquisition of introns.}, }
@article {pmid3914946, year = {1985}, author = {Subramanian, AR}, title = {The ribosome: its evolutionary diversity and the functional role of one of its components.}, journal = {Essays in biochemistry}, volume = {21}, number = {}, pages = {45-85}, pmid = {3914946}, issn = {0071-1365}, mesh = {Bacteria/metabolism ; *Biological Evolution ; Chloroplasts/metabolism ; Genes ; Mitochondria/metabolism ; Plants/metabolism ; RNA, Ribosomal/genetics ; Ribosomal Proteins/genetics/metabolism ; Ribosomes/*metabolism ; }, }
@article {pmid3908651, year = {1985}, author = {Enoki, Y}, title = {[Physiological mechanisms for effective utilization of ambient oxygen--with a special relevance to its phylogenetic aspects and exercise].}, journal = {Nihon seirigaku zasshi. Journal of the Physiological Society of Japan}, volume = {47}, number = {7}, pages = {268-278}, pmid = {3908651}, issn = {0031-9341}, mesh = {Adenosine Triphosphate/biosynthesis ; Animals ; Biological Evolution ; Capillaries/anatomy &amp; histology ; Cats ; Dogs ; Energy Metabolism ; Erythrocytes/metabolism ; Fishes ; Guinea Pigs ; Hemoglobins/metabolism/physiology ; Mice ; Microcirculation ; Mitochondria/metabolism/ultrastructure ; Muscles/blood supply ; Myoglobin/physiology ; Oxygen/blood/*physiology ; Rabbits ; Rats ; Reptiles ; }, }
@article {pmid3881803, year = {1985}, author = {Mathews, FS}, title = {The structure, function and evolution of cytochromes.}, journal = {Progress in biophysics and molecular biology}, volume = {45}, number = {1}, pages = {1-56}, doi = {10.1016/0079-6107(85)90004-5}, pmid = {3881803}, issn = {0079-6107}, support = {GM 20530/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Biological Evolution ; Cytochromes/*metabolism ; Eukaryotic Cells/metabolism ; Mitochondria/metabolism ; Prokaryotic Cells/metabolism ; Protein Conformation ; }, }
@article {pmid3836230, year = {1985}, author = {Else, PL and Hulbert, AJ}, title = {An allometric comparison of the mitochondria of mammalian and reptilian tissues: the implications for the evolution of endothermy.}, journal = {Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology}, volume = {156}, number = {1}, pages = {3-11}, pmid = {3836230}, issn = {0174-1578}, mesh = {Alligators and Crocodiles/anatomy &amp; histology ; Animals ; Biological Evolution ; Body Weight ; Intracellular Membranes/ultrastructure ; Lizards/anatomy &amp; histology ; Mammals/*anatomy &amp; histology ; Marsupialia/anatomy &amp; histology ; Mice/anatomy &amp; histology ; Mitochondria/*ultrastructure ; Organ Size ; Oxygen Consumption ; Rabbits/anatomy &amp; histology ; Rats/anatomy &amp; histology ; Reptiles/*anatomy &amp; histology ; Species Specificity ; Tachyglossidae/anatomy &amp; histology ; Turtles/anatomy &amp; histology ; }, abstract = {The effects of body size and phylogeny on metabolic capacities were examined by comparing the mitochondrial capacities of 6 mammalian and 4 reptilian species representing 100-fold body weight ranges. The mammals examined included 3 eutherian, 2 marsupial and a monotreme species and the reptiles 2 saurian, 1 crocodilian and 1 testudine species. The tissues examined were liver, kidney, brain, heart, lung and skeletal muscle. Allometric equations were derived for tissue weights, mitochondrial volume densities, internal mitochondrial membrane surface area densities, tissue mitochondrial membrane surface areas both per gram and per total tissue and summated tissue mitochondrial membrane surface areas. For the mammals and reptiles studied a 100% increase in body size resulted in average increases of 68% in internal organ size and 107% in skeletal muscle mass. Similarly, total organ mitochondrial membrane surface areas increase in mammals and reptiles by an average 54% and for skeletal muscle by an average 96%. These values are similar to increases in standard (54 and 71%) and maximum (73 and 77%) organismal metabolism values found by other authors for mammals and reptiles respectively. Although the allometric exponents (or rates of change with increasing body size) of the mitochondrial parameters in mammals and reptiles are statistically the same, in general the total amount of mitochondrial membrane surface area in the mammalian tissues are four times greater than found in the reptilian tissues.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid3003521, year = {1985}, author = {Taylor, JW and Smolich, BD and May, G}, title = {An evolutionary comparison of homologous mitochondrial plasmid DNAs from three Neurospora species.}, journal = {Molecular &amp; general genetics : MGG}, volume = {201}, number = {2}, pages = {161-167}, pmid = {3003521}, issn = {0026-8925}, support = {BRSG 84-26/RS/DRS NIH HHS/United States ; }, mesh = {*Biological Evolution ; DNA Restriction Enzymes ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Neurospora/*genetics ; Neurospora crassa/*genetics ; Nucleic Acid Hybridization ; *Plasmids ; Sequence Homology, Nucleic Acid ; Species Specificity ; }, abstract = {We have discovered a mitochondrial DNA plasmid in N. crassa 516 (Roanoke, LA) which is homologous to those previously described from N. intermedia 435 (Fiji) and N. tetrasperma 2510 (Hanalei, HA). Subsequent analysis by DNA-DNA hybridization showed that 6 of 14 other Louisiana N. crassa isolates possessed plasmids homologous to these three plasmids, but at lower copy number. Plasmids from the three named strains were studied to examine possible plasmid diversity within each isolate, the extent of the homology between the plasmids, and the possibility that these plasmids could be inherited separately from their host mitochondria. Comparison of cloned plasmids and covalently closed circular mitochondrial DNA showed that only one plasmid line was present in each of the three intensively studied isolates. DNA-DNA hybridization and restriction endonuclease site mapping showed that the mitochondrial plasmids from the three species were very similar; most of the variation was due to presumed nucleotide substitutions. Plasmids judged identical by our analysis were found in different species. The distribution of the homologous plasmids in nature and the presence of these identical plasmids in different species, suggested that these plasmids could be transmitted between isolates independently of their host mitochondria.}, }
@article {pmid2866624, year = {1985}, author = {Bellini, O and Solcia, E}, title = {Early and late sarcoplasmic reticulum changes in doxorubicin cardiomyopathy. An ultrastructural investigation with the zinc iodide-osmium tetroxide (ZIO) technique.}, journal = {Virchows Archiv. B, Cell pathology including molecular pathology}, volume = {49}, number = {2}, pages = {137-152}, doi = {10.1007/BF02912092}, pmid = {2866624}, issn = {0340-6075}, mesh = {Animals ; Antibiotics, Antineoplastic/pharmacology ; Cardiomyopathies/*chemically induced/pathology ; Doxorubicin/*pharmacology ; Female ; *Iodides ; Mice ; Mice, Inbred Strains ; Microscopy, Electron ; Osmium Tetroxide ; Sarcoplasmic Reticulum/*ultrastructure ; Time Factors ; Zinc ; *Zinc Compounds ; }, abstract = {The sequence of myocardial changes in the mouse induced by doxorubicin (Dx) treatment (10 mg/kg i.v.) has been investigated by electron microscopy with the help of the zinc iodide-osmium tetroxide (ZIO) technique. Accumulation of ZIO-reactive material, possibly oxidized glutathione and other disulfides, in the sarcoplasmic reticulum (S.R.) is among the earliest (1 h after Dx injection), more prominent and persistent findings (up to 100 days). It may have a pathogenic relationship with a number of functional and morphologic changes occurring in myocardial cells, including impairment of calcium transport and contractility, S.R. dilation up to extensive vacuolization, as well as inhibition of DNA, RNA and protein synthesis leading to atrophy and disruption of sarcomeres. The latter finding, first appearing in a few cells 4 to 7 days after Dx and progressively increasing in severity and extension during the next 3 months, may represent a key factor in the evolution of chronic cardiomyopathy to cardiac insufficiency. In most cells, only a minority of mitochondria showed obvious ultrastructural lesions, which were first observed 24 h after treatment and disappeared by the end of the first month, when no more mitochondrial damage was found outside degenerating cells. The myocardium of mice receiving multiple Dx injections (4 mg/Kg, 10 times, or 9 mg/Kg, 5 times) showed the same changes observed in animals treated with a single dose, though they were more severe and extensive.}, }
@article {pmid2581766, year = {1985}, author = {Danchin, A and Slonimski, PP}, title = {Split genes.}, journal = {Endeavour}, volume = {9}, number = {1}, pages = {18-27}, doi = {10.1016/0160-9327(85)90005-5}, pmid = {2581766}, issn = {0160-9327}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Mitochondria/metabolism ; Mutation ; *RNA Splicing ; RNA, Messenger/genetics ; }, }
@article {pmid2417640, year = {1985}, author = {Cedergren, R and Lang, BF}, title = {Probing fungal mitochondrial evolution with tRNA.}, journal = {Bio Systems}, volume = {18}, number = {3-4}, pages = {263-267}, doi = {10.1016/0303-2647(85)90026-7}, pmid = {2417640}, issn = {0303-2647}, mesh = {Base Sequence ; *Biological Evolution ; Fungi/*genetics ; Gene Conversion ; Genes, Fungal ; Mitochondria/metabolism ; RNA/*genetics ; RNA, Fungal/*genetics ; RNA, Mitochondrial ; RNA, Transfer/*genetics ; Time Factors ; }, abstract = {Sequence data are now available for almost the entire complement of mitochondrial rRNAs from five fungi: Schizosaccharomyces pombe, Saccharomyces cerevisiae, Toropulis glabrata, Aspergillus nidulans and Neurospora crassa. Analysis of these data show that the five mitochondria can be related to a common ancestor. The unusually high similarity between some S. pombe mt tRNAs may be due to a process similar to gene conversion. Using the number of differences between tRNA pairs as a measure of the evolutionary rate the yeast-S. pombe branch has paradoxically a high nuclear rate and a low mt rate of evolution as compared with other branches in the phylogenetic tree. Finally the position of mt tRNA genes in S. pombe is abnormally distinct from gene orders in other mitochondria. All of the above factors must be taken into account when describing the relationship between these mitochondria.}, }
@article {pmid2409043, year = {1985}, author = {Rogers, JH}, title = {The origin and evolution of retroposons.}, journal = {International review of cytology}, volume = {93}, number = {}, pages = {187-279}, doi = {10.1016/s0074-7696(08)61375-3}, pmid = {2409043}, issn = {0074-7696}, mesh = {Base Sequence ; *Biological Evolution ; *DNA/*genetics ; DNA, Mitochondrial/genetics ; *Genes ; Mitochondria/physiology ; RNA/genetics ; RNA Processing, Post-Transcriptional ; *RNA Splicing ; RNA, Messenger/genetics ; RNA, Mitochondrial ; RNA, Ribosomal/genetics ; RNA, Small Nuclear ; RNA, Transfer/genetics ; RNA-Directed DNA Polymerase/*genetics ; Repetitive Sequences, Nucleic Acid ; }, }
@article {pmid6096380, year = {1984}, author = {Hod, Y and Morris, SM and Hanson, RW}, title = {Induction by cAMP of the mRNA encoding the cytosolic form of phosphoenolpyruvate carboxykinase (GTP) from the chicken. Identification and characterization of a cDNA clone for the enzyme.}, journal = {The Journal of biological chemistry}, volume = {259}, number = {24}, pages = {15603-15608}, pmid = {6096380}, issn = {0021-9258}, support = {AM-21859/AM/NIADDK NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Chickens ; *Cloning, Molecular ; Cyclic AMP/*pharmacology ; Cytosol/enzymology ; DNA/*isolation &amp; purification ; DNA Restriction Enzymes ; Enzyme Induction ; Kidney/enzymology ; Mitochondria/enzymology ; Nucleic Acid Hybridization ; Phosphoenolpyruvate Carboxykinase (GTP)/biosynthesis/*genetics ; RNA, Messenger/biosynthesis/*genetics ; Transcription, Genetic/drug effects ; }, abstract = {Previous work from our laboratory (Hod, Y., Utter, M. F., and Hanson, R. W. (1982) J. Biol. Chem. 257, 13787-13794) has demonstrated that chicken kidney contains both mitochondrial and cytosolic forms of phosphoenolpyruvate carboxykinase (GTP) (EC 4.1.1.32) and that the two forms are distinct proteins. Using poly(A+) RNA from chicken kidney, a double-stranded cDNA library was constructed. DNA clones containing sequences complementary to the mRNA for the cytosolic form of phosphoenolpyruvate carboxykinase were initially identified by colony hybridization with 32P-labeled cDNA transcribed from an RNA fraction enriched for the enzyme mRNA. The identity of plasmids containing phosphoenolpyruvate carboxykinase cDNA was confirmed by hybrid-selected translation. Mature mRNA for cytosolic phosphoenolpyruvate carboxykinase of the chicken is 2.8 kilobases in length, similar to that previously noted for mRNA coding for the same enzyme in the rat. The cDNA for the chicken enzyme hybridizes with several restriction fragments of the corresponding cDNA for the rat cytosolic phosphoenolpyruvate carboxykinase, indicating conservation of nucleotide sequences during evolution. Wide spread conservation of sequence homology is also demonstrated by the hybridization of the cDNA for the rat phosphoenolpyruvate carboxykinase with a 2.8-kilobase RNA from the livers of a variety of vertebrates including amphibian, avian, and primate species. Specific mRNA coding for the cytosolic form of phosphoenolpyruvate carboxykinase was present in chicken kidney but absent from the liver, even in animals starved for 48 h. However, the administration of cAMP to normal fed chickens caused a rapid induction of phosphoenolpyruvate carboxykinase mRNA. These findings suggest that the gene for the cytosolic enzyme in chicken liver can be expressed if the proper hormonal stimuli are present.}, }
@article {pmid6521672, year = {1984}, author = {Setälä, K}, title = {Carcinogenesis--devolution towards an ancient nucleated pre-eukaryotic level.}, journal = {Medical hypotheses}, volume = {15}, number = {3}, pages = {209-230}, doi = {10.1016/0306-9877(84)90015-x}, pmid = {6521672}, issn = {0306-9877}, mesh = {Animals ; Biological Evolution ; Carcinogens/pharmacology ; Cell Differentiation ; Energy Metabolism ; Eukaryotic Cells/physiology ; Humans ; Mice ; Mitochondria/*physiology ; Mitosis ; Neoplasms/*pathology/physiopathology ; Precancerous Conditions/pathology ; Skin/drug effects ; Skin Neoplasms/etiology/pathology ; Water ; }, abstract = {Because the mitochondria and the cells housing them are obligatory symbionts, the evolutionary history of cells forms the locus minoris resistentiae which is the prerequisite for the carcinogenetic process. During carcinogenesis, the cells devolve towards an ancient anaerobic nucleated pre-eukaryotic level. True carcinogens cause an accumulation of inclusion bodies in the inner, bacterial, mitochondrial membrane. The mitochondrial damage which is detectable only in the early pretumorous stages, results in the respiratory surface with its enzymes being specifically changed, the mitochondrial and nuclear cycles no longer coinciding, the energy generation being forced to reuse the latent, "prehistoric", mode of respiration and the mitochondrial enzyme systems of soil bacterial origin becoming adapted to use other and more versatile metabolic pathways with a wider variety of end-products than classical glycolysis which produces lactate only. Neither external carcinogens nor oncogens are necessary. An increased, prolonged cell replication activity of physiological type is sufficient to initiate and maintain the process in animals with an inherited neoplastic disposition located in the inner mitochondrial membrane. The neoplastic disposition is inherited maternally: in fertilization the ovum does not receive mitochondria from the spermatocyte. The final results are an overall retardation of cell processes and instability in its structural and functional repertoire, the cytoskeleton (differentiation organelle) of the malignant cell manifesting special patterns. The proposed devolutionary mechanism is feasible as DNA packages are physiological components of soil bacterial membrane and can remain dormant (repressed) for years, or for ever, but under suitable conditions can generate seemingly new species, and particularly because enzyme adaptability is the unique privilege of soil bacteria.}, }
@article {pmid6236996, year = {1984}, author = {Ovchinnikov YuA,  and Modyanov, NN and Grinkevich, VA and Aldanova, NA and Kostetsky, PV and Trubetskaya, OE and Hundal, T and Ernster, L}, title = {Oligomycin sensitivity-conferring protein (OSCP) of beef heart mitochondria. Internal sequence homology and structural relationship with other proteins.}, journal = {FEBS letters}, volume = {175}, number = {1}, pages = {109-112}, doi = {10.1016/0014-5793(84)80580-3}, pmid = {6236996}, issn = {0014-5793}, mesh = {Adenosine Triphosphatases/*isolation &amp; purification ; Amino Acid Sequence ; Animals ; Carrier Proteins/*isolation &amp; purification ; Cattle ; Macromolecular Substances ; Membrane Proteins/*isolation &amp; purification ; Mitochondria, Heart/*metabolism ; Mitochondrial ADP, ATP Translocases ; Mitochondrial Proton-Translocating ATPases ; Software ; Structure-Activity Relationship ; }, abstract = {Structural analysis of oligomycin sensitivity-conferring protein (OSCP) revealed repeating sequences (residues 1-89, 105-190) suggesting an evolution of the protein by gene duplication. In addition to the reported homology with the delta-subunit of Escherichia coli F1ATPase, OSCP also shows a certain homology with the b-subunit of E. coli F0 and the ADP/ATP carrier of mitochondria.}, }
@article {pmid6486738, year = {1984}, author = {Sterman, AB}, title = {Hexacarbon neuropathy: cell body changes are early, dynamic, and specific.}, journal = {Annals of neurology}, volume = {16}, number = {3}, pages = {343-348}, doi = {10.1002/ana.410160311}, pmid = {6486738}, issn = {0364-5134}, support = {ES-02650/ES/NIEHS NIH HHS/United States ; ES-03511/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Axons/drug effects ; Female ; Ganglia, Spinal/*drug effects ; Hexanones/*toxicity ; Ketones/*toxicity ; Microscopy, Electron ; Mitochondria/drug effects ; Nerve Degeneration/drug effects ; Neurons/drug effects ; Nissl Bodies/drug effects ; Rats ; Rats, Inbred Strains ; }, abstract = {To study the evolution of cell body alterations during toxic neuropathy we exposed rats to the prototype neurotoxin 2,5-hexanedione and examined perikarya of lumbar dorsal root ganglia with electron microscopy and stereology at three stages of neuropathy. Compared to unintoxicated controls, neurons from rats with incipient (four weeks) and intermediate (six to seven weeks) neuropathy showed dispersion of Nissl substance and significant decreases (p less than 0.001) in the volume fractions of Nissl bodies, but not of mitochondria or Golgi apparatus. However, at advanced (twelve to fourteen weeks) stages the volume fraction of Nissl bodies had increased and no longer differed from that of controls; distinct chromatolysis-like changes also became prominent. To evaluate the specificity of this remodeling we compared current morphometric results to data from rats exposed to acrylamide monomer and found significant differences (p less than 0.001) in the volume fractions of Nissl bodies and mitochondria. We conclude: (1) in axonopathy, cell body remodeling occurs early and advances as a dynamic, evolving process, and (2) distinct differences in the patterns of cell body changes can distinguish the neuropathies studied, implying distinct cell body functions.}, }
@article {pmid6089794, year = {1984}, author = {Young, LJ and Einarsdóttir, O and Vossbrink, CR and Caughey, WS}, title = {Infrared spectra of carbon monoxide bound to mitochondria from diverse species and tissues reveal structurally similar cytochrome c oxidase dioxygen reaction sites.}, journal = {Biochemical and biophysical research communications}, volume = {123}, number = {1}, pages = {247-253}, doi = {10.1016/0006-291x(84)90405-4}, pmid = {6089794}, issn = {0006-291X}, support = {HL-15980/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Binding Sites ; Brain/enzymology ; Carbon Monoxide/*metabolism ; Cattle ; Diptera ; Electron Transport Complex IV/*metabolism ; Kidney/enzymology ; Mitochondria/*enzymology ; Mitochondria, Heart/*enzymology ; Mitochondria, Muscle/*enzymology ; Oxygen ; Protein Binding ; Rats ; Spectrophotometry, Infrared ; Swine ; }, abstract = {Infrared bands for CO bound to mitochondria from bovine and porcine hearts, bovine brain, rat kidney, and blowfly flight muscle and to intact blowfly flight muscle have been measured in the carbon-oxygen stretch region. Each spectrum contains a narrow band near 1963 cm-1 similar to the major band found earlier for the carbonyl cytochrome c oxidase purified from bovine heart. A second band near 1959 cm-1 ascribed to a less stable conformer of the purified oxidase carbonyl is also detected in mitochondria. These spectra support very similar CO (and O2) binding sites among all the oxidases examined whether the enzyme is purified or is still within mitochondria or intact tissue and therefore suggest that the reduced heme A ligand binding site has been highly conserved during evolution.}, }
@article {pmid6089124, year = {1984}, author = {Chao, S and Sederoff, R and Levings, CS}, title = {Nucleotide sequence and evolution of the 18S ribosomal RNA gene in maize mitochondria.}, journal = {Nucleic acids research}, volume = {12}, number = {16}, pages = {6629-6644}, pmid = {6089124}, issn = {0305-1048}, mesh = {Animals ; Base Sequence ; Cloning, Molecular ; DNA Restriction Enzymes ; DNA, Mitochondrial/*genetics ; *Genes ; Humans ; Mitochondria/*metabolism ; Molecular Weight ; Nucleic Acid Conformation ; Plants/*genetics ; RNA, Ribosomal/*genetics ; Species Specificity ; Zea mays/genetics ; }, abstract = {The nucleotide sequence of the gene coding for the 18S ribosomal RNA of maize mitochondria has been determined and a model for the secondary structure is proposed. Dot matrix analysis has been used to compare the extent and distribution of sequence similarities of the entire maize mitochondrial 18S rRNA sequence with that of 15 other small subunit rRNA sequences. The mitochondrial gene shows great similarity to the eubacterial sequences and to the maize chloroplast, and less similarity to mitochondrial rRNA genes in animals and fungi. We propose that this similarity is due to a slow rate of nucleotide divergence in plant mtDNA compared to the mtDNA of animals. Sequence comparisons indicate that the evolution of the maize mitochondrial 18S, chloroplast 16S and nuclear 17S ribosomal genes have been essentially independent, in spite of evidence for DNA transfer between organelles and the nucleus.}, }
@article {pmid6462918, year = {1984}, author = {Gray, MW and Sankoff, D and Cedergren, RJ}, title = {On the evolutionary descent of organisms and organelles: a global phylogeny based on a highly conserved structural core in small subunit ribosomal RNA.}, journal = {Nucleic acids research}, volume = {12}, number = {14}, pages = {5837-5852}, pmid = {6462918}, issn = {0305-1048}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA, Mitochondrial/genetics ; Eukaryotic Cells/physiology ; Nucleic Acid Conformation ; Prokaryotic Cells/physiology ; RNA, Ribosomal/genetics ; Ribosomes/ultrastructure ; }, abstract = {To probe the earliest evolutionary events attending the origin of the five known genome types (archaebacterial, eubacterial, nuclear, mitochondrial and plastid), we have analyzed sequences corresponding to a ubiquitous, highly conserved core of secondary structure in small subunit rRNA. Our results support (i) the existence of three primary lineages (archaebacterial, eubacterial, and nuclear), (ii) a specific eubacterial ancestry for plastids and mitochondria (plant, animal, fungal), and (iii) an endosymbiotic, evolutionary origin of the two types of organelle from within distinct groups of eubacteria (blue-green algae (cyanobacteria) in the case of plastids, nonphotosynthetic aerobic bacteria in the case of mitochondria). In addition, our analysis suggests (iv) a biphyletic origin of mitochondria, with animal and fungal mitochondria branching together but separately from plant mitochondria, and (v) a monophyletic origin of plastids. The method described here provides a powerful and generally applicable molecular taxonomic approach towards a global phylogeny encompassing all organisms and organelles.}, }
@article {pmid6330036, year = {1984}, author = {Natvig, DO and May, G and Taylor, JW}, title = {Distribution and evolutionary significance of mitochondrial plasmids in Neurospora spp.}, journal = {Journal of bacteriology}, volume = {159}, number = {1}, pages = {288-293}, pmid = {6330036}, issn = {0021-9193}, support = {BRSG 81-31/RS/DRS NIH HHS/United States ; }, mesh = {*Biological Evolution ; DNA Restriction Enzymes ; DNA, Mitochondrial/*genetics ; DNA, Recombinant/analysis ; Mitochondria/*physiology ; Neurospora/*genetics ; Neurospora crassa/genetics ; Nucleic Acid Hybridization ; *Plasmids ; Species Specificity ; }, abstract = {A mitochondrial plasmid line in the fungal genus Neurospora is geographically widely distributed and occurs in isolates of at least two species. On the basis of characterization with restriction endonucleases, it is apparent that plasmids from isolates of Neurospora tetrasperma are more closely related to one another than to an evolutionarily homologous plasmid from Neurospora intermedia; N. tetrasperma plasmids from Surinam and Hawaii differed from one another only slightly by our analysis, whereas the plasmid from N. intermedia (Fiji) exhibited substantial restriction site divergence from all N. tetrasperma plasmids. We believe these observations strengthen the presumption that four-spored isolates of Neurospora spp. represent a natural taxonomic grouping (N. tetrasperma). The plasmids from N. tetrasperma and N. intermedia (Fiji), although clearly related to each other as shown by hybridization studies, exhibited no detectable homology with either of two additional plasmid lines from isolates of Neurospora spp. Nor did they exhibit homology with the mitochondrial genome. Despite this lack of homology among three distinct plasmid lines, all the plasmids may possess a common mode of replication.}, }
@article {pmid6427407, year = {1984}, author = {Holdsworth, ES and Appleby, G}, title = {Assays of glucose tolerance factor and its mode of action, studied with brewer's yeast.}, journal = {Journal of inorganic biochemistry}, volume = {21}, number = {1}, pages = {31-44}, doi = {10.1016/0162-0134(84)85037-0}, pmid = {6427407}, issn = {0162-0134}, mesh = {Aerobiosis ; Amino Acids/*metabolism ; Anaerobiosis ; Biological Transport, Active ; Carbon Dioxide/metabolism ; Chromium/*metabolism ; Deoxyglucose/metabolism ; Ethanol/metabolism ; Hydrogen-Ion Concentration ; Mitochondria/metabolism ; Nicotinic Acids/*metabolism ; Pyruvate Carboxylase/metabolism ; Pyruvates/metabolism ; Pyruvic Acid ; Saccharomyces cerevisiae/*metabolism ; }, abstract = {Glucose tolerance factor (GTF) has usually been assayed by manometric measurement of CO2 evolved when glucose was metabolizing glucose. By using 14C labeled substrates it has been shown that GTF increases the decarboxylation of pyruvate to ethanol and CO2. Thus in addition to measuring CO2 evolution, the enzymatic estimation of the increased ethanol production can be used to assay GTF. A further effect of GTF was to cause increased carboxylation of pyruvate to substrates that are used in the biosynthesis of cell substance. The metabolic sites of action of GTF are discussed.}, }
@article {pmid6732765, year = {1984}, author = {Vayssière, JL and Berthelot, F and Croizat, B and Gros, F}, title = {Changes in mitochondrial proteins during neuroblastoma differentiation.}, journal = {Biochemical and biophysical research communications}, volume = {120}, number = {2}, pages = {411-419}, doi = {10.1016/0006-291x(84)91269-5}, pmid = {6732765}, issn = {0006-291X}, mesh = {Animals ; Brain/embryology/metabolism ; Cell Differentiation/drug effects ; Cell Line ; Cyclohexanecarboxylic Acids/pharmacology ; Dimethyl Sulfoxide/pharmacology ; Methionine/metabolism ; Mice ; Mitochondria/*metabolism ; Neuroblastoma/*metabolism/pathology ; *Protein Biosynthesis ; }, abstract = {The evolution of three major mit-proteins was followed in neuroblastoma cells cultured in different conditions of differentiation. 1 methyl cyclohexane carboxylic acid (CCA) was found to stimulate the synthesis of the three mit-protein markers. This result, compared to the effects of oligomycin, an inhibitor of mitochondrial function, favours the hypothesis that CCA induces in vitro neurogenesis through a general metabolic alteration.}, }
@article {pmid6715340, year = {1984}, author = {Seilhamer, JJ and Gutell, RR and Cummings, DJ}, title = {Paramecium mitochondrial genes. II. Large subunit rRNA gene sequence and microevolution.}, journal = {The Journal of biological chemistry}, volume = {259}, number = {8}, pages = {5173-5181}, pmid = {6715340}, issn = {0021-9258}, support = {AG-05221/AG/NIA NIH HHS/United States ; GM-17129/GM/NIGMS NIH HHS/United States ; GM-21948/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA/*genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal ; *Genes ; Macromolecular Substances ; Mitochondria/*metabolism ; Nucleic Acid Conformation ; Paramecium/*genetics ; RNA, Ribosomal/*genetics ; }, abstract = {Mature Paramecium mitochondrial large subunit rRNA consists of two stable segments: a 20 S segment described previously and a unique 283-base segment similar to 5.8 S rRNAs typically found in eucaryotic cytoplasmic RNA. pBR325 clones of both gene regions from both Paramecium primaurelia and Paramecium tetraurelia were sequenced and aligned. The gene segments lie adjacent to each other very near the replicative terminal end of the linear Paramecium mitochondrial genome and are transcribed from a common 23 S precursor. The precise gene ends were determined using nuclease S1 protection; the large subunit rRNA gene complex (consisting of "5.8 S-like" rRNA, a 19-26-base excised region, and 20 S rRNA) spans about 2654 base pairs. The gene complex is preceded by a 15-base poly(T) tract and terminates randomly within a 20-base A + T-rich segment immediately preceding the tRNATyr gene. The sequences from the two species were 4% divergent, the changes consisting of 59% transitions, 38% transversions, and 3% insertions or deletions. The sequences were aligned with Escherichia coli 23 S rRNA, and a secondary structure model is presented for the entire molecule based on structures proposed for E. coli 23 S rRNA.}, }
@article {pmid6371000, year = {1984}, author = {Seilhamer, JJ and Olsen, GJ and Cummings, DJ}, title = {Paramecium mitochondrial genes. I. Small subunit rRNA gene sequence and microevolution.}, journal = {The Journal of biological chemistry}, volume = {259}, number = {8}, pages = {5167-5172}, pmid = {6371000}, issn = {0021-9258}, support = {AG-05221/AG/NIA NIH HHS/United States ; GM-21948/GM/NIGMS NIH HHS/United States ; GM-23464/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA/genetics ; DNA, Mitochondrial/*genetics ; DNA, Ribosomal ; Escherichia coli/genetics ; *Genes ; Macromolecular Substances ; Mitochondria/metabolism ; Nucleic Acid Conformation ; Paramecium/*genetics ; RNA, Ribosomal/*genetics ; Species Specificity ; }, abstract = {The sequences of the small subunit mitochondrial rRNA genes from two divergent species of Paramecium (primaurelia and tetraurelia) were determined. The gene lies near the center of the linear mitochondrial genome, on the same strand as are all other currently identified genes. The sequences generally resemble their counterparts found in cytoplasmic, procaryotic, and other mitochondrial sources. The rDNA gene boundaries were located by nuclease S1 protection. Small subunit rDNA spans about 1680 nucleotides, including an extraneous 83-base pair sequence very near the 3' end which is unique to Paramecium mitochondria. This "insert" occurs at the apex of the highly variable in length penultimate helix, according to proposed models for small subunit rRNA secondary structure. A discontinuity occurs in isolated rRNA near the start of the insert, resulting in a stable 13 S RNA species and a small segment containing the remaining 3' portion of the gene. The overall rRNA gene sequence was 94% conserved between the two species, and the nucleotide differences consisted of 53% transitions, 37% transversions, and 9% insertions plus deletions. These substitutions were somewhat clustered, and the two most divergent regions coincided with the gene boundaries. The sequence was aligned with Escherichia coli 16 S rRNA for direct comparison of sequence and structure.}, }
@article {pmid6201395, year = {1984}, author = {Vogel, DW and Hartmann, RK and Bartsch, M and Subramanian, AR and Kleinow, W and O'Brien, TW and Pieler, T and Erdmann, VA}, title = {Reconstitution of 50 S ribosomal subunits from Bacillus stearothermophilus with 5 S RNA from spinach chloroplasts and low-Mr RNA from mitochondria of Locusta migratoria and bovine liver.}, journal = {FEBS letters}, volume = {169}, number = {1}, pages = {67-72}, doi = {10.1016/0014-5793(84)80291-4}, pmid = {6201395}, issn = {0014-5793}, mesh = {Animals ; Biological Evolution ; Cattle ; Chloroplasts/*analysis ; Geobacillus stearothermophilus/*analysis ; Grasshoppers/analysis ; Mitochondria/*analysis ; Mitochondria, Liver/analysis ; Peptide Biosynthesis ; *Peptides ; Plants ; RNA, Bacterial/physiology ; RNA, Ribosomal/*physiology ; Ribosomes/*physiology ; Species Specificity ; }, abstract = {Reconstitution experiments with 50 S ribosomal subunits from Bacillus stearothermophilus demonstrate that spinach chloroplast 5 S rRNA can be incorporated into the bacterial ribosome and yield biologically active particles, thereby establishing the eubacterial nature of chloroplast 5 S rRNA. In contrast, mitochondria from Locusta migratoria or bovine liver do not appear to contain discrete, low-Mr RNAs, which can replace 5 S rRNA in the functional reconstitution of B. stearothermophilus ribosomes.}, }
@article {pmid6709501, year = {1984}, author = {Van Knippenberg, PH and Van Kimmenade, JM and Heus, HA}, title = {Phylogeny of the conserved 3' terminal structure of the RNA of small ribosomal subunits.}, journal = {Nucleic acids research}, volume = {12}, number = {6}, pages = {2595-2604}, pmid = {6709501}, issn = {0305-1048}, mesh = {Animals ; Bacteria/genetics ; Base Sequence ; Fungi/genetics ; Humans ; Nucleic Acid Conformation ; *Phylogeny ; Plants/genetics ; RNA, Ribosomal/*genetics ; Ribosomes/*metabolism ; Species Specificity ; }, abstract = {The strongest conserved part of the RNA of small ribosomal subunits is probably located near the 3' end. This paper reviews the primary and secondary structures of some 40 sequenced 3' termini and tries to classify these structures according to common features and differences. The regions under consideration contain at the 5' side an almost universal, supposedly single-stranded stretch of nucleotides with the sequence--AAGUCGUAACAAGGU--. This is followed by a stem-loop structure. The stem always contains 9 basepairs (including U-G pairs) and no mismatches or bulged nucleotides. The loop of the hairpin is either (m2)GGm62Am62A (bacteria, chloroplasts and mitochondria) or UGm62Am62A (cytoplasm). The hairpin is, in most cases, followed at the 3' side by--GGAUCA--. Next to it bacteria and chloroplasts contain the so-called "Shine and Dalgarno" sequence --CCUCC--. The stem region of the hairpin contains a conserved A-U U-G junction. The two basepairs between this junction and the loop are either of type 1 (G-C G-C) or type 2 (C-G C-G). Classification according to type links certain bacteria with mitochondria of yeast and plants and others with chloroplasts and with animal mitochondria.}, }
@article {pmid6539426, year = {1984}, author = {Jones, HB and Cavanagh, JB}, title = {The evolution of intracellular responses to acrylamide in rat spinal ganglion neurons.}, journal = {Neuropathology and applied neurobiology}, volume = {10}, number = {2}, pages = {101-121}, doi = {10.1111/j.1365-2990.1984.tb00343.x}, pmid = {6539426}, issn = {0305-1846}, mesh = {Acrylamide ; Acrylamides/*toxicity ; Animals ; Axons/drug effects ; Cytoskeleton/drug effects ; Dose-Response Relationship, Drug ; Endoplasmic Reticulum/drug effects ; Female ; Ganglia, Spinal/*drug effects ; Hindlimb/innervation ; Lysosomes/drug effects ; Microscopy, Electron ; Mitochondria/drug effects ; Neurons/drug effects ; Rats ; Rats, Inbred Strains ; Ribosomes/drug effects ; Sensory Receptor Cells/drug effects ; Tail/innervation ; Wallerian Degeneration/drug effects ; }, abstract = {Acrylamide (30 mg or 50 mg/kg/day, 5 days each week) was injected intraperitoneally into rats for up to 4 weeks. Lumbar spinal ganglia, spinal cord and lumbrical muscle spindles were examined by light and electron microscopy at various times during this period. The first abnormalities in spinal ganglion neurons were seen at 7 days when an apparent increase in numbers of mitochondria, some being hypertrophic, were found in a few large light cells. This was 10 days before any significant Wallerian degeneration was found in muscle spindle sensory fibres. Mitochondrial changes became more marked with time and were later associated with RER disruption, loss of neurofilaments and peripheral displacement of the nucleus thus mimicking chromatolysis of the axon reaction. All these changes began, however, before axon degeneration. Evidence of increased satellite cell activity was maximal at 21 days. These changes are discussed in the light of the possibility that calcium entry into the cell may be seriously increased early in the intoxication as a direct result of the presence of acrylamide and that many of these cellular features are secondary responses to such an event. Distal degeneration of axons seems likely to be secondary to the perikaryal changes.}, }
@article {pmid6323246, year = {1984}, author = {Cann, RL and Brown, WM and Wilson, AC}, title = {Polymorphic sites and the mechanism of evolution in human mitochondrial DNA.}, journal = {Genetics}, volume = {106}, number = {3}, pages = {479-499}, pmid = {6323246}, issn = {0016-6731}, support = {DEB81-12412/DE/NIDCR NIH HHS/United States ; GM30144/GM/NIGMS NIH HHS/United States ; }, mesh = {Base Sequence ; *Biological Evolution ; Codon ; DNA Restriction Enzymes ; DNA, Mitochondrial/*genetics ; Female ; Genetic Variation ; Humans ; Liver/analysis ; Placenta/analysis ; *Polymorphism, Genetic ; Pregnancy ; RNA, Ribosomal/genetics ; RNA, Transfer/genetics ; }, abstract = {Twelve restriction enzymes were used to screen for the presence or absence of cleavage sites at 441 locations in the mitochondrial DNA of 112 humans from four continents. Cleavage maps were constructed by comparison of DNA fragment sizes with those expected from the published sequence for one human mtDNA. One hundred and sixty-three of the sites were polymorphic, i.e., present in some individuals but absent from others, 278 sites being invariant. These polymorphisms probably result from single base substitutions and occur in all functional regions of the genome.--In 77 cases, it was possible to specify the exact nature and location (within a restriction site) of the mutation responsible for the absence of a restriction site in a known human mtDNA sequence and its presence in another human mtDNA. Fifty-two of these 77 gain mutations occur in genes coding for proteins, 34 being silent and 18 causing amino acid replacements; moreover, nine of the replacements are radical.--Notable also is the anomalous ratio of transitions to transversions required to account for these 77 restriction site differences between the known human mtDNA sequences and other human mtDNAs. This ratio is lower for most groups of restriction sites than has been reported from sequence comparisons of limited parts of the mtDNA genome in closely related mammals, perhaps indicating a special functional role or sensitivity to mutagenesis for palindromic regions containing high levels of guanine and cytosine.--From the genomic distribution of the 163 polymorphic sites, it is inferred that the level of point mutational variability in tRNA and rRNA genes is nearly as high as in protein-coding genes but lower than in noncoding mtDNA. Thus, the functional constraints operating on components of the protein-synthetic apparatus may be lower for mitochondria than for other systems. Furthermore, the mitochondrial genes for tRNAs that recognize four codons are more variable than those recognizing only two codons.--Among the more variable of the human mitochondrial genes coding for proteins is that for subunit 2 of cytochrome oxidase; this polypeptide appears to have been evolving about five times faster in primates than in other mammals. Cytochrome c, a nuclearly encoded protein that interacts directly with the oxidase 2 subunit in electron transport, has also evolved faster in primates than in rodents or ungulates. This example, along with that for the mitochondrial rRNA genes and the nuclear genes coding for mitochondrial ribosomal proteins, provides evidence for coevolution between specific nuclear and mitochondrial genes.}, }
@article {pmid6201716, year = {1984}, author = {Mikel'saar, RN}, title = {[The human mitochondrial genome and evolution of transfer methionine RNA].}, journal = {Molekuliarnaia biologiia}, volume = {18}, number = {2}, pages = {323-331}, pmid = {6201716}, issn = {0026-8984}, mesh = {Animals ; Anticodon/genetics ; Bacteria/genetics ; Base Sequence ; *Biological Evolution ; Codon/genetics ; DNA, Mitochondrial/*genetics ; Fungi/genetics ; Humans ; Peptide Elongation Factors/*genetics ; Peptide Initiation Factors/*genetics ; Plants/genetics ; RNA, Bacterial/genetics ; RNA, Fungal/genetics ; RNA, Transfer, Amino Acyl/*genetics ; }, abstract = {The recently deciphered sequence of the human mitochondrial genome is analyzed in the light of an archigenetic hypothesis, according to which mitochondria are derived neither from pro- nor eukaryotes but from more primitive organisms. The possibility that animal mitochondria have only one gene both for elongator and initiator methionine tRNA is supported but C-A pair forming cytosine in the anticodon of these tRNAs is considered to be unmodified. The evolution of the gene and of the codon reading pattern of the methionine tRNA is discussed.}, }
@article {pmid6583663, year = {1984}, author = {Nussinov, R}, title = {Doublet frequencies in evolutionary distinct groups.}, journal = {Nucleic acids research}, volume = {12}, number = {3}, pages = {1749-1763}, pmid = {6583663}, issn = {0305-1048}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; DNA/genetics ; Dinucleoside Phosphates ; Mathematics ; Models, Genetic ; Nucleic Acid Conformation ; Oligonucleotides/*analysis ; Species Specificity ; }, abstract = {We analyze the dinucleotide frequencies of occurrence and preferences separately within the vertebrates, nonvertebrates, DNA viruses, mitochondria, RNA viruses, bacteria and phage sequences. Over half a million nucleotides from more than 400 sequences were used in this study. Distinct patterns are observed. Some of the patterns are common to all sequences, some to either eukaryotes or prokaryotes and others to the subgroups within them. Doublets are the most basic ingredient of order in nucleotide sequences. We suggest that their preferences and the arrangement of nucleotides in the DNA in general is determined to a large extent by the conformational and packaging considerations of the double helix. Some principles of DNA conformation are viewed in light of our results.}, }
@article {pmid6229420, year = {1984}, author = {Ovchinnikov, YA and Modyanov, NN and Grinkevich, VA and Aldanova, NA and Trubetskaya, OE and Nazimov, IV and Hundal, T and Ernster, L}, title = {Amino acid sequence of the oligomycin sensitivity-conferring protein (OSCP) of beef-heart mitochondria and its homology with the delta-subunit of the F1-ATPase of Escherichia coli.}, journal = {FEBS letters}, volume = {166}, number = {1}, pages = {19-22}, doi = {10.1016/0014-5793(84)80036-8}, pmid = {6229420}, issn = {0014-5793}, mesh = {*Adenosine Triphosphatases ; Amino Acid Sequence ; Animals ; Biological Evolution ; *Carrier Proteins ; Cattle ; Escherichia coli/*enzymology ; Macromolecular Substances ; *Membrane Proteins ; Mitochondria, Heart/*enzymology ; Mitochondrial Proton-Translocating ATPases ; Oligomycins/pharmacology ; }, abstract = {The complete amino acid sequence of the oligomycin sensitivity-conferring protein (OSCP) of beef-heart mitochondria is reported. The protein contains 190 amino acids and has a molecular mass of 20 967. Its structure is characterized by a concentration of charged amino acids in the two terminal segments (N 1-77 and C 128-190) of the protein, whereas its central region is more hydrophobic. The earlier reported homology of the protein with the delta-subunit of E. coli F1, based on the terminal amino acid sequences of OSCP, is further substantiated.}, }
@article {pmid6531780, year = {1984}, author = {Smith, DS and Kathirithamby, J}, title = {Atypical 'fibrillar' flight muscle in strepsiptera.}, journal = {Tissue &amp; cell}, volume = {16}, number = {6}, pages = {929-940}, doi = {10.1016/0040-8166(84)90072-7}, pmid = {6531780}, issn = {0040-8166}, mesh = {Actins/analysis ; Animals ; *Flight, Animal ; Insecta/*ultrastructure ; Male ; Microscopy, Electron ; Mitochondria/ultrastructure ; Muscles/ultrastructure ; Myofibrils/ultrastructure ; Myosins/analysis ; Sarcomeres/ultrastructure ; }, abstract = {The fine structure of the principal and ancillary metathoracic flight muscle fibres in the adult male of a strepsipteran, Elenchus tenuicornis, is described. Power-producing dorsal longitudinal and dorso-ventral flight muscles show features consistent with myoneural asynchrony: myofibrils are large and discrete and are separated by large closely packed mitochondria; the sarcoplasmic reticulum is very reduced but engages with T-system membranes in dyads at the mid-sarcomere H-band level. With respect to other asynchronous insect flight muscles, the fibres of Elenchus are anomalous (i) in the small fibre diameter, (ii) in the variable contour of the myofibrils and (iii) in the absence of tracheolar invagination. The functional significance of these structural features is discussed. Ancillary metathoracic muscles are structurally comparable with other synchronous fibres in possessing an extensive SR compartment. Structural evidence for asynchrony in the flight mechanism of Strepsiptera is considered in the context of the evolution of this mechanism throughout the insect Orders.}, }
@article {pmid6429346, year = {1984}, author = {Lanave, C and Preparata, G and Saccone, C and Serio, G}, title = {A new method for calculating evolutionary substitution rates.}, journal = {Journal of molecular evolution}, volume = {20}, number = {1}, pages = {86-93}, pmid = {6429346}, issn = {0022-2844}, mesh = {Animals ; *Biological Evolution ; Cattle ; Codon/genetics ; *Genes ; Humans ; Markov Chains ; Mice ; Mitochondria/metabolism ; Monte Carlo Method ; Proteins/genetics ; Rats ; Stochastic Processes ; }, abstract = {In this paper we present a new method for analysing molecular evolution in homologous genes based on a general stationary Markov process. The elaborate statistical analysis necessary to apply the method effectively has been performed using Monte Carlo techniques. We have applied our method to the silent third position of the codon of the five mitochondrial genes coding for identified proteins of four mammalian species (rat, mouse, cow and man). We found that the method applies satisfactorily to the three former species, while the last appears to be outside the scope of the present approach. The method allows one to calculate the evolutionarily effective silent substitution rate (vs) for mitochondrial genes, which in the species mentioned above is 1.4 X 10(-8) nucleotide substitutions per site per year. We have also determined the divergence time ratios between the couples mouse-cow/rat-mouse and rat-cow/rat-mouse. In both cases this value is approximately 1.4.}, }
@article {pmid6429345, year = {1984}, author = {Hasegawa, M and Yano, T and Miyata, T}, title = {Evolutionary implications of error amplification in the self-replicating and protein-synthesizing machinery.}, journal = {Journal of molecular evolution}, volume = {20}, number = {1}, pages = {77-85}, pmid = {6429345}, issn = {0022-2844}, mesh = {Animals ; *Biological Evolution ; Cytoplasm/metabolism ; DNA Replication ; DNA-Directed DNA Polymerase/genetics ; Fungi/metabolism ; Mitochondria/metabolism ; *Protein Biosynthesis ; Proteins/genetics ; RNA, Transfer/*genetics ; Transcription, Genetic ; }, abstract = {Evolutionary constraints operating on animal mitochondrial tRNA were estimated to be reduced to about 1/30 of those that apply to cytoplasmic tRNA. In the nuclear-cytoplasmic system, an effect of a mutation in tRNA is likely to be amplified through positive feedback loops consisting of DNA polymerases, RNA polymerases, ribosomal proteins, aminoacyl-tRNA synthetases, tRNA processing enzymes, and others. This amplification phenomenon is called an "error cascade" and the loops that cause it are called "error loops." The freedom of evolutionary change of cytoplasmic tRNA is expected to be severely restricted to avoid the error cascade. In fact, cytoplasmic tRNA is highly conserved during evolution. On the other hand, in the animal mitochondrial system, all of the proteins involved in error loops are coded for in the nuclear genome and imported from the cytoplasm, and accordingly the system is free from the error cascade. The difference in constraints operating on animal tRNA between cytoplasm and mitochondria is attributed to the presence or absence of error loops. It is shown that the constraints on mitochondrial tRNA in fungi are not as relaxed as those in animals. This observation is attributed to the presence of an error loop in fungal mitochondria, since at least one protein of the mitochondrial ribosome is coded for in the mitochondrial genome of fungi. The evolutionary rates of proteins involved in the processing of genetic information are discussed in relation to the error cascade.}, }
@article {pmid6399830, year = {1984}, author = {Godlewski, G and Rouy, S and Bureau, JP and Fesquet, J and Eledjam, JJ and Gay, C and Cousineau, J}, title = {The morphological effects in pig liver after Nd-YAG laser resection.}, journal = {Archives d'anatomie, d'histologie et d'embryologie normales et experimentales}, volume = {67}, number = {}, pages = {119-129}, pmid = {6399830}, issn = {0249-5554}, mesh = {Animals ; *Hepatectomy ; *Laser Therapy ; Liver/*anatomy &amp; histology/ultrastructure ; Swine ; }, abstract = {The morphological effects of liver resection in 15 pigs performed with a Nd-YAG laser beam are reported. A regular cut surface was obtained and overlayed an ischemic layer which was thinnest at a 80 W power output and a short exposure time. Hemostasis was satisfying when the encountered vessels did not exceed 4,5 mm in diameter. Semi-thin and electron microscopic examination showed "ghost" cells in the layer of coagulation necrosis, shrunken hepatocytes and red blood cells in oedematous layer and "swollen" mitochondria in the deepest layer. Clamping of the hepatic pedicle - increasing local hyperthermia by suppression of cooling vascular inflow - majorated the depth of cellular alterations and the intensivity of the post-operative inflammatory reaction. Numerous biliary ductules and active hepatocytes meant parenchymal regeneration. Good healing evolution free of complications was observed after a one year's follow up.}, }
@article {pmid6397770, year = {1984}, author = {Delihas, N and Andersen, J and Singhal, RP}, title = {Structure, function and evolution of 5-S ribosomal RNAs.}, journal = {Progress in nucleic acid research and molecular biology}, volume = {31}, number = {}, pages = {161-190}, doi = {10.1016/s0079-6603(08)60377-3}, pmid = {6397770}, issn = {0079-6603}, mesh = {Base Sequence ; *Biological Evolution ; Chloroplasts/physiology ; Eukaryotic Cells/physiology ; Hydrogen Bonding ; Mitochondria/physiology ; Nucleic Acid Conformation ; Prokaryotic Cells/physiology ; Protein Binding ; *RNA, Ribosomal ; Ribosomal Proteins/metabolism ; Ribosomes/*ultrastructure ; Species Specificity ; }, }
@article {pmid6397370, year = {1984}, author = {Doonan, S and Barra, D and Bossa, F}, title = {Structural and genetic relationships between cytosolic and mitochondrial isoenzymes.}, journal = {The International journal of biochemistry}, volume = {16}, number = {12}, pages = {1193-1199}, doi = {10.1016/0020-711x(84)90216-7}, pmid = {6397370}, issn = {0020-711X}, mesh = {Animals ; Aspartate Aminotransferases/genetics ; Biological Evolution ; Cytosol/*enzymology ; Fumarate Hydratase/genetics ; Genes ; Isoenzymes/*genetics ; Mitochondria/*enzymology ; Protein Processing, Post-Translational ; Structure-Activity Relationship ; Superoxide Dismutase/genetics ; }, abstract = {The most common type of genetic relationship between cytosolic and mitochondrial isoenzymes will probably be found to be divergent evolution from a common ancestral form. This is firmly established for the aspartate aminotransferases and less directly so in other cases. The two isoenzymes of aspartate aminotransferase have evolved at roughly equal rates at the level of total amino acid sequence but certain limited surface regions of the mitochondrial form have been much more highly conserved than corresponding regions in the cytosolic protein; these regions probably play a role in topogenesis of the mitochondrial isoenzyme. It is of interest that nearly all mitochondrial proteins are initially synthesised as precursors of molecular weight greater than the mature forms. In the case of aspartate aminotransferase, and possibly of other such isoenzymes, the N-terminus of the mature protein is nearly coincident with that of the cytosolic isoenzyme. Hence during evolution either the gene for the mitochondrial isoenzyme has gained an extra coding region for this N-terminal extension or, less likely, the structural gene for the cytosolic form has suffered a sizeable terminal deletion. Cytosolic and mitochondrial superoxide dismutases have not shared a common ancestral form as shown by the fact that their primary structures are completely unrelated. On the other hand, the mitochondrial and prokaryotic enzymes are clearly related. There is now, however, evidence to suggest that some prokaryotes possess a copper/zinc enzyme related to the eukaryotic cytosolic form. Hence the possibility arises that primitive prokaryotes possessed both proteins. The copper/zinc superoxide dismutase has been retained in the cytosol of eukaryotic cells and a few bacterial species.(ABSTRACT TRUNCATED AT 250 WORDS)}, }
@article {pmid6393247, year = {1984}, author = {Bézard, J and Mauléon, P}, title = {[Female germ cell development during the meiotic prophase in the rat: criteria for cytoplasmic and nuclear identification of the different stages on thin histological slides].}, journal = {Reproduction, nutrition, developpement}, volume = {24}, number = {5A}, pages = {633-654}, pmid = {6393247}, issn = {0181-1916}, mesh = {Animals ; Cell Nucleus/ultrastructure ; Chromosomes/ultrastructure ; Cytoplasm/ultrastructure ; Female ; Gestational Age ; Histological Techniques ; Meiosis ; Models, Biological ; *Oogenesis ; Organoids/ultrastructure ; Ovum/*growth &amp; development/ultrastructure ; Prophase ; Rats/*embryology ; Rats, Inbred Strains ; }, abstract = {The different stages of meiotic prophase in germ cells of the rat ovary were studied cytologically at definite times when there was a dominant nuclear stage. Each stage was identified in 1 mu sections. The usual references for the definition of meiotic nuclear stages according to chromosomal structures wee used and have been described in more detail. It has also been shown that cytological observations such as the organization and distribution of cytoplasmic organelles (mitochondria, Golgi apparatus) equally contributes to the identification of the stages of meiotic prophase.}, }
@article {pmid6099426, year = {1984}, author = {Stewart, KD and Mattox, KR}, title = {The case for a polyphyletic origin of mitochondria: morphological and molecular comparisons.}, journal = {Journal of molecular evolution}, volume = {21}, number = {1}, pages = {54-57}, pmid = {6099426}, issn = {0022-2844}, mesh = {*Biological Evolution ; Cytochrome c Group/genetics ; Mitochondria/*ultrastructure ; *Models, Genetic ; Rhodospirillaceae/genetics/*ultrastructure ; }, abstract = {The comparative morphology and pigmentation of protists suggest that those with tubular mitochondrial cristae belong to a different lineage than those with lamellar cristae and that the evolutionary divergence might have been very early. We propose that the difference in cristal morphology is the result of separate origins of the mitochondria from endosymbionts related to the Rhodospirillaceae (purple nonsulfur bacteria) but differing in the morphology of their internal membranes. Comparisons of the cytochromes c of protists and the Rhodospirillaceae and of 16s rRNA T1 oligonucleotide catalogs in the Rhodospirillaceae do not contradict, and in fact provide support for, the idea. More extensive evidence may be lacking simply because cytochromes c have been studied in very few protists with tubular mitochondrial cristae.}, }
@article {pmid6085867, year = {1984}, author = {Porter, EK and Parry, D and Bird, J and Dickinson, HG}, title = {Nucleic acid metabolism in the nucleus and cytoplasm of angiosperm meiocytes.}, journal = {Symposia of the Society for Experimental Biology}, volume = {38}, number = {}, pages = {363-379}, pmid = {6085867}, issn = {0081-1386}, mesh = {Cell Differentiation ; Chromosomes/ultrastructure ; Cytoplasm/ultrastructure ; DNA/*biosynthesis ; *Meiosis ; Microscopy, Electron ; Plants/*genetics/ultrastructure ; RNA/*metabolism ; RNA, Messenger/biosynthesis ; RNA, Ribosomal/metabolism ; Ribosomes/metabolism ; }, abstract = {Over the course of flowering plant evolution many important stages in the life cycle have become compressed into the period between the premeiotic mitosis and gamete maturation. For this reason the changes in structure or chemistry that take place at this time are not easily ascribed to particular 'developmental stages'. During the meiotic process itself striking changes occur in levels of cytoplasmic and nuclear RNA, while DNA is synthesized in both the chromosomes and organelles. Evidence is presented indicating that a large proportion of the m- and rRNA is purged from the meiocyte cytoplasm by a combination of normal degradation and the activity of specific hydrolases. DNA synthesis in both the plastids and mitochondria precedes the re-differentiation of these organelles, while that in the chromosomes occurs in two major peaks, as has previously been reported (Hotta &amp; Stern, 1971). High-resolution autoradiography did not indicate either peak of DNA synthesis to be localized within the synaptonemal complex, although final confirmation of this conclusion must await further investigation. Examination of these events in organisms where meiosis is removed from other stages of the life cycle suggests that the degradation of RNA and the chromosomal DNA synthesis are features which regularly accompany the meiotic process. The significance of these findings is discussed in terms of the hypothesis that there is at least one stage in the life cycle of all plants at which a purge of information-carrying molecules takes place.}, }
@article {pmid6558300, year = {1983}, author = {Mikelsaar, R}, title = {Human mitochondrial genome and the evolution of methionine transfer ribonucleic acids.}, journal = {Journal of theoretical biology}, volume = {105}, number = {2}, pages = {221-232}, doi = {10.1016/s0022-5193(83)80004-6}, pmid = {6558300}, issn = {0022-5193}, mesh = {Animals ; Anticodon/genetics ; Base Sequence ; *Biological Evolution ; Codon/genetics ; *Genes ; Humans ; Mitochondria/*ultrastructure ; Peptide Elongation Factors/genetics ; Peptide Initiation Factors/genetics ; RNA, Transfer, Amino Acyl/*genetics ; }, abstract = {The recently deciphered sequence of the human mitochondrial genome is analyzed in the light of an archigenetic hypothesis, according to which mitochondria are derived neither from pro- nor eukaryotes but from more primitive organisms. The possibility that animal mitochondria have only one gene both for elongator and initiator methionine tRNA is supported but C-A pair forming cytosine in the anticodon of these tRNAs is considered to be unmodified. The evolution of the gene and of the codon reading pattern of methionine tRNA is discussed.}, }
@article {pmid6353578, year = {1983}, author = {Birky, CW}, title = {Relaxed cellular controls and organelle heredity.}, journal = {Science (New York, N.Y.)}, volume = {222}, number = {4623}, pages = {468-475}, doi = {10.1126/science.6353578}, pmid = {6353578}, issn = {0036-8075}, support = {GM19607/GM/NIGMS NIH HHS/United States ; GM21896/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Biological Evolution ; Cell Cycle ; Cell Nucleus/physiology ; Chromosomes/physiology ; DNA Replication ; Fungi/*genetics ; *Genes ; Mitochondria/physiology ; Organoids/*physiology ; Plants/*genetics ; Recombination, Genetic ; Reproduction ; Saccharomyces cerevisiae/genetics ; }, }
@article {pmid6576816, year = {1983}, author = {Muchi, H and Yamamoto, Y}, title = {Studies on mitochondrial and cytoplasmic malate dehydrogenase in childhood myelodysplastic syndrome.}, journal = {Blood}, volume = {62}, number = {4}, pages = {808-814}, pmid = {6576816}, issn = {0006-4971}, mesh = {Anemia, Aplastic/enzymology ; Bone Marrow Diseases/*enzymology ; Cell Transformation, Neoplastic ; Child ; Colony-Forming Units Assay ; Cytoplasm/enzymology ; Female ; Humans ; Karyotyping ; Leukemia, Myeloid, Acute/mortality ; Malate Dehydrogenase/*deficiency ; Male ; Mitochondria/enzymology ; Neutrophils/*enzymology ; Syndrome ; }, abstract = {Three cases of uncommon childhood hematologic disorders are reported. At presentation, one patient had refractory anemia with an excess of blasts (RAEB) with partial 7-monosomy and was reclassified into RAEB "in transformation" thereafter. Another case was diagnosed as acute myelogenous leukemia with complete 7-monosomy. The other case was diagnosed as RAEB "in transformation" without chromosome aberrations. The cytogenetic studies of the patients with 7-monosomy revealed abnormal karyotypes on bone marrow cells, but normal karyotypes on peripheral blood cells. Polymorphonuclear cells from the two patients with 7-monosomy revealed reduced mitochondrial malate dehydrogenase activity, but those from the patient with RAEB "in transformation" without chromosome aberrations did not. Cytoplasmic malate dehydrogenase activity, having been defined as located on chromosome 2, was within the normal range in those three patients. The decreased mitochondrial enzyme activity in the two patients with 7-monosomy would be a dosage effect of the chromosome aberration, but not caused by their hematologic disorders. The level of mitochondrial enzyme activity in the patients with 7-monosomy was reduced in polymorphonuclear cells, but not in mononuclear cells in peripheral blood. This fact would indicate that such chromosome evolution had involved myeloid cells only, but not lymphoid cells. Both enzymes from leukemic cells of four patients with active disease revealed much higher activities than controls, an expression of partially enhanced oxidative phosphorylation.}, }
@article {pmid6309369, year = {1983}, author = {Doroshow, JH}, title = {Anthracycline antibiotic-stimulated superoxide, hydrogen peroxide, and hydroxyl radical production by NADH dehydrogenase.}, journal = {Cancer research}, volume = {43}, number = {10}, pages = {4543-4551}, pmid = {6309369}, issn = {0008-5472}, support = {31788-03//PHS HHS/United States ; }, mesh = {Animals ; Antibiotics, Antineoplastic/*pharmacology ; Cytochrome Reductases/*metabolism ; Doxorubicin/pharmacology ; Free Radicals ; Hydrogen Peroxide/*metabolism ; Methane/metabolism ; Mitochondria, Heart/enzymology ; NADH Dehydrogenase/*metabolism ; Naphthacenes/pharmacology ; Oxygen/*metabolism ; Oxygen Consumption/drug effects ; Superoxides/*metabolism ; Swine ; }, abstract = {This study investigated the effect of the anthracycline antibiotics on oxygen radical metabolism by cardiac mitochondrial reduced nicotinamide adenine dinucleotide (NADH) dehydrogenase [NADH:(acceptor) oxidoreductase, EC 1.6.99.3]. Superoxide formation by NADH dehydrogenase after anthracycline treatment appeared to follow saturation kinetics with an apparent Km of 167.3, 73.3, 64.0, or 47.6 microM for doxorubicin, daunorubicin, rubidazone, or aclacinomycin A, respectively. Superoxide formation by NADH dehydrogenase after doxorubicin treatment occurred with a pH optimum of 7.6 and was accompanied by the production of hydrogen peroxide. Furthermore, drug-related hydroxyl radical generation was detected in this enzyme system by the evolution of methane gas from dimethyl sulfoxide. Hydroxyl radical production proceeded only in the presence of superoxide anion, hydrogen peroxide, and trace amounts of iron or a chelate of iron and ethylenediaminetetraacetate and thus was probably the by-product of a transition metal-catalyzed Haber-Weiss reaction. The antitumor agents mitoxantrone and actinomycin D did not significantly enhance reactive oxygen metabolism by NADH dehydrogenase. These results suggest that the specific activation of the anthracycline antibiotics to free radicals by NADH dehydrogenase leads to the formation of a variety of reactive oxygen species that may contribute to the mitochondrial toxicity of these drugs.}, }
@article {pmid6353901, year = {1983}, author = {Thiéry, G and Gaffiero, P and Bergeron, M}, title = {Three-dimensional characteristics of the endoplasmic reticulum in the columnar cells of the rat small intestine: an electron microscopy study in thick section.}, journal = {The American journal of anatomy}, volume = {167}, number = {4}, pages = {479-493}, doi = {10.1002/aja.1001670406}, pmid = {6353901}, issn = {0002-9106}, mesh = {Animals ; Endoplasmic Reticulum/*ultrastructure ; Female ; Histological Techniques ; Jejunum/*ultrastructure ; Male ; Osmium ; Rats ; Rats, Inbred Strains ; }, abstract = {The endoplasmic reticulum (ER) of the columnar cells of the rat jejunum was studied with a specific block-staining technique and standard transmission electron microscopy. A new three-dimensional model, based on the analysis of stereo pair photographs, is proposed; this model suggests that the endoplasmic reticulum may constitute a transcellular route. Thick sections (0.5-1 micron) of columnar cells were made after a 5-day impregnation with osmium tetroxide and were examined by standard transmission electron microscopy at 80-100 kV. The evolution of the ER during the cellular ascent of cells from the crypt to the top of the villus is toward a greater complexity. At the base of the crypt of Lieberkühn, no definite organization is noted, and most often only the nuclear envelope and canalicular elements are stained. The endoplasmic reticulum of the mature columnar cells forms a continuous network of canaliculi and fenestrated saccules; it extends from the apex, below the microvilli, to the lateral and basal plasma membranes, and sends many projections to the nuclear envelope. In the basal part of the cell, below the nucleus, the ER consists mainly of tubular canaliculi, whereas mostly saccules are observed in the supranuclear part. The canaliculi have a diameter of 40-60 nm. Fenestrated saccules appear to form a continuous tubular structure surrounding mitochondria; the saccules have a thickness of 25-40 nm and possess irregular perforations of 35-60 nm. Finally, in some cells, the endoplasmic reticulum seems to show functional differences as reflected by the absence of reaction in cells adjacent to well-stained cells in the same part of the villus; thus the osmium impregnation technique appears to be a valid tool for studying the ER organization.}, }
@article {pmid6345546, year = {1983}, author = {Graf-Hausner, U and Wilson, KJ and Christen, P}, title = {The covalent structure of mitochondrial aspartate aminotransferase from chicken. Identification of segments of the polypeptide chain invariant specifically in the mitochondrial isoenzyme.}, journal = {The Journal of biological chemistry}, volume = {258}, number = {14}, pages = {8813-8826}, pmid = {6345546}, issn = {0021-9258}, mesh = {Amino Acid Sequence ; Animals ; *Aspartate Aminotransferases/isolation &amp; purification ; Chickens ; Chymotrypsin ; Cyanogen Bromide ; Endopeptidases ; Isoenzymes/isolation &amp; purification ; Mitochondria, Heart/*metabolism ; Models, Molecular ; Peptide Fragments/analysis ; Protein Conformation ; *Serine Endopeptidases ; Species Specificity ; Swine ; Trypsin ; }, abstract = {The primary structure of mitochondrial aspartate aminotransferase from chicken is reported. The enzyme is a dimer of identical subunits. Each subunit contains 401 amino acid residues; the calculated subunit molecular weight of the apoform is 44,866. The degree of sequence identity with the homologous cytosolic isoenzyme from chicken is 46%. A comparison of the primary structures of the mitochondrial and the cytosolic isoenzyme from pig and chicken shows that 40% of all residues are invariant. The degree of interspecies sequence identity both of the mitochondrial and the cytosolic isoenzyme from chicken and pig (86% and 83%, respectively) markedly exceeds that of the intraspecies identity between mitochondrial and cytosolic aspartate aminotransferase in chicken (46%) or in pig (48%). Based on these values, the duplication of the aspartate aminotransferase ancestral gene is estimated to have occurred approximately 1000 million years ago, i.e. at the time of the emergence of eukaryotic cells. By sequence comparison it is possible to identify amino acid residues and segments of the polypeptide chain that have been conserved specifically in the mitochondrial isoenzyme during phylogenetic evolution. These segments comprise about a third of the total polypeptide chain and appear to cluster in a certain surface region. The cluster carries an excess of positively charged residues which exceeds the overall charge difference between the cytosolic (pI approximately 6) and the mitochondrial isoenzyme (pI approximately 9).}, }
@article {pmid6648454, year = {1983}, author = {Chen, JH}, title = {[Genetic code and its evolution].}, journal = {Sheng li ke xue jin zhan [Progress in physiology]}, volume = {14}, number = {3}, pages = {204-208}, pmid = {6648454}, issn = {0559-7765}, mesh = {Animals ; *Genetic Code ; Humans ; Mitochondria/metabolism ; RNA, Transfer/metabolism ; }, }
@article {pmid6230525, year = {1983}, author = {Turcanu, L and Georgescu, L and Branea, I}, title = {Importance of morpho-clinical correlations in the diagnosis of congestive cardiomyopathies.}, journal = {Morphologie et embryologie}, volume = {29}, number = {3}, pages = {177-181}, pmid = {6230525}, issn = {0377-5038}, mesh = {Biopsy ; Cardiomyopathy, Dilated/*diagnosis/pathology/physiopathology ; Electrocardiography ; Heart Failure/*diagnosis ; Humans ; Mitochondria, Heart/ultrastructure ; Myocardial Contraction ; Myocardium/pathology/ultrastructure ; Prognosis ; Stroke Volume ; }, abstract = {A morphologic score was performed in 17 myocardial biopsy specimens proceeding from patients with congestive cardiomyopathies. The electron microscopic changes were estimated according to their frequency and severity. According to this score, the morphological findings were compared with the clinical data and some echographic indexes of the myocardial contractility. These correlations turned out to be of great value in estimating the prognosis of these patients and allowed to set up three different stages of evolution in the congestive cardiomyopathies.}, }
@article {pmid6574491, year = {1983}, author = {Ohno, S and Epplen, JT}, title = {The primitive code and repeats of base oligomers as the primordial protein-encoding sequence.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {80}, number = {11}, pages = {3391-3395}, pmid = {6574491}, issn = {0027-8424}, support = {AI 15620/AI/NIAID NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; *Biological Evolution ; DNA/*genetics ; *Models, Genetic ; Proteins/*genetics ; RNA, Transfer/*genetics ; }, abstract = {Even if the prebiotic self-replication of nucleic acids and the subsequent emergence of primitive, enzyme-independent tRNAs are accepted as plausible, the origin of life by spontaneous generation still appears improbable. This is because the just-emerged primitive translational machinery had to cope with base sequences that were not preselected for their coding potentials. Particularly if the primitive mitochondria-like code with four chain-terminating base triplets preceded the universal code, the translation of long, randomly generated, base sequences at this critical stage would have merely resulted in the production of short oligopeptides instead of long polypeptide chains. We present the base sequence of a mouse transcript containing tetranucleotide repeats conserved during evolution. Even if translated in accordance with the primitive mitochondria-like code, this transcript in its three reading frames can yield 245-, 246-, and 251-residue-long tetrapeptidic periodical polypeptides that are already acquiring longer periodicities. We contend that the first set of base sequences translated at the beginning of life were such oligonucleotide repeats. By quickly acquiring longer periodicities, their products must have soon gained characteristic secondary structures--alpha-helical or beta-sheet or both.}, }
@article {pmid6365337, year = {1983}, author = {Tashiro, Y}, title = {Subcellular compartments and protein topogenesis.}, journal = {Cell structure and function}, volume = {8}, number = {2}, pages = {91-107}, doi = {10.1247/csf.8.91}, pmid = {6365337}, issn = {0386-7196}, mesh = {Bacteria/metabolism/*ultrastructure ; Bacterial Proteins/*metabolism ; Biological Transport ; *Cell Compartmentation ; Cell Membrane/metabolism ; Cell Nucleus/metabolism ; Cells/*ultrastructure ; Chloroplasts/metabolism ; Endoplasmic Reticulum/metabolism ; Eukaryotic Cells/metabolism/*ultrastructure ; Intracellular Membranes/metabolism ; Membrane Proteins/metabolism ; Microbodies/metabolism ; Mitochondria/metabolism ; Models, Biological ; Phylogeny ; Proteins/*metabolism ; Ribosomes/metabolism ; Symbiosis ; Terminology as Topic ; }, abstract = {A cell is surrounded by a plasma membrane. It contains various organelles, most of which are enclosed by limiting membranes. The intracellular space is thus divided into a number of subcellular compartments. Structurally, a cell is composed of membranes and the spaces enclosed by those membranes. In order to classify these compartments, the extracellular space has been designated S1 and whenever a unit membrane structure is crossed to arrive at the next space, one is added to term; the cytoplasmic space becomes S2, the intraluminal space of the endoplasmic reticulum and the intermembrane space of the mitochondria S3, and the matrix space of the mitochondria S4. Similarly, the plasma membrane is M1, the outer membrane of the mitochondria M2, and the inner counterpart M3. This classification of the subcellular compartments is useful in understanding a number of complicated cellular structures and functions. The intracellular transport of newly synthesized protein (protein topogenesis) and the probable development of subcellular organelles during phylogenesis of eukaryotic cells is discussed in terms of these subcellular compartments.}, }
@article {pmid6873566, year = {1983}, author = {Danan, G and Homberg, JC and Bernuau, J and Roche-Sicot, J and Pessayre, D}, title = {[Iproniazid-induced hepatitis. The diagnostic value of a new antimitochondrial antibody anti-M6].}, journal = {Gastroenterologie clinique et biologique}, volume = {7}, number = {5}, pages = {529-532}, pmid = {6873566}, issn = {0399-8320}, mesh = {Adult ; Antibodies/*analysis ; Chemical and Drug Induced Liver Injury/*diagnosis/etiology/pathology ; Drug Therapy, Combination ; Female ; Humans ; Iproniazid/*adverse effects ; Jaundice/chemically induced/diagnosis/pathology ; Male ; Middle Aged ; Mitochondria, Liver/*immunology ; }, abstract = {The authors report the observations of four patients with iproniazid hepatitis. Three of these patients died. An antimitochondrial antibody was found in the 4 patients at a high titer. This antibody differed from the antimitochondrial antibodies which have been described previously (anti-M1, anti-M5). This new antibody was called anti-M6. The evolution of the anti-M6 titer has been studied in the patient who survived. This titer progressively decreased; the antibody was no longer detectable 6 months after the withdrawal of iproniazid. Anti-M6 has not been found in other hepatic diseases. It was not detected in 15 patients receiving iproniazid without hepatitis or in 6 patients receiving isoniazid. Anti-M6 appears as a useful serologic marker for the diagnosis of iproniazid hepatitis.}, }
@article {pmid6867162, year = {1983}, author = {Dubin, DT and HsuChen, CC}, title = {The 3'-terminal region of mosquito mitochondrial small ribosomal subunit RNA: sequence and localization of methylated residues.}, journal = {Plasmid}, volume = {9}, number = {3}, pages = {307-320}, doi = {10.1016/0147-619x(83)90008-2}, pmid = {6867162}, issn = {0147-619X}, support = {GM-14957/GM/NIGMS NIH HHS/United States ; }, mesh = {Aedes/*genetics ; Animals ; Base Sequence ; Biological Evolution ; Methylation ; Mitochondria/*metabolism ; RNA, Ribosomal/*genetics ; }, abstract = {The 3'-terminal 101 residues of the small ribosomal subunit (SSU) RNA of mosquito cell mitochondria have been determined. This stretch includes the four methylated residues of the molecule: an m4C, an m5C, and two m26A residues. The m26A's occur in a typical m26A "arm," and the methylated Cs in the unique subsequence G x m4C . C . m5C . A, which is homologous in position to a conserved methylated GCCCG subsequence of other SSU RNA classes. There is fairly good overall homology between the mosquito mitochondrial sequence and corresponding regions of other SSU RNA classes, except that a domain of 50-100 residues, previously considered universal, is absent. Comparison with mammalian mitochondrial sequences revealed a marked preponderance of transitional base substitutions, supporting earlier evidence that the 3'-terminal region of SSU RNA is under special structural constraints. The extreme 3' end of the mosquito sequence is heterogeneous, three-fourths of the molecules ending in ... GA and one-fourth ending in ... GAA. Evidence is presented indicating that some, at least, of the 3'-terminal A residues may be added post-transcriptionally, as occurs in mammalian mitochondrial systems. Taken together, the results provide modest support for the monophyletic evolutionary origin of insect and mammalian mitochondria from a primitive procaryotic ancestor.}, }
@article {pmid6840539, year = {1983}, author = {Birky, CW and Maruyama, T and Fuerst, P}, title = {An approach to population and evolutionary genetic theory for genes in mitochondria and chloroplasts, and some results.}, journal = {Genetics}, volume = {103}, number = {3}, pages = {513-527}, pmid = {6840539}, issn = {0016-6731}, support = {GM19607/GM/NIGMS NIH HHS/United States ; }, mesh = {Alleles ; Animals ; Biological Evolution ; Chloroplasts ; *Extrachromosomal Inheritance ; Female ; Gene Frequency ; Genes ; Genetics, Population ; Male ; Mitochondria ; *Models, Genetic ; Sex Factors ; }, abstract = {We developed population genetic theory for organelle genes, using an infinite alleles model appropriate for molecular genetic data, and considering the effects of mutation and random drift on the frequencies of selectively neutral alleles. The effects of maternal inheritance and vegetative segregation of organelle genes are dealt with by defining new effective gene numbers, and substituting these for 2N(e) in classical theory of nuclear genes for diploid organisms. We define three different effective gene numbers. The most general is N(lambda), defined as a function of population size, number of organelle genomes per cell, and proportions of genes contributed by male and female gametes to the zygote. In many organisms, vegetative segregation of organelle genomes and intracellular random drift of organelle gene frequencies combine to produce a predominance of homoplasmic cells within individuals in the population. Then, the effective number of organelle genes is N(eo), a simple function of the numbers of males and females and of the maternal and paternal contributions to the zygote. Finally, when the paternal contribution is very small, N(eo) is closely approximated by the number of females, N(f). Then if the sex ratio is 1, the mean time to fixation or loss of new mutations is approximately two times longer for nuclear genes than for organelle genes, and gene diversity is approximately four times greater. The difference between nuclear and organelle genes disappears or is reversed in animals in which males have large harems. The differences between nuclear and organelle gene behavior caused by maternal inheritance and vegetative segregation are generally small and may be overshadowed by differences in mutation rates to neutral alleles. For monoecious organisms, the effective number of organelle genes is approximately equal to the total population size N. We also show that a population can be effectively subdivided for organelle genes at migration rates which result in panmixis for nuclear genes, especially if males migrate more than females.}, }
@article {pmid6188212, year = {1983}, author = {Grivell, LA}, title = {Mitochondrial DNA.}, journal = {Scientific American}, volume = {248}, number = {3}, pages = {78-89}, doi = {10.1038/scientificamerican0383-78}, pmid = {6188212}, issn = {0036-8733}, mesh = {Base Sequence ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Gene Expression Regulation ; Genes ; Humans ; Mitochondria/metabolism ; RNA/genetics ; RNA, Transfer/genetics ; Yeasts/genetics ; }, }
@article {pmid6835839, year = {1983}, author = {Küntzel, H and Piechulla, B and Hahn, U}, title = {Consensus structure and evolution of 5S rRNA.}, journal = {Nucleic acids research}, volume = {11}, number = {3}, pages = {893-900}, pmid = {6835839}, issn = {0305-1048}, mesh = {Bacteria/genetics ; Base Sequence ; *Biological Evolution ; Models, Genetic ; Nucleic Acid Conformation ; RNA, Ribosomal/*genetics ; Species Specificity ; }, abstract = {A consensus structure model of 5S rRNA presenting all conserved nucleotides in fixed positions has been deduced from the primary and secondary structure of 71 eubacterial, archaebacterial, eukaryotic cytosolic and organellar molecules. Phylogenetically related groups of molecules are characterized by nucleotide deletions in helices III, IV and V, and by potential base pair interactions in helix IV. The group-specific deletions are correlated with the early branching pattern of a dendrogram calculated from nucleotide substitution data: the first major division separates the group of eubacterial and organellar molecules from a second group containing the common ancestors of archaebacterial and eukaryotic/cytosolic molecules. The earliest diverging branch of the eubacterial/organellar group includes molecules from Thermus thermophilus, T. aquaticus, Rhodospirillum rubrum, Paracoccus denitrificans and wheat mitochondria.}, }
@article {pmid6306566, year = {1983}, author = {Christiansen, G and Christiansen, C}, title = {Heterology of mitochondrial DNA from mammals detected by electron microscopic heteroduplex analyses.}, journal = {Nucleic acids research}, volume = {11}, number = {1}, pages = {37-56}, pmid = {6306566}, issn = {0305-1048}, mesh = {Animals ; *Biological Evolution ; Cattle ; Chlorocebus aethiops ; DNA Restriction Enzymes ; DNA, Mitochondrial/*genetics ; Humans ; Mice ; Microscopy, Electron ; Mitochondria, Liver/*analysis ; Rats ; Species Specificity ; }, abstract = {Heteroduplex analysis of mitochondrial DNA (mtDNA) from evolutionary closely related mammals (rat vs. mouse, man vs. monkey) are analyzed and compared to heteroduplex analysis of mt-DNA from more distantly related mammals (rat vs. man, rat vs. monkey, mouse vs. man, mouse vs. monkey and man vs. cow). Each analysis is transformed into a heteroduplex map and all maps are aligned to restriction enzyme maps and to genetic maps and where possible compared with the known sequence. We show that early evolutionary changes are seen mainly in URF2, URFA6L, URF6 and the D-loop region. The regions of rRNA, URF1, COI and COIII are generally very conserved regions but areas with some evolutionary activity can be localized. Heteroduplex analysis between distantly related species show much more heterology than do closely related species and the heteroduplex maps between all the distantly related species show a common pattern of heterology. Comparisons between the DNA sequence of mtDNA from man, cow and mouse and the equivalent heteroduplex maps show that base pair homologies higher than 73% are displayed as homologous regions. In the heteroduplex analysis of mtDNA's from more closely related species very few heterologies are displayed at 50% formamide but an increase in formamide concentration to 65-70% demonstrate also in these instances general heterologous regions.}, }
@article {pmid6823280, year = {1983}, author = {Jukes, TH}, title = {Mitochondrial codes and evolution.}, journal = {Nature}, volume = {301}, number = {5895}, pages = {19-20}, doi = {10.1038/301019a0}, pmid = {6823280}, issn = {0028-0836}, mesh = {Amino Acids/biosynthesis ; Animals ; Anticodon/analysis ; Base Sequence ; *Biological Evolution ; *Genetic Code ; Mitochondria/*analysis ; RNA, Transfer/analysis ; }, }
@article {pmid6862814, year = {1983}, author = {Gentry, GA and Allen, GP and Holton, R and Nevins, RB and McGowan, JJ and Veerisetty, V}, title = {Thymine salvage, mitochondria, and the evolution of the herpesviruses.}, journal = {Intervirology}, volume = {19}, number = {2}, pages = {67-76}, doi = {10.1159/000149340}, pmid = {6862814}, issn = {0300-5526}, support = {DE-5089/DE/NIDCR NIH HHS/United States ; }, mesh = {Biological Evolution ; Cytoplasm/metabolism ; DNA Replication ; Herpesviridae/*physiology ; Mitochondria/*physiology ; Prokaryotic Cells/physiology ; Thymidine Kinase/genetics/metabolism ; Thymine/*metabolism ; }, abstract = {The salvage of thymine is an apparently ubiquitous feature of free-living lifeforms as well as of mitochondria, chloroplasts and most of the large DNA viruses. Assumptions and data are described which explain the evolution of thymine salvage in prokaryotes, animal cells, and large DNA viruses, in terms of deoxythymidine kinase and its relationship to mitochondria. Specifically, it is suggested that regulation of deoxythymidine kinase (by end-product inhibition) has evolved as a means of assuring a constant supply of thymine compounds for the mitochondria and that the degree to which this regulation is present in the deoxythymidine kinases of the various herpesviruses correlates with the degree of dependence of their replicative cycle on the continued health of the mitochondria of their host cells.}, }
@article {pmid6856964, year = {1983}, author = {Katagiri, T and Sasai, Y and Nakamura, N and Minatoguchi, H and Yokoyama, M and Kobayashi, Y and Takeyama, Y and Ozawa, K and Niitani, H}, title = {Acid hydrolases in the initiation of ischemic myocardial necrosis.}, journal = {Advances in myocardiology}, volume = {4}, number = {}, pages = {363-369}, doi = {10.1007/978-1-4757-4441-5_33}, pmid = {6856964}, issn = {0270-4056}, mesh = {Acid Phosphatase/*metabolism ; Animals ; Cathepsins/*metabolism ; Coronary Disease/*enzymology ; Dogs ; Glucuronidase/*metabolism ; Lysosomes/enzymology ; Microsomes/enzymology ; Mitochondria, Heart/enzymology ; }, abstract = {Alterations in myocardial acid hydrolases in acute ischemia were studied in relation to the evolution of cardiac cellular necrosis by the determination of cathepsin D, acid phosphatase (AcPase), and beta-glucuronidase activities of the myocardial fractions and by electron microscopic cytochemical studies on AcPase in the canine heart. In the normal myocardium, the same level of activity of acid hydrolases was found in sarcoplasmic reticulum (SR) as in the lysosome fraction. In electron microscopy, AcPase reaction products were observed markedly in SR and moderately in lysosomes, in residual bodies, and in Golgi apparatus. In the ischemic myocardium, at 20 to 30 min after coronary ligation, activation of these enzymes was observed in both SR and lysosomes, and at 60 to 90 min they were decreased in the particles and, in turn, increased in the cytoplasm accompanying the ischemic fine structural changes. At 2 to 3 hr those acid hydrolase activities in the cytosol were decreased, indicating the loss of enzymes from necrotic myocardial cells. Acid hydrolases are the most important factor for the evolution of ischemic myocardial necrosis by being activated not only in lysosomes but also in SR and by being released to the cytoplasm to disintegrate the cellular structures.}, }
@article {pmid6673807, year = {1983}, author = {Fouquet, JP and Meusy-Dessolle, N and Dang, DC}, title = {Morphometry of fetal Leydig cells in the monkey (Macaca fascicularis), correlation with plasma testosterone.}, journal = {Biology of the cell}, volume = {49}, number = {3}, pages = {267-272}, doi = {10.1111/j.1768-322x.1984.tb00246.x}, pmid = {6673807}, issn = {0248-4900}, mesh = {Animals ; Cell Differentiation ; Endoplasmic Reticulum/ultrastructure ; Fetal Blood/*metabolism ; Gestational Age ; Leydig Cells/metabolism/*ultrastructure ; Lipid Metabolism ; Macaca fascicularis ; Male ; Microscopy, Electron ; Mitochondria/ultrastructure ; Testis/*embryology ; Testosterone/*blood ; }, abstract = {The evolution of Leydig cells in Macaca fascicularis fetuses was followed throughout gestation (50-150 d) by morphometric procedures (volume densities of: cells, SER, mitochondria and lipid droplets). Testosterone from umbilical artery plasma was radioimmunoassayed starting on day 57. After predifferentiation and differentiation phases, Leydig cells entered the maturity phase (57-66 d), they occupied 19% of testicular volume, SER and lipid droplets represented 19% and 5% respectively of cytoplasmic volume. Then Leydig cells regressed dramatically (involution phase I: 66-83 d), their volume density decreased to 8%, that of SER to 12% whereas lipids doubled. Leydig cell volume density diminished to 5% during the second half of gestation (involution phase II), but their ultrastructure was not significantly altered. High plasma testosterone level (2.4 ng/ml) was observed during the maturity phase of Leydig cells, decline of testosterone occurred during involution phases I and II (1.13 and 0.58 ng/ml respectively). Its was shown that from day 57 to the end of fetal development the evolution of the plasma testosterone level correlated with the Leydig cell volume density and the SER volume density.}, }
@article {pmid6635206, year = {1983}, author = {Blobel, G}, title = {Regulation of intracellular protein traffic.}, journal = {Progress in brain research}, volume = {58}, number = {}, pages = {77-93}, doi = {10.1016/S0079-6123(08)60009-6}, pmid = {6635206}, issn = {0079-6123}, mesh = {Animals ; Biological Evolution ; Biological Transport ; Cell Membrane/*metabolism ; Endoplasmic Reticulum/*metabolism ; Intracellular Membranes/*metabolism ; Membrane Proteins/metabolism ; Microbodies/metabolism ; Mitochondria/metabolism ; Proteins/genetics/*metabolism ; }, }
@article {pmid6365727, year = {1983}, author = {Grivell, LA and Bonen, L and Borst, P}, title = {Mosaic genes and RNA processing in mitochondria.}, journal = {Horizons in biochemistry and biophysics}, volume = {7}, number = {}, pages = {279-306}, pmid = {6365727}, issn = {0096-2708}, mesh = {Base Sequence ; Biological Evolution ; Cell Nucleus/physiology ; Chromosome Mapping ; DNA, Mitochondrial/*genetics ; Endoribonucleases/metabolism ; Genes ; Genetic Code ; Nucleic Acid Conformation ; *RNA Processing, Post-Transcriptional ; RNA Splicing ; }, }
@article {pmid6310133, year = {1983}, author = {Johnson, MJ and Wallace, DC and Ferris, SD and Rattazzi, MC and Cavalli-Sforza, LL}, title = {Radiation of human mitochondria DNA types analyzed by restriction endonuclease cleavage patterns.}, journal = {Journal of molecular evolution}, volume = {19}, number = {3-4}, pages = {255-271}, pmid = {6310133}, issn = {0022-2844}, mesh = {DNA Restriction Enzymes ; DNA, Mitochondrial/*genetics/isolation &amp; purification ; Gene Frequency ; Genetic Variation ; Humans ; Mathematics ; Models, Genetic ; Phylogeny ; *Racial Groups ; }, abstract = {Human mitochondrial DNA (mtDNA) restriction endonuclease fragment patterns were analyzed using total blood cell DNA isolated from 200 individuals representing five different populations. Thirty-two fragment patterns (morphs) were observed with the enzymes Hpa I, Bam HI, Hae II, Msp I and Ava II yielding thirty-five different combinations of fragment patterns (mt DNA types). The major ethnic groups exhibit quantitative as well as qualitative differences in their mtDNA types, all of which are related to each other by a tree in which the closely related mtDNA types cluster according to geographic origin. Three mtDNA types are postulated to be 'central' to ethnic radiations due to their high frequencies, their appearance in more than one ethnic group, or their presence in other primate species. Genetic distances among populations were computed and employed in construction of an average linkage tree. If one of the three central mtDNA types is the root of the tree, differences in evolutionary rates among the branches become apparent. In particular, the Bushmen appear to have a higher evolutionary rate for mtDNA than the other four populations. Comparisons with nuclear gene frequencies suggest that this higher evolutionary rate may be the product of an elevated mutation rate or fixation of mutations in mtDNA.}, }
@article {pmid6301949, year = {1983}, author = {Greenberg, BD and Newbold, JE and Sugino, A}, title = {Intraspecific nucleotide sequence variability surrounding the origin of replication in human mitochondrial DNA.}, journal = {Gene}, volume = {21}, number = {1-2}, pages = {33-49}, doi = {10.1016/0378-1119(83)90145-2}, pmid = {6301949}, issn = {0378-1119}, support = {GM07092/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; *Cloning, Molecular ; *DNA Replication ; DNA Restriction Enzymes ; DNA, Mitochondrial/*genetics ; Female ; *Genetic Variation ; Humans ; Placenta/metabolism ; Polymorphism, Genetic ; Pregnancy ; Protein Biosynthesis ; Racial Groups ; }, abstract = {We have cloned the major noncoding region of human mitochondrial DNA (mtDNA) from 11 human placentas. Partial nucleotide sequences of five of these clones have been determined and they share a maximum of 900 bp around the origin of H-strand replication. Alignment of these sequences with others previously determined has revealed a striking pattern of nucleotide substitutions and insertion/deletion events. The level of sequence divergence significantly exceeds the reported estimates of divergence in coding regions. Two particularly hypervariable regions have also been defined. More than 96% of the base changes are transitions, and length alterations have occurred exclusively by addition or deletion of mono-or dinucleotide segments within serially repeating stretches. This region of the mitochondrial genome, which contains the initiation sites for replication and transcription, is the least conserved among species with respect to both sequence and length (Anderson et al., 1981; Walberg and Clayton, 1981). Despite this overall lack of primary sequence conservation, several consistencies appear among the available mammalian mtDNA sequences within this region. Between species, a conserved linear array of characteristic stretches exists which nonetheless differ in primary sequence. Among humans, several conserved blocks of nucleotides appear within domains deleted from the mtDNA of other species. These observations are consistent with both a species-specificity of nucleotide sequence, and a preservation of the necessary genetic functions among species. This provides a model for the evolution of protein-nucleic acid interactions in mammalian mitochondria.}, }
@article {pmid7143702, year = {1982}, author = {Sasai, Y and Nakamura, N and Kobayashi, Y and Katagiri, T}, title = {Studies on intracardiac acid hydrolases in the ischemic myocardial necrosis.}, journal = {Japanese circulation journal}, volume = {46}, number = {12}, pages = {1337-1344}, doi = {10.1253/jcj.46.1337}, pmid = {7143702}, issn = {0047-1828}, mesh = {Acid Phosphatase/metabolism ; Animals ; Cathepsin D ; Cathepsins/metabolism ; Coronary Disease/*enzymology ; Dogs ; Glucuronidase/*metabolism ; Hydrolases/*metabolism ; Lysosomes/enzymology ; Mitochondria, Heart/enzymology ; Myocardium/*enzymology/pathology ; Necrosis ; }, abstract = {Activities and subcellular distributions of acid hydrolases, cathepsin D, acid phosphatase and beta-glucuronidase in myocardial subfractions were determined serially with reference to the initiation of myocardial necrosis in dog hearts with acute ischemia. The following results were obtained: 1) In the normal myocardium, respectable activities of three enzymes were obtained either in the sarcoplasmic reticulum or in the lysosome-containing fraction. 2) Thirty min after coronary ligation, an increase in the activities was observed in both lysosome and sarcoplasmic reticulum fractions of the ischemic heart muscle. After 60 to 90 min these activities were decreased rapidly in both fractions to about 70% of those of the normal myocardium with an increase in the cytosolic activity. Two to 3 hours after ligation, the reduction in the cytosolic activity was noted, indicating an escape of the enzymes from the necrotic myocardium. The subcellular distribution of these enzymes was further altered in the ischemic heart muscle for 12 to 14 hours reflecting an infiltration of the interstitial cells. These findings suggest that activation and release of acid hydrolases not only in lysosomes but also in the sarcoplasmic reticulum are one of the primary and the earliest factors for the evolution of ischemic myocardial injury which leads to necrosis.}, }
@article {pmid6959107, year = {1982}, author = {Birktoft, JJ and Fernley, RT and Bradshaw, RA and Banaszak, LJ}, title = {Amino acid sequence homology among the 2-hydroxy acid dehydrogenases: mitochondrial and cytoplasmic malate dehydrogenases form a homologous system with lactate dehydrogenase.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {79}, number = {20}, pages = {6166-6170}, pmid = {6959107}, issn = {0027-8424}, support = {AM-13362/AM/NIADDK NIH HHS/United States ; GM-13925/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; *Biological Evolution ; Cattle ; Cytoplasm/enzymology ; *L-Lactate Dehydrogenase/genetics ; Macromolecular Substances ; *Malate Dehydrogenase/genetics ; Mitochondria, Heart/enzymology ; Substrate Specificity ; }, abstract = {The amino acid sequence of porcine heart mitochondrial malate dehydrogenase (mMDH; L-malate: NAD+ oxidoreductase, EC 1.1.1.37) has been compared with the sequences of six different lactate dehydrogenases (LDH; L-lactate: NAD+ oxidoreductase, EC 1.1.1.27) and with the "x-ray" sequence of cytoplasmic malate dehydrogenase (sMDH). The main points are that (i) all three enzymes are homologous; (ii) invariant residues in the catalytic center of these enzymes include a histidine and an internally located aspartate that function as a proton relay system; (iii) numerous residues important to coenzyme binding are conserved, including several glycines and charged residues; and (iv) amino acid side chains present in the subunit interface common to the MDHs and LDHs appear to be better conserved than those in the protein interior. It is concluded that LDH, sMDH, and mMDH are derived from a common ancestral gene and probably have similar catalytic mechanisms.}, }
@article {pmid6817826, year = {1982}, author = {Carrascosa, JM and Martinez, P and de Castro, IN}, title = {Ammonium ions enhance the flow through the pyruvate dehydrogenase in Ehrlich ascites tumor cells.}, journal = {Biochimie}, volume = {64}, number = {10}, pages = {949-954}, doi = {10.1016/s0300-9084(82)80358-1}, pmid = {6817826}, issn = {0300-9084}, mesh = {Adenine Nucleotides/metabolism ; Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Carbon Dioxide/metabolism ; Carcinoma, Ehrlich Tumor/*enzymology ; Female ; Mice ; Mitochondria/metabolism ; Pyruvate Dehydrogenase Complex/*metabolism ; Pyruvates/metabolism ; Pyruvic Acid ; Quaternary Ammonium Compounds/*pharmacology ; Starvation/metabolism ; }, abstract = {The flow through pyruvate dehydrogenase was assayed in glycolysing cells by the evolution of 14CO2 from [1-14C] pyruvate. Parallel incubations were carried out in high bicarbonate buffer (25 mM) and in bicarbonate-free buffer. The activation of the complex by NH+4 was only observed in high bicarbonate buffer, because the dilution of labelled CO2 in the presence of an excess of bicarbonate enables the quantitative determination of labelled CO2 evolved from pyruvate in the decarboxylase step. In the bicarbonate-free buffer the activation of the complex was not observed, because the 14CO2 evolved from pyruvate was consumed by biosynthetic processes inside the cell. On the contrary in isolated hepatocytes the NH+4 activation of the pyruvate dehydrogenase was observed in both buffers. In Ehrlich ascites cells, in common with other mammalian tissues, pyruvate dehydrogenase activity was found to be inversely correlated to the intramitochondrial ATP/ADP ratio.}, }
@article {pmid6754571, year = {1982}, author = {Gabius, HJ and Freist, W and Cramer, F}, title = {Phenylalanyl-tRNA synthetases from hen liver cytoplasm and mitochondria, yeast cytoplasm and mitochondria, and from Escherichia coli: substrate specificity relationship with regard to ATP analogs.}, journal = {Hoppe-Seyler's Zeitschrift fur physiologische Chemie}, volume = {363}, number = {10}, pages = {1241-1246}, doi = {10.1515/bchm2.1982.363.2.1241}, pmid = {6754571}, issn = {0018-4888}, mesh = {Adenosine Triphosphate/*analogs &amp; derivatives/metabolism ; Amino Acyl-tRNA Synthetases/*metabolism ; Animals ; Chickens ; Cytoplasm/*enzymology ; Escherichia coli/*enzymology ; Kinetics ; Liver/*enzymology ; Mitochondria/*enzymology ; Mitochondria, Liver/enzymology ; Phenylalanine-tRNA Ligase/*metabolism ; Saccharomyces cerevisiae/*enzymology ; Species Specificity ; Substrate Specificity ; }, abstract = {Twelve structural analogs of ATP have been tested in the aminoacylation reaction of phenylalanyl-tRNA synthetases from hen liver cytoplasm and mitochondria, yeast cytoplasm and mitochondria and E. coli. Three compounds are substrates for all five phenylalanyl-tRNA synthetase, three are completely inactive, while the other ATP analogs show differing properties with the different enzymes. Their Km, Ki and V values have been determined. The importance of the amino group in Position 6, the nitrogen in Position 7 and an unsubstituted Position 8 of the purine moiety as well as the supposed anti-conformation of the glycosidic bond and coordination of the magnesium cation to N-7 appear to be conserved through evolution. Bulky substituents on the 2' and 3' of the ribose moiety are generally not tolerated. Graduation of substrate properties of some analogs are similar for the intracellular heterotopic isoenzymes from yeast and hen liver.}, }
@article {pmid6816225, year = {1982}, author = {Takada, Y and Noguchi, T}, title = {The evolution of peroxisomal and mitochondrial alanine: glyoxylate aminotransferase 1 in mammalian liver.}, journal = {Biochemical and biophysical research communications}, volume = {108}, number = {1}, pages = {153-157}, doi = {10.1016/0006-291x(82)91844-7}, pmid = {6816225}, issn = {0006-291X}, mesh = {Alanine Transaminase/*genetics ; Animals ; *Biological Evolution ; Cats ; Cricetinae ; Dogs ; Guinea Pigs ; Haplorhini ; Humans ; Liver/*enzymology ; Mice ; Microbodies/*enzymology ; Mitochondria, Liver/*enzymology ; Organoids/*enzymology ; Rats ; Species Specificity ; *Transaminases ; }, }
@article {pmid6751874, year = {1982}, author = {Keha, EE and Ronft, H and Kresze, GB}, title = {On the origin of mitochondria: a reexamination of the molecular structure and kinetic properties of pyruvate dehydrogenase complex from brewer's yeast.}, journal = {FEBS letters}, volume = {145}, number = {2}, pages = {289-292}, doi = {10.1016/0014-5793(82)80185-3}, pmid = {6751874}, issn = {0014-5793}, mesh = {*Biological Evolution ; Kinetics ; Mitochondria/*enzymology ; Molecular Weight ; Protein Conformation ; Pyruvate Dehydrogenase Complex/*metabolism ; Saccharomyces/*enzymology ; Saccharomyces cerevisiae/enzymology ; }, }
@article {pmid6216131, year = {1982}, author = {Walker, JE and Eberle, A and Gay, NJ and Runswick, MJ and Saraste, M}, title = {Conservation of structure in proton-translocating ATPases of Escherichia coli and mitochondria.}, journal = {Biochemical Society transactions}, volume = {10}, number = {4}, pages = {203-206}, doi = {10.1042/bst0100203}, pmid = {6216131}, issn = {0300-5127}, mesh = {Adenosine Diphosphate/metabolism ; *Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Biological Evolution ; Cell Membrane/enzymology ; Escherichia coli/*enzymology ; Macromolecular Substances ; Mitochondria/*enzymology ; Protein Conformation ; Proton-Translocating ATPases ; }, }
@article {pmid6180946, year = {1982}, author = {Wells, DE and Bruskin, AM and O'Brochta, DA and Raff, RA}, title = {Prevalent RNA sequences of mitochondrial origin in sea urchin embryos.}, journal = {Developmental biology}, volume = {92}, number = {2}, pages = {557-562}, doi = {10.1016/0012-1606(82)90202-0}, pmid = {6180946}, issn = {0012-1606}, support = {GM7227/GM/NIGMS NIH HHS/United States ; HD 06902/HD/NICHD NIH HHS/United States ; HD 07098/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; Base Sequence ; Biological Evolution ; Embryo, Nonmammalian/*metabolism ; Female ; Mitochondria/*metabolism ; Ovum/metabolism ; Poly A/metabolism ; RNA/*metabolism ; RNA, Messenger ; RNA, Ribosomal/metabolism ; Sea Urchins/embryology/metabolism ; }, }
@article {pmid7050913, year = {1982}, author = {Schnare, MN and Gray, MW}, title = {3'-Terminal sequence of wheat mitochondrial 18S ribosomal RNA: further evidence of a eubacterial evolutionary origin.}, journal = {Nucleic acids research}, volume = {10}, number = {13}, pages = {3921-3932}, pmid = {7050913}, issn = {0305-1048}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Chloroplasts/analysis ; Cricetinae ; Cytosol/analysis ; Mitochondria/*analysis ; Molecular Weight ; Nucleic Acid Hybridization ; Plants/*genetics ; RNA, Ribosomal/*genetics ; Saccharomyces cerevisiae/analysis ; Species Specificity ; Triticum/genetics ; }, abstract = {We have determined the sequences of the 3'-terminal approximately 100 nucleotides of [5' -32P]pCp-labeled wheat mitochondrial, wheat cytosol, and E. coli small sub-unit rRNAs. Sequence comparison demonstrates that within this region, there is a substantially greater degree of homology between wheat mitochondrial 18S and E. coli 16S rRNAs than between either of these and wheat cytosol 18S rRNA. Moreover, at a position occupied by 3-methyluridine in E. coli 16S rRNA, the same (or a very similar) modified nucleoside is present in wheat mitochondrial 18S rRNA but not in wheat cytosol 18S rRNA. Further, E. coli 16S and 23S rRNAs hybridize extensively to wheat mitochondrial 18S and 26S rRNA genes, respectively, but wheat cytosol 18S and 26S rRNAs do not. No other mitochondrial system studies to date has provided comparable evidence that a mitochondrial rRNA is more closely related to its eubacterial homolog than is its counterpart in the cytoplasmic compartment of the same cell. The results reported here provide additional support for the view that plant mitochondria are of endosymbiotic, specifically eubacterial, origin.}, }
@article {pmid6180777, year = {1982}, author = {Grosjean, H and Cedergren, RJ and McKay, W}, title = {Structure in tRNA data.}, journal = {Biochimie}, volume = {64}, number = {6}, pages = {387-397}, doi = {10.1016/s0300-9084(82)80576-2}, pmid = {6180777}, issn = {0300-9084}, mesh = {Animals ; Archaea ; Base Sequence ; Mitochondria/analysis ; *Nucleic Acid Conformation ; RNA, Bacterial/analysis ; RNA, Transfer/*analysis ; }, abstract = {260 sequences of tRNA are compared, after their classification into six categories: prokaryotic (83 sequences) and eukaryotic (83 sequences) elongators, prokaryotic (10 sequences) and eukaryotic (11 sequences), initiators, lower eukaryotic mitochondrial tRNA (53 sequences) and archaebacterial tRNA (20 sequences). Beside the presence of invariable and semi-invariable positions in tRNA, non-random base distribution in almost all positions is also evident; most of them being characteristic of each class of tRNA. Therefore, during evolution it would seem that selectional pressures do act in so called variable positions as well as invariant positions of tRNA molecules. Results are discussed in relation to possible restrictions depending on functional and/or structural constraints of tRNA.}, }
@article {pmid6808279, year = {1982}, author = {Siu, GM and Draper, HH}, title = {Metabolism of malonaldehyde in vivo and in vitro.}, journal = {Lipids}, volume = {17}, number = {5}, pages = {349-355}, pmid = {6808279}, issn = {0024-4201}, mesh = {Acetates/metabolism ; Animals ; Carbon Dioxide/metabolism ; Kinetics ; Male ; Malonates/*metabolism ; Malondialdehyde/*metabolism ; Mitochondria, Liver/metabolism ; Models, Chemical ; Oxygen Consumption ; Rats ; Rats, Inbred Strains ; Succinate Dehydrogenase/metabolism ; Time Factors ; }, abstract = {The metabolism of malonaldehyde (MA) was investigated in vivo using male Wistar rats and in vitro using rat liver mitochondria. Twelve hr after intubation with [1,3-14C] MA, 60-70%, 5-15% and 9-17% of administered radioactivity was recovered in expired CO2, feces and urine, respectively. In rats intubated with [1,2-14C) acetate, the corresponding values were 68-82%, 1-2% and 2.3%. 14CO2 evolution was initially slower after 14C-MA administration than after 14C-acetate administration and more radioactivity was excreted in the feces and urine. In vitro experiments using [1,3-14C] MA showed that MA is metabolized primarily in the mitochondria via reactions involving O2 utilization and 14CO2 production. The apparent Km and Vmax were 0.5 mM and 9.3 nmol/min/mg protein for O2 uptake, respectively, and 2.0 mM and 2.4 nmol/min/mg protein for 14CO2 production. Addition of malonic acid to mitochondrial incubates at concentrations inhibitory to succinate dehydrogenase did not affect MA-induced O2 uptake but enhanced 14CO2 production from 14C-MA. 14C-Acetate appeared to be the major accumulating metabolite in rat liver mitochondrial preparations following a 120-min incubation with 14C-MA. A probable biochemical route for MA metabolism involves oxidation of MA by mitochondrial aldehyde dehydrogenase followed by decarboxylation to produce CO2 and acetate.}, }
@article {pmid7104824, year = {1982}, author = {Cedergren, RJ}, title = {An evaluation of mitochondrial tRNA gene evolution and its relation to the genetic code.}, journal = {Canadian journal of biochemistry}, volume = {60}, number = {4}, pages = {475-479}, doi = {10.1139/o82-056}, pmid = {7104824}, issn = {0008-4018}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; *Genes ; *Genetic Code ; Humans ; Mitochondria/*metabolism ; RNA, Transfer/*genetics ; }, abstract = {Extensive sequence data on mitochondrial (mt) tRNAs give for the first time an opportunity to evaluate tRNA gene evolution in this organelle. Deductions from these gene structures relate to the evolution of tRNA genes in other cellular systems and to the origin of the genetic code. Mt tRNAs, in contrast to the prokaryotic nature of chloroplastic tRNA structure, can not at the present time be definitely related to either prokaryotic or eukaryotic tRNAs, probably because of a higher mutation rate in mitochondria. Fungal mt tRNAs having the same anticodon and function are generally similar enough to be considered homologous. Comparisons af all mt tRNA sequences contained in the same mitochondrion indicate that some tRNAs originated by duplication of a prototypic gene which, after divergence, led to tRNAs having different amino acid specificities. The deviant mt genetic code, although admittedly permitting a simpler decoding mechanism, is not useful in determining whether the origin of mitochondria had preceded or was derived from prokaryotes or eukaryotes, since the genetic code is variable even among mitochondria. Variants of the mt genetic code lead to speculation on the nature of the primordial code and its relation to the present "universal" code.}, }
@article {pmid7200441, year = {1982}, author = {Sukhodolets, VV}, title = {[Evolutionary changes in the genetic code, predictable on basis of the hypothesis of physical predetermination of the structure of codon bases].}, journal = {Genetika}, volume = {18}, number = {3}, pages = {499-502}, pmid = {7200441}, issn = {0016-6758}, mesh = {Amino Acids/genetics ; Animals ; Base Sequence ; *Biological Evolution ; Codon/*genetics ; *Genetic Code ; Mitochondria/ultrastructure ; Neurospora/genetics ; Protein Biosynthesis ; RNA, Messenger/*genetics ; Yeasts/genetics ; }, abstract = {According to the earlier proposed hypothesis on the structural correspondence between amino acids and doublets from the first codon bases (Sukhodolets 1980), the UGA triplet corresponds to tryptophan and the AGX triplets - to the termination codons. It is notably this sense of the UGA and AGA, AGG, respectively, that was reported for mitochondrial codes. Thereby, a proposal is indirectly confirmed that meanings of the UGA (nonsense) and AGA, AGG (arginine) in the normal cytoplasmic code is the result of evolutionary changes.}, }
@article {pmid6178009, year = {1982}, author = {Gray, MW and Doolittle, WF}, title = {Has the endosymbiont hypothesis been proven?.}, journal = {Microbiological reviews}, volume = {46}, number = {1}, pages = {1-42}, pmid = {6178009}, issn = {0146-0749}, mesh = {Amino Acid Sequence ; Bacteria/genetics ; Base Sequence ; *Biological Evolution ; *Cell Nucleus ; DNA ; Fungi/genetics ; Genes ; Genetic Code ; *Mitochondria ; *Plasmids ; Protein Biosynthesis ; Proteins ; RNA ; *Symbiosis ; Transcription, Genetic ; }, }
@article {pmid6805924, year = {1982}, author = {Doolittle, WF}, title = {The Ayerst Award Lecture 1981/La Conférence Ayerst 1981.}, journal = {Canadian journal of biochemistry}, volume = {60}, number = {2}, pages = {83-90}, pmid = {6805924}, issn = {0008-4018}, mesh = {Archaea/genetics ; Base Sequence ; *Biological Evolution ; Cyanobacteria/genetics/physiology ; DNA/physiology ; Electron Transport ; Environment ; Gene Expression Regulation ; Mitochondria/analysis ; Molecular Biology/*trends ; Oxygen Consumption ; Phenotype ; Photosynthesis ; RNA, Ribosomal/analysis ; Rhodophyta/genetics ; }, }
@article {pmid7161808, year = {1982}, author = {Miyata, T and Hayashida, H and Kikuno, R and Hasegawa, M and Kobayashi, M and Koike, K}, title = {Molecular clock of silent substitution: at least six-fold preponderance of silent changes in mitochondrial genes over those in nuclear genes.}, journal = {Journal of molecular evolution}, volume = {19}, number = {1}, pages = {28-35}, pmid = {7161808}, issn = {0022-2844}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Cell Nucleus/*metabolism ; DNA/*metabolism ; *Genes ; Genetic Code ; Humans ; Immunoglobulins/biosynthesis ; Mice ; Mitochondria/*metabolism ; Rabbits ; Rats ; }, }
@article {pmid7156500, year = {1982}, author = {Fouquet, JP}, title = {[Ultrastructural evolution of fetal germinal cells to adult spermatogonia in Macaca fascicularis monkeys].}, journal = {Reproduction, nutrition, developpement}, volume = {22}, number = {5}, pages = {767-783}, pmid = {7156500}, issn = {0181-1916}, mesh = {Aging ; Animals ; Macaca/*anatomy &amp; histology ; Macaca fascicularis/*anatomy &amp; histology/embryology ; Male ; Microscopy, Electron ; Spermatids/ultrastructure ; *Spermatogenesis ; Spermatogonia/ultrastructure ; Spermatozoa/*ultrastructure ; }, abstract = {Ultrastructural changes in the spermatogonial line of the macaque, Macaca fascicularis, were studied during foetal development (from day 37), childhood and puberty. The different cell types and their distinctive morphological characteristics have been identified by studying adjacent thick and thin sections under light and electron microscopy. The main criteria used were: organization of the rough endoplasmic reticulum (RER) and its relation to mitochondria, chromatin distribution, stainability and perichromatin granule content, nucleolar organization and differentiation of the nuclear membrane including the lamina and nuclear vacuoles or cisternae. According to their ultrastructure, the following main cell classes were distinguished: gonocytes (37 to 43-day foetuses), prespermatogonia (50 to 110-day foetuses), pale type A (Ap) and dark type A (Ad) adult-type spermatogonia which differentiated progressively in 120 to 140-day foetuses. During childhood, the testis contained only Ap and Ad spermatogonia. At the onset of meiosis (about 48 months after birth), type B spermatogonia appeared, and the different classes of spermatogonia were found lying directly on the basal lamina of the sex cords. The filiation of the spermatogonial line during development has been discussed.}, }
@article {pmid7120423, year = {1982}, author = {Harington, A and Thornley, AL}, title = {Biochemical and genetic consequences of gene transfer from endosymbiont to host genome.}, journal = {Journal of molecular evolution}, volume = {18}, number = {5}, pages = {287-292}, pmid = {7120423}, issn = {0022-2844}, mesh = {*Biological Evolution ; Chloroplasts/*physiology ; DNA, Mitochondrial/*genetics ; Gene Expression Regulation ; Genes ; Mitochondria/physiology ; Models, Biological ; Permeability ; Phagocytosis ; Proteins/genetics ; Recombination, Genetic ; *Symbiosis ; }, }
@article {pmid7089959, year = {1982}, author = {Taylor, VA and Luke, BM and Lomas, MB}, title = {The giant sperm of a minute beetle.}, journal = {Tissue &amp; cell}, volume = {14}, number = {1}, pages = {113-123}, doi = {10.1016/0040-8166(82)90011-8}, pmid = {7089959}, issn = {0040-8166}, mesh = {Acrosome/ultrastructure ; Animals ; Cell Nucleus/ultrastructure ; Coleoptera/*physiology ; Male ; Microscopy, Electron ; Sperm Tail/ultrastructure ; Spermatozoa/ultrastructure ; }, abstract = {The mature sperm of Ptinella aptera is a helically coiled, flagellate gamete ca. 1.4 mm long-twice the length of the beetle itself. The rod-like acrosome, comprising the anterior part of the sperm, is 0.4 micrometer thick but is expanded as a flange around the nucleus and the base of the tail, increasing the diameter of the sperm to 2 micrometer. The bulk of the tail consists of a pair of bodies with a characteristic ultrastructure of longitudinal tubules beneath a lamellar cortical layer. These bodies are probably homologous with the mitochondria derivatives of other insect sperm. The axoneme is helically coiled and is flanked by a single accessory body. One of the 'structured bodies' is connected to the acrosome and the other to the accessory body. The sperm move actively in the female reproductive tract. The functional significance of this behaviour and of the evolution of the large gamete itself is discussed in relation to existing hypotheses.}, }
@article {pmid7060089, year = {1982}, author = {Carrick, FN and Hughes, RL}, title = {Aspects of the structure and development of monotreme spermatozoa and their relevance to the evolution of mammalian sperm morphology.}, journal = {Cell and tissue research}, volume = {222}, number = {1}, pages = {127-141}, pmid = {7060089}, issn = {0302-766X}, mesh = {Animals ; Epididymis/ultrastructure ; Male ; Microscopy, Electron ; Monotremata/*anatomy &amp; histology/physiology ; Sperm Head/ultrastructure ; Sperm Tail/ultrastructure ; *Spermatogenesis ; Spermatozoa/*ultrastructure ; }, abstract = {The elongated spermatid nuclei of monotremes exhibit a circumferentially arranged spiral pattern of chromatin condensation, and ultimately form helical filiform sperm heads up to 50 microns long and either circular or slightly oval in transverse section. The acrosome is formed by the collapse of the proacrosomal vacuole onto the rostral surface of the elongating nucleus. However, genesis of acrosomal material occurs in the absence of a prominent proacrosomal granule. The flagellum becomes inserted into the distal extremity of the nucleus, the most proximal mitochondria of the midpiece directly abutting the nuclear membrane, so that a prominent neck region is absent. The axoneme is simple and, in the midpiece, small dense peripheral fibres are closely applied to the outer surface of each of the nine microtubule doublets. The cortical fibrous sheath of the principal piece is an anastomosing spiral that lacks lateral columnar elements. The spermatozoal cytoplasmic droplet undergoes migration and is lost during epididymal passage. Monotreme spermatozoa exhibit a montage of features, some of these being also found in marsupials and some in sauropsidan vertebrates, as well as a number of their own distinctive features. It is concluded that monotreme spermatozoa also have a close affinity with the unspecialised spermatozoa of some eutherian mammals.}, }
@article {pmid6960226, year = {1982}, author = {Seilhamer, JJ and Cummings, DJ}, title = {Altered genetic code in Paramecium mitochondria: possible evolutionary trends.}, journal = {Molecular &amp; general genetics : MGG}, volume = {187}, number = {2}, pages = {236-239}, pmid = {6960226}, issn = {0026-8925}, mesh = {Base Sequence ; *Biological Evolution ; DNA ; Mitochondria/*ultrastructure ; Paramecium/*genetics ; RNA, Transfer ; }, abstract = {The sequence and presumptive structure of a tRNA trp gene from Paramecium tetraaurelia are given. The gene is located 1,500 bp downstream from the 13S rRNA gene, in about the middle of the genome. Paramecium tRNA trp has a completely normal TpsiC loop and stem, however its anticodon (UCA) constitutes an alteration in the "universal" genetic code, similar to those seen in fungal and mammalian mitochondria. Most features of Paramecium tRNA trp resemble other mitochondrial counterparts; however, its sequence is more homologous to the "unaltered" tRNA trp (anticodon CCA) from E. coli. Paramecium mitochondria may resemble a primitive stage of organelle evolution.}, }
@article {pmid6807040, year = {1982}, author = {Schwemmler, W}, title = {The endocytobiotic cell theory and the periodic system of cells.}, journal = {Acta biotheoretica}, volume = {31}, number = {1}, pages = {45-68}, pmid = {6807040}, issn = {0001-5342}, mesh = {Animals ; *Biological Evolution ; *Cell Physiological Phenomena ; Cells/ultrastructure ; Chloroplasts/ultrastructure ; Cilia/ultrastructure ; Flagella/ultrastructure ; Liver/ultrastructure ; Mitochondria/ultrastructure ; Plants ; }, abstract = {According to scientific procedure, each discipline first describes the phenomena of its research area, then analyzes them, and finally categorized them in a system. To date, biology has lacked such a system for its smallest building blocks, the cells. Although the theory of evolution explains certain central evolutionary mechanisms of the cell, there existed no generally accepted theory of the organization of the cell. The endocytobiotic cell theory is suggested as a possible basis for a satisfying explanation of the structure, function, information, and evolution of the cell. Furthermore, a hypothetical periodic system of the cell is developed. This system consists of eight groups, including the ecological niches fermentation, respiration, photergy, and photosynthesis (each aerobic and anaerobic) and seven periods with increasing numbers of protein biosynthesis machineries (cytoplasma, mitochondria, plastids, endocytobionts). We find furthermore, a division according to typical animal of plant cells and between these two in fungus-like cells.}, }
@article {pmid6765191, year = {1982}, author = {Scovassi, AI and Torsello, S and Plevani, P and Badaracco, GF and Bertazzoni, U}, title = {Active polypeptide fragments common to prokaryotic, eukaryotic, and mitochondrial DNA polymerases.}, journal = {The EMBO journal}, volume = {1}, number = {10}, pages = {1161-1165}, pmid = {6765191}, issn = {0261-4189}, mesh = {Animals ; Binding Sites ; Cell Line ; DNA-Directed DNA Polymerase/*genetics ; Escherichia coli/enzymology ; Fungi/enzymology ; Humans ; Leukemia, Lymphoid ; Male ; Mitochondria/*enzymology ; Molecular Weight ; Organ Specificity ; Peptide Fragments/analysis ; Plants/enzymology ; Rats ; Species Specificity ; }, abstract = {With a procedure that allows the renaturation of the DNA polymerase catalytic activity in situ after SDS-polyacrylamide gel electrophoresis, we have compared the active polypeptides present in extracts from organisms covering a wide evolutionary range from prokaryotes to eukaryotes, namely: Escherichia coli, Oryza sativa, Daucus carota , Neurospora crassa, Dictyostelium discoideum, Saccharomyces cerevisiae, Ceratitis capitata, Leucophaea maderae , Xenopus laevis, rat tissues and human lymphoblastoid cells. Two main clusters of active peptides are visible in mammalian and adult insect tissues, characterized by a mol. wt. greater than 70000 and less than 50000, respectively. High mol. wt. peptides are heterogeneous in size and correspond to active fragments of DNA polymerase alpha, whereas low mol. wt. peptides show the same migration rate as purified DNA polymerase beta and are not generated by proteolysis of the high mol. wt. cluster, In the three species of fungi studied, only high mol. wt. peptides are found. The same is true in plant cells, where no DNA polymerase beta activity is detectable and the pattern of the high mol. wt. cluster is similar to that observed in E. coli extracts (which also lack low mol. wt. peptides). Also in mitochondria from higher and lower eukaryotes only high mol. wt. species are observed, and the active band(s) range from 70000 to 145000 daltons. Our results indicate that the structure of DNA polymerase has been highly conserved during evolution so that an active fragment of mol. wt. greater than or equal to 70 000 is always found in prokaryotic enzymes and in the replicative species of eukaryotic and mitochondrial DNA polymerases; at a certain stage in evolution, another species of low mol. wt. DNA polymerase (beta or beta-like) appears.}, }
@article {pmid6750830, year = {1982}, author = {Sherlock, S}, title = {Primary biliary cirrhosis: critical evaluation and treatment policies.}, journal = {Scandinavian journal of gastroenterology. Supplement}, volume = {77}, number = {}, pages = {63-74}, pmid = {6750830}, issn = {0085-5928}, mesh = {Adrenal Cortex Hormones/therapeutic use ; Adult ; Antibodies/analysis ; Azathioprine/therapeutic use ; Copper/metabolism ; Female ; Humans ; Liver/pathology ; *Liver Cirrhosis, Biliary/diagnosis/immunology/therapy ; Liver Transplantation ; Male ; Middle Aged ; Mitochondria, Liver/immunology ; Penicillamine/therapeutic use ; Portasystemic Shunt, Surgical ; Prognosis ; }, abstract = {Primary biliary cirrhosis is a disease where small intra-hepatic bile ducts are destroyed as a result of an immunological reaction, presumably by cytotoxic T-lymphocytes on biliary epithelium. Analogies can be made to the graft-versus-host reaction. Hepatic copper retention is secondary to cholestasis. A circulating mitochondrial antibody is virtually constant. A mitochondrial antibody, specific for primary biliary cirrhosis, has been identified. Liver biopsy appearances have been staged but there are difficulties because of the varying rte of evolution in different parts of the liver, the focal nature of the changes and the lack of correlation with the clinical picture. Other diagnostic criteria include female sex, raised serum alkaline phosphatase values and various associated diseases. Many patients are now diagnosed when presymptomatic and such patients, particularly with granulomas in the liver, may have a normal life expectancy. General therapeutic measures include control of pruritus and prevention of fat soluble vitamin and calcium deficiencies. There is no specific treatment but D-penicillamine is useful in the later stages and prolongs survival. The prognosis in those with progressive jaundice is very poor.}, }
@article {pmid6298804, year = {1982}, author = {Cann, RL and Brown, WM and Wilson, AC}, title = {Evolution of human mitochondrial DNA: a preliminary report.}, journal = {Progress in clinical and biological research}, volume = {103 Pt A}, number = {}, pages = {157-165}, pmid = {6298804}, issn = {0361-7742}, mesh = {*Biological Evolution ; DNA Restriction Enzymes ; DNA, Mitochondrial/*genetics ; Humans ; Polymorphism, Genetic ; RNA, Transfer/genetics ; }, abstract = {Preliminary mapping of 346 cleavage sites in the mitochondrial genome of 100 human beings gives evidence that the genes for transfer RNA are highly variable, a result that points to the need for testing the accuracy of mitochondrial protein synthesis. In addition, the map comparisons imply that Australia has as much mtDNA diversity as any other area tested in the Old World. Assuming a model of strictly maternal inheritance, it appears possible to follow individual female lineages back hundreds of generations thereby providing human genetics with an important new measure of population heterogeneity. This measure, when compared with those available from protein and morphologic considerations, will help highlight particular groups of people whose mitochondria may increase greatly our understanding of the historical processes leading to the evolution of our own species.}, }
@article {pmid6179895, year = {1982}, author = {Kuroiwa, T}, title = {Mitochondrial nuclei.}, journal = {International review of cytology}, volume = {75}, number = {}, pages = {1-59}, doi = {10.1016/s0074-7696(08)61001-3}, pmid = {6179895}, issn = {0074-7696}, mesh = {Animals ; Cell Cycle ; Chloroplasts/ultrastructure ; Chromatin/analysis ; Chromosomes ; *DNA, Mitochondrial/analysis ; Fungi/ultrastructure ; Humans ; Mitochondria/analysis/physiology/*ultrastructure ; Models, Biological ; Molecular Weight ; Phylogeny ; Proteins/analysis/physiology ; RNA/analysis ; RNA, Ribosomal/analysis ; }, }
@article {pmid6276013, year = {1981}, author = {Yin, S and Heckman, J and RajBhandary, UL}, title = {Highly conserved GC-rich palindromic DNA sequences flank tRNA genes in Neurospora crassa mitochondria.}, journal = {Cell}, volume = {26}, number = {3 Pt 1}, pages = {325-332}, doi = {10.1016/0092-8674(81)90201-4}, pmid = {6276013}, issn = {0092-8674}, mesh = {Base Sequence ; Biological Evolution ; DNA Restriction Enzymes ; DNA, Mitochondrial/*genetics ; Genetic Linkage ; Neurospora/*genetics ; Neurospora crassa/*genetics ; Nucleic Acid Conformation ; RNA, Transfer/*genetics ; }, abstract = {In sequencing a 2200 bp region of the Neurospora crassa mitochondrial DNA encoding the 3' end of the large rRNA gene and a cluster of six tRNA genes, we have found that the tRNA genes are flanked by highly conserved GC-rich palindromic DNA sequences. An 18 bp long core sequence, 5'-CC CTGCAG TA CTGCAG GG-3', containing two closely spaced Pst I sites, is common to all these palindromic sequences. Each of the eight Pst I sites mapped in the 2200 bp region consists of two closely spaced Pst I sites; thus this 2200 bp long segment actually contains 16 Pst I sites. Between 5-10% of the N. crassa DNA may consist of these GC-rich palindromic sequences that include the 18 base long core sequence. The same core sequence is present within both the 5' and 3' side of the intervening sequence of the large rRNA gene, close to, but not at, the intron-exon boundaries. We discuss probable roles for these sequences in N. crassa mitochondrial function, including their role as signals either in the synthesis or processing (or both) of RNA in the mitochondria.}, }
@article {pmid6121363, year = {1981}, author = {Buligescu, L and Moscaliuc, I and Eşanu, I and Ionică, M}, title = {[Significance of anti-tissue antibodies in the evolution of chronic liver diseases].}, journal = {Revista de medicina interna, neurologe, psihiatrie, neurochirurgie, dermato-venerologie. Medicina interna}, volume = {33}, number = {6}, pages = {445-452}, pmid = {6121363}, issn = {1220-0905}, mesh = {Antibodies, Antinuclear/analysis ; Autoantibodies/*analysis ; Chronic Disease ; Cytoplasm/immunology ; Hepatitis/immunology ; Humans ; Liver Cirrhosis/immunology ; Liver Diseases/*immunology ; Mitochondria, Liver/immunology ; Muscle, Smooth/immunology ; }, }
@article {pmid7324176, year = {1981}, author = {Solcia, E and Ballerini, L and Bellini, O and Magrini, U and Bertazzoli, C and Tosana, G and Sala, L and Balconi, F and Rallo, F}, title = {Cardiomyopathy of doxorubicin in experimental animals, Factors affecting the severity, distribution and evolution of myocardial lesions.}, journal = {Tumori}, volume = {67}, number = {5}, pages = {461-472}, doi = {10.1177/030089168106700512}, pmid = {7324176}, issn = {0300-8916}, mesh = {Animals ; Cardiomyopathies/*chemically induced/pathology ; Dogs ; Dose-Response Relationship, Drug ; Doxorubicin/*toxicity ; Female ; Male ; Mice ; Rabbits ; Rats ; Rats, Inbred Strains ; Time Factors ; }, abstract = {Heart lesions induced in mice, rats, rabbits and dogs by Doxorubicin administered i.v. according to various schedules were studied by light and electron microscopy Vacuolization of myocardial cytoplasm due to distention of the sarcoplasmic reticulum, the T-tubule system and the Golgi vesicles was one of the most common findings. Myocytolysis, clumping and loss of fibrils, fragmentation of sarcomeres, swelling of mitochondria and an increase in lysosomes and residual bodies were also observed. The severity of the cardiomyopathy, quantitatively evaluated by a score system, proved to be dose-dependent. Cardiomyopathy was more severe when the treatment was given in a short period by administration of high doses than when the same cumulative dose was administered as low doses repeated for a long period. The left atrium was more severely affected than the ventricles when high doses were given, whereas it was less affected in animals given low doses. The cardiomyopathy was less severe in animals receiving the same dose in a high volume of solvent and during a long perfusion time. Threshold doses were needed both to induce the cardiomyopathy and to establish it as a progressive disease.}, }
@article {pmid7027053, year = {1981}, author = {Küntzel, H and Köchel, HG}, title = {Evolution of rRNA and origin of mitochondria.}, journal = {Nature}, volume = {293}, number = {5835}, pages = {751-755}, doi = {10.1038/293751a0}, pmid = {7027053}, issn = {0028-0836}, mesh = {Animals ; Aspergillus nidulans/genetics ; Base Sequence ; *Biological Evolution ; DNA, Mitochondrial/*genetics ; Genes ; Humans ; Nucleic Acid Conformation ; Plants/genetics ; RNA, Ribosomal/*genetics ; }, }
@article {pmid7299574, year = {1981}, author = {Komuniecki, R and Komuniecki, PR and Saz, HJ}, title = {Relationships between pyruvate decarboxylation and branched-chain volatile acid synthesis in Ascaris mitochondria.}, journal = {The Journal of parasitology}, volume = {67}, number = {5}, pages = {601-608}, pmid = {7299574}, issn = {0022-3395}, support = {AI-07030/AI/NIAID NIH HHS/United States ; AI-09483/AI/NIAID NIH HHS/United States ; }, mesh = {Adenosine Diphosphate/pharmacology ; Animals ; Ascaris/*metabolism/ultrastructure ; Fatty Acids, Volatile/*biosynthesis ; Fumarates/metabolism ; Malates/metabolism ; Mitochondria/*metabolism ; Oxidation-Reduction ; Oxygen/pharmacology ; Pyruvates/*metabolism ; Pyruvic Acid ; Succinates/metabolism ; Succinic Acid ; }, abstract = {The rate of 14CO2 evolution from 1-[14C]pyruvate by intact Ascaris mitochondria was very slow, but increased with increasing concentrations of pyruvate. At all concentrations of pyruvate, in an aerobic environment, pyruvate decarboxylation was stimulated greatly by the addition of fumarate, malate, or succinate. However, under anaerobic conditions, only malate and fumarate stimulated pyruvate decarboxylation; succinate had no effect. This implies that the aerobic metabolism of succinate, presumably to other dicarboxylic acids, may be required for the stimulation. Incubation of sonicated mitochondria with pyruvate plus fumarate, under rate-limiting concentrations of NAD+, resulted in approximately equal quantities of pyruvate utilized and succinate formed, suggesting that pyruvate oxidation and fumarate reduction may be linked. Branched-chain, volatile fatty acids were not formed during incubations with either malate or succinate, or succinate plus acetate. However, incubations of intact Ascaris mitochondria with pyruvate plus succinate yielded 2-methylbutyrate and 2-methylvalerate, whereas incubations with pyruvate plus propionate yielded almost exclusively 2-methylvalerate. Oxygen dramatically inhibited the synthesis of the branched-chain acids from succinate plus pyruvate, attesting to the apparent anaerobic nature of Ascaris mitochondrial metabolism. Significantly, the addition of glucose plus ADP stimulated the formation of all volatile fatty acids. Therefore, the synthesis of branched-chain acids may be related directly to increased energy generation. Alternatively, they may function in the regulatory role of maintaining the mitochondrial redox balance.}, }
@article {pmid7030741, year = {1981}, author = {Kresze, GB and Ronft, H}, title = {Pyruvate dehydrogenase complex from baker's yeast. 2. Molecular structure, dissociation, and implications for the origin of mitochondria.}, journal = {European journal of biochemistry}, volume = {119}, number = {3}, pages = {581-587}, doi = {10.1111/j.1432-1033.1981.tb05647.x}, pmid = {7030741}, issn = {0014-2956}, mesh = {Biological Evolution ; Chemical Phenomena ; Chemistry ; Flavins/isolation &amp; purification ; *Mitochondria ; Molecular Weight ; Pyruvate Dehydrogenase Complex/*isolation &amp; purification ; Saccharomyces cerevisiae/*enzymology ; }, abstract = {1. Pyruvate dehydrogenase complex from Saccharomyces cerevisiae is similar in size (s20,w 77 S) and flavin content (1.3--1.4 nmol/mg) to the complexes from mammalian mitochondria. 2. The relative molecular masses of the constituent polypeptide chains, as determined by dodecylsulfate gel electrophoresis at different gel concentrations, were: lipoate acetyltransferase (E2), 58 000; lipoamide dehydrogenase (E3), 56 000; pyruvate dehydrogenase (E1), alpha-subunit, 45 000, and beta-subunit, 35 000. Gel chromatography in the presence of 6 M guanidine . HCl gave a value of 52 000 for E2 indicating anomalous electrophoretic migration as described for the E2 components of other pyruvate dehydrogenase complexes. Thus, the organization and subunit Mr values are similar with the mammalian complexes and virtually identical with the complexes of gram-positive bacteria but differ greatly from the pyruvate dehydrogenase complexes of gram-negative bacteria. 3. The complex was resolved into its component enzymes by the following methods. E1 was obtained by treatment of the complex with elastase followed by gel chromatography on Sepharose CL-2B using a reverse ammonium sulfate gradient for elution. E2 was isolated by gel filtration of the complex in the presence of 2 M KBr, and E3 was obtained by hydroxyapatite chromatography in 8 M urea. The isolated enzymes reassociated spontaneously to give pyruvate dehydrogenase overall activity.}, }
@article {pmid7024918, year = {1981}, author = {Zwieb, C and Glotz, C and Brimacombe, R}, title = {Secondary structure comparisons between small subunit ribosomal RNA molecules from six different species.}, journal = {Nucleic acids research}, volume = {9}, number = {15}, pages = {3621-3640}, pmid = {7024918}, issn = {0305-1048}, mesh = {Animals ; Base Sequence ; Chloroplasts/analysis ; Escherichia coli/analysis ; Humans ; Mice ; Mitochondria/analysis ; Molecular Weight ; Nucleic Acid Conformation ; Plants/analysis ; *RNA, Ribosomal ; Saccharomyces cerevisiae/analysis ; Species Specificity ; Xenopus ; Zea mays/analysis ; }, abstract = {Secondary structure models are presented for three pairs of small subunit ribosomal RNA molecules. These are the 16S rRNA from E. coli cytoplasmic and Z. mays chloroplast ribosomes, the 18S rRNA from S. cerevisiae and X. laevis cytoplasmic ribosomes, and the 12S rRNA from human and mouse mitochondrial ribosomes. Using the experimentally-established secondary structure of the E. coli 16S rRNA as a basis, the models were derived both by searching for primary structural homology between the three classes of sequence (12S, 16S, 18S), and also by searching for compensating base changes in putative helical regions of each pair of sequences. The models support the concept that secondary structure of ribosomal RNA has been extensively conserved throughout evolution, differences in length between the three classes of sequence being accommodated in distinct regions of the molecules.}, }
@article {pmid7311594, year = {1981}, author = {Thornley, AL and Harington, A}, title = {Diploidy and sex as the selective advantages for retaining genes transferred from mitochondrial and plastid ancestors in the nuclear genome.}, journal = {Journal of theoretical biology}, volume = {91}, number = {3}, pages = {515-523}, doi = {10.1016/0022-5193(81)90271-x}, pmid = {7311594}, issn = {0022-5193}, mesh = {*Biological Evolution ; DNA ; *Diploidy ; *Genes ; Mitochondria ; Models, Genetic ; Plasmids ; Selection, Genetic ; *Sex ; Symbiosis ; }, }
@article {pmid7284306, year = {1981}, author = {Spencer, DF and Bonen, L and Gray, MW}, title = {Primary sequence of wheat mitochondrial 5S ribosomal ribonucleic acid: functional and evolutionary implications.}, journal = {Biochemistry}, volume = {20}, number = {14}, pages = {4022-4029}, doi = {10.1021/bi00517a011}, pmid = {7284306}, issn = {0006-2960}, mesh = {Base Composition ; Base Sequence ; *Biological Evolution ; Cytosol/analysis ; Mitochondria/*physiology ; Molecular Weight ; Nucleic Acid Conformation ; Plants/*genetics ; Protein Biosynthesis ; RNA, Ribosomal/genetics ; Triticum/genetics ; }, abstract = {Using the procedures of Donis-Keller et al. [Donis-Keller, H., Maxam, A. M., &amp; Gilbert, W. (1977) Nucleic Acids Res. 4, 2527--2538 (1977)] and Peattie [Peattie, D. A. (1979) Proc. Natl. Acad. Sci. U.S.A. 76, 1760--1764], we have determined the nucleotide sequence of wheat mitochondrial 5S ribosomal ribonucleic acid (rRNA). This sequence [Formula: see text] is the first to be reported for a plant mitochondrial RNA. A highly conserved region (underlined) readily identifies the molecule as a structural homologue of other 5S rRNAs, as do potential base-paired regions which are characteristic of all known (prokaryotic, chloroplast, eukaryotic cytosol) 5S rRNA sequences. However, when assessed in terms of those structural features which distinguish prokaryotic from eukaryotic 5S rRNAs, wheat mitochondrial 5S rRNA cannot be classified readily as one or the other but instead displays characteristics of both types. In addition, the mitochondrial 5S rRNA has several unusual features, including (i) a variable number (two to three) of A residues at both the 5' and 3' ends, (ii) a unique sequence (CGACC, italic) in place of the prokaryotic sequence (CGAAC) which has been postulated to interact with aminoacyl-tRNA during translation, and (iii) a novel sequence, AUAUAUAU, immediately following the highly conserved sequence. In terms of overall primary sequence, wheat mitochondrial and cytosol 5S rRNAs seem to be slightly more divergent from each other than either is from Escherichia coli 5S rRNA, with which they are about equally homologous. From these observations, we propose that wheat mitochondrial 5S rRNA represents a distinct class of 5S rRNA. Our observations raise a number of questions about the evolutionary origin and functional role(s) of plant mitochondrial 5S rRNA.}, }
@article {pmid6262320, year = {1981}, author = {Wilson, G and Hodges, R and Hare, JF}, title = {Site of synthesis of the mitochondrial cytochromes in hepatocyte cultures.}, journal = {The Journal of biological chemistry}, volume = {256}, number = {10}, pages = {5197-5203}, pmid = {6262320}, issn = {0021-9258}, support = {AM 25703-02/AM/NIADDK NIH HHS/United States ; }, mesh = {Animals ; Cattle ; Cells, Cultured ; Chloramphenicol/pharmacology ; Cycloheximide/pharmacology ; Cytochrome c Group/biosynthesis ; Electron Transport Complex III ; Electron Transport Complex IV/*biosynthesis/isolation &amp; purification ; Immunoassay ; Liver/*enzymology ; Macromolecular Substances ; Mitochondria, Heart/metabolism ; Mitochondria, Liver/*enzymology ; Multienzyme Complexes/*biosynthesis ; NADH, NADPH Oxidoreductases/*biosynthesis ; *Protein Biosynthesis/drug effects ; Quinone Reductases/*biosynthesis ; Rats ; Subcellular Fractions/enzymology ; }, abstract = {The biosynthesis of mammalian mitochondrial cytochromes was explored in primary hepatocyte cultures. When these were pulsed with [35S]methionine in the presence of cycloheximide, eight discrete mitochondrial polypeptides were detected by fluorography after their resolution under denaturing conditions by polyacrylamide gel electrophoresis. Since the pulse labeling of the polypeptides was sensitive to chloramphenicol, an inhibitor of mitochondrial translation, they must be translated on mitochondrial ribosomes. Three were identified as the largest subunits of cytochrome oxidase by their immunoprecipitation with antibody directed against purified rat liver cytochrome oxidase. Another (Mr = 28,000) was identified as one of eight subunits of purified rat liver cytochrome b-c1 complex by its immunoprecipitation with antibody directed against bovine heart b-c1 complex. Since cytochrome b apoprotein is the only product of the mitochondrial genome in the yeast cytochrome b-c1 complex (Krieke, J., Bechmann, H., van Hemert, F. J., Schweyan, R. J., Boer, P. H., Kaudewitz, F., and Groot, G. S. P. (1979) Eur. J. Bio-chem. 101, 607-617), the results strongly suggest that the Mr = 28,000 subunit of liver b-c1 complex is cytochrome b apoprotein. Thus the contribution of the mitochondrial translation system to the cytochrome complexes in liver is identical to that of yeast and Neurospora, and there appears to be no deletion or transfer to the nuclear genome of structural genes for mitochondrially synthesized cytochromes during eukaryotic evolution.}, }
@article {pmid6941289, year = {1981}, author = {Belknap, WR and Togasaki, RK}, title = {Chlamydomonas reinhardtii cell preparation with altered permeability toward substrates of organellar reactions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {78}, number = {4}, pages = {2310-2314}, pmid = {6941289}, issn = {0027-8424}, support = {PHS GM7227/GM/NIGMS NIH HHS/United States ; }, mesh = {Cell Fractionation/methods ; Chlamydomonas/*physiology/ultrastructure ; Chloroplasts/*physiology ; Darkness ; Intracellular Membranes/*physiology ; Mitochondria/*physiology ; Mutation ; Oxygen Consumption ; Permeability ; Phosphates/pharmacology ; Photosynthesis/drug effects ; }, abstract = {Chlamydomonas reinhardtii cells disrupted under low pressure in a Yeda press yielded a preparation ("presate") with high permeability toward substrates for Class A chloroplasts and intact mitochondria. The stoichiometric rates of CO2 uptake and O2 photoevolution by the wild-type cell pressate were severely suppressed by 10 mM exogenous phosphate, and this suppression could be reversed by the addition of either 3-phosphoglycerate or dihydroxyacetone phosphate. A mutant, F60, which lacks phosphoribulokinase activity and hence CO2-dependent O2 photoevolution, was studied by using intact cells, pressate, and sonicated pressate. In the pressate, the rate of 3-phosphoglycerate-dependent O2 photoevolution was high, whereas that dependent on K3Fe(CN)6 was low; the opposite was true of the sonicated pressate. p-Benzoquinone supported high rates of O2 evolution in both the pressate and the sonicated pressate. The slow O2 uptake in the dark by the dark-adapted wild-type pressate could be increased by the addition of succinate and further stimulated by ADP. Addition of KCN resulted in rapid but only partial suppression of this activity. Dark O2 uptake by the unpressed preparation did not show similar responses. The procedure described here opens the possibility of in situ analysis of Class A chloroplasts from wild-type and mutant strains of C. reinhardtii.}, }
@article {pmid6457986, year = {1981}, author = {Eskenasy, A}, title = {Morphogenesis and pathogenesis of chronic lung diseases. XVII. Ultrastructure of the experimentally induced granulomas of the rabbit lung.}, journal = {Morphologie et embryologie}, volume = {27}, number = {2}, pages = {147-153}, pmid = {6457986}, issn = {0377-5038}, mesh = {Animals ; Granuloma/*pathology ; Lung/*ultrastructure ; Lung Diseases/*pathology ; Microscopy, Electron ; Rabbits ; }, abstract = {Experimentally induced lung granulomas of rabbits challenged by complete Freund's adjuvant with human gammaglobulins were ultrastructurally studied at two moments of their evolution: 10 and 20 days. Granulomas were formed even in the first stage, being composed of histiocytic accumulations around capillaries, sometimes dilated, in which the adjuvant lipidic compounds were embolized: hypertrophy of endothelial cytoplasms, lymphocytic insertions with membrane contacts with the histiocytes, an epithelial covering completed this picture. The 20-day granulomas presented intragranulomatous capillaries with hypertrophied endothelia, macrophages and lymphocytes; the pericapillary granulomatous tissue showed many epithelioid cells with mitochondria and numerous cytoplasmic vesicles of different densities (among them "grey vesicles"), and long cytoplasmic digitations; some histiocytes had an epithelioid aspect. A large granulous alveolocyte was sometimes present at the granuloma periphery. The perinodular veins evinced hypertrophied endothelia with many pinocytotic vesicles and coated caveolae expressing the processing of engulfed transported particles; fibroblasts were active near veins.}, }
@article {pmid6785727, year = {1981}, author = {Küntzel, H and Heidrich, M and Piechulla, B}, title = {Phylogenetic tree derived from bacterial, cytosol and organelle 5S rRNA sequences.}, journal = {Nucleic acids research}, volume = {9}, number = {6}, pages = {1451-1461}, pmid = {6785727}, issn = {0305-1048}, mesh = {Bacteria/*analysis ; Base Sequence ; Chloroplasts/*analysis ; Computers ; Cyanobacteria/*analysis ; Cytosol/analysis ; Mitochondria/analysis ; *Phylogeny ; Plants/*analysis ; *RNA, Ribosomal/genetics ; Species Specificity ; Thermus/analysis ; }, abstract = {A phylogenetic tree was constructed by computer analysis of 47 completely determined 5S rRNA sequences. The wheat mitochondrial sequence is significantly more related to prokaryotic than to eukaryotic sequences, and its affinity to that of the thermophilic Gram-negative bacterium Thermus aquaticus is comparable to the affinity between Anacystis nidulans and chloroplastic sequences. This strongly supports the idea of an endosymbiotic origin of plant mitochondria. A comparison of the plant cytosol and chloroplast sub-trees suggests a similar rate of nucleotide substitution in nuclear genes and chloroplastic genes. Other features of the tree are a common precursor of protozoa and metazoa, which appears to be more related to the fungal than to the plant protosequence, and an early divergence of the archebacterial sequence (Halobacterium cutirubrum) from the prokaryotic branch.}, }
@article {pmid7244315, year = {1981}, author = {Ali, MA}, title = {[Retinal adaptations to habitat].}, journal = {Revue canadienne de biologie}, volume = {40}, number = {1}, pages = {3-17}, pmid = {7244315}, issn = {0035-0915}, mesh = {*Adaptation, Physiological ; Amphibians ; Animals ; Fishes ; Retina/*physiology/ultrastructure ; Species Specificity ; Vertebrates/*physiology ; Vision, Ocular ; }, abstract = {Vertebrates have, through the process of evolution, adapted to their photic environment. This is well manifested in the retinal adaptations to various habitats. Although all vertebrates are considered, emphasis is placed on fishes because they form about 50% of the vertebrate species. In addition, they occupy a wide range of habitats, thus retinal modifications of fishes serve as models for all other vertebrates. The present article reviews morphological, physiological and biochemical retinal adaptations. The quality and quantity of light reaching the aquatic organism are functions of the incident light as well as the aquatic environment. Thus, in well lit, clear waters fishes are arhythmic and possess almost equal populations of rods and cones; whereas fishes in dimly lit environments (due to turbidity or depth) have retinas that are more specialised for high sensitivity-multi-banked retinas, long outer segments, grouped photoreceptors, hypertrophied ellipsoid mitochondria, reflecting tapetum. Similarly, the ratio and distribution of visual pigments (rhodopsin and porphyropsin) and S-potential change with respect to fresh/sea water, clear/turbid water and air/aquatic environments. Thus, in fresh waters, where the photic environment shifts to longer wavelengths, porphyropsin predominates; while in land vertebrates and almost all marine fishes the dominant pigment is rhodopsin. With respect to the latter, fishes in turbid, greenish or yellowish coastal waters have 'rhodopsins' with lambda mas above 500 nm; fishes in clear coastal habitats have 'rhodopsins' with lambda max near 500 nm; while those in the blue-lit environment of deep seas have lambda max below 500 nm. The retinal pigment composition is also associated with habitat changes during diadromous migrations in fishes or during amphibian metamorphosis. It is interesting to note that the dorsal and ventral retinas of Rana catesbeiana and Anableps microlepis which view aquatic and aerial environments, respectively, show a predominately porphyropsin-rich dorsal retina compared to a rhodopsin-rich ventral retina. Similar shifts in the S-potential are observed with change in habitats. Fresh water fishes exhibit L-responses with lambda max in longer wavelengths compared to marine fishes where the maximum of the L-response shifted towards shorter wavelengths.}, }
@article {pmid6261575, year = {1981}, author = {Bhattacharyya, TK and Butler, DG and Youson, JH}, title = {Distribution and structure of the adrenocortical homologue in the garpike.}, journal = {The American journal of anatomy}, volume = {160}, number = {3}, pages = {231-246}, doi = {10.1002/aja.1001600302}, pmid = {6261575}, issn = {0002-9106}, mesh = {3-Hydroxysteroid Dehydrogenases/analysis ; Adrenal Cortex/anatomy &amp; histology/drug effects/*ultrastructure ; Adrenocorticotropic Hormone/pharmacology ; Animals ; Female ; Fishes/*anatomy &amp; histology ; Histocytochemistry ; Inclusion Bodies/ultrastructure ; Lipids ; Male ; Microscopy, Electron ; Organoids/ultrastructure ; Phylogeny ; }, abstract = {The microanatomy of the yellow corpuscles (adrenocortical homologue, AH) in the holostean fish, Lepisosteus spp. was studied by serial sectioning, steroid histochemistry, and electron microscopy. The modification of this tissue to short-term ACTH treatment was also observed. The distribution of the AH within the renal tissue of the garpike phylogenetically represents a more advanced condition than that seen in its closest holostean relative, the bowfin, and appears to approximate that in teleosts. The homology of this tissue of vertebrate adrenocortical tissue was established by the positive identification of the enzyme, gamma 5-3 beta-hydroxysteroid dehydrogenase, and by the ultrastructural features of the cells before and after ACTH administration. The AH cells possess fine structural features characteristic of steroidogenic cells, namely, polymorphic mitochondria with tubular cristae, abundant tubules of smooth endoplasmic reticulum, a prominent Golgi complex, and lipid droplets. Other interesting features include the presence of annulate lamellae and a variety of dense bodies. Digitonin perfusion results in the deposition of presumed, cholesterol-digitonide crystalline spicules on the surface microplicae of the cells and as dense accumulations in association with smooth endoplasmic reticulum. ACTH administration results in swelling of mitochondria, a loss of their cristae, and a smooth decrease in electron density of their matrices. Alterations also occur in the smooth and rough endoplasmic reticulum, and large osmiophilic inclusions of irregular profile appear. Some of the ACTH-induced modifications are similar to those observed in the adrenocortical cells of other vertebrate groups following comparable stimulation.}, }
@article {pmid7008949, year = {1981}, author = {Lagerkvist, U}, title = {Unorthodox codon reading and the evolution of the genetic code.}, journal = {Cell}, volume = {23}, number = {2}, pages = {305-306}, doi = {10.1016/0092-8674(81)90124-0}, pmid = {7008949}, issn = {0092-8674}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; *Codon ; *Genetic Code ; Humans ; Hydrogen Bonding ; Mitochondria ; Models, Genetic ; *RNA, Messenger ; RNA, Transfer/genetics ; }, }
@article {pmid7345968, year = {1981}, author = {Baloyannis, S}, title = {The fine structure of the isomorphic oligodendroglioma.}, journal = {Anticancer research}, volume = {1}, number = {4}, pages = {243-248}, pmid = {7345968}, issn = {0250-7005}, mesh = {Brain Neoplasms/*ultrastructure ; Cell Nucleus/ultrastructure ; Cytoplasm/ultrastructure ; Humans ; Microscopy, Electron ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Oligodendroglioma/*ultrastructure ; Spinal Cord Neoplasms/*ultrastructure ; }, abstract = {The fine structure of 26 isomorphic oligodendrogliomas excised from various areas of the Central Nervous System is described. These tumors are composed mainly of three types of cells: (a) those with large round or ovoid nuclei and scanty cytoplasm, (b) those with abundant cytoplasm, very rich in organelles and (c) cells very fibrillated with long cellular processes. The cytoplasm of the second cell type sometimes included crystalline bodies, numerous microtubules, myelin-like membranous structures and a large number of elongated mitochondria. The cells with the very fibrillated cytoplasm are eigher astrocytes intermixed with the neoplastic cells of the oligodendrocytic line or an astrocytic-like cellular evolution of the immature neoplastic cell of the oligodendrocytic line. Ultrastructural analysis provided evidence that isomorphic oligodendroglioma is not as homogeneous as was considered to be at the light microscopy level.}, }
@article {pmid7337818, year = {1981}, author = {Cavalier-Smith, T}, title = {Eukaryote kingdoms: seven or nine?.}, journal = {Bio Systems}, volume = {14}, number = {3-4}, pages = {461-481}, doi = {10.1016/0303-2647(81)90050-2}, pmid = {7337818}, issn = {0303-2647}, mesh = {Animals ; Bacteria/classification ; Euglena/classification ; Eukaryota/*classification ; Fungi/*classification ; Phycobilisomes ; *Phylogeny ; Plants/classification ; }, abstract = {The primary taxa of eukaryote classification should be monophyletic and based on fundamental cell structure rather than nutritional adaptive zones. The classical two kingdom classification into "plants" and "animals" and the newer four kingdom classifications into "protis", "fungi" "animals" and "plants" are therefore both unsatisfactory. Eukaryotes can be classified into nine kingdoms each defined in terms of a unique constellation of cell structures. Five kingdoms have plate-like mitochondrial cristae: (1) Eufungi (the non-ciliated fungi, which unlike the other eight kingdoms have unstacked Golgi cisternae), (2) Ciliofungi (the posteriorly ciliated fungi), (3) Animalia (Animals, sponges, mesozoa, and choanociliates; phagotrophs with basically posterior ciliation), (4) Biliphyta (Non-phagotrophic, phycobilisome-containing, algae; i.e. theGlaucophyceae and Rhodophyceae), (5) Viridiplantae (Non-phagotrophic green plants, with starch-containing plastids). Kingdom (6), the Euglenozoa, has disc-shaped cristae and an intraciliary dense rod and may be phagotrophic and/or phototrophic with plastids with three-membraned envelopes. Kingdom (7), the cryptophyta, has flattened tubular cristae, tubular mastigonemes on both cilia,m and starch in thecompartment between the plastid endoplasmic reticulum and the plastid envelope; their plastids, if present, have phycobilins inside the paired thylakoids and chlorophyll c2. Kingdom (8), the Chromophyta, has tubular cristae, together with tubular mastigonemes on one anterior cilum and/or a plastid endoplasmic reticulum and chlorophyll c1 + c2. Members of the ninth kingdom, the Protozoa, are mainly phagotrophic, and have tubular or vesicular cristae (or lack mitochondria altogether), and lack tubular mastigonemes on their (primitively anterior) cilia; plastids if present have three-envelop membranes, chlorophyll c2, and no internal starch, and a plastid endoplasmic reticulum is absent. Kingdoms 4-9 are primitively anteriorly biciliate. Detailed definitions of the new kingdoms and lists of the phyla comprising them are given. Advantages of the new system and its main phylogenetic implications are discussed. A simpler system of five kingdoms suitable for very elementary teaching is possible by grouping the photosynthetic and fungal kindoms in pairs. Various compromises are possible between the nine and five kingdoms systems; it is suggested that the best one for general scientific use is a system of seven kingdoms in which the Eufungi and Ciliofungi become subkingdoms of the Kingdom Fungi, and the Cryptophyta andChromophyta subkingdoms of th Kingdom Chromista; the Fungi, Viridiplantae, Biliphyta, and Chromista can be subject to the Botanical Code of Nomenclature, while the Zoological Code can govern the Kingdoms Animalia, Protozoa and Euglenozoa...}, }
@article {pmid7327142, year = {1981}, author = {Wikström, M}, title = {[The inner mitochondrial membrane--inheritance from ancient bacteria].}, journal = {Duodecim; laaketieteellinen aikakauskirja}, volume = {97}, number = {18}, pages = {1546-1553}, pmid = {7327142}, issn = {0012-7183}, mesh = {Animals ; Biological Evolution ; Humans ; Intracellular Membranes/*ultrastructure ; Membrane Proteins/metabolism ; Mitochondria/*ultrastructure ; }, }
@article {pmid7325033, year = {1981}, author = {}, title = {Phylogeny, structure and composition of cell membranes.}, journal = {Advances in experimental medicine and biology}, volume = {140}, number = {}, pages = {1-53}, doi = {10.1007/978-1-4684-4112-3_1}, pmid = {7325033}, issn = {0065-2598}, mesh = {Animals ; Biological Transport, Active ; Calcium/metabolism ; Cell Membrane/*physiology ; Erythrocyte Membrane/physiology ; Humans ; Intracellular Membranes/*physiology ; Lipid Bilayers ; Liposomes ; Membrane Lipids/physiology ; Membrane Proteins/physiology ; Mitochondria/physiology ; *Phylogeny ; }, }
@article {pmid7324860, year = {1981}, author = {Ludatscher, RM and Hashmonai, M and Monies-Chass, I and Schramek, A}, title = {Progressing alterations in transient ischemia of skeletal muscles: an ultrastructural study.}, journal = {Acta anatomica}, volume = {111}, number = {4}, pages = {320-327}, doi = {10.1159/000145483}, pmid = {7324860}, issn = {0001-5180}, mesh = {Animals ; Dogs ; Hindlimb/anatomy &amp; histology ; Ischemic Attack, Transient/*physiopathology ; Microscopy, Electron ; Muscles/*blood supply/ultrastructure ; Time Factors ; }, abstract = {Ultrastructural muscle changes resulting from temporary anoxia and their evolution were studied in dogs. Ischaemia of the hind limb was produced by subcutaneous ligation of all muscles of the thigh and clamping of the femoral artery. Revascularization was obtained by declamping and removal of the muscle ligature. The period of ischaemia ranged from 4 1/2 to 7 h, the latter being the upper limit allowing functional recovery after revascularization. 6-7 h of ischaemia revealed focal degenerative changes of varied intensity. These consisted of enlarged mitochondria with ruptured cristae, small pads of glycogen granules and accumulation of lipid vacuoles. The tubules of sarcoplasmic reticulum contained dense, fine-granular material. Focal myofibrillar destruction and disruption of the Z line were encountered in half of the cases. The myofibrillar damage was more severe 9 days after revascularization of the muscles. The functional recovery of the ischaemic limbs in the present study may be due to the focal nature of these changes.}, }
@article {pmid7272468, year = {1981}, author = {Schiff, JA}, title = {Evolution of the control of pigment and plastid development in photosynthetic organisms.}, journal = {Bio Systems}, volume = {14}, number = {1}, pages = {123-147}, doi = {10.1016/0303-2647(81)90027-7}, pmid = {7272468}, issn = {0303-2647}, support = {GM14595/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; Chloroplasts/*metabolism ; Darkness ; Energy Metabolism ; Light ; Mitochondria/metabolism ; *Photosynthesis ; Pigments, Biological/*metabolism ; Plants/*metabolism ; Species Specificity ; }, abstract = {How do bioenergetic organelles relate to the cells they are in and how was this relationship established over the course of evolution? Plastids and mitochondria are viewed as prokaryotic residents in eukaryotic cells. These organelles are semiautonomous: they perpetuate themselves by division but regulate and are subject to regulation by the cell in which they are residents. Although these organelles are usually constitutive, their development is arrested in certain organisms when an inducing substrate is absent (light, for example, in the case of the chloroplast) with the formation of precursor organelles such as proplastids. Various trends in the evolution of photo-control systems are discussed including those concerned with photoperception and photomorphogenesis. The photocontrol of chloroplast development by blue and red light is discussed in relation to its possible evolutionary origins in a system for finding the right light for photosynthesis. Models for various types of cellular regulation by light during chloroplast development are discussed. Also considered is the evolution of plastid pigments in response to available light. A parallel evolution of accessory pigments and chlorophylls is suggested which led to chlorophyll reaction centers serving as energy sinks for light absorbed by accessory pigments and, therefore, having their absorptions pushed to the longest possible wavelengths as accessory pigments evolved to fill the middle of the spectrum in response to ecological selection. An endosymbiotic origin of bioenergetic organelles is suggested based on polyphyletic origins of chloroplasts from a number of oxygenic procaryotic precursors. The similarity between proplastids and these oxygenic procaryotes suggests that the original invading organelle may have resembled a modern proplastid rather than a mature chloroplast.}, }
@article {pmid7198422, year = {1981}, author = {Euzet, L and Swiderski, Z and Mokhtar-Maamouri, F}, title = {[Comparative fine structure of the cestode spermatozoon. Relationship to phylogenesis].}, journal = {Annales de parasitologie humaine et comparee}, volume = {56}, number = {3}, pages = {247-259}, pmid = {7198422}, issn = {0003-4150}, mesh = {Animals ; Cell Nucleus/ultrastructure ; Cestoda/classification/*ultrastructure ; Cytoplasm/ultrastructure ; Male ; Microscopy, Electron ; Microtubules/ultrastructure ; Phylogeny ; Species Specificity ; Spermatozoa/ultrastructure ; }, abstract = {The comparison of the ultrastructure of spermatozoa in Cestodes from seven different orders shows that they have the same general pattern of organization. The main common features are following: (a) a long thread-like body; (b) an elongated nucleus; (c) cortical microtubules underlying plasma membrane; (d) the absence of mitochondria and of a typical acrosome. The mode of spermatozoon differentiation indicates an inversion of the polarity. The number of axonemes of the 9 + "1" pattern, characteristic of the platyhelminthes, allow us to distinguish two types of spermatozoa among cestodes: --The "two-axonemes"-type is considered as primitive as it has also been found in the free-living platyhelminths. This type has been observed in the Pseudophyllidea, Proteocephalidea, Tetrarhynchidea and Tetraphyllidea (Onchobothriidae). --The "one-axoneme"-type has been found in the Cyclophyllidea, Caryophyllaeidea, Diphyllidea and Tetraphyllidea (Phyllobothriidae). It has been proved that the one axoneme type of the spermatozoon, observed in Tetraphyllidea, Phyllobothriidae arises from the two axoneme type by early abortion of the second axoneme. In all the tetraphyllidean species studied so far, we found an helicoidal body forming so-called "crested body" or "spiral crest" at the proximal end of the spermatozoon, which is opposite to the nuclear part. This division of the cestodes into two groups, according to the number of axonemes in the spermatozoon is compared with the phylogenetic diagrammes of Cestoda proposed by Freeman (1973) and Euzet (1974). As result, two hypothesis can be forwarded to explain the relationships between the Tetraphyllidea, Proteocephalidea and Cyclophyllidea. The importance of data on the cestode spermatozoa as a criterion in analysis of cestode phylogenesis is drawn and discussed.}, }
@article {pmid6941740, year = {1981}, author = {Dayhoff, MO and Schwartz, RM}, title = {Evidence on the origin of eukaryotic mitochondria from protein and nucleic acid sequences.}, journal = {Annals of the New York Academy of Sciences}, volume = {361}, number = {}, pages = {92-104}, doi = {10.1111/j.1749-6632.1981.tb46513.x}, pmid = {6941740}, issn = {0077-8923}, support = {GM-08710/GM/NIGMS NIH HHS/United States ; RR-05681/RR/NCRR NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; Base Sequence ; *Biological Evolution ; *Cells ; Chloroplasts ; *Eukaryotic Cells ; *Mitochondria ; Phylogeny ; Symbiosis ; }, }
@article {pmid6941720, year = {1981}, author = {Gillham, NW and Boynton, JE}, title = {Evolution of organelle genomes and protein-synthesizing systems.}, journal = {Annals of the New York Academy of Sciences}, volume = {361}, number = {}, pages = {20-43}, doi = {10.1111/j.1749-6632.1981.tb46509.x}, pmid = {6941720}, issn = {0077-8923}, support = {GM-19427/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Evolution ; Chloroplasts ; DNA, Mitochondrial ; *Genes ; Mitochondria ; *Organoids ; Phylogeny ; Protein Biosynthesis ; RNA, Ribosomal ; *Ribosomes ; }, }
@article {pmid6941718, year = {1981}, author = {Schiff, JA}, title = {Origin and evolution of the plastid and its function.}, journal = {Annals of the New York Academy of Sciences}, volume = {361}, number = {}, pages = {166-192}, pmid = {6941718}, issn = {0077-8923}, mesh = {*Biological Evolution ; Light ; Mitochondria ; *Organoids/physiology ; Photosynthesis ; Pigmentation ; }, }
@article {pmid6941714, year = {1981}, author = {Locker, J and Synenki, RM and Merten, S and Rabinowitz, M}, title = {Eukaryotic features of mitochondiral transcription and gene structure in yeast.}, journal = {Annals of the New York Academy of Sciences}, volume = {361}, number = {}, pages = {105-118}, pmid = {6941714}, issn = {0077-8923}, support = {HL-04442/HL/NHLBI NIH HHS/United States ; HL-09172/HL/NHLBI NIH HHS/United States ; }, mesh = {Biological Evolution ; Chromosome Mapping ; Genes ; *Mitochondria ; *Transcription, Genetic ; Yeasts/*genetics ; }, }
@article {pmid6801266, year = {1981}, author = {Jukes, TH}, title = {Amino acid codes in mitochondria as possible clues to primitive codes.}, journal = {Journal of molecular evolution}, volume = {18}, number = {1}, pages = {15-17}, pmid = {6801266}, issn = {0022-2844}, mesh = {Amino Acids/metabolism ; Anticodon/physiology ; Base Sequence ; *Biological Evolution ; *DNA, Mitochondrial ; *Genetic Code ; Humans ; Leucine/metabolism ; Neurospora/genetics ; RNA, Transfer/physiology ; Threonine/metabolism ; Yeasts/genetics ; }, abstract = {Differences between mitochondrial codes and the universal code indicate that an evolutionary simplification has taken place, rather than a return to a more primitive code. However, these differences make it evident that the universal code is not the only code possible, and therefore earlier codes may have differed markedly from the previous code. The present universal code is probably a "frozen accident." The change in CUN codons from leucine to threonine (Neurospora vs. yeast mitochondria) indicates that neutral or near-neutral changes occurred in the corresponding proteins when this code change took change took place, caused presumably by a mutation in a tRNA gene.}, }
@article {pmid6268221, year = {1981}, author = {Harris, DA}, title = {The coupling ATPase complex: an evolutionary view.}, journal = {Bio Systems}, volume = {14}, number = {1}, pages = {113-121}, doi = {10.1016/0303-2647(81)90026-5}, pmid = {6268221}, issn = {0303-2647}, mesh = {Adenosine Triphosphatases/*metabolism ; Amino Acid Sequence ; Bacteria/metabolism ; *Biological Evolution ; Energy Metabolism ; Ion Channels/metabolism ; Mitochondria/metabolism ; Oxidative Phosphorylation Coupling Factors/*metabolism ; Proton-Translocating ATPases/*metabolism ; Saccharomyces cerevisiae/enzymology ; }, abstract = {Phospholipid micelles and vesicles, present in the primordial soup, formed both primitive (surface) catalyst and primitive replicative life forms. With the adoption of a common energy source, ATP, integrated biochemical systems within these vesicles became possible - cells. Fermentation within these primitive cells was favoured by the evolution, first of ion channels allowing protons to leak out, and then of an active ATP-driven pump. In the prokaryotic/mitochondria/chloroplast line, the proton channel was such as to be blocked by dicyclohexylcarbodiimide and the adenosine 5' triphosphate phosphohydrolase (ATPase) by 4-chloro 7-nitrobenzofurazan (Nbf-C1). The ATPase was initially simple (4 subunits) but later, possibly concomitant with its evolution to an ATP synthetase, became more complex (8 subunits). One of the steps in evolution probably involved gene duplication and divergence of 2 subunits (alpha and beta) from the largest of the ATPase subunits. From this stage, the general form of the ATPase was fixed, although sensitivity to, for example, oligomycin involved later, after divergence of the mitochondrial and chloroplast lines. A regulatory protein, the ATPase inhibitor, is found associated with a wide spectrum of coupling ATPases.}, }
@article {pmid6264827, year = {1981}, author = {Whatley, FR}, title = {The establishment of mitochondria: Paracoccus and Rhodopseudomonas.}, journal = {Annals of the New York Academy of Sciences}, volume = {361}, number = {}, pages = {330-340}, doi = {10.1111/j.1749-6632.1981.tb46529.x}, pmid = {6264827}, issn = {0077-8923}, mesh = {Biological Evolution ; Cytochrome c Group/metabolism ; Electron Transport ; *Mitochondria/metabolism ; *Paracoccus/metabolism ; *Rhodobacter sphaeroides/metabolism ; *Symbiosis ; }, abstract = {Many aerobic bacteria (both facultative and obligate) possess a number of those biochemical features of mitochondria which are concerned with energy metabolism. However, only restricted number, notably Paracoccus denitrificans and Rhodopseudomonas spheroides, have the majority of these features. The theory of endosymbiosis proposes that a primitive eukaryote took up bacteria to yield mitochondria. The present-day Paracoccus then resembles the ancestral bacterium in many respects the primitive amoeba, Pelomyxa palustris, which lacks mitochondria but contains a permanent population of unique symbiotic bacteria, has many of the characteristics of a present-day transitional form. The evolution of mitochondria from endosymbiotic bacteria would involve their integration with the host cell both biochemically and structurally: a number of the intermediate steps are discussed. Attention is drawn to the existence in some ciliates of hydrogenosomes, which function as anaerobic mitochondria.}, }
@article {pmid6166147, year = {1981}, author = {Nguyen-Legros, J and Cesaro, P and Gay, M and Pollin, B}, title = {[Evolution of the storage site of iron-dextran after retrograde axonal transport in the rat central nervous system (author's transl)].}, journal = {Acta neuropathologica}, volume = {54}, number = {2}, pages = {101-112}, pmid = {6166147}, issn = {0001-6322}, mesh = {Animals ; Axonal Transport ; Brain/*metabolism ; Endocytosis ; Iron/analysis ; Iron-Dextran Complex/*metabolism ; Mitochondria/analysis ; Neuroglia/metabolism ; Neurons/metabolism ; Rats ; Time Factors ; }, abstract = {The uptake, transport, and storage of an iron-dextran complex (used as a neuroanatomical tracer in the nigrostriatal pathway of rat) by neurons of the CNS is described. The complex is taken up by endocytosis and transported by lysosomes. Some iron-containing mitochondria are observed within the nigral cell bodies. The neuronal labelling remains for 10 days. Thereafter, the iron labelling of neurons decreases. No important neuronal degeneration is observed as a result of iron toxicity. The iron lost by neurons is taken up by glial cells. It is converted into ferritin and increases the intracerebral endogenous iron content.}, }
@article {pmid6253835, year = {1980}, author = {Macino, G and Scazzocchio, C and Waring, RB and Berks, MM and Davies, RW}, title = {Conservation and rearrangement of mitochondrial structural gene sequences.}, journal = {Nature}, volume = {288}, number = {5789}, pages = {404-406}, doi = {10.1038/288404a0}, pmid = {6253835}, issn = {0028-0836}, mesh = {Adenosine Triphosphatases/genetics ; Aspergillus nidulans/*genetics ; Biological Evolution ; DNA, Mitochondrial/*genetics ; Electron Transport Complex IV/genetics ; *Genes ; Nucleic Acid Hybridization ; Saccharomyces cerevisiae/genetics ; }, abstract = {Mitochondria contain the simplest DNA molecules that are present in eukaryotes. Mitochondrial DNA (mtDNA) is easily purified, and is an important model system for studying eukaryote gene structure and basic molecular processes. The protein sequences of mitochondrial gene products have been shown to be conserved from yeast to man, and there are definite similarities at the DNA sequence level. In contrast, the overall organization of the mitochondrial genome is drastically different in these organisms. To understand this, we need to extend work on mtDNA to a wider range of species. We have chosen to study the mtDNA of Aspergillus nidulans because a particularly comprehensive analysis of this system can be achieved using genetics as well as biochemistry, and like most eukaryotes it is an obligate aerobe, whereas Saccharomyces cerevisiae is not. We have investigated whether defined pieces of particular yeast mitochondrial genes show enough homology to Aspergillus mtDNA fragments to enable the corresponding Aspergillus genes to be located on the physical map. The results reported here show that this is the case for all five genes tested, and present the first data on the physical organization of the structural genes in the mitochondrial genome of A. nidulans.}, }
@article {pmid7435541, year = {1980}, author = {Reynolds, ES and Moslen, MT and Boor, PJ and Jaeger, RJ}, title = {1,1-Dichloroethylene hepatotoxicity. Time course of GSH changes and biochemical aberrations.}, journal = {The American journal of pathology}, volume = {101}, number = {2}, pages = {331-344}, pmid = {7435541}, issn = {0002-9440}, support = {AM-19814/AM/NIADDK NIH HHS/United States ; ES-00002/ES/NIEHS NIH HHS/United States ; }, mesh = {Chemical and Drug Induced Liver Injury/*etiology ; Dichloroethylenes/metabolism/*toxicity ; Endoplasmic Reticulum/enzymology ; Glutathione/*metabolism ; Hydrocarbons, Chlorinated/*toxicity ; L-Iditol 2-Dehydrogenase/blood ; Liver/*drug effects/pathology ; Mitochondria, Liver/metabolism ; Mixed Function Oxygenases/metabolism ; }, abstract = {Exposure of fasted rats to 200 ppm 1,1-dichloroethylene (1,1-DCE) for 1-4 hours resulted in striking aberrations in hepatic Na, K, Ca, and GSH levels which preceded and/or accompanied catastrophic histologic alterations of the liver. Na levels began to rise during the first hour, and preceded the morphologically apparent injury. Ca levels increased markedly and K levels declined between the second and fourth hour of exposure, and accompanied the catastrophic morphologic alterations. GSH levels were rapidly depleted but began to recover before the end of the exposure to 1,1-DCE. Functions of components of the mixed-function oxidase system of the liver endoplasmic reticulum were not appreciably affected early in the course of 1,1-DCE exposure; but after injury became massive, cytochrome P-450 and oxidative N-demethylase were deactivated. Thus effects on the functional components of the endoplasmic reticulum mixed-function oxidase system do not appear to be primary events in 1,1-DCE cytotoxicity. In contrast, there were progressive declines in mitochondrial K and marked imbalances in mitochondrial Na, Zn, and Mg preceding the massive influx of Ca into the cell, indicating that mitochondria are involved early in he evolution of injurious molecular events elicited by this potent hepatotoxin.}, }
@article {pmid6778858, year = {1980}, author = {Hayasaka, K and Kochi, H and Hiraga, K and Kikuchi, G}, title = {Purification and properties of glycine decarboxylase, a component of the glycine cleavage system, from rat liver mitochondria and immunochemical comparison of this enzyme from various sources.}, journal = {Journal of biochemistry}, volume = {88}, number = {4}, pages = {1193-1199}, doi = {10.1093/oxfordjournals.jbchem.a133074}, pmid = {6778858}, issn = {0021-924X}, mesh = {Amino Acid Oxidoreductases/isolation &amp; purification/*metabolism ; Animals ; Cross Reactions ; Glycine/isolation &amp; purification/metabolism ; Glycine Decarboxylase Complex H-Protein ; Glycine Dehydrogenase (Decarboxylating) ; Humans ; Immunodiffusion ; Kinetics ; Macromolecular Substances ; Male ; Mitochondria, Liver/*enzymology ; Molecular Weight ; Rats ; Species Specificity ; }, abstract = {Glycine decarboxylase, tentatively called P-protein as a constituent of the glycine cleavage system, was purified to near homogeneity from rat liver mitochondria. The purified P-protein was a homodimer with a molecular weight of about 210,000, consisting of identical subunits with a molecular weight of 105,000. In the exchange reaction of the carboxyl carbon of glycine wih CO2 catalyzed by the purified P-protein in the presence of H-protein, the pH optimum was 6.7, Km for glycine was 6.6 mM, and Km for H-protein was 7.4 microM. A specific rabbit antibody against the purified rat liver P-protein was prepared. Ouchterlony double diffusion analysis and immunoinhibition experiments using this antibody revealed immunological cross-reactivity among the P-proteins from various species of animals such as carp, frog, snake, chicken, bovine, and human, suggesting a quite conservative evolution of the glycine cleavage system.}, }
@article {pmid6450888, year = {1980}, author = {Laky, D and Constantinescu, S and Filipescu, G and Ratea, E and Constantinescu, NM and Hălălău, F}, title = {Experimental investigations in prolonged myocardial ischaemia. Note II. Biology of the myocardial fiber during permanent ischaemia.}, journal = {Morphologie et embryologie}, volume = {26}, number = {4}, pages = {365-370}, pmid = {6450888}, issn = {0377-5038}, mesh = {Animals ; Cell Nucleus/pathology ; Cytoskeleton/pathology ; Dogs ; Hydrolases/metabolism ; Mitochondria, Heart/pathology ; Myocardial Infarction/*pathology ; Myocardium/enzymology/*pathology ; Oxidoreductases/metabolism ; Sarcolemma/pathology ; Sarcoplasmic Reticulum/pathology ; }, abstract = {The dynamics of morphologic and biochemical lesions of the myocardial fiber during the first ten days after an experimental myocardial infarction showed an unequal evolution of the lesional picture in the ischaemic area, the intervention of lysosomal hydrolases and the reactions of inflammatory fibrocollagen substitution. Morphologic aspects in the areas neighbouring the infarction and other myocardial areas are discussed.}, }
@article {pmid6450884, year = {1980}, author = {Eskenasy, A and Mangiulea, V}, title = {Ultrastructure of a bronchial mucoepidermoid tumour of a seven-year-old boy.}, journal = {Morphologie et embryologie}, volume = {26}, number = {4}, pages = {335-340}, pmid = {6450884}, issn = {0377-5038}, mesh = {Bronchial Neoplasms/*ultrastructure ; Carcinoma/*ultrastructure ; Cell Nucleus/ultrastructure ; Child ; Cytoplasmic Granules/ultrastructure ; Desmosomes/ultrastructure ; Endoplasmic Reticulum/ultrastructure ; Glycosaminoglycans/analysis ; Golgi Apparatus/ultrastructure ; Humans ; Male ; Mitochondria/ultrastructure ; }, abstract = {A bronchial mucoepidermoid tumour of a 7-year-old boy was histopathologically and electronmicroscopically studied. The light microscopy revealed an epidermoid structure in whose cells an intracellular and extracellular accumulation of acid mucopolysaccharides occurred. The origin of this transformation seems to be located within the cells of a glandular duct. Electron microscopy pointed out the main characteristics of epidermoid cells (tonofibrils, cellular junctions of desmosomal type) and the secretory transformation by the large development of polyribosomes, of the rough endoplasmic reticulum and of dilated cisternae filled with the secretory product. The prolonged evolution with repeated obstructive pneumonitides, the proliferation after partial endoscopic resection, the absence of mitoses and invasion, as well as the late evolution of the case, suggested the semi-malignancy of this tumour and the impossibility of its consideration as a mucoepidermoid carcinoma. The hypothesis of a unique class of tumours with different secretory possibility including carcinoids, cylindromas (adenocystic tumours) and mucoepidermoid tumours is sustainable.}, }
@article {pmid6777503, year = {1980}, author = {Alahiotis, SN}, title = {Adaptation of Drosophila enzymes to temperature. III. Evolutionary conservation in mitochondrial enzymes.}, journal = {Journal of molecular evolution}, volume = {16}, number = {1}, pages = {37-46}, pmid = {6777503}, issn = {0022-2844}, mesh = {Animals ; *Biological Evolution ; Climate ; Cytosol/enzymology ; Drosophila/*enzymology ; Glycerolphosphate Dehydrogenase/*metabolism ; Kinetics ; Malate Dehydrogenase/*metabolism ; Mitochondria/*enzymology ; Temperature ; }, abstract = {The evolutionary behavior of two mitochondrial enzymnes (L-glycerol 3-phosphate:cytochrome c oxidoreductase E.C.1.1.1.95, alpha GPO, and L-malate: NAD+ oxidoreductase, E.C.1.1.1.37, m-MDH) obtained from several temperate and tropical Drosophila species was examined by comparing their catalytic properties, which related to temperature (Km-Ea-Q10-Thermostability). Mitochondrial alpha GPO or m-MDH obtained either from template or from tropical species was found to exhibit similar catalytic properties while for both cytosolic enzymes, the alpha GPDH and s-MDH, Km patterns were similar among species from the same thermal habitat and different thermal habitats. In combination with other observations reported in the literature these facts support the view that the function, and probably the structure, of mitochondrial enzymes are better conserved in evolution than those of the corresponding enzymes found in the cytosol. It is proposed that the relative invariance of the mitochondrial enzymes structure is probably linked to a necessary relative invariance of molecular interactions inside the mitochondrion.}, }
@article {pmid6157106, year = {1980}, author = {Eperon, IC and Anderson, S and Nierlich, DP}, title = {Distinctive sequence of human mitochondrial ribosomal RNA genes.}, journal = {Nature}, volume = {286}, number = {5772}, pages = {460-467}, doi = {10.1038/286460a0}, pmid = {6157106}, issn = {0028-0836}, mesh = {Base Sequence ; Biological Evolution ; Chromosome Mapping ; DNA, Mitochondrial/*genetics ; Genes ; Humans ; Molecular Weight ; RNA, Bacterial/genetics ; RNA, Ribosomal/*genetics ; RNA, Transfer/*genetics ; }, abstract = {The nucleotide sequence spanning the ribosomal RNA (rRNA) genes of cloned human mitochondrial DNA reveals an extremely compact genome organization wherein the putative tRNA genes are probably 'butt-jointed' around the two rRNA genes. The sequences of the rRNA genes are significantly homologous in some regions to eukaryotic and prokaryotic sequences, but distinctive; the tRNA genes also have unusual nucleotide sequences. It seems that human mitochondria did not originate from recognizable relatives of present day organisms.}, }
@article {pmid6453291, year = {1980}, author = {Eskenasy, A}, title = {Bronchiolar pathology. II. Light and electron microscopical changes of bronchiolar epithelial cells in rabbits repeatedly injected intratracheally with a detergent solution.}, journal = {Morphologie et embryologie}, volume = {26}, number = {3}, pages = {279-284}, pmid = {6453291}, issn = {0377-5038}, mesh = {Animals ; Bronchi/*drug effects/pathology/ultrastructure ; Bronchial Diseases/*chemically induced ; Detergents/administration &amp; dosage/*adverse effects ; Epithelium/pathology ; Fatty Alcohols/*adverse effects ; Microscopy, Electron ; Necrosis ; Rabbits ; Surface-Active Agents/*adverse effects ; }, abstract = {Intratracheal administration in rabbits of a detergent solution (Blue Perlan) determined the progressive swelling of bronchiolar epithelial cells, mainly of non-ciliated secretory ones, with hypertrophy of cytoplasms, frequent bleb ruptures and partial cell necroses. Mucoprotein synthesis was not enhanced. Ultrastructurally, the non-ciliated Clara cells were predominating; their cytoplasms were hypertrophied, prominent in bronchiolar lumina, and contained a few mitochondria and numerous dark-stained secretory granules with a thin membrane; glycogen was present in cytosol, and the apical zones of cytoplasms were locally balloonized; nuclei were chromatin-monomorphous and had an evident membrane. Disrupted blebs presented the same granules and glycogen-rich structure as the cytoplasms. Intermingled ciliated cells presented small mitochondria, sometimes modified, and some secretory granules; cilia and basal corpuscles were rarely damaged. Some microvilli intermingled among cilia, but they were extremely rare in non-ciliated secretory hypertrophied cells. Some tight junctions were observed between bronchiolar cell cytoplasms. The evolution to partial necrotizing bronchiolitis was obvious mainly after the third intratracheal injection of the detergent solution.}, }
@article {pmid6997870, year = {1980}, author = {Bonitz, SG and Berlani, R and Coruzzi, G and Li, M and Macino, G and Nobrega, FG and Nobrega, MP and Thalenfeld, BE and Tzagoloff, A}, title = {Codon recognition rules in yeast mitochondria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {77}, number = {6}, pages = {3167-3170}, pmid = {6997870}, issn = {0027-8424}, mesh = {Anticodon/*genetics ; Base Sequence ; Biological Evolution ; Chromosome Mapping ; Codon/*genetics ; DNA, Fungal ; DNA, Mitochondrial/*genetics ; *Genetic Code ; *Mitochondria ; RNA, Messenger/*genetics ; RNA, Transfer/*genetics ; Saccharomyces cerevisiae/*genetics ; }, abstract = {The mitochondrial genome of Saccharomyces cerevisiae codes for 24 tRNAs. The nucleotide sequences of the tRNA genes suggest a unique set of rules that govern the decoding of the mitochondrial genetic code. The four codons of unmixed fmilies are recognized by single tRNAs that always have a U in the wobble position of the anticodon. The codons of the mixed families are read by two different tRNAs. Codons terminating in a C or U are recognized by tRNAs with a G and codons terminating in a G or A are recognized by tRNAs with a U in the corresponding positions of the anticodons. There are two exceptions to these rules. In the AUN family for isoleucine and methionine, the isoleucine tRNA has a G and the methionine tRNA has a C in the wobble position. The tRNA for the arginine CGN family also has an A in the wobble position of the anticodon. It is of interest that the CGN codons have not been found in the mitochondrial genes sequenced to date. The simplified decoding system of yeast mitochondria allows all the codons to be recognized by only 24 tRNAs.}, }
@article {pmid6932013, year = {1980}, author = {Barrell, BG and Anderson, S and Bankier, AT and de Bruijn, MH and Chen, E and Coulson, AR and Drouin, J and Eperon, IC and Nierlich, DP and Roe, BA and Sanger, F and Schreier, PH and Smith, AJ and Staden, R and Young, IG}, title = {Different pattern of codon recognition by mammalian mitochondrial tRNAs.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {77}, number = {6}, pages = {3164-3166}, pmid = {6932013}, issn = {0027-8424}, mesh = {Animals ; Anticodon/*genetics ; Base Sequence ; Biological Evolution ; Cattle ; Codon/*genetics ; Computers ; DNA, Mitochondrial/analysis/*genetics ; *Genetic Code ; Humans ; Mammals/genetics ; Mitochondria ; RNA, Messenger/*genetics ; RNA, Transfer/*genetics ; Uridine/analogs &amp; derivatives ; }, abstract = {Analysis of an almost complete mammalian mitochondrial DNA sequence has identified 23 possible tRNA genes and we speculate here that these are sufficient to translate all the codons of the mitochondrial genetic code. This number is much smaller than the minimum of 31 required by the wobble hypothesis. For each of the eight genetic code boxes with four codons for one amino acid we find a single specific tRNA gene with T in the first (wobble) position of the anticodon. We suggest that these tRNAs with U in the wobble position can recognize all four codons in these genetic code boxes either by a "two out of three" base interaction or by U.N wobble.}, }
@article {pmid6446335, year = {1980}, author = {Gurevich, VS and Tkachenko, EI and Kulikova, OG}, title = {[Role of calcium ions in the evolution of the anticonvulsant effect of taurine].}, journal = {Biulleten' eksperimental'noi biologii i meditsiny}, volume = {89}, number = {4}, pages = {418-420}, pmid = {6446335}, issn = {0365-9615}, mesh = {Animals ; Anticonvulsants/*pharmacology ; Calcium/*metabolism ; Calcium-Transporting ATPases/*antagonists &amp; inhibitors ; Cerebral Cortex/*drug effects/enzymology/metabolism ; Magnesium/pharmacology ; Male ; Microsomes/metabolism ; Mitochondria/metabolism ; Penicillin G ; Rabbits ; Rats ; Seizures/chemically induced/drug therapy ; Species Specificity ; Taurine/*pharmacology/therapeutic use ; }, abstract = {The decreased microsomal Ca++Mg++ATPase activity and lowered level of Ca++ binding by the brain cortex microsomes in seizure prone rats as compared with normal animals have been revealed. Taurine increases these parameters in experiments in vitro. Injection of taurine into the penicillin-provoked epileptogenic focus prevents the seizure reaction in rabbits. This effect is not observed after injection of taurine together with EGTA. The data obtained demonstrate the important role of calcium ions in the anticonvulsant action of taurine.}, }
@article {pmid6446035, year = {1980}, author = {Laky, D and Constantinescu, S and Filipescu, G and Constantinescu, NM and Ratea, E and Hâlâlâu, F}, title = {Experimental investigations in prolonged myocardial ischaemia. Note I. Biology of the myocardial fiber after transient myocardial fiber after transient myocardial ischaemia.}, journal = {Morphologie et embryologie}, volume = {26}, number = {2}, pages = {173-177}, pmid = {6446035}, issn = {0377-5038}, mesh = {Angina Pectoris/*pathology ; Animals ; Cardiomyopathies/*pathology ; Dogs ; Hydrolases/analysis ; Ischemia ; Lysosomes/enzymology ; Mitochondria, Heart/pathology ; Myocardial Infarction/*pathology ; Myocardium/*pathology ; }, abstract = {The first ten days' evolution of post-ischaemic lesions of the premonitory or angina pectoris syndrome type was experimentally studied by the challenge of a short-term (10 and 15 min) ischaemia, of an adaptation to ischaemia and an adaptation followed by prolonged ischaemia (20 and 35 min). Worthy of note was the persistence of reversible lesions after short-term ischaemia and adaptation, and the progressive evolution towards cytolysis and cicatrization of some pancicellular foci after adaptation followed by prolonged ischaemia. The role of mitochondrial lesions, of lysosomal hydrolases, the inefficiency of renewed circulation, as well as problems of diagnosis are discussed.}, }
@article {pmid6929499, year = {1980}, author = {Blobel, G}, title = {Intracellular protein topogenesis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {77}, number = {3}, pages = {1496-1500}, pmid = {6929499}, issn = {0027-8424}, mesh = {Animals ; Biological Transport ; Cell Compartmentation ; Cell Membrane/metabolism ; Endoplasmic Reticulum/metabolism ; Humans ; Intracellular Membranes/metabolism ; Membrane Proteins/*metabolism ; Microbodies/metabolism ; Mitochondria/metabolism ; Protein Biosynthesis ; Proteins/*metabolism ; Ribosomes/metabolism ; }, abstract = {Concurrently with or shortly after their synthesis on ribosomes, numerous specific proteins are unidirectionally translocated across or asymmetrically integrated into distinct cellular membranes. Thereafter, subpopulations of these proteins need to be sorted from each other and routed for export or targeted to other intracellular membranes or compartments. It is hypothesized here that the information for these processes, termed "protein topogenesis," is encoded in discrete "topogenic" sequences that constitute a permanent or transient part of the polypeptide chain. The repertoire of distinct topogenic sequences is predicted to be relatively small because many different proteins would be topologically equivalent-i.e., targeted to the same intracellular address. The information content of topogenic sequences would be decoded and processed by distinct effectors. Four types of topogenic sequences could be distinguished: signal sequences, stop-transfer sequences, sorting sequences, and insertion sequences. Signal sequences initiate translocation of proteins across specific membranes. They would be decoded and processed by protein translocators that, by virtue of their signal sequence-specific domain and their unique location in distinct cellular membranes, effect unidirectional translocation of proteins across specific cellular membranes. Stop-transfer sequences interrupt the translocation process that was previously initiated by a signal sequence and, by excluding a distinct segment of the polypeptide chain from translocation, yield asymmetric integration of proteins into translocation-competent membranes. Sorting sequences would act as determinants for posttranslocational traffic of subpopulations of proteins, originating in translocation-competent donor membranes (and compartments) and going to translocation-incompetent receiver membranes (and compartments). Finally, insertion sequences initiate unilateral integration of proteins into the lipid bilayer without the mediation of a distinct protein effector. Examples are given for topogenic sequences, either alone or in combination, to provide the information for the location of proteins in any of the intracellular compartments or for the asymmetric orientation of proteins and their location in any of the cellular membranes. Proposals are made concerning the evolution of topogenic sequences and the relationship of protein topogenesis to the precellular evolution of membranes and compartments.}, }
@article {pmid6767883, year = {1980}, author = {Carlin, RK}, title = {Poly(A): a new evolutionary probe.}, journal = {Journal of theoretical biology}, volume = {82}, number = {3}, pages = {353-362}, doi = {10.1016/0022-5193(80)90242-8}, pmid = {6767883}, issn = {0022-5193}, mesh = {Animals ; *Biological Evolution ; Euglena gracilis/metabolism ; Humans ; Mitochondria/metabolism ; Origin of Life ; Plants/metabolism ; Poly A/*biosynthesis ; RNA, Messenger/metabolism ; }, }
@article {pmid7377628, year = {1980}, author = {Rohde, K}, title = {Some aspects of the ultrastructure of Gotocotyla secunda and Hexostoma euthynni.}, journal = {Angewandte Parasitologie}, volume = {21}, number = {1}, pages = {32-48}, pmid = {7377628}, issn = {0003-3162}, mesh = {Animals ; Cecum/ultrastructure ; Cell Nucleus/ultrastructure ; Cilia/ultrastructure ; Endoplasmic Reticulum/ultrastructure ; Golgi Apparatus/ultrastructure ; Male ; Membranes/ultrastructure ; Microscopy, Electron ; Mitochondria/ultrastructure ; Organoids/ultrastructure ; Phylogeny ; Spermatozoa/ultrastructure ; Trematoda/*ultrastructure ; }, abstract = {The ultrastructure of the spermatozoon, the protonephridia, the intestine and the tegument of Gotocotyla secunda (Monogenea, Gotocotylidae) and of the intestine of Hexostoma euthynni (Monogenea, Hexostomatidae) is described. The "connecting cells" in the intestine of at least some Monogenea show secretory activity and are possibly involved in extracellular digestion. Sloughing of whole haematin cells appears to be common and may be an important component in the digestive process. Flame cells appear to be a very conservative element and their more or less identical structure in all major groups of parasitic platyhelminths indicates that parasitic platyhelminths have originated from one or a few closely related groups of freeliving Turbellaria with the same type of flame cell.}, }
@article {pmid6892690, year = {1980}, author = {Fishbein, MC and Hare, CA and Gissen, SA and Spadaro, J and Maclean, D and Maroko, PR}, title = {Identification and quantification of histochemical border zones during the evolution of myocardial infarction in the rat.}, journal = {Cardiovascular research}, volume = {14}, number = {1}, pages = {41-49}, doi = {10.1093/cvr/14.1.41}, pmid = {6892690}, issn = {0008-6363}, mesh = {Animals ; Dihydrolipoamide Dehydrogenase/metabolism ; Glycogen/metabolism ; Histocytochemistry ; Lipid Metabolism ; Male ; Mitochondria, Heart/enzymology ; Myocardial Infarction/*metabolism/pathology ; Myocardium/*metabolism/pathology ; Rats ; Succinate Dehydrogenase/metabolism ; Time Factors ; }, }
@article {pmid6453255, year = {1980}, author = {Wilson, TH and Lin, EC}, title = {Evolution of membrane bioenergetics.}, journal = {Journal of supramolecular structure}, volume = {13}, number = {4}, pages = {421-446}, doi = {10.1002/jss.400130403}, pmid = {6453255}, issn = {0091-7419}, support = {AM-05736/AM/NIADDK NIH HHS/United States ; GM-11983/GM/NIGMS NIH HHS/United States ; }, mesh = {Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Bacteria/metabolism ; *Biological Evolution ; Biological Transport ; Cell Membrane/*metabolism ; DNA/metabolism ; Energy Metabolism ; Hydrogen-Ion Concentration ; Mitochondria/metabolism ; Oxidation-Reduction ; Photosynthesis ; Plants/metabolism ; Potassium/metabolism ; Sodium/metabolism ; Vertebrates ; }, abstract = {One of the first problems encountered by primitive cells was that of volume regulation; the continuous entry of ions, (eg, NaCl) and water in response to the internal colloid osmotic pressure threatening to destroy the cell by lysis. We propose that to meet this environmental challenge cells evolved an ATP-driven proton extrusion system plus a membrane carrier that would exchange external protons with internal Na+. With the appearance of the ability to generate proton gradients, additional mechanisms to harness this source of energy emerged. These would include proton-nutrient cotransport, K+ accumulation, nucleic acid entry, and motility. A more efficient system for the uptake of certain carbohydrates by vectorial phosphorylation via the PEP-phosphotransferase system probably appeared rather early in the evolution of anaerobic bacteria. The reversal of the proton-ATPase reaction to give net ATP synthesis became possible with the development of other types of efficient proton transporting machinery. Either light-driven bacterial rhodopsin or a redox system coupled to proton translocation would have served this function. Oxidation of one substrate coupled to the reduction of another substrate by membrane-bound enzymes evolved in such a manner that protons were extruded from the cell during the reaction. The progressive elaboration of this type of redox proton pump permitted the use of exogenous electron acceptors, such as fumarate, sulfate, and nitrate. The stepwise growth of these electron transport chains required the accretion of several flavoproteins, iron-sulfur proteins, quinones, and cytochromes. With modifications of these four basic components a chlorophyll-dependent photosynthetic system was subsequently evolved. The oxygen that was generated by this photosynthetic system from water would eventually accumulate in the atmosphere of the earth. With molecular oxygen present, the emergence of cytochrome oxidase would complete the respiratory chain. The proton economy of membrane energetics has been retained by most present-day microorganisms, mitochondria, chloroplasts, and cells of higher plants. A secondary use of the energy stored as an electrochemical difference of Na+ for powering membrane events probably also evolved in microorganisms. The exclusive age of the Na+ economy is distinctive of the plasma membrane of animal cells; the Na+-K+ ATPase sets up an electrochemical Na+ gradient that provides the energy for osmoregulation, Na+-nutrient co-transport, and the action potential of excitable cells.}, }
@article {pmid6261528, year = {1980}, author = {Del Maestro, RF}, title = {An approach to free radicals in medicine and biology.}, journal = {Acta physiologica Scandinavica. Supplementum}, volume = {492}, number = {}, pages = {153-168}, pmid = {6261528}, issn = {0302-2994}, mesh = {Animals ; *Biological Evolution ; Catalase/metabolism ; Disease/*physiopathology ; *Free Radicals ; Humans ; Hydrogen Peroxide ; Inflammation/metabolism ; Ischemia/physiopathology ; Membranes/metabolism ; Mitochondria/metabolism ; *Oxygen ; Radiation Injuries/physiopathology ; Superoxide Dismutase/metabolism ; Superoxides/metabolism ; }, abstract = {Evolutionary pressure induced by the release of O2 into the environment has necessitated the development of a group of mechanisms to deal with the toxic free radical byproducts of oxidative metabolism. The complete reduction of O2 to H2O2 involves the addition of four electrons which can occur univalently resulting in a series of toxic intermediates or quadrivalently by the mitochondrial cytochrome oxidase system, which avoids these reactive intermediates. Free radical mechanisms have been associated with a large number of disease states including inflammation, irradiation-induced injury and ischemia. The site of free radical generation, that is whether the generation of radical species is predominantly extracellular or intracellular, may determine to a degree, the types of macromolecular and cellular damage which result. A classification of diseases in which radical generating processes may play a role is presented in the hope that it may aid in the understanding and treatment of these diseases.}, }
@article {pmid6249412, year = {1980}, author = {Kulaev, IS and Mansurova, SE and Burlakova, EB and Dukhovich, VF}, title = {Why ATP instead of pyrophosphate? Interrelation between ATP and pyrophosphate production during evolution and in contemporary organisms.}, journal = {Bio Systems}, volume = {12}, number = {3-4}, pages = {177-180}, doi = {10.1016/0303-2647(80)90015-5}, pmid = {6249412}, issn = {0303-2647}, mesh = {*Adenosine Triphosphate ; Animals ; *Biological Evolution ; *Diphosphates ; Intracellular Membranes/metabolism ; Mitochondria, Liver/metabolism ; Oxidative Phosphorylation ; Phosphorylation ; Rats ; }, }
@article {pmid6110267, year = {1980}, author = {Kraus, B and Cain, H}, title = {Giant mitochondria in the human myocardium--morphogenesis and fate.}, journal = {Virchows Archiv. B, Cell pathology including molecular pathology}, volume = {33}, number = {1}, pages = {77-89}, doi = {10.1007/BF02899172}, pmid = {6110267}, issn = {0340-6075}, mesh = {Autophagy ; Biopsy ; Glycogen/analysis ; Heart Failure/pathology ; Humans ; Male ; Microscopy, Electron ; Middle Aged ; Mitochondria, Heart/analysis/*ultrastructure ; Myocardium/pathology ; }, abstract = {Electron-microscopical examination of myocardial biopsy material obtained from a 58-year-old man revealed giant mitochondria having a length of 30 micron. Such giant mitochondria (also called megamitochondria) evolve by fusion of the membranes of numerous large individual organelles. Initially they are polymorphous and of diverse shapes, but later they are seen to be arranged among and parallel with the filaments of the myocardial fibres, where they present a smooth, cigar-like appearance. Deposits of glycogen in the giant mitochondria result from the accidental inclusion of glycogen granules during fusion. The abundance of cristae, which often form dense stacks in the megamitochondria, is evidence for the genuine synthesis of new cristal material. The aetiological and exact pathogenetic mechanisms of the evolution of giant mitochondria in the myocardium, as also their function, remain unclear. Particularly large specimens are obviously inefficient and disturbing to the cell. They are degraded by autophagy.}, }
@article {pmid542702, year = {1979}, author = {de la Fuente-Burguillo, P and Nicolás, G}, title = {Respiratory activity during germination of seeds of Cicer arietinum L. II. Effect of some metabolic inhibitors and mitochondrial activities.}, journal = {Revista espanola de fisiologia}, volume = {35}, number = {4}, pages = {401-407}, pmid = {542702}, issn = {0034-9402}, mesh = {Fabaceae/*metabolism ; Mitochondria/metabolism ; Oxygen Consumption ; *Plants, Medicinal ; Seeds/*metabolism ; }, abstract = {Changes in respiration rate during the early period of germination of Cicer arietinum L. seeds were studied. Three phases were distinguished. During phases I and II the RQ was higher than unity. Sodium fluoride showed no effect on gaseous exchange during phase I while in phases II and III a progressive increase in the inhibition of the respiratory activity was obtained. Iodoacetate inhibited oxygen uptake and carbon dioxide evolution from the beginning of germination. The activities of mitochondrial enzymes increased during the germination period, especially after the first 24 hours. The respiratory control and ADP/O ratio of the isolated mitochondria increased gradually during germination, reaching maximum values at 48 hours, lower, however than the expected theoretical ones.}, }
@article {pmid520336, year = {1979}, author = {Troyer, D and Schwager, P}, title = {Ultrastructure and evolution of a sperm: phylogenetic implications of altered motile machinery in Ophryotrocha puerilis spermatozoon.}, journal = {European journal of cell biology}, volume = {20}, number = {2}, pages = {174-176}, pmid = {520336}, issn = {0171-9335}, mesh = {Acrosome/ultrastructure ; Animals ; *Biological Evolution ; Centrioles/ultrastructure ; Male ; Mitochondria/ultrastructure ; Polychaeta/*physiology ; Sperm Tail/ultrastructure ; Spermatozoa/*ultrastructure ; }, abstract = {Modifications to the mitochondria and flagellum of the Ophryotrocha spermatozoon render it immotile. The sperm may represent an evolutionary unstable intermediate between flagellate and aflagellate sperm types.}, }
@article {pmid293756, year = {1979}, author = {Avise, JC and Giblin-Davidson, C and Laerm, J and Patton, JC and Lansman, RA}, title = {Mitochondrial DNA clones and matriarchal phylogeny within and among geographic populations of the pocket gopher, Geomys pinetis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {76}, number = {12}, pages = {6694-6698}, pmid = {293756}, issn = {0027-8424}, mesh = {Albumins/genetics ; Animals ; Base Sequence ; DNA Restriction Enzymes ; DNA, Mitochondrial/*genetics ; Environment ; Gene Frequency ; Heterozygote ; Isoenzymes/genetics ; Phosphogluconate Dehydrogenase/genetics ; Phylogeny ; Rodentia/*genetics ; }, abstract = {Restriction endonuclease assay of mitochondria DNA (mtDNA) and standard starch-gel electrophoresis of proteins encoded by nuclear genes have been used to analyze phylogenetic relatedness among a large number of pocket gophers (Geomys pinetis) collected throughout the range of the species. The restriction analysis clearly distinguishes two populations within the species, an eastern and a western form, which differ by at least 3% in mtDNA sequence. Qualitative comparisons of the restriction phenotypes can also be used to identify mtDNA "clones" within each form. The mtDNA clones interconnect in a phylogenetic network which represents an estimate of matriarchal phylogeny for G. pinetis. Although the protein electrophoretic data also differentiate the eastern and western forms, the data are of limited usefulness in establishing relationships among more local subpopulations. The comparison between these two data sets suggests that restriction analysis of mtDNA is probably unequalled by other techniques currently available for determining phylogenetic relationships among conspecific organisms.}, }
@article {pmid534540, year = {1979}, author = {Arron, GP and Spalding, MH and Edwards, GE}, title = {Stoichiometry of carbon dioxide release and oxygen uptake during glycine oxidation in mitochondria isolated from spinach (Spinacia oleracea) leaves.}, journal = {The Biochemical journal}, volume = {184}, number = {2}, pages = {457-460}, pmid = {534540}, issn = {0264-6021}, mesh = {Carbon Dioxide/*biosynthesis ; Decarboxylation ; Glycine/*metabolism ; Mitochondria/metabolism ; Oxidation-Reduction ; Oxygen/*metabolism ; Plants/*metabolism ; }, abstract = {Mitochondria isolated from spinach (Spinacia oleracea) leaves oxidized glycine with a stoichiometry of CO2 evolution to O2 uptake of 2 : 1. In the absence of added substrate, the mitochondria exhibited an extremely low endogenous rate of O2 uptake.}, }
@article {pmid116847, year = {1979}, author = {Scovassi, AI and Wicker, R and Bertazzoni, U}, title = {A phylogenetic study on vertebrate mitochondrial DNA polymerase.}, journal = {European journal of biochemistry}, volume = {100}, number = {2}, pages = {491-496}, doi = {10.1111/j.1432-1033.1979.tb04193.x}, pmid = {116847}, issn = {0014-2956}, mesh = {Animals ; Cell Line ; Chick Embryo ; DNA, Mitochondrial/*biosynthesis ; DNA-Directed DNA Polymerase/*analysis ; Female ; Haplorhini ; Liver/enzymology ; Mice ; Mitochondria/*enzymology ; Oocytes/enzymology ; *Phylogeny ; Species Specificity ; Trout ; Turtles ; Xenopus ; }, abstract = {We have started a phylogenetic survey for the mitochondrial DNA polymerase and present in this study the results obtained for all the different classes for the vertebrates. The operating conditions include the purification of mitochondria, the analysis of the DNA polymerase activity in the extract and the determination of the sedimentation coefficient on sucrose gradients. The utilization of digitonin for removing the external membrane of the organelle and contaminating proteins has been generalized since this detergent shows no effect on the activities of either DNA polymerases alpha or gamma. The results obtained for the mitochondria of different classes of vertebrates show that the activity responding to the specific assay of DNA polymerase gamma tended invariably to increase during purification while that of DNA polymerase alpha tended to decrease. Furthermore in almost all the cases the gamma-polymerase represented the only DNA polymerase activity found in the mitochondria after digitonin treatment. The analysis of the sedimentation patterns of the mitochondrial DNA polymerase strongly suggests the presence of a single type of DNA polymerase showing the typical properties of the gamma-polymerase. It is concluded that the vertebrate mitochondria contain a well-defined and unique form of DNA polymerase which corresponds to the DNA polymerase gamma.}, }
@article {pmid575618, year = {1979}, author = {Taga, R and Sesso, A}, title = {Ultrastructural studies on developing parotid gland of the rat at early postnatal periods.}, journal = {Archivum histologicum Japonicum = Nihon soshikigaku kiroku}, volume = {42}, number = {4}, pages = {427-444}, doi = {10.1679/aohc1950.42.427}, pmid = {575618}, issn = {0004-0681}, mesh = {Animals ; Cell Membrane/ultrastructure ; Cell Nucleus/ultrastructure ; Cytoplasmic Granules/ultrastructure ; Cytoskeleton/ultrastructure ; Endoplasmic Reticulum/ultrastructure ; Female ; Golgi Apparatus/ultrastructure ; Male ; Microscopy, Electron ; Mitochondria/ultrastructure ; Morphogenesis ; Myofibrils/ultrastructure ; Parotid Gland/*growth &amp; development/ultrastructure ; Rats ; }, abstract = {An electron microscopic study of the exocrine and myoepithelial cells of the parotid gland of the rat between days 2 and 40 of the postpartum was undertaken. Besides confirming morphological data of the literature on the evolution of the acinar cells, the following observations are reported. 1. At early postnatal development in some acini "mucous-like" cells containing secretory granules with light and dense parts may be observed. Cells with these types of granules were not found after day 20. 2. Morphological differentiation and maturation of the myoepithelial cells were followed. A parallelism was observed between the maturation of these myoepithelial cells and of the acinar cells. Myofilaments first appear around the nucleus at day 5 and between days 20 and 30 a considerable amount of these filaments is found in the already typical myoepithelial cells. 3. Active morphogenesis seems to be occurring in all cellular compartments namely at very early postnatal periods, e.g., between days 2 to 15. 4. The distribution and amount of thin and intermediate sized microfilaments in cells of these compartments varied visibly by various orders of magnitude.}, }
@article {pmid230215, year = {1979}, author = {Mincione, GP and Campana, G and Vannelli, G}, title = {[Study of uveal malignant melanoma with the electron microscope (author's transl)].}, journal = {Journal francais d'ophtalmologie}, volume = {2}, number = {10}, pages = {531-538}, pmid = {230215}, issn = {0181-5512}, mesh = {Adult ; Cell Nucleolus/ultrastructure ; Child ; Choroid Neoplasms/ultrastructure ; Ciliary Body/ultrastructure ; Eye Neoplasms/metabolism/pathology/*ultrastructure ; Humans ; Inclusion Bodies/ultrastructure ; Melanins/biosynthesis ; Melanocytes/ultrastructure ; Melanoma/metabolism/pathology/*ultrastructure ; Mitochondria/ultrastructure ; Ribosomes/ultrastructure ; Uveal Diseases/metabolism/*pathology ; }, abstract = {Twelve cases of uveal malignant melanoma, including the principal histologic types of this neoplasm according to Callender, were studied with the electron microscope. Nuclear inclusions were observed in each case, more frequently in epithelioid cells: they were probably correlated with nuclear hyperactivity. Melanogenesis in neoplastic cells was sometimes abnormal because of the granular structure of the premelanosomes, of the difference in size and in shape melanosomes, of the difference in size and in shape of the pigment granules and of the different stage of evolution of the premelanosomes in the cell. The size and the degree of reticulation of nucleoli and the number of free ribosomes and mitochondria increased from spindle A, to spindle B and epithelioid cells. This behaviour probably depends on an increasing metabolic activity which is related to the increasing degree of malignancy.}, }
@article {pmid501930, year = {1979}, author = {Okuda, M and Lefer, AM}, title = {Lysosomal hypothesis in evolution of myocardial infarction. Subcellular fractionation and electron microscopic cytochemical study.}, journal = {Japanese heart journal}, volume = {20}, number = {5}, pages = {643-656}, doi = {10.1536/ihj.20.643}, pmid = {501930}, issn = {0021-4868}, mesh = {Acid Phosphatase/metabolism ; Animals ; Cathepsins/metabolism ; Cats ; Female ; Glucuronidase/metabolism ; Hydrolases/metabolism ; Lysosomes/*enzymology/ultrastructure ; Male ; Myocardial Infarction/*enzymology/pathology ; Myocardium/enzymology/ultrastructure ; Protein Binding ; Subcellular Fractions/*enzymology/ultrastructure ; }, abstract = {Twenty-two cat hearts were perfused according to Langendorff technique and myocardial regional ischemia was induced by occlusion of left anterior coronary artery. Separation of particulate (bound) from soluble (free) fraction, and subsequent fractionation into plasma membranes, lysosomes, sarcoplasmic reticulum, and mitochondria were performed by sucrose density gradient ultracentrifugation. By ischemia for 60 min, particle-bound activity of cathepsin D decreased from 4.2 +/- 0.24 U/mg protein to 3.2 +/- 0.31 U/mg protein (p less than 0.01). Likewise, the particle-bound activity of beta-glucuronidase decreased from 11.9 +/- 0.92 U/mg protein to 6.2 +/- 1.28 U/mg protein (p less than 0.01). Accordingly, free/bound activity ratios of cathepsin D increased from 0.8 to 1.9 and beta-glucuronidase from 0.9 to 2.8, respectively. Conspicuous fall from 12.8 +/- 0.6 U/mg protein to 8.0 +/- 0.97 U/mg protein (p less than 0.01) in absolute specific activity of cathepsin D bound to the lysosomal fraction, presents definitive evidence of lysosomal release of the acid hydrolases during the early phase of myocardial ischemia. Electron microscopic observation of the ischemic myocytes revealed ultrastructural alterations of the lysosomes suggestive of autophagic degradation of various subcellular organelles.}, }
@article {pmid474592, year = {1979}, author = {Motta, J and Guilleminault, C and Billingham, M and Barry, W and Mason, J}, title = {Cardiac abnormalities in myotonic dystrophy. Electrophysiologic and histopathologic studies.}, journal = {The American journal of medicine}, volume = {67}, number = {3}, pages = {467-473}, doi = {10.1016/0002-9343(79)90795-2}, pmid = {474592}, issn = {0002-9343}, mesh = {Adolescent ; Adult ; Arrhythmias, Cardiac/complications ; Bundle-Branch Block/complications ; *Electrocardiography ; Heart Block/complications ; Humans ; Male ; Myocardium/*ultrastructure ; Myotonic Dystrophy/complications/pathology/*physiopathology ; Organoids/ultrastructure ; }, abstract = {Eight young adult male patients with myotonic dystrophy, mean age 26 years, underwent 24-hour Holter electrocardiographic monitoring and intracardiac electrophysiologic study. Right ventricular endomyocardial biopsies were performed at the end of the electrophysiologic study in five of them. The atrial to His[A-H] interval was 155 msec in one case and less than or equal to 55 msec in all patients. Twenty-four hour Holter electrocardiographic monitoring demonstrated more than 4 premature ventricular contractions per minute in two patients and marked cyclical sinus arrhythmia during sleep in two others. Electron microscopic analysis of the endomyocardial biopsy specimens disclosed no prominent sarcoplasmic reticulum abnormalities but prominent I bands compared to previously obtained controls. Myofibrillar degeneration was seen in all cases and was associated with abnormal mitochondria in two. Cardiac abnormalities can be detected very early in the evolution of myotonic dystrophy, even prior to the onset of cardiac symptoms. The reported abnormalities appear closely related to the pathologic process affecting other skeletal muscles.}, }
@article {pmid518764, year = {1979}, author = {Mazzotti, G and Mosca Bubola, G and Pettazzoni, P and Ruggeri, F and Santi, P and Papa, S and Farulla, A}, title = {[Effects of ionizing radiations on the ultrastructure of the thymus gland].}, journal = {Bollettino della Societa italiana di biologia sperimentale}, volume = {55}, number = {14}, pages = {1334-1340}, pmid = {518764}, issn = {0037-8771}, mesh = {Animals ; Chickens ; Chromatin/radiation effects ; Epithelial Cells ; Lymphocyte Activation/radiation effects ; Lymphocytes/radiation effects ; Macrophages/radiation effects ; Mitochondria/radiation effects ; Thymus Gland/*radiation effects/ultrastructure ; Time Factors ; }, abstract = {Different doses of gamma rays induce ultrastructural alterations in limphoid and epithelial cells of the chick thymus which exhibit a different temporal evolution after the treatment. The main changes which occur in lymphoid cells treated with 50 rads disappear 48 hours after the irradiation, while with 100 rads the radiation damage is still evident in epithelial cells.}, }
@article {pmid113918, year = {1979}, author = {Pinevich, AV and Desnitskiĭ, AG}, title = {[Evolutionary origin of cell organelles].}, journal = {Tsitologiia}, volume = {21}, number = {7}, pages = {755-767}, pmid = {113918}, issn = {0041-3771}, mesh = {Aerobiosis ; Anaerobiosis ; *Biological Evolution ; Cell Compartmentation ; Chloroplasts/metabolism ; Clone Cells/ultrastructure ; Cyanobacteria/metabolism ; Cytogenetics ; Energy Metabolism ; Eukaryotic Cells/ultrastructure ; Mitochondria/metabolism ; Organoids/physiology/*ultrastructure ; Oxygen Consumption ; Phenotype ; Photosynthesis ; Phylogeny ; Symbiosis ; }, abstract = {A review on the evolutionary origin of the energy-yielding eukaryotic organelles is presented. Current autogenetic (endogenous compartmentalization) schemes, as well as different variants of symbiogenesis, are critically envisaged. A new symbiogenetic scheme is put forth, according to which mitochondria and chloroplasts originated divergently from a primordial photosynthetic organelle; the latter was acquired by endosymbiosis of ancient cyanobacteria in the cells of protoeukaryotes.}, }
@article {pmid383249, year = {1979}, author = {Dodson, EO}, title = {Crossing the procaryote--eucaryote border: endosymbiosis or continuous development?.}, journal = {Canadian journal of microbiology}, volume = {25}, number = {6}, pages = {651-674}, doi = {10.1139/m79-096}, pmid = {383249}, issn = {0008-4166}, mesh = {*Biological Evolution ; Cell Nucleus ; *Cell Physiological Phenomena ; Chloroplasts ; DNA ; Endocytosis ; Eukaryotic Cells/*physiology/ultrastructure ; Mitochondria ; Organoids/ultrastructure ; Plasmids ; Prokaryotic Cells/*physiology/ultrastructure ; *Symbiosis ; }, }
@article {pmid221822, year = {1979}, author = {Ambler, RP and Daniel, M and Hermoso, J and Meyer, TE and Bartsch, RG and Kamen, MD}, title = {Cytochrome c2 sequence variation among the recognised species of purple nonsulphur photosynthetic bacteria.}, journal = {Nature}, volume = {278}, number = {5705}, pages = {659-660}, doi = {10.1038/278659a0}, pmid = {221822}, issn = {0028-0836}, mesh = {Amino Acid Sequence ; Bacteria/*genetics ; *Cytochrome c Group/genetics ; Mitochondria/analysis ; Phylogeny ; Species Specificity ; }, }
@article {pmid36627, year = {1979}, author = {Taylor, FJ}, title = {Symbionticism revisited: a discussion of the evolutionary impact of intracellular symbioses.}, journal = {Proceedings of the Royal Society of London. Series B, Biological sciences}, volume = {204}, number = {1155}, pages = {267-286}, doi = {10.1098/rspb.1979.0027}, pmid = {36627}, issn = {0950-1193}, mesh = {Animals ; Bacterial Physiological Phenomena ; *Biological Evolution ; Chloroplasts/physiology ; DNA/metabolism ; Dinoflagellida/physiology ; Mitochondria/physiology ; Photosynthesis ; Protein Biosynthesis ; RNA/metabolism ; Species Specificity ; *Symbiosis ; Transcription, Genetic ; }, abstract = {Wallin (1927) first published the notion that the fusion of bacteria with host cells was the principal source of genetic novelty for speciation. He suggested that mitochondria are transitional elements in this process. While the significance that he attributed to symbiosis now seem excessive, he was one of the first authors to be aware of the evolutionary potential of symbiotic events and his view of mitochondria may not seem strange to many cell biologist today. The most significant evolutionary development which has been attributed to intracellular symbiosis is the origin of eukaryotic cellular organization. The current status of the 'serial endosymbiosis hypothesis' is briefly review. The case for the symbiotic origin of the chloroplast, based principally on 16 S RNA oligonucleotide cataloguing, is very strong. Mitochondrial origins are more obscure but also appear to be symbiotic due to recent 18 S cataloguing from wheat embryos. The probablility of the multiple origin of some eukaryotic organelles is also examined, the processes in question being the acquisition of distinct stocks of chloroplasts from disparate photosynthetic prokaryotes and the secondary donation of organelles from degenerate eukaryotic endosymbionts to their hosts, with specific reference to the dinoflagellates Peridinium balticum, Kryptoperidinium foliaceum and the ciliate Mesodinium rubrum. It is concluded that the evolutionary potential of intracellular symbiosis ('cytobiosis': a term introduced in this paper) is great, with the best established influence being on the origin of eukaryotic chloroplasts. Together with the potential effects of viral vectors, symbiosis serves as a supplementary speciation mechanism capable of producing directed evolutionary changes. It is likely that these processes will explain some of the apparent anomalies in evolutionary rates and direction which are not readily explicable by the conventional synthetic theory of evolution.}, }
@article {pmid36620, year = {1979}, author = {Whatley, JM and John, P and Whatley, FR}, title = {From extracellular to intracellular: the establishment of mitochondria and chloroplasts.}, journal = {Proceedings of the Royal Society of London. Series B, Biological sciences}, volume = {204}, number = {1155}, pages = {165-187}, doi = {10.1098/rspb.1979.0020}, pmid = {36620}, issn = {0950-1193}, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; *Bacterial Physiological Phenomena ; Chloroplasts/*physiology ; Cyanobacteria/*physiology ; Cytochrome c Group/physiology ; Mitochondria/*physiology ; Paracoccus/physiology ; Photosynthesis ; Plants ; Rhodopseudomonas/physiology ; Species Specificity ; Symbiosis ; }, abstract = {Paracoccus and Rhodopseudomonas are unusual among bacteria in having a majority of the biochemical features of mitochondria; blue-green algae have many of the features of chloroplasts. The theory of serial endosymbiosis proposes that a primitive eukaryote successively took up bacteria and blue-green algae to yield mitochondria and chloroplasts respectively. Possible characteristics of transitional forms are indicated both by the primitive amoeba, Pelomyxa, which lacks mitochondria but contains a permanent population of endosymbiotic bacteria, and by several anomalous eukaryotic algae, e.g. Cyanophora, which contain cyanelles instead of chloroplasts. Blue-green algae appear to be obvious precursors of red algal chloroplasts but the ancestry of other chloroplasts is less certain, though the epizoic symbiont, Prochloron, may resemble the ancestral green algal chloroplast. We speculate that the chloroplasts of the remaining algae may have been a eukaryotic origin. The evolution or organelles from endosymbiotic precursors would involve their integration with the host cell biochemically, structurally and numerically.}, }
@article {pmid158138, year = {1979}, author = {Galbenu, P and Gheorghiu, M and Marinescu, D}, title = {Infection in vitro of the human pulmonary macrophage with Staphylococcus aureus (bacteriologic and ultrastructural observations).}, journal = {Morphologie et embryologie}, volume = {25}, number = {2}, pages = {175-184}, pmid = {158138}, issn = {0377-5038}, mesh = {Adult ; Aged ; Carbenicillin/pharmacology ; Humans ; Lung Diseases/*microbiology ; Lung Neoplasms/microbiology ; Macrophages/*microbiology/ultrastructure ; Middle Aged ; Mitochondria/ultrastructure ; Phagocytosis ; Staphylococcal Infections/*microbiology ; Staphylococcus aureus/drug effects/ultrastructure ; }, abstract = {Alveolar macrophages from exeresis fragments taken from patients operated for pulmonary cancer were infected in vitro with Staphylococcus aureus. Part of the investigation was carried out in the presence of an antibiotic (pyopen) introduced in the culture medium. Bacteriologic seeding from an extracellular medium and from lyzed cells showed a greater intracellular multiplication rate. In the presence of pyopen there was a decrease in the number of germs due to the inhibition of multiplication. Electron microscopy revealed reduced phagolysosomal fusion, aspects of bacterial multiplication and the coexistence of intact bacteria and bacteria presenting structural alterations. The results suggest the importance of cellular parasitism in the chronic evolution of infectious bronchopulmonary processes.}, }
@article {pmid109836, year = {1979}, author = {Brown, WM and George, M and Wilson, AC}, title = {Rapid evolution of animal mitochondrial DNA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {76}, number = {4}, pages = {1967-1971}, pmid = {109836}, issn = {0027-8424}, mesh = {Animals ; *Biological Evolution ; Cercopithecus ; Cricetinae ; DNA Restriction Enzymes ; DNA, Mitochondrial/*genetics ; Haplorhini ; Humans ; Kinetics ; Macaca mulatta ; Mice ; Mitochondria, Liver/*analysis ; Nucleic Acid Denaturation ; Papio ; Rats ; Species Specificity ; }, abstract = {Mitochondrial DNA was purified from four species of higher primates (Guinea baboon, rhesus macaque, guenon, and human) and digested with 11 restriction endonucleases. A cleavage map was constructed for the mitochondrial DNA of each species. Comparison of the maps, aligned with respect to the origin and direction of DNA replication, revealed that the species differ from one another at most of the cleavage sites. The degree of divergence in nucleotide sequence at these sites was calculated from the fraction of cleavage sites shared by each pair of species. By plotting the degree of divergence in mitochondrial DNA against time of divergence, the rate of base substitution could be calculated from the initial slope of the curve. The value obtained, 0.02 substitutions per base pair per million years, was compared with the value for single-copy nuclear DNA. The rate of evolution of the mitochondrial genome appears to exceed that of the single-copy fraction of the nuclear genome by a factor of about 10. This high rate may be due, in part, to an elevated rate of mutation in mitochondrial DNA. Because of the high rate of evolution, mitochondrial DNA is likely to be an extremely useful molecule to employ for high-resolution analysis of the evolutionary process.}, }
@article {pmid313252, year = {1979}, author = {Masoni, A and Garcia-Romeu, F}, title = {Moulting in Rana esculenta: development of mitochondria-rich cells, morphological changes of the epithelium and sodium transport.}, journal = {Cell and tissue research}, volume = {197}, number = {1}, pages = {23-38}, pmid = {313252}, issn = {0302-766X}, mesh = {Aldosterone/pharmacology ; Animals ; Anura ; Biological Transport, Active ; Cell Differentiation ; Epithelial Cells ; Rana esculenta/*physiology ; Seasons ; Skin/*cytology/drug effects ; Sodium/*metabolism ; }, abstract = {The present study concerns moulting of the skin in Rana esculenta in vivo and in vitro. The evolution of mitochondria-rich cells (MRC) and changes in the epithelium during moulting were followed. The greater part of the MRC are lost during moulting, either because they remain attached to the old stratum corneum or because they are left in contact with the external medium and degenerate. The cells thus lost leave deep impressions in the new stratum corneum which disappear progressively. Before an MRC is shed, a cell of the stratum intermedium contacting it differentiates to form a new MRC to replace the old. Isolation of the skin triggers moulting in the excised pieces. This moulting does not cause changes in the short-circuit current or in the transepithelial resistance. Aldosterone (10(-6) M) added in vitro to the serous side appeared to facilitate the detachment of the slough, however, no clear-cut moult-inducing effect of the hormone was seen.}, }
@article {pmid218460, year = {1979}, author = {Rossier, BC and Rossier, M and Lo, CS}, title = {Thyroxine and Na+ transport in toad: role in transition from poikilo- to homeothermy.}, journal = {The American journal of physiology}, volume = {236}, number = {3}, pages = {C117-24}, doi = {10.1152/ajpcell.1979.236.3.C117}, pmid = {218460}, issn = {0002-9513}, mesh = {Animals ; Biological Evolution ; *Body Temperature Regulation ; Bufo marinus/physiology ; Female ; Liver/metabolism ; Male ; Oxygen Consumption/*drug effects ; Sodium/*metabolism ; Sodium-Potassium-Exchanging ATPase/*metabolism ; Thyroxine/*pharmacology ; Urinary Bladder/metabolism ; }, abstract = {The effects of thyroxine (T4) on Na+ transport, oxygen consumption (QO2), and Na+-K+-ATPase activity were studied in the urinary bladder and liver of the toad Bufo marinus. In the bladder, T4 in vitro (10(-8) to 10(-6) M) had no significant effect on these parameters during 15 h of incubation. When injected intraperitoneally (approximately 20 microgram/(kg body wt.day) for 6 days), T4 lowered base-line, short-circuit current by 62% (P less than 0.0025) and potential difference by 37% (P less than 0.001), increasing tissue resistance by 40% (P less than 0.02). T4 depressed QO2/DNA (-25%, P less than 0.05) with no significant effect on Na+-K+-ATPase activity. In liver, T4 increased the recovery per cell DNA of mitochondrial proteins by 32% (P less than 0.025), corresponding to an increased QO2 (stage IV) of isolated mitochondria per cell DNA (+54%, P less than 0.01). There was no significant effect on Na+-K+-ATPase activity. These results suggest that, unlike its function in the rat, T4 in the toad does not regulate cellular thermogenesis by inducing Na+-K+-ATPase. This major difference could account at least in part for the transition from poikilothermy to homeothermy. In addition, T4 has a distinct inhibitory effect on Na+ transport in the urinary bladder, which suggests an antagonism to the action of aldosterone.}, }
@article {pmid549104, year = {1979}, author = {Singhal, RP and Fallis, PA}, title = {Structure, function, and evolution of transfer RNAs (with appendix giving complete sequences of 178 tRNAs).}, journal = {Progress in nucleic acid research and molecular biology}, volume = {23}, number = {}, pages = {227-290}, doi = {10.1016/s0079-6603(08)60135-x}, pmid = {549104}, issn = {0079-6603}, mesh = {Base Sequence ; Chemical Phenomena ; Chemistry ; Mitochondria ; Nucleosides/metabolism ; *RNA, Transfer/metabolism ; Ribosomes/metabolism ; }, }
@article {pmid233495, year = {1979}, author = {Margoliash, E}, title = {Evolutionary adaptation of mitochondrial cytochrome c to its functional milieu.}, journal = {UCLA forum in medical sciences}, volume = {}, number = {21}, pages = {299-321}, doi = {10.1016/b978-0-12-643150-6.50024-5}, pmid = {233495}, issn = {0082-7134}, mesh = {*Adaptation, Physiological ; Animals ; *Biological Evolution ; Cytochrome c Group/*genetics/metabolism ; Electron Transport ; Electron Transport Complex IV/metabolism ; Humans ; Kinetics ; Mitochondria/*metabolism ; Mutation ; Oxidoreductases/metabolism ; Selection, Genetic ; Succinates/metabolism ; }, }
@article {pmid115189, year = {1979}, author = {Portelli, C}, title = {The origin of life. A cybernetic and informational process.}, journal = {Acta biotheoretica}, volume = {28}, number = {1}, pages = {19-47}, pmid = {115189}, issn = {0001-5342}, mesh = {Adenine/metabolism ; Amino Acids/biosynthesis ; Biological Evolution ; Chemical Phenomena ; Chemistry ; *Cybernetics ; Histones/biosynthesis ; Membranes/metabolism ; *Models, Biological ; Nucleotides/biosynthesis ; Organoids/metabolism ; *Origin of Life ; Thymine/metabolism ; }, abstract = {According to the model presented in this paper, the beginning of life was marked by the coupling of two complementary nucleotide bases: adenine and thymine. The adenine-thymine system received photons from the sun and stored their energy in the form of a chemical high-energy bond between two phosphoric acid molecules, which were before-hand fixed by adenine from the aqueous environment. The energy of the high-energy bond was then delivered in the form of two waves of electronic excitation. These were utilized to synthesize new molecules, starting from the carbonic acid and ammonia molecules, fixed from the aqueous environment by the polar groups of the nucleotide bases. In this way, a nucleotides-histone protosystem (NHPS) was self-synthesized, evolving step by step towards complexity, by means of some internal cybernetic and informational mechanisms. During its evolution, the NHPS synthesized a limiting membrane, produced the organizing elements of the cellular organelles (chloroplastes, mitochondria, ribosomes etc) and constructed microtubules and microfilaments. Subsequently, the NHPS evolved to the building of DNA-histone system and formed the cellular nucleus.}, }
@article {pmid106191, year = {1978}, author = {Gochlerner, GB}, title = {Free oxygen and evolutionary progress.}, journal = {Journal of theoretical biology}, volume = {75}, number = {4}, pages = {467-486}, doi = {10.1016/0022-5193(78)90357-0}, pmid = {106191}, issn = {0022-5193}, mesh = {Aerobiosis ; Bacteria/metabolism ; *Biological Evolution ; Catalase/metabolism ; Cyanobacteria/metabolism ; Ecology ; Mitochondria/metabolism ; *Oxygen Consumption ; Photosynthesis ; }, }
@article {pmid741024, year = {1978}, author = {de Diego Carmona, JA and Vincent Hamelin, E and Cañizo, JF and Garrido Santo, A and Blanco, J and Molina Triguero, L}, title = {[Evolution of the bioelectric impedance in provoked renal ischemia].}, journal = {Revista clinica espanola}, volume = {151}, number = {5}, pages = {385-388}, pmid = {741024}, issn = {0014-2565}, mesh = {Animals ; Ischemia/*pathology ; Kidney/*blood supply/ultrastructure ; Mitochondria/ultrastructure ; *Plethysmography, Impedance ; Rats ; }, }
@article {pmid737712, year = {1978}, author = {Meyer-Rochow, VB and Walsh, S}, title = {The eyes of mesopelagic crustaceans. III. Thysanopoda tricuspidata (Euphausiacea).}, journal = {Cell and tissue research}, volume = {195}, number = {1}, pages = {59-79}, pmid = {737712}, issn = {0302-766X}, mesh = {Biological Evolution ; Crustacea/*anatomy &amp; histology ; Eye/*ultrastructure ; Microscopy, Electron, Scanning ; Ocular Physiological Phenomena ; Species Specificity ; Vision, Ocular/physiology ; }, abstract = {The compound eyes of the mesopelagic eupausiid Thysanopoda tricuspidata were investigated by light-, scanning-, and transmission electron microscopy. The eyes are spherical and have a diameter that corresponds to 1/6 of the carapace length. The hexagonal facets have strongly curved outer surfaces. Although there are four crystalline cone cells, only two participate in the formation of the cone, which is 90-120 micrometer long and appears to have a radial gradient of refractive index. The clear zone, separating dioptric structures and retinula, is only 90-120 micrometer wide. In it lie the very large oval nuclei of the seven retinula cells. Directly in front of the 70 micrometer long and 15 micrometer thick rhabdom a lens-like structure of 12 micrometer diameter is developed. This structure, known in only a very few arthropods, seems to be present in all species of Euphausiacea studied to date. It is believed that the rhabdom lens improves near-field vision and absolute light sensitivity. Rod-shaped pigment grains and mitochondria of the tubular type are found in the plasma of retinula cells. The position of the proximal screening pigment as well as the microvillar organization in the rhabdom are indicative of light-adapted material. The orthogonal alignment of rhabdovilli suggests polarization sensitivity. Behind each rabdom there is a cup-shaped homogenous structure of unknown, but possibly optical function. Finally, the structure and the function of the euphysiid eye are reviewed and the functional implications of individual components are discussed.}, }
@article {pmid370774, year = {1978}, author = {Martin, RP and Sibler, AP and Schneller, JM and Keith, G and Stahl, AJ and Dirheimer, G}, title = {Primary structure of yeast mitochondrial DNA-coded phenylalanine-tRNA.}, journal = {Nucleic acids research}, volume = {5}, number = {12}, pages = {4579-4592}, pmid = {370774}, issn = {0305-1048}, mesh = {Base Sequence ; DNA, Mitochondrial/*metabolism ; Nucleic Acid Conformation ; Oligoribonucleotides/analysis ; Phenylalanine ; *RNA, Transfer/biosynthesis/isolation &amp; purification ; Ribonucleases ; Saccharomyces cerevisiae/*metabolism ; }, abstract = {Mitochondrial tRNAPhe from Saccharomyces cerevisiae isolated by two-dimensional gel electrophoresis was sequenced by fingerprinting uniformly labeled 32 P-tRNA as well as by 5'-end postlabeling techniques. Its sequence was found to be: pG-C-U-U-U-U-A-U-A-G-C-U-U-A-G-D-G-G-D-A-A-A-G-C-m22G-A-U-A-A-A-phi-U-G-A-A-m1G-A-phi-U-U-A-U-U-U-A-C-A-U-G-U-A-G-U-phi-C-G-A-U-U-C-U-C-A-U-U-A-A-G-G-G-C-A-C-C-A. The secondary structure we propose, in order to maximize base pairing in the phiC stem and to allow tertiary interaction between G15 and C46, excludes U50 from base pairing giving a bulge in the phiC stem. No conclusion can be drawn concerning the endosymbiotic theory of mitochondria evolution by comparing the primary structure of mt. tRNAPhe with other sequenced tRNAsPhe. This mt.tRNAPhe lacks some of the structural elements reported to be involved in the yeast cytoplasmic phenylalanyl-tRNA ligase recognition site and cannot be aminoacylated by purified yeast cytoplasmic phenylalanyl-tRNA ligase.}, }
@article {pmid103657, year = {1978}, author = {Martin, R and Sibler, AP and Schneller, JM and Keith, G and Stahl, AJ and Dirheimer, G}, title = {[Nucleotide sequence determination of yeast mitochondrial phenylalanine-tRNA].}, journal = {Comptes rendus hebdomadaires des seances de l'Academie des sciences. Serie D: Sciences naturelles}, volume = {287}, number = {8}, pages = {845-848}, pmid = {103657}, mesh = {Base Sequence ; Chemical Phenomena ; Chemistry ; Mitochondria/*ultrastructure ; Nucleic Acid Conformation ; Phenylalanine ; *RNA, Transfer ; Saccharomyces cerevisiae/*ultrastructure ; }, abstract = {The primary structure of mitochondrial tRNAPhe from Saccharomyces cerevisiae, purified by two-dimensional polyacrylamide gel electrophoresis, was determined using, standard procedures on in vivo 32P-labeled tRNA, as well as the new 5'-end postlabeling techniques. We propose a cloverleaf model which allows for tertiary interaction between cytosine in position 46 and guanine in position 15 and maximizes base pairing in the psi C stem, thus excluding the uracile in position 50 from base pairing in the psi C stem. Comparison of the primary structure of this tRNA with all other known procaryotic, chloroplastic or cytoplasmic tRNAsPhe sequences does not lead to any conclusion about the endosymbiotic theory of mitochondria evolution.}, }
@article {pmid692687, year = {1978}, author = {Sonderegger, P and Christen, P}, title = {Comparison of the evolution rates of cytosolic and mitochondrial aspartate aminotransferase.}, journal = {Nature}, volume = {275}, number = {5676}, pages = {157-159}, doi = {10.1038/275157a0}, pmid = {692687}, issn = {0028-0836}, mesh = {Animals ; Antigens/analysis ; Aspartate Aminotransferases/*genetics/immunology/metabolism ; *Biological Evolution ; Cytosol/enzymology ; Isoenzymes/*genetics ; Mitochondria/enzymology ; Vertebrates/genetics ; }, }
@article {pmid713490, year = {1978}, author = {Balentine, JD}, title = {Pathology of experimental spinal cord trauma. II. Ultrastructure of axons and myelin.}, journal = {Laboratory investigation; a journal of technical methods and pathology}, volume = {39}, number = {3}, pages = {254-266}, pmid = {713490}, issn = {0023-6837}, mesh = {Animals ; Axons/*ultrastructure ; Calcinosis/pathology ; Endoplasmic Reticulum/ultrastructure ; Ischemia/pathology ; Lysosomes/ultrastructure ; Male ; Microscopy, Electron ; Mitochondria/ultrastructure ; Myelin Sheath/*ultrastructure ; Necrosis/pathology ; Neurofibrils/ultrastructure ; Rats ; Spinal Cord/blood supply ; Spinal Cord Injuries/*pathology ; Time Factors ; Vacuoles/ultrastructure ; }, abstract = {Adult male Sprague Dawley rats were subjected to spinal cord trauma of the lower thoracic-upper lumbar spinal cord using a weight dropping technique onto the surgically exposed dorsal surface. This experimental model, which results in severe paraplegia and development of complete segmental necrosis, was studied in a time sequence varying from immediately to 30 days afterward by electron microscopy, in order to characterize the pathologic changes in axons and myelin in the area of impounding. The results revealed tubulovesiculation within axons immediately posttrauma. Axonal fragmentation, axonal and adaxonal swelling accounted for the progressively increasing spongy appearance of the white matter. Beginning at 30 minutes and progressing until completion of tissue necrosis at 8 to 24 hours, axonal necrosis characterized by a finely granular alteration gradually evolved. Spheroids containing increased mitochondria, neurofilaments, lysosomes, and smooth endoplasmic reticulum appeared both in and peripheral to the zone of necrosis. Axonal calcification, rarely observed within 30 minutes, appeared maximally after the evolution of tissue necrosis. Two basic abnormalities of myelin were found: vesicular degeneration and intramyelinic vacuolization. These characteristically occurred late and involved fibers with abnormal axoplasm and were interpreted as being secondary in origin.}, }
@article {pmid685853, year = {1978}, author = {Banka, VS and Bodenheimer, MM and Ramanathan, KB and Hermann, GA and Helfant, RH}, title = {Progressive transmural electrographic, myocardial potassium ion/sodium ion ratio and ultrastructural changes as a function of time after acute coronary occlusion.}, journal = {The American journal of cardiology}, volume = {42}, number = {3}, pages = {429-443}, doi = {10.1016/0002-9149(78)90938-4}, pmid = {685853}, issn = {0002-9149}, mesh = {Animals ; Dogs ; Electrocardiography ; Heart Conduction System/*physiopathology ; Microscopy, Electron ; Mitochondria, Heart/ultrastructure ; *Myocardial Infarction/metabolism/pathology/physiopathology ; *Myocardium/metabolism/ultrastructure ; Potassium/*metabolism ; Sodium/*metabolism ; Time Factors ; Vacuoles/ultrastructure ; }, abstract = {The progressive transmural electrographic, biochemical and ultrastructural changes as a function of time after acute coronary occlusion were systematically assessed in eight dogs. Transmural plunge electrodes with poles 1 mm apart were placed in the ischemic and nonischemic zones, and coronary occlusion was maintained for 4 hours. Transmural full thickness biopsy specimens were obtained from each zone for electron microscopy before, and 1 and 4 hours after occlusion. Endocardial and epicardial layers were also obtained for assessment of myocardial potassium ion (K+) and sodium ion (Na+) concentrations. Before coronary occlusion, local Q waves were recorded an average depth of 1.0 +/- 0.34 mm from the endocardial surface. After 1 hour of occlusion, Q waves appeared at an average depth of 3.8 +/- 0.67 mm and progressed to a depth of 5.2 +/- 0.7 mm at 2 hours, 6.2 +/- 0.5 mm at 3 hours and 7.0 +/- 0.5 mm at 4 hours. After 1 hour, ultrastructural changes of early ischemia, including a decrease in glycogen and mild mitochondrial swelling, were seen in the endocardial layer; the epicardial layer showed normal morphologic features. After 4 hours, the endocardial layer showed well developed ischemic changes marked by the loss of mitochondrial cristae, vacuolization, the appearance of amorhopous mitochondrial cristae, vacuolization, the appearance of amorphous mitochondrial densities, an increase in interfibrillary space and the appearance of I bands. In contrast, the epicardial layer at this time showed only early ischemic changes. At the end of 4 hours, the endocardial layer showed a marked decrease in myocardial K+ concentration and an increase in Na+ concentration leading to complete reversal of K+/Na+ ratio (0.7 +/- 1.0; P less than 0.001). In the epicardial layer, a smaller decrease in K+ concentration and an increase in Na+ concentration occurred, resulting in a diminution but not a reversal of K+/Na+ ratio (1.4 +/- 0.2; P less than 0.005). Thus, the dynamic evolution of an acute myocardal infarction involves a sequential progression from endocardium to epicardium as a function of time, resulting in an epicardial "border zone" in the early stages after acute coronary occlusion.}, }
@article {pmid207827, year = {1978}, author = {Westfall, JA and Kinnamon, JC}, title = {A second sensory--motor--interneuron with neurosecretory granules in Hydra.}, journal = {Journal of neurocytology}, volume = {7}, number = {3}, pages = {365-379}, doi = {10.1007/BF01176999}, pmid = {207827}, issn = {0300-4864}, mesh = {Animals ; Axons/ultrastructure ; Biological Evolution ; Cilia/ultrastructure ; Cytoplasmic Granules/ultrastructure ; Hydra/*cytology ; Interneurons/*ultrastructure ; Microscopy, Electron ; Neurosecretion ; Synapses/ultrastructure ; Synaptic Transmission ; }, abstract = {Using serial-sectioning techniques for conventional transmission and high-voltage electron microscopy, we characterized the ultrastructural features and synaptic contacts of the sensory cell in tentacles of Hydra. The sensory cell has an apical specialization characterized by a recessed cilium surrounded by three rodlike stereocilia. This ciliary--stereociliary complex constitutes the receptive or dendritic pole of the sensory cell. The dense filamentous cores of the stereocilia project proximally into a narrow circumciliary cytoplasmic region connected by septate junctions to marginal processes of an enveloping epitheliomuscular cell. The central cilium has a characteristic marginal flare midway along its length and a dense filamentous substructure at its base. Pairs of branched, striated rootlets extend from the axial centriole into a mitochondria-rich region of the cell. Pigment-like granules are present in the cytoplasm around the circumciliary space. The perikaryon is characterized by an elongate nucleus surrounded by a narrow rim of cytoplasm containing prominent Golgi complexes, assorted vacuoles and dense-cored vesicles, free ribosomes, short segments of rough endoplasmic reticulum, microtubules, glycogen particles, and lipid droplets. Generally, one or two thin, naked axons extend laterally from the perikaryon into the nerve net region above the myonemes of the large epitheliomuscular cells. Within the axons are found occasional aggregates of dense-cored vesicles and en passant synapses characterized by the presence of clear or dense-cored vesicles in contact with paramembranous densities and associated intracleft cross filaments. Using these ultrastructural criteria, we demonstrated for the first time that the granule-containing sensory cells have synaptic contacts with other neurons, nematocytes, and epitheliomuscular cells hence, we considered these cells to be sensory--motor--interneurons with neurosecretory granules. We hypothesize that this unique, apparently multifunctional neuron may be a modern representative of a primitive stem cell that give rise evolutionarily to the sensory cells, motor neurons, interneurons, and neurosecretory cells of higher animals.}, }
@article {pmid207877, year = {1978}, author = {Lyddiatt, A and Peacock, D and Boulter, D}, title = {Evolutionary change in invertebrate cytochrome C.}, journal = {Journal of molecular evolution}, volume = {11}, number = {1}, pages = {35-45}, pmid = {207877}, issn = {0022-2844}, mesh = {Amino Acid Sequence ; Animals ; Cytochrome c Group/*genetics ; Fungi ; Invertebrates/*genetics ; Mitochondria ; *Phylogeny ; Plants ; Vertebrates ; }, abstract = {Recently published amino acid sequences are compared to those of other cytochromes c. Molecular phylogenies constructed by using an ancestral sequence method are compared to the classical biological view of invertebrate evolution. Problems associated with the analysis of sequences of different chain lengths and of high variability are discussed, and the logistics of increasing the representation of key invertebrate phyla is assessed.}, }
@article {pmid656565, year = {1978}, author = {Powell, MJ}, title = {Phylogenetic implications of the microbody-lipid globule complex in zoosporic fungi.}, journal = {Bio Systems}, volume = {10}, number = {1-2}, pages = {167-180}, doi = {10.1016/0303-2647(78)90038-2}, pmid = {656565}, issn = {0303-2647}, mesh = {Fungi/classification/*ultrastructure ; *Lipids ; Microbodies/physiology/*ultrastructure ; Organoids/*ultrastructure ; *Phylogeny ; Species Specificity ; Spores, Fungal/ultrastructure ; }, abstract = {Chytridiomycetous fungal zoospores contain a unique and intricate association of organelles, the 'microbody-lipid globule complex' (MLC). The spatial arrangement of organelles in the MLC appears important in the utilization of lipid globules for energy, but in addition, the structural association of organelles in the MLC reveals phylogenetic trends within this diverse group of organisms. Variations in the structure of the MLC correlate well with current phylogenetic concepts of aquatic fungi, yet suggest new relationships among these posteriorly uniflagellate zoospores. Based upon the organization of organelles in the MLC, 4 basic patterns of MLCs can be recognized, and these correspond to the 4 orders of Chytridiomycetes. The MLC in its simplest form consists of a microbody appressed to the edge of a lipid globule. In more highly organized MLCs, mitochondria subtend the microbody and a cisterna surmounts one side of the lipid globule. The organization and structure is still more complex in other MLCs where ER is elaborated into a tubular network of membranes or where small microbodies or mitochondria fuse into 'giant' organelles. The structural organization of the MLC provides an additional criterion by which the phylogeny of awuatic fungi can be evaluated.}, }
@article {pmid650262, year = {1978}, author = {Denizot, JP and Kirschbaum, F and Westby, GW and Tsuji, S}, title = {The larval electric organ of the weakly electric fish Pollimyrus (Marcusenius) isidori (Mormyridae, Teleostei).}, journal = {Journal of neurocytology}, volume = {7}, number = {2}, pages = {165-181}, doi = {10.1007/BF01217916}, pmid = {650262}, issn = {0300-4864}, mesh = {Animals ; Biological Evolution ; Electric Organ/anatomy &amp; histology/*cytology/physiology ; Fishes/*anatomy &amp; histology/physiology ; Larva ; Motor Neurons/cytology ; }, abstract = {The larval electric organ of Pollimyrus isidori consists of four longitudinal tubes, a dorsal and a ventral pair, which begin behind the skull, end at the beginning of the caudal peduncle and show myotomic segmentation. The elementary units are, apparently, transformed muscle fibres called electrocytes. They are shorter and thicker than muscle fibres, with long stalks and are found in the medial part of the deep lateral muscle. Electron microscopy reveals a clear difference between the anterior and posterior face of the electrocyte. Anteriorly, deep linear invaginations of the surface membrane together with many small vesicles of about 100 nm diameter can be seen. Posteriorly, many plasma membrane invaginations and vacuoles are found together with numerous cytoplasmic organelles--pleiomorphic nuclei, Golgi apparatus, oblong mitochondria and multivesicular bodies. The stalk originates at the posterior face and the nerve terminals are situated at the distal end of the stalk. In the electrocyte, myofibrils, similar to those found in muscle fibres, can be detected with clearly visible Z lines but with only a suggestion of H zones. Two bundles of myofibrils can be seen arranged orthogonally in the electrocyte. Strong acetylcholinesterase activity was found on the anterior face and on the innervated stalk. Under the given recording conditions the overall discharge amplitude of the larval electric organ reaches a maximum of about 100 mV peak to peak. The pulse duration is 1 millisecond and the main phase is head-positive.}, }
@article {pmid418828, year = {1978}, author = {Taylor, FJ}, title = {Problems in the development of an explicit hypothetical phylogeny of the lower eukaryotes.}, journal = {Bio Systems}, volume = {10}, number = {1-2}, pages = {67-89}, doi = {10.1016/0303-2647(78)90031-x}, pmid = {418828}, issn = {0303-2647}, mesh = {Animals ; Apicomplexa/classification ; Chloroplasts/ultrastructure ; Ciliophora/classification ; Eukaryota/*classification ; Flagella/ultrastructure ; Fossils ; Fungi/*classification ; Mitochondria/ultrastructure ; Photosynthesis ; *Phylogeny ; }, abstract = {A semi-explicit arrangement of the lower eukaryotes is provided to serve as a basis for phyletic discussions. No single character is used to determine the position of all the groups. The tree provides no ready separation of protozoa, algae and fungi, groups assigned to these traditional assemblages being considered to be for the most part inextricably interwoven. Photosynthetic forms, whose relationships seem to be more readily discernable, are considered to have given rise repeatedly to nonphotosynthetic forms. The assumption that there are primitive "preflagellar" eukaryotes (red algae, non-flagellated fungi) is adopted. The potential value of mitochondrial features as indicators of broad affinities is emphasised, particularly in determining the probable affinities of non-photosynthetic forms, and this criterion is contra-indicative of a ciliate ancestry for the Metazoa. In the arrangement provided the distributions of chloroplast, mitochondrial and flagellar features match one another well, suggesting their probable co-evolution.}, }
@article {pmid565824, year = {1978}, author = {Hogan, JC}, title = {An ultrastructural analysis of "cytoplasmic markers" in germ cells of Oryzias latipes.}, journal = {Journal of ultrastructure research}, volume = {62}, number = {3}, pages = {237-250}, doi = {10.1016/s0022-5320(78)80021-5}, pmid = {565824}, issn = {0022-5320}, mesh = {Animals ; Biological Evolution ; Cell Differentiation ; Cell Nucleus/ultrastructure ; Cytoplasm/ultrastructure ; Endoplasmic Reticulum/ultrastructure ; Female ; Fishes/*embryology ; Germ Cells/*ultrastructure ; Mitochondria/ultrastructure ; Oocytes/ultrastructure ; }, }
@article {pmid677683, year = {1978}, author = {Boiron, G and Surléve-Bazeille, JE and Gauthier, Y and Maleville, J}, title = {[Ulstrastructural study of various evolutive stages of pityriasis versicolor (author's transl)].}, journal = {Annales de dermatologie et de venereologie}, volume = {105}, number = {2}, pages = {141-149}, pmid = {677683}, issn = {0151-9638}, mesh = {Adult ; Child ; Female ; Humans ; Male ; Melanocytes/ultrastructure ; Pigmentation Disorders/pathology ; Tinea Versicolor/*pathology ; }, abstract = {Small size, less numerous and sometimes clustered melanosomes, were seen within the melanocytes. The others organites alos showed abnormalities: smaller mitochondria, abundant cytofilaments. Sometimes total degeneration of the melanocyte was seen. These alterations are variable, depending upon the evolutive stage of pityriasis versicolor: either hypopigmented undergoing treatment or not, or hyperpigmented. Reactions of several cellular types of the dermoepidermal unit could be observed: more numerous Langerhans cells located near the base of the epidermis, abundant nerve fibers in the superficial dermis and active fibroblasts of foetal type. A slight inflammatory infiltrate was present in some cases. It is suggested that a toxic effect of the fungus is responsible for the changes of the morphological aspects of the melanocyte.}, }
@article {pmid620833, year = {1978}, author = {Matthews, DE and Hessler, RA and O'Brien, TW}, title = {Rapid evolutionary divergence of proteins in mammalian mitochondrial ribosomes.}, journal = {FEBS letters}, volume = {86}, number = {1}, pages = {76-80}, doi = {10.1016/0014-5793(78)80102-1}, pmid = {620833}, issn = {0014-5793}, mesh = {Animals ; *Biological Evolution ; Cattle ; Macromolecular Substances ; Mitochondria, Liver/*physiology ; Molecular Weight ; Rats ; *Ribosomal Proteins ; Ribosomes/*physiology ; Species Specificity ; }, }
@article {pmid202030, year = {1978}, author = {Schwartz, RM and Dayhoff, MO}, title = {Origins of prokaryotes, eukaryotes, mitochondria, and chloroplasts.}, journal = {Science (New York, N.Y.)}, volume = {199}, number = {4327}, pages = {395-403}, doi = {10.1126/science.202030}, pmid = {202030}, issn = {0036-8075}, mesh = {Amino Acid Sequence ; Base Sequence ; *Biological Evolution ; *Cells ; *Chloroplasts ; Computers ; Cytochrome c Group ; *Eukaryotic Cells ; Ferredoxins ; *Mitochondria ; Nucleic Acids ; *Prokaryotic Cells ; Proteins ; RNA, Ribosomal ; }, }
@article {pmid749395, year = {1978}, author = {Coujard, MF}, title = {[II. Ultrastructure of rat superior cervical ganglion cells in organ culture and grafts].}, journal = {Zeitschrift fur mikroskopisch-anatomische Forschung}, volume = {92}, number = {4}, pages = {655-674}, pmid = {749395}, issn = {0044-3107}, mesh = {Animals ; Ganglia, Autonomic/*cytology/transplantation ; Neck ; Nerve Degeneration ; Neurons/*ultrastructure ; Organ Culture Techniques ; Organoids/ultrastructure ; Rats ; Transplantation, Autologous ; Transplantation, Heterologous ; Transplantation, Homologous ; }, abstract = {Ultrastructural modifications of neurons in organ cultures were more and less obvious, while remaining always identical in cultures at the same age. Between 5 and 6 days after culture, neurons showed numerous dense bodies, nuclear pockets, sparse Nissl's bodies broken into fragments, bundles of microfilaments, elongated mitochondria and a slightly distended Golgi apparatus. Sometimes, the nucleus was indented and the nucleolus was shaded off. S.I.F. cells had indented nucleus, dense bodies and bundles of microfibrils. Neurons from direct grafts presented modifications similar to those observed in cultures at short time intervals. Then the breaking up of Nissl's bodies and mitochondria and the hyalin transformation of dense bodies took place. A restoration, at first involving the nucleus, could occur in relation with immunological conditions. The evolution of S.I.F. cells was quite comparable to that of neurons. In either case, features of cellular degeneracy were always little marked and fugitive.}, }
@article {pmid747394, year = {1978}, author = {Wissocq, JC}, title = {[Evolution of muscles in Nereidae (Annelida polycheta) during epitoky. I and II. Atokous and epitokous longitudinal fibres (author's transl)].}, journal = {Archives d'anatomie microscopique et de morphologie experimentale}, volume = {67}, number = {1}, pages = {37-62}, pmid = {747394}, issn = {0003-9594}, mesh = {Animals ; Cell Nucleus/ultrastructure ; Glycogen/pharmacology ; Mitochondria, Muscle/physiology ; Muscle Contraction/drug effects ; Muscles/*cytology ; Myofibrils/physiology/ultrastructure ; Neuromuscular Junction/cytology ; Polychaeta/*anatomy &amp; histology ; Sarcoplasmic Reticulum ; }, abstract = {The longitudinal fibres from atokous Nereis belong to the double oblique striation type. Their thick myofilaments, paramyosinic (about 145 A periodicity) are arranged in an hexagonal lattice, well preserved after a glycerol treatment. 9 to 13 thin filaments form an orbit around one thick filament (ratio: 6-7/1). The contraction occurs in two processes: a sliding filament mechanism, and a shearing mechanism. This second mechanism consists in a parallel shifting of thick filaments, arising their overlap and decreasing their degree of stagger; it induces the increase of the myofibrillar (A-bands) oblique angle from 10-12 degrees in isolated glycerol extracted fibres, to 35-38 degrees in the same fibres after contraction by the action of ATP-solution. The longitudinal fibres from epitokous Nereis or Heteronereis are characterized also by a double oblique striation. The structural aspects of the contraction are similar to these ones occurring in atokous fibres. Nevertheless, the epitokous fibres are different from the atokous fibres by many characteristic points. Their thick myofilaments, with an hexagonous array, are thinner and shorter than these ones from atokous fibres. The contractile material is only present in the cortex. The axis of epitokous fibres is filled with numerous mitochondria, between them numerous glycogen particles have been synthetised. The sarcoplasm of the fiber's coelomic edge is often devoided of myofilaments but it is full of mitochondria and glycogen granules. The nucleus, with a voluminous nucleolus, is no more placed in the fibre axis, but in a lateral sarcoplasm containing ribosomes, glycogen and mitochondria. The important transformations of longitudinal fibres are discussed in connection with the Heteronereis locomotor behaviour, very different from this one of the atokus Nereis. Particularly, it seems that the abundance of glycogen and mitochondria in epitokous muscles allows a high contraction frequency. The decrease of the diameter and length from the thick filaments should be set in relation with the augmentation of the contraction's swiftness. These results are very similar to these ones occuring in Syllidae with the stolonization mode of reproduction. The Syllis stolonial fibres present the same characteristics than the Nereis epitokous fibres.}, }
@article {pmid274302, year = {1978}, author = {Cannon, B and Nedergaard, J}, title = {Energy dissipation in brown fat.}, journal = {Experientia. Supplementum}, volume = {32}, number = {}, pages = {107-111}, doi = {10.1007/978-3-0348-5559-4_12}, pmid = {274302}, issn = {0071-335X}, mesh = {Adenosine Triphosphate/biosynthesis ; Adipose Tissue, Brown/drug effects/*metabolism/ultrastructure ; Amino Acids/biosynthesis ; Animals ; Carbon Dioxide/pharmacology ; Citric Acid Cycle ; Cricetinae ; *Energy Metabolism/drug effects ; Fatty Acids/metabolism ; In Vitro Techniques ; Mitochondria/metabolism ; Norepinephrine/pharmacology ; Oxygen Consumption/drug effects ; }, abstract = {Heat evolution in isolated brown fat cells has been measured by microcalorimetry. Thermogenesis (= oxygen consumption) is enhanced in the presence of CO2. This effect is probably due to pyruvate carboxylase activity which will increase the mitochondrial concentration of oxaloacetate. Oxaloacetate serves as condensing partner for acetyl-CoA coming from fatty acid oxidation. The high rate of oxygen consumption is impossible in cells when mitochondrial respiration is coupled to ATP synthesis, due to low amounts of ATP synthetase enzyme. A loosening of coupling is therefore required. This is possibly facilitated by acyl-CoA.}, }
@article {pmid914998, year = {1977}, author = {Burton, KP and Hagler, HK and Templeton, GH and Willerson, JT and Buja, LM}, title = {Lanthanum probe studies of cellular pathophysiology induced by hypoxia in isolated cardiac muscle.}, journal = {The Journal of clinical investigation}, volume = {60}, number = {6}, pages = {1289-1302}, pmid = {914998}, issn = {0021-9738}, mesh = {Animals ; Cats ; Cell Membrane/ultrastructure ; Glycogen/metabolism ; Hypoxia/*complications/pathology ; *Lanthanum/metabolism ; Methods ; Microscopy, Electron ; Mitochondria, Muscle/ultrastructure ; Myocardial Infarction/metabolism/*pathology ; Myocardium/metabolism/*ultrastructure ; Myofibrils/ultrastructure ; }, abstract = {This study was undertaken to evaluate directly the relationship between evolution of irreversible myocardial injury induced by hypoxia in an isolated papillary muscle preparation and the development of pathophysiological alterations related to severely impaired membrane function. An ionic lanthanum probe technique was employed as a cytochemical marker to monitor the progression of cellular injury, and data from this cytologic technique were correlated with ultrastructure and measurements of contractile parameters in a total of 67 muscles subjected to control conditions or to graded intervals of hypoxia with or without reoxygenation. Marked depression of developed tension and rate of tension development occurred after 30 min of hypoxia. Contractile function showed significant recovery with reoxygenation after 1 h and 15 min of hypoxia but remained depressed when reoxygenation was provided after 2 or 3 h of hypoxia. Examination by transmission and analytical electron microscopy (energy dispersive X-ray microanalysis) revealed lanthanum deposition only in extracellular regions of control muscles and muscles subjected to 30 min of hypoxia. After hypoxic intervals of over 1 h, abnormal intracytoplasmic and intramitochondrial localization of lanthanum were detected. After 1 h and 15 min of hypoxia, abnormal intracellular lanthanum accumulation was associated with only minimal ultrastructural evidence of injury; muscle provided reoxygenation after 1 h and 15 min of hypoxia showed improved ultrastructure and did not exhibit intracellular lanthanum deposits upon exposure to lanthanum during the reoxygenation period. After 2 to 3 h of hypoxia, abnormal intracellular lanthanum accumulation was associated with ultrastructural evidence of severe muscle injury which persisted after reoxygenation. Thus, the data support the conclusion that cellular and membrane alterations responsible for abnormal intracellular lanthanum deposition precede the development of irreversible injury but evolve at a transitional stage in the progression from reversible to irreversible injury induced by hypoxia in isolated feline papillary muscles.}, }
@article {pmid592424, year = {1977}, author = {Woese, CR}, title = {Endosymbionts and mitochondrial origins.}, journal = {Journal of molecular evolution}, volume = {10}, number = {2}, pages = {93-96}, pmid = {592424}, issn = {0022-2844}, mesh = {*Biological Evolution ; Chloroplasts ; DNA, Mitochondrial/genetics ; Genes ; *Mitochondria ; Oxygen Consumption ; *Symbiosis ; }, abstract = {The possibility is put forth that the mitochondrion did not originate from an endosymbiosis, 1-2 billion years ago, involving an aerobic bacterium. Rather, it arose by endosymbiosis in a much early, anaerobic period, and was initially a photosynthetic organelle, analogous to the modern chloroplast. This suggestion arises from a reconsideration of the nature of endosymbiosis. It explains the remarkable diversity in mitochondrial information storage and processing systems.}, }
@article {pmid611361, year = {1977}, author = {Biagini, G and Misciattelli, ME and Contri Baccarani, M and Vangelista, A and Raffi, GB and Caudarella, R}, title = {[Electron microscopy features of renal changes in chronic lead poisoning (author's transl)].}, journal = {Lavoro umano}, volume = {29}, number = {6}, pages = {179-187}, pmid = {611361}, issn = {0023-9127}, mesh = {Adult ; Aged ; Basement Membrane/ultrastructure ; Chronic Disease ; Endoplasmic Reticulum/ultrastructure ; Humans ; Kidney/*ultrastructure ; Kidney Tubules/ultrastructure ; Lead Poisoning/*pathology ; Microscopy, Electron ; Microvilli/ultrastructure ; Middle Aged ; Mitochondrial Swelling ; }, abstract = {The Authors report the results of a renal morphological study carried out on eight patients with chronic lead poisoning. The ultrastructural analysis showed changes, mainly involving the proximal tubules, as follows: 1) degenerative pattern (swollen mitochondria, dilated endoplasmic reticulum and scanty microvilli); 2) signs of metabolic hyperactivity (intranuclear granular inclusions, odd shaped nuclei); 3) regenerative pattern (poorly differentiated cells with few microvilli, shallow infoldings of basal cell membranes). In the glomeruli the most characteristic finding was a mesangial reaction. The basement membrane, in some cases, appeared to be thickened and the visceral epithelial cells hypertrophic. Interstitial fibrosis was present, as well as, occasionally, a certain degree of arteriolar hyperplasia. These data appear to confirm that chronic lead nephropathy has an extremely slow evolution.}, }
@article {pmid607961, year = {1977}, author = {Bernardi, G}, title = {Organization and evolution of the mitochondrial genome of yeast.}, journal = {Bollettino della Societa italiana di biologia sperimentale}, volume = {53}, number = {18 Pt 2}, pages = {7-17}, pmid = {607961}, issn = {0037-8771}, mesh = {DNA, Mitochondrial ; Genes ; Mitochondria ; Polyploidy ; Yeasts/*genetics ; }, }
@article {pmid197321, year = {1977}, author = {Ostroumov, SA}, title = {Participation of chloroplasts and mitochondria in virus reproduction and the evolution of the eukaryotic cell.}, journal = {Journal of theoretical biology}, volume = {67}, number = {2}, pages = {287-297}, doi = {10.1016/0022-5193(77)90201-6}, pmid = {197321}, issn = {0022-5193}, mesh = {Animals ; *Biological Evolution ; Chloroplasts ; DNA ; Mitochondria ; *Models, Biological ; Plants ; Sarcoma, Avian/ultrastructure ; *Virus Replication ; }, }
@article {pmid193188, year = {1977}, author = {Goldberg, E and Sberna, D and Wheat, TE and Urbanski, GJ and Margoliash, E}, title = {Cytochrome c: immunofluorescent localization of the testis-specific form.}, journal = {Science (New York, N.Y.)}, volume = {196}, number = {4293}, pages = {1010-1012}, doi = {10.1126/science.193188}, pmid = {193188}, issn = {0036-8075}, mesh = {Animals ; Biological Evolution ; Cytochrome c Group/*metabolism ; Fluorescent Antibody Technique ; Genes ; Male ; Mice ; Mitochondria/metabolism ; Seminiferous Epithelium/*metabolism ; Sertoli Cells/metabolism ; Spermatocytes/metabolism ; *Spermatogenesis ; Spermatogonia/metabolism ; Testis/cytology/*metabolism ; }, abstract = {Mouse testes contain a unique form of cytochrome c. As demonstrated by the indirect immunofluorescence technique, the testis-specific cytochrome c is detectable in the primary spermatocyte and in cell types comprising the later stages of spermatogenesis. Interstitial cells, Sertoli cells, and spermatogonia contain the somatic form of cytochrome c, as does heart muscle.}, }
@article {pmid559936, year = {1977}, author = {Dykstra, MJ}, title = {The possible phylogenetic significance of mitochondrial configurations in the acrasid cellular slime molds with reference to members of the Eumycetozoa and fungi.}, journal = {Mycologia}, volume = {69}, number = {3}, pages = {579-591}, pmid = {559936}, issn = {0027-5514}, mesh = {*Biological Evolution ; Dictyostelium/ultrastructure ; Fungi/ultrastructure ; Mitochondria/*ultrastructure ; Myxomycetes/*ultrastructure ; *Phylogeny ; }, }
@article {pmid886245, year = {1977}, author = {Cudennec, C and Nicolas, JF}, title = {Blood formation in a clonal cell line of mouse teratocarcinoma.}, journal = {Journal of embryology and experimental morphology}, volume = {38}, number = {}, pages = {203-210}, pmid = {886245}, issn = {0022-0752}, mesh = {Cell Differentiation ; Cell Line ; Endoderm/ultrastructure ; Endoplasmic Reticulum/ultrastructure ; Epithelial Cells ; Epithelium/ultrastructure ; Erythroblasts/ultrastructure ; *Erythropoiesis ; Golgi Apparatus/ultrastructure ; Intercellular Junctions/ultrastructure ; Mitochondria/ultrastructure ; Organ Culture Techniques ; Polyribosomes/ultrastructure ; *Teratoma ; }, abstract = {Pluripotent cells of a teratocarcinoma clonal line differentiate into various tissues when they are cultivated in submerged cultures. We describe here the formation of endodermal vesicles and blood islands in organotypic cultures of such cells. These are the first macroscopically visible tissues to appear in organ culture and they give rise to megalocytes, the ultimate stage of blood cell evolution in the normal mouse embryo yolk-sac. As in the normal embryo yolk-sac, the formation of haemoglobin-containing cells stops after a while, but it is not replaced by adult haemopoiesis in culture.}, }
@article {pmid557532, year = {1977}, author = {Horten, BC and Urich, H and Rubinstein, LJ and Montague, SR}, title = {The angioblastic meningioma: a reappraisal of the nosological problem. Light-, electron-microscopic, tissue, and organ culture observations.}, journal = {Journal of the neurological sciences}, volume = {31}, number = {3}, pages = {387-410}, doi = {10.1016/0022-510x(77)90217-9}, pmid = {557532}, issn = {0022-510X}, mesh = {Brain Neoplasms/*classification/ultrastructure ; Cells, Cultured ; Endoplasmic Reticulum/ultrastructure ; Hemangiopericytoma/classification/ultrastructure ; Hemangiosarcoma/*classification/ultrastructure ; Humans ; Meningioma/ultrastructure ; Mitochondria/ultrastructure ; Neurofibrils/ultrastructure ; Organ Culture Techniques ; Spinal Cord Neoplasms/*classification/ultrastructure ; }, abstract = {The validity of the concept of the angioblastic meningioma, now in dispute, was reexamined by reviewing 79 meningeal and angioblastic tumors of the central nervous system and by comparing the fine structural characteristics and in vitro evolution of 2 typical meningiomas and 1 intracranial hemangiopericytoma. While most tumors show the consistent features of either hemangiopericytoma or hemangioblastoma, there exist transitional forms between these tumors and typical meningioma. There is also a greater degree of morphological overlap at the electron microscopic level than has been recognized up till now. In view of these findings the concept of the angioblastic meningioma deserves to be retained as a generic term to include craniospinal hemangiopericytomas and transitional forms between hemangiopericytoma, hemangioblastoma and classic meningioma. It is postulated that all these tumors share a common origin from polyblastic mesenchymal cells originating in or derived from the meninges.}, }
@article {pmid866186, year = {1977}, author = {Bonen, L and Cunningham, RS and Gray, MW and Doolittle, WF}, title = {Wheat embryo mitochondrial 18S ribosomal RNA: evidence for its prokaryotic nature.}, journal = {Nucleic acids research}, volume = {4}, number = {3}, pages = {663-671}, pmid = {866186}, issn = {0305-1048}, mesh = {Base Sequence ; Biological Evolution ; Chemical Phenomena ; Chemistry ; Cytosol/analysis ; Embryo, Mammalian/analysis ; Embryo, Nonmammalian ; Mitochondria/*analysis ; Oligonucleotides ; *RNA, Ribosomal/isolation &amp; purification ; Ribonucleases ; Ribonucleotides/*analysis ; Species Specificity ; Triticum/*analysis ; }, abstract = {We present a catalog of sequences of oligonucleotides produced by T1 ribonuclease digestion of 32P-labeled small-ribosomal-subunit RNA ("18S rRNA) isolated from purified wheat embryo mitochondria. This catalog is compared to catalogs published for prokaryotic and chloroplast 16S rRNAs and to preliminary results for wheat cytosol 18S rRNA. These comparisons indicate that: (1) wheat mitochondrial 18S rRNA is clearly prokaryotic in nature, showing significantly more sequence homology with 16S rRNAs than can be expected to arise by chance (p less than 0.000001); (2) shared oligonucleotide sequences include an especially high proportion of those identified as conserved in the evolution of prokaryotic rRNAs; and (3) wheat embryo mitochondrial and cytosol 18S rRNAs retain no more, and perhaps less, than the minimum sequence homology detectable by this sensitive method. These results argue in favor of an endosymbiotic origin for mitochondria.}, }
@article {pmid190357, year = {1977}, author = {Spencer, PS and Schaumburg, HH}, title = {Ultrastructural studies of the dying-back process. III. The evolution of experimental peripheral giant axonal degeneration.}, journal = {Journal of neuropathology and experimental neurology}, volume = {36}, number = {2}, pages = {276-299}, doi = {10.1097/00005072-197703000-00005}, pmid = {190357}, issn = {0022-3069}, mesh = {Alkanes/adverse effects ; Animals ; Axons/*ultrastructure ; Hexanones/adverse effects ; Methyl n-Butyl Ketone/adverse effects ; *Nerve Degeneration ; Nerve Fibers, Myelinated/pathology/ultrastructure ; Nerve Regeneration ; Peripheral Nerves/*ultrastructure ; Peripheral Nervous System Diseases/chemically induced/*pathology ; Rats ; Time Factors ; }, abstract = {The spatio-temporal evolution of peripheral giant axonal degeneration has been studied in rats during the development of concurrent peripheral (PNS) and central (CNS) nervous system dying-back disease after chronic intoxication with the neurotoxic hexacarbons n-hexane (CH3CH2CH2CH2CH2CH3), methyl n-butyl ketone (MBK) (CH3COCH2CH2CH2CH3), or 2,5-hexanedione (CH3COCH2CH2CHOCH3), a neurotoxic metabolite of MBK. Each compound caused animals insidiously to develop identical, symmetrical peripheral neuropathies characterized by eversion and drop of hindfeet, inability to extend hindlimbs and upper extremity weakness. Teased fiber studies demonstrated that giant axonal swellings first developed on the proximal sides of multiple paranodes sited in distal, non-terminal regions of large myelinated fibers. Later, swellings developed at internodal sites. Smaller myelinated and unmyelinated fibers also underwent multifocal, giant axonal swelling. In affected myelinated fibers, swollen nodal and paranodal axons were frequently associated with retracted paranodal myelin sheaths. Adjacent distal internodes were attenuated and corrugated. Demyelinated paranodes apparently underwent local shrinkage and remyelination before complete distal fiber breakdown commenced. The proximal limits of chains of homogeneous myelin ovoids were interfaced with proximal, preserved regions at sites of giant axonal swellings. Regeneration of myelinated axons also occurred during intoxication. Regenerating fibers wre composed of multiple, short, branched internodes which sometimes appeared multifocally swollen. Interfaces between regenerating and preserved portions of fibers were unswollen. Thick section studies showed that pronounced endoneurial edema accompanied fiber degeneration in peripheral nerve trunks. Ultrastructural studies revealed multifocal, giant axonal swellings containing masses of 10 nm neurofilaments and sometimes, clustered mitochondria, neurotubules and smooth endoplasmic reticulum. Enlarged granular mitochondria, interdigitated Schwann cell/axon networks and corrugated myelin sheaths were common findings. Dense granules, vesicles and hexagonal particles were also noted in the axoplasm. These findings provide new insights into the nature of the dying-back process: although there was a retrograde, temporal spread of axonal swelling up affected nerve trunks, axonal degeneration neither began in the nerve terminal nor spread seriatim centripetally along individual nerve fibers. The dying-back process was further examined in a companion study in this issue (32) which analyzed some of the factors determining the differential vulnerability of PNS and CNS fibers in animals intoxicated either with these neurotoxic hexacarbons or with acrylamide.}, }
@article {pmid576735, year = {1977}, author = {Vuia, O}, title = {Congenital spongy degeneration of the brain (van Bogaert - Bertrand) associated with micrencephaly and ponto - cerebellar atrophy (contributions to the pathology of glial dystrophy of intrauterin origin).}, journal = {Neuropadiatrie}, volume = {8}, number = {1}, pages = {73-87}, doi = {10.1055/s-0028-1091507}, pmid = {576735}, issn = {0028-3797}, mesh = {Atrophy ; Brain/*abnormalities ; Cerebellum/abnormalities/pathology ; *Diseases in Twins ; Humans ; Infant, Newborn ; Lipidoses/*pathology ; Male ; Microscopy, Electron ; Neuroglia ; Pons/abnormalities/pathology ; Purkinje Cells/ultrastructure ; Syndrome ; }, abstract = {The present paper reports on two twin brothers who presented clinically at birth a syndrome characterized by progressive development of muscular hypertonia, opisthotonus, micrencephaly, amaurosis and short, localized clonic seizures. Both children died soon after one year of age. The anatomic examination performed in one case revealed a spongy degeneration of the brain of van Bogaert-Bertrand type. Associated to the cerebral degenerative syndrome was a severe malformative syndrome characterized by micrencephaly, internal hydrocephalus and pontocerebellar atrophy. The ultrastructure of the cerebellar cortex showed degenerative phenomena in the Purkinje and glial cells, demonstrating the evolutive character of the ponto-cerebellar lesions. The degenerative process consisted of the accumulation of lamellar bodies within the mitochondria and free in the cellular cytoplasm with tendency to form inclusions of the multilamellar or finger-print type. Association of the degenerative with the malformative process is not considered to be accidental but based upon the same fundamental pathologic process: glial dystrophy. It may be assumed that the pathologic defect, which as a rule produces syndromes that appear after birth (spongy degeneration of the brain, ponto-cerebellar atrophy), may in some instances act at an early date in intrauterine life, the glial dystrophy that appears so early producing both the degenerative and the malformative process.}, }
@article {pmid556886, year = {1977}, author = {Gutierrez, JA and Norenberg, MD}, title = {Ultrastructural study of methionine sulfoximine-induced Alzheimer type II astrocytosis.}, journal = {The American journal of pathology}, volume = {86}, number = {2}, pages = {285-300}, pmid = {556886}, issn = {0002-9440}, mesh = {Alzheimer Disease/chemically induced/*pathology ; Animals ; Astrocytes/drug effects/*ultrastructure ; Cerebral Cortex/ultrastructure ; Dementia/*pathology ; Endoplasmic Reticulum/ultrastructure ; Humans ; Male ; *Methionine Sulfoximine/administration &amp; dosage ; Mitochondria/ultrastructure ; Neuroglia/*ultrastructure ; Rats ; Seizures/*chemically induced ; Vacuoles/ultrastructure ; }, abstract = {An ultrastructural study of cerebral cortex was performed in rats during the preictal period following the administration of the convulsant methionine sulfoximine (MSO). The morphologic changes were restricted to astrocytes and consisted of cytoplasmic enlargement, mitochondrial and rough endoplasmic reticulum proliferation, accumulation of glycogen, development of cisternal and saccular smooth endoplasmic reticulum, nuclear chromatin clumping, and hydropic degenerative changes. These findings resemble those seen in experimental ammonia encephalopathy, suggesting an important role of ammonia in the evolution of these morphologic changes. The findings, moreover, suggest that the primary effect of MSO is on astrocytes and that abnormalities in astrocytes may play a role in the development of MSO-induced seizures.}, }
@article {pmid194036, year = {1977}, author = {Fenchel, T and Perry, T and Thane, A}, title = {Anaerobiosis and symbiosis with bacteria in free-living ciliates.}, journal = {The Journal of protozoology}, volume = {24}, number = {1}, pages = {154-163}, doi = {10.1111/j.1550-7408.1977.tb05294.x}, pmid = {194036}, issn = {0022-3921}, mesh = {Anaerobiosis ; Biological Evolution ; Ciliophora/*metabolism/microbiology/ultrastructure ; Electron Transport Complex IV/metabolism ; Microscopy, Electron ; Microscopy, Electron, Scanning ; Mitochondria/ultrastructure ; Sulfides/metabolism ; Symbiosis ; }, abstract = {Marine, sediment-dwelling ciliates were examined for cytochrome oxidase activity by a cytochemical method and for fine structural details. Species of Plagiopylidae (Trichostomatida), i.e. Plagiopyla frontata, Sonderia vorax and Sonderia sp., and of Heterotrichda, i.e., Parablepharisma pellitum, Parablepharisma sp., Metopus contortus, Metopus vestitus and Caenomorpha capucina; previously considered to be obligate anaerobes because of their sulfide-containing habitat, do not have cytochrome oxidase activity or mitochondria with cristae or tubuli. The evolutionary origin and significance of anaerobic ciliates is discussed. Most of the anaerobic ciliates harbor a flora of ecto- and endosymbiotic bacteria as demonstrated by transmission and scanning electron micrographs. It is speculated that the bacteria may utilize the metabolic end products of the protozoa for growth and energy yielding processes. These associations are also compared with other, previously described cases of symbiosis involving prokaryotes and protozoa.}, }
@article {pmid14427, year = {1977}, author = {Ojeda, F and Schraub, A and Sattler, EL}, title = {[Radiation response of mitochondria in dependence on their metabolic status (author's transl)].}, journal = {Strahlentherapie}, volume = {153}, number = {2}, pages = {117-123}, pmid = {14427}, issn = {0039-2073}, mesh = {Animals ; Female ; Hydroxybutyrates/pharmacology ; Mitochondria, Liver/drug effects/metabolism/*radiation effects ; NAD/metabolism ; NADP/metabolism ; Rats ; }, abstract = {The influence of the metabolic status of mitochondria upon their radiation response was studied. It turned out that the reduction of pyridine nucleotides by addition of beta-hydroxybutyrate (BOH) and the decrease through respiration were distinctly impaired in mitochondria with a substrate deficit by an irradiation with 2.7 krd already. The evolution of the lesion depends on the incubation conditions following irradiation, a presence of BOH having protective effects. The general redox level seems to be essential for radiation response of mitochondria. An exit of NAD from mitochondria has proved to be the main cause for inhibition of the respiratory BOH-consumption.}, }
@article {pmid401816, year = {1977}, author = {Sonderegger, P and Gehring, H and Christen, P}, title = {Interspecies comparison of cytosolic and mitochondrial aspartate aminotransferases. Evidence for a more conservative evolution of the mitochondrial isoenzyme.}, journal = {The Journal of biological chemistry}, volume = {252}, number = {2}, pages = {609-612}, pmid = {401816}, issn = {0021-9258}, mesh = {Animals ; Aspartate Aminotransferases/immunology/*metabolism ; *Biological Evolution ; Chickens ; Complement Fixation Tests ; Cross Reactions ; Cytosol/*enzymology ; Immunodiffusion ; Isoenzymes/*metabolism ; Mitochondria, Muscle/*enzymology ; Myocardium/*enzymology ; Species Specificity ; Swine ; }, abstract = {The degree of structural similarity between the mitochondrial isoenzymes of aspartate aminotransferase from pig heart and chicken heart was determined by means of their immunological cross-reactivity and compared with the degree of similarity between the cytosolic isoenzymes from the same two species. Quantitative microcomplement fixation revealed a remarkable similarity of the two mitochondrial isoenzymes corresponding to an immunological distance of 104. The structures of the two cytosolic isoenzymes, on the other hand, diverge with an immunological distance of 203. The apparent conservatism of mitochondrial aspartate aminotransferase indicates additional evolutionary constraints on the structure of this organelle-confined isoenzyme.}, }
@article {pmid837393, year = {1977}, author = {Hama, K and Yamada, Y}, title = {Fine structure of the ordinary lateral line organ. II. The lateral line canal organ of spotted shark, Mustelus manazo.}, journal = {Cell and tissue research}, volume = {176}, number = {1}, pages = {23-36}, pmid = {837393}, issn = {0302-766X}, mesh = {Animals ; Biological Evolution ; Cilia/ultrastructure ; Fishes/anatomy &amp; histology ; Lampreys/anatomy &amp; histology ; Mechanoreceptors/*ultrastructure ; Microscopy, Electron ; Sharks/*anatomy &amp; histology ; Water Movements ; }, abstract = {The lateral line organ of the spotted shark is characterized by its semi-cylindrical shape. Each organ (neuromast) is so closely apposed to the next that the individual neuromasts are almost continuous. The neuromast is composed of receptor cells, supporting cells and mantle cells. The receptor cells bear one kinocilium and up to 40 stereocilia. Bi-directional arrangement of the receptor cells as occurs in teleosts was demonstrated. Afferent and efferent nerve endings were found at the base of the receptor cells. The supporting cells extend from the basal lamina to the free surface. Long microvilli and a cilium-like "ciliary rod" project from the top of each supporting cell. The cell contains relatively few elements of the Golgi apparatus and little rough endoplasmic reticulum, but mitochondria and filaments are abundant. The mantle cell limits the lateral margin of the neuromast. It is distinguished from the supporting cell because of its long crescent-shaped nucleus and scarce, short microvilli. Myelinated nerve fibres are found in the subepithelial connective tissue but not in the epithelium. The fine structure of the shark lateral line organ suggests that this organ is in an intermediated step of evolution between that of lamphrey and teleost.}, }
@article {pmid610007, year = {1977}, author = {Noirot, C and Noirot-Timothée, C}, title = {Fine structure of the rectum in termites (Isoptera): a comparative study.}, journal = {Tissue &amp; cell}, volume = {9}, number = {4}, pages = {693-710}, doi = {10.1016/0040-8166(77)90036-2}, pmid = {610007}, issn = {0040-8166}, mesh = {Animals ; Biological Evolution ; Cell Nucleus/ultrastructure ; Insecta/*ultrastructure ; Intercellular Junctions/ultrastructure ; Mitochondria/ultrastructure ; Rectum/ultrastructure ; Species Specificity ; }, }
@article {pmid328366, year = {1977}, author = {Neupert, W}, title = {Mitochondrial ribosomes.}, journal = {Horizons in biochemistry and biophysics}, volume = {3}, number = {}, pages = {257-296}, pmid = {328366}, issn = {0096-2708}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Biological Evolution ; Cytoplasm ; DNA, Mitochondrial/metabolism ; Drug Resistance ; Eukaryota ; Fungi ; Mitochondria/*metabolism ; Molecular Weight ; Mutation ; Neurospora/metabolism ; Nucleotides/analysis ; Plants ; Protein Biosynthesis ; RNA, Ribosomal/analysis/biosynthesis ; Ribosomal Proteins/analysis/biosynthesis ; Ribosomes/analysis/*metabolism/ultrastructure ; }, }
@article {pmid264684, year = {1977}, author = {Yang, NS and Sorenson, JC and Scandalios, JG}, title = {Genetic control of mitochondrial malate dehydrogenases: evidence for duplicated chromosome segments.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {74}, number = {1}, pages = {310-314}, pmid = {264684}, issn = {0027-8424}, mesh = {Alleles ; Biological Evolution ; *Chromosome Aberrations ; Cytoplasm/enzymology ; *Genes ; Genetic Linkage ; Isoenzymes/*metabolism ; Malate Dehydrogenase/*metabolism ; Mitochondria/*enzymology ; Models, Biological ; Zea mays/enzymology ; }, abstract = {The genetic control of the major mitochondrial isoenzymes of malate dehydrogenase (L-malate:NAD+ oxidoreductase; EC 1.1.1.37) has been investigated in Zea mays. The mitochondrial isozymes are coded at four nuclear gene loci. Two of the loci (mdh1 and mdh2) are diallelic and tightly linked. The other two loci (mdh3 and mdh4) appear to have arisen by duplication of the chromosome segment carrying mdh1 and mdh2, but are not linked to them. The segregation of such a duplicate segment can explain anomalous backcross and F2 segregation ratios.}, }
@article {pmid143673, year = {1977}, author = {Welch, GR}, title = {On the role of organized multienzyme systems in cellular metabolism: a general synthesis.}, journal = {Progress in biophysics and molecular biology}, volume = {32}, number = {2}, pages = {103-191}, pmid = {143673}, issn = {0079-6107}, mesh = {Biological Evolution ; Catalysis ; Cells/enzymology ; Diffusion ; Escherichia coli/enzymology ; Euglena gracilis/enzymology ; Fatty Acid Synthases/physiology ; Fatty Acids/biosynthesis ; Kinetics ; Mathematics ; Mitochondria/enzymology ; Models, Biological ; Multienzyme Complexes/*physiology ; Neurospora crassa/enzymology ; Prephenate Dehydratase/physiology ; Protein Conformation ; Pyruvate Dehydrogenase Complex/physiology ; Saccharomyces cerevisiae/enzymology ; Tetrahydrofolates/biosynthesis ; Tryptophan Synthase/physiology ; }, }
@article {pmid798040, year = {1976}, author = {Bernardi, G}, title = {Organization and evolution of the mitochondrial genome of yeast.}, journal = {Journal of molecular evolution}, volume = {9}, number = {1}, pages = {25-35}, pmid = {798040}, issn = {0022-2844}, mesh = {*Biological Evolution ; Crosses, Genetic ; DNA ; DNA Restriction Enzymes ; Deoxyribonucleases ; Electrophoresis, Polyacrylamide Gel ; Escherichia coli/metabolism ; *Genotype ; Micrococcal Nuclease ; Mitochondria/*physiology ; Pancreas/enzymology ; Recombination, Genetic ; Saccharomyces/*physiology ; Saccharomyces cerevisiae/*physiology ; }, abstract = {The mitochondrial genome of yeast (S. cerevisiae or S. carlsbergensis) appears to be formed by 60-70 genetic units, each one of which is formed by (1) a GC-rich sequence, possibly having a regulatory role; (2) a gene, and (3) an AT-rich spacer, which probably is not transcribed. Recombination in this genome appears to underlie a number of important phenomena. The organization of the mitochondrial genome of yeast and these recombinational events are discussed in relationship with the organization and evolution of the nuclear genome of eukaryotes.}, }
@article {pmid983936, year = {1976}, author = {Kraikitpanitch, S and Haygood, CC and Baxter, DJ and Yunice, AA and Lindeman, RD}, title = {Effects of acetylsalicylic acid, dipyridamole, and hydrocortisone on epinephrine-induced myocardial injury in dogs.}, journal = {American heart journal}, volume = {92}, number = {5}, pages = {615-622}, doi = {10.1016/s0002-8703(76)80081-6}, pmid = {983936}, issn = {0002-8703}, mesh = {Acute Disease ; Animals ; Aspartate Aminotransferases/blood ; Aspirin/*pharmacology ; Calcium/blood ; Calcium Chloride/adverse effects ; Cardiomyopathies/*chemically induced/metabolism ; Dipyridamole/*pharmacology ; Dogs ; Drug Therapy, Combination ; Electrolytes/metabolism ; Epinephrine/*adverse effects ; Hydrocortisone/*pharmacology ; Mitochondria, Muscle/metabolism ; Myocardial Contraction/drug effects ; Myocardial Infarction/prevention &amp; control ; Myocardium/metabolism ; Necrosis ; Premedication ; }, abstract = {A reproducible model for producing diffuse myocardial injury (epinephrine infusion) has been developed to study the cardioprotective effects of agents or maneuvers which might alter the evolution of acute myocardial infarction. Infusions of epinephrine (4 mug per kilogram per minute for 6 hours) increased radiocalcium uptakes into intact myocardium and each of its subcellular components with the mitochondrial fraction showing the most consistent changes when compared to saline-infused control animals (4,957 vs. 827 counts per minute per gram of dried tissue or fraction). Myocardial concentrations of calcium also increased significantly (12.0 vs. 5.0 mg.per 100 Gm. of fat-free dry weight). Infusions of calcium chloride sufficient to raise serum calcium concentrations 2 mEq. per liter failed to increase calcium influx into the myocardial cell. Mitochondrial radiocalcium uptakes were significantly decreased in animals pretreated with acetylsalicylic acid or dipyridamole or when hydrocortisone was added to the epinephrine infusion (2,682,2,803, and 3,424 counts per minute per gram of dried fraction, respectively). Myocardial calcium concentrations also were decreased (11.2, 8.3, and 8.9 mg. per 100 Gm. of fat-free dry weight, respectively) in the three treatment groups, being significantly decreased only in the last two. Evidence of microscopic damage was graded as less severe in the three treatment groups. Acetylsalicylic acid, dipyridamole, and hydrocortisone all appear to have cardioprotective effects when tested in this model.}, }
@article {pmid780131, year = {1976}, author = {Wills, C}, title = {Controlling protein evolution.}, journal = {Federation proceedings}, volume = {35}, number = {10}, pages = {2098-2101}, pmid = {780131}, issn = {0014-9446}, mesh = {Alcohol Oxidoreductases/metabolism ; *Biological Evolution ; Cytoplasm/enzymology ; Electrophoresis ; Kinetics ; Mitochondria/enzymology ; Mutation ; Polymorphism, Genetic ; *Proteins ; Saccharomyces cerevisiae/enzymology/ultrastructure ; }, abstract = {A method is presented for selecting, with a high degree of specificity, mutants for the enzyme alcohol dehydrogenase (ADH) of Saccharomyces cerevisiae having altered kinetics. The method depends on the facts that a) petite yeast strains (those unable to respire aerobically) have an absolute dependence on the presence of cytoplasmic alcohol dehydrogenase, and b) allyl alcohol is readily oxidized by yeast ADH to the highly poisonous product acrolein. If petite yeast are grown in the presence of allyl alcohol surviving mutants show alterations that can be traced to the ADH structural gene. Eight out of nine spontaneous mutant enzymes and five out of five mutants enzymes induced by nitrosoguanidine exhibited a slower electrophoresis mobility than wild type. There may therefore be some correlation between electrophoretic mobility and function. Of three mutant enzymes purified, one of spontaneous origin and two induced by nitrosoguanidine, each showed a different pattern of altered kinetics and a different specific activity. This strongly suggests that, despite the considerable specificity of the selective procedure, there are many ways in which an enzyme can be altered in response to an environmental stimulus. The implications of these results for the study of protein evolution and some directions for future research are briefly discussed.}, }
@article {pmid181273, year = {1976}, author = {Dayhoff, MO}, title = {The origin and evolution of protein superfamilies.}, journal = {Federation proceedings}, volume = {35}, number = {10}, pages = {2132-2138}, pmid = {181273}, issn = {0014-9446}, mesh = {Amino Acid Sequence ; *Biological Evolution ; Chorionic Gonadotropin ; Cytochrome c Group ; Gonadotropins, Pituitary ; Models, Biological ; Mutation ; Pituitary Hormone-Releasing Hormones ; Protein Conformation ; *Proteins/classification ; Thyrotropin ; }, abstract = {The organization of proteins into superfamilies based primarily on their sequences is introduced: examples are given of the methods used to cluster the related sequences and to elucidate the evolutionary history of the corresponding genes within each superfamily. Within the framework of this organization, the amount of sequence information currently and potentially available in all living forms can be discussed. The 116 superfamilies already sampled reflect possibly 10% of the total number. There are related proteins from many species in all of these superfamilies, suggesting that the origin of a new superfamily is rare indeed. The proteins so far sequenced are so rigorously conserved by the evolutionary process that we would expect to recognize as related descendants of any protein found in the ancestral vertebrate. The evolutionary history of the thyrotropin-gonadotropin beta chain superfamily is discussed in detail as an example. Some proteins are so constrained in structure that related forms can be recognized in prokaryotes and eukaryotes. Evolution in these superfamilies can be traced back close to the origin of life itself. From the evolutionary tree of the c-type cytochromes the identity of the prokaryote types involved in the symbiotic origin of mitochondria and chloroplasts begins to emerge.}, }
@article {pmid181272, year = {1976}, author = {Margoliash, E and Ferguson-Miller, S and Kang, CH and Brautigan, DL}, title = {Do evolutionary changes in cytochrome c structure reflect functional adaptations?.}, journal = {Federation proceedings}, volume = {35}, number = {10}, pages = {2124-2130}, pmid = {181272}, issn = {0014-9446}, mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; *Cytochrome c Group/metabolism ; Electron Transport ; Electron Transport Complex IV/metabolism ; Humans ; Kinetics ; Mitochondria/enzymology/metabolism ; Protein Conformation ; Species Specificity ; }, abstract = {Following the demonstration that the rate of evolutionary change in the amino acid sequences of cytochromes c of eukaryotic species was not constant either for a single line of phylogenetic descent during different evolutionary intervals or for separate lines of descent, the concept that neutral mutations account for the vast majority of the evolutionary variations could no longer be accepted. Previous studies had shown that all eukaryotic cytochromes c tested appeared to be functionally indistinguishable in their reaction with mitochondrial respiratory chain components. However, an examination of the kinetics at low ionic strength led to the discovery of a high affinity reaction of cytochrome c with cytochrome c oxidase that revealed large differences in activity between the cytochromes of the horse, baker's yeast and the protist Euglena. Observed Km values for this reaction of 10(-7) to 10(-8) M appear to represent actual dissociation constants, as demonstrated by direct binding studies of cytochrome c with purified cytochrome c oxidase. The high affinity reaction is sensitive to ionic strength and inhibited by ADP and ATP in the range of physiological concentrations, ATP being three times as effective as ADP. The possibility is discussed that this effect of ATP on cytochrome c binding to its oxidase could provide the basis of a mechanism for mitochondrial respiratory control. The demonstration of differences between cytochrome c of various species in this kinetic system opens the way to a systematic study of the possible evolutionary adaptations of cytochromes c to their oxidases.}, }
@article {pmid1034454, year = {1976}, author = {Marty-Double, C and Demêmes, D and Marty, R}, title = {[Intraventricular glial tumor. in the evolution of Bourneville tuberous sclerosis: ultrastructural study].}, journal = {Annales d'anatomie pathologique}, volume = {21}, number = {3}, pages = {329-338}, pmid = {1034454}, issn = {0003-3871}, mesh = {Astrocytoma/complications/*ultrastructure ; Cerebral Ventricle Neoplasms/complications/ultrastructure ; Endoplasmic Reticulum/ultrastructure ; Golgi Apparatus/ultrastructure ; Humans ; Lysosomes/ultrastructure ; Mitochondria/ultrastructure ; Tuberous Sclerosis/complications/*pathology ; }, abstract = {Ultrastructural study of an intraventricular tumour in a child with Bourneville tuberose sclerosis showed the presence of marked glial astrocytic proliferation. All the tumour cells were undoubtedly of astrocytic type, as shown by the presence of gliofilaments and beta-type glycogenic particles. They were also characterized by an abundant ergastoplasm of an original type (lamellar stacking of the saccules), a well developed Golgi apparatus, a multitude of mitochondria and numerous dense lysosomic bodies, indicative of metabolic hyperactivity. On the basis of these morphological date, the tumour may be defined as an astrocytoma, the blastic tendency of which cannot be affirmed, other than on the basis of the presence of mitotic figures.}, }
@article {pmid824879, year = {1976}, author = {Hildebrand, HF}, title = {[Electron microscopic investigation on the evolution stages of the trophozoite of Didymophyes gigantea (Sporozoa, Gregarinida). I. The fine structure of the proto- and epimerite and the relationship between host and parasite (author's transl)].}, journal = {Zeitschrift fur Parasitenkunde (Berlin, Germany)}, volume = {49}, number = {3}, pages = {193-215}, pmid = {824879}, issn = {0044-3255}, mesh = {Animals ; Apicomplexa/growth &amp; development/*ultrastructure ; Coleoptera/parasitology ; Microscopy, Electron ; }, abstract = {The fine structure of the epimerite and the protomerite of D. gigantea was investigated following the different stages of the evolution of the trophozoite. The first stage is mononucleate and very poor of cytoplasmic structures (Fig. 1). All following stages are polynucleate (Fig. 3). The septum between protomerite and deutomerite appears at the third stage (Fig. 22). The body of the gregarine is in all stages surrounded by a thick cell-wall constituted of three membranes. The limit between epimerite and protomerite is indicated by the existence of an osmiophilic basal ring just under the parasite's cell-wall. This basal ring has a transverse substructure with a periodical distance of 450 A (Fig. 12). The two inner membranes join together just beneath the basal ring, whereas the outer membrane continues and forms the single cell membrane of the epimerite (Fig.9). The epimerite displays a large number of microvillosities and evaginations of the membrane which increase considerably its surface (Figs. 11-14). The epimerite essentially contains ribosomes and mitochondria (Fig.6). The protomerite contains in addition to the usual cell organites cytoplasmic agglomerations consisting of endoplasmic reticulum, ribonucleoprotein and peripheric mitochondria. During evolution from stage IV to V, these agglomerations produce osmiophilic granula of different form and size, most of which are surrounded by an elementary membrane (Fig. 18). Beside these granula one can observe sometimes small spherical or lamellar structures (Fig. 21). Large bundles of microtubules run from the protomerite into the epimerite where they generally branch off and penetrate into the mitochondrial layer (Figs. 6, 19, 20). Between the parasite and the host-cell exists a space, the periparasitic space, without any cytoplasmic inclusions. The cell membrane of the host-cell has in the periparasitic space an outer cell-coat with a ripped pattern (Fig. 13). The microvillosities of the cell membrane disappear at this place. The host-cell cytoplasm displays a large number of microtubules and a fibrillar network (Figs. 13, 14). The importance of these structures for the relationship between parasite and host-cell is discussed.}, }
@article {pmid132964, year = {1976}, author = {Riebeling, V and Jungermann, K}, title = {Properties and function of clostridial membrane ATPase.}, journal = {Biochimica et biophysica acta}, volume = {430}, number = {3}, pages = {434-444}, doi = {10.1016/0005-2728(76)90019-0}, pmid = {132964}, issn = {0006-3002}, mesh = {2,6-Dichloroindophenol/pharmacology ; Adenosine Triphosphatases/isolation &amp; purification/*metabolism ; Calcium/pharmacology ; Cell Membrane/enzymology ; Clostridium/*enzymology ; Kinetics ; Magnesium/pharmacology ; Manganese/pharmacology ; Oligomycins/pharmacology ; Potassium/pharmacology ; Sodium/pharmacology ; Solubility ; }, abstract = {ATPase (ATP phosphohydrolase, EC 3.6.1.3) was detected in the membrane fraction of the strict anaerobic bacterium, Clostridium pasteurianum. About 70% of the total activity was found in the particulate fraction. The enzyme was Mg2+ dependent; Co2+ and Mn2+ but not Ca2+ could replace Mg2+ to some extent; the activation by Mg2+ was slightly antagonized by Ca2+. Even in the presence of Mg2+, Na+ or K+ had no stimulatory effect. The ATPase reaction was effectively inhibited by one of its products, ADP, and only slightly by the other product, inorganic phosphate. Of the nucleoside triphosphates tested ATP was hydrolyzed with highest affinity ([S]0.5 v = 1.3 mM) and maximal activity (120 U/g). The ATPase activity could be nearly completely solubilized by treatment of the membranes with 2 M LiCl in the absence of Mg2+. Solubilization, however, led to instability of the enzyme. The clostridial solubilized and membrane-bound ATPase showed different properties similar to the "allotopic" properties of mitochondrial and other bacterial ATPases. The membrane-bound ATPase in contrast to the soluble ATPase was sensitive to the ATPase inhibitor dicyclohexylcarbodiimide (DCCD). DCCD, at 10(-4) M, led to 80% inhibition of the membrane-bound enzyme; oligomycin ouabain, or NaN3 had no effect. The membrane-bound ATPase could not be stimulated by trypsin pretreatment. Since none of the mono- or divalent cations had any truly stimulatory effect, and since a pH gradient (interior alkaline), which was sensitive to the ATPase inhibitor DCCD, was maintained during growth of C. pasteurianum, it was concluded that the function of the clostridial ATPase was the same as that of the rather similar mitochondrial enzyme, namely H+ translocation. A H+-translocating, ATP-consuming ATPase appears to be intrinsic equipment of all prolaryotic cells and as such to be phylogenetically very old; in the course of evolution the enzyme might have been developed to a H+-(re)translocating, ATP-forming ATPase as probably realized in aerobic bacteria, mitochondria and chloroplasts.}, }
@article {pmid188170, year = {1976}, author = {Bakouche, P and Lamotte-Barrillon, S and Lagarde, P}, title = {[Downward-turning ocular myopathy with mitochondrial abnormalities].}, journal = {La semaine des hopitaux : organe fonde par l'Association d'enseignement medical des hopitaux de Paris}, volume = {52}, number = {16}, pages = {1013-1016}, pmid = {188170}, mesh = {Adult ; Biopsy ; Eye Diseases/enzymology/pathology ; Humans ; Lipid Metabolism ; Male ; Mitochondria, Muscle/enzymology/metabolism/*ultrastructure ; Muscular Diseases/enzymology/pathology ; Oculomotor Muscles/enzymology/*ultrastructure ; }, }
@article {pmid816668, year = {1976}, author = {Margulis, L}, title = {Genetic and evolutionary consequences of symbiosis.}, journal = {Experimental parasitology}, volume = {39}, number = {2}, pages = {277-349}, doi = {10.1016/0014-4894(76)90127-2}, pmid = {816668}, issn = {0014-4894}, mesh = {Amoeba/microbiology ; Animals ; Bacteria/metabolism ; Base Sequence ; Biological Evolution ; Blastocladiella ; DNA ; Drosophila melanogaster/microbiology ; Insecta/microbiology ; Methane/biosynthesis ; Mitochondria/metabolism ; Mollusca/microbiology ; Nematoda/microbiology ; Nitrogen Fixation ; Nucleic Acid Hybridization ; Paramecium/microbiology ; Photosynthesis ; Plants/microbiology ; Protein Biosynthesis ; RNA, Ribosomal ; Rhodospirillaceae/metabolism ; Selection, Genetic ; Sex Ratio ; *Symbiosis ; Transcription, Genetic ; }, }
@article {pmid57191, year = {1976}, author = {Buja, LM and Dees, JH and Harling, DF and Willerson, JT}, title = {Analytical electron microscopic study of mitochondrial inclusions in canine myocardial infarcts.}, journal = {The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society}, volume = {24}, number = {3}, pages = {508-516}, doi = {10.1177/24.3.57191}, pmid = {57191}, issn = {0022-1554}, mesh = {Animals ; Dogs ; Histocytochemistry ; Inclusion Bodies/*ultrastructure ; Microscopy, Electron, Scanning/methods ; Mitochondria, Muscle/*ultrastructure ; Myocardial Infarction/*pathology ; Myocardium/*pathology ; Staining and Labeling ; }, abstract = {An analytical electron microscopic study, utilizing scanning transmission electron microscopy and energy-dispersive x-ray spectroscopy, was made of two types of mitochondrial inclusions identified in canine myocardial infarcts. The data were obtained from thin sections of tissues that were fixed in aldehyde, osmicated and embedded in epoxy resin. Calcium peaks of variable intensity were detected in inclusions which contained very electron-dense spicular material and which were localized to muscle cells at the peripheries of the infarcts. These findings indicate that the spicular inclusions represent early stages in the process of mitochondrial calcification in myocardial infarcts. In contrast, calcium or other trace elements were not detected in moderately electron-dense amorphous inclusions which were present in mitochondria of muscle cells throughout the infarcts. With the tissue preparative techniques employed, the possibility cannot be excluded that the amorphous inclusions contained calcium, either in small amounts or in a readily diffusable state, in vivo. The data, however, are in accord with the previously advanced hypothesis that the amorphous inclusions represent precipitates of denatured mitochondrial protein formed during the evolution of irreversible cellular injury. This study provides further evidence that analytical electron microscopy can yield important information regarding the nature of various inclusions occurring in normal and diseased tissues.}, }
@article {pmid1267748, year = {1976}, author = {Salas, M and Tuchweber, B and Kovacs, K and Garg, BD}, title = {Effect of cerium on the rat liver: an ultrastructural and biochemical study.}, journal = {Beitrage zur Pathologie}, volume = {157}, number = {1}, pages = {23-44}, doi = {10.1016/s0005-8165(76)80146-1}, pmid = {1267748}, issn = {0005-8165}, mesh = {Adenine/pharmacology ; Adenosine Triphosphate/metabolism/pharmacology ; Alanine Transaminase/blood ; Animals ; Bilirubin/blood ; Cell Nucleus/ultrastructure ; Cerium/*toxicity ; Chemical and Drug Induced Liver Injury/*etiology/metabolism/pathology/prevention &amp; control ; Endoplasmic Reticulum/ultrastructure ; Fatty Liver/chemically induced ; Female ; Golgi Apparatus/ultrastructure ; Liver/*drug effects/ultrastructure ; Liver Glycogen/metabolism ; Mitochondria/ultrastructure ; Rats ; Time Factors ; Triglycerides/metabolism ; Tryptophan/pharmacology ; }, abstract = {In rats, liver steatosis and necrosis were induced by cerous chloride (CeCl3) and the evolution of these changes was examined. By electron microscopy, 17 hours after CeCl3 treatment, dilation, disorganization and degranulation of the rough endoplasmic reticulum (RER) were noted with an increase in the number and electron density of lysosome-like bodies. In addition, nuclear chromatin showed showed a marked focal electron density, and the nuclear membrane appeared to be interrupted. At 24 hours, the RER was markedly dilated and degranulated, with free ribosomes aggregated in the cytoplasm. The Golgi cisternae appeared to be empty. There was an increase in the number and size of lipid droplets, with depletion of glycogen. At 48 hours, a massive proliferation of smooth endoplasmic reticulum (SER) vesicles occurred. Large lipid droplets were scattered throughout the cytoplasm, while the mitochondria displayed mild changes. By the 8th day, the number of lipid droplets returned to normal; no abnormalities were detected in the other cell organelles. Biochemically, the total hepatic ATP levels fell significantly by the 12th hour, dropping to a minimum by the 48th hour. The liver was gradually depleted of glycogen within the first 48 hours, while hepatic triglycerides increased rapidly, reaching a peak at 96 hours. Exogenous administration of adenine, ATP (adenosine triphosphate), or tryptophan completely prevented CeCl3-induced mortality; hepatic fat accumulation and necrosis were markedly decreased. Glucose, dl-methionine, and choline had no protective effect. It appears that a defect in hepatocellular lipoprotein synthesis and/or release may be responsible for lipid accumulation.}, }
@article {pmid1247225, year = {1976}, author = {Hayes, JA and Snider, GL and Palmer, KC}, title = {The evolution of biochemical damage in the rat lung after acute cadmium exposure.}, journal = {The American review of respiratory disease}, volume = {113}, number = {2}, pages = {121-130}, doi = {10.1164/arrd.1976.113.2.121}, pmid = {1247225}, issn = {0003-0805}, mesh = {Aerosols ; Animals ; Cadmium/*adverse effects ; Glucosephosphate Dehydrogenase/metabolism ; Isocitrate Dehydrogenase/metabolism ; L-Lactate Dehydrogenase/metabolism ; Lipid Metabolism ; Lung/*drug effects/enzymology ; Malate Dehydrogenase/metabolism ; Mitochondria/enzymology ; Rats ; Sodium Chloride/pharmacology ; }, abstract = {Rats were exposed once to a polydisperse aerosol of 0.005 M cadmium chloride for 2 hours. Controls were saline-exposed rats and unexposed rats. Total extractable lipid, malate, lactate, isocitrate, and glucose-6-phosphate dehydrogenases were measured on the organelle-free cytosol from homogenized lungs at periods up to 10 days after exposure. The wet weight, dry weight, ribonucleic acid, and deoxyribonucleic acid content of the lungs were also determined. Ultrastructural appearances were studied at the same time intervals in a separate experiment. Total lipid content, lactate dehydrogenase, and glucose-6-phosphate dehydrogenase activities showed approximate doubling by the fourth day after exposure, this change coinciding with doubling of wet lung weight and total lung deoxyribonucleic acid content. Malate dehydrogenase activity showed a high peak 1 hour after exposure before decreasing to follow the pattern of lactate and glucose-6-phosphate dehydrogenase. The changes found may be a nonspecific reaction to lung injury, comparable with oxygen, ozone, and nitrogen dioxide. These results in Type II cell proliferation, which would enhance glucose-6-phosphate dehydrogenase content and resistance to peroxidation. Lipid accumulation could be a similar response. However, the initial elevation in malate dehydrogenase activity is more in keeping with a specific mitochondrial injury (with some ultrastructural support), perhaps with leakage of mitochondrial enzymes. This suggests that there may be more than one mechanism at work in the injury. It is significant that despite the marked structural and functional changes, none of the rats died after the exposure, which makes the injury a model worthy of further investigation.}, }
@article {pmid1253564, year = {1976}, author = {Waters, BK and Wallace, RB and Freeman, KB}, title = {Characterization of cytosol and mitochondrial rRNA of reptiles in relation to evolution.}, journal = {Comparative biochemistry and physiology. B, Comparative biochemistry}, volume = {53}, number = {3}, pages = {283-286}, doi = {10.1016/0305-0491(76)90326-6}, pmid = {1253564}, issn = {0305-0491}, mesh = {Animals ; *Biological Evolution ; Centrifugation, Density Gradient ; Cytosol/*analysis/metabolism ; Electrophoresis, Polyacrylamide Gel ; Female ; Fibroblasts/metabolism ; Mitochondria/*analysis/metabolism ; Molecular Weight ; Ovary/analysis ; *RNA, Ribosomal/*metabolism ; Rats ; Ribonucleotides/analysis ; Species Specificity ; Turtles/*metabolism ; Xenopus/*metabolism ; }, }
@article {pmid1244358, year = {1976}, author = {Nakao, T}, title = {An electron microscopic study of the neuromuscular junction in the myotomes of larval lamprey, Lampetra japonica.}, journal = {The Journal of comparative neurology}, volume = {165}, number = {1}, pages = {1-15}, doi = {10.1002/cne.901650102}, pmid = {1244358}, issn = {0021-9967}, mesh = {Animals ; Biological Evolution ; Fishes/*anatomy &amp; histology ; Lampreys/*anatomy &amp; histology ; Larva ; Microscopy, Electron ; Neuromuscular Junction/*ultrastructure ; }, abstract = {The neuromuscular junction in the myotomes of larval and adult lampreys, Lampetra japonica, was studied with the electron microscope. In larval lampreys of 26 days after artificial insemination, the myotome consists of triangular lamellae of muscle cell with their bases laterally and apexes medially oriented and placed one on the other. The lateral aspect of the myotome is covered by a layer of flattened cell, and the other aspect is covered by an external lamina which does not extend into the intercellular space between adjacent cells within a myotome. A bundle of thin axons was found in a depression at the middle of medial edge (apex) of each muscle lamella of the myotome and neuromuscular junction was formed here. No nerve endings were found at the myoseptal ends or at the lateral borders of the muscle lamellae. Enlarged axon terminals contained numerous clear vesicles with a few cored vesicles, mitochondria and neurofilaments. The presynaptic axolemma was separated from the postsynaptic sarcolemma by an interspace (50-55 mmu wide) with an interposed external lamina. In the trunk musculature of adult lampreys, nerve endings were found on the surface of the parietal fibers whereas they were seen on both the myoseptal ends near the myotendinous junction along the medial border of each central fiber. Thickening and enhancement in the electron density and accumulation of filamentous material on the sarcoplasmic surface of the postsynaptic sarcolemma were noted in both the larval and adult lampreys. Any other specific alterations were not found on both the pre- and postsynaptic membrane in the neuromuscular junctions of larval and adult lampreys. A brief comment was made on the relationship in development of the characteristic muscle units and patterns of the motor innervation in the larval and adult lampreys. The significance of the neuromuscular junction in the very young larvae reported here was also discussed in respect to the evolution of the neuromuscular junction, particularly in lower chordates, and it was presumed to be the most primitive pattern of innervation in the vertebrate skeletal muscle.}, }
@article {pmid1107820, year = {1976}, author = {Baccetti, B and Afzelius, BA}, title = {The biology of the sperm cell.}, journal = {Monographs in developmental biology}, volume = {}, number = {10}, pages = {1-254}, pmid = {1107820}, issn = {0077-0825}, mesh = {Acrosome/ultrastructure ; Animals ; Cell Membrane/ultrastructure ; Cell Nucleus/ultrastructure ; Chromosomes/ultrastructure ; Environment ; Fertilization ; Flagella/ultrastructure ; Glycoproteins ; Humans ; Invertebrates ; Male ; Mammals ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Phylogeny ; Polysaccharides ; Sperm Capacitation ; Sperm Motility ; Sperm Tail/ultrastructure ; Spermatozoa/*physiology/ultrastructure ; }, }
@article {pmid1020018, year = {1976}, author = {Margaritis, LH and Politof, TK and Koliopoulos, JX}, title = {Quantitative and comparative ultrastructure of the vertebrate cornea. I. Urodele Amphibia.}, journal = {Tissue &amp; cell}, volume = {8}, number = {4}, pages = {591-602}, doi = {10.1016/0040-8166(76)90033-1}, pmid = {1020018}, issn = {0040-8166}, mesh = {Animals ; Basement Membrane/ultrastructure ; Collagen ; Cornea/*ultrastructure ; Descemet Membrane/ultrastructure ; Endoplasmic Reticulum/ultrastructure ; Epithelial Cells ; Epithelium/ultrastructure ; Humans ; Mitochondria/ultrastructure ; Rabbits ; Sharks/anatomy &amp; histology ; Triturus/*anatomy &amp; histology ; }, abstract = {The cornea of the urodele amphibian Triturus c. cristatus was studied ultrastructurally in order to provide the basis for a comparison among corneas throughout the vertebrate phylum. The cornea of this salamander consists of relatively thick epithelium and basement membrane and thin Descemet's membrane, unlike the mammalian corneas. The outermost epithelial cells contain Ruthenium Red stainable extracellular filaments and intracellular vesicles which are thought to play a role in the process of lubricating the corneal surface. Occluding junctions have been observed in the apical region of the superficial epithelial cells and are considered as barriers to the intercellular passage of material. A thin substantia propria (stroma) consists of about 40 collagenous highly organized lamellae. The thicknesses of the basement membrane, Descemet's membrane and the epithelium are believed to represent the primitive situation in the process of corneal evolution.}, }
@article {pmid980364, year = {1976}, author = {Lupulescu, A and Pinkus, H}, title = {Electron microscopic observations on rat epidermis during experimental carcinogenesis.}, journal = {Oncology}, volume = {33}, number = {1}, pages = {24-28}, doi = {10.1159/000225096}, pmid = {980364}, issn = {0030-2414}, mesh = {Animals ; Carcinoma/chemically induced/*ultrastructure ; Carcinoma, Basal Cell/chemically induced/*ultrastructure ; Endoplasmic Reticulum/ultrastructure ; Female ; Methylcholanthrene ; Microscopy, Electron ; Neoplasms, Experimental/chemically induced/ultrastructure ; Polyribosomes/ultrastructure ; Rats ; Ribosomes/ultrastructure ; Skin Neoplasms/chemically induced/*ultrastructure ; }, abstract = {Early ultrastructural changes and their progressive evolution were studied in rat epidermis following topical application of carcinogen (3-methylcholanthrene) and were compared to ultrastructural features of fully developed tumors (sebaceous epithelioma and basal cell epithelioma) in animals of the same group. Similar cytologic alterations were found, such as a marked increase in free ribosomes and polysomes, extensive endoplasmic reticulum, considerable increase of mitochondria, and dilated intercellular spaces, occupied by cytoplasmic projections. Predominance of dark cells, considered by us to be only phenotypically different from normal (light) cells, was also observed. A two-stage or multiple-stage of neoplastic evolution was suggested.}, }
@article {pmid968313, year = {1976}, author = {Vuia, O}, title = {[Morphological aspects (optical and ultrastructural) of hypertrophy of the olivary bulb].}, journal = {Revue neurologique}, volume = {132}, number = {1}, pages = {51-61}, pmid = {968313}, issn = {0035-3787}, mesh = {Adult ; Aged ; Brain Diseases/*pathology ; Brain Neoplasms/ultrastructure ; Humans ; Hypertrophy ; Male ; Neurons/ultrastructure ; Olivary Nucleus/*ultrastructure ; Plasmacytoma/ultrastructure ; Trigeminal Neuralgia/pathology ; }, abstract = {The present paper is an anatomical study of 3 cases which evolved with hypertrophy of the inferior olives: a case of zoster encephalitis, a multifocal leucoencephalopathy and a post-traumatic encephalopathy. In all three cases a relationship was demonstrated between the dentate nucleus and dento-olivary pathway - a relation of topical order in some instances - and the hypertrophic lesion of the inferior olive. Examination in the electron microscope revealed in the hypertrophic olivary cell not only dystrophic lesions but also progressive intracellular phenomena, such as maintenance of the Nissl bodies, multiplication of the mitochondria and especially marked proliferation of the neuro-filaments. This shows that, at least in some of the evolutive phases, hypertrophy of the inferior olives is based upon a real hypertrophy of the olivary cell. In addition, lesions of the glial system of the hypertrophic inferior olives were noted with the presence of osmiophil degeneration whose morphology clearly differed from that of Rosenthal's fibres.}, }
@article {pmid941681, year = {1976}, author = {Varakis, JN and ZuRhein, GM}, title = {Experimental pineocytoma of the Syrian hamster induced by a human papovavirus (JC). A light and electron microscopic study.}, journal = {Acta neuropathologica}, volume = {35}, number = {3}, pages = {243-264}, pmid = {941681}, issn = {0001-6322}, mesh = {Animals ; Cell Differentiation ; Cricetinae ; Female ; Mesocricetus ; Microtubules/ultrastructure ; Neoplasms, Experimental ; Organoids/ultrastructure ; *Papillomaviridae ; Photoreceptor Cells/ultrastructure ; Phylogeny ; Pineal Gland/ultrastructure ; Pinealoma/microbiology/*pathology ; *Polyomaviridae ; }, abstract = {The gross, light and electron microscopic features of a pineocytoma of the Syrian hamster (mesocricetus auratus) which had been induced by a human oncogenic virus (JC papovavirus) have been defined. For comparison, adult hamster pineal tissue was studied, and the literature was consulted in regard to other pineal parenchymal tumors, and to pineal cell differentiation during ontogeny and phylogeny. Many differentiated tumor cells contained organelles, such as vesicle-crowned lamellae (synaptic ribbons) and microtubular sheaves, as consistent with adult hamster pineocytes. Some cells showed rudimentary photoreceptor-like differentiation as consistent with fetal hamster pineocytes and with cells seen in the pineal systems of some lower vertebrate species. Such tumor cells had lumen-directed specialized cytoplasmic extensions which, by their richness in mitochondria and presence of centrioles and striated rootlets, resembled inner segments. Extending 9+0 cilia were accompanied by occasional lamellar whorls. Oncogenesis seems to have simulated different stages of hamster pineal ontogeny. This observation would support the theory that the secretory mammalian pineocyte derived phylogenetically from the true photoreceptor cell of the pineal system of fishes and amphibians. The possible influences of host and of virus in the accomplishment of tumor morphology were discussed. This tumor differed considerably in pattern and cell detail from the only other pineocytoma studied previously by electron microscopy. It is the first experimentally induced pineocytoma.}, }
@article {pmid770372, year = {1976}, author = {Szarski, H}, title = {Cell size and nuclear DNA content in vertebrates.}, journal = {International review of cytology}, volume = {44}, number = {}, pages = {93-111}, doi = {10.1016/s0074-7696(08)61648-4}, pmid = {770372}, issn = {0074-7696}, mesh = {Adaptation, Physiological ; Animals ; Biological Evolution ; Cell Division ; Cell Nucleus/*analysis ; *Cells/metabolism/ultrastructure ; Cytoplasm ; DNA/*analysis ; Endoplasmic Reticulum/ultrastructure ; Erythrocytes/metabolism ; Genes ; Genes, Regulator ; Mitochondria/ultrastructure ; Osmolar Concentration ; Oxygen Consumption ; Polyploidy ; Species Specificity ; }, }
@article {pmid174805, year = {1976}, author = {Reddy, JK and Svoboda, DJ and Rao, MS}, title = {Induction of liver tumors by aflatoxin B1 in the tree shrew (Tupaia glis), a nonhuman primate.}, journal = {Cancer research}, volume = {36}, number = {1}, pages = {151-160}, pmid = {174805}, issn = {0008-5472}, mesh = {Aflatoxins/*toxicity ; Animals ; Dose-Response Relationship, Drug ; Endoplasmic Reticulum/ultrastructure ; Female ; Inclusion Bodies/ultrastructure ; Liver/ultrastructure ; Liver Neoplasms/*chemically induced/pathology ; Male ; Mitochondria/ultrastructure ; Neoplasms, Experimental/chemically induced/pathology ; *Shrews ; Time Factors ; }, abstract = {The epidemiological studies suggest that aflatoxins, the toxic metabolites of the ubiquitous mold Aspergillus flavus, may play a significant role in the evolution of hepatocellular carcinoma in man in certain geographic areas of the world. To ascertain their carcinogenicity in nonhuman primates, we have administered highly purified aflatoxin B1, intermittently in the diet at 2 ppm, to 10 female and 8 male tree shrews. The tree shrew (Tupaia glis) is a nonhuman primate occurring throughout Southeast Asia which can be reared easily in captivity. Of 12 animals that survived, 6 of 6 female (100%) and 3 of 6 male (50%) tree shrews developed hepatocellular carcinomas between 74 and 172 weeks after the beginning of the experiment. None of the 8 control animals developed liver cancers. The estimated total amount of aflatoxin B1 consumed by these animals ranged from 24 to 66 mg. The development of liver tumors did not follow a specific pattern; considerable variation in hepatocellular responses to aflatoxin B1 was noted in these animals. In 2 tree shrews, the liver tumors were associated with severe post necrotic scarring; in the other 7 tumor-bearing livers, only mild to moderate portal fibrosis was encountered. This individual variation in hepatocellular response and in the amount of aflatoxin B1 required to induce hepatocellular carcinomas is attributed to inherent differences in the susceptibility within a given species of outbred animals and suggests extreme caution in proposing the "permissible" or "safe" levels of contamination of carcinogens in the food-stuffs.}, }
@article {pmid1203955, year = {1975}, author = {Lamer, HI and Chavin, W}, title = {Ultrastructure of the integumental melanophores of the coelacanth, Latimeria chalumnae.}, journal = {Cell and tissue research}, volume = {163}, number = {3}, pages = {383-394}, pmid = {1203955}, issn = {0302-766X}, mesh = {Animals ; Chromatophores/*ultrastructure ; Fishes/*anatomy &amp; histology ; Melanocytes/ultrastructure ; Melanophores/*ultrastructure ; Microtubules/ultrastructure ; Organoids/ultrastructure ; Phylogeny ; Skin Pigmentation ; }, abstract = {The integumental melanophores of Latimeria chalumnae were studied by light and electron microscopy. The epidermal melanophore located in the mid-epidermis consists of a round perikaryon with long slender dendrites extending into epidermal cells and intercellular spaces. The dermal melanophores occur in the loose dermal matrix underlying a relatively thick layer of collagen fibers. The dermal melanophores are usually flattened and their dendrites lie parallel to the collagen layer. Both epidermal and dermal melanophores contain oval, electron-opaque melanosomes, large mitochondria, agranular vacuoles of endoplasmic reticulum and microtubules. Microfilaments and RNP particles are less conspicuous. While the peripheral cytoplasm of both dermal and epidermal melanophores is filled with a large number of melanosomes, the perinuclear cytoplasm of many dermal melanophores is occupied by premelanosomes in various stages of differentiation, and that of the epidermal melanophore contains numerous large vacuoles. Despite the scarcity of epidermal melanophores, the epidermal melanin unit is present in the form of melanosome complexes. In addition, the melanophores of Latimeria possess the basic characteristics common to other vertebrates, but they more closely resemble those of lungfish and other aquatic vertebrates.}, }
@article {pmid1203951, year = {1975}, author = {Morris, R and Pickering, AD}, title = {Ultrastructure of the presumed ion-transporting cells in the gills of ammocoete lampreys, Lampetra fluviatilis (L.) and Lampetra planeri (Bloch).}, journal = {Cell and tissue research}, volume = {163}, number = {3}, pages = {327-341}, pmid = {1203951}, issn = {0302-766X}, mesh = {Animals ; Biological Evolution ; Biological Transport, Active ; Cell Nucleus/ultrastructure ; Chlorides/metabolism ; Fishes/*anatomy &amp; histology ; Gills/metabolism/*ultrastructure ; Ions/*metabolism ; Lampreys/*anatomy &amp; histology ; Larva ; Mitochondria/metabolism/ultrastructure ; Organoids/ultrastructure ; Water-Electrolyte Balance ; }, abstract = {Mitochondria-rich cells were located in the interplatelet area of gill filaments from ammocoete Lampetra fluviatilis and L. planeri. The ultrastructure of this cell type differs from typical teleost 'chloride cells' by the absence of a tubular, smooth endoplasmic reticulum (SER). This difference is discussed in relation to the presumed functions of the cell and to the evolutionary histories of lampreys and teleosts. It is concluded that the mitochondria-rich cell is responsible for the active uptake of ions by the ammocoete gill.}, }
@article {pmid813866, year = {1975}, author = {Chambon, M and Morat, M and Chevalier, M and Dufaure, JP}, title = {[Mitochondrial reorganization after HCG stimulation of Leydig cells from hypophysectomized hogs].}, journal = {Comptes rendus hebdomadaires des seances de l'Academie des sciences. Serie D: Sciences naturelles}, volume = {281}, number = {14}, pages = {1011-1014}, pmid = {813866}, mesh = {Animals ; Chorionic Gonadotropin/*pharmacology ; Hypophysectomy ; Leydig Cells/*drug effects/ultrastructure ; Male ; Microscopy, Electron ; Mitochondria/*ultrastructure ; Organ Culture Techniques ; Swine ; Time Factors ; }, abstract = {One to three months after hypophysectomy, porcine Leydig cells contain numerous dense bodies surrounded by a single membrane and crowded with dense rods geometrically arranged. In organotypic culture with HCG they undergo a striking evolution which leads first to intermediate bodies looking like peroxysomes and then to mitochondrial structures. This evolution is quantitatively reduced in a medium without HCG.}, }
@article {pmid169987, year = {1975}, author = {Bedrossian, CW and Weilbaecher, DG and Bentinck, DC and Greenberg, SD}, title = {Ultrastructure of human bronchiolo-alveolar cell carcinoma.}, journal = {Cancer}, volume = {36}, number = {4}, pages = {1399-1413}, doi = {10.1002/1097-0142(197510)36:4&lt;1399::aid-cncr2820360432&gt;3.0.co;2-s}, pmid = {169987}, issn = {0008-543X}, mesh = {Adenocarcinoma, Bronchiolo-Alveolar/*pathology ; Aged ; Cell Membrane/ultrastructure ; Cell Nucleus/ultrastructure ; Cilia/ultrastructure ; Cytoplasm/ultrastructure ; Desmosomes/ultrastructure ; Female ; Humans ; Lung Neoplasms/*pathology ; Male ; Middle Aged ; Mitochondria/ultrastructure ; Vacuoles/ultrastructure ; }, abstract = {Ultrastructural features were correlated with a series of special staining reactions in eight cases of bronchiolo-alveolar carcinoma. Ultrastructural, all tumors were similarly composed of large cells with abundant cytoplasm and small nuclei in close contact with each other. Straight membranes or complex interdigitations occurred within adjacent tumor cells, attached to each other by scattered desmosomes. Microvilli or cilia abutted from free surfaces of the cells, and were noted in different stages of evolution. Numerous organelles were seen in the cytoplasm, including prominent mitochondria and single or coalescent secretory vacuoles with granular matrix resembling mucin. Other cytosomes less commonly found were irregular, partially lamellated inclusions and dark, homogeneous structures without limiting membranes. The stroma of the tumors was rich in elastin and collagen. Both the number of secretory vacuoles in the cytoplasm of tumor cells and the amount of connective tissue fibrils in the stroma of the tumors correlated well with the findings in the series of special staining reactions. No definite ultrastructural feature was present to identify the tumors as orginating from Type II alveolar epithelial cells, but the possibility exists that they arose in the bronchiole, from undifferentiated basal cells or mucinous cells per se. Our impression in these eight cases studied is consistent with the view that bronchiolo-alveolar carcinomas are indistinguishable at the ultrastructural level from other bronchogenic adenocarcinomas.}, }
@article {pmid1211654, year = {1975}, author = {Collet, AJ and Des Biens, G}, title = {Evolution of mesenchymal cells in fetal rat lung.}, journal = {Anatomy and embryology}, volume = {147}, number = {3}, pages = {273-292}, pmid = {1211654}, issn = {0340-2061}, mesh = {Animals ; Bronchi/embryology ; Cell Differentiation ; Cell Nucleolus/ultrastructure ; Cell Nucleus/ultrastructure ; Collagen ; Connective Tissue/*ultrastructure ; *Connective Tissue Cells ; Cytoplasm/ultrastructure ; Cytoplasmic Granules/ultrastructure ; Endoplasmic Reticulum/ultrastructure ; Epithelial Cells ; Epithelium/ultrastructure ; Fibroblasts/ultrastructure ; Golgi Apparatus/ultrastructure ; Heterochromatin/ultrastructure ; Lung/*embryology/ultrastructure ; Macrophages/ultrastructure ; Mitochondria/ultrastructure ; Mitosis ; Neutrophils/ultrastructure ; Pulmonary Alveoli/embryology ; Rats ; Vacuoles/ultrastructure ; }, abstract = {The evolution of connective tissue cells in the developing fetal rat lung is studied under the electron microscope from the 15th until the 21st day of gestation and is compared to the evolution of epithelial cells. Three successive types of stem cells ("mesocytoblasts") are present during the first stages of lung development studied (15 to 18 days of gestation). These stem cells appear to be able to differentiate into fibroblasts or into smooth muscle cells, according to their localization along the broncho-alveolar tubule. Myoblasts are situated near the bronchial epithelium, whereas fibroblasts occur under the alveolar epithelium. Epithelo-mesenchymal interactions are assumed to play a role in this differentiation process. Synthesis of both, collagen and elastic fibers and of cytoplasmic filaments by fibroblasts as well as by myoblasts reveal the multiple potentialities of the mesenchymal stem cell and suggest a common origin. The early fibroblast in characterized by long cytoplasmic processes which contain numerous cytofilaments, and by the presence of collagen fibers in the vicinity of the cell. Later on, (20 days of gestation) the mature fibroblast of the lung mesenchyme shows areas of RER, glycogen and lipidic vacuoles in its cytoplasm. Cytofilaments are numerous within very long cytoplasmic processes and elastic and collagen fibers are very frequent beside the cytoplasmic membrane. The earliest fibroblast differentiation occurs under the epithelium of primitive respiratory bronchioles, which indicate the limit between the bronchial and the alveolar territories. Later on, differentiating fibroblasts are found throughout the whole alveolar walls. Connective tissue cells other than mesenchymal stem cells, fibroblasts or myoblasts are observed during lung development. Vacuolar cells, similar to Hofbauer cells, transiently appear on the 16th day of gestation. On the 20th and the 21st day macrophage-like cells are present in the septal space of the alveolar wall. The absence of intermediate stages of differentiation and parallel evolution of blood cells suggest that those connective tissue cells are differentiated elsewhere and have then migrated from blood into lung mesenchyme. No cell death has been observed in the developing lung.}, }
@article {pmid809342, year = {1975}, author = {Garcia, JH}, title = {The neuropathology of stroke.}, journal = {Human pathology}, volume = {6}, number = {5}, pages = {583-598}, doi = {10.1016/s0046-8177(75)80043-8}, pmid = {809342}, issn = {0046-8177}, mesh = {Animals ; Brain/*pathology ; Cerebral Cortex/ultrastructure ; Cerebral Hemorrhage/pathology ; Cerebrovascular Circulation ; Cerebrovascular Disorders/*pathology/physiopathology ; Encephalomalacia/pathology ; Haplorhini ; Humans ; Intracranial Aneurysm/pathology ; Intracranial Arteriosclerosis/pathology ; Intracranial Embolism and Thrombosis/pathology ; Ischemic Attack, Transient/pathology/physiopathology ; Microcirculation ; Mitochondria/ultrastructure ; Neurons/pathology ; Pan troglodytes ; Saimiri ; }, abstract = {Vascular-circulatory derangements affecting the function of the central nervous system may result in parenchymal lesions that are hemorrhagic, ischemic, or mixed. Most nontraumatic intraparenchymal brain hemorrhages are found in asssociation with cerebral arteriolar sclerosis and other stigmata of hypertensive disease, such as hypertrophy of the left cardiac ventricle and granular kidneys. Global temporary ischemia, the type that exists during severe and transient hypotension, results in a wide variety of parenchymal lesions that may be bilateral, hypotension, results in a wide variety of parenchymal lesions that may be bilateral, unilateral, supratenorial, or infratentorial. The cerebral and cerebellar cortices, white matter, basal ganglia, brain stem, and spinal cord may be involved simulatenously or there may be isolated, focal lesions that are confined occasionally to any one of these areas. Regions ischemia, the type induced through the occlusion of a major intracranial artery, evolves through a stage of acute encephalomalacia, during which the morphologic change consists of alternating cellular swelling and shrinkage. This is followed by leukocytic inflammation at three to four days and the beginning of resolution at about the tenth day after arterial occlusion. In the evolution of this form of abnormal circulation, after a few minutes, some neurons in the most distal arterial territories show the first recognizable changes. In these neurons the mitochondria swell massively. Astrocytes and neurites in the same foci are selectively swollen, whereas oligodendrocytes and capillaries remain structurally unchanged during the initial stages of ischemic injury.}, }
@article {pmid808560, year = {1975}, author = {Pinckard, RN and Olson, MS and Giclas, PC and Terry, R and Boyer, JT and O'Rourke, RA}, title = {Consumption of classical complement components by heart subcellular membranes in vitro and in patients after acute myocardial infarction.}, journal = {The Journal of clinical investigation}, volume = {56}, number = {3}, pages = {740-750}, pmid = {808560}, issn = {0021-9738}, mesh = {Autoantibodies/analysis ; Complement C1/metabolism ; Complement C2/metabolism ; Complement C3/metabolism ; Complement C4/metabolism ; Complement C6/metabolism ; Complement System Proteins/*metabolism ; Egtazic Acid/pharmacology ; Humans ; In Vitro Techniques ; Membranes/immunology ; Mitochondria, Muscle/drug effects/immunology ; Myocardial Infarction/*immunology ; Myocardium/*immunology ; Subcellular Fractions/immunology ; Time Factors ; }, abstract = {Experiments were conducted to characterize the antibody-independent activation of complement in human serum by isolated human heart mitochondrial membranes in vitro and to determine whether similar patterns of complement consumption occurred in patients after acute myocardial infarction. Direct evidence for the interaction of C1 and heart mitochondrial membranes was obtained by mitochondria-C1 binding and elution experiments. Exposure of normal human sera to isolated human heart mitochondria at 37 degrees C resulted in the consumption of C1, C4, C2, and C3 without significant consumption of the terminal components of the complement system (C6 through C9). The consumption occurred in the absence of detectable anti-heart mitochondria autoantibody, was demonstrated to be calcium dependent, and was inhibited by either 0.01 M EDTA or ethylene glycol bis(bets-aminoethyl ether) N,N,N',N',-tetraacetic acid (EDTA). Although specific absorption of C1q from human sera inhibited the mitochondria-dependent activation of C4, C3 donsumption was not affected. These data indicate that the consumption of C4 and C2 likely occurred due to the mitochondrial membrane-mediated activation of C1, but that the consumption of the C3 did not necessarily involve either the classical or alternative complement pathways. After the in vitro characterization of the mitochondria-dependent activation of the complement system, additional studies were performed to determine whether similar consumption occurred in patients after acute myocaridal infarction. During a 72-h period after hospital admission significant decreases in C1, C4, and C3 occurred in six patients with recent chest pain but no evidence of acute myocardial infarction. These studies suggest that myocardial cell necrosis results in the release of subcellular membrane constituents capable of activating the complement system in the absence of detectable anti-heart autoantibodies; such activation may be responsible in part for the development of acute inflammation and evolution of the infarct size following coronary artery occulusion.}, }
@article {pmid1160997, year = {1975}, author = {Wickramashighe, RH and Villee, CA}, title = {Early role during chemical evolution for cytochrome P450 in oxygen detoxification.}, journal = {Nature}, volume = {256}, number = {5517}, pages = {509-510}, doi = {10.1038/256509a0}, pmid = {1160997}, issn = {0028-0836}, mesh = {Animals ; Apoproteins/analysis ; Bacteria/enzymology ; *Biological Evolution ; Biotransformation ; Cytochrome P-450 Enzyme System/analysis/*metabolism ; Hydroxylation ; Microsomes/enzymology ; Mitochondria/enzymology ; Molecular Weight ; Oxidation-Reduction ; Oxygen/*metabolism ; }, }
@article {pmid808732, year = {1975}, author = {Cavalier-tsmith, T}, title = {The origin of nuclei and of eukaryotic cells.}, journal = {Nature}, volume = {256}, number = {5517}, pages = {463-468}, doi = {10.1038/256463a0}, pmid = {808732}, issn = {0028-0836}, mesh = {*Biological Evolution ; Cell Membrane/metabolism ; *Cell Nucleus ; Cells/*ultrastructure ; Chloroplasts ; Cyanobacteria/ultrastructure ; Endoplasmic Reticulum ; Golgi Apparatus ; Lysosomes ; Microbodies ; Microtubules ; Mitochondria ; Mitosis ; Models, Biological ; Phagocytosis ; Sex Factors ; Symbiosis ; }, }
@article {pmid1099218, year = {1975}, author = {Reijnders, L}, title = {The origin of mitochondria.}, journal = {Journal of molecular evolution}, volume = {5}, number = {3}, pages = {167-176}, pmid = {1099218}, issn = {0022-2844}, mesh = {Bacteria/ultrastructure ; *Biological Evolution ; Cell Nucleus/metabolism ; DNA/metabolism ; DNA, Mitochondrial/metabolism ; Genes ; *Mitochondria/metabolism ; Models, Biological ; Plasmids ; Symbiosis ; }, abstract = {The endosymbiont and episome theories about the origin of mitochondria are reviewed. Biochemical and genetic data, relevant to these theories are discussed. An alternative theory is also proposed; this theory is that nuclear and mitochondrial DNAs developed from compartmentalized duplicate prokaryote DNAs.}, }
@article {pmid1146380, year = {1975}, author = {Fournier, A}, title = {[The eyespots of the oncomiracidium of Euzetrema knoepffleri (Monogenea): ultrastructure and evolution during the life-cycle (author's transl)].}, journal = {Zeitschrift fur Parasitenkunde (Berlin, Germany)}, volume = {46}, number = {3}, pages = {203-209}, pmid = {1146380}, issn = {0044-3255}, mesh = {Animals ; Cell Nucleus ; Cytoplasmic Granules ; Desmosomes ; Ecology ; Eye/embryology/growth &amp; development/*ultrastructure ; Larva/ultrastructure ; Lens, Crystalline/ultrastructure ; Light ; Locomotion ; Mitochondria ; Pigments, Biological ; Trematoda/embryology/growth &amp; development/ultrastructure ; }, abstract = {Euzetrema knoepffleri (Monogenea, Monopisthocotylea) is a parasite of the urinary bladder of Euproctus montanus (Amphibia, Urodela). The eyespots of the oncomiracidium of E. knoepffleri are rhabdomeric; each anterior pigmented cell has one rhabdomere, each posterior pigmented cell has two rhabdomeres. This pattern is quite similar to that of the eyespot of another Monopisthocotylea, Entobdella soleae but the lack of cristalline lens in E. knoepffleri appears as a new feature of the Monopisthocotylea. The symmetry of the pigmented structures seems to be effectively connected with the swimming mode of the larva. Moreover, the ultrastructural differences between the two species Euzetrema knoepffleri and Entobdella soleae may be in relation with their different behaviour concerning light. After the fixation of the larva on its host, the comparative study of the evolution of the eyespots, shows the disappearance of the cristalline lens in Entobdella, and the loss of rhabdomeric structures in Euzetrema. These differences seem related with the nature of the microbiotope of the adult: Entobdella soleae is a skin parasite, Euzetrema knoepffleri a reno-vesical one.}, }
@article {pmid1169263, year = {1975}, author = {Demski, LS and Evan, AP and Saland, LC}, title = {The structure of the inferior lobe of the teleost hypothalamus.}, journal = {The Journal of comparative neurology}, volume = {161}, number = {4}, pages = {483-497}, doi = {10.1002/cne.901610402}, pmid = {1169263}, issn = {0021-9967}, mesh = {Aggression/physiology ; Animals ; Dendrites/ultrastructure ; Endoplasmic Reticulum/ultrastructure ; Feeding Behavior/physiology ; Fishes/*anatomy &amp; histology ; Golgi Apparatus/ultrastructure ; Humans ; Hypothalamus/*anatomy &amp; histology ; Hypothalamus, Anterior/*anatomy &amp; histology ; Microscopy, Electron ; Mitochondria/ultrastructure ; Neurofibrils/ultrastructure ; Synapses/ultrastructure ; Synaptic Vesicles/ultrastructure ; }, abstract = {Electron microscopic and Golgi studies on the inferior lobes of sunfish and goldfish are described. The inferior lobe consists primarily of a nucleus ventricularis of densely packed cells surrounding the lateral recess of the third ventricle, and a peripherally situated nucleus diffusus consisting mostly of scattered neurons. A cell-sparse zone of dense neuropil is located between the two cellular areas. Neurons of both nuclei have spiny dendrites and axons which originate from basal dendrites. In some cases axons are found to send a collateral into the cell-sparse zone. Neurons of the nucleus diffusus possess collaterals that extend a considerable distance within the nucleus itself. The ultrastructure of cells of both nuclei reveals cytoplasmic organelles typical of most neurons. Synapses containing dense-cored and clear vesicles are present on the spines and shafts of the dendrites of both neuronal types. In only rare cases synapses were observed on the soma of neurons of the nucleus ventricularis. Possible anatomical substrates involved in the control of feeding and aggression in teleosts are considered in light of the present findings. Morphological similarities of the inferior lobes and related areas in various fishes and amphibians are discussed and their possible significance for the understanding of the evolution of hypothalamic mechanisms is considered.}, }
@article {pmid1136100, year = {1975}, author = {Dionne, GP and Bovill, EG and Seemayer, TA}, title = {New fine structural observations in testicular malakoplakia: role of the Sertoli cell.}, journal = {Urology}, volume = {5}, number = {6}, pages = {828-834}, doi = {10.1016/0090-4295(75)90368-4}, pmid = {1136100}, issn = {0090-4295}, mesh = {Adult ; Cell Membrane/ultrastructure ; Cell Nucleolus/ultrastructure ; Cell Nucleus/ultrastructure ; Cytoplasm/ultrastructure ; Endoplasmic Reticulum/ultrastructure ; Histiocytes/ultrastructure ; Humans ; Malacoplakia/etiology/*pathology ; Male ; Microscopy, Electron ; Sertoli Cells/*ultrastructure ; Testicular Diseases/etiology/*pathology ; Vacuoles/ultrastructure ; }, abstract = {A case of testicular malakoplakia is described in which cells other than histiocytes were involved in the tissue response. The abundant cell junctions, some closely related to mitochondria, and the peripheral displacement of rough endoplasmic reticulum by abundant phagolysosomes, suggest involvement of Sertoli cells, in addition to histiocytes. It is suggested that, perhaps, some forms of granulomatous orchitis and malakoplakia represent a single disease process observed at a different stage in its evolution.}, }
@article {pmid807395, year = {1975}, author = {Deleurance, S and Charpin, P}, title = {[Ultrastructural changes in the corpora allata of the last larval instar of Choleva angustata Fab. (Catopidae). The effect of fasting, with or without ecdysterone].}, journal = {Comptes rendus hebdomadaires des seances de l'Academie des sciences. Serie D: Sciences naturelles}, volume = {280}, number = {18}, pages = {2113-2116}, pmid = {807395}, mesh = {Age Factors ; Animals ; Cholestenes/*physiology ; Ecdysterone/*physiology ; Endoplasmic Reticulum/ultrastructure ; *Fasting ; Insecta/*physiology ; Juvenile Hormones/physiology ; Larva ; Microscopy, Electron ; Mitochondria/ultrastructure ; Neurosecretory Systems/physiology/*ultrastructure ; }, abstract = {Fasting experiments show striking changes at the ultrastructural level in the corpora allata of the last larval instar of Choleva angustata Fab: increase of the glandular volume and development of the smooth reticulum. These findings suggest that fasting leads to a continuous activity of the corpora allata.}, }
@article {pmid807383, year = {1975}, author = {Charpin, P}, title = {[Ultrastructural development of the corpora allata during the last larval stage of Choleva angustata Fab. (Coleoptera Catopidae of the subfamily Catopinae)].}, journal = {Comptes rendus hebdomadaires des seances de l'Academie des sciences. Serie D: Sciences naturelles}, volume = {280}, number = {17}, pages = {1997-1999}, pmid = {807383}, mesh = {Age Factors ; Animals ; Coleoptera/*physiology ; Endoplasmic Reticulum/ultrastructure ; Feeding Behavior ; Larva ; *Metamorphosis, Biological ; Microscopy, Electron ; Mitochondria/ultrastructure ; Neurosecretory Systems/*physiology/ultrastructure ; Pupa ; Vacuoles/ultrastructure ; }, abstract = {The ultrastructure of the corpora allata of the last larvar instar of Choleva angustata Fab. was studied. In normal development a complex pattern of changes in the ultrastructure of the corpora allata occurs in relation to the larval age in the active and inactive stages. Towards the end of the active stage, a drastic change occurs, involving an increase in number and volume of vacuoles which fill up the cells. During the fasting stage (in the nymphal clay case) the smooth endoplasmic reticulum disappears while the rough endoplasmic reticulum forms long and sinuous cisternae. Towards the end of the instar, numerous vacuoles appear.}, }
@article {pmid1212765, year = {1975}, author = {Biard, ML}, title = {[Progressive myogenic external ophthalmoplegia with ultrastructural anomalies].}, journal = {Bulletin des societes d'ophtalmologie de France}, volume = {75}, number = {5-6}, pages = {515-522}, pmid = {1212765}, issn = {0081-1270}, mesh = {Adolescent ; Humans ; Male ; Mitochondria, Muscle/ultrastructure ; Oculomotor Muscles/*ultrastructure ; Ophthalmoplegia/*pathology ; }, }
@article {pmid235742, year = {1975}, author = {John, P and Whatley, FR}, title = {Paracoccus denitrificans and the evolutionary origin of the mitochondrion.}, journal = {Nature}, volume = {254}, number = {5500}, pages = {495-498}, doi = {10.1038/254495a0}, pmid = {235742}, issn = {0028-0836}, mesh = {Adenosine Triphosphate/biosynthesis ; *Biological Evolution ; Cell Membrane/metabolism ; Electron Transport ; Micrococcus/*metabolism ; Mitochondria/enzymology/*metabolism/ultrastructure ; *Models, Biological ; Oxidative Phosphorylation ; Oxidoreductases/metabolism ; Paracoccus denitrificans/enzymology/*metabolism/ultrastructure ; }, }
@article {pmid1217906, year = {1975}, author = {Boivin, G}, title = {[Cutaneous calcinosis induced by topical calciphylaxis in rats. I. Ultrastructural aspcts].}, journal = {Archives d'anatomie microscopique et de morphologie experimentale}, volume = {64}, number = {2}, pages = {183-205}, pmid = {1217906}, issn = {0003-9594}, mesh = {Animals ; Calcinosis/chemically induced/*pathology ; Chlorides ; Dihydrotachysterol ; Female ; Ferrous Compounds ; Rats ; Skin/*ultrastructure ; Skin Diseases/chemically induced/*pathology ; }, abstract = {Skin calcification induced by topical calciphylaxis was provoked by a subcutaneous injection of iron chloride in rats previously sensitized by D.H.T. and studied by electron microscope. The evolution of the calciphylatic response can be resumed as follows: -- early appearance of numberous granules in the mitochondria of the cells of the connective tissue; their inorganic nature was revealed by microincineration and it is highly probable that they are a reserve of mineral ions; -- between the 6 hr, and the 18 hr, stages the interfibrillar matrix contained rounded vesicular structures, enclosed by a triple mambrane, which must surely be of cellular origin; they progressively incorporated more and more mineral particles which confirm their primordial role in the initial phases of mineralization; -- from the 14 hr. stage onward, mineral rodlets composed of chains of little dots appeared in the intercellular matrix and then on the collagen fibrils, probably in contact with the mucopolysaccharides; -- starting at the 24 hr, stage, the mineralization progressed without a vesicular intermediary forming increasingly dense and widespread plaques; the presence of needles of homogenous aspect indicated the appearance of a crystalline mineral deposit; an intrafibrillar mineral deposit becomes visible later. These results are compared with those obtained previously in other studies of experimental or pathological calcinosis and of mineralization of skeletal tissues.}, }
@article {pmid235330, year = {1975}, author = {Flatmark, T and Pedersen, JI}, title = {Brown adipose tissue mitochondria.}, journal = {Biochimica et biophysica acta}, volume = {416}, number = {1}, pages = {53-103}, doi = {10.1016/0304-4173(75)90013-0}, pmid = {235330}, issn = {0006-3002}, mesh = {Adaptation, Physiological ; Adenosine Diphosphate/metabolism ; Adenosine Triphosphate/metabolism ; Adipose Tissue, Brown/*metabolism ; Animals ; Animals, Newborn ; Biological Evolution ; Body Temperature Regulation ; Cell Differentiation ; Cell Fractionation ; Cold Temperature ; Cytochromes/metabolism ; Electron Transport ; Energy Transfer ; Fatty Acids/metabolism ; Guanine Nucleotides/pharmacology ; Guinea Pigs ; Hydrogen-Ion Concentration ; Kinetics ; Mitochondria/*metabolism/ultrastructure ; Norepinephrine/pharmacology ; Oxidative Phosphorylation/drug effects ; Oxygen Consumption ; Time Factors ; }, }
@article {pmid1142221, year = {1975}, author = {Ceccarelli, B and Clemente, F and Meldolesi, J}, title = {Secretion of calcium in pancreatic juice.}, journal = {The Journal of physiology}, volume = {245}, number = {3}, pages = {617-638}, pmid = {1142221}, issn = {0022-3751}, mesh = {Animals ; Calcium/analysis/*metabolism ; Ceruletide/pharmacology ; Cytoplasm/analysis ; Guinea Pigs ; Leucine/metabolism ; Microsomes/analysis ; Mitochondria/analysis ; Pancreas/analysis/drug effects ; Pancreatic Juice/*metabolism ; Proteins/analysis ; Secretin/pharmacology ; Sorbitol/metabolism ; Subcellular Fractions/analysis ; }, abstract = {1. The orgin of the calcium secreted by the pancreas has been investigated in vivo in the guinea-pig by a study carried out in parallel (a) in the juice secreted in response to the injection of either secretin or caerulein and (b) in the pancreatic tissue and in cell fractions isolated thereform. 2. In agreement with previous findings we observed that the concentration of calcium is low in the secretin-stimulated and high in the caerulein-stimulated juice. In the latter calcium and protein are proportional (cal0 n-mole:mg). 3. After I.V. injection of 45Ca the radioactivity decreases rapidly and quasi-exponentially in the blood plasma. A roughly parallel time course is found in the secretin-stimulated juice: the evolution of the juice: plasma radioactivity ratio resembles that observed with the extraceullar space marker [3H]D-sorbitol. In contrast, the time course of 45Ca in plasma and caerulein-stimulated juice are not proportional: the high levels characteristic of this juice are reached several minutes after the injection and maintained thereafter. This increase is followed ca. 50 min later by the appearance of the newly synthesized [3H]L-leucine-labelled proteins. 4. The pancreatic tissue is rich in calcium which is localized primarily in zymogen granules (Ca.36 n-mole:mg protein) and mitochondria; the soluble cytoplasm is low in calcium. 5. The injected 45Ca accumulates in zymogen granules faster than [3H]L-leucine-labelled proteins. The 45Ca:protein ratio of these organelles is considerably lower than that of the caerulein-stimulated juice. 6. It is concluded (a) that calcium is secreted in to the pancreatic juice in two fractions, one (possibly released by simple diffusion) associated with the electrolyte component, the other with protein of the juice, (b) that zymogen granules are the major, but not the only source of the latter fraction, and (c) that the zymogen granule-associated calcium joins the exportable proteins some time after their synthesis, possibly in the Golgi complex and/or in the condensing vacuoles.}, }
@article {pmid168599, year = {1975}, author = {Duchesne, J and Goutier, R and Maréchal, R and Van de Vorst, A}, title = {Free radical evolution in rat liver following the ingestion of DAB.}, journal = {Physics in medicine and biology}, volume = {20}, number = {2}, pages = {305-309}, doi = {10.1088/0031-9155/20/2/012}, pmid = {168599}, issn = {0031-9155}, mesh = {Animals ; Electron Spin Resonance Spectroscopy ; Free Radicals ; Liver/*drug effects ; Male ; Mitochondria, Liver/drug effects ; Neoplasms/analysis ; Rats ; p-Dimethylaminoazobenzene/*pharmacology ; }, abstract = {The effect of the ingestion of the carcinogenic substance DAB on the density and distribution of organic free radicals in rat liver is studied by the electron spin resonance method. There is a remarkable parallelism between what is known about the evolution of the activity of mitochondria and the concentration variations of free radicals.}, }
@article {pmid124043, year = {1975}, author = {Herlicoviez, D}, title = {[Mitochondrial abnormalities and ocular myopathies with downward-spreading evolution. Apropos of 2 new cases].}, journal = {Pathologie-biologie}, volume = {23}, number = {2}, pages = {107-117}, pmid = {124043}, issn = {0369-8114}, mesh = {Adenoma/complications ; Adenosine Triphosphatases/metabolism ; Adult ; Biopsy ; Cytoplasmic Granules/ultrastructure ; Emaciation/complications ; Female ; Glycerolphosphate Dehydrogenase/metabolism ; Histocytochemistry ; Humans ; Middle Aged ; Mitochondria, Muscle/*ultrastructure ; Muscles/pathology ; Muscular Atrophy/complications/metabolism/*pathology ; Myofibrils/ultrastructure ; NADH Tetrazolium Reductase/metabolism ; Ophthalmoplegia/*complications ; Phosphorylases/metabolism ; Sarcolemma/ultrastructure ; Succinate Dehydrogenase/metabolism ; Thyroid Neoplasms/complications ; Vitamin K ; }, abstract = {Two cases, one being probably familial, of ocular myopathy are reported. In both the onset was in childhood by ptosis of the eyelids and the course lasted more than 20 years. The patients (32 and 49 years) presented involvement of the ocular muscles as well as of the facial, pharyngolaryngeal, neck and limb muscles. There was, in both cases, marked body weight loss which could not be explained by the muscular atrophy alone, and a thyroid nodule which was not accompanied by evident change in thyroid function. Muscle biopsy studies were carried out : electron microscopy showed in both cases aggregates of mitochondria exhibiting various changes ; in one case histochemistry demonstrated that these changes were confined to type 1 muscle fibres. These cases of descending ocular myopathy can be included therefore in the group of the smaller than myopathies with abnormal mitochondria greater than.}, }
@article {pmid1118075, year = {1975}, author = {Cantoni, L and Andreuzzi, P and Curri, SB and Rocchetti, P}, title = {[Total and fractionized plasma phospholipids in chronic liver diseases].}, journal = {Minerva medica}, volume = {66}, number = {3}, pages = {101-128}, pmid = {1118075}, issn = {0026-4806}, mesh = {Adult ; Analysis of Variance ; Chromatography, Thin Layer ; Chronic Disease ; Female ; Humans ; Liver Cirrhosis/blood ; Liver Diseases/*blood ; Male ; Middle Aged ; Mitochondria, Liver/metabolism ; Phosphatidylcholines/blood ; Phosphatidylethanolamines/blood ; Phosphatidylserines/blood ; Phospholipids/*blood ; Sphingomyelins/blood ; }, abstract = {The literature data relating to the importance of the liver in fat metabolism, and the behaviour of plasma and red cell phospholipids, cholesterol, triglycerides, fatty acids and lipoproteins in acute and chronic liver disease is reviewed. The results of an investigation of the diagnostic and prognostic significance of total and single plasma phospholipid levels in a series of 70 cases (5 chronic aggressive hepatitis, 12 compensated cirrhosis, 41 uncompensated cirrhosis, and 12 controls) are presented. Quantitative assessment by means of thin-layer chromatography showed four features of marked prognostic interest: a) a significant decrease in total phospholipids; b) increased phosphatidyl choline; c) increased phosphatidyl ethanolamine; d) decreased sphingomyelin. In discussing the results, stress is laid on the fact that this method offers a sufficient close evaluation of the clinical picture with respect to both the evolution of cirrogenic liver diseases and the effectiveness of their treatment. It also enables an assessment to be made of liver cell mitochondria function.}, }
@article {pmid1234809, year = {1975}, author = {Pác, L}, title = {Ultrastructure of the joint receptors of the tortoise (Testudo graeca. Emys orbicularis).}, journal = {Zeitschrift fur mikroskopisch-anatomische Forschung}, volume = {89}, number = {6}, pages = {1068-1078}, pmid = {1234809}, issn = {0044-3107}, mesh = {Animals ; Extremities ; Joints/*innervation ; Mechanoreceptors/*ultrastructure ; Phylogeny ; Turtles/*anatomy &amp; histology ; }, abstract = {The ultrastructure of the spray-like ramified encapsulated corpuscles with the primitive inner core from the joint capsules of the large limb joints of the tortoise (Testudo graeca and Emys orbicularis) was examined. Each of the branches of the receptor consists of three components. Through the middle of the receptor branche runs the nerve terminal, containing in the receptor matrix numerous mitochondria, tiny light vesicles and neurofilaments and neurotubules running in the axial way. The nerve terminal gives off on some places among the inner core cells tiny finger-like processes. The axon is surrounded by the inner core cells and their irregular plasmatic processes. Among the inner core cells and their irregular plasmatic processes there is a labyrinth of spaces, connected centrally with the periaxonal space and with the boundary space on the periphery. The inner core cells are covered on the surface, turning to the boundary space by the basal membrane. The inner core has a very primitive structure, it still lacks the typical lamellar structure. The capsule of the receptor is formed by flat cells, which surround the inner core in 1--3 layers. Between the capsule of the receptor and the inner core is the boundary space, containihg sporadical collagenous fibrils. The structure of the spray-like ramified encapsulated corpuscles with the primitive inner core from the joint capsules of the tortoise is analogous to the simple lamellar receptors from the skin of some reptiles (Von Düring 1973, 1974). The primitive structure of the inner core of the joint receptors in the tortoise reminds of the structure of the inner core of the developing simple (paciniform) corpuscles (Poláĉek and Halata 1970) and Pacinian corpuscles (Malinovský 1974). The observed nerve endings represent a primitive, early stage in phylogeny development of the lamellar mechanoreceptors.}, }
@article {pmid1145607, year = {1975}, author = {Rieger, RM and Rieger, GE}, title = {Fine structure of the pharyngeal bulb in Trilobodrilus and its phylogenetic significance within archiannelida.}, journal = {Tissue &amp; cell}, volume = {7}, number = {2}, pages = {267-279}, doi = {10.1016/0040-8166(75)90005-1}, pmid = {1145607}, issn = {0040-8166}, mesh = {Animals ; Annelida/classification/*ultrastructure ; Cell Nucleus/ultrastructure ; Membranes/ultrastructure ; Mitochondria, Muscle/ultrastructure ; Models, Structural ; Muscle Contraction ; Muscles ; Myofibrils/ultrastructure ; Pharynx/ultrastructure ; Phylogeny ; Sarcoplasmic Reticulum/ultrastructure ; }, abstract = {Transmission electron microscopical studies of the pharyngeal bulb in the archiannelid Trilobodrilus sp. proved the presence of two opposing myofilament systems in the plate muscle cells forming this bulb. These muscles are obliquely striated. The significance as well as the origin of this specialized plate-muscle cells in the pharyngeal bulb of archiannelids is discussed in the light of their controversial phylogenetic and systematic position. In addition a hypothesis is suggested to explain the origin of the special arrangement of two opposing systems of myofilaments in one single muscle cell.}, }
@article {pmid1103284, year = {1975}, author = {Hall, DO and Rao, KK and Cammack, R}, title = {The iron-sulphur proteins: structure, function and evolution of a ubiquitous group of proteins.}, journal = {Science progress}, volume = {62}, number = {246}, pages = {285-317}, pmid = {1103284}, issn = {0036-8504}, mesh = {Amino Acid Sequence ; Animals ; Bacteria/enzymology ; Biological Evolution ; *Cysteine ; Electron Transport ; Ferredoxins ; *Iron ; Mitochondria/enzymology ; Plants/enzymology ; *Proteins/metabolism ; Structure-Activity Relationship ; }, }
@article {pmid1089067, year = {1975}, author = {Bridgen, J and Harris, JI and Northrop, F}, title = {Evolutionary relationships in superoxide dismutase.}, journal = {FEBS letters}, volume = {49}, number = {3}, pages = {392-395}, doi = {10.1016/0014-5793(75)80793-9}, pmid = {1089067}, issn = {0014-5793}, mesh = {Amino Acid Sequence ; Amino Acids/analysis ; Animals ; Bacillus/enzymology ; *Biological Evolution ; Cattle ; Chickens ; Erythrocytes/enzymology ; Escherichia coli/analysis ; Mitochondria, Liver/enzymology ; Species Specificity ; *Superoxide Dismutase/blood ; }, }
@article {pmid1041247, year = {1975}, author = {}, title = {Mitochondria, chloroplasts, and energy transfer: a discussion.}, journal = {Ciba Foundation symposium}, volume = {}, number = {31}, pages = {63-68}, pmid = {1041247}, issn = {0300-5208}, mesh = {Adenosine Triphosphate/metabolism ; Bacteria/metabolism ; Biological Evolution ; Biological Transport, Active ; Chloroplasts/*metabolism ; Cytosol/metabolism ; Energy Metabolism ; Energy Transfer ; Enzyme Induction ; Ions/metabolism ; Membranes/metabolism ; Mitochondria/*metabolism ; Oxidative Phosphorylation ; Oxygen/pharmacology ; Photosynthesis ; }, }
@article {pmid822529, year = {1975}, author = {Margulis, L}, title = {Symbiotic theory of the origin of eukaryotic organelles; criteria for proof.}, journal = {Symposia of the Society for Experimental Biology}, volume = {}, number = {29}, pages = {21-38}, pmid = {822529}, issn = {0081-1386}, mesh = {Aerobiosis ; Animal Population Groups/classification ; Animals ; Bacteria ; *Biological Evolution ; Chloroplasts ; Cilia ; Cyanobacteria ; DNA, Mitochondrial ; Eukaryota ; Extrachromosomal Inheritance ; Flagella ; Genetics ; Mitochondria/metabolism ; Mitosis ; *Models, Biological ; *Organoids ; Paramecium ; Photosynthesis ; Phylogeny ; Plants/classification ; Recombination, Genetic ; *Symbiosis ; Tubulin ; }, abstract = {The purpose of a scientific theory is to unite apparently disparate observations into a coherent set of generalizations with predictive power. Historical theories, which necessarily treat complex irreversible events, can never be directly tested. However they certainly can lead to predictions. The 'extreme' version of the serial endosymbiotic theory argues that three classes of eukaryotic organelles had free-living ancestors: mitochondria, basal bodies/flagella/cilia [(9 + 2) homologues] and photosynthetic plastids. Many lines of evidence support this theory and can be interpreted in relation to one another on the basis of this theory. Even if this theory should eventually be proved wrong it has the real advantage of generating a large number of unique experimentally verifiable hypotheses.}, }
@article {pmid238809, year = {1975}, author = {Whatley, FR}, title = {Chloroplasts.}, journal = {Ciba Foundation symposium}, volume = {}, number = {31}, pages = {41-61}, doi = {10.1002/9780470720134.ch4}, pmid = {238809}, issn = {0300-5208}, mesh = {Adenosine Triphosphate/biosynthesis ; Binding Sites ; Biological Transport, Active ; Chlorides/pharmacology ; Chloroplasts/*metabolism/ultrastructure ; Cytochromes/metabolism ; Energy Transfer ; Ferredoxins/metabolism ; Hydrogen-Ion Concentration ; Membranes/metabolism/ultrastructure ; Models, Biological ; NADP/metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; Photochemistry ; Photophosphorylation ; *Photosynthesis ; Plastoquinone/metabolism ; Spectrum Analysis ; }, abstract = {Illuminated chloroplast fragments, which can convert light into chemical energy (NADPH2 and ATP), contain a number of soluble and insoluble electron carriers that have been arranged, on the basis of their redox potentials and on kinetic and other evidence, in sequences (analogous to those in mitochondria) to describe the events involved in the light reactions of photosynthesis. Fractionation of chloroplasts allows separation of two light-dependent partial reactions: the evolution of oxygen and the reduction of pyridine nucleotide, accompanied by ATP synthesis. The stoichiometry of the latter reaction is still uncertain. Chloroplasts contain a directional proton-translocating ATPase (CF1) needed for the phosphorylation of ADP in the light. The CF1 also catalyses synthesis of ATP from ADP. When a pH gradient is applied in the dark across the phosphorylating membranes, the amount of ATP synthesized is related to both the change in pH and the electrical potential. During its catalytic activity, the CF1 protein undergoes reversible conformational changes, but this is not the source of the driving force for ATP synthesis.}, }
@article {pmid183302, year = {1975}, author = {John, P and Whatley, FR}, title = {Paracoccus denitrificans: a present-day bacterium resembling the hypothetical free-living ancestor of the mitochondrion.}, journal = {Symposia of the Society for Experimental Biology}, volume = {}, number = {29}, pages = {39-40}, pmid = {183302}, issn = {0081-1386}, mesh = {*Biological Evolution ; Cytochrome c Group/analysis ; Membranes/enzymology ; *Mitochondria/enzymology/metabolism ; *Models, Biological ; Oxidative Phosphorylation ; *Paracoccus denitrificans/enzymology/metabolism ; }, }
@article {pmid131111, year = {1975}, author = {Mahler, HR and Raff, RA}, title = {The evolutionary origin of the mitochondrion: a nonsymbiotic model.}, journal = {International review of cytology}, volume = {43}, number = {}, pages = {1-124}, doi = {10.1016/s0074-7696(08)60067-4}, pmid = {131111}, issn = {0074-7696}, mesh = {Adenosine Triphosphatases/metabolism ; Aerobiosis ; Animals ; Bacteria/ultrastructure ; *Biological Evolution ; DNA, Mitochondrial ; DNA-Directed RNA Polymerases/metabolism ; Electron Transport ; Extrachromosomal Inheritance ; Fossils ; Genes ; Heme/biosynthesis ; History, Ancient ; Membranes/physiology ; *Mitochondria/metabolism/ultrastructure ; *Models, Biological ; Origin of Life ; Oxygen/toxicity ; Oxygen Consumption ; Plasmids ; Protein Biosynthesis ; RNA, Messenger/metabolism ; RNA, Ribosomal/metabolism ; Symbiosis ; Transcription, Genetic ; }, }
@article {pmid125189, year = {1975}, author = {Lipmann, F}, title = {The roots of bioenergetics.}, journal = {Ciba Foundation symposium}, volume = {}, number = {31}, pages = {3-22}, doi = {10.1002/9780470720134.ch2}, pmid = {125189}, issn = {0300-5208}, mesh = {Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Biochemistry/*history ; Biological Evolution ; Creatine/metabolism ; Cytochromes/metabolism ; *Energy Metabolism ; Fermentation ; Flavoproteins/metabolism ; Fructosephosphates/metabolism ; Glyceric Acids/metabolism ; Glycolysis ; History, 20th Century ; Membrane Potentials ; Microscopy, Electron ; Mitochondria/ultrastructure ; Muscle Contraction ; Myosin Subfragments/metabolism ; Nucleotides/metabolism ; Oxidative Phosphorylation ; Phosphates/metabolism ; Photophosphorylation ; Pyridines/metabolism ; Pyruvates/metabolism ; Thermodynamics ; }, abstract = {Understanding metabolic energy transformation began with the realization of an 'intrusion' of phosphate into the mechanism of alcoholic fermentation. The discovery of an analogous participation of phosphate in muscle glycolysis connected the metabolic generation of energy-rich phosphate bonds fed into a common transmitter, adenosine triphosphate (ATP), with the production of mechanical energy through the finding that the phosphoryl group of creatine phosphate transferred to ATP could supply the energy for muscle contraction. In this way, a functional applicability of the energy of the phosphate bond was first shown. This observation was soon followed by the recognition that the phosphoanhydride bond of ATP provided the driving force in biosynthetic reactions; in this type of bond, metabolic energy apparently collects before it is transmitted for functional and biosynthetic use. The storage of energy in ATP was first detected in anaerobic energy-yielding reactions but soon was also found in respiratory and photosynthetic energy production. However, the mechanism by which energy derived from metabolites was converted into phosphate-bond energy in the latter processes appeared to differ from that of anaerobic energy transmission. Whereas phosphorylated compounds mediate the latter in homogeneous solutions, aerobic phosphorylation and photophosphorylation in prokaryotes seem to require special submembranous structures; and in eukaryotes, energy conversion is a function of special organelles, the mitochondria and chloroplasts. The evolutionary aspects of the transition from prokaryotes to eukaryotes are of considerable interest. In conclusion, the relevance of an apparent prokaryotic origin of the energy-transforming organelles in the eukaryotes will be commented on.}, }
@article {pmid60787, year = {1975}, author = {Raff, RA and Mahler, HR}, title = {The symbiont that never was: an inquiry into the evolutionary origin of the mitochondrion.}, journal = {Symposia of the Society for Experimental Biology}, volume = {6}, number = {29}, pages = {41-92}, pmid = {60787}, issn = {0081-1386}, mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; Cell Nucleus/enzymology ; Complement Fixation Tests ; Cytoplasm/metabolism ; DNA, Mitochondrial/analysis ; DNA-Directed RNA Polymerases/metabolism ; Electron Transport ; Ferredoxins/analysis ; Genes ; *Mitochondria/enzymology ; Mixed Function Oxygenases/analysis ; *Models, Biological ; Nucleotides/analysis ; Oxygen ; Phylogeny ; Plasmids ; RNA, Messenger/analysis ; RNA, Ribosomal/analysis ; RNA-Directed DNA Polymerase/metabolism ; *Symbiosis ; }, abstract = {Intraoperative real-time sonography was used to monitor surgical reduction of acute thoracolumbar burst fractures in eight patients. Real-time sonography was performed after laminectomy through a saline-filled operative field using either a 5.0 or a 7.5 MHz transducer. Sonography was performed during Harrington rod distraction and during fracture reduction to confirm adequacy of decompression of the spinal canal. This technique is useful to monitor surgery and in defining adequate fracture reduction.}, }
@article {pmid4413751, year = {1974}, author = {Broniszewska-Ardelt, B and Miller AT Jr+MILLER, AT}, title = {Hypoxic changes in brain hexokinase distribution: phylogenetic and developmental considerations.}, journal = {Comparative biochemistry and physiology. B, Comparative biochemistry}, volume = {49}, number = {1B}, pages = {151-156}, doi = {10.1016/0305-0491(74)90234-x}, pmid = {4413751}, issn = {0305-0491}, mesh = {Acidosis/enzymology ; Aging ; Animals ; *Biological Evolution ; Brain/cytology/*enzymology/growth &amp; development ; Cytoplasm/enzymology ; Hexokinase/*metabolism ; Hypoxia/*enzymology ; Mitochondria/enzymology ; *Phylogeny ; Rats ; Species Specificity ; Spectrophotometry, Ultraviolet ; Time Factors ; Turtles ; }, }
@article {pmid4426877, year = {1974}, author = {Wintenberger-Torrés, S and Fléchon, JE}, title = {Ultrastructural evolution of the trophoblast cells of the pre-implantation sheep blastocyst from day 8 to day 18.}, journal = {Journal of anatomy}, volume = {118}, number = {Pt 1}, pages = {143-153}, pmid = {4426877}, issn = {0021-8782}, mesh = {Animals ; Basement Membrane/ultrastructure ; Blastocyst/*ultrastructure ; Cell Membrane/ultrastructure ; Cell Nucleolus/ultrastructure ; Cell Nucleus/ultrastructure ; Cytoplasm/ultrastructure ; Desmosomes/ultrastructure ; Embryo Implantation ; Endoderm/ultrastructure ; Endoplasmic Reticulum/ultrastructure ; Female ; Glycogen/analysis ; Golgi Apparatus/ultrastructure ; Heterochromatin/ultrastructure ; Liposomes/ultrastructure ; Microtubules/ultrastructure ; Mitochondria/ultrastructure ; Phagocytosis ; Pinocytosis ; Polyribosomes/ultrastructure ; Pregnancy ; Ribosomes/ultrastructure ; Sheep/*physiology ; Trophoblasts/*ultrastructure ; }, }
@article {pmid4370101, year = {1974}, author = {Dayhoff, MO and Barker, WC and McLaughlin, PJ}, title = {Inferences from protein and nucleic acid sequences: early molecular evolution, divergence of kingdoms and rates of change.}, journal = {Origins of life}, volume = {5}, number = {3}, pages = {311-330}, pmid = {4370101}, issn = {0302-1688}, mesh = {Amino Acid Sequence ; Animals ; Bacterial Proteins ; Base Sequence ; *Biological Evolution ; Chromosome Aberrations ; Cytochrome c Group ; Electron Transport ; Ferredoxins ; Genetic Code ; Humans ; Mitochondria ; Mutation ; *Nucleic Acids ; Plants ; Polynucleotides ; *Proteins ; RNA, Ribosomal ; RNA, Transfer ; }, }
@article {pmid4832979, year = {1974}, author = {Uzzell, T and Spolsky, C}, title = {Mitochondria and plastids as endosymbionts: a revival of special creation?.}, journal = {American scientist}, volume = {62}, number = {3}, pages = {334-343}, pmid = {4832979}, issn = {0003-0996}, mesh = {Animals ; Bacteria/cytology ; Biological Evolution ; DNA/analysis ; DNA, Mitochondrial/analysis ; Eukaryota/cytology ; Mice ; Mitochondria/*analysis ; Organoids/*analysis ; Rats ; *Symbiosis ; }, }
@article {pmid4856973, year = {1974}, author = {Dubin, DT and Friend, DA}, title = {Methylation properties of mitochondrion-specific transfer RNA from cultured hamster cells.}, journal = {Biochimica et biophysica acta}, volume = {340}, number = {3}, pages = {269-277}, doi = {10.1016/0005-2787(74)90272-x}, pmid = {4856973}, issn = {0006-3002}, mesh = {Adenine/metabolism ; Adenine Nucleotides/analysis ; Animals ; Biological Evolution ; Carbon Radioisotopes ; Cell Line ; Chromatography, Paper ; Cricetinae ; Cytosine/metabolism ; Electrophoresis, Paper ; Electrophoresis, Polyacrylamide Gel ; Ethidium/pharmacology ; Guanine/metabolism ; Kidney ; Methionine ; Methylation ; Mitochondria/drug effects/*metabolism ; Phosphorus Radioisotopes ; RNA, Transfer/*metabolism ; Ribose/metabolism ; Species Specificity ; }, }
@article {pmid4597494, year = {1974}, author = {Fridovich, I}, title = {Evidence for the symbiotic origin of mitochondria.}, journal = {Life sciences}, volume = {14}, number = {5}, pages = {819-826}, doi = {10.1016/0024-3205(74)90071-x}, pmid = {4597494}, issn = {0024-3205}, mesh = {Aerobiosis ; Amino Acid Sequence ; Animals ; *Biological Evolution ; Chloramphenicol/pharmacology ; Cycloheximide/pharmacology ; Cytoplasm/enzymology/metabolism ; DNA/metabolism ; DNA Nucleotidyltransferases/metabolism ; Escherichia coli/enzymology ; Mitochondria/drug effects/*metabolism ; Mitochondria, Liver/enzymology ; Oxygen Consumption ; Peptide Elongation Factors ; Protein Biosynthesis ; Rats ; Ribosomes/metabolism ; Species Specificity ; Superoxide Dismutase/metabolism ; *Symbiosis ; }, }
@article {pmid4600296, year = {1974}, author = {Wickramasinghe, RH and McIntosh, EN}, title = {Adrenodoxin, ferredoxins and other iron-sulphur (nonheme-iron) proteins. I.}, journal = {Enzyme}, volume = {17}, number = {4}, pages = {210-226}, doi = {10.1159/000459332}, pmid = {4600296}, issn = {0013-9432}, mesh = {Adrenal Glands/metabolism ; Amino Acid Sequence ; Animals ; Bacteria/metabolism ; Binding Sites ; Biological Evolution ; *Carrier Proteins ; Cattle ; Corpus Luteum/metabolism ; Electron Transport ; Female ; *Ferredoxins ; Humans ; Hydroxylation ; Male ; *Metalloproteins ; Mitochondria/metabolism ; Molecular Conformation ; Molecular Weight ; Oxidation-Reduction ; Oxidoreductases/metabolism ; Plants/metabolism ; Potentiometry ; Protein Binding ; Rubredoxins ; Testis/metabolism ; }, }
@article {pmid4377493, year = {1974}, author = {Vinnikov, YA}, title = {Differentiation of photoreceptor cells and morphogenetic function of biomembranes.}, journal = {Zeitschrift fur mikroskopisch-anatomische Forschung}, volume = {88}, number = {4}, pages = {759-773}, pmid = {4377493}, issn = {0044-3107}, mesh = {Animals ; Biological Evolution ; Cell Differentiation ; Cell Membrane/physiology/ultrastructure ; Chick Embryo ; Dendrites/ultrastructure ; Eels ; Flagella/ultrastructure ; Golgi Apparatus/ultrastructure ; Membrane Potentials ; Mitochondria/ultrastructure ; Permeability ; Photoreceptor Cells/*cytology/ultrastructure ; Potassium ; Receptors, Neurotransmitter/ultrastructure ; Rhodopsin/biosynthesis/isolation &amp; purification ; Ribosomes/ultrastructure ; Sodium ; Synaptic Membranes/physiology ; }, abstract = {Photoreceptor cells of eyes in vertebrate animals have been chosen as an example to illustrate the morphogenetic function of biomembranes in differentiation of the eye outer segments -- rods and cones. Morphogenetic function of biomembranes in photoreceptor cells involves an insertion of the heterogeneous molecule of visual pigment into the original plasma membrane. Depending on some features of visual pigment in one case cones may be produced or rods as more complicated structures may be differentiated in the other one. Some evolution aspects of photoreceptor cell differentiation have also been under discussion.}, }
@article {pmid4377067, year = {1974}, author = {Malassiné, A}, title = {[Ultrastructural evolution of the placental labyrinth of the cat (author's transl)].}, journal = {Anatomy and embryology}, volume = {146}, number = {1}, pages = {1-20}, pmid = {4377067}, issn = {0340-2061}, mesh = {Animals ; Capillaries/ultrastructure ; Cats ; Decidua/ultrastructure ; Endoplasmic Reticulum/metabolism ; Endothelium/ultrastructure ; Female ; Fetus/ultrastructure ; Gestational Age ; Glycogen ; Golgi Apparatus/immunology ; Hormones/biosynthesis ; Inclusion Bodies/ultrastructure ; Lipids ; Microscopy, Electron ; Mitochondria/ultrastructure ; Pinocytosis ; Placenta/*ultrastructure ; Pregnancy ; Protein Biosynthesis ; Ribosomes/ultrastructure ; Steroids/biosynthesis ; Trophoblasts/ultrastructure ; }, }
@article {pmid4376458, year = {1974}, author = {Koopowitz, H and Chien, P}, title = {Ultrastructure of the nerve plexus in flatworms. I. Peripheral organization.}, journal = {Cell and tissue research}, volume = {155}, number = {3}, pages = {337-351}, pmid = {4376458}, issn = {0302-766X}, mesh = {Animals ; Axons ; Biological Evolution ; Epithelial Cells ; Epithelium/ultrastructure ; Inclusion Bodies ; Microscopy, Electron ; Microtubules ; Mitochondria ; Muscles/ultrastructure ; Nervous System/*ultrastructure ; Neuroglia/ultrastructure ; Neurons/ultrastructure ; Synapses/ultrastructure ; Turbellaria/*ultrastructure ; Vacuoles ; }, }
@article {pmid4370692, year = {1974}, author = {Garaci, E and Djaczenko, W}, title = {Ultrastructural evolution of experimentally induced lipid inclusions in rat and mouse hepatocytes indicative for the recovery of livers from effects of benzidamine and triacetyloleandomycin.}, journal = {Annali Sclavo; rivista di microbiologia e di immunologia}, volume = {16}, number = {1}, pages = {18-28}, pmid = {4370692}, mesh = {Animals ; Benzyl Compounds/pharmacology ; Dimethylamines/pharmacology ; Inclusion Bodies/*metabolism ; Indazoles/*pharmacology ; *Lipid Metabolism ; Liver/drug effects/*metabolism/ultrastructure ; Liver Regeneration/*drug effects ; Mice ; Microscopy, Electron ; Mitochondria, Liver/*metabolism/ultrastructure ; Oleandomycin/*pharmacology ; Pyrazoles/*pharmacology ; Rats ; }, }
@article {pmid4218927, year = {1974}, author = {Schwemmler, W}, title = {[Endosymoiosis of leafhoppers: A model for the evolution of the eukaryotic cell (author's transl)].}, journal = {Acta biotheoretica}, volume = {23}, number = {3-4}, pages = {132-169}, pmid = {4218927}, issn = {0001-5342}, mesh = {Acculturation ; Animals ; *Cell Nucleus ; Chloroplasts/ultrastructure ; Hemolymph ; Hydrogen-Ion Concentration ; *Insecta ; Mitochondria/ultrastructure ; Models, Biological ; Osmotic Pressure ; *Symbiosis ; }, }
@article {pmid4590170, year = {1973}, author = {Steinman, HM and Hill, RL}, title = {Sequence homologies among bacterial and mitochondrial superoxide dismutases.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {70}, number = {12}, pages = {3725-3729}, pmid = {4590170}, issn = {0027-8424}, mesh = {Amino Acid Sequence ; Animals ; Autoanalysis ; Biological Evolution ; Cattle ; Chickens ; Erythrocytes/enzymology ; Escherichia coli/*enzymology ; Iron ; Manganese ; Mitochondria, Liver/*enzymology ; Superoxide Dismutase/*analysis/blood/isolation &amp; purification ; }, abstract = {Superoxide dismutase from chicken-liver mitochondria (manganese enzyme) and the two dismutases from Escherichia coli (manganese and iron enzymes) were analyzed through 29 cycles of automated Edman degradations. The high degree of homology among the amino-terminal sequences of these three dismutases corroborates their known similarity of structural and functional properties, and serves as further evidence for the endosymbiotic origin of mitochondria. In contrast, these three sequences exhibit no significant homology with the amino-terminal sequence of bovine-erythrocyte superoxide dismutase, which is consistent with the classification of eukaryotic copper-zinc dismutases as a family distinct from the manganese enzymes in stability and catalytic properties.}, }
@article {pmid4274132, year = {1973}, author = {Weltman, JK and Dowben, RM}, title = {Relatedness among contractile and membrane proteins: evidence for evolution from common ancestral genes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {70}, number = {11}, pages = {3230-3234}, pmid = {4274132}, issn = {0027-8424}, mesh = {Actins ; Adenosine Triphosphatases ; Amino Acid Sequence ; Animals ; Bacillus/analysis ; Bacterial Proteins ; *Biological Evolution ; Cell Membrane/*analysis ; Chloroplasts/analysis ; Enterococcus faecalis/analysis ; Genetic Code ; Humans ; Mollusca ; *Muscle Proteins ; Myocardium/analysis ; Myosin Subfragments ; Myosins ; Oxidative Phosphorylation Coupling Factors ; *Proteins ; Proteus vulgaris/analysis ; Rabbits ; Salmonella/analysis ; Tetrahymena/analysis ; Tropomyosin ; }, abstract = {A statistical method for quantifying the relatedness among proteins was used to perform 2926 paired comparisons of amino-acid composition among 77 contractile and membrane-associated proteins from diverse species and sources. Relatedness of amino-acid compositions correlates with homology of amino-acid sequence. A high degree of relatedness was detected among K(+)-dependent membrane ATPase of Streptococcus faecalis, coupling factors F(1) and CF(1) from mitochondria and chloroplasts, outer fiber protein of cilia, ciliary dynein, tubulin, various actins, and myosin subfragment S-1. Heavy meromyosin and tropomyosin were related to each other but not to the first group of proteins. Differences in the degree of methylation may account for some differences in physiological function. Because of their diverse sources, the high degree of relatedness among these proteins is more compatible with evolution from common ancestral genes than with convergent evolution. Squid axon filarin, molluscan paramyosin, and bacterial flagellins appear to be unrelated either to each other or to any of the other proteins studied. Existence of persistent homologies among so many diverse proteins implies conservation of genetic information during evolution by utilization of codons for preferred amino-acid sequences in various proteins.}, }
@article {pmid4365747, year = {1973}, author = {Anzanel, D and Dieterlen-Lièvre, F and Salvatorelli, G}, title = {[Influence of different hormones on the evolution of embryonic chicken liver in organotypic culture].}, journal = {Comptes rendus hebdomadaires des seances de l'Academie des sciences. Serie D: Sciences naturelles}, volume = {277}, number = {17}, pages = {1809-1811}, pmid = {4365747}, mesh = {Animals ; Cell Differentiation/*drug effects ; Chick Embryo/*drug effects ; Endoplasmic Reticulum/drug effects ; Glucagon/pharmacology ; Hormones/*pharmacology ; Hydrocortisone/pharmacology ; Inclusion Bodies/drug effects ; Insulin/pharmacology ; Lipid Metabolism ; Liver/cytology/*embryology/growth &amp; development/metabolism ; Liver Glycogen/*biosynthesis ; Microscopy, Electron ; Mitochondria, Liver/drug effects ; Organ Culture Techniques ; }, }
@article {pmid4730058, year = {1973}, author = {De Duve, C}, title = {Origin of mitochondria.}, journal = {Science (New York, N.Y.)}, volume = {182}, number = {4107}, pages = {85}, doi = {10.1126/science.182.4107.85}, pmid = {4730058}, issn = {0036-8075}, mesh = {Aerobiosis ; Bacteria/cytology/*metabolism ; Biological Evolution ; Mitochondria/*metabolism ; }, }
@article {pmid4366949, year = {1973}, author = {Laffargue, P and Adechy-Benkoel, L}, title = {[Ultrastructure of the human corpus luteum. 2. Evolution during pregnancy].}, journal = {Annales d'anatomie pathologique}, volume = {18}, number = {4}, pages = {389-403}, pmid = {4366949}, issn = {0003-3871}, mesh = {Cell Nucleolus ; Cell Nucleus ; *Corpus Luteum ; Endoplasmic Reticulum ; Female ; Gestational Age ; Histological Techniques ; Humans ; Inclusion Bodies ; Infant ; Menstruation ; Microscopy, Electron ; Mitochondria ; *Pregnancy ; }, }
@article {pmid4356037, year = {1973}, author = {Brandenburger, JL and Woollacott, RM and Eakin, RM}, title = {Fine structure of eyespots in tornarian larvae (phylum: Hemichordata).}, journal = {Zeitschrift fur Zellforschung und mikroskopische Anatomie (Vienna, Austria : 1948)}, volume = {142}, number = {1}, pages = {89-102}, pmid = {4356037}, issn = {0340-0336}, mesh = {Animals ; Axons ; Biological Evolution ; Cell Nucleus ; Chordata, Nonvertebrate/*cytology ; Cilia ; Inclusion Bodies ; Larva/*cytology ; Light ; Microscopy, Electron ; Mitochondria ; Photoreceptor Cells/*cytology ; Pigments, Biological ; }, }
@article {pmid4700607, year = {1973}, author = {Uzzell, T and Spolsky, C}, title = {Origin of mitochondria.}, journal = {Science (New York, N.Y.)}, volume = {180}, number = {4085}, pages = {516-517}, doi = {10.1126/science.180.4085.516}, pmid = {4700607}, issn = {0036-8075}, mesh = {Aerobiosis ; Anaerobiosis ; Bacteria/cytology ; *Biological Evolution ; *Mitochondria ; *Symbiosis ; }, }
@article {pmid4709980, year = {1973}, author = {Smith, CL}, title = {Thermostability of some mitochondrial enzymes of lower vertebrates. I. General survey.}, journal = {Comparative biochemistry and physiology. B, Comparative biochemistry}, volume = {44}, number = {3}, pages = {779-788}, doi = {10.1016/0305-0491(73)90227-7}, pmid = {4709980}, issn = {0305-0491}, mesh = {Animals ; Anura ; Biological Evolution ; Chickens ; Colorimetry ; Columbidae ; Cricetinae ; Drug Stability ; Fishes ; Guinea Pigs ; Hot Temperature ; Lizards ; Mitochondria, Liver/*enzymology ; Monoamine Oxidase/*metabolism ; Polarography ; Rabbits ; Rats ; Snakes ; Species Specificity ; Succinate Dehydrogenase/*metabolism ; Time Factors ; Turtles ; Urodela ; Vertebrates/*metabolism ; }, }
@article {pmid4692357, year = {1973}, author = {Meyer, RR}, title = {On the evolutionary origin of mitochondrial DNA.}, journal = {Journal of theoretical biology}, volume = {38}, number = {3}, pages = {647-653}, doi = {10.1016/0022-5193(73)90264-6}, pmid = {4692357}, issn = {0022-5193}, mesh = {Acridines/pharmacology ; Animals ; Bacteria ; *Biological Evolution ; Cell Membrane ; *DNA/biosynthesis ; DNA Replication ; DNA, Circular ; DNA, Mitochondrial ; Ethidium/pharmacology ; Extrachromosomal Inheritance ; Genetics, Microbial ; Humans ; *Mitochondria ; Models, Biological ; Molecular Weight ; Symbiosis ; }, }
@article {pmid4702922, year = {1973}, author = {Westfall, JA}, title = {Ultrastructural evidence for a granule-containing sensory-motor-interneuron in Hydra littoralis.}, journal = {Journal of ultrastructure research}, volume = {42}, number = {3}, pages = {268-282}, doi = {10.1016/s0022-5320(73)90055-5}, pmid = {4702922}, issn = {0022-5320}, mesh = {Animals ; Biological Evolution ; Cell Nucleolus ; Cell Nucleus ; Cilia ; *Cytoplasmic Granules ; Golgi Apparatus ; Hydra/*cytology ; Microscopy, Electron ; Microtubules ; Mitochondria ; Motor Neurons/*cytology ; Nerve Net/cytology ; Neuromuscular Junction/cytology ; Neurons/*cytology ; Ribosomes ; Synapses/cytology ; Synaptic Vesicles ; }, }
@article {pmid4196498, year = {1973}, author = {Regard, E and Mauchamp, J}, title = {[Development of peroxidase activity and organification of iodide in the thyroid gland of Xenopus laevis (Daudin) during metamorphosis].}, journal = {Comptes rendus hebdomadaires des seances de l'Academie des sciences. Serie D: Sciences naturelles}, volume = {276}, number = {1}, pages = {121-123}, pmid = {4196498}, mesh = {Animals ; Endoplasmic Reticulum ; Golgi Apparatus ; Histocytochemistry ; Iodides/*metabolism ; Iodine Isotopes ; Larva/metabolism ; *Metamorphosis, Biological ; Mitochondria ; Peroxidases/*analysis ; Thyroid Gland/enzymology/*metabolism ; Xenopus/*metabolism ; }, }
@article {pmid4803168, year = {1973}, author = {Levy, M and Joncourt, M}, title = {[Changes in the phospholipids of liver cell mitochondrial internal membranes in the course of the development of the rat].}, journal = {Comptes rendus des seances de la Societe de biologie et de ses filiales}, volume = {167}, number = {6}, pages = {848-851}, pmid = {4803168}, issn = {0037-9026}, mesh = {Age Factors ; Animals ; Cardiolipins/metabolism ; Chromatography, Thin Layer ; Female ; Liver/*growth &amp; development/metabolism ; Male ; Mitochondria, Liver/*metabolism ; Phosphatidylcholines/metabolism ; Phosphatidylethanolamines/metabolism ; Phospholipids/*metabolism ; Pregnancy ; Proteins/metabolism ; Rats ; Sphingomyelins/metabolism ; }, }
@article {pmid4785084, year = {1973}, author = {Faugier, S}, title = {[Ultrastructural study of the evolution of interneuronal junctions during the maturation of the central nervous system of Triturus alpestris (Amphibian, Urodele)].}, journal = {Comptes rendus des seances de la Societe de biologie et de ses filiales}, volume = {167}, number = {3}, pages = {480-483}, pmid = {4785084}, issn = {0037-9026}, mesh = {Amphibians/*embryology ; Animals ; Desmosomes ; Epithelial Cells ; Microscopy, Electron ; Mitochondria ; Nervous System/growth &amp; development ; Synapses/*cytology ; Synaptic Membranes ; Synaptic Vesicles ; }, }
@article {pmid4776371, year = {1973}, author = {Laborit, H and Thuret, F}, title = {[Ineffectiveness of injections of mitochondria ruptured by osmotic shock, of chloroplast, of ethidium bromide, of isometamidium, and of ethidium chloride on the evolution of ascitic cancer in mice].}, journal = {Agressologie: revue internationale de physio-biologie et de pharmacologie appliquees aux effets de l'agression}, volume = {14}, number = {2}, pages = {105-110}, pmid = {4776371}, issn = {0002-1148}, mesh = {Amidines/therapeutic use ; Animals ; Azo Compounds/therapeutic use ; Body Weight ; Carcinoma, Ehrlich Tumor/*therapy ; Cell Wall ; *Chloroplasts ; Ethidium/*therapeutic use ; Male ; Mice ; *Mitochondria, Liver ; Phenanthridines/*therapeutic use ; Time Factors ; }, }
@article {pmid4741798, year = {1973}, author = {Franquinet, R and Lender, T}, title = {[Ultrastructural study of testis of Polycelis tenuis and Polycelis nigra (Planarians). Evolution of male germ cells before spermatogenesis].}, journal = {Zeitschrift fur mikroskopisch-anatomische Forschung}, volume = {87}, number = {1}, pages = {4-22}, pmid = {4741798}, issn = {0044-3107}, mesh = {Animals ; Cell Nucleolus ; Cell Nucleus ; Endoplasmic Reticulum ; Germ Cells/*physiology ; Golgi Apparatus ; Male ; Meiosis ; Microscopy, Electron ; Microtubules ; Mitochondria ; Mitosis ; Platyhelminths/*anatomy &amp; histology ; *Spermatogenesis ; Spermatozoa/*cytology ; Testis/*cytology ; }, }
@article {pmid4578665, year = {1973}, author = {Bak, AL}, title = {DNA base composition in mycoplasma, bacteria and yeast.}, journal = {Current topics in microbiology and immunology}, volume = {61}, number = {}, pages = {89-149}, doi = {10.1007/978-3-642-65531-9_3}, pmid = {4578665}, issn = {0070-217X}, mesh = {Absorption ; Bacteria/analysis ; Biological Evolution ; Bromine ; Cytosine/analysis ; DNA/*analysis/radiation effects ; Densitometry ; Guanine/analysis ; Methods ; Mitochondria/analysis ; Mycoplasma/analysis ; Nucleic Acid Denaturation ; Spectrum Analysis ; Temperature ; Ultraviolet Rays ; Yeasts/analysis ; }, }
@article {pmid4209315, year = {1973}, author = {Cohen, SS}, title = {Recent studies on the origins of cellular organelles.}, journal = {Basic life sciences}, volume = {2}, number = {}, pages = {27-52}, doi = {10.1007/978-1-4684-2880-3_3}, pmid = {4209315}, issn = {0090-5542}, mesh = {Bacteria/cytology ; Biological Evolution ; Cell Nucleus ; *Chloroplasts/drug effects/enzymology/metabolism ; Cyanobacteria/cytology ; DNA/biosynthesis ; *Genetics, Microbial ; *Mitochondria/drug effects/enzymology/metabolism ; Molecular Biology ; Mutation ; Protein Biosynthesis ; RNA/biosynthesis ; RNA, Messenger/biosynthesis ; Viruses ; }, }
@article {pmid4654230, year = {1972}, author = {Schwemmler, W}, title = {[Endosymbiosis of grasshoppers: structure of eucytes and a functional and evolutionary model].}, journal = {Experientia}, volume = {28}, number = {12}, pages = {1511-1512}, pmid = {4654230}, issn = {0014-4754}, mesh = {Animals ; Bacteria/growth &amp; development ; *Biological Evolution ; Grasshoppers/growth &amp; development ; Hydrogen-Ion Concentration ; Mitochondria ; *Models, Biological ; Rickettsia/growth &amp; development ; *Symbiosis ; Time Factors ; }, }
@article {pmid4678324, year = {1972}, author = {}, title = {The mystery of the mitochondria.}, journal = {JAMA}, volume = {222}, number = {11}, pages = {1422}, pmid = {4678324}, issn = {0098-7484}, mesh = {Biological Evolution ; Ecology ; *Mitochondria ; }, }
@article {pmid5075787, year = {1972}, author = {Dawid, IB}, title = {Evolution of mitochondrial DNA sequences in Xenopus.}, journal = {Developmental biology}, volume = {29}, number = {2}, pages = {139-151}, doi = {10.1016/0012-1606(72)90051-6}, pmid = {5075787}, issn = {0012-1606}, mesh = {Animals ; Base Sequence ; Biological Evolution ; Cell Fractionation ; Centrifugation, Density Gradient ; DNA/*analysis ; Electrophoresis, Polyacrylamide Gel ; Female ; Hot Temperature ; Microscopy, Electron ; Mitochondria/*analysis ; Molecular Weight ; Nucleic Acid Denaturation ; Nucleic Acid Hybridization ; Nucleic Acid Renaturation ; Ovary/analysis ; Phosphorus Isotopes ; RNA, Ribosomal ; RNA, Transfer ; Tritium ; Xenopus/*physiology ; }, }
@article {pmid4352002, year = {1972}, author = {Laffargue, P and Adechy-Benkoël, L}, title = {[The ultrastructure of the human corpus luteum. I. Evolution during the menstrual cycle].}, journal = {Annales d'anatomie pathologique}, volume = {17}, number = {4}, pages = {425-448}, pmid = {4352002}, issn = {0003-3871}, mesh = {Cell Nucleus ; Cell Wall ; Corpus Luteum/*cytology/metabolism ; Cytoplasm ; Endoplasmic Reticulum ; Female ; Golgi Apparatus ; Humans ; Inclusion Bodies ; Lysosomes ; *Menstruation ; Microscopy, Electron ; Microtubules ; Mitochondria ; Ovulation ; }, }
@article {pmid4340327, year = {1972}, author = {Raff, RA and Mahler, HR}, title = {The non symbiotic origin of mitochondria.}, journal = {Science (New York, N.Y.)}, volume = {177}, number = {4049}, pages = {575-582}, doi = {10.1126/science.177.4049.575}, pmid = {4340327}, issn = {0036-8075}, mesh = {Aerobiosis ; Anaerobiosis ; Animals ; Ascomycota/enzymology/metabolism ; Bacteria/metabolism ; *Biological Evolution ; DNA Replication ; Genetic Code ; Genetics, Microbial ; Inclusion Bodies ; Mammals ; *Mitochondria/metabolism/physiology ; Models, Biological ; Neurospora/enzymology ; Oxygen Consumption ; Peptide Chain Elongation, Translational ; Peptide Chain Initiation, Translational ; Protein Biosynthesis ; RNA/biosynthesis ; *Symbiosis ; Yeasts/metabolism ; }, }
@article {pmid4403906, year = {1972}, author = {Bennett, AF}, title = {A comparison of activities of metabolic enzymes in lizards and rats.}, journal = {Comparative biochemistry and physiology. B, Comparative biochemistry}, volume = {42}, number = {4}, pages = {637-647}, doi = {10.1016/0305-0491(72)90325-2}, pmid = {4403906}, issn = {0305-0491}, mesh = {Aerobiosis ; Anaerobiosis ; Animals ; Biological Evolution ; Electron Transport Complex IV/metabolism ; Isocitrate Dehydrogenase/metabolism ; L-Lactate Dehydrogenase/metabolism ; Liver/cytology/*enzymology ; Lizards/*metabolism ; Mitochondria, Liver/enzymology ; Mitochondria, Muscle/enzymology ; Muscles/cytology/*enzymology ; NAD ; NADP ; Oxidoreductases/*metabolism ; Phosphofructokinase-1/metabolism ; Phosphotransferases/*metabolism ; Pyruvate Kinase/metabolism ; Rats ; Solubility ; Species Specificity ; Succinate Dehydrogenase/metabolism ; }, }
@article {pmid5053471, year = {1972}, author = {Bawdon, RE and Garrison, RG and Fina, LR}, title = {Deoxyribonucleic acid base composition of the yeastlike and mycelial phases of Histoplasma capsulatum and Blastomyces dermatitidis.}, journal = {Journal of bacteriology}, volume = {111}, number = {2}, pages = {593-596}, pmid = {5053471}, issn = {0021-9193}, mesh = {Biological Evolution ; Blastomyces/*analysis/classification/cytology/growth &amp; development ; Cell Nucleus/analysis ; Centrifugation, Density Gradient ; Cesium ; Chlorides ; Culture Media ; Cytosine/analysis ; DNA/*analysis/isolation &amp; purification ; Densitometry ; Guanine/analysis ; Histoplasma/*analysis/classification/cytology/growth &amp; development ; Hot Temperature ; Mitochondria/analysis ; Nucleic Acid Denaturation ; Spectrophotometry ; }, abstract = {The base composition in moles percent guanine plus cytosine (%GC) of both nuclear and mitochondrial deoxyribonucleic acid (DNA) isolated from the yeastlike and mycelial phases of the dimorphic fungal pathogens Histoplasma capsulatum and Blastomyces dermatitidis was determined by techniques of thermal denaturation and CsCl buoyant density gradient equilibrium centrifugation. The mean observed values for GC content of nuclear DNA from H. capsulatum and B. dermatitidis were 47.3 and 48.2%, respectively. What is speculated to be mitochondrial DNA was found to be 34.0% for H. capsulatum and 34.3% for B. dermatitidis. Thermal denaturation curves for Blastomyces DNA indicated a bimodality in thermal denaturation profiles, thereby suggesting a significant mitochondrial DNA contamination. Mitochondrial DNA appeared to represent a smaller percentage of the total DNA prepared from Histoplasma, and was not observed consistently to affect%GC values as determined by thermal denaturation profiles. On the basis of the now known perfect stage of B. dermatitidis (Ajellomyces dermatitidis) as a member of the family Gymnoascaceae, the close approximation of%GC content of nuclear DNA of this fungal organism with that of H. capsulatum suggests possible phylogenetic relationship. It is suggested that the just reported, but as yet unclassified, perfect stage of H. capsulatum may be found to be phylogenetically a primitive form of the Gymnoascaceae.}, }
@article {pmid5045924, year = {1972}, author = {Towers, NR and Dixon, H and Kellerman, GM and Linnane, AW}, title = {Biogenesis of mitochondria. 22. The sensitivity of rat liver mitochondria to antibiotics; a phylogenetic difference between a mammalian system and yeast.}, journal = {Archives of biochemistry and biophysics}, volume = {151}, number = {2}, pages = {361-369}, doi = {10.1016/0003-9861(72)90510-3}, pmid = {5045924}, issn = {0003-9861}, mesh = {Adenosine Triphosphate/biosynthesis ; Animals ; Anti-Bacterial Agents/*pharmacology ; Biological Evolution ; Carbon Isotopes ; Chloramphenicol/pharmacology ; Depression, Chemical ; Dinitrophenols/pharmacology ; Erythromycin/pharmacology ; In Vitro Techniques ; Leucine/metabolism ; Leucomycins/pharmacology ; Lincomycin/pharmacology ; Mitochondria, Liver/*drug effects/metabolism ; Mitochondrial Swelling ; Oxygen Consumption/drug effects ; Paromomycin/pharmacology ; Protein Binding ; Protein Biosynthesis ; Rats ; Ribosomes ; Yeasts/cytology ; }, }
@article {pmid4580899, year = {1972}, author = {La Placa, R and Malini, PL and Montroni, M and Dalmonte, PR and Danieli, G}, title = {[Changes in humoral immunity in progressive liver diseases: study of 64 patients].}, journal = {Giornale di clinica medica}, volume = {53}, number = {8}, pages = {353-370}, pmid = {4580899}, issn = {0017-0275}, mesh = {*Antibody Formation ; Autoantibodies/analysis ; Chronic Disease ; Fluorescent Antibody Technique ; Humans ; Immunity, Cellular ; Immunoglobulins/analysis ; Liver Diseases/*immunology ; Mitochondria, Liver/immunology ; Muscle, Smooth/immunology ; }, }
@article {pmid4342288, year = {1972}, author = {Rahil, KS and Narbaitz, R}, title = {Evolution of the lining bodies in the embryonic chick gonad.}, journal = {Journal of embryology and experimental morphology}, volume = {28}, number = {1}, pages = {133-140}, pmid = {4342288}, issn = {0022-0752}, mesh = {Animals ; Cell Differentiation ; *Chick Embryo ; Cytoplasm ; Endoplasmic Reticulum ; Epithelium ; Female ; Golgi Apparatus ; Inclusion Bodies ; Male ; Mitochondria ; Ovarian Follicle ; Ovary/cytology/*embryology ; Testis/cytology/*embryology ; Time Factors ; }, }
@article {pmid5077189, year = {1972}, author = {Loo, SK and Kanagasunteram, R}, title = {The vomeronasal organ in tree shrew and slow loris.}, journal = {Journal of anatomy}, volume = {112}, number = {Pt 2}, pages = {165-172}, pmid = {5077189}, issn = {0021-8782}, mesh = {Animals ; Biological Evolution ; Cell Nucleus ; Cilia ; Cytoplasmic Granules ; Endoplasmic Reticulum ; Epithelial Cells ; Golgi Apparatus ; Microscopy, Electron ; Mitochondria ; Nasal Septum/*cytology ; Nose/*cytology ; Primates/*anatomy &amp; histology ; Shrews/*anatomy &amp; histology ; }, }
@article {pmid4344699, year = {1972}, author = {Brown, RH and Richardson, M and Boulter, D and Ramshaw, JA and Jefferies, RP}, title = {The amino acid sequence of cytochrome c from Helix aspersa Müller (garden snail).}, journal = {The Biochemical journal}, volume = {128}, number = {4}, pages = {971-974}, pmid = {4344699}, issn = {0264-6021}, mesh = {Amino Acid Sequence ; Animals ; Biological Evolution ; Cytochrome c Group/*analysis ; Mitochondria ; Peptides/analysis ; *Snails ; }, abstract = {The amino acid sequence of a snail cytochrome c has been determined. The molecule consists of a single polypeptide chain of 104 residues, and is homologous with other mitochondrial cytochromes c. Unlike the cytochromes c from vertebrates, there is no acetyl blocking group at the N-terminus. A change in an otherwise invariant position has been observed in position 87. Comparison with amino acid sequences of cytochromes c from other sources indicates that the point of divergence of the molluscs and the vertebrates in evolutionary time was 720 million years ago. Experimental details are given in a supplementary paper that has been deposited as Supplementary Publication SUP 50009 at the National Lending Library for Science and Technology, Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1972), 126, 5.}, }
@article {pmid4199803, year = {1972}, author = {Flavell, R}, title = {Mitochondria and chloroplasts as descendants of prokaryotes.}, journal = {Biochemical genetics}, volume = {6}, number = {4}, pages = {275-291}, pmid = {4199803}, issn = {0006-2928}, mesh = {Biochemical Phenomena ; Biochemistry ; *Biological Evolution ; *Chloroplasts ; DNA, Mitochondrial ; Fungi ; Genetics ; *Mitochondria ; Plants ; Rickettsiaceae ; }, }
@article {pmid4403759, year = {1972}, author = {Utevskiĭ, AM and Rasin, MS}, title = {[Catecholamines and corticosteroids (molecular aspects of the interrelations of 2 basic adaptational systems)].}, journal = {Uspekhi sovremennoi biologii}, volume = {73}, number = {3}, pages = {323-341}, pmid = {4403759}, issn = {0042-1324}, mesh = {Adrenocorticotropic Hormone/pharmacology ; Amphibians ; Animals ; Biological Evolution ; Birds ; Brain/metabolism ; *Catecholamines/metabolism/pharmacology ; Chromaffin System ; Fishes ; *Glucocorticoids/metabolism/pharmacology ; Hypophysectomy ; Insecta ; Methyltransferases/metabolism ; Mitochondria/metabolism ; Monoamine Oxidase/metabolism ; Myocardium/metabolism ; *Pituitary-Adrenal System/drug effects ; Rabbits ; Rats ; Receptors, Adrenergic ; Reserpine/pharmacology ; Stress, Physiological/metabolism ; Tyrosine 3-Monooxygenase/metabolism ; }, }
@article {pmid4402967, year = {1972}, author = {Alexandrov, VY}, title = {The problem of behaviour at the cellular level (cytoethology).}, journal = {Journal of theoretical biology}, volume = {35}, number = {1}, pages = {1-26}, doi = {10.1016/0022-5193(72)90189-0}, pmid = {4402967}, issn = {0022-5193}, mesh = {Animals ; Anura ; Biological Evolution ; Calcium Carbonate ; Cats ; Cell Differentiation ; *Cell Movement ; Cell Nucleus ; *Cell Physiological Phenomena ; Chloroplasts ; Chordata, Nonvertebrate/cytology ; Cilia ; Cnidaria/anatomy &amp; histology ; Cytoplasm ; Epithelial Cells ; Eukaryota/cytology ; Female ; Fertilization ; Golgi Apparatus ; Macrophages ; Male ; Mitochondria ; Mitosis ; Ovum ; Porifera/cytology ; Scorpions/cytology ; Spermatozoa ; }, }
@article {pmid4551646, year = {1972}, author = {Adoutte, A and Beisson, J}, title = {Evolution of mixed populations of genetically different mitochondria in Paramecium aurelia.}, journal = {Nature}, volume = {235}, number = {5338}, pages = {393-396}, doi = {10.1038/235393b0}, pmid = {4551646}, issn = {0028-0836}, mesh = {Anti-Bacterial Agents/pharmacology ; Conjugation, Genetic ; Crosses, Genetic ; Drug Resistance, Microbial ; *Genetics, Microbial ; Genotype ; *Mitochondria ; Mutation ; *Paramecium/drug effects ; Radiation Genetics ; Recombination, Genetic ; Temperature ; }, }
@article {pmid5082439, year = {1972}, author = {Bosquet, G}, title = {[Changes in oxygen consumption during starvation in Bombyx mori L. Effect of digestion and realimentation].}, journal = {Annales de la nutrition et de l'alimentation}, volume = {26}, number = {4}, pages = {121-131}, pmid = {5082439}, issn = {0003-4037}, mesh = {*Animal Nutritional Physiological Phenomena ; Animals ; Bombyx/*metabolism ; *Digestion ; Methods ; Mitochondria ; *Oxygen Consumption ; Starvation/*metabolism ; Time Factors ; }, }
@article {pmid5068919, year = {1972}, author = {Ovtscharoff, W and Gossrau, R}, title = {[Histochemistry and ultrastructure of the red nucleus of hens (Gallus domesticus)].}, journal = {Histochemie. Histochemistry. Histochimie}, volume = {30}, number = {1}, pages = {73-81}, pmid = {5068919}, issn = {0018-2222}, mesh = {Animals ; Biological Evolution ; Blood-Brain Barrier ; Chickens/*anatomy &amp; histology ; Glycolysis ; Golgi Apparatus ; Histocytochemistry ; Lysosomes ; Microscopy, Electron ; Mitochondria ; Neurons/*cytology/metabolism ; Organoids ; Parasympathetic Nervous System ; Red Nucleus/anatomy &amp; histology/*cytology/innervation/metabolism ; }, }
@article {pmid4636686, year = {1972}, author = {Soyer, MO}, title = {[Ultrastructure of the nucleus of Noctiluca (free living dinoflagellate) during sporulation].}, journal = {Chromosoma}, volume = {39}, number = {4}, pages = {419-441}, pmid = {4636686}, issn = {0009-5915}, mesh = {Animals ; Biological Evolution ; Cell Division ; Cell Nucleolus ; *Cell Nucleus ; Chromatids ; Chromosomes ; Cytoplasmic Granules ; DNA ; Eukaryota/*cytology/growth &amp; development ; Flagella ; Golgi Apparatus ; Microscopy ; Microscopy, Electron ; Mitochondria ; Mitosis ; Spores/growth &amp; development ; }, }
@article {pmid4569009, year = {1972}, author = {Sternlieb, I}, title = {Evolution of the hepatic lesion in Wilson's disease (hepatolenticular degeneration).}, journal = {Progress in liver diseases}, volume = {4}, number = {}, pages = {511-525}, pmid = {4569009}, issn = {1060-913X}, mesh = {Adolescent ; Adult ; Biopsy ; Ceruloplasmin/analysis/metabolism ; Child ; Child, Preschool ; Copper/analysis/metabolism ; Cornea/pathology ; Endoplasmic Reticulum ; Female ; *Hepatolenticular Degeneration/diagnosis/genetics/metabolism/pathology ; Humans ; Liver/analysis/metabolism/pathology ; Male ; Mitochondria, Liver ; Radioisotopes ; }, }
@article {pmid4563438, year = {1972}, author = {Borst, P}, title = {Mitochondrial nucleic acids.}, journal = {Annual review of biochemistry}, volume = {41}, number = {}, pages = {333-376}, doi = {10.1146/annurev.bi.41.070172.002001}, pmid = {4563438}, issn = {0066-4154}, mesh = {Acridines ; Base Sequence ; Biological Evolution ; Chemical Phenomena ; Chemistry ; *DNA/biosynthesis ; DNA Repair ; Ethidium ; Genes ; *Mitochondria/metabolism ; Polynucleotides ; Proteins/metabolism ; *RNA/biosynthesis ; RNA, Messenger/metabolism ; RNA, Ribosomal ; RNA, Transfer ; Ribonucleotides ; Ribosomes ; Trypanosoma ; Virus Replication ; Yeasts ; }, }
@article {pmid4558510, year = {1972}, author = {Sparrow, AH and Price, HJ and Underbrink, AG}, title = {A survey of DNA content per cell and per chromosome of prokaryotic and eukaryotic organisms: some evolutionary considerations.}, journal = {Brookhaven symposia in biology}, volume = {23}, number = {}, pages = {451-494}, pmid = {4558510}, issn = {0068-2799}, mesh = {Animals ; Bacteria ; *Biological Evolution ; Cell Nucleus ; Chloroplasts/analysis ; *Chromosomes/analysis ; *DNA/analysis ; DNA, Bacterial/analysis ; DNA, Viral/analysis ; Haploidy ; Invertebrates ; Mitochondria/analysis ; Plants ; Vertebrates ; Viruses ; }, }
@article {pmid4553984, year = {1972}, author = {Whitfield, PJ}, title = {The ultrastructure of the spermatozoon of the hoplonemertine, Emplectonema neesii.}, journal = {Zeitschrift fur Zellforschung und mikroskopische Anatomie (Vienna, Austria : 1948)}, volume = {128}, number = {3}, pages = {303-316}, pmid = {4553984}, issn = {0340-0336}, mesh = {Animals ; Biological Evolution ; Cell Nucleus/analysis ; Cytoplasmic Granules ; Flagella/cytology ; Glycogen/analysis ; Male ; Microscopy, Electron ; Microscopy, Phase-Contrast ; Mitochondria/analysis ; Platyhelminths/*analysis ; Spermatozoa/*cytology ; }, }
@article {pmid4551614, year = {1972}, author = {Rank, GH and Bech-Hansen, NT}, title = {Genetic evidence for "Darwinian" selection at the molecular level. 3. The effect of the suppressive factor on nuclearly and cytoplasmically inherited chloramphenicol resistance in S. cerevisiae.}, journal = {Canadian journal of microbiology}, volume = {18}, number = {1}, pages = {1-7}, doi = {10.1139/m72-001}, pmid = {4551614}, issn = {0008-4166}, mesh = {Biological Evolution ; Cell Nucleus ; Chloramphenicol/*pharmacology ; Crosses, Genetic ; Culture Media ; Cytoplasm ; DNA ; DNA Replication ; Diploidy ; *Drug Resistance, Microbial ; Genetics, Microbial ; Glucose ; Glycerol ; Haploidy ; Mitochondria ; Mutation ; Saccharomyces/*drug effects ; Saccharomyces cerevisiae/cytology/drug effects/growth &amp; development/metabolism ; *Selection, Genetic ; }, }
@article {pmid4346122, year = {1972}, author = {Dahl, E}, title = {Studies of the fine structure of ovarian interstitial tissue. 7. The postnatal evolution of the thecal gland in the domestic fowl.}, journal = {Zeitschrift fur Zellforschung und mikroskopische Anatomie (Vienna, Austria : 1948)}, volume = {135}, number = {4}, pages = {553-561}, pmid = {4346122}, issn = {0340-0336}, mesh = {Animals ; Cell Nucleolus ; Cell Nucleus ; Chickens ; Connective Tissue Cells ; Cytoplasmic Granules ; Endoplasmic Reticulum ; Epithelial Cells ; Female ; Inclusion Bodies ; Lipids ; Microscopy ; Microscopy, Electron ; Mitochondria ; Ovary/cytology/*growth &amp; development ; Regeneration ; Steroids/biosynthesis ; }, }
@article {pmid4344753, year = {1972}, author = {Lyons, KM}, title = {Ultrastructural observations on the epidermis of the polyopisthocotylinean monogeneans Rajonchocotyle emarginata and Plectanocotyle gurnardi.}, journal = {Zeitschrift fur Parasitenkunde (Berlin, Germany)}, volume = {40}, number = {2}, pages = {87-100}, pmid = {4344753}, issn = {0044-3255}, mesh = {Actins ; Animals ; Biological Evolution ; Cell Nucleus ; Cytoplasmic Granules ; Fish Diseases ; Fishes ; Golgi Apparatus ; Inclusion Bodies ; Lanthanum ; Microscopy, Electron ; Mitochondria ; Myofibrils ; Ribosomes ; Species Specificity ; Thorium Dioxide ; Trematoda/*cytology ; Trematode Infections/veterinary ; }, }
@article {pmid4344459, year = {1972}, author = {Marin, L and Dameron, F}, title = {[Differentiation of chick embryo lung buds in heterochronic grafts: an ultra structural study of lamellay and granular inclusions].}, journal = {Zeitschrift fur Anatomie und Entwicklungsgeschichte}, volume = {138}, number = {2}, pages = {111-126}, pmid = {4344459}, issn = {0044-2232}, mesh = {Age Factors ; Animals ; Cell Differentiation ; Cell Nucleus ; Chick Embryo ; Cytoplasmic Granules ; Epithelial Cells ; Inclusion Bodies ; Lipids ; Lung/cytology/*embryology ; Lung Transplantation ; Microscopy ; Microscopy, Electron ; Mitochondria ; Organoids ; Transplantation, Homologous ; }, }
@article {pmid4336216, year = {1972}, author = {Huet, M}, title = {[Ultrastructural study and development of the neuroepithelial cells of regenerating epidermic arm cells in Asterina gibbosa Penn].}, journal = {Zeitschrift fur Zellforschung und mikroskopische Anatomie (Vienna, Austria : 1948)}, volume = {126}, number = {1}, pages = {75-89}, pmid = {4336216}, issn = {0340-0336}, mesh = {Animals ; Cell Differentiation ; Cell Nucleolus ; Cell Nucleus ; Chromatin ; Cilia ; Desmosomes ; Epithelial Cells ; Golgi Apparatus ; Inclusion Bodies ; Microscopy, Electron ; Microtubules ; Mitochondria ; Neurons/cytology ; RNA/biosynthesis ; *Regeneration ; Ribosomes ; Skin/*cytology ; Starfish/*cytology ; }, }
@article {pmid5116522, year = {1971}, author = {Stegeman, JJ and Goldberg, E}, title = {Distribution and characterization of hexose 6-phosphate dehydrogenase in trout.}, journal = {Biochemical genetics}, volume = {5}, number = {6}, pages = {579-589}, pmid = {5116522}, issn = {0006-2928}, mesh = {Alleles ; Animals ; Biological Evolution ; Cell Nucleus/enzymology ; Electrophoresis, Disc ; Genetic Code ; Genotype ; Glucosephosphate Dehydrogenase/*analysis/classification ; Liver/*enzymology ; Microsomes, Liver/enzymology ; Mitochondria, Liver/enzymology ; Molecular Weight ; Phenotype ; Polymorphism, Genetic ; Salmonidae/*enzymology ; Spectrophotometry ; }, }
@article {pmid5131735, year = {1971}, author = {Thompson, EW and Notton, BA and Richardson, M and Boulter, D}, title = {The amino acid sequence of cytochrome c from Abutilon theophrasti Medic. and Gossypium barbadense L. (cotton).}, journal = {The Biochemical journal}, volume = {124}, number = {4}, pages = {787-791}, pmid = {5131735}, issn = {0264-6021}, mesh = {*Amino Acid Sequence ; Amino Acids/analysis ; Biological Evolution ; Cytochromes/*analysis ; Gossypium/enzymology ; Mitochondria/enzymology ; Plants/classification/*enzymology ; }, abstract = {The amino acid sequences of Abutilon and Gossypium cytochromes c were determined on 1mumol of protein. The molecules consist of 111 residues and are homologous with other mitochondrial plant cytochromes c. Experimental details are given in a supplementary paper that has been deposited as Supplementary Publication SUP 50005 at the National Lending Library for Science and Technology, Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1971), 121, 7.}, }
@article {pmid4106520, year = {1971}, author = {Roy, S and Ramalingaswami, V and Nayak, NC}, title = {An ultrastructural study of the liver in Indian childhood cirrhosis with particular reference to the structure of cytoplasmic hyaline.}, journal = {Gut}, volume = {12}, number = {9}, pages = {693-701}, pmid = {4106520}, issn = {0017-5749}, mesh = {Bile ; Cell Membrane ; Child ; Collagen ; Cytoplasm ; Dilatation ; Endoplasmic Reticulum ; Humans ; *Hyalin ; Liver Cirrhosis/*pathology ; Microscopy, Electron ; Mitochondria, Liver ; Pigments, Biological ; Ribosomes ; }, abstract = {Ultrastructural features of the liver in eight cases of Indian childhood cirrhosis, a fatal and elusive liver disease in India, have been described. Severe parenchymal damage, diffuse creeping fibrosis, and other light microscopic alterations, including the frequent presence of cytoplasmic hyaline, reported earlier are confirmed in the present study. The hyaline is predominantly comprised of tangled masses of fibrils and some electron-dense particles possibly derived from endoplasmic reticulum. The morphological features of this hyaline are identical to those of alcoholic hyaline described by Biava and Smuckler. Mitochondria do not seem to participate in the structural evolution of hyaline.}, }
@article {pmid4396690, year = {1971}, author = {Stevenson, RM and LéJohn, HB}, title = {Glutamic dehydrogenases of Oomycetes. Kinetic mechanism and possible vvolutionary history.}, journal = {The Journal of biological chemistry}, volume = {246}, number = {7}, pages = {2127-2135}, pmid = {4396690}, issn = {0021-9258}, mesh = {Adenine Nucleotides ; Adenosine Triphosphate ; Biological Evolution ; Citrates ; Coenzyme A ; Drug Stability ; Enzyme Activation ; Fungi/*enzymology ; *Glutamate Dehydrogenase/antagonists &amp; inhibitors ; Guanine Nucleotides ; Hot Temperature ; Hydrogen-Ion Concentration ; Kinetics ; Mitochondria/enzymology ; NAD ; NADP ; Protein Denaturation ; Pyruvates ; }, }
@article {pmid5553680, year = {1971}, author = {Flavell, RA and Jones, IG}, title = {Paramecium mitochondrial DNA. Renaturation and hybridisation studies.}, journal = {Biochimica et biophysica acta}, volume = {232}, number = {2}, pages = {255-260}, pmid = {5553680}, issn = {0006-3002}, mesh = {Animals ; Biological Evolution ; Cell Nucleus ; Centrifugation, Density Gradient ; Chromatography ; Coliphages ; Cytosine/analysis ; *DNA/analysis ; DNA, Viral ; Densitometry ; Guanine/analysis ; Hot Temperature ; Kinetics ; *Mitochondria ; Nucleic Acid Denaturation ; Nucleic Acid Hybridization ; Paramecium/*cytology/growth &amp; development ; Spectrophotometry ; Tetrahymena/cytology ; Ultraviolet Rays ; Vibration ; }, }
@article {pmid5555017, year = {1971}, author = {Hirumi, H and Raski, DJ and Jones, NO}, title = {Primitive muscle cells of nematodes: morphological aspects of platymyarian and shallow coelomyarian muscles in two plant parasitic nematodes, Trichodorus christiei and Longidorus elongatus.}, journal = {Journal of ultrastructure research}, volume = {34}, number = {5}, pages = {517-543}, doi = {10.1016/s0022-5320(71)80062-x}, pmid = {5555017}, issn = {0022-5320}, mesh = {Animals ; Biological Evolution ; Cell Membrane ; Cytoplasm ; Endoplasmic Reticulum ; Glycogen ; Microscopy, Electron ; Mitochondria, Muscle ; Muscle Contraction ; Muscles/*cytology ; Myofibrils ; Nematoda/*cytology ; }, }
@article {pmid4995226, year = {1971}, author = {Scheib, D}, title = {[Observations on the evolution of the fine structure of interstitial cells in the postnatal testis of white mice: continuity or perenniality of these cells].}, journal = {Comptes rendus hebdomadaires des seances de l'Academie des sciences. Serie D: Sciences naturelles}, volume = {272}, number = {6}, pages = {837-840}, pmid = {4995226}, mesh = {Animals ; Cell Differentiation ; Cytoplasm ; Fibroblasts ; Leydig Cells/*cytology ; Lipids/analysis ; Lysosomes ; Male ; Mice ; Microscopy, Electron ; Mitochondria ; Testis/analysis/anatomy &amp; histology/*cytology/*growth &amp; development ; }, }
@article {pmid5545444, year = {1971}, author = {Mira-Moser, F}, title = {[The ultrastructure of the adenohypophysis in the toad, Bufo bufo L. II. On the formtion of glycoprotein containing cells of type II (perivascular basophils) after thyroidectomy].}, journal = {Zeitschrift fur Zellforschung und mikroskopische Anatomie (Vienna, Austria : 1948)}, volume = {112}, number = {2}, pages = {266-286}, pmid = {5545444}, issn = {0340-0336}, mesh = {Animals ; *Anura ; Endoplasmic Reticulum ; Glycoproteins/analysis ; Golgi Apparatus ; Microscopy, Electron ; Mitochondria ; Pituitary Gland/*cytology/metabolism/physiology ; Thyroid Gland/physiology/surgery ; Thyroidectomy ; Thyrotropin/metabolism ; }, }
@article {pmid5543784, year = {1971}, author = {Moreland, DE and Boots, MR}, title = {Effects of optically active 1-(alpha-methylbenzyl)-3-(3,4-dichlorophenyl)urea on reactions of mitochondria and chloroplasts.}, journal = {Plant physiology}, volume = {47}, number = {1}, pages = {53-58}, pmid = {5543784}, issn = {0032-0889}, mesh = {Chloroplasts/*drug effects/metabolism ; }, abstract = {Effects of the R- and S-isomers and racemate of 1-(alpha-methylbenzyl)-3-(3,4-dichlorophenyl)urea (MBPU) were measured on phosphorylation and electron transport in mung bean (Phaseolus aureus L.) mitochondria and spinach (Spinacia oleracea L.) chloroplasts.In chloroplasts, S-MBPU inhibited basal and methylamine-uncoupled electron transport with ferricyanide as the oxidant, both photoreduction and coupled photophosphorylation with water as the electron donor and with ferricyanide and nicotinamide adenine dinucleotide phosphate (NADP) as oxidants, and cyclic photophosphorylation with phenazine methosulfate as the electron mediator under an argon gas phase. With ascorbate 2,6-dichloro-phenolindophenol as the electron donor, phosphorylation coupled to NADP reduction was inhibited, but the reduction of NADP was not inhibited. The R-isomer of MBPU, like the S-isomer, inhibited all of the photophosphorylation reactions studied. However, unlike the S-isomer, the R-isomer either did not inhibit or was a very weak inhibitor of all photoreduction reactions. The effects of the MBPUs on the chloroplast reactions can be explained by action at two different sites: an optically specific site near photosystem II and the oxygen evolution pathway, and a second optically nonspecific site associated with the generation of ATP.In mitochondria, both the R- and S-isomers stimulated state 4 respiration, inhibited state 3 respiration, and released oligomycin-inhibited respiration with malate, succinate, and NADH as substrates. Both enantiomers were equally active in all studies with malate and succinate as substrates. However, with NADH as substrate, R-MBPU was a stronger inhibitor of state 3 respiration and a weaker stimulator of state 4 respiration than S-MBPU.}, }
@article {pmid5099151, year = {1971}, author = {Myers, RB and Cantino, EC}, title = {DNA profile of the spore of Blastocladiella emersonii: evidence for -particle DNA.}, journal = {Archiv fur Mikrobiologie}, volume = {78}, number = {3}, pages = {252-267}, pmid = {5099151}, issn = {0003-9276}, mesh = {Biological Evolution ; Cell Nucleolus/analysis ; Cell Nucleus/analysis ; Chromatin/analysis ; Culture Media ; DNA/*isolation &amp; purification ; Fungi/*analysis/cytology/enzymology ; Methods ; Microscopy, Electron ; Mitochondria/analysis ; Phenotype ; Polysaccharides ; Spores, Fungal/analysis ; }, }
@article {pmid4330578, year = {1971}, author = {Hess, B and Boiteux, A}, title = {Oscillatory phenomena in biochemistry.}, journal = {Annual review of biochemistry}, volume = {40}, number = {}, pages = {237-258}, doi = {10.1146/annurev.bi.40.070171.001321}, pmid = {4330578}, issn = {0066-4154}, mesh = {Animals ; Biological Evolution ; Biological Transport ; Circadian Rhythm ; Cytochromes ; Enzymes ; Feedback ; *Glycolysis ; Guinea Pigs ; Kinetics ; Macromolecular Substances ; Mathematics ; Membrane Potentials ; Metabolism ; *Mitochondria/metabolism ; Mitochondrial Swelling ; Models, Biological ; Models, Chemical ; Models, Theoretical ; Muscle Contraction ; NAD ; Oxidation-Reduction ; Oxygen Consumption ; *Periodicity ; Photosynthesis ; Protein Biosynthesis ; Thermodynamics ; Yeasts ; }, }
@article {pmid4330242, year = {1971}, author = {Fujita, H and Nanba, H}, title = {Fine structure and its functional properties of the endostyle of ascidians, Ciona intestinalis. A part of phylogenetic studies of the thyroid gland.}, journal = {Zeitschrift fur Zellforschung und mikroskopische Anatomie (Vienna, Austria : 1948)}, volume = {121}, number = {4}, pages = {455-469}, pmid = {4330242}, issn = {0340-0336}, mesh = {Animals ; Autoradiography ; *Biological Evolution ; Cell Membrane ; Cell Nucleus ; Chordata, Nonvertebrate/*anatomy &amp; histology ; Cilia ; Cytoplasmic Granules ; Digestion ; Endoplasmic Reticulum ; Fishes/anatomy &amp; histology ; Golgi Apparatus ; Inclusion Bodies ; Intestinal Mucosa/metabolism ; Intestines/*cytology ; Iodine/metabolism ; Iodine Isotopes ; Larva/anatomy &amp; histology ; Lipids ; Lysosomes ; Microscopy, Electron ; Mitochondria ; Mucoproteins/metabolism ; Proteins/metabolism ; Thyroglobulin ; Thyroid Gland/*cytology ; Time Factors ; }, }
@article {pmid4330182, year = {1971}, author = {Holmberg, K}, title = {The hagfish retina: electron microscopic study comparing receptor and epithelial cells in the Pacific hagfish, Polistotrema stouti, with those in the Atlantic hagfish, Myxine glutinosa.}, journal = {Zeitschrift fur Zellforschung und mikroskopische Anatomie (Vienna, Austria : 1948)}, volume = {121}, number = {2}, pages = {249-269}, pmid = {4330182}, issn = {0340-0336}, mesh = {Animals ; Biological Evolution ; Capillaries ; Cell Membrane ; Cilia ; Cytoplasmic Granules ; Endoplasmic Reticulum ; Epithelial Cells ; Female ; Fishes/*anatomy &amp; histology ; Golgi Apparatus ; Histological Techniques ; Inclusion Bodies ; Intercellular Junctions ; Male ; Microscopy, Electron ; Mitochondria ; Morphogenesis ; Neuroglia ; Phagocytosis ; Photoreceptor Cells/*cytology ; Retina/*cytology/growth &amp; development ; Vitreous Body/cytology ; }, }
@article {pmid4329954, year = {1971}, author = {Schmitt, J and Kömpf, J and Ritter, H}, title = {Transspecific variability of mitochondrial NAD-malate dehydrogenase (E.C.: 1.1.1.37) in Primates.}, journal = {Humangenetik}, volume = {13}, number = {1}, pages = {69-71}, pmid = {4329954}, issn = {0018-7348}, mesh = {Animals ; Biological Evolution ; Electrophoresis ; Haplorhini ; Hedgehogs ; Hominidae ; Macaca ; *Malate Dehydrogenase ; Mitochondria/*enzymology ; Mitochondria, Liver ; Mitochondria, Muscle ; Molecular Biology ; NAD ; Papio ; Phenotype ; Polymorphism, Genetic ; *Primates ; Starch ; }, }
@article {pmid4326860, year = {1971}, author = {Jacobson, KB}, title = {Reaction of aminoacyl-tRNA synthetases with heterologous tRNA's.}, journal = {Progress in nucleic acid research and molecular biology}, volume = {11}, number = {}, pages = {461-488}, doi = {10.1016/s0079-6603(08)60335-9}, pmid = {4326860}, issn = {0079-6603}, mesh = {Amino Acids ; Base Sequence ; Binding Sites ; Biological Evolution ; Diphosphates ; Escherichia coli ; Hydrolysis ; Kinetics ; *Ligases/antagonists &amp; inhibitors ; Mitochondria ; Neurospora/enzymology/metabolism ; Organ Specificity ; RNA, Bacterial ; RNA, Neoplasm ; *RNA, Transfer/isolation &amp; purification ; Sodium Chloride ; Species Specificity ; Spermine ; }, }
@article {pmid4326435, year = {1971}, author = {Meiniel, A and Collin, JP}, title = {[The pineal complex of the ammocoete (Lampetra planeri). Connections of the pineal and parapineal organs with the epithalamic roof].}, journal = {Zeitschrift fur Zellforschung und mikroskopische Anatomie (Vienna, Austria : 1948)}, volume = {117}, number = {3}, pages = {354-380}, pmid = {4326435}, issn = {0340-0336}, mesh = {Animals ; Axons/cytology ; Biological Evolution ; Fishes/*anatomy &amp; histology ; Ganglia/cytology ; Golgi Apparatus ; Inclusion Bodies ; Microscopy ; Microscopy, Electron ; Mitochondria ; Nerve Fibers, Myelinated ; Nerve Net ; Neurofibrils ; Neurons/cytology ; Pineal Gland/cytology/*innervation ; Synapses/cytology ; }, }
@article {pmid4326063, year = {1971}, author = {Altenähr, E and Seifert, G}, title = {[Ultrastructural comparison of human parathyroid glands in secondary hyperparathyroidism and primary parathyroid adenoma].}, journal = {Virchows Archiv. A, Pathology. Pathologische Anatomie}, volume = {353}, number = {1}, pages = {60-86}, pmid = {4326063}, issn = {0042-6423}, mesh = {Adenoma/*pathology ; Adolescent ; Adult ; Autopsy ; Biological Evolution ; Biopsy ; Cell Membrane ; Cell Nucleus ; Cilia ; Cytoplasmic Granules ; Endoplasmic Reticulum ; Female ; Glycogen ; Golgi Apparatus ; Humans ; Hyperparathyroidism, Secondary/*pathology ; Hyperplasia ; Inclusion Bodies ; Lipids ; Lysosomes ; Male ; Microscopy, Electron ; Middle Aged ; Mitochondria ; Organoids ; Parathyroid Glands/cytology/metabolism/*pathology ; Parathyroid Neoplasms/*pathology ; Ribosomes ; }, }
@article {pmid4323433, year = {1970}, author = {Levy, M and Toury, R}, title = {[Study on the evolution of mitochondrial enzyme activities in hepatocyte during rat development].}, journal = {Biochimica et biophysica acta}, volume = {216}, number = {2}, pages = {318-327}, doi = {10.1016/0005-2728(70)90223-9}, pmid = {4323433}, issn = {0006-3002}, mesh = {Animals ; Animals, Newborn ; Citrates ; Citric Acid Cycle ; Cytochromes ; Electron Transport ; Electron Transport Complex IV/metabolism ; Endoplasmic Reticulum/enzymology ; Female ; Fumarates ; Glutamate Dehydrogenase/metabolism ; Hydro-Lyases/metabolism ; Isocitrate Dehydrogenase/metabolism ; Liver/cytology/embryology/*growth &amp; development ; Malate Dehydrogenase/metabolism ; Membranes/enzymology ; Mitochondria, Liver/*enzymology ; NAD ; Oxidoreductases/metabolism ; Oxygen Consumption ; Pregnancy ; Rats ; }, }
@article {pmid4988062, year = {1970}, author = {Raven, PH}, title = {A multiple origin for plastids and mitochondria.}, journal = {Science (New York, N.Y.)}, volume = {169}, number = {3946}, pages = {641-646}, doi = {10.1126/science.169.3946.641}, pmid = {4988062}, issn = {0036-8075}, mesh = {Biological Evolution ; Carotenoids ; Chlorophyta/cytology ; *Chloroplasts ; Cyanobacteria/cytology ; DNA/metabolism ; Escherichia coli/cytology ; Euglena/cytology ; Eukaryota/*cytology ; *Mitochondria ; Neurospora/cytology ; Photosynthesis ; *Symbiosis ; }, abstract = {The impressive homologies between mitochondria and plastids, on the one hand, and procaryotic organisms, on the other, make it almost certain that these important cellular organelles had their origin as independent organisms. The vast number of symbiotic relationships of all degrees of evolutionary antiquity which have been found in contemporary organisms point to the ease with which such relationships can be established.}, }
@article {pmid5449178, year = {1970}, author = {Cushman, SW}, title = {Structure-function relationships in the adipose cell. I. Ultrastructure of the isolated adipose cell.}, journal = {The Journal of cell biology}, volume = {46}, number = {2}, pages = {326-341}, pmid = {5449178}, issn = {0021-9525}, mesh = {Adipose Tissue/*cytology/drug effects/metabolism/*physiology ; Animals ; Carbon Dioxide/biosynthesis ; Carbon Isotopes ; Cell Membrane ; Cytoplasm ; Endoplasmic Reticulum ; Epinephrine/pharmacology ; Glucose/metabolism ; Golgi Apparatus ; Insulin/pharmacology ; Male ; Microscopy, Electron ; Mitochondria ; Rats ; }, abstract = {A method is described for preparing isolated rat adipose cells for electron microscopy. The ultrastructure of such cells and their production of (14)CO(2) from U-glucose-(14)C were studied simultaneously in the presence of insulin or epinephrine. Each adipose cell consists of a large lipid droplet surrounded by a thin rim of cytoplasm. In addition to typical subcellular organelles, a variety of small lipid droplets and an extensive system of membranes characterize the cell's cytoplasm. A fenestrated envelope surrounds the large, central lipid droplet. Similar envelopes surround cytoplasmic lipid droplets occurring individually or as aggregates of very small, amorphous droplets. Groups of individual droplets of smaller size also occur without envelopes. The system of membranes consists of invaginations of the cell membrane, vesicles possibly of pinocytic origin, simple and vesiculated vacuoles, vesicles deeper in the cytoplasm, flattened and vesicular smooth surfaced endoplasmic reticulum, and Golgi complexes. Neither insulin nor epinephrine produced detectable ultrastructural alterations even when cells were incubated under optimal conditions for the stimulation of (14)CO(2) evolution. Structural responses of the isolated adipose cell to hormones, if such occur, must, therefore, be dynamic rather than qualitative in nature; the extensive system of smooth surfaced membranes is suggestive of compartmentalized transport and metabolism.}, }
@article {pmid4274113, year = {1970}, author = {Perlman, PS and Mahler, HR}, title = {Formation of yeast mitochondria. 3. Biochemical properties of mitochondria isolated from a cytoplasmic petite mutant.}, journal = {Journal of bioenergetics}, volume = {1}, number = {2}, pages = {113-138}, pmid = {4274113}, issn = {0449-5705}, mesh = {Adenosine Triphosphatases/analysis ; Biological Evolution ; Citrate (si)-Synthase/analysis ; Isocitrate Dehydrogenase/analysis ; Malate Dehydrogenase/analysis ; Microscopy, Electron ; *Mitochondria/analysis/enzymology ; *Mutation ; Saccharomyces cerevisiae/*cytology ; Spheroplasts ; }, }
@article {pmid4988449, year = {1970}, author = {Migita, LK and Doi, RH}, title = {Formylation of methionyl-transfer RNA from prokaryotes and eukaryotes by Bacillus subtilis transformylase.}, journal = {Archives of biochemistry and biophysics}, volume = {138}, number = {2}, pages = {457-463}, doi = {10.1016/0003-9861(70)90369-3}, pmid = {4988449}, issn = {0003-9861}, mesh = {Animals ; Anura ; Bacillus subtilis/*enzymology ; Biological Evolution ; Carbon Isotopes ; Cell-Free System ; Chemical Phenomena ; Chemistry ; Drosophila ; Electrophoresis ; *Formates ; Kinetics ; *Methionine ; Mitochondria/metabolism ; Myocardium ; *RNA, Transfer ; Saccharomyces ; Transferases/metabolism ; Tritium ; }, }
@article {pmid5440477, year = {1970}, author = {Cohen, SS}, title = {Are/were mitochondria and chloroplasts microorganisms?.}, journal = {American scientist}, volume = {58}, number = {3}, pages = {281-289}, pmid = {5440477}, issn = {0003-0996}, mesh = {*Biological Evolution ; *Chloroplasts ; *Mitochondria ; *Molecular Biology ; }, }
@article {pmid4259116, year = {1970}, author = {Stinson, RA and Spencer, M}, title = {Respiratory control, oxidative phosphorylation, respiration, rate of ATP hydrolysis, and ethylene evolution in subcellular particulate fractions from cotyledons of germinating seedlings.}, journal = {Canadian journal of biochemistry}, volume = {48}, number = {5}, pages = {541-546}, doi = {10.1139/o70-089}, pmid = {4259116}, issn = {0008-4018}, mesh = {Adenosine Diphosphate/metabolism ; Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/*metabolism ; Electron Transport ; Ethylenes/metabolism ; Hydrolysis ; Mitochondria/metabolism ; Oxidative Phosphorylation ; Oxygen Consumption ; Plant Cells ; Plant Development ; Plants/*metabolism ; Subcellular Fractions/metabolism ; Time Factors ; }, }
@article {pmid4193097, year = {1970}, author = {Hadziyannis, S and Scheuer, PJ and Feizi, T and Naccarato, R and Doniach, D and Sherlock, S}, title = {Immunological and histological studies in primary biliary cirrhosis.}, journal = {Journal of clinical pathology}, volume = {23}, number = {2}, pages = {95-98}, pmid = {4193097}, issn = {0021-9746}, mesh = {Antibodies ; Antibodies, Antinuclear ; Cholestasis/complications ; Complement Fixation Tests ; Humans ; Immunoglobulin M ; Liver/pathology ; Liver Cirrhosis, Biliary/complications/*immunology/*pathology ; Mitochondria ; gamma-Globulins ; }, abstract = {Thirty-one patients with primary biliary cirrhosis in whom adequate histological liver material was available were studied by immunological and histological methods. There was no statistically significant correlation between individual histological features and the level of serum mitochondrial antibodies. A relationship between the duration of symptoms and histological stage of the disease supports the present concept of its evolution. However, several stages were often identified in the same specimen. Four cases with negative mitochondrial antibodies were similar to the other 27 clinically and histologically.}, }
@article {pmid5409474, year = {1970}, author = {Wang, JH}, title = {Oxidative and photosynthetic phosphorylation mechanisms.}, journal = {Science (New York, N.Y.)}, volume = {167}, number = {3914}, pages = {25-30}, doi = {10.1126/science.167.3914.25}, pmid = {5409474}, issn = {0036-8075}, mesh = {Adenosine Triphosphate/biosynthesis ; Biological Evolution ; Chloroplasts/metabolism ; Electron Transport ; Energy Transfer ; Light ; Mitochondria/metabolism ; *Models, Chemical ; *Oxidative Phosphorylation ; *Photosynthesis ; }, }
@article {pmid4930354, year = {1970}, author = {Noll, H}, title = {Organelle integration and the evolution of ribosome structure and function.}, journal = {Symposia of the Society for Experimental Biology}, volume = {24}, number = {}, pages = {419-447}, pmid = {4930354}, issn = {0081-1386}, mesh = {Amino Acid Sequence ; Animals ; *Biological Evolution ; Chromosome Aberrations ; Cytoplasm ; DNA ; Escherichia coli ; Genetic Code ; Mitochondria ; Molecular Biology ; Molecular Weight ; Rats ; *Ribosomes ; Ultracentrifugation ; }, }
@article {pmid4920823, year = {1970}, author = {Ashwell, M and Work, TS}, title = {The biogenesis of mitochondria.}, journal = {Annual review of biochemistry}, volume = {39}, number = {}, pages = {251-290}, doi = {10.1146/annurev.bi.39.070170.001343}, pmid = {4920823}, issn = {0066-4154}, mesh = {Animals ; Bacteria ; Biological Evolution ; DNA/biosynthesis/metabolism ; Humans ; Mice ; Mitochondria/*growth &amp; development/metabolism ; Mitochondria, Liver ; Mutation ; Protein Biosynthesis ; Proteins/metabolism ; RNA/biosynthesis/metabolism ; Rats ; Ribosomes/metabolism ; }, }
@article {pmid4913287, year = {1970}, author = {Broda, E}, title = {The evolution of bioenergetic processes.}, journal = {Progress in biophysics and molecular biology}, volume = {21}, number = {}, pages = {143-208}, pmid = {4913287}, issn = {0079-6107}, mesh = {Adenine Nucleotides/metabolism ; *Biological Evolution ; Carbon Dioxide/metabolism ; Electron Transport ; *Energy Transfer ; Eukaryota/metabolism ; Fermentation ; Fungi/metabolism ; Geological Phenomena ; Geology ; Mitochondria ; Origin of Life ; Oxygen Consumption ; Pentosephosphates/metabolism ; Phosphorus/metabolism ; Photosynthesis ; Plants/metabolism ; Thermodynamics ; }, }
@article {pmid4401045, year = {1970}, author = {Kröger, A and Klingenberg, M}, title = {Quinones and nicotinamide nucleotides associated with electron transfer.}, journal = {Vitamins and hormones}, volume = {28}, number = {}, pages = {533-574}, doi = {10.1016/s0083-6729(08)60910-3}, pmid = {4401045}, issn = {0083-6729}, mesh = {Animals ; Antimycin A ; Bacteria ; Biological Evolution ; Chemical Phenomena ; Chemistry ; Chemistry, Physical ; *Electron Transport ; Kinetics ; Membranes ; Mitochondria/analysis/enzymology ; Models, Biological ; *NAD ; *NADP ; Oxidation-Reduction ; Oxidative Phosphorylation ; Oxidoreductases ; *Quinones ; Rats ; Succinate Dehydrogenase ; Ubiquinone ; Vitamin K ; }, }
@article {pmid4393176, year = {1970}, author = {Wolf, U and Engel, W and Faust, J}, title = {[The mechanism of diploidization in vertebrate evolution: coexistence of tetrasomic and disomic gene loci for the isocitrate dehydrogenases in trout (salmo irideus)].}, journal = {Humangenetik}, volume = {9}, number = {2}, pages = {150-156}, pmid = {4393176}, issn = {0018-7348}, mesh = {Agar ; Alleles ; Animals ; Biological Evolution ; Diploidy ; Electrophoresis ; Fishes/*enzymology ; Gels ; *Genes ; Isocitrate Dehydrogenase/analysis ; Isoenzymes/analysis ; Liver/enzymology ; Mitochondria ; Molecular Biology ; Myocardium/enzymology ; NADP/analysis ; Phenotype ; Polymorphism, Genetic ; *Polyploidy ; Salmonidae/*enzymology ; }, }
@article {pmid4193491, year = {1970}, author = {Dhainaut, A}, title = {[Cytochemical and ultrastructural study of oocyte development in Nereis pelagica L. (Annelida Polychaeta). II. Development in the absence of brain hormone].}, journal = {Zeitschrift fur Zellforschung und mikroskopische Anatomie (Vienna, Austria : 1948)}, volume = {104}, number = {3}, pages = {390-404}, pmid = {4193491}, issn = {0340-0336}, mesh = {Animals ; Annelida/cytology/*growth &amp; development ; Cell Nucleus ; Cytoplasm ; Endoplasmic Reticulum ; Female ; Glycosaminoglycans ; Golgi Apparatus ; Histocytochemistry ; Invertebrate Hormones/*physiology ; Microscopy, Electron ; Mitochondria ; Ovum/cytology/*growth &amp; development ; Proteins ; Staining and Labeling ; }, }
@article {pmid4193490, year = {1970}, author = {Dhainaut, A}, title = {[Cytochemical and ultrastructural study of oocyte development in Nereis pelagica L. (Annelida Polychaeta). I. Normal ovogenesis].}, journal = {Zeitschrift fur Zellforschung und mikroskopische Anatomie (Vienna, Austria : 1948)}, volume = {104}, number = {3}, pages = {375-389}, pmid = {4193490}, issn = {0340-0336}, mesh = {Animals ; Annelida/cytology/*growth &amp; development ; Cytoplasm ; Cytoplasmic Granules ; Endoplasmic Reticulum ; Female ; Glycosaminoglycans ; Golgi Apparatus ; Histocytochemistry ; Lipids ; Microscopy, Electron ; Mitochondria ; Ovum/cytology/*growth &amp; development ; Proteins ; Staining and Labeling ; }, }
@article {pmid5770525, year = {1969}, author = {Christiansen, EN and Pedersen, JI and Grav, HJ}, title = {Uncoupling and recoupling of oxidative phosphorylation in brown adipose tissue mitochondria.}, journal = {Nature}, volume = {222}, number = {5196}, pages = {857-860}, doi = {10.1038/222857a0}, pmid = {5770525}, issn = {0028-0836}, mesh = {Adaptation, Physiological ; Adenine Nucleotides/pharmacology ; Adipose Tissue/*physiology ; Adipose Tissue, Brown/physiology ; Aging ; Animals ; Animals, Newborn ; Biological Evolution ; *Body Temperature Regulation ; Cold Temperature ; Guinea Pigs ; Hibernation ; *Mitochondria ; Oligomycins/pharmacology ; *Oxidative Phosphorylation ; }, }
@article {pmid4387871, year = {1969}, author = {Koler, RD and Vanbellinghen, PJ and Fellman, JH and Jones, RT and Behrman, RE}, title = {Ontogeny of soluble and mitochondrial tyrosine aminotransferases.}, journal = {Science (New York, N.Y.)}, volume = {163}, number = {3873}, pages = {1348-1350}, doi = {10.1126/science.163.3873.1348}, pmid = {4387871}, issn = {0036-8075}, mesh = {Aging ; Animals ; Animals, Newborn ; Biological Evolution ; Female ; Fetus ; Haplorhini ; Mitochondria, Liver/enzymology ; Pregnancy ; Tyrosine/blood ; *Tyrosine Transaminase ; }, abstract = {The development of the soluble and mitochondrial forms of tyrosine aminotransferase was observed in fetal and neonatal rhesus monkey tissues. The mitochondrial activity is detectable in early fetal life; the soluble form reaches significant activity just before the birth of the animal.}, }
@article {pmid5766382, year = {1969}, author = {Afifi, AK and Bergman, RA}, title = {Steroid myopathy. A study of the evolution of the muscle lesion in rabbits.}, journal = {The Johns Hopkins medical journal}, volume = {124}, number = {2}, pages = {66-86}, pmid = {5766382}, issn = {0021-7263}, mesh = {Animals ; Basement Membrane ; Cortisone/*adverse effects ; Diaphragm/pathology ; Microscopy, Electron ; Mitochondria ; Muscles/*pathology ; Muscular Diseases/*chemically induced/pathology ; Rabbits ; Regeneration ; Ribosomes ; }, }
@article {pmid4304157, year = {1969}, author = {Graham, AB and Park, MV}, title = {A product-inhibition study of the mechanism of mitochondrial octanoly-coenzyme A synthetase.}, journal = {The Biochemical journal}, volume = {111}, number = {3}, pages = {257-262}, pmid = {4304157}, issn = {0264-6021}, mesh = {Adenine Nucleotides/metabolism ; Adenosine Triphosphate/metabolism ; Animals ; Caprylates/*metabolism ; Cattle ; Coenzyme A/*metabolism ; Depression, Chemical ; Diphosphates/metabolism ; In Vitro Techniques ; Kinetics ; Ligases/*metabolism ; Mitochondria, Liver/*enzymology ; Models, Chemical ; }, abstract = {By a study of the product-inhibition kinetics of the octanoyl-CoA synthetase from ox liver mitochondria, evidence was obtained consistent with the hypothesis that the enzyme reacts by a Bi Uni Uni Bi Ping Pong type of mechanism in which the order of addition and evolution of substrates and products is CoA, octanoate, octanoyl-CoA, ATP, PP(i) and AMP. There is also evidence that more than one molecule of CoA can add to the enzyme and that it may act as an allosteric activator.}, }
@article {pmid4973141, year = {1969}, author = {Amaldi, F}, title = {Non-random variability in evolution of base compositions of ribosomal RNA.}, journal = {Nature}, volume = {221}, number = {5175}, pages = {95-96}, doi = {10.1038/221095a0}, pmid = {4973141}, issn = {0028-0836}, mesh = {Adenine/*analysis ; Amphibians ; Animals ; Bacillus ; Bacillus subtilis ; *Biological Evolution ; Birds ; Chlamydia ; Cytosine/*analysis ; Drosophila ; Echinodermata ; Enterobacter ; Escherichia coli ; Fungi ; Guanine/*analysis ; Humans ; Mammals ; Mitochondria ; Plants, Edible ; Pseudomonas ; RNA/*analysis ; *Ribosomes ; Species Specificity ; Uracil/*analysis ; Zea mays ; }, }
@article {pmid5814431, year = {1969}, author = {Halstead, LB}, title = {Are mitochondria directly involved in biological mineralisation? The mitochondrion and the origin of bone.}, journal = {Calcified tissue research}, volume = {3}, number = {1}, pages = {103-105}, pmid = {5814431}, issn = {0008-0594}, mesh = {Animals ; Biological Evolution ; *Bone and Bones ; *Calcification, Physiologic ; Calcium/analysis ; *Mitochondria ; Vertebrates ; }, }
@article {pmid5004398, year = {1969}, author = {Hruban, Z and Rechcigl, M}, title = {Microbodies and related particles. Morphology, biochemistry, and physiology.}, journal = {International review of cytology}, volume = {}, number = {}, pages = {Suppl 1:1-296}, pmid = {5004398}, issn = {0074-7696}, mesh = {Aging ; Anatomy, Comparative ; Animals ; Animals, Newborn ; Biological Evolution ; Cats ; Cattle ; *Cell Biology ; Chick Embryo ; Cricetinae ; Crystallization ; Cytoplasm ; Dogs ; Endoplasmic Reticulum ; Enzymes/analysis ; Eukaryota/cytology ; Fetus ; Golgi Apparatus ; Guinea Pigs ; Haplorhini ; Histological Techniques ; Humans ; Kidney/cytology ; Liver/cytology ; Lysosomes ; Mice ; Microscopy, Electron ; *Microsomes/drug effects/enzymology/metabolism ; Microsomes, Liver ; Microtubules ; Mitochondria ; Neoplasms/pathology ; Origin of Life ; Pharmacology ; Plant Cells ; Rats ; }, }
@article {pmid4914411, year = {1969}, author = {Pollock, MR}, title = {The changing concept of organism in microbiology.}, journal = {Progress in biophysics and molecular biology}, volume = {19}, number = {2}, pages = {271-305}, pmid = {4914411}, issn = {0079-6107}, mesh = {Bacteria ; Biological Evolution ; *Cell Biology ; Cell Membrane ; Chloroplasts ; Cytoplasm/physiology ; Drug Resistance, Microbial ; Escherichia ; Extrachromosomal Inheritance ; Genes ; Microbiology ; Mitochondria ; Nucleic Acids ; Protein Biosynthesis ; Salmonella ; Transformation, Genetic ; Viruses ; }, }
@article {pmid4908552, year = {1969}, author = {Heggtveit, HA}, title = {Contributions of electron microscopy to the study of myocardial ischaemia.}, journal = {Bulletin of the World Health Organization}, volume = {41}, number = {6}, pages = {865-872}, pmid = {4908552}, issn = {0042-9686}, mesh = {Animals ; Cats ; Coronary Disease/metabolism/*pathology ; Disease Models, Animal ; Dogs ; Glycogen/metabolism ; Humans ; Hypoxia/pathology ; Magnesium Deficiency/pathology ; *Microscopy, Electron ; Mitochondria ; Myocardium/pathology ; Myofibrils ; Organoids ; Postmortem Changes ; Rabbits ; Rats ; }, abstract = {Electron-microscope studies of experimental models of myocardial ischaemia have provided basic information on the pathogenesis of hypoxic heart injury. Correlation of ultrastructural changes with biochemical data confirms the importance of catecholamine release and ionic shifts in the early evolution of ischaemic injury. An altered cellular metabolism induced by ischaemia causes rapid depletion of glycogen and is followed quickly by alterations in the nucleus, the mitochondria and the sarcotubular system; the myofibril is the organelle most resistant to hypoxia.Postmortem autolysis mimics early ischaemic change very closely and it probably has an initial hypoxic basis. Significant hypoxic-autolytic changes may begin during the agonal state. The time elapsing and the techniques of tissue preservation are critical in determining the amount of artefact. At present it is unrealistic to expect to obtain acutely ischaemic human myocardium soon enough after death to be of value in the estimation of the degree or duration of ischaemia by electron-microscope techniques. Rapidly progressive autolytic changes preclude the meaningful morphological assessment of hypoxic change at the ultrastructural level.}, }
@article {pmid4235914, year = {1968}, author = {Sarlospv, DS}, title = {[Problem of the stimulation of myocardial regeneration and ways of its solution].}, journal = {Kardiologiia}, volume = {8}, number = {8}, pages = {142-150}, pmid = {4235914}, issn = {0022-9040}, mesh = {Animals ; Biological Evolution ; Cardiomegaly ; Cicatrix ; Granulation Tissue ; Hyperplasia ; Hypertrophy ; Mitochondria ; Models, Structural ; Myocardial Infarction ; *Myocardium ; Organoids ; *Regeneration ; Ribosomes ; }, }
@article {pmid4892070, year = {1968}, author = {Nass, MM}, title = {Mitochondrial DNA: advances, problems, and goals.}, journal = {Science (New York, N.Y.)}, volume = {165}, number = {3888}, pages = {25-35}, pmid = {4892070}, issn = {0036-8075}, mesh = {Animals ; Biological Evolution ; Chemical Phenomena ; Chemistry, Physical ; *DNA ; Genetic Code ; Humans ; Membranes ; Microscopy, Electron ; *Mitochondria ; Molecular Weight ; Nucleic Acid Denaturation ; Nucleosides/analysis ; }, }
@article {pmid5656454, year = {1968}, author = {Le Moigne, A}, title = {[Electron microscopic study of the fate of x-irradiated embryonic planarian structures].}, journal = {Journal of embryology and experimental morphology}, volume = {19}, number = {2}, pages = {181-192}, pmid = {5656454}, issn = {0022-0752}, mesh = {Animals ; Cell Differentiation ; Cell Division ; Cell Membrane ; Cytoplasm ; Microscopy, Electron ; Mitochondria ; *Radiation Effects ; Ribosomes ; Turbellaria/cytology/*embryology/*radiation effects ; }, }
@article {pmid5727114, year = {1968}, author = {Sarkisov, DS}, title = {[Regeneration and hypertrophy].}, journal = {Arkhiv patologii}, volume = {30}, number = {7}, pages = {3-12}, pmid = {5727114}, issn = {0004-1955}, mesh = {Animals ; Biological Evolution ; Bone Marrow Cells ; Bone and Bones ; Cicatrix ; Cytoplasm ; Endoplasmic Reticulum ; Gastric Mucosa/cytology ; Humans ; Hyperplasia ; *Hypertrophy ; Intestinal Mucosa/cytology ; Liver Regeneration ; Mammals ; Microscopy, Electron ; Mitochondria ; Models, Biological ; Myocardium/cytology ; Organoids ; *Regeneration ; Skin/cytology ; Wounds and Injuries ; }, }
@article {pmid5641404, year = {1968}, author = {Dawid, IB and Wolstenholme, DR}, title = {Renaturation and hybridization studies of mitochondrial DNA.}, journal = {Biophysical journal}, volume = {8}, number = {1}, pages = {65-81}, pmid = {5641404}, issn = {0006-3495}, mesh = {Animals ; Anura ; Cell Nucleus ; Centrifugation, Density Gradient ; *DNA ; Hybridization, Genetic ; Mice ; Microscopy, Electron ; *Mitochondria ; Nucleic Acid Denaturation ; Urodela ; }, abstract = {The products of the renaturation reaction of mitochondrial DNA from oocytes of Xenopus laevis have been studied by electron microscopy and CsCl equilibrium density gradient centrifugation. The reaction leads to the formation of intermediates containing single-stranded and double-stranded regions. Further reactions of these intermediates result in large complexes of interlinking double-stranded filaments. The formation of circular molecules of the same length as native circles of mitochondrial DNA was also observed. The formation of common high molecular weight complexes during joint reannealing of two DNA's with complementary sequences was used as a method to detect sequence homology in different DNA samples. Although this method does not produce quantitative data it offers several advantages in the present study. No homologies could be detected between the nuclear DNA and the mitochondrial DNA of X. laevis or of Rana pipiens. In interspecies comparisons homologies were found between the nuclear DNA's of X. laevis and the mouse and between the mitochondrial DNA's of X. laevis and the chick, but none between the mitochondrial DNA's of X. laevis and yeast. These results are interpreted as indicating the continuity of mitochondrial DNA during evolution.}, }
@article {pmid6064364, year = {1967}, author = {Ohad, I and Siekevitz, P and Palade, GE}, title = {Biogenesis of chloroplast membranes. I. Plastid dedifferentiation in a dark-grown algal mutant (Chlamydomonas reinhardi).}, journal = {The Journal of cell biology}, volume = {35}, number = {3}, pages = {521-552}, pmid = {6064364}, issn = {0021-9525}, mesh = {Autoradiography ; Cell Differentiation ; Cell Division ; Chlorophyll/biosynthesis ; *Chloroplasts/metabolism ; Darkness ; Enzymes/metabolism ; Eukaryota/*cytology ; Light ; Lipid Metabolism ; *Membranes ; Microscopy, Electron ; Mitochondria ; Mutation ; *Photosynthesis ; }, abstract = {This paper describes the morphology and photosynthetic activity of a mutant of Chlamydomonas reinhardi (y-1) which is unable to synthesize chlorophyll in the dark. When grown heterotrophically in the light, the mutant is indistinguishable from the wild type Chlamydomonas. When grown in the dark, chlorophyll is diluted through cell division and the photosynthetic activity (oxygen evolution, Hill reaction, and photoreduction of NADP) decays at a rate equal to or faster than that of chlorophyll dilution. However, soluble enzymes associated with the photosynthetic process (alkaline FDPase, NADP-linked G-3-P dehydrogenase, RuDP carboxylase), as well as cytochrome f and ferredoxin, continue to be present in relatively high concentrations. The enzymes involved in the synthesis of the characteristic lipids of the chloroplast (including mono- and digalactoside glycerides, phosphatidyl glycerol, and sulfolipid) are still detectable in dark-grown cells. Such cells accumulate large amounts of starch granules in their plastids. On onset of illumination, dark-grown cells synthesize chlorophyll rapidly, utilizing their starch reserve in the process. At the morphological level, it was observed that during growth in the dark the chloroplast lamellar system is gradually disorganized and drastically decreased in extent, while other subchloroplast components are either unaffected (pyrenoid and its tubular system, matrix) or much less affected (eyespot, ribosomes). It is concluded that the dark-grown mutant possesses a partially differentiated plastid and the enzymic apparatus necessary for the synthesis of the chloroplast membranes (discs). The advantage provided by such a system for the study of the biogenesis of the chloroplast photosynthetic membranes is discussed.}, }
@article {pmid5615439, year = {1967}, author = {Motta, P}, title = {[On the fine structure of human luteinic cell during some stages of its evolution cycle with special reference to its secretory activity].}, journal = {Biologica Latina}, volume = {20}, number = {3}, pages = {201-224}, pmid = {5615439}, issn = {0006-3150}, mesh = {Cell Differentiation ; Corpus Luteum/*cytology/metabolism ; Corpus Luteum Hormones/*biosynthesis ; Female ; Humans ; Microscopy, Electron ; Mitochondria ; *Ovulation ; Pregnancy ; }, }
@article {pmid5630196, year = {1967}, author = {Shirai, T and Welsh, GW and Sims, EA}, title = {Diabetes mellitus in the Chinese hamster. II. The evolution of renal glomerulopathy.}, journal = {Diabetologia}, volume = {3}, number = {2}, pages = {266-286}, pmid = {5630196}, issn = {0012-186X}, mesh = {Animals ; Basement Membrane ; Capillaries/pathology ; *Cricetinae ; Cytoplasm ; Diabetes Mellitus/pathology/*veterinary ; Diabetic Nephropathies/pathology/*veterinary ; Female ; Kidney Glomerulus/*pathology ; Male ; Medical Illustration ; Microscopy, Electron ; Mitochondria ; Sclerosis ; }, }
@article {pmid4168867, year = {1967}, author = {Teodori, U and Gentilini, P and Surrenti, C}, title = {Electron microscope observations of some forms of viral hepatitis. Contribution to the understanding of the morphological evolution and pathogenetic mechanism of jaundice.}, journal = {Gastroenterologia}, volume = {108}, number = {3}, pages = {105-120}, doi = {10.1159/000201596}, pmid = {4168867}, issn = {0301-164X}, mesh = {Bile Ducts, Intrahepatic/pathology ; Biopsy ; Cell Membrane ; Endoplasmic Reticulum ; Golgi Apparatus ; Hepatitis A/classification/*pathology ; Histological Techniques ; Humans ; Jaundice/etiology ; Liver/*pathology ; Lysosomes ; Macrophages ; Microscopy, Electron ; Microscopy, Phase-Contrast ; Mitochondria ; Phagocytosis ; Staining and Labeling ; }, }
@article {pmid5971968, year = {1966}, author = {Bassot, JM}, title = {[A microtubular and a paracrystalline form in the endoplasmic reticulum of the photocytes of annelids, Polynoinae].}, journal = {The Journal of cell biology}, volume = {31}, number = {1}, pages = {135-158}, pmid = {5971968}, issn = {0021-9525}, mesh = {Annelida/*cytology ; Cell Membrane ; Cell Membrane Permeability ; Crystallization ; *Endoplasmic Reticulum ; Epithelial Cells ; Glycogen/analysis ; Golgi Apparatus ; Histocytochemistry ; Microscopy, Electron ; Mitochondria ; *Organoids ; }, abstract = {Luminous cells of polynoid worm elytra have been examined by methods of electron microscopy, with special attention focused on the fine structure of photogenic grains. These cells send apical prolongations into the mid-part of the elytra. The plasma membrane is very sinuous, and a special kind of desmosome links two portions of the same membrane. In addition to all the organelles which can be found in nonluminescent epithelial cells of the elytra, numerous photogenic grains are contained in their cytoplasm. These grains are composed of undulating microtubules measuring 200 A in diameter; their disposition in the grain is highly regular, and the grains appear as paracrystals. At the borders of the grains, the walls of the microtubules are often in continuity with those of the endoplasmic reticulum and with the external membrane of the nuclear envelope. Because of this fact, the microtubules of the grains may be considered a cytoplasmic organelle, representing a specialized form of the endoplasmic reticulum. The microtubules permit the repartition, inside and outside their walls, of two different products, one being forty-three times more abundant than the other; thus, the contact surface, in comparison to the volume, is greatly increased. The induction of the luminous reaction by change in the permeability of the microtubule walls, allowing contact between the two substances, is suggested as a working hypothesis. There is an evolution of the grains along the axis of the photocytes. The grains are often surrounded by progressively increasing amounts of glycogen. Their paracrystalline disposition is altered at the apex of the luminous cells.}, }
@article {pmid5934524, year = {1966}, author = {Glinsmann, WH and Ericsson, JL}, title = {Observations on the subcellular organization of hepatic parenchymal cells. II. Evolution of reversible alterations induced by hypoxia.}, journal = {Laboratory investigation; a journal of technical methods and pathology}, volume = {15}, number = {4}, pages = {762-777}, pmid = {5934524}, issn = {0023-6837}, mesh = {Animals ; Hypoxia/*pathology ; Liver/*pathology ; Microscopy, Electron ; Mitochondria ; *Organoids ; Rats ; }, }
@article {pmid4954168, year = {1965}, author = {Thomas, JA}, title = {[Morphological development of desoxyribonucleic acid in the mitochondria of cells infected by a virus (BHK 21/13 subline and H54 cancer strains)].}, journal = {Comptes rendus hebdomadaires des seances de l'Academie des sciences. Serie D: Sciences naturelles}, volume = {260}, number = {26}, pages = {7054-7057}, pmid = {4954168}, mesh = {Animals ; *DNA ; In Vitro Techniques ; Microscopy, Electron ; *Mitochondria ; Neoplasms/*pathology ; *Virus Cultivation ; }, }
@article {pmid5840027, year = {1965}, author = {Fabro, SP and Rinaldini, LM}, title = {Loss of ascorbic acid synthesis in embryonic development.}, journal = {Developmental biology}, volume = {11}, number = {3}, pages = {468-488}, doi = {10.1016/0012-1606(65)90051-5}, pmid = {5840027}, issn = {0012-1606}, mesh = {Alcohol Oxidoreductases/*metabolism ; Animals ; Ascorbic Acid/*biosynthesis ; Biological Evolution ; Brain/enzymology ; Chick Embryo ; Embryo, Mammalian/*enzymology ; *Embryo, Nonmammalian ; Eye/enzymology ; Intestines/enzymology ; Kidney/cytology ; Lactones/metabolism ; Liver/enzymology ; Microscopy, Electron ; Microsomes ; Mitochondria ; Muscles/enzymology ; Myocardium/enzymology ; Stomach/enzymology ; }, }
@article {pmid5844054, year = {1965}, author = {Idèo, G and Mannucci, PM and Coghe, A and Fiorelli, G and Dioguardi, N}, title = {[Behavior of cytoplasmatic and mitochondrial glutamic oxalacetic transaminase in the serum of subjects affected by acute viral hepatitis of diverse evolution].}, journal = {Rassegna medica sarda}, volume = {68}, number = {3}, pages = {191-203}, pmid = {5844054}, issn = {0033-9776}, mesh = {*Aspartate Aminotransferases ; Blood ; *Clinical Enzyme Tests ; Cytoplasm ; Hepatitis A/*diagnosis ; Humans ; Isoenzymes ; Liver/enzymology ; Mitochondria ; }, }